Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 174 of 425
Found at i:52674701 original size:46 final size:47
Alignment explanation
Indices: 52674522--52674720 Score: 120
Period size: 46 Copynumber: 4.2 Consensus size: 47
52674512 ACATGTGTGT
* * *
52674522 TAGTGTAAGACATGCCTGGGACATGCATC-AGCCAC-ATTATGA-GAGC
1 TAGTGTAAGACATGTCTGGGACATGCATCGA-CCTCGA-GATGACGAGC
* * *** * *
52674568 CAGTGTAAGACATGTCTAGGACATGCATTTTCCTCGAGA-GATGCAAAC
1 TAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATGA--CGAGC
* * * ** *** *
52674616 CAATGTAAGACATGTTTGGGACATTTATCGGTATTGAGATGA-GAGC
1 TAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATGACGAGC
* * *
52674662 TAGTGTAAGACATGTCTGGGACATGCATCGACTTCGAGATATACAAGC
1 TAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGAT-GACGAGC
52674710 TAGTGTAAGAC
1 TAGTGTAAGAC
52674721 CTATTTGAGA
Statistics
Matches: 112, Mismatches: 33, Indels: 14
0.70 0.21 0.09
Matches are distributed among these distances:
45 2 0.02
46 62 0.55
47 2 0.02
48 44 0.39
49 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (47 bp):
TAGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATGACGAGC
Found at i:52674733 original size:94 final size:94
Alignment explanation
Indices: 52674560--52674733 Score: 222
Period size: 94 Copynumber: 1.9 Consensus size: 94
52674550 CAGCCACATT
*** *
52674560 ATGAGAGCCAGTGTAAGACATGTCTAGGACATGCATTTTCCTCGAGAGATGCAAACCAATGTAAG
1 ATGAGAGCCAGTGTAAGACATGTCTAGGACATGCATCGACCTCGAGAGATACAAACCAATGTAAG
* *
52674625 ACATGTTTGGGACATTTATCGGTATTGAG
66 ACATATTTGAGACATTTATCGGTATTGAG
* * * * * * *
52674654 ATGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACTTCGAGATATACAAGCTAGTGTAAG
1 ATGAGAGCCAGTGTAAGACATGTCTAGGACATGCATCGACCTCGAGAGATACAAACCAATGTAAG
*
52674719 ACCTATTTGAGACAT
66 ACATATTTGAGACAT
52674734 GGCGTCAGCT
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
94 66 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (94 bp):
ATGAGAGCCAGTGTAAGACATGTCTAGGACATGCATCGACCTCGAGAGATACAAACCAATGTAAG
ACATATTTGAGACATTTATCGGTATTGAG
Found at i:52674810 original size:49 final size:48
Alignment explanation
Indices: 52674754--52674928 Score: 165
Period size: 49 Copynumber: 3.6 Consensus size: 48
52674744 TGTTGTGTGT
* *
52674754 CAGTGTAAGACCTGTCTGGGACATGGCATCGACACTGATAGATGAGAGC
1 CAGTGTAAAACCTGTCTGGGACATGGCATCGAC-CTGATAGATGAAAGC
* * * * * *
52674803 CAGTGTAAAACCTGTCTCGGACAAGGCATCGGCCTCTATATATGAAAGT
1 CAGTGTAAAACCTGTCTGGGACATGGCATCGACCT-GATAGATGAAAGC
* ** * **
52674852 TAGTGTAAAACCTGTCTACGACATGGCATCGACTTTGAT-G-TGCTAGC
1 CAGTGTAAAACCTGTCTGGGACATGGCATCGAC-CTGATAGATGAAAGC
*
52674899 CAGTGTAAGACCATGTCTGGGACATGGCAT
1 CAGTGTAAAACC-TGTCTGGGACATGGCAT
52674929 TGGCATCTTA
Statistics
Matches: 100, Mismatches: 23, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
47 14 0.14
48 17 0.17
49 68 0.68
50 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (48 bp):
CAGTGTAAAACCTGTCTGGGACATGGCATCGACCTGATAGATGAAAGC
Found at i:52674856 original size:142 final size:145
Alignment explanation
Indices: 52674652--52674928 Score: 325
Period size: 142 Copynumber: 1.9 Consensus size: 145
52674642 ATCGGTATTG
* * * * *
52674652 AGATGAGAGCTAGTGTAAGACATGTCTGGGACATGCATCGACTTCGAGATATACAAGCTAGTGTA
1 AGATGAGAGCCAGTGTAAAACATGTCTCGGACAGGCATCGACCTCGAGATATACAAGCTAGTGTA
* * * * *
52674717 AGACCTATTTGA-GACATGGCGTC-AGC-TTGTTGTG-T-GTCAGTGTAAGACC-TGTCTGGGAC
66 AAACCTATCT-ACGACATGGCATCGA-CTTTGATGTGCTAGCCAGTGTAAGACCATGTCTGGGAC
52674776 ATGGCATCGACACTGAT
129 ATGGCATCGACACTGAT
* * * * *
52674793 AGATGAGAGCCAGTGTAAAACCTGTCTCGGACAAGGCATCGGCCTCTATATATGA-AAGTTAGTG
1 AGATGAGAGCCAGTGTAAAACATGTCTCGGAC-AGGCATCGACCTCGAGATAT-ACAAGCTAGTG
*
52674857 TAAAACCTGTCTACGACATGGCATCGACTTTGATGTGCTAGCCAGTGTAAGACCATGTCTGGGAC
64 TAAAACCTATCTACGACATGGCATCGACTTTGATGTGCTAGCCAGTGTAAGACCATGTCTGGGAC
52674922 ATGGCAT
129 ATGGCAT
52674929 TGGCATCTTA
Statistics
Matches: 112, Mismatches: 16, Indels: 11
0.81 0.12 0.08
Matches are distributed among these distances:
141 29 0.26
142 43 0.38
143 9 0.08
144 1 0.01
145 13 0.12
146 17 0.15
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (145 bp):
AGATGAGAGCCAGTGTAAAACATGTCTCGGACAGGCATCGACCTCGAGATATACAAGCTAGTGTA
AAACCTATCTACGACATGGCATCGACTTTGATGTGCTAGCCAGTGTAAGACCATGTCTGGGACAT
GGCATCGACACTGAT
Found at i:52690470 original size:27 final size:28
Alignment explanation
Indices: 52690440--52690539 Score: 121
Period size: 27 Copynumber: 3.5 Consensus size: 28
52690430 ATAGTGAGTC
52690440 CGCACACTTAGTGCTATAAAATC-AACT
1 CGCACACTTAGTGCTATAAAATCAAACT
* *
52690467 CGCACACCTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
52690495 CGCACACTTAGTGCTGTACAAATTTAAAACC
1 CGCACACTTAGTGCTATA-AAA--TCAAACT
52690526 CGCACACTTAGTGC
1 CGCACACTTAGTGC
52690540 AATCTCATGA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
27 21 0.34
28 20 0.32
29 2 0.03
31 19 0.31
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:52691393 original size:7 final size:7
Alignment explanation
Indices: 52691383--52691407 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52691373 TCATCACCAC
52691383 AACATCA
1 AACATCA
52691390 AACATCA
1 AACATCA
52691397 AACATCA
1 AACATCA
52691404 AACA
1 AACA
52691408 AGAAGACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (7 bp):
AACATCA
Found at i:52695633 original size:93 final size:93
Alignment explanation
Indices: 52695520--52695690 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
52695510 GCCCCTAAGT
* * * *
52695520 GAACTCAGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACACAACGAGCTCAGACATTCGCATCCATAACTGAACTCGGACTCAACTCAA
*
52695585 CGAGTTCGGATGCCTATTTACATTTCAC
66 CGAGTTCAGATGCCTATTTACATTTCAC
* *
52695613 GAACTCGGACTCAACACAACGAGTTCAGACATTCGCATCCATAACTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACACAACGAGCTCAGACATTCGCATCCATAACTGAACTCGGACTCAACTCAA
52695678 CGAGTTCAGATGC
66 CGAGTTCAGATGC
52695691 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACACAACGAGCTCAGACATTCGCATCCATAACTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTATTTACATTTCAC
Found at i:52695685 original size:46 final size:46
Alignment explanation
Indices: 52695519--52695687 Score: 182
Period size: 46 Copynumber: 3.7 Consensus size: 46
52695509 CGCCCCTAAG
* * * * *
52695519 TGAACTCAGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAC
* ** * *
52695565 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTATTTACAT--TTCAC
1 TGAACTCGGACTCAACTCAACGAGTTC--A-GAC-ATTCGCATCCATAAC
*
52695613 -GAACTCGGACTCAACACAACGAGTTCAGACATTCGCATCCATAAC
1 TGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAC
52695658 TGAACTCGGACTCAACTCAACGAGTTCAGA
1 TGAACTCGGACTCAACTCAACGAGTTCAGA
52695688 TGCTCAACCA
Statistics
Matches: 99, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 4 0.04
46 53 0.54
47 25 0.25
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAC
Found at i:52707781 original size:30 final size:30
Alignment explanation
Indices: 52707747--52707807 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52707737 TCCTTAACTC
52707747 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
52707777 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
52707807 A
1 A
52707808 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:52712315 original size:30 final size:30
Alignment explanation
Indices: 52712281--52712341 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
52712271 TCCTTAACTC
52712281 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
52712311 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
52712341 A
1 A
52712342 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:52719171 original size:17 final size:18
Alignment explanation
Indices: 52719129--52719177 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
52719119 AGTTGAAAAG
52719129 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
52719148 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
52719165 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
52719178 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:52720163 original size:40 final size:39
Alignment explanation
Indices: 52719999--52720181 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
52719989 AAATTGAATG
* *
52719999 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
52720038 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
52720078 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
52720118 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
52720157 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
52720182 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 25, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 15 0.13
40 92 0.81
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:52720206 original size:80 final size:81
Alignment explanation
Indices: 52720038--52720226 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
52720028 GCTGGAAATT
* * * *
52720038 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
52720103 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
52720119 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
52720182 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
52720198 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
52720227 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:52722777 original size:24 final size:23
Alignment explanation
Indices: 52722745--52722792 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 23
52722735 CAACATTGTG
52722745 GCAAATGGCATTCGGGGAGCTGTT
1 GCAAATGGCATTCGGGG-GCTGTT
52722769 GCAAATGGCATTCGGGGGCTGTT
1 GCAAATGGCATTCGGGGGCTGTT
52722792 G
1 G
52722793 GTTTCGTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.19, C:0.17, G:0.40, T:0.25
Consensus pattern (23 bp):
GCAAATGGCATTCGGGGGCTGTT
Found at i:52728166 original size:40 final size:40
Alignment explanation
Indices: 52728100--52728250 Score: 146
Period size: 40 Copynumber: 3.8 Consensus size: 40
52728090 AAATTGAATG
* * *
52728100 ATATCCGGGCTAA-TCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* * ****
52728139 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
* *
52728179 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GAAATT
* *
52728219 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
52728251 ACATGGTTAT
Statistics
Matches: 89, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
39 15 0.17
40 72 0.81
41 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGAAATT
Found at i:52728264 original size:40 final size:40
Alignment explanation
Indices: 52728137--52728266 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
52728127 ATGCTGGAAA
* * * *
52728137 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
* * * **
52728177 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGA-CA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
*
52728217 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-ATGG
52728257 TTATATCCGG
1 TTATATCCGG
52728267 TTATATTCCG
Statistics
Matches: 71, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
39 2 0.03
40 69 0.97
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATGG
Found at i:52732369 original size:27 final size:27
Alignment explanation
Indices: 52732329--52732440 Score: 138
Period size: 27 Copynumber: 4.1 Consensus size: 27
52732319 AGGAAGCGTC
*
52732329 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
52732356 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
*
52732383 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
52732411 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
52732437 CTGG
1 CTGG
52732441 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.11
27 49 0.65
28 18 0.24
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:52732435 original size:54 final size:54
Alignment explanation
Indices: 52732329--52732440 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
52732319 AGGAAGCGTC
* *
52732329 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
52732383 CTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
52732437 CTGG
1 CTGG
52732441 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:52733628 original size:16 final size:16
Alignment explanation
Indices: 52733602--52733645 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
52733592 TATGAATCGG
52733602 TAAAA-GCCGAAATGC
1 TAAAATGCCGAAATGC
52733617 TAAAATGCCGAAATGC
1 TAAAATGCCGAAATGC
52733633 TAAAATGCCGAAA
1 TAAAATGCCGAAA
52733646 AGCCGAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (16 bp):
TAAAATGCCGAAATGC
Found at i:52733650 original size:24 final size:25
Alignment explanation
Indices: 52733618--52733669 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 25
52733608 CCGAAATGCT
52733618 AAAATGCCGAAATGCT-AAAATGCCG
1 AAAATGCCGAAATGCTGAAAA-GCCG
52733643 AAAA-GCCGAAATGCTGAAAAGCCG
1 AAAATGCCGAAATGCTGAAAAGCCG
52733667 AAA
1 AAA
52733670 GTTTGGCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (25 bp):
AAAATGCCGAAATGCTGAAAAGCCG
Found at i:52733654 original size:16 final size:16
Alignment explanation
Indices: 52733619--52733669 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
52733609 CGAAATGCTA
* **
52733619 AAATGCCGAAATGCTA
1 AAATGCCGAAAAGCCG
52733635 AAATGCCGAAAAGCCG
1 AAATGCCGAAAAGCCG
*
52733651 AAATGCTGAAAAGCCG
1 AAATGCCGAAAAGCCG
52733667 AAA
1 AAA
52733670 GTTTGGCTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.12
Consensus pattern (16 bp):
AAATGCCGAAAAGCCG
Found at i:52733924 original size:28 final size:28
Alignment explanation
Indices: 52733880--52733994 Score: 113
Period size: 29 Copynumber: 4.0 Consensus size: 28
52733870 GTGAGCATGA
* * **
52733880 ATATGAATGTGACTGGGCCTAGCGGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
*
52733908 ATATAAATGTGATTGGGGCCTAATGGACC
1 ATATAAATGTGATT-GGGCCTAATGGGCC
* *
52733937 ATATACAGGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGA-TTGGGCCTAATGGGCC
* * * *
52733966 ATATAAATATGAATGGGCTTAATTGGCC
1 ATATAAATGTGATTGGGCCTAATGGGCC
52733994 A
1 A
52733995 GATACAGGTA
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
28 26 0.37
29 43 0.61
30 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (28 bp):
ATATAAATGTGATTGGGCCTAATGGGCC
Found at i:52733965 original size:58 final size:57
Alignment explanation
Indices: 52733893--52734003 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 57
52733883 TGAATGTGAC
* * * *
52733893 TGGGCCTAGCGGGCCATATAAATGTGATTGGGGCCTAA-TGGACCATATACAGGTGATT
1 TGGGCCTAACGGGCCATATAAATATGAAT-GGGCCTAATTGG-CCAGATACAGGTGATT
* *
52733951 TGGGCCTAATGGGCCATATAAATATGAATGGGCTTAATTGGCCAGATACAGGT
1 TGGGCCTAACGGGCCATATAAATATGAATGGGCCTAATTGGCCAGATACAGGT
52734004 ATGTGAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 18 0.39
58 28 0.61
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (57 bp):
TGGGCCTAACGGGCCATATAAATATGAATGGGCCTAATTGGCCAGATACAGGTGATT
Found at i:52738362 original size:28 final size:28
Alignment explanation
Indices: 52738283--52738362 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 28
52738273 GTGAGCATGA
*
52738283 ATATGAATGTGAATGGGCCTAACGGGCC
1 ATATGAATGTGAATGGGCCTAATGGGCC
* *
52738311 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGA-ATGGGCCTAATGGGCC
* *
52738340 ATATGAATATGAATGGGCATAAT
1 ATATGAATGTGAATGGGCCTAAT
52738363 AGCCTAGATA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 20 0.45
29 24 0.55
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.28
Consensus pattern (28 bp):
ATATGAATGTGAATGGGCCTAATGGGCC
Found at i:52739480 original size:17 final size:18
Alignment explanation
Indices: 52739448--52739481 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52739438 TTTAAGAAGA
52739448 GTTTTCAATGAAAACACG
1 GTTTTCAATGAAAACACG
*
52739466 GTTTTCACT-AAAACAC
1 GTTTTCAATGAAAACAC
52739482 TTCAATGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (18 bp):
GTTTTCAATGAAAACACG
Found at i:52749448 original size:40 final size:40
Alignment explanation
Indices: 52749340--52749589 Score: 385
Period size: 40 Copynumber: 6.2 Consensus size: 40
52749330 CGGGATTTAA
* * * * *
52749340 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
52749380 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
52749420 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
52749460 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
52749500 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
52749540 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
52749580 CCGGATATAT
1 CCGGATATAT
52749590 TTCCAATGTT
Statistics
Matches: 193, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 1 0.01
40 192 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:52755475 original size:40 final size:40
Alignment explanation
Indices: 52755398--52755659 Score: 393
Period size: 40 Copynumber: 6.6 Consensus size: 40
52755388 AAACCCAGTA
* * * *
52755398 CCTTCGGGAATTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCACACAAATG
* *
52755437 CCTTCGGGATTTAGCCTGGTTATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCACACAAATG
*
52755477 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCACACAAATG
* **
52755517 CCTTCGGGACTTAGCCCGGATATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCACACAAATG
52755557 CCTTCGGGACTTAGCCCGGTTATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCACACAAATG
*
52755597 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCACACAAATG
*
52755637 CCTTCAGGACTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
52755660 CATCCAAATA
Statistics
Matches: 206, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 14 0.07
40 192 0.93
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCACACAAATG
Found at i:52758576 original size:19 final size:18
Alignment explanation
Indices: 52758539--52758582 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
52758529 ATACATACAG
52758539 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
52758556 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
52758575 TACTAATT
1 TAATAATT
52758583 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:52765099 original size:32 final size:33
Alignment explanation
Indices: 52765062--52765166 Score: 131
Period size: 32 Copynumber: 3.0 Consensus size: 33
52765052 GGGTATCACA
52765062 ACTCGCACAATTGCCTTCGGGCTTAGCCCGGAT
1 ACTCGCACAATTGCCTTCGGGCTTAGCCCGGAT
*
52765095 -CTCGCACCATTGCCTTCGGGCTTAGCCCGGATAT
1 ACTCGCACAATTGCCTTCGGGCTTAGCCCGG--AT
*
52765129 CACAACTTGCACAATTGCCTTCGGGCTTAGCCCGGAT
1 ----ACTCGCACAATTGCCTTCGGGCTTAGCCCGGAT
52765166 A
1 A
52765167 TCACAATTCG
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
32 29 0.47
33 1 0.02
34 2 0.03
37 2 0.03
39 28 0.45
ACGTcount: A:0.19, C:0.33, G:0.23, T:0.25
Consensus pattern (33 bp):
ACTCGCACAATTGCCTTCGGGCTTAGCCCGGAT
Found at i:52765157 original size:39 final size:39
Alignment explanation
Indices: 52765096--52765180 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
52765086 AGCCCGGATC
*
52765096 TCGCACCATTGCCTTCGGGCTTAGCCCGGATATCACAACT
1 TCGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAA-T
52765136 T-GCACAATTGCCTTCGGGCTTAGCCCGGATATCACAAT
1 TCGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAAT
52765174 TCGCACA
1 TCGCACA
52765181 TTCATACACA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
38 2 0.05
39 40 0.93
40 1 0.02
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.25
Consensus pattern (39 bp):
TCGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAAT
Found at i:52772397 original size:21 final size:21
Alignment explanation
Indices: 52772373--52772414 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52772363 TCATCAGATC
*
52772373 TACACCTTGAGGCATCGGGGG
1 TACACCTTGAGGAATCGGGGG
**
52772394 TACAGGTTGAGGAATCGGGGG
1 TACACCTTGAGGAATCGGGGG
52772415 AGGTGGGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.43, T:0.19
Consensus pattern (21 bp):
TACACCTTGAGGAATCGGGGG
Found at i:52779928 original size:21 final size:21
Alignment explanation
Indices: 52779904--52779944 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52779894 TCATCAGATC
*
52779904 TACACCTTGAGGCATCGGGGG
1 TACACCTTGAGGAATCGGGGG
**
52779925 TACAGGTTGAGGAATCGGGG
1 TACACCTTGAGGAATCGGGG
52779945 AGGTGGGGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.17, G:0.41, T:0.20
Consensus pattern (21 bp):
TACACCTTGAGGAATCGGGGG
Found at i:52789724 original size:5 final size:5
Alignment explanation
Indices: 52789714--52789739 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52789704 TTTTTCTTGC
52789714 AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT A
52789740 TTCTTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:52793890 original size:40 final size:40
Alignment explanation
Indices: 52793787--52793987 Score: 273
Period size: 40 Copynumber: 5.1 Consensus size: 40
52793777 GGAATTTAGT
* ** *
52793787 CGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACC
1 CGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACC
* * *
52793827 CGG-TATAGCAACTCGCACAAATGCCTTTGGGTCTTAGCC
1 CGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACC
52793866 CGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACC
1 CGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACC
*
52793906 CGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAACC
1 CGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACC
* * *
52793946 CGGATATAATC-ACTAGCATAAATGCCTTCGGG-CTTAGCC
1 CGGATATAA-CAACTCGCACAAATGCCTTCGGGTCTTAACC
52793985 CGG
1 CGG
52793988 GTATCATTCA
Statistics
Matches: 144, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 41 0.28
40 102 0.71
41 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
CGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACC
Found at i:52796161 original size:13 final size:13
Alignment explanation
Indices: 52796143--52796167 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52796133 AACAATGCCA
52796143 GACACGACCGTGC
1 GACACGACCGTGC
52796156 GACACGACCGTG
1 GACACGACCGTG
52796168 TGCACCCACA
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:0.24, C:0.36, G:0.32, T:0.08
Consensus pattern (13 bp):
GACACGACCGTGC
Found at i:52798040 original size:22 final size:22
Alignment explanation
Indices: 52798001--52798059 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
52797991 GTTTTAAGAA
*
52798001 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
52798022 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
52798044 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
52798060 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:52798076 original size:26 final size:24
Alignment explanation
Indices: 52798030--52798089 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
52798020 ATTTGTTTTA
*
52798030 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
52798054 ATATTTGATTTATTATATTTTTAAAT
1 ATATTT-ATTT-TTATATTTTTAAAT
* *
52798080 TTTTTTATTT
1 ATATTTATTT
52798090 AATGAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.68
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:52807293 original size:37 final size:38
Alignment explanation
Indices: 52807229--52807302 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 38
52807219 CAATATTCTC
52807229 AGTTTTCAATTACTTTTTTTTATTTACCATTACAATTT
1 AGTTTTCAATTACTTTTTTTTATTTACCATTACAATTT
*
52807267 AGTTTTCAATTGC-TTTTTTTATTTACCATTACAATT
1 AGTTTTCAATTACTTTTTTTTATTTACCATTACAATT
52807303 CATGCCATGT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 23 0.66
38 12 0.34
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.57
Consensus pattern (38 bp):
AGTTTTCAATTACTTTTTTTTATTTACCATTACAATTT
Found at i:52815344 original size:2 final size:2
Alignment explanation
Indices: 52815337--52815366 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52815327 ATGTATCATG
52815337 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52815367 CTAGTCTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52818562 original size:68 final size:66
Alignment explanation
Indices: 52818490--52818661 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
52818480 CATCATGTGT
* * * *
52818490 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
52818553 TGTAG
62 TGTAG
** * *
52818558 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
52818623 AG
65 AG
* * * *
52818625 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
52818662 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:52818595 original size:64 final size:64
Alignment explanation
Indices: 52818514--52818697 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
52818504 AGACATTATG
* * *
52818514 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
52818578 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
52818643 AA
63 AA
* * *
52818645 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
52818698 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:52821354 original size:17 final size:18
Alignment explanation
Indices: 52821318--52821355 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
52821308 TAGGAAATAA
*
52821318 AAATAAACACCTAAAAAT
1 AAATAAACAACTAAAAAT
*
52821336 AAATAAA-AACTAAAGAT
1 AAATAAACAACTAAAAAT
52821353 AAA
1 AAA
52821356 AAATTCCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.71, C:0.11, G:0.03, T:0.16
Consensus pattern (18 bp):
AAATAAACAACTAAAAAT
Found at i:52823248 original size:17 final size:18
Alignment explanation
Indices: 52823226--52823294 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 18
52823216 AAACATAAAC
52823226 AAATTAAATAAAAA-TTA
1 AAATTAAATAAAAATTTA
* **
52823243 AAATTAAAGAAAAAGATA
1 AAATTAAATAAAAATTTA
52823261 AAA--AAATAAAAATTTTA
1 AAATTAAATAAAAA-TTTA
* *
52823278 AAATTAATTAGAAATTT
1 AAATTAAATAAAAATTT
52823295 CTTTTCAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
16 8 0.20
17 18 0.44
18 8 0.20
19 7 0.17
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (18 bp):
AAATTAAATAAAAATTTA
Found at i:52823987 original size:15 final size:15
Alignment explanation
Indices: 52823948--52824027 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
52823938 GTATCTTGGG
*
52823948 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
52823963 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
52823978 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
52823993 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
52824008 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
52824022 TTTCTT
1 TTTCTT
52824028 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:52824017 original size:30 final size:30
Alignment explanation
Indices: 52823939--52824026 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
52823929 CATAGTATCG
* * *
52823939 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
52823969 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
52823999 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
52824027 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:52826522 original size:47 final size:46
Alignment explanation
Indices: 52826403--52826576 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
52826393 GGGATATTTG
*
52826403 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGA
* * *
52826450 -GCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATG---CGA
*
52826496 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGA
* * *
52826543 -AC-GCCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
52826577 TATGGGCGGG
Statistics
Matches: 109, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
43 4 0.04
45 32 0.29
46 34 0.31
47 33 0.30
48 2 0.02
50 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGA
Found at i:52826570 original size:45 final size:46
Alignment explanation
Indices: 52826407--52826581 Score: 225
Period size: 45 Copynumber: 3.8 Consensus size: 46
52826397 TATTTGGGCA
*
52826407 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
52826453 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
52826498 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
52826546 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52826582 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 38 0.34
46 29 0.26
47 29 0.26
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:52830045 original size:10 final size:10
Alignment explanation
Indices: 52830030--52830056 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
52830020 TGAAACAAGC
52830030 CTAATTCATA
1 CTAATTCATA
52830040 CTAATTCATA
1 CTAATTCATA
52830050 CTAATTC
1 CTAATTC
52830057 CACACTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (10 bp):
CTAATTCATA
Found at i:52830487 original size:31 final size:31
Alignment explanation
Indices: 52830449--52830512 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
52830439 TTATAGTTCG
52830449 ATAGTGTGATGCAGTCTCCGACGACTCCCAA
1 ATAGTGTGATGCAGTCTCCGACGACTCCCAA
* *
52830480 ATAGTGTGATGCGGTCTCCGACGTCTCCCAA
1 ATAGTGTGATGCAGTCTCCGACGACTCCCAA
52830511 AT
1 AT
52830513 TTGAGCTAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (31 bp):
ATAGTGTGATGCAGTCTCCGACGACTCCCAA
Found at i:52838722 original size:13 final size:13
Alignment explanation
Indices: 52838706--52838738 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
52838696 TTTAATTAAA
*
52838706 TTAGTTAATTAGT
1 TTAGATAATTAGT
52838719 TTAGATAATTAGT
1 TTAGATAATTAGT
52838732 TTA-ATAA
1 TTAGATAA
52838739 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:52844561 original size:25 final size:25
Alignment explanation
Indices: 52844533--52844611 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
52844523 ACTCGGCCCT
52844533 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
52844558 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
52844580 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
52844605 ATCACAT
1 ATCACAT
52844612 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:52844657 original size:49 final size:49
Alignment explanation
Indices: 52844483--52844832 Score: 541
Period size: 49 Copynumber: 7.3 Consensus size: 49
52844473 CCCTTCGGGA
* * * * * *
52844483 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGACCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
52844530 CCTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52844577 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52844624 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
52844673 CTTATCACATGTATATACAATTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52844722 TTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52844771 CTTATCACATGTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52844820 CTTATCACATATA
1 CTTATCACATATA
52844833 CTATCATGTA
Statistics
Matches: 283, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
46 1 0.00
47 91 0.32
49 191 0.67
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52848767 original size:6 final size:6
Alignment explanation
Indices: 52848756--52848825 Score: 54
Period size: 6 Copynumber: 11.2 Consensus size: 6
52848746 TTATTTCTTC
* *
52848756 TTATTT TTA-TT TTA-TT TTATTTAT GTTATTT TTATTT TTCTTT TCATTT
1 TTATTT TTATTT TTATTT TTA-TT-T -TTATTT TTATTT TTATTT TTATTT
*
52848805 TTCTTT TTATTATT TTATTT T
1 TTATTT TTA-T-TT TTATTT T
52848826 GAAAGACATA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
5 10 0.19
6 27 0.52
7 4 0.08
8 8 0.15
9 3 0.06
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.79
Consensus pattern (6 bp):
TTATTT
Found at i:52848818 original size:42 final size:42
Alignment explanation
Indices: 52848739--52848819 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 42
52848729 TTGAATCCTC
*
52848739 TTATTTTTTATTTCTTCTTATTTTTATTTTATTTTATTTATG
1 TTATTTTTTATTTCTTCTTATTTTTATTTTATATTATTTATG
* *
52848781 TTATTTTTATTTTTCTT-TTCATTTTTCTTTT-TATTATTT
1 TTATTTTT-TATTTCTTCTT-ATTTTTATTTTATATTATTT
52848820 TATTTTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 17 0.50
43 17 0.50
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (42 bp):
TTATTTTTTATTTCTTCTTATTTTTATTTTATATTATTTATG
Found at i:52850155 original size:1 final size:1
Alignment explanation
Indices: 52850149--52850173 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
52850139 TGTGAGAAAC
52850149 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
52850174 GAAGTTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:52850965 original size:2 final size:2
Alignment explanation
Indices: 52850958--52850983 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52850948 TTATTTGATG
52850958 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
52850984 GTATTCGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52851351 original size:2 final size:2
Alignment explanation
Indices: 52851346--52851370 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52851336 CATATATAGG
52851346 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
52851371 GTATGCCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52853364 original size:2 final size:2
Alignment explanation
Indices: 52853357--52853385 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52853347 TATTCAAAGG
52853357 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52853386 GACAGCCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52863940 original size:17 final size:17
Alignment explanation
Indices: 52863918--52863951 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52863908 GTTCATAAGT
52863918 AAAACATGATATTATAA
1 AAAACATGATATTATAA
*
52863935 AAAACATGATGTTATAA
1 AAAACATGATATTATAA
52863952 GTATGTTTTG
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:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (17 bp):
AAAACATGATATTATAA
Found at i:52865858 original size:25 final size:25
Alignment explanation
Indices: 52865829--52865876 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
52865819 TTATACCATG
* * *
52865829 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
52865854 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
52865877 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:52865944 original size:20 final size:20
Alignment explanation
Indices: 52865919--52865977 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
52865909 TAAATATGGT
52865919 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
52865939 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
52865959 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
52865978 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:52865959 original size:11 final size:11
Alignment explanation
Indices: 52865923--52865977 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
52865913 TATGGTATGT
52865923 ATGATATGCAC
1 ATGATATGCAC
* *
52865934 ATGAAATG--T
1 ATGATATGCAC
52865943 ATGATATGCAC
1 ATGATATGCAC
*
52865954 ATGATATG--T
1 ATGATATGCAC
52865963 ATGATATGCAC
1 ATGATATGCAC
52865974 ATGA
1 ATGA
52865978 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:52866055 original size:24 final size:24
Alignment explanation
Indices: 52866028--52866168 Score: 200
Period size: 24 Copynumber: 6.0 Consensus size: 24
52866018 GGAGGAAGTG
52866028 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
52866052 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
52866076 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
52866099 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* *
52866122 GAAAGGGCTT-TGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
52866145 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
52866169 ATGATAAAGT
Statistics
Matches: 110, Mismatches: 2, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
22 22 0.20
23 18 0.16
24 62 0.56
25 8 0.07
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:52866165 original size:70 final size:70
Alignment explanation
Indices: 52866029--52866169 Score: 214
Period size: 70 Copynumber: 2.0 Consensus size: 70
52866019 GAGGAAGTGA
*
52866029 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTAGGCCCCA
52866094 GTTAT
66 GTTAT
** *
52866099 AAAGGGCTTATGCCCCAGTTATTGAAAGGGCTT-TGCCCCAGTTATTAAAAGAGGC-TAGGCCTC
1 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAG-GGCTTAGGCC-C
52866162 CAGTTAT
64 CAGTTAT
52866169 A
1 A
52866170 TGATAAAGTA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
69 22 0.34
70 43 0.66
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (70 bp):
AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTAGGCCCCA
GTTAT
Found at i:52866393 original size:31 final size:31
Alignment explanation
Indices: 52866358--52866421 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
52866348 CGTTTACAGT
52866358 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
52866389 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
52866420 AA
1 AA
52866422 TATGAAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:52870669 original size:29 final size:29
Alignment explanation
Indices: 52870635--52870707 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 29
52870625 TACTCGATTT
* *
52870635 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATGCCATTCAAGCC
* * *
52870664 CGCACAC--AGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATGCCATTCAAGCC
52870691 CGCACACTTAGTGCCAT
1 CGCACACTTAGTGCCAT
52870708 ATATTTCCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.59
29 15 0.41
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.22
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCCATTCAAGCC
Found at i:52870750 original size:26 final size:27
Alignment explanation
Indices: 52870691--52870760 Score: 106
Period size: 26 Copynumber: 2.6 Consensus size: 27
52870681 CCTTCGAGCT
52870691 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATA--TCCAGCA
*
52870720 TGCACACTTAGTGCCATATA-CCAGCA
1 CGCACACTTAGTGCCATATATCCAGCA
52870746 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
52870761 GAAAGCAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
26 20 0.51
29 19 0.49
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (27 bp):
CGCACACTTAGTGCCATATATCCAGCA
Found at i:52878490 original size:29 final size:29
Alignment explanation
Indices: 52878456--52878530 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
52878446 TACTCGATTT
* *
52878456 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATGCCATTCAAGCC
** * * *
52878485 CGCACACACAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATGCCATTCAAGCC
52878514 CGCACACTTAGTGCCAT
1 CGCACACTTAGTGCCAT
52878531 ATATTTCCAG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCCATTCAAGCC
Found at i:52878547 original size:29 final size:29
Alignment explanation
Indices: 52878514--52878586 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
52878504 CCTTCGAGCT
52878514 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
52878543 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
52878572 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
52878587 GAAAGCAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:52878548 original size:58 final size:58
Alignment explanation
Indices: 52878455--52878586 Score: 131
Period size: 58 Copynumber: 2.3 Consensus size: 58
52878445 ATACTCGATT
* * * * *
52878455 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
* * * ** * *
52878513 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACACAGTGCCATACACTTCCAGC
*
52878571 ACGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
52878587 GAAAGCAAAC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 56 0.93
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.25
Consensus pattern (58 bp):
TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
Found at i:52881080 original size:27 final size:27
Alignment explanation
Indices: 52881042--52881436 Score: 306
Period size: 27 Copynumber: 14.6 Consensus size: 27
52881032 TTAGTTTACC
* *
52881042 AAATTACTAAAATGCCCTCAATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
*
52881069 AAATTACTAAAATACCC-CTGGTTTGTA
1 AAATTACTAAAATACCCTC-GATTTGTA
* * *
52881096 AAATTACCAAAATACCCT-TAGTTTGTG
1 AAATTACTAAAATACCCTCGA-TTTGTA
* *
52881123 AAATTACCAAAATACCC-CTAATTTG-A
1 AAATTACTAAAATACCCTC-GATTTGTA
* *
52881149 GAAATTACTGAAATACCCTCGACTTGTA
1 -AAATTACTAAAATACCCTCGATTTGTA
* *
52881177 AAATTAC-CAAATAACCCT-GATTTGTG
1 AAATTACTAAAAT-ACCCTCGATTTGTA
* * *
52881203 AAATTACTGAAATACCCTTGACTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* * * * **
52881230 AAATTACCAAAATAACCTTGGTTTACA
1 AAATTACTAAAATACCCTCGATTTGTA
* *
52881257 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACTAAAATACCCTC-GATTTGTA
* *
52881284 AAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACTAAAATACCCTC-GATTTGTA
52881311 AAATTA-TCAAAATACCCTC-AGTTTGTA
1 AAATTACT-AAAATACCCTCGA-TTTGTA
*
52881338 AAATTACTAAAATACCCTCAATTTGTA
1 AAATTACTAAAATACCCTCGATTTGTA
* * *
52881365 AAATTACTGAAATACCCTCGACTTATA
1 AAATTACTAAAATACCCTCGATTTGTA
* * * **
52881392 AACATTACCAAAGTACCCCCGATTTACA
1 AA-ATTACTAAAATACCCTCGATTTGTA
* *
52881420 AAATTATTGAAATACCC
1 AAATTACTAAAATACCC
52881437 CTATAGGGTA
Statistics
Matches: 302, Mismatches: 48, Indels: 36
0.78 0.12 0.09
Matches are distributed among these distances:
26 24 0.08
27 251 0.83
28 27 0.09
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACTAAAATACCCTCGATTTGTA
Found at i:52881108 original size:54 final size:54
Alignment explanation
Indices: 52881042--52881425 Score: 344
Period size: 54 Copynumber: 7.1 Consensus size: 54
52881032 TTAGTTTACC
* * * *
52881042 AAATTACTAAAATGCCCTCAATTTGTAAAATTACTAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTGTA
* * * *
52881096 AAATTACCAAAATACCCTTAGTTTGTGAAATTACCAAAATACCCCTAATTTG-A
1 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTGTA
** * * * *
52881149 GAAATTACTGAAATACCCTCGACTTGTAAAATTACC-AAATAACCCTGATTTGTG
1 -AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTGTA
** ** * * * * **
52881203 AAATTACTGAAATACCCTTGACTTGTAAAATTACCAAAATAACCTTGGTTTACA
1 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTGTA
** *
52881257 AAATTACCAAAATACCC-CTGGTTTGTAAAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCTC-AATTTGTAAAATTACCAAAATACCCCTGATTTGTA
* * * *
52881311 AAATTATCAAAATACCCTCAGTTTGTAAAATTACTAAAATA-CCCTCAATTTGTA
1 AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCT-GATTTGTA
** * * * * * **
52881365 AAATTACTGAAATACCCTCGACTTATAAACATTACCAAAGTACCCCCGATTTACA
1 AAATTACCAAAATACCCTCAATTTGTAAA-ATTACCAAAATACCCCTGATTTGTA
52881420 AAATTA
1 AAATTA
52881426 TTGAAATACC
Statistics
Matches: 269, Mismatches: 53, Indels: 15
0.80 0.16 0.04
Matches are distributed among these distances:
53 53 0.20
54 191 0.71
55 22 0.08
56 3 0.01
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (54 bp):
AAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTGTA
Found at i:52881451 original size:27 final size:27
Alignment explanation
Indices: 52881421--52881506 Score: 154
Period size: 27 Copynumber: 3.2 Consensus size: 27
52881411 CGATTTACAA
52881421 AATTATTGAAATACCCCTATAGGGTAG
1 AATTATTGAAATACCCCTATAGGGTAG
*
52881448 AATTATCGAAATACCCCTATAGGGTAG
1 AATTATTGAAATACCCCTATAGGGTAG
*
52881475 AATTACTGAAATACCCCTATAGGGTAG
1 AATTATTGAAATACCCCTATAGGGTAG
52881502 AATTA
1 AATTA
52881507 CCGAGATACC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (27 bp):
AATTATTGAAATACCCCTATAGGGTAG
Found at i:52881526 original size:27 final size:27
Alignment explanation
Indices: 52881428--52881535 Score: 153
Period size: 27 Copynumber: 4.0 Consensus size: 27
52881418 CAAAATTATT
*
52881428 GAAATACCCCTATAGGGTAGAATTATC
1 GAAATACCCCTATAGGGTAGAATTACC
*
52881455 GAAATACCCCTATAGGGTAGAATTACT
1 GAAATACCCCTATAGGGTAGAATTACC
52881482 GAAATACCCCTATAGGGTAGAATTACC
1 GAAATACCCCTATAGGGTAGAATTACC
* * * * *
52881509 GAGATACCCTTGTGGGGTAAAATTACC
1 GAAATACCCCTATAGGGTAGAATTACC
52881536 ATTTTGCCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
GAAATACCCCTATAGGGTAGAATTACC
Found at i:52881527 original size:54 final size:54
Alignment explanation
Indices: 52881419--52881534 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
52881409 CCCGATTTAC
* *
52881419 AAAATTATTGAAATACCCCTATAGGGTAGAATTATCGAAATACCCCTATAGGGT
1 AAAATTACTGAAATACCCCTATAGGGTAGAATTACCGAAATACCCCTATAGGGT
* * * * *
52881473 AGAATTACTGAAATACCCCTATAGGGTAGAATTACCGAGATACCCTTGTGGGGT
1 AAAATTACTGAAATACCCCTATAGGGTAGAATTACCGAAATACCCCTATAGGGT
52881527 AAAATTAC
1 AAAATTAC
52881535 CATTTTGCCC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (54 bp):
AAAATTACTGAAATACCCCTATAGGGTAGAATTACCGAAATACCCCTATAGGGT
Found at i:52896509 original size:40 final size:39
Alignment explanation
Indices: 52896432--52896513 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 39
52896422 TAACGACTTA
**
52896432 TCGACTAAAATGGCACTTAGTGTACGGTTCGAAATAGCT
1 TCGACTAAAATGGCACTTAGTGTACAATTCGAAATAGCT
* * * *
52896471 TCGACTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCT
1 TCGACTAAAA-TGGCACTTAGTGTACAATTCGAAATAGCT
52896511 TCG
1 TCG
52896514 GCTATATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 10 0.28
40 26 0.72
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (39 bp):
TCGACTAAAATGGCACTTAGTGTACAATTCGAAATAGCT
Found at i:52908211 original size:29 final size:30
Alignment explanation
Indices: 52908165--52908223 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
52908155 TTCCCGAGCC
* *
52908165 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATATAATTATGCAAAAGTT
* *
52908195 TAGGGG-AAAAATATAATTTTGCCAAAGTT
1 TAGGGGCAAAAATATAATTATGCAAAAGTT
52908224 CATATTAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.41, C:0.07, G:0.24, T:0.29
Consensus pattern (30 bp):
TAGGGGCAAAAATATAATTATGCAAAAGTT
Found at i:52912133 original size:45 final size:45
Alignment explanation
Indices: 52912079--52912252 Score: 152
Period size: 50 Copynumber: 3.7 Consensus size: 45
52912069 CATGTGAGCT
* *
52912079 AGTGTAAGACCATGTCTGGGACATGGCATTGGCTTGATATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATTGACTCGATATGTGTC
* * * * *
52912124 AGTGTAAGACCATGTTTGGGATATGGCATCAGCCTCGATATAAGAGAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCAT-TGACTCGATAT----GTGTC
* * * *
52912174 AGTGTAAGACCATGTCTGGGATATGGCATCGACTCAATATTTGATTAC
1 AGTGTAAGACCATGTCTGGGACATGGCATTGACTCGATATGTG--T-C
*
52912222 A-TGGAAGACCATGTCTGGGACATTGGCATTG
1 AGTGTAAGACCATGTCTGGGACA-TGGCATTG
52912253 TATTGTGATT
Statistics
Matches: 105, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
45 28 0.27
46 8 0.08
47 20 0.19
48 9 0.09
49 8 0.08
50 32 0.30
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (45 bp):
AGTGTAAGACCATGTCTGGGACATGGCATTGACTCGATATGTGTC
Found at i:52912292 original size:43 final size:43
Alignment explanation
Indices: 52912245--52912340 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 43
52912235 TCTGGGACAT
** * *
52912245 TGGCATTGTAT-TGTGATTTCGTGTAAGACCCTATGTAGGATA
1 TGGCATTGTATATGTGATAACATGTAAGACCATATGTAGGATA
** *
52912287 GTGGCAACG-ATATGTGATAACATGTAAGACCATATTTAGGATA
1 -TGGCATTGTATATGTGATAACATGTAAGACCATATGTAGGATA
52912330 TGGCATTGTAT
1 TGGCATTGTAT
52912341 GAGCTATATG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
42 8 0.19
43 34 0.81
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.34
Consensus pattern (43 bp):
TGGCATTGTATATGTGATAACATGTAAGACCATATGTAGGATA
Found at i:52916296 original size:40 final size:39
Alignment explanation
Indices: 52916219--52916304 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 39
52916209 TAACGACTTA
* **
52916219 TCGGCCAAAATGGCACTTAGTGTGCCGTTCGAAATAGCT
1 TCGGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCT
* * *
52916258 TCGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TGGCACTTAGTGTGCAATTCGAAATAGCT
*
52916298 TTGGCTA
1 TCGGCTA
52916305 CATTTATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 9 0.23
40 30 0.77
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (39 bp):
TCGGCTAAAATGGCACTTAGTGTGCAATTCGAAATAGCT
Found at i:52925665 original size:38 final size:38
Alignment explanation
Indices: 52925618--52925695 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
52925608 TGATGTGCGA
52925618 GTAAGACTATGACATCGACATGTGACTCCGATATATGT
1 GTAAGACTATGACATCGACATGTGACTCCGATATATGT
52925656 GTAAGACTATGACATCGACATGTGACTCCGATATATGT
1 GTAAGACTATGACATCGACATGTGACTCCGATATATGT
52925694 GT
1 GT
52925696 GTGAGTAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (38 bp):
GTAAGACTATGACATCGACATGTGACTCCGATATATGT
Found at i:52936773 original size:40 final size:39
Alignment explanation
Indices: 52936714--52936920 Score: 227
Period size: 40 Copynumber: 5.2 Consensus size: 39
52936704 TGGATTACAA
* *
52936714 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA-CACTTGCACAAATGCCTTCGGGTCTTAGC
*
52936754 CCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAAC-ACTTGCACAAATGCCTTCGGGTCTTAGC
* *
52936794 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAAC-ACTTGCACAAATGCCTTCGGGTCTTAGC
* * * * * *
52936834 CCGGATGTAGTCACTAGCACAATTGCCTTCAGGTCTTAAC
1 CCGGATATA-ACACTTGCACAAATGCCTTCGGGTCTTAGC
* * * *
52936874 CCGGATATAATTACTAGCACAAATGTCTTCGGGACTTAGC
1 CCGGATATAA-CACTTGCACAAATGCCTTCGGGTCTTAGC
52936914 CC-GATAT
1 CCGGATAT
52936921 CATTCAATTG
Statistics
Matches: 142, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
39 6 0.04
40 135 0.95
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
CCGGATATAACACTTGCACAAATGCCTTCGGGTCTTAGC
Found at i:52940571 original size:14 final size:14
Alignment explanation
Indices: 52940552--52940582 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
52940542 AAGACTAAGC
52940552 GTAGTAAAGTTATT
1 GTAGTAAAGTTATT
52940566 GTAGTAAAGTTATT
1 GTAGTAAAGTTATT
52940580 GTA
1 GTA
52940583 ATTCGGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (14 bp):
GTAGTAAAGTTATT
Found at i:52944429 original size:10 final size:10
Alignment explanation
Indices: 52944407--52944458 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
52944397 AAATCTGTCG
*
52944407 AAAA-TAATC
1 AAAATTAATT
52944416 AAAATTAATT
1 AAAATTAATT
52944426 AAAATTAATTAT
1 AAAATTAA-T-T
52944438 AAAATTAATT
1 AAAATTAATT
*
52944448 AAAATTCATT
1 AAAATTAATT
52944458 A
1 A
52944459 TGTTAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 4 0.11
10 23 0.61
11 2 0.05
12 9 0.24
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATTAATT
Found at i:52944442 original size:12 final size:12
Alignment explanation
Indices: 52944416--52944448 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
52944406 GAAAATAATC
52944416 AAAATTAA-T-T
1 AAAATTAATTAT
52944426 AAAATTAATTAT
1 AAAATTAATTAT
52944438 AAAATTAATTA
1 AAAATTAATTA
52944449 AAATTCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.38
11 1 0.05
12 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATTAATTAT
Found at i:52944468 original size:22 final size:22
Alignment explanation
Indices: 52944416--52944459 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
52944406 GAAAATAATC
52944416 AAAATTAATTAAAATTAATTAT
1 AAAATTAATTAAAATTAATTAT
*
52944438 AAAATTAATTAAAATTCATTAT
1 AAAATTAATTAAAATTAATTAT
52944460 GTTAATAATA
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:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTAATTAAAATTAATTAT
Found at i:52949286 original size:43 final size:43
Alignment explanation
Indices: 52949137--52949285 Score: 147
Period size: 43 Copynumber: 3.5 Consensus size: 43
52949127 TATAAACTCA
* * * * *
52949137 GACCACTCAACGAGCTCAGATGCTCACATCTATAATGAACTTG
1 GACCACTCAATGAGCTCGGATGCTCACATATATCACGAACTTG
* **
52949180 GACCACTCAATGTGCTCGGATGC-CTTATATATCACGAACTTG
1 GACCACTCAATGAGCTCGGATGCTCACATATATCACGAACTTG
* ** * * *
52949222 GATCACTCAACAAGCTTGGATTCTCACATATATCACGAACTCG
1 GACCACTCAATGAGCTCGGATGCTCACATATATCACGAACTTG
* *
52949265 GACCGCTTAATGAGCTCGGAT
1 GACCACTCAATGAGCTCGGAT
52949286 TTCTTAATTC
Statistics
Matches: 82, Mismatches: 23, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
42 31 0.38
43 51 0.62
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (43 bp):
GACCACTCAATGAGCTCGGATGCTCACATATATCACGAACTTG
Found at i:52949790 original size:30 final size:30
Alignment explanation
Indices: 52949754--52949812 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
52949744 TTCAAAAACC
*
52949754 AAACTTTTACAAATTTACA-TTTTGACCCCT
1 AAACTTTCACAAATTTACACTTTTG-CCCCT
*
52949784 AAACTTTCACACATTTACACTTTTGCCCC
1 AAACTTTCACAAATTTACACTTTTGCCCC
52949813 AATGTTCGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.31, C:0.29, G:0.03, T:0.37
Consensus pattern (30 bp):
AAACTTTCACAAATTTACACTTTTGCCCCT
Found at i:52951274 original size:40 final size:40
Alignment explanation
Indices: 52951181--52951324 Score: 207
Period size: 40 Copynumber: 3.5 Consensus size: 40
52951171 TGAATTCTCA
* *
52951181 CACACTAAGTGCCAATACATAGCTGAAGCTATTTTAATATCG
1 CACACTAAGTGCC-ATACATAGCAGAAGCTATCTTAA-ATCG
* *
52951223 CACACTAAGTGCCATACATAGCCGAAGCTATCTCAAATCG
1 CACACTAAGTGCCATACATAGCAGAAGCTATCTTAAATCG
* * *
52951263 CACAGTAAGTGCCATACATAGCAGAAGCTATCTTGAATTG
1 CACACTAAGTGCCATACATAGCAGAAGCTATCTTAAATCG
52951303 CACACTAAGTGCCATACATAGC
1 CACACTAAGTGCCATACATAGC
52951325 TGAATTGTTA
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 60 0.65
41 20 0.22
42 13 0.14
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (40 bp):
CACACTAAGTGCCATACATAGCAGAAGCTATCTTAAATCG
Found at i:52957004 original size:27 final size:28
Alignment explanation
Indices: 52956948--52957017 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
52956938 AAATTTGTAC
52956948 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
52956976 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
52957003 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
52957018 GACTCACTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:52961473 original size:19 final size:19
Alignment explanation
Indices: 52961449--52961486 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
52961439 GGAAGTGTAC
52961449 TATAACTCTGCTGCAAATA
1 TATAACTCTGCTGCAAATA
*
52961468 TATAACTCTGTTGCAAATA
1 TATAACTCTGCTGCAAATA
52961487 CTATTTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (19 bp):
TATAACTCTGCTGCAAATA
Found at i:52967469 original size:46 final size:46
Alignment explanation
Indices: 52967402--52967509 Score: 207
Period size: 46 Copynumber: 2.3 Consensus size: 46
52967392 TAGCCAAGCT
52967402 ACTCAACGAGTTCGGACATTCGCATCCATAAGTAAACTCGGACTCA
1 ACTCAACGAGTTCGGACATTCGCATCCATAAGTAAACTCGGACTCA
*
52967448 ACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCA
1 ACTCAACGAGTTCGGACATTCGCATCCATAAGTAAACTCGGACTCA
52967494 ACTCAACGAGTTCGGA
1 ACTCAACGAGTTCGGA
52967510 TGCCCAAATA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 61 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.21
Consensus pattern (46 bp):
ACTCAACGAGTTCGGACATTCGCATCCATAAGTAAACTCGGACTCA
Found at i:52969940 original size:30 final size:30
Alignment explanation
Indices: 52969895--52969983 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
52969885 CAAAGATAAC
*
52969895 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
52969924 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
52969954 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
52969984 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 34 0.68
31 7 0.14
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:52969943 original size:15 final size:14
Alignment explanation
Indices: 52969895--52969977 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
52969885 CAAAGATAAC
*
52969895 AAGAAAACCGAATA
1 AAGAAACCCGAATA
* *
52969909 AAGAAATCCAAGATA
1 AAGAAACCCGA-ATA
*
52969924 GAGAAACCCGGAATA
1 AAGAAACCC-GAATA
*
52969939 AAGAAATCCAGAATA
1 AAGAAA-CCCGAATA
* * *
52969954 AAGAGATCCAGGATA
1 AAGA-AACCCGAATA
52969969 AAGAAACCC
1 AAGAAACCC
52969978 AAGATACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.22
15 38 0.70
16 4 0.07
ACGTcount: A:0.55, C:0.17, G:0.18, T:0.10
Consensus pattern (14 bp):
AAGAAACCCGAATA
Found at i:52969983 original size:15 final size:15
Alignment explanation
Indices: 52969906--52969983 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
52969896 AGAAAACCGA
52969906 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
52969921 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
52969935 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
52969950 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
52969966 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
52969981 ATA
1 ATA
52969984 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:52973071 original size:88 final size:89
Alignment explanation
Indices: 52972909--52973075 Score: 284
Period size: 88 Copynumber: 1.9 Consensus size: 89
52972899 CGCCCATAAG
* *
52972909 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAGTGAACTCGGACTCAACTCAA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAA
52972974 CGAGTTCGGATGCCTAGTTATTCA
66 CGAGTTCGGATGCCTAGTTATTCA
*
52972998 CGAACTCGGACTCAACTCAACGAGTTC-GACATTCGCATCCATAAGTGAACTC-GACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCAT-AGTGAACTCGGACTCAACTCA
52973061 ACGAGTTCGGATGCC
65 ACGAGTTCGGATGCC
52973076 CAAATATCCC
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
88 39 0.53
89 35 0.47
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.22
Consensus pattern (89 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTATTCA
Found at i:52974406 original size:27 final size:27
Alignment explanation
Indices: 52974350--52974470 Score: 163
Period size: 27 Copynumber: 4.5 Consensus size: 27
52974340 AAATCAAGAT
* * *
52974350 ATTACAGAAATA-CCACAGTTTGTAAA
1 ATTACCGAAATACCCCCAATTTGTAAA
52974376 ATTACCGAAATACCCCCAATTTGTAAA
1 ATTACCGAAATACCCCCAATTTGTAAA
* *
52974403 ATTACTGAAATACCCCCAGTTTGTAAA
1 ATTACCGAAATACCCCCAATTTGTAAA
**
52974430 ATTACTAAAATACCCCCAATTTGTAAA
1 ATTACCGAAATACCCCCAATTTGTAAA
*
52974457 AGTACCGAAATACC
1 ATTACCGAAATACC
52974471 TTTATAGTGT
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
26 11 0.13
27 73 0.87
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.26
Consensus pattern (27 bp):
ATTACCGAAATACCCCCAATTTGTAAA
Found at i:52974426 original size:54 final size:54
Alignment explanation
Indices: 52974350--52974470 Score: 181
Period size: 54 Copynumber: 2.3 Consensus size: 54
52974340 AAATCAAGAT
*
52974350 ATTACAGAAATA-CCACAGTTTGTAAAATTACCGAAATACCCCCAATTTGTAAA
1 ATTACAGAAATACCCACAGTTTGTAAAATTACCAAAATACCCCCAATTTGTAAA
* * *
52974403 ATTACTGAAATACCCCCAGTTTGTAAAATTACTAAAATACCCCCAATTTGTAAA
1 ATTACAGAAATACCCACAGTTTGTAAAATTACCAAAATACCCCCAATTTGTAAA
* *
52974457 AGTACCGAAATACC
1 ATTACAGAAATACC
52974471 TTTATAGTGT
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
53 11 0.18
54 50 0.82
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.26
Consensus pattern (54 bp):
ATTACAGAAATACCCACAGTTTGTAAAATTACCAAAATACCCCCAATTTGTAAA
Found at i:52974494 original size:54 final size:53
Alignment explanation
Indices: 52974356--52974499 Score: 157
Period size: 54 Copynumber: 2.7 Consensus size: 53
52974346 AGATATTACA
* * * * *
52974356 GAAATA-CCACAGTTTGTAAAATTACCGAAATACCCCCAATTTGTAAAATTACT
1 GAAATACCCCCAGTGTGTAAAATTA-CAAAATACCCCCAATTTGTAAAAGTACC
*
52974409 GAAATACCCCCAGTTTGTAAAATTACTAAAATACCCCCAATTTGTAAAAGTACC
1 GAAATACCCCCAGTGTGTAAAATTAC-AAAATACCCCCAATTTGTAAAAGTACC
***
52974463 GAAATACCTTTA-TAGTGTAAAATTATCAAAATACCCC
1 GAAATACCCCCAGT-GTGTAAAATTA-CAAAATACCCC
52974500 TGTAGGGTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
53 8 0.10
54 70 0.89
55 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.28
Consensus pattern (53 bp):
GAAATACCCCCAGTGTGTAAAATTACAAAATACCCCCAATTTGTAAAAGTACC
Found at i:52977005 original size:23 final size:23
Alignment explanation
Indices: 52976975--52977021 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
52976965 TCAAACTTTC
52976975 ATAATTCATCATTTAACATCACA
1 ATAATTCATCATTTAACATCACA
52976998 ATAATTCATCATTTAACATCACA
1 ATAATTCATCATTTAACATCACA
52977021 A
1 A
52977022 CACTCATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (23 bp):
ATAATTCATCATTTAACATCACA
Found at i:52979749 original size:29 final size:28
Alignment explanation
Indices: 52979689--52979766 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 28
52979679 CATACATGCT
*
52979689 TATGGCCCACTAGGCCCAATCTCATTCA
1 TATGGCCCACTAGGCCCAATCACATTCA
* *
52979717 TATGGCCTATTAGGCCCAAATCACA-TCTA
1 TATGGCCCACTAGGCCC-AATCACATTC-A
*
52979746 TATGG-CCACTA-GACCAATCAC
1 TATGGCCCACTAGGCCCAATCAC
52979767 TTTTATAGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 6 0.14
27 3 0.07
28 21 0.50
29 12 0.29
ACGTcount: A:0.29, C:0.32, G:0.14, T:0.24
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACATTCA
Found at i:52979999 original size:16 final size:16
Alignment explanation
Indices: 52979978--52980044 Score: 107
Period size: 16 Copynumber: 4.2 Consensus size: 16
52979968 GTAGCCAAAC
52979978 TTTCAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
*
52979994 TTTCAGCTTTTCGGTA
1 TTTCAGCTTTTCGGCA
*
52980010 TTTTAGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
*
52980026 TTTCAGCTTTTCGGGA
1 TTTCAGCTTTTCGGCA
52980042 TTT
1 TTT
52980045 GCCGATCTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.49
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:52984618 original size:22 final size:22
Alignment explanation
Indices: 52984593--52984668 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
52984583 AGATATGTAT
52984593 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * ***
52984615 ATGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCCG-AA-TGGCCA
52984639 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
52984662 ATGTGAT
1 ATGTGAT
52984669 GAATGTGAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 15 0.38
23 8 0.21
24 8 0.21
25 8 0.21
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:52984643 original size:25 final size:25
Alignment explanation
Indices: 52984615--52984693 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
52984605 CGAATGGCCA
52984615 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* * ***
52984640 ATGTGAT-AAGGCCG-AA-TGGCCA-
1 ATGTGATGAATG-TGAAAGTGTATAT
*
52984662 ATGTGATGAATGTGAAAGTATATAT
1 ATGTGATGAATGTGAAAGTGTATAT
52984687 ATGTGAT
1 ATGTGAT
52984694 AGGGCCAAGT
Statistics
Matches: 38, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
22 8 0.21
23 8 0.21
24 7 0.18
25 15 0.39
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:52984643 original size:47 final size:47
Alignment explanation
Indices: 52984590--52984884 Score: 484
Period size: 47 Copynumber: 6.3 Consensus size: 47
52984580 ACAAGATATG
52984590 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
52984637 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
52984684 TATATGTGATAGGGCC-AAGTGGCCAACGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAA-TGGCCAATGTGATGAATGTGAAAGTGTA
* *
52984731 GATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTATA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* **
52984778 TATATGTGATAGGGCCGAGCGGCCAATGTGATGAATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
52984825 TATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
52984872 TAAATGTGATAAG
1 TATATGTGATAAG
52984885 TCCCGAAGGG
Statistics
Matches: 228, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
46 2 0.01
47 224 0.98
48 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.27
Consensus pattern (47 bp):
TATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:52986706 original size:28 final size:28
Alignment explanation
Indices: 52986674--52986743 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
52986664 AATGAGATTG
*
52986674 GCACTAAGTGTGCGAGTTTAATT-GTATA
1 GCACTAAGTGTGCGAGTTTAATTATTA-A
* *
52986702 GCACTAAGTGTACGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTATTAA
52986730 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
52986744 GACTTACTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 35 0.95
29 2 0.05
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATTAA
Found at i:52990763 original size:40 final size:39
Alignment explanation
Indices: 52990719--52990929 Score: 246
Period size: 40 Copynumber: 5.3 Consensus size: 39
52990709 GCACAAACGT
* * **
52990719 CTTCGGGTCTTAGCCCGG-ATATAGCAACTCATACATATGC
1 CTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACA-ATGC
52990759 CTTCGGGACTTAGCCCGGAATTAGTAACTCGCACCAATGC
1 CTTCGGGACTTAGCCCGGAATTAGTAACTCGCA-CAATGC
* *
52990799 CTTCGGGACTTGGCCCGGAATTAGTATCTCGCACAATTGC
1 CTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAA-TGC
52990839 CTTCGGGACTTAGCCCGG-ATGTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCAC-AATGC
* * * *
52990879 CTTCGGGACTTAGCCCGGAATTAATCACTAGCACAAATGT
1 CTTCGGGACTTAGCCCGGAATTAGTAACTCGCAC-AATGC
*
52990919 CTTCGGAACTT
1 CTTCGGGACTT
52990930 GACCCCATTA
Statistics
Matches: 152, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
39 5 0.03
40 139 0.91
41 8 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAATGC
Found at i:52998956 original size:40 final size:40
Alignment explanation
Indices: 52998883--52999146 Score: 281
Period size: 40 Copynumber: 6.7 Consensus size: 40
52998873 CGGATATAAC
* * * *
52998883 CACTCGCAC-AAGGCCGTCGGGTCTTAGCCCGG-ATATGGT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT
* * * *
52998922 CACTAGCACAAATGTCTTCGTGTCTTAGCCCGG-ATATAG-
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT
*
52998961 CAACTCGGACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
1 C-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
* * *
52999002 AACTCGCACCAATGCCTTCGGGACTTGGCCCGGAATTAGT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
*
52999042 -ATCTCGCACAATTGCCTTCGGGACTTAGCCCGG-ATGTAGT
1 CA-CTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT
* *
52999082 AACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAAT
1 CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
* *
52999122 CACTAGC-CAAATGTCTTCGGGACTT
1 CACTCGCACAAATGCCTTCGGGACTT
52999147 GACGCCGTTA
Statistics
Matches: 194, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
39 29 0.15
40 160 0.82
41 5 0.03
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
Found at i:52999070 original size:120 final size:119
Alignment explanation
Indices: 52998927--52999147 Score: 325
Period size: 120 Copynumber: 1.8 Consensus size: 119
52998917 ATGGTCACTA
* * * *
52998927 GCACAAATGTCTTCGTGTCTTAGCCCGGATATAGCAACTCGGACAAATGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCC
* * *
52998992 CGGAATTAGTAACTCGCACCAATGCCTTCGGGACTTGGCCCGGAATTAGTATCTC
66 CGGAATTAATAACTAGC-CAAATGCCTTCGGGACTTGGCCCGGAATTAGTATCTC
* * *
52999047 GCACAATTGCCTTCGGGACTTAGCCCGGATGTAGTAACTCGCACAAATGCCTTCGGGACTTAGCC
1 GCACAAATGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCC
* *
52999112 CGGAATTAATCACTAGCCAAATGTCTTCGGGACTTG
66 CGGAATTAATAACTAGCCAAATGCCTTCGGGACTTG
52999148 ACGCCGTTAG
Statistics
Matches: 89, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
119 17 0.19
120 72 0.81
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (119 bp):
GCACAAATGCCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCC
CGGAATTAATAACTAGCCAAATGCCTTCGGGACTTGGCCCGGAATTAGTATCTC
Found at i:53004852 original size:2 final size:2
Alignment explanation
Indices: 53004845--53004870 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53004835 CACATTCGGC
53004845 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
53004871 AATGTATGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53005491 original size:28 final size:28
Alignment explanation
Indices: 53005424--53005493 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
53005414 AATGAGATTG
*
53005424 GCACTAAGTGTACGAGTTTAATTGTATA
1 GCACTAAGTGTGCGAGTTTAATTGTATA
* *
53005452 GCACTAAGTGTGCGAGTTTGATTAT-TAA
1 GCACTAAGTGTGCGAGTTTAATTGTAT-A
53005480 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
53005494 GACTTACTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTGTATA
Found at i:53009406 original size:29 final size:29
Alignment explanation
Indices: 53009347--53009449 Score: 109
Period size: 29 Copynumber: 3.6 Consensus size: 29
53009337 GTGACGAGAT
* * * *
53009347 TGGCACTGAGTGTGTGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* *
53009376 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGGAATATA
* * *
53009405 TGGCACTATGTGTGCGGGCTT-GAATCACA
1 TGGCACTAAGTGTGCGAGCTTGGAAT-ATA
53009434 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
53009450 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 3 0.05
29 58 0.95
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGGAATATA
Found at i:53012830 original size:29 final size:29
Alignment explanation
Indices: 53012798--53012870 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
53012788 CTTCGAGCTC
* *
53012798 GCACACCCAGTGCCGTCTATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
** *
53012827 GCACACTTAGTGCCATATATTTCTAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
53012856 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
53012871 ATCTCGTCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.25, C:0.32, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:53020635 original size:29 final size:29
Alignment explanation
Indices: 53020620--53020704 Score: 161
Period size: 29 Copynumber: 2.9 Consensus size: 29
53020610 CAGTGCTGTC
53020620 TATTTCCAGCATGCACACTTAGTGCCATA
1 TATTTCCAGCATGCACACTTAGTGCCATA
53020649 TATTTCCAGCATGCACACTTAGTGCCATA
1 TATTTCCAGCATGCACACTTAGTGCCATA
*
53020678 TATTTCCAGCATGCACAGTTAGTGCCA
1 TATTTCCAGCATGCACACTTAGTGCCA
53020705 ATCTCATCAC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (29 bp):
TATTTCCAGCATGCACACTTAGTGCCATA
Found at i:53023324 original size:22 final size:22
Alignment explanation
Indices: 53023299--53023342 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
53023289 AATTATTAAC
*
53023299 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTTTAATTAATTTT
* *
53023321 ATAATAAATTTTGATTATTTTT
1 ATAATAAATTTTAATTAATTTT
53023343 TATTATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
ATAATAAATTTTAATTAATTTT
Found at i:53032140 original size:49 final size:49
Alignment explanation
Indices: 53032075--53032442 Score: 646
Period size: 49 Copynumber: 7.5 Consensus size: 49
53032065 TACATATATG
* *
53032075 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATA
* *
53032124 TGTGATGAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATA
*
53032173 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATA
53032222 TGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATA
*
53032271 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATA
*
53032320 TGTGATGAGTCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATA
* *
53032369 TGTGATGAGGCCTAATGGCCGATGTGGTGAACGTGAAACTGTATGTATA
1 TGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATA
*
53032418 TGTGATGAGGCCTAATGGCCAATGT
1 TGTGATGAGGCCTAATGGCCGATGT
53032443 AAAATATATG
Statistics
Matches: 306, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 306 1.00
ACGTcount: A:0.28, C:0.10, G:0.33, T:0.30
Consensus pattern (49 bp):
TGTGATGAGGCCTAATGGCCGATGTGATGAACGTGAAAGTGTATGTATA
Found at i:53032587 original size:37 final size:37
Alignment explanation
Indices: 53032544--53032621 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
53032534 GTTCCGGGCG
53032544 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
53032581 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
53032618 AGAC
1 AGAC
53032622 TTCTTTTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.28, C:0.19, G:0.32, T:0.21
Consensus pattern (37 bp):
AGACCCGATGACTACGTGTGGAGATTATGACCGGGTA
Found at i:53036145 original size:8 final size:8
Alignment explanation
Indices: 53036132--53036184 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
53036122 AACGCCCCAA
*
53036132 AAATCCCG
1 AAATCCAG
*
53036140 AAATCCCG
1 AAATCCAG
*
53036148 AAATCCAA
1 AAATCCAG
*
53036156 AAATCCTG
1 AAATCCAG
*
53036164 AAATCCAA
1 AAATCCAG
*
53036172 AAATCCTG
1 AAATCCAG
53036180 AAATC
1 AAATC
53036185 TTTAATTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.47, C:0.28, G:0.08, T:0.17
Consensus pattern (8 bp):
AAATCCAG
Found at i:53036153 original size:16 final size:16
Alignment explanation
Indices: 53036140--53036184 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
53036130 AAAAATCCCG
*
53036140 AAATCCCGAAATCCAA
1 AAATCCTGAAATCCAA
53036156 AAATCCTGAAATCCAA
1 AAATCCTGAAATCCAA
53036172 AAATCCTGAAATC
1 AAATCCTGAAATC
53036185 TTTAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.49, C:0.27, G:0.07, T:0.18
Consensus pattern (16 bp):
AAATCCTGAAATCCAA
Found at i:53036184 original size:24 final size:24
Alignment explanation
Indices: 53036128--53036177 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
53036118 GTGTAACGCC
**
53036128 CCAAAAATCCCGAAATCCCGAAAT
1 CCAAAAATCCCGAAATCCAAAAAT
*
53036152 CCAAAAATCCTGAAATCCAAAAAT
1 CCAAAAATCCCGAAATCCAAAAAT
53036176 CC
1 CC
53036178 TGAAATCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.32, G:0.06, T:0.14
Consensus pattern (24 bp):
CCAAAAATCCCGAAATCCAAAAAT
Done.