Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007993.1 Hibiscus syriacus cultivar Beakdansim tig00110443_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: 2245901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 12
Found at i:1777513 original size:52 final size:53
Alignment explanation
Indices: 1777400--1777516 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1777390 GAAATTAAAA
1777400 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1777453 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1777505 TCGCATTGCGAT
1 TCGCATTGCGAT
1777517 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1777524 original size:19 final size:19
Alignment explanation
Indices: 1777419--1777516 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1777409 GATTCTCTCG
1777419 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1777439 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1777458 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1777472 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1777491 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1777510 TTGCGAT
1 TTGCGAT
1777517 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1777642 original size:14 final size:14
Alignment explanation
Indices: 1777623--1777659 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1777613 CATCAATTAC
1777623 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1777637 ACAAATCATCTTTT
1 ACAAATCAACTTTT
*
1777651 ATAAATCAA
1 ACAAATCAA
1777660 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1779623 original size:19 final size:19
Alignment explanation
Indices: 1779581--1779753 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
1779571 TAGTTTACTT
* *
1779581 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
1779601 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
1779620 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
1779639 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1779658 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1779677 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1779691 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1779710 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1779724 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1779743 TCGCAATGCGA
1 TCGCAACGCGA
1779754 TTTTGGTTTC
Statistics
Matches: 130, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
14 16 0.12
16 11 0.08
17 11 0.08
19 80 0.62
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1779694 original size:14 final size:14
Alignment explanation
Indices: 1779675--1779731 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1779665 GCGAAATGAA
*
1779675 AATCGCAACGACAG
1 AATCGCAACGAAAG
1779689 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1779706 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1779722 AATCGCAACG
1 AATCGCAACG
1779732 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1779702 original size:33 final size:33
Alignment explanation
Indices: 1779656--1779748 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1779646 GCGAAACCAA
*
1779656 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1779689 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1779722 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1779749 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1779765 original size:19 final size:19
Alignment explanation
Indices: 1779749--1779863 Score: 141
Period size: 19 Copynumber: 6.3 Consensus size: 19
1779739 AAAATCGCAA
1779749 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1779768 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1779787 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1779801 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1779820 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1779839 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1779859 TGCGA
1 TGCGA
1779864 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
14 11 0.13
16 1 0.01
17 1 0.01
18 1 0.01
19 56 0.67
20 13 0.16
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1780027 original size:93 final size:93
Alignment explanation
Indices: 1779911--1780472 Score: 1108
Period size: 93 Copynumber: 6.1 Consensus size: 93
1779901 ATGGATTGCA
1779911 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1779975 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1780003 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1780068 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1780096 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1780161 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1780189 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1780254 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1780282 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1780347 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1780375 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1780440 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1780468 TTACT
1 TTACT
1780473 AAGCAATCTA
Statistics
Matches: 468, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
92 4 0.01
93 464 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1782203 original size:20 final size:20
Alignment explanation
Indices: 1782172--1782268 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
1782162 TTTTGGTTGA
1782172 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
1782192 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1782212 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
1782231 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
1782246 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1782266 AAT
1 AAT
1782269 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1782224 original size:21 final size:21
Alignment explanation
Indices: 1782170--1782234 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1782160 TCTTTTGGTT
1782170 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
1782191 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1782211 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1782232 GAA
1 GAA
1782235 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1782238 original size:14 final size:14
Alignment explanation
Indices: 1782219--1782275 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1782209 GAGAAATGAA
1782219 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1782233 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1782252 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1782266 AATCGCAACG
1 AATCGCAACG
1782276 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1782251 original size:33 final size:33
Alignment explanation
Indices: 1782170--1782292 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
1782160 TCTTTTGGTT
*
1782170 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
1782211 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1782244 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1782277 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1782293 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1782335 original size:21 final size:21
Alignment explanation
Indices: 1782309--1782378 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
1782299 TTTGGTTTCG
1782309 CGTTGCGATTTTCATTTCTCT
1 CGTTGCGATTTTCATTTCTCT
***
1782330 CGTTGCGACAGTCA-TTCTCT
1 CGTTGCGATTTTCATTTCTCT
*
1782350 CGTTGCGATTTTCATTTATCT
1 CGTTGCGATTTTCATTTCTCT
*
1782371 CATTGCGA
1 CGTTGCGA
1782379 CTCTTCTGCA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.43
21 23 0.57
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.44
Consensus pattern (21 bp):
CGTTGCGATTTTCATTTCTCT
Found at i:1782364 original size:20 final size:20
Alignment explanation
Indices: 1782309--1782365 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1782299 TTTGGTTTCG
1782309 CGTTGCGATTTTCATTTCTCT
1 CGTTGCGATTTTCA-TTCTCT
***
1782330 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATTCTCT
1782350 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
1782366 TATCTCATTG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTCTCT
Found at i:1782500 original size:33 final size:33
Alignment explanation
Indices: 1782458--1782528 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1782448 AATACTAACT
*
1782458 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1782491 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1782524 TGAAA
1 TGAAA
1782529 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1782762 original size:22 final size:22
Alignment explanation
Indices: 1782710--1782764 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1782700 TGGTTTTGAG
**
1782710 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1782732 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1782754 GGATTTCTTCG
1 GGATTTCTTCG
1782765 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1782936 original size:20 final size:20
Alignment explanation
Indices: 1782911--1783104 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1782901 CTTTAAATAT
1782911 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1782931 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1782953 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1782972 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1782992 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1783012 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1783032 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1783052 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1783072 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1783092 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1783105 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1783098 original size:60 final size:60
Alignment explanation
Indices: 1782911--1783104 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1782901 CTTTAAATAT
**
1782911 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1782972 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1783032 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1783092 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1783105 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1783121 original size:21 final size:21
Alignment explanation
Indices: 1783091--1783173 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1783081 ATTTTCATAT
*
1783091 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1783112 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1783133 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1783154 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1783174 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1783164 original size:42 final size:43
Alignment explanation
Indices: 1783071--1783169 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1783061 ATTTATGTGT
* *
1783071 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1783112 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1783154 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1783170 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1783349 original size:19 final size:16
Alignment explanation
Indices: 1783309--1783340 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1783299 GCGATTTTCT
*
1783309 CTAATAATAATAATAG
1 CTAATAAGAATAATAG
1783325 CTAATAAGAATAATAG
1 CTAATAAGAATAATAG
1783341 TACGTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.28
Consensus pattern (16 bp):
CTAATAAGAATAATAG
Found at i:1783451 original size:19 final size:20
Alignment explanation
Indices: 1783424--1783550 Score: 79
Period size: 19 Copynumber: 6.6 Consensus size: 20
1783414 AATAATAAAG
*
1783424 ATAAGAATAATA-TATGATA
1 ATAATAATAATACTATGATA
* *
1783443 ATAATAATACACACTA--CTA
1 ATAATAATA-ATACTATGATA
* *
1783462 ATAATAGTAATAGTAT-AGTA
1 ATAATAATAATACTATGA-TA
****
1783482 ATAAT-ATAATAAGGGGATA
1 ATAATAATAATACTATGATA
*
1783501 ATAATAATAGTACT-TGATA
1 ATAATAATAATACTATGATA
* *
1783520 ATAATAATAGTACT-TTATA
1 ATAATAATAATACTATGATA
1783539 ATAATAATAATA
1 ATAATAATAATA
1783551 ATACTTTATA
Statistics
Matches: 84, Mismatches: 18, Indels: 12
0.74 0.16 0.11
Matches are distributed among these distances:
18 4 0.05
19 63 0.75
20 15 0.18
21 2 0.02
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (20 bp):
ATAATAATAATACTATGATA
Found at i:1783523 original size:22 final size:22
Alignment explanation
Indices: 1783498--1783571 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
1783488 TAATAAGGGG
*
1783498 ATAATAATAATAGTAC--T-TG
1 ATAATAATAATAGTACTTTATA
1783517 ATAATAATAATAGTACTTTATA
1 ATAATAATAATAGTACTTTATA
*
1783539 ATAATAATAATAATACTTTATA
1 ATAATAATAATAGTACTTTATA
*
1783561 TGTAATAATAA
1 -ATAATAATAA
1783572 ATGGACTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 16 0.33
21 1 0.02
22 22 0.46
23 9 0.19
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.39
Consensus pattern (22 bp):
ATAATAATAATAGTACTTTATA
Found at i:1783571 original size:3 final size:3
Alignment explanation
Indices: 1783367--1783553 Score: 69
Period size: 3 Copynumber: 61.3 Consensus size: 3
1783357 CATTAACGAA
* * * *
1783367 AAT AAT AAT AGCT AAT AAC AAT AGT AAT AAT ACT -AT AAT -AT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * *
1783411 GTT AAT AAT AA- AGAT AAG AAT AAT ATAT GAT AAT AAT AAT ACAC ACT
1 AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT AAT AAT A-AT AAT
* * * * * *
1783458 ACT AAT AAT AGT AAT AGT -AT AGT AAT AAT -AT AAT AAGGG GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA--T AAT AAT
* * * * * *
1783503 AAT AAT AGT ACTT GAT AAT AAT AAT AGT ACTT TAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
1783550 AAT A
1 AAT A
1783554 CTTTATATGT
Statistics
Matches: 131, Mismatches: 40, Indels: 26
0.66 0.20 0.13
Matches are distributed among these distances:
2 7 0.05
3 114 0.87
4 9 0.07
5 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1784550 original size:16 final size:16
Alignment explanation
Indices: 1784529--1784562 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1784519 CATCTCCCGC
1784529 CTCCATTGTGCCAAGA
1 CTCCATTGTGCCAAGA
1784545 CTCCATTGTGCCAAGA
1 CTCCATTGTGCCAAGA
1784561 CT
1 CT
1784563 ACCTGACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (16 bp):
CTCCATTGTGCCAAGA
Found at i:1785478 original size:21 final size:21
Alignment explanation
Indices: 1785453--1785493 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1785443 GGAGCGATGT
*
1785453 TGTTATTATTATTTAATAAAA
1 TGTTATAATTATTTAATAAAA
* *
1785474 TGTTATAATTGTTTATTAAA
1 TGTTATAATTATTTAATAAA
1785494 TATCATAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (21 bp):
TGTTATAATTATTTAATAAAA
Found at i:1787137 original size:17 final size:17
Alignment explanation
Indices: 1787097--1787178 Score: 78
Period size: 17 Copynumber: 4.8 Consensus size: 17
1787087 ATTCATGCAT
1787097 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
1787114 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* * *
1787132 TTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
1787149 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
*
1787166 CTAGCTC-TTAATT
1 CTAGTTCATTAATT
1787179 GTTTCATGCA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
16 5 0.09
17 37 0.67
18 13 0.24
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:1787531 original size:26 final size:26
Alignment explanation
Indices: 1787492--1787547 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
1787482 AGTTTGAGCA
1787492 AAGAAAGAGCCCTTTCATCTTCTACC
1 AAGAAAGAGCCCTTTCATCTTCTACC
*
1787518 AAGAAAGAGTCCTTTCATCTTCTACC
1 AAGAAAGAGCCCTTTCATCTTCTACC
1787544 AAGA
1 AAGA
1787548 GACAAGCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (26 bp):
AAGAAAGAGCCCTTTCATCTTCTACC
Found at i:1790980 original size:17 final size:17
Alignment explanation
Indices: 1790959--1791012 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
1790949 ATTCATGCAT
1790959 CTAGTTCATTAATTAAA
1 CTAGTTCATTAATTAAA
* * * *
1790976 TTAGTTAATTCATCAAA
1 CTAGTTCATTAATTAAA
*
1790993 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
1791010 CTA
1 CTA
1791013 ACTCTTAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.43
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:1794797 original size:7 final size:7
Alignment explanation
Indices: 1794774--1794853 Score: 57
Period size: 7 Copynumber: 12.0 Consensus size: 7
1794764 CCGACTTTAA
1794774 CTTTCTT
1 CTTTCTT
1794781 C-TT-TT
1 CTTTCTT
1794786 C-TTCTT
1 CTTTCTT
1794792 CTTTCTT
1 CTTTCTT
*
1794799 C-CTCTT
1 CTTTCTT
1794805 -TTCTCTT
1 CTT-TCTT
1794812 CTTTCTT
1 CTTTCTT
1794819 CCTTT-TT
1 -CTTTCTT
*
1794826 -TCTCTT
1 CTTTCTT
1794832 CTTTCTT
1 CTTTCTT
*
1794839 CTTCCCTT
1 CTT-TCTT
1794847 CTTTCTT
1 CTTTCTT
1794854 TCACTCCCGG
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
5 7 0.12
6 11 0.19
7 28 0.48
8 12 0.21
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (7 bp):
CTTTCTT
Found at i:1794813 original size:20 final size:20
Alignment explanation
Indices: 1794780--1794839 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
1794770 TTAACTTTCT
1794780 TCTTTTCTTCTTCTTTCTTCC
1 TCTTTTC-TCTTCTTTCTTCC
1794801 TCTTTTCTCTTCTTTCTTCC
1 TCTTTTCTCTTCTTTCTTCC
*
1794821 TTTTTTCTCTTCTTTCTTC
1 TCTTTTCTCTTCTTTCTTC
1794840 TTCCCTTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 31 0.82
21 7 0.18
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (20 bp):
TCTTTTCTCTTCTTTCTTCC
Found at i:1794848 original size:20 final size:20
Alignment explanation
Indices: 1794776--1794855 Score: 101
Period size: 20 Copynumber: 4.0 Consensus size: 20
1794766 GACTTTAACT
1794776 TTCTTCTTTTCTTCTTCTTTC
1 TTCTTCTTTTC-TCTTCTTTC
*
1794797 TTCCTCTTTTCTCTTCTTTC
1 TTCTTCTTTTCTCTTCTTTC
1794817 TTCCTT-TTTTCTCTTCTTTC
1 TT-CTTCTTTTCTCTTCTTTC
**
1794837 TTCTTCCCTTCT-TTCTTTC
1 TTCTTCTTTTCTCTTCTTTC
1794856 ACTCCCGGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
19 10 0.19
20 31 0.58
21 12 0.23
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTTCTTTTCTCTTCTTTC
Found at i:1794850 original size:27 final size:27
Alignment explanation
Indices: 1794779--1794855 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
1794769 TTTAACTTTC
* *
1794779 TTCTTTTCTT-CTTCTTTCTTCCTCTT
1 TTCTCTTCTTCCTTCTTTCTTTCTCTT
*
1794805 TTCTCTTCTTTCTTCCTTT-TTTCTCTT
1 TTCTCTTCTTCCTT-CTTTCTTTCTCTT
1794832 CTT-TCTTCTTCCCTTCTTTCTTTC
1 -TTCTCTTCTT-CCTTCTTTCTTTC
1794856 ACTCCCGGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
26 9 0.21
27 21 0.49
28 13 0.30
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (27 bp):
TTCTCTTCTTCCTTCTTTCTTTCTCTT
Found at i:1794894 original size:2 final size:2
Alignment explanation
Indices: 1794887--1794930 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1794877 CCCTACATCC
1794887 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1794929 TA
1 TA
1794931 AAACCCAACC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1796049 original size:20 final size:20
Alignment explanation
Indices: 1796024--1796071 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1796014 ATATATTATT
1796024 TTTTCGAGTTGCTCGCAAAC
1 TTTTCGAGTTGCTCGCAAAC
1796044 TTTTCGAGTTGCTCGCAAAC
1 TTTTCGAGTTGCTCGCAAAC
1796064 TTTTCGAG
1 TTTTCGAG
1796072 CCGAGTATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.38
Consensus pattern (20 bp):
TTTTCGAGTTGCTCGCAAAC
Found at i:1802528 original size:3 final size:3
Alignment explanation
Indices: 1802503--1802550 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
1802493 ATATAAACAA
* *
1802503 AAT AAT TAT AAAT AAT AAC AAT AAT AAT AAT AAT AAT ATAT AA- AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
1802549 AA
1 AA
1802551 ATAACATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.82
4 5 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1802989 original size:133 final size:133
Alignment explanation
Indices: 1802758--1803061 Score: 398
Period size: 133 Copynumber: 2.3 Consensus size: 133
1802748 GGTGACACAG
* * * * *
1802758 CTCCTACGTGATGAGGAGATCTGGTTGGGGGATGACACTTCTCATACGTGATGAAGGGTTCTGGT
1 CTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGTCTCATACGTGATGAAGAGTTCTGGC
* * * ** *
1802823 CATCTTTAGGGAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATC-AGGGGCGAC
66 CATCTTTAGGAAGGGCGATAACACAGTTCCTACGCAATAAGGACGGCTGGTTATCTA-GGGCGAC
1802887 ACGA
130 ACGA
* *
1802891 CTCCTACGTGATGAGCAGGTCTAGTCGGGGGATGGA-ACGTCTCATACGTGATGAAGAGTTCTGG
1 CTCCTACGTGATGAGGAGGTCTGGTCGGGGGAT-GACACGTCTCATACGTGATGAAGAGTTCTGG
* *
1802955 CCATCTTTAGGAAGGGCGATAACACAGTTCCTACGCAATAAGGACGGCTGGTTATCTAGGGTGAT
65 CCATCTTTAGGAAGGGCGATAACACAGTTCCTACGCAATAAGGACGGCTGGTTATCTAGGGCGAC
*
1803020 ACGG
130 ACGA
* * *
1803024 CTCCTGCATGATGAGGAGGTCTGGTC-GGGGATAACACG
1 CTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACG
1803062 ATTTTGATGC
Statistics
Matches: 147, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
131 1 0.01
132 9 0.06
133 134 0.91
134 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (133 bp):
CTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGTCTCATACGTGATGAAGAGTTCTGGC
CATCTTTAGGAAGGGCGATAACACAGTTCCTACGCAATAAGGACGGCTGGTTATCTAGGGCGACA
CGA
Found at i:1803448 original size:64 final size:64
Alignment explanation
Indices: 1803243--1803464 Score: 204
Period size: 64 Copynumber: 3.5 Consensus size: 64
1803233 AGGGATAATG
* * * ** * * *
1803243 GTTTCAAGGGAAACTGACTCAAAGATTGGTTTTTGATAGAAACTGTCTCAAGGGAGACAAAA-TT
1 GTTTCAAGAGAAACAGATTCAAAGATT--TTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTT
*
1803307 C
64 T
* * * *
1803308 GTTTCAAG-GTAAAC-GTTCTCAAAGATGATTTTCAAAAGAAATTGTCT-TA-AGAGATAAAACT
1 GTTTCAAGAG-AAACAGAT-TCAAAGAT-TTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACT
1803369 TT
63 TT
*
1803371 GTTTCAA-AGGAAACAAATTCAAAGATTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTT
1 GTTTCAAGA-GAAACAGATTCAAAGATTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTT
* *
1803435 GTTTCAAGAGAAACAGACTCAAATATTTTT
1 GTTTCAAGAGAAACAGATTCAAAGATTTTT
1803465 GTTTCAAAAG
Statistics
Matches: 128, Mismatches: 19, Indels: 21
0.76 0.11 0.12
Matches are distributed among these distances:
62 27 0.21
63 23 0.18
64 57 0.45
65 21 0.16
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (64 bp):
GTTTCAAGAGAAACAGATTCAAAGATTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTT
Found at i:1803492 original size:29 final size:29
Alignment explanation
Indices: 1803432--1803518 Score: 138
Period size: 29 Copynumber: 3.0 Consensus size: 29
1803422 GAGACAAAAC
* *
1803432 TTTGTTTCAAGAGAAACAGACTCAAATATT
1 TTTGTTTCAAAAGAAAC-GACTCAAAGATT
1803462 TTTGTTTCAAAAGAAACGACTCAAAGATT
1 TTTGTTTCAAAAGAAACGACTCAAAGATT
*
1803491 TTTGTCTCAAAAGAAACGACTCAAAGAT
1 TTTGTTTCAAAAGAAACGACTCAAAGAT
1803519 GATGGTTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 38 0.70
30 16 0.30
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (29 bp):
TTTGTTTCAAAAGAAACGACTCAAAGATT
Found at i:1803746 original size:36 final size:35
Alignment explanation
Indices: 1803701--1803822 Score: 111
Period size: 34 Copynumber: 3.4 Consensus size: 35
1803691 AAAGGAAAAA
**
1803701 TGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAAT
1 TGTCTCAAGCGAGAAAAAATTTGTTTT-AAAGAAAT
* * * * *
1803737 TGTCTCAAGCAAGAAAAAAATTATTTTAGA-AAAC
1 TGTCTCAAGCGAGAAAAAATTTGTTTTAAAGAAAT
* *
1803771 TGTCTCAAACGAGAAAAAATTTGTTTTTCAAAAGAAGT
1 TGTCTCAAGCGAGAAAAAATTTG-TTTT--AAAGAAAT
*
1803809 TGTCTCTAGCGAGA
1 TGTCTCAAGCGAGA
1803823 CAATATTTTG
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
34 22 0.33
35 6 0.09
36 22 0.33
37 2 0.03
38 14 0.21
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (35 bp):
TGTCTCAAGCGAGAAAAAATTTGTTTTAAAGAAAT
Found at i:1803993 original size:32 final size:32
Alignment explanation
Indices: 1803925--1803996 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 32
1803915 TTCGCATCAA
*
1803925 GATGTTGAATCCCCAAAGATATCCCAATATTT
1 GATGTTGAATCCCCAAAGATATCCCAATATTC
*
1803957 GATGTTGAATCTCCAAAGATGA-CCC-ATCATTC
1 GATGTTGAATCCCCAAAGAT-ATCCCAAT-ATTC
1803989 GATGTTGA
1 GATGTTGA
1803997 TTGCTTCAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
31 2 0.06
32 33 0.92
33 1 0.03
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGATATCCCAATATTC
Found at i:1807965 original size:198 final size:198
Alignment explanation
Indices: 1807610--1807986 Score: 549
Period size: 198 Copynumber: 1.9 Consensus size: 198
1807600 CTGCTTCGTC
1807610 TCGTATCTTCGTATTTGGAACTGATACCCCTCAATGCTCTGTAACCTAACTCGGTTAATGCCCCT
1 TCGTATCTTCGTATTTGGAACTGATACCCCTCAATGCTCTGTAACCTAACTCGGTTAATGCCCCT
*** * * * * *
1807675 GCAGTGGTAAAGTTGGTGTGTCACTCCCTGATAACTAGCAATGAAATTATTGTAGATGAGAATCT
66 GCAGTGGTAAAGTCAATGCGTCACTCCCTGATAACTAGAAATGAAATGATTGTAGATAAGAATCC
** * * **
1807740 ACTGTTGGATTACTCTTTGGCTCAATGGATCATCATTTCAGTCTCGAATGTTGCACAATCTTTGA
131 ACTACTGAATTACTCCTTGAATCAATGGATCATCATTTCAGTCTCGAATGTTGCACAATCTTTGA
1807805 GTT
196 GTT
*
1807808 TCGTATCTTCGTATTTGGAACTGATGCCCCTCAATGCTCTGTAACCTAACTCGGTTAATGCCCCT
1 TCGTATCTTCGTATTTGGAACTGATACCCCTCAATGCTCTGTAACCTAACTCGGTTAATGCCCCT
* * * * * *
1807873 GCGGTGGTAAAGTCAATGCGTCGCTCCTTGATGACTAGAAATGACATGATTGTAGATAAGACTCC
66 GCAGTGGTAAAGTCAATGCGTCACTCCCTGATAACTAGAAATGAAATGATTGTAGATAAGAATCC
1807938 ACTACTGAATTAC-CGCTTGAATCAATGGATCATCATTTCAGTCTCGAAT
131 ACTACTGAATTACTC-CTTGAATCAATGGATCATCATTTCAGTCTCGAAT
1807987 ATTACACGAT
Statistics
Matches: 157, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
197 1 0.01
198 156 0.99
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (198 bp):
TCGTATCTTCGTATTTGGAACTGATACCCCTCAATGCTCTGTAACCTAACTCGGTTAATGCCCCT
GCAGTGGTAAAGTCAATGCGTCACTCCCTGATAACTAGAAATGAAATGATTGTAGATAAGAATCC
ACTACTGAATTACTCCTTGAATCAATGGATCATCATTTCAGTCTCGAATGTTGCACAATCTTTGA
GTT
Found at i:1811681 original size:3 final size:3
Alignment explanation
Indices: 1811666--1811710 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
1811656 TATAATTATA
*
1811666 AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1811711 ATAACATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1811714 original size:9 final size:10
Alignment explanation
Indices: 1811657--1811714 Score: 56
Period size: 9 Copynumber: 6.4 Consensus size: 10
1811647 TGCAAAATGT
*
1811657 ATAATTATAA
1 ATAATAATAA
*
1811667 ATAATAA-CA
1 ATAATAATAA
1811676 ATAATAAT-A
1 ATAATAATAA
1811685 ATAATAAT-A
1 ATAATAATAA
1811694 ATAATAAT--
1 ATAATAATAA
1811702 ATAA-AATAA
1 ATAATAATAA
1811711 ATAA
1 ATAA
1811715 CATAAAAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
7 3 0.07
8 4 0.09
9 30 0.70
10 6 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAATAATAA
Found at i:1812937 original size:36 final size:36
Alignment explanation
Indices: 1812880--1812948 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
1812870 CTTCATCTCT
* *
1812880 ACTTCTTCTTCCTCTCCTTCTTTATGGAAATAATCG
1 ACTTATTCTTCCTCTCCTTCTTTATGAAAATAATCG
*
1812916 ACTTATTCTTCCTCTCTTTCTTTATGAAAATAA
1 ACTTATTCTTCCTCTCCTTCTTTATGAAAATAA
1812949 AGGATTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.06, T:0.46
Consensus pattern (36 bp):
ACTTATTCTTCCTCTCCTTCTTTATGAAAATAATCG
Found at i:1814921 original size:5 final size:5
Alignment explanation
Indices: 1814899--1814939 Score: 55
Period size: 5 Copynumber: 8.0 Consensus size: 5
1814889 ATATGAGAAA
* *
1814899 AATTC AATTT AAATTT AAATT AATTT AATTT AATTT AATTT
1 AATTT AATTT -AATTT AATTT AATTT AATTT AATTT AATTT
1814940 TAAAATAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (5 bp):
AATTT
Found at i:1814933 original size:26 final size:27
Alignment explanation
Indices: 1814899--1814954 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1814889 ATATGAGAAA
*
1814899 AATTCAATTTAAATTTAAATTAAT-TT
1 AATTCAATTTAAATTTAAAATAATGTT
* *
1814925 AATTTAATTTAATTTTAAAATAATGTT
1 AATTCAATTTAAATTTAAAATAATGTT
1814952 AAT
1 AAT
1814955 AAATAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (27 bp):
AATTCAATTTAAATTTAAAATAATGTT
Found at i:1815696 original size:81 final size:82
Alignment explanation
Indices: 1815596--1815970 Score: 429
Period size: 81 Copynumber: 4.6 Consensus size: 82
1815586 TCTTTTCCTT
* *
1815596 ATCATCA-GGTGATTTTTCACCAGCGAACGGACTCTCTTGTTCGACGTCTTCTCCCAATGATCTT
1 ATCATCATCGTGATTTTTCACCAGCGAACGGACTCTCTTGTTCAACGTCTTCTCCCAATGATCTT
* **
1815660 CCTGCCTTTTCTCCCTC
66 CCTGGCTTCCCTCCCTC
* * * * * *
1815677 ATCA-CCTCGTGATTTTTCACCAGCGAACGGACTATCTTTTTCAACGTCTTCTCCTAGTAATCTT
1 ATCATCATCGTGATTTTTCACCAGCGAACGGACTCTCTTGTTCAACGTCTTCTCCCAATGATCTT
* *
1815741 CCCGGCTTCCCTTCCTC
66 CCTGGCTTCCCTCCCTC
* **
1815758 ATCATC--CGGTGGTTTTTCACCAGCGAACATACTCTCTTGTTCAACGTCTTCTCCCAATGATCT
1 ATCATCATC-GTGATTTTTCACCAGCGAACGGACTCTCTTGTTCAACGTCTTCTCCCAATGATCT
1815821 TCCTGGCTTCCCTTCCTCATC
65 TCCTGGCTTCCC-TCC-C-TC
* * * * *
1815842 ATCATTATCAGGTGGTTCTTT-ACCAGCGAACGAACTCTCTTCTTCAATGTCTTCTCCCAATGAT
1 ATCATCATC--GTGATT-TTTCACCAGCGAACGGACTCTCTTGTTCAACGTCTTCTCCCAATGAT
*
1815906 CTTCCTGGCATCCCTCCCTC
63 CTTCCTGGCTTCCCTCCCTC
* *
1815926 ATCATCATC-TGATTTTTCACCAGCGAACGGACTCTCCTCTTCAAC
1 ATCATCATCGTGATTTTTCACCAGCGAACGGACTCTCTTGTTCAAC
1815971 AGCTTGCAGA
Statistics
Matches: 249, Mismatches: 34, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
80 5 0.02
81 156 0.63
82 3 0.01
83 1 0.00
84 17 0.07
85 1 0.00
86 4 0.02
87 59 0.24
88 3 0.01
ACGTcount: A:0.18, C:0.34, G:0.13, T:0.35
Consensus pattern (82 bp):
ATCATCATCGTGATTTTTCACCAGCGAACGGACTCTCTTGTTCAACGTCTTCTCCCAATGATCTT
CCTGGCTTCCCTCCCTC
Found at i:1815798 original size:162 final size:167
Alignment explanation
Indices: 1815590--1815970 Score: 459
Period size: 168 Copynumber: 2.3 Consensus size: 167
1815580 CTGATTTCTT
* * *
1815590 TTCCTTATCATCAGGTGATTTTTCACCAGCGAACGGACTCTCTTGTTCGACGTCTTCTCCCAATG
1 TTCCTCATCATCAGGTGATTTTTCACCAGCGAACAGACTCTCTTGTTCAACGTCTTCTCCCAATG
** * *
1815655 ATCTTCCTGCCTTTTC-TCC-C-TCATCA-CCTC-GTGATT-TTTCACCAGCGAACGGACTATCT
66 ATCTTCCTGCCTTCCCTTCCTCATCATCATCATCAGTGATTCTTT-ACCAGCGAACGAACTATCT
* * * *
1815714 TTTTCAACGTCTTCTCCTAGTAATCTTCCCGGCTTCCC
130 TCTTCAACGTCTTCTCCCAATAATCTTCCCGGCATCCC
* * *
1815752 TTCCTCATCATCCGGTGGTTTTTCACCAGCGAACATACTCTCTTGTTCAACGTCTTCTCCCAATG
1 TTCCTCATCATCAGGTGATTTTTCACCAGCGAACAGACTCTCTTGTTCAACGTCTTCTCCCAATG
* * * *
1815817 ATCTTCCTGGCTTCCCTTCCTCATCATCATTATCAGGTGGTTCTTTACCAGCGAACGAACTCTCT
66 ATCTTCCTGCCTTCCCTTCCTCATCATCATCATCA-GTGATTCTTTACCAGCGAACGAACTATCT
* * *
1815882 TCTTCAATGTCTTCTCCCAATGATCTTCCTGGCATCCC
130 TCTTCAACGTCTTCTCCCAATAATCTTCCCGGCATCCC
* ** * * *
1815920 TCCCTCATCATCATCTGATTTTTCACCAGCGAACGGACTCTCCTCTTCAAC
1 TTCCTCATCATCAGGTGATTTTTCACCAGCGAACAGACTCTCTTGTTCAAC
1815971 AGCTTGCAGA
Statistics
Matches: 182, Mismatches: 30, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
162 72 0.40
163 3 0.02
164 1 0.01
165 6 0.03
166 2 0.01
168 95 0.52
169 3 0.02
ACGTcount: A:0.18, C:0.34, G:0.13, T:0.35
Consensus pattern (167 bp):
TTCCTCATCATCAGGTGATTTTTCACCAGCGAACAGACTCTCTTGTTCAACGTCTTCTCCCAATG
ATCTTCCTGCCTTCCCTTCCTCATCATCATCATCAGTGATTCTTTACCAGCGAACGAACTATCTT
CTTCAACGTCTTCTCCCAATAATCTTCCCGGCATCCC
Found at i:1828254 original size:61 final size:61
Alignment explanation
Indices: 1828174--1828296 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 61
1828164 TACTCCACTT
* * *
1828174 TTAATATAAAACGATCATTAATTTTCGGCAATCAAAACCAAACTCTGTTCGATGAATGCTA
1 TTAATATAAAAAGAACATTAAATTTCGGCAATCAAAACCAAACTCTGTTCGATGAATGCTA
*
1828235 TTAATATAAAAAGAACATTAAATTTCGGCAATCAAGACCAAACTCTGTTCGATGAATGCTA
1 TTAATATAAAAAGAACATTAAATTTCGGCAATCAAAACCAAACTCTGTTCGATGAATGCTA
1828296 T
1 T
1828297 AGGAACAGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (61 bp):
TTAATATAAAAAGAACATTAAATTTCGGCAATCAAAACCAAACTCTGTTCGATGAATGCTA
Found at i:1829609 original size:25 final size:25
Alignment explanation
Indices: 1829576--1829623 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1829566 TCAAATTTAA
*
1829576 AATCTTAAAAA-TAATAATATTTTTT
1 AATCATAAAAACTAATAA-ATTTTTT
1829601 AATCATAAAAACTAATAAATTTT
1 AATCATAAAAACTAATAAATTTT
1829624 GATTTTTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (25 bp):
AATCATAAAAACTAATAAATTTTTT
Found at i:1830468 original size:16 final size:16
Alignment explanation
Indices: 1830447--1830477 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1830437 TACAAAATCT
1830447 AATAATTCATAATATA
1 AATAATTCATAATATA
*
1830463 AATAATTCATTATAT
1 AATAATTCATAATAT
1830478 TATATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:1830479 original size:5 final size:5
Alignment explanation
Indices: 1830471--1830500 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1830461 TAAATAATTC
1830471 ATTAT ATTAT ATTAT ATTAT A-TAT ATTAT A
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
1830501 AAAATAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATTAT
Found at i:1830481 original size:19 final size:19
Alignment explanation
Indices: 1830447--1830502 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
1830437 TACAAAATCT
1830447 AATAATTCA-TA-A-TATA
1 AATAATTCATTATATTATA
1830463 AATAATTCATTATATTAT-
1 AATAATTCATTATATTATA
*
1830481 ATTATATT-ATATATATTATA
1 AATA-ATTCAT-TATATTATA
1830501 AA
1 AA
1830503 AATAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 9 0.28
17 2 0.06
18 6 0.19
19 14 0.44
20 1 0.03
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (19 bp):
AATAATTCATTATATTATA
Found at i:1835331 original size:29 final size:29
Alignment explanation
Indices: 1835299--1835392 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
1835289 ATTAGTCTTT
1835299 AAACTTTTAAACATTTCAATTTCATCCCC
1 AAACTTTTAAACATTTCAATTTCATCCCC
* * * * **
1835328 AAACTATGACTATCA-TTCTAAATT-AGTCCTT
1 AAACTTTTA--AACATTTC-AATTTCA-TCCCC
*
1835359 AAACTTTTAAACATTGCAATTTCATCCCC
1 AAACTTTTAAACATTTCAATTTCATCCCC
1835388 AAACT
1 AAACT
1835393 ATGAATCTCA
Statistics
Matches: 46, Mismatches: 13, Indels: 12
0.65 0.18 0.17
Matches are distributed among these distances:
29 22 0.48
30 7 0.15
31 17 0.37
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (29 bp):
AAACTTTTAAACATTTCAATTTCATCCCC
Found at i:1835361 original size:60 final size:60
Alignment explanation
Indices: 1835268--1835485 Score: 262
Period size: 60 Copynumber: 3.6 Consensus size: 60
1835258 ACATGTTTCT
* *
1835268 AAACTATGACTCTTATT-TCAAATTAGTCTTTAAACTTTTAAACATTTCAATTTCATCCCC
1 AAACTATGACTCTCATTCT-AAATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCCCC
* *
1835328 AAACTATGACTATCATTCTAAATTAGTCCTTAAACTTTTAAACATTGCAATTTCATCCCC
1 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCCCC
* * * * * * *
1835388 AAACTATGAATCTCATTCTAAATTGGTCCCTAAACTTTT-GA-ATCTTCTAGTTTCATTCCT
1 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACAT-TTC-AATTTCATCCCC
* * *
1835448 AAACTATGACTTTCATTCTAAATTGGTCCATAAACTTT
1 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTT
1835486 GGATCTTCTA
Statistics
Matches: 139, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
58 2 0.01
59 3 0.02
60 133 0.96
61 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCCCC
Found at i:1836988 original size:3 final size:3
Alignment explanation
Indices: 1836980--1837058 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
1836970 TGAATGTTGG
1836980 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1837028 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1837059 TATATTGTAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1837397 original size:13 final size:15
Alignment explanation
Indices: 1837364--1837394 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1837354 AATATTCTTC
1837364 AAATAATTTTAAGAA
1 AAATAATTTTAAGAA
1837379 AAATAATTTTAA-AA
1 AAATAATTTTAAGAA
1837393 AA
1 AA
1837395 TAAAAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
AAATAATTTTAAGAA
Found at i:1838536 original size:3 final size:3
Alignment explanation
Indices: 1838528--1838704 Score: 87
Period size: 3 Copynumber: 55.7 Consensus size: 3
1838518 AAACAAACAA
1838528 AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT GCAAT -AT ATAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT --AAT AAT A-AT A-AT
* * * *
1838577 ATAT AAT AAT AAT AAG ATAT AGT ATTT AAT AA- AA- AAG AAT AA- AAT
1 A-AT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* * *
1838622 AAAT AAAT AAAT AAAG AAC AAT AAT AAT AAT AAA AGAT AAT AA- AAT
1 -AAT -AAT -AAT -AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* *
1838668 ACAT ATAT AAT ATT AGGT AA- AAT AAT AAT AAT AAT AA
1 A-AT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AA
1838705 AAAGTAAAAA
Statistics
Matches: 144, Mismatches: 15, Indels: 30
0.76 0.08 0.16
Matches are distributed among these distances:
2 12 0.08
3 87 0.60
4 42 0.29
5 3 0.02
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1838727 original size:2 final size:2
Alignment explanation
Indices: 1838722--1838766 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1838712 AAAAAAGTAA
1838722 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
1838764 AT A
1 AT A
1838767 AATGTATAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1839377 original size:548 final size:544
Alignment explanation
Indices: 1838774--1839868 Score: 2019
Period size: 548 Copynumber: 2.0 Consensus size: 544
1838764 ATAAATGTAT
*
1838774 AAAAAATTAGAAAAAAAGTAAAAGAAAGAAAAGTAAATAATAAATAATAATAATAATAAAAACCA
1 AAAAAAATAGAAAAAAAGTAAAAGAAAGAAAAGTAAATAATAAATAATAATAATAATAAAAACCA
1838839 CAAATTAAAGAAAATAGTAAAAAAGGAATAAAAAATAATAAAAAGAAACAAATAAAAATATATGT
66 CAAATTAAAGAAAATAGTAAAAAAGGAATAAAAAATAATAAAAAGAAACAAATAAAAATATATGT
*
1838904 ATATTAATAATAATAGTGGATTAAGTTGAAAAGGAAATGAATTAGGGGTCGAATTTAGGAATAAA
131 ATATTAATAATAATAGTGGATTAAATTGAAAAGGAAATGAATTAGGGGTCGAATTTAGGAATAAA
*
1838969 TTACCGTGAAAATCGAATATAGGGACTTTTAAATGATCTTTTAAAACAAGGGGGACTAGAAGTAT
196 TTACCGTGAAAATCGAATATAGGGACTTTTAAATGATCTTTTAAAACAAGGAGGACTAGAAGTAT
*
1839034 AATTTGCCCATCAATTCGGTAAAACACGCGGGTCTAACGTGGGCATGGGTCGGGTCATGGAGGTC
261 AATTTGCCCATCAATTCGGTAAAACACGCGGGTCTAACGTGGGCATGGGTCGGGTCATGGAAGTC
1839099 CGATGGGTTCAGTATGAAGCCAACATTTTTTTTAAATCTCATTTCTTCTCTTCTCACGCCAAAAA
326 CGATGGGTTCAGTATGAAGCCAACA-TTTTTTTAAATCTCATTTCTTCTCTTCTCACGCCAAAAA
1839164 CTCCCCCCATTCAGTTTTCCTCTCATTTGTTATTCACAAATGAAGAACATGGGTCGTGGTTTTCA
390 CT-CCCCCATTCAGTTTTCCTCTCATTTGTTATTCACAAATGAAGAACATGGGTCGTGGTTTTCA
* *
1839229 GAAATTGGCCATCGGCCGCCTCGCGGTGTTCATCGGTGGTAAAATTTGATTTTTTTTTTGTTTTT
454 AAAATTGGCCATCGACCGCCTCGCGGTGTTCATCGGTGGTAAAATTTGA-TTTTTTTTTGTTTTT
1839294 CGAAAGCCTTACCCTACACCAACTCAA
518 CGAAAGCCTTACCCTACACCAACTCAA
1839321 AAAAAAATAGAAAAGAAAGTAAAAGAAAGAAAAGTAAATAATAAATAATAATAATAATAAAAACC
1 AAAAAAATAGAAAA-AAAGTAAAAGAAAGAAAAGTAAATAATAAATAATAATAATAATAAAAACC
1839386 ACAAATTAAAGAAAATAGTAAAAAAGGAATAAAAAATAATAAAAAGAAACAAATAAAAATATATG
65 ACAAATTAAAGAAAATAGTAAAAAAGGAATAAAAAATAATAAAAAGAAACAAATAAAAATATATG
1839451 TATATTAATAATAATAGTGGATTAAATTGAAAAGGAAATGAATTAGGGGTCGAATTTAGGAATAA
130 TATATTAATAATAATAGTGGATTAAATTGAAAAGGAAATGAATTAGGGGTCGAATTTAGGAATAA
* *
1839516 ATTAGCGTGAAAATCGAATATAGGGACTTTTAAATGATCTTTTAAAATAAGGAGGACTAGAAGTA
195 ATTACCGTGAAAATCGAATATAGGGACTTTTAAATGATCTTTTAAAACAAGGAGGACTAGAAGTA
* * *
1839581 TAATTTGCCCATCAATTCGGTAACACACGCGGGTCTAACGTGGGCATGGTTTGGGTCATGGAAGT
260 TAATTTGCCCATCAATTCGGTAAAACACGCGGGTCTAACGTGGGCATGGGTCGGGTCATGGAAGT
*
1839646 CCGATGGGTTCAGTATGAAGCCAACATTTTTTTAAATCTCATTTCTTCTCTTCTCACGCCAAAAG
325 CCGATGGGTTCAGTATGAAGCCAACATTTTTTTAAATCTCATTTCTTCTCTTCTCACGCCAAAAA
*
1839711 CTCCCCCATTCAGTTTTCCTCTCCTTTGTTATTCACAAATGAAGAACATGGGTCGTGGTTTTCAA
390 CTCCCCCATTCAGTTTTCCTCTCATTTGTTATTCACAAATGAAGAACATGGGTCGTGGTTTTCAA
1839776 AAATTGGCCATCGACCGCCTCGCGGTGTTCATCGGTGGTAAAATTTGATTTTTTTTTGTTTTTCG
455 AAATTGGCCATCGACCGCCTCGCGGTGTTCATCGGTGGTAAAATTTGATTTTTTTTTGTTTTTCG
* *
1839841 AAAGCTTTTCCCTACACCAACTCAA
520 AAAGCCTTACCCTACACCAACTCAA
1839866 AAA
1 AAA
1839869 CAACCTTGGA
Statistics
Matches: 532, Mismatches: 15, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
545 43 0.08
546 108 0.20
547 53 0.10
548 328 0.62
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (544 bp):
AAAAAAATAGAAAAAAAGTAAAAGAAAGAAAAGTAAATAATAAATAATAATAATAATAAAAACCA
CAAATTAAAGAAAATAGTAAAAAAGGAATAAAAAATAATAAAAAGAAACAAATAAAAATATATGT
ATATTAATAATAATAGTGGATTAAATTGAAAAGGAAATGAATTAGGGGTCGAATTTAGGAATAAA
TTACCGTGAAAATCGAATATAGGGACTTTTAAATGATCTTTTAAAACAAGGAGGACTAGAAGTAT
AATTTGCCCATCAATTCGGTAAAACACGCGGGTCTAACGTGGGCATGGGTCGGGTCATGGAAGTC
CGATGGGTTCAGTATGAAGCCAACATTTTTTTAAATCTCATTTCTTCTCTTCTCACGCCAAAAAC
TCCCCCATTCAGTTTTCCTCTCATTTGTTATTCACAAATGAAGAACATGGGTCGTGGTTTTCAAA
AATTGGCCATCGACCGCCTCGCGGTGTTCATCGGTGGTAAAATTTGATTTTTTTTTGTTTTTCGA
AAGCCTTACCCTACACCAACTCAA
Found at i:1841368 original size:120 final size:120
Alignment explanation
Indices: 1841201--1841424 Score: 380
Period size: 120 Copynumber: 1.9 Consensus size: 120
1841191 GATGCTTCTT
*
1841201 GTGGACACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCATTGTGAAGTTGAGC
1 GTGGACACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCATTGTGAAGTTGAGC
1841266 CTTC-AATTGGATATCCTTCGT-TGTGAAATTGAAATCCAAGTATTGTATGTTGCTG
66 C-TCGAATTGGATATCCTTCGTCT-TGAAATTGAAATCCAAGTATTGTATGTTGCTG
**
1841321 GTGGACACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGACCCCTTTGTTGTGAAGTTGAGC
1 GTGGACACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCATTGTGAAGTTGAGC
*
1841386 CTCGAATTGGATATCCTTCGTCTTGAAGTTGAAATCCAA
66 CTCGAATTGGATATCCTTCGTCTTGAAATTGAAATCCAA
1841425 TCTTGAGTAA
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
119 2 0.02
120 95 0.97
121 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (120 bp):
GTGGACACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGACCCCTTCATTGTGAAGTTGAGC
CTCGAATTGGATATCCTTCGTCTTGAAATTGAAATCCAAGTATTGTATGTTGCTG
Found at i:1841534 original size:59 final size:55
Alignment explanation
Indices: 1841396--1841534 Score: 165
Period size: 55 Copynumber: 2.5 Consensus size: 55
1841386 CTCGAATTGG
* * ***
1841396 ATATCCTTCGTCT-TGAAGTTGAAATCCAATCTTGAGTAAGTTGGTTTTGAGTTGG
1 ATATCCTTCGT-TGTGAAGTTGAAATCCAATCTCGAGTAAGATGGTTTTGAGTCCA
1841451 ATATCCTTCGTTGTGAAGTTGAAATCCAATCTCGAGTAA-ATGGTGTCGCTTCGAGTCCA
1 ATATCCTTCGTTGTGAAGTTGAAATCCAATCTCGAGTAAGATGGT-T---TT-GAGTCCA
1841510 ATATCCTTCGTTGTGAAGTTGAAAT
1 ATATCCTTCGTTGTGAAGTTGAAAT
1841535 TGACTCTAGC
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
54 5 0.07
55 37 0.51
58 2 0.03
59 29 0.40
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (55 bp):
ATATCCTTCGTTGTGAAGTTGAAATCCAATCTCGAGTAAGATGGTTTTGAGTCCA
Found at i:1842334 original size:19 final size:19
Alignment explanation
Indices: 1842297--1842334 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1842287 CCACCTTATT
*
1842297 TTCTTTTTATTTTCTTTTA
1 TTCTTTTTATTTTCATTTA
1842316 TTCTTTTT-TTTTCAATTTA
1 TTCTTTTTATTTTC-ATTTA
1842335 GGGCGTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (19 bp):
TTCTTTTTATTTTCATTTA
Found at i:1852721 original size:17 final size:16
Alignment explanation
Indices: 1852699--1852784 Score: 73
Period size: 17 Copynumber: 4.9 Consensus size: 16
1852689 AAAATCAAGA
*
1852699 AAATAAAAAAATACAT
1 AAATAAAAAAATAAAT
*
1852715 AAGATAAAGAAAATAAAG
1 AA-ATAAA-AAAATAAAT
* *
1852733 ACAATATATAAATAAATGT
1 A-AATAAAAAAATAAA--T
1852752 AAGATAAAAAAATAAAT
1 AA-ATAAAAAAATAAAT
1852769 AAATAATAAAAATAAA
1 AAATAA-AAAAATAAA
1852785 AAAAAGTAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
16 6 0.11
17 24 0.43
18 13 0.23
19 13 0.23
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (16 bp):
AAATAAAAAAATAAAT
Found at i:1852726 original size:35 final size:35
Alignment explanation
Indices: 1852686--1852784 Score: 96
Period size: 35 Copynumber: 2.8 Consensus size: 35
1852676 ATATAAAATC
*
1852686 AAGAAAATCAAGAAAATAAAAAAATACA-TAAGATA
1 AAGAAAAT-AAGAAAATAAAAAAATAAAGTAAGATA
* * *
1852721 AAGAAAATAAAGACAATATATAAATAAATGTAAGATA
1 AAGAAAAT-AAGAAAATAAAAAAATAAA-GTAAGATA
1852758 AA-AAAATAA-ATAAATAATAAAAATAAA
1 AAGAAAATAAGA-AAATAA-AAAAATAAA
1852785 AAAAAGTAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
34 1 0.02
35 29 0.56
36 13 0.25
37 9 0.17
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.18
Consensus pattern (35 bp):
AAGAAAATAAGAAAATAAAAAAATAAAGTAAGATA
Found at i:1852732 original size:9 final size:8
Alignment explanation
Indices: 1852698--1852788 Score: 56
Period size: 8 Copynumber: 10.5 Consensus size: 8
1852688 GAAAATCAAG
1852698 AAAATAAA
1 AAAATAAA
*
1852706 AAAATACAT
1 AAAATA-AA
*
1852715 AAGATAAA
1 AAAATAAA
1852723 GAAAATAAA
1 -AAAATAAA
* *
1852732 GACAATATA
1 -AAAATAAA
*
1852741 TAAATAAA
1 AAAATAAA
*
1852749 TGTAAGATAAA
1 ---AAAATAAA
1852760 AAAATAAA
1 AAAATAAA
*
1852768 TAAATAATA
1 AAAATAA-A
1852777 AAAATAAA
1 AAAATAAA
1852785 AAAA
1 AAAA
1852789 AGTAAGTGAA
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
8 30 0.48
9 27 0.43
11 6 0.10
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (8 bp):
AAAATAAA
Found at i:1852765 original size:27 final size:25
Alignment explanation
Indices: 1852690--1852788 Score: 101
Period size: 27 Copynumber: 3.8 Consensus size: 25
1852680 AAAATCAAGA
* *
1852690 AAATCAAGAAAATAAAAAAATACAT
1 AAATAAAGAAAATAAAAAAATAAAT
* *
1852715 AAGATAAAGAAAATAAAGACAATATAT
1 AA-ATAAAGAAAATAAA-AAAATAAAT
*
1852742 AAATAAATGTAAGATAAAAAAATAAAT
1 AAATAAA-G-AAAATAAAAAAATAAAT
1852769 AAATAATA-AAAATAAAAAAA
1 AAATAA-AGAAAATAAAAAAA
1852789 AGTAAGTGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
25 13 0.21
26 18 0.29
27 23 0.37
28 8 0.13
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (25 bp):
AAATAAAGAAAATAAAAAAATAAAT
Found at i:1859530 original size:3 final size:3
Alignment explanation
Indices: 1859522--1859554 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1859512 GACACGTCAT
1859522 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1859555 TATGTAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1867199 original size:24 final size:24
Alignment explanation
Indices: 1867167--1867220 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1867157 TTACCTTTTC
1867167 TTGATTGATCAGATCTTGAAATGA
1 TTGATTGATCAGATCTTGAAATGA
1867191 TTGATTGATCAGATCTTGAAATGA
1 TTGATTGATCAGATCTTGAAATGA
1867215 TTGATT
1 TTGATT
1867221 TTGGGTATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.41
Consensus pattern (24 bp):
TTGATTGATCAGATCTTGAAATGA
Found at i:1867777 original size:20 final size:20
Alignment explanation
Indices: 1867749--1867805 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
1867739 TACTTTACAT
*
1867749 AGTAGTATCGATACCATAGG
1 AGTAATATCGATACCATAGG
1867769 AGTAATATCGATACCATAGG
1 AGTAATATCGATACCATAGG
1867789 AGTAATATCGATACCAT
1 AGTAATATCGATACCAT
1867806 CAGGCCCTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (20 bp):
AGTAATATCGATACCATAGG
Found at i:1872029 original size:28 final size:28
Alignment explanation
Indices: 1871989--1872060 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 28
1871979 GAGGAACACC
1871989 AACTGTCCCTCCACGTTTCAGCTCCACT
1 AACTGTCCCTCCACGTTTCAGCTCCACT
*
1872017 AACTGTCCCTCCAGGTTTCAGCTCCACT
1 AACTGTCCCTCCACGTTTCAGCTCCACT
* *
1872045 AGCTATCCCTCCACGT
1 AACTGTCCCTCCACGT
1872061 CCTGAATCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.18, C:0.42, G:0.12, T:0.28
Consensus pattern (28 bp):
AACTGTCCCTCCACGTTTCAGCTCCACT
Found at i:1873045 original size:14 final size:14
Alignment explanation
Indices: 1873015--1873048 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1873005 TTTTCATTTA
*
1873015 TTTAATTTCAATCC
1 TTTAATTTCAATAC
*
1873029 TTTAATTTCACTAC
1 TTTAATTTCAATAC
1873043 TTTAAT
1 TTTAAT
1873049 ATTCTAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTAATTTCAATAC
Found at i:1873073 original size:14 final size:14
Alignment explanation
Indices: 1873056--1873082 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1873046 AATATTCTAA
1873056 CTTTTTATTTTTTT
1 CTTTTTATTTTTTT
1873070 CTTTTTATTTTTT
1 CTTTTTATTTTTT
1873083 AATATTTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (14 bp):
CTTTTTATTTTTTT
Found at i:1873300 original size:18 final size:17
Alignment explanation
Indices: 1873277--1873312 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
1873267 TAATTTAGTA
1873277 ATTTAATTATTATTCTTT
1 ATTTAATTATTATT-TTT
1873295 ATTTAATTATTATTTTT
1 ATTTAATTATTATTTTT
1873312 A
1 A
1873313 ATTATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTAATTATTATTTTT
Found at i:1873439 original size:2 final size:2
Alignment explanation
Indices: 1873432--1873499 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1873422 ACCTTACTTA
1873432 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
1873474 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
1873500 TGTAGACTCC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1878789 original size:19 final size:18
Alignment explanation
Indices: 1878765--1878803 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
1878755 AATGATACCT
1878765 TTTGTAATTGCATTTAGCA
1 TTTGTAATTGCATTT-GCA
*
1878784 TTTGTATTTGCATTTGCA
1 TTTGTAATTGCATTTGCA
1878802 TT
1 TT
1878804 ACATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (18 bp):
TTTGTAATTGCATTTGCA
Found at i:1883067 original size:37 final size:37
Alignment explanation
Indices: 1883012--1883164 Score: 184
Period size: 37 Copynumber: 4.1 Consensus size: 37
1883002 CACATGAGAT
*
1883012 TGAAGCAAAGTCAATCTTAAGCCTTCACCGAAAATGAG
1 TGAAGCAAA-TCAATCTTAAGCCTTCACCGAAAAGGAG
*
1883050 TGAAGCAAATCAATCTTAAGCCTTTACC-AAAGAGGAG
1 TGAAGCAAATCAATCTTAAGCCTTCACCGAAA-AGGAG
* *
1883087 TGAAGCAAA-CCATCTTAAGCCTTCACCAAAAAGGAG
1 TGAAGCAAATCAATCTTAAGCCTTCACCGAAAAGGAG
* * * * *
1883123 GGAATCAAATCAATTTGTAAGCCTTCACCGAAGAGTAG
1 TGAAGCAAATCAATCT-TAAGCCTTCACCGAAAAGGAG
1883161 TGAA
1 TGAA
1883165 CCACCACCTT
Statistics
Matches: 99, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
36 31 0.31
37 38 0.38
38 30 0.30
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (37 bp):
TGAAGCAAATCAATCTTAAGCCTTCACCGAAAAGGAG
Found at i:1883108 original size:73 final size:72
Alignment explanation
Indices: 1883025--1883215 Score: 215
Period size: 73 Copynumber: 2.6 Consensus size: 72
1883015 AGCAAAGTCA
*
1883025 ATCTTAAGCCTTCACCGAAAATGAGTGAAGCAAATCAATCT-TAAGCCTTTACCAAAGAGGAGTG
1 ATCTTAAGCCTTCACCGAAAATGAGTGAAGCAAATCAATCTGTAAGCCTTCACCAAAGAGGAGTG
1883089 AAGCAAACC
66 AA-C-AACC
* * * * * * *
1883098 ATCTTAAGCCTTCACCAAAAAGGAGGGAATCAAATCAATTTGTAAGCCTTCACCGAAGAGTAGTG
1 ATCTTAAGCCTTCACCGAAAATGAGTGAAGCAAATCAATCTGTAAGCCTTCACCAAAGAGGAGTG
*
1883163 AACCACC
66 AACAACC
* * * * *
1883170 ACCTTGAGCCTTCACAGAAGAAT-AGTGAAGCAAACCAATCAGTAAG
1 ATCTTAAGCCTTCACCGAA-AATGAGTGAAGCAAATCAATCTGTAAG
1883216 TCTTTCGAGC
Statistics
Matches: 97, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
72 36 0.37
73 39 0.40
74 22 0.23
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (72 bp):
ATCTTAAGCCTTCACCGAAAATGAGTGAAGCAAATCAATCTGTAAGCCTTCACCAAAGAGGAGTG
AACAACC
Found at i:1883109 original size:36 final size:36
Alignment explanation
Indices: 1883025--1883206 Score: 156
Period size: 36 Copynumber: 5.0 Consensus size: 36
1883015 AGCAAAGTCA
* *
1883025 ATCTTAAGCCTTCACCGAAA-ATGAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACC-AAAGAGGAGTGAAGCAAA-CC
*
1883062 ATCTTAAGCCTTTACCAAAGAGGAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
* * * *
1883098 ATCTTAAGCCTTCACCAAAAAGGAGGGAATCAAATCA
1 ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAA-CC
* * * *
1883135 ATTTGTAAGCCTTCACCGAAGAGTAGTGAA-C-CACC
1 ATCT-TAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
* * **
1883170 ACCTTGAGCCTTCA-CAGAAGAATAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCA-AAGAGGAGTGAAGCAAACC
1883206 A
1 A
1883207 ATCAGTAAGT
Statistics
Matches: 118, Mismatches: 21, Indels: 13
0.78 0.14 0.09
Matches are distributed among these distances:
33 1 0.01
34 20 0.17
35 4 0.03
36 39 0.33
37 33 0.28
38 21 0.18
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
Found at i:1884088 original size:215 final size:214
Alignment explanation
Indices: 1883207--1884395 Score: 1772
Period size: 214 Copynumber: 5.5 Consensus size: 214
1883197 AAGCAAACCA
**
1883207 ATCAGTAAGTCTTTCGAGCATGATGCTTAAATTCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
1 ATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
* * *
1883272 TGATAAGTCATTCGGGCCATCCATAAGACATTTGGGTAGGATGTTTTCACATGAATTTGGAAATA
66 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGGAAATA
*
1883337 AAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAA
131 AAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATACGATTTTCAAAATTTCACAA
1883402 TTTATAAGTCCTTCGGGCC
196 TTTATAAGTCCTTCGGGCC
1883421 ATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
1 ATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
* *
1883486 TGATAAGTCCTTCGGGCCATCCATTAGACCTTCGGGTATGATGTTTTCACATGAATTTGGAAATA
66 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGGAAATA
* *
1883551 AAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATCCGATTTTAAAAATTTCACAA
131 AAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATACGATTTTCAAAATTTCACAA
1883616 TTTATAAGTCCTTCGGGCC
196 TTTATAAGTCCTTCGGGCC
* * *
1883635 ATTAGTAAGTCTTTCGAGCATGATGCTTAAAACATTCAGGTCATCTGTAAGCCTTTAGAGCAAGA
1 ATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
* * * *
1883700 TGATAAGTCCTTCGGGACATCCATAAGACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATG
66 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGGAAATA
* * * *
1883765 AAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCATAA
131 AAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATACGATTTTCAAAATTTCACAA
*
1883830 TTTATAAGTCTTTCGGGCC
196 TTTATAAGTCCTTCGGGCC
* * *
1883849 ATCAATAAGTCTTTCGATCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
1 ATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
*
1883914 TGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGGAAATA
66 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGGAAAT-
* *
1883979 AAAAAATGATGTTTTAAGAAGATGGAATATTTGAAAACGAAGAATAAGATTTTCAAAATTTCACA
130 AAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATACGATTTTCAAAATTTCACA
1884044 ATTTATAAGTCCTTCGGGCC
195 ATTTATAAGTCCTTCGGGCC
* *
1884064 ATCAGTAAGTCTTTCGAGCATGATGCTTAAAACATTCGGGTCATCTGTAAGCCTTTAGAGCATGA
1 ATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
* * *
1884129 TGATATGTCCTTCGGGCCATCTATAAG-TCTTCTGGGTAGGATGTTTTCACATGAATTTGAAAAT
66 TGATAAGTCCTTCGGGCCATCCATAAGACCTTC-GGGTAGGATGTTTTCACATGAATTTG-----
* * * * * * * *
1884193 GAAAATAAGAAAATGATGTTTGAAGATGATGAAATTTTTGGAAACTAGGAATACGATTTCCGAAA
125 G-AAATAA-AAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATACGATTTTCAAAA
*
1884258 TTTCAC-A-CTAGTAAGTCCTTCGGGCC
188 TTTCACAATTTA-TAAGTCCTTCGGGCC
* * * * * * * * *
1884284 ATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTAGGGTCATTTGTGAGTCTCTCGAGCAAGA
1 ATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
* * * *
1884349 TGATAAATCCTTCGGGTCATCCATAAGATCTTCGGGCAGGATGTTTT
66 TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTT
1884396 TCACCAAGAT
Statistics
Matches: 886, Mismatches: 78, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
214 527 0.59
215 187 0.21
219 2 0.00
220 109 0.12
221 61 0.07
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Consensus pattern (214 bp):
ATCAGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGA
TGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGGAAATA
AAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAAGAATACGATTTTCAAAATTTCACAA
TTTATAAGTCCTTCGGGCC
Found at i:1884467 original size:37 final size:36
Alignment explanation
Indices: 1884423--1884568 Score: 184
Period size: 37 Copynumber: 3.9 Consensus size: 36
1884413 CCTCCGGGCC
*
1884423 ATCTTAAGCCTTCACCAAAACGTAGTGAAACAAATCA
1 ATCTTAAGCCTTCACCAAAA-GTAGTGAAGCAAATCA
* * *
1884460 ATCTTAAGACTTAATCAAAGAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACCAAA-AGTAGTGAAGCAAATCA
* * *
1884497 ATCTTAAGCCTTCACTGAAGAGTATTGAAGCAAATCA
1 ATCTTAAGCCTTCAC-CAAAAGTAGTGAAGCAAATCA
*
1884534 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
1 ATCTTAAGCCTTCACC-AAAAGTAGTGAAGCAAAT
1884569 TGATCTCGAG
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
37 91 0.97
38 3 0.03
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCAAAAGTAGTGAAGCAAATCA
Found at i:1884555 original size:74 final size:74
Alignment explanation
Indices: 1884423--1884568 Score: 204
Period size: 74 Copynumber: 2.0 Consensus size: 74
1884413 CCTCCGGGCC
*
1884423 ATCTTAAGCCTTCACCAAAACGTAGTGAAACAAATCAATCTTAAGACTTAATCAAAGAGTAGTGA
1 ATCTTAAGCCTTCACCAAAACGTAGTGAAACAAATCAATCTTAAGACTTAACCAAAGAGTAGTGA
1884488 AGCAAATCA
66 AGCAAATCA
* * * * * * *
1884497 ATCTTAAGCCTTCACTGAAGA-GTATTGAAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTG
1 ATCTTAAGCCTTCAC-CAAAACGTAGTGAAACAAATCAATCTTAAGACTTAACCAAAGAGTAGTG
1884561 AAGCAAAT
65 AAGCAAAT
1884569 TGATCTCGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 60 0.95
75 3 0.05
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (74 bp):
ATCTTAAGCCTTCACCAAAACGTAGTGAAACAAATCAATCTTAAGACTTAACCAAAGAGTAGTGA
AGCAAATCA
Found at i:1884763 original size:3 final size:3
Alignment explanation
Indices: 1884750--1884796 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
1884740 AGCTTAAAAA
* *
1884750 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TA- TAA TAA TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1884795 TA
1 TA
1884797 ACATAATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1884802 original size:20 final size:20
Alignment explanation
Indices: 1884766--1884803 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1884756 TTATTATTAT
**
1884766 TATTATTATTATTATAATAA
1 TATTATTATTAACATAATAA
1884786 TATTATTATTAACATAAT
1 TATTATTATTAACATAAT
1884804 TTTTTTACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTATTATTAACATAATAA
Found at i:1884803 original size:17 final size:17
Alignment explanation
Indices: 1884748--1884796 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1884738 CGAGCTTAAA
*
1884748 AATATTAATTATTATTATT
1 AATATT-ATTATTA-TAAT
*
1884767 ATTATTATTATTATAAT
1 AATATTATTATTATAAT
1884784 AATATTATTATTA
1 AATATTATTATTA
1884797 ACATAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 15 0.56
18 7 0.26
19 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATATTATTATTATAAT
Found at i:1887050 original size:2 final size:2
Alignment explanation
Indices: 1887045--1887092 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1887035 AACTGTTTCG
1887045 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
1887087 AT AT AT
1 AT AT AT
1887093 TTACTTTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1888303 original size:13 final size:12
Alignment explanation
Indices: 1888275--1888309 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1888265 TACTAACCAT
*
1888275 TTTATTTTTTTC
1 TTTATTTTTTTA
1888287 TTTATTATTTTTA
1 TTTATT-TTTTTA
1888300 TTTATTTTTT
1 TTTATTTTTT
1888310 ATTGTTCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTATTTTTTTA
Found at i:1888310 original size:20 final size:21
Alignment explanation
Indices: 1888274--1888312 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1888264 GTACTAACCA
*
1888274 TTTTATTTTTTTCTTTATTAT
1 TTTTATTTATTTCTTTATTAT
1888295 TTTTATTTATTT-TTTATT
1 TTTTATTTATTTCTTTATT
1888313 GTTCATACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTATTTATTTCTTTATTAT
Found at i:1890621 original size:11 final size:11
Alignment explanation
Indices: 1890605--1890658 Score: 83
Period size: 11 Copynumber: 4.9 Consensus size: 11
1890595 TTCAAATAGC
1890605 AAAAAAGAAAA
1 AAAAAAGAAAA
1890616 AAAAAAG-AAA
1 AAAAAAGAAAA
1890626 AAAAAAGAAAA
1 AAAAAAGAAAA
*
1890637 AAAAAGGAAAA
1 AAAAAAGAAAA
1890648 AAGAAAAGAAA
1 AA-AAAAGAAA
1890659 GAGAATAAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
10 10 0.26
11 22 0.56
12 7 0.18
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:1890631 original size:21 final size:22
Alignment explanation
Indices: 1890605--1890658 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
1890595 TTCAAATAGC
1890605 AAAAAAGAAAAAAAAAAG-AAA
1 AAAAAAGAAAAAAAAAAGAAAA
*
1890626 AAAAAAGAAAAAAAAAGGAAAA
1 AAAAAAGAAAAAAAAAAGAAAA
1890648 AAGAAAAGAAA
1 AA-AAAAGAAA
1890659 GAGAATAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 17 0.57
22 5 0.17
23 8 0.27
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (22 bp):
AAAAAAGAAAAAAAAAAGAAAA
Found at i:1890663 original size:11 final size:10
Alignment explanation
Indices: 1890605--1890649 Score: 72
Period size: 10 Copynumber: 4.3 Consensus size: 10
1890595 TTCAAATAGC
1890605 AAAAAAGAAAA
1 AAAAAAG-AAA
1890616 AAAAAAGAAA
1 AAAAAAGAAA
1890626 AAAAAAGAAA
1 AAAAAAGAAA
1890636 AAAAAAGGAAA
1 AAAAAA-GAAA
1890647 AAA
1 AAA
1890650 GAAAAGAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 19 0.58
11 14 0.42
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1891857 original size:54 final size:54
Alignment explanation
Indices: 1891781--1891918 Score: 204
Period size: 54 Copynumber: 2.6 Consensus size: 54
1891771 GAACATCTAG
* * *
1891781 GCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACAAACATCTGT
1 GCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACAAACATATGT
* * *
1891835 GTAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACGAGCATATGT
1 GCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACAAACATATGT
* *
1891889 GCAGAAACAACAGGAAATGATGAATGTGTT
1 GCAGAAGCCACAGGAAATGATGAATGTGTT
1891919 ACGAACCAGT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 75 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (54 bp):
GCAGAAGCCACAGGAAATGATGAATGTGTTGTCAAATGTTTTACAAACATATGT
Found at i:1893005 original size:73 final size:73
Alignment explanation
Indices: 1892923--1893249 Score: 501
Period size: 73 Copynumber: 4.5 Consensus size: 73
1892913 TTCTCAAAGA
*
1892923 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTGGAGAAAATTTCATTT
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTGGAGAAAATTTCACTT
1892988 GAAATAGC
66 GAAATAGC
* * * *
1892996 AATTTATCTCACTTGAGATTTTTTTTCTTAAAACAAATTGTTTCTCGCTGGAGTAAGTTTCACTT
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTGGAGAAAATTTCACTT
1893061 GAAATAGC
66 GAAATAGC
* * * *
1893069 AATTTATCTCACTTGAGATTATTTTTCTTAAAACAAAATGTTTCTCGCTTGAGAAAATTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTGGAGAAAATTTCACTT
* *
1893134 GAAACAGG
66 GAAATAGC
* * * *
1893142 AATTTATTTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTTGCTTGAGCAAATTTCACTT
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTGGAGAAAATTTCACTT
*
1893207 AAAATAGC
66 GAAATAGC
*
1893215 AATTTATTTCACTTGAGATTGTTTTTCTTAAAACA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1893250 TTTCTAGAAG
Statistics
Matches: 232, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 232 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.41
Consensus pattern (73 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGTTTCTCGCTGGAGAAAATTTCACTT
GAAATAGC
Found at i:1893464 original size:123 final size:123
Alignment explanation
Indices: 1893260--1893601 Score: 546
Period size: 123 Copynumber: 2.8 Consensus size: 123
1893250 TTTCTAGAAG
1893260 GAGTTCGTAATAAGAAGAACTCCTCTGAAGA-G--GAAGAAGTTCATAGTCTGAAGAACTTATTC
1 GAGTTCGTAATAAGAAGAACTCCTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTC
*
1893322 AACTTTTTGCTTGACTCTATCACAGAAGGAGATAGAGCAGCAGAACCATTTCCAGACA
66 AACCTTTTGCTTGACTCTATCACAGAAGGAGATAGAGCAGCAGAACCATTTCCAGACA
* *
1893380 GAGTTCGTAAGAAGAAGAACTCCTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAAATTATTC
1 GAGTTCGTAATAAGAAGAACTCCTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTC
** *
1893445 AACCTTTTGCTTGACTCTATCGTAGAAGGAGATAGAGCAGCAGAACCATTTCTAGACA
66 AACCTTTTGCTTGACTCTATCACAGAAGGAGATAGAGCAGCAGAACCATTTCCAGACA
* * * *
1893503 GAGTTCGTAATAAGAAGAACTCATCTGAAGAGGAAGAAAAAATTCATAATCTGAAGAACTTATTC
1 GAGTTCGTAATAAGAAGAACTCCTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTC
* * *
1893568 AACCTTTTGATCGATTCTATCACAGAAGGAGATA
66 AACCTTTTGCTTGACTCTATCACAGAAGGAGATA
1893602 AATCAACATC
Statistics
Matches: 202, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
120 30 0.15
121 1 0.00
123 171 0.85
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (123 bp):
GAGTTCGTAATAAGAAGAACTCCTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTC
AACCTTTTGCTTGACTCTATCACAGAAGGAGATAGAGCAGCAGAACCATTTCCAGACA
Found at i:1894876 original size:15 final size:15
Alignment explanation
Indices: 1894836--1894878 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1894826 AATTTCACTA
*
1894836 CTTTA-ATTTTCTAT
1 CTTTATATTTTTTAT
* *
1894850 CTTTTTATTTTTTTT
1 CTTTATATTTTTTAT
1894865 CTTTATATTTTTTA
1 CTTTATATTTTTTA
1894879 ATATTTTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTATATTTTTTAT
Found at i:1895106 original size:11 final size:11
Alignment explanation
Indices: 1895084--1895113 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1895074 AATTTAATTA
1895084 TTATTCTTTATT
1 TTATT-TTTATT
1895096 TTATTTTTATT
1 TTATTTTTATT
1895107 TTATTTT
1 TTATTTT
1895114 AATCATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:1895283 original size:2 final size:2
Alignment explanation
Indices: 1895241--1895266 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1895231 ACCTTACTTA
1895241 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
1895267 TTACTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1895914 original size:21 final size:21
Alignment explanation
Indices: 1895888--1895927 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1895878 GCAACACAGG
1895888 TTCCAAAATCGCAACGCGATT
1 TTCCAAAATCGCAACGCGATT
*
1895909 TTCCAAATTCGCAACGCGA
1 TTCCAAAATCGCAACGCGA
1895928 ATAGTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
TTCCAAAATCGCAACGCGATT
Found at i:1895942 original size:20 final size:20
Alignment explanation
Indices: 1895893--1896050 Score: 135
Period size: 20 Copynumber: 7.8 Consensus size: 20
1895883 ACAGGTTCCA
* * **
1895893 AAATCGCAACGCGATTTTCC
1 AAATCGCAACGCGAATATGT
1895913 AAATTCGCAACGCGAATA-GTT
1 AAA-TCGCAACGCGAATATG-T
**
1895934 AAATCGCAACGATAATATGT
1 AAATCGCAACGCGAATATGT
1895954 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
*
1895974 AAATCGCAACGCGAATTTGT
1 AAATCGCAACGCGAATATGT
* *
1895994 AAATCGCAACAC--ATAAGT
1 AAATCGCAACGCGAATATGT
* *
1896012 CAAATTCGCAACACGAA-ATTT
1 -AAA-TCGCAACGCGAATATGT
1896033 CAAATTCGCAACGCGAAT
1 -AAA-TCGCAACGCGAAT
1896051 TTATTTTTCA
Statistics
Matches: 115, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.03
19 3 0.03
20 73 0.63
21 34 0.30
22 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:1897888 original size:42 final size:42
Alignment explanation
Indices: 1897829--1897925 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
1897819 GTGAATCGGG
* *
1897829 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGGGAGGGACCTCTTGAACGATGACAAGGGC
* * * *
1897871 CTCTTGAACGATGGGAGGGGCCTCTTGAAGGATGATAATGGC
1 CTCTTGAACGATGGGAGGGACCTCTTGAACGATGACAAGGGC
1897913 CTCTTGAACGATG
1 CTCTTGAACGATG
1897926 ACAGGTGAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGATGGGAGGGACCTCTTGAACGATGACAAGGGC
Found at i:1897926 original size:21 final size:21
Alignment explanation
Indices: 1897829--1897930 Score: 114
Period size: 21 Copynumber: 4.9 Consensus size: 21
1897819 GTGAATCGGG
* ** *
1897829 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGACAGGGGC
1897850 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGACAGGGGC
**
1897871 CTCTTGAACGATGGGAGGGGC
1 CTCTTGAACGATGACAGGGGC
* * **
1897892 CTCTTGAAGGATGATAATGGC
1 CTCTTGAACGATGACAGGGGC
1897913 CTCTTGAACGATGACAGG
1 CTCTTGAACGATGACAGG
1897931 TGAATTGAGC
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 66 1.00
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGACAGGGGC
Found at i:1898455 original size:21 final size:21
Alignment explanation
Indices: 1898429--1898479 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1898419 TTTCATGCAT
1898429 TTAGGTCCTCTACCAATAATA
1 TTAGGTCCTCTACCAATAATA
1898450 TTAGGTCCTCTACCAATAATA
1 TTAGGTCCTCTACCAATAATA
1898471 TTAGGTCCT
1 TTAGGTCCT
1898480 TAGAAATAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (21 bp):
TTAGGTCCTCTACCAATAATA
Found at i:1899412 original size:19 final size:18
Alignment explanation
Indices: 1899373--1899428 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
1899363 TCTGAAACTT
*
1899373 AAAATCACAACATGAAAATG
1 AAAATCAC-A-ATGCAAATG
1899393 AAAATCACAATGCGAAATG
1 AAAATCACAATGC-AAATG
*
1899412 AAAATCGCAATGCAAAT
1 AAAATCACAATGCAAAT
1899429 TTCATTTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.21
19 18 0.55
20 8 0.24
ACGTcount: A:0.55, C:0.16, G:0.12, T:0.16
Consensus pattern (18 bp):
AAAATCACAATGCAAATG
Found at i:1899856 original size:22 final size:22
Alignment explanation
Indices: 1899828--1899878 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1899818 ATAGAGGGGG
* * *
1899828 GTCGCCGGATATGTGGACGGAT
1 GTCGCCGGAGATGGGGACAGAT
*
1899850 GTCGCCGGAGATGGGGATAGAT
1 GTCGCCGGAGATGGGGACAGAT
1899872 GTCGCCG
1 GTCGCCG
1899879 TAGAGAGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.20, G:0.43, T:0.20
Consensus pattern (22 bp):
GTCGCCGGAGATGGGGACAGAT
Found at i:1900004 original size:19 final size:20
Alignment explanation
Indices: 1899982--1900019 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1899972 AATATCGTGT
1899982 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
1900001 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
1900020 CGTGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:1900067 original size:20 final size:20
Alignment explanation
Indices: 1900026--1900067 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1900016 TAAACGTGCT
*
1900026 TTGCGAATTTGACTTCTATG
1 TTGCGAATTTGACTTATATG
*
1900046 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATATG
1900066 TT
1 TT
1900068 ACGATTTACA
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:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (20 bp):
TTGCGAATTTGACTTATATG
Found at i:1900095 original size:20 final size:20
Alignment explanation
Indices: 1900069--1900154 Score: 93
Period size: 20 Copynumber: 4.3 Consensus size: 20
1900059 TTATGTGTTA
1900069 CGATTTACAAATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
* *
1900089 TGATTTACATATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
* **
1900109 CGATTTACATATTATCGTTG
1 CGATTTACAAATTCGCGTTG
* *
1900129 CAATTTA-ACTATTCGCGTTG
1 CGATTTACA-AATTCGCGTTG
1900149 CGATTT
1 CGATTT
1900155 TGGAACCTGT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
19 1 0.02
20 55 0.98
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.42
Consensus pattern (20 bp):
CGATTTACAAATTCGCGTTG
Found at i:1900128 original size:40 final size:40
Alignment explanation
Indices: 1900069--1900154 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
1900059 TTATGTGTTA
* **
1900069 CGATTTACAAATTCGCGTTGTGATTT-ACATATTCGCGTTG
1 CGATTTACAAATTAGCGTTGCAATTTAAC-TATTCGCGTTG
* *
1900109 CGATTTACATATTATCGTTGCAATTTAACTATTCGCGTTG
1 CGATTTACAAATTAGCGTTGCAATTTAACTATTCGCGTTG
1900149 CGATTT
1 CGATTT
1900155 TGGAACCTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 38 0.95
41 2 0.05
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.42
Consensus pattern (40 bp):
CGATTTACAAATTAGCGTTGCAATTTAACTATTCGCGTTG
Found at i:1900344 original size:19 final size:19
Alignment explanation
Indices: 1900320--1900357 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1900310 TGTGATATGT
1900320 TGATACATTCATACATACA
1 TGATACATTCATACATACA
1900339 TGATACATTCATACATACA
1 TGATACATTCATACATACA
1900358 CGTTTTGCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (19 bp):
TGATACATTCATACATACA
Found at i:1908012 original size:31 final size:31
Alignment explanation
Indices: 1907953--1908012 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1907943 TCGGTGGTGA
* **
1907953 TGGTGCTTGTTGTGAAGGTGGTGGTGGTGCG
1 TGGTGCTTGTTGTGAAGATGGTAATGGTGCG
**
1907984 TGGTGCTTGTTGTGACTATGGTAATGGTG
1 TGGTGCTTGTTGTGAAGATGGTAATGGTG
1908013 GCGGTGGCAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.10, C:0.07, G:0.45, T:0.38
Consensus pattern (31 bp):
TGGTGCTTGTTGTGAAGATGGTAATGGTGCG
Found at i:1908284 original size:12 final size:12
Alignment explanation
Indices: 1908267--1908291 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1908257 CTCAAACAGA
1908267 GAGAATGAACGT
1 GAGAATGAACGT
1908279 GAGAATGAACGT
1 GAGAATGAACGT
1908291 G
1 G
1908292 TTGCATGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:1908353 original size:29 final size:29
Alignment explanation
Indices: 1908320--1908375 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1908310 TCCTAACACA
1908320 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
1908349 TAGGTCGTCATGCCCTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
1908376 ACACATGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.11, C:0.38, G:0.30, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:1908388 original size:22 final size:22
Alignment explanation
Indices: 1908357--1908399 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1908347 TGTAGGTCGT
* *
1908357 CATGCCCTCCGGGCGACCTACA
1 CATGCACTCCGGACGACCTACA
1908379 CATGCACTCCGGACGACCTAC
1 CATGCACTCCGGACGACCTAC
1908400 CCTCGCTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.44, G:0.21, T:0.14
Consensus pattern (22 bp):
CATGCACTCCGGACGACCTACA
Found at i:1908522 original size:34 final size:35
Alignment explanation
Indices: 1908449--1908537 Score: 117
Period size: 34 Copynumber: 2.5 Consensus size: 35
1908439 TCGGTTGCTC
* * * *
1908449 TCGGATGCCCTCGTATAGCTCGTTCGGATGGTCTTGG
1 TCGGATGGCCTCGGAT-GCTCG-TCGGATGGCCTCGG
1908486 TCGGATGGCCTCGGATGCTC-TCGGATGGCCTCGG
1 TCGGATGGCCTCGGATGCTCGTCGGATGGCCTCGG
1908520 TCGGATGGCCTCGGATGC
1 TCGGATGGCCTCGGATGC
1908538 CCAGCGTGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
34 30 0.62
36 4 0.08
37 14 0.29
ACGTcount: A:0.10, C:0.27, G:0.36, T:0.27
Consensus pattern (35 bp):
TCGGATGGCCTCGGATGCTCGTCGGATGGCCTCGG
Found at i:1908525 original size:14 final size:14
Alignment explanation
Indices: 1908506--1908533 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1908496 TCGGATGCTC
1908506 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1908520 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1908534 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:1908536 original size:10 final size:10
Alignment explanation
Indices: 1908486--1908519 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1908476 ATGGTCTTGG
1908486 TCGGATGGCC
1 TCGGATGGCC
1908496 TCGGAT-GCTC
1 TCGGATGGC-C
1908506 TCGGATGGCC
1 TCGGATGGCC
1908516 TCGG
1 TCGG
1908520 TCGGATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:1922900 original size:20 final size:21
Alignment explanation
Indices: 1922875--1922926 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
1922865 TCTAGGTAAA
1922875 TTTCTAATT-CTTCTCTAATT
1 TTTCTAATTCCTTCTCTAATT
1922895 TTTCT-ATTCCTTCTCTAATT
1 TTTCTAATTCCTTCTCTAATT
1922915 TTTCT-ATTCCTT
1 TTTCTAATTCCTT
1922927 ATTTATTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTCTAATTCCTTCTCTAATT
Found at i:1923656 original size:3 final size:3
Alignment explanation
Indices: 1923648--1923707 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
1923638 TATGTAACAT
* * *
1923648 TAA TAA TAA TAA TAA TATA TTA TAA T-A TAA TAG TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1923693 TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA T
1923708 TTTAATATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.08
3 42 0.88
4 2 0.04
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1923713 original size:11 final size:12
Alignment explanation
Indices: 1923664--1923723 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 12
1923654 TAATAATAAT
1923664 ATATTATAATATA
1 ATATT-TAATATA
1923677 ATAGTTATAATAATA
1 ATA-TT-TAAT-ATA
*
1923692 ATAATAATAATATA
1 AT-AT-TTAATATA
1923706 AT-TTTAATATA
1 ATATTTAATATA
1923717 ATATTTA
1 ATATTTA
1923724 TAACCCATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
11 9 0.22
12 5 0.12
13 3 0.08
14 12 0.30
15 10 0.25
16 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (12 bp):
ATATTTAATATA
Done.