Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008979.1 Hibiscus syriacus cultivar Beakdansim tig00112339_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: 1115631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1039445 original size:19 final size:19
Alignment explanation
Indices: 1039377--1039563 Score: 208
Period size: 19 Copynumber: 10.6 Consensus size: 19
1039367 GCAACGAGAG
1039377 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1039396 ATCCCAA--C---ATGAAA
1 ATCGCAATGCGAAATGAAA
1039410 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1039430 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1039449 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1039467 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1039481 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1039500 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1039519 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1039533 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
*
1039552 ATCGCATTGCGA
1 ATCGCAATGCGA
1039564 TTCTCCCGTT
Statistics
Matches: 143, Mismatches: 8, Indels: 34
0.77 0.04 0.18
Matches are distributed among these distances:
13 1 0.01
14 31 0.22
15 1 0.01
16 7 0.05
17 3 0.02
18 11 0.08
19 73 0.51
20 16 0.11
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1039489 original size:32 final size:34
Alignment explanation
Indices: 1039363--1039525 Score: 183
Period size: 32 Copynumber: 4.7 Consensus size: 34
1039353 CGGAAATTAC
*
1039363 AATCGCAACGA-G-AGATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
1039395 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAA
1039429 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-A
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
*
1039466 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
1039499 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAA--CG--ATGAAAATCGCAA
1039526 CGAGAGAATC
Statistics
Matches: 112, Mismatches: 5, Indels: 22
0.81 0.04 0.16
Matches are distributed among these distances:
31 1 0.01
32 28 0.25
33 21 0.19
34 15 0.13
35 4 0.04
36 1 0.01
37 10 0.09
38 16 0.14
39 16 0.14
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:1039509 original size:70 final size:72
Alignment explanation
Indices: 1039377--1039525 Score: 250
Period size: 70 Copynumber: 2.1 Consensus size: 72
1039367 GCAACGAGAG
1039377 ATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCGA
1 ATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCGA
1039442 AATGAAA
66 AATGAAA
* *
1039449 ATCGCAATGCGAAATG-AAATCGCAACGA-GAGAATCGCAATGC-GAAATGAAAATCGCAATGCG
1 ATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1039511 AAATGAAA
65 AAATGAAA
1039519 ATCGCAA
1 ATCGCAA
1039526 CGAGAGAATC
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
70 35 0.47
71 22 0.30
72 17 0.23
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (72 bp):
ATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAATGCGA
AATGAAA
Found at i:1039543 original size:52 final size:52
Alignment explanation
Indices: 1039363--1039563 Score: 263
Period size: 52 Copynumber: 3.9 Consensus size: 52
1039353 CGGAAATTAC
*
1039363 AATCGCAACGAGAG-ATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
1039409 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-A
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1039466 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
1039518 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
1039564 TTCTCCCGTT
Statistics
Matches: 137, Mismatches: 5, Indels: 20
0.85 0.03 0.12
Matches are distributed among these distances:
46 8 0.06
48 1 0.01
49 1 0.01
51 39 0.28
52 48 0.35
53 25 0.18
54 1 0.01
55 2 0.01
57 9 0.07
58 3 0.02
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:1039543 original size:103 final size:101
Alignment explanation
Indices: 1039363--1039563 Score: 266
Period size: 103 Copynumber: 2.0 Consensus size: 101
1039353 CGGAAATTAC
1039363 AATCGCAACGAGAGATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGA
1 AATCGCAACGAGAGATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAA-GCGG-AATGA
1039428 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
64 AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
*
1039466 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G-
1 AATCGCAACGAGAG-ATCGCAATGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAAGCGGA
* * *
1039528 A-GAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
60 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
1039564 TTCTCCCGTT
Statistics
Matches: 88, Mismatches: 4, Indels: 12
0.85 0.04 0.12
Matches are distributed among these distances:
103 46 0.52
104 26 0.30
106 2 0.02
107 1 0.01
109 13 0.15
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (101 bp):
AATCGCAACGAGAGATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAAGCGGAATGAAA
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
Found at i:1039612 original size:19 final size:19
Alignment explanation
Indices: 1039572--1039669 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1039562 GATTCTCCCG
1039572 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1039592 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1039611 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1039625 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1039644 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1039663 TTGCGAT
1 TTGCGAT
1039670 AGTCAATTTT
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:1039666 original size:52 final size:53
Alignment explanation
Indices: 1039553--1039669 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
1039543 GAAATTAAAA
1039553 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
1039606 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1039658 TCGCATTGCGAT
1 TCGCATTGCGAT
1039670 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1039795 original size:14 final size:14
Alignment explanation
Indices: 1039776--1039812 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1039766 CATCAATTAC
1039776 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1039790 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1039804 ACAAATCAA
1 ACAAATCAA
1039813 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:1041785 original size:14 final size:14
Alignment explanation
Indices: 1041766--1041822 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1041756 GCGAAATGAA
*
1041766 AATCGCAACGACAG
1 AATCGCAACGAAAG
1041780 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1041797 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1041813 AATCGCAACG
1 AATCGCAACG
1041823 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:1041793 original size:33 final size:33
Alignment explanation
Indices: 1041747--1041838 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1041737 GCGAAACCAA
*
1041747 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1041780 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1041813 AATCGCAACGCGAAATG-AAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1041839 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 9 0.16
33 47 0.84
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1041804 original size:19 final size:19
Alignment explanation
Indices: 1041710--1041843 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1041700 TAGTTTACTT
* *
1041710 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1041730 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1041749 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1041768 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1041782 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1041801 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1041815 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
1041833 TCGCAATGCGA
1 TCGCAACGCGA
1041844 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
18 12 0.12
19 35 0.36
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1041861 original size:19 final size:19
Alignment explanation
Indices: 1041839--1041967 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1041829 GAAATCGCAA
1041839 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1041858 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1041872 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1041891 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
** *
1041905 TGCGATTTTCATTTCACGT
1 TGCGATTTTGGTTTCGCGT
1041924 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1041943 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1041963 TGCGA
1 TGCGA
1041968 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1041881 original size:33 final size:33
Alignment explanation
Indices: 1041839--1041930 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
1041829 GAAATCGCAA
1041839 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1041872 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
1041905 TGCGATTTTCATTTCACGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1041931 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1042471 original size:91 final size:93
Alignment explanation
Indices: 1042015--1042570 Score: 1027
Period size: 93 Copynumber: 6.1 Consensus size: 93
1042005 ATGGATTGCA
* *
1042015 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATA-T-TTTCACAATGTTAAAGAATACATAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1042077 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1042105 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1042170 TAGCAGAATTGGCAGCAACCAAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1042198 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1042263 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1042291 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1042356 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1042384 TTAC-TTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1042447 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1042475 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAG-ATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1042538 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1042566 TTACT
1 TTACT
1042571 AAGCAATCTA
Statistics
Matches: 456, Mismatches: 5, Indels: 9
0.97 0.01 0.02
Matches are distributed among these distances:
90 4 0.01
91 148 0.32
92 63 0.14
93 241 0.53
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1044282 original size:33 final size:33
Alignment explanation
Indices: 1044242--1044356 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1044232 TCTTTTGGTT
*
1044242 GAAATGAAAATCGCAACGAGAGAATCGTAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1044275 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1044308 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1044341 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1044357 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1044321 original size:19 final size:19
Alignment explanation
Indices: 1044264--1044361 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1044254 GCAACGAGAG
*
1044264 AATCGTAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
1044283 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
1044297 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1044316 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1044330 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1044349 AATCGCAATGCGA
1 AATCGCAACGCGA
1044362 TTTTGGTTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.33
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 31 0.51
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1044335 original size:14 final size:14
Alignment explanation
Indices: 1044250--1044339 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
1044240 TTGAAATGAA
1044250 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
1044264 AATCGTAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1044283 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
1044297 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1044316 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1044330 AATCGCAACG
1 AATCGCAACG
1044340 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 20
0.67 0.09 0.23
Matches are distributed among these distances:
14 29 0.50
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 19 0.33
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1044392 original size:14 final size:14
Alignment explanation
Indices: 1044373--1044429 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1044363 TTTGGTTTCG
1044373 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1044387 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1044406 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1044420 CGTTGCGATT
1 CGTTGCGATT
1044430 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1044405 original size:33 final size:33
Alignment explanation
Indices: 1044357--1044437 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1044347 AAAATCGCAA
**
1044357 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1044390 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1044423 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1044438 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1044440 original size:21 final size:21
Alignment explanation
Indices: 1044414--1044489 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1044404 CGCGTTGCGA
1044414 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1044435 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1044455 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1044476 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1044490 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1044470 original size:41 final size:41
Alignment explanation
Indices: 1044413--1044490 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1044403 TCGCGTTGCG
*
1044413 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1044454 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1044491 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1044611 original size:33 final size:33
Alignment explanation
Indices: 1044569--1044639 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1044559 AATACTAACT
*
1044569 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1044602 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1044635 TGAAA
1 TGAAA
1044640 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:1044870 original size:21 final size:22
Alignment explanation
Indices: 1044819--1044872 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
1044809 TGGTTGTGAG
**
1044819 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1044841 GGAAATCTTCGGAGAT-GGGAC
1 GGATTTCTTCGGAGATGGGGAC
1044862 GGATTTCTTCG
1 GGATTTCTTCG
1044873 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1045042 original size:20 final size:20
Alignment explanation
Indices: 1045017--1045170 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1045007 CTTTAAATAT
1045017 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1045037 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1045059 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1045078 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1045098 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1045118 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1045138 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1045158 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1045171 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1045144 original size:40 final size:40
Alignment explanation
Indices: 1045016--1045170 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
1045006 GCTTTAAATA
*
1045016 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
1045057 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
1045097 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
1045137 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
1045171 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:1045187 original size:21 final size:21
Alignment explanation
Indices: 1045157--1045239 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1045147 ATTTTCATAT
*
1045157 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1045178 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1045199 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1045220 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1045240 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:1045230 original size:42 final size:43
Alignment explanation
Indices: 1045137--1045235 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1045127 ATTTATGTGT
* *
1045137 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1045178 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1045220 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1045236 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:1047975 original size:38 final size:37
Alignment explanation
Indices: 1047927--1048016 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 37
1047917 TATTAAAAAT
*
1047927 AATTATTATATATATATAATATTAATAAATT-TA-ATTTA
1 AATTAATATATATATAT-ATA-TAAT-AATTATATATTTA
*
1047965 AATTAATATATATATATATATAATATTTATATATTTA
1 AATTAATATATATATATATATAATAATTATATATTTA
*
1048002 ATTTAA-ATATATATA
1 AATTAATATATATATA
1048017 CCCAGCCCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
35 3 0.06
36 15 0.32
37 13 0.28
38 16 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (37 bp):
AATTAATATATATATATATATAATAATTATATATTTA
Found at i:1047990 original size:17 final size:17
Alignment explanation
Indices: 1047968--1048016 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
1047958 TAATTTAAAT
1047968 TAATATATATATATATA
1 TAATATATATATATATA
*
1047985 TAATAT-T-TATATATT
1 TAATATATATATATATA
* *
1048000 TAATTTAAATATATATA
1 TAATATATATATATATA
1048017 CCCAGCCCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 12 0.46
16 1 0.04
17 13 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATATATATATATATA
Found at i:1047991 original size:42 final size:40
Alignment explanation
Indices: 1047933--1048016 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 40
1047923 AAATAATTAT
1047933 TATATATATATAATATTAATAAATTTAATTTAAATTAATATA
1 TATATATATATAATATTAATAAATTTAATTTAAA-T-ATATA
* *
1047975 TATATATATATAATATTTATATATTTAATTTAAATATATA
1 TATATATATATAATATTAATAAATTTAATTTAAATATATA
1048015 TA
1 TA
1048017 CCCAGCCCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 7 0.17
41 1 0.03
42 32 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (40 bp):
TATATATATATAATATTAATAAATTTAATTTAAATATATA
Found at i:1049707 original size:22 final size:22
Alignment explanation
Indices: 1049679--1049720 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1049669 TCGGTAGAAG
*
1049679 TGGTATAGTTCAAGGGCAAAAA
1 TGGTATAGTCCAAGGGCAAAAA
1049701 TGGTATAGTCCAAGGGCAAA
1 TGGTATAGTCCAAGGGCAAA
1049721 TGTGCATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (22 bp):
TGGTATAGTCCAAGGGCAAAAA
Found at i:1049741 original size:2 final size:2
Alignment explanation
Indices: 1049734--1049780 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1049724 GCATTTAAGT
1049734 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
1049776 TA TA T
1 TA TA T
1049781 GTTTTGGCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1058602 original size:23 final size:22
Alignment explanation
Indices: 1058559--1058607 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
1058549 CACCTAACTA
*
1058559 AATTGATGTAAGCATCTTCATC
1 AATTGATGTAAGCATCGTCATC
1058581 TAATTGATGTAAGCAAT-GTCATC
1 -AATTGATGTAAGC-ATCGTCATC
1058604 AATT
1 AATT
1058608 TAGTTTGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 18 0.75
24 2 0.08
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (22 bp):
AATTGATGTAAGCATCGTCATC
Found at i:1065087 original size:16 final size:15
Alignment explanation
Indices: 1065066--1065108 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
1065056 GATCCGCCCG
1065066 CCCCCATCCATCCGCC
1 CCCCCATCCATCCG-C
*
1065082 CCCCCATCCATCTGC
1 CCCCCATCCATCCGC
*
1065097 CCCACATCCATC
1 CCCCCATCCATC
1065109 TGTCCACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.16, C:0.63, G:0.05, T:0.16
Consensus pattern (15 bp):
CCCCCATCCATCCGC
Found at i:1065099 original size:15 final size:16
Alignment explanation
Indices: 1065066--1065110 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
1065056 GATCCGCCCG
*
1065066 CCCCCATCCATCCGCC
1 CCCCCATCCATCTGCC
1065082 CCCCCATCCATCTG-C
1 CCCCCATCCATCTGCC
*
1065097 CCCACATCCATCTG
1 CCCCCATCCATCTG
1065111 TCCACTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 14 0.52
16 13 0.48
ACGTcount: A:0.16, C:0.60, G:0.07, T:0.18
Consensus pattern (16 bp):
CCCCCATCCATCTGCC
Found at i:1065338 original size:29 final size:28
Alignment explanation
Indices: 1065305--1065410 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 28
1065295 CTTTTTCATT
1065305 TAAGTACCTAAAGTATTTTTTAGTCAAAA
1 TAAGTACCTAAAGTATTTTTT-GTCAAAA
** *
1065334 TAAGTATTTAAAATAATCTTTTTGATCAAAA
1 TAAGTACCTAAAGT-AT-TTTTTG-TCAAAA
* *
1065365 TAGGTACCTAAAGTATCTTTTGGTCAAAA
1 TAAGTACCTAAAGTAT-TTTTTGTCAAAA
* *
1065394 TAGGTACTTAAAGTATT
1 TAAGTACCTAAAGTATT
1065411 CAAAATTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 1 0.02
29 32 0.49
30 11 0.17
31 21 0.32
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (28 bp):
TAAGTACCTAAAGTATTTTTTGTCAAAA
Found at i:1069232 original size:13 final size:14
Alignment explanation
Indices: 1069214--1069251 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
1069204 AAATGTTTTT
1069214 TAGGTTTAGTGG-G
1 TAGGTTTAGTGGAG
*
1069227 TAGGTTTAGTGGAT
1 TAGGTTTAGTGGAG
1069241 TAGGTTTAGTG
1 TAGGTTTAGTG
1069252 ATTTGGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.42
Consensus pattern (14 bp):
TAGGTTTAGTGGAG
Found at i:1069246 original size:14 final size:14
Alignment explanation
Indices: 1069213--1069264 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
1069203 TAAATGTTTT
1069213 TTAGGTTTAGTGG-
1 TTAGGTTTAGTGGA
*
1069226 GTAGGTTTAGTGGA
1 TTAGGTTTAGTGGA
1069240 TTAGGTTTAGT-GA
1 TTAGGTTTAGTGGA
*
1069253 TTTGGGTTTAGT
1 -TTAGGTTTAGT
1069265 TTTTAATGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 14 0.41
14 20 0.59
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.46
Consensus pattern (14 bp):
TTAGGTTTAGTGGA
Found at i:1069413 original size:34 final size:34
Alignment explanation
Indices: 1069370--1069434 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
1069360 ATGATGACGA
* *
1069370 TGGTGGCTCGGCAAAGACTGGAATGTTGGCTCGT
1 TGGTGGCTCGACAAAGACTGGAACGTTGGCTCGT
* *
1069404 TGGTGGCTCGACGACGACTGGAACGTTGGCT
1 TGGTGGCTCGACAAAGACTGGAACGTTGGCT
1069435 TGGTGGAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.17, C:0.20, G:0.38, T:0.25
Consensus pattern (34 bp):
TGGTGGCTCGACAAAGACTGGAACGTTGGCTCGT
Found at i:1070276 original size:127 final size:127
Alignment explanation
Indices: 1069954--1070588 Score: 676
Period size: 127 Copynumber: 5.0 Consensus size: 127
1069944 TTGACACGAT
* * * * ** *
1069954 TCCTACATAATGAGGAAATCTAGTCGGGTAATGACACAGCTCATACG-TGATGAATAGT-TCTGG
1 TCCTACATAATGAGGAAATCTGGTCAGGTGATGACACTGCTCATTTGTTCATG---AGTCT-TGG
** * *
1070017 CCATCTAAATGTGATAACACGGTTCCTATGTGATGAGGACGGTTGGA-TATCT-GGGTTGACACA
62 CCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCT-GATTATCTGGGGTTGACACA
1070080 GC
126 GC
* * *
1070082 TCCTACATAATGAAGATATCTGGTCAGGTGATGACACTGCTCATCTGTTCATGAGTCTTGGCCAT
1 TCCTACATAATGAGGAAATCTGGTCAGGTGATGACACTGCTCATTTGTTCATGAGTCTTGGCCAT
* * *
1070147 CTAAGGGTGATAACACAGTTCCTACGTGATGAGGACGACTGATTATCT-GAGTTGACACAGC
66 CTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGATTATCTGGGGTTGACACAGC
* *
1070208 TCCTTACATAATGAGGAGATCTGGTCATGTGATGACACTGCTCATTTGTTCATGAGTCTTGGCCA
1 TCC-TACATAATGAGGAAATCTGGTCAGGTGATGACACTGCTCATTTGTTCATGAGTCTTGGCCA
* *
1070273 TCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCT-AGTTATCTGGGGTTGACACGGT
65 TCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGA-TTATCTGGGGTTGACACAGC
* * * * *
1070336 TCCTACGTGATGAGAAAATCAGGTCGGGTGATGACACTGCTCATTTGTTCATGAGTCTTGGCCAT
1 TCCTACATAATGAGGAAATCTGGTCAGGTGATGACACTGCTCATTTGTTCATGAGTCTTGGCCAT
* ** *
1070401 CTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGGTTGACATGGT
66 CTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGATTATCTGGGGTTGACACAGC
* * * * * * ** * * *
1070463 TCCTACGTGATGAGGAAAAT-AGGTCAGGTGATGATA-TGGTTCCTACG-TGATGAGGACGGTAG
1 TCCTACATAATGAGG-AAATCTGGTCAGGTGATGACACT-GCTCATTTGTTCATGA-GTC--TTG
* * * * *
1070525 GTCATCTAAGGTTGATAACATGGTTCCTACGTGATGAGGACGACTGGTTTATCTGGGGTTGACA
61 GCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCT-GATTATCTGGGGTTGACA
1070589 TGGCTCTTAT
Statistics
Matches: 445, Mismatches: 49, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
125 2 0.00
126 71 0.16
127 252 0.57
128 56 0.13
129 47 0.11
130 17 0.04
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (127 bp):
TCCTACATAATGAGGAAATCTGGTCAGGTGATGACACTGCTCATTTGTTCATGAGTCTTGGCCAT
CTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGATTATCTGGGGTTGACACAGC
Found at i:1070465 original size:43 final size:44
Alignment explanation
Indices: 1070417--1070608 Score: 173
Period size: 40 Copynumber: 4.4 Consensus size: 44
1070407 GTGATAACAC
*
1070417 GGTTCCTACGTGATGAGGACGGCT-GGTTATCTGGGGTTGACAT
1 GGTTCCTACGTGATGAGGACGACTAGGTTATCTGGGGTTGACAT
* * * * * *
1070460 GGTTCCTACGTGATGAGGA-AAATAGG---TCAGGTGATGATAT
1 GGTTCCTACGTGATGAGGACGACTAGGTTATCTGGGGTTGACAT
* * **
1070500 GGTTCCTACGTGATGAGGACG-GTAGGTCATCTAAGGTTGATAACAT
1 GGTTCCTACGTGATGAGGACGACTAGGTTATCTGGGGTTG---ACAT
1070546 GGTTCCTACGTGATGAGGACGACT-GGTTTATCTGGGGTTGACAT
1 GGTTCCTACGTGATGAGGACGACTAGG-TTATCTGGGGTTGACAT
* * *
1070590 GGCTCTTATGTGATGAGGA
1 GGTTCCTACGTGATGAGGA
1070609 GATCAAGTCG
Statistics
Matches: 117, Mismatches: 22, Indels: 19
0.74 0.14 0.12
Matches are distributed among these distances:
40 33 0.28
42 1 0.01
43 26 0.22
44 20 0.17
46 26 0.22
47 11 0.09
ACGTcount: A:0.22, C:0.14, G:0.34, T:0.30
Consensus pattern (44 bp):
GGTTCCTACGTGATGAGGACGACTAGGTTATCTGGGGTTGACAT
Found at i:1070558 original size:46 final size:46
Alignment explanation
Indices: 1070398--1070566 Score: 169
Period size: 46 Copynumber: 3.9 Consensus size: 46
1070388 GAGTCTTGGC
* *
1070398 CATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCT-GGT
1 CATCTAAGGTTGATAACATGGTTCCTACGTGATGAGGACGG-TAGGT
* ** ***
1070444 TATCTGGGGTTG---ACATGGTTCCTACGTGATGAGGAAAATAGG-
1 CATCTAAGGTTGATAACATGGTTCCTACGTGATGAGGACGGTAGGT
* *
1070486 --TC--AGG-TGATGATATGGTTCCTACGTGATGAGGACGGTAGGT
1 CATCTAAGGTTGATAACATGGTTCCTACGTGATGAGGACGGTAGGT
1070527 CATCTAAGGTTGATAACATGGTTCCTACGTGATGAGGACG
1 CATCTAAGGTTGATAACATGGTTCCTACGTGATGAGGACG
1070567 ACTGGTTTAT
Statistics
Matches: 98, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
37 2 0.02
38 2 0.02
40 28 0.29
42 1 0.01
43 26 0.27
45 3 0.03
46 36 0.37
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (46 bp):
CATCTAAGGTTGATAACATGGTTCCTACGTGATGAGGACGGTAGGT
Found at i:1070636 original size:130 final size:128
Alignment explanation
Indices: 1070018--1070672 Score: 547
Period size: 127 Copynumber: 5.1 Consensus size: 128
1070008 TAGTTCTGGC
** * * * ** *
1070018 CATCTAAATGTGATAACACGGTTCCTATGTGATGAGGACGGTTGGATATCT-GGGTTGACACAGC
1 CATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGGTTGACATGGT
* * * * * * * * * * * * *
1070082 TCCTACATAATGAAGATATCTGGTCAGGTGATGACACTGCTCAT-CTGTTCATGA-GTC-TTGGC
66 TCCTACGTGATGAGGAAATCAGGTCGGGTGATGACACGGTTCCTAC-G-TGATGAGGACGTAGGT
* * * * ** *
1070144 CATCTAAGGGTGATAACACAGTTCCTACGTGATGAGGACGACTGATTATCT-GAGTTGACACAGC
1 CATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGGTTGACATGGT
* * * * ** * * * ** * * * *
1070208 TCCTTACATAATGAGGAGATCTGGTCATGTGATGACACTGCTCATTTGTTCATGA-GTC-TTGGC
66 TCC-TACGTGATGAGGAAATCAGGTCGGGTGATGACACGGTTCCTACG-TGATGAGGACGTAGGT
* *
1070271 CATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTAGTTATCTGGGGTTGACACGGT
1 CATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGGTTGACATGGT
* * * * ** * * * *
1070336 TCCTACGTGATGAGAAAATCAGGTCGGGTGATGACACTGCTCATTTGTTCATGA-GTC-TTGGC
66 TCCTACGTGATGAGGAAATCAGGTCGGGTGATGACACGGTTCCTACG-TGATGAGGACGTAGGT
1070398 CATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGGTTGACATGGT
1 CATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGGTTGACATGGT
* * *
1070463 TCCTACGTGATGAGGAAAAT-AGGTCAGGTGATGATATGGTTCCTACGTGATGAGGACGGTAGGT
66 TCCTACGTGATGAGG-AAATCAGGTCGGGTGATGACACGGTTCCTACGTGATGAGGAC-GTAGGT
* * *
1070527 CATCTAAGGTTGATAACATGGTTCCTACGTGATGAGGACGACTGGTTTATCTGGGGTTGACATGG
1 CATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG-TTATCTGGGGTTGACATGG
* * * * * *
1070592 CTCTTATGTGATGAGGAGATCAAGTCGGGTGATGACACGGTTCCTACGCGATGAGGACGATAGGT
65 TTCCTACGTGATGAGGAAATCAGGTCGGGTGATGACACGGTTCCTACGTGATGAGGACG-TAGGT
*
1070657 CATCCAAGGGTGATAA
1 CATCTAAGGGTGATAA
1070673 TGGTTTCAAA
Statistics
Matches: 463, Mismatches: 56, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
126 63 0.14
127 251 0.54
128 17 0.04
129 49 0.11
130 83 0.18
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (128 bp):
CATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGGGGTTGACATGGT
TCCTACGTGATGAGGAAATCAGGTCGGGTGATGACACGGTTCCTACGTGATGAGGACGTAGGT
Found at i:1070810 original size:63 final size:66
Alignment explanation
Indices: 1070736--1070863 Score: 172
Period size: 68 Copynumber: 2.0 Consensus size: 66
1070726 AAGAGACAAA
* * *
1070736 ATTCATTTCAAGGG-AATGA-CTCAAAGATG-GTTTTGTTTCAAGATAAACAAACTCAAAGATTT
1 ATTCATTTCAAGGGAAACGATATCAAAGATGTGTTTTGTTTCAAGAGAAACAAACTCAAAGATTT
1070798 T
66 T
* *
1070799 ATTCGTTTCAAGGGAAACGATATCAAAGATGTTTGTTTTGTTTCAAGGGAAACAAACTCAAAGAT
1 ATTCATTTCAAGGGAAACGATATCAAAGATG--TGTTTTGTTTCAAGAGAAACAAACTCAAAGAT
1070864 GGTTATTTCA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
63 13 0.24
64 4 0.07
65 9 0.16
68 29 0.53
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (66 bp):
ATTCATTTCAAGGGAAACGATATCAAAGATGTGTTTTGTTTCAAGAGAAACAAACTCAAAGATTT
T
Found at i:1070845 original size:35 final size:35
Alignment explanation
Indices: 1070754--1070864 Score: 126
Period size: 35 Copynumber: 3.3 Consensus size: 35
1070744 CAAGGGAATG
**
1070754 ACTCAAAGATG---GTTTTGTTTCAAGATAAACAA
1 ACTCAAAGATGTTTGTTTTGTTTCAAGGGAAACAA
* * *
1070786 ACTCAAAGAT-TTT-ATTCGTTTCAAGGGAAACGAT
1 ACTCAAAGATGTTTGTTTTGTTTCAAGGGAAAC-AA
1070820 A-TCAAAGATGTTTGTTTTGTTTCAAGGGAAACAA
1 ACTCAAAGATGTTTGTTTTGTTTCAAGGGAAACAA
1070854 ACTCAAAGATG
1 ACTCAAAGATG
1070865 GTTATTTCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
32 10 0.16
33 22 0.34
34 7 0.11
35 25 0.39
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.32
Consensus pattern (35 bp):
ACTCAAAGATGTTTGTTTTGTTTCAAGGGAAACAA
Found at i:1071019 original size:33 final size:33
Alignment explanation
Indices: 1070971--1071055 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
1070961 AAAATAAGAT
* *
1070971 TTGTTTCAAGAGAAACAATCTCAAAGATGGTTG
1 TTGTTTCAAGTGAAACAATCTCAAAGATGATTG
* * *
1071004 TTGTTTCCAGTGAAACGGA-CTCAAAGATGATTT
1 TTGTTTCAAGTGAAAC-AATCTCAAAGATGATTG
* *
1071037 TTATTTTAAGTGAAACAAT
1 TTGTTTCAAGTGAAACAAT
1071056 TTCAGAATTT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
32 1 0.02
33 39 0.95
34 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (33 bp):
TTGTTTCAAGTGAAACAATCTCAAAGATGATTG
Found at i:1071466 original size:20 final size:20
Alignment explanation
Indices: 1071441--1071500 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
1071431 TTTGTTATGA
1071441 GAAATTGTCTCAAGTGAGAT
1 GAAATTGTCTCAAGTGAGAT
*
1071461 GAAATTTGT-T----T-TGA-
1 GAAA-TTGTCTCAAGTGAGAT
1071475 GAAATTGTCTCAAGTGAGAT
1 GAAATTGTCTCAAGTGAGAT
1071495 GAAATT
1 GAAATT
1071501 TGTTTTGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 16
0.62 0.04 0.33
Matches are distributed among these distances:
13 4 0.13
14 5 0.17
15 2 0.07
16 1 0.03
18 1 0.03
19 2 0.07
20 11 0.37
21 4 0.13
ACGTcount: A:0.35, C:0.07, G:0.23, T:0.35
Consensus pattern (20 bp):
GAAATTGTCTCAAGTGAGAT
Found at i:1071535 original size:34 final size:34
Alignment explanation
Indices: 1071374--1071527 Score: 245
Period size: 34 Copynumber: 4.5 Consensus size: 34
1071364 TCTCAGAGAA
*
1071374 AAATTGTCTCAAGCGAGATGAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGATGAAATTTGTTTTGAG
* * *
1071408 AAATTGTTTCAAGTGAGACGAAATTTGTTATGAG
1 AAATTGTCTCAAGTGAGATGAAATTTGTTTTGAG
1071442 AAATTGTCTCAAGTGAGATGAAATTTGTTTTGAG
1 AAATTGTCTCAAGTGAGATGAAATTTGTTTTGAG
*
1071476 AAATTGTCTCAAGTGAGATGAAATTTGTTTTGGG
1 AAATTGTCTCAAGTGAGATGAAATTTGTTTTGAG
* *
1071510 AAATTATCTCAAGCGAGA
1 AAATTGTCTCAAGTGAGA
1071528 CAAAATTTTT
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 110 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (34 bp):
AAATTGTCTCAAGTGAGATGAAATTTGTTTTGAG
Found at i:1071874 original size:24 final size:23
Alignment explanation
Indices: 1071821--1071885 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
1071811 TTTTTTATTT
1071821 TCAAA-AGTTTTGAAAATATCAA
1 TCAAAGAGTTTTGAAAATATCAA
* * *
1071843 TTAGAAGAGTTTTGAAAATGTTTAA
1 TCA-AAGAGTTTTGAAAAT-ATCAA
1071868 TCAAAGA--TTTGAAAATAT
1 TCAAAGAGTTTTGAAAATAT
1071886 TGCCCCTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
21 1 0.03
22 11 0.31
23 2 0.06
24 16 0.46
25 5 0.14
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (23 bp):
TCAAAGAGTTTTGAAAATATCAA
Found at i:1072729 original size:7 final size:6
Alignment explanation
Indices: 1072702--1072768 Score: 72
Period size: 6 Copynumber: 12.0 Consensus size: 6
1072692 ATTCTCATCC
* * *
1072702 CTTTTT C-TTTA CTTTTT CTTTTT CCTTTT -TTGTT CTTTTT C-TTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
1072747 C-TTTT CTTTTT CTTTTT -TTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT
1072769 GCTCTTTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
5 22 0.42
6 30 0.58
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:1072740 original size:16 final size:15
Alignment explanation
Indices: 1072702--1072766 Score: 85
Period size: 16 Copynumber: 4.0 Consensus size: 15
1072692 ATTCTCATCC
1072702 CTTTTTCTTTACTTTTT
1 CTTTTTCTTT--TTTTT
1072719 CTTTTTCCTTTTTTGTT
1 CTTTTT-CTTTTTT-TT
1072736 CTTTTTCTTTTCTTTT
1 CTTTTTCTTTT-TTTT
1072752 CTTTTTCTTTTTTTT
1 CTTTTTCTTTTTTTT
1072767 TTGCTCTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.09
16 21 0.47
17 16 0.36
18 4 0.09
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (15 bp):
CTTTTTCTTTTTTTT
Found at i:1072766 original size:34 final size:34
Alignment explanation
Indices: 1072702--1072765 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
1072692 ATTCTCATCC
1072702 CTTTTTCTTTACTTTTTCTTTTTCCTTTTTTGTT
1 CTTTTTCTTTACTTTTTCTTTTTCCTTTTTTGTT
* *
1072736 CTTTTTCTTTTC-TTTTCTTTTTCTTTTTTT
1 CTTTTTCTTTACTTTTTCTTTTTCCTTTTTT
1072766 TTTGCTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (34 bp):
CTTTTTCTTTACTTTTTCTTTTTCCTTTTTTGTT
Found at i:1072768 original size:11 final size:11
Alignment explanation
Indices: 1072702--1072787 Score: 73
Period size: 11 Copynumber: 7.6 Consensus size: 11
1072692 ATTCTCATCC
* *
1072702 CTTTTTCTTTA
1 CTTTTTTTTTT
1072713 CTTTTTCTTTTT
1 CTTTTT-TTTTT
* *
1072725 CCTTTTTTGTT
1 CTTTTTTTTTT
*
1072736 CTTTTTCTTTT
1 CTTTTTTTTTT
*
1072747 CTTTTCTTTTT
1 CTTTTTTTTTT
1072758 CTTTTTTTTTT
1 CTTTTTTTTTT
* **
1072769 GCTCTTTTTGCT
1 -CTTTTTTTTTT
1072781 CTTTTTT
1 CTTTTTT
1072788 ATTCTCTTTG
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
11 43 0.73
12 16 0.27
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.78
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:1072785 original size:39 final size:38
Alignment explanation
Indices: 1072704--1072777 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 38
1072694 TCTCATCCCT
*
1072704 TTTTCTTTACTTTTTCTTTTTCCTTTTTTGTTCTTTTTC
1 TTTTCTTTACTTTTTCTTTTT-CTTTTTTGCTCTTTTTC
*
1072743 TTTTCTTTTCTTTTTC-TTTT-TTTTTTGCTCTTTTT
1 TTTTCTTTACTTTTTCTTTTTCTTTTTTGCTCTTTTT
1072778 GCTCTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 14 0.42
38 4 0.12
39 15 0.45
ACGTcount: A:0.01, C:0.16, G:0.03, T:0.80
Consensus pattern (38 bp):
TTTTCTTTACTTTTTCTTTTTCTTTTTTGCTCTTTTTC
Found at i:1072787 original size:23 final size:21
Alignment explanation
Indices: 1072713--1072796 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 21
1072703 TTTTTCTTTA
1072713 CTTTTTCTTTTTCCTTTTTTGTT
1 CTTTTT-TTTTT-CTTTTTTGTT
* *
1072736 CTTTTTCTTTTCTTTTCTTTTT
1 CTTTTTTTTTTCTTTT-TTGTT
*
1072758 CTTTTTTTTTTGCTCTTTTTGCT
1 CTTTTTTTTTT-CT-TTTTTGTT
*
1072781 CTTTTTTATTCTCTTT
1 CTTTTTT-TTTTCTTT
1072797 GCTTTAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
21 5 0.10
22 20 0.39
23 20 0.39
24 6 0.12
ACGTcount: A:0.01, C:0.18, G:0.04, T:0.77
Consensus pattern (21 bp):
CTTTTTTTTTTCTTTTTTGTT
Found at i:1073995 original size:15 final size:13
Alignment explanation
Indices: 1073969--1074011 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1073959 CTTAAAAATG
*
1073969 AAATGCAGATGCA
1 AAATGAAGATGCA
1073982 AAATGCAAAGATGC-
1 AAATG--AAGATGCA
1073996 AAATGAAGATGCA
1 AAATGAAGATGCA
1074009 AAA
1 AAA
1074012 ATGTTGAGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 7 0.27
13 8 0.31
14 5 0.19
15 6 0.23
ACGTcount: A:0.53, C:0.12, G:0.21, T:0.14
Consensus pattern (13 bp):
AAATGAAGATGCA
Found at i:1074762 original size:32 final size:32
Alignment explanation
Indices: 1074726--1074786 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1074716 ATGAAAAATG
*
1074726 ACACAAACAAAAGAAAAGAAATAAGTTAGTGT
1 ACACAAACAAAACAAAAGAAATAAGTTAGTGT
* *
1074758 ACACAAACTAAACAAAAGAAATTAGTTAG
1 ACACAAACAAAACAAAAGAAATAAGTTAG
1074787 CACAGGTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAACAAAAGAAATAAGTTAGTGT
Found at i:1077026 original size:13 final size:14
Alignment explanation
Indices: 1077008--1077045 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
1076998 AAATGTTTTT
1077008 TAGGTTTAGTGG-G
1 TAGGTTTAGTGGAG
*
1077021 TAGGTTTAGTGGAT
1 TAGGTTTAGTGGAG
1077035 TAGGTTTAGTG
1 TAGGTTTAGTG
1077046 ATTTGGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.42
Consensus pattern (14 bp):
TAGGTTTAGTGGAG
Found at i:1077040 original size:14 final size:14
Alignment explanation
Indices: 1077007--1077058 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
1076997 TAAATGTTTT
1077007 TTAGGTTTAGTGG-
1 TTAGGTTTAGTGGA
*
1077020 GTAGGTTTAGTGGA
1 TTAGGTTTAGTGGA
1077034 TTAGGTTTAGT-GA
1 TTAGGTTTAGTGGA
*
1077047 TTTGGGTTTAGT
1 -TTAGGTTTAGT
1077059 TTTTTAATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 14 0.41
14 20 0.59
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.46
Consensus pattern (14 bp):
TTAGGTTTAGTGGA
Found at i:1077489 original size:24 final size:24
Alignment explanation
Indices: 1077457--1077507 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1077447 CAATACCATC
1077457 AAGTGAATTCCACATTTCCAATCG
1 AAGTGAATTCCACATTTCCAATCG
*
1077481 AAGTGAATTCCGCATTTCCAATCG
1 AAGTGAATTCCACATTTCCAATCG
1077505 AAG
1 AAG
1077508 AACCGGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (24 bp):
AAGTGAATTCCACATTTCCAATCG
Found at i:1079283 original size:2 final size:2
Alignment explanation
Indices: 1079278--1079307 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1079268 AAATATGAAG
*
1079278 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1079308 CATTATGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1080055 original size:13 final size:13
Alignment explanation
Indices: 1080037--1080084 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1080027 AAATGCAAAC
1080037 TAAAATTAAATAT
1 TAAAATTAAATAT
*
1080050 TAAAATTGAAATGTTT
1 TAAAATT-AAA--TAT
*
1080066 TAAAATTCAATAT
1 TAAAATTAAATAT
1080079 TAAAAT
1 TAAAAT
1080085 AGATACAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 15 0.52
14 3 0.10
15 2 0.07
16 9 0.31
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (13 bp):
TAAAATTAAATAT
Found at i:1080871 original size:7 final size:7
Alignment explanation
Indices: 1080859--1080899 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
1080849 TGGTGAGCTT
1080859 AACGAGC
1 AACGAGC
1080866 AACGAG-
1 AACGAGC
1080872 -ACGAGC
1 AACGAGC
1080878 AACGAGC
1 AACGAGC
1080885 TTAACGAGC
1 --AACGAGC
1080894 AACGAG
1 AACGAG
1080900 TTGAGCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 5 0.17
7 18 0.60
9 7 0.23
ACGTcount: A:0.41, C:0.24, G:0.29, T:0.05
Consensus pattern (7 bp):
AACGAGC
Found at i:1080893 original size:16 final size:16
Alignment explanation
Indices: 1080853--1080899 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
1080843 AAATTTTGGT
1080853 GAGCTTAACGAGCAAC
1 GAGCTTAACGAGCAAC
1080869 GAG----ACGAGCAAC
1 GAGCTTAACGAGCAAC
1080881 GAGCTTAACGAGCAAC
1 GAGCTTAACGAGCAAC
1080897 GAG
1 GAG
1080900 TTGAGCAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 12 0.44
16 15 0.56
ACGTcount: A:0.38, C:0.23, G:0.30, T:0.09
Consensus pattern (16 bp):
GAGCTTAACGAGCAAC
Found at i:1080924 original size:48 final size:48
Alignment explanation
Indices: 1080872--1080974 Score: 143
Period size: 48 Copynumber: 2.1 Consensus size: 48
1080862 GAGCAACGAG
* * * *
1080872 ACGAGCAACGAGCTTAACGAGCAACGAGTTGAGCAATAACTTTTCTTA
1 ACGAGCAACAAGCTTAACGAGCAACGAGCTGAGCAACAAATTTTCTTA
* *
1080920 ACGAGCAACAAGCTTAATGAGCAATGAGCTGAGCAACAAATTTTCTTA
1 ACGAGCAACAAGCTTAACGAGCAACGAGCTGAGCAACAAATTTTCTTA
*
1080968 ACAAGCA
1 ACGAGCA
1080975 TGAGTCGAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (48 bp):
ACGAGCAACAAGCTTAACGAGCAACGAGCTGAGCAACAAATTTTCTTA
Found at i:1081014 original size:31 final size:31
Alignment explanation
Indices: 1080950--1081024 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
1080940 GCAATGAGCT
* ** *
1080950 GAGCAACAAATTTTCTTAACAAGCATGAGTC
1 GAGCAACAAATTTTATTAACAAGCACAAATC
*
1080981 GAGCAACAAATTTTATTAACGAGCACAAATC
1 GAGCAACAAATTTTATTAACAAGCACAAATC
1081012 GAGC-A-AAATTTTA
1 GAGCAACAAATTTTA
1081025 ACGAGCTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 8 0.21
30 1 0.03
31 30 0.77
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (31 bp):
GAGCAACAAATTTTATTAACAAGCACAAATC
Found at i:1085959 original size:22 final size:23
Alignment explanation
Indices: 1085910--1085969 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1085900 ATTCCCCTGT
1085910 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
1085933 AGGGGGAATCGGTT-CCCTT--A
1 GGGGGGAATCGGTTCCCCTTCAA
* *
1085953 GGGGGGGATCGATTCCC
1 GGGGGGAATCGGTTCCC
1085970 TCTGCACCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.38
21 2 0.06
22 5 0.16
23 13 0.41
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.22
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:1089818 original size:22 final size:21
Alignment explanation
Indices: 1089776--1089815 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1089766 GAGTTTGTTT
*
1089776 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1089797 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1089816 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1094679 original size:24 final size:24
Alignment explanation
Indices: 1094652--1094699 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1094642 AGTCTGTGAA
1094652 ATAATAAGAAGGAAACATGCGTTT
1 ATAATAAGAAGGAAACATGCGTTT
* *
1094676 ATAATAAGAAGGAAATATGTGTTT
1 ATAATAAGAAGGAAACATGCGTTT
1094700 TTTCCTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAATAAGAAGGAAACATGCGTTT
Found at i:1094989 original size:17 final size:17
Alignment explanation
Indices: 1094967--1095007 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1094957 TGTAGGGCCC
*
1094967 TGCGCCGTCGCGTAGTA
1 TGCGCCGTCGCGCAGTA
1094984 TGCGCCGTCGCGCAGTA
1 TGCGCCGTCGCGCAGTA
1095001 TGCGCCG
1 TGCGCCG
1095008 GCTCTGCCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.10, C:0.34, G:0.37, T:0.20
Consensus pattern (17 bp):
TGCGCCGTCGCGCAGTA
Found at i:1095822 original size:27 final size:27
Alignment explanation
Indices: 1095786--1095842 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
1095776 GTCGATAGAA
1095786 AAATGATCATTGATAGGGGTAAATGAG
1 AAATGATCATTGATAGGGGTAAATGAG
1095813 AAATGATCATTGATAGGGGTAAATGAG
1 AAATGATCATTGATAGGGGTAAATGAG
1095840 AAA
1 AAA
1095843 ATAAATATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.44, C:0.04, G:0.28, T:0.25
Consensus pattern (27 bp):
AAATGATCATTGATAGGGGTAAATGAG
Found at i:1097727 original size:28 final size:28
Alignment explanation
Indices: 1097687--1097751 Score: 130
Period size: 28 Copynumber: 2.3 Consensus size: 28
1097677 TGTCAGGTTC
1097687 TTTGGGTTCTCACATTATTTTACTTTGT
1 TTTGGGTTCTCACATTATTTTACTTTGT
1097715 TTTGGGTTCTCACATTATTTTACTTTGT
1 TTTGGGTTCTCACATTATTTTACTTTGT
1097743 TTTGGGTTC
1 TTTGGGTTC
1097752 ATTGAAAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.57
Consensus pattern (28 bp):
TTTGGGTTCTCACATTATTTTACTTTGT
Found at i:1099634 original size:4 final size:4
Alignment explanation
Indices: 1099611--1099646 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1099601 CATATCTAGG
* *
1099611 TAAA TGAA TAAA TAAT TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1099647 AGGGACTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:1100802 original size:7 final size:7
Alignment explanation
Indices: 1100790--1100849 Score: 63
Period size: 7 Copynumber: 8.9 Consensus size: 7
1100780 AAAACGATAA
1100790 AATAAAT
1 AATAAAT
1100797 AAT-AA-
1 AATAAAT
*
1100802 AACAAA-
1 AATAAAT
*
1100808 AACAAAT
1 AATAAAT
1100815 AATAAAT
1 AATAAAT
1100822 AATAAAT
1 AATAAAT
1100829 AATAAAT
1 AATAAAT
*
1100836 AAATAAAG
1 -AATAAAT
1100844 AATAAA
1 AATAAA
1100850 ATACTAGATG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
5 2 0.04
6 10 0.21
7 29 0.62
8 6 0.13
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (7 bp):
AATAAAT
Found at i:1100836 original size:18 final size:18
Alignment explanation
Indices: 1100788--1100849 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
1100778 AAAAAACGAT
1100788 AAAATAAATAATAAA-ACA
1 AAAATAAATAATAAATA-A
*
1100806 AAAACAAATAATAAATAA
1 AAAATAAATAATAAATAA
*
1100824 TAAAT-AATAAATAAATAA
1 AAAATAAAT-AATAAATAA
*
1100842 AGAATAAA
1 AAAATAAA
1100850 ATACTAGATG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 3 0.08
18 30 0.83
19 3 0.08
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAATAAATAATAAATAA
Found at i:1101958 original size:82 final size:80
Alignment explanation
Indices: 1101850--1102199 Score: 439
Period size: 82 Copynumber: 4.3 Consensus size: 80
1101840 CCTCTAAATA
*
1101850 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1101915 CCCTCGAAGCTTGAGTG
66 CCCTCG-AGC-TGAGTG
** *
1101932 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * *
1101997 CCGTTGAGCTGAGCG
66 CCCTCGAGCTGAGTG
* * * * * * * *
1102012 TAGTCAAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
1 TAATCGAACTCGAAGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
*
1102077 TGTGCCCTCGGAGCTGAGTA
62 TGTGCCCTC-GAGCTGAGTG
*
1102097 TAATCGAACCCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* * *
1102162 CCTTGGAGCTGAGCG
66 CCCTCGAGCTGAGTG
* *
1102177 TAGTCGAACTCAAAGGTCTTTGG
1 TAATCGAACTCGAAGGTCTTTGG
1102200 TTGGCAGACA
Statistics
Matches: 225, Mismatches: 38, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
80 47 0.21
81 47 0.21
82 65 0.29
84 43 0.19
85 23 0.10
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (80 bp):
TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCCTCGAGCTGAGTG
Found at i:1102131 original size:165 final size:166
Alignment explanation
Indices: 1101873--1102197 Score: 501
Period size: 165 Copynumber: 2.0 Consensus size: 166
1101863 AGGTCTTTAG
* * *
1101873 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTTGAGTGTAATCG
1 CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTTGAGTATAATCG
* **
1101938 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-
66 AACCCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTG
*
1102002 GAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTCA
130 GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCA
* * * * *
1102039 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGGAGC-TGAGTATAATCG
1 CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTTGAGTATAATCG
*
1102103 AACCCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACCCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGG
*
1102168 AGCTGAGCGTAGTCGAACTCAAAGGTCTTT
131 AGCTGAGCGTAGTCAAACTCAAAGGTCTTT
1102198 GGTTGGCAGA
Statistics
Matches: 144, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
164 2 0.01
165 97 0.67
166 45 0.31
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (166 bp):
CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTTGAGTATAATCG
AACCCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCA
Found at i:1102581 original size:105 final size:105
Alignment explanation
Indices: 1102398--1103657 Score: 2008
Period size: 105 Copynumber: 12.0 Consensus size: 105
1102388 TATTGTTCCA
* ** * * *
1102398 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTATGGAACTG-GAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAA-TGTTTGTTGACAA
*
1102462 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1102504 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
*
1102569 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1102609 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGCTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
*
1102674 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1102714 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAAC
*
1102779 CAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTG-CTTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGG
*
1102820 AGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AA-GTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
* *
1102883 AGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
1102923 AGTCCAATATCCTTCGATGTGAAGTTGAAATTGACTCTGAAATTGGGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAAC
*
1102988 CAGCGGT-CCTTCGTCGTGAAGTTGAACTTGCGTTATCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1103028 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAAC
*
1103093 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1103134 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAAC
*
1103199 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1103240 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
*
1103305 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** * * *
1103345 AGTCCAATATCCTTCGTTGTGAAGACGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAGCC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
1103410 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
1103450 AGTCCAATATCCTTCGTTATGAAGTCGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
*
1103515 AGCGGTCCCTTCGTCGTGAAGTTGCACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1103555 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
*
1103620 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
1103658 TGAGCGACCC
Statistics
Matches: 1078, Mismatches: 68, Indels: 17
0.93 0.06 0.01
Matches are distributed among these distances:
103 92 0.09
104 2 0.00
105 648 0.60
106 335 0.31
107 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1102800 original size:211 final size:210
Alignment explanation
Indices: 1102398--1103657 Score: 2008
Period size: 211 Copynumber: 6.0 Consensus size: 210
1102388 TATTGTTCCA
* ** * * *
1102398 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTATGGAACTG-GAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AAA-TGTTTGTTGACAA
*
1102462 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCTTCGTTGTGAA
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
1102527 GTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
129 GTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
1102592 GAACTTGCGTTGTCTAG
194 GAACTTGCGTTGTCTGG
* * *
1102609 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGCTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
* *
1102674 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * * *
1102739 TGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGCCGTGAAGTTG
131 TGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
1102804 AACTTGCGTTG-CTTGG
195 AACTTGCGTTGTC-TGG
*
1102820 AGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG-AA-GTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
* * *
1102883 AGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGATGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * *
1102948 TGAAATTGACTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGT-CCTTCGTCGTGAAGTTG
131 TGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
1103012 AACTTGCGTTATCTGG
195 AACTTGCGTTGTCTGG
* * *
1103028 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAAC
*
1103093 CAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
*
1103158 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
130 TTGAAATTGGCTCTGAAATTGAGAA-ATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
*
1103223 GAACTTACGTTGTCTGG
194 GAACTTGCGTTGTCTGG
1103240 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
* *
1103305 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * *
1103370 CGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAGCCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
1103435 ACTTGCGTTGTCTGG
196 ACTTGCGTTGTCTGG
* * * *
1103450 AGTCCAATATCCTTCGTTATGAAGTCGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
*
1103515 AGCGGTCCCTTCGTCGTGAAGTTGCACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
1103580 TGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
*
1103645 ACTTGCATTGTCT
196 ACTTGCGTTGTCT
1103658 TGAGCGACCC
Statistics
Matches: 976, Mismatches: 65, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
208 73 0.07
209 121 0.12
210 349 0.36
211 354 0.36
212 79 0.08
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (210 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
ACTTGCGTTGTCTGG
Found at i:1107504 original size:14 final size:14
Alignment explanation
Indices: 1107482--1107517 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1107472 ACTAAAAAAT
*
1107482 AAAAAAATAATAAC
1 AAAATAATAATAAC
*
1107496 AAAATAATAATAAT
1 AAAATAATAATAAC
1107510 AAAATAAT
1 AAAATAAT
1107518 TAAATAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAATAATAAC
Found at i:1107515 original size:8 final size:8
Alignment explanation
Indices: 1107477--1107523 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
1107467 TTGTAACTAA
*
1107477 AAAATAAA
1 AAAATAAT
1107485 AAAATAAT
1 AAAATAAT
1107493 AACAA-AAT
1 AA-AATAAT
1107501 AATAATAAT
1 AA-AATAAT
1107510 AAAATAAT
1 AAAATAAT
*
1107518 TAAATA
1 AAAATA
1107524 GAGATAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 27 0.79
9 7 0.21
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAATAAT
Found at i:1107515 original size:11 final size:11
Alignment explanation
Indices: 1107474--1107546 Score: 53
Period size: 11 Copynumber: 6.6 Consensus size: 11
1107464 ATATTGTAAC
1107474 TAAAA-AATAA
1 TAAAATAATAA
*
1107484 AAAAATAATAA
1 TAAAATAATAA
*
1107495 CAAAATAATAA
1 TAAAATAATAA
1107506 TAATAA-AATAA
1 TAA-AATAATAA
* *
1107517 TTAAATAGA-GA
1 TAAAATA-ATAA
*
1107528 TAAAATAATGA
1 TAAAATAATAA
1107539 TGAAAATA
1 T-AAAATA
1107547 CGATAAAACA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
10 7 0.14
11 35 0.69
12 9 0.18
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.23
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:1108837 original size:7 final size:7
Alignment explanation
Indices: 1108825--1108883 Score: 56
Period size: 6 Copynumber: 9.1 Consensus size: 7
1108815 AAAACGATAA
1108825 AATAAAT
1 AATAAAT
1108832 AAT-AA-
1 AATAAAT
*
1108837 AACAAA-
1 AATAAAT
*
1108843 AACAAAT
1 AATAAAT
1108850 AATAAAT
1 AATAAAT
1108857 AATAAAT
1 AATAAAT
1108864 -ATAAAT
1 AATAAAT
*
1108870 AA-AAAG
1 AATAAAT
1108876 AATAAAT
1 AATAAAT
1108883 A
1 A
1108884 CTATATGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 2 0.05
6 21 0.48
7 21 0.48
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (7 bp):
AATAAAT
Found at i:1108880 original size:13 final size:13
Alignment explanation
Indices: 1108823--1108883 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
1108813 AAAAAACGAT
1108823 AAAATAAATAAT-
1 AAAATAAATAATA
* *
1108835 AAAACAAA-AACA
1 AAAATAAATAATA
1108847 AATAATAAATAATA
1 AA-AATAAATAATA
*
1108861 AATATAAATAA-A
1 AAAATAAATAATA
1108873 AAGAATAAATA
1 AA-AATAAATA
1108884 CTATATGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
11 2 0.05
12 12 0.31
13 20 0.51
14 5 0.13
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (13 bp):
AAAATAAATAATA
Found at i:1109028 original size:31 final size:33
Alignment explanation
Indices: 1108963--1109037 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
1108953 TATAAATTTA
*
1108963 AAAAACGTTTTAAAACTATATGTTATAGTTTTC
1 AAAAACGTTTTAAAACTATATGTTATAGTATTC
1108996 AAAAACGTTTTAAAACTATA--TTATA-TGATTC
1 AAAAACGTTTTAAAACTATATGTTATAGT-ATTC
*
1109027 AAAAATGTTTT
1 AAAAACGTTTT
1109038 TTTAACTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 1 0.03
31 18 0.46
33 20 0.51
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (33 bp):
AAAAACGTTTTAAAACTATATGTTATAGTATTC
Found at i:1109127 original size:37 final size:36
Alignment explanation
Indices: 1108893--1109220 Score: 145
Period size: 35 Copynumber: 9.3 Consensus size: 36
1108883 ACTATATGAT
* *
1108893 AAAATGTTTT-AAAACTTTATATAATAT-A-TATTTC
1 AAAATGTTTTAAAAACTATATATTATATAAGT-TTTC
* * * **
1108927 AAAGATATTTTCAAAA-TCATATATTATATAAATTTAA
1 AAA-ATGTTTTAAAAACT-ATATATTATATAAGTTTTC
* *
1108964 AAAACGTTTT-AAAACTATAT-GT-TAT-AGTTTTC
1 AAAATGTTTTAAAAACTATATATTATATAAGTTTTC
* *
1108996 AAAAACGTTTT-AAAAC--TATATTATAT--G-ATTC
1 -AAAATGTTTTAAAAACTATATATTATATAAGTTTTC
*** *
1109027 AAAAATGTTTTTTTAACTATATATTATATAAATTTT-
1 -AAAATGTTTTAAAAACTATATATTATATAAGTTTTC
* * *
1109063 AAAAT-TATTTTACAACTATATCTTATATAAGTTTTC
1 AAAATGT-TTTAAAAACTATATATTATATAAGTTTTC
* * *
1109099 AAAATGGTTTTAAAAACTATATAATATATATGGTTTC
1 AAAAT-GTTTTAAAAACTATATATTATATAAGTTTTC
*** * * * *
1109136 AAAAAAAAATTCAAAAATTATATAATATATATGTTTTC
1 --AAAATGTTTTAAAAACTATATATTATATAAGTTTTC
*
1109174 AAGAAATGTTTTCAAAAAGC-AAATATTATAT-A-TTTTC
1 -A-AAATGTTTT-AAAAA-CTATATATTATATAAGTTTTC
1109211 AAAATGTTTT
1 AAAATGTTTT
1109221 CTTTTTAGAA
Statistics
Matches: 228, Mismatches: 42, Indels: 47
0.72 0.13 0.15
Matches are distributed among these distances:
31 16 0.07
32 9 0.04
33 21 0.09
34 15 0.07
35 53 0.23
36 25 0.11
37 38 0.17
38 33 0.14
39 18 0.08
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATATTATATAAGTTTTC
Found at i:1109606 original size:13 final size:11
Alignment explanation
Indices: 1109578--1109620 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
1109568 TTATACAACG
*
1109578 AATATAAAATA
1 AATAAAAAATA
1109589 AATAAAAAGATAA
1 AATAAAAA-AT-A
1109602 AATAAGAAAATA
1 AATAA-AAAATA
1109614 AATAAAA
1 AATAAAA
1109621 TAATGAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 9 0.32
12 8 0.29
13 8 0.29
14 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (11 bp):
AATAAAAAATA
Found at i:1109634 original size:17 final size:17
Alignment explanation
Indices: 1109581--1109623 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
1109571 TACAACGAAT
1109581 ATAAAATAA-ATAAA-AA
1 ATAAAATAAGA-AAATAA
1109597 GATAAAATAAGAAAATAA
1 -ATAAAATAAGAAAATAA
1109615 ATAAAATAA
1 ATAAAATAA
1109624 TGAAGATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (17 bp):
ATAAAATAAGAAAATAA
Found at i:1114193 original size:9 final size:9
Alignment explanation
Indices: 1114162--1114233 Score: 63
Period size: 9 Copynumber: 7.4 Consensus size: 9
1114152 CTGTGGAAAA
1114162 CGGTTTGAC
1 CGGTTTGAC
*
1114171 CAGTTTTTGAAC
1 C-G-GTTTG-AC
1114183 CGGTTTGAC
1 CGGTTTGAC
*
1114192 CGGTTCGAAC
1 CGGTTTG-AC
1114202 CGGTTTGAC
1 CGGTTTGAC
* *
1114211 CAGTCTGAAC
1 CGGTTTG-AC
1114221 CGGTTTGAC
1 CGGTTTGAC
1114230 CGGT
1 CGGT
1114234 CTAAACCAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
9 22 0.44
10 20 0.40
11 5 0.10
12 3 0.06
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.31
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:1114203 original size:19 final size:20
Alignment explanation
Indices: 1114162--1114250 Score: 96
Period size: 19 Copynumber: 4.5 Consensus size: 20
1114152 CTGTGGAAAA
* *
1114162 CGGTTTGACCAGTTTTTGAAC
1 CGGTTTGACC-GGTTCTGAAC
1114183 CGGTTTGACCGGTTC-GAAC
1 CGGTTTGACCGGTTCTGAAC
*
1114202 CGGTTTGACCAG-TCTGAAC
1 CGGTTTGACCGGTTCTGAAC
*
1114221 CGGTTTGACCGG-TCTAAAC
1 CGGTTTGACCGGTTCTGAAC
1114240 CAGG-TTGACCG
1 C-GGTTTGACCG
1114251 ACCCGACTGT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
18 2 0.03
19 44 0.72
20 5 0.08
21 10 0.16
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (20 bp):
CGGTTTGACCGGTTCTGAAC
Found at i:1114264 original size:16 final size:15
Alignment explanation
Indices: 1114243--1114296 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 15
1114233 TCTAAACCAG
1114243 GTTGACCGACCCGAC
1 GTTGACCGACCCGAC
1114258 TGTTGACCCGACCCGAC
1 -GTTGA-CCGACCCGAC
1114275 GTTGACCGA--CGACC
1 GTTGACCGACCCGA-C
1114289 GTTGACCG
1 GTTGACCG
1114297 TTGACCGTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.08
14 9 0.25
15 4 0.11
16 10 0.28
17 10 0.28
ACGTcount: A:0.19, C:0.37, G:0.28, T:0.17
Consensus pattern (15 bp):
GTTGACCGACCCGAC
Found at i:1114295 original size:7 final size:7
Alignment explanation
Indices: 1114274--1114320 Score: 69
Period size: 7 Copynumber: 6.9 Consensus size: 7
1114264 CCCGACCCGA
1114274 CGTTGAC
1 CGTTGAC
**
1114281 CGACGAC
1 CGTTGAC
1114288 CGTTGAC
1 CGTTGAC
1114295 CGTTGAC
1 CGTTGAC
1114302 CG-TGAC
1 CGTTGAC
1114308 CGTTGAC
1 CGTTGAC
1114315 CGTTGA
1 CGTTGA
1114321 TCTTTGACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 6 0.17
7 29 0.83
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
CGTTGAC
Found at i:1114309 original size:13 final size:13
Alignment explanation
Indices: 1114285--1114317 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1114275 GTTGACCGAC
1114285 GACCGTTGACCGTT
1 GACCG-TGACCGTT
1114299 GACCGTGACCGTT
1 GACCGTGACCGTT
1114312 GACCGT
1 GACCGT
1114318 TGATCTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Done.