Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 37 of 208
Found at i:10274037 original size:12 final size:12
Alignment explanation
Indices: 10274005--10274039 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
10273995 ATTTTTGCAT
*
10274005 CAGCAGCAACAA
1 CAGCAGCAGCAA
10274017 CAGCAGCAGCAA
1 CAGCAGCAGCAA
10274029 CAGCAGCAGCA
1 CAGCAGCAGCA
10274040 GTTGCTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.43, C:0.34, G:0.23, T:0.00
Consensus pattern (12 bp):
CAGCAGCAGCAA
Found at i:10291090 original size:22 final size:22
Alignment explanation
Indices: 10291062--10291106 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
10291052 TGTACCAATC
10291062 AATTCTCAATCCACTCGATCCG
1 AATTCTCAATCCACTCGATCCG
10291084 AATTCTCAATCCACTCGATCCG
1 AATTCTCAATCCACTCGATCCG
10291106 A
1 A
10291107 TCAACTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.36, G:0.09, T:0.27
Consensus pattern (22 bp):
AATTCTCAATCCACTCGATCCG
Found at i:10302024 original size:110 final size:110
Alignment explanation
Indices: 10301831--10302051 Score: 442
Period size: 110 Copynumber: 2.0 Consensus size: 110
10301821 ATTATGGAAA
10301831 ACCGGAATTTGGGATCCCTTCATTGTTCAGATCAGGCTGGACAATCACTTGTGAGTATGGTGAAA
1 ACCGGAATTTGGGATCCCTTCATTGTTCAGATCAGGCTGGACAATCACTTGTGAGTATGGTGAAA
10301896 GAGCCAAAAATATAACTTATTTGGGTTTCAGCATTCCCAGACCAG
66 GAGCCAAAAATATAACTTATTTGGGTTTCAGCATTCCCAGACCAG
10301941 ACCGGAATTTGGGATCCCTTCATTGTTCAGATCAGGCTGGACAATCACTTGTGAGTATGGTGAAA
1 ACCGGAATTTGGGATCCCTTCATTGTTCAGATCAGGCTGGACAATCACTTGTGAGTATGGTGAAA
10302006 GAGCCAAAAATATAACTTATTTGGGTTTCAGCATTCCCAGACCAG
66 GAGCCAAAAATATAACTTATTTGGGTTTCAGCATTCCCAGACCAG
10302051 A
1 A
10302052 AAGATCTTAG
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 111 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (110 bp):
ACCGGAATTTGGGATCCCTTCATTGTTCAGATCAGGCTGGACAATCACTTGTGAGTATGGTGAAA
GAGCCAAAAATATAACTTATTTGGGTTTCAGCATTCCCAGACCAG
Found at i:10310961 original size:31 final size:31
Alignment explanation
Indices: 10310915--10310994 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
10310905 GTCGAGCAAG
* *
10310915 TTTACAATTTGGTCACTCAATTATTAGTAAA
1 TTTACAATTTAGTCACTCAACTATTAGTAAA
*
10310946 TTTATAATTTAGTCACTCAACTATTAGTAAA
1 TTTACAATTTAGTCACTCAACTATTAGTAAA
10310977 TTTACAATTTAGTCACTC
1 TTTACAATTTAGTCACTC
10310995 TTTGCATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (31 bp):
TTTACAATTTAGTCACTCAACTATTAGTAAA
Found at i:10323395 original size:46 final size:46
Alignment explanation
Indices: 10323328--10323576 Score: 357
Period size: 46 Copynumber: 5.5 Consensus size: 46
10323318 TGATCAGTGA
* *
10323328 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTAACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
*
10323374 CAAGTAACAAAGTGATAAGTGGTAGCCTCAGCTACACTTATCT-AT
1 CAAGTAACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
* *
10323419 CAAGTGAA-AAAGTGATAAGTGGTAGCCTTAGTTACACTTATCTAAT
1 CAAGT-AACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
10323465 CAAGTGAA-AAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
1 CAAGT-AACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
* *
10323511 CAAGTGACAAAGTGATAAGTGGTAGCC-TAGCTACACTTATTTGAT
1 CAAGTAACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
**
10323556 C-AGGGAC-AAGTGATAAGTGGT
1 CAAGTAACAAAGTGATAAGTGGT
10323577 CATACGTAAG
Statistics
Matches: 190, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
43 14 0.07
44 5 0.03
45 59 0.31
46 112 0.59
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (46 bp):
CAAGTAACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
Found at i:10323483 original size:91 final size:92
Alignment explanation
Indices: 10323328--10323576 Score: 382
Period size: 91 Copynumber: 2.8 Consensus size: 92
10323318 TGATCAGTGA
*
10323328 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGT-AACAAAGTGATAA
1 CAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAA-AAAGTGATAA
10323392 GTGGTAGCCTCAGCTACACTTATCT-AT
65 GTGGTAGCCTCAGCTACACTTATCTGAT
* * *
10323419 CAAGTGAAAAAGTGATAAGTGGTAGCCTTAGTTACACTTATCTAATCAAGTGAAAAAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAG
*
10323484 TGGTAGCCTTAGCTACACTTATCTGAT
66 TGGTAGCCTCAGCTACACTTATCTGAT
* * *
10323511 CAAGTGACAAAGTGATAAGTGGTAGCC-TAGCTACACTTATTTGATC-AG-GGACAAGTGATAAG
1 CAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAG
10323573 TGGT
66 TGGT
10323577 CATACGTAAG
Statistics
Matches: 145, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
89 16 0.11
90 2 0.01
91 97 0.67
92 30 0.21
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (92 bp):
CAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAG
TGGTAGCCTCAGCTACACTTATCTGAT
Found at i:10324585 original size:49 final size:49
Alignment explanation
Indices: 10324509--10324658 Score: 176
Period size: 49 Copynumber: 3.0 Consensus size: 49
10324499 ATGTGAAAAT
*
10324509 GTGATTATGTGATTTCTGTGTAAGACCATAGCTGGGCTATGACATCGGAAA
1 GTGA-TATGTGATTTC-GTGTAAGACCATAGCTGGGCTATGGCATCGGAAA
** * *
10324560 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATTAGTAT
1 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGAAA
* * * *
10324609 GTGATTTGTGATTAT-GTGTAAGACTATAGTTGGACTATGGCATCGAGAAA
1 GTGATATGTGATT-TCGTGTAAGACCATAGCTGGGCTATGGCATCG-GAAA
10324659 ACGAAGTACT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
49 66 0.79
50 14 0.17
51 4 0.05
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.33
Consensus pattern (49 bp):
GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGAAA
Found at i:10328369 original size:46 final size:46
Alignment explanation
Indices: 10328290--10328585 Score: 472
Period size: 46 Copynumber: 6.5 Consensus size: 46
10328280 TGATCAGTGA
* * * *
10328290 CAAGTGACAAAGTAATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGAT
*
10328336 CAAGTGACAAAGTGATAAGTGGTAACCTCAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGAT
*
10328382 CAAGTGACAAAGTGATAAGTGGTAGCCTCAGCTTCACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGAT
*
10328428 CAAGTGAAAAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGAT
* *
10328474 CAAGTGAAAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGAT
*
10328520 CAAGTGACAAAGTGATAAGTGGTAGCCT-AGCTACACTTATTTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGAT
*
10328565 C-AGGGAC-AAGTGATAAGTGGT
1 CAAGTGACAAAGTGATAAGTGGT
10328586 CGTACGTAAG
Statistics
Matches: 237, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
43 14 0.06
44 5 0.02
45 17 0.07
46 201 0.85
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGAT
Found at i:10333358 original size:46 final size:46
Alignment explanation
Indices: 10333259--10333511 Score: 357
Period size: 46 Copynumber: 5.7 Consensus size: 46
10333249 CTTACGTATG
* *
10333259 ACCACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAACT-AGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
* *
10333302 ACCACTTATCACTTTGTCACTTGATTAGATAAGTGTAGCTAAAGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
* *
10333348 ACCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTATGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
*
10333394 ACCACTTATCATTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
*
10333440 ACCACTTATCACTTTTTCAC----T----TAAGTGTAGCTAAGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
10333478 ACCACTTATCACTTTGTCACTTGATCAGATAAGT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGT
10333512 ACTCAAATCT
Statistics
Matches: 185, Mismatches: 14, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
38 36 0.19
42 2 0.01
43 12 0.06
44 5 0.03
45 18 0.10
46 112 0.61
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
Found at i:10333465 original size:38 final size:38
Alignment explanation
Indices: 10333423--10333499 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
10333413 CTTGATCAGA
*
10333423 TAAGTGTAGCTAAGGCTACCACTTATCACTTTTTCACT
1 TAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCACT
10333461 TAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCACT
1 TAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCACT
10333499 T
1 T
10333500 GATCAGATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (38 bp):
TAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCACT
Found at i:10336928 original size:19 final size:18
Alignment explanation
Indices: 10336904--10336950 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
10336894 TTTCTATATA
*
10336904 TTTTATAATTTTAATGAT
1 TTTTATAATTTTAATGCT
*
10336922 TTTT-TATATTTTTATGCT
1 TTTTATA-ATTTTAATGCT
10336940 TTTTATAATTT
1 TTTTATAATTT
10336951 CAAAATGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 21 0.84
19 2 0.08
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (18 bp):
TTTTATAATTTTAATGCT
Found at i:10337778 original size:31 final size:31
Alignment explanation
Indices: 10337743--10337826 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 31
10337733 AAGAGTTCAA
*
10337743 AATTTGAAAAGTATAGGGACTAAAATTGACC
1 AATTTGAAAAGTATAAGGACTAAAATTGACC
* * *
10337774 AATTTGAAAAGTAAAAGAACTAAAATTGATC
1 AATTTGAAAAGTATAAGGACTAAAATTGACC
*
10337805 AAATT-AAAA-TATAAGGACTAAA
1 AATTTGAAAAGTATAAGGACTAAA
10337827 TCCATAACTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
29 11 0.24
30 4 0.09
31 31 0.67
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (31 bp):
AATTTGAAAAGTATAAGGACTAAAATTGACC
Found at i:10340763 original size:24 final size:25
Alignment explanation
Indices: 10340723--10340784 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 25
10340713 TCAGGTAAAA
*
10340723 TTGAGTTTACAAA-GAAGAGAAA-AAC
1 TTGA-TTTTCAAAGGAAG-GAAAGAAC
10340748 -TGATTTTCAAAGGAAGGAAAGAAC
1 TTGATTTTCAAAGGAAGGAAAGAAC
*
10340772 TTTATTTTCAAAG
1 TTGATTTTCAAAG
10340785 AAAGCAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 11 0.34
24 10 0.31
25 11 0.34
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.27
Consensus pattern (25 bp):
TTGATTTTCAAAGGAAGGAAAGAAC
Found at i:10346638 original size:17 final size:17
Alignment explanation
Indices: 10346616--10346653 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
10346606 TCTACTGCAT
*
10346616 GGTCGTGTGTCCCGCAC
1 GGTCGTGTGTCCCACAC
10346633 GGTCGTGTGTCCCACAC
1 GGTCGTGTGTCCCACAC
10346650 GGTC
1 GGTC
10346654 CTTACATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.08, C:0.34, G:0.34, T:0.24
Consensus pattern (17 bp):
GGTCGTGTGTCCCACAC
Found at i:10353747 original size:18 final size:18
Alignment explanation
Indices: 10353724--10353761 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
10353714 AATCCAAGTC
10353724 AAATAA-AAAAATTAAAAT
1 AAATAACAAAAA-TAAAAT
*
10353742 AAATAACTAAAATAAAAT
1 AAATAACAAAAATAAAAT
10353760 AA
1 AA
10353762 TCAATCAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
AAATAACAAAAATAAAAT
Found at i:10353759 original size:14 final size:14
Alignment explanation
Indices: 10353724--10353761 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
10353714 AATCCAAGTC
* *
10353724 AAATAAAAAAATTA
1 AAATAAAATAACTA
10353738 AAAT-AAATAACTA
1 AAATAAAATAACTA
10353751 AAATAAAATAA
1 AAATAAAATAA
10353762 TCAATCAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAACTA
Found at i:10362123 original size:114 final size:113
Alignment explanation
Indices: 10361769--10362124 Score: 292
Period size: 114 Copynumber: 3.1 Consensus size: 113
10361759 TTTGAAACCG
* * *
10361769 AAACGCAACATTTCGTCTTGAGCTATAGCGCCTTTAGCGGCGCTTAGCCGAAAACGCCGCTATAT
1 AAACGCAACGTTTCGTCTTGAGCTATAGCGCCTTTAGTGGCGCTTACCCGAAAACGCCGCTATAT
* * * * * *
10361834 ATCAGCTTTTCGTGGCGCTATTCCTGAATCGCCGCAAATATTTTGAACA
66 ATCAGCTTTTAGTGGCGCT-TTACTAAAACGCCGCAAAAATTTTGACCA
** * ** * * * * *
10361883 AAACGCATTG-TTCGGGCTTGA-CGTATAAAGGCATTAGTGGCGCTTACCTGCAAATGCCGCTAT
1 AAACGCAACGTTTC-GTCTTGAGC-TATAGCGCCTTTAGTGGCGCTTACCCGAAAACGCCGCTAT
** ** * ** * *
10361946 ATCCCA--TAAATAGCGGCG-TTTAACTAAAAAATACCG-AAAAATTTTAAACCG
64 ATATCAGCT-TTTAGTGGCGCTTT-ACT--AAAACGCCGCAAAAATTTT-GACCA
*
10361997 AAACGCAACGTTTCGTCTTGAGCTATAGCGCCTTTAGTGGCGCTTACCCGTAAACGCCGCTATAT
1 AAACGCAACGTTTCGTCTTGAGCTATAGCGCCTTTAGTGGCGCTTACCCGAAAACGCCGCTATAT
* * *
10362062 ATCAGCTTTTAGTGGCGCTTCTGCTTAAGCGCCGCAAAAATTTTGACCA
66 ATCAGCTTTTAGTGGCGCTT-TACTAAAACGCCGCAAAAATTTTGACCA
*
10362111 AAACGCATCGTTTC
1 AAACGCAACGTTTC
10362125 AGCTTCACGT
Statistics
Matches: 177, Mismatches: 51, Indels: 28
0.69 0.20 0.11
Matches are distributed among these distances:
111 2 0.01
112 4 0.02
113 18 0.10
114 127 0.72
115 20 0.11
116 5 0.03
117 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (113 bp):
AAACGCAACGTTTCGTCTTGAGCTATAGCGCCTTTAGTGGCGCTTACCCGAAAACGCCGCTATAT
ATCAGCTTTTAGTGGCGCTTTACTAAAACGCCGCAAAAATTTTGACCA
Found at i:10362137 original size:228 final size:229
Alignment explanation
Indices: 10361758--10362174 Score: 606
Period size: 228 Copynumber: 1.8 Consensus size: 229
10361748 ACGCCGGAAC
*
10361758 TTTTGAAACCGAAACGCAACATTTCGTCTTGAGCTATAGCGCCTTTAGCGGCGCTTAGCCGAAAA
1 TTTTGAAACCGAAACGCAACATTTCGTCTTGAGCTATAGCGCCTTTAGCGGCGCTTACCCGAAAA
* * *
10361823 CGCCGCTATATATCAGCTTTTCGTGGCGCTATTCCTGAATCGCCGCAAATATTTTGAACAAAACG
66 CGCCGCTATATATCAGCTTTTAGTGGCGCTATTCCTGAAGCGCCGCAAAAATTTTGAACAAAACG
* * * * *
10361888 CATTGTTCGGGCTTGACGTATAAAGGCATTAGTGGCGCTTACCTGCAAATGCCGCTATATCCCAT
131 CATCGTTCGAGCTTCACGTATAAAGGCATTAGCGGCGCTTACCTGCAAACGCCGCTATATCCCAT
10361953 AAATAGCGGCGTTTAACTAAAAAATACCGAAAAA
196 AAATAGCGGCGTTTAACTAAAAAATACCGAAAAA
* * *
10361987 TTTT-AAACCGAAACGCAACGTTTCGTCTTGAGCTATAGCGCCTTTAGTGGCGCTTACCCGTAAA
1 TTTTGAAACCGAAACGCAACATTTCGTCTTGAGCTATAGCGCCTTTAGCGGCGCTTACCCGAAAA
* * *
10362051 CGCCGCTATATATCAGCTTTTAGTGGCGCT-TCTGCTTAAGCGCCGCAAAAATTTTGACCAAAAC
66 CGCCGCTATATATCAGCTTTTAGTGGCGCTAT-TCCTGAAGCGCCGCAAAAATTTTGAACAAAAC
* ** ** *
10362115 GCATCGTTTC-AGCTTCACGTATAGATTCATTAGCGGCGCTTATTTGGAAACGCCGCTATA
130 GCATCG-TTCGAGCTTCACGTATAAAGGCATTAGCGGCGCTTACCTGCAAACGCCGCTATA
10362175 GAGTAACTTT
Statistics
Matches: 165, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
227 1 0.01
228 157 0.95
229 7 0.04
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (229 bp):
TTTTGAAACCGAAACGCAACATTTCGTCTTGAGCTATAGCGCCTTTAGCGGCGCTTACCCGAAAA
CGCCGCTATATATCAGCTTTTAGTGGCGCTATTCCTGAAGCGCCGCAAAAATTTTGAACAAAACG
CATCGTTCGAGCTTCACGTATAAAGGCATTAGCGGCGCTTACCTGCAAACGCCGCTATATCCCAT
AAATAGCGGCGTTTAACTAAAAAATACCGAAAAA
Found at i:10362138 original size:114 final size:112
Alignment explanation
Indices: 10361769--10362197 Score: 271
Period size: 114 Copynumber: 3.8 Consensus size: 112
10361759 TTTGAAACCG
* * * *
10361769 AAACGCAACATTTCGTCTTGA-GCTATAGCGCCTTTAGCGGCGCTTAGCCGAAAACGCCGCTATA
1 AAACGCATCGTTTCG-CTTGACG-TATAGCGCCTTTAGTGGCGCTTACCCGAAAACGCCGCTATA
* * * * * *
10361833 TATCAGCTTTTCGTGGCGCTATTCCTGAATCGCCGCAAATATTTTGAACA
64 TATCAGCTTTTAGTGGCGCT-TTACTAAAACGCCGCAAAAATTTTGACCA
* ** * * * * *
10361883 AAACGCATTG-TTCGGGCTTGACGTATAAAGGCATTAGTGGCGCTTACCTGCAAATGCCGCTATA
1 AAACGCATCGTTTC--GCTTGACGTATAGCGCCTTTAGTGGCGCTTACCCGAAAACGCCGCTATA
** ** * ** * *
10361947 TCCCA--TAAATAGCGGCG-TTTAACTAAAAAATACCG-AAAAATTTTAAACCG
64 TATCAGCT-TTTAGTGGCGCTTT-ACT--AAAACGCCGCAAAAATTTT-GACCA
* *
10361997 AAACGCAACGTTTCGTCTTGA-GCTATAGCGCCTTTAGTGGCGCTTACCCGTAAACGCCGCTATA
1 AAACGCATCGTTTCG-CTTGACG-TATAGCGCCTTTAGTGGCGCTTACCCGAAAACGCCGCTATA
* * *
10362061 TATCAGCTTTTAGTGGCGCTTCTGCTTAAGCGCCGCAAAAATTTTGACCA
64 TATCAGCTTTTAGTGGCGCTT-TACTAAAACGCCGCAAAAATTTTGACCA
* *** * * *** * *
10362111 AAACGCATCGTTTCAGCTTCACGTATAGATTCATTAGCGGCGCTTATTTGGAAACGCCGCTATAG
1 AAACGCATCGTTTC-GCTTGACGTATAGCGCCTTTAGTGGCGCTTACCCGAAAACGCCGCTATAT
*
10362176 AGT-AACTTTTAGTGGCGCTTTA
65 A-TCAGCTTTTAGTGGCGCTTTA
10362198 GATTAAAAAT
Statistics
Matches: 234, Mismatches: 62, Indels: 39
0.70 0.19 0.12
Matches are distributed among these distances:
111 2 0.01
112 4 0.02
113 20 0.09
114 178 0.76
115 24 0.10
116 5 0.02
117 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (112 bp):
AAACGCATCGTTTCGCTTGACGTATAGCGCCTTTAGTGGCGCTTACCCGAAAACGCCGCTATATA
TCAGCTTTTAGTGGCGCTTTACTAAAACGCCGCAAAAATTTTGACCA
Found at i:10362504 original size:13 final size:14
Alignment explanation
Indices: 10362486--10362526 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
10362476 TTTCCAAAGA
10362486 TATGGTTTAGGA-T
1 TATGGTTTAGGACT
*
10362499 TATGGTTTATGACT
1 TATGGTTTAGGACT
*
10362513 TACGGTTTA-GACT
1 TATGGTTTAGGACT
10362526 T
1 T
10362527 TAGGGGCTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.22, C:0.07, G:0.24, T:0.46
Consensus pattern (14 bp):
TATGGTTTAGGACT
Found at i:10362940 original size:15 final size:16
Alignment explanation
Indices: 10362908--10362946 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
10362898 GATATTCTAG
10362908 ATTAATATAAATGAAA
1 ATTAATATAAATGAAA
10362924 A-TAATATAAAT-ATAA
1 ATTAATATAAATGA-AA
10362939 ATTAATAT
1 ATTAATAT
10362947 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.05
15 13 0.62
16 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTAATATAAATGAAA
Found at i:10363595 original size:17 final size:19
Alignment explanation
Indices: 10363575--10363617 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 19
10363565 CTATCATCTC
10363575 CCCCAAATCCCTAA-A-TT
1 CCCCAAATCCCTAACAGTT
*
10363592 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAACAGTT
10363611 CCCCAAA
1 CCCCAAA
10363618 CCCGACGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 13 0.59
18 1 0.05
19 8 0.36
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (19 bp):
CCCCAAATCCCTAACAGTT
Found at i:10365075 original size:21 final size:21
Alignment explanation
Indices: 10365049--10365091 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
10365039 TCGGACTTCT
10365049 TACTGACATAATTGAGTTGGA
1 TACTGACATAATTGAGTTGGA
10365070 TACTGACATAATTGAGTTGGA
1 TACTGACATAATTGAGTTGGA
10365091 T
1 T
10365092 TACTATGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (21 bp):
TACTGACATAATTGAGTTGGA
Found at i:10367215 original size:21 final size:21
Alignment explanation
Indices: 10367189--10367236 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
10367179 CTACAACTTA
* *
10367189 AAGCAGAGGCGGCATCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
*
10367210 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
10367231 AAGCAG
1 AAGCAG
10367237 GGGTTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.19, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:10367483 original size:24 final size:26
Alignment explanation
Indices: 10367456--10367506 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
10367446 ATGAATTCAC
* *
10367456 TTTTATTTA-TTAATTT-TAATATTA
1 TTTTATTCATTTAATTTGAAATATTA
10367480 TTTTATTCATTTAATTTGAAATATTA
1 TTTTATTCATTTAATTTGAAATATTA
10367506 T
1 T
10367507 AAAAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 8 0.35
25 7 0.30
26 8 0.35
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTTATTCATTTAATTTGAAATATTA
Found at i:10367820 original size:42 final size:43
Alignment explanation
Indices: 10367609--10367872 Score: 297
Period size: 43 Copynumber: 6.2 Consensus size: 43
10367599 AATCCCAAAA
* * * * * * *
10367609 TTAGTGGCGTTTTTCATAAAAACACCGCTAAA-ACTCATGTTCT
1 TTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGA-ACATGATCT
*
10367652 CTAGCGGCGTTTGTGA-AGAAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTGTGATA-AAAGCGCCGCTAAAGAACATGATCT
10367695 TTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAACATGATCT
*
10367738 TTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAGCATGATCT
1 TTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAACATGATCT
* * * *
10367781 TTAACGGCGTTTTTCG-T-TAAGCGCCGCTAAAGAATATGATCT
1 TTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAGAACATGATCT
* * **
10367823 TTACCGGCGTTTTTAGAT--AAGCGCCGCTAAAGAACATGGCCT
1 TTAGCGGCGTTTGT-GATAAAAGCGCCGCTAAAGAACATGATCT
10367865 TTAGCGGC
1 TTAGCGGC
10367873 ATTTTTTTCT
Statistics
Matches: 195, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
42 65 0.33
43 127 0.65
44 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGAACATGATCT
Found at i:10382397 original size:42 final size:42
Alignment explanation
Indices: 10382272--10382573 Score: 407
Period size: 42 Copynumber: 7.2 Consensus size: 42
10382262 ACTAGCACTT
* *
10382272 AGCCTGCTAGACTTAAAG-CTTGAT-TTAG-TACACCGGCACTT-
1 AGCCTGCTAGACGTAAAGTC-TGATATT-GTTTCACCGGCA-TTA
* * * *
10382313 AGCCTACTAGACATATAGTCTGA-AATGTTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
10382354 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
* * *
10382396 AGCCTGCTAGACGTAAAGTTTGAAATTATTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
*
10382438 AGCCTTCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
* *
10382480 AGCCTGCTAGACGTAAAGTCTGAAATTATTTCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
* * *
10382522 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGGTAATA
1 AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
10382564 AGCCTGCTAG
1 AGCCTGCTAG
10382574 GTGCTAAGCC
Statistics
Matches: 232, Mismatches: 24, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
40 3 0.01
41 48 0.21
42 181 0.78
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (42 bp):
AGCCTGCTAGACGTAAAGTCTGATATTGTTTCACCGGCATTA
Found at i:10383620 original size:4 final size:4
Alignment explanation
Indices: 10383611--10383702 Score: 175
Period size: 4 Copynumber: 23.0 Consensus size: 4
10383601 TACAATAGAT
10383611 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
10383659 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
10383703 TGATTTGATA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 86 1.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:10385921 original size:26 final size:26
Alignment explanation
Indices: 10385865--10385921 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
10385855 TATGAGATGT
*
10385865 TTATACAAAATTGTTATATAAATTAG
1 TTATACAAAATTGTTATATAAATCAG
* * *
10385891 ATATACAGAA-TGATTATATGAATCAG
1 TTATACAAAATTG-TTATATAAATCAG
10385917 TTATA
1 TTATA
10385922 TGGAAAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.39
Consensus pattern (26 bp):
TTATACAAAATTGTTATATAAATCAG
Found at i:10389570 original size:29 final size:29
Alignment explanation
Indices: 10389489--10389559 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
10389479 AATTTTAAAA
* *
10389489 TTATACATAAACTTTAGTCTAATGTGCAATT
1 TTATACATAAACTTTAAT-T-TTGTGCAATT
*
10389520 TTATACATGAACTTTAATTTTGTGCAATT
1 TTATACATAAACTTTAATTTTGTGCAATT
10389549 TTATACATAAA
1 TTATACATAAA
10389560 ATTTTGATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 19 0.53
30 1 0.03
31 16 0.44
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (29 bp):
TTATACATAAACTTTAATTTTGTGCAATT
Found at i:10391566 original size:20 final size:21
Alignment explanation
Indices: 10391519--10391566 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
10391509 TTCTGTAGTG
*
10391519 AAGAATATGAGAAGAGAGAAA
1 AAGAAAATGAGAAGAGAGAAA
* *
10391540 AA-TAAATGGGAAGA-AGAAA
1 AAGAAAATGAGAAGAGAGAAA
10391559 AAGAAAAT
1 AAGAAAAT
10391567 AAAGAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 7 0.32
20 13 0.59
21 2 0.09
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (21 bp):
AAGAAAATGAGAAGAGAGAAA
Found at i:10391699 original size:23 final size:25
Alignment explanation
Indices: 10391668--10391715 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
10391658 AGAAGAAAAT
10391668 AGAAAAT-AAAG-AAAAAAATTAAA
1 AGAAAATAAAAGAAAAAAAATTAAA
*
10391691 AGAACATAAAAGAAAAAAAATTAAA
1 AGAAAATAAAAGAAAAAAAATTAAA
10391716 TAGCTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.27
24 4 0.18
25 12 0.55
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.12
Consensus pattern (25 bp):
AGAAAATAAAAGAAAAAAAATTAAA
Found at i:10393007 original size:15 final size:15
Alignment explanation
Indices: 10392984--10393013 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10392974 GATTTTGATG
*
10392984 TTTTGAAATTTAAAA
1 TTTTAAAATTTAAAA
10392999 TTTTAAAATTTAAAA
1 TTTTAAAATTTAAAA
10393014 AAAATTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TTTTAAAATTTAAAA
Found at i:10429808 original size:3 final size:3
Alignment explanation
Indices: 10429800--10429830 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
10429790 TACAGCTTTG
10429800 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
10429831 ACATTCTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:10440705 original size:10 final size:10
Alignment explanation
Indices: 10440690--10440714 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10440680 GGGAGTTGTG
10440690 ACCTTTGATT
1 ACCTTTGATT
10440700 ACCTTTGATT
1 ACCTTTGATT
10440710 ACCTT
1 ACCTT
10440715 GACCATCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (10 bp):
ACCTTTGATT
Found at i:10445323 original size:29 final size:30
Alignment explanation
Indices: 10445267--10445345 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
10445257 AATCTTAAAA
* * *
10445267 TTATAAATCAATTTTGATTTAATGTGTAATT
1 TTATATATAAATTTTGATTT-AGGTGTAATT
*
10445298 TTATATATGAATTTTGATTT-GGTGTAATT
1 TTATATATAAATTTTGATTTAGGTGTAATT
*
10445327 ATATATATAAAATTTTGAT
1 TTATATAT-AAATTTTGAT
10445346 CGTAGTTCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 15 0.36
30 9 0.21
31 18 0.43
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.52
Consensus pattern (30 bp):
TTATATATAAATTTTGATTTAGGTGTAATT
Found at i:10452765 original size:3 final size:3
Alignment explanation
Indices: 10452757--10452781 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10452747 TTGGGACTTG
10452757 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
10452782 GTACTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:10454107 original size:14 final size:15
Alignment explanation
Indices: 10454085--10454161 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
10454075 CAATCAAACA
10454085 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
10454099 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
10454114 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
10454134 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
10454148 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
10454162 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:10454126 original size:20 final size:20
Alignment explanation
Indices: 10454101--10454140 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
10454091 AATATTTTCC
*
10454101 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
10454121 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
10454141 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:10454146 original size:34 final size:35
Alignment explanation
Indices: 10454089--10454155 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
10454079 CAAACACCAG
*
10454089 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
10454124 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
10454156 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:10459485 original size:16 final size:16
Alignment explanation
Indices: 10459464--10459495 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10459454 GATCCTCACT
10459464 ATATTTTCTTTCTTTC
1 ATATTTTCTTTCTTTC
*
10459480 ATATTTTCTTTGTTTC
1 ATATTTTCTTTCTTTC
10459496 TTTTTATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.16, G:0.03, T:0.69
Consensus pattern (16 bp):
ATATTTTCTTTCTTTC
Found at i:10460721 original size:21 final size:22
Alignment explanation
Indices: 10460679--10460721 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10460669 TAGACGAAGT
* *
10460679 ACAATATTATTTAACTACATAA
1 ACAATATAATTTAACTAAATAA
10460701 ACAATATAATTT-ACTAAATAA
1 ACAATATAATTTAACTAAATAA
10460722 TTACATGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
ACAATATAATTTAACTAAATAA
Found at i:10461802 original size:20 final size:21
Alignment explanation
Indices: 10461769--10461808 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
10461759 ATGACTAAGC
10461769 CTATCTTCAATTTTACTTGAT
1 CTATCTTCAATTTTACTTGAT
*
10461790 CTAT-TTCATTTTTACTTGA
1 CTATCTTCAATTTTACTTGA
10461809 ACTTGGAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.23, C:0.17, G:0.05, T:0.55
Consensus pattern (21 bp):
CTATCTTCAATTTTACTTGAT
Found at i:10464977 original size:13 final size:14
Alignment explanation
Indices: 10464959--10464996 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
10464949 ATCCCACCCC
10464959 AAATACAGATACA-
1 AAATACAGATACAG
*
10464972 AAATACAAATACAG
1 AAATACAGATACAG
10464986 AAATAACAGAT
1 AAAT-ACAGAT
10464997 TTAACATGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 4 0.19
15 5 0.24
ACGTcount: A:0.63, C:0.13, G:0.08, T:0.16
Consensus pattern (14 bp):
AAATACAGATACAG
Found at i:10465947 original size:17 final size:17
Alignment explanation
Indices: 10465925--10465959 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10465915 CATTAACTTC
10465925 CCACTAACCCACTAAAT
1 CCACTAACCCACTAAAT
*
10465942 CCACTAACCTACTAAAT
1 CCACTAACCCACTAAAT
10465959 C
1 C
10465960 TCAACTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (17 bp):
CCACTAACCCACTAAAT
Found at i:10467850 original size:42 final size:42
Alignment explanation
Indices: 10467787--10467904 Score: 145
Period size: 42 Copynumber: 2.8 Consensus size: 42
10467777 TGTGATTACG
*
10467787 TGTAAGACCATGTCTGAGACATTGGCATTGATATAAGATTCA
1 TGTAAGACCATGTCTGAGACATTGGCATCGATATAAGATTCA
* * *
10467829 TGTAAGACCATGTCT-AGGACATTGGCATCGATTTGAGATTCG
1 TGTAAGACCATGTCTGA-GACATTGGCATCGATATAAGATTCA
10467871 TGTAAGACCATAG-CTG-G-CTATTGGCATCGATATA
1 TGTAAGACCAT-GTCTGAGAC-ATTGGCATCGATATA
10467905 TGATAGTTTG
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
40 1 0.02
41 15 0.23
42 49 0.74
43 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGAGACATTGGCATCGATATAAGATTCA
Found at i:10467938 original size:42 final size:40
Alignment explanation
Indices: 10467787--10467938 Score: 128
Period size: 42 Copynumber: 3.6 Consensus size: 40
10467777 TGTGATTACG
* * * * *
10467787 TGTAAGACCATGTCTGAGACATTGGCATTGATATAAGATTC
1 TGTAAGACCATATCTG-GATATTGGCATCGATTTGAGATTC
* *
10467828 ATGTAAGACCATGTCTAGGACATTGGCATCGATTTGAGATTC
1 -TGTAAGACCATATCT-GGATATTGGCATCGATTTGAGATTC
* * *
10467870 GTGTAAGACCATAGCTGGCTATTGGCATCGATATATGATAGTT-
1 -TGTAAGACCATATCTGGATATTGGCATCGAT-T-TGAGA-TTC
10467913 TGTAAGACCATATCTGGGATA-TGGCA
1 TGTAAGACCATATCT-GGATATTGGCA
10467939 CTGTGCGAGT
Statistics
Matches: 94, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
41 14 0.15
42 69 0.73
43 9 0.10
44 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (40 bp):
TGTAAGACCATATCTGGATATTGGCATCGATTTGAGATTC
Found at i:10474095 original size:42 final size:43
Alignment explanation
Indices: 10473989--10474102 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 43
10473979 TGATGTAGAA
* * *
10473989 AAATGCCGCTATAGAATATGACCTTTAGCGGTGCTTTTCCTAC
1 AAATGCCGCTATAGAACATGACCTTTAGCGGTGCATTTCCCAC
** * * * *
10474032 AAATGCCATTAAAGAAGATGACATTTAGCGTTG-ATTTCCCAC
1 AAATGCCGCTATAGAACATGACCTTTAGCGGTGCATTTCCCAC
*
10474074 AAATGACGCTATAGAACATGACCTTTAGC
1 AAATGCCGCTATAGAACATGACCTTTAGC
10474103 AGCATGTTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
42 30 0.53
43 27 0.47
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (43 bp):
AAATGCCGCTATAGAACATGACCTTTAGCGGTGCATTTCCCAC
Found at i:10476577 original size:24 final size:24
Alignment explanation
Indices: 10476533--10476579 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
10476523 AACAAAATAT
*
10476533 AAATGAAAACATAAATCAATAAAC
1 AAATGAAAACATAAATAAATAAAC
*
10476557 AAATGAAGGACATAAA-AAATAAA
1 AAATGAA-AACATAAATAAATAAA
10476580 AAAAATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.15
Consensus pattern (24 bp):
AAATGAAAACATAAATAAATAAAC
Found at i:10477253 original size:21 final size:19
Alignment explanation
Indices: 10477216--10477290 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
10477206 AATCATATCT
10477216 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
10477235 TCCAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
10477256 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
10477275 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
10477291 CTTGAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
21 18 0.35
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:10479179 original size:107 final size:107
Alignment explanation
Indices: 10478890--10479428 Score: 798
Period size: 107 Copynumber: 5.0 Consensus size: 107
10478880 TGGACTGAGA
* * * ** **
10478890 TTTAAGAGAATATTT-GCCTATTTGGTCAAACG-GGAAATCGAAACCCAGCACATTAGCACACGT
1 TTTAAAAGGATATTTAG-CTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGT
* *
10478953 TTCCTCGAATTTCTAAACGCAAAATATTGCCTTACTTTGAAAT
65 TTTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
* *
10478996 TTTAAAAGGATATTTGGCTATTTGGTCGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGT
1 TTTAAAAGGATATTTAGCTATTTGGTCGAACGA-AAAAATCGAAACCCAGCACATTAGGGCACGT
* *
10479061 TTTCTCGAATTTCCAAGCGCAAAATATTGCCTTACTTTGAATT
65 TTTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
* *
10479104 TTTAAAAGAATATTTAGCTATTTGATCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTT
1 TTTAAAAGGATATTTAGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTT
*
10479169 TTCTCGAATTTCTAAACGCAAAATATTGCCTTACTTTGAAAT
66 TTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
* * * *
10479211 TTTAAAAGGATATTTAGCTATTTAGTCGAATGAAAAAATCGAAACCTAACACATTAGGGCACGTT
1 TTTAAAAGGATATTTAGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTT
*
10479276 TTCTCGAATTTCCAAACGCAAAATATTCCCTTACTTTGAAAT
66 TTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
* *
10479318 TTTAAAAGGATATTTAGCTATTTGGTTGAACAAAAAAATCGAAACCCAGCACATTAGGGCACGTT
1 TTTAAAAGGATATTTAGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTT
10479383 TTCTCGAATTTCCAAATC-CAAAATATTGCCTTA-TTTAGAAAAT
66 TTCTCGAATTTCCAAA-CGCAAAATATTGCCTTACTTT-G-AAAT
10479426 TTT
1 TTT
10479429 TCTTTTTTGA
Statistics
Matches: 393, Mismatches: 34, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
106 30 0.08
107 260 0.66
108 103 0.26
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (107 bp):
TTTAAAAGGATATTTAGCTATTTGGTCGAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTT
TTCTCGAATTTCCAAACGCAAAATATTGCCTTACTTTGAAAT
Found at i:10479493 original size:20 final size:21
Alignment explanation
Indices: 10479450--10479494 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
10479440 GTAAGGTGTT
*
10479450 AATATGCATAATGTAATAATA
1 AATATGCATAATGTAACAATA
10479471 AATATG-ATAATGTGAACAA-A
1 AATATGCATAATGT-AACAATA
10479491 AATA
1 AATA
10479495 ATATGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (21 bp):
AATATGCATAATGTAACAATA
Found at i:10479657 original size:30 final size:27
Alignment explanation
Indices: 10479623--10479681 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 27
10479613 TATCATCAAG
*
10479623 TAAAACAATAATAACAATA-AAGAAACTAGA
1 TAAAAAAAT-ATAA-AATATAA-AAA-TAGA
10479653 TAAAAAAATATAAAATATAAAAATAGA
1 TAAAAAAATATAAAATATAAAAATAGA
10479680 TA
1 TA
10479682 TGTACACGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 6 0.22
28 7 0.26
29 6 0.22
30 8 0.30
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.20
Consensus pattern (27 bp):
TAAAAAAATATAAAATATAAAAATAGA
Found at i:10479926 original size:2 final size:2
Alignment explanation
Indices: 10479921--10479961 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
10479911 ATGTACATGG
*
10479921 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10479962 AATTCTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:10489938 original size:2 final size:2
Alignment explanation
Indices: 10489931--10489957 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10489921 TTAAACATTA
10489931 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 A
10489958 CAACATTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10491033 original size:231 final size:233
Alignment explanation
Indices: 10490620--10491072 Score: 865
Period size: 231 Copynumber: 1.9 Consensus size: 233
10490610 GAAAAATAAA
10490620 CCATAACCAAATAAATCATCTCAATGATATTATAATTCAATTTGACTAGGCCGCCGAATTTAGCA
1 CCATAACCAAATAAATCATCTCAATGATATTATAATTCAATTTGACTAGG-CGCCGAATTTAGCA
10490685 AATCTCAACCACACATACATTTATCATACTCGTAAATTCTTATGACCACATTAAGTAACTTCACT
65 AATCTCAACCACACATACATTTATCATACTCGTAAATTCTTATGACCACATTAAGTAACTTCACT
10490750 TATCTTATTTATCAATGAACATATAAACCATGCTTTCAAATTCAACCATTTCAATCTCATTTATC
130 TATCTTATTTATCAATGAACATATAAACCATGCTTTCAAATTCAACCATTTCAATCTCATTTATC
10490815 AATTCAAAATTCAAATTAACTACCATAAAGCTTAGTAAG
195 AATTCAAAATTCAAATTAACTACCATAAAGCTTAGTAAG
*
10490854 CCATAAGCAAATAAATCATCTCAATGATATTATAATTCAATTTGACTA-G-GCCGAATTTAGCAA
1 CCATAACCAAATAAATCATCTCAATGATATTATAATTCAATTTGACTAGGCGCCGAATTTAGCAA
10490917 ATCTCAACCACACATACATTTATCATACTCGTAAATTCTTATGACCACATTAAGTAACTTCACTT
66 ATCTCAACCACACATACATTTATCATACTCGTAAATTCTTATGACCACATTAAGTAACTTCACTT
*
10490982 ATCTTATTTATCAATGAACATATAAACCATGCTTTCAAATTCAACCATTTCAATCTCATTTGTCA
131 ATCTTATTTATCAATGAACATATAAACCATGCTTTCAAATTCAACCATTTCAATCTCATTTATCA
10491047 ATTCAAAATTCAAATTAACTACCATA
196 ATTCAAAATTCAAATTAACTACCATA
10491073 CATCAAAGTC
Statistics
Matches: 217, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
231 169 0.78
233 1 0.00
234 47 0.22
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (233 bp):
CCATAACCAAATAAATCATCTCAATGATATTATAATTCAATTTGACTAGGCGCCGAATTTAGCAA
ATCTCAACCACACATACATTTATCATACTCGTAAATTCTTATGACCACATTAAGTAACTTCACTT
ATCTTATTTATCAATGAACATATAAACCATGCTTTCAAATTCAACCATTTCAATCTCATTTATCA
ATTCAAAATTCAAATTAACTACCATAAAGCTTAGTAAG
Found at i:10493948 original size:15 final size:15
Alignment explanation
Indices: 10493928--10493958 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
10493918 TTATTGTTAA
10493928 AAAAAATAAAATTTT
1 AAAAAATAAAATTTT
10493943 AAAAAATAAAATTTT
1 AAAAAATAAAATTTT
10493958 A
1 A
10493959 TATTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAAAATAAAATTTT
Found at i:10494494 original size:16 final size:14
Alignment explanation
Indices: 10494449--10494484 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
10494439 TGGAGAATAT
*
10494449 TTTTAATTAATTCAA
1 TTTTAATTAATT-TA
10494464 TTTTAATTAATTTA
1 TTTTAATTAATTTA
10494478 TTTTAAT
1 TTTTAAT
10494485 ATTATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTAATTAATTTA
Found at i:10494705 original size:14 final size:14
Alignment explanation
Indices: 10494686--10494733 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
10494676 TTAGTACTTA
10494686 AATTTTTAATATTT
1 AATTTTTAATATTT
**
10494700 AATTTTTAACCTTT
1 AATTTTTAATATTT
* *
10494714 ATTTTTTAATTTTAT
1 AATTTTTAATATT-T
10494729 AATTT
1 AATTT
10494734 AATTTAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
14 22 0.81
15 5 0.19
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (14 bp):
AATTTTTAATATTT
Found at i:10503740 original size:29 final size:30
Alignment explanation
Indices: 10503698--10503781 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 30
10503688 TAAAATTAAT
*
10503698 AAAAATAAGT-AAAATATTTAAAATTTTATA
1 AAAAATAA-TAAAAATATTTAAAATCTTATA
** *
10503728 AAAGGT-ATAAAAAT-TCTTAAAAACTTATA
1 AAAAATAATAAAAATAT-TTAAAATCTTATA
10503757 AAAAATAATAAAAATATTATAAAAT
1 AAAAATAATAAAAATATT-TAAAAT
10503782 ATTAAAATTG
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
28 2 0.05
29 21 0.50
30 13 0.31
31 6 0.14
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAAATAATAAAAATATTTAAAATCTTATA
Found at i:10503742 original size:20 final size:20
Alignment explanation
Indices: 10503717--10503760 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
10503707 TAAAATATTT
*
10503717 AAAATT-TTATAAAAGGTATA
1 AAAATTCTTA-AAAACGTATA
*
10503737 AAAATTCTTAAAAACTTATA
1 AAAATTCTTAAAAACGTATA
10503757 AAAA
1 AAAA
10503761 ATAATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAATTCTTAAAAACGTATA
Found at i:10504195 original size:10 final size:9
Alignment explanation
Indices: 10504180--10504266 Score: 63
Period size: 9 Copynumber: 9.7 Consensus size: 9
10504170 AATTTAAATA
10504180 TATTTTTAT
1 TATTTTTAT
*
10504189 TAGTTTTAT
1 TATTTTTAT
* *
10504198 AAATTTTTAG
1 -TATTTTTAT
*
10504208 AATTTATTAT
1 TATTT-TTAT
*
10504218 AATTTTTA-
1 TATTTTTAT
10504226 TATTTTTA-
1 TATTTTTAT
10504234 TATTTTTAT
1 TATTTTTAT
* *
10504243 GATATTTAT
1 TATTTTTAT
10504252 TAGTTTTTAT
1 TA-TTTTTAT
10504262 T-TTTT
1 TATTTT
10504267 ATAATTTTAA
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
8 19 0.30
9 24 0.38
10 21 0.33
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (9 bp):
TATTTTTAT
Found at i:10504231 original size:7 final size:8
Alignment explanation
Indices: 10504178--10504275 Score: 72
Period size: 8 Copynumber: 11.2 Consensus size: 8
10504168 AAAATTTAAA
10504178 TATATTTT
1 TATATTTT
10504186 TATTAGTTTT
1 TA-TA-TTTT
*
10504196 ATAAATTTT
1 -TATATTTT
*
10504205 TAGAATTTAT
1 TA-TATTT-T
10504215 TATAATTTT
1 TAT-ATTTT
10504224 TATATTTT
1 TATATTTT
10504232 TATATTTT
1 TATATTTT
*
10504240 TATGATATT
1 TAT-ATTTT
10504249 TATTAGTTTT
1 TA-TA-TTTT
10504259 TAT-TTTT
1 TATATTTT
*
10504266 TATAATTT
1 TATATTTT
10504274 TA
1 TA
10504276 AAAGTTTATG
Statistics
Matches: 75, Mismatches: 5, Indels: 20
0.75 0.05 0.20
Matches are distributed among these distances:
7 7 0.09
8 25 0.33
9 23 0.31
10 18 0.24
11 2 0.03
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (8 bp):
TATATTTT
Found at i:10504258 original size:19 final size:16
Alignment explanation
Indices: 10504214--10504275 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
10504204 TTAGAATTTA
*
10504214 TTATAATTTTTATATTT
1 TTAT-ATTTTTATATAT
10504231 TTATATTTTTATGATAT
1 TTATATTTTTAT-ATAT
*
10504248 TTATTAGTTTTTAT-TTT
1 TTA-TA-TTTTTATATAT
*
10504265 TTATAATTTTA
1 TTATATTTTTA
10504276 AAAGTTTATG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 5 0.13
16 10 0.26
17 15 0.38
18 2 0.05
19 7 0.18
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
TTATATTTTTATATAT
Found at i:10504275 original size:25 final size:25
Alignment explanation
Indices: 10504224--10504275 Score: 52
Period size: 26 Copynumber: 2.0 Consensus size: 25
10504214 TTATAATTTT
* *
10504224 TATATTTTTATATTTTTATGATATT-
1 TATATTTTTAT-TTTTTATAATTTTA
10504249 TATTAGTTTTTATTTTTTATAATTTTA
1 TA-TA-TTTTTATTTTTTATAATTTTA
10504276 AAAGTTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
25 2 0.09
26 13 0.59
27 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (25 bp):
TATATTTTTATTTTTTATAATTTTA
Found at i:10504281 original size:25 final size:25
Alignment explanation
Indices: 10504209--10504282 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
10504199 AATTTTTAGA
* *
10504209 ATTTATTATAATTTTTATA-TTTTT
1 ATTTTTTATAATTTTAATAGTTTTT
* *
10504233 ATATTTTTATGATATTTATTAGTTTTT
1 AT-TTTTTATAAT-TTTAATAGTTTTT
*
10504260 ATTTTTTATAATTTTAAAAGTTT
1 ATTTTTTATAATTTTAATAGTTT
10504283 ATGTCAATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
24 2 0.05
25 17 0.43
26 14 0.35
27 7 0.17
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (25 bp):
ATTTTTTATAATTTTAATAGTTTTT
Found at i:10504326 original size:34 final size:35
Alignment explanation
Indices: 10504192--10504327 Score: 106
Period size: 34 Copynumber: 3.9 Consensus size: 35
10504182 TTTTTATTAG
*
10504192 TTTTATAAATTTTTA-GAATTTATTATAATTTTTATAT
1 TTTTA-AAATTTTTATGAATTTATTAGAA-TTTTA-AT
* * *
10504229 TTTT-ATATTTTTATGATATTTATTAG-TTTTTATT
1 TTTTAAAATTTTTATGA-ATTTATTAGAATTTTAAT
* * *
10504263 TTTTATAA-TTTTA-AAAGTTTATGT-CAATTTTAAT
1 TTTTAAAATTTTTATGAA-TTTAT-TAGAATTTTAAT
10504297 TTTTAAAATTTTTATG-ATTTATTAGAATTTT
1 TTTTAAAATTTTTATGAATTTATTAGAATTTT
10504328 TATTCATTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
32 1 0.01
33 7 0.09
34 35 0.45
35 20 0.26
36 2 0.03
37 12 0.16
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (35 bp):
TTTTAAAATTTTTATGAATTTATTAGAATTTTAAT
Found at i:10504346 original size:10 final size:9
Alignment explanation
Indices: 10504294--10504388 Score: 75
Period size: 10 Copynumber: 10.0 Consensus size: 9
10504284 TGTCAATTTT
10504294 AATTTTTAA
1 AATTTTTAA
*
10504303 AATTTTTAT
1 AATTTTTAA
* *
10504312 GATTTATTAG
1 AATTT-TTAA
*
10504322 AATTTTTATT
1 AATTTTTA-A
*
10504332 CATTTTATAA
1 AATTTT-TAA
10504342 AA-TTTTAA
1 AATTTTTAA
10504350 ATATTTTTAA
1 A-ATTTTTAA
10504360 AATATTTTAA
1 AAT-TTTTAA
*
10504370 AATATTTTAT
1 AAT-TTTTAA
10504380 AATTTTTAA
1 AATTTTTAA
10504389 TTTTTATAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
8 4 0.06
9 26 0.37
10 38 0.54
11 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (9 bp):
AATTTTTAA
Found at i:10504420 original size:35 final size:35
Alignment explanation
Indices: 10504373--10504439 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
10504363 ATTTTAAAAT
*
10504373 ATTTTATAATTTTTAAT-TTTTATAAGTTTATATCA
1 ATTTTATAATTTTTAATCTTTAATAA-TTTATATCA
10504408 ATTTTA-ATATTTTTAATCTTTAATAATTTATA
1 ATTTTATA-ATTTTTAATCTTTAATAATTTATA
10504440 ATTTTTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 1 0.03
35 21 0.72
36 7 0.24
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (35 bp):
ATTTTATAATTTTTAATCTTTAATAATTTATATCA
Found at i:10504423 original size:9 final size:9
Alignment explanation
Indices: 10504295--10504454 Score: 52
Period size: 10 Copynumber: 17.7 Consensus size: 9
10504285 GTCAATTTTA
*
10504295 ATTTTTAAA
1 ATTTTTAAT
10504304 ATTTTT-AT
1 ATTTTTAAT
10504312 GATTTATTAGA-
1 -ATTT-TTA-AT
*
10504323 ATTTTTATT
1 ATTTTTAAT
*
10504332 CATTTTATAAA
1 -ATTTT-TAAT
*
10504343 ATTTTAAAT
1 ATTTTTAAT
*
10504352 ATTTTTAAA
1 ATTTTTAAT
*
10504361 ATATTTTAAA
1 AT-TTTTAAT
10504371 ATATTTT-AT
1 AT-TTTTAAT
10504380 AATTTTT-A-
1 -ATTTTTAAT
10504388 ATTTTT-AT
1 ATTTTTAAT
**
10504396 AAGTTTATAT
1 ATTTTTA-AT
*
10504406 CAATTTTAAT
1 -ATTTTTAAT
10504416 ATTTTT-A-
1 ATTTTTAAT
*
10504423 ATCTTTAAT
1 ATTTTTAAT
*
10504432 AATTTATAAT
1 -ATTTTTAAT
10504442 -TTTTT-AT
1 ATTTTTAAT
10504449 ATTTTT
1 ATTTTT
10504455 TTTGATTTGT
Statistics
Matches: 117, Mismatches: 17, Indels: 35
0.69 0.10 0.21
Matches are distributed among these distances:
7 14 0.12
8 16 0.14
9 35 0.30
10 43 0.37
11 8 0.07
12 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:10504441 original size:17 final size:16
Alignment explanation
Indices: 10504410--10504452 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
10504400 TTATATCAAT
*
10504410 TTTAATATTTTTAATC
1 TTTAATATTTATAATC
*
10504426 TTTAATAATTTATAATT
1 TTTAAT-ATTTATAATC
*
10504443 TTTTATATTT
1 TTTAATATTT
10504453 TTTTTGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAATATTTATAATC
Found at i:10504471 original size:28 final size:30
Alignment explanation
Indices: 10504436--10504492 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
10504426 TTTAATAATT
10504436 TATAATTTTTT-ATATTTTTTT-TGATTTG
1 TATAATTTTTTCATATTTTTTTATGATTTG
* *
10504464 TATAATTTTTTCCTCTTTTTTTATGATTT
1 TATAATTTTTTCATATTTTTTTATGATTT
10504493 TTATGAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.44
29 8 0.32
30 6 0.24
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.70
Consensus pattern (30 bp):
TATAATTTTTTCATATTTTTTTATGATTTG
Found at i:10504892 original size:21 final size:21
Alignment explanation
Indices: 10504865--10504910 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
10504855 TAAACAAAAT
*
10504865 AATATATTTATATATTTTAATAA
1 AATAT-TTTAT-TAATTTAATAA
10504888 AATATTTTATTAATTTAA-AA
1 AATATTTTATTAATTTAATAA
10504908 AAT
1 AAT
10504911 TATACAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 7 0.32
22 5 0.23
23 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATTTTATTAATTTAATAA
Found at i:10506938 original size:20 final size:19
Alignment explanation
Indices: 10506915--10506977 Score: 83
Period size: 20 Copynumber: 3.3 Consensus size: 19
10506905 TTGCAAAAAG
10506915 AAATTCAAAATAATTTTTAA
1 AAATTCAAAAT-ATTTTTAA
*
10506935 AAATTCAAAATGATTTTT-G
1 AAATTCAAAAT-ATTTTTAA
*
10506954 AAATTCAAAATATTTATAA
1 AAATTCAAAATATTTTTAA
10506973 AAATT
1 AAATT
10506978 TCAGAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 5 0.13
19 16 0.42
20 17 0.45
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (19 bp):
AAATTCAAAATATTTTTAA
Found at i:10506976 original size:19 final size:19
Alignment explanation
Indices: 10506915--10506977 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
10506905 TTGCAAAAAG
10506915 AAATTCAAAATAATTTTTAA
1 AAATTCAAAATAA-TTTTAA
* **
10506935 AAATTCAAAATGATTTTTG
1 AAATTCAAAATAATTTTAA
10506954 AAATTCAAAAT-ATTTATAA
1 AAATTCAAAATAATTT-TAA
10506973 AAATT
1 AAATT
10506978 TCAGAATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
18 4 0.11
19 21 0.57
20 12 0.32
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (19 bp):
AAATTCAAAATAATTTTAA
Found at i:10512022 original size:69 final size:69
Alignment explanation
Indices: 10511936--10512091 Score: 195
Period size: 69 Copynumber: 2.3 Consensus size: 69
10511926 ATATATACAC
** * * *
10511936 TGCCATGGTCCAACCATGACCTTATGTATGAAAAACTATTATAGCCTCGCTATGGTTTTACGTGA
1 TGCCATGGTCCAACCATGACCTTACATATGAAAAACTATCATAGCCTCGCTATGGTCTTACGTAA
*
10512001 ATAT
66 ACAT
** * * * *
10512005 TGCCATGGTCCAACCATGGTCTTGCATCTGAAAAACTATCATAGTCTCGCTATGGTCTTATGTAA
1 TGCCATGGTCCAACCATGACCTTACATATGAAAAACTATCATAGCCTCGCTATGGTCTTACGTAA
10512070 ACAT
66 ACAT
*
10512074 TACCATGGTCCAACCATG
1 TGCCATGGTCCAACCATG
10512092 GTTATGTACA
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 74 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (69 bp):
TGCCATGGTCCAACCATGACCTTACATATGAAAAACTATCATAGCCTCGCTATGGTCTTACGTAA
ACAT
Found at i:10512092 original size:69 final size:69
Alignment explanation
Indices: 10511964--10512093 Score: 197
Period size: 69 Copynumber: 1.9 Consensus size: 69
10511954 ACCTTATGTA
* * * * *
10511964 TGAAAAACTATTATAGCCTCGCTATGGTTTTACGTGAATATTGCCATGGTCCAACCATGGTCTTG
1 TGAAAAACTATCATAGCCTCGCTATGGTCTTACGTAAACATTACCATGGTCCAACCATGGTCTTG
10512029 CATC
66 CATC
* *
10512033 TGAAAAACTATCATAGTCTCGCTATGGTCTTATGTAAACATTACCATGGTCCAACCATGGT
1 TGAAAAACTATCATAGCCTCGCTATGGTCTTACGTAAACATTACCATGGTCCAACCATGGT
10512094 TATGTACATC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 54 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (69 bp):
TGAAAAACTATCATAGCCTCGCTATGGTCTTACGTAAACATTACCATGGTCCAACCATGGTCTTG
CATC
Found at i:10515504 original size:26 final size:26
Alignment explanation
Indices: 10515468--10515521 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
10515458 ATCGTCCTCC
10515468 CCACATGCATATGCAACGCAATCATT
1 CCACATGCATATGCAACGCAATCATT
*
10515494 CCACATGCATATGCAATGCAATCATT
1 CCACATGCATATGCAACGCAATCATT
10515520 CC
1 CC
10515522 TTAATGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.31, G:0.11, T:0.24
Consensus pattern (26 bp):
CCACATGCATATGCAACGCAATCATT
Found at i:10521875 original size:14 final size:14
Alignment explanation
Indices: 10521841--10521876 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
10521831 TTATTTCACT
*
10521841 AAAAATATTTTTTA
1 AAAAATAATTTTTA
*
10521855 AATAATAATTTTTA
1 AAAAATAATTTTTA
10521869 AAAAATAA
1 AAAAATAA
10521877 ATAATTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAAAATAATTTTTA
Found at i:10538613 original size:87 final size:86
Alignment explanation
Indices: 10538467--10538630 Score: 247
Period size: 87 Copynumber: 1.9 Consensus size: 86
10538457 TTTAAGTTCG
* * * *
10538467 GTGAATTCATCAAGTTAGTCTCAATAGGACCACCCAAACTTTGGGATATTAACTGATTAAGAGTA
1 GTGAATTCATAAAGTTAGTCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGTA
*
10538532 AGAAACTTAACTTCACATGTCA
66 AG-AACTCAACTTCACATGTCA
* * *
10538554 GTGAATTCATAAAGTTTGTCTCAATAGGATCACCCAAACTCTGGGATATGAATTCATTAAGAGTA
1 GTGAATTCATAAAGTTAGTCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGTA
10538619 AGAACTCAACTT
66 AGAACTCAACTT
10538631 TATACATGTA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
86 9 0.13
87 60 0.87
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (86 bp):
GTGAATTCATAAAGTTAGTCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGTA
AGAACTCAACTTCACATGTCA
Found at i:10538651 original size:30 final size:30
Alignment explanation
Indices: 10538617--10538677 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
10538607 TCATTAAGAG
10538617 TAAGAACTCAACTTTATACATGTAAATCAT
1 TAAGAACTCAACTTTATACATGTAAATCAT
*
10538647 TAAGAACTCAACTTTATGCATGTAAATCAT
1 TAAGAACTCAACTTTATACATGTAAATCAT
10538677 T
1 T
10538678 TTCCATAGGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.34
Consensus pattern (30 bp):
TAAGAACTCAACTTTATACATGTAAATCAT
Found at i:10539888 original size:30 final size:30
Alignment explanation
Indices: 10539852--10539912 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
10539842 GCTTTGGAGC
10539852 TTGTTTGAGACAATAGAAAAATTTTTTTAG
1 TTGTTTGAGACAATAGAAAAATTTTTTTAG
*
10539882 TTGTTTGAGACAATAGAAAGATTTTTTTAG
1 TTGTTTGAGACAATAGAAAAATTTTTTTAG
10539912 T
1 T
10539913 CTGCAAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.44
Consensus pattern (30 bp):
TTGTTTGAGACAATAGAAAAATTTTTTTAG
Found at i:10544194 original size:27 final size:26
Alignment explanation
Indices: 10544139--10544212 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 26
10544129 TATTTTTTCG
*
10544139 AAATTTTACCAAGGTTAAAATCCTCAA
1 AAATTTTACCAAGGGTAAAATCCTC-A
* ** *
10544166 AAATTATACCAAGGGTAAAATTTTTA
1 AAATTTTACCAAGGGTAAAATCCTCA
* *
10544192 AAATTTTACTAGGGGTAAAAT
1 AAATTTTACCAAGGGTAAAAT
10544213 AGATATGAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 19 0.49
27 20 0.51
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (26 bp):
AAATTTTACCAAGGGTAAAATCCTCA
Found at i:10546717 original size:2 final size:2
Alignment explanation
Indices: 10546710--10546737 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10546700 TCAATTTAAT
10546710 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
10546738 CACATAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10547056 original size:23 final size:21
Alignment explanation
Indices: 10546995--10547056 Score: 54
Period size: 23 Copynumber: 2.9 Consensus size: 21
10546985 CCTAATTTTG
* *
10546995 TTTTCAGATTAA-CATTAACA
1 TTTTTAGATTAATCATTCACA
* **
10547015 TTTTTAAATTAATTTTTCACGA
1 TTTTTAGATTAATCATTCAC-A
10547037 TTTTATAGATTAATCATTCA
1 TTTT-TAGATTAATCATTCA
10547057 AGTCCATCTG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 10 0.32
21 4 0.13
22 5 0.16
23 12 0.39
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.48
Consensus pattern (21 bp):
TTTTTAGATTAATCATTCACA
Found at i:10560840 original size:29 final size:30
Alignment explanation
Indices: 10560739--10560869 Score: 140
Period size: 29 Copynumber: 4.4 Consensus size: 30
10560729 AAAAAAATAT
** * *
10560739 AAATTACATTTCAACCCCTAAACTTTTTTCA
1 AAATTACATTTTGACCCCTTAACTTTCTT-A
** *
10560770 AAATTGTATCTTGACCCCTTAACTTTCTTA
1 AAATTACATTTTGACCCCTTAACTTTCTTA
*
10560800 AAATTTCATTTTGACCCCTTAACTTTC-TA
1 AAATTACATTTTGACCCCTTAACTTTCTTA
* * *
10560829 AAATTACATTTTGGCCCCGT-ATTTTCTTA
1 AAATTACATTTTGACCCCTTAACTTTCTTA
10560858 AAATTACATTTT
1 AAATTACATTTT
10560870 TCCCCAGAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
28 5 0.06
29 33 0.39
30 25 0.29
31 22 0.26
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.44
Consensus pattern (30 bp):
AAATTACATTTTGACCCCTTAACTTTCTTA
Found at i:10561189 original size:15 final size:15
Alignment explanation
Indices: 10561165--10561195 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10561155 ACCACCCTCG
10561165 CGCAAACACCACCAC
1 CGCAAACACCACCAC
*
10561180 CGCAACCACCACCAC
1 CGCAAACACCACCAC
10561195 C
1 C
10561196 ACTACAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.58, G:0.06, T:0.00
Consensus pattern (15 bp):
CGCAAACACCACCAC
Found at i:10561441 original size:12 final size:12
Alignment explanation
Indices: 10561424--10561482 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
10561414 AGGAAGAGGG
10561424 GAGAAAGAAAGA
1 GAGAAAGAAAGA
*
10561436 GAGAAAGGAAAAA
1 GAGAAA-GAAAGA
10561449 G-GAAAG---GA
1 GAGAAAGAAAGA
10561457 GAGAAAGAAA-A
1 GAGAAAGAAAGA
*
10561468 GAGAAAAAAAGA
1 GAGAAAGAAAGA
10561480 GAG
1 GAG
10561483 GAGATACCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
8 2 0.05
9 5 0.13
11 11 0.29
12 14 0.37
13 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
GAGAAAGAAAGA
Found at i:10561473 original size:20 final size:19
Alignment explanation
Indices: 10561427--10561473 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
10561417 AAGAGGGGAG
10561427 AAAGAAAGAGAGAAAGGAA
1 AAAGAAAGAGAGAAAGGAA
10561446 AAAGGAAAGGAGAGAAA-GAA
1 AAA-GAAA-GAGAGAAAGGAA
10561466 AAGAGAAA
1 AA-AGAAA
10561474 AAAAGAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 3 0.12
20 13 0.52
21 9 0.36
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAGAGAAAGGAA
Found at i:10561480 original size:21 final size:22
Alignment explanation
Indices: 10561424--10561481 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
10561414 AGGAAGAGGG
10561424 GAGAAAGAAAGAGAGAAAGGAAAA
1 GAGAAA-AAA-AGAGAAAGGAAAA
* **
10561448 -AGGAAAGGAGAGAAA-GAAAA
1 GAGAAAAAAAGAGAAAGGAAAA
10561468 GAGAAAAAAAGAGA
1 GAGAAAAAAAGAGA
10561482 GGAGATACCG
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
20 5 0.19
21 17 0.63
22 1 0.04
23 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (22 bp):
GAGAAAAAAAGAGAAAGGAAAA
Found at i:10561606 original size:6 final size:6
Alignment explanation
Indices: 10561578--10561656 Score: 53
Period size: 6 Copynumber: 13.5 Consensus size: 6
10561568 GAAGGGGAAG
10561578 AAAGAA AATAGAA AGAA-AA AAAGAA AAAG-- AAAGAA AAAGAA AAA-ATA
1 AAAGAA AA-AGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGA-A
* * *
10561625 GAAGAA ATAGAA GAAA-AA GAA-AA AAAGAA AAA
1 AAAGAA AAAGAA -AAAGAA AAAGAA AAAGAA AAA
10561657 AGAATAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
4 4 0.07
5 9 0.16
6 35 0.60
7 9 0.16
8 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:10561610 original size:18 final size:17
Alignment explanation
Indices: 10561578--10561667 Score: 85
Period size: 18 Copynumber: 5.1 Consensus size: 17
10561568 GAAGGGGAAG
10561578 AAAGAAAATAGAAAGAAAA
1 AAAGAAAA-A-AAAGAAAA
10561597 AAAGAAAAAGAAAG--AA
1 AAAGAAAAA-AAAGAAAA
*
10561613 AAAGAAAAAATAGAAGAA
1 AAAGAAAAAAAAGAA-AA
* *
10561631 ATAGAAGAAAAAGAAAA
1 AAAGAAAAAAAAGAAAA
*
10561648 AAAGAAAAAAGAATAAAA
1 AAAGAAAAAA-AAGAAAA
10561666 AA
1 AA
10561668 CAGCAGCAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.05
16 11 0.18
17 10 0.17
18 28 0.47
19 8 0.13
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (17 bp):
AAAGAAAAAAAAGAAAA
Found at i:10561614 original size:9 final size:10
Alignment explanation
Indices: 10561575--10561654 Score: 84
Period size: 9 Copynumber: 8.6 Consensus size: 10
10561565 GAAGAAGGGG
10561575 AAGAAAGAAA
1 AAGAAAGAAA
10561585 ATAGAAAG-AA
1 A-AGAAAGAAA
10561595 AA-AAAGAAA
1 AAGAAAGAAA
10561604 AAGAAAGAAA
1 AAGAAAGAAA
10561614 AAGAAA-AAA
1 AAGAAAGAAA
*
10561623 TAG-AAGAAA
1 AAGAAAGAAA
*
10561632 TAG-AAGAAA
1 AAGAAAGAAA
10561641 AAG-AA-AAA
1 AAGAAAGAAA
10561649 AAGAAA
1 AAGAAA
10561655 AAAGAATAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
8 12 0.19
9 28 0.44
10 17 0.27
11 6 0.10
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:10561639 original size:37 final size:35
Alignment explanation
Indices: 10561582--10561657 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 35
10561572 GGGAAGAAAG
10561582 AAAATAGAAAGAAAAAAAGAAAAAGAAAGAAAAAGAA
1 AAAATAGAAAGAAAAAAAGAAAAAG-AA-AAAAAGAA
*
10561619 AAAATAG-AAGAAATAGAAGAAAAAGAAAAAAAGAA
1 AAAATAGAAAGAAA-AAAAGAAAAAGAAAAAAAGAA
10561654 AAAA
1 AAAA
10561658 GAATAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
35 12 0.32
36 8 0.22
37 17 0.46
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (35 bp):
AAAATAGAAAGAAAAAAAGAAAAAGAAAAAAAGAA
Found at i:10561656 original size:9 final size:9
Alignment explanation
Indices: 10561575--10561667 Score: 73
Period size: 9 Copynumber: 10.0 Consensus size: 9
10561565 GAAGAAGGGG
10561575 AAGAAAGAAA
1 AAGAAA-AAA
10561585 ATAGAAAGAAA
1 A-AGAAA-AAA
*
10561596 AA-AAGAAA
1 AAGAAAAAA
10561604 AAGAAAGAAA
1 AAGAAA-AAA
10561614 AAGAAAAAA
1 AAGAAAAAA
* *
10561623 TAGAAGAAA
1 AAGAAAAAA
* *
10561632 TAGAAGAAA
1 AAGAAAAAA
10561641 AAG-AAAAA
1 AAGAAAAAA
10561649 AAGAAAAAA
1 AAGAAAAAA
*
10561658 GAATAAAAAA
1 -AAGAAAAAA
10561668 CAGCAGCAGC
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
8 12 0.17
9 30 0.42
10 19 0.27
11 10 0.14
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:10561787 original size:36 final size:36
Alignment explanation
Indices: 10561743--10561845 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
10561733 CCACAACCCG
10561743 CAGCAGGCCACTGCCCAGCCCAACGCCCAGCAGCTC
1 CAGCAGGCCACTGCCCAGCCCAACGCCCAGCAGCTC
* *
10561779 CAGTAGGCCACTGCCTAGCCCAACGCCCAGCAGCTC
1 CAGCAGGCCACTGCCCAGCCCAACGCCCAGCAGCTC
10561815 CAGCAGGCCA--GCATCCAGCCCAACGCCCAGC
1 CAGCAGGCCACTGC--CCAGCCCAACGCCCAGC
10561846 GGCCCAATCT
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
34 2 0.03
36 59 0.97
ACGTcount: A:0.23, C:0.48, G:0.22, T:0.07
Consensus pattern (36 bp):
CAGCAGGCCACTGCCCAGCCCAACGCCCAGCAGCTC
Found at i:10561879 original size:13 final size:13
Alignment explanation
Indices: 10561857--10561902 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
10561847 GCCCAATCTG
10561857 CAAAAA-AAAAAA
1 CAAAAAGAAAAAA
10561869 CAAAAAGAAAAAA
1 CAAAAAGAAAAAA
*
10561882 GAAAAAGAAAAAAA
1 CAAAAAG-AAAAAA
10561896 CAAAAAG
1 CAAAAAG
10561903 GCCCGAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 6 0.20
13 12 0.40
14 12 0.40
ACGTcount: A:0.85, C:0.07, G:0.09, T:0.00
Consensus pattern (13 bp):
CAAAAAGAAAAAA
Found at i:10562366 original size:17 final size:17
Alignment explanation
Indices: 10562346--10562480 Score: 71
Period size: 17 Copynumber: 7.6 Consensus size: 17
10562336 AATTTGCCGT
10562346 TTTTCAAAAATTTCGAG
1 TTTTCAAAAATTTCGAG
* **
10562363 TTTTAAAAAAAATCGAG
1 TTTTCAAAAATTTCGAG
*
10562380 TTTTCAAAAAAATTTTCTCACG
1 TTTTC--AAAAA-TTTC-GA-G
*
10562402 -TTTCACAAATTTTC-ATG
1 TTTTCA-AAAATTTCGA-G
**
10562419 TTTTCAAAAA-TTCTTG
1 TTTTCAAAAATTTCGAG
*
10562435 TGTTTCAAAAATTTTCGCG
1 T-TTTCAAAAA-TTTCGAG
*
10562454 TTTTCAAAAATTTTCGTG
1 TTTTCAAAAA-TTTCGAG
10562472 TTTT-AAAAA
1 TTTTCAAAAA
10562481 AAATTTCATA
Statistics
Matches: 93, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
16 5 0.05
17 37 0.40
18 25 0.27
19 15 0.16
20 5 0.05
21 5 0.05
22 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (17 bp):
TTTTCAAAAATTTCGAG
Found at i:10562429 original size:18 final size:18
Alignment explanation
Indices: 10562402--10562829 Score: 196
Period size: 18 Copynumber: 24.5 Consensus size: 18
10562392 TTTTCTCACG
* *
10562402 TTTCACAAATTTTCATGT
1 TTTCAAAAATTTTCGTGT
10562420 TTTCAAAAATTCTT-GTG-
1 TTTCAAAAATT-TTCGTGT
*
10562437 TTTCAAAAATTTTCGCGT
1 TTTCAAAAATTTTCGTGT
10562455 TTTCAAAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
* * * *
10562473 TTTAAAAAAAATTTCAT-A
1 TTT-CAAAAATTTTCGTGT
* *
10562491 TTTCAAAAATATTCCTGT
1 TTTCAAAAATTTTCGTGT
* ***
10562509 TTT-AAAAA--AT--AAA
1 TTTCAAAAATTTTCGTGT
** * ** * *
10562522 AATAAAAAAGAATCCAT-T
1 TTTCAAAAA-TTTTCGTGT
*
10562540 TTTC-AAAATTCTCGTGT
1 TTTCAAAAATTTTCGTGT
*
10562557 TTTC-AAAA-TTCCAGTG-
1 TTTCAAAAATTTTC-GTGT
*
10562573 TTTCAAAAATTTTCATGT
1 TTTCAAAAATTTTCGTGT
* *
10562591 TTTCAAAAA-TTCCAATGT
1 TTTCAAAAATTTTC-GTGT
* *
10562609 TTT-AAAAATTTCCGTAT
1 TTTCAAAAATTTTCGTGT
* *
10562626 TTTAAAAAATTTCCGTGT
1 TTTCAAAAATTTTCGTGT
* *
10562644 TTTAAAAAATCTTCGTGT
1 TTTCAAAAATTTTCGTGT
* **
10562662 TTTCAAGAATCCTCGTGT
1 TTTCAAAAATTTTCGTGT
** *
10562680 TTTC-TTAA-TTCCG-GT
1 TTTCAAAAATTTTCGTGT
*
10562695 GTTTCAAAAATTTTCATGT
1 -TTTCAAAAATTTTCGTGT
*
10562714 TTTCAAAAATTCTCGTGT
1 TTTCAAAAATTTTCGTGT
*
10562732 TTT-AAAAATTTCCGTGT
1 TTTCAAAAATTTTCGTGT
* * *
10562749 TTTAAAAAATTTTCATATT
1 TTTCAAAAATTTTCGT-GT
* *
10562768 TTTTAAGAATTTTCGTG-
1 TTTCAAAAATTTTCGTGT
* * * *
10562785 TCTCTAAAATTCTCGTGC
1 TTTCAAAAATTTTCGTGT
10562803 TTT-AAAAATTTTTCGTGT
1 TTTCAAAAA-TTTTCGTGT
10562821 TTTCAAAAA
1 TTTCAAAAA
10562830 AATAATTGTT
Statistics
Matches: 309, Mismatches: 73, Indels: 55
0.71 0.17 0.13
Matches are distributed among these distances:
13 1 0.00
14 5 0.02
15 3 0.01
16 16 0.05
17 97 0.31
18 154 0.50
19 33 0.11
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:10562447 original size:35 final size:35
Alignment explanation
Indices: 10562401--10562480 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
10562391 ATTTTCTCAC
* *
10562401 GTTTCACAAATTTTCATGTTTTCAAAAATTCTT-GT
1 GTTTCAAAAATTTTCACGTTTTCAAAAATT-TTCGT
*
10562436 GTTTCAAAAATTTTCGCGTTTTCAAAAATTTTCGT
1 GTTTCAAAAATTTTCACGTTTTCAAAAATTTTCGT
*
10562471 GTTTTAAAAA
1 GTTTCAAAAA
10562481 AAATTTCATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 2 0.05
35 38 0.95
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.46
Consensus pattern (35 bp):
GTTTCAAAAATTTTCACGTTTTCAAAAATTTTCGT
Found at i:10562700 original size:123 final size:122
Alignment explanation
Indices: 10562539--10562760 Score: 365
Period size: 123 Copynumber: 1.8 Consensus size: 122
10562529 AAGAATCCAT
*
10562539 TTTTCAAAATTCTCGTGTTTTCAAAATTCCAGTGTTTCAAAAATTTTCATGTTTTCAAAAATTC-
1 TTTTCAAAATCCTCGTGTTTTCAAAATTCCAGTGTTTCAAAAATTTTCATGTTTTCAAAAATTCT
10562603 CAATGTTTTAAAAATTTCCGTATTTTAAAAAATTTCCGTGTTTTAAAAAATCTTCGTG
66 C-ATGTTTTAAAAATTTCCGTATTTTAAAAAATTTCCGTGTTTTAAAAAATCTTCGTG
** *
10562661 TTTTCAAGAATCCTCGTGTTTTCTTAATTCCGGTGTTTCAAAAATTTTCATGTTTTCAAAAATTC
1 TTTTCAA-AATCCTCGTGTTTTCAAAATTCCAGTGTTTCAAAAATTTTCATGTTTTCAAAAATTC
* *
10562726 TCGTGTTTTAAAAATTTCCGTGTTTTAAAAAATTT
65 TCATGTTTTAAAAATTTCCGTATTTTAAAAAATTT
10562761 TCATATTTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
122 7 0.08
123 84 0.91
124 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (122 bp):
TTTTCAAAATCCTCGTGTTTTCAAAATTCCAGTGTTTCAAAAATTTTCATGTTTTCAAAAATTCT
CATGTTTTAAAAATTTCCGTATTTTAAAAAATTTCCGTGTTTTAAAAAATCTTCGTG
Found at i:10562715 original size:52 final size:53
Alignment explanation
Indices: 10562544--10562829 Score: 201
Period size: 53 Copynumber: 5.4 Consensus size: 53
10562534 TCCATTTTTC
* * * * * * * *
10562544 AAAATTCTCGTGTTTTCAAAATTCC-AGTGTTTCAAAAATTTTCATGTTTTCA
1 AAAATTTTCATGTTTTCAAAAATCCTCGTGTTTTAAAAATTTCCGTGTTTTAA
* * *
10562596 AAAA-TTCCAATGTTTT-AAAAAT-TTCCGTATTTTAAAAAATTTCCGTGTTTTAA
1 AAAATTTTC-ATGTTTTCAAAAATCCT-CGTGTTTT-AAAAATTTCCGTGTTTTAA
* * * *** *
10562649 AAAATCTTCGTGTTTTCAAGAATCCTCGTGTTTTCTTAA-TTCCG-GTGTTTCA
1 AAAATTTTCATGTTTTCAAAAATCCTCGTGTTTTAAAAATTTCCGTGT-TTTAA
*
10562701 AAAATTTTCATGTTTTCAAAAATTCTCGTGTTTTAAAAATTTCCGTGTTTTAA
1 AAAATTTTCATGTTTTCAAAAATCCTCGTGTTTTAAAAATTTCCGTGTTTTAA
* * * ** * *
10562754 AAAATTTTCATATTTTTTAAGAATTTTCGTGTCTCT-AAAA-TTCTCGTGCTTTAA
1 AAAATTTTCAT-GTTTTCAAAAATCCTCGTGT-TTTAAAAATTTC-CGTGTTTTAA
* *
10562808 AAATTTTTCGTGTTTTCAAAAA
1 AAAATTTTCATGTTTTCAAAAA
10562830 AATAATTGTT
Statistics
Matches: 181, Mismatches: 40, Indels: 25
0.74 0.16 0.10
Matches are distributed among these distances:
51 9 0.05
52 56 0.31
53 59 0.33
54 54 0.30
55 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (53 bp):
AAAATTTTCATGTTTTCAAAAATCCTCGTGTTTTAAAAATTTCCGTGTTTTAA
Found at i:10562725 original size:35 final size:35
Alignment explanation
Indices: 10562544--10562759 Score: 135
Period size: 35 Copynumber: 6.2 Consensus size: 35
10562534 TCCATTTTTC
*
10562544 AAAATTCTCGTGTTTTC-AAAA-TTCCA-GTGTTTCA
1 AAAATTCTCGTG-TTTCAAAAATTTCCATGT-TTTAA
* *
10562578 AAAATTTTCATGTTTTCAAAAA-TTCCAATGTTTTAA
1 AAAATTCTCGTG-TTTCAAAAATTTCC-ATGTTTTAA
* * * *
10562614 AAATTTC-CGTATTTTAAAAAATTTCCGTGTTTTAA
1 AAAATTCTCGT-GTTTCAAAAATTTCCATGTTTTAA
* * * *
10562649 AAAA-TCTTCGTGTTTTCAAGAA-TCCTCGTGTTTT-C
1 AAAATTC-TCGTG-TTTCAAAAATTTC-CATGTTTTAA
** * *
10562684 TTAATTC-CGGTGTTTCAAAAATTTTCATGTTTTCA
1 AAAATTCTC-GTGTTTCAAAAATTTCCATGTTTTAA
* *
10562719 AAAATTCTCGTGTTTTAAAAATTTCCGTGTTTTAA
1 AAAATTCTCGTGTTTCAAAAATTTCCATGTTTTAA
10562754 AAAATT
1 AAAATT
10562760 TTCATATTTT
Statistics
Matches: 140, Mismatches: 28, Indels: 27
0.72 0.14 0.14
Matches are distributed among these distances:
34 33 0.24
35 70 0.50
36 35 0.25
37 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.44
Consensus pattern (35 bp):
AAAATTCTCGTGTTTCAAAAATTTCCATGTTTTAA
Found at i:10562800 original size:123 final size:122
Alignment explanation
Indices: 10562542--10562812 Score: 357
Period size: 123 Copynumber: 2.2 Consensus size: 122
10562532 AATCCATTTT
10562542 TCAAAATTCTCGTGTTTTCAAAATTCCAGTGTTTCAAAAATTTTCATGTTTTCAAAAATTCCAAT
1 TCAAAATTCTCGTGTTTTCAAAATTCCAGTGTTTCAAAAATTTTCATGTTTTCAAAAATTCCAAT
* *
10562607 GTTTTAAAAATTTCCGTATTTTAAAAAATTTCCGTGTTTTAAAAAATCTTCGTGTTT
66 GTTTTAAAAATTTCCGTATTTTAAAAAATTTCCATGTTTTAAAAAATCTTCGTGTTC
* ** *
10562664 TCAAGAATCCTCGTGTTTTCTTAATTCCGGTGTTTCAAAAATTTTCATGTTTTCAAAAATTCTC-
1 TCAA-AATTCTCGTGTTTTCAAAATTCCAGTGTTTCAAAAATTTTCATGTTTTCAAAAATTC-CA
* * * * * * *
10562728 GTGTTTTAAAAATTTCCGTGTTTTAAAAAATTTTCATATTTTTTAAGAATTTTCGTG-TC
64 ATGTTTTAAAAATTTCCGTATTTTAAAAAATTTCCAT-GTTTTAAAAAATCTTCGTGTTC
* *
10562787 TCTAAAATTCTCGTGCTTTAAAAATT
1 TC-AAAATTCTCGTGTTTTCAAAATT
10562813 TTTCGTGTTT
Statistics
Matches: 127, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
122 4 0.03
123 105 0.83
124 18 0.14
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (122 bp):
TCAAAATTCTCGTGTTTTCAAAATTCCAGTGTTTCAAAAATTTTCATGTTTTCAAAAATTCCAAT
GTTTTAAAAATTTCCGTATTTTAAAAAATTTCCATGTTTTAAAAAATCTTCGTGTTC
Found at i:10562807 original size:54 final size:53
Alignment explanation
Indices: 10562544--10562829 Score: 178
Period size: 52 Copynumber: 5.4 Consensus size: 53
10562534 TCCATTTTTC
* * * * * *
10562544 AAAATTCTCGTGTTTTC-AAAATTC-CAGTGTT-TCAAAAATTTTCATGTTTTCA
1 AAAATTTTCATGTTTTCAAAAATTCTC-GTGTTCT-AAAAATTTCCGTGCTTTAA
* * * *
10562596 AAAA-TTCCAATGTTTT-AAAAATT-TCCGTATTTTAAAAAATTTCCGTGTTTTAA
1 AAAATTTTC-ATGTTTTCAAAAATTCT-CGTGTTCT-AAAAATTTCCGTGCTTTAA
* * * * * *** *
10562649 AAAATCTTCGTGTTTTCAAGAATCCTCGTGTTTTCTTAA-TTCCGGTG-TTTCA
1 AAAATTTTCATGTTTTCAAAAATTCTCGTGTTCTAAAAATTTCC-GTGCTTTAA
* *
10562701 AAAATTTTCATGTTTTCAAAAATTCTCGTGTTTTAAAAATTTCCGTGTTTTAA
1 AAAATTTTCATGTTTTCAAAAATTCTCGTGTTCTAAAAATTTCCGTGCTTTAA
* * * *
10562754 AAAATTTTCATATTTTTTAAGAATTTTCGTGTCTCT-AAAA-TTCTCGTGCTTTAA
1 AAAATTTTCAT-GTTTTCAAAAATTCTCGTGT-TCTAAAAATTTC-CGTGCTTTAA
* *
10562808 AAATTTTTCGTGTTTTCAAAAA
1 AAAATTTTCATGTTTTCAAAAA
10562830 AATAATTGTT
Statistics
Matches: 183, Mismatches: 37, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
51 2 0.01
52 63 0.34
53 63 0.34
54 52 0.28
55 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (53 bp):
AAAATTTTCATGTTTTCAAAAATTCTCGTGTTCTAAAAATTTCCGTGCTTTAA
Found at i:10573851 original size:11 final size:11
Alignment explanation
Indices: 10573832--10573902 Score: 61
Period size: 12 Copynumber: 5.9 Consensus size: 11
10573822 TATTATGCCT
10573832 AAAAAAAAAAC
1 AAAAAAAAAAC
*
10573843 AAAACAAAAAC
1 AAAAAAAAAAC
*
10573854 AAAAAATAAAAA
1 AAAAAA-AAAAC
*
10573866 AATAAAAAAATAA
1 AA-AAAAAAA-AC
10573879 AAAAGCAAAAAAGC
1 AAAA--AAAAAA-C
10573893 AAAAAAAAAA
1 AAAAAAAAAA
10573903 AGTAAAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
11 15 0.30
12 17 0.34
13 9 0.18
14 9 0.18
ACGTcount: A:0.86, C:0.07, G:0.03, T:0.04
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:10573872 original size:37 final size:36
Alignment explanation
Indices: 10573831--10573911 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 36
10573821 ATATTATGCC
10573831 TAAAAAAA-AAACAAAAC-AAAAACAAAAAATAAAAAAA
1 TAAAAAAATAAA-AAAACAAAAAAC-AAAAA-AAAAAAA
* *
10573868 TAAAAAAATAAAAAAGCAAAAAAGCAAAAAAAAAAAG
1 TAAAAAAATAAAAAAACAAAAAA-CAAAAAAAAAAAA
10573905 TAAAAAA
1 TAAAAAA
10573912 GAAGAAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 25 0.64
38 13 0.33
39 1 0.03
ACGTcount: A:0.84, C:0.06, G:0.04, T:0.06
Consensus pattern (36 bp):
TAAAAAAATAAAAAAACAAAAAACAAAAAAAAAAAA
Found at i:10573909 original size:7 final size:7
Alignment explanation
Indices: 10573870--10573924 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
10573860 TAAAAAAATA
*
10573870 AAAAAAT
1 AAAAAAG
10573877 AAAAAAG
1 AAAAAAG
10573884 CAAAAAAG
1 -AAAAAAG
*
10573892 CAAAAA-
1 AAAAAAG
10573898 AAAAAAG
1 AAAAAAG
10573905 TAAAAAAG
1 -AAAAAAG
*
10573913 -AAGAAG
1 AAAAAAG
10573919 AAAAAA
1 AAAAAA
10573925 TCAAGATGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
6 10 0.26
7 15 0.38
8 14 0.36
ACGTcount: A:0.82, C:0.04, G:0.11, T:0.04
Consensus pattern (7 bp):
AAAAAAG
Found at i:10573909 original size:8 final size:8
Alignment explanation
Indices: 10573854--10573912 Score: 54
Period size: 8 Copynumber: 7.9 Consensus size: 8
10573844 AAACAAAAAC
10573854 AAAAAA-T
1 AAAAAAGT
*
10573861 AAAAAAAT
1 AAAAAAGT
*
10573869 AAAAAAAT
1 AAAAAAGT
*
10573877 AAAAAAGC
1 AAAAAAGT
10573885 AAAAAAG-
1 AAAAAAGT
*
10573892 CAAAAA--
1 AAAAAAGT
10573898 AAAAAAGT
1 AAAAAAGT
10573906 AAAAAAG
1 AAAAAAG
10573913 AAGAAGAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
6 5 0.11
7 11 0.24
8 29 0.64
ACGTcount: A:0.83, C:0.03, G:0.07, T:0.07
Consensus pattern (8 bp):
AAAAAAGT
Found at i:10573923 original size:1 final size:1
Alignment explanation
Indices: 10573832--10573903 Score: 54
Period size: 1 Copynumber: 72.0 Consensus size: 1
10573822 TATTATGCCT
* * * * * * ** **
10573832 AAAAAAAAAACAAAACAAAAACAAAAAATAAAAAAATAAAAAAATAAAAAAGCAAAAAAGCAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10573897 AAAAAAA
1 AAAAAAA
10573904 GTAAAAAAGA
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.86, C:0.07, G:0.03, T:0.04
Consensus pattern (1 bp):
A
Found at i:10573923 original size:14 final size:12
Alignment explanation
Indices: 10573832--10573924 Score: 64
Period size: 13 Copynumber: 7.4 Consensus size: 12
10573822 TATTATGCCT
*
10573832 AAAAAAAAAACA
1 AAAAAAAAAAGA
10573844 AAACAAAAACAA-A
1 AAA-AAAAA-AAGA
*
10573857 AAATAAAAAAATA
1 AAA-AAAAAAAGA
*
10573870 AAAAAATAAA-A
1 AAAAAAAAAAGA
**
10573881 AAGCAAAAAAGCA
1 AAAAAAAAAAG-A
10573894 AAAAAAAAAAGTA
1 AAAAAAAAAAG-A
*
10573907 AAAAAGAAGAAGA
1 AAAAA-AAAAAGA
10573920 AAAAA
1 AAAAA
10573925 TCAAGATGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
11 8 0.12
12 11 0.17
13 40 0.61
14 7 0.11
ACGTcount: A:0.84, C:0.05, G:0.06, T:0.04
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:10573924 original size:21 final size:21
Alignment explanation
Indices: 10573871--10573912 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
10573861 AAAAAAATAA
10573871 AAAAATAAAAAAGCAAAAAAGC
1 AAAAA-AAAAAAGCAAAAAAGC
*
10573893 AAAAAAAAAAAGTAAAAAAG
1 AAAAAAAAAAAGCAAAAAAG
10573913 AAGAAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.81, C:0.05, G:0.10, T:0.05
Consensus pattern (21 bp):
AAAAAAAAAAAGCAAAAAAGC
Found at i:10574910 original size:77 final size:76
Alignment explanation
Indices: 10574778--10575341 Score: 648
Period size: 77 Copynumber: 7.4 Consensus size: 76
10574768 TCAAGAATTA
* *
10574778 TATTCTTTTAAATTTCTATTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
1 TATT-TTTT-AATTTCTTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
* *
10574842 AGTCACG-TCAAGG
64 GGTCACGCT-GAGG
* *
10574855 TATTTTTTTAA-TTCTTTCTTTTCAAAAAAATCAACTCATATTGCGAGAGTTGAGTTGAGCCTCG
1 TA-TTTTTTAATTTCTTT-TTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
10574919 GGTCACGCTGAGG
64 GGTCACGCTGAGG
* * *
10574932 TATTTTTTAATTTTCGTTTTTTCAAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCAG
1 TATTTTTTAA-TTTCTTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGG
10574996 GTCACGCTGAGG
65 GTCACGCTGAGG
*
10575008 TTTTTTTTTTTTAATTTCTATTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCC
1 ----TATTTTTTAATTTCT-TTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCC
*
10575072 TCGGGTCACGCTGACG
61 TCGGGTCACGCTGAGG
** * * *
10575088 TA-TTTTCGATTTCTGTTTTTC--AAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGA
1 TATTTTTTAATTTCTTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
10575150 TCACGCTGAGG
66 TCACGCTGAGG
* * * * *
10575161 TA-TTTTCAATTTCTATTTTTCAAGAAAAAATGAACTCATAATGCGAGAGGTGGGTTGAGCATCG
1 TATTTTTTAATTTCTTTTTTTC-A-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
*
10575225 GGTTACGCTGAGG
64 GGTCACGCTGAGG
* * * * *
10575238 TA-TTTTTAATTTCCGTTTTTTCAAAAAAATCAAGTCATAGTGCGAGAAGG-GGGTTGAGCCTTG
1 TATTTTTTAATTT-CTTTTTTTCAAAAAAATCAACTCATAATGCGAG-AGGTGAGTTGAGCCTCG
10575301 GGTCACGCTGAGG
64 GGTCACGCTGAGG
* *
10575314 TA-TTTTCAATTTCTGTTTTTCAAAAAAA
1 TATTTTTTAATTTCTTTTTTTCAAAAAAA
10575342 AAAAAAGAGA
Statistics
Matches: 430, Mismatches: 39, Indels: 38
0.85 0.08 0.07
Matches are distributed among these distances:
73 68 0.16
74 6 0.01
75 29 0.07
76 100 0.23
77 143 0.33
78 15 0.03
79 23 0.05
80 46 0.11
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.36
Consensus pattern (76 bp):
TATTTTTTAATTTCTTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
TCACGCTGAGG
Found at i:10575343 original size:153 final size:150
Alignment explanation
Indices: 10574796--10575341 Score: 656
Period size: 153 Copynumber: 3.6 Consensus size: 150
10574786 TAAATTTCTA
* * *
10574796 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACG-TCAAGGTATTT
1 TTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCT-GAGGTA--T
* * *
10574860 TTTTAA-TTCTTTCTTTTCAAAAAAATCAACTCATATTGCGAGAGTTGAGTTGAGCCTCGGGTCA
63 TTTCAATTTCTTT-TTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
10574924 CGCTGAGGTATTTTTTAATTTTCGT
127 CGCTGAGGTA-TTTTTAATTTCCGT
* *
10574949 TTTTTCAAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTTTTT
1 TTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG-----
* *
10575013 TTTTTTTAATTTCTATTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
60 TATTTTCAATTTCT-TTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG
* ** *
10575077 TCACGCTGACGTATTTTCGATTTCTG-
124 TCACGCTGAGGTATTTTTAATTTCCGT
* *
10575103 TTTTTC-AAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGATCACGCTGAGGTATTTT
1 TTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
* * * * *
10575167 CAATTTCTATTTTTCAAGAAAAAATGAACTCATAATGCGAGAGGTGGGTTGAGCATCGGGTTACG
66 CAATTTCTTTTTTTC-A-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACG
10575232 CTGAGGTATTTTTAATTTCCGT
129 CTGAGGTATTTTTAATTTCCGT
* * * *
10575254 TTTTTCAAAAAAATCAAGTCATAGTGCGAGAAGG-GGGTTGAGCCTTGGGTCACGCTGAGGTATT
1 TTTTTC-AAAAAATCAACTCATAATGCGAG-AGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
10575318 TTCAATTTCTGTTTTTCAAAAAAA
64 TTCAATTTCTTTTTTTCAAAAAAA
10575342 AAAAAAGAGA
Statistics
Matches: 343, Mismatches: 33, Indels: 36
0.83 0.08 0.09
Matches are distributed among these distances:
147 6 0.02
148 12 0.03
150 60 0.17
151 12 0.03
152 19 0.06
153 126 0.37
154 28 0.08
155 9 0.03
156 59 0.17
157 9 0.03
158 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (150 bp):
TTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
CAATTTCTTTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCT
GAGGTATTTTTAATTTCCGT
Found at i:10576442 original size:21 final size:21
Alignment explanation
Indices: 10576412--10576463 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
10576402 AGGGGAGAAA
10576412 GAAA-GAGAGAAAGGAAAA-AG
1 GAAAGGAGAGAAA-GAAAAGAG
10576432 GAAAGGAGAGAAAGAAAAGAG
1 GAAAGGAGAGAAAGAAAAGAG
* *
10576453 AAAAGAAGAGA
1 GAAAGGAGAGA
10576464 GGAGATACCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (21 bp):
GAAAGGAGAGAAAGAAAAGAG
Found at i:10576443 original size:33 final size:33
Alignment explanation
Indices: 10576393--10576455 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
10576383 GTCAAAATAG
*
10576393 AAAAGGAAGAGGGGAGAAAGAAAGAGAGAAAGGA
1 AAAAGGAAGAGGAGAGAAAGAAA-AGAGAAAGGA
10576427 AAAAGGAA-AGGAGAGAAAGAAAAGAGAAA
1 AAAAGGAAGAGGAGAGAAAGAAAAGAGAAA
10576456 AGAAGAGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 7 0.25
33 13 0.46
34 8 0.29
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (33 bp):
AAAAGGAAGAGGAGAGAAAGAAAAGAGAAAGGA
Found at i:10576584 original size:19 final size:19
Alignment explanation
Indices: 10576560--10576639 Score: 85
Period size: 18 Copynumber: 4.2 Consensus size: 19
10576550 GAAGGGGAAG
10576560 AAAGAAAATAGAAAGAAAA
1 AAAGAAAATAGAAAGAAAA
10576579 AAAGAAAA-AGAAAGAAAA
1 AAAGAAAATAGAAAGAAAA
10576597 AGAA-AAAATAG-AAGAAAA
1 A-AAGAAAATAGAAAGAAAA
* *
10576615 AGAAAAAAATAATAAAGAATAA
1 A-AAGAAAAT-AGAAAGAA-AA
10576637 AAA
1 AAA
10576640 ACAGCAGCAG
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
18 26 0.48
19 17 0.31
20 1 0.02
21 7 0.13
22 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (19 bp):
AAAGAAAATAGAAAGAAAA
Found at i:10576588 original size:6 final size:6
Alignment explanation
Indices: 10576560--10576621 Score: 60
Period size: 6 Copynumber: 10.5 Consensus size: 6
10576550 GAAGGGGAAG
10576560 AAAGAA AATAGAA AGAA-AA AAAGAA AAAG-- AAAGAA AAAGAA AAA-ATA
1 AAAGAA AA-AGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGA-A
*
10576607 GAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAA
10576622 AATAATAAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
4 4 0.09
5 3 0.06
6 32 0.68
7 7 0.15
8 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:10576598 original size:24 final size:24
Alignment explanation
Indices: 10576571--10576621 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
10576561 AAGAAAATAG
10576571 AAAGAAAAAA-AGAAAAAGAAAGAA
1 AAAGAAAAAATAGAAAAA-AAAGAA
*
10576595 AAAGAAAAAATAGAAGAAAAAGAA
1 AAAGAAAAAATAGAAAAAAAAGAA
10576619 AAA
1 AAA
10576622 AATAATAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (24 bp):
AAAGAAAAAATAGAAAAAAAAGAA
Found at i:10576611 original size:28 final size:29
Alignment explanation
Indices: 10576557--10576639 Score: 100
Period size: 28 Copynumber: 2.9 Consensus size: 29
10576547 GAAGAAGGGG
10576557 AAGAAAGAAAATAGAAAGAAAAAAAGAAA
1 AAGAAAGAAAATAGAAAGAAAAAAAGAAA
*
10576586 AAGAAAGAAAA-AGAAA-AAATAGAAGAAA
1 AAGAAAGAAAATAGAAAGAAA-AAAAGAAA
*
10576614 AAGAAA-AAAATAATAAAGAATAAAAA
1 AAGAAAGAAAAT-AGAAAGAA-AAAAA
10576640 ACAGCAGCAG
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 7 0.15
28 18 0.39
29 15 0.33
30 5 0.11
31 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (29 bp):
AAGAAAGAAAATAGAAAGAAAAAAAGAAA
Done.