Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 43 of 208
Found at i:11823160 original size:31 final size:31
Alignment explanation
Indices: 11823081--11823165 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
11823071 AATGAAAAAA
* * *
11823081 CCATCATAGCCGGGCAATCTAGGGTGGTAAG
1 CCATCATTGCCGAGCAATCTAGGGTAGTAAG
11823112 CCATCATTGCC-AGGCAATCTAGGGTAGT-AG
1 CCATCATTGCCGA-GCAATCTAGGGTAGTAAG
* * *
11823142 ATCATCGTTGCCGAGCAATATAGG
1 -CCATCATTGCCGAGCAATCTAGG
11823166 ATGACAGATA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
30 2 0.04
31 42 0.93
32 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.22
Consensus pattern (31 bp):
CCATCATTGCCGAGCAATCTAGGGTAGTAAG
Found at i:11837278 original size:27 final size:27
Alignment explanation
Indices: 11837234--11837327 Score: 125
Period size: 27 Copynumber: 3.5 Consensus size: 27
11837224 CTTGTCAGCT
* * * *
11837234 TTTGTGGCATACTCTGAAAGAATTGCC
1 TTTGTGGCGTACTATGAATGAATCGCC
* *
11837261 TTTGTGGCGTATTATGAATGAATCACC
1 TTTGTGGCGTACTATGAATGAATCGCC
11837288 TTTGTGGCGTACTATGAATGAATCGCC
1 TTTGTGGCGTACTATGAATGAATCGCC
*
11837315 TTTGTGGCATACT
1 TTTGTGGCGTACT
11837328 CTATATAGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (27 bp):
TTTGTGGCGTACTATGAATGAATCGCC
Found at i:11837901 original size:28 final size:28
Alignment explanation
Indices: 11837868--11837924 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
11837858 ATGTCTAAAG
11837868 ATAAAATTAATGGTATCTAGTTCTACAT
1 ATAAAATTAATGGTATCTAGTTCTACAT
11837896 ATAAAATTAATGGTATCTAGTTCTACAT
1 ATAAAATTAATGGTATCTAGTTCTACAT
11837924 A
1 A
11837925 GGTATTTGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.39
Consensus pattern (28 bp):
ATAAAATTAATGGTATCTAGTTCTACAT
Found at i:11849565 original size:5 final size:5
Alignment explanation
Indices: 11849555--11849581 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
11849545 TTATCTTAAT
11849555 ATTTA ATTTA ATTTA ATTTA ATTTA AT
1 ATTTA ATTTA ATTTA ATTTA ATTTA AT
11849582 GTTTATCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:11856496 original size:43 final size:44
Alignment explanation
Indices: 11856377--11856525 Score: 125
Period size: 42 Copynumber: 3.5 Consensus size: 44
11856367 CCGTTACTCG
* * *
11856377 GTGGATTCAGCACTTAGCAACTACC-TTAAATTC-AGTGATTAC
1 GTGGAATCAGCACTTAGCAACCACCTTTAAAGTCAAGTGATTAC
* * * *
11856419 GGGGAATCAGCACATAACAACC-CCTTTCACAGTCAAG-GA-TAC
1 GTGGAATCAGCACTTAGCAACCACCTTT-AAAGTCAAGTGATTAC
* *
11856461 GATGGAATCAGCACTTAGTAACCACCTTTAAAGTCAA-TAATT-C
1 G-TGGAATCAGCACTTAGCAACCACCTTTAAAGTCAAGTGATTAC
*
11856504 AG-GTAATCAGCACTTAGCAACC
1 -GTGGAATCAGCACTTAGCAACC
11856526 CCTCGAGAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
41 2 0.02
42 41 0.49
43 32 0.38
44 9 0.11
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (44 bp):
GTGGAATCAGCACTTAGCAACCACCTTTAAAGTCAAGTGATTAC
Found at i:11873502 original size:6 final size:6
Alignment explanation
Indices: 11873493--11873524 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
11873483 TCTTCGTCTT
11873493 CATCTC CATCTC CATCTC CATCTC CATCTC CA
1 CATCTC CATCTC CATCTC CATCTC CATCTC CA
11873525 CTTCCACTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.50, G:0.00, T:0.31
Consensus pattern (6 bp):
CATCTC
Found at i:11878615 original size:20 final size:20
Alignment explanation
Indices: 11878590--11878628 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
11878580 AACTTTCTTC
11878590 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
11878610 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
11878629 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:11878956 original size:50 final size:50
Alignment explanation
Indices: 11878893--11879025 Score: 160
Period size: 50 Copynumber: 2.7 Consensus size: 50
11878883 AAATGTCATA
* * ** * *
11878893 TCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACAGGAGACCTCTCATATCGGTGCCAACGCCATG
* * *
11878943 TCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACAGGAGACCTCTCATATCGGTGCCAACGCCATG
*
11878993 TCCCAGACATGGTCTTACGTGGA-ACCTCTCATA
1 TCCCAGACATGGTCTTAC-AGGAGACCTCTCATA
11879026 ACCTCAATAA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
50 68 0.97
51 2 0.03
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACAGGAGACCTCTCATATCGGTGCCAACGCCATG
Found at i:11882977 original size:9 final size:9
Alignment explanation
Indices: 11882963--11882990 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
11882953 TGCAACTGAG
11882963 CTTTCAATT
1 CTTTCAATT
11882972 CTTTCAATT
1 CTTTCAATT
11882981 CTTTCAATT
1 CTTTCAATT
11882990 C
1 C
11882991 CAACGGGGCC
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:0.21, C:0.25, G:0.00, T:0.54
Consensus pattern (9 bp):
CTTTCAATT
Found at i:11886305 original size:20 final size:20
Alignment explanation
Indices: 11886280--11886318 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
11886270 TACTTTCTTC
11886280 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
11886300 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
11886319 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:11890312 original size:12 final size:13
Alignment explanation
Indices: 11890280--11890317 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
11890270 CAAAGAAAGG
*
11890280 ATAGAAAAAGAGA
1 ATAGAAACAGAGA
11890293 ATAGAAACAGAGA
1 ATAGAAACAGAGA
11890306 A-AGAAACAGAGA
1 ATAGAAACAGAGA
11890318 GCAAAACGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.66, C:0.05, G:0.24, T:0.05
Consensus pattern (13 bp):
ATAGAAACAGAGA
Found at i:11891411 original size:24 final size:24
Alignment explanation
Indices: 11891379--11891461 Score: 91
Period size: 25 Copynumber: 3.5 Consensus size: 24
11891369 ACTTTAGCGC
*
11891379 GCTCTCTGATATTAGCACGTTGGT
1 GCTCTCTGATATTAGCACGTTAGT
**
11891403 GCTCTCTGATATTTAGCACGGCAGT
1 GCTCTCTGATA-TTAGCACGTTAGT
* *
11891428 GCTCTCTG-T-TTAGCACATTTGT
1 GCTCTCTGATATTAGCACGTTAGT
11891450 GCTCTCT-ATATT
1 GCTCTCTGATATT
11891462 TGTTCCGTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
22 17 0.35
23 2 0.04
24 12 0.24
25 18 0.37
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (24 bp):
GCTCTCTGATATTAGCACGTTAGT
Found at i:11892324 original size:17 final size:17
Alignment explanation
Indices: 11892281--11892327 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
11892271 GGCATGTACT
*
11892281 TAAGTAATGTACATACC
1 TAAGTAATGTATATACC
11892298 TAAGTAATGTATATACC
1 TAAGTAATGTATATACC
* *
11892315 TAGGTGATGTATA
1 TAAGTAATGTATA
11892328 GGGATTAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (17 bp):
TAAGTAATGTATATACC
Found at i:11898480 original size:51 final size:51
Alignment explanation
Indices: 11898419--11898525 Score: 135
Period size: 51 Copynumber: 2.1 Consensus size: 51
11898409 AGAAATGATG
* * * *
11898419 AAATAGAGAAATAGGAA-CATTTCGAAATGATTATGATTTTCTCCAAAATGA
1 AAATGGAGAAAT-GAAATCATTTCGAAATAAATATGATTTTCTCCAAAATGA
* * *
11898470 AAATGGAGAAATGAAATCATTTGGAAATAAATGTGGTTTTCTCCAAAATGA
1 AAATGGAGAAATGAAATCATTTCGAAATAAATATGATTTTCTCCAAAATGA
11898521 AAATG
1 AAATG
11898526 AAAATGGCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 3 0.06
51 45 0.94
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (51 bp):
AAATGGAGAAATGAAATCATTTCGAAATAAATATGATTTTCTCCAAAATGA
Found at i:11904284 original size:57 final size:57
Alignment explanation
Indices: 11904217--11904336 Score: 161
Period size: 57 Copynumber: 2.1 Consensus size: 57
11904207 AGAAATGATG
* * * *
11904217 AAATAGAGAAATAGGAA-CATTTGGAAATGATTATGATTTTCTCCAAAATGAAAATGA
1 AAATGGAGAAA-AGAAATCATTTGAAAATGAATATGATTTTCTCCAAAATGAAAATGA
* * *
11904274 AAATGGAGAAACGAAATCATTTGAAAATGAATGTGGTTTTCTCCAAAATGAAAATGA
1 AAATGGAGAAAAGAAATCATTTGAAAATGAATATGATTTTCTCCAAAATGAAAATGA
11904331 AAATGG
1 AAATGG
11904337 CCTGAAAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
56 3 0.05
57 52 0.95
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.27
Consensus pattern (57 bp):
AAATGGAGAAAAGAAATCATTTGAAAATGAATATGATTTTCTCCAAAATGAAAATGA
Found at i:11907939 original size:20 final size:20
Alignment explanation
Indices: 11907914--11907957 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
11907904 AGAAGCATTA
11907914 GGACTTTAATGGTTTAATGT
1 GGACTTTAATGGTTTAATGT
11907934 GGACTTTAATGGTTTAATGT
1 GGACTTTAATGGTTTAATGT
11907954 GGAC
1 GGAC
11907958 ATGGCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (20 bp):
GGACTTTAATGGTTTAATGT
Found at i:11908810 original size:2 final size:2
Alignment explanation
Indices: 11908803--11908837 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11908793 TGCGTGGAGG
*
11908803 TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11908838 TTGTTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:11912871 original size:57 final size:57
Alignment explanation
Indices: 11912784--11912902 Score: 220
Period size: 57 Copynumber: 2.1 Consensus size: 57
11912774 TGATATGGAG
*
11912784 TTATTTTATTCAAACGATTCAAAATCCCTAGTAGTTGGCTATACTGATACTGGAAAT
1 TTATTTTATTCAAACGATTCAAAATCCCTAGTAGTCGGCTATACTGATACTGGAAAT
*
11912841 TTATTTTATTCAAATGATTCAAAATCCCTAGTAGTCGGCTATACTGATACTGGAAAT
1 TTATTTTATTCAAACGATTCAAAATCCCTAGTAGTCGGCTATACTGATACTGGAAAT
11912898 TTATT
1 TTATT
11912903 GAATCCACAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (57 bp):
TTATTTTATTCAAACGATTCAAAATCCCTAGTAGTCGGCTATACTGATACTGGAAAT
Found at i:11920860 original size:2 final size:2
Alignment explanation
Indices: 11920853--11920888 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
11920843 TTAAATCAAC
*
11920853 AT AT AT AT AT AT AT AT AT AT AT 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
11920889 CTATTGTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11921035 original size:114 final size:114
Alignment explanation
Indices: 11920865--11921115 Score: 432
Period size: 114 Copynumber: 2.2 Consensus size: 114
11920855 ATATATATAT
*
11920865 ATATATATATATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATATAAAT
1 ATATATATAAATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATATAAAT
*
11920930 TGAAATTAGTTAAGTATGAATGTTATATATATGCATAAATGAAGTTCGA
66 TGAAATTAGTTAAGTATGAATGTTATATATATGCATAAATGAAATTCGA
* *
11920979 ATATATGTAAATATATATGTATATCTATTGTATATTTGATGAGCTATAATTGAAAGTATATAAAT
1 ATATATATAAATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATATAAAT
11921044 TGAAATTAGTTAAGTATGAATGTTATATATATGCATAAATGAAATTCGA
66 TGAAATTAGTTAAGTATGAATGTTATATATATGCATAAATGAAATTCGA
* *
11921093 ATATGTATATATGA-ATATGTATA
1 ATATATATAAAT-ATATATGTATA
11921116 AGATCTTGAG
Statistics
Matches: 129, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
114 128 0.99
115 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.41
Consensus pattern (114 bp):
ATATATATAAATATATATGTATATCTATTGTATATTTGATGAGCTATAATTAAAAGTATATAAAT
TGAAATTAGTTAAGTATGAATGTTATATATATGCATAAATGAAATTCGA
Found at i:11921073 original size:60 final size:60
Alignment explanation
Indices: 11920895--11921073 Score: 164
Period size: 60 Copynumber: 3.1 Consensus size: 60
11920885 ATATCTATTG
*
11920895 TATATTTGATGAGCTATAATTAAAAGTATATAAATTGAAATTAGTTAAGTATGAATGTTA
1 TATATTTGATGAGCTATAATTGAAAGTATATAAATTGAAATTAGTTAAGTATGAATGTTA
* ** * * * *
11920955 TATA--T-AT--GC-ATAAATG-AAGT-TCGAATATATGTAAA-TA-TATATGTAT-ATCTATTG
1 TATATTTGATGAGCTATAATTGAAAGTATATAA-AT-TG-AAATTAGT-TAAGTATGA-ATGTTA
11921009 TATATTTGATGAGCTATAATTGAAAGTATATAAATTGAAATTAGTTAAGTATGAATGTTA
1 TATATTTGATGAGCTATAATTGAAAGTATATAAATTGAAATTAGTTAAGTATGAATGTTA
11921069 TATAT
1 TATAT
11921074 ATGCATAAAT
Statistics
Matches: 88, Mismatches: 15, Indels: 32
0.65 0.11 0.24
Matches are distributed among these distances:
52 3 0.03
53 8 0.09
54 22 0.25
55 5 0.06
56 1 0.01
57 4 0.05
58 1 0.01
59 5 0.06
60 28 0.32
61 8 0.09
62 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.41
Consensus pattern (60 bp):
TATATTTGATGAGCTATAATTGAAAGTATATAAATTGAAATTAGTTAAGTATGAATGTTA
Found at i:11921633 original size:41 final size:41
Alignment explanation
Indices: 11921583--11921729 Score: 215
Period size: 41 Copynumber: 3.6 Consensus size: 41
11921573 CAGACTTTAC
* *
11921583 GTCTAGCAGGCTAAGTGCCAGTGATCTGAAACAGGCTATAA
1 GTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
*
11921624 GTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
1 GTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
**
11921665 ACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
1 GTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
* *
11921706 G-CTTAGCAAGTTAAGTGCCGGTGA
1 GTC-TAGCAGGCTAAGTGCCGGTGA
11921730 ATATGTTAAA
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 1 0.01
41 95 0.99
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (41 bp):
GTCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
Found at i:11922645 original size:11 final size:11
Alignment explanation
Indices: 11922631--11922687 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
11922621 ATATCCAAAT
11922631 AATAATAACAA
1 AATAATAACAA
*
11922642 AATATTAACAA
1 AATAATAACAA
*
11922653 TATAATAACAA
1 AATAATAACAA
* *
11922664 AATGATAGCAA
1 AATAATAACAA
* *
11922675 AACAACAACAA
1 AATAATAACAA
11922686 AA
1 AA
11922688 CAACTTATTC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 36 1.00
ACGTcount: A:0.67, C:0.12, G:0.04, T:0.18
Consensus pattern (11 bp):
AATAATAACAA
Found at i:11924804 original size:58 final size:58
Alignment explanation
Indices: 11924721--11924924 Score: 263
Period size: 52 Copynumber: 3.7 Consensus size: 58
11924711 CATTTCCGAG
* **
11924721 TCATTTTCATTT-GGAGAAAACCACATTCGTTTTCAAATGTCCCCTATTTCTCCATTT
1 TCATTTTCATTTGGGAGAAAACCACATTCATTTTCAAATGTTTCCTATTTCTCCATTT
11924778 TCATTTTCATTTGGGAGAAAACCACATTCATTTTCAAATGTTTCCTA----T--ATTT
1 TCATTTTCATTTGGGAGAAAACCACATTCATTTTCAAATGTTTCCTATTTCTCCATTT
*
11924830 TCATTTTCATTTGGGATAAAACCACATTCATTTTCAAATGTTTCCTATTTCTCCATTT
1 TCATTTTCATTTGGGAGAAAACCACATTCATTTTCAAATGTTTCCTATTTCTCCATTT
* *
11924888 TCA---T--TTT-GGAAAAAACCACATCCATTTTCAAATGTTT
1 TCATTTTCATTTGGGAGAAAACCACATTCATTTTCAAATGTTT
11924925 TTCATTTCTT
Statistics
Matches: 134, Mismatches: 6, Indels: 19
0.84 0.04 0.12
Matches are distributed among these distances:
52 78 0.58
53 3 0.02
54 1 0.01
55 1 0.01
56 1 0.01
57 12 0.09
58 38 0.28
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (58 bp):
TCATTTTCATTTGGGAGAAAACCACATTCATTTTCAAATGTTTCCTATTTCTCCATTT
Found at i:11924940 original size:110 final size:106
Alignment explanation
Indices: 11924721--11924924 Score: 297
Period size: 110 Copynumber: 1.9 Consensus size: 106
11924711 CATTTCCGAG
*
11924721 TCATTTTCATTTGGAGAAAACCACATTCGTTTTCAAATGTCCCCTATTTCTCCATTTTCATTTTC
1 TCATTTTCATTTGGAGAAAACCACATTCATTTTCAAATGTCCCCTATTTCTCCATTTTCA--TT-
* *
11924786 ATTTGGGAGAAAACCACATTCATTTTCAAATGTTTCCTATATTT
63 ATTTGGGAAAAAACCACATCCATTTTCAAATGTTTCCTATATTT
* **
11924830 TCATTTTCATTTGGGATAAAACCACATTCATTTTCAAATGTTTCCTATTTCTCCATTTTCA-T-T
1 TCATTTTCATTT-GGAGAAAACCACATTCATTTTCAAATGTCCCCTATTTCTCCATTTTCATTAT
11924893 TT-GGAAAAAACCACATCCATTTTCAAATGTTT
65 TTGGGAAAAAACCACATCCATTTTCAAATGTTT
11924925 TTCATTTCTT
Statistics
Matches: 88, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
104 28 0.32
105 3 0.03
107 1 0.01
109 12 0.14
110 44 0.50
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (106 bp):
TCATTTTCATTTGGAGAAAACCACATTCATTTTCAAATGTCCCCTATTTCTCCATTTTCATTATT
TGGGAAAAAACCACATCCATTTTCAAATGTTTCCTATATTT
Found at i:11925857 original size:33 final size:33
Alignment explanation
Indices: 11925820--11925887 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
11925810 CGGACATGTT
11925820 TAGGTTTGCCTACTAATAGAAGTTGTATTTCTG
1 TAGGTTTGCCTACTAATAGAAGTTGTATTTCTG
11925853 TAGGTTTGCCTACTAATAGAAGTTGTATTTCTG
1 TAGGTTTGCCTACTAATAGAAGTTGTATTTCTG
11925886 TA
1 TA
11925888 TCACGATCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.43
Consensus pattern (33 bp):
TAGGTTTGCCTACTAATAGAAGTTGTATTTCTG
Found at i:11929182 original size:12 final size:12
Alignment explanation
Indices: 11929165--11929190 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11929155 CTATTGAGTC
11929165 TAGGTCAACAAT
1 TAGGTCAACAAT
11929177 TAGGTCAACAAT
1 TAGGTCAACAAT
11929189 TA
1 TA
11929191 TGGATGAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (12 bp):
TAGGTCAACAAT
Found at i:11933261 original size:41 final size:41
Alignment explanation
Indices: 11933180--11933536 Score: 570
Period size: 41 Copynumber: 8.7 Consensus size: 41
11933170 TTAATTTAAA
* ** *
11933180 CAGATTCACTGGCACTTAGCCCTATTAGGCTTAAAGCCTGATT
1 CAGA-TCACCGGCACTTAG-CCTGCTAGGCTTATAGCCTGATT
* *
11933223 CAGATCACCGACACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* *
11933264 TAGATCACCGGCACTTAACCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
11933305 CAGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
11933346 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTTATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
11933387 CAGATCACCGGCACTTAGCTTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
* *
11933428 CAGATCACCGGCACTTAGTCTGCTAGGCTTATAGCCTTATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
11933469 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
*
11933510 CAGTTCACCGGCACTTAGCCTGCTAGG
1 CAGATCACCGGCACTTAGCCTGCTAGG
11933537 TTTTAAAACC
Statistics
Matches: 291, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
41 275 0.95
42 12 0.04
43 4 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
Found at i:11934015 original size:2 final size:2
Alignment explanation
Indices: 11934008--11934037 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
11933998 CGAGCATAAC
*
11934008 AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11934038 GTATCTAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:11941564 original size:8 final size:8
Alignment explanation
Indices: 11941551--11941577 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
11941541 AGTATATTCG
11941551 TTTGTAAA
1 TTTGTAAA
11941559 TTTGTAAA
1 TTTGTAAA
11941567 TTTGTAAA
1 TTTGTAAA
11941575 TTT
1 TTT
11941578 TTTTGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (8 bp):
TTTGTAAA
Found at i:11941862 original size:169 final size:170
Alignment explanation
Indices: 11941558--11941868 Score: 536
Period size: 170 Copynumber: 1.8 Consensus size: 170
11941548 TCGTTTGTAA
* * *
11941558 ATTTGTAAATTTGTAAATTTTTTTGAAAAAATTGTTTTATTAACCAATGTAACAATCAATGAATT
1 ATTTGTAAACTTGTAAACTTTTTCGAAAAAATTGTTTTATTAACCAATGTAACAATCAATGAATT
* *
11941623 TATTTTATTAACCAATCTGTTCAAAAAAAATTACAAGTTTACAGATGAATACACTACACTTAGGG
66 TATTTTATTAACCAATCTGTTCAAAAAAAATTACAAGTTTACAGACGAATACACTACACTCAGGG
11941688 CATTAGATCCAACACTCAGGGCTCTGAGTGTAGTATATTC
131 CATTAGATCCAACACTCAGGGCTCTGAGTGTAGTATATTC
*
11941728 ATTTGTAAACTTGT-AACTTTTTCGAAAAAAATTGTTTTATTAACCAATGTCACAATCAATGAAT
1 ATTTGTAAACTTGTAAACTTTTTCG-AAAAAATTGTTTTATTAACCAATGTAACAATCAATGAAT
*
11941792 TTATTTTATTAACCAATCTGTTCAAAAAAAA-TACAAGTTTACAGACGAATATACTACACTCAGG
65 TTATTTTATTAACCAATCTGTTCAAAAAAAATTACAAGTTTACAGACGAATACACTACACTCAGG
11941856 GCATTAGATCCAA
130 GCATTAGATCCAA
11941869 TAGTCTTTCA
Statistics
Matches: 133, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
169 51 0.38
170 82 0.62
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.35
Consensus pattern (170 bp):
ATTTGTAAACTTGTAAACTTTTTCGAAAAAATTGTTTTATTAACCAATGTAACAATCAATGAATT
TATTTTATTAACCAATCTGTTCAAAAAAAATTACAAGTTTACAGACGAATACACTACACTCAGGG
CATTAGATCCAACACTCAGGGCTCTGAGTGTAGTATATTC
Found at i:11943617 original size:30 final size:33
Alignment explanation
Indices: 11943555--11943617 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 33
11943545 AGTTTTAGGG
* **
11943555 TTAGGTTTTCTTTTCTTTCTTTTTTATTTTAGA
1 TTAGGTTTTCTTCTCTTTCTTTTTTAGATTAGA
11943588 TTAGGTTTT-TTCT-TTTC-TTTTTAGATTAGA
1 TTAGGTTTTCTTCTCTTTCTTTTTTAGATTAGA
11943618 CTCTATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.41
31 4 0.15
32 3 0.11
33 9 0.33
ACGTcount: A:0.14, C:0.08, G:0.11, T:0.67
Consensus pattern (33 bp):
TTAGGTTTTCTTCTCTTTCTTTTTTAGATTAGA
Found at i:11957438 original size:14 final size:15
Alignment explanation
Indices: 11957412--11957484 Score: 66
Period size: 14 Copynumber: 5.0 Consensus size: 15
11957402 TATAGAATAG
11957412 TATAGATTA-TGAAAC
1 TATAGA-TACTGAAAC
11957427 T-TAGATACTGAAAAC
1 TATAGATACTG-AAAC
*
11957442 TATAGATACTGATAC
1 TATAGATACTGAAAC
11957457 TATAG-TGAC-GAAAC
1 TATAGAT-ACTGAAAC
*
11957471 TTTAGA-ACTGAAAC
1 TATAGATACTGAAAC
11957485 ATTCTGAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
13 4 0.08
14 20 0.41
15 16 0.33
16 9 0.18
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (15 bp):
TATAGATACTGAAAC
Found at i:11957461 original size:15 final size:16
Alignment explanation
Indices: 11957423--11957453 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11957413 ATAGATTATG
11957423 AAACT-TAGATACTGA
1 AAACTATAGATACTGA
11957438 AAACTATAGATACTGA
1 AAACTATAGATACTGA
11957454 TACTATAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (16 bp):
AAACTATAGATACTGA
Found at i:11969474 original size:25 final size:25
Alignment explanation
Indices: 11969425--11969474 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
11969415 GGTTTTTTTA
*
11969425 TTATTTAATATTAACATAATTATTT
1 TTATTTAATATTAACATAATAATTT
*
11969450 TTATTTAAATATTAATATAA-AATTT
1 TTATTT-AATATTAACATAATAATTT
11969475 AAATTTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATTTAATATTAACATAATAATTT
Found at i:11974307 original size:13 final size:13
Alignment explanation
Indices: 11974289--11974314 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11974279 ATTTTAACTG
11974289 TTTTCATTTCTAT
1 TTTTCATTTCTAT
11974302 TTTTCATTTCTAT
1 TTTTCATTTCTAT
11974315 AGATAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTCATTTCTAT
Found at i:11982588 original size:43 final size:43
Alignment explanation
Indices: 11982522--11982647 Score: 143
Period size: 41 Copynumber: 3.0 Consensus size: 43
11982512 GGCTCGTACA
**
11982522 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTGAACACATATCG
1 ATGCCAATATCCCAGACAG-GGTCTTACATGTGAACACATATCG
* *
11982565 ATGCCACTATCCCAGACAGGGTCTTACA--TGAATCAAATA-CG
1 ATGCCAATATCCCAGACAGGGTCTTACATGTGAA-CACATATCG
* * *
11982606 ATGCCAATGTCCCAGACATGGTCTTACATGTAAACACATATC
1 ATGCCAATATCCCAGACAGGGTCTTACATGTGAACACATATC
11982648 AAAAATCCTA
Statistics
Matches: 69, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
41 31 0.45
42 10 0.14
43 27 0.39
44 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAATATCCCAGACAGGGTCTTACATGTGAACACATATCG
Found at i:11983399 original size:10 final size:10
Alignment explanation
Indices: 11983386--11983414 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
11983376 TCAAAAACAT
11983386 AACAAAATCG
1 AACAAAATCG
11983396 AACAAAATCG
1 AACAAAATCG
11983406 AACAAAATC
1 AACAAAATC
11983415 CATACCGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.21, G:0.07, T:0.10
Consensus pattern (10 bp):
AACAAAATCG
Found at i:11983549 original size:23 final size:23
Alignment explanation
Indices: 11983521--11983567 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
11983511 TTAATTTGTT
11983521 TTATTAA-ACATATATTAACCTTA
1 TTATTAATAC-TATATTAACCTTA
11983544 TTATTAATTTACTATATTAACCTT
1 TTATTAA--TACTATATTAACCTT
11983568 TACTAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.33
25 12 0.57
26 2 0.10
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATTAATACTATATTAACCTTA
Found at i:11997381 original size:25 final size:25
Alignment explanation
Indices: 11997318--11997383 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
11997308 GTACATATAT
** * * *
11997318 GCTCATATGAGCTATGAATCGGTAT
1 GCTCATACAAGCTGTGAATCGATAA
11997343 GCTC-TCACAAGCTGTGAATCGATAA
1 GCTCAT-ACAAGCTGTGAATCGATAA
11997368 GCTCATACAAGCTGTG
1 GCTCATACAAGCTGTG
11997384 GTGTGTTCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.03
25 32 0.94
26 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (25 bp):
GCTCATACAAGCTGTGAATCGATAA
Found at i:12002898 original size:32 final size:32
Alignment explanation
Indices: 12002862--12002948 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
12002852 ACTTTTCCGA
*
12002862 AAAATATTTTCAGGAAATC-TGCCAAACAACAG
1 AAAATATTTTCAGCAAATCAT-CCAAACAACAG
* *
12002894 AAAATATTTTACA-CAGATTCATCCAAACACCAG
1 AAAATATTTT-CAGCA-AATCATCCAAACAACAG
*
12002927 AAAATATTTTTCAGTAAATCAT
1 AAAATA-TTTTCAGCAAATCAT
12002949 TTTCCAGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
32 11 0.24
33 28 0.62
34 6 0.13
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (32 bp):
AAAATATTTTCAGCAAATCATCCAAACAACAG
Found at i:12002964 original size:20 final size:20
Alignment explanation
Indices: 12002939--12002978 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12002929 AATATTTTTC
12002939 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
12002959 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
12002979 TCATTTTCCG
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:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:12002980 original size:34 final size:33
Alignment explanation
Indices: 12002928--12002992 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
12002918 AAACACCAGA
*
12002928 AAATATTTTTCAGTAAATCATTTTCCAGAAAAGT
1 AAATATTTTCCAGTAAATCATTTTCC-GAAAAGT
12002962 AAATCATTTTCCAG-AAATCATTTTCCGAAAA
1 AAAT-ATTTTCCAGTAAATCATTTTCCGAAAA
12002993 ACATTTTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 5 0.17
34 16 0.55
35 8 0.28
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (33 bp):
AAATATTTTCCAGTAAATCATTTTCCGAAAAGT
Found at i:12002981 original size:14 final size:13
Alignment explanation
Indices: 12002962--12002991 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
12002952 CCAGAAAAGT
12002962 AAATCATTTTCCAG
1 AAATCATTTTCC-G
12002976 AAATCATTTTCCG
1 AAATCATTTTCCG
12002989 AAA
1 AAA
12002992 AACATTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (13 bp):
AAATCATTTTCCG
Found at i:12005760 original size:63 final size:62
Alignment explanation
Indices: 12005640--12005791 Score: 146
Period size: 63 Copynumber: 2.4 Consensus size: 62
12005630 CTCACACGAA
* * * *
12005640 CTAGGGAAACGGGCGTGTGTCCAGACTGTATAACTCATTGTTTGTAATTGGGCGTCACATAGG
1 CTAGGGACAC-GGCGTGTGTCCAGGCTGTATAACTCATTGTTTGGAATTAGGCGTCACATAGG
* * * * *
12005703 TTAGGGACACGGACGTGTGTCCAGGTTGTGTAACTCACTAT-TTTGGATTTAGG-GTCACATGGG
1 CTAGGGACACGG-CGTGTGTCCAGGCTGTATAACTCA-T-TGTTTGGAATTAGGCGTCACATAGG
* *
12005766 CCAAGGACACAGGCGTGTGTCCAGGC
1 CTAGGGACAC-GGCGTGTGTCCAGGC
12005792 CGTGTGAGGG
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
62 2 0.03
63 57 0.79
64 12 0.17
65 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (62 bp):
CTAGGGACACGGCGTGTGTCCAGGCTGTATAACTCATTGTTTGGAATTAGGCGTCACATAGG
Found at i:12006394 original size:23 final size:23
Alignment explanation
Indices: 12006364--12006414 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
12006354 CCCTATATGG
*
12006364 TGTGTTAGGATGGTCGGGGATGA
1 TGTGTTAGGATGGTCGGAGATGA
*
12006387 TGTGTTAGGATGGTCGGAGATGG
1 TGTGTTAGGATGGTCGGAGATGA
12006410 TGTGT
1 TGTGT
12006415 AGTGGATAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.16, C:0.04, G:0.47, T:0.33
Consensus pattern (23 bp):
TGTGTTAGGATGGTCGGAGATGA
Found at i:12008696 original size:3 final size:3
Alignment explanation
Indices: 12008688--12008728 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
12008678 AATATAAACA
12008688 AAC AAC AAC AAC AAC AAC AAC AAC AAC AGAGC AAC AA- AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC A-A-C AAC AAC AAC A
12008729 GTGACAGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 29 0.83
4 2 0.06
5 2 0.06
ACGTcount: A:0.66, C:0.29, G:0.05, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:12009663 original size:23 final size:22
Alignment explanation
Indices: 12009610--12009671 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
12009600 TTTAAGCTTG
*
12009610 ATATTATTTTAAATTCATCATTA
1 ATATTA-TTTAAATTTATCATTA
12009633 ATA-T-TTTAAATTTATCATATA
1 ATATTATTTAAATTTATCAT-TA
* *
12009654 TTATTATTTACATTTATC
1 ATATTATTTAAATTTATC
12009672 GTCTATTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 13 0.39
21 4 0.12
22 2 0.06
23 14 0.42
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATTATTTAAATTTATCATTA
Found at i:12011856 original size:14 final size:14
Alignment explanation
Indices: 12011791--12011856 Score: 55
Period size: 14 Copynumber: 4.5 Consensus size: 14
12011781 TTGACCAAGT
* *
12011791 ATAAATTATTAATA
1 ATAAATAATTTATA
12011805 ATAAAT-ATTATATA
1 ATAAATAATT-TATA
12011819 ATTAAATTAACTTTA-A
1 A-TAAA-TAA-TTTATA
12011835 TATAAATAATTTATA
1 -ATAAATAATTTATA
12011850 ATAAATA
1 ATAAATA
12011857 CTATATATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
13 3 0.07
14 21 0.48
15 8 0.18
16 6 0.14
17 4 0.09
18 2 0.05
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAAATAATTTATA
Found at i:12015420 original size:12 final size:12
Alignment explanation
Indices: 12015405--12015437 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
12015395 AACTGAGCCG
12015405 TAAATATTTTTA
1 TAAATATTTTTA
12015417 TAAATATTTTTA
1 TAAATATTTTTA
12015429 TAAATATTT
1 TAAATATTT
12015438 ACGGAGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAAATATTTTTA
Found at i:12017608 original size:50 final size:51
Alignment explanation
Indices: 12017452--12017629 Score: 306
Period size: 51 Copynumber: 3.5 Consensus size: 51
12017442 ATCAGTGGCA
*
12017452 AGTGACAAGTGACAAGTGATAAGTGGTAGCATT-AGCTACACTTATCTGATC
1 AGTGACAAGTGACAAGTGATAAGTGATAGC-TTCAGCTACACTTATCTGATC
*
12017503 AGTGACAAGTAACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATC
1 AGTGACAAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATC
12017554 AGTGACAAGTGACAAGTGATAAGTGATAG-TTCAGCTACACTTATCTGATC
1 AGTGACAAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATC
*
12017604 AGTGACAAGTGACAAGTGACAAGTGA
1 AGTGACAAGTGACAAGTGATAAGTGA
12017630 CAAGTGATAA
Statistics
Matches: 122, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
50 48 0.39
51 74 0.61
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (51 bp):
AGTGACAAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATC
Found at i:12017616 original size:7 final size:7
Alignment explanation
Indices: 12017604--12017642 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
12017594 TTATCTGATC
12017604 AGTGACA
1 AGTGACA
12017611 AGTGACA
1 AGTGACA
12017618 AGTGACA
1 AGTGACA
12017625 AGTGACA
1 AGTGACA
*
12017632 AGTGATA
1 AGTGACA
12017639 AGTG
1 AGTG
12017643 GTAGCATTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.31, T:0.18
Consensus pattern (7 bp):
AGTGACA
Found at i:12017670 original size:115 final size:114
Alignment explanation
Indices: 12017401--12017737 Score: 386
Period size: 115 Copynumber: 3.0 Consensus size: 114
12017391 ACTTCTAATC
* * *
12017401 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGGCAAGTGACAAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
* * * *
12017466 AGTGATAAG-T-GGTAGCA-TTAGCT-A-CACTTATC---TGATC-AGTGACA
66 AGTGAT-AGTTAGCTA-CACTTATCTGATCAGTGA-CAAGTGA-CAAGTGACA
* * *
12017510 AGTAACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
12017575 AGTGATAGTTCAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGACA
66 AGTGATAGTT-AGCTACACTTATCTGATCAGTGACAAGTGACAAGTGACA
* * * * * *
12017625 AGTGACAAGTGATAAGTGGTAGCATTAGCTACACTTATCTAATCAGTGATAAGCGGCAAGAGATA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
* * *
12017690 AGTGGTAGCTTAGCTACACTTATCTGATCAGGGACAAGTGATAAGTGA
66 AGTGATAG-TTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGA
12017738 TCATACGTTA
Statistics
Matches: 195, Mismatches: 22, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
108 2 0.01
109 66 0.34
110 2 0.01
111 8 0.04
112 2 0.01
113 4 0.02
114 1 0.01
115 108 0.55
116 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (114 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
AGTGATAGTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGACA
Found at i:12017693 original size:65 final size:64
Alignment explanation
Indices: 12017557--12017693 Score: 186
Period size: 65 Copynumber: 2.1 Consensus size: 64
12017547 TCTGATCAGT
* * *
12017557 GACAAGTGACAAGTGATAAGTGATAGTTCAGCTACACTTATCTGATCAGTGACAAGTGACAAGT
1 GACAAGTGACAAGTGATAAGTGATAGTTCAGCTACACTTATCTAATCAGTGACAAGCGACAAGA
* * *
12017621 GACAAGTGACAAGTGATAAGTGGTAGCATT-AGCTACACTTATCTAATCAGTGATAAGCGGCAAG
1 GACAAGTGACAAGTGATAAGTGATAG--TTCAGCTACACTTATCTAATCAGTGACAAGCGACAAG
12017685 A
64 A
*
12017686 GATAAGTG
1 GACAAGTG
12017694 GTAGCTTAGC
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
64 25 0.39
65 37 0.58
66 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (64 bp):
GACAAGTGACAAGTGATAAGTGATAGTTCAGCTACACTTATCTAATCAGTGACAAGCGACAAGA
Found at i:12019046 original size:28 final size:28
Alignment explanation
Indices: 12019006--12019104 Score: 153
Period size: 28 Copynumber: 3.5 Consensus size: 28
12018996 TGATTTTCGA
12019006 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAATTTAATTGTAAAG
*
12019034 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAATTTAATTGTAAAG
* * * *
12019062 CACCAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAATTTAATTGTAAAG
12019090 CACTAAGTGTGCGAA
1 CACTAAGTGTGCGAA
12019105 CTTATTAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (28 bp):
CACTAAGTGTGCGAATTTAATTGTAAAG
Found at i:12019858 original size:23 final size:23
Alignment explanation
Indices: 12019831--12020312 Score: 359
Period size: 23 Copynumber: 20.6 Consensus size: 23
12019821 TTATGCTTAA
*
12019831 ATGCTGTCCAATTTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
* *
12019854 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
12019877 ATGCTGTCCAATTTTGATGTAAAA
1 ATGCTGTCCAA-TTTGTTGTATAT
* *
12019901 ATGCTG-CTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* * * *
12019924 ATGCTGCCCAAATTGTTGCACAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
12019947 ATGCTGTCAAATTTTTATGCTA-AA
1 ATGCTGTCCAATTTGT-TG-TATAT
*
12019971 ATGCTGTCCAATTTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
* * * *
12019994 ATGCTGCCCAAATTGGTGCATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
12020017 ATGCTGTCAAATTTTTATGCTA-AA
1 ATGCTGTCCAATTTGT-TG-TATAT
*
12020041 ATGCTGTCCAATTTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
* * *
12020064 ATGCTGCCCAAATTGTTGCATAT
1 ATGCTGTCCAATTTGTTGTATAT
* *
12020087 ATGCTGTCCAATTTTTATGCT-TAA
1 ATGCTGTCCAATTTGT-TG-TATAT
* *
12020111 ATGCTGCCCAATTTGTTGTATTT
1 ATGCTGTCCAATTTGTTGTATAT
* *
12020134 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
* * * *
12020157 ATGCTGTCCGATTTTGATGTAAAA
1 ATGCTGTCC-AATTTGTTGTATAT
*
12020181 ATGCTG-CTCAATTTGGTATATATAT
1 ATGCTGTC-CAATTT-GT-TGTATAT
* *
12020206 AGGCTGCCCTAA-TTGTTGTATAT
1 ATGCTGTCC-AATTTGTTGTATAT
* *
12020229 ATGCTGTCCAATTTTTATGCTA-AA
1 ATGCTGTCCAATTTGT-TG-TATAT
*
12020253 ATGCTG-CTCAATTTGATGTATAT
1 ATGCTGTC-CAATTTGTTGTATAT
* *
12020276 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGTTGTATAT
12020299 ATGCTGTCCAATTT
1 ATGCTGTCCAATTT
12020313 TTGGTGTGAA
Statistics
Matches: 353, Mismatches: 82, Indels: 48
0.73 0.17 0.10
Matches are distributed among these distances:
22 9 0.03
23 220 0.62
24 105 0.30
25 16 0.05
26 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.42
Consensus pattern (23 bp):
ATGCTGTCCAATTTGTTGTATAT
Found at i:12019905 original size:70 final size:70
Alignment explanation
Indices: 12019816--12020314 Score: 702
Period size: 70 Copynumber: 7.1 Consensus size: 70
12019806 ATATTCATGT
*
12019816 AATTTTTATGCTTAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
12019881 TGTCC
66 TGTCC
* * * * * *
12019886 AATTTTGATG-TAAAAATGCTG-CTCAATTTGGTATATATATGCTGCCCAAATTGTTGCACATAT
1 AATTTTTATGCT-AAAATGCTGTC-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATAT
*
12019949 GCTGTCA
64 GCTGTCC
* *
12019956 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGGTGCATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
*
12020021 TGTCA
66 TGTCC
*
12020026 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGCATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
12020091 TGTCC
66 TGTCC
* *
12020096 AATTTTTATGCTTAAATGCTGCCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
1 AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
12020161 TGTCC
66 TGTCC
* * * * * *
12020166 GATTTTGATG-TAAAAATGCTG-CTCAATTTGGTATATATATAGGCTGCCCTAATTGTTGTATAT
1 AATTTTTATGCT-AAAATGCTGTC-CAATTT-GT-TGTATTTATGCTGCCCAAATTGTTGTATAT
12020229 ATGCTGTCC
62 ATGCTGTCC
* *
12020238 AATTTTTATGCTAAAATGCTG-CTCAATTTGATGTATATATGCTGCCCAAATTGTTGTATATATG
1 AATTTTTATGCTAAAATGCTGTC-CAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATG
12020302 CTGTCC
65 CTGTCC
12020308 AATTTTT
1 AATTTTT
12020315 GGTGTGAAAA
Statistics
Matches: 388, Mismatches: 32, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
69 4 0.01
70 318 0.82
71 5 0.01
72 60 0.15
73 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (70 bp):
AATTTTTATGCTAAAATGCTGTCCAATTTGTTGTATTTATGCTGCCCAAATTGTTGTATATATGC
TGTCC
Found at i:12027126 original size:14 final size:14
Alignment explanation
Indices: 12027061--12027126 Score: 55
Period size: 14 Copynumber: 4.5 Consensus size: 14
12027051 TTGACCAAGT
* *
12027061 ATAAATTATTAATA
1 ATAAATAATTTATA
12027075 ATAAAT-ATTATATA
1 ATAAATAATT-TATA
12027089 ATTAAATTAACTTTA-A
1 A-TAAA-TAA-TTTATA
12027105 TATAAATAATTTATA
1 -ATAAATAATTTATA
12027120 ATAAATA
1 ATAAATA
12027127 CTATATATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
13 3 0.07
14 21 0.48
15 8 0.18
16 6 0.14
17 4 0.09
18 2 0.05
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAAATAATTTATA
Found at i:12033280 original size:27 final size:29
Alignment explanation
Indices: 12033226--12033280 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
12033216 AGAAAAAATT
* *
12033226 TAAATAAATCACTTAAAATATAACAAAAC
1 TAAAAAAATCACTTAAAATATAAAAAAAC
12033255 TAAAAAAATCA-TT-AAATATAAAAAAA
1 TAAAAAAATCACTTAAAATATAAAAAAA
12033281 ATAGAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.50
28 2 0.08
29 10 0.42
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (29 bp):
TAAAAAAATCACTTAAAATATAAAAAAAC
Found at i:12038577 original size:25 final size:25
Alignment explanation
Indices: 12038496--12038579 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
12038486 CGGATACACC
*
12038496 ACAACTCATATGAGCTTACCGATTT
1 ACAACTCGTATGAGCTTACCGATTT
** *
12038521 GTAGCTCGTGA-GAG-TTACCGATTCT
1 ACAACTCGT-ATGAGCTTACCGATT-T
* *
12038546 -CAGCTCGTATTAGCTTACCGATTT
1 ACAACTCGTATGAGCTTACCGATTT
12038570 ACAACTCGTA
1 ACAACTCGTA
12038580 ATAGCATATT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
23 1 0.02
24 19 0.40
25 26 0.55
26 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (25 bp):
ACAACTCGTATGAGCTTACCGATTT
Found at i:12042592 original size:44 final size:44
Alignment explanation
Indices: 12042487--12042783 Score: 153
Period size: 44 Copynumber: 6.6 Consensus size: 44
12042477 TTCAGTCTAT
* ** * * *
12042487 TCCACTGTAATCTCAGGGAGATAAGA-CC-CGA-TGCGATCTAC
1 TCCACTGTAATCTCAGAGAGATAAGATCCTTTATTTCAATCTGC
* * *
12042528 TCTACTGTAA-CTTCATAGAGATAAGATCCTTTATTTTAATCTGC
1 TCCACTGTAATC-TCAGAGAGATAAGATCCTTTATTTCAATCTGC
* * *
12042572 TCCACTGTAATCTCAGAGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGAGAGATAAGATCCT-TTA-TTTCAATCTGC
* * * * *
12042616 TCCACTGTAATCTCAGGGAGATAAGTTTCAAGCTTCAATCTGATGCGATCTAC
1 TCCACTGTAATCTCAGAGAGATAAG-ATC---CTT-TAT-T--T-CAATCTGC
* * *
12042669 TCTACTGTAA-CTTTAGAGAGATAAGATCCTTTATTTTAATCTGC
1 TCCACTGTAATC-TCAGAGAGATAAGATCCTTTATTTCAATCTGC
* * * *
12042713 TCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCTGC
1 TCCACTGTAATCTCAGAGAGATAAGATCCT-TTA-TTTCAATCTGC
* * *
12042757 TCCGCTGTAATCTCAGGGAGATGAGAT
1 TCCACTGTAATCTCAGAGAGATAAGAT
12042784 TTCTGGCTTC
Statistics
Matches: 193, Mismatches: 41, Indels: 41
0.70 0.15 0.15
Matches are distributed among these distances:
40 1 0.01
41 21 0.11
42 4 0.02
43 5 0.03
44 119 0.62
45 4 0.02
47 1 0.01
48 2 0.01
49 3 0.02
50 3 0.02
52 4 0.02
53 26 0.13
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
TCCACTGTAATCTCAGAGAGATAAGATCCTTTATTTCAATCTGC
Found at i:12042770 original size:141 final size:142
Alignment explanation
Indices: 12042516--12042796 Score: 492
Period size: 141 Copynumber: 2.0 Consensus size: 142
12042506 GATAAGACCC
*
12042516 GATGCGATCTACTCTACTGTAACTTCATAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTA
1 GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTA
12042581 ATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAG-TTTC
66 ATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTC
12042645 AAGCTTCAATCT
131 AAGCTTCAATCT
*
12042657 GATGCGATCTACTCTACTGTAACTTTAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTA
1 GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTA
* * *
12042722 ATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATGAGATTTC
66 ATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTC
**
12042787 TGGCTTCAAT
131 AAGCTTCAAT
12042797 TTGCTCTACT
Statistics
Matches: 132, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
141 120 0.91
142 12 0.09
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (142 bp):
GATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTA
ATCTCAGAGAGATAGGATTACTAGCTTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTC
AAGCTTCAATCT
Found at i:12042793 original size:44 final size:43
Alignment explanation
Indices: 12042706--12042828 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 43
12042696 CCTTTATTTT
12042706 AATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATA-GATTACTAGCTTC
* * *
12042750 AATCTGCTCCGCTGTAATCTCAGGGAGATGAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGAT-AGATTACTAGCTTC
* * *
12042794 AATTTGCTCTACTGTAA-CATCAAGGAGATAAGATT
1 AATCTGCTCCACTGTAATC-TCAGGGAGAT-AGATT
12042829 CACCATTTCC
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
43 1 0.01
44 67 0.97
45 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (43 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAGATTACTAGCTTC
Found at i:12043104 original size:131 final size:131
Alignment explanation
Indices: 12042873--12043282 Score: 619
Period size: 131 Copynumber: 3.2 Consensus size: 131
12042863 CACTGTAATC
* * * * * * * **
12042873 TCAGGGAGATAAGACCTGTGGCTTAAATCTGCTTCCTTACACTTA---AAGATAAGATTTACCGT
1 TCAGGGACATAGGACGTGTGGCTTAAATCTGTTTCCCTACTCCTAGGGAAGATAAGATTCGCCGT
* * *
12042935 CTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTACTCCACTGCTG
66 CTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTG
12043000 G
131 G
*
12043001 TCAGGGACATAGGACGTGTGGCTTAAATCTGTTTCCCTACTCCTAGGGAAGATAAGATTCGCCAT
1 TCAGGGACATAGGACGTGTGGCTTAAATCTGTTTCCCTACTCCTAGGGAAGATAAGATTCGCCGT
*
12043066 CTTCGATCTGATCTGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTG
66 CTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTG
12043131 G
131 G
* *
12043132 TCAGGGACATAGGACGTATGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGT
1 TCAGGGACATAGGACGTGTGGCTTAAATCTGTTTCCCTACTCCTAGGGAAGATAAGATTCGCCGT
* *
12043197 CTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAGATCTCCAATTTCCAACCTATTCCACTACTG
66 CTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTG
12043262 G
131 G
* *
12043263 CCAGGGACATAGGACTTGTG
1 TCAGGGACATAGGACGTGTG
12043283 ATTTCACCGA
Statistics
Matches: 256, Mismatches: 23, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
128 38 0.15
131 218 0.85
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (131 bp):
TCAGGGACATAGGACGTGTGGCTTAAATCTGTTTCCCTACTCCTAGGGAAGATAAGATTCGCCGT
CTTCGATCTGCTCTGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTG
G
Found at i:12044109 original size:25 final size:24
Alignment explanation
Indices: 12044080--12044162 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 24
12044070 GGATACACCA
*
12044080 CAGCTCATATGAGCTTACCGATTT
1 CAGCTCGTATGAGCTTACCGATTT
*
12044104 GTAGCTCGTGA-GAG-TTACCGATTCT
1 -CAGCTCGT-ATGAGCTTACCGATT-T
*
12044129 CAGCTCGTATTAGCTTACCGATTT
1 CAGCTCGTATGAGCTTACCGATTT
*
12044153 ACAACTCGTA
1 -CAGCTCGTA
12044163 ATAGCATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
23 1 0.02
24 19 0.40
25 27 0.56
26 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (24 bp):
CAGCTCGTATGAGCTTACCGATTT
Found at i:12048918 original size:22 final size:24
Alignment explanation
Indices: 12048888--12048931 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
12048878 GCAATGGTGA
*
12048888 AAGGCTAGTC-CTTGAG-TAAATG
1 AAGGATAGTCTCTTGAGCTAAATG
12048910 AAGGATAGTCTCTTGAGCTAAA
1 AAGGATAGTCTCTTGAGCTAAA
12048932 GAGGAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 6 0.32
24 4 0.21
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (24 bp):
AAGGATAGTCTCTTGAGCTAAATG
Found at i:12049321 original size:16 final size:16
Alignment explanation
Indices: 12049300--12049331 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12049290 ATTGGGGCCT
12049300 TGTTTTCGTAATTTAA
1 TGTTTTCGTAATTTAA
12049316 TGTTTTCGTAATTTAA
1 TGTTTTCGTAATTTAA
12049332 GGCTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.56
Consensus pattern (16 bp):
TGTTTTCGTAATTTAA
Found at i:12066611 original size:22 final size:22
Alignment explanation
Indices: 12066539--12066613 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
12066529 TGTTACTATT
*
12066539 TTACTGTCATTTCACTATTATA
1 TTACTATCATTTCACTATTATA
* * ** * *
12066561 TTGCTGTTACTATTTCGTTACTATT
1 TTACT-AT-C-ATTTCACTATTATA
12066586 TTACTATCATTTCACTATTATA
1 TTACTATCATTTCACTATTATA
12066608 TTACTA
1 TTACTA
12066614 CTATTTTTTG
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
22 20 0.53
23 2 0.05
24 2 0.05
25 14 0.37
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.52
Consensus pattern (22 bp):
TTACTATCATTTCACTATTATA
Found at i:12071866 original size:20 final size:21
Alignment explanation
Indices: 12071836--12071877 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
12071826 CATGGAAAAG
12071836 TTTTAATTTAAATAAATTTAA
1 TTTTAATTTAAATAAATTTAA
* *
12071857 TTTT-ATTTAATTAATTTTAA
1 TTTTAATTTAAATAAATTTAA
12071877 T
1 T
12071878 CTAAAAGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTAATTTAAATAAATTTAA
Found at i:12075518 original size:26 final size:26
Alignment explanation
Indices: 12075482--12075535 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
12075472 AATTTTTAAC
12075482 ATAGTTTTCATCTCAATGAACTGAAA
1 ATAGTTTTCATCTCAATGAACTGAAA
12075508 ATAGTTTTCATCTCAATGAACTGAAA
1 ATAGTTTTCATCTCAATGAACTGAAA
12075534 AT
1 AT
12075536 CATTAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (26 bp):
ATAGTTTTCATCTCAATGAACTGAAA
Found at i:12083207 original size:12 final size:12
Alignment explanation
Indices: 12083192--12083241 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
12083182 TTCCTTGCTA
*
12083192 TTTTTTACTGTT
1 TTTTTTACTATT
12083204 TTTTTTACTA-T
1 TTTTTTACTATT
* *
12083215 TTTCTTATTATT
1 TTTTTTACTATT
12083227 TTTTTTCACTATT
1 TTTTTT-ACTATT
12083240 TT
1 TT
12083242 GCTATTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 9 0.29
12 15 0.48
13 7 0.23
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTTTACTATT
Found at i:12083229 original size:24 final size:24
Alignment explanation
Indices: 12083202--12083251 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
12083192 TTTTTTACTG
12083202 TTTTTTTT-ACTATTTT-CTTATTA
1 TTTTTTTTCACTATTTTGC-TATTA
12083225 TTTTTTTTCACTATTTTGCTATTA
1 TTTTTTTTCACTATTTTGCTATTA
12083249 TTT
1 TTT
12083252 CAATAATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 8 0.32
24 16 0.64
25 1 0.04
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTTTTTTCACTATTTTGCTATTA
Found at i:12083698 original size:19 final size:16
Alignment explanation
Indices: 12083663--12083694 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12083653 AAATTAACTG
12083663 AAAATTAATATTTTTA
1 AAAATTAATATTTTTA
12083679 ATAAATTAATATTTTT
1 A-AAATTAATATTTTT
12083695 TTAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATTAATATTTTTA
Found at i:12088298 original size:21 final size:21
Alignment explanation
Indices: 12088272--12088314 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
12088262 TTTGGGTGGA
*
12088272 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
12088293 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTCTGT
12088314 T
1 T
12088315 GGCGTGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (21 bp):
TCAGCTCTCACGAGCTTCTGT
Found at i:12092210 original size:20 final size:20
Alignment explanation
Indices: 12092185--12092224 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
12092175 TGGAAAACGA
*
12092185 TTTCTGGAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
12092205 TTTCTGAAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
12092225 GGAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:12093645 original size:32 final size:32
Alignment explanation
Indices: 12093599--12093659 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
12093589 TGCCAATTAT
12093599 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
*
12093631 TTCAATATCTAACAAGCTTAAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
12093660 CAATATCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:12093666 original size:27 final size:30
Alignment explanation
Indices: 12093599--12093672 Score: 100
Period size: 32 Copynumber: 2.5 Consensus size: 30
12093589 TGCCAATTAT
*
12093599 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCTTAAAAC--AATAAA
12093631 TTCAATATCTAACAAGCTTAAAAC-AT-AA
1 TTCAATATCTAACAAGCTTAAAACAATAAA
12093659 -TCAATATCTAACAA
1 TTCAATATCTAACAA
12093673 ATTCAAGACA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 14 0.34
28 2 0.05
29 2 0.05
32 23 0.56
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (30 bp):
TTCAATATCTAACAAGCTTAAAACAATAAA
Found at i:12093683 original size:27 final size:27
Alignment explanation
Indices: 12093600--12093686 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 27
12093590 GCCAATTATT
* *
12093600 TCAATATCCAACAAGCTTAAAACATAATAAA
1 TCAATATCTAACAAGATTAAAAC---AT-AA
*
12093631 TTCAATATCTAACAAGCTTAAAACATAA
1 -TCAATATCTAACAAGATTAAAACATAA
*
12093659 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
12093686 T
1 T
12093687 AATTTCAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.04
27 23 0.45
28 2 0.04
29 2 0.04
32 22 0.43
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:12095139 original size:27 final size:27
Alignment explanation
Indices: 12095079--12095139 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
12095069 ATACCACACA
* **
12095079 AATATTTGATCACTATAAAAAAGATTT
1 AATATTTGATCAATATAAAAAAGATAC
* * *
12095106 AAAATTTGATCAATATAAAATATATAC
1 AATATTTGATCAATATAAAAAAGATAC
12095133 AATATTT
1 AATATTT
12095140 TAGATCGATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.38
Consensus pattern (27 bp):
AATATTTGATCAATATAAAAAAGATAC
Found at i:12097081 original size:18 final size:18
Alignment explanation
Indices: 12097058--12097096 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12097048 TTTGGCTGAG
12097058 AAAGAATGAAGGAAA-GAA
1 AAAGAATGAA-GAAAGGAA
12097076 AAAGAATGAAGAAAGGAA
1 AAAGAATGAAGAAAGGAA
12097094 AAA
1 AAA
12097097 AGGGATCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (18 bp):
AAAGAATGAAGAAAGGAA
Found at i:12098788 original size:29 final size:29
Alignment explanation
Indices: 12098746--12098803 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
12098736 AATATTAATG
12098746 ATAATATCATTATTGCTCAAGAGATTACT
1 ATAATATCATTATTGCTCAAGAGATTACT
* *
12098775 ATAATATCATTATTGCTCGAGAGGTTACT
1 ATAATATCATTATTGCTCAAGAGATTACT
12098804 CACTCCGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (29 bp):
ATAATATCATTATTGCTCAAGAGATTACT
Found at i:12099561 original size:22 final size:23
Alignment explanation
Indices: 12099528--12099574 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
12099518 CCATTTGAGG
12099528 TTAATTTTCTCCTAA-GTGCCAAT
1 TTAATTTTCTCC-AAGGTGCCAAT
*
12099551 TTAA-TTTCTCCAAGGTTCCAAT
1 TTAATTTTCTCCAAGGTGCCAAT
12099573 TT
1 TT
12099575 CAAATTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 2 0.09
22 16 0.73
23 4 0.18
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.45
Consensus pattern (23 bp):
TTAATTTTCTCCAAGGTGCCAAT
Found at i:12100113 original size:14 final size:14
Alignment explanation
Indices: 12100096--12100123 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12100086 TTGGCTTTGT
12100096 TAATTCCATTTATC
1 TAATTCCATTTATC
12100110 TAATTCCATTTATC
1 TAATTCCATTTATC
12100124 ATATACTAGT
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:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTCCATTTATC
Found at i:12103827 original size:18 final size:18
Alignment explanation
Indices: 12103781--12103831 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
12103771 AGCTCTCAGG
12103781 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* * ***
12103799 TAGTAAGCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
12103817 CATTCTTCTCCCTTC
1 CATTCTTCTCCCTTC
12103832 CTTCATTCCT
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.41, G:0.04, T:0.41
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:12107356 original size:14 final size:15
Alignment explanation
Indices: 12107334--12107410 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
12107324 CAATCAAACA
12107334 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
12107348 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
12107363 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
12107383 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
12107397 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
12107411 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:12107375 original size:20 final size:20
Alignment explanation
Indices: 12107350--12107389 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12107340 AATATTTTCC
*
12107350 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
12107370 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
12107390 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:12107395 original size:34 final size:35
Alignment explanation
Indices: 12107338--12107404 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
12107328 CAAACACCAG
*
12107338 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
12107373 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
12107405 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:12107411 original size:14 final size:14
Alignment explanation
Indices: 12107373--12107412 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
12107363 ACAGAAAAGT
*
12107373 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
12107387 AAATCATTTTACGG
1 AAAACATTTTACAG
12107401 AAAACATTTTAC
1 AAAACATTTTAC
12107413 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:12109078 original size:18 final size:18
Alignment explanation
Indices: 12109055--12109106 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
12109045 ACAATGCGAG
*
12109055 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
*
12109073 AAATGATGCTCACATTTC
1 AAATGATGTTCACATTTC
12109091 AAATGATGTTCACATT
1 AAATGATGTTCACATT
12109107 GATGGAAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:12112704 original size:26 final size:26
Alignment explanation
Indices: 12112639--12112705 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
12112629 ATAATTGTAC
12112639 TCAATACTTATATTTACCAAAAAAATT
1 TCAATACTTA-ATTTACCAAAAAAATT
* *
12112666 TCTAATA-TAAATTTAGCAGAAAAAA-T
1 TC-AATACTTAATTTACCA-AAAAAATT
12112692 TCAATACTTAATTT
1 TCAATACTTAATTT
12112706 TTCAGCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 4 0.12
26 16 0.47
27 10 0.29
28 4 0.12
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.37
Consensus pattern (26 bp):
TCAATACTTAATTTACCAAAAAAATT
Found at i:12117363 original size:30 final size:27
Alignment explanation
Indices: 12117328--12117389 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 27
12117318 ATTTTATATC
*
12117328 TTTTAAAAAAATTAAATTAATAATTATTAA
1 TTTTAAAAAAATTAAAGT-ATAATT-TT-A
*
12117358 TTTTAAAGAAATTAAAGTATAATTTTA
1 TTTTAAAAAAATTAAAGTATAATTTTA
12117385 TTTTA
1 TTTTA
12117390 TATTAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 6 0.20
28 2 0.07
29 6 0.20
30 16 0.53
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (27 bp):
TTTTAAAAAAATTAAAGTATAATTTTA
Found at i:12118482 original size:38 final size:39
Alignment explanation
Indices: 12118425--12118560 Score: 190
Period size: 38 Copynumber: 3.5 Consensus size: 39
12118415 ATTTTAAAAA
12118425 TTAAAA-T-AAAAATTAAAAAAAGTATTTTAAAAATATT
1 TTAAAATTAAAAAATTAAAAAAAGTATTTTAAAAATATT
*
12118462 TTAAAATTAAAAAATT-AAAAAAGTATTTTAAAAAAATT
1 TTAAAATTAAAAAATTAAAAAAAGTATTTTAAAAATATT
* *
12118500 TTAAAATTAAAAAAATTAATAAAAAGTATTTTAAGAGTATT
1 TTAAAATT-AAAAAATTAA-AAAAAGTATTTTAAAAATATT
*
12118541 TTAAAGTTAAAAAA-TAAAAA
1 TTAAAATTAAAAAATTAAAAA
12118561 TAAAAATATT
Statistics
Matches: 89, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
37 6 0.07
38 33 0.37
39 18 0.20
40 7 0.08
41 25 0.28
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (39 bp):
TTAAAATTAAAAAATTAAAAAAAGTATTTTAAAAATATT
Found at i:12118531 original size:30 final size:29
Alignment explanation
Indices: 12118472--12118533 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
12118462 TTAAAATTAA
*
12118472 AAAATTAAAAAAGTATTTTAAAAAAATTTT
1 AAAATTAAAAAAG-ATTATAAAAAAATTTT
*
12118502 AAAATTAAAAAA-ATTAATAAAAAGTATTTT
1 AAAATTAAAAAAGATT-ATAAAAA-AATTTT
12118532 AA
1 AA
12118534 GAGTATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 3 0.11
29 6 0.21
30 19 0.68
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTAAAAAAGATTATAAAAAAATTTT
Found at i:12121120 original size:22 final size:20
Alignment explanation
Indices: 12121095--12121142 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
12121085 TTAATAGCAT
12121095 TAATTAGTATATTTAGAGATTA
1 TAATTAGT-T-TTTAGAGATTA
* *
12121117 TAATTGGTTTTTAGAGATTC
1 TAATTAGTTTTTAGAGATTA
12121137 TAATTA
1 TAATTA
12121143 AGAGATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 15 0.65
21 1 0.04
22 7 0.30
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (20 bp):
TAATTAGTTTTTAGAGATTA
Found at i:12121301 original size:21 final size:23
Alignment explanation
Indices: 12121277--12121318 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12121267 TCATGTTATC
12121277 AGATTT-TTTATT-TGATTTTTG
1 AGATTTCTTTATTCTGATTTTTG
*
12121298 AGATTTCTTTCTTCTGATTTT
1 AGATTTCTTTATTCTGATTTT
12121319 CAATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 5 0.28
23 7 0.39
ACGTcount: A:0.17, C:0.07, G:0.12, T:0.64
Consensus pattern (23 bp):
AGATTTCTTTATTCTGATTTTTG
Found at i:12128837 original size:28 final size:28
Alignment explanation
Indices: 12128773--12128837 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
12128763 TATGAAAATA
* * *
12128773 TAAAAAACATATAAGTATGTGTATATATT
1 TAAAAAA-ATAAAAATATGTATATATATT
* **
12128802 CATGAAAATAAAAATATGTATATATATT
1 TAAAAAAATAAAAATATGTATATATATT
12128830 TAAAAAAA
1 TAAAAAAA
12128838 ATTATACAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (28 bp):
TAAAAAAATAAAAATATGTATATATATT
Found at i:12128990 original size:3 final size:3
Alignment explanation
Indices: 12128982--12129062 Score: 87
Period size: 3 Copynumber: 28.0 Consensus size: 3
12128972 TAAATATTTG
*
12128982 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
12129029 TTA GTA ATA ATA CT- ATT TTA A-A ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12129063 GCAAAAATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
2 4 0.06
3 61 0.94
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:12129071 original size:18 final size:18
Alignment explanation
Indices: 12129048--12129110 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
12129038 ATACTATTTT
12129048 AAAATAATAATAATAGCA
1 AAAATAATAATAATAGCA
* * *
12129066 AAAATAATGAT-ATTGTTA
1 AAAATAATAATAATAG-CA
*
12129084 AAATTAATTAATTAATAGCA
1 AAAATAA-TAA-TAATAGCA
12129104 AAAATAA
1 AAAATAA
12129111 CAAAAAGGGA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 3 0.09
18 17 0.52
19 2 0.06
20 8 0.24
21 3 0.09
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.30
Consensus pattern (18 bp):
AAAATAATAATAATAGCA
Found at i:12129104 original size:38 final size:34
Alignment explanation
Indices: 12129034--12129110 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 34
12129024 CAATATTAGT
12129034 AATAATACTATTTTAAAATAATAATAATAGCAAA
1 AATAATACTATTTTAAAATAATAATAATAGCAAA
12129068 AATAATGA-TATTGTTAAAATTAATTAATTAATAGCAAA
1 AATAAT-ACTATT-TTAAAA-TAA-TAA-TAATAGCAAA
12129106 AATAA
1 AATAA
12129111 CAAAAAGGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
34 10 0.26
35 7 0.18
36 3 0.08
37 3 0.08
38 15 0.39
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (34 bp):
AATAATACTATTTTAAAATAATAATAATAGCAAA
Found at i:12130235 original size:30 final size:30
Alignment explanation
Indices: 12130201--12130265 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
12130191 TGGGATTTTG
* *
12130201 TTGGGCATCGGTTTGGGTTTGTAATGGGTT
1 TTGGGCATCGGGTAGGGTTTGTAATGGGTT
* * * *
12130231 TTGGGTATTGGGTAGGTTTTTTAATGGGTT
1 TTGGGCATCGGGTAGGGTTTGTAATGGGTT
12130261 TTGGG
1 TTGGG
12130266 TTGGGCACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.11, C:0.03, G:0.40, T:0.46
Consensus pattern (30 bp):
TTGGGCATCGGGTAGGGTTTGTAATGGGTT
Found at i:12134892 original size:18 final size:18
Alignment explanation
Indices: 12134871--12134905 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12134861 AATATATAAA
12134871 AATTGATGA-ACCTGGAAT
1 AATTGA-GATACCTGGAAT
12134889 AATTGAGATACCTGGAA
1 AATTGAGATACCTGGAA
12134906 CAAATTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (18 bp):
AATTGAGATACCTGGAAT
Found at i:12144325 original size:20 final size:20
Alignment explanation
Indices: 12144297--12144341 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
12144287 TAATATGTCT
*
12144297 TGTCCTAACTGAATTAATGG
1 TGTCTTAACTGAATTAATGG
* *
12144317 TGTCTTAACTTAATTAATTG
1 TGTCTTAACTGAATTAATGG
12144337 TGTCT
1 TGTCT
12144342 CGTTTTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (20 bp):
TGTCTTAACTGAATTAATGG
Found at i:12145317 original size:45 final size:45
Alignment explanation
Indices: 12145236--12145399 Score: 213
Period size: 45 Copynumber: 3.6 Consensus size: 45
12145226 GACCTTTTTG
* *
12145236 ATCCATTTTCGTACCAAAACTTATACC-TTTTGTACCTACACCAAA
1 ATCCA-TTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
*
12145281 ATCCATGTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
1 ATCCATTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
* * * *
12145326 ATCTATTTTGTACCAAAACCTATATCATTTCGTACCTATACCAAA
1 ATCCATTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
* * * *
12145371 ACCCATTTCCTACCAAAACCGATATCATT
1 ATCCATTTCGTACCAAAACCTATACCATT
12145400 CCATAATTAA
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
44 19 0.18
45 86 0.82
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (45 bp):
ATCCATTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
Found at i:12145378 original size:23 final size:22
Alignment explanation
Indices: 12145267--12145390 Score: 86
Period size: 23 Copynumber: 5.5 Consensus size: 22
12145257 TATACCTTTT
* *
12145267 GTACCTACACCAAAATCCATGTC
1 GTACCTAAACCAAAA-CCATTTC
* * *
12145290 GTACCAAAACCTATACCATTTC
1 GTACCTAAACCAAAACCATTTC
* * *
12145312 GTACCTACACCAAAATCTATTTT
1 GTACCTAAACCAAAA-CCATTTC
* * * *
12145335 GTACCAAAACCTATATCATTTC
1 GTACCTAAACCAAAACCATTTC
*
12145357 GTACCTATACCAAAACCCATTTC
1 GTACCTAAACCAAAA-CCATTTC
* *
12145380 CTACCAAAACC
1 GTACCTAAACC
12145391 GATATCATTC
Statistics
Matches: 73, Mismatches: 26, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
22 32 0.44
23 41 0.56
ACGTcount: A:0.36, C:0.32, G:0.05, T:0.27
Consensus pattern (22 bp):
GTACCTAAACCAAAACCATTTC
Found at i:12145672 original size:29 final size:29
Alignment explanation
Indices: 12145637--12145697 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
12145627 ATCGAAATTA
*
12145637 AAAAAAAATATATATGAAATTAAAAAAAAAG
1 AAAAAAAATAT-T-CGAAATTAAAAAAAAAG
**
12145668 AAAAAAAATATTCGTGATTAAAAAAAAAG
1 AAAAAAAATATTCGAAATTAAAAAAAAAG
12145697 A
1 A
12145698 GGAATCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 15 0.56
30 1 0.04
31 11 0.41
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (29 bp):
AAAAAAAATATTCGAAATTAAAAAAAAAG
Found at i:12147838 original size:38 final size:41
Alignment explanation
Indices: 12147788--12147872 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 41
12147778 AAAACAAAAG
* **
12147788 AAAAGAGTGAAAA-T-CAAAAGGAAAAT-AAAATTGAG-AAA
1 AAAAGAGGGAAAATTGCAAAA-GAAAATGAAAAGAGAGTAAA
12147826 AAAAGAGGGAAAATTGCAAAAGAAAATGAAAAGAGAGTAAA
1 AAAAGAGGGAAAATTGCAAAAGAAAATGAAAAGAGAGTAAA
12147867 AAAAGA
1 AAAAGA
12147873 AATCAATGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
38 12 0.30
39 7 0.17
40 12 0.30
41 9 0.22
ACGTcount: A:0.66, C:0.02, G:0.21, T:0.11
Consensus pattern (41 bp):
AAAAGAGGGAAAATTGCAAAAGAAAATGAAAAGAGAGTAAA
Found at i:12152147 original size:22 final size:22
Alignment explanation
Indices: 12152073--12152230 Score: 138
Period size: 23 Copynumber: 7.1 Consensus size: 22
12152063 TTTGATCCAT
**
12152073 TTTCGTACCAAAACTTATACC-
1 TTTCGTACCAAAACCAATACCA
* * * *
12152094 TTTCGTACCTACACCAAAATCTA
1 TTTCGTACCAAAACCAATA-CCA
* *
12152117 TTTCATACCAAAACCTATACCA
1 TTTCGTACCAAAACCAATACCA
* * * *
12152139 TTTAGTACCTACACCAAAATCCA
1 TTTCGTACCAAAACCAATA-CCA
*
12152162 TTTCGTACCAAAACCTATACCA
1 TTTCGTACCAAAACCAATACCA
* * *
12152184 TTTCGTACCTATACCAAAACCCA
1 TTTCGTACCAAAACCAATA-CCA
12152207 TTTCGTACCAAAACCAATACCA
1 TTTCGTACCAAAACCAATACCA
12152229 TT
1 TT
12152231 CCATAATTAA
Statistics
Matches: 103, Mismatches: 30, Indels: 7
0.74 0.21 0.05
Matches are distributed among these distances:
21 14 0.14
22 39 0.38
23 50 0.49
ACGTcount: A:0.37, C:0.31, G:0.04, T:0.28
Consensus pattern (22 bp):
TTTCGTACCAAAACCAATACCA
Found at i:12152157 original size:45 final size:45
Alignment explanation
Indices: 12152067--12152230 Score: 249
Period size: 45 Copynumber: 3.6 Consensus size: 45
12152057 GTCCTTTTTG
*
12152067 ATCCATTTTCGTACCAAAACTTATACC-TTTCGTACCTACACCAAA
1 ATCCA-TTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
* * *
12152112 ATCTATTTCATACCAAAACCTATACCATTTAGTACCTACACCAAA
1 ATCCATTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
*
12152157 ATCCATTTCGTACCAAAACCTATACCATTTCGTACCTATACCAAA
1 ATCCATTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
* *
12152202 ACCCATTTCGTACCAAAACCAATACCATT
1 ATCCATTTCGTACCAAAACCTATACCATT
12152231 CCATAATTAA
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 19 0.18
45 89 0.82
ACGTcount: A:0.37, C:0.31, G:0.04, T:0.29
Consensus pattern (45 bp):
ATCCATTTCGTACCAAAACCTATACCATTTCGTACCTACACCAAA
Found at i:12152249 original size:45 final size:44
Alignment explanation
Indices: 12152073--12152262 Score: 143
Period size: 45 Copynumber: 4.3 Consensus size: 44
12152063 TTTGATCCAT
** * * * * *
12152073 TTTCGTACCAAAACTTATACC-TTTCGTACCTACACCAAAATCTA
1 TTTCGTACCAAAACCAATACCATTCCATAACTAAACCAAAA-CCA
* * * * *
12152117 TTTCATACCAAAACCTATACCATT-TAGTACCTACACCAAAATCCA
1 TTTCGTACCAAAACCAATACCATTCCA-TAACTAAACCAAAA-CCA
* * * * *
12152162 TTTCGTACCAAAACCTATACCATTTCGTACCTATACCAAAACCCA
1 TTTCGTACCAAAACCAATACCATTCCATAACTAAACCAAAA-CCA
* *
12152207 TTTCGTACCAAAACCAATACCATTCCATAATTAAACCTAAACCA
1 TTTCGTACCAAAACCAATACCATTCCATAACTAAACCAAAACCA
12152251 TATTCG-ACCAAA
1 T-TTCGTACCAAA
12152263 CTTAGCCTAC
Statistics
Matches: 125, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
44 29 0.23
45 96 0.77
ACGTcount: A:0.38, C:0.31, G:0.04, T:0.27
Consensus pattern (44 bp):
TTTCGTACCAAAACCAATACCATTCCATAACTAAACCAAAACCA
Found at i:12156256 original size:36 final size:35
Alignment explanation
Indices: 12156211--12156328 Score: 150
Period size: 34 Copynumber: 3.4 Consensus size: 35
12156201 GTTACACTGT
*
12156211 TCCCGCACATGGAGGAAGGCTTACAGGGGGTCTTGC
1 TCCCACACATGG-GGAAGGCTTACAGGGGGTCTTGC
** * *
12156247 TCCCACACATGGGGGTGGCTTACA-GGAGTCCTGC
1 TCCCACACATGGGGAAGGCTTACAGGGGGTCTTGC
* *
12156281 TCCCACACATGGGGAAGGCTTAC-GAGGGTTTTGC
1 TCCCACACATGGGGAAGGCTTACAGGGGGTCTTGC
12156315 TCCCACACATGGGG
1 TCCCACACATGGGG
12156329 GACACTTATA
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
34 49 0.70
35 10 0.14
36 11 0.16
ACGTcount: A:0.19, C:0.27, G:0.33, T:0.20
Consensus pattern (35 bp):
TCCCACACATGGGGAAGGCTTACAGGGGGTCTTGC
Found at i:12159718 original size:20 final size:20
Alignment explanation
Indices: 12159680--12159718 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12159670 ACCTACATGA
* *
12159680 GACACACAGCTGTGTCACAT
1 GACACACAGCTGAGACACAT
*
12159700 GACACACGGCTGAGACACA
1 GACACACAGCTGAGACACA
12159719 CATCTGTGTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.31, G:0.23, T:0.13
Consensus pattern (20 bp):
GACACACAGCTGAGACACAT
Found at i:12165740 original size:16 final size:16
Alignment explanation
Indices: 12165708--12165758 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
12165698 TCTATATATA
*
12165708 TTATAATTTACAT-ATT
1 TTATAA-TTAAATAATT
12165724 TTATAATTAAATAATTT
1 TTATAATTAAATAA-TT
12165741 TTATTAA-TAAATAATT
1 TTA-TAATTAAATAATT
12165757 TT
1 TT
12165759 CAAAATACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 5 0.16
16 11 0.35
17 12 0.39
18 3 0.10
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATAATTAAATAATT
Found at i:12165744 original size:17 final size:17
Alignment explanation
Indices: 12165722--12165758 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
12165712 AATTTACATA
12165722 TTTTA-TAATTAAATAAT
1 TTTTATTAA-TAAATAAT
12165739 TTTTATTAATAAATAAT
1 TTTTATTAATAAATAAT
12165756 TTT
1 TTT
12165759 CAAAATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTATTAATAAATAAT
Found at i:12172665 original size:8 final size:8
Alignment explanation
Indices: 12172652--12173140 Score: 602
Period size: 8 Copynumber: 61.1 Consensus size: 8
12172642 AAGAAGTTTT
12172652 TGTATGTA
1 TGTATGTA
12172660 TGTATGTA
1 TGTATGTA
12172668 TGTATGTA
1 TGTATGTA
*
12172676 TGTATGCA
1 TGTATGTA
12172684 TGTATGTA
1 TGTATGTA
12172692 TGTATGTA
1 TGTATGTA
12172700 TGTATGTA
1 TGTATGTA
12172708 TGTATGTA
1 TGTATGTA
12172716 TGTATGTA
1 TGTATGTA
12172724 TGTATGTA
1 TGTATGTA
12172732 TGTATGTA
1 TGTATGTA
12172740 TGTATGTA
1 TGTATGTA
12172748 TGTATGTA
1 TGTATGTA
* *
12172756 TATATGCA
1 TGTATGTA
* *
12172764 TGCACGTA
1 TGTATGTA
* *
12172772 TGCACGTA
1 TGTATGTA
12172780 TAG-ATGTA
1 T-GTATGTA
*
12172788 TGTTTGTA
1 TGTATGTA
12172796 TGTATGTA
1 TGTATGTA
12172804 TGTATGTA
1 TGTATGTA
* *
12172812 TGCATGCA
1 TGTATGTA
*
12172820 TGCATGTA
1 TGTATGTA
*
12172828 TGGATGTA
1 TGTATGTA
*
12172836 TGTTTGTA
1 TGTATGTA
12172844 TGTATGTA
1 TGTATGTA
12172852 TGTATGTA
1 TGTATGTA
12172860 TGTATGTA
1 TGTATGTA
*
12172868 TGCATGTA
1 TGTATGTA
12172876 TGTATGTA
1 TGTATGTA
*
12172884 TGCATGTA
1 TGTATGTA
12172892 TGTATGTA
1 TGTATGTA
*
12172900 TGCATGTA
1 TGTATGTA
*
12172908 TGCATGTA
1 TGTATGTA
*
12172916 TGCATGTA
1 TGTATGTA
*
12172924 TGCATGTA
1 TGTATGTA
*
12172932 TGCATGTA
1 TGTATGTA
*
12172940 TGTATGCA
1 TGTATGTA
*
12172948 TGTATGCA
1 TGTATGTA
12172956 TGTATGTA
1 TGTATGTA
*
12172964 TGCATGTA
1 TGTATGTA
*
12172972 TGCATGTA
1 TGTATGTA
*
12172980 TGCATGTA
1 TGTATGTA
*
12172988 TGCATGTA
1 TGTATGTA
*
12172996 TGCATGTA
1 TGTATGTA
12173004 TGTATGTA
1 TGTATGTA
*
12173012 TGTATGCA
1 TGTATGTA
12173020 TGTATGTA
1 TGTATGTA
*
12173028 TGTATGCA
1 TGTATGTA
*
12173036 TGTATGCA
1 TGTATGTA
*
12173044 TGTATGCA
1 TGTATGTA
*
12173052 TGTATGCA
1 TGTATGTA
*
12173060 TGTATGCA
1 TGTATGTA
12173068 TGTATGTA
1 TGTATGTA
*
12173076 TGCATGTA
1 TGTATGTA
*
12173084 TGCATGTA
1 TGTATGTA
*
12173092 TGTATGCA
1 TGTATGTA
*
12173100 TGTATGCA
1 TGTATGTA
*
12173108 TGTATGCA
1 TGTATGTA
*
12173116 TGTATGCA
1 TGTATGTA
*
12173124 TGTATGCA
1 TGTATGTA
12173132 TGTATGTA
1 TGTATGTA
12173140 T
1 T
12173141 NNNNNNNNNN
Statistics
Matches: 443, Mismatches: 36, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
7 1 0.00
8 441 1.00
9 1 0.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (8 bp):
TGTATGTA
Found at i:12173255 original size:4 final size:4
Alignment explanation
Indices: 12173241--12173940 Score: 1109
Period size: 4 Copynumber: 175.5 Consensus size: 4
12173231 NNNNNNNNNN
* * * *
12173241 GTAT ATAT GTAT GTAT GCAT GTAT GTAT GCAT GTAT GGAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
12173289 GGAT GTAT GTTT GTAT GTAT GTAT GTAT GTAT GTAT GTTT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * *
12173337 GTTT GTAT GTAT GTAT GTAT GTAT TTAT GTAT GTAT ATAT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
**
12173385 ACAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
12173433 GCAT GTAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12173481 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12173529 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * * *
12173577 GTAT GTAT GTAT GTAT GTAT GTAT GTAT ATAT GCAT GCAC GTAT GCAC
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
12173625 GTAT AG-AT GTAT GTTT GTAT GTAT GTAT GTAT GTAT GCAT GCAT GTAT
1 GTAT -GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
12173673 GTTT GTAT GTAT GTTT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* *
12173721 GTAT GTAT GTAT GTAT GTAT GTAT GTAT G--T GTGT GTGT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
12173767 GTAT GTAT GTAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12173815 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12173863 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
12173911 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
12173941 TGAGTGAAAT
Statistics
Matches: 643, Mismatches: 49, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
2 2 0.00
3 1 0.00
4 639 0.99
5 1 0.00
ACGTcount: A:0.24, C:0.02, G:0.25, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:12176994 original size:25 final size:26
Alignment explanation
Indices: 12176966--12177021 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 26
12176956 GTTTCGAAAA
12176966 CCTTTATAGGGATTTATTT-GAGAAG
1 CCTTTATAGGGATTTATTTGGAGAAG
* *
12176991 CCTTTATAGTGATTTATTTGGGGAAG
1 CCTTTATAGGGATTTATTTGGAGAAG
12177017 CCTTT
1 CCTTT
12177022 GTGGCAAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (26 bp):
CCTTTATAGGGATTTATTTGGAGAAG
Found at i:12177101 original size:25 final size:25
Alignment explanation
Indices: 12177014--12177104 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 25
12177004 TTATTTGGGG
12177014 AAGCCTTTGTGGCAAGTCACCTGTA
1 AAGCCTTTGTGGCAAGTCACCTGTA
* * * * ** **
12177039 AATCCTTTGTGGTAATTTATTTGGGG
1 AAGCCTTTGTGGCAAGTCACCT-GTA
12177065 AAGCCTTTGTGGCAAGTCACCTGTA
1 AAGCCTTTGTGGCAAGTCACCTGTA
12177090 CAA-CCTTTGTGGCAA
1 -AAGCCTTTGTGGCAA
12177105 TTTATTCGGG
Statistics
Matches: 48, Mismatches: 16, Indels: 4
0.71 0.24 0.06
Matches are distributed among these distances:
25 29 0.60
26 19 0.40
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (25 bp):
AAGCCTTTGTGGCAAGTCACCTGTA
Found at i:12177121 original size:25 final size:25
Alignment explanation
Indices: 12177042--12177128 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 25
12177032 ACCTGTAAAT
* *
12177042 CCTTTGTGGTAATTTATTTGGGGAAG
1 CCTTTGTGGCAATTTA-TTCGGGAAG
* * * * * *
12177068 CCTTTGTGGCAAGTCA-CCTGTACAA
1 CCTTTGTGGCAATTTATTCGGGA-AG
12177093 CCTTTGTGGCAATTTATTCGGGAAG
1 CCTTTGTGGCAATTTATTCGGGAAG
12177118 CCTTTGTGGCA
1 CCTTTGTGGCA
12177129 GGTTATCTGT
Statistics
Matches: 45, Mismatches: 14, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
24 2 0.04
25 27 0.60
26 16 0.36
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (25 bp):
CCTTTGTGGCAATTTATTCGGGAAG
Found at i:12177139 original size:50 final size:51
Alignment explanation
Indices: 12177002--12177128 Score: 213
Period size: 51 Copynumber: 2.5 Consensus size: 51
12176992 CTTTATAGTG
*
12177002 ATTTATTTGGGGAAGCCTTTGTGGCAAGTCACCTGTAAATCCTTTGTGGTA
1 ATTTATTTGGGGAAGCCTTTGTGGCAAGTCACCTGTAAATCCTTTGTGGCA
12177053 ATTTATTTGGGGAAGCCTTTGTGGCAAGTCACCTGTACAA-CCTTTGTGGCA
1 ATTTATTTGGGGAAGCCTTTGTGGCAAGTCACCTGTA-AATCCTTTGTGGCA
*
12177104 ATTTA-TTCGGGAAGCCTTTGTGGCA
1 ATTTATTTGGGGAAGCCTTTGTGGCA
12177129 GGTTATCTGT
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
50 19 0.26
51 52 0.71
52 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.35
Consensus pattern (51 bp):
ATTTATTTGGGGAAGCCTTTGTGGCAAGTCACCTGTAAATCCTTTGTGGCA
Found at i:12177149 original size:50 final size:50
Alignment explanation
Indices: 12177002--12177151 Score: 187
Period size: 51 Copynumber: 3.0 Consensus size: 50
12176992 CTTTATAGTG
* *
12177002 ATTTATTTGGGGAAGCCTTTGTGGCAAGTCACCTGTAAATCCTTTGTGGTA
1 ATTTATTTGGGGAAGCCTTTGTGGCAAGTCACCTGTAACT-CTTTGTGGCA
12177053 ATTTATTTGGGGAAGCCTTTGTGGCAAGTCACCTGTACAAC-CTTTGTGGCA
1 ATTTATTTGGGGAAGCCTTTGTGGCAAGTCACCTGT--AACTCTTTGTGGCA
* * * * *
12177104 ATTTA-TTCGGGAAGCCTTTGTGGCAGGTTATCTGTAACGTATTTGTGG
1 ATTTATTTGGGGAAGCCTTTGTGGCAAGTCACCTGTAAC-TCTTTGTGG
12177152 TAGGCTACCT
Statistics
Matches: 88, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
48 3 0.03
50 33 0.38
51 50 0.57
53 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.37
Consensus pattern (50 bp):
ATTTATTTGGGGAAGCCTTTGTGGCAAGTCACCTGTAACTCTTTGTGGCA
Done.