Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007744.1 Hibiscus syriacus cultivar Beakdansim tig00110007_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4276731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 16
Found at i:216842 original size:56 final size:57
Alignment explanation
Indices: 216757--216909 Score: 177
Period size: 62 Copynumber: 2.6 Consensus size: 57
216747 ACGATGACAG
* * *
216757 GGGA-CTCTTGAACGGTGGGAGGGGACTCTTGAACGGT-GGAGGGG-GAATGGTGGGA
1 GGGACCTCTTGAACGATGAGAGGGGACTCTTGAACGGTGGGAGGGGTGAACGGT-GGA
*
216812 GGGACCTCTTGAACGATGACAGGGGACTCTTGAACGGTGGGAGGGGACTCTTGAACGGTGGA
1 GGGACCTCTTGAACGATGAGAGGGGACTCTTGAACGGTGGGAGGGG-----TGAACGGTGGA
* *
216874 GGGGCCTCTTGAACGATGAGAGGGGCCTCTTGAACG
1 GGGACCTCTTGAACGATGAGAGGGGACTCTTGAACG
216910 ATAGGAGGCG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
55 4 0.05
56 30 0.36
57 7 0.08
62 36 0.43
63 6 0.07
ACGTcount: A:0.21, C:0.16, G:0.44, T:0.19
Consensus pattern (57 bp):
GGGACCTCTTGAACGATGAGAGGGGACTCTTGAACGGTGGGAGGGGTGAACGGTGGA
Found at i:216851 original size:77 final size:77
Alignment explanation
Indices: 216724--216877 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
216714 TCGGGCTCTT
216724 GAATGGTGGGAGGGACCTCTTGAACGATGACAGGGGACTCTTGAACGGTGGGAGGGGACTCTTGA
1 GAATGGTGGGAGGGACCTCTTGAACGATGACAGGGGACTCTTGAACGGTGGGAGGGGACTCTTGA
216789 ACGGTGGAGGGG
66 ACGGTGGAGGGG
216801 GAATGGTGGGAGGGACCTCTTGAACGATGACAGGGGACTCTTGAACGGTGGGAGGGGACTCTTGA
1 GAATGGTGGGAGGGACCTCTTGAACGATGACAGGGGACTCTTGAACGGTGGGAGGGGACTCTTGA
216866 ACGGTGGAGGGG
66 ACGGTGGAGGGG
216878 CCTCTTGAAC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.22, C:0.14, G:0.45, T:0.18
Consensus pattern (77 bp):
GAATGGTGGGAGGGACCTCTTGAACGATGACAGGGGACTCTTGAACGGTGGGAGGGGACTCTTGA
ACGGTGGAGGGG
Found at i:216931 original size:21 final size:20
Alignment explanation
Indices: 216732--216933 Score: 164
Period size: 21 Copynumber: 10.1 Consensus size: 20
216722 TTGAATGGTG
*
216732 GGAGGGACCTCTTGAACGAT
1 GGAGGGGCCTCTTGAACGAT
* * *
216752 GACAGGGGACTCTTGAACGGT
1 G-GAGGGGCCTCTTGAACGAT
* *
216773 GGGAGGGGACTCTTGAACGGT
1 -GGAGGGGCCTCTTGAACGAT
* *
216794 GGAGGGG------GAATGGT
1 GGAGGGGCCTCTTGAACGAT
*
216808 GGGAGGGACCTCTTGAACGAT
1 -GGAGGGGCCTCTTGAACGAT
* * *
216829 GACAGGGGACTCTTGAACGGT
1 G-GAGGGGCCTCTTGAACGAT
* *
216850 GGGAGGGGACTCTTGAACGGT
1 -GGAGGGGCCTCTTGAACGAT
216871 GGAGGGGCCTCTTGAACGAT
1 GGAGGGGCCTCTTGAACGAT
216891 GAGAGGGGCCTCTTGAACGAT
1 G-GAGGGGCCTCTTGAACGAT
*
216912 AGGAGGCGCCTCTTGAACGAT
1 -GGAGGGGCCTCTTGAACGAT
216933 G
1 G
216934 ATAGGTGCAT
Statistics
Matches: 152, Mismatches: 17, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
14 6 0.04
15 6 0.04
20 29 0.19
21 108 0.71
22 3 0.02
ACGTcount: A:0.22, C:0.17, G:0.42, T:0.19
Consensus pattern (20 bp):
GGAGGGGCCTCTTGAACGAT
Found at i:219086 original size:20 final size:19
Alignment explanation
Indices: 219034--219086 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
219024 AATCGCAACA
*
219034 CGAATTTAGTTTTGCGTTG
1 CGAATTTAGTTTCGCGTTG
* * *
219053 CGATTTTCATTTTCGTGTTG
1 CGAATTT-AGTTTCGCGTTG
219073 CGAATTTAAGTTTC
1 CGAATTT-AGTTTC
219087 AAAATCTATT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.49
Consensus pattern (19 bp):
CGAATTTAGTTTCGCGTTG
Found at i:219584 original size:20 final size:20
Alignment explanation
Indices: 219559--219637 Score: 131
Period size: 20 Copynumber: 4.0 Consensus size: 20
219549 ATAAACGCGC
* *
219559 TTTGACTTCTGTGTTGCAAA
1 TTTGACTTATGTGTTGCGAA
219579 TTTGACTTATGTGTTGCGAA
1 TTTGACTTATGTGTTGCGAA
219599 TTTGACTTATGTGTTGCGAA
1 TTTGACTTATGTGTTGCGAA
*
219619 TTTGACTTCTGTGTTGCGA
1 TTTGACTTATGTGTTGCGA
219638 TTTACAAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.18, C:0.13, G:0.24, T:0.46
Consensus pattern (20 bp):
TTTGACTTATGTGTTGCGAA
Found at i:219652 original size:20 final size:20
Alignment explanation
Indices: 219631--219697 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
219621 TGACTTCTGT
*
219631 GTTGCGATTTACAAATTAGT
1 GTTGCGATTTACAAATTAGC
*
219651 GTTGCGATTTACAAATTTGC
1 GTTGCGATTTACAAATTAGC
* *
219671 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTAGC
219691 GTTGCGA
1 GTTGCGA
219698 ATTTGAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACAAATTAGC
Found at i:219653 original size:40 final size:38
Alignment explanation
Indices: 219569--219703 Score: 116
Period size: 40 Copynumber: 3.4 Consensus size: 38
219559 TTTGACTTCT
*
219569 GTGTTGCAAATTTGACTTATGTGTTGCGAATTTGAC--TTA
1 GTGTTGCGAATTTGACTT-TGTGTTGCG-ATTT-ACAATTA
219608 TGTGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTA
1 -GTGTTGCGAATTTGACTT-TGTGTTGCGATTTAC-AATTA
* *
219649 GTGTTGCG-ATTT-ACAAATTTGCGTTGCGATTTACATATTC
1 GTGTTGCGAATTTGAC---TTTGTGTTGCGATTTACA-ATTA
*
219689 GCGTTGCGAATTTGA
1 GTGTTGCGAATTTGA
219704 AAAATCGCAA
Statistics
Matches: 81, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
38 4 0.05
39 9 0.11
40 58 0.72
41 9 0.11
42 1 0.01
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.42
Consensus pattern (38 bp):
GTGTTGCGAATTTGACTTTGTGTTGCGATTTACAATTA
Found at i:219711 original size:21 final size:21
Alignment explanation
Indices: 219693--219738 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
219683 ATATTCGCGT
219693 TGCGAATTT-GAAAAATCGCAA
1 TGCGAATTTAG-AAAATCGCAA
219714 TGCGAATTTAGAAAATCGCAA
1 TGCGAATTTAGAAAATCGCAA
219735 TGCG
1 TGCG
219739 TTTCATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (21 bp):
TGCGAATTTAGAAAATCGCAA
Found at i:233662 original size:28 final size:29
Alignment explanation
Indices: 233582--233665 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 29
233572 TATATAATCG
* *
233582 TTCTGATTT-TGCACGGGATTATAT-CCT
1 TTCTGATTTCTGCATGGGATCATATCCCT
* *
233609 TGTCTGATTTCTACATGAGA-CAATATCCCT
1 T-TCTGATTTCTGCATGGGATC-ATATCCCT
233639 TTCT-ATTTCTGCATGGGATCATATCCC
1 TTCTGATTTCTGCATGGGATCATATCCC
233666 CGTCTTGCTA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
27 1 0.02
28 27 0.59
29 14 0.30
30 4 0.09
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (29 bp):
TTCTGATTTCTGCATGGGATCATATCCCT
Found at i:234424 original size:27 final size:27
Alignment explanation
Indices: 234386--234449 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
234376 TGTACCATTT
234386 TTAGTTCATTAAATGTTGGTTTGATTG
1 TTAGTTCATTAAATGTTGGTTTGATTG
234413 TTAGTTCATTAAATGTTGGTTTGATTG
1 TTAGTTCATTAAATGTTGGTTTGATTG
*
234440 TTAGCTCATT
1 TTAGTTCATT
234450 GAGCACATGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.22, C:0.06, G:0.20, T:0.52
Consensus pattern (27 bp):
TTAGTTCATTAAATGTTGGTTTGATTG
Found at i:242229 original size:46 final size:46
Alignment explanation
Indices: 242146--242258 Score: 158
Period size: 46 Copynumber: 2.5 Consensus size: 46
242136 GCAATGCATA
* *
242146 ATGGTGTAT-AAAGGCATGAAAGGATGCCACAAAATGAAATGTATG
1 ATGGTGTATAAAAGGCATGAAAAGATGCCACAAAATGAAATGTATC
* *
242191 ATGGTGTATAAAAGGGCATGAAAAGATTCCA-TAAATGAAATGTATC
1 ATGGTGTATAAAA-GGCATGAAAAGATGCCACAAAATGAAATGTATC
*
242237 ATGGTATATAAAAGGCATGAAA
1 ATGGTGTATAAAAGGCATGAAA
242259 GAATGTATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
45 18 0.30
46 28 0.46
47 15 0.25
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (46 bp):
ATGGTGTATAAAAGGCATGAAAAGATGCCACAAAATGAAATGTATC
Found at i:246703 original size:94 final size:94
Alignment explanation
Indices: 246506--246711 Score: 215
Period size: 94 Copynumber: 2.2 Consensus size: 94
246496 CGATATCATG
* * * * *
246506 GTAAGGGTATCGATACCAAGCAACATCGAATCTAAATTTGGTATCGATACTGGAAGGGGTATCAG
1 GTAAGAGTATCGATACTAAGAAACATCGAACCTAAATTTAGTATCGATACTGGAAGGGGTATCAG
* **
246571 TACAAGTGTATTATAGTATCGATACCATT
66 TACAAGTGTATTAAAGTATCGATACCAGA
* *
246600 TTAAGAGTATCGATACTAGGAAACATCGAACCT-AATTTAGTATCGATAGC-GGAAGGGGGTATC
1 GTAAGAGTATCGATACTAAGAAACATCGAACCTAAATTTAGTATCGATA-CTGGAA-GGGGTATC
* *
246663 AGTACCA-TAGTA-TAGAAGTATCGGTACCAGA
64 AGTACAAGT-GTATTA-AAGTATCGATACCAGA
*
246694 GT-AGTAGTATTGATACTA
1 GTAAG-AGTATCGATACTA
246712 TAGTACCAGA
Statistics
Matches: 93, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
93 23 0.25
94 70 0.75
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (94 bp):
GTAAGAGTATCGATACTAAGAAACATCGAACCTAAATTTAGTATCGATACTGGAAGGGGTATCAG
TACAAGTGTATTAAAGTATCGATACCAGA
Found at i:247129 original size:55 final size:55
Alignment explanation
Indices: 247050--247317 Score: 296
Period size: 55 Copynumber: 4.9 Consensus size: 55
247040 GTGTGCATTT
* * * *
247050 CACGGAATTCATCAT-ATGTGGATGAATAGCCATTTC-GGCACTATGTGTGTAAATC
1 CACGGAATTCATCATGA-GTTGATGAATAACCA-TACAGGCACTATGTGTGCAAATC
* * * *
247105 CACGAAATTCATCATGAGTTGATGAATAATC-TACAGGCAGTATGTGTGAAAATC
1 CACGGAATTCATCATGAGTTGATGAATAACCATACAGGCACTATGTGTGCAAATC
* *
247159 CACGAAATTCATCATGAGTTGATGAATAACCACACAGGCACTATGTGTGCAAATC
1 CACGGAATTCATCATGAGTTGATGAATAACCATACAGGCACTATGTGTGCAAATC
* * * * *
247214 CATGGAATTCATGATGAGTTGATGAATAACGA-A-TGACACTATGTGTGCAAATC
1 CACGGAATTCATCATGAGTTGATGAATAACCATACAGGCACTATGTGTGCAAATC
* * * *
247267 CACGGAATTCATTATGAGTTGATAAATAA-TAGTACAGGCACTACGTGTGCA
1 CACGGAATTCATCATGAGTTGATGAATAACCA-TACAGGCACTATGTGTGCA
247318 TCTTAATAAA
Statistics
Matches: 183, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
52 1 0.01
53 46 0.25
54 49 0.27
55 86 0.47
56 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (55 bp):
CACGGAATTCATCATGAGTTGATGAATAACCATACAGGCACTATGTGTGCAAATC
Found at i:247274 original size:53 final size:53
Alignment explanation
Indices: 247086--247295 Score: 269
Period size: 54 Copynumber: 3.9 Consensus size: 53
247076 TAGCCATTTC
* *
247086 GGCACTATGTGTGTAAATCCACGAAATTCATCATGAGTTGATGAATAATCTACA
1 GGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAA-CCACA
* *
247140 GGCAGTATGTGTGAAAATCCACGAAATTCATCATGAGTTGATGAATAACCACACA
1 GGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAA-C-CACA
* * * *
247195 GGCACTATGTGTGCAAATCCATGGAATTCATGATGAGTTGATGAATAACGA-A
1 GGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCACA
* * * *
247247 TGACACTATGTGTGCAAATCCACGGAATTCATTATGAGTTGATAAATAA
1 -GGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAA
247296 TAGTACAGGC
Statistics
Matches: 140, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
52 1 0.01
53 45 0.32
54 48 0.34
55 46 0.33
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (53 bp):
GGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCACA
Found at i:247304 original size:108 final size:109
Alignment explanation
Indices: 247086--247317 Score: 299
Period size: 108 Copynumber: 2.1 Consensus size: 109
247076 TAGCCATTTC
* * * *
247086 GGCACTATGTGTGTAAATCCACGAAATTCATCATGAGTTGATGAATAATCTACAGGCAGTATGTG
1 GGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAATCGACAGACACTATGTG
*
247151 TGAAAATCCACGAAATTCATCATGAGTTGATGAATAACCACACA
66 TGAAAATCCACGAAATTCATCATGAGTTGATAAATAACCACACA
* * *
247195 GGCACTATGTGTGCAAATCCATGGAATTCATGATGAGTTGATGAATAA-CGA-ATGACACTATGT
1 GGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAATCGACA-GACACTATGT
* * * * *
247258 GTGCAAATCCACGGAATTCATTATGAGTTGATAAATAA-TAGTACA
65 GTGAAAATCCACGAAATTCATCATGAGTTGATAAATAACCA-CACA
*
247303 GGCACTACGTGTGCA
1 GGCACTATGTGTGCA
247318 TCTTAATAAA
Statistics
Matches: 107, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
107 2 0.02
108 61 0.57
109 44 0.41
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (109 bp):
GGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAATCGACAGACACTATGTG
TGAAAATCCACGAAATTCATCATGAGTTGATAAATAACCACACA
Found at i:247633 original size:47 final size:45
Alignment explanation
Indices: 247565--247678 Score: 167
Period size: 46 Copynumber: 2.5 Consensus size: 45
247555 ACAATGCATA
247565 ATGGTGTATAAAAGGCATGAAAGGATGCCACAAAATGAAATGTATG
1 ATGGTGTATAAAAGGCATGAAAGGATGCCA-AAAATGAAATGTATG
* *
247611 ATGGTGTATAAAAAGGCATGAAAAGATGCCATAAATGAAATGTATG
1 ATGGTGTAT-AAAAGGCATGAAAGGATGCCAAAAATGAAATGTATG
* *
247657 -TGATATATAAAAGGCATGAAAG
1 ATGGTGTATAAAAGGCATGAAAG
247679 AATGTATAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
44 13 0.21
45 6 0.10
46 23 0.37
47 20 0.32
ACGTcount: A:0.46, C:0.07, G:0.25, T:0.23
Consensus pattern (45 bp):
ATGGTGTATAAAAGGCATGAAAGGATGCCAAAAATGAAATGTATG
Found at i:250663 original size:20 final size:19
Alignment explanation
Indices: 250640--250680 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
250630 TTGACTTTTT
250640 GGTCAAAGTCAACAGTCAAC
1 GGTCAAAGTCAA-AGTCAAC
250660 GGTCAAAGTCAAAGTCAAC
1 GGTCAAAGTCAAAGTCAAC
250679 GG
1 GG
250681 GCATGTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (19 bp):
GGTCAAAGTCAAAGTCAAC
Found at i:257723 original size:21 final size:20
Alignment explanation
Indices: 257682--257724 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
257672 TTTTTGTTCC
* * *
257682 TTAGTTCTTGTAGTTGTATA
1 TTAGTTCATGTAGCTGCATA
257702 TTAGTTGCATGTAGCTGCATA
1 TTAGTT-CATGTAGCTGCATA
257723 TT
1 TT
257725 TCATGAATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.49
Consensus pattern (20 bp):
TTAGTTCATGTAGCTGCATA
Found at i:269694 original size:251 final size:251
Alignment explanation
Indices: 269251--269746 Score: 992
Period size: 251 Copynumber: 2.0 Consensus size: 251
269241 CCTTTCAAAG
269251 AACTCCAAGCTCATGATTTGGTTTTTAACTAACTTGTAACTCTAGGGAAGTCATCTAAACATCTT
1 AACTCCAAGCTCATGATTTGGTTTTTAACTAACTTGTAACTCTAGGGAAGTCATCTAAACATCTT
269316 TAACTAACACATTATCATCTATGCAAGGACGAACCTACAATGTAGGTAGGAGGGGGAATCGCACG
66 TAACTAACACATTATCATCTATGCAAGGACGAACCTACAATGTAGGTAGGAGGGGGAATCGCACG
269381 CTCCCAAACTTTGGTGGTTTTCACTATAGCAAGCTTGATATTTAATGACATTTTTAGCAGCGTTA
131 CTCCCAAACTTTGGTGGTTTTCACTATAGCAAGCTTGATATTTAATGACATTTTTAGCAGCGTTA
269446 ACTAAAAAACATCACTAATATTGTAAATCTCACGACGTTTAACATAAAACCAAAAT
196 ACTAAAAAACATCACTAATATTGTAAATCTCACGACGTTTAACATAAAACCAAAAT
269502 AACTCCAAGCTCATGATTTGGTTTTTAACTAACTTGTAACTCTAGGGAAGTCATCTAAACATCTT
1 AACTCCAAGCTCATGATTTGGTTTTTAACTAACTTGTAACTCTAGGGAAGTCATCTAAACATCTT
269567 TAACTAACACATTATCATCTATGCAAGGACGAACCTACAATGTAGGTAGGAGGGGGAATCGCACG
66 TAACTAACACATTATCATCTATGCAAGGACGAACCTACAATGTAGGTAGGAGGGGGAATCGCACG
269632 CTCCCAAACTTTGGTGGTTTTCACTATAGCAAGCTTGATATTTAATGACATTTTTAGCAGCGTTA
131 CTCCCAAACTTTGGTGGTTTTCACTATAGCAAGCTTGATATTTAATGACATTTTTAGCAGCGTTA
269697 ACTAAAAAACATCACTAATATTGTAAATCTCACGACGTTTAACATAAAAC
196 ACTAAAAAACATCACTAATATTGTAAATCTCACGACGTTTAACATAAAAC
269747 GGCACGAAAT
Statistics
Matches: 245, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
251 245 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (251 bp):
AACTCCAAGCTCATGATTTGGTTTTTAACTAACTTGTAACTCTAGGGAAGTCATCTAAACATCTT
TAACTAACACATTATCATCTATGCAAGGACGAACCTACAATGTAGGTAGGAGGGGGAATCGCACG
CTCCCAAACTTTGGTGGTTTTCACTATAGCAAGCTTGATATTTAATGACATTTTTAGCAGCGTTA
ACTAAAAAACATCACTAATATTGTAAATCTCACGACGTTTAACATAAAACCAAAAT
Found at i:278152 original size:16 final size:17
Alignment explanation
Indices: 278133--278176 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
278123 CTTTCATGTC
278133 TTTTTTTTCGAACAG-T
1 TTTTTTTTCGAACAGCT
*
278149 TTTTTTTTCGAACTGCT
1 TTTTTTTTCGAACAGCT
*
278166 ATTTTTTTCGA
1 TTTTTTTTCGA
278177 TGGAGAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.16, C:0.14, G:0.11, T:0.59
Consensus pattern (17 bp):
TTTTTTTTCGAACAGCT
Found at i:283526 original size:20 final size:19
Alignment explanation
Indices: 283484--283526 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
283474 AATAGTAATA
* *
283484 TTTTTTCATGAATACTCAG
1 TTTTTTCACGAATACTCAC
*
283503 TTTTTTCACGAATAAGTCAC
1 TTTTTTCACGAAT-ACTCAC
283523 TTTT
1 TTTT
283527 ACTCATACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.49
Consensus pattern (19 bp):
TTTTTTCACGAATACTCAC
Found at i:284194 original size:19 final size:19
Alignment explanation
Indices: 284154--284196 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
284144 TTTTCTGATG
* *
284154 CTTTTTCTTTTGCAATTTC
1 CTTTTTCTTTTGCAACTCC
284173 CTTTCTTCTTTTGC-ACTCC
1 CTTT-TTCTTTTGCAACTCC
284192 CTTTT
1 CTTTT
284197 GATAATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 11 0.52
20 9 0.43
ACGTcount: A:0.07, C:0.28, G:0.05, T:0.60
Consensus pattern (19 bp):
CTTTTTCTTTTGCAACTCC
Found at i:285447 original size:20 final size:20
Alignment explanation
Indices: 285393--285448 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
285383 CTCCAACTGT
*
285393 CTTTAGTCTTCAACTCAACTA
1 CTTT-GTCTTCAGCTCAACTA
285414 CTTTGTCTTCAGCTCAACTA
1 CTTTGTCTTCAGCTCAACTA
*
285434 CTTTGTCTTTAGCTC
1 CTTTGTCTTCAGCTC
285449 CCTCCCACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 29 0.88
21 4 0.12
ACGTcount: A:0.20, C:0.29, G:0.09, T:0.43
Consensus pattern (20 bp):
CTTTGTCTTCAGCTCAACTA
Found at i:285499 original size:11 final size:11
Alignment explanation
Indices: 285479--285511 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
285469 CTCAATCAGC
285479 TCCTTTAGCTA
1 TCCTTTAGCTA
*
285490 TCCTTCAGCTA
1 TCCTTTAGCTA
285501 TCCTTTAGCTA
1 TCCTTTAGCTA
285512 GTTTCCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.18, C:0.30, G:0.09, T:0.42
Consensus pattern (11 bp):
TCCTTTAGCTA
Found at i:285706 original size:3 final size:3
Alignment explanation
Indices: 285698--285732 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
285688 CCTTCTACTT
285698 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
285733 GTTGTAGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:288106 original size:131 final size:129
Alignment explanation
Indices: 287860--288225 Score: 411
Period size: 131 Copynumber: 2.8 Consensus size: 129
287850 CGATATTGAG
* * *
287860 AATAGTAATATCTTTTCATTTCAGTTGGAGTAATAAATGACTGCTTTAAGG-TGAGAGGTCATTT
1 AATAGT-A-ATCTCTTCATTTCAGTTGGAGTAATAAATGATTGCTTTAAGGATAAGAGGTCATTT
* * * * *
287924 ATTCTCGATTGGAAATAATTTGATATTGTCGTTTT-ATCTCGAATCAATATTGATTTTTAAGACG
64 ATTCTCGATTGGAAATAATTAGATATTATCATTTTCATCTCAAATCAATATTGAATTTTAAGACG
*
287988 G
129 A
* **
287989 AATCGTGACATCTCTTCATTTCAGTTGGAAAAATAAATGATTGCTTTAAGGTATAAGAGGTCATT
1 AATAGT-A-ATCTCTTCATTTCAGTTGGAGTAATAAATGATTGCTTTAAGG-ATAAGAGGTCATT
* * * *
288054 TATTCTCGATTGGAAATCATCAGATATTATCATTTTCAT-TCAAATCGATATTGAATTTTAAGAT
63 TATTCTCGATTGGAAATAATTAGATATTATCATTTTCATCTCAAATCAATATTGAATTTTAAGAC
288118 GA
128 GA
* * *
288120 AATAGTAATGCATCTTCATTTC-GATTGGAGTAATAAATGATTGTTTTAATGAATGAA-ATGTCA
1 AATAGTAAT-C-TCTTCATTTCAG-TTGGAGTAATAAATGATTGCTTTAA-GGAT-AAGAGGTCA
* *
288183 TTTATTCTCGATCGGAAATAATTAGATATTATTATTTTC-TCTC
61 TTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCATCTC
288226 TTAAAATTAT
Statistics
Matches: 200, Mismatches: 28, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
129 46 0.23
130 4 0.02
131 145 0.73
132 5 0.03
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (129 bp):
AATAGTAATCTCTTCATTTCAGTTGGAGTAATAAATGATTGCTTTAAGGATAAGAGGTCATTTAT
TCTCGATTGGAAATAATTAGATATTATCATTTTCATCTCAAATCAATATTGAATTTTAAGACGA
Found at i:292922 original size:6 final size:5
Alignment explanation
Indices: 292892--292921 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
292882 CTTACCATTT
292892 TTTTC TTTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTT
292922 TATATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:295384 original size:21 final size:21
Alignment explanation
Indices: 295360--295403 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
295350 AATTTAAATT
295360 GTGTATCGATGCAATGCTACA
1 GTGTATCGATGCAATGCTACA
*
295381 GTGTATCGATGCACTGCTACA
1 GTGTATCGATGCAATGCTACA
295402 GT
1 GT
295404 AACTACTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (21 bp):
GTGTATCGATGCAATGCTACA
Found at i:295887 original size:48 final size:48
Alignment explanation
Indices: 295831--295931 Score: 139
Period size: 48 Copynumber: 2.1 Consensus size: 48
295821 CAATATATTT
* * *
295831 ACCATTTATCCCGTAAACTCGTAAGCTTATATTACCAACATACTATAA
1 ACCATTTATCCCATAAACTCATAAGCTTATATTACCAACATACCATAA
* * * *
295879 ACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAATATACCATAA
1 ACCATTTATCCCATAAACTCATAAGCTTATATTACCAACATACCATAA
295927 ACCAT
1 ACCAT
295932 AGACATTAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.33
Consensus pattern (48 bp):
ACCATTTATCCCATAAACTCATAAGCTTATATTACCAACATACCATAA
Found at i:299012 original size:20 final size:22
Alignment explanation
Indices: 298974--299020 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
298964 CACGTTTTCA
298974 AAAGCTATTATTTTCCTATTCG
1 AAAGCTATTATTTTCCTATTCG
*
298996 AAAGCTATT-TTTT-CTATTTG
1 AAAGCTATTATTTTCCTATTCG
299016 AAAGC
1 AAAGC
299021 AGAAAAACAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.46
21 4 0.17
22 9 0.38
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.45
Consensus pattern (22 bp):
AAAGCTATTATTTTCCTATTCG
Found at i:299516 original size:41 final size:41
Alignment explanation
Indices: 299471--299582 Score: 122
Period size: 41 Copynumber: 2.7 Consensus size: 41
299461 TTGGCATTGA
299471 TCTAAAAATGCCACTATAAACAAACCTATTGCGGCGTTTGT
1 TCTAAAAATGCCACTATAAACAAACCTATTGCGGCGTTTGT
* * *
299512 TCTAAAAATGCCGCCA-AATTAC-TACTCTATTGCGGCGTTTGT
1 TCTAAAAATGCCACTATAA--ACAAAC-CTATTGCGGCGTTTGT
** *
299554 T-GGAAAATGCCACTATAAACAACCCTATT
1 TCTAAAAATGCCACTATAAACAAACCTATT
299583 CTAACATTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
40 9 0.16
41 27 0.47
42 21 0.37
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (41 bp):
TCTAAAAATGCCACTATAAACAAACCTATTGCGGCGTTTGT
Found at i:299688 original size:83 final size:83
Alignment explanation
Indices: 299527--299729 Score: 282
Period size: 83 Copynumber: 2.5 Consensus size: 83
299517 AAATGCCGCC
*
299527 AAATTACTACTCTATTGCGGCGTTTGTTGG-AAAATGCCACTATAAACAACCCTATTCTAACATT
1 AAATTACTACTCTATTGCGGCGTTTGTTGGAAAAACGCCACTATAAACAACCCTATTCTAACATT
* *
299591 TATGCTATAAACGCCATT
66 TATGATATAAACGCCACT
* * * ***
299609 AAATTGCTACTCTATTACGGCGTTTGTTGGAAAAACGCCACTATAAACTACCCTATTCTGGTATT
1 AAATTACTACTCTATTGCGGCGTTTGTTGGAAAAACGCCACTATAAACAACCCTATTCTAACATT
* *
299674 TGTGATATAAACGCCGCT
66 TATGATATAAACGCCACT
* *
299692 ACATTACTACTCTATTGCGGCGTTTATTGGAAAAACGC
1 AAATTACTACTCTATTGCGGCGTTTGTTGGAAAAACGC
299730 TGCTAAAGTA
Statistics
Matches: 105, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
82 28 0.27
83 77 0.73
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.33
Consensus pattern (83 bp):
AAATTACTACTCTATTGCGGCGTTTGTTGGAAAAACGCCACTATAAACAACCCTATTCTAACATT
TATGATATAAACGCCACT
Found at i:299728 original size:42 final size:39
Alignment explanation
Indices: 299615--299734 Score: 98
Period size: 41 Copynumber: 2.9 Consensus size: 39
299605 CATTAAATTG
* *
299615 CTACTCTATTACGGCGTTTGTTGGAAAAACGCCACTATAAA
1 CTACTCTATT-CGGCGTTT-TTGGAAAAACGCCGCTACAAA
* * * *
299656 CTACCCTATTCTG-GTATTTGTGATATAAACGCCGCTACATTA
1 CTACTCTATTCGGCGTTTTTG-GA-A-AAACGCCGCTACA-AA
*
299698 CTACTCTATTGCGGCGTTTATTGGAAAAACGCTGCTA
1 CTACTCTATT-CGGCGTTT-TTGGAAAAACGCCGCTA
299735 AAGTATCTTT
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
38 3 0.05
39 5 0.08
40 3 0.05
41 20 0.32
42 20 0.32
43 3 0.05
44 5 0.08
45 3 0.05
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.33
Consensus pattern (39 bp):
CTACTCTATTCGGCGTTTTTGGAAAAACGCCGCTACAAA
Found at i:306536 original size:18 final size:18
Alignment explanation
Indices: 306513--306556 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
306503 GCATACACAA
306513 TAATTTGCTCAAAATCTT
1 TAATTTGCTCAAAATCTT
306531 TAATTTGCTCAAAATCTT
1 TAATTTGCTCAAAATCTT
306549 TAATTTGC
1 TAATTTGC
306557 AACCACCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.07, T:0.45
Consensus pattern (18 bp):
TAATTTGCTCAAAATCTT
Found at i:311049 original size:36 final size:39
Alignment explanation
Indices: 311009--311098 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 39
310999 AATTTTTGTT
311009 TATTATATACTATTAATATTA-TA-TATTTATTACT-T-A
1 TATTATATACTATTAATATTATTATTA-TTATTACTATGA
* * * *
311045 TATTATATAGTGTTACTATTATTATTATTATTACTATGT
1 TATTATATACTATTAATATTATTATTATTATTACTATGA
*
311084 TATTATATATTATTA
1 TATTATATACTATTA
311099 TTTTGCTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
36 18 0.41
37 10 0.23
38 3 0.07
39 13 0.30
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (39 bp):
TATTATATACTATTAATATTATTATTATTATTACTATGA
Found at i:311127 original size:20 final size:21
Alignment explanation
Indices: 311058--311130 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 21
311048 TATATAGTGT
*
311058 TACTATTAT-TATTATTATTA
1 TACTATTATATACTATTATTA
* * *
311078 CTATGTTATTATATATTATTATTT
1 -TA--CTATTATATACTATTATTA
*
311102 TGCTATTA-ATACTATTATTA
1 TACTATTATATACTATTATTA
311122 TACTATTAT
1 TACTATTAT
311131 TCCAATATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
20 17 0.41
21 7 0.17
23 7 0.17
24 10 0.24
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.58
Consensus pattern (21 bp):
TACTATTATATACTATTATTA
Found at i:311144 original size:3 final size:3
Alignment explanation
Indices: 311008--311131 Score: 58
Period size: 3 Copynumber: 40.7 Consensus size: 3
310998 TAATTTTTGT
* *
311008 TTA TTA TATA CTA TTA ATA TTA TATA TTTA TTA CTTA -TA TTA TATA
1 TTA TTA T-TA TTA TTA TTA TTA T-TA -TTA TTA -TTA TTA TTA T-TA
* * * * *
311054 GTG TTA CTA TTA TTA TTA TTA TTA CTA -TG TTA TTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* * * * *
311099 TT- TTG CTA TTA ATA CTA TTA TTA -TA CTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
311132 CCAATATATT
Statistics
Matches: 91, Mismatches: 20, Indels: 20
0.69 0.15 0.15
Matches are distributed among these distances:
2 7 0.08
3 69 0.76
4 14 0.15
5 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:311262 original size:30 final size:30
Alignment explanation
Indices: 311226--311286 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
311216 AAAATGAATG
311226 AATGGGTTTTTATTGATATTTAATTATTTT
1 AATGGGTTTTTATTGATATTTAATTATTTT
311256 AATGGGTTTTTATTGATATTTAATTATTTT
1 AATGGGTTTTTATTGATATTTAATTATTTT
311286 A
1 A
311287 CAGACCCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (30 bp):
AATGGGTTTTTATTGATATTTAATTATTTT
Found at i:312523 original size:41 final size:41
Alignment explanation
Indices: 312413--312523 Score: 125
Period size: 40 Copynumber: 2.7 Consensus size: 41
312403 CCGTAAACGG
* ** ** * *
312413 TCGTACTTTAGTGGCGTTTTTATATTAATGGTGCTGAATAC
1 TCGTACTTTAGTGGCGTTTTTATATAAATGCCGCAAAAAAA
* * *
312454 T-ATACTTTAGTGGCGTTTGTATACAAATGCCGCAAAAAAA
1 TCGTACTTTAGTGGCGTTTTTATATAAATGCCGCAAAAAAA
312494 TCGTACTTTAGTGGCGTTTTTATATAAATG
1 TCGTACTTTAGTGGCGTTTTTATATAAATG
312524 ATGCTAAAGA
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
40 30 0.54
41 26 0.46
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.40
Consensus pattern (41 bp):
TCGTACTTTAGTGGCGTTTTTATATAAATGCCGCAAAAAAA
Found at i:312542 original size:41 final size:41
Alignment explanation
Indices: 312416--312554 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
312406 TAAACGGTCG
* * * *
312416 TACTTTAGTGGCGTTTTTATATTAATGGTGCTGAATACT-A
1 TACTTTAGTGGCGTTTTTATATAAATGATGCTAAAAACTCA
* * ** * * *
312456 TACTTTAGTGGCGTTTGTATACAAATGCCGCAAAAAAATCG
1 TACTTTAGTGGCGTTTTTATATAAATGATGCTAAAAACTCA
*
312497 TACTTTAGTGGCGTTTTTATATAAATGATGCTAAAGACTCA
1 TACTTTAGTGGCGTTTTTATATAAATGATGCTAAAAACTCA
*
312538 TACTTTAGTGGTGTTTT
1 TACTTTAGTGGCGTTTT
312555 AAGCACAAAC
Statistics
Matches: 79, Mismatches: 19, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
40 30 0.38
41 49 0.62
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40
Consensus pattern (41 bp):
TACTTTAGTGGCGTTTTTATATAAATGATGCTAAAAACTCA
Found at i:312585 original size:42 final size:40
Alignment explanation
Indices: 312449--312626 Score: 132
Period size: 41 Copynumber: 4.4 Consensus size: 40
312439 AATGGTGCTG
* * *
312449 AATACT-ATACTTTAGTGGCGTTTGTATACAAATGCCGCAA
1 AATACTCATACTTTAGTGTCGTTT-TATACAAATACCGCTA
* * * * * *
312489 AAAAATCGTACTTTAGTGGCGTTTTTATATAAATGA-TGCTA
1 AATACTCATACTTTAGTGTCG-TTTTATACAAAT-ACCGCTA
*
312530 AAGACTCATACTTTAGTGGT-GTTTTA-AGCACAA-ACGTCGCTA
1 AATACTCATACTTTAGT-GTCGTTTTATA-CA-AATAC--CGCTA
* *
312572 AATACTCCTACTTTGGTGTCGTTTTATACAAATACCGCTA
1 AATACTCATACTTTAGTGTCGTTTTATACAAATACCGCTA
*
312612 AATACTCGTACTTTA
1 AATACTCATACTTTA
312627 AAATCACGAC
Statistics
Matches: 108, Mismatches: 18, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
39 2 0.02
40 28 0.26
41 45 0.42
42 32 0.30
43 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (40 bp):
AATACTCATACTTTAGTGTCGTTTTATACAAATACCGCTA
Found at i:322273 original size:56 final size:56
Alignment explanation
Indices: 322126--322520 Score: 668
Period size: 56 Copynumber: 7.1 Consensus size: 56
322116 ATTTCCAAGT
* *
322126 TTTTACACATATAGTGCCCATAC-AGAAATTCATTCACTTAGTATTAATTTCTTAAG
1 TTTTACACATATAGTGCCCATACGA-AAATTCATCCACTTAGTATGAATTTCTTAAG
* * * *
322182 -TTTAAACATAAAGTGCCTATACAAAAATTCATCCACTTAGTATGAATTTCTTAAG
1 TTTTACACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG
* *
322237 TTTTACACATATAGTGTCCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAG
1 TTTTACACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG
322293 TTTTACACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG
1 TTTTACACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG
322349 TTTTACACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG
1 TTTTACACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG
322405 TTTTACACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG
1 TTTTACACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG
* * *
322461 TTTTACACATATAGTACCCATACCAAAATTCATCCACTTAGTATGAATTTCTTATG
1 TTTTACACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG
322517 TTTT
1 TTTT
322521 TGCACACTTA
Statistics
Matches: 321, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
55 48 0.15
56 273 0.85
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (56 bp):
TTTTACACATATAGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG
Found at i:322915 original size:19 final size:20
Alignment explanation
Indices: 322868--322926 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
322858 ATCCATACCC
*
322868 CTACCATGGTATCGATACTA
1 CTACTATGGTATCGATACTA
*
322888 CCGTACTATGGTACCGATACT-
1 -C-TACTATGGTATCGATACTA
322909 CTACTATGGTATCGATAC
1 CTACTATGGTATCGATAC
322927 CATTTTTTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 16 0.47
20 1 0.03
21 1 0.03
22 16 0.47
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (20 bp):
CTACTATGGTATCGATACTA
Found at i:328854 original size:20 final size:20
Alignment explanation
Indices: 328825--328865 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
328815 TACAGTGCCC
* *
328825 ATACAGAAATTTATTCACTT
1 ATACAGAAATTCATCCACTT
*
328845 ATACATAAATTCATCCACTT
1 ATACAGAAATTCATCCACTT
328865 A
1 A
328866 GTATGAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (20 bp):
ATACAGAAATTCATCCACTT
Found at i:330270 original size:13 final size:14
Alignment explanation
Indices: 330252--330301 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
330242 CATTATTCAG
330252 TTATAT-TTTAATT
1 TTATATATTTAATT
*
330265 TTATATGTTT-ATT
1 TTATATATTTAATT
330278 TTAATATATTTAATT
1 TT-ATATATTTAATT
330293 ATTAT-TATT
1 -TTATATATT
330302 ATTATTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.34
14 14 0.44
15 5 0.16
16 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:330284 original size:14 final size:13
Alignment explanation
Indices: 330252--330342 Score: 52
Period size: 12 Copynumber: 7.3 Consensus size: 13
330242 CATTATTCAG
330252 TTATAT-TTTAATT
1 TTATATATTT-ATT
*
330265 TTATATGTTTATT
1 TTATATATTTATT
*
330278 TTAATATATTTA-A
1 TT-ATATATTTATT
330291 TTAT-TA-TTATT
1 TTATATATTTATT
*
330302 ATTAT-TATTTA-A
1 -TTATATATTTATT
* *
330314 TCATATATATA-T
1 TTATATATTTATT
*
330326 ATATATATTTATT
1 TTATATATTTATT
330339 TTAT
1 TTAT
330343 TTATATTAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 5 0.08
12 21 0.35
13 20 0.33
14 11 0.18
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (13 bp):
TTATATATTTATT
Found at i:331178 original size:26 final size:28
Alignment explanation
Indices: 331132--331189 Score: 86
Period size: 26 Copynumber: 2.1 Consensus size: 28
331122 TTTTATATTT
331132 TTTATATATACTTATTATTTTCA-TAATA
1 TTTATATATACTTATTATTTT-ATTAATA
331160 TTTATATATA-TTATT-TTTTATTAATA
1 TTTATATATACTTATTATTTTATTAATA
331186 TTTA
1 TTTA
331190 CTTTAGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 1 0.03
26 13 0.45
27 5 0.17
28 10 0.34
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTATATATACTTATTATTTTATTAATA
Found at i:332106 original size:36 final size:35
Alignment explanation
Indices: 332045--332113 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
332035 CGAGCTATGC
* * *
332045 ACACAAAGATCCTGTATATTAATACCAAAAGTATT
1 ACACAAAGAACCTGCAGATTAATACCAAAAGTATT
332080 ACACAAAGAACCTGCCAGATTAATACCAAAAGTA
1 ACACAAAGAACCTG-CAGATTAATACCAAAAGTA
332114 GTCTATGGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 13 0.43
36 17 0.57
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.22
Consensus pattern (35 bp):
ACACAAAGAACCTGCAGATTAATACCAAAAGTATT
Found at i:336071 original size:7 final size:7
Alignment explanation
Indices: 336070--336125 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
336060 AAAAAAGAAA
336070 AAAAAAG
1 AAAAAAG
336077 AAAAAAG
1 AAAAAAG
*
336084 AGATAAA-
1 A-AAAAAG
*
336091 AAAGAAG
1 AAAAAAG
336098 AAAAAAGG
1 AAAAAA-G
*
336106 AAAAAGG
1 AAAAAAG
*
336113 AAAGAAG
1 AAAAAAG
336120 AAAAAA
1 AAAAAA
336126 ATTGAATCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
6 3 0.08
7 25 0.66
8 10 0.26
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:336093 original size:21 final size:19
Alignment explanation
Indices: 336059--336125 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 19
336049 CATTCATCAG
336059 GAAAAAA-G-AAAAAAAAA
1 GAAAAAAGGAAAAAAAAAA
*
336076 GAAAAAAGAGATAAAAAAGAA
1 GAAAAAAG-GA-AAAAAAAAA
336097 GAAAAAAGGAAAAAGGAAAGAA
1 GAAAAAAGGAAAAA--AAA-AA
336119 GAAAAAA
1 GAAAAAA
336126 ATTGAATCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
17 7 0.17
19 5 0.12
20 2 0.05
21 18 0.44
22 9 0.22
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (19 bp):
GAAAAAAGGAAAAAAAAAA
Found at i:340306 original size:54 final size:54
Alignment explanation
Indices: 340221--340328 Score: 144
Period size: 54 Copynumber: 2.0 Consensus size: 54
340211 ATGACCAGAA
* *
340221 ATCTGGGCAGAAGCCAAAGGAAAAGAGGAATGTGTTATCAAATGTTTTATGAAC
1 ATCTGGGCAGAAACCAAAGGAAAAGAGGAATGTGTTATCAAATGTTTTACGAAC
* * * * * *
340275 ATCTGGGCAGAAACCACATGAGATGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGGGCAGAAACCAAAGGAAAAGAGGAATGTGTTATCAAATGTTTTACGAAC
340329 CAGTTATTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (54 bp):
ATCTGGGCAGAAACCAAAGGAAAAGAGGAATGTGTTATCAAATGTTTTACGAAC
Found at i:340749 original size:22 final size:22
Alignment explanation
Indices: 340693--340737 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
340683 ACATCTACAT
340693 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
340715 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
340737 T
1 T
340738 TTTTGAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:341306 original size:20 final size:20
Alignment explanation
Indices: 341251--341309 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
341241 TGCCAGGTAG
341251 AGTTCATAATGAGAAGAACA
1 AGTTCATAATGAGAAGAACA
*
341271 A-ATC-TGAA-GAAGGAAGAACA
1 AGTTCAT-AATG-A-GAAGAACA
341291 AGTTCATAATGAGAAGAAC
1 AGTTCATAATGAGAAGAAC
341310 TTGTTCAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
18 2 0.06
19 5 0.16
20 17 0.55
21 5 0.16
22 2 0.06
ACGTcount: A:0.51, C:0.10, G:0.22, T:0.17
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACA
Found at i:341412 original size:113 final size:113
Alignment explanation
Indices: 341103--341663 Score: 808
Period size: 113 Copynumber: 5.0 Consensus size: 113
341093 GCAAAGATTT
* * * *
341103 GAATCCATCACTCGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATATGAAG
1 GAATTCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
341168 AAGGAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* **
341216 AAATTCATCA-TTCGATGGATCAACA-TGCCAGGTAGAGTTCATAATGAGAAGAACAAATCTGAA
1 GAATTCATCACTT-GATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAA
*
341279 GAAGGAAGAACAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
***
341328 GAATTCATCACTTGATGGATTGGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 GAATTCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
341393 AAGGAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * *
341441 AAATTCATCACTTGATGGATAAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAG
1 GAATTCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * ** *
341506 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATATTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * * * *
341554 GAATTCATCACTCGATGGATCAACTTTTCCAAAG-AAAGTTCATAATAAGAAGAACTCATCTGAA
1 GAATTCATCACTTGATGGATCAACATTGCC-AGGTAGAGTTCATAATGAGAAGAACTCATCTGAA
341618 GAA-GAAGAA-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT
341664 TGACTCTATC
Statistics
Matches: 404, Mismatches: 40, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
111 33 0.08
112 107 0.26
113 262 0.65
114 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
GAATTCATCACTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
Found at i:343476 original size:13 final size:14
Alignment explanation
Indices: 343458--343507 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
343448 AATTATTCAG
343458 TTATAT-TTTAATT
1 TTATATATTTAATT
*
343471 TTATATGTTT-ATT
1 TTATATATTTAATT
343484 TTAATATATTTAATT
1 TT-ATATATTTAATT
343499 ATTAT-TATT
1 -TTATATATT
343508 ATTTTTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 11 0.34
14 14 0.44
15 5 0.16
16 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:343740 original size:14 final size:14
Alignment explanation
Indices: 343691--343742 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
343681 CCATTTTCTG
343691 ATATTTTTAAATAA
1 ATATTTTTAAATAA
*
343705 ATAAATATTTTAAATTA
1 AT--AT-TTTTAAATAA
* *
343722 TTATTTTTAGATAA
1 ATATTTTTAAATAA
343736 ATATTTT
1 ATATTTT
343743 ATTAATATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
14 16 0.53
15 2 0.07
16 2 0.07
17 10 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
ATATTTTTAAATAA
Found at i:343847 original size:2 final size:2
Alignment explanation
Indices: 343835--343872 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
343825 ATATCTTATT
*
343835 TA TA AA 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
343873 CTAATAGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:344357 original size:56 final size:56
Alignment explanation
Indices: 344271--344598 Score: 541
Period size: 56 Copynumber: 5.9 Consensus size: 56
344261 CGATTACGAC
*
344271 AGTGCCCATACTG-AAATTCATCCACTTAGTATGAATTTATTAAGTTTTACACATAT
1 AGTGCCCATAC-GAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAT
*
344327 AGTGCTCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAT
1 AGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAT
*
344383 AGTGCCCATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAT
1 AGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAT
* * *
344439 AGTGCTCATATGAAAATTCATCCACATAGTATGAATTTCTTAAGTTTTACACATAT
1 AGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAT
* * * *
344495 AGTGCCCATACGGAAATTCATCCACTTAGTATGAATTTATTAAGTTCTACGCATAT
1 AGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAT
*
344551 AGTGCCCATACGAAAATTCATCCACTGAGTATGAATTTCTTAAGTTTT
1 AGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTT
344599 TGCACACTTA
Statistics
Matches: 252, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
55 1 0.00
56 251 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (56 bp):
AGTGCCCATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTTACACATAT
Found at i:367911 original size:3 final size:3
Alignment explanation
Indices: 367903--367972 Score: 117
Period size: 3 Copynumber: 23.7 Consensus size: 3
367893 TTCAATAACT
367903 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
367951 ATA ATA A-A ATCA A-A ATA ATA AT
1 ATA ATA ATA AT-A ATA ATA ATA AT
367973 TCGTTTTAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.06
3 58 0.91
4 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:369793 original size:3 final size:3
Alignment explanation
Indices: 369774--369844 Score: 106
Period size: 3 Copynumber: 23.0 Consensus size: 3
369764 TTGTAATATT
* *
369774 TAA TAAA TAA TATA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
369821 TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
369845 ATTTAAATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
3 56 0.90
4 6 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:370261 original size:76 final size:77
Alignment explanation
Indices: 369978--370297 Score: 534
Period size: 77 Copynumber: 4.2 Consensus size: 77
369968 GATGAAAATG
* * *
369978 TTTGGAAACATCATGCACTGTAGGACTCACAGATAACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
370043 CCCGAAGGCTTT
66 CCCGAAGGCTTT
*
370055 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
370120 CCCGAAGGCTTT
66 CCCGAAGGCTTT
*
370132 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGTT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
370197 CCCGAAGGC-TT
66 CCCGAAGGCTTT
* * * *
370208 TTTGGAAACATCATGCACTGAAGGGCTTCCAGATGACCCGAAGGCTTTTAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
370273 CCCGAAGGCTTT
66 CCCGAAGGCTTT
* *
370285 TTTGAAAATATCA
1 TTTGGAAACATCA
370298 AAAAGTTCAT
Statistics
Matches: 230, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
76 71 0.31
77 159 0.69
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (77 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTT
Found at i:370298 original size:108 final size:108
Alignment explanation
Indices: 370177--370404 Score: 379
Period size: 108 Copynumber: 2.1 Consensus size: 108
370167 ACCCTAAGGC
* *
370177 TTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTCCAGAT
1 TTTGAAAACATCAAAAAGTTCACGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
370242 GACCCGAAGGCTTTT-AAAACATCAAAAAGCTCCCGAAGGCTTT
66 GACCCGAAGG-TTTTGAAAACATCAAAAAGCTCCCGAAGGCTTT
* *
370285 TTTGAAAATATCAAAAAGTTCATGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGTTCACGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
*
370350 GACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGC-TT
66 GACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTT
*
370392 TTTGGAAACATCA
1 TTTGAAAACATCA
370405 TGCACTGAAG
Statistics
Matches: 112, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
107 17 0.15
108 95 0.85
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (108 bp):
TTTGAAAACATCAAAAAGTTCACGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
GACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTT
Found at i:370312 original size:32 final size:32
Alignment explanation
Indices: 370246--370328 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
370236 CCAGATGACC
*
370246 CGAAGGC--TTTT-AAAACATCAAAAAGCTCC
1 CGAAGGCTTTTTTGAAAACATCAAAAAGCTCA
* *
370275 CGAAGGCTTTTTTGAAAATATCAAAAAGTTCA
1 CGAAGGCTTTTTTGAAAACATCAAAAAGCTCA
* *
370307 TGAAGGC-TTTTTGGAAACATCA
1 CGAAGGCTTTTTTGAAAACATCA
370329 TGCACTGAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 7 0.16
31 17 0.38
32 21 0.47
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (32 bp):
CGAAGGCTTTTTTGAAAACATCAAAAAGCTCA
Found at i:370350 original size:184 final size:184
Alignment explanation
Indices: 370100--370474 Score: 635
Period size: 184 Copynumber: 2.0 Consensus size: 184
370090 ACCCTAAGGC
*
370100 TTTGAAAACATCAAAAAGATCCCGAAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
1 TTTGAAAACATCAAAAAGATCACGAAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
*
370165 TGACCCTAAGGCTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
66 TGACCCGAAGGCTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
* *
370230 GGGCTTCCAGATGACCCGAAGGCTTTTAAAACATCAAAAAGCTCCCGAAGGCTTT
131 GGGCTTACAGATGACCCGAAGGCTTTGAAAAC-TCAAAAAGCTCCCGAAGGCTTT
* * * *
370285 TTTGAAAATATCAAAAAGTTCATGAAGGC-TTTTTGGAAACATCATGCACTGAAGGGCTTACAGA
1 TTTGAAAACATCAAAAAGATCACGAAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
*
370349 TGACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
66 TGACCCGAAGGCTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
*
370414 GGGCTTACAGATGACCCGAAGGCTTTGAAAACTCAAAAAGTTCCCGAAGGCTTT
131 GGGCTTACAGATGACCCGAAGGCTTTGAAAACTCAAAAAGCTCCCGAAGGCTTT
*
370468 TTGGAAA
1 TTTGAAA
370475 TCATGCACTG
Statistics
Matches: 179, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
183 27 0.15
184 127 0.71
185 25 0.14
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.25
Consensus pattern (184 bp):
TTTGAAAACATCAAAAAGATCACGAAGGCTTTTTTGGAAACATCATGCACTGAAGGACTTACAGA
TGACCCGAAGGCTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAA
GGGCTTACAGATGACCCGAAGGCTTTGAAAACTCAAAAAGCTCCCGAAGGCTTT
Found at i:370367 original size:76 final size:76
Alignment explanation
Indices: 370285--370873 Score: 989
Period size: 76 Copynumber: 7.9 Consensus size: 76
370275 CGAAGGCTTT
* * **
370285 TTTGAAAATATCAAAAAGTTCATGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
*
370350 GACCCGAAGGT
66 GACCCGAAGGC
*
370361 TTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
370426 GACCCGAAGGC
66 GACCCGAAGGC
* *
370437 TTTGAAAAC-TCAAAAAGTTCCCGAAGGCTTTTTGG-AA-ATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
370499 GACCCGAAGGC
66 GACCCGAAGGC
*
370510 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT-G-AACATCATGCAATGAA-GGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
370572 GACCCGAAGGC
66 GACCCGAAGGC
*
370583 TTTGAAAACATCTAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
370648 GACCCGAAGGC
66 GACCCGAAGGC
*
370659 TTTGAAAACATC-AAAAGCTCCCGAAGGC-TTTTGAAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
370722 GA-CCGAAGGC
66 GACCCGAAGGC
*
370732 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
*
370797 GACCCGAAGGT
66 GACCCGAAGGC
*
370808 TTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
370873 G
66 G
370874 TGGGAAATAG
Statistics
Matches: 491, Mismatches: 14, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
73 121 0.25
74 90 0.18
75 94 0.19
76 186 0.38
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (76 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
GACCCGAAGGC
Found at i:370501 original size:149 final size:152
Alignment explanation
Indices: 370285--370873 Score: 989
Period size: 149 Copynumber: 3.9 Consensus size: 152
370275 CGAAGGCTTT
* * **
370285 TTTGAAAATATCAAAAAGTTCATGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
* *
370350 GACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
66 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
370415 GGCTTACAGATGACCCGAAGGC
131 GGCTTACAGATGACCCGAAGGC
* *
370437 TTTGAAAAC-TCAAAAAGTTCCCGAAGGCTTTTTGG-AA-ATCATGCACTGAAGGACTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
*
370499 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT-G-AACATCATGCAATGAA-
66 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
370561 GGCTTACAGATGACCCGAAGGC
131 GGCTTACAGATGACCCGAAGGC
*
370583 TTTGAAAACATCTAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
*
370648 GACCCGAAGGCTTTGAAAACATC-AAAAGCTCCCGAAGGC-TTTTGAAAACATCATGCACTGAAG
66 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
370711 GGCTTACAGATGA-CCGAAGGC
131 GGCTTACAGATGACCCGAAGGC
*
370732 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
* *
370797 GACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
66 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
370862 GGCTTACAGATG
131 GGCTTACAGATG
370874 TGGGAAATAG
Statistics
Matches: 412, Mismatches: 17, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
146 31 0.08
147 43 0.10
148 19 0.05
149 222 0.54
150 30 0.07
151 59 0.14
152 8 0.02
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (152 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
GGCTTACAGATGACCCGAAGGC
Found at i:370592 original size:222 final size:224
Alignment explanation
Indices: 370285--370873 Score: 999
Period size: 222 Copynumber: 2.6 Consensus size: 224
370275 CGAAGGCTTT
* * **
370285 TTTGAAAATATCAAAAAGTTCATGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT-GAAACATCATGCACTGAAGGGCTTACAGAT
370350 GACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
65 GACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
* *
370415 GGCTTACAGATGACCCGAAGGCTTTGAAAAC-TCAAAAAGTTCCCGAAGGCTTTTTG-GAA-ATC
130 GGCTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCTCCCGAAGGC-TTTTGAAAACATC
370477 ATGCACTGAAGGACTTACAGATGACCCGAAGGC
193 ATGCACTGAAGGACTTACAGATGA-CCGAAGGC
*
370510 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTG-AACATCATGCAATGAA-GGCTTACAGATG
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAACATCATGCACTGAAGGGCTTACAGATG
* * *
370573 ACCCGAAGGCTTTGAAAACATCTAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
66 ACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
370638 GCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAGCTCCCGAAGGCTTTTGAAAACATCATG
131 GCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAGCTCCCGAAGGCTTTTGAAAACATCATG
*
370703 CACTGAAGGGCTTACAGATGACCGAAGGC
196 CACTGAAGGACTTACAGATGACCGAAGGC
370732 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGAT
1 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTG-AAACATCATGCACTGAAGGGCTTACAGAT
370797 GACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
65 GACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAG
370862 GGCTTACAGATG
130 GGCTTACAGATG
370874 TGGGAAATAG
Statistics
Matches: 343, Mismatches: 15, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
221 5 0.01
222 164 0.48
223 43 0.13
224 16 0.05
225 115 0.34
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (224 bp):
TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAAACATCATGCACTGAAGGGCTTACAGATG
ACCCGAAGGTTTTGAAAACATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGG
GCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAGCTCCCGAAGGCTTTTGAAAACATCATG
CACTGAAGGACTTACAGATGACCGAAGGC
Found at i:372158 original size:118 final size:120
Alignment explanation
Indices: 371996--372225 Score: 446
Period size: 118 Copynumber: 1.9 Consensus size: 120
371986 TATGATGTAC
371996 AGACCATTTGAGAACAAAACTCCATGGGGATTCAAGTGTGATGTTGGTATGACAAAAAAAA-TGA
1 AGACCATTTGAGAACAAAACTCCATGGGGATTCAAGTGTGATGTTGGTATGACAAAAAAAATTGA
372060 TCAATTTCTCAAGATATGCTAG-GTTGAATTGAATAGGAGACACTAAATGTCACA
66 TCAATTTCTCAAGATATGCTAGTGTTGAATTGAATAGGAGACACTAAATGTCACA
372114 AGACCATTTGAGAACAAAACTCCATGGGGATTCAAGTGTGATGTTGGTATGACAAAAAAAATTGA
1 AGACCATTTGAGAACAAAACTCCATGGGGATTCAAGTGTGATGTTGGTATGACAAAAAAAATTGA
372179 TCAATTTCTCAAGATATGCTAGTGTTGAATTGAATAGGAGACACTAA
66 TCAATTTCTCAAGATATGCTAGTGTTGAATTGAATAGGAGACACTAA
372226 CTGATCTTGA
Statistics
Matches: 110, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
118 61 0.55
119 25 0.23
120 24 0.22
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (120 bp):
AGACCATTTGAGAACAAAACTCCATGGGGATTCAAGTGTGATGTTGGTATGACAAAAAAAATTGA
TCAATTTCTCAAGATATGCTAGTGTTGAATTGAATAGGAGACACTAAATGTCACA
Found at i:374247 original size:114 final size:114
Alignment explanation
Indices: 374047--374272 Score: 362
Period size: 114 Copynumber: 2.0 Consensus size: 114
374037 GATCATGCAG
* * * * * * *
374047 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATTAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGATTCTGGAGTTCATACCAAATCAAATCAGATAACTCAAAGA
374112 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* *
374161 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATCGATTCTGGAGTTCATACCAAATCAAATCAGATAACTCAAAGA
*
374226 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCA
374273 CATGGCACTT
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 102 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATCGATTCTGGAGTTCATACCAAATCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:382812 original size:157 final size:152
Alignment explanation
Indices: 382526--382835 Score: 566
Period size: 157 Copynumber: 2.0 Consensus size: 152
382516 TGAAGAAATA
382526 CCTTCGGGTATTTCGAATAATTAGTCTGCCCGTAGCGTCTTCGATCACCGGTGGCTTCTCGGAAA
1 CCTTCGGGTATTTCGAATAATTAGTCTGCCCGTAGCGTCTTCGATCACCGGTGGCTTCTCGGAAA
382591 GCTTTCCCTTCTTTTTGGTTTCTATTTTTTGTGTTTTGGTTGTTGCTGGGTTGTATTTGTGTCTC
66 GCTTTCCCTTCTTTTTGGTTTCTATTTTTTGTGTTTTGGTTGTTGCTGGGTTGTATTTGTGTCTC
382656 TCTTCGGTTCCTTTATCTCTAT
131 TCTTCGGTTCCTTTATCTCTAT
382678 CCTTCGGGTATTTCGAATAATTTAGTCTGCCCGTAGCGTCTTCGATCACCGGTGGCTTCCTCGGA
1 CCTTCGGGTATTTCGAATAA-TTAGTCTGCCCGTAGCGTCTTCGATCACCGGTGGCTT-CTCGGA
382743 AAGCTTTCCCTTCTTTCTTGGTTTCTATTTTTTTGTGGTTTTGGTTGTTGCTGGGTTGTATTTGT
64 AAGCTTTCCCTTCTTT-TTGGTTTCTA-TTTTTTGT-GTTTTGGTTGTTGCTGGGTTGTATTTGT
*
382808 GTCTCTCTTCGGTTCCTTTCTCTCTAT
126 GTCTCTCTTCGGTTCCTTTATCTCTAT
382835 C
1 C
382836 TTTGTTGGCA
Statistics
Matches: 152, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
152 20 0.13
153 37 0.24
154 22 0.14
155 10 0.07
156 8 0.05
157 55 0.36
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (152 bp):
CCTTCGGGTATTTCGAATAATTAGTCTGCCCGTAGCGTCTTCGATCACCGGTGGCTTCTCGGAAA
GCTTTCCCTTCTTTTTGGTTTCTATTTTTTGTGTTTTGGTTGTTGCTGGGTTGTATTTGTGTCTC
TCTTCGGTTCCTTTATCTCTAT
Found at i:383203 original size:7 final size:7
Alignment explanation
Indices: 383193--383248 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 7
383183 TTGGGTTTTG
*
383193 TAATATT
1 TAATATA
*
383200 TAATAAA
1 TAATATA
383207 TAATATA
1 TAATATA
383214 TAATA-A
1 TAATATA
383220 TAATA-A
1 TAATATA
383226 TAATA-A
1 TAATATA
383232 TAATA-A
1 TAATATA
383238 TAATA-A
1 TAATATA
383244 TAATA
1 TAATA
383249 ATTTAAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
6 30 0.65
7 16 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
TAATATA
Found at i:383219 original size:3 final size:3
Alignment explanation
Indices: 383200--383250 Score: 84
Period size: 3 Copynumber: 16.3 Consensus size: 3
383190 TTGTAATATT
383200 TAA TAAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
383247 TAA T
1 TAA T
383251 TTAAATTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:385635 original size:3 final size:3
Alignment explanation
Indices: 385629--385654 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
385619 AACTTATAAT
385629 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
385655 AACCCAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:387768 original size:71 final size:71
Alignment explanation
Indices: 387688--387827 Score: 271
Period size: 71 Copynumber: 2.0 Consensus size: 71
387678 GACAAAGTAG
387688 AGATCATAAATCCTATTGATATAGTTGATCCTTTGGCTGATGAATTTTTAAGGACTAATTTTTCT
1 AGATCATAAATCCTATTGATATAGTTGATCCTTTGGCTGATGAATTTTTAAGGACTAATTTTTCT
387753 TTTGTA
66 TTTGTA
*
387759 AGATCATAAATCCTATTGATATAGTTGATCCTTTGGCTGATGGATTTTTAAGGACTAATTTTTCT
1 AGATCATAAATCCTATTGATATAGTTGATCCTTTGGCTGATGAATTTTTAAGGACTAATTTTTCT
387824 TTTG
66 TTTG
387828 ATCTATGCAG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.45
Consensus pattern (71 bp):
AGATCATAAATCCTATTGATATAGTTGATCCTTTGGCTGATGAATTTTTAAGGACTAATTTTTCT
TTTGTA
Found at i:391695 original size:29 final size:29
Alignment explanation
Indices: 391643--391861 Score: 280
Period size: 29 Copynumber: 7.6 Consensus size: 29
391633 GACCTGACCC
391643 GGGTGCTATTTTCGTAAATATTTTTAAAA
1 GGGTGCTATTTTCGTAAATATTTTTAAAA
*
391672 AGGTGCTATTTT-GTAAATATTTTTAAAA
1 GGGTGCTATTTTCGTAAATATTTTTAAAA
391700 GGGTGAC-ATTTTCGTAAATATTTTTAAAA
1 GGGTG-CTATTTTCGTAAATATTTTTAAAA
** * ** *
391729 AAGTGATATACTCGTAATTATTTTTAAAA
1 GGGTGCTATTTTCGTAAATATTTTTAAAA
* *
391758 GGGTGCTATTTACATAAATATTTTTAAAA
1 GGGTGCTATTTTCGTAAATATTTTTAAAA
*
391787 GGGTGTTATTTTCGTAAATATTTTTAAAA
1 GGGTGCTATTTTCGTAAATATTTTTAAAA
* * *
391816 AGGTGTTATTTTCATAAATATTTTTAAAA
1 GGGTGCTATTTTCGTAAATATTTTTAAAA
* *
391845 GGGTGTTAGTTTCGTAA
1 GGGTGCTATTTTCGTAA
391862 TTAATTTATG
Statistics
Matches: 163, Mismatches: 24, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
28 25 0.15
29 138 0.85
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.44
Consensus pattern (29 bp):
GGGTGCTATTTTCGTAAATATTTTTAAAA
Found at i:400682 original size:5 final size:5
Alignment explanation
Indices: 400672--400770 Score: 81
Period size: 5 Copynumber: 18.8 Consensus size: 5
400662 TTCGTTCTAT
* * * * * *
400672 TTTTA TTTTA TTTCA TTTCA TTTCA TTTAA TTTTCA TTTCA TTTAA TTTTCA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTT-A
* *
400724 TTTTAA TTTTCA TTTCA TTTTA TTTTG TTTTA TTTTCA TTTTA TTTT
1 TTTT-A TTTT-A TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTT
400771 TATCAAACTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
5 56 0.71
6 23 0.29
ACGTcount: A:0.20, C:0.09, G:0.01, T:0.70
Consensus pattern (5 bp):
TTTTA
Found at i:400689 original size:16 final size:16
Alignment explanation
Indices: 400670--400770 Score: 82
Period size: 16 Copynumber: 6.3 Consensus size: 16
400660 ATTTCGTTCT
* *
400670 ATTTTTATTTTATTTC
1 ATTTTCATTTTATTTA
*
400686 A-TTTCATTTCATTTA
1 ATTTTCATTTTATTTA
*
400701 ATTTTCATTTCATTTA
1 ATTTTCATTTTATTTA
*
400717 ATTTTCATTTTAATTTTC
1 ATTTTCATTTT-A-TTTA
*
400735 A-TTTCATTTTATTTT
1 ATTTTCATTTTATTTA
* *
400750 GTTTT-ATTTTCATTTT
1 ATTTTCATTTT-ATTTA
400766 ATTTT
1 ATTTT
400771 TATCAAACTT
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
15 20 0.28
16 38 0.53
17 10 0.14
18 4 0.06
ACGTcount: A:0.21, C:0.09, G:0.01, T:0.69
Consensus pattern (16 bp):
ATTTTCATTTTATTTA
Found at i:405434 original size:22 final size:21
Alignment explanation
Indices: 405406--405447 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
405396 CATTTTATCT
405406 TTATTATTATCTTTAAAAATTA
1 TTATTATTAT-TTTAAAAATTA
*
405428 TTATTATTATTTTAATAATT
1 TTATTATTATTTTAAAAATT
405448 TTTCCCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATTATTATTTTAAAAATTA
Found at i:407446 original size:133 final size:133
Alignment explanation
Indices: 407088--407504 Score: 527
Period size: 134 Copynumber: 3.1 Consensus size: 133
407078 TTTTCTTTAT
* * *
407088 GGAAGATTGAATCGAGGTAGACTTGTTCCACTATTTCTCATGGAAGATCAAATCTTGAACGAAAG
1 GGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCAGGGAAGATCAAATCTTGAAAGAAAG
* * * *
407153 GGATCTGTTTCGCTTCTTCATGAGGGAAAAT-CATCTATGGGTATGTTGATTCATTC-CACTATT
66 GGATCTGTTTCGCTTCTTCTTGAGGGAAAATAAATC--TGGGGACGTTGATTCATTCTC-CTATT
407216 CTAT-AG
128 CT-TCAG
* * * *
407222 GGAAGATTGAATCGAGGTAGACTTGTTCCACTTTTACTCAGGAAAGATCAAATCTTAAAAGAGAG
1 GGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCAGGGAAGATCAAATCTTGAAAGAAAG
* * * * * *
407287 GGGTATGTTCCGCTTCTTCTTGAGGGAAAAATAAATCTGGGGACGTTCATTAATTCTCCTGTTCT
66 GGATCTGTTTCGCTTCTTCTTGAGGG-AAAATAAATCTGGGGACGTTGATTCATTCTCCTATTCT
407352 TCAG
130 TCAG
* * * *
407356 GGAAGATTGAATCGAGGCATACTTGTTCCAC-ATTACTCAGGGAAGATCAAAACTTGAAAGAAAA
1 GGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCAGGGAAGATCAAATCTTGAAAGAAAG
** * *
407420 AAATCTGTTTCGCTTCTTCTTGAGGGAAAATCATATCTTGGGACGTTGATTCATTCTCCTATTCT
66 GGATCTGTTTCGCTTCTTCTTGAGGGAAAAT-AAATCTGGGGACGTTGATTCATTCTCCTATTCT
407485 TCAG
130 TCAG
407489 GGAAGATTGAATCGAG
1 GGAAGATTGAATCGAG
407505 TTTGATTCAG
Statistics
Matches: 243, Mismatches: 35, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
132 5 0.02
133 97 0.40
134 132 0.54
135 6 0.02
136 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (133 bp):
GGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTCAGGGAAGATCAAATCTTGAAAGAAAG
GGATCTGTTTCGCTTCTTCTTGAGGGAAAATAAATCTGGGGACGTTGATTCATTCTCCTATTCTT
CAG
Found at i:408840 original size:41 final size:40
Alignment explanation
Indices: 408725--408847 Score: 103
Period size: 40 Copynumber: 3.1 Consensus size: 40
408715 TTTTTTTCTA
* * *
408725 TTTTTC-TATTTTCT-TTCTTTTCTCTTTCATTTTCTTTTC
1 TTTTTCATTTTTTCTATTTTTTTCTTTTTCATTTTC-TTTC
* * *
408764 TTTTTCATTTTCTC-ATTTTCCCTT-TTCTTCATTTTCTTTC
1 TTTTTCATTTTTTCTATTTT--TTTCTTTTTCATTTTCTTTC
*
408804 TTTTAT-ATTTTTTCTATTTTTTTCTTTTTCATTTTTCATTC
1 TTTT-TCATTTTTTCTATTTTTTTCTTTTTCA-TTTTCTTTC
408845 TTT
1 TTT
408848 AGACGAAGTA
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
39 8 0.12
40 29 0.44
41 27 0.41
42 2 0.03
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (40 bp):
TTTTTCATTTTTTCTATTTTTTTCTTTTTCATTTTCTTTC
Found at i:408847 original size:17 final size:16
Alignment explanation
Indices: 408712--408839 Score: 57
Period size: 16 Copynumber: 7.5 Consensus size: 16
408702 ATCTTCAACC
408712 CTATTTTTTTCTATTTTT
1 CTATTTTTTTC--TTTTT
408730 CTATTTTCTTTCTTTTCT
1 CTATTTT-TTTCTTTT-T
408748 CTTTCATTTTCTTTTCTTTTT
1 C--T-A-TTT-TTTTCTTTTT
* *
408769 C-A-TTTTCTCATTTT
1 CTATTTTTTTCTTTTT
** * *
408783 CCCTTTTCTTCATTTT
1 CTATTTTTTTCTTTTT
*
408799 CT-TTCTTTTATATTTTTT
1 CTATT-TTTT-T-CTTTTT
408817 CTATTTTTTTCTTTTT
1 CTATTTTTTTCTTTTT
408833 C-ATTTTT
1 CTATTTTT
408840 CATTCTTTAG
Statistics
Matches: 87, Mismatches: 10, Indels: 29
0.69 0.08 0.23
Matches are distributed among these distances:
14 9 0.10
15 10 0.11
16 20 0.23
17 7 0.08
18 19 0.22
19 6 0.07
20 1 0.01
21 3 0.03
22 11 0.13
23 1 0.01
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (16 bp):
CTATTTTTTTCTTTTT
Found at i:411191 original size:19 final size:21
Alignment explanation
Indices: 411155--411204 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
411145 ATTCAATCAA
411155 TATCAATACCGAAAGGGAA-G
1 TATCAATACCGAAAGGGAAGG
*
411175 TATCGATACCG-AAGGGAAGG
1 TATCAATACCGAAAGGGAAGG
411195 TATCAATACC
1 TATCAATACC
411205 ATTTCAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (21 bp):
TATCAATACCGAAAGGGAAGG
Found at i:411796 original size:54 final size:54
Alignment explanation
Indices: 411620--412045 Score: 352
Period size: 54 Copynumber: 7.9 Consensus size: 54
411610 ACCAAACAGG
* ** *
411620 CACTAAGTGTGCATCTCACTA-AATTCATCCACTATG--GATGAATGTCCATTTCGA
1 CACTAAGTGTGCATTTCAC-AGAATTCAT-C-CTATGTAGATGAATAACCGTTTCGA
* * *
411674 CACTAAGGGTGCATTTCAC-GAATTCATCCTATG-AGGATG-ATAACCGTTTTGG
1 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTA-GATGAATAACCGTTTCGA
*
411726 CACTAA-TGGTGTATTTCACAGAATTCATCCTATGTAGATGAATAACCGTTTCGA
1 CACTAAGT-GTGCATTTCACAGAATTCATCCTATGTAGATGAATAACCGTTTCGA
* * * * *
411780 CACTAAGTATGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTTGT
1 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTAGATGAATAACCGTTTCGA
* * * * * *
411834 CACTAAGTGTGCATTTTACAAAATTCATCCTACGTGGATGAATAACCGTATCGG
1 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTAGATGAATAACCGTTTCGA
* * *
411888 CACTAAATGTGCATTTCAC-GTAATTCATCCTATGTGGATGAATAACCATTTCAGA
1 CACTAAGTGTGCATTTCACAG-AATTCATCCTATGTAGATGAATAACCGTTTC-GA
* * ** * * * * * *
411943 -ACTAAAG-GTGCAATACATGGAATTCATCATAAGTTGATGAATAATCG-TACAGG
1 CACT-AAGTGTGCATTTCACAGAATTCATCCTATGTAGATGAATAACCGTTTC-GA
** * * *
411996 CACTGTGTGTGCAAATTCACAGAATTCATCATAAGTAGATGAATAACCGT
1 CACTAAGTGTGC-ATTTCACAGAATTCATCCTATGTAGATGAATAACCGT
412046 ACAAGCACTG
Statistics
Matches: 306, Mismatches: 50, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
51 5 0.02
52 25 0.08
53 34 0.11
54 206 0.67
55 36 0.12
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACAGAATTCATCCTATGTAGATGAATAACCGTTTCGA
Found at i:411874 original size:108 final size:108
Alignment explanation
Indices: 411618--411934 Score: 417
Period size: 108 Copynumber: 3.0 Consensus size: 108
411608 TTACCAAACA
* * * ** * *
411618 GGCACTAAGTGTGCATCTCACTAAATTCATCC-ACTATGGATGAATGTCCATTTCGACACTAAGG
1 GGCACTAAGTGTGCATTTCACAAAATTCATCCTAC-GTGGATGAATAACCGTTTCGACACTAAGT
*
411682 GTGCATTTCAC-GAATTCATCCTATGAGGATG-ATAACCGTTTT
65 GTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTT
* * * *
411724 GGCACTAA-TGGTGTATTTCACAGAATTCATCCTATGTAGATGAATAACCGTTTCGACACTAAGT
1 GGCACTAAGT-GTGCATTTCACAAAATTCATCCTACGTGGATGAATAACCGTTTCGACACTAAGT
*
411788 ATGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTT
65 GTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTT
* * * * *
411832 GTCACTAAGTGTGCATTTTACAAAATTCATCCTACGTGGATGAATAACCGTATCGGCACTAAATG
1 GGCACTAAGTGTGCATTTCACAAAATTCATCCTACGTGGATGAATAACCGTTTCGACACTAAGTG
*
411897 TGCATTTCACGTAATTCATCCTATGTGGATGAATAACC
66 TGCATTTCACGGAATTCATCCTATGTGGATGAATAACC
411935 ATTTCAGAAC
Statistics
Matches: 182, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
105 1 0.01
106 59 0.32
107 20 0.11
108 101 0.55
109 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (108 bp):
GGCACTAAGTGTGCATTTCACAAAATTCATCCTACGTGGATGAATAACCGTTTCGACACTAAGTG
TGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTT
Found at i:411930 original size:162 final size:161
Alignment explanation
Indices: 411620--411947 Score: 396
Period size: 160 Copynumber: 2.0 Consensus size: 161
411610 ACCAAACAGG
* * **
411620 CACTAAGTGTGCATCTCACTAAATTCATCCACTATGGATGAATGTCCATTTCGACACTAAGGGTG
1 CACTAAGTATGCATCTCACGAAATTCATCCACTATGGATGAATAACCATTTCGACACTAAGGGTG
* * * * *
411685 CATTTCACGAATTCATCCTATGAGGATGATAACCGTTTTGGCACTAATGGTGTATTTCACAGAAT
66 CATTTCACAAATTCATCCTACGAGGATGATAACCGTATCGGCACTAATGGTGCATTTCACAGAAT
*
411750 TCATCCTATGTAGATGAATAACCGTTTC-GA
131 TCATCCTATGTAGATGAATAACCATTTCAGA
* * * * * * *
411780 CACTAAGTATGCATTTCACGGAATTCATCCTA-TGTGGATGAATAACCGTTTTGTCACTAAGTGT
1 CACTAAGTATGCATCTCACGAAATTCATCC-ACTATGGATGAATAACCATTTCGACACTAAGGGT
* *
411844 GCATTTTACAAAATTCATCCTACGTGGATGAATAACCGTATCGGCACTAAAT-GTGCATTTCAC-
65 GCATTTCAC-AAATTCATCCTACGAGGATG-ATAACCGTATCGGCACT-AATGGTGCATTTCACA
*
411907 GTAATTCATCCTATGTGGATGAATAACCATTTCAGA
127 G-AATTCATCCTATGTAGATGAATAACCATTTCAGA
411943 -ACTAA
1 CACTAA
411948 AGGTGCAATA
Statistics
Matches: 142, Mismatches: 20, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
160 59 0.42
161 19 0.13
162 59 0.42
163 5 0.04
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Consensus pattern (161 bp):
CACTAAGTATGCATCTCACGAAATTCATCCACTATGGATGAATAACCATTTCGACACTAAGGGTG
CATTTCACAAATTCATCCTACGAGGATGATAACCGTATCGGCACTAATGGTGCATTTCACAGAAT
TCATCCTATGTAGATGAATAACCATTTCAGA
Found at i:411967 original size:162 final size:160
Alignment explanation
Indices: 411674--411986 Score: 391
Period size: 162 Copynumber: 1.9 Consensus size: 160
411664 TCCATTTCGA
* * * * *
411674 CACTAAGGGTGCATTTCACGAATTCATCCTATGAGGATGATAACCGTTTTGGCACTAATGGTGTA
1 CACTAAGGGTGCATTTCACAAATTCATCCTACGAGGATGATAACCGTATCGGCACTAATGGTGCA
* * *
411739 TTTCACAGAATTCATCCTATGTAGATGAATAACCGTTTCGACACTAAGTATGCATTTCACGGAAT
66 TTTCACAGAATTCATCCTATGTAGATGAATAACCATTTCGACACTAAGTATGCAATACACGGAAT
* *
411804 TCATCCTATGTGGATGAATAACCGTTTTGT
131 TCATCATAAGTGGATGAATAACCGTTTTGT
* * *
411834 CACTAAGTGTGCATTTTACAAAATTCATCCTACGTGGATGAATAACCGTATCGGCACTAAAT-GT
1 CACTAAGGGTGCATTTCAC-AAATTCATCCTACGAGGATG-ATAACCGTATCGGCACT-AATGGT
* *
411898 GCATTTCAC-GTAATTCATCCTATGTGGATGAATAACCATTTCAGA-ACTAAAG-GTGCAATACA
63 GCATTTCACAG-AATTCATCCTATGTAGATGAATAACCATTTC-GACACT-AAGTATGCAATACA
* *
411960 TGGAATTCATCATAAGTTGATGAATAA
125 CGGAATTCATCATAAGTGGATGAATAA
411987 TCGTACAGGC
Statistics
Matches: 130, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
160 17 0.13
161 18 0.14
162 87 0.67
163 8 0.06
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (160 bp):
CACTAAGGGTGCATTTCACAAATTCATCCTACGAGGATGATAACCGTATCGGCACTAATGGTGCA
TTTCACAGAATTCATCCTATGTAGATGAATAACCATTTCGACACTAAGTATGCAATACACGGAAT
TCATCATAAGTGGATGAATAACCGTTTTGT
Found at i:412031 original size:55 final size:55
Alignment explanation
Indices: 411962--412221 Score: 312
Period size: 55 Copynumber: 4.7 Consensus size: 55
411952 GCAATACATG
* *
411962 GAATTCATCATAAGTTGATGAATAATCGTACAGGCACTGTGTGTGCAAATTCACA
1 GAATTCATCATAAGTTGATGAATAACCGTACAGGCACTGTGTGTGCAAATCCACA
* * *
412017 GAATTCATCATAAGTAGATGAATAACCGTACAAGCACTGTGTGTACAAATCCACA
1 GAATTCATCATAAGTTGATGAATAACCGTACAGGCACTGTGTGTGCAAATCCACA
* * * * *
412072 GAATTCATCATGAGTTGATAAATAGCCGTACATGCACTATGTGTATGCAAATCCAC-
1 GAATTCATCATAAGTTGATGAATAACCGTACAGGCAC--TGTGTGTGCAAATCCACA
* * * *
412128 GAAATTCATCATAAGTTGATGAATAGCCGTACAGG-AGCTGTGTGTGTACAT--ACGT
1 G-AATTCATCATAAGTTGATGAATAACCGTACAGGCA-CTGTGTGTGCAAATCCAC-A
412183 GAAATTCATCATAAGTTGATGAATAACCGTACAGGCACT
1 G-AATTCATCATAAGTTGATGAATAACCGTACAGGCACT
412222 AAGTATGCAT
Statistics
Matches: 179, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
53 2 0.01
55 128 0.72
56 3 0.02
57 46 0.26
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (55 bp):
GAATTCATCATAAGTTGATGAATAACCGTACAGGCACTGTGTGTGCAAATCCACA
Found at i:412158 original size:112 final size:112
Alignment explanation
Indices: 411962--412222 Score: 325
Period size: 112 Copynumber: 2.3 Consensus size: 112
411952 GCAATACATG
* * *
411962 GAATTCATCATAAGTTGATGAATAATCGTACAGGCAC--TGTGTGTGCAAATTCACAGAATTCAT
1 GAATTCATCATAAGTTGATGAATAACCGTACAGGCACTATGTGTATGCAAATCCACAGAATTCAT
412025 CATAAGTAGATGAATAACCGTACA-AGCACTGTGTGTACAAATCCACA
66 CATAAGTAGATGAATAACCGTACAGAGCACTGTGTGTACAAA-CCACA
* * * *
412072 GAATTCATCATGAGTTGATAAATAGCCGTACATGCACTATGTGTATGCAAATCCAC-GAAATTCA
1 GAATTCATCATAAGTTGATGAATAACCGTACAGGCACTATGTGTATGCAAATCCACAG-AATTCA
* * ** * ***
412136 TCATAAGTTGATGAATAGCCGTACAGGAGCTGTGTGTGTACATACGTGA
65 TCATAAGTAGATGAATAACCGTACA-GAGCACTGTGTGTACAAACCACA
412185 -AATTCATCATAAGTTGATGAATAACCGTACAGGCACTA
1 GAATTCATCATAAGTTGATGAATAACCGTACAGGCACTA
412223 AGTATGCATA
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
110 32 0.25
111 1 0.01
112 78 0.61
113 2 0.02
114 14 0.11
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (112 bp):
GAATTCATCATAAGTTGATGAATAACCGTACAGGCACTATGTGTATGCAAATCCACAGAATTCAT
CATAAGTAGATGAATAACCGTACAGAGCACTGTGTGTACAAACCACA
Found at i:412963 original size:45 final size:45
Alignment explanation
Indices: 412926--413051 Score: 189
Period size: 45 Copynumber: 2.8 Consensus size: 45
412916 GTATAAAAGG
* *
412926 CATGAAATGATGCCATAATTGAAACGCATATGGGTGTATTATCGA
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGTATTATCGA
* * *
412971 CATGAAAGGATGTCATAACTGAAATGCATATGGGTGCATTATCGA
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGTATTATCGA
* *
413016 CATGAAAGGATGCGATAATTGAAATGCATATAGGTG
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTG
413052 CATCATAAAC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 72 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.27
Consensus pattern (45 bp):
CATGAAAGGATGCCATAATTGAAATGCATATGGGTGTATTATCGA
Found at i:413052 original size:45 final size:44
Alignment explanation
Indices: 412926--413073 Score: 188
Period size: 45 Copynumber: 3.3 Consensus size: 44
412916 GTATAAAAGG
* * *
412926 CATGAAATGATGCCATAATTGAAACGCATATGGGTGTATTATCGA
1 CATGAAAGGATG-CATAATTGAAATGCATATGGGTGCATTATCGA
*
412971 CATGAAAGGATGTCATAACTGAAATGCATATGGGTGCATTATCGA
1 CATGAAAGGATG-CATAATTGAAATGCATATGGGTGCATTATCGA
* * **
413016 CATGAAAGGATGCGATAATTGAAATGCATATAGGTGCATCATAAA
1 CATGAAAGGATGC-ATAATTGAAATGCATATGGGTGCATTATCGA
*
413061 CATGAATGGATGC
1 CATGAAAGGATGC
413074 TATCAATGAA
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
44 1 0.01
45 90 0.99
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (44 bp):
CATGAAAGGATGCATAATTGAAATGCATATGGGTGCATTATCGA
Found at i:416840 original size:20 final size:20
Alignment explanation
Indices: 416812--416852 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
416802 TAATCTAGTA
*
416812 CGAAAGGAAAGTATCGATAC
1 CGAAAGGAAAGTATCAATAC
* *
416832 CGAAGGGAAGGTATCAATAC
1 CGAAAGGAAAGTATCAATAC
416852 C
1 C
416853 ATTTCAAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.27, T:0.15
Consensus pattern (20 bp):
CGAAAGGAAAGTATCAATAC
Found at i:417386 original size:53 final size:53
Alignment explanation
Indices: 417268--417638 Score: 428
Period size: 54 Copynumber: 6.9 Consensus size: 53
417258 TTACCAAATA
417268 GGCACTAAGTGTGCATTTCACGGAATT-ATCCGT-TGTGGATGAATAACCGTTTC
1 GGCACTAAG-GTGCATTTCACGGAATTCATCC-TATGTGGATGAATAACCGTTTC
* * *
417321 -GCACTAAGGGTGCATTTCACGGAATTCATCTTATATGGATG-ATGACCGTTTC
1 GGCACTAA-GGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * *
417373 AGCACTAATGGTGCATTTCAC-GAATTTATCCTATGTAGATGAATAATCGTTTC
1 GGCACTAA-GGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
417426 GGCACTAATCGTGCATTTCACGGAATTCATCCTACGTGGATGAATAATCATTTT
1 GGCACTAA-GGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
417480 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCATTTC
1 GGCACTAAG-GTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
417534 GGAACTAAGTGTGCATTTCATGGAATTCATTCTATGTGGATGAATAACCGTTTC
1 GGCACTAAG-GTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * * *
417588 GGTACTAAAGGTGCAATACACGGAATTCATCATAAGTTGATGAATAACCGT
1 GGCACT-AAGGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGT
417639 ACAAGCACAA
Statistics
Matches: 277, Mismatches: 33, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
52 51 0.18
53 58 0.21
54 165 0.60
55 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.33
Consensus pattern (53 bp):
GGCACTAAGGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:417654 original size:108 final size:108
Alignment explanation
Indices: 417268--417693 Score: 390
Period size: 108 Copynumber: 4.0 Consensus size: 108
417258 TTACCAAATA
*
417268 GGCACT-AAGTGTGCATTTCACGGAATT-ATCCGT-TGTGGATGAATAACCGTTTC-GCACTAA-
1 GGCACTAAAG-GTGCATTTCACGGAATTCATCC-TATGTAGATGAATAACCG-TTCGGCACTAAT
* * *
417328 GGGTGCATTTCACGGAATTCA-TCTTATATGGATG-ATGACCGTTTC
63 GTGTGCATTTCACGGAATTCATTC-TATGTGGATGAATAACCGTTTC
* * * * *
417373 AGCACTAATGGTGCATTTCAC-GAATTTATCCTATGTAGATGAATAATCGTTTCGGCACTAAT-C
1 GGCACTAAAGGTGCATTTCACGGAATTCATCCTATGTAGATGAATAACCG-TTCGGCACTAATGT
* * * * *
417436 GTGCATTTCACGGAATTCATCCTACGTGGATGAATAATCATTTT
65 GTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTC
* ** *
417480 GGCACT-AAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCATTTCGGAACTAA-G
1 GGCACTAAAG-GTGCATTTCACGGAATTCATCCTATGTAGATGAATAA-CCGTTCGGCACTAATG
*
417543 TGTGCATTTCATGGAATTCATTCTATGTGGATGAATAACCGTTTC
64 TGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTC
* * * * * * * *
417588 GGTACTAAAGGTGCAATACACGGAATTCATCATAAGTTGATGAATAACCGTACAAGCAC-AATGT
1 GGCACTAAAGGTGCATTTCACGGAATTCATCCTATGTAGATGAATAACCGTTC-GGCACTAATGT
* * * * * *
417652 GTGCAAATCCACGAAATTCATTATAAGTTGATGAATAACCGT
65 GTGC-ATTTCACGGAATTCATTCTATGTGGATGAATAACCGT
417694 AGAGGCACTG
Statistics
Matches: 261, Mismatches: 45, Indels: 26
0.79 0.14 0.08
Matches are distributed among these distances:
104 6 0.02
105 38 0.15
106 38 0.15
107 29 0.11
108 117 0.45
109 33 0.13
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (108 bp):
GGCACTAAAGGTGCATTTCACGGAATTCATCCTATGTAGATGAATAACCGTTCGGCACTAATGTG
TGCATTTCACGGAATTCATTCTATGTGGATGAATAACCGTTTC
Found at i:417685 original size:55 final size:54
Alignment explanation
Indices: 417609--417857 Score: 259
Period size: 55 Copynumber: 4.5 Consensus size: 54
417599 TGCAATACAC
**
417609 GGAATTCATCATAAGTTGATGAATAACCGTACAAGCACAATGTGTGCAAATCCA
1 GGAATTCATCATAAGTTGATGAATAACCGTACAAGCACTGTGTGTGCAAATCCA
* * * *
417663 CGAAATTCATTATAAGTTGATGAATAACCGTAGAGGCACTGTGTGTGCAAATCCAA
1 -GGAATTCATCATAAGTTGATGAATAACCGTACAAGCACTGTGTGTGCAAATCC-A
* * * * * *
417719 AGAATTCATTATGAGTTAATGAATAGCCGTA-AAGGC-CTGTGTGTGTGCAAATCAA
1 GGAATTCATCATAAGTTGATGAATAACCGTACAA-GCAC--TGTGTGTGCAAATCCA
* * * *
417774 TGGAATTCATCATGAGTTGATGAATAGCCGTACATGTACTGTGTGTGCAAATCCGA
1 -GGAATTCATCATAAGTTGATGAATAACCGTACAAGCACTGTGTGTGCAAATCC-A
**
417830 GGAATTCATCATAAAATGATGAATAACC
1 GGAATTCATCATAAGTTGATGAATAACC
417858 TTGTAGGCAC
Statistics
Matches: 163, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
54 2 0.01
55 114 0.70
56 45 0.28
57 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (54 bp):
GGAATTCATCATAAGTTGATGAATAACCGTACAAGCACTGTGTGTGCAAATCCA
Found at i:417852 original size:111 final size:111
Alignment explanation
Indices: 417649--417854 Score: 268
Period size: 111 Copynumber: 1.9 Consensus size: 111
417639 ACAAGCACAA
* * *
417649 TGTGTGCAAATCCACGAAATTCATTATAAGTTGATGAATAACCGTAGAGGCACTGTGTGTGCAAA
1 TGTGTGCAAATCAACGAAATTCATCATAAGTTGATGAATAACCGTACAGGCACTGTGTGTGCAAA
* * **
417714 TCCAAAGAATTCATTATGAGTTAATGAATAGCCGTAAAGGCCTGTG
66 TCCAAAGAATTCATCATAAAATAATGAATAGCCGTAAAGGCCTGTG
* * * * * *
417760 TGTGTGCAAATCAATGGAATTCATCATGAGTTGATGAATAGCCGTACATGTACTGTGTGTGCAAA
1 TGTGTGCAAATCAACGAAATTCATCATAAGTTGATGAATAACCGTACAGGCACTGTGTGTGCAAA
* * *
417825 TCCGAGGAATTCATCATAAAATGATGAATA
66 TCCAAAGAATTCATCATAAAATAATGAATA
417855 ACCTTGTAGG
Statistics
Matches: 79, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
111 79 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (111 bp):
TGTGTGCAAATCAACGAAATTCATCATAAGTTGATGAATAACCGTACAGGCACTGTGTGTGCAAA
TCCAAAGAATTCATCATAAAATAATGAATAGCCGTAAAGGCCTGTG
Found at i:418405 original size:68 final size:68
Alignment explanation
Indices: 418273--418405 Score: 169
Period size: 68 Copynumber: 2.0 Consensus size: 68
418263 ATTAATGGAT
* * * *
418273 TAACTGTGCATTTGACAGAAAGGTGTCAACCATGCAAGTTAGATGAAAGGCTAAGTGCCTTTGAG
1 TAACTGTGAAATTGACAGAAAGGTGTCAAACATGCAAGTTAGATGAAAGGCTAAGTGCCGTTGAG
418338 GCC
66 GCC
* * * * *
418341 TAACTGTGAAATTGGCAGAAAGGTGTCAAATATG-ACAGTTAGATGAATGGTTAAGTGTCGTTGA
1 TAACTGTGAAATTGACAGAAAGGTGTCAAACATGCA-AGTTAGATGAAAGGCTAAGTGCCGTTGA
418405 G
65 G
418406 TAAACAATTA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
67 1 0.02
68 54 0.98
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.27
Consensus pattern (68 bp):
TAACTGTGAAATTGACAGAAAGGTGTCAAACATGCAAGTTAGATGAAAGGCTAAGTGCCGTTGAG
GCC
Found at i:418486 original size:81 final size:81
Alignment explanation
Indices: 418337--418486 Score: 183
Period size: 81 Copynumber: 1.9 Consensus size: 81
418327 GTGCCTTTGA
* * * * **
418337 GGCCTAACTGTGAAATTGGCAGAAAGGTGTCAAATATGACAGTTAGATGAATGGTTAAGTGTCGT
1 GGCCTAACTGTGAAATTGACAGAAAGATGTCAAATATGACAGTTAGATGAAAGGTTAAATACCGT
418402 TGAGTAAACAATTAAT
66 TGAGTAAACAATTAAT
* * * * * * *
418418 GGCCTAGCTGTGCATTTGACAGAAATATGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTT
1 GGCCTAACTGTGAAATTGACAGAAAGATGTCAAATATGACAGTTAGATGAAAGGTTAAATACCGT
418483 TGAG
66 TGAG
418487 AAAGACTAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
81 56 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (81 bp):
GGCCTAACTGTGAAATTGACAGAAAGATGTCAAATATGACAGTTAGATGAAAGGTTAAATACCGT
TGAGTAAACAATTAAT
Found at i:418633 original size:45 final size:45
Alignment explanation
Indices: 418569--418691 Score: 210
Period size: 45 Copynumber: 2.7 Consensus size: 45
418559 GTGTATAAAA
*
418569 GGCATGAAAGGATGCCATAATTGAAATGCATATGCGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGCGTACATTATC
*
418614 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTACATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGCGTACATTATC
* *
418659 GGCATGAAAGGATGCCATAATTAAAATTCATAT
1 GGCATGAAAGGATGCCATAATTGAAATGCATAT
418692 AGGTTCATCA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAATTGAAATGCATATGCGTACATTATC
Found at i:428497 original size:14 final size:14
Alignment explanation
Indices: 428478--428522 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
428468 CCAATGACGA
428478 AAGTTTATGCCATT
1 AAGTTTATGCCATT
*
428492 AAGTTTAT-CCTTCT
1 AAGTTTATGCCAT-T
428506 AAAGTTTATGCCATT
1 -AAGTTTATGCCATT
428521 AA
1 AA
428523 ATCTACAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.12
14 11 0.42
15 9 0.35
16 3 0.12
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (14 bp):
AAGTTTATGCCATT
Found at i:428523 original size:15 final size:15
Alignment explanation
Indices: 428477--428523 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
428467 ACCAATGACG
428477 AAAGTTTATGCCATT
1 AAAGTTTATGCCATT
*
428492 -AAGTTTAT-CCTTCT
1 AAAGTTTATGCCAT-T
428506 AAAGTTTATGCCATT
1 AAAGTTTATGCCATT
428521 AAA
1 AAA
428524 TCTACAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 9 0.33
15 12 0.44
16 3 0.11
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (15 bp):
AAAGTTTATGCCATT
Found at i:433564 original size:23 final size:23
Alignment explanation
Indices: 433538--433590 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
433528 CGTAGTGTCA
* * *
433538 CATAGATTTGTCCCGAAGGACCG
1 CATAGAATTATCCCGAAAGACCG
433561 CATAGAATTATCCCGAAAGACCG
1 CATAGAATTATCCCGAAAGACCG
*
433584 CGTAGAA
1 CATAGAA
433591 CCCTCGACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CATAGAATTATCCCGAAAGACCG
Found at i:433733 original size:15 final size:15
Alignment explanation
Indices: 433693--433777 Score: 89
Period size: 15 Copynumber: 5.7 Consensus size: 15
433683 AAGTATCATT
* *
433693 TATTCACGTAGACCA
1 TATTCACATAGAACA
* *
433708 CATTCAAATAGAACA
1 TATTCACATAGAACA
*
433723 TATCCACATAGAACA
1 TATTCACATAGAACA
* *
433738 TTTTCACGTAGAACA
1 TATTCACATAGAACA
*
433753 TATTCACATATAACA
1 TATTCACATAGAACA
*
433768 CATTCACATA
1 TATTCACATA
433778 CTAATAAAAT
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 56 1.00
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (15 bp):
TATTCACATAGAACA
Found at i:434784 original size:18 final size:19
Alignment explanation
Indices: 434761--434796 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
434751 AAGCTTCTAT
*
434761 ACCAA-CCAAAGATTCAAA
1 ACCAACCCAAAAATTCAAA
434779 ACCAACCCAAAAATTCAA
1 ACCAACCCAAAAATTCAA
434797 GAAACAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.56, C:0.31, G:0.03, T:0.11
Consensus pattern (19 bp):
ACCAACCCAAAAATTCAAA
Found at i:446320 original size:16 final size:16
Alignment explanation
Indices: 446299--446330 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
446289 TTAGGTTCCC
446299 AAATCTTGTCTTACCT
1 AAATCTTGTCTTACCT
*
446315 AAATCTTGTTTTACCT
1 AAATCTTGTCTTACCT
446331 TCGGTAGGGT
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:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (16 bp):
AAATCTTGTCTTACCT
Found at i:457530 original size:363 final size:364
Alignment explanation
Indices: 456849--457544 Score: 1063
Period size: 363 Copynumber: 1.9 Consensus size: 364
456839 CAAATGTTTG
456849 AACCACATTTTAACATGCTCTCATGTGGGAGGTATCTACTGGCAGCCTCTTAAGAGTGACTAAGG
1 AACCACATTTTAACATGCTCTCATGTGGGAGGTATCTACTGGCAGCCTCTTAAGAGTGACTAAGG
456914 GCATCAAGTTAAGGGAAGAGCCATTGTCTAAATAGTACACTAGGTAGGGAATGTCACTTACAATG
66 GCATCAAGTTAAGGGAAGAGCCATTGTCTAAATAGTACACTAGGTAGGGAATGTCACTTACAATG
* * *
456979 GGTATTGATGTGTAATGCCTTTGCTCTGCCCCTACCCTCAAGCTGAATCTCATCATCAAAAAATA
131 GGCAGTGATGTGTAATGCCTTTGCTCTGCCCCTACCATCAAGCTGAATCTCATCATCAAAAAATA
* * *
457044 AGATAAGATTATCAACTTAGATATTGTTAACCAGTCAATATAGCTTGTTGACTAGTATGTGTTTC
196 AGATAAGATTATCAACTTAGATATTGTTAACCAATCAATATAGCTTATTGACTAGTATGTATTTC
* * *
457109 AGCAAAAATATCTTACTCAAGACCTTTAGCAACGCCTCACTATATGCTTCTGAACTCAGCAACAA
261 AGCAAAAATATCTGACTCAAGACCTTTAGCAACGCCTCACTATATGCCTCTAAACTCAGCAACAA
457174 TGCCAACAGTGCCTTCTTTTTCATCCTATCGAATATTCA
326 TGCCAACAGTGCCTTCTTTTTCATCCTATCGAATATTCA
* * *
457213 AACCACATTTTGACATGCTCTCATGTGGGAGGTATCTACTGGTAGCCTCTTGAGAGTGACTAAGG
1 AACCACATTTTAACATGCTCTCATGTGGGAGGTATCTACTGGCAGCCTCTTAAGAGTGACTAAGG
* * * * *
457278 GCATCACGTTAAGGGTAGAGCCATTGTCT-ATTAGTACACTAGGTAGGGCATGTCACTTGCAATG
66 GCATCAAGTTAAGGGAAGAGCCATTGTCTAAATAGTACACTAGGTAGGGAATGTCACTTACAATG
* * ** * *
457342 GGCAGTGATGTGTAATGCCTTTTCTCTGCCCCTACTATCGGGTTGAATCTCATCATCAAAAAATG
131 GGCAGTGATGTGTAATGCCTTTGCTCTGCCCCTACCATCAAGCTGAATCTCATCATCAAAAAATA
* * *
457407 AGATAAGGTTATCAGCTTGGATATTGTTAACCAATCAATATAGCTTATTGACTAGTATGTATTTC
196 AGATAAGATTATCAACTTAGATATTGTTAACCAATCAATATAGCTTATTGACTAGTATGTATTTC
* * *** * *
457472 AGCACAAATATCTGACTCAAGGCCTTTAGCTGTGCCTC-CTTGTGTGCCTCTAAACTCAGCAACA
261 AGCAAAAATATCTGACTCAAGACCTTTAGCAACGCCTCAC-TATATGCCTCTAAACTCAGCAACA
*
457536 ATGCTAACA
325 ATGCCAACA
457545 TTGAAATACT
Statistics
Matches: 297, Mismatches: 34, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
362 1 0.00
363 207 0.70
364 89 0.30
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (364 bp):
AACCACATTTTAACATGCTCTCATGTGGGAGGTATCTACTGGCAGCCTCTTAAGAGTGACTAAGG
GCATCAAGTTAAGGGAAGAGCCATTGTCTAAATAGTACACTAGGTAGGGAATGTCACTTACAATG
GGCAGTGATGTGTAATGCCTTTGCTCTGCCCCTACCATCAAGCTGAATCTCATCATCAAAAAATA
AGATAAGATTATCAACTTAGATATTGTTAACCAATCAATATAGCTTATTGACTAGTATGTATTTC
AGCAAAAATATCTGACTCAAGACCTTTAGCAACGCCTCACTATATGCCTCTAAACTCAGCAACAA
TGCCAACAGTGCCTTCTTTTTCATCCTATCGAATATTCA
Found at i:473266 original size:22 final size:19
Alignment explanation
Indices: 473216--473285 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 19
473206 ACAAAAATTT
473216 TATCAATACCATAGTAGGG
1 TATCAATACCATAGTAGGG
**
473235 TATCGGTACCATAGTATGGTAG
1 TATCAATACCATAGTA-GG--G
* *
473257 TATCCATACCATGGTAGGGG
1 TATCAATACCATAGTA-GGG
*
473277 TATCGATAC
1 TATCAATAC
473286 TGAAGAGCCA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 14 0.34
20 11 0.27
22 16 0.39
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (19 bp):
TATCAATACCATAGTAGGG
Found at i:473799 original size:58 final size:58
Alignment explanation
Indices: 473612--473945 Score: 489
Period size: 58 Copynumber: 5.8 Consensus size: 58
473602 ATGGCACTAA
*
473612 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTC-GTATTTGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
* * **
473669 GTGTGAAAAAAGTTAAGAAATTCATACTAAG-GTATAAATTT-TGTATTGAACACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
473725 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
* *
473783 GTGTGCAAAAATTTAAGAAATTCATATTAAGTGTATGAATTT-TCGTATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGCACTTC
* * * *
473841 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTACGGATTTTTGTATTGGGTACTT-
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
* * * *
473898 GGGTGCCAAAAGTTAAGAGATTCATACTAAGTGTATGAATTTCCGTAT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTAT
473946 GGGAAATATG
Statistics
Matches: 249, Mismatches: 23, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
56 50 0.20
57 81 0.33
58 117 0.47
59 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
Found at i:479640 original size:58 final size:58
Alignment explanation
Indices: 479577--479972 Score: 585
Period size: 58 Copynumber: 6.8 Consensus size: 58
479567 ATGGAACTAA
* *
479577 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGGCATTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* *
479635 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTATATGAATTTTCGTATTGTGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* * * * *
479693 ATGTGCAAAAAGTTAATAAATTCATACTAAGTGTATGAATTTCCGCATTGGGCACTTA
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* *
479751 ATGTGCAAAAAGTTAAGAAATTCATATTAAGTGTATGAATTTTCGTATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* * * * *
479809 GTGTGGAAAAAGTTAAGAAATTCATACTAACTGTATAAATTTCCATATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* * * *
479867 GTGTACAAAAAGTTAAGAAATTAATACTAAGTGTATGAATTTTCATATTGGACACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* * *
479925 ATGTGCAAAAAGTTAAGAGATTCATACTAAGTGTATGAATTTCCGTAT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
479973 GGGAAATGTG
Statistics
Matches: 302, Mismatches: 36, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 302 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
Found at i:493279 original size:13 final size:13
Alignment explanation
Indices: 493261--493296 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
493251 CAGAACTGAA
493261 CTAAGGCTCAAAT
1 CTAAGGCTCAAAT
*
493274 CTAAGGCTCGAAT
1 CTAAGGCTCAAAT
*
493287 CAAAGGCTCA
1 CTAAGGCTCA
493297 TCTACTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (13 bp):
CTAAGGCTCAAAT
Found at i:495430 original size:176 final size:175
Alignment explanation
Indices: 495220--495568 Score: 567
Period size: 176 Copynumber: 2.0 Consensus size: 175
495210 TGTATCATAT
*
495220 AATCAAATATAAAGCTAAAAAATTAAAATTAAATCAAGATAAATAAAT-AATAAACTTCTCATTC
1 AATCAAATATAAAACTAAAAAATTAAAATTAAATCAAGATAAATAAATAAATAAA-TTCTCATTC
* * * *
495284 AAAATCCACCACTGATTTTCATTAAGAAATCTCAAAGAAGGCTTGATTTATGAAGATCTAATTGA
65 AAAATCCACCACTGATTTTCATTAAGAAACCTCAAAGAAGGCTTAATTCATGAAAATCTAATTGA
495349 AAGCCTTTTCCTTAT-TCATTGGTTCTCTCATTCAATGGGATTTTAA
130 AAGCCTTTTCCTTATAT-ATTGGTTCTCTCATTCAATGGGATTTTAA
** *
495395 AATCAAATATAAAACTCAAAATTTTAAAATTAAATCAAGATAAATAAATAAATAAATTTTCATTC
1 AATCAAATATAAAACT-AAAAAATTAAAATTAAATCAAGATAAATAAATAAATAAATTCTCATTC
* *
495460 AAAATCCACCACTGATTTTCATTGAGAAACCTCAAGGAAGGCTTAATTCATGAAAATCTAATTGA
65 AAAATCCACCACTGATTTTCATTAAGAAACCTCAAAGAAGGCTTAATTCATGAAAATCTAATTGA
495525 AAGCCTTTTCCTTATATATTGGTTCTCTCATTCAATGGGATTTT
130 AAGCCTTTTCCTTATATATTGGTTCTCTCATTCAATGGGATTTT
495569 CAAACAACAT
Statistics
Matches: 161, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
175 15 0.09
176 139 0.86
177 7 0.04
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (175 bp):
AATCAAATATAAAACTAAAAAATTAAAATTAAATCAAGATAAATAAATAAATAAATTCTCATTCA
AAATCCACCACTGATTTTCATTAAGAAACCTCAAAGAAGGCTTAATTCATGAAAATCTAATTGAA
AGCCTTTTCCTTATATATTGGTTCTCTCATTCAATGGGATTTTAA
Found at i:501295 original size:18 final size:18
Alignment explanation
Indices: 501272--501309 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
501262 CGTGAGGATT
501272 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
501290 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
501308 GG
1 GG
501310 CATCTGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.21, G:0.47, T:0.16
Consensus pattern (18 bp):
GGGCAGTGGTCCAGCATG
Found at i:509781 original size:18 final size:18
Alignment explanation
Indices: 509758--509795 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
509748 CGTGAGGATT
*
509758 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAACATG
509776 GGGCAGTGGTCCAACATG
1 GGGCAGTGGTCCAACATG
509794 GG
1 GG
509796 CATCTGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.21, G:0.45, T:0.16
Consensus pattern (18 bp):
GGGCAGTGGTCCAACATG
Found at i:513019 original size:19 final size:20
Alignment explanation
Indices: 512987--513029 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
512977 AAACTAGAAT
512987 ATTTTATATATTTAAAAATA
1 ATTTTATATATTTAAAAATA
*
513007 ATTTTATAT-TTTAAAATTA
1 ATTTTATATATTTAAAAATA
513026 ATTT
1 ATTT
513030 AATTTAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTATATATTTAAAAATA
Found at i:518425 original size:2 final size:2
Alignment explanation
Indices: 518412--518454 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
518402 AGTTCATTAT
*
518412 TA TA TA TT 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
518454 T
1 T
518455 GGAGCATAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:519377 original size:33 final size:33
Alignment explanation
Indices: 519308--519380 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
519298 CCCTAAACAT
* * * *
519308 ACCCGAATATCATACTTAAAAAAATCCGACCTG
1 ACCCGAATATCAAACTTAAAAAAACCCAACCAG
*
519341 ACCCGAATATCAAAACTT-AAAAAACCCAATCAG
1 ACCCGAATATC-AAACTTAAAAAAACCCAACCAG
519374 ACCCGAA
1 ACCCGAA
519381 CCTGATTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 29 0.85
34 5 0.15
ACGTcount: A:0.47, C:0.29, G:0.08, T:0.16
Consensus pattern (33 bp):
ACCCGAATATCAAACTTAAAAAAACCCAACCAG
Found at i:522930 original size:39 final size:39
Alignment explanation
Indices: 522887--522969 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
522877 AAAACTTTTC
** *
522887 AATTCACAATAAAACACTCTAACACCCCAGAGATTCTTA
1 AATTCACAATAAAACACTCTAACACCAAAGAGACTCTTA
* *
522926 AATTCACAATAAAACACTTTAACTCCAAAGAGACTCTTA
1 AATTCACAATAAAACACTCTAACACCAAAGAGACTCTTA
522965 AATTC
1 AATTC
522970 CCCCTTAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (39 bp):
AATTCACAATAAAACACTCTAACACCAAAGAGACTCTTA
Found at i:536906 original size:206 final size:206
Alignment explanation
Indices: 536661--537071 Score: 781
Period size: 207 Copynumber: 2.0 Consensus size: 206
536651 TTCAATTACG
536661 ATTTTTCTATATATTCAAATTTAAGAATTCAAATATTTATTT-ATTTATTATCCTTTTATTCCCT
1 ATTTTTCTATATATTCAAATTTAAGAATTCAAATATTTATTTAATTTATTATCCTTTTATTCCCT
536725 AAGTAAAATATTTTAACGTAATTAAAGATTTTTTAGAGAGACACACAATATTTGTCTATTTCTAA
66 AAGTAAAATATTTTAACGTAATTAAAGATTTTTTAGAGAGACACACAATATTTGTCTATTTCTAA
*
536790 TTAAATAAGAAAACTAACCCCTTAATCGAAATAAGACAATTATTTCTTA-TTTTTAATCGAAACA
131 TTAAATAAG-AAACTAACCCCTTAATCGAAATAAGACAATTATTTCTTATTTTTTAATCAAAACA
536854 ATGAAATATTGA
195 ATGAAATATTGA
536866 ATTTTTCTATATATTCAAAATTTAAGAATTCAAATATTTATTTAATTTATTATCCTTTTATTCCC
1 ATTTTTCTATATATTC-AAATTTAAGAATTCAAATATTTATTTAATTTATTATCCTTTTATTCCC
536931 TAAGTAAAATATTTTAACGTAATTAAAGATTTTTTAGAGAGACACACAATATTTGTCTATTTCTA
65 TAAGTAAAATATTTTAACGTAATTAAAGATTTTTTAGAGAGACACACAATATTTGTCTATTTCTA
536996 ATTAAATAAGAAACTAACCCCTTAATCGAAATAAGACAATTATTTCTTATTTTTTAATCAAAACA
130 ATTAAATAAGAAACTAACCCCTTAATCGAAATAAGACAATTATTTCTTATTTTTTAATCAAAACA
537061 ATGAAATATTG
195 ATGAAATATTG
537072 TCATCCTTAA
Statistics
Matches: 202, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
205 16 0.08
206 65 0.32
207 121 0.60
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (206 bp):
ATTTTTCTATATATTCAAATTTAAGAATTCAAATATTTATTTAATTTATTATCCTTTTATTCCCT
AAGTAAAATATTTTAACGTAATTAAAGATTTTTTAGAGAGACACACAATATTTGTCTATTTCTAA
TTAAATAAGAAACTAACCCCTTAATCGAAATAAGACAATTATTTCTTATTTTTTAATCAAAACAA
TGAAATATTGA
Found at i:539184 original size:43 final size:43
Alignment explanation
Indices: 539123--539229 Score: 153
Period size: 43 Copynumber: 2.5 Consensus size: 43
539113 GTAGCAGTAC
*
539123 TGATCCAACTCCTTCTGTGAAGAATCAAGC-ATAAGGTTATCGT
1 TGATCCAACTCCTTCTGTGAAGAATCAAGCGA-AAGGTTATCAT
* * *
539166 TGATCCAACTCCTTCTGTGAAGGATCGAGCGAAAGGTTGTCAT
1 TGATCCAACTCCTTCTGTGAAGAATCAAGCGAAAGGTTATCAT
*
539209 TGATCCAACTCCTTATGTGAA
1 TGATCCAACTCCTTCTGTGAA
539230 TGATCGAGTG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 57 0.98
44 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (43 bp):
TGATCCAACTCCTTCTGTGAAGAATCAAGCGAAAGGTTATCAT
Found at i:547373 original size:21 final size:20
Alignment explanation
Indices: 547358--547409 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
547348 ATGAATATGG
547358 AAATGTGAACTTTGAATCAAT
1 AAATGTGAACTTTGAAT-AAT
*
547379 AAATGTGAACTTTGAATTAGT
1 AAATGTGAACTTTGAA-TAAT
*
547400 GAATGTGAAC
1 AAATGTGAAC
547410 AGACTCTACG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (20 bp):
AAATGTGAACTTTGAATAAT
Found at i:547578 original size:21 final size:21
Alignment explanation
Indices: 547539--547594 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
547529 GTCGAGGGTC
*
547539 TTAT-TGGTCATT-TGGACAA
1 TTATGTGGTCATTCGGGACAA
547558 TTATGTGGTCATTCGGGACAA
1 TTATGTGGTCATTCGGGACAA
*
547579 ATATGTGG-CACTTCGG
1 TTATGTGGTCA-TTCGG
547595 TGCAAACCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.12
20 10 0.31
21 18 0.56
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (21 bp):
TTATGTGGTCATTCGGGACAA
Done.