Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 21
Found at i:3549436 original size:14 final size:14
Alignment explanation
Indices: 3549417--3549473 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3549407 GAGAAATGAA
3549417 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3549431 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3549450 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3549464 AATCGCAACG
1 AATCGCAACG
3549474 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:3549447 original size:33 final size:33
Alignment explanation
Indices: 3549409--3549490 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
3549399 TGCAACGAGA
3549409 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3549442 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
3549475 GAAACCAAAATCGCAA
1 GAAATGAAAATCGCAA
3549491 TGCGATTTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.48, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3549455 original size:19 final size:19
Alignment explanation
Indices: 3549368--3549495 Score: 69
Period size: 19 Copynumber: 7.1 Consensus size: 19
3549358 GCAACGAGAT
*
3549368 AAATGAAAATCGCAACGTG
1 AAATGAAAATCGCAACGCG
** *
3549387 AAAATGACTATCTGCAACGAGAG
1 -AAATGAAAATC-GCAAC--GCG
3549410 AAATGAAAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
3549427 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
3549443 AAATGAAAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
3549460 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
** *
3549476 AAACCAAAATCGCAATGCG
1 AAATGAAAATCGCAACGCG
3549495 A
1 A
3549496 TTTTCATTTC
Statistics
Matches: 83, Mismatches: 12, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
14 20 0.24
15 2 0.02
16 4 0.05
17 3 0.04
18 2 0.02
19 23 0.28
20 9 0.11
21 9 0.11
22 9 0.11
23 2 0.02
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:3549526 original size:14 final size:14
Alignment explanation
Indices: 3549507--3549563 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3549497 TTTCATTTCG
3549507 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3549521 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
3549540 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
3549554 CGTTGCGATT
1 CGTTGCGATT
3549564 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3549533 original size:33 final size:33
Alignment explanation
Indices: 3549491--3549612 Score: 163
Period size: 33 Copynumber: 3.5 Consensus size: 33
3549481 AAAATCGCAA
3549491 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3549524 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
3549557 TGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCGT
3549598 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
3549613 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 44 0.55
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.26
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3549574 original size:21 final size:21
Alignment explanation
Indices: 3549548--3549612 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
3549538 CGCGTTGCGA
3549548 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
3549569 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
3549589 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
3549610 TTC
1 TTC
3549613 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:3551456 original size:93 final size:93
Alignment explanation
Indices: 3551297--3551612 Score: 605
Period size: 93 Copynumber: 3.4 Consensus size: 93
3551287 TAGATTGCTT
*
3551297 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
3551362 TTTATCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
3551390 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3551455 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3551483 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
3551548 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
3551576 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
3551613 AATACCCTGA
Statistics
Matches: 219, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 219 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3551769 original size:19 final size:19
Alignment explanation
Indices: 3551745--3551912 Score: 149
Period size: 19 Copynumber: 9.3 Consensus size: 19
3551735 ACGAGAGAAA
*
3551745 TTGCGATTTTAATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
3551764 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
*
3551778 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
3551797 TTGCGA--TTC-TGT--CG
1 TTGCGATTTTCATTTCGCG
3551811 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
**
3551830 TTGCGATTTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCG
** *
3551849 TTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCG
*
3551868 TTGCGATTCTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
3551887 TTGCGATTTTAAGTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
3551907 TTGCGA
1 TTGCGA
3551913 AAGTAAACTA
Statistics
Matches: 121, Mismatches: 17, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
14 17 0.14
16 8 0.07
17 7 0.06
19 77 0.64
20 12 0.10
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:3551781 original size:14 final size:14
Alignment explanation
Indices: 3551762--3551818 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
3551752 TTTAATTTCG
3551762 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
3551776 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
3551793 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
3551809 CGTTGCGATT
1 CGTTGCGATT
3551819 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:3551785 original size:33 final size:33
Alignment explanation
Indices: 3551745--3551837 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
3551735 ACGAGAGAAA
*
3551745 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
3551778 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
3551811 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
3551838 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:3551870 original size:38 final size:38
Alignment explanation
Indices: 3551745--3551912 Score: 158
Period size: 33 Copynumber: 4.7 Consensus size: 38
3551735 ACGAGAGAAA
*
3551745 TTGCGATTTTAATTTCGCGTTGCGATTCTC---T--CG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCGCG
* *
3551778 TTGCGATTTTCATTTCGCATTGCGA-T-TC-TGT--CG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCGCG
* **
3551811 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCGCG
** *
3551849 TTGCGATTTTGGTTTCTCGTTGCGATTCTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCGCG
* *
3551887 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
3551913 AAGTAAACTA
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 50 0.45
34 1 0.01
35 1 0.01
36 2 0.02
38 44 0.39
39 11 0.10
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (38 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCGCG
Found at i:3553841 original size:14 final size:14
Alignment explanation
Indices: 3553822--3553857 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3553812 ATTGTTTAAT
3553822 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3553836 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3553850 TGATTTGT
1 TGATTTGT
3553858 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:3554037 original size:53 final size:53
Alignment explanation
Indices: 3553964--3554079 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
3553954 AAAAATGACT
*
3553964 ATCGCAATGC-GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGA
3554016 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
3554069 ATCGCAATGCG
1 ATCGCAATGCG
3554080 ATTTTCATTT
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
52 10 0.16
53 45 0.74
54 6 0.10
ACGTcount: A:0.43, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAATCGCAACGAGAGA
Found at i:3554040 original size:20 final size:19
Alignment explanation
Indices: 3553964--3554061 Score: 127
Period size: 19 Copynumber: 5.4 Consensus size: 19
3553954 AAAAATGACT
3553964 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3553983 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3554002 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
3554016 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
3554036 ATCGCAATGCGGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
3554055 ATCGCAA
1 ATCGCAA
3554062 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 11 0.15
15 1 0.01
17 2 0.03
19 37 0.52
20 20 0.28
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3554162 original size:72 final size:70
Alignment explanation
Indices: 3554071--3554364 Score: 275
Period size: 72 Copynumber: 4.2 Consensus size: 70
3554061 ACGAGAGAAT
*
3554071 CGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1 CGCATTGCGATTTTCATTTCG--TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
3554136 TTCATTT-
63 TTCATTTC
* * * * *
3554143 CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGA
1 CGCATTGCGATTTTCATTTCG--TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGA
3554205 TTTTCATTTC
61 TTTTCATTTC
* * *
3554215 CGCATTGCGA--TTC-TATCGTTGCGATTTTCATTTCGCATTGTGATTTTCATTTCGCATTGCGA
1 CGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGA
3554277 TTTTCATTTC
61 TTTTCATTTC
* * *
3554287 CGCATTGCGATTTTCA--T-GTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTA
1 CGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
3554349 ATTTC
66 ATTTC
**
3554354 CGTGTTGCGAT
1 CGCATTGCGAT
3554365 AGTCAAATGC
Statistics
Matches: 186, Mismatches: 21, Indels: 35
0.77 0.09 0.14
Matches are distributed among these distances:
65 8 0.04
66 3 0.02
67 31 0.17
68 2 0.01
69 8 0.04
70 8 0.04
71 18 0.10
72 94 0.51
73 7 0.04
74 7 0.04
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (70 bp):
CGCATTGCGATTTTCATTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
ATTTC
Found at i:3554219 original size:105 final size:109
Alignment explanation
Indices: 3554076--3554345 Score: 416
Period size: 105 Copynumber: 2.6 Consensus size: 109
3554066 AGAATCGCAA
3554076 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
3554141 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-T
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
*
3554181 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTATCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
* *
3554246 TTCGCATTGTGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-AT
*
3554292 TGCGATTTTCA--T-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
3554346 GTAATTTCCG
Statistics
Matches: 154, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
105 119 0.77
106 14 0.09
107 3 0.02
108 3 0.02
109 3 0.02
111 12 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (109 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
Found at i:3554360 original size:53 final size:52
Alignment explanation
Indices: 3554076--3554345 Score: 397
Period size: 53 Copynumber: 5.1 Consensus size: 52
3554066 AGAATCGCAA
3554076 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
3554129 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
3554181 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTATCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
* *
3554234 TGCGATTTTCATTTCGCATTGTGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
3554292 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
3554339 TGCGATT
1 TGCGATT
3554346 GTAATTTCCG
Statistics
Matches: 205, Mismatches: 5, Indels: 20
0.89 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 62 0.30
53 107 0.52
54 3 0.01
55 3 0.01
56 3 0.01
58 12 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:3556857 original size:24 final size:24
Alignment explanation
Indices: 3556823--3556869 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3556813 CTGAAACATC
3556823 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
3556847 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
3556870 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:3557591 original size:20 final size:20
Alignment explanation
Indices: 3557562--3557653 Score: 121
Period size: 20 Copynumber: 4.6 Consensus size: 20
3557552 AAATTTCAGT
* *
3557562 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACAGATTATC
* *
3557582 GTTGCAATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
**
3557602 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTATC
*
3557622 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
3557642 GTTGCGATTTAC
1 GTTGCGATTTAC
3557654 GGATACGCGT
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACAGATTATC
Found at i:3557625 original size:40 final size:40
Alignment explanation
Indices: 3557562--3557790 Score: 232
Period size: 40 Copynumber: 5.7 Consensus size: 40
3557552 AAATTTCAGT
* * * *
3557562 GTTGTGATTTACAGATTCTCGTTGCAATTTACGGATTATC
1 GTTGCGATTTACAGATACGCGTTGCGATTTACGGATTATC
*
3557602 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATACGCGTTGCGATTTACGGATTATC
* *
3557642 GTTGCGATTTACGGATACGCGTTGCGATATACGGA-TA-C
1 GTTGCGATTTACAGATACGCGTTGCGATTTACGGATTATC
* * *
3557680 GCATTGCGATTTACGGATACGCGTTGCTATTTACGGA-TACAC
1 G--TTGCGATTTACAGATACGCGTTGCGATTTACGGATTA-TC
* * * **
3557722 GTTGCGGTTTACGGATACGCGTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACAGATACGCGTTGCGATTTACG-GATTATC
* * *
3557762 GTTGCGATTTTCATATTCGCGTTGCGATT
1 GTTGCGATTTACAGATACGCGTTGCGATT
3557791 CTTGAAAATC
Statistics
Matches: 165, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 157 0.95
41 2 0.01
42 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
GTTGCGATTTACAGATACGCGTTGCGATTTACGGATTATC
Found at i:3557654 original size:20 final size:19
Alignment explanation
Indices: 3557581--3557771 Score: 184
Period size: 20 Copynumber: 9.6 Consensus size: 19
3557571 TACAGATTCT
* *
3557581 CGTTGCAATTTACGGATTAT
1 CGTTGCGATTTACGGA-TAG
* *
3557601 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTACGGA-TAG
*
3557621 CGTTGCGATTTACGGATTAT
1 CGTTGCGATTTACGGA-TAG
3557641 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATA-G
*
3557661 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATA-G
*
3557681 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATA-G
* *
3557701 CGTTGCTATTTACGGATACA
1 CGTTGCGATTTACGGATA-G
*
3557721 CGTTGCGGTTTACGGATACG
1 CGTTGCGATTTACGGATA-G
* * *
3557741 CGTTGCGATTTATGTGTTCG
1 CGTTGCGATTTACG-GATAG
3557761 CGTTGCGATTT
1 CGTTGCGATTT
3557772 TCATATTCGC
Statistics
Matches: 148, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
19 2 0.01
20 144 0.97
21 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (19 bp):
CGTTGCGATTTACGGATAG
Found at i:3557780 original size:20 final size:20
Alignment explanation
Indices: 3557739--3557790 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3557729 TTTACGGATA
* *
3557739 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTTATATATT
3557759 CGCGTTGCGATTT-TCATATT
1 CGCGTTGCGATTTAT-ATATT
3557779 CGCGTTGCGATT
1 CGCGTTGCGATT
3557791 CTTGAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.12, C:0.19, G:0.27, T:0.42
Consensus pattern (20 bp):
CGCGTTGCGATTTATATATT
Found at i:3557785 original size:60 final size:60
Alignment explanation
Indices: 3557562--3557790 Score: 246
Period size: 60 Copynumber: 3.8 Consensus size: 60
3557552 AAATTTCAGT
* * * * * * *
3557562 GTTGTGATTTACAGATTCTCGTTGCAATTTACGGATTA-TCGTTGCGATTTACAGATTCGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACGC
** *
3557622 GTTGCGATTTACGGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
* * * * *
3557682 ATTGCGATTTACGGATACGCGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
* * ** *
3557742 GTTGCGATTTATGTG-TTCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 GTTGCGATTTACG-GATTCGCGTTGCGATTTACGGATACGCGTTGCGATT
3557791 CTTGAAAATC
Statistics
Matches: 141, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
59 2 0.01
60 138 0.98
61 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (60 bp):
GTTGCGATTTACGGATTCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
Found at i:3557843 original size:21 final size:20
Alignment explanation
Indices: 3557758--3557855 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
3557748 ATTTATGTGT
* *
3557758 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
3557778 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
3557799 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
3557820 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
3557841 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
3557856 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:3557851 original size:42 final size:43
Alignment explanation
Indices: 3557758--3557856 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3557748 ATTTATGTGT
* *
3557758 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
3557799 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
3557841 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3557857 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:3561354 original size:16 final size:16
Alignment explanation
Indices: 3561333--3561375 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
3561323 TCGGGTTAGA
3561333 TCGAAACCCATCGGAT
1 TCGAAACCCATCGGAT
*
3561349 TCGAAACCCGTCGGAT
1 TCGAAACCCATCGGAT
*
3561365 TCGAATCCCAT
1 TCGAAACCCAT
3561376 GCCCATCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.21
Consensus pattern (16 bp):
TCGAAACCCATCGGAT
Found at i:3568360 original size:21 final size:21
Alignment explanation
Indices: 3568323--3568405 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
3568313 TTTTGGTGCA
*
3568323 GAGGGAATC-AATCCCCCCAT
1 GAGGGAATCGATTCCCCCCAT
* **
3568343 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCCAT
3568364 GAAGAGGAATCGATTCCCCCCAT
1 G-AG-GGAATCGATTCCCCCCAT
*
3568387 -AGGGGAATCGATACCCCCC
1 GA-GGGAATCGATTCCCCCC
3568406 CTGGGGTTCT
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
20 8 0.16
21 25 0.49
22 3 0.06
23 15 0.29
ACGTcount: A:0.27, C:0.34, G:0.23, T:0.17
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCAT
Found at i:3570664 original size:12 final size:12
Alignment explanation
Indices: 3570647--3570680 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3570637 AAGTAAGTGA
*
3570647 GTGTTTTTAAGT
1 GTGTTTTAAAGT
3570659 GTGTTTTAAAGT
1 GTGTTTTAAAGT
3570671 GTGTTTTAAA
1 GTGTTTTAAA
3570681 ATGATAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (12 bp):
GTGTTTTAAAGT
Found at i:3572048 original size:16 final size:15
Alignment explanation
Indices: 3571968--3572044 Score: 63
Period size: 15 Copynumber: 5.3 Consensus size: 15
3571958 GTGAAATTCT
3571968 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
3571983 AATTATTTATATAAA
1 AATTATTTAAATAAA
* * *
3571998 AA--A-TT-CATCGAT
1 AATTATTTAAAT-AAA
3572010 AATATATTTAAATAAA
1 AAT-TATTTAAATAAA
*
3572026 AATTATTTATATAAA
1 AATTATTTAAATAAA
3572041 AATT
1 AATT
3572045 TATTGATAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
11 2 0.04
12 5 0.10
13 1 0.02
15 32 0.67
16 6 0.12
17 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:3572059 original size:42 final size:43
Alignment explanation
Indices: 3571971--3572059 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
3571961 AAATTCTAAT
*
3571971 TATTTAAATAAAAATTATTTATATAAAAAATTCATCGATAATA
1 TATTTAAATAAAAATTATTTATATAAAAAATTCATCGATAAAA
* *
3572014 TATTTAAATAAAAATTATTTATAT-AAAAATTTATTGATAAAA
1 TATTTAAATAAAAATTATTTATATAAAAAATTCATCGATAAAA
3572056 TATT
1 TATT
3572060 ATTTTATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
42 19 0.44
43 24 0.56
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (43 bp):
TATTTAAATAAAAATTATTTATATAAAAAATTCATCGATAAAA
Found at i:3572109 original size:20 final size:20
Alignment explanation
Indices: 3572084--3572121 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3572074 ATATTTAAAT
*
3572084 ATATATCATTTATTATTTAA
1 ATATATCATGTATTATTTAA
3572104 ATATATCATGTATTATTT
1 ATATATCATGTATTATTT
3572122 TTATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (20 bp):
ATATATCATGTATTATTTAA
Found at i:3578066 original size:9 final size:9
Alignment explanation
Indices: 3578035--3578068 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3578025 ATTTAATTTC
3578035 ATTTTTCTT
1 ATTTTTCTT
*
3578044 ATTATTTATT
1 ATT-TTTCTT
3578054 ATTTTTCTT
1 ATTTTTCTT
3578063 ATTTTT
1 ATTTTT
3578069 TTCGTCTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTTTCTT
Found at i:3580358 original size:21 final size:22
Alignment explanation
Indices: 3580321--3580364 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3580311 CTGAAGTCAT
3580321 AAAAATTCAAATAACCAAATAA
1 AAAAATTCAAATAACCAAATAA
3580343 AAAAATTCAAAT-ACCAAATAA
1 AAAAATTCAAATAACCAAATAA
3580364 A
1 A
3580365 CATCAAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.68, C:0.14, G:0.00, T:0.18
Consensus pattern (22 bp):
AAAAATTCAAATAACCAAATAA
Found at i:3585152 original size:12 final size:12
Alignment explanation
Indices: 3585135--3585159 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3585125 CTTTGAATTA
3585135 TTTTTGATAAAT
1 TTTTTGATAAAT
3585147 TTTTTGATAAAT
1 TTTTTGATAAAT
3585159 T
1 T
3585160 CAATTAAGTC
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TTTTTGATAAAT
Found at i:3595323 original size:42 final size:43
Alignment explanation
Indices: 3595029--3595481 Score: 521
Period size: 43 Copynumber: 10.7 Consensus size: 43
3595019 TGAGAACCAA
* * * *
3595029 AAACGCCGCCATAGGTCAATATCTATAGCGGCGTTTTTGTAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* * * ** *
3595072 AAACGTCGCAAAAGATCGAGATCTATAATGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* *
3595115 AAACGCCGCAAAAGGTCGAGATCTATAGCGGTGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* *
3595158 AAACACCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-AC
* * * *
3595202 AAACGCCGCAGAAGGTC-ATATCTATAGCGTCATTTTTGGAAT
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* * *
3595244 AAACGCCGCAAAATGTCGAGATCTATAACGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* *
3595287 AAACGCCACAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAT
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
3595329 AAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* * * * *
3595371 AAACGCCGC-AAATGTC-ATGTCTATAGCGGCATTTATAGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* ** *
3595412 --A--CCGCAAAAGGTC-ATATATATAGCGGTATTTTTAGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* *
3595450 AAACGCCACAAAAGGTCGAGATCTATAGCGGC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGC
3595482 ATTTGTATCC
Statistics
Matches: 350, Mismatches: 52, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
37 4 0.01
38 27 0.08
39 1 0.00
40 1 0.00
41 27 0.08
42 98 0.28
43 175 0.50
44 17 0.05
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
Found at i:3600121 original size:41 final size:41
Alignment explanation
Indices: 3600076--3600502 Score: 428
Period size: 41 Copynumber: 10.4 Consensus size: 41
3600066 GTAAACTTGT
* *
3600076 GGCGTTTGTATAAAAACGCCACTAAAACACGAGTTTTTAGC
1 GGCGTTTATATAAAAACGCCACTAAAACACGAGTCTTTAGC
* * * * *
3600117 GGCGTTTTTATAAGAAAATGCCACTAAAACAAGAGTCTATAGA
1 GGCGTTTATAT-A-AAAACGCCACTAAAACACGAGTCTTTAGC
* * *
3600160 TGCGTTTATATAAAAACGCTACTAAAACATC-AGTCTTCAGC
1 GGCGTTTATATAAAAACGCCACTAAAACA-CGAGTCTTTAGC
* * *
3600201 GGCGTTTGTATAAAAACGCCAGTAAAACACGAGTTTTTAGC
1 GGCGTTTATATAAAAACGCCACTAAAACACGAGTCTTTAGC
* * * * **
3600242 GGCATTTGTATAAGAACGCCGCTAAAGTACGAGTCTTTTA-C
1 GGCGTTTATATAAAAACGCCACTAAAACACGAGTC-TTTAGC
* * *
3600283 GGCGTTTATATAGAAACGCCACTAAAACAAGAGTCTATAGC
1 GGCGTTTATATAAAAACGCCACTAAAACACGAGTCTTTAGC
* **
3600324 GGCGTTTATATAAAAACGTCACTAAAGTACGAGTCTTTAGC
1 GGCGTTTATATAAAAACGCCACTAAAACACGAGTCTTTAGC
3600365 GGCGTTTATATAAAAACGCCACTAAAACACGAGTCTTTAGC
1 GGCGTTTATATAAAAACGCCACTAAAACACGAGTCTTTAGC
* * * *** * *
3600406 GACGTTTGTATAAAAATGCCACTAACGTATGAGTCTATAGC
1 GGCGTTTATATAAAAACGCCACTAAAACACGAGTCTTTAGC
* * *** * *
3600447 GGCGTTTA-AAAAAAATGCCACTAACGTATGAGTCTATAGC
1 GGCGTTTATATAAAAACGCCACTAAAACACGAGTCTTTAGC
*
3600487 GGCGTTTTTATAAAAA
1 GGCGTTTATATAAAAA
3600503 TTTCACCGCT
Statistics
Matches: 321, Mismatches: 58, Indels: 14
0.82 0.15 0.04
Matches are distributed among these distances:
40 42 0.13
41 240 0.75
42 6 0.02
43 33 0.10
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (41 bp):
GGCGTTTATATAAAAACGCCACTAAAACACGAGTCTTTAGC
Found at i:3600559 original size:42 final size:43
Alignment explanation
Indices: 3600485--3600570 Score: 113
Period size: 42 Copynumber: 2.0 Consensus size: 43
3600475 TGAGTCTATA
3600485 GCGGCGTTTTTATAAAAATTTCACCGCTAAAG-TACTACTTTGTC
1 GCGGCGTTTTTATAAAAA--TCACCGCTAAAGTTACTACTTTGTC
* *
3600529 GCGGCGTTTTGTATAAAAA-CGCCGCTAAAGTTACTATTTTGT
1 GCGGCGTTTT-TATAAAAATCACCGCTAAAGTTACTACTTTGT
3600571 GGCGTTTGGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
42 10 0.26
43 10 0.26
44 10 0.26
45 8 0.21
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (43 bp):
GCGGCGTTTTTATAAAAATCACCGCTAAAGTTACTACTTTGTC
Found at i:3602332 original size:20 final size:20
Alignment explanation
Indices: 3602307--3602356 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3602297 TGCATGTAGA
*
3602307 GGTATCGATACCTCAAGGGT
1 GGTATCGATACCTCAAGGAT
**
3602327 GGTATCGATACCTGTAGGAT
1 GGTATCGATACCTCAAGGAT
3602347 GGTATCGATA
1 GGTATCGATA
3602357 TCCTTAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (20 bp):
GGTATCGATACCTCAAGGAT
Found at i:3602362 original size:147 final size:147
Alignment explanation
Indices: 3602156--3602465 Score: 566
Period size: 147 Copynumber: 2.1 Consensus size: 147
3602146 TACCTGTTGA
* * *
3602156 TAGAGGTATCAATATCTCAAGGGTGGTATCGATATCTGTAGAATGGTATCGATATCCTTAAAACT
1 TAGAGGTATCGATACCTCAAGGGTGGTATCGATACCTGTAGAATGGTATCGATATCCTTAAAACT
*
3602221 TCGAAGGTAATTTCGGTTTTAGTACCTTGAGGAGGTATCAATACCCTAGAAACATCTAACGTAAT
66 TCGAAGGTAATTTCGGTTTCAGTACCTTGAGGAGGTATCAATACCCTAGAAACATCTAACGTAAT
3602286 TTTGATATTGTTGCATG
131 TTTGATATTGTTGCATG
*
3602303 TAGAGGTATCGATACCTCAAGGGTGGTATCGATACCTGTAGGATGGTATCGATATCCTTAAAACT
1 TAGAGGTATCGATACCTCAAGGGTGGTATCGATACCTGTAGAATGGTATCGATATCCTTAAAACT
3602368 TCGAAGGTAATTTCGGTTTCAGTACCTTGAGGAGGTATCAATACCCTAGAAACATCTAACGTAAT
66 TCGAAGGTAATTTCGGTTTCAGTACCTTGAGGAGGTATCAATACCCTAGAAACATCTAACGTAAT
3602433 TTTGATATTGTTGCATG
131 TTTGATATTGTTGCATG
*
3602450 TGGAGGTATCGATACC
1 TAGAGGTATCGATACC
3602466 CTTGAGGGGG
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 157 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (147 bp):
TAGAGGTATCGATACCTCAAGGGTGGTATCGATACCTGTAGAATGGTATCGATATCCTTAAAACT
TCGAAGGTAATTTCGGTTTCAGTACCTTGAGGAGGTATCAATACCCTAGAAACATCTAACGTAAT
TTTGATATTGTTGCATG
Found at i:3602498 original size:20 final size:22
Alignment explanation
Indices: 3602454--3602508 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 22
3602444 TGCATGTGGA
3602454 GGTATCGATACCCTTGAGGGGGT
1 GGTATCGATACCCTTGA-GGGGT
*
3602477 GGTATCGGTACCCTT-A-GGGT
1 GGTATCGATACCCTTGAGGGGT
*
3602497 GGTACCGATACC
1 GGTATCGATACC
3602509 TCTAAGCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.48
22 1 0.03
23 14 0.48
ACGTcount: A:0.18, C:0.22, G:0.35, T:0.25
Consensus pattern (22 bp):
GGTATCGATACCCTTGAGGGGT
Found at i:3603044 original size:21 final size:21
Alignment explanation
Indices: 3603018--3603058 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3603008 GTCGAGGGTC
*
3603018 TATGTGGTCATTCGGGACAAT
1 TATGTGGTCATCCGGGACAAT
*
3603039 TATGTGGTCCTCCGGGACAA
1 TATGTGGTCATCCGGGACAA
3603059 ATACGTAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGTGGTCATCCGGGACAAT
Found at i:3603148 original size:22 final size:21
Alignment explanation
Indices: 3603083--3603151 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
3603073 AGTGCAACCC
*
3603083 TATGTGGCACTTCGGTGCAAAC
1 TATGTGGCACTTC-GTGCAAAT
* * * *
3603105 TATATGGTAATTCG-GGACAAT
1 TATGTGGCACTTCGTGCA-AAT
3603126 TATGTGGCACTTCTGTGCAAAT
1 TATGTGGCACTTC-GTGCAAAT
3603148 TATG
1 TATG
3603152 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
20 2 0.06
21 13 0.37
22 18 0.51
23 2 0.06
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (21 bp):
TATGTGGCACTTCGTGCAAAT
Found at i:3609380 original size:23 final size:23
Alignment explanation
Indices: 3609347--3609392 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
3609337 GCATATGGAT
3609347 GTATCGATACCCTTGAGGG-GGTA
1 GTATCGATACCCTT-AGGGTGGTA
*
3609370 GTATCGGTACCCTTAGGGTGGTA
1 GTATCGATACCCTTAGGGTGGTA
3609393 CCGATACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.20, C:0.17, G:0.35, T:0.28
Consensus pattern (23 bp):
GTATCGATACCCTTAGGGTGGTA
Found at i:3609955 original size:21 final size:21
Alignment explanation
Indices: 3609928--3609977 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3609918 AGTCGAGGGT
*
3609928 ATATGTGGTCATT-CGGGACTA
1 ATATGTGGTC-TTCCGGGACAA
*
3609949 TTATGTGGTCTTCCGGGACAA
1 ATATGTGGTCTTCCGGGACAA
3609970 ATATGTGG
1 ATATGTGG
3609978 CACTTCGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (21 bp):
ATATGTGGTCTTCCGGGACAA
Found at i:3611251 original size:17 final size:19
Alignment explanation
Indices: 3611212--3611256 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
3611202 AAAGTTTATC
* *
3611212 TTTTTAATAAAGAAATATT
1 TTTTTATTAAAGAAATATG
3611231 TTTTTATTAAA-AAAT-TG
1 TTTTTATTAAAGAAATATG
3611248 TTTTTATTA
1 TTTTTATTA
3611257 TAAATATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.42
18 4 0.17
19 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
TTTTTATTAAAGAAATATG
Found at i:3612261 original size:87 final size:87
Alignment explanation
Indices: 3612115--3612277 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 87
3612105 TATGTTATAT
3612115 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
3612180 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * *
3612202 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
3612267 AGCGCTTATAT
66 AGCGCTTATAT
3612278 TGACTTATTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:3613030 original size:200 final size:200
Alignment explanation
Indices: 3612793--3613878 Score: 1992
Period size: 200 Copynumber: 5.4 Consensus size: 200
3612783 GTTTCATTGA
3612793 ACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTA
1 ACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTA
*
3612858 TTGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGA
66 TTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGA
* *
3612923 CACATTATTTAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGAAAAATTAC
131 TACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTAC
3612988 CTATT
196 CTATT
3612993 ACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTA
1 ACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTA
*
3613058 TTGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGA
66 TTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGA
*
3613123 TACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTAC
131 TACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTAC
3613188 CTATT
196 CTATT
*
3613193 ACATTATATTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTA
1 ACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTA
* *
3613258 TTGTTGCACCCTATTTGCCATTCATTCTGGACCAAAAATATCGATACAAACTACAAAAGTGTCGA
66 TTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGA
*
3613323 CACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTAC
131 TACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTAC
3613388 CTATT
196 CTATT
*
3613393 ACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGTATCGACACTTTA
1 ACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTA
*
3613458 TTGTTGTACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGA
66 TTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGA
* * *
3613523 TACATTATTTAGACCTATTCTCTCATAAAACCGATATACTTGTACTGATTAGATTGAAAAATTAC
131 TACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTAC
3613588 CTATT
196 CTATT
* * *
3613593 ACATTATACTTGTGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATTGACACTTTA
1 ACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTA
3613658 TTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGA
66 TTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGA
*
3613723 TACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTAC
131 TACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTAC
3613788 CTATT
196 CTATT
*
3613793 ACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTA
1 ACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTA
*
3613858 TGGTTGCACCCTGTTTGCCAT
66 TTGTTGCACCCTGTTTGCCAT
3613879 ATTGTAAATT
Statistics
Matches: 857, Mismatches: 29, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
200 857 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (200 bp):
ACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTA
TTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGA
TACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTAC
CTATT
Found at i:3614123 original size:18 final size:18
Alignment explanation
Indices: 3614100--3614158 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
3614090 TCTCATTCAT
*
3614100 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
3614118 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
3614137 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
3614156 AAT
1 AAT
3614159 GAACCCTACA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
18 6 0.17
19 30 0.83
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:3614136 original size:19 final size:19
Alignment explanation
Indices: 3614112--3614158 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
3614102 TTATATTCAC
3614112 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
3614131 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
3614150 ATACAAAAT
1 ATACAAAAT
3614159 GAACCCTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:3615751 original size:21 final size:21
Alignment explanation
Indices: 3615726--3615766 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3615716 CCTCCTCATT
3615726 TCTTCCATCTCTTCTTCTTCC
1 TCTTCCATCTCTTCTTCTTCC
* *
3615747 TCTTCCCTCTTTTCTTCTTC
1 TCTTCCATCTCTTCTTCTTC
3615767 ATATTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.56
Consensus pattern (21 bp):
TCTTCCATCTCTTCTTCTTCC
Found at i:3615987 original size:33 final size:33
Alignment explanation
Indices: 3615950--3616015 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3615940 CATCTTAATA
*
3615950 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
3615983 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
3616016 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:3616074 original size:21 final size:21
Alignment explanation
Indices: 3616049--3616113 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
3616039 CCCCTTATGC
* *
3616049 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
3616070 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
3616091 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
3616112 CT
1 CT
3616114 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:3618378 original size:20 final size:19
Alignment explanation
Indices: 3618332--3618378 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
3618322 TCCGGTATCG
3618332 TTTTACCGATTTTATCATT
1 TTTTACCGATTTTATCATT
* *
3618351 TTGATACCGGTTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
3618372 TTTTACC
1 TTTTACC
3618379 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:3618558 original size:20 final size:19
Alignment explanation
Indices: 3618512--3618558 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
3618502 TCCGGTAACG
3618512 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
3618531 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
3618552 TTTTACC
1 TTTTACC
3618559 TGGTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:3618713 original size:182 final size:181
Alignment explanation
Indices: 3618299--3618770 Score: 721
Period size: 182 Copynumber: 2.6 Consensus size: 181
3618289 CGTACTTACG
* *
3618299 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGATTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * *
3618364 TATCATATTTTTACCTGTTATATCGTTGTGAATCGATA-TTTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
3618428 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
3618479 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
3618544 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
3618609 AAGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * **
3618661 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
3618726 TGTCATAGTTTTACCTGTTATATCATTTTGGATCGATACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
3618771 AATTTGGATC
Statistics
Matches: 266, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
180 98 0.37
181 68 0.26
182 100 0.38
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:3618772 original size:181 final size:180
Alignment explanation
Indices: 3618299--3618772 Score: 714
Period size: 180 Copynumber: 2.6 Consensus size: 180
3618289 CGTACTTACG
* *
3618299 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGATTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * ** *
3618364 TATCATATTTTTACCTGTTATATCGTTGTGAATCGATATTTTTTTTAAAGTATCGACACATTATA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATA
* *
3618429 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 AGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
3618479 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
3618544 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTAAAAGTATCGACACATTAT
** *
3618609 AAGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AAGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * **
3618661 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
3618726 TGTCATAGTTTTACCTGTTATATCATTTTGGATCGATACATTTTTAA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAA
3618773 TTTGGATCGA
Statistics
Matches: 267, Mismatches: 25, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
180 98 0.37
181 74 0.28
182 95 0.36
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (180 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATA
AGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:3629754 original size:9 final size:8
Alignment explanation
Indices: 3629742--3629823 Score: 62
Period size: 9 Copynumber: 9.9 Consensus size: 8
3629732 AATATTTTAT
3629742 ATATAATTA
1 ATATAA-TA
*
3629751 ATATAAAA
1 ATATAATA
3629759 ATATAA-A
1 ATATAATA
*
3629766 ATATTATA
1 ATATAATA
3629774 TATATAATTA
1 -ATATAA-TA
*
3629784 ATATAAAAA
1 ATAT-AATA
3629793 ATATAA-A
1 ATATAATA
3629800 ATATAAT-
1 ATATAATA
3629807 ATATATATA
1 ATATA-ATA
3629816 TATATAAT
1 -ATATAAT
3629824 CGGGGCGGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
7 18 0.30
8 12 0.20
9 22 0.36
10 9 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:3629767 original size:33 final size:34
Alignment explanation
Indices: 3629730--3629813 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 34
3629720 CCCGAACCCA
*
3629730 AAAATATTTTATATATAATTAATAT-AAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
3629763 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
*
3629797 AAAATATAATATATATA
1 AAAATATTATATATATA
3629814 TATATATAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 24 0.50
34 24 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:3629768 original size:7 final size:7
Alignment explanation
Indices: 3629750--3629811 Score: 54
Period size: 7 Copynumber: 8.9 Consensus size: 7
3629740 ATATATAATT
3629750 AATATAAA
1 AATAT-AA
3629758 AATATAA
1 AATATAA
*
3629765 AATATTA
1 AATATAA
* *
3629772 TATATAT
1 AATATAA
3629779 AAT-TAA
1 AATATAA
* *
3629785 TATAAAA
1 AATATAA
3629792 AATATAA
1 AATATAA
3629799 AATATAA
1 AATATAA
*
3629806 TATATA
1 AATATA
3629812 TATATATATA
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
6 4 0.10
7 33 0.79
8 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
AATATAA
Found at i:3636975 original size:8 final size:8
Alignment explanation
Indices: 3636962--3637069 Score: 126
Period size: 8 Copynumber: 13.2 Consensus size: 8
3636952 TAATTGCTCG
3636962 AACTCTCA
1 AACTCTCA
3636970 AACTCTCTTA
1 AACTCTC--A
* *
3636980 AATTCTTA
1 AACTCTCA
*
3636988 AACTCTCT
1 AACTCTCA
*
3636996 AACTCTGA
1 AACTCTCA
*
3637004 AACTATCA
1 AACTCTCA
3637012 AACTCTCA
1 AACTCTCA
*
3637020 AACTTTCA
1 AACTCTCA
*
3637028 AACTTTCA
1 AACTCTCA
3637036 AACTCTCA
1 AACTCTCA
3637044 AACTCTCA
1 AACTCTCA
3637052 AACTCTCA
1 AACTCTCA
*
3637060 AATTCTCA
1 AACTCTCA
3637068 AA
1 AA
3637070 ATGACTTCTA
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
8 79 0.93
10 6 0.07
ACGTcount: A:0.38, C:0.30, G:0.01, T:0.31
Consensus pattern (8 bp):
AACTCTCA
Found at i:3637646 original size:59 final size:60
Alignment explanation
Indices: 3637551--3637701 Score: 214
Period size: 59 Copynumber: 2.5 Consensus size: 60
3637541 ATAGGGATGT
* ** * * * *
3637551 ATTCATCTGCCAACTTCTTTGACGTCAATATGGATATGCCTTTTAGTTCC-AGGGGAGAC
1 ATTCATCTGCCAGCTTCTTCAACCTCAATATAGATATGCCTTCTAGTTCCAAGGGGAAAC
*
3637610 ATTCATCTGCTAGCTTCTTCAACCTCAATATAGATATGCCTTCTAGTTCCAAGGGGAAAC
1 ATTCATCTGCCAGCTTCTTCAACCTCAATATAGATATGCCTTCTAGTTCCAAGGGGAAAC
*
3637670 ATTCATCTTCCAGCTTCTTCAACCTCAATATA
1 ATTCATCTGCCAGCTTCTTCAACCTCAATATA
3637702 CAGATGTTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 43 0.53
60 38 0.47
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (60 bp):
ATTCATCTGCCAGCTTCTTCAACCTCAATATAGATATGCCTTCTAGTTCCAAGGGGAAAC
Found at i:3639570 original size:18 final size:19
Alignment explanation
Indices: 3639542--3639577 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3639532 AAACCTAAAA
3639542 ACAATTAAATGAAAATATT
1 ACAATTAAATGAAAATATT
3639561 ACAA-TAAATGAAAATAT
1 ACAATTAAATGAAAATAT
3639578 CATCAACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (19 bp):
ACAATTAAATGAAAATATT
Found at i:3641657 original size:14 final size:14
Alignment explanation
Indices: 3641638--3641665 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3641628 ATAAATTATT
3641638 TAAATAAATTCTAA
1 TAAATAAATTCTAA
3641652 TAAATAAATTCTAA
1 TAAATAAATTCTAA
3641666 CGATTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAATAAATTCTAA
Found at i:3641987 original size:21 final size:21
Alignment explanation
Indices: 3641961--3642009 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
3641951 AATTTTGGAT
3641961 GTGGTTTGTATGAGGTAAGGG
1 GTGGTTTGTATGAGGTAAGGG
3641982 GTGGTTTGTATGAGGTAAGGG
1 GTGGTTTGTATGAGGTAAGGG
3642003 GTGGTTT
1 GTGGTTT
3642010 ATATAGGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.37
Consensus pattern (21 bp):
GTGGTTTGTATGAGGTAAGGG
Found at i:3643387 original size:14 final size:12
Alignment explanation
Indices: 3643351--3643384 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3643341 TATAATCACA
3643351 TATTTGATATTTT
1 TATTT-ATATTTT
3643364 TATTTATATTTT
1 TATTTATATTTT
3643376 TATTTATAT
1 TATTTATAT
3643385 ATTCTCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (12 bp):
TATTTATATTTT
Found at i:3643735 original size:29 final size:30
Alignment explanation
Indices: 3643641--3643735 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
3643631 TACTTTTTCT
*
3643641 TCTTAATTTATTAAATACATTTTATTCTTA
1 TCTTAATTTATTAAATATATTTTATTCTTA
* *
3643671 ACTTAATTTATTAAATAT-TTTATATTATTA
1 TCTTAATTTATTAAATATATTT-TATTCTTA
* *
3643701 -CTTTAAATT-TTAAATATATTTTATTCCTA
1 TC-TTAATTTATTAAATATATTTTATTCTTA
3643730 TCTTAA
1 TCTTAA
3643736 CTTAAAAGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
29 22 0.40
30 33 0.60
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (30 bp):
TCTTAATTTATTAAATATATTTTATTCTTA
Found at i:3643797 original size:29 final size:29
Alignment explanation
Indices: 3643765--3643863 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
3643755 AAAAGTTACT
*
3643765 TTATTCATATCTTAACTTATATATATATA
1 TTATTCTTATCTTAACTTATATATATATA
* * * * *
3643794 TTATTCTTATTTTAACTTAAAAACACATA
1 TTATTCTTATCTTAACTTATATATATATA
*
3643823 TTTATTCTTAACTTAACTTAATATATATATA
1 -TTATTCTTATCTTAACTT-ATATATATATA
*
3643854 TATAATCTTA
1 T-TATTCTTA
3643864 ATTTAAACAT
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 23 0.43
30 17 0.31
31 14 0.26
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (29 bp):
TTATTCTTATCTTAACTTATATATATATA
Found at i:3648108 original size:30 final size:30
Alignment explanation
Indices: 3648072--3648144 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
3648062 TCTGAAGGAC
3648072 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3648102 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
3648132 CTGTCCATAGGTC
1 CTATCCAGAGGTC
3648145 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3648161 original size:30 final size:30
Alignment explanation
Indices: 3648118--3648211 Score: 80
Period size: 31 Copynumber: 3.1 Consensus size: 30
3648108 AGAGGTCATA
* * *
3648118 AAGATCCTCGGTAACTGTCCATAGGTCCCG
1 AAGAACCTAGGTAACTGTCCATATGTCCCG
* * * *
3648148 AAGAACCTAGGTAAACTATACATATGTTCCT
1 AAGAACCTAGGT-AACTGTCCATATGTCCCG
* * *
3648179 TAGAACATAGGTATACTGTCCATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCCATATGTCCCG
3648210 AA
1 AA
3648212 AGACATAGGT
Statistics
Matches: 47, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
30 11 0.23
31 36 0.77
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCCATATGTCCCG
Found at i:3649400 original size:64 final size:63
Alignment explanation
Indices: 3649299--3649419 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 63
3649289 CTTTAGCACG
* *
3649299 TGCATCGATGCACAAAATCACCTTCGATGTTTTCATTTTAAGGGGATGCATCGATGCAATCCTTA
1 TGCATCGATGCACAAAATCA-CTTCGATGTTTCCATTTTAAGAGG-TGCATCGATGCAATCCTTA
* * *
3649364 TGCATCGATGCACCAATTGCA-TTCGATGTTTCCATTTTAATAGGTGCATCGATGCA
1 TGCATCGATGCACAAAAT-CACTTCGATGTTTCCATTTTAAGAGGTGCATCGATGCA
3649420 CTTCCTGTGC
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 12 0.24
64 20 0.40
65 16 0.32
66 2 0.04
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (63 bp):
TGCATCGATGCACAAAATCACTTCGATGTTTCCATTTTAAGAGGTGCATCGATGCAATCCTTA
Found at i:3649432 original size:63 final size:64
Alignment explanation
Indices: 3649298--3649440 Score: 166
Period size: 63 Copynumber: 2.2 Consensus size: 64
3649288 TCTTTAGCAC
* *
3649298 GTGCATCGATGCACAAAATCACCTTCGATGTTTTCATTTTAAGGGGATGCATCGATGCAATCCTT
1 GTGCATCGATGCACAAAATCA-CTTCGATGTTTCCATTTTAAGAGGATGCATCGATGCAATCCTT
* * * * *
3649363 ATGCATCGATGCACCAATTGCA-TTCGATGTTTCCATTTTAATAGG-TGCATCGATGCACTTCC-
1 GTGCATCGATGCACAAAAT-CACTTCGATGTTTCCATTTTAAGAGGATGCATCGATGCA-ATCCT
3649425 T
64 T
*
3649426 GTGCATCGATACACA
1 GTGCATCGATGCACA
3649441 CTGAACAATT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 25 0.38
64 23 0.35
65 16 0.24
66 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCACAAAATCACTTCGATGTTTCCATTTTAAGAGGATGCATCGATGCAATCCTT
Found at i:3652875 original size:30 final size:30
Alignment explanation
Indices: 3652839--3652941 Score: 188
Period size: 30 Copynumber: 3.4 Consensus size: 30
3652829 TCCGAAGGAC
3652839 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3652869 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3652899 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
3652929 CTGTCCATAGGTC
1 CTATCCAGAGGTC
3652942 CCGAAGAACC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3652958 original size:60 final size:61
Alignment explanation
Indices: 3652839--3652964 Score: 182
Period size: 60 Copynumber: 2.1 Consensus size: 61
3652829 TCCGAAGGAC
* * *
3652839 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGT-AA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
* * * *
3652899 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
3652960 CTATC
1 CTATC
3652965 TATATGTTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
60 51 0.88
61 7 0.12
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (61 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
Found at i:3654179 original size:64 final size:63
Alignment explanation
Indices: 3654111--3654230 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 63
3654101 ACAGTACCCG
* * *
3654111 TGCATCGATGCACAAATCACCTTCGATGTTTTCATTTTAAGGGGATGCATCGATGCACTCCTTA
1 TGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAGG-TGCATCGATGCACTCCTTA
* ** *
3654175 TGCATCGATGCACCAATTGCATTCGATGTTTCCATTTTAATAGGTGCATCGATGCA
1 TGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAGGTGCATCGATGCA
3654231 TCGATGCACT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 12 0.24
64 37 0.76
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (63 bp):
TGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAGGTGCATCGATGCACTCCTTA
Found at i:3656699 original size:19 final size:19
Alignment explanation
Indices: 3656662--3656704 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3656652 TTTTTTAATA
3656662 AAATTATTAATTTACTTTT
1 AAATTATTAATTTACTTTT
* *
3656681 TAATTAATTAATTT-TTTTT
1 AAATT-ATTAATTTACTTTT
3656700 AAATT
1 AAATT
3656705 TAATCCAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
AAATTATTAATTTACTTTT
Found at i:3656708 original size:20 final size:19
Alignment explanation
Indices: 3656663--3656701 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3656653 TTTTTAATAA
3656663 AATT-ATTAATTTACTTTTT
1 AATTAATTAATTTA-TTTTT
3656682 AATTAATTAATTT-TTTTT
1 AATTAATTAATTTATTTTT
3656700 AA
1 AA
3656702 ATTTAATCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTAATTAATTTATTTTT
Found at i:3676739 original size:3 final size:3
Alignment explanation
Indices: 3676731--3676767 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3676721 TCTAATTGTA
3676731 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3676768 GCTTATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3677913 original size:19 final size:19
Alignment explanation
Indices: 3677867--3677913 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
3677857 CATTAATTTG
*
3677867 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
3677887 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
3677907 TATATTT
1 TATATTT
3677914 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:3680658 original size:27 final size:30
Alignment explanation
Indices: 3680623--3680682 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
3680613 TTATTTTACA
3680623 TGTACTAACTTA-TT-TTCTCTTTTGTTTG
1 TGTACTAACTTATTTCTTCTCTTTTGTTTG
3680651 TGTA-TAACTTATTTCTTCTCTTTTGTTTG
1 TGTACTAACTTATTTCTTCTCTTTTGTTTG
3680680 TGT
1 TGT
3680683 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 7 0.23
28 6 0.20
29 17 0.57
ACGTcount: A:0.13, C:0.13, G:0.12, T:0.62
Consensus pattern (30 bp):
TGTACTAACTTATTTCTTCTCTTTTGTTTG
Found at i:3682784 original size:22 final size:20
Alignment explanation
Indices: 3682755--3682802 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
3682745 TATTAAAGCG
3682755 AAAAGAAAAAAAAAAGCAACA
1 AAAAGAAAAAAAAAAG-AACA
**
3682776 ACAAAGAAAAAGCAAAGAACA
1 A-AAAGAAAAAAAAAAGAACA
3682797 AAAAGA
1 AAAAGA
3682803 GGACAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.21
21 6 0.25
22 13 0.54
ACGTcount: A:0.77, C:0.10, G:0.12, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAAAAGAACA
Found at i:3682796 original size:18 final size:17
Alignment explanation
Indices: 3682756--3682814 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
3682746 ATTAAAGCGA
3682756 AAAGAA-AAAAAAAAGC
1 AAAGAACAAAAAAAAGC
*
3682772 -AACAACAAAGAAAAAGC
1 AAAGAACAAA-AAAAAGC
* *
3682789 AAAGAACAAAAAGAGGAC
1 AAAGAACAAAAAAAAG-C
3682807 AAAGAACA
1 AAAGAACA
3682815 CAGACAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 4 0.11
16 3 0.09
17 11 0.31
18 17 0.49
ACGTcount: A:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAGAACAAAAAAAAGC
Found at i:3683982 original size:4 final size:4
Alignment explanation
Indices: 3683973--3684007 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
3683963 GAAAGTATAC
3683973 ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
3684008 AAATTTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 27 0.93
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:3683992 original size:18 final size:18
Alignment explanation
Indices: 3683969--3684007 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
3683959 ATCGGAAAGT
3683969 ATACACATACATACATAC
1 ATACACATACATACATAC
3683987 ATACACATACATACATAC
1 ATACACATACATACATAC
3684005 ATA
1 ATA
3684008 AAATTTGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (18 bp):
ATACACATACATACATAC
Found at i:3683994 original size:14 final size:14
Alignment explanation
Indices: 3683977--3684005 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3683967 GTATACACAT
3683977 ACATACATACATAC
1 ACATACATACATAC
3683991 ACATACATACATAC
1 ACATACATACATAC
3684005 A
1 A
3684006 TAAAATTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
ACATACATACATAC
Found at i:3684643 original size:105 final size:101
Alignment explanation
Indices: 3684457--3684694 Score: 275
Period size: 105 Copynumber: 2.3 Consensus size: 101
3684447 TGAGAATTTT
** * *
3684457 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTGAGATACAAATTTTGAATTTGATTCACTA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTGAGATACAAATTTCGAATTTGATTCACTA
*
3684522 AAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 AAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * *
3684561 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCC-TTGAGATACAAATTTCGAATTTGATTCACT
* * *
3684625 ATTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
65 A-AAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
* *
3684663 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTC
3684695 TCTAAAAAAA
Statistics
Matches: 116, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
101 2 0.02
102 29 0.25
103 4 0.03
104 35 0.30
105 46 0.40
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (101 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTGAGATACAAATTTCGAATTTGATTCACTA
AAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:3684685 original size:36 final size:35
Alignment explanation
Indices: 3684640--3684723 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 35
3684630 ACAAAGTTGA
**
3684640 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAA-AAACTTTG
* *
3684676 TCTCGCTTGAGACAATTTCTCTAAAAAAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAAAAACTTTG
*
3684711 TCTCATTTGAGAC
1 TCTCACTTGAGAC
3684724 TATATCTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 25 0.61
36 16 0.39
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (35 bp):
TCTCACTTGAGACAATTTCTCTAAAAAAAACTTTG
Found at i:3684711 original size:35 final size:35
Alignment explanation
Indices: 3684656--3684754 Score: 96
Period size: 35 Copynumber: 2.9 Consensus size: 35
3684646 TTGAGATCGT
*
3684656 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAA-AAATTTTGTCTCGCTTGAGACAA
** *
3684691 TTTCTCTAAAAAAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAAAAATTTTGTCTCGCTTGAGACAA
* **
3684726 TATCT-TAAAGCAAATTTCT-TCTCGCTTGA
1 TTTCTCTAAAAAAAATTT-TGTCTCGCTTGA
3684755 TACATCATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
34 18 0.34
35 30 0.57
36 5 0.09
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.38
Consensus pattern (35 bp):
TTTCTCTAAAAAAAATTTTGTCTCGCTTGAGACAA
Found at i:3685104 original size:29 final size:27
Alignment explanation
Indices: 3684994--3685124 Score: 208
Period size: 27 Copynumber: 4.7 Consensus size: 27
3684984 TTAAAGACAA
3684994 TTTGTTCCTCTTGAAAAAATCTTTGAG
1 TTTGTTCCTCTTGAAAAAATCTTTGAG
3685021 TTTGTTCCTCTTGAAAAAATCTTTGAG
1 TTTGTTCCTCTTGAAAAAATCTTTGAG
3685048 TTTGTTCCTCTTGAAAAAATCTTTGAG
1 TTTGTTCCTCTTGAAAAAATCTTTGAG
* *
3685075 TTTGTTCCTTTTGAATAAAAATCTTGGAG
1 TTTGTTCCTCTTG-A-AAAAATCTTTGAG
*
3685104 TTTGTTCCTTTTGAATAAAAT
1 TTTGTTCCTCTTGAA-AAAAT
3685125 TTTTTTAAGT
Statistics
Matches: 99, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
27 67 0.68
28 7 0.07
29 25 0.25
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.46
Consensus pattern (27 bp):
TTTGTTCCTCTTGAAAAAATCTTTGAG
Found at i:3685252 original size:52 final size:53
Alignment explanation
Indices: 3685174--3685276 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
3685164 CTATTTATTT
*
3685174 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGT-GAAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTAAAAAAATCTTTGAGTC
*
3685226 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTAAAAAAATCTTTGAG
3685277 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 35 0.73
53 13 0.27
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTAAAAAAATCTTTGAGTC
Found at i:3685430 original size:98 final size:98
Alignment explanation
Indices: 3685227--3685492 Score: 395
Period size: 98 Copynumber: 2.8 Consensus size: 98
3685217 CTTTGAGTCT
* * * *
3685227 GAAACAAAGTTTTGTCTCTCTTGAGACAA----TTTTGTAAAAAAATCTTTGAGATTGTTTCTTT
1 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAAAAAATCTTTGAGATTGTTTCTTT
3685288 TGAAAC--AAAAATCTTTGAGTTGGTTTCTTTG
66 TGAAACAAAAAAATCTTTGAGTTGGTTTCTTTG
3685319 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAAAAAATCTTTGAGATTGTTTCTTT
1 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAAAAAATCTTTGAGATTGTTTCTTT
3685384 TGAAACAAAAAAATCTTTGAGTCT-GTTTCTTTG
66 TGAAACAAAAAAATCTTTGAGT-TGGTTTCTTTG
*
3685417 GAAACAAAATTTTGTCTCTTTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAG-TCTGTTTCT
1 GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAA-AAAAATCTTTGAGAT-TGTTTCT
*
3685481 TTGGAAACAAAA
64 TTTGAAACAAAA
3685493 TTTTGTCTCT
Statistics
Matches: 159, Mismatches: 6, Indels: 11
0.90 0.03 0.06
Matches are distributed among these distances:
92 26 0.16
96 37 0.23
98 64 0.40
99 32 0.20
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (98 bp):
GAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAAAAAATCTTTGAGATTGTTTCTTT
TGAAACAAAAAAATCTTTGAGTTGGTTTCTTTG
Found at i:3685450 original size:37 final size:36
Alignment explanation
Indices: 3685409--3685534 Score: 101
Period size: 37 Copynumber: 3.6 Consensus size: 36
3685399 TTTGAGTCTG
3685409 TTTCTTTGGAAACAAAAT-TTTGTCTCTTTTAAGATAA
1 TTTCTTTGGAAACAAAATCTTTGTCTC-TTTAAGAT-A
* **
3685446 TTTCTTTTGAAACAAAAATCTTTGAGTC--T--G---
1 TTTCTTTGGAAAC-AAAATCTTTGTCTCTTTAAGATA
3685476 TTTCTTTGGAAACAAAAT-TTTGTCTCTCTTAAGATA
1 TTTCTTTGGAAACAAAATCTTTGTCTCT-TTAAGATA
*
3685512 TTTTCTTTTGAAA-AAAATCTTTG
1 -TTTCTTTGGAAACAAAATCTTTG
3685535 AATCTGTTTC
Statistics
Matches: 70, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
28 6 0.09
29 5 0.07
30 12 0.17
31 1 0.01
33 1 0.01
34 1 0.01
36 6 0.09
37 27 0.39
38 5 0.07
39 6 0.09
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (36 bp):
TTTCTTTGGAAACAAAATCTTTGTCTCTTTAAGATA
Found at i:3685476 original size:67 final size:67
Alignment explanation
Indices: 3685377--3685545 Score: 279
Period size: 67 Copynumber: 2.5 Consensus size: 67
3685367 TTTGAGATTG
*
3685377 TTTCTTTTGAAACAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAG
1 TTTCTTTTGAAAC--AAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAG
3685442 ATAA
64 ATAA
3685446 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
*
3685511 AT
66 AA
*
3685513 TTTCTTTTG-AA-AAAAATCTTTGAATCTGTTTCT
1 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCT
3685546 CTTAAAATGA
Statistics
Matches: 97, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
65 21 0.22
66 2 0.02
67 61 0.63
69 13 0.13
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:3685569 original size:67 final size:65
Alignment explanation
Indices: 3685390--3685609 Score: 210
Period size: 67 Copynumber: 3.3 Consensus size: 65
3685380 CTTTTGAAAC
* * * * *
3685390 AAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGATAATTTCTTTTG
1 AAAAAAATCTTTGAATCTGTTTCTTTGAAAACAAAATGTTATCTCTCTTAAGATAATTTCTTTTG
* * * * *
3685455 AAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATATTTTCTTT
1 -AA-AAAAATCTTTGAATCTGTTTCTTTGAAAACAAAATGTTATCTCTCTTAAGATAATTTCTTT
3685520 TG
64 TG
* * * *
3685522 AAAAAAATCTTTGAATCTGTTTCTCTT-AAAATGAATTATGTTATCTCTCTTGAA-ACAGTTTCT
1 AAAAAAATCTTTGAATCTGTTTCT-TTGAAAA-CAA-AATGTTATCTCTCTT-AAGATAATTTCT
*
3685585 CTTG
62 TTTG
** *
3685589 AAGTAAATCTTTGAATATGTT
1 AAAAAAATCTTTGAATCTGTT
3685610 CATTTTGAAA
Statistics
Matches: 135, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
65 24 0.18
66 8 0.06
67 101 0.75
68 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (65 bp):
AAAAAAATCTTTGAATCTGTTTCTTTGAAAACAAAATGTTATCTCTCTTAAGATAATTTCTTTTG
Found at i:3685823 original size:120 final size:121
Alignment explanation
Indices: 3685649--3685873 Score: 262
Period size: 120 Copynumber: 1.9 Consensus size: 121
3685639 TTAACAAAAT
* * * *
3685649 CATCTTTGAGTCTATTTCTTTAAAAACATATGTTATCTCTCTTGAGACAGTTTCTAATGA-AAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTATATCTCTTAAGACAATTTCTAATGAGAAAA
*
3685713 CTAA-CTTTTGAGATTGTTTCATTTGAAACAAA-TTTGGTCTTACTTAAGATGTAATC
66 -AAATC-TTTGAGATTGTTTCATTTGAAACAAACTTTGGTCTTACTTAAGATGTAATC
* ** **
3685769 CATCTTTGAGTCTGTTTCTTTTGAAACAAAAT-TT-TATCTCTTAATGACAATTTCTTTTGAGAA
1 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTATATCTCTTAA-GACAATTTCTAATGAGAA
* * *
3685832 AAAAATCTTTGAGTTTGTTTCCTTTGAAACAAACTTTTGTCT
64 AAAAATCTTTGAGATTGTTTCATTTGAAACAAACTTTGGTCT
3685874 CTCGAGACAA
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
119 8 0.09
120 64 0.74
121 15 0.17
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (121 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAATGTTATATCTCTTAAGACAATTTCTAATGAGAAAA
AAATCTTTGAGATTGTTTCATTTGAAACAAACTTTGGTCTTACTTAAGATGTAATC
Found at i:3685851 original size:66 final size:65
Alignment explanation
Indices: 3685770--3685893 Score: 185
Period size: 66 Copynumber: 1.9 Consensus size: 65
3685760 GATGTAATCC
* *
3685770 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAATGACAATTTCTTTTGAGAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTCAA-GACAATTTCTTTTGAGAAAAA
3685835 A
65 A
* * * *
3685836 ATCTTTGAGTTTGTTTCCTTTGAAACAAACTTTTGTCTCTCGAGACAATTTCTTTTGA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTCAAGACAATTTCTTTTGA
3685894 AAATACACAC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
65 15 0.29
66 37 0.71
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (65 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTCAAGACAATTTCTTTTGAGAAAAAA
Found at i:3685918 original size:66 final size:65
Alignment explanation
Indices: 3685782--3685939 Score: 160
Period size: 66 Copynumber: 2.4 Consensus size: 65
3685772 CTTTGAGTCT
* * * * * *
3685782 GTTTCTTTTGAAACAAAATTTTATCTCTTAATGACAATTTCTTTTGAGAAAAAAATCTTTGAGTT
1 GTTTCCTTTGAAAC-AAATTTTGTCTCTCAATGACAATTTCTTTTGAGAAAAAAACCTTCGAGAT
*
3685847 T
65 C
* *
3685848 GTTTCCTTTGAAACAAACTTTTGTCTCTCGA-GACAATTTCTTTTGA-AAATACACACCTTCGAG
1 GTTTCCTTTGAAACAAA-TTTTGTCTCTCAATGACAATTTCTTTTGAGAAA-A-AAACCTTCGAG
3685911 ATC
63 ATC
*
3685914 GTTT-CTATTAAAACAAATTTTGTCTC
1 GTTTCCT-TTGAAACAAATTTTGTCTC
3685940 CCTTAAGACA
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
64 3 0.04
65 30 0.38
66 45 0.58
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (65 bp):
GTTTCCTTTGAAACAAATTTTGTCTCTCAATGACAATTTCTTTTGAGAAAAAAACCTTCGAGATC
Found at i:3686054 original size:15 final size:16
Alignment explanation
Indices: 3686013--3686059 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 16
3686003 CTTTGAGTCG
3686013 TTTCCCTTGAAACAAATT
1 TTTCCCTTGAAAC--ATT
3686031 TTGTCCCTTGAAACA-T
1 TT-TCCCTTGAAACATT
3686047 TTTCCCTT-AAACA
1 TTTCCCTTGAAACA
3686060 AGAACATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.18
15 6 0.21
16 3 0.11
17 1 0.04
18 2 0.07
19 11 0.39
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (16 bp):
TTTCCCTTGAAACATT
Found at i:3686237 original size:101 final size:101
Alignment explanation
Indices: 3686112--3686335 Score: 430
Period size: 101 Copynumber: 2.2 Consensus size: 101
3686102 TTAACATAAT
*
3686112 TCTTTTGAAGAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCACTAAGATACAA
1 TCTTTTCAA-AAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCACTAAGATACAA
3686177 TTTTCTGAAAAACAAAGTTTTGTCTCTTATGACAATG
65 TTTTCTGAAAAACAAAGTTTTGTCTCTTATGACAATG
3686214 TCTTTTCAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCACTAAGATACAAT
1 TCTTTTCAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCACTAAGATACAAT
3686279 TTTCTGAAAAACAAAGTTTTGTCTCTTATGACAATG
66 TTTCTGAAAAACAAAGTTTTGTCTCTTATGACAATG
3686315 TCTTTTCAAAAAAATCTTTGA
1 TCTTTTCAAAAAAATCTTTGA
3686336 ATTGAATCTC
Statistics
Matches: 121, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
101 113 0.93
102 8 0.07
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (101 bp):
TCTTTTCAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCACTAAGATACAAT
TTTCTGAAAAACAAAGTTTTGTCTCTTATGACAATG
Found at i:3686477 original size:35 final size:35
Alignment explanation
Indices: 3686431--3686526 Score: 176
Period size: 35 Copynumber: 2.7 Consensus size: 35
3686421 CAAAATTTAC
3686431 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
1 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
3686466 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
1 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
3686501 CATCTTTGAGATC-GTTTCCCTTGAAA
1 CATCTTTGA-ATCTGTTTCCCTTGAAA
3686527 TGAATTTTGT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
35 57 0.95
36 3 0.05
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (35 bp):
CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
Found at i:3686848 original size:28 final size:28
Alignment explanation
Indices: 3686798--3686851 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
3686788 TCAAAATCCA
* * *
3686798 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTCTCCATTGAAACAC
*
3686826 ATCTTTGAGTTGGTCTCCCTTGAAAC
1 ATCTTTGAGTTGGTCTCCATTGAAAC
3686852 CATTATCCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.43
Consensus pattern (28 bp):
ATCTTTGAGTTGGTCTCCATTGAAACAC
Found at i:3686933 original size:46 final size:45
Alignment explanation
Indices: 3686880--3687156 Score: 176
Period size: 40 Copynumber: 6.4 Consensus size: 45
3686870 CCAGCCGTCC
* *
3686880 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTTATCACC-TTAGATGGCCAGAACTCT
* * *
3686926 TCATCACGTATGAGCCGTGTCATTC-CC--CGA---CCAGATCTCT
1 TCATCACGTATGAGCCGTGTTA-TCACCTTAGATGGCCAGAACTCT
* ** * *
3686966 TCATCACGTATGAGCCGTG---TCACCCTAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTTATCACCTTAGATGGCCAGAAC-TCT
* *
3687008 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTTATCACC-TTAGATGGCCAGAACTCT
* * * *
3687054 TCATCACGTATGAGCCGTGTCATTC-CC--CGA---CCAGATCTCC
1 TCATCACGTATGAGCCGTGTTA-TCACCTTAGATGGCCAGAACTCT
* * * *
3687094 TCATCACGTAGGAGCCGTGTCA-C-CCTTAGATGACCAGACCTCT
1 TCATCACGTATGAGCCGTGTTATCACCTTAGATGGCCAGAACTCT
** *
3687137 TCATTGCGTATGAGCAGTGT
1 TCATCACGTATGAGCCGTGT
3687157 CGTCCCCACC
Statistics
Matches: 183, Mismatches: 29, Indels: 41
0.72 0.11 0.16
Matches are distributed among these distances:
36 2 0.01
37 2 0.01
38 3 0.02
39 2 0.01
40 59 0.32
41 1 0.01
42 23 0.13
43 28 0.15
45 5 0.03
46 53 0.29
47 5 0.03
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (45 bp):
TCATCACGTATGAGCCGTGTTATCACCTTAGATGGCCAGAACTCT
Found at i:3687092 original size:128 final size:129
Alignment explanation
Indices: 3686864--3687130 Score: 500
Period size: 128 Copynumber: 2.1 Consensus size: 129
3686854 TTATCCCTAG
3686864 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
* *
3686929 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCC-T
66 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTT
3686992 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
3687057 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTT
66 TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTT
*
3687121 AGATGACCAG
1 AGATAACCAG
3687131 ACCTCTTCAT
Statistics
Matches: 135, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
128 125 0.93
129 10 0.07
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
TCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTT
Found at i:3687332 original size:3 final size:3
Alignment explanation
Indices: 3687324--3687375 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
3687314 TCTAATTGTA
* *
3687324 ATT ATT ATT -TT A-T ATT ATT A-T ATT ATT ATT ATT ATG CTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
3687369 GTT ATT A
1 ATT ATT A
3687376 ATATATTACA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3689690 original size:22 final size:22
Alignment explanation
Indices: 3689665--3689708 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3689655 TCAAACGATG
*
3689665 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
3689687 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
3689709 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:3692790 original size:25 final size:21
Alignment explanation
Indices: 3692732--3692782 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
3692722 TAACAATTCC
3692732 CCGACCGAACTAATTCGATAG
1 CCGACCGAACTAATTCGATAG
3692753 CCGACCGAACTAATTCGATAG
1 CCGACCGAACTAATTCGATAG
3692774 CCGACCGAA
1 CCGACCGAA
3692783 TTAACTAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.31, G:0.20, T:0.16
Consensus pattern (21 bp):
CCGACCGAACTAATTCGATAG
Found at i:3695069 original size:21 final size:23
Alignment explanation
Indices: 3695036--3695082 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
3695026 TATTTACTAT
*
3695036 AAAGTTAAGAAAAATTAAAATAA
1 AAAGTTAAGAAAAATAAAAATAA
3695059 AAAG-TAA-AAAAATAAAAATAA
1 AAAGTTAAGAAAAATAAAAATAA
3695080 AAA
1 AAA
3695083 TATCAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.70
22 3 0.13
23 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (23 bp):
AAAGTTAAGAAAAATAAAAATAA
Found at i:3695072 original size:15 final size:14
Alignment explanation
Indices: 3695052--3695082 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3695042 AAGAAAAATT
3695052 AAAATAAAAAGTAAA
1 AAAATAAAAA-TAAA
3695067 AAAATAAAAATAAA
1 AAAATAAAAATAAA
3695081 AA
1 AA
3695083 TATCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:3697003 original size:2 final size:2
Alignment explanation
Indices: 3696998--3697027 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3696988 AGATCACAAC
3696998 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3697028 TTCATTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3700614 original size:14 final size:15
Alignment explanation
Indices: 3700586--3700614 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3700576 GGACCAGGTC
3700586 CTCCTATGTTTGCTG
1 CTCCTATGTTTGCTG
3700601 CTCCTATG-TTGCTG
1 CTCCTATGTTTGCTG
3700615 AGTTGAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.07, C:0.28, G:0.21, T:0.45
Consensus pattern (15 bp):
CTCCTATGTTTGCTG
Found at i:3710841 original size:2 final size:2
Alignment explanation
Indices: 3710834--3710868 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3710824 CCAAGATAGT
3710834 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3710869 TATTGTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3710968 original size:2 final size:2
Alignment explanation
Indices: 3710961--3711006 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3710951 ACTTCATGCA
3710961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3711003 -T AT A
1 AT AT A
3711007 AAAGAAAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3715511 original size:33 final size:34
Alignment explanation
Indices: 3715437--3715514 Score: 140
Period size: 34 Copynumber: 2.3 Consensus size: 34
3715427 CAAAAGGGGT
3715437 GGTGGGCACCGCCTAAATGGAAATTAACAAAGGG
1 GGTGGGCACCGCCTAAATGGAAATTAACAAAGGG
*
3715471 GGTGGGCACCGCCTAAATTGAAATTAACAAA-GG
1 GGTGGGCACCGCCTAAATGGAAATTAACAAAGGG
3715504 GGTGGGCACCG
1 GGTGGGCACCG
3715515 GCTTGGTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 13 0.30
34 30 0.70
ACGTcount: A:0.32, C:0.19, G:0.33, T:0.15
Consensus pattern (34 bp):
GGTGGGCACCGCCTAAATGGAAATTAACAAAGGG
Found at i:3717073 original size:20 final size:20
Alignment explanation
Indices: 3717043--3717080 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3717033 CCGTCCCCGA
3717043 ACCCGACCCG-AAATATTAT
1 ACCCGACCCGAAAATATTAT
3717062 ACCCGAACCCGAAAATATT
1 ACCCG-ACCCGAAAATATT
3717081 TTATATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.39, C:0.32, G:0.11, T:0.18
Consensus pattern (20 bp):
ACCCGACCCGAAAATATTAT
Found at i:3717121 original size:2 final size:2
Alignment explanation
Indices: 3717110--3717174 Score: 61
Period size: 2 Copynumber: 35.5 Consensus size: 2
3717100 AATAGATAAA
* * *
3717110 AT AT -T AT AT AT AT A- AT -T A- AT AT AA AA AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3717147 -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3717175 ATCGGGGCGG
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
1 6 0.11
2 48 0.89
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3717166 original size:34 final size:33
Alignment explanation
Indices: 3717073--3717156 Score: 141
Period size: 34 Copynumber: 2.5 Consensus size: 33
3717063 CCCGAACCCG
* *
3717073 AAAATATTTTATATATAATTAATATAAAATAGAT
1 AAAATATTATATATATAATTAATATAAAA-ATAT
3717107 AAAATATTATATATATAATTAATATAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAATAT
3717140 AAAATATTATATATATA
1 AAAATATTATATATATA
3717157 TATATATATA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 20 0.42
34 28 0.58
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (33 bp):
AAAATATTATATATATAATTAATATAAAAATAT
Found at i:3717174 original size:34 final size:33
Alignment explanation
Indices: 3717073--3717175 Score: 136
Period size: 34 Copynumber: 3.1 Consensus size: 33
3717063 CCCGAACCCG
* *
3717073 AAAATATTTTATATATAATTAATATAAAATAGAT
1 AAAATATTATATATATAATTAATAT-AAATATAT
*
3717107 AAAATATTATATATATAATTAATATAAAAATAT
1 AAAATATTATATATATAATTAATATAAATATAT
*
3717140 AAAATATTATATATAT-ATATATATATATATATAT
1 AAAATATTATATATATAAT-TA-ATATAAATATAT
3717174 AA
1 AA
3717176 TCGGGGCGGG
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
32 2 0.03
33 24 0.39
34 36 0.58
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (33 bp):
AAAATATTATATATATAATTAATATAAATATAT
Found at i:3723705 original size:15 final size:16
Alignment explanation
Indices: 3723677--3723708 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3723667 TCTCTCTCTT
3723677 AGAGAGAGAATGAGAA
1 AGAGAGAGAATGAGAA
3723693 AGAGAGA-AATGAGAA
1 AGAGAGAGAATGAGAA
3723708 A
1 A
3723709 ACCGACCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.06
Consensus pattern (16 bp):
AGAGAGAGAATGAGAA
Found at i:3736838 original size:21 final size:21
Alignment explanation
Indices: 3736721--3736858 Score: 68
Period size: 21 Copynumber: 6.7 Consensus size: 21
3736711 ACGCGAAATA
**
3736721 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
3736741 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
* *
3736761 AAAATCGCAACACGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
3736782 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
3736803 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
3736824 AGAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
3736844 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
3736859 ACACATAAAT
Statistics
Matches: 86, Mismatches: 28, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.44
21 45 0.52
22 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:3736887 original size:20 final size:20
Alignment explanation
Indices: 3736826--3737054 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
3736816 GATTTTCCAG
* ** *
3736826 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3736846 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3736866 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
3736886 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3736906 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3736926 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3736946 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3736966 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3736986 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3737006 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3737026 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3737046 AATCACAAC
1 AATCGCAAC
3737055 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3737777 original size:23 final size:23
Alignment explanation
Indices: 3737748--3737792 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3737738 AATTTGGTCT
3737748 TGGTCAATATC-CGGACTTTGATA
1 TGGTCAATA-CACGGACTTTGATA
*
3737771 TGGTCAATACACGGATTTTGAT
1 TGGTCAATACACGGACTTTGAT
3737793 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (23 bp):
TGGTCAATACACGGACTTTGATA
Done.