Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12
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: 24583705
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1509421 characters in sequence are not A, C, G, or T
File 21 of 75
Found at i:5997445 original size:57 final size:58
Alignment explanation
Indices: 5997375--5997492 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 58
5997365 TAGGCCTTGG
* *** *
5997375 TGTAGGAACAATTATCAAGTTCAGGGGGTAACTCG-TAAAAAAAGGTTCAAGCTCCAA
1 TGTAGGAAAAATTATCAAGTTCAGGACCTAACTCGAAAAAAAAAGGTTCAAGCTCCAA
* *
5997432 TGTAGGAAAAATTATCAAGTTCAGGACCTAACTTGAAAAAAAAAGGTTCAGGCTCCAA
1 TGTAGGAAAAATTATCAAGTTCAGGACCTAACTCGAAAAAAAAAGGTTCAAGCTCCAA
5997490 TGT
1 TGT
5997493 GAAAAAGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 30 0.57
58 23 0.43
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (58 bp):
TGTAGGAAAAATTATCAAGTTCAGGACCTAACTCGAAAAAAAAAGGTTCAAGCTCCAA
Found at i:6004887 original size:35 final size:35
Alignment explanation
Indices: 6004843--6004912 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
6004833 TTCGATGAAG
* *
6004843 TGCAAGTGATAAGCACATATATGCATTTAGATATA
1 TGCAAGTGATAAACACATATATACATTTAGATATA
* * *
6004878 TGCAGGTGATAAATACATATATACATTTAGTTATA
1 TGCAAGTGATAAACACATATATACATTTAGATATA
6004913 ATAAGTGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (35 bp):
TGCAAGTGATAAACACATATATACATTTAGATATA
Found at i:6014020 original size:40 final size:40
Alignment explanation
Indices: 6013975--6014052 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
6013965 TTTTCAAATT
*
6013975 CACTTTCGATTCAAT-CACAATTCA-ATTCAATTTCACTTTC
1 CACTTTCGAATCAATACACAATTCAGA-T-AATTTCACTTTC
**
6014015 CACTTTTTAATCAATACACAATTCAGATAATTTCACTT
1 CACTTTCGAATCAATACACAATTCAGATAATTTCACTT
6014053 CGATTCAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 22 0.67
41 10 0.30
42 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (40 bp):
CACTTTCGAATCAATACACAATTCAGATAATTTCACTTTC
Found at i:6016098 original size:25 final size:25
Alignment explanation
Indices: 6016061--6016202 Score: 112
Period size: 25 Copynumber: 5.7 Consensus size: 25
6016051 TAAATAATAC
*
6016061 GCCATAAAGGCTTTTCACAAGATTA
1 GCCACAAAGGCTTTTCACAAGATTA
* * *
6016086 ACCACAAAAGC-TTTC-CAAGTAATA
1 GCCACAAAGGCTTTTCACAAG-ATTA
**
6016110 CGCCACAAAGGCTTTTCACGGGATTA
1 -GCCACAAAGGCTTTTCACAAGATTA
* * * *
6016136 ACCACAAAAGATTTTCAGATA-A-TA
1 GCCACAAAGGCTTTTCACA-AGATTA
* *
6016160 CGCCACAAAGGCTTTTTATAAGATTA
1 -GCCACAAAGGCTTTTCACAAGATTA
6016186 GCCACAAAGGCTTTTCA
1 GCCACAAAGGCTTTTCA
6016203 GAGAATTCTC
Statistics
Matches: 88, Mismatches: 21, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
23 4 0.05
24 10 0.11
25 63 0.72
26 9 0.10
27 2 0.02
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (25 bp):
GCCACAAAGGCTTTTCACAAGATTA
Found at i:6016201 original size:50 final size:50
Alignment explanation
Indices: 6016054--6016204 Score: 205
Period size: 50 Copynumber: 3.0 Consensus size: 50
6016044 GTCTTTCTAA
* *
6016054 ATAATACGCCATAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTCCA-
1 ATAATACGCCACAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTTCAG
** *
6016103 AGTAATACGCCACAAAGGCTTTTCACGGGATTAACCACAAAAGATTTTCAG
1 A-TAATACGCCACAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTTCAG
* * * *
6016154 ATAATACGCCACAAAGGCTTTTTATAAGATTAGCCACAAAGGCTTTTCAG
1 ATAATACGCCACAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTTCAG
6016204 A
1 A
6016205 GAATTCTCGA
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
49 1 0.01
50 86 0.98
51 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (50 bp):
ATAATACGCCACAAAGGCTTTTCACAAGATTAACCACAAAAGCTTTTCAG
Found at i:6018584 original size:16 final size:16
Alignment explanation
Indices: 6018563--6018593 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6018553 CGCTGTATTA
6018563 GAATAGAGGCGTAATG
1 GAATAGAGGCGTAATG
*
6018579 GAATAGAGGTGTAAT
1 GAATAGAGGCGTAAT
6018594 AGTATTCTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.35, T:0.23
Consensus pattern (16 bp):
GAATAGAGGCGTAATG
Found at i:6018799 original size:16 final size:16
Alignment explanation
Indices: 6018762--6018803 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
6018752 TTAATCATAT
*
6018762 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
6018778 TT-AAATATATTATAA
1 TTAAAATATATTATAA
6018793 TTAAAATATAT
1 TTAAAATATAT
6018804 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:6018810 original size:14 final size:15
Alignment explanation
Indices: 6018771--6018812 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6018761 TTTAAACATA
*
6018771 ATTATTATTAAATAT
1 ATTATAATTAAATAT
6018786 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
6018800 A-TATAATTTAATA
1 ATTATAATTAAATA
6018813 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:6037303 original size:4 final size:4
Alignment explanation
Indices: 6037296--6037329 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
6037286 ATTTATTTAT
*
6037296 ATAA ATAA ATGA ATAA ATAAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA A
6037330 ATTCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:6037339 original size:13 final size:13
Alignment explanation
Indices: 6037296--6037331 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
6037286 ATTTATTTAT
*
6037296 ATAAAT-AAATGA
1 ATAAATAAAATAA
6037308 ATAAATAAAATAA
1 ATAAATAAAATAA
6037321 ATAAATAAAAT
1 ATAAATAAAAT
6037332 TCAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (13 bp):
ATAAATAAAATAA
Found at i:6047004 original size:64 final size:64
Alignment explanation
Indices: 6046900--6047028 Score: 215
Period size: 64 Copynumber: 2.0 Consensus size: 64
6046890 GCAAGAAGCG
6046900 TAAGACTATTGCAGGGGTTGTGCACGTCAGTTCTGTGAGTGAGAAAGAAGGAATAATGAACAAT
1 TAAGACTATTGCAGGGGTTGTGCACGTCAGTTCTGTGAGTGAGAAAGAAGGAATAATGAACAAT
* * *
6046964 TAAGACTATTGCAGGGGTTGTGCGCGTCAGTTCT-TCGAGTGAGAAGGAAGGAATAATTAACAAT
1 TAAGACTATTGCAGGGGTTGTGCACGTCAGTTCTGT-GAGTGAGAAAGAAGGAATAATGAACAAT
6047028 T
1 T
6047029 GTAGCTATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
63 1 0.02
64 60 0.98
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (64 bp):
TAAGACTATTGCAGGGGTTGTGCACGTCAGTTCTGTGAGTGAGAAAGAAGGAATAATGAACAAT
Found at i:6048077 original size:140 final size:140
Alignment explanation
Indices: 6047825--6048229 Score: 801
Period size: 140 Copynumber: 2.9 Consensus size: 140
6047815 GGGTAGATAT
6047825 GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
1 GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
*
6047890 GGAAGAACTCTTCAGATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCTTTTG
66 GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCTTTTG
6047955 CTGCGAATGA
131 CTGCGAATGA
6047965 GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
1 GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
6048030 GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCTTTTG
66 GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCTTTTG
6048095 CTGCGAATGA
131 CTGCGAATGA
6048105 GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
1 GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
6048170 GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCC
66 GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCC
6048230 CTTCTAATAA
Statistics
Matches: 264, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 264 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (140 bp):
GGACAAGCTGGGTTTTGAAGTGATTTTTCCTTCTAGCAATGCGTGTGACTCATTTATGTCCACTT
GGAAGAACTCTTCAAATTTTTACTTAGAAGAGGACCTAGTTGGGAATGAGGATGTGGCCCTTTTG
CTGCGAATGA
Found at i:6048591 original size:58 final size:58
Alignment explanation
Indices: 6048496--6048719 Score: 256
Period size: 58 Copynumber: 3.9 Consensus size: 58
6048486 TGTTAGCTGA
* *
6048496 GGATATGAATCTGTGAGCTATTTTATACTTGTAAAAATTTTGAAAGATAATCAACTGG
1 GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCAACTGG
* *
6048554 GGATGTGAATCCGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCAATTGG
1 GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCAACTGG
* * ** * * * *
6048612 GGATGTGAATTTGAGAAATGTTTTATACTTGTGAAAACTTTGAAACATAA-CATATCT-A
1 GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCA-A-CTGG
* * * *
6048670 AGAGTTTGAATCTGCGAGCTGTTTTATACTTGTGAAAATTTTGAAA-ATAA
1 GGA-TGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAA
6048720 CATAGCTGAG
Statistics
Matches: 142, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
57 2 0.01
58 103 0.73
59 37 0.26
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (58 bp):
GGATGTGAATCTGTGAGCTATTTTATACTTGTGAAAATTTTGAAAGATAATCAACTGG
Found at i:6049058 original size:69 final size:69
Alignment explanation
Indices: 6048782--6049067 Score: 236
Period size: 69 Copynumber: 4.1 Consensus size: 69
6048772 ATCCTGCCAA
* ** * * *
6048782 CCTTAGTATGACAGTTGGGAGTTTTACTCTCTTTAATTGTGTTAGAGGTTGCGACTCTTTGCCTA
1 CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAGAGGCTGCGACTCTTCGCCTA
6048847 CGAG
66 CGAG
* * * * * * * *
6048851 CCTAAATATGATAGTTGGGAGTTTTACTCTCATTAACTGTGTTAGAGTCTGCTG-CCCTTCGCAT
1 CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAGAGGCTGC-GACTCTTCGCCT
*
6048915 GCGAG
65 ACGAG
* * * * * ** * * * * * *
6048920 CCTCAATATTACAGCTGGGAGCTCTGTTCTCGCCAACTGTGTTGGAGGTTGCGACTTTTCACCTA
1 CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAGAGGCTGCGACTCTTCGCCTA
6048985 CGAG
66 CGAG
* * *
6048989 CCTTAGTATGACAGTTGGGAGCTTTGCTCTCACTAACTGT-TTTGAAGGCTGCGGCTCTTCG-CT
1 CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAG-AGGCTGCGACTCTTCGCCT
*
6049052 CGCGAG
65 -ACGAG
6049058 CCTTAGTATG
1 CCTTAGTATG
6049068 GCATAAATGT
Statistics
Matches: 169, Mismatches: 44, Indels: 8
0.76 0.20 0.04
Matches are distributed among these distances:
68 6 0.04
69 162 0.96
70 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (69 bp):
CCTTAGTATGACAGTTGGGAGCTTTACTCTCACTAACTGTGTTAGAGGCTGCGACTCTTCGCCTA
CGAG
Found at i:6058744 original size:5 final size:5
Alignment explanation
Indices: 6058734--6058762 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
6058724 GATAATGCAT
6058734 GAGAA GAGAA GAGAA GAGAA GAGAA GAGA
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGA
6058763 GCAGACTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:6060906 original size:2 final size:2
Alignment explanation
Indices: 6060899--6060930 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
6060889 GAGTTTCTAT
6060899 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
6060931 AAAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:6061999 original size:2 final size:2
Alignment explanation
Indices: 6061992--6062035 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
6061982 AAGCTACCCC
* *
6061992 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6062034 AT
1 AT
6062036 GAAATAAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6064836 original size:17 final size:17
Alignment explanation
Indices: 6064800--6064841 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
6064790 GTAAAGTATG
*
6064800 ATAAAAGAAAAGGGAAA
1 ATAAAAGAAAAGAGAAA
6064817 ATAAAAGAAAA-AGAATA
1 ATAAAAGAAAAGAGAA-A
6064834 ATATAAAG
1 ATA-AAAG
6064842 GGAAGAGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 15 0.68
18 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (17 bp):
ATAAAAGAAAAGAGAAA
Found at i:6067093 original size:19 final size:22
Alignment explanation
Indices: 6067047--6067095 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
6067037 AAAAAGAACT
6067047 TATTTTCTGTTGACTTGTAAGTC
1 TATTTTCTGTTGAC-TGTAAGTC
6067070 T-TTTTCTGTTGA-T-TAAG-C
1 TATTTTCTGTTGACTGTAAGTC
6067088 TATTTTCT
1 TATTTTCT
6067096 ATGAAGCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.08
19 10 0.40
20 1 0.04
22 11 0.44
23 1 0.04
ACGTcount: A:0.16, C:0.12, G:0.14, T:0.57
Consensus pattern (22 bp):
TATTTTCTGTTGACTGTAAGTC
Found at i:6067671 original size:23 final size:23
Alignment explanation
Indices: 6067645--6067692 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
6067635 ACCAATATAT
*
6067645 AAATCAAATC-TCTTAAGATTACA
1 AAATCAAATCTTC-TAAAATTACA
6067668 AAATCAAATCTTCTAAAATTACA
1 AAATCAAATCTTCTAAAATTACA
6067691 AA
1 AA
6067693 TCTTCCAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (23 bp):
AAATCAAATCTTCTAAAATTACA
Found at i:6069012 original size:25 final size:24
Alignment explanation
Indices: 6068969--6069021 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
6068959 AAGTTCAAGC
*
6068969 GAGCCATATCAGGAAGCTCATTAA
1 GAGCCATATCAGGAAGCTCATAAA
* *
6068993 GAGCCTATATCGGGACGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCATAAA
6069018 GAGC
1 GAGC
6069022 TATGGTATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.19
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCATAAA
Found at i:6069107 original size:64 final size:64
Alignment explanation
Indices: 6069006--6069158 Score: 234
Period size: 64 Copynumber: 2.4 Consensus size: 64
6068996 CCTATATCGG
* * * *
6069006 GACGCTCATAAAGAGCTATGGTATGTCCACATTATATGCAAGATCCATACCAATCATATAACAA
1 GACGCTCACAAAGAGCTGTAGTATGTCCACATCATATGCAAGATCCATACCAATCATATAACAA
* * *
6069070 GACGCTCACAAAGAGCTGCAGTATGTCCACATCATATGCAAGATTCATACCAATCATATAACAG
1 GACGCTCACAAAGAGCTGTAGTATGTCCACATCATATGCAAGATCCATACCAATCATATAACAA
*
6069134 GATGCTCACAAAGAGCTGTAGTATG
1 GACGCTCACAAAGAGCTGTAGTATG
6069159 ATCGCAACAC
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (64 bp):
GACGCTCACAAAGAGCTGTAGTATGTCCACATCATATGCAAGATCCATACCAATCATATAACAA
Found at i:6078736 original size:19 final size:19
Alignment explanation
Indices: 6078712--6078751 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
6078702 CCGTTAGTTA
6078712 ATGTTAGTTAAGTCTGTTG
1 ATGTTAGTTAAGTCTGTTG
6078731 ATGTTAGTTAAGTCTGTTG
1 ATGTTAGTTAAGTCTGTTG
6078750 AT
1 AT
6078752 TTGGATTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (19 bp):
ATGTTAGTTAAGTCTGTTG
Found at i:6083206 original size:19 final size:19
Alignment explanation
Indices: 6083182--6083220 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6083172 TCGTTAGTTA
6083182 ATGTTAGTTAAGTCTGTTG
1 ATGTTAGTTAAGTCTGTTG
6083201 ATGTTAGTTAAGTCTGTTG
1 ATGTTAGTTAAGTCTGTTG
6083220 A
1 A
6083221 CTTGGATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.46
Consensus pattern (19 bp):
ATGTTAGTTAAGTCTGTTG
Found at i:6084862 original size:24 final size:24
Alignment explanation
Indices: 6084826--6084888 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
6084816 TGGTATAGGA
* * *
6084826 GTCAAAAATTGTATTTGCAGAAAT
1 GTCACAAACTGTATTTACAGAAAT
6084850 GT-AGCAAACTGTATTTACAGAAAT
1 GTCA-CAAACTGTATTTACAGAAAT
*
6084874 GTCACAAATTGTATT
1 GTCACAAACTGTATT
6084889 CTAGAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 1 0.03
24 31 0.94
25 1 0.03
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (24 bp):
GTCACAAACTGTATTTACAGAAAT
Found at i:6085075 original size:54 final size:54
Alignment explanation
Indices: 6085009--6085378 Score: 372
Period size: 54 Copynumber: 6.9 Consensus size: 54
6084999 GTAGTCCTTA
* * ** *
6085009 AGATTC-TAAAAATCTTGTATGTAGAAGGTCGTGATCGTAAATCAGTGGACCATG
1 AGATTCGT-AAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCAGACCGTG
* * *
6085063 AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAACTTAACAGACCGTG
1 AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCAGACCGTG
** ** * * * *
6085117 AGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAATCAGTAGACCGTG
1 AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCAGACCGTG
* * * *
6085171 AGATTTGTAAAATCTCGAAAGTAAAAGGTCGTGATCATAAATC-G-ACGAACCGTG
1 AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCA-G-ACCGTG
* * * * * *
6085225 AGATTTGTAAAATCTCGAAAATAGAAGGTC-TGATCATAAATCAACAGACTGTG
1 AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCAGACCGTG
* * * **
6085278 AGATTCGTAAAATCTTAAAAATAGAAGGTCGTGATTGTAAATCAGCAGACCAAG
1 AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCAGACCGTG
* *
6085332 AAATTCGTAAAAT-TTCAAAAGTAGAAGGTCGTGATCGTAAATCAGCA
1 AGATTCGTAAAATCTT-GAAAGTAGAAGGTCGTGATCGTAAATCAGCA
6085379 TAACAACCCA
Statistics
Matches: 267, Mismatches: 42, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
52 1 0.00
53 48 0.18
54 216 0.81
55 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (54 bp):
AGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGATCGTAAATCAGCAGACCGTG
Found at i:6085199 original size:108 final size:108
Alignment explanation
Indices: 6085030--6085376 Score: 419
Period size: 108 Copynumber: 3.2 Consensus size: 108
6085020 ATCTTGTATG
* *
6085030 TAGAAGGTCGTGATCGTAAATCAGTGGACCATGAGATTCGTAAAATCTTGAAAGTAGAAGGTCGT
1 TAGAAGGTCGTGATCGTAAATCAGTAGACCGTGAGATTCGTAAAATCTTGAAAGTAGAAGGTCGT
* * **
6085095 GATCGTAACTTAACAGACCGTGAGATTCACAAAATCTCAAAAA
66 GATCGTAAATCAACAGACCGTGAGATTCGTAAAATCTCAAAAA
* * * * *
6085138 TAAAAGGTCGTGATTGTAAATCAGTAGACCGTGAGATTTGTAAAATCTCGAAAGTAAAAGGTCGT
1 TAGAAGGTCGTGATCGTAAATCAGTAGACCGTGAGATTCGTAAAATCTTGAAAGTAGAAGGTCGT
* * * *
6085203 GATCATAAATCGAC-GAACCGTGAGATTTGTAAAATCTCGAAAA
66 GATCGTAAATCAACAG-ACCGTGAGATTCGTAAAATCTCAAAAA
* ** * * *
6085246 TAGAAGGTC-TGATCATAAATCAACAGACTGTGAGATTCGTAAAATCTTAAAAATAGAAGGTCGT
1 TAGAAGGTCGTGATCGTAAATCAGTAGACCGTGAGATTCGTAAAATCTTGAAAGTAGAAGGTCGT
* * ** * * *
6085310 GATTGTAAATCAGCAGACCAAGAAATTCGTAAAATTTCAAAAG
66 GATCGTAAATCAACAGACCGTGAGATTCGTAAAATCTCAAAAA
6085353 TAGAAGGTCGTGATCGTAAATCAG
1 TAGAAGGTCGTGATCGTAAATCAG
6085377 CATAACAACC
Statistics
Matches: 197, Mismatches: 39, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
107 85 0.43
108 112 0.57
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (108 bp):
TAGAAGGTCGTGATCGTAAATCAGTAGACCGTGAGATTCGTAAAATCTTGAAAGTAGAAGGTCGT
GATCGTAAATCAACAGACCGTGAGATTCGTAAAATCTCAAAAA
Found at i:6085315 original size:161 final size:162
Alignment explanation
Indices: 6085033--6085377 Score: 460
Period size: 161 Copynumber: 2.1 Consensus size: 162
6085023 TTGTATGTAG
* * * *
6085033 AAGGTCGTGATCGTAAATCAGTGGACCATGAGATTCGTAAAATCTTGAAAGTAGAAGGTCGTGAT
1 AAGGTCGTGATCGTAAATCAGCGAACCATGAGATTCGTAAAATCTCGAAAATAGAAGGTCGTGAT
* * * *
6085098 CGTAACTTAACAGACCGTGAGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAATCAGT
66 CATAAATCAACAGACCGTGAGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAATCAGC
** * * *
6085163 AGACCGTGAGATTTGTAAAATCTCGAAAGTAA
131 AGACCAAGAAATTCGTAAAATCTCAAAAGTAA
* * *
6085195 AAGGTCGTGATCATAAATC-GACGAACCGTGAGATTTGTAAAATCTCGAAAATAGAAGGTC-TGA
1 AAGGTCGTGATCGTAAATCAG-CGAACCATGAGATTCGTAAAATCTCGAAAATAGAAGGTCGTGA
* ** * *
6085258 TCATAAATCAACAGACTGTGAGATTCGTAAAATCTTAAAAATAGAAGGTCGTGATTGTAAATCAG
65 TCATAAATCAACAGACCGTGAGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAATCAG
* *
6085323 CAGACCAAGAAATTCGTAAAATTTCAAAAGTAG
130 CAGACCAAGAAATTCGTAAAATCTCAAAAGTAA
6085356 AAGGTCGTGATCGTAAATCAGC
1 AAGGTCGTGATCGTAAATCAGC
6085378 ATAACAACCC
Statistics
Matches: 157, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
161 105 0.67
162 52 0.33
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (162 bp):
AAGGTCGTGATCGTAAATCAGCGAACCATGAGATTCGTAAAATCTCGAAAATAGAAGGTCGTGAT
CATAAATCAACAGACCGTGAGATTCACAAAATCTCAAAAATAAAAGGTCGTGATTGTAAATCAGC
AGACCAAGAAATTCGTAAAATCTCAAAAGTAA
Found at i:6102902 original size:87 final size:87
Alignment explanation
Indices: 6102756--6102934 Score: 313
Period size: 87 Copynumber: 2.1 Consensus size: 87
6102746 GGTGTGAACG
* *
6102756 GTGTGTTTCCGAGGGGTGATCCAAGCAAGTCTTTTATGTTAATTCGTAGGTGTTTATTACGCAAT
1 GTGTGTTTCCGAGGAGTGATCCAAGCAAGTCTTTTATGTTAATTCGTAGGTGTTTATTACCCAAT
6102821 TATGATTTGGGAAATAAAGGCA
66 TATGATTTGGGAAATAAAGGCA
* *
6102843 GTGTGTTTCCGAGGAGTGATCCAAGCAAGTCTTTTATGTTAATTTGTAGGTGTTTATTACCCATT
1 GTGTGTTTCCGAGGAGTGATCCAAGCAAGTCTTTTATGTTAATTCGTAGGTGTTTATTACCCAAT
6102908 TATGATTTGGGAAATAAAGGCA
66 TATGATTTGGGAAATAAAGGCA
*
6102930 ATGTG
1 GTGTG
6102935 GTAGAACTAT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (87 bp):
GTGTGTTTCCGAGGAGTGATCCAAGCAAGTCTTTTATGTTAATTCGTAGGTGTTTATTACCCAAT
TATGATTTGGGAAATAAAGGCA
Found at i:6104644 original size:114 final size:113
Alignment explanation
Indices: 6104465--6104696 Score: 437
Period size: 114 Copynumber: 2.0 Consensus size: 113
6104455 TTTCTCTCTT
*
6104465 TTTCCTTTCTTCTACACGTTGGAAGCATGGGACATATGAAGACATATCTTCATATTTCCTTAATA
1 TTTCATTTCTTCTACACGTTGGAAGCATGGGACATATGAAGACATATCTTCATATTTCCTTAATA
6104530 ATTATCTTAATAATAAATAATTTAAATAAAAAAATATTCAACATCATAA
66 ATTATCTTAATAATAAATAATTTAAAT-AAAAAATATTCAACATCATAA
*
6104579 TTTCATTTCTTCTACACGTTGGAAGCATGGGACATATGAAGACATTTCTTCATATTTCCTTAATA
1 TTTCATTTCTTCTACACGTTGGAAGCATGGGACATATGAAGACATATCTTCATATTTCCTTAATA
6104644 ATTATCTTAATAATAAATAATTTAAATAAAAAATATTCAACATCATAA
66 ATTATCTTAATAATAAATAATTTAAATAAAAAATATTCAACATCATAA
6104692 TTTCA
1 TTTCA
6104697 ATGTAAGGGC
Statistics
Matches: 116, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
113 26 0.22
114 90 0.78
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (113 bp):
TTTCATTTCTTCTACACGTTGGAAGCATGGGACATATGAAGACATATCTTCATATTTCCTTAATA
ATTATCTTAATAATAAATAATTTAAATAAAAAATATTCAACATCATAA
Found at i:6105376 original size:17 final size:17
Alignment explanation
Indices: 6105326--6105383 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
6105316 GGGTGAGAAG
*
6105326 TAAAAGTTTAGAGGAAAAA
1 TAAAAGTTT-GAGG-GAAA
*
6105345 TAAAAAGTTT-TGGGAAA
1 T-AAAAGTTTGAGGGAAA
6105362 TAAAAGTTTGAGGGAAA
1 TAAAAGTTTGAGGGAAA
6105379 GTAAA
1 -TAAA
6105384 TAGGGGGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 8 0.24
17 10 0.30
18 6 0.18
19 1 0.03
20 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
TAAAAGTTTGAGGGAAA
Found at i:6105502 original size:30 final size:31
Alignment explanation
Indices: 6105463--6105522 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
6105453 GGAGGTGAGA
*
6105463 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
6105494 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
6105523 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:6105691 original size:21 final size:21
Alignment explanation
Indices: 6105657--6105697 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6105647 GGGGGTAAGT
*
6105657 GGGAATAAGTAAAAGTTTTGA
1 GGGAATAAGTAAAAGGTTTGA
6105678 GGGAA-AAGTAAAAAGGTTTG
1 GGGAATAAGT-AAAAGGTTTG
6105698 GGAGTTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (21 bp):
GGGAATAAGTAAAAGGTTTGA
Found at i:6105749 original size:9 final size:9
Alignment explanation
Indices: 6105735--6105762 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
6105725 TATAGTTTGA
6105735 TATTCGAAT
1 TATTCGAAT
6105744 TATTCGAAT
1 TATTCGAAT
6105753 TATTCGAAT
1 TATTCGAAT
6105762 T
1 T
6105763 CGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:6106017 original size:29 final size:30
Alignment explanation
Indices: 6105953--6106063 Score: 100
Period size: 31 Copynumber: 3.7 Consensus size: 30
6105943 ATATCAAAAT
* * *
6105953 TATACAT-AAACTTTGATTTAATGTGCAGTTG
1 TATACATGAAACTTTAATTT--GGTGCAATTG
*
6105984 TATACATG-AACTTTAATTTGGTGCAATTA
1 TATACATGAAACTTTAATTTGGTGCAATTG
* * * *
6106013 TATACGTGAAACTCTAATTGTGGTTCAAATG
1 TATACATGAAACTTTAATT-TGGTGCAATTG
*
6106044 TATACTTGAAACTTTAATTT
1 TATACATGAAACTTTAATTT
6106064 TGATTTAATC
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
29 14 0.21
30 10 0.15
31 42 0.64
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (30 bp):
TATACATGAAACTTTAATTTGGTGCAATTG
Found at i:6106974 original size:26 final size:26
Alignment explanation
Indices: 6106945--6106994 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
6106935 GTTACGGTAG
*
6106945 ATTTCAACCTATTTTTGTAATTAATA
1 ATTTCAACATATTTTTGTAATTAATA
** *
6106971 ATTTTTATATATTTTTGTAATTAA
1 ATTTCAACATATTTTTGTAATTAA
6106995 CTTTTTGTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (26 bp):
ATTTCAACATATTTTTGTAATTAATA
Found at i:6112097 original size:12 final size:13
Alignment explanation
Indices: 6112067--6112107 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
6112057 CAGAGCCCTA
6112067 AACCATGAACT-TCG
1 AACC-TGAACTCT-G
6112081 AACCTGAAC-CTG
1 AACCTGAACTCTG
6112093 AACCTGAACTCTG
1 AACCTGAACTCTG
6112106 AA
1 AA
6112108 TTCAGGGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 10 0.40
13 11 0.44
14 4 0.16
ACGTcount: A:0.37, C:0.29, G:0.15, T:0.20
Consensus pattern (13 bp):
AACCTGAACTCTG
Found at i:6124605 original size:22 final size:22
Alignment explanation
Indices: 6124580--6124621 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6124570 AATATAATAG
*
6124580 CAAAATGGCAACAAAACAACAT
1 CAAAATGACAACAAAACAACAT
* *
6124602 CAAATTGACAGCAAAACAAC
1 CAAAATGACAACAAAACAAC
6124622 GACAGAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.24, G:0.10, T:0.10
Consensus pattern (22 bp):
CAAAATGACAACAAAACAACAT
Found at i:6129505 original size:22 final size:21
Alignment explanation
Indices: 6129458--6129545 Score: 135
Period size: 22 Copynumber: 4.2 Consensus size: 21
6129448 TGGATTAGTA
*
6129458 TTTTGTATGAATATTCTAATT
1 TTTTGTATGAATATTGTAATT
6129479 TTTTGTATGAATATTGTAATTT
1 TTTTGTATGAATATTGTAA-TT
6129501 TTTTGTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
6129520 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
6129541 ATTTT
1 -TTTT
6129546 ATAATTAATT
Statistics
Matches: 62, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
19 19 0.31
21 18 0.29
22 25 0.40
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.58
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:6129525 original size:19 final size:19
Alignment explanation
Indices: 6129457--6129625 Score: 121
Period size: 19 Copynumber: 8.4 Consensus size: 19
6129447 TTGGATTAGT
*
6129457 ATTTTGTATGAATATTCTA
1 ATTTTGTATGAATATTGTA
6129476 ATTTTTTGTATGAATATTGTA
1 A--TTTTGTATGAATATTGTA
6129497 ATTTTTTTGTATGAATATTGTA
1 A---TTTTGTATGAATATTGTA
6129519 ATTTTGTATGAATATTGTA
1 ATTTTGTATGAATATTGTA
*
6129538 ATTATTTTAT-AATTAATTTCGT-
1 ATT-TTGTATGAA-T-A-TT-GTA
* * *
6129560 ATTTATAGTTTTGGAT-TAGT-
1 ATTT-T-G-TATGAATATTGTA
*
6129580 ATTTTGTATGAATTTTGTA
1 ATTTTGTATGAATATTGTA
*
6129599 ATTTTGTATGAATATTGGA
1 ATTTTGTATGAATATTGTA
*
6129618 ATATTGTA
1 ATTTTGTA
6129626 ATCTTTTGTA
Statistics
Matches: 124, Mismatches: 12, Indels: 28
0.76 0.07 0.17
Matches are distributed among these distances:
17 5 0.04
18 4 0.03
19 49 0.40
20 12 0.10
21 21 0.17
22 27 0.22
23 2 0.02
24 3 0.02
25 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (19 bp):
ATTTTGTATGAATATTGTA
Found at i:6129536 original size:41 final size:42
Alignment explanation
Indices: 6129456--6129545 Score: 146
Period size: 41 Copynumber: 2.1 Consensus size: 42
6129446 TTTGGATTAG
6129456 TATTTTGTATGAATATTCTAATTTTTTGTATGAATATTGTAAT
1 TATTTTGTATGAATATTCTAA-TTTTTGTATGAATATTGTAAT
* *
6129499 TTTTTTGTATGAATATTGTAA-TTTTGTATGAATATTGTAAT
1 TATTTTGTATGAATATTCTAATTTTTGTATGAATATTGTAAT
6129540 TATTTT
1 TATTTT
6129546 ATAATTAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 25 0.57
43 19 0.43
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.58
Consensus pattern (42 bp):
TATTTTGTATGAATATTCTAATTTTTGTATGAATATTGTAAT
Found at i:6129909 original size:15 final size:15
Alignment explanation
Indices: 6129868--6129909 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
6129858 GTTAACTCAT
*
6129868 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
6129883 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
6129899 TTAAATTTTAT
1 TTAAATTTTAT
6129910 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:6130073 original size:72 final size:72
Alignment explanation
Indices: 6129991--6130133 Score: 259
Period size: 72 Copynumber: 2.0 Consensus size: 72
6129981 GCAAATTTGT
6129991 AGGAAATGGGTTCTCTAATTAATAATAATAATCACATATCAAATACTATTAATGAGATGGTAATA
1 AGGAAATGGGTTCTCTAATTAATAATAATAATCACATATCAAATACTATTAATGAGATGGTAATA
6130056 AAATTTC
66 AAATTTC
* * *
6130063 AGGAAATGGGTTTTCTGATTAATAATAATAATCACATATCAAGTACTATTAATGAGATGGTAATA
1 AGGAAATGGGTTCTCTAATTAATAATAATAATCACATATCAAATACTATTAATGAGATGGTAATA
6130128 AAATTT
66 AAATTT
6130134 TTATTTGATA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (72 bp):
AGGAAATGGGTTCTCTAATTAATAATAATAATCACATATCAAATACTATTAATGAGATGGTAATA
AAATTTC
Found at i:6132211 original size:26 final size:26
Alignment explanation
Indices: 6132178--6132229 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6132168 GTAATTAAGT
6132178 ACATATTAATTTCTACCCGATTGAGA
1 ACATATTAATTTCTACCCGATTGAGA
6132204 ACATATTAATTTCTACCCGATTGAGA
1 ACATATTAATTTCTACCCGATTGAGA
6132230 CGATTGTCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (26 bp):
ACATATTAATTTCTACCCGATTGAGA
Found at i:6135253 original size:27 final size:27
Alignment explanation
Indices: 6135223--6135283 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
6135213 TCAACATGAC
*
6135223 ACCACTAATGGCGCCTCTCATATAGGT
1 ACCACTAATGGCGCCTCTCAGATAGGT
* * *
6135250 ACCACCATTGGCGCCTCTGAGATAGGT
1 ACCACTAATGGCGCCTCTCAGATAGGT
*
6135277 GCCACTA
1 ACCACTA
6135284 CTATGTATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (27 bp):
ACCACTAATGGCGCCTCTCAGATAGGT
Found at i:6135360 original size:21 final size:22
Alignment explanation
Indices: 6135317--6135360 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
6135307 CTGACCTAGG
***
6135317 AAAAAAATTAATTATATTTTAT
1 AAAAAAATTAATTATAAAATAT
6135339 AAAAAAATTAA-TATAAAATAT
1 AAAAAAATTAATTATAAAATAT
6135360 A
1 A
6135361 TATTGGCGGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAAAATTAATTATAAAATAT
Found at i:6136302 original size:11 final size:11
Alignment explanation
Indices: 6136286--6136311 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6136276 TTGACCCATA
6136286 TAATCGTTAAC
1 TAATCGTTAAC
6136297 TAATCGTTAAC
1 TAATCGTTAAC
6136308 TAAT
1 TAAT
6136312 GGAAGTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (11 bp):
TAATCGTTAAC
Found at i:6145960 original size:73 final size:73
Alignment explanation
Indices: 6145833--6145980 Score: 242
Period size: 73 Copynumber: 2.0 Consensus size: 73
6145823 CAGAGAATAT
* * *
6145833 TTACTATTCATGCATCTTTTCTTGCAGGGACTATTTACTGTTTACGCCATAGAATATTTCCTGTT
1 TTACTATTCATGCATCTTTTCTTGCAGGGAATATTTACTGCTTACGCCAGAGAATATTTCCTGTT
6145898 CACTTGTC
66 CACTTGTC
* **
6145906 TTACTATTCATGCGTCTTTTCTTGCAGGGAATATTTACTGCTTACGTTAGAGAATATTTCCTGTT
1 TTACTATTCATGCATCTTTTCTTGCAGGGAATATTTACTGCTTACGCCAGAGAATATTTCCTGTT
6145971 CACTTGTC
66 CACTTGTC
6145979 TT
1 TT
6145981 TTCTTGCATC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (73 bp):
TTACTATTCATGCATCTTTTCTTGCAGGGAATATTTACTGCTTACGCCAGAGAATATTTCCTGTT
CACTTGTC
Found at i:6159470 original size:11 final size:11
Alignment explanation
Indices: 6159454--6159480 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6159444 ACTATTGGGG
6159454 TCATTCACTCA
1 TCATTCACTCA
6159465 TCATTCACTCA
1 TCATTCACTCA
6159476 TCATT
1 TCATT
6159481 TCTTCTTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (11 bp):
TCATTCACTCA
Found at i:6163096 original size:19 final size:19
Alignment explanation
Indices: 6163072--6163222 Score: 257
Period size: 19 Copynumber: 7.8 Consensus size: 19
6163062 AATTTTTGAG
6163072 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
6163091 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
6163110 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6163129 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
6163150 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6163169 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
6163188 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6163207 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
6163223 ATATATGATT
Statistics
Matches: 124, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
19 105 0.85
21 19 0.15
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:6163136 original size:59 final size:59
Alignment explanation
Indices: 6163073--6163229 Score: 277
Period size: 59 Copynumber: 2.7 Consensus size: 59
6163063 ATTTTTGAGG
*
6163073 ATATGCAATCTTAGATATGATATGCAATCCTAGATATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
6163132 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
6163191 ATAT--AATCTTAGATATGATATGCAATCTTAGA-AT-ATATG
1 ATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATG
6163230 ATTTTGTAAT
Statistics
Matches: 97, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
55 5 0.05
56 2 0.02
57 28 0.29
59 62 0.64
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (59 bp):
ATATGCAATCTTAGATATGATATGCAATCTTAGATATGATATGCAATCTTAGATATGAT
Found at i:6177842 original size:19 final size:19
Alignment explanation
Indices: 6177793--6177866 Score: 80
Period size: 18 Copynumber: 3.9 Consensus size: 19
6177783 AAAATATAAC
*
6177793 AAAACTAAAGAAAAATCATT
1 AAAACTTAA-AAAAATCATT
*
6177813 AAAA-TTCAAAAAATCATT
1 AAAACTTAAAAAAATCATT
* *
6177831 AAAACTTAAAAAAATTATA
1 AAAACTTAAAAAAATCATT
*
6177850 AAAAC-TAAAAGAATCAT
1 AAAACTTAAAAAAATCAT
6177867 AATCTATATT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 24 0.52
19 18 0.39
20 4 0.09
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAACTTAAAAAAATCATT
Found at i:6177942 original size:18 final size:18
Alignment explanation
Indices: 6177891--6177934 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
6177881 ATTTGTGTGC
* *
6177891 AAAATTTTTTAAAAATTT
1 AAAAATTTTCAAAAATTT
*
6177909 AAAAATTTTCATAAATTT
1 AAAAATTTTCAAAAATTT
*
6177927 TAAAATTT
1 AAAAATTT
6177935 CGAAAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AAAAATTTTCAAAAATTT
Found at i:6178092 original size:18 final size:18
Alignment explanation
Indices: 6178069--6178117 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
6178059 TAAATATAGA
6178069 TTATAATTTTTTTTAGTT
1 TTATAATTTTTTTTAGTT
* *
6178087 TTATAA-TTTTCTAAGTT
1 TTATAATTTTTTTTAGTT
6178104 TTAGT-ATTTTTTTT
1 TTA-TAATTTTTTTT
6178118 TGGGATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.69
Consensus pattern (18 bp):
TTATAATTTTTTTTAGTT
Found at i:6187394 original size:20 final size:19
Alignment explanation
Indices: 6187359--6187397 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
6187349 GTTTATATTC
6187359 TTTACATTCCAGTACACTT
1 TTTACATTCCAGTACACTT
6187378 TTTACCATTACCA-TACACTT
1 TTTA-CATT-CCAGTACACTT
6187398 AATCAGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 11 0.61
21 3 0.17
ACGTcount: A:0.28, C:0.28, G:0.03, T:0.41
Consensus pattern (19 bp):
TTTACATTCCAGTACACTT
Found at i:6193843 original size:50 final size:52
Alignment explanation
Indices: 6193789--6193913 Score: 130
Period size: 50 Copynumber: 2.4 Consensus size: 52
6193779 TTCTGCATTT
* *
6193789 AATAAAGTTATGCATTATGTAACTTCTATGCTAG-TTAAGTATGCATCA-GA
1 AATAAAGTTATGCATTATGTAACTCCCATGCTAGTTTAAGTATGCATCATGA
* ** * * *
6193839 AATAATGACATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCATCATTA
1 AATAAAGTTATGCATTATGTAACTCCCATGCTAGTTTAAGTATGCATCATGA
* *
6193891 AATTAAGTCT-TGCATTAAGTAAC
1 AATAAAGT-TATGCATTATGTAAC
6193914 GCATTTAGTT
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
50 28 0.47
51 13 0.22
52 18 0.31
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (52 bp):
AATAAAGTTATGCATTATGTAACTCCCATGCTAGTTTAAGTATGCATCATGA
Found at i:6196406 original size:21 final size:21
Alignment explanation
Indices: 6196355--6196407 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
6196345 TATATGGCTA
* *
6196355 GGCCATGTGCCTTAGGGACAT
1 GGCCATGTGGCTCAGGGACAT
6196376 GGCCATGTGGCTCAGGGACAT
1 GGCCATGTGGCTCAGGGACAT
*
6196397 GGCCGTGTGGC
1 GGCCATGTGGC
6196408 CAAACTATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.15, C:0.25, G:0.40, T:0.21
Consensus pattern (21 bp):
GGCCATGTGGCTCAGGGACAT
Found at i:6198020 original size:36 final size:35
Alignment explanation
Indices: 6197929--6198087 Score: 103
Period size: 36 Copynumber: 4.6 Consensus size: 35
6197919 TTTTAGATAC
** * *
6197929 AAGACCATGGTTGGACCATGG-AAATGTT-TACAT
1 AAGACCATGGTTGGACCATGGCATTTTTTATACGT
* * * *
6197962 AATACCATAGGCTAGG-CTATGGCATTTTTTTATACGC
1 AAGACCAT-GG-TTGGACCATGGCA-TTTTTTATACGT
***
6197999 AAGACCATGGTTGGACCATGGCA-ACGTT-TACGT
1 AAGACCATGGTTGGACCATGGCATTTTTTATACGT
* * * * *
6198032 AAGACCATAGTTGGGCTATGGCAGTTTTTCAGACGT
1 AAGACCATGGTTGGACCATGGCA-TTTTTTATACGT
6198068 AAGACCATGGTTGGACCATG
1 AAGACCATGGTTGGACCATG
6198088 ACAGTGTATA
Statistics
Matches: 91, Mismatches: 26, Indels: 15
0.69 0.20 0.11
Matches are distributed among these distances:
33 31 0.34
34 9 0.10
35 8 0.09
36 33 0.36
37 10 0.11
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (35 bp):
AAGACCATGGTTGGACCATGGCATTTTTTATACGT
Found at i:6198037 original size:33 final size:33
Alignment explanation
Indices: 6197994--6198087 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 33
6197984 CATTTTTTTA
*
6197994 TACGCAAGACCATGGTTGGACCATGGCAACGTT
1 TACGTAAGACCATGGTTGGACCATGGCAACGTT
* * * ***
6198027 TACGTAAGACCATAGTTGGGCTATGGCAGTTTT
1 TACGTAAGACCATGGTTGGACCATGGCAACGTT
6198060 TCAGACGTAAGACCATGGTTGGACCATG
1 T---ACGTAAGACCATGGTTGGACCATG
6198088 ACAGTGTATA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
33 27 0.56
36 21 0.44
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (33 bp):
TACGTAAGACCATGGTTGGACCATGGCAACGTT
Found at i:6198087 original size:69 final size:70
Alignment explanation
Indices: 6197858--6198087 Score: 318
Period size: 70 Copynumber: 3.3 Consensus size: 70
6197848 TAAAAATGTA
* * *
6197858 CAAGACTATGGTTAGACCATGACAATGTTTACATAAGACCATAGGCTAGGCTATGGCAGTTTTTT
1 CAAGACCATGGTTGGACCATGGCAATGTTTACATAAGACCATAGGCTAGGCTATGGCAGTTTTTT
**
6197923 AGATA
66 AGACG
* * *
6197928 CAAGACCATGGTTGGACCATGGAAATGTTTACATAATACCATAGGCTAGGCTATGGCATTTTTTT
1 CAAGACCATGGTTGGACCATGGCAATGTTTACATAAGACCATAGGCTAGGCTATGGCAGTTTTTT
*
6197993 ATACG
66 AGACG
* * * * *
6197998 CAAGACCATGGTTGGACCATGGCAACGTTTACGTAAGACCATA-GTTGGGCTATGGCAGTTTTTC
1 CAAGACCATGGTTGGACCATGGCAATGTTTACATAAGACCATAGGCTAGGCTATGGCAGTTTTTT
6198062 AGACG
66 AGACG
*
6198067 TAAGACCATGGTTGGACCATG
1 CAAGACCATGGTTGGACCATG
6198088 ACAGTGTATA
Statistics
Matches: 141, Mismatches: 19, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
69 41 0.29
70 100 0.71
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (70 bp):
CAAGACCATGGTTGGACCATGGCAATGTTTACATAAGACCATAGGCTAGGCTATGGCAGTTTTTT
AGACG
Found at i:6198326 original size:28 final size:29
Alignment explanation
Indices: 6198274--6198335 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
6198264 TTACAATGTT
6198274 CATCGAATATAAAAAAGGAAGGTTTCGAC
1 CATCGAATATAAAAAAGGAAGGTTTCGAC
* *
6198303 CATCGATTA-AAAAAAGGATA-GTTTCGAT
1 CATCGAATATAAAAAAGGA-AGGTTTCGAC
6198331 CATCG
1 CATCG
6198336 TTTAGCACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (29 bp):
CATCGAATATAAAAAAGGAAGGTTTCGAC
Found at i:6201591 original size:16 final size:17
Alignment explanation
Indices: 6201570--6201601 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
6201560 TATATAATAA
6201570 AAGAAAGAAA-AGAAAT
1 AAGAAAGAAACAGAAAT
6201586 AAGAAAGAAACAGAAA
1 AAGAAAGAAACAGAAA
6201602 GCTTAAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAACAGAAAT
Found at i:6202540 original size:25 final size:24
Alignment explanation
Indices: 6202512--6202623 Score: 108
Period size: 25 Copynumber: 4.7 Consensus size: 24
6202502 GAACTTTAGC
6202512 GTGCTCTCTGATTATTAGCACGTTA
1 GTGCTCTCTG-TTATTAGCACGTTA
*
6202537 GTGCTCTCTGATTACTAGCACGTTA
1 GTGCTCTCTG-TTATTAGCACGTTA
* * *
6202562 GTGCTATCTG-T-TTAGCGCATCTA
1 GTGCTCTCTGTTATTAGCACGT-TA
*
6202585 -TGCTCTCTG-TA-TAGCACTTTA
1 GTGCTCTCTGTTATTAGCACGTTA
6202606 GTGCTCTCTGTTTATTAG
1 GTGCTCTCTG-TTATTAG
6202624 TGCATAATAA
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.03
22 30 0.41
23 3 0.04
24 2 0.03
25 36 0.49
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (24 bp):
GTGCTCTCTGTTATTAGCACGTTA
Found at i:6207575 original size:16 final size:16
Alignment explanation
Indices: 6207554--6207584 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6207544 TTCACTATTA
*
6207554 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
6207570 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
6207585 ACATACATGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:6212507 original size:18 final size:18
Alignment explanation
Indices: 6212484--6212520 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6212474 GGCGGCCCTA
*
6212484 GTGGATCACGCTTCTTTG
1 GTGGATCAAGCTTCTTTG
*
6212502 GTGGATCAAGTTTCTTTG
1 GTGGATCAAGCTTCTTTG
6212520 G
1 G
6212521 CTTTGATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.16, G:0.30, T:0.41
Consensus pattern (18 bp):
GTGGATCAAGCTTCTTTG
Found at i:6241533 original size:19 final size:20
Alignment explanation
Indices: 6241505--6241556 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
6241495 AAATTTTAAT
6241505 AAAA-TATTTT-AAAATTTG
1 AAAATTATTTTGAAAATTTG
**
6241523 AAAATTATTTTGAATTTTTG
1 AAAATTATTTTGAAAATTTG
6241543 AAAATTATTTTGAA
1 AAAATTATTTTGAA
6241557 TTATTTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 4 0.13
19 6 0.20
20 20 0.67
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (20 bp):
AAAATTATTTTGAAAATTTG
Found at i:6241544 original size:20 final size:20
Alignment explanation
Indices: 6241519--6241558 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6241509 TATTTTAAAA
6241519 TTTGAAAATTATTTTGAATT
1 TTTGAAAATTATTTTGAATT
6241539 TTTGAAAATTATTTTGAATT
1 TTTGAAAATTATTTTGAATT
6241559 ATTTTGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (20 bp):
TTTGAAAATTATTTTGAATT
Found at i:6242285 original size:18 final size:19
Alignment explanation
Indices: 6242258--6242295 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
6242248 TTTTTAAATT
*
6242258 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTGAA
6242276 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTGAA
6242295 T
1 T
6242296 CTTTTTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTAAAAATTATTTTGAA
Found at i:6242865 original size:12 final size:12
Alignment explanation
Indices: 6242850--6242879 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6242840 AATAATTAAA
6242850 TAAATTAGAAAT
1 TAAATTAGAAAT
*
6242862 TAAATTGGAAAT
1 TAAATTAGAAAT
6242874 TAAATT
1 TAAATT
6242880 CAGATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (12 bp):
TAAATTAGAAAT
Found at i:6244146 original size:23 final size:23
Alignment explanation
Indices: 6244117--6244284 Score: 223
Period size: 23 Copynumber: 7.3 Consensus size: 23
6244107 ATAAGTGCCA
*
6244117 CACTGATATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
6244140 CACTGATATGTAGCTGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
6244163 CATTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
6244186 CACTGAAATATAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
6244209 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
6244232 CACTGGA-ATGTAGCCGAAGCTAC
1 CACT-GATATGTAGCCGAAGCTAC
6244255 CACTGGA-ATGTAGCCGAAGCTAC
1 CACT-GATATGTAGCCGAAGCTAC
6244278 CACTGAT
1 CACTGAT
6244285 CAATAACACT
Statistics
Matches: 128, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
22 2 0.02
23 124 0.97
24 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:6244228 original size:69 final size:69
Alignment explanation
Indices: 6244117--6244284 Score: 273
Period size: 69 Copynumber: 2.4 Consensus size: 69
6244107 ATAAGTGCCA
* * *
6244117 CACTGATATGTAGTCGAAGCTACCACTGATATGTAGCTGTAGCTACCATTGAAATGTAGCCGAAG
1 CACTGAAATGTAGTCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAAATGTAGCCGAAG
6244182 CTAC
66 CTAC
* *
6244186 CACTGAAATATAGTCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGGAATGTAGCCGAAG
1 CACTGAAATGTAGTCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAAATGTAGCCGAAG
6244251 CTAC
66 CTAC
* *
6244255 CACTGGAATGTAGCCGAAGCTACCACTGAT
1 CACTGAAATGTAGTCGAAGCTACCACTGAT
6244285 CAATAACACT
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 91 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (69 bp):
CACTGAAATGTAGTCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAAATGTAGCCGAAG
CTAC
Found at i:6248292 original size:3 final size:3
Alignment explanation
Indices: 6248284--6248336 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
6248274 TATTTTAATG
* * *
6248284 TTA TTA TTA TTA TTG TTA TCA TTA TTA TTA TTA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6248332 -TA TTA
1 TTA TTA
6248337 ATATAATTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:6248987 original size:109 final size:109
Alignment explanation
Indices: 6248791--6249101 Score: 466
Period size: 109 Copynumber: 2.9 Consensus size: 109
6248781 AAGTTTTTCT
* * * * *
6248791 AAATGAGGCAATATTTAGGGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTTGATT
1 AAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
*
6248856 TTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAATTCA
66 TTTCTCGTTCAACCAAATAGCTAAATATCCTTTCAAAAAATTCA
*
6248900 AAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTTTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
* *
6248965 TTTCTCGTTCAACCAAATAGCTAAATATCCTTTCAGAAATTTCA
66 TTTCTCGTTCAACCAAATAGCTAAATATCCTTTCAAAAAATTCA
* *
6249009 AAATAAGGCAATGTTTTGCGTTTGAAAATTCGAG-GAACGTGCCCTAATGTGCTGGGTTTCG--G
1 AAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
* * * *
6249071 TTTCTCGTTTAACCAATTAGCCAATTATCCT
66 TTTCTCGTTCAACCAAATAGCTAAATATCCT
6249102 CTTGAATTTT
Statistics
Matches: 186, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
106 27 0.15
108 25 0.13
109 134 0.72
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (109 bp):
AAATAAGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
TTTCTCGTTCAACCAAATAGCTAAATATCCTTTCAAAAAATTCA
Found at i:6250107 original size:25 final size:26
Alignment explanation
Indices: 6250060--6250118 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
6250050 TAAGATGGCT
*
6250060 ATATAAAAATTTCAATAAATAAAA-A
1 ATATAAAAATTTAAATAAATAAAATA
*
6250085 ATATAAAAATATTAAAT-ATTAAAATA
1 ATATAAAAAT-TTAAATAAATAAAATA
*
6250111 AAATAAAA
1 ATATAAAA
6250119 TAATTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 16 0.55
26 13 0.45
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (26 bp):
ATATAAAAATTTAAATAAATAAAATA
Found at i:6260787 original size:98 final size:98
Alignment explanation
Indices: 6260617--6261357 Score: 1365
Period size: 98 Copynumber: 7.6 Consensus size: 98
6260607 GTACAATAAA
* * *
6260617 ACTTTAAAAGAACATCCACTAATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
* * * *
6260682 CCTCTAGAATCCCAAGCTCAGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
* * * *
6260715 TCTTTAAAAGAACTTCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
* *
6260780 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
6260813 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
6260878 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
6260911 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
6260976 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
6261009 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
6261074 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
6261107 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
6261172 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
6261205 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
6261270 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
6261303 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTA
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTA
6261358 TAGAGGGGCT
Statistics
Matches: 632, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 632 1.00
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGACACAATT
CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:6261595 original size:19 final size:21
Alignment explanation
Indices: 6261557--6261595 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
6261547 CTTTTTTTAA
*
6261557 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
6261578 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
6261596 AAGAAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:6261813 original size:22 final size:23
Alignment explanation
Indices: 6261764--6261808 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
6261754 GGGTATCTAC
*
6261764 AAATTAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
6261786 AAATCAAATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
6261809 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:6261834 original size:21 final size:19
Alignment explanation
Indices: 6261797--6261889 Score: 150
Period size: 19 Copynumber: 4.8 Consensus size: 19
6261787 AATCAAATCT
*
6261797 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
6261816 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
6261837 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
6261856 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
6261875 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
6261890 ACTCAAAAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 50 0.72
21 19 0.28
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:6261845 original size:40 final size:38
Alignment explanation
Indices: 6261797--6261889 Score: 150
Period size: 40 Copynumber: 2.4 Consensus size: 38
6261787 AATCAAATCT
*
6261797 TCTAAGATTACATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGC--ATATCATA
*
6261837 TCTAAGATTGCATATCATATCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATCATA
6261875 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
6261890 ACTCAAAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
38 23 0.45
40 28 0.55
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (38 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATCATA
Found at i:6272123 original size:22 final size:22
Alignment explanation
Indices: 6272080--6272138 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
6272070 TGTAGTTTTC
6272080 TAGGTGAAAAGA-T-GGATGTGA
1 TAGGTG-AAAGATTAGGATGTGA
*
6272101 TAGGTGAAAGATTAGGATTTGA
1 TAGGTGAAAGATTAGGATGTGA
* *
6272123 TGGGTGAAAGGTTAGG
1 TAGGTGAAAGATTAGG
6272139 GTATTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.15
21 7 0.21
22 21 0.64
ACGTcount: A:0.34, C:0.00, G:0.39, T:0.27
Consensus pattern (22 bp):
TAGGTGAAAGATTAGGATGTGA
Found at i:6272211 original size:25 final size:24
Alignment explanation
Indices: 6272183--6272244 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
6272173 TGGTAGTGTA
*
6272183 AATTTGGGTTTTATTTTTGGGTTTG
1 AATTTGGGTTTTA-TATTGGGTTTG
*
6272208 AATTTGGGTTAGTATATTGGGTTTG
1 AATTTGGGTT-TTATATTGGGTTTG
**
6272233 GGTTTGGGTTTT
1 AATTTGGGTTTT
6272245 GGTTAATGGG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.03
25 28 0.90
26 2 0.06
ACGTcount: A:0.13, C:0.00, G:0.32, T:0.55
Consensus pattern (24 bp):
AATTTGGGTTTTATATTGGGTTTG
Found at i:6272215 original size:12 final size:12
Alignment explanation
Indices: 6272183--6272243 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
6272173 TGGTAGTGTA
*
6272183 AATTTGGGTTTT
1 AATTTGGGTTTG
*
6272195 ATTTTTGGGTTTG
1 A-ATTTGGGTTTG
*
6272208 AATTTGGGTTAG
1 AATTTGGGTTTG
*
6272220 TATATTGGGTTTG
1 AAT-TTGGGTTTG
**
6272233 GGTTTGGGTTT
1 AATTTGGGTTT
6272244 TGGTTAATGG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
12 20 0.51
13 19 0.49
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.54
Consensus pattern (12 bp):
AATTTGGGTTTG
Found at i:6272394 original size:6 final size:6
Alignment explanation
Indices: 6272385--6272429 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
6272375 AAAACAAAAC
6272385 AAAATA AAAATA AAAAT- AAAATA AAATAGTA AAAATA AATAATA A
1 AAAATA AAAATA AAAATA AAAATA AAA-A-TA AAAATA AA-AATA A
6272430 TAAAAGGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.14
6 18 0.51
7 7 0.20
8 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:6272399 original size:16 final size:15
Alignment explanation
Indices: 6272374--6272434 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 15
6272364 GTTTCCCTGC
*
6272374 AAAAACAAAACAAAAT
1 AAAAATAAAA-AAAAT
6272390 AAAAATAAAAATAAAAT
1 AAAAAT-AAAA-AAAAT
6272407 AAAATAGTAAAAATAAAT
1 AAAA-A-TAAAAA-AAAT
*
6272425 AATAATAAAA
1 AAAAATAAAA
6272435 GGAAAATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 10 0.26
17 15 0.39
18 12 0.32
19 1 0.03
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.16
Consensus pattern (15 bp):
AAAAATAAAAAAAAT
Found at i:6272431 original size:19 final size:19
Alignment explanation
Indices: 6272380--6272423 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
6272370 CTGCAAAAAC
*
6272380 AAAACAAAATAAAA-A-TA
1 AAAATAAAATAAAATAGTA
6272397 AAAATAAAATAAAATAGTA
1 AAAATAAAATAAAATAGTA
6272416 AAAATAAA
1 AAAATAAA
6272424 TAATAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.54
18 1 0.04
19 10 0.42
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAATAAAATAAAATAGTA
Found at i:6272453 original size:29 final size:29
Alignment explanation
Indices: 6272385--6272453 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
6272375 AAAACAAAAC
* *
6272385 AAAATAAAAATAAAAATAAAATAAAATAGT
1 AAAATTAAAATAAAAATAAAAGAAAATA-T
* *
6272415 AAAAAT-AAATAATAATAAAAGGAAAAT-T
1 AAAATTAAAATAAAAATAAAA-GAAAATAT
6272443 AAAATTAAAAT
1 AAAATTAAAAT
6272454 GTGTATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 6 0.19
29 17 0.53
30 9 0.28
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (29 bp):
AAAATTAAAATAAAAATAAAAGAAAATAT
Found at i:6282630 original size:2 final size:2
Alignment explanation
Indices: 6282617--6282648 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6282607 GACATAACCA
*
6282617 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6282649 GTAAAAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6289889 original size:51 final size:51
Alignment explanation
Indices: 6289806--6289903 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
6289796 ATTAATGTAC
6289806 AATTAGGACCAAGTTGACATCATATGCAAATTTTGAGGGCTAAATTTGTTA
1 AATTAGGACCAAGTTGACATCATATGCAAATTTTGAGGGCTAAATTTGTTA
* * *
6289857 AATTAGGACCAAGTTGGCATTATTTGTC-AATTTTGAGGGCTAAATTT
1 AATTAGGACCAAGTTGACATCATATG-CAAATTTTGAGGGCTAAATTT
6289904 ATTATATCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (51 bp):
AATTAGGACCAAGTTGACATCATATGCAAATTTTGAGGGCTAAATTTGTTA
Found at i:6290169 original size:19 final size:19
Alignment explanation
Indices: 6290145--6290182 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
6290135 ACGTTCGAGG
6290145 CCATTAATTAGAATGCTAT
1 CCATTAATTAGAATGCTAT
6290164 CCATTAATTAGAATGCTAT
1 CCATTAATTAGAATGCTAT
6290183 GTGATTGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
CCATTAATTAGAATGCTAT
Found at i:6291145 original size:1 final size:1
Alignment explanation
Indices: 6291139--6291178 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
6291129 NNNNNNNNNN
*
6291139 AAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6291179 TCAAACTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6295582 original size:24 final size:24
Alignment explanation
Indices: 6295554--6295617 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
6295544 GGTATTACAG
*
6295554 ATTTAATATTTATTAGTATAATGT
1 ATTTAATATTTATTAGTATAATAT
* **
6295578 TTTTAGCATTTATTAGTATAATAT
1 ATTTAATATTTATTAGTATAATAT
* *
6295602 ATTTGATATTAATTAG
1 ATTTAATATTTATTAG
6295618 AATTAAGTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (24 bp):
ATTTAATATTTATTAGTATAATAT
Found at i:6303789 original size:50 final size:50
Alignment explanation
Indices: 6303651--6303826 Score: 171
Period size: 50 Copynumber: 3.6 Consensus size: 50
6303641 TTACGTGAGG
*
6303651 CCTCTATGGCGAGTCCTCTGTAAAG-C-CTGTGGCGATTTATTTGGGAAA
1 CCTCTATGGCGAGTCCTCTGTAAAGCCTCTGTAGCGATTTATTTGGGAAA
* * * * * * * *
6303699 CCTCTGTTGTGAGTCATCTATAAAACCTTTGTAGCAATTTATTTGGGAAA
1 CCTCTATGGCGAGTCCTCTGTAAAGCCTCTGTAGCGATTTATTTGGGAAA
* * * * *
6303749 CCTCTGTGGCAAGTCC-CTTGTAAAGCCTCTGTTGCGATTTATTTCGGAAG
1 CCTCTATGGCGAGTCCTC-TGTAAAGCCTCTGTAGCGATTTATTTGGGAAA
*
6303799 CCTCTATAGCGAGTCAC-CTGTAAAGCCT
1 CCTCTATGGCGAGTC-CTCTGTAAAGCCT
6303827 TTATGGTAGG
Statistics
Matches: 101, Mismatches: 23, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
48 19 0.19
49 2 0.02
50 78 0.77
51 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (50 bp):
CCTCTATGGCGAGTCCTCTGTAAAGCCTCTGTAGCGATTTATTTGGGAAA
Found at i:6307552 original size:878 final size:881
Alignment explanation
Indices: 6305523--6307688 Score: 3175
Period size: 884 Copynumber: 2.5 Consensus size: 881
6305513 ACGACACACC
* *
6305523 ACCAATAAAACGATTAAGGAAAACTTCAAT-GAA-A-CATAATAAATAAT-AATAAACGAGATGC
1 ACCAATAAAACGATTAAGGAAAACTTCAATGGAACATAATAATAAATAATAAAAAAACGAGATGC
** * * *
6305584 TAGTTTGAGGTTCCTCCGATGCTAATCCGTGTCCTA-TTTTTCTATGTTACCTGAGAGTTAAGGA
66 TAGTCCGAGGTTCCTCCGATGCTAATCCGAGTCCTAGTTTTT-TGTGTTACCTGAGAGGTAA-GA
* * * *
6305648 AAATA-GGGAGTGCGCTTATGACAGCCCAATGTGAGTCTAATTTTTAAACCATTATATATAATTG
129 AAAAAGGGGAGTGAGCTTATGACAGCCCAATGTGAGTTTAATTTTTAAACCATTACATATAATTG
* **
6305712 TTCAAACGACAAAGCATTCAATTTAAAACATCATAGCAAATTAAGCATAATATAAGAAACATTCA
194 TTCAAACGATAAAGCATTCAATTTAAAACATCATAGCAAATTAAGCATAATATAAGGGACATTCA
6305777 GTAAATCAATGCATGTACAAGTTATGTTCATGATGCAATGCAATTATAATTTTAAATTCCCACTC
259 GTAAATCAATGCATGTACAAGTTATGTTCATGATGCAATGCAATTATAATTTTAAATTCCCACTC
* * ** * * * *
6305842 ATCTATCTTATTTGCCCTCGAGCATCACTTGACACTCGAAAACACATTTCAGTAATTGACCGTCT
324 ATCCATCCTATCCGCCCTCGAGCATCACTCGACACTCCAAAACACATTTCAGTAACTGACCATCT
* * * *
6305907 TGGATTT-TTCGGTGACGATGGTCGTTCACTTATCATCCGTGACGATGAATTTTAATACAATAAC
389 TGGATTTCCT-GATGACGATGGTCATTCACTTATCATCCGTGACGATAAATTTTAATACAATAAC
* * ** * * * *
6305971 TTACCAAATGTAACACCCCCGATCTGGATTAGGAGTTTCGAGTAAGTTAAATGCGTTACATTGAT
453 TTACCAAATGTAAAACCCCCGAACCAGATTAGGAGTTTCGACTAAGTCAAAGGAGTTACATTGAT
*
6306036 CACCGAAGTAATCCAATAAAGCCATTCTTTTGCTTGAGTTGAATTGTATGAAAATCACTCTTTTG
518 CACCGAAGTAATCCAATAAAGCCATTCTTTTGATTGAGTTGAATTGTATGAAAATCACTCTTTTG
* * * *
6306101 TTTTTAGGAATGACATTCATTAATTAATCCGACTTTACTTAGTAATCTATCTACAATATTATTAA
583 TTTTTAAGAAAGACATTCATTAATTAATCCGACTTTACTCAATAATCTATCTACAATATTATTAA
* *
6306166 CGTGAAGTTTTTTTTATTTTGAGAAAACGGTTTATGATTTTAAAAGACTTATCAAAACTTTAAGT
648 CGTGAAG---TTTATATTTTGAGAAAACGATTTATGATTTTAAAAGACTTATCAAAACTTTAAGT
*
6306231 ATTTTGCAAAGCAACAGAAACCAATAATAAGGATAATAATTTTCTAAACCAATTAGCATGCAATA
710 ATTTTGCAAAGCAACAGAAACCAATAATAAGAATAATAATTTTCTAAACCAATTAGCATGCAATA
* *
6306296 ATCAGAGTAATAACTAAATGTCATGCTTAAAAATTTATAAGCTAAATAATCCCAAACCACAATTA
775 ATCAAAGTAATAAATAAATGTCATGCTTAAAAATTTATAAGCTAAATAATCCCAAACCACAATTA
**
6306361 TGAAAGCAATAAATAATTAATAGCTTACGACCCAATTAACAA
840 ACAAAGCAATAAATAATTAATAGCTTACGACCCAATTAACAA
* *
6306403 ACCAATAAAACAATTAAGGAAAACTTCAATGGAACATAATAATAAATAATAAAAAAATGAGATGC
1 ACCAATAAAACGATTAAGGAAAACTTCAATGGAACATAATAATAAATAATAAAAAAACGAGATGC
* * * *
6306468 TAGTCCAAGGTTCCTCCGATGCCAATCCGAGTCCTAGTTTTCTGTGTTACCTGAGAGGTAAGGAA
66 TAGTCCGAGGTTCCTCCGATGCTAATCCGAGTCCTAGTTTTTTGTGTTACCTGAGAGGTAAGAAA
** * * * *
6306533 ACTGGAGAGTAAGCTTATGACAGCCTAATATGAGTTTAATTTTTAAACCATTACATATAATTGTT
131 AAAGGGGAGTGAGCTTATGACAGCCCAATGTGAGTTTAATTTTTAAACCATTACATATAATTGTT
* * *
6306598 CAAACGGTAAAGCATTCAATTTAAAACATCATAACAAATTAAGCATAATATAAGGGGCATTCAGT
196 CAAACGATAAAGCATTCAATTTAAAACATCATAGCAAATTAAGCATAATATAAGGGACATTCAGT
* * ** * *
6306663 TAATTAATGCATGTACTCGTTATGTTCATGATGCAATGCAATTATAATTTTAAATTGCCACCCAT
261 AAATCAATGCATGTACAAGTTATGTTCATGATGCAATGCAATTATAATTTTAAATTCCCACTCAT
* * *
6306728 CCATCCTATCCGCCCTCGAGCATCGCTCGACACTCCAAAACACATTTCAGTAACTGACCATCCTA
326 CCATCCTATCCGCCCTCGAGCATCACTCGACACTCCAAAACACATTTCAGTAACTGACCATCTTG
* * * *
6306793 GATTTCCTGATGACGATGGTCATTCACTTGTCATCTGTGATGATAAATTTTACTACAATAACTTA
391 GATTTCCTGATGACGATGGTCATTCACTTATCATCCGTGACGATAAATTTTAATACAATAACTTA
*
6306858 CCAAATGTAAAACCCCC-AACCAGACTTAGGAGTTTTGACTAAGTCAAAGGAGTTACATTGATCA
456 CCAAATGTAAAACCCCCGAACCAGA-TTAGGAGTTTCGACTAAGTCAAAGGAGTTACATTGATCA
* * * * *
6306922 CTGAAGTGATCCAGTAAAGTCATTCTTTTGATTGAGTTGAATTGTATGAAAATCGCTCTTTTGTT
520 CCGAAGTAATCCAATAAAGCCATTCTTTTGATTGAGTTGAATTGTATGAAAATCACTCTTTTGTT
* * *
6306987 TTTAAGAAAGACATTCATTAATTAATCTGGCTTTACTCAATAATCTATCTATAATATTATTAACG
585 TTTAAGAAAGACATTCATTAATTAATCCGACTTTACTCAATAATCTATCTACAATATTATTAACG
* *
6307052 TGAAG-TTAT-TTTTGAGCAAACGATTTATGGTTTTAAAAGACTTATCAAAACTTTAAGTATTTT
650 TGAAGTTTATATTTTGAGAAAACGATTTATGATTTTAAAAGACTTATCAAAACTTTAAGTATTTT
* ** *
6307115 GCAAAGCAACAGAAATCAATAATAAGAATAATGGTTTTCTAAACCAATTAGCATTCAATAATCAA
715 GCAAAGCAACAGAAACCAATAATAAGAATAATAATTTTCTAAACCAATTAGCATGCAATAATCAA
* * *
6307180 AGTAATAAATAAATTTCATGCTT-AAAATTTATAAGCTAAATAATCTCAAACCACAGTTAACAAA
780 AGTAATAAATAAATGTCATGCTTAAAAATTTATAAGCTAAATAATCCCAAACCACAATTAACAAA
*
6307244 GTAATAAATAATTAATAGCTTACGACCCAATTAACAA
845 GCAATAAATAATTAATAGCTTACGACCCAATTAACAA
* *
6307281 ACCAATAAAATGATTAAGGAAAACTTCAATGGAACATAATAATAAATAATAAAAAAACGATATGC
1 ACCAATAAAACGATTAAGGAAAACTTCAATGGAACATAATAATAAATAATAAAAAAACGAGATGC
* * * * *
6307346 TAGTCCGAGGTTCCTTCGATGCTAATTCAAGTCCTAGTTTTTTGTGTTACTTGATAGGTAAGAAA
66 TAGTCCGAGGTTCCTCCGATGCTAATCCGAGTCCTAGTTTTTTGTGTTACCTGAGAGGTAAGAAA
*
6307411 AAAGGGGAGTGAGCTTATGACAGCCCAATGTGAGTTTAATTTTTAAACCATTACAGATAATTGTT
131 AAAGGGGAGTGAGCTTATGACAGCCCAATGTGAGTTTAATTTTTAAACCATTACATATAATTGTT
* * * *
6307476 CAAATGATAAATCATTCAATTTAAAACATCATAGCAAATTAAGCATACTATAAGGGACATTCAAT
196 CAAACGATAAAGCATTCAATTTAAAACATCATAGCAAATTAAGCATAATATAAGGGACATTCAGT
* *
6307541 AAATCAATGCATGTACAAGTTATGTTCATGATGTAATGAAATTATAATTTTAAATTCCCACTCAT
261 AAATCAATGCATGTACAAGTTATGTTCATGATGCAATGCAATTATAATTTTAAATTCCCACTCAT
* * **
6307606 CCATCCTATCCGCCGTCGAGCATCACTCGACATTTTAAAACACATTTCAGTAACTGACCATCTTG
326 CCATCCTATCCGCCCTCGAGCATCACTCGACACTCCAAAACACATTTCAGTAACTGACCATCTTG
**
6307671 GATTTCCAAATGACGATG
391 GATTTCCTGATGACGATG
6307689 TGACGATGAA
Statistics
Matches: 1142, Mismatches: 136, Indels: 18
0.88 0.10 0.01
Matches are distributed among these distances:
878 437 0.38
879 131 0.11
880 32 0.03
881 3 0.00
882 1 0.00
883 20 0.02
884 513 0.45
885 5 0.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (881 bp):
ACCAATAAAACGATTAAGGAAAACTTCAATGGAACATAATAATAAATAATAAAAAAACGAGATGC
TAGTCCGAGGTTCCTCCGATGCTAATCCGAGTCCTAGTTTTTTGTGTTACCTGAGAGGTAAGAAA
AAAGGGGAGTGAGCTTATGACAGCCCAATGTGAGTTTAATTTTTAAACCATTACATATAATTGTT
CAAACGATAAAGCATTCAATTTAAAACATCATAGCAAATTAAGCATAATATAAGGGACATTCAGT
AAATCAATGCATGTACAAGTTATGTTCATGATGCAATGCAATTATAATTTTAAATTCCCACTCAT
CCATCCTATCCGCCCTCGAGCATCACTCGACACTCCAAAACACATTTCAGTAACTGACCATCTTG
GATTTCCTGATGACGATGGTCATTCACTTATCATCCGTGACGATAAATTTTAATACAATAACTTA
CCAAATGTAAAACCCCCGAACCAGATTAGGAGTTTCGACTAAGTCAAAGGAGTTACATTGATCAC
CGAAGTAATCCAATAAAGCCATTCTTTTGATTGAGTTGAATTGTATGAAAATCACTCTTTTGTTT
TTAAGAAAGACATTCATTAATTAATCCGACTTTACTCAATAATCTATCTACAATATTATTAACGT
GAAGTTTATATTTTGAGAAAACGATTTATGATTTTAAAAGACTTATCAAAACTTTAAGTATTTTG
CAAAGCAACAGAAACCAATAATAAGAATAATAATTTTCTAAACCAATTAGCATGCAATAATCAAA
GTAATAAATAAATGTCATGCTTAAAAATTTATAAGCTAAATAATCCCAAACCACAATTAACAAAG
CAATAAATAATTAATAGCTTACGACCCAATTAACAA
Found at i:6308154 original size:15 final size:15
Alignment explanation
Indices: 6308112--6308230 Score: 65
Period size: 13 Copynumber: 8.5 Consensus size: 15
6308102 TGTTCGCATT
*
6308112 TAGGGTTCGCACATA
1 TAGGGTTTGCACATA
* *
6308127 CA-TGTTT-CACATA
1 TAGGGTTTGCACATA
6308140 TAGGGTTTGCACATA
1 TAGGGTTTGCACATA
* *
6308155 TAGAGTTTG--CATG
1 TAGGGTTTGCACATA
*
6308168 TAGGGTTCGCACATA
1 TAGGGTTTGCACATA
* ** * *
6308183 CAAAG-TT-CGCATG
1 TAGGGTTTGCACATA
6308196 TAGGGTTTGCACATA
1 TAGGGTTTGCACATA
*
6308211 CAGGG-TT-CACATA
1 TAGGGTTTGCACATA
*
6308224 TAAGGTT
1 TAGGGTT
6308231 CGCATACTAA
Statistics
Matches: 73, Mismatches: 24, Indels: 15
0.65 0.21 0.13
Matches are distributed among these distances:
13 32 0.44
14 13 0.18
15 28 0.38
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (15 bp):
TAGGGTTTGCACATA
Found at i:6308218 original size:28 final size:28
Alignment explanation
Indices: 6308103--6308234 Score: 131
Period size: 28 Copynumber: 4.7 Consensus size: 28
6308093 TACATAACAT
*
6308103 GTTCGCATTTAGGGTTCGCACATACATG-
1 GTTCGCATGTAGGGTTCGCACATACA-GA
* * * * *
6308131 TTTCACATATAGGGTTTGCACATATAGA
1 GTTCGCATGTAGGGTTCGCACATACAGA
* *
6308159 GTTTGCATGTAGGGTTCGCACATACAAA
1 GTTCGCATGTAGGGTTCGCACATACAGA
* *
6308187 GTTCGCATGTAGGGTTTGCACATACAGG
1 GTTCGCATGTAGGGTTCGCACATACAGA
* * *
6308215 GTTCACATATAAGGTTCGCA
1 GTTCGCATGTAGGGTTCGCA
6308235 TACTAAATCA
Statistics
Matches: 83, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
27 1 0.01
28 82 0.99
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (28 bp):
GTTCGCATGTAGGGTTCGCACATACAGA
Found at i:6308279 original size:24 final size:24
Alignment explanation
Indices: 6308227--6308362 Score: 87
Period size: 24 Copynumber: 5.7 Consensus size: 24
6308217 TCACATATAA
* *
6308227 GGTTCGCATACTAAATCACATGGT
1 GGTTCGCATAATAAATCACATGGG
*
6308251 AGTTCGCATAATAAATCACATGGG
1 GGTTCGCATAATAAATCACATGGG
** ** *
6308275 GGTTCATATACAT-AATCGTATGAG
1 GGTTCGCATA-ATAAATCACATGGG
* * **
6308299 GGTTTGCATATTAAATC-CATAAG
1 GGTTCGCATAATAAATCACATGGG
* * * *
6308322 GGTTCGCATATTAAAACATATAGG
1 GGTTCGCATAATAAATCACATGGG
* *
6308346 GGTTCTCATACTAAATC
1 GGTTCGCATAATAAATC
6308363 CATAAGGGCT
Statistics
Matches: 87, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
23 20 0.23
24 65 0.75
25 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (24 bp):
GGTTCGCATAATAAATCACATGGG
Found at i:6308370 original size:24 final size:24
Alignment explanation
Indices: 6308298--6308379 Score: 89
Period size: 23 Copynumber: 3.5 Consensus size: 24
6308288 AATCGTATGA
*
6308298 GGGTTTGCATATTAAATCCATAA-
1 GGGTTCGCATATTAAATCCATAAG
*
6308321 GGGTTCGCATATTAAA-ACATATAG
1 GGGTTCGCATATTAAATCCATA-AG
* *
6308345 GGGTTCTCATACTAAATCCATAAG
1 GGGTTCGCATATTAAATCCATAAG
*
6308369 GGCTT-GCATAT
1 GGGTTCGCATAT
6308380 AGGGTTCGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 4 0.08
23 20 0.42
24 20 0.42
25 4 0.08
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (24 bp):
GGGTTCGCATATTAAATCCATAAG
Found at i:6308443 original size:58 final size:58
Alignment explanation
Indices: 6308352--6308574 Score: 218
Period size: 58 Copynumber: 3.8 Consensus size: 58
6308342 TAGGGGTTCT
* *
6308352 CATACTAAATC-CATAAGGGCTTGCATATAGGGTTCGCATAATATATAGTAAGAGATCA
1 CATACTAAATCACATAAAGGTTTGCATAT-GGGTTCGCATAATATATAGTAAGAGATCA
* * *
6308410 CATACTAAGTCACATAAAGGTTTGCATATGGGTTAG-ACTAATATATGGTAAGAGAT-A
1 CATACTAAATCACATAAAGGTTTGCATATGGGTTCGCA-TAATATATAGTAAGAGATCA
* * * * * * * * * *
6308467 GTATACTAAATCATATAAAGTTTTTCATACGGGTTCACATTATTTATGGTAAGAGATCG
1 -CATACTAAATCACATAAAGGTTTGCATATGGGTTCGCATAATATATAGTAAGAGATCA
* * * *
6308526 TATACTAAATCATATAAAAGGTTTTCATATAGGTTCGCATAATATATAG
1 CATACTAAATCACAT-AAAGGTTTGCATATGGGTTCGCATAATATATAG
6308575 GGTTCACATA
Statistics
Matches: 136, Mismatches: 23, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
57 2 0.01
58 92 0.68
59 42 0.31
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (58 bp):
CATACTAAATCACATAAAGGTTTGCATATGGGTTCGCATAATATATAGTAAGAGATCA
Found at i:6308584 original size:18 final size:18
Alignment explanation
Indices: 6308552--6308596 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
6308542 AAAGGTTTTC
* *
6308552 ATATA-GGTTCGCATAAT
1 ATATAGGGTTCACATAAG
6308569 ATATAGGGTTCACATAAG
1 ATATAGGGTTCACATAAG
6308587 ATATAGGGTT
1 ATATAGGGTT
6308597 TGCATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (18 bp):
ATATAGGGTTCACATAAG
Found at i:6308780 original size:16 final size:16
Alignment explanation
Indices: 6308743--6308785 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
6308733 TTAATAGTTC
*
6308743 ACCTAA-GGTTCGCAT
1 ACCTAAGGGTTCACAT
* *
6308758 TCATAAGGGTTCACAT
1 ACCTAAGGGTTCACAT
6308774 ACCTAAGGGTTC
1 ACCTAAGGGTTC
6308786 GTATGCATGG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (16 bp):
ACCTAAGGGTTCACAT
Found at i:6308825 original size:15 final size:16
Alignment explanation
Indices: 6308792--6308851 Score: 65
Period size: 15 Copynumber: 3.9 Consensus size: 16
6308782 GTTCGTATGC
6308792 ATGGGGTTTCGCATAT
1 ATGGGGTTTCGCATAT
*
6308808 ATGGGGTTT-GCGTAT
1 ATGGGGTTTCGCATAT
*
6308823 ATGGGAG-TTCGCATAC
1 ATGGG-GTTTCGCATAT
6308839 AT-GGGTTT-GCATA
1 ATGGGGTTTCGCATA
6308852 ACAGATTACC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 6 0.16
15 16 0.42
16 16 0.42
ACGTcount: A:0.20, C:0.12, G:0.33, T:0.35
Consensus pattern (16 bp):
ATGGGGTTTCGCATAT
Found at i:6310977 original size:20 final size:20
Alignment explanation
Indices: 6310954--6310991 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6310944 AAATAATAAA
**
6310954 ATTTAAAATTAAAGTAATAT
1 ATTTAAAAGAAAAGTAATAT
6310974 ATTTAAAAGAAAAGTAAT
1 ATTTAAAAGAAAAGTAAT
6310992 TCAACATAGA
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:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (20 bp):
ATTTAAAAGAAAAGTAATAT
Found at i:6312400 original size:22 final size:22
Alignment explanation
Indices: 6312359--6312400 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6312349 CGTACGGATC
*
6312359 GATTTTTAATACTTTTTTTATA
1 GATTTTTAATACTTTATTTATA
**
6312381 GATTTTTAATGGTTTATTTA
1 GATTTTTAATACTTTATTTA
6312401 ATTGAATTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.02, G:0.10, T:0.62
Consensus pattern (22 bp):
GATTTTTAATACTTTATTTATA
Found at i:6316411 original size:16 final size:16
Alignment explanation
Indices: 6316390--6316441 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
6316380 TTTGGTTCGC
6316390 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
6316406 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
** *
6316422 TGTAACGGAATAGAGG
1 TGTATTGGATTAGAGG
6316438 TGTA
1 TGTA
6316442 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:6316488 original size:45 final size:44
Alignment explanation
Indices: 6316422--6316512 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
6316412 GGATTAGAGG
* *
6316422 TGTAACGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAACGGAATAGAAGCGTAATAG-AAATCAACTGTTTGGTTGAA
* * ***
6316467 TGTAATGGAATAGAAGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAACGGAATAGAAGCGTAATAGAAATCAACTGTTTGGTTGAA
6316511 TG
1 TG
6316513 GAATAGAGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAACGGAATAGAAGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:6316958 original size:44 final size:44
Alignment explanation
Indices: 6316840--6316964 Score: 121
Period size: 44 Copynumber: 2.8 Consensus size: 44
6316830 NNNNNNNNNN
** *
6316840 TATTAAATATAATTTAATAATGATATATAATTTCATAAAATTCTTGA
1 TATTAAATATAATTTAATAATGATATATAA-TT--TAAAATAATTAA
* * *
6316887 TAATAAAT-T-TTCTTATATGAAT-TTATATAATTTAAAATAATTAA
1 TATTAAATATAAT-TTA-AT-AATGATATATAATTTAAAATAATTAA
6316931 TATTAAATATAATTTAATAATGATATATAATTTA
1 TATTAAATATAATTTAATAATGATATATAATTTA
6316965 TACATTTAAC
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
43 3 0.05
44 29 0.46
45 5 0.08
46 7 0.11
47 16 0.25
48 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (44 bp):
TATTAAATATAATTTAATAATGATATATAATTTAAAATAATTAA
Found at i:6318156 original size:77 final size:77
Alignment explanation
Indices: 6318029--6318296 Score: 536
Period size: 77 Copynumber: 3.5 Consensus size: 77
6318019 NNNNNNNNNN
6318029 ATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAATTAATCAATACCATTTTTACCATAGGAC
1 ATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAATTAATCAATACCATTTTTACCATAGGAC
6318094 TAGGAATTGCTA
66 TAGGAATTGCTA
6318106 ATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAATTAATCAATACCATTTTTACCATAGGAC
1 ATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAATTAATCAATACCATTTTTACCATAGGAC
6318171 TAGGAATTGCTA
66 TAGGAATTGCTA
6318183 ATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAATTAATCAATACCATTTTTACCATAGGAC
1 ATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAATTAATCAATACCATTTTTACCATAGGAC
6318248 TAGGAATTGCTA
66 TAGGAATTGCTA
6318260 ATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAA
1 ATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAA
6318297 GGAGAAACTT
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 191 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (77 bp):
ATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAATTAATCAATACCATTTTTACCATAGGAC
TAGGAATTGCTA
Found at i:6321315 original size:18 final size:18
Alignment explanation
Indices: 6321292--6321336 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
6321282 AGAATCTGAT
6321292 TTGTGGATTCATCAACTC
1 TTGTGGATTCATCAACTC
6321310 TTGTGGATTCATCAACTC
1 TTGTGGATTCATCAACTC
6321328 TTGTGGATT
1 TTGTGGATT
6321337 TCTATGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.42
Consensus pattern (18 bp):
TTGTGGATTCATCAACTC
Found at i:6323645 original size:40 final size:40
Alignment explanation
Indices: 6323601--6323804 Score: 246
Period size: 40 Copynumber: 5.1 Consensus size: 40
6323591 CACACTAGAT
* * * *
6323601 AGAAGCTCATAAGAGCTGATCCACCCGAAGCACACCAGAC
1 AGAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
* * *
6323641 AGAAGCTCATAAGAGTTGATCCAACCGTAACATGCCAAAC
1 AGAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
* * **
6323681 AGAAGATCATAAGAGCTGATTCAATAGAAACACGCCAAAC
1 AGAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
* * * *
6323721 AGTAGCTCAGAAGAGCTGATCCAACTGAAACATGCCAAAC
1 AGAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
* * *
6323761 AGAAGCTCATAAGAGTTGATCCAACCGTAACACGCCTAAC
1 AGAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
6323801 AGAA
1 AGAA
6323805 AGTATAACAC
Statistics
Matches: 136, Mismatches: 28, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 136 1.00
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.15
Consensus pattern (40 bp):
AGAAGCTCATAAGAGCTGATCCAACCGAAACACGCCAAAC
Found at i:6332644 original size:19 final size:20
Alignment explanation
Indices: 6332617--6332656 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
6332607 GTAAATACAC
* *
6332617 ATATGTTTATAAT-TGATCA
1 ATATATTTAAAATATGATCA
6332636 ATATATTTAAAATATGATCA
1 ATATATTTAAAATATGATCA
6332656 A
1 A
6332657 CATCATATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (20 bp):
ATATATTTAAAATATGATCA
Found at i:6335665 original size:43 final size:43
Alignment explanation
Indices: 6335576--6335667 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
6335566 GTTGTGGTTG
* * * *
6335576 CTTCCTTTTTTGTTGTTTCTTGGTTGTGGTTGCTTCCATGTTA
1 CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTGCTTCCACGTAA
** *
6335619 CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTTTTTCTACGTAA
1 CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTGCTTCCACGTAA
6335662 CTTCCT
1 CTTCCT
6335668 CTGTCTTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.07, C:0.18, G:0.18, T:0.57
Consensus pattern (43 bp):
CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTGCTTCCACGTAA
Found at i:6336282 original size:21 final size:22
Alignment explanation
Indices: 6336244--6336285 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
6336234 AATAAATGAA
**
6336244 AAGAAAAATTTTATCCACAACC
1 AAGAAAAATTACATCCACAACC
6336266 AAGAAAAATTACA-CCACAAC
1 AAGAAAAATTACATCCACAAC
6336286 TGGCAAGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.55, C:0.24, G:0.05, T:0.17
Consensus pattern (22 bp):
AAGAAAAATTACATCCACAACC
Found at i:6338168 original size:27 final size:27
Alignment explanation
Indices: 6338138--6338223 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 27
6338128 CCCATAAGAG
*
6338138 TATCTCGTATTTAACGTCCCGTCAAAC
1 TATCTCGTGTTTAACGTCCCGTCAAAC
* * *
6338165 TATCCCGTGTTTAACGTCTCGTTAGAA-
1 TATCTCGTGTTTAACGTCCCGTCA-AAC
* *
6338192 TATCTCGTGTTTAATGTCCCGTCAGAC
1 TATCTCGTGTTTAACGTCCCGTCAAAC
6338219 TATCT
1 TATCT
6338224 ATGATGCCAT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
26 1 0.02
27 45 0.94
28 2 0.04
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (27 bp):
TATCTCGTGTTTAACGTCCCGTCAAAC
Found at i:6343568 original size:54 final size:54
Alignment explanation
Indices: 6343509--6343676 Score: 130
Period size: 54 Copynumber: 3.1 Consensus size: 54
6343499 AACATACATT
*
6343509 TACCAAAACCCTATTTACGTGCCACTTAAAATTGAGCCAAAATAAACAAATAGA
1 TACCAAAACCCTATTTACGTGACACTTAAAATTGAGCCAAAATAAACAAATAGA
*** ** ** * * * * * *
6343563 TACCAAAAGAGT-TGAGACACGAAACATAACCAATTGA-TCACAA-ACATAAAT--A
1 TACCAAAACCCTAT-TTACGTGACACTTAA--AATTGAGCCAAAATAAACAAATAGA
* *
6343615 TACCAAAACCCAATTTACGTGTCACTTAAAATTGAGCCAAAATAAACAAATAGA
1 TACCAAAACCCTATTTACGTGACACTTAAAATTGAGCCAAAATAAACAAATAGA
6343669 TACCAAAA
1 TACCAAAA
6343677 GAGTTGACGG
Statistics
Matches: 77, Mismatches: 29, Indels: 16
0.63 0.24 0.13
Matches are distributed among these distances:
50 6 0.08
51 4 0.05
52 23 0.30
53 2 0.03
54 32 0.42
55 4 0.05
56 6 0.08
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.20
Consensus pattern (54 bp):
TACCAAAACCCTATTTACGTGACACTTAAAATTGAGCCAAAATAAACAAATAGA
Found at i:6343608 original size:106 final size:106
Alignment explanation
Indices: 6343475--6343683 Score: 373
Period size: 106 Copynumber: 2.0 Consensus size: 106
6343465 ATCAAATGAA
* * * *
6343475 ACGAAACATAACCAATTGGTCACAAACATACATTTACCAAAACCCTATTTACGTGCCACTTAAAA
1 ACGAAACATAACCAATTGATCACAAACATAAATATACCAAAACCCAATTTACGTGCCACTTAAAA
6343540 TTGAGCCAAAATAAACAAATAGATACCAAAAGAGTTGAGAC
66 TTGAGCCAAAATAAACAAATAGATACCAAAAGAGTTGAGAC
*
6343581 ACGAAACATAACCAATTGATCACAAACATAAATATACCAAAACCCAATTTACGTGTCACTTAAAA
1 ACGAAACATAACCAATTGATCACAAACATAAATATACCAAAACCCAATTTACGTGCCACTTAAAA
6343646 TTGAGCCAAAATAAACAAATAGATACCAAAAGAGTTGA
66 TTGAGCCAAAATAAACAAATAGATACCAAAAGAGTTGA
6343684 CGGATAGTGC
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 98 1.00
ACGTcount: A:0.48, C:0.21, G:0.11, T:0.21
Consensus pattern (106 bp):
ACGAAACATAACCAATTGATCACAAACATAAATATACCAAAACCCAATTTACGTGCCACTTAAAA
TTGAGCCAAAATAAACAAATAGATACCAAAAGAGTTGAGAC
Found at i:6350923 original size:110 final size:110
Alignment explanation
Indices: 6350799--6351035 Score: 474
Period size: 110 Copynumber: 2.2 Consensus size: 110
6350789 TACTTATGTA
6350799 TATATATATACATATATTCGAACCTAATTTATCAATGTTATACATACCTTTGATTTATACTAGGA
1 TATATATATACATATATTCGAACCTAATTTATCAATGTTATACATACCTTTGATTTATACTAGGA
6350864 ATTTATACATATACAACATTTGTACTTTAACTAAACACAAAAACT
66 ATTTATACATATACAACATTTGTACTTTAACTAAACACAAAAACT
6350909 TATATATATACATATATTCGAACCTAATTTATCAATGTTATACATACCTTTGATTTATACTAGGA
1 TATATATATACATATATTCGAACCTAATTTATCAATGTTATACATACCTTTGATTTATACTAGGA
6350974 ATTTATACATATACAACATTTGTACTTTAACTAAACACAAAAACT
66 ATTTATACATATACAACATTTGTACTTTAACTAAACACAAAAACT
6351019 TATATATATACATATAT
1 TATATATATACATATAT
6351036 ATATTCGAAT
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 127 1.00
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (110 bp):
TATATATATACATATATTCGAACCTAATTTATCAATGTTATACATACCTTTGATTTATACTAGGA
ATTTATACATATACAACATTTGTACTTTAACTAAACACAAAAACT
Found at i:6351036 original size:12 final size:12
Alignment explanation
Indices: 6351019--6351072 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 12
6351009 CACAAAAACT
6351019 TATATATATACA
1 TATATATATACA
*
6351031 TATATATATTCGA
1 TATATATATAC-A
6351044 -ATATTATACGTACA
1 TATA-TATA--TACA
6351058 TATATATATACA
1 TATATATATACA
6351070 TAT
1 TAT
6351073 CTTTGTCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
12 20 0.57
13 5 0.14
14 5 0.14
15 5 0.14
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (12 bp):
TATATATATACA
Found at i:6351623 original size:15 final size:15
Alignment explanation
Indices: 6351603--6351634 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
6351593 CAAAATAAGC
6351603 TAGTTTAAATATAAT
1 TAGTTTAAATATAAT
6351618 TAGTTTAAATATAAT
1 TAGTTTAAATATAAT
6351633 TA
1 TA
6351635 CATACAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (15 bp):
TAGTTTAAATATAAT
Found at i:6355511 original size:30 final size:30
Alignment explanation
Indices: 6355452--6355531 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
6355442 ACACAAAGTG
*
6355452 CTTGGAAACTATAA-CACTAGTACATAGTA
1 CTTGGAAACTATAATCACCAGTACATAGTA
* * *
6355481 CTTGGAAACTGTAATCACCGGTATATAGTA
1 CTTGGAAACTATAATCACCAGTACATAGTA
* *
6355511 CCTGGAAACTAAAATCACCAG
1 CTTGGAAACTATAATCACCAG
6355532 CACCTAGTGC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 13 0.31
30 29 0.69
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (30 bp):
CTTGGAAACTATAATCACCAGTACATAGTA
Found at i:6359097 original size:26 final size:26
Alignment explanation
Indices: 6359053--6359151 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
6359043 TATCATCCTT
* ** *
6359053 ATTTTACCTTTAGCGAAATTTTGACG
1 ATTTTACCCTTAGTAAAATTTTGATG
*
6359079 ATTTTACCCTTGGTAAAATTTTGATG
1 ATTTTACCCTTAGTAAAATTTTGATG
6359105 ATTTTACCCTTAGTAAAATTTTGATG
1 ATTTTACCCTTAGTAAAATTTTGATG
* *
6359131 ATTTTGCCCCTAGTAAAATTT
1 ATTTTACCCTTAGTAAAATTT
6359152 CGAGAAAATA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 65 1.00
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.44
Consensus pattern (26 bp):
ATTTTACCCTTAGTAAAATTTTGATG
Done.