Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008413.1 Hibiscus syriacus cultivar Beakdansim tig00111191_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: 2772818
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 10
Found at i:3063 original size:9 final size:9
Alignment explanation
Indices: 3049--3102 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
3039 GGCTGCTGGA
3049 AACCGGTTT
1 AACCGGTTT
3058 AACCGGTTTT
1 AACCGG-TTT
3068 CAACCGGTTCT
1 -AACCGGTT-T
*
3079 GACCGGTTT
1 AACCGGTTT
*
3088 GACCGGTTT
1 AACCGGTTT
3097 CAACCG
1 -AACCG
3103 TTCGAACTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 16 0.41
10 16 0.41
11 7 0.18
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:3074 original size:20 final size:21
Alignment explanation
Indices: 3049--3087 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3039 GGCTGCTGGA
3049 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
3069 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
3088 GACCGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:3094 original size:19 final size:19
Alignment explanation
Indices: 3051--3147 Score: 60
Period size: 19 Copynumber: 5.1 Consensus size: 19
3041 CTGCTGGAAA
* * *
3051 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
3071 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
3090 CCGGTTTCAACC-GTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
*
3109 CTGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
3128 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
3146 CC
1 CC
3148 CGACCCGACC
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
18 12 0.19
19 36 0.57
20 7 0.11
21 8 0.13
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.31
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:3115 original size:28 final size:29
Alignment explanation
Indices: 3050--3147 Score: 103
Period size: 28 Copynumber: 3.4 Consensus size: 29
3040 GCTGCTGGAA
*
3050 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTCTG
3080 ACCGGTTTGACCGGTTTCAACC-GTTC-G
1 ACCGGTTTGACCGGTTTCAACCGGTTCTG
* * * *
3107 AACTGGTTTGACCGGTCTGAATCGGTT-TG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCTG
*
3136 ACCGGTCTGACC
1 ACCGGTTTGACC
3148 CGACCCGACC
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
27 1 0.02
28 32 0.55
29 12 0.21
30 13 0.22
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.31
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:3154 original size:5 final size:5
Alignment explanation
Indices: 3144--3221 Score: 77
Period size: 5 Copynumber: 14.8 Consensus size: 5
3134 TGACCGGTCT
* *
3144 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGT GA-CC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC-C GACCC GACCC
*
3191 GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACC--C GACCC GACCC GACCC GACC
3222 GTTGATCGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
4 2 0.03
5 49 0.80
6 2 0.03
7 8 0.13
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:3170 original size:22 final size:22
Alignment explanation
Indices: 3144--3226 Score: 152
Period size: 22 Copynumber: 3.9 Consensus size: 22
3134 TGACCGGTCT
3144 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
3166 GACCCGACCCGACCG-TGA-CC
1 GACCCGACCCGACCGTTGACCC
3186 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
3208 GACCCGACCCGACCGTTGA
1 GACCCGACCCGACCGTTGA
3227 TCGTTGACCG
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
20 17 0.29
21 6 0.10
22 36 0.61
ACGTcount: A:0.19, C:0.48, G:0.24, T:0.08
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:3195 original size:42 final size:42
Alignment explanation
Indices: 3144--3223 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
3134 TGACCGGTCT
3144 GACCCGACCCGACCGTTGACCCGACCCGACCCGACCGTGACC
1 GACCCGACCCGACCGTTGACCCGACCCGACCCGACCGTGACC
3186 GACCCGACCCGACCGTTGACCCGACCCGACCCGACCGT
1 GACCCGACCCGACCGTTGACCCGACCCGACCCGACCGT
3224 TGATCGTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.19, C:0.50, G:0.24, T:0.07
Consensus pattern (42 bp):
GACCCGACCCGACCGTTGACCCGACCCGACCCGACCGTGACC
Found at i:19002 original size:25 final size:20
Alignment explanation
Indices: 18946--18985 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18936 AATGAAAATG
18946 AAATGGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
18966 AAATGGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
18986 TGAAATGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (20 bp):
AAATGGAAAAAGGAAAGAAT
Found at i:19217 original size:36 final size:36
Alignment explanation
Indices: 19143--19244 Score: 179
Period size: 36 Copynumber: 2.9 Consensus size: 36
19133 AAATGGAATT
**
19143 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
19178 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
19214 TGGTGATGATATAGGCGTGATAATGGTGATG
1 TGGTGATGATATAGGCGTGATAATGGTGATG
19245 AACAGATTGT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.33
36 43 0.67
ACGTcount: A:0.27, C:0.04, G:0.38, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAAGA
Found at i:23530 original size:25 final size:20
Alignment explanation
Indices: 23474--23513 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
23464 AATGAAAATG
23474 AAATGGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
23494 AAATGGAAAAAGGAAAGAAT
1 AAATGGAAAAAGGAAAGAAT
23514 TGAAATGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (20 bp):
AAATGGAAAAAGGAAAGAAT
Found at i:23708 original size:13 final size:12
Alignment explanation
Indices: 23689--23774 Score: 58
Period size: 11 Copynumber: 7.2 Consensus size: 12
23679 ATATATGCGT
23689 GATATGGTGATG
1 GATATGGTGATG
23701 GAATATGGTGAT-
1 G-ATATGGTGATG
*
23713 GATATAGGCG-T-
1 GATAT-GGTGATG
23724 GATAATGGTGATG
1 GAT-ATGGTGATG
23737 GAATATGGTGAT-
1 G-ATATGGTGATG
*
23749 GATATAGGCG-T-
1 GATAT-GGTGATG
23760 GATAATGGTGATG
1 GAT-ATGGTGATG
23773 GA
1 GA
23775 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 22 0.37
12 15 0.25
13 21 0.35
14 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:23739 original size:36 final size:36
Alignment explanation
Indices: 23663--23774 Score: 199
Period size: 36 Copynumber: 3.1 Consensus size: 36
23653 GGAATGGAAA
* *
23663 ATGGAATTTGGTGATGATATATGCGTGAT-ATGGTG
1 ATGGAATATGGTGATGATATAGGCGTGATAATGGTG
23698 ATGGAATATGGTGATGATATAGGCGTGATAATGGTG
1 ATGGAATATGGTGATGATATAGGCGTGATAATGGTG
23734 ATGGAATATGGTGATGATATAGGCGTGATAATGGTG
1 ATGGAATATGGTGATGATATAGGCGTGATAATGGTG
23770 ATGGA
1 ATGGA
23775 CAGATTGTAT
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 27 0.36
36 47 0.64
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (36 bp):
ATGGAATATGGTGATGATATAGGCGTGATAATGGTG
Found at i:25347 original size:16 final size:16
Alignment explanation
Indices: 25323--25355 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
25313 TAGTTAGCTC
25323 ATTTACATTCTAACAT
1 ATTTACATTCTAACAT
*
25339 ATTTGCATTCTAACAT
1 ATTTACATTCTAACAT
25355 A
1 A
25356 GGTGGCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.42
Consensus pattern (16 bp):
ATTTACATTCTAACAT
Found at i:30726 original size:16 final size:16
Alignment explanation
Indices: 30705--30737 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
30695 TAGTTAGCTC
30705 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
30721 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
30737 A
1 A
30738 GGTGGCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:36803 original size:19 final size:20
Alignment explanation
Indices: 36779--36829 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
36769 CGGCCAAGAG
* *
36779 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
36798 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
36818 CATGTATTTTCA
1 CATGTATTTTCA
36830 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:37544 original size:16 final size:16
Alignment explanation
Indices: 37525--37555 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37515 AGAGAAAATC
*
37525 AGAAAAGAAGAAGAAA
1 AGAAAAGAAAAAGAAA
37541 AGAAAAGAAAAAGAA
1 AGAAAAGAAAAAGAA
37556 TTCAAAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAAAAGAAA
Found at i:40851 original size:19 final size:20
Alignment explanation
Indices: 40827--40877 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
40817 CGGCCAAGAG
* *
40827 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
40846 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
40866 CATGTATTTTCA
1 CATGTATTTTCA
40878 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:42133 original size:28 final size:28
Alignment explanation
Indices: 42101--42168 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
42091 TCTTTCTTTT
* *
42101 ATTTTCTTTTCTTCTTTTTGAGTGCTGG
1 ATTTTCTTTTCTTCTTTTGGAGTGCTGC
* *
42129 ATTTTCTTTCCTTCTTTTGGAGTGCTTC
1 ATTTTCTTTTCTTCTTTTGGAGTGCTGC
*
42157 AATTTCTTTTCT
1 ATTTTCTTTTCT
42169 GATTTTCTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.09, C:0.18, G:0.13, T:0.60
Consensus pattern (28 bp):
ATTTTCTTTTCTTCTTTTGGAGTGCTGC
Found at i:44069 original size:15 final size:16
Alignment explanation
Indices: 44033--44069 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
44023 TGATAATTAA
44033 GAAAT-GAAAGTAATG
1 GAAATGGAAAGTAATG
*
44048 GAAATGGAAAG-AATT
1 GAAATGGAAAGTAATG
44063 GAAATGG
1 GAAATGG
44070 TTAGAATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.30, T:0.19
Consensus pattern (16 bp):
GAAATGGAAAGTAATG
Found at i:44255 original size:13 final size:12
Alignment explanation
Indices: 44236--44321 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
44226 ATATAGGCGT
44236 GATATGGTGATG
1 GATATGGTGATG
44248 GAATATGGTGAT-
1 G-ATATGGTGATG
*
44260 GATATAGGCG-T-
1 GATAT-GGTGATG
44271 GATAATGGTGATG
1 GAT-ATGGTGATG
44284 GACTATGGTGAT-
1 GA-TATGGTGATG
*
44296 GATATAGGCG-T-
1 GATAT-GGTGATG
44307 GATAATGGTGATG
1 GAT-ATGGTGATG
44320 GA
1 GA
44322 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:44291 original size:36 final size:36
Alignment explanation
Indices: 44218--44322 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
44208 ATTTATAAGT
* *
44218 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
44253 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
44289 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
44323 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:44703 original size:19 final size:20
Alignment explanation
Indices: 44662--44712 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
44652 GAAACCCCTT
* **
44662 TGAAAAAACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
44682 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
44701 TGAAGATACATG
1 TGAAAATACATG
44713 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:48329 original size:36 final size:36
Alignment explanation
Indices: 48256--48360 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
48246 ATTTATAAGT
* *
48256 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
48291 TGGTGATGATATAGGCGTGATAATAGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
48327 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
48361 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:48741 original size:19 final size:20
Alignment explanation
Indices: 48700--48750 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
48690 TAAACCCCTT
* **
48700 TGAAAAAACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
48720 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
48739 TGAAGATACATG
1 TGAAAATACATG
48751 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:49767 original size:19 final size:20
Alignment explanation
Indices: 49725--49775 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
49715 GAAACCCCTT
49725 TGAAAATACATGACTTTAAA
1 TGAAAATACATGACTTTAAA
*
49745 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGACTTTAAA
*
49764 TGAAGATACATG
1 TGAAAATACATG
49776 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (20 bp):
TGAAAATACATGACTTTAAA
Found at i:51809 original size:21 final size:21
Alignment explanation
Indices: 51757--51810 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
51747 GAAAGAAAAA
51757 TCAACAAAGAAAATAAAAGCAC
1 TCAA-AAAGAAAATAAAAGCAC
* *
51779 TCAAAGAAGAAATTGAAAGCAC
1 TCAAA-AAGAAAATAAAAGCAC
*
51801 TCGAAAAGAA
1 TCAAAAAGAA
51811 GAAGAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.11
Consensus pattern (21 bp):
TCAAAAAGAAAATAAAAGCAC
Found at i:51813 original size:24 final size:22
Alignment explanation
Indices: 51763--51813 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
51753 AAAATCAACA
51763 AAGAAAATAAAAGCACTCAAAG
1 AAGAAAATAAAAGCACTCAAAG
* *
51785 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTC--AAAG
51809 AAGAA
1 AAGAA
51814 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.64
24 9 0.36
ACGTcount: A:0.61, C:0.12, G:0.18, T:0.10
Consensus pattern (22 bp):
AAGAAAATAAAAGCACTCAAAG
Found at i:66254 original size:23 final size:22
Alignment explanation
Indices: 66208--66258 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
66198 AAGAAAAATC
66208 AGAAAAGAAGCACTCAAAAAGA
1 AGAAAAGAAGCACTCAAAAAGA
66230 AGAAAATGAAAGCACTC-AAAAGA
1 AGAAAA-G-AAGCACTCAAAAAGA
66253 AGAAAA
1 AGAAAA
66259 AAGAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 6 0.22
23 13 0.48
24 8 0.30
ACGTcount: A:0.65, C:0.12, G:0.18, T:0.06
Consensus pattern (22 bp):
AGAAAAGAAGCACTCAAAAAGA
Found at i:66259 original size:24 final size:24
Alignment explanation
Indices: 66210--66265 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
66200 GAAAAATCAG
66210 AAAAG-AAGCACTCAAAAAGAAGA
1 AAAAGAAAGCACTCAAAAAGAAGA
*
66233 AAATGAAAGCACTC-AAAAGAAGAA
1 AAAAGAAAGCACTCAAAAAGAAG-A
66257 AAAAGAAAG
1 AAAAGAAAG
66266 AAAAGTTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.66, C:0.11, G:0.18, T:0.05
Consensus pattern (24 bp):
AAAAGAAAGCACTCAAAAAGAAGA
Found at i:67445 original size:35 final size:37
Alignment explanation
Indices: 67394--67473 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
67384 TTTGAGAATT
* *
67394 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATACAGGCGTGATAATGGAAGATGGACTA
*
67429 TGGTGATGATACAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATACAGGCGTGATAATGGAAGATGGACTA
*
67466 TGGGGATG
1 TGGTGATG
67474 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.05, G:0.39, T:0.29
Consensus pattern (37 bp):
TGGTGATGATACAGGCGTGATAATGGAAGATGGACTA
Found at i:67858 original size:19 final size:20
Alignment explanation
Indices: 67812--67861 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
67802 AAATCCCTTA
**
67812 GAAAATACATGATTTTTGAT
1 GAAAATACATGATTTTAAAT
67832 GAAAATACATGA-TTTAAAT
1 GAAAATACATGATTTTAAAT
*
67851 GAAGATACATG
1 GAAAATACATG
67862 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (20 bp):
GAAAATACATGATTTTAAAT
Found at i:79606 original size:24 final size:24
Alignment explanation
Indices: 79579--79630 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
79569 GACATGTCCT
* * *
79579 TTGACGTTCCAACAGTTATGCCAC
1 TTGACGTTCAAAAAGCTATGCCAC
* *
79603 TTGATGTTCAAAAAGCTGTGCCAC
1 TTGACGTTCAAAAAGCTATGCCAC
79627 TTGA
1 TTGA
79631 AGTGCCAAGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (24 bp):
TTGACGTTCAAAAAGCTATGCCAC
Found at i:83995 original size:12 final size:11
Alignment explanation
Indices: 83966--83992 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
83956 ATTGGAGTGC
83966 AAAAAGAAAAT
1 AAAAAGAAAAT
83977 AAAAAGAAAAT
1 AAAAAGAAAAT
83988 AAAAA
1 AAAAA
83993 AGAGAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAGAAAAT
Found at i:88731 original size:21 final size:23
Alignment explanation
Indices: 88684--88731 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
88674 CTTTCTTTTT
**
88684 TTTTGAGTGCTTTCAATTTCTTC
1 TTTTGAGTGCTTTCAATTTCTGA
*
88707 TTTTGAGTGC-TTC-TTTTCTGA
1 TTTTGAGTGCTTTCAATTTCTGA
88728 TTTT
1 TTTT
88732 TTTCTTGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 9 0.41
22 3 0.14
23 10 0.45
ACGTcount: A:0.10, C:0.15, G:0.15, T:0.60
Consensus pattern (23 bp):
TTTTGAGTGCTTTCAATTTCTGA
Found at i:90302 original size:90 final size:91
Alignment explanation
Indices: 90186--90367 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
90176 GGGAAATGAT
*
90186 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATACAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATACAAGGCACATA
*
90250 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* * * * *
90276 GCTTGGTCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATA
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATACAAGGCACATA
* **
90341 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
90367 G
1 G
90368 GTGTTCTAGG
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 58 0.72
91 23 0.28
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATACAAGGCACATA
GGGGCTGGTCACATGCAAAACACATG
Found at i:113480 original size:16 final size:16
Alignment explanation
Indices: 113459--113491 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
113449 TTCTGCCACC
113459 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
113475 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
113491 T
1 T
113492 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:117662 original size:15 final size:17
Alignment explanation
Indices: 117637--117670 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
117627 TAAAGGTCCT
117637 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
117653 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
117669 AA
1 AA
117671 CATATCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:129949 original size:22 final size:23
Alignment explanation
Indices: 129894--129951 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
129884 GTTCTTTCAA
*
129894 CTTTTATTTCTTTCTTTTTGAGTG
1 CTTTGATTTC-TTCTTTTTGAGTG
*
129918 C-TAGATTTTCTTC-TTTTGAGTG
1 CTTTGA-TTTCTTCTTTTTGAGTG
129940 CTTTGATTTCTT
1 CTTTGATTTCTT
129952 TGCTGGATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 16 0.55
23 8 0.28
24 5 0.17
ACGTcount: A:0.10, C:0.14, G:0.14, T:0.62
Consensus pattern (23 bp):
CTTTGATTTCTTCTTTTTGAGTG
Found at i:131073 original size:21 final size:21
Alignment explanation
Indices: 131034--131076 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
131024 AAAGAAGATT
*
131034 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
131055 AATGAAATGA-AATAAATAAGG
1 AATGAAATGATAA-AAATAAGG
131076 A
1 A
131077 TAGAGATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.60, C:0.00, G:0.21, T:0.19
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:133520 original size:24 final size:24
Alignment explanation
Indices: 133493--133551 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
133483 TGTGAATCAC
133493 CAAAAGTCATGGCTATTGGTTTTT
1 CAAAAGTCATGGCTATTGGTTTTT
*** *
133517 CAAAAGTCACATCTTTTGGTTTTT
1 CAAAAGTCATGGCTATTGGTTTTT
*
133541 CAAAAGCCATG
1 CAAAAGTCATG
133552 ATTTTTGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (24 bp):
CAAAAGTCATGGCTATTGGTTTTT
Found at i:134522 original size:22 final size:22
Alignment explanation
Indices: 134478--134522 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
134468 TCAAAACACC
* *
134478 TTGAAGAAGAACATTGAAGCAA
1 TTGAAGAACAACATTAAAGCAA
134500 TTGAAGAACAAC-TTAAAGACAA
1 TTGAAGAACAACATTAAAG-CAA
134522 T
1 T
134523 GCAACTGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (22 bp):
TTGAAGAACAACATTAAAGCAA
Found at i:135438 original size:114 final size:114
Alignment explanation
Indices: 135238--135466 Score: 440
Period size: 114 Copynumber: 2.0 Consensus size: 114
135228 ATGAGGATTC
**
135238 TAAGGAAACTTCCATTCTAAGAGTTATAACCTTTCATGATTCAATGAATACACCTATTTTAGGAC
1 TAAGGAAACTTCCATTCTAAGAGTTATAACCTTTCATGATTCAATGAATACACCTATTGGAGGAC
135303 CAAGGAACATGACTTTTGGGGACATGGTCGTTCAAAGGAACATATATTG
66 CAAGGAACATGACTTTTGGGGACATGGTCGTTCAAAGGAACATATATTG
135352 TAAGGAAACTTCCATTCTAAGAGTTATAACCTTTCATGATTCAATGAATACACCTATTGGAGGAC
1 TAAGGAAACTTCCATTCTAAGAGTTATAACCTTTCATGATTCAATGAATACACCTATTGGAGGAC
135417 CAAGGAACATGACTTTTGGGGACATGGTCGTTCAAAGGAACATATATTG
66 CAAGGAACATGACTTTTGGGGACATGGTCGTTCAAAGGAACATATATTG
135466 T
1 T
135467 GATTCAAAAG
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (114 bp):
TAAGGAAACTTCCATTCTAAGAGTTATAACCTTTCATGATTCAATGAATACACCTATTGGAGGAC
CAAGGAACATGACTTTTGGGGACATGGTCGTTCAAAGGAACATATATTG
Found at i:136870 original size:19 final size:21
Alignment explanation
Indices: 136846--136897 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
136836 CGGCCAAGAG
*
136846 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
136865 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
136886 CATGTATTTTCA
1 CATGTATTTTCA
136898 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:139859 original size:24 final size:24
Alignment explanation
Indices: 139832--139890 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
139822 TGTGAATCAC
139832 CAAAAGTCATGGCTATTGGTTTTT
1 CAAAAGTCATGGCTATTGGTTTTT
*** *
139856 CAAAAGTCACATCTTTTGGTTTTT
1 CAAAAGTCATGGCTATTGGTTTTT
*
139880 CAAAAGCCATG
1 CAAAAGTCATG
139891 ATTTTTGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (24 bp):
CAAAAGTCATGGCTATTGGTTTTT
Found at i:141206 original size:18 final size:18
Alignment explanation
Indices: 141185--141220 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
141175 TTCTTCTTCT
141185 TCTTCCTCTTTCTTTTTG
1 TCTTCCTCTTTCTTTTTG
**
141203 TCTTTTTCTTTCTTTTTG
1 TCTTCCTCTTTCTTTTTG
141221 CACTATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.06, T:0.72
Consensus pattern (18 bp):
TCTTCCTCTTTCTTTTTG
Found at i:141561 original size:22 final size:21
Alignment explanation
Indices: 141533--141573 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
141523 GATGTGGAAT
141533 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
141555 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
141574 ATGGAGATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:144787 original size:19 final size:20
Alignment explanation
Indices: 144763--144813 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
144753 CGGCCAAGAG
* *
144763 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
144782 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
144802 CATGTATTTTCA
1 CATGTATTTTCA
144814 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:148828 original size:19 final size:20
Alignment explanation
Indices: 148804--148854 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
148794 CGGCCAAGAG
* *
148804 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
148823 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
148843 CATGTATTTTCA
1 CATGTATTTTCA
148855 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:157669 original size:24 final size:22
Alignment explanation
Indices: 157635--157679 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
157625 TGCACAAGAT
* *
157635 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGAAATTTAAAAGG
157657 ATGTACCTCTTGAAATTTAAAAG
1 ATGT-CCT-TTGAAATTTAAAAG
157680 AATGAGCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 3 0.16
24 12 0.63
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
ATGTCCTTTGAAATTTAAAAGG
Found at i:165296 original size:19 final size:21
Alignment explanation
Indices: 165253--165304 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
165243 GAAACCCCTT
165253 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
165274 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
165293 TGAAGATACATG
1 TGAAAATACATG
165305 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:169324 original size:19 final size:18
Alignment explanation
Indices: 169300--169348 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
169290 ACCCCTTTGA
169300 AAATACATGCTTTTAAATG
1 AAATACATGCTTTT-AATG
*
169319 AAATACATGATTTTAATG
1 AAATACATGCTTTTAATG
169337 AAGATACATGCT
1 AA-ATACATGCT
169349 CTTGGCCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (18 bp):
AAATACATGCTTTTAATG
Found at i:175656 original size:21 final size:20
Alignment explanation
Indices: 175632--175676 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
175622 TATTTTGAAA
175632 TTTTGGCTTTTTTGGCTCTTT
1 TTTTGGCTTTTTTGGC-CTTT
** *
175653 TTTTGTTTTTTTTTGCCTTT
1 TTTTGGCTTTTTTGGCCTTT
175673 TTTT
1 TTTT
175677 TTTGCCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.76
Consensus pattern (20 bp):
TTTTGGCTTTTTTGGCCTTT
Found at i:175663 original size:10 final size:10
Alignment explanation
Indices: 175650--175702 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
175640 TTTTTGGCTC
175650 TTTTTTTGTT
1 TTTTTTTGTT
175660 TTTTTTTGCCTT
1 TTTTTTTG--TT
*
175672 TTTTTTT-TGC
1 TTTTTTTGT-T
*
175682 CTTTTTTGTT
1 TTTTTTTGTT
175692 TTTTTTTGTT
1 TTTTTTTGTT
175702 T
1 T
175703 ATTTGAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 1 0.03
10 24 0.69
11 1 0.03
12 9 0.26
ACGTcount: A:0.00, C:0.08, G:0.09, T:0.83
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:175675 original size:14 final size:13
Alignment explanation
Indices: 175658--175693 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
175648 TCTTTTTTTG
175658 TTTTTTTTTGCCT
1 TTTTTTTTTGCCT
175671 TTTTTTTTTGCCT
1 TTTTTTTTTGCCT
175684 TTTTTGTTTT
1 TTTTT-TTTT
175694 TTTTTGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (13 bp):
TTTTTTTTTGCCT
Found at i:179734 original size:23 final size:23
Alignment explanation
Indices: 179704--179772 Score: 138
Period size: 23 Copynumber: 3.0 Consensus size: 23
179694 CCTAGTTAGC
179704 TACCAAGACACTCATCTAGCTTA
1 TACCAAGACACTCATCTAGCTTA
179727 TACCAAGACACTCATCTAGCTTA
1 TACCAAGACACTCATCTAGCTTA
179750 TACCAAGACACTCATCTAGCTTA
1 TACCAAGACACTCATCTAGCTTA
179773 CCTTGAAACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (23 bp):
TACCAAGACACTCATCTAGCTTA
Found at i:180775 original size:3 final size:3
Alignment explanation
Indices: 180767--180793 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
180757 AAGCAACGTG
180767 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
180794 AAATACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:195256 original size:43 final size:45
Alignment explanation
Indices: 195157--195261 Score: 126
Period size: 49 Copynumber: 2.3 Consensus size: 45
195147 AGGATCAGAT
* *
195157 TTATTATTTTATTAGGAATTAAGTTGGGTTAAAACAATATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAA--TGAGTTAAAAC-A-ATGTTTAGTTA
195206 TTATTATTTTATTAGGAATT-A-GAGTTAAAAC-ATGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAATGAGTTAAAACAATGTTTAG-TTA
195249 TTATTATTTTATT
1 TTATTATTTTATT
195262 CTTTAGTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
42 7 0.13
43 16 0.30
45 9 0.17
48 1 0.02
49 20 0.38
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (45 bp):
TTATTATTTTATTAGGAATTAATGAGTTAAAACAATGTTTAGTTA
Found at i:206599 original size:24 final size:21
Alignment explanation
Indices: 206564--206606 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
206554 GGCTCATTCT
*
206564 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
206587 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
206607 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:210499 original size:24 final size:21
Alignment explanation
Indices: 210464--210506 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
210454 GGCTCATTCT
*
210464 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
210487 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
210507 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:219078 original size:13 final size:13
Alignment explanation
Indices: 219060--219084 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
219050 ATATAGGCGT
219060 AATATGGTGATGG
1 AATATGGTGATGG
219073 AATATGGTGATG
1 AATATGGTGATG
219085 ATATAGGCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (13 bp):
AATATGGTGATGG
Found at i:219115 original size:36 final size:36
Alignment explanation
Indices: 219042--219142 Score: 150
Period size: 36 Copynumber: 2.8 Consensus size: 36
219032 ATTTATAAGT
* * *
219042 TGGTGATAATATAGGCGTAAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATAGAATA
*
219077 TGGTGATGATATAGGCGTGATAATGGTGATAGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATAGAATA
*
219113 TGGTGATGATATAGGAGTGATAATGGTGAT
1 TGGTGATGATATAGGCGTGATAATGGTGAT
219143 GGACAGATTG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 19 0.32
36 41 0.68
ACGTcount: A:0.32, C:0.03, G:0.34, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATAGAATA
Found at i:223109 original size:13 final size:11
Alignment explanation
Indices: 223089--223173 Score: 75
Period size: 13 Copynumber: 7.2 Consensus size: 11
223079 AATATAGGCG
223089 TGATATGGTGA
1 TGATATGGTGA
223100 TGGAATATGGTGA
1 T-G-ATATGGTGA
223113 TGATATAGGTG-
1 TGATAT-GGTGA
223124 TGATAATGGTGA
1 TGAT-ATGGTGA
223136 TAGACTATGGTGA
1 T-GA-TATGGTGA
*
223149 TGATATAG-GA
1 TGATATGGTGA
223159 GTGATAATGGTGA
1 -TGAT-ATGGTGA
223172 TG
1 TG
223174 GACATATTGT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
10 2 0.03
11 21 0.34
12 16 0.26
13 22 0.35
14 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.35, T:0.33
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:223127 original size:11 final size:12
Alignment explanation
Indices: 223073--223157 Score: 65
Period size: 11 Copynumber: 7.2 Consensus size: 12
223063 TTTATAAGTT
*
223073 GGTGATAATATA
1 GGTGATGATATA
*
223085 GGCG-TGATAT-
1 GGTGATGATATA
223095 GGTGATGGA-ATA
1 GGTGAT-GATATA
223107 TGGTGATGATATA
1 -GGTGATGATATA
223120 GGTG-TGATA-A
1 GGTGATGATATA
223130 TGGTGATAGACTAT-
1 -GGTGAT-GA-TATA
223144 GGTGATGATATA
1 GGTGATGATATA
223156 GG
1 GG
223158 AGTGATAATG
Statistics
Matches: 59, Mismatches: 3, Indels: 22
0.70 0.04 0.26
Matches are distributed among these distances:
10 4 0.07
11 20 0.34
12 16 0.27
13 17 0.29
14 2 0.03
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.32
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:223145 original size:36 final size:36
Alignment explanation
Indices: 223072--223172 Score: 150
Period size: 36 Copynumber: 2.8 Consensus size: 36
223062 ATTTATAAGT
* * *
223072 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGAGTGATAATGGTGATAGAATA
* *
223107 TGGTGATGATATAGGTGTGATAATGGTGATAGACTA
1 TGGTGATGATATAGGAGTGATAATGGTGATAGAATA
223143 TGGTGATGATATAGGAGTGATAATGGTGAT
1 TGGTGATGATATAGGAGTGATAATGGTGAT
223173 GGACATATTG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 19 0.32
36 41 0.68
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.33
Consensus pattern (36 bp):
TGGTGATGATATAGGAGTGATAATGGTGATAGAATA
Found at i:224659 original size:23 final size:24
Alignment explanation
Indices: 224631--224684 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
224621 CAAATCAGCA
224631 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
224654 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
224678 AAGAAAA
1 AAGAAAA
224685 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:224689 original size:24 final size:23
Alignment explanation
Indices: 224631--224690 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
224621 CAAATCAGCA
224631 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
224654 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
224678 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
224691 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.63, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:225933 original size:24 final size:21
Alignment explanation
Indices: 225899--225941 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
225889 TCCACAAGAT
*
225899 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
225921 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
225942 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:229019 original size:11 final size:11
Alignment explanation
Indices: 228996--229079 Score: 82
Period size: 11 Copynumber: 7.2 Consensus size: 11
228986 ACAATCTATC
228996 CATCACCATTAT
1 CATCACCA-TAT
229008 CA-CACCTATAT
1 CATCACC-ATAT
229019 CATCACCATATT
1 CATCACCATA-T
229031 CCATCACCATAT
1 -CATCACCATAT
*
229043 CA-CGCCTATAT
1 CATCACC-ATAT
229054 CATCACCATATT
1 CATCACCATA-T
229066 CCATCACCATAT
1 -CATCACCATAT
229078 CA
1 CA
229080 CGCCTATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 17
0.77 0.02 0.21
Matches are distributed among these distances:
10 3 0.05
11 25 0.40
12 14 0.23
13 20 0.32
ACGTcount: A:0.33, C:0.37, G:0.01, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:229037 original size:13 final size:12
Alignment explanation
Indices: 228996--229077 Score: 68
Period size: 13 Copynumber: 6.9 Consensus size: 12
228986 ACAATCTATC
228996 CATCACCAT-TAT
1 CATCACCATAT-T
229008 CA-CACC-TATAT
1 CATCACCATAT-T
229019 CATCACCATATT
1 CATCACCATATT
229031 CCATCACCATA-T
1 -CATCACCATATT
*
229043 CA-CGCC-TATAT
1 CATCACCATAT-T
229054 CATCACCATATT
1 CATCACCATATT
229066 CCATCACCATAT
1 -CATCACCATAT
229078 CACGCCTATA
Statistics
Matches: 59, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
9 2 0.03
10 4 0.07
11 14 0.24
12 12 0.20
13 27 0.46
ACGTcount: A:0.33, C:0.37, G:0.01, T:0.29
Consensus pattern (12 bp):
CATCACCATATT
Found at i:229051 original size:35 final size:35
Alignment explanation
Indices: 228994--229096 Score: 179
Period size: 35 Copynumber: 2.9 Consensus size: 35
228984 ATACAATCTA
*
228994 TCCATCACCATTATCACACCTATATCATCACCATAT
1 TCCATCACCA-TATCACGCCTATATCATCACCATAT
229030 TCCATCACCATATCACGCCTATATCATCACCATAT
1 TCCATCACCATATCACGCCTATATCATCACCATAT
*
229065 TCCATCACCATATCACGCCTATATTATCACCA
1 TCCATCACCATATCACGCCTATATCATCACCA
229097 ACTTCTAAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 55 0.85
36 10 0.15
ACGTcount: A:0.32, C:0.37, G:0.02, T:0.29
Consensus pattern (35 bp):
TCCATCACCATATCACGCCTATATCATCACCATAT
Found at i:229273 original size:15 final size:17
Alignment explanation
Indices: 229237--229270 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
229227 TTCGATAACA
229237 TTTC-TATCAATTTCCT
1 TTTCTTATCAATTTCCT
229253 TTTCTTATC-ATTTCCT
1 TTTCTTATCAATTTCCT
229269 TT
1 TT
229271 CTTCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTCTTATCAATTTCCT
Found at i:229513 original size:20 final size:20
Alignment explanation
Indices: 229477--229515 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
229467 CAAAAAAAGC
*
229477 AACAAGAAAGAAGGAAAAAA
1 AACAAGAAAGAAAGAAAAAA
229497 AACAA-AAAGAAAAGAAAAA
1 AACAAGAAAG-AAAGAAAAA
229516 GACTCCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (20 bp):
AACAAGAAAGAAAGAAAAAA
Found at i:233494 original size:13 final size:12
Alignment explanation
Indices: 233465--233536 Score: 60
Period size: 13 Copynumber: 5.8 Consensus size: 12
233455 CATCACCATT
233465 ATCACGCATATATC
1 ATCAC-CATAT-TC
233479 ATCACCATATTCC
1 ATCACCATATT-C
*
233492 ATCACCAT-CTC
1 ATCACCATATTC
*
233503 A-CGCC-TATATC
1 ATCACCATAT-TC
233514 ATCACCATATTCC
1 ATCACCATATT-C
233527 ATCACCATAT
1 ATCACCATAT
233537 CACGCCTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
9 1 0.02
10 3 0.06
11 5 0.10
12 6 0.12
13 28 0.58
14 5 0.10
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.29
Consensus pattern (12 bp):
ATCACCATATTC
Found at i:233512 original size:35 final size:35
Alignment explanation
Indices: 233453--233555 Score: 170
Period size: 35 Copynumber: 2.9 Consensus size: 35
233443 ATACAATCTG
*
233453 TCCATCACCATTATCACGCATATATCATCACCATAT
1 TCCATCACCA-TATCACGCCTATATCATCACCATAT
*
233489 TCCATCACCATCTCACGCCTATATCATCACCATAT
1 TCCATCACCATATCACGCCTATATCATCACCATAT
*
233524 TCCATCACCATATCACGCCTATATTATCACCA
1 TCCATCACCATATCACGCCTATATCATCACCA
233556 ACTTCTAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 53 0.84
36 10 0.16
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (35 bp):
TCCATCACCATATCACGCCTATATCATCACCATAT
Found at i:237524 original size:13 final size:12
Alignment explanation
Indices: 237505--237590 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
237495 ATATAGGCGT
237505 GATATGGTGATG
1 GATATGGTGATG
237517 GAATATGGTGAT-
1 G-ATATGGTGATG
*
237529 GATATAGGCG-T-
1 GATAT-GGTGATG
237540 GATAATGGTGATG
1 GAT-ATGGTGATG
237553 GACTATGGTGAT-
1 GA-TATGGTGATG
*
237565 GATATAGGCG-T-
1 GATAT-GGTGATG
237576 GATAATGGTGATG
1 GAT-ATGGTGATG
237589 GA
1 GA
237591 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:237560 original size:36 final size:36
Alignment explanation
Indices: 237487--237591 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
237477 ATTTATAAGT
* *
237487 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
237522 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
237558 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
237592 AGATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:237971 original size:19 final size:20
Alignment explanation
Indices: 237930--237980 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
237920 GAAACCCCTT
* **
237930 TGAAAAAACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
237950 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
237969 TGAAGATACATG
1 TGAAAATACATG
237981 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:240953 original size:27 final size:30
Alignment explanation
Indices: 240922--240977 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
240912 TTGTTTTGTC
240922 TTTCT-TTTTTATT-TTC-TTTTTCTTTCT
1 TTTCTATTTTTATTATTCTTTTTTCTTTCT
*
240949 TTTCTAATTTTTCTTATTCTTTTTTCTTT
1 TTTCT-ATTTTTATTATTCTTTTTTCTTT
240978 TACTCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 5 0.21
29 7 0.29
30 3 0.12
31 9 0.38
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (30 bp):
TTTCTATTTTTATTATTCTTTTTTCTTTCT
Found at i:240963 original size:14 final size:12
Alignment explanation
Indices: 240922--240997 Score: 64
Period size: 14 Copynumber: 5.8 Consensus size: 12
240912 TTGTTTTGTC
*
240922 TTTCTTTTTTAT
1 TTTCTTTTTTCT
240934 TTTCTTTTTCTTTCT
1 TTTC--TTT-TTTCT
240949 TTTCTAATTTTTCT
1 TTTCT--TTTTTCT
240963 TATTCTTTTTTCT
1 T-TTCTTTTTTCT
240976 TTTACTCTTTTTC-
1 TTT-CT-TTTTTCT
240989 TTTCTTTTT
1 TTTCTTTTT
240998 GCACTCCAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 17
0.75 0.01 0.23
Matches are distributed among these distances:
11 4 0.07
12 8 0.15
13 14 0.25
14 15 0.27
15 14 0.25
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:241288 original size:21 final size:21
Alignment explanation
Indices: 241249--241288 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
241239 AAGGAAGATT
*
241249 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
241270 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
241289 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:241724 original size:19 final size:20
Alignment explanation
Indices: 241677--241727 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
241667 ATAACCCCTT
**
241677 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
241697 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
241716 TGAAGATACATG
1 TGAAAATACATG
241728 CTCTTAGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:242409 original size:36 final size:36
Alignment explanation
Indices: 242368--242516 Score: 199
Period size: 36 Copynumber: 4.1 Consensus size: 36
242358 ATTTATAAGT
* * * * *
242368 TGGTGATAATATGGGTGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* *
242404 TGGTGACGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
242440 TGGTGATGATAAAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
242476 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
242512 TGGTG
1 TGGTG
242517 TTGAACAGAT
Statistics
Matches: 99, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 99 1.00
ACGTcount: A:0.30, C:0.04, G:0.38, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:242506 original size:23 final size:23
Alignment explanation
Indices: 242411--242506 Score: 56
Period size: 25 Copynumber: 4.0 Consensus size: 23
242401 ATATGGTGAC
242411 GATATAGGCGTGATAATGGAGAT
1 GATATAGGCGTGATAATGGAGAT
* * *
242434 GGACTAT-GGTGATGATAAAGGCG-T
1 -GA-TATAGGCG-TGATAATGGAGAT
* *
242458 GATA-ATG-GTGATGGACTATGGTGAT
1 GATATAGGCGTGAT--A--ATGGAGAT
242483 GATATAGGCGTGATAATGGAGAT
1 GATATAGGCGTGATAATGGAGAT
242506 G
1 G
242507 GAAGATGGTG
Statistics
Matches: 54, Mismatches: 8, Indels: 21
0.65 0.10 0.25
Matches are distributed among these distances:
20 4 0.07
21 1 0.02
22 4 0.07
23 10 0.19
24 10 0.19
25 18 0.33
26 2 0.04
27 5 0.09
ACGTcount: A:0.31, C:0.05, G:0.36, T:0.27
Consensus pattern (23 bp):
GATATAGGCGTGATAATGGAGAT
Found at i:242925 original size:17 final size:17
Alignment explanation
Indices: 242903--242941 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
242893 ATTTAAATGA
242903 ACATGCTTGAATGATGC
1 ACATGCTTGAATGATGC
242920 ACATGCTTGAATGATGC
1 ACATGCTTGAATGATGC
242937 ACATG
1 ACATG
242942 GCAGCCTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (17 bp):
ACATGCTTGAATGATGC
Found at i:246374 original size:36 final size:36
Alignment explanation
Indices: 246333--246481 Score: 190
Period size: 36 Copynumber: 4.1 Consensus size: 36
246323 ATTTATAAGT
* * * * *
246333 TGGTGATAATATGGGTGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* *
246369 TGGTGACGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * * *
246405 TGGTGATGATAAAGGTGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
246441 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
246477 TGGTG
1 TGGTG
246482 TTGGACAGAT
Statistics
Matches: 97, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 97 1.00
ACGTcount: A:0.30, C:0.03, G:0.38, T:0.29
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:246412 original size:13 final size:13
Alignment explanation
Indices: 246387--246448 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 13
246377 ATATAGGCGT
*
246387 GATAATGGAGATG
1 GATAATGGTGATG
246400 GACT-ATGGTGAT-
1 GA-TAATGGTGATG
*
246412 GATAAAGGTG-T-
1 GATAATGGTGATG
246423 GATAATGGTGATG
1 GATAATGGTGATG
246436 GACT-ATGGTGATG
1 GA-TAATGGTGATG
246449 ATATAGGCGT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
11 11 0.27
12 8 0.20
13 20 0.49
14 2 0.05
ACGTcount: A:0.31, C:0.03, G:0.37, T:0.29
Consensus pattern (13 bp):
GATAATGGTGATG
Found at i:246480 original size:72 final size:72
Alignment explanation
Indices: 246346--246481 Score: 227
Period size: 72 Copynumber: 1.9 Consensus size: 72
246336 TGATAATATG
* **
246346 GGTGTGATAATGGTGGTGGAATATGGTGACGATATAGGCGTGATAATGGAGATGGACTATGGTGA
1 GGTGTGATAATGGTGATGGAATATGGTGACGATATAGGCGTGATAATGGAGATGGAAGATGGTGA
246411 TGATAAA
66 TGATAAA
* *
246418 GGTGTGATAATGGTGATGGACTATGGTGATGATATAGGCGTGATAATGGAGATGGAAGATGGTG
1 GGTGTGATAATGGTGATGGAATATGGTGACGATATAGGCGTGATAATGGAGATGGAAGATGGTG
246482 TTGGACAGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.29, C:0.04, G:0.39, T:0.28
Consensus pattern (72 bp):
GGTGTGATAATGGTGATGGAATATGGTGACGATATAGGCGTGATAATGGAGATGGAAGATGGTGA
TGATAAA
Found at i:249588 original size:24 final size:24
Alignment explanation
Indices: 249561--249614 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
249551 TGTGAATCAC
**
249561 CAAAAGTCATGGCTTTTGGTTATT
1 CAAAAGTCACAGCTTTTGGTTATT
* *
249585 CAAAAGTCACATCTTTTGGTTTTT
1 CAAAAGTCACAGCTTTTGGTTATT
249609 CAAAAG
1 CAAAAG
249615 CCATTATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (24 bp):
CAAAAGTCACAGCTTTTGGTTATT
Found at i:250922 original size:18 final size:18
Alignment explanation
Indices: 250860--250940 Score: 56
Period size: 18 Copynumber: 4.3 Consensus size: 18
250850 TTTCCTTGGT
*
250860 TTTTTTGTCTTTTATTTTTC
1 TTTTTT-TCTTCT-TTTTTC
* * *
250880 TTTTCTTTTCTTCATTTATG
1 -TTT-TTTTCTTCTTTTTTC
*
250900 ATTTTTTCTTCTTTTTTC
1 TTTTTTTCTTCTTTTTTC
*
250918 TTTTTGTCTT-TTTCTTTC
1 TTTTTTTCTTCTTT-TTTC
250936 TTTTT
1 TTTTT
250941 GCACTCCAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
17 3 0.06
18 29 0.60
19 2 0.04
20 4 0.08
21 7 0.15
22 3 0.06
ACGTcount: A:0.05, C:0.14, G:0.04, T:0.78
Consensus pattern (18 bp):
TTTTTTTCTTCTTTTTTC
Found at i:250941 original size:18 final size:18
Alignment explanation
Indices: 250901--250941 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
250891 TCATTTATGA
250901 TTTTT-TCTTCTTTTTTC
1 TTTTTGTCTTCTTTTTTC
250918 TTTTTGTCTT-TTTCTTTC
1 TTTTTGTCTTCTTT-TTTC
250936 TTTTTG
1 TTTTTG
250942 CACTCCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTTGTCTTCTTTTTTC
Found at i:255589 original size:19 final size:20
Alignment explanation
Indices: 255549--255598 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
255539 GAAACCCTTT
**
255549 TGAAAAT-CATGATTTTTTA
1 TGAAAATACATGATTTTAAA
255568 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
255587 TGAAGATACATG
1 TGAAAATACATG
255599 CTCTTGGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:260244 original size:24 final size:25
Alignment explanation
Indices: 260198--260252 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
260188 ACAGTTATAC
*
260198 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
260222 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
260247 CA-TTGA
1 CACTTGA
260253 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:264597 original size:16 final size:16
Alignment explanation
Indices: 264573--264618 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
264563 CCTTGGCTTG
*
264573 TATTGTCTTTCTTTTT
1 TATTTTCTTTCTTTTT
264589 TATTTTCTTT-TTATTT
1 TATTTTCTTTCTT-TTT
*
264605 TCTTTTC-TTCTTTT
1 TATTTTCTTTCTTTT
264619 CTGAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (16 bp):
TATTTTCTTTCTTTTT
Found at i:264601 original size:11 final size:11
Alignment explanation
Indices: 264580--264610 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
264570 TTGTATTGTC
264580 TTTCTTTTTTAT
1 TTTC-TTTTTAT
264592 TTTCTTTTTAT
1 TTTCTTTTTAT
264603 TTTCTTTT
1 TTTCTTTT
264611 CTTCTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTTAT
Found at i:264635 original size:21 final size:18
Alignment explanation
Indices: 264585--264640 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 18
264575 TTGTCTTTCT
264585 TTTTTATT-TTCTTTTTA
1 TTTTTATTCTTCTTTTTA
*
264602 TTTTCTTTTCTTCTTTTCTGAA
1 TTTT-TATTCTTCTTTT-T--A
264624 TTTTTATTCTTCTTTTT
1 TTTTTATTCTTCTTTTT
264641 TCTTTTTGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 4 0.12
18 3 0.09
19 7 0.22
20 2 0.06
21 11 0.34
22 5 0.16
ACGTcount: A:0.09, C:0.12, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTTATTCTTCTTTTTA
Found at i:274986 original size:8 final size:8
Alignment explanation
Indices: 274973--275017 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
274963 ATCTTTTTCT
274973 TTTTCTTC
1 TTTTCTTC
274981 TTTTCTTC
1 TTTTCTTC
274989 TTTTCTTC
1 TTTTCTTC
274997 TTTT-TGTC
1 TTTTCT-TC
275005 TTTTCTTTC
1 TTTTC-TTC
275014 TTTT
1 TTTT
275018 TGTACTCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.03
8 26 0.76
9 6 0.18
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTCTTC
Found at i:275019 original size:17 final size:16
Alignment explanation
Indices: 274964--275020 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
274954 CTTTTTGAAA
*
274964 TCTTTTTCT-TTTTCT
1 TCTTTTTGTCTTTTCT
274979 TCTTTTCT-TCTTTTCT
1 TCTTTT-TGTCTTTTCT
274995 TCTTTTTGTCTTTTCTT
1 TCTTTTTGTCTTTTC-T
275012 TCTTTTTGT
1 TCTTTTTGT
275021 ACTCCAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.21
16 20 0.53
17 10 0.26
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (16 bp):
TCTTTTTGTCTTTTCT
Found at i:294449 original size:17 final size:17
Alignment explanation
Indices: 294429--294467 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
294419 CTTTCTGAAT
294429 TTTTTTCTTCTTT-TTTC
1 TTTTTTCTT-TTTCTTTC
*
294446 TTTTGTCTTTTTCTTTC
1 TTTTTTCTTTTTCTTTC
294463 TTTTT
1 TTTTT
294468 GCACTCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTTCTTTTTCTTTC
Found at i:294751 original size:20 final size:20
Alignment explanation
Indices: 294721--294778 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
294711 AAGATTAATG
294721 AAATG-AAAAAAAAGGAATC
1 AAATGAAAAAAAAAGGAATC
*
294740 AAATGAAAAAAAAAGGAATG
1 AAATGAAAAAAAAAGGAATC
294760 AAATGAAATAAATAAAGGA
1 AAATGAAA-AAA-AAAGGA
294779 TATAGATGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 5 0.14
20 21 0.60
21 3 0.09
22 6 0.17
ACGTcount: A:0.69, C:0.02, G:0.17, T:0.12
Consensus pattern (20 bp):
AAATGAAAAAAAAAGGAATC
Found at i:294831 original size:22 final size:21
Alignment explanation
Indices: 294797--294837 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
294787 GTTGCAGAAT
294797 TGATGGTCCTGATGGATGAAGA
1 TGATGGTCCTGAT-GATGAAGA
**
294819 TGATGGTGTTGATGATGAA
1 TGATGGTCCTGATGATGAA
294838 ATGGAGATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.05, G:0.37, T:0.32
Consensus pattern (21 bp):
TGATGGTCCTGATGATGAAGA
Found at i:296725 original size:35 final size:37
Alignment explanation
Indices: 296657--296736 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
296647 ATACTATTTC
* *
296657 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
296694 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
296729 CATCACCA
1 CATCACCA
296737 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.39, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:301960 original size:35 final size:37
Alignment explanation
Indices: 301892--301971 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
301882 ATACTATTTC
* *
301892 CATCCCCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
301929 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
301964 CATCACCA
1 CATCACCA
301972 AATTCACAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.30, C:0.39, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:307573 original size:19 final size:20
Alignment explanation
Indices: 307526--307576 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
307516 GAAACCCTTT
**
307526 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
307546 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
307565 TGAAGATACATG
1 TGAAAATACATG
307577 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:309507 original size:35 final size:35
Alignment explanation
Indices: 309396--309507 Score: 179
Period size: 36 Copynumber: 3.1 Consensus size: 35
309386 ATACAATCTG
*
309396 TCCATCACCATCATCACGCCTATATCATCACCATCT
1 TCCATCACCAT-ATCACGCCTATATCATCACCATAT
*
309432 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCA-TATCACGCCTATATCATCACCATAT
*
309468 TCCATCACCATATCACGCCTATATCATCACCAAAT
1 TCCATCACCATATCACGCCTATATCATCACCATAT
309503 TCCAT
1 TCCAT
309508 TTTTCATTCC
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 28 0.39
36 42 0.59
37 1 0.01
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.28
Consensus pattern (35 bp):
TCCATCACCATATCACGCCTATATCATCACCATAT
Found at i:309666 original size:15 final size:16
Alignment explanation
Indices: 309641--309670 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
309631 CTTTGATAAC
309641 ATTCTTTTCCATTTCA
1 ATTCTTTTCCATTTCA
309657 ATTC-TTTCCATTTC
1 ATTCTTTTCCATTTC
309671 CATTTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTCTTTTCCATTTCA
Found at i:313103 original size:35 final size:35
Alignment explanation
Indices: 312992--313103 Score: 170
Period size: 36 Copynumber: 3.1 Consensus size: 35
312982 GATACAATCG
*
312992 TCCATCACCATCATCACGCCTATATCATCACCATCT
1 TCCATCACCAT-ATCACGCCTATATCATCACCATAT
* *
313028 TCCATCACCATTGTCACGCCTATATCATCACCATAG
1 TCCATCACCA-TATCACGCCTATATCATCACCATAT
*
313064 TCCATCACCATATCACGCCTATATCATCACCAAAT
1 TCCATCACCATATCACGCCTATATCATCACCATAT
313099 TCCAT
1 TCCAT
313104 TTTTCATTCC
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
35 27 0.39
36 41 0.59
37 1 0.01
ACGTcount: A:0.29, C:0.38, G:0.04, T:0.28
Consensus pattern (35 bp):
TCCATCACCATATCACGCCTATATCATCACCATAT
Found at i:313262 original size:15 final size:16
Alignment explanation
Indices: 313237--313266 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
313227 CTTTGATAAC
313237 ATTCTTTTCCATTTCA
1 ATTCTTTTCCATTTCA
313253 ATTC-TTTCCATTTC
1 ATTCTTTTCCATTTC
313267 CATTTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTCTTTTCCATTTCA
Found at i:313512 original size:24 final size:24
Alignment explanation
Indices: 313472--313518 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
313462 AAAGTGCTAC
313472 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
313497 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
313519 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:314169 original size:19 final size:20
Alignment explanation
Indices: 314131--314171 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
314121 GAAACCCCTT
*
314131 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
314151 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
314170 TG
1 TG
314172 GAGATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:315106 original size:30 final size:31
Alignment explanation
Indices: 315067--315126 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
315057 ACATGCTGCC
**
315067 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
315098 ATGA-ATCTAAAACATATGTAAGCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
315127 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:317882 original size:19 final size:20
Alignment explanation
Indices: 317854--317893 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
317844 GGATAATAAT
317854 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
317874 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
317893 A
1 A
317894 AGAAAGGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:318344 original size:19 final size:20
Alignment explanation
Indices: 318306--318348 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
318296 GAAACCCCTT
*
318306 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
318326 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
318345 TGAA
1 TGAA
318349 GATAAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:337772 original size:17 final size:17
Alignment explanation
Indices: 337743--337775 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
337733 AACAACGTGC
337743 AAAAACAACAAAGAAGA
1 AAAAACAACAAAGAAGA
337760 AAAATACAA-AAAGAAG
1 AAAA-ACAACAAAGAAG
337776 TGCAAGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.76, C:0.09, G:0.12, T:0.03
Consensus pattern (17 bp):
AAAAACAACAAAGAAGA
Found at i:337848 original size:23 final size:24
Alignment explanation
Indices: 337820--337872 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
337810 AAAATCAGCA
337820 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCAAAAAG
* *
337843 AAGAAATTGAAAGCACTCAAAAAG
1 AAGAAAATAAAAGCACTCAAAAAG
337867 AAGAAA
1 AAGAAA
337873 GAAAAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.64, C:0.11, G:0.15, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCAAAAAG
Found at i:344070 original size:23 final size:24
Alignment explanation
Indices: 344044--344097 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
344034 AAATCCAGCA
*
344044 AAGAAAATCAAAGCACTC-AAAAG
1 AAGAAAATCAAAGAACTCGAAAAG
* *
344067 AAGAAATTGAAAGAACTCGAAAAG
1 AAGAAAATCAAAGAACTCGAAAAG
344091 AAGAAAA
1 AAGAAAA
344098 AGAAAGAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATCAAAGAACTCGAAAAG
Found at i:344094 original size:24 final size:23
Alignment explanation
Indices: 344044--344105 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 23
344034 AAATCCAGCA
* *
344044 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATGAAAGAACTCAAAAG
*
344067 AAGAAATTGAAAGAACTCGAAAAG
1 AAGAAAATGAAAGAACTC-AAAAG
*
344091 AAGAAAAAGAAAGAA
1 AAGAAAATGAAAGAA
344106 AGAAAAGTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 15 0.45
24 18 0.55
ACGTcount: A:0.65, C:0.10, G:0.18, T:0.08
Consensus pattern (23 bp):
AAGAAAATGAAAGAACTCAAAAG
Found at i:361532 original size:23 final size:25
Alignment explanation
Indices: 361493--361546 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
361483 TTCTTTTCTC
361493 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
361518 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
361541 TTTCTT
1 TTTCTT
361547 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:365108 original size:24 final size:23
Alignment explanation
Indices: 365080--365139 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
365070 ACTTTTCTTT
*
365080 CTTTCTTTTTCTTCTTTTTGAGTG
1 CTTTCATTTTCTTC-TTTTGAGTG
*
365104 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCATTTTCTTCTTTTGAGTG
*
365127 CTTTGATTTTCTT
1 CTTTCATTTTCTT
365140 TGCTGGATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.08, C:0.17, G:0.12, T:0.63
Consensus pattern (23 bp):
CTTTCATTTTCTTCTTTTGAGTG
Found at i:379337 original size:90 final size:91
Alignment explanation
Indices: 379221--379402 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
379211 GGGAAATGAT
*
379221 GCTTGGCCAAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
*
379285 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* * * * *
379311 GCTTGGTCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
* **
379376 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
379402 G
1 G
379403 GTGTTCTAGG
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 58 0.72
91 23 0.28
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.21
Consensus pattern (91 bp):
GCTTGGCCAAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:382528 original size:23 final size:22
Alignment explanation
Indices: 382502--382560 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 22
382492 ATTTTTTTTC
382502 CTTTTTTTTCTTCTTTTCGAGTG
1 CTTTTTTTTCTTCTTTT-GAGTG
**
382525 CTTTCAATTTCTTCTTTTGAGTG
1 CTTT-TTTTTCTTCTTTTGAGTG
382548 CTTTTATTTTCTT
1 CTTTT-TTTTCTT
382561 TGCTGTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.08, C:0.17, G:0.10, T:0.64
Consensus pattern (22 bp):
CTTTTTTTTCTTCTTTTGAGTG
Done.