Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007777.1 Hibiscus syriacus cultivar Beakdansim tig00110059_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: 1720799
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1211734 original size:43 final size:43
Alignment explanation
Indices: 1211681--1211958 Score: 299
Period size: 43 Copynumber: 6.7 Consensus size: 43
1211671 TTAGCGGCGT
* *
1211681 TTTACAAACGCCGCTATTAACTGTGTATTTAGCGGCGTTTGGC
1 TTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTC
* * *
1211724 TTTATAAACGCCGCTATTGACTTTGTA-TTAGCGGCATTTGTC
1 TTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTC
** * * *
1211766 TTTACAAACGCCAATATTGATTGTGCATTTAGCGGCGTTT-TT
1 TTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTC
* *
1211808 TTTACAAACGCCGCTATTGATTGTATATTTAGCGGCGTTTGTC
1 TTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTC
* * *
1211851 TTTATAAACGCCGCTATTGACTATATATTTAGCGGC----G--
1 TTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTC
* * *
1211888 TTT---AACGCCGCTATTGATTGTGAATTTAGCGGCGTTTTTC
1 TTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTC
* *
1211928 TTTACAAACGTCGCTATTGACTATGTATTTA
1 TTTACAAACGCCGCTATTGACTGTGTATTTA
1211959 ATGTCATTTG
Statistics
Matches: 194, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
34 26 0.13
37 3 0.02
39 1 0.01
40 3 0.02
42 71 0.37
43 90 0.46
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (43 bp):
TTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGTC
Found at i:1211800 original size:85 final size:85
Alignment explanation
Indices: 1211681--1211958 Score: 299
Period size: 85 Copynumber: 3.4 Consensus size: 85
1211671 TTAGCGGCGT
* *
1211681 TTTACAAACGCCGCTATTAACTGTGTATTTAGCGGCGTTTGGCTTTATAAACGCCGCTATTGACT
1 TTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTT-GCTTTACAAACGCCGCTATTGA-T
*
1211746 T-TGTA-TTAGCGGCATTTGTC
64 TGTATATTTAGCGGCATTTGTC
** * * **
1211766 TTTACAAACGCCAATATTGATTGTGCATTTAGCGGCGTTTTTTTTACAAACGCCGCTATTGATTG
1 TTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGCTTTACAAACGCCGCTATTGATTG
*
1211831 TATATTTAGCGGCGTTTGTC
66 TATATTTAGCGGCATTTGTC
* * *
1211851 TTTATAAACGCCGCTATTGACTATATATTTAGCGGC----G-TTT---AACGCCGCTATTGATTG
1 TTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGCTTTACAAACGCCGCTATTGATTG
* *
1211908 TGA-ATTTAGCGGCGTTTTTC
66 T-ATATTTAGCGGCATTTGTC
* *
1211928 TTTACAAACGTCGCTATTGACTATGTATTTA
1 TTTACAAACGCCGCTATTGACTGTGTATTTA
1211959 ATGTCATTTG
Statistics
Matches: 168, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
77 62 0.37
78 1 0.01
80 3 0.02
83 2 0.01
84 22 0.13
85 78 0.46
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (85 bp):
TTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGCTTTACAAACGCCGCTATTGATTG
TATATTTAGCGGCATTTGTC
Found at i:1211825 original size:127 final size:119
Alignment explanation
Indices: 1211680--1211958 Score: 362
Period size: 127 Copynumber: 2.3 Consensus size: 119
1211670 TTTAGCGGCG
*
1211680 TTTTACAAACGCCGCTATTAACTGTGTATTTAGCGGCGTTTGGCTTTATAAACGCCGCTATTGAC
1 TTTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGGCTTTATAAACGCCGCTATTGAC
* * *
1211745 TTTGTA-TTAGCGGCATTTGTCTTTACAAACGCCAATATTGATTGTGCATTTAGCGGCGTTTT
66 TATATATTTAGCGGC----G--TTT---AACGCCAATATTGATTGTGAATTTAGCGGCGTTTT
* * *
1211807 TTTTACAAACGCCGCTATTGATTGTATATTTAGCGGCGTTTGTCTTTATAAACGCCGCTATTGAC
1 TTTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGGCTTTATAAACGCCGCTATTGAC
**
1211872 TATATATTTAGCGGCGTTTAACGCCGCTATTGATTGTGAATTTAGCGGCGTTTT
66 TATATATTTAGCGGCGTTTAACGCCAATATTGATTGTGAATTTAGCGGCGTTTT
* *
1211926 TCTTTACAAACGTCGCTATTGACTATGTATTTA
1 T-TTTACAAACGCCGCTATTGACTGTGTATTTA
1211959 ATGTCATTTG
Statistics
Matches: 137, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
119 33 0.24
120 27 0.20
122 3 0.02
124 1 0.01
127 65 0.47
128 8 0.06
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (119 bp):
TTTTACAAACGCCGCTATTGACTGTGTATTTAGCGGCGTTTGGCTTTATAAACGCCGCTATTGAC
TATATATTTAGCGGCGTTTAACGCCAATATTGATTGTGAATTTAGCGGCGTTTT
Found at i:1211900 original size:34 final size:34
Alignment explanation
Indices: 1211857--1211924 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
1211847 TGTCTTTATA
1211857 AACGCCGCTATTGACTAT-ATATTTAGCGGCGTTT
1 AACGCCGCTATTGACTATGA-ATTTAGCGGCGTTT
* *
1211891 AACGCCGCTATTGATTGTGAATTTAGCGGCGTTT
1 AACGCCGCTATTGACTATGAATTTAGCGGCGTTT
1211925 TTCTTTACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 30 0.97
35 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (34 bp):
AACGCCGCTATTGACTATGAATTTAGCGGCGTTT
Found at i:1211943 original size:77 final size:77
Alignment explanation
Indices: 1211730--1211958 Score: 239
Period size: 77 Copynumber: 2.9 Consensus size: 77
1211720 TGGCTTTATA
* * ** * * **
1211730 AACGCCGCTATTGACTT-TGTA-TTAGCGGCATTTGTCTTTACAAACGCCAATATTGATTGTGCA
1 AACGCCGCTATTGA-TTGTATATTTAGCGGCGTTTGTCTTTACAAACGCCGCTATTGACTATATA
1211793 TTTAGCGGCGTTTTTTTT
65 TTTAGCGGCG-----TTT
*
1211811 ACAAACGCCGCTATTGATTGTATATTTAGCGGCGTTTGTCTTTATAAACGCCGCTATTGACTATA
1 ---AACGCCGCTATTGATTGTATATTTAGCGGCGTTTGTCTTTACAAACGCCGCTATTGACTATA
1211876 TATTTAGCGGCGTTT
63 TATTTAGCGGCGTTT
* * *
1211891 AACGCCGCTATTGATTGTGA-ATTTAGCGGCGTTTTTCTTTACAAACGTCGCTATTGACTATGTA
1 AACGCCGCTATTGATTGT-ATATTTAGCGGCGTTTGTCTTTACAAACGCCGCTATTGACTATATA
1211955 TTTA
65 TTTA
1211959 ATGTCATTTG
Statistics
Matches: 129, Mismatches: 13, Indels: 13
0.83 0.08 0.08
Matches are distributed among these distances:
77 62 0.48
78 1 0.01
80 3 0.02
83 2 0.02
84 17 0.13
85 44 0.34
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (77 bp):
AACGCCGCTATTGATTGTATATTTAGCGGCGTTTGTCTTTACAAACGCCGCTATTGACTATATAT
TTAGCGGCGTTT
Found at i:1215491 original size:13 final size:13
Alignment explanation
Indices: 1215473--1215497 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1215463 CCTGTAGAGT
1215473 AGGGCATAGTAGA
1 AGGGCATAGTAGA
1215486 AGGGCATAGTAG
1 AGGGCATAGTAG
1215498 GGCTCGCACG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.40, T:0.16
Consensus pattern (13 bp):
AGGGCATAGTAGA
Found at i:1215788 original size:36 final size:35
Alignment explanation
Indices: 1215723--1216135 Score: 212
Period size: 39 Copynumber: 11.5 Consensus size: 35
1215713 TTTGACAAAA
* * *
1215723 TATAATATATAATTTTCAGAAAACGATTTTTGAAAA-T
1 TATATTATATAGTTTT-TGAAAAC-A-TTTTGAAAACT
* * *
1215760 GTATATTATATGGTTTTTGAAAATATTTTGAATA-T
1 -TATATTATATAGTTTTTGAAAACATTTTGAAAACT
* *
1215795 ATATAATATATAG--TTTGAAAATATTTTGAAAACATTT
1 -TATATTATATAGTTTTTGAAAACATTTTGAAAAC---T
*
1215832 ATATATTATATAG-TTTTCAAAACATTTTGAAAACT
1 -TATATTATATAGTTTTTGAAAACATTTTGAAAACT
*
1215867 TATATAATATATAGTTTTT-AAAACATTTGGAAAACT
1 TATAT--TATATAGTTTTTGAAAACATTTTGAAAACT
* *
1215903 TATATAGTATATAGTTTTTTAAAACATTTTTGAAAAAAT
1 TATAT--TATATAGTTTTTGAAAACA-TTTTG-AAAACT
* *
1215942 TATATAATATATAG-TTTTAAAAACATTTTTTTGAAAAATCA
1 TATAT--TATATAGTTTTTGAAAACA---TTTTG-AAAA-CT
** * *
1215983 TATAACATATAG-TTTTAAAAACATTTTTGGAAAAAT
1 TATATTATATAGTTTTTGAAAACA-TTTT-GAAAACT
**
1216019 TATATAATATATAGTTTTAAAAAACAATTTTTGAAAACT
1 TATAT--TATATAGTTTTTGAAAAC-A-TTTTGAAAACT
**
1216058 TATA-TA-ATA-TTTTTG-AAGTATTTTGAAAAC-
1 TATATTATATAGTTTTTGAAAACATTTTGAAAACT
* * *
1216088 TATATAATATATTGTTTTGAAAAC-TTTT-TAAA--
1 TATATTATATAGT-TTTTGAAAACATTTTGAAAACT
*
1216120 TATAATATATAGTTTT
1 TATATTATATAGTTTT
1216136 AAAAAATATT
Statistics
Matches: 311, Mismatches: 40, Indels: 55
0.77 0.10 0.14
Matches are distributed among these distances:
30 4 0.01
31 14 0.05
32 14 0.05
33 24 0.08
34 18 0.06
35 25 0.08
36 48 0.15
37 37 0.12
38 52 0.17
39 54 0.17
40 17 0.05
41 4 0.01
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (35 bp):
TATATTATATAGTTTTTGAAAACATTTTGAAAACT
Found at i:1215844 original size:37 final size:37
Alignment explanation
Indices: 1215761--1216067 Score: 299
Period size: 39 Copynumber: 8.2 Consensus size: 37
1215751 TTTGAAAATG
* * * *
1215761 TATATTATATGGTTTTTGAAAATATTTTG--AATA-TA
1 TATAATATATAGTTTTT-AAAACATTTTGAAAACATTA
* *
1215796 TATAATATATAG-TTTGAAAATATTTTGAAAACATTTA
1 TATAATATATAGTTTTTAAAACATTTTGAAAACA-TTA
* *
1215833 TATATTATATAGTTTTCAAAACATTTTGAAAAC-TTA
1 TATAATATATAGTTTTTAAAACATTTTGAAAACATTA
*
1215869 TATAATATATAGTTTTTAAAACATTTGGAAAAC-TTA
1 TATAATATATAGTTTTTAAAACATTTTGAAAACATTA
* *
1215905 TATAGTATATAGTTTTTTAAAACATTTTTGAAAAAATTA
1 TATAATATATAG-TTTTTAAAACA-TTTTGAAAACATTA
* *
1215944 TATAATATATAGTTTTAAAAACATTTTTTTGAAAA-ATCA
1 TATAATATATAGTTTTTAAAACA---TTTTGAAAACATTA
* *
1215983 TATAACATATAGTTTTAAAAACATTTTTGGAAAA-ATTA
1 TATAATATATAGTTTTTAAAACA-TTTT-GAAAACATTA
*
1216021 TATAATATATAGTTTTAAAAAACAATTTTTGAAAAC-TTA
1 TATAATATATAGTTTT-TAAAAC-A-TTTTGAAAACATTA
1216060 TATAATAT
1 TATAATAT
1216068 TTTTGAAGTA
Statistics
Matches: 239, Mismatches: 19, Indels: 24
0.85 0.07 0.09
Matches are distributed among these distances:
33 11 0.05
34 3 0.01
35 13 0.05
36 47 0.20
37 29 0.12
38 59 0.25
39 61 0.26
40 16 0.07
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (37 bp):
TATAATATATAGTTTTTAAAACATTTTGAAAACATTA
Found at i:1215938 original size:38 final size:37
Alignment explanation
Indices: 1215684--1216151 Score: 342
Period size: 38 Copynumber: 12.9 Consensus size: 37
1215674 TATATATATG
* **
1215684 TATATAATAATATAGTTTGTGAAAATGTTTTTGACAAA--
1 TATATAAT-ATATAGTTT-TAAAAACATTTTTGA-AAACT
*
1215722 -ATATAATATATAATTTTCAGAAAACGATTTTTGAAAA-T
1 TATATAATATATAGTTTT-A-AAAAC-ATTTTTGAAAACT
* ** *
1215760 GTATAT--TATATGGTTTTTGAAA-ATATTTTGAATA--
1 -TATATAATATATAGTTTTAAAAACAT-TTTTGAAAACT
* *
1215794 TATATAATATATAG-TTTGAAAATA-TTTTGAAAACATT
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAAC--T
* *
1215831 TATATATTATATAGTTTTCAAAACA-TTTTGAAAACT
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAACT
* *
1215867 TATATAATATATAGTTTTTAAAACA-TTTGGAAAACT
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAACT
* * *
1215903 TATATAGTATATAGTTTTTTAAAACATTTTTGAAAAAAT
1 TATATAATATATAG-TTTTAAAAACATTTTTG-AAAACT
*
1215942 TATATAATATATAGTTTTAAAAACATTTTTTTGAAAAAT
1 TATATAATATATAGTTTTAAAAACA--TTTTTGAAAACT
* * *
1215981 CATATAACATATAGTTTTAAAAACATTTTTGGAAAAAT
1 TATATAATATATAGTTTTAAAAACATTTTT-GAAAACT
1216019 TATATAATATATAGTTTTAAAAAACAATTTTTGAAAACT
1 TATATAATATATAGTTTT-AAAAAC-ATTTTTGAAAACT
* **
1216058 TATAT-A-ATAT--TTTT-GAAGTA-TTTTGAAAAC-
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAACT
* *
1216088 TATATAATATATTGTTTTGAAAAC-TTTTT---AA--
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAACT
*
1216119 -ATATAATATATAGTTTTAAAAAATATTTTTGAA
1 TATATAATATATAGTTTT-AAAAACATTTTTGAA
1216152 GTATATATAT
Statistics
Matches: 358, Mismatches: 38, Indels: 71
0.77 0.08 0.15
Matches are distributed among these distances:
30 21 0.06
31 15 0.04
32 12 0.03
33 15 0.04
34 12 0.03
35 26 0.07
36 58 0.16
37 47 0.13
38 72 0.20
39 64 0.18
40 16 0.04
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (37 bp):
TATATAATATATAGTTTTAAAAACATTTTTGAAAACT
Found at i:1216022 original size:77 final size:75
Alignment explanation
Indices: 1215794--1216064 Score: 318
Period size: 77 Copynumber: 3.6 Consensus size: 75
1215784 ATTTTGAATA
* * ** *
1215794 TATATAATATATAG-TTTGAAAATA-TTTTGAAAACATTTATATATTATATAGTTTTCAAAACA-
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAAC--TTATATAACATATAGTTTTAAAAACAT
*
1215856 TTTT-GAAAACT
64 TTTTGGAAAAAT
* * ** *
1215867 TATATAATATATAGTTTTTAAAACA-TTTGGAAAACTTATATAGTATATAGTTTTTTAAAACATT
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAACTTATATAACATATAG-TTTTAAAAACATT
*
1215931 TTTGAAAAAAT
65 TTTGGAAAAAT
* *
1215942 TATATAATATATAGTTTTAAAAACATTTTTTTGAAAAATCATATAACATATAGTTTTAAAAACAT
1 TATATAATATATAGTTTTAAAAACA--TTTTTGAAAACTTATATAACATATAGTTTTAAAAACAT
1216007 TTTTGGAAAAAT
64 TTTTGGAAAAAT
1216019 TATATAATATATAGTTTTAAAAAACAATTTTTGAAAACTTATATAA
1 TATATAATATATAGTTTT-AAAAAC-ATTTTTGAAAACTTATATAA
1216065 TATTTTTGAA
Statistics
Matches: 172, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
72 14 0.08
73 24 0.14
74 21 0.12
75 29 0.17
77 57 0.33
78 26 0.15
79 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.43
Consensus pattern (75 bp):
TATATAATATATAGTTTTAAAAACATTTTTGAAAACTTATATAACATATAGTTTTAAAAACATTT
TTGGAAAAAT
Found at i:1216148 original size:32 final size:31
Alignment explanation
Indices: 1215943--1216161 Score: 86
Period size: 39 Copynumber: 6.4 Consensus size: 31
1215933 TGAAAAAATT
1215943 ATATAATATATAGTTTTAAAAACATTTTTTTGAAAAA
1 ATATAATATATAGTTTTAAAAA-A--TTTTTG---AA
*
1215980 TCATATAACATATAGTTTTAAAAACATTTTTGGAAAAA
1 --ATATAATATATAGTTTTAAAAA-ATTTTT-G---AA
1216018 TTATATAATATATAGTTTTAAAAAACAATTTTTGAA
1 --ATATAATATATAGTTTT--AAAA-AATTTTTGAA
* * * **
1216054 A-ACTTATATAATATTTTTGAAGTA-TTTTGAAAA
1 ATA-TAATAT-ATAGTTTTAAAAAATTTTTG--AA
* * *
1216087 CTATATAATATATTGTTTTGAAAACTTTTT-AA
1 --ATATAATATATAGTTTTAAAAAATTTTTGAA
1216119 ATATAATATATAGTTTTAAAAAATATTTTTGAA
1 ATATAATATATAGTTTT-AAAAA-ATTTTTGAA
*
1216152 GTAT-ATATAT
1 ATATAATATAT
1216162 TCTATAATTT
Statistics
Matches: 147, Mismatches: 18, Indels: 37
0.73 0.09 0.18
Matches are distributed among these distances:
30 16 0.11
31 9 0.06
32 14 0.10
33 10 0.07
34 15 0.10
35 17 0.12
36 3 0.02
37 5 0.03
38 23 0.16
39 24 0.16
40 10 0.07
41 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (31 bp):
ATATAATATATAGTTTTAAAAAATTTTTGAA
Found at i:1217253 original size:6 final size:6
Alignment explanation
Indices: 1217242--1217281 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
1217232 TTTAATCATT
1217242 TTTTTA TTTTTA TTTTTA TTTTTA --TTTA TTTGTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTTT
1217282 TTGTCTATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 4 0.13
6 21 0.68
7 6 0.19
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:1217263 original size:17 final size:18
Alignment explanation
Indices: 1217242--1217281 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1217232 TTTAATCATT
1217242 TTTTTATTTTTATTT-TTA
1 TTTTTA-TTTTATTTGTTA
1217260 TTTTTA-TTTATTTGTTA
1 TTTTTATTTTATTTGTTA
1217277 TTTTT
1 TTTTT
1217282 TTGTCTATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 8 0.38
18 6 0.29
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTTTATTTTATTTGTTA
Found at i:1217387 original size:24 final size:23
Alignment explanation
Indices: 1217348--1217400 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 23
1217338 TCATTATTTT
1217348 TATTATTTTTCATTTGTTTATA-G
1 TATT-TTTTTCATTTGTTTATATG
1217371 TATTTTTTTCTACTTTGTTTATATG
1 TATTTTTTTC-A-TTTGTTTATATG
1217396 TATTT
1 TATTT
1217401 ACATGTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.22
23 5 0.19
24 10 0.37
25 6 0.22
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.68
Consensus pattern (23 bp):
TATTTTTTTCATTTGTTTATATG
Found at i:1217447 original size:3 final size:3
Alignment explanation
Indices: 1217439--1217468 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1217429 ATATTATAAC
1217439 TAT TAT TAT TAT TAT TATT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA
1217469 ACGTTTATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1221530 original size:163 final size:165
Alignment explanation
Indices: 1221251--1222107 Score: 836
Period size: 163 Copynumber: 5.2 Consensus size: 165
1221241 TTTTAAACAA
* * *
1221251 ATCATTTGCAGCATAACTCAA-TGCTAGAAGGGTTATATGTCACCAAAGACCTTCGAGTTCGGCT
1 ATCATTTGCAGCATAACTCAAGT-CGAGAAGGGTTATCTG--ACCAAAGACCTTCGAGTTCGACT
* *
1221315 CCGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCG-GAAAGGGTTATCTGCCAACA
63 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG-AAGGGTTATCTGCCAACA
* * *
1221379 AAATACCTTTGAGTTCGACTACGTTCAGCTCAAAGGCAC
127 AAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCAC
* * ** * * *
1221418 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGACTATCTG-CCAAAGACC-TCGAGTTCGGCTCCA
1 ATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACG
* * *
1221481 CTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACTAAAG
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAG
* *
1221546 ACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
131 ACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCAC
* * * * * * * *
1221581 ACCATTTGAAGCATAGCTCAAGTCGAGAAGGGTTATCTG-CCAAAGACCCTCGATTTTGATTACA
1 ATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACG
* * * * * * * * ** *
1221645 CTCAGCTTCGAGGAACAT-ATTTACAGCATAACTCAAGGCTATAAGGGTTATCTGTGACCAAAAG
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAG
* *
1221709 ACCTTCGAGTTCGACT-CGCTCAGCTCTAAGGCAT
131 ACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCAC
* *
1221743 ATAATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGACT
* * * *
1221808 ACGCTCAGCT-CAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTG---TC--
63 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
* * * * *
1221867 AAGACCTTCGAGTTTGATTACACTCAGCTTCAAGGGCAT
128 AAGACCTTCGAGTTCGACTACGCTCAGC-TCAAAGGCAC
* * *
1221906 ATCATTTACA-CATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTA
1 ATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATC--TGACCAAAGACCTTCGAGTTCGACTA
* * * * *
1221970 CGTTCAGCTCCAAGGCACATCATTTTGTAGCATAGCTTAAGTCGAGAAGGGCTAT-TG----CTA
64 CGCTCAGCTCCAAGGCACATCA-TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAA
* * *
1222030 AAGACCTTCGAGTTCGATTACACTCAGCTCAAA-GCAA
128 AAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCAC
** * * * *
1222067 ATCAAGTTCACAGCATAGCTCAAGGCAAGAAGGGCTATCTG
1 ATC-A-TTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTG
1222108 TCAATAAATT
Statistics
Matches: 591, Mismatches: 80, Indels: 43
0.83 0.11 0.06
Matches are distributed among these distances:
161 56 0.09
162 101 0.17
163 280 0.47
164 59 0.10
165 8 0.01
166 55 0.09
167 31 0.05
168 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (165 bp):
ATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAG
ACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCAC
Found at i:1221752 original size:246 final size:245
Alignment explanation
Indices: 1221254--1222107 Score: 858
Period size: 246 Copynumber: 3.5 Consensus size: 245
1221244 TAAACAAATC
* * * ** * *
1221254 ATTTGCAGCATAACTCAA-TGCTAGAAGGGTTATATGTC-ACCAAAGACCTTCGAGTTCGGCTCC
1 ATTTGCAGCATAACTTAAGT-CGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTAC
* * * * * *
1221317 GCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCG-GAAAGGGTTATCTGCCAACAAA
65 GCTCAGCT-CAAGGCACACCATTTGAAGCATAGCTCAAGTCGAG-AAGGGCTATCTG-C--C--A
* * * * * ** * * * * * * *
1221381 ATACCTTTGAGTTCGACTACGTTCAGC-TCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
123 AGACCCTCGAGTTTGATTACACTCAGCTTCAAGGGAACATCATTTACA-CATAACTCAAGGCTAG
** * * * *
1221445 AAGGACTATC--TG-CCAAAGACC-TCGAGTTCGGCTCCACTCAGCTCCAAGGCATATC
187 AAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATA
* *
1221500 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACTAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACG
*
1221565 CTCAGCTCCAAGGCACACCATTTGAAGCATAGCTCAAGTCGAGAAGGGTTATCTGCCAAAGACCC
66 CTCAGCT-CAAGGCACACCATTTGAAGCATAGCTCAAGTCGAGAAGGGCTATCTGCC-AAGACCC
* * *
1221630 TCGATTTTGATTACACTCAGCTTCGA-GGAACAT-ATTTACAGCATAACTCAAGGCTATAAGGGT
129 TCGAGTTTGATTACACTCAGCTTCAAGGGAACATCATTTACA-CATAACTCAAGGCTAGAAGGGT
*
1221693 TATCTGTGACCAAAAGACCTTCGAGTTCGACT-CGCTCAGCTCTAAGGCATATA
193 TATCTGTGACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATA
*
1221746 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACG
* * * * * *
1221811 CTCAGCTCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGTCAAGACCTTC
66 CTCAGCTCAAGGCACACCATTTGAAGCATAGCTCAAGTCGAGAAGGGCTATCTGCCAAGACCCTC
* *
1221876 GAGTTTGATTACACTCAGCTTCAAGGGCATATCATTTACACATAACTCAAGGCTAGAAGGGTTAT
131 GAGTTTGATTACACTCAGCTTCAAGGGAACATCATTTACACATAACTCAAGGCTAGAAGGGTTAT
* *
1221941 CTGTGACCAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCA
196 CTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT-A
* * * * * * * *
1221992 TTTTGTAGCATAGCTTAAGTCGAGAAGGGCTAT-T----GCTAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACG
* * * * * * *
1222052 CTCAGCTCAAAGCAAATCAAGTTCACAGCATAGCTCAAGGCAAGAAGGGCTATCTG
66 CTCAGCTCAAGGCACA-CCATTTGA-AGCATAGCTCAAGTCGAGAAGGGCTATCTG
1222108 TCAATAAATT
Statistics
Matches: 520, Mismatches: 73, Indels: 33
0.83 0.12 0.05
Matches are distributed among these distances:
241 36 0.07
242 29 0.06
243 53 0.10
244 56 0.11
245 100 0.19
246 163 0.31
247 82 0.16
248 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (245 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCAAGGCACACCATTTGAAGCATAGCTCAAGTCGAGAAGGGCTATCTGCCAAGACCCTC
GAGTTTGATTACACTCAGCTTCAAGGGAACATCATTTACACATAACTCAAGGCTAGAAGGGTTAT
CTGTGACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATA
Found at i:1221758 original size:83 final size:83
Alignment explanation
Indices: 1221251--1222059 Score: 796
Period size: 83 Copynumber: 9.9 Consensus size: 83
1221241 TTTTAAACAA
* * * * *
1221251 ATCATTTGCAGCATAACTCAA-TGCTAGAAGGGTTATATGTCACCAAAGACCTTCGAGTTCGGCT
1 ATCATTTGCAGCATAACTTAAGT-CGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACT
* *
1221315 CCGCTCAGCTCCAAGGCAT
65 ACGCTCAGCTCCAAGGCAC
** * * *
1221334 ATCATTTGCAGCATAACTTAAGTCG-GAAAGGGTTATCTGCCAACAAAATACCTTTGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAG-AAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGAC
* *
1221398 TACGTTCAGCTCAAAGGCAC
64 TACGCTCAGCTCCAAGGCAC
* ** * *
1221418 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGACTATC--TG-CCAAAGACC-TCGAGTTCGGCTC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTA
* *
1221479 CACTCAGCTCCAAGGCAT
66 CGCTCAGCTCCAAGGCAC
*** * *
1221497 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACTAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-GTGACCAAAGACCTTCGAGTTCGACT
1221562 ACGCTCAGCTCCAAGGCAC
65 ACGCTCAGCTCCAAGGCAC
* * * * * * * *
1221581 ACCATTTGAAGCATAGCTCAAGTCGAGAAGGGTTATC--TG-CCAAAGACCCTCGATTTTGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTA
* * * *
1221643 CACTCAGCTTCGAGGAAC
66 CGCTCAGCTCCAAGGCAC
* * * * *
1221661 AT-ATTTACAGCATAACTCAAGGCTATAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACC-AAAGACCTTCGAGTTCGACT
* *
1221725 -CGCTCAGCTCTAAGGCAT
65 ACGCTCAGCTCCAAGGCAC
* **
1221743 ATAATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-TGACCAAAGACCTTCGAGTTCGACT
1221808 ACGCTCAGCT-CAAGGCAC
65 ACGCTCAGCTCCAAGGCAC
* * * * *
1221826 ATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGT---C-AAGACCTTCGAGTTTGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTA
* * *
1221887 CACTCAGCTTCAAGGGCAT
66 CGCTCAGCTCCAA-GGCAC
* * * *
1221906 ATCATTTACA-CATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTA
*
1221970 CGTTCAGCTCCAAGGCAC
66 CGCTCAGCTCCAAGGCAC
* * * * *
1221988 ATCATTTTGTAGCATAGCTTAAGTCGAGAAGGGCTA--T-TG-CTAAAGACCTTCGAGTTCGATT
1 ATCA-TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACT
*
1222049 ACACTCAGCTC
65 ACGCTCAGCTC
1222060 AAAGCAAATC
Statistics
Matches: 589, Mismatches: 113, Indels: 51
0.78 0.15 0.07
Matches are distributed among these distances:
78 26 0.04
79 113 0.19
80 81 0.14
81 4 0.01
82 27 0.05
83 180 0.31
84 157 0.27
85 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (83 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCAC
Found at i:1222082 original size:409 final size:409
Alignment explanation
Indices: 1221259--1222110 Score: 1173
Period size: 409 Copynumber: 2.1 Consensus size: 409
1221249 AAATCATTTG
* * *
1221259 CAGCATAACTCAATGCTAGAAGGGTTATATGTCACCAAAGACCTTCGAGTTCGGCTCCGCTCAGC
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTCCGCTCAGC
* * *
1221324 TCCAAGGCATATCATTTGCAGCATAACTTAAGTCGGAAAGGGTTATCTGCCAACAAAATACCTTT
66 TCCAAGGCATATAATTTGCAGCATAACTTAAGTCGGAAAGGGTTATCTGCCAACAAAAGACCTTC
*
1221389 GAGTTCGACTACGTTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGACTAT
131 GAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGACTAT
* * * *
1221454 CTGCCAAAGACCTCGAGTTCGGCTCCACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAG
196 CTGCCAAAGACCTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAG
* * *
1221519 TCGAGAAGGGTTATCTACCAACTAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACACC
261 GCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACACC
* * *
1221584 ATTTGAAGCATAGCTCAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGATTTTGATTACACTCA
326 ATTTGAAGCATAGCTCAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
* * *
1221649 GCTTCGAGGAACATATTTA
391 GCTTCAAGAAACATATTCA
* *
1221668 CAGCATAACTCAAGGCTATAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACT-CGCTCAG
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTCCGCTCAG
* *
1221732 CTCTAAGGCATATAATTTGCAGCATAACTTAAGTC-GAGAAGGGTTATCTGCCAACCAAAGACCT
65 CTCCAAGGCATATAATTTGCAGCATAACTTAAGTCGGA-AAGGGTTATCTGCCAACAAAAGACCT
* *
1221796 TCGAGTTCGACTACGCTCAGCTC-AAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCT
129 TCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGACT
* * * *
1221860 ATCTGTC-AAGACCTTCGAGTTTGATTACACTCAGCTTCAAGGGCATATCATTTACA-CATAACT
194 ATCTGCCAAAGACC-TCGAGTTCGACTACACTCAGCTCCAA-GGCATATCATTTACAGCATAACT
* *** *
1221923 CAAGGCTAGAAGGGTTATCT-GTGACCAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCA
257 CAAGGCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
* * * * *
1221987 CATCATTTTGTAGCATAGCTTAAGTCGAGAAGGGCTAT-TGCTAAAGACCTTCGAGTTCGATTAC
322 CACCA-TTTGAAGCATAGCTCAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAC
1222051 ACTCAGC-TCAAAGCAAATCA-AGTTCA
386 ACTCAGCTTC-AAG-AAA-CATA-TTCA
* * *
1222077 CAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCA
1 CAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
1222111 ATAAATTGTC
Statistics
Matches: 389, Mismatches: 45, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
406 2 0.01
407 79 0.20
408 124 0.32
409 165 0.42
410 19 0.05
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (409 bp):
CAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTCCGCTCAGC
TCCAAGGCATATAATTTGCAGCATAACTTAAGTCGGAAAGGGTTATCTGCCAACAAAAGACCTTC
GAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGACTAT
CTGCCAAAGACCTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTACAGCATAACTCAAG
GCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACACC
ATTTGAAGCATAGCTCAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCA
GCTTCAAGAAACATATTCA
Found at i:1222825 original size:23 final size:25
Alignment explanation
Indices: 1222795--1222842 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1222785 TGAAATATAG
*
1222795 ATATATA-TAG-TTTGAAAACATTT
1 ATATATATTAGTTTTCAAAACATTT
1222818 ATATATATTAGTTTTCAAAACATTT
1 ATATATATTAGTTTTCAAAACATTT
1222843 TGAAAACTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 3 0.14
25 12 0.55
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (25 bp):
ATATATATTAGTTTTCAAAACATTT
Found at i:1222882 original size:70 final size:72
Alignment explanation
Indices: 1222816--1223088 Score: 241
Period size: 78 Copynumber: 3.8 Consensus size: 72
1222806 TTGAAAACAT
* *
1222816 TTATATA-TATTAG-TTTTCAAAACA-TTTTGAAAACTTATAT-A-ATATAGTTTTTAAAACATT
1 TTATATAGTA-TAGTTTTTCAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATT
1222876 TGGAAAAC
65 TGGAAAAC
*
1222884 TTATATAGTATAGTTTTTTAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTT
1 TTATATAGTATAGTTTTTCAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACA---
* *
1222949 TTTTTGAAAAA
63 -TTTGGAAAAC
* * *
1222960 TCATATAACATATAG-TTTTAAAAACATTTTTGAAAAAATTATATAATATATAGTTTTAAAAACA
1 TTATAT-A-GTATAGTTTTTCAAAACATTTTTG-AAAAATTATATAATATATAGTTTTAAAAACA
*
1223024 TTTTTTG-AAAC
63 --TTTGGAAAAC
* * * *
1223035 TTATATA--ATA--TTTT-GAAGCA-TTTTG-AAAACTATATAATATATAGTTTTGAAAAC
1 TTATATAGTATAGTTTTTCAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAAC
1223089 TTTTTAATAA
Statistics
Matches: 179, Mismatches: 14, Indels: 26
0.82 0.06 0.12
Matches are distributed among these distances:
66 27 0.15
68 15 0.08
69 16 0.09
70 19 0.11
71 4 0.02
72 16 0.09
74 1 0.01
75 8 0.04
76 20 0.11
77 17 0.09
78 36 0.20
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (72 bp):
TTATATAGTATAGTTTTTCAAAACATTTTTGAAAAATTATATAATATATAGTTTTAAAAACATTT
GGAAAAC
Found at i:1222925 original size:36 final size:35
Alignment explanation
Indices: 1222805--1223045 Score: 238
Period size: 40 Copynumber: 6.6 Consensus size: 35
1222795 ATATATATAG
*
1222805 TTTGAAAACATT-TATATATATTAGTTTTCAAAACA-T
1 TTTGAAAA-ATTATATA-ATA-TAGTTTTAAAAACATT
* *
1222841 TTTGAAAACTTATATAATATAGTTTTTAAAACA-T
1 TTTGAAAAATTATATAATATAGTTTTAAAAACATT
* * * *
1222875 TTGGAAAACTTATATAGTATAGTTTTTTAAAACATT
1 TTTGAAAAATTATATAATATAG-TTTTAAAAACATT
1222911 TTTGAAAAATTATATAATATATAGTTTTAAAAACATTTTT
1 TTTGAAAAATTATAT-A-ATATAGTTTTAAAAACA---TT
*
1222951 TTTGAAAAATCATATAACATATAGTTTTAAAAACATT
1 TTTGAAAAATTATAT-A-ATATAGTTTTAAAAACATT
1222988 TTTGAAAAAATTATATAATATATAGTTTTAAAAACATTT
1 TTTG-AAAAATTATAT-A-ATATAGTTTTAAAAACA-TT
*
1223027 TTTG-AAACTTATATAATAT
1 TTTGAAAAATTATATAATAT
1223046 TTTGAAGCAT
Statistics
Matches: 182, Mismatches: 13, Indels: 21
0.84 0.06 0.10
Matches are distributed among these distances:
34 34 0.19
35 20 0.11
36 27 0.15
37 26 0.14
38 34 0.19
39 6 0.03
40 35 0.19
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (35 bp):
TTTGAAAAATTATATAATATAGTTTTAAAAACATT
Found at i:1222951 original size:38 final size:37
Alignment explanation
Indices: 1222805--1223045 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 37
1222795 ATATATATAG
*
1222805 TTTGAAAACATT-TATATATAT-TAGTTTTCAAAACA-T
1 TTTGAAAA-ATTATATA-ATATATAGTTTTAAAAACATT
* *
1222841 TTTGAAAACTTATAT-A-ATATAGTTTTTAAAACA-T
1 TTTGAAAAATTATATAATATATAGTTTTAAAAACATT
* * * *
1222875 TTGGAAAACTTATAT-A-GTATAGTTTTTTAAAACATT
1 TTTGAAAAATTATATAATATATAG-TTTTAAAAACATT
1222911 TTTGAAAAATTATATAATATATAGTTTTAAAAACATTTTT
1 TTTGAAAAATTATATAATATATAGTTTTAAAAACA---TT
* *
1222951 TTTGAAAAATCATATAACATATAGTTTTAAAAACATT
1 TTTGAAAAATTATATAATATATAGTTTTAAAAACATT
1222988 TTTGAAAAAATTATATAATATATAGTTTTAAAAACATTT
1 TTTG-AAAAATTATATAATATATAGTTTTAAAAACA-TT
*
1223027 TTTG-AAACTTATATAATAT
1 TTTGAAAAATTATATAATAT
1223046 TTTGAAGCAT
Statistics
Matches: 181, Mismatches: 13, Indels: 21
0.84 0.06 0.10
Matches are distributed among these distances:
33 2 0.01
34 35 0.19
35 13 0.07
36 25 0.14
37 31 0.17
38 34 0.19
39 6 0.03
40 35 0.19
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (37 bp):
TTTGAAAAATTATATAATATATAGTTTTAAAAACATT
Found at i:1223082 original size:24 final size:26
Alignment explanation
Indices: 1223055--1223108 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
1223045 TTTTGAAGCA
1223055 TTTTGAAAAC-TAT-ATAATATATAG
1 TTTTGAAAACTTATAATAATATATAG
*
1223079 TTTTGAAAACTTTTTAATAATATATAG
1 TTTTGAAAAC-TTATAATAATATATAG
1223106 TTT
1 TTT
1223109 AAAAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 10 0.38
26 2 0.08
27 14 0.54
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (26 bp):
TTTTGAAAACTTATAATAATATATAG
Found at i:1224205 original size:18 final size:17
Alignment explanation
Indices: 1224155--1224208 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
1224145 ATATTATATA
1224155 TATTTTTATTTTTTCAT
1 TATTTTTATTTTTTCAT
**
1224172 T-TTATTTAATCCTTTCAT
1 TATT-TTT-ATTTTTTCAT
1224190 TATTTTTATTATTTTCAT
1 TATTTTTATT-TTTTCAT
1224208 T
1 T
1224209 TGTTTATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
16 2 0.07
17 6 0.21
18 19 0.66
19 2 0.07
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTTTATTTTTTCAT
Found at i:1226343 original size:202 final size:193
Alignment explanation
Indices: 1225967--1226363 Score: 713
Period size: 202 Copynumber: 2.0 Consensus size: 193
1225957 TCAAACTCTA
1225967 ATTTCTTACACTTTGAATTTTATTACTATTTGAGTGGATTCAGTAATATCTAAATTCTTAATTGG
1 ATTTCTTACACTTTGAATTTTATTACTATTTGAGTGGATTCAGTAATATCTAAATTCTTAATTGG
1226032 ATACACAAAATATGAATTTCTCCTTATGAGAGGATTTGTTAATAAAATAAGAATATATGATACTT
66 ATACACAAAATATGAATTTCTCCTTATGAGAGGATTTGTTAATAAAATAAGAATATATGATACTT
1226097 GATGTATATTTTTATTAGGTAAAGATTAAAAATATCTGTTTAGGTATTGAATTTTTAAAAGAT
131 GATGTATATTTTTATTAGGTAAAGATTAAAAATATCTGTTTAGGTATTGAATTTTTAAAAGAT
1226160 ATTTCTTACACTTTGAATTTTATTACTATTTGAGTTGGATTCAGTAATATCTAAAATTCTTAATT
1 ATTTCTTACACTTTGAATTTTATTACTATTTGAG-TGGATTCAGTAATATCT-AAATTCTTAA-T
1226225 TGGATACACAAAATAATGAATTTCTCCTTAATGAGAGGATTTGTTAATAAAAATAAGAATATATG
63 TGGATACACAAAAT-ATGAATTTCTCCTT-ATGAGAGGATTTGTTAAT-AAAATAAGAATATATG
1226290 ATACTTGAATGTATATTTATTTATTAGGTAAAGATTAAAAATATCTGTTTAGGTATTGAATTTTT
125 ATACTTG-ATGTATA-TT-TTTATTAGGTAAAGATTAAAAATATCTGTTTAGGTATTGAATTTTT
1226355 AAAAGAT
187 AAAAGAT
1226362 AT
1 AT
1226364 AAAAAATGAG
Statistics
Matches: 195, Mismatches: 0, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
193 34 0.17
194 17 0.09
195 10 0.05
196 15 0.08
197 14 0.07
198 18 0.09
199 23 0.12
200 7 0.04
201 2 0.01
202 55 0.28
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (193 bp):
ATTTCTTACACTTTGAATTTTATTACTATTTGAGTGGATTCAGTAATATCTAAATTCTTAATTGG
ATACACAAAATATGAATTTCTCCTTATGAGAGGATTTGTTAATAAAATAAGAATATATGATACTT
GATGTATATTTTTATTAGGTAAAGATTAAAAATATCTGTTTAGGTATTGAATTTTTAAAAGAT
Found at i:1227576 original size:18 final size:18
Alignment explanation
Indices: 1227553--1227594 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1227543 TGTTGTTTCT
1227553 TTAGATATAATACACATA
1 TTAGATATAATACACATA
1227571 TTAGATATAATACACATA
1 TTAGATATAATACACATA
1227589 TTAGAT
1 TTAGAT
1227595 TTGATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (18 bp):
TTAGATATAATACACATA
Found at i:1229449 original size:17 final size:18
Alignment explanation
Indices: 1229427--1229475 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1229417 ACATGTTTCA
*
1229427 ACCCGACCAGTTGA-CCG
1 ACCCGACCCGTTGACCCG
1229444 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
1229462 ACCCGACCCGTTGA
1 ACCCGACCCGTTGA
1229476 TCATTGACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.20, C:0.45, G:0.22, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:1229536 original size:29 final size:29
Alignment explanation
Indices: 1229494--1229626 Score: 121
Period size: 29 Copynumber: 4.6 Consensus size: 29
1229484 CGTTGATCGG
*
1229494 GTGATATTTTGGGAA-TTAATTCGAAATAG
1 GTGATATTTTGGGAATTTAATTCGAAA-AA
* * *
1229523 GTGCTATTTGGGGAATTTAATTTGAAAAAA
1 GTGATATTTTGGGAATTTAATTCG-AAAAA
*
1229553 GT-ACTATTTTAGGAATTTAATTC-AAAAA
1 GTGA-TATTTTGGGAATTTAATTCGAAAAA
*
1229581 GTGATATTTTGGGAA-TTAATTCAAAAATA
1 GTGATATTTTGGGAATTTAATTCGAAAA-A
* * *
1229610 ATGCTATTTTGGTAATT
1 GTGATATTTTGGGAATT
1229627 ATTTTAAAGA
Statistics
Matches: 85, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
27 7 0.08
28 21 0.25
29 27 0.32
30 27 0.32
31 3 0.04
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (29 bp):
GTGATATTTTGGGAATTTAATTCGAAAAA
Found at i:1229560 original size:30 final size:30
Alignment explanation
Indices: 1229498--1229626 Score: 117
Period size: 30 Copynumber: 4.4 Consensus size: 30
1229488 GATCGGGTGA
* * *
1229498 TATTTTGGGAA-TTAATTCGAAATAGGTGC
1 TATTTTGGGAATTTAATTCGAAAAAAGTAC
* *
1229527 TATTTGGGGAATTTAATTTGAAAAAAGTAC
1 TATTTTGGGAATTTAATTCGAAAAAAGTAC
*
1229557 TATTTTAGGAATTTAATTC--AAAAAGTGA-
1 TATTTTGGGAATTTAATTCGAAAAAAGT-AC
* *
1229585 TATTTTGGGAA-TTAATTC-AAAAATAATGC
1 TATTTTGGGAATTTAATTCGAAAAA-AGTAC
*
1229614 TATTTTGGTAATT
1 TATTTTGGGAATT
1229627 ATTTTAAAGA
Statistics
Matches: 82, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
27 7 0.09
28 21 0.26
29 23 0.28
30 31 0.38
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (30 bp):
TATTTTGGGAATTTAATTCGAAAAAAGTAC
Found at i:1236805 original size:12 final size:12
Alignment explanation
Indices: 1236773--1236806 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1236763 TGTTGACCTC
*
1236773 CTTTGACCAGAA
1 CTTTGACCGGAA
1236785 CTTTGACCGGAA
1 CTTTGACCGGAA
1236797 CTTTGACCGG
1 CTTTGACCGG
1236807 CTTTGACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (12 bp):
CTTTGACCGGAA
Found at i:1239333 original size:12 final size:12
Alignment explanation
Indices: 1239316--1239349 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1239306 ATGAACATTA
*
1239316 ATGAACAGTGTC
1 ATGAACAGTGCC
1239328 ATGAACAGTGCC
1 ATGAACAGTGCC
1239340 ATGAACAGTG
1 ATGAACAGTG
1239350 AAATATTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (12 bp):
ATGAACAGTGCC
Found at i:1240120 original size:32 final size:32
Alignment explanation
Indices: 1240069--1240229 Score: 236
Period size: 32 Copynumber: 5.1 Consensus size: 32
1240059 GTTCCTAAGA
1240069 ACATAGGT-A-ACTGTCCATATGTCCCGAAAG
1 ACATAGGTAATACTGTCCATATGTCCCGAAAG
* * *
1240099 ACATATGTAATTCTGTCCATATGTCCCAAAAG
1 ACATAGGTAATACTGTCCATATGTCCCGAAAG
** * *
1240131 ACATAGAAAATAATGTTCATATGTCCCGAAAG
1 ACATAGGTAATACTGTCCATATGTCCCGAAAG
*
1240163 ACATAGGTAATACTGTCCATATGTCCCGAAAC
1 ACATAGGTAATACTGTCCATATGTCCCGAAAG
1240195 ACATAGGTAATACTGTCCATATGTCCCGAAAG
1 ACATAGGTAATACTGTCCATATGTCCCGAAAG
1240227 ACA
1 ACA
1240230 GGTAAAATTT
Statistics
Matches: 113, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 7 0.06
31 1 0.01
32 105 0.93
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (32 bp):
ACATAGGTAATACTGTCCATATGTCCCGAAAG
Found at i:1240189 original size:96 final size:94
Alignment explanation
Indices: 1240055--1240267 Score: 270
Period size: 96 Copynumber: 2.3 Consensus size: 94
1240045 GAACCTATCT
* * * * * *
1240055 ATATGTTCCTAAGAACATAGGT-AACTGTCCATATGTCCCGAAAGACATATGTAATTCTGTCCAT
1 ATATGTCCCAAAGGACATAGGTAAACTGTCCATATGTCCCGAAACACATAGGTAATACTGTCCAT
1240119 ATGTCCCAAAAGACATAG-AAAATAATGTTC
66 ATGTCCCAAAAGACA-AGTAAAAT-ATGTTC
1240149 ATATGTCCCGAAA-GACATAGGTAATACTGTCCATATGTCCCGAAACACATAGGTAATACTGTCC
1 ATATGTCCC-AAAGGACATAGGTAA-ACTGTCCATATGTCCCGAAACACATAGGTAATACTGTCC
* * *
1240213 ATATGTCCCGAAAGACAGGTAAAATTTGTTC
64 ATATGTCCCAAAAGACAAGTAAAATATGTTC
* *
1240244 ATATGTCTCAAAGGACATCGGTAA
1 ATATGTCCCAAAGGACATAGGTAA
1240268 CCATCGACTC
Statistics
Matches: 103, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
94 19 0.18
95 27 0.26
96 57 0.55
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (94 bp):
ATATGTCCCAAAGGACATAGGTAAACTGTCCATATGTCCCGAAACACATAGGTAATACTGTCCAT
ATGTCCCAAAAGACAAGTAAAATATGTTC
Found at i:1245456 original size:22 final size:22
Alignment explanation
Indices: 1245404--1245456 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1245394 TCCATTTTAT
* *
1245404 TACGGAAATGCCTTAGCACTAA
1 TACGGAAGTACCTTAGCACTAA
** *
1245426 TACAAAAGTACCTTAGCACTGA
1 TACGGAAGTACCTTAGCACTAA
1245448 TACGGAAGT
1 TACGGAAGT
1245457 GTATACGCAC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (22 bp):
TACGGAAGTACCTTAGCACTAA
Found at i:1255461 original size:16 final size:16
Alignment explanation
Indices: 1255431--1255461 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1255421 TGAAACTCGA
*
1255431 CTCGAACTCGAAAAAG
1 CTCGAACTCAAAAAAG
1255447 CTCGAACTCAAAAAA
1 CTCGAACTCAAAAAA
1255462 AATTTAAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (16 bp):
CTCGAACTCAAAAAAG
Found at i:1255488 original size:11 final size:11
Alignment explanation
Indices: 1255472--1255616 Score: 83
Period size: 11 Copynumber: 12.5 Consensus size: 11
1255462 AATTTAAGAG
1255472 CTCGATTCAAA
1 CTCGATTCAAA
** *
1255483 CTCGATTTTGAG
1 CTCGA-TTCAAA
*
1255495 CTCGATTGAAAAA
1 CTCGATT--CAAA
* *
1255508 CTCGATGCAAG
1 CTCGATTCAAA
*
1255519 CTCGATTGAGAA
1 CTCGATTCA-AA
*
1255531 GCTCGATTAAAAA
1 -CTCGATT-CAAA
*
1255544 GCTCGATTTTAAA
1 -CTCGA-TTCAAA
*
1255557 CTCGATTCAAG
1 CTCGATTCAAA
* *
1255568 CTCGTTTCAAG
1 CTCGATTCAAA
1255579 CTCGATTCAAA
1 CTCGATTCAAA
* *
1255590 CTCGTTTCAAG
1 CTCGATTCAAA
*
1255601 CTCGATTCAAG
1 CTCGATTCAAA
1255612 CTCGA
1 CTCGA
1255617 AAACGGGTTA
Statistics
Matches: 105, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
11 63 0.60
12 14 0.13
13 25 0.24
14 3 0.03
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (11 bp):
CTCGATTCAAA
Found at i:1255512 original size:36 final size:37
Alignment explanation
Indices: 1255470--1255593 Score: 116
Period size: 36 Copynumber: 3.5 Consensus size: 37
1255460 AAAATTTAAG
**
1255470 AGCTCGATTCAAACTCGATTTTG-AGCTCGATTGAAAA
1 AGCTCGATTCAAACTCGATTGAGAAGCTCGATT-AAAA
* *
1255507 A-CTCGATGCAAGCTCGATTGAGAAGCTCGATTAAAA
1 AGCTCGATTCAAACTCGATTGAGAAGCTCGATTAAAA
* * **
1255543 AGCTCGATTTTAAACTCGATT--CAAGCTCG-TT-TCA
1 AGCTCGA-TTCAAACTCGATTGAGAAGCTCGATTAAAA
1255577 AGCTCGATTCAAACTCG
1 AGCTCGATTCAAACTCG
1255594 TTTCAAGCTC
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
33 9 0.12
34 8 0.11
35 2 0.03
36 29 0.40
37 15 0.21
38 10 0.14
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (37 bp):
AGCTCGATTCAAACTCGATTGAGAAGCTCGATTAAAA
Found at i:1255585 original size:22 final size:22
Alignment explanation
Indices: 1255542--1255615 Score: 112
Period size: 22 Copynumber: 3.3 Consensus size: 22
1255532 CTCGATTAAA
* *
1255542 AAGCTCGATTTTAAACTCGATTC
1 AAGCTCG-TTTCAAGCTCGATTC
1255565 AAGCTCGTTTCAAGCTCGATTC
1 AAGCTCGTTTCAAGCTCGATTC
*
1255587 AAACTCGTTTCAAGCTCGATTC
1 AAGCTCGTTTCAAGCTCGATTC
1255609 AAGCTCG
1 AAGCTCG
1255616 AAAACGGGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 40 0.85
23 7 0.15
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (22 bp):
AAGCTCGTTTCAAGCTCGATTC
Found at i:1255599 original size:33 final size:34
Alignment explanation
Indices: 1255542--1255616 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
1255532 CTCGATTAAA
* *
1255542 AAGCTCGATTTTAAACTCGATTCAAGCTCGTTTC
1 AAGCTCGATTTCAAACTCGATTCAAGCTCGATTC
*
1255576 AAGCTCGA-TTCAAACTCGTTTCAAGCTCGATTC
1 AAGCTCGATTTCAAACTCGATTCAAGCTCGATTC
1255609 AAGCTCGA
1 AAGCTCGA
1255617 AAACGGGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 30 0.79
34 8 0.21
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (34 bp):
AAGCTCGATTTCAAACTCGATTCAAGCTCGATTC
Found at i:1256339 original size:3 final size:3
Alignment explanation
Indices: 1256331--1256358 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1256321 TTCCCCTTGC
1256331 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1256359 TACTTGATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1257200 original size:25 final size:25
Alignment explanation
Indices: 1257174--1257222 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1257164 TAGTTATTTA
1257174 AAATA-TTATCATTAGA-AATATATT
1 AAATATTTATCATTAGATAA-ATATT
*
1257198 AAATATTTGTCATTAGATAAATATT
1 AAATATTTATCATTAGATAAATATT
1257223 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 15 0.68
26 2 0.09
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (25 bp):
AAATATTTATCATTAGATAAATATT
Found at i:1257649 original size:21 final size:22
Alignment explanation
Indices: 1257599--1257650 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
1257589 ATAATTATTT
*
1257599 AAAAAA-TTAAAAAAAATATTA
1 AAAAAATTTAAAAAAAATATCA
* *
1257620 AAAATATTTAATAAAAA-ATCA
1 AAAAAATTTAAAAAAAATATCA
1257641 AAAAAATTTA
1 AAAAAATTTA
1257651 GGTTGAACCG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAAATTTAAAAAAAATATCA
Found at i:1260343 original size:119 final size:117
Alignment explanation
Indices: 1260198--1260415 Score: 305
Period size: 119 Copynumber: 1.8 Consensus size: 117
1260188 AGCCGTCGAT
* * *
1260198 GTTCGAATTCAAAACCTTTAGGAATAATAAATATTCCCTTAA-TCACTGAGTTAATTTGGTTCGT
1 GTTCGAATTCAAAACATTTAAGAATAATAAATATTCCCTTAACT-ACTGAGTTAATTTGATT--T
*
1260262 GTATATTTAATTTTA-TATTAAAATTTAGTCAATTAAAATCACTCATACTGCAGTC
63 GTATATTTAATTTTAGTATT-AAATTTAATCAATTAAAATCACTCATACTGCAGTC
* * * **
1260317 GTTCGAATTCGAAACATTTAAGAATAATAACTATTCTCTTAACTGTTGAGTTAATTTGATTTGTA
1 GTTCGAATTCAAAACATTTAAGAATAATAAATATTCCCTTAACTACTGAGTTAATTTGATTTGTA
1260382 TATTTAATTTTAGTATTAAATTTAATCAATTAAA
66 TATTTAATTTTAGTATTAAATTTAATCAATTAAA
1260416 TATACACAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
117 32 0.36
118 4 0.05
119 51 0.58
120 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (117 bp):
GTTCGAATTCAAAACATTTAAGAATAATAAATATTCCCTTAACTACTGAGTTAATTTGATTTGTA
TATTTAATTTTAGTATTAAATTTAATCAATTAAAATCACTCATACTGCAGTC
Found at i:1264385 original size:114 final size:116
Alignment explanation
Indices: 1264239--1264526 Score: 332
Period size: 117 Copynumber: 2.5 Consensus size: 116
1264229 CAATGGAAGG
* *
1264239 GTTCATAATGAGAAGAACTCGTCTGATAAGG-GAA-AAGTTCATAATGAAAAGAACTTACCCAAC
1 GTTCATAATGAGAAGAACTCATCCGATAAGGAGAAGAAGTTCATAATGAAAAGAACTTACCCAAC
** **
1264302 CTTTGTTCGATTTAATCACAGAAAGAGGTGGATCATTATTTCTACCAGAGA
66 CTTTACTCGATTTAATCACAGAAAGAGGTGGATCAGCATTTCTACCAGAGA
* * * ***
1264353 GTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAATTCATAATGAGAAGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCCGAT-AAGGAGAAGAAGTTCATAATGAAAAGAACTTACCCAA
* * * * ** *
1264418 CCTTTACTCGATTTCATCACAGAAGGAGTTGGATGAGCATTTCTGGCAGATA
65 CCTTTACTCGATTTAATCACAGAAAGAGGTGGATCAGCATTTCTACCAGAGA
* * *
1264470 GTTCAT-ATGAGAATAACTCATCCAATAAGGAAAAGAAGTTCATAAT-AATAAGAACTT
1 GTTCATAATGAGAAGAACTCATCCGATAAGGAGAAGAAGTTCATAATGAA-AAGAACTT
1264527 GTAACTCAAG
Statistics
Matches: 145, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
114 26 0.18
115 28 0.19
116 21 0.14
117 70 0.48
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (116 bp):
GTTCATAATGAGAAGAACTCATCCGATAAGGAGAAGAAGTTCATAATGAAAAGAACTTACCCAAC
CTTTACTCGATTTAATCACAGAAAGAGGTGGATCAGCATTTCTACCAGAGA
Found at i:1266671 original size:15 final size:15
Alignment explanation
Indices: 1266651--1266692 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
1266641 TTCGTCTTCT
*
1266651 TTAAAATGATTTTTC
1 TTAAAATAATTTTTC
1266666 TTAAAATAATTTTTC
1 TTAAAATAATTTTTC
1266681 TTAAAATAATTT
1 TTAAAATAATTT
1266693 AAAAGACGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (15 bp):
TTAAAATAATTTTTC
Found at i:1269886 original size:20 final size:19
Alignment explanation
Indices: 1269854--1269927 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 19
1269844 ATTCTTCTCA
1269854 TTCTATTTCTTTTTCTTATT
1 TTCT-TTTCTTTTTCTTATT
* *
1269874 TTCTTTTCATTTTTTTTCTT
1 TTCTTTTC-TTTTTCTTATT
* * *
1269894 TTCATTT-TTTTTCTTCTCA
1 TTCTTTTCTTTTTCTTAT-T
1269913 TT-TTTTCTTTTTCTT
1 TTCTTTTCTTTTTCTT
1269928 TCTTTTTATG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 12 0.27
19 14 0.31
20 19 0.42
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (19 bp):
TTCTTTTCTTTTTCTTATT
Found at i:1269915 original size:15 final size:15
Alignment explanation
Indices: 1269872--1269918 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
1269862 CTTTTTCTTA
1269872 TTTTCTTTTCATTTT
1 TTTTCTTTTCATTTT
1269887 TTTTCTTTTCATTTT
1 TTTTCTTTTCATTTT
*
1269902 TTTTCTTCTCATTTT
1 TTTTCTTTTCATTTT
1269917 TT
1 TT
1269919 CTTTTTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTTTTCATTTT
Found at i:1269933 original size:15 final size:14
Alignment explanation
Indices: 1269854--1269933 Score: 56
Period size: 15 Copynumber: 5.5 Consensus size: 14
1269844 ATTCTTCTCA
1269854 TTCTATTTCTTTT-T
1 TTCT-TTTCTTTTCT
*
1269868 CTTATTTTCTTTTCAT
1 -TTCTTTTCTTTTC-T
*
1269884 TTTTTTTCTTTTCAT
1 TTCTTTTCTTTTC-T
* * *
1269899 TTTTTTTCTTCTCA
1 TTCTTTTCTTTTCT
1269913 TT-TTTTCTTTTTCT
1 TTCTTTTC-TTTTCT
1269927 TTCTTTT
1 TTCTTTT
1269934 TATGAAATCA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
13 5 0.09
14 16 0.29
15 33 0.60
16 1 0.02
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTTTCTTTTCT
Found at i:1269933 original size:29 final size:28
Alignment explanation
Indices: 1269845--1269934 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 28
1269835 TTCATGCACA
*
1269845 TTCTTCTCATTCTATTTCTTTTTC-TTATT
1 TTCTTCTCATT-T-TTTCTTTTTCTTTTTT
* *
1269874 TTCTTTTCATTTTTTTTCTTTTCATTTTTT
1 TTCTTCTCATTTTTTCT-TTTTC-TTTTTT
1269904 TTCTTCTCATTTTTTCTTTTTCTTTCTTT
1 TTCTTCTCATTTTTTCTTTTTCTTT-TTT
1269933 TT
1 TT
1269935 ATGAAATCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
27 4 0.08
28 9 0.17
29 20 0.38
30 19 0.37
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (28 bp):
TTCTTCTCATTTTTTCTTTTTCTTTTTT
Found at i:1271813 original size:16 final size:15
Alignment explanation
Indices: 1271792--1271821 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1271782 TAAAACTCGA
1271792 CTCGAACTCGAAAAGG
1 CTCGAACTC-AAAAGG
1271808 CTCGAACTCAAAAG
1 CTCGAACTCAAAAG
1271822 AATTTCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (15 bp):
CTCGAACTCAAAAGG
Found at i:1272726 original size:21 final size:21
Alignment explanation
Indices: 1272700--1272741 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1272690 AGACATAAAT
1272700 GGGTTTATG-TGTTAGGGTTTA
1 GGGTTTATGAT-TTAGGGTTTA
1272721 GGGTTTATGATTTAGGGTTTA
1 GGGTTTATGATTTAGGGTTTA
1272742 TAGTTTAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.17, C:0.00, G:0.36, T:0.48
Consensus pattern (21 bp):
GGGTTTATGATTTAGGGTTTA
Found at i:1272734 original size:14 final size:14
Alignment explanation
Indices: 1272716--1272755 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1272706 ATGTGTTAGG
1272716 GTTTAGGGTTTAT-
1 GTTTAGGGTTTATA
1272729 GATTTAGGGTTTATA
1 G-TTTAGGGTTTATA
*
1272744 GTTTAAGGTTTA
1 GTTTAGGGTTTA
1272756 AGGTTCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 22 0.92
15 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (14 bp):
GTTTAGGGTTTATA
Found at i:1272747 original size:21 final size:21
Alignment explanation
Indices: 1272702--1272748 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1272692 ACATAAATGG
*
1272702 GTTTATGTGTTAGGGTTTAGG
1 GTTTATGTGTTAGGGTTTAGA
*
1272723 GTTTATGAT-TTAGGGTTTATA
1 GTTTATG-TGTTAGGGTTTAGA
1272744 GTTTA
1 GTTTA
1272749 AGGTTTAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (21 bp):
GTTTATGTGTTAGGGTTTAGA
Found at i:1272755 original size:21 final size:21
Alignment explanation
Indices: 1272711--1272760 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1272701 GGTTTATGTG
* *
1272711 TTAGGGTTTAGGGTTTATGAT
1 TTAGGGTTTAGAGTTTAAGAT
* *
1272732 TTAGGGTTTATAGTTTAAGGT
1 TTAGGGTTTAGAGTTTAAGAT
*
1272753 TTAAGGTT
1 TTAGGGTT
1272761 CATTACAAAG
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:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (21 bp):
TTAGGGTTTAGAGTTTAAGAT
Found at i:1273648 original size:16 final size:17
Alignment explanation
Indices: 1273621--1273652 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1273611 ATACCAATCC
1273621 TACCCAGACATGCTTTG
1 TACCCAGACATGCTTTG
1273638 TACCC-GACATGCTTT
1 TACCCAGACATGCTTT
1273653 ATTTCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (17 bp):
TACCCAGACATGCTTTG
Found at i:1275025 original size:2 final size:2
Alignment explanation
Indices: 1275018--1275063 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1275008 TGATATGAAC
1275018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1275060 AT AT
1 AT AT
1275064 TAACTAATGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1275470 original size:2 final size:2
Alignment explanation
Indices: 1275463--1275502 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1275453 AATCATAAAG
1275463 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
1275503 TAACTAATGA
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:1275495 original size:439 final size:440
Alignment explanation
Indices: 1275024--1275903 Score: 1744
Period size: 440 Copynumber: 2.0 Consensus size: 440
1275014 GAACATATAT
1275024 ATATATATATATATATATATATATATATATATATATATATTAACTAATGATCATTATTACTTAGT
1 ATATATATATATATATATATATATATATATATATATATATTAACTAATGATCATTATTACTTAGT
1275089 ATAAGAATATTATTACCATTTTAATAAAATA-TTAGGGCATATGGGTCATATTAATACGTAATAA
66 ATAAGAATATTATTACCATTTTAATAAAATATTTAGGGCATATGGGTCATATTAATACGTAATAA
1275153 ATTAAAACAAACATGAATACTACATAAAAAAAAATCAATATACTAAATCAAGACTAAACTAGAAC
131 ATTAAAACAAACATGAATACTACATAAAAAAAAATCAATATACTAAATCAAGACTAAACTAGAAC
1275218 TTCAGGGACCTATCGTCAATAAATCCATATTTTATTCATATAACCTAGTTGAAATAATGATCCAA
196 TTCAGGGACCTATCGTCAATAAATCCATATTTTATTCATATAACCTAGTTGAAATAATGATCCAA
1275283 ATAAATATGTAATAAGTCTAGAAGGGTCTAAGGCATAAATATTACCTAAAATAAACTAAGGATTA
261 ATAAATATGTAATAAGTCTAGAAGGGTCTAAGGCATAAATATTACCTAAAATAAACTAAGGATTA
1275348 AAAGTCATCAAATATGAAATTTAAGGACCATATTAAACATTTGGCCAAAGCATGTAAGACCATAT
326 AAAGTCATCAAATATGAAATTTAAGGACCATATTAAACATTTGGCCAAAGCATGTAAGACCATAT
*
1275413 GTAGTGACTAAAATGAACAAAAAAATAAGTACAGTGCGTAAATCATAAAG
391 GTAGTGACTAAAATGAACAAAAAAATAAGAACAGTGCGTAAATCATAAAG
1275463 ATATATATATATATATATATATATATATATATATATATATTAACTAATGATCATTATTACTTAGT
1 ATATATATATATATATATATATATATATATATATATATATTAACTAATGATCATTATTACTTAGT
1275528 ATAAGAATATTATTACCATTTTAATAAAATATTTAGGGCATATGGGTCATATTAATACGTAATAA
66 ATAAGAATATTATTACCATTTTAATAAAATATTTAGGGCATATGGGTCATATTAATACGTAATAA
1275593 ATTAAAACAAACATGAATACTACATAAAAAAAAATCAATATACTAAATCAAGACTAAACTAGAAC
131 ATTAAAACAAACATGAATACTACATAAAAAAAAATCAATATACTAAATCAAGACTAAACTAGAAC
1275658 TTCAGGGACCTATCGTCAATAAATCCATATTTTATTCATATAACCTAGTTGAAATAATGATCCAA
196 TTCAGGGACCTATCGTCAATAAATCCATATTTTATTCATATAACCTAGTTGAAATAATGATCCAA
1275723 ATAAATATGTAATAAGTCTAGAAGGGTCTAAGGCATAAATATTACCTAAAATAAACTAAGGATTA
261 ATAAATATGTAATAAGTCTAGAAGGGTCTAAGGCATAAATATTACCTAAAATAAACTAAGGATTA
1275788 AAAGTCATCAAATATGAAATTTAAGGACCATATTAAACATTTGGCCAAAGCATGTAAGACCATAT
326 AAAGTCATCAAATATGAAATTTAAGGACCATATTAAACATTTGGCCAAAGCATGTAAGACCATAT
1275853 GTAGTGACTAAAATGAACAAAAAAATAAGAACAGTGCGTAAATCATAAAG
391 GTAGTGACTAAAATGAACAAAAAAATAAGAACAGTGCGTAAATCATAAAG
1275903 A
1 A
1275904 GATAAAACTT
Statistics
Matches: 439, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
439 96 0.22
440 343 0.78
ACGTcount: A:0.47, C:0.12, G:0.11, T:0.30
Consensus pattern (440 bp):
ATATATATATATATATATATATATATATATATATATATATTAACTAATGATCATTATTACTTAGT
ATAAGAATATTATTACCATTTTAATAAAATATTTAGGGCATATGGGTCATATTAATACGTAATAA
ATTAAAACAAACATGAATACTACATAAAAAAAAATCAATATACTAAATCAAGACTAAACTAGAAC
TTCAGGGACCTATCGTCAATAAATCCATATTTTATTCATATAACCTAGTTGAAATAATGATCCAA
ATAAATATGTAATAAGTCTAGAAGGGTCTAAGGCATAAATATTACCTAAAATAAACTAAGGATTA
AAAGTCATCAAATATGAAATTTAAGGACCATATTAAACATTTGGCCAAAGCATGTAAGACCATAT
GTAGTGACTAAAATGAACAAAAAAATAAGAACAGTGCGTAAATCATAAAG
Found at i:1276958 original size:3 final size:3
Alignment explanation
Indices: 1276950--1276980 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1276940 TGGTTTATTG
*
1276950 TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1276981 TTTAGGGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1277441 original size:32 final size:32
Alignment explanation
Indices: 1277386--1277446 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1277376 ATCCAATTTG
*
1277386 ACCCGAATCGAAAACAAATCGAACCGAAATTA
1 ACCCAAATCGAAAACAAATCGAACCGAAATTA
*
1277418 ACCCAAATCGAAAA-TAATCCGAACCGAAA
1 ACCCAAATCGAAAACAAAT-CGAACCGAAA
1277447 GCAACTCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.51, C:0.26, G:0.11, T:0.11
Consensus pattern (32 bp):
ACCCAAATCGAAAACAAATCGAACCGAAATTA
Found at i:1277445 original size:16 final size:16
Alignment explanation
Indices: 1277386--1277446 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
1277376 ATCCAATTTG
* *
1277386 ACCCGAATCGAAAACA
1 ACCCGAACCGAAAATA
** *
1277402 AATCGAACCGAAATTA
1 ACCCGAACCGAAAATA
* *
1277418 ACCCAAATCGAAAATA
1 ACCCGAACCGAAAATA
*
1277434 ATCCGAACCGAAA
1 ACCCGAACCGAAA
1277447 GCAACTCGAA
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.51, C:0.26, G:0.11, T:0.11
Consensus pattern (16 bp):
ACCCGAACCGAAAATA
Found at i:1277958 original size:3 final size:3
Alignment explanation
Indices: 1277950--1277975 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1277940 AATTAATATC
1277950 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1277976 ATTTCTTTGA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1281573 original size:21 final size:19
Alignment explanation
Indices: 1281546--1281602 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 19
1281536 ATCCTCTAGC
*
1281546 AAAAGGATTGATCCCTTTG
1 AAAAGGATCGATCCCTTTG
* *
1281565 ACCAAAGGATCAATCCCCTTG
1 A--AAAGGATCGATCCCTTTG
1281586 AAAAGGATCGATCCCTT
1 AAAAGGATCGATCCCTT
1281603 GGATTCCAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (19 bp):
AAAAGGATCGATCCCTTTG
Found at i:1281600 original size:40 final size:41
Alignment explanation
Indices: 1281526--1281602 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
1281516 ATTTTTGGTA
* *
1281526 CAAAGGATCAATCCTCTAGCAAAAGGATTGATCCCTTTGAC
1 CAAAGGATCAATCCCCTAGCAAAAGGATCGATCCCTTTGAC
*
1281567 CAAAGGATCAATCCCCTTG-AAAAGGATCGATCCCTT
1 CAAAGGATCAATCCCCTAGCAAAAGGATCGATCCCTT
1281603 GGATTCCAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 16 0.48
41 17 0.52
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (41 bp):
CAAAGGATCAATCCCCTAGCAAAAGGATCGATCCCTTTGAC
Found at i:1283103 original size:7 final size:6
Alignment explanation
Indices: 1283062--1283102 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
1283052 AGAAGAAGGG
*
1283062 AAAGAA AAAG-A AAAGAA AGAGAA AAAGAA AAAGATA AAAGA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGA-A AAAGA
1283103 TGTAGGCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
5 5 0.16
6 20 0.65
7 6 0.19
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:1286057 original size:15 final size:16
Alignment explanation
Indices: 1286031--1286060 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1286021 TAGAGAGTAC
1286031 ATAGAGGATGAGCACG
1 ATAGAGGATGAGCACG
1286047 ATAGA-GATGAGCAC
1 ATAGAGGATGAGCAC
1286061 ATGGATGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.13, G:0.33, T:0.13
Consensus pattern (16 bp):
ATAGAGGATGAGCACG
Found at i:1295124 original size:36 final size:37
Alignment explanation
Indices: 1295027--1295158 Score: 157
Period size: 36 Copynumber: 3.6 Consensus size: 37
1295017 TTCTAAATTG
1295027 TTTTTGAAAATACATATATAATATATAG--TTTAAAACA
1 TTTTTGAAAAT--ATATATAATATATAGTTTTTAAAACA
* * *
1295064 TTTTTTGAAAATATGTATATTATATAGTTTTTAAAATA
1 -TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
* *
1295102 TTTTTGAAAAT-TATATAATATATAGTTTTGAAAACG
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
1295138 TTTTT-AAAATATATAT-ATATA
1 TTTTTGAAAATATATATAATATA
1295159 CTTTTGAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
35 10 0.12
36 43 0.52
37 11 0.13
38 19 0.23
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:1295188 original size:33 final size:33
Alignment explanation
Indices: 1295114--1295189 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
1295104 TTTGAAAATT
* * * *
1295114 ATATAATATATAGTTTTGAAAACGTTTTTAAAAT
1 ATAT-ATATATACTTTTGAAAACGTTATGAAAAC
1295148 ATATATATATACTTTTGAAAACGTTATGAAAAC
1 ATATATATATACTTTTGAAAACGTTATGAAAAC
*
1295181 ATTTATATA
1 ATATATATA
1295190 ATATATAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 33 0.89
34 4 0.11
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (33 bp):
ATATATATATACTTTTGAAAACGTTATGAAAAC
Found at i:1295234 original size:15 final size:16
Alignment explanation
Indices: 1295216--1295245 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1295206 AAAAAAACCA
1295216 TTTTGAAAA-TATATT
1 TTTTGAAAATTATATT
1295231 TTTTGAAAATTATAT
1 TTTTGAAAATTATAT
1295246 AATATATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTGAAAATTATATT
Found at i:1295282 original size:37 final size:37
Alignment explanation
Indices: 1295230--1295415 Score: 143
Period size: 37 Copynumber: 5.1 Consensus size: 37
1295220 GAAAATATAT
*
1295230 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAACG
1 TTTTTAAAAATATATATAATATATAGTTTTTGAAACG
* *
1295266 TTTTT-AAAA-ATATAT-ATATATA-CTTTTGAAAATG
1 TTTTTAAAAATATATATAATATATAGTTTTTG-AAACG
* * * * * *
1295300 TTATGAAAACATTTATATAATATATAATTTTTAAAAACC
1 TTTTTAAAA-ATATATATAATATATAGTTTTT-GAAACG
* * *
1295339 ATTTTGAAAATATATATAATATATAGTTTTTTAAAAC-
1 TTTTTAAAAATATATATAATATATAG-TTTTTGAAACG
* * *
1295376 ATTTTAAAAATTTATATATTATAT-GTTTTTGAAAACG
1 TTTTTAAAAATATATATAATATATAGTTTTTG-AAACG
1295413 TTT
1 TTT
1295416 ATATATATAA
Statistics
Matches: 119, Mismatches: 20, Indels: 21
0.74 0.12 0.13
Matches are distributed among these distances:
33 5 0.04
34 14 0.12
35 17 0.14
36 11 0.09
37 28 0.24
38 27 0.23
39 17 0.14
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (37 bp):
TTTTTAAAAATATATATAATATATAGTTTTTGAAACG
Found at i:1295355 original size:38 final size:36
Alignment explanation
Indices: 1295231--1295399 Score: 146
Period size: 38 Copynumber: 4.6 Consensus size: 36
1295221 AAAATATATT
* * *
1295231 TTTTGAAAAT-TATATAATATATAGTTTTTGAAACG
1 TTTTGAAAATATATATAATATATAATTTTTAAAACA
* * * **
1295266 TTTTTAAAA-ATATAT-ATATATACTTTTGAAAATG
1 TTTTGAAAATATATATAATATATAATTTTTAAAACA
* *
1295300 TTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTG-AAA-ATATATATAATATATAATTTTT-AAAA-CA
*
1295340 TTTTGAAAATATATATAATATATAGTTTTTTAAAACA
1 TTTTGAAAATATATATAATATATA-ATTTTTAAAACA
* * *
1295377 TTTTAAAAATTTATATATTATAT
1 TTTTGAAAATATATATAATATAT
1295400 GTTTTTGAAA
Statistics
Matches: 108, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
34 18 0.17
35 16 0.15
36 1 0.01
37 27 0.25
38 30 0.28
39 12 0.11
40 4 0.04
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAATTTTTAAAACA
Found at i:1295356 original size:128 final size:125
Alignment explanation
Indices: 1295102--1295353 Score: 429
Period size: 129 Copynumber: 2.0 Consensus size: 125
1295092 TTTTAAAATA
1295102 TTTTTGAAAATTATATAATATATAGTTTTGAAAACGTTTTTAAAATATATATATATACTTTTGAA
1 TTTTTGAAAATTATATAATATATAGTTTTGAAAACGTTTTTAAAATATATATATATACTTTTGAA
1295167 AACGTTATGAAAACATTTATATAATATATAATTTTTTAAAAAAAAACCATTTTGAAAATATAT
66 AACGTTATGAAAACATTTATATAATATATAATTTTTT---AAAAAACCATTTTGAAAATATAT
1295230 TTTTTGAAAATTATATAATATATAGTTTTTG-AAACGTTTTTAAAAATATATATATATACTTTTG
1 TTTTTGAAAATTATATAATATATAG-TTTTGAAAACGTTTTT-AAAATATATATATATACTTTTG
*
1295294 AAAATGTTATGAAAACATTTATATAATATATAA-TTTTT-AAAAACCATTTTGAAAATATAT
64 AAAACGTTATGAAAACATTTATATAATATATAATTTTTTAAAAAACCATTTTGAAAATATAT
1295354 ATAATATATA
Statistics
Matches: 121, Mismatches: 1, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
124 22 0.18
128 40 0.33
129 59 0.49
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (125 bp):
TTTTTGAAAATTATATAATATATAGTTTTGAAAACGTTTTTAAAATATATATATATACTTTTGAA
AACGTTATGAAAACATTTATATAATATATAATTTTTTAAAAAACCATTTTGAAAATATAT
Found at i:1297070 original size:10 final size:9
Alignment explanation
Indices: 1297035--1297133 Score: 90
Period size: 10 Copynumber: 10.3 Consensus size: 9
1297025 GCTGCTGGAA
*
1297035 ACCGGTTTA
1 ACCGGTTTG
*
1297044 ACCGGTTTTCA
1 ACCGG-TTT-G
1297055 ACCGGTTCTG
1 ACCGGTT-TG
1297065 ACCGGTTTG
1 ACCGGTTTG
*
1297074 ACCGGTTTCA
1 ACCGGTTT-G
*
1297084 ACCGGTTCG
1 ACCGGTTTG
1297093 AACCGGTTTG
1 -ACCGGTTTG
*
1297103 ACCGGTCTG
1 ACCGGTTTG
1297112 ACTCGGTTTG
1 AC-CGGTTTG
*
1297122 ACCGGTCTG
1 ACCGGTTTG
1297131 ACC
1 ACC
1297134 CGACCCGACC
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
9 34 0.45
10 35 0.46
11 7 0.09
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1297079 original size:19 final size:19
Alignment explanation
Indices: 1297036--1297133 Score: 87
Period size: 19 Copynumber: 5.1 Consensus size: 19
1297026 CTGCTGGAAA
* * *
1297036 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
1297056 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
1297075 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
1297095 CCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
1297113 CTCGGTTTGACCGG-TCTGA
1 C-CGGTTTGACCGGTTCTGA
1297132 CC
1 CC
1297134 CGACCCGACC
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
18 6 0.09
19 39 0.57
20 15 0.22
21 8 0.12
ACGTcount: A:0.14, C:0.29, G:0.28, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:1297097 original size:29 final size:30
Alignment explanation
Indices: 1297034--1297108 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
1297024 GGCTGCTGGA
*
1297034 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
1297065 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
1297093 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
1297109 CTGACTCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:1297118 original size:29 final size:28
Alignment explanation
Indices: 1297035--1297133 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 28
1297025 GCTGCTGGAA
* *
1297035 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TCTCAACCGGTTC-G
*
1297065 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTCTCAACCGGTTCG
* *
1297093 AACCGGTTTGACCGGTCT-GACTCGGTTTG
1 -ACCGGTTTGACCGGTCTCAAC-CGGTTCG
*
1297122 ACCGGTCTGACC
1 ACCGGTTTGACC
1297134 CGACCCGACC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
28 14 0.23
29 35 0.56
30 13 0.21
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.29
Consensus pattern (28 bp):
ACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:1297140 original size:5 final size:5
Alignment explanation
Indices: 1297130--1297187 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
1297120 TGACCGGTCT
* *
1297130 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
1297179 GACCC GACC
1 GACCC GACC
1297188 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:1297156 original size:22 final size:22
Alignment explanation
Indices: 1297130--1297194 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
1297120 TGACCGGTCT
1297130 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1297152 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1297174 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
1297195 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:1297196 original size:7 final size:7
Alignment explanation
Indices: 1297184--1297221 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
1297174 GACCCGACCC
1297184 GACCGTT
1 GACCGTT
1297191 GACCGTT
1 GACCGTT
1297198 GACCGTT
1 GACCGTT
1297205 GACCGTT
1 GACCGTT
1297212 GACCGTT
1 GACCGTT
1297219 GAC
1 GAC
1297222 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:1304404 original size:10 final size:9
Alignment explanation
Indices: 1304369--1304467 Score: 90
Period size: 10 Copynumber: 10.3 Consensus size: 9
1304359 GCTGCTGGAA
*
1304369 ACCGGTTTA
1 ACCGGTTTG
*
1304378 ACCGGTTTTCA
1 ACCGG-TTT-G
1304389 ACCGGTTCTG
1 ACCGGTT-TG
1304399 ACCGGTTTG
1 ACCGGTTTG
*
1304408 ACCGGTTTCA
1 ACCGGTTT-G
*
1304418 ACCGGTTCG
1 ACCGGTTTG
1304427 AACCGGTTTG
1 -ACCGGTTTG
*
1304437 ACCGGTCTG
1 ACCGGTTTG
1304446 ACTCGGTTTG
1 AC-CGGTTTG
*
1304456 ACCGGTCTG
1 ACCGGTTTG
1304465 ACC
1 ACC
1304468 CGACCCGACC
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
9 34 0.45
10 35 0.46
11 7 0.09
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1304413 original size:19 final size:19
Alignment explanation
Indices: 1304370--1304467 Score: 87
Period size: 19 Copynumber: 5.1 Consensus size: 19
1304360 CTGCTGGAAA
* * *
1304370 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
1304390 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
1304409 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
1304429 CCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
1304447 CTCGGTTTGACCGG-TCTGA
1 C-CGGTTTGACCGGTTCTGA
1304466 CC
1 CC
1304468 CGACCCGACC
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
18 6 0.09
19 39 0.57
20 15 0.22
21 8 0.12
ACGTcount: A:0.14, C:0.29, G:0.28, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:1304431 original size:29 final size:30
Alignment explanation
Indices: 1304368--1304442 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
1304358 GGCTGCTGGA
*
1304368 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
1304399 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
1304427 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
1304443 CTGACTCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:1304452 original size:29 final size:28
Alignment explanation
Indices: 1304369--1304467 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 28
1304359 GCTGCTGGAA
* *
1304369 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TCTCAACCGGTTC-G
*
1304399 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTCTCAACCGGTTCG
* *
1304427 AACCGGTTTGACCGGTCT-GACTCGGTTTG
1 -ACCGGTTTGACCGGTCTCAAC-CGGTTCG
*
1304456 ACCGGTCTGACC
1 ACCGGTTTGACC
1304468 CGACCCGACC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
28 14 0.23
29 35 0.56
30 13 0.21
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.29
Consensus pattern (28 bp):
ACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:1304474 original size:5 final size:5
Alignment explanation
Indices: 1304464--1304521 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
1304454 TGACCGGTCT
* *
1304464 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
1304513 GACCC GACC
1 GACCC GACC
1304522 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:1304490 original size:22 final size:22
Alignment explanation
Indices: 1304464--1304528 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
1304454 TGACCGGTCT
1304464 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1304486 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1304508 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
1304529 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:1304530 original size:7 final size:7
Alignment explanation
Indices: 1304518--1304555 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
1304508 GACCCGACCC
1304518 GACCGTT
1 GACCGTT
1304525 GACCGTT
1 GACCGTT
1304532 GACCGTT
1 GACCGTT
1304539 GACCGTT
1 GACCGTT
1304546 GACCGTT
1 GACCGTT
1304553 GAC
1 GAC
1304556 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:1306581 original size:20 final size:20
Alignment explanation
Indices: 1306556--1306593 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1306546 CATCCATGTT
* *
1306556 TCTTTTTTTTTCTTTTTCAC
1 TCTTTTATTTTCATTTTCAC
1306576 TCTTTTATTTTCATTTTC
1 TCTTTTATTTTCATTTTC
1306594 GGTTACTTAT
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:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (20 bp):
TCTTTTATTTTCATTTTCAC
Found at i:1306706 original size:25 final size:24
Alignment explanation
Indices: 1306648--1306707 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
1306638 TTATTATTAT
*
1306648 TATTATTATTTTTGATAAATTTTA
1 TATTATCATTTTTGATAAATTTTA
**
1306672 T-TTATCCATTTTTTTTAAATTTTA
1 TATTAT-CATTTTTGATAAATTTTA
1306696 TCATTATCATTT
1 T-ATTATCATTT
1306708 AACTAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 4 0.13
24 17 0.57
25 5 0.17
26 4 0.13
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (24 bp):
TATTATCATTTTTGATAAATTTTA
Found at i:1307966 original size:16 final size:16
Alignment explanation
Indices: 1307945--1307989 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
1307935 TAACACATGA
1307945 ATATATTGTTATATAT
1 ATATATTGTTATATAT
*
1307961 ATATATTGTTATATGT
1 ATATATTGTTATATAT
*
1307977 ATGTATTG-TATAT
1 ATATATTGTTATAT
1307990 GATCATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (16 bp):
ATATATTGTTATATAT
Found at i:1308556 original size:14 final size:15
Alignment explanation
Indices: 1308529--1308558 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1308519 TATTCAGATT
1308529 ATTTTTTTACTTTAA
1 ATTTTTTTACTTTAA
1308544 ATTTTTTTA-TTTAA
1 ATTTTTTTACTTTAA
1308558 A
1 A
1308559 AATTGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTTTACTTTAA
Found at i:1308743 original size:2 final size:2
Alignment explanation
Indices: 1308736--1308762 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1308726 GGATTATGTT
1308736 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 T
1308763 TGCATTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1312996 original size:2 final size:2
Alignment explanation
Indices: 1312989--1313021 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1312979 GTGAGGTACG
*
1312989 AT AT AT AT AT AT AT AT AT AT A- AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1313022 GCGTCTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1323146 original size:14 final size:14
Alignment explanation
Indices: 1323120--1323164 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
1323110 AAGCAGTATC
1323120 GATACCG-AAAGGG
1 GATACCGAAAAGGG
1323133 GATACCGAAAAGGG
1 GATACCGAAAAGGG
*
1323147 GATATCGAAAAGGG
1 GATACCGAAAAGGG
1323161 GATA
1 GATA
1323165 TCGATACTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 7 0.23
14 23 0.77
ACGTcount: A:0.42, C:0.11, G:0.36, T:0.11
Consensus pattern (14 bp):
GATACCGAAAAGGG
Found at i:1323165 original size:14 final size:14
Alignment explanation
Indices: 1323127--1323168 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
1323117 ATCGATACCG
*
1323127 AAAGGGGATACCGA
1 AAAGGGGATATCGA
1323141 AAAGGGGATATCGA
1 AAAGGGGATATCGA
1323155 AAAGGGGATATCGA
1 AAAGGGGATATCGA
1323169 TACTGTGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.36, T:0.12
Consensus pattern (14 bp):
AAAGGGGATATCGA
Found at i:1323823 original size:54 final size:54
Alignment explanation
Indices: 1323628--1324100 Score: 637
Period size: 54 Copynumber: 8.6 Consensus size: 54
1323618 TACAAAAAGT
* * * * * *
1323628 TAAGAAATTCATAATTAGTTTATGAATTTCCGTATGAGCACCT-TGTGTGCAAAAAGT
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCA-CTATGTGTGC--AAA-C
* * * * *
1323685 TAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAGC
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGC--AAA-C
*
1323742 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAC
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGCAAAC
* *
1323796 TAAGAAATTCACACTAAGTGTGTGAATTTCCGTATGAGCACTATGTGTGCAAAC
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGCAAAC
1323850 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTAT-GGCACTATGTGTGCAAAC
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGCAAAC
1323903 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGCAAAC
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGCAAAC
* *
1323957 CAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAAC
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGCAAAC
* * * * *
1324011 CAAGAAATTCATATTAAGTGTGTGAATTTCCGTATGGGAACTATATGTGCAAAGA
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGCAAA-C
* *
1324066 TAAGAAATTCATAATAAGTAG-GTGAATTTCTGTAT
1 TAAGAAATTCATACTAAGT-GTGTGAATTTCCGTAT
1324101 TGGTAGTGGG
Statistics
Matches: 391, Mismatches: 21, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
53 52 0.13
54 205 0.52
55 33 0.08
56 3 0.01
57 98 0.25
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (54 bp):
TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGCAAAC
Found at i:1323922 original size:107 final size:109
Alignment explanation
Indices: 1323623--1324084 Score: 653
Period size: 107 Copynumber: 4.2 Consensus size: 109
1323613 GAGTGTACAA
* * * * * *
1323623 AAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGAGCACCT-TGTGTGCAAAAAGTTA
1 AAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCA-CTATGTGTGC--AAA-CTA
* * * * *
1323687 AGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACTTTGTGTGC
62 AGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGC
1323735 AAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAACTAAG
1 --AAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAACTAAG
* *
1323800 AAATTCACACTAAGTGTGTGAATTTCCGTATGAGCACTATGTGTGC
64 AAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGC
*
1323846 AAA-CTAAGAAATTCATACTAAGTGTGTGAATTTCCGTAT-GGCACTATGTGTGCAAACTAAGAA
1 AAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAACTAAGAA
1323909 ATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGC
66 ATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGC
* *
1323953 AAA-CCAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAACCAAGAA
1 AAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAACTAAGAA
* * *
1324017 ATTCATATTAAGTGTGTGAATTTCCGTATGGGAACTATATGTGC
66 ATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGC
* *
1324061 AAAGATAAGAAATTCATAATAAGT
1 AAAGCTAAGAAATTCATACTAAGT
1324085 AGGTGAATTT
Statistics
Matches: 320, Mismatches: 25, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
107 103 0.32
108 102 0.32
109 20 0.06
111 43 0.13
112 3 0.01
113 2 0.01
114 47 0.15
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.32
Consensus pattern (109 bp):
AAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAACTAAGAA
ATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGC
Found at i:1323942 original size:161 final size:163
Alignment explanation
Indices: 1323629--1324100 Score: 655
Period size: 161 Copynumber: 2.9 Consensus size: 163
1323619 ACAAAAAGTT
* * * * *
1323629 AAGAAATTCATAATTAGTTTATGAATTTCCGTATGAGCACCT-TGTGTGCAAAAAGTTAAGAAAT
1 AAGAAATTCACACTAAGTGTATGAATTTCCGTATGAGCA-CTATGTGTGC--AAA-CTAAGAAAT
* * * *
1323693 TCATAATTAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAGCTAAGAAATTCATACTA
62 TCATAATAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGC--AAAGCTAAGAAATTCATACTA
* *
1323758 AGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAACT
125 AGTGTGTGAATTTCCGTATGGGCACTATGTGTGCAAACC
*
1323797 AAGAAATTCACACTAAGTGTGTGAATTTCCGTATGAGCACTATGTGTGCAAACTAAGAAATTCAT
1 AAGAAATTCACACTAAGTGTATGAATTTCCGTATGAGCACTATGTGTGCAAACTAAGAAATTCAT
*
1323862 ACTAAGTGTGTGAATTTCCGTAT-GGCACTATGTGTGCAAA-CTAAGAAATTCATACTAAGTGTG
66 AATAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGCAAAGCTAAGAAATTCATACTAAGTGTG
1323925 TGAATTTCCGTATGGGCACTATGTGTGCAAACC
131 TGAATTTCCGTATGGGCACTATGTGTGCAAACC
* * *
1323958 AAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTGCAAACCAAGAAATTCAT
1 AAGAAATTCACACTAAGTGTATGAATTTCCGTATGAGCACTATGTGTGCAAACTAAGAAATTCAT
* * * * *
1324023 ATTAAGTGTGTGAATTTCCGTATGGGAACTATATGTGCAAAGATAAGAAATTCATAATAAGTAG-
66 AATAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGCAAAGCTAAGAAATTCATACTAAGT-GT
*
1324087 GTGAATTTCTGTAT
130 GTGAATTTCCGTAT
1324101 TGGTAGTGGG
Statistics
Matches: 277, Mismatches: 23, Indels: 13
0.88 0.07 0.04
Matches are distributed among these distances:
161 137 0.49
162 18 0.06
163 31 0.11
164 14 0.05
165 31 0.11
166 3 0.01
167 2 0.01
168 41 0.15
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (163 bp):
AAGAAATTCACACTAAGTGTATGAATTTCCGTATGAGCACTATGTGTGCAAACTAAGAAATTCAT
AATAAGTGTGTGAATTTCCGTATGGGCACTATGTGTGCAAAGCTAAGAAATTCATACTAAGTGTG
TGAATTTCCGTATGGGCACTATGTGTGCAAACC
Found at i:1329883 original size:22 final size:19
Alignment explanation
Indices: 1329837--1329890 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
1329827 TGCAAAAATG
*
1329837 GTATCGATACCGTAATAGA
1 GTATCGATACCATAATAGA
1329856 GTATCGATACCATAGTATAGTA
1 GTATCGATACCATA--ATAG-A
*
1329878 GTATCGGTACCAT
1 GTATCGATACCAT
1329891 GGTAGGGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 13 0.43
21 4 0.13
22 13 0.43
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (19 bp):
GTATCGATACCATAATAGA
Found at i:1330331 original size:57 final size:57
Alignment explanation
Indices: 1330238--1330405 Score: 255
Period size: 57 Copynumber: 2.9 Consensus size: 57
1330228 ATGACACTGA
* *
1330238 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAAATTCCGTATGGGCACCTT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACATT
* *
1330295 GTGTTCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCATATGGGCACATT
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACATT
* * * * *
1330352 TTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCAC
1 GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCAC
1330406 TATGTATGCA
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 100 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (57 bp):
GTGTGCAAAAAGTTAAGAAATTCATAATTAGTTTATGAATTTCCGTATGGGCACATT
Found at i:1330455 original size:54 final size:54
Alignment explanation
Indices: 1330308--1330670 Score: 451
Period size: 54 Copynumber: 6.6 Consensus size: 54
1330298 TTCAAAAAGT
* * * * * *
1330308 TAAGAAATTCATAATTAGTTTATGAATTTCCATATGGGCAC-ATTTTGTGCAAAAAGC
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTA-TATGTGC--AAA-C
* * *
1330365 TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTATGCAAAC
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATATGTGCAAAC
* **
1330419 TAAAAAATTCATACTAAGTGTGTGAATTTCTATATGGGCACTATATGTGCAAAC
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATATGTGCAAAC
* * *
1330473 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGAGCACTATGTATGCAAAC
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATATGTGCAAAC
* * *
1330527 TATGAAATTCATACTAAGTGTGTGAATTTTCGTATGGGCACTATATGTGTAAAC
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATATGTGCAAAC
* * *
1330581 TAAGAAATTCATACTAAGTGTGTGAATTTCCATATGGGAATTATATGTGCAAAC
1 TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATATGTGCAAAC
* *
1330635 ATAAGAAATTCATAATAAGTAG-GTGAATTTCTGTAT
1 -TAAGAAATTCATACTAAGT-GTGTGAATTTCCGTAT
1330671 TGGTAGTGGG
Statistics
Matches: 270, Mismatches: 33, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
54 193 0.71
55 33 0.12
56 1 0.00
57 42 0.16
58 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (54 bp):
TAAGAAATTCATACTAAGTGTGTGAATTTCCGTATGGGCACTATATGTGCAAAC
Found at i:1332228 original size:20 final size:20
Alignment explanation
Indices: 1332203--1332253 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1332193 GAGGGTTGTA
*
1332203 GTATCGATACCAGATGCTCG
1 GTATCGAGACCAGATGCTCG
* *
1332223 GTATCGAGATCAGATGCTCA
1 GTATCGAGACCAGATGCTCG
*
1332243 GTCTCGAGACC
1 GTATCGAGACC
1332254 GTTGGTCTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.24
Consensus pattern (20 bp):
GTATCGAGACCAGATGCTCG
Found at i:1332287 original size:20 final size:21
Alignment explanation
Indices: 1332264--1332311 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1332254 GTTGGTCTCT
*
1332264 ATACCGAATGACTG-GTATCC
1 ATACCGAAAGACTGAGTATCC
*
1332284 ATACC-AAAGATTGAGTATCC
1 ATACCGAAAGACTGAGTATCC
1332304 ATACCGAA
1 ATACCGAA
1332312 GGCTTGATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 16 0.67
21 2 0.08
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (21 bp):
ATACCGAAAGACTGAGTATCC
Found at i:1339878 original size:20 final size:19
Alignment explanation
Indices: 1339855--1339925 Score: 88
Period size: 20 Copynumber: 3.6 Consensus size: 19
1339845 CGAATGACTA
1339855 GTATCCATACCGAAGGATTG
1 GTATCCATACC-AAGGATTG
*
1339875 GTATCCATACCAAAGATTG
1 GTATCCATACCAAGGATTG
1339894 AGTATCCATACCAAAGGATTG
1 -GTATCCATACC-AAGGATTG
* *
1339915 ATATCGATACC
1 GTATCCATACC
1339926 TAAAGTGGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.16
20 31 0.69
21 7 0.16
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.25
Consensus pattern (19 bp):
GTATCCATACCAAGGATTG
Found at i:1339911 original size:40 final size:41
Alignment explanation
Indices: 1339854--1339930 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
1339844 GCGAATGACT
* *
1339854 AGTATCCATACCGAAGGATTGGTATCCATACC-AAAGATTG
1 AGTATCCATACCAAAGGATTGATATCCATACCTAAAGATTG
*
1339894 AGTATCCATACCAAAGGATTGATATCGATACCTAAAG
1 AGTATCCATACCAAAGGATTGATATCCATACCTAAAG
1339931 TGGTTGAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (41 bp):
AGTATCCATACCAAAGGATTGATATCCATACCTAAAGATTG
Found at i:1347473 original size:24 final size:26
Alignment explanation
Indices: 1347436--1347483 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
1347426 TCATGCATTG
*
1347436 TTTTATAATATGTTTT-TATTTTTAC
1 TTTTATAAGATGTTTTATATTTTTAC
1347461 TTTTA-AAGATGTTTTATATTTTT
1 TTTTATAAGATGTTTTATATTTTT
1347484 TTGTGGACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (26 bp):
TTTTATAAGATGTTTTATATTTTTAC
Found at i:1347761 original size:20 final size:21
Alignment explanation
Indices: 1347737--1347783 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1347727 GCGAATATGT
1347737 AAATT-GCATTGCGATTTTCC
1 AAATTCGCATTGCGATTTTCC
* **
1347757 GAATTCGTGTTGCGATTTTCC
1 AAATTCGCATTGCGATTTTCC
1347778 AAATTC
1 AAATTC
1347784 ACAACGCGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (21 bp):
AAATTCGCATTGCGATTTTCC
Found at i:1347822 original size:20 final size:20
Alignment explanation
Indices: 1347799--1347847 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1347789 GCGAATCTAT
*
1347799 AATTCGCAACACATAAGTCA
1 AATTCGCAACACAGAAGTCA
1347819 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
1347839 AATTCGCAA
1 AATTCGCAA
1347848 AGCGCGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.18
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:1350143 original size:21 final size:21
Alignment explanation
Indices: 1350116--1350165 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1350106 GTTAGGGGAG
* *
1350116 TTACGTGATGAGGTCAATGCT
1 TTACGTGAGGAGGTCAATACT
* *
1350137 TTGCGTGAGGAGGTCGATACT
1 TTACGTGAGGAGGTCAATACT
1350158 TTACGTGA
1 TTACGTGA
1350166 AGACAATGGT
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:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:1350206 original size:21 final size:22
Alignment explanation
Indices: 1350182--1350278 Score: 64
Period size: 21 Copynumber: 4.6 Consensus size: 22
1350172 TGGTGCATGG
*
1350182 CGTGATGAGGTA-CTGTCTTTA
1 CGTGATGAGGTAGATGTCTTTA
* *
1350203 CGTGGTGAGGTAGAGGT-TTTA
1 CGTGATGAGGTAGATGTCTTTA
*
1350224 CGTGATGA---AAATGGTGCTTTA
1 CGTGATGAGGTAGAT-GT-CTTTA
* *
1350245 CGTGGTGAGGT--ATCTACTTTA
1 CGTGATGAGGTAGATGT-CTTTA
1350266 CGTGATGAGGTAG
1 CGTGATGAGGTAG
1350279 CCACTTTACG
Statistics
Matches: 57, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
18 2 0.04
19 2 0.04
21 49 0.86
22 4 0.07
ACGTcount: A:0.22, C:0.10, G:0.34, T:0.34
Consensus pattern (22 bp):
CGTGATGAGGTAGATGTCTTTA
Found at i:1350284 original size:21 final size:21
Alignment explanation
Indices: 1350240--1350291 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1350230 GAAAATGGTG
* * *
1350240 CTTTACGTGGTGAGGTATCTA
1 CTTTACGTGATGAGGTAGCCA
1350261 CTTTACGTGATGAGGTAGCCA
1 CTTTACGTGATGAGGTAGCCA
1350282 CTTTACGTGA
1 CTTTACGTGA
1350292 GATTGTTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (21 bp):
CTTTACGTGATGAGGTAGCCA
Found at i:1350287 original size:63 final size:63
Alignment explanation
Indices: 1350118--1350291 Score: 163
Period size: 63 Copynumber: 2.8 Consensus size: 63
1350108 TAGGGGAGTT
* * * * * *
1350118 ACGTGATGAGGTCAATG-CTTTGCGTGAGGAGGTCGATACTTTACGTGAAGACAATGGTGCATG
1 ACGTGATGAGGT-ACTGACTTTACGTGATGAGGTAGACACTTTACGTGAAGAAAATGGTGCATG
* * * *** * * *
1350181 GCGTGATGAGGTACTGTCTTTACGTGGTGAGGTAGAGGTTTTACGTGATGAAAATGGTGCTTT
1 ACGTGATGAGGTACTGACTTTACGTGATGAGGTAGACACTTTACGTGAAGAAAATGGTGCATG
* *
1350244 ACGTGGTGAGGTATCT-ACTTTACGTGATGAGGTAGCCACTTTACGTGA
1 ACGTGATGAGGTA-CTGACTTTACGTGATGAGGTAGACACTTTACGTGA
1350292 GATTGTTGCA
Statistics
Matches: 88, Mismatches: 21, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
62 3 0.03
63 83 0.94
64 2 0.02
ACGTcount: A:0.23, C:0.13, G:0.33, T:0.31
Consensus pattern (63 bp):
ACGTGATGAGGTACTGACTTTACGTGATGAGGTAGACACTTTACGTGAAGAAAATGGTGCATG
Found at i:1350414 original size:12 final size:12
Alignment explanation
Indices: 1350388--1350429 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1350378 TTTTTCGGCA
1350388 TTATTTATTTG-T
1 TTATTTA-TTGAT
1350400 TTATTTATTGAT
1 TTATTTATTGAT
* *
1350412 TTATGTATTAAT
1 TTATTTATTGAT
1350424 TTATTT
1 TTATTT
1350430 TTAGCGGCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
TTATTTATTGAT
Found at i:1350600 original size:21 final size:21
Alignment explanation
Indices: 1350574--1350711 Score: 143
Period size: 21 Copynumber: 6.6 Consensus size: 21
1350564 TTCACCTGTC
*
1350574 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
*
1350595 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
*
1350616 ATCGTTCAAGAGGCCCCT-AT
1 ATCGTTCAAGAGGCCCCTCCT
* * * *
1350636 CATCCTTTAATAGGCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* **
1350658 ATCATTCAAGAGGCCCCTATT
1 ATCGTTCAAGAGGCCCCTCCT
* *
1350679 ATCGTTCAAGAGGTCCCTCCC
1 ATCGTTCAAGAGGCCCCTCCT
*
1350700 ACCGTTCAAGAG
1 ATCGTTCAAGAG
1350712 CCCGATTTAC
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
20 1 0.01
21 95 0.99
ACGTcount: A:0.22, C:0.34, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:1351892 original size:14 final size:14
Alignment explanation
Indices: 1351873--1351900 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1351863 ATTGATGTAT
1351873 TTTGTAAAAGTTGA
1 TTTGTAAAAGTTGA
1351887 TTTGTAAAAGTTGA
1 TTTGTAAAAGTTGA
1351901 CAAATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.43
Consensus pattern (14 bp):
TTTGTAAAAGTTGA
Found at i:1351996 original size:64 final size:64
Alignment explanation
Indices: 1351883--1352033 Score: 203
Period size: 64 Copynumber: 2.4 Consensus size: 64
1351873 TTTGTAAAAG
**** *
1351883 TTGATTTGTAAAAGTTGACAAATTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAAAAAGAATTATTTTTTGCTTGTTTAA
* * ***
1351947 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAAAAATTCTTATTTTTTGCTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAAAAAGAATTATTTTTTGCTTGTTTAA
*
1352011 TTTATTTGTAAAAGTTGATTTGT
1 TTGATTTGTAAAAGTTGATTTGT
1352034 CGTTTTAAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 76 1.00
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.50
Consensus pattern (64 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAAAAAGAATTATTTTTTGCTTGTTTAA
Found at i:1352453 original size:18 final size:18
Alignment explanation
Indices: 1352430--1352465 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1352420 AAGCCTATTG
*
1352430 TGATTAGGATTTTGATTT
1 TGATTACGATTTTGATTT
1352448 TGATTACGATTTTGATTT
1 TGATTACGATTTTGATTT
1352466 CCTTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (18 bp):
TGATTACGATTTTGATTT
Found at i:1354917 original size:12 final size:12
Alignment explanation
Indices: 1354896--1354929 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1354886 GGTTGCGGGT
*
1354896 TTTGAGATTGTG
1 TTTGATATTGTG
1354908 TTTGATATTGTG
1 TTTGATATTGTG
*
1354920 TTTGGTATTG
1 TTTGATATTG
1354930 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1355560 original size:14 final size:15
Alignment explanation
Indices: 1355524--1355561 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1355514 GAAATCATTG
1355524 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1355539 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1355554 AAAAATTA
1 AAAAATTA
1355562 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1355743 original size:20 final size:20
Alignment explanation
Indices: 1355718--1355788 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1355708 ACTAAAACCT
1355718 GTTGCGAATTCGAAAATCAA
1 GTTGCGAATTCGAAAATCAA
*
1355738 GTTGCGAATTC-AGAAATCGA
1 GTTGCGAATTCGA-AAATCAA
* * *
1355758 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTCGAAAATCA-A
1355779 GTTGCGAATT
1 GTTGCGAATT
1355789 TGGAAAATCG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 1 0.02
20 31 0.72
21 11 0.26
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (20 bp):
GTTGCGAATTCGAAAATCAA
Done.