Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008926.1 Hibiscus syriacus cultivar Beakdansim tig00112231_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: 4069050
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 20
Found at i:3150717 original size:29 final size:30
Alignment explanation
Indices: 3150657--3150728 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
3150647 GGTTCTTTGG
* * * * *
3150657 GACCTATGGACAGTTGCCGAGGTTCTTTGT
1 GACCTCTGGATAGTTACCGAGGGTCTGTGT
3150687 GACCTCTGGATAGTTACCG-GGGTCTGTGT
1 GACCTCTGGATAGTTACCGAGGGTCTGTGT
3150716 GACCTCTGGATAG
1 GACCTCTGGATAG
3150729 GTTCTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.31
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGGTCTGTGT
Found at i:3153813 original size:21 final size:20
Alignment explanation
Indices: 3153727--3153881 Score: 80
Period size: 21 Copynumber: 7.7 Consensus size: 20
3153717 AAATGACCAA
**
3153727 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
3153746 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
3153766 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
3153786 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
3153807 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3153828 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3153848 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
3153869 GAAAATCGCAACG
1 CAAAATCGCAACG
3153882 TGAACACATA
Statistics
Matches: 101, Mismatches: 29, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 38 0.38
21 47 0.47
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3153875 original size:20 final size:19
Alignment explanation
Indices: 3153849--3153903 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
3153839 TGCGATTTTC
*
3153849 CAAAATCGCAACGCGAATA
1 CAAAATCGCAACGCGAACA
* *
3153868 TGAAAATCGCAACGTGAACA
1 -CAAAATCGCAACGCGAACA
3153888 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
3153904 TATCCGTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.13
Consensus pattern (19 bp):
CAAAATCGCAACGCGAACA
Found at i:3153900 original size:40 final size:40
Alignment explanation
Indices: 3153851--3154042 Score: 136
Period size: 40 Copynumber: 4.8 Consensus size: 40
3153841 CGATTTTCCA
*
3153851 AAATCGCAACGCGAATATGAAAATCGCAACGTG-AACACAT
1 AAATCGCAACGCGAATACGAAAATCGCAACGTGTAAC-CAT
* * * * *
3153891 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACGAAAATCGCAACGTGTAACCAT
* ** * * * * *
3153931 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATACGAAAATCGCAACGTGTAACCAT
* * * * * *
3153971 ATATCGCAACGCGTATCCGTAAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGAATACGAAAATCGCAACGTGTAA-CCAT
* * *
3154011 AAAATCGCAACGCGTATCCGTAAATCGCAACG
1 -AAATCGCAACGCGAATACGAAAATCGCAACG
3154043 CGATATTTAA
Statistics
Matches: 130, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
39 2 0.02
40 96 0.74
41 32 0.25
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGAATACGAAAATCGCAACGTGTAACCAT
Found at i:3153913 original size:20 final size:20
Alignment explanation
Indices: 3153890--3154044 Score: 213
Period size: 20 Copynumber: 7.7 Consensus size: 20
3153880 CGTGAACACA
3153890 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
3153910 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
**
3153930 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
3153950 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
3153970 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* * *
3153990 TAAATCGCAACG-ATAATACA
1 TAAATCGCAACGCGT-ATCCG
3154010 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
3154031 TAAATCGCAACGCG
1 TAAATCGCAACGCG
3154045 ATATTTAAAG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 99 0.85
21 15 0.13
22 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:3153935 original size:60 final size:60
Alignment explanation
Indices: 3153851--3154044 Score: 246
Period size: 60 Copynumber: 3.2 Consensus size: 60
3153841 CGATTTTCCA
* ** * *
3153851 AAATCGCAACGCGAATATGAAAATCGCAACGTGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGTGAATACATAAATCGCAACGCGTATCCGT
* * * *** *
3153911 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGTGAATACATAAATCGCAACGCGTATCCGT
*
3153971 ATATCGCAACGCGTATCCGTAAATCGCAACGAT-AATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACG-TGAATACAT-AAATCGCAACGCGTATCCGT
3154032 AAATCGCAACGCG
1 AAATCGCAACGCG
3154045 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGTGAATACATAAATCGCAACGCGTATCCGT
Found at i:3154465 original size:33 final size:33
Alignment explanation
Indices: 3154426--3154496 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
3154416 TTCACTTAGA
* *
3154426 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
3154459 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
3154492 TTTCA
1 TTTCA
3154497 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:3154620 original size:20 final size:20
Alignment explanation
Indices: 3154576--3154685 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
3154566 TGCAGAAGAG
*
3154576 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
3154597 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
3154617 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
3154638 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
3154652 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
3154671 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
3154686 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:3154633 original size:41 final size:38
Alignment explanation
Indices: 3154569--3154685 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
3154559 TTCAATTTGC
* *
3154569 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
3154607 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
3154648 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
3154681 AGAAT
1 AGAAT
3154686 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:3154655 original size:14 final size:14
Alignment explanation
Indices: 3154636--3154692 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3154626 GAGAAATGAA
3154636 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3154650 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3154669 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3154683 AATCGCAACG
1 AATCGCAACG
3154693 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:3154668 original size:33 final size:33
Alignment explanation
Indices: 3154628--3154708 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
3154618 CGCAACGAGA
3154628 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3154661 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
3154694 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
3154709 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:3154726 original size:19 final size:19
Alignment explanation
Indices: 3154704--3154801 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
3154694 GAAACCAAAA
*
3154704 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3154723 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
3154737 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3154756 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
3154770 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
3154789 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3154802 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3154745 original size:14 final size:14
Alignment explanation
Indices: 3154726--3154815 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
3154716 TTTCATTTCG
3154726 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3154740 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3154759 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3154773 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
3154790 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
3154806 CGTTGCGATT
1 CGTTGCGATT
3154816 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3154751 original size:33 final size:33
Alignment explanation
Indices: 3154709--3154823 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
3154699 CAAAATCGCA
3154709 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3154742 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
3154775 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3154808 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
3154824 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3155701 original size:93 final size:93
Alignment explanation
Indices: 3155542--3155804 Score: 508
Period size: 93 Copynumber: 2.8 Consensus size: 93
3155532 TTCCGTGGGG
3155542 TTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTT
1 TTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTT
*
3155607 GAAAGTAAATTTGTTCGGTTGCTGCCAA
66 GAAAGTAAATTTGTTCCGTTGCTGCCAA
3155635 TTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTT
1 TTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTT
3155700 GAAAGTAAATTTGTTCCGTTGCTGCCAA
66 GAAAGTAAATTTGTTCCGTTGCTGCCAA
*
3155728 TTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTT
1 TTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTT
3155793 GAAAGTAAATTT
66 GAAAGTAAATTT
3155805 ATCCATTCAA
Statistics
Matches: 168, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 168 1.00
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
TTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTT
GAAAGTAAATTTGTTCCGTTGCTGCCAA
Found at i:3155888 original size:19 final size:19
Alignment explanation
Indices: 3155848--3155976 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3155838 TAGTTTACTT
* *
3155848 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
3155868 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
3155887 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
3155906 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
3155920 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
3155939 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
3155953 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
3155972 TCGCA
1 TCGCA
3155977 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:3155927 original size:33 final size:32
Alignment explanation
Indices: 3155884--3155976 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
3155874 CGCGAAACCA
**
3155884 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
3155916 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
3155949 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
3155977 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:3155974 original size:52 final size:52
Alignment explanation
Indices: 3155848--3155976 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
3155838 TAGTTTACTT
**
3155848 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
3155900 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
3155953 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
3155977 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:3155994 original size:19 final size:19
Alignment explanation
Indices: 3155972--3156106 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3155962 GAAACCAAAA
*
3155972 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3155991 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
3156007 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
3156024 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
3156040 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
3156057 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
3156076 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
3156096 TCGTGTTGCGA
1 TCGCGTTGCGA
3156107 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:3156013 original size:14 final size:14
Alignment explanation
Indices: 3155994--3156050 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3155984 TTTCATTTCG
3155994 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3156008 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3156025 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
3156041 CGTTGCGATT
1 CGTTGCGATT
3156051 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:3156019 original size:33 final size:33
Alignment explanation
Indices: 3155977--3156069 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
3155967 CAAAATCGCA
*
3155977 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
3156010 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
3156043 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3156070 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:3157669 original size:12 final size:12
Alignment explanation
Indices: 3157652--3157676 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3157642 TCTTCGGGGA
3157652 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3157664 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3157676 C
1 C
3157677 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:3157885 original size:24 final size:24
Alignment explanation
Indices: 3157851--3157897 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3157841 CTGAAACATC
3157851 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3157875 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3157898 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:3158608 original size:20 final size:20
Alignment explanation
Indices: 3158580--3158809 Score: 246
Period size: 20 Copynumber: 11.5 Consensus size: 20
3158570 AAATTTCAGT
* * *
3158580 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
3158600 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATTCGC
**
3158620 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
3158640 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
3158660 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
3158680 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
3158700 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
3158720 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
3158740 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
3158760 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
3158780 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
3158800 GTTGCGATTT
1 GTTGCGATTT
3158810 TGGAAAATCG
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 183 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:3160507 original size:12 final size:13
Alignment explanation
Indices: 3160484--3160525 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
3160474 AACGGTCATC
3160484 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3160497 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
3160509 GGTAAACGGGTCG
1 GGTCAACGGGTCG
3160522 GGTC
1 GGTC
3160526 GGGTAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3160527 original size:18 final size:18
Alignment explanation
Indices: 3160504--3160557 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
3160494 TCGGGTCAAC
3160504 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
3160522 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
3160540 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
3160558 TGACCGGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:3160557 original size:13 final size:13
Alignment explanation
Indices: 3160488--3160524 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
3160478 GTCATCGGTC
*
3160488 AACGGGTCGGGTC
1 AACGGGTCGGGTA
3160501 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
3160513 AACGGGTCGGGT
1 AACGGGTCGGGT
3160525 CGGGTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:3167721 original size:13 final size:13
Alignment explanation
Indices: 3167703--3167743 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3167693 AACGGTCAAC
3167703 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3167716 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
* *
3167728 AGTAAACGGGTCG
1 GGTCAACGGGTCG
3167741 GGT
1 GGT
3167744 TGGGTAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.20, C:0.20, G:0.44, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3167726 original size:7 final size:7
Alignment explanation
Indices: 3167674--3167711 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
3167664 AGAATAGCAC
3167674 CGGTCAA
1 CGGTCAA
3167681 CGGTCAA
1 CGGTCAA
3167688 CGGTCAA
1 CGGTCAA
3167695 CGGTCAA
1 CGGTCAA
3167702 CGGTCAA
1 CGGTCAA
3167709 CGG
1 CGG
3167712 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:3167752 original size:18 final size:18
Alignment explanation
Indices: 3167723--3167776 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
3167713 TCGGGTCAAC
*
3167723 GGTCGAGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
* *
3167741 GGTTGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
3167759 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
3167777 TGACCAGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.19, C:0.15, G:0.46, T:0.20
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:3170535 original size:51 final size:52
Alignment explanation
Indices: 3170475--3170785 Score: 298
Period size: 51 Copynumber: 5.9 Consensus size: 52
3170465 GAAGCAAACT
* *
3170475 CATTTTATGAAGA-TCAAGTCCTATACTCTCTGAAGGAATAGGGAGAGGACA
1 CATTTTATGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
3170526 CATTTTATGAAGA-TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CATTTTATGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
3170577 CGTTTGT-TAAAGATT-GAGTCCTATACTCTCTGAAGGAATA--GAGCGGAC-
1 CATTT-TATGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
3170625 C-TGTTTATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CAT-TTTA-TGAAGA---TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * * **
3170681 CGTTTTATTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCATACA
1 CATTTTA-TGAAGA---TTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
*
3170737 CATTTTATGAAGATTGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGAG
1 CATTTTATGAAGA---TTCGAGTCCTATACTCT-CTGAAGGAATAGGGAG
3170786 TAGACTCATC
Statistics
Matches: 228, Mismatches: 18, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
47 2 0.01
48 3 0.01
49 13 0.06
51 83 0.36
52 4 0.02
53 24 0.11
54 1 0.00
55 45 0.20
56 52 0.23
57 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (52 bp):
CATTTTATGAAGATTCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:3170676 original size:104 final size:102
Alignment explanation
Indices: 3170491--3170781 Score: 295
Period size: 104 Copynumber: 2.7 Consensus size: 102
3170481 ATGAAGATCA
3170491 AGTCCTATACTCTCTGAAGGAATAGGGAGAGGACACATTTTATGAAGATCGAGTCCTATACTCTC
1 AGTCCTATACTCTCTGAAGGAATA--GAGAGGACACATTTTATGAAGATCGAGTCCTATACTCTC
* *
3170556 TGAAGGAATAGGGAGCGGACACG-TTTGTTAAAGATTG-
64 TGAAGGAATAGAGAGCGGACACGTTTTATTAAAGATTGT
* *
3170593 AGTCCTATACTCTCTGAAGGAATAGAGCGGAC-C-TGTTTATTGAAGATTTTTCGAGTTCTATAC
1 AGTCCTATACTCTCTGAAGGAATAGAGAGGACACAT-TTTA-TGAAGA----TCGAGTCCTATAC
* *
3170656 TCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTT
60 TCTCTGAAGGAATAGAGAGCGGACACGTTTTATTAAAGATTG-T
* * * *
3170700 CAAGTCTTATACTCTCTGAATGAATAGAGAGCATACACATTTTATGAAGATTGTTCGAGTCTTAT
1 --AGTCCTATACTCTCTGAAGGAATAGAGAG--GACACATTTTATGAAGA----TCGAGTCCTAT
3170765 ACT-TCCTGAAGGAATAG
58 ACTCT-CTGAAGGAATAG
3170782 GGAGTAGACT
Statistics
Matches: 160, Mismatches: 13, Indels: 23
0.82 0.07 0.12
Matches are distributed among these distances:
98 1 0.01
99 5 0.03
100 13 0.08
102 24 0.15
104 37 0.23
105 12 0.08
109 26 0.16
110 1 0.01
111 35 0.22
112 5 0.03
113 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (102 bp):
AGTCCTATACTCTCTGAAGGAATAGAGAGGACACATTTTATGAAGATCGAGTCCTATACTCTCTG
AAGGAATAGAGAGCGGACACGTTTTATTAAAGATTGT
Found at i:3170804 original size:55 final size:55
Alignment explanation
Indices: 3170488--3170816 Score: 181
Period size: 55 Copynumber: 6.1 Consensus size: 55
3170478 TTTATGAAGA
* * * *
3170488 TCAAGTCCTATACTCTCTGAAGGAATAGGGAG-AGGACACATTTTATGAAGA----
1 TCAAGTCTTATACTCTCTGAAGGAATAGAGAGCA-GACACATATTACGAAGATTGT
* * * * * *
3170539 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTA--AAGATTG-
1 TCAAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACAC--ATATTACGAAGATTGT
* * * * *
3170593 ---AGTCCTATACTCTCTGAAGGAAT--AGAGCGGAC-C-TGTTTATTGAAGATTTT
1 TCAAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACAT-ATTA-CGAAGATTGT
* * * * * *
3170643 TCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGT
1 TCAAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACACATATTA-CGAAGATTGT
* * * *
3170699 TCAAGTCTTATACTCTCTGAATGAATAGAGAGCATACACATTTTATGAAGATTGT
1 TCAAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACATATTACGAAGATTGT
* * * * *
3170754 TCGAGTCTTATACT-TCCTGAAGGAATAGGGAGTAGACTCATCATT-CGAAGATTTT
1 TCAAGTCTTATACTCT-CTGAAGGAATAGAGAGCAGACACAT-ATTACGAAGATTGT
3170809 TCAAGTCT
1 TCAAGTCT
3170817 CGCTTATCCT
Statistics
Matches: 231, Mismatches: 25, Indels: 40
0.78 0.08 0.14
Matches are distributed among these distances:
45 1 0.00
46 3 0.01
48 1 0.00
49 14 0.06
51 63 0.27
53 25 0.11
54 1 0.00
55 67 0.29
56 54 0.23
57 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (55 bp):
TCAAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACATATTACGAAGATTGT
Found at i:3187369 original size:14 final size:15
Alignment explanation
Indices: 3187344--3187372 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3187334 TTGATTAAAT
3187344 TTGTATAATTTTTAA
1 TTGTATAATTTTTAA
3187359 TTGTA-AATTTTTAA
1 TTGTATAATTTTTAA
3187373 GATCCAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (15 bp):
TTGTATAATTTTTAA
Found at i:3189239 original size:30 final size:30
Alignment explanation
Indices: 3189199--3189333 Score: 243
Period size: 30 Copynumber: 4.5 Consensus size: 30
3189189 GGATGAGATT
*
3189199 GGTCGCCATGCAGTCGGGGCGAAGCTTGAA
1 GGTCGCCATGCAGTCGGGGCAAAGCTTGAA
* *
3189229 GGTTGCCATGCAGTTGGGGCAAAGCTTGAA
1 GGTCGCCATGCAGTCGGGGCAAAGCTTGAA
3189259 GGTCGCCATGCAGTCGGGGCAAAGCTTGAA
1 GGTCGCCATGCAGTCGGGGCAAAGCTTGAA
3189289 GGTCGCCATGCAGTCGGGGCAAAGCTTGAA
1 GGTCGCCATGCAGTCGGGGCAAAGCTTGAA
3189319 GGTCGCCATGCAGTC
1 GGTCGCCATGCAGTC
3189334 CTTGAAGGTC
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 100 1.00
ACGTcount: A:0.21, C:0.23, G:0.37, T:0.19
Consensus pattern (30 bp):
GGTCGCCATGCAGTCGGGGCAAAGCTTGAA
Found at i:3189337 original size:21 final size:21
Alignment explanation
Indices: 3189313--3189354 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3189303 CGGGGCAAAG
*
3189313 CTTGAAGGTCGCCATGCAGTC
1 CTTGAAGGTCGCCATACAGTC
*
3189334 CTTGAAGGTCGTCATACAGTC
1 CTTGAAGGTCGCCATACAGTC
3189355 GGGGCGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (21 bp):
CTTGAAGGTCGCCATACAGTC
Found at i:3189359 original size:51 final size:50
Alignment explanation
Indices: 3189283--3189381 Score: 144
Period size: 51 Copynumber: 2.0 Consensus size: 50
3189273 CGGGGCAAAG
* * *
3189283 CTTGAAGGTCGCCATGCAGTCGGGGCAAAGCTTGAAGGTCGCCATGCAGTC
1 CTTGAAGGTCGCCATACAGTCGGGGCAAA-CTTAAAGATCGCCATGCAGTC
* *
3189334 CTTGAAGGTCGTCATACAGTCGGGGCGAACTTAAAGATCGCCATGCAG
1 CTTGAAGGTCGCCATACAGTCGGGGCAAACTTAAAGATCGCCATGCAG
3189382 CCGAGATGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 17 0.40
51 26 0.60
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.20
Consensus pattern (50 bp):
CTTGAAGGTCGCCATACAGTCGGGGCAAACTTAAAGATCGCCATGCAGTC
Found at i:3189766 original size:15 final size:15
Alignment explanation
Indices: 3189746--3189784 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
3189736 TGAAAGGTTC
3189746 GAGCCAAGGTTAGTG
1 GAGCCAAGGTTAGTG
3189761 GAGCCAAGGTTAGTG
1 GAGCCAAGGTTAGTG
3189776 GAGCCAAGG
1 GAGCCAAGG
3189785 ACTTTAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.15, G:0.41, T:0.15
Consensus pattern (15 bp):
GAGCCAAGGTTAGTG
Found at i:3195477 original size:27 final size:27
Alignment explanation
Indices: 3195447--3195508 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
3195437 TACTCAAGAT
3195447 CGACTCGATCAAAACTCAATAAATACA
1 CGACTCGATCAAAACTCAATAAATACA
* *
3195474 CGACTCGATCAAAACTCGATAAATACT
1 CGACTCGATCAAAACTCAATAAATACA
3195501 CGACTCGA
1 CGACTCGA
3195509 ATGGACTCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.19
Consensus pattern (27 bp):
CGACTCGATCAAAACTCAATAAATACA
Found at i:3198141 original size:23 final size:23
Alignment explanation
Indices: 3198110--3198154 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3198100 TTAAAATCTT
*
3198110 TTCTGATGATATTTGTTTATGTG
1 TTCTCATGATATTTGTTTATGTG
3198133 TTCTCATGATATTTGTTTATGT
1 TTCTCATGATATTTGTTTATGT
3198155 AGGACGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.07, G:0.18, T:0.58
Consensus pattern (23 bp):
TTCTCATGATATTTGTTTATGTG
Found at i:3198588 original size:79 final size:79
Alignment explanation
Indices: 3198457--3198624 Score: 327
Period size: 79 Copynumber: 2.1 Consensus size: 79
3198447 GATATGTTCG
*
3198457 AACTCGACTCAGTCAAAATTTAGTAAATGCTCGACTCAGGTTGATTCAACTCAACTCGAGACCTT
1 AACTCGACTAAGTCAAAATTTAGTAAATGCTCGACTCAGGTTGATTCAACTCAACTCGAGACCTT
3198522 AACGAGTTAAGTCC
66 AACGAGTTAAGTCC
3198536 AACTCGACTAAGTCAAAATTTAGTAAATGCTCGACTCAGGTTGATTCAACTCAACTCGAGACCTT
1 AACTCGACTAAGTCAAAATTTAGTAAATGCTCGACTCAGGTTGATTCAACTCAACTCGAGACCTT
3198601 AACGAGTTAAGTCC
66 AACGAGTTAAGTCC
3198615 AACTCGACTA
1 AACTCGACTA
3198625 TATAAGTTCG
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 88 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (79 bp):
AACTCGACTAAGTCAAAATTTAGTAAATGCTCGACTCAGGTTGATTCAACTCAACTCGAGACCTT
AACGAGTTAAGTCC
Found at i:3201313 original size:16 final size:15
Alignment explanation
Indices: 3201279--3201333 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
3201269 TAATAACTCA
*
3201279 TAACAGCTAAAAAAG
1 TAACAACTAAAAAAG
*
3201294 TAACAACTAAAATTAG
1 TAACAACTAAAA-AAG
3201310 TAACAACTAGAAACAA-
1 TAACAACTA-AAA-AAG
3201326 TAACAACT
1 TAACAACT
3201334 TGGATGTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.32
16 19 0.56
17 4 0.12
ACGTcount: A:0.58, C:0.16, G:0.07, T:0.18
Consensus pattern (15 bp):
TAACAACTAAAAAAG
Found at i:3205713 original size:18 final size:18
Alignment explanation
Indices: 3205692--3205748 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
3205682 GATTGCCCAG
3205692 AGGGAACAGATTCCCCCC
1 AGGGAACAGATTCCCCCC
*
3205710 AGGGGGTATC-GATT--CCCC
1 A--GGG-AACAGATTCCCCCC
3205728 -GGGAACAGATTCCCCCC
1 AGGGAACAGATTCCCCCC
3205745 AGGG
1 AGGG
3205749 GTATCGACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 2 0.07
15 7 0.23
17 4 0.13
18 8 0.27
20 7 0.23
21 2 0.07
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (18 bp):
AGGGAACAGATTCCCCCC
Found at i:3205750 original size:34 final size:35
Alignment explanation
Indices: 3205693--3205777 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 35
3205683 ATTGCCCAGA
*
3205693 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGACTCCCC
*
3205728 GGGAACAGATTCCCCCCA-GGGGTATCGACTCCTC
1 GGGAACAGATTCCCCCCAGGGGGTATCGACTCCCC
* *
3205762 GGGTACATATTCCCCC
1 GGGAACAGATTCCCCC
3205778 TGCATGGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 28 0.61
35 18 0.39
ACGTcount: A:0.20, C:0.35, G:0.26, T:0.19
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTATCGACTCCCC
Found at i:3205915 original size:21 final size:21
Alignment explanation
Indices: 3205889--3205930 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3205879 ATTTGAATAT
3205889 TATGAAGGGGTA-TCGATTCCC
1 TATGAAGGGGTACT-GATTCCC
3205910 TATGAAGGGGTACTGATTCCC
1 TATGAAGGGGTACTGATTCCC
3205931 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACTGATTCCC
Found at i:3207157 original size:16 final size:18
Alignment explanation
Indices: 3207138--3207171 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
3207128 TGAAAACGAT
3207138 TTTCTTTT-AAAA-AAAA
1 TTTCTTTTGAAAACAAAA
3207154 TTTCTTTTGAAAACAAAA
1 TTTCTTTTGAAAACAAAA
3207172 ATAGATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 4 0.25
18 4 0.25
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (18 bp):
TTTCTTTTGAAAACAAAA
Found at i:3207180 original size:19 final size:20
Alignment explanation
Indices: 3207158--3207205 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3207148 AAAAAATTTC
*
3207158 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
3207177 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
3207197 TTTTGAAAA
1 TTTTGAAAA
3207206 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:3208630 original size:34 final size:35
Alignment explanation
Indices: 3208573--3208657 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 35
3208563 ATTGCCCAGA
3208573 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
*
3208608 GGGAATAGATTCCCCCCA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
* *
3208642 GGGTACATATTCCCCC
1 GGGAACAGATTCCCCC
3208658 TGTATGGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 29 0.63
35 17 0.37
ACGTcount: A:0.20, C:0.34, G:0.26, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
Found at i:3209150 original size:34 final size:32
Alignment explanation
Indices: 3209092--3209162 Score: 79
Period size: 34 Copynumber: 2.2 Consensus size: 32
3209082 CTTTTGTAAA
* *
3209092 AGGGAAAGGTTCTAGCTAATCCCGTGTAAAAGCT
1 AGGGAAAGGTTCTAGCTAAGCCC--GTAAAAACT
* * *
3209126 AGGGAAAGGTTCTTGTTTAGCCCGTAAAAACT
1 AGGGAAAGGTTCTAGCTAAGCCCGTAAAAACT
3209158 AGGGA
1 AGGGA
3209163 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 13 0.41
34 19 0.59
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.24
Consensus pattern (32 bp):
AGGGAAAGGTTCTAGCTAAGCCCGTAAAAACT
Found at i:3213675 original size:59 final size:59
Alignment explanation
Indices: 3213583--3213696 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
3213573 TGAAGGACTT
* * *
3213583 TTGCTTATTCGAAGTGTTGTGAATCGAGCAAAGGAAATGTTGATCCCTCAAGTGAAACG
1 TTGCTAATTCGAAGTGTTGTGAATCAAGCAAAGGAAATGTTAATCCCTCAAGTGAAACG
* * *
3213642 TTGCTAATTTGAAGTGTTGTGAATCAAGCAAAGGAGATGTTAATCCCTCGAGTGA
1 TTGCTAATTCGAAGTGTTGTGAATCAAGCAAAGGAAATGTTAATCCCTCAAGTGA
3213697 GGCGTAGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (59 bp):
TTGCTAATTCGAAGTGTTGTGAATCAAGCAAAGGAAATGTTAATCCCTCAAGTGAAACG
Found at i:3213798 original size:74 final size:74
Alignment explanation
Indices: 3213704--3214217 Score: 392
Period size: 74 Copynumber: 7.0 Consensus size: 74
3213694 TGAGGCGTAG
* *
3213704 TTTGTTTTAA-AAAAACAATCTTAAGTGAGATAAACTTCTTGTTTCAAGTGAAGCTATCTCAAGC
1 TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAACTTCTTGTTTCAAGTGAAACTATCTCAAGC
3213768 GAGATAAAA
66 GAGATAAAA
** * * *
3213777 TTTACTCTAAGAAAAACAATCTCAAGTGAGATAAATCTT-TAGTTTCAAGTGAAACTGTCTCAAG
1 TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA-CTTCTTGTTTCAAGTGAAACTATCTCAAG
*
3213841 CAAGATAAAA
65 CGAGATAAAA
* * *
3213851 CTTGTTTTAAGAAAAACAATCTCAAGTAAGATAAAACTTC-TATTTCAAGTGAAA-TAATCTCAA
1 TTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAACTTCTTGTTTCAAGTGAAACT-ATCTCAA
*
3213914 GTGAGAT-AAA
64 GCGAGATAAAA
* * *
3213924 TCTTGTTTTAAGAAAAACAATCTCAAGGGAGAT-AATTTC-TGTTTCGAGTGAAACTATCTCAAG
1 T-TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAACTTCTTGTTTCAAGTGAAACTATCTCAAG
*
3213987 CGA-A-ATAA
65 CGAGATAAAA
* ** * * * * *
3213995 TTTTTTTTAAAGAAAAACAATCTTGAGTGAAATGAAATTTCTTGTTTCGAGTAAAAACTGTCTCA
1 TTTGTTTT-AAGAAAAACAATCTCAAGTGAGAT-AAACTTCTTGTTTCAAGT-GAAACTATCTCA
* *
3214060 AGTGAGATAAATC
63 AGCGAGATAAA-A
** ** * ** *
3214073 TTATGTTTCGAGTGAAACTATCTCAAGTGAGATAAA--TCTTGTATT-AAGAAAAACAATCTCAA
1 TT-TGTTTTAAGAAAAACAATCTCAAGTGAGATAAACTTCTTGT-TTCAAGTGAAACTATCTCAA
*
3214135 G-GAAGATAAAT
64 GCG-AGATAAAA
* ** * * * * * ** *
3214146 TTATGTTTTGAGTGAAACTATCTGAAGCGAGATAAA-AT-TTGTTTTAAGAAAAACAATCTCAAG
1 TT-TGTTTTAAGAAAAACAATCTCAAGTGAGATAAACTTCTTGTTTCAAGTGAAACTATCTCAAG
*
3214209 TGAGATAAA
65 CGAGATAAA
3214218 TCTTCGTATT
Statistics
Matches: 366, Mismatches: 53, Indels: 44
0.79 0.11 0.10
Matches are distributed among these distances:
70 6 0.02
71 24 0.07
72 29 0.08
73 81 0.22
74 167 0.46
75 28 0.08
76 3 0.01
77 5 0.01
78 19 0.05
79 4 0.01
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (74 bp):
TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAACTTCTTGTTTCAAGTGAAACTATCTCAAGC
GAGATAAAA
Found at i:3213802 original size:36 final size:36
Alignment explanation
Indices: 3213708--3214217 Score: 250
Period size: 36 Copynumber: 13.9 Consensus size: 36
3213698 GCGTAGTTTG
* *
3213708 TTTTAA-AAAAACAATCTTAAGTGAGATAAACTTCT-
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAAATT-TA
** * * *
3213743 TGTTTCAAGTGAAGCTATCTCAAGCGAGATAAAATTTA
1 T-TTT-AAGAAAAACAATCTCAAGTGAGATAAAATTTA
* * *
3213781 CTCTAAGAAAAACAATCTCAAGTGAGATAAATCTTTA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAA-ATTTA
* ** ** ** * *
3213818 GTTTCAAGTGAAACTGTCTCAAGCAAGATAAAACTTG
1 -TTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTA
*
3213855 TTTTAAGAAAAACAATCTCAAGTAAGATAAAACTTCTA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAAA-TT-TA
* ** * *
3213893 TTTCAAGTGAAATAATCTCAAGTGAGAT-AAATCTTG
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAAAT-TTA
* *
3213929 TTTTAAGAAAAACAATCTCAAGGGAGAT--AATTTC
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTA
* ** * * * *
3213963 TGTTTCGAGTGAAACTATCTCAAGCGA-A-ATAATTTT
1 T-TTT-AAGAAAAACAATCTCAAGTGAGATAAAATTTA
** * * *
3213999 TTTTAAAGAAAAACAATCTTGAGTGAAATGAAATTTCT
1 TTTT-AAGAAAAACAATCTCAAGTGAGATAAAATTT-A
* **
3214037 TGTTTCGAGTAAAAACTGTCTCAAGTGAGAT-AAATCTTA
1 T-TTT-AAG-AAAAACAATCTCAAGTGAGATAAAAT-TTA
* ** * *
3214076 TGTTTCGAGTGAAACTATCTCAAGTGAGAT-AAATCTTG
1 T-TTT-AAGAAAAACAATCTCAAGTGAGATAAAAT-TTA
*
3214114 TATTAAGAAAAACAATCTCAAG-GAAGAT-AAATTTA
1 TTTTAAGAAAAACAATCTCAAGTG-AGATAAAATTTA
* ** * * * *
3214149 TGTTTTGAGTGAAACTATCTGAAGCGAGATAAAATTTG
1 --TTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTA
3214187 TTTTAAGAAAAACAATCTCAAGTGAGATAAA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAA
3214218 TCTTCGTATT
Statistics
Matches: 357, Mismatches: 94, Indels: 47
0.72 0.19 0.09
Matches are distributed among these distances:
34 3 0.01
35 28 0.08
36 146 0.41
37 43 0.12
38 101 0.28
39 18 0.05
40 18 0.05
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (36 bp):
TTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTA
Found at i:3214107 original size:185 final size:187
Alignment explanation
Indices: 3213870--3214204 Score: 516
Period size: 185 Copynumber: 1.8 Consensus size: 187
3213860 AGAAAAACAA
* *
3213870 TCTCAAGTAAGATAAAACTTCTATTTCAAGTGAAATAATCTCAAGTGAGATAAATCTTGTTTTAA
1 TCTCAAGTAAGATAAAACTTATATTTCAAGTGAAATAATCTCAAGTGAGATAAATCTTGTATTAA
* * *
3213935 GAAAAACAATCTCAAGGGAGAT-AATTTCTGTTTCGAGTGAAACTATCTCAAGCGA-A-ATAATT
66 GAAAAACAATCTCAAGGAAGATAAATTTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATT
*
3213997 TTTTTTAAAGAAAAACAATCTTGAGTGAAATGAAATTTCTTGTTTCGAGTAAAAACTG
131 TGTTTT-AAGAAAAACAATCTTGAGTGAAATGAAATTTCTTGTTTCGAGTAAAAACTG
* * * *
3214055 TCTCAAGTGAGATAAATCTTATGTTTCGAGTGAAACT-ATCTCAAGTGAGATAAATCTTGTATTA
1 TCTCAAGTAAGATAAAACTTATATTTCAAGTGAAA-TAATCTCAAGTGAGATAAATCTTGTATTA
* *
3214119 AGAAAAACAATCTCAAGGAAGATAAATTTATGTTTTGAGTGAAACTATCTGAAGCGAGATAAAAT
65 AGAAAAACAATCTCAAGGAAGATAAATTTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAAAT
3214184 TTGTTTTAAGAAAAACAATCT
130 TTGTTTTAAGAAAAACAATCT
3214205 CAAGTGAGAT
Statistics
Matches: 134, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
185 78 0.58
186 31 0.23
187 15 0.11
188 10 0.07
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (187 bp):
TCTCAAGTAAGATAAAACTTATATTTCAAGTGAAATAATCTCAAGTGAGATAAATCTTGTATTAA
GAAAAACAATCTCAAGGAAGATAAATTTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATT
TGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATTTCTTGTTTCGAGTAAAAACTG
Found at i:3214167 original size:73 final size:74
Alignment explanation
Indices: 3214055--3214221 Score: 259
Period size: 73 Copynumber: 2.3 Consensus size: 74
3214045 GTAAAAACTG
*
3214055 TCTCAAGTGAGATAAATCTTATGTTTCGAGTGAAACTATCTCAAGTGAGAT-AAATCTTGTATTA
1 TCTCAAGTGAGATAAATCTTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAAAT-TTGTATTA
3214119 AGAAAAACAA
65 AGAAAAACAA
* * *
3214129 TCTCAAG-GAAGATAAAT-TTATGTTTTGAGTGAAACTATCTGAAGCGAGATAAAATTTGTTTTA
1 TCTCAAGTG-AGATAAATCTTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATTTGTATTA
3214192 AGAAAAACAA
65 AGAAAAACAA
3214202 TCTCAAGTGAGATAAATCTT
1 TCTCAAGTGAGATAAATCTT
3214222 CGTATTAAAT
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
73 63 0.74
74 22 0.26
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (74 bp):
TCTCAAGTGAGATAAATCTTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATTTGTATTAA
GAAAAACAA
Found at i:3214235 original size:73 final size:73
Alignment explanation
Indices: 3214055--3214249 Score: 254
Period size: 73 Copynumber: 2.7 Consensus size: 73
3214045 GTAAAAACTG
*
3214055 TCTCAAGTGAGATAAATCTTATGTTTCGAGTGAAACTATCTCAAGTGAGATAAATCTTGTATTAA
1 TCTCAAGTGAGATAAATCTTATGTTT-GAGTGAAACTATCTCAAGCGAGATAAATCTTGTATTAA
3214120 GAAAAACAA
65 GAAAAACAA
* *
3214129 TCTCAAG-GAAGATAAAT-TTATGTTTTGAGTGAAACTATCTGAAGCGAGATAAAAT-TTGTTTT
1 TCTCAAGTG-AGATAAATCTTATG-TTTGAGTGAAACTATCTCAAGCGAGAT-AAATCTTGTATT
3214191 AAGAAAAACAA
63 AAGAAAAACAA
* * * *
3214202 TCTCAAGTGAGATAAATCTT-CGTATTAAATGAAACTGTCTCAAGCGAG
1 TCTCAAGTGAGATAAATCTTATGT-TTGAGTGAAACTATCTCAAGCGAG
3214250 CCAATTTTTG
Statistics
Matches: 107, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
72 1 0.01
73 81 0.76
74 25 0.23
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (73 bp):
TCTCAAGTGAGATAAATCTTATGTTTGAGTGAAACTATCTCAAGCGAGATAAATCTTGTATTAAG
AAAAACAA
Found at i:3215234 original size:16 final size:16
Alignment explanation
Indices: 3215213--3215246 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3215203 GACATCAGTC
3215213 TAAATATAAAATTCCT
1 TAAATATAAAATTCCT
3215229 TAAATATAAAATTCCT
1 TAAATATAAAATTCCT
3215245 TA
1 TA
3215247 GTACTTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATATAAAATTCCT
Found at i:3215380 original size:2 final size:2
Alignment explanation
Indices: 3215373--3215410 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3215363 ATCTTTATTG
3215373 TA 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
3215411 ATCGCCTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3216710 original size:13 final size:13
Alignment explanation
Indices: 3216694--3216727 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3216684 TCAGATTTTA
*
3216694 TTTGAAAATCATT
1 TTTGAAAATCAAT
3216707 TTTG-AAATCAAT
1 TTTGAAAATCAAT
3216719 TTTGAAAAT
1 TTTGAAAAT
3216728 TACTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:3218477 original size:12 final size:13
Alignment explanation
Indices: 3218454--3218492 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
3218444 ATCCTAATGG
*
3218454 ACAATATTTGAAA
1 ACAATGTTTGAAA
*
3218467 ACTAT-TTTGAAA
1 ACAATGTTTGAAA
3218479 ACAATGTTTGAAA
1 ACAATGTTTGAAA
3218492 A
1 A
3218493 ACAAAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (13 bp):
ACAATGTTTGAAA
Found at i:3219037 original size:44 final size:44
Alignment explanation
Indices: 3218986--3219092 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 44
3218976 CGGTACATTG
* *
3218986 CATAGTGTATCAATGCACATCCAAGGAATGCATCGGTGTACCTT
1 CATAGTGTATCGATGCACATCCAAGGAATGCATCGGTATACCTT
* * * *
3219030 CATAGTGTATCGATGCATATTCAAGGGATGCATCGGTATACTTT
1 CATAGTGTATCGATGCACATCCAAGGAATGCATCGGTATACCTT
* *
3219074 CATTGTGTTTCGATGCACA
1 CATAGTGTATCGATGCACA
3219093 ATGCACAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (44 bp):
CATAGTGTATCGATGCACATCCAAGGAATGCATCGGTATACCTT
Found at i:3226565 original size:28 final size:30
Alignment explanation
Indices: 3226509--3226565 Score: 82
Period size: 28 Copynumber: 1.9 Consensus size: 30
3226499 CTACAAGACC
3226509 AGACAAAAGGAAATCAATGTTAGTAGAAACA
1 AGACAAAA-GAAATCAATGTTAGTAGAAACA
*
3226540 AGACAAAA-AAATCAA-GTTAGTTGAAA
1 AGACAAAAGAAATCAATGTTAGTAGAAA
3226566 TGATTAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 7 0.28
31 8 0.32
ACGTcount: A:0.56, C:0.09, G:0.18, T:0.18
Consensus pattern (30 bp):
AGACAAAAGAAATCAATGTTAGTAGAAACA
Found at i:3227550 original size:21 final size:21
Alignment explanation
Indices: 3227521--3227574 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 21
3227511 AAAATACGTA
3227521 AAAT-AAAATAACAG-TGACT
1 AAATCAAAATAACAGCTGACT
3227540 AAATCAGAAATAAACAGCTGACT
1 AAATCA-AAAT-AACAGCTGACT
*
3227563 AAATTAAAATAA
1 AAATCAAAATAA
3227575 AATAAAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.13
20 1 0.03
21 6 0.20
22 9 0.30
23 10 0.33
ACGTcount: A:0.59, C:0.11, G:0.09, T:0.20
Consensus pattern (21 bp):
AAATCAAAATAACAGCTGACT
Found at i:3227572 original size:22 final size:21
Alignment explanation
Indices: 3227519--3227575 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
3227509 CCAAAATACG
*
3227519 TAAAATAAAAT-AACAGTGAC
1 TAAATTAAAATAAACAGTGAC
*
3227539 TAAATCAGAAATAAACAGCTGAC
1 TAAATTA-AAATAAACAG-TGAC
3227562 TAAATTAAAATAAA
1 TAAATTAAAATAAA
3227576 ATAAAATGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 5 0.16
21 4 0.13
22 12 0.39
23 10 0.32
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.21
Consensus pattern (21 bp):
TAAATTAAAATAAACAGTGAC
Found at i:3231299 original size:23 final size:23
Alignment explanation
Indices: 3231273--3231344 Score: 135
Period size: 23 Copynumber: 3.1 Consensus size: 23
3231263 GAAGGACCAT
3231273 ATAGGTTTGCACCGAAGTGCCAC
1 ATAGGTTTGCACCGAAGTGCCAC
*
3231296 ATAGGTTTGCACCGAAGTACCAC
1 ATAGGTTTGCACCGAAGTGCCAC
3231319 ATAGGTTTGCACCGAAGTGCCAC
1 ATAGGTTTGCACCGAAGTGCCAC
3231342 ATA
1 ATA
3231345 ATTGTCCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (23 bp):
ATAGGTTTGCACCGAAGTGCCAC
Found at i:3231329 original size:46 final size:44
Alignment explanation
Indices: 3231238--3231365 Score: 168
Period size: 46 Copynumber: 2.9 Consensus size: 44
3231228 TCGTAATTTA
* *
3231238 CACCGAAGTGCCACATAATTATCTCGAAGGACCATATAGGTTTG
1 CACCGAAGTGCCACATAATTATCCCGAAGGACCACATAGGTTTG
* *
3231282 CACCGAAGTGCCACATAGGTT-TGCACCGAAGTACCACATAGGTTTG
1 CACCGAAGTGCCACATA-ATTAT-C-CCGAAGGACCACATAGGTTTG
* *
3231328 CACCGAAGTGCCACATAATTGTCCCAAAGGACCACATA
1 CACCGAAGTGCCACATAATTATCCCGAAGGACCACATA
3231366 AATCCCTCGA
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
44 31 0.42
45 6 0.08
46 36 0.49
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (44 bp):
CACCGAAGTGCCACATAATTATCCCGAAGGACCACATAGGTTTG
Found at i:3237081 original size:23 final size:23
Alignment explanation
Indices: 3237020--3237107 Score: 103
Period size: 23 Copynumber: 3.9 Consensus size: 23
3237010 CAGCTCGTAA
*
3237020 TTTGCACTGAAGTGCCACATA--
1 TTTGCACCGAAGTGCCACATAGG
*
3237041 ATTGTC-CCGAA-TGACCACATAGG
1 TTTG-CACCGAAGTG-CCACATAGG
*
3237064 TTTGCATCGAAGTGCCACATAGG
1 TTTGCACCGAAGTGCCACATAGG
3237087 TTTGCACCGAAGTGCCACATA
1 TTTGCACCGAAGTGCCACATA
3237108 ATTGTCCCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.04
21 14 0.25
22 2 0.04
23 36 0.64
24 2 0.04
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAGG
Found at i:3238659 original size:48 final size:48
Alignment explanation
Indices: 3238588--3238683 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
3238578 GGAGTTCACG
3238588 GCACAAAGAAGAAGAGAGCAAGAAATGGGTTCCAGACTTTTTCTCCTT
1 GCACAAAGAAGAAGAGAGCAAGAAATGGGTTCCAGACTTTTTCTCCTT
3238636 GCACAAAGAAGAAGAGAGCAAGAAATGGGTTCCAGACTTTTTCTCCTT
1 GCACAAAGAAGAAGAGAGCAAGAAATGGGTTCCAGACTTTTTCTCCTT
3238684 ATCCAAGTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (48 bp):
GCACAAAGAAGAAGAGAGCAAGAAATGGGTTCCAGACTTTTTCTCCTT
Found at i:3239221 original size:2 final size:2
Alignment explanation
Indices: 3239214--3239239 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3239204 AAGCTAAATA
3239214 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
3239240 TAAATATTTA
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:3244364 original size:3 final size:3
Alignment explanation
Indices: 3244350--3244387 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
3244340 ATTTATTCGA
*
3244350 TAT TAGT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3244388 GTATATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3245096 original size:21 final size:21
Alignment explanation
Indices: 3245059--3245100 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3245049 TTTACTTCCT
*
3245059 TTTATTGTATGTATATATACA
1 TTTATTGTATATATATATACA
3245080 TTTATGTGTATATTATATATA
1 TTTAT-TGTATA-TATATATA
3245101 TGTGTCTGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 5 0.28
23 8 0.44
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTATTGTATATATATATACA
Found at i:3245104 original size:17 final size:18
Alignment explanation
Indices: 3245068--3245105 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3245058 TTTTATTGTA
*
3245068 TGTATATATACATTTATG
1 TGTATATATACATATATG
*
3245086 TGTATAT-TATATATATG
1 TGTATATATACATATATG
3245103 TGT
1 TGT
3245106 CTGCGTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.53
Consensus pattern (18 bp):
TGTATATATACATATATG
Found at i:3245615 original size:2 final size:2
Alignment explanation
Indices: 3245605--3245636 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3245595 AAGAAAAAAT
*
3245605 TA TA AA 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
3245637 CATACACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3246220 original size:21 final size:20
Alignment explanation
Indices: 3246196--3246235 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3246186 ATACAATACT
*
3246196 TTGACCAAAGGATCAATCCCC
1 TTGA-CAAAGAATCAATCCCC
*
3246217 TTGATAAAGAATCAATCCC
1 TTGACAAAGAATCAATCCC
3246236 ATAGATTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.23
Consensus pattern (20 bp):
TTGACAAAGAATCAATCCCC
Found at i:3248226 original size:20 final size:20
Alignment explanation
Indices: 3248203--3248268 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
3248193 CAAAGAATCG
*
3248203 ATCCCCTAGCAAAAGGATCA
1 ATCCCCTTGCAAAAGGATCA
* *
3248223 ATCCCTTTGACTAAAGGATCA
1 ATCCCCTTG-CAAAAGGATCA
* *
3248244 ATCCCCTTGAAAAAGAATCA
1 ATCCCCTTGCAAAAGGATCA
3248264 ATCCC
1 ATCCC
3248269 TTAGAGTACA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 20 0.53
21 18 0.47
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (20 bp):
ATCCCCTTGCAAAAGGATCA
Found at i:3248239 original size:21 final size:20
Alignment explanation
Indices: 3248213--3248270 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 20
3248203 ATCCCCTAGC
3248213 AAAAGGATCAATCCCTTTGA
1 AAAAGGATCAATCCCTTTGA
* *
3248233 CTAAAGGATCAATCCCCTTGA
1 -AAAAGGATCAATCCCTTTGA
*
3248254 AAAAGAATCAATCCCTT
1 AAAAGGATCAATCCCTT
3248271 AGAGTACAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (20 bp):
AAAAGGATCAATCCCTTTGA
Found at i:3248343 original size:21 final size:21
Alignment explanation
Indices: 3248319--3248365 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3248309 AAATGATTGT
*
3248319 TCCCTTTACCAAAAGAATCGA
1 TCCCTTGACCAAAAGAATCGA
** *
3248340 TCCCTTGATGAAAAGGATCGA
1 TCCCTTGACCAAAAGAATCGA
3248361 TCCCT
1 TCCCT
3248366 CGATGACAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (21 bp):
TCCCTTGACCAAAAGAATCGA
Found at i:3248370 original size:21 final size:21
Alignment explanation
Indices: 3248329--3248386 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
3248319 TCCCTTTACC
* *
3248329 AAAAGAATCGATCCCTTGATG
1 AAAAGGATCGATCCCTCGATG
3248350 AAAAGGATCGATCCCTCGATG
1 AAAAGGATCGATCCCTCGATG
*
3248371 ACAAGGATCGATCCCT
1 AAAAGGATCGATCCCT
3248387 TTCCTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (21 bp):
AAAAGGATCGATCCCTCGATG
Found at i:3248402 original size:21 final size:21
Alignment explanation
Indices: 3248378--3248423 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3248368 ATGACAAGGA
*
3248378 TCGATCCCTTTCCTTA-AATGG
1 TCGATCCCCTT-CTTACAATGG
3248399 TCGATCCCCTTCTTACAATGG
1 TCGATCCCCTTCTTACAATGG
3248420 TCGA
1 TCGA
3248424 AATAATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (21 bp):
TCGATCCCCTTCTTACAATGG
Found at i:3254346 original size:21 final size:21
Alignment explanation
Indices: 3254322--3254361 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3254312 TCCGCTAGCA
* *
3254322 AAAGGATCAATCTCTTTGACC
1 AAAGGAACAATCCCTTTGACC
3254343 AAAGGAACAATCCCTTTGA
1 AAAGGAACAATCCCTTTGA
3254362 AAAGAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (21 bp):
AAAGGAACAATCCCTTTGACC
Found at i:3254450 original size:22 final size:23
Alignment explanation
Indices: 3254395--3254450 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 23
3254385 TGTGAGTTTG
*
3254395 GGATCGATCCC-TTTACAAAAAA
1 GGATTGATCCCTTTTACAAAAAA
* * *
3254417 TGATTG-TTCCTTTTAC-CAAAA
1 GGATTGATCCCTTTTACAAAAAA
3254438 GGATTGATCCCTT
1 GGATTGATCCCTT
3254451 CCCTTAAATG
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.34
Consensus pattern (23 bp):
GGATTGATCCCTTTTACAAAAAA
Found at i:3257296 original size:5 final size:5
Alignment explanation
Indices: 3257286--3257315 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3257276 ATCGGAATCA
*
3257286 TACTT TACTT TACTT TACTT TACTT AACTT
1 TACTT TACTT TACTT TACTT TACTT TACTT
3257316 CATGGCATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (5 bp):
TACTT
Found at i:3259969 original size:25 final size:25
Alignment explanation
Indices: 3259933--3259989 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
3259923 TGGTGAAGCA
*
3259933 CGAG-GGAGTGGCGAGCTAGGAGTC
1 CGAGAGGAATGGCGAGCTAGGAGTC
3259957 CGAGAGGAATGGCGAGCTAGGAGTC
1 CGAGAGGAATGGCGAGCTAGGAGTC
3259982 CGAGAGGA
1 CGAGAGGA
3259990 TCTAGCGAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.26, C:0.16, G:0.47, T:0.11
Consensus pattern (25 bp):
CGAGAGGAATGGCGAGCTAGGAGTC
Found at i:3267644 original size:19 final size:20
Alignment explanation
Indices: 3267608--3267646 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3267598 TTGGACAATA
*
3267608 ATGTTAGAGTGTTGAAATTG
1 ATGTTAGAATGTTGAAATTG
3267628 ATGTTAGAATG-TGAAATTG
1 ATGTTAGAATGTTGAAATTG
3267647 GGTCATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.38
Consensus pattern (20 bp):
ATGTTAGAATGTTGAAATTG
Found at i:3270867 original size:42 final size:41
Alignment explanation
Indices: 3270658--3270869 Score: 343
Period size: 42 Copynumber: 5.0 Consensus size: 41
3270648 GAGCCTAGGA
* *
3270658 AAACTGTAAGGTTTATCCTTGCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGT
3270700 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGT
1 AAACTGTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGT
*
3270742 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGT
*
3270784 AAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGT
1 AAACTGTAAGGCTTACC-TTGCACACAGCAAAGGGACCTGGT
3270826 AAACTGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGT
1 AAACTGTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGT
3270868 AA
1 AA
3270870 TACTTCCTTC
Statistics
Matches: 160, Mismatches: 7, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
41 6 0.04
42 152 0.95
43 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (41 bp):
AAACTGTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGT
Found at i:3277846 original size:42 final size:41
Alignment explanation
Indices: 3277745--3277992 Score: 309
Period size: 42 Copynumber: 5.9 Consensus size: 41
3277735 CTATACACCA
* * *
3277745 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGAAAACT
1 GTAAGGCTT-ACCT-TGCACACAGCAAAGGGA-CCT-GGGAAACT
* *
3277789 GTAAGGTTTATCCTTGCACACAGTAAAGGGACCTGGGAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
* * *
3277831 GTAAGTCTTACCCTTGTACACAGCAAAGGGACCTGGTAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
3277873 GTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACT
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAACT
**
3277915 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGATAAACT
1 GTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAACT
*
3277957 GTAAGGCTTACCTTCGCACACAGCAAAGCGACCTGG
1 GTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGG
3277993 TAATACTTCC
Statistics
Matches: 181, Mismatches: 18, Indels: 12
0.86 0.09 0.06
Matches are distributed among these distances:
41 8 0.04
42 141 0.78
43 18 0.10
44 14 0.08
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (41 bp):
GTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAACT
Found at i:3277925 original size:84 final size:84
Alignment explanation
Indices: 3277745--3277992 Score: 349
Period size: 84 Copynumber: 2.9 Consensus size: 84
3277735 CTATACACCA
* * * *
3277745 GTAAGGCTTAACCTGTGCACAAAGCAGA-GGAGCCTAGGA-AAACTGTAAGGTTTATCCTT-GCA
1 GTAAGGCTTACCCT-TGCACACAGCAAAGGGA-CCT--GATAAACTGTAAGGCTTA-CCTTCGCA
*
3277807 CACAGTAAAGGGACCTGGGAAACT
61 CACAGCAAAGGGACCTGGGAAACT
* * *
3277831 GTAAGTCTTACCCTTGTACACAGCAAAGGGACCTGGTAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGATAAACTGTAAGGCTTACCTTCGCACACAG
3277896 CAAAGGGACCTGGGAAACT
66 CAAAGGGACCTGGGAAACT
3277915 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGATAAACTGTAAGGCTTACCTTCGCACACAG
1 GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGATAAACTGTAAGGCTTACCTTCGCACACAG
*
3277980 CAAAGCGACCTGG
66 CAAAGGGACCTGG
3277993 TAATACTTCC
Statistics
Matches: 147, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
83 5 0.03
84 114 0.78
85 13 0.09
86 15 0.10
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (84 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGATAAACTGTAAGGCTTACCTTCGCACACAG
CAAAGGGACCTGGGAAACT
Found at i:3277933 original size:126 final size:128
Alignment explanation
Indices: 3277745--3277995 Score: 341
Period size: 126 Copynumber: 2.0 Consensus size: 128
3277735 CTATACACCA
* * *
3277745 GTAAGGCTTAACCTGTGCACAAAGCAGAGGAGCCTAGGAAAACTGTAAGGTTTATCCTTGCACAC
1 GTAAGGCTTAACCTGTGCACAAAGCAAAGGAGCCTAGGAAAACTGTAAGGCTTACCCTTGCACAC
* * * * *
3277810 AGTAAAGGGACCTGGGAAACTGTAAGTCTTACCCTT-GTACACAGCAAAGGGACCTGGTAAACT
66 AGCAAAGGGACCTGAGAAACTGTAAGGCTTA-CCTTCGCACACAGCAAAGCGACCTGGTAAACT
* *
3277873 GTAAGGCTT-ACCT-TCGCACACAGCAAAGG-GACCT-GGGAAACTGTAAGGCTTACCCTTGCAC
1 GTAAGGCTTAACCTGT-GCACAAAGCAAAGGAG-CCTAGGAAAACTGTAAGGCTTACCCTTGCAC
*
3277934 ACAGCAAAGGGACCTGATAAACTGTAAGGCTTACCTTCGCACACAGCAAAGCGACCTGGTAA
64 ACAGCAAAGGGACCTGAGAAACTGTAAGGCTTACCTTCGCACACAGCAAAGCGACCTGGTAA
3277996 TACTTCCTTC
Statistics
Matches: 109, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
125 4 0.04
126 77 0.71
127 19 0.17
128 9 0.08
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (128 bp):
GTAAGGCTTAACCTGTGCACAAAGCAAAGGAGCCTAGGAAAACTGTAAGGCTTACCCTTGCACAC
AGCAAAGGGACCTGAGAAACTGTAAGGCTTACCTTCGCACACAGCAAAGCGACCTGGTAAACT
Found at i:3279079 original size:23 final size:23
Alignment explanation
Indices: 3279037--3279081 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3279027 GTCAACGGTC
*
3279037 GGGTCGGGTCGGGTCGGGTCAAT
1 GGGTCGGGTCGGATCGGGTCAAT
3279060 GGGTCGGGTCGTGATC-GGTCAA
1 GGGTCGGGTCG-GATCGGGTCAA
3279082 ACCGGTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.11, C:0.18, G:0.49, T:0.22
Consensus pattern (23 bp):
GGGTCGGGTCGGATCGGGTCAAT
Found at i:3279089 original size:9 final size:10
Alignment explanation
Indices: 3279075--3279117 Score: 54
Period size: 9 Copynumber: 4.4 Consensus size: 10
3279065 GGGTCGTGAT
3279075 CGGTC-AAAC
1 CGGTCAAAAC
3279084 CGGTCAAAAC
1 CGGTCAAAAC
3279094 CGGTTCAAAAC
1 CGG-TCAAAAC
*
3279105 CGGT-TAAAC
1 CGGTCAAAAC
3279114 CGGT
1 CGGT
3279118 TTCCAGCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 13 0.42
10 8 0.26
11 10 0.32
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (10 bp):
CGGTCAAAAC
Found at i:3279103 original size:11 final size:11
Alignment explanation
Indices: 3279080--3279118 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
3279070 GTGATCGGTC
3279080 AAACCGG-TCA
1 AAACCGGTTCA
3279090 AAACCGGTTCA
1 AAACCGGTTCA
3279101 AAACCGGTT--
1 AAACCGGTTCA
3279110 AAACCGGTT
1 AAACCGGTT
3279119 TCCAGCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.32
10 7 0.25
11 12 0.43
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.18
Consensus pattern (11 bp):
AAACCGGTTCA
Found at i:3284240 original size:60 final size:59
Alignment explanation
Indices: 3284140--3284305 Score: 167
Period size: 59 Copynumber: 2.8 Consensus size: 59
3284130 ACAAATATGG
* * * **
3284140 AATATTCAAAAGTTTGA-GAATCAATTTAGAA-AGAGGGTCATAGTTTTGGGATAAAATTAA
1 AATATTCAAAAGTTTAAGGACT-AATTTAGAATA-AGAGTCATAGTTTAAGG-TAAAATTAA
* * *
3284200 AATATTCAAAAGTTTAAGGACTAATTTAGAATAAGAGTCATAATTTAAGGTGAAATTAG
1 AATATTCAAAAGTTTAAGGACTAATTTAGAATAAGAGTCATAGTTTAAGGTAAAATTAA
* * * *
3284259 AATACTCAAAAGTTTAAGGGAC-AATTTAAAATGAGAATCATAGTTTA
1 AATATTCAAAAGTTTAA-GGACTAATTTAGAATAAGAGTCATAGTTTA
3284306 GAGATATATG
Statistics
Matches: 90, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
59 44 0.49
60 42 0.47
61 4 0.04
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.31
Consensus pattern (59 bp):
AATATTCAAAAGTTTAAGGACTAATTTAGAATAAGAGTCATAGTTTAAGGTAAAATTAA
Found at i:3284284 original size:28 final size:28
Alignment explanation
Indices: 3284194--3284284 Score: 71
Period size: 28 Copynumber: 3.1 Consensus size: 28
3284184 TTTGGGATAA
* *
3284194 AATTAAAATATTCAAAAGTTTAA-GGAC
1 AATTAGAATACTCAAAAGTTTAAGGGAC
* *
3284221 TAATTTAGAATAAGAGTCATAA-TTTAAGGTGA-
1 -AA-TTAGAAT---ACTCAAAAGTTTAAGG-GAC
3284253 AATTAGAATACTCAAAAGTTTAAGGGAC
1 AATTAGAATACTCAAAAGTTTAAGGGAC
3284281 AATT
1 AATT
3284285 TAAAATGAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
27 8 0.16
28 13 0.26
29 6 0.12
30 7 0.14
31 7 0.14
32 7 0.14
33 2 0.04
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (28 bp):
AATTAGAATACTCAAAAGTTTAAGGGAC
Found at i:3287795 original size:31 final size:32
Alignment explanation
Indices: 3287757--3287819 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
3287747 GAAGAGAAGG
*
3287757 GAAAAA-GGTAAATTACACCATGAGTCATTAA
1 GAAAAAGGGTAAATTACACCATGAGCCATTAA
*
3287788 GAAAAAGGGTAAGTTACACCATGAGCCATTAA
1 GAAAAAGGGTAAATTACACCATGAGCCATTAA
3287820 ACTTTACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 6 0.21
32 23 0.79
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.21
Consensus pattern (32 bp):
GAAAAAGGGTAAATTACACCATGAGCCATTAA
Found at i:3289236 original size:17 final size:17
Alignment explanation
Indices: 3289199--3289232 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3289189 CTTTATTGTC
3289199 ATTTATTTTTTCATTTA
1 ATTTATTTTTTCATTTA
*
3289216 ATTTGTTTTTTC-TTTA
1 ATTTATTTTTTCATTTA
3289232 A
1 A
3289233 ATTTTATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (17 bp):
ATTTATTTTTTCATTTA
Found at i:3292281 original size:7 final size:7
Alignment explanation
Indices: 3292271--3292344 Score: 71
Period size: 7 Copynumber: 10.6 Consensus size: 7
3292261 CTATAATACA
3292271 TAAACCC
1 TAAACCC
3292278 TAAACCC
1 TAAACCC
3292285 TAAACCC
1 TAAACCC
*
3292292 TAAACCT
1 TAAACCC
3292299 TAAATCCC
1 TAAA-CCC
* *
3292307 --ATCACA
1 TAAAC-CC
*
3292313 TAAACTC
1 TAAACCC
*
3292320 TAAACTC
1 TAAACCC
3292327 TAAACCC
1 TAAACCC
3292334 TAAACCC
1 TAAACCC
3292341 TAAA
1 TAAA
3292345 TCTTATCACA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
5 1 0.02
6 2 0.04
7 48 0.87
8 4 0.07
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:3292314 original size:42 final size:42
Alignment explanation
Indices: 3292268--3292357 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
3292258 AACCTATAAT
*
3292268 ACATAAACCCTAAACCCTAAACCCTAAACCTTAAATCCCATC
1 ACATAAACCCTAAACCCTAAACCCTAAACCCTAAATCCCATC
* * **
3292310 ACATAAACTCTAAACTCTAAACCCTAAACCCTAAATCTTATC
1 ACATAAACCCTAAACCCTAAACCCTAAACCCTAAATCCCATC
3292352 ACATAA
1 ACATAA
3292358 TTAGTTATGA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (42 bp):
ACATAAACCCTAAACCCTAAACCCTAAACCCTAAATCCCATC
Found at i:3298742 original size:2 final size:2
Alignment explanation
Indices: 3298735--3298771 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3298725 TATTAATAAT
3298735 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3298772 GCGTATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3299950 original size:51 final size:51
Alignment explanation
Indices: 3299885--3299996 Score: 206
Period size: 51 Copynumber: 2.2 Consensus size: 51
3299875 AAATCCAAAA
3299885 CCCCTTTTTTACAGTATGTTTCCCTCTCATGTTGTCAATGAATCCTGTTCC
1 CCCCTTTTTTACAGTATGTTTCCCTCTCATGTTGTCAATGAATCCTGTTCC
3299936 CCCCTTTTTTACAGTATGTTTCCCTCTCATGTTGTCAATGAATCCTGTTCC
1 CCCCTTTTTTACAGTATGTTTCCCTCTCATGTTGTCAATGAATCCTGTTCC
* *
3299987 CTCATTTTTT
1 CCCCTTTTTT
3299997 CTTTGCTTGC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.15, C:0.29, G:0.11, T:0.46
Consensus pattern (51 bp):
CCCCTTTTTTACAGTATGTTTCCCTCTCATGTTGTCAATGAATCCTGTTCC
Found at i:3301235 original size:90 final size:90
Alignment explanation
Indices: 3301082--3301403 Score: 502
Period size: 90 Copynumber: 3.6 Consensus size: 90
3301072 AAGACTTACA
* * * * * * * * *
3301082 GATGGCCCGGAGGACTTACAAATCAAGAAACTCCCGAAGGTTTAGTTTCTAAAAGCTCGTTTGAA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGATCAGTTTCTTAGATCTCATTTGAA
3301147 AACATCCTGCACTGAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
* * *
3301172 GATGGTCCAAAAGACTTAAAAATCAAGAAACCCCCGAAGGATCAGTTTCTTAGATCTCATTTGAA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGATCAGTTTCTTAGATCTCATTTGAA
3301237 AACATCCTGCACTGAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
*
3301262 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGCTCAGTTTCTTAGATCTCATTTGAA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGATCAGTTTCTTAGATCTCATTTGAA
3301327 AACATCCTGCACTGAAGGTCTTATG
66 AACATCCTGCACTGAAGGTCTTATG
*
3301352 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAA-GACTCAATTTCTTA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGA-TCAGTTTCTTA
3301404 ATTGTCACCA
Statistics
Matches: 213, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
89 1 0.00
90 212 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (90 bp):
GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCCGAAGGATCAGTTTCTTAGATCTCATTTGAA
AACATCCTGCACTGAAGGTCTTATG
Found at i:3301465 original size:43 final size:43
Alignment explanation
Indices: 3301404--3301653 Score: 308
Period size: 43 Copynumber: 5.8 Consensus size: 43
3301394 CAATTTCTTA
* * *
3301404 ATTGTCACCAAGGAACCCCTACATATCATGTTGGTCCCTCAAG
1 ATTGTCATCAAGAAACCCCTACATATCATGATGGTCCCTCAAG
* *
3301447 ATTGTCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAG
1 ATTGTCATCAAGAAACCCCTACATATCATGATGGTCCCTCAAG
* *
3301490 CA-TGTCATCAAGAAACCTCTACATATCATGATGGTCTCTCAAG
1 -ATTGTCATCAAGAAACCCCTACATATCATGATGGTCCCTCAAG
*
3301533 CA-TGTCATCAA-AGAACCCCTACATATCATGATGGTCCTTCAAG
1 -ATTGTCATCAAGA-AACCCCTACATATCATGATGGTCCCTCAAG
* * * * *
3301576 CTTGTTATCAAGGAACCCCTACATATCACGATGGTCCTTCAAG
1 ATTGTCATCAAGAAACCCCTACATATCATGATGGTCCCTCAAG
* * *
3301619 CTTATCATCAAGAAACCCCTACATATCACGATGGT
1 ATTGTCATCAAGAAACCCCTACATATCATGATGGT
3301654 TTCTCAATCT
Statistics
Matches: 186, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
42 1 0.01
43 184 0.99
44 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.26
Consensus pattern (43 bp):
ATTGTCATCAAGAAACCCCTACATATCATGATGGTCCCTCAAG
Found at i:3301525 original size:86 final size:86
Alignment explanation
Indices: 3301406--3301660 Score: 345
Period size: 86 Copynumber: 3.0 Consensus size: 86
3301396 ATTTCTTAAT
* *
3301406 TGTCACCAAGGAACCCCTACATATCATGTTGGTCCCTCAAGATTGTCATCAAGAAACCCCTACAT
1 TGTCATCAAGGAACCCCTACATATCATGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACAT
3301471 ATCACGATGGTCTCTCAAGCA
66 ATCACGATGGTCTCTCAAGCA
* * *
3301492 TGTCATCAAGAAACCTCTACATATCATGATGGTCTCTCAAGCA-TGTCATCAA-AGAACCCCTAC
1 TGTCATCAAGGAACCCCTACATATCATGATGGTCCCTCAAG-ATTGTCATCAAGA-AACCCCTAC
* *
3301555 ATATCATGATGGTC-CTTCAAGCT
64 ATATCACGATGGTCTC-TCAAGCA
* * * * *
3301578 TGTTATCAAGGAACCCCTACATATCACGATGGTCCTTCAAGCTTATCATCAAGAAACCCCTACAT
1 TGTCATCAAGGAACCCCTACATATCATGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACAT
*
3301643 ATCACGATGGTTTCTCAA
66 ATCACGATGGTCTCTCAA
3301661 TCTATTGTGT
Statistics
Matches: 146, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
85 2 0.01
86 141 0.97
87 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (86 bp):
TGTCATCAAGGAACCCCTACATATCATGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACAT
ATCACGATGGTCTCTCAAGCA
Found at i:3301540 original size:22 final size:22
Alignment explanation
Indices: 3301476--3301540 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 22
3301466 TACATATCAC
3301476 GATGGTCTCTCAAGCATGTCAT
1 GATGGTCTCTCAAGCATGTCAT
* * ** * *
3301498 CAAGAAAC-CTCTA-CATATCAT
1 GATG-GTCTCTCAAGCATGTCAT
3301519 GATGGTCTCTCAAGCATGTCAT
1 GATGGTCTCTCAAGCATGTCAT
3301541 CAAAGAACCC
Statistics
Matches: 28, Mismatches: 12, Indels: 6
0.61 0.26 0.13
Matches are distributed among these distances:
20 1 0.04
21 13 0.46
22 13 0.46
23 1 0.04
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (22 bp):
GATGGTCTCTCAAGCATGTCAT
Found at i:3301641 original size:129 final size:129
Alignment explanation
Indices: 3301406--3301660 Score: 386
Period size: 129 Copynumber: 2.0 Consensus size: 129
3301396 ATTTCTTAAT
* *
3301406 TGTCACCAAGGAACCCCTACATATCATGTTGGTCCCTCAAGATTGTCATCAAGAAACCCCTACAT
1 TGTCACCAAAGAACCCCTACATATCATGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACAT
* * *
3301471 ATCACGATGGTCTCTCAAGCATGTCATCAAGAAACCTCTACATATCATGATGGTCTCTCAAGCA
66 ATCACGATGGTCTCTCAAGCATATCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAGCA
* * * * *
3301535 TGTCATCAAAGAACCCCTACATATCATGATGGTCCTTCAAGCTTGTTATCAAGGAACCCCTACAT
1 TGTCACCAAAGAACCCCTACATATCATGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACAT
* *
3301600 ATCACGATGGTC-CTTCAAGCTTATCATCAAGAAACCCCTACATATCACGATGGTTTCTCAA
66 ATCACGATGGTCTC-TCAAGCATATCATCAAGAAACCCCTACATATCACGATGGTCTCTCAA
3301661 TCTATTGTGT
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
128 1 0.01
129 112 0.99
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (129 bp):
TGTCACCAAAGAACCCCTACATATCATGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACAT
ATCACGATGGTCTCTCAAGCATATCATCAAGAAACCCCTACATATCACGATGGTCTCTCAAGCA
Found at i:3301721 original size:39 final size:39
Alignment explanation
Indices: 3301659--3301774 Score: 142
Period size: 39 Copynumber: 2.9 Consensus size: 39
3301649 ATGGTTTCTC
* *
3301659 AATCTATTGTGTTTTAAGCGAAACTATCTCAAGCGAGATAA
1 AATCT-TT-TGTTTCAAGTGAAACTATCTCAAGCGAGATAA
*
3301700 AATCTTTTGTTTCAAGTGAAACAATCTCAAGCGAGATAA
1 AATCTTTTGTTTCAAGTGAAACTATCTCAAGCGAGATAA
* * * * *
3301739 AATCTTATATTTCAAGTGAAATTGTCTCAAGAGAGA
1 AATCTTTTGTTTCAAGTGAAACTATCTCAAGCGAGA
3301775 CTGTCTCAAG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
39 59 0.89
40 2 0.03
41 5 0.08
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (39 bp):
AATCTTTTGTTTCAAGTGAAACTATCTCAAGCGAGATAA
Found at i:3301779 original size:15 final size:15
Alignment explanation
Indices: 3301761--3301805 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
3301751 CAAGTGAAAT
*
3301761 TGTCTCAAGAGAGAC
1 TGTCTCAAGGGAGAC
*
3301776 TGTCTCAAGGGAAAC
1 TGTCTCAAGGGAGAC
3301791 TGTCTCAAGGGAGAC
1 TGTCTCAAGGGAGAC
3301806 AAAATTTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.20
Consensus pattern (15 bp):
TGTCTCAAGGGAGAC
Found at i:3301821 original size:21 final size:21
Alignment explanation
Indices: 3301795--3301859 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
3301785 GGAAACTGTC
3301795 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
** *
3301816 TCAAGGGA-A-ACCA----TC
1 TCAAGGGAGACAAAATTTGTT
3301831 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
3301852 TCAAGGGA
1 TCAAGGGA
3301860 AACCGTCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 9 0.28
16 1 0.03
17 2 0.06
19 2 0.06
20 1 0.03
21 17 0.53
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:3301833 original size:36 final size:36
Alignment explanation
Indices: 3301780--3301877 Score: 178
Period size: 36 Copynumber: 2.7 Consensus size: 36
3301770 AGAGACTGTC
*
3301780 TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAAACCGTCTCAAGGGAGACAAAATTTGTT
*
3301816 TCAAGGGAAACCATCTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAAACCGTCTCAAGGGAGACAAAATTTGTT
3301852 TCAAGGGAAACCGTCTCAAGGGAGAC
1 TCAAGGGAAACCGTCTCAAGGGAGAC
3301878 CGTCTCAAGG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (36 bp):
TCAAGGGAAACCGTCTCAAGGGAGACAAAATTTGTT
Found at i:3301890 original size:15 final size:15
Alignment explanation
Indices: 3301852--3301891 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
3301842 AAAATTTGTT
*
3301852 TCAAGGGAAACCGTC
1 TCAAGGGAGACCGTC
3301867 TCAAGGGAGACCGTC
1 TCAAGGGAGACCGTC
3301882 TCAAGGGAGA
1 TCAAGGGAGA
3301892 TAAATCTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.23, G:0.33, T:0.12
Consensus pattern (15 bp):
TCAAGGGAGACCGTC
Found at i:3301934 original size:39 final size:39
Alignment explanation
Indices: 3301880--3302008 Score: 188
Period size: 39 Copynumber: 3.3 Consensus size: 39
3301870 AGGGAGACCG
* *
3301880 TCTCAAGGGAGAT-AAATCTTTCTGTTTCGAGAGAAACTA
1 TCTCAAGCGAGATAAAATC-TTCTGCTTCGAGAGAAACTA
* *
3301919 TCTCAAGCGAGATAAAATATTCTGCTTCGATAGAAACTA
1 TCTCAAGCGAGATAAAATCTTCTGCTTCGAGAGAAACTA
*
3301958 TCTCAAGCGAGATAAAATCTTCTGCTTCGAGGGAAACTA
1 TCTCAAGCGAGATAAAATCTTCTGCTTCGAGAGAAACTA
*
3301997 TCTCAAGGGAGA
1 TCTCAAGCGAGA
3302009 CTATCTCAAG
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 77 0.95
40 4 0.05
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (39 bp):
TCTCAAGCGAGATAAAATCTTCTGCTTCGAGAGAAACTA
Found at i:3302011 original size:15 final size:15
Alignment explanation
Indices: 3301987--3302073 Score: 84
Period size: 15 Copynumber: 5.5 Consensus size: 15
3301977 TTCTGCTTCG
*
3301987 AGGGAAACTATCTCA
1 AGGGAGACTATCTCA
3302002 AGGGAGACTATCTCA
1 AGGGAGACTATCTCA
*
3302017 AGGGAGACAATTTATTTCA
1 AGGGAGAC----TATCTCA
* *
3302036 AGGGAAACTGTCTCA
1 AGGGAGACTATCTCA
*
3302051 AGGGAGACTGTCTCA
1 AGGGAGACTATCTCA
*
3302066 AGAGAGAC
1 AGGGAGAC
3302074 AATTTGTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
15 48 0.79
19 13 0.21
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (15 bp):
AGGGAGACTATCTCA
Found at i:3302050 original size:49 final size:49
Alignment explanation
Indices: 3301987--3302107 Score: 188
Period size: 49 Copynumber: 2.5 Consensus size: 49
3301977 TTCTGCTTCG
* *
3301987 AGGGAAACTATCTCAAGGGAGACTATCTCAAGGGAGACAATTTATTTCA
1 AGGGAAACTGTCTCAAGGGAGACTATCTCAAGAGAGACAATTTATTTCA
* * *
3302036 AGGGAAACTGTCTCAAGGGAGACTGTCTCAAGAGAGACAATTTGTTTTA
1 AGGGAAACTGTCTCAAGGGAGACTATCTCAAGAGAGACAATTTATTTCA
*
3302085 AGGGAAACCGTCTCAAGGGAGAC
1 AGGGAAACTGTCTCAAGGGAGAC
3302108 AAAATTTGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 66 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (49 bp):
AGGGAAACTGTCTCAAGGGAGACTATCTCAAGAGAGACAATTTATTTCA
Found at i:3302104 original size:15 final size:15
Alignment explanation
Indices: 3301987--3302104 Score: 65
Period size: 15 Copynumber: 7.3 Consensus size: 15
3301977 TTCTGCTTCG
*
3301987 AGGGAAACTATCTCA
1 AGGGAAACTGTCTCA
* *
3302002 AGGGAGACTATCTCA
1 AGGGAAACTGTCTCA
* * *
3302017 AGGGAGACAATTTATTTCA
1 A-GG-GA-AA-CTGTCTCA
3302036 AGGGAAACTGTCTCA
1 AGGGAAACTGTCTCA
*
3302051 AGGGAGACTGTCTCA
1 AGGGAAACTGTCTCA
* * *
3302066 AGAGAGACAATTTGTTTTA
1 AG-G-GA-AA-CTGTCTCA
*
3302085 AGGGAAACCGTCTCA
1 AGGGAAACTGTCTCA
3302100 AGGGA
1 AGGGA
3302105 GACAAAATTT
Statistics
Matches: 79, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
15 45 0.57
16 7 0.09
17 8 0.10
18 5 0.06
19 14 0.18
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (15 bp):
AGGGAAACTGTCTCA
Found at i:3302123 original size:21 final size:21
Alignment explanation
Indices: 3302097--3302161 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
3302087 GGAAACCGTC
3302097 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
* *
3302118 TCAA-GG-G---AAA-CTGTC
1 TCAAGGGAGACAAAATTTGTT
3302133 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
3302154 TCAAGGGA
1 TCAAGGGA
3302162 ATCTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 7 0.21
16 5 0.15
17 1 0.03
19 1 0.03
20 5 0.15
21 15 0.44
ACGTcount: A:0.37, C:0.12, G:0.26, T:0.25
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:3302124 original size:36 final size:36
Alignment explanation
Indices: 3302048--3302172 Score: 191
Period size: 36 Copynumber: 3.5 Consensus size: 36
3302038 GGAAACTGTC
* *
3302048 TCAAGGGAGACTGTCTCAAGAGAGAC--AATTTGTT
1 TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
* *
3302082 TTAAGGGAAACCGTCTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
3302118 TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
1 TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
*
3302154 TCAAGGGAATCTGTCTCAA
1 TCAAGGGAAACTGTCTCAA
3302173 AATTTGTATC
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
34 22 0.27
36 60 0.73
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (36 bp):
TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTT
Found at i:3302232 original size:34 final size:34
Alignment explanation
Indices: 3302191--3302311 Score: 161
Period size: 34 Copynumber: 3.6 Consensus size: 34
3302181 TCTCAGAGAA
*
3302191 AAATTGTCTCAAGCGAGACGGAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
*
3302225 AAATTGTCTCAAGCGAGACGAAATTTATTTTGAG
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
* * * *
3302259 AAAGTGTATCAAGTGAGACAAAATTTGTTTTGAG
1 AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
* * *
3302293 AAATTATCTTAAGTGAGAC
1 AAATTGTCTCAAGCGAGAC
3302312 AAAAAAATTT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 76 1.00
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (34 bp):
AAATTGTCTCAAGCGAGACGAAATTTGTTTTGAG
Found at i:3302560 original size:32 final size:32
Alignment explanation
Indices: 3302426--3302561 Score: 139
Period size: 32 Copynumber: 4.2 Consensus size: 32
3302416 CAGGATATTG
* * * *
3302426 AATGCCCCAATATTCGATATTAAATCTCCAAA
1 AATGCCCCAACATTTGATGTTGAATCTCCAAA
* * *
3302458 TATGACCCAACATTTTAATGTTGAATCTCCAAA
1 AATGCCCCAACA-TTTGATGTTGAATCTCCAAA
* * *
3302491 GATACCCTAACATTTGATGTTGAATC-CCTAAA
1 AATGCCCCAACATTTGATGTTGAATCTCC-AAA
* *
3302523 GATGCCCCAACATTTGATGTTGAATCTTCAAA
1 AATGCCCCAACATTTGATGTTGAATCTCCAAA
3302555 AATGCCC
1 AATGCCC
3302562 TCTATTGCTT
Statistics
Matches: 85, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
31 2 0.02
32 58 0.68
33 25 0.29
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (32 bp):
AATGCCCCAACATTTGATGTTGAATCTCCAAA
Found at i:3303601 original size:14 final size:13
Alignment explanation
Indices: 3303573--3303620 Score: 64
Period size: 11 Copynumber: 3.8 Consensus size: 13
3303563 TTCTCGTCCC
3303573 TTTTTCTTTACTT
1 TTTTTCTTTACTT
*
3303586 TTTTTCTTTGCTTT
1 TTTTTCTTTAC-TT
3303600 TTTTTCTTTA--T
1 TTTTTCTTTACTT
3303611 TTTTTCTTTA
1 TTTTTCTTTA
3303621 TTATCCTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 11 0.34
13 10 0.31
14 11 0.34
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTACTT
Found at i:3303624 original size:14 final size:13
Alignment explanation
Indices: 3303573--3303642 Score: 63
Period size: 14 Copynumber: 5.4 Consensus size: 13
3303563 TTCTCGTCCC
*
3303573 TTTTTCTTTACTT
1 TTTTTCTTTATTT
*
3303586 TTTTTCTTTGCTTT
1 TTTTTCTTT-ATTT
3303600 TTTTTCTTTA--T
1 TTTTTCTTTATTT
3303611 TTTTTCTTTATTAT
1 TTTTTCTTTATT-T
** *
3303625 CCTTGCTTTATTT
1 TTTTTCTTTATTT
3303638 TTTTT
1 TTTTT
3303643 ATTCTCTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
11 11 0.25
13 12 0.27
14 21 0.48
ACGTcount: A:0.07, C:0.13, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTCTTTATTT
Found at i:3303658 original size:25 final size:26
Alignment explanation
Indices: 3303573--3303665 Score: 77
Period size: 27 Copynumber: 3.6 Consensus size: 26
3303563 TTCTCGTCCC
*
3303573 TTTTTCTTTACTTTTTTTCT-TTGCTTT
1 TTTTTCTTTACTTTTTTT-TATT-CTCT
* *
3303600 TTTTTCTTTATTTTTTCTTTATTATC-
1 TTTTTCTTTACTTTTT-TTTATTCTCT
* *
3303626 -CTTGCTTTA-TTTTTTTTATTCTCT
1 TTTTTCTTTACTTTTTTTTATTCTCT
*
3303650 TTTTTCTTTTCTTTTT
1 TTTTTCTTTACTTTTT
3303666 GCTATGTTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 11
0.72 0.12 0.15
Matches are distributed among these distances:
23 8 0.15
24 5 0.10
25 13 0.25
26 5 0.10
27 17 0.33
28 4 0.08
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTTTCTTTACTTTTTTTTATTCTCT
Found at i:3308665 original size:2 final size:2
Alignment explanation
Indices: 3308658--3308684 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3308648 ATTAATAAAT
3308658 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
3308685 GCGTATTAAA
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
Done.