Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009405.1 Hibiscus syriacus cultivar Beakdansim tig00113337_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: 1310060
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1181548 original size:10 final size:10
Alignment explanation
Indices: 1181513--1181565 Score: 65
Period size: 10 Copynumber: 5.5 Consensus size: 10
1181503 TTCAGACTGA
*
1181513 TCAAATCGGT
1 TCAAACCGGT
*
1181523 TCAGACCGG-
1 TCAAACCGGT
1181532 TCAAACCGGT
1 TCAAACCGGT
*
1181542 TCGAACCGGT
1 TCAAACCGGT
1181552 T-AAACCGGT
1 TCAAACCGGT
1181561 TCAAA
1 TCAAA
1181566 ACTGGTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 16 0.44
10 20 0.56
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1183428 original size:23 final size:23
Alignment explanation
Indices: 1183360--1183420 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
1183350 ACACTTTATA
1183360 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1183383 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1183406 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
1183421 TTTATACGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1197208 original size:22 final size:22
Alignment explanation
Indices: 1197128--1197210 Score: 103
Period size: 22 Copynumber: 3.8 Consensus size: 22
1197118 CCATCATATA
*
1197128 ACTAAAGTGCCTTAACACTGAT
1 ACTAAAGTGCCTTAGCACTGAT
* * *
1197150 ACTAAAGTGTCTCATCACTGAT
1 ACTAAAGTGCCTTAGCACTGAT
* **
1197172 ACGAAAGTGTATTAGCACTGAT
1 ACTAAAGTGCCTTAGCACTGAT
1197194 ACTAAAGTGCCTTAGCA
1 ACTAAAGTGCCTTAGCA
1197211 TTGGAGGGAA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (22 bp):
ACTAAAGTGCCTTAGCACTGAT
Found at i:1213775 original size:37 final size:37
Alignment explanation
Indices: 1213699--1213775 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
1213689 TTTTTATATT
*
1213699 TTTAATTTTGTAAAAAAATTATATAAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAAATATTATCAA
* *
1213736 TTTAATTTTTTAAAGAAAA-TATAT-AAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAAATATTAT-CAA
1213773 TTT
1 TTT
1213776 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 8 0.23
37 23 0.66
38 4 0.11
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAATTATATAAAATATTATCAA
Found at i:1213957 original size:20 final size:20
Alignment explanation
Indices: 1213921--1213958 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1213911 ATCCTATTCC
**
1213921 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1213941 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1213959 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1215083 original size:21 final size:20
Alignment explanation
Indices: 1215016--1215090 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
1215006 CAGTTTCCAA
* * *
1215016 AATCGCAACGCGATTCTTGAC
1 AATCGCAATGCGATT-TTCAT
1215037 AATCGCAATGCGATTTTCAT
1 AATCGCAATGCGATTTTCAT
* *
1215057 ATTCGCATTGCGATTTTCCAT
1 AATCGCAATGCGATTTT-CAT
*
1215078 AATCGCAACGCGA
1 AATCGCAATGCGA
1215091 ATATGAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 18 0.40
21 27 0.60
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (20 bp):
AATCGCAATGCGATTTTCAT
Found at i:1215172 original size:20 final size:20
Alignment explanation
Indices: 1215078--1215306 Score: 232
Period size: 20 Copynumber: 11.4 Consensus size: 20
1215068 GATTTTCCAT
* ** *
1215078 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1215098 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1215118 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1215138 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1215158 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1215178 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1215198 TATCGCAACACGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1215218 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* *
1215238 AATCGCAACG-ATAATCTGTA
1 AATCGCAACGCGT-ATCCGTA
*
1215258 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1215278 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1215298 AATCACAAC
1 AATCGCAAC
1215307 ACTGAAATTT
Statistics
Matches: 183, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
19 2 0.01
20 179 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1216036 original size:24 final size:24
Alignment explanation
Indices: 1215997--1216043 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1215987 GAATTTGGTC
1215997 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1216021 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1216044 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1218559 original size:52 final size:52
Alignment explanation
Indices: 1218497--1218666 Score: 170
Period size: 52 Copynumber: 3.2 Consensus size: 52
1218487 TCGCAACGAG
1218497 AATCGCAATGCGAAATGAAAATC-CTAACAAGA-AATCGCAATACGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGC-AACAAGAGAATCGCAATAC-GAAATGAA
* *
1218549 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACAAGAGAATCGCAATACGAAATGAA
* * * * * *
1218601 AATCGTAACGAGAGAATCG-CAAT-GCAGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGCA-ACAA-GAGAATCGCAATACGAAATGAA
*
1218654 AATCGCATTGCGA
1 AATCGCAATGCGA
1218667 TTCTCTCGTT
Statistics
Matches: 100, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
52 51 0.51
53 48 0.48
54 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACAAGAGAATCGCAATACGAAATGAA
Found at i:1218586 original size:33 final size:33
Alignment explanation
Indices: 1218549--1218642 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1218539 CGGAAATGAA
1218549 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
1218582 AATCGCAATGCGAAATGAAAATCGTAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1218615 AATCGCAATGCAGAAATGAAAATCGCAA
1 AATCGCAATGC-GAAATGAAAATCGCAA
1218643 TGCGAAATGA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 43 0.74
34 15 0.26
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:1218665 original size:19 final size:19
Alignment explanation
Indices: 1218497--1218666 Score: 149
Period size: 19 Copynumber: 9.7 Consensus size: 19
1218487 TCGCAACGAG
1218497 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1218516 AATC-CTAA--C--AA-G-A
1 AATCGC-AATGCGAAATGAA
*
1218529 AATCGCAATACGGAAATGAA
1 AATCGCAATGC-GAAATGAA
1218549 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1218568 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1218582 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
1218601 AATCGTAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1218615 AATCGCAATGCAGAAATGAA
1 AATCGCAATGC-GAAATGAA
1218635 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1218654 AATCGCATTGCGA
1 AATCGCAATGCGA
1218667 TTCTCTCGTT
Statistics
Matches: 123, Mismatches: 8, Indels: 40
0.72 0.05 0.23
Matches are distributed among these distances:
13 7 0.06
14 21 0.17
15 5 0.04
16 3 0.02
17 6 0.05
18 4 0.03
19 53 0.43
20 24 0.20
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1218680 original size:86 final size:85
Alignment explanation
Indices: 1218485--1218660 Score: 293
Period size: 86 Copynumber: 2.1 Consensus size: 85
1218475 CGGAAATTAC
*
1218485 AATCGCAAC--GAGAATCGCAATGCGAAATGAAAATCCTAACAAGAAATCGCAATACGGAAATGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCTAACAAGAAATCGCAATACAGAAATGA
1218548 AAATCGCAATGCGAAATGAA
66 AAATCGCAATGCGAAATGAA
* * *
1218568 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGTAACGAGAGAATCGCAATGCAGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCTAACAAGA-AATCGCAATACAGAAATG
1218633 AAAATCGCAATGCGAAATGAA
65 AAAATCGCAATGCGAAATGAA
1218654 AATCGCA
1 AATCGCA
1218661 TTGCGATTCT
Statistics
Matches: 86, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
83 9 0.10
85 33 0.38
86 44 0.51
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (85 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCTAACAAGAAATCGCAATACAGAAATGA
AAATCGCAATGCGAAATGAA
Found at i:1218700 original size:53 final size:52
Alignment explanation
Indices: 1218637--1218752 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
1218627 GAAATGAAAA
*
1218637 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
1218689 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1218742 TCGCATTGCGA
1 TCGCATTGCGA
1218753 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1218715 original size:19 final size:19
Alignment explanation
Indices: 1218675--1218762 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
1218665 GATTCTCTCG
1218675 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1218695 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1218714 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1218728 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1218747 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1218763 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1218872 original size:14 final size:14
Alignment explanation
Indices: 1218853--1218889 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1218843 CATCAATTAC
1218853 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1218867 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1218881 ACAAATCAA
1 ACAAATCAA
1218890 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1220845 original size:19 final size:19
Alignment explanation
Indices: 1220821--1220941 Score: 144
Period size: 19 Copynumber: 6.6 Consensus size: 19
1220811 CACGAAACTT
**
1220821 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
* *
1220840 AGAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAACC
1220859 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
**
1220878 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
1220897 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
1220911 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
1220930 AAAATCGCAACG
1 AAAATCGCAACG
1220942 AGAGAATCGT
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 71 0.83
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:1220848 original size:38 final size:38
Alignment explanation
Indices: 1220806--1220908 Score: 104
Period size: 38 Copynumber: 2.7 Consensus size: 38
1220796 TATTTTACTT
* ** *
1220806 TCGCACACGAAACTTAAAATCGCAACGCGAAATGAGAA
1 TCGCACACGAAACTCAAAATCGCAACGCGAAACCAAAA
1220844 TCGCA-ACGAGAAAC-CAAAATCGCAACGCGAAACCAAAA
1 TCGCACAC--GAAACTCAAAATCGCAACGCGAAACCAAAA
* *
1220882 TCGCAACGCGAAA-TGAAAATCGCAACG
1 TCGC-ACACGAAACTCAAAATCGCAACG
1220909 ACAGAATCGC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
37 2 0.04
38 45 0.83
39 6 0.11
40 1 0.02
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.10
Consensus pattern (38 bp):
TCGCACACGAAACTCAAAATCGCAACGCGAAACCAAAA
Found at i:1220922 original size:33 final size:33
Alignment explanation
Indices: 1220880--1220972 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1220870 GCGAAACCAA
1220880 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
** *
1220913 AATCGCAACGCGAAACCAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
*
1220946 AATCGTAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1220973 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:1220939 original size:52 final size:55
Alignment explanation
Indices: 1220821--1220941 Score: 185
Period size: 52 Copynumber: 2.2 Consensus size: 55
1220811 CACGAAACTT
*
1220821 AAAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAAC-AG-AACCAAAATCGCAACGCGAAACC
*
1220878 AAAATCGCAACGCGAAATGAAAATCGCAAC-G-A-CAGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAATCGCAACGCGAAACC
1220930 AAAATCGCAACG
1 AAAATCGCAACG
1220942 AGAGAATCGT
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
52 31 0.50
53 1 0.02
55 1 0.02
57 29 0.47
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.07
Consensus pattern (55 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACAGAACCAAAATCGCAACGCGAAACC
Found at i:1220969 original size:52 final size:52
Alignment explanation
Indices: 1220839--1220977 Score: 156
Period size: 52 Copynumber: 2.7 Consensus size: 52
1220829 AACGCGAAAT
* * * *
1220839 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGAAACGCGAAACGAAAATCGCAACGCGAAACCAAAATCGCAACGA
** *
1220891 GA-AAT-GAAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGA
1 GAGAATCGAAACGCGAAACGA-A-AATCGCAACGCGAAACCAAAATCGCAACGA
* * *
1220943 GAGAATCGTAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGAAACGCGAAACGAAAATCGCAACGCGA
1220978 TTTTGGTTTC
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
50 8 0.11
51 4 0.06
52 45 0.64
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.24, G:0.21, T:0.09
Consensus pattern (52 bp):
GAGAATCGAAACGCGAAACGAAAATCGCAACGCGAAACCAAAATCGCAACGA
Found at i:1220977 original size:19 final size:19
Alignment explanation
Indices: 1220821--1220977 Score: 136
Period size: 19 Copynumber: 8.8 Consensus size: 19
1220811 CACGAAACTT
*
1220821 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACG
* * *
1220840 AGAATCGCAACGAGAAACC
1 AAAATCGCAACGCGAAACG
*
1220859 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACG
*
1220878 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACG
1220897 AAAATCGCAA--CG--AC-
1 AAAATCGCAACGCGAAACG
* *
1220911 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACG
1220930 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAACG
* * *
1220944 AGAATCGTAACGCGAAATG
1 AAAATCGCAACGCGAAACG
*
1220963 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
1220978 TTTTGGTTTC
Statistics
Matches: 111, Mismatches: 17, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
14 17 0.15
15 2 0.02
16 4 0.04
17 4 0.04
18 3 0.03
19 81 0.73
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACG
Found at i:1221008 original size:14 final size:14
Alignment explanation
Indices: 1220989--1221047 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1220979 TTTGGTTTCG
1220989 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1221003 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
1221020 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
1221036 CGTTGCGATTTT
1 CGTTGCGATTTT
1221048 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1221015 original size:33 final size:33
Alignment explanation
Indices: 1220973--1221096 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
1220963 AAAATCGCAA
*
1220973 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1221006 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
1221039 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* *
1221072 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-GGTTTCGCGTTGCGA
1221097 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1221027 original size:19 final size:18
Alignment explanation
Indices: 1220973--1221064 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
1220963 AAAATCGCAA
1220973 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1220992 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
1221006 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
1221025 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
1221039 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
1221058 TGCGATT
1 TGCGATT
1221065 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:1221074 original size:14 final size:14
Alignment explanation
Indices: 1221022--1221078 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1221012 TTTGGTTTCG
*
1221022 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
1221036 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1221055 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1221069 CGTTGCGATT
1 CGTTGCGATT
1221079 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1223041 original size:20 final size:20
Alignment explanation
Indices: 1223010--1223106 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
1223000 TTTTGGTTGA
1223010 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
1223030 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1223050 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
1223069 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
1223084 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1223104 AAT
1 AAT
1223107 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1223062 original size:21 final size:21
Alignment explanation
Indices: 1223008--1223072 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1222998 TCTTTTGGTT
1223008 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
1223029 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1223049 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1223070 GAA
1 GAA
1223073 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1223076 original size:14 final size:14
Alignment explanation
Indices: 1223057--1223113 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1223047 GAGAAATGAA
1223057 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1223071 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1223090 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1223104 AATCGCAACG
1 AATCGCAACG
1223114 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1223089 original size:33 final size:33
Alignment explanation
Indices: 1223008--1223130 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
1222998 TCTTTTGGTT
*
1223008 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
1223049 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1223082 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1223115 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1223131 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1223183 original size:21 final size:21
Alignment explanation
Indices: 1223158--1223231 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
1223148 GTTGCGATTC
1223158 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
1223179 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
1223200 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
1223221 TCTCGTTGCGA
1 TCTCGTTGCGA
1223232 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:1223353 original size:33 final size:33
Alignment explanation
Indices: 1223311--1223381 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1223301 AATACTAACT
1223311 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* * *
1223344 TGAAAATCGCAACGAGATAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1223377 TGAAA
1 TGAAA
1223382 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1223786 original size:20 final size:20
Alignment explanation
Indices: 1223761--1223893 Score: 205
Period size: 20 Copynumber: 6.7 Consensus size: 20
1223751 CTTTAAAAAT
1223761 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1223781 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1223801 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1223821 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1223841 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1223861 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
1223881 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1223894 TCATATTCAC
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 103 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1223912 original size:60 final size:60
Alignment explanation
Indices: 1223760--1223912 Score: 209
Period size: 60 Copynumber: 2.5 Consensus size: 60
1223750 GCTTTAAAAA
* *
1223760 TCGCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCATTGCGATTTACGGAT
* * *
1223820 ACGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
1 TCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCATTGCGATTTACG-GAT
* ** *
1223880 TCGCGTTGCGATTTTCATATTCACGTTGCGATT
1 TCGCGTTGCGATTTACGGATACACGTTGCGATT
1223913 ATGGAAAATC
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 81 0.99
61 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCATTGCGATTTACGGAT
Found at i:1223941 original size:20 final size:21
Alignment explanation
Indices: 1223906--1223951 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1223896 ATATTCACGT
*
1223906 TGCGATTATGGAAAATCGCAA
1 TGCGAATATGGAAAATCGCAA
*
1223927 TGCGAATAT-GAAAATCGCAT
1 TGCGAATATGGAAAATCGCAA
1223947 TGCGA
1 TGCGA
1223952 TTGTCAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCGAATATGGAAAATCGCAA
Found at i:1227398 original size:2 final size:2
Alignment explanation
Indices: 1227391--1227416 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1227381 TGCCTTAGCG
1227391 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1227417 AAGTTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1232768 original size:59 final size:60
Alignment explanation
Indices: 1232664--1232836 Score: 178
Period size: 60 Copynumber: 2.9 Consensus size: 60
1232654 TATTTGGATG
* * * *
1232664 AATTTGGCGATGAAATTCG-AA-GATCTAAAAGTTT-AGAGACCAATTTGAAATGAGATTCAT
1 AATTTGGGGATGAAATT-GAAATG-TTTAAAAGTTTAAG-GATCAATTTGAAATGAGATACAT
* *
1232724 AATTTTGGGATG-AATT-AGAATGTTTAAAAGTTTAAGGATTAATTT-AAAGTGAGATACAT
1 AATTTGGGGATGAAATTGA-AATGTTTAAAAGTTTAAGGATCAATTTGAAA-TGAGATACAT
* * *
1232783 AGTTTGGGGATGAAATTGAAATTTTTAAGAGTTTAAGGATCAATTTGAAATGAG
1 AATTTGGGGATGAAATTGAAATGTTTAAAAGTTTAAGGATCAATTTGAAATGAG
1232837 GGTCATAGTC
Statistics
Matches: 94, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
58 3 0.03
59 42 0.45
60 45 0.48
61 4 0.04
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (60 bp):
AATTTGGGGATGAAATTGAAATGTTTAAAAGTTTAAGGATCAATTTGAAATGAGATACAT
Found at i:1232828 original size:60 final size:59
Alignment explanation
Indices: 1232689--1232836 Score: 176
Period size: 59 Copynumber: 2.5 Consensus size: 59
1232679 TTCGAAGATC
* * *
1232689 TAAAAGTTT-AGAGACCAATTTGAAATGAGATTCATAATTTTGGGATGAATTAGAATGTT
1 TAAAAGTTTAAG-GATCAATTTGAAATGAGATACATAATTTGGGGATGAATTAGAATGTT
* * *
1232748 TAAAAGTTTAAGGATTAATTT-AAAGTGAGATACATAGTTTGGGGATGAAATT-GAAATTTT
1 TAAAAGTTTAAGGATCAATTTGAAA-TGAGATACATAATTTGGGGATG-AATTAG-AATGTT
*
1232808 TAAGAGTTTAAGGATCAATTTGAAATGAG
1 TAAAAGTTTAAGGATCAATTTGAAATGAG
1232837 GGTCATAGTC
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
58 3 0.04
59 36 0.47
60 34 0.45
61 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.35
Consensus pattern (59 bp):
TAAAAGTTTAAGGATCAATTTGAAATGAGATACATAATTTGGGGATGAATTAGAATGTT
Found at i:1241378 original size:161 final size:161
Alignment explanation
Indices: 1241021--1241416 Score: 656
Period size: 160 Copynumber: 2.5 Consensus size: 161
1241011 AACATTTTTA
*
1241021 GTAAAAAAGTAGAAATTGAAGTTACATA-ATATTCTATTGTGGTATATGAGCATGTGGTTCATAT
1 GTAAAAAAG-AGGAATTGAAGTTACATAGATATTCTATTGTGGTATATGAGCATGTGGTTCATAT
* * *
1241085 TT-G-AAAAAAAAGCGTACTTACAATAAATGATGAATTGAAGAAATAAGGAAATTATGAAAAATT
65 TTGGTAAAAAAAAGCATACTTAAAATAAATGATGAATTGAAGAAATAAGGAAATTATGAAAAAAT
1241148 GAGGGCCTAAATTGAAAAATAAAAAAATTATT
130 GAGGGCCTAAATTGAAAAATAAAAAAATTATT
* *
1241180 GTAAAAAAGAGGAATTGAAGTTACATAGATATTCTATTGTGGTATATGAGCATGTGATTCAGATT
1 GTAAAAAAGAGGAATTGAAGTTACATAGATATTCTATTGTGGTATATGAGCATGTGGTTCATATT
*
1241245 TGGTAAAAAAAA-CATACTTAAAATAAATGATGAATTGAATAAATAAGGAAATTATGAAAAAATG
66 TGGTAAAAAAAAGCATACTTAAAATAAATGATGAATTGAAGAAATAAGGAAATTATGAAAAAATG
1241309 AGGGCCTAAATTGAAAAATAAAAAAATTATT
131 AGGGCCTAAATTGAAAAATAAAAAAATTATT
* * *
1241340 GTCAAAAAAGAGGAATTGAAGTTACATAGGTATTCTATTATGGTATACGAGCATGTGGTTCATAT
1 GT-AAAAAAGAGGAATTGAAGTTACATAGATATTCTATTGTGGTATATGAGCATGTGGTTCATAT
1241405 TTGGTAAAAAAA
65 TTGGTAAAAAAA
1241417 TGATGAATTG
Statistics
Matches: 221, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
158 17 0.08
159 45 0.20
160 82 0.37
161 77 0.35
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (161 bp):
GTAAAAAAGAGGAATTGAAGTTACATAGATATTCTATTGTGGTATATGAGCATGTGGTTCATATT
TGGTAAAAAAAAGCATACTTAAAATAAATGATGAATTGAAGAAATAAGGAAATTATGAAAAAATG
AGGGCCTAAATTGAAAAATAAAAAAATTATT
Found at i:1241535 original size:143 final size:145
Alignment explanation
Indices: 1241263--1241557 Score: 389
Period size: 143 Copynumber: 2.0 Consensus size: 145
1241253 AAAACATACT
* * * * * *
1241263 TAAAATAAATGATGAATTGAATAAATAAGGAAATTATGAAAAAATGAGGGCCTAAATTGAAAAAT
1 TAAAA-AAATGATGAATTGAAGAAAAAAAGAAATTATGAAAAAATGAAGGACAAAATTGAAAAAT
* * * *
1241328 AAAAAAATTATTGTCAAAAAAGAGGAATTGAAGTTACATAGGTATTCTATTATGGTATACGAGCA
65 AAAAAAATAATTATCAAAAAAGAGGAATTGAAGTTACATAGGTATTCTATGATGATATACGAGCA
* *
1241393 TGTGGTTCATATTTGG
130 TGTGGTTAAAATTTGG
* *
1241409 TAAAAAAATGATGAATTGAAGAAAAAAAGAAATTATG-AAAAATTAATGACAAAATTGAAAAATA
1 TAAAAAAATGATGAATTGAAGAAAAAAAGAAATTATGAAAAAATGAAGGACAAAATTGAAAAATA
* * * *
1241473 AAAAAATAATTATC-ACAAAGAGGAATTGAAAG-TACATATGTATTCTATGATGATTTATGAGCA
66 AAAAAATAATTATCAAAAAAGAGGAATTG-AAGTTACATAGGTATTCTATGATGATATACGAGCA
1241536 TGTGGTTAAAATTTGG
130 TGTGGTTAAAATTTGG
1241552 TAAAAA
1 TAAAAA
1241558 TGGACTTAAA
Statistics
Matches: 130, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
143 59 0.45
144 37 0.28
145 29 0.22
146 5 0.04
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.28
Consensus pattern (145 bp):
TAAAAAAATGATGAATTGAAGAAAAAAAGAAATTATGAAAAAATGAAGGACAAAATTGAAAAATA
AAAAAATAATTATCAAAAAAGAGGAATTGAAGTTACATAGGTATTCTATGATGATATACGAGCAT
GTGGTTAAAATTTGG
Found at i:1242321 original size:20 final size:21
Alignment explanation
Indices: 1242296--1242338 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1242286 TGGCCATGGG
* *
1242296 TCGGGTTGGGTTGGGT-TTTT
1 TCGGGTCGGGTCGGGTATTTT
1242316 TCGGGTCGGGTCGGGTATTTT
1 TCGGGTCGGGTCGGGTATTTT
1242337 TC
1 TC
1242339 ACCCTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.02, C:0.12, G:0.42, T:0.44
Consensus pattern (21 bp):
TCGGGTCGGGTCGGGTATTTT
Found at i:1242471 original size:28 final size:28
Alignment explanation
Indices: 1242357--1242481 Score: 142
Period size: 28 Copynumber: 4.2 Consensus size: 28
1242347 ATCGAACTCA
* *
1242357 ACCCAAATATCACACTTTAAAAAAACTGACCCA
1 ACCCGAATATCACAC-TT-AAAAAA---ACCCG
*
1242390 ACCCGAATATCACACTTAAAAAAACACG
1 ACCCGAATATCACACTTAAAAAAACCCG
*
1242418 ACCCAAATATCACACTTAAAAAAACCCG
1 ACCCGAATATCACACTTAAAAAAACCCG
* *
1242446 ACTCGAATATCAAACTTAAAAAAACCCCG
1 ACCCGAATATCACACTTAAAAAAA-CCCG
1242475 ACCCGAA
1 ACCCGAA
1242482 CCCAAATTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
28 50 0.61
29 10 0.12
31 6 0.07
32 2 0.02
33 14 0.17
ACGTcount: A:0.49, C:0.30, G:0.06, T:0.15
Consensus pattern (28 bp):
ACCCGAATATCACACTTAAAAAAACCCG
Found at i:1247763 original size:2 final size:2
Alignment explanation
Indices: 1247758--1247783 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1247748 AATTTTTTTA
1247758 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
1247784 TTACTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1248311 original size:20 final size:20
Alignment explanation
Indices: 1248286--1248330 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1248276 ATATTGCCAT
* *
1248286 TTTTTGACAGAACGTATGAA
1 TTTTTGACAGAACATATAAA
*
1248306 TTTTTGACATAACATATAAA
1 TTTTTGACAGAACATATAAA
1248326 TTTTT
1 TTTTT
1248331 ATTTTTGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (20 bp):
TTTTTGACAGAACATATAAA
Found at i:1249847 original size:22 final size:22
Alignment explanation
Indices: 1249799--1249848 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1249789 CCTTATATAT
* * *
1249799 TTTTTAAATTTTTTAAATTTTA
1 TTTTTAAAATTTTTAAACTGTA
1249821 TTTTTAAAATTTTTAATACTGTA
1 TTTTTAAAATTTTTAA-ACTGTA
1249844 TTTTT
1 TTTTT
1249849 TTAAATTCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTTTAAAATTTTTAAACTGTA
Found at i:1257082 original size:2 final size:2
Alignment explanation
Indices: 1257075--1257133 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1257065 AGGTATTTAG
1257075 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
1257117 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1257134 ATAAAAGCCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1260428 original size:39 final size:40
Alignment explanation
Indices: 1260361--1260446 Score: 140
Period size: 39 Copynumber: 2.2 Consensus size: 40
1260351 TGAAAAAATT
*
1260361 AAACTC-AAAACATTCTAAAACTTAGTTTGATCGAAGCTC
1 AAACTCAAAAACATTCTAAAACTTAGTTTGATCAAAGCTC
*
1260400 AAACTCAAAAACATTCTAAAACTT-GTTTGATTAAAGCTC
1 AAACTCAAAAACATTCTAAAACTTAGTTTGATCAAAGCTC
1260439 AAACTCAA
1 AAACTCAA
1260447 GCTAAACATG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 27 0.61
40 17 0.39
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (40 bp):
AAACTCAAAAACATTCTAAAACTTAGTTTGATCAAAGCTC
Found at i:1260576 original size:39 final size:39
Alignment explanation
Indices: 1260533--1260618 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
1260523 ATAAAAAATT
1260533 AAACTCAAAA-CATTCTAAAACTTAATTTGATCGAAGCTC
1 AAACTCAAAATCATTCTAAAA-TTAATTTGATCGAAGCTC
** *
1260572 AAACTCAAAATCATTCTAAAATTTGTTTGATTGAAGCTC
1 AAACTCAAAATCATTCTAAAATTAATTTGATCGAAGCTC
1260611 AAACTCAA
1 AAACTCAA
1260619 CCTAAACATG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 33 0.77
40 10 0.23
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (39 bp):
AAACTCAAAATCATTCTAAAATTAATTTGATCGAAGCTC
Found at i:1260639 original size:172 final size:172
Alignment explanation
Indices: 1260353--1260707 Score: 622
Period size: 172 Copynumber: 2.1 Consensus size: 172
1260343 CTAGAACTTG
*
1260353 AAAAAATTAAACTCAAAACATTCTAAAACTTAGTTTGATCGAAGCTCAAACTCAAAAACATTCTA
1 AAAAAATTAAACTCAAAACATTCTAAAACTTAATTTGATCGAAGCTCAAACTCAAAAACATTCTA
* *
1260418 AAACTTGTTTGATTAAAGCTCAAACTCAAGCTAAACATGAACTTTAAATACATGAAAACCTTATA
66 AAACTTGTTTGATTAAAGCTCAAACTCAACCTAAACATGAACTTTAAATACATAAAAACCTTATA
1260483 TTGCATTTAATAAAATA-AAATATTTAATATTATTAATAATAT
131 TTGCATTTAATAAAATATAAA-ATTTAATATTATTAATAATAT
*
1260525 AAAAAATTAAACTCAAAACATTCTAAAACTTAATTTGATCGAAGCTCAAACTCAAAATCATTCTA
1 AAAAAATTAAACTCAAAACATTCTAAAACTTAATTTGATCGAAGCTCAAACTCAAAAACATTCTA
* *
1260590 AAATTTGTTTGATTGAAGCTCAAACTCAACCTAAACATGAACTTTAAATACATAAAAACCTTATA
66 AAACTTGTTTGATTAAAGCTCAAACTCAACCTAAACATGAACTTTAAATACATAAAAACCTTATA
*
1260655 TTGCATTTAATAAAATATAAAATTTAATATTATTAATAATTT
131 TTGCATTTAATAAAATATAAAATTTAATATTATTAATAATAT
*
1260697 TAAAAATTAAA
1 AAAAAATTAAA
1260708 AAATTTAATA
Statistics
Matches: 174, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
172 171 0.98
173 3 0.02
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.33
Consensus pattern (172 bp):
AAAAAATTAAACTCAAAACATTCTAAAACTTAATTTGATCGAAGCTCAAACTCAAAAACATTCTA
AAACTTGTTTGATTAAAGCTCAAACTCAACCTAAACATGAACTTTAAATACATAAAAACCTTATA
TTGCATTTAATAAAATATAAAATTTAATATTATTAATAATAT
Found at i:1260722 original size:17 final size:17
Alignment explanation
Indices: 1260659--1260722 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 17
1260649 CTTATATTGC
* *
1260659 ATTTAATAAAATATAAA
1 ATTTAATAAATTAAAAA
* *
1260676 ATTTAATATTATTAATAA
1 ATTTAATA-AATTAAAAA
*
1260694 TTTTAA-AAATTAAAAA
1 ATTTAATAAATTAAAAA
*
1260710 ATTTAATATATTA
1 ATTTAATAAATTA
1260723 TTTTCTCAAG
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
16 12 0.33
17 14 0.39
18 10 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAATAAATTAAAAA
Found at i:1269222 original size:391 final size:390
Alignment explanation
Indices: 1268502--1269284 Score: 1512
Period size: 391 Copynumber: 2.0 Consensus size: 390
1268492 GTAAAGGCAT
1268502 CAATAGCCTATGTTGCTATGGCTATTCGATTTTCGGTTCCAAACATGGAATGGGAATACAACCTT
1 CAATAGCCTATGTTGCTATGGCTATTCGATTTTCGGTTCCAAACATGGAATGGGAATACAACCTT
1268567 CAAAGATCATCCATATCAATGAAAAAGTTAAAGAAAAACACGAACAGAACCATACAGGATATTAG
66 CAAAGATCATCCATATCAATGAAAAAGTTAAAGAAAAACACGAACAGAACCATACAGGATATTAG
*
1268632 GACGCATATACTGAAAAATAAGAAAAAAACCATACAGGACACATACTGATAAACAAGAACAATAT
131 GACGCATATACTGAAAAATAAAAAAAAAACCATACAGGACACATACTGATAAACAAGAACAATAT
1268697 TCTCATTCCATGTTTGGAAATGTATACAGGTTCAACACCAACACAGTCAAAGTAACATAAATGTC
196 TCTCATTCCATGTTTGGAAATGTATACAGGTTCAACACCAACACAGTCAAAGTAACATAAATGTC
1268762 AACTTGGAAAGATAGATAATAGAATCTTCAAAACATCAGTGAATCATGTTTTCATTTTCAAAGGG
261 AACTTGGAAAGATAGATAATAGAATCTTCAAAACATCAGTGAATCATGTTTTCATTTTCAAAGGG
1268827 TGCAACAGCAGCTGATTTTCAGGAATATTCACTTTATTTCACCTGACATTCCAAAAGCAAGTAAC
326 TGCAACAGCAGCTGATTTTCAGGAATATTCACTTTATTTCACCTGACATTCCAAAAGCAAGTAAC
1268892 CAATAGCCTATGTTGCTATGGCTATTCGATTTTCGGTTCCAAACATGGAATGGGAATACAACCTT
1 CAATAGCCTATGTTGCTATGGCTATTCGATTTTCGGTTCCAAACATGGAATGGGAATACAACCTT
1268957 CAAAGATCATCCATATCAATGAAAAAGTTAAAGAAAAACACGAACAGAACCATACAGGATATTAG
66 CAAAGATCATCCATATCAATGAAAAAGTTAAAGAAAAACACGAACAGAACCATACAGGATATTAG
1269022 GACGCATATACTGAAAAATAAAATAAAAAACCATACAGGACACATACTGATAAACAAGAACAATA
131 GACGCATATACTGAAAAATAAAA-AAAAAACCATACAGGACACATACTGATAAACAAGAACAATA
*
1269087 TTCTCATTCCATGTTTGGAAATGTATACAGGTTCAACACCAACAGAGTCAAAGTAACATAAATGT
195 TTCTCATTCCATGTTTGGAAATGTATACAGGTTCAACACCAACACAGTCAAAGTAACATAAATGT
*
1269152 CAACTTGGAAAGATAGATAATAGAATCTTCAAAACATCAGTGACTCATGTTTTCATTTTCAAAGG
260 CAACTTGGAAAGATAGATAATAGAATCTTCAAAACATCAGTGAATCATGTTTTCATTTTCAAAGG
* *
1269217 GTGCAACAGCAGCTGATTTTCAGGAATATTCACTTTATTTCACCTGACATTGCGAAAGCAAGTAA
325 GTGCAACAGCAGCTGATTTTCAGGAATATTCACTTTATTTCACCTGACATTCCAAAAGCAAGTAA
1269282 C
390 C
1269283 CA
1 CA
1269285 GAGAAAAACC
Statistics
Matches: 387, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
390 152 0.39
391 235 0.61
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.25
Consensus pattern (390 bp):
CAATAGCCTATGTTGCTATGGCTATTCGATTTTCGGTTCCAAACATGGAATGGGAATACAACCTT
CAAAGATCATCCATATCAATGAAAAAGTTAAAGAAAAACACGAACAGAACCATACAGGATATTAG
GACGCATATACTGAAAAATAAAAAAAAAACCATACAGGACACATACTGATAAACAAGAACAATAT
TCTCATTCCATGTTTGGAAATGTATACAGGTTCAACACCAACACAGTCAAAGTAACATAAATGTC
AACTTGGAAAGATAGATAATAGAATCTTCAAAACATCAGTGAATCATGTTTTCATTTTCAAAGGG
TGCAACAGCAGCTGATTTTCAGGAATATTCACTTTATTTCACCTGACATTCCAAAAGCAAGTAAC
Found at i:1269481 original size:18 final size:18
Alignment explanation
Indices: 1269458--1269493 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1269448 ATTTCTCCCT
1269458 TGGGGTTGACAATGACAC
1 TGGGGTTGACAATGACAC
1269476 TGGGGTTGACAATGACAC
1 TGGGGTTGACAATGACAC
1269494 CAGCGTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (18 bp):
TGGGGTTGACAATGACAC
Found at i:1269894 original size:17 final size:17
Alignment explanation
Indices: 1269872--1269906 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1269862 TTTCTTGACG
1269872 GTAGTCATGACCATGTC
1 GTAGTCATGACCATGTC
1269889 GTAGTCATGACCATGTC
1 GTAGTCATGACCATGTC
1269906 G
1 G
1269907 CCGACACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (17 bp):
GTAGTCATGACCATGTC
Found at i:1278712 original size:56 final size:53
Alignment explanation
Indices: 1278619--1278738 Score: 143
Period size: 54 Copynumber: 2.2 Consensus size: 53
1278609 CTGTGATTAT
* *
1278619 CAAGAACAGACACATACGCAAACGAATAACTGCATACTTAAAAAAGGAAAAAAA
1 CAAGAACAAACACATACGAAAACGAATAACTGCATACTTAAAAAA-GAAAAAAA
* * * *
1278673 CAAGAACAAACACATATGAAATTACGAATAACTGTATACTTAGAAAAGAAAAGAA
1 CAAGAACAAACACATACGAAA--ACGAATAACTGCATACTTAAAAAAGAAAAAAA
*
1278728 -AAGAAAAAACA
1 CAAGAACAAACA
1278739 AGAACAAACA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
54 28 0.49
55 7 0.12
56 22 0.39
ACGTcount: A:0.59, C:0.15, G:0.12, T:0.13
Consensus pattern (53 bp):
CAAGAACAAACACATACGAAAACGAATAACTGCATACTTAAAAAAGAAAAAAA
Found at i:1279248 original size:21 final size:21
Alignment explanation
Indices: 1279222--1279261 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1279212 TATAATGTAA
* *
1279222 ATTTCAGAATAATTAAATTAG
1 ATTTCAAAATAAATAAATTAG
1279243 ATTTCAAAATAAATAAATT
1 ATTTCAAAATAAATAAATT
1279262 TAATTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTTCAAAATAAATAAATTAG
Found at i:1291512 original size:6 final size:6
Alignment explanation
Indices: 1291501--1291537 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1291491 CAGAATAGAT
1291501 AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC A
1 AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC AGAGCC A
1291538 TTTGAATTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.32, G:0.32, T:0.00
Consensus pattern (6 bp):
AGAGCC
Found at i:1292902 original size:9 final size:10
Alignment explanation
Indices: 1292879--1292903 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1292869 ACTGTACTCA
1292879 TTTTTTATTC
1 TTTTTTATTC
1292889 TTTTTTATTC
1 TTTTTTATTC
1292899 TTTTT
1 TTTTT
1292904 CTTTTCTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTATTC
Found at i:1307292 original size:25 final size:23
Alignment explanation
Indices: 1307258--1307309 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
1307248 ATATGCATTT
1307258 TTCT-AATATTATATATTACTAATG
1 TTCTAAATATT-T-TATTACTAATG
**
1307282 TTCTAAATATTTTATTGTTAATG
1 TTCTAAATATTTTATTACTAATG
1307305 TTCTA
1 TTCTA
1307310 GTTTCAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 14 0.56
24 5 0.20
25 6 0.24
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.54
Consensus pattern (23 bp):
TTCTAAATATTTTATTACTAATG
Done.