Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008071.1 Hibiscus syriacus cultivar Beakdansim tig00110569_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: 1969971
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 3 of 8
Found at i:458124 original size:53 final size:52
Alignment explanation
Indices: 458061--458176 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
458051 GAAATGAAAA
*
458061 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
458113 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
458166 TCGCATTGCGA
1 TCGCATTGCGA
458177 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:458139 original size:19 final size:19
Alignment explanation
Indices: 458099--458186 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
458089 GATTCTCTCG
458099 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
458119 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
458138 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
458152 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
458171 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
458187 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:458296 original size:14 final size:14
Alignment explanation
Indices: 458277--458313 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
458267 CATCAATTAC
458277 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
458291 ACAAATCATCTTTT
1 ACAAATCAACTTTT
458305 ACAAATCAA
1 ACAAATCAA
458314 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:460279 original size:19 final size:19
Alignment explanation
Indices: 460237--460356 Score: 126
Period size: 19 Copynumber: 6.6 Consensus size: 19
460227 TAGTTTACTT
* *
460237 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
460257 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* *
460276 TCGCAACGAGAAA-CAAAA
1 TCGCAACGCGAAATGAAAA
460294 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
460313 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
460327 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
460346 TCGCAATGCGA
1 TCGCAACGCGA
460357 TTTTGGTTTC
Statistics
Matches: 83, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
14 8 0.10
16 5 0.06
17 5 0.06
18 15 0.18
19 38 0.46
20 12 0.14
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:460301 original size:37 final size:33
Alignment explanation
Indices: 460253--460351 Score: 144
Period size: 33 Copynumber: 2.9 Consensus size: 33
460243 CACGAAACTT
*
460253 AAAATCGCAACGCGAAATGAGAATCGCAACGAGAAAC
1 AAAATCGCAACGCGAAATGAAAATCGCAAC--G--AC
460290 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
*
460323 AGAATCGCAACGCGAAATGAAAATCGCAA
1 AAAATCGCAACGCGAAATGAAAATCGCAA
460352 TGCGATTTTG
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.50
35 1 0.02
37 29 0.48
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:460387 original size:14 final size:14
Alignment explanation
Indices: 460368--460426 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
460358 TTTGGTTTCG
460368 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
460382 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
460399 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
460415 CGTTGCGATTTT
1 CGTTGCGATTTT
460427 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:460394 original size:33 final size:33
Alignment explanation
Indices: 460352--460475 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
460342 AAAATCGCAA
*
460352 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
460385 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
460418 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
460451 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
460476 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:460406 original size:19 final size:18
Alignment explanation
Indices: 460352--460443 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
460342 AAAATCGCAA
460352 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
460371 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
460385 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
460404 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
460418 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
460437 TGCGATT
1 TGCGATT
460444 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:460453 original size:14 final size:14
Alignment explanation
Indices: 460401--460457 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
460391 TTTGGTTTCG
*
460401 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
460415 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
460434 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
460448 CGTTGCGATT
1 CGTTGCGATT
460458 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:460732 original size:93 final size:93
Alignment explanation
Indices: 460573--461074 Score: 977
Period size: 93 Copynumber: 5.4 Consensus size: 93
460563 TCAGGGTATT
460573 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
460638 TACTATTTCACAGTATTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
460666 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
460731 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
460759 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
460824 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
460852 AGTTTAGCAGAATTTGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
460917 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
460945 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
461010 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
461038 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
461075 AAGCAATCTA
Statistics
Matches: 405, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 405 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:462802 original size:41 final size:33
Alignment explanation
Indices: 462757--462879 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
462747 TCTTTTGGTT
462757 GAAATGAAAATCGCAACGAGAGAATGACTGTCGTAACGAGA
1 GAAATGAAAATCGCAACGAGAGAAT--C-G-C--AAC--GA
*
462798 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGA
*
462831 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGA
462864 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
462880 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 3 0.04
37 1 0.01
38 1 0.01
39 1 0.01
41 25 0.31
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGA
Found at i:462815 original size:21 final size:21
Alignment explanation
Indices: 462757--462821 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
462747 TCTTTTGGTT
462757 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
*** *
462778 G-AATGACTGTCGTAACGAGA
1 GAAATGAAAATCGCAACGAGA
462798 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
462819 GAA
1 GAA
462822 TCGCAACGCG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.48, C:0.14, G:0.26, T:0.12
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:462825 original size:14 final size:14
Alignment explanation
Indices: 462806--462862 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
462796 GAGAAATGAA
462806 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
462820 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
462839 AATCGCAACGAGAG
1 AATCGCAACGAGAG
462853 AATCGCAACG
1 AATCGCAACG
462863 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:462840 original size:33 final size:33
Alignment explanation
Indices: 462798--462879 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
462788 CGTAACGAGA
462798 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
462831 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
462864 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
462880 TGCGATTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.48, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:462915 original size:14 final size:14
Alignment explanation
Indices: 462896--462952 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
462886 TTTGGTTTCG
462896 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
462910 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
462929 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
462943 CGTTGCGATT
1 CGTTGCGATT
462953 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:462928 original size:33 final size:33
Alignment explanation
Indices: 462880--462959 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
462870 AAAATCGCAA
**
462880 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
462913 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
462946 TGCGATTTTCATTT
1 TGCGATTTTCATTT
462960 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:462965 original size:21 final size:21
Alignment explanation
Indices: 462940--463013 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
462930 GTTGCGATTC
462940 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
462961 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
462982 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
463003 TCTCGTTGCGA
1 TCTCGTTGCGA
463014 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:463135 original size:33 final size:33
Alignment explanation
Indices: 463093--463163 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
463083 AATACTAACT
463093 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
463126 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
463159 TGAAA
1 TGAAA
463164 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:463568 original size:20 final size:20
Alignment explanation
Indices: 463543--463674 Score: 185
Period size: 20 Copynumber: 6.6 Consensus size: 20
463533 CTTTAAAAAT
463543 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
463563 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
463583 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
463603 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
463623 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
463643 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
463663 CGCGTTGCGATT
1 CGCGTTGCGATT
463675 CTGGAAAATC
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
20 101 0.99
21 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:463878 original size:1 final size:1
Alignment explanation
Indices: 463874--463902 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
463864 ACTGAGGCGA
463874 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
463903 GCTTTCTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:464202 original size:20 final size:21
Alignment explanation
Indices: 464169--464215 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
464159 CAAATTGGGG
464169 TAAATTATATA-TTTAATACT
1 TAAATTATATATTTTAATACT
464189 TAAATTATCA-ATTTTAATA-T
1 TAAATTAT-ATATTTTAATACT
464209 CTAAATT
1 -TAAATT
464216 TTTAATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAATTATATATTTTAATACT
Found at i:464905 original size:3 final size:3
Alignment explanation
Indices: 464897--464922 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
464887 ACTGTTTGAT
464897 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
464923 TTAGGAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:472346 original size:26 final size:25
Alignment explanation
Indices: 472316--472372 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
472306 AAGATTTTTG
*
472316 AAAATTTTGAATTTTTTTTAAAAGAA
1 AAAATTTTGAA-GTTTTTTAAAAGAA
* * *
472342 TAAATTTTTAAGTTTTTTAAAATAA
1 AAAATTTTGAAGTTTTTTAAAAGAA
472367 AAAATT
1 AAAATT
472373 CAAAATTACC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (25 bp):
AAAATTTTGAAGTTTTTTAAAAGAA
Found at i:482487 original size:20 final size:21
Alignment explanation
Indices: 482450--482489 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
482440 GTAATTTTTA
*
482450 AATTTTTAAATATGATATAAAC
1 AATTTATAAATA-GATATAAAC
482472 AATTTATAAATA-ATATAA
1 AATTTATAAATAGATATAA
482490 TTAAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (21 bp):
AATTTATAAATAGATATAAAC
Found at i:489741 original size:14 final size:14
Alignment explanation
Indices: 489722--489750 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
489712 ATTAATCGTA
489722 AAATAATTTTTTTC
1 AAATAATTTTTTTC
489736 AAATAATTTTTTTC
1 AAATAATTTTTTTC
489750 A
1 A
489751 CTACAATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AAATAATTTTTTTC
Found at i:498624 original size:105 final size:105
Alignment explanation
Indices: 498481--499199 Score: 1280
Period size: 105 Copynumber: 6.8 Consensus size: 105
498471 GAAGTTGACG
** *** *
498481 GTTGACAGTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTTGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
*
498546 GTTGTGAAGCTGAAATTGGCTCTGAAATTGAGAAATGTTT
66 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
498586 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
* *
498651 GTTGTGAAGTTGAAATTGGCTCTGACATTGAGAAATATTT
66 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
498691 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
498756 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
66 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
498796 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
498861 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
66 GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
*
498901 GGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
*
498966 GCTGTGAAGTTGAAATTGGCTCT-AAATTTGAGAAATGTTT
66 GTTGTGAAGTTGAAATTGGCTCTGAAA-TTGAGAAATGTTT
*
499006 GGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
*
499071 GCTGTGAAGTTGAAATTGGCTCT-AAATTTGAGAAATGTTT
66 GTTGTGAAGTTGAAATTGGCTCTGAAA-TTGAGAAATGTTT
*
499111 GGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
1 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
499176 GTTGTGAAGTTGAAATTGGCTCTG
66 GTTGTGAAGTTGAAATTGGCTCTG
499200 GGTAAAACCT
Statistics
Matches: 598, Mismatches: 14, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
104 3 0.01
105 595 0.99
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
GTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
Found at i:500018 original size:57 final size:57
Alignment explanation
Indices: 499948--500102 Score: 187
Period size: 57 Copynumber: 2.8 Consensus size: 57
499938 TTCTTTTTCC
* * * *
499948 TTTTTTCTGTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACGTTTTTTT
1 TTTTTTTTGTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGTTTTTTT
* * *
500005 TTTTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAAGCG-----TT
1 TTTTTTTTGTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGTTTTTTT
* *
500057 TTTTTTTT-TTTTCAACTTAGGACACCCTCTCGGGTTTTCATCCTAA
1 TTTTTTTTGTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
500103 GCGAAGTATT
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
51 37 0.41
52 10 0.11
57 43 0.48
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.49
Consensus pattern (57 bp):
TTTTTTTTGTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACGTTTTTTT
Found at i:500085 original size:51 final size:51
Alignment explanation
Indices: 500004--500105 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
499994 AACGTTTTTT
*
500004 TTTTTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAAGCG
1 TTTTTTTTTTTTTTCAACTTAGGACACCCTCTCGGGTTTTCATCCTAAGCG
500055 TTTTTTTTTTTTTTCAACTTAGGACACCCTCTCGGGTTTTCATCCTAAGCG
1 TTTTTTTTTTTTTTCAACTTAGGACACCCTCTCGGGTTTTCATCCTAAGCG
500106 AAGTATTTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.47
Consensus pattern (51 bp):
TTTTTTTTTTTTTTCAACTTAGGACACCCTCTCGGGTTTTCATCCTAAGCG
Found at i:506661 original size:21 final size:22
Alignment explanation
Indices: 506636--506684 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
506626 TCTTTATTTG
*
506636 ATCTTCTAATATTTTTATCTTT
1 ATCTTCTAATATTTTTAGCTTT
* *
506658 -TCTTC-CATCTTTTTAGCTTT
1 ATCTTCTAATATTTTTAGCTTT
506678 ATCTTCT
1 ATCTTCT
506685 TCATCAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (22 bp):
ATCTTCTAATATTTTTAGCTTT
Found at i:506809 original size:39 final size:39
Alignment explanation
Indices: 506761--506838 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
506751 TTCGCAGCAG
* *
506761 GTGCAACTTTCGCTTTGGTAAC-GAGTGAGTCCCCGGGTA
1 GTGCAACTTTCCCTTTAGTAACAGA-TGAGTCCCCGGGTA
* * *
506800 GTGCTACTTTCCCTTTAGTAGCAGATGCGTCCCCGGGTA
1 GTGCAACTTTCCCTTTAGTAACAGATGAGTCCCCGGGTA
506839 ATATTCCGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (39 bp):
GTGCAACTTTCCCTTTAGTAACAGATGAGTCCCCGGGTA
Found at i:511143 original size:2 final size:2
Alignment explanation
Indices: 511138--511174 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
511128 TATACAAAAA
511138 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
511175 AAGGAATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:516480 original size:22 final size:22
Alignment explanation
Indices: 516426--516497 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
516416 AGTCGAGGGT
*
516426 TTCATAGGTCCTTCGGGAC-CA
1 TTCATAGGTCCTTCGGGACAAA
*
516447 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
516469 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
516491 TTTCATA
1 -TTCATA
516498 TGCCACTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 18 0.41
22 21 0.48
23 5 0.11
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:517334 original size:25 final size:23
Alignment explanation
Indices: 517293--517341 Score: 55
Period size: 25 Copynumber: 2.0 Consensus size: 23
517283 TTGGTATGGT
*
517293 AATGAGTATGTTGTTTTGCTAATAG
1 AATGAGTATGTTATTTT--TAATAG
517318 AATGA-TATGTTTATTTTTAATAG
1 AATGAGTATG-TTATTTTTAATAG
517341 A
1 A
517342 TGTCCGGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 7 0.32
24 4 0.18
25 11 0.50
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (23 bp):
AATGAGTATGTTATTTTTAATAG
Found at i:523370 original size:22 final size:22
Alignment explanation
Indices: 523316--523387 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
523306 AGTCGAGGGT
*
523316 TTCATAGGTCCTTCGGGAC-CA
1 TTCATAGGTCCTTCGGGACAAA
*
523337 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
523359 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
523381 TTTCATA
1 -TTCATA
523388 TGCCACTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 18 0.41
22 21 0.48
23 5 0.11
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:527374 original size:60 final size:59
Alignment explanation
Indices: 527261--527415 Score: 145
Period size: 60 Copynumber: 2.6 Consensus size: 59
527251 GATAAATTTG
** **
527261 AAATATTCAAAAAGTTTGGGGACCAATTTAGAATGAAGATCAAATTTGGGGATGAAAATA
1 AAATATTC-AAAAGTTTAAGGACCAATTTAGAATGAAGATCAAATTTAAGGATGAAAATA
* * * * *
527321 AAATATTCAAAAGTTTAAGGACTAATTTAGAATGGTAG-TCATAATTTAAGGATGAGATTG
1 AAATATTCAAAAGTTTAAGGACCAATTTAGAAT-GAAGATCA-AATTTAAGGATGAAAATA
* *
527381 AAATGATT-AAAAGTTT-AGATACCAATTTAAAATGA
1 AAAT-ATTCAAAAGTTTAAG-GACCAATTTAGAATGA
527416 GGGTCATAGA
Statistics
Matches: 78, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
59 28 0.36
60 47 0.60
61 3 0.04
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.30
Consensus pattern (59 bp):
AAATATTCAAAAGTTTAAGGACCAATTTAGAATGAAGATCAAATTTAAGGATGAAAATA
Found at i:530772 original size:64 final size:64
Alignment explanation
Indices: 530659--530778 Score: 143
Period size: 64 Copynumber: 1.9 Consensus size: 64
530649 ATGCACAGGA
* *
530659 AGTGCATCGATACACCCCTTAAAAATAGAAACATTGAATGCCATGAGTGTACCGATGCACAATT
1 AGTGCATCGATACACCCCTTAAAAATAGAAACATCGAATGCAATGAGTGTACCGATGCACAATT
* * * * * * *
530723 AGTGCATCGATGCACCCCCTT-GAAATTGAAATATCGAATGTAATTAGTGTATCGAT
1 AGTGCATCGATACA-CCCCTTAAAAATAGAAACATCGAATGCAATGAGTGTACCGAT
530779 ACACTATAGA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
64 40 0.87
65 6 0.13
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (64 bp):
AGTGCATCGATACACCCCTTAAAAATAGAAACATCGAATGCAATGAGTGTACCGATGCACAATT
Found at i:531832 original size:62 final size:63
Alignment explanation
Indices: 531713--531836 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 63
531703 GTCGAGGGTT
* * *
531713 TACCTATGTTCTACGGAACATATGGACAAAATTACCTATGTCTTTCGGGACATATGGACAGTA
1 TACCTATATTCTAAGGAACATATGGACAAAATTACCTAGGTCTTTCGGGACATATGGACAGTA
* ** *
531776 TACCTATATTTTAAGGAACATATGGAC-AGTTTACCTAGGT-TCTTCGGGACCTATGGACAGT
1 TACCTATATTCTAAGGAACATATGGACAAAATTACCTAGGTCT-TTCGGGACATATGGACAGT
531837 TGCCGAGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 1 0.02
62 28 0.53
63 24 0.45
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (63 bp):
TACCTATATTCTAAGGAACATATGGACAAAATTACCTAGGTCTTTCGGGACATATGGACAGTA
Found at i:531837 original size:31 final size:31
Alignment explanation
Indices: 531710--531837 Score: 125
Period size: 31 Copynumber: 4.1 Consensus size: 31
531700 AGAGTCGAGG
*
531710 GTTTACCTATGTTCTACGGAACATATGGACAA
1 GTTTACCTATGTTCTTCGGAACATATGGAC-A
** *
531742 AATTACCTATG-TCTTTCGGGACATATGGACA
1 GTTTACCTATGTTC-TTCGGAACATATGGACA
* * *
531773 GTATACCTATATT-TTAAGGAACATATGGACA
1 GTTTACCTATGTTCTT-CGGAACATATGGACA
* * *
531804 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTTCGGAACATATGGACA
531835 GTT
1 GTT
531838 GCCGAGGTTC
Statistics
Matches: 76, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
30 2 0.03
31 48 0.63
32 26 0.34
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACA
Found at i:532062 original size:35 final size:36
Alignment explanation
Indices: 531985--532077 Score: 95
Period size: 35 Copynumber: 2.6 Consensus size: 36
531975 CATTGAATAC
* *
531985 AATGTATGTGATAT-ATATATGTGTTTTGTGATATG
1 AATGTATATGATATGATATATGTGTTTAGTGATATG
532020 AAT-TATATGATATGATATATGTGTGTTAGTGAT-T-
1 AATGTATATGATATGATATATGTGT-TTAGTGATATG
* *
532054 ATTGTATATGTTATAAGATATATG
1 AATGTATATG--ATATGATATATG
532078 ATATGTACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
34 11 0.22
35 20 0.41
36 7 0.14
37 11 0.22
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.47
Consensus pattern (36 bp):
AATGTATATGATATGATATATGTGTTTAGTGATATG
Found at i:549993 original size:6 final size:6
Alignment explanation
Indices: 549984--550020 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
549974 CATAGACCAC
549984 GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA G
1 GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA GGAAGA G
550021 TTGTTAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (6 bp):
GGAAGA
Found at i:550155 original size:5 final size:6
Alignment explanation
Indices: 550130--550171 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
550120 TCATCCTAGT
* *
550130 AAATAA AAATTA AATTAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
550172 CAAAACCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAATAA
Found at i:550206 original size:6 final size:6
Alignment explanation
Indices: 550172--550205 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
550162 ATAAAAATAA
550172 CAAAAC CAAAAC CAAAAC CAAAAC CAAAA- CAAAA
1 CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAAA
550206 ATAATATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.71, C:0.29, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAC
Found at i:554353 original size:15 final size:15
Alignment explanation
Indices: 554333--554366 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
554323 GCCAATTAAC
554333 TAGCTGATTTAGACT
1 TAGCTGATTTAGACT
554348 TAGCTGATTTAGACT
1 TAGCTGATTTAGACT
554363 TAGC
1 TAGC
554367 CCATAGCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (15 bp):
TAGCTGATTTAGACT
Found at i:557238 original size:16 final size:16
Alignment explanation
Indices: 557217--557249 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
557207 CTCCAAAATA
557217 AAACACATACATAATT
1 AAACACATACATAATT
557233 AAACACATACATAATT
1 AAACACATACATAATT
557249 A
1 A
557250 TAAAAGTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (16 bp):
AAACACATACATAATT
Found at i:557320 original size:9 final size:8
Alignment explanation
Indices: 557306--557411 Score: 67
Period size: 9 Copynumber: 12.9 Consensus size: 8
557296 GGTTTGTATT
557306 ATATAATTA
1 ATATAA-TA
*
557315 ATATAAAA
1 ATATAATA
557323 ATATAA-A
1 ATATAATA
*
557330 ATATTAT-
1 ATATAATA
557337 ATATAATTA
1 ATATAA-TA
557346 ATATAA-A
1 ATATAATA
*
557353 ATATATAAA
1 ATATA-ATA
*
557362 ATATTATA
1 ATATAATA
557370 TATATAATTA
1 -ATATAA-TA
557380 ATATAA-A
1 ATATAATA
*
557387 ATATATAAA
1 ATATA-ATA
*
557396 ATATTATA
1 ATATAATA
557404 TATATAAT
1 -ATATAAT
557412 TGGGGCGGGG
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
7 23 0.29
8 14 0.18
9 39 0.50
10 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAATA
Found at i:557332 original size:7 final size:7
Alignment explanation
Indices: 557314--557399 Score: 50
Period size: 7 Copynumber: 11.7 Consensus size: 7
557304 TTATATAATT
557314 AATATAAA
1 AATAT-AA
557322 AATATAA
1 AATATAA
*
557329 AATATTA
1 AATATAA
*
557336 TATATAA
1 AATATAA
557343 TTAATATAAA
1 --AATAT-AA
557353 ATATATAA
1 A-ATATAA
*
557361 AATATTA
1 AATATAA
* *
557368 TATATAT
1 AATATAA
557375 AAT-TAA
1 AATATAA
*
557381 TATA-AA
1 AATATAA
557387 ATATATAA
1 A-ATATAA
557395 AATAT
1 AATAT
557400 TATATATATA
Statistics
Matches: 59, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
6 6 0.10
7 31 0.53
8 12 0.20
9 8 0.14
10 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATATAA
Found at i:557377 original size:34 final size:34
Alignment explanation
Indices: 557305--557412 Score: 195
Period size: 34 Copynumber: 3.3 Consensus size: 34
557295 GGGTTTGTAT
557305 TATATAATTAATATAAAA-ATATAAAATA-T-TA
1 TATATAATTAATATAAAATATATAAAATATTATA
557336 TATATAATTAATATAAAATATATAAAATATTATA
1 TATATAATTAATATAAAATATATAAAATATTATA
557370 TATATAATTAATATAAAATATATAAAATATTATA
1 TATATAATTAATATAAAATATATAAAATATTATA
557404 TATATAATT
1 TATATAATT
557413 GGGGCGGGGA
Statistics
Matches: 74, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
31 18 0.24
32 10 0.14
33 1 0.01
34 45 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
TATATAATTAATATAAAATATATAAAATATTATA
Found at i:560976 original size:6 final size:6
Alignment explanation
Indices: 560965--561008 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
560955 GCACGAATAT
*
560965 GGATAC GGATAC GGATAC GGATAC GGATAC GGATAT GGATAC GG
1 GGATAC GGATAC GGATAC GGATAC GGATAC GGATAC GGATAC GG
561009 GGACGGGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.32, C:0.14, G:0.36, T:0.18
Consensus pattern (6 bp):
GGATAC
Found at i:561014 original size:18 final size:18
Alignment explanation
Indices: 560961--561008 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
560951 TGTTGCACGA
560961 ATATGGATACGGATACGG
1 ATATGGATACGGATACGG
*
560979 ATACGGATACGGATACGG
1 ATATGGATACGGATACGG
560997 ATATGGATACGG
1 ATATGGATACGG
561009 GGACGGGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.21
Consensus pattern (18 bp):
ATATGGATACGGATACGG
Found at i:562081 original size:3 final size:3
Alignment explanation
Indices: 562073--562097 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
562063 GTTTTACACT
562073 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
562098 AACCCTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:562468 original size:16 final size:15
Alignment explanation
Indices: 562447--562477 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
562437 ATATTTAGGG
562447 TTTTAGGATTTGGGAT
1 TTTTA-GATTTGGGAT
562463 TTTTAGATTTGGGAT
1 TTTTAGATTTGGGAT
562478 AAAAGAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (15 bp):
TTTTAGATTTGGGAT
Found at i:562641 original size:2 final size:2
Alignment explanation
Indices: 562634--562673 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
562624 ATATCTTATG
562634 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
562674 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:563866 original size:3 final size:3
Alignment explanation
Indices: 563858--563894 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
563848 TTGGGGAAAA
563858 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
563895 TTCTCTCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:564502 original size:18 final size:18
Alignment explanation
Indices: 564479--564515 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
564469 TAAAGTTAAT
564479 TTGTTTAGGGGTTATTTG
1 TTGTTTAGGGGTTATTTG
564497 TTGTTTAGGGGTTATTTG
1 TTGTTTAGGGGTTATTTG
564515 T
1 T
564516 GTCTTTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.32, T:0.57
Consensus pattern (18 bp):
TTGTTTAGGGGTTATTTG
Found at i:564710 original size:21 final size:21
Alignment explanation
Indices: 564684--564819 Score: 143
Period size: 21 Copynumber: 6.5 Consensus size: 21
564674 GTTTCCAGAT
* * *
564684 TCGCAACGCGAACTTCGAATA
1 TCGCAATGCGAACTTGGACTA
*
564705 TCGCAATGCGAACTTGGGCTA
1 TCGCAATGCGAACTTGGACTA
564726 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
564747 TCGCAATGC-AAATATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* **
564767 TCGCAATGCGATA-GTCAACTA
1 TCGCAATGCGA-ACTTGGACTA
564788 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
564809 TCGCAATGCGA
1 TCGCAATGCGA
564820 TTTACATATT
Statistics
Matches: 95, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
20 16 0.17
21 78 0.82
22 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:564833 original size:41 final size:41
Alignment explanation
Indices: 564705--564839 Score: 102
Period size: 41 Copynumber: 3.3 Consensus size: 41
564695 ACTTCGAATA
* *
564705 TCGCAATGCGAACTTGGGCTATCGCAATGCGAACTTGGAC-TA-
1 TCGCAATGCGAACTTGGACTATCGCAATGCG-A-TT-TACATAT
* * * *
564747 TCGCAATGC-AAATATGTA-AATCGCAATGCGATAGT-CA-ACT
1 TCGCAATGCGAACT-TGGACTATCGCAATGCGAT-TTACATA-T
564787 ATCGCAATGCGAACTTGGACTATCGCAATGCGATTTACATAT
1 -TCGCAATGCGAACTTGGACTATCGCAATGCGATTTACATAT
*
564829 TCGCATTGCGA
1 TCGCAATGCGA
564840 TTTACATATT
Statistics
Matches: 72, Mismatches: 11, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 1 0.01
41 37 0.51
42 30 0.42
43 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (41 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGATTTACATAT
Found at i:564838 original size:20 final size:20
Alignment explanation
Indices: 564809--564860 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
564799 ACTTGGACTA
*
564809 TCGCAATGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
564829 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
564849 TCGCATTGCGAT
1 TCGCATTGCGAT
564861 AGTCGAAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:564874 original size:21 final size:21
Alignment explanation
Indices: 564848--564942 Score: 106
Period size: 21 Copynumber: 4.6 Consensus size: 21
564838 GATTTACATA
564848 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
564869 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAG
** * *
564889 TATCGCATTGCGATTTTCCAAA
1 T-TCGCATTGCGATAGTCGAAG
564911 TTCG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
*
564930 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
564943 TTATTCCAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
19 15 0.25
20 2 0.03
21 42 0.69
22 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:564880 original size:61 final size:61
Alignment explanation
Indices: 564809--564945 Score: 165
Period size: 61 Copynumber: 2.2 Consensus size: 61
564799 ACTTGGACTA
* *
564809 TCGCAATGCGATTTAC-A-TATTCGCATTGCGA-TTTACATATTCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATTTACGACTA-TCGCATTGCGATTTTACAAATTCG--TTGCGATAGTCGAAGT
* *
564870 TCGCATTGCGATAGT-CGACTATCGCATTGCGATTTTCCAAATTCGTTGCGATAGTCGAAGT
1 TCGCATTGCGAT-TTACGACTATCGCATTGCGATTTTACAAATTCGTTGCGATAGTCGAAGT
*
564931 TCGCGTTGCGATTTA
1 TCGCATTGCGATTTA
564946 TTCCAAATTC
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
60 1 0.02
61 39 0.60
62 13 0.20
63 12 0.18
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (61 bp):
TCGCATTGCGATTTACGACTATCGCATTGCGATTTTACAAATTCGTTGCGATAGTCGAAGT
Found at i:564926 original size:40 final size:42
Alignment explanation
Indices: 564875--564967 Score: 138
Period size: 40 Copynumber: 2.3 Consensus size: 42
564865 GAAGTTCGCA
564875 TTGCGATAGTCG-ACTATCGCATTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCGAACT-TCGCATTGCGATTTATTCCAAATTCG
* *
564915 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAACTTCGCATTGCGATTTATTCCAAATTCG
564957 TTGCGATAGTC
1 TTGCGATAGTC
564968 CAAAATCGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
40 22 0.46
41 4 0.08
42 22 0.46
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
TTGCGATAGTCGAACTTCGCATTGCGATTTATTCCAAATTCG
Found at i:564958 original size:21 final size:20
Alignment explanation
Indices: 564896--564963 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
564886 GACTATCGCA
564896 TTGCGATT-TTCCAAATTCG
1 TTGCGATTATTCCAAATTCG
* * *
564915 TTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATTATTCCAAATT--CG
564936 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAATTCG
564957 TTGCGAT
1 TTGCGAT
564964 AGTCCAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 1 0.03
19 12 0.32
20 1 0.03
21 16 0.42
23 8 0.21
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTATTCCAAATTCG
Found at i:564970 original size:61 final size:60
Alignment explanation
Indices: 564854--564971 Score: 132
Period size: 61 Copynumber: 1.9 Consensus size: 60
564844 CATATTCGCA
* * **
564854 TTGCGATAGTCGAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCATTGCGATAGTCAAATATCG-ATTGCGATAGTCCAAATTCG
* *
564915 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAAT-TCG-TTGCGATAGTCCAAA
1 TTGCGATAGTCGAAGTTCGCATTGCGA--TAGT-CAAATATCGATTGCGATAGTCCAAA
564972 ATCGCAACGA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
61 39 0.81
63 6 0.12
64 3 0.06
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (60 bp):
TTGCGATAGTCGAAGTTCGCATTGCGATAGTCAAATATCGATTGCGATAGTCCAAATTCG
Found at i:564971 original size:19 final size:19
Alignment explanation
Indices: 564905--564971 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
564895 ATTGCGATTT
564905 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * *
564924 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
564947 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
564966 TCCAAA
1 TCCAAA
564972 ATCGCAACGA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 14 0.37
21 16 0.42
23 8 0.21
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:565592 original size:5 final size:5
Alignment explanation
Indices: 565583--565641 Score: 55
Period size: 6 Copynumber: 10.6 Consensus size: 5
565573 CTGTCTCGTC
*
565583 TCGGG ACGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG-GG TCG-GG
565633 TCGTGG TCG
1 TCG-GG TCG
565642 TGGTAATACG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 16 0.31
6 35 0.69
ACGTcount: A:0.02, C:0.19, G:0.53, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:565612 original size:6 final size:6
Alignment explanation
Indices: 565591--565645 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
565581 TCTCGGGACG
565591 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
565637 GGTCGT GGT
1 GGTCGT GGT
565646 AATACGTGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.20
6 39 0.80
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:565764 original size:21 final size:21
Alignment explanation
Indices: 565738--565863 Score: 130
Period size: 21 Copynumber: 5.8 Consensus size: 21
565728 ATTTTGGACT
*
565738 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
565759 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
* *
565782 ATCACAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
565803 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
565824 ATTGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
565845 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
565864 CTATCGCAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
19 10 0.12
21 38 0.44
23 38 0.44
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:565845 original size:42 final size:42
Alignment explanation
Indices: 565731--565872 Score: 221
Period size: 42 Copynumber: 3.3 Consensus size: 42
565721 CGTTGCGATT
565731 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
565773 TTGGAATAAATCACAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
565817 TTCGACTATTGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
565859 TTGGACTATCGCAA
1 TTGGACTATCGCAA
565873 TGCGAATATG
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
42 50 0.56
44 39 0.44
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:565869 original size:21 final size:21
Alignment explanation
Indices: 565738--565878 Score: 112
Period size: 21 Copynumber: 6.6 Consensus size: 21
565728 ATTTTGGACT
*
565738 ATCGCAA-CGAATTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
565759 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAA-GCGAACTTGGAAT-A
* *
565782 ATCACAA-CGAATTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
* *
565803 ATCGCAACGCGAACTTCGACT-
1 ATCGCAA-GCGAACTTGGAATA
*
565824 ATTGCAA-CGAACTTGGAATAA
1 ATCGCAAGCGAACTTGGAAT-A
*
565845 ATCGCAACGCGAACTTGGACT-
1 ATCGCAA-GCGAACTTGGAATA
565866 ATCGCAATGCGAA
1 ATCGCAA-GCGAA
565879 TATGTAAATC
Statistics
Matches: 99, Mismatches: 13, Indels: 16
0.77 0.10 0.12
Matches are distributed among these distances:
19 10 0.10
21 50 0.51
23 39 0.39
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAAGCGAACTTGGAATA
Found at i:569109 original size:4 final size:4
Alignment explanation
Indices: 569100--569125 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
569090 AATCAATTCT
569100 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
569126 ACTACCCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:569640 original size:3 final size:3
Alignment explanation
Indices: 569632--569661 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
569622 TTCGAAACAA
*
569632 CTG CTG CTG CTG CTG CTG CTG CTA CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG
569662 GAGTTACAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.33, G:0.30, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:576572 original size:26 final size:28
Alignment explanation
Indices: 576526--576581 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
576516 CCTTATTATT
576526 ATATTTTAACTTGTAATAAT-ATTTTTA
1 ATATTTTAACTTGTAATAATAATTTTTA
576553 ATATTTTAA-TTG-AATGAATAATTTTTA
1 ATATTTTAACTTGTAAT-AATAATTTTTA
576580 AT
1 AT
576582 TAAAAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
25 3 0.11
26 6 0.22
27 18 0.67
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (28 bp):
ATATTTTAACTTGTAATAATAATTTTTA
Found at i:580942 original size:20 final size:20
Alignment explanation
Indices: 580917--580970 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
580907 AGTTCGGGTT
580917 TTCCATATGGAACCCATTTG
1 TTCCATATGGAACCCATTTG
580937 TTCCATATGGAACCCATTTG
1 TTCCATATGGAACCCATTTG
*
580957 TTCCATATTGAACC
1 TTCCATATGGAACC
580971 GAATATGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (20 bp):
TTCCATATGGAACCCATTTG
Found at i:581046 original size:5 final size:5
Alignment explanation
Indices: 581036--581062 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
581026 AAAACCGAAA
581036 AACCG AACCG AACCG AACCG AACCG AA
1 AACCG AACCG AACCG AACCG AACCG AA
581063 AAATTCGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.37, G:0.19, T:0.00
Consensus pattern (5 bp):
AACCG
Found at i:581205 original size:5 final size:5
Alignment explanation
Indices: 581195--581221 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
581185 TTTGGTAAAA
581195 AACCG AACCG AACCG AACCG AACCG AA
1 AACCG AACCG AACCG AACCG AACCG AA
581222 TACACCCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.37, G:0.19, T:0.00
Consensus pattern (5 bp):
AACCG
Found at i:581595 original size:16 final size:16
Alignment explanation
Indices: 581574--581611 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
581564 CCTAGTAAGA
*
581574 TTTCTTCTTCTCTCCC
1 TTTCTTCTCCTCTCCC
581590 TTTCTTCTCCTCTCCC
1 TTTCTTCTCCTCTCCC
581606 TTTCTT
1 TTTCTT
581612 TACAATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTCTTCTCCTCTCCC
Found at i:584886 original size:17 final size:16
Alignment explanation
Indices: 584864--584902 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
584854 TATATTATCA
584864 ATAAATAAAATTTTTAT
1 ATAAAT-AAATTTTTAT
584881 ATAAAT-AATTTTTAT
1 ATAAATAAATTTTTAT
*
584896 TTAAATA
1 ATAAATA
584903 TTTAGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 14 0.70
17 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAATAAATTTTTAT
Found at i:585094 original size:20 final size:20
Alignment explanation
Indices: 585058--585095 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
585048 ATCATATGCC
**
585058 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
585078 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
585096 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:586184 original size:152 final size:147
Alignment explanation
Indices: 585897--586191 Score: 473
Period size: 152 Copynumber: 2.0 Consensus size: 147
585887 AACTATTTAA
* * *
585897 ATTAGAATCAAATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAGAAACTCGAAA
1 ATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
*
585962 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAATTTTTGAGTCAACTAT
66 ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTAAAATCGAAAATTTTTGAGTCAACTAT
586027 TTTATAAACTGAACTGG
131 TTTATAAACTGAACTGG
*
586044 ATTATAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
1 ATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTC--AA
***
586109 ATTCAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTAAAATCGATTTTTTTTGAGTCA
64 A---AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTAAAATCGAAAATTTTTGAGTCA
586174 ACTATTTTATAAACTGAA
126 ACTATTTTATAAACTGAA
586192 TTGAGTATTT
Statistics
Matches: 135, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
147 58 0.43
149 2 0.01
152 75 0.56
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.39
Consensus pattern (147 bp):
ATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAAA
ATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTAAAATCGAAAATTTTTGAGTCAACTAT
TTTATAAACTGAACTGG
Found at i:586388 original size:35 final size:35
Alignment explanation
Indices: 586349--586439 Score: 94
Period size: 35 Copynumber: 2.6 Consensus size: 35
586339 TGGATTATGG
* *
586349 ATTTGGGGTTGGGCATGTAAATGAAGTATTTTGGA
1 ATTTGGGGTTGAGAATGTAAATGAAGTATTTTGGA
* * * *
586384 ATTTGAGGTTTAGAATGTAATTGAGGTATTTTGGA
1 ATTTGGGGTTGAGAATGTAAATGAAGTATTTTGGA
* * *
586419 TTTTGGAGTTTAGAATG-AAAT
1 ATTTGGGGTTGAGAATGTAAAT
586440 TGATGATTGC
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
34 3 0.07
35 43 0.93
ACGTcount: A:0.29, C:0.01, G:0.30, T:0.41
Consensus pattern (35 bp):
ATTTGGGGTTGAGAATGTAAATGAAGTATTTTGGA
Found at i:586441 original size:35 final size:35
Alignment explanation
Indices: 586374--586442 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
586364 TGTAAATGAA
*
586374 GTATTTTGGAATTTGAGGTTTAGAATGTAATTGAG
1 GTATTTTGGAATTTGAGGTTTAGAATGAAATTGAG
*
586409 GTATTTTGGATTTTG-GAGTTTAGAATGAAATTGA
1 GTATTTTGGAATTTGAG-GTTTAGAATGAAATTGA
586443 TGATTGCGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 1 0.03
35 30 0.97
ACGTcount: A:0.29, C:0.00, G:0.28, T:0.43
Consensus pattern (35 bp):
GTATTTTGGAATTTGAGGTTTAGAATGAAATTGAG
Found at i:587934 original size:16 final size:16
Alignment explanation
Indices: 587908--587954 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
587898 TGAAATATAA
*
587908 AATAT-AATAATCCAT
1 AATATAAATAATCAAT
587923 AATATAAATAATCAAT
1 AATATAAATAATCAAT
* * *
587939 TATATATATAACCAAT
1 AATATAAATAATCAAT
587955 TACTTGGGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATAAATAATCAAT
Found at i:593469 original size:29 final size:31
Alignment explanation
Indices: 593428--593501 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 31
593418 TATGGTCAAA
** *
593428 AATCAATGTGACCACT-AAAC-GTTCAATTG
1 AATCAATCAGACCACTCAAACTATTCAATTG
*
593457 AATCAATCAGACCA-TCAAACTATTTAATTG
1 AATCAATCAGACCACTCAAACTATTCAATTG
* *
593487 ATTCAATCAAACCAC
1 AATCAATCAGACCAC
593502 CGGCCGTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 1 0.03
29 16 0.44
30 19 0.53
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (31 bp):
AATCAATCAGACCACTCAAACTATTCAATTG
Found at i:597529 original size:18 final size:18
Alignment explanation
Indices: 597502--597536 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
597492 GAAATTCCGG
*
597502 AAGAGGAGAAGGAGAAAA
1 AAGAGAAGAAGGAGAAAA
597520 AAGAGAAGAAGGAGAAA
1 AAGAGAAGAAGGAGAAA
597537 GCTTTAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (18 bp):
AAGAGAAGAAGGAGAAAA
Found at i:603311 original size:19 final size:20
Alignment explanation
Indices: 603268--603313 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
603258 TATTTTGCAG
* * *
603268 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAAAATGTT
603288 GAAATTGATGTTAAAATG-T
1 GAAATTGATGTTAAAATGTT
603307 GAAATTG
1 GAAATTG
603314 GATCATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (20 bp):
GAAATTGATGTTAAAATGTT
Found at i:605105 original size:20 final size:20
Alignment explanation
Indices: 605080--605144 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
605070 TACATTGGAC
605080 TATGAATCTGAAAGTGAAGT
1 TATGAATCTGAAAGTGAAGT
* * *
605100 TATGAATATGAAAGTAAAGC
1 TATGAATCTGAAAGTGAAGT
605120 TATGAATCTGAAA-TGAA-T
1 TATGAATCTGAAAGTGAAGT
605138 TATGAAT
1 TATGAAT
605145 TTGGAAAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 7 0.18
19 3 0.08
20 29 0.74
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.31
Consensus pattern (20 bp):
TATGAATCTGAAAGTGAAGT
Found at i:623388 original size:16 final size:16
Alignment explanation
Indices: 623367--623399 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
623357 GAATTTGAAT
623367 ATAAAGTTTGGGGGCC
1 ATAAAGTTTGGGGGCC
623383 ATAAAGTTTGGGGGCC
1 ATAAAGTTTGGGGGCC
623399 A
1 A
623400 ACTTAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.36, T:0.24
Consensus pattern (16 bp):
ATAAAGTTTGGGGGCC
Found at i:625654 original size:12 final size:12
Alignment explanation
Indices: 625639--625669 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
625629 GGAGTTGGGT
625639 TCGGGTTTGGCC
1 TCGGGTTTGGCC
625651 TCGGGTTTGGCC
1 TCGGGTTTGGCC
625663 TCGGGTT
1 TCGGGTT
625670 AGGGATGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.42, T:0.35
Consensus pattern (12 bp):
TCGGGTTTGGCC
Found at i:626969 original size:60 final size:60
Alignment explanation
Indices: 626897--627026 Score: 188
Period size: 60 Copynumber: 2.2 Consensus size: 60
626887 TTAATAGGAT
* * *
626897 AAAGTTACAAGATAATACGCTTACTGTAGAATGTTGTTTTGTTAAGTCCTTAGACGATTA
1 AAAGTTACAAGATAATACGCTGACTATAGAATGTTGTTTTATTAAGTCCTTAGACGATTA
* * * *
626957 AAAGTTACAAGATAATACTCTGACTATAGAATGTTTTTTTATTAAGTCTTTAGACTATTA
1 AAAGTTACAAGATAATACGCTGACTATAGAATGTTGTTTTATTAAGTCCTTAGACGATTA
*
627017 AAAATTACAA
1 AAAGTTACAA
627027 AAAAATGGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (60 bp):
AAAGTTACAAGATAATACGCTGACTATAGAATGTTGTTTTATTAAGTCCTTAGACGATTA
Found at i:628143 original size:185 final size:183
Alignment explanation
Indices: 627829--628198 Score: 607
Period size: 185 Copynumber: 2.0 Consensus size: 183
627819 ATTAAATTTT
* * * *
627829 AAATATTAAATATATTATATATAACATATGGGCTCAGCCTAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGATAAGCCCAAACAATTTAAAACCCAATTAATAA
627894 TTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
66 TTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAA-TTT
* *
627959 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
* *
628014 AAATATTAAATATATTATATATAACATTTGGGATAAGCCCAAACAATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGATAAGCCCAAACAATTTAAAACCCAATTAATAA
* * *
628079 TTTAAGATTCAATAACTTTTAAATCTAAATCAATATTAATTAATT-AAAAATTTATCTGAAATTT
66 TTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATTT
628143 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
628197 AA
1 AA
628199 CATTTAATTT
Statistics
Matches: 173, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
183 15 0.09
184 52 0.30
185 106 0.61
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGATAAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:632029 original size:58 final size:58
Alignment explanation
Indices: 631960--632069 Score: 220
Period size: 58 Copynumber: 1.9 Consensus size: 58
631950 TTCATCATAG
631960 AATTGTAAGTCATCGACTATTTATGTCAAGCGAGTGATTATAAATAATCTCCTATAAT
1 AATTGTAAGTCATCGACTATTTATGTCAAGCGAGTGATTATAAATAATCTCCTATAAT
632018 AATTGTAAGTCATCGACTATTTATGTCAAGCGAGTGATTATAAATAATCTCC
1 AATTGTAAGTCATCGACTATTTATGTCAAGCGAGTGATTATAAATAATCTCC
632070 AAATTATAGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (58 bp):
AATTGTAAGTCATCGACTATTTATGTCAAGCGAGTGATTATAAATAATCTCCTATAAT
Found at i:633458 original size:24 final size:24
Alignment explanation
Indices: 633431--633476 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
633421 AAATAATTTT
633431 CAAATGTGACGTT-TAAATATATAA
1 CAAAT-TGACGTTATAAATATATAA
*
633455 CAAATTGATGTTATAAATATAT
1 CAAATTGACGTTATAAATATAT
633477 TATCATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (24 bp):
CAAATTGACGTTATAAATATATAA
Found at i:635762 original size:12 final size:12
Alignment explanation
Indices: 635745--635783 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
635735 TACATAAATA
635745 TATTTAATATAT
1 TATTTAATATAT
*
635757 TATTTAATATAA
1 TATTTAATATAT
635769 TATTTAATATTAT
1 TATTTAATA-TAT
635782 TA
1 TA
635784 GTTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTTAATATAT
Found at i:635830 original size:23 final size:23
Alignment explanation
Indices: 635792--635849 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
635782 TAGTTATAAT
635792 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
635813 TTTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
635836 TTTTACATAATATA
1 TTTTACATAATATA
635850 TTATTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:643505 original size:85 final size:85
Alignment explanation
Indices: 643362--643533 Score: 335
Period size: 85 Copynumber: 2.0 Consensus size: 85
643352 AAACTGTCTT
643362 GCTGCTACATTAACCATGTAGAAAGAAAAGACATTCTCGCACAGAGCTGCAATCGAGGTTCCCGA
1 GCTGCTACATTAACCATGTAGAAAGAAAAGACATTCTCGCACAGAGCTGCAATCGAGGTTCCCGA
*
643427 CTCCCTGACCGAAAACTCTC
66 CACCCTGACCGAAAACTCTC
643447 GCTGCTACATTAACCATGTAGAAAGAAAAGACATTCTCGCACAGAGCTGCAATCGAGGTTCCCGA
1 GCTGCTACATTAACCATGTAGAAAGAAAAGACATTCTCGCACAGAGCTGCAATCGAGGTTCCCGA
643512 CACCCTGACCGAAAACTCTC
66 CACCCTGACCGAAAACTCTC
643532 GC
1 GC
643534 CGACAACGCG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (85 bp):
GCTGCTACATTAACCATGTAGAAAGAAAAGACATTCTCGCACAGAGCTGCAATCGAGGTTCCCGA
CACCCTGACCGAAAACTCTC
Found at i:651953 original size:31 final size:30
Alignment explanation
Indices: 651884--651998 Score: 117
Period size: 31 Copynumber: 3.7 Consensus size: 30
651874 ATACATAACA
* *
651884 ATAA-ATTTTAATAAGTTTAATAATCTTTTTATT
1 ATAATATTTTAA-AAATTTAATAA-C-TATT-TT
* *
651917 ATAATATTTTAAGAAATTTAGTAACTCTTTT
1 ATAATATTTTAA-AAATTTAATAACTATTTT
*
651948 ATAATATTTTAACAAATTTAATAATTATTTT
1 ATAATATTTTAA-AAATTTAATAACTATTTT
651979 ATAATA-TTTAAAAATTTAAT
1 ATAATATTTTAAAAATTTAAT
651999 GATTAAAAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
29 9 0.12
30 5 0.07
31 35 0.48
32 3 0.04
33 5 0.07
34 16 0.22
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (30 bp):
ATAATATTTTAAAAATTTAATAACTATTTT
Found at i:656573 original size:19 final size:18
Alignment explanation
Indices: 656525--656573 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
656515 TATCAGTTTT
*
656525 AATTTATTTTAATACTTA
1 AATTTATTTTTATACTTA
656543 AATATTCA-TTTTATACTTA
1 AAT-TT-ATTTTTATACTTA
656562 AAGTTTATTTTT
1 AA-TTTATTTTT
656574 TGTTTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 4 0.15
19 20 0.77
20 2 0.08
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (18 bp):
AATTTATTTTTATACTTA
Found at i:663353 original size:19 final size:20
Alignment explanation
Indices: 663326--663367 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
663316 AAACTATCAA
**
663326 TTTGATAATTGAACACTTAT
1 TTTGATAATAAAACACTTAT
*
663346 TTTG-TAATAAAACAGTTAT
1 TTTGATAATAAAACACTTAT
663365 TTT
1 TTT
663368 ATTGGGTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (20 bp):
TTTGATAATAAAACACTTAT
Found at i:663358 original size:98 final size:98
Alignment explanation
Indices: 663239--663415 Score: 291
Period size: 98 Copynumber: 1.8 Consensus size: 98
663229 AAAAATAATA
** * *
663239 AACACTTATTTTGCAATAAAACCTTTATTTTATTGGGTAAACTACGCATTTAGTATCTAAACTAT
1 AACACTTATTTTGCAATAAAACAGTTATTTTATTGGGTAAACTACACATTTAATATCTAAACTAT
*
663304 CTATTTTAACCCAAACTATCAATTTGATAATTG
66 CAATTTTAACCCAAACTATCAATTTGATAATTG
*
663337 AACACTTATTTTGTAATAAAACAGTTATTTTATTGGGTAAACTACACATTTAATATCTAAACTAT
1 AACACTTATTTTGCAATAAAACAGTTATTTTATTGGGTAAACTACACATTTAATATCTAAACTAT
*
663402 CAATTTTAATCCAA
66 CAATTTTAACCCAA
663416 TACCTAAACT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 72 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (98 bp):
AACACTTATTTTGCAATAAAACAGTTATTTTATTGGGTAAACTACACATTTAATATCTAAACTAT
CAATTTTAACCCAAACTATCAATTTGATAATTG
Found at i:665564 original size:2 final size:2
Alignment explanation
Indices: 665552--665589 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
665542 TCCGTATGAG
665552 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
665590 TGTAAGAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:667525 original size:35 final size:35
Alignment explanation
Indices: 667475--667549 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
667465 TCATAACTAA
* * *
667475 TTATGTGATAAGATTTAGGGTTT-AGGATTTAGAGT
1 TTATGTGATAAGATTTAAGATTTAAAG-TTTAGAGT
*
667510 TTATGTGATAGGATTTAAGATTTAAAGTTTAGAGT
1 TTATGTGATAAGATTTAAGATTTAAAGTTTAGAGT
667545 TTATG
1 TTATG
667550 ATTTATGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 33 0.94
36 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (35 bp):
TTATGTGATAAGATTTAAGATTTAAAGTTTAGAGT
Found at i:667552 original size:28 final size:28
Alignment explanation
Indices: 667521--667577 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
667511 TATGTGATAG
667521 GATTTAAGAT-TTAAAGTTTAGAGTTTAT
1 GATTTAAG-TGTTAAAGTTTAGAGTTTAT
* * *
667549 GATTTATGTGTTAAGGTTTAGGGTTTAT
1 GATTTAAGTGTTAAAGTTTAGAGTTTAT
667577 G
1 G
667578 TGTTAGGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (28 bp):
GATTTAAGTGTTAAAGTTTAGAGTTTAT
Found at i:667567 original size:21 final size:21
Alignment explanation
Indices: 667543--667589 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
667533 AAAGTTTAGA
*
667543 GTTTATGATTTATGTGTTAAG
1 GTTTAGGATTTATGTGTTAAG
* *
667564 GTTTAGGGTTTATGTGTTAGG
1 GTTTAGGATTTATGTGTTAAG
667585 GTTTA
1 GTTTA
667590 AGTTATGCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (21 bp):
GTTTAGGATTTATGTGTTAAG
Found at i:667899 original size:11 final size:11
Alignment explanation
Indices: 667885--667949 Score: 53
Period size: 11 Copynumber: 5.6 Consensus size: 11
667875 TTAATCGAGT
*
667885 TCGAGCTTGAA
1 TCGAGCTTCAA
667896 TCGAGC-TCAAAA
1 TCGAGCTTC--AA
667908 TCGAGCTTCAA
1 TCGAGCTTCAA
*
667919 TCGAGC-TCGAGTC
1 TCGAGCTTC-A--A
667932 TCGAGCTTCAA
1 TCGAGCTTCAA
667943 TCGAGCT
1 TCGAGCT
667950 CTTGAATTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
10 3 0.07
11 22 0.50
12 8 0.18
13 9 0.20
14 2 0.05
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (11 bp):
TCGAGCTTCAA
Found at i:667940 original size:24 final size:23
Alignment explanation
Indices: 667879--667950 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
667869 TGAGTTTTAA
*
667879 TCGAGTTCGAGCTTGAATCGAGC
1 TCGAGTTCGAGCTTCAATCGAGC
* **
667902 TCAAAATCGAGCTTCAATCGAGC
1 TCGAGTTCGAGCTTCAATCGAGC
667925 TCGAGTCTCGAGCTTCAATCGAGC
1 TCGAGT-TCGAGCTTCAATCGAGC
667949 TC
1 TC
667951 TTGAATTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 22 0.54
24 19 0.46
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (23 bp):
TCGAGTTCGAGCTTCAATCGAGC
Found at i:669149 original size:17 final size:18
Alignment explanation
Indices: 669114--669151 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
669104 TATTGTATAT
**
669114 TTATACAAAATATTTTTA
1 TTATACAAAATATAATTA
669132 TTATA-AAAATATAATTA
1 TTATACAAAATATAATTA
669149 TTA
1 TTA
669152 ATTTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATACAAAATATAATTA
Found at i:669443 original size:29 final size:29
Alignment explanation
Indices: 669399--669456 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
669389 TAAAATCTTA
*
669399 TTTCGTGTTCATTTTTAAAACATTTAGAT
1 TTTCGTGTTCAGTTTTAAAACATTTAGAT
669428 TTTCGTGTTCAGTTTTAAAACATTTAGAT
1 TTTCGTGTTCAGTTTTAAAACATTTAGAT
669457 ACGAGATTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (29 bp):
TTTCGTGTTCAGTTTTAAAACATTTAGAT
Found at i:669764 original size:128 final size:128
Alignment explanation
Indices: 669533--669784 Score: 432
Period size: 128 Copynumber: 2.0 Consensus size: 128
669523 GAATGTTGAA
* * * *
669533 CCGTTCAACATTCAACGCGTTTGTTTCGCACATTTGAATGATTTAGTGCTGACTGATTTAGCAAA
1 CCGTTCAACATTCAAAGCGTTTGTTTCGCACATCTGAATGATTTAGTGCTGACTGATTCAACAAA
* *
669598 ACAGTGTTGAATGATTCAGCACATAAATACATTCTGAATGATTCAGAATCATTATCAAATAGC
66 ACAGTGTTGAATGATTCAACACATAAATACATTATGAATGATTCAGAATCATTATCAAATAGC
669661 CCGTTCAACATTCAAAGCGTTTGTTTCGCACATCTGAATGATTTAGTGCTGACTGATTCAACAAA
1 CCGTTCAACATTCAAAGCGTTTGTTTCGCACATCTGAATGATTTAGTGCTGACTGATTCAACAAA
* *
669726 ACAGTGTTGAATGATTCAACACATAAGTACATTATGAATGATTCAGAGTCATTATCAAA
66 ACAGTGTTGAATGATTCAACACATAAATACATTATGAATGATTCAGAATCATTATCAAA
669785 CAGCATGTCA
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
128 116 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (128 bp):
CCGTTCAACATTCAAAGCGTTTGTTTCGCACATCTGAATGATTTAGTGCTGACTGATTCAACAAA
ACAGTGTTGAATGATTCAACACATAAATACATTATGAATGATTCAGAATCATTATCAAATAGC
Found at i:670229 original size:15 final size:15
Alignment explanation
Indices: 670209--670238 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
670199 GGTGGGGCGG
670209 GCCGGGTTTTTGGCC
1 GCCGGGTTTTTGGCC
670224 GCCGGGTTTTTGGCC
1 GCCGGGTTTTTGGCC
670239 ACCCCTACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.27, G:0.40, T:0.33
Consensus pattern (15 bp):
GCCGGGTTTTTGGCC
Found at i:670413 original size:43 final size:45
Alignment explanation
Indices: 670349--670437 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 45
670339 GTCAGGAATA
* *
670349 TATTAATATATTTAAATAATTAAAATAAAT-TAATTTATAATGATT
1 TATTAATATATTTAAACAATT-AAATAAATATAATTTATAATAATT
* *
670394 TATT-ATAT-TTTAAACAATTAAATTAATATATTTTATAATAATT
1 TATTAATATATTTAAACAATTAAATAAATATAATTTATAATAATT
670437 T
1 T
670438 TCTACAGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 7 0.18
43 24 0.62
44 4 0.10
45 4 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (45 bp):
TATTAATATATTTAAACAATTAAATAAATATAATTTATAATAATT
Found at i:671035 original size:60 final size:60
Alignment explanation
Indices: 670889--671026 Score: 167
Period size: 60 Copynumber: 2.3 Consensus size: 60
670879 AAAATAATAA
* *
670889 ATAGTT-GAGTGATCATTTTGTAACTTTTAATAGTCGATGAACTCAACAAAACAATACTCT
1 ATAGTTGGAG-GACCATTTTGTAACTTTTAATAGTCAATGAACTCAACAAAACAATACTCT
* * *
670949 ATAGTTGGAGGACCATTTTGTAACTTTTAATAGTCAAT-AGACTTAATAAAATAATA-TCCT
1 ATAGTTGGAGGACCATTTTGTAACTTTTAATAGTCAATGA-ACTCAACAAAACAATACT-CT
671009 ATAGTTAGGA-GACCATTT
1 ATAGTT-GGAGGACCATTT
671027 ATTTACTTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
59 2 0.03
60 61 0.88
61 6 0.09
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (60 bp):
ATAGTTGGAGGACCATTTTGTAACTTTTAATAGTCAATGAACTCAACAAAACAATACTCT
Found at i:671819 original size:19 final size:19
Alignment explanation
Indices: 671795--671834 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
671785 GAATCATGCC
671795 CCGTCGTTTTAGATCTCCT
1 CCGTCGTTTTAGATCTCCT
671814 CCGTCGTTTTAGATCTCCT
1 CCGTCGTTTTAGATCTCCT
671833 CC
1 CC
671835 CTCACCCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.35, G:0.15, T:0.40
Consensus pattern (19 bp):
CCGTCGTTTTAGATCTCCT
Found at i:678986 original size:41 final size:41
Alignment explanation
Indices: 678925--679048 Score: 212
Period size: 41 Copynumber: 3.0 Consensus size: 41
678915 AACGTATAAA
*
678925 TCGAATTAAGTTTTACACTAGTATAAGTAAATCCTATACCG
1 TCGAATTAAGTTTTACACTAGTATAAGTAAATCCTATCCCG
* * *
678966 TCGAACTAAGTTTTAAACTAGTATAAGTAAATCATATCCCG
1 TCGAATTAAGTTTTACACTAGTATAAGTAAATCCTATCCCG
679007 TCGAATTAAGTTTTACACTAGTATAAGTAAATCCTATCCCG
1 TCGAATTAAGTTTTACACTAGTATAAGTAAATCCTATCCCG
679048 T
1 T
679049 GTACATCATA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 76 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (41 bp):
TCGAATTAAGTTTTACACTAGTATAAGTAAATCCTATCCCG
Found at i:690266 original size:26 final size:26
Alignment explanation
Indices: 690232--690284 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
690222 TGAGATTACA
* *
690232 GTTTGGTGGTGGTT-AGTTGGGATTGG
1 GTTTAGTGGTGGTTGA-TTGAGATTGG
690258 GTTTAGTGGTGGTTGATTGAGATTGG
1 GTTTAGTGGTGGTTGATTGAGATTGG
690284 G
1 G
690285 GTTTGTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.11, C:0.00, G:0.47, T:0.42
Consensus pattern (26 bp):
GTTTAGTGGTGGTTGATTGAGATTGG
Found at i:690764 original size:15 final size:15
Alignment explanation
Indices: 690744--690779 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
690734 TGAGTAATTT
*
690744 TTTTTTTATACTCTA
1 TTTTTTGATACTCTA
*
690759 TTTTTTGATATTCTA
1 TTTTTTGATACTCTA
690774 TTTTTT
1 TTTTTT
690780 AATGTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTTTTGATACTCTA
Found at i:693700 original size:33 final size:31
Alignment explanation
Indices: 693638--693710 Score: 92
Period size: 33 Copynumber: 2.3 Consensus size: 31
693628 GCGACCTACC
* * *
693638 CTCGCTTGGTTGCTCGGATTCCCTTGCATAG
1 CTCGCTCGGTTGCTCGGATGCCCTCGCATAG
693669 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTG--CTCGGATGCCCTCGCATAG
*
693702 CTCGTTCGG
1 CTCGCTCGG
693711 ATGGCTTGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 11 0.31
33 25 0.69
ACGTcount: A:0.08, C:0.34, G:0.27, T:0.30
Consensus pattern (31 bp):
CTCGCTCGGTTGCTCGGATGCCCTCGCATAG
Found at i:694769 original size:16 final size:16
Alignment explanation
Indices: 694737--694769 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
694727 TCACATTTAG
694737 ATTTTTTTTAAATAAT
1 ATTTTTTTTAAATAAT
694753 ATTTTATTTTAAA-AAT
1 ATTTT-TTTTAAATAAT
694769 A
1 A
694770 AAAAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTTTTTAAATAAT
Found at i:701736 original size:14 final size:14
Alignment explanation
Indices: 701719--701748 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
701709 AATTTTATAA
*
701719 AAATTTTATAATTT
1 AAATTTAATAATTT
701733 AAATTTAATAATTT
1 AAATTTAATAATTT
701747 AA
1 AA
701749 TCCAAGGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATTTAATAATTT
Found at i:701923 original size:12 final size:12
Alignment explanation
Indices: 701906--701931 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
701896 AGCGCTTTCT
701906 TATCATAATAAA
1 TATCATAATAAA
701918 TATCATAATAAA
1 TATCATAATAAA
701930 TA
1 TA
701932 AGACTGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (12 bp):
TATCATAATAAA
Found at i:702985 original size:101 final size:100
Alignment explanation
Indices: 702766--702988 Score: 272
Period size: 100 Copynumber: 2.2 Consensus size: 100
702756 GTGGGGACAG
* *
702766 TCGTCGTCATAAAATTTTAAAATTATCTTATATTTTAGAATTTGTTTATGTATTTTCTATTAAAA
1 TCGTC-TCCTAAAATTTTAAAATTATCTTATATTTTAGAATTTGTTTATATATTTTCTATTAAAA
* * *
702831 ATTTATTTTCGCTCCTGAAATTTTATAAGTTCAAGT
65 ATCTATTTTCGCCCCTAAAATTTTATAAGTTCAAGT
** * * * *
702867 TCACCCCCTAAAATTTTAATATTA-CATTATATTTTATAATTT-TTCTATATATTTT-TATTAAC
1 TCGTCTCCTAAAATTTTAAAATTATC-TTATATTTTAGAATTTGTT-TATATATTTTCTATTAAA
*
702929 AATCTATTTTTCGCCCACTAAAATTTTATAAGTTTAAGT
64 AATCTA-TTTTCGCCC-CTAAAATTTTATAAGTTCAAGT
702968 TCGTCTCCTAAAATTTTAAAA
1 TCGTCTCCTAAAATTTTAAAA
702989 ATTCAAAATT
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
99 14 0.14
100 48 0.47
101 40 0.39
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (100 bp):
TCGTCTCCTAAAATTTTAAAATTATCTTATATTTTAGAATTTGTTTATATATTTTCTATTAAAAA
TCTATTTTCGCCCCTAAAATTTTATAAGTTCAAGT
Found at i:703809 original size:31 final size:31
Alignment explanation
Indices: 703756--703814 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
703746 CGGTTGAGGG
* * *
703756 ACTAAAATCGAACAGATCGATAATGTTAGGT
1 ACTAAAATCAAACAAATCGATAACGTTAGGT
*
703787 ACTATAATCAAACAAATCGATAACGTTA
1 ACTAAAATCAAACAAATCGATAACGTTA
703815 CCCTTAATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (31 bp):
ACTAAAATCAAACAAATCGATAACGTTAGGT
Done.