Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 7 of 438
Found at i:1999850 original size:43 final size:43
Alignment explanation
Indices: 1999825--1999982 Score: 289
Period size: 43 Copynumber: 3.7 Consensus size: 43
1999815 GTAAAAAAAG
*
1999825 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCCCAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
*
1999868 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTCCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
1999911 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
*
1999954 CGCCGCTAAAAGCCTTGACTTTTAGCGGC
1 CGCCGCTAAAAGCCTTGACCTTTAGCGGC
1999983 ATTTTTTCCC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 111 1.00
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.23
Consensus pattern (43 bp):
CGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCACAAA
Found at i:2000342 original size:60 final size:56
Alignment explanation
Indices: 2000278--2000405 Score: 123
Period size: 60 Copynumber: 2.1 Consensus size: 56
2000268 TGATTTATCG
* * *
2000278 ATTATTTTAAATACTTTCTTTCATATATATATGTATTGTTTAATTTTTAGTTT-TTTATAA
1 ATTATTTTAAATA--TT-TTTCATATATAT-T-TATAGTCTAATTCTTAGTTTGTTTATAA
*
2000338 ATTATATACATTTAAATATTTTTCATATATATTTATAGTCTAATTCTTATTTTGTTTATAA
1 A-T-TAT---TTTAAATATTTTTCATATATATTTATAGTCTAATTCTTAGTTTGTTTATAA
2000399 ATTATTT
1 ATTATTT
2000406 GTTATTTTAG
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
56 2 0.03
59 3 0.05
60 18 0.31
61 10 0.17
62 15 0.26
63 2 0.03
65 8 0.14
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (56 bp):
ATTATTTTAAATATTTTTCATATATATTTATAGTCTAATTCTTAGTTTGTTTATAA
Found at i:2007389 original size:27 final size:27
Alignment explanation
Indices: 2007334--2007394 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
2007324 TGCGCCTGTG
* * *
2007334 TCAGAGGAGCGACTAGTTGAACCTTTC
1 TCAGAGGAGCGACTAATCGAACCTATC
**
2007361 TCAGAGGAGCGACTAATCGTGCCTATC
1 TCAGAGGAGCGACTAATCGAACCTATC
2007388 TCAGAGG
1 TCAGAGG
2007395 CGCAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (27 bp):
TCAGAGGAGCGACTAATCGAACCTATC
Found at i:2008362 original size:60 final size:60
Alignment explanation
Indices: 2008275--2008393 Score: 186
Period size: 60 Copynumber: 2.0 Consensus size: 60
2008265 ATATTAAACT
* * *
2008275 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
*
2008335 AAACACAGAAAATTT-TAACATAGTCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACA-AAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
2008394 TAAAAAACAA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 48 0.89
61 6 0.11
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.34
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:2012837 original size:37 final size:38
Alignment explanation
Indices: 2012737--2012838 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 38
2012727 ATATATTTGG
2012737 TAATAATAATA--TAAAATAATAA-TATGTACATAAAAA
1 TAATAATAATATCTAAAATAA-AAGTATGTACATAAAAA
* *
2012773 TACATATATATATATGCATATAATAAAAGTATGTA-ATAATAA
1 TA-ATA-ATA-ATAT-C-TAAAATAAAAGTATGTACATAAAAA
*
2012815 TAATAATAATATCTACAATAAAAG
1 TAATAATAATATCTAAAATAAAAG
2012839 AAAATATTAG
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
36 2 0.04
37 13 0.24
38 4 0.07
39 7 0.13
40 3 0.05
41 3 0.05
42 10 0.18
43 13 0.24
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (38 bp):
TAATAATAATATCTAAAATAAAAGTATGTACATAAAAA
Found at i:2013557 original size:12 final size:12
Alignment explanation
Indices: 2013540--2013565 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2013530 GTAGACAATA
2013540 GGAGGAAAAATG
1 GGAGGAAAAATG
2013552 GGAGGAAAAATG
1 GGAGGAAAAATG
2013564 GG
1 GG
2013566 GCAAGTGGGA
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:0.46, C:0.00, G:0.46, T:0.08
Consensus pattern (12 bp):
GGAGGAAAAATG
Found at i:2013617 original size:14 final size:14
Alignment explanation
Indices: 2013595--2013628 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2013585 GGTGGCTAGG
2013595 TTTTTTTA-GTTTT
1 TTTTTTTAGGTTTT
2013608 TTTTTGTTAGGTTTT
1 TTTTT-TTAGGTTTT
2013623 TTTTTT
1 TTTTTT
2013629 CTTCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 4 0.21
15 10 0.53
ACGTcount: A:0.06, C:0.00, G:0.12, T:0.82
Consensus pattern (14 bp):
TTTTTTTAGGTTTT
Found at i:2013623 original size:15 final size:13
Alignment explanation
Indices: 2013595--2013641 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2013585 GGTGGCTAGG
2013595 TTTTTTTAGTTTT
1 TTTTTTTAGTTTT
*
2013608 TTTTTGTTAGGTTT
1 TTTTT-TTAGTTTT
*
2013622 TTTTTTT-CTTCTT
1 TTTTTTTAGTT-TT
2013635 TTTTTTT
1 TTTTTTT
2013642 TGGGTTAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 1 0.03
13 16 0.55
14 12 0.41
ACGTcount: A:0.04, C:0.04, G:0.09, T:0.83
Consensus pattern (13 bp):
TTTTTTTAGTTTT
Found at i:2013661 original size:34 final size:33
Alignment explanation
Indices: 2013604--2013692 Score: 139
Period size: 34 Copynumber: 2.8 Consensus size: 33
2013594 GTTTTTTTAG
2013604 TTTTTTTTT--GTTAGG-TTTTTTTTTTCTTCT
1 TTTTTTTTTGGGTTAGGTTTTTTTTTTTCTTCT
2013634 TTTTTTTTTGGGTTAGGTTTTTCTTTTTTCTTCT
1 TTTTTTTTTGGGTTAGGTTTTT-TTTTTTCTTCT
*
2013668 TTTTTTTTGGGGTTAGGTTTTTTTT
1 TTTTTTTTTGGGTTAGGTTTTTTTT
2013693 GGGGGGGCTT
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
30 9 0.17
32 6 0.11
33 7 0.13
34 32 0.59
ACGTcount: A:0.03, C:0.06, G:0.16, T:0.75
Consensus pattern (33 bp):
TTTTTTTTTGGGTTAGGTTTTTTTTTTTCTTCT
Found at i:2014552 original size:30 final size:30
Alignment explanation
Indices: 2014516--2014577 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2014506 TTTTGAAAAA
2014516 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
2014546 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
2014576 CA
1 CA
2014578 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:2014739 original size:87 final size:84
Alignment explanation
Indices: 2014377--2014765 Score: 242
Period size: 87 Copynumber: 4.5 Consensus size: 84
2014367 AGCTCAGCGC
** **
2014377 GTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAACTTAACTTGAAAGG
1 GTGA-CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAACAGAA--T-AAAAA
* *
2014441 CAGATTTTGAAAATACCTCGATAT
61 CAGATATTGAAAATACCTCGACAT
*** *
2014465 GTGATTGGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGA
1 GTGA-CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAG-AA-TAAAA-A
** * * * * *
2014530 CTCA-ACT-CAACT-CTCGCAGAAAT
61 CAGATATTGAAAATAC-CTC-GACAT
* * * *
2014553 -T-A-AAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAGA-A-AA-AAAGACA
1 GTGACCAAGGCTCAACTCACCTCTCGCAATATGAGTTG-A--TTTTTGAAAACAGAATAAAAACA
* * *
2014612 GAAATTGAAAATAGCTC-AGCAC
63 GATATTGAAAATACCTCGA-CAT
** *
2014634 GTGAGCCAAGTTTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATCTAAAAACA
1 GTGA-CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAA--TAAAAACA
*
2014699 GATTTTGAAAATACCTCGACAT
63 GATATTGAAAATACCTCGACAT
* * *
2014721 GTGACCCGAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTT
1 GTGA-CCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
2014766 TTGAAAAATA
Statistics
Matches: 229, Mismatches: 49, Indels: 47
0.70 0.15 0.14
Matches are distributed among these distances:
80 4 0.02
81 6 0.03
82 15 0.07
83 4 0.02
84 32 0.14
85 30 0.13
86 5 0.02
87 79 0.34
88 44 0.19
89 8 0.03
90 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (84 bp):
GTGACCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAATAAAAACAGAT
ATTGAAAATACCTCGACAT
Found at i:2014903 original size:77 final size:78
Alignment explanation
Indices: 2014731--2015486 Score: 266
Period size: 75 Copynumber: 9.4 Consensus size: 78
2014721 GTGACCCGAG
* * *
2014731 GCTCAACTCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCTCA
1 GCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTG-AAAAATACCTCA
* * * *
2014796 GTGTGTGATCTGAA
65 GCGCGTGAGCTCAA
* * *
2014810 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTG-AAAATAGCTCAG
1 GCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
2014874 CGCGTGAGC-CAA
66 CGCGTGAGCTCAA
* * * **
2014886 GTTTCAACTCACTTCTCGCAATATGAGTTGA--TTTTTG-AAAACAG-AATCTGAAAAACAGATT
1 G-CTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAAT-TGAAAAATA-CCT
** **** *
2014947 TTGAAAAT-ACCTCGACA
63 CAGCGCGTGAGCTC-A-A
* * * * * * *
2014964 TGTGACCCGAGGCTCA-A-CTCAC-ATCTCGCAATGTGAGTTGATTTTTTGAAAAATATAAATTG
1 ---G-CTC-A-ACTCACATCTCGCAATAT-G-AGT-TGA--T--TTTTTTGAAAAACAGAAATTG
* * * *
2015026 AAAAAATACCTCAGTGTGTGATCT-GA
53 -AAAAATACCTCAGCGCGTGAGCTCAA
* * *
2015052 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGACAGAAATTG-AAAATAGCTCA
1 GCTCAACTCACATCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAAATTGAAAAATACCTCA
2015116 GCGCGTGAGC-CAA
65 GCGCGTGAGCTCAA
* **
2015129 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAA
1 -GCTCAACTCACATCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAAATTG---AA---AAA
** * * * * **
2015194 TTGAAAAT-ACCTCG-GCGTTTGA
58 -T--ACCTCAGCGCGTGAGCTCAA
* * * * * * * *
2015216 CCTGAGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTTG-ACAACAGAAATTG-AAATTA
1 GCTCA-ACTC-A--C-A-TCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATA
** * *
2015279 CCTCA--GCGTGTCCTGAG
60 CCTCAGCGCGTGAGCTCAA
*
2015296 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTG-AAAATACCTCA-
1 GCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
* * * *
2015359 -GCATG-TCTTGAG
66 CGCGTGAGC-TCAA
** * *
2015371 GCTCAACTCATTTCTCACAATATGAGTTGAATTTTTTTTTTTGAAAGACAGAAATTG-AAAATAC
1 GCTCAACTCACATCTCGCAATATGAGTTG-A----TTTTTTTGAAAAACAGAAATTGAAAAATAC
** * *
2015435 CTCAGCATGTGAAC-CGAG
61 CTCAGCGCGTGAGCTC-AA
* *
2015453 GCTCAACTCACCTCTCGCAATATGAGCTGATTTT
1 GCTCAACTCACATCTCGCAATATGAGTTGATTTT
2015487 GAAAAAGTAG
Statistics
Matches: 510, Mismatches: 107, Indels: 122
0.69 0.14 0.17
Matches are distributed among these distances:
73 3 0.01
74 33 0.06
75 70 0.14
76 9 0.02
77 67 0.13
78 54 0.11
79 70 0.14
80 42 0.08
81 11 0.02
82 41 0.08
83 13 0.03
84 7 0.01
85 7 0.01
86 7 0.01
87 8 0.02
88 4 0.01
89 6 0.01
90 21 0.04
91 21 0.04
92 16 0.03
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (78 bp):
GCTCAACTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAG
CGCGTGAGCTCAA
Found at i:2015011 original size:243 final size:245
Alignment explanation
Indices: 2014356--2015360 Score: 1252
Period size: 243 Copynumber: 4.1 Consensus size: 245
2014346 TTAAAAACAA
2014356 AAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
** ** * *** *
2014421 TTG-AAACTTAA-CTTGAAAGGCAGATTTTGAAAATACCTCGATATGTGATTGGAGGTTCAACTC
66 TTGAAAACAGAATC-TGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTC
* * * * *
2014484 ACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATT-AAAAGACTCAACTCAACTCTCG
130 ACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAA-AAT-ACCTC-AGTGT-G
* *
2014546 CAGAAAT-TAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAGAAAAAAAGA
191 -TG--ATCT--GAAGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTT---G----AAAGA
2014610 CAG
243 CAG
* ** *
2014613 AAATTGAAAATAGCTCAGCACGTGAGCCAAGTTTCAACTCACTTCTCGCAATATGAGTTGA-TTT
1 AAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
2014677 TTGAAAACAGAATCT-AAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCA
66 TTGAAAACAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCA
* * *
2014741 CATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCTCAGTGTGTGATC
131 CATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAAATACCTCAGTGTGTGATC
2014806 TGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAG
196 TGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAG
** *
2014856 AAATTGAAAATAGCTCAGCGCGTGAGCCAAGTTTCAACTCACTTCTCGCAATATGAGTTGA-TTT
1 AAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
2014920 TTGAAAACAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCA
66 TTGAAAACAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCA
* * *
2014985 CATCTCGCAATGTGAGTTGA-TTTTTTGAAAAATATAAATTGAAAAAATACCTCAGTGTGTGATC
131 CATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAAATACCTCAGTGTGTGATC
2015049 TG-AGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAGACAG
196 TGAAGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAGACAG
2015099 AAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT
* * ** * * * *
2015164 TTTTGAAAGGCAGAAAT-TGAAAAACGGAAATTGAAAATACCTCGGCGTTTGACCTGAGGCTCAA
64 TTTTGAAA-ACAG-AATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAA
* * * * * * *
2015228 CTCGCCTCTCACAATACGAGTTGATTTTTTTG-ACAACAGAAATTG--AAATTACCTCAGCGTGT
127 CTCACATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAAATACCTCAGTGTGT
* * *
2015290 --CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAG
192 GATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAG
*
2015342 AAATTGAAAATACCTCAGC
1 AAATTGAAAATAGCTCAGC
2015361 ATGTCTTGAG
Statistics
Matches: 684, Mismatches: 49, Indels: 44
0.88 0.06 0.06
Matches are distributed among these distances:
242 31 0.05
243 242 0.35
244 99 0.14
245 15 0.02
246 9 0.01
247 73 0.11
248 10 0.01
250 8 0.01
251 31 0.05
252 2 0.00
253 1 0.00
254 1 0.00
255 1 0.00
256 69 0.10
257 68 0.10
258 20 0.03
259 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (245 bp):
AAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TTGAAAACAGAATCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCA
CATCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAAATACCTCAGTGTGTGATC
TGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAG
Found at i:2015087 original size:78 final size:77
Alignment explanation
Indices: 2014934--2015486 Score: 355
Period size: 78 Copynumber: 7.0 Consensus size: 77
2014924 AAACAGAATC
** * * * *
2014934 TGAAAAACAGATTTTGAAAATACCTC-GACATGTGACCCGAGGCTCAACTCACATCTCGCAATGT
1 TGAAAAACAGAAATTGAAAATACCTCAG-CGTGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
2014998 GAGTTGA-TTTTT
65 GAGTTGATTTTTT
* * * *
2015010 TGAAAAATATAAATTGAAAAAATACCTCAGTGTGTGATCTGA-GCTCAACTCACCTCTCGCAATA
1 TGAAAAACAGAAATTG--AAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
2015074 TGAGTTGATTTTTTT
64 TGAGTTGA-TTTTTT
* * * *
2015089 TGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATAT
1 TGAAAAACAGAAATTGAAAATACCTCAGCGTGTGA-CCTGAGGCTCAACTCACCTCTCGCAATAT
2015153 GAGTTGATTTTTTT
65 GAGTTGA-TTTTTT
** ** *** * * *
2015167 TGAAAGGCAGAAATTGAAAA-A-CGGAAATTGAAAAT-ACCTCGGCGTTTGACCTGAGGCTCAAC
1 TGAAAAACAGAAATTGAAAATACCTCAGCGTG----TGACCT--GAG---G--CTCA-ACTC-AC
* * ** *
2015229 TCGCCTCTCACAAT-A--CGAGTTGATTTT
53 -C-TCTCGCAATATGAGTTGA-TT--TTTT
* *
2015256 TTTG-ACAACAGAAATTGAAATTACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATA
1 --TGAAAAACAGAAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
2015318 TGAGTTGATTTTTT
64 TGAGTTGATTTTTT
* * ** *
2015332 TGAAAAACAGAAATTGAAAATACCTCAGCATGT--CTTGAGGCTCAACTCATTTCTCACAATATG
1 TGAAAAACAGAAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATG
2015395 AGTTGAATTTTTTTTTT
66 AGTTG-A----TTTTTT
* *
2015412 TGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATAT
1 TGAAAAACAGAAATTGAAAATACCTCAGCGTGTG-ACCTGAGGCTCAACTCACCTCTCGCAATAT
*
2015476 GAGCTGATTTT
65 GAGTTGATTTT
2015487 GAAAAAGTAG
Statistics
Matches: 371, Mismatches: 65, Indels: 81
0.72 0.13 0.16
Matches are distributed among these distances:
74 2 0.01
75 58 0.16
76 27 0.07
77 52 0.14
78 81 0.22
79 25 0.07
80 42 0.11
81 2 0.01
82 29 0.08
83 1 0.00
84 1 0.00
85 2 0.01
86 3 0.01
87 10 0.03
88 3 0.01
89 6 0.02
90 20 0.05
91 3 0.01
92 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (77 bp):
TGAAAAACAGAAATTGAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTT
Found at i:2015249 original size:92 final size:90
Alignment explanation
Indices: 2015088--2015275 Score: 236
Period size: 92 Copynumber: 2.1 Consensus size: 90
2015078 TTGATTTTTT
* * * *
2015088 TTGAAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCACAATAC
2015153 GAGTTGATTTTTTTTGA-AAGGCAGAAA
66 GAGTTGA-TTTTTTTGACAA--CAGAAA
* * ** * *
2015180 TTGAAAAACGGAAATTGAAAATACCTCGGCGTTTGA-CCTGAGGCTCAACTCGCCTCTCACAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCC-AAGGCTCAACTCACCTCTCACAATA
2015244 CGAGTTGATTTTTTTGACAACAGAAA
65 CGAGTTGATTTTTTTGACAACAGAAA
2015270 TTGAAA
1 TTGAAA
2015276 TTACCTCAGC
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
90 12 0.14
91 11 0.13
92 61 0.73
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (90 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCACAATAC
GAGTTGATTTTTTTGACAACAGAAA
Found at i:2015316 original size:166 final size:167
Alignment explanation
Indices: 2015028--2015486 Score: 474
Period size: 157 Copynumber: 2.8 Consensus size: 167
2015018 ATAAATTGAA
* * * *
2015028 AAAATACCTCAGTGTGTGATCTGAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAA
1 AAAATACCTCAGCGTGTGACCTGAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTTGAA
*
2015093 AGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTT
66 AGACAGAAATTGAAAATACCTCA-CGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTT
**
2015158 GATTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
130 GA-TTTTTTTGAAAAACAGAAATTGAAAAACGGAAATTG
* * *
2015197 AAAATACCTCGGCGTTTGACCTGAGGCTCAACTCGCCTCTCACAATACGAGTTGA-TTTTTTTGA
1 AAAATACCTCAGCGTGTGACCTGA-GCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTTGA
* * * *
2015261 CA-ACAGAAATTGAAATTACCTCA-GCGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
65 AAGACAGAAATTGAAAATACCTCACGCGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGT
2015323 TGATTTTTTTGAAAAAC------------A--GAAATTG
129 TGATTTTTTTGAAAAACAGAAATTGAAAAACGGAAATTG
* * ** *
2015348 AAAATACCTCAGCATGT--CTTGAGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTTTTTT
1 AAAATACCTCAGCGTGTGACCTGA-GCTCAACTCACCTCTCACAATACGAGTTG-A---TTTTTT
* *
2015411 TTGAAAGACAGAAATTGAAAATACCTCA-GCATGTGAACCGAGGCTCAACTCACCTCTCGCAATA
61 TTGAAAGACAGAAATTGAAAATACCTCACGC--GTGAGCCAAGGCTCAACTCACCTCTCGCAATA
*
2015475 TGAGCTGATTTT
124 TGAGTTGATTTT
2015487 GAAAAAGTAG
Statistics
Matches: 253, Mismatches: 26, Indels: 34
0.81 0.08 0.11
Matches are distributed among these distances:
149 30 0.12
150 1 0.00
151 21 0.08
153 1 0.00
154 10 0.04
155 22 0.09
157 39 0.15
158 2 0.01
165 14 0.06
166 37 0.15
168 19 0.08
169 30 0.12
170 27 0.11
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (167 bp):
AAAATACCTCAGCGTGTGACCTGAGCTCAACTCACCTCTCACAATACGAGTTGATTTTTTTTGAA
AGACAGAAATTGAAAATACCTCACGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTTTGAAAAACAGAAATTGAAAAACGGAAATTG
Found at i:2015344 original size:486 final size:491
Alignment explanation
Indices: 2014348--2015525 Score: 1305
Period size: 500 Copynumber: 2.4 Consensus size: 491
2014338 AACAAGCATT
*
2014348 AAAAACAAAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
** ** * *** *
2014413 TTGATTTTTTGAAACTTAACTTGAAAGGCAGATTTTGAAAATACCTCGATATGTGATTGGAGGTT
66 TTGATTTTTTGAAACAGAACTTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCT
* *
2014478 CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGACTCAACTCAACTC
131 CAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGAATCAACTCAACTC
2014543 TCGCAGAAATTAAAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAGAAAAAAA
196 TCGCAG-AATT--AAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTT-AAG---AAAA
** *
2014608 GACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGTTTCAACTCACTTCTCGCAATATGAGTTG
254 GACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTG
**
2014673 ATTTTTGAAAACAGAATCTAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCTCAAC
319 ATTTTTGAAAACAGAATCTAAAAACAGAAATTGAAAATACCTCGACATGTGACCCGAGGCTCAAC
* ** * * *
2014738 TCACATCTCGCAATGTGAGTTGATTTTTTTGAAAAATATAAATTGAAAAAATACCTCAGTGTGTG
384 TCACATCTCACAATACGAGTTGATTTTTTTGAAAAACAGAAATTG-AAAAATACCTCAGCGTGT-
*
2014803 ATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
447 ACCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* ** *
2014848 AAAGACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGTTTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
2014913 TTGA-TTTTTGAAAACAGAA-TCTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGG
66 TTGATTTTTTG-AAACAGAACT-TGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGG
* * * *
2014976 CTCAACTCACATCTCGCAATGTGAGTTGATTTTTTGAAAAATATAAATTGAAAA-AAT-ACCTC-
129 CTCAACTCACATCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATT-AAAAGAATCAACTCA
* * * * *
2015038 AGTGT-G-TG-ATCT-GAGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTT-TG-AAAGA
192 ACTCTCGCAGAAT-TAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTAAGAAAAGA
*
2015096 CAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
256 CAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
* * * * * *
2015161 TTTTTTTGAAAGGCAGAAAT-TGAAAAACGGAAATTGAAAATACCTCGGCGTTTGACCTGAGGCT
320 --TTTTTGAAA-ACAG-AATCT-AAAAACAGAAATTGAAAATACCTCGACATGTGACCCGAGGCT
* * * *
2015225 CAACTCGCCTCTCACAATACGAGTTGATTTTTTTG-ACAACAGAAATTG-AAATTACCTCAGCGT
380 CAACTCACATCTCACAATACGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGT
*
2015288 GT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
445 GTACCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
* * * ** ** *
2015334 AAAAACAGAAATTGAAAATACCTCA--GCATG-TCTTGAGGCTCAACTCATTTCTCACAATATGA
1 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGA
*** * ** *
2015396 GTTGAATTTTTT-------TTTTTGAAAGACAGAAATTGAAAATACCTC-AGCATGTGAACCGAG
65 GTTG-ATTTTTTGAAACAGAACTTGAAAAACAGATTTTGAAAATACCTCGA-CATGTGACCCGAG
* * * ** *
2015453 GCTCAACTCACCTCTCGCAATATGAGCTGA-TTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCA
128 GCTCAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAA-CAGAAATTAAAAGAATCAACTCA
*
2015517 CCTCTCGCA
192 ACTCTCGCA
2015526 ATATGAGTTG
Statistics
Matches: 579, Mismatches: 77, Indels: 63
0.81 0.11 0.09
Matches are distributed among these distances:
476 14 0.02
477 9 0.02
478 65 0.11
479 3 0.01
480 1 0.00
483 1 0.00
484 31 0.05
485 1 0.00
486 135 0.23
488 15 0.03
489 9 0.02
490 15 0.03
491 68 0.12
492 8 0.01
493 30 0.05
495 2 0.00
496 1 0.00
497 1 0.00
498 1 0.00
499 10 0.02
500 136 0.23
501 19 0.03
502 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (491 bp):
AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTGAAACAGAACTTGAAAAACAGATTTTGAAAATACCTCGACATGTGACCCGAGGCT
CAACTCACATCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGAATCAACTCAACTC
TCGCAGAATTAAAGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTAAGAAAAGACAGAA
ATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
AAAACAGAATCTAAAAACAGAAATTGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACATC
TCACAATACGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTACCTGAAGC
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
Found at i:2015439 original size:80 final size:75
Alignment explanation
Indices: 2015180--2015486 Score: 366
Period size: 75 Copynumber: 4.0 Consensus size: 75
2015170 AAGGCAGAAA
* * * * * *
2015180 TTGAAAAACGGAAATTGAAAATACCTCGGCGTTTGACCTGAGGCTCAACTCGCCTCTCACAATAC
1 TTGAAAAACAGAAATTGAAAATACCTCAGC--ATGTCCTGAGGCTCAACTCACCTCTCACAATAT
2015245 GAGTTGATTTTT
64 GAGTTGATTTTT
* * * *
2015257 TTG-ACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
2015321 GTTGATTTTT
66 GTTGATTTTT
* **
2015331 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
2015396 GTTGAATTTTTTTTT
66 GTTG-A----TTTTT
* *
2015411 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGT---CCTGAGGCTCAACTCACCTCTCACAATA
*
2015475 TGAGCTGATTTT
63 TGAGTTGATTTT
2015487 GAAAAAGTAG
Statistics
Matches: 199, Mismatches: 22, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
74 43 0.22
75 58 0.29
76 23 0.12
77 7 0.04
80 38 0.19
81 1 0.01
82 28 0.14
83 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (75 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
GTTGATTTTT
Found at i:2015555 original size:54 final size:54
Alignment explanation
Indices: 2015455--2015560 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 54
2015445 GAACCGAGGC
*
2015455 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTA-AAATTGAAAAGGT
* *
2015509 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAACAACGT-AAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAA-AAAGTAAAATTGAAAA
2015561 CAGAAATTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
54 33 0.72
55 9 0.20
56 4 0.09
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (54 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAAAATTGAAAAGGT
Found at i:2015598 original size:222 final size:211
Alignment explanation
Indices: 2015335--2015744 Score: 552
Period size: 222 Copynumber: 1.9 Consensus size: 211
2015325 ATTTTTTTGA
* * **
2015335 AAAACAGAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
* * * *
2015400 AATTTTTTTTTTTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACC
66 AA--------ATTAAAACACAAAAATTGAAAATACCTCAGC--GTGAACCGAGGCTCAACTCACC
* * *
2015465 TCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATTAAAAGG-TTCAACCCACCTCTCGCAATA
121 TCTAGCAATATGAGCTGATTTTGAAAAA-CAAAAATTAAAAGGCTT-AACCCACCTCTCGCAATA
2015529 TGAGTTGATTCTTGAACAACGTAAATTG
184 TGAGTTGATTCTTGAACAACGTAAATTG
* *
2015557 AAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
**
2015622 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
66 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGAACCGAGGCTCAACTCACCTCTAGCAATA
* *
2015687 TGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGT
131 TGAGCTGATTTTGAAAAACAAAAATTAAAAGGCTTAACCCACCTCTCGCAATATGAGT
2015745 CAATTTAAAA
Statistics
Matches: 170, Mismatches: 17, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
211 34 0.20
212 48 0.28
214 27 0.16
222 61 0.36
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (211 bp):
AAAACAGAAATTGAAAATACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGTTG
AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGAACCGAGGCTCAACTCACCTCTAGCAATA
TGAGCTGATTTTGAAAAACAAAAATTAAAAGGCTTAACCCACCTCTCGCAATATGAGTTGATTCT
TGAACAACGTAAATTG
Found at i:2015685 original size:72 final size:71
Alignment explanation
Indices: 2015551--2015716 Score: 244
Period size: 72 Copynumber: 2.3 Consensus size: 71
2015541 TGAACAACGT
* * * *
2015551 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
2015616 GAGTTG
66 GAGTTG
*
2015622 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
2015687 TGAGTTG
65 TGAGTTG
**
2015694 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
2015717 GGCTTAACTC
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
71 12 0.14
72 70 0.81
73 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:2015872 original size:71 final size:70
Alignment explanation
Indices: 2015751--2015973 Score: 306
Period size: 70 Copynumber: 3.1 Consensus size: 70
2015741 GAGTCAATTT
*
2015751 AAAACTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTG
1 AAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCAC-TCTCGCAATATGAGTTGATTTTG
2015816 AAAACA
65 AAAACA
* * ** *
2015822 ACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGA--TTA
1 AAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTG
2015885 AAACACA
65 AAA-ACA
* * *
2015892 AAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTG
1 AAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTG
2015957 AAAAACA
65 -AAAACA
2015964 AAAATTAAAA
1 AAAATTAAAA
2015974 GGCTTAACTC
Statistics
Matches: 131, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
69 5 0.04
70 55 0.42
71 53 0.40
72 15 0.11
73 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (70 bp):
AAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTCTCGCAATATGAGTTGATTTTGA
AAACA
Found at i:2015933 original size:257 final size:258
Alignment explanation
Indices: 2015554--2016140 Score: 1072
Period size: 257 Copynumber: 2.3 Consensus size: 258
2015544 ACAACGTAAA
* * * * *
2015554 TTGAAAACAGA-AATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAACA-ACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGA
2015618 GTTGAAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGC
65 GTTG--ATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGC
2015683 AATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAA
128 AATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAA
*
2015748 TTTAAAACT-AAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
193 TTTAAAACTAAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGAT
2015812 T
258 T
2015813 TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
2015878 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
66 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
2015943 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
131 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
2016008 AAAACTAAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
196 AAAACTAAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
2016071 TTG-AAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
2016135 TTGATT
66 TTGATT
2016141 TTCCTTGAAA
Statistics
Matches: 320, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
257 200 0.62
258 59 0.18
259 61 0.19
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (258 bp):
TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
AAAACTAAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
Found at i:2015942 original size:70 final size:69
Alignment explanation
Indices: 2015716--2015973 Score: 294
Period size: 70 Copynumber: 3.7 Consensus size: 69
2015706 AAAAATTAAA
* ** *
2015716 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAAC------TAAAAATACCTCAGCGTGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAAACAAAAATTAAAAATACCTCAGCGTGT
2015775 CCCG
66 CCCG
* * * *
2015779 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAACAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTAAAAACAAAAATTAAAAATACCTCAGCGT
**
2015844 GTCTTG
64 GTCCCG
* *
2015850 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAA-ACAAAAATTAAAAATACCTCAGCGTG
*
2015915 CCCCG
65 TCCCG
*
2015920 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT-AAAAACAAAAATTAAAA
2015974 GGCTTAACTC
Statistics
Matches: 163, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
63 28 0.17
65 7 0.04
69 5 0.03
70 55 0.34
71 50 0.31
72 14 0.09
73 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (69 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAAACAAAAATTAAAAATACCTCAGCGTGT
CCCG
Found at i:2026946 original size:11 final size:12
Alignment explanation
Indices: 2026926--2026951 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2026916 GGTAGACAAT
2026926 GGAGGAAAAATG
1 GGAGGAAAAATG
2026938 GGAGGAAAAATG
1 GGAGGAAAAATG
2026950 GG
1 GG
2026952 GCAAGTGGAA
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:0.46, C:0.00, G:0.46, T:0.08
Consensus pattern (12 bp):
GGAGGAAAAATG
Found at i:2027048 original size:35 final size:35
Alignment explanation
Indices: 2026989--2027080 Score: 145
Period size: 34 Copynumber: 2.7 Consensus size: 35
2026979 GTTTTTTTAG
*
2026989 TTTTTTTT-GTTAGGTTTTTCTTTTTTCTTCT-TT
1 TTTTTTTTGGTTAGGTTTTTCTTTTTTTTTCTCTT
*
2027022 TTTTTTTTGGTTAGGTTTTTCTTTTTTTTTTTCTT
1 TTTTTTTTGGTTAGGTTTTTCTTTTTTTTTCTCTT
2027057 TTTTTTTTGGTTAGGTTTTT-TTTT
1 TTTTTTTTGGTTAGGTTTTTCTTTT
2027081 GGGGGGCTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
33 8 0.15
34 25 0.45
35 22 0.40
ACGTcount: A:0.03, C:0.05, G:0.12, T:0.79
Consensus pattern (35 bp):
TTTTTTTTGGTTAGGTTTTTCTTTTTTTTTCTCTT
Found at i:2027051 original size:29 final size:29
Alignment explanation
Indices: 2026980--2027060 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 29
2026970 GGTGGCTAGG
**
2026980 TTTTTTTAGTTTTTTTTGTTAGGTTTTTC
1 TTTTTTTTTTTTTTTTTGTTAGGTTTTTC
2027009 TTTTTTCTTCTTTTTTTTTTTGGTTAGGTTTTTC
1 --TTTT-TT-TTTTTTTTTTT-GTTAGGTTTTTC
2027043 TTTTTTTTTTTCTTTTTT
1 TTTTTTTTTTT-TTTTTT
2027061 TTTTGGTTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
30 5 0.11
31 12 0.27
32 6 0.14
33 9 0.20
34 12 0.27
ACGTcount: A:0.04, C:0.06, G:0.10, T:0.80
Consensus pattern (29 bp):
TTTTTTTTTTTTTTTTTGTTAGGTTTTTC
Found at i:2027052 original size:12 final size:12
Alignment explanation
Indices: 2027009--2027064 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 12
2026999 TAGGTTTTTC
*
2027009 TTTTTTCTTCTT
1 TTTTTTTTTCTT
**
2027021 TTTTTTTTTGGT
1 TTTTTTTTTCTT
***
2027033 TAGGTTTTTCTT
1 TTTTTTTTTCTT
2027045 TTTTTTTTTCTT
1 TTTTTTTTTCTT
2027057 TTTTTTTT
1 TTTTTTTT
2027065 GGTTAGGTTT
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:2029599 original size:61 final size:61
Alignment explanation
Indices: 2029499--2029631 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
2029489 ATGTTGAGGG
* * *
2029499 CTAAATTTATTGATTTTTTAGAATTCAAATTAAAATGACA-AATTTTATAAACATTGAAGG-
1 CTAAATTTGTTGATTTTTTAGAATTCAAATCAAAATGACATAA-TGTATAAACATTGAAGGA
* * * *
2029559 TTAAATTTGTTGAATTTTTTAG-ATTTAGAATCGAATTGACATAATGTATAAACATTGAAGGA
1 CTAAATTTGTTG-ATTTTTTAGAATTCA-AATCAAAATGACATAATGTATAAACATTGAAGGA
2029621 CTAAATTTGTT
1 CTAAATTTGTT
2029632 ATTAAGCCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
60 14 0.23
61 35 0.57
62 12 0.20
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (61 bp):
CTAAATTTGTTGATTTTTTAGAATTCAAATCAAAATGACATAATGTATAAACATTGAAGGA
Found at i:2030063 original size:19 final size:20
Alignment explanation
Indices: 2030026--2030063 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2030016 ATGTTTCACA
2030026 TTCATATAACTAATATTTAT
1 TTCATATAACTAATATTTAT
2030046 TTCAT-TAACATAAT-TTTA
1 TTCATATAAC-TAATATTTA
2030064 ACTTAATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (20 bp):
TTCATATAACTAATATTTAT
Found at i:2032173 original size:15 final size:14
Alignment explanation
Indices: 2032155--2032185 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
2032145 TTAATTTATT
2032155 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
2032170 TAATAATAATCTAA
1 TAATAATAATCTAA
2032184 TA
1 TA
2032186 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:2032196 original size:21 final size:21
Alignment explanation
Indices: 2032172--2032240 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
2032162 AATGCTAATA
2032172 ATAATAATCTAATATAAAACC
1 ATAATAATCTAATATAAAACC
* **
2032193 ATAAT-GT-TAAT-TAATAATT
1 ATAATAATCTAATATAA-AACC
2032212 ATAATAATCTAATATAAAACC
1 ATAATAATCTAATATAAAACC
2032233 ATAATAAT
1 ATAATAAT
2032241 GATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.09, G:0.01, T:0.35
Consensus pattern (21 bp):
ATAATAATCTAATATAAAACC
Found at i:2044344 original size:19 final size:19
Alignment explanation
Indices: 2044320--2044370 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
2044310 ATTAAAGGGT
*
2044320 TTTATCATATATTATTTAA
1 TTTATCATATATTATATAA
2044339 TTTATCATATATTATATAA
1 TTTATCATATATTATATAA
*
2044358 TGTATACATATAT
1 TTTAT-CATATAT
2044371 CTACTTAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 22 0.76
20 7 0.24
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTATCATATATTATATAA
Found at i:2045494 original size:131 final size:131
Alignment explanation
Indices: 2045260--2045518 Score: 428
Period size: 131 Copynumber: 2.0 Consensus size: 131
2045250 TAATTATTCG
* ** *
2045260 TTTAAAAATTCTTTCAAACGAAGGCGATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
1 TTTAAAAATTCTTTAAAACGAAGGAAATGTTCGATGTTTGGCAACTCGGGGAATCGTGCCCTATC
* * **
2045325 GTGCTGGGTTGCAATTTCCTATTTGTTCAAAATAATCGAATATCCCTTTGGAATTTCACTCATAT
66 GTGCTGGGTTACAATTTCCCATTTGTTCAAAATAATCGAATATCCCTTTAAAATTTCACTCATAT
2045390 C
131 C
*
2045391 TTTAAAAATTCTTTAAAACGGAGGAAATGTTCGATGTTTGGCAACTCGGGGAATCGTGCCCTATC
1 TTTAAAAATTCTTTAAAACGAAGGAAATGTTCGATGTTTGGCAACTCGGGGAATCGTGCCCTATC
*
2045456 GTGCTGGGTTACAATTTCCCGTTTGTTCAAAATAATCGAATATCCCTTTAAAATTTCACTCAT
66 GTGCTGGGTTACAATTTCCCATTTGTTCAAAATAATCGAATATCCCTTTAAAATTTCACTCAT
2045519 GTTTTCTAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 118 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (131 bp):
TTTAAAAATTCTTTAAAACGAAGGAAATGTTCGATGTTTGGCAACTCGGGGAATCGTGCCCTATC
GTGCTGGGTTACAATTTCCCATTTGTTCAAAATAATCGAATATCCCTTTAAAATTTCACTCATAT
C
Found at i:2048378 original size:8 final size:9
Alignment explanation
Indices: 2048355--2048380 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2048345 GTTCAATCAA
2048355 AATTTTTAT
1 AATTTTTAT
2048364 AATTTTTAT
1 AATTTTTAT
2048373 AATTTTTA
1 AATTTTTA
2048381 CAATAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
AATTTTTAT
Found at i:2049195 original size:20 final size:21
Alignment explanation
Indices: 2049158--2049197 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2049148 ATTAGCAAAT
2049158 TCAATTTATTAAATTTTGCTA
1 TCAATTTATTAAATTTTGCTA
*
2049179 TCAATTT-TTATATTTTGCT
1 TCAATTTATTAAATTTTGCT
2049198 GAAGTTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.57
Consensus pattern (21 bp):
TCAATTTATTAAATTTTGCTA
Found at i:2052589 original size:23 final size:23
Alignment explanation
Indices: 2052572--2052614 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2052562 TTATAGTTTA
2052572 ATTT-TTATTTTGTTTATAAATT
1 ATTTGTTATTTTGTTTATAAATT
*
2052594 ATTTGTTATTTTGGTTA-AAAT
1 ATTTGTTATTTTGTTTATAAAT
2052615 AAATTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (23 bp):
ATTTGTTATTTTGTTTATAAATT
Found at i:2053177 original size:52 final size:52
Alignment explanation
Indices: 2053120--2053224 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
2053110 AACCAACAAC
2053120 TCATAAATTATAATATAAAGCAGGAGTACAAATATTTGATCTACACACCACA
1 TCATAAATTATAATATAAAGCAGGAGTACAAATATTTGATCTACACACCACA
2053172 TCATAAATTATAATATAAAGCAGGAGTACAAATATTTGATCTACACACCACA
1 TCATAAATTATAATATAAAGCAGGAGTACAAATATTTGATCTACACACCACA
2053224 T
1 T
2053225 AAAGATAGCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.28
Consensus pattern (52 bp):
TCATAAATTATAATATAAAGCAGGAGTACAAATATTTGATCTACACACCACA
Found at i:2056646 original size:88 final size:88
Alignment explanation
Indices: 2056495--2056669 Score: 332
Period size: 88 Copynumber: 2.0 Consensus size: 88
2056485 TTACAGTCAG
*
2056495 TTATTACCGGACAAAATGAAATTAGGTAGGTATGGGACAAAATGAAAGTGAGAAAAAGCATATTT
1 TTATTACCGGACAAAATGAAATTAGGTAGGTATGGAACAAAATGAAAGTGAGAAAAAGCATATTT
2056560 AATGATTTATTTTAAGTAATTAA
66 AATGATTTATTTTAAGTAATTAA
*
2056583 TTATTACCGGACAAAATGAAATTAGGTAGGTATGGAACAAAATGAAAGTGAGAAAAAGTATATTT
1 TTATTACCGGACAAAATGAAATTAGGTAGGTATGGAACAAAATGAAAGTGAGAAAAAGCATATTT
2056648 AATGATTTATTTTAAGTAATTA
66 AATGATTTATTTTAAGTAATTA
2056670 GCTATTATTG
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (88 bp):
TTATTACCGGACAAAATGAAATTAGGTAGGTATGGAACAAAATGAAAGTGAGAAAAAGCATATTT
AATGATTTATTTTAAGTAATTAA
Found at i:2068217 original size:60 final size:61
Alignment explanation
Indices: 2068142--2068283 Score: 144
Period size: 60 Copynumber: 2.3 Consensus size: 61
2068132 CCTTTTGTTT
* * * * * *
2068142 TTGAAATTTTAAGAATTAGACCTAAATTGTCATATTATGTAAATGTTGAGGGCTAAATTTA
1 TTGAATTTTTAAGAATTAGAACTAAAATGACAAATTATGTAAATATTGAGGGCTAAATTTA
* * * * *
2068203 TTG-ATTTTTTAGAATTCA-AACTAAAATGACAAATTTTGTAAATATTGATGGTTAAATTTG
1 TTGAATTTTTAAGAATT-AGAACTAAAATGACAAATTATGTAAATATTGAGGGCTAAATTTA
* *
2068263 TTGAATTTTTCAGATTTAGAA
1 TTGAATTTTTAAGAATTAGAA
2068284 AGAAGTTGAT
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
60 48 0.74
61 17 0.26
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (61 bp):
TTGAATTTTTAAGAATTAGAACTAAAATGACAAATTATGTAAATATTGAGGGCTAAATTTA
Found at i:2071835 original size:17 final size:18
Alignment explanation
Indices: 2071813--2071852 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2071803 AAAAAAAAAG
2071813 AAAATAATT-TAACA-ATA
1 AAAATAATTATAA-ATATA
2071830 AAAATAATTATAAATATA
1 AAAATAATTATAAATATA
2071848 AAAAT
1 AAAAT
2071853 TCAAATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATAATTATAAATATA
Found at i:2078132 original size:14 final size:14
Alignment explanation
Indices: 2078115--2078157 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2078105 ATTCTTATAA
2078115 AATATTTTTTATTT
1 AATATTTTTTATTT
**
2078129 AATATTTACTATTTT
1 AATATTTTTTA-TTT
2078144 ATATATTTTTTATT
1 A-ATATTTTTTATT
2078158 AAACTTTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 9 0.39
15 6 0.26
16 8 0.35
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTTATTT
Found at i:2083928 original size:20 final size:20
Alignment explanation
Indices: 2083903--2083942 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2083893 GAATGAACTT
* *
2083903 ATTATTTTGCTTTTTAACCA
1 ATTATTGTGCTTTTGAACCA
*
2083923 ATTATTGTGGTTTTGAACCA
1 ATTATTGTGCTTTTGAACCA
2083943 TCCCTATCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (20 bp):
ATTATTGTGCTTTTGAACCA
Found at i:2096372 original size:2 final size:2
Alignment explanation
Indices: 2096365--2096407 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2096355 AAAATTTCAT
2096365 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2096407 T
1 T
2096408 TATCATGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2099266 original size:24 final size:23
Alignment explanation
Indices: 2099223--2099268 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2099213 AGTGTTGTTA
*
2099223 ATATATTTTGAAAACAAATTTAG
1 ATATATTCTGAAAACAAATTTAG
2099246 ATATATTACTGAAAATC-AATTTA
1 ATATATT-CTGAAAA-CAAATTTA
2099269 TTTTCCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 12 0.60
25 1 0.05
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (23 bp):
ATATATTCTGAAAACAAATTTAG
Found at i:2100019 original size:16 final size:16
Alignment explanation
Indices: 2099998--2100030 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2099988 ATCTTTTTAA
2099998 AATTATT-TTATCAAAT
1 AATTATTATT-TCAAAT
2100014 AATTATTATTTCAAAT
1 AATTATTATTTCAAAT
2100030 A
1 A
2100031 GAATCTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTATTATTTCAAAT
Found at i:2100057 original size:2 final size:2
Alignment explanation
Indices: 2100050--2100079 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2100040 TTCAATTATT
2100050 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2100080 AAAGTTAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2102977 original size:31 final size:29
Alignment explanation
Indices: 2102942--2103002 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
2102932 ATGTTATATT
*
2102942 TAGTATTTATACTTTCATAAATTATCTAATG
1 TAGTACTTATACTTTCA-AAA-TATCTAATG
* *
2102973 TAGTACTTGTACTTTGAAAATATCTAATG
1 TAGTACTTATACTTTCAAAATATCTAATG
2103002 T
1 T
2103003 GATACTTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 10 0.37
30 3 0.11
31 14 0.52
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (29 bp):
TAGTACTTATACTTTCAAAATATCTAATG
Found at i:2103024 original size:29 final size:29
Alignment explanation
Indices: 2102964--2103024 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
2102954 TTTCATAAAT
* * *
2102964 TATCTAATGTAGTACTTGTACTTTGAAAA
1 TATCTAATGTAGTACTTGAACTATCAAAA
*
2102993 TATCTAATGT-GATACTTGAACTATCAATA
1 TATCTAATGTAG-TACTTGAACTATCAAAA
2103022 TAT
1 TAT
2103025 TTTTTTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (29 bp):
TATCTAATGTAGTACTTGAACTATCAAAA
Found at i:2103600 original size:30 final size:30
Alignment explanation
Indices: 2103566--2103628 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2103556 CCACTAACCC
2103566 TTTTCTGTTACAAACGTAACGGAGCTACCA
1 TTTTCTGTTACAAACGTAACGGAGCTACCA
* * *
2103596 TTTTCTGTTACAAACTTAATGGAGCTGCCA
1 TTTTCTGTTACAAACGTAACGGAGCTACCA
2103626 TTT
1 TTT
2103629 CCTATCCCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.37
Consensus pattern (30 bp):
TTTTCTGTTACAAACGTAACGGAGCTACCA
Found at i:2104768 original size:30 final size:30
Alignment explanation
Indices: 2104734--2104790 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
2104724 CAGGGGATGG
2104734 AAAATGGCAGCTCCATTAAGTCTGTAATGA
1 AAAATGGCAGCTCCATTAAGTCTGTAATGA
* * *
2104764 AAAATGGTAGCTCCGTTATGTCTGTAA
1 AAAATGGCAGCTCCATTAAGTCTGTAA
2104791 CAGAAAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (30 bp):
AAAATGGCAGCTCCATTAAGTCTGTAATGA
Found at i:2104798 original size:30 final size:29
Alignment explanation
Indices: 2104733--2104798 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
2104723 ACAGGGGATG
*
2104733 GAAAATGGCAGCTCCATTAAGTCTGTAAT
1 GAAAATGGCAGCTCCATTAAGTCTGTAAA
* * *
2104762 GAAAAATGGTAGCTCCGTTATGTCTGTAACA
1 G-AAAATGGCAGCTCCATTAAGTCTGTAA-A
2104793 GAAAAT
1 GAAAAT
2104799 AGTTAGTGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 1 0.03
30 29 0.94
31 1 0.03
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.27
Consensus pattern (29 bp):
GAAAATGGCAGCTCCATTAAGTCTGTAAA
Found at i:2105030 original size:24 final size:24
Alignment explanation
Indices: 2105003--2105048 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2104993 GGTAAAATGA
* *
2105003 ATTATGCTAATAAATGCTAAATAT
1 ATTATACTAATAAATACTAAATAT
2105027 ATTATACTAATAAATACTAAAT
1 ATTATACTAATAAATACTAAAT
2105049 CTTCTAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (24 bp):
ATTATACTAATAAATACTAAATAT
Found at i:2105678 original size:32 final size:32
Alignment explanation
Indices: 2105637--2105702 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
2105627 AGTATCCTAA
2105637 AATATATAATACTTAAAAAAATGCTCACTTTC
1 AATATATAATACTTAAAAAAATGCTCACTTTC
*
2105669 AATATATAATACTTAAAAAAATGGTCACTTTC
1 AATATATAATACTTAAAAAAATGCTCACTTTC
2105701 AA
1 AA
2105703 ATTTCATACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (32 bp):
AATATATAATACTTAAAAAAATGCTCACTTTC
Found at i:2105908 original size:18 final size:17
Alignment explanation
Indices: 2105882--2105919 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2105872 ATGATTATAC
2105882 TTTTTATT-AATTTGATT
1 TTTTTATTAAATTT-ATT
2105899 TTTTTAATTAAATTTATT
1 TTTTT-ATTAAATTTATT
2105917 TTT
1 TTT
2105920 GGTTGCACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 9 0.47
19 5 0.26
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTATTAAATTTATT
Found at i:2107702 original size:15 final size:15
Alignment explanation
Indices: 2107684--2107718 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2107674 TTTCTTCTTT
*
2107684 TTTTTTTGGGTTAGG
1 TTTTTTTGGGGTAGG
2107699 TTTTTTTGGGGTAGG
1 TTTTTTTGGGGTAGG
2107714 TTTTT
1 TTTTT
2107719 CTTTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.00, G:0.31, T:0.63
Consensus pattern (15 bp):
TTTTTTTGGGGTAGG
Found at i:2108595 original size:30 final size:30
Alignment explanation
Indices: 2108559--2108649 Score: 150
Period size: 29 Copynumber: 3.1 Consensus size: 30
2108549 TTTTGAAAAA
2108559 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
2108589 CAGAAATTAAAAAGCTCAACTC-ACTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
*
2108618 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
2108648 CA
1 CA
2108650 ATATGAGTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
29 29 0.50
30 24 0.41
31 5 0.09
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.20
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:2108764 original size:13 final size:13
Alignment explanation
Indices: 2108746--2108779 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2108736 TGAGTTGATT
2108746 TTTGAAAACAGAA
1 TTTGAAAACAGAA
*
2108759 TTTGAAAACAGAT
1 TTTGAAAACAGAA
2108772 TTTGAAAA
1 TTTGAAAA
2108780 TACCTCGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAGAA
Found at i:2108887 original size:79 final size:75
Alignment explanation
Indices: 2108759--2109138 Score: 362
Period size: 79 Copynumber: 5.0 Consensus size: 75
2108749 GAAAACAGAA
** * * * * * *
2108759 TTTGAAAACAGATTTTGAAAATACCTC-GACATGTAACCCGAGGCTCAACTCACATCTCGCAATG
1 TTTGAAAACAGAAATTGAAAATACCTCAG-CGTGT-ATCTGAAGCTCAACTCACCTCTCGCAATA
2108823 TGAGTTGATTTT
64 TGAGTTGATTTT
* * *
2108835 TTTGAAAAATATAAATTGAAAAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAA
1 TTTG-AAAACAGAAATTG--AAAATACCTCAGCGTGT-ATCTGAAGCTCAACTCACCTCTCGCAA
2108900 TATGAGTTGATTTT
62 TATGAGTTGATTTT
* * * * *
2108914 TTTGAAAGATAGAAATTGAAAATAGCTCAGCGCATG-AGC-CAAGGGTCAACTCACCTCTCGCAA
1 TTTGAAA-ACAGAAATTGAAAATACCTCAGCG--TGTATCTGAA-GCTCAACTCACCTCTCGCAA
*
2108977 TATAAGTTGA-TTT
62 TATGAGTTGATTTT
* * * ** *
2108990 TTTGAAAACAGAAATTGAAAATACCTCAACGTGTCT-TGAGGCTCAACTCATTTCTCACAATATG
1 TTTGAAAACAGAAATTGAAAATACCTCAGCGTGTATCTGAAGCTCAACTCACCTCTCGCAATATG
*
2109054 AGTTGA--AT
66 AGTTGATTTT
* * * *
2109062 TTTGAAAACAGAAATTGAAATTACCTCAGCGTGT-CCCGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAACAGAAATTGAAAATACCTCAGCGTGTATCTGAAGCTCAACTCACCTCTCGCAATATG
2109126 AGTTGATTTT
66 AGTTGATTTT
2109136 TTT
1 TTT
2109139 TTTTTTTGAA
Statistics
Matches: 251, Mismatches: 40, Indels: 28
0.79 0.13 0.09
Matches are distributed among these distances:
72 63 0.25
73 27 0.11
74 5 0.02
75 21 0.08
76 16 0.06
77 51 0.20
78 3 0.01
79 64 0.25
80 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (75 bp):
TTTGAAAACAGAAATTGAAAATACCTCAGCGTGTATCTGAAGCTCAACTCACCTCTCGCAATATG
AGTTGATTTT
Found at i:2109080 original size:72 final size:73
Alignment explanation
Indices: 2108759--2109137 Score: 393
Period size: 72 Copynumber: 5.0 Consensus size: 73
2108749 GAAAACAGAA
** * * *
2108759 TTTGAAAACAGATTTTGAAAATACCTC-GACATGTAACCCGAGGCTCAACTCACATCTCGCAATG
1 TTTGAAAACAGAAATTGAAAATACCTCAG-CGTGT--CCCGAGGCTCAACTCACCTCTCGCAATA
2108823 TGAGTTGATTTT
63 TGAGTTGA-TTT
* * * * * *
2108835 TTTGAAAAATATAAATTGAAAAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAA
1 TTTG-AAAACAGAAATTG--AAAATACCTCAGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAA
2108900 TATGAGTTGATTTT
61 TATGAGTTGA-TTT
* * ** * *
2108914 TTTGAAAGATAGAAATTGAAAATAGCTCAGCGCATGAGCCAAGGGTCAACTCACCTCTCGCAATA
1 TTTGAAA-ACAGAAATTGAAAATACCTCAGCG--TGTCCCGAGGCTCAACTCACCTCTCGCAATA
*
2108979 TAAGTTGATTT
63 TGAGTTGATTT
* ** ** *
2108990 TTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCACAATATGA
1 TTTGAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
*
2109055 GTTGA-AT
66 GTTGATTT
*
2109062 TTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTTGAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
2109127 GTTGATTT
66 GTTGATTT
2109135 TTT
1 TTT
2109138 TTTTTTTTGA
Statistics
Matches: 251, Mismatches: 44, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
72 64 0.25
73 33 0.13
75 21 0.08
76 14 0.06
77 51 0.20
78 3 0.01
79 64 0.25
80 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (73 bp):
TTTGAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:2109282 original size:171 final size:168
Alignment explanation
Indices: 2108994--2109471 Score: 702
Period size: 164 Copynumber: 2.9 Consensus size: 168
2108984 TGATTTTTTG
* * * ** * *
2108994 AAAACAGAAATTGAAAATACCTCAACGTGT-CT-TGAGGCTCAACTCATTTCTCACAATATGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
* * *
2109057 TGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCA
66 TGATTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
* *
2109121 ATATGAGTTGATTTTTTTTTTTTTTGAAATGCAGAAATTGA
131 ATATGAGTTGA---TTTTTTTTTTTGAAAGGCAAAAATTGA
*
2109162 AAAATGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
2109227 TGACTTTTTTGACAA-AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGA-TTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
2109291 AATATGAGTTGA----TTTTTTTGAAAGGCAAAAATTGA
130 AATATGAGTTGATTTTTTTTTTTGAAAGGCAAAAATTGA
* * * *
2109326 AAAACGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGT
1 AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
2109391 TGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
66 TGA-TTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC
2109456 AATATGAGTTGATTTT
130 AATATGAGTTGATTTT
2109472 GAAAAAGTAG
Statistics
Matches: 282, Mismatches: 19, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
164 95 0.34
165 61 0.22
168 27 0.10
169 1 0.00
170 30 0.11
171 60 0.21
172 8 0.03
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (168 bp):
AAAACGGAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGT
TGATTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCA
ATATGAGTTGATTTTTTTTTTTGAAAGGCAAAAATTGA
Found at i:2109289 original size:73 final size:74
Alignment explanation
Indices: 2109168--2109311 Score: 220
Period size: 73 Copynumber: 1.9 Consensus size: 74
2109158 TTGAAAAATG
*
2109168 GAAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
1 GAAATTGAAAATACCTCGACGTGT-ACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
2109233 TTTTGACAAA
65 TTTTGACAAA
* * *
2109243 GAAATTGAAATTACCTC-AGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 GAAATTGAAAATACCTCGA-CGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTT
2109306 TTTTGA
65 TTTTGA
2109312 AAGGCAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
73 42 0.66
74 1 0.02
75 21 0.33
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (74 bp):
GAAATTGAAAATACCTCGACGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
TTTGACAAA
Found at i:2109323 original size:75 final size:74
Alignment explanation
Indices: 2109169--2109328 Score: 209
Period size: 73 Copynumber: 2.1 Consensus size: 74
2109159 TGAAAAATGG
*
2109169 AAATTGAAAATACCTCGACGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
1 AAATTGAAAATACCTCGACGTGT-ACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
*
2109234 TTTGACAAAG
65 TTTGACAAAA
* * *
2109244 AAATTGAAATTACCTC-AGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTGAAAATACCTCGA-CGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTT
2109307 TTTGA-AAGGCAA
65 TTTGACAA---AA
2109319 AAATTGAAAA
1 AAATTGAAAA
2109329 ACGGAAATTG
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
72 2 0.03
73 42 0.56
74 1 0.01
75 30 0.40
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (74 bp):
AAATTGAAAATACCTCGACGTGTACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTTT
TTGACAAAA
Found at i:2109457 original size:74 final size:75
Alignment explanation
Indices: 2109332--2109471 Score: 219
Period size: 74 Copynumber: 1.9 Consensus size: 75
2109322 TTGAAAAACG
* *
2109332 GAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCGCCACTCGCAATACGAGTTGATTT
1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTT
2109397 TTTTGACAACA
65 TTTTGACAACA
* * *
2109408 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
2109472 GAAAAAGTAG
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
74 37 0.63
76 22 0.37
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (75 bp):
GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAATACGAGTTGATTTT
TTTGACAACA
Found at i:2109652 original size:71 final size:71
Alignment explanation
Indices: 2109536--2109700 Score: 244
Period size: 71 Copynumber: 2.3 Consensus size: 71
2109526 TGAACAACGT
* * *
2109536 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTGAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
2109601 GAGTTG
66 GAGTTG
*
2109607 AAATT-AAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTGAAA-ACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATA
2109671 TGAGTTG
65 TGAGTTG
**
2109678 ATTTTGAAAAACAAAAATT-AAAA
1 AAATTG-AAAACAAAAATTGAAAA
2109701 GGCTTAACTC
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
70 3 0.04
71 70 0.82
72 9 0.11
73 3 0.04
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.22
Consensus pattern (71 bp):
AAATTGAAAACAAAAATTGAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:2109843 original size:71 final size:71
Alignment explanation
Indices: 2109700--2109963 Score: 356
Period size: 70 Copynumber: 3.7 Consensus size: 71
2109690 AAAAATTAAA
* * * * *
2109700 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTT-AAAACATAAACTAAAAATACCTCAGCGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
2109763 GCCCCG
66 GCCCCG
* *
2109769 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
* **
2109834 GTCTTG
66 GCCCCG
* * *
2109840 AGGCTCAACTCATCTCTCGCAATATGAGTTGA--TTAAAACACAAAAATTGAAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAA-ACAAAAATTAAAAATACCTCAGCG
2109903 TGCCCCG
65 TGCCCCG
*
2109910 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAAAAATTAAAA
2109964 GGCTTAACTC
Statistics
Matches: 167, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
69 31 0.19
70 61 0.37
71 58 0.35
72 14 0.08
73 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (71 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAGCGT
GCCCCG
Found at i:2109921 original size:70 final size:69
Alignment explanation
Indices: 2109700--2109963 Score: 339
Period size: 71 Copynumber: 3.7 Consensus size: 69
2109690 AAAAATTAAA
* ** * * *
2109700 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCAGCGTGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAAACAAAAATTAAAAATACCTCAGCGTGC
2109765 CCCG
66 CCCG
* * *
2109769 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACAAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTAAAAACAAAAATTAAAAATACCTCAGCGT
* **
2109834 GTCTTG
64 GCCCCG
* *
2109840 AGGCTCAACTCATCTCTCGCAATATGAGTTGATTAAAACACAAAAATTGAAAATACCTCAGCGTG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAA-ACAAAAATTAAAAATACCTCAGCGTG
2109905 CCCCG
65 CCCCG
*
2109910 AGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT-AAAAACAAAAATTAAAA
2109964 GGCTTAACTC
Statistics
Matches: 167, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
69 33 0.20
70 56 0.34
71 60 0.36
72 14 0.08
73 4 0.02
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (69 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTAAAAACAAAAATTAAAAATACCTCAGCGTGC
CCCG
Found at i:2109950 original size:263 final size:256
Alignment explanation
Indices: 2109539--2110130 Score: 1031
Period size: 257 Copynumber: 2.3 Consensus size: 256
2109529 ACAACGTAAA
* * * * * *
2109539 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
2109604 TTGAAATTAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAA
66 TTG--ATTAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAA
2109669 TATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATT
129 TATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATT
2109734 TAAAACATAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTT
194 T-----A-AAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTT
2109799 GATT
253 GATT
2109803 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
2109868 TTGATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
66 TTGATT-AAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAAT
2109933 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
130 ATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
*
2109998 AAAACTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
195 AAAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
*
2110060 TTGAAAACAACAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
2110125 TTGATT
66 TTGATT
2110131 TTCCTTGAAA
Statistics
Matches: 319, Mismatches: 8, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
257 130 0.41
258 1 0.00
262 3 0.01
263 123 0.39
264 62 0.19
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.26
Consensus pattern (256 bp):
TTGAAAACAAAAATTAAAAATACCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAG
TTGATTAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
TGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTTA
AAACTAAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATT
Found at i:2115174 original size:12 final size:12
Alignment explanation
Indices: 2115154--2115189 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2115144 TGGGATATGC
*
2115154 AATGTATGAATG
1 AATGCATGAATG
2115166 AATGCATGAATG
1 AATGCATGAATG
2115178 AATGCATGAATG
1 AATGCATGAATG
2115190 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:2117765 original size:15 final size:15
Alignment explanation
Indices: 2117747--2117781 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2117737 TTCTTCTTTT
*
2117747 TTTTTTTGGGTTAGG
1 TTTTTTTGGGGTAGG
2117762 TTTTTTTGGGGTAGG
1 TTTTTTTGGGGTAGG
2117777 TTTTT
1 TTTTT
2117782 CTTTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.00, G:0.31, T:0.63
Consensus pattern (15 bp):
TTTTTTTGGGGTAGG
Found at i:2117807 original size:12 final size:11
Alignment explanation
Indices: 2117777--2117810 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
2117767 TTGGGGTAGG
2117777 TTTTTCTTTTTC
1 TTTTT-TTTTTC
2117789 TTTTTTTTTTC
1 TTTTTTTTTTC
2117800 TTTGTTTTTTT
1 TTT-TTTTTTT
2117811 TTGGGTTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:2120966 original size:6 final size:6
Alignment explanation
Indices: 2120957--2121004 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
2120947 TTATAATTAT
* * *
2120957 TTAATA TTAATA TTAATA TTAATA TCAAT- TTTATA TT-ATT TTAATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA
2121003 TT
1 TT
2121005 TTCTGTTGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 7 0.20
6 28 0.80
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (6 bp):
TTAATA
Found at i:2122365 original size:22 final size:21
Alignment explanation
Indices: 2122336--2122376 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
2122326 GATTAAAATA
2122336 TTTTATT-AATTTGATTTTTAT
1 TTTTATTAAATTT-ATTTTTAT
2122357 TTTTAATTAAATTTATTTTT
1 TTTT-ATTAAATTTATTTTT
2122377 TGGTTGCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTATTAAATTTATTTTTAT
Found at i:2122636 original size:22 final size:22
Alignment explanation
Indices: 2122602--2122644 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2122592 TAATATCTAA
2122602 ATAATAATAAAATAGTAGCAAT
1 ATAATAATAAAATAGTAGCAAT
* *
2122624 ATAATAGTGAAATAGTAGCAA
1 ATAATAATAAAATAGTAGCAA
2122645 CATATTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.26
Consensus pattern (22 bp):
ATAATAATAAAATAGTAGCAAT
Found at i:2126389 original size:22 final size:22
Alignment explanation
Indices: 2126363--2126408 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2126353 GTGTTAGCAT
*
2126363 TCTCCTCCTTAAAATTTGGGTC
1 TCTCCACCTTAAAATTTGGGTC
2126385 TCTCCACCTTAAAATTTGGGTC
1 TCTCCACCTTAAAATTTGGGTC
2126407 TC
1 TC
2126409 ATGTTGCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.28, G:0.13, T:0.39
Consensus pattern (22 bp):
TCTCCACCTTAAAATTTGGGTC
Found at i:2131339 original size:144 final size:144
Alignment explanation
Indices: 2131063--2131340 Score: 344
Period size: 144 Copynumber: 1.9 Consensus size: 144
2131053 TTAAACCAAT
* * * *
2131063 AACTTTTGTTAGCTTGACTGACTAGTGCTGGGCACACATTTGTCGGTATAACCGACTAGCGCTGG
1 AACTTTTGTCAGCTTGACTGACTAGTGCTGGGCACACAATTGTCGGTACAACCGACTAGCGCTAG
* ** * ** **
2131128 GCTCAAACATCGTTGGTTTACCCAAATAGAGCTAGGCTCACTATGGATTTTGTCGATATATTTGA
66 GCTCAAACATCGTTGGTTTACCCAAATAGAGCTAGGCTCACAATCAATATCATCGATATATCCGA
2131193 CTAGTGCTGGGTGC
131 CTAGTGCTGGGTGC
* * * **
2131207 AACTTTTGTCAGCTTGTCTGGCTAGTGCTGGGCACACAATTGTTGGTACAATTGACTAGCGCTAG
1 AACTTTTGTCAGCTTGACTGACTAGTGCTGGGCACACAATTGTCGGTACAACCGACTAGCGCTAG
* * *
2131272 G-TGCAAACATCGTTGGTTTATCCAATTAGAGCTGGGCTCACAATCAATATCATCGACTA-ATCC
66 GCT-CAAACATCGTTGGTTTACCCAAATAGAGCTAGGCTCACAATCAATATCATCGA-TATATCC
2131335 GACTAG
129 GACTAG
2131341 CACTGGGCGC
Statistics
Matches: 112, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
143 1 0.01
144 109 0.97
145 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (144 bp):
AACTTTTGTCAGCTTGACTGACTAGTGCTGGGCACACAATTGTCGGTACAACCGACTAGCGCTAG
GCTCAAACATCGTTGGTTTACCCAAATAGAGCTAGGCTCACAATCAATATCATCGATATATCCGA
CTAGTGCTGGGTGC
Found at i:2145554 original size:18 final size:18
Alignment explanation
Indices: 2145528--2145566 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2145518 AACAGGTTGA
*
2145528 GAAAGAAAAGGGAATCGG
1 GAAAAAAAAGGGAATCGG
2145546 GAAAAAAAAGGGAATCGG
1 GAAAAAAAAGGGAATCGG
2145564 GAA
1 GAA
2145567 GATAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.36, T:0.05
Consensus pattern (18 bp):
GAAAAAAAAGGGAATCGG
Found at i:2145623 original size:44 final size:44
Alignment explanation
Indices: 2145546--2145643 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 44
2145536 AGGGAATCGG
*
2145546 GAAAAAAAAGGGAATCGGGAAGATAAATAAAACGACATCGTTTGC
1 GAAAGAAAAGGGAATCGGGAAGA-AAATAAAACGACATCGTTTGC
* *
2145591 GAAAGAAAAGGGAATTGGGGAAG-AAATAAAACGGCATCGTTTGC
1 GAAAGAAAAGGGAA-TCGGGAAGAAAATAAAACGACATCGTTTGC
2145635 GAAAGAAAA
1 GAAAGAAAA
2145644 AAGAAATCGG
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
44 29 0.59
45 13 0.27
46 7 0.14
ACGTcount: A:0.49, C:0.09, G:0.28, T:0.14
Consensus pattern (44 bp):
GAAAGAAAAGGGAATCGGGAAGAAAATAAAACGACATCGTTTGC
Found at i:2146334 original size:48 final size:48
Alignment explanation
Indices: 2146242--2146332 Score: 114
Period size: 48 Copynumber: 1.9 Consensus size: 48
2146232 TTAATTAATT
* **
2146242 TTTTAAAATTTTAATATATTAAAAACTATCTTTTTATAATTTTTATAG
1 TTTTAAAATTTTAATATATTAAAAAATAGATTTTTATAATTTTTATAG
* *
2146290 TTTTAATAATTTTAAT-TTTTAAAAAATAGA-TTTTGTAATTTTT
1 TTTTAA-AATTTTAATATATTAAAAAATAGATTTTTATAATTTTT
2146333 TAAATTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
47 12 0.32
48 16 0.43
49 9 0.24
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.56
Consensus pattern (48 bp):
TTTTAAAATTTTAATATATTAAAAAATAGATTTTTATAATTTTTATAG
Found at i:2153513 original size:93 final size:93
Alignment explanation
Indices: 2153401--2153571 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
2153391 GCCCATAAGT
* *
2153401 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
2153466 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
2153494 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
2153559 CGAGTTCGGATGC
66 CGAGTTCGGATGC
2153572 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:2153587 original size:46 final size:46
Alignment explanation
Indices: 2153393--2153573 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
2153383 TGTAACCCGC
* * *
2153393 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
2153439 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
2153489 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
*
2153532 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
2153574 AACCATCCTA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 72 0.62
47 32 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:2156786 original size:22 final size:22
Alignment explanation
Indices: 2156761--2156819 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 22
2156751 GCCACACAGC
2156761 CGTGTGTCTCCTTTCACACGGA
1 CGTGTGTCTCCTTTCACACGGA
* * *
2156783 CGTGTG-C-CTTTTTACATGGA
1 CGTGTGTCTCCTTTCACACGGA
2156803 CGTGTGTCT-CTTTCACA
1 CGTGTGTCTCCTTTCACA
2156820 TGGGTGTGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
20 16 0.53
21 8 0.27
22 6 0.20
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.37
Consensus pattern (22 bp):
CGTGTGTCTCCTTTCACACGGA
Found at i:2159651 original size:48 final size:48
Alignment explanation
Indices: 2159546--2159655 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 48
2159536 CAACATTTAA
*
2159546 TTAA-TTTTTTAAAATTTTAAAAATTAAAAACTATCTTTTTATAATTT
1 TTAATTTTTTTAAAATTTTAAAAATTAAAAACTATATTTTTATAATTT
* *** *
2159593 TT-ATACTTTTTAATAATTTTAATTTTTAAAAA-TATATTTTTTTAATTT
1 TTAAT-TTTTTTAA-AATTTTAAAAATTAAAAACTATATTTTTATAATTT
2159641 TTAATTTTTTTAAAA
1 TTAATTTTTTTAAAA
2159656 AAATTAAATG
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
46 1 0.02
47 4 0.08
48 30 0.58
49 17 0.33
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (48 bp):
TTAATTTTTTTAAAATTTTAAAAATTAAAAACTATATTTTTATAATTT
Found at i:2170752 original size:2 final size:2
Alignment explanation
Indices: 2170745--2170774 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2170735 GTAAGCATTC
2170745 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
2170775 GTTAGCTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2174918 original size:2 final size:2
Alignment explanation
Indices: 2174911--2174957 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2174901 TTCTAACCCT
2174911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2174953 TA TA T
1 TA TA T
2174958 GTCCATATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2176688 original size:2 final size:2
Alignment explanation
Indices: 2176681--2176710 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2176671 ACTGATTTGA
2176681 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
2176711 TTAAATGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2178234 original size:21 final size:22
Alignment explanation
Indices: 2178210--2178266 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 22
2178200 TACTTGGGTA
*
2178210 TTATATATATATTTTTATA-TG
1 TTATATATATATTTTAATATTG
2178231 TTATATATATACTTTTAATATTG
1 TTATATATATA-TTTTAATATTG
*
2178254 TATTTATATATAT
1 T-TATATATATAT
2178267 CATATATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 11 0.35
22 7 0.23
23 4 0.13
24 9 0.29
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
TTATATATATATTTTAATATTG
Found at i:2178278 original size:31 final size:28
Alignment explanation
Indices: 2178231--2178295 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 28
2178221 TTTTTATATG
2178231 TTATATATATACTTTTAATATTGTATTTA
1 TTATATATATACTTTTAATATTGTA-TTA
* *
2178260 TATATATCATATATTTTTAATGTTGTATTA
1 T-TATAT-ATATACTTTTAATATTGTATTA
2178290 TTATAT
1 TTATAT
2178296 TTTAATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 6 0.19
30 9 0.28
31 17 0.53
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (28 bp):
TTATATATATACTTTTAATATTGTATTA
Found at i:2178368 original size:25 final size:25
Alignment explanation
Indices: 2178340--2178416 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
2178330 TATATACATG
2178340 TATTTTATATATATTATCATGTATA
1 TATTTTATATATATTATCATGTATA
* *
2178365 TATTTTGATAT-TACTAGTTATGTAT-
1 TATTTT-ATATATATTA-TCATGTATA
* *
2178390 TA-CTTATATAT-TT-CCATGTATA
1 TATTTTATATATATTATCATGTATA
2178412 TATTT
1 TATTT
2178417 ATACTGTCCC
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
21 6 0.15
22 2 0.05
23 6 0.15
24 3 0.08
25 12 0.30
26 11 0.28
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (25 bp):
TATTTTATATATATTATCATGTATA
Found at i:2180486 original size:29 final size:30
Alignment explanation
Indices: 2180427--2180488 Score: 72
Period size: 35 Copynumber: 1.9 Consensus size: 30
2180417 AGGAAAAAGG
2180427 CAACAACAAAGTAGCATGTGATTTGTTTAAAAAAA
1 CAACAACAAAGTAGCATGTGA-----TTAAAAAAA
2180462 CAACAACAAAGTAGCATGTGA-TAAAAA
1 CAACAACAAAGTAGCATGTGATTAAAAA
2180489 TATTTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
29 6 0.22
35 21 0.78
ACGTcount: A:0.52, C:0.13, G:0.15, T:0.21
Consensus pattern (30 bp):
CAACAACAAAGTAGCATGTGATTAAAAAAA
Found at i:2191745 original size:22 final size:22
Alignment explanation
Indices: 2191703--2191745 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2191693 GTCTTTTATT
* *
2191703 TATTTTTTATTTAAATCGGATG
1 TATTTTTAATTTAAATAGGATG
2191725 TATTTTTAATTTCAAA-AGGAT
1 TATTTTTAATTT-AAATAGGAT
2191746 ATTCGGTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.51
Consensus pattern (22 bp):
TATTTTTAATTTAAATAGGATG
Found at i:2192015 original size:5 final size:5
Alignment explanation
Indices: 2191991--2192017 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2191981 AAAACAAGAC
2191991 AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA
2192018 TGAGATAATA
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2199749 original size:19 final size:20
Alignment explanation
Indices: 2199706--2199754 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2199696 TGCCTCTTTT
*
2199706 TGCATT-CATTTCATTCATC
1 TGCATTACATTTCATTCATA
*
2199725 TACATTACATTTCA-TCATA
1 TGCATTACATTTCATTCATA
2199744 TGCATTA-ATTT
1 TGCATTACATTT
2199755 TCATAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 15 0.58
20 7 0.27
ACGTcount: A:0.29, C:0.20, G:0.04, T:0.47
Consensus pattern (20 bp):
TGCATTACATTTCATTCATA
Found at i:2206430 original size:31 final size:31
Alignment explanation
Indices: 2206394--2206463 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
2206384 CAGAAAAAAG
2206394 AAGACTAAGTTGATAAAAGATTTCAAATCCA
1 AAGACTAAGTTGATAAAAGATTTCAAATCCA
*
2206425 AAGACTAAGTTTATAAAAGATTTCAAATCCA
1 AAGACTAAGTTGATAAAAGATTTCAAATCCA
*
2206456 AAGGCTAA
1 AAGACTAA
2206464 ATGTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (31 bp):
AAGACTAAGTTGATAAAAGATTTCAAATCCA
Found at i:2207421 original size:39 final size:39
Alignment explanation
Indices: 2207329--2207428 Score: 173
Period size: 39 Copynumber: 2.6 Consensus size: 39
2207319 AAAATTATTA
*
2207329 TTTTAAAAAAATTTAAAAATTTAATTTTCTTTAGAATTT
1 TTTTAAAAAAATTTCAAAATTTAATTTTCTTTAGAATTT
2207368 TTTTAAAAAAATTTCAAAATTTAATTTTCTTTAGAATTT
1 TTTTAAAAAAATTTCAAAATTTAATTTTCTTTAGAATTT
* *
2207407 TTTTTAAAAAATTTCATAATTT
1 TTTTAAAAAAATTTCAAAATTT
2207429 GTAAAAATAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (39 bp):
TTTTAAAAAAATTTCAAAATTTAATTTTCTTTAGAATTT
Found at i:2207442 original size:17 final size:17
Alignment explanation
Indices: 2207422--2207455 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2207412 AAAAAATTTC
2207422 ATAATTTGTAAAAATAT
1 ATAATTTGTAAAAATAT
* *
2207439 ATAATTTTTATAAATAT
1 ATAATTTGTAAAAATAT
2207456 TTTTAATTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATAATTTGTAAAAATAT
Found at i:2208337 original size:11 final size:11
Alignment explanation
Indices: 2208290--2208349 Score: 52
Period size: 11 Copynumber: 5.2 Consensus size: 11
2208280 TTGAATAACC
2208290 AATTAAAAATTT
1 AATTAAAAA-TT
2208302 AATT-AAAA-T
1 AATTAAAAATT
2208311 AATTAAAAATACAT
1 AATTAAAAAT---T
*
2208325 TATATAAAAATT
1 AAT-TAAAAATT
2208337 AATTAAAAATT
1 AATTAAAAATT
2208348 AA
1 AA
2208350 ATGTGTTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
9 5 0.12
10 4 0.10
11 14 0.35
12 7 0.17
14 3 0.08
15 7 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
AATTAAAAATT
Found at i:2209281 original size:12 final size:13
Alignment explanation
Indices: 2209258--2209286 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2209248 TAGCAATCTT
2209258 TTTAATATATATA
1 TTTAATATATATA
2209271 TTTAA-ATATATA
1 TTTAATATATATA
2209283 TTTA
1 TTTA
2209287 TGTAAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTAATATATATA
Found at i:2213569 original size:14 final size:12
Alignment explanation
Indices: 2213535--2213576 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
2213525 TAAAAAAGTC
2213535 AAAATATTAAAT
1 AAAATATTAAAT
*
2213547 AATATATTAAACTT
1 AAAATATTAAA--T
2213561 AAAATATT-AAT
1 AAAATATTAAAT
2213572 AAAAT
1 AAAAT
2213577 TTTGAAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 6 0.23
12 10 0.38
13 2 0.08
14 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAATATTAAAT
Found at i:2214606 original size:12 final size:12
Alignment explanation
Indices: 2214589--2214613 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2214579 ATTATCAAAG
2214589 AATAATTTTTTT
1 AATAATTTTTTT
2214601 AATAATTTTTTT
1 AATAATTTTTTT
2214613 A
1 A
2214614 TTTGATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATAATTTTTTT
Found at i:2216761 original size:20 final size:19
Alignment explanation
Indices: 2216723--2216771 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
2216713 TCTTTATAAA
*
2216723 TATTTTTAA-TTTTAAAAT
1 TATTTTGAATTTTTAAAAT
2216741 TATTTTGAATTTTTGAAAAT
1 TATTTTGAATTTTT-AAAAT
2216761 TATTTTGAATT
1 TATTTTGAATT
2216772 ATTATGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 8 0.29
19 4 0.14
20 16 0.57
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (19 bp):
TATTTTGAATTTTTAAAAT
Found at i:2217648 original size:26 final size:26
Alignment explanation
Indices: 2217602--2217651 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2217592 TTAATTACAA
*
2217602 TAATTAAAAATACATTATATAAAAAC
1 TAATTAAAAATACAATATATAAAAAC
*
2217628 TAATTAAAAATTA-AATGTATAAAA
1 TAATTAAAAA-TACAATATATAAAA
2217652 TCACATGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (26 bp):
TAATTAAAAATACAATATATAAAAAC
Found at i:2220569 original size:14 final size:15
Alignment explanation
Indices: 2220535--2220572 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2220525 TTTTCAATAT
2220535 TTTTAATTTTTATTAA
1 TTTT-ATTTTTATTAA
*
2220551 TTTTATTTTTGTTAA
1 TTTTATTTTTATTAA
2220566 -TTTATTT
1 TTTTATTT
2220573 GTTTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 10 0.48
16 4 0.19
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTATTTTTATTAA
Found at i:2224055 original size:21 final size:20
Alignment explanation
Indices: 2224026--2224064 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2224016 ACGCCTACGA
*
2224026 AAAGATCGCTTGGATTTAAG
1 AAAGATCGCTTGAATTTAAG
2224046 AAAGAGTCGCTTGAATTTA
1 AAAGA-TCGCTTGAATTTA
2224065 TCCATGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (20 bp):
AAAGATCGCTTGAATTTAAG
Found at i:2224198 original size:15 final size:16
Alignment explanation
Indices: 2224178--2224207 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2224168 AGGATTTGGT
2224178 TTGTTTATT-TTATTA
1 TTGTTTATTATTATTA
2224193 TTGTTTATTATTATT
1 TTGTTTATTATTATT
2224208 TATCATTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (16 bp):
TTGTTTATTATTATTA
Found at i:2224260 original size:18 final size:19
Alignment explanation
Indices: 2224218--2224275 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 19
2224208 TATCATTTCA
2224218 ATATATAATTTAAATATA-T
1 ATATA-AATTTAAATATATT
2224237 ATATAAATTTAAATATATT
1 ATATAAATTTAAATATATT
*
2224256 A-ATAATATATAAA-ATATT
1 ATATAA-ATTTAAATATATT
2224274 AT
1 AT
2224276 TGTGTAGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 22 0.63
19 13 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATAAATTTAAATATATT
Found at i:2228090 original size:11 final size:11
Alignment explanation
Indices: 2228074--2228098 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2228064 CAAAAATTCT
2228074 AATAAATTAAA
1 AATAAATTAAA
2228085 AATAAATTAAA
1 AATAAATTAAA
2228096 AAT
1 AAT
2228099 TTTATACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAATTAAA
Found at i:2228250 original size:10 final size:10
Alignment explanation
Indices: 2228151--2228243 Score: 60
Period size: 11 Copynumber: 8.7 Consensus size: 10
2228141 AAATATATTT
2228151 AAAATAATAA
1 AAAATAATAA
*
2228161 AAAATTAATAT
1 AAAA-TAATAA
* *
2228172 ATAATATCTAA
1 AAAATA-ATAA
* *
2228183 ATAATAATGAT
1 AAAATAAT-AA
2228194 AAAATAATAA
1 AAAATAATAA
*
2228204 CAACATAATAA
1 -AAAATAATAA
* *
2228215 TAAAATGACAA
1 -AAAATAATAA
2228226 TAAAATAATAA
1 -AAAATAATAA
2228237 AAAATAA
1 AAAATAA
2228244 AAGAAAAACA
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
10 15 0.23
11 49 0.77
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (10 bp):
AAAATAATAA
Found at i:2235197 original size:4 final size:4
Alignment explanation
Indices: 2235188--2235213 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2235178 GCTCCAAGTA
2235188 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
2235214 TTTGAATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:2238212 original size:12 final size:12
Alignment explanation
Indices: 2238197--2238222 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2238187 CATAGTTTGT
2238197 TAGGACCAATGG
1 TAGGACCAATGG
2238209 TAGGACCAATGG
1 TAGGACCAATGG
2238221 TA
1 TA
2238223 CCATCAGTTC
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:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (12 bp):
TAGGACCAATGG
Found at i:2238517 original size:17 final size:17
Alignment explanation
Indices: 2238494--2238541 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2238484 CATCTAAATA
2238494 ATTTTTTAAATACTAAT
1 ATTTTTTAAATACTAAT
* * ** *
2238511 TTTTTTTATATTTTTAT
1 ATTTTTTAAATACTAAT
2238528 ATTTTTTAAATACT
1 ATTTTTTAAATACT
2238542 TTTAATGATT
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTTAAATACTAAT
Found at i:2238576 original size:23 final size:24
Alignment explanation
Indices: 2238550--2238595 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2238540 CTTTTAATGA
2238550 TTTTAA-ATTTTAAAAAATAATTT
1 TTTTAATATTTTAAAAAATAATTT
*
2238573 TTTTAATTTTTTAAAAAATAATT
1 TTTTAATATTTTAAAAAATAATT
2238596 AAATACTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTAATATTTTAAAAAATAATTT
Found at i:2238736 original size:24 final size:24
Alignment explanation
Indices: 2238694--2238739 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2238684 TAATTTAACC
* *
2238694 AAAAAAAACGTAAATTTAAATACT
1 AAAAAAAACGAAAAATTAAATACT
*
2238718 AAAAAAGACGAAAAATTAAATA
1 AAAAAAAACGAAAAATTAAATA
2238740 AAAGTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (24 bp):
AAAAAAAACGAAAAATTAAATACT
Found at i:2248199 original size:18 final size:18
Alignment explanation
Indices: 2248168--2248202 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2248158 GACTAATAAT
2248168 TAAAAATTTATAAAAATC
1 TAAAAATTTATAAAAATC
* *
2248186 TAAAAGTTTTTAAAAAT
1 TAAAAATTTATAAAAAT
2248203 AGAAAATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (18 bp):
TAAAAATTTATAAAAATC
Found at i:2253163 original size:24 final size:26
Alignment explanation
Indices: 2253136--2253184 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2253126 TTTATCTATA
*
2253136 AATAAAT-AAAATA-ATTATTTTTAT
1 AATAAATAAAAATATATTAATTTTAT
*
2253160 AATAATTAAAAATATATTAATTTTA
1 AATAAATAAAAATATATTAATTTTA
2253185 AGGGGTAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 6 0.29
26 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AATAAATAAAAATATATTAATTTTAT
Found at i:2257323 original size:1 final size:1
Alignment explanation
Indices: 2257317--2257343 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2257307 CCTACAGTGG
2257317 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
2257344 GCATTTCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2267982 original size:29 final size:29
Alignment explanation
Indices: 2267949--2268006 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2267939 TTCTAATTCC
2267949 TTAAAAACAATTATTCACTTTGTATCAAA
1 TTAAAAACAATTATTCACTTTGTATCAAA
2267978 TTAAAAACAATTATTCACTTTGTATCAAA
1 TTAAAAACAATTATTCACTTTGTATCAAA
2268007 ATGAAACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (29 bp):
TTAAAAACAATTATTCACTTTGTATCAAA
Found at i:2276408 original size:15 final size:16
Alignment explanation
Indices: 2276379--2276411 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2276369 TTTTTAGTGC
*
2276379 TTTTAGTATATTATAT
1 TTTTAATATATTATAT
2276395 TTTTAATATA-TATAT
1 TTTTAATATATTATAT
2276410 TT
1 TT
2276412 AAATAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTTAATATATTATAT
Found at i:2282516 original size:2 final size:2
Alignment explanation
Indices: 2282509--2282547 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2282499 ATATAAGTAA
2282509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2282548 AAGCTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2285366 original size:17 final size:16
Alignment explanation
Indices: 2285346--2285389 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
2285336 TTTATTATTT
*
2285346 ATATAATTTTTTTATAA
1 ATAT-ATTTTTATATAA
2285363 ATATATTTATTATATAA
1 ATATATTT-TTATATAA
*
2285380 TTATATTTTT
1 ATATATTTTT
2285390 CACCTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATATTTTTATATAA
Done.