Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009043.1 Hibiscus syriacus cultivar Beakdansim tig00112453_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: 500226
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:155930 original size:41 final size:41
Alignment explanation
Indices: 155845--155930 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 41
155835 GCCTGGCCTG
* * * * *
155845 GCCTATTTAACTAAACAGGCCAGGCCCAGGCCTTTTTAACA
1 GCCTATTTAACTAAACAGACCAGGCCCAGGCATATTAAAAA
**
155886 GCCTATTTAACTAAACAGACCAGGCTTAGGCATATTAAAAA
1 GCCTATTTAACTAAACAGACCAGGCCCAGGCATATTAAAAA
155927 GCCT
1 GCCT
155931 TATAAGCCTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (41 bp):
GCCTATTTAACTAAACAGACCAGGCCCAGGCATATTAAAAA
Found at i:156850 original size:59 final size:59
Alignment explanation
Indices: 156758--156875 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
156748 TGTAGGTATG
156758 CACTGACCTTAGATTAAGAGAGTCACCCTGACCTAAACTTTTTTATGCAAAAAAAAAAA
1 CACTGACCTTAGATTAAGAGAGTCACCCTGACCTAAACTTTTTTATGCAAAAAAAAAAA
* *
156817 CACTGACCTTAGATTGAGAGAGTTACCCTGACCTAAACTTTTTTATGCAAAAAAAAAAA
1 CACTGACCTTAGATTAAGAGAGTCACCCTGACCTAAACTTTTTTATGCAAAAAAAAAAA
156876 AAAACTAGAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (59 bp):
CACTGACCTTAGATTAAGAGAGTCACCCTGACCTAAACTTTTTTATGCAAAAAAAAAAA
Found at i:157453 original size:14 final size:14
Alignment explanation
Indices: 157434--157463 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
157424 TCGACCCTAT
157434 CTATATCATTTGTA
1 CTATATCATTTGTA
157448 CTATATCATTTGTA
1 CTATATCATTTGTA
157462 CT
1 CT
157464 TTGCTCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (14 bp):
CTATATCATTTGTA
Found at i:158540 original size:15 final size:16
Alignment explanation
Indices: 158520--158549 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
158510 ATATATATAC
158520 TTTTTT-GGGGCCCTA
1 TTTTTTGGGGGCCCTA
158535 TTTTTTGGGGGCCCT
1 TTTTTTGGGGGCCCT
158550 GCTCGGTCGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.03, C:0.20, G:0.30, T:0.47
Consensus pattern (16 bp):
TTTTTTGGGGGCCCTA
Found at i:159889 original size:31 final size:32
Alignment explanation
Indices: 159828--159904 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
159818 CGAGGCCATG
*
159828 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACACATCTCAGGGCCGCA
* **
159860 GGGCCTACCCAAGAA-TGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACACATCTCAGGGCCGCA
*
159891 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
159905 GTCACATTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 25 0.64
32 14 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (32 bp):
GGGCCTACCTAAGAACACATCTCAGGGCCGCA
Found at i:162902 original size:13 final size:13
Alignment explanation
Indices: 162884--162923 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
162874 ATTGAAATTA
162884 ACGATTCACGACG
1 ACGATTCACGACG
162897 ACGATTCACGACG
1 ACGATTCACGACG
162910 ACGATTCACGACG
1 ACGATTCACGACG
162923 A
1 A
162924 AAGGCTTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.15
Consensus pattern (13 bp):
ACGATTCACGACG
Found at i:165514 original size:18 final size:17
Alignment explanation
Indices: 165487--165522 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
165477 GGACTTTTTG
165487 ATTTAGATAAAGATAAA
1 ATTTAGATAAAGATAAA
165504 ATTTCAGATAAAGATAAA
1 ATTT-AGATAAAGATAAA
165522 A
1 A
165523 AAACGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.28
Consensus pattern (17 bp):
ATTTAGATAAAGATAAA
Found at i:166451 original size:23 final size:21
Alignment explanation
Indices: 166412--166464 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
166402 ATAGCCTTCA
166412 AAATCCTAAAAACAAGATAAAG
1 AAATCCTAAAAACAAGA-AAAG
*
166434 ATAATCCTAAAATA-AAGAAAAT
1 A-AATCCTAAAA-ACAAGAAAAG
166456 AAATCCTAA
1 AAATCCTAA
166465 TTAATTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 8 0.29
22 5 0.18
23 14 0.50
24 1 0.04
ACGTcount: A:0.62, C:0.13, G:0.06, T:0.19
Consensus pattern (21 bp):
AAATCCTAAAAACAAGAAAAG
Found at i:174572 original size:15 final size:15
Alignment explanation
Indices: 174552--174583 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
174542 GCTTCTTTTC
*
174552 ATTGAATTGTTTCTT
1 ATTGAATTATTTCTT
174567 ATTGAATTATTTCTT
1 ATTGAATTATTTCTT
174582 AT
1 AT
174584 GTTTTAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.09, T:0.59
Consensus pattern (15 bp):
ATTGAATTATTTCTT
Found at i:177943 original size:21 final size:21
Alignment explanation
Indices: 177883--177951 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
177873 GGCTTTGGAA
* * *
177883 TTTTTCATAGAATGCAACCAG
1 TTTTTCATGGGATGCAACTAG
* *
177904 CTTTTCCTGGGATGCAACTAG
1 TTTTTCATGGGATGCAACTAG
*
177925 TTTTTCATGGGATGTAACTAG
1 TTTTTCATGGGATGCAACTAG
*
177946 TATTTC
1 TTTTTC
177952 TTGTGAAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTTTCATGGGATGCAACTAG
Found at i:185461 original size:12 final size:12
Alignment explanation
Indices: 185444--185468 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
185434 ACAAAGCACC
185444 ATTTGGTGCCTA
1 ATTTGGTGCCTA
185456 ATTTGGTGCCTA
1 ATTTGGTGCCTA
185468 A
1 A
185469 ATTATTTGAC
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:190084 original size:12 final size:12
Alignment explanation
Indices: 190067--190091 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
190057 ACAAAGCACC
190067 ATTTGGTGTCTA
1 ATTTGGTGTCTA
190079 ATTTGGTGTCTA
1 ATTTGGTGTCTA
190091 A
1 A
190092 ATTATTTGAC
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:0.20, C:0.08, G:0.24, T:0.48
Consensus pattern (12 bp):
ATTTGGTGTCTA
Found at i:191233 original size:6 final size:6
Alignment explanation
Indices: 191222--191254 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
191212 AACCCACTCT
191222 CCCTCC CCCTCC CCCTCC CCCTCCC CCCTCC CC
1 CCCTCC CCCTCC CCCTCC CCCT-CC CCCTCC CC
191255 GACCTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.00, C:0.85, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCTCC
Found at i:193686 original size:24 final size:25
Alignment explanation
Indices: 193659--193705 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
193649 CAATTATTTC
193659 GCTTCAATCGAGC-TCGAATTTTAG
1 GCTTCAATCGAGCTTCGAATTTTAG
*
193683 GCTTCAATCGAGCTTCTAATTTT
1 GCTTCAATCGAGCTTCGAATTTT
193706 TTTTTGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (25 bp):
GCTTCAATCGAGCTTCGAATTTTAG
Found at i:195615 original size:29 final size:29
Alignment explanation
Indices: 195583--195651 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
195573 ATAATTCATC
195583 GTTCTGATTCTACATGGGATTAATTACCT
1 GTTCTGATTCTACATGGGATTAATTACCT
* * * * *
195612 GTTCTAATTCTGCTTGTGATTAATTCCCT
1 GTTCTGATTCTACATGGGATTAATTACCT
*
195641 GTTTTGATTCT
1 GTTCTGATTCT
195652 GTATGGATTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (29 bp):
GTTCTGATTCTACATGGGATTAATTACCT
Found at i:195723 original size:28 final size:29
Alignment explanation
Indices: 195664--195733 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
195654 ATGGATTAAT
195664 GGATTAATTCCTCATTCTATTTCTACATG
1 GGATTAATTCCTCATTCTATTTCTACATG
* * *
195693 GGATCAATTCC-CCTTCTGATTT-TACTTG
1 GGATTAATTCCTCATTCT-ATTTCTACATG
195721 GGATTAATTCCTC
1 GGATTAATTCCTC
195734 GTTTTGACTC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 20 0.57
29 15 0.43
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (29 bp):
GGATTAATTCCTCATTCTATTTCTACATG
Found at i:196642 original size:3 final size:3
Alignment explanation
Indices: 196629--196692 Score: 112
Period size: 3 Copynumber: 21.7 Consensus size: 3
196619 CATTTGTTTG
*
196629 TAT TA- TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
196676 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
196693 CAGTTCCAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:198557 original size:20 final size:19
Alignment explanation
Indices: 198528--198590 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
198518 TTTGCAATAG
198528 TATTTTATTATTACTTTTA
1 TATTTTATTATTACTTTTA
*
198547 TATTTTAATTATTGCTTTAATTA
1 TATTTT-ATTATTAC-TT--TTA
*
198570 TTATTTTATTATTATTTTTA
1 -TATTTTATTATTACTTTTA
198590 T
1 T
198591 CTTATTCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
19 7 0.19
20 10 0.28
21 2 0.06
22 2 0.06
23 9 0.25
24 6 0.17
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (19 bp):
TATTTTATTATTACTTTTA
Found at i:198590 original size:12 final size:12
Alignment explanation
Indices: 198547--198587 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
198537 ATTACTTTTA
198547 TATTTTAATTAT
1 TATTTTAATTAT
**
198559 TGCTTTAATTAT
1 TATTTTAATTAT
198571 TATTTT-ATTAT
1 TATTTTAATTAT
198582 TATTTT
1 TATTTT
198588 TATCTTATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:198596 original size:14 final size:11
Alignment explanation
Indices: 198528--198587 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
198518 TTTGCAATAG
198528 TATTTTATTAT
1 TATTTTATTAT
198539 TACTTTTA-TA-
1 TA-TTTTATTAT
*
198549 T-TTTAATTAT
1 TATTTTATTAT
* *
198559 TGCTTTAATTAT
1 T-ATTTTATTAT
198571 TATTTTATTAT
1 TATTTTATTAT
198582 TATTTT
1 TATTTT
198588 TATCTTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 2 0.05
11 18 0.44
12 15 0.37
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:204212 original size:15 final size:15
Alignment explanation
Indices: 204194--204228 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
204184 AAAAAAACAA
204194 AAAAAACAAAAAAGG
1 AAAAAACAAAAAAGG
**
204209 AAAAATGAAAAAAGG
1 AAAAAACAAAAAAGG
204224 AAAAA
1 AAAAA
204229 GGGAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAAACAAAAAAGG
Found at i:207605 original size:75 final size:74
Alignment explanation
Indices: 207523--207694 Score: 202
Period size: 74 Copynumber: 2.3 Consensus size: 74
207513 GATTACAAGA
* *
207523 AGCAAATGTTGGGGCATGCTGAAAGCCCGTTTCAAACATAATCAAGAATATTGACT-CTTTTTGA
1 AGCAAATGTTGGGGCATGCTGAAAGCCC-TTTCAAACAGAATCAAGAATATTG-CTGCATTTTGA
*
207587 ACATTTGTATC
64 ACATCTGTATC
* * * * * * *
207598 AGCAAATGCTGGGACATGCTGAAAGCCCTTTTAATCAGAATCAGGAATGTTGGTGCATTTTGAAC
1 AGCAAATGTTGGGGCATGCTGAAAGCCCTTTCAAACAGAATCAAGAATATTGCTGCATTTTGAAC
*
207663 GTCTGTATC
66 ATCTGTATC
* *
207672 AGCAAATGTTAGGGCATGTTGAA
1 AGCAAATGTTGGGGCATGCTGAA
207695 GACCCATATC
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
73 1 0.01
74 54 0.67
75 26 0.32
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (74 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCTTTCAAACAGAATCAAGAATATTGCTGCATTTTGAAC
ATCTGTATC
Found at i:209538 original size:114 final size:112
Alignment explanation
Indices: 209238--209573 Score: 412
Period size: 112 Copynumber: 3.0 Consensus size: 112
209228 TTAGCAAAGA
* * * * *
209238 TTTGAATCCATCATTCAATAGATCAACATTTT-CAG-GTAGAGTTCATAATGAGAAGAACTCATC
1 TTTGAATTCATCATTCGATGGATCAA-ATTTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATC
* *
209301 TGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTG
64 TGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTG
* * * * *
209350 CTTGAATTCATCATTTGATGTATCAGCA-TTGCCAGAGAAAGTTCATAATGAGAAGAACTTATCT
1 TTTGAATTCATCATTCGATGGATCA-AATTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCT
*
209414 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACCTTTTG
65 GAAG-AGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC-AACCTTTTG
* *
209464 TTTGAATTCATCACTCGATGGATCAAATTTTCCAGAGAAAAGTTCATAATGAGAATAACTTATCT
1 TTTGAATTCATCATTCGATGGATCAAATTTTCCAGAG-AAAGTTCATAATGAGAAGAACTTATCT
** *
209529 GAAGAGGAAGAAGAAGA-TCAT-CCGAGAAGAACTTGTTCAGCCTTT
65 GAAGAGGAAGAAGAA-ATTCATAATGAGAAGAACTTGTTCAACCTTT
209574 GCATGATTAC
Statistics
Matches: 192, Mismatches: 24, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
111 2 0.01
112 57 0.30
113 49 0.26
114 53 0.28
115 31 0.16
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
TTTGAATTCATCATTCGATGGATCAAATTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTG
AAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTG
Found at i:209812 original size:3 final size:3
Alignment explanation
Indices: 209800--209858 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
209790 CTATTTGTTT
*
209800 TTA TTA -TA TTA TTG 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
209847 TTA TTA TTA TTA
1 TTA TTA TTA TTA
209859 CAATTCCAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:211729 original size:20 final size:19
Alignment explanation
Indices: 211700--211762 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
211690 TTTGCAATAG
211700 TATTTTATTATTACTTTTA
1 TATTTTATTATTACTTTTA
*
211719 TATTTTAATTATTTCTTTAATTA
1 TATTTT-ATTATTAC-TT--TTA
*
211742 TTATTTTATTATTATTTTTA
1 -TATTTTATTATTACTTTTA
211762 T
1 T
211763 CTTATTCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
19 7 0.19
20 10 0.28
21 2 0.06
22 2 0.06
23 9 0.25
24 6 0.17
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTTTATTATTACTTTTA
Found at i:211762 original size:12 final size:12
Alignment explanation
Indices: 211719--211759 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
211709 ATTACTTTTA
211719 TATTTTAATTAT
1 TATTTTAATTAT
211731 T-TCTTTAATTAT
1 TAT-TTTAATTAT
211743 TATTTT-ATTAT
1 TATTTTAATTAT
211754 TATTTT
1 TATTTT
211760 TATCTTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 12 0.44
12 14 0.52
13 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:211768 original size:14 final size:11
Alignment explanation
Indices: 211700--211759 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
211690 TTTGCAATAG
211700 TATTTTATTAT
1 TATTTTATTAT
211711 TACTTTTA-TA-
1 TA-TTTTATTAT
*
211721 T-TTTAATTAT
1 TATTTTATTAT
211731 T-TCTTTAATTAT
1 TAT-TTT-ATTAT
211743 TATTTTATTAT
1 TATTTTATTAT
211754 TATTTT
1 TATTTT
211760 TATCTTATTC
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 3 0.07
11 17 0.41
12 14 0.34
13 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:215662 original size:29 final size:29
Alignment explanation
Indices: 215617--215864 Score: 163
Period size: 29 Copynumber: 8.7 Consensus size: 29
215607 TGATGCATTC
* * *
215617 CTGATTCTGCATTGGATTAATTCTACATT
1 CTGATTCTGCATGGGATTAATTCTCCGTT
*
215646 TTGATTCTGCATGGGATTAA-TC-CACGTT
1 CTGATTCTGCATGGGATTAATTCTC-CGTT
* ** * *
215674 CTGATTATAAATGGGATTAATTCCCCATT
1 CTGATTCTGCATGGGATTAATTCTCCGTT
*
215703 CT-ATTTCTGCATGAGATTAATT-TCCCGTT
1 CTGA-TTCTGCATGGGATTAATTCT-CCGTT
**
215732 CT-AGTTCTGCATGGGATTAATTCTTTGTT
1 CTGA-TTCTGCATGGGATTAATTCTCCGTT
* *
215761 CT-ATTTCTGCATGAGATTAATTCCCCGTT
1 CTGA-TTCTGCATGGGATTAATTCTCCGTT
* *
215790 CTGATTCTACGTGGGATTAATTC-CTCGTT
1 CTGATTCTGCATGGGATTAATTCTC-CGTT
* * ** * *
215819 TTGACTCTATATGGG-TTAGTTCTCCATT
1 CTGATTCTGCATGGGATTAATTCTCCGTT
* *
215847 TTG-TTCTGTATGGGATTA
1 CTGATTCTGCATGGGATTA
215865 TATCCCCATT
Statistics
Matches: 174, Mismatches: 35, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
27 9 0.05
28 38 0.22
29 124 0.71
30 3 0.02
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (29 bp):
CTGATTCTGCATGGGATTAATTCTCCGTT
Found at i:215753 original size:58 final size:58
Alignment explanation
Indices: 215617--215813 Score: 211
Period size: 58 Copynumber: 3.4 Consensus size: 58
215607 TGATGCATTC
* * ** * * *
215617 CTGATTCTGCATTGGATTAATTCTACATTTTGA-TTCTGCATGGGATTAA-TCCACGTT
1 CTGATTCTACATGGGATTAATTCCCCATTCT-ATTTCTGCATGAGATTAATTCCCCGTT
* * *
215674 CTGATTATAAATGGGATTAATTCCCCATTCTATTTCTGCATGAGATTAATTTCCCGTT
1 CTGATTCTACATGGGATTAATTCCCCATTCTATTTCTGCATGAGATTAATTCCCCGTT
* ****
215732 CT-AGTTCTGCATGGGATTAATTCTTTGTTCTATTTCTGCATGAGATTAATTCCCCGTT
1 CTGA-TTCTACATGGGATTAATTCCCCATTCTATTTCTGCATGAGATTAATTCCCCGTT
*
215790 CTGATTCTACGTGGGATTAATTCC
1 CTGATTCTACATGGGATTAATTCC
215814 TCGTTTTGAC
Statistics
Matches: 115, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
56 1 0.01
57 40 0.35
58 73 0.63
59 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (58 bp):
CTGATTCTACATGGGATTAATTCCCCATTCTATTTCTGCATGAGATTAATTCCCCGTT
Found at i:220145 original size:226 final size:228
Alignment explanation
Indices: 219727--220212 Score: 874
Period size: 226 Copynumber: 2.1 Consensus size: 228
219717 GTTATATTGT
* * *
219727 AAAGTATCTATCTTTTTTATAAAA--GTCCATACTTATTTCACTGTGAAAATATATTTATTATTA
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
*
219790 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAAAATATTTTATAAAATATCAAAACAATCAAAT
66 TATTTGGTTAATATTGTTAAATTTAAATTCTAAAAATATTTTATAAAATATCAAAACAATCAAAT
219855 AATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA
131 AATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA
219920 AAAATTGAAACAT-AATTACATAACTTT-AAAA
196 AAAATTGAAACATAAATTACATAACTTTAAAAA
219951 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
*
220016 TATTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAAA
66 TATTTGGTTAATATTGTTAAATTTAAATTCTAAA-AATATTTTATAAAATATCAAAACAATCAAA
*
220080 TAATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
130 TAATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAA
220145 AAAAATTGAAACATAAATTACATAACTTTAAAAA
195 AAAAATTGAAACATAAATTACATAACTTTAAAAA
220179 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
1 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
220213 GTATAAAAGT
Statistics
Matches: 251, Mismatches: 6, Indels: 6
0.95 0.02 0.02
Matches are distributed among these distances:
224 22 0.09
226 159 0.63
227 32 0.13
228 38 0.15
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (228 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
TATTTGGTTAATATTGTTAAATTTAAATTCTAAAAATATTTTATAAAATATCAAAACAATCAAAT
AATTTTGTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAA
AAAATTGAAACATAAATTACATAACTTTAAAAA
Found at i:220586 original size:161 final size:161
Alignment explanation
Indices: 220344--220673 Score: 464
Period size: 161 Copynumber: 2.0 Consensus size: 161
220334 TATAGAAATG
* * * * *
220344 ATAAAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAATGATCGACAC
1 ATAAAACCAGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACAC
* * **
220409 TTCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTAAAAAATGTAT
66 TTCGTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATAC-TTTAAAAAAAATAT
* *
220474 TGATCCAAAACGATATACCAGGTAAAAATATA
130 CGATCCAAAACGATATAACAGGTAAAAATATA
* *
220506 ATAAAACCAGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACAC
1 ATAAAACCAGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACAC
* ** *
220570 TTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAATGTGTCGATACTTTAAAAAAAATATC
66 TTCGTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAAATATC
* * *
220635 GATCCACAATGATATAACAGGTAAAAATATG
131 GATCCAAAACGATATAACAGGTAAAAATATA
220666 ATAAAACC
1 ATAAAACC
220674 GTAGATACCG
Statistics
Matches: 148, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
160 47 0.32
161 59 0.40
162 42 0.28
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (161 bp):
ATAAAACCAGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACAC
TTCGTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAAAAAAAATATC
GATCCAAAACGATATAACAGGTAAAAATATA
Found at i:222917 original size:21 final size:21
Alignment explanation
Indices: 222891--222955 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
222881 AAGACAATCA
*
222891 AGAGTCGAAAAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
222912 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
222933 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
222954 AG
1 AG
222956 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.43, C:0.11, G:0.31, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:223031 original size:33 final size:33
Alignment explanation
Indices: 222989--223054 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
222979 AAATAGATGG
*
222989 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
223022 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
223055 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:224867 original size:19 final size:19
Alignment explanation
Indices: 224843--224891 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
224833 AATGTAGGGT
224843 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
224862 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
224881 TATTTTTGTAT
1 TAATTTTGTAT
224892 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:225699 original size:198 final size:198
Alignment explanation
Indices: 225010--225781 Score: 1418
Period size: 199 Copynumber: 3.9 Consensus size: 198
225000 CAATATGGCC
* *
225010 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
*
225075 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATAAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
225140 GAATATGTCTAAATAATGTGTCGACACAATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACAC-TTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
225205 TGGAA
194 TGGAA
*
225210 AACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
225275 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
225340 AATATGTCTAAATAATGTGTCAACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
225405 GGAA
195 GGAA
225409 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
225474 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* * *
225539 AATATGTCTAACTAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAATG
225604 GAA
196 GAA
* *
225607 AACAGGGTGCACCCATAAAGTGTCGATCCATTTATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
225672 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
225737 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATA
225782 CTAATTTAAA
Statistics
Matches: 556, Mismatches: 15, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
198 210 0.38
199 287 0.52
200 59 0.11
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAATG
GAA
Found at i:225745 original size:397 final size:398
Alignment explanation
Indices: 225010--225781 Score: 1422
Period size: 397 Copynumber: 1.9 Consensus size: 398
225000 CAATATGGCC
225010 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAAACATCGAAAA
225075 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATAAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATAAGA
* *
225140 GAATATGTCTAAATAATGTGTCGACACAATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACAATTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAA
225205 TGGAAAACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATC
196 TGGAAAACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATC
225270 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT
261 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT
225335 GAGAGAATATGTCTAAATAATGTGTCAACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAA
326 GAGAGAATATGTCTAAATAATGTGTCAACACT-TTTTAGTTTGTGTCGATATTTTTGTTCCAGAA
225400 TGAATGGAA
390 TGAATGGAA
* *
225409 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAAACATCGAAAA
*
225473 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATAAGA
* *
225538 GAATATGTCTAACTAATGTGTCGACAC-TTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACAATTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAA
* * *
225602 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATTTATAAAAAGTGTCGATCCCAAAAACATC
196 TGGAAAACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATC
225667 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT
261 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT
*
225732 GAGAGAATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATA
326 GAGAGAATATGTCTAAATAATGTGTCAACACTTTTTAGTTTGTGTCGATA
225782 CTAATTTAAA
Statistics
Matches: 362, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
396 18 0.05
397 192 0.53
398 92 0.25
399 60 0.17
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (398 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAAACATCGAAAA
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATAAGA
GAATATGTCTAAATAATGTGTCGACACAATTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAA
TGGAAAACAGGGTGCAACCATAAAATGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATC
GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTAT
GAGAGAATATGTCTAAATAATGTGTCAACACTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAAT
GAATGGAA
Found at i:227261 original size:6 final size:6
Alignment explanation
Indices: 227237--227328 Score: 78
Period size: 6 Copynumber: 15.3 Consensus size: 6
227227 AGCGGTCGCA
* * * * *
227237 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACA-AT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA-AGAT GAAGAT
* * * * *
227285 GACGAT GAAGAT GATGAT GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
227329 TGATCCAAAC
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
5 1 0.01
6 70 0.99
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (6 bp):
GAAGAT
Found at i:227272 original size:3 final size:3
Alignment explanation
Indices: 227252--227332 Score: 81
Period size: 3 Copynumber: 27.0 Consensus size: 3
227242 TGAAGCTGAC
* * * * * * * *
227252 GAT GAA GAT GAC GAT GAT GAT GAC AAT GAA GCT GAC GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
227300 GAT GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
227333 CCAAACAAGT
Statistics
Matches: 60, Mismatches: 18, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:227288 original size:36 final size:36
Alignment explanation
Indices: 227241--227310 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
227231 GTCGCAGAAG
227241 ATGAAGCTGACGATGAAGATGACGATGATGATGACA
1 ATGAAGCTGACGATGAAGATGACGATGATGATGACA
*
227277 ATGAAGCTGACGATGAAGATGATGATGATGATGA
1 ATGAAGCTGACGATGAAGATGACGATGATGATGA
227311 TGATGATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.39, C:0.09, G:0.31, T:0.21
Consensus pattern (36 bp):
ATGAAGCTGACGATGAAGATGACGATGATGATGACA
Found at i:227332 original size:12 final size:12
Alignment explanation
Indices: 227240--227328 Score: 97
Period size: 12 Copynumber: 7.4 Consensus size: 12
227230 GGTCGCAGAA
*
227240 GATGAAGCTGAC
1 GATGAAGATGAC
227252 GATGAAGATGAC
1 GATGAAGATGAC
*
227264 GATGATGATGAC
1 GATGAAGATGAC
* *
227276 AATGAAGCTGAC
1 GATGAAGATGAC
*
227288 GATGAAGATGAT
1 GATGAAGATGAC
* *
227300 GATGATGATGAT
1 GATGAAGATGAC
* *
227312 GATGATGATGAA
1 GATGAAGATGAC
227324 GATGA
1 GATGA
227329 TGATCCAAAC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 67 1.00
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:227332 original size:18 final size:18
Alignment explanation
Indices: 227237--227328 Score: 87
Period size: 18 Copynumber: 5.1 Consensus size: 18
227227 AGCGGTCGCA
*
227237 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
* *
227255 GAAGATGACGATGATGAT
1 GAAGATGAAGATGACGAT
*
227273 GACA-ATGAAGCTGACGAT
1 GA-AGATGAAGATGACGAT
* *
227291 GAAGATGATGATGATGAT
1 GAAGATGAAGATGACGAT
* * *
227309 GATGATGATGATGAAGAT
1 GAAGATGAAGATGACGAT
227327 GA
1 GA
227329 TGATCCAAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
17 1 0.02
18 59 0.97
19 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:228557 original size:16 final size:16
Alignment explanation
Indices: 228525--228558 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
228515 TATCCACAAC
* *
228525 AAAGTGTCGATTTAAA
1 AAAGTGTCGACTGAAA
228541 AAAGTGTCGACTGAAA
1 AAAGTGTCGACTGAAA
228557 AA
1 AA
228559 TGTAATAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (16 bp):
AAAGTGTCGACTGAAA
Found at i:228950 original size:23 final size:23
Alignment explanation
Indices: 228919--228991 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
228909 ATAGGTAAAA
*
228919 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
228942 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
228965 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
228988 ATAT
1 ATAT
228992 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:229312 original size:34 final size:31
Alignment explanation
Indices: 229257--229319 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 31
229247 TGAAACATAC
* *
229257 TTAAAAAAAATTGAAACTTAAATTACATATCT
1 TTAAAAAAAAGTGAAAATTAAATTA-ATATCT
229289 TTAAAAAAAAGTGAAATTATTAAATTAATAT
1 TTAAAAAAAAGTGAAA--ATTAAATTAATAT
229320 TGTAGGTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 15 0.56
33 4 0.15
34 8 0.30
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (31 bp):
TTAAAAAAAAGTGAAAATTAAATTAATATCT
Found at i:229319 original size:88 final size:88
Alignment explanation
Indices: 229212--229385 Score: 339
Period size: 88 Copynumber: 2.0 Consensus size: 88
229202 TTAGTGCAAA
*
229212 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAAATTGAAACTTA
1 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAAATTGAAACATA
229277 AATTACATATCTTTAAAAAAAAG
66 AATTACATATCTTTAAAAAAAAG
229300 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAAATTGAAACATA
1 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAAATTGAAACATA
229365 AATTACATATCTTTAAAAAAA
66 AATTACATATCTTTAAAAAAA
229386 GTATCGATCC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (88 bp):
TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAAATTGAAACATA
AATTACATATCTTTAAAAAAAAG
Found at i:229487 original size:22 final size:22
Alignment explanation
Indices: 229438--229509 Score: 99
Period size: 23 Copynumber: 3.2 Consensus size: 22
229428 ATAGGTAAAA
* *
229438 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTATCG-TT
229461 ATATAATGTAATAGGTATCGTT
1 ATATAATGTAATAGGTATCGTT
*
229483 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTA-TCGTT
229506 ATAT
1 ATAT
229510 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 19 0.42
23 26 0.58
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (22 bp):
ATATAATGTAATAGGTATCGTT
Found at i:229643 original size:518 final size:515
Alignment explanation
Indices: 228782--229812 Score: 1895
Period size: 518 Copynumber: 2.0 Consensus size: 515
228772 TTTGTGCAAA
*
228782 TGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATAA
1 TGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTGTAAAAAAAATTGAAACATAA
*
228847 ATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTGCAATATAATA
66 ATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTGCAATATAATA
228912 GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
131 GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
228977 AGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTG
196 AGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTG
*
229042 AAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCG
261 AAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAAGCG
229107 TCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTTAATATTATT
326 TCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTTAATATTATT
229172 TTATAAAATATCAAAACAATCAAATAATTTTTAGTGCAAATGAAATTATTAAATTAATATTGTAG
391 TTATAAAATATCAAAACAATCAAATAATTTTTAGTGCAAATGAAATTATTAAATTAATATTGTAG
*
229237 GTGGAAAACATGAAACATACTTAAAAAAAATTGAAACTTAAATTACATATCTTTAAAAAAAAG
456 GT-GAAAACATGAAACATACTT--AAAAAATTGAAACATAAATTACATATCTTTAAAAAAAAG
*
229300 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACT-TAAAAAAAATTGAAACAT
1 TGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAAC--ACTGTAAAAAAAATTGAAACAT
* *
229364 AAATTACATATCTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
64 AAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTGCAATATAA
229429 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCG-TTATATAATGTA
129 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTA
*
229493 ATAGGTAGTGGTTATATTGTAAAGTATTTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTG
194 ATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTG
* *
229558 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATCTTAATTTAGTAATTATAAG
259 TGAAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAAG
*
229623 CGTCTAATGGTTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTTAATATTA
324 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTTAATATTA
*
229688 TTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATTGT
389 TTTTATAAAATATCAAAACAATCAAATAATTTTTAGTGCAAATGAAATTATTAAATTAATATTGT
229753 AGGTGAAAACATGAAACATACTTAAAAAATTGAAACATAAATTACATATCTTTAAAAAAA
454 AGGTGAAAACATGAAACATACTTAAAAAATTGAAACATAAATTACATATCTTTAAAAAAA
229813 GTATCGATCA
Statistics
Matches: 499, Mismatches: 12, Indels: 7
0.96 0.02 0.01
Matches are distributed among these distances:
515 36 0.07
517 19 0.04
518 310 0.62
519 131 0.26
520 3 0.01
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (515 bp):
TGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTGTAAAAAAAATTGAAACATAA
ATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTGCAATATAATA
GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAAT
AGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTG
AAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAAGCG
TCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTTAATATTATT
TTATAAAATATCAAAACAATCAAATAATTTTTAGTGCAAATGAAATTATTAAATTAATATTGTAG
GTGAAAACATGAAACATACTTAAAAAATTGAAACATAAATTACATATCTTTAAAAAAAAG
Found at i:229896 original size:23 final size:23
Alignment explanation
Indices: 229865--229937 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
229855 ATAGGTAAAA
*
229865 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
229888 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
229911 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
229934 ATAT
1 ATAT
229938 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:229962 original size:46 final size:45
Alignment explanation
Indices: 229865--229962 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
229855 ATAGGTAAAA
* * *
229865 ATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATATCTATCCTTT
* *
229911 ATATAATGTAATAGGTAGTGGTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TATCTATCCTTT
*
229957 TTATAA
1 ATATAA
229963 AAGTGTCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATATCTATCCTTT
Found at i:230145 original size:428 final size:429
Alignment explanation
Indices: 229300--230280 Score: 1858
Period size: 428 Copynumber: 2.3 Consensus size: 429
229290 TAAAAAAAAG
229300 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAAATTGAAACATA
1 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTT-AAAAAAATTGAAACATA
229365 AATTACATATCTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
65 AATTACATATCTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
229430 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTATATAATGTAAT
130 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTATATAATGTAAT
* *
229495 AGGTAGTGGTTATATTGTAAAGTATTTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTG
195 AGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTAACTGTG
229560 GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATCTTAATTTAGTAATTATAAGCG
260 GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATCTTAATTTAGTAATTATAAGCG
*
229625 TCTAATGGTTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTTAATATTATT
325 TCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTTAATATTATT
229690 TTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAA
390 TTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAA
229730 TGAAATTATTAAATTAATATTGTAGGT-GAAAACATGAAACATACTT-AAAAAATTGAAACATAA
1 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAATTGAAACATAA
*
229793 ATTACATATCTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATAATA
66 ATTACATATCTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATA
*
229858 GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATATGTATCGTTTATATAATGTAAT
131 GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCG-TTATATAATGTAAT
229923 AGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTAACTGTG
195 AGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTAACTGTG
* *
229988 GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATCTTAATTTAGTAATTATAGGTG
260 GAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATCTTAATTTAGTAATTATAAGCG
*
230053 TCTAATGATTTATTTTTTACGTTACTATATATATTATTATTAAATTAAAAATTCTTAATATTATT
325 TCTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTTAATATTATT
230118 TTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAA
390 TTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAA
230158 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAATTGAAACATAA
1 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAATTGAAACATAA
230223 ATTACATATCTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAA
66 ATTACATATCTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAA
230281 CATATTATAA
Statistics
Matches: 539, Mismatches: 9, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
427 130 0.24
428 270 0.50
429 38 0.07
430 101 0.19
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (429 bp):
TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACATACTTAAAAAAATTGAAACATAA
ATTACATATCTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATA
GGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTATATAATGTAATA
GGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTAACTGTGG
AAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATCTTAATTTAGTAATTATAAGCGT
CTAATGATTTATTTTTTACGTTACGATATATATTATTATTAAATTAAAAATTCTTAATATTATTT
TATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAA
Found at i:230592 original size:183 final size:182
Alignment explanation
Indices: 230317--230977 Score: 1119
Period size: 183 Copynumber: 3.7 Consensus size: 182
230307 GCAATGCTAT
*
230317 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTAT-AATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
230382 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTGTCAAAAAGTGTCGAC
65 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATT-TAAAAAAGTGTCGAC
* *
230446 ATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
129 ATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
* * *
230500 CGGTATAAATATACCGATTTTATGCGTGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTAT-AATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
230565 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACA
65 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACA
*
230630 TTTACACATCGAAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
130 TTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
230683 CGGTATAA-ATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACAC-TTTTAATATTG
1 CGGTATAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTG
230746 TGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTT-AAAAAGTGTCGACAT
66 TGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACAT
230810 TTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
131 TTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
230862 CGG-----TATA-CGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACA-TTTTCTAATATT
1 CGGTATAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTT-TAATATT
* *
230920 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTATCGATACCATTTAAAAAAGT
65 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGT
230978 TTCGGTAATT
Statistics
Matches: 461, Mismatches: 12, Indels: 17
0.94 0.02 0.03
Matches are distributed among these distances:
174 42 0.09
175 58 0.13
176 7 0.02
179 69 0.15
180 60 0.13
181 41 0.09
182 2 0.00
183 179 0.39
184 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (182 bp):
CGGTATAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTG
TGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACAT
TTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:233478 original size:25 final size:25
Alignment explanation
Indices: 233450--233514 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
233440 TTATCATTAA
233450 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
233475 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
233500 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
233515 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:233892 original size:23 final size:23
Alignment explanation
Indices: 233861--233933 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
233851 ATAGGTAAAA
*
233861 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
233884 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
233907 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
233930 ATAT
1 ATAT
233934 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:234667 original size:18 final size:18
Alignment explanation
Indices: 234646--234682 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
234636 GTAATTGGAG
234646 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
234664 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
234682 T
1 T
234683 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:234690 original size:24 final size:24
Alignment explanation
Indices: 234638--234684 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
234628 TTTCATATGT
* *
234638 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
234662 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
234685 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:234996 original size:39 final size:39
Alignment explanation
Indices: 234953--235039 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
234943 TCCGATGCTC
*
234953 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
234992 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
235031 ATCAAAATC
1 ATCAAAATC
235040 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:235487 original size:23 final size:23
Alignment explanation
Indices: 235456--235528 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
235446 ATAGGTAAAA
* *
235456 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGATT
* *
235479 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGATT
*
235502 ATATAATGTAATAGGTAGTGATT
1 ATATAATGTAATAGGTAGCGATT
235525 ATAT
1 ATAT
235529 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGATT
Found at i:235919 original size:23 final size:23
Alignment explanation
Indices: 235888--235960 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
235878 ATAGGTAAAA
*
235888 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
235911 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
235934 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
235957 ATAT
1 ATAT
235961 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:236349 original size:23 final size:23
Alignment explanation
Indices: 236318--236390 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
236308 ATAGGTAAAA
*
236318 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
236341 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
236364 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
236387 ATAT
1 ATAT
236391 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:236465 original size:430 final size:430
Alignment explanation
Indices: 235254--236740 Score: 2805
Period size: 430 Copynumber: 3.5 Consensus size: 430
235244 GTTAATGTTG
* *
235254 TTAAATT-TAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
235318 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATA
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
235383 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
131 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
235448 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
196 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
* *
235513 TAGGTAGTGATTATATTGTAAAGTATTTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
261 TAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
*
235578 GGAAAACATTAATTTAAGGTTATCATTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
326 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
*
235643 GTCTAATAATTTATTTTTTACGTTACGATATATATTATTA
391 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
235683 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
235748 CTGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAATTGAAACA
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT--AAAAAAATTGAAACA
*
235813 TAAATTACATAACTTTAAAAGAAGTATCGATCCATTTTATAAAAAGTATGGACACTTTCAATATA
129 TAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATA
235878 ATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGT
194 ATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGT
*
235943 AATAGGTAGTGGTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACTTTTTTCACT
259 AATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACT
236008 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
324 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
236073 GCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
389 GCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
236115 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
236180 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAATATA
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
236245 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
131 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
*
236310 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAA
196 AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
*
236375 TAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTTCATACTTTTTTCACTGT
261 TAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
236440 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
326 GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
236505 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
* *
236545 TTAAATTAAAAATTATAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
*
236610 ATGAAATTATTAAATTAATATTTTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
236675 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
131 AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
236740 A
196 A
236741 TAATGTAATA
Statistics
Matches: 1035, Mismatches: 20, Indels: 5
0.98 0.02 0.00
Matches are distributed among these distances:
429 7 0.01
430 605 0.58
432 423 0.41
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (430 bp):
TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATA
AATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAAT
AGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAA
TAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGT
GGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGC
GTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
Found at i:241978 original size:21 final size:21
Alignment explanation
Indices: 241950--242126 Score: 162
Period size: 21 Copynumber: 8.6 Consensus size: 21
241940 TATCGCAAAT
241950 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
241971 TCGTGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
241992 TCGTGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
242012 TCGCGTTGCGATAGTTGAGAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
242033 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
242053 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
242074 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
242094 TCACGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
242115 TCGCGTTGCGAT
1 TCGCGTTGCGAT
242127 TTTCCATTTC
Statistics
Matches: 117, Mismatches: 36, Indels: 6
0.74 0.23 0.04
Matches are distributed among these distances:
20 42 0.36
21 75 0.64
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:242023 original size:41 final size:41
Alignment explanation
Indices: 241975--242167 Score: 316
Period size: 41 Copynumber: 4.7 Consensus size: 41
241965 TGAAAATCGT
*
241975 GTTGCGATAGTTGAAAATCGTGTTGCGATTTTCCATTTCGC
1 GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGC
*
242016 GTTGCGATAGTTGAGAATCGCGTTGCGATTTTCCATTTCGC
1 GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGC
*
242057 GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCAC
1 GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGC
242098 GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGC
1 GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGC
* * *
242139 ATTGCGATAGTCT-ACAGTCGCGTTGCGAT
1 GTTGCGATAGT-TGAAAATCGCGTTGCGAT
242168 GGAATACAGT
Statistics
Matches: 143, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
41 142 0.99
42 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (41 bp):
GTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGC
Found at i:242160 original size:103 final size:103
Alignment explanation
Indices: 242074--242271 Score: 285
Period size: 103 Copynumber: 1.9 Consensus size: 103
242064 TAGTTGAAAA
*
242074 TCGCGTTGCGATTTTCCATTTCACGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-ATTT
1 TCGCGTTGCGATTTTCCATTTCACGTTGCGATAGTCT-AAAATCGTCGTTGCGATTTTCCAAATT
242136 CGCATTGCGATAGTCTACAGTCGCGTTGCGATGGAATACAG
65 CG--TTGCGATAGTCTACAGTCGCGTTGCGATGGAATACAG
* * * *
242177 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTC
1 TCGCGTTGCGATTTTCCATTTCACGTTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCAAATTC
*
242242 GTTGCGATAGTCTACAGTTGTCGTTGCGAT
66 GTTGCGATAGTCTACAGTCG-CGTTGCGAT
242272 TTTCCAAATT
Statistics
Matches: 85, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
103 56 0.66
104 24 0.28
105 5 0.06
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (103 bp):
TCGCGTTGCGATTTTCCATTTCACGTTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCAAATTC
GTTGCGATAGTCTACAGTCGCGTTGCGATGGAATACAG
Found at i:242163 original size:62 final size:60
Alignment explanation
Indices: 241949--242230 Score: 237
Period size: 62 Copynumber: 4.5 Consensus size: 60
241939 CTATCGCAAA
* * *
241949 TTCGCGTTGCGATAGTTGAAAATCGTGTTGCGATAGTTGAAAATCGTGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTT-ACAATCGCGTTGCGAT-GTTGAAAATCGCGTTGCGATTTTCCAT
* * ** ** * ** *
242011 TTCGCGTTGCGATAGTTGAGAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGATAGTT-ACAATCGCGTTGCGATGTTGAAAATCGCGTTGCGAT-TTTCCAT
* * * * *
242073 ATCGCGTTGCGAT-TTTCCATTTCACGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTACA-ATCGCGTTGCGAT-GTTGAAAATCGCGTTGCGATTTTCCAT
* *
242134 TTCGCATTGCGATAGTCTACAGTCGCGTTGCGATG--GAATACAGTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGT-TACAATCGCGTTGCGATGTTGAA-A-A-TCGCGTTGCGATTTTCCAT
* *
242196 TTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGAT
1 TTCGCGTTGCGATAGT-TACAATCG-CGTTGCGAT
242231 TTTCCAAATT
Statistics
Matches: 176, Mismatches: 35, Indels: 17
0.77 0.15 0.07
Matches are distributed among these distances:
59 3 0.02
60 2 0.01
61 43 0.24
62 116 0.66
63 12 0.07
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
TTCGCGTTGCGATAGTTACAATCGCGTTGCGATGTTGAAAATCGCGTTGCGATTTTCCAT
Found at i:242164 original size:21 final size:21
Alignment explanation
Indices: 242135--242271 Score: 93
Period size: 21 Copynumber: 6.6 Consensus size: 21
242125 ATTTTCCATT
*
242135 TCGCATTGCGATAGTCTACAG
1 TCGCGTTGCGATAGTCTACAG
* **
242156 TCGCGTTGCGATGGAATACAG
1 TCGCGTTGCGATAGTCTACAG
* * *
242177 TCGCGTTGCGAT--TTTCCATT
1 TCGCGTTGCGATAGTCTACA-G
242197 TCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATAGTCTACAG
* ** * *
242218 TTGTCGTTGCGATTTTCCA-AA
1 TCG-CGTTGCGATAGTCTACAG
*
242239 T-TCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATAGTCTACAG
*
242259 TTGTCGTTGCGAT
1 TCG-CGTTGCGAT
242272 TTTCCAAATT
Statistics
Matches: 87, Mismatches: 22, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
19 15 0.17
20 14 0.16
21 33 0.38
22 25 0.29
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCTACAG
Found at i:242201 original size:41 final size:42
Alignment explanation
Indices: 242156--242283 Score: 172
Period size: 41 Copynumber: 3.1 Consensus size: 42
242146 TAGTCTACAG
* ** * *
242156 TCGCGTTGCGATGGAATACAGTCG-CGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAT
242197 TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCC-AAT
242240 T--CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCC-AAT
242281 TCG
1 TCG
242284 TTGTGATAGT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
41 61 0.78
42 14 0.18
43 3 0.04
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (42 bp):
TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAT
Found at i:242245 original size:19 final size:19
Alignment explanation
Indices: 242221--242286 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
242211 TCTACAGTTG
242221 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
242240 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
242261 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
242281 TCGTTG
1 TCGTTG
242287 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:242284 original size:41 final size:41
Alignment explanation
Indices: 242172--242293 Score: 185
Period size: 41 Copynumber: 3.0 Consensus size: 41
242162 TGCGATGGAA
* *
242172 TACAGTCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTC
1 TACAGTTGTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTC
242213 TACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATAGTC
1 TACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATAGTC
*
242254 TACAGTTGTCGTTGCGATTTTCCAAATTCGTTGTGATAGT
1 TACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATAGT
242294 TAAAAAAAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
41 59 0.78
42 14 0.18
43 3 0.04
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (41 bp):
TACAGTTGTCGTTGCGATTTTCCAAATTCGTTGCGATAGTC
Found at i:242382 original size:6 final size:6
Alignment explanation
Indices: 242371--242425 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
242361 GACACGTATT
242371 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
242419 ACCACG A
1 ACCACG A
242426 GACGAGACGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:242432 original size:5 final size:5
Alignment explanation
Indices: 242422--242487 Score: 118
Period size: 5 Copynumber: 13.6 Consensus size: 5
242412 GACCACGACC
242422 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG AC--G ACGAG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG
242470 ACGAG ACGAG ACGAG ACG
1 ACGAG ACGAG ACGAG ACG
242488 GCGGCGGCGG
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.05
5 56 0.95
ACGTcount: A:0.39, C:0.21, G:0.39, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:242984 original size:6 final size:6
Alignment explanation
Indices: 242973--243004 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
242963 GTCTCGTCTC
242973 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
243005 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:243136 original size:20 final size:20
Alignment explanation
Indices: 243111--243162 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
243101 ACCGTAGACT
243111 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
243131 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
243151 ATCGCAACGCGA
1 ATCGCAACGCGA
243163 TTTTCAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:243183 original size:41 final size:41
Alignment explanation
Indices: 243131--243317 Score: 196
Period size: 41 Copynumber: 4.4 Consensus size: 41
243121 GAAATGGAAA
243131 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
* ***
243172 ATCGCAACGCGAATTTGCGATGATGGAGATCGCGTTGCGA-TTTCAACT
1 ATCGCAACGCGAA-ATG-GA--A---A-ATCGCAACGCGATTTTCAACT
* * * * *
243220 ATCGCAATGTGAAATGGAAAATCGCAACGCAATCTCCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
*
243261 ATCGCAACGCGAAATGGAAAAACGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
*
243302 ATCGCAATGCGAAATG
1 ATCGCAACGCGAAATG
243318 CAACGTGAAT
Statistics
Matches: 117, Mismatches: 20, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
40 8 0.07
41 70 0.60
42 2 0.02
43 2 0.02
44 1 0.01
45 1 0.01
46 2 0.02
47 2 0.02
48 20 0.17
49 9 0.08
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
Found at i:243321 original size:21 final size:21
Alignment explanation
Indices: 243215--243321 Score: 67
Period size: 21 Copynumber: 5.2 Consensus size: 21
243205 GTTGCGATTT
* *
243215 CAACTATCGCAATGTGAAATG
1 CAACTATCGCAACGCGAAATG
* * * *
243236 GAA-AATCGCAACGC-AATCTC
1 CAACTATCGCAACGCGAA-ATG
243256 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
243277 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
243297 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
243318 CAAC
1 CAAC
243322 GTGAATTTGC
Statistics
Matches: 59, Mismatches: 23, Indels: 8
0.66 0.26 0.09
Matches are distributed among these distances:
19 2 0.03
20 25 0.42
21 30 0.51
22 2 0.03
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:244693 original size:23 final size:23
Alignment explanation
Indices: 244667--244711 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
244657 AAATATGATG
* *
244667 TAATAGGTAGTGTTTATATAATC
1 TAATAGGTAGCGCTTATATAATC
244690 TAATAGGTAGCGCTTATATAAT
1 TAATAGGTAGCGCTTATATAAT
244712 AAAATAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.40
Consensus pattern (23 bp):
TAATAGGTAGCGCTTATATAATC
Found at i:244717 original size:23 final size:23
Alignment explanation
Indices: 244668--244718 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
244658 AATATGATGT
* * **
244668 AATAGGTAGTGTTTATATAATCT
1 AATAGGTAGCGCTTATATAATAA
244691 AATAGGTAGCGCTTATATAATAA
1 AATAGGTAGCGCTTATATAATAA
244714 AATAG
1 AATAG
244719 ATTAATTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (23 bp):
AATAGGTAGCGCTTATATAATAA
Found at i:244839 original size:23 final size:23
Alignment explanation
Indices: 244766--244844 Score: 113
Period size: 23 Copynumber: 3.4 Consensus size: 23
244756 TAAGATATCA
*
244766 CTTATATAATGTAATAGGTAGCA
1 CTTATATAATGTAATAGGTAGCG
244789 CTTATATAATGTAATAGGTAGCG
1 CTTATATAATGTAATAGGTAGCG
* ** *
244812 TTTATATAATGTAATAAATAACG
1 CTTATATAATGTAATAGGTAGCG
244835 CTTATATAAT
1 CTTATATAAT
244845 AAAACATGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (23 bp):
CTTATATAATGTAATAGGTAGCG
Found at i:245276 original size:23 final size:23
Alignment explanation
Indices: 245236--245285 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
245226 ACATATTTTA
* * *
245236 TTATATAAGCACTACCTATTACG
1 TTATATAAGAAATACCTAATACG
* *
245259 TTATATAAGAAATGCCTAATATG
1 TTATATAAGAAATACCTAATACG
245282 TTAT
1 TTAT
245286 TGTGCTTAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (23 bp):
TTATATAAGAAATACCTAATACG
Found at i:245351 original size:87 final size:86
Alignment explanation
Indices: 245218--245476 Score: 306
Period size: 87 Copynumber: 3.0 Consensus size: 86
245208 TAACAAATTA
* * *
245218 AATAATTAACATATTTTATTATATAAGCACTACCTATTACGTTATATAAGAAATGCCTAATATGT
1 AATAATTAACATATTTTATTATATAAGC-CTACCTATTACATTATATAAGAAGTACCTAATATGT
* *
245283 TATTGTGCTTAATAATATTTAT
65 TATTGTACTTGATAATATTTAT
* **
245305 AATAATTAACATATTTTATTATATAAGCGCTACTTATTACATTATATAAGTTGTACCTAATATGT
1 AATAATTAACATATTTTATTATATAAGC-CTACCTATTACATTATATAAGAAGTACCTAATATGT
* * * *
245370 TATTATATTTGATAATGTTTCT
65 TATTGTACTTGATAATATTTAT
** * *
245392 TGTAATTAACCA-ATTTTATTATATAAGTCATACCTATTACATTATATAA-ACGGTACCTAATAT
1 AATAATTAA-CATATTTTATTATATAAG-CCTACCTATTACATTATATAAGA-AGTACCTAATAT
*
245455 TTTATTGTACTTGATAATATTT
63 GTTATTGTACTTGATAATATTT
245477 TCGGTTAAAT
Statistics
Matches: 146, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
87 143 0.98
88 3 0.02
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (86 bp):
AATAATTAACATATTTTATTATATAAGCCTACCTATTACATTATATAAGAAGTACCTAATATGTT
ATTGTACTTGATAATATTTAT
Found at i:246934 original size:27 final size:27
Alignment explanation
Indices: 246870--246934 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
246860 CTTTCTTCAT
* *
246870 TTCAGTTTCAATTTGATTTCGAGTTTG
1 TTCAGTTTCAGTTTAATTTCGAGTTTG
*
246897 TTCAGTTTCAGTTTAATTTTGAGTTTG
1 TTCAGTTTCAGTTTAATTTCGAGTTTG
*
246924 TTCATTTTCAG
1 TTCAGTTTCAG
246935 GCTGCAGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.18, C:0.11, G:0.17, T:0.54
Consensus pattern (27 bp):
TTCAGTTTCAGTTTAATTTCGAGTTTG
Found at i:252191 original size:18 final size:18
Alignment explanation
Indices: 252164--252216 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
252154 GTTCCAACCT
*
252164 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTGACCC
*
252182 GACCCAACCCGTTGACCC
1 GACCCGACCCGTTGACCC
252200 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
252217 TGGTGATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:252337 original size:29 final size:29
Alignment explanation
Indices: 252298--252377 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 29
252288 TTTTAGGTGA
*
252298 TATTTTTGTAATTATTTTGAAAATGATGG
1 TATTTTTGTAATTATTTTGAAAATGATGC
* * *
252327 TATTTTGGTAATTATTTTGGAAATGGTGC
1 TATTTTTGTAATTATTTTGAAAATGATGC
* *
252356 T-TTTTTGTAATTTTTTTTAAAA
1 TATTTTTGTAATTATTTTGAAAA
252378 AATTGATAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 17 0.40
29 26 0.60
ACGTcount: A:0.28, C:0.01, G:0.16, T:0.55
Consensus pattern (29 bp):
TATTTTTGTAATTATTTTGAAAATGATGC
Found at i:253127 original size:24 final size:24
Alignment explanation
Indices: 253100--253228 Score: 159
Period size: 24 Copynumber: 5.4 Consensus size: 24
253090 CTGATTTTTA
253100 ACCTGAATTTTGATATGATACTTG
1 ACCTGAATTTTGATATGATACTTG
*
253124 ACCTGAATTTTGATATGCTACTTG
1 ACCTGAATTTTGATATGATACTTG
* *
253148 ACCTGGATTTTTATATGATACTTG
1 ACCTGAATTTTGATATGATACTTG
* * *
253172 ACCTGGATTTTTATGTGATACTTG
1 ACCTGAATTTTGATATGATACTTG
* * * * *
253196 ACATGGATTCTGATCTGCTACTTG
1 ACCTGAATTTTGATATGATACTTG
253220 ACCTGAATT
1 ACCTGAATT
253229 ATGTTTTAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 93 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.42
Consensus pattern (24 bp):
ACCTGAATTTTGATATGATACTTG
Found at i:259457 original size:17 final size:18
Alignment explanation
Indices: 259393--259445 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
259383 GGTTCCAACT
*
259393 CGACCCGTTTA-CCGACC
1 CGACCCGTTGACCCGACC
* *
259410 CAACCCATTGACCCGACC
1 CGACCCGTTGACCCGACC
259428 CGACCCGTTGACCCGACC
1 CGACCCGTTGACCCGACC
259446 TGACTGTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 8 0.27
18 22 0.73
ACGTcount: A:0.21, C:0.49, G:0.17, T:0.13
Consensus pattern (18 bp):
CGACCCGTTGACCCGACC
Found at i:259504 original size:28 final size:29
Alignment explanation
Indices: 259458--259595 Score: 77
Period size: 29 Copynumber: 5.1 Consensus size: 29
259448 ACTGTTGACC
* *
259458 TGGTGATATTTTGGTAATTATTTTGAAAA
1 TGGTGATATTTTGATAATTATTTTAAAAA
* *
259487 TGGTGTTATTTT-ATAATTTTTTTAAAAA
1 TGGTGATATTTTGATAATTATTTTAAAAA
* *
259515 --ATGATATTTTCAT-A--ATTTT----A
1 TGGTGATATTTTGATAATTATTTTAAAAA
259535 -GGTGATATTTTTG-TAATTATTTTAAAAA
1 TGGTGATA-TTTTGATAATTATTTTAAAAA
* * * *
259563 TGAT-AGTATTCTGGTAATTATTTTGAAAA
1 TGGTGA-TATTTTGATAATTATTTTAAAAA
259592 TGGT
1 TGGT
259596 TGATCATATC
Statistics
Matches: 83, Mismatches: 13, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
20 1 0.01
21 6 0.07
22 5 0.06
24 9 0.11
26 9 0.11
27 2 0.02
28 19 0.23
29 32 0.39
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.51
Consensus pattern (29 bp):
TGGTGATATTTTGATAATTATTTTAAAAA
Found at i:260300 original size:24 final size:24
Alignment explanation
Indices: 260273--260467 Score: 304
Period size: 24 Copynumber: 8.2 Consensus size: 24
260263 CTGATTTTTA
*
260273 ACCTGAATTTTGATATGATACTTG
1 ACCTGGATTTTGATATGATACTTG
260297 ACCTGGATTTTGATATGATACTTG
1 ACCTGGATTTTGATATGATACTTG
*
260321 ACTTGGATTTTGATATGATACTTG
1 ACCTGGATTTTGATATGATACTTG
260345 ACCTGGATTTTGATATGATACTTG
1 ACCTGGATTTTGATATGATACTTG
*
260369 ACTTGGATTTTGATATGATACTTG
1 ACCTGGATTTTGATATGATACTTG
260393 ACCTGGA-TTT-ATATGATACTTG
1 ACCTGGATTTTGATATGATACTTG
*
260415 ACCTGGATTTTTATATGATACTTG
1 ACCTGGATTTTGATATGATACTTG
* * * *
260439 ACATGGATTCTGATCTGCTACTTG
1 ACCTGGATTTTGATATGATACTTG
260463 ACCTG
1 ACCTG
260468 AATTATGTTT
Statistics
Matches: 158, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
22 19 0.12
23 6 0.04
24 133 0.84
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (24 bp):
ACCTGGATTTTGATATGATACTTG
Found at i:261827 original size:16 final size:15
Alignment explanation
Indices: 261807--261867 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 15
261797 TTTTAAATTA
*
261807 TAAATATAAAATTAT
1 TAAATATAAAAATAT
261822 TCAAATATTCAAAAA-AT
1 T-AAATA-T-AAAAATAT
261839 TAAATATAAAAAATAT
1 TAAATAT-AAAAATAT
261855 TAAATATAAAAAT
1 TAAATATAAAAAT
261868 TAAATATTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 13 0.32
16 19 0.47
17 4 0.10
18 4 0.10
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAATATAAAAATAT
Found at i:261827 original size:23 final size:23
Alignment explanation
Indices: 261784--261827 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
261774 TAATTTATTT
*
261784 TAAAAATAAAATATTTTAAATTA
1 TAAAAATAAAATATTTCAAATTA
*
261807 TAAATATAAAAT-TATTCAAAT
1 TAAAAATAAAATAT-TTCAAAT
261828 ATTCAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAAATAAAATATTTCAAATTA
Found at i:261837 original size:48 final size:45
Alignment explanation
Indices: 261785--261877 Score: 107
Period size: 48 Copynumber: 2.0 Consensus size: 45
261775 AATTTATTTT
***
261785 AAAAATAAAATATTTTAAAT-TATAAATATAAAATTATTCAAATATTCA
1 AAAAATAAAATATAAAAAATAT-TAAATATAAAA--ATT-AAATATTCA
*
261833 AAAAATTAAATATAAAAAATATTAAATATAAAAATTAAATATTCA
1 AAAAATAAAATATAAAAAATATTAAATATAAAAATTAAATATTCA
261878 TATTAGAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 9 0.22
46 3 0.08
48 27 0.68
49 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (45 bp):
AAAAATAAAATATAAAAAATATTAAATATAAAAATTAAATATTCA
Found at i:262203 original size:25 final size:25
Alignment explanation
Indices: 262175--262222 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
262165 GTAAATTTCG
262175 ACTAATCCAAAATTTA-TAAATCTAA
1 ACTAAT-CAAAATTTATTAAATCTAA
**
262200 ACTAATTTAAATTTATTAAATCT
1 ACTAATCAAAATTTATTAAATCT
262223 TGATTAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (25 bp):
ACTAATCAAAATTTATTAAATCTAA
Found at i:266147 original size:66 final size:66
Alignment explanation
Indices: 266037--266163 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
266027 GGTATGAAGA
* * * * *
266037 CTCTGTCAGGTTCAGTCGCTGCTGGTAATTCCTTATATATGTTCAGCACCGACTGATAATTATTA
1 CTCTGGCAGGTTCAGTCGCTGCTGGTAACTCATTATATAAGTTCAACACCGACTGATAATTATTA
266102 T
66 T
* * * *
266103 CTCTGGCAGGTTCAGTCGTTG-TCGGTAACTCATTGTATAAGTTCAACAGCGACTGGTAATT
1 CTCTGGCAGGTTCAGTCGCTGCT-GGTAACTCATTATATAAGTTCAACACCGACTGATAATT
266164 CCTTATGGAC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 1 0.02
66 50 0.98
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (66 bp):
CTCTGGCAGGTTCAGTCGCTGCTGGTAACTCATTATATAAGTTCAACACCGACTGATAATTATTA
T
Found at i:266238 original size:31 final size:31
Alignment explanation
Indices: 266185--266254 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
266175 TCAGGCAACC
* *
266185 CTTGGGTAGGCACTGTAACCCTGAG-ATTTT
1 CTTGGGTAGGCACCGTAACCCTGAGAACTTT
* **
266215 ACTTGGGTAGGCCCCGTGGCCCTGAGAACTTT
1 -CTTGGGTAGGCACCGTAACCCTGAGAACTTT
266247 CTTGGGTA
1 CTTGGGTA
266255 TATGCTCTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (31 bp):
CTTGGGTAGGCACCGTAACCCTGAGAACTTT
Found at i:271207 original size:12 final size:12
Alignment explanation
Indices: 271140--271209 Score: 65
Period size: 12 Copynumber: 6.0 Consensus size: 12
271130 TAGTCAGCGA
*
271140 CTGATGTGGAAG
1 CTGATGTGGTAG
271152 CTGATGTGG-AG
1 CTGATGTGGTAG
* *
271163 ATTATGTGGTAG
1 CTGATGTGGTAG
*
271175 CTGACGTGGTTA-
1 CTGATGTGG-TAG
*
271187 -TGATTTGGTAG
1 CTGATGTGGTAG
271198 CTGATGTGGTAG
1 CTGATGTGGTAG
271210 GTGACGTAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
10 2 0.04
11 15 0.33
12 27 0.59
13 2 0.04
ACGTcount: A:0.20, C:0.07, G:0.39, T:0.34
Consensus pattern (12 bp):
CTGATGTGGTAG
Found at i:271207 original size:23 final size:23
Alignment explanation
Indices: 271141--271207 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
271131 AGTCAGCGAC
* *
271141 TGATGTGGAAGCTGATGTGGAGA
1 TGATGTGGTAGCTGATGTGGTGA
* * *
271164 TTATGTGGTAGCTGACGTGGTTA
1 TGATGTGGTAGCTGATGTGGTGA
*
271187 TGATTTGGTAGCTGATGTGGT
1 TGATGTGGTAGCTGATGTGGT
271208 AGGTGACGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.06, G:0.39, T:0.36
Consensus pattern (23 bp):
TGATGTGGTAGCTGATGTGGTGA
Found at i:271256 original size:23 final size:23
Alignment explanation
Indices: 271221--271265 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
271211 TGACGTAGCA
271221 CCCAATCAACAGCTTCTAGAAGG
1 CCCAATCAACAGCTTCTAGAAGG
* *
271244 CCCAGTCAGCAGCTTCTAGAAG
1 CCCAATCAACAGCTTCTAGAAG
271266 ATCCAATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (23 bp):
CCCAATCAACAGCTTCTAGAAGG
Found at i:271834 original size:29 final size:29
Alignment explanation
Indices: 271794--271849 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
271784 GGTGTTGAAT
*
271794 TAATAAGTGATTGTCGCTATTAACTCAAA
1 TAATAAGTGATTGTCCCTATTAACTCAAA
271823 TAATAAGTGATTGTCCCTATTAACTCA
1 TAATAAGTGATTGTCCCTATTAACTCA
271850 CAAAGAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (29 bp):
TAATAAGTGATTGTCCCTATTAACTCAAA
Found at i:280212 original size:233 final size:234
Alignment explanation
Indices: 279803--280271 Score: 897
Period size: 233 Copynumber: 2.0 Consensus size: 234
279793 GCTGATAGGT
279803 ATTTTTCACAATACCCAAGTGTAGTCTAGTGGTTTGGTTTTTATCTACATATTCTAGTGGAAATA
1 ATTTTTCACAATACCCAAGTGTAGTCTAGTGGTTTGG-TTTTATCTACATATTCTAGTGGAAATA
279868 AGCTAATTTATTAAGTTAGCATGAACACAAGTCTAGCCTAGTTCAGTAAAATAATTGATTAATTT
65 AGCTAATTTATTAAGTTAGCATGAACACAAGTCTAGCCTAGTTCAGTAAAATAATTGATTAATTT
279933 CTCTTTTACTTTCAATGTTTTGTTTATAAATATATATATATATTTGCATTGGCTAGTTTAATTTA
130 CTCTTTTACTTTCAATGTTTTGTTTATAAATATATATATATATTTGCATTGGCTAGTTTAATTTA
279998 TTTGCAAAGCGGCTCTAGGTGTTAACCAAATTACAAATTA
195 TTTGCAAAGCGGCTCTAGGTGTTAACCAAATTACAAATTA
280038 ATTTTTCACAATACCCAAGTGTAGTCTAGTGGTTTGG-TTT-TCTACATATTCTAGTTGGAAATA
1 ATTTTTCACAATACCCAAGTGTAGTCTAGTGGTTTGGTTTTATCTACATATTCTAG-TGGAAATA
*
280101 AGCTAATTTATTAAGTTAGCATGCACACAAGTCTAGCCTAGTTCAGTAAAATAATTGATTAATTT
65 AGCTAATTTATTAAGTTAGCATGAACACAAGTCTAGCCTAGTTCAGTAAAATAATTGATTAATTT
280166 CTCTTTTACTTTCAATGTTTTGTTTATAAATATATATATATATTTGCATTGGCTAGTTTAATTTA
130 CTCTTTTACTTTCAATGTTTTGTTTATAAATATATATATATATTTGCATTGGCTAGTTTAATTTA
280231 TTTGCAAAGCGGCTCTAGGTGTTAACCAAATTACAAATTA
195 TTTGCAAAGCGGCTCTAGGTGTTAACCAAATTACAAATTA
280271 A
1 A
280272 CCTTAACATG
Statistics
Matches: 232, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
232 14 0.06
233 181 0.78
235 37 0.16
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (234 bp):
ATTTTTCACAATACCCAAGTGTAGTCTAGTGGTTTGGTTTTATCTACATATTCTAGTGGAAATAA
GCTAATTTATTAAGTTAGCATGAACACAAGTCTAGCCTAGTTCAGTAAAATAATTGATTAATTTC
TCTTTTACTTTCAATGTTTTGTTTATAAATATATATATATATTTGCATTGGCTAGTTTAATTTAT
TTGCAAAGCGGCTCTAGGTGTTAACCAAATTACAAATTA
Found at i:284463 original size:29 final size:29
Alignment explanation
Indices: 284411--284478 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
284401 CATTTTACAC
* *
284411 AAATAGCACCCTTTTTAAAATAATCACCA
1 AAATAGCACCCATTTCAAAATAATCACCA
* *
284440 AAATAGCACCCATTTCAAATTAATTACCA
1 AAATAGCACCCATTTCAAAATAATCACCA
*
284469 GAATAGCACC
1 AAATAGCACC
284479 AAAATCGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (29 bp):
AAATAGCACCCATTTCAAAATAATCACCA
Found at i:284489 original size:29 final size:29
Alignment explanation
Indices: 284457--284536 Score: 135
Period size: 29 Copynumber: 2.8 Consensus size: 29
284447 ACCCATTTCA
*
284457 AATTAATTACCAGAATAGCACCAAAA-TCG
1 AATTATTTACCAGAATAGCACCAAAACT-G
284486 AATTATTTACCAGAATAGCACCAAAACTG
1 AATTATTTACCAGAATAGCACCAAAACTG
284515 AATTATTTACCAGAATAGCACC
1 AATTATTTACCAGAATAGCACC
284537 GGTCAACTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 48 0.98
30 1 0.02
ACGTcount: A:0.45, C:0.21, G:0.10, T:0.24
Consensus pattern (29 bp):
AATTATTTACCAGAATAGCACCAAAACTG
Found at i:291779 original size:29 final size:29
Alignment explanation
Indices: 291744--291817 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
291734 TTCGAAGTAA
291744 TTACCAGAATAGCACCAAAA-TCAAATTAT
1 TTACCAGAATAGCACCAAAACT-AAATTAT
*
291773 TTACCAGAATAGCACCAAAACTTAATTAT
1 TTACCAGAATAGCACCAAAACTAAATTAT
291802 TTACCAGAATAGCACC
1 TTACCAGAATAGCACC
291818 GGTCAACGGT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
29 42 0.98
30 1 0.02
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.24
Consensus pattern (29 bp):
TTACCAGAATAGCACCAAAACTAAATTAT
Found at i:291853 original size:13 final size:13
Alignment explanation
Indices: 291835--291859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291825 GGTCAACAAT
291835 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
291848 CGGGTCGGGTCA
1 CGGGTCGGGTCA
291860 GTTCAACGGG
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:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:291857 original size:18 final size:18
Alignment explanation
Indices: 291834--291877 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
291824 CGGTCAACAA
291834 TCGGGTCGGGTCAACGGG
1 TCGGGTCGGGTCAACGGG
* *
291852 TCGGGTCAGTTCAACGGG
1 TCGGGTCGGGTCAACGGG
291870 TCGGGTCG
1 TCGGGTCG
291878 TGACCGGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.11, C:0.23, G:0.45, T:0.20
Consensus pattern (18 bp):
TCGGGTCGGGTCAACGGG
Found at i:292196 original size:37 final size:38
Alignment explanation
Indices: 292146--292225 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
292136 GTGGACTCGG
292146 AACGGCACAAGGAAC-CGATGGTGCGGGAGGTGTCGTA
1 AACGGCACAAGGAACACGATGGTGCGGGAGGTGTCGTA
292183 AACGGCACAAGGAACACGATGGTGCGGGAGGTGTCGTA
1 AACGGCACAAGGAACACGATGGTGCGGGAGGTGTCGTA
292221 AACGG
1 AACGG
292226 AGCAACGATC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 15 0.36
38 27 0.64
ACGTcount: A:0.29, C:0.19, G:0.40, T:0.12
Consensus pattern (38 bp):
AACGGCACAAGGAACACGATGGTGCGGGAGGTGTCGTA
Found at i:295576 original size:24 final size:24
Alignment explanation
Indices: 295546--295603 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
295536 ATGAACTGAC
*
295546 ATAAACGAATATACACCAACATAA
1 ATAAACGAACATACACCAACATAA
* ***
295570 ATGAACGAACATACATGGACATAA
1 ATAAACGAACATACACCAACATAA
295594 ATAAACGAAC
1 ATAAACGAAC
295604 GGATTAATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.55, C:0.19, G:0.10, T:0.16
Consensus pattern (24 bp):
ATAAACGAACATACACCAACATAA
Found at i:295983 original size:31 final size:31
Alignment explanation
Indices: 295933--295996 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
295923 ATTATGATGA
* * *
295933 TTGATAAAATTATTGATAGA-AGAAAATGTTT
1 TTGAAAAAATGATTGATAGATA-AAAATATTT
*
295964 TTGAAAAAATGATTTATAGATAAAAATATTT
1 TTGAAAAAATGATTGATAGATAAAAATATTT
295995 TT
1 TT
295997 TATCATCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (31 bp):
TTGAAAAAATGATTGATAGATAAAAATATTT
Found at i:298197 original size:42 final size:42
Alignment explanation
Indices: 298145--298233 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
298135 GTACCTACAG
* *
298145 GTTCTGGTTTCGGATCCCAATTTGTAGGAACCGGATG-AACAA
1 GTTCCGGTTTCGGATCCCAATTTGTAGGAACCAG-TGCAACAA
* * *
298187 GTTCCGGTTTCGGTTCCCATTTTTTAGGAACCAGTGCAACAA
1 GTTCCGGTTTCGGATCCCAATTTGTAGGAACCAGTGCAACAA
298229 GTTCC
1 GTTCC
298234 AATTCCAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 2 0.05
42 39 0.95
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (42 bp):
GTTCCGGTTTCGGATCCCAATTTGTAGGAACCAGTGCAACAA
Found at i:298245 original size:42 final size:42
Alignment explanation
Indices: 298159--298248 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
298149 TGGTTTCGGA
* ** * *
298159 TCCCAATTTGTAGGAACCGGATGAACAAGTTCCGGTTTCGGT
1 TCCCAATTTGTAGGAACCAGATGAACAAGTTCCAATTCCAGT
* *
298201 TCCCATTTTTTAGGAACCAG-TGCAACAAGTTCCAATTCCAGT
1 TCCCAATTTGTAGGAACCAGATG-AACAAGTTCCAATTCCAGT
298243 TCCCAA
1 TCCCAA
298249 AAAAATAAGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 2 0.05
42 37 0.95
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (42 bp):
TCCCAATTTGTAGGAACCAGATGAACAAGTTCCAATTCCAGT
Found at i:302599 original size:53 final size:53
Alignment explanation
Indices: 302388--302601 Score: 277
Period size: 53 Copynumber: 4.0 Consensus size: 53
302378 TTTTAGATAC
* * *
302388 TAAGATATTGAGAGATGTACATACTTACACCAGTGTAAGTATATGTTAATTGC
1 TAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTAATTGT
* ** **
302441 TATGATATTGAGAGATACACATACTTACACATGTGTAAGTATGTGTTAATT-T
1 TAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTAATTGT
* * * * *
302493 CTAAGATATTGAGAGATGTAAATACTTATATCGGTGTAAATTTGTGTTAATTGT
1 -TAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTAATTGT
* *
302547 TAAGATATCGAGAGATGTACATACTTATACCGGTGTAAGTATGTGTTAATTGT
1 TAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTAATTGT
302600 TA
1 TA
302602 CATTTTTATA
Statistics
Matches: 137, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
53 136 0.99
54 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (53 bp):
TAAGATATTGAGAGATGTACATACTTACACCGGTGTAAGTATGTGTTAATTGT
Found at i:308425 original size:49 final size:51
Alignment explanation
Indices: 308324--308425 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 51
308314 AACCGAATTT
**
308324 TATATAAAATAATATTTTTTAAAATTTTATAATATTCAAAATAATATTAATA
1 TATATAAAATAATATTTTTTAAAA-TTTATAATATTCAAAATAATAAAAATA
* *
308376 TATATATAAT-ATATTTTTTTAAA-TTATAATATT-AAAAGGT-ATAAAAATA
1 TATATAAAATAATATTTTTTAAAATTTATAATATTCAAAA--TAATAAAAATA
308425 T
1 T
308426 TACAATTCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
48 4 0.09
49 18 0.41
50 1 0.02
51 12 0.27
52 9 0.20
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (51 bp):
TATATAAAATAATATTTTTTAAAATTTATAATATTCAAAATAATAAAAATA
Found at i:313403 original size:24 final size:24
Alignment explanation
Indices: 313371--313433 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
313361 TCCAAGGCTT
313371 CAAGCTTCTCGAGATCTAGTGATC
1 CAAGCTTCTCGAGATCTAGTGATC
313395 CAAGCTTCTCGAGATCTAGTGATC
1 CAAGCTTCTCGAGATCTAGTGATC
* *
313419 CTAGCTTCTCAAGAT
1 CAAGCTTCTCGAGAT
313434 TGATGGATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (24 bp):
CAAGCTTCTCGAGATCTAGTGATC
Found at i:319858 original size:20 final size:20
Alignment explanation
Indices: 319833--319879 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
319823 ACAGTGTCGT
319833 TGCGATACTGACTATCACAA
1 TGCGATACTGACTATCACAA
* *
319853 TGCGATACTTACTATCGCAA
1 TGCGATACTGACTATCACAA
319873 TGCGATA
1 TGCGATA
319880 ATACAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (20 bp):
TGCGATACTGACTATCACAA
Found at i:319936 original size:20 final size:20
Alignment explanation
Indices: 319890--319940 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
319880 ATACAAAATT
* *
319890 GCAACGAGATACTGACTTTC
1 GCAACGCGATTCTGACTTTC
319910 GCAACGCGATTCTGACTTTC
1 GCAACGCGATTCTGACTTTC
319930 GCAACGCGATT
1 GCAACGCGATT
319941 TACATAGCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (20 bp):
GCAACGCGATTCTGACTTTC
Found at i:320518 original size:19 final size:19
Alignment explanation
Indices: 320494--320538 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
320484 GCAACGAGAG
* *
320494 AATCGCAACGTGAAATAAA
1 AATCGCAACGCGAAACAAA
*
320513 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
320532 AATCGCA
1 AATCGCA
320539 TTGCGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:320556 original size:19 final size:19
Alignment explanation
Indices: 320534--320679 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
320524 GAAACCAAAA
*
320534 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
320553 TCGCGTTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
320572 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
320586 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
320605 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
320619 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
320638 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
320658 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
320678 TC
1 TC
320680 AACCAAAAGA
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
14 19 0.19
16 4 0.04
17 5 0.05
19 39 0.39
20 31 0.31
21 1 0.01
ACGTcount: A:0.13, C:0.25, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:320609 original size:33 final size:33
Alignment explanation
Indices: 320567--320654 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
320557 GTTGCAATTT
320567 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
320600 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
320633 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
320655 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.11, C:0.27, G:0.23, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:322842 original size:21 final size:21
Alignment explanation
Indices: 322818--322968 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
322808 TCATTCCTCG
322818 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** *
322839 AGAGGCCACTGTCATCC-CTCA
1 AGAGTCCCCTCCCA-CCGTTCA
* * * *
322860 AGAGTCCACTCCTATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
* ** *
322881 AGAGGCCCCTATCATTCC--TCG
1 AGAGTCCCCTCCCA--CCGTTCA
322902 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
322923 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
322944 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
322965 AGAG
1 AGAG
322969 CCCGATTCAC
Statistics
Matches: 86, Mismatches: 37, Indels: 15
0.62 0.27 0.11
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 78 0.91
22 3 0.03
23 1 0.01
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:322842 original size:42 final size:42
Alignment explanation
Indices: 322766--322968 Score: 203
Period size: 42 Copynumber: 4.8 Consensus size: 42
322756 GACTCGCCTG
* * * * * * *
322766 TCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
322808 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * * * * * *
322850 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
322892 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
322934 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
322969 CCCGATTCAC
Statistics
Matches: 132, Mismatches: 27, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
41 4 0.03
42 126 0.95
43 2 0.02
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:322947 original size:84 final size:84
Alignment explanation
Indices: 322763--322938 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
322753 CCCGACTCGC
322763 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
322828 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
*
322847 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
322912 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
322931 CTGTCATC
1 CTGTCATC
322939 GTTGAAGAGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:322968 original size:84 final size:84
Alignment explanation
Indices: 322763--322968 Score: 297
Period size: 84 Copynumber: 2.5 Consensus size: 84
322753 CCCGACTCGC
* * * *
322763 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
322828 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * * *
322847 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
322912 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** *
322931 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
322969 CCCGATTCAC
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
84 109 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:324334 original size:14 final size:14
Alignment explanation
Indices: 324315--324350 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
324305 ATTGTTTAAT
324315 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
324329 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
324343 TGATTTGT
1 TGATTTGT
324351 TAATTGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Done.