Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009463.1 Hibiscus syriacus cultivar Beakdansim tig00113726_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: 3931635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 20
Found at i:2522085 original size:84 final size:84
Alignment explanation
Indices: 2521901--2522076 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
2521891 CCCGACTCGC
*
2521901 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
2521966 CCCACCATTCAAGAGGCCA
66 CCCACCATTCAAGAGGCCA
2521985 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
* *
2522050 CCCACCGTTTAAGAGGCCA
66 CCCACCATTCAAGAGGCCA
2522069 CTGTCATC
1 CTGTCATC
2522077 GTTGAAGAGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCATTCAAGAGGCCA
Found at i:2522106 original size:84 final size:84
Alignment explanation
Indices: 2521901--2522106 Score: 288
Period size: 84 Copynumber: 2.5 Consensus size: 84
2521891 CCCGACTCGC
* * * *
2521901 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
2521966 CCCACCATTCAAGAGGCCA
66 CCCACCATTCAAGAGGCCA
* * *
2521985 CTGTCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
* *
2522050 CCCACCGTTTAAGAGGCCA
66 CCCACCATTCAAGAGGCCA
** *
2522069 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
2522107 CCCGATTCAC
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 108 0.96
85 4 0.04
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCATTCAAGAGGCCA
Found at i:2523483 original size:14 final size:14
Alignment explanation
Indices: 2523464--2523498 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2523454 TTGTTTAATA
2523464 GATTTGTAAAAGGT
1 GATTTGTAAAAGGT
*
2523478 GATTTGTAAAAGTT
1 GATTTGTAAAAGGT
2523492 GATTTGT
1 GATTTGT
2523499 TTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (14 bp):
GATTTGTAAAAGGT
Found at i:2523681 original size:20 final size:19
Alignment explanation
Indices: 2523614--2523664 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
2523604 TATCACAATG
2523614 CGAAATGAAAATCGC-A-A
1 CGAAATGAAAATCGCAACA
*
2523631 CG--A-GAGAATCGCAACA
1 CGAAATGAAAATCGCAACA
2523647 CGAAATGAAAATCGCAAC
1 CGAAATGAAAATCGCAAC
2523665 GCGCAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
15 2 0.07
16 3 0.11
17 2 0.07
18 1 0.04
19 11 0.41
ACGTcount: A:0.49, C:0.22, G:0.20, T:0.10
Consensus pattern (19 bp):
CGAAATGAAAATCGCAACA
Found at i:2523705 original size:19 final size:19
Alignment explanation
Indices: 2523677--2523807 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
2523667 GCAAATTAAA
*
2523677 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
2523696 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
* *
2523712 CTCG--TTGCAATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
2523729 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
2523743 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
2523762 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
2523778 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
2523795 TTTGCATTGCGAT
1 TTCGCATTGCGAT
2523808 AGTAATTTCC
Statistics
Matches: 81, Mismatches: 16, Indels: 30
0.64 0.13 0.24
Matches are distributed among these distances:
14 22 0.27
16 13 0.16
17 12 0.15
19 34 0.42
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:2523725 original size:33 final size:32
Alignment explanation
Indices: 2523681--2523807 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
2523671 ATTAAATTCG
2523681 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
2523714 CGTTGCAATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
2523747 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
2523780 CGTTGCGATTTTCATTTTGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2523808 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:2523782 original size:66 final size:66
Alignment explanation
Indices: 2523674--2523806 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
2523664 CGCGCAAATT
*
2523674 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
2523739 G
66 G
* * *
2523740 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
2523805 G
66 G
2523806 A
1 A
2523807 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
G
Found at i:2526116 original size:12 final size:12
Alignment explanation
Indices: 2526099--2526135 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
2526089 TCTTCGGGGA
*
2526099 CTTTTTGTTCTT
1 CTTTTTCTTCTT
2526111 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2526123 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2526135 C
1 C
2526136 AGGATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2527173 original size:20 final size:21
Alignment explanation
Indices: 2527148--2527199 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2527138 TTTTCCTAAT
*
2527148 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
2527168 TCGCAATGTGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2527189 TCGCAATGCGA
1 TCGCAATGCGA
2527200 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2527273 original size:20 final size:20
Alignment explanation
Indices: 2527184--2527275 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
2527174 TGTGAATTTG
* *
2527184 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
2527204 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
2527224 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
2527245 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
2527265 GAAAATCGCAA
1 GAAAATCGCAA
2527276 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:2527559 original size:19 final size:20
Alignment explanation
Indices: 2527509--2527559 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2527499 GAAAATGGCT
2527509 ATCGCAATT-CGAAATGAAAA
1 ATCGC-ATTGCGAAATGAAAA
**
2527529 ATCGCAAAGCGAAATG-AAA
1 ATCGCATTGCGAAATGAAAA
2527548 ATCGCATTGCGA
1 ATCGCATTGCGA
2527560 TTTTCATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCATTGCGAAATGAAAA
Found at i:2527739 original size:14 final size:14
Alignment explanation
Indices: 2527720--2527756 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2527710 CATCAATTAA
2527720 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2527734 ACAAATCATCTTTT
1 ACAAATCAACATTT
2527748 ACAAATCAA
1 ACAAATCAA
2527757 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2529652 original size:20 final size:20
Alignment explanation
Indices: 2529626--2529693 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
2529616 GAAACTTAAA
2529626 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
2529646 ATTGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
* **
2529666 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
2529685 ATCGCAACG
1 ATCGCAACG
2529694 ACAAAATTGC
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 13 0.33
20 26 0.67
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2529734 original size:14 final size:14
Alignment explanation
Indices: 2529682--2529772 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
2529672 ATGCGAAATG
2529682 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
2529696 AAAATTGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
2529715 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2529729 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
2529745 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2529761 AAAATCGCAACG
1 AAAATCGCAACG
2529773 CGAAACACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 9 0.15
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2529757 original size:32 final size:33
Alignment explanation
Indices: 2529666--2529777 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
2529656 GGAAATGGCT
2529666 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2529699 ATTGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
2529732 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2529764 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
2529778 CACAAATCGC
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 29 0.38
33 47 0.62
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2529785 original size:65 final size:66
Alignment explanation
Indices: 2529666--2529788 Score: 196
Period size: 65 Copynumber: 1.9 Consensus size: 66
2529656 GGAAATGGCT
* * *
2529666 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATTGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
2529731 A
66 A
2529732 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
2529789 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 1 0.02
65 36 0.68
66 16 0.30
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:2529823 original size:14 final size:14
Alignment explanation
Indices: 2529800--2529863 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 14
2529790 TGCGATTTTC
2529800 ATTTTG-CGTTGCG
1 ATTTTGTCGTTGCG
2529813 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
*
2529827 ATTTCATTTCGCATTGCG
1 ATTT--TGTCG--TTGCG
2529845 ATTTTGTCGTTGCG
1 ATTTTGTCGTTGCG
2529859 ATTTT
1 ATTTT
2529864 CATTTCGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 6 0.14
14 21 0.48
16 8 0.18
18 9 0.20
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
ATTTTGTCGTTGCG
Found at i:2529870 original size:33 final size:33
Alignment explanation
Indices: 2529789--2529879 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
2529779 ACAAATCGCA
* *
2529789 TTGCGATTTTCATTTTGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2529822 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2529854 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2529880 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:2529878 original size:19 final size:19
Alignment explanation
Indices: 2529784--2529899 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 19
2529774 GAAACACAAA
2529784 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* * *
2529803 TTGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
2529819 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
2529835 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
2529851 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
***
2529868 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATTTTCATT
2529887 TCCGCATTGCGAT
1 T-CGCATTGCGAT
2529900 AGTCATTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.19
15 3 0.04
16 11 0.14
17 4 0.05
18 12 0.16
19 21 0.27
20 11 0.14
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2529918 original size:20 final size:20
Alignment explanation
Indices: 2529864--2529907 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2529854 TTGCGATTTT
2529864 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
2529883 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
2529903 CATTT
1 CATTT
2529908 TCGTGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:2531784 original size:20 final size:20
Alignment explanation
Indices: 2531759--2531796 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2531749 AATAGTTTCT
2531759 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
2531779 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
2531797 GCAAATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:2532107 original size:22 final size:22
Alignment explanation
Indices: 2532080--2532123 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2532070 GATGGAGATA
2532080 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2532102 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2532124 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2532397 original size:20 final size:20
Alignment explanation
Indices: 2532291--2532425 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
2532281 CGCTTTGAAA
*
2532291 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
2532312 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
2532332 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
2532352 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
2532373 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
2532393 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
2532413 ATCGCATTGCGAT
1 ATCGCATTGCGAT
2532426 TTTACCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:2532397 original size:61 final size:61
Alignment explanation
Indices: 2532291--2532428 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
2532281 CGCTTTGAAA
* * * *
2532291 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
2532352 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
2532413 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
2532429 ACCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:2532444 original size:61 final size:61
Alignment explanation
Indices: 2532291--2532446 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
2532281 CGCTTTGAAA
* ** * * * *
2532291 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
2532352 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
2532413 ATCGCATTGCGATTTTACCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
2532447 TTACTTATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 77 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:2532456 original size:20 final size:21
Alignment explanation
Indices: 2532414--2532465 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
2532404 ATAGTCAGTA
2532414 TCGCATTGCGATTTTACCAAT
1 TCGCATTGCGATTTTACCAAT
* **
2532435 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
2532455 TCGCATTGCGA
1 TCGCATTGCGA
2532466 ATTTGCGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:2535753 original size:20 final size:20
Alignment explanation
Indices: 2535728--2535820 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
2535718 TTTTCCCAAT
2535728 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
2535748 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
2535768 CTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
2535789 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
2535810 TCGCAATGCGA
1 TCGCAATGCGA
2535821 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:2535773 original size:41 final size:41
Alignment explanation
Indices: 2535728--2535820 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
2535718 TTTTCCCAAT
*
2535728 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAC
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
2535769 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
2535810 TCGCAATGCGA
1 TCGCAATGCGA
2535821 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:2535833 original size:41 final size:41
Alignment explanation
Indices: 2535747--2535881 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
2535737 GAATAAGTAA
* * *
2535747 ATCGCAACGCGAATTGGGAAACTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
2535788 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
2535829 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
2535870 TTCGCAACGCGA
1 ATCGCAACGCGA
2535882 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:2535834 original size:20 final size:20
Alignment explanation
Indices: 2535809--2535923 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
2535799 AATTGGGAAA
*
2535809 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
2535829 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
2535850 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
2535870 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2535890 TTCGCAACGCGATATTGACT
1 ATCGCAACGCGATACTGACT
*
2535910 TTCGCAACGCGATA
1 ATCGCAACGCGATA
2535924 ATACATAATC
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 66 0.82
21 14 0.17
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2536139 original size:22 final size:22
Alignment explanation
Indices: 2536111--2536154 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2536101 CACTCTCTCA
2536111 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2536133 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2536155 TATCTAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2536443 original size:20 final size:20
Alignment explanation
Indices: 2536418--2536455 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2536408 CGATTCTCTC
2536418 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
2536438 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
2536456 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:2537795 original size:18 final size:18
Alignment explanation
Indices: 2537774--2537818 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2537764 TCCACTTCGG
*
2537774 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
2537792 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
2537810 AAGCCATCA
1 GAGCCATCA
2537819 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.44, G:0.13, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2538310 original size:20 final size:20
Alignment explanation
Indices: 2538285--2538330 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2538275 TAGTTTACTT
2538285 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* *
2538305 TCGCAACACGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
2538325 TCGCAA
1 TCGCAA
2538331 TGCGAAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:2538347 original size:18 final size:19
Alignment explanation
Indices: 2538324--2538372 Score: 82
Period size: 18 Copynumber: 2.6 Consensus size: 19
2538314 GGAAATGGCT
2538324 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
2538342 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2538361 ATCGCAATGCGA
1 ATCGCAATGCGA
2538373 TTTGTGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2538403 original size:14 final size:14
Alignment explanation
Indices: 2538384--2538441 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2538374 TTGTGTTTCG
2538384 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2538398 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2538414 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2538430 CGTTGCGATTTT
1 CGTTGCGATTTT
2538442 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2538418 original size:32 final size:33
Alignment explanation
Indices: 2538379--2538457 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
2538369 GCGATTTGTG
2538379 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
2538411 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
2538444 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
2538458 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:2538456 original size:19 final size:19
Alignment explanation
Indices: 2538398--2538515 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
2538388 GCGATTTTGT
2538398 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2538416 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
2538430 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
2538449 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
2538469 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
2538488 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
2538508 TGTTGCGA
1 CGTTGCGA
2538516 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:2540535 original size:19 final size:19
Alignment explanation
Indices: 2540513--2540580 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
2540503 ATCGCAACGA
*
2540513 GAAAATCGTAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2540532 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2540551 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
2540565 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
2540581 TTTTCATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 29 0.64
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:2540656 original size:20 final size:20
Alignment explanation
Indices: 2540599--2540656 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
2540589 TCGCATTGCG
* *
2540599 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
2540619 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2540639 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
2540657 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:2541715 original size:24 final size:24
Alignment explanation
Indices: 2541688--2541741 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2541678 GTATTCGAAA
* *
2541688 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
2541712 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
2541736 TTTGAT
1 TTTGAT
2541742 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:2541933 original size:12 final size:12
Alignment explanation
Indices: 2541916--2541940 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2541906 ATATAATCCT
2541916 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2541928 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2541940 G
1 G
2541941 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2543273 original size:19 final size:19
Alignment explanation
Indices: 2543251--2543381 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
2543241 GGAAATTACT
2543251 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2543270 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2543284 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
2543303 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
2543317 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
2543336 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
2543350 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2543369 ATCGCAACGCGAA
1 ATCGCAATGCGAA
2543382 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2543293 original size:33 final size:33
Alignment explanation
Indices: 2543251--2543377 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
2543241 GGAAATTACT
2543251 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
2543284 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
2543316 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
2543350 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2543378 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2543358 original size:66 final size:66
Alignment explanation
Indices: 2543252--2543384 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
2543242 GAAATTACTA
*
2543252 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2543317 T
66 T
*
2543318 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
2543383 T
66 T
2543384 T
1 T
2543385 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:2543399 original size:19 final size:20
Alignment explanation
Indices: 2543377--2543417 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2543367 AAATCGCAAC
2543377 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
2543396 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
2543416 GC
1 GC
2543418 TATTCTCTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.44
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:2543578 original size:14 final size:14
Alignment explanation
Indices: 2543559--2543595 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2543549 CATCAATTAA
2543559 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2543573 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2543587 ACAAATCAA
1 ACAAATCAA
2543596 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2545028 original size:42 final size:42
Alignment explanation
Indices: 2544982--2545065 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
2544972 CGATGACAGT
* * * *
2544982 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGAGACTCTCGAGGAATGATAGG
* * *
2545024 GGCCTCTTCAACGATAGGAGTAGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGAGACTCTCGAGGAATGATAGG
2545066 CGAGTCGGGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGAGACTCTCGAGGAATGATAGG
Found at i:2547082 original size:20 final size:20
Alignment explanation
Indices: 2547057--2547116 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
2547047 CTTTTGGTTG
2547057 AAATGAAAATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
* * *
2547077 AAATGAGAATCGCAACGCGG
1 AAATGAAAATCGCAACGAGA
**
2547097 AAATGACTATCGCAACGAGA
1 AAATGAAAATCGCAACGAGA
2547117 GAATCGCAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (20 bp):
AAATGAAAATCGCAACGAGA
Found at i:2547138 original size:33 final size:33
Alignment explanation
Indices: 2547081--2547179 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
2547071 ACGAGAAAAT
2547081 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
* * *
2547115 GAGAATCGCAACGCGAAATGACTACCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
2547148 GACAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
2547180 CGAAATGAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
33 42 0.75
34 14 0.25
ACGTcount: A:0.39, C:0.26, G:0.24, T:0.10
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:2547173 original size:19 final size:19
Alignment explanation
Indices: 2547151--2547201 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
2547141 GCGACCAGAC
2547151 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
2547170 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2547189 AATCGCAATGCGA
1 AATCGCAACGCGA
2547202 TTTGGTTTCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2547218 original size:18 final size:18
Alignment explanation
Indices: 2547197--2547240 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
2547187 AAAATCGCAA
*
2547197 TGCGATTTGGTTTCGCGT
1 TGCGATTTGATTTCGCGT
*
2547215 TGCGATTTTTATTTCGCGT
1 TGCGA-TTTGATTTCGCGT
2547234 TGCGATT
1 TGCGATT
2547241 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (18 bp):
TGCGATTTGATTTCGCGT
Found at i:2547231 original size:19 final size:19
Alignment explanation
Indices: 2547207--2547276 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 19
2547197 TGCGATTTGG
2547207 TTTCGCGTTGCGATTTTTA
1 TTTCGCGTTGCGATTTTTA
2547226 TTTCGCGTTGCGA---TTA
1 TTTCGCGTTGCGATTTTTA
* **
2547242 --TCTCGTTGCGATAGTTA
1 TTTCGCGTTGCGATTTTTA
2547259 TTTCCGCGTTGCGATTTT
1 TTT-CGCGTTGCGATTTT
2547277 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
14 10 0.24
16 3 0.07
17 3 0.07
19 14 0.34
20 11 0.27
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTTA
Found at i:2547866 original size:21 final size:21
Alignment explanation
Indices: 2547833--2547933 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
2547823 TGCGAAAGTA
* * *
2547833 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
2547854 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
2547874 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
2547896 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
2547917 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
2547934 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:2547889 original size:20 final size:20
Alignment explanation
Indices: 2547796--2547889 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
2547786 CGCTATGTAA
*
2547796 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
2547816 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
2547836 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
2547857 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
2547877 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
2547890 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:2547908 original size:41 final size:41
Alignment explanation
Indices: 2547817--2547951 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
2547807 AAAGTCAGTA
* * * ** *
2547817 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
2547857 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
2547899 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
2547940 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2547952 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:2547943 original size:21 final size:20
Alignment explanation
Indices: 2547878--2547970 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2547868 ATAGTCAGTA
*
2547878 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
2547899 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
2547919 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
2547940 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
2547960 TCGCATTGCGA
1 TCGCATTGCGA
2547971 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:2547952 original size:41 final size:41
Alignment explanation
Indices: 2547878--2547970 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
2547868 ATAGTCAGTA
2547878 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
2547919 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
2547960 TCGCATTGCGA
1 TCGCATTGCGA
2547971 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2548863 original size:2 final size:2
Alignment explanation
Indices: 2548856--2548891 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2548846 TATTTTTAAA
2548856 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
2548892 GGAAGAGTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2553477 original size:19 final size:19
Alignment explanation
Indices: 2553434--2553484 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2553424 AAATGACCAA
*
2553434 CAAATTCGCAACACGATCT
1 CAAATTCGCAACACGAACT
**
2553453 CAAATTCGCAATGCGAACT
1 CAAATTCGCAACACGAACT
*
2553472 CCAATTTCGCAAC
1 -CAAATTCGCAAC
2553485 CCAGTTTCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.22
Consensus pattern (19 bp):
CAAATTCGCAACACGAACT
Found at i:2553580 original size:40 final size:40
Alignment explanation
Indices: 2553533--2553681 Score: 167
Period size: 40 Copynumber: 3.7 Consensus size: 40
2553523 TGCGATTTTC
* * * *
2553533 CAAATTCGCAATGTGAATCTGT-AAA-TCGCAATACAGAAGT
1 CAAATTCGCAATGCG-AT-AGTCAAATTCGCAACACAAAAGT
2553573 CAAATTCGCAATGCGATAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAATGCGATAGTCAAATTCGCAACACAAAAGT
* * ** * *
2553613 CAAATTCGCAAAGCGATAGTCAAATTCACAATGCGATAGT
1 CAAATTCGCAATGCGATAGTCAAATTCGCAACACAAAAGT
*
2553653 CAAATTCGCAACGCGATAGTCAAATTCGC
1 CAAATTCGCAATGCGATAGTCAAATTCGC
2553682 GTTGTAAATC
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
38 2 0.02
39 5 0.05
40 88 0.93
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (40 bp):
CAAATTCGCAATGCGATAGTCAAATTCGCAACACAAAAGT
Found at i:2553581 original size:20 final size:20
Alignment explanation
Indices: 2553558--2553681 Score: 144
Period size: 20 Copynumber: 6.2 Consensus size: 20
2553548 AATCTGTAAA
2553558 TCGCAATACAGA-AGTCAAAT
1 TCGCAATAC-GATAGTCAAAT
*
2553578 TCGCAATGCGATAGTCAAAT
1 TCGCAATACGATAGTCAAAT
* * *
2553598 TCGCAACACAAAAGTCAAAT
1 TCGCAATACGATAGTCAAAT
2553618 TCGCAA-AGCGATAGTCAAAT
1 TCGCAATA-CGATAGTCAAAT
* *
2553638 TCACAATGCGATAGTCAAAT
1 TCGCAATACGATAGTCAAAT
**
2553658 TCGCAACGCGATAGTCAAAT
1 TCGCAATACGATAGTCAAAT
2553678 TCGC
1 TCGC
2553682 GTTGTAAATC
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.03
20 87 0.97
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
TCGCAATACGATAGTCAAAT
Found at i:2553862 original size:22 final size:22
Alignment explanation
Indices: 2553837--2553878 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2553827 GCGACATCCA
2553837 TCCCCATCTCCGACGAAATCTG
1 TCCCCATCTCCGACGAAATCTG
*
2553859 TCCCCATCTCCGGCGAAATC
1 TCCCCATCTCCGACGAAATC
2553879 CGTCTATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.43, G:0.14, T:0.21
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCTG
Found at i:2554277 original size:14 final size:14
Alignment explanation
Indices: 2554260--2554292 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2554250 ACGCGATTTT
2554260 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
*
2554274 ATTTTCTCGTTGCG
1 ATTTTCGCGTTGCG
2554288 ATTTT
1 ATTTT
2554293 TATTTTCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.18, G:0.21, T:0.52
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:2556276 original size:4 final size:4
Alignment explanation
Indices: 2556267--2556308 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
2556257 TTTTTCTGCA
* * *
2556267 TTAT TTAT TTAT TTAT TTAT TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
2556309 TCAGCGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:2556543 original size:21 final size:22
Alignment explanation
Indices: 2556479--2556549 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 22
2556469 CCTCCTATCA
* *
2556479 TTCAGGAGACCCCT-CCCACCG
1 TTCAAGAGGCCCCTGCCCACCG
* *
2556500 TTCAAGAGGCCCCTG-TCATCG
1 TTCAAGAGGCCCCTGCCCACCG
* *
2556521 TTCAAGAGGTCTC-GCCCACCG
1 TTCAAGAGGCCCCTGCCCACCG
2556542 TTCAAGAG
1 TTCAAGAG
2556550 CCCAATTCAT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.03
21 39 0.98
ACGTcount: A:0.21, C:0.37, G:0.23, T:0.20
Consensus pattern (22 bp):
TTCAAGAGGCCCCTGCCCACCG
Found at i:2557959 original size:69 final size:68
Alignment explanation
Indices: 2557883--2558055 Score: 223
Period size: 67 Copynumber: 2.6 Consensus size: 68
2557873 GTATACTTTG
2557883 TTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAA-TTGATAAGGAAATAAGAA
1 TTTGCTTGTTTAATTGAATTTGT--A---AAAGTTGATTTGTTTAATTTGATAAGGAAATAAGAA
2557946 TTA-T-TT
61 TTATTATT
** *
2557952 TTTGCTTGTTTAATTG-ATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATT
1 TTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTTGATAAGGAAATAAGAATTATT
2558016 ATT
66 ATT
*
2558019 TTTTCTTGTTTAATTG-ATTTGTAAAAGTTGATTTGTT
1 TTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTT
2558056 GTTTTAAATC
Statistics
Matches: 96, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
64 17 0.18
65 18 0.19
66 1 0.01
67 39 0.41
68 4 0.04
69 17 0.18
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.52
Consensus pattern (68 bp):
TTTGCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTTGATAAGGAAATAAGAATTATT
ATT
Found at i:2557991 original size:64 final size:67
Alignment explanation
Indices: 2557911--2558055 Score: 233
Period size: 67 Copynumber: 2.2 Consensus size: 67
2557901 TTTTACATTG
2557911 AAAGTTGATTTGTTTAA-TTGATAAGGAAATAAGAATTA-T-TTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTAATTTGATAAGGAAATAAGAATTATTATTTTTGCTTGTTTAATTGATTTG
2557973 TA
66 TA
** * *
2557975 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTATTTTTTCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTAATTTGATAAGGAAATAAGAATTATTATTTTTGCTTGTTTAATTGATTTG
2558040 TA
66 TA
2558042 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
2558056 GTTTTAAATC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
64 17 0.23
65 18 0.24
66 1 0.01
67 38 0.51
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (67 bp):
AAAGTTGATTTGTTTAATTTGATAAGGAAATAAGAATTATTATTTTTGCTTGTTTAATTGATTTG
TA
Found at i:2558249 original size:20 final size:20
Alignment explanation
Indices: 2558205--2558243 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2558195 TCGCGTTGTG
* *
2558205 AATTTGACTTTCGCATTGCA
1 AATTTGACTATCGCAATGCA
2558225 AATTTGACTATCGCAATGC
1 AATTTGACTATCGCAATGC
2558244 TTATTTTGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (20 bp):
AATTTGACTATCGCAATGCA
Found at i:2558554 original size:6 final size:6
Alignment explanation
Indices: 2558543--2558577 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2558533 AATCAAAAGA
**
2558543 GATTTT GATTTT GATTTT GATTGC GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
2558578 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:2559553 original size:18 final size:18
Alignment explanation
Indices: 2559530--2559566 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2559520 CAAAATTTAT
2559530 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2559548 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2559566 A
1 A
2559567 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2560462 original size:18 final size:18
Alignment explanation
Indices: 2560439--2560474 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2560429 AAGCCGGTTG
2560439 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
2560457 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
2560475 CATTTTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:2562676 original size:24 final size:24
Alignment explanation
Indices: 2562625--2562676 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2562615 ATCCGAGTAT
** *
2562625 TGACCAAGATCAAAGTTTGGGTAT
1 TGACCAAGATCAAAGTTTGAATAC
2562649 TGACCAAGATCAAA-TTTCGAATAC
1 TGACCAAGATCAAAGTTT-GAATAC
2562673 TGAC
1 TGAC
2562677 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTTGAATAC
Found at i:2562809 original size:12 final size:12
Alignment explanation
Indices: 2562788--2562821 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2562778 GGTTGTGGGT
*
2562788 TTTGAGATTGTG
1 TTTGATATTGTG
2562800 TTTGATATTGTG
1 TTTGATATTGTG
*
2562812 TTTGGTATTG
1 TTTGATATTG
2562822 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2563483 original size:22 final size:24
Alignment explanation
Indices: 2563445--2563491 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
2563435 AATAGAGATG
*
2563445 GGGAAGGGAGTGTCGTTTGATATA
1 GGGAAGGGAGTGTCGTTGGATATA
2563469 GGGAA-GGA-TGTCGTTGGATATA
1 GGGAAGGGAGTGTCGTTGGATATA
2563491 G
1 G
2563492 AACAGATGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
23 3 0.14
24 5 0.23
ACGTcount: A:0.26, C:0.04, G:0.43, T:0.28
Consensus pattern (24 bp):
GGGAAGGGAGTGTCGTTGGATATA
Found at i:2563641 original size:19 final size:18
Alignment explanation
Indices: 2563598--2563644 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2563588 CAAAACATTT
2563598 GTGTTGCGAAACTAAAAC
1 GTGTTGCGAAACTAAAAC
* * *
2563616 CTGTTGCGAAATTAAATTC
1 GTGTTGCGAAACTAAA-AC
2563635 GTGTTGCGAA
1 GTGTTGCGAA
2563645 TTCGAAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (18 bp):
GTGTTGCGAAACTAAAAC
Found at i:2563678 original size:19 final size:20
Alignment explanation
Indices: 2563618--2563884 Score: 140
Period size: 20 Copynumber: 13.4 Consensus size: 20
2563608 ACTAAAACCT
* *
2563618 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* * *
2563637 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTCGA
2563657 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
*
2563676 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-CGA
** * *
2563697 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTCGA
* *
2563717 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGA
* *
2563737 GTTGCGAATTTG-ACTTCTA
1 GTTGCGAATTTGAAATTCGA
*
2563756 TGTTGCG-ATTTAAAAATTCGA
1 -GTTGCGAATTT-GAAATTCGA
* * *
2563777 GTTGCAAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGA
*
2563797 GTTGCGAATTTG-ACTATC-A
1 GTTGCGAATTTGAAAT-TCGA
* * *
2563816 CGTTGCGAATTTGAATTTTGT
1 -GTTGCGAATTTGAAATTCGA
* * *
2563837 GTTACGAATTTG-ACTTCTGT
1 GTTGCGAATTTGAAATTC-GA
* *
2563857 GTTGCG-ATTTACAAATTCGC
1 GTTGCGAATTT-GAAATTCGA
2563877 GTTGCGAA
1 GTTGCGAA
2563885 ATTGGAAACT
Statistics
Matches: 195, Mismatches: 37, Indels: 30
0.74 0.14 0.11
Matches are distributed among these distances:
19 43 0.22
20 121 0.62
21 31 0.16
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:2563861 original size:40 final size:39
Alignment explanation
Indices: 2563676--2563863 Score: 180
Period size: 40 Copynumber: 4.7 Consensus size: 39
2563666 TTGAAATTCA
*
2563676 GTTGCGAATTTGAAATTCCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTG-ACTT-CGCGTTGCGAATTTGACTTTTGT
* *
2563717 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTAT
1 GTTGCGAATTTGACT-TCGCGTTGCGAATTTGACTTTTGT
* * * * * * *
2563757 GTTGCG-ATTTAAAAATTCGAGTTGCAAATTTGACTATCGC
1 GTTGCGAATTT--GACTTCGCGTTGCGAATTTGACTTTTGT
* *
2563797 GTTGCGAATTTGACTATCACGTTGCGAATTTGAATTTTGT
1 GTTGCGAATTTGACT-TCGCGTTGCGAATTTGACTTTTGT
* *
2563837 GTTACGAATTTGACTTCTGTGTTGCGA
1 GTTGCGAATTTGACTTC-GCGTTGCGA
2563864 TTTACAAATT
Statistics
Matches: 117, Mismatches: 24, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
39 8 0.07
40 90 0.77
41 19 0.16
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (39 bp):
GTTGCGAATTTGACTTCGCGTTGCGAATTTGACTTTTGT
Found at i:2563863 original size:60 final size:60
Alignment explanation
Indices: 2563676--2563851 Score: 212
Period size: 60 Copynumber: 2.9 Consensus size: 60
2563666 TTGAAATTCA
* ** *
2563676 GTTGCGAATTTGAAATTCCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTG-ACTTCTACGTTGCGAATTTGAATTTTGTGTTGCGAATTTGACTATCGC
* * * * * *
2563737 GTTGCGAATTTGACTTCTATGTTGCG-ATTTAAAAATTCGAGTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTTCTACGTTGCGAATTT-GAATTTTGTGTTGCGAATTTGACTATCGC
*
2563797 GTTGCGAATTTGACTATC-ACGTTGCGAATTTGAATTTTGTGTTACGAATTTGACT
1 GTTGCGAATTTGACT-TCTACGTTGCGAATTTGAATTTTGTGTTGCGAATTTGACT
2563852 TCTGTGTTGC
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
59 4 0.04
60 73 0.77
61 18 0.19
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (60 bp):
GTTGCGAATTTGACTTCTACGTTGCGAATTTGAATTTTGTGTTGCGAATTTGACTATCGC
Found at i:2563925 original size:100 final size:99
Alignment explanation
Indices: 2563741--2563928 Score: 229
Period size: 100 Copynumber: 1.9 Consensus size: 99
2563731 TATCGCGTTG
*
2563741 CGAATTTGACTTCTATGTTGCGATTTAAAAATTCGAGTTGCAAATTTGACTATCGCGTTGCGAAT
1 CGAATTTGACTTCTATGTTGCGATTTAAAAATTCGAGTTGCAAATTGGACTA-CGCGTTGCGAAT
* * *
2563806 TTGACTATCACGTTGCGAATTTGAATTTTGTGTTA
65 TGGACTATCACATTACGAATTTGAATTTTGTGTTA
* * *
2563841 CGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGAAATTGGAAACTA-G-GTTGCGA
1 CGAATTTGACTTCTATGTTGCGATTTAAAAATTCGAGTTGC-AAATTGG--ACTACGCGTTGCG-
* *
2563904 AATTGGAGT-TCGCATTACGAATTTG
62 AATTGGACTATCACATTACGAATTTG
2563929 TTGGTCATTT
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
100 57 0.76
101 14 0.19
103 4 0.05
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (99 bp):
CGAATTTGACTTCTATGTTGCGATTTAAAAATTCGAGTTGCAAATTGGACTACGCGTTGCGAATT
GGACTATCACATTACGAATTTGAATTTTGTGTTA
Found at i:2565828 original size:31 final size:31
Alignment explanation
Indices: 2565793--2565853 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2565783 GTATGCGTCG
* *
2565793 TTAGTGGCGTTTACCAAAAAATGCCACCTTT
1 TTAGTGGAGTTTACCAAAAAATACCACCTTT
2565824 TTAGTGGAGTTTACCAAAAAATACCACCTT
1 TTAGTGGAGTTTACCAAAAAATACCACCTT
2565854 ATAAGAGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (31 bp):
TTAGTGGAGTTTACCAAAAAATACCACCTTT
Found at i:2571708 original size:223 final size:225
Alignment explanation
Indices: 2571318--2571766 Score: 884
Period size: 223 Copynumber: 2.0 Consensus size: 225
2571308 GGATCCCCTT
2571318 AAATATTTGTTGTAAATCTACTGCTATTAGACCCTTACGGATGAATGCTTGAACTACGATTTGAA
1 AAATATTTGTTGTAAATCTACTGCTATTAGACCCTTACGGATGAATGCTTGAACTACGATTTGAA
2571383 GCTTATCTTTAAGAAGTTTGGTTCGACCTCGTGTGATAGGGCCAAGTGGTTAGTAAATTCATCAT
66 GCTTATCTTTAAGAAGTTTGGTTCGACCTCGTGTGATAGGGCCAAGTGGTTAGTAAATTCATCAT
2571448 CCTTAGCTTTAGGGCGTGTGGTGCATGTATCATCTCCCCCTTCCTTAAAATGATTTGTCCACGAA
131 CCTTAGCTTTAGGGCGTGTGGTGCATGTATCATCTCCCCCTTCCTTAAAATGATTTGTCCACGAA
2571513 TCTGAAATATCAAAAGGAGATAAGTCAGAA
196 TCTGAAATATCAAAAGGAGATAAGTCAGAA
2571543 AAATATTTGTTGTAAATCTACTGCTATTAGACCC-TACGGATGAATGCTTGAACTACGA-TTGAA
1 AAATATTTGTTGTAAATCTACTGCTATTAGACCCTTACGGATGAATGCTTGAACTACGATTTGAA
2571606 GCTTATCTTTAAGAAGTTTGGTTCGACCTCGTGTGATAGGGCCAAGTGGTTAGTAAATTCATCAT
66 GCTTATCTTTAAGAAGTTTGGTTCGACCTCGTGTGATAGGGCCAAGTGGTTAGTAAATTCATCAT
2571671 CCTTAGCTTTAGGGCGTGTGGTGCATGTATCATCTCCCCCTTCCTTAAAATGATTTGTCCACGAA
131 CCTTAGCTTTAGGGCGTGTGGTGCATGTATCATCTCCCCCTTCCTTAAAATGATTTGTCCACGAA
2571736 TCTGAAATATCAAAAGGAGATAAGTCAGAA
196 TCTGAAATATCAAAAGGAGATAAGTCAGAA
2571766 A
1 A
2571767 TATTAAAGGA
Statistics
Matches: 224, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
223 166 0.74
224 24 0.11
225 34 0.15
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (225 bp):
AAATATTTGTTGTAAATCTACTGCTATTAGACCCTTACGGATGAATGCTTGAACTACGATTTGAA
GCTTATCTTTAAGAAGTTTGGTTCGACCTCGTGTGATAGGGCCAAGTGGTTAGTAAATTCATCAT
CCTTAGCTTTAGGGCGTGTGGTGCATGTATCATCTCCCCCTTCCTTAAAATGATTTGTCCACGAA
TCTGAAATATCAAAAGGAGATAAGTCAGAA
Found at i:2576263 original size:71 final size:71
Alignment explanation
Indices: 2576180--2576323 Score: 243
Period size: 71 Copynumber: 2.0 Consensus size: 71
2576170 AAAGCAAGAA
* * * *
2576180 ACCTCACAAGTCACTCCAAGAAAGTAATACATCGATAGGAAAGTAAGTCGATCTTATACTCTTTA
1 ACCTCACAAGTCACTCCAAGAAAGTAATACAACGATAGAAAAGTAAGCCAATCTTATACTCTTTA
2576245 AAACTC
66 AAACTC
*
2576251 ACCTCACAAGTCACTCCAAGAAAGTAATACAACGATATAAAAGTAAGCCAATCTTATACTCTTTA
1 ACCTCACAAGTCACTCCAAGAAAGTAATACAACGATAGAAAAGTAAGCCAATCTTATACTCTTTA
2576316 AAACTC
66 AAACTC
2576322 AC
1 AC
2576324 TTTACCAAGT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.24
Consensus pattern (71 bp):
ACCTCACAAGTCACTCCAAGAAAGTAATACAACGATAGAAAAGTAAGCCAATCTTATACTCTTTA
AAACTC
Found at i:2578318 original size:19 final size:18
Alignment explanation
Indices: 2578291--2578494 Score: 153
Period size: 19 Copynumber: 10.8 Consensus size: 18
2578281 TGATTAACGC
*
2578291 GGAAGCCTGATTTTGAGTT
1 GGAAACCTGATTTT-AGTT
2578310 GGAAACCTGATTTTAGATT
1 GGAAACCTGATTTTAG-TT
** *
2578329 -GAAAAATAAGTTTTAGGTT
1 GGAAACCTGA-TTTTA-GTT
*
2578348 GGAAACCTAATTTTAAGTT
1 GGAAACCTGATTTT-AGTT
*
2578367 GGAAACCTGATTTTACTTT
1 GGAAACCTGATTTTA-GTT
* *
2578386 GGAAAACAT-ATATTAGGTT
1 GG-AAACCTGATTTTA-GTT
*
2578405 GGGAACCTGATTTTAAGTT
1 GGAAACCTGATTTT-AGTT
*
2578424 GGAAACATGATTTTAGTTT
1 GGAAACCTGATTTTAG-TT
* *
2578443 GGAAA-ATAGGTTTTAGGTT
1 GGAAACCT-GATTTTA-GTT
*
2578462 GGAAATCTGATTTTAGGTT
1 GGAAACCTGATTTTA-GTT
2578481 GGAAACCTGATTTT
1 GGAAACCTGATTTT
2578495 GGGATTGGAA
Statistics
Matches: 151, Mismatches: 21, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
18 17 0.11
19 117 0.77
20 17 0.11
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (18 bp):
GGAAACCTGATTTTAGTT
Found at i:2578402 original size:57 final size:56
Alignment explanation
Indices: 2578291--2578494 Score: 259
Period size: 57 Copynumber: 3.6 Consensus size: 56
2578281 TGATTAACGC
* * *
2578291 GGAAGCCTGATTTTGAGTTGGAAACCTGATTTTAGATT-GAAAAATAAGTTTTAGGTT
1 GGAAACCTGATTTTAAGTTGGAAACCTGATTTTAGTTTGGAAAAAT-A-TTTTAGGTT
* * *
2578348 GGAAACCTAATTTTAAGTTGGAAACCTGATTTTACTTTGGAAAACATATATTAGGTT
1 GGAAACCTGATTTTAAGTTGGAAACCTGATTTTAGTTTGGAAAA-ATATTTTAGGTT
* *
2578405 GGGAACCTGATTTTAAGTTGGAAACATGATTTTAGTTTGG-AAAATAGGTTTTAGGTT
1 GGAAACCTGATTTTAAGTTGGAAACCTGATTTTAGTTTGGAAAAATA--TTTTAGGTT
* *
2578462 GGAAATCTGATTTTAGGTTGGAAACCTGATTTT
1 GGAAACCTGATTTTAAGTTGGAAACCTGATTTT
2578495 GGGATTGGAA
Statistics
Matches: 128, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
55 3 0.02
56 3 0.02
57 114 0.89
58 6 0.05
59 2 0.02
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (56 bp):
GGAAACCTGATTTTAAGTTGGAAACCTGATTTTAGTTTGGAAAAATATTTTAGGTT
Found at i:2578613 original size:68 final size:67
Alignment explanation
Indices: 2578522--2578665 Score: 189
Period size: 68 Copynumber: 2.1 Consensus size: 67
2578512 TCTACGAAGT
* * * **
2578522 ATTAGAGTGACTCACACGGGAGCATCTAATCATATTATTTTGGGTGGCTCGCATGGGAGCCCCAA
1 ATTAGAGTGACTCACACGGGAGCACCTAATCATATTATTTCGGGTGACTCGCACAGGAG-CCCAA
2578587 AGG
65 AGG
* ** * *
2578590 ATTAGAGTGACTCGCACTTGAGCACCTAATCATATTATTTCGGGTGACTCGTACAGGAGCCCGAA
1 ATTAGAGTGACTCACACGGGAGCACCTAATCATATTATTTCGGGTGACTCGCACAGGAGCCCAAA
2578655 GG
66 GG
2578657 ATTAGAGTG
1 ATTAGAGTG
2578666 CCTAATCAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
67 16 0.24
68 50 0.76
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (67 bp):
ATTAGAGTGACTCACACGGGAGCACCTAATCATATTATTTCGGGTGACTCGCACAGGAGCCCAAA
GG
Found at i:2578702 original size:52 final size:53
Alignment explanation
Indices: 2578614--2578717 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 53
2578604 CACTTGAGCA
* ** *
2578614 CCTAATCATATTATTTCGGGTGACTCGTACAGGAG-CCCGAAGGATTAGAGTG
1 CCTAATCAAATTATTAAGGGTGACTCGCACAGGAGCCCCGAAGGATTAGAGTG
* *
2578666 CCTAATCAAATTATTAAGGGTGACTTGCACATGAGCCCCGAAGGATTAGAGT
1 CCTAATCAAATTATTAAGGGTGACTCGCACAGGAGCCCCGAAGGATTAGAGT
2578718 AACTAGCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
52 29 0.64
53 16 0.36
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (53 bp):
CCTAATCAAATTATTAAGGGTGACTCGCACAGGAGCCCCGAAGGATTAGAGTG
Found at i:2584827 original size:57 final size:57
Alignment explanation
Indices: 2584748--2584857 Score: 184
Period size: 57 Copynumber: 1.9 Consensus size: 57
2584738 GAAGTCTGAT
* * *
2584748 TTTGAGTTGGAAACCTGATTTTAGTTTGGAAAATAGGTTTTAGGTTGGAAACCCAAG
1 TTTGAGTTGGAAACCTGATTTTACTTAGGAAAATAAGTTTTAGGTTGGAAACCCAAG
*
2584805 TTTGAGTTGGAAACCTGGTTTTACTTAGGAAAATAAGTTTTAGGTTGGAAACC
1 TTTGAGTTGGAAACCTGATTTTACTTAGGAAAATAAGTTTTAGGTTGGAAACC
2584858 TGATTTTAGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.35
Consensus pattern (57 bp):
TTTGAGTTGGAAACCTGATTTTACTTAGGAAAATAAGTTTTAGGTTGGAAACCCAAG
Found at i:2584872 original size:57 final size:55
Alignment explanation
Indices: 2584746--2584931 Score: 180
Period size: 57 Copynumber: 3.3 Consensus size: 55
2584736 TGGAAGTCTG
* * * *
2584746 ATTTTGAGTTGGAAACCTGATTTTAGTTTGGAAAATAGGTTTTAGGTTGGAAACCCA
1 ATTTT-AGTTGGAAACCTGGTTTTA-CTTGGAAAATAAGTTTTAGGTTGGAAACCTA
* *
2584803 AGTTTGAGTTGGAAACCTGGTTTTACTTAGGAAAATAAGTTTTAGGTTGGAAACCTG
1 A-TTTTAGTTGGAAACCTGGTTTTACTT-GGAAAATAAGTTTTAGGTTGGAAACCTA
* * *
2584860 ATTTTAGTTTGGAAA-ATAGGTTTTACATTGGAAACCTAA-TTTTAGGTT-TAAACCCTA
1 ATTTTAG-TTGGAAACCT-GGTTTTAC-TTGGAAA-ATAAGTTTTAGGTTGGAAA-CCTA
2584917 ATTTTAGGTTGGAAA
1 ATTTTA-GTTGGAAA
2584932 ATAGGTTTTA
Statistics
Matches: 110, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
56 11 0.10
57 90 0.82
58 9 0.08
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.38
Consensus pattern (55 bp):
ATTTTAGTTGGAAACCTGGTTTTACTTGGAAAATAAGTTTTAGGTTGGAAACCTA
Found at i:2584932 original size:57 final size:57
Alignment explanation
Indices: 2584766--2584941 Score: 182
Period size: 57 Copynumber: 3.1 Consensus size: 57
2584756 GGAAACCTGA
* * * * * *
2584766 TTTTAGTTTGGAAAATAGGTTTTAGGTTGGAAACCCAAGTTT-GAGTTGGAAACCT-GG
1 TTTTACTTAGGAAAATAAGTTTTAGGTTGGAAACCTAATTTTAG-GTTGGAAA-ATAGG
* *
2584823 TTTTACTTAGGAAAATAAGTTTTAGGTTGGAAACCTGATTTTAGTTTGGAAAATAGG
1 TTTTACTTAGGAAAATAAGTTTTAGGTTGGAAACCTAATTTTAGGTTGGAAAATAGG
* *
2584880 TTTTACATT-GGAAACCTAA-TTTTAGGTT-TAAACCCTAATTTTAGGTTGGAAAATAGG
1 TTTTAC-TTAGGAAA-ATAAGTTTTAGGTTGGAAA-CCTAATTTTAGGTTGGAAAATAGG
2584937 TTTTA
1 TTTTA
2584942 GGTTAGAAAC
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
56 4 0.04
57 92 0.90
58 6 0.06
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (57 bp):
TTTTACTTAGGAAAATAAGTTTTAGGTTGGAAACCTAATTTTAGGTTGGAAAATAGG
Found at i:2584940 original size:19 final size:20
Alignment explanation
Indices: 2584753--2584951 Score: 125
Period size: 19 Copynumber: 10.4 Consensus size: 20
2584743 CTGATTTTGA
*
2584753 GTTGGAAACCT-GATTTTAG
1 GTTGGAAACCTAGGTTTTAG
* *
2584772 TTTGGAAA-ATAGGTTTTAG
1 GTTGGAAACCTAGGTTTTAG
* * *
2584791 GTTGGAAACCCAAGTTTGA-
1 GTTGGAAACCTAGGTTTTAG
2584810 GTTGGAAACCT-GGTTTTA-
1 GTTGGAAACCTAGGTTTTAG
* * *
2584828 CTTAGGAAA-ATAAGTTTTAG
1 GTT-GGAAACCTAGGTTTTAG
*
2584848 GTTGGAAACCT-GATTTTAG
1 GTTGGAAACCTAGGTTTTAG
* * *
2584867 TTTGGAAA-ATAGGTTTTAC
1 GTTGGAAACCTAGGTTTTAG
* *
2584886 ATTGGAAACCTA-ATTTTAG
1 GTTGGAAACCTAGGTTTTAG
* *
2584905 GTT-TAAACCCTA-ATTTTAG
1 GTTGGAAA-CCTAGGTTTTAG
*
2584924 GTTGGAAA-ATAGGTTTTAG
1 GTTGGAAACCTAGGTTTTAG
*
2584943 GTTAGAAAC
1 GTTGGAAAC
2584952 TTGATTTTGG
Statistics
Matches: 136, Mismatches: 32, Indels: 23
0.71 0.17 0.12
Matches are distributed among these distances:
18 15 0.11
19 107 0.79
20 14 0.10
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.37
Consensus pattern (20 bp):
GTTGGAAACCTAGGTTTTAG
Found at i:2585251 original size:136 final size:136
Alignment explanation
Indices: 2584994--2585238 Score: 305
Period size: 136 Copynumber: 1.8 Consensus size: 136
2584984 AGTATTAGAG
**
2584994 TGACTCGCACTGGAGCACCTAATCATATTATTCCAAGCAACTCGCACGGGAGCCCCGAAGAATTA
1 TGACTCGCACTGGAGCACCTAATCATATTATTCCAAGCAACTCGCACAAGAGCCCCGAAGAATTA
* *
2585059 GAGTAACTCGTACAAGAGCACTTAATCATATTATTCCGGGTGACCCACAAGGGAGCTCCAAAGAA
66 GAGTAACTCGCACAAGAGCACTTAATCATATTATTCCAGGTGACCCACAAGGGAGCTCCAAAGAA
2585124 TTAAAA
131 TTAAAA
* * ** ** * *
2585130 TGACTTGCAC-GGAAGCACCTTATCATATTATTCCGGGTGATTCGCACAAGAGCCCTGAAGAATT
1 TGACTCGCACTGG-AGCACCTAATCATATTATTCCAAGCAACTCGCACAAGAGCCCCGAAGAATT
* *** *
2585194 AGAGTGACTCGCATGGGAGCAAC-TAATCATATTATTCTAGGTGAC
65 AGAGTAACTCGCACAAGAGC-ACTTAATCATATTATTCCAGGTGAC
2585239 TTGCACGGGA
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
135 2 0.02
136 86 0.96
137 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.23
Consensus pattern (136 bp):
TGACTCGCACTGGAGCACCTAATCATATTATTCCAAGCAACTCGCACAAGAGCCCCGAAGAATTA
GAGTAACTCGCACAAGAGCACTTAATCATATTATTCCAGGTGACCCACAAGGGAGCTCCAAAGAA
TTAAAA
Found at i:2585264 original size:68 final size:68
Alignment explanation
Indices: 2584981--2585250 Score: 254
Period size: 68 Copynumber: 4.0 Consensus size: 68
2584971 CCAAATTCTA
* * * * **
2584981 CGAAGTATTAGAGTGACTCGCACTGGAGCACCTAATCATATTATTCCAAGCAACTCGCACGGGAG
1 CGAAGAATTAGAGTGACTCGCACGGGAGCAACTAATCATATTATTCCAGGTGACTCGCACGGGAG
2585046 CCC
66 CCC
* * ** * * * *
2585049 CGAAGAATTAGAGTAACTCGTACAAGAGC-ACTTAATCATATTATTCCGGGTGACCCACAAGGGA
1 CGAAGAATTAGAGTGACTCGCACGGGAGCAAC-TAATCATATTATTCCAGGTGACTCGCACGGGA
*
2585113 GCTC
65 GCCC
* * * * * * * * * **
2585117 CAAAGAATTAAAATGACTTGCACGGAAGCACCTTATCATATTATTCCGGGTGATTCGCACAAGAG
1 CGAAGAATTAGAGTGACTCGCACGGGAGCAACTAATCATATTATTCCAGGTGACTCGCACGGGAG
2585182 CCC
66 CCC
* * * *
2585185 TGAAGAATTAGAGTGACTCGCATGGGAGCAACTAATCATATTATTCTAGGTGACTTGCACGGGAG
1 CGAAGAATTAGAGTGACTCGCACGGGAGCAACTAATCATATTATTCCAGGTGACTCGCACGGGAG
2585250 C
66 C
2585251 TTTGAAGGAT
Statistics
Matches: 153, Mismatches: 47, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
67 1 0.01
68 151 0.99
69 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (68 bp):
CGAAGAATTAGAGTGACTCGCACGGGAGCAACTAATCATATTATTCCAGGTGACTCGCACGGGAG
CCC
Found at i:2592887 original size:21 final size:22
Alignment explanation
Indices: 2592818--2592899 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 22
2592808 TTAGTACAGA
* *
2592818 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
*
2592840 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCC-TTGAAG
2592863 GGGAACCGATTCCCTCCTTG-A-
1 GGGAACCGATTCCC-CCTTGAAG
* *
2592884 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
2592900 CACGGGTTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
20 2 0.04
21 12 0.23
22 15 0.28
23 22 0.42
24 2 0.04
ACGTcount: A:0.23, C:0.32, G:0.24, T:0.21
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:2598133 original size:21 final size:21
Alignment explanation
Indices: 2598107--2598159 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2598097 GTTTCCAGAT
2598107 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
2598128 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
2598149 TCGCAATGCGA
1 TCGCAACGCGA
2598160 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:2598212 original size:42 final size:42
Alignment explanation
Indices: 2598155--2598473 Score: 497
Period size: 42 Copynumber: 7.7 Consensus size: 42
2598145 ACTATCGCAA
*
2598155 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCTAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
2598195 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* * *
2598237 TGTGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
*
2598277 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* *
2598319 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCAT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* *
2598361 TGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
* *
2598401 TGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
2598443 TGCGATTTATTCCAAATTCGTTGCGATAGTC
1 TGCGATTTATTCCAAATTCGTTGCGATAGTC
2598474 CAAAATCGCA
Statistics
Matches: 257, Mismatches: 16, Indels: 10
0.91 0.06 0.04
Matches are distributed among these distances:
40 78 0.30
41 2 0.01
42 177 0.69
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (42 bp):
TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:2598271 original size:82 final size:83
Alignment explanation
Indices: 2598155--2598473 Score: 493
Period size: 82 Copynumber: 3.9 Consensus size: 83
2598145 ACTATCGCAA
*
2598155 TGCGATT-TTCCAAATTCGTTGCGATAGTCTAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
1 TGCGATTATTCCAAATTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
2598219 GATAGTCGAAGTTCGCGT
66 GATAGTCGAAGTTCGCGT
* * * * *
2598237 TGTGA-TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGC
1 TGCGATTATTCCAAATTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
2598301 GATAGTCGAAGTTCGCGT
66 GATAGTCGAAGTTCGCGT
* * * *
2598319 TGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGA--TAGTCCAAGTTCGTTG
1 TGCGA-TTATTCCAAATTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
2598382 CGATAGTCGAAGTTCGCGT
65 CGATAGTCGAAGTTCGCGT
*
2598401 TGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
1 TGCGA-TTATTCCAAATTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
2598466 CGATAGTC
65 CGATAGTC
2598474 CAAAATCGCA
Statistics
Matches: 216, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
81 1 0.00
82 157 0.73
84 58 0.27
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (83 bp):
TGCGATTATTCCAAATTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGC
GATAGTCGAAGTTCGCGT
Found at i:2598483 original size:124 final size:124
Alignment explanation
Indices: 2598155--2598476 Score: 576
Period size: 124 Copynumber: 2.6 Consensus size: 124
2598145 ACTATCGCAA
* *
2598155 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCTAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
* * *
2598218 CGATAGTCGAAGTTCGCGTTGTGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
66 CGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
*
2598277 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
2598342 CGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
66 CGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
2598401 TGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
2598466 CGATAGTCCAA
66 CGATAGTCCAA
2598477 AATCGCAACG
Statistics
Matches: 192, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
122 5 0.03
123 2 0.01
124 185 0.96
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (124 bp):
TGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
CGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:2599316 original size:42 final size:42
Alignment explanation
Indices: 2599255--2599422 Score: 258
Period size: 42 Copynumber: 4.1 Consensus size: 42
2599245 GTCTTCGACT
2599255 ATCGCAA--CGAACTTGGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
* * *
2599295 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACT--
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
*
2599335 ATCGCAACGCGAACTTGGACTATCGCAGCGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
2599377 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGG-A-AA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
2599417 ATCGCA
1 ATCGCA
2599423 TTGCGATAGT
Statistics
Matches: 116, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
40 51 0.44
41 1 0.01
42 64 0.55
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (42 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAA
Found at i:2599342 original size:61 final size:60
Alignment explanation
Indices: 2599247--2599422 Score: 209
Period size: 61 Copynumber: 2.9 Consensus size: 60
2599237 TAATACGTGT
2599247 CTTCGACTATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAA
1 CTTCGACTATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAA-GCGAA
* *
2599308 CTTCGACTATCGCAACGAACTTGGACTATCGCAACGCGAACTTGGACT--ATCGC-AGCGAA
1 CTTCGACTATCGCAACGAACTTGGACTATCGCAA--CGAATTTGGAATAAATCGCAAGCGAA
* * *
2599367 TTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGG-A-AAATCGCA
1 CTTCGACT--ATCGCAA--CGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCA
2599423 TTGCGATAGT
Statistics
Matches: 99, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
59 10 0.10
60 1 0.01
61 59 0.60
63 29 0.29
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (60 bp):
CTTCGACTATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAAGCGAA
Found at i:2599386 original size:82 final size:80
Alignment explanation
Indices: 2599251--2599414 Score: 283
Period size: 82 Copynumber: 2.0 Consensus size: 80
2599241 ACGTGTCTTC
2599251 GACTATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 GACTATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
2599316 ATCGCAACGAACTTG
66 ATCGCAACGAACTTG
* *
2599331 GACTATCGCAACGCGAACTTGGACTATCGCAGCGAATTTGGAATAAATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGA
*
2599396 CTATCGCAACGAATTTG
64 CTATCGCAACGAACTTG
2599413 GA
1 GA
2599415 AAATCGCATT
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
80 11 0.14
82 68 0.86
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (80 bp):
GACTATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
ATCGCAACGAACTTG
Found at i:2600319 original size:7 final size:6
Alignment explanation
Indices: 2600299--2600344 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
2600289 CTATTTCCTC
*
2600299 TTTCTT TTTCTT TTGCTT TTTC-- TTTCGTT TTTCTT TTT-TT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT
2600345 GATTTCTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.12
5 5 0.15
6 21 0.62
7 4 0.12
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:2600319 original size:12 final size:12
Alignment explanation
Indices: 2600302--2600344 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
2600292 TTTCCTCTTT
2600302 CTTTTTCTTTTG
1 CTTTTTCTTTTG
*
2600314 CTTTTTCTTTCG
1 CTTTTTCTTTTG
2600326 -TTTTTCTTTT-
1 CTTTTTCTTTTG
*
2600336 TTTTTTCTT
1 CTTTTTCTT
2600345 GATTTCTCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (12 bp):
CTTTTTCTTTTG
Found at i:2600322 original size:22 final size:22
Alignment explanation
Indices: 2600297--2600344 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2600287 TTCTATTTCC
2600297 TCTTTC-TTTTTCTTTTGCTTTT
1 TCTTTCGTTTTTCTTTT-CTTTT
*
2600319 TCTTTCGTTTTTCTTTTTTTTT
1 TCTTTCGTTTTTCTTTTCTTTT
2600341 TCTT
1 TCTT
2600345 GATTTCTCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (22 bp):
TCTTTCGTTTTTCTTTTCTTTT
Found at i:2600329 original size:11 final size:11
Alignment explanation
Indices: 2600297--2600344 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
2600287 TTCTATTTCC
2600297 TCTTTC-TTTT
1 TCTTTCGTTTT
*
2600307 TCTTTTGCTTTT
1 TCTTTCG-TTTT
2600319 TCTTTCGTTTT
1 TCTTTCGTTTT
**
2600330 TCTTTTTTTTT
1 TCTTTCGTTTT
2600341 TCTT
1 TCTT
2600345 GATTTCTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 5 0.16
11 17 0.53
12 10 0.31
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (11 bp):
TCTTTCGTTTT
Found at i:2600358 original size:29 final size:29
Alignment explanation
Indices: 2600299--2600363 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
2600289 CTATTTCCTC
*
2600299 TTTCTTTTTCTTTTGCTTTTTCTTTCGTT
1 TTTCTTTTTCTTTTGCTTTTTCTCTCGTT
*
2600328 TTTCTTTTT-TTTTTCTTGATTTCTCTC-TT
1 TTTCTTTTTCTTTTGCTT--TTTCTCTCGTT
2600357 TTTCTTT
1 TTTCTTT
2600364 CTTAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 7 0.22
29 18 0.56
30 7 0.22
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.77
Consensus pattern (29 bp):
TTTCTTTTTCTTTTGCTTTTTCTCTCGTT
Found at i:2608910 original size:15 final size:14
Alignment explanation
Indices: 2608881--2608919 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2608871 GTACTATTAT
*
2608881 TTTCTTTTACATTTA
1 TTTCTTTTTC-TTTA
2608896 TTTCTATTTTCTTTA
1 TTTCT-TTTTCTTTA
2608911 TTTCTTTTT
1 TTTCTTTTT
2608920 TAATTCATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCTTTTTCTTTA
Found at i:2616277 original size:99 final size:102
Alignment explanation
Indices: 2616104--2616346 Score: 323
Period size: 99 Copynumber: 2.4 Consensus size: 102
2616094 CCAATTTCTT
* * * *
2616104 AACCAATTTCAACTTCACAGCGAATGATATTGGACCCAAGATAACACAAGCTCAACTTCACGGCG
1 AACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACGGCA
*
2616169 AAGGGGCGGCTAATTGTCAACAAACAATTTT-CA-A-
66 AAGGGGCGGCTAACTGTCAACAAACAATTTTCCACAG
* * * *
2616203 ATCCAATTTCAACTTCACAGCGAAGGATATTGGACTGAAGACAGCACAAGCTTAACTTCACGGCA
1 AACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACGGCA
*
2616268 AAGGGGCGGCTGACTGTCAACAAACAATTTTCCAGTTCCAG
66 AAGGGGCGGCTAACTGTCAACAAACAATTTTCCA----CAG
2616309 AACCAATTTCAACTTCAC-GACGAAGGATATTGGACTCA
1 AACCAATTTCAACTTCACAG-CGAAGGATATTGGACTCA
2616347 GAGCAATACA
Statistics
Matches: 124, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
99 86 0.69
100 2 0.02
105 2 0.02
106 34 0.27
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (102 bp):
AACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACGGCA
AAGGGGCGGCTAACTGTCAACAAACAATTTTCCACAG
Found at i:2618494 original size:15 final size:14
Alignment explanation
Indices: 2618465--2618503 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2618455 GTACTATTAT
*
2618465 TTTCTTTTACATTTA
1 TTTCTTTTTC-TTTA
2618480 TTTCTATTTTCTTTA
1 TTTCT-TTTTCTTTA
2618495 TTTCTTTTT
1 TTTCTTTTT
2618504 TAATTCATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCTTTTTCTTTA
Found at i:2625223 original size:16 final size:16
Alignment explanation
Indices: 2625202--2625240 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
2625192 CATAAAAAAA
*
2625202 AAACATTTCCATTAAG
1 AAACATATCCATTAAG
2625218 AAACATATCCATTAAG
1 AAACATATCCATTAAG
2625234 AAACATA
1 AAACATA
2625241 ATAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (16 bp):
AAACATATCCATTAAG
Found at i:2642126 original size:12 final size:12
Alignment explanation
Indices: 2642109--2642137 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2642099 CCCATGAATA
2642109 ATTTGGAACTCT
1 ATTTGGAACTCT
2642121 ATTTGGAACTCT
1 ATTTGGAACTCT
2642133 ATTTG
1 ATTTG
2642138 TAATGTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (12 bp):
ATTTGGAACTCT
Found at i:2644729 original size:16 final size:16
Alignment explanation
Indices: 2644710--2644783 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 16
2644700 TAACCCAATC
2644710 CAAAAGTAACTCGAAT
1 CAAAAGTAACTCGAAT
*
2644726 C-AAAGTTAAC-CTGAAC
1 CAAAAG-TAACTC-GAAT
* *
2644742 CGAAAA-TAATTTGAAT
1 C-AAAAGTAACTCGAAT
2644758 CAAAAGTAACAT-GAAT
1 CAAAAGTAAC-TCGAAT
2644774 CAAAAGTAAC
1 CAAAAGTAAC
2644784 CCAAATCCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
15 9 0.20
16 33 0.72
17 1 0.02
18 3 0.07
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.20
Consensus pattern (16 bp):
CAAAAGTAACTCGAAT
Found at i:2645471 original size:18 final size:18
Alignment explanation
Indices: 2645448--2645483 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2645438 AACATATGGT
2645448 TGAAATTT-TAATTAAAAA
1 TGAAATTTATAA-TAAAAA
2645466 TGAAATTTATAATAAAAA
1 TGAAATTTATAATAAAAA
2645484 AATATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (18 bp):
TGAAATTTATAATAAAAA
Found at i:2645483 original size:19 final size:18
Alignment explanation
Indices: 2645448--2645484 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2645438 AACATATGGT
*
2645448 TGAAATTTTAATTAAAAA
1 TGAAATTTTAATAAAAAA
2645466 TGAAATTTATAATAAAAAA
1 TGAAATTT-TAATAAAAAA
2645485 ATATTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TGAAATTTTAATAAAAAA
Found at i:2653219 original size:27 final size:27
Alignment explanation
Indices: 2653173--2653226 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2653163 TGTTTTCGAA
* *
2653173 ATCTATTATTTCCCTTTTCGGAAGCAG
1 ATCTATTATTTCCCTATTCGAAAGCAG
**
2653200 ATCTATTATTTTTCTATTCGAAAGCAG
1 ATCTATTATTTCCCTATTCGAAAGCAG
2653227 TAAAACACTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.43
Consensus pattern (27 bp):
ATCTATTATTTCCCTATTCGAAAGCAG
Found at i:2656384 original size:32 final size:32
Alignment explanation
Indices: 2656341--2656466 Score: 96
Period size: 32 Copynumber: 3.9 Consensus size: 32
2656331 CTAATCTAAA
2656341 CCAAAAATCAACCG-ATCCGATATTAACCCGAT
1 CCAAAAATCAACCGAAT-CGATATTAACCCGAT
* * *
2656373 CCAAAACTCAACTGAATCGATATTGACTCCGAT
1 CCAAAAATCAACCGAATCGATATTAAC-CCGAT
* * * * * *
2656406 TC-GAAATCTAACTGAATTGATATTAACCTGAC
1 CCAAAAATC-AACCGAATCGATATTAACCCGAT
* *
2656438 CCAAAAATCAATCG-ATCCAATATTAACCC
1 CCAAAAATCAACCGAAT-CGATATTAACCC
2656467 AAATCAAAAA
Statistics
Matches: 72, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
31 2 0.03
32 41 0.57
33 29 0.40
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.24
Consensus pattern (32 bp):
CCAAAAATCAACCGAATCGATATTAACCCGAT
Found at i:2661744 original size:20 final size:20
Alignment explanation
Indices: 2661721--2661768 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
2661711 CCTTTAACTG
2661721 TTGACTTTCACTTTGACCCA
1 TTGACTTTCACTTTGACCCA
2661741 TTGACTTTCACTTTGACCCA
1 TTGACTTTCACTTTGACCCA
2661761 TTGACTTT
1 TTGACTTT
2661769 TTTCTAGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.27, G:0.10, T:0.44
Consensus pattern (20 bp):
TTGACTTTCACTTTGACCCA
Found at i:2662490 original size:43 final size:42
Alignment explanation
Indices: 2662374--2662500 Score: 121
Period size: 42 Copynumber: 3.0 Consensus size: 42
2662364 ATTCTTGTCT
* * * *
2662374 TGATTCTACATAGGATCCTCTAC-GAAGGGCATCATCCTCATCT
1 TGATTCTGCAT-GAATCCTCTACAGAA-GGCATCATCCTCGTCA
* * *
2662417 TGGTTCTGCATGAATCCTCTACAGAGGGCATCATCCCCGTCA
1 TGATTCTGCATGAATCCTCTACAGAAGGCATCATCCTCGTCA
* ** *
2662459 TGATTCTGCATGAAATCCTTTATGGAAGGCATAATCCTCGTC
1 TGATTCTGCATG-AATCCTCTACAGAAGGCATCATCCTCGTC
2662501 CTGGTTTTCT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 34 0.50
43 34 0.50
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (42 bp):
TGATTCTGCATGAATCCTCTACAGAAGGCATCATCCTCGTCA
Found at i:2664576 original size:18 final size:18
Alignment explanation
Indices: 2664536--2664577 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2664526 CTTCTGAAAA
2664536 TTTTAAATTTTTTATAGT
1 TTTTAAATTTTTTATAGT
* *
2664554 ATTTAAATTTTTTATATT
1 TTTTAAATTTTTTATAGT
2664572 TTTTAA
1 TTTTAA
2664578 TAATTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTAAATTTTTTATAGT
Found at i:2664587 original size:25 final size:26
Alignment explanation
Indices: 2664536--2664589 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
2664526 CTTCTGAAAA
2664536 TTTTAAATTTTTTATAGTATTTAAATT
1 TTTTAAATTTTTTATAG-ATTTAAATT
*
2664563 TTTTATATTTTTTAATA-ATTT-AATT
1 TTTTAAATTTTTT-ATAGATTTAAATT
2664588 TT
1 TT
2664590 ACACCTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 6 0.24
26 4 0.16
27 12 0.48
28 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTTAAATTTTTTATAGATTTAAATT
Done.