Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 91 of 150
Found at i:28512386 original size:163 final size:164
Alignment explanation
Indices: 28512101--28512405 Score: 404
Period size: 163 Copynumber: 1.9 Consensus size: 164
28512091 CGCTAGTTCC
* * * *
28512101 CAGATCTTTAGCGGCGTTTTTGTAAAATCGCCGCTAATGCTCAGATCTTTAGCGACGTTTTTTGA
1 CAGATCTTTAGCAGCGTTTTTGTAAAATCGCCGCTAATGCTCAAATCTTTAGCGACGTTTATAGA
* *
28512166 GAAGCATCGCTAATGCTCAGATCTTTAGCAGCGTTTTTGAAAAAGCGCCAGTAATGCTCAGATAT
66 AAAGCACCGCTAATGCTCAGATCTTTAGCAGCGTTTTTGAAAAAGCGCCAGTAATGCTCAGATAT
28512231 TTAGCGACGTTTCTGTAGAAGCGCCGCTAAAGCT
131 TTAGCGACGTTTCTGTAGAAGCGCCGCTAAAGCT
* *
28512265 CAGATCTTT-GTCAGCGTTTTT-TCAAAATCGCCGC-GATGCTCAAATCTTTAGCGGCGTTTATA
1 CAGATCTTTAG-CAGCGTTTTTGT-AAAATCGCCGCTAATGCTCAAATCTTTAGCGACGTTTATA
* * ** * *
28512327 GAAAAGCGCCGCTAATGCTCAGATCTTTAGC-GATGTTTTTGGTAAAGCGTC-GCTAATGCTCCG
64 GAAAAGCACCGCTAATGCTCAGATCTTTAGCAG-CGTTTTTGAAAAAGCGCCAG-TAATGCTCAG
*
28512390 ATATTTAGCGGCGTTT
127 ATATTTAGCGACGTTT
28512406 TTGAAAATGC
Statistics
Matches: 122, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
162 2 0.02
163 91 0.75
164 29 0.24
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (164 bp):
CAGATCTTTAGCAGCGTTTTTGTAAAATCGCCGCTAATGCTCAAATCTTTAGCGACGTTTATAGA
AAAGCACCGCTAATGCTCAGATCTTTAGCAGCGTTTTTGAAAAAGCGCCAGTAATGCTCAGATAT
TTAGCGACGTTTCTGTAGAAGCGCCGCTAAAGCT
Found at i:28512460 original size:20 final size:18
Alignment explanation
Indices: 28512435--28512472 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
28512425 ACATTTCATC
28512435 TGTTTATTTACTATGTAATT
1 TGTTTATTTA-TAT-TAATT
28512455 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
28512473 AAATTCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 10 0.56
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:28512833 original size:14 final size:15
Alignment explanation
Indices: 28512805--28512837 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
28512795 AAGGTTTATA
28512805 GATTATGGAATTAGG
1 GATTATGGAATTAGG
28512820 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
28512834 GATT
1 GATT
28512838 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:28513671 original size:25 final size:25
Alignment explanation
Indices: 28513623--28513672 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
28513613 TCATTTAAGA
* * * *
28513623 TATTTCAGAGATGTATAGTTTATAT
1 TATTTAAGAGATATATAATATATAT
28513648 TATTTAAGAGATATATAATATATAT
1 TATTTAAGAGATATATAATATATAT
28513673 ATATATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (25 bp):
TATTTAAGAGATATATAATATATAT
Found at i:28517401 original size:2 final size:2
Alignment explanation
Indices: 28517345--28517388 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
28517335 NNNNNNNNCT
28517345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28517387 TA
1 TA
28517389 CACACTTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28519599 original size:19 final size:19
Alignment explanation
Indices: 28519575--28519621 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
28519565 TCTCTTTCTT
28519575 TTTGCATT-CATTCCATGCA
1 TTTGCATTACATTCCAT-CA
*
28519594 TTTGCATTACATTGCATCA
1 TTTGCATTACATTCCATCA
*
28519613 TATGCATTA
1 TTTGCATTA
28519622 GATTTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.43
Consensus pattern (19 bp):
TTTGCATTACATTCCATCA
Found at i:28519780 original size:12 final size:12
Alignment explanation
Indices: 28519763--28519796 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28519753 TTAGAGCAAT
28519763 TGCAAGAACAGA
1 TGCAAGAACAGA
**
28519775 TGCAAGCCCAGA
1 TGCAAGAACAGA
28519787 TGCAAGAACA
1 TGCAAGAACA
28519797 ACTAGAAAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.09
Consensus pattern (12 bp):
TGCAAGAACAGA
Found at i:28522096 original size:16 final size:15
Alignment explanation
Indices: 28522075--28522118 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
28522065 AAAGAATGTT
28522075 CAAAAAAAAAAACAAA
1 CAAAAAAAAAAA-AAA
28522091 CAAAAAAAGAAAAAAA
1 CAAAAAAA-AAAAAAA
*
28522107 TAAAAAAGAAAA
1 CAAAAAA-AAAA
28522119 GGAAAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.86, C:0.07, G:0.05, T:0.02
Consensus pattern (15 bp):
CAAAAAAAAAAAAAA
Found at i:28522105 original size:20 final size:18
Alignment explanation
Indices: 28522076--28522151 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 18
28522066 AAGAATGTTC
* *
28522076 AAAAAA-AAAAACAAACA
1 AAAAAAGAAAAAAAAAAA
28522093 AAAAAAGAAAAAAATAAAA
1 AAAAAAGAAAAAAA-AAAA
28522112 AAGAAAAGGAAAAAAGAAAAGA
1 AA-AAAA-GAAAAAA-AAAA-A
*
28522134 AAAGAAGAAAAAGAAAAA
1 AAAAAAGAAAAA-AAAAA
28522152 GGAGAGGCAT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
17 6 0.12
18 6 0.12
19 5 0.10
20 14 0.29
21 14 0.29
22 4 0.08
ACGTcount: A:0.84, C:0.03, G:0.12, T:0.01
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAAAA
Found at i:28522111 original size:13 final size:12
Alignment explanation
Indices: 28522076--28522152 Score: 64
Period size: 13 Copynumber: 6.0 Consensus size: 12
28522066 AAGAATGTTC
*
28522076 AAAAAAAAAAAC
1 AAAAAAAAAAAG
*
28522088 AAACAAAAAAAGAA
1 AAA-AAAAAAA-AG
28522102 AAAAATAAAAAAG
1 AAAAA-AAAAAAG
*
28522115 AAAAGGAAAAAAG
1 AAAA-AAAAAAAG
*
28522128 AAAAGAAAAGAAG
1 AAAA-AAAAAAAG
*
28522141 AAAAAGAAAAAG
1 AAAAAAAAAAAG
28522153 GAGAGGCATA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
12 9 0.17
13 36 0.67
14 9 0.17
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.01
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:28522124 original size:26 final size:26
Alignment explanation
Indices: 28522095--28522151 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
28522085 AACAAACAAA
* *
28522095 AAAAGAAAAAAATAAAA-AAGAAAAGG
1 AAAA-AAAAAAAGAAAAGAAGAAAAAG
*
28522121 AAAAAAGAAAAGAAAAGAAGAAAAAG
1 AAAAAAAAAAAGAAAAGAAGAAAAAG
28522147 AAAAA
1 AAAAA
28522152 GGAGAGGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (26 bp):
AAAAAAAAAAAGAAAAGAAGAAAAAG
Found at i:28523718 original size:46 final size:46
Alignment explanation
Indices: 28523651--28523977 Score: 458
Period size: 46 Copynumber: 7.1 Consensus size: 46
28523641 GAACAGATTA
*
28523651 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
*
28523697 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGAGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* *
28523743 TAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATTG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
28523789 TAGATAGCAGATCTTGTCTTCCTATTTTTGGCAGCGGAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * * *
28523835 GAGATAGCAGATATTGTCTTCCTGTATTTGGCAGTGAAGTAGATTG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * *
28523881 AAGATAGCAGATCTTATCTTCCTATATTTGGCAACGGAGTAGATC-
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
* * * * *
28523926 ATAGATAGTAGATCTTGTCTTCCTGTATTTGGTAGTGGAGTAGGTTG
1 A-AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
28523973 AAGAT
1 AAGAT
28523978 TACAGATTCT
Statistics
Matches: 249, Mismatches: 30, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
45 1 0.00
46 247 0.99
47 1 0.00
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (46 bp):
AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCG
Found at i:28523984 original size:92 final size:92
Alignment explanation
Indices: 28523652--28523977 Score: 510
Period size: 92 Copynumber: 3.5 Consensus size: 92
28523642 AACAGATTAA
*
28523652 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTAGATCGAAGATAGCAGATCTTGTCTT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTAGATTGAAGATAGCAGATCTTGTCTT
*
28523717 CCTGTATTTGGCAGA-GGAGTAGATCGT
66 CCTATATTTGGCA-ACGGAGTAGATCGT
* *
28523744 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATTGTAGATAGCAGATCTTGTCTT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTAGATTGAAGATAGCAGATCTTGTCTT
* * *
28523809 CCTATTTTTGGCAGCGGAGTAGATCGG
66 CCTATATTTGGCAACGGAGTAGATCGT
* * *
28523836 AGATAGCAGATATTGTCTTCCTGTATTTGGCAGTGAAGTAGATTGAAGATAGCAGATCTTATCTT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTAGATTGAAGATAGCAGATCTTGTCTT
*
28523901 CCTATATTTGGCAACGGAGTAGATCAT
66 CCTATATTTGGCAACGGAGTAGATCGT
* * *
28523928 AGATAGTAGATCTTGTCTTCCTGTATTTGGTAGTGGAGTAGGTTGAAGAT
1 AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTAGATTGAAGAT
28523978 TACAGATTCT
Statistics
Matches: 212, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
92 212 1.00
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (92 bp):
AGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTAGATTGAAGATAGCAGATCTTGTCTT
CCTATATTTGGCAACGGAGTAGATCGT
Found at i:28524583 original size:44 final size:44
Alignment explanation
Indices: 28524501--28524586 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 44
28524491 GATCGTAACC
* * *
28524501 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTGAAGCTACT
1 AATCCTATCTCCCTGAAGTTACAGTGGAACAAACTGAAGCTACT
* * * *
28524545 AATCCTATTTCCCTGAAGTTACGGTGGAACAGATTGAAGCTA
1 AATCCTATCTCCCTGAAGTTACAGTGGAACAAACTGAAGCTA
28524587 TAAGTTGCAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (44 bp):
AATCCTATCTCCCTGAAGTTACAGTGGAACAAACTGAAGCTACT
Found at i:28527029 original size:19 final size:19
Alignment explanation
Indices: 28527002--28527046 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
28526992 TTATATACAG
28527002 TTTTAATATATATATT-AAAA
1 TTTT-ATATATAT-TTGAAAA
28527022 TTTTATATATATTTGAAAA
1 TTTTATATATATTTGAAAA
*
28527041 ATTTAT
1 TTTTAT
28527047 CAATCATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 17 0.74
20 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTATATATATTTGAAAA
Found at i:28527125 original size:12 final size:11
Alignment explanation
Indices: 28527108--28527254 Score: 64
Period size: 12 Copynumber: 13.6 Consensus size: 11
28527098 TACACAACAC
28527108 ATAACTTACAT
1 ATAACTTACAT
28527119 AATAACTTAC--
1 -ATAACTTACAT
*
28527129 ATAACTTATAT
1 ATAACTTACAT
*
28527140 ATAAACTTATAT
1 AT-AACTTACAT
28527152 ATAACTTACAT
1 ATAACTTACAT
*
28527163 ACATAACTTAAAT
1 --ATAACTTACAT
* *
28527176 A-AAGTTTATAT
1 ATAA-CTTACAT
28527187 ATAAACTTAC--
1 AT-AACTTACAT
*
28527197 ACAAC--AC--
1 ATAACTTACAT
*
28527204 ATAACTTACACA
1 ATAACTTACA-T
28527216 ATAACTTAC--
1 ATAACTTACAT
*
28527225 ATAACTTATAT
1 ATAACTTACAT
*
28527236 ATAAACTTATAT
1 AT-AACTTACAT
28527248 ATAACTT
1 ATAACTT
28527255 TCACAACTTA
Statistics
Matches: 109, Mismatches: 10, Indels: 33
0.72 0.07 0.22
Matches are distributed among these distances:
7 6 0.06
9 21 0.19
10 3 0.03
11 24 0.22
12 43 0.39
13 12 0.11
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (11 bp):
ATAACTTACAT
Found at i:28527132 original size:21 final size:21
Alignment explanation
Indices: 28527106--28527177 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
28527096 CTTACACAAC
28527106 ACATAACTTACATAATAACTT
1 ACATAACTTACATAATAACTT
*
28527127 ACATAACTTATAT-ATAAACTTAT
1 ACATAACTTACATAAT-AAC-T-T
*
28527150 ATATAACTTACATACATAACTT
1 ACATAACTTACATA-ATAACTT
*
28527172 AAATAA
1 ACATAA
28527178 AGTTTATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
20 2 0.05
21 15 0.36
22 7 0.17
23 13 0.31
24 3 0.07
25 2 0.05
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (21 bp):
ACATAACTTACATAATAACTT
Found at i:28527155 original size:23 final size:23
Alignment explanation
Indices: 28527129--28527195 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
28527119 AATAACTTAC
*
28527129 ATAACTTATATATAAACTTATAT
1 ATAACTTATATATAAACTTAAAT
* *
28527152 ATAACTTACATACATAACTTAAAT
1 ATAACTTATATATA-AACTTAAAT
*
28527176 A-AAGTTTATATATAAACTTA
1 ATAA-CTTATATATAAACTTA
28527196 CACAACACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 20 0.56
24 16 0.44
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.39
Consensus pattern (23 bp):
ATAACTTATATATAAACTTAAAT
Found at i:28527225 original size:96 final size:95
Alignment explanation
Indices: 28527052--28527254 Score: 352
Period size: 96 Copynumber: 2.1 Consensus size: 95
28527042 TTTATCAATC
* *
28527052 ATATCATAATTTACATACATAACATATATAAATTTATATATAAACTTACACAACACATAACTTAC
1 ATAT-ATAACTTACATACATAACATAAATAAATTTATATATAAACTTACACAACACATAACTTAC
*
28527117 ATAATAACTTACATAACTTATATATAAACTT
65 ACAATAACTTACATAACTTATATATAAACTT
*
28527148 ATATATAACTTACATACATAACTTAAATAAAGTTTATATATAAACTTACACAACACATAACTTAC
1 ATATATAACTTACATACATAACATAAATAAA-TTTATATATAAACTTACACAACACATAACTTAC
28527213 ACAATAACTTACATAACTTATATATAAACTT
65 ACAATAACTTACATAACTTATATATAAACTT
28527244 ATATATAACTT
1 ATATATAACTT
28527255 TCACAACTTA
Statistics
Matches: 102, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 24 0.24
96 78 0.76
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (95 bp):
ATATATAACTTACATACATAACATAAATAAATTTATATATAAACTTACACAACACATAACTTACA
CAATAACTTACATAACTTATATATAAACTT
Found at i:28527237 original size:49 final size:49
Alignment explanation
Indices: 28527056--28527464 Score: 233
Period size: 50 Copynumber: 7.9 Consensus size: 49
28527046 TCAATCATAT
* * * *
28527056 CATAATTTACATACATAACATATATAAATTTATATATAAACTTACACAACA
1 CATAACTTACATA-ATAACTTACAT-AACTTATATATAAACTTACACAACA
*
28527107 CATAACTTACATAATAACTTACATAACTTATATATAAACTT-----ATA
1 CATAACTTACATAATAACTTACATAACTTATATATAAACTTACACAACA
* * *
28527151 TATAACTTACATACATAACTTAAATAAAGTTTATATATAAACTTACACAACA
1 CATAACTTACATA-ATAACTTACAT-AA-CTTATATATAAACTTACACAACA
* * * *
28527203 CATAACTTACACAATAACTTACATAACTTATATATAAACTTATATATAACTTT
1 CATAACTTACATAATAACTTACATAACTTATATATAAAC-T-TACACAAC--A
* ** * * * *
28527256 CACAACTTACTTATAATAACTTACATAACACATACCCTACATGACTTACATAATA
1 CATAACTTAC--ATAATAACTTACATAACTTATA---TATA-AACTTACACAACA
* * *
28527311 CACAACTT--A-AATAACTTAAATAACTTACATAATACATAGCTTACATTACACACAACTTA
1 CATAACTTACATAATAACTTACATAACTT--AT-AT--ATA---AAC-TT--ACACAAC--A
* *
28527370 CATAACTTACATTCATAACTTGA-ATAAAATTTATATATAAACTTACACAACA
1 CATAACTTACA-TAATAACTT-ACAT--AACTTATATATAAACTTACACAACA
*
28527422 CATAGCTTACATATATAACTTACATAACTTATATATAAACTTA
1 CATAACTTACATA-ATAACTTACATAACTTATATATAAACTTA
28527465 TATATAACTT
Statistics
Matches: 280, Mismatches: 39, Indels: 79
0.70 0.10 0.20
Matches are distributed among these distances:
44 14 0.05
45 10 0.04
46 2 0.01
47 14 0.05
49 28 0.10
50 44 0.16
51 31 0.11
52 37 0.13
53 10 0.04
54 10 0.04
55 29 0.10
56 2 0.01
57 13 0.05
58 4 0.01
59 10 0.04
60 3 0.01
61 1 0.00
62 2 0.01
63 11 0.04
64 1 0.00
65 4 0.01
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.33
Consensus pattern (49 bp):
CATAACTTACATAATAACTTACATAACTTATATATAAACTTACACAACA
Found at i:28527271 original size:32 final size:32
Alignment explanation
Indices: 28527078--28527271 Score: 117
Period size: 32 Copynumber: 6.2 Consensus size: 32
28527068 ACATAACATA
*
28527078 TATAAATTTATATATAAACTTACACAAC--AC-
1 TATAAACTTATATAT-AACTTACACAACTTACT
* *
28527108 -AT-AACTTACATAATAACTTACATAACTTA-T
1 TATAAACTTATAT-ATAACTTACACAACTTACT
* *
28527138 ATATAAACTTATATATAACTTACA-TACATAACT
1 -TATAAACTTATATATAACTTACACAAC-TTACT
*
28527171 TAAATAAAGTTTATATATAAACTTACACAAC--AC-
1 T--ATAAA-CTTATATAT-AACTTACACAACTTACT
* * *
28527204 -AT-AACTTACACAATAACTTACATAACTTA-T
1 TATAAACTTATA-TATAACTTACACAACTTACT
*
28527234 ATATAAACTTATATATAACTTTCACAACTTACT
1 -TATAAACTTATATATAACTTACACAACTTACT
28527267 TATAA
1 TATAA
28527272 TAACTTACAT
Statistics
Matches: 126, Mismatches: 16, Indels: 42
0.68 0.09 0.23
Matches are distributed among these distances:
28 33 0.26
29 8 0.06
30 4 0.03
31 2 0.02
32 37 0.29
33 17 0.13
34 7 0.06
35 8 0.06
36 8 0.06
37 2 0.02
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.35
Consensus pattern (32 bp):
TATAAACTTATATATAACTTACACAACTTACT
Found at i:28527378 original size:9 final size:9
Alignment explanation
Indices: 28527271--28527616 Score: 119
Period size: 9 Copynumber: 40.9 Consensus size: 9
28527261 CTTACTTATA
28527271 ATAACTTAC
1 ATAACTTAC
28527280 ATAAC--AC
1 ATAACTTAC
* *
28527287 ATACCCTAC
1 ATAACTTAC
*
28527296 ATGACTTAC
1 ATAACTTAC
28527305 ATAA--TAC
1 ATAACTTAC
* *
28527312 ACAACTTAA
1 ATAACTTAC
*
28527321 ATAACTTAA
1 ATAACTTAC
28527330 ATAACTTAC
1 ATAACTTAC
28527339 ATAA--TAC
1 ATAACTTAC
*
28527346 ATAGCTTAC
1 ATAACTTAC
*
28527355 ATTAC--AC
1 ATAACTTAC
*
28527362 ACAACTTAC
1 ATAACTTAC
28527371 ATAACTTAC
1 ATAACTTAC
28527380 ---A-TT-C
1 ATAACTTAC
28527384 ATAACTTGA-
1 ATAACTT-AC
* *
28527393 ATAAAATTTATAT
1 AT--AA-CT-TAC
28527406 ATAAACTTAC
1 AT-AACTTAC
*
28527416 ACAAC--AC
1 ATAACTTAC
*
28527423 ATAGCTTAC
1 ATAACTTAC
28527432 AT-A--T--
1 ATAACTTAC
28527436 ATAACTTAC
1 ATAACTTAC
*
28527445 ATAACTTATAT
1 ATAAC-T-TAC
*
28527456 ATAAACTTATAT
1 AT-AAC-T-TAC
*
28527468 ATAACTTTC
1 ATAACTTAC
28527477 ATAACTTAC
1 ATAACTTAC
*
28527486 -TTA-TT--
1 ATAACTTAC
28527491 ATAACTTAC
1 ATAACTTAC
28527500 ATAA--TAC
1 ATAACTTAC
* *
28527507 ATAGCCTAC
1 ATAACTTAC
*
28527516 ATGACTTAC
1 ATAACTTAC
28527525 ATAA--TAC
1 ATAACTTAC
* *
28527532 ACAACTTAA
1 ATAACTTAC
28527541 ATAACTTAC
1 ATAACTTAC
28527550 ATAA--TAC
1 ATAACTTAC
*
28527557 ATAACTTTC
1 ATAACTTAC
28527566 ATAACTTAC
1 ATAACTTAC
*
28527575 ATTA--TAC
1 ATAACTTAC
* *
28527582 ACAACTTAT
1 ATAACTTAC
28527591 ATAACTTAC
1 ATAACTTAC
28527600 ATAACTTAC
1 ATAACTTAC
*
28527609 ATAGCTTA
1 ATAACTTA
28527617 ATTATACTTA
Statistics
Matches: 250, Mismatches: 46, Indels: 82
0.66 0.12 0.22
Matches are distributed among these distances:
4 3 0.01
5 3 0.01
6 4 0.02
7 58 0.23
8 4 0.02
9 144 0.58
10 5 0.02
11 10 0.04
12 16 0.06
13 3 0.01
ACGTcount: A:0.45, C:0.20, G:0.02, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:28527382 original size:25 final size:25
Alignment explanation
Indices: 28527271--28527381 Score: 100
Period size: 25 Copynumber: 4.4 Consensus size: 25
28527261 CTTACTTATA
* * *
28527271 ATAACTTACATAACACATACCCTAC
1 ATAACTTACATAACACACAACTTAC
* * *
28527296 ATGACTTACATAATACACAACTTAA
1 ATAACTTACATAACACACAACTTAC
* *
28527321 ATAACTTAAATAACTTACATAA--TAC
1 ATAACTTACATAAC--ACACAACTTAC
* *
28527346 ATAGCTTACATTACACACAACTTAC
1 ATAACTTACATAACACACAACTTAC
28527371 ATAACTTACAT
1 ATAACTTACAT
28527382 TCATAACTTG
Statistics
Matches: 66, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
23 5 0.08
25 56 0.85
27 5 0.08
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.29
Consensus pattern (25 bp):
ATAACTTACATAACACACAACTTAC
Found at i:28527468 original size:10 final size:11
Alignment explanation
Indices: 28527432--28527474 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 11
28527422 CATAGCTTAC
28527432 ATATATAAC-T
1 ATATATAACTT
*
28527442 -TACATAACTT
1 ATATATAACTT
28527452 ATATATAAACTT
1 ATATAT-AACTT
28527464 ATATATAACTT
1 ATATATAACTT
28527475 TCATAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 7 0.25
10 1 0.04
11 9 0.32
12 11 0.39
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATATAACTT
Found at i:28527485 original size:220 final size:218
Alignment explanation
Indices: 28527152--28527602 Score: 733
Period size: 220 Copynumber: 2.1 Consensus size: 218
28527142 AAACTTATAT
*
28527152 ATAACTTACATACATAACTTAAATAAAGTTTATATATAAACTTACACAACACATAACTTACACAA
1 ATAACTTACATACATAACTTAAATAAAATTTATATATAAACTTACACAACACATAACTTACACAA
28527217 TAACTTACATAACTTATATATAAACTTATATATAACTTTCACAACTTACTTATAATAACTTACAT
66 TAACTTACATAACTTATATATAAACTTATATATAACTTTCACAACTTACTTATAATAACTTACAT
28527282 AACACATACCCTACATGACTTACATAATACACAACTTAAATAACTTAAATAACTTACATAA-TAC
131 AACACATACCCTACATGACTTACATAATACACAACTTAAATAACTTAAATAA--TACATAACTAC
*
28527346 ATAGCTTACATTACACACAACTTAC
194 ATAACTTACATTACACACAACTTAC
* * * *
28527371 ATAACTTACATTCATAACTTGAATAAAATTTATATATAAACTTACACAACACATAGCTTACATAT
1 ATAACTTACATACATAACTTAAATAAAATTTATATATAAACTTACACAACACATAACTTACACA-
* *
28527436 ATAACTTACATAACTTATATATAAACTTATATATAACTTTCATAACTTACTTATTATAACTTACA
65 ATAACTTACATAACTTATATATAAACTTATATATAACTTTCACAACTTACTTATAATAACTTACA
* * * *
28527501 TAATACATAGCCTACATGACTTACATAATACACAACTTAAATAACTTACATAATACATAACTTTC
130 TAACACATACCCTACATGACTTACATAATACACAACTTAAATAACTTAAATAATACATAAC-TAC
* *
28527566 ATAACTTACATTATACACAACTTAT
194 ATAACTTACATTACACACAACTTAC
28527591 ATAACTTACATA
1 ATAACTTACATA
28527603 ACTTACATAG
Statistics
Matches: 214, Mismatches: 15, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
218 7 0.03
219 59 0.28
220 148 0.69
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (218 bp):
ATAACTTACATACATAACTTAAATAAAATTTATATATAAACTTACACAACACATAACTTACACAA
TAACTTACATAACTTATATATAAACTTATATATAACTTTCACAACTTACTTATAATAACTTACAT
AACACATACCCTACATGACTTACATAATACACAACTTAAATAACTTAAATAATACATAACTACAT
AACTTACATTACACACAACTTAC
Found at i:28527523 original size:25 final size:25
Alignment explanation
Indices: 28527491--28527603 Score: 145
Period size: 25 Copynumber: 4.5 Consensus size: 25
28527481 CTTACTTATT
* *
28527491 ATAACTTACATAATACATAGCCTAC
1 ATAACTTACATAATACATAACTTAC
* * *
28527516 ATGACTTACATAATACACAACTTAA
1 ATAACTTACATAATACATAACTTAC
*
28527541 ATAACTTACATAATACATAACTTTC
1 ATAACTTACATAATACATAACTTAC
* * *
28527566 ATAACTTACATTATACACAACTTAT
1 ATAACTTACATAATACATAACTTAC
28527591 ATAACTTACATAA
1 ATAACTTACATAA
28527604 CTTACATAGC
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (25 bp):
ATAACTTACATAATACATAACTTAC
Found at i:28527558 original size:50 final size:50
Alignment explanation
Indices: 28527491--28527613 Score: 174
Period size: 50 Copynumber: 2.4 Consensus size: 50
28527481 CTTACTTATT
*
28527491 ATAACTTACATAATACATAGCCTACATGACTTACATAATACACAACTTAA
1 ATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTAA
* * * * *
28527541 ATAACTTACATAATACATAACTTTCATAACTTACATTATACACAACTTAT
1 ATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTAA
28527591 ATAACTTACATAACTTACATAGC
1 ATAACTTACATAA--TACATAGC
28527614 TTAATTATAC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
50 57 0.89
52 7 0.11
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (50 bp):
ATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTAA
Found at i:28533198 original size:66 final size:66
Alignment explanation
Indices: 28533037--28533200 Score: 181
Period size: 66 Copynumber: 2.5 Consensus size: 66
28533027 AGCAAATTAC
* *
28533037 ACAACTTAAAG-AGGAGGCAACATCGAGAGAAGCGGAGGTTCAAAAAAGATATGAAGAACTCCAG
1 ACAACTTAAAGCA-GATGCAACAGCGAGAGAAGCGGAGGTTCAAAAAAGATATGAAGAACTCCAG
28533101 CT
65 CT
* * * * * *
28533103 ACAACTTAAAGTAGATGCAATAGCAAGAGAAGCTGAGGTTCAACGAAAG-TATGAAGAACTCTAG
1 ACAACTTAAAGCAGATGCAACAGCGAGAGAAGCGGAGGTTCAA-AAAAGATATGAAGAACTCCAG
28533167 C-
65 CT
* **
28533168 AGCAGCTTAAAGCAGATGCGGCAGCGAGAGAAG
1 A-CAACTTAAAGCAGATGCAACAGCGAGAGAAG
28533201 TAGAGGCTGG
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
65 1 0.01
66 76 0.93
67 5 0.06
ACGTcount: A:0.42, C:0.16, G:0.27, T:0.15
Consensus pattern (66 bp):
ACAACTTAAAGCAGATGCAACAGCGAGAGAAGCGGAGGTTCAAAAAAGATATGAAGAACTCCAGC
T
Found at i:28533238 original size:21 final size:21
Alignment explanation
Indices: 28533188--28533247 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
28533178 AGCAGATGCG
*
28533188 GCAGCGAGAGAAGTAGAGGCT
1 GCAGCGAGGGAAGTAGAGGCT
*
28533209 GGAGCGAGGGAAGTAGAGGCT
1 GCAGCGAGGGAAGTAGAGGCT
* *
28533230 GCAGTGAGGGAAGCAGAG
1 GCAGCGAGGGAAGTAGAG
28533248 CAGCATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.48, T:0.08
Consensus pattern (21 bp):
GCAGCGAGGGAAGTAGAGGCT
Found at i:28533763 original size:43 final size:43
Alignment explanation
Indices: 28533575--28533902 Score: 257
Period size: 43 Copynumber: 7.6 Consensus size: 43
28533565 AAATTAGTAC
* * ** *
28533575 CGTTTGTGGGAAAAGTGCCGCTAAAGATCATGGTCTTCAGCGG
1 CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGACCTTTAGCGG
* * * * * * **
28533618 CGTTT-TCTGGAAAGGCACCGCTAACGATCAGGGTCTTTAGCGG
1 CGTTTGT-GGGAAAAGCGCCGCTAAAGACCATGACCTTTAGCGG
* * * * * *
28533661 CGTTT-TCTGGAGAAGCGCCGCTAAAGATCATTATCGTTAGCGG
1 CGTTTGT-GGGAAAAGCGCCGCTAAAGACCATGACCTTTAGCGG
** * *
28533704 CGTTTGTTTTG-TAAGTGCCGCTAAAGACCATGACCTTTAGCGG
1 CGTTTG-TGGGAAAAGCGCCGCTAAAGACCATGACCTTTAGCGG
* *** * * * * * *
28533747 TGTTTGTCATAAAAGTGTCGTTAAAGAGCGTGATCTTTAGCGG
1 CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGACCTTTAGCGG
*
28533790 CGTTTGTGGGAAAAGCGCCGCTGAAGACCATGACCTTTAGCGG
1 CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGACCTTTAGCGG
* *
28533833 CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGGCCTTCAGCGG
1 CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGACCTTTAGCGG
* **
28533876 CATTTGTGGTTAAAGCGCCGCTAAAGA
1 CGTTTGTGGGAAAAGCGCCGCTAAAGA
28533903 TCTTGGTCTT
Statistics
Matches: 232, Mismatches: 49, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
42 2 0.01
43 227 0.98
44 2 0.01
45 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (43 bp):
CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGACCTTTAGCGG
Found at i:28533901 original size:129 final size:128
Alignment explanation
Indices: 28533575--28533916 Score: 332
Period size: 129 Copynumber: 2.6 Consensus size: 128
28533565 AAATTAGTAC
* * * * *
28533575 CGTTTGTGGGAAAAGTGCCGCTAAAGATCATGGTCTTCAGCGGCGTTTTCTGG-AAAGGCACCGC
1 CGTTTGTGGGAAAAGTGCCGCTAAAGACCATGGCCTTCAGCGGC-ATTTGTGGTAAA-GCGCCGC
* * * * * *
28533639 TAACGATCAG-GGTCTTTAGCGGCGTTTTCTGGAGAAGCGCCGCTAAAGATCATTATCGTTAGCG
64 TAAAGATC-GTGGTCTTTAGCGGCGTTTTCGGGAAAAGCGCCGCTAAAGACCATGACCGTTAGCG
28533703 G
128 G
** * * * ** ** * * *
28533704 CGTTTGTTTTG-TAAGTGCCGCTAAAGACCATGACCTTTAGCGGTGTTTGTCATAAAAGTGTCGT
1 CGTTTG-TGGGAAAAGTGCCGCTAAAGACCATGGCCTTCAGCGGCATTTGTGGT-AAAGCGCCGC
* * * *
28533768 TAAAGAGCGTGATCTTTAGCGGCGTTTGT-GGGAAAAGCGCCGCTGAAGACCATGACCTTTAGCG
64 TAAAGATCGTGGTCTTTAGCGGCGTTT-TCGGGAAAAGCGCCGCTAAAGACCATGACCGTTAGCG
28533832 G
128 G
*
28533833 CGTTTGTGGGAAAAGCGCCGCTAAAGACCATGGCCTTCAGCGGCATTTGTGGTTAAAGCGCCGCT
1 CGTTTGTGGGAAAAGTGCCGCTAAAGACCATGGCCTTCAGCGGCATTTGTGG-TAAAGCGCCGCT
*
28533898 AAAGATCTTGGTCTTTAGC
65 AAAGATCGTGGTCTTTAGC
28533917 AGCATTTATT
Statistics
Matches: 164, Mismatches: 42, Indels: 14
0.75 0.19 0.06
Matches are distributed among these distances:
128 7 0.04
129 150 0.91
130 7 0.04
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.27
Consensus pattern (128 bp):
CGTTTGTGGGAAAAGTGCCGCTAAAGACCATGGCCTTCAGCGGCATTTGTGGTAAAGCGCCGCTA
AAGATCGTGGTCTTTAGCGGCGTTTTCGGGAAAAGCGCCGCTAAAGACCATGACCGTTAGCGG
Found at i:28534022 original size:22 final size:22
Alignment explanation
Indices: 28533994--28534036 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
28533984 TTACGGCGCT
*
28533994 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
28534016 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
28534037 GTCTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:28553211 original size:15 final size:15
Alignment explanation
Indices: 28553191--28553222 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
28553181 TGTAGTAAAC
28553191 ATGTAATTATTTTCT
1 ATGTAATTATTTTCT
28553206 ATGTAATTATTTTCT
1 ATGTAATTATTTTCT
28553221 AT
1 AT
28553223 ATATTTGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.59
Consensus pattern (15 bp):
ATGTAATTATTTTCT
Found at i:28554973 original size:12 final size:12
Alignment explanation
Indices: 28554941--28554974 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
28554931 TATTAATTTA
28554941 ATAATATTTAAT
1 ATAATATTTAAT
28554953 ATTAA-ATTTAAT
1 A-TAATATTTAAT
28554965 ATAATATTTA
1 ATAATATTTA
28554975 TCTTGATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.15
12 14 0.70
13 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATAATATTTAAT
Found at i:28555490 original size:77 final size:77
Alignment explanation
Indices: 28555362--28555507 Score: 229
Period size: 77 Copynumber: 1.9 Consensus size: 77
28555352 ATGAAGGAAG
*** *
28555362 ATGTAATGACTACCATGAGATAAAATAGGAGCATATTGGAAGAATGTATATTGTCCCAAAGAGAT
1 ATGTAATGACTACCATGAGATAAAATAGGAGCATATTGGAAGAAAAAATATTCTCCCAAAGAGAT
28555427 TAAGAATATTCT
66 TAAGAATATTCT
** *
28555439 ATGTAATGGTTACCATGAGATAAAATAGGAGCATATTGGGAGAAAAAATATTCTCCCAAAGAGAT
1 ATGTAATGACTACCATGAGATAAAATAGGAGCATATTGGAAGAAAAAATATTCTCCCAAAGAGAT
28555504 TAAG
66 TAAG
28555508 GACAAGGTGA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 62 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (77 bp):
ATGTAATGACTACCATGAGATAAAATAGGAGCATATTGGAAGAAAAAATATTCTCCCAAAGAGAT
TAAGAATATTCT
Found at i:28558342 original size:15 final size:15
Alignment explanation
Indices: 28558322--28558350 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28558312 AATGTCGCGA
28558322 CAACAAAGCAAGCTT
1 CAACAAAGCAAGCTT
28558337 CAACAAAGCAAGCT
1 CAACAAAGCAAGCT
28558351 GAATTTTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.14, T:0.10
Consensus pattern (15 bp):
CAACAAAGCAAGCTT
Found at i:28575667 original size:22 final size:23
Alignment explanation
Indices: 28575618--28575680 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
28575608 CTCTCTAATT
*
28575618 ATTAGCACATT-ACTGCTCTGTG
1 ATTAGCACATTCACTGCTCTCTG
28575640 ATTAGCACATTCA-TGCTCTCTG
1 ATTAGCACATTCACTGCTCTCTG
*
28575662 -TATAGCAC-TTCAGTGCTCT
1 AT-TAGCACATTCACTGCTCT
28575681 TTGTTCATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 5 0.14
22 31 0.84
23 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (23 bp):
ATTAGCACATTCACTGCTCTCTG
Found at i:28582777 original size:51 final size:50
Alignment explanation
Indices: 28582710--28582905 Score: 205
Period size: 51 Copynumber: 3.9 Consensus size: 50
28582700 CAATGATGTT
* * * *
28582710 CGGTTCACATAGTAGCCTGCACATAGAACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATC
* * * * * * *
28582761 CGATACATGTAGTAGCCTGCACATAGTACTACATACATGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATC
* * * * * *
28582812 CGGTACGCATAGTAGCCTGCACATAGCACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TC
28582862 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
28582906 CACTTTCACT
Statistics
Matches: 113, Mismatches: 29, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
49 2 0.02
50 40 0.35
51 69 0.61
52 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCATC
Found at i:28582925 original size:101 final size:99
Alignment explanation
Indices: 28582716--28582897 Score: 258
Period size: 101 Copynumber: 1.8 Consensus size: 99
28582706 TGTTCGGTTC
* *
28582716 ACATAGTAGCCTGCACATAGAACTACACATGTGACCATTACCATCCGATACATGTAGTAGCCTGC
1 ACATAGTAGCCTGCACATAGAACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCTGC
* *
28582781 ACATAGTACTACATACATGATCGAAACTATCCGGT
65 ACATAGTACTACACACATGATCCAAACTATCCGGT
* * *
28582816 ACGCATAGTAGCCTGCACATAGCACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCT
1 A--CATAGTAGCCTGCACATAGAACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCT
28582880 GCACATAGTACTACACAC
63 GCACATAGTACTACACAC
28582898 GTGACCATCA
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
100 5 0.07
101 35 0.48
102 33 0.45
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (99 bp):
ACATAGTAGCCTGCACATAGAACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACATGATCCAAACTATCCGGT
Found at i:28587027 original size:20 final size:19
Alignment explanation
Indices: 28586990--28587029 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
28586980 ACAAAGGCCC
*
28586990 CAAAGTGCAGACAGGGGCA
1 CAAAGTGCAAACAGGGGCA
*
28587009 CAAATGTGCAAACATGGGCA
1 CAAA-GTGCAAACAGGGGCA
28587029 C
1 C
28587030 CGTAGTGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.38, C:0.23, G:0.30, T:0.10
Consensus pattern (19 bp):
CAAAGTGCAAACAGGGGCA
Found at i:28592583 original size:20 final size:21
Alignment explanation
Indices: 28592550--28592606 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
28592540 GCATCATAGA
28592550 TGCATAACAGGGGCACCAAA-G
1 TGCA-AACAGGGGCACCAAATG
*
28592571 TGCAAACAAGGGCA-CAAATG
1 TGCAAACAGGGGCACCAAATG
28592591 TGCAAACAGGGGCACC
1 TGCAAACAGGGGCACC
28592607 GTAGTGTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.12
20 23 0.72
21 5 0.16
ACGTcount: A:0.39, C:0.25, G:0.28, T:0.09
Consensus pattern (21 bp):
TGCAAACAGGGGCACCAAATG
Found at i:28602789 original size:25 final size:25
Alignment explanation
Indices: 28602755--28602825 Score: 124
Period size: 25 Copynumber: 2.8 Consensus size: 25
28602745 CCTTTACATA
*
28602755 TATGCTCACATGAGCTGTGAATAAG
1 TATGCTCACATGAGCTATGAATAAG
28602780 TATGCTCACATGAGCTATGAATAAG
1 TATGCTCACATGAGCTATGAATAAG
*
28602805 TATGCTCACTTGAGCTATGAA
1 TATGCTCACATGAGCTATGAA
28602826 AATGGGCCTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (25 bp):
TATGCTCACATGAGCTATGAATAAG
Found at i:28607554 original size:24 final size:24
Alignment explanation
Indices: 28607509--28607554 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
28607499 ATCGGTTATT
*
28607509 ATATTCATGTTATTTAATTGAATG
1 ATATTCATGTTATTTAAATGAATG
28607533 ATATT-ATGTTATTTATAATGAA
1 ATATTCATGTTATTTA-AATGAA
28607555 AATTATTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (24 bp):
ATATTCATGTTATTTAAATGAATG
Found at i:28609974 original size:14 final size:14
Alignment explanation
Indices: 28609955--28609983 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28609945 CGAGAAAGAA
28609955 TTTGTATGACTCAG
1 TTTGTATGACTCAG
28609969 TTTGTATGACTCAG
1 TTTGTATGACTCAG
28609983 T
1 T
28609984 AAGTATGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.45
Consensus pattern (14 bp):
TTTGTATGACTCAG
Found at i:28622246 original size:20 final size:20
Alignment explanation
Indices: 28622221--28622260 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28622211 ATGAGTTATT
28622221 CAAGTAAGCA-AGTAAGTAAA
1 CAAGTAAG-AGAGTAAGTAAA
28622241 CAAGTAAGAGAGTAAGTAAA
1 CAAGTAAGAGAGTAAGTAAA
28622261 GAAGAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.55, C:0.07, G:0.23, T:0.15
Consensus pattern (20 bp):
CAAGTAAGAGAGTAAGTAAA
Found at i:28629512 original size:56 final size:51
Alignment explanation
Indices: 28629452--28629644 Score: 176
Period size: 50 Copynumber: 3.7 Consensus size: 51
28629442 GGGAATGAGA
*
28629452 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTCTGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA--ACTGAGG---TGAGAGG
**
28629508 TCCCACGTAAGACCATGTCTGGGACATGGTGTTGGC-ACTGAGGTGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACTGAGGTGAGAGG
* * * ** **
28629558 TCCCCCGTAAGACCATGT-TAGGGACATGGCATGGGCAGC-GATATGAGAAC
1 TCCCACGTAAGACCATGTCT-GGGACATGGCATTGGCAACTGAGGTGAGAGG
* * * * *
28629608 TCTCATGTAAGACCATATCTGGGAAATGGCTTTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
28629645 TGTTATTATC
Statistics
Matches: 115, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
49 1 0.01
50 72 0.63
51 2 0.02
53 6 0.05
56 34 0.30
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.24
Consensus pattern (51 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCAACTGAGGTGAGAGG
Found at i:28643136 original size:16 final size:16
Alignment explanation
Indices: 28643115--28643149 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28643105 ATGCCACTGC
28643115 AAACTCCTCCTCAATT
1 AAACTCCTCCTCAATT
*
28643131 AAACTCTTCCTCAATT
1 AAACTCCTCCTCAATT
28643147 AAA
1 AAA
28643150 TCATCTAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.31, G:0.00, T:0.31
Consensus pattern (16 bp):
AAACTCCTCCTCAATT
Found at i:28651089 original size:20 final size:21
Alignment explanation
Indices: 28651061--28651103 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
28651051 ATAGTAAAAT
28651061 AAAGAAGGA-AATGGAAGAGAG
1 AAAGAAGGAGAAT-GAAGAGAG
*
28651082 AAAG-AGGAGAATGAATAGAG
1 AAAGAAGGAGAATGAAGAGAG
28651102 AA
1 AA
28651104 TTTAGAGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.07
Consensus pattern (21 bp):
AAAGAAGGAGAATGAAGAGAG
Found at i:28651450 original size:33 final size:33
Alignment explanation
Indices: 28651413--28651475 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
28651403 TTGTTAGATC
28651413 AGTCCTCTTTTACTTAGAACAATTAGGCCACTT
1 AGTCCTCTTTTACTTAGAACAATTAGGCCACTT
28651446 AGTCCTCTTTTACTTAGAACAATTAGGCCA
1 AGTCCTCTTTTACTTAGAACAATTAGGCCA
28651476 TTTTCTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.35
Consensus pattern (33 bp):
AGTCCTCTTTTACTTAGAACAATTAGGCCACTT
Found at i:28657367 original size:17 final size:19
Alignment explanation
Indices: 28657335--28657369 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
28657325 ACGTTTGGGG
28657335 ACTAAATTTAGTAAAAAGA
1 ACTAAATTTAGTAAAAAGA
28657354 ACTAAA-TT-GTAAAAAG
1 ACTAAATTTAGTAAAAAG
28657370 TGAAAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (19 bp):
ACTAAATTTAGTAAAAAGA
Found at i:28658507 original size:50 final size:50
Alignment explanation
Indices: 28658401--28658631 Score: 198
Period size: 50 Copynumber: 4.5 Consensus size: 50
28658391 GGGAATGAGA
*
28658401 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA-TA--AGAGG
* *
28658457 TCGCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
** * * * * * **
28658507 TCCCCCGTAAGACCATGTCTAGGACATGACATGGGCACCGATATGAGGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT-AAGAGG
* * * * * *
28658558 TCCCATGTAAGACCATATCTGGGATATGGCATTGGAAATACAAGA-AACA--
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG-CA-CCGAGATAAGAGG
28658607 TCCCATGTAAGACCATGTCTGGGAC
1 TCCCATGTAAGACCATGTCTGGGAC
28658632 TTAGCTTTGG
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
49 23 0.16
50 41 0.29
51 33 0.23
52 3 0.02
53 7 0.05
55 1 0.01
56 35 0.24
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
Found at i:28665865 original size:56 final size:50
Alignment explanation
Indices: 28665783--28666025 Score: 159
Period size: 50 Copynumber: 4.8 Consensus size: 50
28665773 GGGAATGAGA
* *
28665783 TCCCATGTAAGACCATGTCTGAGACATGGAATTGGCATCATTTAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATC---GAGA-TA--AGAGG
**
28665839 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCGAGATAAGAGG
** * * * * * * **
28665889 TCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCGAGATAAGAGG
* * * * * * * *
28665939 TCCCGTGTAAGACTATATCTGGGATATAGCATTGGCAGTACAAGA-AACA--
1 TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCA-T-CGAGATAAGAGG
** **
28665988 TCCCATGTAAGACCATGTCTATGACATGGCTTTGGCAT
1 TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCAT
28666026 ATTTCTATTT
Statistics
Matches: 150, Mismatches: 35, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
48 1 0.01
49 29 0.19
50 74 0.49
51 2 0.01
52 5 0.03
53 3 0.02
56 36 0.24
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCGAGATAAGAGG
Found at i:28665949 original size:50 final size:49
Alignment explanation
Indices: 28665839--28666024 Score: 160
Period size: 50 Copynumber: 3.8 Consensus size: 49
28665829 TTATGAGAGG
* * * **
28665839 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATAAGAGG
1 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA-CGATATAAGAAC
** * *
28665889 TCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA-CGATATAAGAAC
* * * * * * *
28665939 TCCCGTGTAAGACTATATCTGGGATATAGCATTGGCA-G-TACAAGAAAC
1 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACGATATAAG-AAC
* *
28665987 ATCCCATGTAAGACCATGTCTATGACATGGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA
28666025 TATTTCTATT
Statistics
Matches: 106, Mismatches: 28, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
47 4 0.04
48 4 0.04
49 29 0.27
50 69 0.65
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACGATATAAGAAC
Found at i:28665974 original size:100 final size:99
Alignment explanation
Indices: 28665830--28666017 Score: 218
Period size: 100 Copynumber: 1.9 Consensus size: 99
28665820 TCATTTAGAT
** * * * * *
28665830 TATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-T-CGAGATAAGAGGTCCC
1 TATGAGAACTCCCATGTAAGACCATATCTGGGACATAGCATTGGCAGTACAAGA-AACA--TCCC
*
28665893 CCGTAAGACCATGTCTAGGACATGGCATGGGCACCGA
63 ACGTAAGACCATGTCTAGGACATGGCATGGGCACCGA
* * * *
28665930 TATGAGAACTCCCGTGTAAGACTATATCTGGGATATAGCATTGGCAGTACAAGAAACATCCCATG
1 TATGAGAACTCCCATGTAAGACCATATCTGGGACATAGCATTGGCAGTACAAGAAACATCCCACG
*
28665995 TAAGACCATGTCTATGACATGGC
66 TAAGACCATGTCTAGGACATGGC
28666018 TTTGGCATAT
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
99 27 0.37
100 38 0.52
101 4 0.05
102 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (99 bp):
TATGAGAACTCCCATGTAAGACCATATCTGGGACATAGCATTGGCAGTACAAGAAACATCCCACG
TAAGACCATGTCTAGGACATGGCATGGGCACCGA
Found at i:28674212 original size:50 final size:50
Alignment explanation
Indices: 28674142--28674274 Score: 230
Period size: 50 Copynumber: 2.7 Consensus size: 50
28674132 AAATGCGCTA
*
28674142 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAATGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGC
*
28674192 CATGTCCCAGACATGGTCTTACAAGGGACCTCTCATCTCGGTGCCAACGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGC
* *
28674242 CATGTTCTAGACATGGTCTTACATGGGACCTCT
1 CATGTCCCAGACATGGTCTTACATGGGACCTCT
28674275 TTACCCAAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGC
Found at i:28677412 original size:27 final size:27
Alignment explanation
Indices: 28677379--28677435 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
28677369 GGGGTCATTC
*
28677379 TACAAGGGGCAATAGAAATGGGAGTTG
1 TACAAGGGCCAATAGAAATGGGAGTTG
28677406 TACAAGGGCCAATAGAAATGGGAGTTG
1 TACAAGGGCCAATAGAAATGGGAGTTG
28677433 TAC
1 TAC
28677436 CTGGAACCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.11, G:0.33, T:0.19
Consensus pattern (27 bp):
TACAAGGGCCAATAGAAATGGGAGTTG
Found at i:28680904 original size:89 final size:93
Alignment explanation
Indices: 28680798--28681028 Score: 254
Period size: 100 Copynumber: 2.5 Consensus size: 93
28680788 TTTCTTGTAC
* * * **
28680798 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTG-C-CCATG-C-CA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCACCATGCCACA
** *
28680859 TGGTCTTACCGGGGACCTCTCATCTTGG
66 TGGTCTTACAAGGGACCTCTCATCTCGG
* * * *
28680887 TGCCAACGCCATGTCCCATACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAAGCCATGTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGGTGCC--A-CCATG--
28680952 CCAGACATGGTCTTACAAGGGACCTCTCATCTCGG
61 CC--ACATGGTCTTACAAGGGACCTCTCATCTCGG
*
28680987 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCT
28681029 TTACCCAAAT
Statistics
Matches: 118, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
89 43 0.36
90 1 0.01
94 5 0.04
97 1 0.01
100 68 0.58
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.26
Consensus pattern (93 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCACCATGCCACA
TGGTCTTACAAGGGACCTCTCATCTCGG
Found at i:28680926 original size:50 final size:50
Alignment explanation
Indices: 28680857--28681028 Score: 290
Period size: 50 Copynumber: 3.4 Consensus size: 50
28680847 GTGCCCATGC
** * *
28680857 CATGGTCTTACCGGGGACCTCTCATCTTGGTGCCAACGCCATGTCCCATA
1 CATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGA
*
28680907 CATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAAGCCATGTCCCAGA
1 CATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGA
*
28680957 CATGGTCTTACAAGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGA
1 CATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGA
28681007 CATGGTCTTACATGGGACCTCT
1 CATGGTCTTACATGGGACCTCT
28681029 TTACCCAAAT
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 114 1.00
ACGTcount: A:0.20, C:0.33, G:0.22, T:0.25
Consensus pattern (50 bp):
CATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGA
Found at i:28683874 original size:18 final size:17
Alignment explanation
Indices: 28683827--28683875 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
28683817 TTCTTGTCCG
28683827 AAAATAAACT-AAAACA
1 AAAATAAACTAAAAACA
* *
28683843 AAAAAAAAGATAAAAACCA
1 AAAATAAA-CTAAAAA-CA
28683862 AAAATAAACTAAAA
1 AAAATAAACTAAAA
28683876 TGAAAAATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.27
17 1 0.04
18 9 0.35
19 9 0.35
ACGTcount: A:0.78, C:0.10, G:0.02, T:0.10
Consensus pattern (17 bp):
AAAATAAACTAAAAACA
Found at i:28701652 original size:50 final size:50
Alignment explanation
Indices: 28701524--28701815 Score: 282
Period size: 50 Copynumber: 5.7 Consensus size: 50
28701514 GATAATAACA
* * ** * * *
28701524 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * * ** **
28701573 TACCAATTCCATATCCCAGATATCATCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
28701623 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** * *
28701673 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTGTTTAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
28701723 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATC----GG
*
28701778 ATGCCAATTCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
28701816 TCTTTTTACC
Statistics
Matches: 196, Mismatches: 39, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
48 1 0.01
49 34 0.17
50 123 0.63
51 1 0.01
55 2 0.01
56 35 0.18
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:28702196 original size:30 final size:30
Alignment explanation
Indices: 28702162--28702219 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
28702152 CCTCGACTCT
28702162 AACTTTGT-CAAAATTACAATTTTGCCCCTA
1 AACTTT-TACAAAATTACAATTTTGCCCCTA
* * *
28702192 AACTTTTACATAATTACACTTTTTCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
28702220 AAAGCTCGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.40
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:28724332 original size:21 final size:20
Alignment explanation
Indices: 28724286--28724342 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
28724276 ATCAGCACAC
28724286 TCAAATGCATCCACAACAAAG
1 TCAAATGCATCCAC-ACAAAG
*
28724307 CCAAATGCATCCACACTAGAA-
1 TCAAATGCATCCACAC-A-AAG
*
28724328 TCAAATGCAGCCACA
1 TCAAATGCATCCACA
28724343 ACACTCTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.44, C:0.32, G:0.11, T:0.14
Consensus pattern (20 bp):
TCAAATGCATCCACACAAAG
Found at i:28726477 original size:23 final size:23
Alignment explanation
Indices: 28726443--28726493 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
28726433 TGAAGACAAA
*
28726443 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
28726466 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
28726489 AGTAA
1 TGTAA
28726494 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:28730110 original size:18 final size:18
Alignment explanation
Indices: 28730087--28730123 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28730077 TGCAACCACA
28730087 TCTGTGGCTGAGGAAAAC
1 TCTGTGGCTGAGGAAAAC
28730105 TCTGTGGCTGAGGAAAAC
1 TCTGTGGCTGAGGAAAAC
28730123 T
1 T
28730124 GAGTTAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.24
Consensus pattern (18 bp):
TCTGTGGCTGAGGAAAAC
Found at i:28733584 original size:21 final size:21
Alignment explanation
Indices: 28733558--28733600 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28733548 ATGGGAGAAG
28733558 TAAAAATGAAGAAATGTTTAT
1 TAAAAATGAAGAAATGTTTAT
28733579 TAAAAATGAAGAAATGTTTAT
1 TAAAAATGAAGAAATGTTTAT
28733600 T
1 T
28733601 CTTACCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (21 bp):
TAAAAATGAAGAAATGTTTAT
Found at i:28740061 original size:37 final size:34
Alignment explanation
Indices: 28739977--28740077 Score: 103
Period size: 37 Copynumber: 2.8 Consensus size: 34
28739967 AGATGCTCAA
* * *
28739977 AAGAGCTAATCCACCCAAAACACACGAGTTGCTC
1 AAGAGCTAGTCCACCCGAAACACACTAGTTGCTC
* *
28740011 ATGCGAGCCAGTCCACCCGATAACACACTAGTTGCTTC
1 A--AGAGCTAGTCCACCCGA-AACACACTAGTTGC-TC
*
28740049 GAAGAGCTAGTCCAACCGAAACACACTAG
1 -AAGAGCTAGTCCACCCGAAACACACTAG
28740078 AAGAGGGAGT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
34 1 0.02
36 23 0.43
37 27 0.50
38 2 0.04
39 1 0.02
ACGTcount: A:0.35, C:0.32, G:0.18, T:0.16
Consensus pattern (34 bp):
AAGAGCTAGTCCACCCGAAACACACTAGTTGCTC
Found at i:28744974 original size:33 final size:33
Alignment explanation
Indices: 28744937--28745007 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
28744927 TCTCTGTTTG
*
28744937 GTGTGTTGGTTGGACTATCTCTTATGAGCACTT-
1 GTGTGTTGGTTGGACTAGCTCTTATGAGCA-TTA
* * *
28744970 GTGTGTTGGTTGTATTAGCTCTTCTGAGCATTA
1 GTGTGTTGGTTGGACTAGCTCTTATGAGCATTA
28745003 GTGTG
1 GTGTG
28745008 CTGGAGGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.14, C:0.13, G:0.30, T:0.44
Consensus pattern (33 bp):
GTGTGTTGGTTGGACTAGCTCTTATGAGCATTA
Found at i:28746176 original size:20 final size:20
Alignment explanation
Indices: 28746138--28746176 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28746128 CCCTGTAGTC
* * *
28746138 TAAAATTTTCAACTTTTTCT
1 TAAAATTTCCAAATGTTTCT
28746158 TAAAATTTCCAAATGTTTC
1 TAAAATTTCCAAATGTTTC
28746177 CAATTTAGTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (20 bp):
TAAAATTTCCAAATGTTTCT
Found at i:28748791 original size:17 final size:18
Alignment explanation
Indices: 28748769--28748802 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28748759 AACTCTAGCC
28748769 AATAG-AAGACACAAAAG
1 AATAGAAAGACACAAAAG
*
28748786 AATAGAAAGCCACAAAA
1 AATAGAAAGACACAAAA
28748803 AACTATGCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.15, G:0.15, T:0.06
Consensus pattern (18 bp):
AATAGAAAGACACAAAAG
Found at i:28750180 original size:19 final size:19
Alignment explanation
Indices: 28750153--28750245 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
28750143 TTATTCCAAC
*
28750153 AACTTAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
*
28750172 AACTCAATTAACTTAGATG
1 AACTCAATTAACTAAGATG
* * * * *
28750191 -AGT-AATTTATTCCAG--C
1 AACTCAATTAACT-AAGATG
*
28750207 AACTTAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
28750226 AACTCAATTAACTAAGATG
1 AACTCAATTAACTAAGATG
28750245 A
1 A
28750246 GTAATTTATT
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
17 10 0.18
18 10 0.18
19 36 0.64
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (19 bp):
AACTCAATTAACTAAGATG
Found at i:28750259 original size:54 final size:54
Alignment explanation
Indices: 28750088--28750264 Score: 275
Period size: 54 Copynumber: 3.3 Consensus size: 54
28750078 ACATTAAAAG
* * * *
28750088 TTTAATCCAGCAAC-TAAGTGAACTAAGTTGAACTTAATTAACTAAGATGAGTAA
1 TTTATTCCAGCAACTTAA-TTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
* *
28750142 TTTATTCCAACAACTTAATTAACTAAGATGAACTCAATTAACTTAGATGAGTAA
1 TTTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
28750196 TTTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
1 TTTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
*
28750250 TTTATTCCAGGAACT
1 TTTATTCCAGCAACT
28750265 AAATACTTAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
54 110 0.97
55 3 0.03
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (54 bp):
TTTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAGATGAGTAA
Found at i:28750591 original size:15 final size:17
Alignment explanation
Indices: 28750565--28750604 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
28750555 CTATTTGAGA
28750565 CCTTTATTTTTCTT-TTT
1 CCTTT-TTTTTCTTCTTT
28750582 -CTTTTTTTTCTTCTTT
1 CCTTTTTTTTCTTCTTT
28750598 CCTTTTT
1 CCTTTTT
28750605 AGGCCTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (17 bp):
CCTTTTTTTTCTTCTTT
Found at i:28751106 original size:27 final size:27
Alignment explanation
Indices: 28751072--28751133 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
28751062 TAAGTAAGTG
28751072 TTACATTTTAATGAAACCATAAAGTTT
1 TTACATTTTAATGAAACCATAAAGTTT
* ** *
28751099 TTATATTTTAATGAAACTGTAAGGTTT
1 TTACATTTTAATGAAACCATAAAGTTT
28751126 TTACATTT
1 TTACATTT
28751134 GGATTTAGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (27 bp):
TTACATTTTAATGAAACCATAAAGTTT
Found at i:28757642 original size:26 final size:28
Alignment explanation
Indices: 28757602--28757653 Score: 90
Period size: 26 Copynumber: 1.9 Consensus size: 28
28757592 TTGTTAAAAC
28757602 TCTTCTAAAAGAAAACTC-AAGAGAAAT
1 TCTTCTAAAAGAAAACTCAAAGAGAAAT
28757629 TCTTC-AAAAGAAAACTCAAAGAGAA
1 TCTTCTAAAAGAAAACTCAAAGAGAA
28757654 TTTTATTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.19
Consensus pattern (28 bp):
TCTTCTAAAAGAAAACTCAAAGAGAAAT
Found at i:28758275 original size:22 final size:23
Alignment explanation
Indices: 28758228--28758282 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
28758218 ATGCAATCTT
* *
28758228 AGATATGA-TATGTAATCTAAGA
1 AGATATGATTTTGTAATATAAGA
*
28758250 AGATATGATTTTGTAATATTAG-
1 AGATATGATTTTGTAATATAAGA
*
28758272 AGATTTGATTT
1 AGATATGATTT
28758283 GTAGATACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (23 bp):
AGATATGATTTTGTAATATAAGA
Found at i:28763361 original size:22 final size:23
Alignment explanation
Indices: 28763333--28763377 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28763323 ATTCAATCTT
*
28763333 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATATTAGA
*
28763355 AGATATGATTTTGTAATATTAGA
1 AGATATGATTATGTAATATTAGA
28763378 TATTTGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATATTAGA
Found at i:28765739 original size:22 final size:22
Alignment explanation
Indices: 28765699--28765762 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
28765689 GTACGTGAAA
28765699 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
28765721 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * *
28765743 CATGAGGGTTTAGTTCGTTA
1 CATGAGAGCTTAGTACGTTA
28765763 AACATGATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:28765768 original size:22 final size:22
Alignment explanation
Indices: 28765687--28765769 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 22
28765677 TTGAATTCCA
*
28765687 TAGTACGTGAAACATGAGAGCT
1 TAGTACGTTAAACATGAGAGCT
**
28765709 TAGTACGTTAGCCATGAGAGCT
1 TAGTACGTTAAACATGAGAGCT
** * *
28765731 TAGTACGTTAGCCATGAGGGTT
1 TAGTACGTTAAACATGAGAGCT
*
28765753 TAGTTCGTTAAACATGA
1 TAGTACGTTAAACATGA
28765770 TTTATATAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (22 bp):
TAGTACGTTAAACATGAGAGCT
Found at i:28769822 original size:21 final size:22
Alignment explanation
Indices: 28769772--28769829 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
28769762 GGGGAAAGAC
* *
28769772 ACATGTTAAAATGTCATTTTTAT
1 ACAT-TTAAAATTTAATTTTTAT
28769795 ACATTTAAAATTTAATTTTTAT
1 ACATTTAAAATTTAATTTTTAT
*
28769817 A-TTTTAAAATTTA
1 ACATTTAAAATTTA
28769830 TTAATATGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 11 0.34
22 17 0.53
23 4 0.12
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (22 bp):
ACATTTAAAATTTAATTTTTAT
Found at i:28774055 original size:39 final size:39
Alignment explanation
Indices: 28774006--28774084 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
28773996 TCCTGACTTG
* *
28774006 ATTTATTTACAAACTTAAGCAACACCATATTTAATTCAT
1 ATTTATTTACAAACTTAAACAACACCACATTTAATTCAT
*
28774045 ATTTATTTACAAACTTAAACAACGCCACATTTAATTCAT
1 ATTTATTTACAAACTTAAACAACACCACATTTAATTCAT
28774084 A
1 A
28774085 CTTACCATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.37
Consensus pattern (39 bp):
ATTTATTTACAAACTTAAACAACACCACATTTAATTCAT
Found at i:28777007 original size:32 final size:32
Alignment explanation
Indices: 28776966--28777029 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
28776956 GGGAAGAATG
28776966 TTAATTGATGTGCAGAAAGGTGAACTCACTAT
1 TTAATTGATGTGCAGAAAGGTGAACTCACTAT
28776998 TTAATTGATGTGCAGAAAGGTGAACTCACTAT
1 TTAATTGATGTGCAGAAAGGTGAACTCACTAT
28777030 GCGAGTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (32 bp):
TTAATTGATGTGCAGAAAGGTGAACTCACTAT
Found at i:28780129 original size:12 final size:12
Alignment explanation
Indices: 28780104--28780142 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28780094 ACTCGCTTCT
* *
28780104 TTACTTACTCAC
1 TTACTTGCTTAC
*
28780116 TTACTTGTTTAC
1 TTACTTGCTTAC
28780128 TTACTTGCTTAC
1 TTACTTGCTTAC
28780140 TTA
1 TTA
28780143 AATAACTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:28780458 original size:50 final size:50
Alignment explanation
Indices: 28780394--28780588 Score: 210
Period size: 50 Copynumber: 3.8 Consensus size: 50
28780384 TCTGTACTGA
* * * **
28780394 CAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGC
* ** * *
28780444 CCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTTC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGC
* *
28780494 CAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTGC
* *
28780550 CAATGCCATGCCCCAGACATGGTCTTACATGGGATCTCT
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
28780589 TTACCCAAAT
Statistics
Matches: 119, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 78 0.66
53 2 0.02
56 39 0.33
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGC
Found at i:28788354 original size:48 final size:48
Alignment explanation
Indices: 28788277--28788394 Score: 139
Period size: 48 Copynumber: 2.5 Consensus size: 48
28788267 ACTTAATTGC
* *
28788277 GTTGTGGTCAAGCCACTCAATCACATTGTGG-CAAAGCCACTCAACATT
1 GTTGTGGTCAAGCCACACAATAACATTGTGGAC-AAGCCACTCAACATT
* * * **
28788325 GTTGTGTTCAAGCCACACAATAACGTTGTGGACAAGCCACTCAATAGC
1 GTTGTGGTCAAGCCACACAATAACATTGTGGACAAGCCACTCAACATT
* *
28788373 GTTGTGGCCAAGCCACTCAATA
1 GTTGTGGTCAAGCCACACAATA
28788395 TTGTAGTAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 58 0.98
49 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (48 bp):
GTTGTGGTCAAGCCACACAATAACATTGTGGACAAGCCACTCAACATT
Found at i:28788394 original size:24 final size:24
Alignment explanation
Indices: 28788275--28788394 Score: 125
Period size: 24 Copynumber: 5.0 Consensus size: 24
28788265 GAACTTAATT
*
28788275 GCGTTGTGGTCAAGCCACTCAATCA
1 GCGTTGTGGCCAAGCCACTCAAT-A
* * *
28788300 -CATTGTGGCAAAGCCACTCAACA
1 GCGTTGTGGCCAAGCCACTCAATA
** ** *
28788323 TTGTTGTGTTCAAGCCACACAATA
1 GCGTTGTGGCCAAGCCACTCAATA
* *
28788347 ACGTTGTGGACAAGCCACTCAATA
1 GCGTTGTGGCCAAGCCACTCAATA
28788371 GCGTTGTGGCCAAGCCACTCAATA
1 GCGTTGTGGCCAAGCCACTCAATA
28788395 TTGTAGTAAA
Statistics
Matches: 76, Mismatches: 18, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
23 1 0.01
24 75 0.99
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (24 bp):
GCGTTGTGGCCAAGCCACTCAATA
Found at i:28791423 original size:25 final size:25
Alignment explanation
Indices: 28791377--28791424 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
28791367 ATGATTAAGC
* * *
28791377 TAATTAAGTTAGATTAATTAAATCT
1 TAATTAAGGTAGATAAACTAAATCT
*
28791402 TAATTAAGGTATATAAACTAAAT
1 TAATTAAGGTAGATAAACTAAAT
28791425 TTAGTGGAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (25 bp):
TAATTAAGGTAGATAAACTAAATCT
Found at i:28793601 original size:40 final size:40
Alignment explanation
Indices: 28793552--28793631 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
28793542 ATGAGTGTTC
*
28793552 GGGGTACCGAAGTACGAATAGGGGCAAGTATGTGCATTCA
1 GGGGTACCGAAGTACAAATAGGGGCAAGTATGTGCATTCA
* * *
28793592 GGGGTACCGAAGTATAAATAGGTGCATGTATGTGCATTCA
1 GGGGTACCGAAGTACAAATAGGGGCAAGTATGTGCATTCA
28793632 TACAATAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.30, C:0.14, G:0.33, T:0.24
Consensus pattern (40 bp):
GGGGTACCGAAGTACAAATAGGGGCAAGTATGTGCATTCA
Found at i:28800783 original size:29 final size:29
Alignment explanation
Indices: 28800751--28800989 Score: 190
Period size: 29 Copynumber: 8.2 Consensus size: 29
28800741 ATAGCTTCGG
* *
28800751 CTATTGATTATGAAGAGGGATGGTGACGA
1 CTATCGATTATGAAAAGGGATGGTGACGA
* **
28800780 CTATCAACAATGAAAAGGGATGGTGACGA
1 CTATCGATTATGAAAAGGGATGGTGACGA
* * * ***
28800809 CCATCGAATATGAAAAGGGATAGCCTCGA
1 CTATCGATTATGAAAAGGGATGGTGACGA
* * * ** *
28800838 CGATCGATTATGGAAAGGGATAGTTTCGG
1 CTATCGATTATGAAAAGGGATGGTGACGA
* * *
28800867 CTATTGATTATGAAAAAGGATGGTGATGA
1 CTATCGATTATGAAAAGGGATGGTGACGA
* * * *
28800896 CCATCAACTATGAAAAGGGATGGTGACCA
1 CTATCGATTATGAAAAGGGATGGTGACGA
**
28800925 CTATCGATTAATGAAAAGGGATGGTTTCGA
1 CTATCGATT-ATGAAAAGGGATGGTGACGA
* * * *
28800955 CCATCGAATATGAAAAGGGACGGTTACGA
1 CTATCGATTATGAAAAGGGATGGTGACGA
*
28800984 CCATCG
1 CTATCG
28800990 TTTAGCACAC
Statistics
Matches: 164, Mismatches: 45, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
29 140 0.85
30 24 0.15
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (29 bp):
CTATCGATTATGAAAAGGGATGGTGACGA
Found at i:28800828 original size:87 final size:87
Alignment explanation
Indices: 28800731--28800916 Score: 214
Period size: 87 Copynumber: 2.1 Consensus size: 87
28800721 TCATCGACCA
* * * * *
28800731 ATGAAAAGGGATAGCTTCGGCTATTGATTAT-GAAGAGGGATGGTGACGACTATCAACAATGAAA
1 ATGAAAAGGGATAGCCTCGACGATCGATTATGGAA-AGGGATAGTGACGACTATCAACAATGAAA
*
28800795 AGGGATGGTGACGACCATCGAA-T
65 AAGGATGGTGACGACCATC-AACT
** * ** **
28800818 ATGAAAAGGGATAGCCTCGACGATCGATTATGGAAAGGGATAGTTTCGGCTATTGATTATGAAAA
1 ATGAAAAGGGATAGCCTCGACGATCGATTATGGAAAGGGATAGTGACGACTATCAACAATGAAAA
*
28800883 AGGATGGTGATGACCATCAACT
66 AGGATGGTGACGACCATCAACT
28800905 ATGAAAAGGGAT
1 ATGAAAAGGGAT
28800917 GGTGACCACT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
86 2 0.02
87 78 0.94
88 3 0.04
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (87 bp):
ATGAAAAGGGATAGCCTCGACGATCGATTATGGAAAGGGATAGTGACGACTATCAACAATGAAAA
AGGATGGTGACGACCATCAACT
Found at i:28800931 original size:87 final size:88
Alignment explanation
Indices: 28800789--28800989 Score: 226
Period size: 87 Copynumber: 2.3 Consensus size: 88
28800779 ACTATCAACA
* * * *
28800789 ATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGATAGCCTCGACGATCGATT-ATGGAA
1 ATGAAAAAGGATGGTGACGACCATCGAATATGAAAAGGGATAGCCACCACGATCGATTAATGAAA
28800853 AGGGATAGTTTCGGCTATTGATT
66 AGGGATAGTTTCGGCTATTGATT
* * ** *
28800876 ATGAAAAAGGATGGTGATGACCATC-AACTATGAAAAGGGATGGTGACCACTATCGATTAATGAA
1 ATGAAAAAGGATGGTGACGACCATCGAA-TATGAAAAGGGATAGCCACCACGATCGATTAATGAA
* * * * *
28800940 AAGGGATGGTTTCGACCATCGAAT
65 AAGGGATAGTTTCGGCTATTGATT
* * *
28800964 ATGAAAAGGGACGGTTACGACCATCG
1 ATGAAAAAGGATGGTGACGACCATCG
28800990 TTTAGCACAC
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
86 2 0.02
87 47 0.51
88 44 0.47
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.22
Consensus pattern (88 bp):
ATGAAAAAGGATGGTGACGACCATCGAATATGAAAAGGGATAGCCACCACGATCGATTAATGAAA
AGGGATAGTTTCGGCTATTGATT
Found at i:28802988 original size:13 final size:13
Alignment explanation
Indices: 28802970--28802995 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28802960 AAAGTATTTG
28802970 GAATGAATGTGTT
1 GAATGAATGTGTT
28802983 GAATGAATGTGTT
1 GAATGAATGTGTT
28802996 TTTAAAGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (13 bp):
GAATGAATGTGTT
Found at i:28813191 original size:22 final size:25
Alignment explanation
Indices: 28813124--28813191 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
28813114 GTCATGCATG
* *
28813124 ATTAAATTAAATAATAATTTATAAA
1 ATTATATTTAATAATAATTTATAAA
*
28813149 ATTATATTTAATAATTTATTT-TAAA
1 ATTATATTTAATAA-TAATTTATAAA
*
28813174 A-TAT-TTTATTAATAATTT
1 ATTATATTTAATAATAATTT
28813192 CGGTTTTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 5 0.14
23 7 0.19
24 3 0.08
25 17 0.46
26 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTATATTTAATAATAATTTATAAA
Found at i:28814993 original size:20 final size:20
Alignment explanation
Indices: 28814970--28815054 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
28814960 GAACTGCAGA
28814970 CAAGCTGCCAGTAATGTAGT
1 CAAGCTGCCAGTAATGTAGT
* *
28814990 CAAGC-GACCAGTATTGCAGAT
1 CAAGCTG-CCAGTAATGTAG-T
* **
28815011 -AAACTGTTAGTAATGTAGT
1 CAAGCTGCCAGTAATGTAGT
* * *
28815030 CAAGCTACCAGTAATATGGT
1 CAAGCTGCCAGTAATGTAGT
28815050 CAAGC
1 CAAGC
28815055 CACTAATGAT
Statistics
Matches: 48, Mismatches: 13, Indels: 8
0.70 0.19 0.12
Matches are distributed among these distances:
19 2 0.04
20 44 0.92
21 2 0.04
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (20 bp):
CAAGCTGCCAGTAATGTAGT
Found at i:28815000 original size:40 final size:40
Alignment explanation
Indices: 28814950--28815040 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 40
28814940 AATTTGTGGA
*
28814950 CAAGCCACCAGAACTGCAGACAAGCTGCCAGTAATGTAGT
1 CAAGCCACCAGAACTGCAGACAAACTGCCAGTAATGTAGT
* * * * **
28814990 CAAGCGACCAGTATTGCAGATAAACTGTTAGTAATGTAGT
1 CAAGCCACCAGAACTGCAGACAAACTGCCAGTAATGTAGT
*
28815030 CAAGCTACCAG
1 CAAGCCACCAG
28815041 TAATATGGTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (40 bp):
CAAGCCACCAGAACTGCAGACAAACTGCCAGTAATGTAGT
Found at i:28818858 original size:21 final size:21
Alignment explanation
Indices: 28818832--28818874 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
28818822 GTTACAACCC
*
28818832 TCCCTAGTAAAGGAATTTTCG
1 TCCCTAGTAAAAGAATTTTCG
28818853 TCCCTAGTAAAAGAATTTTCG
1 TCCCTAGTAAAAGAATTTTCG
28818874 T
1 T
28818875 TCTTGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (21 bp):
TCCCTAGTAAAAGAATTTTCG
Found at i:28826077 original size:23 final size:23
Alignment explanation
Indices: 28826051--28826126 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
28826041 ATAAGTGTCA
28826051 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
28826074 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
28826097 CACTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
28826120 CACTGAT
1 CACTGAT
28826127 CAATAACACT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:28832521 original size:12 final size:12
Alignment explanation
Indices: 28832506--28832543 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
28832496 GTAATGGACA
28832506 TTGGACATTTAT
1 TTGGACATTTAT
28832518 TTGGACATTTAT
1 TTGGACATTTAT
28832530 TTGGACATTTAT
1 TTGGACATTTAT
28832542 TT
1 TT
28832544 TGGTGATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (12 bp):
TTGGACATTTAT
Found at i:28837655 original size:12 final size:12
Alignment explanation
Indices: 28837622--28837702 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
28837612 TTTCCACTCG
28837622 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
28837633 AGCTCTCTTTCA
1 ATTTCTTTTTCA
28837645 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
28837658 CTCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
28837671 --TTCTCTTTCA
1 ATTTCTTTTTCA
28837681 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
28837693 ATCTCTTTTT
1 ATTTCTTTTT
28837703 GCTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.25, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:28837663 original size:21 final size:20
Alignment explanation
Indices: 28837637--28837692 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 20
28837627 TTTTCAAGCT
28837637 CTCTTTCAATTTCTTTTTCCA
1 CTCTTTCAATTTCTTTTT-CA
*
28837658 CTCTTTC--TTT-TTCTT--
1 CTCTTTCAATTTCTTTTTCA
28837673 CTCTTTCAATTTCTTTTTCA
1 CTCTTTCAATTTCTTTTTCA
28837693 ATCTCTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.25
17 3 0.11
18 8 0.29
19 3 0.11
21 7 0.25
ACGTcount: A:0.11, C:0.27, G:0.00, T:0.62
Consensus pattern (20 bp):
CTCTTTCAATTTCTTTTTCA
Found at i:28837755 original size:15 final size:15
Alignment explanation
Indices: 28837732--28837778 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
28837722 TTTTGAAATC
28837732 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
28837747 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
28837762 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
28837778 T
1 T
28837779 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:28838855 original size:16 final size:19
Alignment explanation
Indices: 28838834--28838872 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
28838824 CTTTTTTTTC
28838834 TTTTTTTG-T-AC-TCTTT
1 TTTTTTTGCTCACTTCTTT
28838850 TTTTTTTGCTCACTTCTTT
1 TTTTTTTGCTCACTTCTTT
28838869 TTTT
1 TTTT
28838873 CTTTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 8 0.40
17 1 0.05
18 2 0.10
19 9 0.45
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTTTGCTCACTTCTTT
Found at i:28838894 original size:12 final size:12
Alignment explanation
Indices: 28838879--28838905 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28838869 TTTTCTTTTC
28838879 TTTTTTTTGAAT
1 TTTTTTTTGAAT
28838891 TTTTTTTTGAAT
1 TTTTTTTTGAAT
28838903 TTT
1 TTT
28838906 GATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:28840426 original size:20 final size:20
Alignment explanation
Indices: 28840403--28840449 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28840393 GGGTTAAACT
*
28840403 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
28840423 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
28840443 TGAGCTG
1 TGAGCTG
28840450 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:28843193 original size:50 final size:50
Alignment explanation
Indices: 28843082--28843331 Score: 302
Period size: 50 Copynumber: 4.9 Consensus size: 50
28843072 ATTTGGGTAA
* * *
28843082 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATG
* * *
28843138 AGAGGTCCCATGTAAGACCATGTTTGGTACATGGCGTTGGCATCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
28843188 AGAGGTCTCATGTAAGAACATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
28843238 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * *
28843288 AGAGGTCCCCCGTAAGACCATGTCTGGGAAATGGCATGGGCACC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACC
28843332 TATATAAGAA
Statistics
Matches: 171, Mismatches: 23, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
50 130 0.76
53 3 0.02
56 38 0.22
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:28843354 original size:100 final size:100
Alignment explanation
Indices: 28843143--28843363 Score: 253
Period size: 100 Copynumber: 2.2 Consensus size: 100
28843133 TTATGAGAGG
* * * * * * *
28843143 TCCCATGTAAGACCATGTTTGGTACATGGCGTTGGCATCGAGATGAGAGGTCTCATGTAAGAACA
1 TCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTCCCACGTAAGAACA
* * * * **
28843208 TGTCTAGGACATGGCGTTGGCACCGAGATGAGAGG
66 TGTCTAGGAAATGGCATGGGCACCGAGATAAGAAC
* *
28843243 TCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTCCCCCGTAAGACCA
1 TCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTCCCACGTAAGAACA
* * *
28843308 TGTCTGGGAAATGGCATGGGCACCTATATAAGAAC
66 TGTCTAGGAAATGGCATGGGCACCGAGATAAGAAC
* * *
28843343 TCTCATTTAAGACCATATCTG
1 TCCCATATAAGACCATGTCTG
28843364 AGATATGACA
Statistics
Matches: 100, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (100 bp):
TCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTCCCACGTAAGAACA
TGTCTAGGAAATGGCATGGGCACCGAGATAAGAAC
Found at i:28843378 original size:150 final size:152
Alignment explanation
Indices: 28843082--28843418 Score: 324
Period size: 150 Copynumber: 2.2 Consensus size: 152
28843072 ATTTGGGTAA
* *
28843082 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCC
1 AGAGATCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCA-T-AG--TATGAGAGGTCCC
* * * * * * * * ** *
28843147 ATGTAAGACCATGTTTGGTACATGGCGTTGGCATCGAGATGAGAGGTCTCATGTAAGAACATGTC
62 ACGTAAGACCATGTCTGGGAAATGGCATGGGCACCGAGATAAGAACTCTCATGTAAGAACATATC
* *
28843212 TAGGACATGGCGTTGGCACCGAGATG
127 TAGGACATGACATTGGCACCGAGATG
* * *
28843238 AGAGGTCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCA-AG-ATGAGAGGTCCCCCGT
1 AGAGATCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCATAGTATGAGAGGTCCCACGT
* * * *
28843301 AAGACCATGTCTGGGAAATGGCATGGGCACCTATATAAGAACTCTCATTTAAGACCATATCT-GA
66 AAGACCATGTCTGGGAAATGGCATGGGCACCGAGATAAGAACTCTCATGTAAGAACATATCTAG-
* * *
28843365 GATATGACATTGGCA--GTACAAG
130 GACATGACATTGGCACCG-AGATG
* * * *
28843387 AAACATCCCATGTAAGACTATGTCTGGGACAT
1 AGAGATCCCATATAAGACCATGTCTGGGACAT
28843419 ACCTTTGGCA
Statistics
Matches: 149, Mismatches: 30, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
148 1 0.01
149 31 0.21
150 74 0.50
153 2 0.01
156 41 0.28
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (152 bp):
AGAGATCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCATAGTATGAGAGGTCCCACGT
AAGACCATGTCTGGGAAATGGCATGGGCACCGAGATAAGAACTCTCATGTAAGAACATATCTAGG
ACATGACATTGGCACCGAGATG
Found at i:28851248 original size:50 final size:50
Alignment explanation
Indices: 28851123--28851449 Score: 357
Period size: 50 Copynumber: 6.4 Consensus size: 50
28851113 ATTTGGGTAA
* *** *
28851123 AGAGATCCCATGTAAGACCATGTCTGGGACATGAAATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCA---AG---ATG
* * *
28851179 AGAGGTCCCATGTAAGACCATGTCTGGTACATGGCGTTGCCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
* * * * *
28851229 AAAGGTCTCATGTAAGACCATGTCTGGGATAGGGCATTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
* * **
28851279 AGAGGTCCCATGTAAGACCATGTCTGGGACACGGTGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
*
28851329 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCTCCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
** * * * *
28851379 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
** *
28851429 AGAACTCTCATGTAAGACCAT
1 AGAGGTCCCATGTAAGACCAT
28851450 ATCTTGGATA
Statistics
Matches: 230, Mismatches: 41, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
50 191 0.83
53 2 0.01
56 37 0.16
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
Found at i:28851361 original size:150 final size:153
Alignment explanation
Indices: 28851123--28851449 Score: 419
Period size: 150 Copynumber: 2.1 Consensus size: 153
28851113 ATTTGGGTAA
*
28851123 AGAGATCCCATGTAAGACCATGTCTGGGACATGAAATTGGCATCATTGAGATTATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACACGAAATTGGCATCA-TGAG--TATGAGAGGTCCC
* * * *
28851188 ATGTAAGACCATGTCTGGTACATGGCGTTGCCACCGAGATGAAAGGTCTCATGTAAGACCATGTC
63 ATGTAAGACCATGTCTGGGACATGGCGTTGCCACCAAGATGAAAGGTCCCACGTAAGACCATGTC
* *
28851253 TGGGATAGGGCATTGGCACCAAGATG
128 TGGGACAGGGCATGGGCACCAAGATG
* ***
28851279 AGAGGTCCCATGTAAGACCATGTCTGGGACACGGTGTTGGCA-C-TGAG-ATGAGAGGTCCCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACACGAAATTGGCATCATGAGTATGAGAGGTCCCATG
* * * *
28851341 TAAGACCATGTCTGGGACATGGCGTTGGCTCCAAGATGAGAGGTCCCCCGTAAGACCATGTCTGG
66 TAAGACCATGTCTGGGACATGGCGTTGCCACCAAGATGAAAGGTCCCACGTAAGACCATGTCTGG
* * *
28851406 GACATGGCATGGGCACCTATATG
131 GACAGGGCATGGGCACCAAGATG
*
28851429 AGA-ACTCTCATGTAAGACCAT
1 AGAGA-TCCCATGTAAGACCAT
28851450 ATCTTGGATA
Statistics
Matches: 150, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
150 108 0.72
153 4 0.03
155 1 0.01
156 37 0.25
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (153 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACACGAAATTGGCATCATGAGTATGAGAGGTCCCATG
TAAGACCATGTCTGGGACATGGCGTTGCCACCAAGATGAAAGGTCCCACGTAAGACCATGTCTGG
GACAGGGCATGGGCACCAAGATG
Found at i:28851421 original size:100 final size:100
Alignment explanation
Indices: 28851123--28851519 Score: 372
Period size: 100 Copynumber: 3.9 Consensus size: 100
28851113 ATTTGGGTAA
* **
28851123 AGAGATCCCATGTAAGACCATGTCTGGGACATGAAATTGGCAT-CATTGAGATTATGAGAGGTCC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGC-TCCA---AG---ATGAGAGGTCC
* * *
28851187 CATGTAAGACCATGTCTGGTACATGGCGTTGCCACCGAGATG
59 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
* * * * *
28851229 AAAGGTCTCATGTAAGACCATGTCTGGGATAGGGCATTGGCACCAAGATGAGAGGTCCCATGTAA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCTCCAAGATGAGAGGTCCCATGTAA
* *
28851294 GACCATGTCTGGGACACGGTGTTGGCACTGAGATG
66 GACCATGTCTGGGACATGGCGTTGGCACTGAGATG
* **
28851329 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCTCCAAGATGAGAGGTCCCCCGTAA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCTCCAAGATGAGAGGTCCCATGTAA
* * *
28851394 GACCATGTCTGGGACATGGCATGGGCACCT-ATATG
66 GACCATGTCTGGGACATGGCGTTGGCA-CTGAGATG
** * * * * * * * **
28851429 AGAACTCTCATGTAAGACCATATCTTGGATATGACATTTGCAGTACAAGA--A-ACATCCCATGT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGC--TCCAAGATGAGAGGTCCCATGT
* * *
28851491 AAGACTATGTCTGGGACATAGCTTTGGCA
64 AAGACCATGTCTGGGACATGGCGTTGGCA
28851520 TGTTATATTT
Statistics
Matches: 243, Mismatches: 44, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
99 32 0.13
100 165 0.68
101 2 0.01
102 6 0.02
103 2 0.01
106 36 0.15
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (100 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCTCCAAGATGAGAGGTCCCATGTAA
GACCATGTCTGGGACATGGCGTTGGCACTGAGATG
Found at i:28851760 original size:15 final size:15
Alignment explanation
Indices: 28851735--28851770 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
28851725 ACTCAATTCG
*
28851735 ATCATGAAAGAAGTT
1 ATCAAGAAAGAAGTT
*
28851750 GTCAAGAAAGAAGTT
1 ATCAAGAAAGAAGTT
28851765 ATCAAG
1 ATCAAG
28851771 TGGCTTGATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.22
Consensus pattern (15 bp):
ATCAAGAAAGAAGTT
Found at i:28851953 original size:27 final size:27
Alignment explanation
Indices: 28851921--28851972 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
28851911 GAGAGTATGC
28851921 ATAGACTATCGCAAGCTTAACAAGGCA
1 ATAGACTATCGCAAGCTTAACAAGGCA
*
28851948 ATAGACTATTGCAAGCTTAACAAGG
1 ATAGACTATCGCAAGCTTAACAAGG
28851973 AAACTAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (27 bp):
ATAGACTATCGCAAGCTTAACAAGGCA
Found at i:28857991 original size:50 final size:52
Alignment explanation
Indices: 28857885--28858005 Score: 174
Period size: 50 Copynumber: 2.4 Consensus size: 52
28857875 ATGAACAAAT
* * * *
28857885 GAGTTACTTAATACATGACTTAATTTAATGATGCAAACTTTAACTAACATGG
1 GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
*
28857937 GAGTTACATAATGCATGTCATAATTT-ATGATGCAAAC-TTAACTAACATGA
1 GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
*
28857987 GAGTTACAGAATGCATGAC
1 GAGTTACATAATGCATGAC
28858006 TTTATTAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 29 0.47
51 11 0.18
52 22 0.35
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (52 bp):
GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
Found at i:28860027 original size:18 final size:18
Alignment explanation
Indices: 28859999--28860043 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
28859989 TTTCTTTCAA
28859999 TTTATTTTTCTCACATTT-T
1 TTTA-TTTTCTCA-ATTTCT
*
28860018 TTTCTTTTCTCAATTTCT
1 TTTATTTTCTCAATTTCT
28860036 TTTATTTT
1 TTTATTTT
28860044 TCGCTCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 16 0.70
19 3 0.13
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTTCTCAATTTCT
Found at i:28862325 original size:50 final size:52
Alignment explanation
Indices: 28862215--28862335 Score: 174
Period size: 50 Copynumber: 2.4 Consensus size: 52
28862205 ATGAACAAAT
* * * *
28862215 GAGTTACTTAATGCATGACTTAATTTAATGATGCTAACTTTAACTAACATGG
1 GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
*
28862267 GAGTTACATAATGCATGTCATAATTT-ATGATGCAAAC-TTAACTAACATGA
1 GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
*
28862317 GAGTTACATAATACATGAC
1 GAGTTACATAATGCATGAC
28862336 TTTATTAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 29 0.47
51 10 0.16
52 23 0.37
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (52 bp):
GAGTTACATAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
Found at i:28870409 original size:51 final size:51
Alignment explanation
Indices: 28870273--28870465 Score: 214
Period size: 51 Copynumber: 3.8 Consensus size: 51
28870263 TGAAAGTGGA
* * * *
28870273 AGTGATTG-TCACATGTGTAGTACTATGTGCAGGCTACAAAGTGTACCAGA-
1 AGTGA-TGATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT
* *
28870323 A-TGATAGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT
1 AGTGAT-GATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT
** * * * *
28870374 AGCTTCT-ATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
1 AG-TGATGATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT
*
28870425 AGTGATGGTCACATGTGTAGTACTATGTGCAGGCTACTATG
1 AGTGATGATCACATGTGTAGTACTATGTGCAGGCTACTATG
28870466 TGAACCGGTA
Statistics
Matches: 119, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
48 1 0.01
49 4 0.03
50 40 0.34
51 72 0.61
53 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (51 bp):
AGTGATGATCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGAT
Found at i:28870464 original size:102 final size:101
Alignment explanation
Indices: 28870281--28870465 Score: 291
Period size: 101 Copynumber: 1.8 Consensus size: 101
28870271 GAAGTGATTG
*
28870281 TCACATGTGTAGTACTATGTGCAGGCTACAAAGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTATGTGCAGGCTACAAAGTGTACCAGAATGATAGGTCACATGTGTAGTAC
28870346 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCTA
66 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCTA
* * * * *
28870382 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAGGCTACAAAGTGTACCAGA-A-TGATAGGTCACATGTGTAGT
28870446 ACTATGTGCAGGCTACTATG
64 ACTATGTGCAGGCTACTATG
28870466 TGAACCGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 37 0.49
102 35 0.46
103 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGTGCAGGCTACAAAGTGTACCAGAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGGATAGCTTCTA
Found at i:28870467 original size:26 final size:26
Alignment explanation
Indices: 28870387--28870467 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
28870377 TTCTATCACG
28870387 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
28870413 CGTGTA-T-CGGATAGTG-ATGG-TCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
28870438 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
28870464 TGTG
1 TGTG
28870468 AACCGGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:28870473 original size:102 final size:101
Alignment explanation
Indices: 28870281--28870473 Score: 289
Period size: 102 Copynumber: 1.9 Consensus size: 101
28870271 GAAGTGATTG
*
28870281 TCACATGTGTAGTACTATGTGCAGGCTACAAAGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTATGTGCAGGCTACAAAGTGTACCAGAATGATAGGTCACATGTGTAGTAC
*
28870346 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCTA
66 TATGTGCAGGCTACTATGCGAACCGGATAGCTTCTA
* * * * *
28870382 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACATGTGTAGTACTATGTGCAGGCTACAAAGTGTACCAGA-A-TGATAGGTCACATGTGTAGT
*
28870446 ACTATGTGCAGGCTACTATGTGAACCGG
64 ACTATGTGCAGGCTACTATGCGAACCGG
28870474 TATCATTAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 37 0.45
102 41 0.50
103 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (101 bp):
TCACATGTGTAGTACTATGTGCAGGCTACAAAGTGTACCAGAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGAACCGGATAGCTTCTA
Found at i:28870560 original size:46 final size:43
Alignment explanation
Indices: 28870469--28870567 Score: 101
Period size: 46 Copynumber: 2.2 Consensus size: 43
28870459 TACTATGTGA
* * *
28870469 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGTTGATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTACGTGCTGATCCC
* *
28870512 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGCGTGCTGAAT-CC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTACGTGCTG-ATCCC
28870558 ACCGTGTATC
1 ACCG-GTATC
28870568 TGTTATTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
43 5 0.11
44 11 0.24
45 2 0.04
46 25 0.54
47 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTACGTGCTGATCCC
Found at i:28870712 original size:16 final size:16
Alignment explanation
Indices: 28870691--28870722 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28870681 TGATTGAAAG
*
28870691 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
28870707 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
28870723 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Done.