Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009463.1 Hibiscus syriacus cultivar Beakdansim tig00113726_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: 3931635
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 20
Found at i:3417611 original size:15 final size:14
Alignment explanation
Indices: 3417587--3417628 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
3417577 TTTTCATACA
3417587 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
3417600 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
3417615 TTCATTGTGCATTT
1 TGCATTTTGCATTT
3417629 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:3417696 original size:6 final size:6
Alignment explanation
Indices: 3417687--3417738 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
3417677 ACATTCACAT
* * * * *
3417687 ATTTAC ATTTGC ATTTAC ATTTGC ATTTAC ATTTGC ATTTAC CTTTGC
1 ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC
3417735 ATTT
1 ATTT
3417739 TTTACGTTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (6 bp):
ATTTAC
Found at i:3417717 original size:24 final size:24
Alignment explanation
Indices: 3417687--3417765 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
3417677 ACATTCACAT
3417687 ATTTACATTTGCATTTACATTTGC
1 ATTTACATTTGCATTTACATTTGC
*
3417711 ATTTACATTTGCATTTACCTTTGC
1 ATTTACATTTGCATTTACATTTGC
* * *
3417735 ATTTTTTACGTTTGTATTTACATTTTC
1 A---TTTACATTTGCATTTACATTTGC
3417762 ATTT
1 ATTT
3417766 TTACATAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
24 27 0.57
27 20 0.43
ACGTcount: A:0.22, C:0.15, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTACATTTGCATTTACATTTGC
Found at i:3417765 original size:12 final size:12
Alignment explanation
Indices: 3417687--3417738 Score: 95
Period size: 12 Copynumber: 4.3 Consensus size: 12
3417677 ACATTCACAT
3417687 ATTTACATTTGC
1 ATTTACATTTGC
3417699 ATTTACATTTGC
1 ATTTACATTTGC
3417711 ATTTACATTTGC
1 ATTTACATTTGC
*
3417723 ATTTACCTTTGC
1 ATTTACATTTGC
3417735 ATTT
1 ATTT
3417739 TTTACGTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:3420168 original size:12 final size:12
Alignment explanation
Indices: 3420151--3420184 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3420141 CTATACTCGT
3420151 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
3420163 AAAAAAAAGGAA
1 AAAAAAAAAGAA
3420175 AAAGAAAAAA
1 AAA-AAAAAA
3420185 AAAGGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:3420182 original size:17 final size:18
Alignment explanation
Indices: 3420155--3420193 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
3420145 ACTCGTAAAA
3420155 AAAAAGAAAAAAAAAAGG
1 AAAAAGAAAAAAAAAAGG
3420173 AAAAAG-AAAAAAAAAGG
1 AAAAAGAAAAAAAAAAGG
3420190 AAAA
1 AAAA
3420194 TGGGTGACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAGG
Found at i:3421905 original size:114 final size:114
Alignment explanation
Indices: 3421705--3421926 Score: 345
Period size: 114 Copynumber: 1.9 Consensus size: 114
3421695 CACGTTCTCG
* *
3421705 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAACATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * *
3421770 GGTATAAACCCCAAAACCAATCATTAGATTTGAAATATGAATTTGCTCA
66 GGTAGAAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
* * *
3421819 TAGTAGAAATAAGGAGACCCAATAACATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAACATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * *
3421884 GGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAATT
66 GGTAGAAACCCCAAAACCAATCATTAGAATTGAAAGATGAATT
3421927 GCATGATCGT
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAACATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGAAACCCCAAAACCAATCATTAGAATTGAAAGATGAATTTGCTCA
Found at i:3422140 original size:31 final size:31
Alignment explanation
Indices: 3422102--3422164 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
3422092 GCACATATAA
* *
3422102 AATCTGTCAACTCTGCAATTGATGAATTCAG
1 AATCTGTCAACTCTACAATTGATAAATTCAG
3422133 AATCTGTCAACTCTACAATTGATAAATTCAG
1 AATCTGTCAACTCTACAATTGATAAATTCAG
3422164 A
1 A
3422165 CCACATCTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (31 bp):
AATCTGTCAACTCTACAATTGATAAATTCAG
Found at i:3422960 original size:35 final size:34
Alignment explanation
Indices: 3422909--3422974 Score: 114
Period size: 35 Copynumber: 1.9 Consensus size: 34
3422899 TTCAACCAGA
3422909 AATAGAATATTGGGGCATTTTGAAGGCTCATAGC
1 AATAGAATATTGGGGCATTTTGAAGGCTCATAGC
*
3422943 AATATGAATATTTGGGCATTTTGAAGGCTCAT
1 AATA-GAATATTGGGGCATTTTGAAGGCTCAT
3422975 CTCAACAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 4 0.13
35 26 0.87
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (34 bp):
AATAGAATATTGGGGCATTTTGAAGGCTCATAGC
Found at i:3423149 original size:76 final size:77
Alignment explanation
Indices: 3423020--3423192 Score: 233
Period size: 76 Copynumber: 2.3 Consensus size: 77
3423010 TCTGTATCGG
* * *
3423020 AAAATGTTGGGGCATGCTGAAAACCTTTTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAAT
1 AAAATGTTGGGGCATGCTGAAAACCTGTTTTCAATCAGAATCAAGAAGGTTGATGTATCCTGAAC
*
3423085 GTTTATATCAGC
66 GTTCATATCAGC
* * * **
3423097 AAAATGCTGGGGCATGCTGAAAGCC-GTTTTCAATCAGAATGAAGAAGGTTGATGTATTTTGAAC
1 AAAATGTTGGGGCATGCTGAAAACCTGTTTTCAATCAGAATCAAGAAGGTTGATGTATCCTGAAC
*
3423161 GTTCGTATCAGC
66 GTTCATATCAGC
*
3423173 -AATTGTTGGGGCATGCTGAA
1 AAAATGTTGGGGCATGCTGAA
3423193 GGCCCATATC
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
75 18 0.21
76 43 0.51
77 23 0.27
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (77 bp):
AAAATGTTGGGGCATGCTGAAAACCTGTTTTCAATCAGAATCAAGAAGGTTGATGTATCCTGAAC
GTTCATATCAGC
Found at i:3424593 original size:22 final size:22
Alignment explanation
Indices: 3424562--3424616 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3424552 ATCTACACTC
*
3424562 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
3424584 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
*
3424606 TTCAAACATGA
1 TTCAAAGATGA
3424617 AAGCGTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:3426371 original size:113 final size:113
Alignment explanation
Indices: 3425023--3426369 Score: 2417
Period size: 113 Copynumber: 11.9 Consensus size: 113
3425013 AGTTCAAATC
3425023 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
3425088 ATAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
3425136 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
3425201 ATAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTAAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
*
3425249 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
3425314 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
*
3425362 CATCATTCGATGGATCAGCATTACCAGGTTGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
3425427 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
*
3425475 CATCATTCGATGGATCATCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
3425540 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* *
3425588 CATCATTCGATGGATCAGCATTACCAGATCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
3425653 AGAAGAAGTTCATAATGAGATGAACTTGTTCAACTTTTCGGTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* *
3425701 CATTATTCGATGGATCATCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
3425766 ATAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
3425814 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
3425879 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
3425927 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
3425992 AGAAGAAGTTTATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
3426040 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
3426105 AGAGGAAGTTTATAATGAGAAGAACTTGTTCAACTTTTCACTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * * *
3426153 CATCATTTGATGGATCAGCATTGCCAGGGCGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
3426218 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
* * * * *
3426266 CATCATTCGATGGATTAACTTTTCCAGAG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTCGATGGATCAGCATTACCAG-GTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
3426330 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
3426370 GCATGATTCT
Statistics
Matches: 1190, Mismatches: 42, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
113 1184 0.99
114 6 0.01
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (113 bp):
CATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
Found at i:3426720 original size:3 final size:3
Alignment explanation
Indices: 3426712--3426794 Score: 96
Period size: 3 Copynumber: 28.0 Consensus size: 3
3426702 ATTTGGTTTT
* * * * *
3426712 TTA TTA TTA TTT TTA TTA TTT TTA TTT TTA TTA CTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
3426760 TTA ATA TTA TTA TTA TTA ATA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3426795 CAGATACAAC
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
2 2 0.03
3 63 0.97
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3426730 original size:15 final size:15
Alignment explanation
Indices: 3426708--3426794 Score: 106
Period size: 15 Copynumber: 5.9 Consensus size: 15
3426698 TTATATTTGG
3426708 TTTT-TTATTATTAT
1 TTTTATTATTATTAT
*
3426722 TTTTATTATTTTTAT
1 TTTTATTATTATTAT
*
3426737 TTTTATTACTATTAT
1 TTTTATTATTATTAT
*
3426752 TTTTATTATTAATAT
1 TTTTATTATTATTAT
* *
3426767 TATTATTATTAATAT
1 TTTTATTATTATTAT
*
3426782 TATTATT-TTATTA
1 TTTTATTATTATTA
3426795 CAGATACAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 9 0.14
15 56 0.86
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATTATTATTAT
Found at i:3427354 original size:17 final size:18
Alignment explanation
Indices: 3427332--3427368 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3427322 AACAGGAGAG
3427332 ACGAACACA-CAACAGCA
1 ACGAACACATCAACAGCA
3427349 ACGAACACATCAACAGCA
1 ACGAACACATCAACAGCA
3427367 AC
1 AC
3427369 TGAGACCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.51, C:0.35, G:0.11, T:0.03
Consensus pattern (18 bp):
ACGAACACATCAACAGCA
Found at i:3438111 original size:21 final size:20
Alignment explanation
Indices: 3438069--3438112 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3438059 TTGTATACAC
**
3438069 TTTCAAATATTTATTATTTA
1 TTTCAAATATTTATTAAATA
*
3438089 TTTCATAATATTTCTTAAATA
1 TTTCA-AATATTTATTAAATA
3438110 TTT
1 TTT
3438113 ATGTTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTCAAATATTTATTAAATA
Found at i:3444129 original size:45 final size:44
Alignment explanation
Indices: 3444078--3444175 Score: 160
Period size: 45 Copynumber: 2.2 Consensus size: 44
3444068 TATTTATACC
* *
3444078 ATTTATTTTATTTATAGTTGTATATTGGTATAGATATGATCTATA
1 ATTTATTTCA-TTATAGTTGTATATTGGTATAGATATGATATATA
3444123 ATTTATTATCATTATAGTTGTATATTGGTATAGATATGATATATA
1 ATTTATT-TCATTATAGTTGTATATTGGTATAGATATGATATATA
3444168 ATTTATTT
1 ATTTATTT
3444176 ATAAACCTTC
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
44 1 0.02
45 47 0.94
46 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (44 bp):
ATTTATTTCATTATAGTTGTATATTGGTATAGATATGATATATA
Found at i:3446156 original size:41 final size:41
Alignment explanation
Indices: 3446044--3446481 Score: 275
Period size: 41 Copynumber: 10.8 Consensus size: 41
3446034 TATACAAACA
* * * *
3446044 CCACTAAAGTACGAGTATTTACCAGCGTTTGTTAAAAAAATG
1 CCACTAAAGTACGAGTATTTAGCGGCGTTT-ATATAAAAATG
* * * *
3446086 CCACTAAAGTACGAGTCTTGAACGTCGTTTATATAAAAATG
1 CCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAATG
* * * *
3446127 CCATTAAAGTACGAGTATTTATCGGCGTTTTTTAAAAAAAAT-
1 CCACTAAAGTACGAGTATTTAGCGGCG-TTTAT-ATAAAAATG
* * * *
3446169 -CACAAAAGTA-TAATATTTAGCGGCATTTATATAAAAATG
1 CCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAATG
* * * * * **
3446208 CCACTAAAATACAAGTGTTTAGC-G-GTTTTTGTAAAAAAA
1 CCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAATG
* * *
3446247 CCACTAAAGTAC-AATATTTAACGGTGTTTATATAAAAATG
1 CCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAATG
* * * * * * * *
3446287 CCTCTAAAGGATGAGTATTTACCGACGTTTGT-TCGAAGAACG
1 CCACTAAAGTACGAGTATTTAGCGGCGTTTATAT--AAAAATG
* * * * *
3446329 ACACTAAATTAC-AATATTTAGCGGCGTTTATATCAAAACG
1 CCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAATG
* * * * *
3446369 CCACTAAAATACGAGTCTTTAGCGGCGTTTGTAAAAAAACG
1 CCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAATG
* *** * *
3446410 CCACTAACGTAC-A-TAATTTCTAGGCATTTAAATAAAAATG
1 CCACTAAAGTACGAGT-ATTTAGCGGCGTTTATATAAAAATG
* * *
3446450 CCACTAAAGTGCGAGTATTTAACTGCGTTTAT
1 CCACTAAAGTACGAGTATTTAGCGGCGTTTAT
3446482 TCAAAAAATG
Statistics
Matches: 294, Mismatches: 87, Indels: 31
0.71 0.21 0.08
Matches are distributed among these distances:
38 14 0.05
39 27 0.09
40 83 0.28
41 120 0.41
42 43 0.15
43 7 0.02
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (41 bp):
CCACTAAAGTACGAGTATTTAGCGGCGTTTATATAAAAATG
Found at i:3446361 original size:161 final size:161
Alignment explanation
Indices: 3446034--3446422 Score: 417
Period size: 161 Copynumber: 2.4 Consensus size: 161
3446024 GAGGCACTTG
* * * * * * *
3446034 TATACAAACACCACTAAAGTACGAGTATTTACCAGCGTTTGTTAAAAAAATGCCACTAAAGTACG
1 TATAAAAACGCCACTAAAATACAAGTCTTTAGCGGCGTTTG-TAAAAAAA-GCCACTAAAGTAC-
* * * * * *
3446099 AGTCTTGAACGTCGTTTATATAAAAATGCCATTAAAGTACGAGTATTTATCGGCGTTTTTTAAAA
63 AATATTGAACGTCGTTTATATAAAAATGCCATTAAAGGACGAGTATTTACCGACGTTTTTGAAAA
*
3446164 AAAATCACAAAAGTATAATATTTAGCGGCATTTA
128 AAAATCACAAAAGTACAATATTTAGCGGCATTTA
* * **
3446198 TATAAAAATGCCACTAAAATACAAGTGTTTAGCGGTTTTTGTAAAAAAA-CCACTAAAGTACAAT
1 TATAAAAACGCCACTAAAATACAAGTCTTTAGCGGCGTTTGTAAAAAAAGCCACTAAAGTACAAT
* * *
3446262 ATTTAACGGT-GTTTATATAAAAATGCC-TCTAAAGGATGAGTATTTACCGACGTTTGTTCGAAG
66 ATTGAAC-GTCGTTTATATAAAAATGCCAT-TAAAGGACGAGTATTTACCGACGTTT-TT-GAAA
** * * *
3446325 AACGA-CACTAAATTACAATATTTAGCGGCGTTTA
127 AAAAATCACAAAAGTACAATATTTAGCGGCATTTA
* * *
3446359 TATCAAAACGCCACTAAAATACGAGTCTTTAGCGGCGTTTGTAAAAAAACGCCACTAACGTACA
1 TATAAAAACGCCACTAAAATACAAGTCTTTAGCGGCGTTTGTAAAAAAA-GCCACTAAAGTACA
3446423 TAATTTCTAG
Statistics
Matches: 187, Mismatches: 32, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
159 1 0.01
160 46 0.25
161 84 0.45
162 5 0.03
163 20 0.11
164 31 0.17
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.29
Consensus pattern (161 bp):
TATAAAAACGCCACTAAAATACAAGTCTTTAGCGGCGTTTGTAAAAAAAGCCACTAAAGTACAAT
ATTGAACGTCGTTTATATAAAAATGCCATTAAAGGACGAGTATTTACCGACGTTTTTGAAAAAAA
ATCACAAAAGTACAATATTTAGCGGCATTTA
Found at i:3446398 original size:82 final size:80
Alignment explanation
Indices: 3446044--3446489 Score: 367
Period size: 81 Copynumber: 5.5 Consensus size: 80
3446034 TATACAAACA
* * * * * * *
3446044 CCACTAAAGTACGAGTATTTACCAGCGTTTGTTAAAAAAATGCCACTAAAGTACGAGTCTTGAAC
1 CCACTAAAATACGAGTATTTAGCGGCGTTTGTTAAAAAAA--CCACTAAAGTAC-AATATTTAGC
*
3446109 GTCGTTTATATAAAAATG
63 GGCGTTTATATAAAAATG
* * * * * * *
3446127 CCATTAAAGTACGAGTATTTATCGGCGTTTTTTAAAAAAAATCACAAAAGTATAATATTTAGCGG
1 CCACTAAAATACGAGTATTTAGCGGCGTTTGTT-AAAAAAACCACTAAAGTACAATATTTAGCGG
*
3446192 CATTTATATAAAAATG
65 CGTTTATATAAAAATG
* * ** * *
3446208 CCACTAAAATACAAGTGTTTAGCGGTTTTTG-TAAAAAAACCACTAAAGTACAATATTTAACGGT
1 CCACTAAAATACGAGTATTTAGCGGCGTTTGTTAAAAAAACCACTAAAGTACAATATTTAGCGGC
3446272 GTTTATATAAAAATG
66 GTTTATATAAAAATG
* ** * * * ** * *
3446287 CCTCTAAAGGATGAGTATTTACCGACGTTTGTTCGAAGAACGACACTAAATTACAATATTTAGCG
1 CCACTAAAATACGAGTATTTAGCGGCGTTTGTTAAAAAAAC--CACTAAAGTACAATATTTAGCG
* *
3446352 GCGTTTATATCAAAACG
64 GCGTTTATATAAAAATG
* * ***
3446369 CCACTAAAATACGAGTCTTTAGCGGCGTTTG-TAAAAAAACGCCACTAACGTAC-ATAATTTCTA
1 CCACTAAAATACGAGTATTTAGCGGCGTTTGTTAAAAAAA--CCACTAAAGTACAAT-ATTTAGC
* *
3446432 GGCATTTAAATAAAAATG
63 GGCGTTTATATAAAAATG
* * * * * *
3446450 CCACTAAAGTGCGAGTATTTAACTGCGTTTATTCAAAAAA
1 CCACTAAAATACGAGTATTTAGCGGCGTTTGTTAAAAAAA
3446490 TGCCGCTATT
Statistics
Matches: 284, Mismatches: 71, Indels: 17
0.76 0.19 0.05
Matches are distributed among these distances:
79 62 0.22
80 9 0.03
81 102 0.36
82 74 0.26
83 30 0.11
84 7 0.02
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (80 bp):
CCACTAAAATACGAGTATTTAGCGGCGTTTGTTAAAAAAACCACTAAAGTACAATATTTAGCGGC
GTTTATATAAAAATG
Found at i:3451101 original size:18 final size:18
Alignment explanation
Indices: 3451078--3451123 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
3451068 CTCAATTAAA
3451078 TTCGAATCAAGCAGGAAT
1 TTCGAATCAAGCAGGAAT
3451096 TTCGAATCAAGCAGGAAT
1 TTCGAATCAAGCAGGAAT
3451114 TTCGAATCAA
1 TTCGAATCAA
3451124 TTACACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (18 bp):
TTCGAATCAAGCAGGAAT
Found at i:3452242 original size:51 final size:51
Alignment explanation
Indices: 3452144--3452266 Score: 167
Period size: 51 Copynumber: 2.4 Consensus size: 51
3452134 GTAGAAGATA
* * * * *
3452144 GTCTTGAGGGTGATGAAAATGTTGTTGAAGTTACTGTTGTAATAGAGGGTG
1 GTCTTGAGGGTGATGGAGATGTTGTTGAAGTTACTGCTGCAACAGAGGGTG
*
3452195 GTCTTGAGGGTGATGGAGATGTTGTTGAAAG-TGCTGCTGCAACAGAGGGTG
1 GTCTTGAGGGTGATGGAGATGTTGTTG-AAGTTACTGCTGCAACAGAGGGTG
*
3452246 GTCTTAAGGGTGATGGAGATG
1 GTCTTGAGGGTGATGGAGATG
3452267 GTGATGTAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
51 61 0.95
52 3 0.05
ACGTcount: A:0.24, C:0.07, G:0.39, T:0.31
Consensus pattern (51 bp):
GTCTTGAGGGTGATGGAGATGTTGTTGAAGTTACTGCTGCAACAGAGGGTG
Found at i:3453139 original size:35 final size:35
Alignment explanation
Indices: 3453100--3453166 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
3453090 ATAATCGATC
* *
3453100 TAGATGGTTGTTTCCTTAAGGGCTCATTCAAATGT
1 TAGATGGATGTTTCCTTAAGGGCCCATTCAAATGT
3453135 TAGATGGATGTTTCCTTAAGGGCCCATTCAAA
1 TAGATGGATGTTTCCTTAAGGGCCCATTCAAA
3453167 GGTATATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.36
Consensus pattern (35 bp):
TAGATGGATGTTTCCTTAAGGGCCCATTCAAATGT
Found at i:3455269 original size:30 final size:30
Alignment explanation
Indices: 3455235--3455292 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3455225 ATGATCATTT
*
3455235 ACTTCGCATTACACACTTTCATTCTCTTTC
1 ACTTCGCATTACACACTTTCACTCTCTTTC
* *
3455265 ACTTCGCTTTGCACACTTTCACTCTCTT
1 ACTTCGCATTACACACTTTCACTCTCTT
3455293 CCAATGACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.17, C:0.34, G:0.05, T:0.43
Consensus pattern (30 bp):
ACTTCGCATTACACACTTTCACTCTCTTTC
Found at i:3456546 original size:21 final size:21
Alignment explanation
Indices: 3456495--3456553 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
3456485 AAATCAGTTC
3456495 CCAGAATCGCAATGCGATAGT
1 CCAGAATCGCAATGCGATAGT
* * **
3456516 ACA-AATTCGCATTGCGATTTT
1 CCAGAA-TCGCAATGCGATAGT
*
3456537 CCAGAATCGCAACGCGA
1 CCAGAATCGCAATGCGA
3456554 ATATGAAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (21 bp):
CCAGAATCGCAATGCGATAGT
Found at i:3456566 original size:20 final size:20
Alignment explanation
Indices: 3456541--3456755 Score: 134
Period size: 20 Copynumber: 10.6 Consensus size: 20
3456531 GATTTTCCAG
*
3456541 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
3456561 AATCGCAATGCGAATA-TATA
1 AATCGCAACGCGAATACGA-A
* *
3456581 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * *
3456601 TATCGCAACGAGTAT-CTGTAA
1 AATCGCAACGCGAATAC-G-AA
* * *
3456622 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
3456642 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * * * *
3456663 AATCACAACACGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
3456683 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * *
3456703 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
3456723 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
3456744 AATCGCAACGCG
1 AATCGCAACGCG
3456756 TATCCGTAAA
Statistics
Matches: 152, Mismatches: 31, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
19 3 0.02
20 104 0.68
21 44 0.29
22 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:3456645 original size:81 final size:80
Alignment explanation
Indices: 3456602--3456768 Score: 264
Period size: 81 Copynumber: 2.0 Consensus size: 80
3456592 GATTCTGACT
*
3456602 ATCGCAACGAGTAT-CTGTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAAT
1 ATCGCAACGAGAATAC-GT-AAATCGCAACGCGTATCCGTAAATCGCAACGACAATAC-TAAAAT
* *
3456666 CACAACACGTATCCGTAA
63 CGCAACGCGTATCCGTAA
3456684 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCG
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAAATCGCAACGACAATAC-TAAAATCG
3456749 CAACGCGTATCCGTAA
65 CAACGCGTATCCGTAA
3456765 ATCG
1 ATCG
3456769 TAATGCGATC
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
81 65 0.80
82 15 0.19
83 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (80 bp):
ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACTAAAATCGC
AACGCGTATCCGTAA
Found at i:3456647 original size:41 final size:41
Alignment explanation
Indices: 3456618--3456768 Score: 268
Period size: 41 Copynumber: 3.7 Consensus size: 41
3456608 ACGAGTATCT
3456618 GTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATAC
1 GTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATAC
* * *
3456659 GTAAAATCACAACACGTATCCGTAAATCGCAACGAGAATAC
1 GTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATAC
3456700 GT-AAATCGCAACGCGTATCCGTAAATCGCAACGACAATAC
1 GTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATAC
3456740 GTAAAATCGCAACGCGTATCCGTAAATCG
1 GTAAAATCGCAACGCGTATCCGTAAATCG
3456769 TAATGCGATC
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 37 0.36
41 66 0.64
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (41 bp):
GTAAAATCGCAACGCGTATCCGTAAATCGCAACGACAATAC
Found at i:3456768 original size:20 final size:20
Alignment explanation
Indices: 3456602--3456768 Score: 176
Period size: 20 Copynumber: 8.2 Consensus size: 20
3456592 GATTCTGACT
* *
3456602 ATCGCAACGAGTATCTGTAAA
1 ATCGCAACGCGTATCCGT-AA
3456623 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
3456643 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
* *
3456664 ATCACAACACGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
3456684 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
3456704 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
3456724 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
3456745 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
3456765 ATCG
1 ATCG
3456769 TAATGCGATC
Statistics
Matches: 120, Mismatches: 20, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
20 72 0.60
21 48 0.40
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:3456912 original size:20 final size:20
Alignment explanation
Indices: 3456887--3457014 Score: 168
Period size: 20 Copynumber: 6.4 Consensus size: 20
3456877 TTTTCTTAAT
*
3456887 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
3456907 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* *
3456927 TCGTAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
* **
3456947 TCGTAACGCGGTTACGTAAA
1 TCGCAACGCGAATACGTAAA
3456967 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* *
3456987 TCGCAATGCGAACT-TGTAAA
1 TCGCAACGCGAA-TACGTAAA
3457007 TCGCAACG
1 TCGCAACG
3457015 AGATCCTGAC
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 96 0.99
21 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:3457901 original size:24 final size:24
Alignment explanation
Indices: 3457874--3457927 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3457864 GTATTCGAAA
3457874 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
3457898 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
3457922 TTTGAT
1 TTTGAT
3457928 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:3460391 original size:20 final size:20
Alignment explanation
Indices: 3460368--3460442 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
3460358 CAACGCGAAT
3460368 ATGACTATCGCAACACGGAA
1 ATGACTATCGCAACACGGAA
**
3460388 ATGACTATCGCAATGCGGAA
1 ATGACTATCGCAACACGGAA
* *
3460408 TTGACTATCGCAACGCGGAA
1 ATGACTATCGCAACACGGAA
3460428 ATGACTATCGCAACA
1 ATGACTATCGCAACA
3460443 AGAGAATCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (20 bp):
ATGACTATCGCAACACGGAA
Found at i:3460427 original size:40 final size:41
Alignment explanation
Indices: 3460335--3460440 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 41
3460325 GACATTCATT
*
3460335 TGACTATCGCAACACGG-AA--A-T-T-GCAACGC-GAATA
1 TGACTATCGCAACACGGAAATGACTATCGCAATGCGGAATA
3460369 TGACTATCGCAACACGGAAATGACTATCGCAATGCGGAAT-
1 TGACTATCGCAACACGGAAATGACTATCGCAATGCGGAATA
*
3460409 TGACTATCGCAACGCGGAAATGACTATCGCAA
1 TGACTATCGCAACACGGAAATGACTATCGCAA
3460441 CAAGAGAATC
Statistics
Matches: 63, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
34 17 0.27
35 2 0.03
37 1 0.02
38 1 0.02
39 1 0.02
40 37 0.59
41 4 0.06
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.19
Consensus pattern (41 bp):
TGACTATCGCAACACGGAAATGACTATCGCAATGCGGAATA
Found at i:3460502 original size:34 final size:33
Alignment explanation
Indices: 3460414--3460509 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
3460404 GGAATTGACT
* ** *
3460414 ATCGCAACGCGGAAATGACTATCGCAACAAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
3460448 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3460481 ATCGTAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
3460510 CGAAATTAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3460586 original size:33 final size:33
Alignment explanation
Indices: 3460524--3460619 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
3460514 ATTAGTTTCG
*
3460524 CGTTGCGATTTTCATTTTCGCATTACGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
* **
3460558 CGTTGCAATTTTCATTTCGCATTGCGATTTTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
3460591 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
3460620 AGTCTGTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 30 0.57
34 23 0.43
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:3460740 original size:14 final size:14
Alignment explanation
Indices: 3460721--3460757 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3460711 CATCAATTAA
3460721 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3460735 ACAAATCATCTTTT
1 ACAAATCAACATTT
3460749 ACAAATCAA
1 ACAAATCAA
3460758 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3462165 original size:42 final size:42
Alignment explanation
Indices: 3462098--3462189 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
3462088 GTGAATTGGG
* * *
3462098 CTCTAGAATGTTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
* ** *
3462140 CTCTTGAATGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGGGGC
3462182 CTCTTGAA
1 CTCTTGAA
3462190 CGATAGGGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 38 0.90
43 4 0.10
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (42 bp):
CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
Found at i:3462724 original size:20 final size:20
Alignment explanation
Indices: 3462699--3462767 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
3462689 GAAACTTAAA
*
3462699 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
3462719 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
3462739 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
3462759 ATCGCAACG
1 ATCGCAACG
3462768 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3462877 original size:31 final size:32
Alignment explanation
Indices: 3462810--3462886 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 32
3462800 GCGATTATAG
* * *
3462810 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGAATCTCTCGTTGCGA-TTTCA
3462843 TTTCGCGTTGCGAATCTCTCGTTGCGA-TTCA
1 TTTCGCGTTGCGAATCTCTCGTTGCGATTTCA
3462874 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
3462887 TAGTCATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 17 0.41
33 24 0.59
ACGTcount: A:0.10, C:0.22, G:0.25, T:0.43
Consensus pattern (32 bp):
TTTCGCGTTGCGAATCTCTCGTTGCGATTTCA
Found at i:3463140 original size:94 final size:94
Alignment explanation
Indices: 3462975--3463354 Score: 674
Period size: 94 Copynumber: 4.1 Consensus size: 94
3462965 ATGGATTGCA
* *
3462975 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
3463039 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
3463068 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
3463133 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
3463162 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
3463227 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
3463256 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAATAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
3463320 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
3463350 TTACT
1 TTACT
3463355 AAGCAATATA
Statistics
Matches: 278, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
93 23 0.08
94 255 0.92
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3465066 original size:20 final size:20
Alignment explanation
Indices: 3465043--3465117 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
3465033 TGAAATGAAA
3465043 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
3465063 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
* **
3465083 ATCGCAACGCGA-AATGAAA
1 ATCGCAACGAGAGAATGACT
*
3465102 ATCGCAAAGAGAGAAT
1 ATCGCAACGAGAGAAT
3465118 CGCAACGCGA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
19 16 0.34
20 31 0.66
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:3465098 original size:19 final size:19
Alignment explanation
Indices: 3465043--3465099 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 19
3465033 TGAAATGAAA
*
3465043 ATCGCAACGAGAGAATGACT
1 ATCGCAACGCGA-AATGACT
3465063 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
3465083 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
3465100 AAATCGCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 7 0.20
20 26 0.74
21 2 0.06
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3465105 original size:19 final size:19
Alignment explanation
Indices: 3465034--3465179 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
3465024 TCTTTTGGTT
*
3465034 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
3465053 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3465073 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
3465093 GAAATGAAAATCGCAA---
1 GAAATGAAAATCGCAACGC
* *
3465109 -AGA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3465126 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
3465143 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3465159 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3465178 GA
1 GA
3465180 TTTTGGTTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 19 0.19
15 3 0.03
16 2 0.02
17 2 0.02
18 3 0.03
19 39 0.39
20 31 0.31
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3465125 original size:33 final size:33
Alignment explanation
Indices: 3465083--3465174 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
3465073 GGAAATGACT
3465083 ATCGCAACGCGAAATGAAAATCGCAAAGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAAAGAGAGA
* *
3465116 ATCGCAACGCGAAATTAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAAAGAGAGA
3465149 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
3465175 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAAAGAGAGA
Found at i:3465238 original size:20 final size:20
Alignment explanation
Indices: 3465186--3465263 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
3465176 GCGATTTTGG
*
3465186 TTTCGCGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
**
3465206 TTCTC-TCGTTGCGATAGTCAT
1 TT-TCGT-GTTGCGATTTTCAT
3465227 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
*
3465247 TTTCATGTTGCGATTTT
1 TTTCGTGTTGCGATTTT
3465264 AAGTTTAGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 32 0.65
21 17 0.35
ACGTcount: A:0.12, C:0.18, G:0.19, T:0.51
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTCAT
Found at i:3465846 original size:20 final size:20
Alignment explanation
Indices: 3465821--3466095 Score: 181
Period size: 20 Copynumber: 13.6 Consensus size: 20
3465811 CTTTAAAAAT
3465821 CGCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACAGATA
*
3465841 CGCGTTGCGATTTTACATAT-
1 CGCGTTGCGA-TTTACAGATA
* *
3465861 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACAGATA
* * *
3465882 CACATTGCGATTTAC-GTATT
1 CGCGTTGCGATTTACAG-ATA
*
3465902 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACAGATA
* * *
3465922 CACGTTGCGATCTAC-GTATT
1 CGCGTTGCGATTTACAG-ATA
* *
3465942 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACAGATA
3465962 CGCGTTGCGATTTTAC-G-TA
1 CGCGTTGCGA-TTTACAGATA
*
3465981 TTGTCGTTGCGATTTAC-GAATA
1 -CG-CGTTGCGATTTACAG-ATA
*
3466003 CGCGTTGCGATTTTACAAATA
1 CGCGTTGCGA-TTTACAGATA
* *
3466024 CTCGTTGCGATAGT-CAGA-A
1 CGCGTTGCGAT-TTACAGATA
* *
3466043 TCGCGTTGCGATTTATATG-TT
1 -CGCGTTGCGATTTACA-GATA
* * *
3466064 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACAGATA
*
3466084 CGCGTTGTGATT
1 CGCGTTGCGATT
3466096 CTGGAAAATC
Statistics
Matches: 203, Mismatches: 32, Indels: 40
0.74 0.12 0.15
Matches are distributed among these distances:
19 6 0.03
20 144 0.71
21 51 0.25
22 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACAGATA
Found at i:3465907 original size:40 final size:41
Alignment explanation
Indices: 3465823--3466034 Score: 293
Period size: 41 Copynumber: 5.2 Consensus size: 41
3465813 TTAAAAATCG
* * *
3465823 CGTTGCGATTTACAGATACGCGTTGCGATTTTACATATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
3465864 CGTTGCGATTTACGGATACACATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
3465904 CGTTGCGATTTACAGATACACGTTGCGA-TCTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
3465944 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* ** *
3465985 CGTTGCGATTTACGAATACGCGTTGCGATTTTACAAATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
3466026 CGTTGCGAT
1 CGTTGCGAT
3466035 AGTCAGAATC
Statistics
Matches: 153, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 73 0.48
41 80 0.52
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:3465950 original size:60 final size:59
Alignment explanation
Indices: 3465823--3466034 Score: 174
Period size: 61 Copynumber: 3.5 Consensus size: 59
3465813 TTAAAAATCG
* *** *
3465823 CGTTGCGATTTACAGATACGCGTTGCGATTTTACATATTGTCGTTGCGATTTACGGATACA
1 CGTTGCGATTTAC-GATACGCGTTGCGA-TTTACAGATACACGTTGCGATCTACGGATACA
* * * * * *
3465884 CATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACACGTTGCGATCTACGTATTCT
1 CGTTGCGATTTACG-ATACGCGTTGCGATTTACAGATACACGTTGCGATCTACGGATACA
*** * * *
3465944 CGTTGCGATTTACGGATACGCGTTGCGATTTTAC-GTATTGTCGTTGCGATTTACGAATACG
1 CGTTGCGATTTAC-GATACGCGTTGCGA-TTTACAG-ATACACGTTGCGATCTACGGATACA
* *
3466005 CGTTGCGATTTTACAAATACTCGTTGCGAT
1 CGTTGCGA-TTTAC-GATACGCGTTGCGAT
3466035 AGTCAGAATC
Statistics
Matches: 122, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
60 49 0.40
61 56 0.46
62 17 0.14
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (59 bp):
CGTTGCGATTTACGATACGCGTTGCGATTTACAGATACACGTTGCGATCTACGGATACA
Found at i:3466087 original size:40 final size:40
Alignment explanation
Indices: 3465820--3466095 Score: 256
Period size: 40 Copynumber: 6.8 Consensus size: 40
3465810 GCTTTAAAAA
3465820 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACATAT
1 TCGCGTTGCGATTTACAGATACGCGTTGCGA-TTTACATAT
* * * *
3465861 T-GTCGTTGCGATTTACGGATACACATTGCGATTTACGTAT
1 TCG-CGTTGCGATTTACAGATACGCGTTGCGATTTACATAT
* * * *
3465901 TCTCGTTGCGATTTACAGATACACGTTGCGATCTACGTAT
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTACATAT
* * *
3465941 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
1 TCGCGTTGCGATTTACAGATACGCGTTGCGA-TTTACATAT
*
3465982 T-GTCGTTGCGATTTAC-GAATACGCGTTGCGATTTTACAAAT
1 TCG-CGTTGCGATTTACAG-ATACGCGTTGCGA-TTTACATAT
* * * * *
3466023 ACTCGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGT
1 TCGCGTTGCGAT-TTACAGATA-CGCGTTGCGATTTACATAT
* * * *
3466063 TCGCGTTGCGATTTTCATATTCGCGTTGTGATT
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATT
3466096 CTGGAAAATC
Statistics
Matches: 198, Mismatches: 26, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.01
40 105 0.53
41 90 0.45
42 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
TCGCGTTGCGATTTACAGATACGCGTTGCGATTTACATAT
Found at i:3469810 original size:21 final size:21
Alignment explanation
Indices: 3469786--3469852 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
3469776 TGCAATCTTA
*
3469786 TCTTCTTCTGTTAATTCTAGT
1 TCTTCTTCTGTTAATTCTAGG
* *
3469807 TCTTCTTCTGTGAATTCTGGG
1 TCTTCTTCTGTTAATTCTAGG
*
3469828 TCTTCTTCTGTTAATTCTTGG
1 TCTTCTTCTGTTAATTCTAGG
3469849 TCTT
1 TCTT
3469853 GATCTTGGGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.10, C:0.19, G:0.15, T:0.55
Consensus pattern (21 bp):
TCTTCTTCTGTTAATTCTAGG
Found at i:3490773 original size:23 final size:23
Alignment explanation
Indices: 3490747--3490799 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
3490737 TTTGTCTTGA
3490747 CCACATAGGTTTGCACCAAAGTG
1 CCACATAGGTTTGCACCAAAGTG
*
3490770 CCACATAGGTTTGCACCGAAGTG
1 CCACATAGGTTTGCACCAAAGTG
3490793 CCACATA
1 CCACATA
3490800 ATTATCCTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (23 bp):
CCACATAGGTTTGCACCAAAGTG
Found at i:3495390 original size:22 final size:22
Alignment explanation
Indices: 3495365--3495415 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
3495355 AGTGCCTCAG
*
3495365 CACTGTTAAGGAAGTGCATTAA
1 CACTGTTAAGGAAGTACATTAA
** * *
3495387 CACTAATACGGAAGTACATTAG
1 CACTGTTAAGGAAGTACATTAA
3495409 CACTGTT
1 CACTGTT
3495416 GGGGGATTTA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (22 bp):
CACTGTTAAGGAAGTACATTAA
Found at i:3495593 original size:14 final size:14
Alignment explanation
Indices: 3495574--3495600 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3495564 GCACACAATT
3495574 TCATTATTATTATC
1 TCATTATTATTATC
3495588 TCATTATTATTAT
1 TCATTATTATTAT
3495601 AAATCTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (14 bp):
TCATTATTATTATC
Found at i:3499887 original size:54 final size:54
Alignment explanation
Indices: 3499773--3499890 Score: 137
Period size: 54 Copynumber: 2.2 Consensus size: 54
3499763 ATATGTGTAC
* * *
3499773 TTTCGGCACTATGTATGCAACCCACAAAATTCATAATGAGTTTATGAATGATCG
1 TTTCAGCACTATGTATGCAACCCACAAAATTCATAATAAGTTTATGAATGATCA
* * * ** * **
3499827 TATCAGCACTATGTGTGCAATCCATGAAATTCATAATAAGTTTTTGAATTTTCA
1 TTTCAGCACTATGTATGCAACCCACAAAATTCATAATAAGTTTATGAATGATCA
3499881 TTTCAGCACT
1 TTTCAGCACT
3499891 TTGGGGCAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (54 bp):
TTTCAGCACTATGTATGCAACCCACAAAATTCATAATAAGTTTATGAATGATCA
Found at i:3501961 original size:20 final size:20
Alignment explanation
Indices: 3501938--3501997 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
3501928 TTGTTCACAC
3501938 AGTATCAATACTATTCATAA
1 AGTATCAATACTATTCATAA
* * * *
3501958 AGTATTAGTATTATTCATAC
1 AGTATCAATACTATTCATAA
3501978 AGTA-CAATACTATTCATAA
1 AGTATCAATACTATTCATAA
3501997 A
1 A
3501998 AACATTTTTG
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 12 0.38
20 20 0.62
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (20 bp):
AGTATCAATACTATTCATAA
Found at i:3503588 original size:18 final size:18
Alignment explanation
Indices: 3503565--3503612 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
3503555 GTTGACTACT
3503565 TCATCTTCATCATTGGAG
1 TCATCTTCATCATTGGAG
3503583 TCATCTTCATCATTGGAG
1 TCATCTTCATCATTGGAG
3503601 TCATCTTCATCA
1 TCATCTTCATCA
3503613 CTCCAAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (18 bp):
TCATCTTCATCATTGGAG
Found at i:3505489 original size:19 final size:20
Alignment explanation
Indices: 3505445--3505494 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3505435 ACATTATCGA
* *
3505445 TACTACTCATACAGTACAGG
1 TACTATTCATACAATACAGG
*
3505465 TACTATTCATACAATACA-T
1 TACTATTCATACAATACAGG
3505484 TACTATTCATA
1 TACTATTCATA
3505495 AAAACATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (20 bp):
TACTATTCATACAATACAGG
Found at i:3508349 original size:10 final size:10
Alignment explanation
Indices: 3508334--3508375 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
3508324 AGCTTGAGGA
3508334 ATGAAGAATG
1 ATGAAGAATG
*
3508344 ATGAAGAA-A
1 ATGAAGAATG
* *
3508353 AGGGAGAATG
1 ATGAAGAATG
3508363 ATGAAGAATG
1 ATGAAGAATG
3508373 ATG
1 ATG
3508376 GGAGAAATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
9 6 0.24
10 19 0.76
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (10 bp):
ATGAAGAATG
Found at i:3512440 original size:16 final size:18
Alignment explanation
Indices: 3512393--3512443 Score: 81
Period size: 17 Copynumber: 3.0 Consensus size: 18
3512383 GCTACATTTA
3512393 TATTGTTTAGATTGATT-
1 TATTGTTTAGATTGATTG
3512410 TATTGTTTAGATTGATTG
1 TATTGTTTAGATTGATTG
3512428 T-TTGTTT-GATTGATTG
1 TATTGTTTAGATTGATTG
3512444 GAAATTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
16 9 0.27
17 23 0.70
18 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.59
Consensus pattern (18 bp):
TATTGTTTAGATTGATTG
Found at i:3512544 original size:16 final size:18
Alignment explanation
Indices: 3512497--3512547 Score: 81
Period size: 17 Copynumber: 3.0 Consensus size: 18
3512487 GCTACATTTA
3512497 TATTGTTTAGATTGATT-
1 TATTGTTTAGATTGATTG
3512514 TATTGTTTAGATTGATTG
1 TATTGTTTAGATTGATTG
3512532 T-TTGTTT-GATTGATTG
1 TATTGTTTAGATTGATTG
3512548 GAAATTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
16 9 0.27
17 23 0.70
18 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.59
Consensus pattern (18 bp):
TATTGTTTAGATTGATTG
Found at i:3512551 original size:104 final size:103
Alignment explanation
Indices: 3512367--3512577 Score: 413
Period size: 104 Copynumber: 2.0 Consensus size: 103
3512357 ATCTACGAGG
3512367 TGTGTCTCTAATCTATGCTACATTTATATTGTTTAGATTGATTTATTGTTTAGATTGATTGTTTG
1 TGTGTCTCTAATCTATGCTACATTTATATTGTTTAGATTGATTTATTGTTTAGATTGATTGTTTG
3512432 TTTGATTGATTGGAAATTTATTTGTGAGCATGTCTAAT
66 TTTGATTGATTGGAAATTTATTTGTGAGCATGTCTAAT
3512470 TGTGCTCTCTAATCTATGCTACATTTATATTGTTTAGATTGATTTATTGTTTAGATTGATTGTTT
1 TGTG-TCTCTAATCTATGCTACATTTATATTGTTTAGATTGATTTATTGTTTAGATTGATTGTTT
3512535 GTTTGATTGATTGGAAATTTATTTGTGAGCATGTCTAAT
65 GTTTGATTGATTGGAAATTTATTTGTGAGCATGTCTAAT
3512574 TGTG
1 TGTG
3512578 GAAACGACTG
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
103 4 0.04
104 103 0.96
ACGTcount: A:0.23, C:0.07, G:0.19, T:0.51
Consensus pattern (103 bp):
TGTGTCTCTAATCTATGCTACATTTATATTGTTTAGATTGATTTATTGTTTAGATTGATTGTTTG
TTTGATTGATTGGAAATTTATTTGTGAGCATGTCTAAT
Found at i:3514883 original size:294 final size:295
Alignment explanation
Indices: 3514343--3514938 Score: 1072
Period size: 294 Copynumber: 2.0 Consensus size: 295
3514333 TGTTTGATCA
*
3514343 TTTTGGGACATTGAACACAAATTTTGTTTTGGACTTTAATATTTGAATTTTGAATTTGATAAACA
1 TTTTGTGACATTGAACACAAATTTTGTTTTGGACTTTAATATTTGAATTTTGAATTTGATAAACA
* *
3514408 TTTAATTTATATTTTTAGTTATTGTTGATTTATTTTGATTACTTAAAGTATTTGAAATCAATAAA
66 TTTAATTTATATTTTTAGTTATTGTTGATTTATTTTGATTACATAAAGAATTTGAAATCAATAAA
*
3514473 TACGAGGGTAAATTTTCAATGTATTTAAAGTAATGTTTAGGTATGATTTTGGGGAAATTAGTTAA
131 TACGAGAGTAAATTTTCAATGTATTTAAAGTAATGTTTAGGTATGATTTTGGGGAAATTAGTTAA
3514538 TGTGCCTTCTGGATCCGACCTATTTCATCTAAGTCGGGTAAAGGAGATTACA-AGTAC-AGACAA
196 TGTGCCTTCTGGATCCGACCTATTTCATCTAAGTCGGGTAAAGGAGATTACAGA-TACGA-ACAA
3514601 AGTTTAAAGGAGTGATCAAAGAGCCTCATTTATGTGT
259 AGTTTAAAGGAGTGATCAAAGAGCCTCATTTATGTGT
*
3514638 TTTTGTGATATTGAACACAAATTTTGTTTTGGACTTTAATATTTGAATTTTGAATTTGATAAACA
1 TTTTGTGACATTGAACACAAATTTTGTTTTGGACTTTAATATTTGAATTTTGAATTTGATAAACA
*
3514703 TTTAATTTATA-TTTTAGTTATTGTTGATTTATTTTGATTACATAAAGAATTTGTAATCAATAAA
66 TTTAATTTATATTTTTAGTTATTGTTGATTTATTTTGATTACATAAAGAATTTGAAATCAATAAA
*
3514767 TACGAGAGTAAATTTTCAATGTATTTAAAGTAATTTTTAGGTATGATTTTGGGGAAATTAGTTAA
131 TACGAGAGTAAATTTTCAATGTATTTAAAGTAATGTTTAGGTATGATTTTGGGGAAATTAGTTAA
*
3514832 TGTGCCTTCTGGATCCGACCTATTTCATCTAAGTCGGGTAAAGGTGATTACAGATACGAACAAAG
196 TGTGCCTTCTGGATCCGACCTATTTCATCTAAGTCGGGTAAAGGAGATTACAGATACGAACAAAG
*
3514897 TTTGAAGGAGTGATCAAAGAGCCTCATTTATGTGT
261 TTTAAAGGAGTGATCAAAGAGCCTCATTTATGTGT
3514932 TTTTGTG
1 TTTTGTG
3514939 CAAGATAATA
Statistics
Matches: 290, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
294 214 0.74
295 76 0.26
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (295 bp):
TTTTGTGACATTGAACACAAATTTTGTTTTGGACTTTAATATTTGAATTTTGAATTTGATAAACA
TTTAATTTATATTTTTAGTTATTGTTGATTTATTTTGATTACATAAAGAATTTGAAATCAATAAA
TACGAGAGTAAATTTTCAATGTATTTAAAGTAATGTTTAGGTATGATTTTGGGGAAATTAGTTAA
TGTGCCTTCTGGATCCGACCTATTTCATCTAAGTCGGGTAAAGGAGATTACAGATACGAACAAAG
TTTAAAGGAGTGATCAAAGAGCCTCATTTATGTGT
Found at i:3521258 original size:23 final size:24
Alignment explanation
Indices: 3521222--3521271 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
3521212 AAATATATTT
3521222 TATTATTAACTTAA-TTTAAAAAA
1 TATTATTAACTTAATTTTAAAAAA
3521245 TATT-TTAACTTTAATTTTAAAAAA
1 TATTATTAAC-TTAATTTTAAAAAA
3521269 TAT
1 TAT
3521272 ATTTTATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 5 0.20
23 8 0.32
24 12 0.48
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TATTATTAACTTAATTTTAAAAAA
Found at i:3521404 original size:57 final size:58
Alignment explanation
Indices: 3521282--3521405 Score: 128
Period size: 57 Copynumber: 2.1 Consensus size: 58
3521272 ATTTTATGTT
* * * *
3521282 AAAATTAAGATAAAAATAAAATATATTTAATAATTTAAAGTAATTATATAATATATCTAA
1 AAAATTAAGATAAAAAT--AATATATTTAATAAGTTAAAATAATGATAAAATATATCTAA
* * *
3521342 TAAATTAAGAT-AAAAT-ATATACTTTGAA-AAGTTAAAATAATGATAAAATATTTTTAA
1 AAAATTAAGATAAAAATAATATA-TTT-AATAAGTTAAAATAATGATAAAATATATCTAA
3521399 AAAATTA
1 AAAATTA
3521406 CATTGAAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
56 5 0.09
57 32 0.59
58 2 0.04
59 5 0.09
60 10 0.19
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (58 bp):
AAAATTAAGATAAAAATAATATATTTAATAAGTTAAAATAATGATAAAATATATCTAA
Found at i:3521454 original size:25 final size:26
Alignment explanation
Indices: 3521426--3521510 Score: 77
Period size: 25 Copynumber: 3.2 Consensus size: 26
3521416 AAATATATGT
*
3521426 TTTTATATTAAATTAAAAAT-AAATA
1 TTTTAAATTAAATTAAAAATAAAATA
* *
3521451 TTTTAAATTAAGTTAATAATAAAATA
1 TTTTAAATTAAATTAAAAATAAAATA
*
3521477 TATTT-AA-TAAGTTAATATAATAAAATA
1 T-TTTAAATTAAATTAA-A-AATAAAATA
3521504 TATTTAA
1 T-TTTAA
3521511 TAAGTTAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
25 25 0.49
26 8 0.16
27 17 0.33
28 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TTTTAAATTAAATTAAAAATAAAATA
Found at i:3521454 original size:26 final size:26
Alignment explanation
Indices: 3521415--3521483 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 26
3521405 ACATTGAAAT
* * *
3521415 AAAATATATGTTTTTATATTAAATTA
1 AAAATAAATATTTTTAAATTAAATTA
*
3521441 AAAATAAATA-TTTTAAATTAAGTTA
1 AAAATAAATATTTTTAAATTAAATTA
* *
3521466 ATAATAAAATATATTTAA
1 AAAAT-AAATATTTTTAA
3521484 TAAGTTAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
25 17 0.49
26 13 0.37
27 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
AAAATAAATATTTTTAAATTAAATTA
Found at i:3521486 original size:14 final size:14
Alignment explanation
Indices: 3521467--3521513 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
3521457 ATTAAGTTAA
3521467 TAATAAAATATATT
1 TAATAAAATATATT
** *
3521481 TAATAAGTTA-ATA
1 TAATAAAATATATT
3521494 TAATAAAATATATT
1 TAATAAAATATATT
3521508 TAATAA
1 TAATAA
3521514 GTTAATATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.38
14 16 0.62
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
TAATAAAATATATT
Found at i:3521493 original size:17 final size:17
Alignment explanation
Indices: 3521473--3521522 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 17
3521463 TTAATAATAA
3521473 AATATATTTAATAAGTT
1 AATATATTTAATAAGTT
3521490 -A-ATA--TAATAA---
1 AATATATTTAATAAGTT
3521500 AATATATTTAATAAGTT
1 AATATATTTAATAAGTT
3521517 AATATA
1 AATATA
3521523 ACAAAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 14
0.65 0.00 0.35
Matches are distributed among these distances:
11 1 0.04
12 3 0.12
13 6 0.23
14 6 0.23
15 3 0.12
16 1 0.04
17 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (17 bp):
AATATATTTAATAAGTT
Found at i:3521496 original size:27 final size:27
Alignment explanation
Indices: 3521446--3521531 Score: 124
Period size: 27 Copynumber: 3.2 Consensus size: 27
3521436 AATTAAAAAT
3521446 AAATAT-TTTAAATTAAGTT-A-ATAATA
1 AAATATATTT-AA-TAAGTTAATATAATA
3521472 AAATATATTTAATAAGTTAATATAATA
1 AAATATATTTAATAAGTTAATATAATA
*
3521499 AAATATATTTAATAAGTTAATATAACA
1 AAATATATTTAATAAGTTAATATAATA
3521526 AAATAT
1 AAATAT
3521532 TTCTTAAAGT
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
25 6 0.11
26 9 0.16
27 41 0.73
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (27 bp):
AAATATATTTAATAAGTTAATATAATA
Found at i:3522443 original size:29 final size:29
Alignment explanation
Indices: 3522426--3522606 Score: 188
Period size: 28 Copynumber: 6.3 Consensus size: 29
3522416 TCATGTAAAG
3522426 TCAGGACGAGGATATAAT-CCATGCAGAA
1 TCAGGACGAGGATATAATCCCATGCAGAA
* *
3522454 TCAGGATGAGAATATAATCCCATGCAGAA
1 TCAGGACGAGGATATAATCCCATGCAGAA
* * *
3522483 CCAGGATGAGGATATAGTCCCATGCAGAA
1 TCAGGACGAGGATATAATCCCATGCAGAA
*
3522512 TCAGGACG-GGATATAATCCCATGCAAAA
1 TCAGGACGAGGATATAATCCCATGCAGAA
* * *
3522540 TTAGGACG-GAATATAATCCAATGCAGAA
1 TCAGGACGAGGATATAATCCCATGCAGAA
* * ** *** *
3522568 TTAGAACGATAATATAATATAATACAGAA
1 TCAGGACGAGGATATAATCCCATGCAGAA
3522597 TCAGGACGAG
1 TCAGGACGAG
3522607 ATTATAACCT
Statistics
Matches: 130, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
28 65 0.50
29 65 0.50
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (29 bp):
TCAGGACGAGGATATAATCCCATGCAGAA
Found at i:3522458 original size:28 final size:29
Alignment explanation
Indices: 3522426--3522613 Score: 193
Period size: 29 Copynumber: 6.6 Consensus size: 29
3522416 TCATGTAAAG
*
3522426 TCAGGACGAGGATATAAT-CCATGCAGAA
1 TCAGGACGAGAATATAATCCCATGCAGAA
*
3522454 TCAGGATGAGAATATAATCCCATGCAGAA
1 TCAGGACGAGAATATAATCCCATGCAGAA
* * * *
3522483 CCAGGATGAGGATATAGTCCCATGCAGAA
1 TCAGGACGAGAATATAATCCCATGCAGAA
* *
3522512 TCAGGACG-GGATATAATCCCATGCAAAA
1 TCAGGACGAGAATATAATCCCATGCAGAA
* *
3522540 TTAGGACG-GAATATAATCCAATGCAGAA
1 TCAGGACGAGAATATAATCCCATGCAGAA
* * * *** *
3522568 TTAGAACGATAATATAATATAATACAGAA
1 TCAGGACGAGAATATAATCCCATGCAGAA
*
3522597 TCAGGACGAGATTATAA
1 TCAGGACGAGAATATAA
3522614 CCTCCGTAGA
Statistics
Matches: 136, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
28 65 0.48
29 71 0.52
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (29 bp):
TCAGGACGAGAATATAATCCCATGCAGAA
Found at i:3522583 original size:57 final size:57
Alignment explanation
Indices: 3522410--3522585 Score: 194
Period size: 57 Copynumber: 3.1 Consensus size: 57
3522400 TGACGAATAC
* * * *
3522410 ATAATCTCATGTAAAGTCAGGACGAGGATATAATCCATGCAGAATCAGGATGAGAAT
1 ATAATCCCATGCAAAATCAGGACGAGGATATAATCCATGCAGAATCAGGACGAGAAT
* * * * *
3522467 ATAATCCCATGCAGAACCAGGATGAGGATATAGTCCCATGCAGAATCAGGACG-GGAT
1 ATAATCCCATGCAAAATCAGGACGAGGATATAAT-CCATGCAGAATCAGGACGAGAAT
* * * * *
3522524 ATAATCCCATGCAAAATTAGGACG-GAATATAATCCAATGCAGAATTAGAACGATAAT
1 ATAATCCCATGCAAAATCAGGACGAGGATATAATCC-ATGCAGAATCAGGACGAGAAT
3522581 ATAAT
1 ATAAT
3522586 ATAATACAGA
Statistics
Matches: 97, Mismatches: 19, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
55 2 0.02
56 21 0.22
57 57 0.59
58 17 0.18
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (57 bp):
ATAATCCCATGCAAAATCAGGACGAGGATATAATCCATGCAGAATCAGGACGAGAAT
Found at i:3522583 original size:85 final size:86
Alignment explanation
Indices: 3522426--3522606 Score: 204
Period size: 85 Copynumber: 2.1 Consensus size: 86
3522416 TCATGTAAAG
* * * * *
3522426 TCAGGACGAGGATATAATCCATGCAGAATCAGGATGAGAATATAATCCCATGCAGAACCAGGATG
1 TCAGGACGAGGATATAATCCATGCAAAATCAGGACGAGAATATAATCCAATGCAGAACCAGAACG
*
3522491 AGGATATAGTCCCATGCAGAA
66 AGAATATAGTCCCATGCAGAA
* **
3522512 TCAGGACG-GGATATAATCCCATGCAAAATTAGGACG-GAATATAATCCAATGCAGAATTAGAAC
1 TCAGGACGAGGATATAAT-CCATGCAAAATCAGGACGAGAATATAATCCAATGCAGAACCAGAAC
* * *** *
3522575 GATAATATAATATAATACAGAA
65 GAGAATATAGTCCCATGCAGAA
3522597 TCAGGACGAG
1 TCAGGACGAG
3522607 ATTATAACCT
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
85 54 0.69
86 24 0.31
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (86 bp):
TCAGGACGAGGATATAATCCATGCAAAATCAGGACGAGAATATAATCCAATGCAGAACCAGAACG
AGAATATAGTCCCATGCAGAA
Found at i:3523230 original size:20 final size:20
Alignment explanation
Indices: 3523205--3523242 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3523195 TTACAAAAAA
3523205 GTCAATGGGTC-AAAGTCAGG
1 GTCAAT-GGTCAAAAGTCAGG
3523225 GTCAATGGTCAAAAGTCA
1 GTCAATGGTCAAAAGTCA
3523243 AATTCAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (20 bp):
GTCAATGGTCAAAAGTCAGG
Found at i:3526041 original size:31 final size:31
Alignment explanation
Indices: 3525995--3526093 Score: 162
Period size: 31 Copynumber: 3.2 Consensus size: 31
3525985 TTATCTTATG
*
3525995 GTGACCACATCTTAATTAAATAAAAATGAAA
1 GTGACCATATCTTAATTAAATAAAAATGAAA
*
3526026 GTGATCATATCTTAATTAAATAAAAATGAAA
1 GTGACCATATCTTAATTAAATAAAAATGAAA
* *
3526057 ATGACCATATCTTAATTAAATAAAAATGGAA
1 GTGACCATATCTTAATTAAATAAAAATGAAA
3526088 GTGACC
1 GTGACC
3526094 GTATATTATA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (31 bp):
GTGACCATATCTTAATTAAATAAAAATGAAA
Found at i:3528264 original size:2 final size:2
Alignment explanation
Indices: 3528257--3528299 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3528247 GTACTCGATT
3528257 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3528299 T
1 T
3528300 TAAAAAAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3531869 original size:35 final size:34
Alignment explanation
Indices: 3531800--3531912 Score: 145
Period size: 35 Copynumber: 3.3 Consensus size: 34
3531790 AAAACAGTCC
* *
3531800 TCAATTTTATTCTAAACCCAAATTCTAAAGTAAT
1 TCAATTTAATTCTAAACCCAAATTCTAAAATAAT
* *
3531834 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTAATTCTAAACCC-AAATTCTAAAATAAT
* * *
3531869 TCAATTAAATTCTAAACTCAAAATTCTAAAATACT
1 TCAATTTAATTCTAAAC-CCAAATTCTAAAATAAT
3531904 TCAATTTAA
1 TCAATTTAA
3531913 GGTTTAGAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
34 18 0.26
35 49 0.72
36 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.01, T:0.36
Consensus pattern (34 bp):
TCAATTTAATTCTAAACCCAAATTCTAAAATAAT
Found at i:3532508 original size:35 final size:35
Alignment explanation
Indices: 3532462--3532570 Score: 155
Period size: 35 Copynumber: 3.1 Consensus size: 35
3532452 AAACCTTAAG
* * * **
3532462 TTGAAGTATTTTAGAATTTTGGGTTTAGAATGTAA
1 TTGAATTATTTTGGAATTTAGGGTTTAGAATAAAA
3532497 TTGAATTATTTTGGAATTTAGGGTTTAGAATAAAA
1 TTGAATTATTTTGGAATTTAGGGTTTAGAATAAAA
* *
3532532 TTGAATTACTTTGGAATTTGGGGTTTAGAATAAAA
1 TTGAATTATTTTGGAATTTAGGGTTTAGAATAAAA
3532567 TTGA
1 TTGA
3532571 GGACTATTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.34, C:0.01, G:0.22, T:0.43
Consensus pattern (35 bp):
TTGAATTATTTTGGAATTTAGGGTTTAGAATAAAA
Found at i:3536886 original size:16 final size:16
Alignment explanation
Indices: 3536865--3536895 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3536855 CACCTTTTAG
3536865 GTGTAGAAAACAGACT
1 GTGTAGAAAACAGACT
3536881 GTGTAGAAAACAGAC
1 GTGTAGAAAACAGAC
3536896 ATGTCTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.13, G:0.26, T:0.16
Consensus pattern (16 bp):
GTGTAGAAAACAGACT
Found at i:3539197 original size:51 final size:51
Alignment explanation
Indices: 3539121--3539221 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
3539111 TAAGGAAAGG
* * *
3539121 ATAGGCTGTAAAGAAATATCGGTTTGAACATGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTAAAATTCCTTGTAACTA
3539172 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTAAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTAAAATTCCTTGTAACT
3539222 CTCCCCCTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.32
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTAAAATTCCTTGTAACTA
Found at i:3542311 original size:54 final size:55
Alignment explanation
Indices: 3542198--3542364 Score: 182
Period size: 54 Copynumber: 3.0 Consensus size: 55
3542188 CTTAGGTCTG
* *
3542198 AGACACTGGTGCAAGTGTCCGACAGGGAGGTTCAAGATCA-AGT-TTCGTGCTTGCCA
1 AGACACTGGTGCAAGTGTCCGACAAGGAGG-TCAAGAT-AGAGTATT-GAGCTTGCCA
* *
3542254 AGACAGTGGTGCAAGTGTCCGACAAGGA-GTCAAGATAGAGTATTGGGCTTGCCA
1 AGACACTGGTGCAAGTGTCCGACAAGGAGGTCAAGATAGAGTATTGAGCTTGCCA
* ** *
3542308 AGACATTGGTGCAAGTGTCCGA-AAGGGAATCTCAAGATAGA-TATCGAGCTTGCCA
1 AGACACTGGTGCAAGTGTCCGACAA-GG-AGGTCAAGATAGAGTATTGAGCTTGCCA
3542363 AG
1 AG
3542365 GCCACTAGAC
Statistics
Matches: 99, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
53 3 0.03
54 42 0.42
55 18 0.18
56 36 0.36
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.22
Consensus pattern (55 bp):
AGACACTGGTGCAAGTGTCCGACAAGGAGGTCAAGATAGAGTATTGAGCTTGCCA
Found at i:3550589 original size:209 final size:210
Alignment explanation
Indices: 3550227--3550813 Score: 885
Period size: 209 Copynumber: 2.8 Consensus size: 210
3550217 ATTTGTCAAT
* * * * * *
3550227 GACCACTAAACTATTTAATTGGATCCAATCAAACCACAAAGGCTAAAATTTAATAGAAGTGTTGA
1 GACCACTAAATTATTTAATTGTATCCAATCAAACCACCAACGCTAAAATTTAATAGAAGTATCGA
*
3550292 CATGACAGTTAATAAATATTTGTATTAAGATTTAATCATCTAACTAAATTATGACACATCTTACC
66 CATGACAGTTAATAAATATTTGTATTAAGATTTAATCATCTAACCAAATTATGACACATCTTACC
3550357 GATCTTGAAGTGCTTATGACACATCTTACCAAGTATTATCATCTGGTTGGAGTTAAAA-TAATAA
131 GATCTTGAAGTGCTTATGACACATCTTACCAAGTATTATCATCTGGTTGGAGTTAAAACTAATAA
3550421 CAATTTTATCAATCA
196 CAATTTTATCAATCA
* *
3550436 GACCACTAAATTATTTAATTGTATCCAATCAAACCACCGACGCTAAAATTTAATAGAAATATCGA
1 GACCACTAAATTATTTAATTGTATCCAATCAAACCACCAACGCTAAAATTTAATAGAAGTATCGA
*
3550501 CATGACAGTTAATAAATATTTGTATCAAGATTTAATCATCTAACCAAATTATGACACATCTTACC
66 CATGACAGTTAATAAATATTTGTATTAAGATTTAATCATCTAACCAAATTATGACACATCTTACC
* * *
3550566 GATCTTAAAGTGCTCAGGACACATCTTACCAAGTATTATCATCTGGTTGGAGTTAAAACTAATAA
131 GATCTTGAAGTGCTTATGACACATCTTACCAAGTATTATCATCTGGTTGGAGTTAAAACTAATAA
*
3550631 CAATTTTGTCAATCA
196 CAATTTTATCAATCA
* *
3550646 GACCACTAAATTATTTAATTGTATCCAATCAAACCACCAACGCTAAAATTTAACAGAAGTA-CTA
1 GACCACTAAATTATTTAATTGTATCCAATCAAACCACCAACGCTAAAATTTAATAGAAGTATC-G
** * * *
3550710 ACAT-AGCAGTTTCCT-AATATTTGTATTAAGATTTAATAATCTAACCAAATTATGACATATATT
65 ACATGA-CAG-TTAATAAATATTTGTATTAAGATTTAATCATCTAACCAAATTATGACACATCTT
* * * * *
3550773 ACCGGTTTTGAATTGTTTATGACACATATTACCAAGTATTA
128 ACCGATCTTGAAGTGCTTATGACACATCTTACCAAGTATTA
3550814 CTAGAGATGG
Statistics
Matches: 342, Mismatches: 32, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
209 177 0.52
210 162 0.47
211 3 0.01
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (210 bp):
GACCACTAAATTATTTAATTGTATCCAATCAAACCACCAACGCTAAAATTTAATAGAAGTATCGA
CATGACAGTTAATAAATATTTGTATTAAGATTTAATCATCTAACCAAATTATGACACATCTTACC
GATCTTGAAGTGCTTATGACACATCTTACCAAGTATTATCATCTGGTTGGAGTTAAAACTAATAA
CAATTTTATCAATCA
Found at i:3550992 original size:32 final size:33
Alignment explanation
Indices: 3550977--3551042 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
3550967 GGTGATTATT
3550977 GGATCAGTTG-TTTTTCGGTTCGGGTCAATATC
1 GGATCAGTTGATTTTTCGGTTCGGGTCAATATC
* * *
3551009 GGATCGGTTGATTTTT-TGATCGGGTCAATATC
1 GGATCAGTTGATTTTTCGGTTCGGGTCAATATC
3551041 GG
1 GG
3551043 GCCGGGTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 25 0.83
33 5 0.17
ACGTcount: A:0.17, C:0.14, G:0.30, T:0.39
Consensus pattern (33 bp):
GGATCAGTTGATTTTTCGGTTCGGGTCAATATC
Found at i:3560109 original size:96 final size:96
Alignment explanation
Indices: 3559938--3560133 Score: 275
Period size: 96 Copynumber: 2.0 Consensus size: 96
3559928 ATTCCTTTAA
* * * *
3559938 AGGTGCAAAGGCCAAGATGTTGACTCAAGATATAGATACTGTCATACCAAGGAGGAGAAGTCCCT
1 AGGTGCAAAGGCCAAGATGTTGACTCAAGAGATAGATACAGTAATACCAAGGAGGAGAAGACCCT
* * * * *
3560003 TCACAGAGACATGAAGATCGCTTCGCATTGG
66 TCACAAAGACACGAAGACCACTTCACATTGG
* *
3560034 AGGTGCAAAGGCTAAGATGTTGACTCAAGAGATAGATACAGTAATACCAAGGATGAGAAGACCCT
1 AGGTGCAAAGGCCAAGATGTTGACTCAAGAGATAGATACAGTAATACCAAGGAGGAGAAGACCCT
* *
3560099 TTATAAAGACACGAAGACCACTTCACATTGG
66 TCACAAAGACACGAAGACCACTTCACATTGG
3560130 AGGT
1 AGGT
3560134 AAGAATGGAG
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 87 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.20
Consensus pattern (96 bp):
AGGTGCAAAGGCCAAGATGTTGACTCAAGAGATAGATACAGTAATACCAAGGAGGAGAAGACCCT
TCACAAAGACACGAAGACCACTTCACATTGG
Found at i:3567395 original size:22 final size:21
Alignment explanation
Indices: 3567353--3567392 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3567343 GAGTTTATTT
*
3567353 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3567374 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3567393 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3569418 original size:45 final size:46
Alignment explanation
Indices: 3569332--3569420 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 46
3569322 GGTACACTAA
** * * *
3569332 GAGTGCATTGATGCATGGTCTTGTGCATTGATGCATCAAATGCACT
1 GAGTGCATCAATGCATGGTCATGTGCATCGATACATCAAATGCACT
3569378 GAGTGCATCAATGCATGGT-ATGTGCATCGATACA-CAAAATGCA
1 GAGTGCATCAATGCATGGTCATGTGCATCGATACATC-AAATGCA
3569421 TTCGATGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 1 0.03
45 19 0.51
46 17 0.46
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (46 bp):
GAGTGCATCAATGCATGGTCATGTGCATCGATACATCAAATGCACT
Found at i:3569465 original size:20 final size:20
Alignment explanation
Indices: 3569440--3569477 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3569430 TGAAAAATTA
3569440 ATTGGTGCATCGATGCATAG
1 ATTGGTGCATCGATGCATAG
* *
3569460 ATTGGTGTATCGGTGCAT
1 ATTGGTGCATCGATGCAT
3569478 CACTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.13, G:0.32, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATAG
Found at i:3570103 original size:12 final size:12
Alignment explanation
Indices: 3570086--3570129 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
3570076 TTCAAGCTTG
3570086 AATCGAGCTCAA
1 AATCGAGCTCAA
**
3570098 AATCGAGCT-TT
1 AATCGAGCTCAA
3570109 AATCGAGCTCAA
1 AATCGAGCTCAA
*
3570121 AATTGAGCT
1 AATCGAGCT
3570130 TTAATCGAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (12 bp):
AATCGAGCTCAA
Found at i:3570112 original size:11 final size:11
Alignment explanation
Indices: 3570098--3570151 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
3570088 TCGAGCTCAA
3570098 AATCGAGCTTT
1 AATCGAGCTTT
**
3570109 AATCGAGCTCAA
1 AATCGAGCT-TT
*
3570121 AATTGAGCTTT
1 AATCGAGCTTT
*
3570132 AATCGAGCTTC
1 AATCGAGCTTT
*
3570143 AATTGAGCT
1 AATCGAGCT
3570152 CCTGATTTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
11 26 0.76
12 8 0.24
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (11 bp):
AATCGAGCTTT
Found at i:3570112 original size:23 final size:23
Alignment explanation
Indices: 3570080--3570140 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
3570070 GGTGAGTTCA
*
3570080 AGCTTGAATCGAGCTCAAAATCG
1 AGCTTTAATCGAGCTCAAAATCG
*
3570103 AGCTTTAATCGAGCTCAAAATTG
1 AGCTTTAATCGAGCTCAAAATCG
3570126 AGCTTTAATCGAGCT
1 AGCTTTAATCGAGCT
3570141 TCAATTGAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (23 bp):
AGCTTTAATCGAGCTCAAAATCG
Found at i:3581705 original size:48 final size:48
Alignment explanation
Indices: 3581641--3581738 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
3581631 CAAAAAGAGA
*
3581641 GAGACTCATTGGGGAAAAGAGGAAGCTCGCCAGAGTGAGAGAAAAACT
1 GAGACTCATTGGGGAAAAGAGGAAACTCGCCAGAGTGAGAGAAAAACT
* *
3581689 GAGATTCATTGGGGAAAAGAGGAAACTCGCTAGAGTGAGAGAAAAACT
1 GAGACTCATTGGGGAAAAGAGGAAACTCGCCAGAGTGAGAGAAAAACT
3581737 GA
1 GA
3581739 CTCTTTGTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.41, C:0.12, G:0.33, T:0.14
Consensus pattern (48 bp):
GAGACTCATTGGGGAAAAGAGGAAACTCGCCAGAGTGAGAGAAAAACT
Found at i:3582050 original size:18 final size:17
Alignment explanation
Indices: 3582027--3582073 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
3582017 TGTTTATTAG
3582027 GGAATTGAAATCTGTGAA
1 GGAATTGAAATCTGT-AA
*
3582045 GGAATT-AGAATCTGTCA
1 GGAATTGA-AATCTGTAA
*
3582062 GGAATTGGAATC
1 GGAATTGAAATC
3582074 CAATTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.28
Consensus pattern (17 bp):
GGAATTGAAATCTGTAA
Found at i:3584084 original size:22 final size:22
Alignment explanation
Indices: 3584041--3584086 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3584031 TTTTATGTAT
*
3584041 TTATTTATTTACCATTGTTTAC
1 TTATTTATTTACCATTGCTTAC
* *
3584063 TTATTTATTTATCTTTGCTTAC
1 TTATTTATTTACCATTGCTTAC
3584085 TT
1 TT
3584087 TTATTATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.13, G:0.04, T:0.63
Consensus pattern (22 bp):
TTATTTATTTACCATTGCTTAC
Found at i:3584109 original size:18 final size:19
Alignment explanation
Indices: 3584023--3584111 Score: 53
Period size: 18 Copynumber: 4.8 Consensus size: 19
3584013 GTTTTTTAGT
*
3584023 TTTATTTA-TT-TTATGTA
1 TTTATTTATTTATTATATA
** *
3584040 TTTATTTATTTACCAT-TG
1 TTTATTTATTTATTATATA
* *
3584058 TTTACTTATTTATT-TATC
1 TTTATTTATTTATTATATA
**
3584076 TTTGCTTACTTTTATTATAT-
1 TTTATTTA--TTTATTATATA
3584096 TTTATTTATTTATTAT
1 TTTATTTATTTATTAT
3584112 GTTGATATTT
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
17 9 0.16
18 30 0.54
19 2 0.04
20 12 0.21
21 3 0.05
ACGTcount: A:0.22, C:0.07, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTATTTATTTATTATATA
Found at i:3585343 original size:36 final size:36
Alignment explanation
Indices: 3585296--3585373 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
3585286 ATGCTTGTAG
3585296 TGAACCATAAAATGCTCACCCTAGGTAGAGCTATAC
1 TGAACCATAAAATGCTCACCCTAGGTAGAGCTATAC
*
3585332 TGAACCATAAAATGTTCACCCTAGGTAGAGCTATAC
1 TGAACCATAAAATGCTCACCCTAGGTAGAGCTATAC
3585368 TGAACC
1 TGAACC
3585374 TCTATCCTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (36 bp):
TGAACCATAAAATGCTCACCCTAGGTAGAGCTATAC
Found at i:3589131 original size:29 final size:29
Alignment explanation
Indices: 3589022--3589148 Score: 103
Period size: 29 Copynumber: 4.3 Consensus size: 29
3589012 TGTATTTTGA
* * * *
3589022 TAAAATGTCCAATGTGGTTCTTTTACTTT
1 TAAAATGTCTAATGTGGTACATGTACTTT
* * *
3589051 TAAAATGTTTAATATAGTACATGTA-TTT
1 TAAAATGTCTAATGTGGTACATGTACTTT
* * *
3589079 TGACACGATGTCTTATGTGATACATGTACTTT
1 T-A-A-AATGTCTAATGTGGTACATGTACTTT
*
3589111 TAAAATATCTAATGTGGTACATGTACTTT
1 TAAAATGTCTAATGTGGTACATGTACTTT
* *
3589140 GACAATGTC
1 TAAAATGTC
3589149 CAATTGATAC
Statistics
Matches: 74, Mismatches: 20, Indels: 8
0.73 0.20 0.08
Matches are distributed among these distances:
28 4 0.05
29 47 0.64
30 2 0.03
31 17 0.23
32 4 0.05
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.43
Consensus pattern (29 bp):
TAAAATGTCTAATGTGGTACATGTACTTT
Found at i:3600253 original size:12 final size:12
Alignment explanation
Indices: 3600236--3600269 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3600226 TAGAGTTGAT
3600236 AAGTTGAATTTG
1 AAGTTGAATTTG
3600248 AAGTTGAATTTG
1 AAGTTGAATTTG
*
3600260 AAGTTAAATT
1 AAGTTGAATT
3600270 CGACTTGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:3600912 original size:2 final size:2
Alignment explanation
Indices: 3600907--3601049 Score: 286
Period size: 2 Copynumber: 71.5 Consensus size: 2
3600897 GTGTTGTGTG
3600907 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3600949 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3600991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3601033 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
3601050 CGTGTGTGTG
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 141 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3601620 original size:39 final size:39
Alignment explanation
Indices: 3601575--3601694 Score: 170
Period size: 39 Copynumber: 3.0 Consensus size: 39
3601565 AGTCGAGGGT
*
3601575 TACAGTGGTCCTTTGGGACATAGTGGTCCTTCGAGACAA
1 TACAGTGGTCCTTTGGGACATAGTGGTCCTTCGGGACAA
*
3601614 TACAGTGGTCCTTCGGGACAATACAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTTGGGAC-AT--AGTGGTCCTTCGGGACAA
*
3601656 TACAGTGGTCCTACT-GGACATAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCT-TTGGGACATAGTGGTCCTTCGGGACAA
3601695 ATTTCAGTGC
Statistics
Matches: 73, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
39 36 0.49
40 2 0.03
41 2 0.03
42 33 0.45
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (39 bp):
TACAGTGGTCCTTTGGGACATAGTGGTCCTTCGGGACAA
Found at i:3601622 original size:21 final size:21
Alignment explanation
Indices: 3601575--3601694 Score: 162
Period size: 21 Copynumber: 6.0 Consensus size: 21
3601565 AGTCGAGGGT
*
3601575 TACAGTGGTCCTTTGGGAC-A
1 TACAGTGGTCCTTCGGGACAA
*
3601595 T--AGTGGTCCTTCGAGACAA
1 TACAGTGGTCCTTCGGGACAA
3601614 TACAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
3601635 TACAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
* *
3601656 TACAGTGGTCCTACTGGAC-A
1 TACAGTGGTCCTTCGGGACAA
3601676 T--AGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACAA
3601695 ATTTCAGTGC
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
18 28 0.31
19 3 0.03
20 3 0.03
21 55 0.62
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (21 bp):
TACAGTGGTCCTTCGGGACAA
Found at i:3601681 original size:60 final size:59
Alignment explanation
Indices: 3601575--3601694 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 59
3601565 AGTCGAGGGT
* *
3601575 TACAGTGGTCCTTTGGGACATAGTGGTCCTTCGAGACAATACAGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGACATAGTGGTCCTACGAGACAATA-AGTGGTCCTTCGGGACAA
3601635 TACAGTGGTCCTTCGGGACAATACAGTGGTCCTACTG-GAC-AT-AGTGGTCCTTCGGGACAA
1 TACAGTGGTCCTTCGGGAC-AT--AGTGGTCCTAC-GAGACAATAAGTGGTCCTTCGGGACAA
3601695 ATTTCAGTGC
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
60 36 0.67
61 2 0.04
62 2 0.04
63 13 0.24
64 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (59 bp):
TACAGTGGTCCTTCGGGACATAGTGGTCCTACGAGACAATAAGTGGTCCTTCGGGACAA
Found at i:3603259 original size:187 final size:185
Alignment explanation
Indices: 3603018--3604070 Score: 1129
Period size: 187 Copynumber: 5.6 Consensus size: 185
3603008 TAGGTTGTTC
* * *
3603018 CGAAAATATTATCAGAGTTTAAGTTGACGGAGCGTTGTATTATCCCAA-TATAAGAAAATAAGTT
1 CGAAAATGTTATCAGAGTTTAAGTTGATGGAGCATTGTATTAT-CCAAGTATAAGAAAATAAGTT
* * * * * * * *
3603082 TAAAATTAAAAATGTTACGATCATGTATAAGAAATACGGTTGCACCCAATAATGCGACGATTCGA
65 TAAAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCACCCAATAATGC-ATGGTTCAA
* *
3603147 TAATAAAAAATGTTGTAATCTGGAATGTTAATACTTTTAATAATAAAACAGGTTACGT
129 TAATAAAAAA-GTTGTAATCTAGAATGTTAATACTTTTAATAATAAAATAGGTTACGT
3603205 CGAAAATGTTATCAGAGTTTAAGTTGATGGAGTC-TTAG-ATTATCCAAGTATAAGAAAATAAGT
1 CGAAAATGTTATCAGAGTTTAAGTTGATGGAG-CATT-GTATTATCCAAGTATAAGAAAATAAGT
* * * * *
3603268 TTAAAACTGAAAATGTTATGAATATATATAAGAAATA-TGTTGCATCTAATAATTTCATGGTTCA
64 TTAAAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCACCCAATAA-TGCATGGTTCA
* *
3603332 ATAATAAAAAATGTTGTAATCTAGAATGTTAATATTTTTAATAATAAAGTAGGTTACG-
128 ATAATAAAAAA-GTTGTAATCTAGAATGTTAATACTTTTAATAATAAAATAGGTTACGT
* * * *
3603390 CCAAAATATTATCAGAGTTTAAGTTGATGGAGCCTTGTATTATTCC-ATTATAAGAAAATAAGTT
1 CGAAAATGTTATCAGAGTTTAAGTTGATGGAGCATTGTATTA-TCCAAGTATAAGAAAATAAGTT
* * * *
3603454 TAAAACTGAAAATGTTATGAATATATATAAAAAATACGGTTGCACCCAATAATATCATGATTCAA
65 TAAAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCACCCAATAAT-GCATGGTTCAA
* * * *
3603519 TAATAAAAGAGATTGTAATAT-GAAATGTTAATACTTTTAATAATAAAATAGGTTATGC
129 TAATAAAAAAG-TTGTAATCTAG-AATGTTAATACTTTTAATAATAAAATAGGTTACGT
* ** * * * * *
3603577 CAAAAATGTTATTTGAGTTTAAGGTAATGGAGCCTTGGATTATCCTAA-TATAAGAAAATAAATT
1 CGAAAATGTTATCAGAGTTTAAGTTGATGGAGCATTGTATTATCC-AAGTATAAGAAAATAAGTT
* * * *
3603641 TAAAACTGAAAATGTTATGAACATATATAAGAAATACGATTGCGCTCAATAATATCATGGTTCAA
65 TAAAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCACCCAATAAT-GCATGGTTCAA
* * * * *
3603706 TAATAAAAGAGATTGTAATATAGAATGTTAATTCTTTTAGTAATAAAACAGGGTT--GT
129 TAATAAAAAAG-TTGTAATCTAGAATGTTAATACTTTTAATAATAAAATA-GGTTACGT
* * * * *
3603763 GCTGAAAATGTTATTAGATTTTAAGCTGATGGAGCATTGAATTATCCCAGTATAAGAAAATAAGT
1 -C-GAAAATGTTATCAGAGTTTAAGTTGATGGAGCATTGTATTATCCAAGTATAAGAAAATAAGT
* * * * ** * * *
3603828 TTGAAAAATTAAAATGTTATGAACATATATAATAAATATGGTTGCACAAAAAAATGTAATGGTTA
64 TT-AAAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCACCCAATAATG-CATGGTTC
* * * * * * *
3603893 AAAAATAAAACAGGTTCTAATCTAGAATATTAATATTTTTAATAATAAAATTGGTTAAGT
127 AATAATAAAA-AAGTTGTAATCTAGAATGTTAATACTTTTAATAATAAAATAGGTTACGT
* * * * *
3603953 CGAAAATGTTATCAAAGTTTAAG-CGAATGGGGCATTGGATTATCCGAGTATAAGAAAATAAGTT
1 CGAAAATGTTATCAGAGTTTAAGTTG-ATGGAGCATTGTATTATCCAAGTATAAGAAAATAAGTT
* * * *
3604017 TAAAACTGAAAATATTATGAACATATATAAAAAATACGGTTGCGCCCATTAATG
65 TAAAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCACCCAATAATG
3604071 TAATAGGTCA
Statistics
Matches: 742, Mismatches: 99, Indels: 50
0.83 0.11 0.06
Matches are distributed among these distances:
184 2 0.00
185 91 0.12
186 152 0.20
187 285 0.38
188 120 0.16
189 89 0.12
190 3 0.00
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33
Consensus pattern (185 bp):
CGAAAATGTTATCAGAGTTTAAGTTGATGGAGCATTGTATTATCCAAGTATAAGAAAATAAGTTT
AAAACTGAAAATGTTATGAACATATATAAGAAATACGGTTGCACCCAATAATGCATGGTTCAATA
ATAAAAAAGTTGTAATCTAGAATGTTAATACTTTTAATAATAAAATAGGTTACGT
Found at i:3603974 original size:376 final size:371
Alignment explanation
Indices: 3603009--3604061 Score: 1272
Period size: 372 Copynumber: 2.8 Consensus size: 371
3602999 TGAACATTTT
* * *
3603009 AGGTTGTTCCGAAAATATTATCAGAGTTTAAGTTGACGGAGCGTTGTATTATCCCAATATAAGAA
1 AGGTTG-TGCGAAAATATTATCAGAGTTTAAGTTGATGGAGCATTGTATTATCCCAATATAAGAA
* * * * **
3603074 AATAAGTTT-AAAATTAAAAATGTTACGATCATGTATAAGAAATACGGTTGCACCCAATAATGCG
65 AATAAGTTTAAAAATT-AAAATGTTATGAACATATATAAAAAATACGGTTGCACCCAATAATGTA
* * * * *
3603138 ACGATTCGATAATAAAAAATGTTGTAATCTGGAATGTTAATACTTTTAATAATAAAACAGGTTAC
129 ATGATTCAATAATAAAAAAGGTTGTAATCT-GAATGTTAATACTTTTAATAATAAAATAGGTTAA
* * * *
3603203 GTCGAAAATGTTATCAGAGTTTAAGTTGATGGAGTCTTAGATTATCCAAGTATAAGAAAATAAGT
193 GTCGAAAATGTTATCAGAGTTTAAGGTAATGGAGCCTTGGATTATCCAA-TATAAGAAAATAAGT
* * * *
3603268 TTAAAACTGAAAATGTTATGAATATATATAAGAAATATGTTGC-ATCTAATAATTTCATGGTTCA
257 TTAAAACTGAAAATGTTATGAACATATATAAGAAATACGTTGCGCTCTAATAATATCATGGTTCA
* **
3603332 ATAATAAAAAATGTTGTAATCTAGAATGTTAATATTTTTAATAATAAAGT
322 ATAATAAAAAATGTTGTAATATAGAATGTTAATATTTTTAATAATAAAAC
** * * * *
3603382 AGGTTACGCCAAAATATTATCAGAGTTTAAGTTGATGGAGCCTTGTATTATTCCATTATAAGAAA
1 AGGTTGTGCGAAAATATTATCAGAGTTTAAGTTGATGGAGCATTGTATTATCCCAATATAAGAAA
* * * * *
3603447 ATAAGTTTAAAACTGAAAATGTTATGAATATATATAAAAAATACGGTTGCACCCAATAATATCAT
66 ATAAGTTTAAAAATTAAAATGTTATGAACATATATAAAAAATACGGTTGCACCCAATAATGTAAT
* * * * *
3603512 GATTCAATAATAAAAGAGATTGTAATATGAAATGTTAATACTTTTAATAATAAAATAGGTTATGC
131 GATTCAATAATAAAAAAGGTTGTAATCTG-AATGTTAATACTTTTAATAATAAAATAGGTTAAGT
* ** *
3603577 CAAAAATGTTATTTGAGTTTAAGGTAATGGAGCCTTGGATTATCCTAATATAAGAAAATAAATTT
195 CGAAAATGTTATCAGAGTTTAAGGTAATGGAGCCTTGGATTATCC-AATATAAGAAAATAAGTTT
3603642 AAAACTGAAAATGTTATGAACATATATAAGAAATACGATTGCGCTC-AATAATATCATGGTTCAA
259 AAAACTGAAAATGTTATGAACATATATAAGAAATACG-TTGCGCTCTAATAATATCATGGTTCAA
* *
3603706 TAATAAAAGA-GATTGTAATATAGAATGTTAAT-TCTTTTAGTAATAAAAC
323 TAATAAAAAATG-TTGTAATATAGAATGTTAATAT-TTTTAATAATAAAAC
* * * * * *
3603755 AGGGTTGTGCTGAAAATGTTATTAGATTTTAAGCTGATGGAGCATTGAATTATCCCAGTATAAGA
1 A-GGTTGTGC-GAAAATATTATCAGAGTTTAAGTTGATGGAGCATTGTATTATCCCAATATAAGA
* * ** *
3603820 AAATAAGTTTGAAAAATTAAAATGTTATGAACATATATAATAAATATGGTTGCACAAAAAAATGT
64 AAATAAGTTT-AAAAATTAAAATGTTATGAACATATATAAAAAATACGGTTGCACCCAATAATGT
* * * * * * * *
3603885 AATGGTTAAAAAATAAAACAGGTTCTAATCTAGAATATTAATATTTTTAATAATAAAATTGGTTA
128 AATGATTCAATAATAAAAAAGGTTGTAATCT-GAATGTTAATACTTTTAATAATAAAATAGGTTA
* * * *
3603950 AGTCGAAAATGTTATCAAAGTTTAAGCG-AATGGGGCATTGGATTATCCGAGTATAAGAAAATAA
192 AGTCGAAAATGTTATCAGAGTTTAAG-GTAATGGAGCCTTGGATTATCC-AATATAAGAAAATAA
* *
3604014 GTTTAAAACTGAAAATATTATGAACATATATAAAAAATACGGTTGCGC
255 GTTTAAAACTGAAAATGTTATGAACATATATAAGAAATAC-GTTGCGC
3604062 CCATTAATGT
Statistics
Matches: 579, Mismatches: 88, Indels: 23
0.84 0.13 0.03
Matches are distributed among these distances:
371 1 0.00
372 247 0.43
373 73 0.13
374 8 0.01
375 55 0.09
376 192 0.33
377 3 0.01
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (371 bp):
AGGTTGTGCGAAAATATTATCAGAGTTTAAGTTGATGGAGCATTGTATTATCCCAATATAAGAAA
ATAAGTTTAAAAATTAAAATGTTATGAACATATATAAAAAATACGGTTGCACCCAATAATGTAAT
GATTCAATAATAAAAAAGGTTGTAATCTGAATGTTAATACTTTTAATAATAAAATAGGTTAAGTC
GAAAATGTTATCAGAGTTTAAGGTAATGGAGCCTTGGATTATCCAATATAAGAAAATAAGTTTAA
AACTGAAAATGTTATGAACATATATAAGAAATACGTTGCGCTCTAATAATATCATGGTTCAATAA
TAAAAAATGTTGTAATATAGAATGTTAATATTTTTAATAATAAAAC
Found at i:3604651 original size:18 final size:18
Alignment explanation
Indices: 3604630--3604665 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3604620 AGATCCCAAT
3604630 AAAATATTGGCAATGAAA
1 AAAATATTGGCAATGAAA
3604648 AAAATATTGGCAATGAAA
1 AAAATATTGGCAATGAAA
3604666 GGTTCCGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (18 bp):
AAAATATTGGCAATGAAA
Found at i:3605352 original size:13 final size:13
Alignment explanation
Indices: 3605334--3605367 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3605324 GTAACTTAGT
3605334 CGACCAAGTTTGG
1 CGACCAAGTTTGG
*
3605347 CGACCAAATTTGG
1 CGACCAAGTTTGG
*
3605360 CAACCAAG
1 CGACCAAG
3605368 GGACAACCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (13 bp):
CGACCAAGTTTGG
Found at i:3607075 original size:99 final size:99
Alignment explanation
Indices: 3606898--3607101 Score: 236
Period size: 99 Copynumber: 2.1 Consensus size: 99
3606888 ATGTATACGA
* * * *
3606898 TTTCAGCCTATAACTTAACCAGTTAACATAACAAGAAGGTGCAACCTATAATGTTATAGTGGAAA
1 TTTCAGCCTAAAACTTAACAAGTTAACATAACAACAAGGTGCAACCTATAATGTTATAAT-GAAA
* * *
3606963 CCATGTTTGTTTTACT-TTTT-GATAATATACACT-G
65 CCAAGTTTATTTTA-TATTTTCCATAATATACA-TGG
* * *
3606997 TTTCAGCCTAAAACTTAACAAGTTAACCTAAGAACAAGGTGCAACTTATAATGTTATCAAAT-AA
1 TTTCAGCCTAAAACTTAACAAGTTAACATAACAACAAGGTGCAACCTATAATGTTAT--AATGAA
*
3607061 ATCAAGTTTATTTTATATTTTCCATAATATACATGG
64 ACCAAGTTTATTTTATATTTTCCATAATATACATGG
3607097 TTTCA
1 TTTCA
3607102 TGGGTCAATA
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
98 1 0.01
99 70 0.79
100 16 0.18
101 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (99 bp):
TTTCAGCCTAAAACTTAACAAGTTAACATAACAACAAGGTGCAACCTATAATGTTATAATGAAAC
CAAGTTTATTTTATATTTTCCATAATATACATGG
Found at i:3607800 original size:12 final size:12
Alignment explanation
Indices: 3607783--3607811 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3607773 ATATTGATAT
3607783 CATAAAAGTGAG
1 CATAAAAGTGAG
3607795 CAT-AAAGTGAG
1 CATAAAAGTGAG
3607806 CATAAA
1 CATAAA
3607812 TTGAAAGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.17
Consensus pattern (12 bp):
CATAAAAGTGAG
Found at i:3609740 original size:23 final size:25
Alignment explanation
Indices: 3609694--3609742 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
3609684 ATTTCAAAAA
**
3609694 ATTTCAAAACTATCGATATTTATGT
1 ATTTCAAAACTATCGATACATATGT
3609719 ATTT-AAAA-TATCGATACATATGT
1 ATTTCAAAACTATCGATACATATGT
3609742 A
1 A
3609743 CTGAATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 4 0.18
25 4 0.18
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (25 bp):
ATTTCAAAACTATCGATACATATGT
Found at i:3610002 original size:99 final size:98
Alignment explanation
Indices: 3609817--3610189 Score: 290
Period size: 99 Copynumber: 3.8 Consensus size: 98
3609807 GTTAGTCCCT
* * * * * *
3609817 ATAACATAAACGGTTGACAATATAAGCAGGCTCTACATGTATTGTTATAAATATAATCCTGTTTT
1 ATAACTTAAACGGTTGACAAAATAAGAAGACACTACTTGTATTGTTATAAATATAA-CCTGTTTT
* *
3609882 GTCTTAC-ATAATCATAGTAAAAAAGGTTTCACAC
65 GTCTTACAAT-TTCATAATAAAAAAGGTTTCACAC
* * * *
3609916 ACAACTTAAACGGTTGGCAAAATAAGAAGACACTACTTGTATTGTTATAAATTTACACATGTTTT
1 ATAACTTAAACGGTTGACAAAATAAGAAGACACTACTTGTATTGTTATAAATATA-ACCTGTTTT
* * *
3609981 CTCTTACAATTTCTTAATAAAAAA-GTTTCAAAC
65 GTCTTACAATTTCATAATAAAAAAGGTTTCACAC
* * * * *
3610014 TTATCATGTAAACGGTTGACAATAA-AAAAAGA-AGCTACTTGTGTTGTTATAAATATAACGTGT
1 ATAAC-T-TAAACGGTTGACAA-AATAAGAAGACA-CTACTTGTATTGTTATAAATATAACCTGT
* * ** * *
3610077 TTAGTCTTATACGTTCATAATGAAAAAGATTTCACAC
62 TTTGTCTTACAATTTCATAATAAAAAAGGTTTCACAC
* * * * * ** * *
3610114 ATATAACTTAAATGATTAACAATATAA-AAAAGTGCTACTTGTATTGTTATGAATTTAAACCTGT
1 --ATAACTTAAACGGTTGACAAAATAAGAAGA-CACTACTTGTATTGTTATAAATAT-AACCTGT
3610178 TTT-TCTTACAAT
62 TTTGTCTTACAAT
3610190 GTATTAGTAA
Statistics
Matches: 213, Mismatches: 48, Indels: 25
0.74 0.17 0.09
Matches are distributed among these distances:
98 10 0.05
99 101 0.47
100 88 0.41
101 11 0.05
102 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.35
Consensus pattern (98 bp):
ATAACTTAAACGGTTGACAAAATAAGAAGACACTACTTGTATTGTTATAAATATAACCTGTTTTG
TCTTACAATTTCATAATAAAAAAGGTTTCACAC
Found at i:3610066 original size:100 final size:99
Alignment explanation
Indices: 3609816--3610203 Score: 270
Period size: 100 Copynumber: 3.9 Consensus size: 99
3609806 GGTTAGTCCC
* * ** *** * * *
3609816 TATAACATAAACGGTTGACAATATAAGCAGGCTCTACATGTATTGTTATAAATATAATCCTGTTT
1 TATAACTTAAACGGTTGACAATAAAAAAAGAAGCTACTTGTATTGTTATAAATTTAA-CATGTTT
* * * *
3609881 TGTCTTAC-ATAATCATAGTAAAAAAGGTTTC--ACA
65 T-TCTTACAAT-TTCTTAATAAAAAAGATTTCAAACA
* * * *
3609915 CACAACTTAAACGGTTGGCAA-AATAAGAAGACA-CTACTTGTATTGTTATAAATTTACACATGT
1 TATAACTTAAACGGTTGACAATAA-AAAAAGA-AGCTACTTGTATTGTTATAAATTTA-ACATGT
*
3609978 TTTCTCTTACAATTTCTTAATAAAAAAG-TTTCAAACT
63 TTT-TCTTACAATTTCTTAATAAAAAAGATTTCAAACA
* * * *
3610015 TATCA-TGTAAACGGTTGACAATAAAAAAAGAAGCTACTTGTGTTGTTATAAATATAACGTGTTT
1 TATAACT-TAAACGGTTGACAATAAAAAAAGAAGCTACTTGTATTGTTATAAATTTAACATGTTT
* * ** * * *
3610079 AGTCTTATACGTTCATAATGAAAAAGATTTCACACA
65 -TTCTTACAATTTCTTAATAAAAAAGATTTCAAACA
* * * * * *
3610115 TATAACTTAAATGATTAACAATATAAAAAAG-TGCTACTTGTATTGTTATGAATTTAAACCTGTT
1 TATAACTTAAACGGTTGACAATA-AAAAAAGAAGCTACTTGTATTGTTATAAATTT-AACATGTT
* * *
3610179 TTTCTTACAATGTATTAGTAAAAAA
64 TTTCTTACAATTTCTTAATAAAAAA
3610204 AGGTTTTGAA
Statistics
Matches: 225, Mismatches: 50, Indels: 27
0.75 0.17 0.09
Matches are distributed among these distances:
98 5 0.02
99 96 0.43
100 106 0.47
101 18 0.08
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (99 bp):
TATAACTTAAACGGTTGACAATAAAAAAAGAAGCTACTTGTATTGTTATAAATTTAACATGTTTT
TCTTACAATTTCTTAATAAAAAAGATTTCAAACA
Found at i:3610422 original size:202 final size:202
Alignment explanation
Indices: 3609829--3610527 Score: 499
Period size: 202 Copynumber: 3.5 Consensus size: 202
3609819 AACATAAACG
** * * *
3609829 GTTGACAATATAAGCAGGCTCTACAT-GTATTGTTATAAATATAATCCTGTTTTGTCTTACATAA
1 GTTGACAATATAAAAAAGCACTAC-TCGTATTGTTATAAATATAACCCTGTTTTGTCTTACATAA
* * * * * ** ** * * **
3609893 TCAT-AGTAAAAAAGGTTTCACAC--ACAACTTAAACGGTTGGCAAAAT-AAGAAGACACTACTT
65 CCGTCA-TGAAAAAGATTTCACACATATAACTTAAACAATTAACAATATAAAAAAG-TGCTACTT
* * * * * * * ** *
3609954 GTATTGTTATAAATTTACACATGTTTTCTCTTACAATTTCTTAAT-AAAAAA-GTTTCAAACTTA
128 ATAATGTTATAAATTTAAACCTG-TTTATCTTACAATGTATTAATAAAAAAAGGTTTTGAACATA
* **
3610017 TCATGTAAACG
192 TCAAGTAAATA
* * * * * * ***
3610028 GTTGACAATA-AAAAAAGAAGCTACTTGTGTTGTTATAAATATAA-CGTGTTTAGTCTTATACGT
1 GTTGACAATATAAAAAAGCA-CTACTCGTATTGTTATAAATATAACCCTGTTTTGTCTTACATAA
* * * ** *
3610091 TCATAATGAAAAAGATTTCACACATATAACTTAAATGATTAACAATATAAAAAAGTGCTACTTGT
65 CCGTCATGAAAAAGATTTCACACATATAACTTAAACAATTAACAATATAAAAAAGTGCTACTTAT
* * * *
3610156 ATTGTTATGAATTTAAACCTGTTTTTCTTACAATGTATTAGTAAAAAAAGGTTTTGAACATATCA
130 AATGTTATAAATTTAAACCTGTTTATCTTACAATGTATTAATAAAAAAAGGTTTTGAACATATCA
* *
3610221 CGTAAATG
195 AGTAAATA
* * ** *
3610229 GTTGATACTATAAAAAAGCGTTAC-CGATATTGTTATAAATATAACCTTGTTTTGTCTTACATAA
1 GTTGACAATATAAAAAAGCACTACTCG-TATTGTTATAAATATAACCCTGTTTTGTCTTACATAA
* * *
3610293 CCGTCATGAAAAATG-TTTGACACATATAGCTTAAAACAATTAACAATATAAAAAAGTTCTAGC-
65 CCGTCATGAAAAA-GATTTCACACATATAACTT-AAACAATTAACAATATAAAAAAGTGCTA-CT
* * * * * * * *
3610356 TATAATGTTATAAATTTAAACTTGTTTATGTTATAGTTTCTTAAT-AATAAAGGTTTCT-ATCAT
127 TATAATGTTATAAATTTAAACCTGTTTATCTTACAATGTATTAATAAAAAAAGGTTT-TGAACAT
3610419 ATCAAGTAAATA
191 ATCAAGTAAATA
** * * *
3610431 GTTGACAATATAAGGAAGCACTACTTGTATTGTTATAAATATAACCCTGTTTTGTCTTATATATC
1 GTTGACAATATAAAAAAGCACTACTCGTATTGTTATAAATATAACCCTGTTTTGTCTTACATAAC
* * * * * *
3610496 CATAATGACACATATTTCACATATATAACTTA
66 CGTCATGAAAAAGATTTCACACATATAACTTA
3610528 CACGGTTGAC
Statistics
Matches: 394, Mismatches: 89, Indels: 32
0.77 0.17 0.06
Matches are distributed among these distances:
198 37 0.09
199 49 0.12
200 50 0.13
201 51 0.13
202 144 0.37
203 62 0.16
204 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (202 bp):
GTTGACAATATAAAAAAGCACTACTCGTATTGTTATAAATATAACCCTGTTTTGTCTTACATAAC
CGTCATGAAAAAGATTTCACACATATAACTTAAACAATTAACAATATAAAAAAGTGCTACTTATA
ATGTTATAAATTTAAACCTGTTTATCTTACAATGTATTAATAAAAAAAGGTTTTGAACATATCAA
GTAAATA
Found at i:3615270 original size:6 final size:6
Alignment explanation
Indices: 3615259--3615328 Score: 79
Period size: 6 Copynumber: 11.7 Consensus size: 6
3615249 TAAGGTAAAG
* * ** *
3615259 AAAATA AAAAT- AAAATG AAGATA AATAGGA TAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AA-AATA AAAATA AAAATA AAAATA
3615307 AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAA
3615329 AAGATATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
5 5 0.09
6 46 0.87
7 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:3615291 original size:40 final size:41
Alignment explanation
Indices: 3615207--3615284 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 41
3615197 ATGAAAATAA
*
3615207 ATAAGTTAAAAAACAATAAAAAAACAAATGAAATAAATGAG
1 ATAAGGTAAAAAACAATAAAAAAACAAATGAAATAAATGAG
* *
3615248 ATAAGGTAAAGAA-AATAAAAATA-AAATGAAGATAAAT
1 ATAAGGTAAAAAACAATAAAAAAACAAATGAA-ATAAAT
3615285 AGGATAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 7 0.21
40 15 0.45
41 11 0.33
ACGTcount: A:0.68, C:0.03, G:0.12, T:0.18
Consensus pattern (41 bp):
ATAAGGTAAAAAACAATAAAAAAACAAATGAAATAAATGAG
Found at i:3615306 original size:36 final size:34
Alignment explanation
Indices: 3615187--3615309 Score: 104
Period size: 36 Copynumber: 3.3 Consensus size: 34
3615177 TTAGAAGGGA
* *
3615187 AAAAATAATAATGAAAATAAATAAGTTAAAAAACAAT
1 AAAAATAA-AATG-AAATAAATAGGATAAAAAA-AAT
*
3615224 AAAAAAACAAATGAAATAAAT-GAGATAAGGTAAAGAAAAT
1 AAAAATA-AAATGAAATAAATAG-GAT-A---AAA-AAAAT
3615264 AAAAATAAAATGAAGATAAATAGGATAAATAAAAAT
1 AAAAATAAAATGAA-ATAAATAGGATAAA-AAAAAT
3615300 AAAAATAAAA
1 AAAAATAAAA
3615310 ATAAAAATAA
Statistics
Matches: 72, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
36 27 0.38
37 12 0.17
38 1 0.01
39 8 0.11
40 21 0.29
41 3 0.04
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.18
Consensus pattern (34 bp):
AAAAATAAAATGAAATAAATAGGATAAAAAAAAT
Found at i:3615324 original size:30 final size:30
Alignment explanation
Indices: 3615259--3615344 Score: 61
Period size: 28 Copynumber: 2.8 Consensus size: 30
3615249 TAAGGTAAAG
*
3615259 AAAATAAAAATAAAATGAAGATAAATAGGATAAAT
1 AAAATAAAAAT-AAAT-AAGAAAAATA--A-AAAT
*
3615294 AAAAATAAAAATAAA-AATAAAAATAAAAAT
1 -AAAATAAAAATAAATAAGAAAAATAAAAAT
* *
3615324 AAAA-AAAGATATA-AAGAAAAA
1 AAAATAAAAATAAATAAGAAAAA
3615345 GAAATATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
28 14 0.31
29 4 0.09
30 4 0.09
31 1 0.02
33 8 0.18
35 3 0.07
36 11 0.24
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (30 bp):
AAAATAAAAATAAATAAGAAAAATAAAAAT
Found at i:3615400 original size:2 final size:2
Alignment explanation
Indices: 3615395--3615423 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3615385 TATATAAAAA
3615395 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3615424 AGTACGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3615521 original size:2 final size:2
Alignment explanation
Indices: 3615514--3615539 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3615504 AAATAAAATA
3615514 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3615540 TGTATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3615561 original size:15 final size:15
Alignment explanation
Indices: 3615543--3615591 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 15
3615533 TATATATTGT
3615543 ATAAAAAATAAAAAA
1 ATAAAAAATAAAAAA
*
3615558 ATAAGAAAT---AAA
1 ATAAAAAATAAAAAA
3615570 ATAAAAAATAAGAAAA
1 ATAAAAAATAA-AAAA
3615586 ATAAAA
1 ATAAAA
3615592 GGATTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
12 11 0.39
15 8 0.29
16 9 0.32
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.14
Consensus pattern (15 bp):
ATAAAAAATAAAAAA
Found at i:3615577 original size:19 final size:20
Alignment explanation
Indices: 3615547--3615584 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
3615537 TATTGTATAA
3615547 AAAATAAAAAAATAAGAAAT
1 AAAATAAAAAAATAAGAAAT
3615567 AAAAT-AAAAAATAAGAAA
1 AAAATAAAAAAATAAGAAA
3615585 AATAAAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (20 bp):
AAAATAAAAAAATAAGAAAT
Found at i:3616946 original size:67 final size:67
Alignment explanation
Indices: 3616741--3616956 Score: 234
Period size: 67 Copynumber: 3.2 Consensus size: 67
3616731 CAGATGATGC
** ** * * * * *
3616741 TTCAAGAGAAGTTGTCTCAAAAGAGACATAATTCGTTTCAAGGGAAACGATCTCAATGATATTTG
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAATTTCAAAGAT-TTTG
3616806 TTGT
65 -TGT
* * * * * * *
3616810 TTCATGAGAAACGGTCTCATGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGATTTTG
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACAATTTCAAAGATTTTG
3616875 TGT
65 TGT
* *
3616878 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGGAAACAATTTCAAAGGTTTTGT
1 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAATTTCAAAGATTTTGT
3616943 GT
66 GT
*
3616945 TTCAAGGGAAAC
1 TTCAAGAGAAAC
3616957 AATTTCAAAG
Statistics
Matches: 120, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
67 42 0.35
68 30 0.25
69 26 0.22
70 22 0.18
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (67 bp):
TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAATTTCAAAGATTTTGT
GT
Done.