Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 43
Found at i:172224 original size:23 final size:24
Alignment explanation
Indices: 172194--172243 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
172184 TTTTTATTTA
172194 ATAATTAA-TTAATAA-TTT-AAAT
1 ATAATTAACTTAA-AATTTTAAAAT
172216 ATAATTTAACTTAAAATTTTAAAAT
1 ATAA-TTAACTTAAAATTTTAAAAT
172241 ATA
1 ATA
172244 TAAATGATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.17
23 6 0.25
24 7 0.29
25 7 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATTAACTTAAAATTTTAAAAT
Found at i:172720 original size:2 final size:2
Alignment explanation
Indices: 172692--172793 Score: 93
Period size: 2 Copynumber: 51.0 Consensus size: 2
172682 ACTTATAGTC
* * * * *
172692 TA TA -A TA TA AA TA TA TA AA CTA GA TA TA TA TA AA GTA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA
* *
172735 CTA TA TG TA TG TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
172777 TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA
172794 GTTCTTCTAA
Statistics
Matches: 80, Mismatches: 14, Indels: 12
0.75 0.13 0.11
Matches are distributed among these distances:
1 3 0.04
2 74 0.93
3 3 0.04
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:176802 original size:18 final size:20
Alignment explanation
Indices: 176759--176805 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
176749 TATTTATATG
176759 AAATAA-TAAATTTAAAATT
1 AAATAATTAAATTTAAAATT
*
176778 TAA-AATTAAA-TTAAAA-T
1 AAATAATTAAATTTAAAATT
176795 AAATAATTAAA
1 AAATAATTAAA
176806 AAAAATGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 3 0.12
18 15 0.62
19 6 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATAATTAAATTTAAAATT
Found at i:182156 original size:23 final size:23
Alignment explanation
Indices: 182126--182185 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
182116 TCGTATAAAG
182126 GCACCGAAGTGCCACATAGAATT
1 GCACCGAAGTGCCACATAGAATT
* *
182149 GCACCGAAGTGCCTCGTAGAATT
1 GCACCGAAGTGCCACATAGAATT
*
182172 GCACCGTAGTGCCA
1 GCACCGAAGTGCCA
182186 TATAAGCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.18
Consensus pattern (23 bp):
GCACCGAAGTGCCACATAGAATT
Found at i:183831 original size:13 final size:14
Alignment explanation
Indices: 183801--183832 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
183791 GATATGTATC
183801 TTTTATTTTATTAA
1 TTTTATTTTATTAA
183815 -TTTATTTT-TTAA
1 TTTTATTTTATTAA
183827 TTTTAT
1 TTTTAT
183833 AAAAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTTATTAA
Found at i:187031 original size:20 final size:20
Alignment explanation
Indices: 187006--187062 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
186996 TAAAAAAATG
*
187006 TGTAGTATCGATACTCTAGT
1 TGTAGTATCGATACCCTAGT
187026 TGTAGTATCGATACCCTAG-
1 TGTAGTATCGATACCCTAGT
*
187045 GGTCAAGTATCGATACCC
1 TGT--AGTATCGATACCC
187063 CTATGAGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 18 0.55
21 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTAGTATCGATACCCTAGT
Found at i:204787 original size:2 final size:2
Alignment explanation
Indices: 204780--204845 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
204770 CACCATAACT
204780 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
204821 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
204846 GCTCATCCTT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:205708 original size:43 final size:43
Alignment explanation
Indices: 205651--205733 Score: 148
Period size: 43 Copynumber: 1.9 Consensus size: 43
205641 TTTGTCGACT
*
205651 ACAAACGCCGCTAAAGGTTATGATATTTAGCGGCGTTGTTTCC
1 ACAAACGCCACTAAAGGTTATGATATTTAGCGGCGTTGTTTCC
*
205694 ACAAATGCCACTAAAGGTTATGATATTTAGCGGCGTTGTT
1 ACAAACGCCACTAAAGGTTATGATATTTAGCGGCGTTGTT
205734 GAAGAACGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (43 bp):
ACAAACGCCACTAAAGGTTATGATATTTAGCGGCGTTGTTTCC
Found at i:207070 original size:21 final size:21
Alignment explanation
Indices: 207044--207117 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
207034 GAAATGGAAA
207044 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
207065 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
207085 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
207106 ATCTCAACGCGA
1 ATCGCAACGCGA
207118 AATGCAACGC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:207090 original size:20 final size:20
Alignment explanation
Indices: 207034--207096 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
207024 TAAAGAAACA
207034 GAAATGGAAAATCGCAACGC
1 GAAATGGAAAATCGCAACGC
** ** *
207054 GATTTTCAACTATCGCAACGC
1 GAAATGGAA-AATCGCAACGC
207075 GAAATGGAAAATCGCAACGC
1 GAAATGGAAAATCGCAACGC
207095 GA
1 GA
207097 TTTTCAACTA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
GAAATGGAAAATCGCAACGC
Found at i:207138 original size:41 final size:41
Alignment explanation
Indices: 207034--207121 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
207024 TAAAGAAACA
207034 GAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGC
1 GAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGC
*
207075 GAAATGGAAAATCGCAACGCGATTTTCAACTATCTCAACGC
1 GAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGC
207116 GAAATG
1 GAAATG
207122 CAACGCGAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (41 bp):
GAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGC
Found at i:209611 original size:28 final size:28
Alignment explanation
Indices: 209571--209634 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
209561 TTTGAAAACT
* *
209571 GGTTCAACTGGAAATCGTTACCTAGTCC
1 GGTTCAATTGGAAACCGTTACCTAGTCC
*
209599 GGTTCAATTGGAAACCGTTACTTAGTCC
1 GGTTCAATTGGAAACCGTTACCTAGTCC
*
209627 AGTTCAAT
1 GGTTCAAT
209635 CTACATCGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (28 bp):
GGTTCAATTGGAAACCGTTACCTAGTCC
Found at i:210566 original size:17 final size:17
Alignment explanation
Indices: 210544--210577 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
210534 GACCGATTCG
210544 CTAACCGGTCCGGTTCT
1 CTAACCGGTCCGGTTCT
210561 CTAACCGGTCCGGTTCT
1 CTAACCGGTCCGGTTCT
210578 GAAAACCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.24, T:0.29
Consensus pattern (17 bp):
CTAACCGGTCCGGTTCT
Found at i:211999 original size:42 final size:42
Alignment explanation
Indices: 211936--212066 Score: 201
Period size: 42 Copynumber: 3.1 Consensus size: 42
211926 ATAATCGTGT
* * *
211936 CGTTTATTATAAAAACACCACTAAGGTACATGACTATTGCGG
1 CGTTTATTACAAAAACACCACTAAAGTACATGATTATTGCGG
211978 CGTTTATTACAAAAA-AGCCACTAAAGTACATGATTATTGCGG
1 CGTTTATTACAAAAACA-CCACTAAAGTACATGATTATTGCGG
* *
212020 CGTTTATTACAAAAATACCACTAAAGTACATGATTATTGTGG
1 CGTTTATTACAAAAACACCACTAAAGTACATGATTATTGCGG
212062 CGTTT
1 CGTTT
212067 GAACAAAAAC
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
41 1 0.01
42 81 0.98
43 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (42 bp):
CGTTTATTACAAAAACACCACTAAAGTACATGATTATTGCGG
Found at i:212085 original size:41 final size:41
Alignment explanation
Indices: 211936--212129 Score: 187
Period size: 42 Copynumber: 4.7 Consensus size: 41
211926 ATAATCGTGT
* * *
211936 CGTTTATTATAAAAACACCACTAAGGTACATGACTATTGCGG
1 CGTTTA-TACAAAAACACCACTAAAGTACATGATTATTGCGG
211978 CGTTTATTACAAAAA-AGCCACTAAAGTACATGATTATTGCGG
1 CGTTTA-TACAAAAACA-CCACTAAAGTACATGATTATTGCGG
* *
212020 CGTTTATTACAAAAATACCACTAAAGTACATGATTATTGTGG
1 CGTTTA-TACAAAAACACCACTAAAGTACATGATTATTGCGG
* * * * *
212062 CGTTTGA-ACAAAAACGCTACTAAAATACAAG-TCTATAGCGG
1 CGTTT-ATACAAAAACACCACTAAAGTACATGAT-TATTGCGG
* * * *
212103 CATTTGTATAAAAACGCCACTAAAGTA
1 CGTTTATACAAAAACACCACTAAAGTA
212130 TGAGCCTATA
Statistics
Matches: 131, Mismatches: 16, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
40 1 0.01
41 47 0.36
42 81 0.62
43 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (41 bp):
CGTTTATACAAAAACACCACTAAAGTACATGATTATTGCGG
Found at i:212297 original size:41 final size:41
Alignment explanation
Indices: 212251--212386 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
212241 CATTGAGCCG
* *
212251 TTTGTTTAAAAAAGCCGCTAAAGTACAACTCTGTTGCGGCA
1 TTTGTTGAAAAAAGCCGCTAAAGTACAACTCTATTGCGGCA
* * * * * *
212292 TTTGTTGAAAAACGCCACTATAG-ATGAATTCTATTGCAGCA
1 TTTGTTGAAAAAAGCCGCTAAAGTA-CAACTCTATTGCGGCA
* * * * *
212333 TTTGTAT-AAAAACGCCGCTAAAGTACTACTATATTGCGACG
1 TTTGT-TGAAAAAAGCCGCTAAAGTACAACTCTATTGCGGCA
212374 TTTGTTGAAAAAA
1 TTTGTTGAAAAAA
212387 TATCACTATA
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
40 2 0.03
41 69 0.95
42 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (41 bp):
TTTGTTGAAAAAAGCCGCTAAAGTACAACTCTATTGCGGCA
Found at i:212418 original size:42 final size:42
Alignment explanation
Indices: 212369--212462 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
212359 TACTATATTG
* *
212369 CGACGTTTGTTGAAAAAATATCACTATAAATGAACCCTATTA
1 CGACGTTTGTTGAAAAAATACCACTATAAATGAACCCAATTA
* * * * * *
212411 CGGCGTTTATTGAAAAAATGCCACTATAGATTAATCCAATTA
1 CGACGTTTGTTGAAAAAATACCACTATAAATGAACCCAATTA
212453 CGACGTTTGT
1 CGACGTTTGT
212463 ATATAAACGC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (42 bp):
CGACGTTTGTTGAAAAAATACCACTATAAATGAACCCAATTA
Found at i:212514 original size:12 final size:12
Alignment explanation
Indices: 212497--212522 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
212487 TTTGTGGCGT
212497 TTCTAATGGAAA
1 TTCTAATGGAAA
212509 TTCTAATGGAAA
1 TTCTAATGGAAA
212521 TT
1 TT
212523 TCGCTATATG
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:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (12 bp):
TTCTAATGGAAA
Found at i:213236 original size:14 final size:13
Alignment explanation
Indices: 213209--213274 Score: 66
Period size: 14 Copynumber: 5.1 Consensus size: 13
213199 GTTGAATAAA
*
213209 AAATAATTATATT
1 AAATAATTAAATT
213222 AAATATATTAAATT
1 AAATA-ATTAAATT
*
213236 ACAA-AAATAAA--
1 A-AATAATTAAATT
213247 AAATAATTAAATT
1 AAATAATTAAATT
213260 AAATATATTAAATT
1 AAATA-ATTAAATT
213274 A
1 A
213275 TAAAAATAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
10 2 0.05
11 7 0.16
13 15 0.34
14 18 0.41
15 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATAATTAAATT
Found at i:213296 original size:38 final size:38
Alignment explanation
Indices: 213203--213283 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 38
213193 CTATCTGTTG
*
213203 AATAAAAAATAATTATATTAAATATATTAAATTACAAA
1 AATAAAAAATAATTAAATTAAATATATTAAATTACAAA
*
213241 AATAAAAAATAATTAAATTAAATATATTAAATTATAAA
1 AATAAAAAATAATTAAATTAAATATATTAAATTACAAA
213279 AATAA
1 AATAA
213284 CTTTTTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (38 bp):
AATAAAAAATAATTAAATTAAATATATTAAATTACAAA
Found at i:214300 original size:14 final size:15
Alignment explanation
Indices: 214281--214309 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
214271 TAATTGGAGG
214281 ATTAAATT-TAATAA
1 ATTAAATTATAATAA
214295 ATTAAATTATAATAA
1 ATTAAATTATAATAA
214310 TGACTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAAATTATAATAA
Found at i:215299 original size:2 final size:2
Alignment explanation
Indices: 215294--215322 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
215284 TTACACACCC
215294 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
215323 CTTTAGACAA
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:227624 original size:29 final size:29
Alignment explanation
Indices: 227582--227664 Score: 148
Period size: 29 Copynumber: 2.8 Consensus size: 29
227572 CTCATCTAAC
*
227582 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATATAAGCAATGACATCATTACT
227612 TAAATGATATAAGCAATGACATCATTACT
1 TAAATGATATAAGCAATGACATCATTACT
227641 TAAATGATATAAGCAATGACATCA
1 TAAATGATATAAGCAATGACATCA
227665 ATTTAGTTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 48 0.92
30 4 0.08
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (29 bp):
TAAATGATATAAGCAATGACATCATTACT
Found at i:229678 original size:20 final size:20
Alignment explanation
Indices: 229655--229698 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
229645 CAAAGGAACC
229655 AACAAACGGAAAAAGTGTGA
1 AACAAACGGAAAAAGTGTGA
229675 AACAAACGGAAAAAGTGTGA
1 AACAAACGGAAAAAGTGTGA
229695 AACA
1 AACA
229699 CTCGACTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.57, C:0.11, G:0.23, T:0.09
Consensus pattern (20 bp):
AACAAACGGAAAAAGTGTGA
Found at i:231374 original size:20 final size:17
Alignment explanation
Indices: 231333--231367 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
231323 AAATCAGTTA
231333 AACATCACAAGTTGTCC
1 AACATCACAAGTTGTCC
231350 AACATCACAAGTTGTCC
1 AACATCACAAGTTGTCC
231367 A
1 A
231368 CCAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (17 bp):
AACATCACAAGTTGTCC
Found at i:234400 original size:37 final size:39
Alignment explanation
Indices: 234322--234401 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
234312 AACAAGTTGG
* *
234322 AAAATATTTATATATTTTCTTTAAAAATTTTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAATTTGAAAATCAT
234361 AAAAT-TTATATATATTTT-TTTACAAAA-TTGAAAAT-AT
1 AAAATATT-TATATATTTTCTTTA-AAAATTTGAAAATCAT
234398 AAAA
1 AAAA
234402 AGGTTAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 6 0.16
38 12 0.32
39 19 0.51
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAATTTGAAAATCAT
Found at i:240029 original size:12 final size:12
Alignment explanation
Indices: 240012--240038 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
240002 TTTGATCTAT
240012 AAAAAACAAAAC
1 AAAAAACAAAAC
240024 AAAAAACAAAAC
1 AAAAAACAAAAC
240036 AAA
1 AAA
240039 CTCAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAC
Found at i:240036 original size:17 final size:17
Alignment explanation
Indices: 240012--240051 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
240002 TTTGATCTAT
240012 AAAAAACAAA-ACAAAA
1 AAAAAACAAACACAAAA
*
240028 AACAAAACAAACTCAAAA
1 AA-AAAACAAACACAAAA
240046 AAAAAA
1 AAAAAA
240052 AGGAAGACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 12 0.57
18 7 0.33
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (17 bp):
AAAAAACAAACACAAAA
Found at i:240366 original size:23 final size:23
Alignment explanation
Indices: 240311--240364 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
240301 TGCCAATGTT
240311 GCACGTTTTCATATGCTTTTATG
1 GCACGTTTTCATATGCTTTTATG
*
240334 GCACGTTTTCTTATGCTTTT-TG
1 GCACGTTTTCATATGCTTTTATG
*
240356 GCATGTTTT
1 GCACGTTTT
240365 TCGATTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.13, C:0.17, G:0.19, T:0.52
Consensus pattern (23 bp):
GCACGTTTTCATATGCTTTTATG
Found at i:243380 original size:21 final size:22
Alignment explanation
Indices: 243356--243407 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
243346 AAATAATTGA
* *
243356 AAATTTATATAAT-TTAAAAAT
1 AAATTTATAAAATATAAAAAAT
243377 AAATTTA-AAAATATAAAAAAT
1 AAATTTATAAAATATAAAAAAT
*
243398 AAAATTATAA
1 AAATTTATAA
243408 GATTACAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 20 0.77
22 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATTTATAAAATATAAAAAAT
Found at i:243409 original size:99 final size:98
Alignment explanation
Indices: 243302--243653 Score: 351
Period size: 99 Copynumber: 3.5 Consensus size: 98
243292 TAATAGTTAT
* *
243302 AATT-TAAGATTACAACTAAATTTAAAATAATTTAAGATTAAAATAAATAATTGAAAATTTATAT
1 AATTATAAGATTACAACAAAATTTAAAATAATTTAAAATT-AAATAAATAATTGAAAATTTATAT
243366 AATTTAAAAATAAATTTAAAAATATAAAAAATAA
65 AATTTAAAAATAAATTTAAAAATATAAAAAATAA
** * * ** **
243400 AATTATAAGATTACAACAAAATTTAAAATAATTT----TTATTTTATTTTTTTTAAATTTATAAT
1 AATTATAAGATTACAACAAAATTTAAAATAATTTAAAATTAAATAAATAATTGAAAATTTAT-AT
* * *
243461 ATTTTTTAAAAA-ACATATAAAAA-ATAAAATTAA-AA
65 A--ATTTAAAAATAAATTTAAAAATATAAAA--AATAA
* * * * * *
243496 AATCAAAAGTTTATACATAAAATTTAAGATTACAAAATTTAAAAATTAAATAAATAATTGAAAAT
1 AATTATAAGATTACA-ACAAAATTT-A-A--A-ATAATTT-AAAATTAAATAAATAATTGAAAAT
243561 TTATATAATTTAAAAATAAATTTAAAAATATAAAAAATAA
59 TTATATAATTTAAAAATAAATTTAAAAATATAAAAAATAA
243601 AATTATAAGATTACAACAAAATTTAAAATAATTTAAAATTAAAATAAATAATT
1 AATTATAAGATTACAACAAAATTTAAAATAATTTAAAATT-AAATAAATAATT
243654 TAAATGTTAA
Statistics
Matches: 198, Mismatches: 35, Indels: 41
0.72 0.13 0.15
Matches are distributed among these distances:
94 14 0.07
95 11 0.06
96 22 0.11
97 18 0.09
98 11 0.06
99 47 0.24
100 1 0.01
101 1 0.01
102 7 0.04
103 1 0.01
104 18 0.09
105 22 0.11
106 9 0.05
107 16 0.08
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (98 bp):
AATTATAAGATTACAACAAAATTTAAAATAATTTAAAATTAAATAAATAATTGAAAATTTATATA
ATTTAAAAATAAATTTAAAAATATAAAAAATAA
Found at i:243581 original size:21 final size:21
Alignment explanation
Indices: 243557--243657 Score: 68
Period size: 21 Copynumber: 4.9 Consensus size: 21
243547 AAATAATTGA
*
243557 AAATTTATATAATTTAAAAAT
1 AAATTTAAATAATTTAAAAAT
*
243578 AAATTTAAA-AATATAAAAAAT
1 AAATTTAAATAAT-TTAAAAAT
* * *
243599 AAAATT--ATAAGATTACAACA-
1 AAATTTAAATAA-TTTA-AAAAT
*
243619 AAATTTAAAATAATTTAAAATT
1 AAATTT-AAATAATTTAAAAAT
*
243641 AAA-ATAAATAATTTAAA
1 AAATTTAAATAATTTAAA
243658 TGTTAAGTTG
Statistics
Matches: 61, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
19 1 0.02
20 24 0.39
21 26 0.43
22 6 0.10
23 4 0.07
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (21 bp):
AAATTTAAATAATTTAAAAAT
Found at i:243647 original size:217 final size:212
Alignment explanation
Indices: 243212--243634 Score: 681
Period size: 201 Copynumber: 2.0 Consensus size: 212
243202 AAAATTAAGA
243212 TTTTATTTTATTTTTTTATAAAATTTATAATATTTTTTAAAAAAACATATAAAAAATAAAATTAA
1 TTTTATTTTATTTTTTTATAAAATTTATAATATTTTTTAAAAAAACATATAAAAAATAAAATTAA
243277 AAAATCAAAAGTTTATAATAGTTATAATTTAAGATTACAACTAAATTTAAAATAATTTAAGATTA
66 AAAATCAAAAGTTTATAATA--TATAATTTAAGATTACAAC-AAATTT---ATAA--TAAGATTA
243342 AAATAAATAATTGAAAATTTATATAATTTAAAAATAAATTTAAAAATATAAAAAATAAAATTATA
123 AAATAAATAATTGAAAATTTATATAATTTAAAAATAAATTTAAAAATATAAAAAATAAAATTATA
243407 AGATTACAACAAAATTTAAAATAAT
188 AGATTACAACAAAATTTAAAATAAT
243432 TTTTATTTTATTTTTTT-T-AAATTTATAATATTTTTT-AAAAAACATATAAAAAATAAAATTAA
1 TTTTATTTTATTTTTTTATAAAATTTATAATATTTTTTAAAAAAACATATAAAAAATAAAATTAA
243494 AAAATCAAAAGTTTATACATA-A-AATTTAAGATTAC-A-AAA-TT-TAA-AA-ATT-AAATAAA
66 AAAATCAAAAGTTTATA-ATATATAATTTAAGATTACAACAAATTTATAATAAGATTAAAATAAA
243550 TAATTGAAAATTTATATAATTTAAAAATAAATTTAAAAATATAAAAAATAAAATTATAAGATTAC
130 TAATTGAAAATTTATATAATTTAAAAATAAATTTAAAAATATAAAAAATAAAATTATAAGATTAC
243615 AACAAAATTTAAAATAAT
195 AACAAAATTTAAAATAAT
243633 TT
1 TT
243635 AAAATTAAAA
Statistics
Matches: 202, Mismatches: 0, Indels: 21
0.91 0.00 0.09
Matches are distributed among these distances:
201 92 0.46
202 3 0.01
203 2 0.01
206 3 0.01
210 2 0.01
211 3 0.01
213 1 0.00
214 13 0.06
215 1 0.00
217 43 0.21
218 21 0.10
219 1 0.00
220 17 0.08
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (212 bp):
TTTTATTTTATTTTTTTATAAAATTTATAATATTTTTTAAAAAAACATATAAAAAATAAAATTAA
AAAATCAAAAGTTTATAATATATAATTTAAGATTACAACAAATTTATAATAAGATTAAAATAAAT
AATTGAAAATTTATATAATTTAAAAATAAATTTAAAAATATAAAAAATAAAATTATAAGATTACA
ACAAAATTTAAAATAAT
Found at i:243710 original size:38 final size:37
Alignment explanation
Indices: 243641--243714 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 37
243631 ATTTAAAATT
* *
243641 AAAATAAATAATTTAAATGTTAAGTTGAAATAATTTG
1 AAAATAAATAATTTAAATGTTAAGGTAAAATAATTTG
*
243678 AAAA-AAATAGATTTAGAATGTTAGGGTAAAATAATTT
1 AAAATAAATA-ATTTA-AATGTTAAGGTAAAATAATTT
243715 TCAAATTAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 5 0.16
37 9 0.28
38 18 0.56
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (37 bp):
AAAATAAATAATTTAAATGTTAAGGTAAAATAATTTG
Found at i:243765 original size:17 final size:19
Alignment explanation
Indices: 243724--243767 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
243714 TTCAAATTAG
*
243724 AAATAAAAA-AACTAATGT
1 AAATAAAAATAACTAATGA
243742 AAA-AAAAATAA-TAAT-A
1 AAATAAAAATAACTAATGA
243758 AAATAAAAAT
1 AAATAAAAAT
243768 GAAAAATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 3 0.13
17 15 0.65
18 5 0.22
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (19 bp):
AAATAAAAATAACTAATGA
Found at i:254770 original size:2 final size:2
Alignment explanation
Indices: 254763--254789 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
254753 TATTTTAAAT
254763 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
254790 TACAGAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:254778 original size:27 final size:26
Alignment explanation
Indices: 254729--254781 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
254719 TCATGAATTT
*
254729 TTTTAAATATATAATTATTTATATTA
1 TTTTAAATATATAATTATATATATTA
254755 TTTTAAATTATATATATATATATATAT
1 TTTTAAA-TATATA-AT-TATATATAT
254782 ATATATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 6 0.26
28 2 0.09
29 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTAAATATATAATTATATATATTA
Found at i:257981 original size:21 final size:21
Alignment explanation
Indices: 257937--258037 Score: 86
Period size: 21 Copynumber: 4.9 Consensus size: 21
257927 CGTTGTGACA
257937 AAGGGATCGAT-CTTTTAAGG-G
1 AAGGGATCGATCCTTTT--GGTG
257958 AAGGGATCGATCCTTTTGGTG
1 AAGGGATCGATCCTTTTGGTG
* * *
257979 AAGGCATAGATCCTTTT--TC
1 AAGGGATCGATCCTTTTGGTG
*
257998 AAGGGGATCGATCC-TTTGGTCA
1 AA-GGGATCGATCCTTTTGGT-G
*
258020 AAGGGATCGATTCTTTTG
1 AAGGGATCGATCCTTTTG
258038 CTAGGGGATT
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
19 6 0.09
20 11 0.17
21 38 0.58
22 11 0.17
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.33
Consensus pattern (21 bp):
AAGGGATCGATCCTTTTGGTG
Found at i:258012 original size:20 final size:20
Alignment explanation
Indices: 257960--258046 Score: 68
Period size: 21 Copynumber: 4.2 Consensus size: 20
257950 TTTAAGGGAA
*
257960 GGGATCGATCCTTTTGGTGAA-
1 GGGATCGATCCTTTT--TCAAG
* *
257981 GGCATAGATCCTTTTTCAAG
1 GGGATCGATCCTTTTTCAAG
* *
258001 GGGATCGATCCTTTGGTCAAA
1 GGGATCGATCCTTT-TTCAAG
* * *
258022 GGGATCGATTCTTTTGCTAG
1 GGGATCGATCCTTTTTCAAG
258042 GGGAT
1 GGGAT
258047 TGATTACAAC
Statistics
Matches: 52, Mismatches: 12, Indels: 5
0.75 0.17 0.07
Matches are distributed among these distances:
19 3 0.06
20 19 0.37
21 30 0.58
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (20 bp):
GGGATCGATCCTTTTTCAAG
Found at i:258036 original size:41 final size:41
Alignment explanation
Indices: 257960--258046 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
257950 TTTAAGGGAA
* *
257960 GGGATCGATCCTTTTGGTGAAGGCATAGATCCTTTTTCAAG
1 GGGATCGATCCTTTTGGTAAAGGCATAGATCCTTTTGCAAG
* * * *
258001 GGGATCGATCC-TTTGGTCAAAGGGATCGATTCTTTTGCTAG
1 GGGATCGATCCTTTTGGT-AAAGGCATAGATCCTTTTGCAAG
258042 GGGAT
1 GGGAT
258047 TGATTACAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 6 0.15
41 33 0.85
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (41 bp):
GGGATCGATCCTTTTGGTAAAGGCATAGATCCTTTTGCAAG
Found at i:258377 original size:367 final size:367
Alignment explanation
Indices: 257683--258379 Score: 1238
Period size: 367 Copynumber: 1.9 Consensus size: 367
257673 ACAAGTGTGT
257683 TTACAACAAATAATTTTACAAATTAACCACAAAACTAAGCTTTGATGTTGGTAGATTAGTTCAAT
1 TTACAACAAATAATTTTACAAATTAACCACAAAACTAAGCTTTGATGTTGGTAGATTAGTTCAAT
257748 ATGATTCTTGATGACCTTGGGAAACTTTTACCTTCAATTTATACCTTCTCCATTAATTCTAGTCG
66 ATGATTCTTGATGACCTTGGGAAACTTTTACCTTCAATTTATACCTTCTCCATTAATTCTAGTCG
257813 TTTGGAGCCGTTGGCGATCATTATAACCGTTACCTAAAACCAAAAAACAACATTTAATGCACAAG
131 TTTGGAGCCGTTGGCGATCATTATAACCGTTACCTAAAACCAAAAAACAACATTTAATGCACAAG
257878 GGATCGATCCTTTGTTGAAAGGGATCAATTCATCTTAAAAAAATTTGATCGTTGTGACAAAGGGA
196 GGATCGATCCTTTGTTGAAAGGGATCAATTCATCTTAAAAAAATTTGATCGTTGTGACAAAGGGA
* *
257943 TCGATCTTTTAAGGGAAGGGATCGATCCTTTTGGTGAAGGCATAGATCCTTTTTCAAGGGGATCG
261 TCGATCTTTTAAGGGAAGGGATCGATCCTTTTGATGAAGGCATAGATCCTTTTTCAAGGGCATCG
258008 ATCCTTTGGTCAAAGGGATCGATTCTTTTGCTAGGGGATTGA
326 ATCCTTTGGTCAAAGGGATCGATTCTTTTGCTAGGGGATTGA
*
258050 TTACAACAAATAATTTTACAAATTAACCACAAAACTAAGCTTTGATGTTGGTAGATTGGTTCAAT
1 TTACAACAAATAATTTTACAAATTAACCACAAAACTAAGCTTTGATGTTGGTAGATTAGTTCAAT
258115 ATGATTCTTGATGACCTTGGGAAACTTTTACCTTCAATTTATACCTTCTCCATTAATTCTAGTCG
66 ATGATTCTTGATGACCTTGGGAAACTTTTACCTTCAATTTATACCTTCTCCATTAATTCTAGTCG
*
258180 TTTGGAGCCGTTGGCGATCATTATAATCGTTACCTAAAACC-AAAAACAACATTTAATGCACAAG
131 TTTGGAGCCGTTGGCGATCATTATAACCGTTACCTAAAACCAAAAAACAACATTTAATGCACAAG
* * *
258244 GGATCGATCCTTTGTTGAAAGGGATCAATTTATTTTAAAAAATTTTGATCGTTGTGACAAAGGGA
196 GGATCGATCCTTTGTTGAAAGGGATCAATTCATCTTAAAAAAATTTGATCGTTGTGACAAAGGGA
* * * * *
258309 TCGATCTTTTAAGGGAATGGATCGATCCTTTTTATCG-AGGGATCGATCCTTTTGGTGAA-GGCA
261 TCGATCTTTTAAGGGAAGGGATCGATCCTTTTGAT-GAAGGCATAGATCCTTTT--TCAAGGGCA
258372 TCGATCCT
323 TCGATCCT
258380 AAACTCATTG
Statistics
Matches: 315, Mismatches: 12, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
366 131 0.42
367 181 0.57
368 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (367 bp):
TTACAACAAATAATTTTACAAATTAACCACAAAACTAAGCTTTGATGTTGGTAGATTAGTTCAAT
ATGATTCTTGATGACCTTGGGAAACTTTTACCTTCAATTTATACCTTCTCCATTAATTCTAGTCG
TTTGGAGCCGTTGGCGATCATTATAACCGTTACCTAAAACCAAAAAACAACATTTAATGCACAAG
GGATCGATCCTTTGTTGAAAGGGATCAATTCATCTTAAAAAAATTTGATCGTTGTGACAAAGGGA
TCGATCTTTTAAGGGAAGGGATCGATCCTTTTGATGAAGGCATAGATCCTTTTTCAAGGGCATCG
ATCCTTTGGTCAAAGGGATCGATTCTTTTGCTAGGGGATTGA
Found at i:258423 original size:20 final size:20
Alignment explanation
Indices: 258398--258463 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
258388 TGTTATCCAA
258398 GGGATCGATCCTTTTTCAAG
1 GGGATCGATCCTTTTTCAAG
* *
258418 GGGATCGATCCTTTGGTCAAA
1 GGGATCGATCCTTT-TTCAAG
* * *
258439 GGGATCGATTCTTTTGCTAG
1 GGGATCGATCCTTTTTCAAG
258459 GGGAT
1 GGGAT
258464 TGATACTTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (20 bp):
GGGATCGATCCTTTTTCAAG
Found at i:258442 original size:21 final size:20
Alignment explanation
Indices: 258396--258452 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
258386 ATTGTTATCC
*
258396 AAGGGATCGATCCTTTTTCA
1 AAGGGATCGATCCTTTGTCA
*
258416 AGGGGATCGATCCTTTGGTCA
1 AAGGGATCGATCCTTT-GTCA
*
258437 AAGGGATCGATTCTTT
1 AAGGGATCGATCCTTT
258453 TGCTAGGGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (20 bp):
AAGGGATCGATCCTTTGTCA
Found at i:258453 original size:41 final size:41
Alignment explanation
Indices: 258396--258473 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
258386 ATTGTTATCC
* *
258396 AAGGGATCGATCCTTTTTCAAGGGGATCGATCCTTTGGTCA
1 AAGGGATCGATCCTTTTGCAAGGGGATCGATACTTTGGTCA
* * *
258437 AAGGGATCGATTCTTTTGCTAGGGGATTGATACTTTG
1 AAGGGATCGATCCTTTTGCAAGGGGATCGATACTTTG
258474 AGCCAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (41 bp):
AAGGGATCGATCCTTTTGCAAGGGGATCGATACTTTGGTCA
Found at i:259385 original size:43 final size:43
Alignment explanation
Indices: 259338--259482 Score: 200
Period size: 43 Copynumber: 3.4 Consensus size: 43
259328 CGCCGTTAAT
*
259338 GAACATGATTTTTTGCGGCATTTGTATGTAAAACACCACTAAA
1 GAACATGACTTTTTGCGGCATTTGTATGTAAAACACCACTAAA
* *
259381 GAACATGACATTTTGCGGCATTTGTATGTGAAACACCACTAAA
1 GAACATGACTTTTTGCGGCATTTGTATGTAAAACACCACTAAA
* * ** * *
259424 GAACATGACTTTTTACGACATTTGTATACAAAACATCATTAAA
1 GAACATGACTTTTTGCGGCATTTGTATGTAAAACACCACTAAA
*
259467 GAACATGACTTGTTGC
1 GAACATGACTTTTTGC
259483 AACGTTTGTT
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 89 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (43 bp):
GAACATGACTTTTTGCGGCATTTGTATGTAAAACACCACTAAA
Found at i:263257 original size:3 final size:3
Alignment explanation
Indices: 263249--263306 Score: 82
Period size: 3 Copynumber: 19.3 Consensus size: 3
263239 TTTTATTTAT
* *
263249 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TAA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
263296 TATA TTA TTA T
1 T-TA TTA TTA T
263307 ATATATTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:263307 original size:12 final size:11
Alignment explanation
Indices: 263245--263314 Score: 79
Period size: 12 Copynumber: 6.0 Consensus size: 11
263235 CCCATTTTAT
263245 TTATT-TATTA
1 TTATTATATTA
263255 TTATTATTATTA
1 TTATTA-TATTA
*
263267 TAATTATTATTA
1 TTATTA-TATTA
263279 TTATTATAATTA
1 TTATTAT-ATTA
263291 TTATATATATTA
1 TTAT-TATATTA
263303 TTATATATATTA
1 TTAT-TATATTA
263315 AAAAAATAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
10 5 0.09
11 1 0.02
12 45 0.83
13 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATTATATTA
Found at i:263314 original size:9 final size:8
Alignment explanation
Indices: 263241--263303 Score: 67
Period size: 9 Copynumber: 7.5 Consensus size: 8
263231 TTTACCCATT
263241 TTAT-TTA
1 TTATATTA
263248 TT-TATTA
1 TTATATTA
263255 TTATTATTA
1 TTA-TATTA
263264 TTATAATTA
1 TTAT-ATTA
263273 TTATTATTA
1 TTA-TATTA
263282 TTATAATTA
1 TTAT-ATTA
263291 TTATATATA
1 TTATAT-TA
263300 TTAT
1 TTAT
263304 TATATATATT
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
6 1 0.02
7 7 0.14
8 4 0.08
9 36 0.73
10 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTATATTA
Found at i:264517 original size:20 final size:21
Alignment explanation
Indices: 264471--264517 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
264461 CTGCTTTTAA
264471 ATATATTGTTCTTATTGTATT
1 ATATATTGTTCTTATTGTATT
*
264492 -TTTATTGTT-TTATTTGT-TT
1 ATATATTGTTCTTA-TTGTATT
264511 ATATATT
1 ATATATT
264518 TAAATACTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.21, C:0.02, G:0.09, T:0.68
Consensus pattern (21 bp):
ATATATTGTTCTTATTGTATT
Found at i:264569 original size:23 final size:24
Alignment explanation
Indices: 264531--264585 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
264521 ATACTTTTAT
*
264531 TATAATTATATAGTTATAAATATA
1 TATAATAATATAGTTATAAATATA
* *
264555 TATAATAAT-TAGTTATATATATT
1 TATAATAATATAGTTATAAATATA
*
264578 TTTAATAA
1 TATAATAA
264586 ATTATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TATAATAATATAGTTATAAATATA
Found at i:265269 original size:30 final size:30
Alignment explanation
Indices: 265235--265294 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
265225 TAATTCTTTC
*
265235 TTTTCAAAATTTTTATATATATACTTATTA
1 TTTTCAAAATATTTATATATATACTTATTA
* * * *
265265 TTTTCATAGTATTTATATATTTTCTTATTA
1 TTTTCAAAATATTTATATATATACTTATTA
265295 ATATTTCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.60
Consensus pattern (30 bp):
TTTTCAAAATATTTATATATATACTTATTA
Found at i:266982 original size:14 final size:14
Alignment explanation
Indices: 266963--267005 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
266953 TTTTAAATAA
266963 TTTACATTTACATT
1 TTTACATTTACATT
* *
266977 TTTACATTCACATA
1 TTTACATTTACATT
*
266991 TTTACATTTGCATT
1 TTTACATTTACATT
267005 T
1 T
267006 GGCATTTGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.28, C:0.16, G:0.02, T:0.53
Consensus pattern (14 bp):
TTTACATTTACATT
Found at i:269915 original size:2 final size:2
Alignment explanation
Indices: 269908--269936 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
269898 TCATTTATCT
269908 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
269937 CCTTTGTTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:270250 original size:18 final size:16
Alignment explanation
Indices: 270227--270269 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
270217 CTCATCCAGC
270227 AAAGAAAGAAGAAAAAAA
1 AAAGAAA-AA-AAAAAAA
270245 AAAGAAAAAAAAAGAAA
1 AAAGAAAAAAAAA-AAA
*
270262 AAGGAAAA
1 AAAGAAAA
270270 TTGAATCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 12 0.52
18 7 0.30
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAAAAA
Found at i:270251 original size:11 final size:11
Alignment explanation
Indices: 270235--270263 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
270225 GCAAAGAAAG
270235 AAGAAAAAAAA
1 AAGAAAAAAAA
270246 AAG-AAAAAAA
1 AAGAAAAAAAA
270256 AAGAAAAA
1 AAGAAAAA
270264 GGAAAATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:272787 original size:114 final size:114
Alignment explanation
Indices: 272519--272858 Score: 538
Period size: 114 Copynumber: 3.0 Consensus size: 114
272509 AAGTGCCATG
272519 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
272584 TGGTTTGGTATGAACCTCAAAAACCAATCATTGGATTTTAAAGATGAATT
66 TGGTTTGGTATGAACC-CCAAAACCAATCATTGGATTTAAAAGATGAATT
* *
272634 TGCTCATAGTAAAAATAAGAAGATTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
272699 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
* *
272748 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * * *
272813 TGATTCGGTAGGAA-CCCAGAACCGATCATTGGAATTGAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAA
272859 CTGCATGATC
Statistics
Matches: 208, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 27 0.13
114 102 0.49
115 79 0.38
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATT
Found at i:275321 original size:22 final size:22
Alignment explanation
Indices: 275290--275344 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
275280 ATCTACACTC
* *
275290 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTACCTT
* *
275312 TTTAAAGATGACAGATTATCTT
1 TTCAAAGATGACAGATTACCTT
275334 TTCAAAGATGA
1 TTCAAAGATGA
275345 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTACCTT
Found at i:275928 original size:113 final size:113
Alignment explanation
Indices: 275730--276389 Score: 965
Period size: 113 Copynumber: 5.8 Consensus size: 113
275720 TAGCAAAGAT
* *
275730 TCAAATCCATCA-TCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATTAGAAGAACTCATCTG
1 TCAAATCCATCACT-TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* *
275794 AAGAAGGAAAAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
275843 TCAAATCCATCA-TCTGATGGATCAGCTTTTCCAGAGAAAGTCCATAATAAGAAGAACTCATCTG
1 TCAAATCCATCACT-TGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* *
275907 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTTC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
275956 CCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
276021 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
276069 TCAAATCTATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATTTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
276134 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * * * *
276182 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTATAGTTCATAATGAGAAGAACTCGTCAT
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCAT
**
276246 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAT
62 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
276298 TCAAATCCATCACTTGATAGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT--
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
276361 -GAA-GAAGAAGAAGTTCATAATGAGAAGAA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAA
276390 CTAATCTGAA
Statistics
Matches: 498, Mismatches: 43, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
109 26 0.05
110 3 0.01
112 1 0.00
113 367 0.74
114 2 0.00
115 1 0.00
116 97 0.19
117 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:276382 original size:36 final size:36
Alignment explanation
Indices: 276335--276424 Score: 144
Period size: 36 Copynumber: 2.5 Consensus size: 36
276325 TTTCCAGAGA
* *
276335 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
1 AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
276371 AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
1 AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
* *
276407 AAGTTCACAATGAAAAGA
1 AAGTTCATAATGAGAAGA
276425 GCTTGTTCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.51, C:0.10, G:0.20, T:0.19
Consensus pattern (36 bp):
AAGTTCATAATGAGAAGAACTAATCTGAAAAAGAAG
Found at i:276677 original size:3 final size:3
Alignment explanation
Indices: 276669--276738 Score: 115
Period size: 3 Copynumber: 23.3 Consensus size: 3
276659 CCCATTTTAT
276669 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
276717 TAA TTA TTA -TA TATA TTA TTA T
1 TTA TTA TTA TTA T-TA TTA TTA T
276739 ATATATTAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 58 0.92
4 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:277993 original size:23 final size:24
Alignment explanation
Indices: 277955--278009 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
277945 ATACTTTTAT
*
277955 TATAATTATATAGTTATAAATATA
1 TATAATAATATAGTTATAAATATA
* *
277979 TATAATAAT-TAGTTATATATATT
1 TATAATAATATAGTTATAAATATA
*
278002 TTTAATAA
1 TATAATAA
278010 ATTATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TATAATAATATAGTTATAAATATA
Found at i:281068 original size:2 final size:2
Alignment explanation
Indices: 281061--281097 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
281051 ACATACATGC
281061 AT AT AT AT 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 AT AT AT AT A
281098 ACAATCAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:295022 original size:30 final size:29
Alignment explanation
Indices: 294988--295105 Score: 82
Period size: 30 Copynumber: 4.0 Consensus size: 29
294978 TATTATTTAT
294988 CATATTATTATTAAAATATATCTAAAATAA
1 CATATTATTATTAAAATATAT-TAAAATAA
* * *
295018 CATATTATCAATAAATATAAATTTAATAATTAA
1 CATATTATTATTAAA-ATATA-TTAA-AA-TAA
* *
295051 CAT-TT-TTGTTAAAATGATATTAAAACAA
1 CATATTATTATTAAAAT-ATATTAAAATAA
* * *
295079 TATATTAATATT-ACATATA-TAAAATAA
1 CATATTATTATTAAAATATATTAAAATAA
295106 TAACGTACTA
Statistics
Matches: 68, Mismatches: 13, Indels: 17
0.69 0.13 0.17
Matches are distributed among these distances:
27 7 0.10
28 7 0.10
29 7 0.10
30 22 0.32
31 14 0.21
32 5 0.07
33 6 0.09
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (29 bp):
CATATTATTATTAAAATATATTAAAATAA
Found at i:296380 original size:3 final size:3
Alignment explanation
Indices: 296367--296416 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
296357 TGAAATTTAA
296367 TAT TCAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
296413 TAT T
1 TAT T
296417 GATAAAAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:298955 original size:3 final size:3
Alignment explanation
Indices: 298947--299017 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
298937 TTTTTACCCA
*
298947 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
298995 TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
299018 AATATATATT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:300474 original size:13 final size:13
Alignment explanation
Indices: 300458--300504 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
300448 ATATAATAAA
300458 TAAATATTTATTT
1 TAAATATTTATTT
*
300471 TAAATAAATTATTT
1 TAAAT-ATTTATTT
300485 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
300498 TCAATAT
1 TAAATAT
300505 CAAAAAGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:301197 original size:18 final size:19
Alignment explanation
Indices: 301158--301200 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
301148 TCTTTTCAAA
301158 ATTTTTATATATACTTATT
1 ATTTTTATATATACTTATT
*
301177 ATTTTTCATA-ATATTTA-T
1 ATTTTT-ATATATACTTATT
301195 ATTTTT
1 ATTTTT
301201 TTTATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 12 0.55
20 3 0.14
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTTATATATACTTATT
Found at i:301197 original size:21 final size:23
Alignment explanation
Indices: 301173--301223 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
301163 TATATATACT
301173 TATTATTTTTCA-TAATATTT-A
1 TATTATTTTTCATTAATATTTCA
*
301194 TATT-TTTTTTATTAATATTTCA
1 TATTATTTTTCATTAATATTTCA
*
301216 TTTTATTT
1 TATTATTT
301224 GCAAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.24
21 12 0.48
22 4 0.16
23 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTATTTTTCATTAATATTTCA
Found at i:301201 original size:20 final size:20
Alignment explanation
Indices: 301173--301238 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
301163 TATATATACT
301173 TATTATTTTTCATAATATTTA
1 TATT-TTTTTCATAATATTTA
*
301194 TATTTTTTTTATTAATATTTCA
1 TATTTTTTTCA-TAATATTT-A
*
301216 T-TTTATTTGCA-AATATTT-
1 TATTT-TTTTCATAATATTTA
301234 TATTT
1 TATTT
301239 CATTAATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
18 1 0.03
19 3 0.08
20 13 0.34
21 15 0.39
22 6 0.16
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTTTTTTCATAATATTTA
Found at i:307598 original size:21 final size:21
Alignment explanation
Indices: 307572--307641 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
307562 CAATGATGAT
307572 GCTCTTGAATGCTCTTTCCGA
1 GCTCTTGAATGCTCTTTCCGA
* **
307593 GCTCTTGAAT--T-TGT-AAA
1 GCTCTTGAATGCTCTTTCCGA
307610 TGCTCTTGAATGCTCTTTCCGA
1 -GCTCTTGAATGCTCTTTCCGA
307632 GCTCTTGAAT
1 GCTCTTGAAT
307642 TTGTAAATGC
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
17 1 0.03
18 12 0.32
19 1 0.03
20 1 0.03
21 22 0.58
22 1 0.03
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.40
Consensus pattern (21 bp):
GCTCTTGAATGCTCTTTCCGA
Found at i:307624 original size:39 final size:39
Alignment explanation
Indices: 307570--307651 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
307560 ACCAATGATG
307570 ATGCTCTTGAATGCTCTTTCCGAGCTCTTGAATTTGTAA
1 ATGCTCTTGAATGCTCTTTCCGAGCTCTTGAATTTGTAA
307609 ATGCTCTTGAATGCTCTTTCCGAGCTCTTGAATTTGTAA
1 ATGCTCTTGAATGCTCTTTCCGAGCTCTTGAATTTGTAA
307648 ATGC
1 ATGC
307652 AACCTTTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (39 bp):
ATGCTCTTGAATGCTCTTTCCGAGCTCTTGAATTTGTAA
Found at i:311825 original size:10 final size:10
Alignment explanation
Indices: 311823--311859 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
311813 AAAATGAAGA
311823 AAAAAGAAAAG
1 AAAAA-AAAAG
311834 AAAAAAAAAG
1 AAAAAAAAAG
311844 AAAAAAAAAG
1 AAAAAAAAAG
311854 AAAAAA
1 AAAAAA
311860 GAAAAAAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 21 0.81
11 5 0.19
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:311831 original size:7 final size:7
Alignment explanation
Indices: 311819--311867 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
311809 GAGAAAAATG
311819 AAGAAAA
1 AAGAAAA
311826 AAG--AA
1 AAGAAAA
311831 AAGAAAA
1 AAGAAAA
311838 AA-AAAGA
1 AAGAAA-A
311845 AA-AAAA
1 AAGAAAA
311851 AAGAAAA
1 AAGAAAA
311858 AAGAAAA
1 AAGAAAA
311865 AAG
1 AAG
311868 GGGGGGTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.13
6 6 0.16
7 27 0.71
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:311842 original size:15 final size:15
Alignment explanation
Indices: 311822--311866 Score: 60
Period size: 13 Copynumber: 3.2 Consensus size: 15
311812 AAAAATGAAG
311822 AAAAAAGAAAAGAAA
1 AAAAAAGAAAAGAAA
311837 AAAAAAG-AAA-AAA
1 AAAAAAGAAAAGAAA
*
311850 AAAGAA-AAAAGAAA
1 AAAAAAGAAAAGAAA
311864 AAA
1 AAA
311867 GGGGGGGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 11 0.41
14 9 0.33
15 7 0.26
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAGAAA
Found at i:311850 original size:25 final size:24
Alignment explanation
Indices: 311812--311867 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
311802 TATGCTTGAG
* *
311812 AAAAATGAAGAAAAAAGAAAAGAAA
1 AAAAAAGAAAAAAAAAGAAAA-AAA
*
311837 AAAAAAGAAAAAAAAAGAAAAAAG
1 AAAAAAGAAAAAAAAAGAAAAAAA
311861 AAAAAAG
1 AAAAAAG
311868 GGGGGGTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (24 bp):
AAAAAAGAAAAAAAAAGAAAAAAA
Found at i:311864 original size:5 final size:5
Alignment explanation
Indices: 311824--311857 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
311814 AAATGAAGAA
* *
311824 AAAAG AAAAG AAAAA AAAAG AAAAA AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
311858 AAGAAAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:313199 original size:82 final size:83
Alignment explanation
Indices: 312999--313227 Score: 408
Period size: 82 Copynumber: 2.8 Consensus size: 83
312989 CATTAAATGA
*
312999 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-TAG
313063 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTTAG
*
313082 AAGATGAATTTGCCAATAGCATCTTCTGGATGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-A
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGA
313146 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTAG
*
313164 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGTAG
1 AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAG
313228 GAACTACAGA
Statistics
Matches: 140, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
82 80 0.57
83 56 0.40
84 4 0.03
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (83 bp):
AAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGA
ACCAATCATTGAATTTAG
Found at i:314509 original size:116 final size:115
Alignment explanation
Indices: 313953--314737 Score: 1010
Period size: 114 Copynumber: 6.9 Consensus size: 115
313943 ATTCAAATCT
* *
313953 ATCATTTGATGGATTATCTTTT-CCAGAGAAGGTTCATAATGAGAAGAACTCATCATCTGAAGGA
1 ATCAATTGATGGATTAT-TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTC-TCATCTGAAGAA
*
314017 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTC
64 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
* * *
314069 ATCACTTGATGGATTATTTTTGCCAAAGAA-GTTCATAATGAGAAGAA--CTCATTTGAAGAAGG
1 ATCAATTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCTCATCTGAAGAAGG
*
314131 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
66 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
* *
314181 ATCAAATTGATGGATTAGCTTTT-CCAGAAGAA-GTTCATAATGAGAAGAA--CTCATTTGAAGA
1 ATC-AATTGATGGATTA-TTTTTGCCAG-AGAAGGTTCATAATGAGAAGAACTCTCATCTGAAGA
*
314242 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
63 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
* * *
314295 ATCAAATTGATGGATTAGCTTTT-CCAGAAAAAGTTCATAATGAGAAGAA--CTCATCTGAAGAA
1 ATC-AATTGATGGATTA-TTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCTCATCTGAAGAA
* * * *
314357 TGAAGAAGAAGTCCATAATGAGAAGAATTTATTCAACCTTTTGTCTGAATTC
64 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
*
314409 ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 ATCAATTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTC-TCATCTGAAGAAG
* * *
314474 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTTTTTGAATTC
65 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
* * *** *
314525 ATCATTTGATGGATCAACGTTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCAATTGATGGATTATTTTTGCCAGAGAAG-GTTCATAATGAGAAGAACTC-TCATCTGAAGAA
* *
314589 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTG---GAATTC
64 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
* *** *
314638 ATC-ATTGGATGGATCAACATTGCCA-AGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
1 ATCAATT-GATGGATTATTTTTGCCAGAGAAG-GTTCATAATGAGAAGAACTC-TCATCTGAAGA
* *
314701 AGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
63 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
314738 TAATTCTATC
Statistics
Matches: 618, Mismatches: 39, Indels: 27
0.90 0.06 0.04
Matches are distributed among these distances:
112 69 0.11
113 154 0.25
114 196 0.32
115 25 0.04
116 174 0.28
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (115 bp):
ATCAATTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCTCATCTGAAGAAGG
AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC
Found at i:314675 original size:229 final size:224
Alignment explanation
Indices: 313953--314737 Score: 999
Period size: 229 Copynumber: 3.4 Consensus size: 224
313943 ATTCAAATCT
* * * *
313953 ATCATTTGATGGATTATCTTTTCCAGAGAAG-GTTCATAATGAGAAGAACTCATCATCTGAAGGA
1 ATCA-TTGATGGATTAACTTTGCCA-AGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
* * * *
314017 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGA
64 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTATTTGAATTCATCAATTGATGGA
** *
314082 TTATTTTTGCCA-AAGAAGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAGAAGTTCATA
129 TTAACTTTGCCAGAAG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* *
314146 ATGAGAAGAATTTGTTCAACCTTTTATTTGAATTC
193 ATGAGAAGAATTTGTTCAA--TCTT-TTGGAATTC
* * *
314181 ATCAAATTGATGGATTAGCTTTTCC-AGAAGAAGTTCATAATGAGAAGAA--C-TCATTTGAAGA
1 ATC--ATTGATGGATTAACTTTGCCAAGAAG-AGTTCATAATGAGAAGAACTCGTCATCTGAAGA
*
314242 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATTTGAATTCATCAAATTGATG
63 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTATTTGAATTCATC-AATTGATG
* * * * *
314307 GATTAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAGTCCA
127 GATTAACTTTGCCAG-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* *
314372 TAATGAGAAGAATTTATTCAACCTTTTGTCTGAATTC
191 TAATGAGAAGAATTTGTTCAATCTTTTG---GAATTC
**
314409 ATCACTTGATGGATTATTTTTGCCAGAGAAG-GTTCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATCA-TTGATGGATTAACTTTGCCA-AGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA
* * *
314473 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTTTTTGAATTCATCATTTGATGGA
64 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTATTTGAATTCATCAATTGATGGA
* * *
314538 TCAACGTTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
129 TTAACTTTGCCA-GAAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTC
*
314603 ATAATGAGAAGAACTTGTTCAATCTTTTGGAATTC
190 ATAATGAGAAGAATTTGTTCAATCTTTTGGAATTC
* * *
314638 ATCATTGGATGGATCAACATTGCCAAGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 ATCATT-GATGGATTAACTTTGCCAAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
*
314703 GAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA
65 GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
314738 TAATTCTATC
Statistics
Matches: 493, Mismatches: 42, Indels: 43
0.85 0.07 0.07
Matches are distributed among these distances:
225 2 0.00
226 66 0.13
227 57 0.12
228 81 0.16
229 171 0.35
230 65 0.13
231 1 0.00
232 50 0.10
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (224 bp):
ATCATTGATGGATTAACTTTGCCAAGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGG
AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTATTTGAATTCATCAATTGATGGATT
AACTTTGCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAATTTGTTCAATCTTTTGGAATTC
Found at i:315062 original size:3 final size:3
Alignment explanation
Indices: 315054--315109 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
315044 TTTTTACCCA
* *
315054 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT GAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
315102 TAT TAT TA
1 TAT TAT TA
315110 AATATATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:316567 original size:13 final size:13
Alignment explanation
Indices: 316551--316597 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
316541 ATATAATAAA
316551 TAAATATTTATTT
1 TAAATATTTATTT
*
316564 TAAATAAATTATTT
1 TAAAT-ATTTATTT
316578 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
316591 TCAATAT
1 TAAATAT
316598 CAAAGAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:330095 original size:12 final size:12
Alignment explanation
Indices: 330078--330102 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
330068 TTCAGGTTGA
330078 CTTCTACCTCTT
1 CTTCTACCTCTT
330090 CTTCTACCTCTT
1 CTTCTACCTCTT
330102 C
1 C
330103 CTCTTTGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCTACCTCTT
Found at i:336146 original size:64 final size:64
Alignment explanation
Indices: 336071--336216 Score: 206
Period size: 64 Copynumber: 2.3 Consensus size: 64
336061 CACCATTTCG
* * * *
336071 AATGCATTTTATGCATTGATGCACTG-TCATGCATCGATGCACTCAGG-TTTTTATGAAAACATC
1 AATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTT-TG-AAACATC
336134 A
64 A
* *
336135 AATGTATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTTTGAAACATCG
1 AATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTTTGAAACATCA
336199 AATGCATTTTATGCATCG
1 AATGCATTTTATGCATCG
336217 GTACACCCTT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
64 47 0.64
65 22 0.30
66 4 0.05
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (64 bp):
AATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCAGGCTTGTTTGAAACATCA
Found at i:342629 original size:2 final size:2
Alignment explanation
Indices: 342622--342656 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
342612 TCGTAAATTT
342622 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
342657 TGTAGATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:344130 original size:2 final size:2
Alignment explanation
Indices: 344123--344161 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
344113 TACACATTTA
344123 AT AT AT AT AT 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 AT AT AT AT AT A
344162 AATTAATAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:350953 original size:49 final size:51
Alignment explanation
Indices: 350900--351007 Score: 130
Period size: 51 Copynumber: 2.2 Consensus size: 51
350890 TACACCAGTG
* *
350900 TAAGTATGTTTT-ACTTCTACGC-TTTTTATATTATTCACTTACAACGATA
1 TAAGTATGTTTTAACTGCTACACTTTTTTATATTATTCACTTACAACGATA
* * * * *
350949 TAAGTATATTTTAAGTGCTACACTTTTTTATTTTATTCACTTACACCGGTA
1 TAAGTATGTTTTAACTGCTACACTTTTTTATATTATTCACTTACAACGATA
*
351000 TAAATATG
1 TAAGTATG
351008 GTGTAAGTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
49 11 0.23
50 7 0.15
51 30 0.62
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (51 bp):
TAAGTATGTTTTAACTGCTACACTTTTTTATATTATTCACTTACAACGATA
Found at i:356035 original size:60 final size:60
Alignment explanation
Indices: 355971--356088 Score: 164
Period size: 60 Copynumber: 2.0 Consensus size: 60
355961 TTTGTATACC
* *
355971 AATTTAGAAAGAGGGTCATAGCTTAAGAATGAAATTAGAATATTCAAAAGTATAAGGATT
1 AATTTAGAAAGAGAGTCATAGCTTAAGAATGAAATTAGAATATTCAAAAATATAAGGATT
* ** * * *
356031 AATTTAGAATGAGAGTCATATTTTGAGGATGAAATTAGAATATTCAAAAATTTAAGGA
1 AATTTAGAAAGAGAGTCATAGCTTAAGAATGAAATTAGAATATTCAAAAATATAAGGA
356089 CTACTATAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (60 bp):
AATTTAGAAAGAGAGTCATAGCTTAAGAATGAAATTAGAATATTCAAAAATATAAGGATT
Found at i:362480 original size:21 final size:20
Alignment explanation
Indices: 362443--362486 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
362433 CAAAGAATAA
* *
362443 ATCATTTTTCAATGGGATCG
1 ATCATTTATCAAAGGGATCG
*
362463 ATCATTTGATCAAAGGGATTG
1 ATCATTT-ATCAAAGGGATCG
362484 ATC
1 ATC
362487 CTTTTGCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (20 bp):
ATCATTTATCAAAGGGATCG
Found at i:372874 original size:102 final size:101
Alignment explanation
Indices: 372688--372966 Score: 353
Period size: 102 Copynumber: 2.7 Consensus size: 101
372678 CCGGATTTGA
* * * *
372688 GTATTTTGATC-ATCTCTAATTTTAGCTCGGTGGTTCTCGGTGACTTTATATATGCATCTGTGCT
1 GTATTTTGA-CAATCTCTAGTTTTAGCTCGGTTGTTCTCGATGACTTCATATATGCATCTGTGC-
* * * *
372752 TTGCTTGATCTTGTTGTTTCTGGATCCATGGGGTTCAG
64 TTGCTTGATCTTGCTGTTTCTCGACCCATCGGGTTCAG
** *
372790 GTATTTTGGGAATCTCTAGTTTTAGCTCGGTTGTTCTCGATGACTTCATATATGCATATGTGCTT
1 GTATTTTGACAATCTCTAGTTTTAGCTCGGTTGTTCTCGATGACTTCATATATGCATCTGTGCTT
* *
372855 GCTTGATCTTGCTGTTTTCTCGACCCGTCGTGTTCAG
66 GCTTGATCTTGCTG-TTTCTCGACCCATCGGGTTCAG
** * * *
372892 GTATTTTGACCGTTTCTAGTATTAGCTCGGTTGTTCTCGATGAATTCATATATGCATCTGTGCTT
1 GTATTTTGACAATCTCTAGTTTTAGCTCGGTTGTTCTCGATGACTTCATATATGCATCTGTGCTT
*
372957 GCCTGATCTT
66 GCTTGATCTT
372967 TGTTTGTTTT
Statistics
Matches: 153, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
101 15 0.10
102 138 0.90
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.44
Consensus pattern (101 bp):
GTATTTTGACAATCTCTAGTTTTAGCTCGGTTGTTCTCGATGACTTCATATATGCATCTGTGCTT
GCTTGATCTTGCTGTTTCTCGACCCATCGGGTTCAG
Found at i:377117 original size:409 final size:402
Alignment explanation
Indices: 376345--377164 Score: 1434
Period size: 410 Copynumber: 2.0 Consensus size: 402
376335 AAAATCATCC
*
376345 AGTCTGGCATACTAATATCAACAATTTGCTCAAACATTAATACAATGATATGCCTACAAATTGGG
1 AGTCTGGCATACTAATATCAACAATTTGCTCAAACATTAATACAATGATATACCTACAAATT-GG
376410 AAAATTATAAGATGCCTTAACTTACAAGGTACACCATTAACATGCTAGTAGTAGTCGTTTCACTT
65 ---A-TATAAGATGCCTTAACTTACAAGGTACACCATTAACATGCTAGTAGTAGTCGTTTCACTT
376475 TGATCCTCCTTACAAGTGATGAACTTCTGACATCTAACTAACGAAAGAGACAGAGTTCTATACAT
126 TGATCCTCCTTACAAGTGATGAACTTCTGACATCTAACTAACGAAAGAGACAGAGTTCTATACAT
376540 TGCTCTAATCAGCAACTTTTATGCAAAATTGATAGAAGGCTAATTACCAACCTCCCCAACAACCC
191 TGCTCTAATCAGCAACTTTTATGCAAAATTGATAGAAGGCTAATTACCAACCTCCCCAACAACCC
376605 TTCAAGAAAAAAAGAAAAAGAAATTTAAAGAATCGAAAATGAAAAAAAAATAGTATAAAGGACAA
256 TTCAAGAAAAAAAGAAAAAGAAATTTAAAGAATCGAAAATG-AAAAAAAATAGTATAAAGGACAA
376670 ATAGCATGCACAAATTACCAAAAGCACAGACAGATTCTGCAAATGACATGAAACGTTGAGAAATA
320 ATAGCATGCACAAATTACCAAAAGCACAGACAGATTCTGC-AA-GACATGAAACGTTGAGAAATA
376735 GAGATACATAAACCTACCCT
383 GAGATACATAAACCTACCCT
376755 AGTCTGGCATACTAATATCAACAATTTGCTCAAACATTAATACAATGATATACCTACAAATT-G-
1 AGTCTGGCATACTAATATCAACAATTTGCTCAAACATTAATACAATGATATACCTACAAATTGGA
376818 TATAAGATGCCTTAACTTACAAGGTACACCATTAACATGCTAGTAGTAGTCG-TTCACTTTGATC
66 TATAAGATGCCTTAACTTACAAGGTACACCATTAACATGCTAGTAGTAGTCGTTTCACTTTGATC
376882 CTCCTTACAAGTGATGAACTTCTGAACCATCTAACTAACTATCGAAAGAGACAGAGTTCTATACA
131 CTCCTTACAAGTGATGAACTTCTG-A-CATCTAACT-A--A-CGAAAGAGACAGAGTTCTATACA
376947 TTGCTCTAATCAGCAACTTTTATGCAAAATTGATAGAAAGGCTAATTACCAACCTCCCCAACAAC
190 TTGCTCTAATCAGCAACTTTTATGCAAAATTGATAG-AAGGCTAATTACCAACCTCCCCAACAAC
377012 CCTTCAAGAAGAAAAAAGAAAAAAGAAATTTAAAGAATCGAAAATG-AAAAAAATAGTATAAAGG
254 CCTTCAAG-A-AAAAAAG-AAAAAGAAATTTAAAGAATCGAAAATGAAAAAAAATAGTATAAAGG
377076 -CAAATAGCATGCACAAATTACCAAAAGCACAGACAGATTCTGCAAGACATGAAACGTTGAGAAA
316 ACAAATAGCATGCACAAATTACCAAAAGCACAGACAGATTCTGCAAGACATGAAACGTTGAGAAA
377140 TAGAGATACATAAACCTACCCT
381 TAGAGATACATAAACCTACCCT
377162 AGT
1 AGT
377165 GCACTTACAA
Statistics
Matches: 399, Mismatches: 1, Indels: 23
0.94 0.00 0.05
Matches are distributed among these distances:
402 36 0.09
403 53 0.13
404 9 0.02
405 1 0.00
407 45 0.11
408 62 0.16
409 79 0.20
410 80 0.20
411 7 0.02
412 27 0.07
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (402 bp):
AGTCTGGCATACTAATATCAACAATTTGCTCAAACATTAATACAATGATATACCTACAAATTGGA
TATAAGATGCCTTAACTTACAAGGTACACCATTAACATGCTAGTAGTAGTCGTTTCACTTTGATC
CTCCTTACAAGTGATGAACTTCTGACATCTAACTAACGAAAGAGACAGAGTTCTATACATTGCTC
TAATCAGCAACTTTTATGCAAAATTGATAGAAGGCTAATTACCAACCTCCCCAACAACCCTTCAA
GAAAAAAAGAAAAAGAAATTTAAAGAATCGAAAATGAAAAAAAATAGTATAAAGGACAAATAGCA
TGCACAAATTACCAAAAGCACAGACAGATTCTGCAAGACATGAAACGTTGAGAAATAGAGATACA
TAAACCTACCCT
Found at i:381398 original size:176 final size:176
Alignment explanation
Indices: 381097--381423 Score: 500
Period size: 176 Copynumber: 1.9 Consensus size: 176
381087 AAGATCTACA
*
381097 ATTGGATATGTTTTTACTCTTGGTGGAGGGCCTATATGTTGGAAGTCAACTGTTAAGTCTATTGT
1 ATTGGATATGTTTTTACTCATGGTGGAGGGCCTATATGTTGGAAGTCAACTGTTAAGTCTATTGT
*
381162 GACATTATCTACAACTGAAGCTAAATATGACAACATCTAAAGCTGCAAAAAACGTTATGGCTTAC
66 GACATTATCTACAACTGAAGCTAAATATGACAACATCTAAAGATGCAAAAAACGTTATGGCTTAC
381227 TGGGCCAGTAAATGAATTGGGAGGTCCAGTTCAAAATTGCATTGTG
131 TGGGCCAGTAAATGAATTGGGAGGTCCAGTTCAAAATTGCATTGTG
*
381273 ATTGGGTATGTTTTTACTCATGGTGGAGGGCCTATATGTTGGAAGTCAACTGTTCAA-TCTATTG
1 ATTGGATATGTTTTTACTCATGGTGGAGGGCCTATATGTTGGAAGTCAACTGTT-AAGTCTATTG
* * * * *
381337 -G-CATTATCTACAACTGAAGCTGAATATGGA-AGCATCTGAATATGCAAAAGAAGCTTTATGGC
65 TGACATTATCTACAACTGAAGCTAAATAT-GACAACATCTAAAGATGCAAAA-AA-CGTTATGGC
* *
381399 TTACTGGGCTAGTGAATGAATTGGG
127 TTACTGGGCCAGTAAATGAATTGGG
381424 TGTTAGCAAG
Statistics
Matches: 137, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
174 40 0.29
175 5 0.04
176 90 0.66
177 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (176 bp):
ATTGGATATGTTTTTACTCATGGTGGAGGGCCTATATGTTGGAAGTCAACTGTTAAGTCTATTGT
GACATTATCTACAACTGAAGCTAAATATGACAACATCTAAAGATGCAAAAAACGTTATGGCTTAC
TGGGCCAGTAAATGAATTGGGAGGTCCAGTTCAAAATTGCATTGTG
Found at i:382009 original size:17 final size:18
Alignment explanation
Indices: 381984--382018 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
381974 ACTCGTTAAA
*
381984 TCTTGTGTTC-TTTATTT
1 TCTTCTGTTCGTTTATTT
382001 TCTTCTGTTCGTTTATTT
1 TCTTCTGTTCGTTTATTT
382019 CATGTGTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.06, C:0.14, G:0.11, T:0.69
Consensus pattern (18 bp):
TCTTCTGTTCGTTTATTT
Found at i:391640 original size:17 final size:18
Alignment explanation
Indices: 391614--391652 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
391604 TTTGAGGAGA
*
391614 AATTACATTTAATATA-T
1 AATTAAATTTAATATATT
*
391631 AATTAAATTTAGTATATT
1 AATTAAATTTAATATATT
391649 AATT
1 AATT
391653 TATATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
AATTAAATTTAATATATT
Found at i:391712 original size:17 final size:17
Alignment explanation
Indices: 391692--391724 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
391682 ATATTTATTT
*
391692 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
391709 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
391725 TATGGTAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:391762 original size:16 final size:17
Alignment explanation
Indices: 391743--391779 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
391733 TAAAATATTA
391743 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
391759 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
391776 TTTT
1 TTTT
391780 TTCATCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:392366 original size:31 final size:32
Alignment explanation
Indices: 392331--392407 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 32
392321 TTTTAAAAAA
*
392331 TAAGATATGGTCATTTTTA-TTTTTATTTAAT
1 TAAGATATGGTCATCTTTAGTTTTTATTTAAT
*
392362 TAAGATATGTTCA-CTTTAGTTTTTATTTAAT
1 TAAGATATGGTCATCTTTAGTTTTTATTTAAT
392393 TAAGATATGGTCATC
1 TAAGATATGGTCATC
392408 ACGAGTTAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
30 4 0.10
31 36 0.88
32 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (32 bp):
TAAGATATGGTCATCTTTAGTTTTTATTTAAT
Found at i:392610 original size:29 final size:29
Alignment explanation
Indices: 392547--392610 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
392537 TTTTTAAATG
** *
392547 AAAATAAAAAATATTTTTAAATTAAGTTA
1 AAAATAAAAAATATTTAAAAAGTAAGTTA
* *
392576 ATAATAAAATATATTTAAAAAGTAA-TATA
1 AAAATAAAAAATATTTAAAAAGTAAGT-TA
392605 AAAATA
1 AAAATA
392611 TTTTTTAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATAAAAAATATTTAAAAAGTAAGTTA
Found at i:392624 original size:23 final size:24
Alignment explanation
Indices: 392549--392627 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 24
392539 TTTAAATGAA
* *
392549 AATAAAAAATATTTTTAAATTAAGTT
1 AATATAAAATATATTT--ATTAAGTT
**
392575 AATAATAAAATATATTTAAAAAG-T
1 AAT-ATAAAATATATTTATTAAGTT
*
392599 AATATAAAA-ATATTTTTTAAGTT
1 AATATAAAATATATTTATTAAGTT
392622 AATATA
1 AATATA
392628 TATAAAATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
22 9 0.20
23 13 0.30
24 4 0.09
25 4 0.09
26 3 0.07
27 11 0.25
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
AATATAAAATATATTTATTAAGTT
Found at i:392628 original size:25 final size:25
Alignment explanation
Indices: 392567--392638 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 25
392557 ATATTTTTAA
392567 ATTAAGTTAATA-ATAAAATATATTT
1 ATTAAGTTAATATATAAAA-ATATTT
**
392592 AAAAAG-T-A-ATATAAAAATATTT
1 ATTAAGTTAATATATAAAAATATTT
*
392614 TTTAAGTTAATATATATAAAATATT
1 ATTAAGTTAATATATA-AAAATATT
392639 ATGAATTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
22 10 0.27
23 8 0.22
24 2 0.05
25 9 0.24
26 8 0.22
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (25 bp):
ATTAAGTTAATATATAAAAATATTT
Found at i:393018 original size:37 final size:38
Alignment explanation
Indices: 392925--393017 Score: 131
Period size: 37 Copynumber: 2.5 Consensus size: 38
392915 GTAATAGTGT
* *
392925 TAATCAATAGTGGCGTTTTTAGATAACGCCACATATTT
1 TAATCAATAGTGGCGTTTTTAGAAAACGCCACATATTG
392963 TAAT-AATAGTGGCGTTTTTA-ACAAACGCCACA-A-TG
1 TAATCAATAGTGGCGTTTTTAGA-AAACGCCACATATTG
392998 TAATCAATAGTGGCGTTTTT
1 TAATCAATAGTGGCGTTTTT
393018 TTGTATAAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
35 5 0.10
36 17 0.33
37 25 0.49
38 4 0.08
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (38 bp):
TAATCAATAGTGGCGTTTTTAGAAAACGCCACATATTG
Found at i:393880 original size:8 final size:8
Alignment explanation
Indices: 393869--393907 Score: 78
Period size: 8 Copynumber: 4.9 Consensus size: 8
393859 GAAAACTGGA
393869 AATAAGCT
1 AATAAGCT
393877 AATAAGCT
1 AATAAGCT
393885 AATAAGCT
1 AATAAGCT
393893 AATAAGCT
1 AATAAGCT
393901 AATAAGC
1 AATAAGC
393908 GATTCGTGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (8 bp):
AATAAGCT
Found at i:400483 original size:30 final size:29
Alignment explanation
Indices: 400435--400499 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
400425 AAGCGAAAAT
*
400435 GAAGCAGGGAAACAGAGAGAGCAA-CAGCG
1 GAAGCAGCGAAACAGAGAGAG-AAGCAGCG
400464 GAAGCAGCGAAAGCAGAGAGAGAAGCAGCG
1 GAAGCAGCGAAA-CAGAGAGAGAAGCAGCG
*
400494 GCAGCA
1 GAAGCA
400500 CAGAGAGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.43, C:0.18, G:0.38, T:0.00
Consensus pattern (29 bp):
GAAGCAGCGAAACAGAGAGAGAAGCAGCG
Found at i:400515 original size:21 final size:21
Alignment explanation
Indices: 400464--400529 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
400454 AGCAACAGCG
** *
400464 GAAGCAGCGAAAGCAGAGAGA
1 GAAGCAGCGGCAGCACAGAGA
400485 GAAGCAGCGGCAGCACAGAGA
1 GAAGCAGCGGCAGCACAGAGA
* *
400506 GAGGCAGCGGCAGAACA-AGA
1 GAAGCAGCGGCAGCACAGAGA
400526 GAAG
1 GAAG
400530 TATATCAGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 6 0.15
21 33 0.85
ACGTcount: A:0.42, C:0.18, G:0.39, T:0.00
Consensus pattern (21 bp):
GAAGCAGCGGCAGCACAGAGA
Found at i:401027 original size:43 final size:44
Alignment explanation
Indices: 400966--401089 Score: 155
Period size: 43 Copynumber: 2.9 Consensus size: 44
400956 TTTTTGAAGA
* *
400966 AAACGCCGCTAAACATCAACGA-CTATTGCGGCGTTTGT-CTGCT
1 AAACGCCGCTAAATATCAAC-ACCTATTGCGGCGTTTGTAATGCT
* * *
401009 AAATGCCGTTAAATATCAACACCTATTGCGGCGTTT-TAATTCT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTAATGCT
* *
401052 AAACGCCGCTAAATATCAATACCTTTTGCGGCGTTTGT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT
401090 TGAACAATCG
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.03
43 66 0.96
44 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (44 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTAATGCT
Found at i:401043 original size:86 final size:87
Alignment explanation
Indices: 400864--401045 Score: 189
Period size: 86 Copynumber: 2.1 Consensus size: 87
400854 CACACATTTA
*
400864 GCGGCGTTTTTGATAAAAACGCCGTGAAATCTCAAGACATATTCTGCGGCGTTTGTAGGAAAACG
1 GCGGCGTTTTTGATAAAAACGCCGTGAAATCTCAAGACATATTCTGCGGCGTTTGTAGCAAAACG
*
400929 CCGGTAAAAATAAACATCTACT
66 CCGGTAAAAATAAACACCTACT
* *
400951 GC-GCGTTTTTGA-AGAAAACGCCGCT-AAA-CATCAACGAC-TA-T-TGCGGCGTTTGTCTGCT
1 GCGGCGTTTTTGATA-AAAACGCCG-TGAAATC-TCAA-GACATATTCTGCGGCGTTTGT-AGCA
* * * * *
401009 AAATGCCGTTAAATATCAACACCTATT
61 AAACGCCGGTAAAAATAAACACCTACT
401036 GCGGCGTTTT
1 GCGGCGTTTT
401046 AATTCTAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
84 12 0.15
85 27 0.34
86 35 0.44
87 6 0.08
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (87 bp):
GCGGCGTTTTTGATAAAAACGCCGTGAAATCTCAAGACATATTCTGCGGCGTTTGTAGCAAAACG
CCGGTAAAAATAAACACCTACT
Found at i:401102 original size:43 final size:43
Alignment explanation
Indices: 400908--401105 Score: 128
Period size: 43 Copynumber: 4.7 Consensus size: 43
400898 AGACATATTC
* * * * * *
400908 TGCGGCGTTTGTAGGAA-AA-CGCCGGTAAAAATAAACATCTAC
1 TGCGGCGTTTGT-TGAACAATCGCCGCTAAATATCAACACCTAT
* * *
400950 TGC-GCGTTT-TTGAAGAAAACGCCGCTAAACATCAACGA-CTAT
1 TGCGGCGTTTGTTGAA-CAATCGCCGCTAAATATCAAC-ACCTAT
* *
400992 TGCGGCGTTTGTCTGCTA-AAT-GCCGTTAAATATCAACACCTAT
1 TGCGGCGTTTGT-TG-AACAATCGCCGCTAAATATCAACACCTAT
* * *
401035 TGCGGCG-TT-TT-AATTCTAAACGCCGCTAAATATCAATACCTTT
1 TGCGGCGTTTGTTGAA--C-AATCGCCGCTAAATATCAACACCTAT
401078 TGCGGCGTTTGTTGAACAATCGCCGCTA
1 TGCGGCGTTTGTTGAACAATCGCCGCTA
401106 TATGTTGTAA
Statistics
Matches: 124, Mismatches: 15, Indels: 33
0.72 0.09 0.19
Matches are distributed among these distances:
38 1 0.01
39 3 0.02
40 2 0.02
41 9 0.07
42 28 0.23
43 68 0.55
44 6 0.05
45 4 0.03
46 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (43 bp):
TGCGGCGTTTGTTGAACAATCGCCGCTAAATATCAACACCTAT
Found at i:401185 original size:12 final size:13
Alignment explanation
Indices: 401153--401190 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
401143 ACGCCGCAAA
401153 TTTTAGCGGCGCTAT
1 TTTTAGCGGCGC--T
401168 TTTTAGCGGCGC-
1 TTTTAGCGGCGCT
401180 TTTTAGCGGCG
1 TTTTAGCGGCG
401191 TTTGTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.48
15 12 0.52
ACGTcount: A:0.11, C:0.21, G:0.32, T:0.37
Consensus pattern (13 bp):
TTTTAGCGGCGCT
Found at i:403421 original size:18 final size:18
Alignment explanation
Indices: 403391--403430 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
403381 ATGTGTGCAT
*
403391 GTAT-CATGTATGTGTAG
1 GTATGCATGCATGTGTAG
403408 GTATGCATGCATGTGTAG
1 GTATGCATGCATGTGTAG
403426 GTATG
1 GTATG
403431 TATGTGTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.23, C:0.07, G:0.33, T:0.38
Consensus pattern (18 bp):
GTATGCATGCATGTGTAG
Found at i:403437 original size:14 final size:14
Alignment explanation
Indices: 403396--403476 Score: 67
Period size: 14 Copynumber: 5.5 Consensus size: 14
403386 TGCATGTATC
403396 ATGTATGTGTAGGT
1 ATGTATGTGTAGGT
403410 ATGCATGCATGTGTAGGT
1 ATG--T--ATGTGTAGGT
403428 ATGTATGTGTAGGT
1 ATGTATGTGTAGGT
* *
403442 ATAGGTA--TGTATGC
1 AT--GTATGTGTAGGT
*
403456 ATGTATGTGTAGAT
1 ATGTATGTGTAGGT
403470 ATGTATG
1 ATGTATG
403477 CATGTATGAG
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
12 3 0.06
14 33 0.61
16 5 0.09
18 13 0.24
ACGTcount: A:0.25, C:0.04, G:0.32, T:0.40
Consensus pattern (14 bp):
ATGTATGTGTAGGT
Found at i:403481 original size:18 final size:18
Alignment explanation
Indices: 403400--403459 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
403390 TGTATCATGT
*
403400 ATGTGTAGGTATGCATGC
1 ATGTGTAGGTATGTATGC
*
403418 ATGTGTAGGTATGTATGTGT
1 ATGTGTAGGTATGTA--TGC
* *
403438 AGGTATAGGTATGTATGC
1 ATGTGTAGGTATGTATGC
403456 ATGT
1 ATGT
403460 ATGTGTAGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 19 0.56
20 15 0.44
ACGTcount: A:0.23, C:0.05, G:0.33, T:0.38
Consensus pattern (18 bp):
ATGTGTAGGTATGTATGC
Found at i:412075 original size:21 final size:21
Alignment explanation
Indices: 412033--412080 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
412023 ATAGGGAAAA
*
412033 GAGGACGATGATGACGAGGAC
1 GAGGATGATGATGACGAGGAC
** *
412054 GAGGATGATGATGGTGATGAC
1 GAGGATGATGATGACGAGGAC
412075 GAGGAT
1 GAGGAT
412081 TAACAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.44, T:0.17
Consensus pattern (21 bp):
GAGGATGATGATGACGAGGAC
Found at i:429398 original size:2 final size:2
Alignment explanation
Indices: 429391--429427 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
429381 TATAAAATTC
429391 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
429428 TTAAATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:439701 original size:4 final size:4
Alignment explanation
Indices: 439692--439721 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
439682 AATTTAATGG
*
439692 GTAT GTAT GTAT GTAT GTAT CTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
439722 GAATTATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:442378 original size:13 final size:13
Alignment explanation
Indices: 442362--442392 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
442352 TCTCAATTTA
442362 CTTTCTTATTTTT
1 CTTTCTTATTTTT
442375 CTTTCTTATTTTT
1 CTTTCTTATTTTT
442388 CTTTC
1 CTTTC
442393 AAATCTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.74
Consensus pattern (13 bp):
CTTTCTTATTTTT
Found at i:445902 original size:2 final size:2
Alignment explanation
Indices: 445895--445924 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
445885 GAAAAGAATA
445895 AT 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 AT
445925 GGTTAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:446849 original size:21 final size:21
Alignment explanation
Indices: 446811--446862 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
446801 CATATACATA
*
446811 TTCCAAAGGACCAAATATGTG
1 TTCCAAAGGACCAAATATATG
**
446832 -TCTCAAAGGACCGCATATATG
1 TTC-CAAAGGACCAAATATATG
446853 TTCCAAAGGA
1 TTCCAAAGGA
446863 TTACATATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 2 0.08
21 22 0.85
22 2 0.08
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (21 bp):
TTCCAAAGGACCAAATATATG
Found at i:454544 original size:22 final size:20
Alignment explanation
Indices: 454503--454603 Score: 130
Period size: 20 Copynumber: 4.9 Consensus size: 20
454493 CAGATTGTCA
*
454503 AGGGGGTACAGATTTCCCCCT
1 AGGGGGTACAGA-TTCCCCCC
454524 AGGGGGTACAGATTCCTCCCCC
1 AGGGGGTACAGATT-C-CCCCC
*
454546 AGGGGGTACTGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
* *
454566 AGGAGGAACAGATTCCCCCC
1 AGGGGGTACAGATTCCCCCC
*
454586 AGGGGGTACCGATTCCCC
1 AGGGGGTACAGATTCCCC
454604 TTGTCTAGCG
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
20 39 0.56
21 14 0.20
22 17 0.24
ACGTcount: A:0.20, C:0.34, G:0.29, T:0.18
Consensus pattern (20 bp):
AGGGGGTACAGATTCCCCCC
Found at i:454990 original size:34 final size:32
Alignment explanation
Indices: 454951--455020 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
454941 TTTTGTAAAG
* *
454951 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
454985 GGGAAAGGTTATAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
455017 GGGA
1 GGGA
455021 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 12 0.38
33 1 0.03
34 19 0.59
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:457397 original size:21 final size:21
Alignment explanation
Indices: 457355--457458 Score: 131
Period size: 20 Copynumber: 5.0 Consensus size: 21
457345 TCAGATTGTC
457355 CAGGGGGTACAGATTCCTCCCT
1 CAGGGGGTACAGATTCC-CCCT
*
457377 CAGGGGGAACAGATTCCCCCT
1 CAGGGGGTACAGATTCCCCCT
*
457398 -AGGGGGTACCGATTCCCCC-
1 CAGGGGGTACAGATTCCCCCT
* * *
457417 CAGGGGGAATAGATTCCCCCC
1 CAGGGGGTACAGATTCCCCCT
*
457438 CAGGGGGTACCGATTCCCCCT
1 CAGGGGGTACAGATTCCCCCT
457459 GTTTAACGGT
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
20 33 0.47
21 21 0.30
22 16 0.23
ACGTcount: A:0.19, C:0.35, G:0.29, T:0.17
Consensus pattern (21 bp):
CAGGGGGTACAGATTCCCCCT
Found at i:457449 original size:41 final size:41
Alignment explanation
Indices: 457354--457458 Score: 158
Period size: 41 Copynumber: 2.5 Consensus size: 41
457344 ATCAGATTGT
*
457354 CCAGGGGGTACAGATTCCTCCCTCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACCGATTCC-CCCTCAGGGGGAACAGATTCCCC
* *
457396 CTAGGGGGTACCGATTCCCCC-CAGGGGGAATAGATTCCCCC
1 CCAGGGGGTACCGATTCCCCCTCAGGGGGAACAGATT-CCCC
457437 CCAGGGGGTACCGATTCCCCCT
1 CCAGGGGGTACCGATTCCCCCT
457459 GTTTAACGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
40 14 0.25
41 27 0.47
42 16 0.28
ACGTcount: A:0.19, C:0.35, G:0.29, T:0.17
Consensus pattern (41 bp):
CCAGGGGGTACCGATTCCCCCTCAGGGGGAACAGATTCCCC
Done.