Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 97507971
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: 97507971
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 232 characters in sequence are not A, C, G, or T
File 143 of 328
Found at i:41690902 original size:40 final size:40
Alignment explanation
Indices: 41690857--41691023 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
41690847 CGGAATATAA
*
41690857 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-AGCACAAATGCCTTCGGGTCTTAGC
* ** * *
41690897 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
41690937 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * *
41690977 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
41691016 CCGGATAT
1 CCGGATAT
41691024 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 13 0.12
40 91 0.87
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41691007 original size:80 final size:79
Alignment explanation
Indices: 41690873--41691023 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
41690863 ATAACCATGT
*
41690873 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGG-CTTAGCC
41690938 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
41690953 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGCTTAGC
41691016 CCGGATAT
64 CCGGATAT
41691024 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:41696635 original size:27 final size:28
Alignment explanation
Indices: 41696579--41696648 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
41696569 AAATTTGTAC
41696579 AGCACTAAGTGTGCGAGTTTGATCATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
41696607 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
41696634 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
41696649 GACTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 24 0.59
28 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:41696659 original size:27 final size:27
Alignment explanation
Indices: 41696579--41696660 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
41696569 AAATTTGTAC
* *
41696579 AGCACTAAGTGTGCGAGTTTGA-TCATAT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
41696607 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
41696634 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
41696661 GCTTTTGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.61
28 18 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:41706276 original size:51 final size:51
Alignment explanation
Indices: 41706202--41706304 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
41706192 AATAATTAAG
41706202 TTGTTAAATTTCAGCTTTAAAAGTTAGCAAGTAAATTAAATGGACATAATA
1 TTGTTAAATTTCAGCTTTAAAAGTTAGCAAGTAAATTAAATGGACATAATA
*
41706253 TTGTTAAATTTCAGCTTTGAAAGTTAGCAAGTAAATTAAATGGACATAATA
1 TTGTTAAATTTCAGCTTTAAAAGTTAGCAAGTAAATTAAATGGACATAATA
41706304 T
1 T
41706305 AGTGGTACCA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.36
Consensus pattern (51 bp):
TTGTTAAATTTCAGCTTTAAAAGTTAGCAAGTAAATTAAATGGACATAATA
Found at i:41707851 original size:40 final size:38
Alignment explanation
Indices: 41707802--41707909 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
41707792 ATCACGATTT
*
41707802 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
41707842 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
41707882 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
41707910 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:41707869 original size:80 final size:80
Alignment explanation
Indices: 41707761--41707909 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
41707751 TATGGTAACC
* * * *
41707761 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
41707825 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
41707841 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
41707906 CCGG
66 CCGG
41707910 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:41715945 original size:80 final size:80
Alignment explanation
Indices: 41715861--41716009 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
41715851 TATGGTAACC
* * * *
41715861 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
41715925 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
41715941 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
41716006 CCGG
66 CCGG
41716010 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:41715951 original size:40 final size:38
Alignment explanation
Indices: 41715902--41716009 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
41715892 ATCACGATTT
*
41715902 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
41715942 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
41715982 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
41716010 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:41717741 original size:29 final size:29
Alignment explanation
Indices: 41717708--41717781 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
41717698 CCTTCGAGCT
41717708 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
41717737 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
41717766 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
41717782 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:41717742 original size:58 final size:58
Alignment explanation
Indices: 41717649--41717781 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
41717639 ATACTCGATT
* * * * *
41717649 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
* * * ** * *
41717707 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACACAGTGCCATACACTTCCAGC
*
41717765 ACGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
41717782 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (58 bp):
TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
Found at i:41725605 original size:29 final size:29
Alignment explanation
Indices: 41725572--41725645 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
41725562 CCTTCGAGCT
41725572 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
41725601 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
41725630 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
41725646 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:41725606 original size:58 final size:58
Alignment explanation
Indices: 41725513--41725645 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
41725503 ATACTCGATT
* * * * *
41725513 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
* * * ** * *
41725571 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACACAGTGCCATACACTTCCAGC
*
41725629 ACGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
41725646 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (58 bp):
TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
Found at i:41733484 original size:29 final size:29
Alignment explanation
Indices: 41733451--41733524 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
41733441 CCTTCGAGCT
41733451 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
41733480 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
41733509 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
41733525 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:41733485 original size:58 final size:58
Alignment explanation
Indices: 41733392--41733524 Score: 133
Period size: 58 Copynumber: 2.3 Consensus size: 58
41733382 ATACTCGATT
* * * * *
41733392 TCGCACACTTAGTGCCATGCGATTTAAGCCCGCACACACAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
* * * ** * *
41733450 TCGCACACTTAGTGCCAT-ATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGC
1 TCGCACACTTAGTGCCATGAGATTT-AAGCACGCACACACAGTGCCATACACTTCCAGC
*
41733508 ACGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
41733525 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
57 4 0.07
58 57 0.93
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (58 bp):
TCGCACACTTAGTGCCATGAGATTTAAGCACGCACACACAGTGCCATACACTTCCAGC
Found at i:41739515 original size:49 final size:49
Alignment explanation
Indices: 41739408--41739581 Score: 238
Period size: 49 Copynumber: 3.7 Consensus size: 49
41739398 GACGTAAGCC
*
41739408 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CT-GCAATATG-T-G-T
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCG-AAGATGATAGCT
41739451 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAAGATGATAGCT
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAAGATGATAGCT
* *
41739501 AGTGTAAGACCATGTCTGGGACATGGGATCAGCCTCGAAGATGATAGC-
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAAGATGATAGCT
*
41739549 AGTGTAAGACCATGTCTGAGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
41739582 ACCTTACCCA
Statistics
Matches: 117, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
44 9 0.08
45 14 0.12
46 7 0.06
47 7 0.06
48 32 0.27
49 47 0.40
50 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAAGATGATAGCT
Found at i:41746622 original size:30 final size:30
Alignment explanation
Indices: 41746588--41746645 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
41746578 TTTTTGAGGA
41746588 TAGGGGCAAAATGGTCATTTTGCCAAAGTC
1 TAGGGGCAAAATGGTCATTTTGCCAAAGTC
41746618 TAGGGGCAAAATGGTCATTTTGCCAAAG
1 TAGGGGCAAAATGGTCATTTTGCCAAAG
41746646 GTGTAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.26
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTGCCAAAGTC
Found at i:41747098 original size:46 final size:46
Alignment explanation
Indices: 41746970--41747134 Score: 188
Period size: 46 Copynumber: 3.5 Consensus size: 46
41746960 TGTGAGCTAA
* * * * *
41746970 TGTAAAACATGTCTGGGACATGCATCAGCCACAATATGAGAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCGGCCTCAAGAGGAGAGCCAG
* * * * *
41747016 TGTAAGACCATGTCTGAGACGTGGCATCGGCATCAAGAGGAGTGCTAG
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCAAGAGGAGAGCCAG
*
41747064 TGTAAGACATGTCTGGGACATGCATCGGCCTCAAGACGTA-AGCCAG
1 TGTAAGACATGTCTGGGACATGCATCGGCCTCAAGA-GGAGAGCCAG
*
41747110 TGTAAGACATGTCCGGGACATGCAT
1 TGTAAGACATGTCTGGGACATGCAT
41747135 TAGTAGCGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
46 48 0.48
47 26 0.26
48 25 0.25
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCTCAAGAGGAGAGCCAG
Found at i:41754758 original size:93 final size:93
Alignment explanation
Indices: 41754629--41754800 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
41754619 CGCCCATAAG
* * *
41754629 CGAACTCGGACTCAACTCAATAAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
41754694 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
41754722 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
41754787 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
41754801 TCAACCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACAAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:41754797 original size:46 final size:46
Alignment explanation
Indices: 41754622--41754797 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
41754612 TGTAACCCGC
** * * *
41754622 CCATAAGCGAACTCGGACTCAACTCAATAAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
41754668 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
41754718 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
41754761 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
41754798 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:41754816 original size:46 final size:44
Alignment explanation
Indices: 41754673--41754816 Score: 141
Period size: 46 Copynumber: 3.1 Consensus size: 44
41754663 CGCATCCATA
41754673 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT
* * * *
41754720 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCT
41754766 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CT
41754812 AGTGA
1 AGTGA
41754817 CATGTCACTT
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
44 9 0.11
45 1 0.01
46 33 0.41
47 31 0.39
48 1 0.01
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCT
Found at i:41756168 original size:46 final size:48
Alignment explanation
Indices: 41756097--41756295 Score: 146
Period size: 46 Copynumber: 4.2 Consensus size: 48
41756087 CACAAGTGCT
* *
41756097 AGTGTAAGATATGTCTAGGACAT-GCATTGGC-CTCAAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATAGCATTGGCACT-AAGATGTAGAGCC
* * * *
41756143 AGTGTAAGACATGTCTGGGAAAT-GCATTGGCAGTGAGATGT---GTC
1 AGTGTAAGACATGTCTGGGACATAGCATTGGCACTAAGATGTAGAGCC
** *** *
41756187 AGTGTAAGACCATGTCTGGGACATAGCATCAGCACTTTTATGTGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACATAGCATTGGCACTAAGATGT-AGAGCC
* * *
41756237 AGTGTAAGACCATGTCCGAGACATAGCATTGGC-CTCAAAGATG-ATAGCC
1 AGTGTAAGA-CATGTCTGGGACATAGCATTGGCACT--AAGATGTAGAGCC
41756286 AGTGTAAGAC
1 AGTGTAAGAC
41756296 CATCTCCGAG
Statistics
Matches: 120, Mismatches: 24, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
44 11 0.09
45 13 0.11
46 46 0.38
47 1 0.01
48 1 0.01
49 15 0.12
50 30 0.25
51 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATAGCATTGGCACTAAGATGTAGAGCC
Found at i:41756363 original size:49 final size:49
Alignment explanation
Indices: 41756186--41756350 Score: 177
Period size: 49 Copynumber: 3.3 Consensus size: 49
41756176 TGAGATGTGT
* * * *** * *
41756186 CAGTGTAAGACCATGTCTGGGACATAGCATCAGCACTTTTATGTGAGAGC
1 CAGTGTAAGACCATGTCCGAGACATAGCATCGGC-CTCAAATATGATAGC
* * *
41756236 TAGTGTAAGACCATGTCCGAGACATAGCATTGGCCTCAAAGATGATAGC
1 CAGTGTAAGACCATGTCCGAGACATAGCATCGGCCTCAAATATGATAGC
* * *
41756285 CAGTGTAAGACCATCTCCGAGACATGGCATCGGCCTCGAATATGATAGC
1 CAGTGTAAGACCATGTCCGAGACATAGCATCGGCCTCAAATATGATAGC
* *
41756334 CAATATAAGACCATGTC
1 CAGTGTAAGACCATGTC
41756351 TGGGACATGG
Statistics
Matches: 95, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
49 66 0.69
50 29 0.31
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (49 bp):
CAGTGTAAGACCATGTCCGAGACATAGCATCGGCCTCAAATATGATAGC
Found at i:41759693 original size:55 final size:55
Alignment explanation
Indices: 41759612--41759726 Score: 176
Period size: 55 Copynumber: 2.1 Consensus size: 55
41759602 TGGTCGAGAA
* ** *
41759612 AGAAAAATTTTAGTGTACAAGGCCGGGTAGTATGGCTACAAAAGGGAGACATTCG
1 AGAAAAATTTCAAAGTACAAGGCCGGGTAGTACGGCTACAAAAGGGAGACATTCG
* *
41759667 AGAAAAATTTCAAAGTACAAGGCCGGGTAGTACGGTTACAAAAGGGAGACCTTCG
1 AGAAAAATTTCAAAGTACAAGGCCGGGTAGTACGGCTACAAAAGGGAGACATTCG
41759722 AGAAA
1 AGAAA
41759727 TGGCAGTAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.39, C:0.14, G:0.28, T:0.19
Consensus pattern (55 bp):
AGAAAAATTTCAAAGTACAAGGCCGGGTAGTACGGCTACAAAAGGGAGACATTCG
Found at i:41762263 original size:29 final size:29
Alignment explanation
Indices: 41762229--41762333 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
41762219 TACTCGATTT
* * *
41762229 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
41762258 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
41762287 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
41762316 TGCACACTTAGTGCCATA
1 CGCACACTTAGTGCCATA
41762334 TATTTCCAGC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:41762321 original size:58 final size:59
Alignment explanation
Indices: 41762267--41762389 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 59
41762257 CCGCACACAC
* *
41762267 AGTGCCATACCCTTCGAGC-TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
* * * *
41762325 AGTGCCATATATTTCCAGCAT-GCACACTCAGTGCCATATTTTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
41762383 AGTGCCA
1 AGTGCCA
41762390 ATCTCGTCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 57 0.98
59 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.28
Consensus pattern (59 bp):
AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
Found at i:41762334 original size:29 final size:29
Alignment explanation
Indices: 41762288--41762389 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
41762278 CTTCGAGCTC
41762288 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41762317 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
* *
41762346 GCACACTCAGTGCCATATTTTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41762375 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
41762390 ATCTCGTCAC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:41770249 original size:29 final size:29
Alignment explanation
Indices: 41770187--41770252 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
41770177 ATACTCGATT
* * *
41770187 TCGCACACTTAGTGCCATGCGATTTAAGC
1 TCGCACACATAGTGCCATGCCATTCAAGC
* * *
41770216 CCGCACACATAGTGCCATGCCCTTCGAGC
1 TCGCACACATAGTGCCATGCCATTCAAGC
41770245 TCGCACAC
1 TCGCACAC
41770253 TTAGCAACCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (29 bp):
TCGCACACATAGTGCCATGCCATTCAAGC
Found at i:41772533 original size:29 final size:29
Alignment explanation
Indices: 41772499--41772603 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
41772489 TACTCGATTT
* * *
41772499 CGCACACTTAGTGCCATGCGATTTAAGCC
1 CGCACACTTAGTGCCATACCATTCAAGCC
** * * *
41772528 CGCACACACAGTGCCATACCCTTCGAGCT
1 CGCACACTTAGTGCCATACCATTCAAGCC
* * *
41772557 CGCACACTTAGTGCCATA-TATTTCCAGCA
1 CGCACACTTAGTGCCATACCA-TTCAAGCC
*
41772586 TGCACACTTAGTGCCATA
1 CGCACACTTAGTGCCATA
41772604 TATTTCCAGC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACCATTCAAGCC
Found at i:41772591 original size:58 final size:59
Alignment explanation
Indices: 41772537--41772659 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 59
41772527 CCGCACACAC
* *
41772537 AGTGCCATACCCTTCGAGC-TCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
* * * *
41772595 AGTGCCATATATTTCCAGCAT-GCACACTCAGTGCCATATTTTTCCAGCATGCACACTT
1 AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
41772653 AGTGCCA
1 AGTGCCA
41772660 ATCTCGTCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 57 0.98
59 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.28
Consensus pattern (59 bp):
AGTGCCATACACTTCCAGCATCGCACACTTAGTGCCATATATTTCCAGCATGCACACTT
Found at i:41772604 original size:29 final size:29
Alignment explanation
Indices: 41772558--41772659 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
41772548 CTTCGAGCTC
41772558 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41772587 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
* *
41772616 GCACACTCAGTGCCATATTTTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41772645 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
41772660 ATCTCGTCAC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:41783853 original size:25 final size:25
Alignment explanation
Indices: 41783800--41783927 Score: 102
Period size: 25 Copynumber: 5.1 Consensus size: 25
41783790 ATGTCATTAG
* *
41783800 GCTTACCAAT-TTCATCTCTTATGA
1 GCTTACCAATATTCAGCTCGTATGA
*
41783824 GCTTACCAATACTCAGCTCGTATGA
1 GCTTACCAATATTCAGCTCGTATGA
* * *
41783849 GCTTACCATTATTCAGCTCGAAAAAGGA
1 GCTTACCAATATTCAGCTCG---TATGA
* *
41783877 GCTTACCATTATTCAGCTTAG-ATGA
1 GCTTACCAATATTCAGC-TCGTATGA
*
41783902 GCTTACC-GT-TTACAGCTCGTATGA
1 GCTTACCAATATT-CAGCTCGTATGA
41783926 GC
1 GC
41783928 ATACATGTAC
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
23 4 0.05
24 21 0.24
25 39 0.45
28 20 0.23
29 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (25 bp):
GCTTACCAATATTCAGCTCGTATGA
Found at i:41791340 original size:25 final size:24
Alignment explanation
Indices: 41791305--41791352 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
41791295 CACTTTTGTC
41791305 TTTATTTATCTTC-TTTAAGTACTT
1 TTTATTTATCTTCATTTAA-TACTT
41791329 TTTATTTTATCTTCATTTAATACT
1 TTTA-TTTATCTTCATTTAATACT
41791353 GTGTCATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 13 0.59
26 5 0.23
ACGTcount: A:0.23, C:0.12, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTATTTATCTTCATTTAATACTT
Found at i:41791361 original size:26 final size:25
Alignment explanation
Indices: 41791309--41791362 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
41791299 TTTGTCTTTA
* *
41791309 TTTATCTTCTTTAAGTACTTTTTAT
1 TTTATCTTCTTTAAGTACTTGTCAT
41791334 TTTATCTTCATTTAA-TACTGTGTCAT
1 TTTATCTTC-TTTAAGTACT-TGTCAT
41791360 TTT
1 TTT
41791363 TAGGTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.20, C:0.13, G:0.06, T:0.61
Consensus pattern (25 bp):
TTTATCTTCTTTAAGTACTTGTCAT
Found at i:41792955 original size:23 final size:23
Alignment explanation
Indices: 41792925--41792972 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
41792915 AATGCTCAAC
41792925 TTGGAATGTTTGAACCTTTGATA
1 TTGGAATGTTTGAACCTTTGATA
41792948 TTGGAATGTTTGAACCTTTGATA
1 TTGGAATGTTTGAACCTTTGATA
41792971 TT
1 TT
41792973 CTTCTAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.46
Consensus pattern (23 bp):
TTGGAATGTTTGAACCTTTGATA
Found at i:41816988 original size:27 final size:27
Alignment explanation
Indices: 41816950--41817107 Score: 129
Period size: 27 Copynumber: 5.9 Consensus size: 27
41816940 GTCATTAAGA
41816950 ATTTGTAAAATTACCAAAATACCCCTG
1 ATTTGTAAAATTACCAAAATACCCCTG
*
41816977 ATTTGTGAAATTACCAAAATACCTCC-G
1 ATTTGTAAAATTACCAAAATACC-CCTG
** ** *
41817004 GGTCATAAAATTACCGAAATACCCCTG
1 ATTTGTAAAATTACCAAAATACCCCTG
* * * ** * *
41817031 ACTTGTGAAACTACTGAAATACCTCTA
1 ATTTGTAAAATTACCAAAATACCCCTG
* * *
41817058 ATTTTTAAAATTATCGAAATACCCCTG
1 ATTTGTAAAATTACCAAAATACCCCTG
* * *
41817085 GTTTGTAAAATGACCATAATACC
1 ATTTGTAAAATTACCAAAATACC
41817108 TCTTTAGGGT
Statistics
Matches: 99, Mismatches: 30, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
26 2 0.02
27 95 0.96
28 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.30
Consensus pattern (27 bp):
ATTTGTAAAATTACCAAAATACCCCTG
Found at i:41817037 original size:54 final size:54
Alignment explanation
Indices: 41816955--41817109 Score: 166
Period size: 54 Copynumber: 2.9 Consensus size: 54
41816945 TAAGAATTTG
* **
41816955 TAAAATTACCAAAATACCCCTGATTTGTGAAATTACCAAAATACCTCCGGGTCA
1 TAAAATTACCGAAATACCCCTGATTTGTGAAATTACCAAAATACCTCCAAGTCA
* * ** * * **
41817009 TAAAATTACCGAAATACCCCTGACTTGTGAAACTACTGAAATACCTCTAATTTT
1 TAAAATTACCGAAATACCCCTGATTTGTGAAATTACCAAAATACCTCCAAGTCA
* * * * *
41817063 TAAAATTATCGAAATACCCCTGGTTTGTAAAATGACCATAATACCTC
1 TAAAATTACCGAAATACCCCTGATTTGTGAAATTACCAAAATACCTC
41817110 TTTAGGGTAA
Statistics
Matches: 81, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 81 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCCTGATTTGTGAAATTACCAAAATACCTCCAAGTCA
Found at i:41817119 original size:27 final size:27
Alignment explanation
Indices: 41817089--41817152 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
41817079 CCCCTGGTTT
* *
41817089 GTAAAATGACCATAATACCTCTTTAGG
1 GTAAAATGACCATAATACCCCTGTAGG
* *
41817116 GTAAAATGACCGTAATACCCCTGTATG
1 GTAAAATGACCATAATACCCCTGTAGG
41817143 GTAAAATGAC
1 GTAAAATGAC
41817153 AATTATGCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (27 bp):
GTAAAATGACCATAATACCCCTGTAGG
Found at i:41817369 original size:26 final size:27
Alignment explanation
Indices: 41817308--41817371 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
41817298 GTGACTATGT
* *
41817308 CACATTCACTGATACTGGTGGCTACAC
1 CACATTTACTGATACTGATGGCTACAC
* *
41817335 CACAATTACTGATACTGATGGCT-TAC
1 CACATTTACTGATACTGATGGCTACAC
41817361 CACATTTACTG
1 CACATTTACTG
41817372 TTTCTGCCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 12 0.38
27 20 0.62
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.30
Consensus pattern (27 bp):
CACATTTACTGATACTGATGGCTACAC
Found at i:41817618 original size:33 final size:33
Alignment explanation
Indices: 41817561--41817653 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 33
41817551 GCCCACACTA
* *
41817561 TTACTGTATGGGGCTAA-AGGCCAGACTGT-TCTG
1 TTACTGTATAGGGCTAAGA-CCCAGACTGTAT-TG
41817594 TTACTGTATAGGGCTAAGACCCAGACTGTATTG
1 TTACTGTATAGGGCTAAGACCCAGACTGTATTG
* * * * *
41817627 ATACTGGATAGGACTTAGGCCCAGACT
1 TTACTGTATAGGGCTAAGACCCAGACT
41817654 ATTACTGCAG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
33 49 0.96
34 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (33 bp):
TTACTGTATAGGGCTAAGACCCAGACTGTATTG
Found at i:41821635 original size:24 final size:24
Alignment explanation
Indices: 41821608--41821670 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
41821598 CTTATTATGT
41821608 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
41821632 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
41821656 TCGCACACATAGTGC
1 TCGCACACATAGTGC
41821671 ATTTGAGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:41824405 original size:31 final size:29
Alignment explanation
Indices: 41824369--41824472 Score: 109
Period size: 29 Copynumber: 3.5 Consensus size: 29
41824359 CTTCGAGCTC
* *
41824369 GCACACCCAGTGCCGTATTTTTTTCCAGCAT
1 GCACACCCAGTGCC--ATATATTTCCAGCAT
**
41824400 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
** *
41824429 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
41824458 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
41824473 ATCTCGTCAC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
29 56 0.82
31 12 0.18
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:41824414 original size:60 final size:58
Alignment explanation
Indices: 41824339--41824472 Score: 144
Period size: 60 Copynumber: 2.3 Consensus size: 58
41824329 AATTTAAGCC
* * * * *
41824339 CGCACACATAGTGCCATACCCTTCGAGC-TCGCACACCCAGTGCCGTATTTTTTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCAT-GCACACCCAGTGCC--ATATATTTCCAGCA
* * * **
41824399 TGCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCA
41824457 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
41824473 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
58 27 0.44
60 34 0.55
61 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.27
Consensus pattern (58 bp):
CGCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCA
Found at i:41824430 original size:29 final size:29
Alignment explanation
Indices: 41824390--41824472 Score: 157
Period size: 29 Copynumber: 2.9 Consensus size: 29
41824380 GCCGTATTTT
41824390 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
41824419 TTTCCAGCATGCACACTTAGTGCCATATA
1 TTTCCAGCATGCACACTTAGTGCCATATA
*
41824448 TTTCCAGCACGCACACTTAGTGCCA
1 TTTCCAGCATGCACACTTAGTGCCA
41824473 ATCTCGTCAC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (29 bp):
TTTCCAGCATGCACACTTAGTGCCATATA
Found at i:41824597 original size:2 final size:2
Alignment explanation
Indices: 41824590--41824618 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41824580 ATACAATTTC
41824590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41824619 GCATCCATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41830241 original size:29 final size:29
Alignment explanation
Indices: 41830151--41830310 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
41830141 ACTCGATTTC
* * **
41830151 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
41830180 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
41830208 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
41830238 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41830267 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
41830296 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
41830311 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:41840681 original size:40 final size:39
Alignment explanation
Indices: 41840636--41840765 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
41840626 CGGAATATAA
41840636 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
41840676 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
41840716 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
41840756 CCGGATATAA
1 CCGGATATAA
41840766 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:41840780 original size:40 final size:40
Alignment explanation
Indices: 41840652--41840803 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
41840642 ATAACCATGT
* * *
41840652 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
41840692 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
41840732 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
41840772 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
41840804 CATTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:41840786 original size:80 final size:80
Alignment explanation
Indices: 41840652--41840801 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
41840642 ATAACCATGT
*
41840652 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
41840716 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
41840732 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
41840795 CCCGGAT
64 CCCGGAT
41840802 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:41843942 original size:18 final size:20
Alignment explanation
Indices: 41843902--41843946 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
41843892 TTGTATCTTT
41843902 TATATTATTGCTATTCATTTG
1 TATATTATTGCTATTCA-TTG
*
41843923 TATATTATT-TTATTCA-TG
1 TATATTATTGCTATTCATTG
41843941 TATATT
1 TATATT
41843947 GTCCATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
20 6 0.26
21 9 0.39
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (20 bp):
TATATTATTGCTATTCATTG
Found at i:41847416 original size:19 final size:19
Alignment explanation
Indices: 41847392--41847436 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41847382 CGACGCATTT
*
41847392 TGCATT-CATTCCATGCATC
1 TGCATTACATTACAT-CATC
*
41847411 TGCATTACATTACATCATG
1 TGCATTACATTACATCATC
41847430 TGCATTA
1 TGCATTA
41847437 GAGTCCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (19 bp):
TGCATTACATTACATCATC
Found at i:41866072 original size:44 final size:44
Alignment explanation
Indices: 41866024--41866298 Score: 173
Period size: 44 Copynumber: 6.2 Consensus size: 44
41866014 AGCCACCGGC
* * *
41866024 CTTATCTCTCTGAAGTAGAAAGGGAGCAGGCTAAAGATTGTAGT
1 CTTATCTCTCTGAAGTAGCAAGGGAGCAGACTGAAGATTGTAGT
* *
41866068 CTTATCT-TCCTGAGGTAGCAAGGGAGCAGAATGAAGATTGTAGAT
1 CTTATCTCT-CTGAAGTAGCAAGGGAGCAGACTGAAGATTGTAG-T
* * * * * ** * *
41866113 CTTGTCTCCCTGAAATAG-TAGTGGAGCAGA-TCAAAGACGGCGAAT
1 CTTATCTCTCTGAAGTAGCAAG-GGAGCAGACT-GAAGATTG-TAGT
** * ** **** *
41866158 CTTATCT-TCCCAAGGTAGCAAGGGAGCAGATTTTAGCCACTAGC
1 CTTATCTCTCTGAA-GTAGCAAGGGAGCAGACTGAAGATTGTAGT
* * *
41866202 CTTATCTCTCTGAGGTAGCAAGGGAGCAGGCTGAATATTGTAGT
1 CTTATCTCTCTGAAGTAGCAAGGGAGCAGACTGAAGATTGTAGT
* * *
41866246 CTTATCT-TCCTGAGGTAGTAAAGGAGCAGACTGAAGATTGTAGAT
1 CTTATCTCT-CTGAAGTAGCAAGGGAGCAGACTGAAGATTGTAG-T
41866291 CTTATCTC
1 CTTATCTC
41866299 CCTAAGCAGT
Statistics
Matches: 172, Mismatches: 46, Indels: 24
0.71 0.19 0.10
Matches are distributed among these distances:
43 2 0.01
44 107 0.62
45 59 0.34
46 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (44 bp):
CTTATCTCTCTGAAGTAGCAAGGGAGCAGACTGAAGATTGTAGT
Found at i:41866244 original size:178 final size:178
Alignment explanation
Indices: 41865930--41866392 Score: 685
Period size: 178 Copynumber: 2.6 Consensus size: 178
41865920 TCGGTGAATT
* * *
41865930 TAGATTTTGTCTCCCTGAAATAGCAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTCCCGAGG
1 TAGATCTTGTCTCCCTGAAATAGTAGTGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCGAGG
*
41865995 TAGCAGGGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTGAAGTAGAAAGGGAGCAGGCTAAAG
66 TAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGAAAGGGAGCAGGCTAAAG
*
41866060 ATTGTAGTCTTATCTTCCTGAGGTAGCAAGGGAGCAGAATGAAGATTG
131 ATTGTAGTCTTATCTTCCTGAGGTAGCAAAGGAGCAGAATGAAGATTG
*
41866108 TAGATCTTGTCTCCCTGAAATAGTAGTGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCAAGG
1 TAGATCTTGTCTCCCTGAAATAGTAGTGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCGAGG
* * * * * *
41866173 TAGCAAGGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAGGTAGCAAGGGAGCAGGCTGAAT
66 TAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGAAAGGGAGCAGGCTAAAG
* *
41866238 ATTGTAGTCTTATCTTCCTGAGGTAGTAAAGGAGCAGACTGAAGATTG
131 ATTGTAGTCTTATCTTCCTGAGGTAGCAAAGGAGCAGAATGAAGATTG
* ** * * * * *
41866286 TAGATCTTATCTCCCT-AAGCAGTAATGGAGTAGATCGAAGATGGCGAATCTTATCTTCCCGAGC
1 TAGATCTTGTCTCCCTGAAATAGTAGTGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCGAGG
* * * *
41866350 TAGCAGGGGAGTAGAGTTTAGCCTCCAGCCTTATCTCCCTGAA
66 TAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAA
41866393 ATTGCAGTGG
Statistics
Matches: 255, Mismatches: 30, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
177 76 0.30
178 179 0.70
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (178 bp):
TAGATCTTGTCTCCCTGAAATAGTAGTGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCGAGG
TAGCAGGGGAGCAGATTTTAGCCACCAGCCTTATCTCTCTGAAGTAGAAAGGGAGCAGGCTAAAG
ATTGTAGTCTTATCTTCCTGAGGTAGCAAAGGAGCAGAATGAAGATTG
Found at i:41866327 original size:44 final size:44
Alignment explanation
Indices: 41866224--41866315 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
41866214 AGGTAGCAAG
* * * * *
41866224 GGAGCAGGCTGAATATTGTAGTCTTATCTTCCTGAGGTAGTAAA
1 GGAGCAGACTGAAGATTGTAGTCTTATCTCCCTGAAGCAGTAAA
*
41866268 GGAGCAGACTGAAGATTGTAGATCTTATCTCCCT-AAGCAGTAAT
1 GGAGCAGACTGAAGATTGTAG-TCTTATCTCCCTGAAGCAGTAAA
41866312 GGAG
1 GGAG
41866316 TAGATCGAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 30 0.73
45 11 0.27
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (44 bp):
GGAGCAGACTGAAGATTGTAGTCTTATCTCCCTGAAGCAGTAAA
Found at i:41875007 original size:29 final size:28
Alignment explanation
Indices: 41874973--41875075 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
41874963 TACTCAATCA
*
41874973 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
41875002 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
41875031 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
41875060 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
41875076 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:41883018 original size:29 final size:28
Alignment explanation
Indices: 41882984--41883086 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
41882974 TACTCAATCA
*
41882984 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
41883013 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
41883042 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
41883071 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
41883087 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:41886395 original size:29 final size:28
Alignment explanation
Indices: 41886361--41886463 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
41886351 TACTCAATCA
*
41886361 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
41886390 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
41886419 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
41886448 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
41886464 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:41894408 original size:29 final size:28
Alignment explanation
Indices: 41894374--41894476 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
41894364 TACTCAATCA
*
41894374 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
41894403 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
41894432 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
41894461 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
41894477 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:41919523 original size:48 final size:48
Alignment explanation
Indices: 41919467--41919700 Score: 200
Period size: 48 Copynumber: 4.9 Consensus size: 48
41919457 ATGTGAGTAT
*
41919467 TGAGATCCCGTATAAGACCATATTTGGGATATGGTATTGGCATCAAGA
1 TGAGATCCCGTATAAGACCATATCTGGGATATGGTATTGGCATCAAGA
* * * *** *** * *
41919515 TGAGATCCCGTGTAAGACCGTATCTAGGATATAACACCAGCATCGATA
1 TGAGATCCCGTATAAGACCATATCTGGGATATGGTATTGGCATCAAGA
* * * *
41919563 TGAGATCCCGTATAAGACCATGTCTGGGACATGGCATTGGCATCATTG-
1 TGAGATCCCGTATAAGACCATATCTGGGATATGGTATTGGCATCA-AGA
* * * * * *
41919611 TGAGATCCCATGTAAGATCATATCTGGGATATGGTATTGGTATCGATA
1 TGAGATCCCGTATAAGACCATATCTGGGATATGGTATTGGCATCAAGA
* * * * * *
41919659 TCAGGTCCCGTCTAAGACCATGTCTGGGACATGGTATCGGCA
1 TGAGATCCCGTATAAGACCATATCTGGGATATGGTATTGGCA
41919701 CCGTTATGAA
Statistics
Matches: 140, Mismatches: 44, Indels: 4
0.74 0.23 0.02
Matches are distributed among these distances:
48 140 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (48 bp):
TGAGATCCCGTATAAGACCATATCTGGGATATGGTATTGGCATCAAGA
Found at i:41919615 original size:96 final size:96
Alignment explanation
Indices: 41919467--41919692 Score: 265
Period size: 96 Copynumber: 2.4 Consensus size: 96
41919457 ATGTGAGTAT
* * * * *
41919467 TGAGATCCCGTATAAGACCATATTTGGGATATGGTATTGGCATCAAGATGAGATCCCGTGTAAGA
1 TGAGATCCCGTATAAGACCATGTCTGGGACATGGCATTGGCATCAAGATGAGATCCCATGTAAGA
*
41919532 CCGTATCTAGGATATAACACCAGCATCGATA
66 CCATATCTAGGATATAACACCAGCATCGATA
*
41919563 TGAGATCCCGTATAAGACCATGTCTGGGACATGGCATTGGCATCATTG-TGAGATCCCATGTAAG
1 TGAGATCCCGTATAAGACCATGTCTGGGACATGGCATTGGCATCA-AGATGAGATCCCATGTAAG
* * *** *** *
41919627 ATCATATCTGGGATATGGTATTGGTATCGATA
65 ACCATATCTAGGATATAACACCAGCATCGATA
* * *
41919659 TCAGGTCCCGTCTAAGACCATGTCTGGGACATGG
1 TGAGATCCCGTATAAGACCATGTCTGGGACATGG
41919693 TATCGGCACC
Statistics
Matches: 110, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
96 109 0.99
97 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (96 bp):
TGAGATCCCGTATAAGACCATGTCTGGGACATGGCATTGGCATCAAGATGAGATCCCATGTAAGA
CCATATCTAGGATATAACACCAGCATCGATA
Found at i:41924235 original size:47 final size:48
Alignment explanation
Indices: 41924177--41924307 Score: 133
Period size: 47 Copynumber: 2.8 Consensus size: 48
41924167 GTACGAATAA
* * **
41924177 TACCTTAATTTGGCTACGGGCCATGATATAGGTATTTTGAA-A-AGAGG
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTTCCAAGATA-AGG
* ** * *
41924224 TACCTTGATTTGGTTGTGGGCCATGGTATAGGTA-CTCCAAGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTTCCAAGATAAGG
**
41924271 TACCTTGATTTGGCTACAAGCCATGGTATAGGTATTT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTT
41924308 ATCGATTATG
Statistics
Matches: 66, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
46 3 0.05
47 61 0.92
48 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (48 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTTCCAAGATAAGG
Found at i:41925304 original size:28 final size:28
Alignment explanation
Indices: 41925272--41925329 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
41925262 TACCTTACAG
** *
41925272 GTTTGACACGGCCTGGATACACGGGCGT
1 GTTTGACACAACCTGGACACACGGGCGT
*
41925300 GTTTGACACAACCTGGACATACGGGCGT
1 GTTTGACACAACCTGGACACACGGGCGT
41925328 GT
1 GT
41925330 GACTGACCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.24, G:0.33, T:0.22
Consensus pattern (28 bp):
GTTTGACACAACCTGGACACACGGGCGT
Found at i:41926519 original size:17 final size:17
Alignment explanation
Indices: 41926497--41926529 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41926487 ATTAAATGAG
41926497 TTAAATTTGTTATTATT
1 TTAAATTTGTTATTATT
41926514 TTAAATTTGTTATTAT
1 TTAAATTTGTTATTAT
41926530 AGATCAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (17 bp):
TTAAATTTGTTATTATT
Found at i:41933699 original size:40 final size:40
Alignment explanation
Indices: 41933650--41933801 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
41933640 ACAACCACAA
* * *** *
41933650 GCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
*
41933690 GCACCATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
* *
41933730 GCACGAA-TGCCTTCGGGTCTTAGCCCGGACATAATC-ACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAA-CAACTC
* * * *
41933770 GCATAAATGCCTTCGGGACTTAGCCCGAATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
41933802 CATTCAAATG
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.02
40 91 0.96
41 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
Found at i:41941677 original size:40 final size:40
Alignment explanation
Indices: 41941628--41941778 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
41941618 ACAACCACAA
* * *** *
41941628 GCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
*
41941668 GCACCATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
* *
41941708 GCACGAA-TGCCTTCGGGTCTTAGCCCGGACATAATC-ACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAA-CAACTC
* * *
41941748 GCATAAATGCCTTCGGGACTTAGCCC-GATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
41941779 CATTCAAATG
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
39 6 0.06
40 87 0.92
41 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACAACTC
Found at i:41947838 original size:47 final size:47
Alignment explanation
Indices: 41947781--41947880 Score: 193
Period size: 47 Copynumber: 2.1 Consensus size: 47
41947771 TCACGAAATC
41947781 ACGCGATCACTTTCGCATGAGAAGAATGGAAAAATACCTAAAACGAT
1 ACGCGATCACTTTCGCATGAGAAGAATGGAAAAATACCTAAAACGAT
41947828 ACGCGATCACTTTCGCATGAGAAGAATGGAAAAATACCTAAAACGAT
1 ACGCGATCACTTTCGCATGAGAAGAATGGAAAAATACCTAAAACGAT
41947875 AC-CGAT
1 ACGCGAT
41947881 GAGAGCCTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 4 0.08
47 49 0.92
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (47 bp):
ACGCGATCACTTTCGCATGAGAAGAATGGAAAAATACCTAAAACGAT
Found at i:41948759 original size:13 final size:13
Alignment explanation
Indices: 41948707--41948771 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
41948697 ATTTTAACAT
*
41948707 TTTTGTATA-ATA
1 TTTTATATATATA
* *
41948719 TTTTATATAAATG
1 TTTTATATATATA
*
41948732 TTTT-TATACATTA
1 TTTTATATATA-TA
41948745 TTTTATATATATA
1 TTTTATATATATA
*
41948758 TTATATATATATA
1 TTTTATATATATA
41948771 T
1 T
41948772 ATTCATAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
12 13 0.30
13 26 0.59
14 5 0.11
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (13 bp):
TTTTATATATATA
Found at i:41949497 original size:13 final size:13
Alignment explanation
Indices: 41949479--41949503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41949469 TATTAGGTTA
41949479 TATATTATTTTTG
1 TATATTATTTTTG
41949492 TATATTATTTTT
1 TATATTATTTTT
41949504 ATTTTTTTTG
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:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TATATTATTTTTG
Found at i:41954592 original size:40 final size:40
Alignment explanation
Indices: 41954547--41954713 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
41954537 CGGAATATAA
41954547 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
41954587 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
41954627 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * *
41954667 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
41954706 CCGGATAT
1 CCGGATAT
41954714 CATTCAATTT
Statistics
Matches: 104, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
39 14 0.13
40 90 0.87
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41962558 original size:40 final size:40
Alignment explanation
Indices: 41962513--41962679 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
41962503 CGGAATATAA
41962513 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
41962553 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
41962593 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * *
41962633 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
41962672 CCGGATAT
1 CCGGATAT
41962680 CATTCAATTT
Statistics
Matches: 104, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
39 14 0.13
40 90 0.87
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:41970781 original size:40 final size:40
Alignment explanation
Indices: 41970730--41970955 Score: 321
Period size: 40 Copynumber: 5.7 Consensus size: 40
41970720 GAATATAGCT
* *
41970730 ACTCGCTCAAATGCCTTCGGGACGTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
**
41970770 GTTCGCACAAATGCCTTCGGGACTTAGCCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
*
41970810 ACTCGCACAAATGCCTTCGGGACTTAGCTCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
41970850 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* * *
41970890 ACTAGCACAAATGCCTTCGGGACTTAGCCCGAAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
41970930 ACTAGCACAAATGCCTTTGGGACTTA
1 ACTCGCACAAATGCCTTCGGGACTTA
41970956 CCCCCATTAT
Statistics
Matches: 173, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 171 0.99
41 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:41970856 original size:80 final size:79
Alignment explanation
Indices: 41970704--41970955 Score: 321
Period size: 80 Copynumber: 3.2 Consensus size: 79
41970694 AAACCAAGTA
* * * * *
41970704 CCTTCGGGATTTA-ACCGAATATAGCTACTCGCTCAAATGCCTTCGGGACGTAGCCCGG-ATATA
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TA
**
41970767 GTAGTTCGCACAAATG
64 GTAACTCGCACAAATG
*
41970783 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTCGGAATTAG
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAG
41970848 TAACTCGCACAAATG
65 TAACTCGCACAAATG
* *
41970863 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGAAATTA
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
* *
41970927 GTCACTAGCACAAATG
64 GTAACTCGCACAAATG
*
41970943 CCTTTGGGACTTA
1 CCTTCGGGACTTA
41970956 CCCCCATTAT
Statistics
Matches: 154, Mismatches: 15, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
79 14 0.09
80 138 0.90
81 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGT
AACTCGCACAAATG
Found at i:41979937 original size:14 final size:14
Alignment explanation
Indices: 41979918--41979948 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41979908 TCTGCTTGGC
*
41979918 CGGTTCGGTTCACT
1 CGGTTCGGTTCAAT
41979932 CGGTTCGGTTCAAT
1 CGGTTCGGTTCAAT
41979946 CGG
1 CGG
41979949 ACCATTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.26, G:0.32, T:0.32
Consensus pattern (14 bp):
CGGTTCGGTTCAAT
Found at i:41983341 original size:42 final size:43
Alignment explanation
Indices: 41983241--41983399 Score: 155
Period size: 43 Copynumber: 3.7 Consensus size: 43
41983231 AGCATATACA
* * * * * *
41983241 ATGCCAACGTCCCAGACGTGGTCTTATATGTAATCAAACATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAATTAGATATCG
41983284 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATTAGATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAATTAGATATCG
** *
41983326 ATGCCAACGTCCCAGATATGGTCTTACACGCAAAATAG-TAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG-AAATTAGATA-TCG
**
41983370 ATGCCAACGTATCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
41983400 CAGAACAGAT
Statistics
Matches: 96, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
42 30 0.31
43 37 0.39
44 29 0.30
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAATTAGATATCG
Found at i:41983392 original size:44 final size:43
Alignment explanation
Indices: 41983282--41983410 Score: 129
Period size: 44 Copynumber: 3.0 Consensus size: 43
41983272 AATCAAACAT
* * *
41983282 CGATGCC-ACTGTCCCAGACAGGGTCTTACACG-AAATTAGATA
1 CGATGCCAAC-GTACCAGACATGGTCTTACACGCAAAATAGATA
* *
41983324 CGATGCCAACGTCCCAGATATGGTCTTACACGCAAAATAG-TA
1 CGATGCCAACGTACCAGACATGGTCTTACACGCAAAATAGATA
* * * *
41983366 GTCGATGCCAACGTATCAGACGTGGTCTTACACGCAGAACAGATA
1 --CGATGCCAACGTACCAGACATGGTCTTACACGCAAAATAGATA
41983411 TCGAAAATCC
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
42 29 0.40
43 8 0.11
44 34 0.47
45 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.21
Consensus pattern (43 bp):
CGATGCCAACGTACCAGACATGGTCTTACACGCAAAATAGATA
Found at i:41984833 original size:11 final size:11
Alignment explanation
Indices: 41984817--41984856 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
41984807 TCTTATCATT
41984817 ATTCATTTCCA
1 ATTCATTTCCA
41984828 ATTCATTTCCA
1 ATTCATTTCCA
* *
41984839 ATTCGTAT-CA
1 ATTCATTTCCA
41984849 ATTCATTT
1 ATTCATTT
41984857 GTTATTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.28, C:0.23, G:0.03, T:0.47
Consensus pattern (11 bp):
ATTCATTTCCA
Found at i:41992426 original size:46 final size:46
Alignment explanation
Indices: 41992359--41992533 Score: 210
Period size: 46 Copynumber: 3.8 Consensus size: 46
41992349 AACCCGCCCC
* *
41992359 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCA
* * * * *
41992405 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAG-TTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG-TTCGCATCCA
* * **
41992451 TTTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCA
41992498 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATG
41992534 CTCAACCATC
Statistics
Matches: 104, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
45 2 0.02
46 67 0.64
47 33 0.32
48 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCGCATCCA
Found at i:41992471 original size:93 final size:93
Alignment explanation
Indices: 41992364--41992534 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
41992354 GCCCCTAAGT
***
41992364 GAACTCGGACTCAACTCAACGAGCTCGGGTGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
41992429 TGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
41992457 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41992522 CGAGTTCGGATGC
66 CGAGTTCGGATGC
41992535 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:41994649 original size:27 final size:27
Alignment explanation
Indices: 41994592--41994651 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
41994582 ACCCAGAGTC
* *
41994592 ATTTTACCACATAAGGGCAAAACAATC
1 ATTTTACCACATAAGGGAAAAACAATA
* * *
41994619 ATTTTACCCCATAAGGGAAAAATAGTA
1 ATTTTACCACATAAGGGAAAAACAATA
41994646 ATTTTA
1 ATTTTA
41994652 TTAATTTGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (27 bp):
ATTTTACCACATAAGGGAAAAACAATA
Found at i:41998552 original size:28 final size:29
Alignment explanation
Indices: 41998483--41998554 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 29
41998473 GACAAGATTG
* *
41998483 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-AAATTATACA
* *
41998513 GCACTAAGTGTGCGAGTTT-GATTATATA
1 GCACTAAGTGTGCGAGTTTAAATTATACA
41998541 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41998555 GATTCACTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 20 0.53
30 18 0.47
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.31
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGTTTAAATTATACA
Found at i:42003700 original size:11 final size:11
Alignment explanation
Indices: 42003684--42003712 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
42003674 AAACACTAAT
42003684 TCGAGGTTAGA
1 TCGAGGTTAGA
42003695 TCGAGGTTAGA
1 TCGAGGTTAGA
42003706 TCGAGGT
1 TCGAGGT
42003713 AAGTTCGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.24, C:0.10, G:0.38, T:0.28
Consensus pattern (11 bp):
TCGAGGTTAGA
Found at i:42005316 original size:21 final size:22
Alignment explanation
Indices: 42005290--42005340 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
42005280 CCTCTAGCAT
*
42005290 GGGCGTGT-CCTAGGGTCACAC
1 GGGCGTGTCCCTAGGGCCACAC
*
42005311 GGGCGTGTCCCTTGGGCCACAC
1 GGGCGTGTCCCTAGGGCCACAC
*
42005333 AGGCGTGT
1 GGGCGTGT
42005341 TAGCCCTGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.12, C:0.29, G:0.39, T:0.20
Consensus pattern (22 bp):
GGGCGTGTCCCTAGGGCCACAC
Found at i:42014283 original size:13 final size:13
Alignment explanation
Indices: 42014265--42014293 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42014255 TTTAGTTTAA
42014265 TTAGTTAATTAGT
1 TTAGTTAATTAGT
42014278 TTAGTTAATTAGT
1 TTAGTTAATTAGT
42014291 TTA
1 TTA
42014294 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:42014595 original size:3 final size:3
Alignment explanation
Indices: 42014587--42014628 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
42014577 CAATTTAATT
*
42014587 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42014629 CTAATTAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:42016850 original size:80 final size:80
Alignment explanation
Indices: 42016697--42016866 Score: 191
Period size: 80 Copynumber: 2.1 Consensus size: 80
42016687 GAGTTTCTTT
* * * **
42016697 GGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCAGATTTGGTAACT
1 GGAACTTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCAGATATAATAACT
*
42016761 TGCACAAATGCCTTC
66 AGCACAAATGCCTTC
** ** * * *
42016776 GGGTCTTAGCCCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAATCAC
1 GGAACTTAGCCCGGATATAACAACAAGCAC-AATTGCCTTCGGGTCTTAACCCAGATATAATAAC
*
42016840 TAGCATAAATGCCTTC
65 TAGCACAAATGCCTTC
42016856 GGAACTTAGCC
1 GGAACTTAGCC
42016867 TGGGTATCAT
Statistics
Matches: 73, Mismatches: 16, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
79 6 0.08
80 65 0.89
81 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (80 bp):
GGAACTTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCAGATATAATAACT
AGCACAAATGCCTTC
Found at i:42016864 original size:40 final size:40
Alignment explanation
Indices: 42016702--42016866 Score: 172
Period size: 40 Copynumber: 4.2 Consensus size: 40
42016692 TCTTTGGAAT
* * *
42016702 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* * * *** *
42016741 TTAACCCAGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
42016781 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* **
42016821 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGAAC
1 TTAGCCCGGATATAA-CAACTAGCACAAATGCCTTCGGGTC
42016861 TTAGCC
1 TTAGCC
42016867 TGGGTATCAT
Statistics
Matches: 101, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 3 0.03
40 97 0.96
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
Found at i:42024068 original size:13 final size:13
Alignment explanation
Indices: 42024050--42024078 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
42024040 TTTAGTTTAA
42024050 TTAGTTAATTAGT
1 TTAGTTAATTAGT
42024063 TTAGTTAATTAGT
1 TTAGTTAATTAGT
42024076 TTA
1 TTA
42024079 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:42030058 original size:9 final size:9
Alignment explanation
Indices: 42030052--42030077 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
42030042 AACTAACATA
42030052 AAGAACAAC
1 AAGAACAAC
42030061 AAGAACAAC
1 AAGAACAAC
42030070 AAGAACAA
1 AAGAACAA
42030078 GAAGTAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.19, G:0.12, T:0.00
Consensus pattern (9 bp):
AAGAACAAC
Found at i:42030460 original size:20 final size:21
Alignment explanation
Indices: 42030426--42030464 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
42030416 TCCTCCTTGG
*
42030426 AAGGTGGATATCGCGATACGC
1 AAGGTGGATACCGCGATACGC
42030447 AAGG-GGATACCGCGATAC
1 AAGGTGGATACCGCGATAC
42030465 CACTAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (21 bp):
AAGGTGGATACCGCGATACGC
Found at i:42033735 original size:22 final size:22
Alignment explanation
Indices: 42033704--42033750 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
42033694 AAAATAAAAT
*
42033704 AGGGTTGGTATTGCGATATT-G
1 AGGGTTGGTATCGCGATATTAG
42033725 AGGGTATGGTATCGCGATATTAG
1 AGGGT-TGGTATCGCGATATTAG
42033748 AGG
1 AGG
42033751 CAGACCACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 14 0.61
23 4 0.17
ACGTcount: A:0.23, C:0.06, G:0.38, T:0.32
Consensus pattern (22 bp):
AGGGTTGGTATCGCGATATTAG
Found at i:42035163 original size:28 final size:28
Alignment explanation
Indices: 42035102--42035199 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
42035092 TCACAAATTG
** * *
42035102 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
42035131 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
42035159 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
42035187 GCACTAAGTGTGC
1 GCACTAAGTGTGC
42035200 GGGCTTATGG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:42042840 original size:28 final size:28
Alignment explanation
Indices: 42042779--42042876 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
42042769 TCACAAATTG
** * *
42042779 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
42042808 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
42042836 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
42042864 GCACTAAGTGTGC
1 GCACTAAGTGTGC
42042877 GGGCTTATGC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:42047255 original size:2 final size:2
Alignment explanation
Indices: 42047250--42047293 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
42047240 AAAAAGGTTG
* * *
42047250 AT AT AT AC AT AT AT AT AT AC AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42047292 AT
1 AT
42047294 CTGGTAGCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:42047267 original size:12 final size:12
Alignment explanation
Indices: 42047250--42047293 Score: 70
Period size: 12 Copynumber: 3.5 Consensus size: 12
42047240 AAAAAGGTTG
42047250 ATATATACATAT
1 ATATATACATAT
42047262 ATATATACATATAT
1 ATATATAC--ATAT
42047276 ATATATACATAT
1 ATATATACATAT
42047288 ATATAT
1 ATATAT
42047294 CTGGTAGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 18 0.60
14 12 0.40
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATACATAT
Found at i:42047275 original size:14 final size:14
Alignment explanation
Indices: 42047250--42047293 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
42047240 AAAAAGGTTG
42047250 ATATATAC--ATAT
1 ATATATACATATAT
42047262 ATATATACATATAT
1 ATATATACATATAT
42047276 ATATATACATATAT
1 ATATATACATATAT
42047290 ATAT
1 ATAT
42047294 CTGGTAGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.27
14 22 0.73
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATACATATAT
Found at i:42052289 original size:2 final size:2
Alignment explanation
Indices: 42052284--42052325 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
42052274 AAAAAGGTTG
* * *
42052284 AT AT AT AC AT AT AT AT AT AC AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42052326 TTCTGGTAGC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:42052301 original size:12 final size:12
Alignment explanation
Indices: 42052284--42052325 Score: 84
Period size: 12 Copynumber: 3.5 Consensus size: 12
42052274 AAAAAGGTTG
42052284 ATATATACATAT
1 ATATATACATAT
42052296 ATATATACATAT
1 ATATATACATAT
42052308 ATATATACATAT
1 ATATATACATAT
42052320 ATATAT
1 ATATAT
42052326 TTCTGGTAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATACATAT
Found at i:42054833 original size:39 final size:40
Alignment explanation
Indices: 42054775--42054875 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
42054765 AAATTGAATG
* *
42054775 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
42054814 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
42054854 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
42054876 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:42054868 original size:40 final size:40
Alignment explanation
Indices: 42054775--42054957 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
42054765 AAATTGAATG
* * * * *
42054775 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
42054814 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
42054854 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
42054894 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
42054934 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
42054958 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 32 0.26
40 87 0.72
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:42062864 original size:39 final size:40
Alignment explanation
Indices: 42062806--42062906 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
42062796 AAATTGAATG
* *
42062806 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
42062845 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
42062885 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
42062907 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:42062899 original size:40 final size:40
Alignment explanation
Indices: 42062806--42062988 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
42062796 AAATTGAATG
* * * * *
42062806 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
42062845 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
42062885 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
42062925 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
42062965 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
42062989 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 32 0.26
40 87 0.72
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:42064511 original size:17 final size:15
Alignment explanation
Indices: 42064491--42064555 Score: 66
Period size: 15 Copynumber: 4.5 Consensus size: 15
42064481 ATTTATCTGT
*
42064491 TTATATTTGTACTATTA
1 TTATATTTCTA-T-TTA
42064508 TTATATTTCTATTTA
1 TTATATTTCTATTTA
42064523 TTATATTTCTA--T-
1 TTATATTTCTATTTA
*
42064535 TTCTATTTCTATTTA
1 TTATATTTCTATTTA
42064550 -TATATT
1 TTATATT
42064556 AATATTATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
12 10 0.24
13 1 0.02
14 6 0.14
15 14 0.33
16 1 0.02
17 10 0.24
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:42064522 original size:29 final size:28
Alignment explanation
Indices: 42064474--42064565 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 28
42064464 GTTATTCTAA
*
42064474 TACTATTATTTA--TCTGTTTATAT-TT
1 TACTATTATTTATTTCTATTTATATATT
42064499 GTACTATTATTATATTTCTATTTATTATATT
1 -TACTATTATT-TATTTCTATTTA-TATATT
*
42064530 T-CTATT-TCTATTTCTATTTATATA-T
1 TACTATTATTTATTTCTATTTATATATT
*
42064555 TAATATTATTT
1 TACTATTATTT
42064566 TCATTATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
25 2 0.04
26 18 0.33
27 16 0.29
28 1 0.02
29 12 0.22
30 4 0.07
31 2 0.04
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (28 bp):
TACTATTATTTATTTCTATTTATATATT
Found at i:42064523 original size:12 final size:12
Alignment explanation
Indices: 42064508--42064552 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
42064498 TGTACTATTA
42064508 TTATATTTCTATTT
1 TTATATTTCTA--T
42064522 ATTATATTTCTAT
1 -TTATATTTCTAT
*
42064535 TTCTATTTCTAT
1 TTATATTTCTAT
42064547 TTATAT
1 TTATAT
42064553 ATTAATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 16 0.57
13 1 0.04
15 11 0.39
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATTTCTAT
Found at i:42064564 original size:23 final size:23
Alignment explanation
Indices: 42064494--42064565 Score: 56
Period size: 23 Copynumber: 3.0 Consensus size: 23
42064484 TATCTGTTTA
* *
42064494 TATTTGTACTATTATTA-TATTTC
1 TATTTATA-TATTAATATTATTTC
* *
42064517 TATTTATTATATTTCTATTTCTATTTC
1 TATTTA-TATA-TT-AATAT-TATTTC
42064544 TATTTATATATTAATATTATTT
1 TATTTATATATTAATATTATTT
42064566 TCATTATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
23 12 0.32
24 7 0.18
25 3 0.08
26 4 0.11
27 12 0.32
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (23 bp):
TATTTATATATTAATATTATTTC
Found at i:42064696 original size:3 final size:3
Alignment explanation
Indices: 42064690--42064743 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
42064680 TATCATCGTC
42064690 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42064738 ATT ATT
1 ATT ATT
42064744 TAACTGTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:42064952 original size:3 final size:3
Alignment explanation
Indices: 42064946--42065035 Score: 60
Period size: 3 Copynumber: 30.3 Consensus size: 3
42064936 TATTCGTTAC
* * * *
42064946 TAT TAT TAT TAT TGT TGT TAT TAT TAT TAT TGT TAT TAT TAT CAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
42064993 TTT TAT CAT TGT TAT T-T ATAT TGT TGT T-T TCAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT T-AT TAT TAT TAT T
42065036 CTATTATGCA
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
2 5 0.07
3 62 0.89
4 3 0.04
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42064966 original size:9 final size:9
Alignment explanation
Indices: 42064933--42065008 Score: 64
Period size: 9 Copynumber: 8.4 Consensus size: 9
42064923 GAAAAACTTA
42064933 TATTATTCGT
1 TATTATT-GT
* *
42064943 TACTATTAT
1 TATTATTGT
42064952 TATTATTGT
1 TATTATTGT
* *
42064961 TGTTATTAT
1 TATTATTGT
42064970 TATTATTGT
1 TATTATTGT
*
42064979 TATTATTAT
1 TATTATTGT
* *
42064988 CATT-TTTT
1 TATTATTGT
*
42064996 TATCATTGT
1 TATTATTGT
42065005 TATT
1 TATT
42065009 TATATTGTTG
Statistics
Matches: 50, Mismatches: 15, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
8 5 0.10
9 39 0.78
10 6 0.12
ACGTcount: A:0.24, C:0.05, G:0.07, T:0.64
Consensus pattern (9 bp):
TATTATTGT
Found at i:42064967 original size:18 final size:18
Alignment explanation
Indices: 42064933--42064987 Score: 83
Period size: 18 Copynumber: 3.0 Consensus size: 18
42064923 GAAAAACTTA
*
42064933 TATTATTCGTTACTATTAT
1 TATTATT-GTTATTATTAT
*
42064952 TATTATTGTTGTTATTAT
1 TATTATTGTTATTATTAT
42064970 TATTATTGTTATTATTAT
1 TATTATTGTTATTATTAT
42064988 CATTTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 26 0.79
19 7 0.21
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (18 bp):
TATTATTGTTATTATTAT
Found at i:42064968 original size:15 final size:15
Alignment explanation
Indices: 42064948--42065032 Score: 74
Period size: 15 Copynumber: 5.9 Consensus size: 15
42064938 TTCGTTACTA
*
42064948 TTATTATTATTGTTG
1 TTATTATTATTATTG
42064963 TTATTATTATTATTG
1 TTATTATTATTATTG
*
42064978 TTATTATTATCA-T-
1 TTATTATTATTATTG
*
42064991 TT-TT-TTATCATTG
1 TTATTATTATTATTG
*
42065004 TTATT-TATATTGTTG
1 TTATTAT-TATTATTG
42065019 TT-TTCATTATTATT
1 TTATT-ATTATTATT
42065033 ATTCTATTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
11 6 0.10
12 3 0.05
13 4 0.07
14 6 0.10
15 39 0.66
16 1 0.02
ACGTcount: A:0.22, C:0.04, G:0.07, T:0.67
Consensus pattern (15 bp):
TTATTATTATTATTG
Found at i:42067742 original size:27 final size:27
Alignment explanation
Indices: 42067712--42068062 Score: 458
Period size: 27 Copynumber: 13.0 Consensus size: 27
42067702 AAAGTACTCC
42067712 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
42067739 CGATTTTTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
42067766 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
42067793 C-AGTTTACAGAATTACCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
42067820 CGATTTACAGAATTAACGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
42067847 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
42067874 CAATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
42067901 C-AGTTTACAAAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
42067928 CAATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
42067955 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
42067982 CGATTTACAGAATTACTGGTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
42068009 C-AGTTTACAAAATTATCATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
42068036 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
42068063 TAATTGTGAA
Statistics
Matches: 284, Mismatches: 32, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
26 4 0.01
27 276 0.97
28 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:42068102 original size:27 final size:27
Alignment explanation
Indices: 42068072--42068264 Score: 210
Period size: 27 Copynumber: 7.2 Consensus size: 27
42068062 TTAATTGTGA
*
42068072 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* * *
42068099 AATTTTCGAAATACCCCTATATGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* * *
42068126 AATTA-CTGAAATACCCTTATAGGATAG
1 AATTATC-GAAATACCCCTGTAGGGTAG
* *
42068153 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* *
42068180 AATTATCGAAATAACCTTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
*
42068207 AAATATCGAAATA-CCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* * * * *
42068233 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTATCGAAATACCCCTGTAGGGTAG
42068260 AATTA
1 AATTA
42068265 CCATTTTGCC
Statistics
Matches: 139, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
26 23 0.17
27 115 0.83
28 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (27 bp):
AATTATCGAAATACCCCTGTAGGGTAG
Found at i:42068429 original size:16 final size:16
Alignment explanation
Indices: 42068408--42068438 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42068398 CAAATATGGG
*
42068408 CATGACATTTTGCATA
1 CATGACATGTTGCATA
42068424 CATGACATGTTGCAT
1 CATGACATGTTGCAT
42068439 GGGTTGGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (16 bp):
CATGACATGTTGCATA
Found at i:42068508 original size:27 final size:26
Alignment explanation
Indices: 42068469--42068547 Score: 95
Period size: 27 Copynumber: 3.0 Consensus size: 26
42068459 GGAAGCGTTT
*
42068469 TGGTGGCTATGCCACAAATATCTGTTC
1 TGGTGGCTCTGCCAC-AATATCTGTTC
* *
42068496 TGGTGGCTCTGCCACAATATTTGTATT
1 TGGTGGCTCTGCCACAATATCTGT-TC
* *
42068523 TGGTGACTCTGTCACAATATCTGTT
1 TGGTGGCTCTGCCACAATATCTGTT
42068548 GACCGATCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 9 0.20
27 36 0.80
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (26 bp):
TGGTGGCTCTGCCACAATATCTGTTC
Found at i:42068667 original size:22 final size:22
Alignment explanation
Indices: 42068635--42068693 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
42068625 CCCGTTATTA
*
42068635 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
42068657 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
42068679 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
42068694 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:42068880 original size:27 final size:27
Alignment explanation
Indices: 42068858--42068931 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
42068848 TAGGTGGGTT
*
42068858 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGGCTC
*
42068885 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGGCTC
* *
42068912 TGTCACGATATCTGT-TCTGG
1 TGCCACAATATCTGTATCTGG
42068932 CAGCCATGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 5 0.12
27 36 0.86
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGGCTC
Found at i:42069058 original size:6 final size:6
Alignment explanation
Indices: 42069049--42069150 Score: 86
Period size: 6 Copynumber: 16.8 Consensus size: 6
42069039 CTGCATTCAC
*
42069049 ATTCTG ATTCTG ATTCTG --TCACG AAATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTC-TG -A-TTCTG ATTCTG ATTCTG ATTCTG
* * * *
42069098 ATACTA ATAT-TG ATTTTA ATTCTG ATTCT- ATTACTG ATTCTG ATTCTG
1 ATTCTG AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
42069146 ATTCT
1 ATTCT
42069151 CATTTTGGTT
Statistics
Matches: 78, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
4 2 0.03
5 5 0.06
6 64 0.82
7 4 0.05
8 1 0.01
9 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:42074585 original size:40 final size:40
Alignment explanation
Indices: 42074504--42074688 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
42074494 TCGAATGATG
* * *
42074504 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
42074543 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
42074583 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
** * *
42074623 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGCTACTATAA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* * *
42074664 -CCGGGCTATGTCCCGAAGGTATTTG
1 TCCGGACTAAGTCCCGAAGGCATTTG
42074689 AACGAGTAGC
Statistics
Matches: 130, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
39 25 0.19
40 103 0.79
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42074695 original size:80 final size:79
Alignment explanation
Indices: 42074556--42074711 Score: 183
Period size: 80 Copynumber: 2.0 Consensus size: 79
42074546 GGACTAAGAT
* **
42074556 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTA-CT
1 CCGAAGGCATTTGTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAG-TAGCT
42074620 AAATCCGGGTTAAGTC
65 AAATCC-GGTTAAGTC
* * * *
42074636 CCGAAGGCCTTTGTGCGAGCTACTATAA-CCGGGCTATG-TCCCGAAGGTATTTGAACGAGTAGC
1 CCGAAGGCATTTGTGCGAGCTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTAGC
*
42074699 TATATCCGGTTAA
64 TAAATCCGGTTAA
42074712 ACTCCGAAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
79 9 0.14
80 54 0.83
81 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTAGCTA
AATCCGGTTAAGTC
Found at i:42082619 original size:40 final size:40
Alignment explanation
Indices: 42082538--42082722 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
42082528 TCGAATGATG
* * *
42082538 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
42082577 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
42082617 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
** * *
42082657 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGCTACTATAA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* * *
42082698 -CCGGGCTATGTCCCGAAGGTATTTG
1 TCCGGACTAAGTCCCGAAGGCATTTG
42082723 AACGAGTAGC
Statistics
Matches: 130, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
39 25 0.19
40 103 0.79
41 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Done.