Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008280.1 Hibiscus syriacus cultivar Beakdansim tig00110940_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: 3557051
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 17
Found at i:1010447 original size:24 final size:24
Alignment explanation
Indices: 1010407--1010481 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
1010397 GATTGGGTTA
*
1010407 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
1010431 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
1010455 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
1010479 AAC
1 AAC
1010482 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1016063 original size:21 final size:20
Alignment explanation
Indices: 1016036--1016134 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
1016026 AATCAGTTTC
1016036 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1016057 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1016078 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1016098 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1016119 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1016135 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1016150 original size:40 final size:40
Alignment explanation
Indices: 1016101--1016255 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
1016091 CGATTTTCCA
* ** *
1016101 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
1016141 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
1016181 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
1016221 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1016256 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:1016163 original size:20 final size:20
Alignment explanation
Indices: 1016101--1016254 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1016091 CGATTTTCCA
* ** *
1016101 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1016121 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1016141 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1016161 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1016181 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1016201 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1016221 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1016242 AAATCGCAACGCG
1 AAATCGCAACGCG
1016255 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1016676 original size:33 final size:33
Alignment explanation
Indices: 1016637--1016707 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1016627 TTCACTTAGA
*
1016637 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1016670 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1016703 TTTCA
1 TTTCA
1016708 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1016831 original size:20 final size:20
Alignment explanation
Indices: 1016787--1016896 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
1016777 TGCAGAAGAG
*
1016787 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
1016808 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
1016828 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
1016849 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
1016863 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
1016882 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1016897 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1016844 original size:41 final size:38
Alignment explanation
Indices: 1016780--1016896 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
1016770 TTCAATTTGC
* *
1016780 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1016818 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1016859 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1016892 AGAAT
1 AGAAT
1016897 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:1016866 original size:14 final size:14
Alignment explanation
Indices: 1016847--1016903 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1016837 GAGAAATGAA
1016847 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1016861 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1016880 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1016894 AATCGCAACG
1 AATCGCAACG
1016904 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1016879 original size:33 final size:33
Alignment explanation
Indices: 1016839--1016919 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1016829 CGCAACGAGA
1016839 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1016872 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1016905 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1016920 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1016937 original size:19 final size:19
Alignment explanation
Indices: 1016915--1017012 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
1016905 GAAACCAAAA
*
1016915 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1016934 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1016948 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1016967 TCGCGTTGCGA--TT-A--
1 TCGCGTTGCGATTTTCATT
* *
1016981 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
1017000 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1017013 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1016956 original size:14 final size:14
Alignment explanation
Indices: 1016937--1017026 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
1016927 TTTCATTTCG
1016937 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1016951 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
1016970 CGTTGCGATTATCT
1 CGTTGCGATTCTCT
*
1016984 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
1017003 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1017017 CGTTGCGATT
1 CGTTGCGATT
1017027 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 1 0.02
16 4 0.07
17 4 0.07
18 1 0.02
19 20 0.33
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1016962 original size:33 final size:33
Alignment explanation
Indices: 1016920--1017034 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1016910 CAAAATCGCA
1016920 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1016953 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1016986 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1017019 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1017035 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1018893 original size:93 final size:93
Alignment explanation
Indices: 1018730--1019470 Score: 1401
Period size: 93 Copynumber: 8.1 Consensus size: 93
1018720 TTAGATGCTT
*
1018730 AGTAAATTTATTCGGTTGCTGCCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGT
1 AGTAAATTTGTTCGGTTGCTG-CCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1018794 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1018823 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1018888 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1018915 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1018980 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1019008 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1019073 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1019101 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1019166 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1019194 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1019259 TTTGTCTTTGTTTTGTCTTTT-G--GAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1019284 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1019349 TTTGTCTTTGTTTTGTC-TTT--TTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1019374 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1019439 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1019466 AGTAA
1 AGTAA
1019471 TGCAATCCAT
Statistics
Matches: 640, Mismatches: 1, Indels: 15
0.98 0.00 0.02
Matches are distributed among these distances:
89 3 0.00
90 170 0.27
91 3 0.00
92 135 0.21
93 329 0.51
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1019558 original size:19 final size:19
Alignment explanation
Indices: 1019518--1019646 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1019508 TAGTTTACTT
* *
1019518 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1019538 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1019557 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1019576 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1019590 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
1019609 TCGCAA--CG--A-TAAGA
1 TCGCAACGCGAAACCAAAA
1019623 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1019642 TCGCA
1 TCGCA
1019647 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1019597 original size:33 final size:32
Alignment explanation
Indices: 1019554--1019646 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
1019544 CGCGAAACCA
**
1019554 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
1019586 AGAATCGCAACGCGAAACCAAAATCGCAACGAT
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1019619 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1019647 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1019644 original size:52 final size:52
Alignment explanation
Indices: 1019518--1019646 Score: 138
Period size: 52 Copynumber: 2.5 Consensus size: 52
1019508 TAGTTTACTT
** *
1019518 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
* * * *
1019570 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGATAAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAA-A
*
1019623 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1019647 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.69
53 2 0.03
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
Found at i:1019664 original size:19 final size:19
Alignment explanation
Indices: 1019642--1019776 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1019632 GAAACCAAAA
*
1019642 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1019661 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1019677 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1019694 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1019710 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1019727 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1019746 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1019766 TCGTGTTGCGA
1 TCGCGTTGCGA
1019777 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1019683 original size:14 final size:14
Alignment explanation
Indices: 1019664--1019720 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1019654 TTTCATTTCG
1019664 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1019678 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1019695 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1019711 CGTTGCGATT
1 CGTTGCGATT
1019721 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1019689 original size:33 final size:33
Alignment explanation
Indices: 1019647--1019739 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1019637 CAAAATCGCA
*
1019647 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1019680 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1019713 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1019740 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1020951 original size:14 final size:14
Alignment explanation
Indices: 1020932--1020967 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1020922 ATTGTTTAAT
1020932 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1020946 TGATTTGTATAAGT
1 TGATTTGTAAAAGA
1020960 TGATTTGT
1 TGATTTGT
1020968 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1021090 original size:19 final size:19
Alignment explanation
Indices: 1021074--1021171 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1021064 AAAAATGACT
1021074 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1021093 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1021112 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
1021126 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1021145 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1021165 ATCGCAA
1 ATCGCAA
1021172 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1021203 original size:53 final size:53
Alignment explanation
Indices: 1021074--1021189 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
1021064 AAAAATGACT
*
1021074 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1021126 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1021179 ATCGCAATGCG
1 ATCGCAATGCG
1021190 TTTATAATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1021242 original size:19 final size:19
Alignment explanation
Indices: 1021218--1021401 Score: 227
Period size: 19 Copynumber: 10.4 Consensus size: 19
1021208 GATTCTCTCG
1021218 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1021237 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1021256 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1021270 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1021289 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1021308 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1021327 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1021341 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1021361 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
1021375 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1021394 TTGCGATT
1 TTGCGATT
1021402 CTCTCGTTGC
Statistics
Matches: 143, Mismatches: 6, Indels: 32
0.79 0.03 0.18
Matches are distributed among these distances:
14 23 0.16
16 16 0.11
17 13 0.09
18 3 0.02
19 76 0.53
20 12 0.08
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1021253 original size:52 final size:52
Alignment explanation
Indices: 1021196--1021401 Score: 276
Period size: 52 Copynumber: 3.9 Consensus size: 52
1021186 TGCGTTTATA
1021196 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1021248 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* * * * *
1021300 ATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* *
1021352 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATT
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATT
1021402 CTCTCGTTGC
Statistics
Matches: 135, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
50 9 0.07
51 5 0.04
52 86 0.64
53 23 0.17
54 5 0.04
55 6 0.04
56 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1021296 original size:71 final size:72
Alignment explanation
Indices: 1021218--1021434 Score: 347
Period size: 71 Copynumber: 3.1 Consensus size: 72
1021208 GATTCTCTCG
1021218 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1021283 TT-CGCA
66 TTCCGCA
1021289 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1021354 TTCCGCA
66 TTCCGCA
* * *
1021361 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
**
1021421 TTCCGTG
66 TTCCGCA
1021428 TTGCGAT
1 TTGCGAT
1021435 AGTCAAATGC
Statistics
Matches: 140, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
67 55 0.39
69 1 0.01
70 1 0.01
71 67 0.48
72 16 0.11
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCCGCA
Found at i:1021423 original size:33 final size:33
Alignment explanation
Indices: 1021237--1021415 Score: 261
Period size: 33 Copynumber: 5.2 Consensus size: 33
1021227 TCATTTCGCA
1021237 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1021270 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
1021306 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
1021341 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
1021375 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1021408 TTGCGATT
1 TTGCGATT
1021416 GTAATTTCCG
Statistics
Matches: 132, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
32 1 0.01
33 62 0.47
34 29 0.22
35 8 0.06
36 7 0.05
38 25 0.19
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:1024634 original size:20 final size:20
Alignment explanation
Indices: 1024606--1024835 Score: 228
Period size: 20 Copynumber: 11.5 Consensus size: 20
1024596 AAATTTCAGT
* * *
1024606 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1024626 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1024646 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1024666 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1024686 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1024706 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1024726 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1024746 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
1024766 GTTGCGATTTACGGATACGT
1 GTTGCGATTTACGGATTCGC
*
1024786 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1024806 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1024826 GTTGCGATTT
1 GTTGCGATTT
1024836 TGGAAAATCG
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1024852 original size:21 final size:21
Alignment explanation
Indices: 1024822--1024904 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
1024812 ATTTTCATAT
*
1024822 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1024843 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1024864 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
* *
1024885 TCGCGTTACGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1024905 CTGATTTGCG
Statistics
Matches: 46, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.02
21 43 0.93
22 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1028946 original size:21 final size:22
Alignment explanation
Indices: 1028913--1028962 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1028903 TTTAAGTTTT
*
1028913 TTTTTTAGGAAATAAAAAATTGA
1 TTTTTTA-GAAATAAAAAATTAA
*
1028936 TTTTTTA-AAATTAAAAATTAA
1 TTTTTTAGAAATAAAAAATTAA
1028957 TTTTTT
1 TTTTTT
1028963 GTTAACCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.72
23 7 0.28
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (22 bp):
TTTTTTAGAAATAAAAAATTAA
Found at i:1029620 original size:4 final size:4
Alignment explanation
Indices: 1029611--1029635 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1029601 CACGCATCTG
1029611 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1029636 GTTGATGCTT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1036555 original size:31 final size:29
Alignment explanation
Indices: 1036508--1036620 Score: 118
Period size: 31 Copynumber: 3.7 Consensus size: 29
1036498 TAAAAAATCA
*
1036508 TTAAAATTAAAGATTAAATTAATATTTTAT
1 TTAAAATTTAAGATTAAATTAATATTTT-T
1036538 TTAAAATTTTAAGATTAAATTAATATTTTT
1 TTAAAA-TTTAAGATTAAATTAATATTTTT
* * *
1036568 TAAAAAAATTTAAAATTAAATTAATATTCTGT
1 T--TAAAATTTAAGATTAAATTAATATT-TTT
**
1036600 CCAAAATTTATAGATTAAATT
1 TTAAAATTTA-AGATTAAATT
1036621 GAAATTAATT
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
30 16 0.23
31 49 0.69
32 6 0.08
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (29 bp):
TTAAAATTTAAGATTAAATTAATATTTTT
Found at i:1039590 original size:365 final size:366
Alignment explanation
Indices: 1038908--1039651 Score: 1019
Period size: 365 Copynumber: 2.0 Consensus size: 366
1038898 TGATGGGCTT
* *
1038908 TGATTCAAATTTGGTTGCATTAAATTGTTTAGTTGATGGGTTGTGTAAAGTCGGTCAGACTAAGG
1 TGATTCAAATTTGATTGCATTAAATTGTTTAGTCGATGGGTTGTGTAAAGTCGGTCAGACTAAGG
* * *
1038973 ATGCAATGAAAGTCTATAAATCAATGGAGGTAAGAGATTCTTTTACCTACTCCTCTTTGGTGCAC
66 ATGCAATGAAAATCTATAAATCAATGGAGGTAAGAGATTATTATACCTACTCCTCTTTGGTGCAC
** * * * *
1039038 AACCTTTGCAGGGAAAGGAAGTACCATTCTGCGGCCAAGCTCCTGCTAACTTGTTTACGAAGTGG
131 AACCTTCACAGGGAAAGGAAGAACCATTCTGCAGCCAA-------CT-ACTTGTTCACGAAATGG
* *
1039103 CATGAAAATACTAAAGTCTGCTCAACGGGCTGTCCTGCTTGGTCTTCGCCATTCTGGTTTTCCTG
188 CATGAAAATACTAAAGTCTGCTCAACAGGCTGTCCTGCTTGGTCTTCGCCATTCTGGATTTCCTG
* ** *
1039168 GAGAGGCAAAAAAGCTTAAGTCTAAGATTCGCATTTCTCGAATATTGAGTCACTGATAATTTAAC
253 GAGAGGCAAAAAAGCTTAAGTCTAAGATTCACATCGCTCGAATATTGAGTCACTGATAATATAAC
*
1039233 CATTACTTTC-GATTTCAGTGA-TAGAAGCTGGAAGATTATTTAGTTCAGC
318 CATTACTTTCAG-TTTCAGT-ACTAGAAGCTAGAAGATTATTTAGTTCAGC
* * * * * * *
1039282 TGATTCAGATTTGATTGCATTTAATTGTTTGGTCGGTGGGTTGTGTAAAGTCGGTCTGACTGATG
1 TGATTCAAATTTGATTGCATTAAATTGTTTAGTCGATGGGTTGTGTAAAGTCGGTCAGACTAAGG
*
1039347 ATGCAATGAAAATCTATAACTCAATGGAGGTAAGAGATTATATATACCTACTCCTCTTTGGTGCA
66 ATGCAATGAAAATCTATAAATCAATGGAGGTAAGAGATTAT-TATACCTACTCCTCTTTGGTGCA
* * *
1039412 CAACCTTCACAGGGACAGGAGGAACCATTCTGCAGCCAA-T-CTTGTTCATGAAATGGCATGAAA
130 CAACCTTCACAGGGAAAGGAAGAACCATTCTGCAGCCAACTACTTGTTCACGAAATGGCATGAAA
* * * * *
1039475 ATATTGAAGTCTGCTCAACAGGCTGTCCTGCTTGGTCTTTGCCATTTTGGATTTCCTGGAGAGGT
195 ATACTAAAGTCTGCTCAACAGGCTGTCCTGCTTGGTCTTCGCCATTCTGGATTTCCTGGAGAGGC
* * * *
1039540 GAAAAAGCTTCAGTCTAAGATTCACATCGCTCGAATATTGAGTTACTGATAATATAACCATTATT
260 AAAAAAGCTTAAGTCTAAGATTCACATCGCTCGAATATTGAGTCACTGATAATATAACCATTACT
1039605 TTCAGTTTCAGTACTAGAAGCTAGAAGATTATTTAGTTCAGC
325 TTCAGTTTCAGTACTAGAAGCTAGAAGATTATTTAGTTCAGC
1039647 TGATT
1 TGATT
1039652 TACCATTGAG
Statistics
Matches: 329, Mismatches: 38, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
364 1 0.00
365 177 0.54
366 1 0.00
367 1 0.00
374 94 0.29
375 55 0.17
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (366 bp):
TGATTCAAATTTGATTGCATTAAATTGTTTAGTCGATGGGTTGTGTAAAGTCGGTCAGACTAAGG
ATGCAATGAAAATCTATAAATCAATGGAGGTAAGAGATTATTATACCTACTCCTCTTTGGTGCAC
AACCTTCACAGGGAAAGGAAGAACCATTCTGCAGCCAACTACTTGTTCACGAAATGGCATGAAAA
TACTAAAGTCTGCTCAACAGGCTGTCCTGCTTGGTCTTCGCCATTCTGGATTTCCTGGAGAGGCA
AAAAAGCTTAAGTCTAAGATTCACATCGCTCGAATATTGAGTCACTGATAATATAACCATTACTT
TCAGTTTCAGTACTAGAAGCTAGAAGATTATTTAGTTCAGC
Found at i:1040313 original size:2 final size:2
Alignment explanation
Indices: 1040306--1040338 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1040296 TGCATGTCTG
1040306 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1040339 GAAGGTGGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1052676 original size:13 final size:14
Alignment explanation
Indices: 1052643--1052673 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1052633 CAAACACTGT
*
1052643 AAAATGTTTTCTGG
1 AAAATGTTTTCCGG
1052657 AAAATGTTTTCCGG
1 AAAATGTTTTCCGG
1052671 AAA
1 AAA
1052674 TGTAATTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (14 bp):
AAAATGTTTTCCGG
Found at i:1053569 original size:56 final size:56
Alignment explanation
Indices: 1053446--1053575 Score: 161
Period size: 56 Copynumber: 2.3 Consensus size: 56
1053436 AAATATTTTT
* * ** * * *
1053446 TAGATATATTCAATTCCGGGGTCCATATTTTTATGTTTTTTAATAAAAACAATTGA
1 TAGATATATTCGATTTCGGGACCCATATTTTTATGCTTATTAATAAAAACAACTGA
* ***
1053502 TAGATATATTCGATTTCGGGACCCCTATTTTTATGCTTATTAATGGCAACAACTGA
1 TAGATATATTCGATTTCGGGACCCATATTTTTATGCTTATTAATAAAAACAACTGA
1053558 TAGATATATTCGATTTCG
1 TAGATATATTCGATTTCG
1053576 ATGCTTCTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (56 bp):
TAGATATATTCGATTTCGGGACCCATATTTTTATGCTTATTAATAAAAACAACTGA
Found at i:1053876 original size:56 final size:56
Alignment explanation
Indices: 1053815--1053996 Score: 210
Period size: 56 Copynumber: 3.2 Consensus size: 56
1053805 TGATAAATAG
* * * * *
1053815 AGATATATTTGATTTCGGAATCTCTATTTTTATATTTTTTAATGGAAATAACTGAT
1 AGATATATTCGATTTCGGAATCTCTATTTTTATACTTATTAATGGCAACAACTGAT
* *
1053871 AGATATACTT-GATTTCGGGA-CTTCTATTTTTGTACTTATTAATGGCAACAACTGAT
1 AGATATA-TTCGATTTCGGAATC-TCTATTTTTATACTTATTAATGGCAACAACTGAT
* *
1053927 AGATATATTCGATTTC-GAGGTC-CTTATTTTTATACTTATTAATAGCAACAACTGAT
1 AGATATATTCGATTTCGGA-ATCTC-TATTTTTATACTTATTAATGGCAACAACTGAT
*
1053983 AAATATATTCGATT
1 AGATATATTCGATT
1053997 CAAAACCCCT
Statistics
Matches: 109, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
55 5 0.05
56 101 0.93
57 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (56 bp):
AGATATATTCGATTTCGGAATCTCTATTTTTATACTTATTAATGGCAACAACTGAT
Found at i:1054013 original size:56 final size:56
Alignment explanation
Indices: 1053894--1054012 Score: 159
Period size: 56 Copynumber: 2.1 Consensus size: 56
1053884 TTCGGGACTT
* * * * ***
1053894 CTATTTTTGTACTTATTAATGGCAACAACTGATAGATATATTCGATTTCGAGGTCC
1 CTATTTTTATACTTATTAATAGCAACAACTGATAAATATATTCGATTTCAAAACCC
*
1053950 TTATTTTTATACTTATTAATAGCAACAACTGATAAATATATTCGA-TTCAAAACCC
1 CTATTTTTATACTTATTAATAGCAACAACTGATAAATATATTCGATTTCAAAACCC
1054005 CTATTTTT
1 CTATTTTT
1054013 TGAGACCCTA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
55 13 0.24
56 41 0.76
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (56 bp):
CTATTTTTATACTTATTAATAGCAACAACTGATAAATATATTCGATTTCAAAACCC
Found at i:1056768 original size:22 final size:20
Alignment explanation
Indices: 1056743--1056788 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
1056733 TAAAATTTTA
*
1056743 AGATAAATATTATCAATAAAAT
1 AGATAAATAATAT-AA-AAAAT
*
1056765 AGATGAATAATATAAAAAAT
1 AGATAAATAATATAAAAAAT
1056785 AGAT
1 AGAT
1056789 TTTAGTACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 2 0.09
22 11 0.50
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.28
Consensus pattern (20 bp):
AGATAAATAATATAAAAAAT
Found at i:1057714 original size:20 final size:21
Alignment explanation
Indices: 1057689--1057740 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1057679 TTTTCCCAAT
*
1057689 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* *
1057709 TCGCAACGCGAATTAGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1057730 TCGCAATGCGA
1 TCGCAATGCGA
1057741 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1057754 original size:20 final size:20
Alignment explanation
Indices: 1057729--1057843 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
1057719 AATTAGGAAA
*
1057729 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1057749 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1057769 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1057790 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1057810 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1057830 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1057844 ATACATAATC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 65 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1057773 original size:61 final size:61
Alignment explanation
Indices: 1057708--1057857 Score: 194
Period size: 61 Copynumber: 2.5 Consensus size: 61
1057698 GAATAAGTAA
* * * * *
1057708 ATCGCAACGCGA-ATTAGGAAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAATA-CAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
* * *
1057769 ATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
* *
1057830 TTCGCAACGCGATAATACATAATCGCAA
1 ATCGCAACGCGATAATACAAAATCGCAA
1057858 TACGATTTTC
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
61 74 0.96
62 3 0.04
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (61 bp):
ATCGCAACGCGATAATACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
Found at i:1058059 original size:22 final size:22
Alignment explanation
Indices: 1058031--1058074 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1058021 CACTCTCTCA
*
1058031 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
*
1058053 CCCATCTCCGGCAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
1058075 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:1058377 original size:20 final size:20
Alignment explanation
Indices: 1058318--1058381 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
1058308 GCGATTTTAG
*
1058318 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
1058338 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
1058358 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
1058378 TTTC
1 TTTC
1058382 AGAAACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:1058572 original size:25 final size:24
Alignment explanation
Indices: 1058518--1058572 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1058508 TGTTTATTAT
* *
1058518 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1058542 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1058568 TGTTT
1 TGTTT
1058573 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1060257 original size:19 final size:20
Alignment explanation
Indices: 1060203--1060269 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1060193 TAGTTTACTT
* *
1060203 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1060223 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1060243 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1060262 TCGCAACG
1 TCGCAACG
1060270 ACAAAATCGT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1060277 original size:14 final size:14
Alignment explanation
Indices: 1060258--1060315 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1060248 ATGCGAAATG
1060258 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
1060272 AAAATCGTAATGCGAA
1 AAAATCGCAA--CGAC
1060288 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1060304 AAAATCGCAACG
1 AAAATCGCAACG
1060316 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1060300 original size:32 final size:33
Alignment explanation
Indices: 1060242--1060332 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1060232 GGAAATGGCT
1060242 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1060275 ATCGTAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1060307 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1060333 TGCAATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1060413 original size:33 final size:33
Alignment explanation
Indices: 1060356--1060455 Score: 166
Period size: 33 Copynumber: 3.1 Consensus size: 33
1060346 TCGCGTTACA
*
1060356 ATTTTATCGTTGCGA-TTTCATTTCGCATTGCG
1 ATTTTGTCGTTGCGATTTTCATTTCGCATTGCG
**
1060388 ATTTTGTCGTTGCGATTTTCATTTCGCACAGCG
1 ATTTTGTCGTTGCGATTTTCATTTCGCATTGCG
1060421 ATTTTGTCGTTGCGATTTTCATTTCGCATTGCG
1 ATTTTGTCGTTGCGATTTTCATTTCGCATTGCG
1060454 AT
1 AT
1060456 AGCCATTTCC
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 14 0.23
33 48 0.77
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.46
Consensus pattern (33 bp):
ATTTTGTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:1060474 original size:20 final size:19
Alignment explanation
Indices: 1060440--1060495 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1060430 TTGCGATTTT
*
1060440 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1060459 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1060479 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
1060496 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1060592 original size:27 final size:26
Alignment explanation
Indices: 1060526--1060594 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
1060516 AGTAAACTAT
*
1060526 TCTT-CTTCTGGAATGTTTATATATG
1 TCTTACTTCTGGAATGTTTATATAAG
* * **
1060551 TTTTCCTT-TTAAATGTTTATATAAG
1 TCTTACTTCTGGAATGTTTATATAAG
1060576 TGCTTACTTCTGGAATGTT
1 T-CTTACTTCTGGAATGTT
1060595 ATCTGAGCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
25 18 0.55
26 8 0.24
27 7 0.21
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (26 bp):
TCTTACTTCTGGAATGTTTATATAAG
Found at i:1062384 original size:14 final size:14
Alignment explanation
Indices: 1062365--1062400 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1062355 ATTGTTTAAT
1062365 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1062379 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1062393 TGATTTGT
1 TGATTTGT
1062401 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1062546 original size:14 final size:14
Alignment explanation
Indices: 1062527--1062580 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1062517 GAAACTGACT
1062527 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1062541 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1062560 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1062574 ATCGCAA
1 ATCGCAA
1062581 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1062691 original size:20 final size:20
Alignment explanation
Indices: 1062646--1062699 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1062636 CGATTTTTCA
* *
1062646 TTTCGAATTGTGATAGCCAT
1 TTTCGCATTGCGATAGCCAT
1062666 TTTCGCATTGCGATAGCCAT
1 TTTCGCATTGCGATAGCCAT
*
1062686 TTTCGCGTTGCGAT
1 TTTCGCATTGCGAT
1062700 TTCCCCGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
TTTCGCATTGCGATAGCCAT
Found at i:1062938 original size:20 final size:20
Alignment explanation
Indices: 1062913--1063004 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
1062903 TTGAAGATGA
1062913 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
1062933 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* * **
1062953 TTACGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
1062974 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
1062994 TTGCGATTTTC
1 TTGCGATTTTC
1063005 CAAATTCGCA
Statistics
Matches: 52, Mismatches: 19, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 38 0.73
21 14 0.27
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:1063033 original size:20 final size:21
Alignment explanation
Indices: 1062989--1063038 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1062979 ATAGTCAGTA
*
1062989 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1063010 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1063030 TCGCATTGC
1 TCGCATTGC
1063039 AAATTAGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1063256 original size:12 final size:12
Alignment explanation
Indices: 1063237--1063271 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1063227 CTCTCCGGCG
1063237 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1063249 ATATCCGTTCCT
1 ACATCCGTTCCT
*
1063261 ACATCCTTTCC
1 ACATCCGTTCC
1063272 CATCCGGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.17, C:0.40, G:0.06, T:0.37
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1063852 original size:24 final size:24
Alignment explanation
Indices: 1063825--1063879 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
1063815 GTATTCGAAA
*
1063825 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1063849 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1063873 TTTGATA
1 TTTGATA
1063880 ATGTTTCAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1064065 original size:6 final size:6
Alignment explanation
Indices: 1064054--1064089 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1064044 TATAATCCTA
* *
1064054 AAAAAG AAAAAG AAGAAG AAAAAG AAGAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
1064090 TCCCCGAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1064074 original size:12 final size:12
Alignment explanation
Indices: 1064057--1064089 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1064047 AATCCTAAAA
1064057 AAGAAAAAGAAG
1 AAGAAAAAGAAG
1064069 AAGAAAAAGAAG
1 AAGAAAAAGAAG
1064081 AAGAAAAAG
1 AAGAAAAAG
1064090 TCCCCGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAAG
Found at i:1066409 original size:33 final size:33
Alignment explanation
Indices: 1066367--1066493 Score: 157
Period size: 33 Copynumber: 3.8 Consensus size: 33
1066357 GGAAATTACT
1066367 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * **
1066400 ATCGCAATGCGAAATAAAAATTGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * * *
1066432 TTTCGTAACGCGAAATGAAAATCGCAATGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1066466 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1066494 CGAATTTCAT
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
32 1 0.01
33 73 0.97
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1066486 original size:66 final size:66
Alignment explanation
Indices: 1066375--1066501 Score: 209
Period size: 66 Copynumber: 1.9 Consensus size: 66
1066365 CTATCGCAAT
* *
1066375 GCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAAAAATTGCAACGCTAATTTCGTAA
1 GCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAAAAATCGCAACGCGAATTTCGTAA
1066440 C
66 C
* * *
1066441 GCGAAATGAAAATCGCAATGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTC
1 GCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAAAAATCGCAACGCGAATTTC
1066502 ATTTCGCGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (66 bp):
GCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATAAAAATCGCAACGCGAATTTCGTAA
C
Found at i:1066528 original size:19 final size:19
Alignment explanation
Indices: 1066493--1066568 Score: 90
Period size: 19 Copynumber: 4.3 Consensus size: 19
1066483 AAATCGCAAC
*
1066493 GCGAATTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
1066512 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
1066531 GCGA--TTC---TCTCGTT
1 GCGATTTTCATTTCGCGTT
*
1066545 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCGTT
1066564 GCGAT
1 GCGAT
1066569 AGTACTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
14 10 0.21
16 3 0.06
17 3 0.06
19 32 0.67
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:1066694 original size:14 final size:14
Alignment explanation
Indices: 1066675--1066711 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1066665 CATCAATTAA
1066675 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1066689 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1066703 ACAAATCAA
1 ACAAATCAA
1066712 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1068112 original size:21 final size:21
Alignment explanation
Indices: 1068082--1068247 Score: 77
Period size: 21 Copynumber: 7.9 Consensus size: 21
1068072 TGAATGGTGG
*
1068082 GAGGGACCTCTTCAACGATGA
1 GAGGGGCCTCTTCAACGATGA
* * * * *
1068103 CAGTGGCCTCTTGAACGGTGG
1 GAGGGGCCTCTTCAACGATGA
* * *
1068124 GAGGGGACTC-TCGAGGAATGA
1 GAGGGGCCTCTTCAACG-ATGA
*
1068145 TAGGGGCCTCTTCAACGAT-A
1 GAGGGGCCTCTTCAACGATGA
* * * **
1068165 GGAGTGGACTCTTGAGGGATGA
1 -GAGGGGCCTCTTCAACGATGA
* * * * *
1068187 CAGTGGCCTCTTGAACGGTGG
1 GAGGGGCCTCTTCAACGATGA
* *
1068208 GAGGGGCCTC-TCGAGGAATGA
1 GAGGGGCCTCTTCAACG-ATGA
*
1068229 TAGGGGCCTCTTCAACGAT
1 GAGGGGCCTCTTCAACGAT
1068248 AGGAGTGGAC
Statistics
Matches: 99, Mismatches: 40, Indels: 12
0.66 0.26 0.08
Matches are distributed among these distances:
20 7 0.07
21 83 0.84
22 9 0.09
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
GAGGGGCCTCTTCAACGATGA
Found at i:1068127 original size:42 final size:41
Alignment explanation
Indices: 1068068--1068273 Score: 164
Period size: 42 Copynumber: 4.9 Consensus size: 41
1068058 GTGAATCGGG
* *
1068068 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
1068110 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
1068152 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * * *
1068194 CTCTTGAACGGTGGGAGGGGC-CTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGACTCT-TCAAGG-ATGACAGTGGC
* * * * *
1068236 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
1068274 GCGAGTCGGG
Statistics
Matches: 126, Mismatches: 30, Indels: 16
0.73 0.17 0.09
Matches are distributed among these distances:
40 2 0.02
41 11 0.09
42 98 0.78
43 13 0.10
44 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:1068209 original size:84 final size:84
Alignment explanation
Indices: 1068098--1068273 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
1068088 CCTCTTCAAC
1068098 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1068163 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
1068182 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGCCTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1068247 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1068266 GATGACAG
1 GATGACAG
1068274 GCGAGTCGGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:1068672 original size:91 final size:93
Alignment explanation
Indices: 1068492--1068676 Score: 288
Period size: 91 Copynumber: 2.0 Consensus size: 93
1068482 ATTTCAAACT
1068492 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1068557 AGAATTGGCAGCAACCGAATAAATTTAC
66 AGAATTGGCAGCAACCGAATAAATTTAC
* *
1068585 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAA-A-A-ATTTTA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
**
1068646 GCATTATTGGCAGCAACCGAATAAATTTAC
64 GCAGAATTGGCAGCAACCGAATAAATTTAC
1068676 T
1 T
1068677 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 34 0.40
92 1 0.01
93 20 0.23
94 4 0.05
95 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (93 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
AGAATTGGCAGCAACCGAATAAATTTAC
Found at i:1073100 original size:20 final size:20
Alignment explanation
Indices: 1073075--1073112 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1073065 TCTTTTGGTT
1073075 GAAATGAAAATCGCAACGCG
1 GAAATGAAAATCGCAACGCG
**
1073095 GAAATGACTATCGCAACG
1 GAAATGAAAATCGCAACG
1073113 AGAGAATCGC
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:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (20 bp):
GAAATGAAAATCGCAACGCG
Found at i:1073137 original size:33 final size:33
Alignment explanation
Indices: 1073083--1073167 Score: 152
Period size: 33 Copynumber: 2.5 Consensus size: 33
1073073 TTGAAATGAA
1073083 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGACTATCGCAACGAGAG
*
1073117 AATCGCAACGCGAAATGACTATCGCGACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
1073150 AATCGCAACGCGAAATGA
1 AATCGCAACGCGAAATGA
1073168 AAATCGCTAC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 39 0.78
34 11 0.22
ACGTcount: A:0.39, C:0.24, G:0.26, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAG
Found at i:1073172 original size:19 final size:19
Alignment explanation
Indices: 1073075--1073214 Score: 120
Period size: 19 Copynumber: 7.8 Consensus size: 19
1073065 TCTTTTGGTT
1073075 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
1073094 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1073112 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1073128 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
1073145 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1073161 GAAATGAAAATCGCTACGC
1 GAAATGAAAATCGCAACGC
*
1073180 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
1073199 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1073215 TGGGATTTTG
Statistics
Matches: 95, Mismatches: 15, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
14 17 0.18
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 52 0.55
20 14 0.15
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1073174 original size:33 final size:33
Alignment explanation
Indices: 1073083--1073214 Score: 138
Period size: 33 Copynumber: 3.8 Consensus size: 33
1073073 TTGAAATGAA
**
1073083 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
** *
1073117 AATCGCAACGCGAAATGACTATCGCGACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* *
1073150 AATCGCAACGCGAAATGAAAATCGCTACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGC-A-ACG--A-GAG
*
1073188 AATCACAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1073215 TGGGATTTTG
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
33 44 0.52
34 11 0.13
35 2 0.02
37 2 0.02
38 26 0.31
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:1073802 original size:20 final size:20
Alignment explanation
Indices: 1073777--1073829 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1073767 ACGCTATGTA
1073777 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1073797 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1073817 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1073830 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1073889 original size:21 final size:21
Alignment explanation
Indices: 1073860--1073915 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1073850 ATAGTAAGTA
*
1073860 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
1073881 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
1073902 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1073916 ACTTATTCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:1073890 original size:41 final size:41
Alignment explanation
Indices: 1073798--1073892 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
1073788 GAAAGTCAGA
* * * * ** *
1073798 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
1073839 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
1073881 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1073893 TTTCCCAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:1073925 original size:20 final size:21
Alignment explanation
Indices: 1073860--1073932 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
1073850 ATAGTAAGTA
* *
1073860 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTACCAAT
*
1073881 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTACCAAT
**
1073902 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTACCAAT
*
1073922 TCGCATTGCGA
1 TCGCGTTGCGA
1073933 ATTGGGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 16 0.34
21 31 0.66
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTTTACCAAT
Found at i:1074003 original size:21 final size:21
Alignment explanation
Indices: 1073963--1074003 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1073953 ACTGTAGACC
** *
1073963 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
1073984 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
1074004 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:1075736 original size:18 final size:19
Alignment explanation
Indices: 1075712--1075756 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
1075702 TCCAGTAATC
1075712 ATATTCT-CTGATAATCTT
1 ATATTCTACTGATAATCTT
*
1075730 TTATTCTCACTGATAATCTT
1 ATATTCT-ACTGATAATCTT
1075750 ATATTCT
1 ATATTCT
1075757 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
20 17 0.74
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (19 bp):
ATATTCTACTGATAATCTT
Found at i:1075744 original size:20 final size:20
Alignment explanation
Indices: 1075719--1075756 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1075709 ATCATATTCT
*
1075719 CTGATAATCTTTTATTCTCA
1 CTGATAATCTTATATTCTCA
1075739 CTGATAATCTTATATTCT
1 CTGATAATCTTATATTCT
1075757 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.50
Consensus pattern (20 bp):
CTGATAATCTTATATTCTCA
Found at i:1076602 original size:28 final size:26
Alignment explanation
Indices: 1076567--1076624 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 26
1076557 AAAAGTTTTG
*
1076567 ATATTTTAAAAATTTATTTAATTATAAA
1 ATATTTTAAAAATATA-TT-ATTATAAA
*
1076595 ATATTTTAAAAATATATTATTTTAAA
1 ATATTTTAAAAATATATTATTATAAA
1076621 ATAT
1 ATAT
1076625 AACACAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 11 0.39
27 2 0.07
28 15 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATTTTAAAAATATATTATTATAAA
Found at i:1076623 original size:15 final size:16
Alignment explanation
Indices: 1076596--1076625 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1076586 AATTATAAAA
1076596 TATTTTAAAAATATAT
1 TATTTTAAAAATATAT
1076612 TATTTT-AAAATATA
1 TATTTTAAAAATATA
1076626 ACACAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTTAAAAATATAT
Found at i:1077304 original size:22 final size:22
Alignment explanation
Indices: 1077276--1077328 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1077266 GCAACACCCT
*
1077276 CAAGACGTCGGGAGATCCCAAA
1 CAAGACGCCGGGAGATCCCAAA
1077298 CAAGACGCCGGGAGATCCCAAA
1 CAAGACGCCGGGAGATCCCAAA
*
1077320 CAAAACGCC
1 CAAGACGCC
1077329 AAAAAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.32, G:0.25, T:0.06
Consensus pattern (22 bp):
CAAGACGCCGGGAGATCCCAAA
Found at i:1085054 original size:19 final size:19
Alignment explanation
Indices: 1085030--1085070 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1085020 AACATACACA
1085030 TCTGGACATCTATCAAAAT
1 TCTGGACATCTATCAAAAT
1085049 TCTGGACATCTATCAAAAT
1 TCTGGACATCTATCAAAAT
1085068 TCT
1 TCT
1085071 TAACCCATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (19 bp):
TCTGGACATCTATCAAAAT
Found at i:1094426 original size:41 final size:40
Alignment explanation
Indices: 1094368--1094449 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 40
1094358 CTACTAAGAG
*
1094368 GGAGGTTTTTAAAGAGGCATTCTATTCCTATCAAAAAAAAA
1 GGAGGTTTTTAAAGAGGCATTCAATTCCTAT-AAAAAAAAA
* *
1094409 GGAGGTTTTTAATGAGGCCTTCAATTCCTATAAAAAAAAA
1 GGAGGTTTTTAAAGAGGCATTCAATTCCTATAAAAAAAAA
1094449 G
1 G
1094450 TTGAACAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
40 10 0.26
41 28 0.74
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (40 bp):
GGAGGTTTTTAAAGAGGCATTCAATTCCTATAAAAAAAAA
Found at i:1120900 original size:48 final size:48
Alignment explanation
Indices: 1120828--1120922 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
1120818 TTTTAATAGG
*
1120828 CAATAATTCAGCAAAGATAGGACCAACATTCTCTGATAATGAACACAA
1 CAATAATTCAGCAAAGATAAGACCAACATTCTCTGATAATGAACACAA
1120876 CAATAATTCAGCAAAGATAAGACCAACATTCTCTGATAATGAACACA
1 CAATAATTCAGCAAAGATAAGACCAACATTCTCTGATAATGAACACA
1120923 GCAGCACACG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.21
Consensus pattern (48 bp):
CAATAATTCAGCAAAGATAAGACCAACATTCTCTGATAATGAACACAA
Found at i:1122766 original size:23 final size:23
Alignment explanation
Indices: 1122740--1122808 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1122730 CACCACAGCT
* *
1122740 CGTATAATTGCACCGAAGTGTCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
1122763 CGTAGAATTGCATCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
1122786 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1122809 TATAATAATG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1137585 original size:15 final size:15
Alignment explanation
Indices: 1137567--1137599 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1137557 AAATTCTAAA
1137567 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1137582 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1137597 TAT
1 TAT
1137600 ATTTCTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1145374 original size:31 final size:31
Alignment explanation
Indices: 1145335--1145437 Score: 88
Period size: 31 Copynumber: 3.3 Consensus size: 31
1145325 AACCGATTTG
*
1145335 GGGA-CCAAATTAAATGTTTTTCAAAACAGA
1 GGGAGCCAAATTGAATGTTTTTCAAAACAGA
* * ** *
1145365 GGGAGCCAAAATGAA-G-TTTACCCAACCGA
1 GGGAGCCAAATTGAATGTTTTTCAAAACAGA
1145394 TTTGGG-GACCAAATTGAATGTTTTTCAAAACAGA
1 ---GGGAG-CCAAATTGAATGTTTTTCAAAACAGA
1145428 GGGAGCCAAA
1 GGGAGCCAAA
1145438 ACGCAGTTTG
Statistics
Matches: 54, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
29 9 0.17
30 5 0.09
31 17 0.31
32 13 0.24
33 1 0.02
34 9 0.17
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (31 bp):
GGGAGCCAAATTGAATGTTTTTCAAAACAGA
Found at i:1145446 original size:63 final size:63
Alignment explanation
Indices: 1145325--1145446 Score: 217
Period size: 63 Copynumber: 1.9 Consensus size: 63
1145315 AGGGAAATTA
*
1145325 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAACGAAGTTTACCC
* *
1145388 AACCGATTTGGGGACCAAATTGAATGTTTTTCAAAACAGAGGGAGCCAAAACGCAGTTT
1 AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAACGAAGTTT
1145447 GCCCCTTTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (63 bp):
AACCGATTTGGGGACCAAATTAAATGTTTTTCAAAACAGAGGGAGCCAAAACGAAGTTTACCC
Found at i:1146630 original size:20 final size:20
Alignment explanation
Indices: 1146607--1146648 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1146597 GAATCCTTCG
*
1146607 TCGTGAAATTGAAATCAAAC
1 TCGTGAAACTGAAATCAAAC
* *
1146627 TCGTGAAGCTGAAATCGAAC
1 TCGTGAAACTGAAATCAAAC
1146647 TC
1 TC
1146649 AGAGTTCTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGTGAAACTGAAATCAAAC
Found at i:1147090 original size:105 final size:105
Alignment explanation
Indices: 1146706--1147761 Score: 1860
Period size: 105 Copynumber: 10.0 Consensus size: 105
1146696 CGTTGTGGAG
* *
1146706 CTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
1146771 CTGGAGTCCAATATCCTTCGTTGTGACGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
1146811 CTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTG
1 CTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
* *
1146876 TCTTGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
1146917 CTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 CTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1146982 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
1147023 ATGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1147088 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
1147128 CTGAAATTGAGAAGTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1147193 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* * *
1147233 CTGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1147298 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
1147338 CTGACATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 CTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
*
1147403 TCTGGAGTCCAATATCCTTCGTTGTGAGGTTGAAATTGGCT
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
1147444 ATGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1147509 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* * *
1147549 CTGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1147614 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
1147654 CTGACATTGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1147719 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
1147759 CTG
1 CTG
1147762 GGTAAAACCT
Statistics
Matches: 910, Mismatches: 39, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
105 611 0.67
106 299 0.33
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
Found at i:1147363 original size:316 final size:315
Alignment explanation
Indices: 1146706--1147761 Score: 1898
Period size: 316 Copynumber: 3.3 Consensus size: 315
1146696 CGTTGTGGAG
* * *
1146706 CTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 CTGACATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
1146771 CTGGAGTCCAATATCCTTCGTTGTGACGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG-TGTTTGTTGA
* * *
1146836 CAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGATGT
130 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
* * *
1146901 GAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGA
195 GAAGTTGAAATTGGCTCTGTATTTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGA
*
1146966 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
259 AGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
1147023 ATGA-ATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 CTGACA-TTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1147087 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTGTTTGTTGA
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTGTTTGTTGA
*
1147152 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGT
130 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
1147217 GAAGTTGAAATTGGCTCTGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
195 GAAGTTGAAATTGGCTCTGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
1147282 GTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
260 GTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
1147338 CTGACATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 CTGACATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
* * * *
1147403 TCTGGAGTCCAATATCCTTCGTTGTGAGGTTGAAATTGGCTATGAATTTGAGAAATGTTTGTTGA
65 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTGTTTGTTGA
1147468 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
130 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
1147533 GAAGTTGAAATTGGCTCTGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
195 GAAGTTGAAATTGGCTCTGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
1147598 GTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
260 GTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
1147654 CTGACATTGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGACATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1147719 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1147762 GGTAAAACCT
Statistics
Matches: 713, Mismatches: 23, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
315 191 0.27
316 409 0.57
317 113 0.16
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (315 bp):
CTGACATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTGTTTGTTGAC
AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
AAGTTGAAATTGGCTCTGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
TTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
Found at i:1147491 original size:421 final size:420
Alignment explanation
Indices: 1146706--1147761 Score: 1932
Period size: 421 Copynumber: 2.5 Consensus size: 420
1146696 CGTTGTGGAG
* **
1146706 CTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
* *
1146771 CTGGAGTCCAATATCCTTCGTTGTGACGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGA
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGAGAA-ATGTTTGTTGA
* * *
1146836 CAACCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGATGT
129 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
1146901 GAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGA
194 GAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGA
1146966 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAATTT
259 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAATTT
1147031 GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
324 GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
1147096 CAATATCCTTCGTTGTGAAGTTGAAATTGGCT
389 CAATATCCTTCGTTGTGAAGTTGAAATTGGCT
*
1147128 CTGAAATTGAGAAGTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
*
1147193 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTATTTGAGAAATGTTTGTTGAC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGAGAAATGTTTGTTGAC
*
1147258 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTG
130 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
*
1147323 AAGTTGAAATTGGCTCTGACATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
195 AAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
*
1147388 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAGGTTGAAATTGGCTATGAATTTG
260 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAATTTG
1147453 AGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
325 AGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1147518 AATATCCTTCGTTGTGAAGTTGAAATTGGCT
390 AATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
1147549 CTGTATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
1 CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
*
1147614 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGACATTGAGAAATATTTGTTGAC
66 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATTGAGAAATGTTTGTTGAC
1147679 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
130 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
1147744 AAGTTGAAATTGGCTCTG
195 AAGTTGAAATTGGCTCTG
1147762 GGTAAAACCT
Statistics
Matches: 613, Mismatches: 20, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
420 1 0.00
421 501 0.82
422 111 0.18
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (420 bp):
CTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGT
CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAGAAATGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
AGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAATTTGA
GAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTGGCT
Found at i:1148595 original size:58 final size:58
Alignment explanation
Indices: 1148508--1148620 Score: 167
Period size: 58 Copynumber: 1.9 Consensus size: 58
1148498 TTCTTTTCTC
* *
1148508 TTTTTTTTTTTTTTTTTTTTTAATTTTAGGGCGCCCT-TCCGGGTTTTCACCCTAAACG
1 TTTTTTTTTTTTTTTTTTTTTAATCTTAGGACGCCCTCT-CGGGTTTTCACCCTAAACG
*
1148566 TTTTTTTTTTTTTTTTTTTTTCAA-CTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTTTTTTTTTTTTTTTTT-AATCTTAGGACGCCCTCTCGGGTTTTCACCCTAA
1148621 GCGAAGTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
58 47 0.94
59 3 0.06
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (58 bp):
TTTTTTTTTTTTTTTTTTTTTAATCTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
Found at i:1159478 original size:62 final size:60
Alignment explanation
Indices: 1159360--1159478 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 60
1159350 AGGAAATTAA
*
1159360 ACCGATTTGGGACCAAATTAAATGTTTTTTTCAAACAGAGGAGCCAAAATGAAGTTTACCC
1 ACCGATTTGGGACCAAATTAAATG-TTTTTTCAAACAGAGGAGCCAAAACGAAGTTTACCC
* *
1159421 ACCGATTTGGGGACCAAATTGAATG-TTTTTCAAAACAGAGGGAGCCAAAACGCAGTTT
1 ACCGATTT-GGGACCAAATTAAATGTTTTTTC-AAACAGA-GGAGCCAAAACGAAGTTT
1159479 GCCCCTTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
60 6 0.12
61 15 0.29
62 31 0.60
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (60 bp):
ACCGATTTGGGACCAAATTAAATGTTTTTTCAAACAGAGGAGCCAAAACGAAGTTTACCC
Found at i:1165007 original size:27 final size:27
Alignment explanation
Indices: 1164969--1165037 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
1164959 AGTAAAATAG
1164969 TTCTGAATGATTCAGCACTGAAGTACA
1 TTCTGAATGATTCAGCACTGAAGTACA
1164996 TTCTGAATGATTCAGCACTGAAGTACA
1 TTCTGAATGATTCAGCACTGAAGTACA
1165023 TTCTGAATGATTCAG
1 TTCTGAATGATTCAG
1165038 AGTCATTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (27 bp):
TTCTGAATGATTCAGCACTGAAGTACA
Found at i:1165110 original size:16 final size:16
Alignment explanation
Indices: 1165089--1165133 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1165079 ACAGAGCCTC
1165089 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
1165105 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
*
1165121 TGAATAATTCAGC
1 TGAATCATTCAGC
1165134 GCTTATCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:1168301 original size:159 final size:158
Alignment explanation
Indices: 1167985--1168301 Score: 625
Period size: 158 Copynumber: 2.0 Consensus size: 158
1167975 TGATCAGCTG
1167985 CAATTATTGATTGAATACACCCCAATGGGTCATTCTTTTGATTATGTGGCTGGAATCCAAAACAG
1 CAATTATTGATTGAATACACCCCAATGGGTCATTCTTTTGATTATGTGGCTGGAATCCAAAACAG
1168050 ATAAAGACATACCATAATGTCCCTAAAGAACTGATGTCTTTGATTCAATAATGGAAGGATAAAGT
66 ATAAAGACATACCATAATGTCCCTAAAGAACTGATGTCTTTGATTCAATAATGGAAGGATAAAGT
1168115 CCTGCACATGCAACAGTAGGGCAGTATC
131 CCTGCACATGCAACAGTAGGGCAGTATC
1168143 CAATTATTGATTGAATACACCCCAATGGGTCATTCTTTTGATTATGTGGCTGGAATCCAAAACAG
1 CAATTATTGATTGAATACACCCCAATGGGTCATTCTTTTGATTATGTGGCTGGAATCCAAAACAG
1168208 ATAAAGACATACCAGTAATGTCCCTAAAGAACTGATGTCTTTGATTCAATAATGGAAGGATAAAG
66 ATAAAGACATACCA-TAATGTCCCTAAAGAACTGATGTCTTTGATTCAATAATGGAAGGATAAAG
1168273 TCCTGCACATGCAACAGTAGGGCAGTATC
130 TCCTGCACATGCAACAGTAGGGCAGTATC
1168302 AAATCTCTAC
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
158 79 0.50
159 79 0.50
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (158 bp):
CAATTATTGATTGAATACACCCCAATGGGTCATTCTTTTGATTATGTGGCTGGAATCCAAAACAG
ATAAAGACATACCATAATGTCCCTAAAGAACTGATGTCTTTGATTCAATAATGGAAGGATAAAGT
CCTGCACATGCAACAGTAGGGCAGTATC
Found at i:1193092 original size:217 final size:215
Alignment explanation
Indices: 1192719--1193151 Score: 848
Period size: 217 Copynumber: 2.0 Consensus size: 215
1192709 CTTCATACCT
1192719 TGCTTTAACTGAAGAATTGGACGACTGGGATACCTCCCTTACATGTTCCAATGAATCTTACCAAA
1 TGCTTTAACTGAAGAATTGGACGACTGGGATACCTCCCTTACATGTTCCAATGAATCTTACCAAA
1192784 CTTCTCCAAACCCTTCTATACACTCTATCATAAAAGCTGATAGACACTTCAGTATCCGAACAAGC
66 CTTCTCCAAACCCTTCTATACACTCTATCATAAAAGCTGATAGACACTTCAGTATCCGAACAAGC
1192849 ACTTCCTGAATTACGTGGAGCAATTCTCAACTTTCTTCGATTAACCATACTTTTAGGCCGAGGAT
131 ACTTCCTGAATTACGTGGAGCAATTCTCAACTTTCTTCGATTAACCATACTTTTAGGCCGAGGAT
1192914 AGACTGTTCCTGATGTTCAG
196 AGACTGTTCCTGATGTTCAG
1192934 TGCTTTAACTGAAGAATTGGACGACTGGGATACCTCCCTTACATGTTCCAATGAATCTCTTACCA
1 TGCTTTAACTGAAGAATTGGACGACTGGGATACCTCCCTTACATGTTCCAATGAA--TCTTACCA
1192999 AACTTCTCCAAACCCTTCTATACACTCTATCATAAAAGCTGATAGACACTTCAGTATCCGAACAA
64 AACTTCTCCAAACCCTTCTATACACTCTATCATAAAAGCTGATAGACACTTCAGTATCCGAACAA
1193064 GCACTTCCTGAATTACGTGGAGCAATTCTCAACTTTCTTCGATTAACCATACTTTTAGGCCGAGG
129 GCACTTCCTGAATTACGTGGAGCAATTCTCAACTTTCTTCGATTAACCATACTTTTAGGCCGAGG
1193129 ATAGACTGTTCCTGATGTTCAG
194 ATAGACTGTTCCTGATGTTCAG
1193151 T
1 T
1193152 ATGAGGAAGA
Statistics
Matches: 216, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
215 55 0.25
217 161 0.75
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (215 bp):
TGCTTTAACTGAAGAATTGGACGACTGGGATACCTCCCTTACATGTTCCAATGAATCTTACCAAA
CTTCTCCAAACCCTTCTATACACTCTATCATAAAAGCTGATAGACACTTCAGTATCCGAACAAGC
ACTTCCTGAATTACGTGGAGCAATTCTCAACTTTCTTCGATTAACCATACTTTTAGGCCGAGGAT
AGACTGTTCCTGATGTTCAG
Found at i:1201320 original size:2 final size:2
Alignment explanation
Indices: 1201313--1201357 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1201303 TTTAAATTTA
1201313 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
1201355 AT A
1 AT A
1201358 AGAGATAAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1201710 original size:22 final size:23
Alignment explanation
Indices: 1201667--1201712 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1201657 ATTAATAGAC
*
1201667 ACCATTATCAACAGTAAAATAAA
1 ACCATTATCAACACTAAAATAAA
* *
1201690 ACCA-TATCAATACTAATATAAA
1 ACCATTATCAACACTAAAATAAA
1201712 A
1 A
1201713 TTAATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (23 bp):
ACCATTATCAACACTAAAATAAA
Found at i:1229722 original size:188 final size:191
Alignment explanation
Indices: 1229296--1229788 Score: 579
Period size: 188 Copynumber: 2.5 Consensus size: 191
1229286 GCGACAATAG
* * *
1229296 TCACATCTATAATATAGTATATTTATTAGTTTTGGGATTTATTGCTTTTAGTTGCTCTCTTTGCA
1 TCACATCTCTAATATAGTATATTTATTAGTTTTGGGATTTATTGCTTTCAGTTGTTCTCTTTGCA
* * *
1229361 TTCAAGTAAGTTCTTGATCACTCTCTTCG-TTTCTTTATCTTCTCATAAATCTTGCCACTTTTAT
66 TTCAAGT-A-TTCTTGATCACTCTTTTCGTTTTCTTTAT-TTCTAATAAATATTGCCAC---T-T
* * * * *
1229425 TTTATTATTTCAGATATGTTCTTGAGTGATGTCAATTTGTTTCTTGCACATTAATGCCATCTCCA
124 TTTATTACTCCAGATAGGTTCATGAGTGATGTCAATTTGTTTCTTGCACATTAATACCATCTCCA
*
1229490 TAG
189 TAA
* * * * *
1229493 CCACATCTCTAATACAGTATATTCATTAGTTTTGTGATTTATTGCTTTCAGTTGTTCTCTTTGAA
1 TCACATCTCTAATATAGTATATTTATTAGTTTTGGGATTTATTGCTTTCAGTTGTTCTCTTTGCA
* *
1229558 TTCAAGT-TT-TTGATCACTTTATTTTGTTTTCTTTATTTCCTAATAAATATT-CTCAC-TTTT-
66 TTCAAGTATTCTTGATCACTCT-TTTCGTTTTCTTTATTT-CTAATAAATATTGC-CACTTTTTA
* *
1229618 TT-CTCCAGATAGGTTCATGAGTGATGTCAATTTGTTTCTTGCACATTAATACTATTTCCATAA
128 TTACTCCAGATAGGTTCATGAGTGATGTCAATTTGTTTCTTGCACATTAATACCATCTCCATAA
* *
1229681 TCACATCTCTAATATAATATATTTATTAATTTTGGGATTTATTGCTTTTCA-TTCGTTCTCTTTG
1 TCACATCTCTAATATAGTATATTTATTAGTTTTGGGATTTATTGC-TTTCAGTT-GTTCTCTTTG
*
1229745 CATTCAAGTAAGTTCTTGATCACTGTCTTTCGTTTTCTTTATTT
64 CATTCAAGT-A-TTCTTGATCACTCT-TTTCGTTTTCTTTATTT
1229789 TATTCCCTAA
Statistics
Matches: 255, Mismatches: 31, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
188 94 0.37
189 25 0.10
190 4 0.02
192 2 0.01
193 36 0.14
194 8 0.03
195 22 0.09
197 64 0.25
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (191 bp):
TCACATCTCTAATATAGTATATTTATTAGTTTTGGGATTTATTGCTTTCAGTTGTTCTCTTTGCA
TTCAAGTATTCTTGATCACTCTTTTCGTTTTCTTTATTTCTAATAAATATTGCCACTTTTTATTA
CTCCAGATAGGTTCATGAGTGATGTCAATTTGTTTCTTGCACATTAATACCATCTCCATAA
Found at i:1234642 original size:34 final size:34
Alignment explanation
Indices: 1234604--1234674 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
1234594 TTATCATTAC
1234604 ATTTAAATTAACTTATTAAAAATTATAAATAAAA
1 ATTTAAATTAACTTATTAAAAATTATAAATAAAA
** * * *
1234638 ATTTACTTTGACTTCTTAAAAATTATAAATGAAA
1 ATTTAAATTAACTTATTAAAAATTATAAATAAAA
1234672 ATT
1 ATT
1234675 ACTTTTAGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.41
Consensus pattern (34 bp):
ATTTAAATTAACTTATTAAAAATTATAAATAAAA
Found at i:1235665 original size:5 final size:5
Alignment explanation
Indices: 1235648--1235686 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
1235638 ATCTCTCTTG
*
1235648 CTCTC CTCCC CTCTC CTCTC CTCTC CTCTC CTCTC CTCT
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC CTCT
1235687 TGACTTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (5 bp):
CTCTC
Found at i:1243518 original size:48 final size:48
Alignment explanation
Indices: 1243452--1243544 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
1243442 TGTTGTTGTT
* *
1243452 GTTGTTGTTGTTGACGCTGATCACTGTACGAATTGGAATGCTGCAGCG
1 GTTGTTGCTGTTGACGCTGATCACTGTACGAATTGGAACGCTGCAGCG
* *
1243500 GTTGTTGCTGTTGGCGCTGATCATTGTACGAATTGGAACGCTGCA
1 GTTGTTGCTGTTGACGCTGATCACTGTACGAATTGGAACGCTGCA
1243545 AAAGCTGAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.18, C:0.17, G:0.31, T:0.33
Consensus pattern (48 bp):
GTTGTTGCTGTTGACGCTGATCACTGTACGAATTGGAACGCTGCAGCG
Found at i:1254527 original size:27 final size:27
Alignment explanation
Indices: 1254489--1254558 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1254479 GTGTAGGAAT
*
1254489 TATAGAGTTATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
1254516 TATAGAGATATGATTTGTTATCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
1254543 TATAGAGATATGATTT
1 TATAGAGATATGATTT
1254559 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:1258276 original size:27 final size:27
Alignment explanation
Indices: 1258236--1258357 Score: 194
Period size: 27 Copynumber: 4.6 Consensus size: 27
1258226 GTGTAGGAAT
1258236 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
1258261 TATAGAGTTATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
1258288 TATATAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
1258315 TATAGAGATATGATTTGTTATCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
1258342 TATAGAAATATGATTT
1 TATAGAGATATGATTT
1258358 TGTAAATAGA
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 7 0.08
27 83 0.92
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:1265338 original size:18 final size:18
Alignment explanation
Indices: 1265311--1265351 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1265301 TCATTGTCCG
* *
1265311 TATTATTATTCTTATCAT
1 TATTAGTATTATTATCAT
*
1265329 TATTAGTATTATTTTCAT
1 TATTAGTATTATTATCAT
1265347 TATTA
1 TATTA
1265352 TCTCTTAGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TATTAGTATTATTATCAT
Found at i:1265636 original size:23 final size:23
Alignment explanation
Indices: 1265594--1265637 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1265584 CATATGAATT
*
1265594 TGTCCCGAAAGACCGCGTAGAGA
1 TGTCCCGAAAGACCACGTAGAGA
* *
1265617 TGTCCCGAATGACCATGTAGA
1 TGTCCCGAAAGACCACGTAGA
1265638 ACCCTCGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAAGACCACGTAGAGA
Found at i:1267590 original size:24 final size:20
Alignment explanation
Indices: 1267537--1267594 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1267527 TTCCAATTGA
*
1267537 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
1267557 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
1267580 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1267595 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:1271697 original size:20 final size:20
Alignment explanation
Indices: 1271672--1271710 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1271662 TTCCCATTGA
**
1271672 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGACGCATTCTTC
1271692 AGTGCATCGACGCATTCTT
1 AGTGCATCGACGCATTCTT
1271711 TAACATGTGC
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:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (20 bp):
AGTGCATCGACGCATTCTTC
Found at i:1274837 original size:28 final size:28
Alignment explanation
Indices: 1274804--1274857 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
1274794 AAAATAAATG
1274804 TAAAAAATA-ATCTAACAA-TAAAAAAAAC
1 TAAAAAATATAT-TAA-AAGTAAAAAAAAC
1274832 TAAAAAATATATTAAAAGTAAAAAAA
1 TAAAAAATATATTAAAAGTAAAAAAA
1274858 TTATTATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 2 0.08
28 20 0.83
29 2 0.08
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.20
Consensus pattern (28 bp):
TAAAAAATATATTAAAAGTAAAAAAAAC
Found at i:1278488 original size:38 final size:38
Alignment explanation
Indices: 1278444--1278520 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
1278434 ATCCGAAGCC
1278444 AACCCATTATATTCATCTAATAGCTCATCAAACGAATA
1 AACCCATTATATTCATCTAATAGCTCATCAAACGAATA
*
1278482 AACCCATTATATTCCTCTAATAGCTCATCAAACGAATA
1 AACCCATTATATTCATCTAATAGCTCATCAAACGAATA
1278520 A
1 A
1278521 TCTTCAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.25, G:0.05, T:0.29
Consensus pattern (38 bp):
AACCCATTATATTCATCTAATAGCTCATCAAACGAATA
Found at i:1280451 original size:22 final size:22
Alignment explanation
Indices: 1280424--1280485 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
1280414 AAACCATTCA
1280424 GGGGGAATCAGTTCCCTCCTTG
1 GGGGGAATCAGTTCCCTCCTTG
1280446 GGGGGAATCAGTTCCCTCCTTG
1 GGGGGAATCAGTTCCCTCCTTG
*
1280468 GGGGGAATCGGTTCCCTC
1 GGGGGAATCAGTTCCCTC
1280486 TGGGCAATCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.13, C:0.27, G:0.34, T:0.26
Consensus pattern (22 bp):
GGGGGAATCAGTTCCCTCCTTG
Found at i:1282879 original size:20 final size:20
Alignment explanation
Indices: 1282854--1282892 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1282844 AAGGTGGTGA
1282854 CGCGTTCGTTTATAAAATTC
1 CGCGTTCGTTTATAAAATTC
1282874 CGCGTTCGTTTATAAAATT
1 CGCGTTCGTTTATAAAATT
1282893 GGCAGAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (20 bp):
CGCGTTCGTTTATAAAATTC
Found at i:1283276 original size:12 final size:12
Alignment explanation
Indices: 1283254--1283295 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1283244 TTAAAAGTTT
*
1283254 TATATTTTAAAA
1 TATAATTTAAAA
1283266 T-TAAATTTAAAA
1 TAT-AATTTAAAA
1283278 TATAATTTAAAAA
1 TATAATTT-AAAA
1283291 TATAA
1 TATAA
1283296 AAATGAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 1 0.04
12 15 0.58
13 10 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TATAATTTAAAA
Found at i:1283290 original size:13 final size:13
Alignment explanation
Indices: 1283254--1283295 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1283244 TTAAAAGTTT
* *
1283254 TATATTTTAAAAT
1 TATAATTTAAAAA
1283267 TA-AATTT-AAAA
1 TATAATTTAAAAA
1283278 TATAATTTAAAAA
1 TATAATTTAAAAA
1283291 TATAA
1 TATAA
1283296 AAATGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 5 0.20
12 9 0.36
13 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TATAATTTAAAAA
Found at i:1283414 original size:18 final size:19
Alignment explanation
Indices: 1283384--1283437 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
1283374 TTATATTTAC
1283384 ATTTATAATTTAATATT-T
1 ATTTATAATTTAATATTAT
1283402 -TTTATATATTTAA-ATTAT
1 ATTTATA-ATTTAATATTAT
1283420 ATTT-TAAATTTAATATTA
1 ATTTAT-AATTTAATATTA
1283438 AAATATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
17 9 0.29
18 14 0.45
19 8 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTTATAATTTAATATTAT
Found at i:1283430 original size:29 final size:30
Alignment explanation
Indices: 1283371--1283430 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1283361 ACAAATTGTG
*
1283371 TTTTTATATTTACATTTATAATTTAATATT
1 TTTTTATATTTACAATTATAATTTAATATT
*
1283401 TTTTATATATTTA-AATTATATTTTAA-ATT
1 TTTT-TATATTTACAATTATAATTTAATATT
1283430 T
1 T
1283431 AATATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 4 0.15
30 15 0.56
31 8 0.30
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTTATATTTACAATTATAATTTAATATT
Found at i:1290240 original size:21 final size:21
Alignment explanation
Indices: 1290183--1290241 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
1290173 AACCCTGCAG
**
1290183 CGGTGGCATCTGACCTGGCTA
1 CGGTGGCATCTGATATGGCTA
*
1290204 CGGTGGCATCTTATATGGCTA
1 CGGTGGCATCTGATATGGCTA
1290225 CGGTGGCATCTGATATG
1 CGGTGGCATCTGATATG
1290242 AAAACGGTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.17, C:0.22, G:0.32, T:0.29
Consensus pattern (21 bp):
CGGTGGCATCTGATATGGCTA
Found at i:1290248 original size:21 final size:21
Alignment explanation
Indices: 1290203--1290252 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1290193 TGACCTGGCT
* ***
1290203 ACGGTGGCATCTTATATGGCT
1 ACGGTGGCATCTGATATGAAA
1290224 ACGGTGGCATCTGATATGAAA
1 ACGGTGGCATCTGATATGAAA
1290245 ACGGTGGC
1 ACGGTGGC
1290253 GTCTAACTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (21 bp):
ACGGTGGCATCTGATATGAAA
Done.