Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 159 of 167
Found at i:52298290 original size:43 final size:43
Alignment explanation
Indices: 52298216--52298298 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
52298206 ATCGACATCG
* * *
52298216 TATTTGATTTCGTGTAAGACCCTATCTAGGACAG-TGGCATCAA
1 TATTTGATTACATGTAAGACCCTATCGAGGAC-GTTGGCATCAA
52298259 TATTTGATTACATGTAAGACCAC-ATCGAGGACGTTGGCAT
1 TATTTGATTACATGTAAGACC-CTATCGAGGACGTTGGCAT
52298299 TGTACGAGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.03
43 33 0.94
44 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (43 bp):
TATTTGATTACATGTAAGACCCTATCGAGGACGTTGGCATCAA
Found at i:52299151 original size:19 final size:19
Alignment explanation
Indices: 52299127--52299164 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
52299117 TGTATGATTT
52299127 GGATTTGAAATTGGTTGAA
1 GGATTTGAAATTGGTTGAA
52299146 GGATTTGAAATTGGTTGAA
1 GGATTTGAAATTGGTTGAA
52299165 AATATGATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.37
Consensus pattern (19 bp):
GGATTTGAAATTGGTTGAA
Found at i:52304104 original size:27 final size:27
Alignment explanation
Indices: 52304064--52304118 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
52304054 CTTGACGACC
*
52304064 CTAAGAAGTTATTTAAGTAGATGAGGT
1 CTAAGAAGTAATTTAAGTAGATGAGGT
52304091 CTAAGAAGTAATTTAAGTAGATGAGGT
1 CTAAGAAGTAATTTAAGTAGATGAGGT
52304118 C
1 C
52304119 AGAAGAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.31
Consensus pattern (27 bp):
CTAAGAAGTAATTTAAGTAGATGAGGT
Found at i:52304172 original size:55 final size:55
Alignment explanation
Indices: 52304111--52304234 Score: 194
Period size: 55 Copynumber: 2.3 Consensus size: 55
52304101 ATTTAAGTAG
*
52304111 ATGAGGTCAGAAGAATAGTCTATTGAGCATCTCTCAACTTGTCCTAGTTTGAACT
1 ATGAGGTCAGAAGAATAGTCTATTGAGCATCTCTCAACTTATCCTAGTTTGAACT
* * * * *
52304166 ATGAGGTCGGAAGAATTGTCTATTGAGCATCTCTTAACTTATCCTGGTTTGAATT
1 ATGAGGTCAGAAGAATAGTCTATTGAGCATCTCTCAACTTATCCTAGTTTGAACT
52304221 ATGAGGTCAGAAGA
1 ATGAGGTCAGAAGA
52304235 TAAGTAGTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 62 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (55 bp):
ATGAGGTCAGAAGAATAGTCTATTGAGCATCTCTCAACTTATCCTAGTTTGAACT
Found at i:52323683 original size:27 final size:27
Alignment explanation
Indices: 52323652--52323829 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
52323642 TAAATTGTAC
52323652 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
52323679 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
52323705 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
52323733 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
52323761 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
52323788 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
52323815 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
52323830 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:52323766 original size:82 final size:81
Alignment explanation
Indices: 52323653--52323808 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
52323643 AAATTGTACA
* *
52323653 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
52323717 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
52323734 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
52323799 TGCGAGTTGA
65 TGCGAATTGA
52323809 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:52323820 original size:82 final size:81
Alignment explanation
Indices: 52323649--52323829 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
52323639 GATTAAATTG
* *
52323649 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
52323714 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
52323730 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
52323794 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
52323812 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
52323830 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:52333965 original size:18 final size:19
Alignment explanation
Indices: 52333936--52333971 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52333926 GCATGTTTGC
*
52333936 TTAAGTTGAAATGAATGAT
1 TTAAGTTGAAATCAATGAT
52333955 TTAAG-TGAAATCAATGA
1 TTAAGTTGAAATCAATGA
52333972 CGCTATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.33
Consensus pattern (19 bp):
TTAAGTTGAAATCAATGAT
Found at i:52339314 original size:44 final size:43
Alignment explanation
Indices: 52339251--52339404 Score: 163
Period size: 44 Copynumber: 3.6 Consensus size: 43
52339241 TATGTGTTAT
*
52339251 CGTGTAAGACCAAGTCTGGGACGTTGGCATCGATTTATGATTTA
1 CGTGTAAGACCATGTCTGGGACGTTGGCATCGATTT-TGATTTA
* * *
52339295 CGTGTAAGACCATGTCTGGGATGTTGGCATTGTTTTTGATTT-
1 CGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTTGATTTA
* * *
52339337 CGTGTAAGACCCTGTCTGGGA-GAGTGGCATCGATACTTGA-TTA
1 CGTGTAAGACCATGTCTGGGACG-TTGGCATCGAT-TTTGATTTA
* *
52339380 CATGTACA-ACCACGTCTGGGACGTT
1 CGTGTA-AGACCATGTCTGGGACGTT
52339405 TTGTACGAGC
Statistics
Matches: 92, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
41 1 0.01
42 30 0.33
43 27 0.29
44 34 0.37
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (43 bp):
CGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTTGATTTA
Found at i:52339353 original size:42 final size:43
Alignment explanation
Indices: 52339250--52339404 Score: 156
Period size: 43 Copynumber: 3.6 Consensus size: 43
52339240 ATATGTGTTA
*
52339250 TCGTGTAAGACCAAGTCTGGGACGTTGGCATCGATTTATGATT
1 TCGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTATGATT
* * *
52339293 TACGTGTAAGACCATGTCTGGGATGTTGGCATTG-TTTTTGATT
1 T-CGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTATGATT
* * *
52339336 TCGTGTAAGACCCTGTCTGGGA-GAGTGGCATCGATACT-TGATT
1 TCGTGTAAGACCATGTCTGGGACG-TTGGCATCGAT-TTATGATT
* * *
52339379 ACATGTACA-ACCACGTCTGGGACGTT
1 TCGTGTA-AGACCATGTCTGGGACGTT
52339405 TTGTACGAGC
Statistics
Matches: 93, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
41 1 0.01
42 27 0.29
43 33 0.35
44 32 0.34
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (43 bp):
TCGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTATGATT
Found at i:52344979 original size:53 final size:53
Alignment explanation
Indices: 52344899--52345004 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
52344889 CAAGTCCAAA
52344899 GGGTCCACAACCCACAACAAACGGGTAGTCCTATACATGCCATTTCGAAGTTC
1 GGGTCCACAACCCACAACAAACGGGTAGTCCTATACATGCCATTTCGAAGTTC
*
52344952 GGGTCCACGACCCACAACAAACGGGTAGTCCTATACATGCCATTTCGAAGTTC
1 GGGTCCACAACCCACAACAAACGGGTAGTCCTATACATGCCATTTCGAAGTTC
52345005 AACCAAAATT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (53 bp):
GGGTCCACAACCCACAACAAACGGGTAGTCCTATACATGCCATTTCGAAGTTC
Found at i:52345338 original size:64 final size:64
Alignment explanation
Indices: 52345237--52345361 Score: 241
Period size: 64 Copynumber: 2.0 Consensus size: 64
52345227 CGTACTTGCG
52345237 TCACATTATCAACCCTTATGTACATACACAAAAGATCAACTCAGCCAAAGGCCGGTAGCTCGTT
1 TCACATTATCAACCCTTATGTACATACACAAAAGATCAACTCAGCCAAAGGCCGGTAGCTCGTT
*
52345301 TCACATTCTCAACCCTTATGTACATACACAAAAGATCAACTCAGCCAAAGGCCGGTAGCTC
1 TCACATTATCAACCCTTATGTACATACACAAAAGATCAACTCAGCCAAAGGCCGGTAGCTC
52345362 ATTTATCAAC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (64 bp):
TCACATTATCAACCCTTATGTACATACACAAAAGATCAACTCAGCCAAAGGCCGGTAGCTCGTT
Found at i:52345635 original size:79 final size:78
Alignment explanation
Indices: 52345532--52345756 Score: 247
Period size: 79 Copynumber: 2.8 Consensus size: 78
52345522 GCTCCTCGTT
*** *
52345532 CAAATGCCTTCGGGACAAAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCTGG
1 CAAATGCCTTCGGGTTTAA-CCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
52345597 ATTTAGTAACTAGCA
64 ATTTAGTAACTAGCA
*
52345612 CAAATGCCTTCGGGTTTAACCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGTTTAACCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCCGG
* *
52345676 ATTTAGTATCTCGCA
64 ATTTAGTAACTAGCA
* ** * * * *
52345691 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGT-TTAACCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAACCCG
52345755 GA
63 GA
52345757 CATCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
78 3 0.02
79 65 0.52
80 46 0.37
81 9 0.07
82 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGTTTAACCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGGAT
TTAGTAACTAGCA
Found at i:52345642 original size:39 final size:40
Alignment explanation
Indices: 52345532--52345756 Score: 244
Period size: 40 Copynumber: 5.7 Consensus size: 40
52345522 GCTCCTCGTT
* *
52345532 CAAATGCCTTCGGGAC-AAAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAA-CCCGGATT-TAGTAACTCGCA
* *
52345572 CAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTAGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
52345612 CAAATGCCTTCGGG-TTTAACCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
52345651 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
52345691 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
52345732 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
52345757 CATCATTCAA
Statistics
Matches: 160, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
39 37 0.23
40 108 0.68
41 15 0.09
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:52352722 original size:40 final size:40
Alignment explanation
Indices: 52352678--52352939 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
52352668 GCTCCTCGTT
* *
52352678 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
52352718 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52352758 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52352797 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
52352836 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
52352875 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
52352916 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52352940 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:52356877 original size:42 final size:42
Alignment explanation
Indices: 52356772--52356931 Score: 171
Period size: 43 Copynumber: 3.7 Consensus size: 42
52356762 ATATGTGTTA
* * *
52356772 TCGTGTAAGACCATGTCTGGGACGTTGGCATC-AACTTATGATT
1 TCGTGTAAGACCACGTCTGGGACATTGGCATCGTA-TT-TGATT
*
52356815 TACGTGTAAGACCACATCTGGGACATTGGCATCGTATTTGATT
1 T-CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATT
* * *
52356858 TCGTGTAAGACC-CTGTCTGGGACAGTGGCATTGATATTGGATT
1 TCGTGTAAGACCAC-GTCTGGGACATTGGCATCG-TATTTGATT
* * *
52356901 ACATGTAAGACCACGTCTGGGACGTTGGCAT
1 TCGTGTAAGACCACGTCTGGGACATTGGCAT
52356932 TGTACGAGCT
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
41 1 0.01
42 27 0.27
43 40 0.40
44 31 0.31
45 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (42 bp):
TCGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATT
Found at i:52358424 original size:42 final size:42
Alignment explanation
Indices: 52358372--52358487 Score: 148
Period size: 43 Copynumber: 2.8 Consensus size: 42
52358362 GTTAGGGGTG
*
52358372 TTACA-GTAAGACCATACTTGGGATATGGCATCGATATAAGA
1 TTACATGTAAGACCATACTTGGGATATGGCATCGATACAAGA
**
52358413 CTT-TTTGTAAGACCATAGC-TGGGATATTGGCATCGATACAAGA
1 -TTACATGTAAGACCATA-CTTGGGATA-TGGCATCGATACAAGA
*
52358456 TTACATGTAAGACCATATTTGGGATATGGCAT
1 TTACATGTAAGACCATACTTGGGATATGGCAT
52358488 TGGTATGGTA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
42 28 0.44
43 35 0.56
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (42 bp):
TTACATGTAAGACCATACTTGGGATATGGCATCGATACAAGA
Found at i:52359042 original size:56 final size:56
Alignment explanation
Indices: 52358980--52359098 Score: 202
Period size: 56 Copynumber: 2.1 Consensus size: 56
52358970 ACTCAATGCA
52358980 ATGGCTTATAATCGTCAAAGGCTTGTTTTACTATTTGGCCATGTAAGTTGGCTTAT
1 ATGGCTTATAATCGTCAAAGGCTTGTTTTACTATTTGGCCATGTAAGTTGGCTTAT
* * *
52359036 ATGGCTTGTAATCGTCAAAGGCTTGTTTTGCTATTTGGTCATGTAAGTTGGCTTAT
1 ATGGCTTATAATCGTCAAAGGCTTGTTTTACTATTTGGCCATGTAAGTTGGCTTAT
52359092 ATTGGCT
1 A-TGGCT
52359099 AACATGGTTG
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
56 54 0.92
57 5 0.08
ACGTcount: A:0.21, C:0.13, G:0.24, T:0.42
Consensus pattern (56 bp):
ATGGCTTATAATCGTCAAAGGCTTGTTTTACTATTTGGCCATGTAAGTTGGCTTAT
Found at i:52359134 original size:14 final size:14
Alignment explanation
Indices: 52359115--52359144 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
52359105 GTTGTAAGCC
52359115 TAAGTATACTCATA
1 TAAGTATACTCATA
52359129 TAAGTATACTCATA
1 TAAGTATACTCATA
52359143 TA
1 TA
52359145 TGGTGATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (14 bp):
TAAGTATACTCATA
Found at i:52363366 original size:176 final size:177
Alignment explanation
Indices: 52363066--52363418 Score: 647
Period size: 176 Copynumber: 2.0 Consensus size: 177
52363056 GAAAGAAAAA
52363066 CAAAGAAAAAAAAATTACTCATCCTTTGGTTCATCCTTGGCCAAAAATTTTAAGGAGGAAAGAAG
1 CAAAGAAAAAAAAATTACTCATCCTTTGGTTCATCCTTGGCCAAAAATTTTAAGGAGGAAAGAAG
*
52363131 AAGAAAGGTGAAGAGATTCGGCCATGCATGTAGCTAGGCTAAGGTATGTTGATGATGTTCCATGA
66 AAGAAAGGTGAAGAGATTCGGCCATGCATGTAGCTAGGCTAAGGGATGTTGATGATGTTCCATGA
52363196 GATGCATGCATGTTTTAGTTGTTAGCTTGAGTTCTACCTAGCCCATG
131 GATGCATGCATGTTTTAGTTGTTAGCTTGAGTTCTACCTAGCCCATG
* *
52363243 CAAAG-AAAAAAAA-TGCTCATCCTTTGGTTCATCCTTGGCCAAAAATTTTAAGGAGGAAGGAAG
1 CAAAGAAAAAAAAATTACTCATCCTTTGGTTCATCCTTGGCCAAAAATTTTAAGGAGGAAAGAAG
*
52363306 AAGAAAGGTTGAAGAGGTTCGGCCATGCATGTAGCTAGGCTAAGGGATGTTGATGATGTTCCATG
66 AAGAAAGG-TGAAGAGATTCGGCCATGCATGTAGCTAGGCTAAGGGATGTTGATGATGTTCCATG
52363371 AGATGCATGCATGTTTTAGTTGTTAGCTTGAGTTCTACCTAGCCCATG
130 AGATGCATGCATGTTTTAGTTGTTAGCTTGAGTTCTACCTAGCCCATG
52363419 GTCTAAATCT
Statistics
Matches: 171, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
175 56 0.33
176 110 0.64
177 5 0.03
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (177 bp):
CAAAGAAAAAAAAATTACTCATCCTTTGGTTCATCCTTGGCCAAAAATTTTAAGGAGGAAAGAAG
AAGAAAGGTGAAGAGATTCGGCCATGCATGTAGCTAGGCTAAGGGATGTTGATGATGTTCCATGA
GATGCATGCATGTTTTAGTTGTTAGCTTGAGTTCTACCTAGCCCATG
Found at i:52364288 original size:40 final size:40
Alignment explanation
Indices: 52364257--52364387 Score: 192
Period size: 40 Copynumber: 3.3 Consensus size: 40
52364247 GGACTAAGAT
*
52364257 CCGAAGGCATTTGTGCAAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* * *
52364297 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
* *
52364337 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTATT-AATTCCGGGTTAAGTC
52364377 CCGAAGGCATT
1 CCGAAGGCATT
52364388 GTATGAGTTA
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 80 0.99
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
Found at i:52364408 original size:39 final size:38
Alignment explanation
Indices: 52364257--52364424 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 38
52364247 GGACTAAGAT
* * *
52364257 CCGAAGGCATTTGTGCAAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCA-TTGTGCGAGTTACTAA-ACCGGGTTAAGTC
* * *
52364297 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGG-CATTGTGCGAGTTACTAA-ACCGGGTTAAGTC
*
52364337 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTC
1 CCGAAGGCATT-GTGCGAGTTACT-AAA-CCGGGTTAAGTC
** * *
52364377 CCGAAGGCATTGTATGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTGTGCGAGTTACTA-AACCGGGTTAAGTC
52364416 CCGAAGGCA
1 CCGAAGGCA
52364425 CTTGAACAAG
Statistics
Matches: 109, Mismatches: 13, Indels: 13
0.81 0.10 0.10
Matches are distributed among these distances:
39 31 0.28
40 77 0.71
41 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (38 bp):
CCGAAGGCATTGTGCGAGTTACTAAACCGGGTTAAGTC
Found at i:52367518 original size:13 final size:13
Alignment explanation
Indices: 52367500--52367531 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
52367490 ATGCTGTTGA
*
52367500 CCGTGGTGGCACT
1 CCGTGGCGGCACT
52367513 CCGTGGCGGCACT
1 CCGTGGCGGCACT
52367526 CCGTGG
1 CCGTGG
52367532 ATGAGCCGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.34, G:0.41, T:0.19
Consensus pattern (13 bp):
CCGTGGCGGCACT
Found at i:52370089 original size:17 final size:17
Alignment explanation
Indices: 52370067--52370099 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52370057 ACCCCCCCCC
52370067 CCAAAACAA-AAAAAAAA
1 CCAAAA-AACAAAAAAAA
52370084 CCAAAAAACAAAAAAA
1 CCAAAAAACAAAAAAA
52370100 GAGAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (17 bp):
CCAAAAAACAAAAAAAA
Found at i:52370701 original size:17 final size:17
Alignment explanation
Indices: 52370679--52370712 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52370669 ATCCACTAAT
*
52370679 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
52370696 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
52370713 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:52371741 original size:12 final size:12
Alignment explanation
Indices: 52371724--52371749 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52371714 ATTTTGAGCT
52371724 ACACTGATGGTC
1 ACACTGATGGTC
52371736 ACACTGATGGTC
1 ACACTGATGGTC
52371748 AC
1 AC
52371750 CCTGTTGTCA
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:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (12 bp):
ACACTGATGGTC
Found at i:52376397 original size:17 final size:17
Alignment explanation
Indices: 52376375--52376407 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52376365 ACCCCCCCCC
52376375 CCAAAACAA-AAAAAAAA
1 CCAAAA-AACAAAAAAAA
52376392 CCAAAAAACAAAAAAA
1 CCAAAAAACAAAAAAA
52376408 GAGAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (17 bp):
CCAAAAAACAAAAAAAA
Found at i:52381119 original size:15 final size:14
Alignment explanation
Indices: 52381085--52381119 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
52381075 TCATATTTGA
52381085 AATTTAATTTTTAT
1 AATTTAATTTTTAT
*
52381099 ATTTTAATTTATTAT
1 AATTTAATTT-TTAT
52381114 AATTTA
1 AATTTA
52381120 GTTCTCTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTTAATTTTTAT
Found at i:52381329 original size:17 final size:17
Alignment explanation
Indices: 52381296--52381345 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
52381286 CATAATAAAT
52381296 ATATATATG-TA--GTA
1 ATATATATGTTAGGGTA
52381310 ATATATATGTTAGGGTA
1 ATATATATGTTAGGGTA
*
52381327 ATATCTATGTTAGGGTA
1 ATATATATGTTAGGGTA
52381344 AT
1 AT
52381346 GTTCAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 9 0.28
15 2 0.06
17 21 0.66
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.42
Consensus pattern (17 bp):
ATATATATGTTAGGGTA
Found at i:52384068 original size:3 final size:3
Alignment explanation
Indices: 52384060--52384100 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
52384050 GGCAGTAGGT
*
52384060 GAA GAA GAA G-A GAA GAA AAA GAA -AA -AA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
52384101 CAAGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 6 0.18
3 28 0.82
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:52390160 original size:21 final size:21
Alignment explanation
Indices: 52390110--52390160 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
52390100 TGCAGCGATA
52390110 TCATGACACAAGGGTTCTATG
1 TCATGACACAAGGGTTCTATG
*** *
52390131 TCGCAACACCAGGGTTCGT-TG
1 TCATGACACAAGGGTTC-TATG
52390152 TCATGACAC
1 TCATGACAC
52390161 GCTTTGAAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (21 bp):
TCATGACACAAGGGTTCTATG
Found at i:52391167 original size:18 final size:17
Alignment explanation
Indices: 52391140--52391176 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
52391130 CAGATTGTGT
52391140 AATTATTATATACATGA
1 AATTATTATATACATGA
*
52391157 AATTGATTATATATATGA
1 AATT-ATTATATACATGA
52391175 AA
1 AA
52391177 GTGTCTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (17 bp):
AATTATTATATACATGA
Found at i:52395055 original size:64 final size:64
Alignment explanation
Indices: 52394954--52395082 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
52394944 GGCCGTGTGT
*
52394954 CACACACAGCTAAGACACACGCCTGTGTCTCTGCCCATATGGACAAAATAAGGCCATTTCCAAG
1 CACACACAGCTAAGACACACGCCTGTGTCTCTACCCATATGGACAAAATAAGGCCATTTCCAAG
* *
52395018 CACACACGGCTAAGACACACGCTTGTGTCTCTACCCATATGGACAAAATAAGGCCATTTCCAAG
1 CACACACAGCTAAGACACACGCCTGTGTCTCTACCCATATGGACAAAATAAGGCCATTTCCAAG
52395082 C
1 C
52395083 CTTATTTCTC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (64 bp):
CACACACAGCTAAGACACACGCCTGTGTCTCTACCCATATGGACAAAATAAGGCCATTTCCAAG
Found at i:52395980 original size:25 final size:25
Alignment explanation
Indices: 52395936--52396009 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 25
52395926 AGCCCTCTCT
* *
52395936 CGAGCCATATAAC-AGAAAGCTCATG
1 CGAGCAATATAACGAG-AAGCTCATC
* ** *
52395961 TGAGCTGTATAACGAGAAGCTTATC
1 CGAGCAATATAACGAGAAGCTCATC
52395986 CGAGCAATATAACGAGAAGCTCAT
1 CGAGCAATATAACGAGAAGCTCAT
52396010 AAGAGCCATA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
25 37 0.95
26 2 0.05
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (25 bp):
CGAGCAATATAACGAGAAGCTCATC
Found at i:52408457 original size:21 final size:21
Alignment explanation
Indices: 52408433--52408475 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
52408423 GGTTCGCTGT
*
52408433 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
52408454 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
52408475 A
1 A
52408476 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:52408475 original size:16 final size:16
Alignment explanation
Indices: 52408456--52408488 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
52408446 TGTATTGGAT
*
52408456 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
52408472 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
52408488 T
1 T
52408489 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:52408533 original size:45 final size:44
Alignment explanation
Indices: 52408467--52408561 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
52408457 GGATTAGAGG
* *
52408467 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
52408512 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
52408556 TGTAAT
1 TGTAAT
52408562 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:52416236 original size:20 final size:20
Alignment explanation
Indices: 52416199--52416241 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
52416189 ATTCAACCAG
* *
52416199 TTTTGGGTCTTAGTCTCAGT
1 TTTTGGGTCTTAGGCTCAAT
* *
52416219 TTTTGGTTCTTGGGCTCAAT
1 TTTTGGGTCTTAGGCTCAAT
52416239 TTT
1 TTT
52416242 CGATCTCAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.23, T:0.53
Consensus pattern (20 bp):
TTTTGGGTCTTAGGCTCAAT
Found at i:52427629 original size:4 final size:4
Alignment explanation
Indices: 52427616--52427683 Score: 56
Period size: 4 Copynumber: 17.5 Consensus size: 4
52427606 ATTAAAACGT
* *
52427616 TTTC -TTC TTTC TTTTC TTTT TTTC TTTC -TT- TTTC TTTTC TTTT TTTC
1 TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
52427663 TTTC -TT- TTTC TTTTC TTTC TT
1 TTTC TTTC TTTC -TTTC TTTC TT
52427684 GATATTTGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
3 11 0.21
4 29 0.56
5 12 0.23
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (4 bp):
TTTC
Found at i:52427632 original size:12 final size:11
Alignment explanation
Indices: 52427615--52427680 Score: 87
Period size: 12 Copynumber: 5.7 Consensus size: 11
52427605 GATTAAAACG
52427615 TTTTCTTCTTTC
1 TTTTCTT-TTTC
*
52427627 TTTTCTTTTTT
1 TTTTCTTTTTC
52427638 TCTTTCTTTTTC
1 T-TTTCTTTTTC
*
52427650 TTTTCTTTTTT
1 TTTTCTTTTTC
52427661 TCTTTCTTTTTC
1 T-TTTCTTTTTC
52427673 TTTTCTTT
1 TTTTCTTT
52427681 CTTGATATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
11 21 0.44
12 27 0.56
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:52427652 original size:23 final size:23
Alignment explanation
Indices: 52427616--52427680 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
52427606 ATTAAAACGT
52427616 TTTCTTCTTTCTTTTCTTTTTTTC
1 TTTCTT-TTTCTTTTCTTTTTTTC
52427640 TTTCTTTTTCTTTTCTTTTTTTC
1 TTTCTTTTTCTTTTCTTTTTTTC
52427663 TTTCTTTTTCTTTTCTTT
1 TTTCTTTTTCTTTTCTTT
52427681 CTTGATATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 35 0.85
24 6 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTCTTTTTCTTTTCTTTTTTTC
Found at i:52428378 original size:63 final size:63
Alignment explanation
Indices: 52428257--52428383 Score: 175
Period size: 63 Copynumber: 2.0 Consensus size: 63
52428247 GTCATGTGGT
* * * *
52428257 AGGTCGTGTAACTCACTATTTTGGAATTAAAGTCACACGGGTCAGAGATATAGACGTGTGTCC
1 AGGTCGTGTAACTCACTATTTTGGAATTAAAGTCACACGAGCCAGAGACAGAGACGTGTGTCC
* * *
52428320 AGGTCGTGTAACTCACTGTTTTGGAATTAGAGTCATACGAGCCAGAGACACGAG-CGTGTGTCC
1 AGGTCGTGTAACTCACTATTTTGGAATTAAAGTCACACGAGCCAGAGACA-GAGACGTGTGTCC
52428383 A
1 A
52428384 AGCCGTGTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 54 0.96
64 2 0.04
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (63 bp):
AGGTCGTGTAACTCACTATTTTGGAATTAAAGTCACACGAGCCAGAGACAGAGACGTGTGTCC
Found at i:52429123 original size:22 final size:22
Alignment explanation
Indices: 52429095--52429139 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
52429085 GGTAGGAATT
52429095 TGCATCTGTATCTGATATGTTC
1 TGCATCTGTATCTGATATGTTC
* *
52429117 TGCATCTGTATTTGATCTGTTC
1 TGCATCTGTATCTGATATGTTC
52429139 T
1 T
52429140 ATATCTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (22 bp):
TGCATCTGTATCTGATATGTTC
Found at i:52429145 original size:22 final size:22
Alignment explanation
Indices: 52429097--52429150 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
52429087 TAGGAATTTG
*
52429097 CATCTGTATCTGATATGTTCTG
1 CATCTGTATCTGATATGTTCTA
* *
52429119 CATCTGTATTTGATCTGTTCTA
1 CATCTGTATCTGATATGTTCTA
* *
52429141 TATCTATATC
1 CATCTGTATC
52429151 GAGTATCCTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.48
Consensus pattern (22 bp):
CATCTGTATCTGATATGTTCTA
Found at i:52432914 original size:20 final size:20
Alignment explanation
Indices: 52432889--52432928 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
52432879 GTAATAATAG
*
52432889 TAATTCAACCATATTAACAC
1 TAATTCAACCATATAAACAC
*
52432909 TAATTCATCCATATAAACAC
1 TAATTCAACCATATAAACAC
52432929 ATACCTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (20 bp):
TAATTCAACCATATAAACAC
Found at i:52433131 original size:23 final size:23
Alignment explanation
Indices: 52433105--52433165 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
52433095 CGCTATTGAA
52433105 CTGAAATGGTAAGCTC-TATCAAG
1 CTGAAATGGTAAGCTCATA-CAAG
* *
52433128 CTGAACA--ATAAGCTCATACTAG
1 CTGAA-ATGGTAAGCTCATACAAG
52433150 CTGAAATGGTAAGCTC
1 CTGAAATGGTAAGCTC
52433166 CAATGAGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 1 0.03
22 15 0.48
23 14 0.45
24 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (23 bp):
CTGAAATGGTAAGCTCATACAAG
Found at i:52435821 original size:43 final size:44
Alignment explanation
Indices: 52435668--52435832 Score: 139
Period size: 43 Copynumber: 3.8 Consensus size: 44
52435658 TTCCAACATG
* * *
52435668 TGATTTCGTGTAAGACCATGTCTGGGA-AGTTGGCATCGACT-TGA
1 TGATTACGTGTAAGACCATGTCTGGGACAGCTGGCATC-AATAT-A
* *
52435712 -GATCTACGTGTAAAACCATGTCTGGGACA--TAGGCATC-GTATA
1 TGAT-TACGTGTAAGACCATGTCTGGGACAGCT-GGCATCAATATA
* * * *
52435754 TGATTTCGTGTATGACCTTGTCTGGGACAG-TGGCATCAATATT
1 TGATTACGTGTAAGACCATGTCTGGGACAGCTGGCATCAATATA
* *
52435797 TGATTACATGTAAGACCACGTCTGGGAC-GCTGGCAT
1 TGATTACGTGTAAGACCATGTCTGGGACAGCTGGCAT
52435833 TGTACAGGCT
Statistics
Matches: 99, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
42 30 0.30
43 41 0.41
44 27 0.27
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (44 bp):
TGATTACGTGTAAGACCATGTCTGGGACAGCTGGCATCAATATA
Found at i:52456999 original size:16 final size:16
Alignment explanation
Indices: 52456967--52456999 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52456957 ATTATCTATC
*
52456967 TTATTTTATTTTATTT
1 TTATTTTATTATATTT
52456983 TTATTTTATTA-ATTT
1 TTATTTTATTATATTT
52456998 TT
1 TT
52457000 GAAGATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTATTATATTT
Found at i:52465842 original size:39 final size:39
Alignment explanation
Indices: 52465788--52465867 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
52465778 ACCAAAATAC
52465788 ATAGATTCAAAAGTACCAAACTGATAGCTTGATAGTGTG
1 ATAGATTCAAAAGTACCAAACTGATAGCTTGATAGTGTG
*
52465827 ATAGATTCAAAAGTACCAAAGTGATAGCTTGATAGTGTG
1 ATAGATTCAAAAGTACCAAACTGATAGCTTGATAGTGTG
52465866 AT
1 AT
52465868 GAGGTCTTCG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (39 bp):
ATAGATTCAAAAGTACCAAACTGATAGCTTGATAGTGTG
Found at i:52469706 original size:47 final size:47
Alignment explanation
Indices: 52469583--52469717 Score: 166
Period size: 47 Copynumber: 2.9 Consensus size: 47
52469573 AATAAAGTAC
* * *
52469583 CAATGCCATGTCCCCGACATGGTCTTACATGAATC-CACATATCATAG
1 CAATGCCATGTCCCAGACATGGTCTTACA-CAAGCACACATATCATAG
* *
52469630 TCAATGCCATGTCCCAGACATGTTTTTACACAAGCACACATATCATTA-
1 -CAATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCA-TAG
* *
52469678 CGATGCCATGTCCCAGACATGGTCTTACACAGGCACACAT
1 CAATGCCATGTCCCAGACATGGTCTTACACAAGCACACAT
52469718 TAATATGGTG
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
47 39 0.51
48 35 0.46
49 2 0.03
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (47 bp):
CAATGCCATGTCCCAGACATGGTCTTACACAAGCACACATATCATAG
Found at i:52473550 original size:39 final size:40
Alignment explanation
Indices: 52473505--52473676 Score: 204
Period size: 40 Copynumber: 4.3 Consensus size: 40
52473495 GCTCCTCGTT
* * *
52473505 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
52473545 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
52473584 CGAATGCCTTCGAGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
52473624 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
*
52473664 CCAATGCCTTCGG
1 CAAATGCCTTCGG
52473677 ATCTTAGTCC
Statistics
Matches: 116, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 35 0.30
40 77 0.66
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:52473689 original size:80 final size:78
Alignment explanation
Indices: 52473507--52473729 Score: 225
Period size: 80 Copynumber: 2.8 Consensus size: 78
52473497 TCCTCGTTCA
* * * * *
52473507 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-AT
1 AATGCCTTC-GGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGAAT
*
52473571 TTAATAACTCGCACG
64 TTAATAACTCGCACC
* *
52473586 AATGCCTTCGAGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAA
1 AATGCCTTCG-GACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAA
* *
52473651 TTT-GTATCTCGCACC
63 TTTAATAACTCGCACC
* * * * *
52473666 AATGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
52473730 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
78 2 0.02
79 35 0.29
80 70 0.58
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (78 bp):
AATGCCTTCGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTT
AATAACTCGCACC
Found at i:52473879 original size:105 final size:105
Alignment explanation
Indices: 52473696--52473906 Score: 386
Period size: 105 Copynumber: 2.0 Consensus size: 105
52473686 CGGATATATT
52473696 CACTTAGCACAAAGCCTTCGGGACTTAGCCCGGACAGCATTCAATTAATCATGCACATCTAACAA
1 CACTTAGCACAAAGCCTTCGGGACTTAGCCCGGACAGCATTCAATTAATCATGCACATCTAACAA
*
52473761 TAATTCATAGCACATTCATATTTCATTTTCGTTTACGAAA
66 TAATTCATAGCACATTCATATTTCATTTTCATTTACGAAA
*
52473801 CACTTAGCACAAAGCCTTCGGGACTTAGCCCGGGCAGCATTCAATTAATCATGCACATCTAACAA
1 CACTTAGCACAAAGCCTTCGGGACTTAGCCCGGACAGCATTCAATTAATCATGCACATCTAACAA
* *
52473866 TAATTCATGGCACATTCATATTTCATTTTCATTTGCGAAA
66 TAATTCATAGCACATTCATATTTCATTTTCATTTACGAAA
52473906 C
1 C
52473907 TCAAACACAA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (105 bp):
CACTTAGCACAAAGCCTTCGGGACTTAGCCCGGACAGCATTCAATTAATCATGCACATCTAACAA
TAATTCATAGCACATTCATATTTCATTTTCATTTACGAAA
Found at i:52481459 original size:40 final size:40
Alignment explanation
Indices: 52481408--52481832 Score: 735
Period size: 40 Copynumber: 10.6 Consensus size: 40
52481398 CATTTGAATG
52481408 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
52481448 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
52481488 ATATCCAGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
52481528 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
52481568 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
52481608 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
52481648 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* * *
52481688 ATATTCGGGCTAAGACCCGACGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
52481728 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * *
52481768 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
52481808 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
52481833 ATTGAGCTTG
Statistics
Matches: 366, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
39 2 0.01
40 363 0.99
41 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:52522431 original size:30 final size:30
Alignment explanation
Indices: 52522378--52522435 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
52522368 ACGGTCATGA
* * **
52522378 CACACGGGCGTGTGGTTTGCCCGTGTGCCT
1 CACACGGGCATGTGGATAACCCGTGTGCCT
52522408 CACACGGGCATGTGGATAACCCGTGTGC
1 CACACGGGCATGTGGATAACCCGTGTGC
52522436 AAGTGTTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.14, C:0.29, G:0.34, T:0.22
Consensus pattern (30 bp):
CACACGGGCATGTGGATAACCCGTGTGCCT
Found at i:52531095 original size:25 final size:25
Alignment explanation
Indices: 52531067--52531117 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
52531057 CCCACAGGAA
52531067 AGTCGCTTGCATCGCACATAACTTC
1 AGTCGCTTGCATCGCACATAACTTC
52531092 AGTCGCTTGCATCGCACATAACTTC
1 AGTCGCTTGCATCGCACATAACTTC
52531117 A
1 A
52531118 AAAGGTGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (25 bp):
AGTCGCTTGCATCGCACATAACTTC
Found at i:52540519 original size:29 final size:28
Alignment explanation
Indices: 52540485--52540595 Score: 127
Period size: 29 Copynumber: 3.9 Consensus size: 28
52540475 AATCTCATTT
52540485 ATATGGCCCATCCA-GCCCAATTCACGTTC
1 ATATGGCCCAT-CAGGCCCAATTCAC-TTC
52540514 ATATGGCCCATCAGGCCCAATTCACATTC
1 ATATGGCCCATCAGGCCCAATTCAC-TTC
* * *
52540543 GTATGGCCCATTAGGCCCAATCTCA-TTT
1 ATATGGCCCATCAGGCCCAAT-TCACTTC
* *
52540571 ATATGGCCCATCTGGCCCAAATCAC
1 ATATGGCCCATCAGGCCCAATTCAC
52540596 ATTATATTCA
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
27 3 0.04
28 21 0.30
29 44 0.62
30 3 0.04
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.25
Consensus pattern (28 bp):
ATATGGCCCATCAGGCCCAATTCACTTC
Found at i:52546354 original size:50 final size:49
Alignment explanation
Indices: 52546236--52546467 Score: 279
Period size: 49 Copynumber: 4.7 Consensus size: 49
52546226 CTAGTACGCA
* *
52546236 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCT-AGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGA-TACACG
**
52546285 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCTGATACACG
* * * * *
52546335 TAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCTGATACACG
* * *
52546386 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTAT-TCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCT-GATACACG
* *
52546435 TAGTAGCTTGCACTTAGCACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
52546468 TCACAATAGA
Statistics
Matches: 157, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
49 70 0.45
50 48 0.31
51 39 0.25
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCTGATACACG
Found at i:52548974 original size:15 final size:15
Alignment explanation
Indices: 52548936--52548980 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
52548926 CAAGCCCAGA
*
52548936 ATAAGGAAATCCAAG
1 ATAAGGAAATCCATG
*
52548951 ATAAAGAAATCCATG
1 ATAAGGAAATCCATG
*
52548966 ATATGGAAATACCAT
1 ATAAGGAAAT-CCAT
52548981 TTACAGCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.51, C:0.13, G:0.16, T:0.20
Consensus pattern (15 bp):
ATAAGGAAATCCATG
Found at i:52552013 original size:49 final size:49
Alignment explanation
Indices: 52551784--52552014 Score: 237
Period size: 49 Copynumber: 4.7 Consensus size: 49
52551774 TGGTATGCAC
* * * * *
52551784 AGTAGCCTGCACTTAGTACTACACATGCAACCAATTATTCGGTGCACGT
1 AGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGATACACGT
* * * ** *
52551833 AGTAGCCTACACTTAGTACTACACACGTGAGCTAACCATCTGATACACGT
1 AGTAGCCTGCACTTAGTACTACACACGCGA-CCAATTATCCGATACACGT
* ** * * * *
52551883 AGTAGCCTGCACTTAGTACTACAGACATGATCGAAGTTATCCGGTACGCAT
1 AGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCCGATACACGT
* *
52551934 AGTAGCCTGCACTTAGTATTACACATGCGACCAATTATCCGATACACGT
1 AGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGATACACGT
**
52551983 AGTAGCCTATACTTAGTACTACACACGCGACC
1 AGTAGCCTGCACTTAGTACTACACACGCGACC
52552015 TCACAATAGA
Statistics
Matches: 145, Mismatches: 35, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
49 66 0.46
50 45 0.31
51 34 0.23
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
AGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGATACACGT
Found at i:52553263 original size:115 final size:115
Alignment explanation
Indices: 52553126--52553340 Score: 315
Period size: 115 Copynumber: 1.9 Consensus size: 115
52553116 ATTTTCAAGA
* **
52553126 AATCATTCCGTAAAATCTTAGACCATAAAAATAAAATAAAAATGAAATTTTTCTCATCGGATTTG
1 AATCATTCCGTAAAATCGTAGACCATAAAAATAAAATAAAAATGAAATTTTT-TCATCAAATTTG
52553191 GGGTCCCGAAACCACTGTTC-CACTAAGCCCAAAATTAGAAATTTTTATGG
65 GGGTCCCGAAACCACTGTTCTCACTAAGCCCAAAATTAGAAATTTTTATGG
** * * *
52553241 AATCATTCCGTGCAATCGTAGACCATAAAAATATAATAAAAATTAAATTTTTTCATCAAATTTGT
1 AATCATTCCGTAAAATCGTAGACCATAAAAATAAAATAAAAATGAAATTTTTTCATCAAATTTGG
* * *
52553306 GGTCTCGAAACCACTGTTCTGACTAATCCCAAAAT
66 GGTCCCGAAACCACTGTTCTCACTAAGCCCAAAAT
52553341 CAGGATGTTA
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
114 28 0.32
115 60 0.68
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.31
Consensus pattern (115 bp):
AATCATTCCGTAAAATCGTAGACCATAAAAATAAAATAAAAATGAAATTTTTTCATCAAATTTGG
GGTCCCGAAACCACTGTTCTCACTAAGCCCAAAATTAGAAATTTTTATGG
Found at i:52554238 original size:87 final size:87
Alignment explanation
Indices: 52554056--52554621 Score: 310
Period size: 88 Copynumber: 6.3 Consensus size: 87
52554046 TCATTCTAAC
* * * * * * * *
52554056 CCACTACAACCTCAGGG-GTATAAAAATTGTAGTTTCAATATGATCCACTGTAACTTCAGGGATA
1 CCACTGCAACTTCAGGGAG-ATAAGATTTGTAGCTTCAATCTGATCCACTGCAACTTCAGGGGTA
*
52554120 TAGGAGTTGTAGCTTCATCTTGCT
65 TAAGA-TTGTAGCTTCATCTTGCT
* * *
52554144 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGTTCGACTGCAACTTTAGGGGTAT
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGATCCACTGCAACTTCAGGGGTAT
*
52554209 AAGATTGTATCTTCAAT-TTGCT
66 AAGATTGTAGCTTC-ATCTTGCT
* * * *
52554231 CCACTGCAAGTTTAGGGAGATAAGATTTGTAACTGCAATCT-ACTCCACTGCAACTTCAGGGAG-
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGA-TCCACTGCAACTTCAGGG-GT
* * * * * *
52554294 ATAAGATT-CACCATCGTAATTTTATTCCAA
64 ATAAGATTGTAGC-T--TCA---TCTTGC-T
* * * * * *
52554324 CCTACTACAAATTCAAGGG-TATAGAGATTT-TAGCTTCAATTTGATCCACTGCAACTTTAGGGA
1 CC-ACTGCAACTTC-AGGGAGATA-AGATTTGTAGCTTCAATCTGATCCACTGCAACTTCAGGGG
* *
52554387 TATAGGATTCGTCA-CTTCATCTTGCC
63 TATAAGATT-GT-AGCTTCATCTTGCT
* * * * ** * * *
52554413 CCACTACAACTTTAGGGAGATAAGATTTGTCATCGTAGTTTCATTCCAACCCACTACAACTTCAA
1 CCACTGCAACTTCAGGGAGATAAGA--T-T--T-GTAGCTTCAATCTGATCCACTGCAACTTCAG
* * * * * *
52554478 GTGTTTAGAAATTGAAGCTTCAATC-CGAT
60 GGGTATA-AGATTGTAGCTTC-ATCTTGCT
* * *
52554507 CCACTGCAACTTCAGGGATATAAGATTTGTAGCTTC-ATCTTGCTCCACTGCAACTTTAGGGAG-
1 CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATC-TGATCCACTGCAACTTCAGGG-GT
52554570 ATAAGATTTGTAGCTTCATCTCT-CT
64 ATAAGA-TTGTAGCTTCATCT-TGCT
* * * *
52554595 CCACTGTAACTTTAGGGTGATGAGATT
1 CCACTGCAACTTCAGGGAGATAAGATT
52554622 CGCCACCGTA
Statistics
Matches: 358, Mismatches: 84, Indels: 72
0.70 0.16 0.14
Matches are distributed among these distances:
86 2 0.01
87 90 0.25
88 125 0.35
89 7 0.02
90 5 0.01
91 2 0.01
92 5 0.01
93 5 0.01
94 97 0.27
95 18 0.05
96 1 0.00
97 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (87 bp):
CCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGATCCACTGCAACTTCAGGGGTAT
AAGATTGTAGCTTCATCTTGCT
Found at i:52554542 original size:182 final size:183
Alignment explanation
Indices: 52554330--52554762 Score: 529
Period size: 182 Copynumber: 2.4 Consensus size: 183
52554320 CCAACCTACT
* * *
52554330 ACAAATTCAAGGG-TATAGAGATTT-TAGCTTCAAT-TTGATCCACTGCAACTTTAGGGATATAG
1 ACAACTTC-AGGGATATA-AGATTTGTAGCTTCAATCTTGATCCACTGCAACTTTAGGGAGATAA
* * *
52554392 GATTCGTCA-CTTCATCT-TGCCCCACTACAACTTTAGGGAGATAAGATTTGTCATCGTAGTTTC
64 GATTCGT-AGCTTCATCTCT-CCCCACTACAACTTTAGGGAGATAAGATTCGCCACCGTAGTTTC
* * * *
52554455 ATTCCAACCCACTACAACTTCAAGTGTTTAGAAATTGAAGCTTCAATCCGATCCACT
127 ATTCCAACCCACTACAACTTCAAGGGTATAAAAATTGAAGCTTCAATCCGATCCACA
* *
52554512 GCAACTTCAGGGATATAAGATTTGTAGCTTC-ATCTTGCTCCACTGCAACTTTAGGGAGATAAGA
1 ACAACTTCAGGGATATAAGATTTGTAGCTTCAATCTTGATCCACTGCAACTTTAGGGAGATAAGA
* * ** * *
52554576 TTTGTAGCTTCATCTCTCTCCACTGTAACTTTAGGGTGATGAGATTCGCCACCGTAGTTTCATTC
66 TTCGTAGCTTCATCTCTCCCCACTACAACTTTAGGGAGATAAGATTCGCCACCGTAGTTTCATTC
* * *
52554641 CAACCTACTGCAACTTCAAGGGTATAAAAATTGTAGCTTCAATCCGATCCACA
131 CAACCCACTACAACTTCAAGGGTATAAAAATTGAAGCTTCAATCCGATCCACA
* * * * * * *
52554694 ACAACTTTAGGGATATAAGATTTGTAACTTC-ATCTTGCTCTACTACAACTTCAGGGAGACAAGA
1 ACAACTTCAGGGATATAAGATTTGTAGCTTCAATCTTGATCCACTGCAACTTTAGGGAGATAAGA
52554758 TTCGT
66 TTCGT
52554763 TATGGCAGAT
Statistics
Matches: 217, Mismatches: 29, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
181 13 0.06
182 203 0.94
183 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (183 bp):
ACAACTTCAGGGATATAAGATTTGTAGCTTCAATCTTGATCCACTGCAACTTTAGGGAGATAAGA
TTCGTAGCTTCATCTCTCCCCACTACAACTTTAGGGAGATAAGATTCGCCACCGTAGTTTCATTC
CAACCCACTACAACTTCAAGGGTATAAAAATTGAAGCTTCAATCCGATCCACA
Found at i:52554578 original size:138 final size:138
Alignment explanation
Indices: 52553994--52554580 Score: 571
Period size: 138 Copynumber: 4.3 Consensus size: 138
52553984 AGTATCACGA
* * * * * * ** *
52553994 CTTCATCTTGCTCTATTACAACTTCAAGGAGATAAGGTTTGTTATTATAGCTTCATTCTAACCCA
1 CTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCGTAGCTTCATTCCAACCCA
* * * * * * *
52554059 CTACAACCTCAGGGGTATAAAAATTGTAGTTTCAATATGATCCACTGTAACTTCAGGGATATAGG
66 CTACAACTTCAAGGGTATAGAAATTGTAGCTTCAATTTGATCCACTGCAACTTCAGGGATATAAG
*
52554124 AGTTGTAG
131 ATTTGTAG
* **** *
52554132 CTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGA--T-T--T-GTAGCTTCAATCTGTTCGA
1 CTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCGTAGCTTCATTCCAACCCA
* * * * * * * * *
52554191 CTGCAACTTTAGGGGTATA-AGATTGTATCTTCAATTTGCTCCACTGCAAGTTTAGGGAGATAAG
66 CTACAACTTCAAGGGTATAGAAATTGTAGCTTCAATTTGATCCACTGCAACTTCAGGGATATAAG
*
52554255 ATTTGTAA
131 ATTTGTAG
* * *** ** * *
52554263 CTGCAATC-TACTCCACTGCAACTTCAGGGAGATAAGATTCACCATCGTAATTTTATTCCAACCT
1 CTTC-ATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCGTAGCTTCATTCCAACCC
* * * * *
52554327 ACTACAAATTCAAGGGTATAGAGATTTTAGCTTCAATTTGATCCACTGCAACTTTAGGGATATAG
65 ACTACAACTTCAAGGGTATAGAAATTGTAGCTTCAATTTGATCCACTGCAACTTCAGGGATATAA
*
52554392 GATTCGTCA-
130 GATTTGT-AG
* * * *
52554401 CTTCATCTTGCCCCACTACAACTTTAGGGAGATAAGATTTGTCATCGTAGTTTCATTCCAACCCA
1 CTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCGTAGCTTCATTCCAACCCA
* * * **
52554466 CTACAACTTCAAGTGTTTAGAAATTGAAGCTTCAATCCGATCCACTGCAACTTCAGGGATATAAG
66 CTACAACTTCAAGGGTATAGAAATTGTAGCTTCAATTTGATCCACTGCAACTTCAGGGATATAAG
52554531 ATTTGTAG
131 ATTTGTAG
*
52554539 CTTCATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTTGT
1 CTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT
52554581 AGCTTCATCT
Statistics
Matches: 364, Mismatches: 74, Indels: 22
0.79 0.16 0.05
Matches are distributed among these distances:
131 72 0.20
132 32 0.09
133 1 0.00
135 1 0.00
136 2 0.01
137 29 0.08
138 226 0.62
139 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (138 bp):
CTTCATCTTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTCATCGTAGCTTCATTCCAACCCA
CTACAACTTCAAGGGTATAGAAATTGTAGCTTCAATTTGATCCACTGCAACTTCAGGGATATAAG
ATTTGTAG
Found at i:52554588 original size:44 final size:44
Alignment explanation
Indices: 52554099--52554621 Score: 275
Period size: 44 Copynumber: 11.6 Consensus size: 44
52554089 TTCAATATGA
* * * * *
52554099 TCCACTGTAACTTCAGGGATATAGGAGTTGTAGCTTCATCTTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTCATCTTGC
* *
52554143 TCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATC-TGT
1 TCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTC-ATCTTGC
* *
52554187 TCGACTGCAACTTTAGGG-GTATAAGA-TTGTATCTTCAAT-TTGC
1 TCCACTGCAACTTTAGGGAG-ATAAGATTTGTAGCTTC-ATCTTGC
* * * *
52554230 TCCACTGCAAGTTTAGGGAGATAAGATTTGTAACTGCAATC-TAC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTC-ATCTTGC
* * * * *
52554274 TCCACTGCAACTTCAGGGAGATAAGATTCACCATCGTA-ATT-TTATTCC
1 TCCACTGCAACTTTAGGGAGATAAGATT-----T-GTAGCTTCATCTTGC
* * * * * *
52554322 AACCTACTACAAATTCAAGGG-TATAGAGATTT-TAGCTTCAAT-TTGA
1 -TCC-ACTGCAACTT-TAGGGAGATA-AGATTTGTAGCTTC-ATCTTGC
* * *
52554368 TCCACTGCAACTTTAGGGATATAGGATTCGTCA-CTTCATCTTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGT-AGCTTCATCTTGC
* * * * *
52554412 CCCACTACAACTTTAGGGAGATAAGATTTGTCATCGTAGT-TTCATTCC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGT-AGC-T--TCATC-TTGC
* * * * * * * * * * *
52554460 AACCCACTACAACTTCA-AGTGTTTAGAAATTGAAGCTTCAATC-CGA
1 --TCCACTGCAACTTTAGGGAGATAAG-ATTTGTAGCTTC-ATCTTGC
* *
52554506 TCCACTGCAACTTCAGGGATATAAGATTTGTAGCTTCATCTTGC
1 TCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTCATCTTGC
52554550 TCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTCATCTCT-C
1 TCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTCATCT-TGC
* * *
52554594 TCCACTGTAACTTTAGGGTGATGAGATT
1 TCCACTGCAACTTTAGGGAGATAAGATT
52554622 CGCCACCGTA
Statistics
Matches: 370, Mismatches: 72, Indels: 74
0.72 0.14 0.14
Matches are distributed among these distances:
43 50 0.14
44 236 0.64
45 14 0.04
46 5 0.01
47 4 0.01
48 9 0.02
49 11 0.03
50 32 0.09
51 9 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (44 bp):
TCCACTGCAACTTTAGGGAGATAAGATTTGTAGCTTCATCTTGC
Found at i:52554719 original size:44 final size:44
Alignment explanation
Indices: 52554493--52554725 Score: 170
Period size: 44 Copynumber: 5.2 Consensus size: 44
52554483 TAGAAATTGA
*
52554493 AGCTTCAATCCGATCCACTGCAACTTCAGGGATATAAGATTTGT
1 AGCTTCAATCCGATCCACTGCAACTTTAGGGATATAAGATTTGT
* * *
52554537 AGCTTC-ATCTTGCTCCACTGCAACTTTAGGGAGATAAGATTTGT
1 AGCTTCAATC-CGATCCACTGCAACTTTAGGGATATAAGATTTGT
** * * *
52554581 AGCTTC-ATCTCTCTCCACTGTAACTTTAGGG-TGATGAGATTCGCCACCGT
1 AGCTTCAATC-CGATCCACTGCAACTTTAGGGAT-ATAAGATT------TGT
* * * * * *
52554631 AGTTTCATTCC-AACCTACTGCAACTTCAAGGG-TATAAAAATTGT
1 AGCTTCAATCCGATCC-ACTGCAACTT-TAGGGATATAAGATTTGT
**
52554675 AGCTTCAATCCGATCCACAACAACTTTAGGGATATAAGATTTGT
1 AGCTTCAATCCGATCCACTGCAACTTTAGGGATATAAGATTTGT
*
52554719 AACTTCA
1 AGCTTCA
52554726 TCTTGCTCTA
Statistics
Matches: 147, Mismatches: 29, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
43 7 0.05
44 106 0.72
45 3 0.02
49 2 0.01
50 22 0.15
51 7 0.05
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (44 bp):
AGCTTCAATCCGATCCACTGCAACTTTAGGGATATAAGATTTGT
Found at i:52554789 original size:138 final size:138
Alignment explanation
Indices: 52554496--52554802 Score: 325
Period size: 138 Copynumber: 2.2 Consensus size: 138
52554486 AAATTGAAGC
* * * * * * **
52554496 TTCAATCCGATCCACTGCAACTTC-AGGGATATAAGATTTGTAGCTTCATCTTGCTCCACTGCAA
1 TTCAATTCGACCCACTGCAACTTCAAGGG-TATAAAAATTGTAGCTTCATCTCGATCCACAACAA
* ** * * **
52554560 CTTTAGGGAGATAAGATTTGTAGCTTCATCTCTCTCCACTGTAACTTTAGGGTGATGAGATTCGC
65 CTTTAGGGAGATAAGATTTGTAACTTCATCTCTCTCCACTACAACTTCAGGGAGACAAGATTCGC
* *
52554625 CACCGTAGT
130 CACCGCAGA
* *
52554634 TTC-ATTCCAACCTACTGCAACTTCAAGGGTATAAAAATTGTAGCTTCAATC-CGATCCACAACA
1 TTCAATT-CGACCCACTGCAACTTCAAGGGTATAAAAATTGTAGCTTC-ATCTCGATCCACAACA
* *
52554697 ACTTTAGGGATATAAGATTTGTAACTTCATCT-TGCTCTACTACAACTTCAGGGAGACAAGATTC
64 ACTTTAGGGAGATAAGATTTGTAACTTCATCTCT-CTCCACTACAACTTCAGGGAGACAAGATTC
** **
52554761 GTTATGGCAGA
128 GCCACCGCAGA
52554772 TTCAATTCGACCCACTGCAACTTCAAGGGTA
1 TTCAATTCGACCCACTGCAACTTCAAGGGTA
52554803 CAGGATTTCT
Statistics
Matches: 137, Mismatches: 27, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
137 3 0.02
138 124 0.91
139 10 0.07
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (138 bp):
TTCAATTCGACCCACTGCAACTTCAAGGGTATAAAAATTGTAGCTTCATCTCGATCCACAACAAC
TTTAGGGAGATAAGATTTGTAACTTCATCTCTCTCCACTACAACTTCAGGGAGACAAGATTCGCC
ACCGCAGA
Found at i:52558965 original size:27 final size:27
Alignment explanation
Indices: 52558917--52559129 Score: 233
Period size: 27 Copynumber: 7.9 Consensus size: 27
52558907 GCGAGGCTGC
* * *
52558917 CAGATATTGTGAC-GAAGTCACCATATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
52558944 CAGATATTGTGGTAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
52558970 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
52558997 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
52559024 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
52559051 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
52559078 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
52559105 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
52559130 GACGCTTCCT
Statistics
Matches: 160, Mismatches: 14, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
26 12 0.08
27 141 0.88
28 7 0.04
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:52559020 original size:54 final size:54
Alignment explanation
Indices: 52558959--52559129 Score: 333
Period size: 54 Copynumber: 3.2 Consensus size: 54
52558949 ATTGTGGTAG
52558959 AGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAT
1 AGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAT
52559013 AGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAT
1 AGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAT
*
52559067 AGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCAT
1 AGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAT
52559121 AGCCACCAG
1 AGCCACCAG
52559130 GACGCTTCCT
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 116 1.00
ACGTcount: A:0.35, C:0.25, G:0.24, T:0.16
Consensus pattern (54 bp):
AGCCACCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATCGTGGCAT
Found at i:52559269 original size:26 final size:27
Alignment explanation
Indices: 52559233--52559308 Score: 91
Period size: 26 Copynumber: 2.8 Consensus size: 27
52559223 CAAAAGTAAC
* *
52559233 CCTAGGGGTATAATGGTAATTTTGC-A
1 CCTAGGGGTATAATAGTAATTTTCCAA
*
52559259 CCTAGGGGTATAACAGTAATTTTCCATA
1 CCTAGGGGTATAATAGTAATTTTCCA-A
* *
52559287 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATAATAGTAATTT
52559309 AGCTACTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 22 0.52
28 20 0.48
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (27 bp):
CCTAGGGGTATAATAGTAATTTTCCAA
Found at i:52560781 original size:26 final size:26
Alignment explanation
Indices: 52560750--52560857 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
52560740 TGAAATTCCC
*
52560750 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
52560776 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
52560802 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
52560828 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
52560854 ATCA
1 ATCA
52560858 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:52566199 original size:27 final size:27
Alignment explanation
Indices: 52566151--52566255 Score: 124
Period size: 27 Copynumber: 3.9 Consensus size: 27
52566141 GTGAGGCTGC
* * * *
52566151 CAGATATTGTGACGAAGTCACCATATA
1 CAGATATTGTGGCAAAGCCACCAGATA
52566178 CAGATATTGTGGCAAAGCCACCAGA-A
1 CAGATATTGTGGCAAAGCCACCAGATA
*
52566204 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAAAGCCACCAGATA
*
52566231 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAAAGCCACCAG
52566256 GACGCTTCCT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.12
27 59 0.86
28 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (27 bp):
CAGATATTGTGGCAAAGCCACCAGATA
Found at i:52566395 original size:26 final size:27
Alignment explanation
Indices: 52566359--52566434 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 27
52566349 CAAAAGTAAC
*
52566359 CCTAGGGGTATAATGGTAATTT-TGCA
1 CCTAGGGGTATAATAGTAATTTCTGCA
*
52566385 CCTAGGGGTATAATAGTAATTTTCTGTA
1 CCTAGGGGTATAATAGTAA-TTTCTGCA
* *
52566413 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATAATAGTAATTT
52566435 AGCTGCTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 18 0.41
27 6 0.14
28 20 0.45
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (27 bp):
CCTAGGGGTATAATAGTAATTTCTGCA
Found at i:52567907 original size:26 final size:26
Alignment explanation
Indices: 52567876--52567983 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
52567866 TGAAATGCCC
*
52567876 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
52567902 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
52567928 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
52567954 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
52567980 ATCA
1 ATCA
52567984 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:52571482 original size:20 final size:19
Alignment explanation
Indices: 52571436--52571482 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
52571426 GTAATTCATG
52571436 TTTAATTGCTGAATGGAGT
1 TTTAATTGCTGAATGGAGT
* *
52571455 TTTGAATTGGTAGAATTGAGT
1 TTT-AATTGCT-GAATGGAGT
52571476 TTTAATT
1 TTTAATT
52571483 TTAAGAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 10 0.42
21 11 0.46
ACGTcount: A:0.28, C:0.02, G:0.23, T:0.47
Consensus pattern (19 bp):
TTTAATTGCTGAATGGAGT
Found at i:52575660 original size:20 final size:20
Alignment explanation
Indices: 52575635--52575675 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
52575625 ATCTATCAAC
52575635 TATAACCCAGATCGCATCTT
1 TATAACCCAGATCGCATCTT
52575655 TATAACCCAGATCGCATCTT
1 TATAACCCAGATCGCATCTT
52575675 T
1 T
52575676 CTTTTTCGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.32
Consensus pattern (20 bp):
TATAACCCAGATCGCATCTT
Found at i:52580896 original size:22 final size:22
Alignment explanation
Indices: 52580840--52580889 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
52580830 TGCACAATTC
*
52580840 ATACCAT-ATCCATTTCAAGCAA
1 ATACCATAAT-CAATTCAAGCAA
*
52580862 ATTCCATAATCAATTCAAGCCAA
1 ATACCATAATCAATTCAAG-CAA
52580885 ATACC
1 ATACC
52580890 TATTCAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.42, C:0.28, G:0.04, T:0.26
Consensus pattern (22 bp):
ATACCATAATCAATTCAAGCAA
Found at i:52581623 original size:47 final size:47
Alignment explanation
Indices: 52581565--52581692 Score: 202
Period size: 47 Copynumber: 2.7 Consensus size: 47
52581555 AATAGATAAG
* *
52581565 TACCTACACCATGGCCCGTAGCCAAATCAAGGTAACTTATCTCGGAA
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCGGAA
* * *
52581612 TACCTATACCATGGCCAGTAGCCAAATCAAGGTAACTCCTCTCTGAA
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCGGAA
*
52581659 TACCTATACCATGCCCCGTAGCCAAATCAAGGTA
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTA
52581693 TTATTTGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 74 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (47 bp):
TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCGGAA
Found at i:52591320 original size:46 final size:47
Alignment explanation
Indices: 52591270--52591451 Score: 180
Period size: 46 Copynumber: 3.9 Consensus size: 47
52591260 CACTGACACA
* *
52591270 TCTCGTA-GCCGATGCATGTCCCAGACATGTCTTATACTAGCTTATG
1 TCTCGTAGGCCGATGCATGTCCCAAACATGTCTTACACTAGCTTATG
*
52591316 TCTCG-AGGCCGATGCATGTCCCAAACATGTCTTACACTAGCACT-TG
1 TCTCGTAGGCCGATGCATGTCCCAAACATGTCTTACACTAGC-TTATG
* * *
52591362 TCTC-AATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCAT-
1 TCTCGTAGGCCGATG-CATGTCCCAAACAT-GTCTTACACTAGCT-T-ATG
** * *
52591411 AAT-GT-GGCCGATGCATGTCCCAGATATGTCTTACACTAGCT
1 TCTCGTAGGCCGATGCATGTCCCAAACATGTCTTACACTAGCT
52591452 CACAATAACC
Statistics
Matches: 114, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
45 1 0.01
46 64 0.56
47 27 0.24
48 20 0.18
49 1 0.01
50 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (47 bp):
TCTCGTAGGCCGATGCATGTCCCAAACATGTCTTACACTAGCTTATG
Found at i:52591428 original size:47 final size:44
Alignment explanation
Indices: 52591231--52591452 Score: 146
Period size: 46 Copynumber: 4.8 Consensus size: 44
52591221 GTATATCTGT
* * * * * *
52591231 GCCGATGCCATGTCCTAGACATGGTCTTACACTGACACATCTC-GTA
1 GCCGATG-CATGTCCCAAACAT-GTCTTACACTGGCTC-TCTCAATG
* * * * *
52591277 GCCGATGCATGTCCCAGACATGTCTTATACTAGCTTATGTCTCGA-G
1 GCCGATGCATGTCCCAAACATGTCTTACACTGGC---TCTCTCAATG
* *
52591323 GCCGATGCATGTCCCAAACATGTCTTACACTAGCACTTGTCTCAAT-
1 GCCGATGCATGTCCCAAACATGTCTTACACT-G-GC-TCTCTCAATG
52591369 GCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCAT-AATGTG
1 GCCGATG-CATGTCCCAAACAT-GTCTTACACTGGCTCTC-TCAA--TG
* * *
52591417 GCCGATGCATGTCCCAGATATGTCTTACACTAGCTC
1 GCCGATGCATGTCCCAAACATGTCTTACACTGGCTC
52591453 ACAATAACCC
Statistics
Matches: 144, Mismatches: 19, Indels: 26
0.76 0.10 0.14
Matches are distributed among these distances:
44 10 0.07
45 18 0.12
46 70 0.49
47 28 0.19
48 18 0.12
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (44 bp):
GCCGATGCATGTCCCAAACATGTCTTACACTGGCTCTCTCAATG
Found at i:52593454 original size:12 final size:13
Alignment explanation
Indices: 52593437--52593474 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
52593427 ATCCTGGAAT
52593437 ATTAAG-ACAAGA
1 ATTAAGAACAAGA
*
52593449 ATTAAGAACACATA
1 ATTAAGAACA-AGA
52593463 ATTAAGAACAAG
1 ATTAAGAACAAG
52593475 TCAAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 12 0.55
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (13 bp):
ATTAAGAACAAGA
Found at i:52599148 original size:53 final size:53
Alignment explanation
Indices: 52599067--52599171 Score: 176
Period size: 53 Copynumber: 2.0 Consensus size: 53
52599057 CTTTAAACTG
52599067 AACTTGAATTATGGAATGTATAAGCTAGTTTTGAGGTTAAATACTTTGGAAAA
1 AACTTGAATTATGGAATGTATAAGCTAGTTTTGAGGTTAAATACTTTGGAAAA
* *
52599120 AACTTGAATTATGGCATGTAT-AGACTAGTTTTGAGGTTAAATATTTTGGAAA
1 AACTTGAATTATGGAATGTATAAG-CTAGTTTTGAGGTTAAATACTTTGGAAA
52599172 TGAATGCATA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 2 0.04
53 47 0.96
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.37
Consensus pattern (53 bp):
AACTTGAATTATGGAATGTATAAGCTAGTTTTGAGGTTAAATACTTTGGAAAA
Found at i:52609161 original size:30 final size:30
Alignment explanation
Indices: 52609121--52609180 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
52609111 AATGTTCTAA
*
52609121 TGATCTAAACTTAAAAAAAACCCTTTCATT
1 TGATCCAAACTTAAAAAAAACCCTTTCATT
* *
52609151 TGATCCAAACTTAAAACAACCCCTTTCATT
1 TGATCCAAACTTAAAAAAAACCCTTTCATT
52609181 CCTTCGGCCC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.32
Consensus pattern (30 bp):
TGATCCAAACTTAAAAAAAACCCTTTCATT
Found at i:52633128 original size:22 final size:21
Alignment explanation
Indices: 52633103--52633151 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
52633093 TTTATACTTA
52633103 AATTATTAACATAATTAATTTT
1 AATTATT-ACATAATTAATTTT
**
52633125 AATTAATTTTATAATTAATTTT
1 AATT-ATTACATAATTAATTTT
*
52633147 TATTA
1 AATTA
52633152 ATTTTGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.83
23 3 0.13
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
AATTATTACATAATTAATTTT
Found at i:52633129 original size:10 final size:10
Alignment explanation
Indices: 52633114--52633165 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
52633104 ATTATTAACA
52633114 TAATTAATTT
1 TAATTAATTT
52633124 TAATTAATTTT
1 TAATTAA-TTT
52633135 ATAATTAATTT
1 -TAATTAATTT
*
52633146 TTATTAATTT
1 TAATTAATTT
*
52633156 TGATT-ATTT
1 TAATTAATTT
52633165 T
1 T
52633166 TGATAGATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 5 0.13
10 20 0.53
11 6 0.16
12 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (10 bp):
TAATTAATTT
Found at i:52633152 original size:22 final size:22
Alignment explanation
Indices: 52633113--52633156 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
52633103 AATTATTAAC
52633113 ATAATTAATTTTAATTAATTTT
1 ATAATTAATTTTAATTAATTTT
*
52633135 ATAATTAATTTTTATTAATTTT
1 ATAATTAATTTTAATTAATTTT
52633157 GATTATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATAATTAATTTTAATTAATTTT
Found at i:52633777 original size:21 final size:21
Alignment explanation
Indices: 52633735--52633777 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
52633725 CAATTTTCTC
*
52633735 TCTTTATTTCTCGTCCATTTT
1 TCTTTATTTCTCGTCCAATTT
*
52633756 TCTTTA-TTCTCTTGCCAATTT
1 TCTTTATTTCTCGT-CCAATTT
52633777 T
1 T
52633778 ACCTCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.12, C:0.23, G:0.05, T:0.60
Consensus pattern (21 bp):
TCTTTATTTCTCGTCCAATTT
Found at i:52639715 original size:26 final size:26
Alignment explanation
Indices: 52639685--52639737 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
52639675 CAAAACTTAA
52639685 GGTCCTTATATGGTAATTAGACCATT
1 GGTCCTTATATGGTAATTAGACCATT
52639711 GGTCCTTATATGGTAATTAGACCATT
1 GGTCCTTATATGGTAATTAGACCATT
52639737 G
1 G
52639738 AAGGGTAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (26 bp):
GGTCCTTATATGGTAATTAGACCATT
Found at i:52645187 original size:94 final size:93
Alignment explanation
Indices: 52645082--52645252 Score: 225
Period size: 94 Copynumber: 1.8 Consensus size: 93
52645072 ACATCCTCGA
* * * * * ** *
52645082 GGTTGATGCATGTCTCAGACATGTCTTACACTGGCACTCACCTCTATGCCGATGCCTTGTCTCAG
1 GGTTGATGCATGTCCCAAACATGTATTACACTAGCACT-ACCTCAATGCCGATGCCACGTCCCAG
*
52645147 ACGTGGTCTTATAAGGGCTATCATGATGC
65 ACATGGTCTTATAAGGGCTATCATGATGC
* **
52645176 GGTTGATGCATGTCCCAAACATGTATTACACTAGCCCTGTCTCAATGCCGATGCCACGTCCCAGA
1 GGTTGATGCATGTCCCAAACATGTATTACACTAGCACTACCTCAATGCCGATGCCACGTCCCAGA
52645241 CATGGTCTTATA
66 CATGGTCTTATA
52645253 CTGGCTCTCA
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
93 32 0.49
94 33 0.51
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (93 bp):
GGTTGATGCATGTCCCAAACATGTATTACACTAGCACTACCTCAATGCCGATGCCACGTCCCAGA
CATGGTCTTATAAGGGCTATCATGATGC
Found at i:52652346 original size:13 final size:13
Alignment explanation
Indices: 52652328--52652352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52652318 AACCCAATTT
52652328 TTATTTTATTTTA
1 TTATTTTATTTTA
52652341 TTATTTTATTTT
1 TTATTTTATTTT
52652353 TGGATGTTGA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:52652592 original size:75 final size:74
Alignment explanation
Indices: 52652439--52652667 Score: 350
Period size: 75 Copynumber: 3.1 Consensus size: 74
52652429 AAAAAATTGC
*
52652439 AGCCAAATAGCCTTTATTCCATCCCTATTCTAGCCGGAATAGTGCGTTCCTGCCTTAGACTCCCC
1 AGCCAAATAGCCTTTATTCCATCCCTATTCTAGCTGGAATAGTGCGTTCCTGCCTTAGACTCCCC
*
52652504 AAAACCTGC
66 AAAACCTGT
* * * * * *
52652513 AGCCAAACAACCTTTATTCCATCCCTATTCTAGCATGGAATAGTGCGTTCTTACCCTAAACTCCC
1 AGCCAAATAGCCTTTATTCCATCCCTATTCTAGC-TGGAATAGTGCGTTCCTGCCTTAGACTCCC
52652578 CAAAACCTGT
65 CAAAACCTGT
* *
52652588 AGCCAAATAGCCTTTATTCCATCCCTATTATAGCCTGGAATAGTGCGTTCCTGCCTTAGACTCCA
1 AGCCAAATAGCCTTTATTCCATCCCTATTCTAG-CTGGAATAGTGCGTTCCTGCCTTAGACTCCC
52652653 CAAAACCTGT
65 CAAAACCTGT
52652663 AGCCA
1 AGCCA
52652668 GACACCCCCT
Statistics
Matches: 137, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
74 32 0.23
75 104 0.76
76 1 0.01
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.28
Consensus pattern (74 bp):
AGCCAAATAGCCTTTATTCCATCCCTATTCTAGCTGGAATAGTGCGTTCCTGCCTTAGACTCCCC
AAAACCTGT
Found at i:52655703 original size:10 final size:10
Alignment explanation
Indices: 52655690--52655737 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
52655680 TTATTTTCAT
52655690 TTATCTTTAA
1 TTATCTTTAA
52655700 TTATCTTTAA
1 TTATCTTTAA
*
52655710 TTATCTTTAT
1 TTATCTTTAA
*
52655720 TTAT-TTGTAT
1 TTATCTT-TAA
52655730 TTATCTTT
1 TTATCTTT
52655738 TAGAATTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
9 2 0.06
10 31 0.89
11 2 0.06
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:52656551 original size:39 final size:38
Alignment explanation
Indices: 52656503--52656579 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 38
52656493 ATTTTTGAAA
52656503 TTCCAATCAAAACTTTTAATTCTATTTTTATTTTATTT
1 TTCCAATCAAAACTTTTAATTCTATTTTTATTTTATTT
* * *
52656541 TTCCAGATCAAAACTTTTAATTTTGTTTTTCTTTTATTT
1 TTCCA-ATCAAAACTTTTAATTCTATTTTTATTTTATTT
52656580 CTTTCCCAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 5 0.14
39 30 0.86
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.58
Consensus pattern (38 bp):
TTCCAATCAAAACTTTTAATTCTATTTTTATTTTATTT
Found at i:52662407 original size:50 final size:51
Alignment explanation
Indices: 52662282--52662457 Score: 191
Period size: 50 Copynumber: 3.5 Consensus size: 51
52662272 TGAGGTCGCA
* * *
52662282 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACACGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACACGATAACTTAGATCACG
** *
52662333 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCA-GAT-GGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CACGATAACTTAGATCACG
* * * *
52662383 TGTGTAGTACTAAGTGCAGACTACTACGTGTAC-CGGATAA-TT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACAC-GATAACTTAGATCACG
* *
52662432 TGTGTAGTACTATGTACAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
52662458 TGCGTACCAG
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
49 29 0.27
50 44 0.41
51 33 0.31
52 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (51 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACACGATAACTTAGATCACG
Found at i:52667473 original size:18 final size:18
Alignment explanation
Indices: 52667450--52667484 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52667440 TCCTCGGGTG
52667450 ATAATCAATCAATAACTC
1 ATAATCAATCAATAACTC
**
52667468 ATAATCTTTCAATAACT
1 ATAATCAATCAATAACT
52667485 TGAGCCATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATCAATCAATAACTC
Found at i:52680136 original size:40 final size:40
Alignment explanation
Indices: 52679951--52680136 Score: 211
Period size: 40 Copynumber: 4.7 Consensus size: 40
52679941 GCTCCTCGTT
* * *
52679951 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
* *
52679991 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAAC-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGT-ACTTCGCA
*
52680031 CAAATGTCTTCGGGACTTAGCCCGGA-ATTAGTA-TCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTACT-TCGCA
* * *
52680071 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGT-ACTTCGCA
52680112 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52680137 CATCATTCAA
Statistics
Matches: 124, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
39 4 0.03
40 105 0.85
41 14 0.11
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTACTTCGCA
Found at i:52682346 original size:37 final size:36
Alignment explanation
Indices: 52682296--52682368 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 36
52682286 AATGATCATG
*
52682296 GTGGTTCGAGGAGTTTATACTCTTCATTCCTGCTAT
1 GTGGTTCGAGGAGTTTATACTCCTCATTCCTGCTAT
*
52682332 NGTGGTTCGAGGAGTTTATATTCCTCATTCCTGCTAT
1 -GTGGTTCGAGGAGTTTATACTCCTCATTCCTGCTAT
52682369 CAATCTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.41
Consensus pattern (36 bp):
GTGGTTCGAGGAGTTTATACTCCTCATTCCTGCTAT
Found at i:52688175 original size:21 final size:22
Alignment explanation
Indices: 52688134--52688175 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
52688124 GTCTACGATT
52688134 TCACGAAATGATTATGGTCTAA
1 TCACGAAATGATTATGGTCTAA
52688156 TCACGAAATGATTA-GGTCTA
1 TCACGAAATGATTATGGTCTA
52688176 GTCAAAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (22 bp):
TCACGAAATGATTATGGTCTAA
Found at i:52696176 original size:22 final size:22
Alignment explanation
Indices: 52696150--52696192 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52696140 GAAAATAATC
*
52696150 AAAATTAATCAAAATTAATTAT
1 AAAATCAATCAAAATTAATTAT
* *
52696172 AAAATCAATTAAAATTCATTA
1 AAAATCAATCAAAATTAATTA
52696193 CGTTAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATCAATCAAAATTAATTAT
Found at i:52703068 original size:20 final size:20
Alignment explanation
Indices: 52703026--52703068 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
52703016 TTATCTATGA
* * *
52703026 ATAACTTTTCAATTTCTACC
1 ATAAATTTTAAATTTCCACC
*
52703046 ATAAATTTTAAATTTCCAGC
1 ATAAATTTTAAATTTCCACC
52703066 ATA
1 ATA
52703069 TTCATCCATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (20 bp):
ATAAATTTTAAATTTCCACC
Found at i:52704771 original size:31 final size:31
Alignment explanation
Indices: 52704736--52704797 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
52704726 TCCATGGTAA
*
52704736 CTCTTTCCTATTTCCATTCCGATATTATAAT
1 CTCTTTCCCATTTCCATTCCGATATTATAAT
* *
52704767 CTCTTTCCCATTTCCATTCCGTTATTGTAAT
1 CTCTTTCCCATTTCCATTCCGATATTATAAT
52704798 TGGTTGCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.19, C:0.27, G:0.05, T:0.48
Consensus pattern (31 bp):
CTCTTTCCCATTTCCATTCCGATATTATAAT
Found at i:52725502 original size:22 final size:22
Alignment explanation
Indices: 52725474--52725517 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
52725464 ATATAGCATA
52725474 AATTTCTAGAATTGGAACTAAG
1 AATTTCTAGAATTGGAACTAAG
52725496 AATTTCTAGAATTGGAACTAAG
1 AATTTCTAGAATTGGAACTAAG
52725518 TATATGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (22 bp):
AATTTCTAGAATTGGAACTAAG
Found at i:52733414 original size:17 final size:17
Alignment explanation
Indices: 52733392--52733426 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
52733382 TTTTTGGAAG
52733392 AAAGGCTGTGCTAAAAA
1 AAAGGCTGTGCTAAAAA
52733409 AAAGGCTGTGCTAAAAA
1 AAAGGCTGTGCTAAAAA
52733426 A
1 A
52733427 GTTACTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.23, T:0.17
Consensus pattern (17 bp):
AAAGGCTGTGCTAAAAA
Found at i:52733613 original size:9 final size:9
Alignment explanation
Indices: 52733556--52733619 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
52733546 TTTAAATTAC
52733556 AAATTTTTA
1 AAATTTTTA
*
52733565 CAATTTTTA
1 AAATTTTTA
*
52733574 ATATTTTTTTA
1 A-A-ATTTTTA
*
52733585 TAATTTTTA
1 AAATTTTTA
*
52733594 CAATATTTTA
1 AAAT-TTTTA
52733604 AAATTTTTA
1 AAATTTTTA
*
52733613 ATATTTT
1 AAATTTT
52733620 AATATTATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 28 0.64
10 10 0.23
11 6 0.14
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (9 bp):
AAATTTTTA
Found at i:52734183 original size:21 final size:21
Alignment explanation
Indices: 52734152--52734198 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
52734142 ATTTAATTTC
52734152 TTTTATAAAATTTA-TAAT-T
1 TTTTATAAAATTTAGTAATAT
52734171 TTTTATAATAAATTTAGTAATAT
1 TTTTAT-A-AAATTTAGTAATAT
52734194 TTTTA
1 TTTTA
52734199 GTTTAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 1 0.04
21 7 0.29
22 4 0.17
23 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTATAAAATTTAGTAATAT
Found at i:52745528 original size:29 final size:29
Alignment explanation
Indices: 52745495--52745554 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
52745485 ATTTATCTAC
52745495 AAGATAAATATTAAATTAAATCCAATATT
1 AAGATAAATATTAAATTAAATCCAATATT
* **
52745524 AAGATAAGTATTAAATTAAATTTAATATT
1 AAGATAAATATTAAATTAAATCCAATATT
52745553 AA
1 AA
52745555 ATTTATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (29 bp):
AAGATAAATATTAAATTAAATCCAATATT
Found at i:52754691 original size:11 final size:11
Alignment explanation
Indices: 52754675--52754701 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
52754665 CTAAAATATC
52754675 TAGATAAAATA
1 TAGATAAAATA
52754686 TAGATAAAATA
1 TAGATAAAATA
52754697 TAGAT
1 TAGAT
52754702 TGATTCCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (11 bp):
TAGATAAAATA
Found at i:52770978 original size:15 final size:15
Alignment explanation
Indices: 52770941--52770970 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52770931 AAGACTTTTT
*
52770941 TTATAATAAATATCA
1 TTATAATAAAAATCA
52770956 TTATAATAAAAATCA
1 TTATAATAAAAATCA
52770971 GTTAAATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
TTATAATAAAAATCA
Found at i:52771777 original size:14 final size:14
Alignment explanation
Indices: 52771758--52771794 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
52771748 GCTTAATATT
52771758 TATTATAAACAATA
1 TATTATAAACAATA
* *
52771772 TATTATGAATAATA
1 TATTATAAACAATA
52771786 TATTATAAA
1 TATTATAAA
52771795 AAAATGAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (14 bp):
TATTATAAACAATA
Found at i:52772837 original size:24 final size:24
Alignment explanation
Indices: 52772795--52772843 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
52772785 ATTCAGATTC
* *
52772795 GTTACTTGGGGCTGATGAGGATGA
1 GTTACTTCGGGCTCATGAGGATGA
* *
52772819 GTTACTTCGGGCTCTTGAGGGTGA
1 GTTACTTCGGGCTCATGAGGATGA
52772843 G
1 G
52772844 GAATCCGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.16, C:0.12, G:0.41, T:0.31
Consensus pattern (24 bp):
GTTACTTCGGGCTCATGAGGATGA
Found at i:52776582 original size:11 final size:11
Alignment explanation
Indices: 52776560--52776594 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
52776550 TATTTATACT
52776560 TATATACATATG
1 TATAT-CATATG
*
52776572 TGTATCATATG
1 TATATCATATG
52776583 TATATCATATG
1 TATATCATATG
52776594 T
1 T
52776595 TATAAACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (11 bp):
TATATCATATG
Found at i:52790570 original size:211 final size:211
Alignment explanation
Indices: 52790206--52790631 Score: 807
Period size: 211 Copynumber: 2.0 Consensus size: 211
52790196 TTTGACAAAG
* *
52790206 GGTGGGAAGACTTCGCCTTAGTATAATTGGGTAAATCACTATTAGGAGAATAAGGGAGCTTATGA
1 GGTGGGAAGACTTCGCCTTAGTATAATCGGGTAAATCACTATTAGGAGAATAAGGGAGCTTACGA
52790271 AAAGGGCTATCAAACGGCTGTGACTTTCAATTGGCCTTGTCTCGCTTAACTCGTCGAGTAATGAT
66 AAAGGGCTATCAAACGGCTGTGACTTTCAATTGGCCTTGTCTCGCTTAACTCGTCGAGTAATGAT
*
52790336 TATCCTAGAAGGAAGATCTGTTCGAAAGGTCTCGCCAAAAATCCGTATAATGATTAGCTCCTAGC
131 TATCCCAGAAGGAAGATCTGTTCGAAAGGTCTCGCCAAAAATCCGTATAATGATTAGCTCCTAGC
52790401 CCCTGCTTCTTGAATT
196 CCCTGCTTCTTGAATT
52790417 GGTGGGAAGACTTCGCCTTAGTATAATCGGGTAAATCACTATTAGGAGAATAAGGGAGCTTACGA
1 GGTGGGAAGACTTCGCCTTAGTATAATCGGGTAAATCACTATTAGGAGAATAAGGGAGCTTACGA
*
52790482 AAAGGGCTATCAAACGGCTGTGACTTTCAATTGGCCTTGTCTCGCTTAACTCGTCGAGTAGTGAT
66 AAAGGGCTATCAAACGGCTGTGACTTTCAATTGGCCTTGTCTCGCTTAACTCGTCGAGTAATGAT
*
52790547 TATCCCGGAAGGAAGATCTGTTCGAAAGGTCTCGCCAAAAATCCGTATAATGATTAGCTCCTAGC
131 TATCCCAGAAGGAAGATCTGTTCGAAAGGTCTCGCCAAAAATCCGTATAATGATTAGCTCCTAGC
52790612 CCCTGCTTCTTGAATT
196 CCCTGCTTCTTGAATT
52790628 GGTG
1 GGTG
52790632 ACCCATTCCG
Statistics
Matches: 210, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
211 210 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (211 bp):
GGTGGGAAGACTTCGCCTTAGTATAATCGGGTAAATCACTATTAGGAGAATAAGGGAGCTTACGA
AAAGGGCTATCAAACGGCTGTGACTTTCAATTGGCCTTGTCTCGCTTAACTCGTCGAGTAATGAT
TATCCCAGAAGGAAGATCTGTTCGAAAGGTCTCGCCAAAAATCCGTATAATGATTAGCTCCTAGC
CCCTGCTTCTTGAATT
Found at i:52802860 original size:41 final size:41
Alignment explanation
Indices: 52802803--52802885 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
52802793 GTCTAGGAGA
*
52802803 TGGCATCGAAAAGGAGAAGTCAAAGGGACTAAGAAAGAGTG
1 TGGCATCGAAAAGGAGAAGGCAAAGGGACTAAGAAAGAGTG
52802844 TGGCATCGAAAAGGAGAAGGCAAAGGGACTAAGAAAGAGTG
1 TGGCATCGAAAAGGAGAAGGCAAAGGGACTAAGAAAGAGTG
52802885 T
1 T
52802886 CTCGAGAAGG
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:0.43, C:0.10, G:0.35, T:0.12
Consensus pattern (41 bp):
TGGCATCGAAAAGGAGAAGGCAAAGGGACTAAGAAAGAGTG
Found at i:52811785 original size:40 final size:40
Alignment explanation
Indices: 52811733--52811964 Score: 365
Period size: 40 Copynumber: 5.8 Consensus size: 40
52811723 ATAACCACAA
* * * *
52811733 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
52811773 GCACGAATGCCTTCGGGTCTTAGCCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
52811813 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATGTCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATA--TCAACTC
52811855 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
52811895 GCACAAATGCCTTCGGGTCTTAGTCCGGATATATCAACTT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
52811935 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT
52811965 GTATTCAAAT
Statistics
Matches: 177, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
40 139 0.79
42 38 0.21
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:52811885 original size:82 final size:81
Alignment explanation
Indices: 52811733--52811964 Score: 378
Period size: 82 Copynumber: 2.9 Consensus size: 81
52811723 ATAACCACAA
* * *
52811733 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAG-CAACTCGCACGAATGCCTTCGGGTCTTAGC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGTCAACTCGCACAAATGCCTTCGGGTCTTAGC
*
52811797 CCGGATATATCAACTT
66 CCGGATATATCAACTC
52811813 GCACAATTGCCTTCGGGTCTTAGCCCGGATATATGTCAACTCGCACAAATGCCTTCGGGTCTTAG
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATA-GTCAACTCGCACAAATGCCTTCGGGTCTTAG
52811878 CCCGGATATATCAACTC
65 CCCGGATATATCAACTC
* * *
52811895 GCACAAATGCCTTCGGGTCTTAGTCCGGATATA-TCAACTTGCACAAATGCCTTCGGGTCTTAGC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGTCAACTCGCACAAATGCCTTCGGGTCTTAGC
52811959 CCGGAT
66 CCGGAT
52811965 GTATTCAAAT
Statistics
Matches: 143, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
80 67 0.47
81 1 0.01
82 75 0.52
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (81 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGTCAACTCGCACAAATGCCTTCGGGTCTTAGC
CCGGATATATCAACTC
Found at i:52811950 original size:122 final size:121
Alignment explanation
Indices: 52811733--52811972 Score: 399
Period size: 122 Copynumber: 2.0 Consensus size: 121
52811723 ATAACCACAA
* * *
52811733 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCC
*
52811798 CGGATATATCAACTTGCACAATTGCCTTCGGGTCTTAGCCCGGATATATGTCAACTC
66 CGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAT-TCAACTC
* * *
52811855 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCC
*
52811920 CGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATGTATTCAA
66 CGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATATTCAA
52811973 ATGCTCATGC
Statistics
Matches: 110, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
121 4 0.04
122 106 0.96
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (121 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCC
CGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATATTCAACTC
Found at i:52815431 original size:53 final size:53
Alignment explanation
Indices: 52815373--52815479 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
52815363 GCATAATAAA
*
52815373 AAAGAAGAAAGTCCGATTCCTCTTATTCCTCCAGTCCTACCCACTCTTAACTC
1 AAAGAAGAAAGTCCGATTCCTCTGATTCCTCCAGTCCTACCCACTCTTAACTC
* *
52815426 AAAGAAGAAAGTCCGATTCCTCTGATTCCTCCAGTCCTGCCCACTCTTCACTC
1 AAAGAAGAAAGTCCGATTCCTCTGATTCCTCCAGTCCTACCCACTCTTAACTC
52815479 A
1 A
52815480 TCTTTTTATG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.27, C:0.35, G:0.11, T:0.27
Consensus pattern (53 bp):
AAAGAAGAAAGTCCGATTCCTCTGATTCCTCCAGTCCTACCCACTCTTAACTC
Found at i:52818040 original size:6 final size:6
Alignment explanation
Indices: 52818029--52818072 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
52818019 ACCTATAGCC
52818029 TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TT
1 TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TTAGAT TT
52818073 TGATCTATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TTAGAT
Found at i:52819266 original size:48 final size:48
Alignment explanation
Indices: 52819195--52819291 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
52819185 ATAAAAAAGA
* *
52819195 AGAAAGTTCGATTCCTCTGATTCCTCCAGTCCTGCCCTCTCTTAACTC
1 AGAAAGTCCGATTCCTCTGATTCCTCCAGTCCTGCCCACTCTTAACTC
*
52819243 AGAAAGTCCGATTCCTCTGATTCCTCCAGTCCTGCCCACTCTTCACTC
1 AGAAAGTCCGATTCCTCTGATTCCTCCAGTCCTGCCCACTCTTAACTC
52819291 A
1 A
52819292 TCTTTTTATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.20, C:0.37, G:0.12, T:0.31
Consensus pattern (48 bp):
AGAAAGTCCGATTCCTCTGATTCCTCCAGTCCTGCCCACTCTTAACTC
Found at i:52842166 original size:22 final size:22
Alignment explanation
Indices: 52842141--52842204 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
52842131 TGAGAACGAA
52842141 TCAAATCAGATGGTTCTATTTC
1 TCAAATCAGATGGTTCTATTTC
52842163 TC-AATC---T--TTCTGA--TC
1 TCAAATCAGATGGTTCT-ATTTC
52842178 ATCAAATCAGATGGTTCTATTTC
1 -TCAAATCAGATGGTTCTATTTC
52842201 TCAA
1 TCAA
52842205 TCTTTCTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 20
0.62 0.00 0.38
Matches are distributed among these distances:
15 2 0.06
16 6 0.19
17 5 0.16
18 1 0.03
20 1 0.03
21 5 0.16
22 10 0.31
23 2 0.06
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (22 bp):
TCAAATCAGATGGTTCTATTTC
Done.