Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_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: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 33
Found at i:18607 original size:20 final size:20
Alignment explanation
Indices: 18584--18635 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
18574 AACGCGATCC
18584 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
18604 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
18624 CCAAAATCGCAA
1 CCAGAATCGCAA
18636 CGCGATTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:18652 original size:21 final size:21
Alignment explanation
Indices: 18626--18748 Score: 63
Period size: 21 Copynumber: 5.7 Consensus size: 21
18616 ATCAGTTTCC
18626 AAAATCGCAACGCGATTATGG
1 AAAATCGCAACGCGATTATGG
* *
18647 AAAATCGCAATGCGAGCGATTCTTG
1 AAAATCGCAA--C--GCGATTATGG
* * *
18672 AAAATCGCGATGCGA-TA-GT
1 AAAATCGCAACGCGATTATGG
** * **
18691 ACAAATTCGCATTGCGATTTTCC
1 A-AAA-TCGCAACGCGATTATGG
* *
18714 ATAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTATGG
18734 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
18749 ACACATAAAT
Statistics
Matches: 75, Mismatches: 19, Indels: 17
0.68 0.17 0.15
Matches are distributed among these distances:
19 1 0.01
20 18 0.24
21 34 0.45
22 3 0.04
23 2 0.03
25 17 0.23
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (21 bp):
AAAATCGCAACGCGATTATGG
Found at i:18674 original size:25 final size:25
Alignment explanation
Indices: 18637--18686 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
18627 AAATCGCAAC
18637 GCGATTATGGAAAATCGCAATGCGA
1 GCGATTATGGAAAATCGCAATGCGA
* * *
18662 GCGATTCTTGAAAATCGCGATGCGA
1 GCGATTATGGAAAATCGCAATGCGA
18687 TAGTACAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (25 bp):
GCGATTATGGAAAATCGCAATGCGA
Found at i:18785 original size:60 final size:60
Alignment explanation
Indices: 18716--18907 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
18706 GATTTTCCAT
** * *
18716 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * * *** *
18776 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT-
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
18835 -ATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
18895 AATCGCAACGCGA
1 AATCGCAACGCGA
18908 TATTTAAAGC
Statistics
Matches: 109, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
58 31 0.28
59 19 0.17
60 48 0.44
61 11 0.10
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGAATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:18810 original size:20 final size:20
Alignment explanation
Indices: 18716--18906 Score: 210
Period size: 20 Copynumber: 9.6 Consensus size: 20
18706 GATTTTCCAT
* ** *
18716 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
18736 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
18756 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
18776 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
18796 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
18816 AATCGCAATGCGTATCCGT-
1 AATCGCAACGCGTATCCGTA
18835 -ATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
18854 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
18875 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
18895 AATCGCAACGCG
1 AATCGCAACGCG
18907 ATATTTAAAG
Statistics
Matches: 143, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
18 17 0.12
19 2 0.01
20 106 0.74
21 17 0.12
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:18855 original size:78 final size:79
Alignment explanation
Indices: 18757--18902 Score: 224
Period size: 78 Copynumber: 1.9 Consensus size: 79
18747 GAACACATAA
* * * **
18757 ATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGT-AAATCGCAACGCGTATGGGTAAATC
1 ATCGCAACGCGTATCCGTAAATCGCAACGAT-AATACATAAAATCGCAACGCGTATCCGTAAATC
18820 GCAATGCGTATCCGT
65 GCAATGCGTATCCGT
18835 ATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCG
1 ATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCG
18900 CAA
66 CAA
18903 CGCGATATTT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
78 33 0.54
79 28 0.46
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (79 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCG
CAATGCGTATCCGT
Found at i:19324 original size:33 final size:33
Alignment explanation
Indices: 19285--19355 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
19275 TTCACTTAGA
*
19285 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
19318 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
19351 TTTCA
1 TTTCA
19356 GTTAGTATTT
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:19494 original size:14 final size:14
Alignment explanation
Indices: 19475--19529 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
19465 AGAATGACTG
19475 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
19489 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
19508 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
19522 TCGCAACG
1 TCGCAACG
19530 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:19512 original size:33 final size:33
Alignment explanation
Indices: 19475--19545 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
19465 AGAATGACTG
**
19475 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
19508 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
19541 TCGCA
1 TCGCA
19546 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:19563 original size:19 final size:19
Alignment explanation
Indices: 19541--19637 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
19531 GAAACCAAAA
*
19541 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
19560 TCGCGTTGCGA---TC---
1 TCGCGTTGCGATTTTCATT
*
19573 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
19592 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
19606 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
19625 TCGCGTTGCGATT
1 TCGCGTTGCGATT
19638 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 6, Indels: 22
0.69 0.07 0.25
Matches are distributed among these distances:
13 10 0.16
14 10 0.16
16 6 0.10
17 3 0.05
19 32 0.52
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:19613 original size:33 final size:33
Alignment explanation
Indices: 19546--19659 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
19536 CAAAATCGCA
19546 TTGCGATTTTCATTTCGCGTTGCGA-TCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
19578 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
19611 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
19644 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
19660 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 25 0.32
33 52 0.68
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:19614 original size:14 final size:14
Alignment explanation
Indices: 19563--19651 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
19553 TTTCATTTCG
19563 CGTTGCGA-TCTCT
1 CGTTGCGATTCTCT
*
19576 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
19595 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
19609 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
19626 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
19642 CGTTGCGATT
1 CGTTGCGATT
19652 TTCATTTCAA
Statistics
Matches: 63, Mismatches: 2, Indels: 21
0.73 0.02 0.24
Matches are distributed among these distances:
13 8 0.13
14 20 0.32
15 1 0.02
16 7 0.11
17 8 0.13
18 1 0.02
19 18 0.29
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:20820 original size:184 final size:182
Alignment explanation
Indices: 20432--20892 Score: 856
Period size: 184 Copynumber: 2.5 Consensus size: 182
20422 TAGATTGCTT
*
20432 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
20496 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCCAATTCTGCTAAACTGTG
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCCAATTCTGCTAAACTGTG
20561 TATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
20613 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT-A-ACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
20676 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGG-T--TGCCAATTCTGCTAAACT
20741 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
128 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
20797 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
20862 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGT
20893 TTCAATTTGC
Statistics
Matches: 272, Mismatches: 1, Indels: 9
0.96 0.00 0.03
Matches are distributed among these distances:
179 6 0.02
180 51 0.19
181 48 0.18
183 43 0.16
184 78 0.29
185 1 0.00
186 45 0.17
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (182 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCCAATTCTGCTAAACTGTG
TATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:20821 original size:93 final size:93
Alignment explanation
Indices: 20432--20892 Score: 864
Period size: 93 Copynumber: 5.0 Consensus size: 93
20422 TAGATTGCTT
*
20432 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
20496 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
20524 AGTAAATTTGTTCGG-T--TGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
20585 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
20613 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT-A-ACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
20676 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
20704 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
20769 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
20797 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
20862 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
20890 AGT
1 AGT
20893 TTCAATTTGC
Statistics
Matches: 361, Mismatches: 1, Indels: 13
0.96 0.00 0.03
Matches are distributed among these distances:
89 83 0.23
90 16 0.04
91 80 0.22
92 44 0.12
93 138 0.38
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:20964 original size:19 final size:19
Alignment explanation
Indices: 20924--21052 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
20914 TAGTTTACTT
* *
20924 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
20944 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
20963 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
20982 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
20996 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
21015 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
21029 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
21048 TCGCA
1 TCGCA
21053 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:21003 original size:33 final size:32
Alignment explanation
Indices: 20960--21052 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
20950 CGCGAAACCA
**
20960 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
20992 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
21025 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
21053 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:21050 original size:52 final size:52
Alignment explanation
Indices: 20924--21052 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
20914 TAGTTTACTT
**
20924 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
20976 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
21029 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
21053 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:21070 original size:19 final size:19
Alignment explanation
Indices: 21048--21182 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
21038 GAAACCAAAA
*
21048 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
21067 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
21083 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
21100 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
21116 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
21133 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
21152 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
21172 TCGTGTTGCGA
1 TCGCGTTGCGA
21183 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:21089 original size:14 final size:14
Alignment explanation
Indices: 21070--21126 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
21060 TTTCATTTCG
21070 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
21084 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
21101 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
21117 CGTTGCGATT
1 CGTTGCGATT
21127 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:21095 original size:33 final size:33
Alignment explanation
Indices: 21053--21145 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
21043 CAAAATCGCA
*
21053 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
21086 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
21119 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
21146 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:23121 original size:14 final size:14
Alignment explanation
Indices: 23102--23137 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
23092 ATTGTTTAAT
23102 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
23116 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
23130 TGATTTGT
1 TGATTTGT
23138 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:23260 original size:19 final size:19
Alignment explanation
Indices: 23244--23345 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
23234 AAAAATGACT
23244 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
23263 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
23282 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
23296 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
23315 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
23335 ATCGCAATGCG
1 ATCGCAATGCG
23346 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:23394 original size:33 final size:33
Alignment explanation
Indices: 23352--23675 Score: 257
Period size: 33 Copynumber: 9.5 Consensus size: 33
23342 TGCGTTTATA
23352 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
23385 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
23418 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
*
23451 ATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
23491 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
23522 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TT-ATCTCG--TTGCGATT-T-TC
* * * * *
23562 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTATCTCGTTGCGATTTTC
*
23593 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
* *
23626 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTATC-TCGTTGCGATTTTC
*
23660 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
23676 GTATTTTCCG
Statistics
Matches: 238, Mismatches: 29, Indels: 48
0.76 0.09 0.15
Matches are distributed among these distances:
31 18 0.08
32 8 0.03
33 123 0.52
34 31 0.13
35 7 0.03
36 7 0.03
37 4 0.02
38 16 0.07
39 6 0.03
40 18 0.08
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTC
Found at i:23398 original size:19 final size:19
Alignment explanation
Indices: 23374--23675 Score: 331
Period size: 19 Copynumber: 17.4 Consensus size: 19
23364 GATTATCTCG
23374 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
23393 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
23407 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
23426 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
23440 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
23459 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
23478 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
23492 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
23511 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
23530 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
23549 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
23563 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
23582 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
23601 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
23615 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
23635 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
23649 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
23668 TTGCGATT
1 TTGCGATT
23676 GTATTTTCCG
Statistics
Matches: 242, Mismatches: 10, Indels: 62
0.77 0.03 0.20
Matches are distributed among these distances:
14 41 0.17
16 39 0.16
17 35 0.14
18 3 0.01
19 112 0.46
20 12 0.05
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:23412 original size:14 final size:14
Alignment explanation
Indices: 23360--23447 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 14
23350 TAATTTCGCA
* *
23360 TTGCGATTATCTCG
1 TTGCGATTCTTTCG
23374 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
23391 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
23407 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
23424 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
23440 TTGCGATT
1 TTGCGATT
23448 TTCATTTCGC
Statistics
Matches: 62, Mismatches: 2, Indels: 20
0.74 0.02 0.24
Matches are distributed among these distances:
14 20 0.32
16 15 0.24
17 15 0.24
19 12 0.19
ACGTcount: A:0.12, C:0.20, G:0.19, T:0.48
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:23430 original size:52 final size:52
Alignment explanation
Indices: 23374--23647 Score: 343
Period size: 52 Copynumber: 5.2 Consensus size: 52
23364 GATTATCTCG
23374 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
*
23426 TTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCA
*
23478 TTGCGA--TTC-TGTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCA
*
23530 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
*
23582 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTT-CGCA
23635 TTGCGATTTTCAT
1 TTGCGATTTTCAT
23648 GTTGGGATTT
Statistics
Matches: 206, Mismatches: 5, Indels: 21
0.89 0.02 0.09
Matches are distributed among these distances:
47 6 0.03
49 8 0.04
50 8 0.04
52 147 0.71
53 17 0.08
54 7 0.03
55 7 0.03
57 6 0.03
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
Found at i:23526 original size:71 final size:71
Alignment explanation
Indices: 23440--23608 Score: 320
Period size: 71 Copynumber: 2.4 Consensus size: 71
23430 GATTCTTTCG
*
23440 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
23505 TTCGCA
66 TTCGCA
*
23511 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
23576 TTCGCA
66 TTCGCA
23582 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
23609 CTCTCGTTGC
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 96 1.00
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCA
Found at i:25968 original size:12 final size:12
Alignment explanation
Indices: 25951--25975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25941 TTCTTCGGGA
25951 CTTTTTCTTCTT
1 CTTTTTCTTCTT
25963 CTTTTTCTTCTT
1 CTTTTTCTTCTT
25975 C
1 C
25976 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:26184 original size:24 final size:24
Alignment explanation
Indices: 26150--26196 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26140 CTGAAACATC
26150 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
26174 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
26197 GACCAAATTT
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:26906 original size:20 final size:20
Alignment explanation
Indices: 26878--27246 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
26868 AAATTTCAGT
* * * *
26878 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
26898 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
26918 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
26938 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
26958 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
26978 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
26998 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
27018 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
27038 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
27058 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
27078 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
27098 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
27118 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
27138 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
27158 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
27178 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
27198 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
27218 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
27238 GTTGCGATT
1 GTTGCGATT
27247 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:35599 original size:16 final size:16
Alignment explanation
Indices: 35578--35624 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
35568 ATTATTAATT
35578 TATTTTAATTTTTTTA
1 TATTTTAATTTTTTTA
* *
35594 TATTTTCATTTTATTA
1 TATTTTAATTTTTTTA
* *
35610 T-TATTATTTTTTTTA
1 TATTTTAATTTTTTTA
35625 CTAATTTCAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTAATTTTTTTA
Found at i:35606 original size:27 final size:30
Alignment explanation
Indices: 35576--35642 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 30
35566 TTATTATTAA
*
35576 TTTATTTTA-A-TTTTTTTA-TATTTTCAT
1 TTTATTTTATATTTTTTTTACTAATTTCAT
35603 TTTATTATTATTATTTTTTTTACTAATTTCAT
1 TTTATT-TTA-TATTTTTTTTACTAATTTCAT
35635 TTATATTT
1 TT-TATTT
35643 ATTTGTCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
27 6 0.18
28 3 0.09
30 1 0.03
31 8 0.24
32 11 0.33
33 4 0.12
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (30 bp):
TTTATTTTATATTTTTTTTACTAATTTCAT
Found at i:35618 original size:14 final size:14
Alignment explanation
Indices: 35560--35619 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
35550 TTCTTGGTTA
*
35560 ATTTAATTATTATT
1 ATTTTATTATTATT
*
35574 AATTTATT-TTAATT
1 ATTTTATTATT-ATT
*
35588 TTTTTA-TATT-TT
1 ATTTTATTATTATT
35600 CATTTTATTATTATT
1 -ATTTTATTATTATT
35615 ATTTT
1 ATTTT
35620 TTTTACTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
12 2 0.06
13 8 0.22
14 24 0.67
15 2 0.06
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTATTATTATT
Found at i:35638 original size:44 final size:41
Alignment explanation
Indices: 35560--35642 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
35550 TTCTTGGTTA
*
35560 ATTTAATTATTATTAATTTATTTTAATTTTTTTATATTTTC
1 ATTTAATTATTATTAATTTATTTTAATTTATTTATATTTTC
* * *
35601 ATTTTATTATTATTATTTTTTTTACTAATTTCATTTATATTT
1 ATTTAATTATTATTAATTTATTT--TAATTT-ATTTATATTT
35643 ATTTGTCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 20 0.57
43 6 0.17
44 9 0.26
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (41 bp):
ATTTAATTATTATTAATTTATTTTAATTTATTTATATTTTC
Found at i:35645 original size:31 final size:31
Alignment explanation
Indices: 35577--35641 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
35567 TATTATTAAT
* *
35577 TTATT-TTAATTTTTTTATATTTTCATTTTA
1 TTATTATTATTTTTTTTATAATTTCATTTTA
35607 TTATTATTATTTTTTTTACTAATTTCATTTATA
1 TTATTATTATTTTTTTTA-TAATTTCATTT-TA
35640 TT
1 TT
35642 TATTTGTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 5 0.17
31 11 0.37
32 10 0.33
33 4 0.13
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.71
Consensus pattern (31 bp):
TTATTATTATTTTTTTTATAATTTCATTTTA
Found at i:40002 original size:84 final size:82
Alignment explanation
Indices: 39647--40508 Score: 846
Period size: 84 Copynumber: 10.4 Consensus size: 82
39637 GCTCAAGGCC
* * * * * * *
39647 AGAAGGGCTATCTGCCATC-AAGACCTTCAAGTTCAACTACGCTCAGCTTCGAGGGCATATCATT
1 AGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
*
39711 TACAGCATAACTTAAGTCG
64 TGCAGCATAACTTAAGTCG
* * * * *
39730 AGAAGGGTTATTTGCCAACCAAAAGACCTTTGAGTTCAACTACGCTCATCTCCAAGGCATATCAT
1 AGAAGGGTTATCTG-C-ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
*
39795 TTGCAGCATAGCTTAAGTCG
63 TTGCAGCATAACTTAAGTCG
* * * * * * * * *
39815 AGAAGGGCTATATG--CCAAAGACCTTCAAGTTTGATTACACTCAGCTTCGAGGGCATATCATTT
1 AGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTT
** * *
39878 ATAGCATAACTTAAGGCT
65 GCAGCATAACTTAAGTCG
* * *
39896 AGAAGGGTTATCTGTCACCAAAGACCTTCAAGTTCGACTCCGCTCAGCTCCAAGGCATATCATTT
1 AGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
*
39961 GCAGCATAACTTAAATCG
65 GCAGCATAACTTAAGTCG
* *
39979 AGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATT
1 AGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
40044 TGCAGCATAACTTAAGTCG
64 TGCAGCATAACTTAAGTCG
* * * * ****
40063 AGAAGGGATATCTG--CCAAAGACCCTCGAGTTCGATTACACTCAGCTTTGTGGGCACATCATTT
1 AGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTT
* * * * *
40126 ACAGCATAAGTCAAGGCT
65 GCAGCATAACTTAAGTCG
* * * ** *
40144 AGAAGGGTTATATGTGACCAAAAGACATTCGAGTTCGACCCCGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTG-CACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
40209 TGCAGCATAACTTAAGTCG
64 TGCAGCATAACTTAAGTCG
*
40228 AGAACGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTG-C-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
40293 TGAAGCATAGCTTAAGTCG
64 TGCAGCATAACTTAAGTCG
* * * * * *
40312 AGAAGGGCTATCT--ATCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGC-GGGCACATCATT
1 AGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TC-CAAGGCACATCATT
* * * * *
40374 T-AAGTATACCTCAAGTCT
64 TGCAGCATAACTTAAGTCG
* *
40392 AGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATTT
1 AGAAGGGTTATCTG-CACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
*
40457 GCAGCATAGCTTAAGTCG
65 GCAGCATAACTTAAGTCG
* * *
40475 AGAAGGGCTATTTG--CTAAAGACCTTCGAGTTCGA
1 AGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGA
40509 TTATATTCAA
Statistics
Matches: 645, Mismatches: 113, Indels: 45
0.80 0.14 0.06
Matches are distributed among these distances:
80 122 0.19
81 96 0.15
82 14 0.02
83 108 0.17
84 211 0.33
85 69 0.11
86 25 0.04
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (82 bp):
AGAAGGGTTATCTGCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
CAGCATAACTTAAGTCG
Found at i:40208 original size:249 final size:247
Alignment explanation
Indices: 39638--40478 Score: 1207
Period size: 249 Copynumber: 3.4 Consensus size: 247
39628 TGCAGCTTAG
* * ** * * * * * *
39638 CTCAAGGCCAGAAGGGCTATCTGCCATC-AAGACCTTCAAGTTCAACTACGCTCAGCTTCGAGGG
1 CTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTCCGCTCAGC-TCCAAGG
* * * *
39702 CATATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATTTGCCAACCAAAAGACCTTTGAGTTC
65 CATATCATTTGCAGCATAACTTAAGTCGAGAAAGGTTATCTGCCAACC-AAAGACCTTCGAGTTC
* * * *
39767 AACTACGCTCATCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATATGCCA
129 GACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
* * * *
39832 AAGACCTTCAAGTTTGATTACACTCAGCTTCGAGGGCATATCATTTATAGCATAA
194 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA-AGCATAA
* * *
39887 CTTAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCAAGTTCGACTCCGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGC
*
39952 ATATCATTTGCAGCATAACTTAAATCGAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
66 ATATCATTTGCAGCATAACTTAAGTCGAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
* * *
40017 CTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGATATCTGCCAAA
131 CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
* *
40082 GACCCTCGAGTTCGATTACACTCAGCTTTGTGGGCACATCATTTACAGCATAA
196 GACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA-AGCATAA
* * * *
40135 GTCAAGGCTAGAAGGGTTATATGTGACCAAAAGACATTCGAGTTCGACCCCGCTCAGCTCCAAGG
1 CTCAAGGCTAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGG
*
40200 CATATCATTTGCAGCATAACTTAAGTCGAGAACGGTTATCTGCCAACCAAAGACCTTCGAGTTCG
65 CATATCATTTGCAGCATAACTTAAGTCGAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCG
* **
40265 ACTACGCTCAGCTCCAAGGCACATCATTTGAAGCATAGCTTAAGTCGAGAAGGGCTATCTATCAA
130 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
* * *
40330 AGACCCTCGAGTTCGATTACACTCAGCTTCGCGGGCACATCATTTAAGTATAC
195 AGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAAGCATAA
* *
40383 CTCAAGTCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1 CTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGC
* * *
40448 ACATTATTTGCAGCATAGCTTAAGTCGAGAA
66 ATATCATTTGCAGCATAACTTAAGTCGAGAA
40479 GGGCTATTTG
Statistics
Matches: 534, Mismatches: 56, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
247 62 0.12
248 175 0.33
249 271 0.51
250 26 0.05
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (247 bp):
CTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGC
ATATCATTTGCAGCATAACTTAAGTCGAGAAAGGTTATCTGCCAACCAAAGACCTTCGAGTTCGA
CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
GACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAAGCATAA
Found at i:41576 original size:26 final size:26
Alignment explanation
Indices: 41547--41602 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
41537 GAATGTCTCC
*
41547 AGAAGCAGAAAAGAGAGAAGGAATAG
1 AGAAGCAAAAAAGAGAGAAGGAATAG
* *
41573 AGAAGCAAAAAAGAGAGAATGAATGG
1 AGAAGCAAAAAAGAGAGAAGGAATAG
41599 AGAA
1 AGAA
41603 ATAACAAAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.59, C:0.04, G:0.32, T:0.05
Consensus pattern (26 bp):
AGAAGCAAAAAAGAGAGAAGGAATAG
Found at i:41971 original size:20 final size:19
Alignment explanation
Indices: 41948--41986 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
41938 TCTTGGTTAA
41948 TTTAATTATTTATTA-ATTTT
1 TTTAATT-TTT-TTATATTTT
41968 TTTAATTTTTTTATATTTT
1 TTTAATTTTTTTATATTTT
41987 CATTATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 8 0.44
20 7 0.39
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTAATTTTTTTATATTTT
Found at i:41985 original size:10 final size:9
Alignment explanation
Indices: 41948--41986 Score: 51
Period size: 9 Copynumber: 4.0 Consensus size: 9
41938 TCTTGGTTAA
41948 TTTAATTATT
1 TTTAATT-TT
41958 TATTAATTTT
1 T-TTAATTTT
41968 TTTAATTTT
1 TTTAATTTT
41977 TTTATATTTT
1 TTTA-ATTTT
41987 CATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 12 0.44
10 9 0.33
11 6 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTAATTTT
Found at i:42688 original size:13 final size:15
Alignment explanation
Indices: 42657--42688 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42647 TTGATTTTAA
42657 ATTTTTAGAATACAT
1 ATTTTTAGAATACAT
42672 ATTTTTA-AATA-AT
1 ATTTTTAGAATACAT
42685 ATTT
1 ATTT
42689 ATGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 4 0.24
15 7 0.41
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTTTAGAATACAT
Found at i:52251 original size:16 final size:16
Alignment explanation
Indices: 52230--52267 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
52220 TTCAAAACCT
52230 TATTATTTGCTTACTC
1 TATTATTTGCTTACTC
52246 TATTATTTGCTTACTC
1 TATTATTTGCTTACTC
52262 TATTAT
1 TATTAT
52268 ATCTTGCAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (16 bp):
TATTATTTGCTTACTC
Found at i:55890 original size:67 final size:68
Alignment explanation
Indices: 55776--55905 Score: 190
Period size: 67 Copynumber: 1.9 Consensus size: 68
55766 TTTTAGAATA
* * * *
55776 CTTTTATTTAATAATATTTATGAAAAAAGATTTTTAACTTTTTTAAATAGTAACCAAAAATATCA
1 CTTTAATTTAATAATATTTATGAAAAAAGATTTTTAACTCTCTTAAATAATAACCAAAAATATCA
55841 TAC
66 TAC
* * *
55844 CTTTAATTTAATGATATTTATG-AAAAATATTTTTAACTCTCTTAAATAATATCCAAAAATAT
1 CTTTAATTTAATAATATTTATGAAAAAAGATTTTTAACTCTCTTAAATAATAACCAAAAATAT
55906 ATAGGGTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
67 35 0.64
68 20 0.36
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (68 bp):
CTTTAATTTAATAATATTTATGAAAAAAGATTTTTAACTCTCTTAAATAATAACCAAAAATATCA
TAC
Found at i:56798 original size:13 final size:13
Alignment explanation
Indices: 56780--56805 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56770 AACCCGACCA
56780 AAGAAAAAAAATT
1 AAGAAAAAAAATT
56793 AAGAAAAAAAATT
1 AAGAAAAAAAATT
56806 GATTCGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AAGAAAAAAAATT
Found at i:57197 original size:66 final size:68
Alignment explanation
Indices: 57073--57202 Score: 165
Period size: 66 Copynumber: 1.9 Consensus size: 68
57063 TTTTAGAATA
* * * * * *
57073 CTTTTATTTAATAATATTTATGAAAAAAATATTTTTAACTTTTTTAAATAGTAACAAAA-ATATC
1 CTTTAATTTAATAATATTTATG-AAAAAAGATTTTTAAATCTCTTAAATAATAACAAAATATATC
57137 ATAC
65 ATAC
* *
57141 CTTTAATTTAATGATATTTATG-AAAAAGATTTTTAAATCTCTTAAATAATATCAAAATATAT
1 CTTTAATTTAATAATATTTATGAAAAAAGATTTTTAAATCTCTTAAATAATAACAAAATATAT
57203 ATAGGGTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
66 29 0.55
67 4 0.08
68 20 0.38
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (68 bp):
CTTTAATTTAATAATATTTATGAAAAAAGATTTTTAAATCTCTTAAATAATAACAAAATATATCA
TAC
Found at i:58778 original size:16 final size:17
Alignment explanation
Indices: 58747--58779 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
58737 ATGATATATA
58747 TATATATCTTACATACG
1 TATATATCTTACATACG
*
58764 TATAT-TCTTATATACG
1 TATATATCTTACATACG
58780 AACAAGGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (17 bp):
TATATATCTTACATACG
Found at i:60785 original size:32 final size:36
Alignment explanation
Indices: 60743--60813 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 36
60733 TTATTTCTTA
60743 TTTTCTTCCTT-ATTT-TTAAT-ATTTTTTATTCAT
1 TTTTCTTCCTTGATTTATTAATCATTTTTTATTCAT
* * *
60776 TTTTC-TCCTTGATTTATTTATCCTTTTTTATTTAT
1 TTTTCTTCCTTGATTTATTAATCATTTTTTATTCAT
60811 TTT
1 TTT
60814 ATTTTTATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 5 0.16
33 9 0.28
34 4 0.12
35 14 0.44
ACGTcount: A:0.15, C:0.13, G:0.01, T:0.70
Consensus pattern (36 bp):
TTTTCTTCCTTGATTTATTAATCATTTTTTATTCAT
Found at i:63431 original size:19 final size:19
Alignment explanation
Indices: 63407--63468 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
63397 AAACCAAAAC
63407 CGGTTTTTTCGATTCGGTT
1 CGGTTTTTTCGATTCGGTT
** *
63426 CGGTTTTTTTTAAT-GGTT
1 CGGTTTTTTCGATTCGGTT
* *
63444 CGGGTTTTTCGGTTCGGTT
1 CGGTTTTTTCGATTCGGTT
63463 CGGTTT
1 CGGTTT
63469 ATCGGTTTTT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
18 13 0.39
19 20 0.61
ACGTcount: A:0.05, C:0.13, G:0.29, T:0.53
Consensus pattern (19 bp):
CGGTTTTTTCGATTCGGTT
Found at i:63467 original size:18 final size:19
Alignment explanation
Indices: 63440--63475 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
63430 TTTTTTTAAT
*
63440 GGTTCGGGTTTTTCGGTTC
1 GGTTCGGGTTTATCGGTTC
63459 GGTTC-GGTTTATCGGTT
1 GGTTCGGGTTTATCGGTT
63476 TTTCCATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.03, C:0.14, G:0.36, T:0.47
Consensus pattern (19 bp):
GGTTCGGGTTTATCGGTTC
Found at i:74795 original size:25 final size:25
Alignment explanation
Indices: 74757--74834 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 25
74747 CATATTTTTC
* *
74757 ATAAAAAAAATATATATATAAAAAA
1 ATAAAAATATTATATATATAAAAAA
74782 ATAAAAATATTATATATAATTAATATAAAAA
1 ATAAAAATA-T-TATAT-A-T-ATA-AAAAA
74813 ATAAAAAATATTATATATATAA
1 AT-AAAAATATTATATATATAA
74835 TTAATATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
25 8 0.18
26 1 0.02
27 8 0.18
28 2 0.05
29 2 0.05
30 8 0.18
31 8 0.18
32 7 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (25 bp):
ATAAAAATATTATATATATAAAAAA
Found at i:74808 original size:34 final size:34
Alignment explanation
Indices: 74772--74903 Score: 162
Period size: 34 Copynumber: 3.9 Consensus size: 34
74762 AAAAATATAT
74772 ATATAAAAAA-ATAAAAATAT-TATATATAATTA
1 ATATAAAAAATATAAAAATATATATATATAATTA
74804 ATATAAAAAATA-AAAAATATTATATATATAATTA
1 ATATAAAAAATATAAAAATA-TATATATATAATTA
* * * * *
74838 ATATAAAATATAGAAAATTCTATATATATAGTTA
1 ATATAAAAAATATAAAAATATATATATATAATTA
*
74872 ATATAAAAAATATAAAAAATATTATCTATATA
1 ATATAAAAAATAT-AAAAATA-TATATATATA
74904 TAATCGGGGC
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
32 17 0.20
33 2 0.02
34 47 0.55
35 10 0.12
36 9 0.11
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (34 bp):
ATATAAAAAATATAAAAATATATATATATAATTA
Found at i:76994 original size:3 final size:3
Alignment explanation
Indices: 76988--77055 Score: 86
Period size: 3 Copynumber: 22.0 Consensus size: 3
76978 ATTTGGTTTT
76988 TTA TTA TTTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
77035 TTTA TTAA TT- TTA TTA -TA TTA
1 -TTA TT-A TTA TTA TTA TTA TTA
77056 CAGGCCCAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.07
3 43 0.73
4 12 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:77004 original size:13 final size:13
Alignment explanation
Indices: 76988--77055 Score: 93
Period size: 13 Copynumber: 5.0 Consensus size: 13
76978 ATTTGGTTTT
76988 TTATTATTTATTA
1 TTATTATTTATTA
77001 TTATTATTTATTA
1 TTATTATTTATTA
77014 TTATTATTATTATTA
1 TTATTA-T-TTATTA
77029 TTATTATTTATTAA
1 TTATTATTTATT-A
77043 TT-TTATTATATTA
1 TTATTATT-TATTA
77056 CAGGCCCAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
13 30 0.59
14 9 0.18
15 12 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:78358 original size:16 final size:17
Alignment explanation
Indices: 78322--78363 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
78312 ATTGCTTTTA
*
78322 AATTTATTTTAAATATT
1 AATTTATTATAAATATT
78339 -ATTTATTAT-AATATT
1 AATTTATTATAAATATT
*
78354 AATTTGTTAT
1 AATTTATTAT
78364 TACTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
AATTTATTATAAATATT
Found at i:78382 original size:17 final size:17
Alignment explanation
Indices: 78360--78393 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
78350 TATTAATTTG
78360 TTATTACTTTT-ATATTA
1 TTATTA-TTTTCATATTA
78377 TTATTATTTTCATATTA
1 TTATTATTTTCATATTA
78394 GTCACATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTTCATATTA
Found at i:78410 original size:2 final size:2
Alignment explanation
Indices: 78403--78428 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
78393 AGTCACATAA
78403 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
78429 TTTAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78558 original size:31 final size:33
Alignment explanation
Indices: 78523--78585 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
78513 ATAATTAAAC
78523 ATTATAAAAATTAT-A-ATTTAGTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
* * *
78554 ATTATTAAAATTTTAATATTTATTTTTATTTA
1 ATTATAAAAATTATAATATTTAGTTTTATTTA
78586 TTAATATCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 12 0.44
32 1 0.04
33 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
ATTATAAAAATTATAATATTTAGTTTTATTTAA
Found at i:78673 original size:29 final size:30
Alignment explanation
Indices: 78636--78696 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
78626 TCCTTTTCTG
* *
78636 ATATTTTTAAATAAATAAATTTT-TTATAA
1 ATATATTTAAATAAATAAATTTTCTTAAAA
* *
78665 ATATATTTAAATTAATATATTTTCTTAAAA
1 ATATATTTAAATAAATAAATTTTCTTAAAA
78695 AT
1 AT
78697 TATAGTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
ATATATTTAAATAAATAAATTTTCTTAAAA
Found at i:79333 original size:21 final size:21
Alignment explanation
Indices: 79309--79348 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
79299 CAACCTCAAA
79309 TAAAAAGT-TAATTTTTAAATT
1 TAAAAA-TATAATTTTTAAATT
79330 TAAAAATATAATTTTTAAA
1 TAAAAATATAATTTTTAAA
79349 AATCTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TAAAAATATAATTTTTAAATT
Found at i:86700 original size:23 final size:22
Alignment explanation
Indices: 86655--86703 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 22
86645 GAGCATTGAG
86655 TTGATGAATTTTCTTGATTTTTT
1 TTGATGAATTTTCTTGA-TTTTT
86678 TTGATAGAAGTTTTCTTGATTTTT
1 TTGAT-GAA-TTTTCTTGATTTTT
86702 TT
1 TT
86704 TGTTTAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.21
24 10 0.42
25 9 0.38
ACGTcount: A:0.18, C:0.04, G:0.14, T:0.63
Consensus pattern (22 bp):
TTGATGAATTTTCTTGATTTTT
Found at i:86712 original size:24 final size:25
Alignment explanation
Indices: 86655--86705 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
86645 GAGCATTGAG
86655 TTGAT-GAA-TTTTCTTGATTTTTT
1 TTGATAGAAGTTTTCTTGATTTTTT
86678 TTGATAGAAGTTTTCTTGATTTTTT
1 TTGATAGAAGTTTTCTTGATTTTTT
86703 TTG
1 TTG
86706 TTTAAGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 5 0.19
24 3 0.12
25 18 0.69
ACGTcount: A:0.18, C:0.04, G:0.16, T:0.63
Consensus pattern (25 bp):
TTGATAGAAGTTTTCTTGATTTTTT
Found at i:87468 original size:2 final size:2
Alignment explanation
Indices: 87463--87489 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
87453 TCTCTCTCTC
87463 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
87490 TAGTTACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:92187 original size:16 final size:17
Alignment explanation
Indices: 92166--92198 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
92156 AAATTTTAGA
*
92166 TTTATTG-TTATATTTT
1 TTTATTGATAATATTTT
92182 TTTATTGATAATATTTT
1 TTTATTGATAATATTTT
92199 CTTCTCCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (17 bp):
TTTATTGATAATATTTT
Found at i:92391 original size:24 final size:24
Alignment explanation
Indices: 92355--92415 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
92345 GGAAGGGTGA
* *
92355 TGGGGGACATGTTCCCACGACTGC
1 TGGGGAACCTGTTCCCACGACTGC
92379 -GTGGGAACCTGTTCCCACGACTGC
1 TG-GGGAACCTGTTCCCACGACTGC
92403 TGGGGAACCTGTT
1 TGGGGAACCTGTT
92416 ATTCATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 1 0.03
24 31 0.94
25 1 0.03
ACGTcount: A:0.16, C:0.28, G:0.33, T:0.23
Consensus pattern (24 bp):
TGGGGAACCTGTTCCCACGACTGC
Found at i:93215 original size:14 final size:14
Alignment explanation
Indices: 93185--93226 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
93175 AGGTCTGTAA
*
93185 ACGAACCGAACGCAC
1 ACGAA-CGAACGTAC
*
93200 ACGAATGAACGTAC
1 ACGAACGAACGTAC
93214 ACGAACGAACGTA
1 ACGAACGAACGTA
93227 TGTTCATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.43, C:0.29, G:0.21, T:0.07
Consensus pattern (14 bp):
ACGAACGAACGTAC
Found at i:93357 original size:10 final size:10
Alignment explanation
Indices: 93342--93419 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 10
93332 CATTTAAATG
93342 ATAAACGAAC
1 ATAAACGAAC
*
93352 ATAAACGAAT
1 ATAAACGAAC
*
93362 GTGAACGAACGAAC
1 AT-AA---ACGAAC
*
93376 ATAAACTAAC
1 ATAAACGAAC
93386 ATAAACGAACAC
1 ATAAACG-A-AC
93398 AATAAACGAAC
1 -ATAAACGAAC
*
93409 ATAAATGAAC
1 ATAAACGAAC
93419 A
1 A
93420 ACTCAAACAC
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
10 31 0.57
11 5 0.09
12 3 0.06
13 9 0.17
14 6 0.11
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.13
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:93392 original size:24 final size:24
Alignment explanation
Indices: 93345--93418 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
93335 TTAAATGATA
** *
93345 AACGAACATAAACGAATGTGAACG
1 AACGAACATAAACGAACATAAACG
*
93369 AACGAACATAAACTAACATAAACG
1 AACGAACATAAACGAACATAAACG
*
93393 AAC--ACAATAAACGAACATAAATG
1 AACGAAC-ATAAACGAACATAAACG
93416 AAC
1 AAC
93419 AACTCAAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
22 2 0.05
23 18 0.42
24 23 0.53
ACGTcount: A:0.57, C:0.19, G:0.12, T:0.12
Consensus pattern (24 bp):
AACGAACATAAACGAACATAAACG
Found at i:93427 original size:23 final size:23
Alignment explanation
Indices: 93376--93419 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
93366 ACGAACGAAC
*
93376 ATAAACTAACATAAACGAACACA
1 ATAAACGAACATAAACGAACACA
*
93399 ATAAACGAACATAAATGAACA
1 ATAAACGAACATAAACGAACA
93420 ACTCAAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.18, G:0.07, T:0.14
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACACA
Found at i:104287 original size:17 final size:17
Alignment explanation
Indices: 104265--104311 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
104255 GCATATTTTT
104265 TGGTTCAGTTTTTTTAA
1 TGGTTCAGTTTTTTTAA
104282 TGGTTCAAG--TTTTTAA
1 TGGTTC-AGTTTTTTTAA
104298 TGGTTCAGGTTTTT
1 TGGTTCA-GTTTTT
104312 CATGATGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 14 0.54
17 6 0.23
18 5 0.19
ACGTcount: A:0.17, C:0.06, G:0.21, T:0.55
Consensus pattern (17 bp):
TGGTTCAGTTTTTTTAA
Found at i:104294 original size:16 final size:16
Alignment explanation
Indices: 104275--104311 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
104265 TGGTTCAGTT
104275 TTTTTAATGGTTCAAG
1 TTTTTAATGGTTCAAG
*
104291 TTTTTAATGGTTCAGG
1 TTTTTAATGGTTCAAG
104307 TTTTT
1 TTTTT
104312 CATGATGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.57
Consensus pattern (16 bp):
TTTTTAATGGTTCAAG
Found at i:105053 original size:121 final size:123
Alignment explanation
Indices: 104837--105079 Score: 472
Period size: 121 Copynumber: 2.0 Consensus size: 123
104827 TTGCGGGACT
104837 TTTTATTGATTTTGAATTTTTTTTTGCTATTGCTTCGAAGGAGAAGATGACCTTGTCCACTCTAA
1 TTTTATTGATTTTGAATTTTTTTTTGCTATTGCTTCGAAGGAGAAGATGACCTTGTCCACTCTAA
104902 CAAACATATTTCTCGATTTGAAGCAAGGCATAAAGAGTTTTTCAATAATAGTGCATTC
66 CAAACATATTTCTCGATTTGAAGCAAGGCATAAAGAGTTTTTCAATAATAGTGCATTC
104960 TTTTATTGA-TTTGAA-TTTTTTTTGCTATTGCTTCGAAGGAGAAGATGACCTTGTCCACTCTAA
1 TTTTATTGATTTTGAATTTTTTTTTGCTATTGCTTCGAAGGAGAAGATGACCTTGTCCACTCTAA
105023 CAAACATATTTCTCGATTTGAAGCAAGGCATAAAGAGTTTTTCAATAATAGTGCATT
66 CAAACATATTTCTCGATTTGAAGCAAGGCATAAAGAGTTTTTCAATAATAGTGCATT
105080 GTATTTCTCG
Statistics
Matches: 120, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
121 105 0.88
122 6 0.05
123 9 0.08
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (123 bp):
TTTTATTGATTTTGAATTTTTTTTTGCTATTGCTTCGAAGGAGAAGATGACCTTGTCCACTCTAA
CAAACATATTTCTCGATTTGAAGCAAGGCATAAAGAGTTTTTCAATAATAGTGCATTC
Found at i:105107 original size:52 final size:52
Alignment explanation
Indices: 105029--105132 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
105019 CTAACAAACA
105029 TATTTCTCGATTTGAAGCAAGGCATAAAGAGTTTTTCAATAATAGTGCATTG
1 TATTTCTCGATTTGAAGCAAGGCATAAAGAGTTTTTCAATAATAGTGCATTG
105081 TATTTCTCGATTTGAAGCAAGGCATAAAGAGTTTTTCAATAATAGTGCATTG
1 TATTTCTCGATTTGAAGCAAGGCATAAAGAGTTTTTCAATAATAGTGCATTG
105133 GTTCATGCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.37
Consensus pattern (52 bp):
TATTTCTCGATTTGAAGCAAGGCATAAAGAGTTTTTCAATAATAGTGCATTG
Found at i:118702 original size:13 final size:13
Alignment explanation
Indices: 118684--118713 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
118674 GGTCAACGCC
*
118684 GGTCAACGGGTCG
1 GGTCAACAGGTCG
118697 GGTCAACAGGTCG
1 GGTCAACAGGTCG
118710 GGTC
1 GGTC
118714 GGGTAAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:118711 original size:18 final size:18
Alignment explanation
Indices: 118690--118734 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
118680 CGCCGGTCAA
*
118690 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTAAACAGGT
*
118708 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACAGGT
118726 CGGGTCGGG
1 CGGGTCGGG
118735 GTGTGACCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.51, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTAAACAGGT
Found at i:120876 original size:24 final size:24
Alignment explanation
Indices: 120848--120919 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
120838 GGTAACGGAG
*
120848 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
120872 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
120896 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
120919 A
1 A
120920 GGTAACGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 15 0.36
24 27 0.64
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:120879 original size:12 final size:12
Alignment explanation
Indices: 120852--120920 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
120842 ACGGAGATAT
* *
120852 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
120864 CAGAATTCATAT
1 CAGAATTCAGAA
120876 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
120888 CAGAATCCAGAT
1 CAGAATTCAGAA
120900 CAGAA-TCAGAA
1 CAGAATTCAGAA
120911 CAGAATTCAG
1 CAGAATTCAG
120921 GTAACGTATC
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 11 0.24
12 32 0.71
13 2 0.04
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:120936 original size:24 final size:23
Alignment explanation
Indices: 120857--120943 Score: 84
Period size: 24 Copynumber: 3.7 Consensus size: 23
120847 GATATCAGAA
* * *
120857 ATCAAAACAGAATTCATATCAGAT
1 ATCAGAACAGAATTCAGATAAG-T
* * *
120881 ATCAGAACAGAATCCAGATCAGA
1 ATCAGAACAGAATTCAGATAAGT
*
120904 ATCAGAACAGAATTCAGGTAACGT
1 ATCAGAACAGAATTCAGATAA-GT
*
120928 ATCAGAACAAAATTCA
1 ATCAGAACAGAATTCA
120944 ATTTGAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.34
24 35 0.66
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (23 bp):
ATCAGAACAGAATTCAGATAAGT
Found at i:123332 original size:13 final size:13
Alignment explanation
Indices: 123314--123345 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
123304 CAACTGTCAA
*
123314 CGGGTCAACGGGT
1 CGGGTCAACAGGT
123327 CGGGTCAACAGGT
1 CGGGTCAACAGGT
123340 CGGGTC
1 CGGGTC
123346 TGGTCAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.25, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACAGGT
Found at i:123345 original size:18 final size:18
Alignment explanation
Indices: 123322--123358 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
123312 AACGGGTCAA
123322 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
* *
123340 CGGGTCTGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
123358 C
1 C
123359 AGGTAAACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.24, G:0.43, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:123353 original size:31 final size:31
Alignment explanation
Indices: 123316--123376 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
123306 ACTGTCAACG
* *
123316 GGTCAACGGGTCGGGTCAACAGGTCGGGTCT
1 GGTCAACGGGTCAGGTAAACAGGTCGGGTCT
*
123347 GGTCAACGGGTCAGGTAAACGGGTCGGGTC
1 GGTCAACGGGTCAGGTAAACAGGTCGGGTC
123377 GGGTTGTGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.18, C:0.21, G:0.43, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCAGGTAAACAGGTCGGGTCT
Found at i:126004 original size:16 final size:16
Alignment explanation
Indices: 125983--126027 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
125973 ACAAAATAGT
125983 AATTTACTATTCACAA-
1 AATTTACTATTCA-AAG
125999 AATTTACTATTCAAAG
1 AATTTACTATTCAAAG
*
126015 AATTCACTATTCA
1 AATTTACTATTCA
126028 TGTAAATAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 2 0.07
16 25 0.93
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (16 bp):
AATTTACTATTCAAAG
Found at i:126572 original size:52 final size:53
Alignment explanation
Indices: 126500--126605 Score: 171
Period size: 53 Copynumber: 2.0 Consensus size: 53
126490 GTTTGGCAAC
126500 CAATTTGACAACCAATTTCT-C-ATATTGCTATTTATTGCACCTGCAAGTTTGA
1 CAATTTGACAACCAATTTCTCCTATATTGC-ATTTATTGCACCTGCAAGTTTGA
* *
126552 CAATTTGACAACCAATTTCTCCTATATTTCATTTATTGCAGCTGCAAGTTTGA
1 CAATTTGACAACCAATTTCTCCTATATTGCATTTATTGCACCTGCAAGTTTGA
126605 C
1 C
126606 CAACAGTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
52 20 0.40
53 24 0.48
54 6 0.12
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (53 bp):
CAATTTGACAACCAATTTCTCCTATATTGCATTTATTGCACCTGCAAGTTTGA
Found at i:132138 original size:28 final size:28
Alignment explanation
Indices: 132098--132152 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
132088 CAGATGGTAG
132098 AGTGATGATTGATAAACTCTGTTCACGT
1 AGTGATGATTGATAAACTCTGTTCACGT
132126 AGTGATGATTGATAAACTCTGTTCACG
1 AGTGATGATTGATAAACTCTGTTCACG
132153 GTAGCCCGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Consensus pattern (28 bp):
AGTGATGATTGATAAACTCTGTTCACGT
Found at i:141158 original size:17 final size:19
Alignment explanation
Indices: 141133--141181 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 19
141123 AAACTGGTTT
*
141133 TTCGGTTCAGTTTTTTTAA
1 TTCGGTTCAGTTTTTTCAA
*
141152 -T-GGTTCAGGTTTTTCAA
1 TTCGGTTCAGTTTTTTCAA
141169 TTCGGTTCAGTTT
1 TTCGGTTCAGTTT
141182 GATTTATCGG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 14 0.56
18 2 0.08
19 9 0.36
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.53
Consensus pattern (19 bp):
TTCGGTTCAGTTTTTTCAA
Found at i:141328 original size:32 final size:32
Alignment explanation
Indices: 141287--141361 Score: 150
Period size: 32 Copynumber: 2.3 Consensus size: 32
141277 TGAAAAACCC
141287 AAACCGAACCGAATCAAAAGAATTAAGACTTT
1 AAACCGAACCGAATCAAAAGAATTAAGACTTT
141319 AAACCGAACCGAATCAAAAGAATTAAGACTTT
1 AAACCGAACCGAATCAAAAGAATTAAGACTTT
141351 AAACCGAACCG
1 AAACCGAACCG
141362 TATAATGCCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.16
Consensus pattern (32 bp):
AAACCGAACCGAATCAAAAGAATTAAGACTTT
Found at i:149812 original size:45 final size:45
Alignment explanation
Indices: 149748--149842 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
149738 GTCATTAATT
149748 AACTAATATTTTACTTGTTTCTACATTGTTTATTTATCAATAGGC
1 AACTAATATTTTACTTGTTTCTACATTGTTTATTTATCAATAGGC
149793 AACTAATATTTTACTTGTTTCTACATTGTTTATTTATCAATAGGC
1 AACTAATATTTTACTTGTTTCTACATTGTTTATTTATCAATAGGC
149838 AACTA
1 AACTA
149843 TTGATATCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (45 bp):
AACTAATATTTTACTTGTTTCTACATTGTTTATTTATCAATAGGC
Found at i:150726 original size:16 final size:16
Alignment explanation
Indices: 150705--150747 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
150695 CCGACCAAAT
150705 TTTACTATTCACA-GAA
1 TTTACTATTCA-AGGAA
150721 TTTACTATTCAAGGAA
1 TTTACTATTCAAGGAA
*
150737 TTCACTATTCA
1 TTTACTATTCA
150748 TGTAAATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 1 0.04
16 24 0.96
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.40
Consensus pattern (16 bp):
TTTACTATTCAAGGAA
Found at i:151308 original size:53 final size:50
Alignment explanation
Indices: 151210--151313 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 50
151200 GTTTGGCAAC
151210 CAATTTGACAACCAATTTTCTCATGCTATTTATTGCACCTGCAAGTTTGA
1 CAATTTGACAACCAATTTTCTCATGCTATTTATTGCACCTGCAAGTTTGA
* *
151260 CAATTTGACAACCAATTTCTCCTATATG-TCATTTATTGCAGCTGCAAGTTTGA
1 CAATTTGACAACCAATTT-T-CT-CATGCT-ATTTATTGCACCTGCAAGTTTGA
151313 C
1 C
151314 CAATAGTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
50 18 0.38
51 1 0.02
52 3 0.06
53 26 0.54
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (50 bp):
CAATTTGACAACCAATTTTCTCATGCTATTTATTGCACCTGCAAGTTTGA
Found at i:171702 original size:15 final size:15
Alignment explanation
Indices: 171682--171711 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
171672 CTTTCTAATA
171682 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
171697 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
171712 CCAGCCTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:176621 original size:21 final size:21
Alignment explanation
Indices: 176579--176653 Score: 105
Period size: 21 Copynumber: 3.5 Consensus size: 21
176569 AATTTATCCC
*
176579 GAAGGACCACGTAGAAATGTCCT
1 GAAGGACCACATAG--ATGTCCT
*
176602 GAAGGACCACATATATGTCCT
1 GAAGGACCACATAGATGTCCT
*
176623 GAAGGACCACATAGATGTCCC
1 GAAGGACCACATAGATGTCCT
176644 GAAGGACCAC
1 GAAGGACCAC
176654 TCCTTAAGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 36 0.75
23 12 0.25
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (21 bp):
GAAGGACCACATAGATGTCCT
Found at i:178569 original size:14 final size:14
Alignment explanation
Indices: 178550--178584 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
178540 TAACACCATC
178550 ACTATTAGTAGCGG
1 ACTATTAGTAGCGG
178564 ACTATTAGTAGCGG
1 ACTATTAGTAGCGG
178578 ATCTATT
1 A-CTATT
178585 GTATATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (14 bp):
ACTATTAGTAGCGG
Found at i:186803 original size:16 final size:15
Alignment explanation
Indices: 186784--186843 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 15
186774 AATATATCAT
*
186784 AAAAATAAAACTATTA
1 AAAAATAAAA-AATTA
*
186800 AAAACTAAAAAATTA
1 AAAAATAAAAAATTA
*
186815 AAAAATTAAAAAATTG
1 AAAAA-TAAAAAATTA
186831 AAAAATAATAAAA
1 AAAAATAA-AAAA
186844 CAATTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
15 11 0.29
16 27 0.71
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAAATAAAAAATTA
Found at i:186816 original size:8 final size:8
Alignment explanation
Indices: 186799--186836 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
186789 TAAAACTATT
*
186799 AAAAACTA
1 AAAAATTA
186807 AAAAATTA
1 AAAAATTA
186815 AAAAATTA
1 AAAAATTA
*
186823 AAAAATTG
1 AAAAATTA
186831 AAAAAT
1 AAAAAT
186837 AATAAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (8 bp):
AAAAATTA
Found at i:187248 original size:15 final size:16
Alignment explanation
Indices: 187217--187254 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
187207 TTTATCGCTC
* *
187217 AATAATTATTTTTATT
1 AATAATTATTATAATT
187233 -ATAATTATTATAATT
1 AATAATTATTATAATT
187248 AATAATT
1 AATAATT
187255 TAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATAATTATTATAATT
Found at i:187269 original size:14 final size:15
Alignment explanation
Indices: 187250--187282 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
187240 TTATAATTAA
187250 TAATTTAA-ATATTT
1 TAATTTAACATATTT
187264 TAATTTAATCATATTT
1 TAATTTAA-CATATTT
187280 TAA
1 TAA
187283 CTACACATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
16 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTTAACATATTT
Found at i:190045 original size:2 final size:2
Alignment explanation
Indices: 190034--190081 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
190024 GCTTACGTTT
190034 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
190075 TA TA TA T
1 TA TA TA T
190082 TATTTTTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:190642 original size:17 final size:17
Alignment explanation
Indices: 190603--190643 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
190593 ACGCATACCA
190603 GTTTTTGTCTTAAAAAT
1 GTTTTTGTCTTAAAAAT
* *
190620 GATTTTTTTCTTAAAATT
1 G-TTTTTGTCTTAAAAAT
190638 GTTTTT
1 GTTTTT
190644 AAAAGACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.61
Consensus pattern (17 bp):
GTTTTTGTCTTAAAAAT
Found at i:204932 original size:3 final size:3
Alignment explanation
Indices: 204924--205064 Score: 282
Period size: 3 Copynumber: 47.0 Consensus size: 3
204914 GTTTGAGTTG
204924 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
204972 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
205020 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
205065 CTAACAACAA
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 138 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:210420 original size:366 final size:370
Alignment explanation
Indices: 209727--210421 Score: 1013
Period size: 372 Copynumber: 1.9 Consensus size: 370
209717 TTCTTGATAT
* ** *
209727 GATCGAGTCATTCATTTTTCGAACAACTTCCCAGTGAGTCGCCCATCTTTGAATTACTCTGGTTC
1 GATCGACTCATTCATTTTTCGAACAACTTCCCAGTGAGTCAACCATCCTTGAATTACTCTGGTTC
* * * *
209792 AAGCACGCTTAACTACAGAGTTCTGAAGCGAATGGTTAATATTCATTCTTAAAACCAATTAGTGA
66 AAGCACACTTAACTACAGAGTTCTGAAGCGAATGATCAACATTCATTCTTAAAACCAATTAGTGA
* *
209857 TAAGTAAGTGGGTCATTTTAACCTCATATCTTTGTAGTGGGTGATCACTAGTTTCCCCCAAGCCA
131 TAAGTAA--GGATCATTTTAACCTCATATCTTTGTAGCGGGTGATCACTAGTTTCCCCCAAGCCA
* * *
209922 AGGTGGATTCTTGTGGGGCACCCCCCACAGTTCACCACGGCATTGCAGAGCCCTGCATCTATAGC
194 AGGTGGATTCTTATGAGGCACCCCCCACAATTCACCACGGCATTGCAGAGCCCTGCATCTATAGC
* * * * * *
209987 GTGTTGCGGGCTGGCCTAGGGGCTTCGCAAGGCACACGTGGGCCTTGGCAGGTTGGGCTGTCACG
259 GTGCTGCAGGCTGGCCTAAGGGCTTCGCAAGGCACACGTAGGCCTCGGCAGGTTGGGCTATCACG
210052 CACCTAGGGGATTCGAACTTGCAACCTGCTCTGATACCACTTGTTAG
324 CACCTAGGGGATTCGAACTTGCAACCTGCTCTGATACCACTTGTTAG
* *
210099 GATCGACTCATTCATTTTTCGAACAACTTCCCAGTGGGTCAACCATCCTTGGATTACTCTGGTTC
1 GATCGACTCATTCATTTTTCGAACAACTTCCCAGTGAGTCAACCATCCTTGAATTACTCTGGTTC
* * * * *
210164 AAGCACACTTAACTATAGAGTTCTGAAGCGAATGATCACCATTCCTTCTTAAAATCAA-TGGTGA
66 AAGCACACTTAACTACAGAGTTCTGAAGCGAATGATCAACATTCATTCTTAAAACCAATTAGTGA
* *
210228 TAAGT-A-GATCATTTTAACCTCATATCTTTGTAGCGGGTGATCATTGGTTTCCCCCAAGCCAAG
131 TAAGTAAGGATCATTTTAACCTCATATCTTTGTAGCGGGTGATCACTAGTTTCCCCCAAGCCAAG
** *
210291 GTGGATTCTTATGAGGCA-CCCTTACAATTCACCACGGCATTTCAGAG-CCTCGCATCTATAGCG
196 GTGGATTCTTATGAGGCACCCCCCACAATTCACCACGGCATTGCAGAGCCCT-GCATCTATAGCG
* * * *
210354 TGCTGTAGGCTGGCCTAAGGGCTTCGTAAGGCACACGTAGGTCTCGGCAGGTTGGGTTATCACGC
260 TGCTGCAGGCTGGCCTAAGGGCTTCGCAAGGCACACGTAGGCCTCGGCAGGTTGGGCTATCACGC
210419 ACC
325 ACC
210422 AGATATCAGA
Statistics
Matches: 287, Mismatches: 35, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
365 3 0.01
366 95 0.33
367 69 0.24
370 1 0.00
371 10 0.03
372 109 0.38
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.29
Consensus pattern (370 bp):
GATCGACTCATTCATTTTTCGAACAACTTCCCAGTGAGTCAACCATCCTTGAATTACTCTGGTTC
AAGCACACTTAACTACAGAGTTCTGAAGCGAATGATCAACATTCATTCTTAAAACCAATTAGTGA
TAAGTAAGGATCATTTTAACCTCATATCTTTGTAGCGGGTGATCACTAGTTTCCCCCAAGCCAAG
GTGGATTCTTATGAGGCACCCCCCACAATTCACCACGGCATTGCAGAGCCCTGCATCTATAGCGT
GCTGCAGGCTGGCCTAAGGGCTTCGCAAGGCACACGTAGGCCTCGGCAGGTTGGGCTATCACGCA
CCTAGGGGATTCGAACTTGCAACCTGCTCTGATACCACTTGTTAG
Found at i:212322 original size:16 final size:16
Alignment explanation
Indices: 212278--212321 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
212268 ATATTGAAAC
212278 TTGAACTCGAAAAGGG
1 TTGAACTCGAAAAGGG
*
212294 TTGAATTCGAAAAGGG
1 TTGAACTCGAAAAGGG
212310 TTGAACTC-AAAA
1 TTGAACTCGAAAA
212322 AAAATTAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.41, C:0.11, G:0.25, T:0.23
Consensus pattern (16 bp):
TTGAACTCGAAAAGGG
Found at i:212366 original size:13 final size:13
Alignment explanation
Indices: 212348--212374 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
212338 TTGAAGCCTA
212348 AAATTCGAGCTTG
1 AAATTCGAGCTTG
212361 AAATTCGAGCTTG
1 AAATTCGAGCTTG
212374 A
1 A
212375 TTGAAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (13 bp):
AAATTCGAGCTTG
Found at i:212836 original size:22 final size:24
Alignment explanation
Indices: 212787--212836 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
212777 GTGATATAAA
212787 AAATATTTTTTATTAAATATTTTT
1 AAATATTTTTTATTAAATATTTTT
*
212811 -AATA-TTTTTATTTAAT-TTTTT
1 AAATATTTTTTATTAAATATTTTT
212832 AAATA
1 AAATA
212837 ATTATGACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 15 0.62
23 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
AAATATTTTTTATTAAATATTTTT
Found at i:222084 original size:15 final size:14
Alignment explanation
Indices: 222064--222111 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
222054 TGAATAAGAT
222064 AATAATAATTATAAA
1 AATAATAATT-TAAA
222079 AATAATAATTTAAA
1 AATAATAATTTAAA
* *
222093 CAT-ATAAATTAAA
1 AATAATAATTTAAA
222106 ATATAA
1 A-ATAA
222112 ATAACAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 9 0.32
14 8 0.29
15 11 0.39
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATAATTTAAA
Found at i:223425 original size:11 final size:11
Alignment explanation
Indices: 223409--223452 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
223399 TTTGGGCTTG
* *
223409 TAATAATTATT
1 TAATAATAATA
223420 TAATAATAATA
1 TAATAATAATA
*
223431 TAATAATAAAA
1 TAATAATAATA
*
223442 TATTAATAATA
1 TAATAATAATA
223453 ATAAATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAATAATAATA
Found at i:223426 original size:3 final size:3
Alignment explanation
Indices: 223420--223471 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
223410 AATAATTATT
* *
223420 TAA TAA TAA T-A TAA TAA TAA -AA TAT TAA TAA TAA TAA -ATT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
223463 TAA TAA TAA
1 TAA TAA TAA
223472 AATTAAATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 5 0.12
3 35 0.85
4 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:223428 original size:14 final size:14
Alignment explanation
Indices: 223409--223471 Score: 71
Period size: 14 Copynumber: 4.6 Consensus size: 14
223399 TTTGGGCTTG
*
223409 TAATAATTATTTAA
1 TAATAATAATTTAA
223423 TAATAAT-A--TAA
1 TAATAATAATTTAA
223434 TAATAA-AATATTAA
1 TAATAATAAT-TTAA
223448 TAATAATAAATTTAA
1 TAATAAT-AATTTAA
223463 TAATAATAA
1 TAATAATAA
223472 AATTAAATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
11 10 0.23
13 1 0.02
14 18 0.42
15 11 0.26
16 3 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATAATAATTTAA
Found at i:223464 original size:15 final size:15
Alignment explanation
Indices: 223430--223477 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
223420 TAATAATAAT
223430 ATAATAATAAAATATTA
1 ATAATAAT-AAAT-TTA
223447 ATAATAATAAATTTA
1 ATAATAATAAATTTA
*
223462 ATAATAATAAAATTA
1 ATAATAATAAATTTA
223477 A
1 A
223478 ATGAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 18 0.60
16 4 0.13
17 8 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAATAATAAATTTA
Found at i:223789 original size:75 final size:76
Alignment explanation
Indices: 223597--224368 Score: 1250
Period size: 75 Copynumber: 10.5 Consensus size: 76
223587 GATGGAAATG
* * *
223597 TTTGAAAACATCATGCACTGAAGGGCTTAC-GATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
223660 CCCGAAGGC-T
66 CCCGAAGGCTT
* * *
223670 TTTGGAAAACATCATGCACTGTAGGACTTACAGATTACCC-AAGGCTTTAAAAACATCAAAAAGC
1 TTTGG-AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
*
223734 T-CTGAAGGCTT
65 TCCCGAAGGCTT
* * *
223745 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTCGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
223810 CCCGAAGGC-T
66 CCCGAAGGCTT
223820 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCT---GCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
223882 CCCGAAGGC-T
66 CCCGAAGGCTT
*
223892 TTTGGAAACATCATGC-TTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
223956 CCCGAAGGCTT
66 CCCGAAGGCTT
223967 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTG-AAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
224030 CCCGAAGGC-T
66 CCCGAAGGCTT
224040 TTTGG-AA-A-CAT-CA-TGAAGGACTTACAGATGACCCTAAGGC-TTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
224099 -CCGAAGGCTT
66 CCCGAAGGCTT
224109 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGC-TTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
224173 CCCGAAGGCTT
66 CCCGAAGGCTT
*
224184 TTTGGAAACATCATGCACTGAAGGACTTACAGATTACCCTAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
224248 CCCGAAGGCTT
66 CCCGAAGGCTT
*
224259 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
224323 CCCGAAGGCTT
66 CCCGAAGGCTT
224334 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
224369 TGGGAAATAG
Statistics
Matches: 658, Mismatches: 20, Indels: 40
0.92 0.03 0.06
Matches are distributed among these distances:
67 3 0.00
68 42 0.06
69 15 0.02
70 5 0.01
71 24 0.04
72 52 0.08
73 12 0.02
74 162 0.25
75 294 0.45
76 49 0.07
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:224668 original size:181 final size:185
Alignment explanation
Indices: 224316--224843 Score: 940
Period size: 181 Copynumber: 2.9 Consensus size: 185
224306 TGAAAACATC
* *
224316 AAAAGATCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGTGGGAAATAGTT
1 AAAAGATCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGAAATAGTT
*
224381 TATTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAGAAAAGAT
66 TACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAGAAAAGAT
* *
224446 TGAATGAGAAATTATGGAAATCATTTTCTCATTATTTTTCAAAATAACAACGTCA
131 TGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACAACGTCA
224501 AAAAGATCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGAAATAG-T
1 AAAAGATCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGAAATAGTT
224565 TACTAAGTAAAAAAACTAAGGAAATCG-TTT-TT-CTTTTCAACAATTTCATTTTTAGAAAAGAT
66 TACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAGAAAAGAT
224627 TGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACAACGTCA
131 TGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACAACGTCA
224682 AAAAGATCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGAAATAGTT
1 AAAAGATCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGAAATAGTT
224747 TACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCA-TTTTAGAAAAGAT
66 TACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAGAAAAGAT
** * *
224811 AAAATGAGAAACTAAGAAAATCGTTTTCTCATT
131 TGAATGAGAAACTATGGAAATCGTTTTCTCATT
224844 CTGTTTTTTT
Statistics
Matches: 330, Mismatches: 9, Indels: 9
0.95 0.03 0.03
Matches are distributed among these distances:
181 146 0.44
182 30 0.09
183 6 0.02
184 71 0.22
185 77 0.23
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (185 bp):
AAAAGATCCCAAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGAAATAGTT
TACTAAGTAAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAGAAAAGAT
TGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACAACGTCA
Found at i:225904 original size:54 final size:53
Alignment explanation
Indices: 225769--225923 Score: 195
Period size: 53 Copynumber: 2.9 Consensus size: 53
225759 ATAATCACTG
* * * * *
225769 GTTCATAAAACATTTGATAATACATTCATCTTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCAT-AAACATTTGACAACACATTCATCATTTCTTGTGGTTTCTGCTCAGAC
** *
225823 GTTTGTAAACATTTGACAACACATTCATCATTTCTTGTGGTTTTTGCTCAGAC
1 GTTCATAAACATTTGACAACACATTCATCATTTCTTGTGGTTTCTGCTCAGAC
*
225876 GTTCATAAAGCGTTTGACAACACATTCATCATTT-TCTGTGGTTTCTGC
1 GTTCATAAA-CATTTGACAACACATTCATCATTTCT-TGTGGTTTCTGC
225924 CAAGATTTCT
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
53 49 0.56
54 38 0.44
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (53 bp):
GTTCATAAACATTTGACAACACATTCATCATTTCTTGTGGTTTCTGCTCAGAC
Found at i:227313 original size:389 final size:385
Alignment explanation
Indices: 226601--227375 Score: 1446
Period size: 389 Copynumber: 2.0 Consensus size: 385
226591 TGACACATGG
226601 TAAGAAGATTGGGTATTTGAAAACATATTTGCTGAGTAGATATTTTTCAACAACATGATCATAAT
1 TAAGAAGATTGGGTATTTGAAAACATATTTGCTGAGTAGATATTTTTCAACAACATGATCATAAT
226666 GTAACTGCCTGATGAACGAAGCAATTATGTATAGTCAGCTTCATGTCATTGTTCACCATTTTCTT
66 GTAACTGCCTGATGAACGAAGCAATTATGTATAGTCAGCTTCATGTCATTGTTCACCATTTTCTT
226731 CTTCATACCTTTCTGTCTCATTGGAAAAATCTGTTCAAGTCATGATCTTGACACATGATGATGTG
131 CTTCATACCTTTCTGTCTCATTGGAAAAATCTGTTCAAGTCATGATCTTGACACATGATGATGTG
226796 GGCCTTCAGCATGCCCCAACATTTGCTGATACGATCGTTCAAAAAATGCATAAACAGTCCTAATT
196 GGCCTTCAGCATGCCCCAACATTTGCTGATACGATCGTTCAAAAAATGCATAAACAGTCCTAATT
226861 CTGATGAAATGGGCTTTCAGCATGCCCCGATATTTGCTTCTTGTTAATCTGAGCCTTCAAAATGC
261 CTGATGAAATGGGCTTTCAGCATGCCCCGATATTTGCTTCTTGTTAATCTGAGCCTTCAAAATGC
226926 CCACATGGA-TCTGAAGGAACCTTTAAAATGCCCCAACATTTGCTGATACAGATGTTAGT
326 CCACATGGATTCTGAAGGAACCTTTAAAATGCCCCAACATTTGCTGATACAGATGTTAGT
226985 TAAGAAGATTGGGTATTTGAAAACATATTTGCTGAGTAGATATTTTTTCAACAACATGATCATAA
1 TAAGAAGATTGGGTATTTGAAAACATATTTGCTGAGTAGATA-TTTTTCAACAACATGATCATAA
227050 TGTAACTGCCTGATGAACGAAGCAATTATGTATAGTCAGCTTCATTGTCATTGTTTCACCATTTT
65 TGTAACTGCCTGATGAACGAAGCAATTATGTATAGTCAGCTTCA-TGTCATTG-TTCACCATTTT
*
227115 CATTCTTCATACCTTTCTGTCTCATTGGAAATATCTGTTCAAGTCAATGATCTTGACACATGATG
128 C-TTCTTCATACCTTTCTGTCTCATTGGAAAAATCTGTTCAAGTC-ATGATCTTGACACATGATG
227180 ATGTGGGCCTTCAGCATGCCCCAACATTTGCTGATACGATCGTTC-AAAAATGCATAAACAGTCC
191 ATGTGGGCCTTCAGCATGCCCCAACATTTGCTGATACGATCGTTCAAAAAATGCATAAACAGTCC
227244 TAATTCTGATTGAAATGGGCTTTCAGCATGCCCCGATATTTGCTTCTTGTTAATCTGAGCCTTCA
256 TAATTCTGA-TGAAATGGGCTTTCAGCATGCCCCGATATTTGCTTCTTGTTAATCTGAGCCTTCA
227309 AAATGCCCACATGGATCTGTCTGAAGGAACCTTTAAAATGCCCCAACATTTGCTGATACAGATGT
320 AAATGCCCACATGGA--T-TCTGAAGGAACCTTTAAAATGCCCCAACATTTGCTGATACAGATGT
227374 TA
382 TA
227376 AAAGTGTGCT
Statistics
Matches: 380, Mismatches: 1, Indels: 11
0.97 0.00 0.03
Matches are distributed among these distances:
384 42 0.11
385 66 0.17
386 8 0.02
387 12 0.03
388 70 0.18
389 134 0.35
393 48 0.13
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (385 bp):
TAAGAAGATTGGGTATTTGAAAACATATTTGCTGAGTAGATATTTTTCAACAACATGATCATAAT
GTAACTGCCTGATGAACGAAGCAATTATGTATAGTCAGCTTCATGTCATTGTTCACCATTTTCTT
CTTCATACCTTTCTGTCTCATTGGAAAAATCTGTTCAAGTCATGATCTTGACACATGATGATGTG
GGCCTTCAGCATGCCCCAACATTTGCTGATACGATCGTTCAAAAAATGCATAAACAGTCCTAATT
CTGATGAAATGGGCTTTCAGCATGCCCCGATATTTGCTTCTTGTTAATCTGAGCCTTCAAAATGC
CCACATGGATTCTGAAGGAACCTTTAAAATGCCCCAACATTTGCTGATACAGATGTTAGT
Found at i:228730 original size:115 final size:114
Alignment explanation
Indices: 228410--228750 Score: 565
Period size: 114 Copynumber: 3.0 Consensus size: 114
228400 GATCATGCAG
* * * * * *
228410 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCTTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
228475 ACACTTCCAGAAGATGTTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
* *
228524 TTCATCTTTCAAATCCAATGATTAGTTTTGGGGTTCATACCAAACCATATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
228589 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
*
228638 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAAATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
228703 AACACTTCTAGAAGATGCTATTGAGTCTTCTTATTTCTAGTATGAGCA
65 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
228751 CATGGCACTT
Statistics
Matches: 212, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
114 129 0.61
115 83 0.39
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:236509 original size:15 final size:14
Alignment explanation
Indices: 236489--236518 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
236479 ATAAGATAAC
236489 AATAATTATAAAAAT
1 AATAATT-TAAAAAT
236504 AATAATTTAAAAAT
1 AATAATTTAAAAAT
236518 A
1 A
236519 TAAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATTTAAAAAT
Found at i:237878 original size:3 final size:3
Alignment explanation
Indices: 237872--237928 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
237862 AATAATTATT
* *
237872 TAA TAA T-A TAA TAA TAA TAA TAA TATT TAA TAA TAA TAA -ATT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA
237917 TAA TAA TAA TAA
1 TAA TAA TAA TAA
237929 AATTTAAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 3 0.07
3 40 0.87
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:237895 original size:28 final size:31
Alignment explanation
Indices: 237861--237926 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
237851 TTTGGGCTTG
237861 TAATAATTATTTAATAAT-AT-AA-TAATAA
1 TAATAATTATTTAATAATAATAAATTAATAA
237889 TAATAA-TATTTAATAATAATAAATTTAATAA
1 TAATAATTATTTAATAATAATAAA-TTAATAA
237920 TAATAAT
1 TAATAAT
237927 AAAATTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
27 11 0.33
28 8 0.24
29 2 0.06
31 12 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
TAATAATTATTTAATAATAATAAATTAATAA
Found at i:237923 original size:34 final size:33
Alignment explanation
Indices: 237872--237935 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
237862 AATAATTATT
*
237872 TAATAATATAATAATAATAATAATATTTAATAA
1 TAATAATATAATAATAATAATAAAATTTAATAA
*
237905 TAATAAATTTAATAATAATAATAAAATTTAA
1 TAAT-AATATAATAATAATAATAAAATTTAA
237936 ATGAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
TAATAATATAATAATAATAATAAAATTTAATAA
Found at i:239665 original size:18 final size:18
Alignment explanation
Indices: 239624--239665 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
239614 GATAAGTGGC
*
239624 ATATTTATAAATTTAAAA
1 ATATTAATAAATTTAAAA
*
239642 AAATTAATAAATTTAAAA
1 ATATTAATAAATTTAAAA
*
239660 TTATTA
1 ATATTA
239666 TTATTTTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATTAATAAATTTAAAA
Found at i:239720 original size:19 final size:17
Alignment explanation
Indices: 239673--239721 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
239663 TTATTATTTT
*
239673 TAAAAGTCTAAAAAAATTC
1 TAAAA-TCT-AAAAAAGTC
239692 TAAAATCTAAAAAAGTC
1 TAAAATCTAAAAAAGTC
239709 TCAAAATCCTAAA
1 T-AAAAT-CTAAA
239722 TCTAAAAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 9 0.33
18 8 0.30
19 10 0.37
ACGTcount: A:0.57, C:0.14, G:0.04, T:0.24
Consensus pattern (17 bp):
TAAAATCTAAAAAAGTC
Found at i:240604 original size:80 final size:79
Alignment explanation
Indices: 240458--240616 Score: 255
Period size: 80 Copynumber: 2.0 Consensus size: 79
240448 ATATAGTTAT
*
240458 TATTTGGTATTTGATTTTTCTTATAAACGTCATGTTATATTTTTAATTGATTTAATATCTATATT
1 TATTTGGTATTTGATTTTTCTTATAAACGTCATGTTATATTTTTAATTGATTTAATATCTAAATT
240523 TTTCAAACACTATA
66 TTTCAAACACTATA
* * **
240537 TATTTGGTATTTGATTTTTCTTATAAACGTGATATTTATATTTTTAATTGATTTGGTATCTAAAT
1 TATTTGGTATTTGATTTTTCTTATAAACGTCAT-GTTATATTTTTAATTGATTTAATATCTAAAT
*
240602 TTTTCAAGCACTATA
65 TTTTCAAACACTATA
240617 CCTTTGATAT
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 32 0.44
80 41 0.56
ACGTcount: A:0.30, C:0.08, G:0.09, T:0.53
Consensus pattern (79 bp):
TATTTGGTATTTGATTTTTCTTATAAACGTCATGTTATATTTTTAATTGATTTAATATCTAAATT
TTTCAAACACTATA
Found at i:242756 original size:9 final size:10
Alignment explanation
Indices: 242727--242754 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
242717 ATTTAAAAAT
242727 ATATTTTTTA
1 ATATTTTTTA
242737 ATATTTTTTA
1 ATATTTTTTA
242747 ATATTTTT
1 ATATTTTT
242755 AAAAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
ATATTTTTTA
Done.