Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 7 of 175
Found at i:2015783 original size:23 final size:23
Alignment explanation
Indices: 2015756--2015815 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
2015746 TTATATGTTC
*
2015756 ATGAACATATTCGTTTAATGTT-T
1 ATGAACATATTCGTTTAA-GTTAA
* * *
2015779 GTGAACATGTTCGATTAAGTTAA
1 ATGAACATATTCGTTTAAGTTAA
2015802 ATGAACATATTCGT
1 ATGAACATATTCGT
2015816 GAGCATTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
22 3 0.10
23 26 0.90
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (23 bp):
ATGAACATATTCGTTTAAGTTAA
Found at i:2016065 original size:3 final size:3
Alignment explanation
Indices: 2016057--2016102 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2016047 CTAATTGATG
2016057 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2016103 CTTGAGCCCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2019813 original size:47 final size:47
Alignment explanation
Indices: 2019759--2019909 Score: 248
Period size: 47 Copynumber: 3.2 Consensus size: 47
2019749 TTAGGATTTT
** *
2019759 ATGTGATGAATGTGAATGTGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
2019806 ATGTGATGAATGTGAACATGCATGTATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
2019853 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
2019900 ATGTGATGAA
1 ATGTGATGAA
2019910 ATATGTATGA
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 97 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:2019859 original size:22 final size:22
Alignment explanation
Indices: 2019831--2019906 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
2019821 ACATGCATGT
2019831 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* *
2019853 ATGTGATGAATGTG-AGCAT-G-CA
1 ATGTGAT-AA-G-GCCGAATGGCCA
2019875 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
2019900 ATGTGAT
1 ATGTGAT
2019907 GAAATATGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 16 0.39
23 8 0.20
24 8 0.20
25 9 0.22
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:2019965 original size:48 final size:48
Alignment explanation
Indices: 2019865--2020012 Score: 199
Period size: 48 Copynumber: 3.0 Consensus size: 48
2019855 GTGATGAATG
* *
2019865 TGAG-CATGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAAATATGTA
1 TGAGACATGCATATGTG-G-TAAAGCCGAATGG-CTA-GTG-TGAAATATGTA
*
2019917 TGAGACATGCATATGTGGTAAAGCTGAATGGCTAGTGTGAAATATGTA
1 TGAGACATGCATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
* *
2019965 TGAGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TGAGACATGCATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
2020013 GGCGATGTGC
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
48 56 0.63
49 3 0.03
50 2 0.02
51 11 0.12
52 5 0.06
53 12 0.13
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (48 bp):
TGAGACATGCATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
Found at i:2020267 original size:37 final size:37
Alignment explanation
Indices: 2020159--2020267 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
2020149 GGAAATATAT
*
2020159 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
2020196 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
2020233 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
2020268 CGTCTGAGCT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:2042784 original size:2 final size:2
Alignment explanation
Indices: 2042777--2042817 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2042767 GGCATTGTTT
2042777 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2042818 TTGTAAATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2044348 original size:12 final size:11
Alignment explanation
Indices: 2044311--2044352 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
2044301 CTGAAAAATA
2044311 AAATAAAA-AC
1 AAATAAAAGAC
*
2044321 AAATAACAAGAA
1 AAATAA-AAGAC
2044333 AAATAAAAGTAC
1 AAATAAAAG-AC
2044345 AAATAAAA
1 AAATAAAA
2044353 ATAAAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 6 0.22
11 5 0.19
12 16 0.59
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.12
Consensus pattern (11 bp):
AAATAAAAGAC
Found at i:2044358 original size:24 final size:22
Alignment explanation
Indices: 2044304--2044373 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 22
2044294 CATAATTCTG
2044304 AAAAAT-AAAATAAAAACAAAT
1 AAAAATAAAAATAAAAACAAAT
* *
2044325 AACAAGAAAAATAAAAGTACAAAT
1 AAAAATAAAAATAAAA--ACAAAT
* *
2044349 AAAAATAAAAA-GAAAATAAAT
1 AAAAATAAAAATAAAAACAAAT
2044370 AAAA
1 AAAA
2044374 CACAAAACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
21 13 0.32
22 9 0.22
23 3 0.08
24 15 0.38
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAATAAAAACAAAT
Found at i:2048941 original size:27 final size:27
Alignment explanation
Indices: 2048886--2048943 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
2048876 TTTAAATAGT
** **
2048886 TATAATTCTTTGTCAAAAATCAAGTGA
1 TATAATTCTTTACCAAAAATCAAAAGA
*
2048913 TATAATTCTTTACCAATAATCAAAAGA
1 TATAATTCTTTACCAAAAATCAAAAGA
2048940 TATA
1 TATA
2048944 TTCCAACAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (27 bp):
TATAATTCTTTACCAAAAATCAAAAGA
Found at i:2049826 original size:13 final size:13
Alignment explanation
Indices: 2049808--2049832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2049798 ATTTACAAGA
2049808 TTACATAATCAAT
1 TTACATAATCAAT
2049821 TTACATAATCAA
1 TTACATAATCAA
2049833 ATCCAATCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:2051216 original size:29 final size:29
Alignment explanation
Indices: 2051183--2051241 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2051173 ATCACAAAGA
2051183 AAACATTTCAAATTGCCTATCTTTTTGTT
1 AAACATTTCAAATTGCCTATCTTTTTGTT
2051212 AAACATTTCAAATTGCCTATCTTTTTGTT
1 AAACATTTCAAATTGCCTATCTTTTTGTT
2051241 A
1 A
2051242 GGTTTCTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.47
Consensus pattern (29 bp):
AAACATTTCAAATTGCCTATCTTTTTGTT
Found at i:2054330 original size:4 final size:4
Alignment explanation
Indices: 2054321--2054378 Score: 116
Period size: 4 Copynumber: 14.5 Consensus size: 4
2054311 ATCAGGTAAA
2054321 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
2054369 ATGT ATGT AT
1 ATGT ATGT AT
2054379 ACCTCATGGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2055576 original size:71 final size:71
Alignment explanation
Indices: 2055492--2055635 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 71
2055482 TCATTTACTC
*
2055492 GTTAGTTCGAGTTCAATTCACATTTATTCATTGGCAAGATAATGGTATGGTTGATGCTCTGGCAA
1 GTTAGTTCGAGTTCAATTCACATTTATTCACTGGCAAGATAATGGTATGGTTGATGCTCTGGCAA
2055557 AAGCAG
66 AAGCAG
2055563 GTTAGTTCGAGTTCAATTCACATTTATTCACTGGCAAGATAATGGTATGGTTGATGCTCTGGCAA
1 GTTAGTTCGAGTTCAATTCACATTTATTCACTGGCAAGATAATGGTATGGTTGATGCTCTGGCAA
2055628 AAGCAG
66 AAGCAG
2055634 GT
1 GT
2055636 GTAAGGAGAC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (71 bp):
GTTAGTTCGAGTTCAATTCACATTTATTCACTGGCAAGATAATGGTATGGTTGATGCTCTGGCAA
AAGCAG
Found at i:2056131 original size:23 final size:23
Alignment explanation
Indices: 2056105--2056153 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
2056095 ACGTTAGAAG
*
2056105 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAAGATGAAA
2056128 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAAGATGAAA
2056151 AGT
1 AGT
2056154 TTCACACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.29, T:0.20
Consensus pattern (23 bp):
AGTGAAGAGACTTGAAGATGAAA
Found at i:2056168 original size:42 final size:42
Alignment explanation
Indices: 2056121--2056204 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
2056111 GAGACTTGAA
*
2056121 TATGAAAAGTGAAGAGACTTGAAGATGAAAAGTTTCACACAT
1 TATGAAAAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
* * *
2056163 TATGAAGAGTGAAGAGACTTGAATATGAAAGGTTACACACAT
1 TATGAAAAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
2056205 GCATGAATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.24
Consensus pattern (42 bp):
TATGAAAAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
Found at i:2060622 original size:23 final size:23
Alignment explanation
Indices: 2060596--2060686 Score: 100
Period size: 23 Copynumber: 4.1 Consensus size: 23
2060586 TGAAAAGTTA
2060596 GAAGAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
*
2060619 GAAGAGTGAAGAGACTTGAAGAT
1 GAAGAGTGAAGAGACTTGAATAT
* * * * *
2060642 GAAAAGTTACG-CAC---ATTAT
1 GAAGAGTGAAGAGACTTGAATAT
2060661 GAAGAGTGAAGAGACTTGAATAT
1 GAAGAGTGAAGAGACTTGAATAT
2060684 GAA
1 GAA
2060687 AGGTTACACA
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
19 11 0.21
20 2 0.04
22 2 0.04
23 37 0.71
ACGTcount: A:0.44, C:0.07, G:0.29, T:0.21
Consensus pattern (23 bp):
GAAGAGTGAAGAGACTTGAATAT
Found at i:2060663 original size:42 final size:42
Alignment explanation
Indices: 2060616--2060699 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
2060606 GAGACTTGAA
*
2060616 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACGCACAT
1 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
* *
2060658 TATGAAGAGTGAAGAGACTTGAATATGAAAGGTTACACACAT
1 TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
2060700 GCATGAATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.43, C:0.10, G:0.25, T:0.23
Consensus pattern (42 bp):
TATGAAGAGTGAAGAGACTTGAAGATGAAAAGTTACACACAT
Found at i:2062051 original size:17 final size:18
Alignment explanation
Indices: 2062031--2062067 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2062021 AAATATATTG
*
2062031 TTGC-TTTAAATTTTTAA
1 TTGCATTTAAATTTTGAA
2062048 TTGCATTTAAATTTTGAA
1 TTGCATTTAAATTTTGAA
2062066 TT
1 TT
2062068 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (18 bp):
TTGCATTTAAATTTTGAA
Found at i:2063715 original size:43 final size:43
Alignment explanation
Indices: 2063667--2063765 Score: 153
Period size: 43 Copynumber: 2.3 Consensus size: 43
2063657 TTATATGAAA
** *
2063667 AAACGCCGCTAAAGATCATGGTCTTTACCGGCGCTTCTGACAC
1 AAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTCTGACAC
* *
2063710 AAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTTTGCCAC
1 AAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTCTGACAC
2063753 AAACGCCGCTAAA
1 AAACGCCGCTAAA
2063766 ACATGCTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGACCTTTAACGGCGCTTCTGACAC
Found at i:2064840 original size:47 final size:46
Alignment explanation
Indices: 2064786--2064877 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
2064776 CCCTACATGT
*
2064786 GCCATCATGTCAGATGTAGAAAAGGCTTAATATGTAATGATAAAAAG
1 GCCATCAT-TCAGATGTAGAAAAGGCTTAATATGTAATGACAAAAAG
**** *
2064833 GCCATCATTTTTTTGTGGAAAAGGCTTAATATGTAATGACAAAAA
1 GCCATCATTCAGATGTAGAAAAGGCTTAATATGTAATGACAAAAA
2064878 TGGAAGCAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 31 0.79
47 8 0.21
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (46 bp):
GCCATCATTCAGATGTAGAAAAGGCTTAATATGTAATGACAAAAAG
Found at i:2068111 original size:39 final size:40
Alignment explanation
Indices: 2067976--2068118 Score: 164
Period size: 40 Copynumber: 3.6 Consensus size: 40
2067966 TTTTACGGTG
* * * * * *
2067976 TTTTTAAAATAGAGCTGCTAAAGCTCAATCTATAGCGGC-A
1 TTTTTAAAA-AGCGCCGCTAATGCTCGATCTATAGTGGCGT
***
2068016 TTTTTAAAGAAAAACCGCTAATGCTCGATCTATAGTGGCGT
1 TTTTTAAA-AAGCGCCGCTAATGCTCGATCTATAGTGGCGT
*
2068057 TTTTTAAAAAGCGCCGCTAATGCTCTATCTATAGTGGCGT
1 TTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCGT
2068097 TTTTT-AAAAGCGCCGCTAATGC
1 TTTTTAAAAAGCGCCGCTAATGC
2068119 CTTTTATTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 17 0.19
40 64 0.71
41 9 0.10
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (40 bp):
TTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGTGGCGT
Found at i:2068430 original size:27 final size:27
Alignment explanation
Indices: 2068369--2068437 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
2068359 AAATTAACCA
* * *
2068369 TTCAATACATATAAAGTATACTCATAT
1 TTCAATACATTTAAACTACACTCATAT
*
2068396 TTAAAATA-ATTTAAACTACACTCATAAT
1 TT-CAATACATTTAAACTACACTCAT-AT
*
2068424 TTCAATATATTTAA
1 TTCAATACATTTAA
2068438 TTTATTATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
27 20 0.59
28 14 0.41
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.39
Consensus pattern (27 bp):
TTCAATACATTTAAACTACACTCATAT
Found at i:2068571 original size:14 final size:14
Alignment explanation
Indices: 2068552--2068601 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
2068542 AATCCTAAAT
2068552 CCCTAACTCTTAAC
1 CCCTAACTCTTAAC
2068566 CCCTAACATC-TAAC
1 CCCTAAC-TCTTAAC
*
2068580 CCCTAAACCCTTAAC
1 CCCT-AACTCTTAAC
*
2068595 CCATAAC
1 CCCTAAC
2068602 CCCTAAACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.34, C:0.44, G:0.00, T:0.22
Consensus pattern (14 bp):
CCCTAACTCTTAAC
Found at i:2068588 original size:22 final size:22
Alignment explanation
Indices: 2068563--2068610 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2068553 CCTAACTCTT
*
2068563 AACCCCTAACATC-TAACCCCTA
1 AACCCCTAAC-CCATAACCCCTA
*
2068585 AACCCTTAACCCATAACCCCTA
1 AACCCCTAACCCATAACCCCTA
2068607 AACC
1 AACC
2068611 TTAAATCCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.17
Consensus pattern (22 bp):
AACCCCTAACCCATAACCCCTA
Found at i:2068628 original size:14 final size:15
Alignment explanation
Indices: 2068609--2068647 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
2068599 AACCCCTAAA
2068609 CCTTAAATCC-CAAT
1 CCTTAAATCCACAAT
2068623 CCTTAAA-CCACAAT
1 CCTTAAATCCACAAT
*
2068637 CCCTAAATCCA
1 CCTTAAATCCA
2068648 GACTCCCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 2 0.09
14 17 0.77
15 3 0.14
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.23
Consensus pattern (15 bp):
CCTTAAATCCACAAT
Found at i:2068889 original size:297 final size:299
Alignment explanation
Indices: 2068436--2069034 Score: 845
Period size: 297 Copynumber: 2.0 Consensus size: 299
2068426 CAATATATTT
2068436 AATTTATTATTATCTCTTTTACAATTATATAAGAACATAGTTAAAATATAAATTAAAAAAATAAT
1 AATTTATTATTATCTCTTTTACAATTATATAAGAACATAGTTAAAATATAAATTAAAAAAATAAT
*
2068501 TAATCTAAACCCAAAACCCTAACTCGACCCCTGAATCCCTAAATCCTAAATCCCTAACTCTTAAC
66 TAATCTAAACCCAAAACCCTAACTCGACCCCTGAATCCCTAAATCCTAAATACCTAACTCTTAAC
* *
2068566 CCCTAACATCTAACCCCTAAACCCTTAACCCATAACCCCT-AA-A-CCTTAAATCC-CAATCCTT
131 CCCTAACATCTAACCCCTAAACCCTT-ACCCATAAACCCTAAATACCCTTAAA-CCACAATCCCT
* * *
2068627 AAACCAC-AATCCCTAAATCCAGACTCCCTAAACCTTAAAATA-TGAAAT-CTAAAACCGGTCTT
194 AAACC-CTAATCCCTAAACCCAGACTCCCTAAACATTAAAATAGT-AAATCCT-AAACCGGCCTT
* *
2068689 AAATCTTAAATTAATCATATACCCTAAACTAAAAACCCTAAACA
256 AAATCTTAAATAAATCATATACCCTAAACCAAAAACCCTAAACA
*
2068733 AATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAAATAAT
1 AATTTATTATTATCTCTTTTACAATTATATAAGAACATAGTTAAAATATAAATTAAAAAAATAAT
* * *
2068798 TAATCTAAACTCAAAACCCTAACTCGACCCTTGAATCCTTAAA-CCTTAAATACCTAACTCTTAA
66 TAATCTAAACCCAAAACCCTAACTCGACCCCTGAATCCCTAAATCC-TAAATACCTAACTCTTAA
* * ** * * *
2068862 TCCTTAATGTCTAACCCCTAAACCCTTACCCCTAAACCTTAAATCTTGACCCTTAAACCATAATC
130 CCCCTAACATCTAACCCCTAAACCCTTACCCATAAACCCTAAA---T-ACCCTTAAACCACAATC
* * * *
2068927 CCTAATCCCTAATCCCTAAACCCATACTCCCTAAACATTAAAATAGTAACTCCTAAACTGGCCTT
191 CCTAAACCCTAATCCCTAAACCCAGACTCCCTAAACATTAAAATAGTAAATCCTAAACCGGCCTT
2068992 AAATCTTAAATAAATCATATACCCTAAACCAAAAACCCTAAAC
256 AAATCTTAAATAAATCATATACCCTAAACCAAAAACCCTAAAC
2069035 TATAGTGATA
Statistics
Matches: 267, Mismatches: 23, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
296 12 0.04
297 146 0.55
302 4 0.01
303 102 0.38
304 3 0.01
ACGTcount: A:0.42, C:0.27, G:0.03, T:0.28
Consensus pattern (299 bp):
AATTTATTATTATCTCTTTTACAATTATATAAGAACATAGTTAAAATATAAATTAAAAAAATAAT
TAATCTAAACCCAAAACCCTAACTCGACCCCTGAATCCCTAAATCCTAAATACCTAACTCTTAAC
CCCTAACATCTAACCCCTAAACCCTTACCCATAAACCCTAAATACCCTTAAACCACAATCCCTAA
ACCCTAATCCCTAAACCCAGACTCCCTAAACATTAAAATAGTAAATCCTAAACCGGCCTTAAATC
TTAAATAAATCATATACCCTAAACCAAAAACCCTAAACA
Found at i:2068896 original size:21 final size:21
Alignment explanation
Indices: 2068872--2068962 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 21
2068862 TCCTTAATGT
*
2068872 CTAACCCCTAAACCCTTACCC
1 CTAAACCCTAAACCCTTACCC
* *
2068893 CTAAACCTTAAA-TCTTGACCC
1 CTAAACCCTAAACCCTT-ACCC
* * * * *
2068914 TTAAACCATAATCCCTAATCC
1 CTAAACCCTAAACCCTTACCC
* *
2068935 CTAATCCCTAAACCCATACTCC
1 CTAAACCCTAAACCCTTAC-CC
2068957 CTAAAC
1 CTAAAC
2068963 ATTAAAATAG
Statistics
Matches: 50, Mismatches: 17, Indels: 5
0.69 0.24 0.07
Matches are distributed among these distances:
20 3 0.06
21 38 0.76
22 9 0.18
ACGTcount: A:0.34, C:0.41, G:0.01, T:0.24
Consensus pattern (21 bp):
CTAAACCCTAAACCCTTACCC
Found at i:2068934 original size:7 final size:7
Alignment explanation
Indices: 2068922--2068960 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
2068912 CCTTAAACCA
2068922 TAATCCC
1 TAATCCC
2068929 TAATCCC
1 TAATCCC
2068936 TAATCCC
1 TAATCCC
*
2068943 TAAACCC
1 TAATCCC
*
2068950 ATACTCCC
1 -TAATCCC
2068958 TAA
1 TAA
2068961 ACATTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 22 0.81
8 5 0.19
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26
Consensus pattern (7 bp):
TAATCCC
Found at i:2068959 original size:15 final size:15
Alignment explanation
Indices: 2068915--2068962 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
2068905 TCTTGACCCT
2068915 TAAA-CCATAATCCC
1 TAAACCCATAATCCC
*
2068929 TAATCCC-TAATCCC
1 TAAACCCATAATCCC
*
2068943 TAAACCCATACTCCC
1 TAAACCCATAATCCC
2068958 TAAAC
1 TAAAC
2068963 ATTAAAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.38, C:0.40, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAACCCATAATCCC
Found at i:2069536 original size:124 final size:122
Alignment explanation
Indices: 2069309--2069579 Score: 321
Period size: 124 Copynumber: 2.2 Consensus size: 122
2069299 ATAAAATGTT
* * * * * * *
2069309 TTTAGCGGCACTTTTTCAAAAACGGCGCTAAAGCACCCAGCATTAGCGGCGCTTTTTAAAAACGT
1 TTTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACACACAGCATTAGCGGCGCTTTTCAAAAACGC
* *
2069374 ACTTAAAACACCGAGCATTAGTGGCGCTTTTTCAAAAACGCCACTAAA-ACCCTGAGC
66 ACTTAAAACACCGAGCATTAGCGGCGCATTTTCAAAAACGCCACTAAAGACCCT-AGC
* * *
2069431 TTTAGCGACGCTTTTTAAAAAAACGCCGCTAAAACACAGAGTATTAGCGGCGCTTTTCCAAAAAC
1 TTTAGCGGCGCTTTTT-AAAAAACGCCGCTAAAACACACAGCATTAGCGGCGCTTTT-CAAAAAC
* * ** *
2069496 GCCAC-TAAATCCCCGAGCATTAGCGGCGCATTTTCAAAAACGCTGCTAAAGCCCCTAGC
64 G-CACTTAAAACACCGAGCATTAGCGGCGCATTTTCAAAAACGCCACTAAAGACCCTAGC
* *
2069555 ATTAGCGGCGCTTTTTTAAAAACGC
1 TTTAGCGGCGCTTTTTAAAAAACGC
2069580 TACTAAAGCC
Statistics
Matches: 125, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
122 14 0.11
123 42 0.34
124 63 0.50
125 6 0.05
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.24
Consensus pattern (122 bp):
TTTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACACACAGCATTAGCGGCGCTTTTCAAAAACGC
ACTTAAAACACCGAGCATTAGCGGCGCATTTTCAAAAACGCCACTAAAGACCCTAGC
Found at i:2069587 original size:41 final size:41
Alignment explanation
Indices: 2069310--2069593 Score: 295
Period size: 41 Copynumber: 6.9 Consensus size: 41
2069300 TAAAATGTTT
* * *
2069310 TTAGCGGCACTTTTTCAAAAACGGCGCTAAAGCACCC-AGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCACTAAAGC-CCCGAGCA
* * *
2069351 TTAGCGGCGCTTTTT-AAAAACG-TACTTAAAACACCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCAC-TAAAGCCCCGAGCA
* * * *
2069391 TTAGTGGCGCTTTTTCAAAAACGCCACTAAAACCCTGAGCT
1 TTAGCGGCGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCA
* * * * * * *
2069432 TTAGCGACGCTTTTTAAAAAAACGCCGCTAAAACACAGAGTA
1 TTAGCGGCGCTTTTT-CAAAAACGCCACTAAAGCCCCGAGCA
* *
2069474 TTAGCGGCGCTTTTCCAAAAACGCCACTAAATCCCCGAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCA
* ** *
2069515 TTAGCGGCGCATTTTCAAAAACGCTGCTAAAGCCCCTAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCA
* *
2069556 TTAGCGGCGCTTTTTTAAAAACGCTACTAAAGCCCCGA
1 TTAGCGGCGCTTTTTCAAAAACGCCACTAAAGCCCCGA
2069594 AAGGTAAGAA
Statistics
Matches: 202, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
39 3 0.01
40 30 0.15
41 134 0.66
42 35 0.17
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAACGCCACTAAAGCCCCGAGCA
Found at i:2075219 original size:21 final size:22
Alignment explanation
Indices: 2075193--2075238 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
2075183 AATCTATATA
2075193 TATACATGT-ATATTTATTTTT
1 TATACATGTAATATTTATTTTT
2075214 TATACATGTACATATTTATTTTT
1 TATACATGTA-ATATTTATTTTT
2075237 TA
1 TA
2075239 ACTAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (22 bp):
TATACATGTAATATTTATTTTT
Found at i:2075592 original size:20 final size:19
Alignment explanation
Indices: 2075566--2075616 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2075556 CTCTCTTTTC
*
2075566 TTTATTTATTTTTTAT-TT
1 TTTATTTATTTTTCATATT
2075584 TGTTGATTTATGTTTTCATATT
1 T-TT-ATTTAT-TTTTCATATT
2075606 TTTATTTATTT
1 TTTATTTATTT
2075617 GATACTTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 4 0.14
20 12 0.43
21 8 0.29
22 3 0.11
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.75
Consensus pattern (19 bp):
TTTATTTATTTTTCATATT
Found at i:2076551 original size:15 final size:15
Alignment explanation
Indices: 2076522--2076569 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
2076512 TTCATATTAA
*
2076522 CTTTCAATT-TTCAT
1 CTTTCATTTGTTCAT
2076536 CTTTCATTTGTTCAT
1 CTTTCATTTGTTCAT
2076551 CTCTT-ATTTGTTCAT
1 CT-TTCATTTGTTCAT
2076566 CTTT
1 CTTT
2076570 TTTTTCCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 10 0.32
15 19 0.61
16 2 0.06
ACGTcount: A:0.15, C:0.21, G:0.04, T:0.60
Consensus pattern (15 bp):
CTTTCATTTGTTCAT
Found at i:2088283 original size:17 final size:17
Alignment explanation
Indices: 2088261--2088294 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2088251 GAATGATTGT
2088261 GATTCTGGATAATTGAC
1 GATTCTGGATAATTGAC
2088278 GATTCTGGATAATTGAC
1 GATTCTGGATAATTGAC
2088295 TATAGTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (17 bp):
GATTCTGGATAATTGAC
Found at i:2091686 original size:23 final size:23
Alignment explanation
Indices: 2091660--2091709 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
2091650 TTGACTCAAT
2091660 TAATAATTGGTCATTAAATTTAG
1 TAATAATTGGTCATTAAATTTAG
*
2091683 TAATAATTTGTCATTAAATTTAG
1 TAATAATTGGTCATTAAATTTAG
2091706 TAAT
1 TAAT
2091710 TATGGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (23 bp):
TAATAATTGGTCATTAAATTTAG
Found at i:2093155 original size:13 final size:13
Alignment explanation
Indices: 2093133--2093167 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
2093123 AGTTGTATAT
*
2093133 ATTTATATTTTAA
1 ATTTAAATTTTAA
2093146 ATTTAAA-TTTAA
1 ATTTAAATTTTAA
2093158 ATTTAAATTT
1 ATTTAAATTT
2093168 AATTTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTAAATTTTAA
Found at i:2093173 original size:5 final size:6
Alignment explanation
Indices: 2093141--2093173 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
2093131 ATATTTATAT
2093141 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
2093174 TATTATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:2093182 original size:12 final size:11
Alignment explanation
Indices: 2093145--2093188 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
2093135 TTATATTTTA
2093145 AATTTAAATTT
1 AATTTAAATTT
2093156 AAATTTAAATTT
1 -AATTTAAATTT
*
2093168 AATTTATATTAT
1 AATTTAAATT-T
*
2093180 AATATAAAT
1 AATTTAAAT
2093189 AGTTTTCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:2095912 original size:42 final size:42
Alignment explanation
Indices: 2095852--2096055 Score: 166
Period size: 42 Copynumber: 4.9 Consensus size: 42
2095842 ATACTAAGAT
*
2095852 GTGATTACGTGTAAGACCATGTCTGGGACATTGGCATTC-TTAC
1 GTGATT-CGTGTAAGACCATGTCTGGGACATTGGCA-TCGATAC
* *
2095895 GTGATTCATGTAAGACCATGTATGGGACATTGGCATCGATAC
1 GTGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGATAC
* * ** * * *
2095937 GAGATTCGTGTAAGACCATGTCTAGGATGTTGGCAGCGGTAT
1 GTGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGATAC
** * *
2095979 GAAATTCGTGTAAGACCATAGT-T-GG-CTATTGGCATTGATAT
1 GTGATTCGTGTAAGACCAT-GTCTGGGAC-ATTGGCATCGATAC
* * * *
2096020 GTGATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 GTGAT-TCGTGTAAGACCATGTCTGGGACATTGGCAT
2096056 TGTGCGAGTT
Statistics
Matches: 130, Mismatches: 24, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
41 18 0.14
42 101 0.78
43 11 0.08
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (42 bp):
GTGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGATAC
Found at i:2100587 original size:42 final size:42
Alignment explanation
Indices: 2100527--2100732 Score: 204
Period size: 42 Copynumber: 4.9 Consensus size: 42
2100517 ATACTAAGAT
* *
2100527 GTGATTACGTGTAAGACCATGTCTGGGAAATTGGCATTGTTAC
1 GTGATT-CGTGTAAGACCATGTCTGGGATATTGGCATTGATAC
* * *
2100570 GTGATTCGTGTAAGACCATGTATGGGACATTGGCATCGATAC
1 GTGATTCGTGTAAGACCATGTCTGGGATATTGGCATTGATAC
* * *
2100612 GAT-ATTCGTGTCAGACCATGTCTGGGATGTTGGCATTGATAT
1 G-TGATTCGTGTAAGACCATGTCTGGGATATTGGCATTGATAC
** * * *
2100654 GAAATTCGTTTAAGACCATAGT-T-GGCTATTGGCATTGATAT
1 GTGATTCGTGTAAGACCAT-GTCTGGGATATTGGCATTGATAC
* * *
2100695 GTGATAACATGTAAGACCATATCTGGGATA-TGGCATTG
1 GTGAT-TCGTGTAAGACCATGTCTGGGATATTGGCATTG
2100733 TGCGAGTTAT
Statistics
Matches: 135, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
41 20 0.15
42 102 0.76
43 13 0.10
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.33
Consensus pattern (42 bp):
GTGATTCGTGTAAGACCATGTCTGGGATATTGGCATTGATAC
Found at i:2102393 original size:42 final size:42
Alignment explanation
Indices: 2102304--2102400 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
2102294 GATGTGATTA
* **
2102304 CGTGTAAGACCATGTCTGGGACATTGGCATTCTTACGTGATT
1 CGTGTAAGACCATGTCTGGGACATTGGCATTCGTACGAAATT
** *
2102346 CGTGTAAGACCATGTCTGGGATGTTGGCA-TCGGTATGAAATT
1 CGTGTAAGACCATGTCTGGGACATTGGCATTC-GTACGAAATT
*
2102388 TGTGTAAGACCAT
1 CGTGTAAGACCAT
2102401 AGTTGGCTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 2 0.04
42 45 0.96
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATTCGTACGAAATT
Found at i:2106987 original size:42 final size:42
Alignment explanation
Indices: 2106927--2107116 Score: 215
Period size: 42 Copynumber: 4.5 Consensus size: 42
2106917 GGATACTAAG
*
2106927 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGCT
1 ATGTGATT-CGTGTAAGACCATGTCTGGGACATTGGCATCGAT
*
2106970 ATGTGATTCGTGTAAGACCATGTATGGGACATTGGCATCGAT
1 ATGTGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
* * ** *
2107012 ACGAGATTCGTGTAAGACCATGTCTGGGATGTTGGCATCGGT
1 ATGTGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
** *
2107054 ATGAAATTCGTGTAAGACCATAGT-T-GG-CTATTGGCATTGAT
1 ATGTGATTCGTGTAAGACCAT-GTCTGGGAC-ATTGGCATCGAT
* *
2107095 ATGTGATCACATGTAAGACCAT
1 ATGTGAT-TCGTGTAAGACCAT
2107117 ATCTAGGATA
Statistics
Matches: 126, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
41 16 0.13
42 100 0.79
43 10 0.08
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (42 bp):
ATGTGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
Found at i:2107110 original size:84 final size:84
Alignment explanation
Indices: 2106927--2107132 Score: 240
Period size: 84 Copynumber: 2.5 Consensus size: 84
2106917 GGATACTAAG
* **
2106927 ATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGCTATGTGATTCGTGTAAGACCATG
1 ATGTGA-TACGTGTAAGACCATGTCTGGGATATTGGCATCGCTATGAAATTCGTGTAAGACCATG
2106992 TATGGGACATTGGCATCGAT
65 TATGGGACATTGGCATCGAT
* * * * *
2107012 ACGAGATTCGTGTAAGACCATGTCTGGGATGTTGGCATCGGTATGAAATTCGTGTAAGACCATAG
1 ATGTGATACGTGTAAGACCATGTCTGGGATATTGGCATCGCTATGAAATTCGTGTAAGACCAT-G
*
2107077 T-T-GG-CTATTGGCATTGAT
65 TATGGGAC-ATTGGCATCGAT
* * *
2107095 ATGTGATCACATGTAAGACCATATCTAGGATA-TGGCAT
1 ATGTGAT-ACGTGTAAGACCATGTCTGGGATATTGGCAT
2107133 TGTACGAGTT
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
82 1 0.01
83 24 0.24
84 71 0.70
85 6 0.06
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (84 bp):
ATGTGATACGTGTAAGACCATGTCTGGGATATTGGCATCGCTATGAAATTCGTGTAAGACCATGT
ATGGGACATTGGCATCGAT
Found at i:2111673 original size:42 final size:42
Alignment explanation
Indices: 2111603--2111808 Score: 177
Period size: 42 Copynumber: 4.9 Consensus size: 42
2111593 GGATACTGAG
* * * * * *
2111603 ATGTGATTACGTGAAACACCGTGCCTGGGCCATTGGCATCGTT
1 ATGTGATT-CGTGTAAGACCATGTCTGGGACATTGGCATCGAT
*
2111646 ATGTGATTCGTGAAAGACCATGTCTGGGACATTGGCATCGAT
1 ATGTGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
* * * ** *
2111688 ACGAGATTCGTGTAAGACCTTGTCTGGGATGTTGGCATCGGT
1 ATGTGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
** *
2111730 ATGACATTCGTGTAAGACCATAG-CT-GG-CTATTGGCATTGAT
1 ATGTGATTCGTGTAAGACCAT-GTCTGGGAC-ATTGGCATCGAT
* * *
2111771 ATGTGATATCATGTAAGACCATATCTGGGATA-TGGCAT
1 ATGTGAT-TCGTGTAAGACCATGTCTGGGACATTGGCAT
2111809 TGTGCGAGTT
Statistics
Matches: 133, Mismatches: 24, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
41 16 0.12
42 105 0.79
43 12 0.09
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (42 bp):
ATGTGATTCGTGTAAGACCATGTCTGGGACATTGGCATCGAT
Found at i:2111810 original size:42 final size:42
Alignment explanation
Indices: 2111634--2111808 Score: 183
Period size: 42 Copynumber: 4.2 Consensus size: 42
2111624 TGCCTGGGCC
* * * * *
2111634 ATTGGCATCGTTATGTGATTCGTGAAAGACCATGTCTGGGAC
1 ATTGGCATCGATATGAGATTCGTGTAAGACCATATCTGGGAT
* * *
2111676 ATTGGCATCGATACGAGATTCGTGTAAGACCTTGTCTGGGAT
1 ATTGGCATCGATATGAGATTCGTGTAAGACCATATCTGGGAT
* * * * *
2111718 GTTGGCATCGGTATGACATTCGTGTAAGACCATAGCT-GGCT
1 ATTGGCATCGATATGAGATTCGTGTAAGACCATATCTGGGAT
* * *
2111759 ATTGGCATTGATATGTGATATCATGTAAGACCATATCTGGGAT
1 ATTGGCATCGATATGAGAT-TCGTGTAAGACCATATCTGGGAT
2111802 A-TGGCAT
1 ATTGGCAT
2111809 TGTGCGAGTT
Statistics
Matches: 109, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
41 17 0.16
42 88 0.81
43 4 0.04
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (42 bp):
ATTGGCATCGATATGAGATTCGTGTAAGACCATATCTGGGAT
Found at i:2119390 original size:101 final size:102
Alignment explanation
Indices: 2119275--2119459 Score: 313
Period size: 101 Copynumber: 1.8 Consensus size: 102
2119265 AAAGTGATGG
*
2119275 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-AGA-A-TGATAGGTCGCATGTGTAG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGA-ATAGTGAT-GGTCACATGTGTAG
2119337 TACTATGTGCAGGCTACTATGCGTACCAGATAGCTTCGA
64 TACTATGTGCAGGCTACTATGCGTACCAGATAGCTTCGA
*
2119376 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAGTGATGGTCACATGTGTAGTA
2119441 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
2119460 TGCACCGGTA
Statistics
Matches: 79, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
101 39 0.49
102 36 0.46
103 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCAGATAGCTTCGA
Found at i:2119405 original size:51 final size:49
Alignment explanation
Indices: 2119272--2119457 Score: 223
Period size: 51 Copynumber: 3.7 Consensus size: 49
2119262 GTGAAAGTGA
*
2119272 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATA-G-T
* * * *
2119322 AGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGCT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAG-T
* * *
2119372 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GAATAGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAG-ATAGT
2119422 GATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
2119458 TGTGCACCGG
Statistics
Matches: 116, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
50 44 0.38
51 71 0.61
52 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGT
Found at i:2119461 original size:26 final size:26
Alignment explanation
Indices: 2119381--2119461 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
2119371 TTCGATCACG
2119381 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* *
2119407 CGTGTA-T-CGAATAGTG-ATGG-TCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
2119432 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
2119458 TGTG
1 TGTG
2119462 CACCGGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:2119536 original size:46 final size:43
Alignment explanation
Indices: 2119462--2119561 Score: 121
Period size: 46 Copynumber: 2.2 Consensus size: 43
2119452 CTACTATGTG
*
2119462 CACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCT-AATCC
1 CACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-C
* *
2119505 CACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATC
1 CACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATC
2119551 CACCGTGTATC
1 CACCG-GTATC
2119562 TGTTATTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 6 0.12
44 11 0.22
45 2 0.04
46 26 0.53
47 4 0.08
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (43 bp):
CACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATC
Found at i:2121593 original size:31 final size:31
Alignment explanation
Indices: 2121548--2121610 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
2121538 CCATTGAAGC
*
2121548 ATATAAAATGTGATAGATAATTAGATATTAG
1 ATATAAAATGTGATAGATAATTAGAAATTAG
* *
2121579 ATATAGAATTTGATAGATAATTAGAAATTAG
1 ATATAAAATGTGATAGATAATTAGAAATTAG
2121610 A
1 A
2121611 CGTGGGGAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (31 bp):
ATATAAAATGTGATAGATAATTAGAAATTAG
Found at i:2124479 original size:20 final size:20
Alignment explanation
Indices: 2124454--2124492 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2124444 TATTATGCAT
2124454 TATTA-TTTATAATTTATCAA
1 TATTATTTTA-AATTTATCAA
2124474 TATTATTTTAAATTTATCA
1 TATTATTTTAAATTTATCA
2124493 TTAACTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTATTTTAAATTTATCAA
Found at i:2125880 original size:40 final size:41
Alignment explanation
Indices: 2125802--2125882 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 41
2125792 TGTTACTGAA
* * *
2125802 TACTGCATAACTGCTACTGATACTGTGATGGGCAAAGGCCC
1 TACTGCATAACTGATACTGATACTGAGATGAGCAAAGGCCC
** *
2125843 TACTGCATATTTGATACTG-TACTGAGATGAGCTAAGGCCC
1 TACTGCATAACTGATACTGATACTGAGATGAGCAAAGGCCC
2125883 AAACTGCTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 18 0.53
41 16 0.47
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (41 bp):
TACTGCATAACTGATACTGATACTGAGATGAGCAAAGGCCC
Found at i:2126959 original size:9 final size:9
Alignment explanation
Indices: 2126945--2126975 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2126935 GTTAAACGAA
2126945 TCGAGTTAT
1 TCGAGTTAT
*
2126954 TCGAGTTAA
1 TCGAGTTAT
2126963 TCGAGTTAT
1 TCGAGTTAT
2126972 TCGA
1 TCGA
2126976 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:2127045 original size:9 final size:9
Alignment explanation
Indices: 2127028--2127082 Score: 92
Period size: 9 Copynumber: 6.1 Consensus size: 9
2127018 TGAGTTTTCG
2127028 AATTCGAAT
1 AATTCGAAT
*
2127037 AACTCGAAT
1 AATTCGAAT
2127046 AATTCGAAT
1 AATTCGAAT
*
2127055 AACTCGAAT
1 AATTCGAAT
2127064 AATTCGAAT
1 AATTCGAAT
2127073 AATTCGAAT
1 AATTCGAAT
2127082 A
1 A
2127083 TCAAACTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2130684 original size:6 final size:6
Alignment explanation
Indices: 2130675--2130702 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2130665 TTATATTTTG
2130675 AATTTA AATTTA AATTTA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATT
2130703 ATATTATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:2134548 original size:12 final size:12
Alignment explanation
Indices: 2134531--2134556 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2134521 ATATTTTGAG
2134531 TTTAAATTTAAA
1 TTTAAATTTAAA
2134543 TTTAAATTTAAA
1 TTTAAATTTAAA
2134555 TT
1 TT
2134557 ATATTATAAT
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:0.00, T:0.54
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:2138754 original size:6 final size:6
Alignment explanation
Indices: 2138745--2138770 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2138735 ATATTTTGAG
2138745 TTTAAA TTTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
2138771 ATATTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:2140597 original size:28 final size:28
Alignment explanation
Indices: 2140555--2140676 Score: 156
Period size: 28 Copynumber: 4.4 Consensus size: 28
2140545 TATTCAGTAG
*
2140555 TAGT-ACAGTGTGGGCCTTAGCCCGATA
1 TAGTAACAGTGTGGGCCTTAGCCCAATA
* * *
2140582 TAGTAATAATATGGGCCTTAGCCCAATA
1 TAGTAACAGTGTGGGCCTTAGCCCAATA
* *
2140610 TAGTAACAGTGTGGACCTTAGCCCAAAA
1 TAGTAACAGTGTGGGCCTTAGCCCAATA
*
2140638 TAGTAACAGTGTGGGGCTTAGCCCAATA
1 TAGTAACAGTGTGGGCCTTAGCCCAATA
* *
2140666 CAGAAACAGTG
1 TAGTAACAGTG
2140677 CAGTGCAATA
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 4 0.05
28 76 0.95
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (28 bp):
TAGTAACAGTGTGGGCCTTAGCCCAATA
Found at i:2140632 original size:56 final size:56
Alignment explanation
Indices: 2140522--2140676 Score: 166
Period size: 56 Copynumber: 2.7 Consensus size: 56
2140512 ATACAACATG
* * * * * *
2140522 TAGTAATAGTATGGGCCTGAGCCTATTCAGTAGTAGTACAGTGTGGGCCTTAGCCCGATA
1 TAGTAATAGTATGGGCCTTAGCCCAAT-A-TAGTA--ACAGTGTGGACCTTAGCCCAAAA
*
2140582 TAGTAATAATATGGGCCTTAGCCCAATATAGTAACAGTGTGGACCTTAGCCCAAAA
1 TAGTAATAGTATGGGCCTTAGCCCAATATAGTAACAGTGTGGACCTTAGCCCAAAA
* * * * *
2140638 TAGTAACAGTGTGGGGCTTAGCCCAATACAGAAACAGTG
1 TAGTAATAGTATGGGCCTTAGCCCAATATAGTAACAGTG
2140677 CAGTGCAATA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
56 53 0.65
58 5 0.06
59 1 0.01
60 23 0.28
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (56 bp):
TAGTAATAGTATGGGCCTTAGCCCAATATAGTAACAGTGTGGACCTTAGCCCAAAA
Found at i:2140856 original size:26 final size:26
Alignment explanation
Indices: 2140778--2140857 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 26
2140768 AACACACCAA
* *
2140778 TATCGCAGCAAAGCTGCCAATAATAG
1 TATCGCATCAAAGCTGCCAATAACAG
* * * * *
2140804 CATCGTAGT-ACAGCTGCCAGTATCAG
1 TATCGCA-TCAAAGCTGCCAATAACAG
*
2140830 TATCGCATCAAAGCTACCAATAACAG
1 TATCGCATCAAAGCTGCCAATAACAG
2140856 TA
1 TA
2140858 CATGTGGCAA
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
25 1 0.03
26 38 0.97
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (26 bp):
TATCGCATCAAAGCTGCCAATAACAG
Found at i:2141111 original size:27 final size:27
Alignment explanation
Indices: 2141090--2141617 Score: 461
Period size: 27 Copynumber: 19.8 Consensus size: 27
2141080 AGGGGTATAA
*
2141090 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTAATT
** * *
2141117 TGGTCATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTAATT
* * * *
2141144 TAGTTATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGTAATT
* *
2141171 C-GATCATTTTACCCTATGAGGGTATTT
1 CAG-TCATTTTACCCTATGGGGGTAATT
* *
2141198 C-GATCATTTTACCCTATGAGGGTATTT
1 CAG-TCATTTTACCCTATGGGGGTAATT
* * *
2141225 CGGTCATTTTACTCTATGGAGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATT
* * *
2141252 CAGTCATTTTACCTTGTGAGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATT
*
2141279 TAGTCATTTTACCCTATGGGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATT
* * * *
2141306 CGGTCATTTTTCTCTGTGGGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATT
* ***
2141333 CAGTCATTTTACCCTGTAAAGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATT
*
2141360 CTA-TCATTTTACCCTGTGGGGGTAATT
1 C-AGTCATTTTACCCTATGGGGGTAATT
* * * *
2141387 CAATCATTTTATCCTGTGGGGGTAATA
1 CAGTCATTTTACCCTATGGGGGTAATT
*
2141414 C-GATCATTTTATCCTATGGGGGTAATT
1 CAG-TCATTTTACCCTATGGGGGTAATT
* * *
2141441 CGGTCATTTTACTCTGTGGGGGGT-A--
1 CAGTCATTTTACCCTAT-GGGGGTAATT
* * *
2141466 -A---ATTTTATCTTGTGGGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATT
* *
2141489 CGGTCATTTTACCCTGTGGGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATT
* *
2141516 C-GATCATTTTACCCTGTGAGGGTAATT
1 CAG-TCATTTTACCCTATGGGGGTAATT
* * *
2141543 CGGTTATTTTACCCTTTGGGGGTAATT
1 CAGTCATTTTACCCTATGGGGGTAATT
*
2141570 C-GATCATTTTACCCTGTGGGGGTAATT
1 CAG-TCATTTTACCCTATGGGGGTAATT
*
2141597 CGGTCATTTTACCCTATGGGG
1 CAGTCATTTTACCCTATGGGG
2141618 CAATTCGATC
Statistics
Matches: 424, Mismatches: 59, Indels: 36
0.82 0.11 0.07
Matches are distributed among these distances:
20 6 0.01
21 10 0.02
26 4 0.01
27 393 0.93
28 11 0.03
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGGGGGTAATT
Found at i:2146829 original size:6 final size:6
Alignment explanation
Indices: 2146818--2146842 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2146808 AATGATAGTG
2146818 CAGCAC CAGCAC CAGCAC CAGCAC C
1 CAGCAC CAGCAC CAGCAC CAGCAC C
2146843 CTCTAATGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CAGCAC
Found at i:2147601 original size:20 final size:20
Alignment explanation
Indices: 2147576--2147629 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2147566 ATATTTTACG
*
2147576 TAACATATCATATCG-ATACA
1 TAACATAGCATATCGAAT-CA
*
2147596 TAACATGGCATATCGAATCA
1 TAACATAGCATATCGAATCA
2147616 TAACATAGCATATC
1 TAACATAGCATATC
2147630 TTATCAGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (20 bp):
TAACATAGCATATCGAATCA
Found at i:2160068 original size:18 final size:17
Alignment explanation
Indices: 2160048--2160113 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 17
2160038 AACCCGAATG
2160048 TTATATTAATTATATAT
1 TTATATTAATTATATAT
*
2160065 GTTAAATAATAATTGTATATAT
1 -TT--ATATTAA-T-TATATAT
2160087 TTATATTTATATT-TATAT
1 TTATA-TTA-ATTATATAT
2160105 TTATATTAA
1 TTATATTAA
2160114 ATCACTAATC
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
16 1 0.03
17 3 0.08
18 12 0.30
19 4 0.10
20 9 0.22
21 4 0.10
22 7 0.17
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTATATTAATTATATAT
Found at i:2160093 original size:6 final size:6
Alignment explanation
Indices: 2160082--2160111 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2160072 AATAATTGTA
2160082 TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT
2160112 AAATCACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:2164385 original size:39 final size:39
Alignment explanation
Indices: 2164326--2164405 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
2164316 CTGTCAGTCA
2164326 TGTATTTAGCCGGGAGTGCTTATAGTTATGATCACATAT
1 TGTATTTAGCCGGGAGTGCTTATAGTTATGATCACATAT
* * *
2164365 TGTATTTAGCCGGGATTGCTTATAGTTATTATCAGATAT
1 TGTATTTAGCCGGGAGTGCTTATAGTTATGATCACATAT
2164404 TG
1 TG
2164406 AATTAAGCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (39 bp):
TGTATTTAGCCGGGAGTGCTTATAGTTATGATCACATAT
Found at i:2169691 original size:35 final size:35
Alignment explanation
Indices: 2169602--2169945 Score: 332
Period size: 35 Copynumber: 9.5 Consensus size: 35
2169592 ACCTAAACAT
* * *
2169602 GTCTGTCCCAACCTTTTTTAAAGGTTGCTTTAGACAAT
1 GTCTATCCCAACC-TTTTT-AAGGTTGCCTTAGAC-AG
* * *
2169640 GTCTATCCCAACCTTTTTAAGTTTGCCTTATACGG
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAG
* * * *
2169675 GTCTATCCAAATCTTTTTTAAAGGTTGCTTTACACAAG
1 GTCTATCCCAA-CCTTTTT-AAGGTTGCCTTAGAC-AG
2169713 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAG
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAG
* *
2169748 GTCTATCCCAACCTTTTTTAAAGGTTGCCTTTGATAAG
1 GTCTATCCCAACC-TTTTT-AAGGTTGCCTTAGA-CAG
* * *
2169786 GTCTATCCCGACTTTTTTAAGGTTGCCTTAGACAT
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAG
* * *
2169821 GTCTATCCTAACCCTTTTAAGGTTGCCTTAGA-TG
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAG
* *
2169855 AGTCTATCCCAACCTTTTTTAAAGGTTGACTTAGATAAG
1 -GTCTATCCCAACC-TTTTT-AAGGTTGCCTTAGA-CAG
* * *
2169894 GCCTATCCCAACCTTTTTAAGGTTGACTTAGA-TG
1 GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAG
*
2169928 AGTTTATCCCAACCTTTT
1 -GTCTATCCCAACCTTTT
2169946 GCAAATGTTG
Statistics
Matches: 257, Mismatches: 37, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
34 1 0.00
35 81 0.32
36 67 0.26
37 59 0.23
38 48 0.19
39 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (35 bp):
GTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAG
Found at i:2169733 original size:73 final size:72
Alignment explanation
Indices: 2169609--2169945 Score: 344
Period size: 73 Copynumber: 4.7 Consensus size: 72
2169599 CATGTCTGTC
* * * * *
2169609 CCAACCTTTTTTAAAGGTTGCTTTAGACAATGTCTATCCCAACCTTTTTAAGTTTGCCTTATACG
1 CCAAACTTTTTTAAAGGTTGCTTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACA
2169674 GGTCTAT
66 GGTCTAT
*
2169681 CCAAATCTTTTTTAAAGGTTGCTTTACACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGAC
1 CCAAA-CTTTTTTAAAGGTTGCTTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGAC
2169746 AGGTCTAT
65 AGGTCTAT
* * * *
2169754 CCCAACCTTTTTTAAAGGTTGCCTTT-GATAAGGTCTATCCCGACTTTTTTAAGGTTGCCTTAGA
1 -CCAAACTTTTTTAAAGGTTG-CTTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGA
*
2169818 CATGTCTAT
64 CAGGTCTAT
* ** * ** *
2169827 CCTAACCCTTTT-AAGGTTGCCTTAGATGA-GTCTATCCCAACCTTTTTTAAAGGTTGACTTAGA
1 CCAAACTTTTTTAAAGGTTGCTTTAGACAAGGTCTATCCCAACC-TTTTT-AAGGTTGCCTTAGA
* *
2169890 TAAGGCCTAT
64 -CAGGTCTAT
* * ** *
2169900 CCCAACCTTTTT-AAGGTTGAC-TTAGATGA-GTTTATCCCAACCTTTT
1 CCAAACTTTTTTAAAGGTTG-CTTTAGACAAGGTCTATCCCAACCTTTT
2169946 GCAAATGTTG
Statistics
Matches: 230, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
70 14 0.06
71 16 0.07
72 29 0.13
73 162 0.70
74 9 0.04
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (72 bp):
CCAAACTTTTTTAAAGGTTGCTTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACA
GGTCTAT
Found at i:2169847 original size:108 final size:108
Alignment explanation
Indices: 2169598--2169945 Score: 393
Period size: 108 Copynumber: 3.2 Consensus size: 108
2169588 ATTTACCTAA
* * *
2169598 ACATGTCTGTCCCAACCTTTTTTAAAGGTTGCTTTAGACAATGTCTATCCCAACC-TTTTT-AAG
1 ACATGTCTATCCCAACC-TTTTT-AAGGTTGCCTTAGAC-AGGTCTATCCCAACCTTTTTTAAAG
* * * * *
2169661 TTTGCC-TT-ATACGGGTCTATCCAAATCTTTTTTAAAGGTTGCTTTAC
63 GTTGCCTTTGATA-AGGTCTATCCCAA-CTTTTTT-AAGGTTGCCTTAG
*
2169708 ACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACCTTTTTTAAAGGT
1 AC-ATGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACCTTTTTTAAAGGT
*
2169773 TGCCTTTGATAAGGTCTATCCCGACTTTTTTAAGGTTGCCTTAG
65 TGCCTTTGATAAGGTCTATCCCAACTTTTTTAAGGTTGCCTTAG
* * *
2169817 ACATGTCTATCCTAACCCTTTTAAGGTTGCCTTAGA-TGAGTCTATCCCAACCTTTTTTAAAGGT
1 ACATGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAG-GTCTATCCCAACCTTTTTTAAAGGT
* * * * *
2169881 TGACTTAGATAAGGCCTATCCCAACCTTTTTAAGGTTGACTTAG
65 TGCCTTTGATAAGGTCTATCCCAACTTTTTTAAGGTTGCCTTAG
* *
2169925 ATGA-GTTTATCCCAACCTTTT
1 A-CATGTCTATCCCAACCTTTT
2169946 GCAAATGTTG
Statistics
Matches: 207, Mismatches: 24, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
107 1 0.00
108 123 0.59
109 33 0.16
110 22 0.11
111 25 0.12
112 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (108 bp):
ACATGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACAGGTCTATCCCAACCTTTTTTAAAGGTT
GCCTTTGATAAGGTCTATCCCAACTTTTTTAAGGTTGCCTTAG
Found at i:2169942 original size:181 final size:183
Alignment explanation
Indices: 2169614--2169945 Score: 483
Period size: 181 Copynumber: 1.8 Consensus size: 183
2169604 CTGTCCCAAC
* * * * *
2169614 CTTTTTTAAAGGTTGCTTTAGACAATGTCTATCCCAACCTTTTTAAGTTTGCCTTATACGGGTCT
1 CTTTTTTAAAGGTTGCCTTAGACAATGTCTATCCCAACCCTTTTAAGGTTGCCTTAGACGAGTCT
* * *
2169679 ATCCAAATCTTTTTTAAAGGTTGCTTTACACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAG
66 ATCCAAACCTTTTTTAAAGGTTGCTTTACACAAGGCCTATCCCAACCTTTTTAAGGTTGACTTAG
2169744 ACAGGTCTATCCCAACCTTTTTTAAAGGTTGCCTTTGATAAGGTCTATCCCGA
131 ACAGGTCTATCCCAACCTTTTTTAAAGGTTGCCTTTGATAAGGTCTATCCCGA
* *
2169797 CTTTTTT-AAGGTTGCCTTAGAC-ATGTCTATCCTAACCCTTTTAAGGTTGCCTTAGATGAGTCT
1 CTTTTTTAAAGGTTGCCTTAGACAATGTCTATCCCAACCCTTTTAAGGTTGCCTTAGACGAGTCT
* * *
2169860 ATCCCAACCTTTTTTAAAGGTTGAC-TTAGATAAGGCCTATCCCAACCTTTTTAAGGTTGACTTA
66 ATCCAAACCTTTTTTAAAGGTTG-CTTTACACAAGGCCTATCCCAACCTTTTTAAGGTTGACTTA
* *
2169924 GA-TGAGTTTATCCCAACCTTTT
130 GACAG-GTCTATCCCAACCTTTT
2169946 GCAAATGTTG
Statistics
Matches: 132, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
180 1 0.01
181 109 0.83
182 15 0.11
183 7 0.05
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (183 bp):
CTTTTTTAAAGGTTGCCTTAGACAATGTCTATCCCAACCCTTTTAAGGTTGCCTTAGACGAGTCT
ATCCAAACCTTTTTTAAAGGTTGCTTTACACAAGGCCTATCCCAACCTTTTTAAGGTTGACTTAG
ACAGGTCTATCCCAACCTTTTTTAAAGGTTGCCTTTGATAAGGTCTATCCCGA
Found at i:2170085 original size:12 final size:12
Alignment explanation
Indices: 2170068--2170092 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2170058 TGATGTTTTC
2170068 AGAAGCATCGGG
1 AGAAGCATCGGG
2170080 AGAAGCATCGGG
1 AGAAGCATCGGG
2170092 A
1 A
2170093 TGACCTATGC
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:0.16, G:0.40, T:0.08
Consensus pattern (12 bp):
AGAAGCATCGGG
Found at i:2172081 original size:59 final size:59
Alignment explanation
Indices: 2172009--2172125 Score: 225
Period size: 59 Copynumber: 2.0 Consensus size: 59
2171999 TGAATCATAT
*
2172009 AAGTTTAATTCTTGATTATTTCTTCTAATTTTTGTGGTTTTGATACTTTTACAATTAGA
1 AAGTTTAATTCTTGATTATTTCTTCTAATTTTAGTGGTTTTGATACTTTTACAATTAGA
2172068 AAGTTTAATTCTTGATTATTTCTTCTAATTTTAGTGGTTTTGATACTTTTACAATTAG
1 AAGTTTAATTCTTGATTATTTCTTCTAATTTTAGTGGTTTTGATACTTTTACAATTAG
2172126 GTCCAACTAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.26, C:0.09, G:0.12, T:0.54
Consensus pattern (59 bp):
AAGTTTAATTCTTGATTATTTCTTCTAATTTTAGTGGTTTTGATACTTTTACAATTAGA
Found at i:2172835 original size:46 final size:45
Alignment explanation
Indices: 2172782--2173015 Score: 240
Period size: 36 Copynumber: 5.6 Consensus size: 45
2172772 TTTGAGTACT
* *
2172782 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
* *
2172828 TCTGATCAAGTGATAGAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
2172864 TCTGATCAAGAT-ACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAG-TGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
2172910 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
2172946 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
2172991 TCTGATC-AGGGACAAA-TGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
2173016 ATCATACGTA
Statistics
Matches: 160, Mismatches: 7, Indels: 45
0.75 0.03 0.21
Matches are distributed among these distances:
36 59 0.37
37 5 0.03
40 4 0.03
42 4 0.03
43 9 0.06
44 9 0.06
45 21 0.13
46 49 0.31
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:2172885 original size:82 final size:82
Alignment explanation
Indices: 2172782--2173015 Score: 377
Period size: 82 Copynumber: 2.9 Consensus size: 82
2172772 TTTGAGTACT
* * * *
2172782 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGATAGAGT
1 TCTGATCAAGATACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
2172847 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
2172864 TCTGATCAAGATACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGATACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
2172929 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
* *
2172946 TCTGATCAAG-TGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATC-AGGGACAAA-
1 TCTGATCAAGAT-ACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAG
2173007 TGATAAGTG
65 TGATAAGTG
2173016 ATCATACGTA
Statistics
Matches: 145, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
79 9 0.06
80 7 0.05
81 21 0.14
82 108 0.74
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGATACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:2180555 original size:36 final size:36
Alignment explanation
Indices: 2180485--2180636 Score: 191
Period size: 36 Copynumber: 4.0 Consensus size: 36
2180475 GGTAGCTTTA
2180485 GCTACACTTATCTGAT-AAGTGAC-AAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
*
2180519 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGACAAAGTGAT-A-----AG---T
*
2180564 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
2180600 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
2180636 G
1 G
2180637 GTAGCTTAGC
Statistics
Matches: 103, Mismatches: 4, Indels: 20
0.81 0.03 0.16
Matches are distributed among these distances:
34 16 0.16
35 6 0.06
36 44 0.43
37 1 0.01
39 2 0.02
42 2 0.02
44 1 0.01
45 31 0.30
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
Found at i:2180573 original size:45 final size:45
Alignment explanation
Indices: 2180518--2180678 Score: 209
Period size: 45 Copynumber: 3.8 Consensus size: 45
2180508 AAGTGATAAG
*
2180518 TGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTT
1 TGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTT
*
2180563 TGCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---
1 TGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTT
2180599 TGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTT
1 TGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTT
* *
2180644 AGCTACACTTATCTGATC-AGGGACAAA-TGATAAGT
1 TGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
2180679 TATCATACGT
Statistics
Matches: 102, Mismatches: 5, Indels: 20
0.80 0.04 0.16
Matches are distributed among these distances:
36 32 0.31
37 1 0.01
39 2 0.02
42 2 0.02
43 8 0.08
44 9 0.09
45 48 0.47
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (45 bp):
TGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTT
Found at i:2180625 original size:81 final size:81
Alignment explanation
Indices: 2180449--2180678 Score: 369
Period size: 81 Copynumber: 2.9 Consensus size: 81
2180439 TTGGAGTACT
* *
2180449 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT-AAGTG-ACAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT-GCTACACTTATCTGATCAAGTGAAAAAGT
2180512 GATAAGTGCTACACTTA
65 GATAAGTGCTACACTTA
2180529 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTGCTACACTTATCTGATCAAGTGAAAAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTGCTACACTTATCTGATCAAGTGAAAAAGTG
2180594 ATAAGTGCTACACTTA
66 ATAAGTGCTACACTTA
* * * *
2180610 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATC-AGGGACAAA-TG
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTGCTACACTTATCTGATCAAGTGAAAAAGTG
2180673 ATAAGT
66 ATAAGT
2180679 TATCATACGT
Statistics
Matches: 142, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
79 24 0.17
80 46 0.32
81 72 0.51
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (81 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTGCTACACTTATCTGATCAAGTGAAAAAGTG
ATAAGTGCTACACTTA
Found at i:2182548 original size:23 final size:24
Alignment explanation
Indices: 2182521--2182567 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2182511 TGCATAATAT
2182521 TTAAATATT-TAAAAATTTGATTA
1 TTAAATATTCTAAAAATTTGATTA
**
2182544 TTAAATATTCTTGAAATTTGATTA
1 TTAAATATTCTAAAAATTTGATTA
2182568 AAATTATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (24 bp):
TTAAATATTCTAAAAATTTGATTA
Found at i:2184650 original size:3 final size:3
Alignment explanation
Indices: 2184642--2184668 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2184632 GATGAGATGT
2184642 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2184669 ACATTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2187543 original size:23 final size:23
Alignment explanation
Indices: 2187516--2187613 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
2187506 AGTGTTATTG
2187516 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2187539 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2187562 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2187584 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2187607 ATCAGTG
1 ATCAGTG
2187614 TGGCACTTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
22 21 0.30
23 50 0.70
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2187582 original size:45 final size:45
Alignment explanation
Indices: 2187518--2187606 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
2187508 TGTTATTGAT
*
2187518 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
2187563 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
2187607 ATCAGTGTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.30
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:2190925 original size:23 final size:23
Alignment explanation
Indices: 2190897--2190942 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2190887 AGAAATTTAC
* *
2190897 TTTTTACTTTTAGATATGGTTTT
1 TTTTTACTATTAGATACGGTTTT
*
2190920 TTTTTACTATTAGTTACGGTTTT
1 TTTTTACTATTAGATACGGTTTT
2190943 GTTTGCCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.17, C:0.07, G:0.13, T:0.63
Consensus pattern (23 bp):
TTTTTACTATTAGATACGGTTTT
Found at i:2193155 original size:39 final size:39
Alignment explanation
Indices: 2193087--2193200 Score: 186
Period size: 39 Copynumber: 3.1 Consensus size: 39
2193077 GAAAGAGTAC
2193087 TGAGGAAGATGTGGTGGTATCAATC------AAGTGTTG
1 TGAGGAAGATGTGGTGGTATCAATCAGGGTGAAGTGTTG
2193120 TGAGGAAGATGTGGTGGTATCAATCAGGGTGAAGTGTTG
1 TGAGGAAGATGTGGTGGTATCAATCAGGGTGAAGTGTTG
2193159 TGAGGAAGATGTGGTGGTATCAATCAGGGTGAAGTGTTG
1 TGAGGAAGATGTGGTGGTATCAATCAGGGTGAAGTGTTG
2193198 TGA
1 TGA
2193201 AGAGTCGGAA
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
33 25 0.33
39 50 0.67
ACGTcount: A:0.26, C:0.05, G:0.39, T:0.29
Consensus pattern (39 bp):
TGAGGAAGATGTGGTGGTATCAATCAGGGTGAAGTGTTG
Found at i:2193753 original size:23 final size:22
Alignment explanation
Indices: 2193711--2193753 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
2193701 ATTTTAACGA
*
2193711 AAATTTAATTATTAAAATATAT
1 AAATTTAATTATAAAAATATAT
2193733 AAATATTAA-TATAAAAGATAT
1 AAAT-TTAATTATAAAA-ATAT
2193754 TCTTTTGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATTTAATTATAAAAATATAT
Found at i:2196958 original size:18 final size:18
Alignment explanation
Indices: 2196898--2196958 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
2196888 TTTATATTAA
* *
2196898 AAAATAAATAGTAATAAT
1 AAAAGAAATAATAATAAT
2196916 AAATA-AAATAA-AATAA-
1 AAA-AGAAATAATAATAAT
2196932 AAAAGGAAATAATAATAAT
1 AAAA-GAAATAATAATAAT
2196951 AAAAGAAA
1 AAAAGAAA
2196959 AGAAAAGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
15 1 0.03
16 3 0.08
17 11 0.30
18 17 0.46
19 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (18 bp):
AAAAGAAATAATAATAAT
Found at i:2215917 original size:19 final size:20
Alignment explanation
Indices: 2215893--2215941 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
2215883 AAAATCATAT
2215893 GTATCGATACCC-TAGTA-AA
1 GTATCGATACCCTTA-TATAA
*
2215912 GTATCGGTACCCTTATATAA
1 GTATCGATACCCTTATATAA
2215932 GTATCGATAC
1 GTATCGATAC
2215942 TTTAGTCCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (20 bp):
GTATCGATACCCTTATATAA
Found at i:2216982 original size:16 final size:16
Alignment explanation
Indices: 2216936--2217016 Score: 69
Period size: 16 Copynumber: 4.9 Consensus size: 16
2216926 CAAGATAAAC
2216936 ATTAAATTTAATA--T
1 ATTAAATTTAATATTT
2216950 ATTAAATTAATAGAATATTT
1 ATTAAATT--T--AATATTT
*
2216970 ATTAAATTTAATATTAA
1 ATTAAATTTAATATT-T
**
2216987 ATT-AATAGAATATTT
1 ATTAAATTTAATATTT
2217002 ATTAAATTTAATATT
1 ATTAAATTTAATATT
2217017 AAATTAATAA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
14 8 0.15
15 3 0.06
16 25 0.47
17 3 0.06
18 5 0.09
20 9 0.17
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
ATTAAATTTAATATTT
Found at i:2216986 original size:12 final size:12
Alignment explanation
Indices: 2216969--2217025 Score: 54
Period size: 11 Copynumber: 5.2 Consensus size: 12
2216959 ATAGAATATT
2216969 TATTAAATTTAA
1 TATTAAATTTAA
2216981 TATTAAA-TTAA
1 TATTAAATTTAA
*
2216992 TA--GAATATT--
1 TATTAAAT-TTAA
2217001 TATTAAATTTAA
1 TATTAAATTTAA
2217013 TATTAAA-TTAA
1 TATTAAATTTAA
2217024 TA
1 TA
2217026 AAATACTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
9 4 0.11
10 2 0.05
11 17 0.46
12 14 0.38
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (12 bp):
TATTAAATTTAA
Found at i:2216989 original size:32 final size:32
Alignment explanation
Indices: 2216936--2217030 Score: 163
Period size: 32 Copynumber: 2.9 Consensus size: 32
2216926 CAAGATAAAC
2216936 ATTAAATTTAATATATTAAATTAATAGAATATTT
1 ATTAAATTT-A-ATATTAAATTAATAGAATATTT
2216970 ATTAAATTTAATATTAAATTAATAGAATATTT
1 ATTAAATTTAATATTAAATTAATAGAATATTT
*
2217002 ATTAAATTTAATATTAAATTAATAAAATA
1 ATTAAATTTAATATTAAATTAATAGAATA
2217031 CTATTAGGAT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 50 0.83
33 1 0.02
34 9 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (32 bp):
ATTAAATTTAATATTAAATTAATAGAATATTT
Found at i:2216993 original size:45 final size:48
Alignment explanation
Indices: 2216885--2216993 Score: 140
Period size: 49 Copynumber: 2.4 Consensus size: 48
2216875 ACATAATCAC
2216885 TTTAATATTAAATT--T-TATTAAATTAATAGAATATTTATTTACAAG
1 TTTAATATTAAATTAATATATTAAATTAATAGAATATTTATTTACAAG
* * *
2216930 ATAAACATTAAATTTAATATATTAAATTAATAGAATATTTA-TTA-AA-
1 TTTAATATTAAA-TTAATATATTAAATTAATAGAATATTTATTTACAAG
2216976 TTTAATATTAAATTAATA
1 TTTAATATTAAATTAATA
2216994 GAATATTTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
45 15 0.28
46 11 0.20
47 2 0.04
48 4 0.07
49 22 0.41
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.46
Consensus pattern (48 bp):
TTTAATATTAAATTAATATATTAAATTAATAGAATATTTATTTACAAG
Found at i:2217030 original size:16 final size:16
Alignment explanation
Indices: 2216936--2217030 Score: 63
Period size: 16 Copynumber: 6.1 Consensus size: 16
2216926 CAAGATAAAC
*
2216936 ATTAAATT--TAATAT
1 ATTAAATTAATAAAAT
*
2216950 ATTAAATTAATAGAAT
1 ATTAAATTAATAAAAT
* **
2216966 ATT-TATTAAATTTAAT
1 ATTAAATT-AATAAAAT
*
2216982 ATTAAATTAATAGAAT
1 ATTAAATTAATAAAAT
* **
2216998 ATT-TATTAAATTTAAT
1 ATTAAATT-AATAAAAT
2217014 ATTAAATTAATAAAAT
1 ATTAAATTAATAAAAT
2217030 A
1 A
2217031 CTATTAGGAT
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
14 8 0.13
15 6 0.10
16 41 0.67
17 6 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
ATTAAATTAATAAAAT
Found at i:2218356 original size:16 final size:16
Alignment explanation
Indices: 2218335--2218366 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2218325 ACCATGAATG
*
2218335 TCACAAATGGATTAAT
1 TCACAAACGGATTAAT
2218351 TCACAAACGGATTAAT
1 TCACAAACGGATTAAT
2218367 AATTAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (16 bp):
TCACAAACGGATTAAT
Found at i:2218933 original size:15 final size:17
Alignment explanation
Indices: 2218901--2218933 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2218891 AGGTGATCTG
2218901 ACCGACACATTCTACAA
1 ACCGACACATTCTACAA
2218918 ACCGACA-ATT-TACAA
1 ACCGACACATTCTACAA
2218933 A
1 A
2218934 GAAAAGGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.45, C:0.30, G:0.06, T:0.18
Consensus pattern (17 bp):
ACCGACACATTCTACAA
Found at i:2220865 original size:44 final size:45
Alignment explanation
Indices: 2220795--2220884 Score: 164
Period size: 44 Copynumber: 2.0 Consensus size: 45
2220785 TTGATGTGAT
*
2220795 TGAATTTTCATAAAAGGAATATGTAATGGTTACCATGAGATAAAA
1 TGAATTTTCATAAAAGGAAGATGTAATGGTTACCATGAGATAAAA
2220840 TGAATTTTCAT-AAAGGAAGATGTAATGGTTACCATGAGATAAAA
1 TGAATTTTCATAAAAGGAAGATGTAATGGTTACCATGAGATAAAA
2220884 T
1 T
2220885 AGGATCATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 33 0.75
45 11 0.25
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (45 bp):
TGAATTTTCATAAAAGGAAGATGTAATGGTTACCATGAGATAAAA
Found at i:2222501 original size:20 final size:20
Alignment explanation
Indices: 2222473--2222510 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2222463 ACTAGAACTA
2222473 TGTGATCTGAGCTCATGAGT
1 TGTGATCTGAGCTCATGAGT
* *
2222493 TGTGGTCTGAGTTCATGA
1 TGTGATCTGAGCTCATGA
2222511 ATATGTGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.37
Consensus pattern (20 bp):
TGTGATCTGAGCTCATGAGT
Found at i:2224721 original size:23 final size:23
Alignment explanation
Indices: 2224694--2224791 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
2224684 AGTGTTATTG
2224694 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2224717 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
2224740 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2224762 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
2224785 ATCAGTG
1 ATCAGTG
2224792 TGGCACTTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
22 21 0.30
23 50 0.70
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:2224760 original size:45 final size:45
Alignment explanation
Indices: 2224696--2224784 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
2224686 TGTTATTGAT
*
2224696 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
2224741 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
2224785 ATCAGTGTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.30
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:2226985 original size:14 final size:14
Alignment explanation
Indices: 2226966--2226996 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2226956 TGATTGTTTT
*
2226966 TAATCTAAATTTAC
1 TAATCTAAATTAAC
2226980 TAATCTAAATTAAC
1 TAATCTAAATTAAC
2226994 TAA
1 TAA
2226997 GAACGCGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:2241844 original size:68 final size:68
Alignment explanation
Indices: 2241763--2241903 Score: 237
Period size: 68 Copynumber: 2.1 Consensus size: 68
2241753 TTTGAAAAAC
* * *
2241763 CCACTGCCTAGTTTAAAATGTATCCGTAAGTACAGACTACATTTCTTTTTACTCTCAAAATGGCT
1 CCACTGCCCAGTTTAAAACGTATACGTAAGTACAGACTACATTTCTTTTTACTCTCAAAATGGCT
2241828 TTT
66 TTT
**
2241831 CCACTGCCCAGTTTAAAACGTATACGTAAGTACAGACTATGTTTCTTTTTACTCTCAAAATGGCT
1 CCACTGCCCAGTTTAAAACGTATACGTAAGTACAGACTACATTTCTTTTTACTCTCAAAATGGCT
2241896 TTT
66 TTT
2241899 CCACT
1 CCACT
2241904 TATGAAAGTT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (68 bp):
CCACTGCCCAGTTTAAAACGTATACGTAAGTACAGACTACATTTCTTTTTACTCTCAAAATGGCT
TTT
Found at i:2248159 original size:19 final size:21
Alignment explanation
Indices: 2248137--2248175 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
2248127 CAGAAAAGTT
2248137 AATTTTAAA-TATTT-TTATA
1 AATTTTAAATTATTTATTATA
2248156 AATTTTAAATTATTTATTAT
1 AATTTTAAATTATTTATTAT
2248176 CATGACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 5 0.28
21 4 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTTTAAATTATTTATTATA
Found at i:2255950 original size:29 final size:28
Alignment explanation
Indices: 2255895--2255950 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
2255885 CCTTTTTTGT
* *
2255895 TTTTTAATAAATGGTCCAACATTTTTAC
1 TTTTTAATAAATGGCCCAACATGTTTAC
*
2255923 TTTTTACATAAATGGCCCAATATGTTTA
1 TTTTTA-ATAAATGGCCCAACATGTTTA
2255951 TACTTCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (28 bp):
TTTTTAATAAATGGCCCAACATGTTTAC
Found at i:2255975 original size:21 final size:21
Alignment explanation
Indices: 2255949--2255991 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2255939 CCAATATGTT
2255949 TATACTTCTTCTTCTTCTCCA
1 TATACTTCTTCTTCTTCTCCA
2255970 TATACTTCTTCTTCTTCTCCA
1 TATACTTCTTCTTCTTCTCCA
2255991 T
1 T
2255992 CCCAAGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.33, G:0.00, T:0.53
Consensus pattern (21 bp):
TATACTTCTTCTTCTTCTCCA
Found at i:2258161 original size:40 final size:41
Alignment explanation
Indices: 2258079--2258179 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 41
2258069 TGAGACTGAC
* * * *
2258079 ACTGAACTGAATTATGGAA-TATTGAATATTGTATTTGAGT
1 ACTGAATTGAATTATGAAATTACTGAATATTGTATATGAGT
* *
2258119 ACTGAATTGAATTGTGAAATTACTGAATATTGT-TATGTGT
1 ACTGAATTGAATTATGAAATTACTGAATATTGTATATGAGT
* *
2258159 ACTGCATTGAACTATGAAATT
1 ACTGAATTGAATTATGAAATT
2258180 GTTGAAGTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 39 0.76
41 12 0.24
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.40
Consensus pattern (41 bp):
ACTGAATTGAATTATGAAATTACTGAATATTGTATATGAGT
Found at i:2258477 original size:39 final size:43
Alignment explanation
Indices: 2258390--2258483 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 43
2258380 CTGACTGCTA
*
2258390 TTACTGTTACCGATTCAACACTTTGTGTGTCAAATACTATTACCG
1 TTACTGTTACAGATTCAACACTTTGTGTGTCAAATACTATT--CG
* *
2258435 TTACTGTTACAGATTCAGCACTTTGTGTGT-AGA-A-TATT-G
1 TTACTGTTACAGATTCAACACTTTGTGTGTCAAATACTATTCG
2258474 TTACTGTTAC
1 TTACTGTTAC
2258484 TGCTACCGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
39 11 0.24
42 4 0.09
43 1 0.02
44 2 0.04
45 28 0.61
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (43 bp):
TTACTGTTACAGATTCAACACTTTGTGTGTCAAATACTATTCG
Found at i:2259711 original size:3 final size:3
Alignment explanation
Indices: 2259705--2259748 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
2259695 TTTTTCTTCT
* * **
2259705 TCC TCC TCC TCC TCC TCC TCT TCT TTT TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
2259749 AGCCCAGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (3 bp):
TCC
Found at i:2259735 original size:24 final size:24
Alignment explanation
Indices: 2259699--2259748 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2259689 TTCTTCTTTT
2259699 TCTTCTTCCTCCTCCTCCTCCTCC
1 TCTTCTTCCTCCTCCTCCTCCTCC
**
2259723 TCTTCTTTTTCCTCCTCCTCCTCC
1 TCTTCTTCCTCCTCCTCCTCCTCC
2259747 TC
1 TC
2259749 AGCCCAGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (24 bp):
TCTTCTTCCTCCTCCTCCTCCTCC
Found at i:2260241 original size:24 final size:24
Alignment explanation
Indices: 2260200--2260271 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
2260190 TTATCAAAAT
*
2260200 ATAATTAAAA-TATAAAAATATTTA
1 ATAA-TAAAAGTATTAAAATATTTA
*
2260224 ATAATAAAAGTATTAAAATA-GTA
1 ATAATAAAAGTATTAAAATATTTA
**
2260247 ATTAATGTAAGTA-TAAAATATTTA
1 A-TAATAAAAGTATTAAAATATTTA
2260271 A
1 A
2260272 AAAATTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 15 0.38
24 25 0.62
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (24 bp):
ATAATAAAAGTATTAAAATATTTA
Found at i:2264529 original size:19 final size:19
Alignment explanation
Indices: 2264505--2264546 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2264495 CATGCTTTCT
* *
2264505 ATTCACATTTTCATATTCA
1 ATTCACATTTTCAAATTAA
2264524 ATTCACATTTTCAAATTAA
1 ATTCACATTTTCAAATTAA
2264543 ATTC
1 ATTC
2264547 TACAATCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTCACATTTTCAAATTAA
Found at i:2264870 original size:23 final size:23
Alignment explanation
Indices: 2264718--2264868 Score: 200
Period size: 23 Copynumber: 6.7 Consensus size: 23
2264708 ATCAGTATAG
2264718 GACACAT-AAGTGCCTG--ATAC
1 GACACATAAAGTGCCTGAAATAC
** * *
2264738 GACACACGAGGTGCCTGAAATAT
1 GACACATAAAGTGCCTGAAATAC
** *
2264761 GACACATAAAGTTTCTGATATAC
1 GACACATAAAGTGCCTGAAATAC
2264784 GACACATAAAGTGCCTGAAATAC
1 GACACATAAAGTGCCTGAAATAC
2264807 GACACATAAAGTGCCTGAAATAC
1 GACACATAAAGTGCCTGAAATAC
* *
2264830 GACACATAAAGTTCCTAAAATAC
1 GACACATAAAGTGCCTGAAATAC
2264853 GACACATAAAGTGCCT
1 GACACATAAAGTGCCT
2264869 AATCGGCATA
Statistics
Matches: 112, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
20 6 0.05
21 8 0.07
23 98 0.88
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (23 bp):
GACACATAAAGTGCCTGAAATAC
Found at i:2268709 original size:13 final size:14
Alignment explanation
Indices: 2268679--2268725 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
2268669 TGAAATGGTC
2268679 TAAAATATTAAATA
1 TAAAATATTAAATA
* *
2268693 TAAAA-ATTAACTT
1 TAAAATATTAAATA
2268706 TAAAATAGTTAAAATA
1 TAAAATA-TT-AAATA
2268722 TAAA
1 TAAA
2268726 TAAAATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 11 0.42
14 6 0.23
15 2 0.08
16 7 0.27
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (14 bp):
TAAAATATTAAATA
Found at i:2269752 original size:18 final size:19
Alignment explanation
Indices: 2269725--2269767 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2269715 GCACAAATAT
*
2269725 ATTTTATTTTTT-CTTTTTC
1 ATTTT-TTTTTTCCTCTTTC
2269744 -TTTTTTTTTTCCTCTTTC
1 ATTTTTTTTTTCCTCTTTC
2269762 ATTTTT
1 ATTTTT
2269768 CCAATTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.29
18 10 0.48
19 5 0.24
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (19 bp):
ATTTTTTTTTTCCTCTTTC
Found at i:2277027 original size:50 final size:50
Alignment explanation
Indices: 2276963--2277538 Score: 402
Period size: 50 Copynumber: 11.5 Consensus size: 50
2276953 TTTGGAAAGT
* * * *
2276963 AAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCTGGGAGGC
* * * ** * ** * *
2277013 AAGATTTATCGTTGTGGCTTTAATCTGTTCCACTACACCGCCTGGGAGGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCTGGGAGGC
* * * * *
2277063 AAGATT-AGCTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGC
1 AAGATTCA-CCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCTGGGAGGC
* ** ** * * *
2277113 AA-AGTTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAAGT
1 AAGA-TTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCTGGGAGGC
* * * * ** **
2277163 AAGATTCGCTGCTGTAGCTTTAATCTTTTTAACCCCAATGTCAAGGAGGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCTGGGAGGC
* * ** ** * *
2277213 AAGATTCACCATTGTGGCTTTAATCTATTCCACTGCACCGCCTGGGAGGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCTGGGAGGC
* * * * *
2277263 AAGATTCACTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCTGGGAGGC
* * ** ** * * *
2277313 AAGATTCACCATTGTGGCTTTAATCTGTTCCACTGCACCGCCTGTGAGGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCTGGGAGGC
* * * * *
2277363 AAGATTCACTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGC
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCTGGGAGGC
* ** ** * * * *
2277413 AAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCACCGCCTAGGAAGT
1 AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCTGGGAGGC
* * * * * * *
2277463 AAGATTC-CTTGCTGTAGCTTTAATCTTTTTAACTGTAGTGTCGGGGAAGC
1 AAGATTCAC-CGTTGTGGCTTTAATCTTTTTAACTGCAATGTCTGGGAGGC
2277513 AAGATTCACCGTTGTGGCTTTAATCT
1 AAGATTCACCGTTGTGGCTTTAATCT
2277539 GCTCCACTGC
Statistics
Matches: 376, Mismatches: 144, Indels: 12
0.71 0.27 0.02
Matches are distributed among these distances:
49 3 0.01
50 370 0.98
51 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (50 bp):
AAGATTCACCGTTGTGGCTTTAATCTTTTTAACTGCAATGTCTGGGAGGC
Found at i:2277134 original size:100 final size:100
Alignment explanation
Indices: 2276961--2277569 Score: 902
Period size: 100 Copynumber: 6.1 Consensus size: 100
2276951 CTTTTGGAAA
* * * * * * * *
2276961 GTAAGATTCGCTGTTGTGGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTTATCGTT
1 GTAAGATTAGCTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTT
*
2277026 GTGGCTTTAATCTGTTCCACTACACCGCCTGGGAG
66 GTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAG
2277061 GTAAGATTAGCTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAA-AGTTCACCGT
1 GTAAGATTAGCTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGA-TTCACCGT
*
2277125 TGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAA
65 TGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAG
* * * *
2277161 GTAAGATTCGCTGCTGTAGCTTTAATCTTTTTAACCCCAATGTCAAGGAGGCAAGATTCACCATT
1 GTAAGATTAGCTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTT
*
2277226 GTGGCTTTAATCTATTCCACTGCACCGCCTGGGAG
66 GTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAG
*
2277261 GTAAGATTCA-CTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCAT
1 GTAAGATT-AGCTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGT
*
2277325 TGTGGCTTTAATCTGTTCCACTGCACCGCCTGTGAG
65 TGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAG
2277361 GTAAGATTCA-CTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGT
1 GTAAGATT-AGCTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGT
* *
2277425 TGTGGCTTTAATCTGTTCCACTGCACCGCCTAGGAA
65 TGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAG
* * * * * *
2277461 GTAAGATT-CCTTGCTGTAGCTTTAATCTTTTTAACTGTAGTGTCGGGGAAGCAAGATTCACCGT
1 GTAAGATTAGC-TGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGT
* *
2277525 TGTGGCTTTAATCTGCTCCACTGCACTGCCTGGGAG
65 TGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAG
2277561 AGTAAGATT
1 -GTAAGATT
2277570 TCAAATTTTC
Statistics
Matches: 469, Mismatches: 34, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
99 2 0.00
100 458 0.98
101 9 0.02
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (100 bp):
GTAAGATTAGCTGCTGTAGCTTTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTT
GTGGCTTTAATCTGTTCCACTGCACCGCCTGGGAG
Found at i:2280349 original size:14 final size:14
Alignment explanation
Indices: 2280330--2280357 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2280320 CAGAGGTTTC
2280330 ATTCCTAAAATCTT
1 ATTCCTAAAATCTT
2280344 ATTCCTAAAATCTT
1 ATTCCTAAAATCTT
2280358 GAATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTCCTAAAATCTT
Found at i:2280549 original size:21 final size:21
Alignment explanation
Indices: 2280508--2280550 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2280498 AATAAAGTAG
*
2280508 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
2280529 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
2280550 A
1 A
2280551 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:2280868 original size:50 final size:49
Alignment explanation
Indices: 2280773--2280869 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 49
2280763 TTACAACATT
* * *
2280773 ATTCCATTTAACCAAACACAAGAATACTATTACAGTTTTATTCCATTCC
1 ATTCCATTCAACCAAACACAAGAATACTATTACAGATCTATTCCATTCC
*
2280822 ATTCCATTCAACCAAACA-ATTGAATTACTATTAC-GCATCTATTCCATT
1 ATTCCATTCAACCAAACACA-AGAA-TACTATTACAG-ATCTATTCCATT
2280870 ACAGCTCTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
48 1 0.02
49 21 0.51
50 19 0.46
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (49 bp):
ATTCCATTCAACCAAACACAAGAATACTATTACAGATCTATTCCATTCC
Found at i:2280878 original size:16 final size:16
Alignment explanation
Indices: 2280859--2280906 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
2280849 CTATTACGCA
2280859 TCTATTCCATTACAGC
1 TCTATTCCATTACAGC
* *
2280875 TCTATTCCGTTACACC
1 TCTATTCCATTACAGC
2280891 TCTATTCCATTACAGC
1 TCTATTCCATTACAGC
2280907 GAATCAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (16 bp):
TCTATTCCATTACAGC
Found at i:2281668 original size:7 final size:7
Alignment explanation
Indices: 2281656--2281795 Score: 61
Period size: 7 Copynumber: 19.7 Consensus size: 7
2281646 ACTAGTTAAT
2281656 CTAAACC
1 CTAAACC
2281663 CTAAACC
1 CTAAACC
*
2281670 ATAAA-C
1 CTAAACC
2281676 CTAAACC
1 CTAAACC
*
2281683 CTAAAATC
1 CT-AAACC
*
2281691 TTAAACC
1 CTAAACC
2281698 CTAAACC
1 CTAAACC
* *
2281705 CTTAACA
1 CTAAACC
*
2281712 C-ATAACAT
1 CTA-AAC-C
2281720 CTAAACC
1 CTAAACC
*
2281727 TTAAACC
1 CTAAACC
*
2281734 C-CAACC
1 CTAAACC
*
2281740 TTTAAACC
1 -CTAAACC
*
2281748 ATAAACC
1 CTAAACC
* *
2281755 ATAAATC
1 CTAAACC
* *
2281762 ATAACCC
1 CTAAACC
2281769 CTAAACC
1 CTAAACC
*
2281776 CATAATCC
1 C-TAAACC
*
2281784 ATAAACC
1 CTAAACC
*
2281791 TTAAA
1 CTAAA
2281796 ATAGTAACTC
Statistics
Matches: 99, Mismatches: 26, Indels: 16
0.70 0.18 0.11
Matches are distributed among these distances:
6 9 0.09
7 71 0.72
8 18 0.18
9 1 0.01
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Done.