Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 186 of 322
Found at i:61214678 original size:9 final size:9
Alignment explanation
Indices: 61214664--61214688 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
61214654 GATCAAGTAA
61214664 AATTAAATT
1 AATTAAATT
61214673 AATTAAATT
1 AATTAAATT
61214682 AATTAAA
1 AATTAAA
61214689 ATCAATATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AATTAAATT
Found at i:61215395 original size:17 final size:18
Alignment explanation
Indices: 61215375--61215417 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
61215365 CCAAAAATAA
* *
61215375 TAATATTTTAATAT-ATT
1 TAATATTTAAATATAATC
61215392 TAATA-TTAAATATAATC
1 TAATATTTAAATATAATC
61215409 TAATATTTA
1 TAATATTTA
61215418 TCTTGATAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 12 0.55
18 3 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATATTTAAATATAATC
Found at i:61219255 original size:40 final size:40
Alignment explanation
Indices: 61219165--61219526 Score: 507
Period size: 40 Copynumber: 9.1 Consensus size: 40
61219155 NNNNNNNNNN
* * *
61219165 AAGGCATTTGTGCTAGTGACTA-ATTCTGGGCTAAG-CCCG
1 AAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCCCG
61219204 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
* * * *
61219244 AAGGCATTTGTGCTAGTGACTAAATTCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
* * *
61219284 AAGGCATTTGTGCTAGTGACTAAATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
* *
61219324 ATGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCTCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
61219364 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
*
61219404 AAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
* *
61219444 AAGGCATTTGTGTGAGTTACTATAACCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
* * * *
61219484 AAGGCATTTGAGCAAG-TAGCTATATCC-GGCTAAATTCCG
1 AAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCCCG
61219523 AAGG
1 AAGG
61219527 TGCTTGGTTT
Statistics
Matches: 297, Mismatches: 23, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
39 46 0.15
40 251 0.85
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
Found at i:61222170 original size:39 final size:38
Alignment explanation
Indices: 61222115--61222192 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 38
61222105 CCCGAGATTG
*
61222115 TCTGAACAGAATGTAAATCAGAGTGGGAAACCTGGTGC
1 TCTGAACAGAACGTAAATCAGAGTGGGAAACCTGGTGC
61222153 TNCTGAACAGAACGTAAATCAGAGTGGGAAACCTGGTGC
1 T-CTGAACAGAACGTAAATCAGAGTGGGAAACCTGGTGC
61222192 T
1 T
61222193 ACTACTGCTC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 1 0.03
39 37 0.97
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.21
Consensus pattern (38 bp):
TCTGAACAGAACGTAAATCAGAGTGGGAAACCTGGTGC
Found at i:61225859 original size:42 final size:42
Alignment explanation
Indices: 61225807--61225891 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
61225797 TTAAATATGA
* *
61225807 TAATTATTGTCTAAAATATGTGAATATGAATGTGTGAAAGTT
1 TAATGATTGTCTAAAATATGTGAATATGAATGTGCGAAAGTT
61225849 TAATGATTGTCTAAAATATGTGAATATGAATGTGCGAAAGTT
1 TAATGATTGTCTAAAATATGTGAATATGAATGTGCGAAAGTT
61225891 T
1 T
61225892 TAAGCCTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.39
Consensus pattern (42 bp):
TAATGATTGTCTAAAATATGTGAATATGAATGTGCGAAAGTT
Found at i:61227482 original size:151 final size:151
Alignment explanation
Indices: 61227208--61227508 Score: 593
Period size: 151 Copynumber: 2.0 Consensus size: 151
61227198 TAGCTCAAGA
61227208 GCTTAGAGGACCAAAGTTGGATAAGGGAAAGGAAAAAGTGATCGAATAGCCGCCGAAATCGTTCG
1 GCTTAGAGGACCAAAGTTGGATAAGGGAAAGGAAAAAGTGATCGAATAGCCGCCGAAATCGTTCG
61227273 ACAACATCCGAGGTAAGTTTTTGAGTAATGGATCTTAAATTATGATTCGATTAGATCATGTTTTA
66 ACAACATCCGAGGTAAGTTTTTGAGTAATGGATCTTAAATTATGATTCGATTAGATCATGTTTTA
61227338 AGTAAATCAAAATCATGCTCC
131 AGTAAATCAAAATCATGCTCC
61227359 GCTTAGAGGACCAAAGTTGGATAAGGGAAAGGAAAAAGTGATCGAATAGCCGCCGAAATCGTTCG
1 GCTTAGAGGACCAAAGTTGGATAAGGGAAAGGAAAAAGTGATCGAATAGCCGCCGAAATCGTTCG
*
61227424 ACAACATCCGAGGTAAGTTTTTGAGTAATGGATCTTAGATTATGATTCGATTAGATCATGTTTTA
66 ACAACATCCGAGGTAAGTTTTTGAGTAATGGATCTTAAATTATGATTCGATTAGATCATGTTTTA
61227489 AGTAAATCAAAATCATGCTC
131 AGTAAATCAAAATCATGCTC
61227509 TTTGTATGTA
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 149 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (151 bp):
GCTTAGAGGACCAAAGTTGGATAAGGGAAAGGAAAAAGTGATCGAATAGCCGCCGAAATCGTTCG
ACAACATCCGAGGTAAGTTTTTGAGTAATGGATCTTAAATTATGATTCGATTAGATCATGTTTTA
AGTAAATCAAAATCATGCTCC
Found at i:61227742 original size:40 final size:40
Alignment explanation
Indices: 61227637--61227893 Score: 378
Period size: 40 Copynumber: 6.5 Consensus size: 40
61227627 CGGATGATAA
* *
61227637 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
61227677 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
61227716 CCGGGCTACGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
61227756 CCGGGCTACGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
61227796 CCGGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
61227836 CCGGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
61227876 CC-GGCTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
61227894 TACTTGGTTT
Statistics
Matches: 202, Mismatches: 12, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
39 50 0.25
40 152 0.75
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:61235636 original size:18 final size:18
Alignment explanation
Indices: 61235615--61235662 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
61235605 ATAATAATGT
61235615 AAATAATAATATACAT-GA
1 AAATAATAATATA-ATAGA
61235633 AAAT-ATATATATAATAGA
1 AAATAATA-ATATAATAGA
*
61235651 TAATAATAATAT
1 AAATAATAATAT
61235663 GTAATAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.19
18 18 0.69
19 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (18 bp):
AAATAATAATATAATAGA
Found at i:61235654 original size:30 final size:30
Alignment explanation
Indices: 61235599--61235658 Score: 75
Period size: 33 Copynumber: 1.9 Consensus size: 30
61235589 TCAATTTAAT
*
61235599 ATGAAAATAATAATGTAAATAATAATATAC
1 ATGAAAATAATAATATAAATAATAATATAC
*
61235629 ATGAAAATATATATATAATAGATAATAATA
1 ATGAAAATA-ATA-AT-ATAAATAATAATA
61235659 ATATGTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
31 3 0.12
32 2 0.08
33 11 0.44
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.32
Consensus pattern (30 bp):
ATGAAAATAATAATATAAATAATAATATAC
Found at i:61235791 original size:81 final size:82
Alignment explanation
Indices: 61235641--61235792 Score: 182
Period size: 81 Copynumber: 1.9 Consensus size: 82
61235631 GAAAATATAT
* * * * *
61235641 ATATAATAGATAATAATAATATGTAATAATGTATTGTTAAAATGTAAAATAATATAAAAATATAT
1 ATATAATA-ATAATAATAATAAGTAATAATATATTGTTAAAATATAAAATAATATAAAAATAGAA
61235706 AAATATTATGTGATAAAA
65 AAATATTATGTGATAAAA
* * * * *
61235724 ATATAAT-ATAATAAATAATAAGTAATGATATA-TGTTAAAATATATATTAATATGATAATAGAA
1 ATATAATAATAAT-AATAATAAGTAATAATATATTGTTAAAATATAAAATAATATAAAAATAGAA
61235787 AAATAT
65 AAATAT
61235793 GAAGTAATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
81 35 0.60
82 16 0.28
83 7 0.12
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (82 bp):
ATATAATAATAATAATAATAAGTAATAATATATTGTTAAAATATAAAATAATATAAAAATAGAAA
AATATTATGTGATAAAA
Found at i:61235909 original size:26 final size:26
Alignment explanation
Indices: 61235854--61235911 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
61235844 TATATTTATA
*
61235854 TTAAAATAAAATAATATATATACAAT
1 TTAAAATAAAATAATATATAAACAAT
*
61235880 TTAAAAT-AAATAAGT-TATAAATAAT
1 TTAAAATAAAATAA-TATATAAACAAT
61235905 CTTAAAA
1 -TTAAAA
61235912 GGGATAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (26 bp):
TTAAAATAAAATAATATATAAACAAT
Found at i:61247823 original size:48 final size:48
Alignment explanation
Indices: 61247761--61247920 Score: 169
Period size: 48 Copynumber: 3.3 Consensus size: 48
61247751 GATACCATGC
* *
61247761 CCCAGACATGGTCTTATACGGGACCTCATATCGATGCCAATGCCATAT
1 CCCAGACATGGTCTTATACGGGATCTCATATCGATGCCGATGCCATAT
* * * * *
61247809 CCCAGATATGGTCTTACATGAGATCTCATA-CTGATGCCGATGCCATGT
1 CCCAGACATGGTCTTATACGGGATCTCATATC-GATGCCGATGCCATAT
* * ** * * *
61247857 CCTAGACGTCATCTTATACGGGATCTCTTATCAATGTCGATGCCATAT
1 CCCAGACATGGTCTTATACGGGATCTCATATCGATGCCGATGCCATAT
*
61247905 CCCAGATATGGTCTTA
1 CCCAGACATGGTCTTA
61247921 CATGGGATAT
Statistics
Matches: 86, Mismatches: 24, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
47 1 0.01
48 84 0.98
49 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (48 bp):
CCCAGACATGGTCTTATACGGGATCTCATATCGATGCCGATGCCATAT
Found at i:61247836 original size:95 final size:96
Alignment explanation
Indices: 61247720--61247924 Score: 245
Period size: 96 Copynumber: 2.1 Consensus size: 96
61247710 ACAACTTAGC
* * * **
61247720 TATGGTCTTACACGAAGTCTCATAAC-GGTG-TGATACCATGCCCCAGACATGGTCTTATACGGG
1 TATGGTCTTACATGAAGTCTCAT-ACTGATGCCGATACCATGCCCCAGACATCATCTTATACGGG
*
61247783 ACCTCATATCGATGCCAATGCCATATCCCAGA
65 ACCTCATATCAATGCCAATGCCATATCCCAGA
* * * *
61247815 TATGGTCTTACATG-AGATCTCATACTGATGCCGATGCCATGTCCTAGACGTCATCTTATACGGG
1 TATGGTCTTACATGAAG-TCTCATACTGATGCCGATACCATGCCCCAGACATCATCTTATACGGG
* * * *
61247879 ATCTCTTATCAATGTCGATGCCATATCCCAGA
65 ACCTCATATCAATGCCAATGCCATATCCCAGA
61247911 TATGGTCTTACATG
1 TATGGTCTTACATG
61247925 GGATATCAAT
Statistics
Matches: 93, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
94 4 0.04
95 22 0.24
96 67 0.72
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (96 bp):
TATGGTCTTACATGAAGTCTCATACTGATGCCGATACCATGCCCCAGACATCATCTTATACGGGA
CCTCATATCAATGCCAATGCCATATCCCAGA
Found at i:61249044 original size:11 final size:11
Alignment explanation
Indices: 61249016--61249056 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
61249006 GCCCAAACGT
61249016 CAAAATTTTCAAA
1 CAAAATTTTC--A
*
61249029 CAAAATTTTGA
1 CAAAATTTTCA
61249040 CAAAATTTTCA
1 CAAAATTTTCA
61249051 CAAAAT
1 CAAAAT
61249057 CATTTTGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 17 0.65
13 9 0.35
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (11 bp):
CAAAATTTTCA
Found at i:61260113 original size:27 final size:26
Alignment explanation
Indices: 61260040--61260117 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 26
61260030 AAATTGTCAT
61260040 CATTTTCTATTCGTTTATTTTTC-TTTC
1 CATTTTCTATTC--TTATTTTTCTTTTC
* * *
61260067 TATTGTTCTTTTCTTGTTTTTCTTTTC
1 CATT-TTCTATTCTTATTTTTCTTTTC
*
61260094 CATTTTCAATTCTTAATTTTTCTT
1 CATTTTCTATTCTT-ATTTTTCTT
61260118 CGTTTTAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 16 0.39
27 18 0.44
28 7 0.17
ACGTcount: A:0.12, C:0.17, G:0.04, T:0.68
Consensus pattern (26 bp):
CATTTTCTATTCTTATTTTTCTTTTC
Found at i:61260906 original size:63 final size:63
Alignment explanation
Indices: 61260820--61260954 Score: 162
Period size: 63 Copynumber: 2.1 Consensus size: 63
61260810 GCACAAGATA
* * * * * * * *
61260820 AGGATCACATGGGTTAGGGACACTGGCGTGTGTCCAGGTCTTGTGACTTACTGTTTACAATAT
1 AGGACCACATGGGCTAGAGACACTAGCGTGTGTCCAGGCCGTGTGACTCACTGTTTAAAATAT
* * *
61260883 AGGACCACATGGGCTAGAGACACTAGTGTGTGTCCAGGCCGTGTGACTCACTTTTTAAAATTT
1 AGGACCACATGGGCTAGAGACACTAGCGTGTGTCCAGGCCGTGTGACTCACTGTTTAAAATAT
*
61260946 AAGACCACA
1 AGGACCACA
61260955 CAGGCAGACG
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (63 bp):
AGGACCACATGGGCTAGAGACACTAGCGTGTGTCCAGGCCGTGTGACTCACTGTTTAAAATAT
Found at i:61260968 original size:63 final size:63
Alignment explanation
Indices: 61260838--61260968 Score: 147
Period size: 63 Copynumber: 2.1 Consensus size: 63
61260828 ATGGGTTAGG
* * * * * * **
61260838 GACACTGGCGTGTGTCCAGGTCTTGTGACTTACTGTTTACAATATAGGACCACATGGGCTAGA
1 GACACTAGCGTGTGTCCAGGCCGTGTGACTCACTGTTTAAAATATAAGACCACACAGGCTAGA
* * *
61260901 GACACTAGTGTGTGTCCAGGCCGTGTGACTCACTTTTTAAAATTTAAGACCACACAGGC-AGA
1 GACACTAGCGTGTGTCCAGGCCGTGTGACTCACTGTTTAAAATATAAGACCACACAGGCTAGA
61260963 CGACAC
1 -GACAC
61260969 CGGCATGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 3 0.05
63 53 0.95
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (63 bp):
GACACTAGCGTGTGTCCAGGCCGTGTGACTCACTGTTTAAAATATAAGACCACACAGGCTAGA
Found at i:61268581 original size:4 final size:4
Alignment explanation
Indices: 61268572--61268605 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
61268562 AAGTTTTATT
61268572 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA
61268606 AATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:61268613 original size:22 final size:22
Alignment explanation
Indices: 61268555--61268614 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
61268545 AAGTGGCCCA
*
61268555 AGTTGTAAAGTTTTATTTTTATTT
1 AGTT-TAAATTTTTA-TTTTATTT
*
61268579 A-TTT-ATTTATTTATTTTATTT
1 AGTTTAAATT-TTTATTTTATTT
61268600 AGTTTAAATTTTTAT
1 AGTTTAAATTTTTAT
61268615 ATTCAGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 11 0.37
22 13 0.43
23 5 0.17
24 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
AGTTTAAATTTTTATTTTATTT
Found at i:61275521 original size:15 final size:15
Alignment explanation
Indices: 61275501--61275542 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
61275491 TGTTGTAATG
61275501 GGATTTCCTTATCA-T
1 GGATTTCCTTAT-ATT
*
61275516 GGATTTCTTTATATT
1 GGATTTCCTTATATT
61275531 GGATTTCCTTAT
1 GGATTTCCTTAT
61275543 TCTGGACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 1 0.04
15 23 0.96
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (15 bp):
GGATTTCCTTATATT
Found at i:61275548 original size:15 final size:15
Alignment explanation
Indices: 61275501--61275548 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
61275491 TGTTGTAATG
61275501 GGATTTCCTTA-TCAT
1 GGATTTCCTTATTC-T
*
61275516 GGATTTCTTTATAT-T
1 GGATTTCCTTAT-TCT
61275531 GGATTTCCTTATTCT
1 GGATTTCCTTATTCT
61275546 GGA
1 GGA
61275549 CTTTTTCGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
17 1 0.04
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.50
Consensus pattern (15 bp):
GGATTTCCTTATTCT
Found at i:61275755 original size:36 final size:36
Alignment explanation
Indices: 61275708--61275779 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
61275698 TAATGTGGTG
61275708 AAATTTCAAGTCCTAATGTGTATGGTGGATTTCCTT
1 AAATTTCAAGTCCTAATGTGTATGGTGGATTTCCTT
61275744 AAATTTCAAGTCCTAATGTGTATGGTGGATTTCCTT
1 AAATTTCAAGTCCTAATGTGTATGGTGGATTTCCTT
61275780 TCTCAAGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (36 bp):
AAATTTCAAGTCCTAATGTGTATGGTGGATTTCCTT
Found at i:61277098 original size:6 final size:6
Alignment explanation
Indices: 61277087--61277122 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
61277077 AAAAATTTTG
61277087 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT
61277123 TAACTAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
GAAAAT
Found at i:61283050 original size:22 final size:22
Alignment explanation
Indices: 61283022--61283066 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
61283012 GATCCTTAAC
61283022 TTTGAAAGTAATTTAATGAAAT
1 TTTGAAAGTAATTTAATGAAAT
61283044 TTTGAAAGTAATTTAATGAAAT
1 TTTGAAAGTAATTTAATGAAAT
61283066 T
1 T
61283067 CAAGCTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (22 bp):
TTTGAAAGTAATTTAATGAAAT
Found at i:61283492 original size:18 final size:17
Alignment explanation
Indices: 61283464--61283498 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
61283454 ATTATTAAGA
*
61283464 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
61283481 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
61283499 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:61283500 original size:28 final size:27
Alignment explanation
Indices: 61283468--61283540 Score: 76
Period size: 28 Copynumber: 2.7 Consensus size: 27
61283458 TTAAGAATTT
61283468 TATTAAATTATATATTTTAATTAAAATA
1 TATTAAATTATATATTTT-ATTAAAATA
* * * *
61283496 TATTAAATAATA-ATTATGTTTAAATA
1 TATTAAATTATATATTTTATTAAAATA
*
61283522 TGATTAAATTATTTATTTT
1 T-ATTAAATTATATATTTT
61283541 TGATAATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 8 0.22
27 13 0.36
28 15 0.42
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (27 bp):
TATTAAATTATATATTTTATTAAAATA
Found at i:61283709 original size:44 final size:45
Alignment explanation
Indices: 61283660--61283754 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
61283650 TTACACCTCT
* *
61283660 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
61283704 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
61283749 ATTACA
1 ATTACA
61283755 CCTCTATTCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:61283754 original size:16 final size:16
Alignment explanation
Indices: 61283733--61283802 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
61283723 TTGATTTGCT
*
61283733 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
61283749 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
61283765 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
61283781 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
61283797 AATACA
1 ATTACA
61283803 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:61299068 original size:29 final size:31
Alignment explanation
Indices: 61299035--61299120 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
61299025 GATTTAATGC
*
61299035 GCAATTGTATACATG-AACTTTAGTT-TGGT
1 GCAATTGTATACATGAAACTTTAATTGTGGT
* * *
61299064 GCAATTATACACGTGAAACTTTAATTGTGGT
1 GCAATTGTATACATGAAACTTTAATTGTGGT
* * *
61299095 TCAAATGTATACTTGAAACTTTAATT
1 GCAATTGTATACATGAAACTTTAATT
61299121 TTGATTTAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
29 12 0.26
30 9 0.20
31 25 0.54
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (31 bp):
GCAATTGTATACATGAAACTTTAATTGTGGT
Found at i:61309810 original size:27 final size:26
Alignment explanation
Indices: 61309758--61309817 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
61309748 ACATATATAT
*
61309758 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
61309784 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
61309811 ATATCTG
1 ATATCTG
61309818 GCAGCCTCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:61320893 original size:39 final size:40
Alignment explanation
Indices: 61320850--61320950 Score: 118
Period size: 39 Copynumber: 2.6 Consensus size: 40
61320840 ACTAGCTCGA
* * *
61320850 AGCCTGCGGGA-CTTTAGCCCGGAAATATTTCCAGCACGT
1 AGCCTGCGGGACCTTAAGCCCGGAAATAATTCCAGCACAT
* *
61320889 AGCCTGC-GGACCTTAAGTCCGGATATAATTCCAGCACAT
1 AGCCTGCGGGACCTTAAGCCCGGAAATAATTCCAGCACAT
* *
61320928 AGCCTGC-GGACCCTAAGTCCGGA
1 AGCCTGCGGGACCTTAAGCCCGGA
61320951 TATACATCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 3 0.05
39 52 0.95
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.21
Consensus pattern (40 bp):
AGCCTGCGGGACCTTAAGCCCGGAAATAATTCCAGCACAT
Found at i:61320951 original size:39 final size:39
Alignment explanation
Indices: 61320868--61320954 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
61320858 GGACTTTAGC
* * * *
61320868 CCGGAAATATTTCCAGCACGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
61320907 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
61320946 CCGGATATA
1 CCGGATATA
61320955 CATCACTGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:61324866 original size:12 final size:12
Alignment explanation
Indices: 61324849--61324877 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
61324839 CCACACATGC
61324849 CCGTGTGCTAGG
1 CCGTGTGCTAGG
61324861 CCGTGTGCTAGG
1 CCGTGTGCTAGG
61324873 CCGTG
1 CCGTG
61324878 CAACTCATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.28, G:0.41, T:0.24
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:61326316 original size:89 final size:89
Alignment explanation
Indices: 61326209--61326382 Score: 296
Period size: 89 Copynumber: 2.0 Consensus size: 89
61326199 TTACCTCAAC
* *
61326209 AACTAGGGTTGTAGTAGTAGAGTCGAACTAATTCGAAGCTTTAGCTTTCCCTTGATTTAAG-TCT
1 AACTAGGATTGTAGTAGTAGAGTCGAACTAATTCGAAGCTTCAGCTTTCCCTTGATTTAAGTTC-
61326273 AATTGTGGTTTATCTTGATCTCGAT
65 AATTGTGGTTTATCTTGATCTCGAT
* *
61326298 AACTAGGATTGTAGTAGTAGAGTTGAACTAATTCGAAGCTTCAGCTTTTCCTTGATTTAAGTTCA
1 AACTAGGATTGTAGTAGTAGAGTCGAACTAATTCGAAGCTTCAGCTTTCCCTTGATTTAAGTTCA
61326363 ATTGTGGTTTATCTTGATCT
66 ATTGTGGTTTATCTTGATCT
61326383 AAATAAATAA
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 78 0.98
90 2 0.03
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (89 bp):
AACTAGGATTGTAGTAGTAGAGTCGAACTAATTCGAAGCTTCAGCTTTCCCTTGATTTAAGTTCA
ATTGTGGTTTATCTTGATCTCGAT
Found at i:61337471 original size:8 final size:7
Alignment explanation
Indices: 61337451--61337492 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
61337441 GATGACATAG
61337451 AATTTTT
1 AATTTTT
61337458 AATTTTT
1 AATTTTT
61337465 AATTTTT
1 AATTTTT
*
61337472 ATTTTTT
1 AATTTTT
* *
61337479 CATTGTT
1 AATTTTT
61337486 -ATTTTT
1 AATTTTT
61337492 A
1 A
61337493 TTAAATTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (7 bp):
AATTTTT
Found at i:61339169 original size:40 final size:40
Alignment explanation
Indices: 61339094--61339270 Score: 216
Period size: 40 Copynumber: 4.4 Consensus size: 40
61339084 NNNNNNNNNN
* *
61339094 GGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACTATATCCG
1 GGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACTATATCCG
* *
61339134 GACTAAGATCCGAAGGCATTTGTGCGAGTTG-CTATATCCG
1 GGCTAAGATCCGAAGGCATTTGTGCTAG-TGACTATATCCG
* *
61339174 GGCTAAGACCCGAAGGCATTTGTGCTAGTGACCATATCCG
1 GGCTAAGATCCGAAGGCATTTGTGCTAGTGACTATATCCG
* * *
61339214 GGCTAAG-TCCCGAAGGCATTTATGCTAGTGACCATAACCG
1 GGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACTATATCCG
*
61339254 GGCTAAGACCCGAAGGC
1 GGCTAAGATCCGAAGGC
61339271 CTGTGCGAGT
Statistics
Matches: 120, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
39 2 0.02
40 115 0.96
41 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
GGCTAAGATCCGAAGGCATTTGTGCTAGTGACTATATCCG
Found at i:61339227 original size:80 final size:80
Alignment explanation
Indices: 61339094--61339270 Score: 241
Period size: 80 Copynumber: 2.2 Consensus size: 80
61339084 NNNNNNNNNN
* * * *
61339094 GGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGATCCGAAGGCATTTGTGC
1 GGCTAAGACCCGAAGGCATTTATGCTAGTGACCATATCCGGACTAAGATCCGAAGGCATTTATGC
* *
61339159 GAGTTG-CTATATCCG
66 GAG-TGACCATAACCG
* *
61339174 GGCTAAGACCCGAAGGCATTTGTGCTAGTGACCATATCCGGGCTAAG-TCCCGAAGGCATTTATG
1 GGCTAAGACCCGAAGGCATTTATGCTAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTATG
*
61339238 CTAGTGACCATAACCG
65 CGAGTGACCATAACCG
61339254 GGCTAAGACCCGAAGGC
1 GGCTAAGACCCGAAGGC
61339271 CTGTGCGAGT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 3 0.03
80 83 0.97
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (80 bp):
GGCTAAGACCCGAAGGCATTTATGCTAGTGACCATATCCGGACTAAGATCCGAAGGCATTTATGC
GAGTGACCATAACCG
Found at i:61346926 original size:40 final size:40
Alignment explanation
Indices: 61346685--61346919 Score: 384
Period size: 40 Copynumber: 5.9 Consensus size: 40
61346675 NNNNNNNNNN
*
61346685 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTAACTACTTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAACTACTTCC
*
61346725 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTAACTACTTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAACTACTTCC
*
61346765 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTAACTACTTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAACTACTTCC
*
61346805 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAACTACT-TCC
*
61346845 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAACTACT-TCC
*
61346885 GGGCTAAGTCCCGAAGGCATTTGAGCGAGTAACTA
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAACTA
61346920 TATCCGGTTA
Statistics
Matches: 190, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
39 1 0.01
40 189 0.99
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTAACTACTTCC
Found at i:61352982 original size:39 final size:40
Alignment explanation
Indices: 61352887--61353148 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
61352877 TTGAATGATG
*
61352887 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
61352925 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
61352966 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
61353005 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
61353044 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
61353083 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
* *
61353122 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
61353149 AACGAGGAGC
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
39 132 0.65
40 59 0.29
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:61372973 original size:21 final size:21
Alignment explanation
Indices: 61372947--61372988 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
61372937 TTTGACCAAG
61372947 TTAACTTATAGATGCCATTAT
1 TTAACTTATAGATGCCATTAT
61372968 TTAACTTATAGATGCCATTAT
1 TTAACTTATAGATGCCATTAT
61372989 ACCAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (21 bp):
TTAACTTATAGATGCCATTAT
Found at i:61381375 original size:47 final size:47
Alignment explanation
Indices: 61381321--61381450 Score: 170
Period size: 47 Copynumber: 2.8 Consensus size: 47
61381311 GTGCGAATAA
* * * * *
61381321 TACCTTGATTTGGCTATGGGTCATGATATAGGTATTCTGAGAGGAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTCCGAGAGAAGT
* * *
61381368 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCGGGATAAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTCCGAGAGAAGT
* *
61381415 TACCTTGGTTGGGCTATGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACT
61381451 TATCGGTTGT
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTCCGAGAGAAGT
Found at i:61389655 original size:14 final size:14
Alignment explanation
Indices: 61389621--61389662 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
61389611 ACATATTCTT
61389621 ATAAAAAAAT-ATA
1 ATAAAAAAATGATA
**
61389634 ATCCAAAAATGATA
1 ATAAAAAAATGATA
*
61389648 ATAAAAAAAAGATA
1 ATAAAAAAATGATA
61389662 A
1 A
61389663 ACCAATGCCC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (14 bp):
ATAAAAAAATGATA
Found at i:61399704 original size:18 final size:19
Alignment explanation
Indices: 61399671--61399710 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
61399661 TATCCTTGTA
* *
61399671 TTTTTTTATTATTTTCT-T
1 TTTTTTTATAAATTTCTCT
61399689 TTTTTTTATAAATTTCTCT
1 TTTTTTTATAAATTTCTCT
61399708 TTT
1 TTT
61399711 CTCTCTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTTATAAATTTCTCT
Found at i:61401563 original size:27 final size:27
Alignment explanation
Indices: 61401533--61401710 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
61401523 ATATTGAGTC
* * * *
61401533 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
61401560 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
61401587 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
61401615 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
61401642 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
61401669 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
61401696 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
61401711 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:61401672 original size:82 final size:81
Alignment explanation
Indices: 61401554--61401709 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
61401544 TGCTATATAA
* *
61401554 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
61401619 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
61401636 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
61401700 CACTTAGTGC
65 CACTTAGTGC
61401710 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:61409615 original size:27 final size:27
Alignment explanation
Indices: 61409585--61409762 Score: 164
Period size: 27 Copynumber: 6.6 Consensus size: 27
61409575 ATATTGAGCC
* *
61409585 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
61409612 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
61409639 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAATCA-ACT
** ** *
61409667 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
61409694 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
*
61409721 CGCACACTTAGTGCAACA-AAGTCGAA-T
1 CGCACACTTAGTGCTACATAA-TC-AACT
61409748 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
61409763 GTACAATTTA
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 100 0.79
28 25 0.20
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:61409724 original size:82 final size:81
Alignment explanation
Indices: 61409606--61409761 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
61409596 TGCTATATAA
* * * *
61409606 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACAAAGTC-GAATCGCA
61409671 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
61409688 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACAAAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACAAAGTCGAATCGCA
61409752 CACTTAGTGC
65 CACTTAGTGC
61409762 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 19 0.29
82 46 0.71
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACAAAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:61413931 original size:19 final size:19
Alignment explanation
Indices: 61413907--61413944 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
61413897 CTAAAAGAGT
61413907 TGAGAGAATGATGA-ATGAG
1 TGAGAG-ATGATGAGATGAG
61413926 TGAGAGATGATGAGATGAG
1 TGAGAGATGATGAGATGAG
61413945 GGATGATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (19 bp):
TGAGAGATGATGAGATGAG
Found at i:61416033 original size:30 final size:30
Alignment explanation
Indices: 61415997--61416058 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
61415987 TGAATTATTT
* * *
61415997 TTAAAAATTTGGTTACTATTTTTGTAAATA
1 TTAAAAATTAGATGACTATTTTTGTAAATA
* *
61416027 TTAAAAATTAGATGCCTCTTTTTGTAAATA
1 TTAAAAATTAGATGACTATTTTTGTAAATA
61416057 TT
1 TT
61416059 TTCAAAAAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (30 bp):
TTAAAAATTAGATGACTATTTTTGTAAATA
Found at i:61423187 original size:16 final size:17
Alignment explanation
Indices: 61423156--61423190 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
61423146 ATAGGCCTCG
*
61423156 GTAAAATGCTTGACTAA
1 GTAAAATGCATGACTAA
61423173 GTAAAAT-CATGACTAA
1 GTAAAATGCATGACTAA
61423189 GT
1 GT
61423191 TATTCTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (17 bp):
GTAAAATGCATGACTAA
Found at i:61428190 original size:14 final size:15
Alignment explanation
Indices: 61428164--61428193 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
61428154 TCAATGTAAA
61428164 ATAAAATATAATTAC
1 ATAAAATATAATTAC
61428179 ATAAAA-ATAATTAC
1 ATAAAATATAATTAC
61428193 A
1 A
61428194 AACTAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAAATATAATTAC
Found at i:61443176 original size:15 final size:15
Alignment explanation
Indices: 61443148--61443180 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
61443138 CTTTGTTGTA
61443148 AATTTATTTATTTTT
1 AATTTATTTATTTTT
61443163 AATTATATTT-TTTTT
1 AATT-TATTTATTTTT
61443178 AAT
1 AAT
61443181 AAATGTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
AATTTATTTATTTTT
Found at i:61444203 original size:26 final size:26
Alignment explanation
Indices: 61444174--61444225 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
61444164 AGTGATTTGG
* *
61444174 TTTATATTCTAATGTTAGTTTCTTAT
1 TTTATATTCCAATGTTAATTTCTTAT
61444200 TTTATATTCCAATGTTAATTTCTTAT
1 TTTATATTCCAATGTTAATTTCTTAT
61444226 GTCCCATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.60
Consensus pattern (26 bp):
TTTATATTCCAATGTTAATTTCTTAT
Found at i:61447074 original size:25 final size:25
Alignment explanation
Indices: 61446989--61447074 Score: 61
Period size: 25 Copynumber: 3.3 Consensus size: 25
61446979 ATTAGAATTT
* * *
61446989 TAGATTTTTAT-TTCAGATTTTATGG
1 TAGATTTTTATATT-AGAATTTAAGC
61447014 TAGATTTTT-TAATTAG-ATTGTAAGATGC
1 TAGATTTTTAT-ATTAGAATT-T-A-A-GC
*
61447042 TATATTTTTATATTAGAATTTAAGC
1 TAGATTTTTATATTAGAATTTAAGC
61447067 TAGATTTT
1 TAGATTTT
61447075 AGGATTTTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
24 3 0.06
25 21 0.44
26 4 0.08
27 1 0.02
28 15 0.31
29 4 0.08
ACGTcount: A:0.30, C:0.03, G:0.14, T:0.52
Consensus pattern (25 bp):
TAGATTTTTATATTAGAATTTAAGC
Found at i:61447304 original size:129 final size:131
Alignment explanation
Indices: 61447099--61447365 Score: 351
Period size: 129 Copynumber: 2.0 Consensus size: 131
61447089 TTATATTTAT
* * * * *
61447099 ATTTATATTAGAATTAGATTTTTAGAATTTAAGATTTTGTAGTAGTTTCTTTTAAATGGATTCTA
1 ATTT-TATTAGAATTAGATTTTTAGAATTTAAGAGTTTATAGTAGATTCTTTTAAATAGATTATA
* * * ** * *
61447164 GGATTTCATATTTTTATATAAGAATAGATTGTAGATTTTCGGAGTTTTATATT-GAAATTTAAGT
65 GGATTTCATATTTGTATATAAGAATAGAATCTAGACCTTAGGAGTTTTATATTAG-AATTTAAGC
61447228 TAG
129 TAG
* *
61447231 ATTTTATTAGAATTAGA-TTTTGGAATTTAAGAGTTTATAGTAGATT-TTTTAATTAGATTATAG
1 ATTTTATTAGAATTAGATTTTTAGAATTTAAGAGTTTATAGTAGATTCTTTTAAATAGATTATAG
* *
61447294 GATTTCATATTTGTATATTAGAATAGAATCTAGACCTTAGGATTTTTATATTAGAATTTAAGCTA
66 GATTTCATATTTGTATATAAGAATAGAATCTAGACCTTAGGAGTTTTATATTAGAATTTAAGCTA
61447359 G
131 G
61447360 ATTTTA
1 ATTTTA
61447366 GAATTTTTTA
Statistics
Matches: 118, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
129 75 0.64
130 26 0.22
131 13 0.11
132 4 0.03
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.48
Consensus pattern (131 bp):
ATTTTATTAGAATTAGATTTTTAGAATTTAAGAGTTTATAGTAGATTCTTTTAAATAGATTATAG
GATTTCATATTTGTATATAAGAATAGAATCTAGACCTTAGGAGTTTTATATTAGAATTTAAGCTA
G
Found at i:61447360 original size:33 final size:33
Alignment explanation
Indices: 61447302--61447377 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
61447292 AGGATTTCAT
* * *
61447302 ATTTGTATATTAGAATAGAATCTAGACCTTAGG
1 ATTTTTATATTAGAATAGAAGCTAGACCTTAGA
** **
61447335 ATTTTTATATTAGAATTTAAGCTAGATTTTAGA
1 ATTTTTATATTAGAATAGAAGCTAGACCTTAGA
61447368 ATTTTT-TATT
1 ATTTTTATATT
61447378 TATATTAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 4 0.11
33 32 0.89
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (33 bp):
ATTTTTATATTAGAATAGAAGCTAGACCTTAGA
Found at i:61447510 original size:33 final size:32
Alignment explanation
Indices: 61447449--61447521 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
61447439 TTTCATTTTT
*
61447449 TTTATATTAGAATATATTCTAGACTTTAGGACA
1 TTTATATTAGAATATAGTCTAGACTTTAGGA-A
* * *
61447482 TTTATATTAGAATTTAAGT-TAGATTTTAGGAT
1 TTTATATTAGAATAT-AGTCTAGACTTTAGGAA
61447514 TTTATATT
1 TTTATATT
61447522 TATATTAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 8 0.23
33 25 0.71
34 2 0.06
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.49
Consensus pattern (32 bp):
TTTATATTAGAATATAGTCTAGACTTTAGGAA
Found at i:61447532 original size:38 final size:38
Alignment explanation
Indices: 61447481--61447706 Score: 129
Period size: 38 Copynumber: 6.1 Consensus size: 38
61447471 ACTTTAGGAC
*
61447481 ATTTATATTAGAATTTAAGTTAGATTTTAGGATTTTAT
1 ATTTATATTAGAATTTAATTTAGATTTTAGGATTTTAT
* * *
61447519 ATTTATATTAGAATTATATTTTAGAATTTAAGA---T-T
1 ATTTATATTAGAATT-TAATTTAGATTTTAGGATTTTAT
* **
61447554 -TTTATAGTAGAATTTTTAA-TTAGATGCTAGGATTTTAT
1 ATTTATATTAGAA--TTTAATTTAGATTTTAGGATTTTAT
** * * *
61447592 ATTTTTATATTAGAATAGATTTTATACTTTAGG-----AT
1 A--TTTATATTAGAATTTAATTTAGATTTTAGGATTTTAT
* * *
61447627 -TTTATATTAGAATATAAATT-GACTTTTAGGAATTTAT
1 ATTTATATTAGAATTTAATTTAGA-TTTTAGGATTTTAT
* * *
61447664 ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTT-T
1 ATTTATATTAGAATTTAA-TTTAGATTTTAGGATTTTAT
61447702 ATTTA
1 ATTTA
61447707 AGATTTTATA
Statistics
Matches: 139, Mismatches: 29, Indels: 40
0.67 0.14 0.19
Matches are distributed among these distances:
31 1 0.01
32 23 0.17
34 20 0.14
35 5 0.04
36 3 0.02
37 3 0.02
38 37 0.27
39 26 0.19
40 10 0.07
41 11 0.08
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.51
Consensus pattern (38 bp):
ATTTATATTAGAATTTAATTTAGATTTTAGGATTTTAT
Found at i:61447540 original size:32 final size:32
Alignment explanation
Indices: 61447504--61447692 Score: 85
Period size: 32 Copynumber: 5.4 Consensus size: 32
61447494 TTTAAGTTAG
61447504 ATTTTAGGATTTTATATTTATATTAGAATTAT
1 ATTTTAGGATTTTATATTTATATTAGAATTAT
* * * * *
61447536 ATTTTAGAATTTAAGATTTTTATAGTAGAATTTTT
1 ATTTTAGGATTT--TATATTTATATTAGAA-TTAT
*
61447571 AATTAGATGCTAGGATTTTATATTTTTATATTAGAA-TAG
1 -ATT---T--TAGGATTTTATA--TTTATATTAGAATTAT
* * *
61447610 ATTTTA-TACTTTAGGATTTTATATTAGAATATAAATT
1 ATTTTAGGATTTTA-TA-TTTATATTAGAAT-T--A-T
* *
61447647 GACTTTTAGGAATTTATATTTATATTAGAATTAA
1 -A-TTTTAGGATTTTATATTTATATTAGAATTAT
*
61447681 ATTTTAGAATTT
1 ATTTTAGGATTT
61447693 AAGATTTTTA
Statistics
Matches: 116, Mismatches: 21, Indels: 40
0.66 0.12 0.23
Matches are distributed among these distances:
32 38 0.33
33 4 0.03
34 14 0.12
35 5 0.04
36 4 0.03
37 1 0.01
38 17 0.15
39 10 0.09
40 5 0.04
41 18 0.16
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (32 bp):
ATTTTAGGATTTTATATTTATATTAGAATTAT
Found at i:61447654 original size:145 final size:144
Alignment explanation
Indices: 61447231--61447700 Score: 633
Period size: 144 Copynumber: 3.3 Consensus size: 144
61447221 TTTAAGTTAG
* * * * **
61447231 ATTT-TATTAGAATTAGATTTTGGAATTTAAGAGTTTATAGTAGATTTTTTAATTAGATTATAGG
1 ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTTATAGTAGAATTTTTAATTAGATGCTAGG
* * * * * *
61447295 ATTTCATATTTGTATATTAGAATAGAATCTAGACCTTAGGATTTTTATATTAGAATTTAAGCTAG
66 ATTTCATATTTTTATATTAGAATAGATTCTAGACTTTAGGACTTTTATATTAGAATTTAA-ATTG
* *
61447360 ATTTTAGAATTTTTT
130 ATTTTAGGATTTTAT
*
61447375 ATTTATATTA-AATTAAATTTTAGAATTTAAGATTTTATAGTAG-ATTTTAAATTAGATGCTAGG
1 ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTTATAGTAGAATTTTTAATTAGATGCTAGG
* * * * *
61447438 GTTTCATTTTTTTTATATTAGAATATATTCTAGACTTTAGGACATTTATATTAGAATTTAAGTTA
66 ATTTCA-TATTTTTATATTAGAATAGATTCTAGACTTTAGGACTTTTATATTAGAATTTAAATT-
61447503 GATTTTAGGATTTTAT
129 GATTTTAGGATTTTAT
*
61447519 ATTTATATTAGAATTATATTTTAGAATTTAAGATTTTTATAGTAGAATTTTTAATTAGATGCTAG
1 ATTTATATTAGAATTAAATTTTAGAATTTAAGA-TTTTATAGTAGAATTTTTAATTAGATGCTAG
* * * *
61447584 GATTTTATATTTTTATATTAGAATAGATTTTATACTTTAGGA-TTTTATATTAGAATATAAATTG
65 GATTTCATATTTTTATATTAGAATAGATTCTAGACTTTAGGACTTTTATATTAGAATTTAAATTG
*
61447648 ACTTTTAGGAATTTAT
130 A-TTTTAGGATTTTAT
61447664 ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTT
1 ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTT
61447701 TATTTAAGAT
Statistics
Matches: 287, Mismatches: 32, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
143 22 0.08
144 111 0.39
145 89 0.31
146 42 0.15
147 23 0.08
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (144 bp):
ATTTATATTAGAATTAAATTTTAGAATTTAAGATTTTATAGTAGAATTTTTAATTAGATGCTAGG
ATTTCATATTTTTATATTAGAATAGATTCTAGACTTTAGGACTTTTATATTAGAATTTAAATTGA
TTTTAGGATTTTAT
Found at i:61447715 original size:12 final size:13
Alignment explanation
Indices: 61447689--61447713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61447679 AAATTTTAGA
61447689 ATTTAAGATTTTT
1 ATTTAAGATTTTT
61447702 ATTTAAGATTTT
1 ATTTAAGATTTT
61447714 ATAGTAGCTT
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
ATTTAAGATTTTT
Found at i:61448312 original size:158 final size:158
Alignment explanation
Indices: 61448024--61448338 Score: 551
Period size: 158 Copynumber: 2.0 Consensus size: 158
61448014 AACAGATTCT
61448024 TGGAGATTCAACCGAACCTTCTCCACAATTCAAAACTAACTCGTCATTTATCTTGAGACTTCCGT
1 TGGAGATTCAACCGAACCTTCTCCACAATTCAAAACTAACTCGTCATTTATCTTGAGACTTCCGT
* *
61448089 ACCCACGCAATCCAATCCTTTCTCACCGTCGTTAGAACCAGATCCGATACATCCGTAGCCCAGTT
66 ACCCACGCAATCCAATCCTTTCTCACCGCCGTCAGAACCAGATCCGATACATCCGTAGCCCAGTT
61448154 CCAGCAGTCCCCTTTCCTCCGTCCTTCA
131 CCAGCAGTCCCCTTTCCTCCGTCCTTCA
*
61448182 TGGAGATTCAACCGAACCTTCTCCA-AAGTTCAAAACTAACTCGTCATTTATCTTGCGACTTCCG
1 TGGAGATTCAACCGAACCTTCTCCACAA-TTCAAAACTAACTCGTCATTTATCTTGAGACTTCCG
* *
61448246 TACCCACGCAATCCAGTCCTTTCTCACCGCCGTCAGAACCAGATCCGGTACATCCGTAGCCCAGT
65 TACCCACGCAATCCAATCCTTTCTCACCGCCGTCAGAACCAGATCCGATACATCCGTAGCCCAGT
**
61448311 TCTGGCAGTCCCCTTTCCTCCGTCCTTC
130 TCCAGCAGTCCCCTTTCCTCCGTCCTTC
61448339 GATAGCTAGA
Statistics
Matches: 149, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
157 2 0.01
158 147 0.99
ACGTcount: A:0.23, C:0.36, G:0.14, T:0.27
Consensus pattern (158 bp):
TGGAGATTCAACCGAACCTTCTCCACAATTCAAAACTAACTCGTCATTTATCTTGAGACTTCCGT
ACCCACGCAATCCAATCCTTTCTCACCGCCGTCAGAACCAGATCCGATACATCCGTAGCCCAGTT
CCAGCAGTCCCCTTTCCTCCGTCCTTCA
Found at i:61453731 original size:55 final size:55
Alignment explanation
Indices: 61453648--61453755 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
61453638 TAGCTTTTCT
* *
61453648 TTTAAAAAAGAATAGATTTTAGACTTTAGGATTTTTTATTAGAATCTAAATTGTC
1 TTTAAAAAAGAATAGATTTTAGAATTTAGGATTTTATATTAGAATCTAAATTGTC
* *
61453703 TTTAAAAAAGATTATATTTTAGAATTTAGGATTTTATATTAGAATCTAAATTG
1 TTTAAAAAAGAATAGATTTTAGAATTTAGGATTTTATATTAGAATCTAAATTG
61453756 AATTTTAGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (55 bp):
TTTAAAAAAGAATAGATTTTAGAATTTAGGATTTTATATTAGAATCTAAATTGTC
Found at i:61454258 original size:15 final size:15
Alignment explanation
Indices: 61454221--61454250 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61454211 GTTAGTATCA
*
61454221 AGTTTTTTTTTATTT
1 AGTTATTTTTTATTT
61454236 AGTTATTTTTTATTT
1 AGTTATTTTTTATTT
61454251 GTTCATTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (15 bp):
AGTTATTTTTTATTT
Found at i:61457542 original size:19 final size:19
Alignment explanation
Indices: 61457518--61457567 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
61457508 ATCTTTCAAG
61457518 ATTGCATATCATATCCAAA
1 ATTGCATATCATATCCAAA
* *
61457537 ATTGCATATATCATATCTAAG
1 ATTGC--ATATCATATCCAAA
61457558 ATTGCATATC
1 ATTGCATATC
61457568 CTTGAAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 10 0.37
21 17 0.63
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (19 bp):
ATTGCATATCATATCCAAA
Found at i:61457549 original size:21 final size:21
Alignment explanation
Indices: 61457523--61457566 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
61457513 TCAAGATTGC
61457523 ATATCATATCCAAAATTGCAT
1 ATATCATATCCAAAATTGCAT
* *
61457544 ATATCATATCTAAGATTGCAT
1 ATATCATATCCAAAATTGCAT
61457565 AT
1 AT
61457567 CCTTGAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (21 bp):
ATATCATATCCAAAATTGCAT
Found at i:61458128 original size:44 final size:44
Alignment explanation
Indices: 61458058--61458357 Score: 352
Period size: 44 Copynumber: 6.8 Consensus size: 44
61458048 ACCACTATGG
* *
61458058 GAAGACAAAATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* *
61458102 GAAAACAAGATTTGCTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* * * * * *
61458146 AAAAACAATATCT-ATCATATTTGATCTACTTCACGCCAATATAT
1 GAAGACAAGATCTGCT-ATCTTTGATCTACTTCACGCCAATACAT
* * * * * ***
61458190 GGAGACAAGATCTGCTTTCTTTGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTC-ACGCCAATACAT
* * *
61458235 GAAGACAAGATCTGTTATCTTCGATCTACTTCACACCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
*
61458279 GAAGACAAGATCTGCCATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
*
61458323 GAAGACAAGATCTGCT-TTTTTCGATCTACTTCACG
1 GAAGACAAGATCTGCTATCTTT-GATCTACTTCACG
61458358 ACAACCCAGG
Statistics
Matches: 215, Mismatches: 37, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
43 5 0.02
44 174 0.81
45 36 0.17
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
Found at i:61458128 original size:118 final size:119
Alignment explanation
Indices: 61457914--61458143 Score: 329
Period size: 118 Copynumber: 1.9 Consensus size: 119
61457904 GAATTGTATT
* * * * * * *
61457914 TTCGATCTACTTTGCCACCAGTGTGGGAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGA
1 TTCGATCTACTTTGCCACCACTATGGGAAGACAAAATCTGCTACCTTCGATCTACTTCACGCCAA
**
61457979 TACATGAGGACAAGATCTGCTTCTTTCGATCTACTT-CGCCAATACCTACTTTC
66 TACATGAAAACAAGATCTGCTTCTTTCGATCTACTTACGCCAATACCTACTTTC
*
61458032 TTCGATCTACTTTGCCACCACTATGGGAAGACAAAATCTGCTATCTTCGATCTACTTCACGCCAA
1 TTCGATCTACTTTGCCACCACTATGGGAAGACAAAATCTGCTACCTTCGATCTACTTCACGCCAA
*
61458097 TACATGAAAACAAGATTTGCTATCTTT-GATCTACTTCACGCCAATAC
66 TACATGAAAACAAGATCTGCT-TCTTTCGATCTACTT-ACGCCAATAC
61458144 ATAAAAACAA
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
118 84 0.86
119 5 0.05
120 9 0.09
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (119 bp):
TTCGATCTACTTTGCCACCACTATGGGAAGACAAAATCTGCTACCTTCGATCTACTTCACGCCAA
TACATGAAAACAAGATCTGCTTCTTTCGATCTACTTACGCCAATACCTACTTTC
Found at i:61458261 original size:133 final size:133
Alignment explanation
Indices: 61458106--61458354 Score: 374
Period size: 133 Copynumber: 1.9 Consensus size: 133
61458096 ATACATGAAA
* * * * *
61458106 ACAAGATTTGCTATCTTTGATCTACTTCACGCCAATACATAAAAACAATATCTATCATATTTGAT
1 ACAAGATCTGCTATCTTCGATCTACTTCACACCAATACATAAAAACAAGATCTACCATATTTGAT
* *
61458171 CTACTTCACGCCAATATATGGAGACAAGATCTGCTTTCTTT-GATCTACTTCGCCACCAGTATGG
66 CTACTTCACGCCAATACATGAAGACAAGATCTGCTTT-TTTCGATCTACTTCGCCACCAGTATGG
61458235 GAAG
130 GAAG
* * * * *
61458239 ACAAGATCTGTTATCTTCGATCTACTTCACACCAATACATGAAGACAAGATCTGCCATCTTTGAT
1 ACAAGATCTGCTATCTTCGATCTACTTCACACCAATACATAAAAACAAGATCTACCATATTTGAT
61458304 CTACTTCACGCCAATACATGAAGACAAGATCTGCTTTTTTCGATCTACTTC
66 CTACTTCACGCCAATACATGAAGACAAGATCTGCTTTTTTCGATCTACTTC
61458355 ACGACAACCC
Statistics
Matches: 103, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
132 3 0.03
133 100 0.97
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (133 bp):
ACAAGATCTGCTATCTTCGATCTACTTCACACCAATACATAAAAACAAGATCTACCATATTTGAT
CTACTTCACGCCAATACATGAAGACAAGATCTGCTTTTTTCGATCTACTTCGCCACCAGTATGGG
AAG
Found at i:61458351 original size:177 final size:177
Alignment explanation
Indices: 61458027--61458357 Score: 511
Period size: 177 Copynumber: 1.9 Consensus size: 177
61458017 CCAATACCTA
*
61458027 CTTTCTTCGATCTACTTTGCCACCACTATGGGAAGACAAAATCTGCTATCTTCGATCTACTTCAC
1 CTTTCTTCGATCTACTTCGCCACCACTATGGGAAGACAAAATCTGCTATCTTCGATCTACTTCAC
* * * *
61458092 GCCAATACATGAAAACAAGATTTGCTATCTTTGATCTACTTCACGCCAATACATAAAAACAATAT
66 ACCAATACATGAAAACAAGATCTGCCATCTTTGATCTACTTCACGCCAATACATAAAAACAAGAT
*
61458157 CTATCATATTTGATCTACTTCACGCCAATATATGGAGACAAGATCTG
131 CTAGCATATTTGATCTACTTCACGCCAATATATGGAGACAAGATCTG
* * * *
61458204 CTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTTATCTTCGATCTACTTCAC
1 CTTTCTTCGATCTACTTCGCCACCACTATGGGAAGACAAAATCTGCTATCTTCGATCTACTTCAC
* * *
61458269 ACCAATACATGAAGACAAGATCTGCCATCTTTGATCTACTTCACGCCAATACATGAAGACAAGAT
66 ACCAATACATGAAAACAAGATCTGCCATCTTTGATCTACTTCACGCCAATACATAAAAACAAGAT
* *
61458334 CT-GCTTTTTTCGATCTACTTCACG
131 CTAGCATATTT-GATCTACTTCACG
61458358 ACAACCCAGG
Statistics
Matches: 138, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
176 5 0.04
177 133 0.96
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (177 bp):
CTTTCTTCGATCTACTTCGCCACCACTATGGGAAGACAAAATCTGCTATCTTCGATCTACTTCAC
ACCAATACATGAAAACAAGATCTGCCATCTTTGATCTACTTCACGCCAATACATAAAAACAAGAT
CTAGCATATTTGATCTACTTCACGCCAATATATGGAGACAAGATCTG
Found at i:61458409 original size:88 final size:88
Alignment explanation
Indices: 61458295--61459144 Score: 1103
Period size: 88 Copynumber: 9.7 Consensus size: 88
61458285 AAGATCTGCC
* * * * * * * * * * * * *
61458295 ATCTTTGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTTTTTTCGATCTACTTCACGA
1 ATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
61458359 CAACCCAGGGAGGCAAGGCTGGT
66 CAACCCAGGGAGGCAAGGCTGGT
* * * *
61458382 ATCTTTGATCTGCTTCATTGTCGATACAGTAAGGCAAGATCTGCTATCTTCAACCTACTCCACTA
1 ATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
*
61458447 CGACCCAGGGAGGCAAGGCTGGT
66 CAACCCAGGGAGGCAAGGCTGGT
* *
61458470 ATCTTTGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
1 ATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
61458535 CAACCCAGGGAGGCAAGGCTGGT
66 CAACCCAGGGAGGCAAGGCTGGT
* * ** * * * *
61458558 ATCTTCGATCTGTTTCGCTGTCGATGTAAGAATGCAAGATCTACTATCTTTAACCTGCTCCACTA
1 ATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
*
61458623 CAACCTAGGGAGGCAAGGCTGGT
66 CAACCCAGGGAGGCAAGGCTGGT
*
61458646 ATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
1 ATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
61458711 CAACCCAGGGAGGCAAGGCTGGT
66 CAACCCAGGGAGGCAAGGCTGGT
* * ** * * * *
61458734 ATCTTCGATCTGTTTCGCTGTCGATGTAAGAATGCAAGATCTACTATCTTTAACCTGCTCCACTA
1 ATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
*
61458799 CAACCTAGGGAGGCAAGGCTGGT
66 CAACCCAGGGAGGCAAGGCTGGT
* * * *
61458822 ATCTTCGATCTGCTTCACTGTTGATACAGGAATGCAAGATCTACTATTTTCAACCTGCTCCACTA
1 ATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
* *
61458887 CAACTCAGGAAGGCAAGGCTGGT
66 CAACCCAGGGAGGCAAGGCTGGT
* *
61458910 ATCTTCGATCTGCTTCACTGTCGGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCAACTA
1 ATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
* *
61458975 CAACCTAGGGAGGCAGGGCTGGT
66 CAACCCAGGGAGGCAAGGCTGGT
* * * * *
61458998 ATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTACTATCTTCAACTTACTCCACTA
1 ATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
* * *
61459063 CAATCTAGGGAGGCAAGGCT-AT
66 CAACCCAGGGAGGCAAGGCTGGT
* * * * * *
61459085 ATCTTCGATCTGCTTCACCGTC-AGTACAGGAAGGCAAAATATGTTATTTTCAACATGCTC
1 ATCTTCGATCTGCTTCACTGTCGA-TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
61459145 TGCTGCAAAC
Statistics
Matches: 670, Mismatches: 91, Indels: 4
0.88 0.12 0.01
Matches are distributed among these distances:
86 1 0.00
87 65 0.10
88 604 0.90
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (88 bp):
ATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
CAACCCAGGGAGGCAAGGCTGGT
Found at i:61460757 original size:15 final size:15
Alignment explanation
Indices: 61460737--61460765 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
61460727 AAGAAGAGTT
61460737 TTTTTCTTTTTTTTC
1 TTTTTCTTTTTTTTC
61460752 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
61460766 GCACTATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTCTTTTTTTTC
Found at i:61467890 original size:19 final size:19
Alignment explanation
Indices: 61467819--61467890 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
61467809 CATATCTTTC
* *
61467819 AAGATTGCATATTATATCC
1 AAGATTGCATATCATATCT
61467838 AAGATTGCATATATCATATCT
1 AAGATTGC--ATATCATATCT
61467859 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCT
*
61467878 AAGATTGGATATC
1 AAGATTGCATATC
61467891 CTTGAAGATT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 31 0.65
21 17 0.35
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (19 bp):
AAGATTGCATATCATATCT
Found at i:61480837 original size:15 final size:15
Alignment explanation
Indices: 61480812--61480850 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
61480802 TTCTTCTTAT
*
61480812 TCAAATTTCTTTGCA
1 TCAATTTTCTTTGCA
* *
61480827 TCCATTTTCTTTGCT
1 TCAATTTTCTTTGCA
61480842 TCAATTTTC
1 TCAATTTTC
61480851 ATTAGTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.18, C:0.23, G:0.05, T:0.54
Consensus pattern (15 bp):
TCAATTTTCTTTGCA
Found at i:61481491 original size:2 final size:2
Alignment explanation
Indices: 61481479--61481522 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
61481469 TATTTTTCTC
* * *
61481479 AT AT TT AT AT AT AT AT AT GT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61481521 AT
1 AT
61481523 TTTAAATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61482214 original size:2 final size:2
Alignment explanation
Indices: 61482202--61482245 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
61482192 TATTTTTCTC
* * *
61482202 AT AT TT AT AT AT AT AT AT GT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61482244 AT
1 AT
61482246 TTTAAATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61482850 original size:701 final size:701
Alignment explanation
Indices: 61481932--61483333 Score: 2777
Period size: 701 Copynumber: 2.0 Consensus size: 701
61481922 AATTTGATCC
61481932 ATTTGAACGGCGCCGTTTTAGAGGAGAAGGGAAAATTTCCCTTCCAGCCCCTCTATGTAATTCGC
1 ATTTGAACGGCGCCGTTTTAGAGGAGAAGGGAAAATTTCCCTTCCAGCCCCTCTATGTAATTCGC
61481997 GCGTTCAAATTAGACCTTTTACTTTTATTTATTTGCAGATTTACCCCAGATTTTTTAATTGCAAT
66 GCGTTCAAATTAGACCTTTTACTTTTATTTATTTGCAGATTTACCCCAGATTTTTTAATTGCAAT
61482062 TCAATTTAGTTTTTTTTATGTTCTTTTTATTTATTTTATTAATTAATAATGTAATTATTATTTTT
131 TCAATTTAGTTTTTTTTATGTTCTTTTTATTTATTTTATTAATTAATAATGTAATTATTATTTTT
*
61482127 ATTTTTATTTTTTTAAAAATCTATATATGTATATTTTTATGAACATACTTATTTTTTTCAGCTAA
196 ATTTTCATTTTTTTAAAAATCTATATATGTATATTTTTATGAACATACTTATTTTTTTCAGCTAA
61482192 TATTTTTCTCATATTTATATATATATATGTATATATACATATATATATATATATTTTAAATTAAT
261 TATTTTTCTCATATTTATATATATATATGTATATATACATATATATATATATATTTTAAATTAAT
61482257 TTTGATAATGTACTCATTATTTAATTTTTTTTATCTATGTATATTCCTTTTATATGTACATGTAT
326 TTTGATAATGTACTCATTATTTAATTTTTTTTATCTATGTATATTCCTTTTATATGTACATGTAT
61482322 TTTTTTAACGAATATTTTCCTATATTTTTTTAAAGAATATTTTCATATTTATATGTATATATTTA
391 TTTTTTAACGAATATTTTCCTATATTTTTTTAAAGAATATTTTCATATTTATATGTATATATTTA
61482387 CGTTTTTTTTAAATGATTAAATACTCACTTTTTCTTTTTTAAAATATACCTATTTTTTATTATTT
456 CGTTTTTTTTAAATGATTAAATACTCACTTTTTCTTTTTTAAAATATACCTATTTTTTATTATTT
61482452 TATATATGTACGTATAATTATATTTTTTTCTTTATTTGCATAAGTATATTATGTATTGTATTTAT
521 TATATATGTACGTATAATTATATTTTTTTCTTTATTTGCATAAGTATATTATGTATTGTATTTAT
61482517 ATATAAATTCTATAACCCAAAATTTTATTTGTAAATTTTTTTTTAATCTTCATAATTTTCATGTG
586 ATATAAATTCTATAACCCAAAATTTTATTTGTAAATTTTTTTTTAATCTTCATAATTTTCATGTG
61482582 TATATTATATATCTTCTGATCTTTATTTATTTTGTTTGCTTTCCCATTCGT
651 TATATTATATATCTTCTGATCTTTATTTATTTTGTTTGCTTTCCCATTCGT
61482633 ATTTGAACGGCGCCGTTTTAGAGGAGAAGGGAAAATTTCCCTTCCAGCCCCTCTATGTAATTCGC
1 ATTTGAACGGCGCCGTTTTAGAGGAGAAGGGAAAATTTCCCTTCCAGCCCCTCTATGTAATTCGC
*
61482698 GCGTTCAAATTAGACCTTTTACTTTTATTTATTTGCGGATTTACCCCAGATTTTTTAATTGCAAT
66 GCGTTCAAATTAGACCTTTTACTTTTATTTATTTGCAGATTTACCCCAGATTTTTTAATTGCAAT
*
61482763 TCAATTTAGTTTTTTTTATGTTCTTTTTATTTATTTTATTAATTAATAGTGTAATTATTATTTTT
131 TCAATTTAGTTTTTTTTATGTTCTTTTTATTTATTTTATTAATTAATAATGTAATTATTATTTTT
61482828 ATTTTCATTTTTTTAAAAATCTATATATGTATATTTTTATGAACATACTTATTTTTTTCAGCTAA
196 ATTTTCATTTTTTTAAAAATCTATATATGTATATTTTTATGAACATACTTATTTTTTTCAGCTAA
61482893 TATTTTTCTCATATTTATATATATATATGTATATATACATATATATATATATATTTTAAATTAAT
261 TATTTTTCTCATATTTATATATATATATGTATATATACATATATATATATATATTTTAAATTAAT
61482958 TTTGATAATGTACTCATTATTTAATTTTTTTTATCTATGTATATTCCTTTTATATGTACATGTAT
326 TTTGATAATGTACTCATTATTTAATTTTTTTTATCTATGTATATTCCTTTTATATGTACATGTAT
61483023 TTTTTTAACGAATATTTTCCTATATTTTTTTAAAGAATATTTTCATATTTATATGTATATATTTA
391 TTTTTTAACGAATATTTTCCTATATTTTTTTAAAGAATATTTTCATATTTATATGTATATATTTA
61483088 CGTTTTTTTTAAATGATTAAATACTCACTTTTTCTTTTTTAAAATATACCTATTTTTTATTATTT
456 CGTTTTTTTTAAATGATTAAATACTCACTTTTTCTTTTTTAAAATATACCTATTTTTTATTATTT
61483153 TATATATGTACGTATAATTATATTTTTTTCTTTATTTGCATAAGTATATTATGTATTGTATTTAT
521 TATATATGTACGTATAATTATATTTTTTTCTTTATTTGCATAAGTATATTATGTATTGTATTTAT
61483218 ATATAAATTCTATAACCCAAAATTTTATTTGTAAATTTTTTTTTAATCTTCATAATTTTCATGTG
586 ATATAAATTCTATAACCCAAAATTTTATTTGTAAATTTTTTTTTAATCTTCATAATTTTCATGTG
61483283 TATATTATATATCTTCTGATCTTTATTTATTTTGTTTGCTTTCCCATTCGT
651 TATATTATATATCTTCTGATCTTTATTTATTTTGTTTGCTTTCCCATTCGT
61483334 TGTATAATTG
Statistics
Matches: 698, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
701 698 1.00
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (701 bp):
ATTTGAACGGCGCCGTTTTAGAGGAGAAGGGAAAATTTCCCTTCCAGCCCCTCTATGTAATTCGC
GCGTTCAAATTAGACCTTTTACTTTTATTTATTTGCAGATTTACCCCAGATTTTTTAATTGCAAT
TCAATTTAGTTTTTTTTATGTTCTTTTTATTTATTTTATTAATTAATAATGTAATTATTATTTTT
ATTTTCATTTTTTTAAAAATCTATATATGTATATTTTTATGAACATACTTATTTTTTTCAGCTAA
TATTTTTCTCATATTTATATATATATATGTATATATACATATATATATATATATTTTAAATTAAT
TTTGATAATGTACTCATTATTTAATTTTTTTTATCTATGTATATTCCTTTTATATGTACATGTAT
TTTTTTAACGAATATTTTCCTATATTTTTTTAAAGAATATTTTCATATTTATATGTATATATTTA
CGTTTTTTTTAAATGATTAAATACTCACTTTTTCTTTTTTAAAATATACCTATTTTTTATTATTT
TATATATGTACGTATAATTATATTTTTTTCTTTATTTGCATAAGTATATTATGTATTGTATTTAT
ATATAAATTCTATAACCCAAAATTTTATTTGTAAATTTTTTTTTAATCTTCATAATTTTCATGTG
TATATTATATATCTTCTGATCTTTATTTATTTTGTTTGCTTTCCCATTCGT
Found at i:61482915 original size:2 final size:2
Alignment explanation
Indices: 61482903--61482946 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
61482893 TATTTTTCTC
* * *
61482903 AT AT TT AT AT AT AT AT AT GT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61482945 AT
1 AT
61482947 TTTAAATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61483834 original size:98 final size:98
Alignment explanation
Indices: 61483732--61483928 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
61483722 TTAAAAATAA
* *
61483732 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGAGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGAGATTTC
61483797 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
61483830 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGAGATTTC
*
61483895 TTAAATCTTGGATAAGTGGATGTTTTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
61483928 T
1 T
61483929 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGAGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:61503297 original size:5 final size:5
Alignment explanation
Indices: 61503287--61503314 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
61503277 ATTTGTTTAT
61503287 GGATG GGATG GGATG GGATG GGATG GGA
1 GGATG GGATG GGATG GGATG GGATG GGA
61503315 CTGGACGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.61, T:0.18
Consensus pattern (5 bp):
GGATG
Found at i:61503324 original size:15 final size:15
Alignment explanation
Indices: 61503286--61503330 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
61503276 AATTTGTTTA
61503286 TGGATGGGATGGGA-
1 TGGATGGGATGGGAC
61503300 TGGGATGGGATGGGAC
1 T-GGATGGGATGGGAC
* *
61503316 TGGACGGGACGGGAC
1 TGGATGGGATGGGAC
61503331 CATTCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 1 0.04
15 25 0.93
16 1 0.04
ACGTcount: A:0.20, C:0.09, G:0.56, T:0.16
Consensus pattern (15 bp):
TGGATGGGATGGGAC
Found at i:61505323 original size:31 final size:31
Alignment explanation
Indices: 61505288--61505374 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
61505278 GATGAACTGA
* * *
61505288 CTATTCTGTGTTTATTGTCCTAACAGATTGT
1 CTATTTTGTGTTTACTATCCTAACAGATTGT
*
61505319 CTATTTTGTGTTTACTATCCTAACGGATTGT
1 CTATTTTGTGTTTACTATCCTAACAGATTGT
*
61505350 CTGTTTTGTGTTTACTATCCTAACA
1 CTATTTTGTGTTTACTATCCTAACA
61505375 AACTTACCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (31 bp):
CTATTTTGTGTTTACTATCCTAACAGATTGT
Found at i:61507901 original size:8 final size:8
Alignment explanation
Indices: 61507888--61507924 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
61507878 TGGTCTCTGT
61507888 TTCTTTTA
1 TTCTTTTA
*
61507896 TTCTTTTGT
1 TTCTTTT-A
61507905 TTCTTTTA
1 TTCTTTTA
61507913 TTCTTTTA
1 TTCTTTTA
61507921 TTCT
1 TTCT
61507925 ATTCCTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.08, C:0.14, G:0.03, T:0.76
Consensus pattern (8 bp):
TTCTTTTA
Found at i:61507907 original size:17 final size:17
Alignment explanation
Indices: 61507885--61507919 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
61507875 GAATGGTCTC
61507885 TGTTTCTTTTATTCTTT
1 TGTTTCTTTTATTCTTT
61507902 TGTTTCTTTTATTCTTT
1 TGTTTCTTTTATTCTTT
61507919 T
1 T
61507920 ATTCTATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.11, G:0.06, T:0.77
Consensus pattern (17 bp):
TGTTTCTTTTATTCTTT
Found at i:61507972 original size:22 final size:24
Alignment explanation
Indices: 61507944--61507990 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
61507934 ATGTATTAGT
61507944 TAATAAT-A-ATAACAATATATTA
1 TAATAATCATATAACAATATATTA
* *
61507966 TAATAATCATATAATAATATTTTA
1 TAATAATCATATAACAATATATTA
61507990 T
1 T
61507991 TCACAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 13 0.62
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATAATCATATAACAATATATTA
Found at i:61508123 original size:3 final size:3
Alignment explanation
Indices: 61508115--61508142 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
61508105 ATTTCACAAT
61508115 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
61508143 CATATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:61510813 original size:26 final size:26
Alignment explanation
Indices: 61510784--61510868 Score: 62
Period size: 27 Copynumber: 3.2 Consensus size: 26
61510774 TGGATTTAAA
*
61510784 CATAGCTACAGGAGAAAATGTTTCAT
1 CATAGCTACAGAAGAAAATGTTTCAT
* ** * * * * *
61510810 CATAGTCAACACCATAAATTTATTTAAA
1 CATAG-CTACAGAAGAAA-ATGTTTCAT
*
61510838 CATAGCTACAGAAGAAAAGGTTTCAT
1 CATAGCTACAGAAGAAAATGTTTCAT
61510864 CATAG
1 CATAG
61510869 TCAACACCAT
Statistics
Matches: 40, Mismatches: 17, Indels: 4
0.66 0.28 0.07
Matches are distributed among these distances:
26 14 0.35
27 16 0.40
28 10 0.25
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.27
Consensus pattern (26 bp):
CATAGCTACAGAAGAAAATGTTTCAT
Found at i:61510836 original size:54 final size:54
Alignment explanation
Indices: 61510777--61510884 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
61510767 ATCCTAATGG
* *
61510777 ATTTAAACATAGCTACAGGAGAAAATGTTTCATCATAGTCAACACCATAAATTT
1 ATTTAAACATAGCTACAGAAGAAAAGGTTTCATCATAGTCAACACCATAAATTT
61510831 ATTTAAACATAGCTACAGAAGAAAAGGTTTCATCATAGTCAACACCATAAATTT
1 ATTTAAACATAGCTACAGAAGAAAAGGTTTCATCATAGTCAACACCATAAATTT
61510885 GGCGAAAACC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (54 bp):
ATTTAAACATAGCTACAGAAGAAAAGGTTTCATCATAGTCAACACCATAAATTT
Found at i:61515071 original size:5 final size:5
Alignment explanation
Indices: 61515061--61515088 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
61515051 ATTTGTTTAT
61515061 GGATG GGATG GGATG GGATG GGATG GGA
1 GGATG GGATG GGATG GGATG GGATG GGA
61515089 CTGGACGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.61, T:0.18
Consensus pattern (5 bp):
GGATG
Found at i:61515098 original size:15 final size:15
Alignment explanation
Indices: 61515060--61515104 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
61515050 AATTTGTTTA
61515060 TGGATGGGATGGGA-
1 TGGATGGGATGGGAC
61515074 TGGGATGGGATGGGAC
1 T-GGATGGGATGGGAC
* *
61515090 TGGACGGGACGGGAC
1 TGGATGGGATGGGAC
61515105 CATTCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 1 0.04
15 25 0.93
16 1 0.04
ACGTcount: A:0.20, C:0.09, G:0.56, T:0.16
Consensus pattern (15 bp):
TGGATGGGATGGGAC
Found at i:61515855 original size:106 final size:102
Alignment explanation
Indices: 61515585--61516609 Score: 440
Period size: 108 Copynumber: 9.5 Consensus size: 102
61515575 CAGGTATTTG
** ** * * *
61515585 TCTGTCAATGGCCGGCACCAAAATATGAAAAAAGGTAAAAAAAAATTTGGTGGTGGTCTGCCAAT
1 TCTGTCAATGGTAGGCACCAGTATACGAAAAAA-GTAAAAAAAAATTTTGTGGTGGCCTGCCAAT
* ****
61515650 GGCCGGCACCACC-TTAAAAAGTAATTTTTTTTTTACTTTTTT
65 GGTCGGCACCACCTTTTTCCA--AA--TTTTTTTTAC-TTTTT
* * * * * *
61515692 TGTGTCAATTGTAGGCACCAGTAT-------AAG-AAAAAAAAAATTAGTGGTAGCCTGCTAATG
1 TCTGTCAATGGTAGGCACCAGTATACGAAAAAAGTAAAAAAAAATTTTGTGGTGGCCTGCCAATG
*
61515749 GTCGGCACCACCTTTTTTCAAATTTTTTTTACTTTTT
66 GTCGGCACCACCTTTTTCCAAATTTTTTTTACTTTTT
* * *
61515786 TCATGTCAATGGTAGGAACCAATATACGAAAAAAAGTAAAAAAGAAAATTTGATGGTGGCCTGCC
1 TC-TGTCAATGGTAGGCACCAGTATACG-AAAAAAGTAAAAAA-AAATTTTG-TGGTGGCCTGCC
* *****
61515851 AATGG-CTGGCACCACCTTTTTGCAAA-AAAAATTACTTTTT
62 AATGGTC-GGCACCACCTTTTTCCAAATTTTTTTTACTTTTT
** * * *
61515891 TC-GT--ATACTAGTGCTTGCCATTGAAACGAAAAAAGTAAAAAAAAATTGTTTTGTTGGTGGCC
1 TCTGTCAATGGTAG-GC--ACCAGT-ATACGAAAAAAGTAAAAAAAAA---TTTTG-TGGTGGCC
* * *
61515953 TGCCAATGGCCGGCATCACCTTTTTCCCAAATTTTTTTTACTTTTGG
58 TGCCAATGGTCGGCACCACCTTTTT-CCAAATTTTTTTTACTTTT-T
* * ***
61516000 TCTGTCAATGGCCA-GCACCAGTATACGAAAAAAGGGGAAAAAATGTTTTTTTGTGGTGGCCTGC
1 TCTGTCAATGG-TAGGCACCAGTATACGAAAAAA--GTAAAAAA--AAATTTTGTGGTGGCCTGC
* * * * *
61516064 CAATGATTGGCTCCACCTGTTTCCAATTTTTTTTTA-TTTTT
61 CAATGGTCGGCACCACCTTTTTCCAAATTTTTTTTACTTTTT
* *
61516105 AGTCTGTCAATGGTTGGCATCAGTATACGAAAAAAGTAAAAAAAAATTGTTTTGGTGGTGGCCTG
1 --TCTGTCAATGGTAGGCACCAGTATACGAAAAAAGTAAAAAAAAA---TTTT-GTGGTGGCCTG
* ** * ** ** ****
61516170 CCAATGGCCTTTTTTTGTGGTGGCCTGCCAATGGCCAGCACCACCTTTTTCCCAATTTTTTTTAC
60 CCAATGG--------T-CGG-CACC-ACCTTTTTCCA--A-ATTTTTTT-------------TAC
61516235 TTTTT
98 TTTTT
** *
61516240 TCGTGTCAATGGCCGGCACCAGTATACGAAAAAAG--AAAAAAAATTTGGTGGTGGCCTGCCAAT
1 TC-TGTCAATGGTAGGCACCAGTATACGAAAAAAGTAAAAAAAAATTTTGTGGTGGCCTGCCAAT
* * * *
61516303 GGCCAGCTCCACCTGTTTCC-AATTTTTTTTA-TTTTT
65 GGTCGGCACCACCTTTTTCCAAATTTTTTTTACTTTTT
* *
61516339 GGTCTGTCAATGGCT-GGCACCAGTATACGAAAAAAGTAAAAAAAAAAATTTGGTGGGGGCCTGC
1 --TCTGTCAATGG-TAGGCACCAGTATACGAAAAAAGT--AAAAAAAAATTTTGTGGTGGCCTGC
** * *
61516403 CAATGGTTTGCTCCACCTGTTTCCAAATTTTGTTTCTTTTTACTTTTT
61 CAATGGTCGGCACCACCTTTTTCCAAA-----TTT-TTTTTACTTTTT
* * * *
61516451 TCATGTTAATGGCAGGCATCAGTATACGAAAAAAGTAAAAAAAATTATTTTTTGGTGGTGGCTTG
1 TC-TGTCAATGGTAGGCACCAGTATACGAAAAAAGTAAAAAAAA--A--TTTT-GTGGTGGCCTG
*
61516516 CCAATGGTCGGCAACACCTGTTTT--AAATTTTTTTTTACTTTTT
60 CCAATGGTCGGCACCACCT-TTTTCCAAA-TTTTTTTTACTTTTT
* *
61516559 TGGTGTCAATGGTAGGCACCAGTAAACGAAAAAAGTAAAAAAAAAATTTTG
1 T-CTGTCAATGGTAGGCACCAGTATACGAAAAAAGT-AAAAAAAAATTTTG
61516610 AAAACAGGTG
Statistics
Matches: 702, Mismatches: 122, Indels: 191
0.69 0.12 0.19
Matches are distributed among these distances:
94 6 0.01
95 29 0.04
97 2 0.00
98 36 0.05
99 9 0.01
100 34 0.05
101 7 0.01
102 1 0.00
103 8 0.01
104 69 0.10
105 36 0.05
106 75 0.11
107 83 0.12
108 87 0.12
109 30 0.04
110 14 0.02
111 38 0.05
112 7 0.01
113 11 0.02
114 25 0.04
115 4 0.01
116 3 0.00
117 7 0.01
118 8 0.01
119 1 0.00
120 1 0.00
121 4 0.01
128 18 0.03
129 3 0.00
132 8 0.01
133 2 0.00
134 31 0.04
135 5 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (102 bp):
TCTGTCAATGGTAGGCACCAGTATACGAAAAAAGTAAAAAAAAATTTTGTGGTGGCCTGCCAATG
GTCGGCACCACCTTTTTCCAAATTTTTTTTACTTTTT
Found at i:61516133 original size:107 final size:108
Alignment explanation
Indices: 61515916--61516175 Score: 321
Period size: 107 Copynumber: 2.4 Consensus size: 108
61515906 TGCCATTGAA
* *
61515916 ACGAAAAAAGTAAAAAAAAATTG-TTTTGTTGGTGGCCTGCCAATGGCCGGCATCACCTTTTTCC
1 ACGAAAAAAGTAAAAAAAAATTGTTTTTG-TGGTGGCCTGCCAATGACCGGCATCACCTGTTTCC
*
61515980 CAAATTTTTTTTACTTTTGGTCTGTCAATGGCCAGCACCAGTAT
65 CAAATTTTTTTTACTTTTAGTCTGTCAATGGCCAGCACCAGTAT
*** * **
61516024 ACGAAAAAAG-GGGAAAAAATGTTTTTTTGTGGTGGCCTGCCAATGATTGGC-TCCACCTGTTT-
1 ACGAAAAAAGTAAAAAAAAAT-TGTTTTTGTGGTGGCCTGCCAATGACCGGCAT-CACCTGTTTC
* * *** *
61516086 CCAATTTTTTTTTATTTTTAGTCTGTCAATGGTTGGCATCAGTAT
64 CCAAATTTTTTTTACTTTTAGTCTGTCAATGGCCAGCACCAGTAT
*
61516131 ACGAAAAAAGTAAAAAAAAATTGTTTTGGTGGTGGCCTGCCAATG
1 ACGAAAAAAGTAAAAAAAAATTGTTTTTGTGGTGGCCTGCCAATG
61516176 GCCTTTTTTT
Statistics
Matches: 128, Mismatches: 20, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
107 78 0.61
108 45 0.35
109 5 0.04
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (108 bp):
ACGAAAAAAGTAAAAAAAAATTGTTTTTGTGGTGGCCTGCCAATGACCGGCATCACCTGTTTCCC
AAATTTTTTTTACTTTTAGTCTGTCAATGGCCAGCACCAGTAT
Found at i:61516190 original size:27 final size:27
Alignment explanation
Indices: 61516154--61516205 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
61516144 AAAAAAATTG
61516154 TTTTGGTGGTGGCCTGCCAATGGCCTT
1 TTTTGGTGGTGGCCTGCCAATGGCCTT
*
61516181 TTTTTGTGGTGGCCTGCCAATGGCC
1 TTTTGGTGGTGGCCTGCCAATGGCC
61516206 AGCACCACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.08, C:0.23, G:0.33, T:0.37
Consensus pattern (27 bp):
TTTTGGTGGTGGCCTGCCAATGGCCTT
Found at i:61516484 original size:104 final size:100
Alignment explanation
Indices: 61516186--61516601 Score: 315
Period size: 104 Copynumber: 4.0 Consensus size: 100
61516176 GCCTTTTTTT
* * *
61516186 GTGGTGGCCTGCCAATGGCCAGCACCACCTTTTTCCCAA---TTTTTTTTACTTTTTTCGTGTCA
1 GTGGGGGCCTGCCAATGGCCAGCTCCACCTGTTT-CCAATTTTTTTTTTTACTTTTTTC-TGTCA
*
61516248 ATGGCCGGCACCAGTATACGAAAAAAGAAAAAAAATTTG
64 ATGGCAGGCACCAGTATACG-AAAAA-AAAAAAAATTTG
* * **
61516287 GTGGTGGCCTGCCAATGGCCAGCTCCACCTGTTTCCAATTTTTTTTATT--TTTGGTCTGTCAAT
1 GTGGGGGCCTGCCAATGGCCAGCTCCACCTGTTTCCAATTTTTTTTTTTACTTTTTTCTGTCAAT
*
61516350 GGCTGGCACCAGTATACGAAAAAAGTAAAAAAAAAAATTTG
66 GGCAGGCACCAGTATACG----AA--AAAAAAAAAAATTTG
***
61516391 GTGGGGGCCTGCCAATGGTTTGCTCCACCTGTTTCCAAATTTTGTTTCTTTTTACTTTTTTCATG
1 GTGGGGGCCTGCCAATGGCCAGCTCCACCTGTTTCC-AA-TTT-TTT-TTTTTACTTTTTTC-TG
* *
61516456 TTAATGGCAGGCATCAGTATACGAAAAAAGTAAAAAAAATTATTTTTTG
61 TCAATGGCAGGCACCAGTATACG--AAAA--AAAAAAAA--A---TTTG
* * * * ** * * *
61516505 GTGGTGGCTTGCCAATGGTCGGCAACACCTGTTT-TAA-ATTTTTTTTTACTTTTTTGGTGTCAA
1 GTGGGGGCCTGCCAATGGCCAGCTCCACCTGTTTCCAATTTTTTTTTTTACTTTTTT-CTGTCAA
* *
61516568 TGGTAGGCACCAGTAAACGAAAAAAGTAAAAAAA
65 TGGCAGGCACCAGTATACGAAAAAA--AAAAAAA
61516602 AAATTTTGAA
Statistics
Matches: 261, Mismatches: 29, Indels: 47
0.77 0.09 0.14
Matches are distributed among these distances:
100 28 0.11
101 37 0.14
103 10 0.04
104 47 0.18
105 5 0.02
106 13 0.05
107 5 0.02
108 38 0.15
109 15 0.06
110 6 0.02
111 23 0.09
112 2 0.01
114 32 0.12
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (100 bp):
GTGGGGGCCTGCCAATGGCCAGCTCCACCTGTTTCCAATTTTTTTTTTTACTTTTTTCTGTCAAT
GGCAGGCACCAGTATACGAAAAAAAAAAAAATTTG
Found at i:61516708 original size:221 final size:209
Alignment explanation
Indices: 61516225--61516730 Score: 526
Period size: 221 Copynumber: 2.4 Consensus size: 209
61516215 TTTTTCCCAA
*
61516225 TTTTTTTTACTTTTTTCGTGTCAATGGCCGGCACCAGTATACGAAAAAAG--AAAAAAAATTTGG
1 TTTTTTTTACTTTTTTC-TGTTAATGGCCGGCACCAGTATACGAAAAAAGTAAAAAAAAATTTGG
** *
61516288 TGGTGGCCTGCCAATGGCCAGCTCCACCTGTTTCCAATTTTTTTTATTTTTGGTCTGTCAATGGC
65 TGGTGGCCTGCCAATGGCCAGCAACACCTGTTTCAAATTTTTTTTATTTTTGG-CTGTCAATGGC
* ** * ***
61516353 TGGCACCAGTATACGAAAAAAGTAAAAAAAAAAATTTGGTGGGGGCCTGCCAATGGTTTGCTCCA
129 TGGCACCAGTAAACGAAAAAAGTAAAAAAAAAAATTTGCAGGGGGCCGGCCAATGGCAAGC-CCA
61516418 CCTGTTTCCAAATTTTG
193 CCTGTTTCCAAATTTTG
* *
61516435 TTTCTTTTTACTTTTTTCATGTTAATGGCAGGCATCAGTATACGAAAAAAGTAAAAAAAATTATT
1 TTT-TTTTTACTTTTTTC-TGTTAATGGCCGGCACCAGTATACGAAAAAAGTAAAAAAAA--A--
* * * *
61516500 TTTTGGTGGTGGCTTGCCAATGGTCGGCAACACCTGTTTTAAATTTTTTTTTACTTTTTTGG-TG
60 -TTTGGTGGTGGCCTGCCAATGGCCAGCAACACCTGTTTCAAA-TTTTTTTTA--TTTTTGGCTG
* *
61516564 TCAATGG-TAGGCACCAGTAAACGAAAAAAGTAAAAAAAAAATTTTGAAAACAGGTGCTGCCGGC
121 TCAATGGCT-GGCACCAGTAAACGAAAAAAGTAAAAAAAAAAATTTG----CAGG-G-GGCCGGC
* *
61516628 CATTGGCAAG-CCACCTTTTTTCC-AATTTT-
179 CAATGGCAAGCCCACC-TGTTTCCAAATTTTG
* *
61516657 TTTTTTTTACTTTTGGTT-TGTTAATGGCCTGCACCAGTATACGAGAAAAGTAAAAAAAAA-TTG
1 TTTTTTTTACTTTT--TTCTGTTAATGGCCGGCACCAGTATACGAAAAAAGTAAAAAAAAATTTG
*
61516720 GTGATGGCCTG
64 GTGGTGGCCTG
61516731 TAAATGACCG
Statistics
Matches: 247, Mismatches: 28, Indels: 37
0.79 0.09 0.12
Matches are distributed among these distances:
210 3 0.01
211 43 0.17
213 7 0.03
215 13 0.05
218 36 0.15
219 54 0.22
221 55 0.22
222 3 0.01
223 15 0.06
224 7 0.03
225 11 0.04
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (209 bp):
TTTTTTTTACTTTTTTCTGTTAATGGCCGGCACCAGTATACGAAAAAAGTAAAAAAAAATTTGGT
GGTGGCCTGCCAATGGCCAGCAACACCTGTTTCAAATTTTTTTTATTTTTGGCTGTCAATGGCTG
GCACCAGTAAACGAAAAAAGTAAAAAAAAAAATTTGCAGGGGGCCGGCCAATGGCAAGCCCACCT
GTTTCCAAATTTTG
Found at i:61519555 original size:31 final size:31
Alignment explanation
Indices: 61519517--61519597 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
61519507 GATGAACTAA
* * *
61519517 CTATTCTGTGTTTATTGTCCTAACAGATTGT
1 CTATTCTGTGTTTACTATCATAACAGATTGT
* *
61519548 CTATTCTGTGTTTACTATCATAGCGGATTGT
1 CTATTCTGTGTTTACTATCATAACAGATTGT
*
61519579 CTATTTTGTGTTTACTATC
1 CTATTCTGTGTTTACTATC
61519598 CCAACAAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (31 bp):
CTATTCTGTGTTTACTATCATAACAGATTGT
Found at i:61522194 original size:36 final size:36
Alignment explanation
Indices: 61522148--61522229 Score: 146
Period size: 36 Copynumber: 2.3 Consensus size: 36
61522138 GTTAGCCATG
61522148 TATACTAGCAGTCATGTATAACAACATAAGCAACAA
1 TATACTAGCAGTCATGTATAACAACATAAGCAACAA
* *
61522184 TATACCAGCAGTCATGTATAACAACATACGCAACAA
1 TATACTAGCAGTCATGTATAACAACATAAGCAACAA
61522220 TATACTAGCA
1 TATACTAGCA
61522230 ACAATATTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.45, C:0.22, G:0.11, T:0.22
Consensus pattern (36 bp):
TATACTAGCAGTCATGTATAACAACATAAGCAACAA
Found at i:61526346 original size:126 final size:126
Alignment explanation
Indices: 61526100--61526382 Score: 347
Period size: 126 Copynumber: 2.2 Consensus size: 126
61526090 AGCCAAACAG
* * *
61526100 GAGCTACTGTAGCAAAAAATGCGTCCATGT-GTAAGCTTCTTTCAATACTTTTGCTGACAAAGCA
1 GAGCTACTGTAGCAAAAAA--CGTCCACGTGGGAAGCTTCTTTCAATACTTTTACTGACAAAGCA
* * * * * *
61526164 TCCTGTTTAAGGTATTTTTTACACTATTTGCTCAAAAACGTCTACTCGAAATTATTTTTTC-G
64 TCCTGCTTAAAGCATTTTTAACACTATTTGCTCAAAAACGTCTACTCAAAATTATTTTTTCAA
* *
61526226 GAAGCTACTGTAACAAAAGAACGTCCACGTGGGAA-CTTCTTTCAATACTTTTACTGACAATGCA
1 G-AGCTACTGTAGCAAAA-AACGTCCACGTGGGAAGCTTCTTTCAATACTTTTACTGACAAAGCA
* * * *
61526290 TCCTGCTTAAAGCGTTTTTAACATTATTTGCTCAGAAACGTCTTCTCAAAATTATTTTTTCAA
64 TCCTGCTTAAAGCATTTTTAACACTATTTGCTCAAAAACGTCTACTCAAAATTATTTTTTCAA
* *
61526353 GAGCTATTATAGCAAAACAACGTCCACGTG
1 GAGCTACTGTAGCAAAA-AACGTCCACGTG
61526383 AAAGCTTTTT
Statistics
Matches: 134, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
126 113 0.84
127 19 0.14
128 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (126 bp):
GAGCTACTGTAGCAAAAAACGTCCACGTGGGAAGCTTCTTTCAATACTTTTACTGACAAAGCATC
CTGCTTAAAGCATTTTTAACACTATTTGCTCAAAAACGTCTACTCAAAATTATTTTTTCAA
Found at i:61526490 original size:97 final size:95
Alignment explanation
Indices: 61526407--61526642 Score: 237
Period size: 95 Copynumber: 2.5 Consensus size: 95
61526397 TTAACAAATA
* * *
61526407 ATTTAATTAACCCTA-AACCCAAAACCCTAATTTATTTGAGTTTTTTCTTAAAAACCCTAAACAC
1 ATTTAATTAACCCAAGAACCCAAAACCCTAATTTATTT-AATTTTTCCTTAAAAACCCTAAACAC
* * *
61526471 TAAA-CATTAATCTAATTTTTTTAAAATTTAT
65 CAAAGC-CTAATCTAATTTTTTTAAAATATAT
* * * * *
61526502 ATTTAATTGACTCAAGTAACCCTAAACTCTAATTTATTTAATTTTTCCTTAAAAACCCTTAACAC
1 ATTTAATTAACCCAAG-AACCCAAAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTAAACAC
* *
61526567 CAAAGCCTAATCTAATTTTTTAAAAAT-TTT
65 CAAAGCCTAATCTAATTTTTTTAAAATATAT
* * * * *
61526597 AATTAATTTACTCAAGTAATCCTAAACCCTAATTTAATTT-ATTTTT
1 ATTTAATTAACCCAAG-AACCCAAAACCCTAATTT-ATTTAATTTTT
61526643 AAAAAAACTA
Statistics
Matches: 121, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
95 51 0.42
96 49 0.40
97 21 0.17
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.41
Consensus pattern (95 bp):
ATTTAATTAACCCAAGAACCCAAAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTAAACACC
AAAGCCTAATCTAATTTTTTTAAAATATAT
Found at i:61526621 original size:95 final size:96
Alignment explanation
Indices: 61526422--61526697 Score: 305
Period size: 96 Copynumber: 2.9 Consensus size: 96
61526412 ATTAACCCTA
* * * * *
61526422 AACCCAAAACCCTAATTTATTTGAGTTTTTTCTTAAAAACCCTAAACACTAAACATTAATCTAAT
1 AACCCTAAACCCTAATTTATTT-AATTTTTCCTTAAAAACCCTAAACACCAAACACTAATCTAAT
* *
61526487 TTTTTTAAAATTTATATTTAATTGACTCAAGT
65 TTTTTAAAAATTTATAATTAATTGACTCAAGT
* *
61526519 AACCCTAAACTCTAATTTATTTAATTTTTCCTTAAAAACCCTTAACACCAAAGC-CTAATCTAAT
1 AACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTAAACACCAAA-CACTAATCTAAT
*
61526583 TTTTTAAAAATTT-TAATTAATTTACTCAAGT
65 TTTTTAAAAATTTATAATTAATTGACTCAAGT
* ** ** * * *
61526614 AATCCTAAACCCTAATTTAATTT-ATTTTT--AAAAAAACTATAAAGACGAAACCCTAATCTAA-
1 AACCCTAAACCCTAATTT-ATTTAATTTTTCCTTAAAAACCCTAAACACCAAACACTAATCTAAT
61526675 -TTTTAAAAATTTTATAATTAATT
65 TTTTTAAAAA-TTTATAATTAATT
61526698 TAATTAAAAA
Statistics
Matches: 155, Mismatches: 19, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
91 9 0.06
92 4 0.03
93 32 0.21
95 38 0.25
96 51 0.33
97 21 0.14
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.39
Consensus pattern (96 bp):
AACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAAACCCTAAACACCAAACACTAATCTAATT
TTTTAAAAATTTATAATTAATTGACTCAAGT
Found at i:61526790 original size:7 final size:7
Alignment explanation
Indices: 61526771--61526813 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
61526761 TAAAATCCCC
61526771 AAACCCT
1 AAACCCT
61526778 -AACCCT
1 AAACCCT
61526784 AAACCCT
1 AAACCCT
*
61526791 AAACCCA
1 AAACCCT
*
61526798 AAACCCA
1 AAACCCT
61526805 AAACCCT
1 AAACCCT
61526812 AA
1 AA
61526814 CAGTAACAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 6 0.18
7 27 0.82
ACGTcount: A:0.49, C:0.42, G:0.00, T:0.09
Consensus pattern (7 bp):
AAACCCT
Found at i:61526808 original size:21 final size:20
Alignment explanation
Indices: 61526756--61526813 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
61526746 TTAAAAATCT
* *
61526756 AAACCTAAAATCCCCAAACCC
1 AAACCCAAAA-CCCTAAACCC
* *
61526777 TAACCCTAAACCCTAAACCC
1 AAACCCAAAACCCTAAACCC
61526797 AAAACCCAAAACCCTAA
1 -AAACCCAAAACCCTAA
61526814 CAGTAACAGG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 9 0.30
21 21 0.70
ACGTcount: A:0.48, C:0.41, G:0.00, T:0.10
Consensus pattern (20 bp):
AAACCCAAAACCCTAAACCC
Found at i:61533008 original size:37 final size:37
Alignment explanation
Indices: 61532956--61533026 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
61532946 TTATTATTAA
* *
61532956 ATTTTAATAGGATTATTATTAAATATAATTTAATCAT
1 ATTTTAATAGAATTATTATTAAATAAAATTTAATCAT
*
61532993 ATTTTAATATAATTATTATTAAATAAAATTTAAT
1 ATTTTAATAGAATTATTATTAAATAAAATTTAAT
61533027 AAAAATGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (37 bp):
ATTTTAATAGAATTATTATTAAATAAAATTTAATCAT
Found at i:61537866 original size:5 final size:5
Alignment explanation
Indices: 61537850--61537880 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
61537840 TGAGCATTCG
*
61537850 ATCGA ATAGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
61537881 AATTTTCGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:61547031 original size:13 final size:12
Alignment explanation
Indices: 61547010--61547042 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
61547000 CCCCCTCAAA
61547010 AAAAT-AAAAAT
1 AAAATAAAAAAT
61547021 AAAACTAAAAAAT
1 AAAA-TAAAAAAT
61547034 AAAATAAAA
1 AAAATAAAA
61547043 TCAAACCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 6 0.30
13 10 0.50
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:61547830 original size:7 final size:7
Alignment explanation
Indices: 61547820--61547847 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
61547810 ATAAACTCTA
61547820 AACCCCT
1 AACCCCT
61547827 AACCCCT
1 AACCCCT
61547834 AACCCCT
1 AACCCCT
61547841 AACCCCT
1 AACCCCT
61547848 CTTTTACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.57, G:0.00, T:0.14
Consensus pattern (7 bp):
AACCCCT
Found at i:61547965 original size:21 final size:20
Alignment explanation
Indices: 61547936--61547978 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
61547926 GACCCTAAAT
*
61547936 CTCTAAACCCTAAAATACTAA
1 CTCTTAACCCTAAAAT-CTAA
*
61547957 CTCTTAACCTCTAACATCTAA
1 CTCTTAACC-CTAAAATCTAA
61547978 C
1 C
61547979 CCCTAACCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.28
Consensus pattern (20 bp):
CTCTTAACCCTAAAATCTAA
Found at i:61547984 original size:7 final size:7
Alignment explanation
Indices: 61547974--61548025 Score: 63
Period size: 7 Copynumber: 7.6 Consensus size: 7
61547964 CCTCTAACAT
61547974 CTAACCC
1 CTAACCC
61547981 CTAACCC
1 CTAACCC
**
61547988 CTAACTA
1 CTAACCC
61547995 CTAACCTC
1 CTAACC-C
61548003 C-AACCC
1 CTAACCC
61548009 C-AACCC
1 CTAACCC
61548015 CTAACCC
1 CTAACCC
61548022 CTAA
1 CTAA
61548026 ACATTATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
6 8 0.21
7 30 0.77
8 1 0.03
ACGTcount: A:0.33, C:0.52, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAACCC
Found at i:61547985 original size:21 final size:19
Alignment explanation
Indices: 61547961--61548025 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 19
61547951 TACTAACTCT
61547961 TAACCTCTAACATCTAACCCC
1 TAACC-CTAAC-TCTAACCCC
61547982 TAACCCCTAACTACTAACCTCC
1 TAA-CCCTAACT-CTAACC-CC
* *
61548004 -AACCCCAACCCCTAACCCC
1 TAACCCTAA-CTCTAACCCC
61548023 TAA
1 TAA
61548026 ACATTATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
19 2 0.05
20 14 0.38
21 17 0.46
22 4 0.11
ACGTcount: A:0.34, C:0.48, G:0.00, T:0.18
Consensus pattern (19 bp):
TAACCCTAACTCTAACCCC
Found at i:61548202 original size:14 final size:15
Alignment explanation
Indices: 61548179--61548211 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
61548169 CTTAAACCAG
*
61548179 AATCCTTAA-TCCAT
1 AATCCCTAATTCCAT
61548193 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
61548208 AATC
1 AATC
61548212 TATAAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:61548778 original size:40 final size:40
Alignment explanation
Indices: 61548722--61548858 Score: 197
Period size: 40 Copynumber: 3.5 Consensus size: 40
61548712 TGGGCTTAGG
*
61548722 TTTTT-GCGGCGCTTTTTTTAAAAACGCCGCTAATGCTC-A
1 TTTTTAGCGGCG-TTTTTTGAAAAACGCCGCTAATGCTCGA
* *
61548761 TTTTTAGCGGCGTTTTTTGAAAAGCACCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTTGAAAAACGCCGCTAATGCTCGA
* **
61548801 TCTTTAGCGGCGTTTTTTGAAAAGTGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTTGAAAAACGCCGCTAATGCTCGA
61548841 TTTTTAGCGGCGTTTTTT
1 TTTTTAGCGGCGTTTTTT
61548859 ATCCAAACGC
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 28 0.31
40 61 0.69
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTTTGAAAAACGCCGCTAATGCTCGA
Found at i:61551279 original size:15 final size:16
Alignment explanation
Indices: 61551259--61551288 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61551249 TTTAAAATTT
61551259 TAATAATA-AATATTA
1 TAATAATATAATATTA
61551274 TAATAATATAATATT
1 TAATAATATAATATT
61551289 TTAGAATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAATATAATATTA
Found at i:61551315 original size:16 final size:16
Alignment explanation
Indices: 61551253--61551315 Score: 51
Period size: 18 Copynumber: 3.9 Consensus size: 16
61551243 TATGTATTTA
61551253 AAATTTTA-AT-A-AT
1 AAATTTTATATGATAT
* *
61551266 AAATATTATAATAATAT
1 AAATTTTAT-ATGATAT
*
61551283 AATATTTTAGAATGATAT
1 AA-ATTTTA-TATGATAT
61551301 AAATTTTATATGATA
1 AAATTTTATATGATA
61551316 AAAACTTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
13 7 0.18
15 2 0.05
16 7 0.18
17 10 0.26
18 13 0.33
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (16 bp):
AAATTTTATATGATAT
Found at i:61560263 original size:39 final size:39
Alignment explanation
Indices: 61560220--61560296 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
61560210 ATCTATAAAT
*
61560220 ATGTTATGA-GATTAAATGTA-TATTGTGAAATATGCTTGA
1 ATGTTAT-ATGATTAAATG-AGTATTATGAAATATGCTTGA
* *
61560259 ATGTTATATGATTATATGAGTATTATGATATATGCTTG
1 ATGTTATATGATTAAATGAGTATTATGAAATATGCTTG
61560297 CTTGAATGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.06
39 31 0.94
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (39 bp):
ATGTTATATGATTAAATGAGTATTATGAAATATGCTTGA
Found at i:61560314 original size:43 final size:43
Alignment explanation
Indices: 61560252--61560338 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
61560242 TTGTGAAATA
* *
61560252 TGCTTGAATGTTATATGATTATATGAGT-ATTATGATATATGCT
1 TGCTTGAATGTTAGATGATTATATGAGTAATAAT-ATATATGCT
* *
61560295 TGCTTGAATGTTAGGTGATTATATGCGTAATAATATATATGCT
1 TGCTTGAATGTTAGATGATTATATGAGTAATAATATATATGCT
61560338 T
1 T
61560339 AAACGTGAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 35 0.90
44 4 0.10
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.45
Consensus pattern (43 bp):
TGCTTGAATGTTAGATGATTATATGAGTAATAATATATATGCT
Found at i:61569918 original size:25 final size:25
Alignment explanation
Indices: 61569871--61569919 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
61569861 CTATTTTTTA
* *
61569871 TAGTATATCCTGAAACTGCTATAGG
1 TAGTATATACTGAAACTACTATAGG
* *
61569896 TAGTATATACTGAGACTATTATAG
1 TAGTATATACTGAAACTACTATAG
61569920 ATAAACTGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATAGG
Found at i:61572590 original size:43 final size:43
Alignment explanation
Indices: 61572529--61572615 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
61572519 TTACGGAAAG
61572529 TAACATTTCTGGGCCATGTGGTTTCTGCTCAGGGGATTAGGGT
1 TAACATTTCTGGGCCATGTGGTTTCTGCTCAGGGGATTAGGGT
* *
61572572 TAACATTTTTGGGCCATGTGGTTTCTGCTGAGGGGATTAGGGT
1 TAACATTTCTGGGCCATGTGGTTTCTGCTCAGGGGATTAGGGT
61572615 T
1 T
61572616 GATCCTCGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.16, C:0.14, G:0.33, T:0.37
Consensus pattern (43 bp):
TAACATTTCTGGGCCATGTGGTTTCTGCTCAGGGGATTAGGGT
Found at i:61577315 original size:27 final size:26
Alignment explanation
Indices: 61577275--61577684 Score: 309
Period size: 27 Copynumber: 15.2 Consensus size: 26
61577265 GTGAGGTTAA
* *
61577275 TAAAATAACTGAAATACCCCCGTAGGG
1 TAAAATGAC-GAAATACCCCCATAGGG
* *
61577302 TAAAATAATCGAAATACCCCCATAGAG
1 TAAAATGA-CGAAATACCCCCATAGGG
* ** *
61577329 TAGAATGATCGAAATACCTTCGTAGGG
1 TAAAATGA-CGAAATACCCCCATAGGG
* *
61577356 TAAAATGACCAAAATACCCCCATAGAG
1 TAAAATGA-CGAAATACCCCCATAGGG
*
61577383 TAGAATGACCGAAATACCCCCATAGGG
1 TAAAATGA-CGAAATACCCCCATAGGG
* *
61577410 TAGAATGACTGAAATACCCTCATAGGG
1 TAAAATGAC-GAAATACCCCCATAGGG
* * *
61577437 TAGAATGACTAAAATACCCCTATAGGG
1 TAAAATGAC-GAAATACCCCCATAGGG
* * **
61577464 TAGAATGACCAAAATACCCTTATAGGG
1 TAAAATGA-CGAAATACCCCCATAGGG
* * *
61577491 TAAAATGACATAAATA-CCCTATAGGA
1 TAAAATGAC-GAAATACCCCCATAGGG
* *
61577517 TAGAATGACTGAAATACCCCCATTGGG
1 TAAAATGAC-GAAATACCCCCATAGGG
** *
61577544 TTGAATAACCGAAATACCCCCATAGGG
1 TAAAATGA-CGAAATACCCCCATAGGG
* *
61577571 TAAAATGATCGAAATACCTCCATAAGG
1 TAAAATGA-CGAAATACCCCCATAGGG
* * * *
61577598 TAAAATAACAAAAATACCCCTATAAGG
1 TAAAATGAC-GAAATACCCCCATAGGG
* * ** *
61577625 TAGAATGAACGAAATGCCTTCGTAGGG
1 TAAAATG-ACGAAATACCCCCATAGGG
* *
61577652 TAAAATGACCAAAATATCCCCATAGGG
1 TAAAATGA-CGAAATACCCCCATAGGG
61577679 TAAAAT
1 TAAAAT
61577685 AACTATTAAA
Statistics
Matches: 312, Mismatches: 62, Indels: 18
0.80 0.16 0.05
Matches are distributed among these distances:
26 25 0.08
27 282 0.90
28 5 0.02
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (26 bp):
TAAAATGACGAAATACCCCCATAGGG
Found at i:61577413 original size:81 final size:81
Alignment explanation
Indices: 61577275--61577689 Score: 410
Period size: 81 Copynumber: 5.1 Consensus size: 81
61577265 GTGAGGTTAA
* * * * * * * *
61577275 TAAAATAACTGAAATACCCCCGTAGGGTAAAATAATCGAAATACCCCCATAGAGTAGAATGATC-
1 TAAAATGACTAAAATACCCCCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGA-CA
* *
61577339 GAAATACCTTCGTAGGG
65 GAAATACCCTCATAGGG
* * * *
61577356 TAAAATGACCAAAATACCCCCATAGAGTAGAATGACCGAAATACCCCCATAGGGTAGAATGACTG
1 TAAAATGACTAAAATACCCCCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGACAG
61577421 AAATACCCTCATAGGG
66 AAATACCCTCATAGGG
* * * ** *
61577437 TAGAATGACTAAAATACCCCTATAGGGTAGAATGACCAAAATACCCTTATAGGGTAAAATGACAT
1 TAAAATGACTAAAATACCCCCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGACAG
*
61577502 AAATACCCT-ATAGGA
66 AAATACCCTCATAGGG
* * * * *
61577517 TAGAATGACTGAAATACCCCCATTGGGTTGAATAACCGAAATACCCCCATAGGGTAAAATGATC-
1 TAAAATGACTAAAATACCCCCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGA-CA
*
61577581 GAAATA-CCTCCATAAGG
65 GAAATACCCT-CATAGGG
* * * * * * ** *
61577598 TAAAATAACAAAAATACCCCTATAAGGTAGAATGAACGAAATGCCTTCGTAGGGTAAAATGACCA
1 TAAAATGACTAAAATACCCCCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGA-CA
61577663 -AAATATCCC-CATAGGG
65 GAAATA-CCCTCATAGGG
*
61577679 TAAAATAACTA
1 TAAAATGACTA
61577690 TTAAACCCCT
Statistics
Matches: 277, Mismatches: 50, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
79 3 0.01
80 65 0.23
81 207 0.75
83 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (81 bp):
TAAAATGACTAAAATACCCCCATAGGGTAGAATGACCGAAATACCCCCATAGGGTAAAATGACAG
AAATACCCTCATAGGG
Found at i:61578099 original size:28 final size:28
Alignment explanation
Indices: 61578059--61578161 Score: 145
Period size: 28 Copynumber: 3.7 Consensus size: 28
61578049 TGCATTGTTA
61578059 CTGTATTGGGCTAAGGCCCACACTGATT
1 CTGTATTGGGCTAAGGCCCACACTGATT
*
61578087 CTGTATTGGGCTAATGCCCACACTGATT
1 CTGTATTGGGCTAAGGCCCACACTGATT
* *
61578115 CTATATTGGGCTAAGGCCCACACT-TTT
1 CTGTATTGGGCTAAGGCCCACACTGATT
* *
61578142 ACTGCATTGGGTTAAGGCCC
1 -CTGTATTGGGCTAAGGCCC
61578162 TCATTGTACT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 2 0.03
28 65 0.97
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.30
Consensus pattern (28 bp):
CTGTATTGGGCTAAGGCCCACACTGATT
Done.