Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003756.1 Hibiscus syriacus cultivar Beakdansim tig00008048_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: 116497
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:4771 original size:5 final size:5
Alignment explanation
Indices: 4761--4812 Score: 50
Period size: 5 Copynumber: 9.6 Consensus size: 5
4751 AACGGTCAAC
* *
4761 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
4810 GGT
1 GGT
4813 TAGACCGATC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 31 0.79
7 8 0.21
ACGTcount: A:0.08, C:0.21, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:4781 original size:7 final size:7
Alignment explanation
Indices: 4734--4764 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4724 GTCAAAGAAA
4734 GTCAACG
1 GTCAACG
*
4741 GTTAACG
1 GTCAACG
4748 GTCAACG
1 GTCAACG
4755 GTCAACG
1 GTCAACG
4762 GTC
1 GTC
4765 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:4789 original size:22 final size:22
Alignment explanation
Indices: 4747--4812 Score: 105
Period size: 22 Copynumber: 2.9 Consensus size: 22
4737 AACGGTTAAC
*
4747 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
4771 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
4793 GGTCAACGGTCGGGTCGGGT
1 GGTCAACGGTCGGGTCGGGT
4813 TAGACCGATC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 30 0.73
24 11 0.27
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:4812 original size:17 final size:17
Alignment explanation
Indices: 4754--4791 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
4744 AACGGTCAAC
4754 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
4771 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
4788 GGTC
1 GGTC
4792 GGGTCAACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:4875 original size:10 final size:10
Alignment explanation
Indices: 4862--4947 Score: 76
Period size: 10 Copynumber: 8.8 Consensus size: 10
4852 AGACCGGTCA
4862 AACCGGTTCG
1 AACCGGTTCG
4872 AACCGGTT-G
1 AACCGGTTCG
*
4881 AAACCGG-TCA
1 -AACCGGTTCG
4891 AACCGG-TCAG
1 AACCGGTTC-G
4901 AACCGGTTCG
1 AACCGGTTCG
4911 AACCGGTT-G
1 AACCGGTTCG
*
4920 AAACCGG-TCA
1 -AACCGGTTCG
4930 AACCGG-TCAG
1 AACCGGTTC-G
4940 AACCGGTT
1 AACCGGTT
4948 GAAAACCGGT
Statistics
Matches: 64, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
9 20 0.31
10 41 0.64
11 3 0.05
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (10 bp):
AACCGGTTCG
Found at i:4886 original size:29 final size:28
Alignment explanation
Indices: 4824--4946 Score: 110
Period size: 29 Copynumber: 4.2 Consensus size: 28
4814 AGACCGATCA
* *
4824 AACCGGCTCAGACCGGTCAAACC-GTCTC-
1 AACCGG-TCAAACCGGTCGAACCGGT-TCG
4852 AGACCGGTCAAACCGGTTCGAACCGGTT-G
1 A-ACCGGTCAAACCGG-TCGAACCGGTTCG
4881 AAACCGGTCAAACCGGTCAGAACCGGTTCG
1 -AACCGGTCAAACCGGTC-GAACCGGTTCG
* *
4911 AACCGGTTGAAACCGGTCAAACCGG-TCAG
1 AACCGG-TCAAACCGGTCGAACCGGTTC-G
4940 AACCGGT
1 AACCGGT
4947 TGAAAACCGG
Statistics
Matches: 82, Mismatches: 4, Indels: 18
0.79 0.04 0.17
Matches are distributed among these distances:
28 14 0.17
29 54 0.66
30 14 0.17
ACGTcount: A:0.28, C:0.31, G:0.27, T:0.15
Consensus pattern (28 bp):
AACCGGTCAAACCGGTCGAACCGGTTCG
Found at i:4905 original size:39 final size:39
Alignment explanation
Indices: 4854--4966 Score: 187
Period size: 39 Copynumber: 2.9 Consensus size: 39
4844 ACCGTCTCAG
4854 ACCGGTCA-AACCGGTTCGAACCGGTTGAAACCGGTCAA
1 ACCGGTCAGAACCGGTTCGAACCGGTTGAAACCGGTCAA
4892 ACCGGTCAGAACCGGTTCGAACCGGTTGAAACCGGTCAA
1 ACCGGTCAGAACCGGTTCGAACCGGTTGAAACCGGTCAA
4931 ACCGGTCAGAACCGGTT-GAAAACCGGTT-AAACCGGT
1 ACCGGTCAGAACCGGTTCG--AACCGGTTGAAACCGGT
4967 TTCCAGCAGC
Statistics
Matches: 72, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
38 9 0.12
39 55 0.76
40 8 0.11
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (39 bp):
ACCGGTCAGAACCGGTTCGAACCGGTTGAAACCGGTCAA
Found at i:4946 original size:19 final size:20
Alignment explanation
Indices: 4816--4967 Score: 133
Period size: 19 Copynumber: 7.8 Consensus size: 20
4806 GTCGGGTTAG
* *
4816 ACCGATCAAACCGGCTCAG-
1 ACCGGTCAAACCGGTTCAGA
4835 ACCGGTCAAACC-GTCTCAG-
1 ACCGGTCAAACCGGT-TCAGA
4854 ACCGGTCAAACCGGTTC-GA
1 ACCGGTCAAACCGGTTCAGA
*
4873 ACCGGTTGAAACCGG-TCA-A
1 ACCGG-TCAAACCGGTTCAGA
4892 ACCGGTCAGAACCGGTTC-GA
1 ACCGGTCA-AACCGGTTCAGA
*
4912 ACCGGTTGAAACCGG-TCA-A
1 ACCGG-TCAAACCGGTTCAGA
* *
4931 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGGTTCAGA
*
4952 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
4968 TCCAGCAGCC
Statistics
Matches: 112, Mismatches: 8, Indels: 25
0.77 0.06 0.17
Matches are distributed among these distances:
18 6 0.05
19 62 0.55
20 34 0.30
21 10 0.09
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.16
Consensus pattern (20 bp):
ACCGGTCAAACCGGTTCAGA
Found at i:4947 original size:29 final size:28
Alignment explanation
Indices: 4821--4966 Score: 102
Period size: 29 Copynumber: 5.0 Consensus size: 28
4811 GTTAGACCGA
*
4821 TCAAACCGGCTCAG-ACCGGTCAAACCGTC
1 TCAAACCGG-TCAGAACCGGTCAAACCG-G
* *
4850 TCAGACCGGTCA-AACCGGTTCGAACCGG
1 TCAAACCGGTCAGAACCGG-TCAAACCGG
*
4878 TTGAAACCGGTCA-AACCGGTCAGAACCGG
1 -TCAAACCGGTCAGAACCGGTCA-AACCGG
* *
4907 TTCGAACCGGT-TGAAACCGGTCAAACCGG
1 -TCAAACCGGTCAG-AACCGGTCAAACCGG
* * *
4936 TCAGAACCGGTTGAAAACCGGTTAAACCGG
1 TCA-AACCGG-TCAGAACCGGTCAAACCGG
4966 T
1 T
4967 TTCCAGCAGC
Statistics
Matches: 95, Mismatches: 13, Indels: 17
0.76 0.10 0.14
Matches are distributed among these distances:
28 12 0.13
29 58 0.61
30 25 0.26
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (28 bp):
TCAAACCGGTCAGAACCGGTCAAACCGG
Found at i:5913 original size:14 final size:14
Alignment explanation
Indices: 5879--5921 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
5869 GCTACAAATC
*
5879 GATTTTTTTATATCT
1 GATTTTTTTA-AACT
*
5894 GTTTTTTTTAAACT
1 GATTTTTTTAAACT
5908 GATTTTTTTCAAAC
1 GATTTTTTT-AAAC
5922 CGAAACCGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.60
Consensus pattern (14 bp):
GATTTTTTTAAACT
Found at i:22847 original size:13 final size:14
Alignment explanation
Indices: 22822--22850 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
22812 TAAAACGTTC
22822 ATCATTATACATTT
1 ATCATTATACATTT
22836 ATCATT-TACATTT
1 ATCATTATACATTT
22849 AT
1 AT
22851 ACGTTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (14 bp):
ATCATTATACATTT
Found at i:23404 original size:24 final size:23
Alignment explanation
Indices: 23376--23441 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
23366 AGCTCGTATA
23376 AATTTGCACCATAGTGCCACGTAG
1 AATTTGCACC-TAGTGCCACGTAG
*
23400 AATTTGCACCTAAGTGCCGCGTAG
1 AATTTGCACCT-AGTGCCACGTAG
*
23424 AA-ATGCACCGTAGTGCCA
1 AATTTGCACC-TAGTGCCA
23442 TATAAGATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 13 0.35
24 24 0.65
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
AATTTGCACCTAGTGCCACGTAG
Found at i:31943 original size:14 final size:14
Alignment explanation
Indices: 31910--31945 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
31900 TTGTGAAACT
*
31910 TAGGTTCTTACCAT
1 TAGGTTCTTACCAA
*
31924 TGGGTTCTTACCAA
1 TAGGTTCTTACCAA
31938 TAGGTTCT
1 TAGGTTCT
31946 GGTGTCTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (14 bp):
TAGGTTCTTACCAA
Found at i:39970 original size:3 final size:3
Alignment explanation
Indices: 39962--39986 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39952 CAACTTGACA
39962 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
39987 TTAAATTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:40602 original size:2 final size:2
Alignment explanation
Indices: 40595--40619 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40585 ATGTATTAAT
40595 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 T
40620 TTGTGTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41259 original size:35 final size:35
Alignment explanation
Indices: 41209--41281 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
41199 TCCGGGTTTT
* *
41209 TTATCGTTATTTTATTATTATTATTATTA-TTATTA
1 TTATCGTCATCTTATTATT-TTATTATTATTTATTA
*
41244 TTATCGTCATCTTATTATTTTATTTTTATTTATTA
1 TTATCGTCATCTTATTATTTTATTATTATTTATTA
41279 TTA
1 TTA
41282 CAAATTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 8 0.24
35 26 0.76
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (35 bp):
TTATCGTCATCTTATTATTTTATTATTATTTATTA
Found at i:41262 original size:3 final size:3
Alignment explanation
Indices: 41215--41247 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
41205 TTTTTTATCG
41215 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
41248 CGTCATCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:48380 original size:19 final size:21
Alignment explanation
Indices: 48358--48396 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48348 AGCAAAGAGA
48358 AAAGAGCA-A-AGAAAAAAAC
1 AAAGAGCAGAGAGAAAAAAAC
48377 AAAGAGCAGAGAGAAAAAAA
1 AAAGAGCAGAGAGAAAAAAA
48397 ATCAAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.72, C:0.08, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAGAGCAGAGAGAAAAAAAC
Found at i:48389 original size:26 final size:24
Alignment explanation
Indices: 48350--48397 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
48340 CATATTAAAG
48350 CAAAGAGAAAAGAGCAAAGAAAAAAA
1 CAAAGAGAAAAGAG-AAA-AAAAAAA
* *
48376 CAAAGAGCAGAGAGAAAAAAAA
1 CAAAGAGAAAAGAGAAAAAAAA
48398 TCAAAGCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 3 0.15
26 12 0.60
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (24 bp):
CAAAGAGAAAAGAGAAAAAAAAAA
Found at i:48418 original size:22 final size:24
Alignment explanation
Indices: 48393--48443 Score: 88
Period size: 22 Copynumber: 2.2 Consensus size: 24
48383 CAGAGAGAAA
48393 AAAAATCAAAGCAAAAA-CAAA-G
1 AAAAATCAAAGCAAAAATCAAAGG
48415 AAAAATCAAAGCAAAAATCAAAGG
1 AAAAATCAAAGCAAAAATCAAAGG
48439 AAAAA
1 AAAAA
48444 AGCAAAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 17 0.63
23 4 0.15
24 6 0.22
ACGTcount: A:0.73, C:0.12, G:0.10, T:0.06
Consensus pattern (24 bp):
AAAAATCAAAGCAAAAATCAAAGG
Found at i:48432 original size:12 final size:12
Alignment explanation
Indices: 48393--48443 Score: 79
Period size: 12 Copynumber: 4.4 Consensus size: 12
48383 CAGAGAGAAA
48393 AAAAATCAAAGC
1 AAAAATCAAAGC
48405 AAAAA-CAAAG-
1 AAAAATCAAAGC
48415 AAAAATCAAAGC
1 AAAAATCAAAGC
*
48427 AAAAATCAAAGG
1 AAAAATCAAAGC
48439 AAAAA
1 AAAAA
48444 AGCAAAGAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
10 5 0.14
11 10 0.28
12 21 0.58
ACGTcount: A:0.73, C:0.12, G:0.10, T:0.06
Consensus pattern (12 bp):
AAAAATCAAAGC
Found at i:49637 original size:4 final size:4
Alignment explanation
Indices: 49628--49869 Score: 475
Period size: 4 Copynumber: 60.5 Consensus size: 4
49618 AGAAAAGTAT
*
49628 ATAC ATAC ATAC ACAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
49676 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
49724 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
49772 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
49820 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
49868 AT
1 AT
49870 GATACATAAA
Statistics
Matches: 236, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 236 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:50517 original size:105 final size:102
Alignment explanation
Indices: 50330--50568 Score: 250
Period size: 105 Copynumber: 2.3 Consensus size: 102
50320 GGAGAATTTT
** * * * * *
50330 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTTGTCTCGCTTGAGACACTTTCCCTTTAAGATACAAATTTAGAATTCGATTCACT
*
50395 AAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 AAAAACAAAATTAATCTCA-CTTGAGATCG-T-TTTC--TCA
* * *
50435 AAAACAAATTTTGTCTCGCTTGAGACCCTTTCCCTTTAAGATCCAAATTTAGAATTCGTTTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACACTTTCCCTTTAAGATACAAATTTAGAATTCGATTCACT
* * *
50499 ATTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 A-AAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
* * *
50537 AAAACAAACTTTGTATCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACACTTTC
50569 TCTAAAAACA
Statistics
Matches: 113, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
101 2 0.02
102 28 0.25
103 4 0.04
104 5 0.04
105 74 0.65
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (102 bp):
AAAACAAATTTTGTCTCGCTTGAGACACTTTCCCTTTAAGATACAAATTTAGAATTCGATTCACT
AAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:50596 original size:36 final size:36
Alignment explanation
Indices: 50530--50632 Score: 113
Period size: 36 Copynumber: 2.9 Consensus size: 36
50520 TTGAGATCGT
* *
50530 TTTCTC-AAAAACAAACTTTGTATCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
** *
50565 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * *
50601 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGAC
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGAC
50633 GTCATTGTCT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
34 22 0.39
35 7 0.12
36 28 0.49
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:50952 original size:56 final size:55
Alignment explanation
Indices: 50884--51010 Score: 188
Period size: 56 Copynumber: 2.3 Consensus size: 55
50874 TTCTTTTGAG
50884 GAAAAAATCTTTGAGTTTGTTCCTCTTG-A-AAAAATCTTTGAGTT-TGTTCATTTT
1 GAAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAATCTTTGAGTTGT-TTC-TTTT
*
50938 GAATAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTTGAGTTGTTTCTTTT
1 G-A-AAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAATCTTTGAGTTGTTTCTTTT
50995 GAAAAAATCTTTGAGT
1 GAAAAAATCTTTGAGT
51011 CTATTTATTT
Statistics
Matches: 67, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
54 1 0.01
55 15 0.22
56 26 0.39
57 6 0.09
58 18 0.27
59 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (55 bp):
GAAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAATCTTTGAGTTGTTTCTTTT
Found at i:50955 original size:29 final size:28
Alignment explanation
Indices: 50885--51025 Score: 173
Period size: 29 Copynumber: 5.1 Consensus size: 28
50875 TCTTTTGAGG
* *
50885 AAAAAATCTTTGAGTTTGTTCCTCTTG-
1 AAAAAATCTTTGAGTTTGTTCATTTTGA
50912 AAAAAATCTTTGAGTTTGTTCATTTTGA
1 AAAAAATCTTTGAGTTTGTTCATTTTGA
*
50940 ATAAAAATCTTTGAGTTTGTTCCTTTTGA
1 A-AAAAATCTTTGAGTTTGTTCATTTTGA
50969 ATAAAAATCTTTGAG-TTGTTTC-TTTTG-
1 A-AAAAATCTTTGAGTTTG-TTCATTTTGA
* * *
50996 AAAAAATCTTTGAGTCTATTTATTTTGA
1 AAAAAATCTTTGAGTTTGTTCATTTTGA
51024 AA
1 AA
51026 CGAAGTTTTG
Statistics
Matches: 102, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
26 15 0.15
27 32 0.31
28 11 0.11
29 44 0.43
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.47
Consensus pattern (28 bp):
AAAAAATCTTTGAGTTTGTTCATTTTGA
Found at i:51025 original size:27 final size:27
Alignment explanation
Indices: 50884--51010 Score: 184
Period size: 29 Copynumber: 4.6 Consensus size: 27
50874 TTCTTTTGAG
*
50884 GAAAAAATCTTTGAGTTTGTTCCTCTT
1 GAAAAAATCTTTGAGTTTGTTCCTTTT
*
50911 GAAAAAATCTTTGAGTTTGTTCATTTT
1 GAAAAAATCTTTGAGTTTGTTCCTTTT
50938 GAATAAAAATCTTTGAGTTTGTTCCTTTT
1 G-A-AAAAATCTTTGAGTTTGTTCCTTTT
*
50967 GAATAAAAATCTTTGAG-TTGTTTCTTTT
1 G-A-AAAAATCTTTGAGTTTGTTCCTTTT
50995 GAAAAAATCTTTGAGT
1 GAAAAAATCTTTGAGT
51011 CTATTTATTT
Statistics
Matches: 93, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
26 13 0.14
27 27 0.29
28 12 0.13
29 41 0.44
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (27 bp):
GAAAAAATCTTTGAGTTTGTTCCTTTT
Found at i:51087 original size:61 final size:61
Alignment explanation
Indices: 50997--51124 Score: 184
Period size: 61 Copynumber: 2.1 Consensus size: 61
50987 TTTCTTTTGA
* *
50997 AAAAATCTTTGAGTCTATTTATTTTGAAACGAAGTTTTGTCTCGCTTGAGACAATTTCGTG
1 AAAAATCTTTGAGTCTATTTATTTGGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCGTG
* * * * * *
51058 AAAAATCTTTGATTTTGTTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTG
1 AAAAATCTTTGAGTCTATTTATTTGGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCGTG
51119 AAAAAT
1 AAAAAT
51125 TTTTAAGATA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (61 bp):
AAAAATCTTTGAGTCTATTTATTTGGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCGTG
Found at i:51140 original size:61 final size:61
Alignment explanation
Indices: 51013--51152 Score: 181
Period size: 61 Copynumber: 2.3 Consensus size: 61
51003 CTTTGAGTCT
* * * ** *
51013 ATTTATTTTGAAACGAAGTTTTGTCTCGCTTGAGACAATTTCGTGAAAAATCTTTGATTTT
1 ATTTCTTTTGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCGTGAAAAATCTTTAAGATA
* * * * *
51074 GTTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAATTTTTAAGATA
1 ATTTCTTTTGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCGTGAAAAATCTTTAAGATA
51135 ATTTCTTTTGAAACAAAG
1 ATTTCTTTTGAAACAAAG
51153 ATCTTTGAAT
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.43
Consensus pattern (61 bp):
ATTTCTTTTGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCGTGAAAAATCTTTAAGATA
Found at i:51724 original size:15 final size:16
Alignment explanation
Indices: 51683--51730 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
51673 CTTTGAGTCG
51683 TTTCCCTTGAAACAAATT
1 TTTCCCTTGAAAC--ATT
51701 TTGTCCCTTGAAACA-T
1 TT-TCCCTTGAAACATT
*
51717 TTTCCCTTCAAACA
1 TTTCCCTTGAAACA
51731 AGAACATCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
17 1 0.04
18 2 0.07
19 11 0.39
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.38
Consensus pattern (16 bp):
TTTCCCTTGAAACATT
Found at i:52061 original size:35 final size:35
Alignment explanation
Indices: 52015--52145 Score: 237
Period size: 35 Copynumber: 3.7 Consensus size: 35
52005 CAAAGTTTAC
52015 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
1 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
52050 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
1 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
*
52085 CATCTTTGAATATGTTTCCCTTGAAACAAAACAAA
1 CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
52120 CATCTTTGAGATC-GTTTCCCTTGAAA
1 CATCTTTGA-ATCTGTTTCCCTTGAAA
52146 TGAATTTTGT
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
35 91 0.98
36 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (35 bp):
CATCTTTGAATCTGTTTCCCTTGAAACAAAACAAA
Found at i:52204 original size:66 final size:63
Alignment explanation
Indices: 52120--52298 Score: 180
Period size: 66 Copynumber: 2.8 Consensus size: 63
52110 ACAAAACAAA
52120 CATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCATTTGAGACAATTTCCCATGAAACGC
1 CATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTC-TTTGAGACAA-TTCCCATGAAACGC
* * * * * * * *
52185 CGATCTTTGAGAACGTTTCCCTTAAAAATAAATTTTGTCTCGCTTAAGACAATTCCCTTTAAATG
1 C-ATCTTTGAGATCGTTTCCCTT-GAAATGAATTTTGTCTC-TTTGAGACAATTCCCATGAAACG
52250 C
63 C
* * * * *
52251 CATCTTTG-GGTTGTTTCCTTTGAAACGAATCTTGTCTCTTTCGAGACA
1 CATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCTTT-GAGACA
52299 GTTGCTTTGG
Statistics
Matches: 92, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
62 2 0.02
63 18 0.20
64 9 0.10
65 8 0.09
66 32 0.35
67 23 0.25
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (63 bp):
CATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCTTTGAGACAATTCCCATGAAACGC
Found at i:52562 original size:46 final size:44
Alignment explanation
Indices: 52501--52822 Score: 181
Period size: 46 Copynumber: 7.4 Consensus size: 44
52491 GCCGTCCTCG
* *
52501 TCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 TCACGTAGGAGCCGTGTCATCACC-TTAGAT-GCCAGAACTCTTCA
* * *
52547 TCACGTATGAGCCGTGTCATTC-CC--CGA--CCAGATCTCTTCA
1 TCACGTAGGAGCCGTGTCA-TCACCTTAGATGCCAGAACTCTTCA
* * * *
52587 TCACGTAGGAGCCGTGTCA--ACCATAGATAACCAG-CCGTCCTCA
1 TCACGTAGGAGCCGTGTCATCACCTTAGAT-GCCAGAAC-TCTTCA
* * *
52630 TCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 TCACGTAGGAGCCGTGTCATCACC-TTAGAT-GCCAGAACTCTTCA
* * * *
52676 TCACGTATGAGCCGTGTCATC-CC-CAGA--CCAGATCTCCTCA
1 TCACGTAGGAGCCGTGTCATCACCTTAGATGCCAGAACTCTTCA
* * * * *
52716 TCACGTAGGAGCCGTGTCA--ACCATAGATAACCAG-CCGTCCTCG
1 TCACGTAGGAGCCGTGTCATCACCTTAGAT-GCCAGAAC-TCTTCA
** * *
52759 TCACGTAGGAATCGTGTTATCACCTTTAGACGACCCA-AACTCTTCA
1 TCACGTAGGAGCCGTGTCATCACC-TTAGATG--CCAGAACTCTTCA
* *
52805 TCACGTATGAGCAGTGTC
1 TCACGTAGGAGCCGTGTC
52823 GTCCCCAACA
Statistics
Matches: 210, Mismatches: 42, Indels: 48
0.70 0.14 0.16
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 64 0.30
42 2 0.01
43 55 0.26
45 8 0.04
46 70 0.33
47 7 0.03
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (44 bp):
TCACGTAGGAGCCGTGTCATCACCTTAGATGCCAGAACTCTTCA
Found at i:52633 original size:43 final size:43
Alignment explanation
Indices: 52573--52768 Score: 168
Period size: 43 Copynumber: 4.6 Consensus size: 43
52563 TCATTCCCCG
* *
52573 ACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
* * * * *
52616 ACCAG-CCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATG
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-ATAGATA
* * * * * **
52662 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCAG---
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
*
52702 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
*
52745 ACCAG-CCGTCCTCGTCACGTAGGA
1 ACCAGACC-TCCTCATCACGTAGGA
52769 ATCGTGTTAT
Statistics
Matches: 118, Mismatches: 26, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
40 33 0.28
42 2 0.02
43 48 0.41
44 2 0.02
45 3 0.03
46 29 0.25
47 1 0.01
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (43 bp):
ACCAGACCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
Found at i:52717 original size:129 final size:129
Alignment explanation
Indices: 52482--52829 Score: 592
Period size: 129 Copynumber: 2.7 Consensus size: 129
52472 ATTATCCTAG
52482 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
*
52547 TCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
* *
52611 AGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGATGGCCAGAACTCTTCA
1 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
52676 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
66 TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
* * *
52740 AGATAACCAGCCGTCCTCGTCACGTAGGAATCGTGTTATCACCTTTAGACGACCCA-AACTCTTC
1 AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATG-GCCAGAACTCTTC
* *
52804 ATCACGTATGAGCAGTGTCGTCCCCA
65 ATCACGTATGAGCCGTGTCATCCCCA
52830 ACAACCAATA
Statistics
Matches: 207, Mismatches: 10, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
128 5 0.02
129 199 0.96
130 3 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (129 bp):
AGATAACCAGCCGTCCTCGTCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCA
TCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCAT
Found at i:52718 original size:40 final size:40
Alignment explanation
Indices: 52534--52734 Score: 163
Period size: 40 Copynumber: 4.8 Consensus size: 40
52524 CTTTAGATGG
*
52534 CCAGAACTCTTCATCACGTATGAGCCGTGTCATTCCCC-GA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCA-TCCCCAGA
* * **
52574 CCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAG---A
* * * * * *
52617 CCAG-CCGTCCTCATCACGTAGGAACCATGTTATCACCTTTAGA
1 CCAGAAC-TCTTCATCACGTAGGAGCCGTGTCATC-CC--CAGA
*
52660 TGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCAGA
1 ---CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAGA
* *
52703 CCAGATCTCCTCATCACGTAGGAGCCGTGTCA
1 CCAGAACTCTTCATCACGTAGGAGCCGTGTCA
52735 ACCATAGATA
Statistics
Matches: 127, Mismatches: 22, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
39 2 0.02
40 60 0.47
42 1 0.01
43 31 0.24
44 1 0.01
45 2 0.02
46 29 0.23
47 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (40 bp):
CCAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAGA
Found at i:53023 original size:35 final size:35
Alignment explanation
Indices: 52973--53045 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
52963 TCCGTGTTTT
*
52973 TTATCGTAATTTTATTATTATTATTATTA-TTATTA
1 TTATCGTAATCTTATTATT-TTATTATTATTTATTA
* *
53008 TTATCGTCATCTTATTATTTTATTTTTATTTATTA
1 TTATCGTAATCTTATTATTTTATTATTATTTATTA
53043 TTA
1 TTA
53046 CAAATTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 8 0.24
35 26 0.76
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.64
Consensus pattern (35 bp):
TTATCGTAATCTTATTATTTTATTATTATTTATTA
Found at i:53026 original size:3 final size:3
Alignment explanation
Indices: 52984--53011 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
52974 TATCGTAATT
52984 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
53012 CGTCATCTTA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:60327 original size:16 final size:17
Alignment explanation
Indices: 60294--60327 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
60284 GAATTATCTT
*
60294 TAGGAATTATCTTTTTA
1 TAGGAATTATCATTTTA
60311 TAGGAATTAT-ATTTTA
1 TAGGAATTATCATTTTA
60327 T
1 T
60328 TTGTTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (17 bp):
TAGGAATTATCATTTTA
Found at i:64505 original size:12 final size:12
Alignment explanation
Indices: 64488--64516 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
64478 TAAGCAATAC
64488 TTCTTCTTCTTT
1 TTCTTCTTCTTT
64500 TTCTTCTTCTTT
1 TTCTTCTTCTTT
64512 TTCTT
1 TTCTT
64517 TCACCAATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:66382 original size:25 final size:26
Alignment explanation
Indices: 66336--66384 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
66326 AAGCCTAATG
*
66336 AAATCATCCTTTCTTTAGTTTAATAA
1 AAATCATCCTTTCTTTACTTTAATAA
* *
66362 AAATCAT-TTTTCTTTTCTTTAAT
1 AAATCATCCTTTCTTTACTTTAAT
66385 TTTCTTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.31, C:0.14, G:0.02, T:0.53
Consensus pattern (26 bp):
AAATCATCCTTTCTTTACTTTAATAA
Found at i:66940 original size:12 final size:12
Alignment explanation
Indices: 66906--66951 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
66896 TACCATATTG
*
66906 AATTTTCTTTTA
1 AATTTTCTTTTT
*
66918 AACTTTCTTTTT
1 AATTTTCTTTTT
*
66930 AATTTTATTTTT
1 AATTTTCTTTTT
*
66942 AATCTTCTTT
1 AATTTTCTTT
66952 GAAATTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (12 bp):
AATTTTCTTTTT
Found at i:68348 original size:50 final size:50
Alignment explanation
Indices: 68290--68388 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
68280 TTTAAATTAC
*
68290 ATATGGCAGAAAAATCAGCAGCAAGTTGATTCGCAAGAGTAAAGGGGGAT
1 ATATGGCAGAAAAATCAGCAGCAAGTTGATTCGCAAGAGCAAAGGGGGAT
**
68340 ATATGGCAGAAAAATCAGCAGTGAGTTGATTCGCAAGAGCAAAGGGGGA
1 ATATGGCAGAAAAATCAGCAGCAAGTTGATTCGCAAGAGCAAAGGGGGA
68389 CTATGGTACA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.39, C:0.12, G:0.31, T:0.17
Consensus pattern (50 bp):
ATATGGCAGAAAAATCAGCAGCAAGTTGATTCGCAAGAGCAAAGGGGGAT
Found at i:69377 original size:18 final size:18
Alignment explanation
Indices: 69350--69384 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
69340 TACATTTCAG
69350 GGCTGCTGAATCAAACCA
1 GGCTGCTGAATCAAACCA
* *
69368 GGCTGTTGAATGAAACC
1 GGCTGCTGAATCAAACC
69385 CCTACGTGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (18 bp):
GGCTGCTGAATCAAACCA
Found at i:71490 original size:2 final size:2
Alignment explanation
Indices: 71483--71507 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
71473 TATCTTTTCC
71483 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 T
71508 CACCTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73635 original size:13 final size:13
Alignment explanation
Indices: 73617--73642 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
73607 ATGTTGATAT
73617 GAATTCAAAAAAG
1 GAATTCAAAAAAG
73630 GAATTCAAAAAAG
1 GAATTCAAAAAAG
73643 TTGAAGGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (13 bp):
GAATTCAAAAAAG
Found at i:75273 original size:20 final size:20
Alignment explanation
Indices: 75248--75299 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
75238 ATAGACTGAA
75248 AGTATCGATACTATCCCTGG
1 AGTATCGATACTATCCCTGG
75268 AGTATCGATACTATCCCTGG
1 AGTATCGATACTATCCCTGG
75288 AGTATCGATACT
1 AGTATCGATACT
75300 CCTACTAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTATCCCTGG
Found at i:77690 original size:30 final size:30
Alignment explanation
Indices: 77656--77850 Score: 227
Period size: 30 Copynumber: 6.5 Consensus size: 30
77646 AATGGGGATA
* *
77656 TAATCCCATGAAGATGTCATAACGAGGAAC
1 TAATCCCATGCAGATGTCAGAACGAGGAAC
*
77686 TAATCACATGCAGATGTCAGAAC-AGAGAAC
1 TAATCCCATGCAGATGTCAGAACGAG-GAAC
77716 TAATCCCATGCAGATGTCAGAACGAGGAAC
1 TAATCCCATGCAGATGTCAGAACGAGGAAC
77746 TAATCCCATGCAGATGTCAGAA-G-GGTCAAC
1 TAATCCCATGCAGATGTCAGAACGAGG--AAC
* *
77776 TAATCCCATGCAGATGTCAGAAAGGGGAAC
1 TAATCCCATGCAGATGTCAGAACGAGGAAC
* * * * *
77806 CAATCCCATGTAGATGTCATAATTGA-GAAT
1 TAATCCCATGCAGATGTCAGAA-CGAGGAAC
*
77836 TAATACCATGCAGAT
1 TAATCCCATGCAGAT
77851 CAGAAATACA
Statistics
Matches: 145, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
28 2 0.01
29 3 0.02
30 134 0.92
31 4 0.03
32 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (30 bp):
TAATCCCATGCAGATGTCAGAACGAGGAAC
Found at i:78459 original size:19 final size:19
Alignment explanation
Indices: 78435--78472 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
78425 AAAGTCAACG
78435 GTCAAAGTCAATGGTCAAA
1 GTCAAAGTCAATGGTCAAA
78454 GTCAAAGTCAATGGTCAAA
1 GTCAAAGTCAATGGTCAAA
78473 AGATCAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (19 bp):
GTCAAAGTCAATGGTCAAA
Found at i:78472 original size:13 final size:13
Alignment explanation
Indices: 78425--78458 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
78415 GGTTTTGGAA
78425 AAAGTCAACGGTC
1 AAAGTCAACGGTC
*
78438 AAAGTCAATGGTC
1 AAAGTCAACGGTC
78451 AAAGTCAA
1 AAAGTCAA
78459 AGTCAATGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:78504 original size:13 final size:13
Alignment explanation
Indices: 78425--78506 Score: 58
Period size: 13 Copynumber: 6.2 Consensus size: 13
78415 GGTTTTGGAA
* *
78425 AAAGTCAACGGTC
1 AAAGTCAAAGATC
* *
78438 AAAGTCAATGGTC
1 AAAGTCAAAGATC
78451 AAAGTCAAAG-TC
1 AAAGTCAAAGATC
*
78463 AATGGTCAAAAGATC
1 AA-AGTC-AAAGATC
* *
78478 AACGATCAACGATC
1 AAAG-TCAAAGATC
*
78492 AAAGTCAATGATC
1 AAAGTCAAAGATC
78505 AA
1 AA
78507 CGGGTCAGAT
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
12 4 0.07
13 34 0.59
14 14 0.24
15 6 0.10
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (13 bp):
AAAGTCAAAGATC
Found at i:78569 original size:29 final size:29
Alignment explanation
Indices: 78523--78581 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
78513 AGATCGGATT
**
78523 ACCGATTCAGCCAGTTCGGTTTAAGGGTG
1 ACCGATTCAGCCAGTTCGGTCCAAGGGTG
78552 ACCGATTCAGCC-GATTCGGTCCAAGGGTG
1 ACCGATTCAGCCAG-TTCGGTCCAAGGGTG
78581 A
1 A
78582 TTGGTTCGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.24
Consensus pattern (29 bp):
ACCGATTCAGCCAGTTCGGTCCAAGGGTG
Found at i:79326 original size:19 final size:20
Alignment explanation
Indices: 79302--79351 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
79292 GATAAACTTA
*
79302 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
79321 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
79342 TT-ATAATTTT
1 TTAATAATTTT
79352 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:79328 original size:31 final size:31
Alignment explanation
Indices: 79269--79355 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
79259 TTCGATAATA
* * *
79269 TAATAATTATTTTATAGT-ATTTAGATAAACT
1 TAATAAGTATTTTATAATCTTTTA-ATAAACT
* *
79300 TATTAA-TAATTTTATAATCTTTTAATAAATT
1 TAATAAGT-ATTTTATAATCTTTTAATAAACT
*
79331 TAATAAGTATTTTATAATTTTTTAA
1 TAATAAGTATTTTATAATCTTTTAA
79356 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 41 0.87
32 5 0.11
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (31 bp):
TAATAAGTATTTTATAATCTTTTAATAAACT
Found at i:80122 original size:31 final size:29
Alignment explanation
Indices: 80076--80161 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 29
80066 TCAATAAAGT
80076 TTAAAAAATATAAAATACTTATTAAATTTA
1 TTAAAAAATATAAAATA-TTATTAAATTTA
* *
80106 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAA-AATATAAAA-TATTATTAAATTTA
* *
80137 TCTAAATACTATAAAATAATTATTA
1 T-TAAAAAATATAAAAT-ATTATTA
80162 TATTATCCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
30 7 0.15
31 34 0.72
32 6 0.13
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (29 bp):
TTAAAAAATATAAAATATTATTAAATTTA
Found at i:83015 original size:2 final size:2
Alignment explanation
Indices: 83010--83036 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
83000 TTTCTTGCCT
83010 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
83037 GGGGAATGCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:84609 original size:3 final size:3
Alignment explanation
Indices: 84601--84651 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
84591 CTTTTTTGTA
** *
84601 TAT TAT TAT TAT CGT TAT TTT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
84647 TAT TA
1 TAT TA
84652 ATATATTACA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:88506 original size:31 final size:31
Alignment explanation
Indices: 88470--88530 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
88460 ATTTTACATG
88470 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTC-TTTGTTTGTGTA
88501 TACTAACTTATTTCTTCTCTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTGTTTGTGT
88531 CATTTTGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 24 0.83
32 5 0.17
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (31 bp):
TACTAACTTATTTCTTCTCTTTGTTTGTGTA
Found at i:90988 original size:26 final size:25
Alignment explanation
Indices: 90959--91036 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
90949 AATTTTTGAC
90959 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
90985 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
91005 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
91031 ATTCTT
1 ATTCTT
91037 TCCACCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:90997 original size:20 final size:20
Alignment explanation
Indices: 90974--91048 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
90964 ATCTCTTTGA
90974 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
90994 GACCTTGAAACATTCCCTCTCTTTGA
1 GACCTTGAAATA-T---TCT-TTT-C
91020 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
91039 CACCTTGAAA
1 GACCTTGAAA
91049 CACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:92879 original size:4 final size:4
Alignment explanation
Indices: 92870--92931 Score: 96
Period size: 4 Copynumber: 16.5 Consensus size: 4
92860 AGAAAAGTAT
92870 ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC --AC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
92914 ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC AT
92932 CCATGATACA
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.07
4 50 0.93
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:92898 original size:22 final size:22
Alignment explanation
Indices: 92870--92926 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
92860 AGAAAAGTAT
92870 ATACATACATACACATACATAC
1 ATACATACATACACATACATAC
92892 ATACATACATACACATACATAC
1 ATACATACATACACATACATAC
92914 ATACATACATACA
1 ATACATACATACA
92927 TACATCCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (22 bp):
ATACATACATACACATACATAC
Found at i:93539 original size:105 final size:101
Alignment explanation
Indices: 93398--93635 Score: 264
Period size: 105 Copynumber: 2.3 Consensus size: 101
93388 TGAGAATTTT
* * * *
93398 AAAACAAATTGTGTTTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
** *
93462 TAAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC-
66 T-AAAACAAAATTAATCTCA-CTT-GA-AATCGTTTC--TCA
* * * *
93503 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGGATTTGTTTCACA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* * *
93568 TTAAACAAAGTTGATCTCACTTGAAATCGTTTCTCA
66 TAAAACAAAATTAATCTCACTTGAAATCGTTTCTCA
* *
93604 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTC
93636 TCTAAAAACA
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
100 2 0.02
101 29 0.25
102 6 0.05
103 2 0.02
104 3 0.03
105 71 0.62
106 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (101 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TAAAACAAAATTAATCTCACTTGAAATCGTTTCTCA
Found at i:93626 original size:35 final size:36
Alignment explanation
Indices: 93582--93662 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
93572 ACAAAGTTGA
*
93582 TCTCACTTGAAATC-GTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAAA-CAATTTCTCTAAAAACAAACTTTG
* * *
93617 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAAACAATTTCTCTAAAAACAAACTTTG
*
93653 TCTCATTTGA
1 TCTCACTTGA
93663 GACTATATCT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 1 0.03
35 16 0.42
36 21 0.55
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (36 bp):
TCTCACTTGAAACAATTTCTCTAAAAACAAACTTTG
Found at i:93653 original size:36 final size:36
Alignment explanation
Indices: 93597--93700 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
93587 CTTGAAATCG
*
93597 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
** *
93632 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * *
93668 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
93701 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 22 0.38
35 7 0.12
36 29 0.50
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:94011 original size:29 final size:29
Alignment explanation
Indices: 93942--94107 Score: 196
Period size: 29 Copynumber: 5.8 Consensus size: 29
93932 AAGACAATTT
* *
93942 CTTTTGAAAAAAAAATCTTTGGGTTTGTTT
1 CTTTTG-AAAAAAAATCTTTGAGTTTGTTC
*
93972 CTCTTGAAAAAAAAATCTTTGAGTTTGTTC
1 CTTTTG-AAAAAAAATCTTTGAGTTTGTTC
* *
94002 CTCTTG--AAAAAATCTTTGAGTTTGCTC
1 CTTTTGAAAAAAAATCTTTGAGTTTGTTC
* *
94029 CTTTTGAATAAAAATCTTGGAGTTTGTTC
1 CTTTTGAAAAAAAATCTTTGAGTTTGTTC
* *
94058 CTTTTGAATAAAAATCTTTGAG-TTGTTT
1 CTTTTGAAAAAAAATCTTTGAGTTTGTTC
*
94086 CTTTTG-AAAAATATCTTTGAGT
1 CTTTTGAAAAAAAATCTTTGAGT
94108 CTATTTATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
27 38 0.31
28 11 0.09
29 39 0.32
30 33 0.27
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.45
Consensus pattern (29 bp):
CTTTTGAAAAAAAATCTTTGAGTTTGTTC
Found at i:94036 original size:57 final size:58
Alignment explanation
Indices: 93950--94096 Score: 201
Period size: 57 Copynumber: 2.6 Consensus size: 58
93940 TTCTTTTGAA
* * *
93950 AAAAAAATCTTTGGGTTTGTTTCTCTTGAAAAAAAAATCTTTGAGTTTGTTCCTCTTG
1 AAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAAAATCTTGGAGTTTGTTCCTCTTG
* * * *
94008 -AAAAAATCTTTGAGTTTGCTCCTTTTG-AATAAAAATCTTGGAGTTTGTTCCTTTTG
1 AAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAAAATCTTGGAGTTTGTTCCTCTTG
94064 AATAAAAATCTTTGAG-TTGTTTCTTTTGAAAAA
1 AA-AAAAATCTTTGAGTTTGTTTCTTTTGAAAAA
94097 TATCTTTGAG
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
56 26 0.34
57 34 0.45
58 16 0.21
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.44
Consensus pattern (58 bp):
AAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAAAATCTTGGAGTTTGTTCCTCTTG
Found at i:94052 original size:56 final size:56
Alignment explanation
Indices: 93950--94107 Score: 203
Period size: 56 Copynumber: 2.8 Consensus size: 56
93940 TTCTTTTGAA
* *
93950 AAAAAAATCTTTGGGTTTGTTTCTCTTGAAAAAAAAATCTTTGAGTTTGTTCCTCTTG
1 AAAAAAATCTTTGAGTTTGTTTCTTTTG--AAAAAAATCTTTGAGTTTGTTCCTCTTG
* * * *
94008 -AAAAAATCTTTGAGTTTGCTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTTTTG
1 AAAAAAATCTTTGAGTTTGTTTCTTTTGAA-AAAAATCTTTGAGTTTGTTCCTCTTG
*
94064 AATAAAAATCTTTGAG-TTGTTTCTTTTGAAAAATATCTTTGAGT
1 AA-AAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAATCTTTGAGT
94108 CTATTTATTT
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
55 2 0.02
56 36 0.41
57 36 0.41
58 13 0.15
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (56 bp):
AAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTCCTCTTG
Found at i:94118 original size:28 final size:27
Alignment explanation
Indices: 93980--94122 Score: 96
Period size: 29 Copynumber: 5.1 Consensus size: 27
93970 TTCTCTTGAA
* *
93980 AAAAAAATCTTTGAGTT-TGTTCCTCTTG
1 AAAAAAATCTTTGAGTTAT-TT-ATTTTG
**
94008 -AAAAAATCTTTGAGTT-TGCTCCTTTTG
1 AAAAAAATCTTTGAGTTAT--TTATTTTG
* *
94035 AATAAAAATCTTGGAGTT-TGTTCCTTTTG
1 AA-AAAAATCTTTGAGTTAT-TT-ATTTTG
* *
94064 AATAAAAATCTTTGAGTTGTTTCTTTTG
1 AA-AAAAATCTTTGAGTTATTTATTTTG
*
94092 AAAAATATCTTTGAGTCTATTTATTTTG
1 AAAAAAATCTTTGAGT-TATTTATTTTG
94120 AAA
1 AAA
94123 CAAAGTTTTG
Statistics
Matches: 99, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
27 35 0.35
28 23 0.23
29 40 0.40
30 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.45
Consensus pattern (27 bp):
AAAAAAATCTTTGAGTTATTTATTTTG
Found at i:94196 original size:52 final size:53
Alignment explanation
Indices: 94118--94221 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
94108 CTATTTATTT
94118 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
94170 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
94222 ATTGTTTCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 36 0.73
54 13 0.27
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:94245 original size:27 final size:27
Alignment explanation
Indices: 94208--94264 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
94198 AATTTTGTGA
*
94208 AAAAAATCTTTGAGATT-GTTTCTTTTG
1 AAAAAATCTTTGAG-TTGGTTTCTTTGG
94235 AAAAAATCTTTGAGTTGGTTTCTTTGG
1 AAAAAATCTTTGAGTTGGTTTCTTTGG
94262 AAA
1 AAA
94265 TAAAATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 2 0.07
27 26 0.93
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.44
Consensus pattern (27 bp):
AAAAAATCTTTGAGTTGGTTTCTTTGG
Found at i:94652 original size:63 final size:62
Alignment explanation
Indices: 94550--94672 Score: 174
Period size: 63 Copynumber: 2.0 Consensus size: 62
94540 GATGTAATCC
* * * *
94550 ATCTTTGAGTCTGTTTCTTTTAAAACAAAATTTTATCTCTTAACGACAATTTCTTTTGAAAAA
1 ATCTTTGAGGCTGTTTCTTTGAAAACAAAATTTTATCTCTCAA-GACAACTTCTTTTGAAAAA
* * *
94613 ATCTTTGAGGCTGTTTCTTTGGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAA
1 ATCTTTGAGGCTGTTTCTTTGAAAACAAAATTTTATCTCTCAAGACAACTTCTTTTGAAA
94673 CCACCCACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
62 16 0.30
63 37 0.70
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (62 bp):
ATCTTTGAGGCTGTTTCTTTGAAAACAAAATTTTATCTCTCAAGACAACTTCTTTTGAAAAA
Found at i:94893 original size:36 final size:36
Alignment explanation
Indices: 94820--94894 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
94810 AACAAACATC
*
94820 TTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCA
1 TTTGAGATCATTTCCCTTTAAACGAATTTTGACTCA
* *
94856 TTTGAGA-CAGTTTTCCTTTAAAC-AATCTTTGAGTCA
1 TTTGAGATCA-TTTCCCTTTAAACGAAT-TTTGACTCA
94892 TTT
1 TTT
94895 CCTTTGAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 5 0.15
36 29 0.85
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (36 bp):
TTTGAGATCATTTCCCTTTAAACGAATTTTGACTCA
Found at i:94911 original size:63 final size:63
Alignment explanation
Indices: 94813--94932 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
94803 GAAACAAAAC
*
94813 AAACATCTTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCATTT-GAGACAGTTTTCCTTT
1 AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTTAGAGACAGTTTTCCTTT
*
94875 AAACAATCTTTGAG-TCATTT-CCTTTGAAACAAAATTTTGTCTCTTTTAAGAGACAGTT
1 AAAC-ATCTTTGAGATCATTTCCCTTT-AAAC-AAATTTTGTCTCATTT-AGAGACAGTT
94933 GCTTTTGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
61 5 0.10
62 14 0.27
63 23 0.45
65 9 0.18
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (63 bp):
AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTTAGAGACAGTTTTCCTTT
Found at i:95080 original size:46 final size:45
Alignment explanation
Indices: 95030--95428 Score: 267
Period size: 40 Copynumber: 9.3 Consensus size: 45
95020 CCAGCCGTCC
* * *
95030 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTTATCACC-TTAGATGACCAGAACTCT
* ** *
95076 TCATCACGTATGAGCCGTGTCAT-ACC----CCGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTTATCACCTTAGATGACCAGAACTCT
* * * *
95116 TCATCACGTATGAGCCGTG---TCACCCTAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTTATCACCTTAGATGACCAGAAC-TCT
* *
95158 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGACCAGAACTCT
1 TCATCACGTATGAGCCGTGTTATCACC-TTAGATGACCAGAACTCT
* ** *
95204 TCATCACGTATGAGCCGTGTCAT-ACC----CCGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTTATCACCTTAGATGACCAGAACTCT
* * * * *
95244 TCATCACATATGAGCCGTG---TCACCCTAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTTATCACCTTAGATGACCAGAAC-TCT
* * *
95286 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTTATCACC-TTAGATGACCAGAACTCT
* * *
95332 TCATCACGTATGAGCCGTGTCATTC-CC-----CGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTTA-TCACCTTAGATGACCAGAACTCT
* * * *
95372 TCATCACGTAGGAGCCGTGTCA--ACCATAGATAACCA-AACTCT
1 TCATCACGTATGAGCCGTGTTATCACCTTAGATGACCAGAACTCT
95414 TCATCACGTATGAGC
1 TCATCACGTATGAGC
95429 AGTGGCGTCC
Statistics
Matches: 275, Mismatches: 49, Indels: 62
0.71 0.13 0.16
Matches are distributed among these distances:
37 2 0.01
38 8 0.03
40 89 0.32
41 2 0.01
42 66 0.24
43 4 0.01
45 16 0.06
46 84 0.31
47 4 0.01
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (45 bp):
TCATCACGTATGAGCCGTGTTATCACCTTAGATGACCAGAACTCT
Found at i:95423 original size:128 final size:128
Alignment explanation
Indices: 95020--95407 Score: 722
Period size: 128 Copynumber: 3.0 Consensus size: 128
95010 TTTTAGATGG
95020 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
95085 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
66 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
*
95148 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGACCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
*
95213 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACATATGAGCCGTGTCACCCTAGATAA
66 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
95276 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
* * *
95341 ATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACCATAGATAA
66 ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACCCTAGATAA
95405 CCA
1 CCA
95408 AACTCTTCAT
Statistics
Matches: 252, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
128 239 0.95
129 13 0.05
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (128 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGT
ATGAGCCGTGTCATACCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCACCCTAGATAA
Found at i:95598 original size:3 final size:3
Alignment explanation
Indices: 95590--95634 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
95580 CTTTTTTGTA
** *
95590 TAT TAT TAT TAT CGT TAT TTT TAT TAT TAT TAT TATT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TA
95635 ATATATTACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:95615 original size:18 final size:19
Alignment explanation
Indices: 95590--95634 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
95580 CTTTTTTGTA
*
95590 TATTATTATTATCGTTATT
1 TATTATTATTATCATTATT
*
95609 T-TTATTATTATTATTATT
1 TATTATTATTATCATTATT
95627 TATTATTA
1 TATTATTA
95635 ATATATTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTATTATTATCATTATT
Found at i:111881 original size:22 final size:20
Alignment explanation
Indices: 111843--111882 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
111833 AGATTTAGTG
111843 ACTGCCAAGTAAAAGCTTTA
1 ACTGCCAAGTAAAAGCTTTA
*
111863 ACTGCTAAGGTAACAAGCTT
1 ACTGCCAA-GTAA-AAGCTT
111883 CGGCCATCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (20 bp):
ACTGCCAAGTAAAAGCTTTA
Found at i:112211 original size:30 final size:28
Alignment explanation
Indices: 112177--112233 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
112167 CTTCGTTTAT
112177 TTAGT-ATTTGTTTATTTCTATTTTATTGTC
1 TTAGTAATTT-TTTATTT-TATTTT-TTGTC
112207 TTAGTAATTTTTTATTTTATTTTTTGT
1 TTAGTAATTTTTTATTTTATTTTTTGT
112234 TATAAAACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 4 0.15
29 6 0.23
30 12 0.46
31 4 0.15
ACGTcount: A:0.18, C:0.04, G:0.09, T:0.70
Consensus pattern (28 bp):
TTAGTAATTTTTTATTTTATTTTTTGTC
Found at i:115605 original size:19 final size:19
Alignment explanation
Indices: 115577--115617 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
115567 GATCATCTTT
* *
115577 CATGGTAAGTTTTTGGAAA
1 CATGGAAAGTTTTTAGAAA
115596 CATGGAAAGTTTTTAGAAA
1 CATGGAAAGTTTTTAGAAA
115615 CAT
1 CAT
115618 TAAGACCGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (19 bp):
CATGGAAAGTTTTTAGAAA
Done.