Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 160 of 311
Found at i:54542802 original size:70 final size:70
Alignment explanation
Indices: 54542689--54542830 Score: 257
Period size: 70 Copynumber: 2.0 Consensus size: 70
54542679 AAAATTAAGT
* *
54542689 GATTTGTTTATCTAAACTAGTTAACTAAACTAAAGGTGCACAGAAAGAAAATTAGGAAAAGCTTT
1 GATTTGTTTATCTAAACTAATTAACTAAACTAAAGGTGCACAGAAACAAAATTAGGAAAAGCTTT
54542754 TGGGA
66 TGGGA
*
54542759 GATTTGTTTATCTAAACTAATTAACTAAACTAAGGGTGCACAGAAACAAAATTAGGAAAAGCTTT
1 GATTTGTTTATCTAAACTAATTAACTAAACTAAAGGTGCACAGAAACAAAATTAGGAAAAGCTTT
54542824 TGGGA
66 TGGGA
54542829 GA
1 GA
54542831 ACTCAATTGA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.28
Consensus pattern (70 bp):
GATTTGTTTATCTAAACTAATTAACTAAACTAAAGGTGCACAGAAACAAAATTAGGAAAAGCTTT
TGGGA
Found at i:54547332 original size:28 final size:28
Alignment explanation
Indices: 54547299--54547357 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
54547289 ATTGCATGAC
54547299 TATGAATATGATT-GAGCCTGATGGGCCA
1 TATGAATATGATTGGAGCC-GATGGGCCA
*
54547327 TATGAATGTGATTGGAGCCGATGGGCCA
1 TATGAATATGATTGGAGCCGATGGGCCA
54547355 TAT
1 TAT
54547358 AAATGAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
TATGAATATGATTGGAGCCGATGGGCCA
Found at i:54547362 original size:28 final size:29
Alignment explanation
Indices: 54547307--54547373 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 29
54547297 ACTATGAATA
*
54547307 TGATT-GAGCCTGATGGGCCATATGAATG
1 TGATTGGAGCCTGATGGGCCATATAAATG
54547335 TGATTGGAGCC-GATGGGCCATATAAATG
1 TGATTGGAGCCTGATGGGCCATATAAATG
*
54547363 AGATTGG-GCCT
1 TGATTGGAGCCT
54547374 AAAGGGGCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 3 0.09
28 27 0.77
29 5 0.14
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (29 bp):
TGATTGGAGCCTGATGGGCCATATAAATG
Found at i:54548070 original size:11 final size:11
Alignment explanation
Indices: 54548054--54548079 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54548044 ATTGCATGTA
54548054 TGATATTATTG
1 TGATATTATTG
54548065 TGATATTATTG
1 TGATATTATTG
54548076 TGAT
1 TGAT
54548080 GTGGGCTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (11 bp):
TGATATTATTG
Found at i:54548711 original size:16 final size:17
Alignment explanation
Indices: 54548679--54548711 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54548669 TTTAAAGAAG
54548679 GGTTTTCAAGGAAAACAA
1 GGTTTTCAA-GAAAACAA
54548697 GGTTTTCAA-AAAACA
1 GGTTTTCAAGAAAACA
54548712 CTTCAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (17 bp):
GGTTTTCAAGAAAACAA
Found at i:54552388 original size:28 final size:28
Alignment explanation
Indices: 54552339--54552428 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 28
54552329 TGCATGACTG
54552339 TGAATGTGATTGGGCCTAATGGGCCATA
1 TGAATGTGATTGGGCCTAATGGGCCATA
* *
54552367 TTAATGTGATTAGGGCC-GATGGGCCATA
1 TGAATGTGATT-GGGCCTAATGGGCCATA
* * *
54552395 TGAATGAGATTGGGCCTAAAGGGGCCAAA
1 TGAATGTGATTGGGCCT-AATGGGCCATA
54552424 TGAAT
1 TGAAT
54552429 AAGTGTGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 5 0.10
28 29 0.56
29 18 0.35
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (28 bp):
TGAATGTGATTGGGCCTAATGGGCCATA
Found at i:54558047 original size:55 final size:55
Alignment explanation
Indices: 54557960--54558216 Score: 259
Period size: 55 Copynumber: 4.8 Consensus size: 55
54557950 ATTAGGGTTT
* *
54557960 AAGGATACCGTGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTCTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGTCTCTAAGGC
* * * * * *
54558015 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGT-CTCTAAGGC
* * *
54558070 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-GT-TCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGTCTC-TAAGGC
* *
54558123 AAGGATACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAA-GTTTC-AA---
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGTCTCTAAGGC
* * *
54558172 AAGGATACCACGTAAGACCATGACAAGTCATGGCAA-TGGTAAGGT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGT
54558217 ACCTGCGTAT
Statistics
Matches: 171, Mismatches: 24, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
49 39 0.23
50 2 0.01
52 7 0.04
53 39 0.23
54 13 0.08
55 67 0.39
56 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (55 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATTGGTAAGGTCTCTAAGGC
Found at i:54558166 original size:108 final size:110
Alignment explanation
Indices: 54557970--54558167 Score: 321
Period size: 108 Copynumber: 1.8 Consensus size: 110
54557960 AAGGATACCG
*
54557970 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTCTCTAAGGCAAGGAAATCATGTAAGACCA
1 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTCTCTAAGGCAAGGAAACCATGTAAGACCA
*
54558035 TGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCA
66 TGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
* *
54558080 TGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-GT-TCATAAGGCAAGGATACCATGTAAGACC
1 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTCTC-TAAGGCAAGGAAACCATGTAAGACC
*
54558142 ATGTCAAGACATGGCAATGGTAAGTT
65 ATGTCAAGACATGGCAATGATAAGTT
54558168 TCAAAAGGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 2 0.02
108 49 0.60
109 7 0.09
110 24 0.29
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (110 bp):
TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTCTCTAAGGCAAGGAAACCATGTAAGACCA
TGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
Found at i:54558387 original size:16 final size:16
Alignment explanation
Indices: 54558366--54558396 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54558356 ATAAATTTGA
54558366 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
54558382 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
54558397 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:54561466 original size:44 final size:45
Alignment explanation
Indices: 54561404--54561516 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 45
54561394 AGATGTTAGC
* *
54561404 CAGTGTCAGATATGTCTAGGACATG-AGTCGGCTAC-G-ACATGTG-
1 CAGTGTAAGACATGTCTAGGACATGCA-TCGGC-ACGGTACATGTGT
54561447 CTAGTGTAAGACATGTCTAGGACATGCATCGGCACGGTTACATGTGT
1 C-AGTGTAAGACATGTCTAGGACATGCATCGGCACGG-TACATGTGT
* *
54561494 CAGTGTAAGACCTGTCTGGGACA
1 CAGTGTAAGACATGTCTAGGACA
54561517 CGGCATCGAC
Statistics
Matches: 60, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
43 3 0.05
44 28 0.47
45 1 0.02
46 27 0.45
47 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (45 bp):
CAGTGTAAGACATGTCTAGGACATGCATCGGCACGGTACATGTGT
Found at i:54568007 original size:44 final size:44
Alignment explanation
Indices: 54567852--54568026 Score: 172
Period size: 44 Copynumber: 3.8 Consensus size: 44
54567842 ATGAGATTTG
* * * **
54567852 TGTGCCAGTGTAAGACATGTCTGGGACATGCAGCGAC-AGCGTTA
1 TGTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCTA-CGAGA
* **
54567896 TGATAGCCAGTGTAAGCCCATGTCTAGGACATGGCATCGGCTTTGAGA
1 TG-T-GCCAGTGTAAG-ACATGTCTAGGACAT-GCATCGGCTACGAGA
* * *
54567944 TGAGGGCTAGTGTAAGACATGTCTAGGACATGCGTCGGCTACGAGA
1 T--GTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCTACGAGA
*
54567990 TGTGCTAGTGTAAGACATGTCTAGGACATGCATCGGC
1 TGTGCCAGTGTAAGACATGTCTAGGACATGCATCGGC
54568027 ACGGTTACAT
Statistics
Matches: 108, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
44 36 0.33
45 1 0.01
46 24 0.22
47 27 0.25
48 19 0.18
50 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.24
Consensus pattern (44 bp):
TGTGCCAGTGTAAGACATGTCTAGGACATGCATCGGCTACGAGA
Found at i:54568839 original size:136 final size:136
Alignment explanation
Indices: 54568595--54568866 Score: 517
Period size: 136 Copynumber: 2.0 Consensus size: 136
54568585 ACAAATATTT
54568595 GAGTATGAGCGATTCAATTAAATAAAAGTTATGGCTATCTTTCTCTTCTGAGTATTCTATGTTTT
1 GAGTATGAGCGATTCAATTAAATAAAAGTTATGGCTATCTTTCTCTTCTGAGTATTCTATGTTTT
*
54568660 CCTCAATTCTGGGGAATACGTATGGTTATCCCTTTCGAGTAGGAATTCTATCGTATGAGGATGCT
66 CCTCAATTCTGGGGAATACGTATGGTTATCCCTTTCGAGTAGGAATTCTATCGTACGAGGATGCT
54568725 GGTGAC
131 GGTGAC
*
54568731 GAGTATGAGCGATTCAATTAAATAAAAGTTATGGTTATCTTTCTCTTCTGAGTATTCTATGTTTT
1 GAGTATGAGCGATTCAATTAAATAAAAGTTATGGCTATCTTTCTCTTCTGAGTATTCTATGTTTT
*
54568796 CCTCAATTTTGGGGAATACGTATGGTTATCCCTTTCGAGTAGGAATTCTATCGTACGAGGATGCT
66 CCTCAATTCTGGGGAATACGTATGGTTATCCCTTTCGAGTAGGAATTCTATCGTACGAGGATGCT
54568861 GGTGAC
131 GGTGAC
54568867 TATGATATTA
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 133 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (136 bp):
GAGTATGAGCGATTCAATTAAATAAAAGTTATGGCTATCTTTCTCTTCTGAGTATTCTATGTTTT
CCTCAATTCTGGGGAATACGTATGGTTATCCCTTTCGAGTAGGAATTCTATCGTACGAGGATGCT
GGTGAC
Found at i:54572983 original size:30 final size:31
Alignment explanation
Indices: 54572947--54573029 Score: 125
Period size: 30 Copynumber: 2.7 Consensus size: 31
54572937 CGTTTACAGT
*
54572947 AAAGGCTTCGACCCAGTGATATG-ATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* *
54572977 AAAGGCTTCGGCCCAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
54573008 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
54573030 TTGGGATTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 25 0.52
31 23 0.48
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:54573012 original size:31 final size:30
Alignment explanation
Indices: 54572947--54573024 Score: 120
Period size: 31 Copynumber: 2.6 Consensus size: 30
54572937 CGTTTACAGT
* *
54572947 AAAGGCTTCGACCCAGTGATATGATAATGA
1 AAAGGCTTCGGCCCAGTGACATGATAATGA
*
54572977 AAAGGCTTCGGCCCAGTGACATGAATAATGC
1 AAAGGCTTCGGCCCAGTGACATG-ATAATGA
54573008 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
54573025 ATATGTTGGG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 21 0.48
31 23 0.52
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.21
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTGACATGATAATGA
Found at i:54577391 original size:28 final size:28
Alignment explanation
Indices: 54577330--54577403 Score: 114
Period size: 27 Copynumber: 2.7 Consensus size: 28
54577320 ATTGCATGAC
54577330 TATGAATGTGATTGGGCCTGATAGGCCA
1 TATGAATGTGATTGGGCCTGATAGGCCA
* *
54577358 T-TGAATGTGATTGGGGCTGATGGGCCA
1 TATGAATGTGATTGGGCCTGATAGGCCA
*
54577385 TATGAATGAGATTGGGCCT
1 TATGAATGTGATTGGGCCT
54577404 AAAGGGGCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 25 0.61
28 16 0.39
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.30
Consensus pattern (28 bp):
TATGAATGTGATTGGGCCTGATAGGCCA
Found at i:54577879 original size:20 final size:20
Alignment explanation
Indices: 54577854--54577894 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
54577844 GGCTGGAAAT
54577854 TATGGAACGGAGGATCTATA
1 TATGGAACGGAGGATCTATA
*
54577874 TATGGAACGGAGGATGTATA
1 TATGGAACGGAGGATCTATA
54577894 T
1 T
54577895 GAGGATCGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (20 bp):
TATGGAACGGAGGATCTATA
Found at i:54579867 original size:31 final size:31
Alignment explanation
Indices: 54579832--54579894 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
54579822 TAGTTGAACA
54579832 TAAACATGAAACCATTTCTCATATGTTCGAT
1 TAAACATGAAACCATTTCTCATATGTTCGAT
*
54579863 TAAACATGAAACCATTTCTCATATGTTTGAT
1 TAAACATGAAACCATTTCTCATATGTTCGAT
54579894 T
1 T
54579895 GACATCAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (31 bp):
TAAACATGAAACCATTTCTCATATGTTCGAT
Found at i:54580182 original size:78 final size:79
Alignment explanation
Indices: 54580092--54580295 Score: 279
Period size: 78 Copynumber: 2.5 Consensus size: 79
54580082 GCTAGACCTT
54580092 TAAGTCCGATATCATTTCACCGACATTACGCCTGCTAGGCTCGGAGCCCAATAATATTCACCAGC
1 TAAGTCCGATATCATTTCACCGACATTACGCCTGCTAGGCTCGGAGCCCAATAATATTCACCAGC
**
54580157 TTAAAGCTTTTTAG
66 TTAAAGCTTGCTAG
* * *
54580171 -AAGTCCGATATCATTTCACCTG-CATTACGCCTGCAAGGGTCGGGGCCCAATAATATTCACCAG
1 TAAGTCCGATATCATTTCACC-GACATTACGCCTGCTAGGCTCGGAGCCCAATAATATTCACCAG
54580234 CTTAAAGCTTGCTAG
65 CTTAAAGCTTGCTAG
54580249 ACCTTTAAGTCCGATATCATTTCACC-AGCATTACGCCTGCTAGGCTC
1 -----TAAGTCCGATATCATTTCACCGA-CATTACGCCTGCTAGGCTC
54580296 AAAGCCCGAA
Statistics
Matches: 109, Mismatches: 7, Indels: 13
0.84 0.05 0.10
Matches are distributed among these distances:
78 71 0.65
79 1 0.01
84 37 0.34
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (79 bp):
TAAGTCCGATATCATTTCACCGACATTACGCCTGCTAGGCTCGGAGCCCAATAATATTCACCAGC
TTAAAGCTTGCTAG
Found at i:54587319 original size:43 final size:42
Alignment explanation
Indices: 54587272--54587411 Score: 142
Period size: 43 Copynumber: 3.3 Consensus size: 42
54587262 CGAGATTATG
54587272 TGTAAGACCATGTCTGGGACATTGGTATCATTATGTGATTACA
1 TGTAAGACCATGTCTGGGACATTGG-ATCATTATGTGATTACA
* * * *
54587315 TGTAAGACCATGTCTGGGACATTAAGATCGTTATATGATTTCA
1 TGTAAGACCATGTCTGGGACATT-GGATCATTATGTGATTACA
* * *
54587358 TGTAAGACCATAG-CTGGG-CTATCGGCATCGA-CATGTGATAACA
1 TGTAAGACCAT-GTCTGGGAC-ATTGG-ATC-ATTATGTGATTACA
54587401 TGTAAGACCAT
1 TGTAAGACCAT
54587412 CTCTAGGATA
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
42 2 0.02
43 77 0.95
44 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACATTGGATCATTATGTGATTACA
Found at i:54588258 original size:27 final size:27
Alignment explanation
Indices: 54588227--54588281 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
54588217 TTTCAAAGTT
54588227 ACACTACTACAGTAACTCAAATCTATC
1 ACACTACTACAGTAACTCAAATCTATC
54588254 ACACTACTACAGTAACTCAAATCTATC
1 ACACTACTACAGTAACTCAAATCTATC
54588281 A
1 A
54588282 AGGCTAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.29, G:0.04, T:0.25
Consensus pattern (27 bp):
ACACTACTACAGTAACTCAAATCTATC
Found at i:54592430 original size:22 final size:22
Alignment explanation
Indices: 54592386--54592430 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
54592376 TATTGCTTCT
* *
54592386 ATGGTATCGATATCTCTTTAAA
1 ATGGTATCGATACCTCTTGAAA
54592408 ATGGTATCGATACCATC-TGAAA
1 ATGGTATCGATACC-TCTTGAAA
54592430 A
1 A
54592431 ATCGGTACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (22 bp):
ATGGTATCGATACCTCTTGAAA
Found at i:54598364 original size:27 final size:27
Alignment explanation
Indices: 54598333--54599068 Score: 812
Period size: 27 Copynumber: 27.3 Consensus size: 27
54598323 CCCAAAAGTA
* * *
54598333 GTAAAATGACCATAATACCCCTATAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* *
54598360 GTAAAATGACCATAATGCCCCTATAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
54598387 GTAAAATGACCGTAATGCCCCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* * *
54598414 GTGAAATAACCGTAATGCCCCTGTAAG
1 GTAAAATGACCGTAATGCCCCTGTAGG
54598441 GTAAAATGACCGTAATGCCCCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* * * *
54598468 GTAAAACGACCGTAATGTCCTTTTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* **
54598495 ATAAAATGACCGTAATATCCCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
*
54598522 GTAAAATGA-CGTAATGCCCATGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* * *
54598548 GTAAAATGATCGTAATACCCTTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* * * *
54598575 GTAAAACGACTGTAATGCCCCAGTAGA
1 GTAAAATGACCGTAATGCCCCTGTAGG
* * * *
54598602 GTAAAATGATCGTAATACCCCAGTAGA
1 GTAAAATGACCGTAATGCCCCTGTAGG
* * *
54598629 GTAAAATGACCGTACTACCCCTATAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* ** *
54598656 TTAAAATGACTATAATACCCCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
*
54598683 GTAAAATGACCGTAATGCCCCTATAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* * *
54598710 GTAAAATGACCGTGATGGCCCTATAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* * *
54598737 GTAAAATGACTGTAATGTCCTTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
54598764 GTAAAATG-CCGGTAATGCCCCTGTAGG
1 GTAAAATGACC-GTAATGCCCCTGTAGG
*
54598791 GTAAAATGACCGTAATGCCTCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* * *
54598818 GTAAAAAGATCGTAATGCCCCTATAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* *** * *
54598845 GTAAAATGACCGAAATAAGCCTATATG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* * **
54598872 GTAAAATAACTGTAACACCCCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* *
54598899 GTAAAATGACCGTAATGCCCTTATAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* ** * *
54598926 GAAAAATGACAATAATGCCCTTGTAAG
1 GTAAAATGACCGTAATGCCCCTGTAGG
* *
54598953 GTAAAATGACTG-AATTCCCCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
*
54598979 GTAAAATGACCATAATGCCCCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
54599006 GTAAAATGACCGTAATGCCCCTGTAGG
1 GTAAAATGACCGTAATGCCCCTGTAGG
** ** *
54599033 GTAAAATGACCAAAATAACCCTGTATG
1 GTAAAATGACCGTAATGCCCCTGTAGG
54599060 GTAAAATGA
1 GTAAAATGA
54599069 TGATTATGCC
Statistics
Matches: 599, Mismatches: 106, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
26 45 0.08
27 552 0.92
28 2 0.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
GTAAAATGACCGTAATGCCCCTGTAGG
Found at i:54599249 original size:27 final size:26
Alignment explanation
Indices: 54599205--54599323 Score: 96
Period size: 27 Copynumber: 4.5 Consensus size: 26
54599195 ATGGAGGAAG
* *
54599205 TACTG-TACTGGTGACTATGTCACAT
1 TACTGTTACTGGTGGCTATGCCACAT
*
54599230 TCACTGTTATTGGTGGCTATGCCACAAT
1 T-ACTGTTACTGGTGGCTATGCCAC-AT
* * *
54599258 TACTGATACTGGTCGCTTTGCCACATT
1 TACTGTTACTGGTGGCTATGCCACA-T
* ** *
54599285 TACTGTTTCTGGCAGCTATGCTACAT
1 TACTGTTACTGGTGGCTATGCCACAT
* *
54599311 TATTATTACTGGT
1 TACTGTTACTGGT
54599324 AGCTTTACTG
Statistics
Matches: 73, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
25 1 0.01
26 15 0.21
27 54 0.74
28 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (26 bp):
TACTGTTACTGGTGGCTATGCCACAT
Found at i:54614576 original size:588 final size:588
Alignment explanation
Indices: 54613460--54614638 Score: 2108
Period size: 588 Copynumber: 2.0 Consensus size: 588
54613450 CAAGTTAAAG
* * * * *
54613460 TGTAATAGCTCAAAATTGGGTCTAGTTGGAACAAAGGTTTCGGGACCACAAAAGCTAAGATAGAA
1 TGTAATAGCCCAAAATTGGGTCTAGTTGGAACAAAGGTTTCGAGACCACAAAAGCCAAGACAAAA
* *
54613525 ATAATTATTTTATGATTATTTTGAGGTCTATGATATGATTGCATGATTGTGTGAAATTTTCGTGA
66 ATAATTATTTTATGATTATTTTGAGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCATGA
54613590 AGAAATTCTATGCATAAAGTGCTTAATTTGAAGTTAGGGACTAAATTGAATAAGTTGCAAAACTT
131 AGAAATTCTATGCATAAAGTGCTTAATTTGAAGTTAGGGACTAAATTGAATAAGTTGCAAAACTT
*
54613655 GCATTCTAGAAGTTTCTAGTATGAAATTGCTTTGAAATATTAATTAGGAGGTCTTAAAGAGAAAT
196 GCATTCTAGAAGTTTCTAGTATGAAATTGCTTCGAAATATTAATTAGGAGGTCTTAAAGAGAAAT
54613720 TTGACCAATTTCTAAGTGATGGACAAAAATTGGACATAGATGGAATTTTTGAAAGTTTAATAAGG
261 TTGACCAATTTCTAAGTGATGGACAAAAATTGGACATAGATGGAATTTTTGAAAGTTTAATAAGG
*
54613785 AAGGGCATTTTGGTCATTTGGTAATTAAAAGAAATAAAAAGGGAAAATAAAGCCAAAATTGACTC
326 AAGGGCATTTTGGTCATTTGGTAATTAAAAGAAATAAAAAGGGAAAAAAAAGCCAAAATTGACTC
* *
54613850 ATCTTTCTCATGGAGGCCGAAATTAGCATGGGGGAAGCCATGTCTAGGGTTTTCAAGCTTTCCAA
391 ATCTTTCTCATGGAGGCCGAAATTAGCATGGGGAAAGCCATGGCTAGGGTTTTCAAGCTTTCCAA
*
54613915 GCTCAATAGTAAGTCCGTTATAACCCCATTTTTCAAGTTCTTTACGTTTTTGGAATCTCGATAAT
456 GCTCAATAGTAAGTCCGTTATAACCCCATTTTTCAAGTTCTTTACGTTTTTGGAATCCCGATAAT
* *
54613980 TTGATTAAGCTTATTCTAGCAATAATTTGAGCTAGGGTTCATATTTGGAAAAATAAC-CGTAGGT
521 TTGATTAAGCTTATTCTAGCAATAATTTAAGCTAGGGTTCATATTTGGAAAAAT-ACTCATAGGT
54614044 GAAA
585 GAAA
* *
54614048 TGTAATAGCCCAAAATTGGGTCTAGTTGGAACAGAGGTTTCGAGACCACAAAATCCAAGACAAAA
1 TGTAATAGCCCAAAATTGGGTCTAGTTGGAACAAAGGTTTCGAGACCACAAAAGCCAAGACAAAA
*
54614113 ATAATTATTTTATGATTATTTTGAGGTCTATGATATGATTTCATGATTGTGTGAAAATTTCATGA
66 ATAATTATTTTATGATTATTTTGAGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCATGA
*
54614178 AGACATTCTATGCATAAAGTGCTTAATTTGAAGTTAGGGACTAAATTGAATAAGTTGCAAAACTT
131 AGAAATTCTATGCATAAAGTGCTTAATTTGAAGTTAGGGACTAAATTGAATAAGTTGCAAAACTT
* *
54614243 GCATTCTAGAAGTTTCTAGTATGAAATTGCTTCGAAATATTAATTAGGAGGTCTTAAATAGCAAT
196 GCATTCTAGAAGTTTCTAGTATGAAATTGCTTCGAAATATTAATTAGGAGGTCTTAAAGAGAAAT
* *
54614308 TTGACCAATTTCTAAGTGATGGACAAAAATTGGACATGGATGGAATTTTTGAAAGTTTAGTAAGG
261 TTGACCAATTTCTAAGTGATGGACAAAAATTGGACATAGATGGAATTTTTGAAAGTTTAATAAGG
54614373 AAGGGCATTTTGGTCATTTGGTAATTAAAAGAAATAAAAAGGGAAAAAAAAGCCAAAATTGACTC
326 AAGGGCATTTTGGTCATTTGGTAATTAAAAGAAATAAAAAGGGAAAAAAAAGCCAAAATTGACTC
*
54614438 ATCTTTTTCATGGAGGCCGAAATTAGCATGGGGAAAGCCATGGCTAGGGTTTTCAAGCTTTCCAA
391 ATCTTTCTCATGGAGGCCGAAATTAGCATGGGGAAAGCCATGGCTAGGGTTTTCAAGCTTTCCAA
* * *
54614503 GCTCAATAGTAAGTCCGTTCTAACCCCGTTTTTCAAGTTCTTTACGTTTTTGGAATCCCGGTAAT
456 GCTCAATAGTAAGTCCGTTATAACCCCATTTTTCAAGTTCTTTACGTTTTTGGAATCCCGATAAT
54614568 TTGATTAAGCTTATTCTAGCAATAATTTAAGCTAGGGTTCATATTTGGAAAAATACTCATAGGTG
521 TTGATTAAGCTTATTCTAGCAATAATTTAAGCTAGGGTTCATATTTGGAAAAATACTCATAGGTG
54614633 AAA
586 AAA
54614636 TGT
1 TGT
54614639 GTTTATTTTG
Statistics
Matches: 564, Mismatches: 26, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
587 2 0.00
588 562 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (588 bp):
TGTAATAGCCCAAAATTGGGTCTAGTTGGAACAAAGGTTTCGAGACCACAAAAGCCAAGACAAAA
ATAATTATTTTATGATTATTTTGAGGTCTATGATATGATTGCATGATTGTGTGAAAATTTCATGA
AGAAATTCTATGCATAAAGTGCTTAATTTGAAGTTAGGGACTAAATTGAATAAGTTGCAAAACTT
GCATTCTAGAAGTTTCTAGTATGAAATTGCTTCGAAATATTAATTAGGAGGTCTTAAAGAGAAAT
TTGACCAATTTCTAAGTGATGGACAAAAATTGGACATAGATGGAATTTTTGAAAGTTTAATAAGG
AAGGGCATTTTGGTCATTTGGTAATTAAAAGAAATAAAAAGGGAAAAAAAAGCCAAAATTGACTC
ATCTTTCTCATGGAGGCCGAAATTAGCATGGGGAAAGCCATGGCTAGGGTTTTCAAGCTTTCCAA
GCTCAATAGTAAGTCCGTTATAACCCCATTTTTCAAGTTCTTTACGTTTTTGGAATCCCGATAAT
TTGATTAAGCTTATTCTAGCAATAATTTAAGCTAGGGTTCATATTTGGAAAAATACTCATAGGTG
AAA
Found at i:54615721 original size:64 final size:64
Alignment explanation
Indices: 54615640--54615823 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
54615630 AGACATTATG
* * *
54615640 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
54615704 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAATAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
54615769 AA
63 AA
* * *
54615771 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
54615824 CGAACTATAT
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.19
64 25 0.26
66 21 0.22
67 32 0.33
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:54620921 original size:48 final size:48
Alignment explanation
Indices: 54620799--54621020 Score: 261
Period size: 48 Copynumber: 4.7 Consensus size: 48
54620789 ATGAGATCCG
* * * * * * *
54620799 GTGTAAGACCATGTCTGGGACATGGCGTTGGCATCCGAGATGAGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGT-TGATATGTGTGCCA
* *
54620848 GTGTAAGACCATGTCTAGGATATGGCATCGGCGTTGATATGTGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCCA
** * *
54620896 GTGTAAGACCATGTCTCAGACATGGCATCGGCTTTGATATGTATGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCCA
* * *
54620944 GTGTAAGATCATGTCTGGGACATGGCAT-TG-G-TGATATGTGTGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCCA
*
54620989 GTGTAAGACCATGTCTGGGACATTGCATCGGC
1 GTGTAAGACCATGTCTGGGACATGGCATCGGC
54621021 ACCGATATGA
Statistics
Matches: 147, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
45 38 0.26
46 1 0.01
47 1 0.01
48 78 0.53
49 29 0.20
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.27
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGTGTGCCA
Found at i:54621028 original size:93 final size:96
Alignment explanation
Indices: 54620799--54621031 Score: 285
Period size: 93 Copynumber: 2.4 Consensus size: 96
54620789 ATGAGATCCG
* * *
54620799 GTGTAAGACCATGTCTGGGACATGGCGTTGGCATCCGAGATGAGAGCCAGTGTAAGACCATGTCT
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCA-CCGATATGAGAGCCAGTGTAAGACCATGTCT
*
54620864 AGGATATGGCATCGGCGTTGATATGTGTGCCA
65 AGGACATGGCATCGGCGTTGATATGTGTGCCA
** *** * *
54620896 GTGTAAGACCATGTCTCAGACATGGCATCGGCTTTGATATGTA-TGCCAGTGTAAGATCATGTCT
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCACCGATATG-AGAGCCAGTGTAAGACCATGTCT
* * *
54620960 GGGACATGGCAT-TG-G-TGATATGTGTGCTA
65 AGGACATGGCATCGGCGTTGATATGTGTGCCA
*
54620989 GTGTAAGACCATGTCTGGGACATTGCATCGGCACCGATATGAG
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCACCGATATGAG
54621032 GCTTCGTATA
Statistics
Matches: 114, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
92 1 0.01
93 48 0.42
94 1 0.01
95 1 0.01
96 34 0.30
97 29 0.25
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (96 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCACCGATATGAGAGCCAGTGTAAGACCATGTCTA
GGACATGGCATCGGCGTTGATATGTGTGCCA
Found at i:54624983 original size:19 final size:19
Alignment explanation
Indices: 54624956--54625009 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
54624946 GATGTTTGAA
54624956 TATGTGTATTGACAACGAC
1 TATGTGTATTGACAACGAC
* *
54624975 TATGCGTATTGACCACGAC
1 TATGTGTATTGACAACGAC
*
54624994 TATGTGTATTGGCAAC
1 TATGTGTATTGACAAC
54625010 TTGTGTAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (19 bp):
TATGTGTATTGACAACGAC
Found at i:54630062 original size:40 final size:40
Alignment explanation
Indices: 54629961--54630185 Score: 272
Period size: 40 Copynumber: 5.6 Consensus size: 40
54629951 TATTCGAATG
* *
54629961 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GTGACT
* * * * *
54630002 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGACT
* * *
54630042 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* *
54630082 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
* * * *
54630122 ATATCCGGGCTAAGTCACGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
*
54630162 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
54630186 CTTGTGCAAG
Statistics
Matches: 157, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 127 0.81
41 29 0.18
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGACT
Found at i:54630143 original size:80 final size:80
Alignment explanation
Indices: 54629961--54630221 Score: 294
Period size: 80 Copynumber: 3.3 Consensus size: 80
54629951 TATTCGAATG
* * * *
54629961 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAGACCCGAAGGC
*
54630026 ATTCGTGCGAGTTGCT
65 ATTCGTGCGAGTCGCT
** * * *
54630042 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
54630107 TTTGTGCTAG-CGACT
66 TTCGTGCGAGTCG-CT
* * * * *
54630122 ATATCCGGGCTAAGTCACGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAAGGCC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* * *
54630187 TT-GTGCAAGTAGTT
66 TTCGTGCGAGTCGCT
*
54630201 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
54630222 ATTACTTGAG
Statistics
Matches: 151, Mismatches: 27, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
78 13 0.09
79 14 0.09
80 93 0.62
81 31 0.21
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCGCT
Found at i:54630180 original size:120 final size:120
Alignment explanation
Indices: 54629961--54630221 Score: 316
Period size: 120 Copynumber: 2.2 Consensus size: 120
54629951 TATTCGAATG
* * *
54629961 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
* * * * *
54630026 ATTCGTGCGAGTTGCTATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGA-TT
66 ATTCATGCGAGTTGCCACATCCGGGCTAAAACCCGAAGGC-CTTGTGCAAG-GAGTT
* * *
54630082 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTA-GCGACTATATCCGGGCTAAG-TCACGAAGG
1 ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATC-CGAAGG
* * * *
54630145 CATTTATGCTAG-TGACCACATCCGGGCTAAGACCCGAAGGCCTTGTGCAAGTAGTT
65 CATTCATGCGAGTTG-CCACATCCGGGCTAAAACCCGAAGGCCTTGTGCAAGGAGTT
54630201 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAATCCCGAAG
54630222 ATTACTTGAG
Statistics
Matches: 121, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
118 15 0.12
119 20 0.17
120 55 0.45
121 31 0.26
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (120 bp):
ATATCCGGGCTAAATCCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
ATTCATGCGAGTTGCCACATCCGGGCTAAAACCCGAAGGCCTTGTGCAAGGAGTT
Found at i:54638218 original size:13 final size:13
Alignment explanation
Indices: 54638200--54638224 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54638190 CGTGTATGAC
54638200 ACACGGTCATGTA
1 ACACGGTCATGTA
54638213 ACACGGTCATGT
1 ACACGGTCATGT
54638225 GTCCCTTGGG
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:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (13 bp):
ACACGGTCATGTA
Found at i:54641380 original size:11 final size:11
Alignment explanation
Indices: 54641348--54641382 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
54641338 ATGCCATTTT
*
54641348 CCATCCCTCTT
1 CCATCCCTCTC
54641359 CCATCCCTCTC
1 CCATCCCTCTC
54641370 CCATCCCTCTC
1 CCATCCCTCTC
54641381 CC
1 CC
54641383 TCTCCCCTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.09, C:0.63, G:0.00, T:0.29
Consensus pattern (11 bp):
CCATCCCTCTC
Found at i:54641395 original size:22 final size:22
Alignment explanation
Indices: 54641348--54641397 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
54641338 ATGCCATTTT
* *
54641348 CCATCCCTCTTCCATCCCTCTC
1 CCATCCCTCTTCCATCCCCCTA
*
54641370 CCATCCCTC-TCCCTCTCCCCTA
1 CCATCCCTCTTCCATC-CCCCTA
54641392 CCATCC
1 CCATCC
54641398 ATCCCCTACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.10, C:0.62, G:0.00, T:0.28
Consensus pattern (22 bp):
CCATCCCTCTTCCATCCCCCTA
Found at i:54647028 original size:41 final size:41
Alignment explanation
Indices: 54646983--54647065 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
54646973 AGTTTGGTAT
54646983 TTTTAAAAGTTGGTTTGGTACTTATGGCATGTATAAGCTAA
1 TTTTAAAAGTTGGTTTGGTACTTATGGCATGTATAAGCTAA
*
54647024 TTTTAAAAGTTGGTTTGGTACTTATGGCATGTATATGCTAA
1 TTTTAAAAGTTGGTTTGGTACTTATGGCATGTATAAGCTAA
54647065 T
1 T
54647066 AACTCTTTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (41 bp):
TTTTAAAAGTTGGTTTGGTACTTATGGCATGTATAAGCTAA
Found at i:54649693 original size:39 final size:39
Alignment explanation
Indices: 54649649--54649844 Score: 320
Period size: 39 Copynumber: 5.0 Consensus size: 39
54649639 AATTATATTA
* * *
54649649 CCAGCACAAAGCCTGCGGGACTTTAACCCGGATACGTTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
*
54649688 CCAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
*
54649727 CCAGCACGAAGCCTGCGGGACTTTAGCCCTGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
*
54649766 CCAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* *
54649805 CCAGCACAAAGCCTGCGGGACTTTAGCCAGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
54649844 C
1 C
54649845 TAGTGTCTTG
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 146 1.00
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.21
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
Found at i:54655536 original size:29 final size:29
Alignment explanation
Indices: 54655494--54655552 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
54655484 GTTTTCACTG
54655494 TTAATAATTTGCATGCTTATTAACCCTTA
1 TTAATAATTTGCATGCTTATTAACCCTTA
*
54655523 TTAATAATTTGCATGTTTATTAACCCTTA
1 TTAATAATTTGCATGCTTATTAACCCTTA
54655552 T
1 T
54655553 CTATGTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (29 bp):
TTAATAATTTGCATGCTTATTAACCCTTA
Found at i:54663489 original size:46 final size:46
Alignment explanation
Indices: 54663436--54663644 Score: 119
Period size: 46 Copynumber: 4.5 Consensus size: 46
54663426 TGTGAGCTAT
54663436 TGTAAGACATGTCTGGGACATGCATCAGCCACATTATG-AGAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCAGCCACATTA-GAAGAGCCAG
* * * * * *
54663482 TGTAAGACTATGTCTAGCACTTGGCATAAG---CATTGAGACAAGGGCTAG
1 TGTAAGAC-ATGTCTGGGACAT-GCATCAGCCACATT-AG--AAGAGCCAG
* * * * *
54663530 TGTAAGAGATGTCTGGAACATGCATCGGCCAC--GAGACGTAAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCAGCCACATTAGAAG--AGCCAG
* * ** *
54663576 TGTAAGACATGTCTGGGACATGCATC-GACTACGA-GAGAATCGTCAG
1 TGTAAGACATGTCTGGGACATGCATCAG-CCAC-ATTAGAAGAGCCAG
54663622 TGTAAGACCATGTCTGGGACATG
1 TGTAAGA-CATGTCTGGGACATG
54663645 GAATCGACTT
Statistics
Matches: 125, Mismatches: 23, Indels: 29
0.71 0.13 0.16
Matches are distributed among these distances:
44 2 0.02
45 6 0.05
46 58 0.46
47 35 0.28
48 23 0.18
49 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATGCATCAGCCACATTAGAAGAGCCAG
Found at i:54663670 original size:47 final size:48
Alignment explanation
Indices: 54663528--54663692 Score: 146
Period size: 46 Copynumber: 3.5 Consensus size: 48
54663518 GACAAGGGCT
* * * * * *
54663528 AGTGTAAGA-GATGTCTGGAACAT-GCATCGGCCACGAGACGTA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGAATCGACTACGAGA-GAATAGCC
* * *
54663574 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACTACGAGAGAATCGTC
1 AGTGTAAGACCATGTCTGGGACATGGAATCGACTACGAGAGAATAGCC
* *
54663620 AGTGTAAGACCATGTCTGGGACATGGAATCGACT-TGAGA-TATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGAATCGACTACGAGAGAAT-AGCC
* *
54663667 AGTGTAAGACCGTGTCTAGGACATGG
1 AGTGTAAGACCATGTCTGGGACATGG
54663693 CATCTGCTCC
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
45 2 0.02
46 47 0.47
47 44 0.44
48 8 0.08
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGAATCGACTACGAGAGAATAGCC
Found at i:54668026 original size:18 final size:18
Alignment explanation
Indices: 54667985--54668021 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
54667975 CATAAGCAAC
*
54667985 AAAAATTTTAAAAAATTT
1 AAAAATTTTAAAAAAATT
54668003 AAAAATTTTAATAAAAATT
1 AAAAATTTTAA-AAAAATT
54668022 GAAATATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATTTTAAAAAAATT
Found at i:54668260 original size:22 final size:22
Alignment explanation
Indices: 54668235--54668280 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
54668225 AATTTATAAC
54668235 TAATCAAAACAAA-TAAAAAATA
1 TAATC-AAACAAATTAAAAAATA
**
54668257 TAATCATCCAAATTAAAAAATA
1 TAATCAAACAAATTAAAAAATA
54668279 TA
1 TA
54668281 TAGTCCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (22 bp):
TAATCAAACAAATTAAAAAATA
Found at i:54672094 original size:49 final size:47
Alignment explanation
Indices: 54671983--54672467 Score: 790
Period size: 47 Copynumber: 10.1 Consensus size: 47
54671973 TATGAAATGA
*
54671983 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG
54672030 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATG
54672079 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG
54672126 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATG
54672175 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATG
*
54672224 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG
*
54672271 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG
54672318 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG
*
54672365 TGATAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATG
* * * * * * * *
54672414 TGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATATGTG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG
54672461 TGATAAG
1 TGATAAG
54672468 TCCCGAAGGG
Statistics
Matches: 417, Mismatches: 15, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
47 236 0.57
49 181 0.43
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATG
Found at i:54672467 original size:96 final size:94
Alignment explanation
Indices: 54671983--54672467 Score: 790
Period size: 96 Copynumber: 5.1 Consensus size: 94
54671973 TATGAAATGA
*
54671983 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATGTGATAAGGCCTAATGGCC
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC
54672048 GATGTGATGAATGTGAAAGTGTATATATATG
66 GATGTGATGAATGTGAAAGTG--TATATATG
54672079 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC
54672144 GATGTGATGAATGTGAAAGTGTATATATATG
66 GATGTGATGAATGTGAAAGTG--TATATATG
*
54672175 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGG
54672240 CCGATGTGATGAATGTGAAAGTGTATATATG
64 CCGATGTGATGAATGTGAAAGTGTATATATG
*
54672271 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC
54672336 GATGTGATGAATGTGAAAGTGTATATATG
66 GATGTGATGAATGTGAAAGTGTATATATG
* * * * *
54672365 TGATAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATATGTGACAGGGCCGAGTGG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGG
* * * *
54672430 CCAACGTGATGGATGTGAAAGTGTATATGTG
64 CCGATGTGATGAATGTGAAAGTGTATATATG
54672461 TGATAAG
1 TGATAAG
54672468 TCCCGAAGGG
Statistics
Matches: 371, Mismatches: 14, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
94 91 0.25
96 234 0.63
98 46 0.12
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (94 bp):
TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCC
GATGTGATGAATGTGAAAGTGTATATATG
Found at i:54676706 original size:28 final size:29
Alignment explanation
Indices: 54676615--54676736 Score: 174
Period size: 29 Copynumber: 4.2 Consensus size: 29
54676605 AAGTCTACAT
* *
54676615 ACATGCATATGGCCCACTAGGCCTAAATC
1 ACATTCATATGGCCCATTAGGCCTAAATC
* * *
54676644 TCATACATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCTAAATC
*
54676673 ACATTCGTATGGCCCATTAGGCC-AAATC
1 ACATTCATATGGCCCATTAGGCCTAAATC
*
54676701 ACATTCATATGGCCCATTAGACCTAAATC
1 ACATTCATATGGCCCATTAGGCCTAAATC
54676730 ACATTCA
1 ACATTCA
54676737 CATACATGCT
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
28 26 0.31
29 57 0.69
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.25
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCTAAATC
Found at i:54676717 original size:57 final size:58
Alignment explanation
Indices: 54676622--54676735 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 58
54676612 CATACATGCA
* *
54676622 TATGGCCCACTAGGCCTAAATCTCATACATATGGCCCATTAGGCCCAAATCACATTCG
1 TATGGCCCACTAGGCCTAAATCACATACATATGGCCCATTAGACCCAAATCACATTCG
* * *
54676680 TATGGCCCATTAGGCC-AAATCACATTCATATGGCCCATTAGACCTAAATCACATTC
1 TATGGCCCACTAGGCCTAAATCACATACATATGGCCCATTAGACCCAAATCACATTC
54676736 ACATACATGC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 36 0.71
58 15 0.29
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (58 bp):
TATGGCCCACTAGGCCTAAATCACATACATATGGCCCATTAGACCCAAATCACATTCG
Found at i:54680591 original size:27 final size:28
Alignment explanation
Indices: 54680508--54680604 Score: 128
Period size: 28 Copynumber: 3.5 Consensus size: 28
54680498 CATGAGATAG
* *
54680508 GCACTAAGTGTGCG-GTTTAAATTGT-TCA
1 GCACTAAGTGTGCGAGTTT-GATTATAT-A
54680536 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
54680564 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
54680591 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
54680605 GACTTAATAT
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
27 24 0.38
28 35 0.55
29 5 0.08
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:54680615 original size:27 final size:27
Alignment explanation
Indices: 54680535--54680617 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
54680525 TAAATTGTTC
* *
54680535 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
54680563 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
54680590 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
54680617 A
1 A
54680618 TATTTTTGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:54680618 original size:29 final size:27
Alignment explanation
Indices: 54680508--54680619 Score: 100
Period size: 28 Copynumber: 4.0 Consensus size: 27
54680498 CATGAGATAG
** *
54680508 GCACTAAGTGTGCGGTTTAAATTGT-TCA
1 GCACTAAGTGTGCGACTT-AATTATAT-A
* *
54680536 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
54680564 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
54680591 GCACTGAGTGTGCGGACTTAATATATATA
1 GCACTAAGTGTGC-GACTTAAT-TATATA
54680620 TTTTTGAATC
Statistics
Matches: 73, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
27 23 0.32
28 40 0.55
29 10 0.14
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:54684922 original size:28 final size:26
Alignment explanation
Indices: 54684829--54685026 Score: 131
Period size: 27 Copynumber: 7.4 Consensus size: 26
54684819 ATATTGAGTC
* *
54684829 CGCACACTTCAGTG-TATATAATCAACT
1 CGCACACTT-AGTGCTACATAGTCAA-T
*
54684856 CGCACACTTAGTGCCTAC-TAATCAAAT
1 CGCACACTTAGTG-CTACATAGTC-AAT
54684883 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AA-T
**
54684911 CGCACACTTAGTGCCGCATAGGTCAATT
1 CGCACACTTAGTGCTACATA-GTCAA-T
* *
54684939 CGCACACTTAGT-C-ATCATATTCATTTT
1 CGCACACTTAGTGCTA-CATAGTCA--AT
* *
54684966 CGCACACTTAGTGCAACA-AGACAAT
1 CGCACACTTAGTGCTACATAGTCAAT
* *
54684991 CGCACACTTAGCTG-TACA-ATTTAAT
1 CGCACACTTAG-TGCTACATAGTCAAT
*
54685016 CGCGCACTTAG
1 CGCACACTTAG
54685027 CACATCTCAT
Statistics
Matches: 143, Mismatches: 16, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
25 29 0.20
26 13 0.09
27 56 0.39
28 41 0.29
29 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (26 bp):
CGCACACTTAGTGCTACATAGTCAAT
Found at i:54745972 original size:27 final size:27
Alignment explanation
Indices: 54745942--54746119 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
54745932 ATATTGAGTC
* *
54745942 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
54745969 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
54745996 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
54746024 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
54746051 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
54746078 CGCACACTTAGTGCAACATAGA-CAAAT
1 CGCACACTTAGTGCTACATA-ATCAACT
54746105 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54746120 GTACAATTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 104 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54746081 original size:82 final size:81
Alignment explanation
Indices: 54745963--54746118 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
54745953 TGCTATATAA
* * *
54745963 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGACAAA-TCGCA
54746028 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54746045 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGACAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGACAAATCGCA
54746109 CACTTAGTGC
65 CACTTAGTGC
54746119 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGACAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54757793 original size:41 final size:40
Alignment explanation
Indices: 54757711--54757922 Score: 284
Period size: 41 Copynumber: 5.2 Consensus size: 40
54757701 AAGGGCACAA
* * * *
54757711 GTGC-ATTTAGGGGTACCGAAGTACAATAGGAGCACATAT
1 GTGCAATTCAGGGGTACCGAAGTACAACAGGGGCACGTAT
* *
54757750 GTGCAATTCAGGGGTATC-ATAGTACACATAGGGGCACGTAT
1 GTGCAATTCAGGGGTACCGA-AGTACA-ACAGGGGCACGTAT
*
54757791 GTGCAATTCAGGGGTACCGAAGTACAAACAGGTGCACGTAT
1 GTGCAATTCAGGGGTACCGAAGTAC-AACAGGGGCACGTAT
* * *
54757832 GTGCAATTTAGGGGTACCGGAGTACAACAGGGGCACATAT
1 GTGCAATTCAGGGGTACCGAAGTACAACAGGGGCACGTAT
54757872 GTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACGTAT
1 GTGCAATTCAGGGGTACCGAAGTAC-AACAGGGGCACGTAT
54757913 GTGCAATTCA
1 GTGCAATTCA
54757923 TAATATTCTT
Statistics
Matches: 153, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
39 5 0.03
40 53 0.35
41 93 0.61
42 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.21
Consensus pattern (40 bp):
GTGCAATTCAGGGGTACCGAAGTACAACAGGGGCACGTAT
Found at i:54757807 original size:81 final size:81
Alignment explanation
Indices: 54757692--54757922 Score: 310
Period size: 81 Copynumber: 2.9 Consensus size: 81
54757682 AAGTTACCGG
* * * *
54757692 AGAGTA-AACAAGGGCACA-A-GTGC-ATTTAGGGGTACCGAAGTAC-AATAGGAGCACATATGT
1 AGAGTACAACAGGGGCACATATGTGCAATTCAGGGGTACCGAAGTACAAACAGGAGCACGTATGT
*
54757752 GCAATTCAGGGGTATC
66 GCAATTCAGGGGTACC
* * * *
54757768 ATAGTACACATAGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTACAAACAGGTGCACGTATG
1 AGAGTACA-ACAGGGGCACATATGTGCAATTCAGGGGTACCGAAGTACAAACAGGAGCACGTATG
*
54757833 TGCAATTTAGGGGTACC
65 TGCAATTCAGGGGTACC
* *
54757850 GGAGTACAACAGGGGCACATATGTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGT
1 AGAGTACAACAGGGGCACATATGTGCAATTCAGGGGTACCGAAGTACAAACAGGAGCACGTATGT
54757915 GCAATTCA
66 GCAATTCA
54757923 TAATATTCTT
Statistics
Matches: 133, Mismatches: 16, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
76 5 0.04
77 1 0.01
78 8 0.06
79 1 0.01
80 4 0.03
81 80 0.60
82 34 0.26
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.20
Consensus pattern (81 bp):
AGAGTACAACAGGGGCACATATGTGCAATTCAGGGGTACCGAAGTACAAACAGGAGCACGTATGT
GCAATTCAGGGGTACC
Found at i:54764841 original size:46 final size:46
Alignment explanation
Indices: 54764791--54764880 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
54764781 ATTAGTTAAA
*
54764791 TTTCCCCTATTTTAGTGTTCGATTACTCTGACCTCTGTTCACTAAT
1 TTTCCCCTATTTTAGTGTTCAATTACTCTGACCTCTGTTCACTAAT
54764837 TTTCCCCTATTTTAGTGTTCAATTACTCTGACCTCTGTTCACTA
1 TTTCCCCTATTTTAGTGTTCAATTACTCTGACCTCTGTTCACTA
54764881 CGAATTAATC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.18, C:0.27, G:0.10, T:0.46
Consensus pattern (46 bp):
TTTCCCCTATTTTAGTGTTCAATTACTCTGACCTCTGTTCACTAAT
Found at i:54773131 original size:49 final size:49
Alignment explanation
Indices: 54773020--54773601 Score: 956
Period size: 47 Copynumber: 12.1 Consensus size: 49
54773010 TATGAAATGA
54773020 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
54773067 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
54773116 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
54773165 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA-A-G
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
*
54773212 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAAATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
54773261 TGAT-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
* *
54773309 TGATAGGGCCTAATGCCCGATGTGATGAATGTGAAAGTGTATATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
*
54773358 TGATAAGGCCTAATGGCTGATGTGATGAATGTGAAAGTG--TATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
*
54773405 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
54773452 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
*
54773499 TGATAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
* * * * * * *
54773548 TGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
54773595 TGATAAG
1 TGATAAG
54773602 TCCCGAAGGG
Statistics
Matches: 507, Mismatches: 21, Indels: 14
0.94 0.04 0.03
Matches are distributed among these distances:
47 229 0.45
48 50 0.10
49 228 0.45
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (49 bp):
TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
Found at i:54773208 original size:96 final size:96
Alignment explanation
Indices: 54773020--54773601 Score: 958
Period size: 96 Copynumber: 6.1 Consensus size: 96
54773010 TATGAAATGA
54773020 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG
54773083 CCGATGTGATGAATGTGAAAGTGTATATATATG
66 CCGATGTGATGAATGTGAAAGTG--TATATATG
54773116 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG
*
54773181 CCGATGTGATGAATGTGAAAGTGTATATAAG
66 CCGATGTGATGAATGTGAAAGTGTATATATG
*
54773212 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAAATATGTGAT-AGGCCTAATGG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG
54773276 CCGATGTGATGAATGTGAAAGTGTATATATATG
66 CCGATGTGATGAATGTGAAAGTG--TATATATG
* *
54773309 TGATAGGGCCTAATGCCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG
*
54773374 CTGATGTGATGAATGTGAAAGTGTATATATG
66 CCGATGTGATGAATGTGAAAGTGTATATATG
*
54773405 TGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG
54773468 CCGATGTGATGAATGTGAAAGTGTATATATG
66 CCGATGTGATGAATGTGAAAGTGTATATATG
* * * * *
54773499 TGATAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATATGTGACAGGGCCGAGTGG
1 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG
* * * *
54773564 CCAACGTGATGGATGTGAAAGTGTATAAATG
66 CCGATGTGATGAATGTGAAAGTGTATATATG
54773595 TGATAAG
1 TGATAAG
54773602 TCCCGAAGGG
Statistics
Matches: 460, Mismatches: 19, Indels: 14
0.93 0.04 0.03
Matches are distributed among these distances:
94 91 0.20
95 34 0.07
96 198 0.43
97 57 0.12
98 80 0.17
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (96 bp):
TGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGG
CCGATGTGATGAATGTGAAAGTGTATATATG
Found at i:54773776 original size:37 final size:37
Alignment explanation
Indices: 54773720--54773798 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
54773710 CCGAGCTCTA
* * * *
54773720 AAGACCTGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
54773757 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
54773794 AAGAC
1 AAGAC
54773799 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:54788716 original size:12 final size:12
Alignment explanation
Indices: 54788699--54788724 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54788689 CCACACACGC
54788699 CCGTGTGTTAGG
1 CCGTGTGTTAGG
54788711 CCGTGTGTTAGG
1 CCGTGTGTTAGG
54788723 CC
1 CC
54788725 ATGCCAAACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.23, G:0.38, T:0.31
Consensus pattern (12 bp):
CCGTGTGTTAGG
Found at i:54790094 original size:15 final size:14
Alignment explanation
Indices: 54790056--54790094 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
54790046 GGACACACAA
54790056 CTGTGTAACACGAT
1 CTGTGTAACACGAT
54790070 C-GTGTAACACGACT
1 CTGTGTAACACGA-T
*
54790084 CTGTGTCACAC
1 CTGTGTAACAC
54790095 ACTACTGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (14 bp):
CTGTGTAACACGAT
Found at i:54792659 original size:34 final size:35
Alignment explanation
Indices: 54792620--54792688 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
54792610 GATATGTTAA
* *
54792620 TGGGCTAAGG-CCAGACTGCTACTGTTACTGAAAT
1 TGGGCTAAGGCCCAGACTGCCACTATTACTGAAAT
** *
54792654 TGGGCTCCGGCCCAGACTGCCACTATTGCTGAAAT
1 TGGGCTAAGGCCCAGACTGCCACTATTACTGAAAT
54792689 AGTCTGAGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (35 bp):
TGGGCTAAGGCCCAGACTGCCACTATTACTGAAAT
Found at i:54793998 original size:32 final size:32
Alignment explanation
Indices: 54793962--54794033 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
54793952 GGTCTTGCCG
* *
54793962 TGGTCTTACATTCACATGCCATAACCCGGTTA
1 TGGTCTTACATTCACATGCCATAACCCAGCTA
** ** *
54793994 TGGTCTTATTTTCTGATGCCATAGCCCAGCTA
1 TGGTCTTACATTCACATGCCATAACCCAGCTA
54794026 TGGTCTTA
1 TGGTCTTA
54794034 TTCAGCAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (32 bp):
TGGTCTTACATTCACATGCCATAACCCAGCTA
Found at i:54803962 original size:21 final size:20
Alignment explanation
Indices: 54803933--54803972 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
54803923 CATGTATTTT
54803933 AATGATTGATAATAGATTATG
1 AATGATTGATAATAG-TTATG
* *
54803954 AATGTTTGATCATAGTTAT
1 AATGATTGATAATAGTTAT
54803973 ACAAGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (20 bp):
AATGATTGATAATAGTTATG
Found at i:54805967 original size:13 final size:13
Alignment explanation
Indices: 54805949--54805973 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54805939 CCGAGCACAT
54805949 GCCCGTGTCCCTA
1 GCCCGTGTCCCTA
54805962 GCCCGTGTCCCT
1 GCCCGTGTCCCT
54805974 CACTCGGCCT
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:0.04, C:0.48, G:0.24, T:0.24
Consensus pattern (13 bp):
GCCCGTGTCCCTA
Found at i:54815558 original size:21 final size:22
Alignment explanation
Indices: 54815527--54815573 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 22
54815517 ATTACCGGAC
54815527 AATTCAAAATAT-TTCACA-AT
1 AATTCAAAATATATTCACACAT
54815547 AATTCAAAAATATCATTCACACAT
1 AATTC-AAAATAT-ATTCACACAT
54815571 AAT
1 AAT
54815574 CATAAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.22
21 7 0.30
23 6 0.26
24 5 0.22
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTCAAAATATATTCACACAT
Found at i:54818220 original size:13 final size:13
Alignment explanation
Indices: 54818202--54818226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54818192 ACAAATGATA
54818202 AAATTTTCACACG
1 AAATTTTCACACG
54818215 AAATTTTCACAC
1 AAATTTTCACAC
54818227 ATGTCAATTC
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:54818313 original size:33 final size:33
Alignment explanation
Indices: 54818271--54818344 Score: 139
Period size: 33 Copynumber: 2.2 Consensus size: 33
54818261 TATTTAAATT
*
54818271 TTTTTACTCAAAATTGTGGTCTTGAAACCACTA
1 TTTTGACTCAAAATTGTGGTCTTGAAACCACTA
54818304 TTTTGACTCAAAATTGTGGTCTTGAAACCACTA
1 TTTTGACTCAAAATTGTGGTCTTGAAACCACTA
54818337 TTTTGACT
1 TTTTGACT
54818345 AGGGTCTGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (33 bp):
TTTTGACTCAAAATTGTGGTCTTGAAACCACTA
Found at i:54820144 original size:37 final size:37
Alignment explanation
Indices: 54820094--54820172 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
54820084 TTATTACGAA
* * *
54820094 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
54820131 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
54820168 GTCTT
1 GTCTT
54820173 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:54820369 original size:47 final size:47
Alignment explanation
Indices: 54820291--54820515 Score: 317
Period size: 47 Copynumber: 4.7 Consensus size: 47
54820281 CCCTTCGGGA
* * * * * *
54820291 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54820338 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54820385 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54820432 CTTATCACATATATACACTTTTCACATTCATCAACATCGGCCATTAGGC
1 CTTATCACATATATACAC-TTTCACATTCATC-ACATCGGCCATTAGGC
* * *
54820481 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
54820516 AGAATCCTAA
Statistics
Matches: 162, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
47 107 0.66
48 24 0.15
49 31 0.19
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54822223 original size:29 final size:29
Alignment explanation
Indices: 54822190--54822246 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
54822180 TATTTTATTT
54822190 TTCCATTAACACAACATGTTTTGCCCATG
1 TTCCATTAACACAACATGTTTTGCCCATG
54822219 TTCCATTAACACAACATGTTTTGCCCAT
1 TTCCATTAACACAACATGTTTTGCCCAT
54822247 CATCCCTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (29 bp):
TTCCATTAACACAACATGTTTTGCCCATG
Found at i:54823469 original size:40 final size:40
Alignment explanation
Indices: 54823437--54823898 Score: 463
Period size: 40 Copynumber: 11.6 Consensus size: 40
54823427 CCAGCATGAT
* * * *
54823437 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
54823477 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * *
54823517 TGGTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
54823557 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
54823597 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
54823637 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* ** *
54823677 TGCTCTTTGAAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* * * * * *
54823717 TGCTCTTCGGGACTTAGCCCGGTTATAGTAACTCGTACAAA
1 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAA
* ** * * *
54823758 TGC-CTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAA
* * * * *
54823798 TGC-CTTCGAG-CTTAGCCCGGAATTA-GTAACTCGCACAAA
1 TGCTCTTCGGGACTTAGCCCGG-A-TACATCACTAGCACGAA
* **
54823837 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGA-CTTAGCCCGGATA-CATCAC-TAGCACGAA
*
54823877 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
54823899 CATCATTCGA
Statistics
Matches: 363, Mismatches: 50, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
38 3 0.01
39 29 0.08
40 311 0.86
41 20 0.06
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:54825804 original size:37 final size:37
Alignment explanation
Indices: 54825754--54825832 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
54825744 TTATTACGAA
* * *
54825754 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
54825791 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
54825828 GTCTT
1 GTCTT
54825833 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:54826029 original size:47 final size:47
Alignment explanation
Indices: 54825951--54826455 Score: 868
Period size: 47 Copynumber: 10.7 Consensus size: 47
54825941 CCCTTCGGGA
* * * * * *
54825951 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54825998 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54826045 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54826092 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54826139 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
54826186 CTTTTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
54826233 CTTATCACATATATACACTTTCACAGTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54826280 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54826327 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
54826374 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
54826421 CTTATCTCATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
54826456 AGAATCCTAA
Statistics
Matches: 438, Mismatches: 19, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
46 1 0.00
47 437 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:54834444 original size:43 final size:42
Alignment explanation
Indices: 54834349--54834469 Score: 140
Period size: 44 Copynumber: 2.9 Consensus size: 42
54834339 CCAAAGGCTC
* * *
54834349 ATAT-AATGCCAACGTCCCAGACGTGGTCTTGCATGTAATCAA
1 ATATCAATGCCAA-GTCCCAGACGTGGTCTTACACGAAATCAA
*
54834391 ATATCAATGCCATTGTCCCCAGACAG-GGTCTTACACGAAATCAA
1 ATATCAATGCCA-AGT-CCCAGAC-GTGGTCTTACACGAAATCAA
*
54834435 ATA-CGATGCCAAGTCCCAGACGTGGTCTTACACGA
1 ATATCAATGCCAAGTCCCAGACGTGGTCTTACACGA
54834470 GGGCAAATAT
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
40 1 0.01
41 19 0.28
42 6 0.09
43 16 0.24
44 25 0.37
45 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.23
Consensus pattern (42 bp):
ATATCAATGCCAAGTCCCAGACGTGGTCTTACACGAAATCAA
Found at i:54839412 original size:34 final size:34
Alignment explanation
Indices: 54839365--54839430 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
54839355 AGCATGTTAT
54839365 AAGTTTGGATAGGCTTGGGTAACAAAGAAAATTG
1 AAGTTTGGATAGGCTTGGGTAACAAAGAAAATTG
**
54839399 AAGTTTGTCTAGGCTTGGGTAACAAAGAAAAT
1 AAGTTTGGATAGGCTTGGGTAACAAAGAAAAT
54839431 GAACACATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.27
Consensus pattern (34 bp):
AAGTTTGGATAGGCTTGGGTAACAAAGAAAATTG
Found at i:54841217 original size:46 final size:46
Alignment explanation
Indices: 54841167--54841339 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
54841157 TGGTTGAGCA
*
54841167 TCCGAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54841213 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
**
54841258 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
54841306 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
54841340 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 59 0.56
47 29 0.27
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54841323 original size:93 final size:93
Alignment explanation
Indices: 54841164--54841334 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
54841154 GGATGGTTGA
***
54841164 GCATCCGAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
54841229 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
54841257 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
*
54841322 TGAGTCTGAGTTC
66 TGAGTCCGAGTTC
54841335 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAATTCACTTATGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:54842871 original size:48 final size:48
Alignment explanation
Indices: 54842724--54842848 Score: 180
Period size: 48 Copynumber: 2.6 Consensus size: 48
54842714 GGACTATCGA
* **
54842724 CATCGATATGTGATCCCATGTAAGACCATGT-ATGGGACATAACATTGG
1 CATCGATATGTGATCCCATGTAAGACCATGTCA-AGGACATGGCATTGG
* * *
54842772 CATCGATCTATGATCCCATGTAAGACCATGTCAAGGACATGGCGTTGG
1 CATCGATATGTGATCCCATGTAAGACCATGTCAAGGACATGGCATTGG
54842820 CATCGATATGTGATCCCATGTAAGACCAT
1 CATCGATATGTGATCCCATGTAAGACCAT
54842849 ATCCAGGATA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
48 67 0.99
49 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (48 bp):
CATCGATATGTGATCCCATGTAAGACCATGTCAAGGACATGGCATTGG
Found at i:54850324 original size:17 final size:17
Alignment explanation
Indices: 54850302--54850336 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
54850292 CAAAGTGGGG
54850302 TAATGGGCCCAATAGGC
1 TAATGGGCCCAATAGGC
*
54850319 TAATGGGCCCAATGGGC
1 TAATGGGCCCAATAGGC
54850336 T
1 T
54850337 GTAGGGCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.23, G:0.31, T:0.20
Consensus pattern (17 bp):
TAATGGGCCCAATAGGC
Found at i:54850468 original size:28 final size:29
Alignment explanation
Indices: 54850405--54850492 Score: 99
Period size: 28 Copynumber: 3.1 Consensus size: 29
54850395 AAAGCATGAC
* *
54850405 TATGTATGTGATTTGGGCCTAATGGGCCA
1 TATGAATGTGATGTGGGCCTAATGGGCCA
*
54850434 TACGAATGTGATGTGGGCC-AATGGGCCA
1 TATGAATGTGATGTGGGCCTAATGGGCCA
** * *
54850462 TATGAATAAGAT-TGGGCCTAGTGGGTCA
1 TATGAATGTGATGTGGGCCTAATGGGCCA
54850490 TAT
1 TAT
54850493 ACATGTATGT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 6 0.12
28 28 0.56
29 16 0.32
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.30
Consensus pattern (29 bp):
TATGAATGTGATGTGGGCCTAATGGGCCA
Found at i:54853332 original size:43 final size:46
Alignment explanation
Indices: 54853228--54853385 Score: 121
Period size: 48 Copynumber: 3.4 Consensus size: 46
54853218 GGTTATGTGC
* * * *
54853228 GATCCCATGTAAGACCAT-GTCTGGGACATGGCTTTTGCATCGGTATGT
1 GATCCCATGTAAGACCATAGTCCGGGAC-TTGC--TGGCATCGATATGT
* ** * *
54853276 AATTTCATATAAGACCATAG-CCGGG-CTAT-C-GGCATCTATATGT
1 GATCCCATGTAAGACCATAGTCCGGGACT-TGCTGGCATCGATATGT
*
54853319 GATCCCATGTAAGACCAT-GTCTGGGACTTGGCGTTGGCATCGATATGT
1 GATCCCATGTAAGACCATAGTCCGGGACTT-GC--TGGCATCGATATGT
54853367 GATCCCATGTAAGACCATA
1 GATCCCATGTAAGACCATA
54853386 TCTGGGATAT
Statistics
Matches: 85, Mismatches: 15, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
42 1 0.01
43 29 0.34
44 2 0.02
45 1 0.01
46 2 0.02
47 1 0.01
48 48 0.56
49 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (46 bp):
GATCCCATGTAAGACCATAGTCCGGGACTTGCTGGCATCGATATGT
Found at i:54853365 original size:48 final size:48
Alignment explanation
Indices: 54853306--54853407 Score: 154
Period size: 48 Copynumber: 2.1 Consensus size: 48
54853296 CCGGGCTATC
*
54853306 GGCATCTATATGTGATCCCATGTAAGACCATGTCTGGGACT-TGGCGTT
1 GGCATCGATATGTGATCCCATGTAAGACCATGTCTGGGACTATGGC-TT
*
54853354 GGCATCGATATGTGATCCCATGTAAGACCATATCTGGGA-TATGGCATT
1 GGCATCGATATGTGATCCCATGTAAGACCATGTCTGGGACTATGGC-TT
54853402 GGCATC
1 GGCATC
54853408 CTACCATGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
47 1 0.02
48 49 0.98
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (48 bp):
GGCATCGATATGTGATCCCATGTAAGACCATGTCTGGGACTATGGCTT
Found at i:54854217 original size:80 final size:81
Alignment explanation
Indices: 54854084--54854245 Score: 301
Period size: 80 Copynumber: 2.0 Consensus size: 81
54854074 GATGAATTGT
54854084 GGATATGATCATGTATGTTTGATGATGGAAATGTGGTTAAATGGCATAATAACAACTAAGGCATG
1 GGATATGATCATGTATGTTTGATGATGGAAATGTGGTTAAATGGCATAATAACAACTAAGGCATG
54854149 AATGTATGAAAT-GGA
66 AATGTATGAAATAGGA
54854164 GGATATGATCATGTATGTTTGATGATGGAAATGTGAG-TAAATGGCATAATAACAACTAAGGCAT
1 GGATATGATCATGTATGTTTGATGATGGAAATGTG-GTTAAATGGCATAATAACAACTAAGGCAT
54854228 GAATGTATGAAATAGGA
65 GAATGTATGAAATAGGA
54854245 G
1 G
54854246 TAAATTGAGG
Statistics
Matches: 80, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
80 75 0.94
81 5 0.06
ACGTcount: A:0.38, C:0.06, G:0.27, T:0.29
Consensus pattern (81 bp):
GGATATGATCATGTATGTTTGATGATGGAAATGTGGTTAAATGGCATAATAACAACTAAGGCATG
AATGTATGAAATAGGA
Found at i:54859184 original size:46 final size:46
Alignment explanation
Indices: 54859031--54859250 Score: 216
Period size: 46 Copynumber: 4.7 Consensus size: 46
54859021 TTATTTGTGT
* * * *
54859031 GCTAGTGTAAGACATGTCTAGGACATGCATCGACCAC-ATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGAGA
* * * * * *
54859077 GCCAGTGTAAGACCATGTCTGGGACATGGCATTGACATTGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGAGA
54859125 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-AGA
* *
54859171 GCTAGTGTAAGACATGTCTGGGACATGCATCAG-CTACGAGATGTG-
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAGA
* *
54859216 TC-AGTGTAAGACCATATCTGGGACATGGCATCGGC
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
54859251 ATTATACCCT
Statistics
Matches: 146, Mismatches: 19, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
44 9 0.06
45 16 0.11
46 69 0.47
47 28 0.19
48 23 0.16
49 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAGA
Found at i:54862895 original size:46 final size:46
Alignment explanation
Indices: 54862744--54862960 Score: 192
Period size: 46 Copynumber: 4.7 Consensus size: 46
54862734 TTTGTGTGCT
* * * * *
54862744 AGTGTAAGACATGTCTAGGACATGCATCGACCAC-ATTATGAGAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GATGAGAGCC
* * * * * *
54862790 AGTGTAAGACCATGTCTGGGACATGGCATTGACATTGAGACGAGGGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGAGAGCC
54862838 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATG-AGAGCC
* * * *
54862884 AGTGTAAGACATGTCTGGGACATGAATCAG-CTACGAGAT--GTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGAGAGCC
*
54862928 AGTGTAAGACCATATCTGGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
54862961 AAGGATATGT
Statistics
Matches: 140, Mismatches: 22, Indels: 17
0.78 0.12 0.09
Matches are distributed among these distances:
44 11 0.08
45 15 0.11
46 63 0.45
47 28 0.20
48 22 0.16
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGAGAGCC
Found at i:54878301 original size:46 final size:46
Alignment explanation
Indices: 54878251--54878426 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 46
54878241 TGTTTGGGCA
54878251 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *** * *
54878297 TCCGAACACGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCAT-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
* * * *
54878345 T-CGAGCTCGTTGAGCTGAGTCCGAGTTCACTTATGGATACGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54878390 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54878427 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
44 3 0.03
45 1 0.01
46 66 0.63
47 28 0.27
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54878406 original size:93 final size:93
Alignment explanation
Indices: 54878247--54878418 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
54878237 AGGATGTTTG
* * * *
54878247 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACACGTTGAG
1 GGCATCCGAACTCGTTGAGCTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACACGTTGAG
54878312 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
54878340 GGCATTCGAGCTCGTTGAGCTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGCTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACACGTTGAG
54878405 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
54878419 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGCTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACACGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:54881366 original size:15 final size:15
Alignment explanation
Indices: 54881327--54881406 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
54881317 GTATCTTGGG
*
54881327 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
54881342 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
54881357 TTTCTTTATTTTGGG
1 TTTCTTTATTCTGGA
*
54881372 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
54881387 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
54881401 TTTCTT
1 TTTCTT
54881407 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 9 0.17
15 42 0.79
16 2 0.04
ACGTcount: A:0.10, C:0.16, G:0.14, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:54881373 original size:45 final size:44
Alignment explanation
Indices: 54881322--54881406 Score: 125
Period size: 45 Copynumber: 1.9 Consensus size: 44
54881312 GTATCGTATC
*
54881322 TTGGGTTTCTTTATCCTGGATCTCTTTATTCTGGATTTCTTTATT
1 TTGGGTTTCTCTATCCTGGATCTCTTTATTC-GGATTTCTTTATT
* * *
54881367 TTGGGTTTCTCTATCTTGGATTTCTTTATTCGGTTTTCTT
1 TTGGGTTTCTCTATCCTGGATCTCTTTATTCGGATTTCTT
54881407 GTTATCTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 8 0.22
45 28 0.78
ACGTcount: A:0.09, C:0.15, G:0.16, T:0.59
Consensus pattern (44 bp):
TTGGGTTTCTCTATCCTGGATCTCTTTATTCGGATTTCTTTATT
Found at i:54881387 original size:30 final size:30
Alignment explanation
Indices: 54881318--54881397 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
54881308 ATAAGTATCG
* * *
54881318 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATCTCTC
* * *
54881348 TAT-TCTGGATTTCTTTATTTTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATCTCTC
54881378 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
54881398 GGTTTTCTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.02
30 39 0.95
31 1 0.02
ACGTcount: A:0.11, C:0.16, G:0.15, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATCTCTC
Found at i:54900568 original size:46 final size:46
Alignment explanation
Indices: 54900518--54900694 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
54900508 TGTTTGGGCA
*
54900518 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *** * *
54900564 TCCGAACACGTTGAGTTGAGTTCCGAGTTCGAGAGATGTAACTAG-GCAT-
1 TCCGAACTCGTTGAGTTGAG-TCCGAGTTC-ACTTATG-GA-T-GCGAATG
* * * *
54900613 T-CGAGCTCGTTGAGCTGAGTCCGAGTTCACTTATGGATACGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54900658 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54900695 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 19, Indels: 16
0.75 0.14 0.12
Matches are distributed among these distances:
44 3 0.03
45 1 0.01
46 57 0.55
47 17 0.16
48 19 0.18
49 2 0.02
50 4 0.04
51 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54900675 original size:94 final size:93
Alignment explanation
Indices: 54900514--54900686 Score: 256
Period size: 94 Copynumber: 1.8 Consensus size: 93
54900504 AGGATGTTTG
* * * * *
54900514 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAACACGTTGAG
1 GGCATCCGAACTCGTTGAGCTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACACGTTGAG
54900579 TTGAGTTCCGAGTTCGAGAGATGTAACTA
66 TTGAG-TCCGAGTTCGAGAGATGTAACTA
* * * *
54900608 GGCATTCGAGCTCGTTGAGCTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGCTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACACGTTGAG
54900673 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
54900687 ACTTATGGGC
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
93 9 0.13
94 61 0.87
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGCTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACACGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:54903670 original size:15 final size:15
Alignment explanation
Indices: 54903631--54903692 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
54903621 GTATCTTGGG
*
54903631 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
54903646 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
54903661 TTTCTTTATTTTGG-
1 TTTCTTTATTCTGGA
*
54903675 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
54903690 TTT
1 TTT
54903693 TTTCTTTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
13 1 0.03
14 10 0.26
15 28 0.72
ACGTcount: A:0.11, C:0.16, G:0.13, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:54906147 original size:46 final size:46
Alignment explanation
Indices: 54906095--54906270 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
54906085 TGTTTGGGCA
54906095 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *** * *
54906141 TCCGAACTCGTTCAGTTGAGTTCGAGTTCGAGAGATGTAACTAG-GCAT-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
* *
54906189 T-CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
54906234 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
54906271 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 66 0.62
47 28 0.26
48 2 0.02
49 4 0.04
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:54906251 original size:93 final size:93
Alignment explanation
Indices: 54906091--54906262 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
54906081 AGAATGTTTG
* *
54906091 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTCAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTCAG
*
54906156 TTGAGTTCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
54906184 GGCATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTCAG
54906249 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
54906263 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTCAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:54908895 original size:38 final size:39
Alignment explanation
Indices: 54908796--54908974 Score: 174
Period size: 39 Copynumber: 4.6 Consensus size: 39
54908786 TCGAATGATG
* * *
54908796 TCCGGGCT-AGTCCGGAAGGC-TTT-GTGCTAAGTGACCATA
1 TCCGGGCTAAGTCC-GAAGGCATTTGGTGC-GAGTTACTA-A
*
54908835 TCCGGACTAAGATCCGAAGGCATTTGGTGCGAGTTACTAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGGTGCGAGTTACTAA
*
54908875 TTCGGGCTAAG-CCGAAGGCA-TTGGTGC-AGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGGTGCGAGTTACT-AA
*
54908912 TCCGGGTTAAGTCCGAAGGCATTT-GTGCGAGTTACTATA
1 TCCGGGCTAAGTCCGAAGGCATTTGGTGCGAGTTACTA-A
* *
54908951 ACCGGGCTAAGTCCCAAGAGCATT
1 TCCGGGCTAAGTCCGAAG-GCATT
54908975 CATGCTAGTG
Statistics
Matches: 119, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
36 7 0.06
37 18 0.15
38 23 0.19
39 32 0.27
40 23 0.19
41 12 0.10
42 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGGTGCGAGTTACTAA
Found at i:54909010 original size:40 final size:40
Alignment explanation
Indices: 54908952--54909259 Score: 414
Period size: 40 Copynumber: 7.9 Consensus size: 40
54908942 GTTACTATAA
*
54908952 CCGGGCTAAG-TCCCAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT
*
54908991 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT
*
54909031 CCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT
*
54909071 CCGGGCT-AGTCCCGAAGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT
*
54909110 CCGGGCTAAGTCCCG-AGAGCATTCATGCTAGTGATGTAT
1 CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT
* *
54909149 CCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATAT
1 CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT
* * * * * * *
54909189 CCGTGCTAA--ACCCAAGAGCATTCGTGCTGGTGTTATAT
1 CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT
* * *
54909227 -CGGGCT-AGGTCCGAAGAGCAATCATGCTGGTGA
1 CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGA
54909260 CGTGTATTCG
Statistics
Matches: 246, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
36 1 0.00
37 5 0.02
38 44 0.18
39 87 0.35
40 109 0.44
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTAT
Found at i:54909119 original size:158 final size:155
Alignment explanation
Indices: 54908952--54909259 Score: 483
Period size: 158 Copynumber: 2.0 Consensus size: 155
54908942 GTTACTATAA
54908952 CCGGGCTAAGTCCCAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCG
1 CCGGGCTAAGTCCCAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCG
* * *
54909017 TGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTA-GT
66 TGCTAGTGATATATCCGGGCTAA-ACCC-AAGAGCATTCATGCTAGTGATATAT-CGGGCTAGGT
*
54909081 CCCGAAGAGCATTCATGCTAGTGATGTAT
128 -CCGAAGAGCAATCATGCTAGTGATGTAT
*
54909110 CCGGGCTAAGTCCCGAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCG
1 CCGGGCTAAGTCCCAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCG
* * * *
54909175 TGCTAGTGATATATCCGTGCTAAACCCAAGAGCATTCGTGCTGGTGTTATATCGGGCTAGGTCCG
66 TGCTAGTGATATATCCGGGCTAAACCCAAGAGCATTCATGCTAGTGATATATCGGGCTAGGTCCG
*
54909240 AAGAGCAATCATGCTGGTGA
131 AAGAGCAATCATGCTAGTGA
54909260 CGTGTATTCG
Statistics
Matches: 139, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
155 28 0.20
156 23 0.17
157 3 0.02
158 85 0.61
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (155 bp):
CCGGGCTAAGTCCCAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCG
TGCTAGTGATATATCCGGGCTAAACCCAAGAGCATTCATGCTAGTGATATATCGGGCTAGGTCCG
AAGAGCAATCATGCTAGTGATGTAT
Found at i:54912115 original size:47 final size:47
Alignment explanation
Indices: 54912046--54912632 Score: 1059
Period size: 47 Copynumber: 12.5 Consensus size: 47
54912036 GTGTGTATAC
54912046 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
54912093 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
54912140 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
54912187 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
54912234 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
54912281 GTGAAAGTGTATATATGTGATAAGGCCTAATTGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
54912328 GTGAAAGTGTATATATGTTATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
54912375 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
54912422 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
54912469 GTGAAAGTGTATATATGTGATAAGGCCT-ATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
54912515 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
* * * * * * * * *
54912562 GTTAAAGTGTATATACGTGACAGGGCCGAGTGGCCAACGTGATGGAT
1 GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
*
54912609 GTGAAAGTGTATAAATGTGATAAG
1 GTGAAAGTGTATATATGTGATAAG
54912633 TCCCGAAGGG
Statistics
Matches: 521, Mismatches: 18, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
46 46 0.09
47 475 0.91
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.30
Consensus pattern (47 bp):
GTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
Found at i:54917432 original size:47 final size:45
Alignment explanation
Indices: 54917327--54917449 Score: 178
Period size: 47 Copynumber: 2.7 Consensus size: 45
54917317 CGTCTGTGTT
*
54917327 GATGCCATGTCCCAGACA-GGTCTTACACTAACACATGTCAAGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTAACACATCTCAAGCC
** *
54917371 GATG-CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCAAGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTAAC--ACATCTCAAGCC
54917417 GATGCCATGTCCCAGACATGGTCTTACACTAAC
1 GATGCCATGTCCCAGACATGGTCTTACACTAAC
54917450 TATCATCATC
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
43 13 0.19
44 16 0.23
46 14 0.20
47 26 0.38
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (45 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAACACATCTCAAGCC
Found at i:54919771 original size:37 final size:34
Alignment explanation
Indices: 54919721--54919792 Score: 81
Period size: 37 Copynumber: 2.0 Consensus size: 34
54919711 ATGTGCCATT
* *
54919721 TTTTTCTGACCATCTTTCCTCCTCCTCCTTTCTTTTC
1 TTTTTCTCACCATC-TACCTCCTCCT-C-TTCTTTTC
* *
54919758 TTTTTCTCTCCATCTACCTTCTCCTCTTCTTTTC
1 TTTTTCTCACCATCTACCTCCTCCTCTTCTTTTC
54919792 T
1 T
54919793 CCATAGTCGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 9 0.29
35 1 0.03
36 9 0.29
37 12 0.39
ACGTcount: A:0.06, C:0.38, G:0.01, T:0.56
Consensus pattern (34 bp):
TTTTTCTCACCATCTACCTCCTCCTCTTCTTTTC
Found at i:54920779 original size:31 final size:31
Alignment explanation
Indices: 54920739--54920824 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
54920729 TCAAGCTCAG
*
54920739 CATAT-ACTGGGCCAAAGCCTTTACATTATC
1 CATATCACTGGGCCGAAGCCTTTACATTATC
* * *
54920769 CATGTCACTGGGCCGAAGCCTTTTCATTATT
1 CATATCACTGGGCCGAAGCCTTTACATTATC
54920800 CATATCACTGGGCCGAAGCCTTTAC
1 CATATCACTGGGCCGAAGCCTTTAC
54920825 TGTAAACGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
30 4 0.08
31 45 0.92
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTACATTATC
Found at i:54921063 original size:24 final size:25
Alignment explanation
Indices: 54921036--54921087 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
54921026 CCCTAGCCTC
* *
54921036 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTAGGGAAAAGCCCT
*
54921060 TTTTGATAAACTAGGGAAAAGCCCT
1 TTTTAATAAACTAGGGAAAAGCCCT
54921085 TTT
1 TTT
54921088 CGGTAAACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (25 bp):
TTTTAATAAACTAGGGAAAAGCCCT
Found at i:54921071 original size:25 final size:25
Alignment explanation
Indices: 54921043--54921112 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
54921033 CTCTTTTAAT
*
54921043 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
* * *
54921068 AACTAGGGAAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
54921093 AACTGAGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
54921113 AGCACTTCCT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:54921391 original size:27 final size:27
Alignment explanation
Indices: 54921351--54921435 Score: 152
Period size: 27 Copynumber: 3.1 Consensus size: 27
54921341 CGTTCCACAA
* *
54921351 GGGTATCTCGGTAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
54921378 GGGTATTTCAGTAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
54921405 GGGTATTTCAGTAATTCTACCCTACAG
1 GGGTATTTCAGTAATTCTACCCTACAG
54921432 GGGT
1 GGGT
54921436 TGTAACAGCC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (27 bp):
GGGTATTTCAGTAATTCTACCCTACAG
Found at i:54923398 original size:31 final size:31
Alignment explanation
Indices: 54923282--54923400 Score: 134
Period size: 31 Copynumber: 3.8 Consensus size: 31
54923272 ACAAATGACA
*
54923282 AGTGAAAAGTAGTAGCTTCGGCTACCTGAT-
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * * *
54923312 AGATAAAAAAATGGTAGCTTTGGCAACCTGATC
1 AG-T-GAAAAGTGGTAGCTTCGGCTACCTGATC
*
54923345 AGTGAAAAGTGGTAG-TACCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCT-TCGGCTACCTGATC
*
54923376 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
54923401 AAGTGACAAG
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
30 3 0.04
31 43 0.60
32 24 0.33
33 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:54923536 original size:46 final size:47
Alignment explanation
Indices: 54923469--54923630 Score: 167
Period size: 42 Copynumber: 3.5 Consensus size: 47
54923459 TGCTACTTTA
* *
54923469 TAAGACCATATCTGGGATATGGCAT-TAGTGAGATATGTGATT-CGTG
1 TAAGACCATAGCTGGGCTATGGCATATA-TGAGATATGTGATTACGTG
* *
54923515 TAAGACCATAGCAGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCAT--ATATGAGATATGTGATTACGTG
* * * *
54923564 TAAGACCATAGTTGGGCTATGGC--AT-CGAGATA-G-GAATATGTG
1 TAAGACCATAGCTGGGCTATGGCATATATGAGATATGTGATTACGTG
*
54923606 TAAGACCATAGCTGTGCTATGGCAT
1 TAAGACCATAGCTGGGCTATGGCAT
54923631 CATTATGTGA
Statistics
Matches: 98, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
42 28 0.29
43 1 0.01
44 5 0.05
45 2 0.02
46 22 0.22
48 13 0.13
49 27 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (47 bp):
TAAGACCATAGCTGGGCTATGGCATATATGAGATATGTGATTACGTG
Found at i:54923625 original size:42 final size:44
Alignment explanation
Indices: 54923561--54923677 Score: 152
Period size: 42 Copynumber: 2.8 Consensus size: 44
54923551 ATGTGATTAC
* *
54923561 GTGTAAGACCATAGTTGGGCTATGGCATCGAGATA-G-GAATAT
1 GTGTAAGACCATAGTTGAGCTATGGCATCGAGATATGTGAAGAT
* * *
54923603 GTGTAAGACCATAGCTGTGCTATGGCATC-A-TTATGTGAAGAT
1 GTGTAAGACCATAGTTGAGCTATGGCATCGAGATATGTGAAGAT
*
54923645 GTGTAAGACCATAGTTGAACTATGGCATCGAGA
1 GTGTAAGACCATAGTTGAGCTATGGCATCGAGA
54923678 AAATGAAGTG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
40 2 0.03
41 2 0.03
42 58 0.92
43 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (44 bp):
GTGTAAGACCATAGTTGAGCTATGGCATCGAGATATGTGAAGAT
Found at i:54924514 original size:27 final size:27
Alignment explanation
Indices: 54924483--54924574 Score: 150
Period size: 27 Copynumber: 3.4 Consensus size: 27
54924473 GGGGTGTTAC
54924483 AGGGGTATTTCGGTAATTCTACCTTAT
1 AGGGGTATTTCGGTAATTCTACCTTAT
*
54924510 AGGGGTATTTCGGTAATTCTACCTTAC
1 AGGGGTATTTCGGTAATTCTACCTTAT
* *
54924537 AGGGGTATTTTGGTAATTCTACCCTAT
1 AGGGGTATTTCGGTAATTCTACCTTAT
54924564 A-GGGTATTTCG
1 AGGGGTATTTCG
54924575 ATATTTTACA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
26 9 0.15
27 51 0.85
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (27 bp):
AGGGGTATTTCGGTAATTCTACCTTAT
Found at i:54924614 original size:27 final size:27
Alignment explanation
Indices: 54924567--54924662 Score: 97
Period size: 27 Copynumber: 3.6 Consensus size: 27
54924557 ACCCTATAGG
*
54924567 GTATTTCGAT-ATTTTACAAATC-GAGA
1 GTATTTTGATAATTTTACAAATCAG-GA
* *
54924593 GTATTTTGATAATTTCACAAATCAGGG
1 GTATTTTGATAATTTTACAAATCAGGA
* ** *
54924620 GTATTTTGGTAATTTTACAAGCCAGGG
1 GTATTTTGATAATTTTACAAATCAGGA
*
54924647 GTATTTTGGTAATTTT
1 GTATTTTGATAATTTT
54924663 GTAAACCAAG
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
26 9 0.15
27 51 0.84
28 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (27 bp):
GTATTTTGATAATTTTACAAATCAGGA
Found at i:54924675 original size:27 final size:27
Alignment explanation
Indices: 54924618--54924721 Score: 91
Period size: 27 Copynumber: 3.9 Consensus size: 27
54924608 CACAAATCAG
* ** * *
54924618 GGGTATTTTGGTAATTTTACAAGCCAG
1 GGGTATTTCGGTAATTTTGTAAACCAA
*
54924645 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTCGGTAATTTTGTAAACCAA
** * *
54924672 GGGTATTTCAATAATTTTGTAAATCGA
1 GGGTATTTCGGTAATTTTGTAAACCAA
***
54924699 GGGTAAAACGGTAATTTTGTAAA
1 GGGTATTTCGGTAATTTTGTAAA
54924722 TCGAGAGTAA
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.38
Consensus pattern (27 bp):
GGGTATTTCGGTAATTTTGTAAACCAA
Found at i:54924740 original size:81 final size:81
Alignment explanation
Indices: 54924653--54924946 Score: 340
Period size: 81 Copynumber: 3.6 Consensus size: 81
54924643 AGGGGTATTT
* * ** * *
54924653 TGGTAATTTTGTAAACCAAGGGTATTTCAATAATTTTGTAAATCGAGGGTAAAACGGTAATTTTG
1 TGGTAATTCTATAAACCAAGGGTAAATCGATAATTCTGTAAATCGAGGGTAAAACGGTAATTTTG
*
54924718 TAAATCGAGAGTAAAA
66 TAAATCGAGGGTAAAA
* * * * * * *
54924734 TAGTAATTCTATAAATCGAA-GGTAAAAT-GGTAATTCTATAAATCGAAGGTAAAATGGAAATTT
1 TGGTAATTCTATAAA-CCAAGGGT-AAATCGATAATTCTGTAAATCGAGGGTAAAACGGTAATTT
54924797 TGTAAATCGAGGGTAAAA
64 TGTAAATCGAGGGTAAAA
*** * *
54924815 TGGTAATTCTATAAATTGAGGGTAAAACGATAATTCTGTAAACCGAGGGTAAAACGGTAATTTTG
1 TGGTAATTCTATAAACCAAGGGTAAATCGATAATTCTGTAAATCGAGGGTAAAACGGTAATTTTG
54924880 TAAATCGAGGGTAAAA
66 TAAATCGAGGGTAAAA
* * * * *
54924896 TGGTAATTCTTTAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTA
1 TGGTAATTCTATAAACCAAGGGTAAATCGATAATTCTGTAAATCGAGGGTA
54924947 CTTTGGTAAT
Statistics
Matches: 180, Mismatches: 29, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 4 0.02
81 171 0.95
82 5 0.03
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (81 bp):
TGGTAATTCTATAAACCAAGGGTAAATCGATAATTCTGTAAATCGAGGGTAAAACGGTAATTTTG
TAAATCGAGGGTAAAA
Found at i:54924957 original size:27 final size:27
Alignment explanation
Indices: 54924683--54924946 Score: 348
Period size: 27 Copynumber: 9.8 Consensus size: 27
54924673 GGTATTTCAA
* *
54924683 TAATTTTGTAAATCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
* * *
54924710 TAATTTTGTAAATCGAGAGTAAAATAG
1 TAATTCTGTAAATCGAGGGTAAAATGG
* *
54924737 TAATTCTATAAATCGAAGGTAAAATGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
* *
54924764 TAATTCTATAAATCGAAGGTAAAATGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
* *
54924791 AAATTTTGTAAATCGAGGGTAAAATGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
* * * *
54924818 TAATTCTATAAATTGAGGGTAAAACGA
1 TAATTCTGTAAATCGAGGGTAAAATGG
* *
54924845 TAATTCTGTAAACCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
*
54924872 TAATTTTGTAAATCGAGGGTAAAATGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
* *
54924899 TAATTCTTTAAATCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAATGG
54924926 TAATTCTGTAAATCGAGGGTA
1 TAATTCTGTAAATCGAGGGTA
54924947 CTTTGGTAAT
Statistics
Matches: 208, Mismatches: 29, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 208 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (27 bp):
TAATTCTGTAAATCGAGGGTAAAATGG
Found at i:54924971 original size:81 final size:81
Alignment explanation
Indices: 54924683--54924946 Score: 411
Period size: 81 Copynumber: 3.3 Consensus size: 81
54924673 GGTATTTCAA
* * *
54924683 TAATTTTGTAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGAGTAAAATAGTAATTCTATAA
1 TAATTCTGTAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAA
* *
54924748 ATCGAAGGTAAAATGG
66 ATCGAGGGTAAAACGG
* * * *
54924764 TAATTCTATAAATCGAAGGTAAAATGGAAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAA
1 TAATTCTGTAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAA
* *
54924829 ATTGAGGGTAAAACGA
66 ATCGAGGGTAAAACGG
* *
54924845 TAATTCTGTAAACCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTTTAA
1 TAATTCTGTAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAA
54924910 ATCGAGGGTAAAACGG
66 ATCGAGGGTAAAACGG
54924926 TAATTCTGTAAATCGAGGGTA
1 TAATTCTGTAAATCGAGGGTA
54924947 CTTTGGTAAT
Statistics
Matches: 163, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 163 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (81 bp):
TAATTCTGTAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAATTCTATAA
ATCGAGGGTAAAACGG
Found at i:54926694 original size:47 final size:49
Alignment explanation
Indices: 54926614--54926756 Score: 204
Period size: 47 Copynumber: 3.0 Consensus size: 49
54926604 GCTTTATCAT
* *
54926614 ATAACTGGAGGCCT-AGCCTCTTTTAGTAACTGGGGCA-AAGCCCTTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTTA
*
54926663 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCC-TTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTA
*
54926710 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
54926757 GCACTTCCTC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
47 38 0.44
48 33 0.38
49 15 0.17
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (49 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTA
Found at i:54926715 original size:71 final size:72
Alignment explanation
Indices: 54926614--54926755 Score: 211
Period size: 71 Copynumber: 2.0 Consensus size: 72
54926604 GCTTTATCAT
*
54926614 ATAACTGGAGGCCTAGCCTCTTTTAGTAACTGGGGCA-AAGCCCTTTTTAATAACTGGGGCATAA
1 ATAACTGGAGGCATAGCCTCTTTTAGTAACTGGGGCATAAGCCC-TTTTAATAACTGGGGCATAA
54926678 GCCCTTTA
65 GCCCTTTA
*
54926686 ATAACTGG-GGCATAAGCC-CTTTT-GATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 ATAACTGGAGGCAT-AGCCTCTTTTAG-TAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
54926748 AGCCCTTT
64 AGCCCTTT
54926756 TGCACTTCCT
Statistics
Matches: 65, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
70 1 0.02
71 46 0.71
72 18 0.28
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (72 bp):
ATAACTGGAGGCATAGCCTCTTTTAGTAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAG
CCCTTTA
Found at i:54926757 original size:24 final size:24
Alignment explanation
Indices: 54926614--54926757 Score: 197
Period size: 24 Copynumber: 6.0 Consensus size: 24
54926604 GCTTTATCAT
*
54926614 ATAACTGGAGGCCT-AGCCTCTTTT-
1 ATAACTGG-GGCATAAGCC-CTTTTG
*
54926638 AGTAACTGGGGCA-AAGCCCTTTTTA
1 A-TAACTGGGGCATAAGCCC-TTTTG
*
54926663 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTG
54926686 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54926710 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54926734 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
54926758 CACTTCCTCC
Statistics
Matches: 112, Mismatches: 2, Indels: 12
0.89 0.02 0.10
Matches are distributed among these distances:
23 24 0.21
24 74 0.66
25 14 0.12
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:54926827 original size:9 final size:9
Alignment explanation
Indices: 54926813--54926888 Score: 55
Period size: 9 Copynumber: 7.9 Consensus size: 9
54926803 ATCTCGTGTG
54926813 CATATCATA
1 CATATCATA
* *
54926822 CATATCGTGTG
1 CATATC--ATA
54926833 CATATCATA
1 CATATCATA
*
54926842 CATATCATGTG
1 CATATCA--TA
54926853 CATATCATA
1 CATATCATA
*
54926862 CAT-TCATGTG
1 CATATCA--TA
54926872 CATATCATA
1 CATATCATA
54926881 CATATCAT
1 CATATCAT
54926889 GTTTATCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
8 3 0.06
9 27 0.52
10 4 0.08
11 18 0.35
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (9 bp):
CATATCATA
Found at i:54926829 original size:20 final size:20
Alignment explanation
Indices: 54926809--54926890 Score: 148
Period size: 20 Copynumber: 4.2 Consensus size: 20
54926799 GAACATCTCG
*
54926809 TGTGCATATCATACATATCG
1 TGTGCATATCATACATATCA
54926829 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
54926849 TGTGCATATCATACAT-TCA
1 TGTGCATATCATACATATCA
54926868 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
54926888 TGT
1 TGT
54926891 TTATCAAAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
19 19 0.32
20 41 0.68
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:54926856 original size:11 final size:11
Alignment explanation
Indices: 54926809--54926879 Score: 57
Period size: 9 Copynumber: 7.1 Consensus size: 11
54926799 GAACATCTCG
54926809 TGTGCATATCA
1 TGTGCATATCA
* *
54926820 --TACATATCG
1 TGTGCATATCA
54926829 TGTGCATATCA
1 TGTGCATATCA
*
54926840 --TACATATCA
1 TGTGCATATCA
54926849 TGTGCATATCA
1 TGTGCATATCA
*
54926860 --TACAT-TCA
1 TGTGCATATCA
54926868 TGTGCATATCA
1 TGTGCATATCA
54926879 T
1 T
54926880 ACATATCATG
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
8 3 0.07
9 19 0.42
10 4 0.09
11 19 0.42
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (11 bp):
TGTGCATATCA
Found at i:54926883 original size:39 final size:40
Alignment explanation
Indices: 54926809--54926890 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 40
54926799 GAACATCTCG
*
54926809 TGTGCATATCATACATATCGTGTGCATATCATACATATCA
1 TGTGCATATCATACATATCATGTGCATATCATACATATCA
54926849 TGTGCATATCATACAT-TCATGTGCATATCATACATATCA
1 TGTGCATATCATACATATCATGTGCATATCATACATATCA
54926888 TGT
1 TGT
54926891 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 25 0.61
40 16 0.39
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (40 bp):
TGTGCATATCATACATATCATGTGCATATCATACATATCA
Done.