Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 42
Found at i:2133604 original size:14 final size:14
Alignment explanation
Indices: 2133585--2133621 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2133575 CATCAATTAA
2133585 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2133599 ACAAATCATCTTTT
1 ACAAATCAACATTT
2133613 ACAAATCAA
1 ACAAATCAA
2133622 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2137124 original size:33 final size:33
Alignment explanation
Indices: 2137066--2137161 Score: 147
Period size: 33 Copynumber: 2.9 Consensus size: 33
2137056 TTGAAATGAA
**
2137066 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
*
2137100 AATTGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
2137133 AATCGCAACGCGAAATTAAAATCGCAACG
1 AATCGCAACGCGAAATGAAAATCGCAACG
2137162 CGAAATGAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 47 0.82
34 10 0.18
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:2137128 original size:19 final size:19
Alignment explanation
Indices: 2137058--2137183 Score: 110
Period size: 19 Copynumber: 7.1 Consensus size: 19
2137048 TCTTTTGGTT
2137058 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
2137077 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
* *
2137095 G--A-GAGAATTGCAACGC
1 GAAATGAAAATCGCAACGC
2137111 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2137128 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2137144 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2137163 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2137182 GA
1 GA
2137184 GTTTGGTTTC
Statistics
Matches: 84, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
14 18 0.21
15 2 0.02
16 4 0.05
17 3 0.04
18 3 0.04
19 40 0.48
20 14 0.17
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2137267 original size:20 final size:20
Alignment explanation
Indices: 2137196--2137267 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
2137186 TTGGTTTCGC
*
2137196 GTTGCGATTTTTATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
2137216 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
2137237 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
*
2137257 GTTGCGCTTTT
1 GTTGCGATTTT
2137268 AAGTTTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.11, C:0.17, G:0.19, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:2137888 original size:41 final size:41
Alignment explanation
Indices: 2137831--2138042 Score: 277
Period size: 41 Copynumber: 5.2 Consensus size: 41
2137821 TTAAAAATCG
** *
2137831 CGTTGCGATTTACGGATACACGTAACGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTCT
* *
2137872 CGTTGCGATTTACGGATACACATTGCGA-TTTAAGTATTCT
1 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTCT
* *
2137912 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTCT
* * *
2137952 CGTTGTGATTTACGGATA-AGCGTTGCGATGTTACGTATTGT
1 CGTTGCGATTTACGGATACA-CGTTGCGATTTTACGTATTCT
* * *
2137993 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTCT
2138034 CGTTGCGAT
1 CGTTGCGAT
2138043 AGTCAGAATC
Statistics
Matches: 148, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
40 70 0.47
41 78 0.53
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTCT
Found at i:2138078 original size:81 final size:81
Alignment explanation
Indices: 2137828--2138103 Score: 265
Period size: 81 Copynumber: 3.4 Consensus size: 81
2137818 GCTTTAAAAA
* * ** * *
2137828 TCGCGTTGCGATTTACGGATACACGTAACGATTTTACGTATTGTCGTTGCGATTTACGGATACAC
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
* *
2137893 ATTGCGATTTA-AGTAT
66 GTTGCGATTTATA-TGT
* * *
2137909 TCTCGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGTGATTTACGGATAAGC
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
* *
2137973 GTTGCGATGT-TACGT
66 GTTGCGATTTATATGT
* * * * * *
2137988 ATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-A
1 -TCG-CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGAT-TTACGGATA
*
2138051 TCGCGTTGCAATTTATATGT
63 -CGCGTTGCGATTTATATGT
* * *
2138071 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATT
2138104 CTGGAAAATC
Statistics
Matches: 158, Mismatches: 30, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
79 1 0.01
80 39 0.25
81 80 0.51
82 33 0.21
83 5 0.03
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (81 bp):
TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
GTTGCGATTTATATGT
Found at i:2138100 original size:20 final size:20
Alignment explanation
Indices: 2137828--2138103 Score: 182
Period size: 20 Copynumber: 13.7 Consensus size: 20
2137818 GCTTTAAAAA
2137828 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGAT
* * ** *
2137848 ACACGTAACGATTTTACGTAT
1 TCGCGTTGCGA-TTTACGGAT
2137869 T-GTCGTTGCGATTTACGGAT
1 TCG-CGTTGCGATTTACGGAT
* * * * *
2137889 ACACATTGCGATTTAAGTAT
1 TCGCGTTGCGATTTACGGAT
* *
2137909 TCTCGTTGCGATTTACAGAT
1 TCGCGTTGCGATTTACGGAT
* *
2137929 ACGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGGAT
* *
2137949 TCTCGTTGTGATTTACGGAT
1 TCGCGTTGCGATTTACGGAT
** *
2137969 AAGCGTTGCGATGTTACGTAT
1 TCGCGTTGCGAT-TTACGGAT
2137990 T-GTCGTTGCGATTTACGGAT
1 TCG-CGTTGCGATTTACGGAT
*
2138010 ACGCGTTGCGATTTTACGGAT
1 TCGCGTTGCGA-TTTACGGAT
* * * * *
2138031 ACTCGTTGCGATAGT-CAGAA
1 TCGCGTTGCGAT-TTACGGAT
* **
2138051 TCGCGTTGCAATTTATATG-T
1 TCGCGTTGCGATTTA-CGGAT
* **
2138071 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGAT
2138091 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2138104 CTGGAAAATC
Statistics
Matches: 192, Mismatches: 53, Indels: 22
0.72 0.20 0.08
Matches are distributed among these distances:
19 1 0.01
20 139 0.72
21 52 0.27
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTACGGAT
Found at i:2138117 original size:21 final size:21
Alignment explanation
Indices: 2138091--2138227 Score: 109
Period size: 21 Copynumber: 6.6 Consensus size: 21
2138081 ATTTTCATAT
2138091 TCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGATTCTGGAAAA
2138112 TCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGATTCTGGAAAA
** * **
2138133 TCGCAATGCGAATT-TGTACTA
1 TCGCGTTGCG-ATTCTGGAAAA
* ** *
2138154 TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGATTCTGGAAAA
* *
2138175 TCGCGTTGCGATTCTGGGAAC
1 TCGCGTTGCGATTCTGGAAAA
** **
2138196 T-GATTTGCGATTCTGG-AGT
1 TCGCGTTGCGATTCTGGAAAA
2138215 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2138228 TTTATTTCGC
Statistics
Matches: 91, Mismatches: 22, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
19 2 0.02
20 25 0.27
21 61 0.67
22 3 0.03
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATTCTGGAAAA
Found at i:2138185 original size:42 final size:41
Alignment explanation
Indices: 2138049--2138185 Score: 118
Period size: 42 Copynumber: 3.3 Consensus size: 41
2138039 CGATAGTCAG
* *
2138049 AATCGCGTTGC-AATTTATATGTTCGCGTTGCGATT-TTCAT
1 AATCGCGTTGCGAATTTGTAT-ATCGCGTTGCGATTCTTCAT
* * * ** *
2138089 ATTCGCGTTGCG-ATTCTGGAAAATCGCGTTGCGATTCTGGAA
1 AATCGCGTTGCGAATT-T-GTATATCGCGTTGCGATTCTTCAT
** *
2138131 AATCGCAATGCGAATTTGTACTATCGCATTGCGATTCTTCAT
1 AATCGCGTTGCGAATTTGTA-TATCGCGTTGCGATTCTTCAT
2138173 AATCGCGTTGCGA
1 AATCGCGTTGCGA
2138186 TTCTGGGAAC
Statistics
Matches: 72, Mismatches: 19, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
40 13 0.18
41 16 0.22
42 40 0.56
43 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (41 bp):
AATCGCGTTGCGAATTTGTATATCGCGTTGCGATTCTTCAT
Found at i:2138764 original size:24 final size:24
Alignment explanation
Indices: 2138737--2138786 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2138727 TTTTCATTTA
**
2138737 TTATTATTTTTAAATCTAACTTTT
1 TTATTATACTTAAATCTAACTTTT
2138761 TTATTATACTTAAATCTAACTTTT
1 TTATTATACTTAAATCTAACTTTT
2138785 TT
1 TT
2138787 TCAAGATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATTATACTTAAATCTAACTTTT
Found at i:2143346 original size:28 final size:28
Alignment explanation
Indices: 2143315--2143372 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
2143305 CTAACCAAGA
*
2143315 ATAAGTATAGTTTCAGAGCTAAAGTCTT
1 ATAAGTATAGCTTCAGAGCTAAAGTCTT
2143343 ATAAGTATAGCTTCAGAGCTAAAGTCTT
1 ATAAGTATAGCTTCAGAGCTAAAGTCTT
2143371 AT
1 AT
2143373 CATTTCCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (28 bp):
ATAAGTATAGCTTCAGAGCTAAAGTCTT
Found at i:2144612 original size:3 final size:3
Alignment explanation
Indices: 2144604--2144634 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2144594 TTTATTAATG
2144604 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2144635 CTATATTAGT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2145759 original size:21 final size:21
Alignment explanation
Indices: 2145729--2145772 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2145719 TTAAAATCAC
*
2145729 TTAATAAATTCATTTTTACTA
1 TTAATAAATTCAATTTTACTA
* *
2145750 TTAATGAATTCAATTTTATTA
1 TTAATAAATTCAATTTTACTA
2145771 TT
1 TT
2145773 GAAATTACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAATAAATTCAATTTTACTA
Found at i:2147591 original size:2 final size:2
Alignment explanation
Indices: 2147584--2147696 Score: 94
Period size: 2 Copynumber: 63.5 Consensus size: 2
2147574 ATACAGGATA
2147584 AT AT AT AT -T AT A- AT AT AT -T AT AT A- AT AT AT -T AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2147620 AGT AT -T AT AT AT -T AT AT GT -T AC AT AT -T AT AT AT -T AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2147658 AT -T AT AT AT -T AT AT AT AT AT -T AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2147696 A
1 A
2147697 ATTTTAATAT
Statistics
Matches: 92, Mismatches: 3, Indels: 32
0.72 0.02 0.25
Matches are distributed among these distances:
1 15 0.16
2 75 0.82
3 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2147606 original size:7 final size:7
Alignment explanation
Indices: 2147584--2147696 Score: 122
Period size: 7 Copynumber: 15.7 Consensus size: 7
2147574 ATACAGGATA
2147584 ATATA-T
1 ATATATT
*
2147590 AT-TATA
1 ATATATT
2147596 ATATATT
1 ATATATT
*
2147603 ATATAAT
1 ATATATT
*
2147610 ATATTATA
1 ATA-TATT
2147618 ATAGTATT
1 ATA-TATT
2147626 ATATATT
1 ATATATT
*
2147633 ATATGTT
1 ATATATT
*
2147640 ACATATT
1 ATATATT
2147647 ATATATT
1 ATATATT
2147654 ATATATT
1 ATATATT
2147661 ATATATT
1 ATATATT
2147668 ATATATAT
1 ATATAT-T
2147676 ATTATATAT
1 A-TATAT-T
2147685 ATATATT
1 ATATATT
2147692 ATATA
1 ATATA
2147697 ATTTTAATAT
Statistics
Matches: 91, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
5 2 0.02
6 4 0.04
7 59 0.65
8 18 0.20
9 8 0.09
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (7 bp):
ATATATT
Found at i:2151168 original size:3 final size:3
Alignment explanation
Indices: 2151154--2151217 Score: 69
Period size: 3 Copynumber: 22.0 Consensus size: 3
2151144 TTCACGTTGG
* * * * *
2151154 AGA AGA AAA AGA AGA TGA AGA AG- AGA AGA AGA TGA AGA TGA AGA TGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2151201 AGA AG- AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA
2151218 TAAAGATAGA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
2 4 0.08
3 45 0.92
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (3 bp):
AGA
Found at i:2151216 original size:26 final size:26
Alignment explanation
Indices: 2151154--2151224 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 26
2151144 TTCACGTTGG
* *
2151154 AGAAGAAAAAGAAGATGAAGAAGAGA
1 AGAAGAAGATGAAGATGAAGAAGAGA
2151180 AGAAGATGAAGATGAAGATGAAGAAGAGA
1 AG-A-A-GAAGATGAAGATGAAGAAGAGA
*
2151209 AGAAGAAGATAAAGAT
1 AGAAGAAGATGAAGAT
2151225 AGAAATATCT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
26 13 0.33
27 2 0.05
28 2 0.05
29 22 0.56
ACGTcount: A:0.61, C:0.00, G:0.31, T:0.08
Consensus pattern (26 bp):
AGAAGAAGATGAAGATGAAGAAGAGA
Found at i:2152687 original size:27 final size:27
Alignment explanation
Indices: 2152657--2152708 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2152647 GTATTATTAC
2152657 ATTTCATAAACATTAAAAGTTATAAGA
1 ATTTCATAAACATTAAAAGTTATAAGA
** *
2152684 ATTTCATAAGTATTACAAGTTATAA
1 ATTTCATAAACATTAAAAGTTATAA
2152709 ATAATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.37
Consensus pattern (27 bp):
ATTTCATAAACATTAAAAGTTATAAGA
Found at i:2152726 original size:18 final size:19
Alignment explanation
Indices: 2152703--2152738 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2152693 GTATTACAAG
*
2152703 TTATAAATAATT-TTTTAA
1 TTATAAAGAATTGTTTTAA
2152721 TTATAAAGAATTGTTTTA
1 TTATAAAGAATTGTTTTA
2152739 TTAAATCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
TTATAAAGAATTGTTTTAA
Found at i:2153341 original size:6 final size:6
Alignment explanation
Indices: 2153330--2153386 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
2153320 GAGAACAAGC
2153330 GAGGTT GAGGTT GAGGTT GAGGTT GAGGTT GAGGTT GAGGTT GAGGTT
1 GAGGTT GAGGTT GAGGTT GAGGTT GAGGTT GAGGTT GAGGTT GAGGTT
2153378 GAGGTT GAG
1 GAGGTT GAG
2153387 AATAGAGATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.18, C:0.00, G:0.51, T:0.32
Consensus pattern (6 bp):
GAGGTT
Found at i:2153961 original size:23 final size:23
Alignment explanation
Indices: 2153907--2153961 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
2153897 TCATAGTTTT
*
2153907 TATATTAAAATTGACAGGTTATA
1 TATATTAAAATTGACAGATTATA
* * *
2153930 TAAAATAAAATTTACTA-ATTATA
1 TATATTAAAATTGAC-AGATTATA
2153953 TATATTAAA
1 TATATTAAA
2153962 TAATAATTGA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (23 bp):
TATATTAAAATTGACAGATTATA
Found at i:2153962 original size:27 final size:27
Alignment explanation
Indices: 2153926--2153977 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2153916 ATTGACAGGT
*
2153926 TATATAAAATAA-AATTTACTAATTATA
1 TATATAAAATAATAATTGA-TAATTATA
*
2153953 TATATTAAATAATAATTGATAATTA
1 TATATAAAATAATAATTGATAATTA
2153978 AAAATTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
TATATAAAATAATAATTGATAATTATA
Found at i:2155922 original size:182 final size:181
Alignment explanation
Indices: 2155368--2155965 Score: 840
Period size: 182 Copynumber: 3.3 Consensus size: 181
2155358 GAAAAAATAT
* *
2155368 GACAAAACCGGTAAAGCGCTACCGGATATATTGCATGTGTCGATACTTTAATATAAGTATCGACA
1 GACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
* ** * * *
2155433 CATAGTGAATTTAAAGGAGAAATAATTTTAGCGCCTATAAAGTATCGATTTTTTATAAATATGTA
66 CTTAGTGAATTTAAAGGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATTCTTTATAAATATGTA
* * **
2155498 TCGATCCACAACAATATAACAGGTAAAAATATGACAAAACCGATCAGGAAAA
131 TCGATCCACAACGATATAACA-GTAAAAATATGATAAAACCGATCTCGAAAA
* *** * *
2155550 GACAAAATCGGTAAAGATATATCGGATATATTGCAAGTGTCGATACTTTAATATAAGTATCGACA
1 GACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
**
2155615 CATT-GTGAATTTAAAGGAGAAGCAGTTTTAG-ATCTATAAAGTGTCGATTCTTTATAAATATGT
66 C-TTAGTGAATTTAAAGGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATTCTTTATAAATATGT
*
2155678 ATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTCTCGAAAA
130 ATCGATCCACAACGATATAACA-GTAAAAATATGATAAAACCGATCTCGAAAA
* *
2155731 GATAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATCGACA
1 GACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
* * * *
2155796 CTTAGTGAGTTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTA
66 CTTAGTGAATTTAAAGGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATTCTTTATAAATATGTA
* * ** *
2155861 TCTATCCATAACGATATAACAGATAAAAATATGATAAAACCGATCTTTAAAT
131 TCGATCCACAACGATATAACAG-TAAAAATATGATAAAACCGATCTCGAAAA
* *
2155913 GACAAAACCGGTAAAGCGCTATCGGATATATTAAAAGTGTCGATACTTTAATA
1 GACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
2155966 AGTACGCATA
Statistics
Matches: 368, Mismatches: 44, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
180 2 0.01
181 159 0.43
182 206 0.56
183 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (181 bp):
GACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
CTTAGTGAATTTAAAGGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATTCTTTATAAATATGTA
TCGATCCACAACGATATAACAGTAAAAATATGATAAAACCGATCTCGAAAA
Found at i:2158535 original size:64 final size:63
Alignment explanation
Indices: 2158467--2158624 Score: 140
Period size: 64 Copynumber: 2.5 Consensus size: 63
2158457 TTGAAGGTGT
*** *
2158467 ATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAATCTAA-AAACATCGAATGCAATTAGTG
1 ATCGATGCACAGGTA-TGCATCGATGCATC-CCAATAAT-AAACAAACATCGAATGCAATTAGTG
2158530 C
63 C
* * * * * *
2158531 ATCGATACATAAGGCATGCATCGATGCATCCCAATAATAAACAAACATCGAATGTAGTTTGTGC
1 ATCGATGCA-CAGGTATGCATCGATGCATCCCAATAATAAACAAACATCGAATGCAATTAGTGC
* * *
2158595 ACCGATGCACAAGTATTGCATCGATTCATC
1 ATCGATGCACAGGTA-TGCATCGATGCATC
2158625 GGTAGGGAAT
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
63 5 0.07
64 64 0.86
65 5 0.07
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (63 bp):
ATCGATGCACAGGTATGCATCGATGCATCCCAATAATAAACAAACATCGAATGCAATTAGTGC
Found at i:2159593 original size:103 final size:103
Alignment explanation
Indices: 2159409--2159642 Score: 346
Period size: 103 Copynumber: 2.3 Consensus size: 103
2159399 AGTCGAGGTC
* * *
2159409 TATGTGGTTCTTCGGGACATATATATATTCTTTGGAACATGTGTGAAGTATGGTGAGACATATAC
1 TATGTGGTCCTTTGGGACATATATATATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
* * *
2159474 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
* * *
2159512 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTTTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTTGGGACATATATATATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
*
2159577 TTGATCCCTAGTATATGTATATGATTATTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
2159615 TATGTGGTCCTTAT-GGACAT-TATTATAT
1 TATGTGGTCCTT-TGGGACATATA-TATAT
2159643 GGCACTACGG
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
102 2 0.02
103 115 0.97
104 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (103 bp):
TATGTGGTCCTTTGGGACATATATATATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTATTAAGGAATGA
Found at i:2159710 original size:23 final size:23
Alignment explanation
Indices: 2159633--2159709 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
2159623 CCTTATGGAC
2159633 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATATGGCACTACGGTGCA
* * * *
2159657 ATTCTACACGGCACTCCGGTGCA
1 ATTATATATGGCACTACGGTGCA
* *
2159680 ATTATATGTGGCACTTCGGTGCA
1 ATTATATATGGCACTACGGTGCA
2159703 ATTATAT
1 ATTATAT
2159710 GAGCTGTAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (23 bp):
ATTATATATGGCACTACGGTGCA
Found at i:2162705 original size:20 final size:20
Alignment explanation
Indices: 2162680--2162719 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2162670 TAGAGTCATC
2162680 AGATTTGAAGGAAACATAAA
1 AGATTTGAAGGAAACATAAA
2162700 AGATTTGAAGGAAACATAAA
1 AGATTTGAAGGAAACATAAA
2162720 GTAAGTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (20 bp):
AGATTTGAAGGAAACATAAA
Found at i:2164417 original size:19 final size:19
Alignment explanation
Indices: 2164393--2164443 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
2164383 ATGCAATTAG
2164393 TGCATCGATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
2164412 TGCATCGATGCATAAGGCA
1 TGCATCGATGCATAAGGCA
2164431 TGCATCGATGCAT
1 TGCATCGATGCAT
2164444 CCCAGTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCATAAGGCA
Found at i:2165519 original size:103 final size:103
Alignment explanation
Indices: 2165294--2165511 Score: 366
Period size: 103 Copynumber: 2.1 Consensus size: 103
2165284 GTCGAGGGTC
*
2165294 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGATGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGATGAGACACATAC
*
2165359 TTGATCCTTGACATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTAGACATATGTATATGATTCTTAAGGAATGA
* * *
2165397 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGATGAGACACATAC
*
2165462 TTGATCCCTAG-TATATGTATATGATTCTTAAGGAATGA
66 TTGAT-CCTAGACATATGTATATGATTCTTAAGGAATGA
2165500 TATGTGGTCCTT
1 TATGTGGTCCTT
2165512 ATGGACATTA
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 103 0.96
104 4 0.04
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGATGAGACACATAC
TTGATCCTAGACATATGTATATGATTCTTAAGGAATGA
Found at i:2165594 original size:23 final size:23
Alignment explanation
Indices: 2165518--2165595 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
2165508 CCTTATGGAC
*
2165518 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
2165542 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
2165565 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
2165588 ATTATATG
1 ATTATATG
2165596 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:2167502 original size:25 final size:25
Alignment explanation
Indices: 2167474--2167526 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
2167464 TTGTAGGTAC
2167474 ATTATTTGAACATTGTTATGTATAA
1 ATTATTTGAACATTGTTATGTATAA
2167499 ATTATTTGAACATTGTTATGTATAA
1 ATTATTTGAACATTGTTATGTATAA
2167524 ATT
1 ATT
2167527 TCTTGTGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (25 bp):
ATTATTTGAACATTGTTATGTATAA
Found at i:2167804 original size:15 final size:15
Alignment explanation
Indices: 2167784--2167822 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2167774 TCTCCACAAC
* *
2167784 AAAGTTTTCATACAT
1 AAAGTTTCCAAACAT
*
2167799 AAAGTTTCCAAACTT
1 AAAGTTTCCAAACAT
2167814 AAAGTTTCC
1 AAAGTTTCC
2167823 CATAATGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (15 bp):
AAAGTTTCCAAACAT
Found at i:2168645 original size:400 final size:397
Alignment explanation
Indices: 2167820--2168986 Score: 1739
Period size: 399 Copynumber: 2.9 Consensus size: 397
2167810 ACTTAAAGTT
* * * * ** * *
2167820 TCCCATAATGTGTCGATATAGTTTTAAAAAGTATCGATCCCAGTAACATCAAAATCAATAAATAT
1 TCCCATAAAGTGTCGATACATTTTTAAACAGTATCGATCCCAAAAACATCGAAATCCATAAATAT
* *
2167885 AATGTAATAGGTAATTTTATAATATAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCT
66 AATGTAATAGGTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGTCAGAATAGGTCT
* *
2167950 ACATAATGTGTCGACACTTATTAATGTTGTGTCGATACTTTTTGCCATAATGAATGACCAAAAGG
131 ACATAATGTGTCGACACTT-TTAAAGTTGTGTCGATACTTTTTGCCAGAATGAATG-CCAAAAGG
* * * * *
2168015 GTGAACACATAAAGTGTCGATACAATTATAAAAAGTATTGA-CCCAAAAACATCAAAACCGATAA
194 GTGAACGCATAAAGTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCGATAA
* * * *
2168079 TTATAATGTAATAAGTAAATTTACAATATAACCGGTATAAATAAACCAGTTTTTTGAGAAAATAG
259 TTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATGAACCGGTTTTTTGAGAAAATAG
* *
2168144 ATATACATAATGTATCGACA-GTTGTAGAATTTGTGTCGATACTTTTGGTCCACAAGGAAAATCC
324 GTA-ACATAATGTATCGACACGTTTTAG-ATTTGTGTCGATACTTTTGGTCCACAAGGAAAATCC
2168208 AAAAAGGGTGC
387 AAAAAGGGTGC
*
2168219 ACCCATAAAGTGTCGATACATTTTTAAACAGTATCGATCCCAAAAACATCGAAATCCATAAATAT
1 TCCCATAAAGTGTCGATACATTTTTAAACAGTATCGATCCCAAAAACATCGAAATCCATAAATAT
* * * * * *
2168284 AATGTAATAAGTAATTTTGTAATATAACCGGTATAAATATA-CTAGTTTCATGTTAAAATAGTTC
66 AATGTAATAGGTAATTTTGTAATATAACCGGTATAAATATACCGA-TTTTATGTCAGAATAGGTC
*
2168348 TACATAATGCGTCGACACTTTTGAAAGTTGTGTCGATACTTTTTGCCAGAATGAATGCCCAAAAG
130 TACATAATGTGTCGACACTTTT-AAAGTTGTGTCGATACTTTTTGCCAGAATGAATG-CCAAAAG
* *
2168413 GGTGAACGCATAAAGTGTCAATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACTGATA
193 GGTGAACGCATAAAGTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCGATA
* *
2168478 ATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATGCATCGGTTTTTTGAGAAAATA
258 ATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATGAACCGGTTTTTTGAGAAAATA
* *
2168543 GGTGAATATAATGTATCAACACGTTTTAGATTTGTGTCGATACTTTTGGTCCACAAGGAAAATCC
323 GGT-AACATAATGTATCGACACGTTTTAGATTTGTGTCGATACTTTTGGTCCACAAGGAAAATCC
*
2168608 AAAAAGGTTGC
387 AAAAAGGGTGC
* *
2168619 TCCCATAAAGTGTCGATACATTTTTAAACAGTATCGATCCCTAAAACATCGAAA-CTCATAATTA
1 TCCCATAAAGTGTCGATACATTTTTAAACAGTATCGATCCCAAAAACATCGAAATC-CATAAATA
* **
2168683 TAATGTAATAGGTATTTTTGTAATATAACCAATATAAATATACCGATTTTATGTCAGAATAGGTC
65 TAATGTAATAGGTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGTCAGAATAGGTC
* * * * *
2168748 TACATAATTTGTCGACATTTTTAAATGATGTGTGGATACTTTTTTCCAGAATGAATGCCAAAAGG
130 TACATAATGTGTCGACACTTTTAAA-GTTGTGTCGATACTTTTTGCCAGAATGAATGCCAAAAGG
* *
2168813 GTGAACGCAGAAAGTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATTGAAACCGATAA
194 GTGAACGCATAAAGTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCGATAA
* *
2168878 TTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATGTACCGGTTTTATGAGAAAATAG
259 TTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATGAACCGGTTTTTTGAGAAAATAG
2168943 GTTAACATAATGTATCGACACGTTTTAGATTTGTGTCGATACTT
324 G-TAACATAATGTATCGACACGTTTTAGATTTGTGTCGATACTT
2168987 GTAAATAGCG
Statistics
Matches: 694, Mismatches: 65, Indels: 18
0.89 0.08 0.02
Matches are distributed among these distances:
398 4 0.01
399 380 0.55
400 301 0.43
401 9 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (397 bp):
TCCCATAAAGTGTCGATACATTTTTAAACAGTATCGATCCCAAAAACATCGAAATCCATAAATAT
AATGTAATAGGTAATTTTGTAATATAACCGGTATAAATATACCGATTTTATGTCAGAATAGGTCT
ACATAATGTGTCGACACTTTTAAAGTTGTGTCGATACTTTTTGCCAGAATGAATGCCAAAAGGGT
GAACGCATAAAGTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCGATAATT
ATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATGAACCGGTTTTTTGAGAAAATAGGT
AACATAATGTATCGACACGTTTTAGATTTGTGTCGATACTTTTGGTCCACAAGGAAAATCCAAAA
AGGGTGC
Found at i:2172656 original size:3 final size:3
Alignment explanation
Indices: 2172638--2172731 Score: 66
Period size: 3 Copynumber: 31.7 Consensus size: 3
2172628 AATTTTTGCC
* * * * *
2172638 TAT T-T TAT TTT TAT TAT TAT AAT TAT TAT AAT TGT TAT AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
2172685 AAT TAT TAC TAT TAT TAT CA- TAT TTT TAT TAAT AAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
2172730 TA
1 TA
2172732 CATATTACAG
Statistics
Matches: 66, Mismatches: 22, Indels: 6
0.70 0.23 0.06
Matches are distributed among these distances:
2 3 0.05
3 61 0.92
4 2 0.03
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:2172662 original size:9 final size:9
Alignment explanation
Indices: 2172650--2172702 Score: 81
Period size: 9 Copynumber: 5.9 Consensus size: 9
2172640 TTTTATTTTT
2172650 ATTATTATA
1 ATTATTATA
2172659 ATTATTATA
1 ATTATTATA
*
2172668 ATTGTTATA
1 ATTATTATA
2172677 ATTATTATA
1 ATTATTATA
2172686 ATTATTACT-
1 ATTATTA-TA
2172695 ATTATTAT
1 ATTATTAT
2172703 CATATTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
8 1 0.02
9 39 0.95
10 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (9 bp):
ATTATTATA
Found at i:2174093 original size:30 final size:30
Alignment explanation
Indices: 2174033--2174091 Score: 95
Period size: 28 Copynumber: 2.0 Consensus size: 30
2174023 ATAGTTATTG
*
2174033 TTTAAATTTTATATGATTATTATCAATATA
1 TTTAAATATTATATGATTATTATCAATATA
2174063 TTTAAATATTAT-T-ATTATTATCAATATA
1 TTTAAATATTATATGATTATTATCAATATA
2174091 T
1 T
2174092 ATATAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 16 0.57
29 1 0.04
30 11 0.39
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTAAATATTATATGATTATTATCAATATA
Found at i:2174111 original size:28 final size:28
Alignment explanation
Indices: 2174048--2174105 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
2174038 ATTTTATATG
* *
2174048 ATTATTATCAATATATTTAAATATTATT
1 ATTATTATCAATATATATAAATATAATT
2174076 ATTATTATCAATATATATATAATA-AATT
1 ATTATTATCAATATATATA-AATATAATT
2174104 AT
1 AT
2174106 ATTTATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTATTATCAATATATATAAATATAATT
Found at i:2178171 original size:15 final size:15
Alignment explanation
Indices: 2178151--2178182 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2178141 GATCAATACC
2178151 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
2178166 TTTTGCATACATTCA
1 TTTTGCATACATGCA
2178181 TT
1 TT
2178183 ATTCATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:2185533 original size:17 final size:17
Alignment explanation
Indices: 2185511--2185567 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
2185501 TATTCTTGAA
2185511 AAAAAATGAAGAAAAAG
1 AAAAAATGAAGAAAAAG
*
2185528 AAAAAA-GAAAGAAAGAG
1 AAAAAATG-AAGAAAAAG
* **
2185545 AAAACATGTTGAAAAAG
1 AAAAAATGAAGAAAAAG
2185562 AAAAAA
1 AAAAAA
2185568 ATAGAAAAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 1 0.03
17 30 0.94
18 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.18, T:0.07
Consensus pattern (17 bp):
AAAAAATGAAGAAAAAG
Found at i:2185945 original size:18 final size:18
Alignment explanation
Indices: 2185922--2185956 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2185912 CAAGTTTATC
2185922 TTTTTGAAATTCAATTTA
1 TTTTTGAAATTCAATTTA
2185940 TTTTTGAAATTCAATTT
1 TTTTTGAAATTCAATTT
2185957 GTTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTTTGAAATTCAATTTA
Found at i:2187575 original size:124 final size:122
Alignment explanation
Indices: 2187239--2187612 Score: 615
Period size: 123 Copynumber: 3.0 Consensus size: 122
2187229 CATTTGATGG
*
2187239 ATCAAATTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAGAAGAAGTTCATA
2187304 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
65 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
2187362 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATA
* *
2187427 ATGAGAAGAACTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCATC
65 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
* *
2187485 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAAGTCATCTGAAGAATGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCAT
* * * * *
2187550 AATGATAAGAGCTTGTTCAACCTTTTGTATGA-TCTATCACAGAATGAGATAGATTAGC
64 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
2187608 ATCAA
1 ATCAA
2187613 GAAGAGCTTG
Statistics
Matches: 237, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
123 162 0.68
124 75 0.32
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (122 bp):
ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAA
TGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAAC
Found at i:2187943 original size:3 final size:3
Alignment explanation
Indices: 2187925--2188027 Score: 59
Period size: 3 Copynumber: 34.7 Consensus size: 3
2187915 AAATTTTGTC
* * * * *
2187925 TAT T-T TAT TTT TAT TAT TAT AAT GAT TAT AAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
2187972 TA- TAT TTT TAT TAAT AAA TAT TTT TAT TA- TAT TTT TAT TAAT AAA
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
2188017 TAT TAT TAT TA
1 TAT TAT TAT TA
2188028 CATATTACAG
Statistics
Matches: 72, Mismatches: 23, Indels: 10
0.69 0.22 0.10
Matches are distributed among these distances:
2 6 0.08
3 62 0.86
4 4 0.06
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:2187993 original size:27 final size:27
Alignment explanation
Indices: 2187963--2188027 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
2187953 TAATTATTAC
2187963 TATTATTATTATATTTTTATTAATAAA
1 TATTATTATTATATTTTTATTAATAAA
*
2187990 TATTTTTATTATATTTTTATTAATAAA
1 TATTATTATTATATTTTTATTAATAAA
2188017 TATTATTATTA
1 TATTATTATTA
2188028 CATATTACAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTATTATTATATTTTTATTAATAAA
Found at i:2187994 original size:16 final size:16
Alignment explanation
Indices: 2187973--2188027 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 16
2187963 TATTATTATT
2187973 ATATTTTTATTAATAA
1 ATATTTTTATTAATAA
2187989 ATATTTTTA-T--T--
1 ATATTTTTATTAATAA
2188000 ATATTTTTATTAATAA
1 ATATTTTTATTAATAA
*
2188016 ATATTATTATTA
1 ATATTTTTATTA
2188028 CATATTACAG
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
11 9 0.27
12 1 0.03
13 1 0.03
14 1 0.03
15 1 0.03
16 20 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTTTTATTAATAA
Found at i:2189420 original size:30 final size:30
Alignment explanation
Indices: 2189360--2189418 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
2189350 ATAGTTATTG
* *
2189360 TTTAAATTTTATATGATTATTATCAATATA
1 TTTAAATATTATATGATTATTATAAATATA
2189390 TTTAAATATTAT-T-ATTATTATAAATATA
1 TTTAAATATTATATGATTATTATAAATATA
2189418 T
1 T
2189419 ATATATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 15 0.56
29 1 0.04
30 11 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTAAATATTATATGATTATTATAAATATA
Found at i:2190348 original size:18 final size:18
Alignment explanation
Indices: 2190325--2190361 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2190315 TAGGTATACA
2190325 TAATGTGTCGACACTTTT
1 TAATGTGTCGACACTTTT
*
2190343 TAATGTGTCGATACTTTT
1 TAATGTGTCGACACTTTT
2190361 T
1 T
2190362 TCCAGAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (18 bp):
TAATGTGTCGACACTTTT
Found at i:2190418 original size:196 final size:197
Alignment explanation
Indices: 2190081--2190517 Score: 542
Period size: 196 Copynumber: 2.2 Consensus size: 197
2190071 CGGTTACGAC
* *
2190081 ATAACCGATATAAATATACCAGTTTTATGAGAAAATAGGTCATCATAAAGTATCGACACTTATTA
1 ATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCATCATAAAGTATCGACACTTATTA
* * * * * *
2190146 AGTTTGTGTCGATATATTTTGTCCATAATGAATGTCAGACGGGTGCACTCATAAAGTGTCGATAC
66 A--TTGTGTCGATATATTTTGTCCAGAATGAATGCCAAAAGGGTGAACGCATAAAGTGTCGATAC
* * * *
2190211 ATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTG
129 ATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCCATAATTATAATGTAATAGATAAATTTG
*
2190276 TAAT
194 CAAT
** * * * * *
2190280 ATAACCGGTATATTTATACCGGTTTTATGTGAGAATAGGT-ATACATAATGTGTCGACACTTTTT
1 ATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAT-CATAAAGTATCGACACTTATT
*
2190344 AA-TGTGTCGATACT-TTTT-TCCAGAATGAATGCCCAAAAGGGTGAACGCATATAGTGTCGATA
65 AATTGTGTCGATA-TATTTTGTCCAGAATGAATG-CCAAAAGGGTGAACGCATAAAGTGTCGATA
*
2190406 CATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGATAAATTT
128 CATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCCATAATTATAATGTAATAGATAAATTT
2190471 GCAAT
193 GCAAT
* * * * *
2190476 GTTACAGGTATAAATATACCGG-TTTACTTATAAAATAGGTCA
1 ATAACCGGTATAAATATACCGGTTTTA-TGAGAAAATAGGTCA
2190518 ATATAAGCGC
Statistics
Matches: 202, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
195 16 0.08
196 128 0.63
197 2 0.01
198 2 0.01
199 54 0.27
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (197 bp):
ATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCATCATAAAGTATCGACACTTATTA
ATTGTGTCGATATATTTTGTCCAGAATGAATGCCAAAAGGGTGAACGCATAAAGTGTCGATACAT
TTATAAAAAGTATCGATCCAAAAAACATCGAAACCCATAATTATAATGTAATAGATAAATTTGCA
AT
Found at i:2190618 original size:23 final size:23
Alignment explanation
Indices: 2190592--2190643 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2190582 TCCAGTTAAA
**
2190592 TACCTATTTTATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
*
2190615 TACCTATTACATTATATAAGCGT
1 TACCTATTACATTATATAAGCGC
2190638 TACCTA
1 TACCTA
2190644 ATATGTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (23 bp):
TACCTATTACATTATATAAGCGC
Found at i:2190623 original size:87 final size:87
Alignment explanation
Indices: 2190518--2190680 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
2190508 AAATAGGTCA
*
2190518 ATATAAGCGCTAATTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTAACTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
2190583 CCAGTTAAATACCTATTTTATT
66 CCAGTTAAATACCTATTTTATT
* * *
2190605 ATATAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTAACTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
* *
2190670 TCGGTTAAATA
66 CCAGTTAAATA
2190681 ATATAACATA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTAACTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
CCAGTTAAATACCTATTTTATT
Found at i:2198376 original size:21 final size:20
Alignment explanation
Indices: 2198352--2198412 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
2198342 CAAACATTAC
2198352 CAAACTTTGAAAAACATTTTT
1 CAAA-TTTGAAAAACATTTTT
**
2198373 CAAA---G--AAACATTTAC
1 CAAATTTGAAAAACATTTTT
2198388 CAAATTTTGAAAAACATTTTT
1 CAAA-TTTGAAAAACATTTTT
2198409 CAAA
1 CAAA
2198413 GTTGGTTGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 12 0.40
17 1 0.03
19 1 0.03
21 16 0.53
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (20 bp):
CAAATTTGAAAAACATTTTT
Found at i:2198383 original size:35 final size:36
Alignment explanation
Indices: 2198343--2198413 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
2198333 AACATCTACC
2198343 AAACA-TTACCAAACTTTGAAAAACATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
*
2198378 AAACATTTACCAAATTTTGAAAAACATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
2198414 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:2211940 original size:22 final size:23
Alignment explanation
Indices: 2211899--2211943 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2211889 ATTCTCACAT
* *
2211899 TATTTAGATATTAACTTTTTAAA
1 TATTTAAATATTAACCTTTTAAA
2211922 TATTTAAATA-TAACCTTTTAAA
1 TATTTAAATATTAACCTTTTAAA
2211944 CTTTAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (23 bp):
TATTTAAATATTAACCTTTTAAA
Found at i:2212267 original size:20 final size:20
Alignment explanation
Indices: 2212225--2212416 Score: 244
Period size: 20 Copynumber: 9.6 Consensus size: 20
2212215 GATTTTCAAG
* ** *
2212225 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2212245 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
*
2212265 AATCGCAACGCTTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2212285 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2212305 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2212325 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2212345 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2212365 AATCGCAACG-ATAATCAGTA
1 AATCGCAACGCGT-ATCCGTA
2212385 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2212405 AATCGCAACGCG
1 AATCGCAACGCG
2212417 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 144 0.97
21 3 0.02
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2212833 original size:33 final size:33
Alignment explanation
Indices: 2212794--2212864 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2212784 TTCACTTAGA
2212794 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2212827 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2212860 TTTCA
1 TTTCA
2212865 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2213011 original size:21 final size:20
Alignment explanation
Indices: 2212944--2213049 Score: 100
Period size: 20 Copynumber: 5.5 Consensus size: 20
2212934 TGCAGAAGAG
*
2212944 TCGCAACGAGATAATGAAAA
1 TCGCAACGAGAAAATGAAAA
* **
2212964 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
2212984 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
2213006 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
2213020 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
2213039 TCGCAACGAGA
1 TCGCAACGAGA
2213050 GAATCGCAAC
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 18 0.26
21 15 0.22
22 10 0.14
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:2213023 original size:14 final size:14
Alignment explanation
Indices: 2213004--2213060 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2212994 GAAAAATGAA
2213004 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2213018 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2213037 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2213051 AATCGCAACG
1 AATCGCAACG
2213061 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2213035 original size:33 final size:33
Alignment explanation
Indices: 2212997--2213077 Score: 162
Period size: 33 Copynumber: 2.5 Consensus size: 33
2212987 GCAACGAGAA
2212997 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
2213030 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
2213063 AAATGAAAATCGCAA
1 AAATGAAAATCGCAA
2213078 TGCGATTTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.48, C:0.20, G:0.22, T:0.10
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:2213042 original size:19 final size:19
Alignment explanation
Indices: 2212944--2213082 Score: 91
Period size: 19 Copynumber: 7.6 Consensus size: 19
2212934 TGCAGAAGAG
*
2212944 TCGCAACGAGATAATGAAAA
1 TCGCAACGCGA-AATGAAAA
* **
2212964 TCGCAACGTGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
*
2212984 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGCG--AAATGAAAA
*
2213006 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
2213020 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2213039 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
2213053 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2213072 TCGCAATGCGA
1 TCGCAACGCGA
2213083 TTTTGGTTTC
Statistics
Matches: 94, Mismatches: 12, Indels: 27
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.21
15 2 0.02
16 4 0.04
17 2 0.02
18 2 0.02
19 25 0.27
20 17 0.18
21 12 0.13
22 10 0.11
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2213113 original size:14 final size:14
Alignment explanation
Indices: 2213094--2213150 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2213084 TTTGGTTTCG
2213094 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2213108 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2213127 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2213141 CGTTGCGATT
1 CGTTGCGATT
2213151 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2213126 original size:33 final size:33
Alignment explanation
Indices: 2213078--2213199 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 33
2213068 AAAATCGCAA
**
2213078 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2213111 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
2213144 TGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCGT
2213185 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
2213200 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 42 0.54
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 21 0.27
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2213161 original size:21 final size:21
Alignment explanation
Indices: 2213135--2213199 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
2213125 CGCGTTGCGA
2213135 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2213156 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
2213176 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
2213197 TTC
1 TTC
2213200 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2215331 original size:20 final size:20
Alignment explanation
Indices: 2215303--2215531 Score: 244
Period size: 20 Copynumber: 11.4 Consensus size: 20
2215293 AAATTTCAGT
* * *
2215303 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2215323 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2215343 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
2215363 GTTGCGATTTACTGATTATC
1 GTTGCGATTTACGGATTCGC
*
2215383 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2215403 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2215423 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2215443 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
2215463 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
2215483 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
2215503 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
2215523 GTTGCGATT
1 GTTGCGATT
2215532 CTGTAAAATC
Statistics
Matches: 184, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 183 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:2215549 original size:21 final size:20
Alignment explanation
Indices: 2215525--2215595 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 20
2215515 ATATTCGCGT
2215525 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
2215546 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
**
2215567 TGCGA-TTGTCAAGAATCGCGT
1 TGCGATTTGT-AA-AATCGCAA
2215588 TGCGATTT
1 TGCGATTT
2215596 TGGAAACTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 29 0.73
22 5 0.12
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:2226344 original size:20 final size:20
Alignment explanation
Indices: 2226280--2226348 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
2226270 ACAGTTTCCA
* *
2226280 AATTTGCAACTCAATTTCTG
1 AATTCGCAACTCGATTTCTG
* * * *
2226300 AAATCACAACACGATTTC-A
1 AATTCGCAACTCGATTTCTG
2226319 AATTCGCAACTCGATTTCTG
1 AATTCGCAACTCGATTTCTG
2226339 AATTCGCAAC
1 AATTCGCAAC
2226349 GTGAATCTCT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 15 0.39
20 23 0.61
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (20 bp):
AATTCGCAACTCGATTTCTG
Found at i:2226567 original size:21 final size:21
Alignment explanation
Indices: 2226517--2226567 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
2226507 GTAGTTTTTG
* *
2226517 AAACTTAAATTCGTAACACGA
1 AAACTAAAATTCGCAACACGA
* *
2226538 AAA-TAAAATTTGCAACGCGA
1 AAACTAAAATTCGCAACACGA
2226558 AAACTAAAAT
1 AAACTAAAAT
2226568 CGCGTTGCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.53, C:0.16, G:0.10, T:0.22
Consensus pattern (21 bp):
AAACTAAAATTCGCAACACGA
Found at i:2226620 original size:20 final size:20
Alignment explanation
Indices: 2226597--2226635 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2226587 TCACGTTGCG
2226597 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
*
2226617 ATTTTCGTGTTGTGAATTT
1 ATTTTCGTGTTGCGAATTT
2226636 AAGTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.10, G:0.21, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:2226642 original size:20 final size:20
Alignment explanation
Indices: 2226599--2226642 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2226589 ACGTTGCGAT
* *
2226599 TTTCGTGTTGCGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
*
2226619 TTTCGTGTTGTGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
2226639 TTTC
1 TTTC
2226643 AAAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:2230791 original size:22 final size:25
Alignment explanation
Indices: 2230765--2230816 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 25
2230755 ATATGGGGAC
2230765 GGATGTCGCCG-GAGA-TGAGA-AT
1 GGATGTCGCCGAGAGAGTGAGAGAT
2230787 GGATGTCGCCGTAGAGAGTGAGAGAT
1 GGATGTCGCCG-AGAGAGTGAGAGAT
2230813 GGAT
1 GGAT
2230817 ATGGGACTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 11 0.42
24 4 0.15
25 5 0.19
26 6 0.23
ACGTcount: A:0.27, C:0.12, G:0.42, T:0.19
Consensus pattern (25 bp):
GGATGTCGCCGAGAGAGTGAGAGAT
Found at i:2230931 original size:19 final size:20
Alignment explanation
Indices: 2230909--2230946 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2230899 AATATTGTGT
2230909 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
2230928 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
2230947 TGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:2230942 original size:20 final size:19
Alignment explanation
Indices: 2230917--2230959 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2230907 GTTTCGAATT
*
2230917 CGAAAATAAAATTCGCGTTG
1 CGAAAAT-AAATGCGCGTTG
*
2230937 CGAAAATAAATGCGCTTTG
1 CGAAAATAAATGCGCGTTG
2230956 CGAA
1 CGAA
2230960 TTTGACTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (19 bp):
CGAAAATAAATGCGCGTTG
Found at i:2231223 original size:14 final size:14
Alignment explanation
Indices: 2231204--2231232 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2231194 GAAGTTATTT
2231204 TCTCTATAGTAAAA
1 TCTCTATAGTAAAA
2231218 TCTCTATAGTAAAA
1 TCTCTATAGTAAAA
2231232 T
1 T
2231233 TCTCCTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (14 bp):
TCTCTATAGTAAAA
Found at i:2232639 original size:2 final size:2
Alignment explanation
Indices: 2232632--2232656 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2232622 AATTATGATC
2232632 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2232657 AGCATATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2232938 original size:10 final size:11
Alignment explanation
Indices: 2232923--2232980 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
2232913 GGGGTAAATT
2232923 AAAATA-TAAA
1 AAAATATTAAA
2232933 AAAATATTAAA
1 AAAATATTAAA
**
2232944 AAGTTAATATTTTA
1 AA---AATATTAAA
2232958 AAAATA-TAAA
1 AAAATATTAAA
2232968 AAAATATTAAA
1 AAAATATTAAA
2232979 AA
1 AA
2232981 TTAAAAGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 14 0.36
11 16 0.41
14 9 0.23
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AAAATATTAAA
Found at i:2233167 original size:23 final size:22
Alignment explanation
Indices: 2233134--2233176 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2233124 AGTTTAGTTC
*
2233134 TCTTTATTTCATTTTTTTATTT
1 TCTTTATTTCATTTCTTTATTT
2233156 TCTTTATCTTCATTTCTTTAT
1 TCTTTAT-TTCATTTCTTTAT
2233177 ATCAAATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (22 bp):
TCTTTATTTCATTTCTTTATTT
Found at i:2235055 original size:20 final size:19
Alignment explanation
Indices: 2235030--2235083 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2235020 GCGAAATAAA
2235030 AATCGCAACGTGATCTCCAG
1 AATCGCAACGTGATC-CCAG
** *
2235050 AATCGCAAATTAGTTCCCAG
1 AATCGCAACGT-GATCCCAG
2235070 AATCGCAACGTGAT
1 AATCGCAACGTGAT
2235084 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (19 bp):
AATCGCAACGTGATCCCAG
Found at i:2235175 original size:20 final size:20
Alignment explanation
Indices: 2235133--2235180 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2235123 GATTTTCAAG
* *
2235133 AATCACAACGCGAATATGAA
1 AATCGCAACGCGAACATGAA
2235153 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAACATGA-A
2235173 AATCGCAA
1 AATCGCAA
2235181 TGTGATTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.48, C:0.23, G:0.15, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATGAA
Found at i:2235223 original size:81 final size:80
Alignment explanation
Indices: 2235133--2235408 Score: 297
Period size: 81 Copynumber: 3.4 Consensus size: 80
2235123 GATTTTCAAG
* * * * * * *
2235133 AATCACAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAATGTG-ATTC-TGACTAT
1 AATCGCAACGCGTATCTGTAAATCGCAACGCGAACATATAAATCGCAATGCGTATCCGT-A-AAT
* *
2235196 CGCAACGAGTATCCGTAA
64 CGCAACGAGAATACGT-A
* * * *
2235214 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA-AAATCGCAACGCGTATCCGTAAAT
1 AATCGCAACGCGTATCTGTAAATCGCAACG-CGA-ACATATAAATCGCAATGCGTATCCGTAAAT
2235278 CGCAACGAGAATACGTA
64 CGCAACGAGAATACGTA
* * **
2235295 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGTATCTGTAAATCGCAACGCGAACATATAAATCGCAATGCGTATCCGTAAATCG
* *
2235360 CAATGACAATACGTAA
66 CAACGAGAATACGT-A
*
2235376 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCTGTAAATCGCAACGCGA
2235409 TTTTTAAAGC
Statistics
Matches: 164, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
79 1 0.01
80 38 0.23
81 87 0.53
82 29 0.18
83 8 0.05
84 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (80 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGCGAACATATAAATCGCAATGCGTATCCGTAAATCG
CAACGAGAATACGTA
Found at i:2235238 original size:20 final size:20
Alignment explanation
Indices: 2235194--2235407 Score: 243
Period size: 20 Copynumber: 10.6 Consensus size: 20
2235184 GATTCTGACT
*
2235194 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
2235215 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
2235235 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
2235256 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
2235276 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
2235296 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
2235316 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
2235336 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
2235356 ATCGCAATGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
2235377 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
2235397 ATCGCAACGCG
1 ATCGCAACGCG
2235408 ATTTTTAAAG
Statistics
Matches: 162, Mismatches: 25, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
20 112 0.69
21 50 0.31
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:2235309 original size:40 final size:41
Alignment explanation
Indices: 2235194--2235405 Score: 347
Period size: 41 Copynumber: 5.2 Consensus size: 41
2235184 GATTCTGACT
* *
2235194 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
2235235 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
2235276 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
2235316 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
2235356 ATCGCAATGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
2235397 ATCGCAACG
1 ATCGCAACG
2235406 CGATTTTTAA
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
40 75 0.47
41 84 0.53
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:2236026 original size:21 final size:21
Alignment explanation
Indices: 2235965--2236043 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
2235955 TTCTAAACTT
2235965 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
2235985 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
2236005 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
2236026 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
2236044 TCGCAACGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:2236062 original size:33 final size:34
Alignment explanation
Indices: 2235967--2236100 Score: 128
Period size: 33 Copynumber: 3.8 Consensus size: 34
2235957 CTAAACTTAA
** *
2235967 AATCGCAACATGAAAATGAAAATCGCAACACGAAAATG
1 AATCGCAACGCGAAAATGAAAATCGC-A-ACG-AGA-G
*
2236005 ACTATCGCAACGAGAGAAATGAAAATCGCAACGAGAG
1 A--ATCGCAACGCGA-AAATGAAAATCGCAACGAGAG
* *
2236042 AATCGCAACGC-AAAATGAAAATCACAACGAGAT
1 AATCGCAACGCGAAAATGAAAATCGCAACGAGAG
*
2236075 AATCGCAACGCGAAACT-AAAATCGCA
1 AATCGCAACGCGAAAATGAAAATCGCA
2236101 TTGCGATTCT
Statistics
Matches: 84, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
33 38 0.45
34 5 0.06
35 9 0.11
37 2 0.02
38 3 0.04
39 3 0.04
40 11 0.13
41 13 0.15
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (34 bp):
AATCGCAACGCGAAAATGAAAATCGCAACGAGAG
Found at i:2236168 original size:20 final size:20
Alignment explanation
Indices: 2236106--2236161 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
2236096 TCGCATTGCG
2236106 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
*
2236126 ATT-TCCGCGTTGCGATAGTC
1 ATTCT-CTCGTTGCGATAGTC
2236146 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
2236162 TTTCATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:2238021 original size:94 final size:93
Alignment explanation
Indices: 2237860--2238239 Score: 643
Period size: 94 Copynumber: 4.1 Consensus size: 93
2237850 TAGATTGCTT
* *
2237860 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
2237925 ATTTGTCTTTTGTTTTGTCTTTTAGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
2237954 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2238019 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
2238048 AGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
2238113 ATTTGTCTTTGTTTTGTCTTTTGGTTTAA
66 ATTTGTCTTTGTTTTGTCTTTTGG-TTGA
* * *
2238142 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAATCTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
2238207 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
2238235 AGTAA
1 AGTAA
2238240 TGCAATCCAT
Statistics
Matches: 270, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
93 27 0.10
94 241 0.89
95 2 0.01
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:2238343 original size:19 final size:19
Alignment explanation
Indices: 2238287--2238413 Score: 125
Period size: 19 Copynumber: 6.7 Consensus size: 19
2238277 TAGTTTACTT
* *
2238287 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
2238307 TCGCAACGTGAAAAATGACTA
1 TCGCAACGCG--AAATGAAAA
2238328 TCGCAACGCGAAATG--AA
1 TCGCAACGCGAAATGAAAA
*
2238345 TCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
2238364 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
**
2238383 TCGCAACGC-AAACCAAAA
1 TCGCAACGCGAAATGAAAA
*
2238401 TCGCAATGCGAAA
1 TCGCAACGCGAAA
2238414 CTATAATCGC
Statistics
Matches: 90, Mismatches: 12, Indels: 11
0.80 0.11 0.10
Matches are distributed among these distances:
17 15 0.17
18 15 0.17
19 37 0.41
20 8 0.09
21 12 0.13
22 3 0.03
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2238385 original size:38 final size:38
Alignment explanation
Indices: 2238287--2238413 Score: 125
Period size: 36 Copynumber: 3.3 Consensus size: 38
2238277 TAGTTTACTT
* * **
2238287 TCGCAACACGAAACTTAAAATCGCAACGTGAAAAATGACTA
1 TCGCAACGCGAAA-TGAAAATCGCAAC--GAAAAATGAAAA
*
2238328 TCGCAACGCGAAATG--AATCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAAATGAAAA
* **
2238364 TCGCAACGCGAAATGAAAATCGCAACG-CAAACCAAAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAAATGAAAA
*
2238401 TCGCAATGCGAAA
1 TCGCAACGCGAAA
2238414 CTATAATCGC
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
36 24 0.32
37 19 0.25
38 19 0.25
40 1 0.01
41 12 0.16
ACGTcount: A:0.46, C:0.23, G:0.18, T:0.13
Consensus pattern (38 bp):
TCGCAACGCGAAATGAAAATCGCAACGAAAAATGAAAA
Found at i:2238412 original size:37 final size:36
Alignment explanation
Indices: 2238327--2238413 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 36
2238317 AAAAATGACT
* **
2238327 ATCGCAACGCGAAATGAATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAATGAATCGCAACGACAAACCAAA
2238363 ATCGCAACGCGAAATGAAAATCGCAACG-CAAACCAAA
1 ATCGCAACGCGAAATG--AATCGCAACGACAAACCAAA
*
2238400 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
2238414 CTATAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 16 0.36
37 19 0.42
38 10 0.22
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (36 bp):
ATCGCAACGCGAAATGAATCGCAACGACAAACCAAA
Found at i:2238483 original size:20 final size:20
Alignment explanation
Indices: 2238458--2238504 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2238448 GATTCTCTCG
2238458 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
2238478 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
2238498 TTGCGAT
1 TTGCGAT
2238505 TTTAAGTTTC
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:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:2239079 original size:21 final size:20
Alignment explanation
Indices: 2238988--2239092 Score: 59
Period size: 21 Copynumber: 5.0 Consensus size: 20
2238978 GACTCACCTG
2238988 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-C
* * *
2239008 CCTATCATTCAAGAGGCCCTTA
1 TC-ATCGTTCAAGAGGCCC-TC
** *
2239030 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAG-GCCCTC
* * *
2239051 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
*
2239072 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGG-CCCTC
2239093 CCAACATTCT
Statistics
Matches: 61, Mismatches: 18, Indels: 11
0.68 0.20 0.12
Matches are distributed among these distances:
20 3 0.05
21 49 0.80
22 8 0.13
23 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:2241836 original size:24 final size:24
Alignment explanation
Indices: 2241799--2241852 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2241789 CTAAAAAATC
2241799 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
2241823 ATCAAAGTCTGAGTATTGACCATG
1 ATCAAAATCCGAGTATTGACCAAG
2241847 ATCAAA
1 ATCAAA
2241853 TTTCGAATAC
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:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2242718 original size:20 final size:20
Alignment explanation
Indices: 2242703--2243216 Score: 238
Period size: 20 Copynumber: 25.5 Consensus size: 20
2242693 GTCAGAATCT
2242703 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTACAGATTCG
*
2242723 CATTGCGATTTACAGATTCG
1 CGTTGCGATTTACAGATTCG
2242743 CGTTGCGATTTAC-GTATTCG
1 CGTTGCGATTTACAG-ATTCG
*
2242763 CGTTGCGATTTAC-GTAATCG
1 CGTTGCGATTTACAG-ATTCG
*
2242783 CGTTACGATTTAC-GTATTCG
1 CGTTGCGATTTACAG-ATTCG
* * * *
2242803 CGTTGCGAATTAGGAAAATCG
1 CGTTGCGATTTA-CAGATTCG
*** ** *
2242824 CAACGCGAATTT-GGGAAATCG
1 CGTTGCG-ATTTACAG-ATTCG
** * *
2242845 CAATGCGATAGT-CAGAATCG
1 CGTTGCGAT-TTACAGATTCG
* ** * *
2242865 CGTTGCGAATCTGGAAACT-G
1 CGTTGCG-ATTTACAGATTCG
**
2242885 ATTTGCGA--TACCGGAGA-TCG
1 CGTTGCGATTTA-C--AGATTCG
*
2242905 CGTTGCGAATTATCA-A-TCG
1 CGTTGCGATTTA-CAGATTCG
* *
2242924 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACAGATTCG
2242944 CGTTGCGATTTTAC-GTATT-G
1 CGTTGCGA-TTTACAG-ATTCG
* *
2242964 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACAGATTCG
* *
2242985 CATTGCGATTTAC-GTATTCT
1 CGTTGCGATTTACAG-ATTCG
* *
2243005 CGTTGCGATTTATAGATACG
1 CGTTGCGATTTACAGATTCG
*
2243025 CGTTGCGATTTAC-GTATTCT
1 CGTTGCGATTTACAG-ATTCG
* **
2243045 CGTTGCGATTTACGGATAGG
1 CGTTGCGATTTACAGATTCG
2243065 CGTTGCGATTTTAC-GTATT-G
1 CGTTGCGA-TTTACAG-ATTCG
* *
2243085 CCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACAGATTCG
* * *
2243106 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACAGATTCG
* * *
2243127 CGTTGCGATAGT-CAGAATCA
1 CGTTGCGAT-TTACAGATTCG
*
2243147 CGTTGCGATTTATATG-TTCG
1 CGTTGCGATTTACA-GATTCG
* *
2243167 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACAGATTCG
* *
2243187 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACAGATTCG
2243207 CGTTGCGATT
1 CGTTGCGATT
2243217 ATGGAAAATC
Statistics
Matches: 392, Mismatches: 67, Indels: 70
0.74 0.13 0.13
Matches are distributed among these distances:
17 1 0.00
18 1 0.00
19 22 0.06
20 279 0.71
21 83 0.21
22 6 0.02
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATTTACAGATTCG
Found at i:2242831 original size:21 final size:21
Alignment explanation
Indices: 2242807--2242852 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2242797 TATTCGCGTT
2242807 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
2242828 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2242849 GCGA
1 GCGA
2242853 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2242974 original size:41 final size:41
Alignment explanation
Indices: 2242924--2243216 Score: 332
Period size: 40 Copynumber: 7.2 Consensus size: 41
2242914 TTATCAATCG
*
2242924 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
2242965 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
**
2243005 CGTTGCGATTTATAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
2243045 CGTTGCGATTTACGGATAGGCGTTGCGATTTTACGTATTGC-
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT-CT
* *
2243086 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * * *
2243127 CGTTGCGATAGT-CAGA-ATCACGTTGCGATTTATA--TGTTCG
1 CGTTGCGAT-TTACGGATA-CGCGTTGCGATTT-TACGTATTCT
* ** * * *
2243167 CGTTGCGATTTTCATATTCGCGTTGCGATTTT-CATATTCG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
2243207 CGTTGCGATT
1 CGTTGCGATT
2243217 ATGGAAAATC
Statistics
Matches: 219, Mismatches: 23, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
39 2 0.01
40 116 0.53
41 97 0.44
42 4 0.02
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:2243155 original size:162 final size:161
Alignment explanation
Indices: 2242924--2243216 Score: 394
Period size: 162 Copynumber: 1.8 Consensus size: 161
2242914 TTATCAATCG
* ** * *
2242924 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACG-ATT
* * * *
2242989 GCGATTTACGTATTCTCGTTGCGATTTAT-AGATACGCGTTGCGATTTACGTATTCTCGTTGCGA
65 GCGATTTACATATTCGCGTTGCGATTT-TCAGATACGCGTTGCGATTTACATATTCGCGTTGCGA
2243053 TTTACGGATAGGCGTTGCGATTTTACGTATTGC
129 TTTACGGATAGGCGTTGCGATTTTACGTATTGC
2243086 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAATCACG-
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGAT--TCACGAAT-ACGA
* * * * *
2243149 TTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTCATATTCGCGTTGCG
63 TTGCGATTTACATATTCGCGTTGCGATTTTCAGATACGCGTTGCGATTTACATATTCGCGTTGCG
2243214 ATT
128 ATT
2243217 ATGGAAAATC
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
161 1 0.01
162 104 0.92
163 3 0.03
164 5 0.04
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.38
Consensus pattern (161 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATTCACGAATACGATTG
CGATTTACATATTCGCGTTGCGATTTTCAGATACGCGTTGCGATTTACATATTCGCGTTGCGATT
TACGGATAGGCGTTGCGATTTTACGTATTGC
Found at i:2243171 original size:81 final size:79
Alignment explanation
Indices: 2242921--2243216 Score: 312
Period size: 81 Copynumber: 3.7 Consensus size: 79
2242911 GAATTATCAA
* *
2242921 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGC
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG-
** *
2242986 ATTGCGATTTACGTAT
65 -TTGCGATTTATATGT
* *
2243002 TCTCGTTGCGATTTATAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATAGGC
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA--C
*
2243066 GTTGCGATTT-TACGT
64 GTTGCGATTTATATGT
* * * * * *
2243081 ATTGCCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGAAT
1 -TCG-CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGAT-TTAC-GGAT
2243145 CACGTTGCGATTTATATGT
62 -ACGTTGCGATTTATATGT
* * * * *
2243164 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTT-CATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATT
2243217 ATGGAAAATC
Statistics
Matches: 179, Mismatches: 27, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
79 1 0.01
80 52 0.29
81 82 0.46
82 35 0.20
83 8 0.04
84 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (79 bp):
TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGT
TGCGATTTATATGT
Found at i:2243281 original size:21 final size:20
Alignment explanation
Indices: 2243127--2243279 Score: 96
Period size: 20 Copynumber: 7.5 Consensus size: 20
2243117 TACGGATACT
** * *
2243127 CGTTGCGATAGTCAGAATCA
1 CGTTGCGATTTTCATAATCG
**
2243147 CGTTGCGATTTAT-ATGTTCG
1 CGTTGCGATTT-TCATAATCG
*
2243167 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTTCATAATCG
*
2243187 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTTCATAATCG
** *
2243207 CGTTGCGATTATGGAAAATCG
1 CGTTGCGATT-TTCATAATCG
** *
2243228 CAATACGAATTTGTGC-T-ATCG
1 CGTTGCG-ATTT-T-CATAATCG
*
2243249 CATTGCGATTCTTCATAATCG
1 CGTTGCGATT-TTCATAATCG
2243270 CGTTGCGATT
1 CGTTGCGATT
2243280 CTGGGAACTG
Statistics
Matches: 104, Mismatches: 20, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
19 2 0.02
20 64 0.62
21 35 0.34
22 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTTTCATAATCG
Found at i:2243315 original size:20 final size:20
Alignment explanation
Indices: 2243245--2243319 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
2243235 AATTTGTGCT
** *
2243245 ATCGCATTGCGATTCTTCATA
1 ATCGCATTGCGATTCTGGA-G
*
2243266 ATCGCGTTGCGATTCTGG-G
1 ATCGCATTGCGATTCTGGAG
*
2243285 AACTG-ATTTGCGATTCTGGAG
1 ATC-GCA-TTGCGATTCTGGAG
2243306 ATCGCATTGCGATT
1 ATCGCATTGCGATT
2243320 TTTATTTCGC
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.05
20 22 0.51
21 19 0.44
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATTCTGGAG
Found at i:2245528 original size:37 final size:37
Alignment explanation
Indices: 2245487--2245557 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
2245477 CAAATCAGTG
2245487 TATATATAAATCTGAATAATTGATGATAATTCATATA
1 TATATATAAATCTGAATAATTGATGATAATTCATATA
* * *
2245524 TATATATATATCTGAATGATTGATGATGATTCAT
1 TATATATAAATCTGAATAATTGATGATAATTCAT
2245558 GTATGCAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (37 bp):
TATATATAAATCTGAATAATTGATGATAATTCATATA
Found at i:2247056 original size:46 final size:46
Alignment explanation
Indices: 2246999--2247092 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
2246989 GACATAAATA
* *
2246999 TGTAAGTTATTTAAAACATAACCAGCAAACACAATATTAAAAGTTT
1 TGTAAGCTATTTAAAACATAACCAACAAACACAATATTAAAAGTTT
2247045 TGTAAGCTATTTAAAACATAACCAACAAACACAATATTAAAAGTTT
1 TGTAAGCTATTTAAAACATAACCAACAAACACAATATTAAAAGTTT
2247091 TG
1 TG
2247093 GACCAAATAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.30
Consensus pattern (46 bp):
TGTAAGCTATTTAAAACATAACCAACAAACACAATATTAAAAGTTT
Found at i:2247543 original size:69 final size:69
Alignment explanation
Indices: 2247457--2247597 Score: 282
Period size: 69 Copynumber: 2.0 Consensus size: 69
2247447 ACTTCGACTT
2247457 TATAAACTTCAATTTTAGATATCAAGAGATAAACTTTAAAAAATTTAGAGGAATTGTCAACAAAA
1 TATAAACTTCAATTTTAGATATCAAGAGATAAACTTTAAAAAATTTAGAGGAATTGTCAACAAAA
2247522 TTGA
66 TTGA
2247526 TATAAACTTCAATTTTAGATATCAAGAGATAAACTTTAAAAAATTTAGAGGAATTGTCAACAAAA
1 TATAAACTTCAATTTTAGATATCAAGAGATAAACTTTAAAAAATTTAGAGGAATTGTCAACAAAA
2247591 TTGA
66 TTGA
2247595 TAT
1 TAT
2247598 GATATCGTTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.33
Consensus pattern (69 bp):
TATAAACTTCAATTTTAGATATCAAGAGATAAACTTTAAAAAATTTAGAGGAATTGTCAACAAAA
TTGA
Found at i:2248109 original size:12 final size:12
Alignment explanation
Indices: 2248094--2248118 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2248084 TATATAATAA
2248094 TTTACATATTGT
1 TTTACATATTGT
2248106 TTTACATATTGT
1 TTTACATATTGT
2248118 T
1 T
2248119 CATCAATAAT
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:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TTTACATATTGT
Found at i:2260555 original size:16 final size:17
Alignment explanation
Indices: 2260514--2260567 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
2260504 GTATGATCTG
*
2260514 ATAAAAAAATTAACTAAA
1 ATAAAATAATTAAC-AAA
2260532 ATATAAATAATTAA-AAA
1 ATA-AAATAATTAACAAA
* *
2260549 ATAAAATTATTAACTAA
1 ATAAAATAATTAACAAA
2260566 AT
1 AT
2260568 TTAAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 9 0.29
17 10 0.32
18 3 0.10
19 9 0.29
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAAAATAATTAACAAA
Found at i:2260892 original size:11 final size:10
Alignment explanation
Indices: 2260865--2260900 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
2260855 AGCATTGATG
*
2260865 AAAAATTAAT
1 AAAAATAAAT
2260875 AAAAATAAAT
1 AAAAATAAAT
2260885 AAACAATAAAT
1 AAA-AATAAAT
2260896 AAAAA
1 AAAAA
2260901 AATCATATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:2261913 original size:21 final size:20
Alignment explanation
Indices: 2261889--2261952 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
2261879 AACTTTGAAA
2261889 AAATAGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
*
2261910 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
2261924 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
2261945 AAATGTTT
1 AAATGTTT
2261953 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 8 0.24
21 9 0.26
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:2261980 original size:37 final size:36
Alignment explanation
Indices: 2261881--2261999 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
2261871 TGGTAACCAA
2261881 CTTTGAAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
2261918 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
*
2261953 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAG-TTTTCAAAGTTTGGTAAATGTTT
*
2261990 -ATTGAAAAAT
1 CTTTGAAAAAT
2262000 GATAATGGGA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.45
36 15 0.20
37 27 0.36
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATAGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2266436 original size:21 final size:21
Alignment explanation
Indices: 2266412--2266472 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2266402 AACTTTGAAA
2266412 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
2266433 AAAT-GTTTT-----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
2266447 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
2266468 AAATG
1 AAATG
2266473 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 8 0.26
20 8 0.26
21 10 0.32
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.44
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:2266503 original size:37 final size:37
Alignment explanation
Indices: 2266404--2266522 Score: 165
Period size: 35 Copynumber: 3.3 Consensus size: 37
2266394 TGGTAACCAA
2266404 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
*
2266441 TTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
2266476 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
2266513 -GTTGAAAAAT
1 CTTTGAAAAAT
2266523 GATAATGGGA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
35 29 0.39
36 18 0.24
37 27 0.36
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2268408 original size:2 final size:2
Alignment explanation
Indices: 2268401--2268449 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2268391 ACTTGTTTCT
2268401 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2268443 TA TA TA T
1 TA TA TA T
2268450 TTAAGAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2268928 original size:20 final size:20
Alignment explanation
Indices: 2268905--2268971 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
2268895 GAATATGTAA
* *
2268905 ATCGCAATGCGATTATGACT
1 ATCGCAACGAGATTATGACT
*
2268925 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTATGACT
*
2268945 ATCGCAACGAGATTTTGACT
1 ATCGCAACGAGATTATGACT
2268965 ATCGCAA
1 ATCGCAA
2268972 TGCGATAGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (20 bp):
ATCGCAACGAGATTATGACT
Found at i:2269015 original size:34 final size:34
Alignment explanation
Indices: 2268972--2269065 Score: 143
Period size: 34 Copynumber: 2.8 Consensus size: 34
2268962 ACTATCGCAA
* **
2268972 TGCGATAGTCAAATTCGAGTTGCGATTTTTTCGT
1 TGCGATAGTCAAATTCGCGTTGCGATTTTTGAGT
2269006 TGCGATAGTCAAATTCGCGTTGCGATTTTTGAGT
1 TGCGATAGTCAAATTCGCGTTGCGATTTTTGAGT
* *
2269040 TGCGATAATCAAATTCGCGTTACGAT
1 TGCGATAGTCAAATTCGCGTTGCGAT
2269066 AGTCAAATTC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.37
Consensus pattern (34 bp):
TGCGATAGTCAAATTCGCGTTGCGATTTTTGAGT
Found at i:2269028 original size:20 final size:20
Alignment explanation
Indices: 2269003--2269093 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
2268993 GCGATTTTTT
2269003 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2269023 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
2269037 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2269057 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
2269077 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
2269094 GAATGTGTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
14 11 0.19
16 1 0.02
18 1 0.02
20 44 0.77
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:2269287 original size:18 final size:18
Alignment explanation
Indices: 2269264--2269298 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2269254 AAGCCGGTTG
*
2269264 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2269282 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
2269299 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2270470 original size:23 final size:23
Alignment explanation
Indices: 2270443--2270494 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2270433 TCCTAAAGGA
*
2270443 TGTCATCTGTGTCCCGAAGGACC
1 TGTCATCTGTATCCCGAAGGACC
*
2270466 TGTCATCTGTATCCCGTAGGACC
1 TGTCATCTGTATCCCGAAGGACC
*
2270489 TATCAT
1 TGTCAT
2270495 ATATCTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (23 bp):
TGTCATCTGTATCCCGAAGGACC
Found at i:2270699 original size:46 final size:46
Alignment explanation
Indices: 2270642--2270754 Score: 187
Period size: 46 Copynumber: 2.5 Consensus size: 46
2270632 ATGTGTAACC
2270642 ATAT-ATTTCATATCATATCACATGTATCACGTATTACATATTCAT
1 ATATCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
* *
2270687 ATGTCATTTCATATCATATCACATGTATCACGTATTGCATATTCAT
1 ATATCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
2270733 ATATCATTTCATAT-AT-TCACAT
1 ATATCATTTCATATCATATCACAT
2270755 AGCTTATCTC
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
44 6 0.09
45 5 0.08
46 53 0.83
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (46 bp):
ATATCATTTCATATCATATCACATGTATCACGTATTACATATTCAT
Found at i:2272569 original size:20 final size:20
Alignment explanation
Indices: 2272544--2272651 Score: 144
Period size: 20 Copynumber: 5.4 Consensus size: 20
2272534 GAAATTCAGT
*
2272544 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
2272564 GTTGCGATAGTCAGAATCTC
1 GTTGCGATAGTCAGAATCGC
* *
2272584 GTTGCGATAATCAAAATCGC
1 GTTGCGATAGTCAGAATCGC
2272604 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* * *
2272624 ATTACGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
2272644 ATTGCGAT
1 GTTGCGAT
2272652 TTACATATTC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:2272658 original size:20 final size:20
Alignment explanation
Indices: 2272635--2272690 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
2272625 TTACGATAGT
*
2272635 CATAATCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
2272655 CATATTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
2272675 CATATTCGCATTGCGA
1 CATATTCGCATTGCGA
2272691 ATTCGGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (20 bp):
CATATTCGCATTGCGATTTA
Found at i:2281226 original size:18 final size:20
Alignment explanation
Indices: 2281191--2281227 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2281181 CACGAAATGT
2281191 AAGATTACCAGTGAGAATAA
1 AAGATTACCAGTGAGAATAA
2281211 AAGATTACC-G-GAGAATA
1 AAGATTACCAGTGAGAATA
2281228 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.19
Consensus pattern (20 bp):
AAGATTACCAGTGAGAATAA
Found at i:2289561 original size:61 final size:61
Alignment explanation
Indices: 2289466--2289587 Score: 217
Period size: 61 Copynumber: 2.0 Consensus size: 61
2289456 TGATTGATCT
*
2289466 ATCGATCAGAAACAATTTATGCATGTCACTACACAGTTTCCTGAAGACATATTTTTGGCCA
1 ATCGATCAGAAACAATTTATGCATGTCACTACACAGTTTCCTGAAGACATATTTTCGGCCA
* *
2289527 ATCGATCAGAAACAATTTATGCCTGTTACTACACAGTTTCCTGAAGACATATTTTCGGCCA
1 ATCGATCAGAAACAATTTATGCATGTCACTACACAGTTTCCTGAAGACATATTTTCGGCCA
2289588 CTCATTTGGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (61 bp):
ATCGATCAGAAACAATTTATGCATGTCACTACACAGTTTCCTGAAGACATATTTTCGGCCA
Found at i:2290066 original size:30 final size:30
Alignment explanation
Indices: 2290032--2290091 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2290022 AATTCAAATT
*
2290032 AAAGAATAT-ATTTTAATTTATAATATTAAA
1 AAAGAATATGAATTTAATTTA-AATATTAAA
2290062 AAAGAATATGAATTTAATTTAAATATTAAA
1 AAAGAATATGAATTTAATTTAAATATTAAA
2290092 TCTATCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (30 bp):
AAAGAATATGAATTTAATTTAAATATTAAA
Found at i:2298339 original size:41 final size:41
Alignment explanation
Indices: 2298293--2298374 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
2298283 ATCAGTCGTG
*
2298293 ACTAGAGTTTCAAATAG-AGGTCGAATAGAGAAATAGTGGTC
1 ACTAGAGTTTCAAATAGCA-GTCAAATAGAGAAATAGTGGTC
2298334 ACTAGAGTTTCAAATAGCAGTCAAATAGAGAAATAGTGGTC
1 ACTAGAGTTTCAAATAGCAGTCAAATAGAGAAATAGTGGTC
2298375 GCTAATTGCG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 38 0.97
42 1 0.03
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.24
Consensus pattern (41 bp):
ACTAGAGTTTCAAATAGCAGTCAAATAGAGAAATAGTGGTC
Found at i:2299537 original size:23 final size:22
Alignment explanation
Indices: 2299503--2299547 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
2299493 GATCAAATTG
*
2299503 ATTTTTTTAAGTTTAATGGTTT
1 ATTTTTTAAAGTTTAATGGTTT
2299525 ATTTTTTAAAAGTTTAATGGTTT
1 ATTTTTT-AAAGTTTAATGGTTT
2299548 GTTTGAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.27, C:0.00, G:0.13, T:0.60
Consensus pattern (22 bp):
ATTTTTTAAAGTTTAATGGTTT
Done.