Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007970.1 Hibiscus syriacus cultivar Beakdansim tig00110407_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: 487657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 3
Found at i:184376 original size:22 final size:22
Alignment explanation
Indices: 184327--184379 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
184317 TTAATTATGA
184327 TTAA-AATATTTTTTTAATATT
1 TTAATAATATTTTTTTAATATT
184348 TTAAATAATATTTTTATATAA-A-T
1 TT-AATAATATTTTT-T-TAATATT
184371 TTAATAATA
1 TTAATAATA
184380 ATCATAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
21 2 0.07
22 9 0.32
23 12 0.43
24 2 0.07
25 3 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAATAATATTTTTTTAATATT
Found at i:184809 original size:18 final size:18
Alignment explanation
Indices: 184783--184826 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
184773 GAAAGAAGGT
*
184783 GGAATTGGCGTGATCAAA
1 GGAAATGGCGTGATCAAA
184801 GGAAATGGCGTGATCAAA
1 GGAAATGGCGTGATCAAA
184819 GGAAATGG
1 GGAAATGG
184827 AGTTGGTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.36, T:0.18
Consensus pattern (18 bp):
GGAAATGGCGTGATCAAA
Found at i:186655 original size:17 final size:17
Alignment explanation
Indices: 186633--186670 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
186623 AAGTAGGATC
186633 TAATTGAAAAATAATAA
1 TAATTGAAAAATAATAA
186650 TAATTGAAAAATAATAA
1 TAATTGAAAAATAATAA
186667 TAAT
1 TAAT
186671 ATAGAGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
TAATTGAAAAATAATAA
Found at i:187228 original size:20 final size:20
Alignment explanation
Indices: 187191--187228 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
187181 AAGAAAACTC
*
187191 AAATTTCAAGGTAAACACGA
1 AAATTTCAAAGTAAACACGA
*
187211 AAATTTCAAAGTAGACAC
1 AAATTTCAAAGTAAACAC
187229 CATCAACAAA
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:0.50, C:0.16, G:0.13, T:0.21
Consensus pattern (20 bp):
AAATTTCAAAGTAAACACGA
Found at i:187950 original size:20 final size:21
Alignment explanation
Indices: 187925--188017 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
187915 TTTTCCCAAT
*
187925 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
187945 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
187966 TCACAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
187986 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
188007 TCGCAATGCGA
1 TCGCAATGCGA
188018 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:187973 original size:41 final size:41
Alignment explanation
Indices: 187928--188017 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
187918 TCCCAATTCG
187928 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCA
1 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCA
*
187969 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
1 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCA
188010 CAATGCGA
1 CAATGCGA
188018 TACTGACTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (41 bp):
CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCA
Found at i:188030 original size:41 final size:41
Alignment explanation
Indices: 187944--188078 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
187934 GAATAAGTAA
* * *
187944 ATCGCAACGCGAATTGGGAAAATCACAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
187985 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
188026 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
188067 TTCGCAACGCGA
1 ATCGCAACGCGA
188079 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:188031 original size:20 final size:20
Alignment explanation
Indices: 188006--188100 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
187996 AATTGGGAAA
*
188006 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
188026 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
188047 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
188067 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
188087 TTCGCAACGCGATA
1 ATCGCAACGCGATA
188101 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:188315 original size:22 final size:22
Alignment explanation
Indices: 188287--188330 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
188277 CACTCTCTCA
188287 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
188309 CCCATCTCCGGCTAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
188331 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.45, G:0.14, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:189972 original size:18 final size:18
Alignment explanation
Indices: 189951--189995 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
189941 TCCACTTCGG
*
189951 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
189969 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
189987 GAGCCATCA
1 GAGCCATCA
189996 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:190525 original size:19 final size:20
Alignment explanation
Indices: 190482--190526 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
190472 CGCAACACGA
190482 AAATGACTATCACAACGCGG
1 AAATGACTATCACAACGCGG
* * *
190502 AAATGGCTATCGCAATGC-G
1 AAATGACTATCACAACGCGG
190521 AAATGA
1 AAATGA
190527 AAATCGCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAATGACTATCACAACGCGG
Found at i:190545 original size:14 final size:14
Alignment explanation
Indices: 190526--190583 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
190516 ATGCGAAATG
*
190526 AAAATCGCAACGAC
1 AAAATCGCAACGAA
190540 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAA
190556 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
190572 AAAATCGCAACG
1 AAAATCGCAACG
190584 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:190568 original size:32 final size:33
Alignment explanation
Indices: 190510--190600 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
190500 GGAAATGGCT
* *
190510 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
190543 ATCGCAACGCGAAATG-AAATCGCAACGAAAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
190575 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
190601 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
Found at i:190636 original size:14 final size:14
Alignment explanation
Indices: 190617--190674 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
190607 TTGTGTTTCG
190617 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
190631 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
190647 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
190663 CGTTGCGATTTT
1 CGTTGCGATTTT
190675 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:190651 original size:32 final size:33
Alignment explanation
Indices: 190612--190690 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
190602 GCGATTTGTG
190612 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
190644 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
190677 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
190691 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:190689 original size:19 final size:19
Alignment explanation
Indices: 190631--190748 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
190621 GCGATTTTGT
190631 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
190649 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
190663 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
190682 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
190702 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
190721 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
190741 TGTTGCGA
1 CGTTGCGA
190749 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:192754 original size:14 final size:14
Alignment explanation
Indices: 192735--192788 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
192725 CGAAATGGCT
192735 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
192749 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
192768 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
192782 ATCGCAA
1 ATCGCAA
192789 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:192806 original size:33 final size:33
Alignment explanation
Indices: 192716--192793 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
192706 AAAACAGACT
* ***
192716 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
192749 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
192782 ATCGCAATGCGA
1 ATCGCAATGCGA
192794 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:192869 original size:20 final size:20
Alignment explanation
Indices: 192812--192869 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
192802 TCGCATTGCG
* *
192812 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
192832 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
192852 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
192870 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:193137 original size:33 final size:33
Alignment explanation
Indices: 193086--193148 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
193076 CATGTTAATC
* *
193086 ATCGTTGCCTTTTTCATTTCGCATTGCGATTCT
1 ATCGTTGCCATTTGCATTTCGCATTGCGATTCT
*
193119 ATCGTTGCGATTTGCATTTCGCATTGCGAT
1 ATCGTTGCCATTTGCATTTCGCATTGCGAT
193149 GGTCAAATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.44
Consensus pattern (33 bp):
ATCGTTGCCATTTGCATTTCGCATTGCGATTCT
Found at i:193956 original size:24 final size:24
Alignment explanation
Indices: 193929--193982 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
193919 GTATTCGAAA
* *
193929 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
193953 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
193977 TTTGAT
1 TTTGAT
193983 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:194071 original size:42 final size:42
Alignment explanation
Indices: 194004--194087 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
193994 CGAAGACAGT
* * *
194004 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
194046 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
194088 TGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:196154 original size:19 final size:19
Alignment explanation
Indices: 196089--196259 Score: 181
Period size: 19 Copynumber: 9.1 Consensus size: 19
196079 TCTTTTGGTT
*
196089 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
196108 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
196128 GAAAATGACTATCGCAATGC
1 G-AAATGAAAATCGCAACGC
** *
196148 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
196166 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
196181 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
196201 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
196220 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
196239 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
196258 GA
1 GA
196260 TTTTGGTTTC
Statistics
Matches: 131, Mismatches: 13, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
14 10 0.08
15 2 0.02
18 2 0.02
19 67 0.51
20 49 0.37
21 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:196213 original size:39 final size:38
Alignment explanation
Indices: 196089--196259 Score: 154
Period size: 39 Copynumber: 4.6 Consensus size: 38
196079 TCTTTTGGTT
* * *
196089 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATAAAAATCGCAACGCGA-AATGAAAATCGCAACGC
* ** * ** *
196128 GAAAATGACTATCGCAATGCGAAATGACTATCGCGAC-C
1 G-AAATAAAAATCGCAACGCGAAATGAAAATCGCAACGC
* *
196166 ---A-GACAATCGCAACGCGAAATGAAAATCGCAACCGC
1 GAAATAAAAATCGCAACGCGAAATGAAAATCGCAA-CGC
196201 GAAATAAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATAAAAATCGCAACGCGAAATGAAAATCGCAACGC
* *
196239 GAAATGAAAATCGCAATGCGA
1 GAAATAAAAATCGCAACGCGA
196260 TTTTGGTTTC
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
33 25 0.23
34 2 0.02
35 1 0.01
38 24 0.22
39 41 0.38
40 16 0.15
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (38 bp):
GAAATAAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:196288 original size:19 final size:19
Alignment explanation
Indices: 196255--196335 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
196245 AAAATCGCAA
**
196255 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
196274 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
196293 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
196307 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
196327 TGCGATTTT
1 TGCGATTTT
196336 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:196877 original size:20 final size:20
Alignment explanation
Indices: 196852--196904 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
196842 GCGCTATGTA
196852 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
196872 AATCGCGTTGCGAAAGTCAT
1 AATCGCGTTGCGAAAGTCAG
* *
196892 TATCTCGTTGCGA
1 AATCGCGTTGCGA
196905 TTTTGTATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:196964 original size:21 final size:21
Alignment explanation
Indices: 196935--197026 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
196925 ATAGTAAGTA
196935 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* *
196956 TCGCGTTGCGATTATT---TAT
1 TCGCATTGCGATT-TTCCCAAT
196975 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
196996 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
197016 TCGCATTGCGA
1 TCGCATTGCGA
197027 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.03
19 14 0.24
20 16 0.28
21 24 0.41
22 2 0.03
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:196990 original size:40 final size:41
Alignment explanation
Indices: 196935--197026 Score: 168
Period size: 40 Copynumber: 2.3 Consensus size: 41
196925 ATAGTAAGTA
*
196935 TCGCATTGCGATTTTCCCAATTCGCGTTGCGA-TTATTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
196975 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
197016 TCGCATTGCGA
1 TCGCATTGCGA
197027 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 32 0.64
41 18 0.36
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:197346 original size:39 final size:39
Alignment explanation
Indices: 197292--197372 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
197282 AGTTTTTATC
*
197292 TTTAAGGCTTAATATCAAAATAAGTTATTAAATAATACT
1 TTTAAGGCTTAATATCAAAATAAGTGATTAAATAATACT
* *
197331 TTTAAGGCTTAATATCAAAATAAGTGATTAAATTATATT
1 TTTAAGGCTTAATATCAAAATAAGTGATTAAATAATACT
197370 TTT
1 TTT
197373 TTTGAATGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (39 bp):
TTTAAGGCTTAATATCAAAATAAGTGATTAAATAATACT
Found at i:197903 original size:62 final size:61
Alignment explanation
Indices: 197821--197996 Score: 236
Period size: 56 Copynumber: 2.9 Consensus size: 61
197811 ATTTTTTAAA
*
197821 AAAATTTCGGGATCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTTGGGTCGGGTTTTTTT
1 AAAATTTCAGG-TCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTTGGGTCGGGTTTTTTT
197883 AAAATTTCAGGT----TCGGGTCGGG-TTTTTTAAGTGTGATATTTGGGTCGGGTTTTTTT
1 AAAATTTCAGGTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTTGGGTCGGGTTTTTTT
* * * ** *
197939 AAAGTGTGATATTCGGGTCGGGTCAGGTTTTTTTAAGTGTGATATTTGGGTCGGGTTT
1 AAAATTTCA-GGTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTTGGGTCGGGTTT
197997 AGGGTGAAAA
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
56 40 0.40
57 11 0.11
61 10 0.10
62 40 0.40
ACGTcount: A:0.16, C:0.07, G:0.33, T:0.44
Consensus pattern (61 bp):
AAAATTTCAGGTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTTGGGTCGGGTTTTTTT
Found at i:197937 original size:29 final size:29
Alignment explanation
Indices: 197840--197996 Score: 176
Period size: 29 Copynumber: 5.4 Consensus size: 29
197830 GGATCGGGTC
197840 GGGTCGGG-TTTTTTTAAGTGTGATATTT
1 GGGTCGGGTTTTTTTTAAGTGTGATATTT
* * * * ** *
197868 GGGTCGGGTTTTTTTAAAATTTCAGGTTC
1 GGGTCGGGTTTTTTTTAAGTGTGATATTT
197897 GGGTCGGG--TTTTTTAAGTGTGATATTT
1 GGGTCGGGTTTTTTTTAAGTGTGATATTT
* *
197924 GGGTCGGGTTTTTTTAAAGTGTGATATTC
1 GGGTCGGGTTTTTTTTAAGTGTGATATTT
197953 GGGTCGGGTCAGGTTTTTTTAAGTGTGATATTT
1 GGGTCGGGT----TTTTTTTAAGTGTGATATTT
197986 GGGTCGGGTTT
1 GGGTCGGGTTT
197997 AGGGTGAAAA
Statistics
Matches: 104, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
27 20 0.19
28 8 0.08
29 49 0.47
33 27 0.26
ACGTcount: A:0.15, C:0.06, G:0.33, T:0.46
Consensus pattern (29 bp):
GGGTCGGGTTTTTTTTAAGTGTGATATTT
Found at i:210467 original size:20 final size:20
Alignment explanation
Indices: 210442--210500 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
210432 GTTTGGTTCA
*
210442 CGGAATGTAAGATTATCAGT
1 CGGAATGTAAGATTACCAGT
210462 CGGAATGTAAGATTACCAGT
1 CGGAATGTAAGATTACCAGT
210482 -GAGAATGTAAGATTACCAG
1 CG-GAATGTAAGATTACCAG
210501 GGAATAGGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.25
Consensus pattern (20 bp):
CGGAATGTAAGATTACCAGT
Found at i:213065 original size:33 final size:33
Alignment explanation
Indices: 213007--213091 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
212997 CTTTATTTTG
213007 TTCGGGTCGGGTCGGG-TTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
*
213039 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGTTA
1 TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
*
213072 TTCGGGTCGAGTTCGGGTTT
1 TTCGGGTCG-GGTCGGGTTT
213092 AGGGTGAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 16 0.33
33 24 0.49
34 9 0.18
ACGTcount: A:0.09, C:0.11, G:0.38, T:0.42
Consensus pattern (33 bp):
TTCGGGTCGGGTCGGGTTTTTTTAAGTGTGATA
Found at i:213716 original size:18 final size:18
Alignment explanation
Indices: 213667--213717 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
213657 TGAAATTGGG
* *
213667 TTCCAATT-CCTGACAGA
1 TTCCAATTCCCTCATAGA
**
213684 TTCCAATTCTTTCATAGA
1 TTCCAATTCCCTCATAGA
213702 TTCCAATTCCCTCATA
1 TTCCAATTCCCTCATA
213718 AACATTCCAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.27, C:0.29, G:0.06, T:0.37
Consensus pattern (18 bp):
TTCCAATTCCCTCATAGA
Found at i:214661 original size:17 final size:16
Alignment explanation
Indices: 214531--214662 Score: 54
Period size: 17 Copynumber: 7.9 Consensus size: 16
214521 TTAGACATGA
*
214531 AAAAATAAATAAATATT
1 AAAAA-AAATAAATAAT
*
214548 AAATAATAAGAAAAATAAT
1 AAA-AA-AA-ATAAATAAT
* *
214567 AAATCAAAACAAATAAT
1 AAA-AAAAATAAATAAT
* * *
214584 -TAAAAAATAAATCAG
1 AAAAAAAATAAATAAT
214599 AGAAAAAAATAAATCAAT
1 A-AAAAAAATAAAT-AAT
** *
214617 CGAAAAAA-ACAT-AT
1 AAAAAAAATAAATAAT
* * *
214631 ATACAAAATTAATAAT
1 AAAAAAAATAAATAAT
214647 AAAAATAAATAAATAA
1 AAAAA-AAATAAATAA
214663 ATGAATACGT
Statistics
Matches: 84, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
14 7 0.08
15 11 0.13
16 9 0.11
17 37 0.44
18 8 0.10
19 12 0.14
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAAAAAATAAATAAT
Found at i:215804 original size:14 final size:14
Alignment explanation
Indices: 215785--215825 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
215775 AAAAAGAAAA
215785 TAATAATAAATAAT
1 TAATAATAAATAAT
*
215799 TAATAATTAATAAT
1 TAATAATAAATAAT
215813 TAA-AATAAGATAA
1 TAATAATAA-ATAA
215826 AAATAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
TAATAATAAATAAT
Found at i:215971 original size:37 final size:36
Alignment explanation
Indices: 215844--216166 Score: 375
Period size: 37 Copynumber: 8.7 Consensus size: 36
215834 AAAAGGAATT
* * **
215844 TTTTTAAAACTATATTTTATATATGATTTAAAAAATG
1 TTTTAAAAACTATATATTATATAT-ATTTTCAAAATG
* * * *
215881 TTTTTCAAAACCATATAATATAATATATTTTCAAAAAATA
1 -TTTTAAAAACTATATATTAT-ATATATTTTC--AAAATG
215921 TTTT-AAAACTATATATTATATATATTTTCTAAAATG
1 TTTTAAAAACTATATATTATATATATTTTC-AAAATG
* *
215957 TTTTAAAAATTATATATTATATA-AGTTTTCAAAATAT
1 TTTTAAAAACTATATATTATATATA-TTTTCAAAAT-G
215994 TTTTAAAAACTATATATTATATA-AGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATATA-TTTTCAAAATG
* *
216030 TTTTTAAAAAACTATATATTATATA-AGTTTCCAAAATA
1 -TTTT-AAAAACTATATATTATATATA-TTTTCAAAATG
216068 TTTTAAAAACTATATATTATATATATTTTCAAAAATG
1 TTTTAAAAACTATATATTATATATATTTTC-AAAATG
**
216105 TTTTAAAAACTATATATTATATAGGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATATATTTTCAAAATG
216141 TTTTAAAAACTATATATTATATATAT
1 TTTTAAAAACTATATATTATATATAT
216167 AAATTTTCAA
Statistics
Matches: 252, Mismatches: 23, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
36 68 0.27
37 108 0.43
38 63 0.25
39 8 0.03
40 5 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAATG
Found at i:216929 original size:84 final size:84
Alignment explanation
Indices: 216759--217272 Score: 677
Period size: 84 Copynumber: 6.1 Consensus size: 84
216749 AACTTGACAA
* ** * * * * * * *
216759 TTTTGTTGACAGATAGGCCTTCTTACCTTGAGCTATGCTGTGAATTTTATTTGCCTCTGAGTTGA
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG-CAA-ATGATGTGCCTTTGAGCTGA
*
216824 ATGTAATCAAACTCGAAGGTC
64 GTGTAATCAAACTCGAAGGTC
* * * * * *
216845 TTTTTTTGGCAGATAACCCTTCTTACCTTGAGCTATGTTGTAAACGATGTGCCTTTGAGATGAGT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
216910 GTAATCAAACTCGAAGGTC
66 GTAATCAAACTCGAAGGTC
* * * *
216929 TTTTGTTGGCAGATAACCCTTCTTGCCTTGGGCTATACTGCAAATGATGCGCTTTTGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
216994 GTAATCGAACTCGAAGGTC
66 GTAATCAAACTCGAAGGTC
* * * *
217013 TTTTGTTGGTAGATAACTCTTCTTGCCTTAAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* *
217078 GTAATCAAACTTGAATGTC
66 GTAATCAAACTCGAAGGTC
*
217097 TTTTGTTGGCAGATAACCCTTCTTGCCTTTAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
*
217162 GTAATCGAACTCGAAGGTC
66 GTAATCAAACTCGAAGGTC
* * * * *
217181 TTTTGTTGGCAGATAACCCTTCTCGCCTTGAGTTATACTGCAAATGACGTGCCTTTGAGCTGTGT
1 TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
* *
217246 GTAATCGAACTCAAAGGTC
66 GTAATCAAACTCGAAGGTC
217265 TTTTGTTG
1 TTTTGTTG
217273 AAGGTGCTTT
Statistics
Matches: 379, Mismatches: 49, Indels: 2
0.88 0.11 0.00
Matches are distributed among these distances:
84 342 0.90
85 2 0.01
86 35 0.09
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (84 bp):
TTTTGTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
GTAATCAAACTCGAAGGTC
Found at i:220710 original size:17 final size:17
Alignment explanation
Indices: 220688--220724 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
220678 AAGCTCCATT
220688 GGAGCCCTCTATCAATA
1 GGAGCCCTCTATCAATA
220705 GGAGCCCTCTATCAATA
1 GGAGCCCTCTATCAATA
220722 GGA
1 GGA
220725 ACTATCCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (17 bp):
GGAGCCCTCTATCAATA
Found at i:222336 original size:538 final size:538
Alignment explanation
Indices: 221319--222391 Score: 1858
Period size: 538 Copynumber: 2.0 Consensus size: 538
221309 TAACTCCCTA
*
221319 TACTCTCCCGGTTTAGGTTCTAAAGAGGGTACAGTTAGTTTTTCTTGCTGGTGCCCCCTTGGGCT
1 TACTCTCCCGGTTTAGGTTCTAAAGAGGGTACAGTTAGTTTTCCTTGCTGGTGCCCCCTTGGGCT
* *
221384 TGCTAGACCCTTAGTCTTAAGCCTATTACAAGCTTTTGTTGACTAAGTTAAACTCGAGAGGATAC
66 TGCTAGACCCTTAGTCCTAAGCCTATTACAAGCTTTTGTTAACTAAGTTAAACTCGAGAGGATAC
* * *
221449 ATTCCCTTATACCCTCACGGAGAATAAATTCTCACGAAGGTGTCGCTTTCACCCCACTTAAAAAG
131 ATTCCCTTATACCCGCACGGAGAATAAATTCCCACGAAGGCGTCGCTTTCACCCCACTTAAAAAG
* * * *
221514 GGTTTAGAACTTGGATATAGAGCCTGAGATAATAATTTTGAAAATCTGAAATCATTGAAAAAAAT
196 GGTTTAGAACTTGGATATAAAGCATGAGATAAAAAATTTGAAAATCTGAAATCATTGAAAAAAAT
*
221579 ATCAGTACAACTATTTATTTGAAAAACATACAAAGATAAGTAATAAAAATTGAAAAGTTAAATTA
261 ATCAGTACAACTATTTATTTGAAAAACATACAAAGATAAGTAATAAAAATCGAAAAGTTAAATTA
221644 AAATTTAAACTTACCATTTTCGCTTAAAAAAGAGAATCGAAAAATTAATTCTGGCCTAACTCACT
326 AAATTTAAACTTACCATTTTCGCTTAAAAAAGAGAATCGAAAAATTAATTCTGGCCTAACTCACT
* ***
221709 TACCTGTCGCGGCCGTCTTTCGGTTGGGCCCAAAATTGGGCTTCGACTTGAATAAAATGGATTAG
391 TACCTGTCGCGGCCGTCTTTCGGTTGGGCCCAAAATTGGGCTTCAACTTGAATAAAACAAATTAG
*
221774 AGTCACCATTGATCATTTAAAAACTAGTTTAGATTGATCGAACACCATCTTATCTTATCTGTGTT
456 AGTCACCACTGATCATTTAAAAACTAGTTTAGATTGATCGAACACCATCTTATCTTATCTGTGTT
221839 TTACCAGAAATGTGTTGG
521 TTACCAGAAATGTGTTGG
*
221857 TACTCTCCCGGTTTAGGTTCTAAAGAGGGTACCGTTAGTTTTCCTTGCTGGTGCCCCCTTGGGCT
1 TACTCTCCCGGTTTAGGTTCTAAAGAGGGTACAGTTAGTTTTCCTTGCTGGTGCCCCCTTGGGCT
221922 TGCTAGACCCTTAGTCCTAAGCCTATTACAAGCTTTTGTTAACTAAGTTAAACTCGAGAGGATAC
66 TGCTAGACCCTTAGTCCTAAGCCTATTACAAGCTTTTGTTAACTAAGTTAAACTCGAGAGGATAC
* * *
221987 ATTCCCTTATGCCCGCACGGAGAATAAATTCCCACGAAGGCGTTGCTTTCACTCCACTTAAAAAG
131 ATTCCCTTATACCCGCACGGAGAATAAATTCCCACGAAGGCGTCGCTTTCACCCCACTTAAAAAG
* *
222052 GGTTTAGAGCTTGGGTATAAAGCATGAGATAAAAAATTTGAAAATCTGAAATCATTGAAAAAAAT
196 GGTTTAGAACTTGGATATAAAGCATGAGATAAAAAATTTGAAAATCTGAAATCATTGAAAAAAAT
*
222117 ATCAGTACAACTATTTATTTGAAAAACATTCAAAGATAAGTAATAAAAATCGAAAAGTTAAATTA
261 ATCAGTACAACTATTTATTTGAAAAACATACAAAGATAAGTAATAAAAATCGAAAAGTTAAATTA
*
222182 AAATTTATACTTACCATTTTCGCTTAAAAAAGAGAATCGAAAAATTAATTCTGGCCTAACTCACT
326 AAATTTAAACTTACCATTTTCGCTTAAAAAAGAGAATCGAAAAATTAATTCTGGCCTAACTCACT
* * * *
222247 TACCTGTCGCGGTCGTTTTTCGGTTGGGCCCAGAATTGGGCTTTAACTTGAATAAAACAAATTAG
391 TACCTGTCGCGGCCGTCTTTCGGTTGGGCCCAAAATTGGGCTTCAACTTGAATAAAACAAATTAG
* * * *
222312 AGTCGCCACTGATCATTTAAAAACTATTTTAGATTTATCGAACACCATCTTATCTTATCTTTGTT
456 AGTCACCACTGATCATTTAAAAACTAGTTTAGATTGATCGAACACCATCTTATCTTATCTGTGTT
222377 TTACCAGAAATGTGT
521 TTACCAGAAATGTGT
222392 CGGCTTCGGG
Statistics
Matches: 503, Mismatches: 32, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
538 503 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (538 bp):
TACTCTCCCGGTTTAGGTTCTAAAGAGGGTACAGTTAGTTTTCCTTGCTGGTGCCCCCTTGGGCT
TGCTAGACCCTTAGTCCTAAGCCTATTACAAGCTTTTGTTAACTAAGTTAAACTCGAGAGGATAC
ATTCCCTTATACCCGCACGGAGAATAAATTCCCACGAAGGCGTCGCTTTCACCCCACTTAAAAAG
GGTTTAGAACTTGGATATAAAGCATGAGATAAAAAATTTGAAAATCTGAAATCATTGAAAAAAAT
ATCAGTACAACTATTTATTTGAAAAACATACAAAGATAAGTAATAAAAATCGAAAAGTTAAATTA
AAATTTAAACTTACCATTTTCGCTTAAAAAAGAGAATCGAAAAATTAATTCTGGCCTAACTCACT
TACCTGTCGCGGCCGTCTTTCGGTTGGGCCCAAAATTGGGCTTCAACTTGAATAAAACAAATTAG
AGTCACCACTGATCATTTAAAAACTAGTTTAGATTGATCGAACACCATCTTATCTTATCTGTGTT
TTACCAGAAATGTGTTGG
Found at i:222629 original size:27 final size:27
Alignment explanation
Indices: 222569--222630 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
222559 TGTTAGACAG
* *
222569 AAAAACAATATATAAATATTAAATAAT
1 AAAAAAAATATATAAATAATAAATAAT
* *
222596 AAGAAAAATA-ATAAAATAATAAATCA-
1 AAAAAAAATATAT-AAATAATAAATAAT
222622 AAAAAAAAT
1 AAAAAAAAT
222631 TAGAGAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.23
Consensus pattern (27 bp):
AAAAAAAATATATAAATAATAAATAAT
Found at i:223860 original size:11 final size:10
Alignment explanation
Indices: 223846--223884 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
223836 AATTAATAAC
223846 AAATAAATAAT
1 AAATAAA-AAT
223857 AAAT-AAAAT
1 AAATAAAAAT
223866 AAGATAAAAAT
1 AA-ATAAAAAT
223877 AAATAAAA
1 AAATAAAA
223885 GGAAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 5 0.19
10 10 0.38
11 11 0.42
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:223993 original size:76 final size:72
Alignment explanation
Indices: 223887--224153 Score: 281
Period size: 76 Copynumber: 3.6 Consensus size: 72
223877 AAATAAAAGG
* * * * *
223887 AAAAAATATGTTTTAAAACTATATTTTATATATGATTTAAAAAATGTTTTTTAAAACCATATAAT
1 AAAAAATA--TTTTAAAACTATATATTATATAT-ATTTCAAAAATG-TTTTAAAAACTATATATT
223952 ATAATATATTTTC
62 AT-ATA-ATTTTC
* *
223965 AAAAAATATTTTAAAACTATATATTATATATATTTTCCAAAATGTTTTAAAAATTATATATTATA
1 AAAAAATATTTTAAAACTATATATTATATATA-TTTCAAAAATGTTTTAAAAACTATATATTATA
224030 TAAGTTTTC
65 TAA-TTTTC
*
224039 AAAATAT-TTTTAAAAACTATATATTATATATATATATTCAAAAATGTTTTAAAAACTATATATT
1 AAAAAATATTTT-AAAACTATATA-T-TATATATAT-TTCAAAAATGTTTTAAAAACTATATATT
*
224103 ATATAGGTTTTC
62 ATATA-ATTTTC
* *
224115 --AAAATGTTTTAAAAAT-TATATTATATATATATTCAAAAA
1 AAAAAATATTTTAAAACTATATATTATATATAT-TTCAAAAA
224154 CCATTTACAA
Statistics
Matches: 168, Mismatches: 13, Indels: 23
0.82 0.06 0.11
Matches are distributed among these distances:
71 18 0.11
72 1 0.01
73 9 0.05
74 34 0.20
75 23 0.14
76 75 0.45
78 8 0.05
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (72 bp):
AAAAAATATTTTAAAACTATATATTATATATATTTCAAAAATGTTTTAAAAACTATATATTATAT
AATTTTC
Found at i:224023 original size:37 final size:37
Alignment explanation
Indices: 223889--224181 Score: 296
Period size: 37 Copynumber: 7.9 Consensus size: 37
223879 ATAAAAGGAA
* *
223889 AAAATATGTTTT-AAAACTATATTTTATATATGA-TTTA
1 AAAA-ATGTTTTAAAAACTATATATTATATAT-ATTTTC
* * *
223926 AAAAATGTTTTTTAAAACCATATAATATAATATATTTTC
1 AAAAATG-TTTTAAAAACTATATATTAT-ATATATTTTC
*
223965 AAAAAATATTTT-AAAACTATATATTATATATATTTTC
1 -AAAAATGTTTTAAAAACTATATATTATATATATTTTC
* *
224002 CAAAATGTTTTAAAAATTATATATTATATA-AGTTTTC
1 AAAAATGTTTTAAAAACTATATATTATATATA-TTTTC
224039 AAAATAT-TTTTAAAAACTATATATTATATATATATATTC
1 AAAA-ATGTTTTAAAAACTATATATTATATATAT-T-TTC
**
224078 AAAAATGTTTTAAAAACTATATATTATATAGGTTTTC
1 AAAAATGTTTTAAAAACTATATATTATATATATTTTC
*
224115 -AAAATGTTTTAAAAA-T-TATATTATATATATATTC
1 AAAAATGTTTTAAAAACTATATATTATATATATTTTC
*** * * *
224149 AAAAACCATTTACAAATTATATAATATATATAT
1 AAAAATGTTTTAAAAACTATATATTATATATAT
224182 AGATATATAT
Statistics
Matches: 219, Mismatches: 22, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
34 15 0.07
35 12 0.05
36 29 0.13
37 82 0.37
38 33 0.15
39 42 0.19
40 6 0.03
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (37 bp):
AAAAATGTTTTAAAAACTATATATTATATATATTTTC
Found at i:224179 original size:112 final size:115
Alignment explanation
Indices: 223939--224187 Score: 304
Period size: 112 Copynumber: 2.2 Consensus size: 115
223929 AATGTTTTTT
* *
223939 AAAACCATATAATATA-ATATAT-T-TTCAAAAAATATTTTAAAACTATATATTATATATATTTT
1 AAAACTATATAATATATATATATATATTCAAAAAATATTTTAAAACTATATATTATATAGATTTT
* **
224001 CCAAAATGTTTTAAAAATTATATATTATATAAGTTTTCAAAATATTTTTA
66 CCAAAATGTTTTAAAAATTATATATTATATAAGTATTCAAAATACATTTA
* *
224051 AAAACTATAT-AT-TATATATATATATTC-AAAAATGTTTTAAAAACTATATATTATATAGGTTT
1 AAAACTATATAATATATATATATATATTCAAAAAATATTTT-AAAACTATATATTATATAGATTT
224113 T-CAAAATGTTTTAAAAA-T-TATATTATATATA-TATTCAAAA-ACCATTTA
65 TCCAAAATGTTTTAAAAATTATATATTATATA-AGTATTCAAAATA-CATTTA
* * *
224161 CAAATTATATAATATATATATAGATAT
1 AAAACTATATAATATATATATATATAT
224188 ATATGTAAAA
Statistics
Matches: 119, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
109 1 0.01
110 33 0.28
111 12 0.10
112 48 0.40
113 25 0.21
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (115 bp):
AAAACTATATAATATATATATATATATTCAAAAAATATTTTAAAACTATATATTATATAGATTTT
CCAAAATGTTTTAAAAATTATATATTATATAAGTATTCAAAATACATTTA
Found at i:228777 original size:21 final size:21
Alignment explanation
Indices: 228735--228779 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
228725 AATATGTAAA
**
228735 TCGCATTGCGATTTTATGAAT
1 TCGCATTGCGATTTTACAAAT
* *
228756 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
228777 TCG
1 TCG
228780 TAACGCGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:228810 original size:20 final size:20
Alignment explanation
Indices: 228785--228845 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
228775 ATTCGTAACG
228785 CGAATCTGTAAATCGCAACA
1 CGAATCTGTAAATCGCAACA
*
228805 CGAATCTGTAAATCGCAACG
1 CGAATCTGTAAATCGCAACA
228825 CGAATCTGTAAATCGCAACA
1 CGAATCTGTAAATCGCAACA
228845 C
1 C
228846 AGAAGCCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (20 bp):
CGAATCTGTAAATCGCAACA
Found at i:228865 original size:40 final size:39
Alignment explanation
Indices: 228771--228867 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 39
228761 TTGCGATTTT
* *
228771 CCAAATTCGTAACGCGAATCTGTAAATCGCAACACGAAT
1 CCAAATTCGAAACGCGAATCTGTAAATCGCAACACGAAG
* *
228810 CTGTAAA-TCGCAACGCGAATCTGTAAATCGCAACACAGAAG
1 C--CAAATTCGAAACGCGAATCTGTAAATCGCAACAC-GAAG
228851 CCAAATTCGAAACGCGA
1 CCAAATTCGAAACGCGA
228868 TTTTTAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
39 4 0.08
40 38 0.78
41 7 0.14
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.18
Consensus pattern (39 bp):
CCAAATTCGAAACGCGAATCTGTAAATCGCAACACGAAG
Found at i:228973 original size:20 final size:20
Alignment explanation
Indices: 228894--228977 Score: 82
Period size: 20 Copynumber: 4.2 Consensus size: 20
228884 GCGATTTACA
**
228894 AATTCGCAACACTGAATTTCA
1 AATTCGCAACAC-GAATTTTG
*
228915 AATTCGCAACTCG-ATTTCTG
1 AATTCGCAACACGAATTT-TG
* * *
228935 AATTCACAACTCGATTTTTG
1 AATTCGCAACACGAATTTTG
228955 AATTCGCAACACGAATTTT-
1 AATTCGCAACACGAATTTTG
228974 AATT
1 AATT
228978 TTGCAACAGG
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
19 8 0.15
20 31 0.58
21 14 0.26
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
AATTCGCAACACGAATTTTG
Found at i:229945 original size:24 final size:24
Alignment explanation
Indices: 229918--229971 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
229908 GTATTCGAAA
229918 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
229942 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
229966 TTTGAT
1 TTTGAT
229972 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:230163 original size:12 final size:12
Alignment explanation
Indices: 230146--230173 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
230136 ATATAACCCT
230146 GAAGAAGAAAAA
1 GAAGAAGAAAAA
230158 GAAGAAGAAAAA
1 GAAGAAGAAAAA
230170 GAAG
1 GAAG
230174 TCCCCGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:232933 original size:63 final size:63
Alignment explanation
Indices: 232822--232950 Score: 168
Period size: 63 Copynumber: 2.0 Consensus size: 63
232812 TTAGTAACTT
* * * * * ** *
232822 GAATTTGACTTTCGCAACAATCGCAACGTGAAAATCGTAATGTGAATTTTACTTTCGCGTTGC
1 GAATTTGACTATCGCAACAATCGAAACGAGAAAATCGCAACGCAAATTTGACTTTCGCGTTGC
* *
232885 GAATTTGACTATCGCAACAATCGAAACGAGAAAATTGCAACGCAAATTTGACTTTTGCGTTGC
1 GAATTTGACTATCGCAACAATCGAAACGAGAAAATCGCAACGCAAATTTGACTTTCGCGTTGC
232948 GAA
1 GAA
232951 AGTGTACCTT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (63 bp):
GAATTTGACTATCGCAACAATCGAAACGAGAAAATCGCAACGCAAATTTGACTTTCGCGTTGC
Found at i:233059 original size:25 final size:25
Alignment explanation
Indices: 233023--233070 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
233013 ATCAATTAAT
*
233023 CATTGTTGTGGGCACATTATTTGAA
1 CATTGTTATGGGCACATTATTTGAA
*
233048 CATTGTTATGGGTACATTATTTG
1 CATTGTTATGGGCACATTATTTG
233071 GAAAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (25 bp):
CATTGTTATGGGCACATTATTTGAA
Found at i:233477 original size:18 final size:18
Alignment explanation
Indices: 233456--233492 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
233446 ATAATTGGAG
233456 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
233474 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
233492 T
1 T
233493 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:233500 original size:24 final size:23
Alignment explanation
Indices: 233437--233496 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
233427 TTTCAAATTC
*
233437 ATTTCACATATAATTGGAGTTTGA
1 ATTTCA-ATATAATTTGAGTTTGA
* *
233461 ATTTAAATTTCAATTTGAGTTTGA
1 ATTTCAATAT-AATTTGAGTTTGA
233485 ATTTCAATATAA
1 ATTTCAATATAA
233497 ATTTCGACTC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.45
Consensus pattern (23 bp):
ATTTCAATATAATTTGAGTTTGA
Found at i:234792 original size:29 final size:29
Alignment explanation
Indices: 234711--234784 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
234701 AATTCGCAAC
*
234711 GCGAAAGTCAAATTCGCGTTGCGATTGTT
1 GCGAAAGTCAAATTCGCGTTGCGATTCTT
*
234740 GCGAAAGTTAAATTCGCGTTGCGATTCTT
1 GCGAAAGTCAAATTCGCGTTGCGATTCTT
234769 GCGAAAGTCAAATTCG
1 GCGAAAGTCAAATTCG
234785 AAACGCGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (29 bp):
GCGAAAGTCAAATTCGCGTTGCGATTCTT
Found at i:234825 original size:20 final size:20
Alignment explanation
Indices: 234802--234906 Score: 129
Period size: 20 Copynumber: 5.2 Consensus size: 20
234792 AAATCGCAAC
**
234802 GCGAATTTGACTTTCGTGTT
1 GCGAATTTGACTTTCGCATT
*
234822 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCATT
234842 GCGAATTTGACTTTCGCATT
1 GCGAATTTGACTTTCGCATT
* * * **
234862 GAGAATTTTACTATCGCAAC
1 GCGAATTTGACTTTCGCATT
*
234882 GCGAATTTGACTTTCGCTTT
1 GCGAATTTGACTTTCGCATT
234902 GCGAA
1 GCGAA
234907 AGTGTACCTT
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCATT
Found at i:235034 original size:64 final size:66
Alignment explanation
Indices: 234962--235116 Score: 215
Period size: 64 Copynumber: 2.4 Consensus size: 66
234952 TGAAATTTAA
234962 AACAACAAATCAACTTTTACAAATCAACTAAACAAACAAAAAATAAGAATTATTTACACATCAAT
1 AACAACAAATCAACTTTTACAAATCAACTAAACAAACAAAAAATAAGAATTATTTACACATCAAT
235027 T
66 T
* * *** * *
235028 -A-AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAAT
1 AACAACAAATCAACTTTTACAAATCAACTAAACAAACAAAAAATAAGAATTATTTACACATCAAT
235091 T
66 T
*
235092 AAACAACAAATCAACTTTTATAAAT
1 -AACAACAAATCAACTTTTACAAAT
235117 ACATCAATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 56 0.72
65 1 0.01
66 1 0.01
67 20 0.26
ACGTcount: A:0.53, C:0.18, G:0.01, T:0.28
Consensus pattern (66 bp):
AACAACAAATCAACTTTTACAAATCAACTAAACAAACAAAAAATAAGAATTATTTACACATCAAT
T
Found at i:236522 original size:21 final size:21
Alignment explanation
Indices: 236458--236528 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
236448 GTGAATCGGG
*
236458 CTCTCGAACGGTGGGAGTGA-C
1 CTCTTGAACGGTGGGAG-GAGC
* ** *
236479 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGAGC
236500 CTCTTGAACGGTGGGAGGAGC
1 CTCTTGAACGGTGGGAGGAGC
*
236521 CTTTTGAA
1 CTCTTGAA
236529 GGATGATAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 1 0.03
21 38 0.97
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGAGC
Found at i:236528 original size:42 final size:42
Alignment explanation
Indices: 236458--236580 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 42
236448 GTGAATCGGG
* *
236458 CTCTCGAACGGTGGGAGTGA-CCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAG-GAGCCTTTTGAACGATGACAGGGGC
* *
236500 CTCTTGAACGGTGGGAGGAGCCTTTTGAAGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGAGCCTTTTGAACGATGACAGGGGC
* * *
236542 CTCTTGAATGATAGGA-GAGGCCTTTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGGA-GCCTTTTGAACGATGACAGG
236581 TGCTTCGGGC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 4 0.06
42 66 0.94
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGAGCCTTTTGAACGATGACAGGGGC
Found at i:236543 original size:21 final size:21
Alignment explanation
Indices: 236478--236576 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
236468 GTGGGAGTGA
*
236478 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
236499 CCTCTTGAACGGTGGGAGGAG
1 CCTCTTGAACGATGAGAGGGG
* * *
236520 CCTTTTGAAGGATGATAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
236541 CCTCTTGAATGAT-AGGAGAGG
1 CCTCTTGAACGATGA-GAGGGG
*
236562 CCTTTTGAACGATGA
1 CCTCTTGAACGATGA
236577 CAGGTGCTTC
Statistics
Matches: 60, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 1 0.02
21 58 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:236854 original size:21 final size:21
Alignment explanation
Indices: 236830--236880 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
236820 TGCAACAATC
*
236830 TCACGTAAAGCAGCTACCTCA
1 TCACGTAAAGCAGATACCTCA
*
236851 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGCAGATACCTCA
236872 -CTACGTAAA
1 TC-ACGTAAA
236881 ACACTATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCAGATACCTCA
Found at i:236980 original size:21 final size:21
Alignment explanation
Indices: 236956--237005 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
236946 ACCATTGTCT
* *
236956 TCACGTAAAGTATCGACCTCC
1 TCACGTAAAGCATCGACCTCA
* *
236977 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCATCGACCTCA
236998 TCACGTAA
1 TCACGTAA
237006 CTCCTCTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCATCGACCTCA
Found at i:238764 original size:20 final size:20
Alignment explanation
Indices: 238727--238764 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
238717 CTAAAATCAC
* *
238727 GTTGCGAATTTCATTTTCTT
1 GTTGCGAATTTAAGTTTCTT
238747 GTTGCGAATTTAAGTTTC
1 GTTGCGAATTTAAGTTTC
238765 AAATAGTCTT
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:0.18, C:0.13, G:0.18, T:0.50
Consensus pattern (20 bp):
GTTGCGAATTTAAGTTTCTT
Found at i:239165 original size:22 final size:22
Alignment explanation
Indices: 239085--239165 Score: 103
Period size: 22 Copynumber: 3.8 Consensus size: 22
239075 CTCTGAGACA
*
239085 TGGAGATA--GACGGATTTCGC
1 TGGAGATAGGGACGGATTTCGT
* *
239105 TGGAGATAGGGATGAATTTCGT
1 TGGAGATAGGGACGGATTTCGT
*
239127 TGGAGATAGGGATGGATTTCGT
1 TGGAGATAGGGACGGATTTCGT
*
239149 TGGAGATGGGGACGGAT
1 TGGAGATAGGGACGGAT
239166 GTCGCCGTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 8 0.15
22 45 0.85
ACGTcount: A:0.25, C:0.07, G:0.41, T:0.27
Consensus pattern (22 bp):
TGGAGATAGGGACGGATTTCGT
Found at i:239288 original size:25 final size:25
Alignment explanation
Indices: 239259--239306 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
239249 ATTTGTGTTG
* *
239259 CGAAATTAATATT-GTGTTTCGAATT
1 CGAAAATAA-ATTCGTGTTGCGAATT
239284 CGAAAATAAATTCGTGTTGCGAA
1 CGAAAATAAATTCGTGTTGCGAA
239307 AATAAACGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (25 bp):
CGAAAATAAATTCGTGTTGCGAATT
Found at i:239361 original size:20 final size:20
Alignment explanation
Indices: 239338--239387 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
239328 TGACTTCTGT
239338 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
* *
239358 GTTGCGATTTACATATTCGC
1 GTTGCGAATTACAAATTCGC
239378 GTTGCGAATT
1 GTTGCGAATT
239388 TGGAAACTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:242529 original size:10 final size:10
Alignment explanation
Indices: 242516--242548 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
242506 CGTTCGATAA
242516 TATGTTTGTT
1 TATGTTTGTT
242526 TATGTTTGTT
1 TATGTTTGTT
*
242536 TATGTTCGTT
1 TATGTTTGTT
242546 TAT
1 TAT
242549 ATGCGTTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.12, C:0.03, G:0.18, T:0.67
Consensus pattern (10 bp):
TATGTTTGTT
Found at i:242761 original size:23 final size:23
Alignment explanation
Indices: 242735--242794 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
242725 TCTATTTTCA
242735 TTTATGTTCATTTATTGTGTTCG
1 TTTATGTTCATTTATTGTGTTCG
* *
242758 TTTACGTTTATTTATTGTGTTCG
1 TTTATGTTCATTTATTGTGTTCG
*
242781 TTTATGTTCGTTTA
1 TTTATGTTCATTTA
242795 CACCCGTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.13, C:0.08, G:0.17, T:0.62
Consensus pattern (23 bp):
TTTATGTTCATTTATTGTGTTCG
Found at i:243919 original size:16 final size:16
Alignment explanation
Indices: 243898--244022 Score: 76
Period size: 16 Copynumber: 7.9 Consensus size: 16
243888 AAACTTTAGT
*
243898 TGAACCGAACATAACC
1 TGAACCGAAAATAACC
243914 TGAACC-AAAATGAACC
1 TGAACCGAAAAT-AACC
* *
243930 TAAACCGAAAATAACG
1 TGAACCGAAAATAACC
* * *
243946 TTAACTGAAAACAACC
1 TGAACCGAAAATAACC
** * **
243962 CAAATCGAAAGCAACC
1 TGAACCGAAAATAACC
*
243978 AGAACC-AAAA-AACC
1 TGAACCGAAAATAACC
** *
243992 CAAACCGAAAGTAACC
1 TGAACCGAAAATAACC
*
244008 CGAACCGAAAATAAC
1 TGAACCGAAAATAAC
244023 TCAAATTTAG
Statistics
Matches: 84, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
14 8 0.10
15 10 0.12
16 61 0.73
17 5 0.06
ACGTcount: A:0.52, C:0.27, G:0.11, T:0.10
Consensus pattern (16 bp):
TGAACCGAAAATAACC
Found at i:243992 original size:30 final size:32
Alignment explanation
Indices: 243952--244028 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 32
243942 AACGTTAACT
243952 GAAAACAACCCAAATCGAAAGCAACCAGAACC
1 GAAAACAACCCAAATCGAAAGCAACCAGAACC
* * *
243984 -AAAA-AACCCAAACCGAAAGTAACCCGAACC
1 GAAAACAACCCAAATCGAAAGCAACCAGAACC
* *
244014 GAAAATAACTCAAAT
1 GAAAACAACCCAAAT
244029 TTAGTTTATC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
30 23 0.61
31 8 0.21
32 7 0.18
ACGTcount: A:0.55, C:0.29, G:0.10, T:0.06
Consensus pattern (32 bp):
GAAAACAACCCAAATCGAAAGCAACCAGAACC
Found at i:244018 original size:62 final size:63
Alignment explanation
Indices: 243910--244028 Score: 141
Period size: 62 Copynumber: 1.9 Consensus size: 63
243900 AACCGAACAT
* * *** *
243910 AACCTGAACCAAAATGAACCTAAACCGAAAATAACGTTAACTGAAAACAACCCAAATCGAAAGC
1 AACCAGAACCAAAA-GAACCCAAACCGAAAATAACCCGAACCGAAAACAACCCAAATCGAAAGC
* * *
243974 AACCAGAACCAAAA-AACCCAAACCGAAAGTAACCCGAACCGAAAATAACTCAAAT
1 AACCAGAACCAAAAGAACCCAAACCGAAAATAACCCGAACCGAAAACAACCCAAAT
244029 TTAGTTTATC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
62 33 0.72
64 13 0.28
ACGTcount: A:0.53, C:0.27, G:0.10, T:0.10
Consensus pattern (63 bp):
AACCAGAACCAAAAGAACCCAAACCGAAAATAACCCGAACCGAAAACAACCCAAATCGAAAGC
Found at i:254459 original size:18 final size:18
Alignment explanation
Indices: 254436--254479 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
254426 AAAAATATGG
*
254436 TGGATATTATATGTTTGT
1 TGGATATTATATGTTGGT
* *
254454 TGGATAATATGTGTTGGT
1 TGGATATTATATGTTGGT
*
254472 TAGATATT
1 TGGATATT
254480 GATGTATTGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (18 bp):
TGGATATTATATGTTGGT
Found at i:256933 original size:21 final size:22
Alignment explanation
Indices: 256894--256934 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
256884 GATACTCAAG
256894 AAAGTATAGATACCTTAAACCA
1 AAAGTATAGATACCTTAAACCA
*
256916 AAAGTATCGATA-CTTAAAC
1 AAAGTATAGATACCTTAAAC
256935 TAGAGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.24
Consensus pattern (22 bp):
AAAGTATAGATACCTTAAACCA
Found at i:257019 original size:19 final size:19
Alignment explanation
Indices: 256981--257053 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
256971 AATAAGTCAG
* *
256981 TAGTATCAATACCCAGAGGT
1 TAGTATCGATA-CTAGAGGT
257001 TAGTATCGATACTAGAGGT
1 TAGTATCGATACTAGAGGT
* * *
257020 CAGTACCGATACTGAGAGATT
1 TAGTATCGATACT-AGAG-GT
*
257041 TAGTATCGGTACT
1 TAGTATCGATACT
257054 CACAAATAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
19 18 0.42
20 14 0.33
21 11 0.26
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (19 bp):
TAGTATCGATACTAGAGGT
Found at i:263310 original size:33 final size:34
Alignment explanation
Indices: 263257--263322 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
263247 TGCAGAAAAT
*
263257 ACTGTAGCAGTTACTGTAGCGTATCGATGCATAC
1 ACTGTAGCAGTTACTGTAGCGTATCGAAGCATAC
263291 ACTGTAGCAG-TACTGTAGCGTATCGAAGCATA
1 ACTGTAGCAGTTACTGTAGCGTATCGAAGCATA
263323 ATATTAATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 21 0.68
34 10 0.32
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (34 bp):
ACTGTAGCAGTTACTGTAGCGTATCGAAGCATAC
Found at i:272679 original size:83 final size:82
Alignment explanation
Indices: 272586--272747 Score: 270
Period size: 83 Copynumber: 2.0 Consensus size: 82
272576 GAATTTCAAG
* * * *
272586 AGAGTTTTACTCTAACTAAAACTCTTTTAATATCTAAATTTAAATGGATAATGATATCTTTTAAA
1 AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATATCTTTTAAA
272651 TTTTAAATATTAAACCTA
66 -TTTAAATATTAAACCTA
*
272669 AGAGTTTTACTCAAACCAAAACTCTTTTAATATTTAAATTTAAATAGATAATAATATCTTTTAAA
1 AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATATCTTTTAAA
272734 TTTAAATATTAAAC
66 TTTAAATATTAAAC
272748 AAATATTTCC
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 14 0.19
83 60 0.81
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.41
Consensus pattern (82 bp):
AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATATCTTTTAAA
TTTAAATATTAAACCTA
Found at i:274556 original size:21 final size:21
Alignment explanation
Indices: 274530--274585 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
274520 ACAGTGATAT
*
274530 AGTGTATCGATGCATTGCTAC
1 AGTGTACCGATGCATTGCTAC
274551 AGTGTACCGATGCATTGCTAC
1 AGTGTACCGATGCATTGCTAC
274572 AGTGTACCGATGCA
1 AGTGTACCGATGCA
274586 CAAAAACATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (21 bp):
AGTGTACCGATGCATTGCTAC
Found at i:274632 original size:21 final size:21
Alignment explanation
Indices: 274607--274671 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
274597 AATATAAATT
* *
274607 GTGTATCGATGCACTGCTACA
1 GTGTACCGATGCACTTCTACA
274628 GTGTACCGATGCACTTCTACA
1 GTGTACCGATGCACTTCTACA
274649 GTGTACCGATGCACTTCTACA
1 GTGTACCGATGCACTTCTACA
274670 GT
1 GT
274672 AACTTCAGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (21 bp):
GTGTACCGATGCACTTCTACA
Found at i:282488 original size:82 final size:82
Alignment explanation
Indices: 282351--282514 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
282341 TTTTTTCAAA
282351 GCCTTTAGACAAGGAAAGATTTTGGACACTTAGGAGAGAATTAGGTTTAAATAACCTATCTTCAC
1 GCCTTTAGACAAGGAAAGATTTTGGACACTTAGGAGAGAATTAGGTTTAAATAACCTATCTTCAC
282416 TTAGTGCTTAAAATAAT
66 TTAGTGCTTAAAATAAT
282433 GCCTTTAGACAAGGAAAGATTTTGGACACTTAGGAGAGAATTAGGTTTAAATAACCTATCTTCAC
1 GCCTTTAGACAAGGAAAGATTTTGGACACTTAGGAGAGAATTAGGTTTAAATAACCTATCTTCAC
282498 TTAGTGCTTAAAATAAT
66 TTAGTGCTTAAAATAAT
282515 TTAGCACTTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (82 bp):
GCCTTTAGACAAGGAAAGATTTTGGACACTTAGGAGAGAATTAGGTTTAAATAACCTATCTTCAC
TTAGTGCTTAAAATAAT
Found at i:282783 original size:21 final size:21
Alignment explanation
Indices: 282759--282839 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
282749 TTGGTGCAGA
*
282759 GGGAATCGATACCCCCTGAAG
1 GGGAACCGATACCCCCTGAAG
*
282780 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC--TGAAG
* * *
282803 GGGAACCAATTCCCCCTGTAG
1 GGGAACCGATACCCCCTGAAG
* *
282824 GAGAATCGATACCCCC
1 GGGAACCGATACCCCC
282840 CTGGGGTTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 30 0.60
23 20 0.40
ACGTcount: A:0.26, C:0.32, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCCCTGAAG
Found at i:282805 original size:23 final size:22
Alignment explanation
Indices: 282759--282819 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
282749 TTGGTGCAGA
* *
282759 GGGAATCGATACCCCC-TGAAG
1 GGGAACCGATTCCCCCTTGAAG
282780 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
*
282803 GGGAACCAATTCCCCCT
1 GGGAACCGATTCCCCCT
282820 GTAGGAGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.40
22 1 0.03
23 20 0.57
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:288170 original size:58 final size:57
Alignment explanation
Indices: 288077--288220 Score: 157
Period size: 58 Copynumber: 2.5 Consensus size: 57
288067 GATTCGAGAC
*
288077 TTTCAAGAAATAAATTCAACAATTTATTTCTTTTTACAAGAAGGGAATCATACTTGAT
1 TTTCAAGAAATAAATTCAACAATTTATTTCTTTTTACAA-AAGAGAATCATACTTGAT
* ** * **
288135 TTTCAAGAGATAAATTCAATGATTTAATTTC-TTTTACAAAATAGAATCATACAAGAT
1 TTTCAAGAAATAAATTCAACAATTT-ATTTCTTTTTACAAAAGAGAATCATACTTGAT
* * *
288192 TCT-ATGAATATAAATTTAACAATTTATTT
1 TTTCAAGAA-ATAAATTCAACAATTTATTT
288221 TCTTCTACAA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
56 7 0.10
57 29 0.41
58 30 0.42
59 5 0.07
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (57 bp):
TTTCAAGAAATAAATTCAACAATTTATTTCTTTTTACAAAAGAGAATCATACTTGAT
Found at i:288217 original size:57 final size:56
Alignment explanation
Indices: 288081--288340 Score: 165
Period size: 57 Copynumber: 4.5 Consensus size: 56
288071 CGAGACTTTC
** ** * *
288081 AAGAAATAAATTCAACAATTTATTTCTTTTTACAAGAAGGGAATCATACTTGATTTTC
1 AAGAAATAAATTCAACAATTTATTTC-TTTTACAA-AATAGAATCATACAAGATTCTA
* **
288139 AAGAGATAAATTCAATGATTTAATTTCTTTTACAAAATAGAATCATACAAGATTCT-
1 AAGAAATAAATTCAACAATTT-ATTTCTTTTACAAAATAGAATCATACAAGATTCTA
* * * * *
288195 ATGAATATAAATTTAACAATTTATTTTCTTCTACAAGAT-GAATTCGAT-CAAGATT-TCC
1 AAGAA-ATAAATTCAACAATTTA-TTTCTTTTACAAAATAGAA-TC-ATACAAGATTCT-A
** *
288253 AAGAAAATAAATTTC-ACGTTTTATTTCCTTTT-CAAAGTTAGAATCA-ACGCAAGATTCTA
1 AAG-AAATAAA-TTCAACAATTTATTT-CTTTTACAAA-ATAGAATCATA--CAAGATTCTA
*
288312 AGGTGAAATAAATTCAACAATTTATTTCT
1 A--AGAAATAAATTCAACAATTTATTTCT
288341 CTTTTTCCAA
Statistics
Matches: 157, Mismatches: 26, Indels: 37
0.71 0.12 0.17
Matches are distributed among these distances:
56 8 0.05
57 58 0.37
58 48 0.31
59 25 0.16
60 17 0.11
61 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (56 bp):
AAGAAATAAATTCAACAATTTATTTCTTTTACAAAATAGAATCATACAAGATTCTA
Found at i:289899 original size:84 final size:82
Alignment explanation
Indices: 289798--289955 Score: 262
Period size: 84 Copynumber: 1.9 Consensus size: 82
289788 TTCGAGAAAG
* * *
289798 TTTTGCTCCAACTAAAACTCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAAATTTA
1 TTTTACTCCAACCAAAACTCTTTTAATAACTAAATTTAAACAAATAATAATATCTTTTAAATTT-
289863 AAAATATTAAATCTGAGAA
65 -AAATATTAAATCTGAGAA
*
289882 TTTTACTCCAACCAAAACTCTTTTAATAACTAAATTTAAACATATAATAATATCTTTTAAATTTA
1 TTTTACTCCAACCAAAACTCTTTTAATAACTAAATTTAAACAAATAATAATATCTTTTAAATTTA
289947 AATATTAAA
66 AATATTAAA
289956 CATATATTTC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
82 10 0.14
84 60 0.86
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.40
Consensus pattern (82 bp):
TTTTACTCCAACCAAAACTCTTTTAATAACTAAATTTAAACAAATAATAATATCTTTTAAATTTA
AATATTAAATCTGAGAA
Found at i:298104 original size:29 final size:29
Alignment explanation
Indices: 298069--298150 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
298059 AAACTAAATT
*
298069 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
298098 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
298127 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
298151 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:302812 original size:29 final size:29
Alignment explanation
Indices: 302777--302858 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
302767 AAACTAAATT
*
302777 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
302806 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
302835 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
302859 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:304656 original size:41 final size:41
Alignment explanation
Indices: 304594--304698 Score: 151
Period size: 41 Copynumber: 2.6 Consensus size: 41
304584 CGAACCCTGC
304594 AGCTGTGTTC-AACAACATATAGCTG-TTACCATTCATTTG
1 AGCTGTGTTCAAACAACATATAGCTGTTTACCATTCATTTG
304633 AAGCTGTGTTCAAACAACATATAGCTGTTTACCATTCATTTG
1 -AGCTGTGTTCAAACAACATATAGCTGTTTACCATTCATTTG
* * * *
304675 CGCTGTCTTCAAACCACATGTAGC
1 AGCTGTGTTCAAACAACATATAGC
304699 CGATACACTC
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
40 10 0.17
41 35 0.59
42 14 0.24
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (41 bp):
AGCTGTGTTCAAACAACATATAGCTGTTTACCATTCATTTG
Found at i:306690 original size:28 final size:28
Alignment explanation
Indices: 306659--306714 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
306649 AATATATTTG
*
306659 ATATTATATTTCTATTTTGATAAAATAT
1 ATATGATATTTCTATTTTGATAAAATAT
* *
306687 ATATGATATTTCTGTTTTGCTAAAATAT
1 ATATGATATTTCTATTTTGATAAAATAT
306715 CTAATGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (28 bp):
ATATGATATTTCTATTTTGATAAAATAT
Found at i:307320 original size:20 final size:20
Alignment explanation
Indices: 307295--307346 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
307285 TAGTTGAAAA
307295 TCGCGTTGCGATTTTGT-ATT
1 TCGCGTTGCGATTTT-TCATT
307315 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTTCATT
*
307335 TCGCGTCGCGAT
1 TCGCGTTGCGAT
307347 AGTCTACAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.10, C:0.21, G:0.25, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTTCATT
Found at i:307493 original size:6 final size:6
Alignment explanation
Indices: 307482--307507 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
307472 AGACACGAAT
307482 GACCAC GACCAC GACCAC GACCAC GA
1 GACCAC GACCAC GACCAC GACCAC GA
307508 GACGAGACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.46, G:0.19, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:308232 original size:41 final size:41
Alignment explanation
Indices: 308172--308263 Score: 132
Period size: 41 Copynumber: 2.2 Consensus size: 41
308162 ACTGTAGACT
* * *
308172 ATCGTAACAACAACTGTAGACTATCGCAA-CGAATTTGAAAA
1 ATCGCAACGACAACTGTAGACTATCGCAACCGAA-ATGAAAA
308213 ATCGCAACGACAACTGTAGACTATCGCAACGCGAAATGAAAA
1 ATCGCAACGACAACTGTAGACTATCGCAAC-CGAAATGAAAA
308255 ATCGCAACG
1 ATCGCAACG
308264 CGAAATGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 27 0.59
42 15 0.33
43 4 0.09
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (41 bp):
ATCGCAACGACAACTGTAGACTATCGCAACCGAAATGAAAA
Found at i:308241 original size:22 final size:22
Alignment explanation
Indices: 308154--308243 Score: 96
Period size: 22 Copynumber: 4.2 Consensus size: 22
308144 TGGAAAATCA
*
308154 CAACGACCACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
* *
308176 TAACAACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
** **
308198 CAACGA-ATTTG-A-AAAATCG
1 CAACGACAACTGTAGACTATCG
308217 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
308239 CAACG
1 CAACG
308244 CGAAATGAAA
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
19 11 0.21
20 4 0.08
21 4 0.08
22 33 0.63
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.19
Consensus pattern (22 bp):
CAACGACAACTGTAGACTATCG
Found at i:308260 original size:20 final size:20
Alignment explanation
Indices: 308235--308286 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
308225 ACTGTAGACT
308235 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
308255 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
308275 ATCGCAACGCGA
1 ATCGCAACGCGA
308287 TTTTCAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:308700 original size:24 final size:23
Alignment explanation
Indices: 308636--308737 Score: 80
Period size: 24 Copynumber: 4.3 Consensus size: 23
308626 AACGACCGAT
* * * *
308636 TTTTTTATCGGATTAAAACCCGG
1 TTTTTTAACCGATAAAAAACCGG
308659 TTTTTTTCAAACCGGATAAAAAACCGG
1 -TTTTTT--AACC-GATAAAAAACCGG
* **
308686 TTTTTTATCCAGATAAAAAACCAA
1 TTTTTTAACC-GATAAAAAACCGG
*
308710 TTTTTTAACCGA-AAAAATCCGG
1 TTTTTTAACCGATAAAAAACCGG
308732 TTTTTT
1 TTTTTT
308738 TTTTAAAACC
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
22 13 0.21
23 2 0.03
24 29 0.46
26 8 0.13
27 11 0.17
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (23 bp):
TTTTTTAACCGATAAAAAACCGG
Found at i:315505 original size:20 final size:20
Alignment explanation
Indices: 315456--315510 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
315446 GAATTAGCTA
*
315456 AGTAGTATCGATACTGATTC
1 AGTAGTATCGATACTGACTC
*
315476 AATCAGTATCGATACTGACT-
1 AGT-AGTATCGATACTGACTC
315496 AGGTAGTATCGATAC
1 A-GTAGTATCGATAC
315511 CATGGTAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (20 bp):
AGTAGTATCGATACTGACTC
Found at i:316042 original size:58 final size:59
Alignment explanation
Indices: 315945--316085 Score: 257
Period size: 58 Copynumber: 2.4 Consensus size: 59
315935 ATTACCAAAT
* *
315945 GGCACTACGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
1 GGCACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
316004 GGCACTTCGTGTGCT-AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
1 GGCACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
316062 GGCACTTCGTGTGCTAAAATGTTA
1 GGCACTTCGTGTGCTAAAATGTTA
316086 TAAAAATCAT
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
58 57 0.72
59 22 0.28
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (59 bp):
GGCACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
Found at i:316177 original size:99 final size:99
Alignment explanation
Indices: 316002--316302 Score: 396
Period size: 99 Copynumber: 3.0 Consensus size: 99
315992 ATTTCCATAT
*
316002 AGGGCACTTCGTGTGCT-AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCA
1 AGGGTACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCA
316066 CTTCGTGTGCTAAAATGTTATA-AAAATCATAC-A
66 CTTCGTGTGCTAAAATGTTA-AGAAAATCATACTA
316099 CAGGGTACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGC
1 -AGGGTACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGC
* *
316164 ATTTCGTGTGCTAAAATGTTAAGAAATTCATACTA
65 ACTTCGTGTGCTAAAATGTTAAGAAAATCATACTA
* ** * *
316199 AGTGTA-TAAAGT-TCCATATTAAAATGGTAAGAAATTCATACTAAGTGTATGAATTTCCATATA
1 AGGGTACT-TCGTGTGC----TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATA
* * * *
316262 AGGCACTTCATGTGCTAAAATGCTAAGAAATTCATACTA
61 GGGCACTTCGTGTGCTAAAATGTTAAGAAAATCATACTA
316301 AG
1 AG
316303 TGTATGAATT
Statistics
Matches: 183, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
98 20 0.11
99 82 0.45
100 1 0.01
102 80 0.44
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.33
Consensus pattern (99 bp):
AGGGTACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCA
CTTCGTGTGCTAAAATGTTAAGAAAATCATACTA
Found at i:316216 original size:21 final size:21
Alignment explanation
Indices: 316187--316263 Score: 54
Period size: 20 Copynumber: 3.7 Consensus size: 21
316177 AAATGTTAAG
316187 AAATT-CATACTAAGTGTATA
1 AAATTCCATACTAAGTGTATA
* * *
316207 AAGTTCCATATTAAAATGGTA-A
1 AAATTCCATACT-AAGT-GTATA
*
316229 GAAATT-CATACTAAGTGTATG
1 -AAATTCCATACTAAGTGTATA
*
316250 AATTTCCATA-TAAG
1 AAATTCCATACTAAG
316264 GCACTTCATG
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
20 15 0.35
21 12 0.28
22 9 0.21
23 7 0.16
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (21 bp):
AAATTCCATACTAAGTGTATA
Found at i:316236 original size:43 final size:43
Alignment explanation
Indices: 316175--316260 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
316165 TTTCGTGTGC
*
316175 TAAAATGTTAAGAAATTCATACTAAGTGTATAAAGTTCCATAT
1 TAAAATGGTAAGAAATTCATACTAAGTGTATAAAGTTCCATAT
* *
316218 TAAAATGGTAAGAAATTCATACTAAGTGTATGAATTTCCATAT
1 TAAAATGGTAAGAAATTCATACTAAGTGTATAAAGTTCCATAT
316261 AAGGCACTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (43 bp):
TAAAATGGTAAGAAATTCATACTAAGTGTATAAAGTTCCATAT
Found at i:316276 original size:102 final size:102
Alignment explanation
Indices: 316019--316319 Score: 409
Period size: 102 Copynumber: 3.0 Consensus size: 102
316009 TTCGTGTGCT
316019 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATGT
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATGT
* * * *
316084 TATA-AAAATCATAC-ACAG-G-GT-ACTT-CGTGTGCTA
66 TA-AGAAATTCATACTA-AGTGTATAACTTCCATAT-CTA
*
316118 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTGTGCTAAAATGT
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATGT
*
316183 TAAGAAATTCATACTAAGTGTATAAAGTTCCATAT-TA
66 TAAGAAATTCATACTAAGTGTAT-AACTTCCATATCTA
* * * *
316220 AAATGGTAAGAAATTCATACTAAGTGTATGAATTTCCATATAAGGCACTTCATGTGCTAAAATGC
1 AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATGT
*
316285 TAAGAAATTCATACTAAGTGTATGAATTTCCATAT
66 TAAGAAATTCATACTAAGTGTAT-AACTTCCATAT
316320 AGGGAACTTC
Statistics
Matches: 182, Mismatches: 13, Indels: 11
0.88 0.06 0.05
Matches are distributed among these distances:
98 1 0.01
99 77 0.42
100 2 0.01
101 1 0.01
102 95 0.52
103 3 0.02
104 3 0.02
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (102 bp):
AAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATGT
TAAGAAATTCATACTAAGTGTATAACTTCCATATCTA
Found at i:316291 original size:59 final size:59
Alignment explanation
Indices: 316218--316908 Score: 976
Period size: 59 Copynumber: 11.7 Consensus size: 59
316208 AGTTCCATAT
* * *
316218 TAAAATGGTAAGAAATTCATACTAAGTGTATGAATTTCCATATAAGGCACTTCATGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* * *
316277 TAAAATGCTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGAACTTCGTTTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* **
316336 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTTT
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* *
316395 TAAAATGTTAAAAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
*
316454 TAAAATGGTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* * *
316513 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTTGTGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* *
316572 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTCGTGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* * *
316631 TAAAATGATAAGAAAGTCATACTAAGTGTATGAATTTCCGTATAGGGCATTTCGTGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* * * * *
316690 TAAAAGGATAAGAAAATCATACTAAGTGTATGAATTTCCGTATTGGGCACTAT-GCGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACT-TCGTGTGC
* * * **
316749 TAAAAT-ATTAAGAAATTCATATTAAGTGTATGAATTTCCGTATTGGGCAC-TCGATGTAA
1 TAAAATGA-TAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCG-TGTGC
* * ** * **
316808 AAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTTATGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* *
316867 -AAAAAGATAAGAAACTCATACTAAGTGTATGAATTTCCATAT
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATAT
316909 GAAAAATATA
Statistics
Matches: 579, Mismatches: 47, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
57 1 0.00
58 39 0.07
59 537 0.93
60 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.34
Consensus pattern (59 bp):
TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
Found at i:317238 original size:68 final size:69
Alignment explanation
Indices: 317129--317283 Score: 204
Period size: 68 Copynumber: 2.2 Consensus size: 69
317119 ATTAATAGGT
* * **
317129 CTAACTGTGCAATTGACAGAAAGGAGTCATTTATGCTAGTTAGAT-GAAAGGCTAAGTGCCTTTG
1 CTAACTGTGCATTTGACAGAAAGGAGTCATTTATGCTAGTTAGATAAAAAAACTAAGTGCCTTTG
317193 AGGC
66 AGGC
* * * *
317197 CTAACTGTGCATTTGATAGAAATGTGTCATTTATGCTAGTTAGATAAAAAAAAACTAAGTGCGTT
1 CTAACTGTGCATTTGACAGAAAGGAGTCATTTATGCTAGTTAGAT--AAAAAAACTAAGTGCCTT
317262 TGAGGC
64 TGAGGC
*
317268 CTAACTGTGCGTTTGA
1 CTAACTGTGCATTTGA
317284 GGCCTAACTG
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
68 41 0.55
71 34 0.45
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (69 bp):
CTAACTGTGCATTTGACAGAAAGGAGTCATTTATGCTAGTTAGATAAAAAAACTAAGTGCCTTTG
AGGC
Found at i:317279 original size:19 final size:19
Alignment explanation
Indices: 317255--317302 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
317245 AAAAAACTAA
317255 GTGCGTTTGAGGCCTAACT
1 GTGCGTTTGAGGCCTAACT
317274 GTGCGTTTGAGGCCTAACT
1 GTGCGTTTGAGGCCTAACT
*
317293 GTGCATTTGA
1 GTGCGTTTGA
317303 CAGAAAGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
GTGCGTTTGAGGCCTAACT
Found at i:317388 original size:68 final size:68
Alignment explanation
Indices: 317274--317470 Score: 288
Period size: 68 Copynumber: 2.9 Consensus size: 68
317264 AGGCCTAACT
* *
317274 GTGCGTTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGC
1 GTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGGTATCATTTATGCTAGTTAGATGAAAGGC
317339 TAA
66 TAA
* *
317342 GTGCCTTTGAGGCCTAAATGTGCATTTGATAGAAAGGTATCATTTATGCTAGTTAGATGAAAGGC
1 GTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGGTATCATTTATGCTAGTTAGATGAAAGGC
317407 TAA
66 TAA
* * * * * *
317410 GTGCCTTTGAGGCCTAACTGTGCAATTGGCA-AGAATGTGTCAATTACGCTAGTTAGATGAA
1 GTGCCTTTGAGGCCTAACTGTGCATTTGACAGA-AAGGTATCATTTATGCTAGTTAGATGAA
317471 GGGTTAAATA
Statistics
Matches: 116, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
67 1 0.01
68 115 0.99
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (68 bp):
GTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGGTATCATTTATGCTAGTTAGATGAAAGGC
TAA
Found at i:322131 original size:43 final size:43
Alignment explanation
Indices: 322051--322134 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
322041 AACATATTCG
* * ** *
322051 ATATTTAGCGGCATTTGTAGTCACAAACGTCGTAATAGATTAA
1 ATATTTAGCGACACTTGTAGTCACAAACACCGCAATAGATTAA
* *
322094 ATATTTAGCGACGCTTGTAGTCAGAAACACCGCAATAGATT
1 ATATTTAGCGACACTTGTAGTCACAAACACCGCAATAGATT
322135 TGATATGTAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (43 bp):
ATATTTAGCGACACTTGTAGTCACAAACACCGCAATAGATTAA
Found at i:322146 original size:43 final size:43
Alignment explanation
Indices: 322065--322146 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 43
322055 TTAGCGGCAT
** * *
322065 TTGTAGTCACAAACGTCGTAATAGATTAAATATTTAGCGACGC
1 TTGTAGTCACAAACACCGCAATAGATTAAATATGTAGCGACGC
* **
322108 TTGTAGTCAGAAACACCGCAATAGATTTGATATGTAGCG
1 TTGTAGTCACAAACACCGCAATAGATTAAATATGTAGCG
322147 GCGTGTCTGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (43 bp):
TTGTAGTCACAAACACCGCAATAGATTAAATATGTAGCGACGC
Found at i:322595 original size:21 final size:21
Alignment explanation
Indices: 322566--322630 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
322556 AATGCTACTT
* * *
322566 CTCTTTCTGTTTCTCTCGTTG
1 CTCTCTCTGCTTCTCTCGCTG
322587 CTCTCTCTGCTTCTCTCGCTG
1 CTCTCTCTGCTTCTCTCGCTG
* *
322608 CTCTCTCTACTTCTCTCTCTG
1 CTCTCTCTGCTTCTCTCGCTG
322629 CT
1 CT
322631 TTTTTCGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.02, C:0.38, G:0.11, T:0.49
Consensus pattern (21 bp):
CTCTCTCTGCTTCTCTCGCTG
Found at i:329671 original size:83 final size:83
Alignment explanation
Indices: 329502--329811 Score: 245
Period size: 83 Copynumber: 3.8 Consensus size: 83
329492 GGCATTTTTT
* * ** * *
329502 GAAAAA-GCCACTATAGATGAACCCTATTACGGCGTTTGTATAAAAACACTGCTAAAGTACTACT
1 GAAAAACGCCACTATAGACGAACTCTATTGTGGCATTTGTATAAAAACACCGCTAAAGTACTACT
* * * **
329566 CAAT--TGTGCATTTGTTG
66 CTATCACG-GCGTTTACTG
* * * * *
329583 AAAAAAACGCCACTATAGATGAACTCTATTGTGGTATTTGTATAAAAACGCCGCTAAAGTATTA-
1 -GAAAAACGCCACTATAGACGAACTCTATTGTGGCATTTGTATAAAAACACCGCTAAAGTACTAC
* *
329647 TTTATCACGGCGTTTGCTG
65 TCTATCACGGCGTTTACTG
* * * * * * *
329666 GAAAAACGCTATTA-AGAACG-ATTCATATTGCGGCATTTGTACAAAAACACAGCTAAATTACTA
1 GAAAAACGCCACTATAG-ACGAACTC-TATTGTGGCATTTGTATAAAAACACCGCTAAAGTACTA
* *
329729 CTCTATCACGGTGTTTATTG
64 CTCTATCACGGCGTTTACTG
* * * * * *
329749 GAAAAACGCCACTATAAACGAACCCTATTATGGCGTTTGTTTAAAAACTCCGCTAAAGTACTA
1 GAAAAACGCCACTATAGACGAACTCTATTGTGGCATTTGTATAAAAACACCGCTAAAGTACTA
329812 GTCTTCGCGG
Statistics
Matches: 177, Mismatches: 43, Indels: 15
0.75 0.18 0.06
Matches are distributed among these distances:
81 5 0.03
82 52 0.29
83 116 0.66
84 4 0.02
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (83 bp):
GAAAAACGCCACTATAGACGAACTCTATTGTGGCATTTGTATAAAAACACCGCTAAAGTACTACT
CTATCACGGCGTTTACTG
Found at i:339263 original size:43 final size:43
Alignment explanation
Indices: 339095--339263 Score: 221
Period size: 43 Copynumber: 3.9 Consensus size: 43
339085 CATTTGTTAA
* * * ** **
339095 ACAAACGCCGCAATAGGTGTTGATCTTTAGCGGTGTTTGGCAG
1 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTCCC
* * *
339138 ACAAATGCCGCAATAGGTGTTGATGTTTAGCGGCGTTTTCCCC
1 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTCCC
339181 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTCCC
1 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTCCC
** *
339224 ACAAACGTTGCAGTAGGTGTTGATGTTTAGCGGCATTTTT
1 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTT
339264 ATCGCAAATG
Statistics
Matches: 113, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 113 1.00
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (43 bp):
ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTCCC
Found at i:339284 original size:43 final size:43
Alignment explanation
Indices: 339095--339306 Score: 205
Period size: 43 Copynumber: 5.0 Consensus size: 43
339085 CATTTGTTAA
* ** *
339095 ACAAACGCCGCAATAGGTGTTGATCTTTAGCGG--TGTTTGGCAG
1 ACAAACGCCGCAATAGGTGTTGATGTTTAGCGGCAT-TTTTAC-C
* * **
339138 ACAAATGCCGCAATAGGTGTTGATGTTTAGCGGCGTTTTCCCC
1 ACAAACGCCGCAATAGGTGTTGATGTTTAGCGGCATTTTTACC
* * *
339181 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTCCC
1 ACAAACGCCGCAATAGGTGTTGATGTTTAGCGGCATTTTTACC
** * *
339224 ACAAACGTTGCAGTAGGTGTTGATGTTTAGCGGCATTTTTATC
1 ACAAACGCCGCAATAGGTGTTGATGTTTAGCGGCATTTTTACC
* * * * *
339267 GCAAATGCCGTAATAGGTGTTG-TATATAGCGGCATTTTTA
1 ACAAACGCCGCAATAGGTGTTGATGTTTAGCGGCATTTTTA
339307 GGATACAAAC
Statistics
Matches: 146, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
42 16 0.11
43 125 0.86
44 4 0.03
45 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTGTTGATGTTTAGCGGCATTTTTACC
Found at i:339284 original size:86 final size:86
Alignment explanation
Indices: 339095--339305 Score: 226
Period size: 86 Copynumber: 2.5 Consensus size: 86
339085 CATTTGTTAA
* * ** * *
339095 ACAAACGCCGCAATAGGTGTTGATCTTTAGCGGTGTTTGGCAGACAAATGCCGCAATAGGTGTTG
1 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCACACAAACGCCGCAATAGGTGTTG
* *
339160 ATGTTTAGCGGCGTTTTCCCC
66 ATGTTTAGCGGCATTTTCACC
* * * ** *
339181 ACAAACGCCGCAGTAGGTGTTGATGTTTAGCGGCGTTTTTCCCACAAACGTTGCAGTAGGTGTTG
1 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCACACAAACGCCGCAATAGGTGTTG
* *
339246 ATGTTTAGCGGCATTTTTATC
66 ATGTTTAGCGGCATTTTCACC
* * * * *
339267 GCAAATGCCGTAATAGGTGTTG-TATATAGCGGCATTTTT
1 ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT
339306 AGGATACAAA
Statistics
Matches: 103, Mismatches: 22, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
85 14 0.14
86 89 0.86
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (86 bp):
ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCACACAAACGCCGCAATAGGTGTTG
ATGTTTAGCGGCATTTTCACC
Found at i:339750 original size:21 final size:21
Alignment explanation
Indices: 339683--339777 Score: 77
Period size: 21 Copynumber: 4.5 Consensus size: 21
339673 TTTCTGATAT
* * *
339683 GCTGCTTCTCTCTGTGCTACC
1 GCTGCTGCTCTCTCTGCTTCC
*
339704 GTTGC--CTCTCTCTGTCTTGCC
1 GCTGCTGCTCTCTCTG-CTT-CC
* * *
339725 ACTGCTTCTCTTTCTGCTTCC
1 GCTGCTGCTCTCTCTGCTTCC
**
339746 GCTGCTGCTCTGGCTGCTTCC
1 GCTGCTGCTCTCTCTGCTTCC
339767 GCTGCTGCTCT
1 GCTGCTGCTCT
339778 GGCTGCTGCT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
19 8 0.13
20 2 0.03
21 39 0.65
22 3 0.05
23 8 0.13
ACGTcount: A:0.02, C:0.38, G:0.20, T:0.40
Consensus pattern (21 bp):
GCTGCTGCTCTCTCTGCTTCC
Found at i:339778 original size:21 final size:21
Alignment explanation
Indices: 339738--339784 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
339728 GCTTCTCTTT
339738 CTGCTTCCGCTGCTGCTCTGG
1 CTGCTTCCGCTGCTGCTCTGG
339759 CTGCTTCCGCTGCTGCTCTGG
1 CTGCTTCCGCTGCTGCTCTGG
339780 CTGCT
1 CTGCT
339785 GCTCTCTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.00, C:0.38, G:0.28, T:0.34
Consensus pattern (21 bp):
CTGCTTCCGCTGCTGCTCTGG
Found at i:339782 original size:12 final size:12
Alignment explanation
Indices: 339746--339789 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
339736 TTCTGCTTCC
339746 GCTGCTGCTCTG
1 GCTGCTGCTCTG
*
339758 GCTGCT--TC-C
1 GCTGCTGCTCTG
339767 GCTGCTGCTCTG
1 GCTGCTGCTCTG
339779 GCTGCTGCTCT
1 GCTGCTGCTCT
339790 CTCTGCTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 6 0.22
10 2 0.07
11 2 0.07
12 17 0.63
ACGTcount: A:0.00, C:0.36, G:0.30, T:0.34
Consensus pattern (12 bp):
GCTGCTGCTCTG
Found at i:339795 original size:12 final size:12
Alignment explanation
Indices: 339745--339796 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
339735 TTTCTGCTTC
339745 CGCTGCTGCTCT
1 CGCTGCTGCTCT
*
339757 GGCTGCT--TC-
1 CGCTGCTGCTCT
339766 CGCTGCTGCTCT
1 CGCTGCTGCTCT
*
339778 GGCTGCTGCTCT
1 CGCTGCTGCTCT
*
339790 CTCTGCT
1 CGCTGCT
339797 TCCCTTGCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 2 0.06
12 22 0.69
ACGTcount: A:0.00, C:0.38, G:0.27, T:0.35
Consensus pattern (12 bp):
CGCTGCTGCTCT
Found at i:348032 original size:42 final size:42
Alignment explanation
Indices: 347973--348115 Score: 119
Period size: 42 Copynumber: 3.4 Consensus size: 42
347963 CGTTTATATC
* *
347973 AAAACGCCACTATAGTAAGTGTATTTCGCGGCGTTTGTGCGT
1 AAAACGCCACTAAAGTAAGTGTATTTCGCGGCGTTTGTGCCT
* * * * *
348015 AAAACGCCACTAAAGTAATTGT-TATCTACAGCGTTTGTGCTT
1 AAAACGCCACTAAAGTAAGTGTATTTC-GCGGCGTTTGTGCCT
* * * * ** *
348057 AAAACGTCGCTAGAGTATGTAAAATTCGCGGCGTTT-TGACCT
1 AAAACGCCACTAAAGTAAGTGTATTTCGCGGCGTTTGTG-CCT
*
348099 AAAACGACACTAAAGTA
1 AAAACGCCACTAAAGTA
348116 TGACATTTTG
Statistics
Matches: 77, Mismatches: 21, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
41 5 0.06
42 70 0.91
43 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (42 bp):
AAAACGCCACTAAAGTAAGTGTATTTCGCGGCGTTTGTGCCT
Found at i:352582 original size:21 final size:21
Alignment explanation
Indices: 352530--352576 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
352520 GAAGTCCATT
*
352530 GCTTTTATGTTGTTGTTGATG
1 GCTTTTATGTTGCTGTTGATG
352551 GCTTTTATGTTGCTGTTGATG
1 GCTTTTATGTTGCTGTTGATG
352572 G-TTTT
1 GCTTTT
352577 CCTGTTCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.09, C:0.06, G:0.28, T:0.57
Consensus pattern (21 bp):
GCTTTTATGTTGCTGTTGATG
Found at i:364171 original size:17 final size:17
Alignment explanation
Indices: 364149--364232 Score: 60
Period size: 17 Copynumber: 4.9 Consensus size: 17
364139 AATTAAGAGT
364149 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
364166 TAGTTTAATTAATTAAC
1 TAGTTTAATAAATGAAC
* * *
364183 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
* * * *
364201 TAGATGAATGAATGAAG
1 TAGTTTAATAAATGAAC
* *
364218 TAGCTTACTAAATGA
1 TAGTTTAATAAATGA
364233 TCTAAATATG
Statistics
Matches: 50, Mismatches: 16, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
17 37 0.74
18 13 0.26
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:366370 original size:17 final size:18
Alignment explanation
Indices: 366348--366386 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
366338 AAATTTTCTA
*
366348 TTTTTTCCTTTTATTT-T
1 TTTTTTACTTTTATTTAT
*
366365 TTTTTTATTTTTATTTAT
1 TTTTTTACTTTTATTTAT
366383 TTTT
1 TTTT
366387 AATTTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTACTTTTATTTAT
Done.