Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009245.1 Hibiscus syriacus cultivar Beakdansim tig00112880_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: 119421
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1475 original size:17 final size:18
Alignment explanation
Indices: 1453--1486 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1443 TTCCATCCGG
1453 TCTTAT-ATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1470 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1487 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:2778 original size:15 final size:15
Alignment explanation
Indices: 2748--2803 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
2738 GGTCAACAAT
2748 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
2765 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
*
2780 GGTCAATGGGT---C
1 GGTCAACGGGTCAAC
2792 GGTCAACGGGTC
1 GGTCAACGGGTC
2804 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
12 11 0.31
15 17 0.47
17 8 0.22
ACGTcount: A:0.21, C:0.27, G:0.36, T:0.16
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:2843 original size:13 final size:13
Alignment explanation
Indices: 2803--2851 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
2793 GTCAACGGGT
*
2803 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
* * *
2816 CTGGTTGGATAAA
1 CGGGTCGGGTAAA
2829 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
2842 CGGGTCGGGT
1 CGGGTCGGGT
2852 CGGGTCGGGT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:4901 original size:31 final size:30
Alignment explanation
Indices: 4866--4939 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
4856 GGGGCCGTGG
*
4866 GGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
4897 GGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGCCTACCTAAGAAACATCTCAGGGCCGCA
4927 GAGCCTACCTAAG
1 G-GCCTACCTAAG
4940 TGTCACATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.27, C:0.32, G:0.26, T:0.15
Consensus pattern (30 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:4934 original size:62 final size:63
Alignment explanation
Indices: 4818--4939 Score: 151
Period size: 62 Copynumber: 2.0 Consensus size: 63
4808 ACCTAAGGGA
* * ** *
4818 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
*
4881 ACATCTTAGGGCC-GCAG-GCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
4940 TGTCACATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
61 1 0.02
62 35 0.69
63 15 0.29
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:7751 original size:8 final size:8
Alignment explanation
Indices: 7721--7777 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
7711 GGTCAACAAT
7721 GGTCAACG
1 GGTCAACG
7729 CCGGTCAAC-
1 --GGTCAACG
7738 GGTCAACG
1 GGTCAACG
7746 GGTCAAC-
1 GGTCAACG
*
7753 GGTCAATG
1 GGTCAACG
7761 GGT---CG
1 GGTCAACG
7766 GGTCAACG
1 GGTCAACG
7774 GGTC
1 GGTC
7778 GGGTCGGGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
5 4 0.10
7 13 0.32
8 16 0.40
10 7 0.17
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:7751 original size:15 final size:15
Alignment explanation
Indices: 7721--7777 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
7711 GGTCAACAAT
7721 GGTCAACGCCGGTCAAC
1 GGTCAACG--GGTCAAC
7738 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
* *
7753 GGTCAATGGGTC--G
1 GGTCAACGGGTCAAC
7766 GGTCAACGGGTC
1 GGTCAACGGGTC
7778 GGGTCGGGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 11 0.30
15 18 0.49
17 8 0.22
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:7771 original size:13 final size:13
Alignment explanation
Indices: 7738--7782 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
7728 GCCGGTCAAC
*
7738 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
*
7753 GGTCAATGGGTCG
1 GGTCAACGGGTCG
7766 GGTCAACGGGTCG
1 GGTCAACGGGTCG
7779 GGTC
1 GGTC
7783 GGGTCGGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 16 0.59
15 11 0.41
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:11897 original size:23 final size:24
Alignment explanation
Indices: 11862--11908 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
11852 ACGATCAGAC
*
11862 TGGTCAACGGTCAATGAGTTAACT
1 TGGTCAACAGTCAATGAGTTAACT
11886 TGGTCAA-AGTCAATGAGTTAACT
1 TGGTCAACAGTCAATGAGTTAACT
11909 CAGTGACTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (24 bp):
TGGTCAACAGTCAATGAGTTAACT
Found at i:14787 original size:15 final size:14
Alignment explanation
Indices: 14748--14791 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 14
14738 TTAACTTTTT
14748 CGGTCAAAGT-TAA
1 CGGTCAAAGTCTAA
14761 CGGTCAATAGTCTAA
1 CGGTCAA-AGTCTAA
14776 CCGGTCAAAGTC-AA
1 -CGGTCAAAGTCTAA
14790 CG
1 CG
14792 ATCAGACCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.32
14 5 0.18
15 7 0.25
16 7 0.25
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (14 bp):
CGGTCAAAGTCTAA
Found at i:24681 original size:15 final size:16
Alignment explanation
Indices: 24663--24700 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
24653 TGTTGTTCAA
*
24663 AAAAAAAGAGA-AAAG
1 AAAAAAAGACAGAAAG
24678 AAAAAAAGACATGAAAG
1 AAAAAAAGACA-GAAAG
24695 AAAAAA
1 AAAAAA
24701 TAGAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
17 10 0.50
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAAAAAGACAGAAAG
Found at i:29339 original size:18 final size:18
Alignment explanation
Indices: 29296--29341 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
29286 TTCACGGAAT
*
29296 ATAAGATTATCAGTGGGA
1 ATAAGATTACCAGTGGGA
** *
29314 ATGGGATTACCGGTGGGA
1 ATAAGATTACCAGTGGGA
29332 ATAAGATTAC
1 ATAAGATTAC
29342 TGTGAATGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.30, T:0.26
Consensus pattern (18 bp):
ATAAGATTACCAGTGGGA
Found at i:32388 original size:39 final size:39
Alignment explanation
Indices: 32334--32412 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
32324 AAAATTTCTC
32334 GATGTGTTCGGTTCATTCGGGTTTGTTCTCATGATATGG
1 GATGTGTTCGGTTCATTCGGGTTTGTTCTCATGATATGG
32373 GATGTGTTCGGTTCATTCGGGTTTGTTCTCATGATATGG
1 GATGTGTTCGGTTCATTCGGGTTTGTTCTCATGATATGG
32412 G
1 G
32413 GGTAGTATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.13, C:0.13, G:0.32, T:0.43
Consensus pattern (39 bp):
GATGTGTTCGGTTCATTCGGGTTTGTTCTCATGATATGG
Found at i:33511 original size:100 final size:100
Alignment explanation
Indices: 33338--33599 Score: 456
Period size: 100 Copynumber: 2.6 Consensus size: 100
33328 CTCAAACTCG
* *
33338 AGTATACTTACTTGAGTTTGAAGTTAAATATGAGAATTGAACTTAAATTTTATTAGAAGTGAACG
1 AGTATACATACTTGAGTTTGAAGTTAAATATGAGAATTGAACTTAAATTTTATTAGAAGTGAATG
*
33403 TCTAAACAAGTTTAGTCGAGTCGAGTCGAATTTTA
66 TCTAAACAAGTATAGTCGAGTCGAGTCGAATTTTA
33438 AGTATACATACTTGAGTTTGAAGTTAAATATGAGAATTGAACTTAAATTTTATTAGAAGTGAATG
1 AGTATACATACTTGAGTTTGAAGTTAAATATGAGAATTGAACTTAAATTTTATTAGAAGTGAATG
* *
33503 TCTAAACAAGTATAGTCGAGTTGAGTCTAATTTTA
66 TCTAAACAAGTATAGTCGAGTCGAGTCGAATTTTA
*
33538 AGTATACATACTTGAGTTTGAAGTTAAATATGAGGATTGAACTT-AATTTT-TTAGAAGTGAAT
1 AGTATACATACTTGAGTTTGAAGTTAAATATGAGAATTGAACTTAAATTTTATTAGAAGTGAAT
33600 TTGTGTACGT
Statistics
Matches: 156, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
98 12 0.08
99 6 0.04
100 138 0.88
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (100 bp):
AGTATACATACTTGAGTTTGAAGTTAAATATGAGAATTGAACTTAAATTTTATTAGAAGTGAATG
TCTAAACAAGTATAGTCGAGTCGAGTCGAATTTTA
Found at i:35210 original size:19 final size:19
Alignment explanation
Indices: 35186--35224 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
35176 GATCATTTTT
35186 TTTATTT-CTTGAATTTCGA
1 TTTATTTGCTTG-ATTTCGA
*
35205 TTTATTTGTTTGATTTCGA
1 TTTATTTGCTTGATTTCGA
35224 T
1 T
35225 GTAGCCTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.18, C:0.08, G:0.13, T:0.62
Consensus pattern (19 bp):
TTTATTTGCTTGATTTCGA
Found at i:40411 original size:16 final size:16
Alignment explanation
Indices: 40392--40422 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40382 CCAACGTTTA
40392 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
40408 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
40423 ATTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:51828 original size:14 final size:14
Alignment explanation
Indices: 51809--51835 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51799 TTGATCGGTC
51809 TGACCCGACCCGAT
1 TGACCCGACCCGAT
51823 TGACCCGACCCGA
1 TGACCCGACCCGA
51836 CCGTTGACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.44, G:0.22, T:0.11
Consensus pattern (14 bp):
TGACCCGACCCGAT
Found at i:58888 original size:19 final size:19
Alignment explanation
Indices: 58860--58903 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
58850 GAGGGCTGGA
*
58860 AACCGATTTGACCGGTCTG
1 AACCGATTTGACCAGTCTG
*
58879 AACCGGTTTGACCAGTCTG
1 AACCGATTTGACCAGTCTG
*
58898 ACCCGA
1 AACCGA
58904 CCCGACTGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.23
Consensus pattern (19 bp):
AACCGATTTGACCAGTCTG
Found at i:58912 original size:14 final size:14
Alignment explanation
Indices: 58895--58923 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
58885 TTTGACCAGT
58895 CTGACCCGACCCGA
1 CTGACCCGACCCGA
58909 CTGACCCGACCCGA
1 CTGACCCGACCCGA
58923 C
1 C
58924 CGTTGACCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.52, G:0.21, T:0.07
Consensus pattern (14 bp):
CTGACCCGACCCGA
Found at i:61270 original size:19 final size:20
Alignment explanation
Indices: 61232--61270 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
61222 TGATTGAAAT
* *
61232 ATTTAAAAGTTTGGAAATCA
1 ATTTAAAAGTATGAAAATCA
61252 ATTTAAAA-TATGAAAATCA
1 ATTTAAAAGTATGAAAATCA
61271 TGGTTTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.33
Consensus pattern (20 bp):
ATTTAAAAGTATGAAAATCA
Found at i:61471 original size:22 final size:20
Alignment explanation
Indices: 61446--61490 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
61436 TTTTAATGAC
61446 ATATGACTAAAACATAATAAAA
1 ATATGACTAAAA-ATAA-AAAA
* *
61468 ATATGATTATAAATAAAAAA
1 ATATGACTAAAAATAAAAAA
61488 ATA
1 ATA
61491 ATTAAATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 4 0.19
22 10 0.48
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (20 bp):
ATATGACTAAAAATAAAAAA
Found at i:62127 original size:36 final size:36
Alignment explanation
Indices: 62087--62176 Score: 162
Period size: 36 Copynumber: 2.5 Consensus size: 36
62077 AATCATATAT
*
62087 TCGGGTCGTGTCGGGTCAGGTGAAACCTTAATTTCG
1 TCGGGTCGTGTCGGGTCAGGTGAAACCTTAATTTCA
62123 TCGGGTCGTGTCGGGTCAGGTGAAACCTTAATTTCA
1 TCGGGTCGTGTCGGGTCAGGTGAAACCTTAATTTCA
*
62159 TCGGGTCGGGTCGGGTCA
1 TCGGGTCGTGTCGGGTCA
62177 CGGGTGAAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.16, C:0.20, G:0.36, T:0.29
Consensus pattern (36 bp):
TCGGGTCGTGTCGGGTCAGGTGAAACCTTAATTTCA
Found at i:74131 original size:2 final size:2
Alignment explanation
Indices: 74124--74158 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
74114 ACTTAATAAT
74124 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
74159 GTGTGTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77587 original size:181 final size:182
Alignment explanation
Indices: 77215--77687 Score: 763
Period size: 181 Copynumber: 2.6 Consensus size: 182
77205 AATCCAAATT
* * * **
77215 AAAAATGTATCGATCCACAACGA-AATAA-AAGTTAAAACTATGATAAAATCGATATTGAAATGA
1 AAAAATGTATCGATCCACAACGATAA-AACAAG-TAAAAATATGATAAAACCGGTATCAAAATGA
* * * * *
77278 TAAAACCGGTAAAGCGGTATCGGATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACT
64 TAAAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACT
*
77343 TCGTTAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
129 TCGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* *
77397 AAAAATGTATCGATCCACAACGATAAAACATGTAAAAATATGATAAAACCGGTATCAAAATGATG
1 AAAAATGTATCGATCCACAACGATAAAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
77462 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
77526 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* *
77578 AAAAATGTATCGATCCACAACGATATAACAAGTAAAAATATGATAAAACCTGTATCAAAATGATA
1 AAAAATGTATCGATCCACAACGATAAAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
77643 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT
77688 CGTAAGTACG
Statistics
Matches: 271, Mismatches: 18, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
181 175 0.65
182 92 0.34
183 4 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCACAACGATAAAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:79928 original size:21 final size:21
Alignment explanation
Indices: 79902--79966 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
79892 AAGACAATCA
*
79902 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
*
79923 AGAGTCGAATAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
79944 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
79965 AG
1 AG
79967 GCATAAGGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.42, C:0.11, G:0.29, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:80042 original size:33 final size:33
Alignment explanation
Indices: 80000--80063 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
79990 AAATAGATGG
*
80000 AGTGGTGAAAGAAGTAAAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAAAGGTGTTAAGGGGTGA
**
80033 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGT
1 AGTGGTGAAAGAAGTAAAGGTGTTAAGGGGT
80064 TATCTTAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.45, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAAAGGTGTTAAGGGGTGA
Found at i:81713 original size:19 final size:19
Alignment explanation
Indices: 81668--81716 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
81658 AATGTAGGGT
*
81668 TAATTTTATATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
81687 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
81706 TAATTTTGTAT
1 TAATTTTGTAT
81717 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:82289 original size:200 final size:200
Alignment explanation
Indices: 81946--82305 Score: 693
Period size: 200 Copynumber: 1.8 Consensus size: 200
81936 AATTTACAAT
*
81946 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
82011 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCAGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCAGTTTT
82076 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
82141 AATGA
196 AATGA
82146 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
*
82211 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTT
66 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCAGTTTT
*
82276 ATGAGATAATAGGTGTAATATATGTATCGA
131 ATGAGAGAATAGGTGTAATATATGTATCGA
82306 AACCCAGAAA
Statistics
Matches: 157, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 157 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAGAAACAT
CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCAGTTTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:85341 original size:23 final size:23
Alignment explanation
Indices: 85310--85382 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
85300 ATAGATAAAA
*
85310 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
85333 ATATAATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
85356 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
85379 ATAT
1 ATAT
85383 TGTAAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:86338 original size:87 final size:87
Alignment explanation
Indices: 86242--86404 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
86232 AAACATGTCA
86242 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
*
86307 TCGGTTAAATACCTATTTTATT
66 CCGGTTAAATACCTATTTTATT
* * *
86329 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
86394 CCGGTTAAATA
66 CCGGTTAAATA
86405 ATATAACATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATACCTATTTTATT
Found at i:86376 original size:23 final size:23
Alignment explanation
Indices: 86326--86370 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
86316 TACCTATTTT
* *
86326 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
86349 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
86371 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:86831 original size:30 final size:32
Alignment explanation
Indices: 86780--86839 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
86770 ATATTTAAAA
*
86780 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
86812 TATATTT-TTAATA-TTATAATAAAATAAT
1 TATATTTATTAATATTTATAATAAAATAAT
86840 CAATTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 14 0.52
31 6 0.22
32 7 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:86872 original size:26 final size:26
Alignment explanation
Indices: 86794--86898 Score: 78
Period size: 26 Copynumber: 4.2 Consensus size: 26
86784 TTTATTAATA
86794 TTTATAATAATATAATAT--TATA-T
1 TTTATAATAATATAATATAATATATT
* * *
86817 TTT-TAATATTATAATAAAATA-ATCA
1 TTTATAATAATATAATATAATATAT-T
*
86842 ATTATAATAATATAATATAATATATT
1 TTTATAATAATATAATATAATATATT
** *
86868 TTTATTTTAATA-ATATATAATAAATT
1 TTTATAATAATATA-ATATAATATATT
86894 ATTTA
1 -TTTA
86899 AAAAATTTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
22 12 0.19
23 4 0.06
24 2 0.03
25 3 0.05
26 36 0.57
27 6 0.10
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTATAATAATATAATATAATATATT
Found at i:87047 original size:21 final size:22
Alignment explanation
Indices: 87010--87058 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
87000 AATAAAGATA
*
87010 TTTAAAATATACTATTTAATATT
1 TTTAAAATATAC-ATTTAACATT
87033 TTTAAAATATA-ATTTAACATT
1 TTTAAAATATACATTTAACATT
*
87054 ATTAA
1 TTTAA
87059 TTTAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
23 11 0.46
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAAAATATACATTTAACATT
Found at i:87172 original size:20 final size:20
Alignment explanation
Indices: 87139--87188 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
87129 TAATAAAATT
87139 ATAAAAATAA-TATTTTAATA
1 ATAAAAA-AATTATTTTAATA
*
87159 ATAAATAAATTATTTTAATA
1 ATAAAAAAATTATTTTAATA
*
87179 TTAAAAAAAT
1 ATAAAAAAAT
87189 AATAATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAAAAATTATTTTAATA
Found at i:88783 original size:4 final size:4
Alignment explanation
Indices: 88774--88808 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
88764 AATTAGTATG
88774 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
88809 AGTCGTGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:90088 original size:9 final size:9
Alignment explanation
Indices: 90064--90096 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
90054 TAACTTTAAT
90064 TTAAGAAATA
1 TTAAGAAA-A
90074 TT-AGAAAA
1 TTAAGAAAA
90082 TTAAGAAAA
1 TTAAGAAAA
90091 TTAAGA
1 TTAAGA
90097 CTCGAATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 3 0.14
9 17 0.77
10 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (9 bp):
TTAAGAAAA
Found at i:103360 original size:19 final size:19
Alignment explanation
Indices: 103336--103380 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
103326 TCCTTGAATG
*
103336 AAATGCTGGATTCCTTGCT
1 AAATGCAGGATTCCTTGCT
103355 AAATGCAGGATTCCTTGCT
1 AAATGCAGGATTCCTTGCT
103374 AAATGCA
1 AAATGCA
103381 AGGCGCTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (19 bp):
AAATGCAGGATTCCTTGCT
Found at i:110328 original size:30 final size:29
Alignment explanation
Indices: 110294--110377 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
110284 TAAATTTGAA
110294 GGACTAAAATAATAAAAAAAGAAACTAAAG
1 GGACTAAAATAATAAAAAAAGAAACT-AAG
*** *
110324 GGACTAAAATGGCAAAAATAA-AAACTTAG
1 GGACTAAAATAATAAAAA-AAGAAACTAAG
*
110353 GGACTAAAATAATAAAAATAGAAAC
1 GGACTAAAATAATAAAAAAAGAAAC
110378 CTAGAGGACT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
28 1 0.02
29 21 0.48
30 20 0.45
31 2 0.05
ACGTcount: A:0.62, C:0.08, G:0.14, T:0.15
Consensus pattern (29 bp):
GGACTAAAATAATAAAAAAAGAAACTAAG
Found at i:110479 original size:29 final size:29
Alignment explanation
Indices: 110292--110515 Score: 120
Period size: 30 Copynumber: 7.7 Consensus size: 29
110282 CATAAATTTG
* * *
110292 AAGGACTAAAATAATAAAAAAAGAAACTA
1 AAGGACTAAAATAGTAAAAACAGAAACTT
* * * *
110321 AAGGGACTAAAATGGCAAAAATAAAAACTT
1 AA-GGACTAAAATAGTAAAAACAGAAACTT
* * * *
110351 AGGGACTAAAATAATAAAAATAGAAACCT
1 AAGGACTAAAATAGTAAAAACAGAAACTT
* * *
110380 AGAGGACTAATAT-GACAAAAACAGAAATTT
1 A-AGGACTAAAATAG-TAAAAACAGAAACTT
* *
110410 ACATGG-CTAAAACAG-CAAAAC-GAAACTT
1 A-A-GGACTAAAATAGTAAAAACAGAAACTT
* *
110438 AAAGG-GTATAAATAGTAAAAACAGAAAGTT
1 -AAGGACTA-AAATAGTAAAAACAGAAACTT
* * *
110468 AAGGACTAAAATA-AATAAAATAGAAACTA
1 AAGGACTAAAATAGTA-AAAACAGAAACTT
*
110497 AAGTGGCTAAAATAG-AAAA
1 AAG-GACTAAAATAGTAAAA
110516 TATAGACATT
Statistics
Matches: 148, Mismatches: 34, Indels: 26
0.71 0.16 0.12
Matches are distributed among these distances:
27 4 0.03
28 13 0.09
29 61 0.41
30 67 0.45
31 3 0.02
ACGTcount: A:0.58, C:0.09, G:0.15, T:0.17
Consensus pattern (29 bp):
AAGGACTAAAATAGTAAAAACAGAAACTT
Found at i:111948 original size:3 final size:3
Alignment explanation
Indices: 111935--111967 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
111925 GTAAAATGTA
111935 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
111968 ATAAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:112445 original size:134 final size:133
Alignment explanation
Indices: 112178--112672 Score: 679
Period size: 134 Copynumber: 3.7 Consensus size: 133
112168 GATCTGGTCG
* * * * * *
112178 TCTAAGGGTGACTCGGCTCTTACGTGATGATGAGATCTGGTCAGGGGATGACACTGCTCATACGT
1 TCTAGGGGTGACAC-GCTCCTACGCGATGAGGAGATCTGGTCAGGGGATGACACGGCTCATACGT
112243 GATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCT
65 GATGAAGAGTTC-TGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCT
112308 GGTTA
129 GGTTA
* * * * * *
112313 TCTATGGTTGACACAGCTCCTACGTGATGAGGAGATATGGTCAGGGGATGACACAGCTTATACGT
1 TCTAGGGGTGACAC-GCTCCTACGCGATGAGGAGATCTGGTCAGGGGATGACACGGCTCATACGT
* * * *
112378 GATGAAGAGTTATGGCCATCTTTAGGAAGGGTGATAACTTGGTTCCTACGTGATGAGGATGGCTG
65 GATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTG
112443 GTTA
130 GTTA
*
112447 TCTAGGGGTGACACGACTCCTACGCGATGAGAAGATCTGGTCAGGGGATGACACGGCTCATACGT
1 TCTAGGGGTGACACG-CTCCTACGCGATGAGGAGATCTGGTCAGGGGATGACACGGCTCATACGT
* * * * *
112512 GATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTGCACG-TGAGGACGACTA
65 GATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTG
112576 GTTA
130 GTTA
* *
112580 TCTAGGGGTGACACGGATCCTACGCAATGAGGAGATCTGGTC-GAGGGATGACACGGCTCATACG
1 TCTAGGGGTGACAC-GCTCCTACGCGATGAGGAGATCTGGTCAG-GGGATGACACGGCTCATACG
* **
112644 TGATAAAGAGTTCTGGTTATCTTTAGGAA
64 TGATGAAGAGTTCTGGCCATCTTTAGGAA
112673 TTAAGGTTTC
Statistics
Matches: 323, Mismatches: 34, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
132 1 0.00
133 98 0.30
134 157 0.49
135 67 0.21
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (133 bp):
TCTAGGGGTGACACGCTCCTACGCGATGAGGAGATCTGGTCAGGGGATGACACGGCTCATACGTG
ATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTGG
TTA
Found at i:112516 original size:40 final size:39
Alignment explanation
Indices: 112450--112529 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 39
112440 CTGGTTATCT
*
112450 AGGGGTGACACGACTCCTACGCGATG-AGAAGATCTGGTC
1 AGGGGTGACACGACTCATACGCGATGAAG-AGATCTGGTC
* * *
112489 AGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGTC
1 AGGGG-TGACACGACTCATACGCGATGAAGAGATCTGGTC
112529 A
1 A
112530 TCTTTAGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 5 0.14
40 28 0.80
41 2 0.06
ACGTcount: A:0.26, C:0.20, G:0.34, T:0.20
Consensus pattern (39 bp):
AGGGGTGACACGACTCATACGCGATGAAGAGATCTGGTC
Found at i:112718 original size:28 final size:28
Alignment explanation
Indices: 112678--112748 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
112668 AGGAATTAAG
** * *
112678 GTTTCAAGGGAAACTGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAAATTT
112706 GTTTCAAAAGAAACAGACTCAAAAATTT
1 GTTTCAAAAGAAACAGACTCAAAAATTT
112734 GTTTCAAGAA-AAACA
1 GTTTCAA-AAGAAACA
112749 AACTTAAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 36 0.95
29 2 0.05
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.25
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAAATTT
Found at i:112940 original size:31 final size:32
Alignment explanation
Indices: 112894--112957 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
112884 CAAAGATCGG
* *
112894 TGTTTCGAGAGAAACAAACTCAAA-ATGTTTT
1 TGTTTCAAGAAAAACAAACTCAAAGATGTTTT
* *
112925 TGTTTCAAGAAAAACATACTCAAAGATTTTTT
1 TGTTTCAAGAAAAACAAACTCAAAGATGTTTT
112957 T
1 T
112958 TTGTTTTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (32 bp):
TGTTTCAAGAAAAACAAACTCAAAGATGTTTT
Found at i:113101 original size:173 final size:172
Alignment explanation
Indices: 112812--113158 Score: 613
Period size: 173 Copynumber: 2.0 Consensus size: 172
112802 TTTCAAGGGA
*
112812 AACAACTCAAAGATGATGTTTAAAAGAAACTGTCTCAAGCGAGACAAAATTTGTATTTAAAGGAA
1 AACAACTCAAAGATGACGTTTAAAAGAAACTGTCTCAAGCGAGACAAAATTTGTATTTAAAGGAA
112877 ACGTTCTCAAAGATCGGTGTTTCGAGAGAAACAAACTCAAAATGTTTTTGTTTCAAGAAAAACAT
66 ACGTTCTCAAAGATCGGTGTTTCGAGAGAAACAAACTCAAAATGTTTTTGTTTCAAGAAAAACAT
* *
112942 ACTCAAAGATTTTTTTTTGTTTTGTTTCAAGGGAAACAAACTC
131 ACTCAAAGA-TTTTGTTTGTTTTATTTCAAGGGAAACAAACTC
* * * *
112985 AACAACTCAAAGATGACGTTTAAAGGAAACTGTCTCAAGCGAGATAAAATTTGTGTTTAAGGGAA
1 AACAACTCAAAGATGACGTTTAAAAGAAACTGTCTCAAGCGAGACAAAATTTGTATTTAAAGGAA
*
113050 ACGTTCTCAAAGATCGGTGTTTCGAGAGAGACAAACTCAAAATGTTTTTGTTTCAAGAAAAACAT
66 ACGTTCTCAAAGATCGGTGTTTCGAGAGAAACAAACTCAAAATGTTTTTGTTTCAAGAAAAACAT
113115 ACTCAAAGATTTTGTTTGTTTTATTTCAAGGGAAACAAACTC
131 ACTCAAAGATTTTGTTTGTTTTATTTCAAGGGAAACAAACTC
113157 AA
1 AA
113159 AGATGGTAAA
Statistics
Matches: 166, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
172 33 0.20
173 133 0.80
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (172 bp):
AACAACTCAAAGATGACGTTTAAAAGAAACTGTCTCAAGCGAGACAAAATTTGTATTTAAAGGAA
ACGTTCTCAAAGATCGGTGTTTCGAGAGAAACAAACTCAAAATGTTTTTGTTTCAAGAAAAACAT
ACTCAAAGATTTTGTTTGTTTTATTTCAAGGGAAACAAACTC
Found at i:113290 original size:64 final size:62
Alignment explanation
Indices: 113166--113303 Score: 147
Period size: 64 Copynumber: 2.2 Consensus size: 62
113156 CAAAGATGGT
*
113166 AAATTTTGTTTTCCAAAGAAACAAAATCAAAGATTTTTCTCAAAGAAACTGTCTCGAGAGAAACA
1 AAATTTTG-TTTCCAAAGAAACAAAATCAAAGATTTTTCTCAAAGAAACTGTCTC-A-AGAGACA
* * * *
113231 AAATTTTGTTTCCAAAGAAACAGATTCAATGATTTTT-TCAAA-AGACATCGTCAT-AAGAGACA
1 AAATTTTGTTTCCAAAGAAACAAAATCAAAGATTTTTCTCAAAGAAAC-T-GTC-TCAAGAGACA
*
113293 AAACTTTGTTT
1 AAATTTTGTTT
113304 TTCAGAAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
62 19 0.30
63 7 0.11
64 29 0.45
65 9 0.14
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (62 bp):
AAATTTTGTTTCCAAAGAAACAAAATCAAAGATTTTTCTCAAAGAAACTGTCTCAAGAGACA
Found at i:113541 original size:31 final size:31
Alignment explanation
Indices: 113483--113543 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 31
113473 AAGGGAAATG
113483 ACTCAAAGATAGTTTTATTTCAGGAGAAACAA
1 ACTCAAAGATA-TTTTATTTCAGGAGAAACAA
113515 ACTCAAAGAT-TTTGTATTTCTA-GAGAAAC
1 ACTCAAAGATATTT-TATTTC-AGGAGAAAC
113544 TGTCTCAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 3 0.11
31 13 0.48
32 11 0.41
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (31 bp):
ACTCAAAGATATTTTATTTCAGGAGAAACAA
Found at i:113701 original size:65 final size:64
Alignment explanation
Indices: 113591--113713 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 64
113581 GTGCGTATTT
* * *
113591 TCAAAAGAAATTGTCTCGAGAGGCAAAATTTTGTTTCAAAGGAAACAAACTCGAAGATTTTTTC
1 TCAAAAGAAATTGTCTCGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTC
* * * *
113655 TCAAAAGAAATTGTCTTGAAGAGATAATATTTTGTTTCAAAAGAAACATACTCAAAGAT
1 TCAAAAGAAATTGTCTCG-AGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
113714 AAATTACATC
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
64 17 0.33
65 34 0.67
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (64 bp):
TCAAAAGAAATTGTCTCGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTC
Found at i:114208 original size:36 final size:36
Alignment explanation
Indices: 114168--114277 Score: 143
Period size: 36 Copynumber: 3.1 Consensus size: 36
114158 ATAATTTGGA
*
114168 AAATTGTCTCAAGTGAGACAACATTTGTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
* * * *
114204 AAATTGTCTCAAACGAGACAAAAATTATTTTTAGAG
1 AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
*
114240 AAATTGTCTCAAGCGAGATAA-AGTTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAACA-TTTGTTTTTAGAG
114275 AAA
1 AAA
114278 ACGATATCAA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.11
36 57 0.89
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAACATTTGTTTTTAGAG
Found at i:114429 original size:107 final size:106
Alignment explanation
Indices: 114284--114489 Score: 274
Period size: 107 Copynumber: 1.9 Consensus size: 106
114274 GAAAACGATA
*
114284 TCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGCATTCTCAAAGG-AAAAAT
1 TCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGCA-TATCAAAGGAAAAAAT
*
114348 GCCTCAAACGAGACGAAATTTGTTTTGAA-AGAAATAACAATC
65 GCCTCAAACAAGACGAAATTTGTTTT-AAGAGAAATAACAATC
* * * *
114390 TCAAGTGAGATTAATTTTTGTTTCAA-GTGAATCAAATTCGAAATTTGTATATCAAAGGAAAAAA
1 TCAAGTGAGATCAA-CTTTGTTT-AATGTGAAACAAATTCGAAATTTGCATATCAAAGGAAAAAA
* * *
114454 TGTCTCAAGCAAGACGAAGTTTGTTTTAAGAGAAAT
64 TGCCTCAAACAAGACGAAATTTGTTTTAAGAGAAAT
114490 TGTCTTAAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
106 23 0.26
107 62 0.71
108 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (106 bp):
TCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGCATATCAAAGGAAAAAATG
CCTCAAACAAGACGAAATTTGTTTTAAGAGAAATAACAATC
Found at i:114642 original size:152 final size:154
Alignment explanation
Indices: 114447--114724 Score: 382
Period size: 152 Copynumber: 1.8 Consensus size: 154
114437 TATATCAAAG
* * * * *
114447 GAAAAAATGTCTCAAGCAAGACGAAGTTTGTTTTAAGAGAAATTGTCTTAAATGAGAC-AATTTT
1 GAAAAAATGTCTCAAGCAAGACGAAATTTGCTTTAAGAGAAATTGTCTCAAACGAGACAAAATTT
* * *
114511 TTTTTTAAATTCTCAAAATTTATGG-GAAATGTCTCAAGCGAGA-AAGAATTTTGTTACAAGTAC
66 GTTTTAAAATTCTCAAAATTTATGGAAAAATGTCTCAAGCGAGACAA-AATTTTGTTACAAGTAC
114574 AATAAATTTAAATTTGTATCTTAGA
130 AATAAATTTAAATTTGTATCTTAGA
** * * * *
114599 GAAAAAATGTCTCAAGTGAGACGAAATTTGCTTTGATATAAATTGTCTCAAGCGAGACAAAATTT
1 GAAAAAATGTCTCAAGCAAGACGAAATTTGCTTTAAGAGAAATTGTCTCAAACGAGACAAAATTT
* *
114664 GTTTTAAAATTCTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACAAAATTTTGTTTCAAG
66 GTTTTAAAATTCTCAAAATTTATGGAAAAATGTCTCAAGCGAGACAAAATTTTGTTACAAG
114725 AAAAAACACC
Statistics
Matches: 107, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
152 48 0.45
153 27 0.25
154 30 0.28
155 2 0.02
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (154 bp):
GAAAAAATGTCTCAAGCAAGACGAAATTTGCTTTAAGAGAAATTGTCTCAAACGAGACAAAATTT
GTTTTAAAATTCTCAAAATTTATGGAAAAATGTCTCAAGCGAGACAAAATTTTGTTACAAGTACA
ATAAATTTAAATTTGTATCTTAGA
Found at i:115633 original size:4 final size:4
Alignment explanation
Indices: 115010--115614 Score: 1175
Period size: 4 Copynumber: 152.5 Consensus size: 4
115000 TTTATGTATC
115010 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
115056 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
115104 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
115152 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
115200 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
115248 ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
115295 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
115343 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
115391 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
115439 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
115487 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
115535 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
115581 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
115615 ATGTATGAAC
Statistics
Matches: 596, Mismatches: 0, Indels: 10
0.98 0.00 0.02
Matches are distributed among these distances:
2 4 0.01
3 3 0.01
4 589 0.99
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Done.