Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003352.1 Hibiscus syriacus cultivar Beakdansim tig00007057_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: 159531
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:26752 original size:17 final size:18
Alignment explanation
Indices: 26724--26758 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
26714 TTAAATGGAA
26724 AAAAACCTCTAAATCCTT
1 AAAAACCTCTAAATCCTT
26742 AAAAACC-CTAAATCCTT
1 AAAAACCTCTAAATCCTT
26759 TACCCTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAACCTCTAAATCCTT
Found at i:33686 original size:30 final size:30
Alignment explanation
Indices: 33650--33712 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
33640 AAGGATGCAC
* *
33650 GCACCGAATATGTATAATTTCAATGGGTTG
1 GCACCGAATATGCATAATTTCAATGGGCTG
*
33680 GCACCGAATGTGCATAATTTCAATGGGCTG
1 GCACCGAATATGCATAATTTCAATGGGCTG
33710 GCA
1 GCA
33713 ATTGTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (30 bp):
GCACCGAATATGCATAATTTCAATGGGCTG
Found at i:34138 original size:16 final size:16
Alignment explanation
Indices: 34105--34138 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34095 TTACTATTCA
* *
34105 CGTGAATAGTGAATTT
1 CGTGAATAGTAAAATT
34121 CGTGAATAGTAAAATT
1 CGTGAATAGTAAAATT
34137 CG
1 CG
34139 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTAAAATT
Found at i:38216 original size:30 final size:30
Alignment explanation
Indices: 38180--38242 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
38170 AAGGATGCAC
*
38180 GCACCGAATATGCATAATTTCAATGGGTTG
1 GCACCGAATATGCATAATTTCAATGGGCTG
*
38210 GCACCGAATGTGCATAATTTCAATGGGCTG
1 GCACCGAATATGCATAATTTCAATGGGCTG
38240 GCA
1 GCA
38243 ATTGTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (30 bp):
GCACCGAATATGCATAATTTCAATGGGCTG
Found at i:43209 original size:39 final size:39
Alignment explanation
Indices: 43150--43226 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
43140 TAATGCCATC
* * *
43150 AAAATTTAACAAAGCGATAACTTTTA-TGATTAACATTTA
1 AAAACTTAACAAAGCGATAAC-GTTAGTGATTAAAATTTA
43189 AAAACTTAACGAAA-CGATAACGTTAGTGATTAAAATTT
1 AAAACTTAAC-AAAGCGATAACGTTAGTGATTAAAATTT
43227 TTTAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 3 0.09
39 27 0.82
40 3 0.09
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (39 bp):
AAAACTTAACAAAGCGATAACGTTAGTGATTAAAATTTA
Found at i:43724 original size:21 final size:21
Alignment explanation
Indices: 43698--43835 Score: 181
Period size: 21 Copynumber: 6.7 Consensus size: 21
43688 GCGAATAAGT
43698 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
43719 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
43740 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
43760 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
43781 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
43801 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
43822 AAATCGCAATGCGA
1 AAATCGCAACGCGA
43836 TACTGACTAT
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
20 32 0.33
21 66 0.67
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:43826 original size:62 final size:62
Alignment explanation
Indices: 43683--43835 Score: 191
Period size: 62 Copynumber: 2.5 Consensus size: 62
43673 TTCCCAATTT
* * **
43683 GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAACGCGAATTGGGAAAATC
1 GCAACGCGAATAAGAAAATCGCAACGCGAATTGGGAAAATCGCAACGCGAATTAAGAAAATC
* * * *
43745 GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGCAATGCGAA-TAAGTAAATC
1 GCAACGCGAATAAGAAAATCGCAACGCGAATTGGGAAAATCGCAACGCGAATTAAGAAAATC
** *
43806 GCAACGCGAATTGGGAAAATCGCAATGCGA
1 GCAACGCGAA-TAAGAAAATCGCAACGCGA
43836 TACTGACTAT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
61 16 0.20
62 65 0.80
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (62 bp):
GCAACGCGAATAAGAAAATCGCAACGCGAATTGGGAAAATCGCAACGCGAATTAAGAAAATC
Found at i:43849 original size:20 final size:20
Alignment explanation
Indices: 43824--43917 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
43814 AATTGGGAAA
*
43824 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
43844 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
43865 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
43885 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
43905 TTCGCAACGCGAT
1 ATCGCAACGCGAT
43918 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:43850 original size:41 final size:41
Alignment explanation
Indices: 43719--43835 Score: 234
Period size: 41 Copynumber: 2.9 Consensus size: 41
43709 CGAATTGGGA
43719 AAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGT
1 AAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGT
43760 AAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGT
1 AAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGT
43801 AAATCGCAACGCGAATTGGGAAAATCGCAATGCGA
1 AAATCGCAACGCGAATTGGGAAAATCGCAATGCGA
43836 TACTGACTAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (41 bp):
AAATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGT
Found at i:43866 original size:41 final size:41
Alignment explanation
Indices: 43821--43898 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
43811 GCGAATTGGG
* * *
43821 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
43862 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
43899 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:44473 original size:19 final size:19
Alignment explanation
Indices: 44435--44501 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
44425 TTCGAGAATG
44435 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
44455 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
44474 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
44493 AAAATCGCA
1 AAAATCGCA
44502 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:44543 original size:20 final size:19
Alignment explanation
Indices: 44497--44662 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
44487 GAAACCAAAA
*
44497 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
44516 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
44535 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
44555 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
44571 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
44588 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
44602 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
44621 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
44641 ATCTCGTTGCAATTTTCATT
1 -TCGCGTTGCGATTTTCATT
44661 TC
1 TC
44663 AACCAAAAGA
Statistics
Matches: 118, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.35
20 48 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:44578 original size:39 final size:39
Alignment explanation
Indices: 44502--44578 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
44492 CAAAATCGCA
* **
44502 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
44541 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
44579 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:44587 original size:33 final size:33
Alignment explanation
Indices: 44550--44637 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
44540 GTTGCGATTT
* *
44550 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
44583 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
44616 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
44638 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:46724 original size:42 final size:42
Alignment explanation
Indices: 46664--46786 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
46654 GCCCGACTCG
* * *
46664 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
46706 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
46748 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
46787 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:46744 original size:21 final size:21
Alignment explanation
Indices: 46720--46786 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
46710 TCATTCCTCG
46720 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
46741 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
46762 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
46783 AGAG
1 AGAG
46787 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:48164 original size:14 final size:14
Alignment explanation
Indices: 48145--48180 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
48135 TTTAATTAAT
48145 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
48159 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
48173 TGATTTGT
1 TGATTTGT
48181 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:48406 original size:33 final size:32
Alignment explanation
Indices: 48363--48489 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
48353 ATTAAATTCG
48363 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
48396 CGTTGTGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
48429 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
48462 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
48490 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:48452 original size:66 final size:66
Alignment explanation
Indices: 48356--48488 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
48346 ACGCGAAATT
* *
48356 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGTGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
48421 G
66 G
*
48422 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
48487 G
66 G
48488 A
1 A
48489 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:51002 original size:24 final size:24
Alignment explanation
Indices: 50968--51021 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
50958 CTGAAACATC
* *
50968 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
50992 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
51016 ATCAAA
1 ATCAAA
51022 TTTCGAATAT
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:51032 original size:24 final size:24
Alignment explanation
Indices: 50981--51035 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
50971 AAAATCCGTG
* **
50981 TATTGACCAATATCAAAGTCCGGG
1 TATTGACCAAGATCAAAGTCCGAA
* *
51005 TATTGACCAAGATCAAATTTCGAA
1 TATTGACCAAGATCAAAGTCCGAA
51029 TATTGAC
1 TATTGAC
51036 TAGTACTCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTCCGAA
Found at i:53608 original size:19 final size:19
Alignment explanation
Indices: 53584--53658 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 19
53574 GAAACTTAAA
53584 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
53603 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
53623 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
*
53642 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
53659 AAGCGCAACG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
19 33 0.66
20 17 0.34
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:53627 original size:39 final size:38
Alignment explanation
Indices: 53584--53657 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 38
53574 GAAACTTAAA
**
53584 ATCGCAACGCGAAATGACTATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAATGAAAATCGCAACGC-GAAATGGCT
* *
53623 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATG
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAATG
53658 AAAGCGCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 6 0.19
39 25 0.81
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGGCT
Found at i:53659 original size:19 final size:19
Alignment explanation
Indices: 53567--53660 Score: 89
Period size: 19 Copynumber: 4.8 Consensus size: 19
53557 GTTTACTTTT
* *
53567 GCAACACGAAACTTAAAATC
1 GCAACGCGAAA-TGAAAATC
**
53587 GCAACGCGAAATGACTATC
1 GCAACGCGAAATGAAAATC
***
53606 GCAACGCGGAAATGGCTATC
1 GCAACGC-GAAATGAAAATC
*
53626 GCAATGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
53645 GCAATGCGAAATGAAA
1 GCAACGCGAAATGAAA
53661 GCGCAACGAC
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
19 37 0.58
20 27 0.42
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.15
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:54232 original size:18 final size:18
Alignment explanation
Indices: 54206--54250 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
54196 GTCGATCAGA
*
54206 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
54224 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
54242 TGATGGCTC
1 TGATGGCTC
54251 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:55554 original size:20 final size:20
Alignment explanation
Indices: 55529--55566 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55519 AATAGTTTCT
55529 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
55549 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
55567 GAGAGAATCG
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:55854 original size:22 final size:22
Alignment explanation
Indices: 55829--55872 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55819 GATTTAGATA
55829 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
55851 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
55873 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:56085 original size:20 final size:20
Alignment explanation
Indices: 56060--56153 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
56050 GATTATGTAT
56060 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
56080 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
56100 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
56121 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
56141 TATCGCATTGCGA
1 TATCGCGTTGCGA
56154 TTTTCCCAAT
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):
TATCGCGTTGCGAAAGTCAG
Found at i:56154 original size:20 final size:20
Alignment explanation
Indices: 56040--56154 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
56030 CGCTTTGAAA
*
56040 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
56061 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
56081 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
56101 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
56122 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
56142 ATCGCATTGCGAT
1 ATCGCATTGCGAT
56155 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:56172 original size:21 final size:21
Alignment explanation
Indices: 56143--56235 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
56133 ATAGTCAGTA
56143 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
56164 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
56184 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
56205 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
56225 TCGCATTGCGA
1 TCGCATTGCGA
56236 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 (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:56173 original size:41 final size:41
Alignment explanation
Indices: 56082--56216 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
56072 AAAGTCAGTA
* * * ** *
56082 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
56122 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
56164 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
56205 TCGCGTTGCGAT
1 TCGCGTTGCGAT
56217 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:56217 original size:41 final size:41
Alignment explanation
Indices: 56143--56235 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
56133 ATAGTCAGTA
56143 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
56184 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
56225 TCGCATTGCGA
1 TCGCATTGCGA
56236 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:57173 original size:15 final size:15
Alignment explanation
Indices: 57144--57181 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
57134 ATTAATCAAA
57144 TTATTTAT-CTTCTT
1 TTATTTATACTTCTT
*
57158 TTATTTATATTTCTT
1 TTATTTATACTTCTT
*
57173 TAATTTATA
1 TTATTTATA
57182 AGTTTTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTATACTTCTT
Found at i:57450 original size:39 final size:39
Alignment explanation
Indices: 57391--57467 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
57381 TTACGCCATC
* * * *
57391 AAAATTTAACAAAGCGATAACTTTTA-TGATTAACATTTA
1 AAAACTTAACAAAACGATAAC-GTTAGTGATTAAAATTTA
57430 AAAACTTAACAAAACGATAACGTTAGTGATTAAAATTT
1 AAAACTTAACAAAACGATAACGTTAGTGATTAAAATTT
57468 TTAAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 3 0.09
39 30 0.91
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.32
Consensus pattern (39 bp):
AAAACTTAACAAAACGATAACGTTAGTGATTAAAATTTA
Found at i:61187 original size:44 final size:46
Alignment explanation
Indices: 61121--61209 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 46
61111 TAATTCAAGG
*
61121 CTTTTGATTATTGGTTGTC-AAAACTAAAATCAAATGATTAGTTCC
1 CTTTTGATTATTGGTTGTCAAAAACTAAAATCAAAAGATTAGTTCC
*
61166 CTTTT-ATTATTGTGTTG-CAAAAAGTAAAATCAAAAGATTAGTTC
1 CTTTTGATTATTG-GTTGTCAAAAACTAAAATCAAAAGATTAGTTC
61210 ATTGTGACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 8 0.20
45 32 0.80
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.39
Consensus pattern (46 bp):
CTTTTGATTATTGGTTGTCAAAAACTAAAATCAAAAGATTAGTTCC
Found at i:61451 original size:58 final size:58
Alignment explanation
Indices: 61385--61651 Score: 265
Period size: 58 Copynumber: 4.7 Consensus size: 58
61375 AATCTTGCTT
* * *
61385 TGATTCTAACTTTGTAAGAGAATTATATTGTTGAATTTATTTCCTTGAGGATCTTAAA
1 TGATTCTAACTTTGTAAGAGAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
* * *
61443 TGATTCTAATTAACTTTATAAG-GAAAATAAATTGTTGAATTTATTTCCTTGAGATTCTTGAA
1 TGATTC----TAACTTTGTAAGAG-AAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
61505 TGA---T-A----G---GA-AAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGAGAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
* * *
61551 TGATTTTAACTTTGTAAGAAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGAGAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
** *
61609 TGATTCTATTTTTGTTAA-AGGAAATAAATTGTTAAATTTATTT
1 TGATTCTAACTTTG-TAAGA-GAAATAAATTGTTGAATTTATTT
61652 TCTCATGAAT
Statistics
Matches: 174, Mismatches: 15, Indels: 39
0.76 0.07 0.17
Matches are distributed among these distances:
46 39 0.22
47 1 0.01
49 1 0.01
50 1 0.01
54 2 0.01
55 1 0.01
57 2 0.01
58 55 0.32
59 24 0.14
61 1 0.01
62 47 0.27
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (58 bp):
TGATTCTAACTTTGTAAGAGAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAA
Found at i:61530 original size:46 final size:46
Alignment explanation
Indices: 61463--61554 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
61453 TAACTTTATA
* *
61463 AGGAAAATAAATTGTTGAATTTATTTCCTTGAGATTCTTGAATGAT
1 AGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
61509 AGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
1 AGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
61555 TTTAACTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (46 bp):
AGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAATGAT
Found at i:61598 original size:104 final size:107
Alignment explanation
Indices: 61411--61612 Score: 320
Period size: 104 Copynumber: 1.9 Consensus size: 107
61401 AGAGAATTAT
* *
61411 ATTGTTGAATTTATTTCCTTGAGGATCTTAAATGATTCTAATTAACTTTATAAGGAAAATAAATT
1 ATTGTTGAATTTATTTCCTTGAGAATCTTAAATGATTCT-ATTAACTTTATAAGAAAAATAAATT
* *
61476 GTTGAATTTATTTCCTTGAGATTCTTGAATGATAGGAAAATAA
65 GTTGAATTTATTTCCTTGAGAATCTTAAATGATAGGAAAATAA
*
61519 ATTGTTGAATTTATTTCCTTGAGAATCTTAAATGA-T-T-TTAACTTTGTAAGAAAAATAAATTG
1 ATTGTTGAATTTATTTCCTTGAGAATCTTAAATGATTCTATTAACTTTATAAGAAAAATAAATTG
*
61581 TTGAATTTATTTTCTTGAGAATCTTAAATGAT
66 TTGAATTTATTTCCTTGAGAATCTTAAATGAT
61613 TCTATTTTTG
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
104 52 0.59
106 1 0.01
107 1 0.01
108 34 0.39
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (107 bp):
ATTGTTGAATTTATTTCCTTGAGAATCTTAAATGATTCTATTAACTTTATAAGAAAAATAAATTG
TTGAATTTATTTCCTTGAGAATCTTAAATGATAGGAAAATAA
Found at i:61759 original size:39 final size:39
Alignment explanation
Indices: 61716--61886 Score: 171
Period size: 39 Copynumber: 4.4 Consensus size: 39
61706 TTTATCTTTT
* * *
61716 AAAAGGAAATAAATCATCGGATTTATTTTCCTATTTTGG
1 AAAAGGAAATAAATCATTGAATTTATTTTCCTATTTTGA
* * * * * *
61755 AAAAGGAAACAAATCGTTGAATTTAGTTTCTTGTTTTGT
1 AAAAGGAAATAAATCATTGAATTTATTTTCCTATTTTGA
* * *
61794 AAAAGGAAATAAATCATAGAATTTATTTTCATATTTTAA
1 AAAAGGAAATAAATCATTGAATTTATTTTCCTATTTTGA
* * * * *
61833 AAAATGAAATAAATCGTTGGATTTATTTTTCTATATTGTA
1 AAAAGGAAATAAATCATTGAATTTATTTTCCTATTTTG-A
*
61873 AAAAGCAAATAAAT
1 AAAAGGAAATAAAT
61887 TGAGCAAATC
Statistics
Matches: 105, Mismatches: 26, Indels: 1
0.80 0.20 0.01
Matches are distributed among these distances:
39 92 0.88
40 13 0.12
ACGTcount: A:0.42, C:0.07, G:0.13, T:0.39
Consensus pattern (39 bp):
AAAAGGAAATAAATCATTGAATTTATTTTCCTATTTTGA
Found at i:61872 original size:78 final size:78
Alignment explanation
Indices: 61715--61886 Score: 213
Period size: 78 Copynumber: 2.2 Consensus size: 78
61705 TTTTATCTTT
* * * **
61715 TAAAAGGAAATAAATCATCGGATTTATTTTCCTATTTTGGAAAAGGAAACAAATCGTTGAATTTA
1 TAAAAGGAAATAAATCATAGAATTTATTTTCATATTTTAAAAAAGGAAACAAATCGTTGAATTTA
*
61780 GTTTCTTGTTTTG
66 GTTTCTTCTTTTG
* * *
61793 TAAAAGGAAATAAATCATAGAATTTATTTTCATATTTTAAAAAATGAAATAAATCGTTGGATTTA
1 TAAAAGGAAATAAATCATAGAATTTATTTTCATATTTTAAAAAAGGAAACAAATCGTTGAATTTA
61858 -TTT-TTCTATATTG
66 GTTTCTTCT-T-TTG
*
61871 TAAAAAGCAAATAAAT
1 T-AAAAGGAAATAAAT
61887 TGAGCAAATC
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
76 3 0.04
77 4 0.05
78 61 0.75
79 13 0.16
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (78 bp):
TAAAAGGAAATAAATCATAGAATTTATTTTCATATTTTAAAAAAGGAAACAAATCGTTGAATTTA
GTTTCTTCTTTTG
Found at i:67354 original size:17 final size:18
Alignment explanation
Indices: 67315--67355 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
67305 ATATTATGTA
* *
67315 TTTAATTTATTTAAGTTT
1 TTTACTTTATTTAAGTAT
67333 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
67350 TTTACT
1 TTTACT
67356 AATATAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:69060 original size:18 final size:18
Alignment explanation
Indices: 69037--69071 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
69027 GCAGCCACCG
*
69037 CAGCCATTTATGATGCCA
1 CAGCCATATATGATGCCA
*
69055 CAGCCATATGTGATGCC
1 CAGCCATATATGATGCC
69072 GCCATCGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (18 bp):
CAGCCATATATGATGCCA
Found at i:69635 original size:26 final size:24
Alignment explanation
Indices: 69564--69635 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
69554 TTATATTTGT
69564 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
69589 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
69611 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
69636 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:73467 original size:30 final size:29
Alignment explanation
Indices: 73405--73467 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
73395 TATTACTACG
*
73405 GGTGTTAAATCGAGAAATATAATCTGACC
1 GGTGTTAAATCGAGAAATATAATCTCACC
* *
73434 GGTGTTAGATCGATAAATAT-ATCGATCACC
1 GGTGTTAAATCGAGAAATATAATC--TCACC
73464 GGTG
1 GGTG
73468 ATTTTTCGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 3 0.10
29 18 0.62
30 8 0.28
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (29 bp):
GGTGTTAAATCGAGAAATATAATCTCACC
Found at i:73991 original size:2 final size:2
Alignment explanation
Indices: 73980--74039 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
73970 AAAAGATTTT
73980 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74020 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
74040 AATGTTGAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:75672 original size:30 final size:31
Alignment explanation
Indices: 75630--75704 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
75620 TTAACTCGGG
*
75630 GTGACCACATCTTAATT-AATAAAAACGAAA
1 GTGACCATATCTTAATTAAATAAAAACGAAA
* *
75660 GTGACTATATCTTAATTAAATAAAATCGAAA
1 GTGACCATATCTTAATTAAATAAAAACGAAA
75691 GTGACCATATCTTA
1 GTGACCATATCTTA
75705 TGTTTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 15 0.38
31 25 0.62
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (31 bp):
GTGACCATATCTTAATTAAATAAAAACGAAA
Found at i:87861 original size:40 final size:40
Alignment explanation
Indices: 87806--87967 Score: 306
Period size: 40 Copynumber: 4.0 Consensus size: 40
87796 TGTAGGTTTA
*
87806 TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
87846 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
87886 TAATACACTTCGGCGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
87926 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
87966 TA
1 TA
87968 GCACTACGGT
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 119 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:88196 original size:46 final size:44
Alignment explanation
Indices: 88072--88197 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 44
88062 GTAACCATGC
* *
88072 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATATAA
1 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATATAA
* * * *
88115 AAAAAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA--TAAATGGTAAGTA-TAT-ATAA
* *
88163 AAATAAGCTTATGAGCTTATGGGATAAAAGGTAAG
1 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAG
88198 AAATTTTTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
43 21 0.31
45 1 0.01
46 20 0.29
47 2 0.03
48 24 0.35
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.29
Consensus pattern (44 bp):
AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATATAA
Found at i:88600 original size:12 final size:12
Alignment explanation
Indices: 88583--88607 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88573 AATTTTCAGA
88583 AGTTACTGTAGC
1 AGTTACTGTAGC
88595 AGTTACTGTAGC
1 AGTTACTGTAGC
88607 A
1 A
88608 TGAACAGTAA
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:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (12 bp):
AGTTACTGTAGC
Found at i:93388 original size:28 final size:28
Alignment explanation
Indices: 93343--93408 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
93333 AATTTTTAAA
*
93343 ATGACCAT-ATCATCCACATCTTTGGTT
1 ATGACCATGACCATCCACATCTTTGGTT
93370 ATGACCATGACCATCCACATCTTTGGTT
1 ATGACCATGACCATCCACATCTTTGGTT
93398 ATGACCATGAC
1 ATGACCATGAC
93409 TATGGTCACG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 8 0.22
28 29 0.78
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (28 bp):
ATGACCATGACCATCCACATCTTTGGTT
Found at i:93655 original size:21 final size:21
Alignment explanation
Indices: 93626--93678 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
93616 ATTCTGACTA
*
93626 TCGCATTGCGCTTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
93647 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
* *
93668 TTGCAATGCGA
1 TCGCATTGCGA
93679 ATACGTAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:93712 original size:20 final size:20
Alignment explanation
Indices: 93670--93782 Score: 172
Period size: 20 Copynumber: 5.5 Consensus size: 20
93660 TTCCTAATTT
93670 GCAATGCGAATACGTAAAAATC
1 GCAATGCGAATACGT--AAATC
93692 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
*
93712 GTAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
*
93732 GTAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
*
93752 ACAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
*
93772 GCAACGCGAAT
1 GCAATGCGAAT
93783 CTGACTATCG
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
20 71 0.83
22 15 0.17
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (20 bp):
GCAATGCGAATACGTAAATC
Found at i:94005 original size:22 final size:22
Alignment explanation
Indices: 93980--94045 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
93970 GGCGACATTT
*
93980 GTCCCCATCTCCGAAGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
94002 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
94024 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
94046 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:94450 original size:20 final size:20
Alignment explanation
Indices: 94387--94451 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 20
94377 TCTGTCTATA
*
94387 CGATTTTCA-TTTCGCGTTG
1 CGATTTTCATTTTCGTGTTG
** *
94406 CGATAGTCATATTCGTGTTG
1 CGATTTTCATTTTCGTGTTG
94426 CGATTTTCATTTTCGTGTTG
1 CGATTTTCATTTTCGTGTTG
94446 CGATTT
1 CGATTT
94452 AAAGTTTCAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 7 0.18
20 31 0.82
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.48
Consensus pattern (20 bp):
CGATTTTCATTTTCGTGTTG
Found at i:94459 original size:20 final size:20
Alignment explanation
Indices: 94417--94459 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
94407 GATAGTCATA
** *
94417 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTAAAGT
94437 TTCGTGTTGCGATTTAAAGT
1 TTCGTGTTGCGATTTAAAGT
94457 TTC
1 TTC
94460 AGAAACTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.51
Consensus pattern (20 bp):
TTCGTGTTGCGATTTAAAGT
Found at i:96381 original size:34 final size:34
Alignment explanation
Indices: 96338--96431 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 34
96328 ATAGTTTACT
* * * *
96338 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAATATCGCAACAACAAA
*
96372 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAAATGAATATCGCAACAACAAA
* * *
96405 ATTGCAACGCGAAAATGATTATCGCAA
1 ATCGCAATGCGAAAATGAATATCGCAA
96432 TGCAAATTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 26 0.52
34 24 0.48
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.16
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAATATCGCAACAACAAA
Found at i:96523 original size:20 final size:20
Alignment explanation
Indices: 96498--96624 Score: 155
Period size: 20 Copynumber: 6.3 Consensus size: 20
96488 GATTCTCTCG
96498 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
* *
96518 TTGCGATAGTTAAATTCCCA
1 TTGCGATAGTCAAATTCGCA
*
96538 TTGCGATAGTTAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
96558 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
96578 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
** *
96598 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
96618 TTGCGAT
1 TTGCGAT
96625 TTTAAGTTTC
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 100 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:96610 original size:40 final size:40
Alignment explanation
Indices: 96498--96624 Score: 173
Period size: 40 Copynumber: 3.2 Consensus size: 40
96488 GATTCTCTCG
* ** *
96498 TTGCGATAGTCAAATTCGCATTGCGATAGTTAAATTCCCA
1 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCA
*
96538 TTGCGATAGTTAAATTCGCATTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCA
** * *
96578 TTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCA
96618 TTGCGAT
1 TTGCGAT
96625 TTTAAGTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (40 bp):
TTGCGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCA
Found at i:97200 original size:21 final size:21
Alignment explanation
Indices: 97109--97206 Score: 65
Period size: 21 Copynumber: 4.7 Consensus size: 21
97099 GACTCACATG
97109 TCATCGTTCAAGAGG-CA-TCC
1 TCATCGTTCAAGAGGCCACT-C
* * *
97129 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGGCCACTC
** * *
97151 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCACTC
* * *
97172 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCACTC
*
97193 TCATCGTTGAAGAG
1 TCATCGTTCAAGAG
97207 CTCCATCCCA
Statistics
Matches: 57, Mismatches: 18, Indels: 5
0.71 0.22 0.06
Matches are distributed among these distances:
20 1 0.02
21 53 0.93
22 2 0.04
23 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCACTC
Found at i:98724 original size:34 final size:34
Alignment explanation
Indices: 98681--98776 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
98671 ACTAAATCCG
98681 CGTTGCGATTTTCATTTTCGCGTTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCGTTGCGATTCACT
* *
98715 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCGTTGCGATTCACT
** *
98748 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCGTTGCGAT
98777 AGTCAATTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCGTTGCGATTCACT
Found at i:98773 original size:20 final size:20
Alignment explanation
Indices: 98748--98841 Score: 154
Period size: 20 Copynumber: 4.7 Consensus size: 20
98738 GCGATTCTCT
98748 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
98768 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
98788 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
98808 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
98828 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
98842 AATGAATGTC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 67 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:101038 original size:14 final size:14
Alignment explanation
Indices: 101019--101045 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
101009 TCCTATGGCA
101019 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
101033 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
101046 TTTCTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:101310 original size:24 final size:24
Alignment explanation
Indices: 101259--101310 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
101249 ATCTGAGTAT
** *
101259 TGACCAAGATCAAATTCCGGGTAT
1 TGACCAAGATCAAATTCCGAATAC
**
101283 TGACCAAGATCAAATTTTGAATAC
1 TGACCAAGATCAAATTCCGAATAC
101307 TGAC
1 TGAC
101311 TAGCACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAATTCCGAATAC
Found at i:102163 original size:20 final size:20
Alignment explanation
Indices: 102138--102203 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
102128 AAATTCAGTA
102138 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
102158 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
102178 TTGCGATAGTC-GATTCGCG
1 TTGCGATAGTCAGAATCTCG
102197 TTGCGAT
1 TTGCGAT
102204 TTACATATTC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 13 0.30
20 31 0.70
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:102215 original size:20 final size:20
Alignment explanation
Indices: 102190--102242 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
102180 GCGATAGTCG
*
102190 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACAT
*
102210 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACAT
*
102230 AGTCGCATTGCGA
1 ATTCGCATTGCGA
102243 ATTAGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACAT
Found at i:103601 original size:14 final size:14
Alignment explanation
Indices: 103582--103608 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
103572 ATGGACTAAC
103582 ATATAAGAAAAATA
1 ATATAAGAAAAATA
103596 ATATAAGAAAAAT
1 ATATAAGAAAAAT
103609 GGACGAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (14 bp):
ATATAAGAAAAATA
Found at i:105692 original size:16 final size:17
Alignment explanation
Indices: 105661--105693 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
105651 TTATATTAAC
105661 TTATTAAATATAATTTA
1 TTATTAAATATAATTTA
*
105678 TTATTAACT-TAATTTA
1 TTATTAAATATAATTTA
105694 AAAATATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTAAATATAATTTA
Found at i:105694 original size:27 final size:26
Alignment explanation
Indices: 105650--105726 Score: 70
Period size: 27 Copynumber: 3.0 Consensus size: 26
105640 ATAATATTTT
105650 TTTA-TATTAACTTA-TTAAATATAA
1 TTTATTATTAACTTATTTAAATATAA
*
105674 TTTATTATTAACTTAATTTAAAAAT-A
1 TTTATTATTAACTT-ATTTAAATATAA
* **
105700 TATTATTTTTATTTTCATTTAAATATA
1 T-TTATTATTAACTT-ATTTAAATATA
105727 TATATATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
24 4 0.10
25 9 0.21
26 3 0.07
27 26 0.62
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTATTATTAACTTATTTAAATATAA
Found at i:105935 original size:29 final size:31
Alignment explanation
Indices: 105875--105945 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 31
105865 ACCCGTGATT
*
105875 ATCACATCTTAATTAAATAAAAACGAAAGTG
1 ATCATATCTTAATTAAATAAAAACGAAAGTG
* * *
105906 ATTATATCTTAATT-AA-AAAAATGAATGTG
1 ATCATATCTTAATTAAATAAAAACGAAAGTG
105935 ATCATATCTTA
1 ATCATATCTTA
105946 TGGTTTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 21 0.60
30 2 0.06
31 12 0.34
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (31 bp):
ATCATATCTTAATTAAATAAAAACGAAAGTG
Found at i:112060 original size:16 final size:16
Alignment explanation
Indices: 112039--112105 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 16
112029 GTCTCCAACG
**
112039 TTTATGTTTTTGTTCA
1 TTTATGTTCGTGTTCA
*
112055 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
112071 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
112087 TATATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
112101 TTTAT
1 TTTAT
112106 TAAATGAACG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 4 0.09
15 2 0.04
16 39 0.87
ACGTcount: A:0.12, C:0.09, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:112078 original size:32 final size:32
Alignment explanation
Indices: 112037--112097 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
112027 GGGTCTCCAA
** *
112037 CGTTTATGTTTTTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATATATGTTCGTGTT
*
112069 CGTTTATGTTCGTGTTCGTATATGTTCGT
1 CGTTTATGTTCGTGTTCATATATGTTCGT
112098 TTATTTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.10, C:0.11, G:0.21, T:0.57
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATATATGTTCGTGTT
Found at i:113310 original size:54 final size:54
Alignment explanation
Indices: 113251--113361 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
113241 AACTAATTTG
113251 ATAAGATAAAATTTATAAATAAACATTAAATTATATCAAAATGATATTTTTTAT
1 ATAAGATAAAATTTATAAATAAACATTAAATTATATCAAAATGATATTTTTTAT
* *
113305 ATAAGATAAAATTTATAAATGAACATTAAATTATATCAAAATGATTTTTTTTAT
1 ATAAGATAAAATTTATAAATAAACATTAAATTATATCAAAATGATATTTTTTAT
113359 ATA
1 ATA
113362 CCAAATTTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (54 bp):
ATAAGATAAAATTTATAAATAAACATTAAATTATATCAAAATGATATTTTTTAT
Found at i:130034 original size:15 final size:16
Alignment explanation
Indices: 130014--130043 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
130004 ATAATATTTT
130014 GTTTTAAAAA-AATTA
1 GTTTTAAAAAGAATTA
130029 GTTTTAAAAAGAATT
1 GTTTTAAAAAGAATT
130044 TAGACTTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (16 bp):
GTTTTAAAAAGAATTA
Found at i:133257 original size:14 final size:14
Alignment explanation
Indices: 133238--133264 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
133228 TGATGCAAAC
133238 TGTAGAAAACAGAT
1 TGTAGAAAACAGAT
133252 TGTAGAAAACAGA
1 TGTAGAAAACAGA
133265 CAAGTCTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.22, T:0.19
Consensus pattern (14 bp):
TGTAGAAAACAGAT
Found at i:135567 original size:51 final size:51
Alignment explanation
Indices: 135491--135591 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
135481 TAAGGAAAGG
* *
135491 ATAGGTTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
135542 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
135592 CTCCCCCTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
Found at i:137373 original size:14 final size:14
Alignment explanation
Indices: 137354--137381 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
137344 CCTGATACCA
137354 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
137368 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
137382 AAGTCTGTTA
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:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:148597 original size:3 final size:3
Alignment explanation
Indices: 148589--148619 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
148579 TCAATATTGG
148589 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
148620 GGGGTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:148654 original size:2 final size:2
Alignment explanation
Indices: 148647--148674 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
148637 TTTACCTTTA
148647 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
148675 TAATTAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:149195 original size:27 final size:27
Alignment explanation
Indices: 149157--149304 Score: 251
Period size: 27 Copynumber: 5.5 Consensus size: 27
149147 CATTTATGTT
*
149157 TCTCTCTCTCGGAGAGAGAAACTGAAA
1 TCTCTCTCTAGGAGAGAGAAACTGAAA
*
149184 TCTCTCTCTCGGAGAGAGAAACTGAAA
1 TCTCTCTCTAGGAGAGAGAAACTGAAA
149211 TCTCTCTCTAGGAGAGAGAAACTGAAA
1 TCTCTCTCTAGGAGAGAGAAACTGAAA
149238 TCTCTCTCTAGGAGAGAGAAACTGAAA
1 TCTCTCTCTAGGAGAGAGAAACTGAAA
* * *
149265 TCTATCTCTAGAAGAGAGAAACTAAAA
1 TCTCTCTCTAGGAGAGAGAAACTGAAA
149292 TCTCTCTCTAGGA
1 TCTCTCTCTAGGA
149305 TTCCCTCACC
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 115 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
TCTCTCTCTAGGAGAGAGAAACTGAAA
Found at i:150124 original size:3 final size:3
Alignment explanation
Indices: 150118--150198 Score: 153
Period size: 3 Copynumber: 27.0 Consensus size: 3
150108 ATTTATTATT
*
150118 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
150166 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
150199 AATGGGACAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:150627 original size:124 final size:123
Alignment explanation
Indices: 150341--151013 Score: 1014
Period size: 124 Copynumber: 5.5 Consensus size: 123
150331 AGTTCTTATT
* ** *
150341 ATTATGAACTTCTTCTTCTTCTTTGGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAACGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
* *
150406 ATGCTGCTCTATCTCCTTCTGTGATAGAGTCGAGCAAAAGGTTGAATACGTTCTTCAG
66 ATGATGCTCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAATACGTTCTTCAG
* **
150464 ATTATGAACTTCTTCTTCCTCTTCAGATTAGTTCTTCTTATTACGAACTCCTTCTGGAAATGACG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
* * * *
150529 ATGTTGCCCTATCTCATTCTGCGATAGAGTCAAGCAAAAAGGTTGAATACGTTCTTCAG
66 ATGATGCTCTATCTCCTTCTGTGATAGAGTCAAGC-AAAAGGTTGAATACGTTCTTCAG
* * *
150588 ATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTTATTACGAACTTCTTTTGGAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
150653 ATGATGCTCTATCTCCTTCTGTGATAGAGTCAAGCAAAAAGGTTGAATACGTTCTTCAG
66 ATGATGCTCTATCTCCTTCTGTGATAGAGTCAAGC-AAAAGGTTGAATACGTTCTTCAG
*
150712 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTTCTTCTGGAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
* * * *
150777 ATGATGCTCTATCTCCTTATGTGATAGAATCGAGCAAAAGGTTGAATAAGTTCTTCAG
66 ATGATGCTCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAATACGTTCTTCAG
*
150835 ATTATGAACTTCTTCTTCCTCTTCAGATGAG---TTCTTATTACGAACTCCTTCTGAAAATGTTG
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
* * * * * * *
150897 ATGTTGTTCTCTCTCCTTTTGCGATAGAATC-AGCAAAAGGTTGAATAAGTTCTTCAG
66 ATGATGCTCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAATACGTTCTTCAG
* *
150954 ATTATG-ACTTCTTCTTCCTCTTTAAATGAGTTCTTCTTATTACGAACTCCTTCTGGAAAT
1 ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAAT
151014 AACAATCCAT
Statistics
Matches: 508, Mismatches: 38, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
118 22 0.04
119 32 0.06
120 55 0.11
121 26 0.05
123 141 0.28
124 232 0.46
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (123 bp):
ATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCCTTCTGGAAATGTTG
ATGATGCTCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTGAATACGTTCTTCAG
Found at i:150818 original size:247 final size:246
Alignment explanation
Indices: 150318--151013 Score: 1017
Period size: 247 Copynumber: 2.8 Consensus size: 246
150308 GATTAAAATG
* * * * **
150318 AAAATGTTGAACAAGTTCTT-ATTATTATGAACTTCTTCTTCTTCTTTGGATGAGTTCTTCTTAT
1 AAAAGGTTGAATAAGTTCTTCA-GATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTAT
* *
150382 TACGAACTCCTTCTGGAAACGTTGATGCTGCTCTATCTCCTTCTGTGATAGAGTCGAGCAAAAGG
65 TACGAACTCCTTCTGGAAATGTTGATGATGCTCTATCTCCTTCTGTGATAGAGTC-AGCAAAAGG
*
150447 TTGAATACGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATTAGTTCTTCTTATTACGAAC
129 TTGAATACGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAAC
* * *
150512 TCCTTCTGGAAATGACGATGTTGCCCTATCTCATTCTGCGATAGAGTCAAGCA
194 TCCTTCTGGAAATGACGATGATGCCCTATCTCATTATGCGATAGAATCAAGCA
* *
150565 AAAAGGTTGAATACGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAAATGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* *
150630 ACGAACTTCTTTTGGAAATGTTGATGATGCTCTATCTCCTTCTGTGATAGAGTCAAGCAAAAAGG
66 ACGAACTCCTTCTGGAAATGTTGATGATGCTCTATCTCCTTCTGTGATAGAGTC-AGC-AAAAGG
150695 TTGAATACGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAAC
129 TTGAATACGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAAC
* ** * * * *
150760 TTCTTCTGGAAATGTTGATGATGCTCTATCTCCTTATGTGATAGAATCGAGC-
194 TCCTTCTGGAAATGACGATGATGCCCTATCTCATTATGCGATAGAATCAAGCA
150812 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAG---TTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* * * * * * *
150874 ACGAACTCCTTCTGAAAATGTTGATGTTGTTCTCTCTCCTTTTGCGATAGAATCAGCAAAAGGTT
66 ACGAACTCCTTCTGGAAATGTTGATGATGCTCTATCTCCTTCTGTGATAGAGTCAGCAAAAGGTT
* * *
150939 GAATAAGTTCTTCAGATTATG-ACTTCTTCTTCCTCTTTAAATGAGTTCTTCTTATTACGAACTC
131 GAATACGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTC
151003 CTTCTGGAAAT
196 CTTCTGGAAAT
151014 AACAATCCAT
Statistics
Matches: 408, Mismatches: 39, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
241 51 0.12
242 28 0.07
243 3 0.01
244 53 0.13
247 160 0.39
248 113 0.28
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (246 bp):
AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
ACGAACTCCTTCTGGAAATGTTGATGATGCTCTATCTCCTTCTGTGATAGAGTCAGCAAAAGGTT
GAATACGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTC
CTTCTGGAAATGACGATGATGCCCTATCTCATTATGCGATAGAATCAAGCA
Done.