Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008959.1 Hibiscus syriacus cultivar Beakdansim tig00112293_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: 4521124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 21
Found at i:178343 original size:72 final size:72
Alignment explanation
Indices: 178250--178459 Score: 291
Period size: 72 Copynumber: 2.9 Consensus size: 72
178240 GCAACGAGAG
*
178250 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
178315 AAATGAA
66 AAATGAA
* *
178322 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
178387 AAATGAA
66 AAATGAA
* * * * * *
178394 AATCGCAACGAGAGAATCG-CAATGCGGAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCATT
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAAT
178456 GCGA
63 GCGA
178460 TTATCTCGTT
Statistics
Matches: 124, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
72 100 0.81
73 19 0.15
74 5 0.04
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCGCAACAAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:178371 original size:53 final size:52
Alignment explanation
Indices: 178236--178453 Score: 311
Period size: 53 Copynumber: 4.1 Consensus size: 52
178226 CGGAAATTAC
*
178236 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C--AA-GAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
178283 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
178341 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
178394 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAA
178447 AATCGCA
1 AATCGCA
178454 TTGCGATTAT
Statistics
Matches: 156, Mismatches: 3, Indels: 18
0.88 0.02 0.10
Matches are distributed among these distances:
47 8 0.05
49 1 0.01
50 1 0.01
52 14 0.09
53 116 0.74
55 2 0.01
56 1 0.01
57 2 0.01
58 11 0.07
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:178493 original size:53 final size:52
Alignment explanation
Indices: 178430--178545 Score: 133
Period size: 53 Copynumber: 2.2 Consensus size: 52
178420 GAAATGAAAA
* *
178430 TCGCAATGCGAAATGAAAATCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTATCTCATTGCGATTTTCATT
** ** ** *
178482 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTATCTCATTGCGATTTTCATT
*
178535 TCGTATTGCGA
1 TCGCATTGCGA
178546 TTTTCATTTC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
52 10 0.19
53 43 0.81
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.40
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTATCTCATTGCGATTTTCATT
Found at i:178508 original size:19 final size:19
Alignment explanation
Indices: 178468--178555 Score: 114
Period size: 19 Copynumber: 4.8 Consensus size: 19
178458 GATTATCTCG
178468 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
178488 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
178507 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCA
*
178521 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
178540 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
178556 AACATAATGC
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.17
16 3 0.05
17 3 0.05
19 29 0.48
20 15 0.25
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:178665 original size:14 final size:14
Alignment explanation
Indices: 178646--178682 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
178636 CATCAATTAC
178646 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
178660 ACAAATCATCTTTT
1 ACAAATCAACTTTT
178674 ACAAATCAA
1 ACAAATCAA
178683 TTAAATAATC
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:180647 original size:19 final size:19
Alignment explanation
Indices: 180605--180777 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
180595 TAGTTTACTT
* *
180605 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* *
180625 TCGCAACGCAAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
180644 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
180663 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
180682 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
180701 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
180715 TCGCAAAGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
180734 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
180748 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
180767 TCGCAATGCGA
1 TCGCAACGCGA
180778 TTTTCATTTC
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.06
17 7 0.06
18 1 0.01
19 81 0.64
20 11 0.09
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:180718 original size:14 final size:14
Alignment explanation
Indices: 180699--180755 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
180689 GCGAAATGAA
*
180699 AATCGCAACGACAG
1 AATCGCAACGAAAG
180713 AATCGCAAAGCGAAATG
1 AATCGC-AA-CGAAA-G
*
180730 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
180746 AATCGCAACG
1 AATCGCAACG
180756 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
15 2 0.06
16 5 0.14
17 5 0.14
18 2 0.06
19 6 0.17
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:180726 original size:33 final size:33
Alignment explanation
Indices: 180680--180772 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
180670 GCGAAACCAA
180680 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
180713 AATCGCAAAGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
180746 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
180773 TGCGATTTTC
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:0.22, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:180769 original size:52 final size:52
Alignment explanation
Indices: 180639--180777 Score: 138
Period size: 52 Copynumber: 2.7 Consensus size: 52
180629 AACGCAAAAT
* * * *
180639 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAAAGCGAAACCAAAATCGCAACGA
* ** * **
180691 GA-AAT-GAAAATCGCAACGACAGAATCGCAAAGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAAAGCGAAACCAAAATCGCAACGA
* *
180743 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAAAGCGA
180778 TTTTCATTTC
Statistics
Matches: 67, Mismatches: 16, Indels: 8
0.74 0.18 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 42 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.47, C:0.23, G:0.22, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAAAGCGAAACCAAAATCGCAACGA
Found at i:180812 original size:14 final size:14
Alignment explanation
Indices: 180789--180847 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
180779 TTTCATTTCG
180789 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
180803 CGTTGTGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
180820 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
180836 CGTTGCGATTTT
1 CGTTGCGATTTT
180848 CATTTCGCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 22 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 10 0.28
ACGTcount: A:0.07, C:0.15, G:0.29, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:180821 original size:33 final size:33
Alignment explanation
Indices: 180773--180866 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
180763 AAAATCGCAA
180773 TGCGATTTTCATTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTTTGTCGT
* ** *
180806 TGTGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTTTGTCGT
180839 TGCGATTTTCATTTCGCGTTGCGATTTT
1 TGCGATTTTCATTTCGCGTTGCGATTTT
180867 AAGTTTCGTG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.49
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTTTGTCGT
Found at i:180831 original size:19 final size:18
Alignment explanation
Indices: 180773--180882 Score: 74
Period size: 19 Copynumber: 6.3 Consensus size: 18
180763 AAAATCGCAA
*
180773 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
180792 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
180806 TGTGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
180825 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
180839 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
180858 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
180878 TGCGA
1 TGCGA
180883 AAGTAAACTA
Statistics
Matches: 71, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
14 22 0.31
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 31 0.44
20 12 0.17
ACGTcount: A:0.10, C:0.16, G:0.26, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:181139 original size:93 final size:93
Alignment explanation
Indices: 180980--181295 Score: 623
Period size: 93 Copynumber: 3.4 Consensus size: 93
180970 TCAGGGTATT
180980 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
181045 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
181073 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
181138 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
181166 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
181231 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
181259 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
181296 AAGCAATCTA
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 222 1.00
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:183036 original size:21 final size:21
Alignment explanation
Indices: 182980--183044 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
182970 TCTTTTGGTT
182980 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
183001 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
*
183021 GAAATGAAAATTGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
183042 GAA
1 GAA
183045 TCGCAACGCG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.48, C:0.14, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:183052 original size:14 final size:14
Alignment explanation
Indices: 183033--183085 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
183023 AATGAAAATT
183033 GCAACGAGAGAATC
1 GCAACGAGAGAATC
*
183047 GCAACGCGAAATGAAAATC
1 GCAA--CG--A-GAGAATC
183066 GCAACGAGAGAATC
1 GCAACGAGAGAATC
183080 GCAACG
1 GCAACG
183086 CGAAATGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 16 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.31
ACGTcount: A:0.43, C:0.23, G:0.26, T:0.08
Consensus pattern (14 bp):
GCAACGAGAGAATC
Found at i:183061 original size:33 final size:33
Alignment explanation
Indices: 182980--183102 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
182970 TCTTTTGGTT
*
182980 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
*
183021 GAAATGAAAATTGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
183054 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
183087 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
183103 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
33 49 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 21 0.27
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:183138 original size:14 final size:14
Alignment explanation
Indices: 183119--183175 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
183109 TTTGGTTTCG
183119 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
183133 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
183152 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
183166 CGTTGCGATT
1 CGTTGCGATT
183176 TTCATTTTTC
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:183151 original size:33 final size:33
Alignment explanation
Indices: 183103--183182 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
183093 AAAATCGCAA
**
183103 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
183136 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
183169 TGCGATTTTCATTT
1 TGCGATTTTCATTT
183183 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:183188 original size:21 final size:21
Alignment explanation
Indices: 183163--183236 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
183153 GTTGCGATTC
183163 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
183184 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
183205 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
183226 TCTCGTTGCGA
1 TCTCGTTGCGA
183237 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:183358 original size:33 final size:33
Alignment explanation
Indices: 183316--183386 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
183306 AATACTAACT
183316 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
183349 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
183382 TGAAA
1 TGAAA
183387 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:183791 original size:20 final size:20
Alignment explanation
Indices: 183766--183958 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
183756 CTTTAAAAAT
183766 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
183786 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
183806 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
183827 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
183847 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
183867 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
183887 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
183907 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
183927 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
183947 CGCGTTGCGATT
1 CGCGTTGCGATT
183959 CTGGAAAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
20 134 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:188376 original size:15 final size:15
Alignment explanation
Indices: 188356--188388 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
188346 AAGGAAATCC
188356 AGCTAAATCCTTAGT
1 AGCTAAATCCTTAGT
188371 AGCTAAATCCTTAGT
1 AGCTAAATCCTTAGT
188386 AGC
1 AGC
188389 AATGTTTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (15 bp):
AGCTAAATCCTTAGT
Found at i:195626 original size:26 final size:27
Alignment explanation
Indices: 195587--195638 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
195577 ATTTGTTGTT
* *
195587 AAACTTCTGGATTATTGGATCCCACAA
1 AAACTTCTGAATTATCGGATCCCACAA
195614 AAAC-TCTGAATTATCGGATCCCACA
1 AAACTTCTGAATTATCGGATCCCACA
195639 GTAACTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (27 bp):
AAACTTCTGAATTATCGGATCCCACAA
Found at i:206011 original size:67 final size:67
Alignment explanation
Indices: 205931--206074 Score: 272
Period size: 67 Copynumber: 2.2 Consensus size: 67
205921 TTCAAATGAG
205931 CATGCAAA-CAATTGACTTTAGAAAACTTATTTGCATGTTTCCTTTAGAAAACATGCACTCTTGC
1 CATGCAAAGCAATTGACTTTAGAAAACTTATTTGCATGTTTCCTTTAGAAAACATGCACTCTTGC
205995 AT
66 AT
*
205997 CCTGCAAAGCAATTGACTTTAGAAAACTTATTTGCATGTTTCCTTTAGAAAACATGCACTCTTGC
1 CATGCAAAGCAATTGACTTTAGAAAACTTATTTGCATGTTTCCTTTAGAAAACATGCACTCTTGC
206062 AT
66 AT
206064 CATGCAAAGCA
1 CATGCAAAGCA
206075 CCTCAGTGTT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 7 0.09
67 68 0.91
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (67 bp):
CATGCAAAGCAATTGACTTTAGAAAACTTATTTGCATGTTTCCTTTAGAAAACATGCACTCTTGC
AT
Found at i:206730 original size:23 final size:20
Alignment explanation
Indices: 206682--206730 Score: 53
Period size: 23 Copynumber: 2.3 Consensus size: 20
206672 TAATACATGC
*
206682 AAATTTTAAACTTGAGGAAA
1 AAATTTTAAACTTGAGCAAA
*
206702 ATATTTTGAAAACTTGGAGCAAA
1 AAATTTT--AAACTT-GAGCAAA
206725 AAATTT
1 AAATTT
206731 ATATCAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.26
22 6 0.26
23 11 0.48
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (20 bp):
AAATTTTAAACTTGAGCAAA
Found at i:219347 original size:20 final size:19
Alignment explanation
Indices: 219305--219347 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
219295 TTGGGGTTTT
* * *
219305 AATTCGATGAATAAGTTTT
1 AATTCGATGAAAAAGTATG
219324 AATTCGATGAAGAAAGTATG
1 AATTCGATGAA-AAAGTATG
219344 AATT
1 AATT
219348 GGAGCAAGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.35
Consensus pattern (19 bp):
AATTCGATGAAAAAGTATG
Found at i:220773 original size:33 final size:34
Alignment explanation
Indices: 220736--220806 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 34
220726 GTAAAATGAT
* *
220736 TAAAAAATATTATTTTATATT-CATTTAAATAAA
1 TAAAAAATAATATTTAATATTACATTTAAATAAA
* *
220769 TAAAAAATAATATTTAATTTTATATTTAAATAAA
1 TAAAAAATAATATTTAATATTACATTTAAATAAA
220803 -AAAA
1 TAAAA
220807 TTTGTTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 22 0.67
34 11 0.33
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (34 bp):
TAAAAAATAATATTTAATATTACATTTAAATAAA
Found at i:222345 original size:17 final size:16
Alignment explanation
Indices: 222323--222356 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
222313 TAAAGACAGT
222323 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
222340 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
222356 A
1 A
222357 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:232440 original size:17 final size:16
Alignment explanation
Indices: 232418--232451 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
232408 TAAAGACAGT
232418 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
232435 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
232451 A
1 A
232452 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:237244 original size:21 final size:21
Alignment explanation
Indices: 237218--237285 Score: 66
Period size: 23 Copynumber: 3.1 Consensus size: 21
237208 TGTTAATTTC
237218 TTTTATTATTTGTAATTTTAT
1 TTTTATTATTTGTAATTTTAT
*
237239 TTTTATTCAATTT-TAGTATTTAT
1 TTTTATT--ATTTGTAAT-TTTAT
* *
237262 TTATTTTTTTTTGTAATTTTAT
1 TT-TTATTATTTGTAATTTTAT
237284 TT
1 TT
237286 CTTAATTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
21 7 0.18
22 13 0.34
23 14 0.37
24 4 0.11
ACGTcount: A:0.22, C:0.01, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTTATTATTTGTAATTTTAT
Found at i:242546 original size:20 final size:20
Alignment explanation
Indices: 242521--242561 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
242511 AAACGACAAA
242521 GTGAAACCTTTAGGCAATAC
1 GTGAAACCTTTAGGCAATAC
242541 GTGAAACCTTTAGGCAATAC
1 GTGAAACCTTTAGGCAATAC
242561 G
1 G
242562 CCCAAAGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
GTGAAACCTTTAGGCAATAC
Found at i:249549 original size:91 final size:91
Alignment explanation
Indices: 249395--250101 Score: 1007
Period size: 91 Copynumber: 7.9 Consensus size: 91
249385 AGCTGATCAA
* *
249395 CATTTCCAGTGGAGAGTTCATAAT--G-AGAACTCATCCAACG-AGATAGAAGAAGTTCATAATG
1 CATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAAG-GAGAAGAAGTTCATAATG
249456 AGAAGAACTTGTTCAACCTTGGCTCAG
65 AGAAGAACTTGTTCAACCTTGGCTCAG
* *
249483 CATTTCCAGCGGAGAGTTCATAACGAGAAGAGCTCATCCAACGAAGGAGAAGAAGTTCATAATGA
1 CATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAAGGAGAAGAAGTTCATAATGA
* *
249548 GAAGAATTTGTTCAACCTTAGCTCAG
66 GAAGAACTTGTTCAACCTTGGCTCAG
* * *
249574 CATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACAAAAGGAGAGGAAGTTCATAATG
1 CATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAAC-GAAGGAGAAGAAGTTCATAATG
*
249639 AGAAGAACTTGTTCAACCTTGGCTCAT
65 AGAAGAACTTGTTCAACCTTGGCTCAG
*
249666 CATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGATGGAGAAGAAGTTCATAATGA
1 CATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAAGGAGAAGAAGTTCATAATGA
* *
249731 GAAGAGCTTGTTCAACCTTGGCTCAA
66 GAAGAACTTGTTCAACCTTGGCTCAG
* *
249757 AATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATTCAACGAAGGAGAAGAAGTTCATAATGA
1 CATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAAGGAGAAGAAGTTCATAATGA
249822 GAAGAACTTGTTCAACCTTGGCTCAG
66 GAAGAACTTGTTCAACCTTGGCTCAG
* * * * *
249848 TATTTCCAGCGGAGAGTTCATAATGAGAATAACTCATTCAATGAAGGATAAGAAGTTCATAATGA
1 CATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAAGGAGAAGAAGTTCATAATGA
* * *
249913 GAAGAGCTTGTTCAACCTTGACTCAA
66 GAAGAACTTGTTCAACCTTGGCTCAG
*
249939 CATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAAC-AAGGGAGAACAAGTTCATAATG
1 CATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAA-GGAGAAGAAGTTCATAATG
*
250003 AGAAGAATTTGTTCAACC-T---T-AG
65 AGAAGAACTTGTTCAACCTTGGCTCAG
* * * *
250025 C---T-CA---GAGGGTTCATAATGAGAAGAACTCGTCAAACGAGGGAGAAGAAGTTCATAATGA
1 CATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAAGGAGAAGAAGTTCATAATGA
250083 GAAGAACTTGTTCAACCTT
66 GAAGAACTTGTTCAACCTT
250102 AGATCTACAT
Statistics
Matches: 564, Mismatches: 47, Indels: 24
0.89 0.07 0.04
Matches are distributed among these distances:
79 63 0.11
80 2 0.00
82 2 0.00
83 1 0.00
86 2 0.00
87 1 0.00
88 22 0.04
90 4 0.01
91 380 0.67
92 87 0.15
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (91 bp):
CATTTCCAGCGGAGAGTTCATAATGAGAAGAACTCATCCAACGAAGGAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTGGCTCAG
Found at i:249834 original size:20 final size:19
Alignment explanation
Indices: 249772--249835 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
249762 CCAGCGGAGA
249772 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
249791 CATTCAACGAAGGAGAAGAA--
1 -GTTC-A-TAATGAGAAGAACT
249811 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
249831 GTTCA
1 GTTCA
249836 ACCTTGGCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 10 0.30
18 1 0.03
19 3 0.09
20 8 0.24
21 1 0.03
22 10 0.30
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:249996 original size:39 final size:38
Alignment explanation
Indices: 249953--250090 Score: 125
Period size: 39 Copynumber: 3.5 Consensus size: 38
249943 TCCAGCGGAG
*
249953 AGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAACA
1 AGTTCATAATGAGAAGAACTCGTCCAACAAGGGAGAA-A
* * * * ** *
249992 AGTTCATAATGAGAAGAATTTGTTCAACCTTAGCTCAG-AG
1 AGTTCATAATGAGAAGAACTCGTCCAA-C-AAG-GGAGAAA
* * *
250032 GGTTCATAATGAGAAGAACTCGTCAAACGAGGGAGAAGA
1 AGTTCATAATGAGAAGAACTCGTCCAACAAGGGAGAA-A
250071 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
250091 TGTTCAACCT
Statistics
Matches: 76, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
37 2 0.03
38 3 0.04
39 43 0.57
40 23 0.30
41 3 0.04
42 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (38 bp):
AGTTCATAATGAGAAGAACTCGTCCAACAAGGGAGAAA
Found at i:250085 original size:79 final size:79
Alignment explanation
Indices: 249954--250103 Score: 255
Period size: 79 Copynumber: 1.9 Consensus size: 79
249944 CCAGCGGAGA
* *
249954 GTTCATAATGAGAAGAACTCATCCAACAAGGGAGAACAAGTTCATAATGAGAAGAATTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCAAACAAGGGAGAACAAGTTCATAATGAGAAGAACTTGTTCAA
250019 CCTTAGCTCAGAGG
66 CCTTAGCTCAGAGG
* * *
250033 GTTCATAATGAGAAGAACTCGTCAAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCAAACAAGGGAGAACAAGTTCATAATGAGAAGAACTTGTTCAA
250098 CCTTAG
66 CCTTAG
250104 ATCTACATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (79 bp):
GTTCATAATGAGAAGAACTCATCAAACAAGGGAGAACAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTAGCTCAGAGG
Found at i:250095 original size:20 final size:20
Alignment explanation
Indices: 250033--250096 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
250023 AGCTCAGAGG
*
250033 GTTCATAATGAGAAGAACTC
1 GTTCATAATGAGAAGAACTA
* * **
250053 G-TCA-AACGAGGGAGAAGAA
1 GTTCATAATGA-GAAGAACTA
*
250072 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTA
250092 GTTCA
1 GTTCA
250097 ACCTTAGATC
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 4 0.13
19 9 0.29
20 14 0.45
21 4 0.13
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTA
Found at i:251607 original size:25 final size:25
Alignment explanation
Indices: 251549--251608 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
251539 GTTAATTTCT
*
251549 TTTATTATTT-GTAATTTTATTTTTA
1 TTTATT-TTTAGTAATTTTATATTTA
* *
251574 TTCAATTTTAGTAATTATT-TATTTA
1 TTTATTTTTAGTAATT-TTATATTTA
251599 TTTATTTTTA
1 TTTATTTTTA
251609 TTTTATTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
24 3 0.11
25 23 0.82
26 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (25 bp):
TTTATTTTTAGTAATTTTATATTTA
Found at i:251755 original size:152 final size:151
Alignment explanation
Indices: 251575--251879 Score: 601
Period size: 152 Copynumber: 2.0 Consensus size: 151
251565 TTATTTTTAT
251575 TCAATTTTAGTAATTATTTATTTATTTATTTTTATTTTATTTCTTAATTTGAATTAATATTCGAA
1 TCAATTTTAGTAATTATTTATTTATTTATTTTTATTTTATTTCTTAATTTGAATTAATATTCGAA
251640 TCAAAATTAGAAATTAGGATGACACTCTAGTTTAATTAGGGAGCAATTCGAATTGAGTTTTTCGC
66 TCAAAATTAGAAATTAGGATGACACTCTAGTTTAATTAGGGAGCAATTCGAATTGAG-TTTTCGC
251705 ATTATACGCCCGATTGCTCGAA
130 ATTATACGCCCGATTGCTCGAA
251727 TCAATTTTAGTAATTATTTATTTATTTATTTTTATTTTATTTCTTAATTTGAATTAATATTCGAA
1 TCAATTTTAGTAATTATTTATTTATTTATTTTTATTTTATTTCTTAATTTGAATTAATATTCGAA
251792 TCAAAATTAGAAATTAGGATGACACTCTAGTTTAATTAGGGAGCAATTCGAATTGAGTTTTCGCA
66 TCAAAATTAGAAATTAGGATGACACTCTAGTTTAATTAGGGAGCAATTCGAATTGAGTTTTCGCA
251857 TTATACGCCCGATTGCTCGAA
131 TTATACGCCCGATTGCTCGAA
251878 TC
1 TC
251880 GATTGTTCAA
Statistics
Matches: 153, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
151 31 0.20
152 122 0.80
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (151 bp):
TCAATTTTAGTAATTATTTATTTATTTATTTTTATTTTATTTCTTAATTTGAATTAATATTCGAA
TCAAAATTAGAAATTAGGATGACACTCTAGTTTAATTAGGGAGCAATTCGAATTGAGTTTTCGCA
TTATACGCCCGATTGCTCGAA
Found at i:254886 original size:5 final size:5
Alignment explanation
Indices: 254875--254909 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
254865 ACATAAAATT
* *
254875 TAATC GAATC GAATC TAATC TAATC TAATC TAATC
1 TAATC TAATC TAATC TAATC TAATC TAATC TAATC
254910 ATGTTATGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (5 bp):
TAATC
Found at i:256030 original size:19 final size:18
Alignment explanation
Indices: 255985--256026 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
255975 TTATAAAAAG
255985 TATTTTAATAAAGTACTC
1 TATTTTAATAAAGTACTC
* *
256003 TACTTTAATAAAGTTCTC
1 TATTTTAATAAAGTACTC
256021 TATTTT
1 TATTTT
256027 TAATCAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (18 bp):
TATTTTAATAAAGTACTC
Found at i:258464 original size:18 final size:19
Alignment explanation
Indices: 258441--258476 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
258431 AGATTAATAG
258441 CTTA-TTTCAAATTCATAA
1 CTTATTTTCAAATTCATAA
258459 CTTATTTTCAAATTCATA
1 CTTATTTTCAAATTCATA
258477 GCCCAATGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (19 bp):
CTTATTTTCAAATTCATAA
Found at i:258754 original size:18 final size:19
Alignment explanation
Indices: 258733--258772 Score: 50
Period size: 17 Copynumber: 2.2 Consensus size: 19
258723 TAATTATTAT
258733 ATATTATTCAAT-TATCAA-
1 ATATTA-TCAATATATCAAC
258751 ATA-TATCAATATATCAAC
1 ATATTATCAATATATCAAC
258769 ATAT
1 ATAT
258773 CCAACTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
16 5 0.26
17 8 0.42
18 6 0.32
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATTATCAATATATCAAC
Found at i:264635 original size:34 final size:30
Alignment explanation
Indices: 264597--264665 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
264587 TTGATATAAA
*
264597 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTT
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
264631 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
264660 AATTTA
1 AATTTA
264666 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 9 0.27
30 12 0.36
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:264663 original size:29 final size:31
Alignment explanation
Indices: 264606--264665 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
264596 AAATTTAAGG
*
264606 CAAAATGGTTTTTGGACTTGAATTTAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
264637 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
264666 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:264771 original size:21 final size:21
Alignment explanation
Indices: 264745--264800 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
264735 ACGGTGTCAA
264745 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
264766 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
264787 AGTGCATCCATGCA
1 AGTGCATCCATGCA
264801 TCCATCCACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.39, G:0.20, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:264889 original size:20 final size:20
Alignment explanation
Indices: 264864--265097 Score: 353
Period size: 20 Copynumber: 11.7 Consensus size: 20
264854 AATGCAATTA
264864 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
* *
264884 GTGCATCGATGCATCATTAT
1 GTGCATCGATGCATCCTTCT
* *
264904 GTGCATCGATGCATCATTAT
1 GTGCATCGATGCATCCTTCT
*
264924 GTGCATCGATGCATCATTCT
1 GTGCATCGATGCATCCTTCT
*
264944 GTGCATCGATGCATCATTCT
1 GTGCATCGATGCATCCTTCT
264964 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
264984 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
265004 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
265024 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
***
265044 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTTCT
265065 GTGCATCGATGCATCCTGT-T
1 GTGCATCGATGCATCCT-TCT
*
265085 GTGCATCCATGCA
1 GTGCATCGATGCA
265098 CGAAGGCTGG
Statistics
Matches: 201, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
20 184 0.92
21 17 0.08
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.33
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:265492 original size:34 final size:32
Alignment explanation
Indices: 265453--265522 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
265443 TTTTGTAAAG
* *
265453 GGGAAAGGTTCTAGCTTATCCCGTGTAAAATCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
265487 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
265519 GGGA
1 GGGA
265523 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:266465 original size:21 final size:22
Alignment explanation
Indices: 266441--266486 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
266431 CACTGAGGGG
* *
266441 CATAAT-TATCCCTAAGGACCT
1 CATAATATATCCCGAAGGACCA
266462 CAT-ATATATCCCGAAGGACCA
1 CATAATATATCCCGAAGGACCA
266483 CATA
1 CATA
266487 TAATTCTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (22 bp):
CATAATATATCCCGAAGGACCA
Found at i:266487 original size:21 final size:21
Alignment explanation
Indices: 266447--266593 Score: 100
Period size: 21 Copynumber: 6.9 Consensus size: 21
266437 GGGGCATAAT
* *
266447 TATCCCTAAGGACCTCATATA
1 TATCCCAAAGGACCACATATA
*
266468 TATCCCGAAGGACCACATATA
1 TATCCCAAAGGACCACATATA
266489 -ATTCTCCTTAAA-GACCACATATA
1 TA-TC-CC--AAAGGACCACATATA
* * *
266512 TATTCCAAAAGACCAAATATA
1 TATCCCAAAGGACCACATATA
* * *
266533 TGTCCCAAAGAACCGCATATA
1 TATCCCAAAGGACCACATATA
* * * **
266554 TGTTCCAAAAGAATACATATA
1 TATCCCAAAGGACCACATATA
* *
266575 TGTCCCGAAGGACCACATA
1 TATCCCAAAGGACCACATA
266594 GAACTCTCGA
Statistics
Matches: 98, Mismatches: 22, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
20 4 0.04
21 75 0.77
22 4 0.04
23 12 0.12
24 3 0.03
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (21 bp):
TATCCCAAAGGACCACATATA
Found at i:266511 original size:44 final size:44
Alignment explanation
Indices: 266442--266565 Score: 110
Period size: 44 Copynumber: 2.9 Consensus size: 44
266432 ACTGAGGGGC
* * * * *
266442 ATAATTATCCCTAAGGACCTCATATATATCCCGAAGGACCACAT
1 ATAATTATCCCTAAAGACCACATATATATCCCAAAAGACCAAAT
* * *
266486 ATAATTCTCCTTAAAGACCACATATATATTCCAAAAGACCAAAT
1 ATAATTATCCCTAAAGACCACATATATATCCCAAAAGACCAAAT
* * * *
266530 AT-A-TGTCCC-AAAGAACCGCATATATGTTCCAAAAGA
1 ATAATTATCCCTAAAG-ACCACATATATATCCCAAAAGA
266566 ATACATATAT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 24 0.36
43 1 0.01
44 38 0.57
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (44 bp):
ATAATTATCCCTAAAGACCACATATATATCCCAAAAGACCAAAT
Found at i:266552 original size:42 final size:41
Alignment explanation
Indices: 266498--266593 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 41
266488 AATTCTCCTT
*
266498 AAAGACCACATATATATTCCAAAAGACCAAATATATGTCCC
1 AAAGACCACATATATATTCCAAAAGAACAAATATATGTCCC
* * * *
266539 AAAGAACCGCATATATGTTCCAAAAGAATACATATATGTCCC
1 AAAG-ACCACATATATATTCCAAAAGAACAAATATATGTCCC
*
266581 GAAGGACCACATA
1 -AAAGACCACATA
266594 GAACTCTCGA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 4 0.09
42 39 0.85
43 3 0.07
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.21
Consensus pattern (41 bp):
AAAGACCACATATATATTCCAAAAGAACAAATATATGTCCC
Found at i:271741 original size:21 final size:21
Alignment explanation
Indices: 271713--271883 Score: 100
Period size: 21 Copynumber: 8.1 Consensus size: 21
271703 GGGGCATATA
* * *
271713 ATAT-TGTCCCTAAGGACCTC
1 ATATATGTCCCGAAAGACCAC
271733 ATATATGTCCCGAAAGACCAC
1 ATATATGTCCCGAAAGACCAC
271754 ATATATGTCCCGAAAGACCAC
1 ATATATGTCCCGAAAGACCAC
* * *
271775 ATATAAT-TCTCCTTAAGGGCCAC
1 ATAT-ATGTC-CC-GAAAGACCAC
* * *
271798 ATATATATTCC-AAATGACCAA
1 ATATATGTCCCGAAA-GACCAC
* * *
271819 ATATGTGT-CCAAAAAACCAC
1 ATATATGTCCCGAAAGACCAC
* ** *
271839 ATATATGTTCC-AAAGGATTAT
1 ATATATGTCCCGAAA-GACCAC
**
271860 ATATATGTCCTAAAAGACCAC
1 ATATATGTCCCGAAAGACCAC
271881 ATA
1 ATA
271884 GAACCCTCGA
Statistics
Matches: 117, Mismatches: 24, Indels: 19
0.73 0.15 0.12
Matches are distributed among these distances:
20 22 0.19
21 72 0.62
22 11 0.09
23 12 0.10
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (21 bp):
ATATATGTCCCGAAAGACCAC
Found at i:271778 original size:42 final size:42
Alignment explanation
Indices: 271713--271883 Score: 125
Period size: 41 Copynumber: 4.1 Consensus size: 42
271703 GGGGCATATA
* * *
271713 ATAT-TGTCCCTAAGGACCTCATATATGTCCCGAAAGACCAC
1 ATATATGTCCCAAAGGACCACATATATGTCCCAAAAGACCAC
* * *
271754 ATATATGTCCCGAAA-GACCACATATAAT-TCTCCTTAAGGGCCAC
1 ATATATGTCCC-AAAGGACCACATAT-ATGTC-CC-AAAAGACCAC
* * * * * *
271798 ATATATATTCCAAATGACCAAATATGTGT-CCAAAAAACCAC
1 ATATATGTCCCAAAGGACCACATATATGTCCCAAAAGACCAC
* ** * *
271839 ATATATGTTCCAAAGGATTATATATATGTCCTAAAAGACCAC
1 ATATATGTCCCAAAGGACCACATATATGTCCCAAAAGACCAC
271881 ATA
1 ATA
271884 GAACCCTCGA
Statistics
Matches: 101, Mismatches: 21, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
41 33 0.33
42 32 0.32
43 10 0.10
44 26 0.26
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (42 bp):
ATATATGTCCCAAAGGACCACATATATGTCCCAAAAGACCAC
Found at i:271803 original size:65 final size:64
Alignment explanation
Indices: 271723--271843 Score: 145
Period size: 65 Copynumber: 1.9 Consensus size: 64
271713 ATATTGTCCC
* * * * *
271723 TAAGGACCTCATATATGTCCCGAAA-GACCACATATATGTCCCGAAAGACCACATATAATTCTCC
1 TAAGGACCACATATATATCCC-AAATGACCAAATATATGT-CCAAAAAACCACATATAATTCTCC
271787 T
64 T
* * *
271788 TAAGGGCCACATATATATTCCAAATGACCAAATATGTGTCCAAAAAACCACATATA
1 TAAGGACCACATATATATCCCAAATGACCAAATATATGTCCAAAAAACCACATATA
271844 TGTTCCAAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
64 18 0.38
65 29 0.62
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.24
Consensus pattern (64 bp):
TAAGGACCACATATATATCCCAAATGACCAAATATATGTCCAAAAAACCACATATAATTCTCCT
Found at i:271837 original size:20 final size:21
Alignment explanation
Indices: 271794--271852 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
271784 TCCTTAAGGG
* **
271794 CCACATATATATTCCAAATGA
1 CCACATATATGTTCCAAAAAA
271815 CCA-A-ATATGTGTCCAAAAAA
1 CCACATATATGT-TCCAAAAAA
271835 CCACATATATGTTCCAAA
1 CCACATATATGTTCCAAA
271853 GGATTATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 5 0.16
20 11 0.34
21 10 0.31
22 6 0.19
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.25
Consensus pattern (21 bp):
CCACATATATGTTCCAAAAAA
Found at i:274336 original size:194 final size:193
Alignment explanation
Indices: 274008--274505 Score: 556
Period size: 194 Copynumber: 2.6 Consensus size: 193
273998 TTGTATAAGA
* * * * * * *
274008 TGATGTTATCCATAATCATCATTCATAATATTATTATATAACAACATATCACGTCACTAAAAATG
1 TGATGTTATACATAAACGTCATTCATAATATTATTATGTAATATC-TATTACGTCACTAAAAATG
* * * * *
274073 TAACAATATCTCATTCGTCTCATATAGGTGGATTTTAATGCATTATTCGTGACAATATAAATTAT
65 TGACAATATCTCTTTCGTCACATATAGGTTGATTTTAATGTATTATTCGTGACAATATAAATTAT
* **
274138 CAATAATGAAATCTTATATAATCTAGTGACATAACTA-TTTGTCATGGAATATAAATTAT-AAAG
130 CAATAACGAAATCTTATATAATCTAGTGACATAACTAGTTT-TCATCAAATATAAATTATAAAAG
* * * *
274201 TGATGTTATGCATAAGCGTCATTCATAATATTTTTATGTAATATTTCTATTAAGTCACTAAAAAT
1 TGATGTTATACATAAACGTCATTCATAATATTATTATGTAATA--TCTATTACGTCACTAAAAAT
** *
274266 GTGACAATATAACTTTCGTCACATATAGGTTGATTTTAACGTATTA-TCTGTGACAATATAAATT
64 GTGACAATATCTCTTTCGTCACATATAGGTTGATTTTAATGTATTATTC-GTGACAATATAAATT
* * * * *
274330 ATCAATAACGAAATTTTATATAATTTATTGACATAATTAGTTTTCATCAAATATTAATTATAAAA
128 ATCAATAACGAAATCTTATATAATCTAGTGACATAACTAGTTTTCATCAAATATAAATTATAAAA
274395 G
193 G
* * * * * * * * *
274396 TG-TCATTATATATAAACGTCATTCATATTGTCATTAGGTGATGATATACTACGTCAC-AAAAAT
1 TGAT-GTTATACATAAACGTCATTCATAATATTATTATGTAAT-ATCTATTACGTCACTAAAAAT
* *
274459 GTGACAATATCTCTTTCGTCACATATAAGTTTATTTTAATGTATTAT
64 GTGACAATATCTCTTTCGTCACATATAGGTTGATTTTAATGTATTAT
274506 ATGTCATTCA
Statistics
Matches: 254, Mismatches: 43, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
193 86 0.34
194 129 0.51
195 38 0.15
196 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.39
Consensus pattern (193 bp):
TGATGTTATACATAAACGTCATTCATAATATTATTATGTAATATCTATTACGTCACTAAAAATGT
GACAATATCTCTTTCGTCACATATAGGTTGATTTTAATGTATTATTCGTGACAATATAAATTATC
AATAACGAAATCTTATATAATCTAGTGACATAACTAGTTTTCATCAAATATAAATTATAAAAG
Found at i:275513 original size:17 final size:18
Alignment explanation
Indices: 275491--275539 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
275481 TATTTATTAT
275491 TATTATTATTAT-TACATA
1 TATTATTATTATATA-ATA
275509 T-TTATTA-TATATAATA
1 TATTATTATTATATAATA
*
275525 TATTATTATAATATA
1 TATTATTATTATATA
275540 TTTGCATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 7 0.26
17 14 0.52
18 6 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATTATTATATAATA
Found at i:275533 original size:20 final size:19
Alignment explanation
Indices: 275469--275540 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
275459 TTGTCCGATT
*
275469 TTATTAATTATATATTTATTA
1 TTATT-ATTATATATATA-TA
*
275490 TTATTATTAT-TAT-TACA
1 TTATTATTATATATATATA
275507 -TATTTATTATATATAATATA
1 TTA-TTATTATATAT-ATATA
*
275527 TTATTATAATATAT
1 TTATTATTATATAT
275541 TTGCATTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
16 2 0.05
17 8 0.19
18 5 0.12
19 3 0.07
20 18 0.42
21 7 0.16
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATTATTATATATATATA
Found at i:277481 original size:9 final size:10
Alignment explanation
Indices: 277447--277490 Score: 56
Period size: 9 Copynumber: 4.5 Consensus size: 10
277437 ATTTGTTTTG
277447 TTTTAATTTA
1 TTTTAATTTA
*
277457 ATTTAATTTAA
1 TTTTAATTT-A
277468 TTTTAA-TTA
1 TTTTAATTTA
277477 TTTTAA-TTA
1 TTTTAATTTA
277486 TTTTA
1 TTTTA
277491 CTAACTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
9 15 0.48
10 10 0.32
11 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTAATTTA
Found at i:282303 original size:13 final size:13
Alignment explanation
Indices: 282285--282309 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
282275 GACTCAGATC
282285 AAATGAACTTTAA
1 AAATGAACTTTAA
282298 AAATGAACTTTA
1 AAATGAACTTTA
282310 CGACTCAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
AAATGAACTTTAA
Found at i:283213 original size:23 final size:23
Alignment explanation
Indices: 283187--283238 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
283177 AACATTTTGC
283187 AAGAATGATAGATTCTCTTTTCA
1 AAGAATGATAGATTCTCTTTTCA
283210 AAG-ATGATAGATTCTCTTTTCA
1 AAGAATGATAGATTCTCTTTTCA
283232 AA-AATGA
1 AAGAATGA
283239 GAGCTTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (23 bp):
AAGAATGATAGATTCTCTTTTCA
Found at i:283219 original size:22 final size:22
Alignment explanation
Indices: 283181--283238 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
283171 TATATCAACA
*
283181 TTTTGCAAGAATGATAGATTCTC
1 TTTT-CAAAAATGATAGATTCTC
*
283204 TTTTCAAAGATGATAGATTCTC
1 TTTTCAAAAATGATAGATTCTC
283226 TTTTCAAAAATGA
1 TTTTCAAAAATGA
283239 GAGCTTTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTTTCAAAAATGATAGATTCTC
Found at i:284408 original size:32 final size:32
Alignment explanation
Indices: 284335--284434 Score: 124
Period size: 32 Copynumber: 3.3 Consensus size: 32
284325 TTGTCCGATT
* *
284335 TTATTA-ATTATATAT--TATTAT-TATTACA
1 TTATTATATTATATATAATATAATATATTATA
284363 -TATT-TATTATATATAATATAATATATTATA
1 TTATTATATTATATATAATATAATATATTATA
284393 TTATTATATTATATATAATATAATATATTAT-
1 TTATTATATTATATATAATATAATATATTATA
284424 TATATTATATT
1 T-TATTATATT
284435 TGCATTTAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
27 13 0.21
29 5 0.08
30 6 0.10
31 5 0.08
32 34 0.54
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (32 bp):
TTATTATATTATATATAATATAATATATTATA
Found at i:284434 original size:5 final size:5
Alignment explanation
Indices: 284336--284434 Score: 63
Period size: 5 Copynumber: 20.8 Consensus size: 5
284326 TGTCCGATTT
*
284336 TATTA -ATTA TA-TA TTATTA TTATTACA TATT- TATTA TA-TA TAATA
1 TATTA TATTA TATTA -TATTA -TATT--A TATTA TATTA TATTA TATTA
* * *
284381 TAATA TATTA TA-T- TATTA TATTA TA-TA TAATA TAATA TA-T- TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
284426 TATTA TATT
1 TATTA TATT
284435 TGCATTTAAT
Statistics
Matches: 81, Mismatches: 1, Indels: 24
0.76 0.01 0.23
Matches are distributed among these distances:
3 4 0.05
4 22 0.27
5 43 0.53
6 7 0.09
7 4 0.05
8 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (5 bp):
TATTA
Found at i:286775 original size:23 final size:23
Alignment explanation
Indices: 286749--286819 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
286739 CACCACAACT
286749 CATAAATTTGCACCGAAGAGCCA
1 CATAAATTTGCACCGAAGAGCCA
*
286772 CAT-AA-TTGTC-CTGAA-AGACCA
1 CATAAATTTG-CACCGAAGAG-CCA
** *
286793 CATAGGTTTGCACCGAAGTGCCA
1 CATAAATTTGCACCGAAGAGCCA
286816 CATA
1 CATA
286820 TTTGTCCCGA
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
20 2 0.05
21 13 0.35
22 4 0.11
23 17 0.46
24 1 0.03
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.21
Consensus pattern (23 bp):
CATAAATTTGCACCGAAGAGCCA
Found at i:286818 original size:44 final size:44
Alignment explanation
Indices: 286755--286841 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
286745 AACTCATAAA
*
286755 TTTGCACCGAAGAGCCACATAATTGTCCTGAAAGACCACATAGG
1 TTTGCACCGAAGAGCCACATAATTGTCCCGAAAGACCACATAGG
* * *
286799 TTTGCACCGAAGTGCCACATATTTGTCCCGAAGGACCACATAG
1 TTTGCACCGAAGAGCCACATAATTGTCCCGAAAGACCACATAG
286842 ACCCTCGACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (44 bp):
TTTGCACCGAAGAGCCACATAATTGTCCCGAAAGACCACATAGG
Found at i:286829 original size:21 final size:20
Alignment explanation
Indices: 286761--286840 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 20
286751 TAAATTTGCA
*
286761 CCGAAGAGCCACATAATTGTC
1 CCGAAG-GCCACATATTTGTC
* *
286782 CTGAAAGACCACATAGGTTTG-C
1 CCG-AAGGCCACATA--TTTGTC
286804 ACCGAAGTGCCACATATTTGTC
1 -CCGAAG-GCCACATATTTGTC
286826 CCGAAGGACCACATA
1 CCGAAGG-CCACATA
286841 GACCCTCGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
20 1 0.02
21 26 0.55
22 8 0.17
23 12 0.26
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (20 bp):
CCGAAGGCCACATATTTGTC
Found at i:287271 original size:17 final size:16
Alignment explanation
Indices: 287249--287290 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
287239 TATTTACTTG
287249 TATAAAACATATTCATA
1 TATAAAA-ATATTCATA
*
287266 TAT-AAAATCTTCATA
1 TATAAAAATATTCATA
*
287281 TATAATAATA
1 TATAAAAATA
287291 ATATCATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 11 0.52
16 7 0.33
17 3 0.14
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (16 bp):
TATAAAAATATTCATA
Found at i:287628 original size:55 final size:55
Alignment explanation
Indices: 287559--287705 Score: 224
Period size: 55 Copynumber: 2.7 Consensus size: 55
287549 CATTTCATGC
*
287559 TTTG-GGGTATCGATACACTCCTCAGTGTACCGATACATAAATAACACTCGATGT
1 TTTGAGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACACTCGATGT
* ** * * *
287613 TTTGAGGGTATCGATACACTCCTCAGTGTACCAATACACAAATGGCATTTGGTGT
1 TTTGAGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACACTCGATGT
287668 TTTGAGGGTATCGATACACTCCTCAGTGTACCGATACA
1 TTTGAGGGTATCGATACACTCCTCAGTGTACCGATACA
287706 AACTCACACA
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
54 4 0.05
55 80 0.95
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (55 bp):
TTTGAGGGTATCGATACACTCCTCAGTGTACCGATACACAAATAACACTCGATGT
Found at i:289096 original size:37 final size:37
Alignment explanation
Indices: 289023--289097 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 37
289013 GTTGAAAAAT
*
289023 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
289060 ATTTATATAATTGTT-TTT-AAAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATT-TTCTTTAAAAAAATT-AAAATCATAAA
289097 A
1 A
289098 AGGTTTAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
37 22 0.65
38 10 0.29
39 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:289910 original size:31 final size:31
Alignment explanation
Indices: 289872--289938 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
289862 TCAGAAAAGA
** *
289872 AAGATATGATCATTTTCGTTTTTATTTAATT
1 AAGATATGATCACATTCATTTTTATTTAATT
*
289903 AAGATATGTTCACATTCATTTTTATTTAATT
1 AAGATATGATCACATTCATTTTTATTTAATT
289934 AAGAT
1 AAGAT
289939 GTGGTAATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (31 bp):
AAGATATGATCACATTCATTTTTATTTAATT
Found at i:290137 original size:27 final size:24
Alignment explanation
Indices: 290100--290174 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 24
290090 AAAAGAAAAT
*
290100 AAATATTTTTAAATTAAGTTAATAATA
1 AAATATATTT-AA-TAAGTTAAT-ATA
290127 AAATATATTTAATAAGTTAATATA
1 AAATATATTTAATAAGTTAATATA
* *
290151 AAAAATATCTT-TTAAGTTAATATA
1 AAATATAT-TTAATAAGTTAATATA
290175 TATAAAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
24 22 0.50
25 11 0.25
26 2 0.05
27 9 0.20
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (24 bp):
AAATATATTTAATAAGTTAATATA
Found at i:290175 original size:26 final size:26
Alignment explanation
Indices: 290112--290185 Score: 84
Period size: 24 Copynumber: 3.0 Consensus size: 26
290102 ATATTTTTAA
*
290112 ATTAAGTTAATA-ATAAAATATATTT
1 ATTAAGTTAATATATAAAAAATATTT
*
290137 AATAAGTT-A-ATATAAAAAATATCTT
1 ATTAAGTTAATATATAAAAAATAT-TT
*
290162 -TTAAGTTAATATATATAAAATATT
1 ATTAAGTTAATATATAAAAAATATT
290186 ATGAATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
23 1 0.02
24 17 0.41
25 11 0.27
26 12 0.29
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (26 bp):
ATTAAGTTAATATATAAAAAATATTT
Found at i:300936 original size:12 final size:12
Alignment explanation
Indices: 300916--300953 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
300906 TTTATAAATA
300916 CCTCGCATCTCT
1 CCTCGCATCTCT
*
300928 CCTCACA--TCT
1 CCTCGCATCTCT
300938 CCTCGCATCTCT
1 CCTCGCATCTCT
300950 CCTC
1 CCTC
300954 TCTTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.11, C:0.53, G:0.05, T:0.32
Consensus pattern (12 bp):
CCTCGCATCTCT
Found at i:304372 original size:3 final size:3
Alignment explanation
Indices: 304366--304417 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
304356 GCTGTCATCA
* * * *
304366 TCG TCG TCG TCA TCG TCG TACCA TCG TCA TCG TCG TCA TCG TCG TCG
1 TCG TCG TCG TCG TCG TCG T--CG TCG TCG TCG TCG TCG TCG TCG TCG
304413 TCG TC
1 TCG TC
304418 CTGAGTAGGT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
3 37 0.95
5 2 0.05
ACGTcount: A:0.10, C:0.35, G:0.23, T:0.33
Consensus pattern (3 bp):
TCG
Found at i:304383 original size:9 final size:9
Alignment explanation
Indices: 304369--304417 Score: 64
Period size: 9 Copynumber: 5.6 Consensus size: 9
304359 GTCATCATCG
304369 TCGTCGTCA
1 TCGTCGTCA
304378 TCGTCGT-A
1 TCGTCGTCA
* *
304386 CCATCGTCA
1 TCGTCGTCA
304395 TCGTCGTCA
1 TCGTCGTCA
*
304404 TCGTCGTCG
1 TCGTCGTCA
304413 TCGTC
1 TCGTC
304418 CTGAGTAGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
8 6 0.18
9 28 0.82
ACGTcount: A:0.10, C:0.35, G:0.22, T:0.33
Consensus pattern (9 bp):
TCGTCGTCA
Found at i:304390 original size:26 final size:26
Alignment explanation
Indices: 304361--304410 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
304351 TCCTCGCTGT
*
304361 CATCATCGTCGTCGTCATCGTCGTAC
1 CATCATCATCGTCGTCATCGTCGTAC
*
304387 CATCGTCATCGTCGTCATCGTCGT
1 CATCATCATCGTCGTCATCGTCGT
304411 CGTCGTCCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.14, C:0.34, G:0.20, T:0.32
Consensus pattern (26 bp):
CATCATCATCGTCGTCATCGTCGTAC
Found at i:306468 original size:111 final size:111
Alignment explanation
Indices: 306274--306606 Score: 603
Period size: 111 Copynumber: 3.0 Consensus size: 111
306264 ATTACAAAAA
*
306274 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
306339 AATTAAAATGTTAAAATGTTACCGTATCAGTAAAGTGTCGATATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGATATAT
306385 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
306450 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGATATAT
* *
306496 TTAATTCTTAATCTAATAATTATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
306561 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGATATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGATATAT
306607 ATGATTTCCA
Statistics
Matches: 214, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 214 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGATATAT
Found at i:307349 original size:16 final size:16
Alignment explanation
Indices: 307325--307355 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
307315 AAATTAATCA
*
307325 TTTATTAAAATTATAT
1 TTTAATAAAATTATAT
307341 TTTAATAAAATTATA
1 TTTAATAAAATTATA
307356 ATTATATTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAATAAAATTATAT
Found at i:307435 original size:17 final size:18
Alignment explanation
Indices: 307413--307446 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
307403 TATTAACATC
307413 TTATTTGATTTT-TTTAA
1 TTATTTGATTTTATTTAA
307430 TTATTTGATTTTATTTA
1 TTATTTGATTTTATTTA
307447 TTAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
TTATTTGATTTTATTTAA
Found at i:308509 original size:158 final size:156
Alignment explanation
Indices: 308255--308542 Score: 375
Period size: 158 Copynumber: 1.8 Consensus size: 156
308245 ACAACGTCTT
* * * *
308255 GCTTAGACGACCGTCAAATTTCAACAAAGAAATATGAGTTTGAAATATATGAATAGTCAGGCGAC
1 GCTTAGACGACCGTCAAATTTCAACAAAAAAAGATGAGTTTGAAACATATGAATAGCCAGGCGAC
* * * *
308320 TATTTTATAATTTTTAATAGTTGAAGTACTCAATAGAACAT-TATTTTATAGTC-GAAGAATTTA
66 TATTTTATAATTTTCAATAGTCGAAGGACTCAAT--AACATATATCTTATAGTCGGAA-AATTTA
308383 TATTTTTTAAAAGTTGGGGACTCAACAAA
128 TATTTTTTAAAAGTTGGGGACTCAACAAA
** * * **
308412 GCTTAGACGATTGTCAATTTTTTAACAAAAAAAGATGAGTTTGAAACATATGAATAGCC-GAGTT
1 GCTTAGACGACCGTCAA-ATTTCAACAAAAAAAGATGAGTTTGAAACATATGAATAGCCAG-GCG
308476 ACTATTTTATAATTTTCAATAGTCGAAGGACTCAATAACATAATATCTTATAGTCGGAAAATTTA
64 ACTATTTTATAATTTTCAATAGTCGAAGGACTCAATAACAT-ATATCTTATAGTCGGAAAATTTA
308541 TA
128 TA
308543 AATTTTAATA
Statistics
Matches: 112, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
156 5 0.04
157 16 0.14
158 88 0.79
159 3 0.03
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (156 bp):
GCTTAGACGACCGTCAAATTTCAACAAAAAAAGATGAGTTTGAAACATATGAATAGCCAGGCGAC
TATTTTATAATTTTCAATAGTCGAAGGACTCAATAACATATATCTTATAGTCGGAAAATTTATAT
TTTTTAAAAGTTGGGGACTCAACAAA
Found at i:310098 original size:31 final size:30
Alignment explanation
Indices: 310048--310124 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 30
310038 AAAAAGTTTG
310048 AATAA-TTTAGGTACTTATTTTGACTAAAA
1 AATAACTTTAGGTACTTATTTTGACTAAAA
* *
310077 AGATAACTTTATGTATTTATTTTGACTAAAA
1 A-ATAACTTTAGGTACTTATTTTGACTAAAA
*
310108 AAT-ACTTTAGGCACTTA
1 AATAACTTTAGGTACTTA
310125 AATGAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 12 0.29
30 6 0.15
31 23 0.56
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (30 bp):
AATAACTTTAGGTACTTATTTTGACTAAAA
Found at i:314306 original size:14 final size:14
Alignment explanation
Indices: 314287--314314 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
314277 AATATGTTTG
314287 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
314301 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
314315 AAGTCTGTTA
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:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:316615 original size:51 final size:51
Alignment explanation
Indices: 316539--316639 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
316529 TAAGGAAAGG
* *
316539 ATAGGTTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
316590 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
316640 CTCCCCCTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
Found at i:318420 original size:14 final size:14
Alignment explanation
Indices: 318401--318428 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
318391 CCTGATACCA
318401 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
318415 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
318429 AAGTTTGTTA
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:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
TGTAGAAAACAGAC
Found at i:329816 original size:20 final size:20
Alignment explanation
Indices: 329791--329829 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
329781 TTTGGTAAGT
329791 ATAAATGAAAACTTGAATTC
1 ATAAATGAAAACTTGAATTC
329811 ATAAATGAAAACTTGAATT
1 ATAAATGAAAACTTGAATT
329830 TAAAACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (20 bp):
ATAAATGAAAACTTGAATTC
Found at i:330428 original size:24 final size:25
Alignment explanation
Indices: 330397--330446 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
330387 AATTTAATTT
*
330397 TTAAAAAT-TAAAAAATTATTTAGA
1 TTAAAAATATAAAAAATTATTAAGA
*
330421 TTAAAAATATAAATAATTATTAAGA
1 TTAAAAATATAAAAAATTATTAAGA
330446 T
1 T
330447 AGTCAATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
TTAAAAATATAAAAAATTATTAAGA
Found at i:332271 original size:3 final size:3
Alignment explanation
Indices: 332263--332339 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
332253 TTTTTATCCA
* *
332263 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
332311 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
332340 AATATATTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:333781 original size:13 final size:13
Alignment explanation
Indices: 333729--333806 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 13
333719 TATGTCTTCA
*
333729 TTTATTTTATTGTT
1 TTTATTATATT-TT
* *
333743 TTTAAATATATTGT
1 TTT-ATTATATTTT
*
333757 TTTAATAGTATTTT
1 TTTATTA-TATTTT
*
333771 TTTATTATATTAT
1 TTTATTATATTTT
* * *
333784 ATTATTAAATATT
1 TTTATTATATTTT
333797 TTTA-TATATT
1 TTTATTATATT
333807 CATAAATATA
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
12 4 0.08
13 21 0.43
14 18 0.37
15 6 0.12
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (13 bp):
TTTATTATATTTT
Found at i:334466 original size:7 final size:7
Alignment explanation
Indices: 334454--334485 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
334444 TGTCTCTATT
334454 AATTAAA
1 AATTAAA
334461 AATTAAA
1 AATTAAA
334468 AATTAAA
1 AATTAAA
334475 AATTAAA
1 AATTAAA
334482 AATT
1 AATT
334486 TATATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AATTAAA
Found at i:345211 original size:11 final size:10
Alignment explanation
Indices: 345182--345241 Score: 93
Period size: 10 Copynumber: 5.9 Consensus size: 10
345172 ATTATGCTTG
*
345182 AAGAAAAAGA
1 AAGAAAAAAA
345192 AAGAAAAAAA
1 AAGAAAAAAA
*
345202 AAGAGGAAAAA
1 AAGA-AAAAAA
345213 AAGAAAAAAA
1 AAGAAAAAAA
345223 AAGAAAAAAA
1 AAGAAAAAAA
345233 AAGAAAAAA
1 AAGAAAAAA
345242 GGAAAAAAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
10 37 0.80
11 9 0.20
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:345234 original size:35 final size:35
Alignment explanation
Indices: 345185--345255 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
345175 ATGCTTGAAG
* *
345185 AAAAAGAAAGAAAAA-AAAAGAGGAAAAAAAGAAAA
1 AAAAAGAAAAAAAAAGAAAAAAGG-AAAAAAGAAAA
345220 AAAAAGAAAAAAAAAGAAAAAAGGAAAAAAGAAAA
1 AAAAAGAAAAAAAAAGAAAAAAGGAAAAAAGAAAA
345255 A
1 A
345256 GGGGGTCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 26 0.79
36 7 0.21
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (35 bp):
AAAAAGAAAAAAAAAGAAAAAAGGAAAAAAGAAAA
Found at i:345249 original size:10 final size:10
Alignment explanation
Indices: 345184--345249 Score: 57
Period size: 10 Copynumber: 6.7 Consensus size: 10
345174 TATGCTTGAA
345184 GAAAAAGAAAG
1 GAAAAA-AAAG
*
345195 AAAAAAAAAG
1 GAAAAAAAAG
*
345205 AGGAAAAAAA-
1 -GAAAAAAAAG
*
345215 GAAAAAAAAA
1 GAAAAAAAAG
345225 GAAAAAAAA-
1 GAAAAAAAAG
*
345234 -AGAAAAAAG
1 GAAAAAAAAG
345243 GAAAAAA
1 GAAAAAA
345250 GAAAAAGGGG
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 7 0.16
9 8 0.18
10 18 0.40
11 12 0.27
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAG
Found at i:345254 original size:21 final size:19
Alignment explanation
Indices: 345195--345255 Score: 72
Period size: 17 Copynumber: 3.3 Consensus size: 19
345185 AAAAAGAAAG
*
345195 AAAAAAAAAGAGGAAAAAA
1 AAAAAAAAAAAGGAAAAAA
*
345214 AGAAAAAAAAA-G-AAAAA
1 AAAAAAAAAAAGGAAAAAA
*
345231 AAAAGAAAAAAGGAAAAAA
1 AAAAAAAAAAAGGAAAAAA
345250 GAAAAA
1 -AAAAA
345256 GGGGGTCAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
17 14 0.41
18 2 0.06
19 14 0.41
20 4 0.12
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAGGAAAAAA
Found at i:345256 original size:21 final size:19
Alignment explanation
Indices: 345195--345255 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
345185 AAAAAGAAAG
*
345195 AAAAAAAAAGAGGAAAAAA
1 AAAAAAAAAAAGGAAAAAA
*
345214 AGAAAAAAAAA-G-AAAAA
1 AAAAAAAAAAAGGAAAAAA
*
345231 AAAAGAAAAAAGGAAAAAA
1 AAAAAAAAAAAGGAAAAAA
*
345250 GAAAAA
1 AAAAAA
345256 GGGGGTCAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 14 0.41
18 2 0.06
19 18 0.53
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAGGAAAAAA
Found at i:345256 original size:31 final size:30
Alignment explanation
Indices: 345185--345249 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
345175 ATGCTTGAAG
345185 AAAAAGAAAGAAAAAAAAAGAGGAAAAAAAGA
1 AAAAA-AAAGAAAAAAAAAGA-GAAAAAAAGA
*
345217 AAAAAAAAG-AAAAAAAA-AGAAAAAAGGA
1 AAAAAAAAGAAAAAAAAAGAGAAAAAAAGA
345245 AAAAA
1 AAAAA
345250 GAAAAAGGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 14 0.44
29 1 0.03
30 8 0.25
31 4 0.12
32 5 0.16
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (30 bp):
AAAAAAAAGAAAAAAAAAGAGAAAAAAAGA
Found at i:345593 original size:16 final size:16
Alignment explanation
Indices: 345572--345611 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
345562 ATACAATTCT
345572 ATTTATTTCA-AGTTCA
1 ATTTATTTCAGAG-TCA
*
345588 ATTTATTTGAGAGTCA
1 ATTTATTTCAGAGTCA
345604 ATTTATTT
1 ATTTATTT
345612 TTGGAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (16 bp):
ATTTATTTCAGAGTCA
Found at i:346551 original size:83 final size:83
Alignment explanation
Indices: 346412--346740 Score: 597
Period size: 83 Copynumber: 4.0 Consensus size: 83
346402 CAATATACTT
*
346412 ATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAGTT
346477 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
346495 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAGTT
346560 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
*
346578 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAGTT
*
346643 TGGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
* * *
346661 ATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CAATCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAGTT
346725 TAGAAGATGAATTTGC
66 TAGAAGATGAATTTGC
346741 TCATAGTAAA
Statistics
Matches: 238, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
82 26 0.11
83 212 0.89
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.36
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCAAGCATTGAGTT
TAGAAGATGAATTTGCCA
Found at i:347735 original size:113 final size:113
Alignment explanation
Indices: 347537--348056 Score: 882
Period size: 113 Copynumber: 4.6 Consensus size: 113
347527 ATTTCGAATC
* *
347537 CACTTGATGGATCATTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
347602 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCAT
66 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCAT
* *
347650 CACTTGATGGATCATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGA
1 CACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
347715 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCAT
66 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCAT
* *
347763 CATTTGA-GAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1 CACTTGATG-GATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
347827 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCAT
65 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCAT
* *
347876 CATTTGAGGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* * *
347941 AAAAGTTCATAATTAGAAGAATTTGTTCAACCTTTTACCTGAATTCAT
66 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCAT
* * * *
347989 CAATTGATGGATTATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGA
1 CACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
348053 AGAA
66 AGAA
348057 CTTGTTCAAC
Statistics
Matches: 389, Mismatches: 16, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
112 41 0.11
113 347 0.89
114 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
CACTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCAT
Found at i:348398 original size:3 final size:3
Alignment explanation
Indices: 348390--348466 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
348380 TTTTTATCCA
* *
348390 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
348438 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
348467 AATATATATT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:349905 original size:13 final size:13
Alignment explanation
Indices: 349853--349930 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 13
349843 TATGTCTTCA
*
349853 TTTATTTTATTGTT
1 TTTATTATATT-TT
* *
349867 TTTAAATATATTGT
1 TTT-ATTATATTTT
*
349881 TTTAATAGTATTTT
1 TTTATTA-TATTTT
*
349895 TTTATTATATTAT
1 TTTATTATATTTT
* * *
349908 ATTATTAAATATT
1 TTTATTATATTTT
349921 TTTA-TATATT
1 TTTATTATATT
349931 CATAAATATA
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
12 4 0.08
13 21 0.43
14 18 0.37
15 6 0.12
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (13 bp):
TTTATTATATTTT
Found at i:351537 original size:21 final size:22
Alignment explanation
Indices: 351500--351543 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
351490 AAAAAATTAT
*
351500 TTTTTATTAAATATTTTTGATA
1 TTTTTATTAAATATTTTTAATA
*
351522 TTTTTATTTAAT-TTTTTAATA
1 TTTTTATTAAATATTTTTAATA
351543 T
1 T
351544 AATTATGACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTTATTAAATATTTTTAATA
Found at i:359417 original size:15 final size:15
Alignment explanation
Indices: 359393--359425 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
359383 TAGTGAGGTA
359393 TAAGGCGAGTGCATC
1 TAAGGCGAGTGCATC
*
359408 TAAGGTGAGTGCATC
1 TAAGGCGAGTGCATC
359423 TAA
1 TAA
359426 CTTATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (15 bp):
TAAGGCGAGTGCATC
Found at i:361742 original size:25 final size:25
Alignment explanation
Indices: 361714--361794 Score: 135
Period size: 25 Copynumber: 3.2 Consensus size: 25
361704 GGAAACTATG
*
361714 GTGCAATTCTATAAGGCACTTTCGA
1 GTGCAATTCTACAAGGCACTTTCGA
361739 GTGCAATTCTACAAGGCACTTTCGA
1 GTGCAATTCTACAAGGCACTTTCGA
* *
361764 GTTCAATTCTACAAGGCACTTTCAA
1 GTGCAATTCTACAAGGCACTTTCGA
361789 GTGCAA
1 GTGCAA
361795 ATATTTCTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (25 bp):
GTGCAATTCTACAAGGCACTTTCGA
Found at i:361971 original size:30 final size:29
Alignment explanation
Indices: 361900--361971 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
361890 CCAAAATGTT
* *
361900 TTTAGTAACTAAAGTGTAAGATTTGAAAG
1 TTTAGGAACTAAAGTATAAGATTTGAAAG
*
361929 TTTAGTG-GCTAAAGTATAA-ACTTTGAAAAG
1 TTTAG-GAACTAAAGTATAAGA-TTTG-AAAG
361959 TTTAGGAACTAAA
1 TTTAGGAACTAAA
361972 ATTGTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
28 1 0.03
29 20 0.57
30 14 0.40
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (29 bp):
TTTAGGAACTAAAGTATAAGATTTGAAAG
Found at i:363373 original size:18 final size:18
Alignment explanation
Indices: 363338--363373 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
363328 TTAAGATTTC
*
363338 ATATTCGATTTAAATATT
1 ATATTCGATTCAAATATT
*
363356 ATATTCGATTCAATTATT
1 ATATTCGATTCAAATATT
363374 TGAAAATCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (18 bp):
ATATTCGATTCAAATATT
Found at i:363747 original size:24 final size:24
Alignment explanation
Indices: 363715--363793 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
363705 ACCATGTTCG
**
363715 GTATCGATACTACTTTACATAGTA
1 GTATCGATACTACTGCACATAGTA
*
363739 GTATCGATACTCACTGGAC---G--
1 GTATCGATACT-ACTGCACATAGTA
363759 GTATCGATACTACTGCACATAGTA
1 GTATCGATACTACTGCACATAGTA
363783 GTATCGATACT
1 GTATCGATACT
363794 CCTTGGACAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 6 0.13
20 11 0.24
22 2 0.04
24 22 0.48
25 5 0.11
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (24 bp):
GTATCGATACTACTGCACATAGTA
Found at i:363762 original size:44 final size:44
Alignment explanation
Indices: 363713--363812 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 44
363703 ATACCATGTT
**
363713 CGGTATCGATACTACTTTACATAGTAGTATCGATACTCAC-TGGA
1 CGGTATCGATACTACTGCACATAGTAGTATCGATACTC-CTTGGA
363757 CGGTATCGATACTACTGCACATAGTAGTATCGATACTCCTTGGA
1 CGGTATCGATACTACTGCACATAGTAGTATCGATACTCCTTGGA
**
363801 CAATATCGATAC
1 CGGTATCGATAC
363813 CGTTGAGTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 1 0.02
44 50 0.98
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (44 bp):
CGGTATCGATACTACTGCACATAGTAGTATCGATACTCCTTGGA
Found at i:368164 original size:2 final size:2
Alignment explanation
Indices: 368157--368208 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
368147 TAACAAATGC
368157 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
368199 AT AT AT AT AT
1 AT AT AT AT AT
368209 CATGTAATAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:368754 original size:28 final size:28
Alignment explanation
Indices: 368714--368793 Score: 124
Period size: 28 Copynumber: 2.9 Consensus size: 28
368704 GAAGGATCAC
*
368714 TATGTCCCGAAGGACCACATATAACACA
1 TATGTCCCGAAGGACCACATAGAACACA
* * *
368742 TATGCCCCGAAGGACCACGTCGAACACA
1 TATGTCCCGAAGGACCACATAGAACACA
368770 TATGTCCCGAAGGACCACATAGAA
1 TATGTCCCGAAGGACCACATAGAA
368794 ACCTCGACTC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.15
Consensus pattern (28 bp):
TATGTCCCGAAGGACCACATAGAACACA
Found at i:372528 original size:2 final size:2
Alignment explanation
Indices: 372523--372548 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
372513 AAATCCATGA
372523 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
372549 CATGTAATAA
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:374538 original size:3 final size:3
Alignment explanation
Indices: 374530--374564 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
374520 TGAACACATG
*
374530 AGA AGA AGA A-A GGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
374565 GTTACAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 28 0.97
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:376721 original size:18 final size:18
Alignment explanation
Indices: 376700--376734 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
376690 AAGAAAAATA
376700 TTGTTTTTGATTTAATTG
1 TTGTTTTTGATTTAATTG
376718 TTGTTTTTGATTTAATT
1 TTGTTTTTGATTTAATT
376735 ACATTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (18 bp):
TTGTTTTTGATTTAATTG
Found at i:379023 original size:24 final size:24
Alignment explanation
Indices: 378996--379074 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
378986 ACTATGTTCG
*
378996 GTATCGATACTACTTTACATAGTA
1 GTATCGATACTACTTCACATAGTA
**
379020 GTATCGATACTCACTGGAC---G-A
1 GTATCGATACT-ACTTCACATAGTA
379041 -TATCGATACTA-TTGCACATAGTA
1 GTATCGATACTACTT-CACATAGTA
379064 GTATCGATACT
1 GTATCGATACT
379075 CCTTGGACAG
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 10 0.23
21 1 0.02
22 2 0.05
23 1 0.02
24 21 0.48
25 5 0.11
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (24 bp):
GTATCGATACTACTTCACATAGTA
Found at i:379051 original size:44 final size:44
Alignment explanation
Indices: 378996--379093 Score: 139
Period size: 44 Copynumber: 2.2 Consensus size: 44
378986 ACTATGTTCG
*
378996 GTATCGATACTACTT-TACATAGTAGTATCGATACTCAC-TGGAC-
1 GTATCGATACTA-TTGCACATAGTAGTATCGATACTC-CTTGGACA
379039 GATATCGATACTATTGCACATAGTAGTATCGATACTCCTTGGACA
1 G-TATCGATACTATTGCACATAGTAGTATCGATACTCCTTGGACA
379084 GTATCGATAC
1 GTATCGATAC
379094 CGTTGAGTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
43 4 0.08
44 45 0.90
45 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (44 bp):
GTATCGATACTATTGCACATAGTAGTATCGATACTCCTTGGACA
Found at i:379312 original size:21 final size:22
Alignment explanation
Indices: 379272--379318 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
379262 GCCATTGGTG
379272 ACAATAAGAGAAGCTATAAA-A
1 ACAATAAGAGAAGCTATAAACA
379293 ACAA-AAGAGAAAGCCT-TAAACA
1 ACAATAAGAG-AAG-CTATAAACA
379315 ACAA
1 ACAA
379319 GTTTGAGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.22
21 11 0.48
22 7 0.30
ACGTcount: A:0.62, C:0.15, G:0.13, T:0.11
Consensus pattern (22 bp):
ACAATAAGAGAAGCTATAAACA
Found at i:380088 original size:36 final size:36
Alignment explanation
Indices: 380042--380144 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
380032 ATTTATCCAT
380042 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
*
380078 TATCAACTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
* *
380114 TATCAGCTTTGGTATATTCGTGTATCAATGT
1 TATCAGCTTTGATACATTCGTGTATCAATGT
380145 CCAACATCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (36 bp):
TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
Found at i:380745 original size:12 final size:12
Alignment explanation
Indices: 380708--380762 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
380698 ATACCAGTAT
*
380708 ATACCCGACCCG
1 ATACCCGACCCA
* * *
380720 ATTCTCGGCCCA
1 ATACCCGACCCA
380732 ATACCCGACCCA
1 ATACCCGACCCA
380744 ATACCCGACCCA
1 ATACCCGACCCA
380756 ATACCCG
1 ATACCCG
380763 TTTAAATAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.27, C:0.47, G:0.13, T:0.13
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:381728 original size:76 final size:76
Alignment explanation
Indices: 381623--381763 Score: 201
Period size: 76 Copynumber: 1.9 Consensus size: 76
381613 CAATCACATA
* * * *
381623 TTTGGTAATGGAAGAAATAATTCTTAATTTTTATTTATTAAATATAATTTACAACATTTTTATAT
1 TTTGGTAATCGAAGAAATAATTCTTAATTTGTATTTATTAAATATAATTTAAAACACTTTTATAT
381688 TTTTTAAATTT
66 TTTTTAAATTT
* * * * *
381699 TTTGTTAATCGAAGAAATGATTTTTAATTTGTATTTATTAACTATAATTTAAAACGCTTTTATAT
1 TTTGGTAATCGAAGAAATAATTCTTAATTTGTATTTATTAAATATAATTTAAAACACTTTTATAT
381764 ATTTAATAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 56 1.00
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (76 bp):
TTTGGTAATCGAAGAAATAATTCTTAATTTGTATTTATTAAATATAATTTAAAACACTTTTATAT
TTTTTAAATTT
Found at i:381876 original size:95 final size:96
Alignment explanation
Indices: 381770--381954 Score: 284
Period size: 95 Copynumber: 1.9 Consensus size: 96
381760 ATATATTTAA
* *
381770 TAAATACATATTAACAAAAATAGTTAAAGTAAATAAAAATTTAATATAT-AAAATTTATTGAATA
1 TAAATACATATTAACAAAAATAGTTAAAGTAAATAAAAATTTAATATATGAAAATTTAATAAATA
*
381834 CATATGTGATAAATAT-TTTATTAAAAATGGT
66 CATAT-TAATAAATATATTTATTAAAAATGGT
* ** *
381865 TAAATACATATTAACAAATATTTTTAAAGTAAATAAAAATTTAATATATGAATATTTAATAAATA
1 TAAATACATATTAACAAAAATAGTTAAAGTAAATAAAAATTTAATATATGAAAATTTAATAAATA
381930 CATATTAATAAATATATTTATTAAA
66 CATATTAATAAATATATTTATTAAA
381955 TACAAATTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
95 55 0.68
96 26 0.32
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (96 bp):
TAAATACATATTAACAAAAATAGTTAAAGTAAATAAAAATTTAATATATGAAAATTTAATAAATA
CATATTAATAAATATATTTATTAAAAATGGT
Done.