Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008353.1 Hibiscus syriacus cultivar Beakdansim tig00111088_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: 2583621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 5 of 13
Found at i:982581 original size:19 final size:19
Alignment explanation
Indices: 982554--982598 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
982544 CTGACTTGAT
*
982554 TTTAATTTATTTTAATATA
1 TTTAATTTAATTTAATATA
*
982573 TTTATTTTAATTTAATATA
1 TTTAATTTAATTTAATATA
*
982592 TTAAATT
1 TTTAATT
982599 AAAATAAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTAATTTAATTTAATATA
Found at i:982836 original size:29 final size:29
Alignment explanation
Indices: 982794--982853 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
982784 TGATGATCAC
*
982794 ATCTTAATTAAATAAAAACAAGCGACTAT
1 ATCTTAATTAAATAAAAACAAGCGACCAT
*
982823 ATCTTAATTAAATAAAAACAAGTGACCAT
1 ATCTTAATTAAATAAAAACAAGCGACCAT
982852 AT
1 AT
982854 ATAGTCGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (29 bp):
ATCTTAATTAAATAAAAACAAGCGACCAT
Found at i:988198 original size:29 final size:29
Alignment explanation
Indices: 988156--988215 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
988146 TCTTGGAAAG
988156 AAGTAAACACTGGACGAAGGTAATAAGCA
1 AAGTAAACACTGGACGAAGGTAATAAGCA
*
988185 AAGTAGACACTGGACGAAGGTAATAAGCA
1 AAGTAAACACTGGACGAAGGTAATAAGCA
988214 AA
1 AA
988216 ACGTTAGCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.25, T:0.13
Consensus pattern (29 bp):
AAGTAAACACTGGACGAAGGTAATAAGCA
Found at i:988303 original size:53 final size:53
Alignment explanation
Indices: 988223--988330 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
988213 AAAACGTTAG
* *
988223 CGAGGGTTGCAACTCGTTCCATCTTAATGGAGCGAAACATTCCCAACAGTGTA
1 CGAGGGGTGCAACTCATTCCATCTTAATGGAGCGAAACATTCCCAACAGTGTA
988276 CGAGGGGTGCAACTCATTCCATCTTAATGGAGCGAAACATTCCCAACAGTGTA
1 CGAGGGGTGCAACTCATTCCATCTTAATGGAGCGAAACATTCCCAACAGTGTA
988329 CG
1 CG
988331 GTGGCAACCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (53 bp):
CGAGGGGTGCAACTCATTCCATCTTAATGGAGCGAAACATTCCCAACAGTGTA
Found at i:989095 original size:20 final size:20
Alignment explanation
Indices: 989054--989101 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
989044 TTCCAAAATC
* *
989054 ATCGCAACGCGAATATGAAA
1 ATCGCAACGCGAACATCAAA
989074 ATCGCAACGCGAACA-CATAA
1 ATCGCAACGCGAACATCA-AA
989094 ATCGCAAC
1 ATCGCAAC
989102 TCGTATCCGT
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:0.44, C:0.27, G:0.17, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAACATCAAA
Found at i:989114 original size:20 final size:20
Alignment explanation
Indices: 989072--989281 Score: 210
Period size: 20 Copynumber: 10.5 Consensus size: 20
989062 GCGAATATGA
* *
989072 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
989092 AAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
989112 AAATCACAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
989132 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
989152 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
989172 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
989192 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
989212 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
989232 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
989252 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
989272 AAATCACAAC
1 AAATCGCAAC
989282 ACTGAAATTT
Statistics
Matches: 158, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.01
20 155 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:990002 original size:24 final size:24
Alignment explanation
Indices: 989963--990009 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
989953 AAATTTGGTC
989963 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
989987 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
990010 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:992507 original size:19 final size:19
Alignment explanation
Indices: 992485--992701 Score: 240
Period size: 19 Copynumber: 12.4 Consensus size: 19
992475 CGGAAATTAC
*
992485 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
992504 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
992518 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
992538 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
992552 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
992571 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
992590 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
992604 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
992623 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
992642 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
992656 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
992675 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
992694 AATCGCAA
1 AATCGCAA
992702 CGAGAGAATC
Statistics
Matches: 169, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 42 0.25
15 3 0.02
16 7 0.04
17 6 0.04
18 4 0.02
19 94 0.56
20 13 0.08
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:992572 original size:33 final size:33
Alignment explanation
Indices: 992485--992682 Score: 201
Period size: 33 Copynumber: 5.8 Consensus size: 33
992475 CGGAAATTAC
* *
992485 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
992518 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
992552 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
992590 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
992623 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
992656 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
992683 TGCGAAATGA
Statistics
Matches: 146, Mismatches: 7, Indels: 24
0.82 0.04 0.14
Matches are distributed among these distances:
33 84 0.58
34 31 0.21
35 5 0.03
36 4 0.03
37 2 0.01
38 20 0.14
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:992712 original size:33 final size:33
Alignment explanation
Indices: 992571--992723 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
992561 GCGAAATGAA
992571 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
992604 AATCGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* * * *
992636 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
992675 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
992708 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
992724 TATAAACGCA
Statistics
Matches: 98, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
31 7 0.07
32 7 0.07
33 56 0.57
34 1 0.01
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:992739 original size:52 final size:52
Alignment explanation
Indices: 992513--992723 Score: 413
Period size: 52 Copynumber: 4.0 Consensus size: 52
992503 AAATCCCAAC
992513 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
992566 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
992618 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
992670 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
992722 AT
1 AT
992724 TATAAACGCA
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 142 0.90
53 16 0.10
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:992753 original size:14 final size:14
Alignment explanation
Indices: 992734--992788 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
992724 TATAAACGCA
992734 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
992748 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
992765 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
992781 TTGCGATT
1 TTGCGATT
992789 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:992753 original size:33 final size:33
Alignment explanation
Indices: 992716--992807 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 33
992706 AGAATCGCAA
992716 TGCGAAATT-ATAAACGCATTGCGATTCTCTCGT
1 TGCGAAATTCAT-AACGCATTGCGATTCTCTCGT
** **
992749 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATTCATAACGCATTGCGATTCTCTCGT
** **
992782 TGCGATTTTCATTTCGCATTGCGATT
1 TGCGAAATTCATAACGCATTGCGATT
992808 TTCATTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 52 0.96
34 2 0.04
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.41
Consensus pattern (33 bp):
TGCGAAATTCATAACGCATTGCGATTCTCTCGT
Found at i:992833 original size:19 final size:19
Alignment explanation
Indices: 992748--992825 Score: 112
Period size: 19 Copynumber: 4.4 Consensus size: 19
992738 GATTCTCTCG
992748 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
992767 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
992781 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
992800 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
992819 TTGCGAT
1 TTGCGAT
992826 AGTCATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.12
16 7 0.13
17 7 0.13
19 32 0.62
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:992951 original size:14 final size:14
Alignment explanation
Indices: 992932--992968 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
992922 CATCAATTAC
992932 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
992946 ACAAATCATCTTTT
1 ACAAATCAACTTTT
992960 ACAAATCAA
1 ACAAATCAA
992969 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:994969 original size:33 final size:33
Alignment explanation
Indices: 994923--995015 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
994913 GCGAAACCAA
*
994923 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
994956 AATCGCAATGCGAAATGAAAAGCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
994989 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
995016 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:994997 original size:14 final size:14
Alignment explanation
Indices: 994942--994998 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
994932 GCGAAATGAA
*
994942 AATCGCAACGACAG
1 AATCGCAACGAAAG
994956 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
994973 AAAAGCGCAACGAAAG
1 --AATCGCAACGAAAG
994989 AATCGCAACG
1 AATCGCAACG
994999 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:995013 original size:19 final size:19
Alignment explanation
Indices: 994886--995020 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
994876 TAGTTTACTT
* *
994886 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
994906 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
994925 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
994944 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
994958 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
994977 GCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
994991 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
995010 TCGCAATGCGA
1 TCGCAACGCGA
995021 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:995038 original size:19 final size:18
Alignment explanation
Indices: 995016--995143 Score: 119
Period size: 19 Copynumber: 7.3 Consensus size: 18
995006 AAAATCGCAA
995016 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
995035 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
995049 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
995068 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
995082 TGCGATTTTATTTCGCGT
1 TGCGATTTTGTTTCGCGT
995100 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
995119 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
995139 TGCGA
1 TGCGA
995144 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 8, Indels: 21
0.76 0.07 0.18
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 3 0.03
17 1 0.01
18 14 0.16
19 36 0.40
20 13 0.14
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:995058 original size:33 final size:33
Alignment explanation
Indices: 995016--995106 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
995006 AAAATCGCAA
995016 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
995049 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
*
995082 TGCGATTTT-ATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
995107 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
32 15 0.27
33 39 0.70
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.29, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:995307 original size:93 final size:93
Alignment explanation
Indices: 995191--995659 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
995181 ATGGATTGCA
995191 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
995255 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
995283 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
995348 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
995376 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
995441 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
995469 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCATAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
995534 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
995562 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
995627 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
995655 TTACT
1 TTACT
995660 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 369 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:997374 original size:14 final size:14
Alignment explanation
Indices: 997355--997411 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
997345 TTGAAATGAA
997355 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
997369 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
997388 AATCGCAACGAGAG
1 AATCGCAACGAGAG
997402 AATCGCAACG
1 AATCGCAACG
997412 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:997387 original size:33 final size:33
Alignment explanation
Indices: 997347--997428 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
997337 TCTTTTGGTT
997347 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
997380 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
997413 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
997429 TGCGATTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:997393 original size:19 final size:19
Alignment explanation
Indices: 997369--997433 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
997359 GCAACGAGAG
997369 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
997388 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
997402 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
997421 AATCGCAATGCGA
1 AATCGCAACGCGA
997434 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:997464 original size:14 final size:14
Alignment explanation
Indices: 997445--997501 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
997435 TTTGGTTTCG
997445 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
997459 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
997478 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
997492 CGTTGCGATT
1 CGTTGCGATT
997502 GTCATTTCTC
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:997477 original size:33 final size:33
Alignment explanation
Indices: 997429--997509 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
997419 AAAATCGCAA
**
997429 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
997462 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
997495 TGCGATTGTCATTTC
1 TGCGATTTTCATTTC
997510 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:997512 original size:21 final size:21
Alignment explanation
Indices: 997486--997561 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
997476 CGCGTTGCGA
997486 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
997507 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
* *
997527 TTCTCTTGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
997548 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
997562 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:997542 original size:41 final size:41
Alignment explanation
Indices: 997485--997562 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
997475 TCGCGTTGCG
*
997485 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
* *
997526 ATTCTCTTGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
997563 TCTTCTGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:997683 original size:33 final size:33
Alignment explanation
Indices: 997641--997711 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
997631 AATACTAACT
*
997641 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
997674 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
997707 TGAAA
1 TGAAA
997712 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:998119 original size:20 final size:20
Alignment explanation
Indices: 998094--998287 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
998084 CTTTAAATAT
998094 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
998114 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* * *
998136 -TCGTTGCAATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
998155 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
998175 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
998195 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
998215 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
998235 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
998255 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
998275 CGCGTTGCGATTT
1 CGCGTTGCGATTT
998288 TGGAAAATTG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 14 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:998281 original size:60 final size:60
Alignment explanation
Indices: 998094--998287 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
998084 CTTTAAATAT
** * *
998094 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCAATTTACCGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACAGATA
* * *** * *
998155 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
* * * * *
998215 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
998275 CGCGTTGCGATTT
1 CGCGTTGCGATTT
998288 TGGAAAATTG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 82 0.75
61 28 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
Found at i:998347 original size:42 final size:41
Alignment explanation
Indices: 998254--998347 Score: 93
Period size: 42 Copynumber: 2.3 Consensus size: 41
998244 ATTTATGTGT
* * *
998254 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTCATATTCGCATTGCGATTTTGCAAAA
* **
998295 TTGCAATGCGAATTT-ATACTATCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTCATA-T-TCGCATTGCGATTTTGCAA-AA
998337 TCGCGTTGCGA
1 TCGCGTTGCGA
998348 TTTTGGAAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
40 3 0.07
41 14 0.34
42 24 0.59
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.36
Consensus pattern (41 bp):
TCGCGTTGCGAATTTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1008613 original size:12 final size:12
Alignment explanation
Indices: 1008592--1008621 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1008582 ATATCAATTT
1008592 AAATAT-AATAA
1 AAATATAAATAA
1008603 AAATATAAATAA
1 AAATATAAATAA
1008615 AAATATA
1 AAATATA
1008622 TTTTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATATAAATAA
Found at i:1012755 original size:26 final size:26
Alignment explanation
Indices: 1012719--1012786 Score: 111
Period size: 26 Copynumber: 2.6 Consensus size: 26
1012709 TTCTTAAGGA
*
1012719 GTGGTCCTTCGGGACATATGTGATAT
1 GTGGTCTTTCGGGACATATGTGATAT
1012745 GTGGTCTTTCGGGACATATGTGATAT
1 GTGGTCTTTCGGGACATATGTGATAT
1012771 GTGGT-TCTTCGGGACA
1 GTGGTCT-TTCGGGACA
1012787 AATTCTAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 1 0.03
26 39 0.98
ACGTcount: A:0.18, C:0.15, G:0.32, T:0.35
Consensus pattern (26 bp):
GTGGTCTTTCGGGACATATGTGATAT
Found at i:1021005 original size:17 final size:17
Alignment explanation
Indices: 1020985--1021019 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1020975 ATTATTTTAA
*
1020985 AAATAAAATTATAAATT
1 AAATAAAATTAAAAATT
*
1021002 AAATTAAATTAAAAATT
1 AAATAAAATTAAAAATT
1021019 A
1 A
1021020 TTTCATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATAAAATTAAAAATT
Found at i:1021777 original size:16 final size:15
Alignment explanation
Indices: 1021733--1021779 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1021723 TATAAGGTAA
1021733 TTTTATTATCATT-T
1 TTTTATTATCATTAT
*
1021747 TTTAATTAT-ACTTAT
1 TTTTATTATCA-TTAT
1021762 TGTTTATTATCATTAT
1 T-TTTATTATCATTAT
1021778 TT
1 TT
1021780 GAAAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
13 1 0.04
14 10 0.37
15 3 0.11
16 12 0.44
17 1 0.04
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTTATTATCATTAT
Found at i:1029264 original size:17 final size:17
Alignment explanation
Indices: 1029242--1029319 Score: 74
Period size: 17 Copynumber: 4.7 Consensus size: 17
1029232 TATATGTCAT
1029242 ATATATCACCATTTAAA
1 ATATATCACCATTTAAA
* **
1029259 ATATATAACCA--TACT
1 ATATATCACCATTTAAA
*
1029274 AT-TATTA-CATTTAAAA
1 ATATATCACCATTT-AAA
1029290 TATATATCACCATTTAAA
1 -ATATATCACCATTTAAA
1029308 ATATATCACCAT
1 ATATATCACCAT
1029320 ACTATTATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
13 2 0.04
14 4 0.08
15 5 0.10
16 1 0.02
17 24 0.50
18 7 0.15
19 5 0.10
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATATCACCATTTAAA
Found at i:1029264 original size:19 final size:19
Alignment explanation
Indices: 1029240--1029313 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 19
1029230 TCTATATGTC
1029240 ATATATATCACCATTTAAA
1 ATATATATCACCATTTAAA
1029259 ATATATA--ACCA--T--A
1 ATATATATCACCATTTAAA
* *
1029272 CTAT-TATTA-CATTTAAA
1 ATATATATCACCATTTAAA
1029289 ATATATATCACCATTTAAA
1 ATATATATCACCATTTAAA
1029308 ATATAT
1 ATATAT
1029314 CACCATACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
12 2 0.05
13 6 0.14
14 1 0.02
15 2 0.05
17 8 0.18
18 4 0.09
19 21 0.48
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATATATCACCATTTAAA
Found at i:1029312 original size:49 final size:49
Alignment explanation
Indices: 1029240--1029334 Score: 181
Period size: 49 Copynumber: 1.9 Consensus size: 49
1029230 TCTATATGTC
1029240 ATATATATCACCATTTAAAATATATAACCATACTATTATTACATTTAAA
1 ATATATATCACCATTTAAAATATATAACCATACTATTATTACATTTAAA
*
1029289 ATATATATCACCATTTAAAATATATCACCATACTATTATTACATTT
1 ATATATATCACCATTTAAAATATATAACCATACTATTATTACATTT
1029335 TTTAATATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (49 bp):
ATATATATCACCATTTAAAATATATAACCATACTATTATTACATTTAAA
Found at i:1035603 original size:21 final size:20
Alignment explanation
Indices: 1035565--1035603 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1035555 TATGTAAAGT
*
1035565 TTTTAATCTAACAGTCAATC
1 TTTTAATCTAACAATCAATC
*
1035585 TTTTAATTCTATCAATCAA
1 TTTTAA-TCTAACAATCAA
1035604 ATCACTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.44
Consensus pattern (20 bp):
TTTTAATCTAACAATCAATC
Found at i:1036704 original size:15 final size:15
Alignment explanation
Indices: 1036684--1036712 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1036674 ATTATTATAA
1036684 ATATTTAATGATTTG
1 ATATTTAATGATTTG
1036699 ATATTTAATGATTT
1 ATATTTAATGATTT
1036713 AGTAATGATT
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:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
ATATTTAATGATTTG
Found at i:1036720 original size:11 final size:11
Alignment explanation
Indices: 1036704--1036849 Score: 57
Period size: 11 Copynumber: 12.4 Consensus size: 11
1036694 ATTTGATATT
*
1036704 TAATGATTTAG
1 TAATGATTTAA
1036715 TAATGATTACTAA
1 TAATGATT--TAA
1036728 TAATGATTTATTA
1 TAATGATTTA--A
1036741 TTAAT-ATTTAA
1 -TAATGATTTAA
*
1036752 TAAT--TTGATAC
1 TAATGATT--TAA
*
1036763 TAATGATTTAG
1 TAATGATTTAA
*
1036774 TAATGATTAATAC
1 TAATGATT--TAA
1036787 TAATGAAATTATAA
1 TAATG--ATT-TAA
* *
1036801 TAATTA-ATAA
1 TAATGATTTAA
1036811 TAATGATTACTAA
1 TAATGATT--TAA
*
1036824 TAATTATTTAA
1 TAATGATTTAA
* *
1036835 TAATAATTAAA
1 TAATGATTTAA
1036846 TAAT
1 TAAT
1036850 TAAATATAAT
Statistics
Matches: 107, Mismatches: 12, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
9 2 0.02
10 12 0.11
11 43 0.40
12 1 0.01
13 35 0.33
14 11 0.10
15 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.44
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:1036791 original size:24 final size:23
Alignment explanation
Indices: 1036749--1036829 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 23
1036739 TATTAATATT
*
1036749 TAATAATTTGATACTAATGATTTA
1 TAATAA-TTAATACTAATGATTTA
* *
1036773 GTAATGATTAATACTAATGAAATTA
1 -TAATAATTAATACTAATG-ATTTA
*
1036798 TAATAATTAATAATAATGA-TTA
1 TAATAATTAATACTAATGATTTA
1036820 CTAATAATTA
1 -TAATAATTA
1036830 TTTAATAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
22 3 0.06
23 10 0.20
24 27 0.55
25 9 0.18
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (23 bp):
TAATAATTAATACTAATGATTTA
Found at i:1036791 original size:59 final size:60
Alignment explanation
Indices: 1036675--1036792 Score: 184
Period size: 59 Copynumber: 2.0 Consensus size: 60
1036665 TTTAAGTTCA
* * *
1036675 TTATTATAAATATTTAATGATTTGATATTTAATGATTTAGTAATGATTACTAATAATGAT
1 TTATTATAAATATTTAATAATTTGATATCTAATGATTTAGTAATGATTAATAATAATGAT
* *
1036735 TTATTATTAATATTTAATAATTTGATA-CTAATGATTTAGTAATGATTAATACTAATGA
1 TTATTATAAATATTTAATAATTTGATATCTAATGATTTAGTAATGATTAATAATAATGA
1036793 AATTATAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
59 28 0.53
60 25 0.47
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (60 bp):
TTATTATAAATATTTAATAATTTGATATCTAATGATTTAGTAATGATTAATAATAATGAT
Found at i:1036814 original size:59 final size:59
Alignment explanation
Indices: 1036677--1036811 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 59
1036667 TAAGTTCATT
* * * * *
1036677 ATTATAAATATTTAATGATTTGATATTTAATGATTTAGTAATGATTACTAATAATGATTT
1 ATTATTAATATTTAATAATTTGATATCTAATGATTTAGTAATGATTAATAATAATGA-TA
*
1036737 ATTATTAATATTTAATAATTTGATA-CTAATGATTTAGTAATGATTAATACTAATGA-A
1 ATTATTAATATTTAATAATTTGATATCTAATGATTTAGTAATGATTAATAATAATGATA
*
1036794 ATTA-TAATAATTAATAAT
1 ATTATTAATATTTAATAAT
1036812 AATGATTACT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
56 13 0.19
57 4 0.06
59 28 0.41
60 23 0.34
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (59 bp):
ATTATTAATATTTAATAATTTGATATCTAATGATTTAGTAATGATTAATAATAATGATA
Found at i:1036835 original size:24 final size:23
Alignment explanation
Indices: 1036715--1036859 Score: 79
Period size: 24 Copynumber: 6.2 Consensus size: 23
1036705 AATGATTTAG
* *
1036715 TAATGATTACTAATAATGATTTATTAT
1 TAATGATTA-TAATAAT--TATA-TAA
*
1036742 TAAT-ATT-TAATAATT-TGATAC
1 TAATGATTATAATAATTAT-ATAA
* *
1036763 TAATGATTTAGTAATGATTA-ATAC
1 TAATGA-TTA-TAATAATTATATAA
1036787 TAATGAAATTATAATAATTA-ATAA
1 TAATG--ATTATAATAATTATATAA
*
1036811 TAATGATTACTAATAATTATTTAA
1 TAATGATTA-TAATAATTATATAA
* *
1036835 TAATAATTA-AATAATTAAAT-A
1 TAATGATTATAATAATTATATAA
1036856 TAAT
1 TAAT
1036860 TTATTCAATT
Statistics
Matches: 100, Mismatches: 8, Indels: 26
0.75 0.06 0.19
Matches are distributed among these distances:
21 12 0.12
22 16 0.16
23 11 0.11
24 43 0.43
25 10 0.10
26 4 0.04
27 4 0.04
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (23 bp):
TAATGATTATAATAATTATATAA
Found at i:1037264 original size:17 final size:15
Alignment explanation
Indices: 1037242--1037281 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
1037232 TGAGGTTATG
1037242 TTAAATATTATTAAAA
1 TTAAATATTA-TAAAA
*
1037258 CTTAAATATTATAATA
1 -TTAAATATTATAAAA
1037274 TTAAATAT
1 TTAAATAT
1037282 GCATGTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATTATAAAA
Found at i:1037338 original size:22 final size:22
Alignment explanation
Indices: 1037310--1037351 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1037300 TGTAAAAAGA
1037310 ATAAATTCGACTAT-TTATAACT
1 ATAAATTCGACT-TGTTATAACT
1037332 ATAAATTCGACTTGTTATAA
1 ATAAATTCGACTTGTTATAA
1037352 GTTCAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (22 bp):
ATAAATTCGACTTGTTATAACT
Found at i:1037423 original size:14 final size:13
Alignment explanation
Indices: 1037404--1037450 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
1037394 TTTAAATATT
*
1037404 TAATTATTATTAAA
1 TAATTATTAGT-AA
1037418 TAATTATTAGTAA
1 TAATTATTAGTAA
*
1037431 TCATTATTAGTAA
1 TAATTATTAGTAA
*
1037444 TTATTAT
1 TAATTAT
1037451 AATTTCATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (13 bp):
TAATTATTAGTAA
Found at i:1037431 original size:24 final size:23
Alignment explanation
Indices: 1037400--1037463 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
1037390 TCTATTTAAA
1037400 TATT-TAATTATTATTAAATAAT
1 TATTATAATTATTATTAAATAAT
* *
1037422 TATTAGTAATCATTATT-AGTAAT
1 TATTA-TAATTATTATTAAATAAT
1037445 TATTATAATTTCATTATTA
1 TATTATAA-TT-ATTATTA
1037464 CTAATCATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 7 0.21
23 11 0.32
24 16 0.47
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (23 bp):
TATTATAATTATTATTAAATAAT
Found at i:1037547 original size:16 final size:16
Alignment explanation
Indices: 1037526--1037557 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1037516 ATTATTAGTA
1037526 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
1037542 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
1037558 TAATTATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:1040749 original size:33 final size:33
Alignment explanation
Indices: 1040675--1040813 Score: 183
Period size: 33 Copynumber: 4.2 Consensus size: 33
1040665 TTTTAGTTGG
1040675 CTGTTTATTAAACTTCTCTTGCTAT-GTAGTCTCAT
1 CTGTTTATTAAACTTCTCTTGCTATAGT--TC-CAT
* * *
1040710 CTGTTTATTGAACTTTTCTTTCTATAGTTCCAT
1 CTGTTTATTAAACTTCTCTTGCTATAGTTCCAT
*
1040743 CTGTTTATTAAACTTCTCTTGC-ATAGTCCCAT
1 CTGTTTATTAAACTTCTCTTGCTATAGTTCCAT
* *
1040775 CTGTTCATTAAACTTCTTTTGCTATAGTTCCAT
1 CTGTTTATTAAACTTCTCTTGCTATAGTTCCAT
1040808 CTGTTT
1 CTGTTT
1040814 TAGTTGGCTG
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
32 29 0.32
33 36 0.40
34 2 0.02
35 22 0.24
36 2 0.02
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.50
Consensus pattern (33 bp):
CTGTTTATTAAACTTCTCTTGCTATAGTTCCAT
Found at i:1040804 original size:65 final size:67
Alignment explanation
Indices: 1040675--1040813 Score: 203
Period size: 65 Copynumber: 2.1 Consensus size: 67
1040665 TTTTAGTTGG
* * * *
1040675 CTGTTTATTAAACTTCTCTTGCTATGTAGTCTCATCTGTTTATTGAACTTTTCTTTCTATAGTTC
1 CTGTTTATTAAACTTCTCTTGCTA-GTAGTCCCATCTGTTCATTAAACTTTTCTTGCTATAGTTC
1040740 CAT
65 CAT
1040743 CTGTTTATTAAACTTCTCTTGC-A-TAGTCCCATCTGTTCATTAAACTTCTT-TTGCTATAGTTC
1 CTGTTTATTAAACTTCTCTTGCTAGTAGTCCCATCTGTTCATTAAACTT-TTCTTGCTATAGTTC
1040805 CAT
65 CAT
1040808 CTGTTT
1 CTGTTT
1040814 TAGTTGGCTG
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
65 41 0.62
66 2 0.03
67 1 0.02
68 22 0.33
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.50
Consensus pattern (67 bp):
CTGTTTATTAAACTTCTCTTGCTAGTAGTCCCATCTGTTCATTAAACTTTTCTTGCTATAGTTCC
AT
Found at i:1042473 original size:29 final size:29
Alignment explanation
Indices: 1042440--1042500 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
1042430 AGCAACTTTC
1042440 GTGAAAGACCTCCGTTATAAGTTTCC-TCA
1 GTGAAAGACCTCCGTTATAAG-TTCCTTCA
*
1042469 GTGAAATACCTCCGTTATAAGTTCCTTCA
1 GTGAAAGACCTCCGTTATAAGTTCCTTCA
1042498 GTG
1 GTG
1042501 GGACTCGATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (29 bp):
GTGAAAGACCTCCGTTATAAGTTCCTTCA
Found at i:1049599 original size:16 final size:16
Alignment explanation
Indices: 1049578--1049626 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
1049568 TAATAAATAA
1049578 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1049594 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
1049610 GCGAACATAAACGAAC
1 ACGAACATAAACGAAC
1049626 A
1 A
1049627 TAAATGTTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.55, C:0.22, G:0.14, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1050729 original size:24 final size:24
Alignment explanation
Indices: 1050694--1050744 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1050684 GATTGGGTTA
*
1050694 AACATAAACGAATGAACATAAACG
1 AACATAAACGAACGAACATAAACG
* *
1050718 AACATAACCGAACGAACATAACCG
1 AACATAAACGAACGAACATAAACG
1050742 AAC
1 AAC
1050745 GTTCACGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.24, G:0.12, T:0.10
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:1050731 original size:14 final size:14
Alignment explanation
Indices: 1050714--1050745 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1050704 AATGAACATA
1050714 AACGAACATAACCG
1 AACGAACATAACCG
1050728 AACGAACATAACCG
1 AACGAACATAACCG
1050742 AACG
1 AACG
1050746 TTCACGAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1057444 original size:24 final size:24
Alignment explanation
Indices: 1057404--1057458 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1057394 ATTTGATCTG
* *
1057404 AAAAT-AAAATAATATAATTAATA
1 AAAATAAAAATAAAATAAATAATA
*
1057427 AAAATAAAAATAAAATAAATAATT
1 AAAATAAAAATAAAATAAATAATA
*
1057451 AATATAAA
1 AAAATAAA
1057459 TATACATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (24 bp):
AAAATAAAAATAAAATAAATAATA
Found at i:1057449 original size:28 final size:29
Alignment explanation
Indices: 1057404--1057460 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
1057394 ATTTGATCTG
1057404 AAAATAAAATAATATAATTAATAAAAATA
1 AAAATAAAATAATATAATTAATAAAAATA
*
1057433 AAAATAAAATAA-ATAATTAATATAAATA
1 AAAATAAAATAATATAATTAATAAAAATA
1057461 TACATATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (29 bp):
AAAATAAAATAATATAATTAATAAAAATA
Found at i:1057477 original size:18 final size:19
Alignment explanation
Indices: 1057441--1057540 Score: 67
Period size: 19 Copynumber: 5.5 Consensus size: 19
1057431 TAAAAATAAA
*
1057441 ATAAATAATTAATAT-AAAT
1 ATAAATAA-TACTATGAAAT
*
1057460 ATACAT-ATACTATGAAAT
1 ATAAATAATACTATGAAAT
1057478 ATAAATAATACTAT-ATAAT
1 ATAAATAATACTATGA-AAT
1057497 A-AAAT-ATA-TAT---AT
1 ATAAATAATACTATGAAAT
1057510 ATAATATAATACTAT-AATAT
1 ATAA-ATAATACTATGAA-AT
1057530 ATAATATAATA
1 ATAA-ATAATA
1057541 AATATATATA
Statistics
Matches: 68, Mismatches: 3, Indels: 19
0.76 0.03 0.21
Matches are distributed among these distances:
13 3 0.04
14 2 0.03
15 2 0.03
16 6 0.09
17 11 0.16
18 15 0.22
19 16 0.24
20 13 0.19
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (19 bp):
ATAAATAATACTATGAAAT
Found at i:1057478 original size:24 final size:23
Alignment explanation
Indices: 1057451--1057564 Score: 82
Period size: 24 Copynumber: 5.0 Consensus size: 23
1057441 ATAAATAATT
*
1057451 AATATAAATATAC-ATATACTATGA
1 AATATAAATATACTATATA--ATAA
1057475 AATATAAATAATACTATATAATAA
1 AATATAAAT-ATACTATATAATAA
*
1057499 AATATATATATA-TA-AT-ATAA
1 AATATAAATATACTATATAATAA
*
1057519 TACTAT-AATATA-TAATATAATAA
1 -AATATAAATATACT-ATATAATAA
*
1057542 ATATAT-AT-ATACTATATAATAA
1 A-ATATAAATATACTATATAATAA
1057564 A
1 A
1057565 TATTGTAATA
Statistics
Matches: 76, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
20 10 0.13
21 7 0.09
22 18 0.24
23 12 0.16
24 20 0.26
25 4 0.05
26 5 0.07
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (23 bp):
AATATAAATATACTATATAATAA
Found at i:1057505 original size:2 final size:2
Alignment explanation
Indices: 1057500--1057589 Score: 61
Period size: 2 Copynumber: 47.5 Consensus size: 2
1057490 ATATAATAAA
1057500 AT AT AT AT AT AT A- AT AT A- AT ACT AT A- AT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * *
1057538 AT AA AT AT AT AT AT ACT AT AT A- AT AA AT AT -T GT A- AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1057578 AT TT AT ACT AT A
1 AT AT AT A-T AT A
1057590 ACACAAAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
1 8 0.11
2 56 0.80
3 6 0.09
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1057547 original size:18 final size:18
Alignment explanation
Indices: 1057410--1057550 Score: 96
Period size: 18 Copynumber: 7.6 Consensus size: 18
1057400 TCTGAAAATA
1057410 AAATA-ATATAAT-TAAT
1 AAATATATATAATATAAT
* * *
1057426 AAAAATA-AAAATAAAAT
1 AAATATATATAATATAAT
1057443 AAATA-AT-TAATATAAAT
1 AAATATATATAATAT-AAT
1057460 ATACATATACTATGAAATATAA-
1 A-A-ATATA-TAT--AATATAAT
*
1057482 ATAATACTATATAATAAAAT
1 A-AATA-TATATAATATAAT
*
1057502 ATATATATATAATATAAT
1 AAATATATATAATATAAT
*
1057520 ACTATAATATATAATATAAT
1 A-AAT-ATATATAATATAAT
1057540 AAATATATATA
1 AAATATATATA
1057551 TACTATATAA
Statistics
Matches: 100, Mismatches: 10, Indels: 28
0.72 0.07 0.20
Matches are distributed among these distances:
16 13 0.13
17 12 0.12
18 21 0.21
19 17 0.17
20 17 0.17
21 7 0.07
22 6 0.06
23 2 0.02
24 5 0.05
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.35
Consensus pattern (18 bp):
AAATATATATAATATAAT
Found at i:1057559 original size:42 final size:40
Alignment explanation
Indices: 1057454--1057562 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 40
1057444 AATAATTAAT
*
1057454 ATAAATATACATATACTATGA-AATATAAATAATACTATATA
1 ATAAATATATATATACTAT-ATAATATAAATAATAC-ATATA
1057495 ATAAAATATATATATA-TAATATAATACTATAATATATA-ATATA
1 AT-AAATATATATATACT-ATATAATA-TA-AATA-ATACATATA
1057538 ATAAATATATATATACTATATAATA
1 ATAAATATATATATACTATATAATA
1057563 AATATTGTAA
Statistics
Matches: 60, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
41 4 0.07
42 39 0.65
43 10 0.17
44 4 0.07
45 3 0.05
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.38
Consensus pattern (40 bp):
ATAAATATATATATACTATATAATATAAATAATACATATA
Found at i:1057562 original size:18 final size:18
Alignment explanation
Indices: 1057452--1057567 Score: 81
Period size: 18 Copynumber: 6.7 Consensus size: 18
1057442 TAAATAATTA
*
1057452 ATATAAATATACATATACT
1 ATAT-AATATATATATACT
*
1057471 ATGA-AATATAAATAATACT
1 AT-ATAATATATAT-ATACT
1057490 ATATAATA-A-A-ATA-T
1 ATATAATATATATATACT
*
1057504 ATAT-ATATA-ATATAAT
1 ATATAATATATATATACT
1057520 ACTATAATATATA-ATA-T
1 A-TATAATATATATATACT
1057537 A-ATAAATATATATATACT
1 ATAT-AATATATATATACT
*
1057555 ATATAATAAATAT
1 ATATAATATATAT
1057568 TGTAATATAT
Statistics
Matches: 82, Mismatches: 2, Indels: 27
0.74 0.02 0.24
Matches are distributed among these distances:
13 3 0.04
14 7 0.09
15 8 0.10
16 10 0.12
17 9 0.11
18 28 0.34
19 16 0.20
20 1 0.01
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (18 bp):
ATATAATATATATATACT
Found at i:1059354 original size:43 final size:44
Alignment explanation
Indices: 1059306--1059389 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
1059296 TGAATTTTTC
* * *
1059306 GATATTAACATTTTC-GTTAAAAAATAATATTTTAAATAATTCA
1 GATATTAACATTTCCAGTAAAAAAATAATAATTTAAATAATTCA
* *
1059349 GATATTAATATTTCCAGTAAAAAAATAATAATTTAGATAAT
1 GATATTAACATTTCCAGTAAAAAAATAATAATTTAAATAAT
1059390 ACTCTACCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 13 0.37
44 22 0.63
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (44 bp):
GATATTAACATTTCCAGTAAAAAAATAATAATTTAAATAATTCA
Found at i:1063545 original size:13 final size:13
Alignment explanation
Indices: 1063527--1063906 Score: 64
Period size: 13 Copynumber: 29.8 Consensus size: 13
1063517 AATTGAAAAA
1063527 ATATAATATATAT
1 ATATAATATATAT
*
1063540 ATATAATA-AAATT
1 ATATAATATATA-T
1063553 ATATAACTATAT-T
1 ATATAA-TATATAT
* *
1063566 -TATATTATAAACT
1 ATATAATATATA-T
1063579 ATATAAT-TATA-
1 ATATAATATATAT
*
1063590 A-A-ACTATATAT
1 ATATAATATATAT
*
1063601 ATA-AATTATATTT
1 ATATAA-TATATAT
* *
1063614 ATGTACTATATAT
1 ATATAATATATAT
*
1063627 ATA-AACTATGTAT
1 ATATAA-TATATAT
* *
1063640 ATAATTATAAACTAT
1 AT-ATAATATA-TAT
* * *
1063655 TTATATTATAAACT
1 ATATAATATATA-T
* *
1063669 ATATAAATTATGTTT
1 ATAT-AA-TATATAT
* *
1063684 ATGTGAACTATAGAT
1 ATAT-AA-TATATAT
*
1063699 ATA-AACTATGTAT
1 ATATAA-TATATAT
1063712 ATA-AACTATATAT
1 ATATAA-TATATAT
*
1063725 GTATAA-ACTATA-
1 ATATAATA-TATAT
1063737 A-A-AAGTATATAGT
1 ATATAA-TATATA-T
* * *
1063750 TTATAAAATTTAT
1 ATATAATATATAT
* *
1063763 TTAT-TTATATAGT
1 ATATAATATATA-T
1063776 ATAT-ATATATAT
1 ATATAATATATAT
* *
1063788 A-A-ACTATATGT
1 ATATAATATATAT
*
1063799 ATA-AACTATATAA
1 ATATAA-TATATAT
1063812 ATAT-ATAGT-TAT
1 ATATAATA-TATAT
* *
1063824 ATGTTATA-AT-T
1 ATATAATATATAT
1063835 ATATAATATAGTAT
1 ATATAATATA-TAT
* *
1063849 ATAT-ATGTATGT
1 ATATAATATATAT
*
1063861 ATA-ACTA-ATAT
1 ATATAATATATAT
1063872 A-AGTAATATATAT
1 ATA-TAATATATAT
1063885 ATAT-ATATATAT
1 ATATAATATATAT
1063897 ATAT-ATATAT
1 ATATAATATAT
1063907 TAAAGAACAC
Statistics
Matches: 262, Mismatches: 63, Indels: 85
0.64 0.15 0.21
Matches are distributed among these distances:
9 2 0.01
10 8 0.03
11 30 0.11
12 55 0.21
13 110 0.42
14 33 0.13
15 21 0.08
16 3 0.01
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.44
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:1063581 original size:26 final size:26
Alignment explanation
Indices: 1063527--1063589 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
1063517 AATTGAAAAA
*
1063527 ATATAATATATATATATAATAAAATT
1 ATATAATATATATATATAATAAAACT
* *
1063553 ATATAACTATATTTATATTAT-AAACT
1 ATATAA-TATATATATATAATAAAACT
1063579 ATATAAT-TATA
1 ATATAATATATA
1063590 AAACTATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 3 0.09
25 1 0.03
26 16 0.50
27 12 0.38
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (26 bp):
ATATAATATATATATATAATAAAACT
Found at i:1063595 original size:16 final size:16
Alignment explanation
Indices: 1063549--1063599 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1063539 TATATAATAA
*
1063549 AATTATATAACTATATTT
1 AATTATAAAACTATA--T
1063567 ATATTAT-AAACTATAT
1 A-ATTATAAAACTATAT
1063583 AATTATAAAACTATAT
1 AATTATAAAACTATAT
1063599 A
1 A
1063600 TATAAATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 5 0.17
16 12 0.40
18 8 0.27
19 5 0.17
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTATAAAACTATAT
Found at i:1063731 original size:15 final size:13
Alignment explanation
Indices: 1063566--1063736 Score: 88
Period size: 13 Copynumber: 13.3 Consensus size: 13
1063556 TAACTATATT
1063566 TATAT-TATAAAC
1 TATATATATAAAC
1063578 TATATAATTATAAAAC
1 TATAT-A-TAT-AAAC
*
1063594 TATATATATAAAT
1 TATATATATAAAC
* **
1063607 TATATTTATGTAC
1 TATATATATAAAC
1063620 TATATATATAAAC
1 TATATATATAAAC
*
1063633 TATGTATAT-AA-
1 TATATATATAAAC
* **
1063644 T-TATAAACT-ATT
1 TATATATA-TAAAC
1063656 TATAT-TATAAAC
1 TATATATATAAAC
* *
1063668 TATATAAAT-TA-
1 TATATATATAAAC
* * * *
1063679 TGTTTATGTGAAC
1 TATATATATAAAC
*
1063692 TATAGATATAAAC
1 TATATATATAAAC
*
1063705 TATGTATATAAAC
1 TATATATATAAAC
1063718 TATATATGTATAAAC
1 TATATA--TATAAAC
1063733 TATA
1 TATA
1063737 AAAAGTATAT
Statistics
Matches: 116, Mismatches: 30, Indels: 23
0.69 0.18 0.14
Matches are distributed among these distances:
10 4 0.03
11 9 0.08
12 17 0.15
13 59 0.51
14 3 0.03
15 15 0.13
16 9 0.08
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.43
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:1063737 original size:72 final size:68
Alignment explanation
Indices: 1063571--1063738 Score: 182
Period size: 72 Copynumber: 2.4 Consensus size: 68
1063561 ATATTTATAT
*
1063571 TATAAACTATATAATTATAAAACTAT--ATATATAAATTATATTTATGTACTATATATATAAACT
1 TATAAACTATAT-ATTAT-AAACTATAAATATATAAATTATATTTATGTACTATAGATATAAACT
1063634 ATGTA
64 ATGTA
* * * *
1063639 TATAATTA-TAAACTATT-TATATTATAAACTATATAAATTATGTTTATGTGAACTATAGATATA
1 TATAA--ACTATA-TATTATAAACTATAAA-TATATAAATTATATTTATGT--ACTATAGATATA
1063702 AACTATGTA
60 AACTATGTA
1063711 TATAAACTATATATGTATAAACTATAAA
1 TATAAACTATATAT-TATAAACTATAAA
1063739 AAGTATATAG
Statistics
Matches: 81, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
67 5 0.06
68 6 0.07
69 7 0.09
70 25 0.31
71 4 0.05
72 34 0.42
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.42
Consensus pattern (68 bp):
TATAAACTATATATTATAAACTATAAATATATAAATTATATTTATGTACTATAGATATAAACTAT
GTA
Found at i:1063780 original size:2 final size:2
Alignment explanation
Indices: 1063768--1063906 Score: 89
Period size: 2 Copynumber: 70.5 Consensus size: 2
1063758 TTTATTTATT
* * *
1063768 TA TA TA GTA TA TA TA TA TA TA AA CTA TA TG TA TA AA CTA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* *
1063811 AA TA TA TA GT- TA TA TG T- TA TA -A T- TA TA TA -A TA TA GTA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
1063850 TA TA TG TA TG TA TA -A CTA -A TA TA -A GTA -A 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
1063890 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1063907 TAAAGAACAC
Statistics
Matches: 108, Mismatches: 13, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
1 9 0.08
2 90 0.83
3 9 0.08
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1064291 original size:13 final size:13
Alignment explanation
Indices: 1064240--1064333 Score: 61
Period size: 13 Copynumber: 7.1 Consensus size: 13
1064230 CCCTATTCCC
1064240 ATATGTAACTTAT
1 ATATGTAACTTAT
* *
1064253 AGTATGT-ACATGT
1 A-TATGTAACTTAT
1064266 A-ATGTAAAC-TAT
1 ATATGT-AACTTAT
1064278 ATATGTAACTTATAGT
1 ATATGTAAC-T-TA-T
* *
1064294 ATATGTATACATGT
1 ATATGTA-ACTTAT
*
1064308 A-ATGTAAATTAT
1 ATATGTAACTTAT
1064320 ATATGTAACTTAT
1 ATATGTAACTTAT
1064333 A
1 A
1064334 GTACATGTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
11 4 0.06
12 10 0.16
13 28 0.45
14 7 0.11
15 3 0.05
16 8 0.13
17 2 0.03
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.41
Consensus pattern (13 bp):
ATATGTAACTTAT
Found at i:1064296 original size:18 final size:18
Alignment explanation
Indices: 1064240--1064297 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
1064230 CCCTATTCCC
1064240 ATATGTAACTTATAGTATGT
1 ATATGTAACTTATAGTA--T
* * *
1064260 ACATGTAA-TGTAAACTAT
1 ATATGTAACT-TATAGTAT
1064278 ATATGTAACTTATAGTAT
1 ATATGTAACTTATAGTAT
1064296 AT
1 AT
1064298 GTATACATGT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
18 16 0.53
19 2 0.07
20 12 0.40
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (18 bp):
ATATGTAACTTATAGTAT
Found at i:1064298 original size:16 final size:16
Alignment explanation
Indices: 1064277--1064342 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 16
1064267 ATGTAAACTA
1064277 TATATGTAACTTATAG
1 TATATGTAACTTATAG
1064293 TATATGTATAC--AT-G
1 TATATGTA-ACTTATAG
*
1064307 TA-ATGTAA-AT-TA-
1 TATATGTAACTTATAG
1064319 TATATGTAACTTATAG
1 TATATGTAACTTATAG
*
1064335 TACATGTA
1 TATATGTA
1064343 TGTATAAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
12 4 0.10
13 11 0.28
14 4 0.10
15 4 0.10
16 15 0.38
17 2 0.05
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.42
Consensus pattern (16 bp):
TATATGTAACTTATAG
Found at i:1064302 original size:24 final size:22
Alignment explanation
Indices: 1064275--1064367 Score: 63
Period size: 24 Copynumber: 4.3 Consensus size: 22
1064265 TAATGTAAAC
1064275 TATATATGTAACTTATAGTATATG
1 TATATATGTAAC-TAT-GTATATG
* *
1064299 TATACATGT-A--ATGTAAAT-
1 TATATATGTAACTATGTATATG
*
1064317 TATATATGTAACTTATAGTACATG
1 TATATATGTAAC-TAT-GTATATG
* *
1064341 TATGTAT-AAACTATGTATA-G
1 TATATATGTAACTATGTATATG
1064361 TATATAT
1 TATATAT
1064368 ATATATATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
18 8 0.15
19 6 0.11
20 9 0.16
21 4 0.07
22 5 0.09
23 9 0.16
24 14 0.25
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (22 bp):
TATATATGTAACTATGTATATG
Found at i:1064321 original size:42 final size:42
Alignment explanation
Indices: 1064240--1064343 Score: 162
Period size: 42 Copynumber: 2.6 Consensus size: 42
1064230 CCCTATTCCC
1064240 ATATGTAACTTATAG--TATG--TACATGTAATGTAAACTAT
1 ATATGTAACTTATAGTATATGTATACATGTAATGTAAACTAT
*
1064278 ATATGTAACTTATAGTATATGTATACATGTAATGTAAATTAT
1 ATATGTAACTTATAGTATATGTATACATGTAATGTAAACTAT
*
1064320 ATATGTAACTTATAGTACATGTAT
1 ATATGTAACTTATAGTATATGTAT
1064344 GTATAAACTA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
38 15 0.25
40 4 0.07
42 41 0.68
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (42 bp):
ATATGTAACTTATAGTATATGTATACATGTAATGTAAACTAT
Found at i:1064325 original size:18 final size:18
Alignment explanation
Indices: 1064262--1064327 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 18
1064252 TAGTATGTAC
*
1064262 ATGTAATGTAAACTATAT
1 ATGTAATGTAAATTATAT
* *
1064280 ATGTAACTTATAGTATATGTATAC
1 ATGT-A---AT-GTAAAT-TATAT
1064304 ATGTAATGTAAATTATAT
1 ATGTAATGTAAATTATAT
1064322 ATGTAA
1 ATGTAA
1064328 CTTATAGTAC
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
18 14 0.38
19 6 0.16
20 2 0.05
22 2 0.05
23 5 0.14
24 8 0.22
ACGTcount: A:0.42, C:0.05, G:0.12, T:0.41
Consensus pattern (18 bp):
ATGTAATGTAAATTATAT
Found at i:1064481 original size:20 final size:21
Alignment explanation
Indices: 1064452--1064530 Score: 81
Period size: 20 Copynumber: 3.9 Consensus size: 21
1064442 TATTATATAA
1064452 AAACCCTAAACCTT-AATCAT
1 AAACCCTAAACCTTAAATCAT
* *
1064472 AAACCATAAACTTTAAATC-T
1 AAACCCTAAACCTTAAATCAT
* * ** *
1064492 AAACCTTAACCCTTGCATTAT
1 AAACCCTAAACCTTAAATCAT
1064513 AAACCCTAAACCTTAAAT
1 AAACCCTAAACCTTAAAT
1064531 GAAAAAGACT
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 26 0.58
21 19 0.42
ACGTcount: A:0.44, C:0.27, G:0.01, T:0.28
Consensus pattern (21 bp):
AAACCCTAAACCTTAAATCAT
Found at i:1065388 original size:99 final size:99
Alignment explanation
Indices: 1065218--1065543 Score: 476
Period size: 99 Copynumber: 3.3 Consensus size: 99
1065208 AGGTAAACTC
**
1065218 AACTGTTTAATTTGTAG-TACTGTTGATTTGTTTATGTGTTGGTTGTTCATTCAAATTGCTTTTA
1 AACTGTTTAATTTGTAGCTACTGTTGATTTG-TT-TGTGTTGGTTGTTCATTCGGATTGCTTTTA
1065282 TAAGGTTGTTAGCTGCCTTTATTTACAGTTTAAATA
64 TAAGGTTGTTAGCTGCCTTTATTTACAGTTTAAATA
* * *
1065318 AACTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGGTTTTTCATTCGGATTACTTCTATA
1 AACTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGGTTGTTCATTCGGATTGCTTTTATA
* *
1065383 AGGTTGTTAGCTACCTTTA-TTATAGTTTAAAATA
66 AGGTTGTTAGCTGCCTTTATTTACAGTTT-AAATA
* *
1065417 AACTGTTCAATTTGTTGCTACTGTTGATTTGTTTGTGTTGTTGTTGTTCATTCGGATTGCTTTTA
1 AACTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTG--GTTGTTCATTCGGATTGCTTTTA
*
1065482 TAAGGTTGTTAGTTGCCTTTATTTACAGTTTAAATA
64 TAAGGTTGTTAGCTGCCTTTATTTACAGTTTAAATA
* * *
1065518 AACTATTTAATTTGTTGTTACTGTTG
1 AACTGTTTAATTTGTAGCTACTGTTG
1065544 GTTGTTCATT
Statistics
Matches: 203, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
98 8 0.04
99 88 0.43
100 19 0.09
101 80 0.39
102 8 0.04
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.51
Consensus pattern (99 bp):
AACTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGGTTGTTCATTCGGATTGCTTTTATA
AGGTTGTTAGCTGCCTTTATTTACAGTTTAAATA
Found at i:1067990 original size:11 final size:11
Alignment explanation
Indices: 1067974--1068013 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1067964 TTGAATTGAC
1067974 TTAAATGTTAT
1 TTAAATGTTAT
* *
1067985 TCAAATTTTAT
1 TTAAATGTTAT
1067996 ATTAAATGTTAT
1 -TTAAATGTTAT
1068008 TTAAAT
1 TTAAAT
1068014 TATCATTATC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (11 bp):
TTAAATGTTAT
Found at i:1068282 original size:14 final size:14
Alignment explanation
Indices: 1068263--1068309 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1068253 ATTTTTTCTT
1068263 TATATAAATTAAAC
1 TATATAAATTAAAC
1068277 TATAT-AATT----
1 TATATAAATTAAAC
1068286 TATATAAATTAAAC
1 TATATAAATTAAAC
*
1068300 TATATTAATT
1 TATATAAATT
1068310 TTCCTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:1068287 original size:23 final size:24
Alignment explanation
Indices: 1068261--1068310 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1068251 TTATTTTTTC
1068261 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
1068284 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
1068308 TTT
1 TTT
1068311 TCCTTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:1068587 original size:16 final size:16
Alignment explanation
Indices: 1068565--1068635 Score: 99
Period size: 16 Copynumber: 4.4 Consensus size: 16
1068555 CGGATCATTT
1068565 ACAGGTCAGGTT-AAA
1 ACAGGTCAGGTTGAAA
*
1068580 AGCAGGTCAGGTTAAAA
1 A-CAGGTCAGGTTGAAA
*
1068597 ACATGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
*
1068613 ACAAGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
1068629 ACAGGTC
1 ACAGGTC
1068636 GGGTAATACC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
15 1 0.02
16 45 0.90
17 4 0.08
ACGTcount: A:0.39, C:0.14, G:0.27, T:0.20
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:1074497 original size:15 final size:16
Alignment explanation
Indices: 1074477--1074509 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1074467 AAAGTACAAC
1074477 ATTCTCAG-TAATCTT
1 ATTCTCAGATAATCTT
*
1074492 ATTCTCTGATAATCTT
1 ATTCTCAGATAATCTT
1074508 AT
1 AT
1074510 ATTTTCACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.48
Consensus pattern (16 bp):
ATTCTCAGATAATCTT
Found at i:1078481 original size:18 final size:18
Alignment explanation
Indices: 1078446--1078481 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1078436 GTTCACTCAG
* *
1078446 TTTCTCCTTTTCCCACCC
1 TTTCTCCTTCTCCAACCC
1078464 TTTCTCCTTCTCCAACCC
1 TTTCTCCTTCTCCAACCC
1078482 CTACATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.50, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTCTCCTTCTCCAACCC
Found at i:1080530 original size:14 final size:15
Alignment explanation
Indices: 1080511--1080544 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1080501 TTTAAGAAAA
1080511 TATAATAA-AATATT
1 TATAATAATAATATT
1080525 TATAATAATAATATT
1 TATAATAATAATATT
1080540 T-TAAT
1 TATAAT
1080545 CCTTAAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATAATAATATT
Found at i:1080534 original size:22 final size:21
Alignment explanation
Indices: 1080483--1080534 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
1080473 TTTTTGCATG
* *
1080483 AAATAATATAATAAAGTTTTT
1 AAATAATATAATAAAATATTT
*
1080504 AAGAAAATATAATAAAATATTT
1 AA-ATAATATAATAAAATATTT
1080526 ATAATAATA
1 A-AATAATA
1080535 ATATTTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 2 0.08
22 22 0.88
23 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
AAATAATATAATAAAATATTT
Found at i:1081219 original size:2 final size:2
Alignment explanation
Indices: 1081212--1081266 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1081202 AAATTAATGT
1081212 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
1081254 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1081267 TCAAATTAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1082685 original size:136 final size:136
Alignment explanation
Indices: 1082437--1083200 Score: 1170
Period size: 136 Copynumber: 5.6 Consensus size: 136
1082427 TGTTGATCTG
* * * * *
1082437 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT-TGTTGGACGAATTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* * * * *
1082501 GAACTCTCCATTAGAAATGCCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCGTGAATCG
66 GAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCG
1082566 AGTGAT
131 AGTGAT
*
1082572 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
*
1082637 GAACTCTCAATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCG
66 GAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCG
1082702 AGTGAT
131 AGTGAT
*
1082708 AAGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
** *
1082773 GAACTCTCCATTGGAAATGTCAATCCCTCAAGTAAGGTGTCACTGATTCGAAATGCCATGAATCG
66 GAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCG
1082838 AGTGAT
131 AGTGAT
*** *
1082844 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTATTCTGGCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* * * ** *
1082909 GAACTCTTCACTGGAAATCTTGATCCCTCAAGTGAGGTGTCACTGATTCGAAATGCCGTGAATCG
66 GAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCG
1082974 AGTGAT
131 AGTGAT
**
1082980 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCATTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* * * ** *** * * *
1083045 GAACTCTTCACTGGAAATATTGATCCCTCAAGCGAGACATCACTGATTTGAAATACCATGAATCG
66 GAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCG
1083110 AGTGAT
131 AGTGAT
1083116 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
1083181 GAACTCTCCATTGGAAATGT
66 GAACTCTCCATTGGAAATGT
1083201 TGGTTCACCT
Statistics
Matches: 583, Mismatches: 45, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
135 38 0.07
136 545 0.93
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (136 bp):
AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
GAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGCCGTGAATCG
AGTGAT
Found at i:1084745 original size:13 final size:13
Alignment explanation
Indices: 1084727--1084751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1084717 AGCCATGAGT
1084727 TTCATAATTAATA
1 TTCATAATTAATA
1084740 TTCATAATTAAT
1 TTCATAATTAAT
1084752 GTGAAATGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCATAATTAATA
Found at i:1086901 original size:20 final size:21
Alignment explanation
Indices: 1086855--1086915 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1086845 TCCCCTGTGG
1086855 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1086878 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1086898 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1086916 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1105102 original size:14 final size:15
Alignment explanation
Indices: 1105083--1105116 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1105073 TTTAAGAAAA
1105083 TATAATAA-AATATT
1 TATAATAATAATATT
1105097 TATAATAATAATATT
1 TATAATAATAATATT
1105112 T-TAAT
1 TATAAT
1105117 CCTTAAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATAATAATATT
Found at i:1105106 original size:22 final size:21
Alignment explanation
Indices: 1105055--1105106 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
1105045 TTTTTGCATG
* *
1105055 AAATAATATAATAAAGTTTTT
1 AAATAATATAATAAAATATTT
*
1105076 AAGAAAATATAATAAAATATTT
1 AA-ATAATATAATAAAATATTT
1105098 ATAATAATA
1 A-AATAATA
1105107 ATATTTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 2 0.08
22 22 0.88
23 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
AAATAATATAATAAAATATTT
Found at i:1107219 original size:136 final size:136
Alignment explanation
Indices: 1106971--1107585 Score: 880
Period size: 136 Copynumber: 4.5 Consensus size: 136
1106961 TGTTGATCTG
* * * *
1106971 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT-TGTTGGATGAATTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* * *
1107035 GAACTCTCCA-TTAGAAATATCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCGTGAATC
66 GAACTCTCTACTGA-AAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCGTGAATC
1107099 GAGTGAT
130 GAGTGAT
* * *
1107106 AAGTCGAACAAGCTCTTCTCATTATGAATTTCTTCTCCCTCTGTCGGATGAGTTCTTCTTATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* * * ** *
1107171 GAACACTCTATTGAAAATGTCAATCCCTTAAGTAAGGTGTCACTGATTCAAAATGTCGTGAATCG
66 GAACTCTCTACTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCGTGAATCG
1107236 AGTGAT
131 AGTGAT
*
1107242 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCTTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* * * ** * * *
1107307 GAACTCTTTACTGGAAATCTTGATCCCTCAAGTGAGGTGTCACTGATTCAAAATGACGTGAATCG
66 GAACTCTCTACTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCGTGAATCG
1107372 AGTGAT
131 AGTGAT
**
1107378 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCATTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* ** * *
1107443 GAACTCT-TCACTGGAAATGTTGATCCCTCAAGCGAGGCATCACTGATT-GAAAT-TCCGTGAAT
66 GAACTCTCT-ACTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGT-CGTGAAT
1107505 CGAGTGAT
129 CGAGTGAT
1107513 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
1107578 GAACTCTC
66 GAACTCTC
1107586 CATTAGAAAT
Statistics
Matches: 437, Mismatches: 38, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
135 126 0.29
136 309 0.71
137 2 0.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.35
Consensus pattern (136 bp):
AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
GAACTCTCTACTGAAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCGTGAATCG
AGTGAT
Found at i:1119944 original size:14 final size:15
Alignment explanation
Indices: 1119925--1119958 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1119915 TTTAAGAAAA
1119925 TATAATAA-AATATT
1 TATAATAATAATATT
1119939 TATAATAATAATATT
1 TATAATAATAATATT
1119954 T-TAAT
1 TATAAT
1119959 CCTTAAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAATAATAATATT
Found at i:1119951 original size:25 final size:23
Alignment explanation
Indices: 1119898--1119952 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 23
1119888 TTTTGCATGA
*
1119898 AATAATATAATAAATTTTTTAAG
1 AATAATATAATAAATTTTATAAG
*
1119921 AA-AATATAATAAAATATTTATAAT
1 AATAATATAAT-AAAT-TTTATAAG
1119945 AATAATAT
1 AATAATAT
1119953 TTTAATCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.30
23 6 0.22
24 8 0.30
25 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
AATAATATAATAAATTTTATAAG
Found at i:1125576 original size:15 final size:17
Alignment explanation
Indices: 1125556--1125587 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1125546 CATAATATAA
1125556 TAAATT-CAAG-TAGAT
1 TAAATTACAAGATAGAT
1125571 TAAATTACAAGATAGAT
1 TAAATTACAAGATAGAT
1125588 AAAAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (17 bp):
TAAATTACAAGATAGAT
Found at i:1131026 original size:21 final size:21
Alignment explanation
Indices: 1130989--1131028 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1130979 ACTTTTTTGG
*
1130989 ATATTCAAAATTTTGAATAGT
1 ATATTCAAAATTCTGAATAGT
1131010 ATATTC-AAATATCTGAATA
1 ATATTCAAAAT-TCTGAATA
1131029 TAAACATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
ATATTCAAAATTCTGAATAGT
Found at i:1132911 original size:277 final size:277
Alignment explanation
Indices: 1132417--1132976 Score: 1093
Period size: 277 Copynumber: 2.0 Consensus size: 277
1132407 TCACCGTTAA
1132417 TCTTTTTTAACTTTAATGAGCATTTTATATCTTCCAAAACTTCAATGGCTAAAAGGATCATTTTA
1 TCTTTTTTAACTTTAATGAGCATTTTATATCTTCCAAAACTTCAATGGCTAAAAGGATCATTTTA
1132482 ATAGAGTTTGATGATCATTTACATACTTAACCCTATAATTTGAAATTATGACTTGTGAAACCAAT
66 ATAGAGTTTGATGATCATTTACATACTTAACCCTATAATTTGAAATTATGACTTGTGAAACCAAT
*
1132547 TACATGGGCGGACCAACAGTTCAACACACCCTGTGTGTTTGAACCCGGGCTTGCACGTTTCTTAT
131 TACATGGGCGGACCAACAGTTCAACACACCCTATGTGTTTGAACCCGGGCTTGCACGTTTCTTAT
1132612 TAACACCCAACATCAATAAGAATCCATAGTCATTAGGCCACAATGAGTACGGCCATGGCTGAGGT
196 TAACACCCAACATCAATAAGAATCCATAGTCATTAGGCCACAATGAGTACGGCCATGGCTGAGGT
1132677 ACATAGGCTTCAAATAC
261 ACATAGGCTTCAAATAC
1132694 TCTTTTTTAACTTTAATGAGCATTTTATATCTTCCAAAACTTCAATGGCTAAAAGGATCATTTTA
1 TCTTTTTTAACTTTAATGAGCATTTTATATCTTCCAAAACTTCAATGGCTAAAAGGATCATTTTA
*
1132759 ATAGAGTTTGATGTTCATTTACATACTTAACCCTATAATTTGAAATTATGACTTGTGAAACCAAT
66 ATAGAGTTTGATGATCATTTACATACTTAACCCTATAATTTGAAATTATGACTTGTGAAACCAAT
*
1132824 TACATGGGCGGACCAACAGTTCAACACACCCTATGTGTTTGAACCTGGGCTTGCACGTTTCTTAT
131 TACATGGGCGGACCAACAGTTCAACACACCCTATGTGTTTGAACCCGGGCTTGCACGTTTCTTAT
1132889 TAACACCCAACATCAATAAGAATCCATAGTCATTAGGCCACAATGAGTACGGCCATGGCTGAGGT
196 TAACACCCAACATCAATAAGAATCCATAGTCATTAGGCCACAATGAGTACGGCCATGGCTGAGGT
1132954 ACATAGGCTTCAAATAC
261 ACATAGGCTTCAAATAC
1132971 TCTTTT
1 TCTTTT
1132977 AATAGTAGTA
Statistics
Matches: 280, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
277 280 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (277 bp):
TCTTTTTTAACTTTAATGAGCATTTTATATCTTCCAAAACTTCAATGGCTAAAAGGATCATTTTA
ATAGAGTTTGATGATCATTTACATACTTAACCCTATAATTTGAAATTATGACTTGTGAAACCAAT
TACATGGGCGGACCAACAGTTCAACACACCCTATGTGTTTGAACCCGGGCTTGCACGTTTCTTAT
TAACACCCAACATCAATAAGAATCCATAGTCATTAGGCCACAATGAGTACGGCCATGGCTGAGGT
ACATAGGCTTCAAATAC
Found at i:1137682 original size:2 final size:2
Alignment explanation
Indices: 1137675--1137699 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1137665 CGTTATGGGA
1137675 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
1137700 ATACATGAAA
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:1139492 original size:23 final size:22
Alignment explanation
Indices: 1139452--1139497 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1139442 ATAATATTTA
*
1139452 AATTTATAATTTTAAGTGTTGAT
1 AATTAATAATTTTAAGTG-TGAT
1139475 AATTAATAA-TTTATAGTGTGAT
1 AATTAATAATTTTA-AGTGTGAT
1139497 A
1 A
1139498 GAATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (22 bp):
AATTAATAATTTTAAGTGTGAT
Found at i:1139534 original size:19 final size:19
Alignment explanation
Indices: 1139512--1139554 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1139502 ATATATATAT
*
1139512 ATATATATAAT-ATTTTAAA
1 ATATATATAATCA-TTAAAA
*
1139531 ATATATTTAATCATTAAAA
1 ATATATATAATCATTAAAA
1139550 ATATA
1 ATATA
1139555 CATGTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATATATAATCATTAAAA
Found at i:1140127 original size:15 final size:15
Alignment explanation
Indices: 1140107--1140140 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1140097 CCTTCCCTAT
1140107 TTTTTTATT-AATTAA
1 TTTTTTATTCAA-TAA
1140122 TTTTTTATTCAATAA
1 TTTTTTATTCAATAA
1140137 TTTT
1 TTTT
1140141 ATTAATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTTTATTCAATAA
Found at i:1140468 original size:15 final size:15
Alignment explanation
Indices: 1140449--1140487 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
1140439 AATAATAAAA
1140449 TAATAAAAAATTA-T
1 TAATAAAAAATTACT
1140463 TGAATACAAAAATTACT
1 T-AATA-AAAAATTACT
1140480 TAATAAAA
1 TAATAAAA
1140488 TAATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.05
15 7 0.32
16 12 0.55
17 2 0.09
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (15 bp):
TAATAAAAAATTACT
Found at i:1142998 original size:17 final size:19
Alignment explanation
Indices: 1142980--1143019 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
1142970 GATGAATGAT
*
1142980 TTTTTGAATTGAAGTATTTA
1 TTTTAGAATTGAAGTA-TTA
1143000 TTTTAGGAATTGAAGTATTA
1 TTTTA-GAATTGAAGTATTA
1143020 AGATCAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (19 bp):
TTTTAGAATTGAAGTATTA
Found at i:1151541 original size:58 final size:58
Alignment explanation
Indices: 1151466--1151600 Score: 216
Period size: 58 Copynumber: 2.3 Consensus size: 58
1151456 GATATCTATG
*
1151466 CATTAAATTTTAGGGTTTTCGAGAAATAACAATCATACGTAAATGTGTCAATTTTTTA
1 CATTAAATTTTAGGGTTTTCGAGAAATAACAATCATACGTAAATATGTCAATTTTTTA
* * ** *
1151524 CATTGAATTTTAGGGTTTTCGAGAAGTAACGGTTATACGTAAATATGTCAATTTTTTA
1 CATTAAATTTTAGGGTTTTCGAGAAATAACAATCATACGTAAATATGTCAATTTTTTA
1151582 CATTAAATTTTAGGGTTTT
1 CATTAAATTTTAGGGTTTT
1151601 AGAAAAAATT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 70 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (58 bp):
CATTAAATTTTAGGGTTTTCGAGAAATAACAATCATACGTAAATATGTCAATTTTTTA
Found at i:1153002 original size:60 final size:60
Alignment explanation
Indices: 1152909--1153077 Score: 275
Period size: 60 Copynumber: 2.8 Consensus size: 60
1152899 GAACCAGCAG
* * *
1152909 CAGCAGCAGCAGCATCATCAGTCTTATTTTGCCCTTCACCACCACCACCACCACCACCTA
1 CAGCAGCAGCAACACCATCAGTCTTATTTTGCCCTTCACCACCACCACCACCACCACCAA
* * *
1152969 CAGCAGCAGCAACACCATCAGTCTTATTTTGCCCTTCACCACCACTACTACCACTACCAA
1 CAGCAGCAGCAACACCATCAGTCTTATTTTGCCCTTCACCACCACCACCACCACCACCAA
*
1153029 CAGCAGCAGCAACACCATCAGTCTTATTTTGCCCTTCACCACCGCCACC
1 CAGCAGCAGCAACACCATCAGTCTTATTTTGCCCTTCACCACCACCACC
1153078 CTCATTGTCC
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 100 1.00
ACGTcount: A:0.27, C:0.42, G:0.10, T:0.21
Consensus pattern (60 bp):
CAGCAGCAGCAACACCATCAGTCTTATTTTGCCCTTCACCACCACCACCACCACCACCAA
Found at i:1153980 original size:47 final size:47
Alignment explanation
Indices: 1153905--1153994 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 47
1153895 GATTATTCGG
* *
1153905 TCGATTGAGTTCAGACACGTACACTCTTTCATAAAGAATGTTTTAGA
1 TCGATCGAGTTCAGACACGTACACTCTTTCACAAAGAATGTTTTAGA
* * * * *
1153952 TCGATCGAGTTTAGATACGTGCATTCTTTTACAAAGAATGTTT
1 TCGATCGAGTTCAGACACGTACACTCTTTCACAAAGAATGTTT
1153995 ATATATTAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
47 36 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37
Consensus pattern (47 bp):
TCGATCGAGTTCAGACACGTACACTCTTTCACAAAGAATGTTTTAGA
Found at i:1154049 original size:61 final size:61
Alignment explanation
Indices: 1153950--1154085 Score: 193
Period size: 61 Copynumber: 2.2 Consensus size: 61
1153940 GAATGTTTTA
* *
1153950 GATCGATCGAGTTTAGATACGTGCATTCTTTTACAAAGAATGTTTATATATTAGATGATTC
1 GATCGATCGAGTTTAGAAACATGCATTCTTTTACAAAGAATGTTTATATATTAGATGATTC
* * * * *
1154011 GGTCGATCGAGTTTAGAAATATGCATTGTTTTATAAAGAATGTTTATATATTAGATGCTTC
1 GATCGATCGAGTTTAGAAACATGCATTCTTTTACAAAGAATGTTTATATATTAGATGATTC
*
1154072 GATCCAT-GAGTTTA
1 GATCGATCGAGTTTA
1154086 TACATATATG
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
60 7 0.11
61 59 0.89
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (61 bp):
GATCGATCGAGTTTAGAAACATGCATTCTTTTACAAAGAATGTTTATATATTAGATGATTC
Found at i:1154201 original size:28 final size:28
Alignment explanation
Indices: 1154164--1154225 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
1154154 AATGCTTATA
* *
1154164 TAAGGTTTCAATAAAAGAGGTCAAATGT
1 TAAGTTTTCAATAAAAGAGGTCAAATGC
*
1154192 TAAGTTTTCAATAAAGGAGGTCAAATGC
1 TAAGTTTTCAATAAAAGAGGTCAAATGC
1154220 TAAGTT
1 TAAGTT
1154226 AGAACATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (28 bp):
TAAGTTTTCAATAAAAGAGGTCAAATGC
Found at i:1154675 original size:17 final size:17
Alignment explanation
Indices: 1154661--1154704 Score: 72
Period size: 16 Copynumber: 2.6 Consensus size: 17
1154651 GTAAACCTAT
1154661 TACAAAACAAAACCTTA
1 TACAAAACAAAACCTTA
*
1154678 TACAAAAC-AGACCTTA
1 TACAAAACAAAACCTTA
1154694 TACAAAACAAA
1 TACAAAACAAA
1154705 GCTTAATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.59, C:0.23, G:0.02, T:0.16
Consensus pattern (17 bp):
TACAAAACAAAACCTTA
Found at i:1154693 original size:16 final size:16
Alignment explanation
Indices: 1154661--1154709 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
1154651 GTAAACCTAT
1154661 TACAAAACAAAACCTTA
1 TACAAAAC-AAACCTTA
*
1154678 TACAAAACAGACCTTA
1 TACAAAACAAACCTTA
*
1154694 TACAAAACAAAGCTTA
1 TACAAAACAAACCTTA
1154710 ATAGTTAGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.55, C:0.22, G:0.04, T:0.18
Consensus pattern (16 bp):
TACAAAACAAACCTTA
Found at i:1168263 original size:29 final size:29
Alignment explanation
Indices: 1168216--1168271 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
1168206 TTGTTGGCCA
1168216 TAGGTCGCCATGCCTTCCGGGCGACCTTG
1 TAGGTCGCCATGCCTTCCGGGCGACCTTG
1168245 TAGGTCGCCATGCAC-TCCGGGCGACCT
1 TAGGTCGCCATGC-CTTCCGGGCGACCT
1168272 ACCCTTGCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 25 0.96
30 1 0.04
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCGGGCGACCTTG
Found at i:1168364 original size:29 final size:29
Alignment explanation
Indices: 1168330--1168385 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1168320 TCCCAACACA
*
1168330 TAGGTCGACATGCCCTCCGGGCGACCTTG
1 TAGGTCGACATGCACTCCGGGCGACCTTG
*
1168359 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGACATGCACTCCGGGCGACCT
1168386 ACCCTCGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.36, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGACATGCACTCCGGGCGACCTTG
Found at i:1168441 original size:33 final size:33
Alignment explanation
Indices: 1168389--1168508 Score: 168
Period size: 33 Copynumber: 3.6 Consensus size: 33
1168379 GCGACCTACC
* *
1168389 CTCGCTCGACTGCCCTCGGATTCCCTCGCATAG
1 CTCGTTCGGCTGCCCTCGGATTCCCTCGCATAG
* *
1168422 CTCGTTCGGGTGCCTTCGGATTCCCTCGCATAG
1 CTCGTTCGGCTGCCCTCGGATTCCCTCGCATAG
* *
1168455 CTCGCTCGGCTGCCCTCGGATGCCCTCGCATAG
1 CTCGTTCGGCTGCCCTCGGATTCCCTCGCATAG
* *
1168488 CTCGTTCGGATGGCCTCGGAT
1 CTCGTTCGGCTGCCCTCGGAT
1168509 GCTCTTGGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.10, C:0.38, G:0.27, T:0.26
Consensus pattern (33 bp):
CTCGTTCGGCTGCCCTCGGATTCCCTCGCATAG
Found at i:1168478 original size:10 final size:10
Alignment explanation
Indices: 1168399--1168546 Score: 53
Period size: 10 Copynumber: 13.5 Consensus size: 10
1168389 CTCGCTCGAC
1168399 TGCCCTCGGA
1 TGCCCTCGGA
* *
1168409 TTCCCTCGCA
1 TGCCCTCGGA
* *
1168419 TAGCTCGTTCGGG
1 T-GC-C-CTCGGA
*
1168432 TGCCTTCGGA
1 TGCCCTCGGA
* *
1168442 TTCCCTCGCA
1 TGCCCTCGGA
*
1168452 TAGCTCGCTCGGC
1 T-GC-C-CTCGGA
1168465 TGCCCTCGGA
1 TGCCCTCGGA
*
1168475 TGCCCTCGCA
1 TGCCCTCGGA
*
1168485 TAGCTCGTTCGGA
1 T-GC-C-CTCGGA
*
1168498 TGGCCTCGGA
1 TGCCCTCGGA
* *
1168508 TGCTCTTGGA
1 TGCCCTCGGA
1168518 TAGCCTCGGTCGGA
1 T-GCC-C--TCGGA
*
1168532 TGGCCTCGGA
1 TGCCCTCGGA
1168542 TGCCC
1 TGCCC
1168547 AGCGTGTTGG
Statistics
Matches: 99, Mismatches: 26, Indels: 26
0.66 0.17 0.17
Matches are distributed among these distances:
10 59 0.60
11 9 0.09
12 10 0.10
13 16 0.16
14 5 0.05
ACGTcount: A:0.10, C:0.35, G:0.29, T:0.26
Consensus pattern (10 bp):
TGCCCTCGGA
Found at i:1168507 original size:66 final size:67
Alignment explanation
Indices: 1168388--1168546 Score: 205
Period size: 66 Copynumber: 2.4 Consensus size: 67
1168378 GGCGACCTAC
* * * *
1168388 CCTCGCTCGACTGCCCTCGGATTCCCTCGCATAGCTCGTTCGGGTGCCTTCGGATTCCCTCGCAT
1 CCTCGCTCGGCTGCCCTCGGATGCCCTCGCATAGCTCGTTCGGATGCCTTCGGATGCCCTCGCAT
1168453 AG
66 AG
* * *
1168455 -CTCGCTCGGCTGCCCTCGGATGCCCTCGCATAGCTCGTTCGGATGGCC-TCGGATGCTCTTGGA
1 CCTCGCTCGGCTGCCCTCGGATGCCCTCGCATAGCTCGTTCGGAT-GCCTTCGGATGCCCTCGCA
1168518 TAG
65 TAG
* * *
1168521 CCTCGGTCGGATGGCCTCGGATGCCC
1 CCTCGCTCGGCTGCCCTCGGATGCCC
1168547 AGCGTGTTGG
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
66 55 0.69
67 25 0.31
ACGTcount: A:0.10, C:0.36, G:0.28, T:0.25
Consensus pattern (67 bp):
CCTCGCTCGGCTGCCCTCGGATGCCCTCGCATAGCTCGTTCGGATGCCTTCGGATGCCCTCGCAT
AG
Found at i:1168509 original size:33 final size:33
Alignment explanation
Indices: 1168402--1168546 Score: 175
Period size: 33 Copynumber: 4.4 Consensus size: 33
1168392 GCTCGACTGC
* *
1168402 CCTCGGATTCCCTCGCATAGCTCGTTCGGGT-G
1 CCTCGGATGCCCTCGCATAGCTCGTTCGGATGG
* * * *
1168434 CCTTCGGATTCCCTCGCATAGCTCGCTCGGCTGC
1 CC-TCGGATGCCCTCGCATAGCTCGTTCGGATGG
1168468 CCTCGGATGCCCTCGCATAGCTCGTTCGGATGG
1 CCTCGGATGCCCTCGCATAGCTCGTTCGGATGG
* * * *
1168501 CCTCGGATGCTCTTGGATAGCCTCGGTCGGATGG
1 CCTCGGATGCCCTCGCATAG-CTCGTTCGGATGG
1168535 CCTCGGATGCCC
1 CCTCGGATGCCC
1168547 AGCGTGTTGG
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
32 2 0.02
33 71 0.72
34 25 0.26
ACGTcount: A:0.10, C:0.35, G:0.29, T:0.26
Consensus pattern (33 bp):
CCTCGGATGCCCTCGCATAGCTCGTTCGGATGG
Found at i:1171576 original size:17 final size:17
Alignment explanation
Indices: 1171554--1171593 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1171544 TTGAGAAAAC
1171554 AAAGTGTTCAGTGTGTT
1 AAAGTGTTCAGTGTGTT
1171571 AAAGTGTTCAGTGTGTT
1 AAAGTGTTCAGTGTGTT
*
1171588 TAAGTG
1 AAAGTG
1171594 CTCCGTCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.25, C:0.05, G:0.30, T:0.40
Consensus pattern (17 bp):
AAAGTGTTCAGTGTGTT
Done.