Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold141
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: 2772588
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 118404 characters in sequence are not A, C, G, or T
File 2 of 18
Found at i:168621 original size:62 final size:61
Alignment explanation
Indices: 168486--168646 Score: 215
Period size: 62 Copynumber: 2.7 Consensus size: 61
168476 TGAAAATCGG
* * * *
168486 TTGACTAATTGACATGCTAAAATTATGCCAATTTA---T-TTATATAATCATGGAAATTAG
1 TTGACTAATAGACATGCTAAAATTATGCTAATTTATTGTCTTATATAATCATGGAAATCAA
* *
168543 TTAACTAGTTA-ACATGCTAAAATTATGCTAATTTATTGTCTTAATATAATCATGGAAATCAA
1 TTGACTA-ATAGACATGCTAAAATTATGCTAATTTATTGTCTT-ATATAATCATGGAAATCAA
168605 TTGACTAATAGACATGCTAAAATTATGCTAATTTATTGTCTT
1 TTGACTAATAGACATGCTAAAATTATGCTAATTTATTGTCTT
168647 GCTTGTGATG
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
57 29 0.33
58 1 0.01
60 1 0.01
61 4 0.04
62 54 0.61
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (61 bp):
TTGACTAATAGACATGCTAAAATTATGCTAATTTATTGTCTTATATAATCATGGAAATCAA
Found at i:170314 original size:20 final size:20
Alignment explanation
Indices: 170289--170414 Score: 92
Period size: 20 Copynumber: 5.8 Consensus size: 20
170279 TTTTACCCAG
170289 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
170309 ATGTATTGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
170329 ATGTGTCGATACATTCTTT-A
1 ATGTATCGATACATT-TTTCA
170349 ATGTATCGATACATTCTATCTTTTTACCCA
1 ATGTATCGAT--A--C-A--TTTTT---CA
170379 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
170400 ATGTATCGATACATT
1 ATGTATCGATACATT
170415 CTATCTTTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 26
0.71 0.08 0.22
Matches are distributed among these distances:
20 53 0.63
21 4 0.05
22 1 0.01
24 6 0.07
25 1 0.01
26 4 0.05
27 3 0.04
29 1 0.01
30 1 0.01
31 10 0.12
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:170410 original size:51 final size:50
Alignment explanation
Indices: 170329--170463 Score: 191
Period size: 51 Copynumber: 2.7 Consensus size: 50
170319 ACATGTATGA
*
170329 ATGTGTCGATACATTCTTT-AATGTATCGATACATTCTATCTTTTTACCCAG
1 ATGTATCGATACATT-TTTCAATGTATCGATACATTCTATCTTTTT-CCCAG
* *
170380 ATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTTTTCCAT
1 ATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTTTCCCAG
* * *
170430 ATATATTGATATATTTTTCAATGTATCGATACAT
1 ATGTATCGATACATTTTTCAATGTATCGATACAT
170464 CTAATTAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
50 37 0.48
51 40 0.52
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (50 bp):
ATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTTTCCCAG
Found at i:179652 original size:21 final size:20
Alignment explanation
Indices: 179626--179676 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
179616 GCGAAGGAAA
*
179626 TGTATCGATACGTGCTTACAT
1 TGTATCGATACAT-CTTACAT
* *
179647 TGTATCGATACATTTTTCAT
1 TGTATCGATACATCTTACAT
179667 TGTATCGATA
1 TGTATCGATA
179677 TATTCTAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATCTTACAT
Found at i:180200 original size:20 final size:19
Alignment explanation
Indices: 180177--180227 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
180167 TACATCCAGA
* *
180177 TGTATCGATACATTATGCTT
1 TGTATCGATACATGAT-CAT
*
180197 TGTATCGATACATGCTCAT
1 TGTATCGATACATGATCAT
180216 TGTATCGATACA
1 TGTATCGATACA
180228 AGCACAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:180220 original size:19 final size:19
Alignment explanation
Indices: 180177--180241 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
180167 TACATCCAGA
** *
180177 TGTATCGATACATTATGCTT
1 TGTATCGATACATGCT-CAT
180197 TGTATCGATACATGCTCAT
1 TGTATCGATACATGCTCAT
* *
180216 TGTATCGATACAAGCACAAT
1 TGTATCGATACATGCTC-AT
180236 TGTATC
1 TGTATC
180242 AATATATGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 17 0.44
20 22 0.56
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGCTCAT
Found at i:180239 original size:20 final size:19
Alignment explanation
Indices: 180196--180241 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
180186 ACATTATGCT
* *
180196 TTGTATCGATACATGCTCA
1 TTGTATCGATACAAGCACA
180215 TTGTATCGATACAAGCACAA
1 TTGTATCGATACAAGCAC-A
180235 TTGTATC
1 TTGTATC
180242 AATATATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACAAGCACA
Found at i:180317 original size:13 final size:13
Alignment explanation
Indices: 180299--180323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
180289 CATGGCACTT
180299 TGTATCGATACAG
1 TGTATCGATACAG
180312 TGTATCGATACA
1 TGTATCGATACA
180324 TGATGAATTG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:186467 original size:20 final size:21
Alignment explanation
Indices: 186439--186478 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
186429 ATTTTTCAGA
186439 ATGTATCAATACAT-TGAAAG
1 ATGTATCAATACATCTGAAAG
*
186459 ATGTCTCAATACATCTGAAA
1 ATGTATCAATACATCTGAAA
186479 AAACCCAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (21 bp):
ATGTATCAATACATCTGAAAG
Found at i:188401 original size:31 final size:31
Alignment explanation
Indices: 188366--188512 Score: 267
Period size: 31 Copynumber: 4.7 Consensus size: 31
188356 AAATAAATTT
*
188366 TTATCAAGGGGGAGGAAATTTTTTAAAACGA
1 TTATCAAGGGGGAGAAAATTTTTTAAAACGA
*
188397 TTATCAAGGGGGAGAAAATTTTTTAAAACAA
1 TTATCAAGGGGGAGAAAATTTTTTAAAACGA
188428 TTATCAAGGGGGAGAAAATTTTTTAAAACGA
1 TTATCAAGGGGGAGAAAATTTTTTAAAACGA
188459 TTATCAAGGGGGAGAAAATTTTTTAAAACGA
1 TTATCAAGGGGGAGAAAATTTTTTAAAACGA
*
188490 TTATCAAAGGGGAGAAAATTTTT
1 TTATCAAGGGGGAGAAAATTTTT
188513 AAACGAGAGC
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 112 1.00
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.30
Consensus pattern (31 bp):
TTATCAAGGGGGAGAAAATTTTTTAAAACGA
Found at i:189198 original size:20 final size:20
Alignment explanation
Indices: 189173--189222 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
189163 TCACTGCTTA
189173 TATCGATACATGGCACTTTG
1 TATCGATACATGGCACTTTG
189193 TATCGATACATGGCACTTTG
1 TATCGATACATGGCACTTTG
189213 TATCGATACA
1 TATCGATACA
189223 ATGTATCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (20 bp):
TATCGATACATGGCACTTTG
Found at i:192115 original size:27 final size:27
Alignment explanation
Indices: 192083--192159 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
192073 TTCATTTATT
*
192083 AGAGATATTCCAACCCCATTTTTCCG-
1 AGAGATACTCCAACCCCATTTTTCCGC
* *
192109 AGGAGATACTCCAACCCTATTTTTTCGTC
1 A-GAGATACTCCAACCCCATTTTTCCG-C
192138 AG-GATACTCCAACCCCATTTTT
1 AGAGATACTCCAACCCCATTTTT
192160 AAAAATTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
26 1 0.02
27 41 0.93
28 1 0.02
29 1 0.02
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (27 bp):
AGAGATACTCCAACCCCATTTTTCCGC
Found at i:195822 original size:2 final size:2
Alignment explanation
Indices: 195815--195842 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
195805 CAACCAAAAG
195815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
195843 GGTATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:197093 original size:45 final size:45
Alignment explanation
Indices: 197044--197184 Score: 228
Period size: 45 Copynumber: 3.1 Consensus size: 45
197034 TAATACATAC
*
197044 TAAAAATCTATATAAACTTAAACCCAAACCCAATTAAAACCTAAT
1 TAAAAATCTATATAAACTTAAACCCAAACCCAATTAAAACCCAAT
*
197089 TAAAAATCTATATAAACTTAAACCCAAATCCAATTAAAACCCAAT
1 TAAAAATCTATATAAACTTAAACCCAAACCCAATTAAAACCCAAT
* * * *
197134 TAAAAATCTAAATAAACTTAAACCCAAACCTAATTAAAATCCATT
1 TAAAAATCTATATAAACTTAAACCCAAACCCAATTAAAACCCAAT
197179 TAAAAA
1 TAAAAA
197185 AATAACAAAG
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.25
Consensus pattern (45 bp):
TAAAAATCTATATAAACTTAAACCCAAACCCAATTAAAACCCAAT
Found at i:197117 original size:22 final size:22
Alignment explanation
Indices: 197047--197118 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
197037 TACATACTAA
197047 AAATCTATATAAACTTAAACCC
1 AAATCTATATAAACTTAAACCC
* * * ****
197069 AAACCCA-ATTAAAACCTAATTAA
1 AAATCTATA-T-AAACTTAAACCC
197092 AAATCTATATAAACTTAAACCC
1 AAATCTATATAAACTTAAACCC
197114 AAATC
1 AAATC
197119 CAATTAAAAC
Statistics
Matches: 33, Mismatches: 14, Indels: 6
0.62 0.26 0.11
Matches are distributed among these distances:
21 1 0.03
22 18 0.55
23 13 0.39
24 1 0.03
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (22 bp):
AAATCTATATAAACTTAAACCC
Found at i:197126 original size:22 final size:22
Alignment explanation
Indices: 197056--197126 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
197046 AAAATCTATA
*
197056 TAAACTTAAACCCAAACCCAAT
1 TAAACTTAAACCCAAATCCAAT
* **** *
197078 TAAAACCTAATTAAAAAT-CTAT
1 T-AAACTTAAACCCAAATCCAAT
197100 ATAAACTTAAACCCAAATCCAAT
1 -TAAACTTAAACCCAAATCCAAT
197123 TAAA
1 TAAA
197127 ACCCAATTAA
Statistics
Matches: 33, Mismatches: 13, Indels: 6
0.63 0.25 0.12
Matches are distributed among these distances:
22 19 0.58
23 14 0.42
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAACTTAAACCCAAATCCAAT
Found at i:197217 original size:90 final size:90
Alignment explanation
Indices: 197044--197217 Score: 201
Period size: 90 Copynumber: 1.9 Consensus size: 90
197034 TAATACATAC
* ** *
197044 TAAAAATCTATATAAACTTAAACCCAAACCCAATTAAAACCTAATTAAAAATCTATATAAACTTA
1 TAAAAATCTAAATAAACTTAAACCCAAACCCAATTAAAACCTAATTAAAAAAATATACAAACTTA
** * * *
197109 AACCCAAATCCAATTAAAACCCAAT
66 AACAAAAAACAAAATAAAACCCAAT
* *
197134 TAAAAATCTAAATAAACTTAAACCCAAACCTAATTAAAATCC-ATTTAAAAAAATA-ACAAAGCT
1 TAAAAATCTAAATAAACTTAAACCCAAACCCAATTAAAA-CCTAATTAAAAAAATATACAAA-CT
197197 TAATA-AAAAAACAAAATAAAA
64 TAA-ACAAAAAACAAAATAAAA
197218 TAAAAAAAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
89 4 0.06
90 63 0.90
91 3 0.04
ACGTcount: A:0.58, C:0.18, G:0.01, T:0.23
Consensus pattern (90 bp):
TAAAAATCTAAATAAACTTAAACCCAAACCCAATTAAAACCTAATTAAAAAAATATACAAACTTA
AACAAAAAACAAAATAAAACCCAAT
Found at i:197303 original size:57 final size:57
Alignment explanation
Indices: 197242--197355 Score: 156
Period size: 57 Copynumber: 2.0 Consensus size: 57
197232 ATACACTAGC
* * * * *
197242 AGCAACTAAACTATTAAAACTAACAATAATTGCAATAATCGGCAACAACATTTAGAA
1 AGCAACTAAACTACTAAAACTAACAACAACTACAATAATCGGCAACAACAATTAGAA
* * *
197299 AGCAACTAAACTACTAAACCTAGCAGCAACTACAATAATCGGCAACAACAATTAGAA
1 AGCAACTAAACTACTAAAACTAACAACAACTACAATAATCGGCAACAACAATTAGAA
197356 GTAGATCGAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.50, C:0.21, G:0.10, T:0.19
Consensus pattern (57 bp):
AGCAACTAAACTACTAAAACTAACAACAACTACAATAATCGGCAACAACAATTAGAA
Found at i:197416 original size:18 final size:18
Alignment explanation
Indices: 197390--197425 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
197380 GCAAATTGGC
197390 AGAAACAGATCAGCAACT
1 AGAAACAGATCAGCAACT
* *
197408 AGAAGCAGATCGGCAACT
1 AGAAACAGATCAGCAACT
197426 GCAATATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.11
Consensus pattern (18 bp):
AGAAACAGATCAGCAACT
Found at i:198187 original size:24 final size:25
Alignment explanation
Indices: 198160--198210 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
198150 TTGCCCACCG
198160 TTGTGTTTATAATTATGCTT-ATGC
1 TTGTGTTTATAATTATGCTTAATGC
*
198184 TTGTGTTTATAATTATGTTTAATGC
1 TTGTGTTTATAATTATGCTTAATGC
198209 TT
1 TT
198211 TTCATTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.57
Consensus pattern (25 bp):
TTGTGTTTATAATTATGCTTAATGC
Found at i:199512 original size:1 final size:1
Alignment explanation
Indices: 199506--199534 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
199496 GACTAAGCTT
199506 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
199535 AGGAGACGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:200542 original size:48 final size:48
Alignment explanation
Indices: 200468--200564 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
200458 ACAATAACCG
*
200468 TTAGAAAGCTAACTGGATAAGTCCTATTCGAAAAATATTAAAAAATTA
1 TTAGAAAGCTAACTGGATAAGGCCTATTCGAAAAATATTAAAAAATTA
200516 TTAGAAAGCTAACTGGATAAGGCCTATTCGAAAAATATTAAAAAATTA
1 TTAGAAAGCTAACTGGATAAGGCCTATTCGAAAAATATTAAAAAATTA
200564 T
1 T
200565 CTTTTCTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.29
Consensus pattern (48 bp):
TTAGAAAGCTAACTGGATAAGGCCTATTCGAAAAATATTAAAAAATTA
Found at i:200959 original size:17 final size:18
Alignment explanation
Indices: 200937--200974 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
200927 TCAATAAAGT
200937 TTAAATT-AAAAATCATG
1 TTAAATTCAAAAATCATG
200954 TTAAATTCCAAAAAATCATG
1 TTAAATT-C-AAAAATCATG
200974 T
1 T
200975 AGGTTATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (18 bp):
TTAAATTCAAAAATCATG
Found at i:204394 original size:13 final size:13
Alignment explanation
Indices: 204376--204404 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
204366 AATTTCCTCA
204376 TGTATCGATACAT
1 TGTATCGATACAT
204389 TGTATCGATACAT
1 TGTATCGATACAT
204402 TGT
1 TGT
204405 CCCATGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:204416 original size:33 final size:34
Alignment explanation
Indices: 204355--204419 Score: 107
Period size: 33 Copynumber: 1.9 Consensus size: 34
204345 TTACAAGCAA
204355 TGTATCGATACAATTTCCTCATGTATCGATACAT
1 TGTATCGATACAATTTCCTCATGTATCGATACAT
204389 TGTATCGATAC-ATTGTCC-CATGTATCGATAC
1 TGTATCGATACAATT-TCCTCATGTATCGATAC
204420 TAATAGTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 16 0.53
34 14 0.47
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (34 bp):
TGTATCGATACAATTTCCTCATGTATCGATACAT
Found at i:204494 original size:19 final size:19
Alignment explanation
Indices: 204450--204505 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
204440 CTGCCAATCT
*
204450 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
204470 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
204489 CATGTATCGATACAATG
1 CATGTATCGATACAATG
204506 TATCAATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:205296 original size:19 final size:21
Alignment explanation
Indices: 205274--205320 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
205264 ACACAAACAA
*
205274 TCATAACACAAA-A-TGCATT
1 TCATAAAACAAACATTGCATT
205293 TCATAAAACAAACATTGCATT
1 TCATAAAACAAACATTGCATT
205314 TCATAAA
1 TCATAAA
205321 TTCAAATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 11 0.44
20 1 0.04
21 13 0.52
ACGTcount: A:0.49, C:0.19, G:0.04, T:0.28
Consensus pattern (21 bp):
TCATAAAACAAACATTGCATT
Found at i:207053 original size:13 final size:13
Alignment explanation
Indices: 207035--207076 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
207025 AAATAGTACC
207035 CAATGTATCGATA
1 CAATGTATCGATA
207048 CAATGTATCGATA
1 CAATGTATCGATA
*
207061 TAATGTATCGATA
1 CAATGTATCGATA
207074 CAA
1 CAA
207077 GGAATGTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:213244 original size:20 final size:20
Alignment explanation
Indices: 213219--213283 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
213209 CTGCCAATCT
213219 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
*
213239 CATGTATCGTTAC-A-----
1 CATGTATCGATACAATTGTC
213253 -ATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
213272 CATGTATCGATA
1 CATGTATCGATA
213284 TAATGTATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
19 1 0.03
20 23 0.64
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACAATTGTC
Found at i:213258 original size:13 final size:13
Alignment explanation
Indices: 213240--213299 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 13
213230 ACAATTGTCC
*
213240 ATGTATCGTTACA
1 ATGTATCGATACA
213253 ATGTATCGATACA
1 ATGTATCGATACA
*
213266 A--T-T-G-T-CC
1 ATGTATCGATACA
*
213273 ATGTATCGATATA
1 ATGTATCGATACA
213286 ATGTATCGATACA
1 ATGTATCGATACA
213299 A
1 A
213300 AGCATAATGT
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
7 2 0.06
8 1 0.03
9 2 0.06
10 2 0.06
11 2 0.06
12 1 0.03
13 26 0.72
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:213262 original size:33 final size:33
Alignment explanation
Indices: 213220--213299 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
213210 TGCCAATCTC
*
213220 ATGTATCGATACAATTGTCCATGTATCGTTACA
1 ATGTATCGATACAATTGTCCATGTATCGATACA
*
213253 ATGTATCGATACAATTGTCCATGTATCGATATA
1 ATGTATCGATACAATTGTCCATGTATCGATACA
213286 ATGTATCGATACAA
1 ATGTATCGATACAA
213300 AGCATAATGT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (33 bp):
ATGTATCGATACAATTGTCCATGTATCGATACA
Found at i:213831 original size:18 final size:20
Alignment explanation
Indices: 213808--213847 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
213798 AAGGAGATGT
*
213808 TGGACATGTTA-AAA-TGCA
1 TGGACATGGTACAAAGTGCA
213826 TGGACATGGTACAAAGTGCA
1 TGGACATGGTACAAAGTGCA
213846 TG
1 TG
213848 ATCAAGGGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (20 bp):
TGGACATGGTACAAAGTGCA
Found at i:221640 original size:95 final size:95
Alignment explanation
Indices: 221477--221667 Score: 382
Period size: 95 Copynumber: 2.0 Consensus size: 95
221467 TTTTTGCCAT
221477 CTTTGAAAATTAGCTCCATTAAACTGATTAGATTTGACAAAGTTTGGAGCCAACTTTATTTAGTG
1 CTTTGAAAATTAGCTCCATTAAACTGATTAGATTTGACAAAGTTTGGAGCCAACTTTATTTAGTG
221542 CTCCAATTTCAAAAGCAATCATTGTAGATA
66 CTCCAATTTCAAAAGCAATCATTGTAGATA
221572 CTTTGAAAATTAGCTCCATTAAACTGATTAGATTTGACAAAGTTTGGAGCCAACTTTATTTAGTG
1 CTTTGAAAATTAGCTCCATTAAACTGATTAGATTTGACAAAGTTTGGAGCCAACTTTATTTAGTG
221637 CTCCAATTTCAAAAGCAATCATTGTAGATA
66 CTCCAATTTCAAAAGCAATCATTGTAGATA
221667 C
1 C
221668 CTCATTTTGC
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (95 bp):
CTTTGAAAATTAGCTCCATTAAACTGATTAGATTTGACAAAGTTTGGAGCCAACTTTATTTAGTG
CTCCAATTTCAAAAGCAATCATTGTAGATA
Found at i:222130 original size:51 final size:52
Alignment explanation
Indices: 222069--222184 Score: 157
Period size: 51 Copynumber: 2.2 Consensus size: 52
222059 TTTGGAAAGA
*
222069 AAATGTATCGATACATTTCTCATTGT-TTCGATACATTCTAGG-TTTTAACCC
1 AAATGTATCGATACATTTCTCATTATATT-GATACATTCTAGGTTTTTAACCC
* * *
222120 AAATAG-ATCGATACATTTTTCATTATATTGATACATTCTGGGTTTTTGACCC
1 AAAT-GTATCGATACATTTCTCATTATATTGATACATTCTAGGTTTTTAACCC
222172 AAATGTATCGATA
1 AAATGTATCGATA
222185 TATTGAAGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
51 35 0.61
52 22 0.39
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (52 bp):
AAATGTATCGATACATTTCTCATTATATTGATACATTCTAGGTTTTTAACCC
Found at i:224935 original size:81 final size:80
Alignment explanation
Indices: 224575--224987 Score: 341
Period size: 80 Copynumber: 5.1 Consensus size: 80
224565 TCAAAAAAAG
* * * * * *
224575 TACTCCAACCCCGTTTTTACCTCTAAAACG-TAGAATTTTTTTTTTATCTTTGGGGAAACTCTAA
1 TACTCCAACCCCATTTTTACTTCTAAAACGCT-GAA----TTTTTCATCTTAGGGGATACTCCAA
* * * *
224639 CTCCACTATCTCTGAGGGGA
61 CCCCACCATCTCCGAGAGGA
* * * * * * * * * *
224659 TACTCTAACCCCGTTTTTACTTTTAAAATGCTAAATTTCTCATATT-TGGGATACACTAACCCCA
1 TACTCCAACCCCATTTTTACTTCTAAAACGCTGAATTTTTCATCTTAGGGGATACTCCAACCCCA
** *
224723 CCATCTTTGAGGGGA
66 CCATCTCCGAGAGGA
** * * * *
224738 TACTTTAACCTCGTTTTTACTTCCAAAATGCTGAATTTTTCATCTTAGGGGATACTCCAACCCCA
1 TACTCCAACCCCATTTTTACTTCTAAAACGCTGAATTTTTCATCTTAGGGGATACTCCAACCCCA
* *
224803 CCATCTCCAAGGGGA
66 CCATCTCCGAGAGGA
* * *
224818 TACTCCAAACCCATTTTTACTTCTAAAACGCTGAATTTTTTATCTTAGGGGATACTGCAACCCCA
1 TACTCCAACCCCATTTTTACTTCTAAAACGCTGAATTTTTCATCTTAGGGGATACTCCAACCCCA
* *
224883 CCATCTCTGAGAGAAA
66 CCATCTCCGAGAG-GA
* * ** *
224899 TACTCCAACCCCTTTTTTACATT-TAAAAC-ATCGAATTTTTCAT-TTTTGGGATACTTCAACCC
1 TACTCCAACCCCATTTTTAC-TTCTAAAACGCT-GAATTTTTCATCTTAGGGGATACTCCAACCC
*
224961 TACCATCTCCGAGAGGA
64 CACCATCTCCGAGAGGA
224978 TACTCCAACC
1 TACTCCAACC
224988 ATAATTTTCA
Statistics
Matches: 274, Mismatches: 50, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
79 77 0.28
80 131 0.48
81 35 0.13
82 2 0.01
84 28 0.10
85 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (80 bp):
TACTCCAACCCCATTTTTACTTCTAAAACGCTGAATTTTTCATCTTAGGGGATACTCCAACCCCA
CCATCTCCGAGAGGA
Found at i:225117 original size:26 final size:27
Alignment explanation
Indices: 225073--225133 Score: 90
Period size: 26 Copynumber: 2.3 Consensus size: 27
225063 TATAATAATT
*
225073 GGGGGTA-TTCTAACACCGTATTCTGA
1 GGGGGTACTTCAAACACCGTATTCTGA
225099 GGGGGTACTTCAAAC-CCGTATTCTGA
1 GGGGGTACTTCAAACACCGTATTCTGA
*
225125 GGGGATACT
1 GGGGGTACT
225134 CTAACTCTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 26 0.81
27 6 0.19
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (27 bp):
GGGGGTACTTCAAACACCGTATTCTGA
Found at i:226850 original size:61 final size:61
Alignment explanation
Indices: 226779--226901 Score: 228
Period size: 61 Copynumber: 2.0 Consensus size: 61
226769 TTATTATAGC
*
226779 CATATATTTTTTTAAATTTAATTTATTAATTATTTTGGTTCTTTTTCAATGGGGATTACAT
1 CATACATTTTTTTAAATTTAATTTATTAATTATTTTGGTTCTTTTTCAATGGGGATTACAT
*
226840 CATACATTTTTTTAAATTTAATTTATTAATTGTTTTGGTTCTTTTTCAATGGGGATTACAT
1 CATACATTTTTTTAAATTTAATTTATTAATTATTTTGGTTCTTTTTCAATGGGGATTACAT
226901 C
1 C
226902 CACGCATTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (61 bp):
CATACATTTTTTTAAATTTAATTTATTAATTATTTTGGTTCTTTTTCAATGGGGATTACAT
Found at i:228242 original size:13 final size:13
Alignment explanation
Indices: 228224--228249 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
228214 CAATTTGGTC
228224 ATGTATCGATACA
1 ATGTATCGATACA
228237 ATGTATCGATACA
1 ATGTATCGATACA
228250 TCTTATATGT
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:228356 original size:13 final size:13
Alignment explanation
Indices: 228338--228362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
228328 TACAATGGTC
228338 ATGTATCGATACA
1 ATGTATCGATACA
228351 ATGTATCGATAC
1 ATGTATCGATAC
228363 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:228376 original size:20 final size:20
Alignment explanation
Indices: 228351--228415 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
228341 TATCGATACA
228351 ATGTATCGATACTGTGCATT
1 ATGTATCGATACTGTGCATT
228371 ATGTATCGATA-----CA--
1 ATGTATCGATACTGTGCATT
*
228384 ATGTATCAATACTGTGCATT
1 ATGTATCGATACTGTGCATT
228404 ATGTATCGATAC
1 ATGTATCGATAC
228416 ATCTGAAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
18 2 0.06
20 22 0.61
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACTGTGCATT
Found at i:228380 original size:33 final size:33
Alignment explanation
Indices: 228338--228416 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
228328 TACAATGGTC
*
228338 ATGTATCGATACAATGTATCGATACTGTGCATT
1 ATGTATCGATACAATGTATCAATACTGTGCATT
228371 ATGTATCGATACAATGTATCAATACTGTGCATT
1 ATGTATCGATACAATGTATCAATACTGTGCATT
228404 ATGTATCGATACA
1 ATGTATCGATACA
228417 TCTGAAGGTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (33 bp):
ATGTATCGATACAATGTATCAATACTGTGCATT
Found at i:229056 original size:37 final size:37
Alignment explanation
Indices: 229015--229091 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
229005 TAATCACATG
229015 TTTCCTCACATGTTTCTTTCTCCCCCTTAATCATAAA
1 TTTCCTCACATGTTTCTTTCTCCCCCTTAATCATAAA
229052 TTTCCTCACATGTTTCTTTCTCCCCCTTAATCATAAA
1 TTTCCTCACATGTTTCTTTCTCCCCCTTAATCATAAA
229089 TTT
1 TTT
229092 ATTTACAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.21, C:0.31, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTCCTCACATGTTTCTTTCTCCCCCTTAATCATAAA
Found at i:232691 original size:18 final size:20
Alignment explanation
Indices: 232670--232709 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
232660 TGAGATGCTG
232670 GAAATAT-T-AAAAATGCAT
1 GAAATATATAAAAAATGCAT
232688 GAAATATAATAAAAAATGCAT
1 GAAATAT-ATAAAAAATGCAT
232709 G
1 G
232710 GTCAAAGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
20 1 0.05
21 11 0.58
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.25
Consensus pattern (20 bp):
GAAATATATAAAAAATGCAT
Found at i:233667 original size:20 final size:20
Alignment explanation
Indices: 233620--233694 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
233610 AAAAAGACAT
*
233620 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
233639 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
233660 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
233680 AATGTATCGATACAT
1 AATGTATCGATACAT
233695 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:233688 original size:40 final size:39
Alignment explanation
Indices: 233617--233694 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
233607 GGTAAAAAGA
* *
233617 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
233656 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
233695 CTGGGTAAAA
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:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:235507 original size:28 final size:28
Alignment explanation
Indices: 234296--235509 Score: 1335
Period size: 28 Copynumber: 42.6 Consensus size: 28
234286 CACCAACACG
* * * *
234296 TGTGGGCTTTGAAAAGAGTTACTACTGGCT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* *
234326 TGTGGGCTTTGAAAAGGTGCTACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
234354 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** *
234382 TGTGGGCTTTGAAAAAGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* **
234410 TATGGGC-TTGAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
**
234437 TGTGGGCTTTGAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** *
234465 TGTGGGC-TTGAAAAAGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
**
234492 TGTGGGC-TTGAAAATGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** * *
234519 CATGGGCTTTGAATGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
**
234547 CATGGGCTTTGAAAGGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGG-GTGCCACTGACT
* *
234576 TCGTGGGCTTTGAAATGAGTGCTACTGACT
1 T-GTGGGCTTTGAAA-GGGTGCCACTGACT
*
234606 TGCGTGGGCTTTAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
*
234636 TGCATGGGCTTTGAAAGGATGCCACTGACT
1 TG--TGGGCTTTGAAAGGGTGCCACTGACT
* *
234666 TGTGGGCTTTGAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * **
234694 CGTAGGC-TTGAAAATGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
234721 TGCGTGGGCTTTAAAAGGGTGCCATTGACTT
1 T--GTGGGCTTTGAAAGGGTGCCACTGAC-T
*
234752 GTGTGGGCTTTGAAAGGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
234781 TGTGGGCTTTGAAAGAGTGCCACTGACA
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * * *
234809 CGTGGACTTTGAAAAGGTGCCTCTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
234837 TGCGTGGGCTTTAAAAGTGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
* *
234867 TGCGTGGGCTTTGAAAGAGTGCCACTAACT
1 T--GTGGGCTTTGAAAGGGTGCCACTGACT
* * *
234897 CGTGGGCTTTGAAAAGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** *
234925 CATGGGC-TTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
234952 CGTGGGC-TTGAAAGGGTGCCACTGACA
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
234979 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
235008 TGTGGGCTTTGAAAGAAGTTGCCACCGACTT
1 TGTGGGCTTTGAAAG--GGTGCCACTGAC-T
*
235039 GTGTGGGCTTTGAAAGGAGTGTCACTGACTT
1 -TGTGGGCTTTGAAAGG-GTGCCACTGAC-T
* *
235070 GTGTGGGCTTTGAAAGGATGCCACTAACT
1 -TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
235099 TGTGGGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
235127 TGTGGGCTTCGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
235155 TGTTGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
235183 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
235211 TGTGGGCTCTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
235239 TATGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
235267 TGTGGGCTTTGAAAGAGTGCCACTGAAT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
235295 TGTGGGC-TTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* **
235322 TGTAGGCTTTGAAAAAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
235350 TGTGGGCTTTGAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
235378 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
235406 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
235435 TGTGGGCTTTGAAAAAGGTGCCATTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
* *
235464 CGTGGGCTTTGAAAAGGGTGCCATTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
235493 TGTGGGCTTTGAAAGGG
1 TGTGGGCTTTGAAAGGG
235510 ATGAACATTT
Statistics
Matches: 1030, Mismatches: 130, Indels: 50
0.85 0.11 0.04
Matches are distributed among these distances:
27 163 0.16
28 504 0.49
29 125 0.12
30 179 0.17
31 43 0.04
32 16 0.02
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:236738 original size:13 final size:12
Alignment explanation
Indices: 236718--236804 Score: 77
Period size: 14 Copynumber: 6.8 Consensus size: 12
236708 ATCTAGACCC
236718 TTTTTTTTTTTG
1 TTTTTTTTTTTG
* *
236730 CTATTTTTTCTTGG
1 -T-TTTTTTTTTTG
*
236744 TTCTTTTGTTTTTT
1 TT-TTTT-TTTTTG
236758 TTGTTTTGTTTTTG
1 TT-TTTT-TTTTTG
236772 -TTTTTTTTTTG
1 TTTTTTTTTTTG
236783 TTTTTTTTTTTTG
1 -TTTTTTTTTTTG
236796 TTTTTTTTT
1 TTTTTTTTT
236805 GGTGTAAAGG
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
11 6 0.10
12 14 0.23
13 18 0.29
14 24 0.39
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:236756 original size:1 final size:1
Alignment explanation
Indices: 236747--236804 Score: 62
Period size: 1 Copynumber: 58.0 Consensus size: 1
236737 TTCTTGGTTC
* * * * * *
236747 TTTTGTTTTTTTTGTTTTGTTTTTGTTTTTTTTTTGTTTTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
236805 GGTGTAAAGG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:236788 original size:24 final size:22
Alignment explanation
Indices: 236752--236805 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
236742 GGTTCTTTTG
236752 TTTTTTTTGTTTTGTTTTTGTT
1 TTTTTTTTGTTTTGTTTTTGTT
* *
236774 TTTTTTTTGTTTTTTTTTTTTGT
1 TTTTTTTTGTTTTGTTTTTGT-T
236797 TTTTTTTTG
1 TTTTTTTTG
236806 GTGTAAAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 19 0.66
23 10 0.34
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (22 bp):
TTTTTTTTGTTTTGTTTTTGTT
Found at i:244451 original size:140 final size:140
Alignment explanation
Indices: 244199--244480 Score: 546
Period size: 140 Copynumber: 2.0 Consensus size: 140
244189 GATATTATTT
244199 TAATATGATCCCCTTGAATGCATGAATTTTGTAGAAAAATAAATCCATGTTTGATAAAAGTTTTA
1 TAATATGATCCCCTTGAATGCATGAATTTTGTAGAAAAATAAATCCATGTTTGATAAAAGTTTTA
244264 ATCTCATATGCGCCCCGAAGAGATGGGGAACATAGAGACATAAAATGACCTCTGGATTTCATTTT
66 ATCTCATATGCGCCCCGAAGAGATGGGGAACATAGAGACATAAAATGACCTCTGGATTTCATTTT
244329 GAAAACTGGA
131 GAAAACTGGA
*
244339 TAATATGATCCCCTTGAATGCATGAATTTTGTATAAAAATAAATCCATGTTTGATAAAAGTTTTA
1 TAATATGATCCCCTTGAATGCATGAATTTTGTAGAAAAATAAATCCATGTTTGATAAAAGTTTTA
*
244404 ATCTCATATGCGCCCCGGAGAGATGGGGAACATAGAGACATAAAATGACCTCTGGATTTCATTTT
66 ATCTCATATGCGCCCCGAAGAGATGGGGAACATAGAGACATAAAATGACCTCTGGATTTCATTTT
244469 GAAAACTGGA
131 GAAAACTGGA
244479 TA
1 TA
244481 TTTCGTATCA
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (140 bp):
TAATATGATCCCCTTGAATGCATGAATTTTGTAGAAAAATAAATCCATGTTTGATAAAAGTTTTA
ATCTCATATGCGCCCCGAAGAGATGGGGAACATAGAGACATAAAATGACCTCTGGATTTCATTTT
GAAAACTGGA
Found at i:247200 original size:20 final size:19
Alignment explanation
Indices: 247146--247223 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
247136 GGTAAAAAGA
247146 CATAATGTATCGATACATT
1 CATAATGTATCGATACATT
* * *
247165 GCAGAATATATTGATACATT
1 -CATAATGTATCGATACATT
*
247185 CATACATGTATCGATATATT
1 CATA-ATGTATCGATACATT
* *
247205 GAAAAATGTATCGATACAT
1 -CATAATGTATCGATACAT
247224 CTGGGTAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
19 3 0.07
20 41 0.89
21 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Found at i:247221 original size:40 final size:39
Alignment explanation
Indices: 247146--247223 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
247136 GGTAAAAAGA
* * *
247146 CATAATGTATCGATACATTGCAGAATATATTGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
247185 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
247224 CTGGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:253082 original size:13 final size:13
Alignment explanation
Indices: 253064--253090 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
253054 ACATGCTGCT
253064 TTGTATCGATACA
1 TTGTATCGATACA
253077 TTGTATCGATACA
1 TTGTATCGATACA
253090 T
1 T
253091 GTTCATTGTA
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:253087 original size:33 final size:32
Alignment explanation
Indices: 253045--253109 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
253035 CACACCCAGA
*
253045 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATG-TGCATTGTATCGATACAT
*
253078 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTGCATTGTATCGATACAT
253110 GGACAAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGTATCGATACAT
Found at i:253121 original size:21 final size:19
Alignment explanation
Indices: 253074--253131 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
253064 TTGTATCGAT
*
253074 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
253093 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
253112 ACAAATTGTATCGATACATG
1 AC--ATTGTATCGATACATG
253132 AAACTGGCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:253197 original size:13 final size:13
Alignment explanation
Indices: 253176--253206 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
253166 TGATACATGG
*
253176 TACAATGTATCGA
1 TACATTGTATCGA
253189 TACATTGTATCGA
1 TACATTGTATCGA
253202 TACAT
1 TACAT
253207 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:256673 original size:20 final size:19
Alignment explanation
Indices: 256646--256707 Score: 79
Period size: 20 Copynumber: 3.2 Consensus size: 19
256636 AGTTAGGTAA
256646 AAAAGAAAGAAAGAAAATG
1 AAAAGAAAGAAAGAAAATG
*
256665 AAGAAGAAAGAAAGAAAAAG
1 AA-AAGAAAGAAAGAAAATG
* *
256685 AAAAAAAAGAAAAAAATATG
1 AAAAGAAAGAAAGAAA-ATG
256705 AAA
1 AAA
256708 TGGAGTGGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 14 0.38
20 23 0.62
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (19 bp):
AAAAGAAAGAAAGAAAATG
Found at i:256693 original size:9 final size:9
Alignment explanation
Indices: 256645--256700 Score: 58
Period size: 10 Copynumber: 5.8 Consensus size: 9
256635 AAGTTAGGTA
256645 AAAAAGAAAG
1 AAAAA-AAAG
*
256655 AAAGAAAATG
1 AAA-AAAAAG
*
256665 AAGAAGAAAG
1 AA-AAAAAAG
256675 AAAGAAAAAG
1 AAA-AAAAAG
256685 AAAAAAAAG
1 AAAAAAAAG
256694 AAAAAAA
1 AAAAAAA
256701 TATGAAATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 14 0.36
10 22 0.56
11 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:257255 original size:22 final size:24
Alignment explanation
Indices: 257229--257278 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
257219 AGAAAAGTTC
* *
257229 AAAATTTATGTTT-TTT-TTTTAA
1 AAAATTGATCTTTATTTGTTTTAA
257251 AAAA-TGATCTTTATTTGTTTTAA
1 AAAATTGATCTTTATTTGTTTTAA
257274 AAAAT
1 AAAAT
257279 AAAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 6 0.26
22 7 0.30
23 10 0.43
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (24 bp):
AAAATTGATCTTTATTTGTTTTAA
Found at i:262028 original size:80 final size:79
Alignment explanation
Indices: 261866--262241 Score: 310
Period size: 80 Copynumber: 4.7 Consensus size: 79
261856 TGTCGTTTTT
* * * * * **
261866 TTTTTTATCTTTGGGGAAATTCCAACTCCACTATCTCTGAGGGGATTTTCTAACCCCGTTTTTAC
1 TTTTTCATCTTTGGGGATACTCCAACCCCACCATCTCTGAGGGGATACTCTAA-CCCGTTTTTAC
* * *
261931 TTTCAATATG-CTGAA
65 TTTCAAAACGTC-AAA
* * * *
261946 TTTCTCATCTTTGGGGATACTCTAACCCTACCATCTCTTAGGGGATACTCTAACCTCGTTTTTAC
1 TTTTTCATCTTTGGGGATACTCCAACCCCACCATCTCTGAGGGGATACTCTAACC-CGTTTTTAC
* *
262011 TTTCGAAATGTCAAA
65 TTTCAAAACGTCAAA
* ** * * * *
262026 TTTTTCAACTCAGGGGATACTCCAACCCCACTATCTC-GAAAGGGATACTCCAAACCCATTTTTA
1 TTTTTCATCTTTGGGGATACTCCAACCCCACCATCTCTG-AGGGGATACT-CTAACCCGTTTTTA
262090 C-TTCTAAAACGTCAAA
64 CTTTC-AAAACGTCAAA
** * ** * *
262106 TTTTTCATCTTAT-GGGATACTTTAACCCCGCCATCTCTGAAAGAATACTCCAAACCCGTTTTTA
1 TTTTTCATCTT-TGGGGATACTCCAACCCCACCATCTCTGAGGGGATACT-CTAACCCGTTTTTA
* *
262170 CTTTCAAAACATTAAA
64 CTTTCAAAACGTCAAA
* * * * * *
262186 TTTTTCATTTTTTGGGATATTCCAACCCTACCATCTCCGAGGGGATACTTTAACCC
1 TTTTTCATCTTTGGGGATACTCCAACCCCACCATCTCTGAGGGGATACTCTAACCC
262242 TGATTTTCAC
Statistics
Matches: 236, Mismatches: 51, Indels: 19
0.77 0.17 0.06
Matches are distributed among these distances:
79 11 0.05
80 215 0.91
81 10 0.04
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (79 bp):
TTTTTCATCTTTGGGGATACTCCAACCCCACCATCTCTGAGGGGATACTCTAACCCGTTTTTACT
TTCAAAACGTCAAA
Found at i:269999 original size:23 final size:23
Alignment explanation
Indices: 269967--270012 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
269957 ATGTATGTGT
*
269967 TTACAGCAATATTACATTAGAGG
1 TTACAACAATATTACATTAGAGG
269990 TTACAACAATATTACATTAGAGG
1 TTACAACAATATTACATTAGAGG
270013 CTTGCATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (23 bp):
TTACAACAATATTACATTAGAGG
Found at i:271081 original size:73 final size:71
Alignment explanation
Indices: 270994--271158 Score: 226
Period size: 73 Copynumber: 2.3 Consensus size: 71
270984 TAGGTACTAC
* *
270994 CAATGGTGTGTCGATACAATGAACATGTATCTAAACATTGTA-TCAATACCAAGCAAAATGTATC
1 CAATGGTGTATCGATACAATGAACATGTATCTAAACAATGTACT-AATACCAAGCAAAATGTATC
271058 GATACAATT
65 GATAC-A-T
* * *
271067 CAATGGTGTATCGATACAATGAACATGTATCTAAACAATGTACTGATACTAAGCAAAATGTATTG
1 CAATGGTGTATCGATACAATGAACATGTATCTAAACAATGTACTAATACCAAGCAAAATGTATCG
271132 ATACAT
66 ATACAT
271138 CTAA-GTGTGTATCGATACAAT
1 C-AATG-GTGTATCGATACAAT
271159 CAAGGGTTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
71 3 0.04
72 18 0.21
73 62 0.74
74 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (71 bp):
CAATGGTGTATCGATACAATGAACATGTATCTAAACAATGTACTAATACCAAGCAAAATGTATCG
ATACAT
Found at i:272477 original size:20 final size:21
Alignment explanation
Indices: 272454--272500 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
272444 AGAATATATT
272454 GATACATAAATGAA-TGTATC
1 GATACATAAATGAATTGTATC
* ***
272474 GATATATGTCTGAATTGTATC
1 GATACATAAATGAATTGTATC
272495 GATACA
1 GATACA
272501 AGACCATGTC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (21 bp):
GATACATAAATGAATTGTATC
Found at i:275194 original size:26 final size:28
Alignment explanation
Indices: 275164--275215 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
275154 CTAAATTTCT
* *
275164 CATCTTTG-GG-GATGCTCCAATCTCAC
1 CATCTTTGAGGAGATACTCAAATCTCAC
275190 CATCTTTGAGGAGATACTCAAATCTC
1 CATCTTTGAGGAGATACTCAAATCTC
275216 GTTTTTACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 2 0.09
28 12 0.55
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (28 bp):
CATCTTTGAGGAGATACTCAAATCTCAC
Found at i:275222 original size:80 final size:80
Alignment explanation
Indices: 275085--275261 Score: 203
Period size: 80 Copynumber: 2.2 Consensus size: 80
275075 TTTTCTTTTT
* * * * *
275085 ATCTTTGAGGATACTCTAACCTCACTATTTTTGAGGGAATACTCTAACCCCGCTTTTACTTTCAA
1 ATCTTTGAGGATACTCCAACCTCACCATCTTTGAGGGAATACTCAAACCCCGCTTTTACTTCCAA
* *
275150 AATGCTAAATTTCTC
66 AAAGCCAAATTTCTC
* * * * * *
275165 ATCTTTGGGGATGCTCCAATCTCACCATCTTTGA-GGAGATACTCAAATCTCGTTTTTACTTCCA
1 ATCTTTGAGGATACTCCAACCTCACCATCTTTGAGGGA-ATACTCAAACCCCGCTTTTACTTCCA
*
275229 AAAAGCCAAATTTTTC
65 AAAAGCCAAATTTCTC
*
275245 ATCTTAGAGGATACTCC
1 ATCTTTGAGGATACTCC
275262 CACCCCATTT
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
79 3 0.04
80 76 0.96
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.36
Consensus pattern (80 bp):
ATCTTTGAGGATACTCCAACCTCACCATCTTTGAGGGAATACTCAAACCCCGCTTTTACTTCCAA
AAAGCCAAATTTCTC
Found at i:283316 original size:1 final size:1
Alignment explanation
Indices: 283310--283350 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
283300 CTAAGCTTAA
283310 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
283351 AAGACGTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:284747 original size:17 final size:18
Alignment explanation
Indices: 284725--284762 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
284715 TCAATAAAGT
284725 TTAAATT-AAAAATCATG
1 TTAAATTCAAAAATCATG
284742 TTAAATTCCAAAAAATCATG
1 TTAAATT-C-AAAAATCATG
284762 T
1 T
284763 AGGTTATGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (18 bp):
TTAAATTCAAAAATCATG
Found at i:286244 original size:19 final size:19
Alignment explanation
Indices: 286200--286255 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
286190 CTGCCAGTTT
*
286200 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
286220 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
286239 CATGTATCGATACAATG
1 CATGTATCGATACAATG
286256 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:286258 original size:13 final size:13
Alignment explanation
Indices: 286240--286266 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
286230 TACAATGAGC
286240 ATGTATCGATACA
1 ATGTATCGATACA
286253 ATGTATCGATACA
1 ATGTATCGATACA
286266 A
1 A
286267 AGCATTATGT
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:288669 original size:18 final size:19
Alignment explanation
Indices: 288648--288685 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
288638 TAAATTTTGA
288648 TGAAAAGATGTTGGG-GTT
1 TGAAAAGATGTTGGGTGTT
* *
288666 TGAAAGGATTTTGGGTGTT
1 TGAAAAGATGTTGGGTGTT
288685 T
1 T
288686 TGGGGATAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.37, T:0.39
Consensus pattern (19 bp):
TGAAAAGATGTTGGGTGTT
Found at i:290292 original size:13 final size:13
Alignment explanation
Indices: 290274--290301 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
290264 TTTCATCACA
290274 TATCGATACAATG
1 TATCGATACAATG
290287 TATCGATACAATG
1 TATCGATACAATG
290300 TA
1 TA
290302 CCATGTATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:290390 original size:19 final size:19
Alignment explanation
Indices: 290346--290401 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
290336 CTGCCAGTTT
*
290346 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
290366 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
290385 CATGTATCGATACAATG
1 CATGTATCGATACAATG
290402 TATTGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:291639 original size:25 final size:26
Alignment explanation
Indices: 291611--291660 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
291601 CTTAAGAAGT
*
291611 TCAAAAG-CGAGGTTGGAGTATCCTC
1 TCAAAAGACGAGATTGGAGTATCCTC
*
291636 TCAAAAGAATGAGATTGGAGTATCC
1 TCAAAAG-ACGAGATTGGAGTATCC
291661 CCGATGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
27 14 0.67
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (26 bp):
TCAAAAGACGAGATTGGAGTATCCTC
Found at i:292785 original size:18 final size:20
Alignment explanation
Indices: 292762--292801 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
292752 ATGGAGATGT
*
292762 TGGACATGTTA-AAA-TGCA
1 TGGACATGGTACAAAGTGCA
292780 TGGACATGGTACAAAGTGCA
1 TGGACATGGTACAAAGTGCA
292800 TG
1 TG
292802 ATCAAGGGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (20 bp):
TGGACATGGTACAAAGTGCA
Found at i:299897 original size:18 final size:18
Alignment explanation
Indices: 299862--299900 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
299852 TTAAACTATG
299862 TGATCTTGTGATTTTTGT
1 TGATCTTGTGATTTTTGT
*
299880 TGAT-TTGTGCTTTGTTGT
1 TGATCTTGTGATTT-TTGT
299898 TGA
1 TGA
299901 ATGAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.10, C:0.05, G:0.26, T:0.59
Consensus pattern (18 bp):
TGATCTTGTGATTTTTGT
Found at i:302638 original size:13 final size:13
Alignment explanation
Indices: 302620--302644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
302610 CATTATGCTT
302620 TGTATCGATACAA
1 TGTATCGATACAA
302633 TGTATCGATACA
1 TGTATCGATACA
302645 TACTCATTGT
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:302657 original size:19 final size:20
Alignment explanation
Indices: 302633--302683 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
302623 ATCGATACAA
*
302633 TGTATCGATACATACTC-AT
1 TGTATCGATACATACGCAAT
**
302652 TGTATCGATACATGGGCAAT
1 TGTATCGATACATACGCAAT
302672 TGTATCGATACA
1 TGTATCGATACA
302684 CGAAACTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATACGCAAT
Found at i:306236 original size:21 final size:21
Alignment explanation
Indices: 306212--306267 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
306202 AACATGGTCT
306212 TGTATCGATACATTTGAGACA
1 TGTATCGATACATTTGAGACA
306233 TGTATCGATACATTTGAGACA
1 TGTATCGATACATTTGAGACA
306254 TGTATCGATACATT
1 TGTATCGATACATT
306268 CACTAATTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAGACA
Found at i:310167 original size:17 final size:19
Alignment explanation
Indices: 310145--310182 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
310135 TCAATGAGGT
310145 TTAAATT-A-AAAATCATG
1 TTAAATTCATAAAATCATG
310162 TTAAATTCCATAAAATCATG
1 TTAAATT-CATAAAATCATG
310182 T
1 T
310183 AGGTTTTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (19 bp):
TTAAATTCATAAAATCATG
Found at i:311130 original size:51 final size:52
Alignment explanation
Indices: 311075--311190 Score: 164
Period size: 51 Copynumber: 2.2 Consensus size: 52
311065 TTTGGAAAGA
*
311075 AAATGTATCGATACATTTCTCATTGT-TTCGATACATTCTAGG-TTTTAACCC
1 AAATGTATCGATACATTTCTCATTATATT-GATACATTCTAGGTTTTTAACCC
* * * *
311126 AAATGGATCGATACATTTTTCATTATATTGATACATTCTGGGTTTTTGACCC
1 AAATGTATCGATACATTTCTCATTATATTGATACATTCTAGGTTTTTAACCC
311178 AAATGTATCGATA
1 AAATGTATCGATA
311191 TATTGAAGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 35 0.61
52 22 0.39
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (52 bp):
AAATGTATCGATACATTTCTCATTATATTGATACATTCTAGGTTTTTAACCC
Found at i:311205 original size:52 final size:51
Alignment explanation
Indices: 311104--311205 Score: 114
Period size: 52 Copynumber: 2.0 Consensus size: 51
311094 TCATTGTTTC
*** *
311104 GATACATTCTAGGTTTTAACCCAAATGGATCGATACATTTTTCATTATATT
1 GATACATTCTAGGTTTTAACCCAAATGGATCGATACATTGAACAATATATT
* * * * *
311155 GATACATTCTGGGTTTTTGACCCAAATGTATCGATATATTGAAGAATATAT
1 GATACATTCTAGG-TTTTAACCCAAATGGATCGATACATTGAACAATATAT
311206 CAATACATGT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
51 12 0.29
52 29 0.71
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (51 bp):
GATACATTCTAGGTTTTAACCCAAATGGATCGATACATTGAACAATATATT
Found at i:313585 original size:171 final size:171
Alignment explanation
Indices: 313300--313631 Score: 610
Period size: 171 Copynumber: 1.9 Consensus size: 171
313290 CGAGTCACCT
* * *
313300 TTCCAACGGTTCTTTGTTTACCCCTTGAAACCTCCGGATGAACTTGGAATAACTTCGTAAAGAAA
1 TTCCAACGGTACTTTGTTTACCCCTTGAAACCTCCGGATGAACTTAGAATAACTTCATAAAGAAA
*
313365 GATGATGCAATGCTATTACCTGTTTCAAACCTAATATTTCAAAAATACTCAATTTGAGACGTTCG
66 GATGATGCAATGCTATTACCTGTTTCAAACCTAATATTTCAAAAATACTCAATTTGAGACATTCG
313430 AATGTCTCGAAGAGTATTCGGTTGGCTCTCTAGCAACCTAA
131 AATGTCTCGAAGAGTATTCGGTTGGCTCTCTAGCAACCTAA
*
313471 TTCCAACGGTACTTTGTTTACCCCTTGAAACCTCTGGATGAACTTAGAATAACTTCATAAAGAAA
1 TTCCAACGGTACTTTGTTTACCCCTTGAAACCTCCGGATGAACTTAGAATAACTTCATAAAGAAA
*
313536 GATGATGCAATGCTATTACCTGTTTCAAACCTAATCTTTCAAAAATACTCAATTTGAGACATTCG
66 GATGATGCAATGCTATTACCTGTTTCAAACCTAATATTTCAAAAATACTCAATTTGAGACATTCG
313601 AATGTCTCGAAGAGTATTCGGTTGGCTCTCT
131 AATGTCTCGAAGAGTATTCGGTTGGCTCTCT
313632 CACAACCGAA
Statistics
Matches: 155, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
171 155 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (171 bp):
TTCCAACGGTACTTTGTTTACCCCTTGAAACCTCCGGATGAACTTAGAATAACTTCATAAAGAAA
GATGATGCAATGCTATTACCTGTTTCAAACCTAATATTTCAAAAATACTCAATTTGAGACATTCG
AATGTCTCGAAGAGTATTCGGTTGGCTCTCTAGCAACCTAA
Found at i:313918 original size:79 final size:80
Alignment explanation
Indices: 313756--314164 Score: 358
Period size: 80 Copynumber: 5.1 Consensus size: 80
313746 TCAAAAAAAG
* * * ** * * *
313756 TACTCCAACCCCATTTTTAC-TTCTAAAACGCGATTTTTTTAATCTTTGAGGAAACTCTAACTCC
1 TACTCCAACCCCGTTTTTACTTTC-AAAATGCTAAATTTTTCATCTTTGAGGATACTCTAACCCC
*
313820 ACTATCTCTGAGGGGA
65 ACCATCTCTGAGGGGA
** * *
313836 TACTTTAACCCCGTTTTTACTTTCAAAATGCTAAATTTCTCATCTTTG-GGATACACTAACCCCA
1 TACTCCAACCCCGTTTTTACTTTCAAAATGCTAAATTTTTCATCTTTGAGGATACTCTAACCCCA
313900 CCATCTCTGAGGGGA
66 CCATCTCTGAGGGGA
* * * * * * * *
313915 TACTCTAACCTCGTTTTTACTTCCAAAATGCCAAATTTTTCATCTTAGTGGATACTCCAGCCCCA
1 TACTCCAACCCCGTTTTTACTTTCAAAATGCTAAATTTTTCATCTTTGAGGATACTCTAACCCCA
**
313980 CCATCTCCAAGGGGA
66 CCATCTCTGAGGGGA
* * * * * * * *
313995 TACTCCAAACCCATTTTTACTTTTAAAATGTTGAATTTTTCATCTTAGGGGATATTGC-AACCCC
1 TACTCCAACCCCGTTTTTACTTTCAAAATGCTAAATTTTTCATCTTTGAGGATACT-CTAACCCC
* *
314059 ACCATCTCTGAGAGAA
65 ACCATCTCTGAGGGGA
* *** * * * * *
314075 TACTCCAACCCC-TTTTTACTTTTAAAACATTGAATTTTTCATTTTTGGGGATACTCCAACCCTA
1 TACTCCAACCCCGTTTTTACTTTCAAAATGCTAAATTTTTCATCTTTGAGGATACTCTAACCCCA
* *
314139 CCATCTCCGAGGAGA
66 CCATCTCTGAGGGGA
* *
314154 AACACCAACCC
1 TACTCCAACCC
314165 TGATTTTCAC
Statistics
Matches: 272, Mismatches: 53, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
78 1 0.00
79 133 0.49
80 134 0.49
81 4 0.01
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (80 bp):
TACTCCAACCCCGTTTTTACTTTCAAAATGCTAAATTTTTCATCTTTGAGGATACTCTAACCCCA
CCATCTCTGAGGGGA
Found at i:314111 original size:159 final size:159
Alignment explanation
Indices: 313756--314146 Score: 365
Period size: 159 Copynumber: 2.5 Consensus size: 159
313746 TCAAAAAAAG
* * * ** * * * * * *
313756 TACTCCAACC-CCATTTTTACTTCTAAAACGCGATTTTTTTAATCTTTGAGGAAACTCTAACTCC
1 TACTCCAACCTCC-TTTTTACTTCCAAAACACCAAATTTTTCATCTTAGGGGATACTCCAACCCC
* ** ** * * *
313820 ACTATCTCTGAGGGGATACTTTAACCCCGTTTTTACTTTCAAAATGCTAAATTTCTCATCTTTGG
65 ACCATCTCCAAGGGGATACTCCAAACCCATTTTTACTTTCAAAATGCTAAATTTCTCATCTTGGG
* *
313885 GATACACTAACCCCACCATCTCTGAGGGGA
130 GATACACTAACCCCACCATCTCTGAGAGAA
* * ** * *
313915 TACTCTAACCTCGTTTTTACTTCCAAAATGCCAAATTTTTCATCTTAGTGGATACTCCAGCCCCA
1 TACTCCAACCTCCTTTTTACTTCCAAAACACCAAATTTTTCATCTTAGGGGATACTCCAACCCCA
* * * *
313980 CCATCTCCAAGGGGATACTCCAAACCCATTTTTACTTTTAAAATGTTGAATTTTTCATCTTAGGG
66 CCATCTCCAAGGGGATACTCCAAACCCATTTTTACTTTCAAAATGCTAAATTTCTCATCTT-GGG
**
314045 GATATTGC-AACCCCACCATCTCTGAGAGAA
130 GATA-CACTAACCCCACCATCTCTGAGAGAA
** *** * * *
314075 TACTCCAACC-CCTTTTTACTTTTAAAACATTGAATTTTTCATTTTTGGGGATACTCCAACCCTA
1 TACTCCAACCTCCTTTTTACTTCCAAAACACCAAATTTTTCATCTTAGGGGATACTCCAACCCCA
314139 CCATCTCC
66 CCATCTCC
314147 GAGGAGAAAC
Statistics
Matches: 185, Mismatches: 44, Indels: 6
0.79 0.19 0.03
Matches are distributed among these distances:
159 148 0.80
160 36 0.19
161 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (159 bp):
TACTCCAACCTCCTTTTTACTTCCAAAACACCAAATTTTTCATCTTAGGGGATACTCCAACCCCA
CCATCTCCAAGGGGATACTCCAAACCCATTTTTACTTTCAAAATGCTAAATTTCTCATCTTGGGG
ATACACTAACCCCACCATCTCTGAGAGAA
Found at i:325952 original size:35 final size:35
Alignment explanation
Indices: 325904--326090 Score: 331
Period size: 35 Copynumber: 5.4 Consensus size: 35
325894 TAAAAAAAAA
325904 CATGGAATGATGGGCATGGAATAAAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATAAAAAAATGAAGG
*
325939 CATAGAATGATGGGCATGGAATAAAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATAAAAAAATGAAGG
*
325974 CATGGAATGATGGGCATGGAATATAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATAAAAAAATGAAGG
326009 CATGGAATGATGGGCATGGAATAAAAAAATGAAGG
1 CATGGAATGATGGGCATGGAATAAAAAAATGAAGG
* *
326044 CATAGAATGATGGGCATGGAAT-AAAAAATGAATG
1 CATGGAATGATGGGCATGGAATAAAAAAATGAAGG
326078 CATGGAATGATGG
1 CATGGAATGATGG
326091 ATAAAAATGA
Statistics
Matches: 145, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
34 23 0.16
35 122 0.84
ACGTcount: A:0.45, C:0.06, G:0.30, T:0.19
Consensus pattern (35 bp):
CATGGAATGATGGGCATGGAATAAAAAAATGAAGG
Found at i:327384 original size:28 final size:27
Alignment explanation
Indices: 327316--327384 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
327306 TTCACAATCA
**
327316 GGGATACTCCAACCCCGTTAATCATCG
1 GGGATACTCCAACCCCGTTAATCAGAG
* *
327343 GGGATACTCCAACCCCGTTATTTCCGAG
1 GGGATACTCCAACCCCGTTA-ATCAGAG
*
327371 GGGATACTCTAACC
1 GGGATACTCCAACC
327385 TCGGCTTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (27 bp):
GGGATACTCCAACCCCGTTAATCAGAG
Found at i:327430 original size:79 final size:79
Alignment explanation
Indices: 327339--327909 Score: 955
Period size: 79 Copynumber: 7.2 Consensus size: 79
327329 CCCGTTAATC
* * *
327339 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCTAACCTCGGCTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
327404 ATCAATTTTTCATA
66 ATCAATTTTTCATA
* *
327418 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCTGGCTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
327483 ATCAATTTTTCATA
66 ATCAATTTTTCATA
*
327497 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
327562 ATCAATTTTTCATA
66 ATCAATTTTTCATA
* *
327576 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTTATCTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
327641 ATCAATTTTTCATA
66 ATCAATTTTTCATA
** * **
327655 ATTAGGGATACTCCAATCCCGTTATTTTTGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
327720 ATCAATTTTTCATA
66 ATCAATTTTTCATA
327734 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
*
327799 ACCAATTTTTCATA
66 ATCAATTTTTCATA
*
327813 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
* *
327878 A-CTAATTTTCCTTTA
66 ATC-AATTTTTC-ATA
*
327893 ATCAGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
327910 TCTGATTTTA
Statistics
Matches: 466, Mismatches: 24, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
78 1 0.00
79 447 0.96
80 18 0.04
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
ATCAATTTTTCATA
Found at i:335961 original size:32 final size:33
Alignment explanation
Indices: 335920--335996 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 33
335910 CTCACCTTTG
*
335920 TAAAAGCCCACATAAGTCAGTGGCAACCTCTT-
1 TAAAAGCCCACATAAGTCAGTGGCAACCCCTTC
*
335952 TAAAAGCCCACATAAGTCGGTGGCAACCCCTTC
1 TAAAAGCCCACATAAGTCAGTGGCAACCCCTTC
*
335985 TCAAAGCCCACA
1 TAAAAGCCCACA
335997 ACTCTGTGGC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 30 0.73
33 11 0.27
ACGTcount: A:0.34, C:0.32, G:0.16, T:0.18
Consensus pattern (33 bp):
TAAAAGCCCACATAAGTCAGTGGCAACCCCTTC
Found at i:336165 original size:32 final size:32
Alignment explanation
Indices: 336053--336172 Score: 145
Period size: 32 Copynumber: 3.8 Consensus size: 32
336043 CTTCTCCTTC
* * *
336053 CAAAA-CCCACACAAGTAGATGACAACCTCTT
1 CAAAAGCCCACACAAGTTGGTGGCAACCTCTT
* * * *
336084 CTAAAGCCCATACAAGTTGATAGCAACCTCTT
1 CAAAAGCCCACACAAGTTGGTGGCAACCTCTT
*
336116 CAAAAGCCCACACAAGTTGGTGGTAACCCTCTT
1 CAAAAGCCCACACAAGTTGGTGGCAA-CCTCTT
336149 -AAAAGCCCACACAAGTTGGTGGCA
1 CAAAAGCCCACACAAGTTGGTGGCA
336173 TCTCCTTCCA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
31 4 0.05
32 66 0.87
33 6 0.08
ACGTcount: A:0.36, C:0.29, G:0.16, T:0.19
Consensus pattern (32 bp):
CAAAAGCCCACACAAGTTGGTGGCAACCTCTT
Found at i:336235 original size:49 final size:51
Alignment explanation
Indices: 336182--336320 Score: 183
Period size: 49 Copynumber: 2.8 Consensus size: 51
336172 ATCTCCTTCC
*
336182 AAGTCCAATGTCGCTGGCCTTGAATCAACACATTGGCACC-TTTATCT-TT
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTATCTCTT
* * * * *
336231 AAGTCCAATGTCACTAGCCTTGAATCAGCACATTGACACCTTTTTTTTCTT
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTATCTCTT
* * *
336282 AAGACTAATGTCGCTGGCCTTGAATTAGCACATTGGCAC
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
336321 AAGCCCAATA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
49 36 0.47
50 5 0.07
51 35 0.46
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (51 bp):
AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTTATCTCTT
Found at i:336766 original size:20 final size:20
Alignment explanation
Indices: 336741--336867 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
336731 TTTTCACAAT
336741 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
336761 TTGTATCGATACATTCTGGGTTTTATCTA
1 TTGTATCGATACA-T-T--G---T-TC-A
* *
336790 GATGTATCGATACATT-TCCCA
1 -TTGTATCGATACATTGT-TCA
*
336811 TTGTATCGATACATCGTTCA
1 TTGTATCGATACATTGTTCA
* * *
336831 TTGCATCGATACAGTGTTTA
1 TTGTATCGATACATTGTTCA
*
336851 TTGTATCAATACATTGT
1 TTGTATCGATACATTGT
336868 ATCGATACAT
Statistics
Matches: 83, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
20 58 0.70
21 3 0.04
22 3 0.04
24 1 0.01
27 1 0.01
28 3 0.04
29 2 0.02
30 12 0.14
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:337481 original size:11 final size:12
Alignment explanation
Indices: 337453--337485 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
337443 AATCCCGGAG
337453 CTCCAAAAACAC
1 CTCCAAAAACAC
*
337465 CACCAAAAA-AC
1 CTCCAAAAACAC
337476 CTCCAAAAAC
1 CTCCAAAAAC
337486 TCCATATTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.55, C:0.39, G:0.00, T:0.06
Consensus pattern (12 bp):
CTCCAAAAACAC
Found at i:339357 original size:51 final size:51
Alignment explanation
Indices: 339295--339411 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
339285 TATTTTTGAG
*
339295 GGGATACTCCAACCCCT-ATTTTATTTCTAAAACACCAATTTTTCACAATC
1 GGGATACTCCAACCCCTGATTTAATTTCTAAAACACCAATTTTTCACAATC
*
339345 AGGGATACTCCAA-CTCTGATTTAATTTCTAAAACACCAATTTTTCACAATC
1 -GGGATACTCCAACCCCTGATTTAATTTCTAAAACACCAATTTTTCACAATC
* *
339396 GGGATATTCTAACCCC
1 GGGATACTCCAACCCC
339412 GTTATTTCAT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 13 0.22
51 46 0.78
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (51 bp):
GGGATACTCCAACCCCTGATTTAATTTCTAAAACACCAATTTTTCACAATC
Found at i:339635 original size:79 final size:78
Alignment explanation
Indices: 339427--339714 Score: 237
Period size: 79 Copynumber: 3.7 Consensus size: 78
339417 TTCATTGGAT
** * * *
339427 ATACTCCAACCTTGTTATTTCCGAGAGGATACTCCAACCTCAACTT-TATTTCTAAAATATTAAT
1 ATACTCCAACCACGTTATTTCTGAG-GGATACTCCAACCTCGACTTCTATTTCTAAAATATTGAT
* *
339491 TTCTCACAATTAGGG
65 TTCTCA-AAATCGGG
* * * * * *
339506 ATACTCTAACCTCGTTATTTTCAT-AAGGATACTCCAACC-CTAGTTTTATTTCTAAAATATTGA
1 ATACTCCAACCACGTTA-TTTC-TGAGGGATACTCCAACCTCGACTTCTATTTCTAAAATATTGA
339569 TTTCTCAAAATCGGTG
64 TTTCTCAAAATCGG-G
* * * * * *
339585 ATATTCGAACCCCGTTATTTCTGCGGGAATACTCCAACCTCGA-TTCTATTT-TCAAAACACTGA
1 ATACTCCAACCACGTTATTTCTGAGGG-ATACTCCAACCTCGACTTCTATTTCT-AAAATATTGA
* * *
339648 TTTTTTATAATCAGGG
64 TTTCTCAAAATC-GGG
* *
339664 ATACTCCAACCATGTTATTTCTGAGGGGATACTCCAACCCCGA-TTCTATTT
1 ATACTCCAACCACGTTATTTCTGA-GGGATACTCCAACCTCGACTTCTATTT
339715 TCAGAACATC
Statistics
Matches: 172, Mismatches: 27, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
77 1 0.01
78 16 0.09
79 143 0.83
80 12 0.07
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (78 bp):
ATACTCCAACCACGTTATTTCTGAGGGATACTCCAACCTCGACTTCTATTTCTAAAATATTGATT
TCTCAAAATCGGG
Found at i:339715 original size:79 final size:79
Alignment explanation
Indices: 339427--339748 Score: 223
Period size: 79 Copynumber: 4.1 Consensus size: 79
339417 TTCATTGGAT
* * * * * *
339427 ATACTCCAACCTTGTTATTTCCGAGAGG-ATACTCCAACCTCAACTT-TA-TTTCTAAAATATTA
1 ATACTCCAACCATGTTATTTCTGAG-GGAATACTCCAACCCCGA-TTCTATTTTC-AAAACATCA
* * *
339489 ATTTCTCACAATTAGGG
63 ATTTTTCATAATCAGGG
* * * * *
339506 ATACTCTAACC-TCGTTATTTTCAT-AAGG-ATACTCCAA-CCCTAGTTTTA-TTTCTAAAATAT
1 ATACTCCAACCAT-GTTA-TTTC-TGAGGGAATACTCCAACCCCGA-TTCTATTTTC-AAAACAT
** * *
339566 TGATTTCTCAAAATC-GGTG
61 CAATTTTTCATAATCAGG-G
* * ** * * *
339585 ATATTCGAACCCCGTTATTTCTGCGGGAATACTCCAACCTCGATTCTATTTTCAAAACA-CTGAT
1 ATACTCCAACCATGTTATTTCTGAGGGAATACTCCAACCCCGATTCTATTTTCAAAACATC-AAT
*
339649 TTTTTATAATCAGGG
65 TTTTCATAATCAGGG
* *
339664 ATACTCCAACCATGTTATTTCTGAGGGGATACTCCAACCCCGATTCTATTTTCAGAACATCAATT
1 ATACTCCAACCATGTTATTTCTGAGGGAATACTCCAACCCCGATTCTATTTTCAAAACATCAATT
*
339729 TTTCGTAATCAGGG
66 TTTCATAATCAGGG
339743 ATACTC
1 ATACTC
339749 TAGCCCCGTT
Statistics
Matches: 197, Mismatches: 33, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
77 1 0.01
78 14 0.07
79 167 0.85
80 15 0.08
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.36
Consensus pattern (79 bp):
ATACTCCAACCATGTTATTTCTGAGGGAATACTCCAACCCCGATTCTATTTTCAAAACATCAATT
TTTCATAATCAGGG
Found at i:341830 original size:4 final size:4
Alignment explanation
Indices: 341821--341847 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
341811 TTTTGAGGTG
341821 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
341848 GTTTTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:352179 original size:1 final size:1
Alignment explanation
Indices: 352173--352268 Score: 57
Period size: 1 Copynumber: 96.0 Consensus size: 1
352163 ACCTTCTTTT
* * * * * * * * **
352173 AAAAAAAACACAAAAAAAACAAAAAAAAAACAAAACAAAAAAACAAAATAAAAAAAACAACCAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
352238 AAAAACAAAACAAAGAAAAAAGAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
352269 GAACCTGCTT
Statistics
Matches: 67, Mismatches: 28, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.01
Consensus pattern (1 bp):
A
Found at i:352189 original size:11 final size:11
Alignment explanation
Indices: 352173--352244 Score: 64
Period size: 11 Copynumber: 6.9 Consensus size: 11
352163 ACCTTCTTTT
352173 AAAAAAAACAC
1 AAAAAAAACAC
*
352184 AAAAAAAACAA
1 AAAAAAAACAC
352195 AAAAAAAACA-
1 AAAAAAAACAC
*
352205 AAACAAAAAAAC
1 AAA-AAAAACAC
*
352217 -AAAATAA-A-
1 AAAAAAAACAC
*
352225 AAAAACAAC-C
1 AAAAAAAACAC
352235 AAAAAAAACA
1 AAAAAAAACA
352245 AAACAAAGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
9 7 0.14
10 15 0.30
11 28 0.56
ACGTcount: A:0.85, C:0.14, G:0.00, T:0.01
Consensus pattern (11 bp):
AAAAAAAACAC
Found at i:352191 original size:13 final size:13
Alignment explanation
Indices: 352173--352268 Score: 67
Period size: 13 Copynumber: 7.4 Consensus size: 13
352163 ACCTTCTTTT
352173 AAAAAAAACAC--
1 AAAAAAAACACAA
352184 -AAAAAAA-ACAA
1 AAAAAAAACACAA
352195 AAAAAAAACA-AA
1 AAAAAAAACACAA
*
352207 ACAAAAAAACAAAA
1 A-AAAAAAACACAA
352221 TAAAAAAAACAACCAA
1 -AAAAAAAAC-A-CAA
*
352237 AAAAAACAAAACAA
1 AAAAAA-AACACAA
* * *
352251 AGAAAAAAGAGAA
1 AAAAAAAACACAA
352264 AAAAA
1 AAAAA
352269 GAACCTGCTT
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
9 2 0.03
10 7 0.10
12 10 0.14
13 19 0.28
14 18 0.26
15 9 0.13
16 4 0.06
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.01
Consensus pattern (13 bp):
AAAAAAAACACAA
Found at i:352201 original size:22 final size:23
Alignment explanation
Indices: 352173--352247 Score: 89
Period size: 25 Copynumber: 3.1 Consensus size: 23
352163 ACCTTCTTTT
352173 AAAAAAAAC-ACAAAAAAAACAA
1 AAAAAAAACAACAAAAAAAACAA
*
352195 AAAAAAAACAAAACAAAAAAACAAAA
1 AAAAAAAAC--AACAAAAAAA-ACAA
352221 TAAAAAAAACAACCAAAAAAAACAA
1 -AAAAAAAACAA-CAAAAAAAACAA
352246 AA
1 AA
352248 CAAAGAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
22 9 0.20
24 2 0.04
25 14 0.31
26 11 0.24
27 9 0.20
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.01
Consensus pattern (23 bp):
AAAAAAAACAACAAAAAAAACAA
Found at i:352209 original size:27 final size:27
Alignment explanation
Indices: 352173--352268 Score: 110
Period size: 27 Copynumber: 3.7 Consensus size: 27
352163 ACCTTCTTTT
352173 AAAAAAAACACAAAAAAAACAAAA-AA
1 AAAAAAAACACAAAAAAAACAAAATAA
*
352199 AAAACAAA-AC-AAAAAAACAAAATAA
1 AAAAAAAACACAAAAAAAACAAAATAA
*
352224 AAAAAACAAC-CAAAAAAAACAAAACAA
1 AAAAAA-AACACAAAAAAAACAAAATAA
* * *
352251 AGAAAAAAGAGAAAAAAA
1 AAAAAAAACACAAAAAAA
352269 GAACCTGCTT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
24 12 0.20
25 9 0.15
26 12 0.20
27 26 0.44
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.01
Consensus pattern (27 bp):
AAAAAAAACACAAAAAAAACAAAATAA
Found at i:352266 original size:40 final size:37
Alignment explanation
Indices: 352173--352268 Score: 120
Period size: 40 Copynumber: 2.5 Consensus size: 37
352163 ACCTTCTTTT
*
352173 AAAAAAAACACAAAAAAAACAAAAAAAAAACAAAACA
1 AAAAAAAAAACAAAAAAAACAAAAAAAAAACAAAACA
*
352210 AAAAAACAAAATAAAAAAAACAACCAAAAAAAACAAAACA
1 AAAAAA-AAAACAAAAAAAACAA--AAAAAAAACAAAACA
* *
352250 AAGAAAAAAGAGAAAAAAA
1 AA-AAAAAAAACAAAAAAA
352269 GAACCTGCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
37 6 0.12
38 14 0.27
40 27 0.53
41 4 0.08
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.01
Consensus pattern (37 bp):
AAAAAAAAAACAAAAAAAACAAAAAAAAAACAAAACA
Found at i:353384 original size:60 final size:60
Alignment explanation
Indices: 353230--353628 Score: 541
Period size: 60 Copynumber: 6.6 Consensus size: 60
353220 CCTTTCACTT
* * *
353230 TTCAGTCCTCAAAGAGTAGGACGCCTTCTCGTTTTAAAAGCCCACAAAAGTTGGTGGCACC
1 TTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT-AAAGCCCACACAAGTTGGTGGCACC
*
353291 TTCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACC
1 TT-CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * *
353352 TTCAGTCCTCAAAGAGCAGGATGCATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTT
1 TTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-C
* * *
353413 TTCTAGTCCTCAAAGGGCAGGACGCC-TCTTCCTTTCAAAGCCCATACAAGTTGGTGGCACC
1 TTC-AGTCCTCAAAGAGCAGGACGCCTTC-TCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * * *
353474 ATCAGTGCTCAAAGAGCAAGATGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACC
1 TTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * *
353534 TTCAGTCCTCAAAGAGTAAGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACT
1 TTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
353594 TCTCAGTCCTCAAAGAGCAGGACG-CTCTCTCCTTT
1 T-TCAGTCCTCAAAGAGCAGGACGCCT-TCTCCTTT
353629 CACCCTTTAG
Statistics
Matches: 299, Mismatches: 32, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
60 158 0.53
61 62 0.21
62 79 0.26
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (60 bp):
TTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:353447 original size:122 final size:120
Alignment explanation
Indices: 353230--353628 Score: 541
Period size: 122 Copynumber: 3.3 Consensus size: 120
353220 CCTTTCACTT
* * * *
353230 TTCAGTCCTCAAAGAGTAGGACGCCTTCTCGTTTTAAAAGCCCACAAAAGTTGGTGGCACCTTCC
1 TTCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTT-C
*
353295 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACC
64 AGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
353352 TTCAGTCCTCAAAGAGCAGGATGCATTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
1 TTCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC-
* * *
353417 AGTCCTCAAAGGGCAGGACGCC-TCTTCCTTTCAAAGCCCATACAAGTTGGTGGCACC
64 AGTCCTCAAAGAGCAGGACGCCTTC-TCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * * *
353474 ATCAGTGCTCAAAGAGCAAGATGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCAG
1 TTCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAG
* * * *
353539 TCCTCAAAGAGTAAGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACT
66 TCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
*
353594 TCTCAGTCCTCAAAGAGCAGGACG-CTCTCTCCTTT
1 T-TCAGTCCTCAAAGAGCAGGATGCCT-TCTCCTTT
353629 CACCCTTTAG
Statistics
Matches: 242, Mismatches: 29, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
120 49 0.20
121 58 0.24
122 135 0.56
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (120 bp):
TTCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAG
TCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:353533 original size:182 final size:183
Alignment explanation
Indices: 353225--353630 Score: 631
Period size: 182 Copynumber: 2.2 Consensus size: 183
353215 TTTCTCCTTT
* * *
353225 CACTTTTCAGTCCTCAAAGAGTAGGACGCCT-TCTCGTTTTAAAAGCCCACAAAAGTTGGTGGCA
1 CACTTTTCAGTCCTCAAAGAGCAGGACGCCTCTCTC-CTTTCAAAGCCCACAAAAGTTGGTGGCA
* *
353289 CCTTCCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT
65 CCATCCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT
* *
353354 CAGTCCTCAAAGAGCAGGATGCATTTTCCTTTTAAAGCCCACACAAGTTGGTGG
130 CAGTCCTCAAAGAGCAAGATGCATTCTCCTTTTAAAGCCCACACAAGTTGGTGG
* * *
353408 CACTTTTCTAGTCCTCAAAGGGCAGGACGCCTCT-TCCTTTCAAAGCCCATACAAGTTGGTGGCA
1 CACTTTTC-AGTCCTCAAAGAGCAGGACGCCTCTCTCCTTTCAAAGCCCACAAAAGTTGGTGGCA
* *
353472 CCAT-CAGTGCTCAAAGAGCAAGATGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT
65 CCATCCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT
* *
353536 CAGTCCTCAAAGAGTAAGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGG
130 CAGTCCTCAAAGAGCAAGATGCATTCTCCTTTTAAAGCCCACACAAGTTGGTGG
*
353590 CACTTCTCAGTCCTCAAAGAGCAGGACG-CTCTCTCCTTTCA
1 CACTTTTCAGTCCTCAAAGAGCAGGACGCCTCTCTCCTTTCA
353631 CCCTTTAGTC
Statistics
Matches: 204, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
180 4 0.02
181 27 0.13
182 114 0.56
183 35 0.17
184 23 0.11
185 1 0.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (183 bp):
CACTTTTCAGTCCTCAAAGAGCAGGACGCCTCTCTCCTTTCAAAGCCCACAAAAGTTGGTGGCAC
CATCCAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTTC
AGTCCTCAAAGAGCAAGATGCATTCTCCTTTTAAAGCCCACACAAGTTGGTGG
Found at i:353716 original size:100 final size:100
Alignment explanation
Indices: 353532--353785 Score: 394
Period size: 100 Copynumber: 2.6 Consensus size: 100
353522 GCTGGTGGCA
* *
353532 CCTTCAGTCCTCAAAGAGTAAGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCT
1 CCTTTAGTCCTCAAAGAGTAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCT
* *
353597 CAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCAC
66 CAGTCCTCAAAAAGCAGGACACTCTCTCCTTTCAC
353632 CCTTTAGTCCTCAAAGAGTAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCT
1 CCTTTAGTCCTCAAAGAGTAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCT
* * *
353697 TAGTCCTCAAAAAGTAGGACACTCTCTTCTTTCAC
66 CAGTCCTCAAAAAGCAGGACACTCTCTCCTTTCAC
*
353732 CCTTTAGTCCTCAAAGAGCAGGATGCCTT-T-C----AAAGCCCACACAAGTTGGTGGCA
1 CCTTTAGTCCTCAAAGAGTAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
353786 TTTTCCAGCC
Statistics
Matches: 146, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
94 23 0.16
98 1 0.01
99 1 0.01
100 121 0.83
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (100 bp):
CCTTTAGTCCTCAAAGAGTAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCT
CAGTCCTCAAAAAGCAGGACACTCTCTCCTTTCAC
Found at i:353809 original size:55 final size:55
Alignment explanation
Indices: 353737--353922 Score: 203
Period size: 55 Copynumber: 3.3 Consensus size: 55
353727 TTCACCCTTT
353737 AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * * * **
353792 AGCCCCCAAAGAGCAGGACGCTTTTCAAAGCCCACACAAGCTGGTGGCACCTT-C
1 AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * *
353846 AGTCCTCAGAGAGCAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGA------TGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
353908 AGTCCTCAAAGAGCA
1 AGTCCTCAAAGAGCA
353923 TGGCACCTTT
Statistics
Matches: 104, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
54 16 0.15
55 46 0.44
60 26 0.25
61 2 0.02
62 14 0.13
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:353890 original size:60 final size:62
Alignment explanation
Indices: 353812--353950 Score: 196
Period size: 62 Copynumber: 2.3 Consensus size: 62
353802 GAGCAGGACG
*
353812 CTTTTCAAAGCCCACACAAGCTGGTGGCAC-CTTC-AGTCCTCAGAGAGCA-GG-ACGCTTTTTC
1 CTTTT-AAAGCCCACACAAGCTGGTGGCACTCTTCTAGTCCTCAAAGAGCATGGCAC-C-TTTTC
* *
353873 CTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCATGGCACCTTTTC
1 CTTTTAAAGCCCACACAAGCTGGTGGCACTCTTCTAGTCCTCAAAGAGCATGGCACCTTTTC
353935 CTTTTAAAGCCCACAC
1 CTTTTAAAGCCCACAC
353951 CCATACAAGT
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
60 23 0.32
61 8 0.11
62 35 0.49
63 3 0.04
64 2 0.03
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (62 bp):
CTTTTAAAGCCCACACAAGCTGGTGGCACTCTTCTAGTCCTCAAAGAGCATGGCACCTTTTC
Found at i:354680 original size:20 final size:20
Alignment explanation
Indices: 354655--354706 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
354645 TACCCAGATG
354655 TATCGATACATT-TCCCATTA
1 TATCGATACATTGT-CCATTA
* * *
354675 TATCGATTCATTGTTCATTG
1 TATCGATACATTGTCCATTA
354695 TATCGATACATT
1 TATCGATACATT
354707 ATATCGATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (20 bp):
TATCGATACATTGTCCATTA
Found at i:356408 original size:79 final size:78
Alignment explanation
Indices: 356268--356508 Score: 243
Period size: 79 Copynumber: 3.1 Consensus size: 78
356258 ATGATGAACA
* * * * *
356268 CGTTATTTTTACGGGGATCCTCTAACCTCGATTTTA-TTTCTAAAATATTGATTTCTCATAATCG
1 CGTTATTTCTACGGGGATACTCTAACCCCGATTTTATTTTC-AAAACATCGATTTCT-ATAATCG
* *
356332 GGGATATTCTAACCC
64 GGGATACTCCAACCC
* * * *
356347 CGTTATTTCTACGGGGATACTATAACCCCGATTCTATTTTCAAAACACCGATCTTCTATAATCAG
1 CGTTATTTCTACGGGGATACTCTAACCCCGATTTTATTTTCAAAACATCGAT-TTCTATAATCGG
356412 GGATACTCCAACCC
65 GGATACTCCAACCC
* * * ** * * *
356426 TGTTATTTCTGA-GAGGATACTCTAAACCTAATTTTATTTTCAGAACATCAATTTTCCATAATCG
1 CGTTATTTCT-ACGGGGATACTCTAACCCCGATTTTATTTTCAAAACATCGA-TTTCTATAATCG
*
356490 GGGATACTCCAGCCC
64 GGGATACTCCAACCC
356505 CGTT
1 CGTT
356509 GTTATCCCTA
Statistics
Matches: 133, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
79 123 0.92
80 10 0.08
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (78 bp):
CGTTATTTCTACGGGGATACTCTAACCCCGATTTTATTTTCAAAACATCGATTTCTATAATCGGG
GATACTCCAACCC
Found at i:357700 original size:52 final size:52
Alignment explanation
Indices: 357562--357715 Score: 202
Period size: 52 Copynumber: 3.0 Consensus size: 52
357552 ATTTTCTTTC
* * *
357562 TTAAGTCC-AATATCGCTAGCCTTAAATCAGCATACTAGCACCTTTGTCATCT
1 TTAAG-CCTAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTGTCATCT
* * * *
357614 TCAAGTCTAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCT
1 TTAAGCCTAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTGTCATCT
* * *
357666 TTAAGCCTAATATCGCTGGCCTTAAATCAACATATTGGTACCTTTATCAT
1 TTAAGCCTAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTGTCAT
357716 TCTACGCATC
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
51 1 0.01
52 86 0.99
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (52 bp):
TTAAGCCTAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTTGTCATCT
Found at i:362661 original size:20 final size:19
Alignment explanation
Indices: 362616--362671 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 19
362606 TTGTATCGAT
362616 ACATTGTATC-ATACATGC
1 ACATTGTATCGATACATGC
* *
362634 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
362653 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
362672 AGATTGGCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 9 0.27
19 8 0.24
20 16 0.48
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:362860 original size:24 final size:24
Alignment explanation
Indices: 362828--362877 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
362818 TGGCTACGGG
362828 AAAGCATTAAAACAAGCACCAAAC
1 AAAGCATTAAAACAAGCACCAAAC
*
362852 AAAGCATTAAAACAAGCTCCAAAC
1 AAAGCATTAAAACAAGCACCAAAC
362876 AA
1 AA
362878 GCTTGTAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.24, G:0.08, T:0.10
Consensus pattern (24 bp):
AAAGCATTAAAACAAGCACCAAAC
Found at i:370862 original size:12 final size:12
Alignment explanation
Indices: 370845--370870 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
370835 GGGAAGAAAG
370845 GAGAAAATTTTT
1 GAGAAAATTTTT
370857 GAGAAAATTTTT
1 GAGAAAATTTTT
370869 GA
1 GA
370871 AAATTGCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (12 bp):
GAGAAAATTTTT
Found at i:371494 original size:13 final size:13
Alignment explanation
Indices: 371476--371502 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
371466 ACATTATGCT
371476 TTGTATCGATACA
1 TTGTATCGATACA
371489 TTGTATCGATACA
1 TTGTATCGATACA
371502 T
1 T
371503 GCTCATTGTA
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:371511 original size:19 final size:19
Alignment explanation
Indices: 371486--371581 Score: 104
Period size: 20 Copynumber: 4.9 Consensus size: 19
371476 TTGTATCGAT
371486 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
*
371505 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
371524 ACAATTGTATCGATACATG-
1 AC-ATTGTATCGATACATGC
* * *
371543 AGATTGGTAGTAGATACATGGT
1 ACATT-GTA-TCGATACAT-GC
*
371565 ACAATGTATCGATACAT
1 ACATTGTATCGATACAT
371582 TGCTTGTAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
18 3 0.05
19 23 0.35
20 32 0.49
21 4 0.06
22 3 0.05
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:371719 original size:106 final size:106
Alignment explanation
Indices: 371583--371794 Score: 415
Period size: 106 Copynumber: 2.0 Consensus size: 106
371573 TCGATACATT
371583 GCTTGTAACGGCTATAAACGGCTATAATTTCAAATCAATGTATCGATACATTATTAATTGTATCG
1 GCTTGTAACGGCTATAAACGGCTATAATTTCAAATCAATGTATCGATACATTATTAATTGTATCG
371648 ATACATGGCTACGGGAAAGCATTAAAACAAGCACCAAACAA
66 ATACATGGCTACGGGAAAGCATTAAAACAAGCACCAAACAA
*
371689 GCTTGTAACGGCTATAAATGGCTATAATTTCAAATCAATGTATCGATACATTATTAATTGTATCG
1 GCTTGTAACGGCTATAAACGGCTATAATTTCAAATCAATGTATCGATACATTATTAATTGTATCG
371754 ATACATGGCTACGGGAAAGCATTAAAACAAGCACCAAACAA
66 ATACATGGCTACGGGAAAGCATTAAAACAAGCACCAAACAA
371795 TCATTCAACC
Statistics
Matches: 105, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (106 bp):
GCTTGTAACGGCTATAAACGGCTATAATTTCAAATCAATGTATCGATACATTATTAATTGTATCG
ATACATGGCTACGGGAAAGCATTAAAACAAGCACCAAACAA
Found at i:375818 original size:21 final size:21
Alignment explanation
Indices: 375785--375845 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
375775 GAGATGTTGG
*
375785 ACATA-CTAAAAATGCATGAA
1 ACATAGCTCAAAATGCATGAA
375805 ACATAGCTCAAAATGCATGAA
1 ACATAGCTCAAAATGCATGAA
375826 ACATAGCTCAAAATGCATGA
1 ACATAGCTCAAAATGCATGA
375846 GCATGGGTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
20 5 0.13
21 34 0.87
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (21 bp):
ACATAGCTCAAAATGCATGAA
Found at i:376918 original size:20 final size:21
Alignment explanation
Indices: 376893--376947 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
376883 CATGTGAGGC
376893 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTAT
* *
376913 ATGTATCAATACATTTACTAT
1 ATGTATCGATACATTCACTAT
* *
376934 TTATATCGATACAT
1 ATGTATCGATACAT
376948 ATTGTAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:378344 original size:51 final size:51
Alignment explanation
Indices: 378279--378397 Score: 179
Period size: 51 Copynumber: 2.3 Consensus size: 51
378269 CACATTAAAG
*
378279 AATGTATTGATACATTTAGGTTAAAAAC-CAAAATGTATCGATACAATGAAA
1 AATGTATCGATACATTTAGGTT-AAAACTCAAAATGTATCGATACAATGAAA
* *
378330 AATGTATC-AGTACATTTAGGTTAAGACTCAGAATGTATCGATACAATGAAA
1 AATGTATCGA-TACATTTAGGTTAAAACTCAAAATGTATCGATACAATGAAA
378381 AATGTATCGATACATTT
1 AATGTATCGATACATTT
378398 CCTTTCCAGA
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
50 5 0.08
51 56 0.90
52 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (51 bp):
AATGTATCGATACATTTAGGTTAAAACTCAAAATGTATCGATACAATGAAA
Done.