Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold442
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: 369669
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:138393 original size:130 final size:129
Alignment explanation
Indices: 138048--138394 Score: 391
Period size: 130 Copynumber: 2.7 Consensus size: 129
138038 CAAAACACTA
* **
138048 ATTTTTCACAATCGGGGATAC-CTCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGGCTTT
1 ATTTTTCACAATCGGGGATACTC-CAACCCAGTTATTTTCGAGGGGATACTCCAACCC-GATTTT
* * *
138112 ATTTCCAAAATATTGATTTCTCACAATCAGGGATACTTCAACCACGGCCTTATTTCTAAAATATT
64 ATTTCCAAAATATTAATTTCTCACAATCAGGGACACTTCAACCACGGCCTTATTTCTAAAATATC
138177 G
129 G
* * *
138178 ATTTCTCATAATTGGGGATACTCCAACCCCA-TTATTTTC-ACGGGGATACTCCAATCCCGATTT
1 ATTTTTCACAATCGGGGATACTCCAA-CCCAGTTATTTTCGA-GGGGATACTCCAA-CCCGATTT
*** * * * *
138241 TATTTTTGAAATATCTATTTTCT-ATAATCGGGGACACTTCAACC-CTTGCCTTATTTCT-AAAT
63 TATTTCCAAAATAT-TAATTTCTCACAATCAGGGACACTTCAACCAC-GGCCTTATTTCTAAAAT
138303 CATCG
126 -ATCG
* *
138308 ATTTTTCACAATCGGGGATACTCCAACCCAGTTATTTTCGAGGGGATACTCTAACCCCATTATTA
1 ATTTTTCACAATCGGGGATACTCCAACCCAGTTATTTTCGAGGGGATACTCCAACCCGATT-TTA
*
138373 TCTCCAAAATATTAAATTTCTC
65 TTTCCAAAATATT-AATTTCTC
138395 GTCGGGAGAT
Statistics
Matches: 179, Mismatches: 26, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
129 17 0.09
130 148 0.83
131 14 0.08
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (129 bp):
ATTTTTCACAATCGGGGATACTCCAACCCAGTTATTTTCGAGGGGATACTCCAACCCGATTTTAT
TTCCAAAATATTAATTTCTCACAATCAGGGACACTTCAACCACGGCCTTATTTCTAAAATATCG
Found at i:138524 original size:21 final size:21
Alignment explanation
Indices: 138498--138541 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
138488 CCCCTAGATC
138498 ATTTTTTGAAAACCTCACAGA
1 ATTTTTTGAAAACCTCACAGA
138519 ATTTTTTGAAAACCTCACAGA
1 ATTTTTTGAAAACCTCACAGA
138540 AT
1 AT
138542 CCAATCAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.34
Consensus pattern (21 bp):
ATTTTTTGAAAACCTCACAGA
Found at i:140050 original size:20 final size:20
Alignment explanation
Indices: 140025--140085 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
140015 TTTTTACCCA
* *
140025 AATGTATCAATACATTTTTC
1 AATGTATCGATACATTTATC
* *
140045 AATGTATCGATACATATATG
1 AATGTATCGATACATTTATC
140065 AATGTATCGATACATTCTATC
1 AATGTATCGATACATT-TATC
140086 TTTTTACCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 31 0.91
21 3 0.09
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTATC
Found at i:143571 original size:12 final size:12
Alignment explanation
Indices: 143542--143581 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
143532 AAATCATACA
*
143542 TTTCATACATGC
1 TTTCATGCATGC
143554 -TTCATGCATGC
1 TTTCATGCATGC
*
143565 TTTCATGCATGT
1 TTTCATGCATGC
143577 TTTCA
1 TTTCA
143582 CACATGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (12 bp):
TTTCATGCATGC
Found at i:145422 original size:20 final size:22
Alignment explanation
Indices: 145383--145427 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
145373 TTCGGGTATG
*
145383 AAACGTAATTTTCGAAATTTAA
1 AAACGTAATTTTCAAAATTTAA
145405 AAAC-TAATTTT-AAAATTTAA
1 AAACGTAATTTTCAAAATTTAA
145425 AAA
1 AAA
145428 ACTTTGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
21 7 0.32
22 4 0.18
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (22 bp):
AAACGTAATTTTCAAAATTTAA
Found at i:157587 original size:75 final size:75
Alignment explanation
Indices: 157464--157615 Score: 268
Period size: 75 Copynumber: 2.0 Consensus size: 75
157454 TATCTTGTTA
* * *
157464 CTAGCTTTTGAACCAGAAAAGAATTGTCTAGTTTACTCAAAAACCACAGGCTTAAATTGCTTATT
1 CTAGCTTTTGAACCAGAAAAGAATTCTCTAGTTTACCCAAAAACCACAGGCTCAAATTGCTTATT
157529 TAACAACAGG
66 TAACAACAGG
157539 CTAGCTTTTGAACCAGAAAAGAATTCTCTAGTTTACCCAAAAACCACAGGCTCAAATTGCTTATT
1 CTAGCTTTTGAACCAGAAAAGAATTCTCTAGTTTACCCAAAAACCACAGGCTCAAATTGCTTATT
*
157604 TAACCACAGG
66 TAACAACAGG
157614 CT
1 CT
157616 CAAAGTGCTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (75 bp):
CTAGCTTTTGAACCAGAAAAGAATTCTCTAGTTTACCCAAAAACCACAGGCTCAAATTGCTTATT
TAACAACAGG
Found at i:157614 original size:25 final size:25
Alignment explanation
Indices: 157580--157629 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
157570 TTTACCCAAA
*
157580 AACCACAGGCTCAAATTGCTTATTT
1 AACCACAGGCTCAAAGTGCTTATTT
157605 AACCACAGGCTCAAAGTGCTTATTT
1 AACCACAGGCTCAAAGTGCTTATTT
157630 GAGGCTTGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (25 bp):
AACCACAGGCTCAAAGTGCTTATTT
Found at i:159953 original size:2 final size:2
Alignment explanation
Indices: 159946--159974 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
159936 ATGACTTAAA
159946 AT 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 AT A
159975 AAGTATGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:161367 original size:20 final size:20
Alignment explanation
Indices: 161342--161382 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
161332 TAAATTTTTT
*
161342 ATTTTT-TAAAATGTTTTGAA
1 ATTTTTCTAAAA-ATTTTGAA
161362 ATTTTTCTAAAAATTTTGAA
1 ATTTTTCTAAAAATTTTGAA
161382 A
1 A
161383 AACTGGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (20 bp):
ATTTTTCTAAAAATTTTGAA
Found at i:166364 original size:19 final size:19
Alignment explanation
Indices: 166317--166370 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
166307 CTGCCAATTT
**
166317 CATGTATCGATACAAATTGTC
1 CATGTATCGATAC--ATTGAA
*
166338 CATATATCGATACATTGAA
1 CATGTATCGATACATTGAA
166357 CATGTATCGATACA
1 CATGTATCGATACA
166371 ATGTATCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 17 0.59
21 12 0.41
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACATTGAA
Found at i:166376 original size:13 final size:13
Alignment explanation
Indices: 166358--166384 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
166348 TACATTGAAC
166358 ATGTATCGATACA
1 ATGTATCGATACA
166371 ATGTATCGATACA
1 ATGTATCGATACA
166384 A
1 A
166385 GGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:166943 original size:15 final size:17
Alignment explanation
Indices: 166923--166956 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
166913 GTTTTCGTTT
166923 TTCT-CCCCTTAAA-AA
1 TTCTCCCCCTTAAATAA
166938 TTCTCCCCCTTAAATAA
1 TTCTCCCCCTTAAATAA
166955 TT
1 TT
166957 ATCTTCTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 9 0.53
17 4 0.24
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (17 bp):
TTCTCCCCCTTAAATAA
Found at i:172253 original size:42 final size:42
Alignment explanation
Indices: 172164--172263 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
172154 AAAAAAAATT
*
172164 CAAATGTATCGATACATTTGTGAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGTGAAATGTATCGATACATTTGA
* *
172206 GAAATGTATCGATTCATTTGTGAAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATTTGTGAAATGTATCGATACATT-TGA
*
172248 CAAATGTATTGATACA
1 CAAATGTATCGATACA
172264 GGGTCTCAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 50 0.98
43 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (42 bp):
CAAATGTATCGATACATTTGTGAAATGTATCGATACATTTGA
Found at i:172256 original size:21 final size:21
Alignment explanation
Indices: 172165--172244 Score: 151
Period size: 21 Copynumber: 3.8 Consensus size: 21
172155 AAAAAAATTC
172165 AAATGTATCGATACATTTGTG
1 AAATGTATCGATACATTTGTG
172186 AAATGTATCGATACATTTGTG
1 AAATGTATCGATACATTTGTG
*
172207 AAATGTATCGATTCATTTGTG
1 AAATGTATCGATACATTTGTG
172228 AAATGTATCGATACATT
1 AAATGTATCGATACATT
172245 CTACAAATGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (21 bp):
AAATGTATCGATACATTTGTG
Found at i:172323 original size:19 final size:19
Alignment explanation
Indices: 172299--172366 Score: 78
Period size: 19 Copynumber: 3.9 Consensus size: 19
172289 AATTCAACAA
172299 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
172318 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
172333 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
172350 ATTT-TATCGATACATAA
1 -TTTGTATCGATACATAA
172367 TTAGCTACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 26 0.62
20 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:172338 original size:13 final size:13
Alignment explanation
Indices: 172320--172344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
172310 ACATAAGTTT
172320 TGTATCGATACAA
1 TGTATCGATACAA
172333 TGTATCGATACA
1 TGTATCGATACA
172345 TAAGTATTTT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:172342 original size:32 final size:32
Alignment explanation
Indices: 172301--172363 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
172291 TTCAACAATT
172301 TGTATCGATACATAAGT-TTTGTATCGATACAA
1 TGTATCGATACATAAGTATTT-TATCGATACAA
172333 TGTATCGATACATAAGTATTTTATCGATACA
1 TGTATCGATACATAAGTATTTTATCGATACA
172364 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 27 0.90
33 3 0.10
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTTTATCGATACAA
Found at i:172424 original size:13 final size:13
Alignment explanation
Indices: 172406--172431 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
172396 CATTTTTCTG
172406 TGTATCGATACAT
1 TGTATCGATACAT
172419 TGTATCGATACAT
1 TGTATCGATACAT
172432 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:172428 original size:33 final size:33
Alignment explanation
Indices: 172386--172452 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
172376 ACCAAGGAAA
***
172386 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
172419 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
172452 T
1 T
172453 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:176610 original size:13 final size:13
Alignment explanation
Indices: 176592--176616 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
176582 CAAAGATCAG
176592 TGTATCGATACAA
1 TGTATCGATACAA
176605 TGTATCGATACA
1 TGTATCGATACA
176617 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:176698 original size:33 final size:33
Alignment explanation
Indices: 176656--176725 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
176646 GGCAGTAGCT
*
176656 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCAATACAAAAAAATATGTATCGA
* ***
176689 TACATTGTATCAATACAACATTTTATGTATCGA
1 TACATTGTATCAATACAAAAAAATATGTATCGA
176722 TACA
1 TACA
176726 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (33 bp):
TACATTGTATCAATACAAAAAAATATGTATCGA
Found at i:178505 original size:56 final size:50
Alignment explanation
Indices: 178386--178724 Score: 156
Period size: 51 Copynumber: 6.4 Consensus size: 50
178376 CTCAATTCTC
* * * *
178386 CACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACAAATTTT
*
178436 CTATAATCGGGGATACTCCAACTCCTGATTTTATTTCCAAAAAAAACACCAAATTTT
1 C-ACAATCGGGGATACTCCAACTCC-GATTTTATTTCC----AAAACA-CAAATTTT
* * * * **
178493 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCC-AACCCCGTTATTTT
1 CACAATCGGGGATACTCCAACTCCGATT--T--T-----AT-TTCCAAAACAC-AAATTTT
* * * ** *
178552 --CGA--GGGGATACTCCAAC-CCTGACTTTATTTCCAAAATATTGATTTTT
1 CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAACA-CAAATTTT
* * *
178599 CACAATCGGGGATACTCCAAC-CTCGGTTTTATTTTCAAAACACCAATTTTT
1 CACAATCGGGGATACTCCAACTC-CGATTTTATTTCCAAAACA-CAAATTTT
* * *
178650 C-CTTTGATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACTAATTTTT
1 CAC---AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACAC-AAATTTT
*
178704 CACAATCGAGGATACTCCAAC
1 CACAATCGGGGATACTCCAAC
178725 CTCGTTATCT
Statistics
Matches: 219, Mismatches: 36, Indels: 66
0.68 0.11 0.21
Matches are distributed among these distances:
46 3 0.01
47 8 0.04
49 2 0.01
50 2 0.01
51 57 0.26
52 29 0.13
53 29 0.13
54 19 0.09
55 17 0.08
56 28 0.13
57 10 0.05
58 2 0.01
59 8 0.04
63 2 0.01
64 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (50 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACAAATTTT
Found at i:178567 original size:28 final size:27
Alignment explanation
Indices: 178497--178570 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
178487 AATTTTCACA
178497 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
178524 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
178550 TTCGAGGGGATACTCCAACCC
1 ATC--GGGGATACTCCAACCC
178571 TGACTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 4 0.09
27 23 0.53
28 16 0.37
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.23
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:178748 original size:28 final size:28
Alignment explanation
Indices: 178708--178784 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
178698 ATTTTTCACA
* *
178708 ATCGAGGATACTCCAACCTCGTTA-TCTC
1 ATCGGGGATACTCCAACCCCGTTACT-TC
178736 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
178764 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
178785 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 42 0.98
29 1 0.02
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:178759 original size:212 final size:212
Alignment explanation
Indices: 178381--178832 Score: 642
Period size: 212 Copynumber: 2.1 Consensus size: 212
178371 AGTTTCTCAA
* * *
178381 TTCTCCACAATCGGGGATATTCCAA-CTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCG
1 TTCT-CACAATCGGGGATACTCCAACCTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCG
*
178445 GGGATACTCCAACTCCTGATTTTATTTCCAAAAAAAACACCAAATTTTCACAATCGGGGATACTC
65 GGGATACTCCAACTCCTGATTTTATTTCC--AAAAAACACCAAATTTTCACAATCGAGGATACTC
* * *
178510 CAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTGAC
128 CAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGAC
*
178575 TTTATTTCCAAAATATTGAT
193 TTTATTCCCAAAATATTGAT
* * * *
178595 TTTTCACAATCGGGGATACTCCAACCT-CGGTTTTATTTTCAAAACACCAATTTTTCCTTTGATC
1 TTCTCACAATCGGGGATACTCCAACCTCCGATTTTATTTTCAAAACACCAA-TTTT-CTATAATC
* * *
178659 GGGGATACTCCAACTCC-GATTTTATTTCC-AAAAATACTAATTTTTCACAATCGAGGATACTCC
64 GGGGATACTCCAACTCCTGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCC
* * *
178722 AACCTCGTTATCTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGC
129 AACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGAC
178787 TTTATTCCCAAAATATTGAT
193 TTTATTCCCAAAATATTGAT
* *
178807 TTCTCATAATTGGGGATACTCCAACC
1 TTCTCACAATCGGGGATACTCCAACC
178833 CCGTTATTTT
Statistics
Matches: 213, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
211 39 0.18
212 91 0.43
213 39 0.18
214 21 0.10
215 23 0.11
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (212 bp):
TTCTCACAATCGGGGATACTCCAACCTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
GGATACTCCAACTCCTGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAA
CCCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTT
ATTCCCAAAATATTGAT
Found at i:178887 original size:79 final size:79
Alignment explanation
Indices: 178736--178942 Score: 229
Period size: 79 Copynumber: 2.6 Consensus size: 79
178726 TCGTTATCTC
* * * *
178736 ATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT
* *
178801 ATTGATTTCTCATA
66 ATCGATTTCTCACA
* * * * ** **
178815 ATTGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTC-TGAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT
178879 CATCGATTTCTCACA
66 -ATCGATTTCTCACA
* * *
178894 ATCGAGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCCCG
178943 TTATTATCTC
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
78 7 0.07
79 100 0.93
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT
ATCGATTTCTCACA
Found at i:184679 original size:52 final size:51
Alignment explanation
Indices: 184601--184749 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
184591 CGAAATATGA
184601 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
184653 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
184705 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
184750 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:184756 original size:13 final size:13
Alignment explanation
Indices: 184738--184762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
184728 CAAAGATCAG
184738 TGTATCGATACAA
1 TGTATCGATACAA
184751 TGTATCGATACA
1 TGTATCGATACA
184763 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:184844 original size:13 final size:13
Alignment explanation
Indices: 184826--184850 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
184816 AAAAAAAATA
184826 TGTATCGATACAT
1 TGTATCGATACAT
184839 TGTATCGATACA
1 TGTATCGATACA
184851 ACACTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:185823 original size:52 final size:52
Alignment explanation
Indices: 185686--185897 Score: 217
Period size: 52 Copynumber: 4.2 Consensus size: 52
185676 GAAAAGTGAT
* * * * * * *
185686 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGCTGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-G-A
* * *
185740 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
185793 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
* * *
185836 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
185888 AAAGGTGCCA
1 AAAGGTGCCA
185898 TCGACTTGTG
Statistics
Matches: 132, Mismatches: 16, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
43 38 0.29
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 43 0.33
53 6 0.05
54 5 0.04
55 36 0.27
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
Found at i:185854 original size:43 final size:43
Alignment explanation
Indices: 185793--185882 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
185783 TAAAGATGGA
*
185793 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
185836 AAAGGTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
185879 AAAG
1 AAAG
185883 ATGGAAAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:186000 original size:28 final size:28
Alignment explanation
Indices: 185886--186266 Score: 435
Period size: 28 Copynumber: 13.3 Consensus size: 28
185876 CTTAAAGATG
* *
185886 GAAAAGGTGCCA-TCGACTTGTGGGCTTCG
1 GAAAGGGTGCCACT-GACTTGTGGGCTT-T
*
185915 GAAAAGGGTGCCACTGATTTGTGGGCTTT
1 G-AAAGGGTGCCACTGACTTGTGGGCTTT
*
185944 G-AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAGGGTGCCACTGACTTGTGGGC-TTT
*
185972 GAAAGGGTGCCACTAACTTGTGGGCTTT
1 GAAAGGGTGCCACTGACTTGTGGGCTTT
*
186000 GAAAGGGTGCCACTGACTTGTAGGCTTT
1 GAAAGGGTGCCACTGACTTGTGGGCTTT
* * *
186028 GAAAAGAGTGCCACTAATTTGTGGGCTTT
1 G-AAAGGGTGCCACTGACTTGTGGGCTTT
* * *
186057 GAAAAGAGTGCTACTAACTTGTGGGCTTT
1 G-AAAGGGTGCCACTGACTTGTGGGCTTT
*
186086 GAAATGAGTGCCACTGACTTGTGGGCTTT
1 GAAA-GGGTGCCACTGACTTGTGGGCTTT
* * *
186115 GAAAGAGTGCCACTGAATTGTGGGCTTC
1 GAAAGGGTGCCACTGACTTGTGGGCTTT
* * * *
186143 GTAACGGTGCCACTGAATTGTGGGCTTC
1 GAAAGGGTGCCACTGACTTGTGGGCTTT
186171 GAAAGGGTGCCACTGACTTGCGTGGGCTTT
1 GAAAGGGTGCCACTGACTT--GTGGGCTTT
186201 GAAAAGGGTGCCACTGACTTGTGGGCTTT
1 G-AAAGGGTGCCACTGACTTGTGGGCTTT
* * *
186230 GAAAGAGTGCCACTGACTCGTGGACTTTT
1 GAAAGGGTGCCACTGACTTGTGGGC-TTT
186259 G-AAGGGTG
1 GAAAGGGTG
186267 ATGAATGTCT
Statistics
Matches: 312, Mismatches: 30, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
27 21 0.07
28 127 0.41
29 114 0.37
30 31 0.10
31 19 0.06
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
GAAAGGGTGCCACTGACTTGTGGGCTTT
Found at i:186115 original size:115 final size:111
Alignment explanation
Indices: 185888--186252 Score: 459
Period size: 115 Copynumber: 3.2 Consensus size: 111
185878 TAAAGATGGA
*
185888 AAAG-GTGCCA-TCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGCTTTG-AAGGT
1 AAAGAGTGCCACT-GACTTGTGGGCTTC-GAAAA-GGTGCCACTAATTTGTGGGCTTTGAAAGG-
*
185950 TGCCACTGACTTGTGGGCTTTTGAAAGGGTGCCACTAACTTGTGGGCTTTG
62 TGCCACTGACTTGTGGGC-TTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
186001 AAAGGGTGCCACTGACTTGTAGGCTTTGAAAAGAGTGCCACTAATTTGTGGGCTTTGAAAAGAGT
1 AAAGAGTGCCACTGACTTGTGGGCTTCGAAAAG-GTGCCACTAATTTGTGGGCTTTG-AAAG-GT
* * *
186066 GCTACTAACTTGTGGGCTTTGAAATGAGTGCCACTGACTTGTGGGCTTTG
63 GCCACTGACTTGTGGGCTTTGAAA-GGGTGCCACTGACTTGTGGGCTTTG
* * * *
186116 AAAGAGTGCCACTGAATTGTGGGCTTCGTAACGGTGCCACTGAA-TTGTGGGCTTCGAAAGGGTG
1 AAAGAGTGCCACTGACTTGTGGGCTTCGAAAAGGTGCCACT-AATTTGTGGGCTTTGAAA-GGTG
186180 CCACTGACTTGCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTG
64 CCACTGACTT--GTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
*
186231 AAAGAGTGCCACTGACTCGTGG
1 AAAGAGTGCCACTGACTTGTGG
186253 ACTTTTGAAG
Statistics
Matches: 221, Mismatches: 19, Indels: 22
0.84 0.07 0.08
Matches are distributed among these distances:
112 1 0.00
113 45 0.20
114 45 0.20
115 126 0.57
116 4 0.02
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.28
Consensus pattern (111 bp):
AAAGAGTGCCACTGACTTGTGGGCTTCGAAAAGGTGCCACTAATTTGTGGGCTTTGAAAGGTGCC
ACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:187833 original size:13 final size:13
Alignment explanation
Indices: 187815--187839 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
187805 CATAAAATGT
187815 TGTATCGATACAA
1 TGTATCGATACAA
187828 TGTATCGATACA
1 TGTATCGATACA
187840 TATTTTTTTT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:187924 original size:13 final size:13
Alignment explanation
Indices: 187906--187943 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
187896 ATTACTCACA
187906 TGTATCGATACAT
1 TGTATCGATACAT
187919 TGTATCGATACAT
1 TGTATCGATACAT
187932 TGTATCGATACA
1 TGTATCGATACA
187944 CTGATCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:188010 original size:52 final size:52
Alignment explanation
Indices: 187952--188076 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
187942 CACTGATCTT
*
187952 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
188004 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
188056 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
188077 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:191272 original size:6 final size:6
Alignment explanation
Indices: 191261--191332 Score: 75
Period size: 6 Copynumber: 12.8 Consensus size: 6
191251 GACCCCCTTT
*
191261 TTTTTG TTTTTG --TTTG TTTTT- TTATTG TTTTTG --TTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
*
191304 TTTTTTT TTTTTG TTTTTG TTTTT- TTTTT
1 -TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
191333 TTCGTTTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
4 8 0.14
5 9 0.16
6 34 0.61
7 5 0.09
ACGTcount: A:0.01, C:0.00, G:0.12, T:0.86
Consensus pattern (6 bp):
TTTTTG
Found at i:191276 original size:10 final size:10
Alignment explanation
Indices: 191258--191341 Score: 102
Period size: 10 Copynumber: 8.5 Consensus size: 10
191248 CCGGACCCCC
191258 TTTTT-TTTG
1 TTTTTGTTTG
191267 TTTTTGTTTG
1 TTTTTGTTTG
*
191277 TTTTTTTATTG
1 TTTTTGT-TTG
191288 TTTTTGTTTG
1 TTTTTGTTTG
191298 TTTTTGTTT-
1 TTTTTGTTTG
*
191307 TTTTTTTTTG
1 TTTTTGTTTG
191317 TTTTTGTTT-
1 TTTTTGTTTG
*
191326 TTTTTTTTTCG
1 TTTTTGTTT-G
191337 TTTTT
1 TTTTT
191342 TCATTTTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
9 21 0.32
10 30 0.46
11 14 0.22
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.86
Consensus pattern (10 bp):
TTTTTGTTTG
Found at i:191348 original size:19 final size:20
Alignment explanation
Indices: 191267--191351 Score: 97
Period size: 19 Copynumber: 4.3 Consensus size: 20
191257 CTTTTTTTTG
*
191267 TTTTTGTTTGTTTTT-TTAT
1 TTTTTTTTTGTTTTTGTTAT
191286 TGTTTTTGTTTGTTTTTGTT-T
1 T-TTTTT-TTTGTTTTTGTTAT
191307 TTTTTTTTTGTTTTTGTT-T
1 TTTTTTTTTGTTTTTGTTAT
*
191326 TTTTTTTTTCGTTTTT-TCAT
1 TTTTTTTTT-GTTTTTGTTAT
191346 TTTTTT
1 TTTTTT
191352 CATTTTTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
19 24 0.41
20 22 0.37
21 11 0.19
22 2 0.03
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTGTTTTTGTTAT
Found at i:191351 original size:1 final size:1
Alignment explanation
Indices: 191258--191334 Score: 64
Period size: 1 Copynumber: 77.0 Consensus size: 1
191248 CCGGACCCCC
* * * * * * * * * *
191258 TTTTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTGTTTTTGTTTTTTTTTTTTGTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
191323 TTTTTTTTTTTT
1 TTTTTTTTTTTT
191335 CGTTTTTTCA
Statistics
Matches: 56, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.01, C:0.00, G:0.12, T:0.87
Consensus pattern (1 bp):
T
Found at i:191351 original size:21 final size:19
Alignment explanation
Indices: 191258--191341 Score: 98
Period size: 19 Copynumber: 4.3 Consensus size: 19
191248 CCGGACCCCC
191258 TTTTT-TTTGTTTTTGTTTG
1 TTTTTGTTT-TTTTTGTTTG
*
191277 TTTTTTTATTGTTTTTGTTTG
1 TTTTTGT-TT-TTTTTGTTTG
*
191298 TTTTTGTTTTTTTTTTTTG
1 TTTTTGTTTTTTTTGTTTG
*
191317 TTTTTGTTTTTTTTTTTTCG
1 TTTTTGTTTTTTTTGTTT-G
191337 TTTTT
1 TTTTT
191342 TCATTTTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
19 32 0.53
20 9 0.15
21 19 0.32
ACGTcount: A:0.01, C:0.01, G:0.12, T:0.86
Consensus pattern (19 bp):
TTTTTGTTTTTTTTGTTTG
Found at i:191361 original size:10 final size:9
Alignment explanation
Indices: 191328--191360 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
191318 TTTTGTTTTT
191328 TTTTTTTC-
1 TTTTTTTCA
*
191336 GTTTTTTCA
1 TTTTTTTCA
191345 TTTTTTTCA
1 TTTTTTTCA
191354 TTTTTTT
1 TTTTTTT
191361 TGGAGGACGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.82
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:195700 original size:52 final size:52
Alignment explanation
Indices: 195622--195804 Score: 303
Period size: 52 Copynumber: 3.5 Consensus size: 52
195612 CCCAAAATAT
* *
195622 GAAAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTGTATAATGTATCGATACATCTGG
* *
195674 GAAAATTTTCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTGTATAATGTATCGATACATCTGG
* *
195726 GCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTGTATAATGTATCGATACATCTGG
*
195778 GCAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
195805 AAGATCAGTG
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTGTATAATGTATCGATACATCTGG
Found at i:195831 original size:13 final size:13
Alignment explanation
Indices: 195813--195837 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
195803 CAAAGATCAG
195813 TGTATCGATACAA
1 TGTATCGATACAA
195826 TGTATCGATACA
1 TGTATCGATACA
195838 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:195919 original size:13 final size:13
Alignment explanation
Indices: 195901--195925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
195891 AAAAAAAATA
195901 TGTATCGATACAT
1 TGTATCGATACAT
195914 TGTATCGATACA
1 TGTATCGATACA
195926 ACACTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:197777 original size:33 final size:33
Alignment explanation
Indices: 197739--197805 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 33
197729 GTTACAAGCT
197739 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
*
197772 ATGTATCGATGCATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
197805 A
1 A
197806 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:197874 original size:13 final size:13
Alignment explanation
Indices: 197856--197881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
197846 CAATTTGTCC
197856 ATGTATCGATACA
1 ATGTATCGATACA
197869 ATGTATCGATACA
1 ATGTATCGATACA
197882 TTATACCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:197892 original size:20 final size:20
Alignment explanation
Indices: 197864--197901 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
197854 CCATGTATCG
*
197864 ATACAATGTATCGATACATT
1 ATACAATGTATCAATACATT
*
197884 ATACCATGTATCAATACA
1 ATACAATGTATCAATACA
197902 AATAGTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (20 bp):
ATACAATGTATCAATACATT
Found at i:197901 original size:33 final size:34
Alignment explanation
Indices: 197835--197902 Score: 95
Period size: 33 Copynumber: 2.0 Consensus size: 34
197825 TGCCAATTTC
* *
197835 ATGTATCGATACAATTTGTCCATGTATCGATACA
1 ATGTATCGATACAATTTGACCATGTATCAATACA
197869 ATGTATCGATAC-ATTAT-ACCATGTATCAATACA
1 ATGTATCGATACAATT-TGACCATGTATCAATACA
197902 A
1 A
197903 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
33 18 0.58
34 13 0.42
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (34 bp):
ATGTATCGATACAATTTGACCATGTATCAATACA
Found at i:197904 original size:97 final size:97
Alignment explanation
Indices: 197739--197963 Score: 389
Period size: 97 Copynumber: 2.3 Consensus size: 97
197729 GTTACAAGCT
* * * * *
197739 ATGTATCGATAC-ATTTCTTCATGTATCGATACAATGTATCGATGCATTGTACCATGTATCGATA
1 ATGTATCGATACAATTTGTCCATGTATCGATACAATGTATCGATACATTATACCATGTATCAATA
197803 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
66 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
197835 ATGTATCGATACAATTTGTCCATGTATCGATACAATGTATCGATACATTATACCATGTATCAATA
1 ATGTATCGATACAATTTGTCCATGTATCGATACAATGTATCGATACATTATACCATGTATCAATA
197900 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
66 CAAATAGTGATAGGGTAGCTACTGCCAATTTC
*
197932 ATGTATCGATACAATTTGTCCATGTATTGATA
1 ATGTATCGATACAATTTGTCCATGTATCGATA
197964 TATTAAACAT
Statistics
Matches: 122, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
96 12 0.10
97 110 0.90
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (97 bp):
ATGTATCGATACAATTTGTCCATGTATCGATACAATGTATCGATACATTATACCATGTATCAATA
CAAATAGTGATAGGGTAGCTACTGCCAATTTC
Found at i:197990 original size:13 final size:13
Alignment explanation
Indices: 197972--197998 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
197962 TATATTAAAC
197972 ATGTATCGATACA
1 ATGTATCGATACA
197985 ATGTATCGATACA
1 ATGTATCGATACA
197998 A
1 A
197999 GGCAGCAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:199716 original size:166 final size:163
Alignment explanation
Indices: 199361--199842 Score: 492
Period size: 165 Copynumber: 2.9 Consensus size: 163
199351 AATGTATACA
* * * ** * * *
199361 AAAAATACAAAATTCATG-AAATAAATTGAATTTTTCAAAACTAATTTAAT-TGGAGTTTAATGA
1 AAAAATAAAAAACTCATGAAAATAAA-TAAATTTTTCAAAACCGATTAAATAT-GA-TTAAATAA
* * * *
199424 CAATATTAGATGAATTTTAAAAATTTTAAACCGAGAAAAAT-CTCT--AAAAAACCTTTATGGAA
63 TAATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCCTCTCGAAAAAA--TTTATGGAA
* * * *
199486 TAGAAAATTCAGTTTTTCAAAAATAAGGGCATTTTCAAGG
126 TAGAAAACTCA-TTTTTCGAAAAT-AGGGAAATTTCAAGG
* * * *
199526 AAAAATAAAAAACTCATGAAAATAAAT-GATTTTCTTAAAACCGATTTAATATGAATTAAATGAT
1 AAAAATAAAAAACTCATGAAAATAAATAAATTTT-TCAAAACCGATTAAATATG-ATTAAATAAT
* * * *
199590 GATATTTGATAAATTTTAAAAATTATAAACCAAGAAAAATCCTTTCGAAAAATTTTATGGAATAG
64 AATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCCTCTCGAAAAAATTTATGGAATAG
199655 AAAACTCGATTTTTCGAAAATAGGGAAATTTCAAGG
129 AAAACTC-ATTTTTCGAAAATAGGGAAATTTCAAGG
* * * *
199691 AAAAAATGAAAAACTCATGAAAATAAGTAAATTTTTCAAAACTGATTAAATGTGATTAAATAATA
1 -AAAAATAAAAAACTCATGAAAATAAATAAATTTTTCAAAACCGATTAAATATGATTAAATAATA
* * * * *
199756 ATATTTTATGAATTTTAAAATTTATAAACTAAGAAAAATCCACCCGAAAAAATTTATGGAGA-AG
65 ATATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCCTCTCGAAAAAATTTATGGA-ATAG
*
199820 AAAACTCCATATTTCGAAAATAG
129 AAAACT-CATTTTTCGAAAATAG
199843 TTAGAATTCC
Statistics
Matches: 268, Mismatches: 37, Indels: 24
0.81 0.11 0.07
Matches are distributed among these distances:
164 5 0.02
165 169 0.63
166 83 0.31
167 6 0.02
168 5 0.02
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (163 bp):
AAAAATAAAAAACTCATGAAAATAAATAAATTTTTCAAAACCGATTAAATATGATTAAATAATAA
TATTTGATGAATTTTAAAAATTATAAACCAAGAAAAATCCTCTCGAAAAAATTTATGGAATAGAA
AACTCATTTTTCGAAAATAGGGAAATTTCAAGG
Found at i:199891 original size:165 final size:164
Alignment explanation
Indices: 199389--199927 Score: 441
Period size: 165 Copynumber: 3.3 Consensus size: 164
199379 AAATAAATTG
* * * * * * *
199389 AATTTTTCAAAACTAATTTAAT-TGGAGTTTAATGACAATATTAGATGAATTTTAAAAATTTTAA
1 AATTTTTCAAAACTGATTTAATAT-GA-TTAAATAATAATATTTGATAAATTTTAAAAATTATAA
* * * * * *
199453 ACCGAGAAAAAT---CTCTAAAAAACCTTTATGGAATAGAAAA-TTCAGTTTTTCAAAAATAAGG
64 ACCAAGAAAAATCCACCCGAAAAAA--TTTATGGAATAGAAAACTCCA-TATTTCGAAAAT-AGG
* * * * * * *
199514 GCATTTTCAAGGAAAAATAAAAAACTCATGAAAATAAAT-
125 GAAATTCCAAGAAAAAATCAAAAACGCATGAAAATAAGTA
* * * * *
199553 GATTTTCTTAAAACCGATTTAATATGAATTAAATGATGATATTTGATAAATTTTAAAAATTATAA
1 AATTTT-TCAAAACTGATTTAATATG-ATTAAATAATAATATTTGATAAATTTTAAAAATTATAA
*** * * *
199618 ACCAAGAAAAATCCTTTCGAAAAATTTTATGGAATAGAAAACTCGATTTTTCGAAAATAGGGAAA
64 ACCAAGAAAAATCCACCCGAAAAAATTTATGGAATAGAAAACTCCATATTTCGAAAATAGGGAAA
* * *
199683 TTTCAAGGAAAAAATGAAAAACTCATGAAAATAAGTA
129 TTCCAA-GAAAAAATCAAAAACGCATGAAAATAAGTA
* * * * *
199720 AATTTTTCAAAACTGATTAAATGTGATTAAATAATAATATTTTATGAATTTTAAAATTTATAAAC
1 AATTTTTCAAAACTGATTTAATATGATTAAATAATAATATTTGATAAATTTTAAAAATTATAAAC
* **
199785 TAAGAAAAATCCACCCGAAAAAATTTATGGAGA-AGAAAACTCCATATTTCGAAAATAGTTAGAA
66 CAAGAAAAATCCACCCGAAAAAATTTATGGA-ATAGAAAACTCCATATTTCGAAAATAGGGA-AA
* * *
199849 TTCCAA-AAGAAAATCAATAACGCAT-ACAATCGAAG-G
129 TTCCAAGAA-AAAATCAAAAACGCATGAAAAT--AAGTA
* **
199885 AATTTTTCAAAATTGATTTAATAAAAATTAAATAATAATATTT
1 AATTTTTCAAAACTGATTTAAT-ATGATTAAATAATAATATTT
199928 AAAGAGTTTT
Statistics
Matches: 308, Mismatches: 52, Indels: 28
0.79 0.13 0.07
Matches are distributed among these distances:
164 11 0.04
165 185 0.60
166 98 0.32
167 7 0.02
168 7 0.02
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (164 bp):
AATTTTTCAAAACTGATTTAATATGATTAAATAATAATATTTGATAAATTTTAAAAATTATAAAC
CAAGAAAAATCCACCCGAAAAAATTTATGGAATAGAAAACTCCATATTTCGAAAATAGGGAAATT
CCAAGAAAAAATCAAAAACGCATGAAAATAAGTA
Found at i:202748 original size:22 final size:22
Alignment explanation
Indices: 202690--202766 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
202680 AATGCATATT
202690 TTGTTATAGTGATATATACATA
1 TTGTTATAGTGATATATACATA
*
202712 TAGTTATAGTGATATATACATA
1 TTGTTATAGTGATATATACATA
* * * *
202734 TTGTTATAATAATATGTCCATA
1 TTGTTATAGTGATATATACATA
*
202756 TTGTTACAGTG
1 TTGTTATAGTG
202767 CTATGTACGT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (22 bp):
TTGTTATAGTGATATATACATA
Found at i:203261 original size:22 final size:22
Alignment explanation
Indices: 203214--203262 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
203204 AATTATTATG
** *
203214 ATATGTACATTATGTTATTATG
1 ATATGTACATTATGTTACAATC
203236 ATATGTACATGT-TGTTACAATC
1 ATATGTACAT-TATGTTACAATC
203258 ATATG
1 ATATG
203263 GAATATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (22 bp):
ATATGTACATTATGTTACAATC
Found at i:205160 original size:21 final size:21
Alignment explanation
Indices: 205134--205175 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
205124 AAACCAATTC
205134 TTCACTGAA-GAAACCAACCCT
1 TTCACT-AACGAAACCAACCCT
*
205155 TTCACTAACGAAACTAACCCT
1 TTCACTAACGAAACCAACCCT
205176 ACACAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.38, C:0.33, G:0.07, T:0.21
Consensus pattern (21 bp):
TTCACTAACGAAACCAACCCT
Found at i:209393 original size:16 final size:16
Alignment explanation
Indices: 209368--209406 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
209358 CTCAGGGAGA
*
209368 AGAT-AGGGTGGTTGG
1 AGATAAGGGTGGCTGG
209383 AGATAAGGGTGGCTGG
1 AGATAAGGGTGGCTGG
209399 AGATAAGG
1 AGATAAGG
209407 TTTGGCAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.28, C:0.03, G:0.49, T:0.21
Consensus pattern (16 bp):
AGATAAGGGTGGCTGG
Found at i:209710 original size:13 final size:13
Alignment explanation
Indices: 209692--209717 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
209682 ACAAAGATCC
209692 ATGTATCGATACA
1 ATGTATCGATACA
209705 ATGTATCGATACA
1 ATGTATCGATACA
209718 TTGAGTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:210741 original size:26 final size:26
Alignment explanation
Indices: 210701--210757 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 26
210691 TTTCACATAT
210701 ATTATTATATAAT-AATATA-TA-AA
1 ATTATTATATAATAAATATATTACAA
210724 ATTATTATACTTACATAAATATATTACAA
1 ATTATTATA--TA-ATAAATATATTACAA
210753 ATTAT
1 ATTAT
210758 ATAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 9 0.32
25 2 0.07
26 2 0.07
27 6 0.21
28 2 0.07
29 7 0.25
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTATTATATAATAAATATATTACAA
Found at i:210834 original size:21 final size:20
Alignment explanation
Indices: 210796--210838 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
210786 TTATCAATAA
*
210796 ATATTATAATTACTTAAATT
1 ATATTATAATTACATAAATT
*
210816 ATATTATCTATTACATAAATT
1 ATATTAT-AATTACATAAATT
210837 AT
1 AT
210839 TATGATTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTATAATTACATAAATT
Found at i:211058 original size:20 final size:21
Alignment explanation
Indices: 211021--211060 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
211011 AATATAAAAG
211021 TTACATAAATTATATTATCAA
1 TTACATAAATTATATTATCAA
*
211042 TTACATAAGTT-TATTATCA
1 TTACATAAATTATATTATCA
211061 TATGTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (21 bp):
TTACATAAATTATATTATCAA
Found at i:211467 original size:5 final size:5
Alignment explanation
Indices: 211457--211514 Score: 50
Period size: 5 Copynumber: 11.6 Consensus size: 5
211447 GTAAAAAATT
*
211457 TTATA TTATA TTAT- TT-TA TTAATA TTATA TTATTA TTA-A TAATAA
1 TTATA TTATA TTATA TTATA TT-ATA TTATA TTA-TA TTATA TTAT-A
*
211502 ATATA TTATA TTA
1 TTATA TTATA TTA
211515 ATAAAAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
3 1 0.02
4 7 0.16
5 23 0.53
6 12 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:211483 original size:19 final size:20
Alignment explanation
Indices: 211459--211518 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
211449 AAAAAATTTT
*
211459 ATATTATATTATT-TTATTA
1 ATATTATATTATTATTAATA
211478 ATATTATATTATTATTAATA
1 ATATTATATTATTATTAATA
*
211498 ATAAATATATTA-TATTAATA
1 AT-ATTATATTATTATTAATA
211518 A
1 A
211519 AAATAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 13 0.35
20 16 0.43
21 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTATATTATTATTAATA
Found at i:211516 original size:17 final size:18
Alignment explanation
Indices: 211464--211519 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
211454 ATTTTATATT
* *
211464 ATATTATTTTATTAATATT
1 ATATTATTATATTAATA-A
*
211483 ATATTATTATTAATAATAA
1 ATATTATTA-TATTAATAA
211502 ATA-TATTATATTAATAA
1 ATATTATTATATTAATAA
211519 A
1 A
211520 AATAAATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 9 0.28
18 5 0.16
19 11 0.34
20 7 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTATTATATTAATAA
Found at i:212223 original size:21 final size:20
Alignment explanation
Indices: 212161--212224 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
212151 TTTATGTGTA
*
212161 ACAAATTACATAAAAACATT
1 ACAAGTTACATAAAAACATT
* * *
212181 AGCAAGTTACGTATAAATATT
1 A-CAAGTTACATAAAAACATT
*
212202 ACAGAGTTACTTAAAAACATT
1 ACA-AGTTACATAAAAACATT
212223 AC
1 AC
212225 CGCAACTATA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
20 3 0.09
21 32 0.91
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.28
Consensus pattern (20 bp):
ACAAGTTACATAAAAACATT
Found at i:212582 original size:18 final size:20
Alignment explanation
Indices: 212559--212600 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
212549 TTTTATTAAA
212559 ATATTAAAATTT-TAT-TTT
1 ATATTAAAATTTATATATTT
*
212577 ATATTAATATTTATATATTT
1 ATATTAAAATTTATATATTT
212597 ATAT
1 ATAT
212601 AATAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
19 3 0.14
20 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTAAAATTTATATATTT
Found at i:212613 original size:17 final size:18
Alignment explanation
Indices: 212589--212624 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
212579 ATTAATATTT
212589 ATATATTTATATAATAAAA
1 ATAT-TTTATATAATAAAA
*
212608 ATATTTTTTATAATAAA
1 ATATTTTATATAATAAA
212625 TAGTGATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTTTATATAATAAAA
Found at i:216035 original size:5 final size:5
Alignment explanation
Indices: 216025--216073 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
216015 TACCATGTTA
* * * *
216025 TATTG TATTG TATTG TATTG TATTG CATTA TATTA TATTA TATATG TAT
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TAT-TG TAT
216074 ACTACATTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
5 35 0.90
6 4 0.10
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (5 bp):
TATTG
Found at i:216040 original size:10 final size:10
Alignment explanation
Indices: 216022--216073 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
216012 ATGTACCATG
216022 TTATATTGTA
1 TTATATTGTA
*
216032 TTGTATTGTA
1 TTATATTGTA
* *
216042 TTGTATTGCA
1 TTATATTGTA
*
216052 TTATATTATA
1 TTATATTGTA
216062 TTATATATGTA
1 TTATAT-TGTA
216073 T
1 T
216074 ACTACATTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.58
Consensus pattern (10 bp):
TTATATTGTA
Found at i:224533 original size:14 final size:14
Alignment explanation
Indices: 224514--224543 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
224504 ACCATGAGGG
224514 AAGTCAATCTATCC
1 AAGTCAATCTATCC
224528 AAGTCAATCTATCC
1 AAGTCAATCTATCC
224542 AA
1 AA
224544 AAATGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (14 bp):
AAGTCAATCTATCC
Found at i:230024 original size:65 final size:65
Alignment explanation
Indices: 229920--230049 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
229910 TAGAAAAAAA
229920 CCTAGGGAATGCACTAAGCATCCATTATACCCCTTATCACATTTTTTATCTTTTGAGAAATTTTC
1 CCTAGGGAATGCACTAAGCATCCATTATACCCCTTATCACATTTTTTATCTTTTGAGAAATTTTC
229985 CCTAGGGAATGCACTAAGCATCCATTATACCCCTTATCACATTTTTTATCTTTTGAGAAATTTTC
1 CCTAGGGAATGCACTAAGCATCCATTATACCCCTTATCACATTTTTTATCTTTTGAGAAATTTTC
230050 TCCATCACAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (65 bp):
CCTAGGGAATGCACTAAGCATCCATTATACCCCTTATCACATTTTTTATCTTTTGAGAAATTTTC
Found at i:236971 original size:16 final size:16
Alignment explanation
Indices: 236950--237012 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
236940 ACTTAATTTA
236950 AGTTCGGATCATTTTG
1 AGTTCGGATCATTTTG
*
236966 AGTTC-GAGTCATTTCG
1 AGTTCGGA-TCATTTTG
*
236982 AGTTTAGG-TCATTTTG
1 AG-TTCGGATCATTTTG
* *
236998 GGTTCGGGTCATTTT
1 AGTTCGGATCATTTT
237013 CAGATTTGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
15 6 0.16
16 29 0.76
17 2 0.05
18 1 0.03
ACGTcount: A:0.16, C:0.13, G:0.27, T:0.44
Consensus pattern (16 bp):
AGTTCGGATCATTTTG
Found at i:240933 original size:13 final size:13
Alignment explanation
Indices: 240915--240941 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
240905 ACATTATGCT
240915 TTGTATCGATACA
1 TTGTATCGATACA
240928 TTGTATCGATACA
1 TTGTATCGATACA
240941 T
1 T
240942 GAAACTAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:242613 original size:9 final size:9
Alignment explanation
Indices: 242595--242629 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
242585 AGTCAACCAT
242595 TAATGATGA
1 TAATGATGA
242604 TGAA-GATGA
1 T-AATGATGA
242613 TAATGATGA
1 TAATGATGA
242622 TAATGATG
1 TAATGATG
242630 GTAACTCGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 2 0.08
9 20 0.83
10 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (9 bp):
TAATGATGA
Found at i:243269 original size:20 final size:21
Alignment explanation
Indices: 243228--243270 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
243218 TATTAAAAAG
243228 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAATGAA
243249 TTAGCTAA-GAAAAATAA-GAA
1 TTAGCTAATG-AAAATAATGAA
243269 TT
1 TT
243271 TACATGATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (21 bp):
TTAGCTAATGAAAATAATGAA
Found at i:243420 original size:46 final size:46
Alignment explanation
Indices: 243368--243461 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
243358 GTTTAGGATA
243368 CAATGCCTTCGAGAAAGAAACAAAATTTAAAAATTTCTTTGTTAAG
1 CAATGCCTTCGAGAAAGAAACAAAATTTAAAAATTTCTTTGTTAAG
*
243414 CAATGCCTTTGAGAAAGAAACAAAATTTAAAAATTTCTTTGTTAAG
1 CAATGCCTTCGAGAAAGAAACAAAATTTAAAAATTTCTTTGTTAAG
243460 CA
1 CA
243462 TAATCCACAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (46 bp):
CAATGCCTTCGAGAAAGAAACAAAATTTAAAAATTTCTTTGTTAAG
Found at i:247061 original size:21 final size:21
Alignment explanation
Indices: 247028--247072 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
247018 TTGCAAGTTG
*
247028 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
247050 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
247070 AAA
1 AAA
247073 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:250988 original size:13 final size:13
Alignment explanation
Indices: 250970--251008 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
250960 ACATTTTTCT
250970 TTGTATCGATACA
1 TTGTATCGATACA
250983 TTGTATCGATACA
1 TTGTATCGATACA
250996 TTGTATCGATACA
1 TTGTATCGATACA
251009 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:251817 original size:13 final size:13
Alignment explanation
Indices: 251799--251824 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
251789 CAATTTTTTG
251799 TGTATCGATACAT
1 TGTATCGATACAT
251812 TGTATCGATACAT
1 TGTATCGATACAT
251825 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:252573 original size:21 final size:21
Alignment explanation
Indices: 252532--252575 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
252522 CTCCCCTTTA
* *
252532 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
252553 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
252574 TC
1 TC
252576 ATATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:252595 original size:25 final size:25
Alignment explanation
Indices: 252567--252616 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
252557 CCCCTTAATC
252567 AAGTAATTCATATAAAAAATTTATT
1 AAGTAATTCATATAAAAAATTTATT
*
252592 AAGTAATTCATATCAAAAATTTATT
1 AAGTAATTCATATAAAAAATTTATT
252617 TGCACATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (25 bp):
AAGTAATTCATATAAAAAATTTATT
Found at i:254423 original size:13 final size:13
Alignment explanation
Indices: 254405--254429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
254395 ATAATCACCC
254405 TGTATCGATACAA
1 TGTATCGATACAA
254418 TGTATCGATACA
1 TGTATCGATACA
254430 TTGAATTTCC
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:256507 original size:15 final size:15
Alignment explanation
Indices: 256487--256517 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
256477 ATTTCGTTTG
*
256487 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
256502 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
256517 G
1 G
256518 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:258349 original size:21 final size:21
Alignment explanation
Indices: 258320--258364 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
258310 AAGTTTTCAT
*
258320 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
258340 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
258362 TTT
1 TTT
258365 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:260595 original size:13 final size:13
Alignment explanation
Indices: 260577--260602 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
260567 CAATTTTTTG
260577 TGTATCGATACAT
1 TGTATCGATACAT
260590 TGTATCGATACAT
1 TGTATCGATACAT
260603 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:261109 original size:20 final size:20
Alignment explanation
Indices: 261066--261111 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
261056 AAATCTTTTG
261066 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
261087 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
261107 CAAAA
1 CAAAA
261112 CCAGCATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:263265 original size:20 final size:19
Alignment explanation
Indices: 263219--263274 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
263209 TTTTGTACCA
**
263219 AATGTATCGATACACAATTC
1 AATGTATCGATACA-TGTTC
*
263239 AAAGTATCGATACATGTTGC
1 AATGTATCGATACATGTT-C
263259 AATGTATCGATACATG
1 AATGTATCGATACATG
263275 AAAAAGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (19 bp):
AATGTATCGATACATGTTC
Found at i:263351 original size:13 final size:13
Alignment explanation
Indices: 263333--263358 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
263323 TACAGCAAGT
263333 ATGTATCGATACA
1 ATGTATCGATACA
263346 ATGTATCGATACA
1 ATGTATCGATACA
263359 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:265606 original size:21 final size:21
Alignment explanation
Indices: 265573--265617 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
265563 TTGCAAGTTG
*
265573 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
265595 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
265615 AAA
1 AAA
265618 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:268656 original size:13 final size:13
Alignment explanation
Indices: 268638--268664 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
268628 ACAACATTCC
268638 TTGTATCGATACA
1 TTGTATCGATACA
268651 TTGTATCGATACA
1 TTGTATCGATACA
268664 T
1 T
268665 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:270663 original size:79 final size:78
Alignment explanation
Indices: 270496--270699 Score: 214
Period size: 79 Copynumber: 2.6 Consensus size: 78
270486 GAGATAATAA
* * * ** * *
270496 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTTTGAGAAATCGATGA
1 CGGGGTTGGAGTGTCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
*
270561 TTAGAAAGAAAAAT
66 TTAG-AAGAAAAAC
** *
270575 CGGAATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
1 CGGGGTTGGAGTGTCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
* *
270639 TTTTG-GGAATAAAGC
66 -TTAGAAGAA-AAA-C
* **
270654 CGGGGTTGGAGTGTCCCCTCGGAGGTAACGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTGTCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
270700 GATGAAATAA
Statistics
Matches: 103, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
77 3 0.03
78 4 0.04
79 96 0.93
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTGTCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
TTAGAAGAAAAAC
Found at i:270775 original size:53 final size:53
Alignment explanation
Indices: 270714--270837 Score: 146
Period size: 53 Copynumber: 2.4 Consensus size: 53
270704 AAATAACGAG
* * ** *
270714 GTTGGAGTATCCTCGATTGTGAA-AAAATTGGTGTTTTCGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTAAAGAAAATTGGTGTTTT-AAAAATAAAATCGAA
270767 GTTGGAGTATCCCCGA-T-TAAAGGAAAATTGGTGTTTTAAAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTGTAAA-GAAAATTGGTGTTTTAAAAATAAAATCGAA
* *
270819 GATGGAATATCCCCGATTG
1 GTTGGAGTATCCCCGATTG
270838 CAGAGAATTG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
51 3 0.05
52 27 0.45
53 30 0.50
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTGTAAAGAAAATTGGTGTTTTAAAAATAAAATCGAA
Found at i:270832 original size:52 final size:53
Alignment explanation
Indices: 270737--270836 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 53
270727 CGATTGTGAA
** * * *
270737 AAAATTGGTGTTTTCGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG
1 AAAATTGGTGTTTTCAAAAATAAAATCGAAGATGGAATATCCCCGATTAAAGG
270790 AAAATTGGTGTTTT-AAAAATAAAATCGAAGATGGAATATCCCCGATT
1 AAAATTGGTGTTTTCAAAAATAAAATCGAAGATGGAATATCCCCGATT
270837 GCAGAGAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 28 0.67
53 14 0.33
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (53 bp):
AAAATTGGTGTTTTCAAAAATAAAATCGAAGATGGAATATCCCCGATTAAAGG
Found at i:273212 original size:13 final size:13
Alignment explanation
Indices: 273194--273219 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
273184 ACAAAGATCC
273194 ATGTATCGATACA
1 ATGTATCGATACA
273207 ATGTATCGATACA
1 ATGTATCGATACA
273220 CAGAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:273232 original size:33 final size:33
Alignment explanation
Indices: 273173--273237 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
273163 AAAATTTCCA
**
273173 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGATAAATGTATCGATAC
*
273206 AATGTATCGATACACAGA-AAATTGTATCGATA
1 AATGTATCGATACAAAGATAAA-TGTATCGATA
273238 TATTTCCTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (33 bp):
AATGTATCGATACAAAGATAAATGTATCGATAC
Found at i:273283 original size:19 final size:18
Alignment explanation
Indices: 273259--273358 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
273249 CAGTAGCTAA
273259 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
273278 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
273293 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
273310 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
273325 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
273342 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
273359 TTGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:273299 original size:13 final size:13
Alignment explanation
Indices: 273281--273337 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
273271 ACAATACTTA
273281 TGTATCGATACAT
1 TGTATCGATACAT
273294 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
273312 ATGTATCGATACAT
1 -TGTATCGATACAT
273326 TGTATCGATACA
1 TGTATCGATACA
273338 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:273303 original size:32 final size:32
Alignment explanation
Indices: 273262--273356 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
273252 TAGCTAATTA
*
273262 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
273294 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
273326 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
273357 AATTGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:273419 original size:21 final size:22
Alignment explanation
Indices: 273393--273450 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
273383 GTTGGGACCC
**
273393 TGTATCGATACATTTGTA-GGA
1 TGTATCGATACATTTGTACAAA
*
273414 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTACAAA
273435 TGTATCGATACATTTG
1 TGTATCGATACATTTG
273451 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 4 0.13
21 25 0.81
22 2 0.06
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (22 bp):
TGTATCGATACATTTGTACAAA
Found at i:273707 original size:30 final size:30
Alignment explanation
Indices: 273540--273753 Score: 215
Period size: 28 Copynumber: 7.2 Consensus size: 30
273530 AAAAAAGCAT
** *
273540 TTTCAAAGCCCACACAAGTCAGTAGCACTCC
1 TTTCAAAGCCCATGCAAGTCAGTGGCAC-CC
* * * * *
273571 TTTTAAAGCTCACGCAAGTCAGTGGTACCT
1 TTTCAAAGCCCATGCAAGTCAGTGGCACCC
*
273601 TTTCAAAGCCCA--CAAGTCAGTGGCACTC
1 TTTCAAAGCCCATGCAAGTCAGTGGCACCC
*
273629 TTTCAAAGCCCA--CAAGTCAGTGGCATCC
1 TTTCAAAGCCCATGCAAGTCAGTGGCACCC
* **
273657 TTTCAAAGCCCATG--AGTTAGTGGCATTC
1 TTTCAAAGCCCATGCAAGTCAGTGGCACCC
*
273685 TTTCAAAGCCCATGCAAGTTAGTGGCACCC
1 TTTCAAAGCCCATGCAAGTCAGTGGCACCC
* *
273715 TTTTAAAGCCCATGCAAGTCAATGGCAACCC
1 TTTCAAAGCCCATGCAAGTCAGTGGC-ACCC
273746 TTTTCAAA
1 -TTTCAAA
273754 TCACCACTGT
Statistics
Matches: 156, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
28 77 0.49
30 46 0.29
31 27 0.17
32 6 0.04
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (30 bp):
TTTCAAAGCCCATGCAAGTCAGTGGCACCC
Found at i:274295 original size:20 final size:20
Alignment explanation
Indices: 274267--274341 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
274257 TCATACCCTG
274267 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
274287 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
274307 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
274327 ATGTATCGATACATT
1 ATGTATCGATACATT
274342 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:274334 original size:40 final size:39
Alignment explanation
Indices: 274267--274344 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
274257 TCATACCCTG
* *
274267 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
274307 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
274345 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:286094 original size:15 final size:16
Alignment explanation
Indices: 286074--286103 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
286064 TTTGTCAAAC
286074 CCGCCAGTG-TTGGTA
1 CCGCCAGTGCTTGGTA
286089 CCGCCAGTGCTTGGT
1 CCGCCAGTGCTTGGT
286104 CGTCCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.30, G:0.33, T:0.27
Consensus pattern (16 bp):
CCGCCAGTGCTTGGTA
Found at i:288331 original size:10 final size:10
Alignment explanation
Indices: 288316--288378 Score: 56
Period size: 10 Copynumber: 5.7 Consensus size: 10
288306 CCTTTACACC
288316 CAAAAAAAAA
1 CAAAAAAAAA
288326 CAAAAAAAAAA
1 C-AAAAAAAAA
288337 CAAAACAAAAAAA
1 C--AA-AAAAAAA
288350 CAAAAAAAAA
1 CAAAAAAAAA
288360 -AGAAAAAAATA
1 CA-AAAAAAA-A
288371 GCAAAAAA
1 -CAAAAAA
288379 TAGAAGGGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.02
10 15 0.33
11 13 0.28
12 8 0.17
13 9 0.20
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.02
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:288333 original size:11 final size:11
Alignment explanation
Indices: 288317--288378 Score: 79
Period size: 11 Copynumber: 5.5 Consensus size: 11
288307 CTTTACACCC
288317 AAAAAAAAACA
1 AAAAAAAAACA
288328 AAAAAAAAACAA
1 AAAAAAAAAC-A
288340 AACAAAAAAACA
1 AA-AAAAAAACA
*
288352 AAAAAAAAAGA
1 AAAAAAAAACA
* *
288363 AAAAAATAGCA
1 AAAAAAAAACA
288374 AAAAA
1 AAAAA
288379 TAGAAGGGTC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
11 31 0.69
12 6 0.13
13 8 0.18
ACGTcount: A:0.87, C:0.08, G:0.03, T:0.02
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:288346 original size:24 final size:24
Alignment explanation
Indices: 288319--288365 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
288309 TTACACCCAA
288319 AAAAAAACAAAAAAAAAACAAAAC
1 AAAAAAACAAAAAAAAAACAAAAC
*
288343 AAAAAAACAAAAAAAAAAGAAAA
1 AAAAAAACAAAAAAAAAACAAAA
288366 AAATAGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (24 bp):
AAAAAAACAAAAAAAAAACAAAAC
Found at i:288378 original size:1 final size:1
Alignment explanation
Indices: 288317--288368 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
288307 CTTTACACCC
* * * * *
288317 AAAAAAAAACAAAAAAAAAACAAAACAAAAAAACAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
288369 TAGCAAAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.90, C:0.08, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:289641 original size:29 final size:29
Alignment explanation
Indices: 289599--291116 Score: 2222
Period size: 29 Copynumber: 52.9 Consensus size: 29
289589 AATGTTCATC
289599 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
289628 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
289657 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
289685 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
289713 CCTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
289741 CCTTTCAAAGACCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
289770 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
289798 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
289827 CCTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
289855 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
289884 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
289913 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
289942 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
289970 CCTTTCAAAGCCCACAACTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
289998 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
290027 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
290056 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
290085 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
290113 CCTTTCAAAGCCCAAAAGTCAGTGGCATT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
290142 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
290171 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
290200 CCTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
290229 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
290257 CCTTTTAAAACCCATAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
290285 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
290314 CATTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
** * *
290343 TTTTTCAAAGCCCACAAGTTAGTGGTAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
290371 CCTTTCAAAGCCCACAACTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
290399 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
290428 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
290457 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
290486 CTTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
290514 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
290543 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
290572 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
290601 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
290630 CTTTTCAAAGCTCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
290658 CCTTTCAAAGCTCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
290687 CCTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
290716 CTTTTCAAAGCCCACAAATCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
290745 CTTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
290773 CCTTTCAACGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
290801 CCTTTCAGAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
290829 CCTTTCGAAGCCCACAAGTTAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
290857 CATTACGAAGCCCACAATTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
290886 -CTTTCAAAGCCCACAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
290913 CCTTTTAAAGCCCACACAAGTCAGTAGCACT
1 CCTTTCAAAG-CC-CACAAGTCAGTGGCACT
* * * *
290944 CCTTTTAAAGCTCACGCAAGTTAGTGGTAC-
1 CCTTTCAAAGC-C-CACAAGTCAGTGGCACT
*
290974 CTTTTCAAAGCCCACAAGTCAGTGGCACT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
291003 -CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
* *
291030 CCTTTCAAAGCCCACGAGTTAGTGGCA-T
1 CCTTTCAAAGCCCACAAGTCAGTGGCACT
*
291058 TCTTTCAAAGCCCATGCAAGTCAGTGGCAC-
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCACT
* *
291088 CCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CCTTTCAAAGCCCA--CAAGTCAGTGGCA
291117 ACCCTTTTCA
Statistics
Matches: 1362, Mismatches: 107, Indels: 39
0.90 0.07 0.03
Matches are distributed among these distances:
27 1 0.00
28 568 0.42
29 707 0.52
30 62 0.05
31 24 0.02
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (29 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:289889 original size:86 final size:86
Alignment explanation
Indices: 289598--291116 Score: 2197
Period size: 86 Copynumber: 17.7 Consensus size: 86
289588 GAATGTTCAT
* *
289598 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
289663 AAAGCCCACAAGTCAGTGGCA
66 AAAGCCCACAAGTCAGTGGCA
289684 CCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
*
289747 AAAGACCACAAGTCAGTGGCA
66 AAAGCCCACAAGTCAGTGGCA
*
289768 CTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
*
289832 CAAAGCCCACAAGTTAGTGGCA
65 CAAAGCCCACAAGTCAGTGGCA
289854 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
*
289919 AAAGCCCACAAATCAGTGGCA
66 AAAGCCCACAAGTCAGTGGCA
* * *
289940 CTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAACTTAGTGGCAC-CCTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
290003 CAAAGCCCACAAGTCAGTGGCA
65 CAAAGCCCACAAGTCAGTGGCA
* * *
290025 CTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
*
290090 CAAAGCCCACAAGTTAGTGGCA
65 CAAAGCCCACAAGTCAGTGGCA
* * *
290112 CCCTTTCAAAGCCCAAAAGTCAGTGGCATTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
*
290177 AAAGCCCACAAATCAGTGGCA
66 AAAGCCCACAAGTCAGTGGCA
* *
290198 CTCCTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
* * *
290262 TAAAACCCATAAGTCAGTGGCA
65 CAAAGCCCACAAGTCAGTGGCA
* * **
290284 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCATTTCAAAGCCCACAAATCAGTGGCACTTTTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* *
290349 AAAGCCCACAAGTTAGTGGTA
66 AAAGCCCACAAGTCAGTGGCA
*
290370 CCCTTTCAAAGCCCACAACTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
290434 AAAGCCCACAAGTCAGTGGCA
66 AAAGCCCACAAGTCAGTGGCA
* * * *
290455 CTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
290519 CAAAGCCCACAAGTCAGTGGCA
65 CAAAGCCCACAAGTCAGTGGCA
*
290541 CTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
*
290606 CAAAGCCCACAAATCAGTGGCA
65 CAAAGCCCACAAGTCAGTGGCA
* * * *
290628 CTCTTTTCAAAGCTCACAAGTTAGTGGCAC-CCTTTCAAAGCTCACAAGTCAGTGGCACTCCTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
290692 CAAAGCCCACAAGTCAGTGGCA
65 CAAAGCCCACAAGTCAGTGGCA
* * *
290714 CTCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTT
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTT
* *
290778 CAACGCCCACAAGTTAGTGGCA
65 CAAAGCCCACAAGTCAGTGGCA
* * * * *
290800 CCCTTTCAGAGCCCACAAGTCAGTGGCAC-CCTTTCGAAGCCCACAAGTTAGTGGCAC-CATTAC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* *
290863 GAAGCCCACAATTCAGTGGCA
66 AAAGCCCACAAGTCAGTGGCA
* * *
290884 CTCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTTAAAGCCCACACAAGTCAGTAGCACTCCTT
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG-CC-CACAAGTCAGTGGCACTCCTT
* * * *
290948 TTAAAGCTCACGCAAGTTAGTGGTA
64 TCAAAGC-C-CACAAGTCAGTGGCA
*
290973 CCTTTTCAAAGCCCACAAGTCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTC
1 CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
* *
291036 AAAGCCCACGAGTTAGTGGCA
66 AAAGCCCACAAGTCAGTGGCA
** * *
291057 TTCTTTCAAAGCCCATGCAAGTCAGTGGCAC-CCTTTTAAAGCCCATGCAAGTCAATGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCA
291117 ACCCTTTTCA
Statistics
Matches: 1297, Mismatches: 113, Indels: 44
0.89 0.08 0.03
Matches are distributed among these distances:
84 131 0.10
85 297 0.23
86 577 0.44
87 231 0.18
88 15 0.01
89 46 0.04
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (86 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCTTTC
AAAGCCCACAAGTCAGTGGCA
Found at i:291670 original size:20 final size:20
Alignment explanation
Indices: 291642--291716 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
291632 TCATACCCTG
291642 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
291662 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
291682 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
291702 ATGTATCGATACATT
1 ATGTATCGATACATT
291717 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:291709 original size:40 final size:39
Alignment explanation
Indices: 291642--291719 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
291632 TCATACCCTG
* *
291642 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
291682 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
291720 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:303193 original size:10 final size:10
Alignment explanation
Indices: 303178--303202 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
303168 GCATTTGAAA
303178 TTATAGCCGT
1 TTATAGCCGT
303188 TTATAGCCGT
1 TTATAGCCGT
303198 TTATA
1 TTATA
303203 CAGTTCGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (10 bp):
TTATAGCCGT
Found at i:305385 original size:21 final size:21
Alignment explanation
Indices: 305361--305411 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
305351 GAATTAGAGG
**
305361 AGAAAATGAATGAGTTGGAAA
1 AGAAAATGAATGAGTTACAAA
**
305382 AGAAAAAAAATGAGTTACAAA
1 AGAAAATGAATGAGTTACAAA
305403 ATGAAAATG
1 A-GAAAATG
305412 GTGAATTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.59, C:0.02, G:0.22, T:0.18
Consensus pattern (21 bp):
AGAAAATGAATGAGTTACAAA
Found at i:306970 original size:20 final size:20
Alignment explanation
Indices: 306924--306976 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
306914 ATTTGCCTGT
*
306924 ATGTATCGATATATTGAATA
1 ATGTATCGATACATTGAATA
** * *
306944 ACATATCAATACATTGAATC
1 ATGTATCGATACATTGAATA
306964 ATGTATCGATACA
1 ATGTATCGATACA
306977 AAACTTATGT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:307819 original size:15 final size:15
Alignment explanation
Indices: 307796--307827 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
307786 TATCCAATAT
*
307796 ATCAGTATAGATTTA
1 ATCAATATAGATTTA
307811 ATCAATATAGATTTA
1 ATCAATATAGATTTA
307826 AT
1 AT
307828 GATAGATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (15 bp):
ATCAATATAGATTTA
Found at i:309107 original size:32 final size:32
Alignment explanation
Indices: 309066--309129 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
309056 GAACATTACA
*
309066 AAAAAATGACAAAATCAACTTT-AAAAGATAAT
1 AAAAAATGACAAAAACAA-TTTAAAAAGATAAT
309098 AAAAAATGACAAAAACAATTTAAAAAGATAAT
1 AAAAAATGACAAAAACAATTTAAAAAGATAAT
309130 TGTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 3 0.10
32 27 0.90
ACGTcount: A:0.66, C:0.08, G:0.06, T:0.20
Consensus pattern (32 bp):
AAAAAATGACAAAAACAATTTAAAAAGATAAT
Found at i:309710 original size:15 final size:16
Alignment explanation
Indices: 309679--309711 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
309669 TAAAACCCAA
309679 CTTTAAAGTCAAAACT
1 CTTTAAAGTCAAAACT
*
309695 CTTTAAA-TCAAGACT
1 CTTTAAAGTCAAAACT
309710 CT
1 CT
309712 ATTAGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.33
Consensus pattern (16 bp):
CTTTAAAGTCAAAACT
Found at i:310043 original size:37 final size:39
Alignment explanation
Indices: 309972--310142 Score: 179
Period size: 39 Copynumber: 4.5 Consensus size: 39
309962 GGGTGAAAAA
* * *
309972 GATCAAAACATCCC-TAATAAG-TATTTTATGCCTAACAT
1 GATCAAAATA-CCCTTAAAAAGTTATTTTATGCCTAATAT
* * * *
310010 GACCAAAATACCCTTAAAACGTT-TTTT-TACCTAAAAT
1 GATCAAAATACCCTTAAAAAGTTATTTTATGCCTAATAT
* * * ** *
310047 GATCGAAATATCCGTAAAGGGTTCTTTTATGCCTAATAT
1 GATCAAAATACCCTTAAAAAGTTATTTTATGCCTAATAT
310086 GATCAAAATACCCTTAAAAAGTTATTTTATGCCTAATAT
1 GATCAAAATACCCTTAAAAAGTTATTTTATGCCTAATAT
*
310125 AATCAAAATACCCTTAAA
1 GATCAAAATACCCTTAAA
310143 GGATACATTT
Statistics
Matches: 108, Mismatches: 21, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
37 28 0.26
38 21 0.19
39 59 0.55
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.33
Consensus pattern (39 bp):
GATCAAAATACCCTTAAAAAGTTATTTTATGCCTAATAT
Found at i:310211 original size:39 final size:38
Alignment explanation
Indices: 309973--310231 Score: 152
Period size: 39 Copynumber: 6.7 Consensus size: 38
309963 GGTGAAAAAG
* * *
309973 ATCAAAACATCCCTAATAA-GTA-TTTTATGCCTAACATG
1 ATCAAAATA-CCCTAA-AAGGTACTTTTATGCCTAAAATA
* * * * *
310011 ACCAAAATACCCTTAAAACGT--TTTTTTACCTAAAATG
1 ATCAAAATACCC-TAAAAGGTACTTTTATGCCTAAAATA
* * * * * *
310048 ATCGAAATATCCGTAAAGGGTTCTTTTATGCCTAATATG
1 ATCAAAATA-CCCTAAAAGGTACTTTTATGCCTAAAATA
* *
310087 ATCAAAATACCCTTAAAAAGTTA-TTTTATGCCTAATATA
1 ATCAAAATACCC-T-AAAAGGTACTTTTATGCCTAAAATA
* * **
310126 ATCAAAATACCCTTAAAGGATACATTTA-GACCTTTTAATA
1 ATCAAAATACCCTAAAAGG-TACTTTTATG-CC-TAAAATA
* * *
310166 ACCAAAATACGCTCAAATGGTACTTTTATGCCTAAAATA
1 ATCAAAATACCCT-AAAAGGTACTTTTATGCCTAAAATA
**
310205 ATCAAAATACCCCTAAAATATACTTTT
1 ATCAAAATA-CCCTAAAAGGTACTTTT
310232 TAACCTAAAT
Statistics
Matches: 170, Mismatches: 37, Indels: 27
0.73 0.16 0.12
Matches are distributed among these distances:
37 35 0.21
38 20 0.12
39 78 0.46
40 32 0.19
41 5 0.03
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (38 bp):
ATCAAAATACCCTAAAAGGTACTTTTATGCCTAAAATA
Found at i:313974 original size:18 final size:18
Alignment explanation
Indices: 313936--313984 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
313926 AATATATGAT
313936 TTTTAAAAA-AAAAATTA
1 TTTTAAAAATAAAAATTA
313953 ---TAAAAATAAAAATTA
1 TTTTAAAAATAAAAATTA
313968 TTTTAAAAATATAAAAT
1 TTTTAAAAATA-AAAAT
313985 ATGTAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 6 0.22
15 8 0.30
18 8 0.30
19 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTTAAAAATAAAAATTA
Done.