Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008003.1 Hibiscus syriacus cultivar Beakdansim tig00110462_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: 3297763
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 14
Found at i:870928 original size:19 final size:19
Alignment explanation
Indices: 870888--871037 Score: 194
Period size: 19 Copynumber: 8.4 Consensus size: 19
870878 GATTCTCCCG
870888 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
870908 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
870927 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
870941 TTGCGATTTTCATTCCGCA
1 TTGCGATTTTCATTTCGCA
870960 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
870979 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
870993 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
871012 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
871031 TTGCGAT
1 TTGCGAT
871038 AGTCAATTTT
Statistics
Matches: 114, Mismatches: 6, Indels: 21
0.81 0.04 0.15
Matches are distributed among these distances:
14 12 0.11
16 14 0.12
17 13 0.11
19 60 0.53
20 15 0.13
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:870979 original size:52 final size:52
Alignment explanation
Indices: 870869--871037 Score: 311
Period size: 52 Copynumber: 3.2 Consensus size: 52
870859 GAAATTAAAA
*
870869 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCA-TTCCGCATTGCGATTTTCATT
870922 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTCCGCATTGCGATTTTCATT
*
870974 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTCCGCATTGCGATTTTCATT
871026 TCGCATTGCGAT
1 TCGCATTGCGAT
871038 AGTCAATTTT
Statistics
Matches: 114, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 84 0.74
53 30 0.26
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTCCGCATTGCGATTTTCATT
Found at i:870997 original size:33 final size:33
Alignment explanation
Indices: 870869--871019 Score: 137
Period size: 33 Copynumber: 4.4 Consensus size: 33
870859 GAAATTAAAA
*
870869 TCGCATTGCGATTCTCCCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* *
870902 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 T-CGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TCATT
* * * *
870943 GCG-ATTTTC-ATTC-CGCATTGCGATTTTCATT
1 TCGCA-TTGCGATTCTCTCGTTGCGATTTTCATT
870974 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
871007 TCGCATTGCGATT
1 TCGCATTGCGATT
871020 TTCATTTCGC
Statistics
Matches: 93, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
31 9 0.10
32 6 0.06
33 38 0.41
34 10 0.11
35 1 0.01
36 3 0.03
37 6 0.06
39 10 0.11
40 6 0.06
41 4 0.04
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:871163 original size:14 final size:14
Alignment explanation
Indices: 871144--871180 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
871134 CATCAATTAC
871144 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
871158 ACAAATCATCTTTT
1 ACAAATCAACTTTT
871172 ACAAATCAA
1 ACAAATCAA
871181 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:873146 original size:19 final size:19
Alignment explanation
Indices: 873106--873171 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
873096 TAGTTTACTT
* *
873106 TCGCAACACGAAACATAAAA
1 TCGCAACGCGAAAC-CAAAA
*
873126 TCGCATCGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
873145 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
873164 TCGCAACG
1 TCGCAACG
873172 ACAGAATCGC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:873180 original size:33 final size:33
Alignment explanation
Indices: 873143--873235 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
873133 GCGAAACCAA
*
873143 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
873176 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
873209 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
873236 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:873181 original size:14 final size:14
Alignment explanation
Indices: 873162--873218 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
873152 GCGAAATGAA
*
873162 AATCGCAACGACAG
1 AATCGCAACGAAAG
873176 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
873193 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
873209 AATCGCAACG
1 AATCGCAACG
873219 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:873200 original size:19 final size:19
Alignment explanation
Indices: 873122--873240 Score: 107
Period size: 19 Copynumber: 6.8 Consensus size: 19
873112 CACGAAACAT
**
873122 AAAATCGC-ATCGCGAAACC
1 AAAATCGCAAT-GCGAAATG
*
873141 AAAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
*
873160 AAAATCGCAA--CGACA-G
1 AAAATCGCAATGCGAAATG
873176 --AATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
873193 AAAATCGCAA--CGAAA-G
1 AAAATCGCAATGCGAAATG
*
873209 --AATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
873226 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
873241 TTTTGGTTTC
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
14 16 0.19
16 11 0.13
17 11 0.13
19 44 0.53
20 1 0.01
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:873258 original size:19 final size:19
Alignment explanation
Indices: 873236--873364 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
873226 AAAATCGCAA
873236 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
873255 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
873269 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
873288 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
** *
873302 TGCGATTTTCATTTCGCTT
1 TGCGATTTTGGTTTCGCGT
873321 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
873340 TGCGATTTTATGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
873360 TGCGA
1 TGCGA
873365 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 46 0.52
20 13 0.15
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:873278 original size:33 final size:33
Alignment explanation
Indices: 873236--873327 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
873226 AAAATCGCAA
873236 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
873269 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
873302 TGCGATTTTCATTTCGCTTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
873328 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.27, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:873528 original size:93 final size:93
Alignment explanation
Indices: 873412--873971 Score: 1090
Period size: 93 Copynumber: 6.1 Consensus size: 93
873402 ATGGATTGCA
873412 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
873476 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
873504 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
873568 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
873596 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
873661 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
873689 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
873754 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
873782 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACTGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
873847 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
873875 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
873940 TAGCAGAATTGGCAGCAACCGAA-AAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
873967 TTACT
1 TTACT
873972 AAGCAATCTA
Statistics
Matches: 464, Mismatches: 2, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
92 105 0.23
93 359 0.77
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:875697 original size:14 final size:14
Alignment explanation
Indices: 875678--875734 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
875668 TTGAAATGAA
875678 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
875692 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
875711 AATCGCAACGAGAG
1 AATCGCAACGAGAG
875725 AATCGCAACG
1 AATCGCAACG
875735 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:875710 original size:33 final size:33
Alignment explanation
Indices: 875670--875751 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
875660 TCTTTTGGTT
875670 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
875703 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
875736 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
875752 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:875716 original size:19 final size:19
Alignment explanation
Indices: 875692--875756 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
875682 GCAACGAGAG
875692 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
875711 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
875725 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
875744 AATCGCAATGCGA
1 AATCGCAACGCGA
875757 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:875787 original size:14 final size:14
Alignment explanation
Indices: 875768--875857 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
875758 TTTGGTTTCG
875768 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
875782 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
875801 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
875815 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
875834 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
875848 CGTTGCGATT
1 CGTTGCGATT
875858 TTCATTTATC
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:875800 original size:33 final size:33
Alignment explanation
Indices: 875752--875864 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
875742 AAAATCGCAA
**
875752 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
875785 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
875818 TGCGATTGTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
875851 TGCGATTTTCATTT
1 TGCGATTTTCATTT
875865 ATCTCGTTGC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:875806 original size:19 final size:19
Alignment explanation
Indices: 875782--875843 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
875772 GCGATTCTCT
875782 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
875801 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
875815 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
875834 CGTTGCGATT
1 CGTTGCGATT
875844 CTCTCGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 2 0.06
17 3 0.09
19 20 0.57
ACGTcount: A:0.10, C:0.23, G:0.24, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:875998 original size:33 final size:33
Alignment explanation
Indices: 875956--876026 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
875946 AATACTAACT
*
875956 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
875989 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
876022 TGAAA
1 TGAAA
876027 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:876260 original size:22 final size:22
Alignment explanation
Indices: 876208--876262 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
876198 TGGTTGTGAG
**
876208 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
876230 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
876252 GGATTTCTTCG
1 GGATTTCTTCG
876263 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:876434 original size:20 final size:20
Alignment explanation
Indices: 876409--876562 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
876399 CTTTAAATAT
876409 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
876429 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
876451 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
876470 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
876490 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
876510 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
876530 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
876550 CGCGTTGCGATTT
1 CGCGTTGCGATTT
876563 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:876536 original size:40 final size:40
Alignment explanation
Indices: 876408--876562 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
876398 GCTTTAAATA
*
876408 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
876449 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
876489 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
876529 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
876563 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:876579 original size:21 final size:21
Alignment explanation
Indices: 876549--876631 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
876539 ATTTTCATAT
*
876549 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
876570 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
876591 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
876612 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
876632 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:876622 original size:42 final size:43
Alignment explanation
Indices: 876529--876627 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
876519 ATTTATGTGT
* *
876529 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
876570 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
876612 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
876628 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:880240 original size:14 final size:14
Alignment explanation
Indices: 880221--880256 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
880211 TAACTACCAG
880221 TATTGGTTTAAATT
1 TATTGGTTTAAATT
880235 TATTGGTTTAAATT
1 TATTGGTTTAAATT
880249 TATTGGTT
1 TATTGGTT
880257 GACTCATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (14 bp):
TATTGGTTTAAATT
Found at i:880535 original size:2 final size:2
Alignment explanation
Indices: 880528--880565 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
880518 GATAATTTGA
880528 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
880566 TATTAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:881925 original size:2 final size:2
Alignment explanation
Indices: 881918--881956 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
881908 TATTACGATA
881918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
881957 GATAATATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:881964 original size:8 final size:7
Alignment explanation
Indices: 881915--881964 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 7
881905 AGTTATTACG
881915 ATAATAT
1 ATAATAT
881922 AT-ATAT
1 ATAATAT
881928 AT-ATAT
1 ATAATAT
881934 ATATATAT
1 ATA-ATAT
881942 ATATATAT
1 ATA-ATAT
*
881950 ATGATAT
1 ATAATAT
881957 GATAATAT
1 -ATAATAT
881965 CCTATTACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
6 12 0.32
7 6 0.16
8 20 0.53
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (7 bp):
ATAATAT
Found at i:886859 original size:18 final size:18
Alignment explanation
Indices: 886838--886897 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 18
886828 TTTTTTATGT
886838 ATTAAAATAATATTATTA
1 ATTAAAATAATATTATTA
* *
886856 ATTAATAATATTTTATTATTT
1 ATTAA-AATA--ATATTATTA
886877 ATTAAAA-AATA-TATTA
1 ATTAAAATAATATTATTA
*
886893 GTTAA
1 ATTAA
886898 CTTATTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 8 0.24
17 2 0.06
18 5 0.15
19 5 0.15
20 2 0.06
21 12 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATTAAAATAATATTATTA
Found at i:886910 original size:40 final size:39
Alignment explanation
Indices: 886828--886920 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 39
886818 TAGGGTTGAG
* *
886828 TTTT-TTATGTATTAAAATAATATTATTAATTAATAATA
1 TTTTATTATTTATTAAAAAAATATTATTAATTAATAATA
*
886866 TTTTATTATTTATTAAAAAATATATTAGTTAACTT-ATTAT-
1 TTTTATTATTTATTAAAAAA-ATATTA-TTAA-TTAATAATA
886906 TTTTATTATTTATTA
1 TTTTATTATTTATTA
886921 TTTATTAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
38 4 0.08
39 13 0.27
40 21 0.44
41 8 0.17
42 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (39 bp):
TTTTATTATTTATTAAAAAAATATTATTAATTAATAATA
Found at i:896344 original size:33 final size:34
Alignment explanation
Indices: 896285--896361 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 34
896275 AGTTAGATAT
**
896285 TTTTTTTAGGAAAAATATAAACTAAACCCTTCAA
1 TTTTTTTAAAAAAAATATAAACTAAACCCTTCAA
* *
896319 TTTTTTTAAAAAAAAT-TAATA-TAAACCTTTGAA
1 TTTTTTTAAAAAAAATATAA-ACTAAACCCTTCAA
*
896352 TTTATTTAAA
1 TTTTTTTAAA
896362 GTTTAAATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 22 0.59
34 15 0.41
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (34 bp):
TTTTTTTAAAAAAAATATAAACTAAACCCTTCAA
Found at i:909987 original size:26 final size:26
Alignment explanation
Indices: 909948--909997 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
909938 TTTTATAATA
**
909948 ATAAATTTTTTATAATTTT-AAAAATT
1 ATAAATTTCATAT-ATTTTGAAAAATT
909974 ATAAATTTCATATATTTTGAAAAA
1 ATAAATTTCATATATTTTGAAAAA
909998 AGTATTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
ATAAATTTCATATATTTTGAAAAATT
Found at i:910618 original size:340 final size:334
Alignment explanation
Indices: 909994--910728 Score: 1137
Period size: 340 Copynumber: 2.2 Consensus size: 334
909984 TATATTTTGA
* *
909994 AAAAAGTATTGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTATTT--TA-----
1 AAAAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTATTTAATATTTTT
910052 ATATTTTTAAACAATTAATTTTAAAAGGCAATAATTTTTTCAAAAATATATGAAATTTATAATTT
66 ATATTTTTAAACAATTAATTTTAAAAGGCAAT-ATTTTTTCAAAAATATATGAAATTTATAATTT
*
910117 TTTAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACT
130 TTAAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACT
* *
910182 TTTATAAAATTATTCATATTTTAAAATAATTACCCTCAAAGTTTTTATATACTAGATTATATGTA
195 TTTATAAAATTATTCATATTTTAAAATAATTACCCTCAAAGTTTTCATATACTAGATTATACGTA
** *
910247 TTGTGTAATTTTAATGCAAAAATTTAAATAATTTTATTAAAAATGAATAAACATTATTAGCTGTT
260 TTGTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAACTGTT
*
910312 GTTAAAAATT
325 GTTAAAAAAT
* *
910322 AAAAATTAATGAATAATAATTTATTTGATCTCTCAATTGTAATTAAAAGTTTATGTTAATATTTT
1 AAAAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTAT-TTAATA-TTT
*
910387 TTATATTTTTAAACAATTAATTTTAAAAGGTAAT-TTTTTTC-AAAATATATGAAATTTATAATT
64 TTATATTTTTAAACAATTAATTTTAAAAGGCAATATTTTTTCAAAAATATATGAAATTTATAATT
*
910450 TTTAAAATTATAAAATATTTATTATTATCATCATCATCATTATTTTGTAAAAGAAATACTAGTTA
129 TTTAAAATTAT-AAA-A--TA-T-TTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTA
*
910515 TAAAACTTTTATAAAATTATTCATATTTTAAAATATTTACCCTCAAAGTTTTCATATACTAGATT
188 TAAAACTTTTATAAAATTATTCATATTTTAAAATAATTACCCTCAAAGTTTTCATATACTAGATT
* *
910580 ATACGTATTGTGTAATTTTAATGTAAAAATCAAAATAATTTTATTAAAAATGAATAAATATTATT
253 ATACGTATTGTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATT
910645 AACTGTTGTTAAAAAAT
318 AACTGTTGTTAAAAAAT
* * * *
910662 AAAAATTAATGAATAATAATTCATTTAATCCCTTAATTATAATTAAAAGTTTACTTTAATATTTT
1 AAAAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTA-TTTAATATTTT
910727 TA
65 TA
910729 AACAATTAAT
Statistics
Matches: 370, Mismatches: 21, Indels: 21
0.90 0.05 0.05
Matches are distributed among these distances:
328 50 0.14
329 2 0.01
331 2 0.01
334 32 0.09
335 10 0.03
336 1 0.00
337 31 0.08
338 2 0.01
339 7 0.02
340 232 0.63
341 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.44
Consensus pattern (334 bp):
AAAAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTATTTAATATTTTT
ATATTTTTAAACAATTAATTTTAAAAGGCAATATTTTTTCAAAAATATATGAAATTTATAATTTT
TAAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTT
TTATAAAATTATTCATATTTTAAAATAATTACCCTCAAAGTTTTCATATACTAGATTATACGTAT
TGTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAACTGTTG
TTAAAAAAT
Found at i:920557 original size:26 final size:26
Alignment explanation
Indices: 920518--920567 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
920508 TTTTATAATA
**
920518 ATAAATTTTTTATAATTTT-AAAAATT
1 ATAAATTTCATAT-ATTTTGAAAAATT
920544 ATAAATTTCATATATTTTGAAAAA
1 ATAAATTTCATATATTTTGAAAAA
920568 AGTATTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
ATAAATTTCATATATTTTGAAAAATT
Found at i:921189 original size:341 final size:334
Alignment explanation
Indices: 920564--921299 Score: 1146
Period size: 341 Copynumber: 2.2 Consensus size: 334
920554 TATATTTTGA
* *
920564 AAAAAGTATTGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTATTT--TA-----
1 AAAAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTATTTAATATTTTT
920622 ATATTTTTAAACAATTAATTTTAAAAGGCAATAATTTTTTCAAAAATATATGAAATTTATAATTT
66 ATATTTTTAAACAATTAATTTTAAAAGGCAAT-ATTTTTTCAAAAATATATGAAATTTATAATTT
*
920687 TTTAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACT
130 TTAAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACT
* *
920752 TTTATAAAATTATTCATATTTTAAAATAATTACCCTCAAAGTTTTTATATACTAGATTATATGTA
195 TTTATAAAATTATTCATATTTTAAAATAATTACCCTCAAAGTTTTCATATACTAGATTATACGTA
** *
920817 TTGTGTAATTTTAATGCAAAAATTTAAATAATTTTATTAAAAATGAATAAACATTATTAGCTGTT
260 TTGTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAACTGTT
*
920882 GTTAAAAATT
325 GTTAAAAAAT
* *
920892 AAAAATTAATGAATAATAATTTATTTGATCTCTCAATTGTAATTAAAAGTTTATGTTAATATTTT
1 AAAAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTAT-TTAATA-TTT
*
920957 TTATATTTTTAAACAATTAATTTTAAAAGGTAAT-TTTTTTCAAAAATATATGAAATTTATAATT
64 TTATATTTTTAAACAATTAATTTTAAAAGGCAATATTTTTTCAAAAATATATGAAATTTATAATT
*
921021 TTTAAAATTATAAAATATTTATTATTATCATCATCATCATTATTTTGTAAAAGAAATACTAGTTA
129 TTTAAAATTAT-AAA-A--TA-T-TTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTA
*
921086 TAAAACTTTTATAAAATTATTCATATTTTAAAATATTTACCCTCAAAGTTTTCATATACTAGATT
188 TAAAACTTTTATAAAATTATTCATATTTTAAAATAATTACCCTCAAAGTTTTCATATACTAGATT
* *
921151 ATACGTATTGTGTAATTTTAATGTAAAAATCAAAATAATTTTATTAAAAATGAATAAATATTATT
253 ATACGTATTGTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATT
921216 AACTGTTGTTAAAAAAT
318 AACTGTTGTTAAAAAAT
* * * *
921233 AAAAATTAATGAATAATAATTCATTTAATCCCTTAATTATAATTAAAAGTTTACTTTAATATTTT
1 AAAAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTA-TTTAATATTTT
921298 TA
65 TA
921300 AACAATTAAT
Statistics
Matches: 371, Mismatches: 21, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
328 50 0.13
329 2 0.01
331 2 0.01
335 40 0.11
336 3 0.01
337 32 0.09
339 2 0.01
340 7 0.02
341 232 0.63
342 1 0.00
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.44
Consensus pattern (334 bp):
AAAAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTATTTAATATTTTT
ATATTTTTAAACAATTAATTTTAAAAGGCAATATTTTTTCAAAAATATATGAAATTTATAATTTT
TAAAATTATAAAATATTTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTT
TTATAAAATTATTCATATTTTAAAATAATTACCCTCAAAGTTTTCATATACTAGATTATACGTAT
TGTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAACTGTTG
TTAAAAAAT
Found at i:928814 original size:24 final size:24
Alignment explanation
Indices: 928787--928864 Score: 88
Period size: 24 Copynumber: 3.2 Consensus size: 24
928777 GTTCATTTAT
* *
928787 GTTCATGAACGTTCGGTTATGTTC
1 GTTCATGAATGTTCGTTTATGTTC
*
928811 GTTCA-GTTATGTTCGTTTATGTTC
1 GTTCATG-AATGTTCGTTTATGTTC
928835 GTTCGAT-AATGTTCGTTTATGTTC
1 GTTC-ATGAATGTTCGTTTATGTTC
*
928859 ATTCAT
1 GTTCAT
928865 TTATGTTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.07
24 42 0.91
25 1 0.02
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.49
Consensus pattern (24 bp):
GTTCATGAATGTTCGTTTATGTTC
Found at i:928819 original size:14 final size:14
Alignment explanation
Indices: 928796--928827 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
928786 TGTTCATGAA
*
928796 CGTTCGGTTATGTT
1 CGTTCAGTTATGTT
928810 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
928824 CGTT
1 CGTT
928828 TATGTTCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (14 bp):
CGTTCAGTTATGTT
Found at i:928870 original size:24 final size:23
Alignment explanation
Indices: 928797--928871 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
928787 GTTCATGAAC
*
928797 GTTCGGTTATGTTCGTTCAGTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
*
928821 GTTCGTTTATGTTCGTTCGATAAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
928845 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCA-TTAT
928869 GTT
1 GTT
928872 TAACTCAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.02
24 43 0.96
25 1 0.02
ACGTcount: A:0.15, C:0.12, G:0.20, T:0.53
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:929613 original size:16 final size:16
Alignment explanation
Indices: 929590--929644 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
929580 GGGTCTCCAA
929590 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
929606 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
929622 CGTCTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
929638 CGTTTAT
1 CGTTTAT
929645 TTATTAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.09, C:0.15, G:0.22, T:0.55
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:941216 original size:60 final size:60
Alignment explanation
Indices: 941104--941216 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
941094 TTGAGTGATC
* *
941104 ATTTTATAACTTTTAATAGTCAGAGGACTCGACAAAATAATGTCCTACAGTCGGGAGACT
1 ATTTTATAACTTTTAATAGTCAGAGGACTCAACAAAATAATGTCCCACAGTCGGGAGACT
* *
941164 ATTTTATAACTTTTAATAGT-AGAGGAACTCAACAAAATATTGTCCCATAGTCG
1 ATTTTATAACTTTTAATAGTCAGAGG-ACTCAACAAAATAATGTCCCACAGTCG
941217 AGGGAACATT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 5 0.10
60 43 0.90
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCAGAGGACTCAACAAAATAATGTCCCACAGTCGGGAGACT
Found at i:941495 original size:2 final size:2
Alignment explanation
Indices: 941488--941515 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
941478 ATTAACGTTA
941488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
941516 TATTTTCCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:946657 original size:20 final size:20
Alignment explanation
Indices: 946634--946730 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
946624 ATTCACGTTG
* *
946634 CATTTCGCGTTGTGATTTTT
1 CATTTCGCGTTGCGATTTTC
946654 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* * *
946674 CAGTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* **
946695 AAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
946715 TATTTCGTGTTGCGAT
1 CATTTCGCGTTGCGAT
946731 AGTCTACAGT
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:946750 original size:22 final size:22
Alignment explanation
Indices: 946723--946802 Score: 88
Period size: 22 Copynumber: 3.4 Consensus size: 22
946713 TCTATTTCGT
946723 GTTGCGATAGTCTACAGTTGTC
1 GTTGCGATAGTCTACAGTTGTC
* *
946745 GTTGCGATTTTCCAAATCTACAGTTGTT
1 GTTGCGA---T---AGTCTACAGTTGTC
946773 GTTGCGATAGTCTACAGTTGTC
1 GTTGCGATAGTCTACAGTTGTC
946795 GTTGCGAT
1 GTTGCGAT
946803 TTTCTAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
22 27 0.56
25 2 0.04
28 19 0.40
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (22 bp):
GTTGCGATAGTCTACAGTTGTC
Found at i:946808 original size:22 final size:22
Alignment explanation
Indices: 946702--946808 Score: 76
Period size: 22 Copynumber: 4.7 Consensus size: 22
946692 TTGAAAATCG
*
946702 CGTTGCGATTTTCT--ATTTCGT
1 CGTTGCGATTTTCTACAGTT-GT
**
946723 -GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCTACAGTTGT
946744 CGTTGCGATTTTCCAAATCTACAGTTGT
1 CGTTGCGA-TTT-----TCTACAGTTGT
* **
946772 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCTACAGTTGT
946794 CGTTGCGATTTTCTA
1 CGTTGCGATTTTCTA
946809 AATTCTTTGC
Statistics
Matches: 66, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
20 11 0.17
21 2 0.03
22 33 0.50
23 1 0.02
27 1 0.02
28 18 0.27
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (22 bp):
CGTTGCGATTTTCTACAGTTGT
Found at i:947448 original size:6 final size:6
Alignment explanation
Indices: 947437--947461 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
947427 TCGGGTCAGA
947437 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
947462 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:953549 original size:20 final size:20
Alignment explanation
Indices: 953524--953566 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
953514 AATTTACCAA
953524 AGATGCTCAAAAAGTTTTGC
1 AGATGCTCAAAAAGTTTTGC
953544 AGATGCTCAAAAAGTTTTGC
1 AGATGCTCAAAAAGTTTTGC
953564 AGA
1 AGA
953567 CTTACTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (20 bp):
AGATGCTCAAAAAGTTTTGC
Found at i:953772 original size:18 final size:18
Alignment explanation
Indices: 953749--953785 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
953739 CCCTCAAAAT
*
953749 TAATACAAGTGCCACCCC
1 TAATACAAATGCCACCCC
953767 TAATACAAATGCCACCCC
1 TAATACAAATGCCACCCC
953785 T
1 T
953786 GGGGCTCTTA
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:0.35, C:0.38, G:0.08, T:0.19
Consensus pattern (18 bp):
TAATACAAATGCCACCCC
Found at i:958260 original size:2 final size:2
Alignment explanation
Indices: 958253--958299 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
958243 TAAAAAGAGA
958253 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
958295 AT AT A
1 AT AT A
958300 GTTTTTTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:962513 original size:45 final size:45
Alignment explanation
Indices: 962424--962514 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 45
962414 CTCGGAAACG
* *
962424 ATGATTGCATAAGTCGAATGAACAAAGTTCTGGAATTACCATTTT
1 ATGATTGCATAAGTCGAATGAACAAAGTTCCGGAATTACAATTTT
**
962469 ATGATTGCATATA-TCGAATGAATGAAGTTCCGG-ATCTACAATTTT
1 ATGATTGCATA-AGTCGAATGAACAAAGTTCCGGAAT-TACAATTTT
962514 A
1 A
962515 AGAGTACTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
44 2 0.05
45 37 0.93
46 1 0.03
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (45 bp):
ATGATTGCATAAGTCGAATGAACAAAGTTCCGGAATTACAATTTT
Found at i:964071 original size:22 final size:22
Alignment explanation
Indices: 964046--964094 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
964036 CGAAAAGCAC
964046 AATATTATTTTAAATAAGATAT
1 AATATTATTTTAAATAAGATAT
* * * *
964068 AATATTTTTTTGATTAAGCTAT
1 AATATTATTTTAAATAAGATAT
964090 AATAT
1 AATAT
964095 ATTAGAATGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (22 bp):
AATATTATTTTAAATAAGATAT
Found at i:983557 original size:29 final size:29
Alignment explanation
Indices: 983512--983569 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
983502 GTGTTGGCCG
*
983512 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
983541 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
983570 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:983622 original size:10 final size:10
Alignment explanation
Indices: 983609--983679 Score: 61
Period size: 10 Copynumber: 6.7 Consensus size: 10
983599 ACACGCTGGG
983609 CATCCGAGAC
1 CATCCGAGAC
983619 CATCCGACCGAGGC
1 CATCCGA--GA--C
* *
983633 CATTCGAGAG
1 CATCCGAGAC
*
983643 CATCCGAGGC
1 CATCCGAGAC
*
983653 CATCCGAGAG
1 CATCCGAGAC
*
983663 CATCCGAGGC
1 CATCCGAGAC
983673 CATCCGA
1 CATCCGA
983680 CCGAGGCCAT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
10 37 0.77
12 4 0.08
14 7 0.15
ACGTcount: A:0.25, C:0.37, G:0.27, T:0.11
Consensus pattern (10 bp):
CATCCGAGAC
Found at i:983651 original size:20 final size:20
Alignment explanation
Indices: 983626--983679 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
983616 GACCATCCGA
*
983626 CCGAGGCCATTCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
983646 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAGAGCAT
983666 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
983680 CCGAGGCCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAGAGCAT
Found at i:983685 original size:14 final size:14
Alignment explanation
Indices: 983666--983698 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
983656 CCGAGAGCAT
983666 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
983680 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
983694 ACGAG
1 CCGAG
983699 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:983693 original size:10 final size:10
Alignment explanation
Indices: 983626--983679 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
983616 GACCATCCGA
983626 CCGAGGCCAT
1 CCGAGGCCAT
*
983636 TCGAGAG-CAT
1 CCGAG-GCCAT
983646 CCGAGGCCAT
1 CCGAGGCCAT
983656 CCGAGAG-CAT
1 CCGAG-GCCAT
983666 CCGAGGCCAT
1 CCGAGGCCAT
983676 CCGA
1 CCGA
983680 CCGAGGCCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 2 0.05
10 34 0.89
11 2 0.05
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:983732 original size:33 final size:33
Alignment explanation
Indices: 983690--983764 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
983680 CCGAGGCCAT
* *
983690 CCGAACGAGCTATGCGAGGGCATCCGAGGGTAA-
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGG-AAG
983723 CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAG
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAG
983756 CCGAGCGAG
1 CCGAGCGAG
983765 GGTAGGTCGC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
32 2 0.05
33 37 0.95
ACGTcount: A:0.27, C:0.24, G:0.40, T:0.09
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAG
Found at i:983801 original size:29 final size:29
Alignment explanation
Indices: 983768--983823 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
983758 GAGCGAGGGT
* *
983768 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGACGACCTACA
983797 AGGTCGCCCGGAGGGCATGACGACCTA
1 AGGTCGCCCGGAGGGCATGACGACCTA
983824 TGTGTTGGGA
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:0.21, C:0.30, G:0.36, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGACGACCTACA
Found at i:985614 original size:108 final size:108
Alignment explanation
Indices: 985443--985742 Score: 327
Period size: 108 Copynumber: 2.8 Consensus size: 108
985433 GAATCTTTAG
* * * * * *
985443 AAATCCGACGATAACAAAAGAAGCTAATTACTTAATTTGTTATTAATATTATCAATATATTAGGT
1 AAATCCGACGATAACAAAATATGTTAATTACTTATTTTGTTATTAATATTATTAACATATTAGGT
* *
985508 AGCGCCTAAAATATTA-CAAAAATTTAAGCTT-ATGGGGCATTAA
66 AGCGCCTAAAATATTATC-AAAATTTAAG-TTGATAGAGCATTAA
*
985551 AAATCCGACGATAACAAAATATGTTAATTATTTATTTTGTTATTAATATTATTAACATATTAGGT
1 AAATCCGACGATAACAAAATATGTTAATTACTTATTTTGTTATTAATATTATTAACATATTAGGT
* * * * **
985616 ATCTCCTAAAATGTTATCAAAATTTAAGTTGATAGAGCCTTCG
66 AGCGCCTAAAATATTATCAAAATTTAAGTTGATAGAGCATTAA
* * * * * *
985659 AAATCTC-ATGACAACAAAATATGTTAATTACTTATTTTGTTATAAATAAATAGTAACATATTAA
1 AAATC-CGACGATAACAAAATATGTTAATTACTTATTTTGTTATTAAT-ATTATTAACATATTAG
* *
985723 GTTGCGCCCAATAATATTAT
64 GTAGCGCCTAA-AATATTAT
985743 TGTAAATAAA
Statistics
Matches: 160, Mismatches: 27, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
107 2 0.01
108 129 0.81
109 22 0.14
110 7 0.04
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (108 bp):
AAATCCGACGATAACAAAATATGTTAATTACTTATTTTGTTATTAATATTATTAACATATTAGGT
AGCGCCTAAAATATTATCAAAATTTAAGTTGATAGAGCATTAA
Found at i:986403 original size:76 final size:74
Alignment explanation
Indices: 986310--986544 Score: 317
Period size: 76 Copynumber: 3.1 Consensus size: 74
986300 AAGTTGTAAA
* * * * *
986310 TATTTTACCATTTACATTATTATTATAGCTTTTAACAAATTGATAGTTAGTTTAACGTAATATGT
1 TATTTTA-CGTTTACATTATTATTA-ATCTTTTAACAAATCGATAGCTAGTTTAACGTAATAGGT
986375 AGCACCTATTT
64 AGCACCTATTT
* *
986386 TATTTTATCGTTTACATTATTATTAATCTTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGT
1 TATTTTA-CGTTTACATTATTATTAATCTTTT-AACAAATCGATAGCTAGTTTAACGTAATAGGT
* *
986451 AACACATATTT
64 AGCACCTATTT
* *
986462 TATTTTACTGTTTACATTATTATTAATCTTTAAAACAAATCGATAGCTAGTTTAACGTAATGGGT
1 TATTTTAC-GTTTACATTATTATTAATCTTT-TAACAAATCGATAGCTAGTTTAACGTAATAGGT
986527 AGCACCTATTT
64 AGCACCTATTT
986538 TATTTTA
1 TATTTTA
986545 ACTAGTTAAG
Statistics
Matches: 140, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
75 7 0.05
76 133 0.95
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (74 bp):
TATTTTACGTTTACATTATTATTAATCTTTTAACAAATCGATAGCTAGTTTAACGTAATAGGTAG
CACCTATTT
Found at i:986639 original size:99 final size:100
Alignment explanation
Indices: 986462--986643 Score: 233
Period size: 99 Copynumber: 1.8 Consensus size: 100
986452 ACACATATTT
* * * * * *
986462 TATTTTACTGTTTACATTATTATTAATCTTTAAAACAAATCGATAGCTAGTTTAACGTAATGGGT
1 TATTTTACCGTTTACAATAATATTAACCTTTAAAACAAATCGATAGCTAATTTAACGTAATAGGT
*
986527 AGCACCTATTTTATTTTAACTAGTTAAGTTGTAAA
66 AACACCTATTTTATTTTAACTAGTTAAGTTGTAAA
* * *
986562 TATTTTACCGTTTACAATAATATTATACCTTTAAAA-AAA-CGGTAGGTAATTTAACGTAATATG
1 TATTTTACCGTTTACAATAATATTA-ACCTTTAAAACAAATCGATAGCTAATTTAACGTAATAGG
**
986625 TAACGGCTATTTTATTTTA
65 TAACACCTATTTTATTTTA
986644 TTGTTTACAT
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
99 35 0.51
100 25 0.36
101 9 0.13
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (100 bp):
TATTTTACCGTTTACAATAATATTAACCTTTAAAACAAATCGATAGCTAATTTAACGTAATAGGT
AACACCTATTTTATTTTAACTAGTTAAGTTGTAAA
Found at i:986732 original size:174 final size:176
Alignment explanation
Indices: 986386--986736 Score: 476
Period size: 174 Copynumber: 2.0 Consensus size: 176
986376 GCACCTATTT
* * * * * *
986386 TATTTTATCGTTTACATTATTATTAATCTTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGT
1 TATTTTACCGTTTACAATAATATTAATCCTTTAAACAAAACGGTAGCTAATTTAACGTAATAGGT
*
986451 AACACATATTTTATTTTACTGTTTACATTATTATTAATCTTTAAAACAAATCGATAGCTAGTTTA
66 AACACATATTTTATTTTACTGTTTACATTATTATTAATCTTTAAAACAAACCGATAGCTAGTTTA
** * * * *
986516 ACGTAATGGGTAGCACCTATTTTATTTTAACTAGTTAAGTTGTAAA
131 ACAAAATAGGTAGCACCTATTTTATTTTAACCAATCAAGTTGTAAA
* *
986562 TATTTTACCGTTTACAATAATATT-ATACCTTTAAA-AAAACGGTAGGTAATTTAACGTAATATG
1 TATTTTACCGTTTACAATAATATTAAT-CCTTTAAACAAAACGGTAGCTAATTTAACGTAATAGG
* * * *
986625 TAACGGC-TATTTTATTTTATTGTTTACATTATTATTAA-CTTTTAAACAAACCGATAGGTAGTT
65 TAAC-ACATATTTTATTTTACTGTTTACATTATTATTAATCTTTAAAACAAACCGATAGCTAGTT
*
986688 TAATAAAATAGGTAGCACCTATTTTATTTTAACCAATCAAGTTGTAAA
129 TAACAAAATAGGTAGCACCTATTTTATTTTAACCAATCAAGTTGTAAA
986736 T
1 T
986737 TAATATTATA
Statistics
Matches: 153, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
174 64 0.42
175 60 0.39
176 29 0.19
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.42
Consensus pattern (176 bp):
TATTTTACCGTTTACAATAATATTAATCCTTTAAACAAAACGGTAGCTAATTTAACGTAATAGGT
AACACATATTTTATTTTACTGTTTACATTATTATTAATCTTTAAAACAAACCGATAGCTAGTTTA
ACAAAATAGGTAGCACCTATTTTATTTTAACCAATCAAGTTGTAAA
Found at i:986835 original size:258 final size:251
Alignment explanation
Indices: 986297--986902 Score: 700
Period size: 258 Copynumber: 2.4 Consensus size: 251
986287 ATTTCAAACG
* * * * ** * *
986297 GTTAAGTTGTAAATATTTTACCATTTACATTATTATTATAGCTTTTAACAAATTGATAGTTAGTT
1 GTTAAGTTGTAAATATTTTACCGTTTACATTAATATTATA-CATTTAAAAAAACGGTAGGTAGTT
*
986362 TAACGTAATATGTAGCACCTATTTTATTTTATCGTTTACATTATTATTAATCTTTTAAACAAACC
65 TAACGTAATATGTAACACCTATTTTATTTTATCGTTTACATTATTATTAATCTTTTAAACAAACC
* ** * * *
986427 GGTAGCTAGTTTAACGTAATAGGTAACACATATTTTATTTTACTGTTTACATTATTATTAATCTT
130 GATAGCTAGTTTAACAAAATAGGTAACACATATTTTATTTTACTGTTTAAATTAATATTAACCTT
* *
986492 TAAAACAAATCGATAGCTAGTTTAACGTAATGGGTAGCACCTATTTTATTTTAACTA
195 TAAAACAAATCGATAGCTAGTTTAACGTAATAGGTAGCACCTATTTTATTTTAACCA
* * *
986549 GTTAAGTTGTAAATATTTTACCGTTTACAATAATATTATACCTTTAAAAAAACGGTAGGTAATTT
1 GTTAAGTTGTAAATATTTTACCGTTTACATTAATATTATACATTTAAAAAAACGGTAGGTAGTTT
** *
986614 AACGTAATATGTAACGGCTATTTTATTTTATTGTTTACATTATTATTAA-CTTTTAAACAAACCG
66 AACGTAATATGTAACACCTATTTTATTTTATCGTTTACATTATTATTAATCTTTTAAACAAACCG
* * * *
986678 ATAGGTAGTTTAATAAAATAGGTAGCACCTATTTTATTTTAACCAATCAAGTTGTAAATTAATAT
131 ATAGCTAGTTTAACAAAATAGGTAACACATATTTTATTTT-A-C--T---GTT-TAAATTAATAT
* * *
986743 TATACCTTT-AAAC-AAGCTGGTAAG-TAGTTTAACGTAATAGGTAAG-ACTTATTTTATTTTAA
188 TA-ACCTTTAAAACAAATC-GAT-AGCTAGTTTAACGTAATAGGT-AGCACCTATTTTATTTTAA
986804 CCA
249 CCA
* ** *
986807 GTTAAGTTGTAAATAGTTTATTGTTTACATTAATATTATACATTTAAACAAACCGGTAGGTAGTT
1 GTTAAGTTGTAAATATTTTACCGTTTACATTAATATTATACATTTAAA-AAAACGGTAGGTAGTT
* ** * *
986872 TAACGCAATAAATAACACATATTTTAATTTA
65 TAACGTAATATGTAACACCTATTTTATTTTA
986903 ACCGGTTAAG
Statistics
Matches: 298, Mismatches: 43, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
250 48 0.16
251 64 0.21
252 38 0.13
254 1 0.00
257 6 0.02
258 94 0.32
259 47 0.16
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (251 bp):
GTTAAGTTGTAAATATTTTACCGTTTACATTAATATTATACATTTAAAAAAACGGTAGGTAGTTT
AACGTAATATGTAACACCTATTTTATTTTATCGTTTACATTATTATTAATCTTTTAAACAAACCG
ATAGCTAGTTTAACAAAATAGGTAACACATATTTTATTTTACTGTTTAAATTAATATTAACCTTT
AAAACAAATCGATAGCTAGTTTAACGTAATAGGTAGCACCTATTTTATTTTAACCA
Found at i:986911 original size:100 final size:100
Alignment explanation
Indices: 986735--987103 Score: 463
Period size: 100 Copynumber: 3.7 Consensus size: 100
986725 CAAGTTGTAA
* * * * *
986735 ATTAATATTATACCTTTAAACAAGCTGGTAAGTAGTTTAACGTAATAGGTAAGACTTATTTTATT
1 ATTAATATTATATCTTTAAACAAACCGGTAAGTAGTTTAACGTAATAGGTAACACATATTTTATT
* **
986800 TTAACCAGTTAAGTTGTAAATAGTTTATTGTTTAC
66 TTAACCAGTTAAGTTGTAAATATTTTACCGTTTAC
* * ** *
986835 ATTAATATTATA-CATTTAAACAAACCGGTAGGTAGTTTAACGCAATAAATAACACATATTTTAA
1 ATTAATATTATATC-TTTAAACAAACCGGTAAGTAGTTTAACGTAATAGGTAACACATATTTTAT
*
986899 TTTAACCGGTTAAGTTGTAAATATTTTACCGTTTAC
65 TTTAACCAGTTAAGTTGTAAATATTTTACCGTTTAC
*** * * *
986935 ATTAATATTATATCTTTAAACAAACCGGTAAGTAGTTTAACGTAATAGGTAGTGCCTATATTGTT
1 ATTAATATTATATCTTTAAACAAACCGGTAAGTAGTTTAACGTAATAGGTAACACATATTTTATT
* *
987000 TTAACCAATTAAGTTTTAAATATTTTACCGTTTAC
66 TTAACCAGTTAAGTTGTAAATATTTTACCGTTTAC
* ** * *
987035 TTTAATATTATATCTTTAAACAAACCGGT-AGTTAGTTTAATATAATATGTAACACCTATTTTAT
1 ATTAATATTATATCTTTAAACAAACCGGTAAG-TAGTTTAACGTAATAGGTAACACATATTTTAT
987099 TTTAA
65 TTTAA
987104 TGTTAACTAA
Statistics
Matches: 230, Mismatches: 36, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
99 3 0.01
100 226 0.98
101 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (100 bp):
ATTAATATTATATCTTTAAACAAACCGGTAAGTAGTTTAACGTAATAGGTAACACATATTTTATT
TTAACCAGTTAAGTTGTAAATATTTTACCGTTTAC
Found at i:987097 original size:200 final size:200
Alignment explanation
Indices: 986735--987103 Score: 517
Period size: 200 Copynumber: 1.8 Consensus size: 200
986725 CAAGTTGTAA
* * * *
986735 ATTAATATTATACCTTTAAACAAGCTGGTAAGTAGTTTAACGTAATAGGTAAGACTTATTTTATT
1 ATTAATATTATACCTTTAAACAAACCGGTAAGTAGTTTAACGTAATAGGTAAGACCTATATTATT
* **
986800 TTAACCAGTTAAGTTGTAAATAGTTTATTGTTTACATTAATATTATACATTTAAACAAACCGGTA
66 TTAACCAATTAAGTTGTAAATAGTTTACCGTTTACATTAATATTATACATTTAAACAAACCGGTA
*
986865 GGTAGTTTAACGCAATAAATAACACATATTTTAATTTAACCGGTTAAGTTGTAAATATTTTACCG
131 GGTAGTTTAACACAATAAATAACACATATTTTAATTTAACCGGTTAAGTTGTAAATATTTTACCG
986930 TTTAC
196 TTTAC
* * *
986935 ATTAATATTATATCTTTAAACAAACCGGTAAGTAGTTTAACGTAATAGGT-AGTGCCTATATTGT
1 ATTAATATTATACCTTTAAACAAACCGGTAAGTAGTTTAACGTAATAGGTAAG-ACCTATATTAT
* * *
986999 TTTAACCAATTAAGTTTTAAATATTTTACCGTTTACTTTAATATTATATC-TTTAAACAAACCGG
65 TTTAACCAATTAAGTTGTAAATAGTTTACCGTTTACATTAATATTATA-CATTTAAACAAACCGG
* * * ** * *
987063 TAGTTAGTTTAATATAATATGTAACACCTATTTTATTTTAA
129 TAGGTAGTTTAACACAATAAATAACACATATTTTAATTTAA
987104 TGTTAACTAA
Statistics
Matches: 146, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
199 2 0.01
200 143 0.98
201 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (200 bp):
ATTAATATTATACCTTTAAACAAACCGGTAAGTAGTTTAACGTAATAGGTAAGACCTATATTATT
TTAACCAATTAAGTTGTAAATAGTTTACCGTTTACATTAATATTATACATTTAAACAAACCGGTA
GGTAGTTTAACACAATAAATAACACATATTTTAATTTAACCGGTTAAGTTGTAAATATTTTACCG
TTTAC
Found at i:999057 original size:21 final size:20
Alignment explanation
Indices: 999033--999074 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
999023 GTCATACAAC
*
999033 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
999054 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
999074 T
1 T
999075 TGTAAATTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:1005624 original size:2 final size:2
Alignment explanation
Indices: 1005617--1005642 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1005607 ATGTCTTATC
1005617 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1005643 TCACATTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1006881 original size:24 final size:20
Alignment explanation
Indices: 1006827--1006864 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1006817 TTCCCCTTGA
*
1006827 AGTGCATTGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1006847 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
1006865 TTAACATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1006945 original size:64 final size:63
Alignment explanation
Indices: 1006872--1007032 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 63
1006862 TCTTTAACAT
* * * **
1006872 GTGCATCGATACACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTTA-TTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
* * ** *
1006936 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTTCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
* *
1007000 GTGCATCGATGCACTTCCTGTACATCGATACAC
1 GTGCATCGATGCAC-TCCTATGCATCGATACAC
1007033 TTCCTGTGCA
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 2 0.02
64 70 0.86
65 9 0.11
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:1007027 original size:19 final size:19
Alignment explanation
Indices: 1007003--1007051 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1006993 TTAATGGGTG
*
1007003 CATCGATGCACTTCCTGTA
1 CATCGATACACTTCCTGTA
*
1007022 CATCGATACACTTCCTGTG
1 CATCGATACACTTCCTGTA
1007041 CATCGATACAC
1 CATCGATACAC
1007052 ACTGAACAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (19 bp):
CATCGATACACTTCCTGTA
Found at i:1015812 original size:12 final size:12
Alignment explanation
Indices: 1015795--1015825 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1015785 ATTAAAATCA
1015795 TTAAAATCTATT
1 TTAAAATCTATT
*
1015807 TTAAAATTTATT
1 TTAAAATCTATT
1015819 TTAAAAT
1 TTAAAAT
1015826 ATAGATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAAATCTATT
Found at i:1015840 original size:22 final size:22
Alignment explanation
Indices: 1015812--1016133 Score: 484
Period size: 22 Copynumber: 14.6 Consensus size: 22
1015802 CTATTTTAAA
*
1015812 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
1015834 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
1015856 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
**
1015878 ATTTATTTTAAAATATGGA-AA
1 ATTTATTTTAAAATATGGATTG
1015899 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
1015922 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
1015944 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
*
1015966 ATTTATTTTAAAATATGTATTG
1 ATTTATTTTAAAATATGGATTG
1015988 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
1016010 ATTTATTTTAAAATATAGAAAA
1 ATTTATTTTAAAATATGGATTG
*
1016032 AATTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
1016054 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
1016076 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
*
1016098 ATTTATTTTAAAAATATGAATTG
1 ATTTATTTT-AAAATATGGATTG
1016121 ATTTATTTTAAAA
1 ATTTATTTTAAAA
1016134 AATTTATTAT
Statistics
Matches: 271, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
21 1 0.00
22 249 0.92
23 21 0.08
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:1016192 original size:31 final size:31
Alignment explanation
Indices: 1016157--1016215 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1016147 AGTTGTATGG
1016157 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTATAAAACTAAA
*
1016188 ATTATTTAAATTTCAGTATTGTAAAACT
1 ATTATTTAAATTTCAGTATTATAAAACT
1016216 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTATAAAACTAAA
Found at i:1020824 original size:91 final size:90
Alignment explanation
Indices: 1020664--1020845 Score: 319
Period size: 91 Copynumber: 2.0 Consensus size: 90
1020654 AAATCGCTAC
* * *
1020664 CTTTCAAAACCTATTTAAAACGTACGTCAATAAAAAAATCTATAATTTTTTGAGTTTGAGGCTTT
1 CTTTCAAAACCTATTTAAAACGCACGCCAATAAAAAAATCTACAATTTTTTGAGTTTGAGGCTTT
1020729 CTTAGATTTAAGGTACTTATTTTGT
66 CTTAGATTTAAGGTACTTATTTTGT
1020754 CTTTCAAAACCTATTTAAAACGCACGCCAATAAAAAAAATCTACAATTTTTTGAGTTTGAGGCTT
1 CTTTCAAAACCTATTTAAAACGCACGCCAAT-AAAAAAATCTACAATTTTTTGAGTTTGAGGCTT
*
1020819 TCTTAGATTTAAGGTATTTATTTTGT
65 TCTTAGATTTAAGGTACTTATTTTGT
1020845 C
1 C
1020846 AAAATAAGTA
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
90 29 0.33
91 58 0.67
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.41
Consensus pattern (90 bp):
CTTTCAAAACCTATTTAAAACGCACGCCAATAAAAAAATCTACAATTTTTTGAGTTTGAGGCTTT
CTTAGATTTAAGGTACTTATTTTGT
Found at i:1023400 original size:3 final size:3
Alignment explanation
Indices: 1023392--1023437 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1023382 ACACATCGGG
1023392 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1023438 TTAAACAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1024609 original size:4 final size:4
Alignment explanation
Indices: 1024544--1024595 Score: 77
Period size: 4 Copynumber: 13.0 Consensus size: 4
1024534 ACATCACACG
* * *
1024544 CATA CATA TATA TATA CATA CATA TATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1024592 CATA
1 CATA
1024596 TATATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (4 bp):
CATA
Found at i:1024609 original size:12 final size:12
Alignment explanation
Indices: 1024545--1024607 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
1024535 CATCACACGC
*
1024545 ATACATATATAT
1 ATACATACATAT
1024557 ATACATACATAT
1 ATACATACATAT
*
1024569 ATACATACATAC
1 ATACATACATAT
*
1024581 ATACATACATAC
1 ATACATACATAT
* *
1024593 ATATATATATAT
1 ATACATACATAT
1024605 ATA
1 ATA
1024608 TAGTTTAGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (12 bp):
ATACATACATAT
Found at i:1027879 original size:7 final size:8
Alignment explanation
Indices: 1027862--1027886 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1027852 TCATTTATTT
1027862 AAAAATAA
1 AAAAATAA
1027870 AAAAATAA
1 AAAAATAA
1027878 AAAAATAA
1 AAAAATAA
1027886 A
1 A
1027887 TGTTAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:1029698 original size:2 final size:2
Alignment explanation
Indices: 1029649--1029679 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1029639 CTCCAAATTC
*
1029649 CT CT CT CT AT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1029680 CCTTTCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1031031 original size:2 final size:2
Alignment explanation
Indices: 1031024--1031057 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1031014 TCATATCTAA
1031024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1031058 TTATGTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1044295 original size:29 final size:29
Alignment explanation
Indices: 1044246--1044309 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
1044236 GGATAAAGCA
*
1044246 AAATTTGACTATTCTGATACCCTGTTATT
1 AAATTTGACTATTCTGATACCCTATTATT
*
1044275 AAATTTGACTATT-TTAGTACCCTATTATT
1 AAATTTGACTATTCTGA-TACCCTATTATT
1044304 AAATTT
1 AAATTT
1044310 AATCATTGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 2 0.06
29 30 0.94
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (29 bp):
AAATTTGACTATTCTGATACCCTATTATT
Found at i:1046236 original size:26 final size:26
Alignment explanation
Indices: 1046200--1046256 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
1046190 TTCAACATTG
1046200 AGCTTAGGCAACAAGCTAAACCAGAC
1 AGCTTAGGCAACAAGCTAAACCAGAC
1046226 AGCTTAGGCAACAAGCTAAACCAGAC
1 AGCTTAGGCAACAAGCTAAACCAGAC
1046252 AGCTT
1 AGCTT
1046257 TGTTTTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.14
Consensus pattern (26 bp):
AGCTTAGGCAACAAGCTAAACCAGAC
Found at i:1055185 original size:20 final size:21
Alignment explanation
Indices: 1055147--1055187 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1055137 CAGCCAACAA
*
1055147 TCAGCAAAATCATCGTTTCTT
1 TCAGCAAAATCATCATTTCTT
*
1055168 TCAGCAAATTC-TCATTTCTT
1 TCAGCAAAATCATCATTTCTT
1055188 GTACTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.41
Consensus pattern (21 bp):
TCAGCAAAATCATCATTTCTT
Found at i:1059840 original size:21 final size:21
Alignment explanation
Indices: 1059789--1059841 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1059779 ATTATGACTA
1059789 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
1059810 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1059831 TCGCAATGCGA
1 TCGCAATGCGA
1059842 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1059856 original size:20 final size:21
Alignment explanation
Indices: 1059831--1059882 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1059821 TTTTCCCAAT
*
1059831 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGAAAAA
**
1059851 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGAATAAGAAAAA
1059872 TCGCAATGCGA
1 TCGCAATGCGA
1059883 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATAAGAAAAA
Found at i:1059874 original size:21 final size:20
Alignment explanation
Indices: 1059831--1059904 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
1059821 TTTTCCCAAT
*
1059831 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
1059851 TCGCAATGCGAATTTGAAAAA
1 TCGCAATGCGAATAAG-AAAA
* **
1059872 TCGCAATGCG-ATACTGACTA
1 TCGCAATGCGAATA-AGAAAA
1059892 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1059905 CTTACTATCG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1059896 original size:20 final size:21
Alignment explanation
Indices: 1059871--1059923 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
1059861 AATTTGAAAA
1059871 ATCGCAATGCGATA-CTGACT
1 ATCGCAATGCGATATCTGACT
*
1059891 ATCGCAATGCGA-ATCTTACT
1 ATCGCAATGCGATATCTGACT
1059911 ATCGCAATGCGAT
1 ATCGCAATGCGAT
1059924 TTACATAGCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (21 bp):
ATCGCAATGCGATATCTGACT
Found at i:1060488 original size:19 final size:19
Alignment explanation
Indices: 1060466--1060510 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1060456 GCAACGAGAG
*
1060466 AATCGCAACGCAAAATAAA
1 AATCGCAACGCAAAACAAA
* * *
1060485 AATCACAACGCGAAACCAA
1 AATCGCAACGCAAAACAAA
1060504 AATCGCA
1 AATCGCA
1060511 TTGTGATTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.27, G:0.11, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCAAAACAAA
Found at i:1060537 original size:19 final size:19
Alignment explanation
Indices: 1060515--1060651 Score: 96
Period size: 19 Copynumber: 7.6 Consensus size: 19
1060505 ATCGCATTGT
1060515 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
1060534 GATTTTCATTTTGCGTTGC
1 GATTTTCATTTCGCGTTGC
* *
1060553 -A-ATTC---TCTCGTTGC
1 GATTTTCATTTCGCGTTGC
**
1060567 GATAGTCATTTCGCGTTGC
1 GATTTTCATTTCGCGTTGC
*
1060586 GA--TTC---TCTCGTTGC
1 GATTTTCATTTCGCGTTGC
**
1060600 GATAGTCATTTTCGCGTTGC
1 GATTTTCA-TTTCGCGTTGC
* *
1060620 GATTCTCATTATCTCGTTGC
1 GATTTTCATT-TCGCGTTGC
1060640 GATTTTCATTTC
1 GATTTTCATTTC
1060652 AACCAAAAGA
Statistics
Matches: 92, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
14 17 0.18
15 1 0.01
16 5 0.05
17 5 0.05
18 1 0.01
19 32 0.35
20 31 0.34
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
GATTTTCATTTCGCGTTGC
Found at i:1060576 original size:33 final size:33
Alignment explanation
Indices: 1060528--1060626 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
1060518 TTTCATTTCG
** *
1060528 CGTTGCGATTTTCATTTTGCGTTGCAATTCTCT
1 CGTTGCGATAGTCATTTTGCGTTGCGATTCTCT
*
1060561 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTTGCGTTGCGATTCTCT
1060594 CGTTGCGATAGTCATTTTCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTT-GCGTTGCGATTCTC
1060627 ATTATCTCGT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 46 0.77
34 14 0.23
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTTGCGTTGCGATTCTCT
Found at i:1060643 original size:20 final size:20
Alignment explanation
Indices: 1060591--1060649 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1060581 GTTGCGATTC
** *
1060591 TCTCGTTGCGATAGTCATTT
1 TCTCGTTGCGATTCTCATTA
*
1060611 TCGCGTTGCGATTCTCATTA
1 TCTCGTTGCGATTCTCATTA
*
1060631 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTCTCATT
1060650 TCAACCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (20 bp):
TCTCGTTGCGATTCTCATTA
Found at i:1062820 original size:21 final size:21
Alignment explanation
Indices: 1062796--1062862 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1062786 TCATTCCTCG
1062796 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1062817 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1062838 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1062859 AGAG
1 AGAG
1062863 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1062820 original size:42 final size:42
Alignment explanation
Indices: 1062744--1062862 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1062734 GACTCGTCTG
* * * * * * *
1062744 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1062786 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1062828 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1062863 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1064377 original size:14 final size:14
Alignment explanation
Indices: 1064358--1064414 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1064348 GCGAAATGAA
1064358 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1064372 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1064391 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1064405 AATCGCAACG
1 AATCGCAACG
1064415 CGAAATTAAA
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:1064385 original size:33 final size:33
Alignment explanation
Indices: 1064340--1064420 Score: 153
Period size: 33 Copynumber: 2.5 Consensus size: 33
1064330 AAAAAGTACT
*
1064340 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1064373 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1064406 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
1064421 TAAATTCGTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:1064399 original size:19 final size:19
Alignment explanation
Indices: 1064340--1064400 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1064330 AAAAAGTACT
*
1064340 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1064359 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
1064373 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1064392 ATCGCAACG
1 ATCGCAACG
1064401 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1064472 original size:33 final size:32
Alignment explanation
Indices: 1064430--1064555 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 32
1064420 TTAAATTCGT
1064430 GTTGCGATTTTCATTTCGCATTGCGATTCCCTC
1 GTTGCGATTTTCATTTCGCATTGCGATT-CCTC
*
1064463 GTTGCGATTTTCATTTCGCATTGCGAAATT-CGC
1 GTTGCGATTTTCATTTCGCATTGCG--ATTCCTC
1064496 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTC-CTC
1064529 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
1064556 AGTAATTTCC
Statistics
Matches: 87, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
31 3 0.03
33 81 0.93
35 3 0.03
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCCTC
Found at i:1064488 original size:19 final size:19
Alignment explanation
Indices: 1064431--1064555 Score: 100
Period size: 19 Copynumber: 7.4 Consensus size: 19
1064421 TAAATTCGTG
1064431 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
**
1064450 TTGCGA--TTC-CCTCG--
1 TTGCGATTTTCATTTCGCA
1064464 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1064483 TTGCGA-----AATTCGCG
1 TTGCGATTTTCATTTCGCA
1064497 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1064516 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1064530 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1064549 TTGCGAT
1 TTGCGAT
1064556 AGTAATTTCC
Statistics
Matches: 81, Mismatches: 10, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
14 24 0.30
16 13 0.16
17 13 0.16
19 31 0.38
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1064506 original size:66 final size:66
Alignment explanation
Indices: 1064422--1064554 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1064412 ACGCGAAATT
*
1064422 AAATTCGTGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1064487 G
66 G
*
1064488 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1064553 G
66 G
1064554 A
1 A
1064555 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1066864 original size:12 final size:12
Alignment explanation
Indices: 1066847--1066871 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1066837 TCTTCGGGGA
1066847 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1066859 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1066871 C
1 C
1066872 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1067080 original size:24 final size:24
Alignment explanation
Indices: 1067046--1067099 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1067036 CTGAAACATC
*
1067046 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1067070 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1067094 ATCAAA
1 ATCAAA
1067100 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:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1067909 original size:20 final size:21
Alignment explanation
Indices: 1067884--1067935 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1067874 TTTTTCTAAT
*
1067884 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
1067904 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1067925 TCGCAATGCGA
1 TCGCAATGCGA
1067936 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1068009 original size:20 final size:20
Alignment explanation
Indices: 1067962--1068011 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1067952 GAGATAATAC
*
1067962 AAAATTGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
1067982 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
1068002 AAAATCGCAA
1 AAAATCGCAA
1068012 TCATCTTCAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:1068320 original size:20 final size:20
Alignment explanation
Indices: 1068221--1068312 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
1068211 ATCGCAACGG
1068221 GGAAATCGCAACGCGAAAAT
1 GGAAATCGCAACGCGAAAAT
1068241 GGAAATCGCAACGCGAAAAT
1 GGAAATCGCAACGCGAAAAT
** **
1068261 GGCTATCGCAATTCG-AAAT
1 GGAAATCGCAACGCGAAAAT
*
1068280 GAAAAATCGCAACGCGAAAAT
1 G-GAAATCGCAACGCGAAAAT
**
1068301 GGCTATCGCAAC
1 GGAAATCGCAAC
1068313 TAGAAAATCG
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
19 5 0.09
20 48 0.83
21 5 0.09
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (20 bp):
GGAAATCGCAACGCGAAAAT
Found at i:1068363 original size:33 final size:33
Alignment explanation
Indices: 1068326--1068396 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
1068316 AAAATCGCAA
*
1068326 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCAT
** ** **
1068359 TGCGATTTTCATTTCGCATTGCGATTTTCTCAT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCAT
1068392 TGCGA
1 TGCGA
1068397 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCAT
Found at i:1068380 original size:19 final size:16
Alignment explanation
Indices: 1068339--1068397 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 16
1068329 GAAATGAAAA
1068339 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1068355 TCG--TTGCGATTTTC
1 TCGCATTGCGATTTTC
1068369 ATTTCGCATTGCGATTTTC
1 ---TCGCATTGCGATTTTC
1068388 T--CATTGCGAT
1 TCGCATTGCGAT
1068398 AGTCAGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 20 0.53
16 4 0.11
17 3 0.08
19 11 0.29
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:1068407 original size:21 final size:20
Alignment explanation
Indices: 1068383--1068427 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1068373 CGCATTGCGA
1068383 TTTTCTCATTGCGATAGTCAG
1 TTTTCT-ATTGCGATAGTCAG
* * *
1068404 TTTTGTGTTGCGATAGTCTG
1 TTTTCTATTGCGATAGTCAG
1068424 TTTT
1 TTTT
1068428 GCCTTCAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.13, C:0.13, G:0.22, T:0.51
Consensus pattern (20 bp):
TTTTCTATTGCGATAGTCAG
Found at i:1068416 original size:20 final size:20
Alignment explanation
Indices: 1068391--1068428 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1068381 GATTTTCTCA
1068391 TTGCGATAGTCAGTTTTGTG
1 TTGCGATAGTCAGTTTTGTG
*
1068411 TTGCGATAGTCTGTTTTG
1 TTGCGATAGTCAGTTTTG
1068429 CCTTCAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.11, G:0.29, T:0.47
Consensus pattern (20 bp):
TTGCGATAGTCAGTTTTGTG
Found at i:1070479 original size:19 final size:20
Alignment explanation
Indices: 1070424--1070479 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
1070414 GAAACTTAAA
**
1070424 ATCACAACGCAAAAATGACT
1 ATCACAACGCGGAAATGACT
* *
1070444 ATCGCAACGCGGAAATGGCT
1 ATCACAACGCGGAAATGACT
*
1070464 ATCACAATGC-GAAATG
1 ATCACAACGCGGAAATG
1070480 CAAATCGCAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCACAACGCGGAAATGACT
Found at i:1070510 original size:33 final size:33
Alignment explanation
Indices: 1070468--1070585 Score: 177
Period size: 33 Copynumber: 3.6 Consensus size: 33
1070458 ATGGCTATCA
*
1070468 CAATGCGAAATGCAAATCGCAACGACAAAATAG
1 CAATGCGAAATGCAAATCGCAACGACAAAATCG
*
1070501 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGCAAATCGCAACGACAAAATCG
*
1070534 CAATGCGAAATG-AAATTGCAACGAC-AAATCG
1 CAATGCGAAATGCAAATCGCAACGACAAAATCG
**
1070565 CAATGCGAAACACAAATCGCA
1 CAATGCGAAATGCAAATCGCA
1070586 TTGCGACTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
31 16 0.21
32 19 0.24
33 43 0.55
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.13
Consensus pattern (33 bp):
CAATGCGAAATGCAAATCGCAACGACAAAATCG
Found at i:1070522 original size:19 final size:19
Alignment explanation
Indices: 1070494--1070548 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
1070484 TCGCAACGAC
*
1070494 AAAATAGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
1070513 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
1070527 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
1070546 AAA
1 AAA
1070549 TTGCAACGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 10
0.68 0.07 0.24
Matches are distributed among these distances:
14 10 0.36
15 1 0.04
16 2 0.07
17 2 0.07
18 1 0.04
19 12 0.43
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.13
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:1070532 original size:14 final size:14
Alignment explanation
Indices: 1070481--1070567 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
1070471 TGCGAAATGC
1070481 AAATCGCAACGACA
1 AAATCGCAACGACA
* *
1070495 AAATAGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
1070514 AAATCGCAACGACA
1 AAATCGCAACGACA
*
1070528 AAATCGCAATGCGAAA
1 AAATCGCAA--CGACA
*
1070544 TGAAATTGCAACGAC-
1 --AAATCGCAACGACA
1070559 AAATCGCAA
1 AAATCGCAA
1070568 TGCGAAACAC
Statistics
Matches: 56, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
13 8 0.14
14 18 0.32
15 1 0.02
16 9 0.16
17 2 0.04
18 9 0.16
19 9 0.16
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:1070641 original size:19 final size:19
Alignment explanation
Indices: 1070581--1070664 Score: 70
Period size: 19 Copynumber: 4.6 Consensus size: 19
1070571 GAAACACAAA
*
1070581 TCGCATTGCGACTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1070600 TTGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1070616 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
***
1070633 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATTTTCATT
1070652 TCCGCATTGCGAT
1 T-CGCATTGCGAT
1070665 AGTCATTTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 3 0.06
17 4 0.08
18 3 0.06
19 22 0.42
20 11 0.21
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1070659 original size:20 final size:19
Alignment explanation
Indices: 1070629--1070672 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
1070619 TTGCGATTTT
1070629 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
*
1070648 CATTTCCGCATTGCGATAGT
1 CATTT-CGCATTGCGATAGC
1070668 CATTT
1 CATTT
1070673 TCATGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:1071191 original size:18 final size:18
Alignment explanation
Indices: 1071165--1071209 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1071155 GTCGATCAGA
*
1071165 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1071183 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1071201 TGATGGCTC
1 TGATGGCTC
1071210 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1072554 original size:20 final size:20
Alignment explanation
Indices: 1072529--1072566 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1072519 AATAGTTTCT
1072529 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1072549 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1072567 GCAAATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1072877 original size:22 final size:22
Alignment explanation
Indices: 1072850--1072893 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1072840 GATGGAGATA
1072850 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1072872 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1072894 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1073167 original size:20 final size:20
Alignment explanation
Indices: 1073061--1073191 Score: 113
Period size: 20 Copynumber: 6.5 Consensus size: 20
1073051 CGCTTTGAAA
*
1073061 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1073082 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
1073102 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1073122 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1073143 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
1073163 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1073183 ATCGCATTG
1 ATCGCATTG
1073192 AGATTTTCCC
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 62 0.67
21 23 0.25
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1073197 original size:61 final size:61
Alignment explanation
Indices: 1073061--1073198 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
1073051 CGCTTTGAAA
* * * *
1073061 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
1073122 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
*
1073183 ATCGCATTGAGATTTT
1 ATCGCATTGCGATTTT
1073199 CCCAATTCGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:1073214 original size:61 final size:61
Alignment explanation
Indices: 1073081--1073216 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 61
1073071 GATTATGTAT
* * * * * * ** *
1073081 TATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGAGATTTTCCAA
* * *
1073142 TATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGAGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGAGATTTT-CCAA
1073204 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
1073217 TTACTTATTC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
TATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGAGATTTTCCAA
Found at i:1077840 original size:39 final size:39
Alignment explanation
Indices: 1077796--1077914 Score: 220
Period size: 39 Copynumber: 3.1 Consensus size: 39
1077786 TTGACAGAAA
1077796 CTGCATTCTGTTCAACAGTCGGTTGCATGTCATCACCTG
1 CTGCATTCTGTTCAACAGTCGGTTGCATGTCATCACCTG
1077835 CTGCATTCTGTTCAACAGTCGGTTGCATGTCATCACCTG
1 CTGCATTCTGTTCAACAGTCGGTTGCATGTCATCACCTG
* *
1077874 CTGCATTCTGTTCAACAGTCGGTTGCATGTTATCATCTG
1 CTGCATTCTGTTCAACAGTCGGTTGCATGTCATCACCTG
1077913 CT
1 CT
1077915 ACACCTTTAG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (39 bp):
CTGCATTCTGTTCAACAGTCGGTTGCATGTCATCACCTG
Found at i:1084256 original size:16 final size:16
Alignment explanation
Indices: 1084223--1084256 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1084213 TTACTATTCA
*
1084223 CGTGAATAGTAAATTT
1 CGTGAATAGTAAACTT
*
1084239 CGTGAATAGTGAACTT
1 CGTGAATAGTAAACTT
1084255 CG
1 CG
1084257 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTAAACTT
Done.