Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008426.1 Hibiscus syriacus cultivar Beakdansim tig00111210_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: 4445546
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 18
Found at i:1452573 original size:3 final size:3
Alignment explanation
Indices: 1452565--1452637 Score: 110
Period size: 3 Copynumber: 24.3 Consensus size: 3
1452555 TTGGTTTGTA
* *
1452565 AAT AAT AAT AAT ATT TAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1452613 AAT AAT AAT AAT GAT AAT GAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1452638 TAGGGTAGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1464865 original size:21 final size:20
Alignment explanation
Indices: 1464779--1464936 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1464769 AAATGACCAA
**
1464779 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1464798 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1464818 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1464838 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1464859 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1464880 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1464900 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1464921 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1464937 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1464952 original size:40 final size:40
Alignment explanation
Indices: 1464903--1465057 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
1464893 CGATTTTCCA
* ** *
1464903 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
1464943 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
1464983 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
1465023 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1465058 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:1464965 original size:20 final size:20
Alignment explanation
Indices: 1464903--1465056 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1464893 CGATTTTCCA
* ** *
1464903 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1464923 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1464943 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1464963 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1464983 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1465003 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1465023 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1465044 AAATCGCAACGCG
1 AAATCGCAACGCG
1465057 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:1465476 original size:33 final size:33
Alignment explanation
Indices: 1465437--1465507 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1465427 TTCACTTAGA
*
1465437 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1465470 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1465503 TTTCA
1 TTTCA
1465508 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:1465611 original size:21 final size:20
Alignment explanation
Indices: 1465587--1465692 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
1465577 TGCAGAAGAG
*
1465587 TCGCAATGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
1465608 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
1465628 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
1465649 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
1465663 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
1465682 TCGCAACGAGA
1 TCGCAACGAGA
1465693 GAATCGCAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 16 0.24
21 25 0.37
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1465631 original size:20 final size:20
Alignment explanation
Indices: 1465600--1465696 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
1465590 CAATGAGATA
1465600 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
1465620 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1465640 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
1465659 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
1465674 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1465694 AAT
1 AAT
1465697 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1465644 original size:41 final size:38
Alignment explanation
Indices: 1465580--1465696 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
1465570 TTCAATTTGC
* * *
1465580 AGAAGAGTCGCAATGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1465618 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
1465659 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1465692 AGAAT
1 AGAAT
1465697 CGCAACGCGA
Statistics
Matches: 70, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
33 23 0.33
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.16, G:0.26, T:0.12
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:1465666 original size:14 final size:14
Alignment explanation
Indices: 1465647--1465703 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1465637 GAGAAATGAA
1465647 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1465661 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1465680 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1465694 AATCGCAACG
1 AATCGCAACG
1465704 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:1465679 original size:33 final size:33
Alignment explanation
Indices: 1465639--1465719 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1465629 CGCAACGAGA
1465639 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1465672 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
1465705 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1465720 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:1465756 original size:14 final size:14
Alignment explanation
Indices: 1465737--1465825 Score: 79
Period size: 14 Copynumber: 5.7 Consensus size: 14
1465727 TTTCATTTCG
1465737 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1465751 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
1465769 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1465783 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1465802 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1465816 CGTTGCGATT
1 CGTTGCGATT
1465826 ATCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 30 0.48
15 3 0.05
16 3 0.05
17 6 0.10
18 10 0.16
19 10 0.16
ACGTcount: A:0.09, C:0.25, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1465801 original size:33 final size:33
Alignment explanation
Indices: 1465720--1465833 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1465710 CAAAATCGCA
1465720 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1465753 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1465785 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1465818 TTGCGATTATCATTTC
1 TTGCGATTTTCATTTC
1465834 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
32 32 0.41
33 47 0.59
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1467950 original size:93 final size:93
Alignment explanation
Indices: 1467527--1468172 Score: 1213
Period size: 93 Copynumber: 7.1 Consensus size: 93
1467517 TAGATTGCTT
*
1467527 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1467592 TTTGTC-TT-TTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1467617 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1467681 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1467709 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1467774 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1467801 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1467866 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1467894 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1467958 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1467985 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1468050 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1468078 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1468143 -TTGTCTTTGTTTTGTC-TTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1468168 AGTAA
1 AGTAA
1468173 TGCAATCCAT
Statistics
Matches: 548, Mismatches: 1, Indels: 14
0.97 0.00 0.02
Matches are distributed among these distances:
89 13 0.02
90 64 0.12
91 108 0.20
92 180 0.33
93 183 0.33
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1467957 original size:184 final size:184
Alignment explanation
Indices: 1467527--1468172 Score: 1205
Period size: 184 Copynumber: 3.5 Consensus size: 184
1467517 TAGATTGCTT
*
1467527 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1467592 TTTGTC-TT-TTTTGTCTTTTGGTTGAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 -TTGTCTTTGTTTTGTCTTTTGGTTGAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
1467655 TGTATTCTTTAACACTGTG-AATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1467709 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1467774 TTTGTCTTTGTTTTGTC-TTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 -TTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1467838 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
129 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1467894 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1467958 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
1468023 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1468078 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1468143 TTGTCTTTGTTTTGTC-TTTGGTTGAAGTAA
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAGTAA
1468173 TGCAATCCAT
Statistics
Matches: 457, Mismatches: 1, Indels: 11
0.97 0.00 0.02
Matches are distributed among these distances:
182 70 0.15
183 32 0.07
184 240 0.53
185 115 0.25
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (184 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTGTCTTTGTTTTGTCTTTTGGTTGAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGT
GTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1468278 original size:18 final size:19
Alignment explanation
Indices: 1468220--1468347 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1468210 TAGTTTACTT
* *
1468220 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1468240 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1468259 TCGCAACGCG-AATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1468277 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1468291 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1468310 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1468324 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1468343 TCGCA
1 TCGCA
1468348 TTGCGATTTC
Statistics
Matches: 89, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 6 0.07
17 2 0.02
18 14 0.16
19 33 0.37
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1468315 original size:33 final size:32
Alignment explanation
Indices: 1468256--1468347 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
1468246 CGCGAAACCA
**
1468256 AAATCGCAACGCG-AATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1468287 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1468320 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1468348 TTGCGATTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
31 1 0.02
32 13 0.23
33 42 0.75
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1468428 original size:32 final size:32
Alignment explanation
Indices: 1468348--1468438 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 32
1468338 CAAAATCGCA
* *
1468348 TTGCGATTTCATTTCGCGTTGCGATTCTTTTG
1 TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
*
1468380 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGA-TTTCATTTCGCGTTGCGATTCTGTCG
1468413 TTGCGATTTCATTTCGCGTTGCGATT
1 TTGCGATTTCATTTCGCGTTGCGATT
1468439 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 25 0.46
33 29 0.54
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1468467 original size:20 final size:19
Alignment explanation
Indices: 1468411--1468475 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
1468401 GCGATTCTGT
*
1468411 CGTTGCGATTTCA-TTTCG
1 CGTTGCGATTTTAGTTTCG
*
1468429 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
1468448 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
1468468 TGTTGCGA
1 CGTTGCGA
1468476 AAGTAAACTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.27
19 17 0.41
20 13 0.32
ACGTcount: A:0.11, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:1470394 original size:14 final size:14
Alignment explanation
Indices: 1470375--1470410 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1470365 ATTGTTTAAT
1470375 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1470389 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1470403 TGATTTGT
1 TGATTTGT
1470411 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1470538 original size:19 final size:19
Alignment explanation
Indices: 1470514--1470610 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
1470504 GCAAAAGACT
1470514 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1470533 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1470551 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1470565 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1470584 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1470604 ATCGCAA
1 ATCGCAA
1470611 CGGGAGAATC
Statistics
Matches: 69, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
13 1 0.01
14 9 0.13
16 4 0.06
18 10 0.14
19 29 0.42
20 16 0.23
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1470590 original size:51 final size:53
Alignment explanation
Indices: 1470514--1470629 Score: 209
Period size: 51 Copynumber: 2.2 Consensus size: 53
1470504 GCAAAAGACT
1470514 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
1470565 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1470618 ATCGCAATGCGA
1 ATCGCAATGCGA
1470630 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
51 29 0.47
52 6 0.10
53 27 0.44
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1470647 original size:19 final size:19
Alignment explanation
Indices: 1470619--1470820 Score: 201
Period size: 19 Copynumber: 11.7 Consensus size: 19
1470609 AACGGGAGAA
* *
1470619 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1470638 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1470654 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1470671 TCGCATTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1470690 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1470706 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1470723 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1470742 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1470758 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1470775 TCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATT
*
1470792 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1470808 TCGCATTGCGATT
1 TCGCATTGCGATT
1470821 CTCTCGTTGC
Statistics
Matches: 151, Mismatches: 12, Indels: 40
0.74 0.06 0.20
Matches are distributed among these distances:
14 29 0.19
16 23 0.15
17 22 0.15
19 77 0.51
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1470724 original size:85 final size:87
Alignment explanation
Indices: 1470625--1470834 Score: 279
Period size: 85 Copynumber: 2.5 Consensus size: 87
1470615 AGAATCGCAA
* *
1470625 TGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTC-ATT-TCGCATTACGATTTTCA
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTGCGATTCTCGCATTACGATTTTCA
1470688 TTTCGCATTGCGATTCTC-TCGT
66 TTTCGCATTGCGATTCTCAT-GT
* * * * *
1470710 TGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTTGCGATTCTCGCATTACGATTTTC
*
1470772 ATTTCGCATTGCGATTTTCATGT
65 ATTTCGCATTGCGATTCTCATGT
*
1470795 TGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1470835 GTAATTTCCG
Statistics
Matches: 107, Mismatches: 11, Indels: 12
0.82 0.08 0.09
Matches are distributed among these distances:
83 9 0.08
84 5 0.05
85 83 0.78
86 3 0.03
87 7 0.07
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (87 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTGCGATTCTCGCATTACGATTTTCA
TTTCGCATTGCGATTCTCATGT
Found at i:1470820 original size:52 final size:52
Alignment explanation
Indices: 1470619--1470792 Score: 321
Period size: 52 Copynumber: 3.3 Consensus size: 52
1470609 AACGGGAGAA
* *
1470619 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1470671 TCGCATTACGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1470723 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1470775 TCGCATTGCGATTTTCAT
1 TCGCATTGCGATTTTCAT
1470793 GTTGGGATTT
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 118 1.00
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1470842 original size:33 final size:33
Alignment explanation
Indices: 1470625--1470834 Score: 221
Period size: 33 Copynumber: 6.2 Consensus size: 33
1470615 AGAATCGCAA
*
1470625 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* *
1470658 TGCGATTTTCATTTCGCATTACGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
1470696 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
1470729 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1470762 TGCGATTTTCATTTCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTTCGCATTGCGATTCTC-TCGT
*
1470795 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1470828 TGCGATT
1 TGCGATT
1470835 GTAATTTCCG
Statistics
Matches: 146, Mismatches: 18, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
31 9 0.06
32 6 0.04
33 99 0.68
34 1 0.01
35 5 0.03
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1473332 original size:24 final size:24
Alignment explanation
Indices: 1473298--1473344 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1473288 CTGAAACATC
1473298 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1473322 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1473345 GACCAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1474053 original size:20 final size:20
Alignment explanation
Indices: 1474025--1474294 Score: 281
Period size: 20 Copynumber: 13.5 Consensus size: 20
1474015 AAATTTCAGT
* * *
1474025 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1474045 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1474065 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1474085 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1474105 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1474125 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1474145 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
1474165 GTTGTGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1474185 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
1474205 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1474225 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1474245 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1474265 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1474285 GTTGCGATTT
1 GTTGCGATTT
1474295 TGGAAAATCG
Statistics
Matches: 218, Mismatches: 30, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
20 217 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1475405 original size:2 final size:2
Alignment explanation
Indices: 1475394--1475424 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1475384 TAAATGCATA
1475394 AT AT -T 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
1475425 TAATTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1475475 original size:23 final size:23
Alignment explanation
Indices: 1475433--1475476 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1475423 ATTAATTTAA
*
1475433 AAATATTTTTTATATTACTTATT
1 AAATATTTTTTATATAACTTATT
1475456 AAATATTTTATTAT-TAACTTA
1 AAATATTTT-TTATATAACTTA
1475477 AATTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATATTTTTTATATAACTTATT
Found at i:1476903 original size:18 final size:17
Alignment explanation
Indices: 1476862--1476906 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
1476852 ATATCTATTT
1476862 AAATGATTTTTCTTAAA
1 AAATGATTTTTCTTAAA
1476879 AAA-GATTAATTT-TTAAA
1 AAATGATT--TTTCTTAAA
1476896 AAATGATTTTT
1 AAATGATTTTT
1476907 AAAAGATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 7 0.28
17 11 0.44
18 7 0.28
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
AAATGATTTTTCTTAAA
Found at i:1480126 original size:133 final size:133
Alignment explanation
Indices: 1479847--1480341 Score: 667
Period size: 133 Copynumber: 3.7 Consensus size: 133
1479837 ATGAAATTTG
* * * * * * * *
1479847 AAAAGGGGTCTGCTCCGTTGC-TCTTTAGAGTAGATTAGATATGAAAATGTTGATTCATTCCACT
1 AAAAGGGATCTGCTCCGCTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCCACT
* * * * *
1479911 ACTT-TTCAGGGAAGATTGAATCAAGGCAGACTTGTTCCATTGCTTCTCAGGGAAGATCAAATAT
66 -GTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTACTCCTCAGGGAAGATCAAATAT
1479975 GG-A
130 GGAA
* *
1479978 AAAAGAGGATATGCTCCACTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCCAC
1 AAAAG-GGATCTGCTCCGCTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCCAC
* * * *
1480043 TGTTCTTCAGGGAAGATTGATTCGAGGTAGACTTGTTCAACTACTCCTCAAGGAAGATCAAATAT
65 TGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTACTCCTCAGGGAAGATCAAATAT
1480108 GGAA
130 GGAA
*
1480112 AAAAGGGATCTGCTCCGCTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCAACT
1 AAAAGGGATCTGCTCCGCTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCCACT
* * * * *
1480177 -ATCTTCAGGGAA-ATTGAATCTAGGCAGACTTGTTCCACTACTCCTTAGGGAAGATCAATTTTG
66 GTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTACTCCTCAGGGAAGATCAAATATG
1480240 GAA
131 GAA
* * * *
1480243 AAAAAGGATCTGCTCCGCTGCTTCTTCAGGGTAAATTAGATCTGGAAATGTTGATTCATTCCACT
1 AAAAGGGATCTGCTCCGCTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCCACT
*
1480308 GTTCTTCAGGGAAGATTGAATCGAGACAGACTTG
66 GTTCTTCAGGGAAGATTGAATCGAGGCAGACTTG
1480342 CTTATCTTGT
Statistics
Matches: 319, Mismatches: 39, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
131 111 0.35
132 36 0.11
133 166 0.52
134 6 0.02
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (133 bp):
AAAAGGGATCTGCTCCGCTGCTTCTTCAGGGTAAATCAGATATGGAAACGTTGATTCATTCCACT
GTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTACTCCTCAGGGAAGATCAAATATG
GAA
Found at i:1481696 original size:35 final size:38
Alignment explanation
Indices: 1481623--1481696 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 38
1481613 GGGTCTTTTT
* *
1481623 CTCCCCATTTTTTGATTCGATAGAAGCATTGTAGAGGGG
1 CTCCCCATTTTTTGATTCGA-AGAAGCAATGTAAAGGGG
1481662 CTCCCCATTTTTT-ATTCG-A-AAGCAATGTAAAGGGG
1 CTCCCCATTTTTTGATTCGAAGAAGCAATGTAAAGGGG
1481697 TTTTCTTCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 14 0.42
36 1 0.03
38 5 0.15
39 13 0.39
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (38 bp):
CTCCCCATTTTTTGATTCGAAGAAGCAATGTAAAGGGG
Found at i:1491258 original size:174 final size:176
Alignment explanation
Indices: 1490948--1491275 Score: 509
Period size: 174 Copynumber: 1.9 Consensus size: 176
1490938 GAGCAAGATG
* * * * * *
1490948 ATAAGACCTTCGGACATGTTGTTTTCACGTGATTTTCAAAAAATGAGAAAGCGGTTTCCTAAGTT
1 ATAAGACCTTCGGACAGGATGTTTTCACGTGATTTTCAAAAAATAAGAAAGCGATTTCCAAAGTG
* *
1491013 TCTTATTTAAGTATTTTTAGAAAATGAAATATTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCT
66 TCTCATTTAAGTATTTTCAGAAAATGAAATATTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCT
1491078 TACCCAGTAAACTATTTCCAAAATTGGCAAGTTCTTCGAGCCATCT
131 TACCCAGTAAACTATTTCCAAAATTGGCAAGTTCTTCGAGCCATCT
** *
1491124 ATAAGACCTTCGG-CAGGATGTTTTCACGTGATTTTTTAAAAATAAGAAAGCGATTTTCAAAGTG
1 ATAAGACCTTCGGACAGGATGTTTTCACGTGATTTTCAAAAAATAAGAAAGCGATTTCCAAAGTG
* *
1491188 TCTCATTT-AGTATTTTCAGAAAATGACATTTTTGAAAAGTAAGAAA-ACGATTTCCAAAGTTTC
66 TCTCATTTAAGTATTTTCAGAAAATGAAATATTTGAAAAGTAAGAAAGA-GATTTCCAAAGTTTC
1491251 TTACCCAGTAAACTATTTCCAAAAT
130 TTACCCAGTAAACTATTTCCAAAAT
1491276 CCATAAGTCA
Statistics
Matches: 138, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
173 1 0.01
174 75 0.54
175 49 0.36
176 13 0.09
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (176 bp):
ATAAGACCTTCGGACAGGATGTTTTCACGTGATTTTCAAAAAATAAGAAAGCGATTTCCAAAGTG
TCTCATTTAAGTATTTTCAGAAAATGAAATATTTGAAAAGTAAGAAAGAGATTTCCAAAGTTTCT
TACCCAGTAAACTATTTCCAAAATTGGCAAGTTCTTCGAGCCATCT
Found at i:1494691 original size:41 final size:41
Alignment explanation
Indices: 1494587--1494691 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 41
1494577 TTTCCAAAAT
* * * * * *
1494587 TGATAAGTCCTTTGGGCCATCAATAAATCTTTTGAGCATGA
1 TGATAAATCCTTCGGGCCATCTATAAAGCTTTCGAGCAAGA
* * * *
1494628 TGATTACATCCTTCGGGTCATCTATCAGGCTTTCGAGCAAGA
1 TGA-TAAATCCTTCGGGCCATCTATAAAGCTTTCGAGCAAGA
1494670 TGATAAATCCTTCGGGCCATCT
1 TGATAAATCCTTCGGGCCATCT
1494692 GTAAGACCTT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
41 20 0.39
42 31 0.61
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (41 bp):
TGATAAATCCTTCGGGCCATCTATAAAGCTTTCGAGCAAGA
Found at i:1496012 original size:36 final size:38
Alignment explanation
Indices: 1495938--1496012 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
1495928 GGGTCTTCTT
* *
1495938 CTCCCCATTTTTTGATTTGATAGAAGCATTGTAGAGGGG
1 CTCCCCATTTTTTGATTTGA-AGAAGCAATGTAAAGGGG
1495977 CTCCCCATTTTTTGATTTG-A-AAGCAATGTAAAGGGG
1 CTCCCCATTTTTTGATTTGAAGAAGCAATGTAAAGGGG
1496013 TTTTCTTCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 14 0.41
37 1 0.03
39 19 0.56
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (38 bp):
CTCCCCATTTTTTGATTTGAAGAAGCAATGTAAAGGGG
Found at i:1496649 original size:16 final size:16
Alignment explanation
Indices: 1496618--1496684 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
1496608 CGTTCATTTA
1496618 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
* *
1496632 ATAAATGAAAATGAAC
1 ATAAATGAACACGAAC
*
1496648 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
1496664 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
1496680 ATAAA
1 ATAAA
1496685 CGGACATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 6 0.13
15 2 0.04
16 38 0.83
ACGTcount: A:0.61, C:0.15, G:0.10, T:0.13
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:1496662 original size:32 final size:32
Alignment explanation
Indices: 1496626--1496686 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
1496616 TAATAAATAA
*
1496626 ACGAACATAAATGAAAATGAACATAAACGAAC
1 ACGAACATAAATGAAAACGAACATAAACGAAC
*
1496658 ACGAACATAAATGAACACGAACATAAACG
1 ACGAACATAAATGAAAACGAACATAAACG
1496687 GACATAAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.57, C:0.18, G:0.13, T:0.11
Consensus pattern (32 bp):
ACGAACATAAATGAAAACGAACATAAACGAAC
Found at i:1497456 original size:24 final size:24
Alignment explanation
Indices: 1497420--1497494 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
1497410 GATTGTGTTA
1497420 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAATGAACATAAACG
*
1497444 AACATAATCGAATGAACATGAACG
1 AACATAATCGAATGAACATAAACG
* * * *
1497468 AACATAACCAAACGAACATAACCG
1 AACATAATCGAATGAACATAAACG
1497492 AAC
1 AAC
1497495 GTTCACGAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.13
Consensus pattern (24 bp):
AACATAATCGAATGAACATAAACG
Found at i:1497481 original size:14 final size:14
Alignment explanation
Indices: 1497464--1497495 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1497454 AATGAACATG
1497464 AACGAACATAACCA
1 AACGAACATAACCA
*
1497478 AACGAACATAACCG
1 AACGAACATAACCA
1497492 AACG
1 AACG
1497496 TTCACGAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.28, G:0.12, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCA
Found at i:1498452 original size:44 final size:44
Alignment explanation
Indices: 1498366--1498463 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
1498356 TTTGTGCTTA
*
1498366 ATGCATCGATACACTGAACAGTGCATCGATACATCCCTTTGAAT
1 ATGCATCGATACACTGAACAGTGCACCGATACATCCCTTTGAAT
* *
1498410 ATGCATCGATACACCATGAA-GGTGCACCGATGCA-CTCC-TTGAAT
1 ATGCATCGATACA-C-TGAACAGTGCACCGATACATC-CCTTTGAAT
*
1498454 GTGCATCGAT
1 ATGCATCGAT
1498464 GCATCCGTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
44 29 0.62
45 14 0.30
46 4 0.09
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (44 bp):
ATGCATCGATACACTGAACAGTGCACCGATACATCCCTTTGAAT
Found at i:1499646 original size:22 final size:22
Alignment explanation
Indices: 1499621--1499675 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1499611 CATTACCATT
1499621 TAATTAAAAATTAATCAAGAGA
1 TAATTAAAAATTAATCAAGAGA
1499643 TAATTAAAAATTAATCAAGAGA
1 TAATTAAAAATTAATCAAGAGA
1499665 TAATTAAAAAT
1 TAATTAAAAAT
1499676 GTGCTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (22 bp):
TAATTAAAAATTAATCAAGAGA
Found at i:1500523 original size:7 final size:7
Alignment explanation
Indices: 1500511--1500572 Score: 63
Period size: 7 Copynumber: 9.0 Consensus size: 7
1500501 TTTTTCTTTA
1500511 TTTTTCT
1 TTTTTCT
1500518 TTTTTCT
1 TTTTTCT
*
1500525 TTTTCCT
1 TTTTTCT
*
1500532 TTTTCCT
1 TTTTTCT
*
1500539 TTTTCCT
1 TTTTTCT
*
1500546 TTTTCCT
1 TTTTTCT
1500553 TTTTTC-
1 TTTTTCT
* *
1500559 ATTTTCA
1 TTTTTCT
1500566 TTTTTCT
1 TTTTTCT
1500573 CTTTCTTCAG
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
6 5 0.10
7 44 0.90
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTCT
Found at i:1500533 original size:14 final size:14
Alignment explanation
Indices: 1500511--1500576 Score: 78
Period size: 14 Copynumber: 4.6 Consensus size: 14
1500501 TTTTTCTTTA
*
1500511 TTTTTCTTTTTTCT
1 TTTTTCTTTTTCCT
*
1500525 TTTTCCTTTTTCCT
1 TTTTTCTTTTTCCT
*
1500539 TTTTCCTTTTTCCT
1 TTTTTCTTTTTCCT
* *
1500553 TTTTTCATTTTCAT
1 TTTTTCTTTTTCCT
1500567 TTTTCTCTTT
1 TTTT-TCTTT
1500577 CTTCAGGTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
14 41 0.91
15 4 0.09
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTCTTTTTCCT
Found at i:1500540 original size:21 final size:21
Alignment explanation
Indices: 1500495--1500556 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1500485 TATTTTTTCA
* *
1500495 TTCCTTTTTT-TCTTT-ATTT
1 TTCCTTTTTTCTTTTTCCTTT
1500514 TT-CTTTTTTCTTTTTCCTTT
1 TTCCTTTTTTCTTTTTCCTTT
*
1500534 TTCCTTTTTCCTTTTTCCTTT
1 TTCCTTTTTTCTTTTTCCTTT
1500555 TT
1 TT
1500557 TCATTTTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 7 0.19
19 6 0.16
20 5 0.14
21 19 0.51
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (21 bp):
TTCCTTTTTTCTTTTTCCTTT
Found at i:1500563 original size:21 final size:21
Alignment explanation
Indices: 1500511--1500581 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
1500501 TTTTTCTTTA
* *
1500511 TTTTTCTTTTTTCTTTTTCCT
1 TTTTTCATTTTCCTTTTTCCT
* *
1500532 TTTTCCTTTTTCCTTTTTCCT
1 TTTTTCATTTTCCTTTTTCCT
*
1500553 TTTTTCATTTTCATTTTTCTCT
1 TTTTTCATTTTCCTTTTTC-CT
*
1500575 TTCTTCA
1 TTTTTCA
1500582 GGTGAAGTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 35 0.81
22 8 0.19
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTCATTTTCCTTTTTCCT
Found at i:1506698 original size:20 final size:20
Alignment explanation
Indices: 1506673--1506721 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1506663 AGAGTGTAAT
1506673 GATGCACCAATCCATGCATC
1 GATGCACCAATCCATGCATC
*
1506693 GATGCACCAATCCATGTATC
1 GATGCACCAATCCATGCATC
1506713 GATGCACCA
1 GATGCACCA
1506722 TTGAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (20 bp):
GATGCACCAATCCATGCATC
Found at i:1506803 original size:65 final size:63
Alignment explanation
Indices: 1506734--1506893 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 63
1506724 GAATAAATTG
* * * *
1506734 AACATCGAATTCCTTATATGCATCGATGCACATA-CCATGTATCGATGCACTCAAG-TTTTTATG
1 AACATCGAATGCCTT-TATGCATCGATGCACA-AGACATGCATCGATGCACTCAAGCTATTT-TG
1506797 AA
63 -A
* *
1506799 AACATCGAATGCATTTGATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCCTTT-ATGCATCGATGCACAAGACATGCATCGATGCACTCAAGCTATTTTGA
*
1506863 AACATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGC-CTTTATGCATCGATGCAC
1506894 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
64 29 0.35
65 50 0.60
66 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCCTTTATGCATCGATGCACAAGACATGCATCGATGCACTCAAGCTATTTTGA
Found at i:1506893 original size:17 final size:19
Alignment explanation
Indices: 1506865--1506913 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1506855 TATTTTGAAA
1506865 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
1506883 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
1506902 CACCGATGCACT
1 CATCGATGCACT
1506914 GAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:1512766 original size:44 final size:44
Alignment explanation
Indices: 1512680--1512777 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 44
1512670 TTTGTGCTTA
*
1512680 ATGCATCGATACACTGAACAGTGCATCGATACATCCCTTTGAAT
1 ATGCATCGATACACTGAACAGTGCACCGATACATCCCTTTGAAT
* *
1512724 ATGCATCGATACACCATGAA-GGTGCACCGATGCA-CTCC-TTGAAT
1 ATGCATCGATACA-C-TGAACAGTGCACCGATACATC-CCTTTGAAT
*
1512768 GTGCATCGAT
1 ATGCATCGAT
1512778 TCATCCGTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
44 29 0.62
45 14 0.30
46 4 0.09
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (44 bp):
ATGCATCGATACACTGAACAGTGCACCGATACATCCCTTTGAAT
Found at i:1513943 original size:11 final size:11
Alignment explanation
Indices: 1513929--1513984 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
1513919 GCATTACCAT
1513929 TTAATTAAAAA
1 TTAATTAAAAA
* *
1513940 TTAATCAAGAGA
1 TTAATTAA-AAA
1513952 -TAATTAAAAA
1 TTAATTAAAAA
*
1513962 TTAATTAAGAGA
1 TTAATTAA-AAA
1513974 -TAATTAAAAA
1 TTAATTAAAAA
1513984 T
1 T
1513985 GTGTTTTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
10 4 0.11
11 27 0.77
12 4 0.11
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (11 bp):
TTAATTAAAAA
Found at i:1513955 original size:22 final size:22
Alignment explanation
Indices: 1513930--1513984 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1513920 CATTACCATT
1513930 TAATTAAAAATTAATCAAGAGA
1 TAATTAAAAATTAATCAAGAGA
*
1513952 TAATTAAAAATTAATTAAGAGA
1 TAATTAAAAATTAATCAAGAGA
1513974 TAATTAAAAAT
1 TAATTAAAAAT
1513985 GTGTTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (22 bp):
TAATTAAAAATTAATCAAGAGA
Found at i:1514806 original size:6 final size:6
Alignment explanation
Indices: 1514795--1514923 Score: 158
Period size: 6 Copynumber: 21.2 Consensus size: 6
1514785 ATTTATTTTC
*
1514795 TTTCTT TTTC-- TTTATT TTTCTT TTTCTT TTT-TT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
1514840 TTTCTT TTTCTT TTTCTT TTTCTTT TTTCTTT TTTCTTT TTTCTT TTT-TT
1 TTTCTT TTTCTT TTTCTT TTTC-TT TTTC-TT TTTC-TT TTTCTT TTTCTT
*
1514890 TTTCTTT TTTCTTT TTTCAT TTTCATT TTTCTT T
1 TTTC-TT TTTC-TT TTTCTT TTTC-TT TTTCTT T
1514924 CTTCAGGTGA
Statistics
Matches: 112, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
4 3 0.03
5 10 0.09
6 61 0.54
7 38 0.34
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:1514847 original size:45 final size:43
Alignment explanation
Indices: 1514790--1514926 Score: 141
Period size: 45 Copynumber: 3.0 Consensus size: 43
1514780 CATTTATTTA
*
1514790 TTTTCTTTCTTTTTCTTTATTTTTCTTTTTCTTTTTTTTTTCTT
1 TTTTTTTTCTTTTTCTTT-TTTTTCTTTTTCTTTTTTTTTTCTT
1514834 TTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTTCTTTTTTCTTTTTTCTT
1 TTT-TTTTTCTTTTTC--TTT-TTTTTC-TTTTTC--TTTT-TTTTTTCTT
* * * *
1514885 TTTTTTTTCTTTTT-TCTTTTTTCATTTTCATTTTTCTTTCTT
1 TTTTTTTTCTTTTTCTTTTTTTTCTTTTTCTTTTTTTTTTCTT
1514927 CAGGTGAAGT
Statistics
Matches: 80, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
42 8 0.10
43 3 0.04
44 3 0.04
45 16 0.20
46 6 0.08
47 11 0.14
48 6 0.08
50 15 0.19
51 12 0.15
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (43 bp):
TTTTTTTTCTTTTTCTTTTTTTTCTTTTTCTTTTTTTTTTCTT
Found at i:1514919 original size:1 final size:1
Alignment explanation
Indices: 1514799--1514906 Score: 81
Period size: 1 Copynumber: 108.0 Consensus size: 1
1514789 ATTTTCTTTC
* * * * * * * * * *
1514799 TTTTTCTTTATTTTTCTTTTTCTTTTTTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
1514864 TTTTCTTTTTTCTTTTTTCTTTTTTTTTTCTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1514907 CATTTTCATT
Statistics
Matches: 77, Mismatches: 30, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:1526663 original size:21 final size:22
Alignment explanation
Indices: 1526639--1526691 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
1526629 CCTTTGAATA
1526639 TGCATCGAT-ACACCATGAAGG
1 TGCATCGATCACACCATGAAGG
* * * *
1526660 TGCACCGATGCACTCCTTGAATG
1 TGCATCGAT-CACACCATGAAGG
1526683 TGCATCGAT
1 TGCATCGAT
1526692 GCATCCGTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 8 0.32
23 17 0.68
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (22 bp):
TGCATCGATCACACCATGAAGG
Found at i:1528227 original size:25 final size:24
Alignment explanation
Indices: 1528199--1528246 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
1528189 GGAGCGAGTT
1528199 CTTCACGAGCACCTCCTGCTCCTAG
1 CTTCACGAGCACCTCCT-CTCCTAG
* * *
1528224 CTTCTCGTGCTCCTCCTCTCCTA
1 CTTCACGAGCACCTCCTCTCCTA
1528247 CTCCGGCATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.10, C:0.46, G:0.12, T:0.31
Consensus pattern (24 bp):
CTTCACGAGCACCTCCTCTCCTAG
Found at i:1529517 original size:17 final size:19
Alignment explanation
Indices: 1529495--1529537 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1529485 GGAACATTAA
*
1529495 ATGCACT-TCA-TGCATCG
1 ATGCACTCTCAGTGCACCG
*
1529512 ATGCACTCTTAGTGCACCG
1 ATGCACTCTCAGTGCACCG
1529531 ATGCACT
1 ATGCACT
1529538 AAGGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (19 bp):
ATGCACTCTCAGTGCACCG
Found at i:1530736 original size:207 final size:208
Alignment explanation
Indices: 1530363--1530779 Score: 802
Period size: 207 Copynumber: 2.0 Consensus size: 208
1530353 TGTGATTTCT
1530363 TGCTAGACTCTCCTTCGTCAAGCCTTACACTCTTGATTTCCATTTCGATCATTTCTCTTGCTGTG
1 TGCTAGACTCTCCTTCGTCAAGCCTTACACTCTTGATTTCCATTTCGATCATTTCTCTTGCTGTG
1530428 ACTAAATCAGGAAAACTCTCGGATGAGTTTCCTATGAAGTGGCCAATGAAAGGAGTTCTCAGAGT
66 ACTAAATCAGGAAAACTCTCGGATGAGTTTCCTATGAAGTGGCCAATGAAAGGAGTTCTCAGAGT
*
1530493 GTTTACAAAGAGTGTCGTAACCGGTTTTAACCGGGCACGAAATTTTTACTTGGCGGGAAAATAAC
131 GTTTACAAAGAGTGTCGTAACCGGTTTTAACCGGGCACGAAATTTTTACTTGGCGGAAAAATAAC
1530558 ACGAAT-AATAAA
196 ACGAATAAATAAA
1530570 TGCTAGACTCTCCTTCGTCAAGCCTTACACTCTTGATTTCCATTTCGATCATTTCTCTTGCTGTG
1 TGCTAGACTCTCCTTCGTCAAGCCTTACACTCTTGATTTCCATTTCGATCATTTCTCTTGCTGTG
1530635 ACTAAATCAGGAAAACTCTCGGATGAGTTTCCTATGAAGTGGCCAATGAAAGGAGTTCTCAGAGT
66 ACTAAATCAGGAAAACTCTCGGATGAGTTTCCTATGAAGTGGCCAATGAAAGGAGTTCTCAGAGT
1530700 GTTTACAAAGAGTG-CGTAACCGGTTTTAACCCGGGCACGAAATTTTTACTTGGCGGAAAAATAA
131 GTTTACAAAGAGTGTCGTAACCGGTTTTAA-CCGGGCACGAAATTTTTACTTGGCGGAAAAATAA
1530764 CACGAATAAATAAA
195 CACGAATAAATAAA
1530778 TG
1 TG
1530780 ATTTTATTTT
Statistics
Matches: 207, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
206 15 0.07
207 184 0.89
208 8 0.04
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (208 bp):
TGCTAGACTCTCCTTCGTCAAGCCTTACACTCTTGATTTCCATTTCGATCATTTCTCTTGCTGTG
ACTAAATCAGGAAAACTCTCGGATGAGTTTCCTATGAAGTGGCCAATGAAAGGAGTTCTCAGAGT
GTTTACAAAGAGTGTCGTAACCGGTTTTAACCGGGCACGAAATTTTTACTTGGCGGAAAAATAAC
ACGAATAAATAAA
Found at i:1531603 original size:29 final size:30
Alignment explanation
Indices: 1531549--1531607 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1531539 AATGCAATTA
1531549 AATAGTGACTAAAACATATAAAATTAAAAT
1 AATAGTGACTAAAACATATAAAATTAAAAT
* *
1531579 AATAG-GATTAAAATATA-AAATATTAAAAT
1 AATAGTGACTAAAACATATAAA-ATTAAAAT
1531608 TTACAGCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAGTGACTAAAACATATAAAATTAAAAT
Found at i:1532880 original size:3 final size:3
Alignment explanation
Indices: 1532874--1532944 Score: 67
Period size: 3 Copynumber: 24.3 Consensus size: 3
1532864 TAATTATTTG
* * *
1532874 ATA ATA AT- ATA AT- ATGT ATA AT- ATA ATA ATA ATA ATA TTT ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
1532917 ATA ATA ATA ATA ATT TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1532945 ATTTAAGTAA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
2 6 0.11
3 47 0.85
4 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:1532918 original size:18 final size:18
Alignment explanation
Indices: 1532895--1532949 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
1532885 ATATGTATAA
1532895 TATAATAATAATAATATT
1 TATAATAATAATAATATT
1532913 TATAATAATAATAATAATT
1 TATAATAATAATAAT-ATT
1532932 T-TAATAATAATAA-ATT
1 TATAATAATAATAATATT
1532948 TA
1 TA
1532950 AGTAAAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.11
18 27 0.77
19 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAATAATAATAATATT
Found at i:1532936 original size:15 final size:15
Alignment explanation
Indices: 1532918--1532950 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1532908 ATATTTATAA
*
1532918 TAATAATAATAATTT
1 TAATAATAATAAATT
1532933 TAATAATAATAAATT
1 TAATAATAATAAATT
1532948 TAA
1 TAA
1532951 GTAAAATGAA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATAATAATAAATT
Found at i:1533201 original size:76 final size:76
Alignment explanation
Indices: 1533103--1533360 Score: 444
Period size: 76 Copynumber: 3.4 Consensus size: 76
1533093 GAGGTCTTAA
* * * * *
1533103 AAACATCATGCACTGAAGGACTTACAGATTACCCAAAGGTTTTGAAAACATCATAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1533168 AGGCTTTTTGG
66 AGGCTTTTTGG
1533179 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1533244 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
1533255 AAACATCATGCACTATAGGACTCACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCCA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1533320 AGGCTTTTTGG
66 AGGCTTTTTGG
1533331 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
1533361 TGGGAAATAG
Statistics
Matches: 172, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 172 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1533345 original size:152 final size:152
Alignment explanation
Indices: 1533103--1533848 Score: 675
Period size: 152 Copynumber: 4.7 Consensus size: 152
1533093 GAGGTCTTAA
* * *
1533103 AAACATCATGCACTGA-AGGACTTACAGATTACCCAAAGGTTTTGAAAACATCATAAAGCTCCCG
1 AAACATCATGCACT-ATAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCG
1533167 AAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
1533232 AAAAGCTCCCGAAGGCTTTTTGG
130 AAAAGCTCCCGAAGGCTTTTTGG
* * *
1533255 AAACATCATGCACTATAGGACTCACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCCA
1 AAACATCATGCACTATAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
***** * *
1533320 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGTGGGAAATAGTTTACTAAGTAAAA
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAA-GGCTT--T--G-AAAA
* * ** **
1533385 -AACTAAGGAAATTGTTTTCTTA--CTTTTT--
125 CATC-AA--AAA--GCTCCCGAAGGCTTTTTGG
* * * * * * ** * * *
1533413 -AACA--ATTTCATTTTAGAAAATATA-AAATGAGAAACTATGGAAATCGTTTTCTCATTATTTT
1 AAACATCA-TGCACTATAG-GACT-TACAGAT--G--ACCCT---AA--GGTTT-TGA--A---A
* ** * *
1533474 TCAAAATAACAACACCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATTGAAGGACTTAC
48 AC-ATC----------AAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTAC
1533539 AGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGG
102 AGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT-GG
* *
1533591 AAACAACATTCACTATAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTATAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1533656 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
1533721 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
* * *
1533743 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAATCTCCCGA
1 AAACATCATGCACTATAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
*
1533808 AGGCTTTTTGAAAACATCATGCACTGTAGGACTTACAGATG
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1533849 TGGGAAATAG
Statistics
Matches: 471, Mismatches: 72, Indels: 102
0.73 0.11 0.16
Matches are distributed among these distances:
151 1 0.00
152 202 0.43
153 99 0.21
155 2 0.00
156 7 0.01
157 12 0.03
158 7 0.01
159 1 0.00
160 9 0.02
161 3 0.01
162 4 0.01
163 1 0.00
164 3 0.01
166 3 0.01
167 3 0.01
169 3 0.01
170 4 0.01
172 3 0.01
173 5 0.01
175 12 0.03
177 7 0.01
178 5 0.01
179 9 0.02
180 9 0.02
181 1 0.00
182 3 0.01
183 53 0.11
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (152 bp):
AAACATCATGCACTATAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGG
Found at i:1533711 original size:76 final size:76
Alignment explanation
Indices: 1533484--1533848 Score: 640
Period size: 76 Copynumber: 4.8 Consensus size: 76
1533474 TCAAAATAAC
* * *
1533484 AACACCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCATTGAAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1533549 AAGGCTTTGAA
66 AAGGCTTTGAA
* * *
1533560 AACATCAAAAAGCTCCCGAAGGCTTTTTGGGAAACAACATTCACTATAGGACTTACAGATGACCC
1 AACATCAAAAAGCTCCCGAAGGCTTTTT-GGAAACATCATGCACTGTAGGACTTACAGATGACCC
*
1533625 TAAGGTTTTGAA
65 TAAGGCTTTGAA
1533637 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1533702 AAGGCTTTGAA
66 AAGGCTTTGAA
1533713 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1533778 AAGGCTTTGAA
66 AAGGCTTTGAA
* *
1533789 AACATCAAAAATCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTACAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1533849 TGGGAAATAG
Statistics
Matches: 275, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
76 205 0.75
77 70 0.25
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
AAGGCTTTGAA
Found at i:1544829 original size:29 final size:30
Alignment explanation
Indices: 1544775--1544833 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1544765 AATGCAATTA
1544775 AATAGTGACTAAAACATATAAAATTAAAAT
1 AATAGTGACTAAAACATATAAAATTAAAAT
* *
1544805 AATAG-GATTAAAATATA-AAATATTAAAAT
1 AATAGTGACTAAAACATATAAA-ATTAAAAT
1544834 TTACAACCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAGTGACTAAAACATATAAAATTAAAAT
Found at i:1545069 original size:2 final size:2
Alignment explanation
Indices: 1545056--1545094 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1545046 TTTATCCTAA
*
1545056 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1545095 AATGTAAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1546158 original size:3 final size:3
Alignment explanation
Indices: 1546152--1546225 Score: 73
Period size: 3 Copynumber: 25.3 Consensus size: 3
1546142 TAATTATTTG
* * *
1546152 ATA ATA AT- ATA AT- ATGT ATA AT- ATA ATA ATA ATA ATA TTT ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
1546195 ATA ATA ATA ATA ATA ATT TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1546226 ATTTAAGTAA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
2 6 0.10
3 50 0.86
4 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:1546230 original size:15 final size:15
Alignment explanation
Indices: 1546199--1546231 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1546189 TTTATAATAA
*
1546199 TAATAATAATAATTT
1 TAATAATAATAAATT
1546214 TAATAATAATAAATT
1 TAATAATAATAAATT
1546229 TAA
1 TAA
1546232 GTAAAATGAA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATAATAATAAATT
Found at i:1546485 original size:76 final size:76
Alignment explanation
Indices: 1546383--1546640 Score: 403
Period size: 76 Copynumber: 3.4 Consensus size: 76
1546373 GAGGTCTTAA
* * * *
1546383 AAACATCATGCACTG-AAGAGCTTACAGATTG-CCCAAAGGTTTTGAAAACATCATAAAGCTCCC
1 AAACATCATGCACTGTAGGA-CTTACAGA-TGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCC
1546446 GAAGGCTTTTTGG
64 GAAGGCTTTTTGG
1546459 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
**
1546524 ATTCTTTTTGG
66 AGGCTTTTTGG
* *
1546535 AAACATCATGCACTGTAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCCA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1546600 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1546611 AAACATCATGCACTATAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
1546641 TGGTAAATAG
Statistics
Matches: 168, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
75 2 0.01
76 163 0.97
77 3 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1546991 original size:76 final size:76
Alignment explanation
Indices: 1546764--1547128 Score: 613
Period size: 76 Copynumber: 4.8 Consensus size: 76
1546754 TCAAAATAAC
* * * *
1546764 AACACCAAAAAGCTCCCGAAGGCGTTTTGGAAACATCATGCACTGAATGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1546829 AAGGCTTTGAA
66 AAGGCTTTGAA
* * *
1546840 AACATCAAAAAGCTCCCGAAAGCTTTTTGGAAAACAACATTCACTGTAGGACTTACAGATGACCC
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGG-AAACATCATGCACTGTAGGACTTACAGATGACCC
*
1546905 TAAGGTTTTGAA
65 TAAGGCTTTGAA
*
1546917 AACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1546982 AAGGCTTTGAA
66 AAGGCTTTGAA
*
1546993 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTATAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1547058 AAGGCTTTGAA
66 AAGGCTTTGAA
* *
1547069 AACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTATAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1547129 TGGGAAATAG
Statistics
Matches: 272, Mismatches: 16, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
76 203 0.75
77 69 0.25
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
AAGGCTTTGAA
Found at i:1547112 original size:152 final size:153
Alignment explanation
Indices: 1546764--1547128 Score: 615
Period size: 153 Copynumber: 2.4 Consensus size: 153
1546754 TCAAAATAAC
* * * *
1546764 AACACCAAAAAGCTCCCGAAGGCGTTTTGGAAACATCATGCACTGAATGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
*
1546829 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAAGCTTTTTGGAAAACAACATTCACTGTAGGACTT
66 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAAGCTTTTTGGAAAACAACATGCACTGTAGGACTT
*
1546894 ACAGATGACCCTAAGGTTTTGAA
131 ACAGATGACCCTAAGGCTTTGAA
*
1546917 AACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
* *
1546982 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG-AAACATCATGCACTGTAGGACTT
66 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAAGCTTTTTGGAAAACAACATGCACTGTAGGACTT
*
1547046 ATAGATGACCCTAAGGCTTTGAA
131 ACAGATGACCCTAAGGCTTTGAA
* *
1547069 AACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTATAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1547129 TGGGAAATAG
Statistics
Matches: 199, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
152 99 0.50
153 100 0.50
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (153 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT
AAGGCTTTGAAAACATCAAAAAGCTCCCGAAAGCTTTTTGGAAAACAACATGCACTGTAGGACTT
ACAGATGACCCTAAGGCTTTGAA
Found at i:1551254 original size:3 final size:3
Alignment explanation
Indices: 1551248--1551310 Score: 56
Period size: 3 Copynumber: 20.3 Consensus size: 3
1551238 TAATTATTTG
* *
1551248 ATA ATA ATA TATA TATA AT- ATA CTA ATA ATTT ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA -ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
* *
1551295 ATT TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
1551311 ATTTAAGTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 38 0.78
4 9 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:1551275 original size:22 final size:19
Alignment explanation
Indices: 1551248--1551310 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 19
1551238 TAATTATTTG
1551248 ATAATAATATATATATAAT-
1 ATAATAATA-ATATATAATA
* *
1551267 ATACTAATAATTTATAATA
1 ATAATAATAATATATAATA
*
1551286 ATAATAATAAT-TTTAATA
1 ATAATAATAATATATAATA
1551304 ATAATAA
1 ATAATAA
1551311 ATTTAAGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
18 21 0.54
19 18 0.46
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAATAATAATATATAATA
Found at i:1551284 original size:18 final size:17
Alignment explanation
Indices: 1551251--1551315 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 17
1551241 TTATTTGATA
*
1551251 ATAATATATATATAATAT
1 ATAATA-ATTTATAATAT
1551269 ACTAATAATTTATAATAAT
1 A-TAATAATTTATAAT-AT
1551288 AATAATAATTT-TAATA-
1 -ATAATAATTTATAATAT
1551304 ATAATAAATTTA
1 ATAAT-AATTTA
1551316 AGTAAAATGA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
15 5 0.12
16 5 0.12
17 1 0.02
18 13 0.32
19 16 0.39
20 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATAATAATTTATAATAT
Found at i:1551304 original size:15 final size:15
Alignment explanation
Indices: 1551284--1551316 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1551274 TAATTTATAA
*
1551284 TAATAATAATAATTT
1 TAATAATAATAAATT
1551299 TAATAATAATAAATT
1 TAATAATAATAAATT
1551314 TAA
1 TAA
1551317 GTAAAATGAA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATAATAATAAATT
Found at i:1551839 original size:21 final size:22
Alignment explanation
Indices: 1551797--1551839 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1551787 CATAGCTCTA
* *
1551797 ATTTCTTCTTCTAATTGTTTTG
1 ATTTCTTCCTCTAATTGCTTTG
*
1551819 ATTTC-TCCTCTAGTTGCTTTG
1 ATTTCTTCCTCTAATTGCTTTG
1551840 TCTGCTCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.58
Consensus pattern (22 bp):
ATTTCTTCCTCTAATTGCTTTG
Found at i:1553723 original size:200 final size:200
Alignment explanation
Indices: 1553372--1553773 Score: 664
Period size: 200 Copynumber: 2.0 Consensus size: 200
1553362 ACTTTTTACT
*
1553372 CCTACTCTTGGTTTTTACCTACGCGTGAAAATCATCACACGCTAAGTATAAACTTAGTGAGACAA
1 CCTACTCCTGGTTTTTACCTACGCGTGAAAATCATCACACGCTAAGTATAAACTTAGTGAGACAA
1553437 TTAAAATAATAAACAGTGTAATAAAACTCATGCATGAAATTTAATGTCATTTTCCAATACCATAA
66 TTAAAATAATAAACAGTGTAATAAAACTCATGCATGAAATTTAATGTCATTTTCCAATACCATAA
* * * *
1553502 GATCACTTTATATGTGTGCCCAATATTTTACCATAAACAAAATGATCTAATATAAATATGATCAT
131 GATCACCTTACATGCGTGCCCAATATTTTACCATAAACAAAATGATATAATATAAATATGATCAT
1553567 TTTTA
196 TTTTA
* * *
1553572 CCTACTCCTGGTTTTTACC-AGCTCGTGAAAATCATCACACGCTAAGTATAAACTTTGTGAGGCA
1 CCTACTCCTGGTTTTTACCTA-CGCGTGAAAATCATCACACGCTAAGTATAAACTTAGTGAGACA
* * *
1553636 ATTAAAATAATAAATAGTGTAATACAACTCATGGATGAAATTTAATGTCATTTTCCAATGA-CAT
65 ATTAAAATAATAAACAGTGTAATAAAACTCATGCATGAAATTTAATGTCATTTTCCAAT-ACCAT
*
1553700 AAGATCACCTTACCTGCGTGCCCAATATTTTACCATAAACAAAATGATATAATATAAATATGATC
129 AAGATCACCTTACATGCGTGCCCAATATTTTACCATAAACAAAATGATATAATATAAATATGATC
1553765 ATTTTTA
194 ATTTTTA
1553772 CC
1 CC
1553774 AATAACTATA
Statistics
Matches: 188, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
199 1 0.01
200 186 0.99
201 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (200 bp):
CCTACTCCTGGTTTTTACCTACGCGTGAAAATCATCACACGCTAAGTATAAACTTAGTGAGACAA
TTAAAATAATAAACAGTGTAATAAAACTCATGCATGAAATTTAATGTCATTTTCCAATACCATAA
GATCACCTTACATGCGTGCCCAATATTTTACCATAAACAAAATGATATAATATAAATATGATCAT
TTTTA
Found at i:1556061 original size:62 final size:62
Alignment explanation
Indices: 1555988--1556109 Score: 217
Period size: 62 Copynumber: 2.0 Consensus size: 62
1555978 TTATTGTAAT
* *
1555988 CAAATTCCAAAATCTTTGAAATTAATCTTGGATCTTCTTTGGTAATGATCATTATTGGCAAG
1 CAAATTCCAAAATCTTTGAAATGAATCTTGGATCTTCTTTGGTAATGATCAATATTGGCAAG
*
1556050 CAAATTCCAAAATCTTTGAAATGAATCTTGGATCTTCTTTGGTTATGATCAATATTGGCA
1 CAAATTCCAAAATCTTTGAAATGAATCTTGGATCTTCTTTGGTAATGATCAATATTGGCA
1556110 GTTCACGTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (62 bp):
CAAATTCCAAAATCTTTGAAATGAATCTTGGATCTTCTTTGGTAATGATCAATATTGGCAAG
Found at i:1557262 original size:8 final size:9
Alignment explanation
Indices: 1557238--1557263 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1557228 TGACATTCAT
1557238 TTATTTTTA
1 TTATTTTTA
1557247 TTATTTTTA
1 TTATTTTTA
1557256 TTATTTTT
1 TTATTTTT
1557264 TCCACAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTATTTTTA
Found at i:1559098 original size:45 final size:44
Alignment explanation
Indices: 1558989--1559126 Score: 152
Period size: 45 Copynumber: 3.0 Consensus size: 44
1558979 TATTCTTTAT
* * * * * *
1558989 TTTCATTGATAGCATCCTTTCATCCTTATAATGCACCATTATGCCA
1 TTTCATTTATGGCATCCTTTCATCCTT-TTATACACAATTAT-ACA
* *
1559035 TTTCCATTT-TGGAATCCTTTCATGCCTTTTATACACTATTATACA
1 TTT-CATTTATGGCATCCTTTCAT-CCTTTTATACACAATTATACA
1559080 TTTCATTTATGGCATCCTTTCATTCCTTTTATACACAATTATACA
1 TTTCATTTATGGCATCCTTTCA-TCCTTTTATACACAATTATACA
1559125 TT
1 TT
1559127 GTTATACATC
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
44 5 0.06
45 39 0.49
46 27 0.34
47 8 0.10
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (44 bp):
TTTCATTTATGGCATCCTTTCATCCTTTTATACACAATTATACA
Found at i:1559653 original size:59 final size:59
Alignment explanation
Indices: 1559580--1560055 Score: 670
Period size: 59 Copynumber: 8.1 Consensus size: 59
1559570 CGTAGATTTT
* * * *
1559580 CACACCAAGTGCCCAATACGAAAATTCATACACTTAGTATTAATTTCTTAACAATTTT-G
1 CACACGAAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAAC-ATTTTAG
* * * * *
1559639 CACACAAAATGCCCAATACAGAAATTCATACACTTAGTATGAACTTCTTAACATTTTAG
1 CACACGAAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAG
* * * * * *
1559698 AACACAAAGTACCCTATAAGGAAATTCATACACTTGGTATGAATTTCTTAACATTTTAT
1 CACACGAAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAG
1559757 CACACGAAGTGCCCTATA-GGAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAG
1 CACACGAAGTGCCCTATACGG-AAATTCATACACTTAGTATGAATTTCTTAACATTTTAG
*
1559816 CACGCGAAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAG
1 CACACGAAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAG
* * *
1559875 CACACGAAGTGCTCTATACGGAAATTCATACCCTTAGTATGAATTTCTTAA-TTTTTAG
1 CACACGAAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAG
* * * *
1559933 CACGCGAAGTGCCCTATACGGAAATTTATACACTTAGTTTGAATTTCTTAATATTTTAG
1 CACACGAAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAG
* * *
1559992 CACACGAAGTTCTCTATACGGAAATTCATGCACTTAGTATGAATTTCTTAACATTTTAG
1 CACACGAAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAG
*
1560051 TACAC
1 CACAC
1560056 TTAGTGCCAT
Statistics
Matches: 374, Mismatches: 39, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
58 59 0.16
59 313 0.84
60 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (59 bp):
CACACGAAGTGCCCTATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAG
Found at i:1566237 original size:20 final size:20
Alignment explanation
Indices: 1566214--1566256 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1566204 AATCCACCAC
*
1566214 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
1566234 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
1566254 ATG
1 ATG
1566257 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:1573945 original size:26 final size:26
Alignment explanation
Indices: 1573895--1573954 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
1573885 AACCGAAGTG
***
1573895 ATAATACACATAAGGTTGTGTCCACC
1 ATAATACACATAAGGTTGAACCCACC
1573921 ATAATACACATAAGGTTGAACCCACC
1 ATAATACACATAAGGTTGAACCCACC
1573947 AT-ATACAC
1 ATAATACAC
1573955 TTAGTTCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 6 0.19
26 25 0.81
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (26 bp):
ATAATACACATAAGGTTGAACCCACC
Found at i:1580170 original size:109 final size:109
Alignment explanation
Indices: 1580042--1580249 Score: 242
Period size: 110 Copynumber: 1.9 Consensus size: 109
1580032 GTTTAAATAA
*
1580042 GGGGGACTAAAAAACAAATATTCC-AATAAACACATAACATACAAG-AAAAAATGGTAAATAACA
1 GGGGGACTAAAAAACAAATATCCCAAATAAA-ACATAACATACAAGAAAAAAAT-GTAAATAACA
* ** * *
1580105 ATTTTGGTCCTCGTAGATGACCAACATGCAAAAAATGCTAAACTAT
64 ATTTCGGTCCTCCAAGATGACCAAAATGAAAAAAATGCTAAACTAT
* * * * * *
1580151 GGGGGACTAAACAGA-AAATATCCCAAAATAAAATATGACATGCATGAAAAAAATGTAAATAACG
1 GGGGGACTAAA-AAACAAATATCCC-AAATAAAACATAACATACAAGAAAAAAATGTAAATAACA
*
1580215 ATTTCGGTCCTCCAAGGTGACCAAAATGAAAAAAA
64 ATTTCGGTCCTCCAAGATGACCAAAATGAAAAAAA
1580250 AAACGACTAA
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
109 19 0.23
110 50 0.61
111 13 0.16
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.20
Consensus pattern (109 bp):
GGGGGACTAAAAAACAAATATCCCAAATAAAACATAACATACAAGAAAAAAATGTAAATAACAAT
TTCGGTCCTCCAAGATGACCAAAATGAAAAAAATGCTAAACTAT
Found at i:1581555 original size:19 final size:20
Alignment explanation
Indices: 1581518--1581556 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1581508 CGTTATACAA
*
1581518 GGGGGGAATCGGTACTCCCTG
1 GGGGGGAATCAGTA-TCCCTG
1581539 GGGGGGAATCAGT-TCCCT
1 GGGGGGAATCAGTATCCCT
1581557 CCAAGCATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
21 12 0.71
ACGTcount: A:0.15, C:0.23, G:0.41, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCAGTATCCCTG
Found at i:1584096 original size:20 final size:20
Alignment explanation
Indices: 1584059--1584097 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1584049 AGATTGAGTG
* * *
1584059 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
1584079 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
1584098 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:1584321 original size:23 final size:23
Alignment explanation
Indices: 1584271--1584320 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1584261 ATTCCCCTGT
1584271 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
1584294 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
1584315 GGGGGG
1 GGGGGG
1584321 GTCGATTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:1592096 original size:6 final size:6
Alignment explanation
Indices: 1592085--1592131 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
1592075 TTTATGTTAA
* * *
1592085 ACGGGG ACGGGG ATGGGG ACGGGG ATGGGG ACGGGG ATGGGG ACGGG
1 ACGGGG ACGGGG ACGGGG ACGGGG ACGGGG ACGGGG ACGGGG ACGGG
1592132 TTTGGTAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.11, G:0.66, T:0.06
Consensus pattern (6 bp):
ACGGGG
Found at i:1592104 original size:12 final size:12
Alignment explanation
Indices: 1592087--1592131 Score: 90
Period size: 12 Copynumber: 3.8 Consensus size: 12
1592077 TATGTTAAAC
1592087 GGGGACGGGGAT
1 GGGGACGGGGAT
1592099 GGGGACGGGGAT
1 GGGGACGGGGAT
1592111 GGGGACGGGGAT
1 GGGGACGGGGAT
1592123 GGGGACGGG
1 GGGGACGGG
1592132 TTTGGTAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.16, C:0.09, G:0.69, T:0.07
Consensus pattern (12 bp):
GGGGACGGGGAT
Found at i:1594084 original size:12 final size:12
Alignment explanation
Indices: 1594067--1594091 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1594057 TGTTTACTTA
1594067 TTTACTATATTT
1 TTTACTATATTT
1594079 TTTACTATATTT
1 TTTACTATATTT
1594091 T
1 T
1594092 CCTAACGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTACTATATTT
Found at i:1594252 original size:22 final size:24
Alignment explanation
Indices: 1594217--1594273 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
1594207 CTATTTAGTA
* *
1594217 TTTTATTA-TATTATACATACAT-
1 TTTTATTATTTTTATAAATACATG
*
1594239 TTTTA-TATTTTTATAAATATATG
1 TTTTATTATTTTTATAAATACATG
1594262 TTTTATTATTTT
1 TTTTATTATTTT
1594274 ATTTATACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 2 0.07
22 16 0.55
23 5 0.17
24 6 0.21
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTATTATTTTTATAAATACATG
Found at i:1594420 original size:20 final size:19
Alignment explanation
Indices: 1594393--1594448 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
1594383 TTTTATCTTC
1594393 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
1594412 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
1594432 ATTT-TTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
1594449 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 4 0.13
19 11 0.35
20 16 0.52
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:1598192 original size:25 final size:25
Alignment explanation
Indices: 1598130--1598194 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
1598120 CAATCAGAAC
1598130 AAAAAGGG-CAAAAAAACAAAAAAG
1 AAAAAGGGACAAAAAAACAAAAAAG
* * **
1598154 AAAAGAAGCA-AAAAAAATTAAAAAG
1 AAAA-AGGGACAAAAAAACAAAAAAG
1598179 AAAAAGGGACAAAAAA
1 AAAAAGGGACAAAAAA
1598195 GCACATGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
24 7 0.22
25 25 0.78
ACGTcount: A:0.75, C:0.06, G:0.15, T:0.03
Consensus pattern (25 bp):
AAAAAGGGACAAAAAAACAAAAAAG
Found at i:1599022 original size:23 final size:21
Alignment explanation
Indices: 1598995--1599057 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 21
1598985 TGAAAGAAAC
1598995 AATATTTTCAAAACTTTTGATT
1 AATATTTTCAAAACTTTT-ATT
*
1599017 AAATATTTTTCGAAACTCTTTATT
1 -AATA-TTTTCAAAACT-TTTATT
* *
1599041 GATATTTTCAGAACTTT
1 AATATTTTCAAAACTTT
1599058 GAAAATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 2 0.06
22 9 0.26
23 7 0.21
24 13 0.38
25 3 0.09
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.49
Consensus pattern (21 bp):
AATATTTTCAAAACTTTTATT
Found at i:1601047 original size:106 final size:106
Alignment explanation
Indices: 1599784--1601046 Score: 1927
Period size: 106 Copynumber: 11.9 Consensus size: 106
1599774 CGAGATAACA
* * * * * *
1599784 CAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAAACAACTTCTCAAATTCATAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
1599849 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
1599890 CAAGCTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
1599955 AATTCAACTTCACAACGAATGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
1599996 CAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
1600061 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
1600102 CAAGTTCAACTTCATGACGAAGGGACCACTGGTTGTCAATAAACAACTTCCCTATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
1600167 ATTTCAACTTCACAGCGAAGGATATTGGATTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
1600208 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1600273 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
1600314 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGTCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* *
1600379 ATTTCAACTTCACATCGAAGGATATTGGACTCGAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
1600420 CAAGTTCAACTTCACGACGAAGGGACCTCTAGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
** * * *
1600485 ATTTCAACTTCACGGCGAAAGATATTGGACTCTAGACAATG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * *
1600526 CAAGTTCAACTTCACAACGAATGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
1600591 ATTTCAACTTCACAACGAAGGATATTGGACTCCATACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
1600632 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1600697 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
1600738 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
1600803 ATTTCAACTTCACAGA-GAAGGATATTGGACTCGAGACAACG
66 ATTTCAACTTCACA-ACGAAGGATATTGGACTCCAGACAACG
* * * *
1600844 CAAGTTCAACTTCATGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
* * * *
1600909 ATTTCAACTTCACAACAAATGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * * * *
1600950 CAAGTTCAACTTCACAACGAAGGGA-CGACTAGTTGTCAACAATCAATTTCCCGATTCCAGAGTC
1 CAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCC
* *
1601014 AATTTCAACTTCACGACGGAGGATATTGGACTC
65 AATTTCAACTTCACAACGAAGGATATTGGACTC
1601047 GGAACAATGC
Statistics
Matches: 1065, Mismatches: 89, Indels: 6
0.92 0.08 0.01
Matches are distributed among these distances:
105 3 0.00
106 1061 1.00
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:1601889 original size:37 final size:37
Alignment explanation
Indices: 1601802--1601895 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
1601792 TTTCGTCCTT
* *
1601802 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTCTA
*
1601839 CTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTA
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTCTA
** *
1601876 CTATTATTTAAACTCCTAAA
1 CTAGGATTCAAACTCCTAAA
1601896 GATATGATCC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTCTA
Found at i:1602357 original size:18 final size:19
Alignment explanation
Indices: 1602293--1602349 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
1602283 TTAACCCTTA
*
1602293 TTATTTATATGTATATATGTAT
1 TTATTTA-AT-TATAT-TTTAT
*
1602315 ATATTTAATTATATTTTAT
1 TTATTTAATTATATTTTAT
1602334 TTATTT-ATTATATTTT
1 TTATTTAATTATATTTT
1602350 TTTCATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 10 0.31
19 9 0.28
20 5 0.16
21 2 0.06
22 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (19 bp):
TTATTTAATTATATTTTAT
Found at i:1602412 original size:23 final size:24
Alignment explanation
Indices: 1602367--1602417 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
1602357 TTTCTTTGCG
* *
1602367 TTATATTATATTATTTTCCTATTA
1 TTATATTATATTATATTACTATTA
* *
1602391 TTATA-TATATTATATTATTATTT
1 TTATATTATATTATATTACTATTA
1602414 TTAT
1 TTAT
1602418 CTATGTTTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATATTATATTATATTACTATTA
Found at i:1602554 original size:11 final size:11
Alignment explanation
Indices: 1602540--1602670 Score: 58
Period size: 11 Copynumber: 11.5 Consensus size: 11
1602530 ATTATATGTA
*
1602540 TATTTATTTTT
1 TATTTATTTAT
1602551 TATTTATTTAT
1 TATTTATTTAT
1602562 TA-TTA-TTAT
1 TATTTATTTAT
* *
1602571 TA-CTATTTAG
1 TATTTATTTAT
1602581 TATTTTATATTAT
1 TA-TTTAT-TTAT
* ** *
1602594 ACATACATTTTT
1 -TATTTATTTAT
*
1602606 ATATTTTATATAT
1 -TA-TTTATTTAT
1602619 ATATTT-TTTAT
1 -TATTTATTTAT
1602630 TATTTTATTTAT
1 TA-TTTATTTAT
1602642 ACTATTTATTTAT
1 --TATTTATTTAT
1602655 T-TTTATTATAT
1 TATTTATT-TAT
1602666 T-TTTA
1 TATTTA
1602671 GTTTCTTTTC
Statistics
Matches: 94, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
9 8 0.09
10 16 0.17
11 28 0.30
12 16 0.17
13 23 0.24
14 3 0.03
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (11 bp):
TATTTATTTAT
Found at i:1602577 original size:23 final size:24
Alignment explanation
Indices: 1602551--1602665 Score: 88
Period size: 23 Copynumber: 4.9 Consensus size: 24
1602541 ATTTATTTTT
1602551 TATTTATTTATTATTATTAT-TAC
1 TATTTATTTATTATTATTATATAC
1602574 TATTTAGTATT-TTA-TATTATACATAC
1 TATTTA-T-TTATTATTATTAT--ATAC
1602600 -ATTT-TTATATT-TTA-TATATA-
1 TATTTATT-TATTATTATTATATAC
1602620 TATTT-TTTATTATT-TTATTTATAC
1 TATTTATTTATTATTATTA--TATAC
*
1602644 TATTTATTTATTTTTATTATAT
1 TATTTATTTATTATTATTATAT
1602666 TTTTAGTTTC
Statistics
Matches: 75, Mismatches: 1, Indels: 31
0.70 0.01 0.29
Matches are distributed among these distances:
20 4 0.05
21 13 0.17
22 1 0.01
23 21 0.28
24 16 0.21
25 14 0.19
26 6 0.08
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (24 bp):
TATTTATTTATTATTATTATATAC
Found at i:1602623 original size:13 final size:12
Alignment explanation
Indices: 1602605--1602670 Score: 63
Period size: 13 Copynumber: 5.8 Consensus size: 12
1602595 CATACATTTT
1602605 TATATTTTATATA
1 TATATTTTAT-TA
1602618 TATATTTT-TTA
1 TATATTTTATTA
1602629 T-TATTTTATT-
1 TATATTTTATTA
1602639 TATACTATTTATT-
1 TATA-T-TTTATTA
1602652 TAT-TTTTATTA
1 TATATTTTATTA
1602663 TAT-TTTTA
1 TATATTTTA
1602671 GTTTCTTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
10 13 0.27
11 16 0.33
12 2 0.04
13 17 0.35
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (12 bp):
TATATTTTATTA
Found at i:1602638 original size:28 final size:29
Alignment explanation
Indices: 1602604--1602668 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
1602594 ACATACATTT
1602604 TTATATTTTATA-TATATATTT-TTTATTA
1 TTATATTTTATACTATATATTTATTT-TTA
* *
1602632 TTTTA-TTTATACTATTTATTTATTTTTA
1 TTATATTTTATACTATATATTTATTTTTA
1602660 TTATATTTT
1 TTATATTTT
1602669 TAGTTTCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 6 0.19
28 19 0.61
29 6 0.19
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.71
Consensus pattern (29 bp):
TTATATTTTATACTATATATTTATTTTTA
Found at i:1604279 original size:13 final size:12
Alignment explanation
Indices: 1604250--1604291 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
1604240 TCACCAAACA
*
1604250 CTCTTCCTC-TC
1 CTCTTCATCTTC
*
1604261 CTCTTCATTTTC
1 CTCTTCATCTTC
1604273 TCTCTTCATCTTC
1 -CTCTTCATCTTC
1604286 CTCTTC
1 CTCTTC
1604292 CCAAGTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 7 0.27
12 8 0.31
13 11 0.42
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.52
Consensus pattern (12 bp):
CTCTTCATCTTC
Found at i:1606766 original size:22 final size:22
Alignment explanation
Indices: 1606738--1606783 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1606728 ACCTCGACAT
*
1606738 CCTCATTTACCTAGTTGCTGAC
1 CCTCATTTACCTAGCTGCTGAC
*
1606760 CCTCATTTACCTAGCTGTTGAC
1 CCTCATTTACCTAGCTGCTGAC
1606782 CC
1 CC
1606784 ACCCAGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.35, G:0.13, T:0.35
Consensus pattern (22 bp):
CCTCATTTACCTAGCTGCTGAC
Found at i:1614188 original size:22 final size:22
Alignment explanation
Indices: 1614163--1614207 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1614153 AGGTTTTTTA
1614163 AGGGTGGAATTGAAAAAAAGGC
1 AGGGTGGAATTGAAAAAAAGGC
*
1614185 AGGGTGTAATTGAAAAAAAGGC
1 AGGGTGGAATTGAAAAAAAGGC
1614207 A
1 A
1614208 AACGTTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.04, G:0.33, T:0.16
Consensus pattern (22 bp):
AGGGTGGAATTGAAAAAAAGGC
Found at i:1614216 original size:22 final size:22
Alignment explanation
Indices: 1614170--1614216 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1614160 TTAAGGGTGG
**
1614170 AATTGAAAAAAAGGCAGGGTGT
1 AATTGAAAAAAAGGCAACGTGT
1614192 AATTGAAAAAAAGGCAAACGT-T
1 AATTGAAAAAAAGGC-AACGTGT
1614214 AAT
1 AAT
1614217 GATTCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.51, C:0.06, G:0.23, T:0.19
Consensus pattern (22 bp):
AATTGAAAAAAAGGCAACGTGT
Found at i:1619898 original size:21 final size:21
Alignment explanation
Indices: 1619873--1619949 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
1619863 AGTAGAGGCG
*
1619873 ATATCAATACTCCCCTTGGCG
1 ATATCAATACTCCCCTTGGCA
*
1619894 GTATCAATACTCCCCTTGGCA
1 ATATCAATACTCCCCTTGGCA
1619915 ATATCAATACTCCCCTTGGCA
1 ATATCAATACTCCCCTTGGCA
*
1619936 GTATCAATACTCCC
1 ATATCAATACTCCC
1619950 AGCCCAAATC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.26, C:0.34, G:0.12, T:0.29
Consensus pattern (21 bp):
ATATCAATACTCCCCTTGGCA
Found at i:1621088 original size:47 final size:48
Alignment explanation
Indices: 1621037--1621179 Score: 139
Period size: 47 Copynumber: 2.9 Consensus size: 48
1621027 GTGTCCAAAT
* *
1621037 AATATTTTTATTTAAATTTATCATGTCGACGTGACGAGTTCTAAT-AA
1 AATATTTTTATTTAAATTTATCACGTCGACGTGACGAGTTCAAATAAA
* * * * *
1621084 AATATTTTTA-TTAAATTTTGTCACATCAGA-TTGACAAATTCAAATAAAA
1 AATATTTTTATTTAAA-TTTATCACGTC-GACGTGACGAGTTCAAAT-AAA
* *
1621133 AATATATTTTATTAAAACTTATCACGTCGACGTGACGAGTTTCAAAT
1 AATAT-TTTTATTTAAATTTATCACGTCGACGTGACGAG-TTCAAAT
1621180 TATTATAATA
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
46 5 0.07
47 29 0.39
48 2 0.03
49 9 0.12
50 18 0.24
51 11 0.15
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.39
Consensus pattern (48 bp):
AATATTTTTATTTAAATTTATCACGTCGACGTGACGAGTTCAAATAAA
Found at i:1623017 original size:5 final size:5
Alignment explanation
Indices: 1622997--1623350 Score: 90
Period size: 5 Copynumber: 70.8 Consensus size: 5
1622987 ATAAAAAAGA
* *
1622997 AAAAT AATAAT AAAAAT AAAAT -AAAG AAAAT AAAAA ACAAAT AAAAT
1 AAAAT AA-AAT -AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT
* * * * * * *
1623044 -AAAG AAGAT AAGAT -AAAG CAAGT AAAA- AAAGAT AAAGA- AAAAT TAAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAA-AT AAAAT AAAAT
* * *
1623091 AAGAT AAAGT AAAGAT AAAAA AGTAAAT AAAAT -AAAT AAAAT AAAGAT
1 AAAAT AAAAT AAA-AT AAAAT A--AAAT AAAAT AAAAT AAAAT AAA-AT
* *
1623139 GAAGAT AAAGAT AAAGAT -AAA- AAAAT AAAA- AGATAAA AAAAT -AAAT
1 -AAAAT AAA-AT AAA-AT AAAAT AAAAT AAAAT A-A-AAT AAAAT AAAAT
* * * * *
1623185 -AAAG AAAAT AATAGT AAAGAT AATAT -ATAT ATAAT AGATAAT -AAAT
1 AAAAT AAAAT AA-AAT AAA-AT AAAAT AAAAT AAAAT A-A-AAT AAAAT
* * *
1623231 AAAAA AGAAAG AAAATT AAAAT -AAAT -AAAT -AAAT AAAAT ATAAAG
1 AAAAT A-AAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT
* * *
1623276 AAAAT AAAA- ACGAAT GAAAT AAAGAT AAAAT -AAAT AAAA- ACAAT AAAAAT
1 AAAAT AAAAT A-AAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT -AAAAT
*
1623326 AAGAT -AAA- AAAAT -AAAT -AAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1623351 AAGGAAATAA
Statistics
Matches: 262, Mismatches: 45, Indels: 84
0.67 0.12 0.21
Matches are distributed among these distances:
4 70 0.27
5 118 0.45
6 62 0.24
7 12 0.05
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:1623106 original size:49 final size:47
Alignment explanation
Indices: 1623053--1623207 Score: 138
Period size: 49 Copynumber: 3.1 Consensus size: 47
1623043 TAAAGAAGAT
1623053 AAGATAAAGCAAGTAAAAAAAGATAAAGAAAAATTAAA-AAGATAAAGTA
1 AAGATAAA--AAGTAAAAAAAGATAAA-AAAAATTAAAGAAGATAAAGTA
* * *
1623102 AAGATAAAAAAGTAAATAAA-ATAAATAAAATAAAGATGAAGATAAAGATA
1 AAGAT-AAAAAGTAAAAAAAGATAAAAAAAATTAA-A-GAAGATAAAG-TA
* *
1623152 AAGATAAAAA--AATAAAAAGATAAAAAAATAAATAAAGAAAATAATAGTA
1 AAGATAAAAAGTAA-AAAAAGAT-AAAAAA-AATTAAAGAAGATAA-AGTA
1623201 AAGATAA
1 AAGATAA
1623208 TATATATATA
Statistics
Matches: 88, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
46 7 0.08
47 8 0.09
48 14 0.16
49 37 0.42
50 18 0.20
51 4 0.05
ACGTcount: A:0.72, C:0.01, G:0.12, T:0.16
Consensus pattern (47 bp):
AAGATAAAAAGTAAAAAAAGATAAAAAAAATTAAAGAAGATAAAGTA
Found at i:1623111 original size:38 final size:38
Alignment explanation
Indices: 1623069--1623207 Score: 90
Period size: 38 Copynumber: 3.9 Consensus size: 38
1623059 AAGCAAGTAA
1623069 AAAAAGATAAAGAAAAATTAAAAAGATAAAG-TAAAGAT
1 AAAAAGATAAAGAAAAA-TAAAAAGATAAAGATAAAGAT
* * *
1623107 AAAAA-AGTAAA-TAAAATAAATAAAATAAAGATGAAGAT
1 AAAAAGA-TAAAGAAAAATAAA-AAGATAAAGATAAAGAT
*
1623145 --AAAGATAAAGATAAAA-AAATA-A-AAAGATAAA-A-
1 AAAAAGATAAAGA-AAAATAAAAAGATAAAGATAAAGAT
*
1623177 AAATAA-ATAAAG-AAAAT-AATAG-TAAAGATAA
1 AAA-AAGATAAAGAAAAATAAAAAGATAAAGATAA
1623208 TATATATATA
Statistics
Matches: 83, Mismatches: 6, Indels: 29
0.70 0.05 0.25
Matches are distributed among these distances:
32 8 0.10
33 9 0.11
34 15 0.18
35 3 0.04
36 12 0.14
37 17 0.20
38 19 0.23
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.17
Consensus pattern (38 bp):
AAAAAGATAAAGAAAAATAAAAAGATAAAGATAAAGAT
Found at i:1623148 original size:12 final size:12
Alignment explanation
Indices: 1623071--1623159 Score: 57
Period size: 12 Copynumber: 7.8 Consensus size: 12
1623061 GCAAGTAAAA
*
1623071 AAAGATAAAGAA
1 AAAGATAAAGAT
* *
1623083 AAATTAAAAAGAT
1 AAA-GATAAAGAT
1623096 AAAG-TAAAGAT
1 AAAGATAAAGAT
*
1623107 AAA-A-AAGTAAAT
1 AAAGATAA--AGAT
1623119 AAA-AT-AA-AT
1 AAAGATAAAGAT
1623128 AAA-ATAAAGAT
1 AAAGATAAAGAT
*
1623139 GAAGATAAAGAT
1 AAAGATAAAGAT
1623151 AAAGATAAA
1 AAAGATAAA
1623160 AAAATAAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
9 7 0.11
10 5 0.08
11 13 0.21
12 27 0.44
13 9 0.15
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (12 bp):
AAAGATAAAGAT
Found at i:1623184 original size:66 final size:70
Alignment explanation
Indices: 1623096--1623270 Score: 186
Period size: 66 Copynumber: 2.5 Consensus size: 70
1623086 TTAAAAAGAT
*
1623096 AAAGTAAAGATAAAAAAGTAAATAAAATAAATAAAATAAAGATGAAGATAAAGATAA-AGAT-A-
1 AAAG-AAAGATAAAAAAATAAATAAAATAAATAAAATAAAGAT-AAGATAAAGATAATAGATAAT
1623158 AAA-AAA
64 AAATAAA
* * * * *
1623164 TAA-AAAGATAAAAAAATAAATAAAGA-AAATAATAGTAAAGATAATATATATATAATAGATAAT
1 AAAGAAAGATAAAAAAATAAATAAA-ATAAATAA-AATAAAGATAAGATAAAGATAATAGATAAT
1623227 AAATAAA
64 AAATAAA
1623234 AAAGAAAGA-AAATTAAAATAAAT-AAATAAATAAAATA
1 AAAGAAAGATAAA--AAAATAAATAAAATAAATAAAATA
1623271 TAAAGAAAAT
Statistics
Matches: 89, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
66 36 0.40
67 13 0.15
68 3 0.03
69 3 0.03
70 12 0.13
71 13 0.15
72 9 0.10
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (70 bp):
AAAGAAAGATAAAAAAATAAATAAAATAAATAAAATAAAGATAAGATAAAGATAATAGATAATAA
ATAAA
Found at i:1623186 original size:4 final size:4
Alignment explanation
Indices: 1623155--1623552 Score: 80
Period size: 4 Copynumber: 97.0 Consensus size: 4
1623145 AAAGATAAAG
* * *
1623155 ATAA AAAA ATAA A-AA GATAA AAAA ATAA ATAA AGAAA ATAA TAGTAA
1 ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA A-TAA ATAA -A-TAA
* * * * * *
1623202 AGATA ATAT ATAT AT-A ATAG AT-A ATAA ATAA A-AA AGAA AGAAA ATTAAA
1 ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A-TAA A-T-AA
* * *
1623251 ATAA ATAA ATAA ATAA A-AT ATAA AGAAA ATAA AAACGA ATGAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA A-TAA ATAA ATA--A AT-AA ATAA
* * * *
1623298 AGAT A-AA ATAA ATAA AAACA AT-A A-AA ATAA GATAA AAAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATA-A ATAA ATAA ATAA -ATAA ATAA ATAA ATAA
* * * * *
1623345 ATAA A-AA AGGAA AT-A ATAGT ACAA ATAA TATAT ATATA AT-A ATAT
1 ATAA ATAA A-TAA ATAA ATA-A ATAA ATAA -ATAA ATA-A ATAA ATAA
* * * * *
1623390 TTAA A-AA A-AGA AT-A ATAT ATAT ATATA TTAGA ATATTA ATAA AAAA
1 ATAA ATAA ATA-A ATAA ATAA ATAA ATA-A ATA-A ATA--A ATAA ATAA
* *
1623436 ACAA ATAA ATAA ATATA ATAT ATATA AT-A ATATA ATAA AT-A AT-A ATATA
1 ATAA ATAA ATAA ATA-A ATAA ATA-A ATAA ATA-A ATAA ATAA ATAA ATA-A
* * * * *
1623485 ATAA A-AT ATAT ATAT ATAA TATAA TATAT ATAA TATAA AT-A ATAA ATAT
1 ATAA ATAA ATAA ATAA ATAA -ATAA -ATAA ATAA -ATAA ATAA ATAA ATAA
*
1623534 ATAA ATAA A-AA CTAA ATAA
1 ATAA ATAA ATAA ATAA ATAA
1623553 TAATAATAAT
Statistics
Matches: 292, Mismatches: 58, Indels: 88
0.67 0.13 0.20
Matches are distributed among these distances:
3 49 0.17
4 163 0.56
5 67 0.23
6 12 0.04
7 1 0.00
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1623259 original size:9 final size:9
Alignment explanation
Indices: 1622997--1623350 Score: 115
Period size: 9 Copynumber: 38.4 Consensus size: 9
1622987 ATAAAAAAGA
1622997 AAAAT-AAT
1 AAAATAAAT
1623005 AATAA-AAAT
1 AA-AATAAAT
*
1623014 AAAATAAAG
1 AAAATAAAT
1623023 AAAAT-AA-
1 AAAATAAAT
*
1623030 AAAACAAAT
1 AAAATAAAT
*
1623039 AAAATAAAG
1 AAAATAAAT
*
1623048 AAGATAAGAT
1 AAAATAA-AT
*
1623058 AAAGCAAGTAAAA
1 -AA--AA-TAAAT
*
1623071 AAAGATAAAGA
1 AAA-ATAAA-T
1623082 AAAATTAAA-
1 AAAA-TAAAT
*
1623091 AAGATAAAGT
1 AAAATAAA-T
1623101 AAAGATAAA-
1 AAA-ATAAAT
*
1623110 AAAGTAAAT
1 AAAATAAAT
1623119 AAAATAAAT
1 AAAATAAAT
1623128 AAAATAAAGAT
1 AAAAT-AA-AT
* *
1623139 GAAGATAAAG
1 -AAAATAAAT
* *
1623149 ATAA-AGAT
1 AAAATAAAT
1623157 AAAA-AAAT
1 AAAATAAAT
*
1623165 AAAA-AGAT
1 AAAATAAAT
1623173 AAAA-AAAT
1 AAAATAAAT
*
1623181 -AAATAAAG
1 AAAATAAAT
1623189 AAAATAATAGT
1 AAAATAA-A-T
1623200 AAAGAT-AAT
1 AAA-ATAAAT
*
1623209 ATATATATAAT
1 A-AAATA-AAT
1623220 AGATAATAAAT
1 A-A-AATAAAT
1623231 AAAA-AAGA-
1 AAAATAA-AT
*
1623239 AAGAA-AATT
1 AA-AATAAAT
1623248 AAAATAAAT
1 AAAATAAAT
1623257 -AAATAAAT
1 AAAATAAAT
1623265 AAAAT--AT
1 AAAATAAAT
1623272 AAAGA-AAAT
1 AAA-ATAAAT
1623281 AAAA-ACGAAT
1 AAAATA--AAT
*
1623291 GAAATAAAGAT
1 AAAAT-AA-AT
1623302 AAAATAAAT
1 AAAATAAAT
1623311 AAAA-ACAAT
1 AAAATA-AAT
1623320 AAAAATAAGAT
1 -AAAATAA-AT
1623331 AAAA-AAAT
1 AAAATAAAT
1623339 -AAATAAAT
1 AAAATAAAT
1623347 AAAA
1 AAAA
1623351 AAGGAAATAA
Statistics
Matches: 267, Mismatches: 31, Indels: 95
0.68 0.08 0.24
Matches are distributed among these distances:
7 15 0.06
8 65 0.24
9 94 0.35
10 34 0.13
11 42 0.16
12 12 0.04
13 2 0.01
14 3 0.01
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (9 bp):
AAAATAAAT
Found at i:1623281 original size:50 final size:50
Alignment explanation
Indices: 1623140--1623336 Score: 127
Period size: 50 Copynumber: 3.8 Consensus size: 50
1623130 AATAAAGATG
* *
1623140 AAGATAAAGATAAAGATAAAAA-AATAAAAAGATAAAAAAATAAATAAAGAAAATA
1 AAGATAAA-AT-AA-ATAAAAACAATAAAAAGA-AAATAAA-AAAGAAAG-AAATA
* * * * *
1623195 ATAG-TAAAGATAATATATATATAATAGATAA-TAAATAAAAAAGAAAGAAAATTA
1 A-AGATAAA-ATAA-ATAAAAACAATA-AAAAGAAAATAAAAAAGAAAG-AAA-TA
* * *
1623249 AA-AT-AAATAAATAAATAA-AATATAAAGAAAATAAAAACGAATGAAATA
1 AAGATAAAATAAATAAA-AACAATAAAAAGAAAATAAAAAAGAAAGAAATA
* *
1623297 AAGATAAAATAAATAAAAACAATAAAAATAAGATAAAAAA
1 AAGATAAAATAAATAAAAACAATAAAAAGAAAATAAAAAA
1623337 ATAAATAAAT
Statistics
Matches: 114, Mismatches: 18, Indels: 25
0.73 0.11 0.16
Matches are distributed among these distances:
48 4 0.04
49 9 0.08
50 48 0.42
51 5 0.04
52 2 0.02
53 13 0.11
54 16 0.14
55 12 0.11
56 5 0.04
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.19
Consensus pattern (50 bp):
AAGATAAAATAAATAAAAACAATAAAAAGAAAATAAAAAAGAAAGAAATA
Found at i:1623313 original size:39 final size:34
Alignment explanation
Indices: 1623224--1623341 Score: 103
Period size: 34 Copynumber: 3.3 Consensus size: 34
1623214 TATAATAGAT
* * * *
1623224 AATAAATAAAAAAGAAAGAAAATTAAAATAAATA
1 AATAAATAAAATATAAAGAAAATAAAAACAAATA
*
1623258 AATAAATAAAATATAAAGAAAATAAAAACGAATGA
1 AATAAATAAAATATAAAGAAAATAAAAACAAAT-A
*
1623293 AATAAAGATAAAATAAATAAA-AACAATAAAAATAAGATA
1 AAT-AA-ATAAAAT--ATAAAGAA-AATAAAAACAA-ATA
*
1623332 AAAAAATAAA
1 AATAAATAAA
1623342 TAAATAAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
34 28 0.41
35 4 0.06
36 2 0.03
37 12 0.17
38 4 0.06
39 17 0.25
40 2 0.03
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (34 bp):
AATAAATAAAATATAAAGAAAATAAAAACAAATA
Found at i:1623385 original size:11 final size:10
Alignment explanation
Indices: 1623369--1623537 Score: 94
Period size: 9 Copynumber: 17.4 Consensus size: 10
1623359 AATAGTACAA
1623369 ATAATATATAT
1 ATAATA-ATAT
1623380 ATAATAATAT
1 ATAATAATAT
* *
1623390 TTAA-AA-AA
1 ATAATAATAT
*
1623398 AGAATAATAT
1 ATAATAATAT
1623408 AT-AT-ATAT
1 ATAATAATAT
* *
1623416 ATTAGAATAT
1 ATAATAATAT
1623426 -TAATAA-A-
1 ATAATAATAT
* *
1623433 AAAACAA-AT
1 ATAATAATAT
1623442 A-AATAA-AT
1 ATAATAATAT
1623450 ATAAT-ATAT
1 ATAATAATAT
1623459 ATAATAATAT
1 ATAATAATAT
1623469 AATAAATAATAAT
1 -AT-AATAAT-AT
*
1623482 ATAATAAAAT
1 ATAATAATAT
1623492 ATATATATATAAT
1 ATA-ATA-AT-AT
1623505 ATAAT-ATAT
1 ATAATAATAT
*
1623514 ATAAT-ATAA
1 ATAATAATAT
1623523 ATAATAAATAT
1 ATAAT-AATAT
1623534 ATAA
1 ATAA
1623538 ATAAAAACTA
Statistics
Matches: 125, Mismatches: 16, Indels: 34
0.71 0.09 0.19
Matches are distributed among these distances:
8 23 0.18
9 37 0.30
10 24 0.19
11 23 0.18
12 11 0.09
13 7 0.06
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.36
Consensus pattern (10 bp):
ATAATAATAT
Found at i:1623477 original size:15 final size:15
Alignment explanation
Indices: 1623439--1623560 Score: 96
Period size: 15 Copynumber: 7.9 Consensus size: 15
1623429 TAAAAAAACA
1623439 AATAAAT-A-AATAT
1 AATAAATAATAATAT
1623452 AATATATATAATAATAT
1 AATA-A-ATAATAATAT
1623469 AATAAATAATAATAT
1 AATAAATAATAATAT
1623484 AAT-AA-AATATATAT
1 AATAAATAATA-ATAT
1623498 ATATAATATAATATATAT
1 A-ATAA-ATAATA-ATAT
1623516 AATATAAATAATAA-AT
1 -A-ATAAATAATAATAT
*
1623532 ATATAAATAAAAACTA-
1 A-ATAAATAATAA-TAT
1623548 AAT-AATAATAATA
1 AATAAATAATAATA
1623561 ATGACAAGTA
Statistics
Matches: 95, Mismatches: 2, Indels: 24
0.79 0.02 0.20
Matches are distributed among these distances:
13 10 0.11
14 15 0.16
15 31 0.33
16 6 0.06
17 12 0.13
18 15 0.16
19 6 0.06
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAAATAATAATAT
Done.