Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 37 of 190
Found at i:6398704 original size:20 final size:20
Alignment explanation
Indices: 6398670--6398715 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
6398660 TCTTTTTTTT
*
6398670 TCTTTTTTTCTTTCCTTTCC
1 TCTTTTTTTCTTTCCCTTCC
6398690 TCTTTCTTTTC-TTCCCTTCC
1 TCTTT-TTTTCTTTCCCTTCC
6398710 -CTTTTT
1 TCTTTTT
6398716 GGGCCAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.08
19 4 0.17
20 13 0.54
21 5 0.21
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TCTTTTTTTCTTTCCCTTCC
Found at i:6398752 original size:22 final size:23
Alignment explanation
Indices: 6398726--6398776 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
6398716 GGGCCAATAC
6398726 TTTCTTTTCCCTTTCTCCT-TTT
1 TTTCTTTTCCCTTTCTCCTATTT
* * *
6398748 TTTCTTTTTCTTTTCTCTTATTT
1 TTTCTTTTCCCTTTCTCCTATTT
6398771 TTTCTT
1 TTTCTT
6398777 ATTTTTCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (23 bp):
TTTCTTTTCCCTTTCTCCTATTT
Found at i:6398771 original size:21 final size:21
Alignment explanation
Indices: 6398726--6398794 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 21
6398716 GGGCCAATAC
* * *
6398726 TTTCTTTTCCCTTTCTCCTTTT
1 TTTCTTTTTCTTTTCT-CTTAT
6398748 TTTCTTTTTCTTTTCTCTTAT
1 TTTCTTTTTCTTTTCTCTTAT
* *
6398769 TTT-TTCTTATTTT-TCTTAT
1 TTTCTTTTTCTTTTCTCTTAT
*
6398788 TTCCTTT
1 TTTCTTT
6398795 CCTCTTCATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 8 0.21
20 10 0.26
21 7 0.18
22 14 0.36
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTCTTTTTCTTTTCTCTTAT
Found at i:6398775 original size:34 final size:35
Alignment explanation
Indices: 6398746--6398809 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 35
6398736 CTTTCTCCTT
*
6398746 TTTTTCTT-TTT-CTTTTCTCTT-ATTTTTTCTTA
1 TTTTTCTTATTTCCTTTCCTCTTCATTTTTTCTTA
6398778 TTTTTCTTATTTCCTTTCCTCTTCATTTTTTC
1 TTTTTCTTATTTCCTTTCCTCTTCATTTTTTC
6398810 CCGTCCACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 8 0.29
33 3 0.11
34 9 0.32
35 8 0.29
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.73
Consensus pattern (35 bp):
TTTTTCTTATTTCCTTTCCTCTTCATTTTTTCTTA
Found at i:6400468 original size:144 final size:142
Alignment explanation
Indices: 6400188--6400472 Score: 500
Period size: 144 Copynumber: 2.0 Consensus size: 142
6400178 ATGTAAAATG
* *
6400188 AAATGCAATTTAAGAGTTTGATTCTTAAATATAATGAGACCACCCCGACTCTCCAACATCTAGGC
1 AAATACAATTTAAGAGTTGGATTCTTAAATATAATGAGACCACCCCGACTCTCCAACATCTAGGC
*
6400253 AGAACTTAGGTGCGACTGTTTATATTTAAGATCCCAATTTTATTATACTTTTTTTTATTTATTAA
66 AGAACTTAGGTGCGACTGTTTATATTTAAAATCCCAATTTTATTATAC--TTTTTTATTTATTAA
6400318 TCTTATTATTAATA
129 TCTTATTATTAATA
6400332 AAATACAATTTAAGAGTTGGATTCTTAAATATAATGAGACCACCCCGACTCTCCAACATCTAGGC
1 AAATACAATTTAAGAGTTGGATTCTTAAATATAATGAGACCACCCCGACTCTCCAACATCTAGGC
* *
6400397 AGAGCTTAGGTGCGACTGTTTATATTTAAAATTCCAATTTTATTATAC-TTTTTATTTATTAATC
66 AGAACTTAGGTGCGACTGTTTATATTTAAAATCCCAATTTTATTATACTTTTTTATTTATTAATC
6400461 TTATTATTAATA
131 TTATTATTAATA
6400473 TGAATTATGA
Statistics
Matches: 136, Mismatches: 5, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
141 28 0.21
144 108 0.79
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (142 bp):
AAATACAATTTAAGAGTTGGATTCTTAAATATAATGAGACCACCCCGACTCTCCAACATCTAGGC
AGAACTTAGGTGCGACTGTTTATATTTAAAATCCCAATTTTATTATACTTTTTTATTTATTAATC
TTATTATTAATA
Found at i:6402165 original size:5 final size:5
Alignment explanation
Indices: 6402157--6402207 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
6402147 GTTTGTTTAC
* *
6402157 TTGTT TTGTT TT-TT TCTGTT TTGTT TTTTT TCTTTT TTGTT TTGTT TTGTT
1 TTGTT TTGTT TTGTT T-TGTT TTGTT TTGTT T-TGTT TTGTT TTGTT TTGTT
6402208 AAATATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
4 3 0.07
5 30 0.73
6 8 0.20
ACGTcount: A:0.00, C:0.04, G:0.14, T:0.82
Consensus pattern (5 bp):
TTGTT
Found at i:6402186 original size:16 final size:16
Alignment explanation
Indices: 6402143--6402204 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
6402133 CTTTCTTTTT
* *
6402143 TTTTGTTTGTTTACTTG
1 TTTTGTTTTTTTTC-TG
6402160 TTTTG-TTTTTTTCTG
1 TTTTGTTTTTTTTCTG
*
6402175 TTTTGTTTTTTTTCTT
1 TTTTGTTTTTTTTCTG
6402191 TTTTGTTTTGTTTT
1 TTTTGTTTT-TTTT
6402205 GTTAAATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.17
16 24 0.60
17 9 0.22
ACGTcount: A:0.02, C:0.05, G:0.13, T:0.81
Consensus pattern (16 bp):
TTTTGTTTTTTTTCTG
Found at i:6402448 original size:48 final size:49
Alignment explanation
Indices: 6402375--6402995 Score: 764
Period size: 49 Copynumber: 12.7 Consensus size: 49
6402365 ACAGAAAAGG
* * *
6402375 GCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATTTC-TTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCATTCTTGAAAAA
* *
6402423 GCTCCTCTCAACAGAGGTTCCACAACTTTAAAA-TTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCATTCTTGAAAAA
* * * *
6402471 GCTCCTCTCAATAGAGGCTCTACAACTTTAAAATTCTCATT-TCGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATT-TCATTCTTGAAAAA
* * *
6402520 GCTACTCTCAACAGGGGCTCCACAACTTTAAAATTTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCATTCTTGAAAAA
* * *
6402569 GCTCATCTCAACAGAGGCTCTACAACTTTAAAATTCTCATT-TCAGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATT-TCATTCT-TGAAAAA
*
6402619 -CTCCTCTCAACAGAGGCTCCACAACTTTAAAAATCTCA-TC-TGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTT-AAAATTTCATTCTTGAAAAA
*
6402666 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAAATTTCA-TCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTT-AAAATTTCATTCTTGAAAAA
*
6402715 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAA-TTCTTTCTTGAAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCATTCTTGAAAAA
* *
6402763 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCA-TCTTGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATT-TCATTCTTGAAAAA
*
6402812 GCTCCCCTGCTCTCAGCAGAGGCTCCACAACTTTAAAATTTC-TTCTTGAAAAA
1 GCT---C--CTCTCAACAGAGGCTCCACAACTTTAAAATTTCATTCTTGAAAAA
* * *
6402865 GCTCCTCTCAACAGAAGCTTCACAACTTTAAAATTTTCA-TCTTGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAA-TTTCATTCTTGAAAAA
* * * *
6402914 GCCCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCATT-TCGGAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATT-TCATTCTTGAAAAA
* *
6402963 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
1 GCTCCTCTCAACAGAGGCTCCACAACTTTAAAA
6402996 ATCTCATTTG
Statistics
Matches: 501, Mismatches: 49, Indels: 45
0.84 0.08 0.08
Matches are distributed among these distances:
47 12 0.02
48 187 0.37
49 235 0.47
50 23 0.05
52 1 0.00
53 14 0.03
54 29 0.06
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (49 bp):
GCTCCTCTCAACAGAGGCTCCACAACTTTAAAATTTCATTCTTGAAAAA
Found at i:6402545 original size:97 final size:97
Alignment explanation
Indices: 6402375--6403005 Score: 839
Period size: 97 Copynumber: 6.4 Consensus size: 97
6402365 ACAGAAAAGG
* * * * *
6402375 GCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATT-TCTTCTTGAAAAAGCTCCTCTCAACAGAG
1 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCAT-TTGGAAAAGCTCCTCTCAACAGAG
*
6402439 GTTCCACAACTTTAAAATTCT-TTCTTGAAAAA
65 GCTCCACAACTTTAAAATTCTCTTCTTGAAAAA
* * *
6402471 GCTCCTCTCAATAGAGGCTCTACAACTTTAAAATTCTCATTTCGGAAAAGCTACTCTCAACAGGG
1 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCATTT-GGAAAAGCTCCTCTCAACAGAG
6402536 GCTCCACAACTTTAAAATT-TCTTTCTTGAAAAA
65 GCTCCACAACTTTAAAATTCTC-TTCTTGAAAAA
* * *
6402569 GCTCATCTCAACAGAGGCTCTACAACTTTAAAATTCTCATTTCAGAAAAACTCCTCTCAACAGAG
1 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCATTT-GGAAAAGCTCCTCTCAACAGAG
* *
6402634 GCTCCACAACTTTAAAAATCTCATC-TGAAAAA
65 GCTCCACAACTTTAAAATTCTCTTCTTGAAAAA
*
6402666 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAAATT-TCATCTTGAAAAAGCTCCTCTCAACAGA
1 GCTCCTCTCAACAGAGGCTCTACAACTTT-AAAATTCTCAT-TTGGAAAAGCTCCTCTCAACAGA
6402730 GGCTCCACAACTTTAAAATTCT-TTCTTGAAAAA
64 GGCTCCACAACTTTAAAATTCTCTTCTTGAAAAA
*
6402763 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCATCTTGGAAAAGCTCCCCTGCTCTCAG
1 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCAT-TTGGAAAAGCT---C--CTCTCAA
6402828 CAGAGGCTCCACAACTTTAAAATT-TCTTCTTGAAAAA
60 CAGAGGCTCCACAACTTTAAAATTCTCTTCTTGAAAAA
* * *
6402865 GCTCCTCTCAACAGAAGCT-TCACAACTTTAAAATTTTCATCTTGGAAAAGCCCCTCTCAACAGA
1 GCTCCTCTCAACAGAGGCTCT-ACAACTTTAAAATTCTCAT-TTGGAAAAGCTCCTCTCAACAGA
* * *
6402929 GGCTCTACAACTTTAAAATTCTCATT-TCGGAAAA
64 GGCTCCACAACTTTAAAATTCTC-TTCTTGAAAAA
* * *
6402963 GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCATTTG
1 GCTCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCATTTG
6403006 TTTTCAAATT
Statistics
Matches: 479, Mismatches: 37, Indels: 37
0.87 0.07 0.07
Matches are distributed among these distances:
96 42 0.09
97 201 0.42
98 140 0.29
99 5 0.01
100 1 0.00
101 2 0.00
102 88 0.18
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (97 bp):
GCTCCTCTCAACAGAGGCTCTACAACTTTAAAATTCTCATTTGGAAAAGCTCCTCTCAACAGAGG
CTCCACAACTTTAAAATTCTCTTCTTGAAAAA
Found at i:6417589 original size:61 final size:60
Alignment explanation
Indices: 6417507--6417650 Score: 157
Period size: 61 Copynumber: 2.4 Consensus size: 60
6417497 CATTTTTTAG
* * * *
6417507 GAAAAGTTGAAAATTTAAATTTTCCTGAAATATAAAAATTTCAAAAAA-A-CATTTCTTAAAA
1 GAAAAGTTAAAAATATAAATTTTCCTGAAAAATAAAAATTACAAAAAATATC-TTT-TT-AAA
* * * *
6417568 GAAAAGTTAAAAATATCAATTTTTCTTAAAAATAAAAATTACAAAAAATATCTTTTTAAG
1 GAAAAGTTAAAAATATAAATTTTCCTGAAAAATAAAAATTACAAAAAATATCTTTTTAAA
* *
6417628 GAAAAATTAAAAATATTAATTTT
1 GAAAAGTTAAAAATATAAATTTT
6417651 TCTTGAAGAT
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
60 23 0.32
61 43 0.61
62 4 0.06
63 1 0.01
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (60 bp):
GAAAAGTTAAAAATATAAATTTTCCTGAAAAATAAAAATTACAAAAAATATCTTTTTAAA
Found at i:6417643 original size:60 final size:59
Alignment explanation
Indices: 6417419--6417904 Score: 301
Period size: 60 Copynumber: 8.2 Consensus size: 59
6417409 TTTTTGAATG
* * * * *
6417419 AAATAAAAA-TTCAAAAAAGTATTTTCTCA-GAAAAGATT-GAAATATCAAATTTTC-AAA
1 AAATAAAAATTTCAAAAAA-TATTTTTTAAGGAAAA-ATTAAAAATATCAATTTTTCTTAA
* * * * * * * * *
6417476 AAAGTAAAAAATTTTAGAAAACATTTTTT-AGGAAAAGTTGAAAATTTAAATTTTCCTGAA
1 AAA-T-AAAAATTTCAAAAAATATTTTTTAAGGAAAAATTAAAAATATCAATTTTTCTTAA
* * * * *
6417536 ATATAAAAATTTCAAAAAAACATTTCTTAAAAGAAAAGTTAAAAATATCAATTTTTCTTAA
1 AAATAAAAATTTC-AAAAAATATTT-TTTAAGGAAAAATTAAAAATATCAATTTTTCTTAA
* * *
6417597 AAATAAAAATTACAAAAAATATCTTTTTAAGGAAAAATTAAAAATATTAATTTTTCTTGA
1 AAATAAAAATTTCAAAAAATAT-TTTTTAAGGAAAAATTAAAAATATCAATTTTTCTTAA
* * * * * * * * * * *
6417657 AGATAAAATTTTTAAATAATGTTGTTTTGAGGAAATATTGAAAATATTAATTTTCCTTAG
1 AAATAAAAATTTCAAAAAATATT-TTTTAAGGAAAAATTAAAAATATCAATTTTTCTTAA
* * * ** * * *
6417717 AAATGAATATTTCAAAAGA-ATGATTTAAAGAAAAATT-GAAGTATCAATTTTTCTTAA
1 AAATAAAAATTTCAAAAAATATTTTTTAAGGAAAAATTAAAAATATCAATTTTTCTTAA
* ** * * * *
6417774 AATTAAAAATTTTTAAAAATA-TTTTTCAGGAAAAATTGAAAGTATTAA-TTTTCTTTACA
1 AAATAAAAATTTCAAAAAATATTTTTTAAGGAAAAATTAAAAATATCAATTTTTC-TTA-A
* * * *
6417833 AATATAAAAA-TTAAAAAAAGTA-TTTTTAAAGAAAAGTTAAAAGTATCAATTTTTCTTAA
1 AA-ATAAAAATTTCAAAAAA-TATTTTTTAAGGAAAAATTAAAAATATCAATTTTTCTTAA
*
6417892 ATAAAAAAAATTT
1 A-AATAAAAATTT
6417905 AAGAAAAAGT
Statistics
Matches: 329, Mismatches: 80, Indels: 37
0.74 0.18 0.08
Matches are distributed among these distances:
57 48 0.15
58 35 0.11
59 58 0.18
60 145 0.44
61 43 0.13
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.36
Consensus pattern (59 bp):
AAATAAAAATTTCAAAAAATATTTTTTAAGGAAAAATTAAAAATATCAATTTTTCTTAA
Found at i:6417787 original size:118 final size:115
Alignment explanation
Indices: 6417568--6417897 Score: 298
Period size: 115 Copynumber: 2.8 Consensus size: 115
6417558 TTTCTTAAAA
* * * * * *
6417568 GAAAAGTTAAAAATATCAATTTTTCTTA-AAA-ATAAAAATTACAAAAAA-TATCTTTTTAAGGA
1 GAAAAATTGAAAATATTAATTTTCCTTACAAATAGAAAAATTA-AAAAAAGTA---TTTTAAAGA
* * * * *
6417630 AAAATTAAAAATATTAATTTTTCTTGAAGATAAAATTTTTAAATAATGTTGTTTTGAG
62 AAAATTAAAAGTATCAATTTTTCTT-AAAATAAAATTTTTAAA-AAT-AT-TTTTCAG
* * * * *
6417688 GAAATATTGAAAATATTAATTTTCCTTAGAAAT-GAATATTTCAAAAGAA-TGA-TTTAAAGAAA
1 GAAAAATTGAAAATATTAATTTTCCTTACAAATAGAAAAATT-AAAAAAAGT-ATTTTAAAGAAA
*
6417750 AATT-GAAGTATCAATTTTTCTTAAAATTAAAAATTTTTAAAAATATTTTTCAG
64 AATTAAAAGTATCAATTTTTCTTAAAA-T-AAAATTTTTAAAAATATTTTTCAG
* * *
6417803 GAAAAATTGAAAGTATTAATTTTCTTTACAAATATAAAAATTAAAAAAAGTATTTTTAAAGAAAA
1 GAAAAATTGAAAATATTAATTTTCCTTACAAATAGAAAAATTAAAAAAAGTA-TTTTAAAGAAAA
*
6417868 GTTAAAAGTATCAATTTTTCTT-AAATAAAA
65 ATTAAAAGTATCAATTTTTCTTAAAATAAAA
6417898 AAAATTTAAG
Statistics
Matches: 173, Mismatches: 26, Indels: 27
0.77 0.12 0.12
Matches are distributed among these distances:
115 46 0.27
116 11 0.06
117 35 0.20
118 42 0.24
120 23 0.13
121 14 0.08
122 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (115 bp):
GAAAAATTGAAAATATTAATTTTCCTTACAAATAGAAAAATTAAAAAAAGTATTTTAAAGAAAAA
TTAAAAGTATCAATTTTTCTTAAAATAAAATTTTTAAAAATATTTTTCAG
Found at i:6418104 original size:48 final size:48
Alignment explanation
Indices: 6417968--6418105 Score: 129
Period size: 48 Copynumber: 2.9 Consensus size: 48
6417958 ATATATTTTA
* * ** *
6417968 AAAAATATTTTAAGGAAAAATTGAAAGTATCAATTTTCCTTAACTAAAG
1 AAAAAGATTTTAAGG-AAAATTAAAAGTATCAATTTTTTTTAAATAAAG
* *
6418017 AAAAAATATTTTAAGGAAAAGTTAAAA-TATTAA-TTTTTTTAAATAAAG
1 -AAAAAGATTTTAAGGAAAA-TTAAAAGTATCAATTTTTTTTAAATAAAG
** *
6418065 -AAGGGGTTTTAAGGAGAAATTAAAAGTATCAATTTTTTTTA
1 AAAAAGATTTTAAGGA-AAATTAAAAGTATCAATTTTTTTTA
6418106 GAAAATAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
46 17 0.23
47 8 0.11
48 20 0.27
49 9 0.12
50 20 0.27
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (48 bp):
AAAAAGATTTTAAGGAAAATTAAAAGTATCAATTTTTTTTAAATAAAG
Found at i:6418165 original size:171 final size:171
Alignment explanation
Indices: 6417846--6418186 Score: 428
Period size: 171 Copynumber: 2.0 Consensus size: 171
6417836 ATAAAAATTA
6417846 AAAAAAGTATTTTTAAAGAAAAGTTAAAAGTATCAATTTTTCTTAAATAAAAAAAATTTAAGAAA
1 AAAAAAGTATTTTTAAAGAAAAGTTAAAAGTATCAATTTTTCTTAAATAAAAAAAATTTAAGAAA
* * *
6417911 AAGTTGAAAGTACTAATTTTTTTTAGAAAACAACAATTTTTTCAAAAATATATTTTAAAAAATAT
66 AAGTTAAAAGTACTAATTTTTTTTAGAAAACAACAATTTTTTCAAAAATATATTTCAAAAAACAT
*
6417976 TTTAAGGAAAAATTGAAAGTATCAATTTTCCTTAACTAAAG
131 TTTAAGGAAAAATTGAAAGTATCAATTTTCCTTAAATAAAG
* * ***
6418017 AAAAAA-TA-TTTTAAGGAAAAGTTAAAA-TATTAATTTTT-TTAAATAAAGAAGGGGTTTTAAG
1 AAAAAAGTATTTTTAAAGAAAAGTTAAAAGTATCAATTTTTCTTAAATAAA-AA--AAATTTAA-
* * *
6418078 GAGAAA-TTAAAAGTA-TCAATTTTTTTTAGAAAATAA-AA-TTTTTCAAAACTATATTTCAAAG
62 GAAAAAGTTAAAAGTACT-AATTTTTTTTAGAAAACAACAATTTTTTCAAAAATATATTTCAAA-
* *
6418139 GAAACATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCTTTAAATAAA
125 -AAACA-TTTTAAGGAAAAATTGAAAGTATCAATTTTCCTTAAATAAA
6418187 AATCTTCTCA
Statistics
Matches: 148, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
167 9 0.06
168 32 0.22
169 21 0.14
170 37 0.25
171 49 0.33
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (171 bp):
AAAAAAGTATTTTTAAAGAAAAGTTAAAAGTATCAATTTTTCTTAAATAAAAAAAATTTAAGAAA
AAGTTAAAAGTACTAATTTTTTTTAGAAAACAACAATTTTTTCAAAAATATATTTCAAAAAACAT
TTTAAGGAAAAATTGAAAGTATCAATTTTCCTTAAATAAAG
Found at i:6430418 original size:26 final size:26
Alignment explanation
Indices: 6430324--6430430 Score: 108
Period size: 26 Copynumber: 3.9 Consensus size: 26
6430314 TTATGAAATA
*
6430324 TCAATTTTTCTTAAAAATAAAAATTT
1 TCAATTTTTCTTAGAAATAAAAATTT
* *
6430350 TAAAAATTATTTTTTGAGAAAAATTAAAAA-TT
1 T--CAATT-TTTCTT-AG--AAA-TAAAAATTT
*
6430382 TCAATTTTTCTTAGAAATTAAAATTT
1 TCAATTTTTCTTAGAAATAAAAATTT
6430408 TCAATTTTTCTTAGAAATAAAAA
1 TCAATTTTTCTTAGAAATAAAAA
6430431 ATTAAAAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
25 5 0.08
26 28 0.42
28 6 0.09
29 10 0.15
30 5 0.08
32 6 0.09
33 6 0.09
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (26 bp):
TCAATTTTTCTTAGAAATAAAAATTT
Found at i:6430490 original size:26 final size:26
Alignment explanation
Indices: 6430319--6430491 Score: 73
Period size: 26 Copynumber: 6.2 Consensus size: 26
6430309 GAAAATTATG
6430319 AAATATCAATTTTTCTT-AAAAATAA
1 AAATATCAATTTTTCTTAAAAAATAA
** *
6430344 AAATTTTAAAAATTATTTTTTGAGAAAAATTAA
1 AAA---TATCAATT-TTTCTT-A-AAAAA-TAA
* * *
6430377 AAATTTCAATTTTTCTTAGAAATTAA
1 AAATATCAATTTTTCTTAAAAAATAA
* *
6430403 AATTTTCAATTTTTCTTAGAAATAA-AA
1 AAATATCAATTTTTCTTA-AAA-AATAA
* ** *
6430430 AATTAAAAAAGGTTTTT-TTAAGCAAAAGTTGA
1 AAAT-ATCAA--TTTTTCTTAA--AAAA--TAA
6430462 AAATATCAATTTTTCTTAAAAAATAA
1 AAATATCAATTTTTCTTAAAAAATAA
6430488 AAAT
1 AAAT
6430492 GTTTCAAAAA
Statistics
Matches: 109, Mismatches: 20, Indels: 37
0.66 0.12 0.22
Matches are distributed among these distances:
25 3 0.03
26 26 0.24
27 11 0.10
28 15 0.14
29 20 0.18
30 16 0.15
31 3 0.03
32 9 0.08
33 6 0.06
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (26 bp):
AAATATCAATTTTTCTTAAAAAATAA
Found at i:6430770 original size:47 final size:47
Alignment explanation
Indices: 6430650--6430775 Score: 157
Period size: 49 Copynumber: 2.6 Consensus size: 47
6430640 TTAAAAACGT
* **
6430650 TTTTAAGGAAAAGTTGAAAGTATTAATTTTTCTTAAATAAAAAAGGAGG
1 TTTTAAGGAAAA-TTGAAAGTATCAATTTTTCTTAAATAAAAAA-GAAA
*
6430699 TTTTAA-GAATAAGTTGAAAATATCAATTTTTCTTAAATAAAAAA-AAA
1 TTTTAAGGAA-AA-TTGAAAGTATCAATTTTTCTTAAATAAAAAAGAAA
6430746 TTTTAAGGAGAAATTGAAAGTATCAATTTT
1 TTTTAAGGA-AAATTGAAAGTATCAATTTT
6430776 CTTTTTAGAA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
47 23 0.33
48 7 0.10
49 39 0.57
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (47 bp):
TTTTAAGGAAAATTGAAAGTATCAATTTTTCTTAAATAAAAAAGAAA
Found at i:6430866 original size:24 final size:22
Alignment explanation
Indices: 6430839--6430889 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
6430829 AAGGAAAAGT
*
6430839 TAAAAGTATCAATTTTTCCTTAAA
1 TAAAAGCATCAATTTTT--TTAAA
* *
6430863 TAAAGGCATTAATTTTTTTAAA
1 TAAAAGCATCAATTTTTTTAAA
6430885 TAAAA
1 TAAAA
6430890 ATAAGAAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 9 0.39
24 14 0.61
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (22 bp):
TAAAAGCATCAATTTTTTTAAA
Found at i:6431912 original size:24 final size:24
Alignment explanation
Indices: 6431892--6431937 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
6431882 TTGTTGTGTA
*
6431892 AGTTGTTATTATTATTATTGTTAT
1 AGTTGTTATTACTATTATTGTTAT
* *
6431916 TGTTGTTATTGCTATTATTGTT
1 AGTTGTTATTACTATTATTGTT
6431938 GTTATTATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.02, G:0.15, T:0.63
Consensus pattern (24 bp):
AGTTGTTATTACTATTATTGTTAT
Found at i:6432668 original size:70 final size:64
Alignment explanation
Indices: 6432590--6432723 Score: 178
Period size: 64 Copynumber: 2.0 Consensus size: 64
6432580 AAAAGACAGC
6432590 ATTACTTTGAATATGACGCAAAGTGATAAAAAAAAAAAAAAAAAGAATGTTATTCAAAGTAGATT
1 ATTACTTTGAATATGACGCAAAGTGAT-----AAAAAAAAAAAA-AATGTTATTCAAAGTAGATT
6432655 GCTTT
60 GCTTT
* * **
6432660 ATTACTTTGACTATGATGCAAAGTGATTGAAAAAAAAAAAATGTTATTCAAAGTAGATTGCTTT
1 ATTACTTTGAATATGACGCAAAGTGATAAAAAAAAAAAAAATGTTATTCAAAGTAGATTGCTTT
6432724 GAATTCGATG
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
64 25 0.42
65 10 0.17
70 25 0.42
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.31
Consensus pattern (64 bp):
ATTACTTTGAATATGACGCAAAGTGATAAAAAAAAAAAAAATGTTATTCAAAGTAGATTGCTTT
Found at i:6440137 original size:21 final size:22
Alignment explanation
Indices: 6440094--6440136 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6440084 ATTAATATAA
6440094 AAAAATTATATATATATATTTT
1 AAAAATTATATATATATATTTT
*
6440116 AAAAA-TATATATTTTATATTT
1 AAAAATTATATA-TATATATTT
6440137 ATTTATGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAAATTATATATATATATTTT
Found at i:6440500 original size:23 final size:23
Alignment explanation
Indices: 6440438--6440503 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
6440428 TAATATACTG
*
6440438 TATAAAGATTATTTTAAATATTTAT
1 TATAAA-ATTATTTT-AATAATTAT
* *
6440463 TATGATA-TATATTTAATAATTAT
1 TATAAAATTAT-TTTAATAATTAT
6440486 TATAAAATTATTTTAATA
1 TATAAAATTATTTTAATA
6440504 TTAATAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 23 0.68
24 7 0.21
25 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (23 bp):
TATAAAATTATTTTAATAATTAT
Found at i:6440645 original size:2 final size:2
Alignment explanation
Indices: 6440640--6440679 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
6440630 ATATATTAAA
6440640 AT AT AT AT AT -T A- AT -T AT AT AT -T 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
6440678 AT
1 AT
6440680 TAGTAATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
1 4 0.12
2 30 0.88
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:6440659 original size:11 final size:13
Alignment explanation
Indices: 6440630--6440679 Score: 61
Period size: 12 Copynumber: 4.0 Consensus size: 13
6440620 TATTAAATGC
*
6440630 ATATATTAAAATAT
1 ATATATT-ATATAT
6440644 ATATATTA-AT-T
1 ATATATTATATAT
6440655 ATATATTATATAT
1 ATATATTATATAT
6440668 ATATA-TATATAT
1 ATATATTATATAT
6440680 TAGTAATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.26
12 11 0.32
13 7 0.21
14 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATATTATATAT
Found at i:6441652 original size:24 final size:24
Alignment explanation
Indices: 6441610--6441658 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
6441600 AAGAACATAA
*
6441610 ATATATTAATTTGACTTTTTAAAT
1 ATATATTAATTTAACTTTTTAAAT
* *
6441634 ATATATTAATTTAATTTTTTTAAT
1 ATATATTAATTTAACTTTTTAAAT
6441658 A
1 A
6441659 ATTTCAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATATATTAATTTAACTTTTTAAAT
Found at i:6442385 original size:11 final size:11
Alignment explanation
Indices: 6442371--6442400 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
6442361 TTTTATATTA
6442371 ATAATATAAAT
1 ATAATATAAAT
6442382 ATAATATAAAT
1 ATAATATAAAT
6442393 AGTAATAT
1 A-TAATAT
6442401 TAGTACGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:6442883 original size:23 final size:22
Alignment explanation
Indices: 6442848--6442899 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
6442838 TCCAAATCAC
*
6442848 ATGATATACAATAATATATTATA
1 ATGATATACAATAACAT-TTATA
6442871 ATGATAATA-AATAACATTTATA
1 ATGAT-ATACAATAACATTTATA
*
6442893 ATAATAT
1 ATGATAT
6442900 GAAACCATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.08
22 9 0.35
23 12 0.46
24 3 0.12
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (22 bp):
ATGATATACAATAACATTTATA
Found at i:6443734 original size:24 final size:22
Alignment explanation
Indices: 6443682--6443735 Score: 54
Period size: 24 Copynumber: 2.4 Consensus size: 22
6443672 AAATAAACCT
*
6443682 TTTATCTTATATATATAATATA
1 TTTATATTATATATATAATATA
** *
6443704 TGAATATTATATATTCATAATTTA
1 TTTATATTATATA-T-ATAATATA
6443728 TTTATATT
1 TTTATATT
6443736 TTTATTTATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 10 0.42
23 1 0.04
24 13 0.54
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTATATTATATATATAATATA
Found at i:6444520 original size:30 final size:28
Alignment explanation
Indices: 6444493--6444562 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
6444483 TTATTTTAAT
*
6444493 ATATATGTTTTTTACTCATACATTTTTA
1 ATATATGTTTTTAACTCATACATTTTTA
* *
6444521 ATATATGTTTTTAACTCATACAGTTCTA
1 ATATATGTTTTTAACTCATACATTTTTA
*
6444549 ATGTATGTTTTTAA
1 ATATATGTTTTTAA
6444563 TACATTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (28 bp):
ATATATGTTTTTAACTCATACATTTTTA
Found at i:6444531 original size:28 final size:28
Alignment explanation
Indices: 6444493--6444574 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 28
6444483 TTATTTTAAT
6444493 ATATATGTTTTTTACTCATACATTTTTA
1 ATATATGTTTTTTACTCATACATTTTTA
* * *
6444521 ATATATGTTTTTAACTCATACAGTTCTA
1 ATATATGTTTTTTACTCATACATTTTTA
*
6444549 ATGTATG-TTTTTA---ATACATTTTTA
1 ATATATGTTTTTTACTCATACATTTTTA
6444573 AT
1 AT
6444575 TTGTAGATGG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
24 11 0.23
27 5 0.11
28 31 0.66
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (28 bp):
ATATATGTTTTTTACTCATACATTTTTA
Found at i:6450107 original size:20 final size:21
Alignment explanation
Indices: 6450066--6450111 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
6450056 CCCAAAATTA
6450066 ATAAAATATTATTTTTAAAAT
1 ATAAAATATTATTTTTAAAAT
*
6450087 ATAAAATATTATTTTT-TAAT
1 ATAAAATATTATTTTTAAAAT
6450107 ATAAA
1 ATAAA
6450112 TATAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:6450114 original size:19 final size:19
Alignment explanation
Indices: 6450063--6450114 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 19
6450053 CGACCCAAAA
6450063 TTAATA-AAATATTATTTT
1 TTAATATAAATATTATTTT
*
6450081 TAAAATATAAAATATTATTTT
1 T-TAATAT-AAATATTATTTT
6450102 TTAATATAAATAT
1 TTAATATAAATAT
6450115 AAAAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 1 0.03
19 10 0.34
20 5 0.17
21 13 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATATAAATATTATTTT
Found at i:6450826 original size:21 final size:21
Alignment explanation
Indices: 6450800--6450841 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
6450790 CTCAAACTTC
6450800 TTCAAAAACTA-TCATATATCA
1 TTCAAAAACTACT-ATATATCA
6450821 TTCAAAAACTACTATATATCA
1 TTCAAAAACTACTATATATCA
6450842 ATGTGTGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (21 bp):
TTCAAAAACTACTATATATCA
Found at i:6457115 original size:162 final size:163
Alignment explanation
Indices: 6456837--6457130 Score: 364
Period size: 162 Copynumber: 1.8 Consensus size: 163
6456827 GTGGTTTGGA
* * * * *
6456837 AAGCCTCAACGTAATAGGTAGAGGTGCTAAGGTCACATTAGACGTGATAGCATAAAGCCTTAACG
1 AAGCCTCAACGTAACAGATAAAGGTGCCAAGGTCACATTAGACGTGATAGCATAAAACCTTAACG
* *
6456902 CAAGAGATGAAAATGCTAGGGGCACATTGGGCATGTTGGCATAGGGCCTTAATGAAATAGAT-AA
66 CAAGAGATGAAAATGCTAGGGGCACAATGGGCATGTTGGCATAGAGCCTTAATGAAATAGATGAA
6456966 AGGCGCGCGGGGCATGTTGGGCATGTTAGCGCG
131 AGGCGCGCGGGGCATGTTGGGCATGTTAGCGCG
* *
6456999 AAGCCTCAACGTAACAGATAAAGGTGCCAGAGG-CACATTAGATGTG-TTG-ATACGAAACCTTA
1 AAGCCTCAACGTAACAGATAAAGGTGCCA-AGGTCACATTAGACGTGATAGCATA--AAACCTTA
* * * ** ** *
6457061 ATGCAATAGAT-AAATGTGCTAGGGGCACAATGGGTGTGTTGGTGTAGAGCCTTAATGCAATAGA
63 ACGCAAGAGATGAAA-ATGCTAGGGGCACAATGGGCATGTTGGCATAGAGCCTTAATGAAATAGA
6457125 TGAAAG
127 TGAAAG
6457131 CACACAGGGT
Statistics
Matches: 110, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
160 3 0.03
161 5 0.05
162 95 0.86
163 7 0.06
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.22
Consensus pattern (163 bp):
AAGCCTCAACGTAACAGATAAAGGTGCCAAGGTCACATTAGACGTGATAGCATAAAACCTTAACG
CAAGAGATGAAAATGCTAGGGGCACAATGGGCATGTTGGCATAGAGCCTTAATGAAATAGATGAA
AGGCGCGCGGGGCATGTTGGGCATGTTAGCGCG
Found at i:6457307 original size:77 final size:75
Alignment explanation
Indices: 6457140--6457346 Score: 191
Period size: 77 Copynumber: 2.7 Consensus size: 75
6457130 GCACACAGGG
* * * * * * *
6457140 TGCATTAAGCATGTCCGCAGGAAGTGGGGATTGTGTTAACCCTTATGCCTTAACACAATAGAAAA
1 TGCATTGAGCATGTCAGCAGGAAGTGGGAACTATGTTAACCCATATGCCTTAACACAATAAAAAA
** *
6457205 TGACTTGTAA
66 TGACGCGGAA
* * *
6457215 GGCACGTTGAACATGTCAGCAAGAAGTGGGAACTATGTTAACCCATATGCCTTAACACAATAAAA
1 TGCA--TTGAGCATGTCAGCAGGAAGTGGGAACTATGTTAACCCATATGCCTTAACACAATAAAA
*
6457280 AATGGCACGCGGGA
64 AAT-G-ACGCGGAA
* ** * *
6457294 TGCATTGAGCATGTTAATAGGAAGT-GGAGACTATGTTAACCGATATACCTTAA
1 TGCATTGAGCATGTCAGCAGGAAGTGGGA-ACTATGTTAACCCATATGCCTTAA
6457347 TGCATAAAAA
Statistics
Matches: 105, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
75 3 0.03
76 3 0.03
77 91 0.87
78 1 0.01
79 7 0.07
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.25
Consensus pattern (75 bp):
TGCATTGAGCATGTCAGCAGGAAGTGGGAACTATGTTAACCCATATGCCTTAACACAATAAAAAA
TGACGCGGAA
Found at i:6462598 original size:11 final size:11
Alignment explanation
Indices: 6462584--6462615 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
6462574 ATTTTTTTTC
6462584 TTTTAAGATTT
1 TTTTAAGATTT
6462595 TTTTAAGATTT
1 TTTTAAGATTT
6462606 TTTTAA-ATTT
1 TTTTAAGATTT
6462616 AAAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (11 bp):
TTTTAAGATTT
Found at i:6464189 original size:10 final size:9
Alignment explanation
Indices: 6464187--6464244 Score: 66
Period size: 9 Copynumber: 6.6 Consensus size: 9
6464177 ATTTTGATTT
*
6464187 ATTTTTTGG
1 ATTTTTTTG
6464196 ATTTTTTTG
1 ATTTTTTTG
6464205 AATTTTTTTG
1 -ATTTTTTTG
6464215 -TTTTTTTG
1 ATTTTTTTG
* *
6464223 AATTTTTAG
1 ATTTTTTTG
6464232 ATTTTTTT-
1 ATTTTTTTG
6464240 ATTTT
1 ATTTT
6464245 AAGTTATTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
8 13 0.31
9 20 0.48
10 9 0.21
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (9 bp):
ATTTTTTTG
Found at i:6464210 original size:18 final size:19
Alignment explanation
Indices: 6464187--6464239 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 19
6464177 ATTTTGATTT
*
6464187 ATTTTTTGGATTTTTTTGA
1 ATTTTTTAGATTTTTTTGA
*
6464206 ATTTTTTTG-TTTTTTTGA
1 ATTTTTTAGATTTTTTTGA
6464224 A-TTTTTAGATTTTTTT
1 ATTTTTTAGATTTTTTT
6464240 ATTTTAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 6 0.19
18 17 0.55
19 8 0.26
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.74
Consensus pattern (19 bp):
ATTTTTTAGATTTTTTTGA
Found at i:6464313 original size:34 final size:34
Alignment explanation
Indices: 6464275--6464339 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
6464265 TAATTAGAAG
6464275 CTCCACAACTTTGAAAATAAACTTAAAATCTCAT
1 CTCCACAACTTTGAAAATAAACTTAAAATCTCAT
*
6464309 CTCCATAACTTTGAAAATAAACTTAAAATCT
1 CTCCACAACTTTGAAAATAAACTTAAAATCT
6464340 TCTCTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.31
Consensus pattern (34 bp):
CTCCACAACTTTGAAAATAAACTTAAAATCTCAT
Found at i:6464705 original size:57 final size:56
Alignment explanation
Indices: 6464520--6464862 Score: 243
Period size: 57 Copynumber: 6.1 Consensus size: 56
6464510 AAACTTTGGT
*
6464520 TATCACCACTGAG-AAATG-AAATGACTTTGGATATTGTCACC-T-AAGAGAACTCAGA
1 TATCACCACTGAGTAAATGCAAATGACTTTAGATA---TCACCATAAAGAGAACTCAGA
* * * * ** *
6464575 TATCACCATTGAGTAAATACAGATGATTTTAGATATCACCACCAAGAGAATTCAGA
1 TATCACCACTGAGTAAATGCAAATGACTTTAGATATCACCATAAAGAGAACTCAGA
* * * * * *
6464631 TGTCACCACTAAATAAATGCATATGACTTTAGATATCGCCAGTAAAGAGAACTCAAA
1 TATCACCACTGAGTAAATGCAAATGACTTTAGATATCACCA-TAAAGAGAACTCAGA
** * * * * * *
6464688 TATCACCACTGAGTAAATATAGATAACTTCAGATATCACCATCAAAAAGGACTTTA-A
1 TATCACCACTGAGTAAATGCAAATGACTTTAGATATCACCAT-AAAGAGAAC-TCAGA
* * * * * *
6464745 TGTCACCACCGAGTAAATGCAAATAACTTTGGCTATCATCATTAAAG-GAACTCAGA
1 TATCACCACTGAGTAAATGCAAATGACTTTAGATATCACCA-TAAAGAGAACTCAGA
* * * * *
6464801 TATCACCACTGAGTAAATGTAGAT-AATTTCAAATATCACCACTAAAGAGGACTC-GAA
1 TATCACCACTGAGTAAATGCAAATGACTTT-AGATATCACCA-TAAAGAGAACTCAG-A
6464858 TATCA
1 TATCA
6464863 TCATCCATAA
Statistics
Matches: 222, Mismatches: 54, Indels: 22
0.74 0.18 0.07
Matches are distributed among these distances:
54 5 0.02
55 18 0.08
56 87 0.39
57 109 0.49
58 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (56 bp):
TATCACCACTGAGTAAATGCAAATGACTTTAGATATCACCATAAAGAGAACTCAGA
Found at i:6464852 original size:113 final size:115
Alignment explanation
Indices: 6464562--6464853 Score: 342
Period size: 113 Copynumber: 2.6 Consensus size: 115
6464552 ATTGTCACCT
* * * * * *
6464562 AAGAGAACTCAGATATCACCATTGAGTAAATACAGATGATTTTAGATATCACCAC-CAAGA-GAA
1 AAGAGAACTCAGATATCACCACTGAGTAAATATAGATAATTTCAGATATCACCACTAAAGAGGAC
* * * *
6464625 TTCAGATGTCACCACTAAATAAATGCATATGACTTTAGATATCGCCAGTA
66 TTCAGATGTCACCACCAAATAAATGCAAATAACTTTAGATATCACCAGTA
* * *
6464675 AAGAGAACTCAAATATCACCACTGAGTAAATATAGATAACTTCAGATATCACCA-TCAAAAAGGA
1 AAGAGAACTCAGATATCACCACTGAGTAAATATAGATAATTTCAGATATCACCACT-AAAGAGGA
* * * * * * *
6464739 CTTTA-ATGTCACCACCGAGTAAATGCAAATAACTTTGGCTATCATCATTA
65 CTTCAGATGTCACCACCAAATAAATGCAAATAACTTTAGATATCACCAGTA
* *
6464789 AAG-GAACTCAGATATCACCACTGAGTAAATGTAGATAATTTCAAATATCACCACTAAAGAGGAC
1 AAGAGAACTCAGATATCACCACTGAGTAAATATAGATAATTTCAGATATCACCACTAAAGAGGAC
6464853 T
66 T
6464854 CGAATATCAT
Statistics
Matches: 150, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
113 103 0.69
114 42 0.28
115 5 0.03
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (115 bp):
AAGAGAACTCAGATATCACCACTGAGTAAATATAGATAATTTCAGATATCACCACTAAAGAGGAC
TTCAGATGTCACCACCAAATAAATGCAAATAACTTTAGATATCACCAGTA
Found at i:6464895 original size:58 final size:57
Alignment explanation
Indices: 6464833--6464956 Score: 131
Period size: 58 Copynumber: 2.2 Consensus size: 57
6464823 ATAATTTCAA
* * * * * * *
6464833 ATATCACCACTAAAGAGGACTCGAATATCATCATCCATAAAAATATAGATGACTTTAG
1 ATATCACCACCAAAAAGAACTCGAATATCACCATCCA-AAAAATACAAATGACTCTAG
* * ** *
6464891 ATATCTCCACCAAAAAGAATTCGAATATCACCATTGAAAAAATACAAATGACTCTGG
1 ATATCACCACCAAAAAGAACTCGAATATCACCATCCAAAAAATACAAATGACTCTAG
6464948 ATATCACCA
1 ATATCACCA
6464957 TTGAAGAGAA
Statistics
Matches: 53, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
57 24 0.45
58 29 0.55
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.24
Consensus pattern (57 bp):
ATATCACCACCAAAAAGAACTCGAATATCACCATCCAAAAAATACAAATGACTCTAG
Found at i:6464951 original size:57 final size:57
Alignment explanation
Indices: 6464833--6465071 Score: 178
Period size: 57 Copynumber: 4.2 Consensus size: 57
6464823 ATAATTTCAA
* * * * * * * * *
6464833 ATATCACCACTAAAGAGGACTCGAATATCATCATCCATAAAAATATAGATGACTTTAG
1 ATATCACCACCAAAAAGAATTCGAATATCACCATCGA-AAAAATACAAATGACTTTGG
* * *
6464891 ATATCTCCACCAAAAAGAATTCGAATATCACCATTGAAAAAATACAAATGACTCTGG
1 ATATCACCACCAAAAAGAATTCGAATATCACCATCGAAAAAATACAAATGACTTTGG
*** * * * * *
6464948 ATATCACCATTGAAGAGAATTTGAATATTACCATCGAAAAGATGCAAATGACTTTGG
1 ATATCACCACCAAAAAGAATTCGAATATCACCATCGAAAAAATACAAATGACTTTGG
* **** * *
6465005 ATATC-CTTACCAAAGTCTATTCAAATATCACCAT--AAAAAATATGCAAATGACTTCGG
1 ATATCAC-CACCAAAAAGAATTCGAATATCACCATCGAAAAAATA--CAAATGACTTTGG
6465062 ATATCACCAC
1 ATATCACCAC
6465072 TAAAGACTTA
Statistics
Matches: 140, Mismatches: 37, Indels: 9
0.75 0.20 0.05
Matches are distributed among these distances:
55 6 0.04
56 1 0.01
57 103 0.74
58 30 0.21
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.26
Consensus pattern (57 bp):
ATATCACCACCAAAAAGAATTCGAATATCACCATCGAAAAAATACAAATGACTTTGG
Found at i:6465579 original size:24 final size:22
Alignment explanation
Indices: 6465522--6465579 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
6465512 AAGTTCTTAA
6465522 TTTTTTCTCTTGTTTTCTTGGAT
1 TTTTTTCT-TTGTTTTCTTGGAT
* *
6465545 TTTTTTCCTTTTTTTTTTTGGACT
1 TTTTTT-CTTTGTTTTCTTGGA-T
6465569 CTTTTTTCTTT
1 -TTTTTTCTTT
6465580 AATGTTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 17 0.57
24 7 0.23
25 6 0.20
ACGTcount: A:0.03, C:0.14, G:0.09, T:0.74
Consensus pattern (22 bp):
TTTTTTCTTTGTTTTCTTGGAT
Found at i:6471992 original size:22 final size:22
Alignment explanation
Indices: 6471948--6471992 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
6471938 TATGTTTCGA
* *
6471948 TTTTTTTTATGCTTTTTAGGGT
1 TTTTTTTTATACTTTCTAGGGT
*
6471970 TTTTTTTTATACTTTCTATGGT
1 TTTTTTTTATACTTTCTAGGGT
6471992 T
1 T
6471993 CTTTGGTGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.07, G:0.13, T:0.69
Consensus pattern (22 bp):
TTTTTTTTATACTTTCTAGGGT
Found at i:6473476 original size:28 final size:28
Alignment explanation
Indices: 6473444--6473497 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
6473434 GTGTTTGGTT
*
6473444 TAATGTTGGGTATTGT-ATGGTATGATCA
1 TAATGATGGGTATTGTCAT-GTATGATCA
*
6473472 TAATGATGGGTGTTGTCATGTATGAT
1 TAATGATGGGTATTGTCATGTATGAT
6473498 TTGATGGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.24, C:0.04, G:0.30, T:0.43
Consensus pattern (28 bp):
TAATGATGGGTATTGTCATGTATGATCA
Found at i:6474240 original size:23 final size:23
Alignment explanation
Indices: 6474210--6474255 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6474200 CATGGATCCC
6474210 AAAGTCGTTACTCCAAGACACGT
1 AAAGTCGTTACTCCAAGACACGT
6474233 AAAGTCGTTACTCCAAGACACGT
1 AAAGTCGTTACTCCAAGACACGT
6474256 TTCAACGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (23 bp):
AAAGTCGTTACTCCAAGACACGT
Found at i:6481241 original size:11 final size:11
Alignment explanation
Indices: 6481225--6481249 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6481215 CGGGGAAATT
6481225 CAAAATACAAG
1 CAAAATACAAG
6481236 CAAAATACAAG
1 CAAAATACAAG
6481247 CAA
1 CAA
6481250 GGAATTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.20, G:0.08, T:0.08
Consensus pattern (11 bp):
CAAAATACAAG
Found at i:6488177 original size:19 final size:20
Alignment explanation
Indices: 6488136--6488177 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
6488126 AAAAATTTTT
**
6488136 TAAAAAAAATATTTTAATCA
1 TAAAAAAAATATTTTAAGAA
*
6488156 TAAAAATAATA-TTTAAGAA
1 TAAAAAAAATATTTTAAGAA
6488175 TAA
1 TAA
6488178 TTTTTTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
TAAAAAAAATATTTTAAGAA
Found at i:6488224 original size:22 final size:21
Alignment explanation
Indices: 6488190--6488230 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
6488180 TTTTTTATAA
* *
6488190 ATTTAATTATGAAATTAAAGC
1 ATTTAATAATGAAAGTAAAGC
6488211 ATTTATATAATGAAAGTAAA
1 ATTTA-ATAATGAAAGTAAA
6488231 TCAAATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (21 bp):
ATTTAATAATGAAAGTAAAGC
Found at i:6488267 original size:18 final size:17
Alignment explanation
Indices: 6488237--6488270 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6488227 TAAATCAAAT
*
6488237 ATAAATTCATAATAAAA
1 ATAAAATCATAATAAAA
6488254 ATAAAATCACTAATAAA
1 ATAAAATCA-TAATAAA
6488271 TCAAATGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAATCATAATAAAA
Found at i:6488954 original size:15 final size:15
Alignment explanation
Indices: 6488934--6488995 Score: 58
Period size: 15 Copynumber: 4.1 Consensus size: 15
6488924 TTTATATTTT
6488934 ATAATTTTTTTAATA
1 ATAATTTTTTTAATA
*
6488949 ATAATTTTTTCAATA
1 ATAATTTTTTTAATA
*
6488964 CAT--TTATTTATAAATA
1 -ATAATT-TTT-TTAATA
6488980 ATAA-TTTTTTAATA
1 ATAATTTTTTTAATA
6488994 AT
1 AT
6488996 TTTTGATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
14 9 0.23
15 22 0.56
16 8 0.21
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTTTAATA
Found at i:6488983 original size:31 final size:28
Alignment explanation
Indices: 6488930--6489005 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 28
6488920 TAAATTTATA
*
6488930 TTTT-ATAATTTTT--TTAATAATAATT
1 TTTTAATAATTTTTGATAAATAATAATT
*
6488955 TTTTCAATACATTTATTTATAAATAATAATT
1 TTTT-AATA-ATTT-TTGATAAATAATAATT
6488986 TTTTAATAATTTTTGATAAA
1 TTTTAATAATTTTTGATAAA
6489006 ATTTCACATT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
25 4 0.09
27 3 0.07
28 11 0.26
29 6 0.14
30 4 0.09
31 15 0.35
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (28 bp):
TTTTAATAATTTTTGATAAATAATAATT
Found at i:6497212 original size:52 final size:51
Alignment explanation
Indices: 6497125--6497281 Score: 215
Period size: 52 Copynumber: 3.0 Consensus size: 51
6497115 TGGACAAGAA
* * * *
6497125 GACTTGCAAAAGAAGAATTCCAAGAGAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAG-GGATTCTTAATAGGCAAGTTT
* *
6497177 GACTTGTAAGAGAAGAATTCTAAAAGGGAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGA-GGAAGGGATTCTTAATAGGCAAGTTT
* *
6497229 GACTTACAAGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGA-AGGGATTCTTAATAGGCAAGTTT
6497281 G
1 G
6497282 TATGATTATA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 3 0.03
52 86 0.92
53 4 0.04
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.25
Consensus pattern (51 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAGGGATTCTTAATAGGCAAGTTT
Found at i:6497809 original size:31 final size:31
Alignment explanation
Indices: 6497771--6497852 Score: 119
Period size: 31 Copynumber: 2.6 Consensus size: 31
6497761 CGTTTAGCCT
6497771 AACAAATGGTATCAGAGCTGTGGTGTTCCCC
1 AACAAATGGTATCAGAGCTGTGGTGTTCCCC
* * *
6497802 AACAAATGGTATCAGAACTGTGGTGTTTCCT
1 AACAAATGGTATCAGAGCTGTGGTGTTCCCC
* *
6497833 AACAAGTGGTATCGGAGCTG
1 AACAAATGGTATCAGAGCTG
6497853 AAGGTTCGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (31 bp):
AACAAATGGTATCAGAGCTGTGGTGTTCCCC
Found at i:6497949 original size:50 final size:48
Alignment explanation
Indices: 6497855--6497974 Score: 116
Period size: 50 Copynumber: 2.4 Consensus size: 48
6497845 CGGAGCTGAA
* * * * *
6497855 GGTTCGAAACGTGAGAAGAGTTGAAGATTCAAGATGTGGAAAGAGCCGAT
1 GGTTCGAGACATGGGAAAAGTTGAAGATTCAAGATATGGAAAGAG-C-AT
* * *
6497905 GGTTCGAGACATGGGAAAAGTTGATAG-TTCGAGATATGGGAAGAGCTT
1 GGTTCGAGACATGGGAAAAGTTGA-AGATTCAAGATATGGAAAGAGCAT
*
6497953 GGTTTGAGACATGGGAAGAAGT
1 GGTTCGAGACATGGGAA-AAGT
6497975 AAGCTTAGAG
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
48 17 0.29
49 5 0.08
50 35 0.59
51 2 0.03
ACGTcount: A:0.33, C:0.08, G:0.36, T:0.23
Consensus pattern (48 bp):
GGTTCGAGACATGGGAAAAGTTGAAGATTCAAGATATGGAAAGAGCAT
Found at i:6497966 original size:23 final size:22
Alignment explanation
Indices: 6497904--6497971 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 22
6497894 AAAGAGCCGA
*
6497904 TGGTTCGAGACATGGGAAAAGT
1 TGGTTCGAGACATGGGAAGAGT
*
6497926 TGATAGTTCGAGATATGGGAAGAGCT
1 TG---GTTCGAGACATGGGAAGAG-T
*
6497952 TGGTTTGAGACATGGGAAGA
1 TGGTTCGAGACATGGGAAGA
6497972 AGTAAGCTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.05
23 16 0.42
25 17 0.45
26 3 0.08
ACGTcount: A:0.31, C:0.07, G:0.37, T:0.25
Consensus pattern (22 bp):
TGGTTCGAGACATGGGAAGAGT
Found at i:6498206 original size:11 final size:11
Alignment explanation
Indices: 6498190--6498230 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
6498180 ATCCCATAAG
6498190 AGATTTGTTTA
1 AGATTTGTTTA
6498201 AGATTTG-TTA
1 AGATTTGTTTA
*
6498211 GAGATTTGTTTG
1 -AGATTTGTTTA
6498223 AGATTTGT
1 AGATTTGT
6498231 CAGATATTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 3 0.11
11 22 0.81
12 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (11 bp):
AGATTTGTTTA
Found at i:6498216 original size:22 final size:22
Alignment explanation
Indices: 6498188--6498230 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
6498178 AAATCCCATA
6498188 AGAGATTTGTTTAAGATTTGTT
1 AGAGATTTGTTTAAGATTTGTT
*
6498210 AGAGATTTGTTTGAGATTTGT
1 AGAGATTTGTTTAAGATTTGT
6498231 CAGATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTAAGATTTGTT
Found at i:6498342 original size:52 final size:52
Alignment explanation
Indices: 6498255--6498411 Score: 201
Period size: 52 Copynumber: 3.0 Consensus size: 52
6498245 TGGACAAGAA
* * * *
6498255 GACTTACAAAAGAAGAATTCCAAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTACAAGAGAAGAATTCTAAAAGGAGAG-GGATTCTTAATAGGTAAGTTT
** *
6498307 GACTTGTAAGAGAAGAATTCTAAAAGG-GAAGGGATTCTTAATAGGCAAGTTT
1 GACTTACAAGAGAAGAATTCTAAAAGGAG-AGGGATTCTTAATAGGTAAGTTT
* *
6498359 GACTTACAAGAGAAGAATTCTAAGAGGAGAGGGATTCTTAATGGGTAAGTTT
1 GACTTACAAGAGAAGAATTCTAAAAGGAGAGGGATTCTTAATAGGTAAGTTT
6498411 G
1 G
6498412 TATAATTATA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
52 86 0.96
53 4 0.04
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.26
Consensus pattern (52 bp):
GACTTACAAGAGAAGAATTCTAAAAGGAGAGGGATTCTTAATAGGTAAGTTT
Found at i:6499329 original size:99 final size:99
Alignment explanation
Indices: 6499151--6499331 Score: 256
Period size: 99 Copynumber: 1.8 Consensus size: 99
6499141 ATGCTCTCTT
* * *
6499151 AAGCCTACACTCCAGGTTGACTCAACACATCGCTCACTTGGGTGTGCTGCTTTTTTACATATTAT
1 AAGCCTACACTCCAAGTTGACTCAACACATCGCTCACTTGGATGTACTGCTTTTTTACATATTAT
6499216 CATATACTCACTACATCCAAGTCGAACCTCCTTC
66 CATATACTCACTACATCCAAGTCGAACCTCCTTC
* * * * * *
6499250 AAGCTTACACTCGAAGTTGACTCAACACATTG-TCTACTTGGATGTATTGTTTTTTTGCATATTA
1 AAGCCTACACTCCAAGTTGACTCAACACATCGCTC-ACTTGGATGTACTGCTTTTTTACATATTA
*
6499314 TCATATACTCGCTACATC
65 TCATATACTCACTACATC
6499332 TAAATTGAAC
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 2 0.03
99 69 0.97
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (99 bp):
AAGCCTACACTCCAAGTTGACTCAACACATCGCTCACTTGGATGTACTGCTTTTTTACATATTAT
CATATACTCACTACATCCAAGTCGAACCTCCTTC
Found at i:6500647 original size:17 final size:17
Alignment explanation
Indices: 6500627--6500663 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
6500617 TAAATTAGTT
*
6500627 AATATTAAATTTATTCA
1 AATATTAAAATTATTCA
6500644 AATATTAAAATTATTCA
1 AATATTAAAATTATTCA
6500661 AAT
1 AAT
6500664 TATAATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
AATATTAAAATTATTCA
Found at i:6501127 original size:11 final size:11
Alignment explanation
Indices: 6501113--6501146 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
6501103 TATATTTTAC
*
6501113 TTATCTATATT
1 TTATTTATATT
*
6501124 TTATTTATATA
1 TTATTTATATT
6501135 TTATTTATATT
1 TTATTTATATT
6501146 T
1 T
6501147 ATTGATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTTATATT
Found at i:6517940 original size:19 final size:19
Alignment explanation
Indices: 6517901--6517940 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6517891 CTTCTCTTTC
* *
6517901 AGTAAAGAAAAACAGAGGT
1 AGTAAAGAAAAACAAAAGT
*
6517920 AGTAAAGAAAGACAAAAGT
1 AGTAAAGAAAAACAAAAGT
6517939 AG
1 AG
6517941 AGTTGGCAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.25, T:0.10
Consensus pattern (19 bp):
AGTAAAGAAAAACAAAAGT
Found at i:6518940 original size:25 final size:25
Alignment explanation
Indices: 6518904--6518951 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
6518894 TGAGGAGAAT
6518904 TTTTTCTAGAAATTT-TGGCGAAAAA
1 TTTTTCTAGAAATTTCTGG-GAAAAA
*
6518929 TTTTTCTGGAAATTTCTGGGAAA
1 TTTTTCTAGAAATTTCTGGGAAA
6518952 TTTCCAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (25 bp):
TTTTTCTAGAAATTTCTGGGAAAAA
Found at i:6519019 original size:31 final size:31
Alignment explanation
Indices: 6518970--6519028 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
6518960 TTCCGGTGAA
* *
6518970 AATTCCGGCGAAACTTGAATTTTTCGGCTAC
1 AATTCCGGCGAAACTTGAAGTTTCCGGCTAC
*
6519001 AATTCCGGC-CAACTTTGAAGTTTCCGGC
1 AATTCCGGCGAAAC-TTGAAGTTTCCGGC
6519029 GACCAGTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (31 bp):
AATTCCGGCGAAACTTGAAGTTTCCGGCTAC
Found at i:6519107 original size:19 final size:20
Alignment explanation
Indices: 6519083--6519121 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6519073 TCCAGCCAAC
6519083 TTCCGGCG-AAATTTTCAGA
1 TTCCGGCGAAAATTTTCAGA
6519102 TTCCGGCGAAAATTTTCAGA
1 TTCCGGCGAAAATTTTCAGA
6519122 ATTCGGCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (20 bp):
TTCCGGCGAAAATTTTCAGA
Found at i:6519489 original size:20 final size:20
Alignment explanation
Indices: 6519452--6519489 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6519442 GCTCCAGGTT
* *
6519452 TTTTTTTTTTTTTTTTTGAA
1 TTTTTTTTTATTTCTTTGAA
6519472 TTTTTTTTTATTTCTTTG
1 TTTTTTTTTATTTCTTTG
6519490 TTTATTTGTT
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:0.08, C:0.03, G:0.05, T:0.84
Consensus pattern (20 bp):
TTTTTTTTTATTTCTTTGAA
Found at i:6519501 original size:20 final size:19
Alignment explanation
Indices: 6519475--6519523 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
6519465 TTTTGAATTT
6519475 TTTTTTATTTCT-TTGTTTA
1 TTTTTTATTT-TATTGTTTA
*
6519494 TTTGTTTATTTTATTTTTTA
1 TTT-TTTATTTTATTGTTTA
6519514 TTTTTTATTT
1 TTTTTTATTT
6519524 ATTAGATTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTTTTATTTTATTGTTTA
Found at i:6519539 original size:32 final size:32
Alignment explanation
Indices: 6519475--6519539 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
6519465 TTTTGAATTT
* * * *
6519475 TTTTTTATTTCTTTGTTTATTTGTTTATTTTA
1 TTTTTTATTTCTTTATTTATTAGATTAGTTTA
6519507 TTTTTTATTT-TTTATTTATTAGATTAGGTTTA
1 TTTTTTATTTCTTTATTTATTAGATTA-GTTTA
6519539 T
1 T
6519540 GTAATATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.17, C:0.02, G:0.08, T:0.74
Consensus pattern (32 bp):
TTTTTTATTTCTTTATTTATTAGATTAGTTTA
Found at i:6519686 original size:57 final size:57
Alignment explanation
Indices: 6519604--6519944 Score: 436
Period size: 57 Copynumber: 5.7 Consensus size: 57
6519594 AAAAATTCTA
*
6519604 AAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAAATAT-TTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
6519663 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTCC
*
6519725 AAAATAAAATATTTTT-AGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTC
1 --AA-AAAATATTTTTGA-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
* *
6519785 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-GAGAATCAAAATTTCAA
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AAT--AAATTTC-C
* * *
6519845 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAGAAATAAATTTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
6519902 AAAAAA-AGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATA---TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
6519945 CTAAAAAAAA
Statistics
Matches: 254, Mismatches: 10, Indels: 36
0.85 0.03 0.12
Matches are distributed among these distances:
56 3 0.01
57 76 0.30
58 13 0.05
59 46 0.18
60 58 0.23
61 2 0.01
62 14 0.06
64 3 0.01
65 39 0.15
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (57 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
Found at i:6519740 original size:122 final size:119
Alignment explanation
Indices: 6519592--6519957 Score: 553
Period size: 122 Copynumber: 3.1 Consensus size: 119
6519582 AAATAAAAAT
6519592 AAAAAAA-TTCTAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATA
1 AAAAAAATTTC-AAAAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATA
*
6519656 AATTTCCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGA
64 AATTTTCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGA
6519712 AAAATAAATTTCCAAAATAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 AAAA-AAATTT-CAAAA-AAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* *
6519777 AAATTTTCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT--GAGA
63 AAATTTTCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGA
** * *
6519832 ATCAAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAGAAATAAA
1 AAAAAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA
*
6519897 TTTTCAAAAAA-AGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCCTAAAA-A
66 TTTTCAAAAAATA---TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGA
6519952 AAAAAA
1 AAAAAA
6519958 TCATTCTCTC
Statistics
Matches: 225, Mismatches: 12, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
116 1 0.00
117 59 0.26
118 5 0.02
119 39 0.17
120 14 0.06
121 4 0.02
122 99 0.44
123 4 0.02
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (119 bp):
AAAAAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA
TTTTCAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGA
Found at i:6525465 original size:18 final size:18
Alignment explanation
Indices: 6525427--6525469 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
6525417 ATAAAAAATT
*
6525427 AATCAAATTTATTTATTA
1 AATCAAATTTATTTATCA
6525445 AATC-AATTTATTTAATCA
1 AATCAAATTTATTT-ATCA
6525463 AAT-AAAT
1 AATCAAAT
6525470 CGAATTACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (18 bp):
AATCAAATTTATTTATCA
Found at i:6526305 original size:14 final size:15
Alignment explanation
Indices: 6526276--6526376 Score: 86
Period size: 14 Copynumber: 6.9 Consensus size: 15
6526266 AGATTCCATT
6526276 TATTATAATAATATAA
1 TATT-TAATAATATAA
6526292 TATTTAAT-ATATAA
1 TATTTAATAATATAA
*
6526306 TATTTAA-AATATAT
1 TATTTAATAATATAA
*
6526320 TATTTATTAATATAA
1 TATTTAATAATATAA
* *
6526335 TA--TAATATTAT-T
1 TATTTAATAATATAA
* *
6526347 TATTTATTAATATAT
1 TATTTAATAATATAA
*
6526362 TATTAATATAATATA
1 TATTTA-ATAATATA
6526377 TTAATAGATT
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
12 2 0.03
13 7 0.10
14 31 0.45
15 18 0.26
16 11 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTTAATAATATAA
Found at i:6526332 original size:38 final size:41
Alignment explanation
Indices: 6526284--6526468 Score: 128
Period size: 42 Copynumber: 4.4 Consensus size: 41
6526274 TTTATTATAA
6526284 TAATATAATAT-TTAATA-TATAATATTTA-AAATATATTAT
1 TAATATAATATATTAATATTAT-ATATTTATAAATATATTAT
* * *
6526323 TTAT-TAATATAATATAATATTATTTATTTATTAATATATTAT
1 TAATATAATAT-AT-TAATATTATATATTTATAAATATATTAT
* * * *
6526365 TAATATAATATATTAATA-GATTTTTTTATTAACAATTTATTAT
1 TAATATAATATATTAATATTATATATTTA-T-A-AATATATTAT
* * ** *
6526408 TAATATATAATATATTTATATTAATAAATAAATAATATTGTATTAT
1 T-A-ATATAATATATTAATATT-ATATATTTATAA-A-TATATTAT
6526454 TAATATAATATATTA
1 TAATATAATATATTA
6526469 TTTATTAATA
Statistics
Matches: 114, Mismatches: 17, Indels: 25
0.73 0.11 0.16
Matches are distributed among these distances:
38 6 0.05
39 3 0.03
40 9 0.08
41 17 0.15
42 18 0.16
43 16 0.14
44 14 0.12
45 18 0.16
46 9 0.08
47 4 0.04
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (41 bp):
TAATATAATATATTAATATTATATATTTATAAATATATTAT
Found at i:6526358 original size:51 final size:51
Alignment explanation
Indices: 6526273--6526484 Score: 137
Period size: 51 Copynumber: 4.3 Consensus size: 51
6526263 TTTAGATTCC
* *
6526273 ATTTATT-ATAATAATATAATA-T-TTAATATA-TAATATTTAAAATATATT
1 ATTTATTAAT-ATAATATAATATTATTAATTTATTAATATTTATAATATATT
*
6526321 ATTTATTAATATAATATAATATTATTTATTTATTAATATATTATTAATATA--
1 ATTTATTAATATAATATAATATTATTAATTTATTAATAT-TTA-TAATATATT
* * * * ** ** * *
6526372 ATATATTAATAGATTTTTTTATTAACAATTTATTATTAATATATAATATATT
1 ATTTATTAATATAATATAATATTATTAATTTATTAAT-ATTTATAATATATT
* * *
6526424 -TATATTAATA-AATA-AATA--A-T-ATTGTATTATTA-ATATAATATATT
1 ATTTATTAATATAATATAATATTATTAATT-TATTAATATTTATAATATATT
6526468 ATTTATTAATATAATAT
1 ATTTATTAATATAATAT
6526485 TTAGATAATA
Statistics
Matches: 131, Mismatches: 20, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
44 12 0.09
45 13 0.10
46 11 0.08
47 1 0.01
48 18 0.14
49 5 0.04
50 15 0.11
51 45 0.34
52 5 0.04
53 6 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (51 bp):
ATTTATTAATATAATATAATATTATTAATTTATTAATATTTATAATATATT
Found at i:6526406 original size:43 final size:38
Alignment explanation
Indices: 6526323--6526423 Score: 103
Period size: 38 Copynumber: 2.5 Consensus size: 38
6526313 AATATATTAT
* *
6526323 TTATTAATATAATATAATATTATTTATTTATTAATATA
1 TTATTAATATAATATATTATGATTTATTTATTAATATA
* *
6526361 TTATTAATATAATATATTAATAGATTTTTTTATTAACAATTTA
1 TTATTAATATAATATATT-AT-GATTTATTTATT---AATATA
6526404 TTATTAATATATAATATATT
1 TTATT-A-ATATAATATATT
6526424 TATATTAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
38 17 0.33
39 2 0.04
40 10 0.19
43 10 0.19
44 1 0.02
45 12 0.23
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (38 bp):
TTATTAATATAATATATTATGATTTATTTATTAATATA
Found at i:6526485 original size:15 final size:16
Alignment explanation
Indices: 6526458--6526502 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
6526448 TATTATTAAT
*
6526458 ATAATATATTATTTA-
1 ATAATATAATATTTAG
*
6526473 TTAATATAATATTTAG
1 ATAATATAATATTTAG
*
6526489 ATAATAAAATATTT
1 ATAATATAATATTT
6526503 TTCTTTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATAATATAATATTTAG
Found at i:6526485 original size:62 final size:60
Alignment explanation
Indices: 6526322--6526496 Score: 153
Period size: 62 Copynumber: 2.9 Consensus size: 60
6526312 AAATATATTA
* * * *
6526322 TTTATTAATATAATATAATATTATTTATTTATTAATATATTATTAATATAATATATTAATAGAT
1 TTTATT-AT-TAATATAATA-TA-TTATTTATTAATATAATATTTATATAATAAATAAATAGAT
* * * *
6526386 TTTTTTATT-A-ACAATTTATTA-TTAAT-ATATAATATATTTATATTAATAAATAAATA-AT
1 TTTATTATTAATATAATATATTATTTATTAATAT-A-ATATTTATA-TAATAAATAAATAGAT
*
6526444 ATTGTATTATTAATATAATATATTATTTATTAATATAATATTTAGATAATAAA
1 -TT-TATTATTAATATAATATATTATTTATTAATATAATATTTATATAATAAA
6526497 ATATTTTTCT
Statistics
Matches: 89, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
56 4 0.04
57 5 0.06
58 12 0.13
59 15 0.17
60 10 0.11
61 9 0.10
62 18 0.20
63 7 0.08
64 9 0.10
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (60 bp):
TTTATTATTAATATAATATATTATTTATTAATATAATATTTATATAATAAATAAATAGAT
Found at i:6526490 original size:105 final size:106
Alignment explanation
Indices: 6526293--6526483 Score: 248
Period size: 105 Copynumber: 1.8 Consensus size: 106
6526283 ATAATATAAT
* * *
6526293 ATTTAATATATAATATTTAAAATATATTATTTATTAATATAATATAATATTATTTATTTATTAAT
1 ATTTAATATATAATATATAAAATATATTATTTAATAATATAATATAATATTATTTATTAATTAAT
*
6526358 ATATTATTAATATAATATATTAATAGATTTTTTTATTAACA
66 ATATTATTAATATAATATAATAATAGATTTTTTTATTAACA
* * *
6526399 ATTTATTAT-TAATATATAATATAT-TTATATTAATAA-ATAA-ATAATATTGTATTATTAATAT
1 ATTTAATATATAATATATAAAATATATTAT-TTAATAATATAATATAATATTAT-TTATTAAT-T
*
6526460 AATATATTATTTAT-TAATATAATA
63 AATATATTATTAATATAATATAATA
6526484 TTTAGATAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
103 9 0.12
104 24 0.32
105 33 0.45
106 8 0.11
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (106 bp):
ATTTAATATATAATATATAAAATATATTATTTAATAATATAATATAATATTATTTATTAATTAAT
ATATTATTAATATAATATAATAATAGATTTTTTTATTAACA
Found at i:6526745 original size:20 final size:20
Alignment explanation
Indices: 6526720--6526769 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
6526710 CAATTTTTAA
* *
6526720 AAAACAAAAAATG-AAAACAT
1 AAAACAAAAAACGAAAAAC-G
6526740 AAAACAAAAAACGAAAAACG
1 AAAACAAAAAACGAAAAACG
6526760 AAAACAAAAA
1 AAAACAAAAA
6526770 CAAACAACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.78, C:0.12, G:0.06, T:0.04
Consensus pattern (20 bp):
AAAACAAAAAACGAAAAACG
Found at i:6526749 original size:27 final size:26
Alignment explanation
Indices: 6526718--6526773 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
6526708 TTCAATTTTT
*
6526718 AAAAAACAAAAAATGAAAACATAAAAC
1 AAAAAACAAAAAACGAAAACA-AAAAC
*
6526745 AAAAAACGAAAAACGAAAACAAAAAC
1 AAAAAACAAAAAACGAAAACAAAAAC
6526771 AAA
1 AAA
6526774 CAACCCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.79, C:0.12, G:0.05, T:0.04
Consensus pattern (26 bp):
AAAAAACAAAAAACGAAAACAAAAAC
Found at i:6527416 original size:7 final size:7
Alignment explanation
Indices: 6527404--6527429 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6527394 TAAATGAATT
6527404 TGAAAAA
1 TGAAAAA
6527411 TGAAAAA
1 TGAAAAA
6527418 TGAAAAA
1 TGAAAAA
6527425 TGAAA
1 TGAAA
6527430 TCGCCATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
TGAAAAA
Found at i:6531923 original size:161 final size:159
Alignment explanation
Indices: 6531584--6531932 Score: 407
Period size: 161 Copynumber: 2.2 Consensus size: 159
6531574 ATCTAAAAGT
* * * *
6531584 TTAATTTGTATTTTTGCCTTTAAAAGGCAAAAATAGTCCTAAATAGACGTAAACGATAACTTTTT
1 TTAATTTGTATTTTTACCTTT-AACGGCAAAAATAATCCTAAATAGACGTAAACAATAACTTTTT
* *
6531649 CACACATATCAACCGTAGAAACTAAGTTCAATTATTCAAACAAGTTTAATATTATATATTGAAGC
65 CACACATATCAACCGTAGAAACTAAGTTCAATTATTCAAACAAGTTTAATATCATATATTGAAAC
* *
6531714 TATCAAAATAGTTAAAATAGAATAATAACA
130 TATCAAAATAGTTAAAACAGAACAATAACA
** * *
6531744 ACAATTTTGTACTTTTACCTATTAACGGCACAAAA-AATCCTAAATAGATGTAAACAATAACTTT
1 TTAA-TTTGTATTTTTACCT-TTAACGGCA-AAAATAATCCTAAATAGACGTAAACAATAACTTT
* * * * *** * *
6531808 TTCATATATATCAATCGTGGAAACTAAGTTCAA-TACTTTGGATAAGTTTAATATCATGTATTGA
63 TTCACACATATCAACCGTAGAAACTAAGTTCAATTA-TTCAAACAAGTTTAATATCATATATTGA
*
6531872 AACTATCAAAACTA-TTAAAACAGAACAATAACTG
127 AACTATCAAAA-TAGTTAAAACAGAACAATAAC-A
6531906 TTAATTTGTATTTTTACCTTTTAACGG
1 TTAATTTGTATTTTTACC-TTTAACGG
6531933 GATAAAAAGT
Statistics
Matches: 157, Mismatches: 25, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
160 4 0.03
161 142 0.90
162 11 0.07
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.35
Consensus pattern (159 bp):
TTAATTTGTATTTTTACCTTTAACGGCAAAAATAATCCTAAATAGACGTAAACAATAACTTTTTC
ACACATATCAACCGTAGAAACTAAGTTCAATTATTCAAACAAGTTTAATATCATATATTGAAACT
ATCAAAATAGTTAAAACAGAACAATAACA
Found at i:6536083 original size:17 final size:18
Alignment explanation
Indices: 6536061--6536101 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
6536051 AATTTATGAA
*
6536061 TTTATTTTG-CAAAGATT
1 TTTATTTTGAAAAAGATT
6536078 TTTA-TTTGAAAAAGATT
1 TTTATTTTGAAAAAGATT
6536095 TTT-TTTT
1 TTTATTTT
6536102 ATTGAAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (18 bp):
TTTATTTTGAAAAAGATT
Found at i:6536113 original size:19 final size:21
Alignment explanation
Indices: 6536076--6536119 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
6536066 TTTGCAAAGA
6536076 TTTTTATTTGAAAAAGATTTT
1 TTTTTATTTGAAAAAGATTTT
*
6536097 TTTTTA-TTG-AAAGGATTTT
1 TTTTTATTTGAAAAAGATTTT
6536116 TTTT
1 TTTT
6536120 GTTTTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.59
20 3 0.14
21 6 0.27
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.61
Consensus pattern (21 bp):
TTTTTATTTGAAAAAGATTTT
Found at i:6536310 original size:18 final size:19
Alignment explanation
Indices: 6536240--6536322 Score: 69
Period size: 21 Copynumber: 4.2 Consensus size: 19
6536230 TAAATTTCTC
* *
6536240 AAAAATAAAACCAAAAAACTA
1 AAAAATAAAATCAAAAAA--G
* *
6536261 AAAAATAAAATGAATTAAAG
1 AAAAATAAAATCAA-AAAAG
6536281 ATAAAATAAAATCAAAAAAG
1 A-AAAATAAAATCAAAAAAG
**
6536301 AAAAAT-AAATGGAAAAAG
1 AAAAATAAAATCAAAAAAG
6536319 AAAA
1 AAAA
6536323 CCTTGCGATC
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
18 14 0.27
19 5 0.10
20 6 0.12
21 24 0.46
22 3 0.06
ACGTcount: A:0.75, C:0.05, G:0.07, T:0.13
Consensus pattern (19 bp):
AAAAATAAAATCAAAAAAG
Found at i:6537670 original size:51 final size:51
Alignment explanation
Indices: 6537615--6537726 Score: 143
Period size: 51 Copynumber: 2.2 Consensus size: 51
6537605 TTTACAAAAG
* * *
6537615 TTTTCAAATTCACAAGAATGAAAGATTTGCAAGATGCAAAATTTGTAAGGA
1 TTTTCAAATTCACAAGAAAGAAAGATTCGCAAGATGCAAAATTCGTAAGGA
** ** * *
6537666 TTTTCATGTTCGTAAGAAAGAAAGATTCGCATGATGCAAGATTCGTAAGGA
1 TTTTCAAATTCACAAGAAAGAAAGATTCGCAAGATGCAAAATTCGTAAGGA
6537717 TTTTCAAATT
1 TTTTCAAATT
6537727 TGCAAGACTC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (51 bp):
TTTTCAAATTCACAAGAAAGAAAGATTCGCAAGATGCAAAATTCGTAAGGA
Found at i:6537936 original size:119 final size:119
Alignment explanation
Indices: 6537665--6537937 Score: 386
Period size: 119 Copynumber: 2.3 Consensus size: 119
6537655 ATTTGTAAGG
* * * * * **
6537665 ATTTTCATGTTCGTAAGAAAGAAAGATTCGCATGATGCAAGATTCGTAAGGATTTTCAAATTTGC
1 ATTTTCAAGTTTGTAAGAAAGAAAGATTCGTAAGATGCAAGATTCGTAAGAATTTTCAAATTCAC
** *
6537730 AAGACTCCAAGTTTCATAAAGGTTCTAGATTTGCAAAAATCAAGATTCACAAAG
66 AAGACTCCAAGTTTCATAAAGGTTCTAGATTCACAAAAATCAAGATTCACAAAA
* * *
6537784 ATTTTCAAGTTTGCAAGAAAGAAATATTCGTAAGATGCAAGATTCGTAAGAATTTTTAAATTCAC
1 ATTTTCAAGTTTGTAAGAAAGAAAGATTCGTAAGATGCAAGATTCGTAAGAATTTTCAAATTCAC
*
6537849 AAGACTCCAAGTTTCATAAAGGTTCTAGATTCACAAAGATGCAAGATTCACAAAA
66 AAGACTCCAAGTTTCATAAAGGTTCTAGATTCACAAAAAT-CAAGATTCACAAAA
* *
6537904 ATTTT-TAGTTTGTAAGAAAGAAAGATTTGTAAGA
1 ATTTTCAAGTTTGTAAGAAAGAAAGATTCGTAAGA
6537938 CTCCAAGTTT
Statistics
Matches: 135, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
119 117 0.87
120 18 0.13
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (119 bp):
ATTTTCAAGTTTGTAAGAAAGAAAGATTCGTAAGATGCAAGATTCGTAAGAATTTTCAAATTCAC
AAGACTCCAAGTTTCATAAAGGTTCTAGATTCACAAAAATCAAGATTCACAAAA
Found at i:6539022 original size:11 final size:11
Alignment explanation
Indices: 6538976--6539028 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
6538966 TCATTTGTCT
6538976 TTTTTTTTGTTC
1 TTTTTTTT-TTC
*
6538988 GTTATTTTTTTC
1 -TTTTTTTTTTC
**
6539000 CCTTTTTTTTC
1 TTTTTTTTTTC
6539011 TTTTTTTTTTC
1 TTTTTTTTTTC
6539022 TTTTTTT
1 TTTTTTT
6539029 GTACACCTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 24 0.71
12 3 0.09
13 7 0.21
ACGTcount: A:0.02, C:0.11, G:0.04, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:6543179 original size:22 final size:20
Alignment explanation
Indices: 6543135--6543212 Score: 99
Period size: 19 Copynumber: 3.9 Consensus size: 20
6543125 TAAATTTCTC
*
6543135 AAAAATAAAA-GCAAAAAACT
1 AAAAATAAAATG-AAAAAAAT
6543155 AAAAATAAAATGAATTAAAAAT
1 AAAAATAAAATGAA--AAAAAT
6543177 AAAAATAAAAT-AAAAAAAT
1 AAAAATAAAATGAAAAAAAT
6543196 AAAAA-AAAATGAAAAAA
1 AAAAATAAAATGAAAAAA
6543213 GGAAACCTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
18 5 0.09
19 17 0.32
20 12 0.23
21 3 0.06
22 16 0.30
ACGTcount: A:0.79, C:0.03, G:0.04, T:0.14
Consensus pattern (20 bp):
AAAAATAAAATGAAAAAAAT
Found at i:6543211 original size:11 final size:10
Alignment explanation
Indices: 6543147--6543212 Score: 55
Period size: 11 Copynumber: 6.4 Consensus size: 10
6543137 AAATAAAAGC
*
6543147 AAAAAACTAA
1 AAAAAAATAA
6543157 AAATAAAATGAA
1 AAA-AAAAT-AA
**
6543169 TTAAAAATAA
1 AAAAAAATAA
6543179 AAATAAAAT--
1 AAA-AAAATAA
6543188 AAAAAAATAA
1 AAAAAAATAA
6543198 AAAAAAATGAA
1 AAAAAAAT-AA
6543209 AAAA
1 AAAA
6543213 GGAAACCTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
8 5 0.11
9 3 0.07
10 14 0.31
11 20 0.44
12 3 0.07
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:6543211 original size:36 final size:39
Alignment explanation
Indices: 6543135--6543212 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 39
6543125 TAAATTTCTC
*
6543135 AAAAATAAAAGCAAAAAACTAAAAATAAAATGAATTAAAAAT
1 AAAAATAAAAGCAAAAAAATAAAAATAAAATG-A--AAAAAT
*
6543177 AAAAATAAAA-TAAAAAAATAAAAA-AAAATGAAAAAA
1 AAAAATAAAAGCAAAAAAATAAAAATAAAATGAAAAAA
6543213 GGAAACCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 5 0.15
39 1 0.03
40 6 0.18
41 12 0.35
42 10 0.29
ACGTcount: A:0.79, C:0.03, G:0.04, T:0.14
Consensus pattern (39 bp):
AAAAATAAAAGCAAAAAAATAAAAATAAAATGAAAAAAT
Found at i:6543514 original size:31 final size:31
Alignment explanation
Indices: 6543443--6543518 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
6543433 TGGAAAATCC
* *
6543443 CATCGAAAAATTCATATCTCGTCAAAAAACT
1 CATCAAAAAATTCATATCTCCTCAAAAAACT
* * *
6543474 CATCGAAAAATTCATATCTCACT-AGAAAATT
1 CATCAAAAAATTCATATCTC-CTCAAAAAACT
*
6543505 TATCAAAAAATTCA
1 CATCAAAAAATTCA
6543519 AACATTCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28
Consensus pattern (31 bp):
CATCAAAAAATTCATATCTCCTCAAAAAACT
Found at i:6544038 original size:3 final size:3
Alignment explanation
Indices: 6544030--6544071 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
6544020 ATAAGATTAC
*
6544030 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6544072 CCTATTGACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6547289 original size:63 final size:61
Alignment explanation
Indices: 6547016--6547291 Score: 141
Period size: 62 Copynumber: 4.4 Consensus size: 61
6547006 AAAAAAAATG
* * * * *
6547016 CCTTCAATAATCTTGTCGTAAA-CTTTTAAAGAGA-TTATTGAAGGTGTTTTTTACTACA-AATA
1 CCTTCAATAAT-TT-TCTTAAATTTTTTAAAGAAATTTATTGAAGGTATTTTTT--TGCATAATA
* * ** * *
6547078 CCTTCATTAATTCTT-TCAAAAGTTTTGAAGGAATTTATTGAAGGTA-TTTTTTGCATAATACA
1 CCTTCAATAATT-TTCTTAAATTTTTTAAAGAAATTTATTGAAGGTATTTTTTTGCATAAT--A
* ** * * * ** ** *
6547140 CCTTCAATAA-TCTCTTCTATTTTTATCAGGAGAATATTAGTGAATGCAATTTTTTACCAAAAAT
1 CCTTCAATAATTTTCTTAAATTTTT-TAAAGA-AAT-TTATTGAA-GGTATTTTTTTGC-ATAAT
6547204 A
61 A
* *** *
6547205 CATTCAATAATCCACTCAAATTTTTTAAAGAAATTTATTGAAGGTATTTTTTTGCATAATA
1 CCTTCAATAATTTTCTTAAATTTTTTAAAGAAATTTATTGAAGGTATTTTTTTGCATAATA
6547266 CGCCTTCAATAATTTTCTTAAATTTT
1 --CCTTCAATAATTTTCTTAAATTTT
6547292 AATGAGGAGA
Statistics
Matches: 154, Mismatches: 44, Indels: 31
0.67 0.19 0.14
Matches are distributed among these distances:
59 3 0.02
60 7 0.05
61 26 0.17
62 44 0.29
63 29 0.19
64 10 0.06
65 16 0.10
66 15 0.10
67 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (61 bp):
CCTTCAATAATTTTCTTAAATTTTTTAAAGAAATTTATTGAAGGTATTTTTTTGCATAATA
Found at i:6547435 original size:62 final size:62
Alignment explanation
Indices: 6547365--6547529 Score: 224
Period size: 62 Copynumber: 2.7 Consensus size: 62
6547355 TTTTAAAGGA
* * ** * * *
6547365 AATTATTGAAGGTATTTTTTTTATAAAATGCATTT-AATAATCGTCGTAATATTTTTTGATAG
1 AATTATTGAAGGTGTTTTCTAAAAAAAATGC-TTTCAATAATCCTCGTAATATTTTTGGATAG
* **
6547427 AATTATTGAATGTGTTTTCTAAAAAAAATGCTTTCAATAATCCTTTTAATATTTTTGGATAG
1 AATTATTGAAGGTGTTTTCTAAAAAAAATGCTTTCAATAATCCTCGTAATATTTTTGGATAG
6547489 AATTATTGAAGGTGTTTTCTAAAAAAAATGCTTTCAATAAT
1 AATTATTGAAGGTGTTTTCTAAAAAAAATGCTTTCAATAAT
6547530 TTCCTTTAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
61 3 0.03
62 88 0.97
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (62 bp):
AATTATTGAAGGTGTTTTCTAAAAAAAATGCTTTCAATAATCCTCGTAATATTTTTGGATAG
Found at i:6548076 original size:28 final size:28
Alignment explanation
Indices: 6548030--6548091 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
6548020 TGGTTTGCTT
* ***
6548030 AATGGTATTGTATGATATTTTTTTACTG
1 AATGGTATCGTATGATATTGGCTTACTG
* *
6548058 AATGGTATCGTTTGGTATTGGCTTACTG
1 AATGGTATCGTATGATATTGGCTTACTG
6548086 AATGGT
1 AATGGT
6548092 TTACTAAATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.23, C:0.06, G:0.24, T:0.47
Consensus pattern (28 bp):
AATGGTATCGTATGATATTGGCTTACTG
Found at i:6552590 original size:19 final size:18
Alignment explanation
Indices: 6552565--6552609 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
6552555 ACTTTTTTCT
6552565 TTTTTTTTTCAGCAATTT-
1 TTTTTTTTT-AGCAATTTA
*
6552583 TCTTTTTTTTAGCCATTTA
1 T-TTTTTTTTAGCAATTTA
6552602 TTTTTTTT
1 TTTTTTTT
6552610 ATCACATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.13, C:0.11, G:0.04, T:0.71
Consensus pattern (18 bp):
TTTTTTTTTAGCAATTTA
Found at i:6552605 original size:17 final size:18
Alignment explanation
Indices: 6552566--6552610 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
6552556 CTTTTTTCTT
*
6552566 TTTTTTTTCAGCAATTTTC
1 TTTTTTTT-AGCAATTTTA
*
6552585 TTTTTTTTAGCCA-TTTA
1 TTTTTTTTAGCAATTTTA
6552602 TTTTTTTTA
1 TTTTTTTTA
6552611 TCACATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.50
18 4 0.17
19 8 0.33
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.69
Consensus pattern (18 bp):
TTTTTTTTAGCAATTTTA
Found at i:6553440 original size:141 final size:142
Alignment explanation
Indices: 6553098--6553457 Score: 397
Period size: 145 Copynumber: 2.5 Consensus size: 142
6553088 TTTAAAATAT
* * *
6553098 CAAAAGTTATGAAATATTATAAAATTGAA-ATTTAAAAAGTTTCATAAAAATCCAAGCTTGAAAA
1 CAAAAATTATGAAATATTATAAAA-TAAAGATCTAAAAAGTTTCATAAAAATCCAAGCTTGAAAA
* * * ***
6553162 AGTTAAATTACGAAAATACCTATATAAAGGTATTTTCATAATTTTACATTTTTAAGGGTATTGTT
65 AGTCAAATTACAAAAATACCTATATAAAGGTATTTTCATAATTTCACATTTTTAAGGGTA-TCAA
*
6553227 GTGATTTCAAATGCA
129 CT-ATTTCAAATGCA
* * * * * *
6553242 CAAAAAGTTATGAAATATTATGAAATTAAGATCTGAAAAGTTTCATAAAAATTCAAGCTCGAGAA
1 CAAAAA-TTATGAAATATTATAAAATAAAGATCTAAAAAGTTTCATAAAAATCCAAGCTTGAAAA
* * * * * *
6553307 TGTCAAATTACAAAAATGCCTTTAT-AGGGATATTTTGATAATTTCACACTTTTTGA-GGTA-CA
65 AGTCAAATTACAAAAATACCTATATAAAGG-TATTTTCATAATTTCACA-TTTTTAAGGGTATCA
6553369 ACT-TTTCAAATGCA
128 ACTATTTCAAATGCA
* *
6553383 CCAAAAATTATGAAATATTATAAAATAAAGATCTAAAAAATTTCATGAAAATCCAAGCTTGAAAA
1 -CAAAAATTATGAAATATTATAAAATAAAGATCTAAAAAGTTTCATAAAAATCCAAGCTTGAAAA
*
6553448 GGTCAAATTA
65 AGTCAAATTA
6553458 TGAAAATATC
Statistics
Matches: 181, Mismatches: 30, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
141 70 0.39
142 6 0.03
143 1 0.01
144 11 0.06
145 87 0.48
146 6 0.03
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (142 bp):
CAAAAATTATGAAATATTATAAAATAAAGATCTAAAAAGTTTCATAAAAATCCAAGCTTGAAAAA
GTCAAATTACAAAAATACCTATATAAAGGTATTTTCATAATTTCACATTTTTAAGGGTATCAACT
ATTTCAAATGCA
Found at i:6553489 original size:141 final size:141
Alignment explanation
Indices: 6553098--6553491 Score: 377
Period size: 141 Copynumber: 2.8 Consensus size: 141
6553088 TTTAAAATAT
* * *
6553098 CAAAAGTTATGAAATATTATAAAATTGAA-ATTTAAAAAGTTTCATAAAAATCCAAGCTTGAAAA
1 CAAAAATTATGAAATATTATAAAA-TAAAGATCTAAAAAGTTTCATAAAAATCCAAGCTTGAAAA
* * * **
6553162 AGTTAAATTACGAAAATA-CCTATATAAAGGTATTTTCATAATTTTACATTTTTAAGGGTATTGT
65 AGTCAAATTA-GAAAATATCCTATA-AAAGGTATTTTAATAATTTCACATTTTTAAGGGTA-TCA
**
6553226 TGTGATTTCAAATGCA
127 ACT-ATTTCAAATGCA
* * * * * *
6553242 CAAAAAGTTATGAAATATTATGAAATTAAGATCTGAAAAGTTTCATAAAAATTCAAGCTCGAGAA
1 CAAAAA-TTATGAAATATTATAAAATAAAGATCTAAAAAGTTTCATAAAAATCCAAGCTTGAAAA
* * * * * * *
6553307 TGTCAAATTACAAAA-ATGCCTTTATAGGGATATTTTGATAATTTCACACTTTTTGA-GGTA-CA
65 AGTCAAATTAGAAAATAT-CCTATAAAAGG-TATTTTAATAATTTCACA-TTTTTAAGGGTATCA
6553369 ACT-TTTCAAATGCA
127 ACTATTTCAAATGCA
* *
6553383 CCAAAAATTATGAAATATTATAAAATAAAGATCTAAAAAATTTCATGAAAATCCAAGCTTGAAAA
1 -CAAAAATTATGAAATATTATAAAATAAAGATCTAAAAAGTTTCATAAAAATCCAAGCTTGAAAA
* ** * *
6553448 GGTCAAATTATGAAAATATCCCCTAGAAGGCATTTTAATAATTT
65 AGTCAAATTA-GAAAATATCCTATAAAAGGTATTTTAATAATTT
6553492 TGTACTTTCG
Statistics
Matches: 204, Mismatches: 37, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
141 82 0.40
142 17 0.08
143 4 0.02
144 15 0.07
145 80 0.39
146 6 0.03
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (141 bp):
CAAAAATTATGAAATATTATAAAATAAAGATCTAAAAAGTTTCATAAAAATCCAAGCTTGAAAAA
GTCAAATTAGAAAATATCCTATAAAAGGTATTTTAATAATTTCACATTTTTAAGGGTATCAACTA
TTTCAAATGCA
Found at i:6559311 original size:3 final size:3
Alignment explanation
Indices: 6559305--6559365 Score: 95
Period size: 3 Copynumber: 20.3 Consensus size: 3
6559295 TTGTTGTTTT
*
6559305 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
**
6559353 CCA ATA ATA ATA A
1 ATA ATA ATA ATA A
6559366 AAATGATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:6559903 original size:15 final size:15
Alignment explanation
Indices: 6559853--6559935 Score: 71
Period size: 15 Copynumber: 5.6 Consensus size: 15
6559843 ACCCTAAGTC
*
6559853 AAACCCTAAACCCTTT
1 AAACCCT-AACCCTCT
** *
6559869 AAACCCTAA-AATCG
1 AAACCCTAACCCTCT
6559883 AAACCCTAACCCTCT
1 AAACCCTAACCCTCT
** *
6559898 AAACCCTAAAACT-A
1 AAACCCTAACCCTCT
*
6559912 AAACCCTAACCCTCC
1 AAACCCTAACCCTCT
6559927 AAACCCTAA
1 AAACCCTAA
6559936 AATCAAATCC
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
14 21 0.40
15 24 0.46
16 7 0.13
ACGTcount: A:0.43, C:0.39, G:0.01, T:0.17
Consensus pattern (15 bp):
AAACCCTAACCCTCT
Found at i:6559952 original size:13 final size:13
Alignment explanation
Indices: 6559814--6559950 Score: 69
Period size: 14 Copynumber: 9.8 Consensus size: 13
6559804 CAAATCCTTG
6559814 AAACCCTAAAATC
1 AAACCCTAAAATC
* **
6559827 AAAACCTTAACCTC
1 -AAACCCTAAAATC
*
6559841 AAACCCT-AAGTC
1 AAACCCTAAAATC
* *
6559853 AAACCCTAAACCCTTT
1 AAACCCTAAA---ATC
6559869 AAACCCTAAAATC
1 AAACCCTAAAATC
**
6559882 GAAACCCTAACCCTC
1 -AAACCCTAA-AATC
*
6559897 TAAACCCTAAAACTA
1 -AAACCCTAAAA-TC
**
6559912 AAACCCTAACCCTCC
1 AAACCCTAA-AAT-C
6559927 AAACCCTAAAATC
1 AAACCCTAAAATC
6559940 AAATCCCTAAA
1 AAA-CCCTAAA
6559951 TCCTCCAACC
Statistics
Matches: 92, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
12 10 0.11
13 13 0.14
14 37 0.40
15 21 0.23
16 11 0.12
ACGTcount: A:0.45, C:0.36, G:0.01, T:0.18
Consensus pattern (13 bp):
AAACCCTAAAATC
Found at i:6559976 original size:142 final size:145
Alignment explanation
Indices: 6559713--6559994 Score: 333
Period size: 142 Copynumber: 2.0 Consensus size: 145
6559703 TTTTCTCTAG
* * * * *
6559713 ACCCTAAATCCTTAAAACCCAAAAATCAAAACCCTAAACCTTTGAAACCCTAAAATTAAAATCTT
1 ACCCTAAACCCTTAAAACCCAAAAATCAAAACCCTAAACCTCTGAAACCCTAAAACTAAAACCCT
* *
6559778 AAACCTCAAACTCCAAAATTAAAACCCAAATCCTTGAAACCCTAAAATCAAAACCTT-AA-CC-T
66 AAACCTCAAACTCCAAAATCAAAACCCAAATCCTTCAAACCCTAAAATCAAAACCTTAAACCCTT
6559840 CAAACCCTAAGTCAA
131 CAAACCCTAAGTCAA
* * * *
6559855 ACCCTAAACCCTTTAAACCCTAAAATCGAAACCCTAACCCTCT-AAACCCTAAAACTAAAACCCT
1 ACCCTAAACCCTTAAAACCCAAAAATCAAAACCCTAAACCTCTGAAACCCTAAAACTAAAACCCT
* * * * ** *
6559919 AACCCTCCAAAC-CCTAAAATCAAATCCCTAAATCC-TCCAACCTTAAAATTGACACCTTAAACC
66 AAACCT-CAAACTCC-AAAATCAAAACCC-AAATCCTTCAAACCCTAAAATCAAAACCTTAAACC
6559982 CTTCAAACCCTAA
128 CTTCAAACCCTAA
6559995 AATTAAAACC
Statistics
Matches: 116, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
141 25 0.22
142 70 0.60
143 8 0.07
144 2 0.02
145 11 0.09
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.20
Consensus pattern (145 bp):
ACCCTAAACCCTTAAAACCCAAAAATCAAAACCCTAAACCTCTGAAACCCTAAAACTAAAACCCT
AAACCTCAAACTCCAAAATCAAAACCCAAATCCTTCAAACCCTAAAATCAAAACCTTAAACCCTT
CAAACCCTAAGTCAA
Found at i:6559998 original size:30 final size:30
Alignment explanation
Indices: 6559713--6560013 Score: 241
Period size: 29 Copynumber: 10.4 Consensus size: 30
6559703 TTTTCTCTAG
* * * *
6559713 ACCCTAAATCCTTAAAACCCAAAAATCAAA
1 ACCCTAAACCCTTCAAACCCTAAAATTAAA
* *
6559743 ACCCTAAACCTTTGAAACCCTAAAATTAAA
1 ACCCTAAACCCTTCAAACCCTAAAATTAAA
* *
6559773 ATCTTAAA-CC-TCAAACTCC-AAAATTAAA
1 ACCCTAAACCCTTCAAAC-CCTAAAATTAAA
* * *
6559801 ACCC-AAATCCTTGAAACCCTAAAATCAAA
1 ACCCTAAACCCTTCAAACCCTAAAATTAAA
* * *
6559830 A-CCTTAA-CC-TCAAACCCT--AAGTCAA
1 ACCCTAAACCCTTCAAACCCTAAAATTAAA
* **
6559855 ACCCTAAACCCTTTAAACCCTAAAATCGAA
1 ACCCTAAACCCTTCAAACCCTAAAATTAAA
*
6559885 ACCCT-AACCC-TCTAAACCCTAAAACTAAA
1 ACCCTAAACCCTTC-AAACCCTAAAATTAAA
* *
6559914 ACCCT-AACCCTCCAAACCCTAAAATCAAA
1 ACCCTAAACCCTTCAAACCCTAAAATTAAA
* * * * * *
6559943 TCCCTAAATCC-TCCAACCTTAAAATTGAC
1 ACCCTAAACCCTTCAAACCCTAAAATTAAA
*
6559972 ACCTTAAACCCTTCAAACCCTAAAATTAAA
1 ACCCTAAACCCTTCAAACCCTAAAATTAAA
*
6560002 ACCTTAAACCCT
1 ACCCTAAACCCT
6560014 AAAATCGAAA
Statistics
Matches: 212, Mismatches: 45, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
25 5 0.02
26 5 0.02
27 13 0.06
28 33 0.16
29 85 0.40
30 71 0.33
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.21
Consensus pattern (30 bp):
ACCCTAAACCCTTCAAACCCTAAAATTAAA
Found at i:6560012 original size:21 final size:22
Alignment explanation
Indices: 6559975--6560018 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
6559965 AATTGACACC
*
6559975 TTAAACCCTTCAAACCCTAAAA
1 TTAAAACCTTCAAACCCTAAAA
6559997 TTAAAACCTT-AAACCCTAAAA
1 TTAAAACCTTCAAACCCTAAAA
6560018 T
1 T
6560019 CGAAACGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (22 bp):
TTAAAACCTTCAAACCCTAAAA
Found at i:6560024 original size:21 final size:21
Alignment explanation
Indices: 6559981--6560033 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
6559971 CACCTTAAAC
*
6559981 CCTTCAAACCCTAAAATTAAAA
1 CCTT-AAACCCTAAAATCAAAA
*
6560003 CCTTAAACCCTAAAATCGAAA
1 CCTTAAACCCTAAAATCAAAA
6560024 CGC-TAAACCC
1 C-CTTAAACCC
6560034 CTTTAAACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.45, C:0.32, G:0.04, T:0.19
Consensus pattern (21 bp):
CCTTAAACCCTAAAATCAAAA
Found at i:6560124 original size:29 final size:29
Alignment explanation
Indices: 6560091--6560148 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
6560081 TTTGAAACCC
6560091 TAAAATCCAAAA-TCTAAAACCCTAAATTT
1 TAAAATCCAAAACT-TAAAACCCTAAATTT
*
6560120 TAAAATTCAAAACTTAAAACCCTAAATTT
1 TAAAATCCAAAACTTAAAACCCTAAATTT
6560149 GGTACACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 26 0.96
30 1 0.04
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (29 bp):
TAAAATCCAAAACTTAAAACCCTAAATTT
Found at i:6566116 original size:2 final size:2
Alignment explanation
Indices: 6566109--6566135 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6566099 TTTCTCCGTT
6566109 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
6566136 TGCTTTTTAG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6571941 original size:22 final size:22
Alignment explanation
Indices: 6571889--6571943 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
6571879 TCCTTTCCCT
**
6571889 TTTTTTTTTTTTTAATTTTTGA
1 TTTTTTTTTTTGGAATTTTTGA
** * *
6571911 TTTGGTTTTTTGGGATTTTTGC
1 TTTTTTTTTTTGGAATTTTTGA
6571933 TTTTTTTTTTT
1 TTTTTTTTTTT
6571944 TTGGGGGGGG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.07, C:0.02, G:0.13, T:0.78
Consensus pattern (22 bp):
TTTTTTTTTTTGGAATTTTTGA
Found at i:6573175 original size:21 final size:20
Alignment explanation
Indices: 6573125--6573179 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 20
6573115 CCTTAATTTA
*
6573125 ATAAAAAATTACATTTATAT
1 ATAAAAAATTAAATTTATAT
*
6573145 ATAATTAAATTATAATTTAT-T
1 ATAA-AAAATTA-AATTTATAT
6573166 ATTAAAAAA-TAAAT
1 A-TAAAAAATTAAAT
6573180 ACACATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 3 0.10
20 6 0.21
21 11 0.38
22 9 0.31
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAAAATTAAATTTATAT
Found at i:6575444 original size:18 final size:18
Alignment explanation
Indices: 6575387--6575457 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
6575377 GTATATTTAT
* **
6575387 GATACATTTGTGGTGGGG
1 GATACATTTGAGGTGGAA
*
6575405 GATACATTTGTA-GT-AAA
1 GATACATTTG-AGGTGGAA
6575422 TGATACATTTGAGGTGGAA
1 -GATACATTTGAGGTGGAA
* *
6575441 GATATATTTGAGATGGA
1 GATACATTTGAGGTGGA
6575458 TAATAATCAT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
17 1 0.02
18 39 0.93
19 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (18 bp):
GATACATTTGAGGTGGAA
Found at i:6575824 original size:3 final size:3
Alignment explanation
Indices: 6575805--6575855 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
6575795 AATTTGCACT
* *
6575805 ATC ACC ATC ACC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
6575853 ATC
1 ATC
6575856 TGGACTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.29
Consensus pattern (3 bp):
ATC
Found at i:6577084 original size:58 final size:59
Alignment explanation
Indices: 6577016--6577127 Score: 181
Period size: 58 Copynumber: 1.9 Consensus size: 59
6577006 TGGTTTTGTA
6577016 CAAGAAAAATTGATACTTTCAACTTTTCTTCGAAAAT-AATTTTTAGAAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCTTCGAAAATGAATTTTTAGAAAACTTATTTT
* * **
6577074 CAAGAAAAATTGATACTTTCAACTTTTTTTTGAAAATGTTTTTTTAGAAAACTT
1 CAAGAAAAATTGATACTTTCAACTTTTCTTCGAAAATGAATTTTTAGAAAACTT
6577128 CTTCAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 35 0.71
59 14 0.29
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (59 bp):
CAAGAAAAATTGATACTTTCAACTTTTCTTCGAAAATGAATTTTTAGAAAACTTATTTT
Found at i:6577238 original size:5 final size:5
Alignment explanation
Indices: 6577228--6577252 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6577218 AAAGAAAATC
6577228 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
6577253 GAAATACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:6577300 original size:4 final size:4
Alignment explanation
Indices: 6577280--6577327 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
6577270 TAATCTAATC
6577280 AATA AAT- AAT- AAT- AATA AATA AATA AATA AATAA AATA AA-A AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AAT-A AATA AATA AATA
6577325 AAT
1 AAT
6577328 GAAAAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
3 12 0.29
4 25 0.61
5 4 0.10
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:6577300 original size:17 final size:18
Alignment explanation
Indices: 6577275--6577327 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 18
6577265 AATTCTAATC
6577275 TAATCAATAAAT-AAT-AA
1 TAAT-AATAAATAAATAAA
6577292 TAATAAATAAATAAATAAA
1 TAAT-AATAAATAAATAAA
6577311 TAA-AATAAA-AAATAAA
1 TAATAATAAATAAATAAA
6577327 T
1 T
6577328 GAAAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 8 0.24
17 17 0.52
18 3 0.09
19 5 0.15
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
TAATAATAAATAAATAAA
Found at i:6577332 original size:12 final size:11
Alignment explanation
Indices: 6577280--6577334 Score: 58
Period size: 12 Copynumber: 4.8 Consensus size: 11
6577270 TAATCTAATC
*
6577280 AATAAATAAT-
1 AATAAAAAATA
*
6577290 AATAATAAATA
1 AATAAAAAATA
6577301 AATAAATAAATAA
1 AATAAA-AAAT-A
6577314 AATAAAAAATA
1 AATAAAAAATA
6577325 AATGAAAAAA
1 AAT-AAAAAA
6577335 AAAACCTTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 8 0.21
11 9 0.24
12 14 0.37
13 7 0.18
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (11 bp):
AATAAAAAATA
Done.