Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 31
Found at i:5590766 original size:200 final size:199
Alignment explanation
Indices: 5590366--5591060 Score: 829
Period size: 200 Copynumber: 3.5 Consensus size: 199
5590356 ACCTAAATAT
5590366 GTGTCGATACATTT-TCTAAAAGTATCGA-CCCAAAAAACATCGAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCCAAAAAACATCGAAACCAATAATTATAATGTAA
* * * * * * *
5590429 TAGGTAAATTAACAAGGTAACCGATATAAATATATC-AGTTAATTAGAAAACAGGTCAACATAAT
65 TAGGTAAATTTACAATGTAACCGATATAAATATACCAATTTTATGAGAAAATAGGTC-ACATAA-
* ** * * *
5590493 A-TATCTACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGAATGAAATCCCAAATGAGGTGC
128 AGTATCGACACTTGTTAAATTTGTGTCGATACTT-TTGTTCAGAATG-AATGCCAAACGAGGTGC
*
5590557 ACACATAAA
191 ACGCATAAA
* *
5590566 GTGTCGATACATTTATTAAAAGTATCGATCCCAATAAA-ATCGAAACCGATAATTATAATGTAAT
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAAACATCGAAACCAATAATTATAATGTAAT
* * *
5590630 ATGTAAATTTACAATGTAACTGGTATAAATATACCAATTTTATGAGAAAAATAGGTCAGCATAAA
66 AGGTAAATTTACAATGTAACCGATATAAATATACCAATTTTATGAG-AAAATAGGTCA-CATAAA
* * *
5590695 GAATCGAAACTTGTTAAATTTGTGTCGATACATTTTGTTCATAATGAATGCCAAACGA-GTGCAC
129 GTATCGACACTTGTTAAATTTGTGTCGATAC-TTTTGTTCAGAATGAATGCCAAACGAGGTGCAC
5590759 GCATAAA
193 GCATAAA
* * * *
5590766 GTGTCGATAAATTTATCAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTGAT
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAAACATCGAAACCAATAATTATAATGTAAT
* * * ** * *
5590830 AGGTAAATTTACAATGTACCCGATAGAAATATACCAGTTTTATGAGAAAATAAATCTAAATAATG
66 AGGTAAATTTACAATGTAACCGATATAAATATACCAATTTTATGAGAAAATAGGTC-ACATAAAG
* * *
5590895 TATCGACACTTTTTAAGTTTGTGTCGATACTTTT-TTCCAGAATGAATGTCC-AACGAGGTGCAT
130 TATCGACACTTGTTAAATTTGTGTCGATACTTTTGTT-CAGAATGAATG-CCAAACGAGGTGCAC
5590958 GCATAAA
193 GCATAAA
** *
5590965 GTGTCGATACATTTCA--AATTGTATTGAT-CCAAAAAACATCGAAACCAATAATTATAATGTAA
1 GTGTCGATACATTT-ATTAAAAGTATCGATCCCAAAAAACATCGAAACCAATAATTATAATGTAA
* *
5591027 TAGGTAAATTTACAATGTTACCGGTATAAATATA
65 TAGGTAAATTTACAATGTAACCGATATAAATATA
5591061 TCGGTTTACT
Statistics
Matches: 429, Mismatches: 52, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
197 4 0.01
198 87 0.20
199 70 0.16
200 189 0.44
201 28 0.07
202 49 0.11
203 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (199 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAAACATCGAAACCAATAATTATAATGTAAT
AGGTAAATTTACAATGTAACCGATATAAATATACCAATTTTATGAGAAAATAGGTCACATAAAGT
ATCGACACTTGTTAAATTTGTGTCGATACTTTTGTTCAGAATGAATGCCAAACGAGGTGCACGCA
TAAA
Found at i:5591188 original size:63 final size:63
Alignment explanation
Indices: 5591095--5591221 Score: 184
Period size: 64 Copynumber: 2.0 Consensus size: 63
5591085 ATATAAGCGC
* * *
5591095 TACCTATTACATTATAAAGCGCTGCCTAATATGTTA-TGTATTTGATAATATTTATGGTTAAA
1 TACCTATTACATTATAAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTACGGTTAAA
** *
5591157 TACCTATTTTATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAA
1 TACCTATTACATTATA-AAGCGCTACCTAATATGTTATTGTACTTGATAATATTTACGGTTAAA
5591221 T
1 T
5591222 GATATTACAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
62 14 0.25
63 19 0.33
64 24 0.42
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (63 bp):
TACCTATTACATTATAAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTACGGTTAAA
Found at i:5593401 original size:19 final size:17
Alignment explanation
Indices: 5593360--5593402 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
5593350 TGCCATGAAA
5593360 GGATATATTAACTTCAT
1 GGATATATTAACTTCAT
5593377 GGATATATTAACTTCAT
1 GGATATATTAACTTCAT
5593394 GGATATATT
1 GGATATATT
5593403 CAAAGTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (17 bp):
GGATATATTAACTTCAT
Found at i:5596461 original size:21 final size:21
Alignment explanation
Indices: 5596437--5596489 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5596427 ATTCTGACTA
5596437 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
5596458 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
5596479 TCGCAATGCGA
1 TCGCATTGCGA
5596490 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:5596504 original size:20 final size:20
Alignment explanation
Indices: 5596479--5596543 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
5596469 TTTTCCTAAT
*
5596479 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
** *
5596499 TCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGAA-TACGTAAA
5596520 TCGCAACGCGAATACGT-AA
1 TCGCAACGCGAATACGTAAA
5596539 TCGCA
1 TCGCA
5596544 TTGCGTTTTA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 7 0.19
20 13 0.35
21 17 0.46
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:5597449 original size:24 final size:24
Alignment explanation
Indices: 5597422--5597475 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
5597412 GTATTCAAAA
5597422 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
5597446 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
5597470 TTTGAT
1 TTTGAT
5597476 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:5600003 original size:20 final size:19
Alignment explanation
Indices: 5599975--5600029 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
5599965 CAATCATCTT
*
5599975 AATGTCTATCGCAACGCGAA
1 AATGACTATCGCAACGCG-A
*
5599995 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
5600014 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
5600030 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:5600039 original size:14 final size:14
Alignment explanation
Indices: 5600020--5600071 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
5600010 GCGAAATGAA
5600020 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
5600034 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
5600053 AATCGCAACGAGAG
1 AATCGCAACGAGAG
5600067 AATCG
1 AATCG
5600072 TAATGCGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 15 0.48
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.32
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:5600044 original size:33 final size:33
Alignment explanation
Indices: 5600002--5600128 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
5599992 GAAAATGACT
5600002 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
5600035 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
5600068 ATCGTAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
5600101 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
5600129 TGAATTTAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:5600058 original size:19 final size:18
Alignment explanation
Indices: 5599982--5600126 Score: 89
Period size: 19 Copynumber: 8.4 Consensus size: 18
5599972 CTTAATGTCT
**
5599982 ATCGCAACGCGAAAATGACT
1 ATCGCAA-GCG-AAATGAAA
5600002 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
5600021 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
5600035 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
5600054 ATCGCAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
*
5600068 ATCGTAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
**
5600087 ATCGCAA-CG--A-GGGA
1 ATCGCAAGCGAAATGAAA
5600101 ATCGCAAAGCGAAATGAAA
1 ATCGC-AAGCGAAATGAAA
5600120 ATCGCAA
1 ATCGCAA
5600127 CGTGAATTTA
Statistics
Matches: 97, Mismatches: 13, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
14 26 0.27
15 5 0.05
16 6 0.06
17 6 0.06
18 5 0.05
19 39 0.40
20 10 0.10
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:5600180 original size:33 final size:33
Alignment explanation
Indices: 5600138--5600217 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
5600128 GTGAATTTAG
* *
5600138 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
5600171 TTTCGCGTTGCGATTCTCTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
5600204 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
5600218 AGTAATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:5600181 original size:19 final size:19
Alignment explanation
Indices: 5600157--5600217 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
5600147 GCGATTTTGT
5600157 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
5600176 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
5600190 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
5600209 CATTGCGAT
1 CGTTGCGAT
5600218 AGTAATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
14 9 0.28
16 3 0.09
17 3 0.09
19 17 0.53
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:5600343 original size:14 final size:14
Alignment explanation
Indices: 5600324--5600360 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5600314 CATCAATTAA
5600324 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5600338 ACAAATCATCTTTT
1 ACAAATCAACTTTT
5600352 ACAAATCAA
1 ACAAATCAA
5600361 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:5602290 original size:14 final size:14
Alignment explanation
Indices: 5602268--5602369 Score: 87
Period size: 14 Copynumber: 6.6 Consensus size: 14
5602258 AACGCGAAAT
*
5602268 GAATAGCAACGAGA
1 GAATCGCAACGAGA
5602282 GAATCGCAACGAGA
1 GAATCGCAACGAGA
5602296 GAATCGCAACGCAAAATGA
1 GAATCGCAACG----A-GA
*
5602315 AAATCGCAACGAGA
1 GAATCGCAACGAGA
*
5602329 GAATCGCAACGCGAAA
1 GAATCGCAA--CGAGA
*
5602345 TGAAAACGCAACGAGA
1 -G-AATCGCAACGAGA
5602361 GAATCGCAA
1 GAATCGCAA
5602370 TGCGAAATGA
Statistics
Matches: 72, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
14 41 0.57
15 2 0.03
16 8 0.11
17 1 0.01
18 8 0.11
19 12 0.17
ACGTcount: A:0.47, C:0.21, G:0.25, T:0.08
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:5602360 original size:32 final size:33
Alignment explanation
Indices: 5602283--5602390 Score: 191
Period size: 33 Copynumber: 3.3 Consensus size: 33
5602273 GCAACGAGAG
*
5602283 AATCGCAACGAGAGAATCGCAACGCAAAATGAA
1 AATCGCAACGAGAGAATCGCAACGCGAAATGAA
5602316 AATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAACGCGAAATGAA
*
5602349 AA-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAACGCGAAATGAA
5602381 AATCGCAACG
1 AATCGCAACG
5602391 TAATTATAGT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
32 31 0.43
33 41 0.57
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.09
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAACGCGAAATGAA
Found at i:5602727 original size:94 final size:93
Alignment explanation
Indices: 5602557--5602841 Score: 455
Period size: 94 Copynumber: 3.1 Consensus size: 93
5602547 ATGGATTGCA
* *
5602557 TTACTTCAA-CAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
* *
5602621 TAACAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAATAAAT
5602649 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
5602714 TTAGCAGAATTGGCAGCAATCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAATAAAT
* *
5602743 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAATAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
5602808 TTAGCAGTATTGACAGTAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAATAAAT
5602837 TTACT
1 TTACT
5602842 AAGCAATCTA
Statistics
Matches: 179, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
92 4 0.02
93 24 0.13
94 151 0.84
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAATAAAT
Found at i:5604571 original size:40 final size:38
Alignment explanation
Indices: 5604527--5604639 Score: 130
Period size: 33 Copynumber: 3.1 Consensus size: 38
5604517 TCTTTTGGTT
5604527 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACG-GAGAATGAAAATCGCAACGC
**
5604566 GGAAATGACTATCGCAAC-GAG-A-G--AATCGCAACGC
1 -GAAATGAAAATCGCAACGGAGAATGAAAATCGCAACGC
*
5604600 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACG-GAGAATGAAAATCGCAACGC
5604638 GA
1 GA
5604640 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
33 15 0.24
34 11 0.18
35 3 0.05
36 2 0.03
37 1 0.02
38 15 0.24
40 15 0.24
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGGAGAATGAAAATCGCAACGC
Found at i:5604613 original size:19 final size:19
Alignment explanation
Indices: 5604527--5604639 Score: 128
Period size: 19 Copynumber: 6.1 Consensus size: 19
5604517 TCTTTTGGTT
*
5604527 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
5604546 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
5604566 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
5604584 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
5604600 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
5604619 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
5604638 GA
1 GA
5604640 TTTTGGTTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.03
17 1 0.01
18 2 0.03
19 35 0.44
20 28 0.35
21 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:5604698 original size:20 final size:20
Alignment explanation
Indices: 5604673--5604716 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
5604663 CATTTCTCTC
*
5604673 GTTGTGATAGTCATTTTCGT
1 GTTGTGATAGTCATTTTCAT
5604693 GTTGTGATAGTCATTTTCAT
1 GTTGTGATAGTCATTTTCAT
5604713 GTTG
1 GTTG
5604717 CGATTTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.09, G:0.25, T:0.50
Consensus pattern (20 bp):
GTTGTGATAGTCATTTTCAT
Found at i:5624651 original size:20 final size:20
Alignment explanation
Indices: 5624626--5624669 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5624616 AAAAAAAGGA
*
5624626 GAATGGCAACATGGACGGGT
1 GAATGGCAACATGGACGGCT
*
5624646 GAATGGCAACATGGGCGGCT
1 GAATGGCAACATGGACGGCT
5624666 GAAT
1 GAAT
5624670 TTTGTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.16, G:0.39, T:0.16
Consensus pattern (20 bp):
GAATGGCAACATGGACGGCT
Found at i:5628708 original size:15 final size:14
Alignment explanation
Indices: 5628686--5628715 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5628676 TTACAAGTTA
5628686 TTTTATAATTAATT
1 TTTTATAATTAATT
5628700 TTTTAATAATTAATT
1 TTTT-ATAATTAATT
5628715 T
1 T
5628716 AAATATATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTATAATTAATT
Found at i:5633527 original size:34 final size:36
Alignment explanation
Indices: 5633463--5633556 Score: 122
Period size: 34 Copynumber: 2.6 Consensus size: 36
5633453 TAATAATATA
*
5633463 AAAAATATTTTCCCAAACTTATATAATATATACTTT-T
1 AAAAATATTTT--CAAAATTATATAATATATACTTTCT
*
5633500 AAAAATATTTT-AAAATTATATATTATATACTTTCT
1 AAAAATATTTTCAAAATTATATAATATATACTTTCT
*
5633535 -AAAATGTTTTCAAAATTATATA
1 AAAAATATTTTCAAAATTATATA
5633557 GTTTTTAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
34 29 0.56
35 12 0.23
37 11 0.21
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.45
Consensus pattern (36 bp):
AAAAATATTTTCAAAATTATATAATATATACTTTCT
Found at i:5633637 original size:37 final size:38
Alignment explanation
Indices: 5633581--5633905 Score: 139
Period size: 37 Copynumber: 9.0 Consensus size: 38
5633571 TTTTTAAAAC
*
5633581 TATATATATTTTTCAAAATG-ATTTCAAAAACTATATA
1 TATATTTATTTTTCAAAATGTATTTCAAAAACTATATA
* *
5633618 TATATTTATGTTTTC-AAATGTTTTTTAAAAAC----TA
1 TATATTTAT-TTTTCAAAATGTATTTCAAAAACTATATA
*
5633652 TATA--TATTTTT-AAAATGT-TTTAAAAA-CTATATAA
1 TATATTTATTTTTCAAAATGTATTTCAAAAACTATAT-A
* * * * *
5633686 CATGTAT-TTT--CAAAA-ATATTTTAAAAACTATATA
1 TATATTTATTTTTCAAAATGTATTTCAAAAACTATATA
* * *
5633720 T-TATATAATTTTCAAAATGT-TTTTAAAAACTATATA
1 TATATTTATTTTTCAAAATGTATTTCAAAAACTATATA
* * *
5633756 -ATATATATATTTTCAAAAATGT-TTT-GAAAACCATATA
1 TATATTTAT-TTTTC-AAAATGTATTTCAAAAACTATATA
* * *
5633793 T-TATATTAATTTTCAAAATGT-CTT-AAGAACTATATAA
1 TATAT-TTATTTTTCAAAATGTATTTCAAAAACTATAT-A
** *
5633830 TATATAAATGTTTTCAAACATGCT-TTTC-AAAATTATATA
1 TATATTTAT-TTTTCAAA-ATG-TATTTCAAAAACTATATA
* * *
5633869 TTATATATATATATTAAAAATGT-TTTC--AAACTATATA
1 -TATATTTAT-TTTTCAAAATGTATTTCAAAAACTATATA
5633906 CTGTATATAT
Statistics
Matches: 227, Mismatches: 32, Indels: 58
0.72 0.10 0.18
Matches are distributed among these distances:
29 1 0.00
30 7 0.03
31 10 0.04
32 3 0.01
33 6 0.03
34 23 0.10
35 9 0.04
36 45 0.20
37 49 0.22
38 42 0.19
39 7 0.03
40 25 0.11
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (38 bp):
TATATTTATTTTTCAAAATGTATTTCAAAAACTATATA
Found at i:5633748 original size:100 final size:102
Alignment explanation
Indices: 5633477--5633755 Score: 307
Period size: 100 Copynumber: 2.8 Consensus size: 102
5633467 ATATTTTCCC
* *
5633477 AAACTTATATAATATATACTTTT-AAAAATATTTT-AAAATTATATATTATAT-ACTTTCTAAAA
1 AAAC-TATATAA-ATATA-TTTTCAAAAATATTTTAAAAACTATATATTATATAATTTTC-AAAA
* *
5633539 TG-TTTTCAAAA-T-TATATAGTTTTTAAAAATGTTTTTTA
62 TGTTTTTAAAAACTATATATAGTTTTTAAAAATGTTTTTAA
* * *
5633577 AAACTATAT--ATAT-TTTTC-AAAATGATTTCAAAAACTATATATATATTTATGTTTTC-AAAT
1 AAACTATATAAATATATTTTCAAAAAT-ATTTTAAAAACTATATAT-TATATA-ATTTTCAAAAT
5633637 GTTTTTTAAAAACTATATATA-TTTTT-AAAATG-TTTTAA
63 G-TTTTTAAAAACTATATATAGTTTTTAAAAATGTTTTTAA
*
5633675 AAACTATATAACATGTATTTTCAAAAATATTTTAAAAACTATATATTATATAATTTTCAAAATGT
1 AAACTATATAA-ATATATTTTCAAAAATATTTTAAAAACTATATATTATATAATTTTCAAAATGT
5633740 TTTTAAAAACTATATA
65 TTTTAAAAACTATATA
5633756 ATATATATAT
Statistics
Matches: 152, Mismatches: 11, Indels: 32
0.78 0.06 0.16
Matches are distributed among these distances:
94 9 0.06
95 4 0.03
96 15 0.10
97 9 0.06
98 14 0.09
99 23 0.15
100 32 0.21
101 19 0.12
102 22 0.14
103 5 0.03
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (102 bp):
AAACTATATAAATATATTTTCAAAAATATTTTAAAAACTATATATTATATAATTTTCAAAATGTT
TTTAAAAACTATATATAGTTTTTAAAAATGTTTTTAA
Found at i:5633775 original size:38 final size:36
Alignment explanation
Indices: 5633581--5633915 Score: 264
Period size: 36 Copynumber: 9.2 Consensus size: 36
5633571 TTTTTAAAAC
*
5633581 TATATATATTTTTCAAAATGATTTCAAAAACTATATATA
1 TATATATA-TTTTCAAAATG-TTTTAAAAACTATATA-A
* *
5633620 TATTTATGTTTTC-AAATGTTTTTTAAAAAC----T-A
1 TATATATATTTTCAAAATG--TTTTAAAAACTATATAA
5633652 TATATAT-TTTT-AAAATGTTTTAAAAACTATAT-A
1 TATATATATTTTCAAAATGTTTTAAAAACTATATAA
* * * *
5633685 -ACATGTATTTTCAAAAATATTTTAAAAACTATATAT
1 TATATATATTTTC-AAAATGTTTTAAAAACTATATAA
5633721 TATATA-ATTTTCAAAATGTTTTTAAAAACTATATAA
1 TATATATATTTTCAAAATG-TTTTAAAAACTATATAA
* * *
5633757 TATATATATTTTCAAAAATGTTTTGAAAACCATATAT
1 TATATATATTTTC-AAAATGTTTTAAAAACTATATAA
* *
5633794 TATAT-TAATTTTCAAAATGTCTTAAGAACTATATAA
1 TATATAT-ATTTTCAAAATGTTTTAAAAACTATATAA
* * *
5633830 TATATAAATGTTTTCAAACATGCTTTTCAAAATTATATATTA
1 TATAT--ATATTTTCAAA-ATG-TTTTAAAAACTATATA--A
* * * *
5633872 TATATATATATTAAAAATGTTTT-CAAACTATATAC
1 TATATATATTTTCAAAATGTTTTAAAAACTATATAA
*
5633907 TGTATATAT
1 TATATATAT
5633916 ATATATATAT
Statistics
Matches: 241, Mismatches: 33, Indels: 48
0.75 0.10 0.15
Matches are distributed among these distances:
29 10 0.04
31 9 0.04
32 11 0.05
33 6 0.02
34 1 0.00
35 33 0.14
36 52 0.22
37 48 0.20
38 32 0.13
39 13 0.05
40 20 0.08
42 6 0.02
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATATATTTTCAAAATGTTTTAAAAACTATATAA
Found at i:5634679 original size:84 final size:84
Alignment explanation
Indices: 5634555--5635338 Score: 765
Period size: 84 Copynumber: 9.4 Consensus size: 84
5634545 AAGGTCTTTA
* * *
5634555 GCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTAAGCGGAGTCGA
1 GCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
*
5634620 ACTCGAAGGTCTTTTGGTC
66 ACTCGAAGGTCTTTTGGTG
* * * * * *
5634639 ACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCGTT-GAGCTGAGCGTAGTCG
1 GCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCG
** *
5634703 AACTTAAAGGTCTTTTGTTG
65 AACTCGAAGGTCTTTTGGTG
* * * *
5634723 GCAGACAACCCTTCTAGACTTAAGCTGTGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* *
5634788 ACTCGAAGGTCTCTGGGTG
66 ACTCGAAGGTCTTTTGGTG
* * * * * * * * *
5634807 GTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAATGTGCCCTCGAAGCTGAGTGTAATTG
1 GCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCG
**
5634872 AACTCGGGGGTC--TT--TG
65 AACTCGAAGGTCTTTTGGTG
* * * *
5634888 GCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGATCGTAGTCG
1 GCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCG
* *
5634952 AACTCAAAGGTCTTTTGTTG
65 AACTCGAAGGTCTTTTGGTG
* * * * *
5634972 GCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
5635037 ACTCGAAGGTC-TTTGGTTG
66 ACTCGAAGGTCTTTTGG-TG
* * * * *
5635056 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCG
**
5635121 AACTCGGGGGTC--TT--TG
65 AACTCGAAGGTCTTTTGGTG
* * * *
5635137 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTT-GAGCTGATCGTAGTCG
1 GCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCG
* * *
5635201 AACTCAAAGGTATTTTGGTC
65 AACTCGAAGGTCTTTTGGTG
* * * * * * * * *
5635221 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCG
*
5635286 AACTC-AGGGGTC--TT--TG
65 AACTCGA-AGGTCTTTTGGTG
* * *
5635302 GCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAAT
1 GCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAAT
5635339 AGTTTGTTTA
Statistics
Matches: 568, Mismatches: 115, Indels: 37
0.79 0.16 0.05
Matches are distributed among these distances:
80 42 0.07
81 119 0.21
82 4 0.01
83 11 0.02
84 317 0.56
85 75 0.13
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (84 bp):
GCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
ACTCGAAGGTCTTTTGGTG
Found at i:5635008 original size:249 final size:247
Alignment explanation
Indices: 5634536--5635339 Score: 1053
Period size: 249 Copynumber: 3.2 Consensus size: 247
5634526 TTTAATATAA
* * * *
5634536 TCGAACTCAAAGGTCTT--TAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-
1 TCGAACTCGAAGGTCTTGGTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGC
* * * * * * ** * * * *
5634598 CCTTGGAGCTAAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAG
* * * * *
5634663 TTATGTTGTAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTTAAAGGTCTTTTGTTGGCAGA
127 CTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGA
* *
5634728 CAACCCTTCTAGACTTAAGCTGTGTTGCAAATGATATGCCTTGGAGCTGAGCGTAG
192 CAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
* *
5634784 TCGAACTCGAAGGTCTCTGGGTGGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATAATGT
1 TCGAACTCGAAGGTCT-T-GGTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATGT
*
5634849 GCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
64 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
*
5634914 ATACTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACA
129 ATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACA
*
5634979 ACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
194 ACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
*
5635033 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTC-TTGG-TGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATGT
5635098 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
64 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
* * * ** *
5635163 ATGCTGCAAATGATGTGTCGTTGAGCTGATCGTAGTCGAACTCAAAGGTATTTTGGTCACAGATA
129 ATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACA
* * * * * * * * *
5635228 ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
194 ACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
* * *
5635283 TCGAACTC-AGGGGTCTT--TGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATA
1 TCGAACTCGA-AGGTCTTGGTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATA
5635340 GTTTGTTTAA
Statistics
Matches: 494, Mismatches: 53, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
246 37 0.07
248 17 0.03
249 344 0.70
250 27 0.05
252 45 0.09
253 24 0.05
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (247 bp):
TCGAACTCGAAGGTCTTGGTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGC
CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
GCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAAC
CCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
Found at i:5635202 original size:165 final size:165
Alignment explanation
Indices: 5634536--5635338 Score: 799
Period size: 165 Copynumber: 4.9 Consensus size: 165
5634526 TTTAATATAA
* *
5634536 TCGAACTCAAAGGTC--T--TTAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
* * * * * * *
5634597 G-CCTTGGAGCTAAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTG
66 GCCCTTGAAGCTGAGTGTAGTCGAACTCGAAGGTC-TTTGG---CAGATAACCCTTCTCGACTTA
* * *
5634661 AGTTATGTTGTAAATGATGTGCCGTTGAGCTGAGCGTAG
127 AGTTATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAG
* * * * * *
5634700 TCGAACTTAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGCTGTGTTGCAAATGATAT
1 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
* * *
5634765 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTCTGGGTGGTAGATAACCCTTCTCGACTTA
66 GCCCTTGAAGCTGAGTGTAGTCGAACTCGAAGGTCT-T---TGGCAGATAACCCTTCTCGACTTA
* * * *
5634829 AGTTATGCTGCAAATAATGTGCCCTCGAAGCTGAGTGTAA
127 AGTTATGCTGCAAATGATGTGCCCTTG-AGCTGAGCGTAG
* *** * * *
5634869 TTGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGT
1 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
* * * * *
5634930 GCCGTTG-AGCTGA-TCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTGTAGACTT
66 GCCCTTGAAGCTGAGT-GTAGTCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTCGACTT
* *
5634993 AAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
126 AAGTTATGCTGCAAATGATGTGCCCTT-GAGCTGAGCGTAG
* *
5635033 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
* * ** * *
5635098 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCT
66 GCCCTTGAAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTT
* * *
5635163 ATGCTGCAAATGATGTGTCGTTGAGCTGATCGTAG
131 ATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAG
* ** * * * *
5635198 TCGAACTCAAAGGTATTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCAAAGGT-CTTTGGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATG
* * * *
5635262 TGCCCTCGAAGCTGAGTGTAATCGAACTC-AGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAG
65 TGCCCTTGAAGCTGAGTGTAGTCGAACTCGA-AGGTCTTTGGCAGATAACCCTTCTCGACTTAAG
5635326 TTATGCTGCAAAT
129 TTATGCTGCAAAT
5635339 AGTTTGTTTA
Statistics
Matches: 538, Mismatches: 77, Indels: 47
0.81 0.12 0.07
Matches are distributed among these distances:
164 39 0.07
165 276 0.51
166 15 0.03
167 2 0.00
168 161 0.30
169 41 0.08
170 1 0.00
171 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
TCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
GCCCTTGAAGCTGAGTGTAGTCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGTT
ATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAG
Found at i:5640089 original size:12 final size:12
Alignment explanation
Indices: 5640072--5640098 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5640062 TTATTTGAGA
5640072 AAATTGAAATTT
1 AAATTGAAATTT
5640084 AAATTGAAATTT
1 AAATTGAAATTT
5640096 AAA
1 AAA
5640099 AATTCGGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (12 bp):
AAATTGAAATTT
Found at i:5640475 original size:2 final size:2
Alignment explanation
Indices: 5640468--5640533 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
5640458 AATTCGGAAA
5640468 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
5640510 AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5640534 GGACTAAAAC
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5641829 original size:100 final size:99
Alignment explanation
Indices: 5641683--5641967 Score: 267
Period size: 100 Copynumber: 2.8 Consensus size: 99
5641673 ATATTTTCCC
* * * *
5641683 AAAACTTATATAATATATACTTTT-AAAAATATTT-TAAAATTATATATTATATACT-TTCTAAA
1 AAAAC-TATATAACATATA-TTTTCAAAAATATTTCAAAAACTATATAATATAT-CTGTTCTAAA
* * *
5641745 AATG-TTTTCAAAATTATATAGTTTTTTAAAAATGTTTTTT
63 AATGTTTTTAAAAACTATATA--TTTTT-AAAATG-TTTTA
** * * * *
5641785 AAAACTATATATTATATGTTTTC-AAAATGATTTCAAAAACTATATAATATATTTGTTTTCAAAA
1 AAAACTATATAACATATATTTTCAAAAAT-ATTTCAAAAACTATATAATATATCTGTTCTAAAAA
5641849 TGTTTTTTAAAAACTATATATTTTTAAAATGTTTTA
65 TG-TTTTTAAAAACTATATATTTTTAAAATGTTTTA
* * * * * *
5641885 AAAACTATATAACATGTATTTTCAAAAATATTTTAAAAACTATATATTATAT-TAATTTTCAAAA
1 AAAACTATATAACATATATTTTCAAAAATATTTCAAAAACTATATAATATATCT-GTTCTAAAAA
5641949 TGTTTTTAAAAACTATATA
65 TGTTTTTAAAAACTATATA
5641968 ATATATATAT
Statistics
Matches: 157, Mismatches: 18, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
99 18 0.11
100 64 0.41
101 27 0.17
102 34 0.22
104 14 0.09
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (99 bp):
AAAACTATATAACATATATTTTCAAAAATATTTCAAAAACTATATAATATATCTGTTCTAAAAAT
GTTTTTAAAAACTATATATTTTTAAAATGTTTTA
Found at i:5641842 original size:37 final size:36
Alignment explanation
Indices: 5641759--5642125 Score: 276
Period size: 37 Copynumber: 10.2 Consensus size: 36
5641749 TTTTCAAAAT
* * *
5641759 TATATAGTTTTTTAAAAATGTTTTTTAAAACTATAT-A
1 TATATA-TATTTTCAAAATG-TTTTAAAAACTATATAA
* *
5641796 T-TATATGTTTTCAAAATGATTTCAAAAACTATATAA
1 TATATATATTTTCAAAATG-TTTTAAAAACTATATAA
* * ** *
5641832 TATATTTGTTTTCAAAATGTTTT-TTAA--A-A-AC
1 TATATATATTTTCAAAATGTTTTAAAAACTATATAA
5641863 TATATAT-TTTT-AAAATGTTTTAAAAACTATAT-A
1 TATATATATTTTCAAAATGTTTTAAAAACTATATAA
* * * *
5641896 -ACATGTATTTTCAAAAATATTTTAAAAACTATATAT
1 TATATATATTTTC-AAAATGTTTTAAAAACTATATAA
5641932 TATAT-TAATTTTCAAAATGTTTTTAAAAACTATATAA
1 TATATAT-ATTTTCAAAATG-TTTTAAAAACTATATAA
* * *
5641969 TATATATATTTTCAAAAATGTTTTGAAAACCATATAT
1 TATATATATTTTC-AAAATGTTTTAAAAACTATATAA
* *
5642006 TATAT-TAATTTTCAAAATGTCTTAAGAACTATATAA
1 TATATAT-ATTTTCAAAATGTTTTAAAAACTATATAA
* * * *
5642042 TATATAAATGTTTTCAAACATGCTTTTCAAAATTATATAT
1 TATAT--ATATTTTCAAA-ATG-TTTTAAAAACTATATAA
* * * *
5642082 TATATATATATTAAAAATGTTTT-CAAACTATATAC
1 TATATATATTTTCAAAATGTTTTAAAAACTATATAA
*
5642117 TGTATATAT
1 TATATATAT
5642126 ATATATATAT
Statistics
Matches: 266, Mismatches: 42, Indels: 46
0.75 0.12 0.13
Matches are distributed among these distances:
29 10 0.04
30 6 0.02
31 7 0.03
32 6 0.02
33 6 0.02
35 63 0.24
36 43 0.16
37 81 0.30
38 23 0.09
39 4 0.02
40 17 0.06
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.46
Consensus pattern (36 bp):
TATATATATTTTCAAAATGTTTTAAAAACTATATAA
Found at i:5641877 original size:29 final size:27
Alignment explanation
Indices: 5641840--5641895 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
5641830 AATATATTTG
5641840 TTTTCAAAATGTTTTTTAAAAACTATATA
1 TTTTCAAAATG--TTTTAAAAACTATATA
*
5641869 TTTTTAAAATGTTTTAAAAACTATATA
1 TTTTCAAAATGTTTTAAAAACTATATA
5641896 ACATGTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 16 0.62
29 10 0.38
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (27 bp):
TTTTCAAAATGTTTTAAAAACTATATA
Found at i:5642114 original size:35 final size:35
Alignment explanation
Indices: 5641683--5642127 Score: 273
Period size: 37 Copynumber: 12.6 Consensus size: 35
5641673 ATATTTTCCC
* *
5641683 AAAACT-TATATAATATATACTTTTAAAAATATTTT
1 AAAACTATATATTATATATA-TTTTAAAAATGTTTT
* *
5641718 AAAATTATATATTATATACT-TTCTAAAAATGTTTT
1 AAAACTATATATTATATA-TATTTTAAAAATGTTTT
*
5641753 CAAAA-T-TATA-TA-GT-T-TTTTAAAAATGTTTTTT
1 -AAAACTATATATTATATATATTTTAAAAATG--TTTT
* * *
5641785 AAAACTATATA-T-TATATGTTTTCAAAATGATTTCA
1 AAAACTATATATTATATATATTTTAAAAATG-TTT-T
* * * *
5641820 AAAACTATATAATATATTTGTTTTCAAAATGTTTT
1 AAAACTATATATTATATATATTTTAAAAATGTTTT
** *
5641855 TTAA--A-A-ACTATATAT-TTTT-AAAATGTTTT
1 AAAACTATATATTATATATATTTTAAAAATGTTTT
* * *
5641884 AAAAACTATATA--ACATGTATTTTCAAAAATATTTT
1 -AAAACTATATATTATATATATTTT-AAAAATGTTTT
*
5641919 AAAAACTATATATTATAT-TAATTTTCAAAATGTTTTT
1 -AAAACTATATATTATATAT-ATTTTAAAAATG-TTTT
*
5641956 AAAAACTATATAATATATATATTTTCAAAAATGTTTT
1 -AAAACTATATATTATATATATTTT-AAAAATGTTTT
* * *
5641993 GAAAACCATATATTATAT-TAATTTTCAAAATGTCTT
1 -AAAACTATATATTATATAT-ATTTTAAAAATGTTTT
* * *
5642029 AAGAACTATATAATATATAAATGTTTTCAAACATGCTTTT
1 AA-AACTATAT-AT-TATATATATTTT-AAAAATG-TTTT
* *
5642069 CAAAATTATATATTATATATATATTAAAAATGTTTT
1 -AAAACTATATATTATATATATTTTAAAAATGTTTT
*
5642105 CAAACTATATACTGTATATATAT
1 AAAACTATATA-T-TATATATAT
5642128 ATATATATAT
Statistics
Matches: 329, Mismatches: 44, Indels: 72
0.74 0.10 0.16
Matches are distributed among these distances:
29 10 0.03
30 17 0.05
31 11 0.03
32 12 0.04
33 14 0.04
34 9 0.03
35 74 0.22
36 46 0.14
37 92 0.28
38 24 0.07
39 8 0.02
40 10 0.03
41 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (35 bp):
AAAACTATATATTATATATATTTTAAAAATGTTTT
Found at i:5645936 original size:14 final size:14
Alignment explanation
Indices: 5645917--5645972 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
5645907 CGTTCGTGAA
5645917 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
5645931 CGTTCAGTTATGTT
1 CGTTCAGTTATGTT
5645945 CG-T---TTATGTT
1 CGTTCAGTTATGTT
* *
5645955 TGTTCGGTTATGTT
1 CGTTCAGTTATGTT
5645969 CGTT
1 CGTT
5645973 TATGTTCATT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
13 1 0.03
14 26 0.72
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCAGTTATGTT
Found at i:5645945 original size:24 final size:24
Alignment explanation
Indices: 5645924--5645992 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
5645914 GAACGTTCAG
5645924 TTATGTTCGTTCAGTTATGTTCGT
1 TTATGTTCGTTCAGTTATGTTCGT
* *
5645948 TTATGTTTGTTCGGTTATGTTCGT
1 TTATGTTCGTTCAGTTATGTTCGT
* *
5645972 TTATGTTCATTCATTTATGTT
1 TTATGTTCGTTCAGTTATGTT
5645993 TAAGCCAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.58
Consensus pattern (24 bp):
TTATGTTCGTTCAGTTATGTTCGT
Found at i:5646645 original size:16 final size:16
Alignment explanation
Indices: 5646624--5646690 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
5646614 AATGTTTATG
5646624 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
* *
5646640 TTTATGTTTGTGTTCT
1 TTTATGTTCGTGTTCA
* *
5646656 TTTATGTTTGTGTTCG
1 TTTATGTTCGTGTTCA
5646672 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
5646686 TTTAT
1 TTTAT
5646691 TAAATGAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 39 0.85
ACGTcount: A:0.10, C:0.07, G:0.18, T:0.64
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:5650186 original size:16 final size:16
Alignment explanation
Indices: 5650160--5650200 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
5650150 AAAAAAAAGC
5650160 TAAGATAAATAAATAAA
1 TAAGAT-AATAAATAAA
*
5650177 TAAGATAATAAATTAA
1 TAAGATAATAAATAAA
*
5650193 TAAAATAA
1 TAAGATAA
5650201 AAACAAACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (16 bp):
TAAGATAATAAATAAA
Found at i:5650448 original size:24 final size:23
Alignment explanation
Indices: 5650403--5650450 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
5650393 CCGAAAATAG
*
5650403 AAAAAGGGATACGAATTTAAAAA
1 AAAAAAGGATACGAATTTAAAAA
*
5650426 AAAAAAGGATAC-AGATTTGAAAA
1 AAAAAAGGATACGA-ATTTAAAAA
5650449 AA
1 AA
5650451 GGATAAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.62, C:0.04, G:0.17, T:0.17
Consensus pattern (23 bp):
AAAAAAGGATACGAATTTAAAAA
Found at i:5650463 original size:19 final size:19
Alignment explanation
Indices: 5650426--5650463 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5650416 AATTTAAAAA
*
5650426 AAAAAAGGATACAGATTTG
1 AAAAAAGGATAAAGATTTG
*
5650445 AAAAAAGGATAAAGGTTTG
1 AAAAAAGGATAAAGATTTG
5650464 GTCAGCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.21
Consensus pattern (19 bp):
AAAAAAGGATAAAGATTTG
Found at i:5650742 original size:30 final size:29
Alignment explanation
Indices: 5650703--5650760 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
5650693 AACGTATATA
5650703 AAAAGAATAGAAATAAAATATAAATAAAAG
1 AAAAGAATAGAAATAAAA-ATAAATAAAAG
* * *
5650733 AAAATAATAGTAATATAAATAAATAAAA
1 AAAAGAATAGAAATAAAAATAAATAAAA
5650761 TATTAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (29 bp):
AAAAGAATAGAAATAAAAATAAATAAAAG
Found at i:5651930 original size:13 final size:13
Alignment explanation
Indices: 5651911--5651949 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
5651901 AATAATATTG
5651911 ATATAATATATAT
1 ATATAATATATAT
*
5651924 ATGTAATATATAAT
1 ATATAATATAT-AT
5651938 ATATAA-ATATAT
1 ATATAATATATAT
5651950 GTTCTTTCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 2 0.09
13 14 0.61
14 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:5651932 original size:7 final size:7
Alignment explanation
Indices: 5651911--5651948 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
5651901 AATAATATTG
5651911 ATATAAT
1 ATATAAT
5651918 ATAT-AT
1 ATATAAT
*
5651924 ATGTAAT
1 ATATAAT
5651931 ATATAAT
1 ATATAAT
5651938 ATATAA-
1 ATATAAT
5651944 ATATA
1 ATATA
5651949 TGTTCTTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 10 0.36
7 18 0.64
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:5651947 original size:24 final size:24
Alignment explanation
Indices: 5651903--5651951 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5651893 TTTAAAATAA
* *
5651903 TAATATTGATATAATATATATATG
1 TAATATTAATATAATAAATATATG
5651927 TAATATATAATAT-ATAAATATATG
1 TAATAT-TAATATAATAAATATATG
5651951 T
1 T
5651952 TCTTTCGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TAATATTAATATAATAAATATATG
Found at i:5652200 original size:20 final size:20
Alignment explanation
Indices: 5652177--5652218 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5652167 GAATCCTTCG
5652177 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAGTTGAAATCGAAC
5652197 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAGTTGAAATCGAAC
5652217 TC
1 TC
5652219 AGAGTTCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (20 bp):
TCGTGAAGTTGAAATCGAAC
Found at i:5653045 original size:210 final size:209
Alignment explanation
Indices: 5652276--5653400 Score: 1675
Period size: 210 Copynumber: 5.5 Consensus size: 209
5652266 CGTTGTGAAG
*
5652276 CTGAGATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 CTGA-ATTGAGAAA-TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
5652341 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AA-----GTTGA
64 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGA
** * ** *
5652400 CAGTCAGCGGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGT
129 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGT
5652465 GAAGTTGAAATT-G--
194 GAAGTTGAAATTGGCT
*
5652478 --G----GA-AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 CTGAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
5652536 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AA-----GTTGACA
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
** * ** *
5652595 GTCAGCGGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGTGA
131 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
5652660 AGTTGAAATT-G--
196 AGTTGAAATTGGCT
* *
5652671 --G----GA-AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTT
1 CTGAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* * * *
5652729 TGGAGTCCAATATCCTTCATTCTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGGCA
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
*
5652794 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCATTCGTTGTGA
131 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
5652859 AGTTGAAATTGGCT
196 AGTTGAAATTGGCT
*
5652873 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAA-TTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* *
5652938 CTGGAGTCCAATATCCTTCGTTCTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGAC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAC
* *
5653003 AACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
130 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTG
5653068 AAGTTGAAATTGGCT
195 AAGTTGAAATTGGCT
*
5653083 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAA-TTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
5653148 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGAC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGAC
* * *
5653213 AACCAGTGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
130 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTG
5653278 AAGTTGAAATTGGCT
195 AAGTTGAAATTGGCT
* * *
5653293 CTGAAATTAAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAATTTGAACATGCGTTGT
1 CTG-AATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
5653358 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
5653401 GGTAAAACCT
Statistics
Matches: 873, Mismatches: 32, Indels: 28
0.94 0.03 0.03
Matches are distributed among these distances:
193 291 0.33
194 4 0.00
195 1 0.00
199 74 0.08
200 2 0.00
204 1 0.00
209 2 0.00
210 496 0.57
211 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (209 bp):
CTGAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
AGTTGAAATTGGCT
Found at i:5653149 original size:315 final size:314
Alignment explanation
Indices: 5652276--5653400 Score: 1670
Period size: 315 Copynumber: 3.7 Consensus size: 314
5652266 CGTTGTGAAG
* *
5652276 CTGAGATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 CTGA-ATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
5652341 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AA-G----TTGA
64 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGA
** * *** *
5652400 CAGTCAGCGGTCCCTTCGTCTTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTCGTTGT
129 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGT
* *
5652465 GAAGTTGAAATT-G----G-----GA-AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAA
194 GAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAA
5652519 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
259 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
** * ***
5652575 CTGAAATTGAG-AA-----GTTGACAGTCAGCGGTCCCTTCGTCTTGAAGTTGAACTTGTACTGT
1 CTG-AATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
5652634 CTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGG----GAAA-T------TGTTTATTGAC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGAC
* * *
5652688 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTGGAGTCCAATATCCTTCATTCTG
130 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
*
5652753 AAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGGCAACCAGCGGTCCCTTCGTCGTGAAG
195 AAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
* *
5652818 TTGAACTTGTGTTGTCTGGAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCT
260 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
5652873 CTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
1 CTGAA-TTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
* * *
5652938 CTGGAGTCCAATATCCTTCGTTCTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGAC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGAC
*
5653003 AACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
130 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
5653068 AAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
195 AAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
5653133 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
260 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
* *
5653188 CTGGAATTGAGAAATGTTTGTTGACAACCAGTGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGT
1 CT-GAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
5653253 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAATGTTTATTGAC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGAC
* *
5653318 AACCAGCGGTCCCTTCGTCGTGAATTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
130 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTG
5653383 AAGTTGAAATTGGCTCTG
195 AAGTTGAAATTGGCTCTG
5653401 GGTAAAACCT
Statistics
Matches: 740, Mismatches: 50, Indels: 56
0.87 0.06 0.07
Matches are distributed among these distances:
283 1 0.00
287 72 0.10
288 5 0.01
292 77 0.10
297 4 0.01
298 99 0.13
299 10 0.01
300 1 0.00
304 76 0.10
308 3 0.00
309 1 0.00
315 388 0.52
316 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (314 bp):
CTGAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
AGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
Found at i:5654149 original size:15 final size:16
Alignment explanation
Indices: 5654129--5654161 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5654119 CCGTCTTATC
5654129 TTCTTTTGTT-CTTTT
1 TTCTTTTGTTCCTTTT
*
5654144 TTCTTTTTTTCCTTTT
1 TTCTTTTGTTCCTTTT
5654160 TT
1 TT
5654162 TTCTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTCTTTTGTTCCTTTT
Found at i:5654152 original size:9 final size:9
Alignment explanation
Indices: 5654140--5654172 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
5654130 TCTTTTGTTC
5654140 TTTTTTCTT
1 TTTTTTCTT
*
5654149 TTTTTCCTT
1 TTTTTTCTT
5654158 TTTTTTCTT
1 TTTTTTCTT
5654167 TTTTTT
1 TTTTTT
5654173 TCAACTTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:5660891 original size:152 final size:152
Alignment explanation
Indices: 5660616--5660919 Score: 592
Period size: 152 Copynumber: 2.0 Consensus size: 152
5660606 CGAATGAGTC
5660616 CCGGGTAGTGCTGCTTTCCCTTTAGTAGCAGATGCGTCCCCGGGTAATATTCGGGTGAGATAACC
1 CCGGGTAGTGCTGCTTTCCCTTTAGTAGCAGATGCGTCCCCGGGTAATATTCGGGTGAGATAACC
5660681 ACTTGCGGGGTTGGTGGTATGGCCACCCCCTCGGAAGATATGCCCCCTGATGCACTAGCTTGCTG
66 ACTTGCGGGGTTGGTGGTATGGCCACCCCCTCGGAAGATATGCCCCCTGATGCACTAGCTTGCTG
5660746 TAGA-CCGACAACTTGGCTACG
131 TAGACCCGACAACTTGGCTACG
5660767 CCGGGTAGTGCTGCTTTCCCTTTAGTAGCAGATGCGTCCCCGGGTAATATTTCGGGTGAGATAAC
1 CCGGGTAGTGCTGCTTTCCCTTTAGTAGCAGATGCGTCCCCGGGTAATA-TTCGGGTGAGATAAC
5660832 CACTTGCGGGGTTGGTGGTATGGCCACCCCCTCGGAAGATATGCCCCCTGATGCACTAGCTTGCT
65 CACTTGCGGGGTTGGTGGTATGGCCACCCCCTCGGAAGATATGCCCCCTGATGCACTAGCTTGCT
5660897 GTAGACCCGACAACTTGGCTACG
130 GTAGACCCGACAACTTGGCTACG
5660920 ATTTGGTCGA
Statistics
Matches: 151, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
151 49 0.32
152 85 0.56
153 17 0.11
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.25
Consensus pattern (152 bp):
CCGGGTAGTGCTGCTTTCCCTTTAGTAGCAGATGCGTCCCCGGGTAATATTCGGGTGAGATAACC
ACTTGCGGGGTTGGTGGTATGGCCACCCCCTCGGAAGATATGCCCCCTGATGCACTAGCTTGCTG
TAGACCCGACAACTTGGCTACG
Found at i:5664739 original size:20 final size:20
Alignment explanation
Indices: 5664716--5664762 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
5664706 CCGAAAATAG
5664716 AAAAAGGGATAC-GAATTTAA
1 AAAAAGGGATACAG-ATTTAA
* *
5664736 AAAAAAGGATACAGATTTGA
1 AAAAAGGGATACAGATTTAA
5664756 AAAAAGG
1 AAAAAGG
5664763 ATAAGGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAAAGGGATACAGATTTAA
Found at i:5664944 original size:25 final size:23
Alignment explanation
Indices: 5664903--5664954 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 23
5664893 ATTAACGTAT
5664903 ATAAAAGAAGAGAAATAAAATATAA
1 ATAAAAGAAGAGAAAT--AATATAA
*
5664928 ATAAAAGAATA-ATAATAATATAA
1 ATAAAAGAAGAGA-AATAATATAA
5664951 ATAA
1 ATAA
5664955 TAAAATCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 11 0.44
24 1 0.04
25 13 0.52
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (23 bp):
ATAAAAGAAGAGAAATAATATAA
Found at i:5666111 original size:13 final size:13
Alignment explanation
Indices: 5666092--5666130 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
5666082 AATAATATTG
5666092 ATATAATATATAT
1 ATATAATATATAT
*
5666105 ATGTAATATATAAT
1 ATATAATATAT-AT
5666119 ATATAA-ATATAT
1 ATATAATATATAT
5666131 GTTCTTTCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 2 0.09
13 14 0.61
14 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:5666113 original size:7 final size:7
Alignment explanation
Indices: 5666092--5666129 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
5666082 AATAATATTG
5666092 ATATAAT
1 ATATAAT
5666099 ATAT-AT
1 ATATAAT
*
5666105 ATGTAAT
1 ATATAAT
5666112 ATATAAT
1 ATATAAT
5666119 ATATAA-
1 ATATAAT
5666125 ATATA
1 ATATA
5666130 TGTTCTTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 10 0.36
7 18 0.64
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:5666128 original size:24 final size:24
Alignment explanation
Indices: 5666084--5666132 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5666074 TTTAAAATAA
* *
5666084 TAATATTGATATAATATATATATG
1 TAATATTAATATAATAAATATATG
5666108 TAATATATAATAT-ATAAATATATG
1 TAATAT-TAATATAATAAATATATG
5666132 T
1 T
5666133 TCTTTCGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
TAATATTAATATAATAAATATATG
Found at i:5666517 original size:2 final size:2
Alignment explanation
Indices: 5666428--5666498 Score: 119
Period size: 2 Copynumber: 36.5 Consensus size: 2
5666418 TAGAGAGTAT
5666428 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5666469 TA TA TA TA TA TA TA -A TA TA TA TC TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5666499 TATGTTGTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 63 0.97
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5668065 original size:21 final size:22
Alignment explanation
Indices: 5668034--5668099 Score: 116
Period size: 21 Copynumber: 3.0 Consensus size: 22
5668024 CTCGTATAAA
5668034 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
5668056 TGCA-CGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
5668077 TGCACCGAAGTGCCCGTATAAT
1 TGCACCGAAGTGCCCGTAGAAT
5668099 T
1 T
5668100 TGTCCATAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
21 21 0.50
22 21 0.50
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:5668380 original size:29 final size:29
Alignment explanation
Indices: 5668338--5668409 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
5668328 TTTTCTGCAT
**
5668338 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* *
5668367 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
5668396 ATTCATGTCATGTA
1 ATTCATGTCATGTA
5668410 TCATAATAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:5668846 original size:66 final size:64
Alignment explanation
Indices: 5668716--5668856 Score: 194
Period size: 66 Copynumber: 2.2 Consensus size: 64
5668706 TCATGGGGGA
* * *
5668716 ATCGGTTCCCCCCCTGGGGTATCGATTCCCTTAAGCAATCTGGAATTCATATACGATGAGGGGT
1 ATCGGTTCCCCCCCTGGGGTACCGATTCCCTTAAGCAATCTGGAAATCATATACGATGAAGGGT
* * *
5668780 ATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCGTTGAAGG
1 ATCGGTTCCCCCCCT-GGGGTACCGATT-CCCT-TAAGCAATCTGGAAATCATATACGATGAAGG
5668844 GT
63 GT
5668846 ATCGGTTCCCC
1 ATCGGTTCCCC
5668857 TTGAATGGTA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
64 15 0.22
65 11 0.16
66 41 0.60
67 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.28
Consensus pattern (64 bp):
ATCGGTTCCCCCCCTGGGGTACCGATTCCCTTAAGCAATCTGGAAATCATATACGATGAAGGGT
Found at i:5668866 original size:20 final size:20
Alignment explanation
Indices: 5668837--5668877 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5668827 ATCATATTCG
* *
5668837 TTGAAGGGTATCGGTTCCCC
1 TTGAAGGGTACCGATTCCCC
*
5668857 TTGAATGGTACCGATTCCCC
1 TTGAAGGGTACCGATTCCCC
5668877 T
1 T
5668878 AACCCAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.27, G:0.24, T:0.32
Consensus pattern (20 bp):
TTGAAGGGTACCGATTCCCC
Found at i:5674907 original size:22 final size:22
Alignment explanation
Indices: 5674890--5674956 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
5674880 CTCGTATAAA
5674890 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
5674912 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
5674934 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
5674956 T
1 T
5674957 TTGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:5675226 original size:30 final size:31
Alignment explanation
Indices: 5675176--5675234 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
5675166 TAGACATAGT
*
5675176 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
* *
5675206 ATTTACATACTTTTATCACATAGTGCATA
1 ATTTACATACCTTTAACACATAGTGCATA
5675235 GAACTTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:5675291 original size:29 final size:29
Alignment explanation
Indices: 5675249--5675320 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
5675239 TTTTCTGCAT
**
5675249 ATTCATGTCATGTAATACATATAAGATGA
1 ATTCATGTCATGTAATACATATAAGACAA
* *
5675278 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAAGACAA
5675307 ATTCATGTCATGTA
1 ATTCATGTCATGTA
5675321 TCATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAAGACAA
Found at i:5675742 original size:66 final size:66
Alignment explanation
Indices: 5675627--5675775 Score: 203
Period size: 66 Copynumber: 2.2 Consensus size: 66
5675617 TTTTCTCATG
* * *
5675627 GGGGAATCGGTTCCCCCCCCTGGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGATG
1 GGGGTATCGGTT-CCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATG
5675692 -A
65 AA
* * *
5675693 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCGTT
1 GGGGTATCGGTTCCCCCCCT-GGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACGAT
5675757 GAA
64 GAA
5675760 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
5675776 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
65 8 0.11
66 48 0.65
67 18 0.24
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (66 bp):
GGGGTATCGGTTCCCCCCCTGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATGA
A
Found at i:5675785 original size:21 final size:21
Alignment explanation
Indices: 5675755--5675797 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5675745 ATCATATTCG
* *
5675755 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5675776 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5675797 T
1 T
5675798 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5675787 original size:67 final size:65
Alignment explanation
Indices: 5675627--5675797 Score: 186
Period size: 66 Copynumber: 2.6 Consensus size: 65
5675617 TTTTCTCATG
* * *
5675627 GGGGAATCGGTTCCCCCCCCT-GGGGTATCGATTCCCCTTAAGCAATCTGGAATTCATATACGAT
1 GGGGTATCGGTT--CCCCCCTGGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGAT
5675691 GA
64 GA
* * *
5675693 GGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCT-AGCATTCTGGAAATCATATTCGTT
1 GGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCT-TAAGCAATCTGGAAATCATATACGAT
5675757 GAA
64 G-A
* *
5675760 GGGGTATCGGTT-CCCCTTGAATGGGTACCGATTCCCCT
1 GGGGTATCGGTTCCCCCCTG--GGGGTACCGATTCCCCT
5675798 AACCCAGAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
65 14 0.15
66 48 0.52
67 30 0.33
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.27
Consensus pattern (65 bp):
GGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTTAAGCAATCTGGAAATCATATACGATGA
Found at i:5676853 original size:21 final size:21
Alignment explanation
Indices: 5676813--5676853 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5676803 TAAAAAACGA
*
5676813 AAGAAAATAAAGATATAATAT
1 AAGAAAATAAAGATACAATAT
5676834 AAGAAAATAAA-ATGACAATA
1 AAGAAAATAAAGAT-ACAATA
5676854 AAATACCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.68, C:0.02, G:0.10, T:0.20
Consensus pattern (21 bp):
AAGAAAATAAAGATACAATAT
Found at i:5678054 original size:30 final size:31
Alignment explanation
Indices: 5677994--5678054 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
5677984 GCCAAATCGA
* *
5677994 TATTTTATATAAACTTTATGTATTAAATTAG
1 TATTTTATATAAACTTTAAGTATCAAATTAG
*
5678025 TATTTTATATAAATTTTAAGT-TCAAATTAG
1 TATTTTATATAAACTTTAAGTATCAAATTAG
5678055 CATTATGTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.39, C:0.03, G:0.07, T:0.51
Consensus pattern (31 bp):
TATTTTATATAAACTTTAAGTATCAAATTAG
Found at i:5681801 original size:22 final size:22
Alignment explanation
Indices: 5681764--5681819 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
5681754 TTTTAAAATT
*
5681764 AATAATA--AATTTTTATAATA
1 AATAATATTAATTATTATAATA
* *
5681784 AATAATATTAATTATTATATTC
1 AATAATATTAATTATTATAATA
5681806 AATAAT-TATAATTA
1 AATAATAT-TAATTA
5681820 ATCATTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 7 0.23
21 1 0.03
22 22 0.73
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
AATAATATTAATTATTATAATA
Found at i:5685271 original size:31 final size:31
Alignment explanation
Indices: 5685148--5685272 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
5685138 CCCGAAGGAC
* * *
5685148 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
5685179 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
5685210 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5685241 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5685272 C
1 C
5685273 CCTCGATCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:5686256 original size:21 final size:21
Alignment explanation
Indices: 5686231--5686276 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5686221 TTCTGGTTCG
* * *
5686231 CTTGAGGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
5686252 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
5686273 CTTG
1 CTTG
5686277 CCCATAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:5689489 original size:31 final size:31
Alignment explanation
Indices: 5689366--5689490 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
5689356 CCCGAAGGAC
* * * *
5689366 CAGTCCATA-GATTCCGAAAAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
5689397 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
5689428 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5689459 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5689490 C
1 C
5689491 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:5690474 original size:21 final size:21
Alignment explanation
Indices: 5690449--5690494 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5690439 TTCTGGTTCG
* * *
5690449 CTTGAGGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
5690470 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
5690491 CTTG
1 CTTG
5690495 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.26, G:0.30, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:5692238 original size:277 final size:277
Alignment explanation
Indices: 5691738--5692363 Score: 981
Period size: 277 Copynumber: 2.3 Consensus size: 277
5691728 TACTATTCAC
* * * * *
5691738 GTGAAGGCGCGTTCCCGGGGGCGCTCCTTCCATTATTTTGTCAGAGAATATGTCATCATTTCCCT
1 GTGAAAGCGCGTTTCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* *
5691803 ATTATGTCACTCATGTCCCTTGGGGGCACTATTTATGTCAGTACCTATTATGTTTGAGGGGACTT
66 ATTATGTCACTCATGTCCCTTCGGAGCACTATTTATGTCAGTACCTATTATGTTTGAGGGGACTT
* **
5691868 GGCAAAGTGGTGAAAGCGCGTTTCCGGGGGGCGCATTCCATTATTTTGTTGGAGAATATGTTATC
131 GGCAAAGTGGTGAAAGCGCGTTTCCGGGGGACGCATTCCATTATTTTGTCAGAGAATATGTTATC
5691933 ATTGCCCTATTATGTCACTCATGTCCCTC-GAGGGAACTATTCATGTCAGTACCTATTATGTTTG
196 ATTGCCCTATTATGTCACTCATGTCCCTCAG-GGGAACTATTCATGTCAGTACCTATTATGTTTG
*
5691997 AGGGGACTTAGCAAAGCG
260 AGGGGACTTAGAAAAGCG
5692015 GTGAAAGCGCGTTTCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAAGCGCGTTTCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
5692080 ATTATGTCACTTATGTCCC-TCGGAGCACTATTTATGTCAGTACCTATTATGTTTGAGGGGACTT
66 ATTATGTCACTCATGTCCCTTCGGAGCACTATTTATGTCAGTACCTATTATGTTTGAGGGGACTT
* * *
5692144 GGCAAAGTGGTGAAAGTGCGTTTCCGAGGGGATGCCTTCCATTATTTTGTCAGAGAATATGTTAT
131 GGCAAAGTGGTGAAAGCGCGTTTCCG-GGGGACGCATTCCATTATTTTGTCAGAGAATATGTTAT
*
5692209 CATTGCCCTATTATGTCACTCATGTCCCTCAGGGGCACTATTCATGTCAGTACCTATTATGTTTG
195 CATTGCCCTATTATGTCACTCATGTCCCTCAGGGGAACTATTCATGTCAGTACCTATTATGTTTG
* *
5692274 AGGTGACTTAGAAAAGTG
260 AGGGGACTTAGAAAAGCG
* * * * *
5692292 GTGAAAGCGCG-TTCTCGGGGAG-GCGCCTTCGATTGTTATGTAAGAGAATATGTTATAATTGCC
1 GTGAAAGCGCGTTTC-CGGGG-GCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCC
5692355 CTATTATGT
64 CTATTATGT
5692364 GAGTCATATC
Statistics
Matches: 322, Mismatches: 23, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
276 71 0.22
277 249 0.77
278 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (277 bp):
GTGAAAGCGCGTTTCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
ATTATGTCACTCATGTCCCTTCGGAGCACTATTTATGTCAGTACCTATTATGTTTGAGGGGACTT
GGCAAAGTGGTGAAAGCGCGTTTCCGGGGGACGCATTCCATTATTTTGTCAGAGAATATGTTATC
ATTGCCCTATTATGTCACTCATGTCCCTCAGGGGAACTATTCATGTCAGTACCTATTATGTTTGA
GGGGACTTAGAAAAGCG
Found at i:5692320 original size:139 final size:137
Alignment explanation
Indices: 5691738--5692363 Score: 930
Period size: 138 Copynumber: 4.5 Consensus size: 137
5691728 TACTATTCAC
* * * * *
5691738 GTGAAGGCGCGTTCCCGGGGGCGCTCCTTCCATTATTTTGTCAGAGAATATGTCATCATTTCCCT
1 GTGAAAGCGCGTTTCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* *
5691803 ATTATGTCACTCATGTCCCTTGGGGGCACTATTTATGTCAGTACCTATTATGTTTGAGGGGACTT
65 ATTATGTCACTCATGTCCC-TCGGGGCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTT
*
5691868 GGCAAAGTG
129 AGCAAAGTG
* **
5691877 GTGAAAGCGCGTTTCCGGGGGGCGCATTCCATTATTTTGTTGGAGAATATGTTATCATTGCCCTA
1 GTGAAAGCGCGTTTCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
5691942 TTATGTCACTCATGTCCCTCGAGGGAACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTA
66 TTATGTCACTCATGTCCCTCG-GGGCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTA
*
5692007 GCAAAGCG
130 GCAAAGTG
5692015 GTGAAAGCGCGTTTCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAAGCGCGTTTCCGGGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* * * *
5692080 ATTATGTCACTTATGTCCCTCGGAGCACTATTTATGTCAGTACCTATTATGTTTGAGGGGACTTG
65 ATTATGTCACTCATGTCCCTCGGGGCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTA
5692145 GCAAAGTG
130 GCAAAGTG
* **
5692153 GTGAAAGTGCGTTTCCGAGGGGATGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAAGCGCGTTTCCG-GGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
5692218 ATTATGTCACTCATGTCCCTCAGGGGCACTATTCATGTCAGTACCTATTATGTTTGAGGTGACTT
65 ATTATGTCACTCATGTCCCTC-GGGGCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTT
*
5692283 AGAAAAGTG
129 AGCAAAGTG
* * * * *
5692292 GTGAAAGCGCG-TTCTCGGGGAGGCGCCTTCGATTGTTATGTAAGAGAATATGTTATAATTGCCC
1 GTGAAAGCGCGTTTC-CGGGG-GGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
5692356 TATTATGT
64 TATTATGT
5692364 GAGTCATATC
Statistics
Matches: 442, Mismatches: 39, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
137 2 0.00
138 253 0.57
139 187 0.42
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (137 bp):
GTGAAAGCGCGTTTCCGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGCACTATTCATGTCAGTACCTATTATGTTTGAGGGGACTTAG
CAAAGTG
Found at i:5692568 original size:23 final size:23
Alignment explanation
Indices: 5692520--5692569 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5692510 TGAAGTTTGA
* * *
5692520 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGAATAAAATGTGAAGG
5692543 ATAAATTGAAT-AAATGTGAAGTG
1 ATAAATTGAATAAAATGTGAAG-G
5692566 ATAA
1 ATAA
5692570 GTTGGTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (23 bp):
ATAAATTGAATAAAATGTGAAGG
Found at i:5693403 original size:21 final size:21
Alignment explanation
Indices: 5693377--5693426 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
5693367 GGTGTCATAA
5693377 AACCCTGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
5693398 AACCCTGTGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
5693419 AACCCTGC
1 AACCCTGC
5693427 AGAGATGGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.26, G:0.30, T:0.20
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:5693450 original size:42 final size:42
Alignment explanation
Indices: 5693404--5693509 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 42
5693394 ATGTAACCCT
*
5693404 GTGGGCTAGGAATGTAACCCTGCAGAGATGGCATATGAACTG
1 GTGGGCTAGGAATGTAACCCTGCAGAGATGGCATATGAACCG
* * * * *
5693446 GTGGGCTTGGCATAT-ACCCTTGCGGAGATGGCATCTGAACCG
1 GTGGGCTAGGAATGTAACCC-TGCAGAGATGGCATATGAACCG
* * * *
5693488 GAGGGCTGGGTATGTACCCCTG
1 GTGGGCTAGGAATGTAACCCTG
5693510 TGGCATCATC
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 4 0.08
42 44 0.86
43 3 0.06
ACGTcount: A:0.22, C:0.21, G:0.35, T:0.23
Consensus pattern (42 bp):
GTGGGCTAGGAATGTAACCCTGCAGAGATGGCATATGAACCG
Found at i:5695081 original size:17 final size:17
Alignment explanation
Indices: 5695032--5695082 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
5695022 TTCAAAAAAT
*
5695032 TTAAAATTAAT-ATAAA
1 TTAAAAATAATAATAAA
* *
5695048 TTAAAGATAA-ATTTAAA
1 TTAAAAATAATA-ATAAA
5695065 TTAAAAATAATAATAAA
1 TTAAAAATAATAATAAA
5695082 T
1 T
5695083 ATTAACATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
16 8 0.30
17 18 0.67
18 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
TTAAAAATAATAATAAA
Found at i:5695270 original size:19 final size:19
Alignment explanation
Indices: 5695257--5695294 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5695247 TAAATATTAG
5695257 TTTA-ATAAAAAAATAATA
1 TTTATATAAAAAAATAATA
*
5695275 TTTATATAAATATAATAATA
1 TTTATATAAA-AAAATAATA
5695295 AAAATATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTTATATAAAAAAATAATA
Found at i:5695291 original size:17 final size:17
Alignment explanation
Indices: 5695235--5695291 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
5695225 TTTAAAATAA
*
5695235 ATAATAATTATATAAAT
1 ATAATATTTATATAAAT
* *
5695252 AT--TAGTTTAATAAAAAA
1 ATAATA-TTT-ATATAAAT
5695269 ATAATATTTATATAAAT
1 ATAATATTTATATAAAT
5695286 ATAATA
1 ATAATA
5695292 ATAAAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
15 2 0.06
16 2 0.06
17 22 0.71
18 3 0.10
19 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
ATAATATTTATATAAAT
Found at i:5695294 original size:31 final size:33
Alignment explanation
Indices: 5695227--5695303 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 33
5695217 TTAATTAATT
*
5695227 TAAAATAAATAATAATTATATAAATATTAGTTTAA
1 TAAAA-AAATAATAATTATATAAATATTAG-ATAA
*
5695262 TAAAAAAATAATATTTATATAAATA-TA-ATAA
1 TAAAAAAATAATAATTATATAAATATTAGATAA
*
5695293 TAAAAATATAA
1 TAAAAAAATAA
5695304 CAACTATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 13 0.33
33 2 0.05
34 19 0.49
35 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (33 bp):
TAAAAAAATAATAATTATATAAATATTAGATAA
Found at i:5707824 original size:185 final size:185
Alignment explanation
Indices: 5707503--5707892 Score: 626
Period size: 185 Copynumber: 2.1 Consensus size: 185
5707493 ATTAAATTTT
* * *
5707503 AAATTTTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACTCAATTAATAA
*
5707568 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
*
5707633 TTATTTTATAA-T-TATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAA
131 TTATTTTATAATTATATATATTATTTAAATTAATTATAAAC--TTTTTTTAATTAAA
*
5707688 AAATATTATATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACTCAATTAATAA
* *
5707753 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAA-TT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATTT
5707817 TTTATTTTATAATTATATATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
130 TTTATTTTATAATTATATATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
* * *
5707873 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
5707893 AATTAGAAAA
Statistics
Matches: 190, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
184 8 0.04
185 152 0.80
186 4 0.02
187 26 0.14
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGAGCTAAGCCCAAACCATTTAAAACTCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
TTATTTTATAATTATATATATTATTTAAATTAATTATAAACTTTTTTTAATTAAA
Found at i:5712293 original size:3 final size:3
Alignment explanation
Indices: 5712285--5712309 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5712275 AATTTATATA
5712285 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5712310 TATTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5714000 original size:35 final size:35
Alignment explanation
Indices: 5713954--5714028 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
5713944 CCATACAAGG
*
5713954 AAAAGATTAAAAAATCCAACTAAATAAACTCGAAC
1 AAAAGATTAAAAAATCCAACCAAATAAACTCGAAC
* * *
5713989 AAAAGTTTAAAAAATCTAACCAACTAAACTCGAAC
1 AAAAGATTAAAAAATCCAACCAAATAAACTCGAAC
5714024 AAAAG
1 AAAAG
5714029 GTAGATACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.59, C:0.17, G:0.07, T:0.17
Consensus pattern (35 bp):
AAAAGATTAAAAAATCCAACCAAATAAACTCGAAC
Found at i:5718854 original size:19 final size:19
Alignment explanation
Indices: 5718830--5718868 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5718820 TCGAATGCAT
5718830 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
5718849 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
5718868 T
1 T
5718869 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:5718970 original size:64 final size:65
Alignment explanation
Indices: 5718816--5718974 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 65
5718806 GAATTAATTG
* * *** *
5718816 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
5718881 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
5718944 A
65 A
*
5718945 AACATCGAATGCATTTTATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
5718975 TCCTTAGTGC
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
64 34 0.41
65 49 0.59
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:5725785 original size:21 final size:21
Alignment explanation
Indices: 5725743--5725786 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5725733 ACCCCGGGAG
*
5725743 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
5725764 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
5725785 CT
1 CT
5725787 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:5726863 original size:19 final size:19
Alignment explanation
Indices: 5726839--5726877 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5726829 TCGAATGCAT
5726839 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
5726858 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
5726877 T
1 T
5726878 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:5726982 original size:64 final size:65
Alignment explanation
Indices: 5726825--5726983 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 65
5726815 GAATTAATTG
* * *** *
5726825 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
5726890 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
5726953 A
65 A
* *
5726954 AACATCGAATGCATTTTATGCATTGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
5726984 TCCTTAGTGC
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
64 33 0.40
65 49 0.60
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:5729635 original size:24 final size:24
Alignment explanation
Indices: 5729608--5729659 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5729598 ATATTGTAGG
*
5729608 TAAATTTAT-AAAATTTTAAAAGAA
1 TAAATTTATAAAAAATTTAAAA-AA
*
5729632 TAAATTTTTAAAAAATTTAAAAAA
1 TAAATTTATAAAAAATTTAAAAAA
5729656 TAAA
1 TAAA
5729660 AATAGATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
TAAATTTATAAAAAATTTAAAAAA
Found at i:5729662 original size:26 final size:26
Alignment explanation
Indices: 5729612--5729659 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
5729602 TGTAGGTAAA
*
5729612 TTTATAAAATTTTAAAAGAATAAATT
1 TTTATAAAAATTTAAAAGAATAAATT
5729638 TTTA-AAAAATTTAAAA-AATAAA
1 TTTATAAAAATTTAAAAGAATAAA
5729660 AATAGATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
TTTATAAAAATTTAAAAGAATAAATT
Found at i:5730213 original size:38 final size:38
Alignment explanation
Indices: 5730170--5730245 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
5730160 ATATATATGT
* * *
5730170 CAGAAAACTATATAAAATATATACGTATCAAAATACCG
1 CAGAAAACAATATAAAATATATACGGAACAAAATACCG
*
5730208 CAGAAAACAATATAAAATATTTACGGAACAAAATACCG
1 CAGAAAACAATATAAAATATATACGGAACAAAATACCG
5730246 GTAATACAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.54, C:0.16, G:0.09, T:0.21
Consensus pattern (38 bp):
CAGAAAACAATATAAAATATATACGGAACAAAATACCG
Found at i:5730660 original size:39 final size:39
Alignment explanation
Indices: 5730550--5730664 Score: 123
Period size: 39 Copynumber: 3.0 Consensus size: 39
5730540 AACCATACAC
*
5730550 CAGTAAGGACTTACCCT-ATGCACAAAGCAGAGGAGCCTG
1 CAGTAAGGACTTACCCTGA-GCACAAAGCCGAGGAGCCTG
* * * * *
5730589 CAGTAAGG---T-CCCATGTGTATAAAGTCGAGGAGCCTT
1 CAGTAAGGACTTACCC-TGAGCACAAAGCCGAGGAGCCTG
5730625 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
1 CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
5730664 C
1 C
5730665 GGAAAACGGT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
35 3 0.05
36 25 0.42
39 28 0.47
40 3 0.05
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.17
Consensus pattern (39 bp):
CAGTAAGGACTTACCCTGAGCACAAAGCCGAGGAGCCTG
Found at i:5740948 original size:20 final size:21
Alignment explanation
Indices: 5740907--5740948 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5740897 AATCAGATTG
5740907 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
*
5740928 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
5740949 ATTGTCTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:5743728 original size:20 final size:20
Alignment explanation
Indices: 5743700--5743741 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
5743690 AATCAGATTG
5743700 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
* *
5743720 CCCATGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
5743740 CC
1 CC
5743742 TTGTCTAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.40, G:0.26, T:0.17
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:5746478 original size:20 final size:21
Alignment explanation
Indices: 5746448--5746486 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5746438 AATCAGATTG
5746448 CCCAGGGGGTACAGATTCCTC
1 CCCAGGGGGTACAGATTCCTC
*
5746469 CCCA-GGGGTACCGATTCC
1 CCCAGGGGGTACAGATTCC
5746487 CCCTTGTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.18, C:0.36, G:0.28, T:0.18
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCTC
Found at i:5749498 original size:39 final size:39
Alignment explanation
Indices: 5749439--5749542 Score: 140
Period size: 37 Copynumber: 2.7 Consensus size: 39
5749429 CTTGTACACC
* *
5749439 CAGTAAGGGCTTACCCTGTGCACAAAGCAGAGGAGCCTG
1 CAGTAAGGGCTTACCCTGTGCACAAAGCACAGGAACCTG
* * *
5749478 CAGTAAGGTCTTATCTTGTGCACAAA--ACAGGAACCTG
1 CAGTAAGGGCTTACCCTGTGCACAAAGCACAGGAACCTG
*
5749515 CAGTAAGGGCTTACCCTGAGCACAAAGC
1 CAGTAAGGGCTTACCCTGTGCACAAAGC
5749543 CATGGAGCAT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 31 0.57
39 23 0.43
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (39 bp):
CAGTAAGGGCTTACCCTGTGCACAAAGCACAGGAACCTG
Found at i:5749589 original size:39 final size:39
Alignment explanation
Indices: 5749527--5749628 Score: 125
Period size: 39 Copynumber: 2.6 Consensus size: 39
5749517 GTAAGGGCTT
*
5749527 ACCCTGAGCACAAAGCC-ATGGAGCATGCGGTAATAACTC
1 ACCCTGAGCACAAAGCCGA-GGAGCATGCGGTAAGAACTC
* * * * * *
5749566 ACCCTAAGGACAAAGCCGAGGAGCTTGTGGTAAGGACTT
1 ACCCTGAGCACAAAGCCGAGGAGCATGCGGTAAGAACTC
5749605 ACCCTGAGCACAAAGCCGAGGAGC
1 ACCCTGAGCACAAAGCCGAGGAGC
5749629 CTGCAAAAAG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 52 0.98
40 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.27, T:0.14
Consensus pattern (39 bp):
ACCCTGAGCACAAAGCCGAGGAGCATGCGGTAAGAACTC
Found at i:5751263 original size:2 final size:2
Alignment explanation
Indices: 5751256--5751294 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5751246 AGCCAAATAA
5751256 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
5751295 CCCCACTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5751649 original size:46 final size:45
Alignment explanation
Indices: 5751579--5751686 Score: 146
Period size: 46 Copynumber: 2.4 Consensus size: 45
5751569 CACTAGCGGA
* *
5751579 AATGTTTTAGGTAGCGCCCGATATTAATATTTCCGGTAGAAAAAAAT
1 AATGTTTTAGGTAGCGCCCAATATTAACATTT-CGGTAG-AAAAAAT
* *
5751626 AATG-TTTAGGTAGCGCCCAATATTAACATTTCGGTTGAACAAAT
1 AATGTTTTAGGTAGCGCCCAATATTAACATTTCGGTAGAAAAAAT
*
5751670 AATGTTTTAGATAGCGC
1 AATGTTTTAGGTAGCGC
5751687 TTTACCGGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 10 0.18
45 16 0.29
46 25 0.45
47 4 0.07
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (45 bp):
AATGTTTTAGGTAGCGCCCAATATTAACATTTCGGTAGAAAAAAT
Found at i:5756015 original size:42 final size:41
Alignment explanation
Indices: 5755968--5756059 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
5755958 GTTTTTTGTG
*
5755968 CAAACGCCGTAATAGAGTAGAAATATAGCGGTGTTTTTACCAA
1 CAAACGCCGTAATAGAGT-GAAATATAGCGGCGTTTTT-CCAA
* * ** *
5756011 -AAACGCCGTCATAGGGTGGTATATAGTGGCGTTTTTCCAA
1 CAAACGCCGTAATAGAGTGAAATATAGCGGCGTTTTTCCAA
5756051 CAAACGCCG
1 CAAACGCCG
5756060 CAATTAAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
40 4 0.10
41 23 0.55
42 15 0.36
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.25
Consensus pattern (41 bp):
CAAACGCCGTAATAGAGTGAAATATAGCGGCGTTTTTCCAA
Found at i:5756262 original size:42 final size:41
Alignment explanation
Indices: 5756142--5756270 Score: 113
Period size: 42 Copynumber: 3.1 Consensus size: 41
5756132 AAAAACGTTG
* * * * *
5756142 AATAGAGTATACATTTAGCGGCATTT-TAGCC-CAAACGCTGT
1 AATAGAGTGTAAATGTAGCGGCGTTTATA-CCACAAACGC-AT
*
5756183 AATAGAGTGTTAATGTAGCGGCGTTTATACCACAAACGTCAT
1 AATAGAGTGTAAATGTAGCGGCGTTTATACCACAAACG-CAT
*
5756225 AATAGAGTGGTAAAT-TAGCGGCGTTTATATCTA-AAACGCAT
1 AATAGAGT-GTAAATGTAGCGGCGTTTATA-CCACAAACGCAT
5756266 CAATA
1 -AATA
5756271 TGATTGTTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
41 26 0.35
42 40 0.54
43 8 0.11
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (41 bp):
AATAGAGTGTAAATGTAGCGGCGTTTATACCACAAACGCAT
Found at i:5758292 original size:81 final size:81
Alignment explanation
Indices: 5758156--5758328 Score: 238
Period size: 81 Copynumber: 2.1 Consensus size: 81
5758146 CATTCGAAGC
* * * * ** *
5758156 CGTCATCACCTACACCGTTGTTGCCTGGTACTCAACTACTGCTGCTTTTCGCCGCTTGAAGCCAT
1 CGTCATCACCTACACCGTCGCTGCCCGGTACTCAACTACTACTGCTCGTCCCCGCTTGAAGCCAT
5758221 CGTTCATACTGCTGCT
66 CGTTCATACTGCTGCT
* * *
5758237 CGTCATCACCTACACCGTCGCTGCCCGGTACTCAACTGCTACTGCTCGTCCCCGCTTGAAGTCGT
1 CGTCATCACCTACACCGTCGCTGCCCGGTACTCAACTACTACTGCTCGTCCCCGCTTGAAGCCAT
* *
5758302 CGTTCCTGCTGCTGCT
66 CGTTCATACTGCTGCT
5758318 CGTCATCACCT
1 CGTCATCACCT
5758329 CCATCGTTAC
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.14, C:0.37, G:0.19, T:0.29
Consensus pattern (81 bp):
CGTCATCACCTACACCGTCGCTGCCCGGTACTCAACTACTACTGCTCGTCCCCGCTTGAAGCCAT
CGTTCATACTGCTGCT
Found at i:5766575 original size:43 final size:43
Alignment explanation
Indices: 5766518--5766599 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
5766508 GTTTGTACCC
*
5766518 TAAAAACGCCGCTAAATCTCAACACTTATTGCGGCGTTTGTGA
1 TAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGA
*
5766561 TAAAAACGCTGCTAAATCTCAACACCTATTGCGGCGTTT
1 TAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTT
5766600 TTCGTTAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
TAAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGA
Found at i:5770333 original size:12 final size:12
Alignment explanation
Indices: 5770316--5770354 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5770306 GAGATATAAT
5770316 TTTATTTAGGTG
1 TTTATTTAGGTG
5770328 TTTATTT---T-
1 TTTATTTAGGTG
5770336 TTTATTTAGGTG
1 TTTATTTAGGTG
5770348 TTTATTT
1 TTTATTT
5770355 TTTATTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.30
9 1 0.04
11 1 0.04
12 14 0.61
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (12 bp):
TTTATTTAGGTG
Found at i:5770360 original size:19 final size:20
Alignment explanation
Indices: 5770315--5770357 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
5770305 AGAGATATAA
5770315 TTTTATTTAGGTGTTTATTT
1 TTTTATTTAGGTGTTTATTT
5770335 TTTTATTTAGGTGTTTATTT
1 TTTTATTTAGGTGTTTATTT
5770355 TTT
1 TTT
5770358 ATTAAACCTA
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:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (20 bp):
TTTTATTTAGGTGTTTATTT
Found at i:5771546 original size:26 final size:27
Alignment explanation
Indices: 5771517--5771581 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
5771507 TTAAACTCAA
5771517 ATAACTCACAATC-TCTCATCTCATTT
1 ATAACTCACAATCGTCTCATCTCATTT
* * *
5771543 ATAACTTACATTCTGTCTCGTCTCATTT
1 ATAACTCACAATC-GTCTCATCTCATTT
5771571 ATAACTCACAA
1 ATAACTCACAA
5771582 GAGAGTCGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 11 0.34
28 21 0.66
ACGTcount: A:0.31, C:0.28, G:0.03, T:0.38
Consensus pattern (27 bp):
ATAACTCACAATCGTCTCATCTCATTT
Found at i:5791881 original size:24 final size:24
Alignment explanation
Indices: 5791849--5791900 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
5791839 TCAATAATCT
5791849 CATTCCCTGATAATCTTTTATTCC
1 CATTCCCTGATAATCTTTTATTCC
*
5791873 CATTCCCTGGTAATCTTTTATTCC
1 CATTCCCTGATAATCTTTTATTCC
5791897 CATT
1 CATT
5791901 GGTAATCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (24 bp):
CATTCCCTGATAATCTTTTATTCC
Found at i:5791905 original size:20 final size:22
Alignment explanation
Indices: 5791859--5791909 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
5791849 CATTCCCTGA
5791859 TAATCTTTTATTCCCATTCCCTGG
1 TAATCTTTTATTCCCATT--CTGG
5791883 TAATCTTTTATTCCCA-T-TGG
1 TAATCTTTTATTCCCATTCTGG
5791903 TAATCTT
1 TAATCTT
5791910 ACATTCCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.37
23 1 0.04
24 16 0.59
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.49
Consensus pattern (22 bp):
TAATCTTTTATTCCCATTCTGG
Found at i:5794151 original size:20 final size:20
Alignment explanation
Indices: 5794126--5794252 Score: 134
Period size: 20 Copynumber: 6.3 Consensus size: 20
5794116 AATCTGTAAA
* *
5794126 TCGCAACATAGAAGTTAAAT
1 TCGCAACACAGAAGTCAAAT
*
5794146 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
5794166 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
**
5794186 TCGCAATGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
5794206 TCGCAACACATAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
5794226 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
5794246 TCGCAAC
1 TCGCAAC
5794253 GCGCGAAACA
Statistics
Matches: 89, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.04
20 83 0.93
21 2 0.02
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:5794173 original size:40 final size:40
Alignment explanation
Indices: 5794126--5794252 Score: 209
Period size: 40 Copynumber: 3.2 Consensus size: 40
5794116 AATCTGTAAA
* * *
5794126 TCGCAACATAGAAGTTAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
*
5794166 TCGCAACACAAAAGTCAAATTCGCAATGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
*
5794206 TCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
5794246 TCGCAAC
1 TCGCAAC
5794253 GCGCGAAACA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (40 bp):
TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:5794253 original size:20 final size:20
Alignment explanation
Indices: 5794142--5794255 Score: 167
Period size: 20 Copynumber: 5.7 Consensus size: 20
5794132 CATAGAAGTT
5794142 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACGCGATAGTC
* * *
5794162 AAATTCGCAACACAAAAGTC
1 AAATTCGCAACGCGATAGTC
*
5794182 AAATTCGCAATGCGATAGTC
1 AAATTCGCAACGCGATAGTC
*
5794202 AAATTCGCAACAC-ATAAGTC
1 AAATTCGCAACGCGAT-AGTC
5794222 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACGCGATAGTC
5794242 AAATTCGCAACGCG
1 AAATTCGCAACGCG
5794256 CGAAACACAA
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
19 2 0.02
20 78 0.95
21 2 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATTCGCAACGCGATAGTC
Found at i:5794395 original size:22 final size:22
Alignment explanation
Indices: 5794370--5794420 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5794360 CTACGGCGAC
5794370 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
5794392 ATCCGTCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
5794414 ATCCGTC
1 ATCCGTC
5794421 TATCTCTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:5794802 original size:14 final size:14
Alignment explanation
Indices: 5794770--5794803 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5794760 ACACGAAAAT
5794770 GAAAATCGCAACAC
1 GAAAATCGCAACAC
* *
5794784 CAAAATCGCAACGC
1 GAAAATCGCAACAC
5794798 GAAAAT
1 GAAAAT
5794804 GAAAATCACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.26, G:0.15, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACAC
Found at i:5794843 original size:14 final size:14
Alignment explanation
Indices: 5794844--5794877 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
5794834 TGCGATTTTC
5794844 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
*
5794858 ATTTTCTCGTTGCG
1 ATTTTCGCGTTGCG
5794872 ATTTTC
1 ATTTTC
5794878 ATTTTCGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.21, G:0.21, T:0.50
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:5794883 original size:20 final size:20
Alignment explanation
Indices: 5794826--5794863 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5794816 GCGGTTTTAG
5794826 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
5794846 TTTCGCGTTGCGATTTTC
1 TTTCGCGTTGCGATTTTC
5794864 TCGTTGCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.21, G:0.21, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:5797088 original size:21 final size:21
Alignment explanation
Indices: 5797056--5797154 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
5797046 GATGCACCTA
* *
5797056 TCATCATTCAAGAGGCGCCTC
1 TCATCGTTCAAGAGGCCCCTC
5797077 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
5797098 TCATC-ATCAAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* * *
5797119 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
5797140 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
5797155 TCTCGCCCGT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.05
21 57 0.90
22 3 0.05
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.21
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:5797103 original size:42 final size:42
Alignment explanation
Indices: 5797056--5797154 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
5797046 GATGCACCTA
* * *
5797056 TCATCATTCAAGAGGCGCCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
* *
5797098 TCATCA-TCAAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTC-AAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
*
5797140 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
5797155 TCTCGCCCGT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 2 0.04
42 44 0.92
43 2 0.04
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.21
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:5798606 original size:66 final size:64
Alignment explanation
Indices: 5798450--5798624 Score: 244
Period size: 66 Copynumber: 2.6 Consensus size: 64
5798440 GGTACACTTT
5798450 TTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAATTGATGAGGAAATAAG
1 TTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTGATGAGGAAATAAG
5798514 AATTA
60 AATTA
* * *
5798519 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAATAATTA
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTA
5798584 TTGTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TT-TTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
5798625 GTTTTAAATT
Statistics
Matches: 100, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
64 17 0.17
65 20 0.20
66 38 0.38
67 1 0.01
68 4 0.04
69 20 0.20
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (64 bp):
TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Done.