Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 61 of 127
Found at i:11909790 original size:144 final size:143
Alignment explanation
Indices: 11909607--11910017 Score: 475
Period size: 144 Copynumber: 2.8 Consensus size: 143
11909597 TTTTTGTGAG
* * ** * * * *
11909607 TTTATTGCATTAAAAATCATAGAATAATATTTAATCATGATTTGAAACCTTTCATGAAAAACTAA
1 TTTATTGCACTAAAAATCATAAAATAATATCAAAACATGATCTGAAACTTTTCAAGAAAAACTAA
* *
11909672 CCTCGAAAAAGTCAAATTATGAAAATACCATTAAATGGTATTTTAGTAATTTCACATCTT-TCAA
66 CCTCGAAAAGGTCAAATTATGAAAATACC-TTAAAGGGTATTTTAGTAATTTCACATCTTCT-AA
*
11909736 GGTATGATCAAGGTT
129 GGTATGATCAAGATT
* * * * * *
11909751 TTTATTGTACTAAAAATCATAAAATAATATCAAAACATGATCTAAAACTTTTTACGAAAATCCAA
1 TTTATTGCACTAAAAATCATAAAATAATATCAAAACATGATCTGAAACTTTTCAAGAAAAACTAA
* * * * *
11909816 CCTTGGAAAGGTCAAATTACGAAAATACCCCTAAAGGGTATTTTGGTAATTTCACATCTTCTAAG
66 CCTCGAAAAGGTCAAATTATGAAAATA-CCTTAAAGGGTATTTTAGTAATTTCACATCTTCTAAG
*
11909881 GTGTGATCAAGATT
130 GTATGATCAAGATT
* * * *
11909895 TTTAATGCACCAAAAATCATAAAATAATATCAAAATATGATCTGAAACTTTTCAAAAAAAAAACT
1 TTTATTGCACTAAAAATCATAAAATAATATCAAAACATGATCTGAAACTTTTC--AAGAAAAACT
* * *
11909960 GACCTC-AGAAAGGTCAAATTATAAAAATATCCTTAAAGGGTATTATAGTAATTTCACA
64 AACCTCGA-AAAGGTCAAATTATGAAAATA-CCTTAAAGGGTATTTTAGTAATTTCACA
11910018 CCATCCAATT
Statistics
Matches: 221, Mismatches: 41, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
144 164 0.74
145 3 0.01
146 54 0.24
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (143 bp):
TTTATTGCACTAAAAATCATAAAATAATATCAAAACATGATCTGAAACTTTTCAAGAAAAACTAA
CCTCGAAAAGGTCAAATTATGAAAATACCTTAAAGGGTATTTTAGTAATTTCACATCTTCTAAGG
TATGATCAAGATT
Found at i:11910101 original size:146 final size:146
Alignment explanation
Indices: 11909663--11910101 Score: 382
Period size: 144 Copynumber: 3.0 Consensus size: 146
11909653 ACCTTTCATG
* * ** ** * *
11909663 AAAAACTAACCTC-GAAAAAGTCAAATTATGAAAATACCATTAAATGGTATTTTAGTAATTTCAC
1 AAAAACCAACCTCAG-AAAGGTCAAATTACAAAAATACCCCTAAAGGGTATTATAGTAATTTCAC
* * * * * * * ** *
11909727 ATCTTTCAAGGTATGATCAAGGTTTTTATTGTACTAAAAATCATAAAATAATATCAAAACATGAT
65 ACCATCCAAGGTGTGATCAAGATTTTCAATACACCAAAAATCATAAAATAATATCAAAACATGAT
*
11909792 CTAAAACTTTTTACG--
130 CTAGAACTTTTTACGAA
* ** * * *
11909807 AAAATCCAACCTTGGAAAGGTCAAATTACGAAAATACCCCTAAAGGGTATTTTGGTAATTTCACA
1 AAAAACCAACCTCAGAAAGGTCAAATTACAAAAATACCCCTAAAGGGTATTATAGTAATTTCACA
* * * * * *
11909872 TCTTCTAAGGTGTGATCAAGATTTTTAATGCACCAAAAATCATAAAATAATATCAAAATATGATC
66 CCATCCAAGGTGTGATCAAGATTTTCAATACACCAAAAATCATAAAATAATATCAAAACATGATC
* **
11909937 T-GAAACTTTTCAAAAA
131 TAG-AACTTTTTACGAA
** * * *
11909953 AAAAACTGACCTCAGAAAGGTCAAATTATAAAAATATCCTTAAAGGGTATTATAGTAATTTCACA
1 AAAAACCAACCTCAGAAAGGTCAAATTACAAAAATACCCCTAAAGGGTATTATAGTAATTTCACA
** * * * * * * **
11910018 CCATCCAATTTGTGTTTAAGGTTTTCAATACATCAAAAATCATAAATTCATATTTAAACATGATC
66 CCATCCAAGGTGTGATCAAGATTTTCAATACACCAAAAATCATAAAATAATATCAAAACATGATC
*
11910083 TAGAAGTTTTTACGAA
131 TAGAACTTTTTACGAA
11910099 AAA
1 AAA
11910102 CTAACTTCAA
Statistics
Matches: 238, Mismatches: 52, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
144 120 0.50
145 1 0.00
146 116 0.49
147 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (146 bp):
AAAAACCAACCTCAGAAAGGTCAAATTACAAAAATACCCCTAAAGGGTATTATAGTAATTTCACA
CCATCCAAGGTGTGATCAAGATTTTCAATACACCAAAAATCATAAAATAATATCAAAACATGATC
TAGAACTTTTTACGAA
Found at i:11911636 original size:29 final size:29
Alignment explanation
Indices: 11911568--11911637 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
11911558 TGATAGGTAT
*
11911568 ATATTATTATATTAATAAAAATATTATTTA
1 ATATTATAAT-TTAATAAAAATATTATTTA
*
11911598 ATATTTTAATTTAATAAAAATATTTTATTT-
1 ATATTATAATTTAATAAAAATA--TTATTTA
11911628 ATA-TATAATT
1 ATATTATAATT
11911638 AAGATGTAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 18 0.51
30 11 0.31
31 6 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATATTATAATTTAATAAAAATATTATTTA
Found at i:11913752 original size:2 final size:2
Alignment explanation
Indices: 11913745--11913780 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
11913735 AGCTTCCATA
11913745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11913781 TTTAAAATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11914741 original size:25 final size:25
Alignment explanation
Indices: 11914712--11914763 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
11914702 TACCTATTAG
11914712 TACCACAGGAGATTAAAGTACCAAA
1 TACCACAGGAGATTAAAGTACCAAA
*
11914737 TACCACAGGAGATTAAAGTACTAAA
1 TACCACAGGAGATTAAAGTACCAAA
11914762 TA
1 TA
11914764 TCGACTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.19
Consensus pattern (25 bp):
TACCACAGGAGATTAAAGTACCAAA
Found at i:11914975 original size:21 final size:21
Alignment explanation
Indices: 11914949--11915014 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 21
11914939 AAAACTTAAC
11914949 AAAATATTATTTTATAAATAT
1 AAAATATTATTTTATAAATAT
*
11914970 AAAATATTATTTTTTAAAATAT
1 AAAATATTATTTTAT-AAATAT
* *
11914992 AAATATATCATTATATAAATAT
1 AAA-ATATTATTTTATAAATAT
11915014 A
1 A
11915015 TAAAAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
21 14 0.36
22 16 0.41
23 9 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATATTATTTTATAAATAT
Found at i:11915883 original size:38 final size:38
Alignment explanation
Indices: 11915841--11915917 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
11915831 AAATTAATAA
11915841 TACAATGGCCAGTAGAAGATAGAGAAAAAAAATCATGT
1 TACAATGGCCAGTAGAAGATAGAGAAAAAAAATCATGT
11915879 TACAATGGCCAGTAGAAGATAGAGAAAAAAAATCATGT
1 TACAATGGCCAGTAGAAGATAGAGAAAAAAAATCATGT
11915917 T
1 T
11915918 TCCTTATTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.19
Consensus pattern (38 bp):
TACAATGGCCAGTAGAAGATAGAGAAAAAAAATCATGT
Found at i:11916148 original size:2 final size:2
Alignment explanation
Indices: 11916143--11916173 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11916133 AACAAAAAAC
*
11916143 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11916174 CGAATCATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:11919385 original size:30 final size:30
Alignment explanation
Indices: 11919344--11919404 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 30
11919334 ATTATATTAG
11919344 TTAAAATTTTATA-ATATAATATTAAAAATTT
1 TTAAAATTTTATATA-AT-ATATTAAAAATTT
*
11919375 TTAAAA-TTTATATAATATATTAAATATTT
1 TTAAAATTTTATATAATATATTAAAAATTT
11919404 T
1 T
11919405 ATTATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 13 0.46
30 8 0.29
31 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
TTAAAATTTTATATAATATATTAAAAATTT
Found at i:11920722 original size:3 final size:3
Alignment explanation
Indices: 11920716--11920771 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
11920706 CATGATCATC
11920716 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11920764 ATT ATT AT
1 ATT ATT AT
11920772 CTCTCTTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:11923018 original size:50 final size:50
Alignment explanation
Indices: 11922890--11923010 Score: 163
Period size: 50 Copynumber: 2.4 Consensus size: 50
11922880 TTAAATAGAG
* * * *
11922890 GCTCAACAACTTTTTTAAATAAATTAAAATGAAAGCTCCTTTTATCAAAA
1 GCTCCACAACTTTTATAAATAAATTAAAATGAAAGCTCCTCTCATCAAAA
* *
11922940 GCTTCACAACTTTTATAAATAAATTAAAATGACAGCTCCTCTCATCAAACA
1 GCTCCACAACTTTTATAAATAAATTAAAATGAAAGCTCCTCTCATCAAA-A
*
11922991 -CTCCACAACTTTTAAAAATA
1 GCTCCACAACTTTTATAAATA
11923011 CTTTAAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 61 0.98
51 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (50 bp):
GCTCCACAACTTTTATAAATAAATTAAAATGAAAGCTCCTCTCATCAAAA
Found at i:11923216 original size:120 final size:120
Alignment explanation
Indices: 11923003--11923245 Score: 319
Period size: 120 Copynumber: 2.0 Consensus size: 120
11922993 CCACAACTTT
* * * *
11923003 TAAAAATACTTTAAAAATCTTAACTTGAAAAAGCTCATTTAAACATAGGTATTAGAACCTTAAAA
1 TAAAAATACTTTAAAAATCCTAACTTAAAAAAGCTCATTTAAACAAAGGTATTAGAAACTTAAAA
*
11923068 AACTATCATATAAAAAAGCTCCATTTAACAAATGCT-TTGAAACTTTAAAAAGCTA
66 AACTATCATATAAAAAAGCTCCATTTAACAAA-GCTGTTGAAACTTTAAAAAACTA
* * *
11923123 TAAAAATACTTTAAAAATCCTATCTTAAAAAAGCTCATTTAAATAAAGGTATT-GAAAATTTAAA
1 TAAAAATACTTTAAAAATCCTAACTTAAAAAAGCTCATTTAAACAAAGGTATTAG-AAACTTAAA
* * * * * * *
11923187 AAACTATTATCTGAAAAAGTTCCTTTTAACAAAGGTGTTGAAATTTTAAAAAACTA
65 AAACTATCATATAAAAAAGCTCCATTTAACAAAGCTGTTGAAACTTTAAAAAACTA
11923243 TAA
1 TAA
11923246 TCATCTTCTC
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
119 3 0.03
120 103 0.97
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.32
Consensus pattern (120 bp):
TAAAAATACTTTAAAAATCCTAACTTAAAAAAGCTCATTTAAACAAAGGTATTAGAAACTTAAAA
AACTATCATATAAAAAAGCTCCATTTAACAAAGCTGTTGAAACTTTAAAAAACTA
Found at i:11929442 original size:3 final size:3
Alignment explanation
Indices: 11929414--11929481 Score: 95
Period size: 3 Copynumber: 22.7 Consensus size: 3
11929404 CCTTATAAAA
*
11929414 AAT AAT AA- AAA AAT AACT AA- AGAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT A-AT AAT AAT AAT AAT AAT AAT AAT
11929459 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
11929482 ATTTTATGAA
Statistics
Matches: 60, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
2 3 0.05
3 53 0.88
4 4 0.07
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:11929634 original size:23 final size:23
Alignment explanation
Indices: 11929608--11929691 Score: 73
Period size: 23 Copynumber: 3.6 Consensus size: 23
11929598 ATAAATTTCG
*
11929608 AAACCCCAAAATCCAAAATCCTA
1 AAACCCCAAAATCCAAAATCTTA
** *
11929631 AAACTTC-AAACCCTAAAACTCTTA
1 AAACCCCAAAATCC-AAAA-TCTTA
* *
11929655 AAACCCCAAAAATCC-AAATTTTG
1 AAACCCC-AAAATCCAAAATCTTA
11929678 AAACCCCAAAATCC
1 AAACCCCAAAATCC
11929692 TCAAAACCCT
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
22 12 0.25
23 19 0.40
24 12 0.25
26 5 0.10
ACGTcount: A:0.49, C:0.32, G:0.01, T:0.18
Consensus pattern (23 bp):
AAACCCCAAAATCCAAAATCTTA
Found at i:11929794 original size:3 final size:3
Alignment explanation
Indices: 11929766--11929833 Score: 95
Period size: 3 Copynumber: 22.7 Consensus size: 3
11929756 CCTTATAAAA
*
11929766 AAT AAT AA- AAA AAT AAGT AA- AGAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT A-AT AAT AAT AAT AAT AAT AAT AAT
11929811 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
11929834 ATTTTATGAA
Statistics
Matches: 60, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
2 3 0.05
3 53 0.88
4 4 0.07
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:11929869 original size:352 final size:352
Alignment explanation
Indices: 11929356--11930065 Score: 1321
Period size: 352 Copynumber: 2.0 Consensus size: 352
11929346 GTAAGTAATG
11929356 AAAATAAAGTTCAAAATTTTTTATAGTTTTATTAAAAATTAAAATAAACCTTATAAAAAATAATA
1 AAAATAAAGTTCAAAATTTTTTATAGTTTTATTAAAAATTAAAATAAACCTTATAAAAAATAATA
11929421 AAAAAATAACTAAAGATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAATTT
66 AAAAAATAACTAAAGATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAATTT
* * *
11929486 TATGAAATATGAAATATATGAAAATTTTTAACTAATTTTCAAAAATTATAAAAAGCGAACTTATT
131 TATGAAATAAGAAATATATGAAAAATTTTAACTAATTTTCAAAAATTATAAAAAGCGAACTTACT
11929551 CAGAAAGTCTACCTAGATATAAGAGATTTTTAGAGATGTACTTATTTATAAATTTCGAAACCCCA
196 CAGAAAGTCTACCTAGATATAAGAGATTTTTAGAGATGTACTTATTTATAAATTTCGAAACCCCA
11929616 AAATCCAAAATCCTAAAACTTCAAACCCTAAAACTCTTAAAACCCCAAAAATCCAAATTTTGAAA
261 AAATCCAAAATCCTAAAACTTCAAACCCTAAAACTCTTAAAACCCCAAAAATCCAAATTTTGAAA
11929681 CCCCAAAATCCTCAAAACCCTAAACCT
326 CCCCAAAATCCTCAAAACCCTAAACCT
11929708 AAAATAAAGTTCAAAATTTTTTATAGTTTTATTAAAAATTAAAATAAACCTTATAAAAAATAATA
1 AAAATAAAGTTCAAAATTTTTTATAGTTTTATTAAAAATTAAAATAAACCTTATAAAAAATAATA
*
11929773 AAAAAATAAGTAAAGATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAATTT
66 AAAAAATAACTAAAGATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAATTT
*
11929838 TATGAAATAAGAAATATATGAAAAATTTTAACTAATTTTTAAAAATTATAAAAAGCGAACTTACT
131 TATGAAATAAGAAATATATGAAAAATTTTAACTAATTTTCAAAAATTATAAAAAGCGAACTTACT
* * *
11929903 CCGAAAGTCTACCTAGATATAAGAGATTTTTAGAGATGTACTTATTTATAAATTTTGAAACCCTA
196 CAGAAAGTCTACCTAGATATAAGAGATTTTTAGAGATGTACTTATTTATAAATTTCGAAACCCCA
*
11929968 AAATCCAAAATCCTAAAACTTCAAACTCTAAAACTCTTAAAACCCCAAAAATCCAAATTTTGAAA
261 AAATCCAAAATCCTAAAACTTCAAACCCTAAAACTCTTAAAACCCCAAAAATCCAAATTTTGAAA
*
11930033 CCCCAAAATCTTCAAAACCCTAAACCT
326 CCCCAAAATCCTCAAAACCCTAAACCT
*
11930060 TAAATA
1 AAAATA
11930066 CTCAAAGCCC
Statistics
Matches: 347, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
352 347 1.00
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (352 bp):
AAAATAAAGTTCAAAATTTTTTATAGTTTTATTAAAAATTAAAATAAACCTTATAAAAAATAATA
AAAAAATAACTAAAGATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAATTT
TATGAAATAAGAAATATATGAAAAATTTTAACTAATTTTCAAAAATTATAAAAAGCGAACTTACT
CAGAAAGTCTACCTAGATATAAGAGATTTTTAGAGATGTACTTATTTATAAATTTCGAAACCCCA
AAATCCAAAATCCTAAAACTTCAAACCCTAAAACTCTTAAAACCCCAAAAATCCAAATTTTGAAA
CCCCAAAATCCTCAAAACCCTAAACCT
Found at i:11930132 original size:24 final size:22
Alignment explanation
Indices: 11930077--11930206 Score: 82
Period size: 24 Copynumber: 5.5 Consensus size: 22
11930067 TCAAAGCCCG
*
11930077 AAACCCTCAAAACCTGAAACTCA
1 AAACCCT-AAAACCTAAAACTCA
*
11930100 AAACTCTAAAACCATAAAACCTCA
1 AAACCCTAAAACC-TAAAA-CTCA
* **
11930124 AATCCCTAAAATTTCAAAACTCTA
1 AAACCCTAAAACCT-AAAACTC-A
* *
11930148 AAACCCTCAAAACTCTAAATCT-T
1 AAACCCT-AAAAC-CTAAAACTCA
*
11930171 AAACCTTCAAAATCCTAAATACTCA
1 AAACCCT-AAAA-CCTAAA-ACTCA
*
11930196 AAACCTTAAAA
1 AAACCCTAAAA
11930207 TCCAAAATCC
Statistics
Matches: 84, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
22 6 0.07
23 30 0.36
24 31 0.37
25 16 0.19
26 1 0.01
ACGTcount: A:0.49, C:0.28, G:0.01, T:0.22
Consensus pattern (22 bp):
AAACCCTAAAACCTAAAACTCA
Found at i:11930180 original size:40 final size:40
Alignment explanation
Indices: 11930093--11930182 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
11930083 TCAAAACCTG
11930093 AAAC-TCAAAACTCTAAAACCATAAAACCTCAAATCCCTA
1 AAACTTCAAAACTCTAAAACCATAAAACCTCAAATCCCTA
* * *
11930132 AAATTTCAAAACTCTAAAACCCTCAAAA-CTCTAAAT-CTTA
1 AAACTTCAAAACTCTAAAACCAT-AAAACCTC-AAATCCCTA
*
11930172 AACCTTCAAAA
1 AAACTTCAAAA
11930183 TCCTAAATAC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 3 0.07
40 32 0.74
41 8 0.19
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (40 bp):
AAACTTCAAAACTCTAAAACCATAAAACCTCAAATCCCTA
Found at i:11930251 original size:30 final size:29
Alignment explanation
Indices: 11930178--11930305 Score: 80
Period size: 30 Copynumber: 4.2 Consensus size: 29
11930168 CTTAAACCTT
* * *
11930178 CAAAATCCTAAATACTCAAAACCTTAAAATC
1 CAAAATCATAAACACT-AAAA-CTTAAAACC
* *
11930209 CAAAATCCTAAACACTAAATCTTAAAACC
1 CAAAATCATAAACACTAAAACTTAAAACC
* * *
11930238 CTAAAATTATAAACCCTAAAACTTCAAAATCT
1 C-AAAATCATAAACACTAAAACTT-AAAA-CC
* **
11930270 CAAAACCA-AAATC-CTAAAACCCAAAACC
1 CAAAATCATAAA-CACTAAAACTTAAAACC
11930298 CTAAAATC
1 C-AAAATC
11930306 TCGAAACCTT
Statistics
Matches: 78, Mismatches: 14, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
28 2 0.03
29 18 0.23
30 31 0.40
31 25 0.32
32 2 0.03
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.20
Consensus pattern (29 bp):
CAAAATCATAAACACTAAAACTTAAAACC
Found at i:11930295 original size:15 final size:15
Alignment explanation
Indices: 11930252--11930303 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
11930242 AATTATAAAC
*
11930252 CCTAAAACTTCAAAAT
1 CCTAAAAC-CCAAAAT
11930268 -CTCAAAA-CCAAAAT
1 CCT-AAAACCCAAAAT
*
11930282 CCTAAAACCCAAAAC
1 CCTAAAACCCAAAAT
11930297 CCTAAAA
1 CCTAAAA
11930304 TCTCGAAACC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 10 0.32
15 17 0.55
16 4 0.13
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (15 bp):
CCTAAAACCCAAAAT
Found at i:11935354 original size:14 final size:14
Alignment explanation
Indices: 11935335--11935361 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11935325 CAAAATTTAA
11935335 AGTCATGTTGTTAG
1 AGTCATGTTGTTAG
11935349 AGTCATGTTGTTA
1 AGTCATGTTGTTA
11935362 TATTACTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.44
Consensus pattern (14 bp):
AGTCATGTTGTTAG
Found at i:11937976 original size:82 final size:82
Alignment explanation
Indices: 11937839--11937998 Score: 236
Period size: 82 Copynumber: 1.9 Consensus size: 82
11937829 GACAAATGAA
11937839 AAAGAAAAGAAAAAAAATGAAAAACAATTATAGGGCAAAATGCCAATGTGCTCCACCAATAAAAA
1 AAAGAAAAGAAAAAAAA-GAAAAACAATTATAGGGCAAAATGCCAATGTGCTCCACCAAT-AAAA
*
11937904 CA-AAAGAAAGAGAGAAAG
64 CATAAAAAAAGAGAGAAAG
* *
11937922 AAAGAAGAGAAAAATAAA-AAAAA-AATTGATAGGGCAAAATGCCAATGTGTTCCACCAATAAAA
1 AAAGAAAAGAAAAA-AAAGAAAAACAATT-ATAGGGCAAAATGCCAATGTGCTCCACCAATAAAA
11937985 CATAAAAAAAGAGA
64 CATAAAAAAAGAGA
11937999 TATTGATGAG
Statistics
Matches: 71, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
81 10 0.14
82 45 0.63
83 13 0.18
84 3 0.04
ACGTcount: A:0.60, C:0.11, G:0.16, T:0.12
Consensus pattern (82 bp):
AAAGAAAAGAAAAAAAAGAAAAACAATTATAGGGCAAAATGCCAATGTGCTCCACCAATAAAACA
TAAAAAAAGAGAGAAAG
Found at i:11938641 original size:15 final size:15
Alignment explanation
Indices: 11938621--11938651 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
11938611 TTCTTCTTAT
11938621 CATTCACTAAATGAA
1 CATTCACTAAATGAA
11938636 CATTCACTAAATGAA
1 CATTCACTAAATGAA
11938651 C
1 C
11938652 CAAGAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.06, T:0.26
Consensus pattern (15 bp):
CATTCACTAAATGAA
Found at i:11939355 original size:18 final size:17
Alignment explanation
Indices: 11939334--11939383 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
11939324 CTTATGAATT
*
11939334 TAAAAGTCTTTGTGAACC
1 TAAAA-TCTTTATGAACC
*
11939352 TAAAATCTTTATGAATC
1 TAAAATCTTTATGAACC
* *
11939369 TAAAACCTCTATGAA
1 TAAAATCTTTATGAA
11939384 TCTTGAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (17 bp):
TAAAATCTTTATGAACC
Found at i:11940274 original size:356 final size:356
Alignment explanation
Indices: 11939788--11940712 Score: 961
Period size: 356 Copynumber: 2.6 Consensus size: 356
11939778 CTCGATTTTA
* * * *
11939788 TCCAGATCATTTTCTGACTC-GTGATTTCATCCCGATCAGTCATCTTCGACCTTGACTC-GATCT
1 TCCAGATCATTTTTTGACTCAGAG-TTCCATCCCGATCAGTCATCTTTGACCTTGACTCAG-TCT
* * * * *
11939851 TGGTCACTTTATTTTTAGACTCGTGATTTTGTCTCA-GTCATTCGATCTCGGCTTAGTCTAGATC
64 TGGTCACTTTATCTTTAGACTCATGATTTCGTCT-AGGTCATTCGATCTCAGCTTAGTCTAAATC
* * *
11939915 ATTTAC-TAACTTATGATTCCATCCCAGTTAGTCATTTTTTACCTTGACTCGATCTTAGTTGCTT
128 ATTT-CTTAACTTATGGTTCCATCTC-GTTAGTCATTTTTAACCTTGACTCGATCTTAGTTGCTT
* * *
11939979 TATCTTTAGACTCAC-AGTTTCATTTCAGTTATTTGATCTCGACTTAGTCTAGATCATTT-TCTG
191 TATCTTTAGACTCACGA-TTTCATTTCAATCATTTAATCTCGACTTAGTCTAGATCATTTCT-TG
* * *** * *
11940042 ATTTATGGCATCGTCTTGGTCAATCATCTTCGATCTTGACTTAATCCTGATCGCTTTATCTTTAG
254 ACTCATGGCATCGTCTCAATCAATCATCTTCGACCTTGACTTAATCCTGATCGCTTTATCTTTAA
* ** * *
11940107 ACTCATGATTTTGTC-CTAACCATTCGATCTCAGCTTAG
319 ACTCACGATTTCATCTC-AACCATTAGATCTCAACTTAG
* *** *
11940145 TCTAGATCATTTTTTGA-TCACGA-TTCCATTTTGGTCAGTCATCTTTGACCTTGACTCAGTCTT
1 TCCAGATCATTTTTTGACTCA-GAGTTCCATCCCGATCAGTCATCTTTGACCTTGACTCAGTCTT
* *
11940208 GGTCACTTTATCTTCAGACTCATGATTTCGTCTAGGTCATTCGATCTCAGTTTAGTCTAAATCAT
65 GGTCACTTTATCTTTAGACTCATGATTTCGTCTAGGTCATTCGATCTCAGCTTAGTCTAAATCAT
* ** * * * * *
11940273 TTCTTAACTCATGGTTATATCTCGGTCAATCATTTTCAACCTTGACTCAATCCTAGTTGCTTTAT
130 TTCTTAACTTATGGTTCCATCTC-GTTAGTCATTTTTAACCTTGACTCGATCTTAGTTGCTTTAT
* *
11940338 CTTTAGACTCACGATTTCATTTCAATCATTTAATTTTGACTTAGTCTAGATCATTTCTTGACTCA
194 CTTTAGACTCACGATTTCATTTCAATCATTTAATCTCGACTTAGTCTAGATCATTTCTTGACTCA
** * ** * * * *
11940403 TGGTTTCGTCTCAATCAGTCATCTTCGACCTTGACTTGGTCTTGGTTGTTTTATCTTTAAACTCA
259 TGGCATCGTCTCAATCAATCATCTTCGACCTTGACTTAATCCTGATCGCTTTATCTTTAAACTCA
**
11940468 CGATTTCATCTCAGTCATTAGATCTCAACTTAG
324 CGATTTCATCTCAACCATTAGATCTCAACTTAG
* * * * * * *
11940501 TCCAGATCATTTTTTGACTTATAGTTTCATCCCGATCAATCCTTGTTTGACCTTGACTCAGTCCT
1 TCCAGATCATTTTTTGACTCAGAGTTCCATCCCGATCAGT-CATCTTTGACCTTGACTCAGTCTT
* * * * * * * * *
11940566 GATCGCTTTATCTTTAGACTTACGATTTCATCTCGGTCATTCAATCTCAACTTAGTCCAAATCAT
65 GGTCACTTTATCTTTAGACTCATGATTTCGTCTAGGTCATTCGATCTCAGCTTAGTCTAAATCAT
* * * * * *
11940631 TTCTTGATTTATGGTTCCATCTCGATTAGTCATCTTTGACCTAGACTCGATCTT-GATCGCTTTA
130 TTCTTAACTTATGGTTCCATCTCG-TTAGTCATTTTTAACCTTGACTCGATCTTAG-TTGCTTTA
*
11940695 TTTTTAGACTCACGATTT
193 TCTTTAGACTCACGATTT
11940713 GATCCCGATC
Statistics
Matches: 461, Mismatches: 94, Indels: 25
0.79 0.16 0.04
Matches are distributed among these distances:
355 2 0.00
356 287 0.62
357 33 0.07
358 139 0.30
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (356 bp):
TCCAGATCATTTTTTGACTCAGAGTTCCATCCCGATCAGTCATCTTTGACCTTGACTCAGTCTTG
GTCACTTTATCTTTAGACTCATGATTTCGTCTAGGTCATTCGATCTCAGCTTAGTCTAAATCATT
TCTTAACTTATGGTTCCATCTCGTTAGTCATTTTTAACCTTGACTCGATCTTAGTTGCTTTATCT
TTAGACTCACGATTTCATTTCAATCATTTAATCTCGACTTAGTCTAGATCATTTCTTGACTCATG
GCATCGTCTCAATCAATCATCTTCGACCTTGACTTAATCCTGATCGCTTTATCTTTAAACTCACG
ATTTCATCTCAACCATTAGATCTCAACTTAG
Found at i:11940632 original size:239 final size:238
Alignment explanation
Indices: 11939812--11940770 Score: 750
Period size: 238 Copynumber: 4.0 Consensus size: 238
11939802 TGACTCGTGA
* * * * * * * * **
11939812 TTTCATCCCGATCAGTCATCTTCGACCTTGACTCGATCTTGGTCACTTTATTTTTAGACTCGTGA
1 TTTCATCCCGATCAATCATTTTCAACCTTGACTCAATCCTAGTCGCTTTATCTTTAGACTCACGA
** * * ** * * * * * *
11939877 TTTTGTCTCAGTCATTCGATCTCGGCTTAGTCTAGATCATTTAC-TAACTTATGATTCCATCCCA
66 TTTCATCTCAATCATTCAATCTCAACTTAGTCCAAATCATTT-CTTGACTCATGGTTCCATCTCA
* * * * * * * *
11939941 GTTAGTCATTTTTTACCTTGACTCGATCTTAGTTGCTTTATCTTTAGACTCAC-AGTTTCATTTC
130 ATCAGTCATCTTTGACCTTGACTCGGTCTTGGTCGCTTTATCTTTAGACTCACGA-TTTCATCTC
* * * * * * *
11940005 AGTTATTTGATCTCGACTTAGTCTAGATCATTT-TCTGATTTATGG
194 AGTCATTCGATCTCAACTTAGTCCAAATCATTTCT-TAACTTATGG
** * ** * * * * * *
11940050 CATCGTCTTGGTCAATCATCTTCGATCTTGACTTAATCCT-GATCGCTTTATCTTTAGACTCATG
1 TTTCATCCCGATCAATCATTTTCAACCTTGACTCAATCCTAG-TCGCTTTATCTTTAGACTCACG
** * * * * * * * * * *
11940114 ATTTTGTC-CTAACCATTCGATCTCAGCTTAGTCTAGATCATTTTTTGA-TCACGATTCCATTTT
65 ATTTCATCTC-AATCATTCAATCTCAACTTAGTCCAAATCATTTCTTGACTCATGGTTCCATCTC
** * * * * *
11940177 GGTCAGTCATCTTTGACCTTGACTCAGTCTTGGTCACTTTATCTTCAGACTCATGATTTCGTCT-
129 AATCAGTCATCTTTGACCTTGACTCGGTCTTGGTCGCTTTATCTTTAGACTCACGATTTCATCTC
** * *
11940241 AGGTCATTCGATCTCAGTTTAGTCTAAATCATTTCTTAACTCATGG
194 A-GTCATTCGATCTCAACTTAGTCCAAATCATTTCTTAACTTATGG
* * *
11940287 TTAT-ATCTCGGTCAATCATTTTCAACCTTGACTCAATCCTAGTTGCTTTATCTTTAGACTCACG
1 TT-TCATCCCGATCAATCATTTTCAACCTTGACTCAATCCTAGTCGCTTTATCTTTAGACTCACG
* * * ** * * * *
11940351 ATTTCATTTCAATCATTTAATTTTGACTTAGTCTAGATCATTTCTTGACTCATGGTTTCGTCTCA
65 ATTTCATCTCAATCATTCAATCTCAACTTAGTCCAAATCATTTCTTGACTCATGGTTCCATCTCA
* * * * *
11940416 ATCAGTCATCTTCGACCTTGACTTGGTCTTGGTTGTTTTATCTTTAAACTCACGATTTCATCTCA
130 ATCAGTCATCTTTGACCTTGACTCGGTCTTGGTCGCTTTATCTTTAGACTCACGATTTCATCTCA
* * * * *
11940481 GTCATTAGATCTCAACTTAGTCCAGATCATTTTTTGACTTATAG
195 GTCATTCGATCTCAACTTAGTCCAAATCATTTCTTAACTTATGG
* ** * *
11940525 TTTCATCCCGATCAATCCTTGTTTGACCTTGACTCAGTCCT-GATCGCTTTATCTTTAGACTTAC
1 TTTCATCCCGATCAATCATT-TTCAACCTTGACTCAATCCTAG-TCGCTTTATCTTTAGACTCAC
** * *
11940589 GATTTCATCTCGGTCATTCAATCTCAACTTAGTCCAAATCATTTCTTGATTTATGGTTCCATCTC
64 GATTTCATCTCAATCATTCAATCTCAACTTAGTCCAAATCATTTCTTGACTCATGGTTCCATCTC
* * * * * * *
11940654 GATTAGTCATCTTTGACCTAGACTCGATCTTGATCGCTTTATTTTTAGACTCACGATTTGATC-C
129 AATCAGTCATCTTTGACCTTGACTCGGTCTTGGTCGCTTTATCTTTAGACTCACGATTTCATCTC
* * *
11940718 CGATCATTCGATCTCAACTTAGTCCAAATAATTTCTTAATTTATGG
194 AG-TCATTCGATCTCAACTTAGTCCAAATCATTTCTTAACTTATGG
11940764 TTTCATC
1 TTTCATC
11940771 TCAGTTAGTC
Statistics
Matches: 571, Mismatches: 135, Indels: 29
0.78 0.18 0.04
Matches are distributed among these distances:
236 1 0.00
237 180 0.32
238 207 0.36
239 183 0.32
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (238 bp):
TTTCATCCCGATCAATCATTTTCAACCTTGACTCAATCCTAGTCGCTTTATCTTTAGACTCACGA
TTTCATCTCAATCATTCAATCTCAACTTAGTCCAAATCATTTCTTGACTCATGGTTCCATCTCAA
TCAGTCATCTTTGACCTTGACTCGGTCTTGGTCGCTTTATCTTTAGACTCACGATTTCATCTCAG
TCATTCGATCTCAACTTAGTCCAAATCATTTCTTAACTTATGG
Found at i:11940807 original size:119 final size:121
Alignment explanation
Indices: 11939812--11940851 Score: 556
Period size: 119 Copynumber: 8.7 Consensus size: 121
11939802 TGACTCGTGA
* * * * * * * **
11939812 TTTCATC-CCGATCAGTCATCTTCGACCTTGACTC-GATCTTGGTCACTTTATTTTTAGACTCGT
1 TTTCATCTCAGATCAGTCATCTTTGACCTAGACTCGGTTCTTGATCGCTTTATCTTTAGACTCAC
** ** * * * * *
11939875 GATTTTGTCTC-AGTCATTCGATCTCGGCTTAGTCTAGATCATTTAC-TAACTTATGA
66 GATTTCATCTCGA-TCATTCGATCTCAACTTAGTCCAAATCATTT-CTTGATTTATGG
* * * * * * * *
11939931 TTCCATCCCAG-TTAGTCATTTTTTACCTTGACTC-GATCTT-AGTTGCTTTATCTTTAGACTCA
1 TTTCATCTCAGATCAGTCATCTTTGACCTAGACTCGGTTCTTGA-TCGCTTTATCTTTAGACTCA
* * * * * *
11939993 C-AGTTTCATTTC-AGTTATTTGATCTCGACTTAGTCTAGATCATTT-TCTGATTTATGG
65 CGA-TTTCATCTCGA-TCATTCGATCTCAACTTAGTCCAAATCATTTCT-TGATTTATGG
** * * * * * * * *** * *
11940050 CATCGTCT-TGGTCAATCATCTTCGATCTTGACT-TAATCCTGATCGCTTTATCTTTAGACTCAT
1 TTTCATCTCAGATCAGTCATCTTTGACCTAGACTCGGTTCTTGATCGCTTTATCTTTAGACTCAC
** * * * * * * * * *
11940113 GATTTTGTC-CTAACCATTCGATCTCAGCTTAGTCTAGATCATTTTTTGA-TCACGA
66 GATTTCATCTC-GATCATTCGATCTCAACTTAGTCCAAATCATTTCTTGATTTATGG
* ** * * * * * * *
11940168 TTCCAT-TTTGGTCAGTCATCTTTGACCTTGACTCAG-TCTTGGTCACTTTATCTTCAGACTCAT
1 TTTCATCTCAGATCAGTCATCTTTGACCTAGACTCGGTTCTTGATCGCTTTATCTTTAGACTCAC
* * * ** * * * *
11940231 GATTTCGTCTAGGTCATTCGATCTCAGTTTAGTCTAAATCATTTCTTAACTCATGG
66 GATTTCATCTCGATCATTCGATCTCAACTTAGTCCAAATCATTTCTTGATTTATGG
* * * * ** * * *
11940287 TTAT-ATCTC-GGTCAATCAT-TTTCAACCTTGACTCAATCCTAG-TTGCTTTATCTTTAGACTC
1 TT-TCATCTCAGATCAGTCATCTTT-GACCTAGACTCGGTTCTTGATCGCTTTATCTTTAGACTC
* * ** * ** * * * *
11940348 ACGATTTCATTTCAATCATTTAATTTTGACTTAGTCTAGATCATTTCTTGACTCATGG
64 ACGATTTCATCTCGATCATTCGATCTCAACTTAGTCCAAATCATTTCTTGATTTATGG
* * * * * * * *
11940406 TTTCGTCTCA-ATCAGTCATCTTCGACCTTGACTTGG-TCTTGGTTGTTTTATCTTTAAACTCAC
1 TTTCATCTCAGATCAGTCATCTTTGACCTAGACTCGGTTCTTGATCGCTTTATCTTTAGACTCAC
* * * * *
11940469 GATTTCATCTC-AGTCATTAGATCTCAACTTAGTCCAGATCATTTTTTGACTTATAG
66 GATTTCATCTCGA-TCATTCGATCTCAACTTAGTCCAAATCATTTCTTGATTTATGG
* * * * * * * *
11940525 TTTCATC-CCGATCAATCCTTGTTTGACCTTGACTCAG-TCCTGATCGCTTTATCTTTAGACTTA
1 TTTCATCTCAGATCAGT-CATCTTTGACCTAGACTCGGTTCTTGATCGCTTTATCTTTAGACTCA
* *
11940588 CGATTTCATCTCGGTCATTCAATCTCAACTTAGTCCAAATCATTTCTTGATTTATGG
65 CGATTTCATCTCGATCATTCGATCTCAACTTAGTCCAAATCATTTCTTGATTTATGG
* * * *
11940645 TTCCATCTC-GATTAGTCATCTTTGACCTAGACTC-GATCTTGATCGCTTTATTTTTAGACTCAC
1 TTTCATCTCAGATCAGTCATCTTTGACCTAGACTCGGTTCTTGATCGCTTTATCTTTAGACTCAC
* * * *
11940708 GATTTGATCCCGATCATTCGATCTCAACTTAGTCCAAATAATTTCTTAATTTATGG
66 GATTTCATCTCGATCATTCGATCTCAACTTAGTCCAAATCATTTCTTGATTTATGG
* * * *
11940764 TTTCATCTCAG-TTAGTCATCTTTGACCTAGACTCGGTTC-TGATCGCTTCATCTTTTCGAATCA
1 TTTCATCTCAGATCAGTCATCTTTGACCTAGACTCGGTTCTTGATCGCTTTATC-TTTAGACTCA
* *
11940827 CAATTTCATCAT-GATCATTCAATCT
65 CGATTTCATC-TCGATCATTCGATCT
11940852 TGACTCAACC
Statistics
Matches: 722, Mismatches: 165, Indels: 67
0.76 0.17 0.07
Matches are distributed among these distances:
117 1 0.00
118 102 0.14
119 479 0.66
120 139 0.19
121 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (121 bp):
TTTCATCTCAGATCAGTCATCTTTGACCTAGACTCGGTTCTTGATCGCTTTATCTTTAGACTCAC
GATTTCATCTCGATCATTCGATCTCAACTTAGTCCAAATCATTTCTTGATTTATGG
Found at i:11940835 original size:239 final size:239
Alignment explanation
Indices: 11940179--11940851 Score: 535
Period size: 239 Copynumber: 2.8 Consensus size: 239
11940169 TCCATTTTGG
* * * * * * * * *
11940179 TCAGTCATCTTTGACCTTGACTC-AGTCTTGGTCACTTTATCTTCAGACTCATGATTTCGT-CTA
1 TCAGTCATCTTCGACCTAGACTCGA-TCTTGATCGCTTTATCTTTAAACTCACGATTTCATCCCA
* ** * * * * *
11940242 GGTCATTCGATCTCAGTTTAGTCTAAATCATTTCTTAACTCATGGTTAT-ATCTC-GGTCAAT-C
65 -GTCATTAGATCTCAACTTAGTCCAAATAATTTCTTAACTTATAGTT-TCATC-CAGATCAATCC
* * * * * * *
11940304 AT-TTTCAACCTTGACTCAATCCT-AGTTGCTTTATCTTTAGACTCACGATTTCATTTCA--ATC
127 ATCTTT-GACCTAGACTCAGTCCTGA-TCGCTTCATCTTTAGAATCACAATTTCA--TCATGATC
* * ** * * * *
11940365 ATTTAATTTTGACTTAGTCTAGATCATTTCTTGACTCATGGTTTCGTCTCAA
188 ATTCAATCTCAACTTAGTCCAAATCATTTCTTGACTCATGGTTCCATCTCAA
* * * * * * *
11940417 TCAGTCATCTTCGACCTTGACTTGGTCTTGGTTGTTTTATCTTTAAACTCACGATTTCATCTCAG
1 TCAGTCATCTTCGACCTAGACTCGATCTTGATCGCTTTATCTTTAAACTCACGATTTCATCCCAG
* * * * * * *
11940482 TCATTAGATCTCAACTTAGTCCAGATCATTTTTTGACTTATAGTTTCATCCCGATCAATCCTTGT
66 TCATTAGATCTCAACTTAGTCCAAATAATTTCTTAACTTATAGTTTCATCCAGATCAATCCATCT
* * * * * *
11940547 TTGACCTTGACTCAGTCCTGATCGCTTTATCTTTAGACTTACGATTTCATC-TCGGTCATTCAAT
131 TTGACCTAGACTCAGTCCTGATCGCTTCATCTTTAGAATCACAATTTCATCAT-GATCATTCAAT
* * *
11940611 CTCAACTTAGTCCAAATCATTTCTTGATTTATGGTTCCATCTCGA
195 CTCAACTTAGTCCAAATCATTTCTTGACTCATGGTTCCATCTCAA
* * * * *
11940656 TTAGTCATCTTTGACCTAGACTCGATCTTGATCGCTTTATTTTTAGACTCACGATTTGATCCC-G
1 TCAGTCATCTTCGACCTAGACTCGATCTTGATCGCTTTATCTTTAAACTCACGATTTCATCCCAG
* * * * *
11940720 ATCATTCGATCTCAACTTAGTCCAAATAATTTCTTAATTTATGGTTTCATCTCAG-TTAGT-CAT
66 -TCATTAGATCTCAACTTAGTCCAAATAATTTCTTAACTTATAGTTTCATC-CAGATCAATCCAT
* * *
11940783 CTTTGACCTAGACTCGGTTCTGATCGCTTCATCTTTTCGAATCACAATTTCATCATGATCATTCA
129 CTTTGACCTAGACTCAGTCCTGATCGCTTCATC-TTTAGAATCACAATTTCATCATGATCATTCA
11940848 ATCT
193 ATCT
11940852 TGACTCAACC
Statistics
Matches: 349, Mismatches: 72, Indels: 27
0.78 0.16 0.06
Matches are distributed among these distances:
237 4 0.01
238 126 0.36
239 212 0.61
240 7 0.02
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (239 bp):
TCAGTCATCTTCGACCTAGACTCGATCTTGATCGCTTTATCTTTAAACTCACGATTTCATCCCAG
TCATTAGATCTCAACTTAGTCCAAATAATTTCTTAACTTATAGTTTCATCCAGATCAATCCATCT
TTGACCTAGACTCAGTCCTGATCGCTTCATCTTTAGAATCACAATTTCATCATGATCATTCAATC
TCAACTTAGTCCAAATCATTTCTTGACTCATGGTTCCATCTCAA
Found at i:11942143 original size:18 final size:19
Alignment explanation
Indices: 11942105--11942145 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
11942095 TCCTTTTCCT
**
11942105 TTTTCATTTTATTTTTTTA
1 TTTTCATTTTATTTTAATA
11942124 TTTTCA-TTTATTTTAATA
1 TTTTCATTTTATTTTAATA
11942142 TTTT
1 TTTT
11942146 AAGATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCATTTTATTTTAATA
Found at i:11942174 original size:30 final size:31
Alignment explanation
Indices: 11942119--11942176 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
11942109 CATTTTATTT
*
11942119 TTTTATTTTCATTTATTTTAATATTTTAAGA
1 TTTTATTTTCAGTTATTTTAATATTTTAAGA
* *
11942150 TTTTATTTTTAGTT-TTTTATTATTTTA
1 TTTTATTTTCAGTTATTTTAATATTTTA
11942177 TTATTATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (31 bp):
TTTTATTTTCAGTTATTTTAATATTTTAAGA
Found at i:11942182 original size:11 final size:11
Alignment explanation
Indices: 11942149--11942194 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
11942139 ATATTTTAAG
*
11942149 ATTTTATTTTT
1 ATTTTATTATT
11942160 AGTTTT-TTATT
1 A-TTTTATTATT
11942171 ATTTTATTATT
1 ATTTTATTATT
*
11942182 ATTCTATT-TT
1 ATTTTATTATT
11942192 ATT
1 ATT
11942195 GGTTTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 9 0.29
11 18 0.58
12 4 0.13
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (11 bp):
ATTTTATTATT
Found at i:11942328 original size:21 final size:21
Alignment explanation
Indices: 11942303--11942354 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
11942293 AAAAACAAAA
11942303 AAATAAAAAAA-ATCTTTTCC
1 AAATAAAAAAAGATCTTTTCC
*
11942323 ATAATAAAAAAATGATCTTTTTC
1 A-AATAAAAAAA-GATCTTTTCC
11942346 AAATAAAAA
1 AAATAAAAA
11942355 TCCTTACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.04
21 10 0.36
22 8 0.29
23 9 0.32
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.31
Consensus pattern (21 bp):
AAATAAAAAAAGATCTTTTCC
Found at i:11942333 original size:23 final size:22
Alignment explanation
Indices: 11942307--11942354 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
11942297 ACAAAAAAAT
11942307 AAAAAAAATCTTTTCCATAATAA
1 AAAAAAAATCTTTTCCA-AATAA
** *
11942330 AAAAATGATCTTTTTCAAATAA
1 AAAAAAAATCTTTTCCAAATAA
11942352 AAA
1 AAA
11942355 TCCTTACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAAAAATCTTTTCCAAATAA
Found at i:11947483 original size:32 final size:32
Alignment explanation
Indices: 11947447--11947512 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
11947437 ACTAAGGGGT
11947447 AAATAGAAAGCTTACAAGTTCAATCTTATCAA
1 AAATAGAAAGCTTACAAGTTCAATCTTATCAA
11947479 AAATAGAAAGCTTACAAGTTCAATCTTATCAA
1 AAATAGAAAGCTTACAAGTTCAATCTTATCAA
11947511 AA
1 AA
11947513 CACTAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.27
Consensus pattern (32 bp):
AAATAGAAAGCTTACAAGTTCAATCTTATCAA
Found at i:11947530 original size:32 final size:32
Alignment explanation
Indices: 11947447--11947530 Score: 100
Period size: 32 Copynumber: 2.6 Consensus size: 32
11947437 ACTAAGGGGT
* *
11947447 AAATAGAAAGCTTACAAGTTCAATCTTATCAA
1 AAATAGAAAGCATAAAAGTTCAATCTTATCAA
* *
11947479 AAATAGAAAGCTTACAAGTTCAATCTTATCAA
1 AAATAGAAAGCATAAAAGTTCAATCTTATCAA
11947511 AACACTA-AAAG-ATAAAAGTT
1 AA-A-TAGAAAGCATAAAAGTT
11947531 ATGTTTATCT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
32 41 0.85
33 5 0.10
34 2 0.04
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (32 bp):
AAATAGAAAGCATAAAAGTTCAATCTTATCAA
Found at i:11954751 original size:1 final size:1
Alignment explanation
Indices: 11954745--11954785 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
11954735 CACAAAAGCC
11954745 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11954786 CCTTGGTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11956533 original size:3 final size:3
Alignment explanation
Indices: 11956525--11956552 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
11956515 ACTCTTTCCC
11956525 CCT CCT CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT C
11956553 AAGATACCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:11958786 original size:2 final size:2
Alignment explanation
Indices: 11958779--11958813 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
11958769 CATTATAGTA
11958779 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11958814 TCTATTTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:11958796 original size:21 final size:21
Alignment explanation
Indices: 11958770--11958814 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
11958760 TTCCATGTTC
11958770 ATTATAGTA-ATATATATATAT
1 ATTATA-TATATATATATATAT
11958791 ATTATATATATATATATATAT
1 ATTATATATATATATATATAT
11958812 ATT
1 ATT
11958815 CTATTTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTATATATATATATATATAT
Found at i:11968058 original size:2 final size:2
Alignment explanation
Indices: 11968051--11968078 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11968041 AACGTCTAGA
11968051 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11968079 CAGGATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11969765 original size:16 final size:15
Alignment explanation
Indices: 11969734--11969773 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
11969724 TAATTAATCC
* *
11969734 AAAATAACTAAATTT
1 AAAATAATTGAATTT
11969749 AAAATGAATTGAATTT
1 AAAAT-AATTGAATTT
11969765 AAAATAATT
1 AAAATAATT
11969774 TAAATCCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (15 bp):
AAAATAATTGAATTT
Found at i:11972184 original size:94 final size:94
Alignment explanation
Indices: 11972080--11972270 Score: 258
Period size: 94 Copynumber: 2.0 Consensus size: 94
11972070 ATTTACAAAC
* * * *
11972080 AAAATTAATAAAAATGACGCATAATCTT-TATAAAATTCAAATAAAACCAAATTTAAGTTCATCT
1 AAAATTAAT-AAAATGACGCATAATCTTAAAAAAAATTCAAATAAAACCAAATTTAACTTCAACT
11972144 AAAATTAATGGAATTTAAAACAATCGGACA
65 AAAATTAATGGAATTTAAAACAATCGGACA
* * * *
11972174 AAAATTAATAAAATGACGCGTATTCTTAAAAAAAATTCAAGTAAAGCCAAATTTAACTTCAACTA
1 AAAATTAATAAAATGACGCATAATCTTAAAAAAAATTCAAATAAAACCAAATTTAACTTCAACTA
* * * *
11972239 GAATTTATGGAATTTAAAACAATGGGAGA
66 AAATTAATGGAATTTAAAACAATCGGACA
11972268 AAA
1 AAA
11972271 GAGCCTGTGG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 16 0.19
94 68 0.81
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.28
Consensus pattern (94 bp):
AAAATTAATAAAATGACGCATAATCTTAAAAAAAATTCAAATAAAACCAAATTTAACTTCAACTA
AAATTAATGGAATTTAAAACAATCGGACA
Found at i:11974420 original size:19 final size:19
Alignment explanation
Indices: 11974384--11974428 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
11974374 CTTAAAATTT
* **
11974384 TTAAAAAATATTTGAAAAA
1 TTAAAAAATAATAAAAAAA
*
11974403 TTAAAAAATAATAAAAAAG
1 TTAAAAAATAATAAAAAAA
11974422 TTAAAAA
1 TTAAAAA
11974429 TTGATTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (19 bp):
TTAAAAAATAATAAAAAAA
Found at i:11974639 original size:27 final size:26
Alignment explanation
Indices: 11974604--11974656 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
11974594 ATTTTCTAAT
*
11974604 TTTTAATTTTTTAAAAAAATAATATTTC
1 TTTTAA-TTTTT-AAAAAATAAGATTTC
11974632 TTTT-ATTTTTAAAAAATAAGATTTC
1 TTTTAATTTTTAAAAAATAAGATTTC
11974657 AATTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 14 0.58
26 5 0.21
27 1 0.04
28 4 0.17
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (26 bp):
TTTTAATTTTTAAAAAATAAGATTTC
Found at i:11974662 original size:26 final size:26
Alignment explanation
Indices: 11974611--11974662 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
11974601 AATTTTTAAT
* *
11974611 TTTTTAAAAAAATAATATTTCTTTTA
1 TTTTTAAAAAAATAAGATTTCATTTA
11974637 TTTTT-AAAAAATAAGATTTCAATTTA
1 TTTTTAAAAAAATAAGATTTC-ATTTA
11974663 AAAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTTAAAAAAATAAGATTTCATTTA
Found at i:11976780 original size:29 final size:31
Alignment explanation
Indices: 11976717--11976780 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
11976707 AAATTAAATT
*
11976717 TTATATCTTTTATATATTTTCTTTTCTATTA
1 TTATATCTTTTATATATTTTATTTTCTATTA
11976748 --ATATCTTTTAT-TATTTTATTTT-TATTA
1 TTATATCTTTTATATATTTTATTTTCTATTA
11976775 TTATAT
1 TTATAT
11976781 AATTCCCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
27 5 0.17
28 10 0.33
29 15 0.50
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (31 bp):
TTATATCTTTTATATATTTTATTTTCTATTA
Found at i:11978220 original size:13 final size:12
Alignment explanation
Indices: 11978189--11978219 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
11978179 TTTGCTTCAA
11978189 TTTTTTTATTGG
1 TTTTTTTATTGG
*
11978201 TTTTTTTATTAG
1 TTTTTTTATTGG
11978213 TTTTTTT
1 TTTTTTT
11978220 TGTTTGCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.81
Consensus pattern (12 bp):
TTTTTTTATTGG
Found at i:11979269 original size:31 final size:31
Alignment explanation
Indices: 11979199--11979270 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
11979189 TCGTAGGTTG
* *
11979199 AATGAAATGATTATGATTAAATCACAACTCA
1 AATGAAATGATCAAGATTAAATCACAACTCA
* * * *
11979230 AATAAAATGATCAAGATTAAATCGCAAGTCG
1 AATGAAATGATCAAGATTAAATCACAACTCA
*
11979261 AGTGAAATGA
1 AATGAAATGA
11979271 CGGTTAATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (31 bp):
AATGAAATGATCAAGATTAAATCACAACTCA
Found at i:11979372 original size:22 final size:22
Alignment explanation
Indices: 11979344--11979419 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
11979334 TTTTTATAAG
**
11979344 TGCCAACTAATCTAAGCTTACA
1 TGCCAACTAATCTGGGCTTACA
11979366 TGCCAACTAATCTGGGCTTACA
1 TGCCAACTAATCTGGGCTTACA
*
11979388 TGCCAATTAATCTGGGCTTACA
1 TGCCAACTAATCTGGGCTTACA
11979410 TGCCAACTAA
1 TGCCAACTAA
11979420 GCCCAACCAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (22 bp):
TGCCAACTAATCTGGGCTTACA
Found at i:11979573 original size:33 final size:31
Alignment explanation
Indices: 11979530--11979662 Score: 115
Period size: 32 Copynumber: 4.1 Consensus size: 31
11979520 TAAACTAACC
* *
11979530 TTAAAATTTCATTAGGTGCCAGCTAAACTGGGT
1 TTAAATTTTCATT-GGTGCCAGC-AAACTGAGT
* * * * *
11979563 TTAAGTTTTCATTTGTGCCAACCAACTTGGGT
1 TTAAATTTTCATTGGTGCCAGCAAAC-TGAGT
* *
11979595 TTAAACTATCATTGG-GCCAGACAAACTGAGT
1 TTAAATTTTCATTGGTGCCAG-CAAACTGAGT
*
11979626 TTAAATTTTCATGGAGTGCCAGCTAAACTGAGT
1 TTAAATTTTCATTG-GTGCCAGC-AAACTGAGT
11979659 TTAA
1 TTAA
11979663 TTCTTATAGG
Statistics
Matches: 80, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
31 22 0.28
32 29 0.36
33 29 0.36
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (31 bp):
TTAAATTTTCATTGGTGCCAGCAAACTGAGT
Found at i:11979630 original size:31 final size:33
Alignment explanation
Indices: 11979593--11979662 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
11979583 ACCAACTTGG
*
11979593 GTTTAAACTATCATTG-G-GCCAGAC-AAACTGA
1 GTTTAAACTATCATGGAGTGCCAG-CTAAACTGA
* *
11979624 GTTTAAATTTTCATGGAGTGCCAGCTAAACTGA
1 GTTTAAACTATCATGGAGTGCCAGCTAAACTGA
11979657 GTTTAA
1 GTTTAA
11979663 TTCTTATAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 13 0.39
32 2 0.06
33 18 0.55
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (33 bp):
GTTTAAACTATCATGGAGTGCCAGCTAAACTGA
Found at i:11980017 original size:22 final size:22
Alignment explanation
Indices: 11979971--11980068 Score: 90
Period size: 22 Copynumber: 4.5 Consensus size: 22
11979961 ATACTTTTTT
* *
11979971 AGCTAATATGGGCTTA-AGTGTC
1 AGCTAATTTGGGCTTATA-TGCC
11979993 AGCTAATTTGGGCTTATATGCC
1 AGCTAATTTGGGCTTATATGCC
* ** **
11980015 AGCTAAATTGGATTTATGCGCC
1 AGCTAATTTGGGCTTATATGCC
* *
11980037 AGCTAATTTGAGCTTATATGCT
1 AGCTAATTTGGGCTTATATGCC
*
11980059 AGTTAATTTG
1 AGCTAATTTG
11980069 AACTTTCGTA
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 59 0.98
23 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (22 bp):
AGCTAATTTGGGCTTATATGCC
Found at i:11980199 original size:29 final size:29
Alignment explanation
Indices: 11980131--11980201 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
11980121 TGCTAACTAC
* *
11980131 ACTAGGCTTAAAACTTAAATGTAAGCTAA
1 ACTAGGCTTAAATCTTAAATATAAGCTAA
** * *
11980160 ACTAGATTTAAATCTTAGATATCAGCTAA
1 ACTAGGCTTAAATCTTAAATATAAGCTAA
11980189 ACTAGGCTTAAAT
1 ACTAGGCTTAAAT
11980202 TCTTTCTCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (29 bp):
ACTAGGCTTAAATCTTAAATATAAGCTAA
Found at i:11981203 original size:22 final size:21
Alignment explanation
Indices: 11981155--11981248 Score: 77
Period size: 23 Copynumber: 4.3 Consensus size: 21
11981145 CACCCATTCG
*
11981155 TTTCTTTC-TTTCTTTTTCTTC
1 TTTCTTTCATTT-TTTTTCTTT
*
11981176 TTTCTTTTATTTTTTTTC-TT
1 TTTCTTTCATTTTTTTTCTTT
11981196 TTTCTCTTCACTTTTTTCTT-TTT
1 TTTCT-TTCA-TTTTTT-TTCTTT
* *
11981219 CATTCTTCCACTTTTTTTTCTTT
1 -TTTCTTTCA-TTTTTTTTCTTT
11981242 TTTCTTT
1 TTTCTTT
11981249 AAATGGATCC
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
20 6 0.10
21 16 0.27
22 16 0.27
23 17 0.29
24 4 0.07
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTCTTTCATTTTTTTTCTTT
Found at i:11981209 original size:27 final size:26
Alignment explanation
Indices: 11981163--11981219 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
11981153 CGTTTCTTTC
* *
11981163 TTTCTTTTTCTTCTTTCTTTTATTTTT
1 TTTCTTTTTCTTCTTACTTTT-TTCTT
11981190 TTTCTTTTTC-TCTTCACTTTTTTCTT
1 TTTCTTTTTCTTCTT-ACTTTTTTCTT
11981216 TTTC
1 TTTC
11981220 ATTCTTCCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTCTTTTTCTTCTTACTTTTTTCTT
Found at i:11981235 original size:25 final size:22
Alignment explanation
Indices: 11981162--11981247 Score: 83
Period size: 20 Copynumber: 3.9 Consensus size: 22
11981152 TCGTTTCTTT
*
11981162 CTTTCTTTTTCTTCTTTCT-TTTA
1 CTTT-TTTTTCTT-TTTCTCTTCA
11981185 -TTTTTTTTCTTTTTCTCTTCA
1 CTTTTTTTTCTTTTTCTCTTCA
11981206 C--TTTTTTCTTTTTCATTCTTCCA
1 CTTTTTTTTCTTTTTC--TCTT-CA
11981229 CTTTTTTTTCTTTTT-TCTT
1 CTTTTTTTTCTTTTTCTCTT
11981248 TAAATGGATC
Statistics
Matches: 55, Mismatches: 1, Indels: 15
0.77 0.01 0.21
Matches are distributed among these distances:
20 18 0.33
21 11 0.20
22 11 0.20
23 3 0.05
25 12 0.22
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (22 bp):
CTTTTTTTTCTTTTTCTCTTCA
Found at i:11982500 original size:9 final size:9
Alignment explanation
Indices: 11982478--11982510 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
11982468 TTAAAACTTG
11982478 TTTTTTCCT
1 TTTTTTCCT
11982487 CTTTTTTCCT
1 -TTTTTTCCT
11982497 TTTTTT-CT
1 TTTTTTCCT
11982505 TTTTTT
1 TTTTTT
11982511 TTAAGGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 6 0.26
10 9 0.39
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:11983254 original size:3 final size:3
Alignment explanation
Indices: 11983246--11983333 Score: 61
Period size: 3 Copynumber: 29.7 Consensus size: 3
11983236 ATCATGAATT
* * * * * * *
11983246 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ACA AGA ACA ACA AGA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
11983294 ACA AGA ACA ATA ACA ACA ATA ATA ATA ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
11983334 TTATTATTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
2 2 0.03
3 72 0.97
ACGTcount: A:0.66, C:0.10, G:0.03, T:0.20
Consensus pattern (3 bp):
ATA
Found at i:11983329 original size:9 final size:9
Alignment explanation
Indices: 11983248--11983327 Score: 70
Period size: 9 Copynumber: 8.9 Consensus size: 9
11983238 CATGAATTAT
*
11983248 AATAATAAT
1 AATAATAAC
*
11983257 AATAATAAT
1 AATAATAAC
11983266 AATAATAAC
1 AATAATAAC
* *
11983275 AACAAGAAC
1 AATAATAAC
* *
11983284 AACAAGAAC
1 AATAATAAC
* *
11983293 AACAAGAAC
1 AATAATAAC
*
11983302 AATAACAAC
1 AATAATAAC
*
11983311 AATAATAAT
1 AATAATAAC
11983320 AATAATAA
1 AATAATAA
11983328 TATAATTTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 64 1.00
ACGTcount: A:0.68, C:0.11, G:0.04, T:0.17
Consensus pattern (9 bp):
AATAATAAC
Found at i:11983554 original size:3 final size:3
Alignment explanation
Indices: 11983548--11983603 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
11983538 GTTATTATTA
* * * * *
11983548 TTG TTG TTT TTG TTG TTG TTA TTG TTG TTA TTG TTA TTA TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
11983596 TTG TTG TT
1 TTG TTG TT
11983604 ATTATTATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.07, C:0.00, G:0.23, T:0.70
Consensus pattern (3 bp):
TTG
Found at i:11983560 original size:9 final size:9
Alignment explanation
Indices: 11983560--11983606 Score: 76
Period size: 9 Copynumber: 5.2 Consensus size: 9
11983550 GTTGTTTTTG
11983560 TTGTTGTTA
1 TTGTTGTTA
11983569 TTGTTGTTA
1 TTGTTGTTA
*
11983578 TTGTTATTA
1 TTGTTGTTA
*
11983587 TTGTTGTTG
1 TTGTTGTTA
11983596 TTGTTGTTA
1 TTGTTGTTA
11983605 TT
1 TT
11983607 ATTATTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.11, C:0.00, G:0.21, T:0.68
Consensus pattern (9 bp):
TTGTTGTTA
Found at i:11983608 original size:3 final size:3
Alignment explanation
Indices: 11983602--11983628 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11983592 GTTGTTGTTG
11983602 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
11983629 ATTTACATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11984908 original size:60 final size:61
Alignment explanation
Indices: 11984844--11984995 Score: 168
Period size: 60 Copynumber: 2.5 Consensus size: 61
11984834 CATGTCTTTA
* ** *
11984844 TTCAAGGAAAATTGATACTTTCAACTTTTTTTCAAAAAA-ACATCTTTCAAAATTTTTAT-T
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAATACATCTTTCAAAA-TTTAATCT
* * ** * *
11984904 TTCAAGAAAAATTGATACTCTCAA-TCTTCCCTCAAAAAATATTTTTTTGAAAATTTAATCT
1 TTCAAGAAAAATTGATACTTTCAACT-TTTCCTCAAAAAATACATCTTTCAAAATTTAATCT
11984965 TT-AAGAAAAATTGATACTTTCAACTTTTCCT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCT
11984996 TAAAGTTTAT
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
59 1 0.01
60 62 0.82
61 13 0.17
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.41
Consensus pattern (61 bp):
TTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAATACATCTTTCAAAATTTAATCT
Found at i:11985329 original size:3 final size:3
Alignment explanation
Indices: 11985321--11985352 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11985311 AAATAAGCAA
11985321 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11985353 ACAAATAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11986985 original size:85 final size:85
Alignment explanation
Indices: 11986862--11987057 Score: 284
Period size: 85 Copynumber: 2.3 Consensus size: 85
11986852 AAGAATCCAG
* * * *
11986862 CATAGGTCGAAATCCCAAAACAAAATGACCTAGATTGAACTGAAGTTTTAAATAAATAACCTAGA
1 CATAGGTCAAAAT-CCAAAACAAAATGACCTAAATTGAACTAAAGTTTGAAATAAATAACCTAGA
* * *
11986927 TTGACCCGATGATAGATATGA
65 CTGACCCAAAGATAGATATGA
*
11986948 CATAGGTCAAAATCCAAAACAAAATGACCTAAATTGAACTAAAGTTTGAAATAAGTAACCTAGAC
1 CATAGGTCAAAATCCAAAACAAAATGACCTAAATTGAACTAAAGTTTGAAATAAATAACCTAGAC
*
11987013 TGACCCAAAGATAGATTTGA
66 TGACCCAAAGATAGATATGA
* *
11987033 CATAGTTCAAAATCTAAAACAAAAT
1 CATAGGTCAAAATCCAAAACAAAAT
11987058 AATCTGGATG
Statistics
Matches: 99, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 87 0.88
86 12 0.12
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.23
Consensus pattern (85 bp):
CATAGGTCAAAATCCAAAACAAAATGACCTAAATTGAACTAAAGTTTGAAATAAATAACCTAGAC
TGACCCAAAGATAGATATGA
Found at i:11987087 original size:85 final size:85
Alignment explanation
Indices: 11986913--11987249 Score: 290
Period size: 85 Copynumber: 4.0 Consensus size: 85
11986903 GAAGTTTTAA
* * * * *
11986913 ATAAATAACCTAGATTGACCCGATGATAGATATGACATAGGTCAAAATCCAAAACAAAATGACCT
1 ATAAGTAACCTAGACTGACCCGATGATAGATCTGACATAGGTCAAAATCCAAAACAAAATAATCT
** * *
11986978 AAATTGAA-CTAAAGTTTGAA-
66 GGATGGAATC-AAAGTCT-AAG
* * * * *
11986998 ATAAGTAACCTAGACTGACCCAAAGATAGATTTGACATAGTTCAAAATCTAAAACAAAATAATCT
1 ATAAGTAACCTAGACTGACCCGATGATAGATCTGACATAGGTCAAAATCCAAAACAAAATAATCT
*
11987063 GGATGGAATCGAAGTCTAAG
66 GGATGGAATCAAAGTCTAAG
* * * * * *
11987083 ATAAGTGA-TTCAGACTGACTCGAGGATGGATCTAACATAGGTCAAAATCCAAAACAAAATGAAT
1 ATAAGTAACCT-AGACTGACCCGATGATAGATCTGACATAGGTCAAAATCCAAAACAAAAT-AAT
* *
11987147 -TGGATGAAATTAAAGTCTAAG
64 CTGGATGGAATCAAAGTCTAAG
* * * ** * *
11987168 ATAAGTAACCGAGATTGACCCGATTATAGATCT-AGCATAGGTTGAAATCTAAAACAAAATCA-C
1 ATAAGTAACCTAGACTGACCCGATGATAGATCTGA-CATAGGTCAAAATCCAAAACAAAATAATC
* *
11987231 TTAGATGGAACCAAAGTCT
65 -TGGATGGAATCAAAGTCT
11987250 GAAATGAATA
Statistics
Matches: 201, Mismatches: 43, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
84 5 0.02
85 192 0.96
86 4 0.02
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (85 bp):
ATAAGTAACCTAGACTGACCCGATGATAGATCTGACATAGGTCAAAATCCAAAACAAAATAATCT
GGATGGAATCAAAGTCTAAG
Found at i:11988208 original size:96 final size:95
Alignment explanation
Indices: 11988072--11988363 Score: 390
Period size: 96 Copynumber: 3.1 Consensus size: 95
11988062 TGGCTTTTCG
** * *
11988072 ATTTGAGCC-TTTTTTTTGGAACTCAAACCACCCTTTATGGGTTTTCAATTTGAGCTTTTTTTTT
1 ATTTGAGCCTTTTTTTTTTTAACTCAAACCACTCTTTATGGGTTTTTAATTTGAGCTTTTTTTTT
11988136 TTAACTCAAATCGCCCTTTGTGGGTTTTTA
66 TTAACTCAAATCGCCCTTTGTGGGTTTTTA
11988166 ATTTGAGCCCTTTTTTTTTTTAACTCAAACCACTCTTTATGGGTTTTTAATTTGAGCTTTTTTTT
1 ATTTGAG-CCTTTTTTTTTTTAACTCAAACCACTCTTTATGGGTTTTTAATTTGAGCTTTTTTTT
* *
11988231 TTTAAACTCAAATCGCTCTTTGTGGGTTTTCA
65 TTT-AACTCAAATCGCCCTTTGTGGGTTTTTA
* * * * * *
11988263 ATTTAAGCCTTCTTTTTTTTAACTCAAATC-GTCCTTTGTAGGTTTTTAATTTGAGCTTTTTTTT
1 ATTTGAGCCTTTTTTTTTTTAACTCAAACCACT-CTTTATGGGTTTTTAATTTGAGCTTTTTTTT
* * * *
11988327 TTTAACTCAAACCACCCTTTATGGATTTTTA
65 TTTAACTCAAATCGCCCTTTGTGGGTTTTTA
*
11988358 AATTGA
1 ATTTGA
11988364 ACACTCATCT
Statistics
Matches: 174, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
94 7 0.04
95 29 0.17
96 106 0.61
97 32 0.18
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (95 bp):
ATTTGAGCCTTTTTTTTTTTAACTCAAACCACTCTTTATGGGTTTTTAATTTGAGCTTTTTTTTT
TTAACTCAAATCGCCCTTTGTGGGTTTTTA
Found at i:11988356 original size:47 final size:47
Alignment explanation
Indices: 11988045--11988363 Score: 359
Period size: 47 Copynumber: 6.7 Consensus size: 47
11988035 TCCTTTCTTG
* * * ** * **
11988045 ACTCAAACTGCCCTTCATGGCTTTTCGATTTGAGCCTTTTTTTTGGA
1 ACTCAAACCGCCCTTTATGGGTTTTTAATTTGAGCTTTTTTTTTTTA
* *
11988092 ACTCAAACCACCCTTTATGGGTTTTCAATTTGAGCTTTTTTTTTTTA
1 ACTCAAACCGCCCTTTATGGGTTTTTAATTTGAGCTTTTTTTTTTTA
* *
11988139 ACTCAAATCGCCCTTTGTGGGTTTTTAATTTGAGCCCTTTTTTTTTTTA
1 ACTCAAACCGCCCTTTATGGGTTTTTAATTTGAG--CTTTTTTTTTTTA
* *
11988188 ACTCAAACCACTCTTTATGGGTTTTTAATTTGAGCTTTTTTTTTTTAA
1 ACTCAAACCGCCCTTTATGGGTTTTTAATTTGAGCTTTTTTTTTTT-A
* * * * * *
11988236 ACTCAAATCGCTCTTTGTGGGTTTTCAATTTAAGCCTTCTTTTTTTTA
1 ACTCAAACCGCCCTTTATGGGTTTTTAATTTGAG-CTTTTTTTTTTTA
* * * *
11988284 ACTCAAATCGTCCTTTGTAGGTTTTTAATTTGAGCTTTTTTTTTTTA
1 ACTCAAACCGCCCTTTATGGGTTTTTAATTTGAGCTTTTTTTTTTTA
* * *
11988331 ACTCAAACCACCCTTTATGGATTTTTAAATTGA
1 ACTCAAACCGCCCTTTATGGGTTTTTAATTTGA
11988364 ACACTCATCT
Statistics
Matches: 233, Mismatches: 35, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
47 119 0.51
48 60 0.26
49 54 0.23
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.49
Consensus pattern (47 bp):
ACTCAAACCGCCCTTTATGGGTTTTTAATTTGAGCTTTTTTTTTTTA
Found at i:11995416 original size:59 final size:58
Alignment explanation
Indices: 11995347--11995561 Score: 146
Period size: 59 Copynumber: 3.6 Consensus size: 58
11995337 CATGACTTTA
* * *
11995347 TTCAAAAAAAATTAATGCTTTTAACTTTTCCTCAAAAAAGCATC-TTTGAAATTTTTATC
1 TTCAAAAAAAATTAATACTCTGAACTTTTCCTCAAAAAA--ATCTTTTGAAATTTTTATC
* * ** * *
11995406 TTCAAGAAAAATTGATACTCTGAACTTTTTGTCAAGAAAATCTTTTGAAATTTTTATTT
1 TTCAAAAAAAATTAATACTCTGAACTTTTCCTCAAAAAAATCTTTTGAAATTTTTA-TC
* * * * * * * *
11995465 TTAAAAAAAAATTGATACTCTCAA-TCTTCCCTCGAAAAATATTTCTTTGAAAATTTCATC
1 TTCAAAAAAAATTAATACTCTGAACT-TTTCCTC-AAAAAAATCT-TTTGAAATTTTTATC
* ** * * * *
11995525 TTTAAGGAAAATTGATACTTTCAACTTTTCCTTAAAA
1 TTCAAAAAAAATTAATACTCTGAACTTTTCCTCAAAA
11995562 TGATTTTTTT
Statistics
Matches: 123, Mismatches: 27, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
57 3 0.02
58 14 0.11
59 61 0.50
60 33 0.27
61 12 0.10
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (58 bp):
TTCAAAAAAAATTAATACTCTGAACTTTTCCTCAAAAAAATCTTTTGAAATTTTTATC
Found at i:11995647 original size:57 final size:57
Alignment explanation
Indices: 11995464--11995792 Score: 199
Period size: 59 Copynumber: 5.6 Consensus size: 57
11995454 AATTTTTATT
* ** ** ** * *
11995464 TTTAAAAAAAAATTGATACTCTCAATCTTCCCTCGAAAAATATTTCTTTGAAAATTTCA
1 TTTAAAAAAAAATTGATACTTTCAA-CTTTTCTTTAAGTATATTT-TTTTAAAATTTGA
* ** * * * *
11995523 TCTTTAAGGAAAATTGATACTTTCAACTTTTCCTTAA-AATGATTTTTTTCAAATTTTA
1 T-TTAAAAAAAAATTGATACTTTCAACTTTTCTTTAAGTAT-ATTTTTTTAAAATTTGA
* * *
11995581 TTT-AAAAAAATTTGTTATTTTCAACTTTTTCTTTAAGTATATTTTTTTAAAATTTGA
1 TTTAAAAAAAAATTGATACTTTCAAC-TTTTCTTTAAGTATATTTTTTTAAAATTTGA
*
11995638 TCTTCAAAAAAAATTGATACTTTCAACTTTTCTTTAAAGTAT-TTTTTTTATTGTTTGAAATTTT
1 T-TTAAAAAAAAATTGATACTTTCAACTTTTCTTT-AAGTATATTTTTTTA-------AAA-TTT
*
11995702 TA
56 GA
* * * *
11995704 TTTTTAAAGAAAATTGATACTTTTAAC----CTTAAAG--TATTTTTTTAAAATTTGA
1 -TTTAAAAAAAAATTGATACTTTCAACTTTTCTTTAAGTATATTTTTTTAAAATTTGA
**
11995756 TCTTAAAGGAAAATTGATACTTTCAACTTTTCTTTAA
1 T-TTAAAAAAAAATTGATACTTTCAACTTTTCTTTAA
11995793 AGCATTTTTT
Statistics
Matches: 214, Mismatches: 34, Indels: 47
0.73 0.12 0.16
Matches are distributed among these distances:
51 1 0.00
52 26 0.12
53 3 0.01
56 22 0.10
57 27 0.13
58 34 0.16
59 37 0.17
60 28 0.13
61 3 0.01
62 3 0.01
65 3 0.01
66 26 0.12
67 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (57 bp):
TTTAAAAAAAAATTGATACTTTCAACTTTTCTTTAAGTATATTTTTTTAAAATTTGA
Found at i:11995962 original size:3 final size:3
Alignment explanation
Indices: 11995954--11995989 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
11995944 AAATAAGCAA
*
11995954 AAT AAT AAT AAT ACT AAT AAT AAT AAAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
11995990 ATAAATAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11996836 original size:9 final size:9
Alignment explanation
Indices: 11996822--11996853 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
11996812 TCTGTTTTTA
11996822 TTTATTATT
1 TTTATTATT
11996831 TTTATTATT
1 TTTATTATT
11996840 TTTATTATT
1 TTTATTATT
*
11996849 CTTAT
1 TTTAT
11996854 ATGAAGCTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTATTATT
Found at i:11999347 original size:13 final size:13
Alignment explanation
Indices: 11999315--11999351 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
11999305 ATTAATTTTT
11999315 ATATCTTTTA-T-
1 ATATCTTTTATTA
*
11999326 ATATTTTTTATTA
1 ATATCTTTTATTA
11999339 ATATCTTTTATTA
1 ATATCTTTTATTA
11999352 TTTTATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 9 0.41
12 1 0.05
13 12 0.55
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (13 bp):
ATATCTTTTATTA
Found at i:11999554 original size:16 final size:16
Alignment explanation
Indices: 11999530--11999567 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
11999520 TGCATAAATG
* *
11999530 TAAAATGTATGAAAAA
1 TAAATTGTATCAAAAA
11999546 TAAATTGTATCAAAAA
1 TAAATTGTATCAAAAA
11999562 TAAATT
1 TAAATT
11999568 AACACATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (16 bp):
TAAATTGTATCAAAAA
Found at i:12000906 original size:23 final size:21
Alignment explanation
Indices: 12000870--12000915 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
12000860 CCCATTTTTC
12000870 TTTTCTTTTCTTACTACTAGTT
1 TTTTCTTTTCTTACTACTA-TT
*
12000892 TTTTCATTTTTTTACTACTATT
1 TTTTC-TTTTCTTACTACTATT
12000914 TT
1 TT
12000916 ACTTTCTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTCTTTTCTTACTACTATT
Found at i:12000925 original size:23 final size:21
Alignment explanation
Indices: 12000870--12000927 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 21
12000860 CCCATTTTTC
12000870 TTTTCTTTTCTTACTACTAGTT
1 TTTTCTTTT-TTACTACTAGTT
*
12000892 TTTTCATTTTTTTACTACTATTT
1 TTTTC--TTTTTTACTACTAGTT
12000915 TACTTTCTTTTTT
1 T--TTTCTTTTTT
12000928 TCTTTTACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 5 0.16
23 18 0.58
24 4 0.13
25 4 0.13
ACGTcount: A:0.14, C:0.16, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTCTTTTTTACTACTAGTT
Found at i:12001157 original size:14 final size:15
Alignment explanation
Indices: 12001128--12001158 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12001118 AGGCTTTTCC
12001128 TTTTGTTTGGGTTTT
1 TTTTGTTTGGGTTTT
*
12001143 TTTTTTTTGGGTTTT
1 TTTTGTTTGGGTTTT
12001158 T
1 T
12001159 AAATTTAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (15 bp):
TTTTGTTTGGGTTTT
Found at i:12001495 original size:19 final size:19
Alignment explanation
Indices: 12001457--12001495 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
12001447 GATAATCAAG
* * *
12001457 ATCAAATTACAGAAATTAA
1 ATCAAATTAAAAAAAATAA
12001476 ATCAAATTAAAAAAAATAA
1 ATCAAATTAAAAAAAATAA
12001495 A
1 A
12001496 ATATTTCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.23
Consensus pattern (19 bp):
ATCAAATTAAAAAAAATAA
Found at i:12001600 original size:16 final size:16
Alignment explanation
Indices: 12001566--12001600 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12001556 TTTAATAATT
* *
12001566 AAATTTTAAATTTTGA
1 AAATTTTAAATATTAA
12001582 AAATTTTAAATATTAA
1 AAATTTTAAATATTAA
12001598 AAA
1 AAA
12001601 ATAATTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AAATTTTAAATATTAA
Found at i:12004831 original size:14 final size:14
Alignment explanation
Indices: 12004812--12004840 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
12004802 ATTCATTTTC
12004812 ATTAAATATCTACA
1 ATTAAATATCTACA
12004826 ATTAAATATCTACA
1 ATTAAATATCTACA
12004840 A
1 A
12004841 AGATAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTAAATATCTACA
Found at i:12008132 original size:12 final size:12
Alignment explanation
Indices: 12008115--12008145 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
12008105 AAAGGAAGCC
12008115 ACTTTTGGGACT
1 ACTTTTGGGACT
12008127 ACTTTTGGGACT
1 ACTTTTGGGACT
12008139 ACTTTTG
1 ACTTTTG
12008146 TTTTGAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (12 bp):
ACTTTTGGGACT
Found at i:12008887 original size:14 final size:14
Alignment explanation
Indices: 12008868--12008895 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12008858 TTATAATATT
12008868 ATTTTTAAAAATAA
1 ATTTTTAAAAATAA
12008882 ATTTTTAAAAATAA
1 ATTTTTAAAAATAA
12008896 TGATGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTTTAAAAATAA
Found at i:12008921 original size:34 final size:32
Alignment explanation
Indices: 12008860--12008947 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 32
12008850 TTTCAGTATT
12008860 ATAATATTATTTTTAAAAATAAATTTTTAAAA
1 ATAATATTATTTTTAAAAATAAATTTTTAAAA
*
12008892 ATAATGATGTATTTTTAAAAATCAATTTTTGAAAA
1 ATAAT-AT-TATTTTTAAAAATAAATTTTT-AAAA
* * *
12008927 TACAATATCATTTTTGAAAAT
1 -ATAATATTATTTTTAAAAAT
12008948 TTATTTTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
32 5 0.10
33 2 0.04
34 31 0.65
35 6 0.12
36 4 0.08
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (32 bp):
ATAATATTATTTTTAAAAATAAATTTTTAAAA
Found at i:12008954 original size:34 final size:35
Alignment explanation
Indices: 12008902--12008987 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 35
12008892 ATAATGATGT
* ** * *
12008902 ATTTTTAAAAATCAATTTTTGAAAA-TACAATATC
1 ATTTTTGAAAATTTATTTTTCAAAACTACAACATC
*
12008936 ATTTTTGAAAATTTA-TTTTCAAAACTACCACATC
1 ATTTTTGAAAATTTATTTTTCAAAACTACAACATC
12008970 ATTTTTGAAAATTTATTT
1 ATTTTTGAAAATTTATTT
12008988 CACAAAATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 8 0.18
34 34 0.77
35 2 0.05
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.45
Consensus pattern (35 bp):
ATTTTTGAAAATTTATTTTTCAAAACTACAACATC
Found at i:12010927 original size:19 final size:18
Alignment explanation
Indices: 12010896--12010951 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
12010886 AATAAATTTT
12010896 AATCAAATTTAAATCAAA
1 AATCAAATTTAAATCAAA
* *
12010914 TATCAAATTTTAAATTAAA
1 AATCAAA-TTTAAATCAAA
* *
12010933 AATTAAATTTAAATTAAA
1 AATCAAATTTAAATCAAA
12010951 A
1 A
12010952 TTTTTTATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 18 0.55
19 15 0.45
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
AATCAAATTTAAATCAAA
Found at i:12011462 original size:32 final size:32
Alignment explanation
Indices: 12011400--12011472 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
12011390 TCTTTCATTT
* * *
12011400 AATTTTAAAAATTAAAAATTGTAATTTTAAAA
1 AATTTAAAAAATTAAAAATTGAAATATTAAAA
*
12011432 AATTTAAAAAATTTAAATATT-AAATATTAAAA
1 AATTTAAAAAA-TTAAAAATTGAAATATTAAAA
12011464 ATATTTAAA
1 A-ATTTAAA
12011473 TTCGAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 20 0.57
33 15 0.43
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (32 bp):
AATTTAAAAAATTAAAAATTGAAATATTAAAA
Found at i:12011480 original size:24 final size:23
Alignment explanation
Indices: 12011431--12011481 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
12011421 TAATTTTAAA
*
12011431 AAAT-TTAAAAAATTTAAATATT
1 AAATATTAAAAAATTTAAATATG
12011453 AAATATTAAAAATATTTAAAT-TCG
1 AAATATTAAAAA-ATTTAAATAT-G
12011477 AAATA
1 AAATA
12011482 ATTTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 4 0.16
23 8 0.32
24 13 0.52
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
AAATATTAAAAAATTTAAATATG
Found at i:12011511 original size:16 final size:16
Alignment explanation
Indices: 12011461--12011511 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
12011451 TTAAATATTA
12011461 AAAAT-ATTTAAATTC
1 AAAATAATTTAAATTC
* * *
12011476 GAAATAATTTTAATTT
1 AAAATAATTTAAATTC
*
12011492 AAAATAATTTAAACTC
1 AAAATAATTTAAATTC
12011508 AAAA
1 AAAA
12011512 CAATATAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
15 4 0.14
16 24 0.86
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (16 bp):
AAAATAATTTAAATTC
Found at i:12013839 original size:23 final size:23
Alignment explanation
Indices: 12013815--12013859 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
12013805 AATTATCCAA
*
12013815 TTAAAAAAATAAAAACAAAAAAAT
1 TTAAAAAAAGAAAAA-AAAAAAAT
*
12013839 TTCAAAAAAGAAAAAAAAAAA
1 TTAAAAAAAGAAAAAAAAAAA
12013860 GTGAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.13
Consensus pattern (23 bp):
TTAAAAAAAGAAAAAAAAAAAAT
Found at i:12014063 original size:17 final size:18
Alignment explanation
Indices: 12014025--12014065 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
12014015 GATCAAATTG
*
12014025 AAAAAAGAAAAAAGAACC
1 AAAAAAGAAAAAAGAAAC
*
12014043 AAAAAA-AAAAAAGAAAT
1 AAAAAAGAAAAAAGAAAC
12014060 AAAAAA
1 AAAAAA
12014066 TTTTAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.85, C:0.05, G:0.07, T:0.02
Consensus pattern (18 bp):
AAAAAAGAAAAAAGAAAC
Found at i:12014116 original size:19 final size:20
Alignment explanation
Indices: 12014094--12014131 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12014084 AATAGATCTC
12014094 ATAT-TAAAAAATTAAAAAA
1 ATATATAAAAAATTAAAAAA
* *
12014113 ATATATAAATATTTAAAAA
1 ATATATAAAAAATTAAAAA
12014132 GAAAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATATAAAAAATTAAAAAA
Found at i:12020845 original size:18 final size:19
Alignment explanation
Indices: 12020822--12020862 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
12020812 GAAAAACCTT
*
12020822 AAATTATTTAA-TATTTTA
1 AAATTATTAAATTATTTTA
12020840 AAATTATTAAATTATTTTA
1 AAATTATTAAATTATTTTA
12020859 AAAT
1 AAAT
12020863 CAAATAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTATTAAATTATTTTA
Found at i:12021016 original size:19 final size:19
Alignment explanation
Indices: 12020994--12021036 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12020984 TCAAAATCTG
12020994 AAAAAAAAATATAA-AAATA
1 AAAAAAAAATATAACAAA-A
* *
12021013 AAAATATAATATAACAAAA
1 AAAAAAAAATATAACAAAA
12021032 AAAAA
1 AAAAA
12021037 GTTAAAAGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAAAAAATATAACAAAA
Found at i:12021372 original size:23 final size:24
Alignment explanation
Indices: 12021341--12021392 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
12021331 TTTATTTTTA
**
12021341 AATT-TTATTTTGA-ATTAAAAAT
1 AATTATTATTTTGATAAAAAAAAT
12021363 AATTATTATTTTGATAAAAAAAAT
1 AATTATTATTTTGATAAAAAAAAT
12021387 AATTAT
1 AATTAT
12021393 CTTCTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 4 0.15
23 9 0.35
24 13 0.50
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
AATTATTATTTTGATAAAAAAAAT
Found at i:12021382 original size:21 final size:23
Alignment explanation
Indices: 12021340--12021392 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
12021330 TTTTATTTTT
12021340 AAATT-TTATTTTGAATTAAAAA
1 AAATTATTATTTTGAATTAAAAA
*
12021362 TAATTATTATTTTG-A-TAAAAA
1 AAATTATTATTTTGAATTAAAAA
*
12021383 AAATAATTAT
1 AAATTATTAT
12021393 CTTCTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 14 0.52
22 5 0.19
23 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
AAATTATTATTTTGAATTAAAAA
Found at i:12021703 original size:21 final size:21
Alignment explanation
Indices: 12021672--12021733 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
12021662 TATTTTACGA
12021672 ATAAT-TTTAATTTTATTATT
1 ATAATATTTAATTTTATTATT
* *
12021692 ATAATATTTAATTTCATAATT
1 ATAATATTTAATTTTATTATT
*
12021713 ATAATAATTAATTTTATTATT
1 ATAATATTTAATTTTATTATT
12021734 TTTAATTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 5 0.14
21 31 0.86
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATAATATTTAATTTTATTATT
Found at i:12022863 original size:21 final size:20
Alignment explanation
Indices: 12022830--12022869 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12022820 TTTCTTTTTT
*
12022830 TTTTTAATTTTATTTATTTAC
1 TTTTTAATATTATTT-TTTAC
*
12022851 TTTTTCATATTATTTTTTA
1 TTTTTAATATTATTTTTTA
12022870 TTAAATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTAATATTATTTTTTAC
Found at i:12044941 original size:1 final size:1
Alignment explanation
Indices: 12044935--12044960 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
12044925 TTCTTTCTTC
12044935 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
12044961 GTAACATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12051394 original size:16 final size:15
Alignment explanation
Indices: 12051373--12051402 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
12051363 TGGAAATTTA
12051373 TCTTTTTATTTTTTTC
1 TCTTTTT-TTTTTTTC
12051389 TCTTTTTTTTTTTT
1 TCTTTTTTTTTTTT
12051403 GAAAGGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (15 bp):
TCTTTTTTTTTTTTC
Found at i:12051589 original size:14 final size:14
Alignment explanation
Indices: 12051560--12051598 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
12051550 ACAATGAGTG
12051560 AAAATAAAATAAAATA
1 AAAAT-AAA-AAAATA
*
12051576 GAAATAAAAAAATA
1 AAAATAAAAAAATA
12051590 AAAATAAAA
1 AAAATAAAA
12051599 TGGAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 14 0.67
15 3 0.14
16 4 0.19
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (14 bp):
AAAATAAAAAAATA
Found at i:12051592 original size:24 final size:24
Alignment explanation
Indices: 12051560--12051612 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 24
12051550 ACAATGAGTG
12051560 AAAAT-AAAATAAAATAGAAATAAA
1 AAAATAAAAATAAAATAGAAA-AAA
*
12051584 AAAATAAAAATAAAATGGAAAAAA
1 AAAATAAAAATAAAATAGAAAAAA
12051608 AAAAT
1 AAAAT
12051613 CTACGATCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (24 bp):
AAAATAAAAATAAAATAGAAAAAA
Found at i:12051599 original size:19 final size:20
Alignment explanation
Indices: 12051565--12051612 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
12051555 GAGTGAAAAT
12051565 AAAAT-AAAATAGAAATAAA
1 AAAATAAAAATAGAAATAAA
**
12051584 AAAATAAAAATA-AAATGGA
1 AAAATAAAAATAGAAATAAA
12051603 AAAA-AAAAAT
1 AAAATAAAAAT
12051613 CTACGATCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 6 0.23
19 14 0.54
20 6 0.23
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (20 bp):
AAAATAAAAATAGAAATAAA
Found at i:12051991 original size:10 final size:10
Alignment explanation
Indices: 12051976--12052011 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
12051966 AAAGTTCTTC
12051976 AAAAAATCCA
1 AAAAAATCCA
*
12051986 AAAAAACCCA
1 AAAAAATCCA
*
12051996 AAAAAATTCA
1 AAAAAATCCA
12052006 AAAAAA
1 AAAAAA
12052012 AATTCCTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.75, C:0.17, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATCCA
Found at i:12052423 original size:10 final size:10
Alignment explanation
Indices: 12052408--12052498 Score: 67
Period size: 12 Copynumber: 8.2 Consensus size: 10
12052398 AAAGAATAGA
*
12052408 AAAAAAGAAT
1 AAAAAATAAT
12052418 AAAAAATAA-
1 AAAAAATAAT
12052427 AAAATAATAAT
1 AAAA-AATAAT
*
12052438 AAAAAAATAACA
1 -AAAAAATAA-T
12052450 ATAAAAATAAT
1 A-AAAAATAAT
12052461 AATAACAATAAT
1 AA-AA-AATAAT
12052473 AATAATAATAAT
1 AA-AA-AATAAT
12052485 AATAATAATAAT
1 AA-AA-AATAAT
12052497 AA
1 AA
12052499 TAATAATATT
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
9 4 0.06
10 14 0.20
11 9 0.13
12 43 0.61
ACGTcount: A:0.75, C:0.02, G:0.01, T:0.22
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:12052425 original size:20 final size:20
Alignment explanation
Indices: 12052402--12052443 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12052392 AAAAGGAAAG
12052402 AATAGAAAAA-AAGAATAAAA
1 AATA-AAAAATAAGAATAAAA
*
12052422 AATAAAAAATAATAATAAAA
1 AATAAAAAATAAGAATAAAA
12052442 AA
1 AA
12052444 ATAACAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (20 bp):
AATAAAAAATAAGAATAAAA
Found at i:12052428 original size:17 final size:16
Alignment explanation
Indices: 12052407--12052471 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
12052397 GAAAGAATAG
*
12052407 AAAAAAAGAATAAAAA
1 AAAAAAACAATAAAAA
*
12052423 ATAAAAAATAATAATAAA
1 A-AAAAAACAATAA-AAA
*
12052441 AAAATAACAATAAAAA
1 AAAAAAACAATAAAAA
*
12052457 TAATAATAACAATAA
1 -AA-AAAAACAATAA
12052472 TAATAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 4 0.10
17 23 0.55
18 15 0.36
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAAAAACAATAAAAA
Found at i:12052437 original size:3 final size:3
Alignment explanation
Indices: 12052429--12052513 Score: 118
Period size: 3 Copynumber: 28.7 Consensus size: 3
12052419 AAAAATAAAA
* * * *
12052429 AAT AAT AAT AA- AAA AAT AAC AAT AAA AAT AAT AAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
12052476 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12052514 ACAAGCTCTC
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
2 2 0.03
3 70 0.97
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:12052441 original size:12 final size:12
Alignment explanation
Indices: 12052419--12052514 Score: 108
Period size: 12 Copynumber: 8.2 Consensus size: 12
12052409 AAAAAGAATA
12052419 AAAAATAA-AA-
1 AAAAATAATAAT
*
12052429 AATAATAATAA-
1 AAAAATAATAAT
*
12052440 AAAAATAACAAT
1 AAAAATAATAAT
12052452 AAAAATAATAAT
1 AAAAATAATAAT
*
12052464 AACAATAATAAT
1 AAAAATAATAAT
*
12052476 AATAATAATAAT
1 AAAAATAATAAT
*
12052488 AATAATAATAAT
1 AAAAATAATAAT
* *
12052500 AATAATATTAAT
1 AAAAATAATAAT
12052512 AAA
1 AAA
12052515 CAAGCTCTCC
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
10 7 0.09
11 11 0.14
12 58 0.76
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:12053204 original size:117 final size:115
Alignment explanation
Indices: 12053078--12053295 Score: 267
Period size: 117 Copynumber: 1.9 Consensus size: 115
12053068 ACTGATGTCG
** *
12053078 TGAGTCAAAATAAAGCG-TCCAGGATTGAGTCGAGATAAAAAATGAATGACCGAACTGATGTCAT
1 TGAGTCAAAATAAAGCGAT-CAGGACCGAGTCGAGATAAAAAA-AAATGACCGAACTGATGTCAT
* * ** * *
12053142 GAGTTTGACAATAATCTGATTTGAGTCGAGATCAAATGACTGGGACTATGTTA
64 -AGTCTGAAAATAATCTGACCTAAGTCAAGATCAAATGACTGGGACTATGTTA
* * * * *
12053195 TGAGTCAAAATAAAGCGATTAGGACCGAGTCGAGGTAAAAAAAAATTACTGAATTGATGTCATAG
1 TGAGTCAAAATAAAGCGATCAGGACCGAGTCGAGATAAAAAAAAATGACCGAACTGATGTCATAG
*
12053260 TCTGAAAATGATCTGACCTAAGTCAAGATCAAATGA
66 TCTGAAAATAATCTGACCTAAGTCAAGATCAAATGA
12053296 GTGGATAGTG
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
115 31 0.36
116 17 0.20
117 36 0.42
118 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.25
Consensus pattern (115 bp):
TGAGTCAAAATAAAGCGATCAGGACCGAGTCGAGATAAAAAAAAATGACCGAACTGATGTCATAG
TCTGAAAATAATCTGACCTAAGTCAAGATCAAATGACTGGGACTATGTTA
Found at i:12057278 original size:18 final size:18
Alignment explanation
Indices: 12057234--12057271 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12057224 ACCAGTTGGA
*
12057234 TTTCAAATTATCCAATAT
1 TTTCAAATTATCCAATAC
12057252 TTTCAAATTATCCAAT-C
1 TTTCAAATTATCCAATAC
12057269 TTT
1 TTT
12057272 GATAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTCAAATTATCCAATAC
Found at i:12057554 original size:22 final size:22
Alignment explanation
Indices: 12057509--12057550 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12057499 TTTAGAGGAT
12057509 AAAAATTATTTTTATTTATTTG
1 AAAAATTATTTTTATTTATTTG
12057531 AAAAGATT-TTTTTA-TTATTT
1 AAAA-ATTATTTTTATTTATTT
12057551 TGAAGACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 10 0.53
23 3 0.16
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
AAAAATTATTTTTATTTATTTG
Found at i:12058717 original size:46 final size:46
Alignment explanation
Indices: 12058635--12058726 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
12058625 ACATGTGAAT
* * ** *
12058635 TAATTGCATAAATCAAGCACCGAATTTTTTTACAAAATCTTTAACG
1 TAATTGCATAAATCAAGCACCAAAATTTACTACAAAATCTTCAACG
* *
12058681 TAATTGCATGAATCAAGCACCAAAATTTACTGCAAAATCTTCAACG
1 TAATTGCATAAATCAAGCACCAAAATTTACTACAAAATCTTCAACG
12058727 ATTTTTTCTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (46 bp):
TAATTGCATAAATCAAGCACCAAAATTTACTACAAAATCTTCAACG
Found at i:12072803 original size:19 final size:19
Alignment explanation
Indices: 12072779--12072815 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12072769 ATGAATCCAA
*
12072779 AAATTTTTTAAATCTAAAT
1 AAATTTATTAAATCTAAAT
*
12072798 AAATTTATTAAATTTAAA
1 AAATTTATTAAATCTAAA
12072816 AAAAAAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATTTATTAAATCTAAAT
Found at i:12073424 original size:7 final size:7
Alignment explanation
Indices: 12073392--12073433 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
12073382 TTTGTTATCA
12073392 AAATTTT
1 AAATTTT
*
12073399 -AATTCT
1 AAATTTT
*
12073405 AAATTCT
1 AAATTTT
12073412 AAATTTT
1 AAATTTT
12073419 AAATTTT
1 AAATTTT
*
12073426 AATTTTT
1 AAATTTT
12073433 A
1 A
12073434 TAAATTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (7 bp):
AAATTTT
Found at i:12073433 original size:14 final size:13
Alignment explanation
Indices: 12073392--12073431 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
12073382 TTTGTTATCA
*
12073392 AAATTTTAATTCT
1 AAATTTTAATTTT
*
12073405 AAATTCTAAATTTT
1 AAATT-TTAATTTT
12073419 AAATTTTAATTTT
1 AAATTTTAATTTT
12073432 TATAAATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (13 bp):
AAATTTTAATTTT
Found at i:12073929 original size:20 final size:20
Alignment explanation
Indices: 12073881--12073940 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
12073871 ATTTAAAATT
12073881 TAAATAAATAACAAATAAAAA
1 TAAATAAA-AACAAATAAAAA
* *
12073902 TAATTAAAAACAATTAAATAA
1 TAAATAAAAACAAATAAA-AA
12073923 -AAATAAAATA-AAATAAAA
1 TAAATAAAA-ACAAATAAAA
12073941 CAAACTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.03
20 22 0.67
21 10 0.30
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAATAAAAACAAATAAAAA
Found at i:12074133 original size:25 final size:25
Alignment explanation
Indices: 12074078--12074137 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
12074068 TTTTCTTTTC
* *
12074078 TATTTTCTATTTTTTAATTTTTTAA
1 TATTTTCTATTTTTTAACTATTTAA
*
12074103 TGTTTTCTATTTTTT-ACTATTTAA
1 TATTTTCTATTTTTTAACTATTTAA
12074127 TAATTTT-TATT
1 T-ATTTTCTATT
12074138 CGTAAGGCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 12 0.40
25 18 0.60
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (25 bp):
TATTTTCTATTTTTTAACTATTTAA
Found at i:12074341 original size:17 final size:18
Alignment explanation
Indices: 12074314--12074351 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
12074304 ATGAAAAATA
12074314 TTTATTTTTTTTCAT-ATT
1 TTTATTTTTTTT-ATAATT
12074332 TTTA-TTTTTTTATAATT
1 TTTATTTTTTTTATAATT
12074349 TTT
1 TTT
12074352 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 13 0.68
18 4 0.21
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTATTTTTTTTATAATT
Found at i:12074351 original size:18 final size:18
Alignment explanation
Indices: 12074314--12074354 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12074304 ATGAAAAATA
*
12074314 TTTATTTTTTTTCATATT
1 TTTATTTTTTTTAATATT
*
12074332 TTTATTTTTTTATAATTTT
1 TTTATTTTTTT-TAATATT
12074351 TTTA
1 TTTA
12074355 AATTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATTTTTTTTAATATT
Found at i:12074433 original size:19 final size:20
Alignment explanation
Indices: 12074411--12074452 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
12074401 AATGTCCTAA
12074411 TTTAGTTTT-TTTGTCATTT
1 TTTAGTTTTATTTGTCATTT
* *
12074430 TTTAGTTTTATTTTTTATTT
1 TTTAGTTTTATTTGTCATTT
12074450 TTT
1 TTT
12074453 TTTTACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (20 bp):
TTTAGTTTTATTTGTCATTT
Done.