Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004929.1 Hibiscus syriacus cultivar Beakdansim tig00011093_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: 209567
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:281 original size:6 final size:6
Alignment explanation
Indices: 265--333 Score: 131
Period size: 6 Copynumber: 11.7 Consensus size: 6
255 GCCGTCTCTC
265 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
312 GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTC
334 ATACGTGTCT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.08
6 58 0.92
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:462 original size:20 final size:20
Alignment explanation
Indices: 439--769 Score: 547
Period size: 20 Copynumber: 16.4 Consensus size: 20
429 ATTTTCAACG
*
439 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTATCAATCGCA
* *
459 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATCAATCGCA
*
479 TTGCGATTTTCT-TCTAAATCGCG
1 TTGCGA--TTCTATC--AATCGCA
* *
502 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTATCAATCGCA
* *
522 TTGCGATTATATAAATCGCA
1 TTGCGATTCTATCAATCGCA
542 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
562 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
582 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
602 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
622 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
642 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
662 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
682 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
702 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
722 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
742 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
762 TTGCGATT
1 TTGCGATT
770 TTCTTCTAAA
Statistics
Matches: 293, Mismatches: 13, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
20 271 0.92
21 5 0.02
22 6 0.02
23 11 0.04
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTATCAATCGCA
Found at i:806 original size:21 final size:21
Alignment explanation
Indices: 780--855 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 21
770 TTCTTCTAAA
780 TCGCGTTGCGAACTTGGAAGC
1 TCGCGTTGCGAACTTGGAAGC
* ** *
801 TCGCGTTGCGATTTTCTTCTAA-A
1 TCGCGTTGCGA---ACTTGGAAGC
824 TCGCGTTGCGAACTTGGAAGC
1 TCGCGTTGCGAACTTGGAAGC
845 TCGCGTTGCGA
1 TCGCGTTGCGA
856 TTTTCTTTTG
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
20 5 0.12
21 22 0.51
23 11 0.26
24 5 0.12
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGAACTTGGAAGC
Found at i:812 original size:44 final size:44
Alignment explanation
Indices: 757--862 Score: 203
Period size: 44 Copynumber: 2.4 Consensus size: 44
747 ATTCTATCAA
*
757 TCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAACTTGGAAGC
1 TCGCGTTGCGATTTTCTTCTAAATCGCGTTGCGAACTTGGAAGC
801 TCGCGTTGCGATTTTCTTCTAAATCGCGTTGCGAACTTGGAAGC
1 TCGCGTTGCGATTTTCTTCTAAATCGCGTTGCGAACTTGGAAGC
845 TCGCGTTGCGATTTTCTT
1 TCGCGTTGCGATTTTCTT
863 TTGACCGTTG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.37
Consensus pattern (44 bp):
TCGCGTTGCGATTTTCTTCTAAATCGCGTTGCGAACTTGGAAGC
Found at i:831 original size:23 final size:23
Alignment explanation
Indices: 755--834 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
745 CGATTCTATC
*
755 AATCGCATTGCGATTTTCTTCTA
1 AATCGCGTTGCGATTTTCTTCTA
* **
778 AATCGCGTTGCGA---ACTTGGA
1 AATCGCGTTGCGATTTTCTTCTA
*
798 AGCTCGCGTTGCGATTTTCTTCTA
1 A-ATCGCGTTGCGATTTTCTTCTA
822 AATCGCGTTGCGA
1 AATCGCGTTGCGA
835 ACTTGGAAGC
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
20 5 0.11
21 11 0.25
23 23 0.52
24 5 0.11
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (23 bp):
AATCGCGTTGCGATTTTCTTCTA
Found at i:895 original size:19 final size:20
Alignment explanation
Indices: 848--900 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
838 TGGAAGCTCG
*
848 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
868 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
888 CG-TGCGATTTTCT
1 CGTTGCGATTTTCT
901 AAATCGCGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 11 0.35
20 20 0.65
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.51
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:2365 original size:18 final size:18
Alignment explanation
Indices: 2344--2401 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
2334 ATTTATTAGT
2344 ATTTATAATAATAATATA
1 ATTTATAATAATAATATA
* *
2362 ATTTTTAATATTATATAAATA
1 ATTTATAATA--ATA-ATATA
* *
2383 ATTAATTATAATAATATA
1 ATTTATAATAATAATATA
2401 A
1 A
2402 GATATTATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
18 14 0.45
19 3 0.10
20 3 0.10
21 11 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTATAATAATAATATA
Found at i:2457 original size:26 final size:26
Alignment explanation
Indices: 2391--2481 Score: 87
Period size: 26 Copynumber: 3.3 Consensus size: 26
2381 TAATTAATTA
*
2391 TAATAAT-ATAAGATATTATATTTTATTT
1 TAATAATAATAA-A-ATTAT-TTATATTT
2419 TAATATATAATAAAATT-TTTATATTT
1 TAATA-ATAATAAAATTATTTATATTT
*
2445 TAATAATGAATAATATTATTTATATGTT
1 TAATAAT-AATAAAATTATTTATAT-TT
2473 TAAATAATA
1 T-AATAATA
2482 TTTAATAAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
25 2 0.04
26 20 0.36
27 8 0.15
28 12 0.22
29 9 0.16
30 4 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (26 bp):
TAATAATAATAAAATTATTTATATTT
Found at i:2465 original size:29 final size:28
Alignment explanation
Indices: 2403--2481 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 28
2393 ATAATATAAG
*
2403 ATATTATATTT-TATTTTAATATATAATA
1 ATATTATTTTTATATTTTAATA-ATAATA
2431 A-A--ATTTTTATATTTTAATAATGAATA
1 ATATTATTTTTATATTTTAATAAT-AATA
* * *
2457 ATATTATTTATATGTTTAAATAATA
1 ATATTATTTTTATATTTTAATAATA
2482 TTTAATAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
25 7 0.17
26 15 0.36
27 2 0.05
28 2 0.05
29 16 0.38
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (28 bp):
ATATTATTTTTATATTTTAATAATAATA
Found at i:3901 original size:18 final size:18
Alignment explanation
Indices: 3878--3924 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
3868 CTTTGTGGCC
3878 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
3896 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
3914 GAAGCGTGAGA
1 GAAGCGTGAGA
3925 CTAATATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (18 bp):
GAAGCGTGAGATTCGTCT
Found at i:4956 original size:14 final size:14
Alignment explanation
Indices: 4937--5334 Score: 184
Period size: 14 Copynumber: 30.0 Consensus size: 14
4927 CTTAATAATT
4937 ACTTTAATGATTTA
1 ACTTTAATGATTTA
4951 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
4965 A---TAAT-AATT-
1 ACTTTAATGATTTA
4974 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
4988 ATTTTAATGATTTA
1 ACTTTAATGATTTA
*
5002 A---TAAT-AATT-
1 ACTTTAATGATTTA
5011 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
5025 ATTTTAATGATTTA
1 ACTTTAATGATTTA
5039 A---T-A--ATTTA
1 ACTTTAATGATTTA
5047 ACTTTAATGATTTAATAA
1 ACTTTAATGA-TT--T-A
5065 TACTTTAATGATTTA
1 -ACTTTAATGATTTA
5080 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
5094 A---TAAT-AATT-
1 ACTTTAATGATTTA
5103 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
5117 ATGATTTAATGATTTA
1 A--CTTTAATGATTTA
* *
5133 A-TAATAATTATTTA
1 ACT-TTAATGATTTA
*
5147 ATGATTTAATGATTTA
1 A--CTTTAATGATTTA
*
5163 A---TAAT-AATT-
1 ACTTTAATGATTTA
5172 ACTTTAATGATTTA
1 ACTTTAATGATTTA
*
5186 ACTTTAATGCTTTA
1 ACTTTAATGATTTA
*
5200 A---TAAT-AATT-
1 ACTTTAATGATTTA
5209 ACTTTAATGATTTA
1 ACTTTAATGATTTA
* *
5223 ATGATTTAAT-AATT-
1 A--CTTTAATGATTTA
5237 ACTTTAATGATTTA
1 ACTTTAATGATTTA
* *
5251 ATTTTAATAATTTA
1 ACTTTAATGATTTA
* * *
5265 A-TAATAATTACTTA
1 ACT-TTAATGATTTA
* *
5279 ATTTTAATTATTTA
1 ACTTTAATGATTTA
*
5293 ATTTTAATGATTTA
1 ACTTTAATGATTTA
* * * *
5307 A-TAATAATTACTTG
1 ACT-TTAATGATTTA
5321 ACTTTAATGATTTA
1 ACTTTAATGATTTA
5335 TATTTACTGA
Statistics
Matches: 295, Mismatches: 39, Indels: 100
0.68 0.09 0.23
Matches are distributed among these distances:
8 6 0.02
9 5 0.02
10 15 0.05
11 22 0.07
12 27 0.09
13 21 0.07
14 146 0.49
15 8 0.03
16 30 0.10
17 2 0.01
18 3 0.01
19 10 0.03
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (14 bp):
ACTTTAATGATTTA
Found at i:4964 original size:8 final size:8
Alignment explanation
Indices: 4939--5308 Score: 183
Period size: 8 Copynumber: 48.8 Consensus size: 8
4929 TAATAATTAC
4939 TTTAATGA
1 TTTAATGA
*
4947 TTTAA--C
1 TTTAATGA
4953 TTTAATGA
1 TTTAATGA
4961 TTTAAT-A
1 TTTAATGA
* *
4968 -ATAATTA
1 TTTAATGA
4975 CTTTAATGA
1 -TTTAATGA
4984 TTTAAT--
1 TTTAATGA
4990 TTTAATGA
1 TTTAATGA
4998 TTTAAT-A
1 TTTAATGA
* *
5005 -ATAATTA
1 TTTAATGA
5012 CTTTAATGA
1 -TTTAATGA
5021 TTTAAT--
1 TTTAATGA
5027 TTTAATGA
1 TTTAATGA
*
5035 TTTAATAA
1 TTTAATGA
*
5043 TTTAA--C
1 TTTAATGA
5049 TTTAATGA
1 TTTAATGA
*
5057 TTTAATAATA
1 TTTAAT--GA
5067 CTTTAATGA
1 -TTTAATGA
*
5076 TTTAA--C
1 TTTAATGA
5082 TTTAATGA
1 TTTAATGA
5090 TTTAAT-A
1 TTTAATGA
* *
5097 -ATAATTA
1 TTTAATGA
5104 CTTTAATGA
1 -TTTAATGA
5113 TTTAATGA
1 TTTAATGA
5121 TTTAATGA
1 TTTAATGA
5129 TTTAAT-A
1 TTTAATGA
* *
5136 -ATAATTA
1 TTTAATGA
5143 TTTAATGA
1 TTTAATGA
5151 TTTAATGA
1 TTTAATGA
5159 TTTAAT-A
1 TTTAATGA
* *
5166 -ATAATTA
1 TTTAATGA
5173 CTTTAATGA
1 -TTTAATGA
*
5182 TTTAA--C
1 TTTAATGA
*
5188 TTTAATGC
1 TTTAATGA
5196 TTTAAT-A
1 TTTAATGA
* *
5203 -ATAATTA
1 TTTAATGA
5210 CTTTAATGA
1 -TTTAATGA
5219 TTTAATGA
1 TTTAATGA
*
5227 TTTAATAATTA
1 -TT--TAATGA
5238 CTTTAATGA
1 -TTTAATGA
5247 TTTAAT--
1 TTTAATGA
*
5253 TTTAATAA
1 TTTAATGA
5261 TTTAAT-A
1 TTTAATGA
* *
5268 -ATAATTA
1 TTTAATGA
*
5275 CTTAAT--
1 TTTAATGA
*
5281 TTTAATTA
1 TTTAATGA
5289 TTTAAT--
1 TTTAATGA
5295 TTTAATGA
1 TTTAATGA
5303 TTTAAT
1 TTTAAT
5309 AATAATTACT
Statistics
Matches: 284, Mismatches: 35, Indels: 86
0.70 0.09 0.21
Matches are distributed among these distances:
6 77 0.27
7 13 0.05
8 147 0.52
9 33 0.12
10 1 0.00
11 13 0.05
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (8 bp):
TTTAATGA
Found at i:4973 original size:37 final size:37
Alignment explanation
Indices: 4929--5319 Score: 297
Period size: 37 Copynumber: 10.3 Consensus size: 37
4919 CATCAATACT
*
4929 TAATAATTACTTTAATGATTTAACTTTAATGATTTAA
1 TAATAATTACTTTAATGATTTAATTTTAATGATTTAA
4966 TAATAATTACTTTAATGATTTAATTTTAATGATTTAA
1 TAATAATTACTTTAATGATTTAATTTTAATGATTTAA
5003 TAATAATTACTTTAATGATTTAATTTTAATGATTTAA
1 TAATAATTACTTTAATGATTTAATTTTAATGATTTAA
5040 TAAT--TTAACTTTAATGATTTAA---TAAT-ACTTTAA
1 TAATAATT-ACTTTAATGATTTAATTTTAATGA-TTTAA
* ** *
5073 TGAT--TTAACTTTAATGATTTAATAATAATTACTTTAA
1 TAATAATT-ACTTTAATGATTTAATTTTAATGA-TTTAA
* * ** *
5110 TGATTTAATGA-TTTAATGATTTAATAATAATTATTTAA
1 T-A-ATAATTACTTTAATGATTTAATTTTAATGATTTAA
* * * *
5148 TGATTTAATGA-TTTAATAATAATT-ACTTTAATGATTTAA
1 T-A-ATAATTACTTTAATGAT--TTAATTTTAATGATTTAA
* * * *
5187 CT-TTAA-TGCTTTAATAATAATT-ACTTTAATGATTTAATGA
1 -TAATAATTACTTTAATGAT--TTAATTTTAATGATTT-A--A
*
5227 TTTAATAATTACTTTAATGATTTAATTTTAATAATTTAA
1 --TAATAATTACTTTAATGATTTAATTTTAATGATTTAA
*
5266 TAATAATTACTTAATTTTAATTATTTAATTTTAATGATTTAA
1 TAATAATTAC-----TTTAATGATTTAATTTTAATGATTTAA
5308 TAATAATTACTT
1 TAATAATTACTT
5320 GACTTTAATG
Statistics
Matches: 308, Mismatches: 20, Indels: 52
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.00
33 30 0.10
35 2 0.01
36 19 0.06
37 127 0.41
38 25 0.08
39 35 0.11
40 5 0.02
41 5 0.02
42 49 0.16
43 10 0.03
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (37 bp):
TAATAATTACTTTAATGATTTAATTTTAATGATTTAA
Found at i:5181 original size:106 final size:102
Alignment explanation
Indices: 5086--5319 Score: 315
Period size: 106 Copynumber: 2.2 Consensus size: 102
5076 TTTAACTTTA
* *
5086 ATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATGATTTAATAATAATTATTTAATGA
1 ATGATTTAATAATAATTACTTTAATGATTTAATGATTTAAT-AATTAAT-ATAATGATTTAAT--
*
5151 TTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTA
62 TTTAATAATTTAATAATAATTACTTTAATGATTTAACTTTA
* * *
5192 ATGCTTTAATAATAATTACTTTAATGATTTAATGATTTAATAATTACTTTAATGATTTAATTTTA
1 ATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATAATTAATATAATGATTTAATTTTA
* *
5257 ATAATTTAATAATAATTACTTAATTTTAATTATTTAATTTTA
66 ATAATTTAATAATAATTAC-----TTTAATGATTTAACTTTA
5299 ATGATTTAATAATAATTACTT
1 ATGATTTAATAATAATTACTT
5320 GACTTTAATG
Statistics
Matches: 114, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
102 22 0.19
104 11 0.10
105 5 0.04
106 40 0.35
107 36 0.32
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.50
Consensus pattern (102 bp):
ATGATTTAATAATAATTACTTTAATGATTTAATGATTTAATAATTAATATAATGATTTAATTTTA
ATAATTTAATAATAATTACTTTAATGATTTAACTTTA
Found at i:5819 original size:6 final size:6
Alignment explanation
Indices: 5808--5838 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5798 GGTGAGAAGA
*
5808 ACTCCC ACTCCC ACTCCT ACTCCC ACTCCC A
1 ACTCCC ACTCCC ACTCCC ACTCCC ACTCCC A
5839 GTCCTTCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.19, C:0.61, G:0.00, T:0.19
Consensus pattern (6 bp):
ACTCCC
Found at i:5829 original size:18 final size:18
Alignment explanation
Indices: 5808--5843 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5798 GGTGAGAAGA
5808 ACTCCCACTCCCACTCCT
1 ACTCCCACTCCCACTCCT
*
5826 ACTCCCACTCCCAGTCCT
1 ACTCCCACTCCCACTCCT
5844 TCTTGGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.58, G:0.03, T:0.22
Consensus pattern (18 bp):
ACTCCCACTCCCACTCCT
Found at i:7864 original size:172 final size:173
Alignment explanation
Indices: 7572--7930 Score: 560
Period size: 172 Copynumber: 2.1 Consensus size: 173
7562 CATCAAATAT
* *
7572 AAAATGATCCCTAATTAATATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAAATT
1 AAAACGATCCCTAATTAATATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
*
7637 TATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAAC
66 TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
* * *
7702 TTTTTATAATTTACTCTAATTTCTTAAATTCCTCAAATTTTGC
131 TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
* * *
7745 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAAGTTAGCAATTTAATC-CATAAAT
1 AAAACGATCCCTAATTAATATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-TAAAT
* * *
7809 TT-TAAATTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAGCAA
65 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAA
* *
7873 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
130 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
7917 AAAACGGTCCCTAA
1 AAAACGATCCCTAA
7931 AACTTTAATA
Statistics
Matches: 170, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
172 111 0.65
173 59 0.35
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (173 bp):
AAAACGATCCCTAATTAATATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAAATT
TATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAAC
TTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:8416 original size:23 final size:23
Alignment explanation
Indices: 8390--8433 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
8380 AGTTGCATGC
8390 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
8413 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGACGTGCAG
8434 CCTTGCAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:8494 original size:22 final size:22
Alignment explanation
Indices: 8463--8509 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
8453 CGTGATTTCT
*
8463 GTGCTTTCTCCTTGCAGAACCC
1 GTGCTCTCTCCTTGCAGAACCC
8485 GTGCTCTCTCCTTGCAGAACCC
1 GTGCTCTCTCCTTGCAGAACCC
8507 GTG
1 GTG
8510 ATTCTCACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.36, G:0.21, T:0.30
Consensus pattern (22 bp):
GTGCTCTCTCCTTGCAGAACCC
Found at i:10283 original size:21 final size:21
Alignment explanation
Indices: 10259--10305 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
10249 ATGCGAATGT
10259 GAGCAAGCAGCAATGACATGA
1 GAGCAAGCAGCAATGACATGA
10280 GAGCAAGCAGCAATGACATGA
1 GAGCAAGCAGCAATGACATGA
10301 GAGCA
1 GAGCA
10306 TGGATATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.43, C:0.19, G:0.30, T:0.09
Consensus pattern (21 bp):
GAGCAAGCAGCAATGACATGA
Found at i:12853 original size:8 final size:8
Alignment explanation
Indices: 12840--12880 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
12830 CTCATTTTCA
12840 GAGAATTT
1 GAGAATTT
12848 GAGAATTT
1 GAGAATTT
*
12856 -AGAGTTT
1 GAGAATTT
*
12863 GGGAATTT
1 GAGAATTT
12871 GAGAATTT
1 GAGAATTT
12879 GA
1 GA
12881 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:13165 original size:128 final size:128
Alignment explanation
Indices: 12951--13447 Score: 894
Period size: 128 Copynumber: 3.9 Consensus size: 128
12941 TAATCGGAGT
* *
12951 ACTATTCATATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTA--TT-TCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
13013 CATTGCCCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
13076 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
13141 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
13204 AC-ATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
* *
13268 CATTGCCCTATTAAGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACATATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
13331 ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
13396 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
13448 AATCAGGTAA
Statistics
Matches: 357, Mismatches: 11, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
125 42 0.12
127 125 0.35
128 190 0.53
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:13402 original size:255 final size:252
Alignment explanation
Indices: 12954--13444 Score: 912
Period size: 255 Copynumber: 1.9 Consensus size: 252
12944 TCGGAGTACT
12954 ATTCATATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTCAGAGAATATGTTATCATTGC
1 ATTCATATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTCAGAGAATATGTTATCATTGC
*
13019 CCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCA
66 CCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACATATTATTTCACTATTCA
13084 CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
131 CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
13149 TATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTCAC
196 TATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTCAC
*
13206 ATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCAT
1 ATTCATATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTA--TT-TCAGAGAATATGTTATCAT
13271 TGCCCTATTA-AGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACATATTATTTCACTA
63 TGCCCTATTATA-TCACTCATGTCCCTCGGGGACACTAGATATATCAGTACATATTATTTCACTA
*
13335 TTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATT
127 TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATT
13400 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCA
192 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCA
13445 GTAAATCAGG
Statistics
Matches: 232, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
252 40 0.17
254 3 0.01
255 189 0.81
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (252 bp):
ATTCATATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTCAGAGAATATGTTATCATTGC
CCTATTATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACATATTATTTCACTATTCA
CATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCC
TATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTCAC
Found at i:13883 original size:34 final size:34
Alignment explanation
Indices: 13845--13945 Score: 148
Period size: 34 Copynumber: 3.0 Consensus size: 34
13835 AAATTTAGTG
*
13845 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
13879 TTAAATTTCGAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
13913 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
13946 AACATTTATC
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:14495 original size:21 final size:20
Alignment explanation
Indices: 14468--14558 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 20
14458 GGTATAAAAC
*
14468 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
*
14488 CCTGGCGGGCAAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
* *
14509 CCTTGCAGGCTCGGAATGTAA
1 CC-TGCGGGCTAGGAATGTAA
*
14530 TCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
14551 CCCTGCGG
1 -CCTGCGG
14559 AGATGGCATA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
20 3 0.05
21 55 0.90
22 3 0.05
ACGTcount: A:0.21, C:0.25, G:0.34, T:0.20
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:14588 original size:21 final size:21
Alignment explanation
Indices: 14562--14609 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
14552 CCTGCGGAGA
*
14562 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
14583 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
14604 GGGCAT
1 TGGCAT
14610 GTACCCCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:16374 original size:34 final size:31
Alignment explanation
Indices: 16331--16419 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
16321 TTAATAATTC
*
16331 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
16365 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
16396 TATAAAAAATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
16420 AAAATACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
33 2 0.04
34 22 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:16376 original size:31 final size:33
Alignment explanation
Indices: 16334--16408 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
16324 ATAATTCTAA
* * *
16334 ATAAATAATAATTATATAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
* *
16366 A-AAAAAATAA-TATTTACATAAATATATTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
16397 ATAAAAAATAAT
1 ATAAAAAATAAT
16409 AACTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 7 0.20
31 18 0.51
32 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATAAAAAATAATTATATAAATAAATATATTAAT
Found at i:28633 original size:21 final size:21
Alignment explanation
Indices: 28604--28656 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
28594 ATTCTGACTA
28604 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
28625 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
28646 TCGCAATGCGA
1 TCGCATTGCGA
28657 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:28678 original size:20 final size:20
Alignment explanation
Indices: 28646--28719 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
28636 TTTTCCTAAT
28646 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * ** *
28666 TCACAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
28687 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
28707 TCGCAATGCGAAT
1 TCGCAATGCGAAT
28720 CTGACTATCG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:28692 original size:41 final size:40
Alignment explanation
Indices: 28646--28737 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
28636 TTTTCCTAAT
*
28646 TCGCAATGCGAATACGTAAATCACAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCACAACGCGAATCT-GAAAA
* * * **
28687 TCGCAATGCGATTACGTAAATCGCAATGCGAATCTGACTA
1 TCGCAATGCGAATACGTAAATCACAACGCGAATCTGAAAA
28727 TCGCAATGCGA
1 TCGCAATGCGA
28738 TTTACATAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
40 14 0.31
41 31 0.69
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCACAACGCGAATCTGAAAA
Found at i:28940 original size:22 final size:22
Alignment explanation
Indices: 28915--28980 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
28905 GGCGACATCC
28915 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
28937 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
28959 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
28981 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:29389 original size:20 final size:20
Alignment explanation
Indices: 29316--29406 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
29306 GCGATTCTGT
29316 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
* ** **
29335 CATTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
29355 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
29375 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
29395 TGTTGCGATTTT
1 CGTTGCGATTTT
29407 AAGTTTCAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 11 0.18
20 50 0.82
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:29413 original size:20 final size:20
Alignment explanation
Indices: 29370--29413 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
29360 CGATAGTCAT
* *
29370 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
29390 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
29410 TTTC
1 TTTC
29414 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:31287 original size:20 final size:20
Alignment explanation
Indices: 31262--31438 Score: 166
Period size: 20 Copynumber: 9.5 Consensus size: 20
31252 AGAATAGTTT
31262 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
31282 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
31302 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
31318 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
31335 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
31351 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
31369 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
31389 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
31409 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
31429 ACTATCGCAA
1 ACTATCGCAA
31439 CGAAAGAATC
Statistics
Matches: 133, Mismatches: 10, Indels: 28
0.78 0.06 0.16
Matches are distributed among these distances:
14 14 0.11
16 10 0.08
17 8 0.06
18 5 0.04
19 7 0.05
20 89 0.67
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:31342 original size:33 final size:33
Alignment explanation
Indices: 31285--31365 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
31275 GAAAATGACT
** * * *
31285 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCG-AAATGAAAATCGCAACAACAAA
*
31319 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
31352 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
31366 ATGACTATCG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 30 0.75
34 10 0.25
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:31450 original size:34 final size:38
Alignment explanation
Indices: 31352--31455 Score: 144
Period size: 40 Copynumber: 2.7 Consensus size: 38
31342 CAACAACAAA
31352 ATCGCAACGCGAAAATGACTATCGCAATGCGAATTTGACT
1 ATCGCAA-GCGAAAATGAC-ATCGCAATGCGAATTTGACT
31392 ATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACT
1 ATCGCAA-GCGAAAATGAC-ATCGCAATGCGAATTTGACT
31432 ATCGCAA-CG-AAA-GA-ATCGCAATGC
1 ATCGCAAGCGAAAATGACATCGCAATGC
31456 AAAATGAAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
34 10 0.16
36 2 0.03
37 3 0.05
38 2 0.03
40 46 0.73
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (38 bp):
ATCGCAAGCGAAAATGACATCGCAATGCGAATTTGACT
Found at i:31566 original size:20 final size:20
Alignment explanation
Indices: 31485--31571 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
31475 GATTCTCTCA
** **
31485 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCATTTTCGCG
* **
31505 TTGCGATAGTAATTTTCGTA
1 TTGCGATAGTCATTTTCGCG
31525 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
*
31545 TTGCGATAGTCATTTTCACG
1 TTGCGATAGTCATTTTCGCG
31565 TTGCGAT
1 TTGCGAT
31572 TTTATGTTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:32096 original size:18 final size:19
Alignment explanation
Indices: 32057--32098 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
32047 CTCACCTGTC
32057 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
32078 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
32096 ATC
1 ATC
32099 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:32152 original size:42 final size:42
Alignment explanation
Indices: 32081--32160 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
32071 CTCCCCTATC
*
32081 GTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCTCCTCCCACT
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGTC-CCTCCCACT
* ** *
32123 GTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCC
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCC
32161 AACATTCTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 29 0.91
43 3 0.09
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.24
Consensus pattern (42 bp):
GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACT
Found at i:33555 original size:14 final size:14
Alignment explanation
Indices: 33536--33571 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
33526 ATTGTTTAAT
33536 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
33550 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
33564 TGATTTGT
1 TGATTTGT
33572 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:33716 original size:14 final size:14
Alignment explanation
Indices: 33697--33750 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
33687 GGAAATGACT
33697 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
33711 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
33730 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
33744 ATCGCAA
1 ATCGCAA
33751 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:33765 original size:34 final size:33
Alignment explanation
Indices: 33677--33770 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
33667 AAAACAGACT
* **
33677 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
33711 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
33744 ATCGCAATGCGAAAATGAAAATCGCAA
1 ATCGCAATGCG-AAATGAAAATCGCAA
33771 TGCGAAAATG
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.57
34 24 0.43
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:33768 original size:20 final size:20
Alignment explanation
Indices: 33710--33797 Score: 118
Period size: 20 Copynumber: 4.8 Consensus size: 20
33700 GCAACGAGAG
33710 AATCGCAATGCG-AAATGAA
1 AATCGCAATGCGAAAATGAA
*
33729 AATCGCAA--CG---A-GAG
1 AATCGCAATGCGAAAATGAA
33743 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
33763 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
33783 AATCGCAATGCGAAA
1 AATCGCAATGCGAAA
33798 CTAAATTCGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
19 9 0.15
20 37 0.61
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.14
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Found at i:33866 original size:33 final size:33
Alignment explanation
Indices: 33807--33891 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 33
33797 ACTAAATTCG
33807 CGTTGCGATTTTCATTTTCGCATTGCGATTCA-CT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATT-ATCT
*
33841 CGTTGCGATTTTCATTTCGCTTTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
**
33874 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
33892 CGCGTTGCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
32 1 0.02
33 32 0.68
34 14 0.30
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTATCT
Found at i:33899 original size:20 final size:20
Alignment explanation
Indices: 33874--33942 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
33864 GCGATTATCT
33874 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
33894 CGTTGCAATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCCG
*
33914 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
33934 CGTTGCGAT
1 CGTTGCGAT
33943 TTCCGCGTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:33953 original size:34 final size:33
Alignment explanation
Indices: 33805--33961 Score: 111
Period size: 34 Copynumber: 4.5 Consensus size: 33
33795 AAACTAAATT
** *
33805 CGCGTTGCGATTTTCATTTTCGCATTGCGA-TTC
1 CGCGTTGCGATAGTCA-TTTCGCGTTGCGATTTC
* ** *
33838 ACTCGTTGCGATTTTCATTTCGCTTTGCGATTAT-
1 -CGCGTTGCGATAGTCATTTCGCGTTGCGATT-TC
*
33872 CTCGTTGCGATAGTCATTTCCGCGTTGCAATAGTCATTTC
1 CGCGTTGCGATAGTCATTT-CGCGTTGC----G--ATTTC
* *
33912 TGTGTTGCGATAGTCATATTCGCGTTGCGATTTC
1 CGCGTTGCGATAGTCAT-TTCGCGTTGCGATTTC
33946 CGCGTTGCGATAGTCA
1 CGCGTTGCGATAGTCA
33962 AATGAATGTC
Statistics
Matches: 102, Mismatches: 10, Indels: 22
0.76 0.07 0.16
Matches are distributed among these distances:
33 29 0.28
34 42 0.41
35 1 0.01
36 1 0.01
38 1 0.01
39 1 0.01
40 25 0.25
41 2 0.02
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (33 bp):
CGCGTTGCGATAGTCATTTCGCGTTGCGATTTC
Found at i:37292 original size:20 final size:20
Alignment explanation
Indices: 37267--37333 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
37257 AAATTCAGTA
*
37267 TTGCGATAGTTAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
37287 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
37307 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
37327 TTGCGAT
1 TTGCGAT
37334 TTACAGATTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:37340 original size:20 final size:20
Alignment explanation
Indices: 37278--37476 Score: 135
Period size: 20 Copynumber: 9.9 Consensus size: 20
37268 TGCGATAGTT
* *
37278 AGAATCTCGTTGCGATAGT-C
1 AGAATCGCGTTGCGAT-TTAC
* *
37298 AGAATCTCGTTGCGATAGT-C
1 AGAATCGCGTTGCGAT-TTAC
*
37318 AGAATCTCGTTGCGATTTAC
1 AGAATCGCGTTGCGATTTAC
* *
37338 AGATTCGAGTTGCGATTTAC
1 AGAATCGCGTTGCGATTTAC
*
37358 -GTAATCGCATTGCGATTTAC
1 AG-AATCGCGTTGCGATTTAC
*
37378 -GTAATCGCATTGCGATTTAC
1 AG-AATCGCGTTGCGATTTAC
*
37398 -GTAATCGCATTGCGATTTAC
1 AG-AATCGCGTTGCGATTTAC
* *
37418 -GTAATCGCATTGCGATTTTCC
1 AG-AATCGCGTTGCGA-TTTAC
37439 A-AATTCGCGTTGCGATTTA-
1 AGAA-TCGCGTTGCGATTTAC
* *
37458 TGTATTCGCGTTGCGATTT
1 AG-AATCGCGTTGCGATTT
37477 CGCATTGCGA
Statistics
Matches: 160, Mismatches: 12, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
19 2 0.01
20 143 0.89
21 15 0.09
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (20 bp):
AGAATCGCGTTGCGATTTAC
Found at i:37350 original size:40 final size:40
Alignment explanation
Indices: 37267--37353 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
37257 AAATTCAGTA
* **
37267 TTGCGATAGTTAGAATCTCGTTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCGTTGCGATAGTCAGAATCGAG
* *
37307 TTGCGATAGTCAGAATCTCGTTGCGAT-TTACAGATTCGAG
1 TTGCGATAGTCAGAATCTCGTTGCGATAGT-CAGAATCGAG
37347 TTGCGAT
1 TTGCGAT
37354 TTACGTAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
39 1 0.02
40 40 0.98
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TTGCGATAGTCAGAATCTCGTTGCGATAGTCAGAATCGAG
Found at i:37371 original size:40 final size:40
Alignment explanation
Indices: 37347--37476 Score: 188
Period size: 40 Copynumber: 3.2 Consensus size: 40
37337 CAGATTCGAG
37347 TTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCA
37387 TTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCA
* ** * * * *
37427 TTGCGATTTTCCAAATTCGCGTTGCGATTTATGTATTCGCG
1 TTGCGATTTACGTAA-TCGCATTGCGATTTACGTAATCGCA
37468 TTGCGATTT
1 TTGCGATTT
37477 CGCATTGCGA
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
40 52 0.63
41 30 0.37
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCA
Found at i:37371 original size:60 final size:58
Alignment explanation
Indices: 37307--37476 Score: 175
Period size: 60 Copynumber: 2.8 Consensus size: 58
37297 CAGAATCTCG
*
37307 TTGCGATAGTCAGAATCTCGTTGCGATTTACAG-ATTCGAGTTGCGATTTACGTAATCGCA
1 TTGCGAT--TCAGAATCGCGTTGCGATTTAC-GTATTCGAGTTGCGATTTACGTAATCGCA
* * *
37367 TTGCGATTTACGTAATCGCATTGCGATTTACGTAATCGCA-TTGCGATTTACGTAATCGCA
1 TTGCGATTCA-G-AATCGCGTTGCGATTTACGTATTCG-AGTTGCGATTTACGTAATCGCA
* *
37427 TTGCGATTTTCCA-AATTCGCGTTGCGATTTATGTATTCGCGTTGCGATTT
1 TTGCGA--TT-CAGAA-TCGCGTTGCGATTTACGTATTCGAGTTGCGATTT
37477 CGCATTGCGA
Statistics
Matches: 92, Mismatches: 9, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
58 2 0.02
59 2 0.02
60 55 0.60
61 30 0.33
62 2 0.02
63 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (58 bp):
TTGCGATTCAGAATCGCGTTGCGATTTACGTATTCGAGTTGCGATTTACGTAATCGCA
Found at i:37507 original size:21 final size:21
Alignment explanation
Indices: 37483--37528 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
37473 ATTTCGCATT
37483 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
37504 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
37525 GCGA
1 GCGA
37529 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:53463 original size:32 final size:34
Alignment explanation
Indices: 53391--53466 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 34
53381 TATTATTTTA
* *
53391 ATAAAAA-AATAATATTTACATAAATATATTAAT
1 ATAAAAATAATAATATTTACATAAATATACTAAC
53424 ATAAAAAATAATAACTATTTA-A-AAA-ATACTAAC
1 AT-AAAAATAATAA-TATTTACATAAATATACTAAC
53457 ATAAAAATAA
1 ATAAAAATAA
53467 ATTTCTTACC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 8 0.21
33 10 0.26
34 8 0.21
35 6 0.16
36 6 0.16
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (34 bp):
ATAAAAATAATAATATTTACATAAATATACTAAC
Found at i:64051 original size:2 final size:2
Alignment explanation
Indices: 64044--64070 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
64034 AAGGGCAACA
64044 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
64071 ATCAGTTAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66643 original size:3 final size:3
Alignment explanation
Indices: 66635--66662 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
66625 AACTACTGTT
66635 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
66663 AACCCAATTC
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:66896 original size:14 final size:14
Alignment explanation
Indices: 66877--66915 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
66867 TAATGGGGAG
66877 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
66891 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
66905 GAATCTCTGCA
1 TAATCCCTGCA
66916 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:67901 original size:27 final size:27
Alignment explanation
Indices: 67863--67928 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
67853 TTTGAAGAAA
67863 ATCAGTGTTTGTATTTCTTGCTCAAGG
1 ATCAGTGTTTGTATTTCTTGCTCAAGG
67890 ATCAGTGTTTGTATTTCTTGCTCAAGG
1 ATCAGTGTTTGTATTTCTTGCTCAAGG
67917 ATCAGTGTTTGT
1 ATCAGTGTTTGT
67929 TAGCTGAGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.45
Consensus pattern (27 bp):
ATCAGTGTTTGTATTTCTTGCTCAAGG
Found at i:78359 original size:345 final size:345
Alignment explanation
Indices: 77728--78418 Score: 1382
Period size: 345 Copynumber: 2.0 Consensus size: 345
77718 AAAGAATTCC
77728 ATTTGTTGTAATATTGGCGATATAGTGAAGTTATCATCCGGTATGGTGCCCGAGGAGTATACGAT
1 ATTTGTTGTAATATTGGCGATATAGTGAAGTTATCATCCGGTATGGTGCCCGAGGAGTATACGAT
77793 ATTCTCGTCGAACCTCGTAAATTTGGTGTGTTCTCTCCTTTATTGTTTTTTATTCGGTTCTTTTC
66 ATTCTCGTCGAACCTCGTAAATTTGGTGTGTTCTCTCCTTTATTGTTTTTTATTCGGTTCTTTTC
77858 CATTGTGTTTCAATATTCAATAATTTGACAGGTTTATCCGCTGTGCAACCTTTGGTGGTTTTAAT
131 CATTGTGTTTCAATATTCAATAATTTGACAGGTTTATCCGCTGTGCAACCTTTGGTGGTTTTAAT
77923 TTTGACATTTTAGGTCAATTTTAAAACTACGTTCGTGTGGGAAATAACCCGTTTTCCCCAACAAT
196 TTTGACATTTTAGGTCAATTTTAAAACTACGTTCGTGTGGGAAATAACCCGTTTTCCCCAACAAT
77988 ATGTACATCCATGTTAGACAAGTAATGGGCTTTTATCATTACAAATAATGATATCCTCACCCTTC
261 ATGTACATCCATGTTAGACAAGTAATGGGCTTTTATCATTACAAATAATGATATCCTCACCCTTC
78053 AATTAGTCCCTGCAAACAGA
326 AATTAGTCCCTGCAAACAGA
78073 ATTTGTTGTAATATTGGCGATATAGTGAAGTTATCATCCGGTATGGTGCCCGAGGAGTATACGAT
1 ATTTGTTGTAATATTGGCGATATAGTGAAGTTATCATCCGGTATGGTGCCCGAGGAGTATACGAT
78138 ATTCTCGTCGAACCTCGTAAATTTGGTGTGTTCTCTCCTTTATTGTTTTTTATTCGGTTCTTTTC
66 ATTCTCGTCGAACCTCGTAAATTTGGTGTGTTCTCTCCTTTATTGTTTTTTATTCGGTTCTTTTC
78203 CATTGTGTTTCAATATTCAATAATTTGACAGGTTTATCCGCTGTGCAACCTTTGGTGGTTTTAAT
131 CATTGTGTTTCAATATTCAATAATTTGACAGGTTTATCCGCTGTGCAACCTTTGGTGGTTTTAAT
78268 TTTGACATTTTAGGTCAATTTTAAAACTACGTTCGTGTGGGAAATAACCCGTTTTCCCCAACAAT
196 TTTGACATTTTAGGTCAATTTTAAAACTACGTTCGTGTGGGAAATAACCCGTTTTCCCCAACAAT
78333 ATGTACATCCATGTTAGACAAGTAATGGGCTTTTATCATTACAAATAATGATATCCTCACCCTTC
261 ATGTACATCCATGTTAGACAAGTAATGGGCTTTTATCATTACAAATAATGATATCCTCACCCTTC
78398 AATTAGTCCCTGCAAACAGA
326 AATTAGTCCCTGCAAACAGA
78418 A
1 A
78419 GCAAACCACA
Statistics
Matches: 346, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
345 346 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (345 bp):
ATTTGTTGTAATATTGGCGATATAGTGAAGTTATCATCCGGTATGGTGCCCGAGGAGTATACGAT
ATTCTCGTCGAACCTCGTAAATTTGGTGTGTTCTCTCCTTTATTGTTTTTTATTCGGTTCTTTTC
CATTGTGTTTCAATATTCAATAATTTGACAGGTTTATCCGCTGTGCAACCTTTGGTGGTTTTAAT
TTTGACATTTTAGGTCAATTTTAAAACTACGTTCGTGTGGGAAATAACCCGTTTTCCCCAACAAT
ATGTACATCCATGTTAGACAAGTAATGGGCTTTTATCATTACAAATAATGATATCCTCACCCTTC
AATTAGTCCCTGCAAACAGA
Found at i:84328 original size:28 final size:28
Alignment explanation
Indices: 84287--84353 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
84277 AGTTAACCCT
*
84287 TATTTTTCTATAATCCAGCATACCTATA
1 TATTTTTCTCTAATCCAGCATACCTATA
84315 TATTTTTCTCTAATCCAGCATACCTATA
1 TATTTTTCTCTAATCCAGCATACCTATA
84343 TATTTTTCTCT
1 TATTTTTCTCT
84354 GATATACCTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.27, C:0.22, G:0.03, T:0.48
Consensus pattern (28 bp):
TATTTTTCTCTAATCCAGCATACCTATA
Found at i:87678 original size:21 final size:21
Alignment explanation
Indices: 87653--87698 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
87643 ATTCTGACTA
87653 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
*
87674 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGATTTTCCAAAT
87695 TCGC
1 TCGC
87699 AATGTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:87720 original size:20 final size:20
Alignment explanation
Indices: 87695--87747 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
87685 TTTTCCTAAT
*
87695 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
87715 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
87735 TCACAACGCGAAT
1 TCGCAATGCGAAT
87748 CTGACTATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:87761 original size:20 final size:20
Alignment explanation
Indices: 87747--87820 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
87737 ACAACGCGAA
87747 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
*
87767 TCTGACTATCGCAATGAGAT
1 TCTGACTATCGCAACGAGAT
*
87787 TCTGACTATCGCAACGCGAT
1 TCTGACTATCGCAACGAGAT
87807 TCTGACTATCGCAA
1 TCTGACTATCGCAA
87821 TACTGAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (20 bp):
TCTGACTATCGCAACGAGAT
Found at i:87943 original size:27 final size:27
Alignment explanation
Indices: 87913--87975 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
87903 CGCAGCAGCA
87913 GCAACTCATAACCTAAATCCCTAAATC
1 GCAACTCATAACCTAAATCCCTAAATC
87940 GCAACTCATAACCTAAATCCCTAAATC
1 GCAACTCATAACCTAAATCCCTAAATC
87967 GCAACTCAT
1 GCAACTCAT
87976 TTCATCTCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.22
Consensus pattern (27 bp):
GCAACTCATAACCTAAATCCCTAAATC
Found at i:88699 original size:24 final size:24
Alignment explanation
Indices: 88682--88728 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
88672 GGTCAGTATT
88682 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
* *
88706 CGGACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
88729 TCAGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:88738 original size:24 final size:24
Alignment explanation
Indices: 88687--88740 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
88677 GTATTCGAAA
*
88687 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
88711 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
88735 TTTGAT
1 TTTGAT
88741 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:88950 original size:15 final size:14
Alignment explanation
Indices: 88932--88967 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
88922 GAAAAAGAAG
88932 AAGAAGAAATCCCCA
1 AAGAA-AAATCCCCA
*
88947 AAGAAAAGTCCCCA
1 AAGAAAAATCCCCA
88961 AAGAAAA
1 AAGAAAA
88968 TGCCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.58, C:0.22, G:0.14, T:0.06
Consensus pattern (14 bp):
AAGAAAAATCCCCA
Found at i:91185 original size:20 final size:20
Alignment explanation
Indices: 91160--91233 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
91150 GACATTCATT
91160 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
91180 TGACTATCGCAACACGAAAA
1 TGACTATCGCAACGCGAATA
91200 TGACTATCGCAACGCGGAAT-
1 TGACTATCGCAACGC-GAATA
*
91220 TAACTATCGCAACG
1 TGACTATCGCAACG
91234 AGAGAATCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 45 0.94
21 3 0.06
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:91319 original size:34 final size:34
Alignment explanation
Indices: 91279--91377 Score: 137
Period size: 33 Copynumber: 2.9 Consensus size: 34
91269 GAATTTAGTT
*
91279 TCTCGTTGTGATTTTCATTTTCGCATTGCGATTC
1 TCTCGTTGCGATTTTCATTTTCGCATTGCGATTC
*
91313 TCTCGTTGCAATTTTCA-TTTCGCATTGCGATTC
1 TCTCGTTGCGATTTTCATTTTCGCATTGCGATTC
** * *
91346 TCTCGTTGCGATAGTCATTTCCGCGTTGCGAT
1 TCTCGTTGCGATTTTCATTTTCGCATTGCGAT
91378 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 30 0.53
34 27 0.47
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.44
Consensus pattern (34 bp):
TCTCGTTGCGATTTTCATTTTCGCATTGCGATTC
Found at i:91502 original size:14 final size:14
Alignment explanation
Indices: 91483--91518 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
91473 CATCAATTAA
91483 ACAAATCATCATTT
1 ACAAATCATCATTT
*
91497 ACAAATCATCTTTT
1 ACAAATCATCATTT
91511 ACAAATCA
1 ACAAATCA
91519 ATTAAACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (14 bp):
ACAAATCATCATTT
Found at i:93006 original size:42 final size:42
Alignment explanation
Indices: 92903--93010 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
92893 GAATGTTGGA
* * * *
92903 AGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGTGTG
1 AGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATGTG
* ** *
92945 AGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAG-G
1 AGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGAT-GTG
92987 -GGAGGCCTCTTGAACGATGACAGG
1 AGG-GGCCTCTTGAACGATGACAGG
93011 TGAGTCAGGC
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
41 2 0.04
42 49 0.94
43 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (42 bp):
AGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATGTG
Found at i:93515 original size:20 final size:20
Alignment explanation
Indices: 93490--93538 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
93480 GAAACTTAAA
93490 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
93510 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
93530 ATCGCAACG
1 ATCGCAACG
93539 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:94283 original size:23 final size:23
Alignment explanation
Indices: 94257--94301 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
94247 CACCACAGCT
*
94257 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
94280 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
94302 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:96067 original size:21 final size:21
Alignment explanation
Indices: 96043--96087 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
96033 TTTTGTTCGT
* *
96043 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
96064 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
96085 TTG
1 TTG
96088 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:101024 original size:21 final size:21
Alignment explanation
Indices: 101000--101044 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
100990 TTTTGTTCGT
* *
101000 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
101021 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
101042 TTG
1 TTG
101045 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:101781 original size:20 final size:20
Alignment explanation
Indices: 101756--101822 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
101746 GATTCTCTCG
**
101756 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
101776 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
101796 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
101816 TTGCGAT
1 TTGCGAT
101823 TTTGTTGTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:101867 original size:33 final size:34
Alignment explanation
Indices: 101746--101885 Score: 129
Period size: 40 Copynumber: 4.0 Consensus size: 34
101736 GGATGTTACA
* **
101746 GATTCTCTCGTTGCGATAGTCAAATTCGCATTGC
1 GATTCTCTCATTGCGATAGTCATTTTCGCATTGC
*
101780 GATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGC
1 GAT--TC----TCTCATTGCGATAGTCATTTTCGCATTGC
* * ** **
101820 GATTTTGTTGTTGCGATTTTCA-TTTCGCATTGC
1 GATTCTCTCATTGCGATAGTCATTTTCGCATTGC
101853 GATTCTCTCATTGCGATAGTCATTTTCGCATTG
1 GATTCTCTCATTGCGATAGTCATTTTCGCATTG
101886 AGATATTAAA
Statistics
Matches: 82, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
33 27 0.33
34 24 0.29
36 2 0.02
38 1 0.01
40 28 0.34
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (34 bp):
GATTCTCTCATTGCGATAGTCATTTTCGCATTGC
Found at i:103800 original size:20 final size:20
Alignment explanation
Indices: 103777--103866 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
103767 TCTGAAACTT
103777 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
103797 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
103817 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
103837 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
103856 AAAATCGCAAC
1 AAAATCGCAAC
103867 GACAGAATCG
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 12 0.20
20 49 0.80
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:104265 original size:22 final size:22
Alignment explanation
Indices: 104203--104268 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
104193 TGACTGTGAA
* *
104203 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
104225 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
*
104247 TGATTTCGTCGAAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
104269 GGACGTCACC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:104496 original size:20 final size:20
Alignment explanation
Indices: 104466--104552 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
104456 CGATAGTCAG
*
104466 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
104486 ATTTGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
104506 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
**
104526 ATTCGCATTTTGATTTACGT
1 ATTCGCATTGCGATTTACGT
104546 ATTCGCA
1 ATTCGCA
104553 ACGCGAATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.44
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:104572 original size:21 final size:21
Alignment explanation
Indices: 104548--104600 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
104538 ATTTACGTAT
104548 TCGCAACGCGAATTTGAAAAA
1 TCGCAACGCGAATTTGAAAAA
*
104569 TCGCAACGCGAATTTGGAAAA
1 TCGCAACGCGAATTTGAAAAA
*
104590 TCGCAATGCGA
1 TCGCAACGCGA
104601 TAGTCAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAATTTGAAAAA
Found at i:106676 original size:31 final size:31
Alignment explanation
Indices: 106616--106677 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
106606 TGACCGAGAA
**
106616 ACTAAAATCAAACGGATCGATAATGTTAGGG
1 ACTAAAATCAAACGGATCGATAACATTAGGG
*
106647 ACTAAAATCGAACGGA-CAGATAACATTAGGG
1 ACTAAAATCAAACGGATC-GATAACATTAGGG
106678 CCCATTTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.19
Consensus pattern (31 bp):
ACTAAAATCAAACGGATCGATAACATTAGGG
Found at i:108561 original size:16 final size:16
Alignment explanation
Indices: 108534--108573 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
108524 AAAAAAAGCG
108534 AAGATAAATAAATAAAT
1 AAGAT-AATAAATAAAT
*
108551 AAGATAATAAATTAAT
1 AAGATAATAAATAAAT
*
108567 AAAATAA
1 AAGATAA
108574 AAGCAAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (16 bp):
AAGATAATAAATAAAT
Found at i:108819 original size:20 final size:20
Alignment explanation
Indices: 108778--108820 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
108768 CCGAAAATAG
* *
108778 AAAAAGGGATACGAATTTAA
1 AAAAAAGGATACGAATTAAA
108798 AAAAAAGGATAC-AGATTAAA
1 AAAAAAGGATACGA-ATTAAA
108818 AAA
1 AAA
108821 GGATAAAGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.63, C:0.05, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAAAAGGATACGAATTAAA
Found at i:109098 original size:30 final size:29
Alignment explanation
Indices: 109059--109116 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
109049 AATGTATATA
109059 AAAAGAATAGAAATAAAATATAAATAAAAG
1 AAAAGAATAGAAATAAAA-ATAAATAAAAG
* * *
109089 AAAATAATAGTAATATAAATAAATAAAA
1 AAAAGAATAGAAATAAAAATAAATAAAA
109117 TATTAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (29 bp):
AAAAGAATAGAAATAAAAATAAATAAAAG
Found at i:110997 original size:105 final size:104
Alignment explanation
Indices: 110810--111475 Score: 1052
Period size: 105 Copynumber: 6.4 Consensus size: 104
110800 TGTTTCGAGG
* * * * *
110810 CCAATATCTTTCGCTATGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGAGAAA-TGTTTGTTGACAACCAG
*
110875 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
64 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
110916 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATCTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAT-TGAGAAATGTTTGTTGACAACCAGC
110981 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
65 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
111021 CCAATATCCTTCGTTGTGAAGTTGAAAATTGACTCTGAAATTGGGAAA--ATTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTG-AAATTGGCTCTG-AATTGAGAAATGTTTGTTGACAACCAG
*
111084 CGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGT
64 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
111125 CCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAA--ATTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGAGAAATGTTTGTTGACAACCAGC
111188 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
65 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
111228 CCAATATCCTTCGTTGTGAAGTTTAAATTGGCTCTGAATTTGAGAAATGTTTATTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-TTGAGAAATGTTTGTTGACAACCAGC
*
111293 GGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGT
65 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
111333 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-TTGAGAA-ATGTTTGTTGACAACCAG
*
111398 CGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGT
64 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
111439 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
111476 GTAAAACCTG
Statistics
Matches: 529, Mismatches: 24, Indels: 14
0.93 0.04 0.02
Matches are distributed among these distances:
102 2 0.00
103 117 0.22
104 78 0.15
105 182 0.34
106 147 0.28
107 3 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (104 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAGAAATGTTTGTTGACAACCAGCG
GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:112321 original size:7 final size:8
Alignment explanation
Indices: 112304--112332 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
112294 CATTCTTCTC
112304 TTTTTGTT
1 TTTTTGTT
112312 TTTTTGTT
1 TTTTTGTT
112320 TTTTTGTT
1 TTTTTGTT
112328 TTTTT
1 TTTTT
112333 CAACTTAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (8 bp):
TTTTTGTT
Found at i:122795 original size:16 final size:16
Alignment explanation
Indices: 122768--122807 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
122758 AAAAAAAGCG
122768 AAGATAAATAAATAAAT
1 AAGAT-AATAAATAAAT
*
122785 AAGATAATAAATTAAT
1 AAGATAATAAATAAAT
*
122801 AAAATAA
1 AAGATAA
122808 AAGCAAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (16 bp):
AAGATAATAAATAAAT
Found at i:123348 original size:25 final size:25
Alignment explanation
Indices: 123328--123403 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 25
123318 AAAGAATAGA
123328 AATA-AAATATAAATAAAAGAAAAT
1 AATAGAAATATAAATAAAAGAAAAT
* *
123352 AATAGTAATATAAAT-AAATAAAAT
1 AATAGAAATATAAATAAAAGAAAAT
* * *
123376 TA-AGAAAATATACATATAAATAAAAT
1 AATAG-AAATATAAATA-AAAGAAAAT
123402 AA
1 AA
123404 AACAAATAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
23 2 0.05
24 21 0.50
25 9 0.21
26 10 0.24
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (25 bp):
AATAGAAATATAAATAAAAGAAAAT
Found at i:123356 original size:30 final size:29
Alignment explanation
Indices: 123317--123374 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
123307 AATGTATATA
123317 AAAAGAATAGAAATAAAATATAAATAAAAG
1 AAAAGAATAGAAATAAAA-ATAAATAAAAG
* * *
123347 AAAATAATAGTAATATAAATAAATAAAA
1 AAAAGAATAGAAATAAAAATAAATAAAA
123375 TTAAGAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (29 bp):
AAAAGAATAGAAATAAAAATAAATAAAAG
Found at i:143940 original size:21 final size:22
Alignment explanation
Indices: 143916--143956 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
143906 GTACTTCAAA
143916 ATATTTTA-TATTTTTTAAAAG
1 ATATTTTATTATTTTTTAAAAG
143937 ATATTTTATTATTTTTTAAA
1 ATATTTTATTATTTTTTAAA
143957 TTTTAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
ATATTTTATTATTTTTTAAAAG
Found at i:155896 original size:62 final size:62
Alignment explanation
Indices: 155794--155933 Score: 244
Period size: 62 Copynumber: 2.3 Consensus size: 62
155784 CTTCATTTTC
*
155794 GTGATATTTGAATCGACGGCGAAGTGAAGAGTGAGGAGCGAAACAGAAGGCAATGGAGAAAT
1 GTGACATTTGAATCGACGGCGAAGTGAAGAGTGAGGAGCGAAACAGAAGGCAATGGAGAAAT
* * *
155856 GTGGCATTTGGATCGACGGCGAAGTGACGAGTGAGGAGCGAAACAGAAGGCAATGGAGAAAT
1 GTGACATTTGAATCGACGGCGAAGTGAAGAGTGAGGAGCGAAACAGAAGGCAATGGAGAAAT
155918 GTGACATTTGAATCGA
1 GTGACATTTGAATCGA
155934 AGTGGTGGCT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.36, C:0.11, G:0.36, T:0.17
Consensus pattern (62 bp):
GTGACATTTGAATCGACGGCGAAGTGAAGAGTGAGGAGCGAAACAGAAGGCAATGGAGAAAT
Found at i:159173 original size:12 final size:12
Alignment explanation
Indices: 159156--159180 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
159146 GCATAATTGG
159156 TTTTTTTTTCTC
1 TTTTTTTTTCTC
159168 TTTTTTTTTCTC
1 TTTTTTTTTCTC
159180 T
1 T
159181 GTATGTCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTCTC
Found at i:165689 original size:2 final size:2
Alignment explanation
Indices: 165682--165747 Score: 88
Period size: 2 Copynumber: 35.5 Consensus size: 2
165672 CCGCCCCGAT
165682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
165723 TT TA TA T- TA TA T- TA -A TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
165748 TTTCGGATTC
Statistics
Matches: 58, Mismatches: 1, Indels: 10
0.84 0.01 0.14
Matches are distributed among these distances:
1 5 0.09
2 53 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:167167 original size:20 final size:20
Alignment explanation
Indices: 167123--167168 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
167113 CTAAAAATCG
167123 AAATATTATATTATATTCAT
1 AAATATTATATTATATTCAT
*
167143 TAATATTATCAATT-TATT-AT
1 AAATATTAT--ATTATATTCAT
167163 AAATAT
1 AAATAT
167169 ATGTACTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 15 0.68
21 4 0.18
22 3 0.14
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATATTATATTATATTCAT
Found at i:169933 original size:42 final size:46
Alignment explanation
Indices: 169886--169995 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 46
169876 ATGTTCATCA
* *
169886 AAATATTAT-TTATTTATTTAT-TTATTAA-TAT-TTATAATAATAT
1 AAATATTATATT-TTTATTTATATAAATAATTATATTATAATAATAT
169929 -AATATTATATTTTTAATATTATATAAATAATTATATTATAATAATAT
1 AAATATTATATTTTT-AT-TTATATAAATAATTATATTATAATAATAT
169976 AAGATATTATATTTTTATTT
1 AA-ATATTATATTTTTATTT
169996 TAATAATATA
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
42 11 0.19
43 4 0.07
44 4 0.07
45 5 0.09
46 3 0.05
47 14 0.25
48 3 0.05
49 13 0.23
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (46 bp):
AAATATTATATTTTTATTTATATAAATAATTATATTATAATAATAT
Found at i:169945 original size:31 final size:32
Alignment explanation
Indices: 169900--169968 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
169890 ATTATTTATT
169900 TATT-TATTTATTAATATT-TAT-AATAATATAA
1 TATTATATTTATTAATATTATATAAATAAT-T-A
169931 TATTATATTT-TTAATATTATATAAATAATTA
1 TATTATATTTATTAATATTATATAAATAATTA
169962 TATTATA
1 TATTATA
169969 ATAATATAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
31 20 0.57
32 9 0.26
33 6 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TATTATATTTATTAATATTATATAAATAATTA
Found at i:169971 original size:14 final size:13
Alignment explanation
Indices: 169926--169976 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
169916 TTTATAATAA
169926 TATAATATTATATT
1 TATAATATTATA-T
*
169940 TTTAATATTATA-
1 TATAATATTATAT
169952 TA-AATAATTATAT
1 TATAAT-ATTATAT
*
169965 TATAATAATATA
1 TATAATATTATA
169977 AGATATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 3 0.10
12 7 0.23
13 7 0.23
14 14 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TATAATATTATAT
Found at i:170092 original size:23 final size:23
Alignment explanation
Indices: 170066--170110 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
170056 AATAATATTT
170066 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
170089 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
170111 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:170189 original size:32 final size:29
Alignment explanation
Indices: 170150--170219 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
170140 AATATAATTT
*
170150 ATAATA-TTTTATTTCACTAAAATATAAAAAA
1 ATAATATTTTTA-TT-AATAAAAT-TAAAAAA
*
170181 ATTAATATTTTTATTAATAAAATTATAAAA
1 A-TAATATTTTTATTAATAAAATTAAAAAA
170211 ATAATATTT
1 ATAATATTT
170220 AATAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 8 0.23
30 7 0.20
31 8 0.23
32 7 0.20
33 5 0.14
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (29 bp):
ATAATATTTTTATTAATAAAATTAAAAAA
Found at i:170493 original size:22 final size:22
Alignment explanation
Indices: 170447--170493 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
170437 AACGTTTTTC
*
170447 AAAAATATAATTCATTTTCCAG
1 AAAAATATAATTCATTTTACAG
* *
170469 AAAAATTTAATTCATTTTACGG
1 AAAAATATAATTCATTTTACAG
170491 AAA
1 AAA
170494 TCATTTTCCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (22 bp):
AAAAATATAATTCATTTTACAG
Found at i:170506 original size:70 final size:70
Alignment explanation
Indices: 170392--170540 Score: 282
Period size: 70 Copynumber: 2.1 Consensus size: 70
170382 TTTCCAGATG
*
170392 TTTTCCAG-AAAATTTAATTCATTTTACGGAAATCATTTTTCGGAAAACGTTTTTCAAAAATATA
1 TTTTCCAGAAAAATTTAATTCATTTTACGGAAATCATTTTCCGGAAAACGTTTTTCAAAAATATA
170456 ATTCA
66 ATTCA
170461 TTTTCCAGAAAAATTTAATTCATTTTACGGAAATCATTTTCCGGAAAACGTTTTTCAAAAATATA
1 TTTTCCAGAAAAATTTAATTCATTTTACGGAAATCATTTTCCGGAAAACGTTTTTCAAAAATATA
170526 ATTCA
66 ATTCA
170531 TTTTCCAGAA
1 TTTTCCAGAA
170541 TTCAAATTCC
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
69 8 0.10
70 70 0.90
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (70 bp):
TTTTCCAGAAAAATTTAATTCATTTTACGGAAATCATTTTCCGGAAAACGTTTTTCAAAAATATA
ATTCA
Found at i:171664 original size:2 final size:2
Alignment explanation
Indices: 171657--171694 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
171647 GAAAAACAAG
*
171657 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
171695 ATCATCGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:172313 original size:15 final size:15
Alignment explanation
Indices: 172293--172326 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
172283 TGCCCATAAT
*
172293 TGTAGGATATAAATC
1 TGTAGGAGATAAATC
172308 TGTAGGAGATAAATC
1 TGTAGGAGATAAATC
172323 TGTA
1 TGTA
172327 TGCATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (15 bp):
TGTAGGAGATAAATC
Found at i:183192 original size:21 final size:21
Alignment explanation
Indices: 183163--183215 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
183153 ATTCTGACTA
183163 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
183184 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
183205 TCGCAATGCGA
1 TCGCATTGCGA
183216 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:183237 original size:20 final size:20
Alignment explanation
Indices: 183205--183278 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
183195 TTTTCCTAAT
183205 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * ** *
183225 TCACAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
183246 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
183266 TCGCAATGCGAAT
1 TCGCAATGCGAAT
183279 CTGACTATCG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:183251 original size:41 final size:40
Alignment explanation
Indices: 183205--183296 Score: 121
Period size: 41 Copynumber: 2.3 Consensus size: 40
183195 TTTTCCTAAT
*
183205 TCGCAATGCGAATACGTAAATCACAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCACAACGCGAATCT-GAAAA
* * * **
183246 TCGCAATGCGATTACGTAAATCGCAATGCGAATCTGACTA
1 TCGCAATGCGAATACGTAAATCACAACGCGAATCTGAAAA
183286 TCGCAATGCGA
1 TCGCAATGCGA
183297 TTTACATAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
40 14 0.31
41 31 0.69
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCACAACGCGAATCTGAAAA
Found at i:183500 original size:22 final size:22
Alignment explanation
Indices: 183475--183540 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
183465 GGCGACATCC
183475 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
183497 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
183519 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
183541 TTCACGGTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:183949 original size:20 final size:20
Alignment explanation
Indices: 183876--183966 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
183866 GCGATTCTGT
183876 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
* ** **
183895 CATTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
**
183915 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
183935 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
183955 TGTTGCGATTTT
1 CGTTGCGATTTT
183967 AAGTTTCAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 11 0.18
20 50 0.82
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:183973 original size:20 final size:20
Alignment explanation
Indices: 183930--183973 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
183920 CGATAGTCAT
* *
183930 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
183950 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
183970 TTTC
1 TTTC
183974 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:185850 original size:20 final size:20
Alignment explanation
Indices: 185825--186001 Score: 166
Period size: 20 Copynumber: 9.5 Consensus size: 20
185815 AGAATAGTTT
185825 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
185845 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
185865 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
185881 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
185898 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
185914 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
185932 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
185952 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
185972 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
185992 ACTATCGCAA
1 ACTATCGCAA
186002 CGAAAGAATC
Statistics
Matches: 133, Mismatches: 10, Indels: 28
0.78 0.06 0.16
Matches are distributed among these distances:
14 14 0.11
16 10 0.08
17 8 0.06
18 5 0.04
19 7 0.05
20 89 0.67
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:185905 original size:33 final size:33
Alignment explanation
Indices: 185848--185928 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
185838 GAAAATGACT
** * * *
185848 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCG-AAATGAAAATCGCAACAACAAA
*
185882 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
185915 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
185929 ATGACTATCG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 30 0.75
34 10 0.25
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:186013 original size:34 final size:38
Alignment explanation
Indices: 185915--186018 Score: 144
Period size: 40 Copynumber: 2.7 Consensus size: 38
185905 CAACAACAAA
185915 ATCGCAACGCGAAAATGACTATCGCAATGCGAATTTGACT
1 ATCGCAA-GCGAAAATGAC-ATCGCAATGCGAATTTGACT
185955 ATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACT
1 ATCGCAA-GCGAAAATGAC-ATCGCAATGCGAATTTGACT
185995 ATCGCAA-CG-AAA-GA-ATCGCAATGC
1 ATCGCAAGCGAAAATGACATCGCAATGC
186019 AAAATGAAAA
Statistics
Matches: 63, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
34 10 0.16
36 2 0.03
37 3 0.05
38 2 0.03
40 46 0.73
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (38 bp):
ATCGCAAGCGAAAATGACATCGCAATGCGAATTTGACT
Found at i:186129 original size:20 final size:20
Alignment explanation
Indices: 186048--186134 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
186038 GATTCTCTCA
** **
186048 TTGCGATAGTCAAATTCGTA
1 TTGCGATAGTCATTTTCGCG
* **
186068 TTGCGATAGTAATTTTCGTA
1 TTGCGATAGTCATTTTCGCG
186088 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCG
*
186108 TTGCGATAGTCATTTTCACG
1 TTGCGATAGTCATTTTCGCG
186128 TTGCGAT
1 TTGCGAT
186135 TTTATGTTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCG
Found at i:186659 original size:18 final size:19
Alignment explanation
Indices: 186620--186661 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
186610 CTCACCTGTC
186620 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
186641 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
186659 ATC
1 ATC
186662 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:186715 original size:42 final size:42
Alignment explanation
Indices: 186644--186723 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
186634 CTCCCCTATC
*
186644 GTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCTCCTCCCACT
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGTC-CCTCCCACT
* ** *
186686 GTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCC
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCC
186724 AACATTCTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 29 0.91
43 3 0.09
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.24
Consensus pattern (42 bp):
GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACT
Found at i:188124 original size:14 final size:14
Alignment explanation
Indices: 188105--188140 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
188095 ATTGTTTAAT
188105 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
188119 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
188133 TGATTTGT
1 TGATTTGT
188141 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:188285 original size:14 final size:14
Alignment explanation
Indices: 188266--188319 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
188256 GGAAATGACT
188266 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
188280 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
188299 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
188313 ATCGCAA
1 ATCGCAA
188320 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:188334 original size:34 final size:33
Alignment explanation
Indices: 188246--188339 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
188236 AAAACAGACT
* **
188246 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
188280 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
188313 ATCGCAATGCGAAAATGAAAATCGCAA
1 ATCGCAATGCG-AAATGAAAATCGCAA
188340 TGCGAAAATG
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.57
34 24 0.43
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:188337 original size:20 final size:20
Alignment explanation
Indices: 188279--188366 Score: 118
Period size: 20 Copynumber: 4.8 Consensus size: 20
188269 GCAACGAGAG
188279 AATCGCAATGCG-AAATGAA
1 AATCGCAATGCGAAAATGAA
*
188298 AATCGCAA--CG---A-GAG
1 AATCGCAATGCGAAAATGAA
188312 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
188332 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAAATGAA
188352 AATCGCAATGCGAAA
1 AATCGCAATGCGAAA
188367 CTAAATTCGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
19 9 0.15
20 37 0.61
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.14
Consensus pattern (20 bp):
AATCGCAATGCGAAAATGAA
Done.