Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009387.1 Hibiscus syriacus cultivar Beakdansim tig00113279_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: 929501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:814538 original size:41 final size:41
Alignment explanation
Indices: 814493--814585 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
814483 TTTTCCCAAT
814493 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
814534 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
814575 TCGCAATGCGA
1 TCGCAATGCGA
814586 TACTTACTAT
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:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:814598 original size:41 final size:41
Alignment explanation
Indices: 814512--814646 Score: 157
Period size: 41 Copynumber: 3.3 Consensus size: 41
814502 GAATAAGTAA
** *
814512 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
814553 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** *
814594 ATCGCAATGCGATAAT-ACAAAATCGCAACGCGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
814635 TTCGCAACGCGA
1 ATCGCAACGCGA
814647 TTTACATAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
40 5 0.06
41 75 0.91
42 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:814599 original size:20 final size:20
Alignment explanation
Indices: 814574--814647 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
814564 AATTGGGAAA
*
814574 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
814594 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
814615 ATCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTTACT
*
814635 TTCGCAACGCGAT
1 ATCGCAACGCGAT
814648 TTACATAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 26 0.58
21 13 0.29
22 3 0.07
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:814659 original size:20 final size:20
Alignment explanation
Indices: 814573--814659 Score: 72
Period size: 20 Copynumber: 4.3 Consensus size: 20
814563 GAATTGGGAA
*
814573 AATCGCAATGCGATACTTACT
1 AATCGCAACGCGATA-TTACT
* * *
814594 -ATCGCAATGCGATAATACAA
1 AATCGCAACGCGATATTAC-T
814614 AATCGCAACGCGATACTTACT
1 AATCGCAACGCGATA-TTACT
*
814635 -TTCGCAACGCGAT-TTACAT
1 AATCGCAACGCGATATTAC-T
814654 AATCGC
1 AATCGC
814660 CATTCGTATT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
18 4 0.07
19 4 0.07
20 30 0.56
21 13 0.24
22 3 0.06
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (20 bp):
AATCGCAACGCGATATTACT
Found at i:815206 original size:19 final size:19
Alignment explanation
Indices: 815168--815234 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
815158 TTCGAGAATG
815168 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
815188 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
815207 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
815226 AAAATCGCA
1 AAAATCGCA
815235 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:815276 original size:20 final size:19
Alignment explanation
Indices: 815230--815361 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
815220 GAAACCAAAA
*
815230 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
815249 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
815268 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
815288 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
815304 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
815321 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
* *
815340 ATCTCGTTTCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
815360 TC
1 TC
815362 AACCAAAAGA
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 46 0.49
20 34 0.36
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:815311 original size:39 final size:39
Alignment explanation
Indices: 815235--815311 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
815225 CAAAATCGCA
* **
815235 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
815274 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
815312 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:817424 original size:42 final size:42
Alignment explanation
Indices: 817364--817486 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
817354 GCCCGACTCG
* * *
817364 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
817406 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
817448 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
817487 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:817444 original size:21 final size:21
Alignment explanation
Indices: 817420--817486 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
817410 TCATTCCTCG
817420 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
817441 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
817462 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
817483 AGAG
1 AGAG
817487 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:818860 original size:14 final size:14
Alignment explanation
Indices: 818841--818876 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
818831 ATTGTTTAAT
818841 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
818855 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
818869 TGATTTGT
1 TGATTTGT
818877 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:819078 original size:19 final size:19
Alignment explanation
Indices: 819056--819153 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
819046 CGAAATTAAA
*
819056 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
819075 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
819091 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
819108 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
819124 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
819141 TTCGCATTGCGAT
1 TTCGCATTGCGAT
819154 GGACATTAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 12 0.19
16 13 0.21
17 13 0.21
19 24 0.39
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:819102 original size:33 final size:33
Alignment explanation
Indices: 819060--819153 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
819050 ATTAAATTCG
819060 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
819093 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
819126 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
819154 GGACATTAAG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:821435 original size:12 final size:12
Alignment explanation
Indices: 821418--821442 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
821408 TCTTCGGGGA
821418 CTTTTTCTTCTT
1 CTTTTTCTTCTT
821430 CTTTTTCTTCTT
1 CTTTTTCTTCTT
821442 C
1 C
821443 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:821658 original size:23 final size:23
Alignment explanation
Indices: 821617--821669 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
821607 CTGAAACATC
* *
821617 ATCAAATCCGTGTATTGACCAAT
1 ATCAAATCCGGGTATTGACCAAG
821640 ATCAAAGTCCGGGTA-TGACCAAG
1 ATCAAA-TCCGGGTATTGACCAAG
821663 ATCAAAT
1 ATCAAAT
821670 TTCGAATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 1 0.04
23 19 0.70
24 7 0.26
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (23 bp):
ATCAAATCCGGGTATTGACCAAG
Found at i:822727 original size:20 final size:20
Alignment explanation
Indices: 822702--822759 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
822692 ATTCATTTGA
822702 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
822722 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
822742 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
822760 CGCAATGCGA
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:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:822802 original size:14 final size:14
Alignment explanation
Indices: 822783--822840 Score: 71
Period size: 14 Copynumber: 3.8 Consensus size: 14
822773 GAAAATCACA
822783 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
822797 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
822814 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
822830 TTGCGATTTTC
1 TTGCGATTTTC
822841 ATTTCGCATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 22 0.56
16 3 0.08
17 3 0.08
19 11 0.28
ACGTcount: A:0.10, C:0.21, G:0.19, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:822802 original size:33 final size:33
Alignment explanation
Indices: 822765--822835 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
822755 AAAATCGCAA
822765 TGCGAAATGAAAATCACATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCACATTGCGATTTTCTCGT
** ** ** *
822798 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCACATTGCGATTTTCTCGT
822831 TGCGA
1 TGCGA
822836 TTTTCATTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCACATTGCGATTTTCTCGT
Found at i:822819 original size:19 final size:19
Alignment explanation
Indices: 822797--822931 Score: 208
Period size: 19 Copynumber: 7.4 Consensus size: 19
822787 GATTTTCTCG
822797 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
822816 TTGCGATTTTC---TCG--
1 TTGCGATTTTCATTTCGCA
822830 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
822849 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
822868 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
822887 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
822906 TTGCGATTTCCATTTCGCG
1 TTGCGATTTTCATTTCGCA
822925 TTGCGAT
1 TTGCGAT
822932 AGTCTGTTTT
Statistics
Matches: 107, Mismatches: 4, Indels: 10
0.88 0.03 0.08
Matches are distributed among these distances:
14 11 0.10
16 3 0.03
17 3 0.03
19 90 0.84
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:822836 original size:33 final size:35
Alignment explanation
Indices: 822781--822931 Score: 193
Period size: 38 Copynumber: 4.3 Consensus size: 35
822771 ATGAAAATCA
822781 CATTGCGATTTTC-TCG-TTGCGATTTTCATTTCG
1 CATTGCGATTTTCTTCGATTGCGATTTTCATTTCG
822814 CATTGCGATTTTC-TCG-TTGCGATTTTCATTTCG
1 CATTGCGATTTTCTTCGATTGCGATTTTCATTTCG
822847 CATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 CATTGCGATTTTC--TTCG-ATTGCGATTTTCATTTCG
* *
822885 CATTGCAATTTTCATTTCGCATTGCGATTTCCATTTCG
1 CATTGCGATTTTC--TTCG-ATTGCGATTTTCATTTCG
*
822923 CGTTGCGAT
1 CATTGCGAT
822932 AGTCTGTTTT
Statistics
Matches: 109, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
33 46 0.42
36 3 0.03
38 60 0.55
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (35 bp):
CATTGCGATTTTCTTCGATTGCGATTTTCATTTCG
Found at i:824993 original size:18 final size:18
Alignment explanation
Indices: 824912--825039 Score: 184
Period size: 18 Copynumber: 6.9 Consensus size: 18
824902 ACGAAACTTA
824912 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
824930 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAACGC-GAAAT-G
** *
824951 CTATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
824969 AAAATCGCAACGCGAAATG
1 -AAATCGCAACGCGAAATG
824988 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
825006 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
825024 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
825040 CACAAATCGC
Statistics
Matches: 100, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
18 54 0.54
19 30 0.30
20 15 0.15
21 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:825087 original size:14 final size:14
Alignment explanation
Indices: 825068--825125 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
825058 TTTCATTTCG
825068 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
825082 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
825098 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
825114 CGTTGCGATTTT
1 CGTTGCGATTTT
825126 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:825132 original size:33 final size:33
Alignment explanation
Indices: 825051--825141 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
825041 ACAAATCGCA
*
825051 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
825084 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
825116 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
825142 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:825148 original size:19 final size:19
Alignment explanation
Indices: 825126--825171 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
825116 TTGCGATTTT
825126 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
** *
825145 CATTTCCGTGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
825165 CATTTCG
1 CATTTCG
825172 TGTTGCGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:825160 original size:20 final size:19
Alignment explanation
Indices: 825135--825179 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
825125 TCATTTCGCA
825135 TTGCGATAGCCATTTCCGTG
1 TTGCGATAGCCATTT-CGTG
*
825155 TTGCGATAGTCATTTCGTG
1 TTGCGATAGCCATTTCGTG
825174 TTGCGA
1 TTGCGA
825180 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.38
Consensus pattern (19 bp):
TTGCGATAGCCATTTCGTG
Found at i:825175 original size:19 final size:19
Alignment explanation
Indices: 825115--825179 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
825105 CGATTTTGTC
** *
825115 GTTGCGATTTTCATTTCGC
1 GTTGCGATAGTCATTTCGT
* *
825134 ATTGCGATAGCCATTTCCGT
1 GTTGCGATAGTCATTT-CGT
825154 GTTGCGATAGTCATTTCGT
1 GTTGCGATAGTCATTTCGT
825173 GTTGCGA
1 GTTGCGA
825180 AAGTAAACTA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.58
20 16 0.42
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.40
Consensus pattern (19 bp):
GTTGCGATAGTCATTTCGT
Found at i:825696 original size:18 final size:18
Alignment explanation
Indices: 825652--825696 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
825642 GTCGATCAGA
* *
825652 TGATGGCTCTGGGTGGGG
1 TGATGGCTCTGGGCGAGG
* *
825670 TTATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
825688 TGATGGCTC
1 TGATGGCTC
825697 CCGAAGTGGA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.11, C:0.16, G:0.44, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:827541 original size:20 final size:20
Alignment explanation
Indices: 827518--827569 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
827508 GATTATGTAA
*
827518 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
827538 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
827558 ATCTCGTTGCGA
1 ATCGCGTTGCGA
827570 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:827603 original size:20 final size:20
Alignment explanation
Indices: 827498--827611 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
827488 CGCTTTGAAA
827498 ATCGCATTGCGATTATGTAA--
1 ATCGCATTGCGA-TA-GTAAGT
* * *
827518 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
827538 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * * *
827558 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTAAGT
827579 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
*
827599 ATCGCATTACGAT
1 ATCGCATTGCGAT
827612 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 55 0.72
21 12 0.16
22 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:827612 original size:41 final size:41
Alignment explanation
Indices: 827537--827614 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
827527 CGAAAGTCAG
* * * *
827537 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTACGATTTTGTAT
*
827578 TATCGCATTGCGATAGTAAGTATCGCATTACGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTACGATTTT
827615 CCCAATTCGC
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:0.24, C:0.15, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTACGATTTTGTAT
Found at i:827630 original size:41 final size:41
Alignment explanation
Indices: 827537--827632 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
827527 CGAAAGTCAG
* * * * ** *
827537 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTACGATTTTCCAA
*
827578 TATCGCATTGCGATAGTAAGTATCGCATTACGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTACGATTTT-CCAA
827620 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
827633 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTACGATTTTCCAA
Found at i:827648 original size:20 final size:20
Alignment explanation
Indices: 827619--827712 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
827609 GATTTTCCCA
827619 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
*
827639 ATTCGTGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
827659 ATTCGCATTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
827680 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
*
827700 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
827713 ATTGGGAAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 46 0.74
21 16 0.26
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:827650 original size:61 final size:61
Alignment explanation
Indices: 827585--827704 Score: 188
Period size: 61 Copynumber: 2.0 Consensus size: 61
827575 TATTATCGCA
827585 TTGCGATAGTAAGTA-TCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGTG
1 TTGCGAT-GTAAGTATTCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGTG
* ** *
827646 TTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 TTGCGATGTAAGTATTCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
827705 CATTGCGAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 4 0.07
61 50 0.93
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.42
Consensus pattern (61 bp):
TTGCGATGTAAGTATTCGCATTACGATTTTCCCAATTCGCGTTGCGATTTACTTATTCGTG
Found at i:834642 original size:17 final size:18
Alignment explanation
Indices: 834620--834667 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
834610 CTGACTTACT
*
834620 TTATATTTAT-AGTATAA
1 TTATATATATAAGTATAA
834637 TTATATATATAAGTATATA
1 TTATATATATAAGTATA-A
*
834656 CTTATGTATATA
1 -TTATATATATA
834668 CTTATACATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 9 0.35
18 6 0.23
19 1 0.04
20 10 0.38
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (18 bp):
TTATATATATAAGTATAA
Found at i:834882 original size:12 final size:12
Alignment explanation
Indices: 834803--834882 Score: 52
Period size: 12 Copynumber: 6.4 Consensus size: 12
834793 TAACATAAAG
*
834803 ATATACTTATGT
1 ATATACTTATAT
* * *
834815 ACATACATCATAC
1 ATATAC-TTATAT
*
834828 ATATATTTATAT
1 ATATACTTATAT
*
834840 ATATACCTATATGT
1 ATATA-CT-TATAT
* *
834854 ACATACTTATGT
1 ATATACTTATAT
834866 ATATACTTATAT
1 ATATACTTATAT
*
834878 TTATA
1 ATATA
834883 GCTTGTCGAA
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
12 33 0.65
13 10 0.20
14 8 0.16
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (12 bp):
ATATACTTATAT
Found at i:836592 original size:105 final size:106
Alignment explanation
Indices: 836438--836652 Score: 287
Period size: 105 Copynumber: 2.0 Consensus size: 106
836428 TCAAAATGCA
*
836438 AAAACACGCCTAAATAAGGGAACTAATATAAAATATTCCAGAAAATACATAACATGCATGAAAAC
1 AAAACACGCCTAAATAAGGGAACTAATAGAAAATATTCCAGAAAATACATAACATGCATGAAAAC
* *
836503 GATTAAATAACAA-CTTCGATCCAT-ACCGGTGACCAACATAC
66 GAGTAAATAACAACCTT-GATCC-TCACAGGTGACCAACATAC
* *
836544 AAAACACG-CTAAACTATGGGGACTAAATAGAAAATA-TCCA-AAAATACATAACATGCATGAAA
1 AAAACACGCCTAAA-TAAGGGAACT-AATAGAAAATATTCCAGAAAATACATAACATGCATGAAA
* * *
836606 ACGGGTAAATAACAACCTTGGTTCTCACAGGTGACCAACATAC
64 ACGAGTAAATAACAACCTTGATCCTCACAGGTGACCAACATAC
836649 AAAA
1 AAAA
836653 TATGCCAGAT
Statistics
Matches: 97, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
104 1 0.01
105 63 0.65
106 23 0.24
107 10 0.10
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.19
Consensus pattern (106 bp):
AAAACACGCCTAAATAAGGGAACTAATAGAAAATATTCCAGAAAATACATAACATGCATGAAAAC
GAGTAAATAACAACCTTGATCCTCACAGGTGACCAACATAC
Found at i:837694 original size:3 final size:3
Alignment explanation
Indices: 837662--837742 Score: 91
Period size: 3 Copynumber: 27.7 Consensus size: 3
837652 GCCTGCAGAT
*
837662 ATA AAA ATA A-A ACTA AT- ATA A-A AT- ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
837703 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATTA ATA ATA AT
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA AT
837743 TAACAAGATC
Statistics
Matches: 68, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
2 10 0.15
3 50 0.74
4 8 0.12
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:837736 original size:16 final size:15
Alignment explanation
Indices: 837662--837742 Score: 91
Period size: 16 Copynumber: 5.5 Consensus size: 15
837652 GCCTGCAGAT
*
837662 ATAAAAATAA-AACTA
1 ATAATAATAATAA-TA
837677 AT-ATAA-AAT-ATA
1 ATAATAATAATAATA
837689 ATAATAAT-ATAATA
1 ATAATAATAATAATA
837703 ATAATAAATAATAATA
1 ATAAT-AATAATAATA
837719 ATAATAATAATAATTA
1 ATAATAATAATAA-TA
837735 ATAATAAT
1 ATAATAAT
837743 TAACAAGATC
Statistics
Matches: 58, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
12 4 0.07
13 9 0.16
14 11 0.19
15 13 0.22
16 21 0.36
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAATAATAATAATA
Found at i:839922 original size:19 final size:19
Alignment explanation
Indices: 839898--839946 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
839888 ATGACCAACA
* *
839898 AATTCGCAACGCGATCTCG
1 AATTCGCAACGCGAACTCC
*
839917 AATTCGCAATGCGAACTCC
1 AATTCGCAACGCGAACTCC
839936 AATTTCGCAAC
1 AA-TTCGCAAC
839947 TCAGTTTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (19 bp):
AATTCGCAACGCGAACTCC
Found at i:839983 original size:20 final size:20
Alignment explanation
Indices: 839960--840006 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
839950 GTTTCCAAAT
839960 TCGCAATGCGAATCTGTAAA
1 TCGCAATGCGAATCTGTAAA
*
839980 TCGCAACGCGAATCTGTAAA
1 TCGCAATGCGAATCTGTAAA
*
840000 TCACAAT
1 TCGCAAT
840007 ACTGAATTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATCTGTAAA
Found at i:840891 original size:12 final size:12
Alignment explanation
Indices: 840870--840903 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
840860 ACCACATTTC
*
840870 CAATACCAAACA
1 CAATATCAAACA
840882 CAATATCAAACA
1 CAATATCAAACA
*
840894 CAATCTCAAA
1 CAATATCAAA
840904 ACCCGTAACC
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:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:843169 original size:18 final size:18
Alignment explanation
Indices: 843146--843181 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
843136 AAGCAAAAGG
*
843146 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
843164 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
843182 CAACCGGCTT
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:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:843481 original size:20 final size:20
Alignment explanation
Indices: 843408--843483 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
843398 TGTGAAGTTG
* *
843408 ACTTTCGCGTTGCAAATTTG
1 ACTTTCGCGTTGCGAATTTA
* **
843428 GCTTTCATGTTGCGAATTTA
1 ACTTTCGCGTTGCGAATTTA
* **
843448 ACTATCGCAATGCGAATTTA
1 ACTTTCGCGTTGCGAATTTA
843468 ACTTTCGCGTTGCGAA
1 ACTTTCGCGTTGCGAA
843484 AGTGTACCTT
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
ACTTTCGCGTTGCGAATTTA
Found at i:843646 original size:64 final size:64
Alignment explanation
Indices: 843542--843690 Score: 228
Period size: 64 Copynumber: 2.3 Consensus size: 64
843532 AATTTAAAAC
*
843542 AACAAATCAACTTTTACAAATCAATTAACGAAGCAGAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAACGAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** * *
843606 AACAAATCAACTTTTACAAATCAATTAAAC-AAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATT-AACGAAGCAAAAAATAAGAATTATTTACACATCAATTA
843670 AACAAATCAACTTTTACAAAT
1 AACAAATCAACTTTTACAAAT
843691 ACATCAATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
64 75 0.96
65 3 0.04
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.29
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAACGAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:845069 original size:21 final size:21
Alignment explanation
Indices: 845045--845106 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
845035 CGGGCTCTCG
*
845045 AACGGTGGGAGGGACCTCTTA
1 AACGGTGGGAGGGGCCTCTTA
* ** *
845066 AACGATGACAGGGGCCTCTTG
1 AACGGTGGGAGGGGCCTCTTA
* *
845087 AATGGTTGGAGGGGCCTCTT
1 AACGGTGGGAGGGGCCTCTT
845107 GAAGGATGAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (21 bp):
AACGGTGGGAGGGGCCTCTTA
Found at i:845115 original size:42 final size:42
Alignment explanation
Indices: 845052--845161 Score: 148
Period size: 42 Copynumber: 2.6 Consensus size: 42
845042 TCGAACGGTG
* * * *
845052 GGAGGGACCTCTTAAACGATGACAGGGGCCTCTTGAATGGTT
1 GGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAATGATA
* *
845094 GGAGGGGCCTCTTGAAGGATGATAGGGGCCTCTTGAATGATA
1 GGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAATGATA
* *
845136 GGAGAGGCCTCTTGAATGATGACAGG
1 GGAGGGGCCTCTTGAACGATGACAGG
845162 TGCTTCGGGC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.25, C:0.16, G:0.36, T:0.23
Consensus pattern (42 bp):
GGAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAATGATA
Found at i:845154 original size:21 final size:20
Alignment explanation
Indices: 845052--845156 Score: 102
Period size: 21 Copynumber: 5.0 Consensus size: 20
845042 TCGAACGGTG
* * *
845052 GGAGGGACCTCTTAAACGAT
1 GGAGGGGCCTCTTGAATGAT
* *
845072 GACAGGGGCCTCTTGAATGGTT
1 G-GAGGGGCCTCTTGAAT-GAT
*
845094 GGAGGGGCCTCTTGAAGGAT
1 GGAGGGGCCTCTTGAATGAT
*
845114 GATAGGGGCCTCTTGAATGAT
1 G-GAGGGGCCTCTTGAATGAT
*
845135 AGGAGAGGCCTCTTGAATGAT
1 -GGAGGGGCCTCTTGAATGAT
845156 G
1 G
845157 ACAGGTGCTT
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 5 0.07
21 60 0.87
22 4 0.06
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (20 bp):
GGAGGGGCCTCTTGAATGAT
Found at i:847189 original size:20 final size:20
Alignment explanation
Indices: 847166--847236 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
847156 TCTGAAACTT
*
847166 AAAATTGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
847186 AAAATCGCAACGCGAAAATG
1 AAAATCGCAACGCGAAAATG
**
847206 AAAATCGCAACAAGAAAATG
1 AAAATCGCAACGCGAAAATG
847226 AAAATCGCAAC
1 AAAATCGCAAC
847237 TTAAGTTTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.54, C:0.18, G:0.17, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:847603 original size:22 final size:22
Alignment explanation
Indices: 847576--847622 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
847566 GAGATAGATA
847576 GATTTCGCCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACG
*
847598 GATTTCGTCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACG
847620 GAT
1 GAT
847623 ATCGTCGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.15, G:0.45, T:0.21
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACG
Found at i:847627 original size:22 final size:22
Alignment explanation
Indices: 847584--847629 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
847574 TAGATTTCGC
*
847584 CGGAGATGGGGACGGATTTCGT
1 CGGAGATGGGGACGGATATCGT
847606 CGGAGATGGGGACGGATATCGT
1 CGGAGATGGGGACGGATATCGT
847628 CG
1 CG
847630 TAAAGAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.46, T:0.20
Consensus pattern (22 bp):
CGGAGATGGGGACGGATATCGT
Found at i:847824 original size:20 final size:20
Alignment explanation
Indices: 847777--847827 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
847767 TAAACGCCCT
*
847777 TTGCGAACTTGACTTATGTA
1 TTGCGAATTTGACTTATGTA
* *
847797 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTATGTA
847817 TTGCGAATTTG
1 TTGCGAATTTG
847828 GAAAATCGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTA
Found at i:847847 original size:21 final size:21
Alignment explanation
Indices: 847821--847861 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
847811 TCTGTGTTGC
847821 GAATTTGGAAAATCGCAATGT
1 GAATTTGGAAAATCGCAATGT
847842 GAATTTGGAAAATCGCAATG
1 GAATTTGGAAAATCGCAATG
847862 CGATTTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (21 bp):
GAATTTGGAAAATCGCAATGT
Found at i:848618 original size:25 final size:25
Alignment explanation
Indices: 848585--848645 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
848575 TAAAAGTGTG
848585 AAAATCTAAATCTAAAGGCTCGGTTT
1 AAAA-CTAAATCTAAAGGCTCGGTTT
848611 AAAACTAAATCTAAAGGCTCGGTTT
1 AAAACTAAATCTAAAGGCTCGGTTT
848636 AAAACTAAAT
1 AAAACTAAAT
848646 AATTAATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 31 0.89
26 4 0.11
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (25 bp):
AAAACTAAATCTAAAGGCTCGGTTT
Found at i:849245 original size:21 final size:21
Alignment explanation
Indices: 849173--849289 Score: 121
Period size: 21 Copynumber: 5.7 Consensus size: 21
849163 ATTCTGACTA
*
849173 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCTAAT
* *
849194 TCGCGTTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCTAAT
* *
849215 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCTAAT
* * * *
849236 TCGCAATGCGA-ATACGTAA-
1 TCGCATTGCGATTTCCCTAAT
* *
849255 TCGCATTTCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCTAAT
849276 TCGCATTGCGATTT
1 TCGCATTGCGATTT
849290 AGTAAATCGC
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 9 0.11
20 10 0.12
21 61 0.76
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCTAAT
Found at i:851115 original size:14 final size:14
Alignment explanation
Indices: 851098--851125 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
851088 CAATGCAAAA
851098 TGAAAATCGCAACG
1 TGAAAATCGCAACG
851112 TGAAAATCGCAACG
1 TGAAAATCGCAACG
851126 CGGAAATGAC
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:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:851132 original size:14 final size:14
Alignment explanation
Indices: 851099--851132 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
851089 AATGCAAAAT
*
851099 GAAAATCGCAACGT
1 GAAAATCGCAACGC
851113 GAAAATCGCAACGC
1 GAAAATCGCAACGC
*
851127 GGAAAT
1 GAAAAT
851133 GACTATCGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAACGC
Found at i:851173 original size:53 final size:52
Alignment explanation
Indices: 851087--851195 Score: 155
Period size: 53 Copynumber: 2.1 Consensus size: 52
851077 CGAGAGAATT
* **
851087 GCAATGCAAAATGAAAATCGCAACGTGAAAATCGCAACGCGGAAATGACTATC
1 GCAATGCAAAATGAAAATCGCAACGAGAAAATCGCAACGC-GAAATGAAAATC
* * *
851140 GCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATC
1 GCAATGCAAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAATGAAAATC
851192 GCAA
1 GCAA
851196 CGAGGGAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
52 14 0.28
53 36 0.72
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (52 bp):
GCAATGCAAAATGAAAATCGCAACGAGAAAATCGCAACGCGAAATGAAAATC
Found at i:851176 original size:33 final size:33
Alignment explanation
Indices: 851137--851230 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
851127 GGAAATGACT
851137 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
851170 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
851203 ATCGCAATGCGAATTGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
851231 CGAATTTAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:851236 original size:19 final size:19
Alignment explanation
Indices: 851087--851234 Score: 101
Period size: 19 Copynumber: 8.5 Consensus size: 19
851077 CGAGAGAATT
*
851087 GCAATGCAAAATGAAAATC
1 GCAATGCGAAATGAAAATC
851106 GCAA--CG---TGAAAATC
1 GCAATGCGAAATGAAAATC
* **
851120 GCAACGCGGAAATGACTATC
1 GCAATGC-GAAATGAAAATC
851140 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
*
851159 GCAA--CG--A-GAGAATC
1 GCAATGCGAAATGAAAATC
851173 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
**
851192 GCAA--CG--A-GGGAATC
1 GCAATGCGAAATGAAAATC
*
851206 GCAATGCGAATTGAAAATC
1 GCAATGCGAAATGAAAATC
*
851225 GCAACGCGAA
1 GCAATGCGAA
851235 TTTAGTTTCG
Statistics
Matches: 99, Mismatches: 14, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
14 31 0.31
15 2 0.02
16 5 0.05
17 6 0.06
18 1 0.01
19 42 0.42
20 12 0.12
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (19 bp):
GCAATGCGAAATGAAAATC
Found at i:851265 original size:19 final size:19
Alignment explanation
Indices: 851230--851292 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
851220 AAATCGCAAC
*
851230 GCGAATTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
851249 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
* *
851268 GCGATTTTAATTTCGCATT
1 GCGATTTTAGTTTCGCGTT
851287 GCGATT
1 GCGATT
851293 CTCTAGTTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:851323 original size:19 final size:19
Alignment explanation
Indices: 851240--851324 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
851230 GCGAATTTAG
*
851240 TTTCGCGTTGCGATTTT-A
1 TTTCGCATTGCGATTTTCA
* *
851258 GTTTCGCGTTGCGATTTTAA
1 -TTTCGCATTGCGATTTTCA
851278 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
* *
851294 TCTAG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
851311 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
851325 AGTCATTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.11
16 6 0.11
17 5 0.09
19 36 0.67
20 1 0.02
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:851450 original size:14 final size:14
Alignment explanation
Indices: 851431--851466 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
851421 CATCAATTAA
*
851431 ACAAATCATCTTTT
1 ACAAATCACCTTTT
851445 ACAAATCACCTTTT
1 ACAAATCACCTTTT
851459 ACAAATCA
1 ACAAATCA
851467 ATTAAACAAT
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:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCACCTTTT
Found at i:852900 original size:42 final size:42
Alignment explanation
Indices: 852854--852933 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
852844 CGATGACAGT
* * *
852854 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
852896 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
852934 AAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:853374 original size:19 final size:19
Alignment explanation
Indices: 853358--853459 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
853348 AAAAATGACT
853358 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
853377 ATCGCAATGCGAAACGAAA
1 ATCGCAACGCGAAATGAAA
* *
853396 ATCGTAACGCGAAATAAAA
1 ATCGCAACGCGAAATGAAA
* *
853415 ATTGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
* *
853429 ATCGCAATGCGAAATTAAA
1 ATCGCAACGCGAAATGAAA
853448 ATCGCAACGCGA
1 ATCGCAACGCGA
853460 TTATAGTTTC
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
14 8 0.12
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 50 0.78
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:853508 original size:19 final size:19
Alignment explanation
Indices: 853486--853580 Score: 76
Period size: 19 Copynumber: 5.2 Consensus size: 19
853476 TGATTTTTGG
*
853486 TTTCGCATTACGATTTTCA
1 TTTCGCATTGCGATTTTCA
853505 TTTCG-AGTTGCGA--TTC-
1 TTTCGCA-TTGCGATTTTCA
* *
853521 TCTCG--TTGCGATTTTCG
1 TTTCGCATTGCGATTTTCA
*
853538 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
* *
853557 TTCTCTCGTTGCGATTTTCA
1 TT-TCGCATTGCGATTTTCA
853577 TTTC
1 TTTC
853581 AACCAAAAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
14 6 0.09
16 7 0.11
17 7 0.11
18 1 0.02
19 25 0.39
20 18 0.28
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.48
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:853533 original size:33 final size:34
Alignment explanation
Indices: 853496--853580 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 34
853486 TTTCGCATTA
853496 CGATTTTCATTTCGAGTTGCG-ATTCTCTCGTTG
1 CGATTTTCATTTCGAGTTGCGTATTCTCTCGTTG
* *
853529 CGATTTTCGTTTCGCGTTGCGATTTTCATTCTCTCGTTG
1 CGATTTTCATTTCGAGTTGCG----T-ATTCTCTCGTTG
853568 CGATTTTCATTTC
1 CGATTTTCATTTC
853581 AACCAAAAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
33 19 0.44
39 24 0.56
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.48
Consensus pattern (34 bp):
CGATTTTCATTTCGAGTTGCGTATTCTCTCGTTG
Found at i:853568 original size:20 final size:20
Alignment explanation
Indices: 853517--853578 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
853507 TCGAGTTGCG
853517 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* *
853537 GTT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
853556 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
853576 ATT
1 ATT
853579 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.10, C:0.23, G:0.18, T:0.50
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:853787 original size:94 final size:94
Alignment explanation
Indices: 853671--854046 Score: 604
Period size: 94 Copynumber: 4.1 Consensus size: 94
853661 ATGGATTGCA
* * * *
853671 TTAC-TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTTAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
853735 TTAGCAGAATTGGCAGCAAACGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
853764 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
853829 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
853858 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
853923 TTAGCATAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
853952 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT----A
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAA-AGAATACACA
* *
854011 GTTTAGCAGTATTGGCAGCAACCGAATAAAT
64 GTTTAGCAGAATTGGCAGCAACCGAACAAAT
854042 TTACT
1 TTACT
854047 AAGTAATCTA
Statistics
Matches: 270, Mismatches: 9, Indels: 10
0.93 0.03 0.03
Matches are distributed among these distances:
90 34 0.13
93 23 0.09
94 212 0.79
95 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:855785 original size:19 final size:20
Alignment explanation
Indices: 855741--855789 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
855731 GGTTGAAATG
**
855741 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGAGAGAACC
*
855761 AAAATCGCAACGCGA-AACC
1 AAAATCGCAACGAGAGAACC
855780 AAAATCGCAA
1 AAAATCGCAA
855790 TGTGATTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.51, C:0.22, G:0.18, T:0.08
Consensus pattern (20 bp):
AAAATCGCAACGAGAGAACC
Found at i:855838 original size:33 final size:33
Alignment explanation
Indices: 855801--855870 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
855791 GTGATTTTGG
* *
855801 TTTCGCATTGCAATTCTCTTGTTGCGATTTTTA
1 TTTCGCATTGCAATTCTCTCGTTGCGATTTTCA
* *
855834 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCAATTCTCTCGTTGCGATTTTCA
855867 TTTC
1 TTTC
855871 TCTCTTTGCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.11, C:0.21, G:0.17, T:0.50
Consensus pattern (33 bp):
TTTCGCATTGCAATTCTCTCGTTGCGATTTTCA
Found at i:855873 original size:21 final size:21
Alignment explanation
Indices: 855847--855910 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
855837 CGCGTTGCGA
855847 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* **
855868 TTCTCTCTTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
855889 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
855909 TT
1 TT
855911 TAATGTTGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.11, C:0.20, G:0.16, T:0.53
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:855923 original size:20 final size:19
Alignment explanation
Indices: 855854--855925 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
855844 CGATTCTCTC
*
855854 GTTGCGATTTTCATTTCTCT
1 GTTGCGATTTTCATTT-TAT
* ** *
855874 CTTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTT-AT
855895 GTTGCGATTTTCATTTTAAT
1 GTTGCGATTTTCATTTT-AT
855915 GTTGCGATTTT
1 GTTGCGATTTT
855926 AAGTTTAGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.14, C:0.15, G:0.18, T:0.53
Consensus pattern (19 bp):
GTTGCGATTTTCATTTTAT
Found at i:855932 original size:20 final size:20
Alignment explanation
Indices: 855894--855932 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
855884 GTCATTTTCG
* *
855894 TGTTGCGATTTTCATTTTAA
1 TGTTGCGATTTTAAGTTTAA
855914 TGTTGCGATTTTAAGTTTA
1 TGTTGCGATTTTAAGTTTA
855933 GAAACTATTC
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:0.21, C:0.08, G:0.18, T:0.54
Consensus pattern (20 bp):
TGTTGCGATTTTAAGTTTAA
Found at i:856500 original size:20 final size:20
Alignment explanation
Indices: 856477--856570 Score: 118
Period size: 20 Copynumber: 4.7 Consensus size: 20
856467 CGATAGTCAG
856477 ATTCTCATTGCGATTTACGT
1 ATTCTCATTGCGATTTACGT
* * *
856497 ATTCGCATTGCGATTTTCCT
1 ATTCTCATTGCGATTTACGT
*
856517 AATTCGCATTGCGATTTACGT
1 -ATTCTCATTGCGATTTACGT
*
856538 ATT-TGCTTTGCGATTTACGT
1 ATTCT-CATTGCGATTTACGT
856558 ATTCTCATTGCGA
1 ATTCTCATTGCGA
856571 ATTATGAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
20 44 0.70
21 19 0.30
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (20 bp):
ATTCTCATTGCGATTTACGT
Found at i:856534 original size:41 final size:40
Alignment explanation
Indices: 856477--856570 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
856467 CGATAGTCAG
*
856477 ATTCTCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCTCATTGCGATTTACGTATTCGCATTGCGATTTACCT
* * * *
856517 AATTCGCATTGCGATTTACGTATTTGCTTTGCGATTTACGT
1 -ATTCTCATTGCGATTTACGTATTCGCATTGCGATTTACCT
856558 ATTCTCATTGCGA
1 ATTCTCATTGCGA
856571 ATTATGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 12 0.26
41 35 0.74
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (40 bp):
ATTCTCATTGCGATTTACGTATTCGCATTGCGATTTACCT
Found at i:856593 original size:21 final size:21
Alignment explanation
Indices: 856567--856612 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
856557 TATTCTCATT
856567 GCGAATTAT-GAAAATCGCAAC
1 GCGAATT-TGGAAAATCGCAAC
* *
856588 GCGAATTTGGGAAATCGCAAT
1 GCGAATTTGGAAAATCGCAAC
856609 GCGA
1 GCGA
856613 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:859733 original size:42 final size:40
Alignment explanation
Indices: 859620--859733 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 40
859610 GCCCAAAGGT
* * *
859620 CTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGA
1 CTTATAGAT-GCCCGAAAGACTTATCATCATGCTCGAAAGA
* *
859661 CTTATAGATGACCCGAAAGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATG-CCCGAAAGACTT-ATCATCATGCTCGAAAGA
* *
859703 CTTATTGATAGCCCGAAGGACTTACTCATCA
1 CTTATAGAT-GCCCGAAAGACTTA-TCATCA
859734 AGAAACCCTT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
40 1 0.02
41 19 0.32
42 39 0.65
43 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (40 bp):
CTTATAGATGCCCGAAAGACTTATCATCATGCTCGAAAGA
Found at i:859911 original size:57 final size:57
Alignment explanation
Indices: 859786--859927 Score: 169
Period size: 57 Copynumber: 2.5 Consensus size: 57
859776 GTTTATAGTT
* * * * *
859786 ATCATCAAGAAACTCCTAAAAATTAGGCTTAACTTCTTTTAAAAATTCAATGGGAGA
1 ATCATCAAGAAACCCCTAAAAATCAGGCGTAACTTCTTTTAAAAAATCAATGGAAGA
* *
859843 ATTCATCAAGAAACCCCTAAAAATCAGGCGTATCTTC-TTTAAAAAATCATTGGAAGTA
1 A-TCATCAAGAAACCCCTAAAAATCAGGCGTAACTTCTTTTAAAAAATCAATGGAAG-A
* * *
859901 ATCATCAAGAAAGCTCTGAAAATCAGG
1 ATCATCAAGAAACCCCTAAAAATCAGG
859928 GTAGCTACTT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 40 0.55
58 33 0.45
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (57 bp):
ATCATCAAGAAACCCCTAAAAATCAGGCGTAACTTCTTTTAAAAAATCAATGGAAGA
Found at i:860036 original size:55 final size:55
Alignment explanation
Indices: 859976--860125 Score: 205
Period size: 55 Copynumber: 2.7 Consensus size: 55
859966 GAAAATCAGG
* *
859976 CTTAGTTTCTTTAAAAACTCATTTAAAAATCATCATGAAACTTCTAAAAATCCAA
1 CTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCCAAAAATCCAA
* * * **
860031 GTTAGTTTCTTTGAAAACTCATTTAATAATCATCAAGAAACTTCCAAAAATCGGA
1 CTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCCAAAAATCCAA
*
860086 CTTAGCTTT-TTTCAAAACTCATTTAAAAAT-ATCAAGAAAC
1 CTTAG-TTTCTTTAAAAACTCATTTAAAAATCATCAAGAAAC
860126 CCCTAAGAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
54 10 0.12
55 71 0.85
56 3 0.04
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (55 bp):
CTTAGTTTCTTTAAAAACTCATTTAAAAATCATCAAGAAACTTCCAAAAATCCAA
Found at i:860144 original size:54 final size:54
Alignment explanation
Indices: 859953--860149 Score: 188
Period size: 55 Copynumber: 3.6 Consensus size: 54
859943 GTTCATCATG
*
859953 TCAAGAAAGCT-CTGAAAATCAGGCTTAGTTTCTTTAAAAACTCATTTAAAAATCA
1 TCAAGAAA-CTCCT-AAAATTAGGCTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * * * * *
860008 TCATGAAACTTCTAAAAATCCAAG-TTAGTTTCTTTGAAAACTCATTTAATAATCA
1 TCAAGAAACTCCT-AAAAT-TAGGCTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * *
860063 TCAAGAAACTTCC-AAAAATCGGACTTAGCTTT-TTTCAAAACTCATTTAAAAAT-A
1 TCAAGAAAC-TCCTAAAATTAGG-CTTAG-TTTCTTTAAAAACTCATTTAAAAATCA
*
860117 TCAAGAAACCCCTAAGAATTAGGCTTAGTTTCT
1 TCAAGAAACTCCTAA-AATTAGGCTTAGTTTCT
860150 AAAATTATTT
Statistics
Matches: 117, Mismatches: 16, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
53 6 0.05
54 24 0.21
55 79 0.68
56 8 0.07
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (54 bp):
TCAAGAAACTCCTAAAATTAGGCTTAGTTTCTTTAAAAACTCATTTAAAAATCA
Found at i:866218 original size:6 final size:6
Alignment explanation
Indices: 866209--866274 Score: 60
Period size: 6 Copynumber: 10.3 Consensus size: 6
866199 GTGTAAAGGT
* * *
866209 AAATGC AAATGTGA AAATGC AAATGC ATATGC AAATGTGA AAATGC AAATGC
1 AAATGC AAA--TGC AAATGC AAATGC AAATGC AAA--TGC AAATGC AAATGC
*
866261 ATATGC AAATGC AA
1 AAATGC AAATGC AA
866275 TGAAGGGATT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 38 0.79
8 10 0.21
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (6 bp):
AAATGC
Found at i:866228 original size:14 final size:14
Alignment explanation
Indices: 866209--866259 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
866199 GTGTAAAGGT
866209 AAATGCAAATGTGA
1 AAATGCAAATGTGA
*
866223 AAATGCAAA--TGC
1 AAATGCAAATGTGA
*
866235 ATATGCAAATGTGA
1 AAATGCAAATGTGA
866249 AAATGCAAATG
1 AAATGCAAATG
866260 CATATGCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 10 0.32
14 21 0.68
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.22
Consensus pattern (14 bp):
AAATGCAAATGTGA
Found at i:866247 original size:26 final size:26
Alignment explanation
Indices: 866211--866271 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
866201 GTAAAGGTAA
866211 ATGCAAATGTGAAAATGCAAATGCAT
1 ATGCAAATGTGAAAATGCAAATGCAT
866237 ATGCAAATGTGAAAATGCAAATGCAT
1 ATGCAAATGTGAAAATGCAAATGCAT
866263 ATGCAAATG
1 ATGCAAATG
866272 CAATGAAGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (26 bp):
ATGCAAATGTGAAAATGCAAATGCAT
Found at i:868720 original size:60 final size:60
Alignment explanation
Indices: 868607--868721 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 60
868597 ATAGTCGAGT
* * *
868607 GACTATTTTCTAACTTTTAATAATCATGAGACTCAACAAAGCAACGCCCTATAGTCAAAG
1 GACTATTTTCTAACTTTTAATAATCAGGAGACTCAACAAAGCAACACCATATAGTCAAAG
* * * * * * *
868667 GACTATTTTGTAACTTTTCATAGTCGGGAGATTCAATAAAGCAATACCATATAGT
1 GACTATTTTCTAACTTTTAATAATCAGGAGACTCAACAAAGCAACACCATATAGT
868722 TGGGGATCAT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (60 bp):
GACTATTTTCTAACTTTTAATAATCAGGAGACTCAACAAAGCAACACCATATAGTCAAAG
Found at i:869848 original size:60 final size:61
Alignment explanation
Indices: 869775--869941 Score: 200
Period size: 60 Copynumber: 2.8 Consensus size: 61
869765 TGCATCATAT
* * *
869775 ATTCTTAAACTATGACTCTCATTCTAAATT-GACCTCTAAACTTTTGAATATTATAATTTC
1 ATTCTTAAACTATGACTCTCATTCTAAATTAGTCCTCTAAACTTTTAAACATTATAATTTC
* * * *
869835 ATTCTCAAACTATGA-TATTCATTTTAAATTAGTCCT-TAAACTTTTAAACATTCTAATTTC
1 ATTCTTAAACTATGACT-CTCATTCTAAATTAGTCCTCTAAACTTTTAAACATTATAATTTC
* *
869895 A-TCATTAAACTATGACCCTCATTCTAAATTGGTCC-CTAAACTTTTAA
1 ATTC-TTAAACTATGACTCTCATTCTAAATTAGTCCTCTAAACTTTTAA
869942 CTTTTTTCAA
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
59 3 0.03
60 83 0.92
61 4 0.04
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (61 bp):
ATTCTTAAACTATGACTCTCATTCTAAATTAGTCCTCTAAACTTTTAAACATTATAATTTC
Found at i:872119 original size:228 final size:226
Alignment explanation
Indices: 871718--872164 Score: 788
Period size: 228 Copynumber: 2.0 Consensus size: 226
871708 GTAAATTATC
* * *
871718 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
871783 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAATTTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAATATTTT
871848 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
131 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
871913 AACATAAATTACATAACTTTCAAAAAAGTATA
196 AACATAAATTACATAACTTT-AAAAAAGTATA
*
871945 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
872010 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA-ATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTAT-AAATATCAAAACAATCAAATAATATT
* *
872074 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
129 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
872139 GAAACATAAATTACATAACTTTAAAA
194 GAAACATAAATTACATAACTTTAAAA
872165 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
227 40 0.19
228 148 0.70
229 22 0.10
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAATATCAAAACAATCAAATAATATTTT
GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:872273 original size:20 final size:20
Alignment explanation
Indices: 872229--872274 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
872219 CGATATACCA
*
872229 GGTAAAAATATGATAAAATC
1 GGTAAAAATATGATAAAACC
*
872249 AGTAACAAA-ATGATAAAACC
1 GGTAA-AAATATGATAAAACC
872269 GGTAAA
1 GGTAAA
872275 TTTAAAAGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.20
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:872419 original size:20 final size:19
Alignment explanation
Indices: 872396--872442 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
872386 CGATATAACA
872396 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
872416 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
872436 GGTAAAA
1 GGTAAAA
872443 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:872444 original size:17 final size:19
Alignment explanation
Indices: 872405--872447 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
872395 AGGTAAAAAT
872405 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
872425 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
872442 ATGATA
1 ATGATA
872448 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:874524 original size:19 final size:19
Alignment explanation
Indices: 874500--874548 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
874490 AATGTCGAGT
874500 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
874519 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
874538 TATTTTTGTAT
1 TAATTTTGTAT
874549 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:875646 original size:197 final size:198
Alignment explanation
Indices: 874667--876026 Score: 2486
Period size: 198 Copynumber: 6.9 Consensus size: 198
874657 CAATATGGCC
* * *
874667 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCAATCCCAAAA-CATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
874730 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
874795 GGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
874860 GGAA
195 GGAA
*
874864 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
874929 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
874994 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
*
875059 -TAA
195 GGAA
875062 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
875127 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
875192 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
**
875257 TAAA
195 GGAA
*
875261 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
875325 CC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
875389 GGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
875454 GGAA
195 GGAA
*
875458 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
875523 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
875588 AATATGTCTAAATAATGTGTCGACACT-A-ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAAT
875651 GGAA
195 GGAA
875655 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
875720 CAAAAGTATAATGTAATATGTAATTTTTCAATATAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
875785 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
875850 GAA
196 GAA
875853 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
875917 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
875981 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
876027 CTAATTTAAA
Statistics
Matches: 1134, Mismatches: 19, Indels: 21
0.97 0.02 0.02
Matches are distributed among these distances:
196 95 0.08
197 330 0.29
198 623 0.55
199 86 0.08
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (198 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAA
Found at i:876514 original size:23 final size:23
Alignment explanation
Indices: 876483--876546 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
876473 ATAGGTAAAC
*
876483 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
876506 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
876529 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
876547 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:876553 original size:23 final size:23
Alignment explanation
Indices: 876483--876555 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
876473 ATAGGTAAAC
* **
876483 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
876506 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
876529 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
876552 ATAT
1 ATAT
876556 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:876943 original size:23 final size:23
Alignment explanation
Indices: 876912--876974 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
876902 ATAGGTAAAC
*
876912 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
876935 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
876958 ATATAATGT-ATAGGTAG
1 ATATAATGTAATAGGTAG
876975 TGGTTATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 7 0.20
23 28 0.80
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:876981 original size:22 final size:23
Alignment explanation
Indices: 876912--876983 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
876902 ATAGGTAAAC
* * **
876912 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
876935 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
876958 ATATAATGT-ATAGGTAGT-GGTT
1 ATATAATGTAATAGGTA-TCGGTT
876980 ATAT
1 ATAT
876984 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 14 0.33
23 29 0.67
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:877278 original size:25 final size:25
Alignment explanation
Indices: 877250--877300 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
877240 AACAACAATC
*
877250 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
877275 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
877300 A
1 A
877301 TTGGATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:877569 original size:18 final size:18
Alignment explanation
Indices: 877548--877584 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
877538 GTAATTGGAG
877548 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
877566 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
877584 T
1 T
877585 ATATTTCGGC
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:877883 original size:39 final size:39
Alignment explanation
Indices: 877840--877926 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
877830 TCCGATGCTC
*
877840 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
877879 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
877918 ATCAAAATC
1 ATCAAAATC
877927 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:878358 original size:23 final size:23
Alignment explanation
Indices: 878327--878390 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
878317 ATAGGTAAAC
*
878327 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
878350 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
878373 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
878391 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:878397 original size:23 final size:23
Alignment explanation
Indices: 878327--878399 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
878317 ATAGGTAAAC
* **
878327 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
878350 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
878373 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
878396 ATAT
1 ATAT
878400 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:885883 original size:19 final size:20
Alignment explanation
Indices: 885844--885883 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
885834 TTATTCACGG
* *
885844 AATATAAGATTATCAGTGGA
1 AATAAAAGATTATCAGAGGA
885864 AATAAAAGATTATC-GAGGA
1 AATAAAAGATTATCAGAGGA
885883 A
1 A
885884 TAGGATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (20 bp):
AATAAAAGATTATCAGAGGA
Found at i:886078 original size:49 final size:49
Alignment explanation
Indices: 886021--886117 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
886011 TTTGTTTTTT
886021 TAACAAGTGAAATTCTAAATATTTAAATAAAAATTATTTATATAAAAAC
1 TAACAAGTGAAATTCTAAATATTTAAATAAAAATTATTTATATAAAAAC
886070 TAACAAGTGAAATTCTAAATATTTAAATAAAAATTATTTATATAAAAA
1 TAACAAGTGAAATTCTAAATATTTAAATAAAAATTATTTATATAAAAA
886118 TTCTATTTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (49 bp):
TAACAAGTGAAATTCTAAATATTTAAATAAAAATTATTTATATAAAAAC
Found at i:886107 original size:15 final size:15
Alignment explanation
Indices: 886089--886119 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
886079 AAATTCTAAA
886089 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
886104 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
886119 T
1 T
886120 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:890759 original size:15 final size:15
Alignment explanation
Indices: 890739--890767 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
890729 TGGCCGACCG
890739 AACCGAATTAACCAT
1 AACCGAATTAACCAT
890754 AACCGAATTAACCA
1 AACCGAATTAACCA
890768 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:891117 original size:179 final size:181
Alignment explanation
Indices: 890904--891265 Score: 590
Period size: 179 Copynumber: 2.0 Consensus size: 181
890894 TAAATTAAAT
* *
890904 ATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATAAATAATTATAAAA-TAAAATTTT
1 ATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAATTATAAAATTAAAAATTT
*
890968 AGATAAATTTTTTAATTAATTAATA-TGATTTAAGTTTAAAAGTTATTGGATCTTAAATTATTAA
66 AGAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGAATCTTAAATTATTAA
*
891032 TTGGGTTTTAAATG-GTTGGGCTT-AGCCCATATGTTATATATAATATATTTA
130 TTGGATTTTAAATGAGTTGGG-TTGAGCCCATATGTTATATATAATATATTTA
*
891083 ATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATTAAAAATT
1 ATTTTTTAATTCAAAAAA-AGTTTACAATTAATTTAAATAATAAATAATTATAAAATTAAAAATT
*
891147 TATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGAATCTTAAATTATTAA
65 TAGATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGAATCTTAAATTATTAA
* *
891212 TTGGATTTTTAATGATTTGGGTTGAGCCCATATGTTATATATAATATATTTA
130 TTGGATTTTAAATGAGTTGGGTTGAGCCCATATGTTATATATAATATATTTA
891264 AT
1 AT
891266 ATTTAAAATT
Statistics
Matches: 170, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
178 6 0.04
179 66 0.39
180 63 0.37
181 35 0.21
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (181 bp):
ATTTTTTAATTCAAAAAAAGTTTACAATTAATTTAAATAATAAATAATTATAAAATTAAAAATTT
AGATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTGAATCTTAAATTATTAAT
TGGATTTTAAATGAGTTGGGTTGAGCCCATATGTTATATATAATATATTTA
Found at i:892034 original size:59 final size:60
Alignment explanation
Indices: 891955--892067 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 60
891945 GGAGATCCCC
*
891955 AAACTATAATCCCTATTTTAAATT-GAT-TTATAAACTTTAAAACATTCTATATCAGTCAAT
1 AAACTATAATCCCTATTTTAAATTAG-TCTT-TAAACTTTAAAACATCCTATATCAGTCAAT
* * *
892015 AAACTATGATTCC-ATTTTAAATTAGTCTTTAAACTTTAAAATATCCTATATCA
1 AAACTATAATCCCTATTTTAAATTAGTCTTTAAACTTTAAAACATCCTATATCA
892068 ATCCTCAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 33 0.70
60 14 0.30
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.41
Consensus pattern (60 bp):
AAACTATAATCCCTATTTTAAATTAGTCTTTAAACTTTAAAACATCCTATATCAGTCAAT
Found at i:892078 original size:59 final size:60
Alignment explanation
Indices: 891949--892079 Score: 144
Period size: 59 Copynumber: 2.2 Consensus size: 60
891939 TTTTAAGGAG
* *
891949 ATCCCCAAACTATAATCCCTATTTTAAATTGATTTATAAACTTTAAAACATTCTATATCA
1 ATCCTCAAACTATAATCCCTATTTTAAATTGATTTATAAACTTTAAAACATCCTATATCA
* * * * *
892009 GTCAAT-AAACTATGATTCC-ATTTTAAATT-AGTCTT-TAAACTTTAAAATATCCTATATCA
1 ATC-CTCAAACTATAATCCCTATTTTAAATTGA-T-TTATAAACTTTAAAACATCCTATATCA
892068 ATCCTCAAACTA
1 ATCCTCAAACTA
892080 CCATCATCGT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
58 2 0.03
59 41 0.71
60 15 0.26
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (60 bp):
ATCCTCAAACTATAATCCCTATTTTAAATTGATTTATAAACTTTAAAACATCCTATATCA
Found at i:897822 original size:60 final size:60
Alignment explanation
Indices: 897711--897823 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
897701 TATATCATAC
*
897711 TACTTTGTTGAGTCCTCCAACTATTAAAAGTTACAAAATAATCCCTCGACTATAGGGTGT
1 TACTTTGTTGAGTCCTCCAACTATTAAAAGTTACAAAATAATCACTCGACTATAGGGTGT
* * *
897771 TACTTTGTTGAGTCC-CTCGACTATTAAAAGTTACAAAATAGTCACTTGACTAT
1 TACTTTGTTGAGTCCTC-CAACTATTAAAAGTTACAAAATAATCACTCGACTAT
897824 TCATTATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 1 0.02
60 47 0.98
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (60 bp):
TACTTTGTTGAGTCCTCCAACTATTAAAAGTTACAAAATAATCACTCGACTATAGGGTGT
Found at i:904516 original size:2 final size:2
Alignment explanation
Indices: 904509--904534 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
904499 AAAATAAAAT
904509 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
904535 AAAGAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:908428 original size:30 final size:30
Alignment explanation
Indices: 908392--908449 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
908382 TGAAGCCTGA
*
908392 CAGGATCAACAGCAGTAGGGCGTGGTCCAG
1 CAGGATCAACAGCAGCAGGGCGTGGTCCAG
**
908422 CAGGATCAGTAGCAGCAGGGCGTGGTCC
1 CAGGATCAACAGCAGCAGGGCGTGGTCC
908450 CCTCCTGGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.38, T:0.14
Consensus pattern (30 bp):
CAGGATCAACAGCAGCAGGGCGTGGTCCAG
Found at i:911240 original size:18 final size:19
Alignment explanation
Indices: 911217--911255 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
911207 TTTAAGTAGT
911217 AATAAAAACGATTAAA-TA
1 AATAAAAACGATTAAAGTA
*
911235 AATAAAAGCGATTAAAGTA
1 AATAAAAACGATTAAAGTA
911254 AA
1 AA
911256 ATAATAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (19 bp):
AATAAAAACGATTAAAGTA
Found at i:922996 original size:20 final size:20
Alignment explanation
Indices: 922971--923008 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
922961 TTTTGGTACA
*
922971 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
922991 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
923009 TTTGAAGGGG
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:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:925623 original size:22 final size:23
Alignment explanation
Indices: 925598--925641 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
925588 AATTAAGTTT
925598 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
925620 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
925642 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:926484 original size:18 final size:19
Alignment explanation
Indices: 926461--926503 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
926451 TTTAAGTAGT
926461 AATAAAAACAATTAAA-TA
1 AATAAAAACAATTAAAGTA
* *
926479 AATAAAAGCGATTAAAGTA
1 AATAAAAACAATTAAAGTA
926498 AA-AAAA
1 AATAAAA
926504 TAAGAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.19
Consensus pattern (19 bp):
AATAAAAACAATTAAAGTA
Done.