Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 152 of 427
Found at i:41781670 original size:28 final size:28
Alignment explanation
Indices: 41781599--41781688 Score: 116
Period size: 28 Copynumber: 3.3 Consensus size: 28
41781589 GTGACAGAGT
*
41781599 CACCA-AATACAGATA-TTG-GGGCAGAGC
1 CACCAGAA-ACAGATATTTGTGGG-ATAGC
41781626 CACCAG-AACAGATATTTGTGGGATAGC
1 CACCAGAAACAGATATTTGTGGGATAGC
*
41781653 CACCAGAAACAGATATTTGTGGCATAGC
1 CACCAGAAACAGATATTTGTGGGATAGC
41781681 CACCAGAA
1 CACCAGAA
41781689 TGCTTCCTCC
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
26 7 0.12
27 19 0.33
28 31 0.54
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (28 bp):
CACCAGAAACAGATATTTGTGGGATAGC
Found at i:41782778 original size:18 final size:17
Alignment explanation
Indices: 41782738--41782770 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41782728 GGGTTCAACT
41782738 ATGG-AGAAAAAAAAAG
1 ATGGAAGAAAAAAAAAG
*
41782754 ATGGAAGAAAAGAAAAG
1 ATGGAAGAAAAAAAAAG
41782771 GTGAGAAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.06
Consensus pattern (17 bp):
ATGGAAGAAAAAAAAAG
Found at i:41787357 original size:43 final size:43
Alignment explanation
Indices: 41787296--41787381 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
41787286 AGAGTAACCT
41787296 AGCTAAGTTATTAACCAATATTATAACCGACGAACATCACTTA
1 AGCTAAGTTATTAACCAATATTATAACCGACGAACATCACTTA
41787339 AGCTAAGTTATTAACCAATATTATAACCGACGAACATCACTTA
1 AGCTAAGTTATTAACCAATATTATAACCGACGAACATCACTTA
41787382 TTCTTTGCGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (43 bp):
AGCTAAGTTATTAACCAATATTATAACCGACGAACATCACTTA
Found at i:41789637 original size:29 final size:29
Alignment explanation
Indices: 41789587--41789716 Score: 163
Period size: 29 Copynumber: 4.5 Consensus size: 29
41789577 CCTCCGAGCT
* * * *
41789587 CGCACAC-CAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* * * *
41789615 TGCACACATAGTGTCATATTTTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
41789644 TGCACACTTAGTGCCTTATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
41789673 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
41789702 CGCACACTTAGTGCC
1 CGCACACTTAGTGCC
41789717 GATCTCGTCA
Statistics
Matches: 90, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 6 0.07
29 84 0.93
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.30
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:41789670 original size:58 final size:58
Alignment explanation
Indices: 41789529--41789717 Score: 179
Period size: 58 Copynumber: 3.3 Consensus size: 58
41789519 TACTCGATTT
* * * *** *
41789529 CGCACACTTAGTGCCACGTA-ATTT-AAGCCCGCACACACAGTGCCATA-CCCTCCGAGCT
1 CGCACACTTAGTG-C-CGTATATTTCCAGCACGCACACATAGTGCCATATATTTCC-AGCA
* * ** * *
41789587 CGCACAC-CAGTGCCGTATTTTTCCAGCTTGCACACATAGTGTCATATTTTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
* * *
41789644 TGCACACTTAGTGCCTTATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
41789702 CGCACACTTAGTGCCG
1 CGCACACTTAGTGCCG
41789718 ATCTCGTCAC
Statistics
Matches: 105, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
55 4 0.04
56 4 0.04
57 31 0.30
58 66 0.63
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.26
Consensus pattern (58 bp):
CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
Found at i:41797600 original size:29 final size:29
Alignment explanation
Indices: 41797568--41797702 Score: 155
Period size: 29 Copynumber: 4.7 Consensus size: 29
41797558 ATACCCTCCG
** * *
41797568 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
* * * *
41797597 AGCTTGCACACATAGTGTCATATTTTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
41797626 AGCAT-GCACACTTAGTGCCTTATATTTCC
1 AGC-TCGCACACTTAGTGCCATATATTTCC
*
41797655 AGCACGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCATATATTTCC
*
41797684 AGCACGCACACTTAGTGCC
1 AGCTCGCACACTTAGTGCC
41797703 GATCTCGTCA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 92 0.99
30 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.30
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCATATATTTCC
Found at i:41797635 original size:58 final size:58
Alignment explanation
Indices: 41797514--41797703 Score: 179
Period size: 58 Copynumber: 3.3 Consensus size: 58
41797504 TACTCGATTT
* * * *** *
41797514 CGCACACTTAGTGCCACGTA-ATTT-AAGCCCGCACACACAGTGCCATA-CCCTCCGAGCT
1 CGCACACTTAGTG-C-CGTATATTTCCAGCACGCACACATAGTGCCATATATTTCC-AGCA
** * ** * *
41797572 CGCACACCCAGTGCCGTATTTTTCCAGCTTGCACACATAGTGTCATATTTTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
* * *
41797630 TGCACACTTAGTGCCTTATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
41797688 CGCACACTTAGTGCCG
1 CGCACACTTAGTGCCG
41797704 ATCTCGTCAC
Statistics
Matches: 105, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
56 4 0.04
57 4 0.04
58 94 0.90
59 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.26
Consensus pattern (58 bp):
CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
Found at i:41807460 original size:33 final size:32
Alignment explanation
Indices: 41807423--41807500 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
41807413 TGGGCCTACC
** * *
41807423 ATGGTCTTACATTTGTAGTACCATAACCCAGTT
1 ATGGTCTTACATCAG-AATACCATAACCCAGCT
* *
41807456 ATGGTCTTATCATCAGAATGCCATAGCCCAGCT
1 ATGGTCTTA-CATCAGAATACCATAACCCAGCT
41807489 ATGGTCTTACAT
1 ATGGTCTTACAT
41807501 ATAAATACTG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 3 0.08
33 31 0.82
34 4 0.11
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (32 bp):
ATGGTCTTACATCAGAATACCATAACCCAGCT
Found at i:41807549 original size:101 final size:101
Alignment explanation
Indices: 41807444--41807636 Score: 314
Period size: 101 Copynumber: 1.9 Consensus size: 101
41807434 TTTGTAGTAC
* * * *
41807444 CATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAAATAC
1 CATAACCCAGTTAAGGTCTTATCATCAAAATACCATAGCCCAACTATGGTCTTACATATAAATAC
41807509 TGCCATGGTCCAACCATGGTCTTACGTCCAAGGTGT
66 TGCCATGGTCCAACCATGGTCTTACGTCCAAGGTGT
* *
41807545 CATAACCCAGTTAAGGTCTTTTCATTAAAATACCATAGCCCAACTATGGTCTTACATATAAATAC
1 CATAACCCAGTTAAGGTCTTATCATCAAAATACCATAGCCCAACTATGGTCTTACATATAAATAC
* *
41807610 TGTCATGGTCCTACCATGGTCTTACGT
66 TGCCATGGTCCAACCATGGTCTTACGT
41807637 TCAATTCATC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 84 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (101 bp):
CATAACCCAGTTAAGGTCTTATCATCAAAATACCATAGCCCAACTATGGTCTTACATATAAATAC
TGCCATGGTCCAACCATGGTCTTACGTCCAAGGTGT
Found at i:41811107 original size:26 final size:26
Alignment explanation
Indices: 41811078--41811133 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
41811068 TGATACAAAT
41811078 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41811104 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41811130 TGAT
1 TGAT
41811134 GGGAATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:41819274 original size:25 final size:26
Alignment explanation
Indices: 41819206--41819286 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
41819196 TGATACAAAT
41819206 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
41819232 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41819258 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
41819283 TGAT
1 TGAT
41819287 GGGAATTTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
25 21 0.40
26 32 0.60
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:41827289 original size:29 final size:29
Alignment explanation
Indices: 41827256--41827314 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
41827246 TTCCCGAGCC
41827256 TAGGGG-AAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGC-AAAGTT
* * *
41827285 TAGGGGCAAAATTGTAATTTTGCAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAGTT
41827314 T
1 T
41827315 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (29 bp):
TAGGGGCAAAAGTGTAAATATGCAAAGTT
Found at i:41827965 original size:67 final size:65
Alignment explanation
Indices: 41827824--41827977 Score: 184
Period size: 67 Copynumber: 2.3 Consensus size: 65
41827814 CATCATGTGT
* * *
41827824 ACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTCGCATGAGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTACG-G-GA-TATGATGTAGCTAGGTCGCATGAGTGATACTAGGTGGACACCATG
41827889 TAG
63 TAG
* * *
41827892 ACAAGAGAGCTACGGGATAT-ATGTAGCTAGGTCGCATGCGTGGTTCTAGGTAAAGGACACCATG
1 ACAAGAGAGCTACGGGATATGATGTAGCTAGGTCGCATGAGTGATACTAGGT---GGACACCATG
41827956 TAG
63 TAG
*
41827959 ACAAGAGAGCTACGAGATA
1 ACAAGAGAGCTACGGGATA
41827978 AACTGGCTAG
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
64 27 0.36
65 3 0.04
66 1 0.01
67 31 0.41
68 14 0.18
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (65 bp):
ACAAGAGAGCTACGGGATATGATGTAGCTAGGTCGCATGAGTGATACTAGGTGGACACCATGTAG
Found at i:41832278 original size:10 final size:10
Alignment explanation
Indices: 41832255--41832306 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
41832245 ATGTGAATCT
*
41832255 ATCATAAATAA
1 ATCA-AAATTA
41832266 ATCAAAATTA
1 ATCAAAATTA
41832276 ATCAAAATTTA
1 ATCAAAA-TTA
*
41832287 ATATAAAATTA
1 AT-CAAAATTA
*
41832298 ATTAAAATT
1 ATCAAAATT
41832307 CAACATGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
10 19 0.51
11 14 0.38
12 4 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.35
Consensus pattern (10 bp):
ATCAAAATTA
Found at i:41838130 original size:25 final size:24
Alignment explanation
Indices: 41838103--41838184 Score: 103
Period size: 24 Copynumber: 3.4 Consensus size: 24
41838093 ATGAGCTATG
* *
41838103 AATCAGTAAGCTCATACGAGTTGA
1 AATCGGTAAGCTCATACGAGCTGA
*
41838127 GAATCGGTAAGCTC-TCACAAGCTGA
1 -AATCGGTAAGCTCAT-ACGAGCTGA
*
41838152 AATCGGTACGCTCATACGAGCTGA
1 AATCGGTAAGCTCATACGAGCTGA
41838176 AATCGGTAA
1 AATCGGTAA
41838185 TCCCTAATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
24 29 0.59
25 20 0.41
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (24 bp):
AATCGGTAAGCTCATACGAGCTGA
Found at i:41841767 original size:40 final size:39
Alignment explanation
Indices: 41841722--41841929 Score: 227
Period size: 40 Copynumber: 5.2 Consensus size: 39
41841712 CGGAATACAA
*
41841722 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *
41841762 CCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
41841802 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
41841842 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
41841882 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
41841922 CCGGATAT
1 CCGGATAT
41841930 CATTCAATTG
Statistics
Matches: 144, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
39 1 0.01
40 143 0.99
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:41841862 original size:80 final size:80
Alignment explanation
Indices: 41841722--41841929 Score: 256
Period size: 80 Copynumber: 2.6 Consensus size: 80
41841712 CGGAATACAA
* * *
41841722 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTTGCACAAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
*
41841787 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
* * * *
41841802 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGTC-ACTAGCACAATT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATA-ACGACTAGCACAAAT
*
41841866 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
41841882 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAT
41841930 CATTCAATTG
Statistics
Matches: 109, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 108 0.99
81 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:41849781 original size:40 final size:39
Alignment explanation
Indices: 41849736--41849943 Score: 227
Period size: 40 Copynumber: 5.2 Consensus size: 39
41849726 CGGAATACAA
*
41849736 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *
41849776 CCGGATATAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
41849816 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
41849856 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
41849896 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
41849936 CCGGATAT
1 CCGGATAT
41849944 CATTCAATTG
Statistics
Matches: 144, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
39 1 0.01
40 143 0.99
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:41849876 original size:80 final size:80
Alignment explanation
Indices: 41849736--41849943 Score: 256
Period size: 80 Copynumber: 2.6 Consensus size: 80
41849726 CGGAATACAA
* * *
41849736 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTTGCACAAATG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
*
41849801 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
* * * *
41849816 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGTC-ACTAGCACAATT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATA-ACGACTAGCACAAAT
*
41849880 GCCTTCGGGTCTTAAC
65 GCCTTCGGGTATTAAC
** * ** * *
41849896 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAT
41849944 CATTCAATTG
Statistics
Matches: 109, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
80 108 0.99
81 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:41853529 original size:39 final size:38
Alignment explanation
Indices: 41853486--41853609 Score: 108
Period size: 39 Copynumber: 3.2 Consensus size: 38
41853476 GCCCAAGCTT
* *
41853486 CTTCGGAATACAACCGGATATAACCACATGCACGAATGC
1 CTTCGGAATAC-ACCGGATATAACAACTTGCACGAATGC
** * *
41853525 CTTCGGGTCTTAGC-CCGGATATAACGACTTGCACAAATGC
1 CTTC-GG-AATA-CACCGGATATAACAACTTGCACGAATGC
* *
41853565 CTTCGGTATTAGC-CCGGATTTAACAACTTGCACGAATGC
1 CTTCGG-AATA-CACCGGATATAACAACTTGCACGAATGC
41853604 CTTCGG
1 CTTCGG
41853610 GTCTTAGCCC
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
39 41 0.56
40 29 0.40
41 2 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (38 bp):
CTTCGGAATACACCGGATATAACAACTTGCACGAATGC
Found at i:41853544 original size:40 final size:39
Alignment explanation
Indices: 41853499--41853705 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 39
41853489 CGGAATACAA
*
41853499 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* *
41853539 CCGGATATAACGACTTGCACAAATGCCTTC-GGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
41853578 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
41853618 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
41853658 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
41853698 CCGGATAT
1 CCGGATAT
41853706 CATTCAATTG
Statistics
Matches: 142, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
39 36 0.25
40 106 0.75
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:41853617 original size:79 final size:80
Alignment explanation
Indices: 41853499--41853705 Score: 247
Period size: 79 Copynumber: 2.6 Consensus size: 80
41853489 CGGAATACAA
* * *
41853499 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATATA-ACGACTTGCACAAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAGAC-ACTAGCACAAAT
*
41853563 GCCTTC-GGTATTAGC
65 GCCTTCGGGTATTAAC
* * * *
41853578 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGTCACTAGCACAATTG
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAGACACTAGCACAAATG
*
41853643 CCTTCGGGTCTTAAC
66 CCTTCGGGTATTAAC
** * ** * *
41853658 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGATAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATAT
41853706 CATTCAATTG
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
79 61 0.56
80 47 0.44
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (80 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAGACACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:41856880 original size:96 final size:97
Alignment explanation
Indices: 41856704--41856894 Score: 278
Period size: 96 Copynumber: 2.0 Consensus size: 97
41856694 ATATCGATAC
* * * *
41856704 AACTTCCCAAACTTGTATAAAACAAGTTTAAAACACTTAAAGACATTTTTGATTGACTCAAAAAT
1 AACTTCCCAAACTTGAATAAAACAAGTTTAAAACACTCAAAGACATTTTGGATTGACACAAAAAT
*
41856769 GTTTAGATAAATTAAAATACATTTAAAATAAG
66 ATTTAGATAAATTAAAATACATTTAAAATAAG
** *
41856801 AACTTCCCAAACTTGAATAAAATGAGTTTAAAACAC-CAAA-ATCATTTTGGATTGGCACAAAAA
1 AACTTCCCAAACTTGAATAAAACAAGTTTAAAACACTCAAAGA-CATTTTGGATTGACACAAAAA
*
41856864 TATTTAGATAAATTAAAATACATTTAGAATA
65 TATTTAGATAAATTAAAATACATTTAAAATA
41856895 TAGTTTTGAG
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
95 1 0.01
96 50 0.60
97 33 0.39
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.31
Consensus pattern (97 bp):
AACTTCCCAAACTTGAATAAAACAAGTTTAAAACACTCAAAGACATTTTGGATTGACACAAAAAT
ATTTAGATAAATTAAAATACATTTAAAATAAG
Found at i:41857604 original size:24 final size:24
Alignment explanation
Indices: 41857572--41857630 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
41857562 TGTGTAAAGT
* *
41857572 AATATTAAATATCATCAA-AAATCA
1 AATAATAAATAGC-TCAACAAATCA
*
41857596 AATAATAAA-AGCTCAACATATCA
1 AATAATAAATAGCTCAACAAATCA
41857619 AATAAATAAATA
1 AAT-AATAAATA
41857631 AATTTCTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 4 0.14
23 10 0.34
24 14 0.48
25 1 0.03
ACGTcount: A:0.61, C:0.12, G:0.02, T:0.25
Consensus pattern (24 bp):
AATAATAAATAGCTCAACAAATCA
Found at i:41857773 original size:13 final size:16
Alignment explanation
Indices: 41857737--41857769 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
41857727 ATATCACTTT
41857737 TATT-ATTTTTTTTAA
1 TATTAATTTTTTTTAA
41857752 TATTAATTTTTTTTAA
1 TATTAATTTTTTTTAA
41857768 TA
1 TA
41857770 ATTTCATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTAATTTTTTTTAA
Found at i:41867016 original size:36 final size:36
Alignment explanation
Indices: 41866973--41867046 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
41866963 AGTGACATGA
41866973 ATTTATTATTTGTTATGTTTAATATATGTTTTATTT
1 ATTTATTATTTGTTATGTTTAATATATGTTTTATTT
41867009 ATTTATTATTTGTTATGTTTAATATATGTTTTATTT
1 ATTTATTATTTGTTATGTTTAATATATGTTTTATTT
41867045 AT
1 AT
41867047 ACTTGTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (36 bp):
ATTTATTATTTGTTATGTTTAATATATGTTTTATTT
Found at i:41867042 original size:25 final size:25
Alignment explanation
Indices: 41866997--41867044 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
41866987 ATGTTTAATA
* *
41866997 TATGTTTTATTTATTTATTATTTGT
1 TATGTTTAATATATTTATTATTTGT
41867022 TATGTTTAATATATGTT-TTATTT
1 TATGTTTAATATAT-TTATTATTT
41867045 ATACTTGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (25 bp):
TATGTTTAATATATTTATTATTTGT
Found at i:41867045 original size:16 final size:16
Alignment explanation
Indices: 41866990--41867045 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 16
41866980 ATTTGTTATG
41866990 TTTAATATATGTTTTA
1 TTTAATATATGTTTTA
*
41867006 TTTATTTATTAT-TTGTTA
1 TTTA-ATA-TATGTT-TTA
41867024 TGTTTAATATATGTTTTA
1 --TTTAATATATGTTTTA
41867042 TTTA
1 TTTA
41867046 TACTTGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 8 0.25
17 4 0.12
18 12 0.38
19 4 0.12
20 4 0.12
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (16 bp):
TTTAATATATGTTTTA
Found at i:41871298 original size:23 final size:24
Alignment explanation
Indices: 41871249--41871300 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
41871239 TTGTTTTATT
* *
41871249 TTTA-TTTTATTTTTTTGCCCTTA
1 TTTATTTTTATTTTATTGCCATTA
41871272 -TTATTTTTATTTTATT-CCATTA
1 TTTATTTTTATTTTATTGCCATTA
41871294 TTTATTT
1 TTTATTT
41871301 ATTCATTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTATTTTTATTTTATTGCCATTA
Found at i:41871303 original size:16 final size:16
Alignment explanation
Indices: 41871269--41871308 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
41871259 TTTTTTGCCC
41871269 TTATT-ATT-TTTATT
1 TTATTCATTATTTATT
41871283 TTATTCCATTATTTA-T
1 TTATT-CATTATTTATT
41871299 TTATTCATTA
1 TTATTCATTA
41871309 CTTTTTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.22
15 5 0.22
16 9 0.39
17 4 0.17
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTCATTATTTATT
Found at i:41876564 original size:13 final size:13
Alignment explanation
Indices: 41876546--41876588 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
41876536 TAGATTTTTC
41876546 CTAAATATTATTA
1 CTAAATATTATTA
41876559 CTAAATA--ATT-
1 CTAAATATTATTA
*
41876569 CTAAATATTATCA
1 CTAAATATTATTA
41876582 CTAAATA
1 CTAAATA
41876589 ATTCAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 2 0.08
13 14 0.54
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
CTAAATATTATTA
Found at i:41876576 original size:23 final size:23
Alignment explanation
Indices: 41876546--41876597 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
41876536 TAGATTTTTC
*
41876546 CTAAATATTATTACTAAATAATT
1 CTAAATATTATCACTAAATAATT
41876569 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
*
41876592 CAAAAT
1 CTAAAT
41876598 TTAAAAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:41879839 original size:29 final size:29
Alignment explanation
Indices: 41879806--41879966 Score: 259
Period size: 29 Copynumber: 5.6 Consensus size: 29
41879796 GTGACGAGAT
41879806 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
41879835 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
41879864 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
41879893 TGGCACTAAGTGTGCGTGCTGGAAATATT
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
** *
41879922 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* **
41879951 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
41879967 AGTTCGGAGG
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 123 1.00
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:41887613 original size:29 final size:29
Alignment explanation
Indices: 41887580--41887740 Score: 259
Period size: 29 Copynumber: 5.6 Consensus size: 29
41887570 GTGACGAGAT
41887580 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
41887609 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
41887638 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
41887667 TGGCACTAAGTGTGCGTGCTGGAAATATT
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
** *
41887696 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* **
41887725 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
41887741 AGTTCGGAGG
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 123 1.00
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:41892615 original size:30 final size:30
Alignment explanation
Indices: 41892574--41892653 Score: 144
Period size: 30 Copynumber: 2.7 Consensus size: 30
41892564 GACCACGCGG
*
41892574 GTGGC-CACACGGGCATGTGCCCCACATAC
1 GTGGCTCACACGGCCATGTGCCCCACATAC
41892603 GTGGCTCACACGGCCATGTGCCCCACATAC
1 GTGGCTCACACGGCCATGTGCCCCACATAC
41892633 GTGGCTCACACGGCCATGTGC
1 GTGGCTCACACGGCCATGTGC
41892654 AATTGGGAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 5 0.10
30 44 0.90
ACGTcount: A:0.19, C:0.38, G:0.28, T:0.16
Consensus pattern (30 bp):
GTGGCTCACACGGCCATGTGCCCCACATAC
Found at i:41907716 original size:40 final size:38
Alignment explanation
Indices: 41907661--41907827 Score: 163
Period size: 35 Copynumber: 4.6 Consensus size: 38
41907651 CATGGCAAAG
41907661 TGTGAAATGTAGGTATGG---TATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCATCCATACTGAGT
* *
41907696 TGTGAAAAGTAGGTATGGTA-T-T-ATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCATCCATACTGAGT
*
41907731 TGTGAAATGTAGGTATGGTATTATCAAATCCACACTGAGT
1 TGTGAAATGTAGGTATGGTATTATC--ATCCATACTGAGT
** * *
41907771 TAAGAAATGTAGGTATGGCATT-TC--CCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTATCATCCATACTGAGT
** *
41907806 TGAAAAATATAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
41907828 TCAATGAGGA
Statistics
Matches: 111, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
35 75 0.68
36 2 0.02
37 2 0.02
39 2 0.02
40 30 0.27
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (38 bp):
TGTGAAATGTAGGTATGGTATTATCATCCATACTGAGT
Found at i:41907799 original size:75 final size:75
Alignment explanation
Indices: 41907661--41907831 Score: 194
Period size: 75 Copynumber: 2.4 Consensus size: 75
41907651 CATGGCAAAG
* ** *
41907661 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAAAGTAGGTATGGTATTATC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCACACTGAGTTAAGAAAAGTAGGTATGGCATTATC
*
41907721 CATACTGAGC
66 CATACCGAGC
*
41907731 TGTGAAATGTAGGTATGGTATTATCAAATCCACACTGAGTTAAGAAATGTAGGTATGGCATT-TC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCACACTGAGTTAAGAAAAGTAGGTATGGCATTAT-
*
41907795 CCATACCGAGT
65 CCATACCGAGC
** *
41907806 TGAAAAATATAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
41907832 TGAGGAAAAC
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 58 0.68
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCACACTGAGTTAAGAAAAGTAGGTATGGCATTATC
CATACCGAGC
Found at i:41910516 original size:71 final size:71
Alignment explanation
Indices: 41910432--41910595 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41910422 CGATTTGTCT
41910432 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
41910497 CTTTCA
66 CTTTCA
41910503 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
41910568 CTTTCA
66 CTTTCA
41910574 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
41910596 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:41910633 original size:71 final size:70
Alignment explanation
Indices: 41910432--41910629 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
41910422 CGATTTGTCT
* * * *
41910432 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
41910497 CTTTCA
65 CTTTCA
* * * *
41910503 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
41910568 CTTTCA
65 CTTTCA
* *
41910574 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
41910630 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:41916465 original size:69 final size:69
Alignment explanation
Indices: 41916381--41916540 Score: 302
Period size: 69 Copynumber: 2.3 Consensus size: 69
41916371 CGATTTGTCT
41916381 CGTAGCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTATCT
1 CGTAGCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTATCT
41916446 TTCA
66 TTCA
41916450 CGTAGCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTATCT
1 CGTAGCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTATCT
41916515 TTCA
66 TTCA
41916519 CGTAGCTCTCTTGTCTACATGG
1 CGTAG--CTCTTGTCTACATGG
41916541 GATACATCTC
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
69 74 0.83
71 15 0.17
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (69 bp):
CGTAGCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTATCT
TTCA
Found at i:41924025 original size:71 final size:71
Alignment explanation
Indices: 41923941--41924104 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41923931 CGATTTGTCT
41923941 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
41924006 CTTTCA
66 CTTTCA
41924012 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
41924077 CTTTCA
66 CTTTCA
41924083 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
41924105 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:41924142 original size:71 final size:70
Alignment explanation
Indices: 41923941--41924138 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
41923931 CGATTTGTCT
* * * *
41923941 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
41924006 CTTTCA
65 CTTTCA
* * * *
41924012 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
41924077 CTTTCA
65 CTTTCA
* *
41924083 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
41924139 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:41925526 original size:68 final size:68
Alignment explanation
Indices: 41925422--41925664 Score: 267
Period size: 68 Copynumber: 3.6 Consensus size: 68
41925412 TGTCCAAGTG
* * *
41925422 GACTCCATATGTTGCCATAGTCAAGCTATGGGCTTACACAATGTAACCCCATGTTTACTGTCCTG
1 GACTCCATATATTGCCATAGTCAAGCTATGGTCTTACACAATGTAACCCCATGTTTATTGTCCTG
41925487 GCA
66 GCA
* ** * * ** * *
41925490 GACTCCATATTTTTACATAGTTAAGCCATGGTCTTACACAATGTAATACCAT-ATTATTGTCTTG
1 GACTCCATATATTGCCATAGTCAAGCTATGGTCTTACACAATGTAACCCCATGTTTATTGTCCTG
41925554 G-A
66 GCA
* *
41925556 GGACTCCATATATTGCCATAG-CAGAGCTATGATCTTACACAATGTAACCCCATGTTTTTTGTCC
1 -GACTCCATATATTGCCATAGTCA-AGCTATGGTCTTACACAATGTAACCCCATGTTTATTGTCC
*
41925620 TAGCA
64 TGGCA
* * * * *
41925625 GACTCTATTTGTTGCCATAGCCGAGCTATGGTCTTACACA
1 GACTCCATATATTGCCATAGTCAAGCTATGGTCTTACACA
41925665 TTAAACCCCT
Statistics
Matches: 142, Mismatches: 28, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
66 2 0.01
67 52 0.37
68 86 0.61
69 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (68 bp):
GACTCCATATATTGCCATAGTCAAGCTATGGTCTTACACAATGTAACCCCATGTTTATTGTCCTG
GCA
Found at i:41925656 original size:135 final size:135
Alignment explanation
Indices: 41925421--41925664 Score: 341
Period size: 135 Copynumber: 1.8 Consensus size: 135
41925411 TTGTCCAAGT
* *
41925421 GGACTCCATATGTTGCCATAGTCAAGCTATGGGCTTACACAATGTAACCCCATGTTTACTGTCCT
1 GGACTCCATATATTGCCATAGTCAAGCTATGAGCTTACACAATGTAACCCCATGTTTACTGTCCT
* **
41925486 GGCAGACTCCATATTTTTACATAGTTAAGCCATGGTCTTACACAATGTAATACCATATTATTGTC
66 AGCAGACTCCATATTTTTACATAGCCAAGCCATGGTCTTACACAATGTAATACCATATTATTGTC
41925551 TTGGA
131 TTGGA
* **
41925556 GGACTCCATATATTGCCATAG-CAGAGCTATGATCTTACACAATGTAACCCCATGTTTTTTGTCC
1 GGACTCCATATATTGCCATAGTCA-AGCTATGAGCTTACACAATGTAACCCCATGTTTACTGTCC
* * *
41925620 TAGCAGACT-C-TATTTGTTGCCATAGCCGAGCTATGGTCTTACACA
65 TAGCAGACTCCATATTT-TT-ACATAGCCAAGCCATGGTCTTACACA
41925665 TTAAACCCCT
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
133 5 0.05
134 5 0.05
135 85 0.89
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (135 bp):
GGACTCCATATATTGCCATAGTCAAGCTATGAGCTTACACAATGTAACCCCATGTTTACTGTCCT
AGCAGACTCCATATTTTTACATAGCCAAGCCATGGTCTTACACAATGTAATACCATATTATTGTC
TTGGA
Found at i:41930480 original size:27 final size:28
Alignment explanation
Indices: 41930420--41930497 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 28
41930410 AAAATAACTG
*
41930420 AAATA-CCCCAAAGGGTAAAATGA-TCA
1 AAATACCCCCATAGGGTAAAATGACTCA
**
41930446 AAATACCCCCATAGGGTAAAATGACTTT
1 AAATACCCCCATAGGGTAAAATGACTCA
***
41930474 AAA-ACCCTTGTAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
41930498 AGTTTTGCCC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 5 0.11
27 35 0.80
28 4 0.09
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.21
Consensus pattern (28 bp):
AAATACCCCCATAGGGTAAAATGACTCA
Found at i:41930508 original size:27 final size:27
Alignment explanation
Indices: 41930490--41930685 Score: 234
Period size: 27 Copynumber: 7.3 Consensus size: 27
41930480 CTTGTAGGGT
41930490 AAAATGAC-AGTTTTGCCCTTATGTGGC
1 AAAATGACTA-TTTTGCCCTTATGTGGC
41930517 AAAATGACTATTTTGCCCTTATGTGGC
1 AAAATGACTATTTTGCCCTTATGTGGC
**
41930544 AAAATGACTATTTTGCCCTTATGTGTT
1 AAAATGACTATTTTGCCCTTATGTGGC
* * * **
41930571 AAATTGACGATTTTGCCCTTGTGTGTT
1 AAAATGACTATTTTGCCCTTATGTGGC
* **
41930598 AAAATGA-TGATTTTTCCCTTATGTGAT
1 AAAATGACT-ATTTTGCCCTTATGTGGC
41930625 AAAATGACTATTTTGCCCTTATGTGGC
1 AAAATGACTATTTTGCCCTTATGTGGC
* * * *
41930652 AAAAAGACTATTTTGCCATTATATGGT
1 AAAATGACTATTTTGCCCTTATGTGGC
41930679 AAAATGA
1 AAAATGA
41930686 TTGAAATGCC
Statistics
Matches: 148, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
27 146 0.99
28 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.39
Consensus pattern (27 bp):
AAAATGACTATTTTGCCCTTATGTGGC
Found at i:41932999 original size:17 final size:18
Alignment explanation
Indices: 41932961--41932999 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41932951 GGTTTTGAGG
41932961 TTTTGCTCTTCAATTCAT
1 TTTTGCTCTTCAATTCAT
*
41932979 TTTTGGCTCTTC-TTTCAT
1 TTTT-GCTCTTCAATTCAT
41932997 TTT
1 TTT
41933000 ATTTTCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.10, C:0.21, G:0.08, T:0.62
Consensus pattern (18 bp):
TTTTGCTCTTCAATTCAT
Found at i:41933765 original size:24 final size:24
Alignment explanation
Indices: 41933732--41933777 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
41933722 GTGGAACTAC
*
41933732 AAAGGCTGAAAAGCTGAAAAGTCA
1 AAAGGATGAAAAGCTGAAAAGTCA
* *
41933756 AAAGGATGAAAAGTTGGAAAGT
1 AAAGGATGAAAAGCTGAAAAGT
41933778 GGGTTGTCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.28, T:0.15
Consensus pattern (24 bp):
AAAGGATGAAAAGCTGAAAAGTCA
Found at i:41935439 original size:40 final size:40
Alignment explanation
Indices: 41935358--41935538 Score: 251
Period size: 40 Copynumber: 4.6 Consensus size: 40
41935348 AAACCAAGTA
** * *
41935358 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
41935397 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
41935437 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * *
41935477 CCTTCGGGACTTGGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
41935517 CCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
41935539 CAATCCGAAT
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
39 25 0.19
40 104 0.81
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:41937461 original size:27 final size:27
Alignment explanation
Indices: 41937431--41937519 Score: 106
Period size: 27 Copynumber: 3.3 Consensus size: 27
41937421 TATTTACTTG
* *
41937431 AAAATGACCGAAATACCCCCACAGGGT
1 AAAATGACCAAAATACCCCCATAGGGT
*
41937458 AAAATGACCAAAATACCCCCATTGGGT
1 AAAATGACCAAAATACCCCCATAGGGT
*** **
41937485 AAAATGACTTTAATACCCCTGTAGGGT
1 AAAATGACCAAAATACCCCCATAGGGT
41937512 AAAATGAC
1 AAAATGAC
41937520 GGTTTTACCC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATACCCCCATAGGGT
Found at i:41937528 original size:27 final size:25
Alignment explanation
Indices: 41937480--41937545 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 25
41937470 ATACCCCCAT
41937480 TGGGTAAAATGACTTTAATACCCCTGTA
1 TGGGTAAAATGACTTT-ATA-CCCT-TA
41937508 -GGGTAAAATGACGGTTT-TACCCTTA
1 TGGGTAAAATGAC--TTTATACCCTTA
41937533 TGTGGTAAAATGA
1 TG-GGTAAAATGA
41937546 TTATTTTGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
25 2 0.06
26 5 0.15
27 24 0.71
29 3 0.09
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (25 bp):
TGGGTAAAATGACTTTATACCCTTA
Found at i:41937552 original size:27 final size:27
Alignment explanation
Indices: 41937509--41937707 Score: 202
Period size: 27 Copynumber: 7.4 Consensus size: 27
41937499 ACCCCTGTAG
** *
41937509 GGTAAAATGACGGTTTTACCCTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
* *
41937536 GGTAAAATGATTATTTTGCCTTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
*
41937563 GTTAAAATGACTATTTTGCCCTTATGT
1 GGTAAAATGACTATTTTGCCCTTATGT
* * ** *
41937590 GTTAAATTGACGGTTTTGCCCTTGTGT
1 GGTAAAATGACTATTTTGCCCTTATGT
*
41937617 GTTAAAATGA-TGATTTTGCCCTTATGT
1 GGTAAAATGACT-ATTTTGCCCTTATGT
* * * *
41937644 GATAAAATGACTGTTTTGTCCTTGTGT
1 GGTAAAATGACTATTTTGCCCTTATGT
* * * *
41937671 GGCAAAAAGAATATTTTGCCCTTCTGT
1 GGTAAAATGACTATTTTGCCCTTATGT
41937698 GGTAAAATGA
1 GGTAAAATGA
41937708 TTGAAATGCC
Statistics
Matches: 141, Mismatches: 29, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
27 140 0.99
28 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.41
Consensus pattern (27 bp):
GGTAAAATGACTATTTTGCCCTTATGT
Found at i:41937570 original size:81 final size:81
Alignment explanation
Indices: 41937484--41937655 Score: 206
Period size: 81 Copynumber: 2.1 Consensus size: 81
41937474 CCCCATTGGG
41937484 TAAAATGACT-TTAATACCCCTGTA-G-GGTAAAATGACGGTTTTACCCTTATGTGGTAAAATGA
1 TAAAATGACTATT--TACCCCT-TATGTGGTAAAATGACGGTTTTACCCTTATGTGGTAAAATGA
* * *
41937546 TTATTTTGCCTTTATGTGT
63 TGATTTTGCCCTTATGTGA
** * * * * *
41937565 TAAAATGACTATTTTGCCCTTATGTGTTAAATTGACGGTTTTGCCCTTGTGTGTTAAAATGATGA
1 TAAAATGACTATTTACCCCTTATGTGGTAAAATGACGGTTTTACCCTTATGTGGTAAAATGATGA
41937630 TTTTGCCCTTATGTGA
66 TTTTGCCCTTATGTGA
41937646 TAAAATGACT
1 TAAAATGACT
41937656 GTTTTGTCCT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
79 2 0.03
80 6 0.08
81 68 0.87
82 2 0.03
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (81 bp):
TAAAATGACTATTTACCCCTTATGTGGTAAAATGACGGTTTTACCCTTATGTGGTAAAATGATGA
TTTTGCCCTTATGTGA
Found at i:41937661 original size:81 final size:81
Alignment explanation
Indices: 41937511--41937708 Score: 234
Period size: 81 Copynumber: 2.4 Consensus size: 81
41937501 CCCTGTAGGG
* * *
41937511 TAAAATGACGGTTTTACCCTTATGTGGTAAAATGATTATTTTGCCTTTATGTGTTAAAATGACTA
1 TAAAATGACGGTTTTACCCTTATGTGGTAAAATGATGATTTTGCCCTTATGTGATAAAATGACTA
41937576 TTTTGCCCTTATGTGT
66 TTTTGCCCTTATGTGT
* * * * *
41937592 TAAATTGACGGTTTTGCCCTTGTGTGTTAAAATGATGATTTTGCCCTTATGTGATAAAATGACTG
1 TAAAATGACGGTTTTACCCTTATGTGGTAAAATGATGATTTTGCCCTTATGTGATAAAATGACTA
* * *
41937657 TTTTGTCCTTGTGTGG
66 TTTTGCCCTTATGTGT
* * *** * *
41937673 CAAAAAGAATATTTTGCCCTTCTGTGGTAAAATGAT
1 TAAAATGACGGTTTTACCCTTATGTGGTAAAATGAT
41937709 TGAAATGCCC
Statistics
Matches: 98, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 98 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.42
Consensus pattern (81 bp):
TAAAATGACGGTTTTACCCTTATGTGGTAAAATGATGATTTTGCCCTTATGTGATAAAATGACTA
TTTTGCCCTTATGTGT
Found at i:41937718 original size:81 final size:82
Alignment explanation
Indices: 41937522--41937752 Score: 225
Period size: 81 Copynumber: 2.9 Consensus size: 82
41937512 AAAATGACGG
* * * *
41937522 TTTTACCCTTATGTGGTAAAATGATT-ATTTTGCCTTTATGTGTTAAAATGACTATTTTGCCCTT
1 TTTTGCCCTTATGTGGTAAAATGATTGATTTTGCCCTTATGTGATAAAATGACTGTTTTGCCCTT
** ** * *
41937586 ATGTGTTAAATTGACGG
66 ATGTGGCAAAAAGAAGA
* * *
41937603 TTTTGCCCTTGTGTGTTAAAATGA-TGATTTTGCCCTTATGTGATAAAATGACTGTTTTGTCCTT
1 TTTTGCCCTTATGTGGTAAAATGATTGATTTTGCCCTTATGTGATAAAATGACTGTTTTGCCCTT
* *
41937667 GTGTGGCAAAAAGAATA
66 ATGTGGCAAAAAGAAGA
* ** * ** * * *
41937684 TTTTGCCCTTCTGTGGTAAAATGATTGA-AATGCCCCTACATGGTAAATTGACTGTTTTGCCCCT
1 TTTTGCCCTTATGTGGTAAAATGATTGATTTTGCCCTTATGTGATAAAATGACTGTTTTGCCCTT
41937748 ATGTG
66 ATGTG
41937753 ATGTACGTTT
Statistics
Matches: 121, Mismatches: 27, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
80 1 0.01
81 117 0.97
82 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (82 bp):
TTTTGCCCTTATGTGGTAAAATGATTGATTTTGCCCTTATGTGATAAAATGACTGTTTTGCCCTT
ATGTGGCAAAAAGAAGA
Found at i:41938058 original size:18 final size:19
Alignment explanation
Indices: 41938031--41938081 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
41938021 TGTTTGCATT
* *
41938031 CTGCACTGATTACT-TTTA
1 CTGCATTGATTACTGGTTA
*
41938049 CTGCATTGATCA-TGGTTA
1 CTGCATTGATTACTGGTTA
41938067 CTGCATTGATTACTG
1 CTGCATTGATTACTG
41938082 CCACTACTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 1 0.04
18 24 0.89
19 2 0.07
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (19 bp):
CTGCATTGATTACTGGTTA
Found at i:41944361 original size:18 final size:19
Alignment explanation
Indices: 41944338--41944388 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
41944328 TGCCCAACAA
41944338 TCTCCTTTTAAACAATA-G
1 TCTCCTTTTAAACAATAGG
* * * *
41944356 TCTCCTATTGAGCAGTAGG
1 TCTCCTTTTAAACAATAGG
41944375 T-TCCTTTTAAACAA
1 TCTCCTTTTAAACAA
41944389 GGTGTTTTTT
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (19 bp):
TCTCCTTTTAAACAATAGG
Found at i:41952435 original size:15 final size:16
Alignment explanation
Indices: 41952412--41952446 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
41952402 TGAATATGAG
*
41952412 ATGAGAAAATATTGAA
1 ATGAGAAAATATAGAA
41952428 ATGA-AAAATATAGAA
1 ATGAGAAAATATAGAA
41952443 ATGA
1 ATGA
41952447 TTATGATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (16 bp):
ATGAGAAAATATAGAA
Found at i:41952446 original size:42 final size:45
Alignment explanation
Indices: 41952377--41952476 Score: 127
Period size: 42 Copynumber: 2.3 Consensus size: 45
41952367 TATGTGATTG
*
41952377 ATATTGAATTGACAAAAATGAGAAATGAATATGAGATGAG-AA-A
1 ATATTGAAATGACAAAAATGAGAAATGAATATGAGATGAGAAATA
* *
41952420 ATATTGAAATGA-AAAATAT-AGAAATGATTATGATATGAGAAATA
1 ATATTGAAATGACAAAA-ATGAGAAATGAATATGAGATGAGAAATA
41952464 ATATGTGAAATGA
1 ATAT-TGAAATGA
41952477 TGAATTGAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
42 22 0.44
43 15 0.30
44 5 0.10
45 8 0.16
ACGTcount: A:0.53, C:0.01, G:0.19, T:0.27
Consensus pattern (45 bp):
ATATTGAAATGACAAAAATGAGAAATGAATATGAGATGAGAAATA
Found at i:41954263 original size:29 final size:29
Alignment explanation
Indices: 41954231--41954306 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
41954221 ATCATATTCG
*
41954231 TATGGCCCATTAGGCCCAAATCACCTGTA
1 TATGGCCCATTAGGCCCAAATCACATGTA
*
41954260 TATGGCCCATTAGGCCCAAATCACATTTA
1 TATGGCCCATTAGGCCCAAATCACATGTA
*
41954289 TATGGCCCGTTAGGCCCA
1 TATGGCCCATTAGGCCCA
41954307 GTCACATTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.25
Consensus pattern (29 bp):
TATGGCCCATTAGGCCCAAATCACATGTA
Found at i:41955836 original size:8 final size:8
Alignment explanation
Indices: 41955819--41955851 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
41955809 AAAAATTCAA
*
41955819 GATTTCGG
1 GATTTTGG
41955827 GATTTTGG
1 GATTTTGG
41955835 GATTTTGG
1 GATTTTGG
41955843 GATTTTGG
1 GATTTTGG
41955851 G
1 G
41955852 GGCGTTACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.12, C:0.03, G:0.39, T:0.45
Consensus pattern (8 bp):
GATTTTGG
Found at i:41958825 original size:20 final size:20
Alignment explanation
Indices: 41958769--41958816 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
41958759 AAAAGAAATG
* * *
41958769 AGCTGAAACGATCTAAAATCA
1 AGCTCAAACGAGCTGAAA-CA
41958790 AGCTCAAACGAGCTGAAACA
1 AGCTCAAACGAGCTGAAACA
41958810 AGCTCAA
1 AGCTCAA
41958817 GTGAGCTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
AGCTCAAACGAGCTGAAACA
Found at i:41962047 original size:40 final size:39
Alignment explanation
Indices: 41961882--41962065 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
41961872 AAATTGAATG
* * *
41961882 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
41961922 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
41961962 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
41962002 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
41962041 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
41962066 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:41962090 original size:80 final size:81
Alignment explanation
Indices: 41961922--41962110 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
41961912 GCTGGAAATT
* * * *
41961922 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
41961987 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
41962003 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
41962066 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
41962082 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
41962111 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:41964320 original size:18 final size:19
Alignment explanation
Indices: 41964298--41964341 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
41964288 TTCACTCTCG
41964298 TTCTTTTTTC-TTTTC-C-
1 TTCTTTTTTCTTTTTCACT
41964314 TTCTCTTTTTCTTTTTCACT
1 TTCT-TTTTTCTTTTTCACT
41964334 TTCTTTTT
1 TTCTTTTT
41964342 CAATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 4 0.17
17 6 0.25
18 5 0.21
19 5 0.21
20 4 0.17
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (19 bp):
TTCTTTTTTCTTTTTCACT
Found at i:41964342 original size:18 final size:17
Alignment explanation
Indices: 41964298--41964342 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
41964288 TTCACTCTCG
41964298 TTCT-TTTTTCTTTTCC
1 TTCTCTTTTTCTTTTCC
41964314 TTCTCTTTTTCTTTTTCAC
1 TTCTCTTTTTC-TTTTC-C
41964333 TT-TCTTTTTC
1 TTCTCTTTTTC
41964343 AATTTTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.15
17 6 0.23
18 13 0.50
19 3 0.12
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (17 bp):
TTCTCTTTTTCTTTTCC
Found at i:41964352 original size:40 final size:41
Alignment explanation
Indices: 41964251--41964352 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 41
41964241 TCAGACTCAA
*
41964251 TTTCTTTTTCAATTTTCTTTTTCTTCTCATATTCTTTTTCAC
1 TTTCTTTTTCAA-TTTCTTTTCCTTCTCATATTCTTTTTCAC
* * *
41964293 TCTCGTTCTTT---TTTCTTTTCCTTCTCTTTTTCTTTTTCAC
1 TTTC-TT-TTTCAATTTCTTTTCCTTCTCATATTCTTTTTCAC
41964333 TTTCTTTTTCAATTT-TTTTC
1 TTTCTTTTTCAATTTCTTTTC
41964353 TTTTTCTCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
38 3 0.06
39 2 0.04
40 34 0.68
41 3 0.06
42 3 0.06
43 2 0.04
44 3 0.06
ACGTcount: A:0.08, C:0.23, G:0.01, T:0.69
Consensus pattern (41 bp):
TTTCTTTTTCAATTTCTTTTCCTTCTCATATTCTTTTTCAC
Found at i:41964390 original size:51 final size:45
Alignment explanation
Indices: 41964301--41964393 Score: 114
Period size: 51 Copynumber: 1.9 Consensus size: 45
41964291 ACTCTCGTTC
**
41964301 TTTTTTCTTTTCCTTCTCTTTTTCTTTTTCACTTTCTTTTTCAAT
1 TTTTTTCTTTTCCTTCTCTTTTTCTTTTTCACACTCTTTTTCAAT
41964346 TTTTTTCTTTTTCTCATTCTCTTTTTGCTTTCTTTCACACTCTTTTTC
1 TTTTTTC-TTTTC-C-TTCTCTTTTT-C-TT-TTTCACACTCTTTTTC
41964394 TGTCATTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
45 7 0.17
46 5 0.12
47 1 0.03
48 10 0.25
49 1 0.03
50 2 0.05
51 14 0.35
ACGTcount: A:0.06, C:0.24, G:0.01, T:0.69
Consensus pattern (45 bp):
TTTTTTCTTTTCCTTCTCTTTTTCTTTTTCACACTCTTTTTCAAT
Found at i:41964406 original size:15 final size:15
Alignment explanation
Indices: 41964386--41964416 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41964376 TCTTTCACAC
41964386 TCTTTTTCTGTCATT
1 TCTTTTTCTGTCATT
*
41964401 TCTTTTTCTTTCATT
1 TCTTTTTCTGTCATT
41964416 T
1 T
41964417 TTTCATTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.71
Consensus pattern (15 bp):
TCTTTTTCTGTCATT
Found at i:41965414 original size:16 final size:16
Alignment explanation
Indices: 41965390--41965421 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41965380 ACGAAAATAC
*
41965390 AATTTGAATTTTTTTT
1 AATTCGAATTTTTTTT
41965406 AATTCGAATTTTTTTT
1 AATTCGAATTTTTTTT
41965422 CACAACGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.66
Consensus pattern (16 bp):
AATTCGAATTTTTTTT
Found at i:41967427 original size:52 final size:52
Alignment explanation
Indices: 41967349--41967449 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
41967339 GCAGATGACA
*
41967349 AAACAGAAGATGCTTAGGAAGCCATTGAATGTAACAGTCCGGTTTAGACACG
1 AAACAGAAGATGCTTAGGAAGCCATTGAATATAACAGTCCGGTTTAGACACG
*
41967401 AAACAGAAGATGCTTGGGAAGCCATTGAATATAACAGTCCGGTTTAGAC
1 AAACAGAAGATGCTTAGGAAGCCATTGAATATAACAGTCCGGTTTAGAC
41967450 CCTAGTCGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.22
Consensus pattern (52 bp):
AAACAGAAGATGCTTAGGAAGCCATTGAATATAACAGTCCGGTTTAGACACG
Found at i:41968101 original size:230 final size:230
Alignment explanation
Indices: 41967698--41968156 Score: 882
Period size: 230 Copynumber: 2.0 Consensus size: 230
41967688 AAGGCCATTG
41967698 TATGATAGTGGGAGACATGGTTTGGCAATATAGTAAATAGATAAAATTTTAAAGGATGGTTAGGT
1 TATGATAGTGGGAGACATGGTTTGGCAATATAGTAAATAGATAAAATTTTAAAGGATGGTTAGGT
41967763 AATTAGGTAATATATGTTATTAAATAAAACAAATGCATGAAAATTTGTCCATTCAGGCATATACT
66 AATTAGGTAATATATGTTATTAAATAAAACAAATGCATGAAAATTTGTCCATTCAGGCATATACT
*
41967828 TGCCAAAAATACAGACGAAAAAGAGAGGAAAAGAACAAGCTAGGTTTTGGCACTTTGATCCTTGA
131 TGCCAAAAATACAAACGAAAAAGAGAGGAAAAGAACAAGCTAGGTTTTGGCACTTTGATCCTTGA
*
41967893 TTAAGGTATTGATTTTTGTCCGTTTTTGATAATTA
196 TTAAGGTATGGATTTTTGTCCGTTTTTGATAATTA
41967928 TATGATAGTGGGAGACATGGTTTGGCAATATAGTAAATAGATAAAATTTTAAAGGATGGTTAGGT
1 TATGATAGTGGGAGACATGGTTTGGCAATATAGTAAATAGATAAAATTTTAAAGGATGGTTAGGT
* *
41967993 AATTAGGTAATATATGTTATTAAATAAAACAAATGCATGAAAATTTGTTCATTCATGCATATACT
66 AATTAGGTAATATATGTTATTAAATAAAACAAATGCATGAAAATTTGTCCATTCAGGCATATACT
41968058 TGCCAAAAATACAAACGAAAAAGAGAGGAAAAGAACAAGCTAGGTTTTGGCACTTTGATCCTTGA
131 TGCCAAAAATACAAACGAAAAAGAGAGGAAAAGAACAAGCTAGGTTTTGGCACTTTGATCCTTGA
41968123 TTAAGGTATGGATTTTTGTCCGTTTTTGATAATT
196 TTAAGGTATGGATTTTTGTCCGTTTTTGATAATT
41968157 TCTACGTTTC
Statistics
Matches: 225, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
230 225 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (230 bp):
TATGATAGTGGGAGACATGGTTTGGCAATATAGTAAATAGATAAAATTTTAAAGGATGGTTAGGT
AATTAGGTAATATATGTTATTAAATAAAACAAATGCATGAAAATTTGTCCATTCAGGCATATACT
TGCCAAAAATACAAACGAAAAAGAGAGGAAAAGAACAAGCTAGGTTTTGGCACTTTGATCCTTGA
TTAAGGTATGGATTTTTGTCCGTTTTTGATAATTA
Found at i:41970373 original size:28 final size:27
Alignment explanation
Indices: 41970310--41970379 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
41970300 ATAGTGAGTC
*
41970310 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
41970337 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
41970365 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41970380 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:41978302 original size:28 final size:27
Alignment explanation
Indices: 41978239--41978308 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
41978229 ATAGTGAGTC
*
41978239 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
*
41978266 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
41978294 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41978309 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:41981077 original size:40 final size:40
Alignment explanation
Indices: 41981011--41981177 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
41981001 AAATTGAATG
* * *
41981011 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
41981050 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
41981090 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
41981130 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
41981170 ATATCCGG
1 ATATCCGG
41981178 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41989069 original size:40 final size:40
Alignment explanation
Indices: 41989003--41989169 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
41988993 AAATTGAATG
* * *
41989003 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
41989042 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
41989082 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
41989122 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
41989162 ATATCCGG
1 ATATCCGG
41989170 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:42001304 original size:39 final size:40
Alignment explanation
Indices: 42001261--42001359 Score: 134
Period size: 39 Copynumber: 2.5 Consensus size: 40
42001251 AATATAAATC
*
42001261 AACAATAATAATAACTAACAATAAT-TAGGGTTTTTTACT
1 AACAATAATAATAACTAACAATAATATAAGGTTTTTTACT
*
42001300 AACAAT-A-ACTAACTAACAATAATAATAAGGTTTTTTACT
1 AACAATAATAATAACTAACAATAAT-ATAAGGTTTTTTACT
42001339 AACAATAATAACTAAC-AACAA
1 AACAATAATAA-TAACTAACAA
42001360 AAAAACAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
37 15 0.29
38 1 0.02
39 25 0.48
40 1 0.02
41 6 0.12
42 4 0.08
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (40 bp):
AACAATAATAATAACTAACAATAATATAAGGTTTTTTACT
Found at i:42001511 original size:37 final size:37
Alignment explanation
Indices: 42001442--42001514 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
42001432 AAAATTATAC
* *
42001442 CTTCTCTTTTCTATTTTTTTTCCTTCTCCTTCTTCTT
1 CTTCTCTTCTCTATTTTCTTTCCTTCTCCTTCTTCTT
* *
42001479 CTTCTCTTCTC-ATTTTCTTTCTTTTTCTCTTCTTCT
1 CTTCTCTTCTCTATTTTCTTTCCTTCTC-CTTCTTCT
42001515 CCTTGCTGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 13 0.42
37 18 0.58
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (37 bp):
CTTCTCTTCTCTATTTTCTTTCCTTCTCCTTCTTCTT
Found at i:42005148 original size:25 final size:25
Alignment explanation
Indices: 42005119--42005174 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
42005109 AGATTAATTT
* *
42005119 ATATTTTATGTATCATTATATTTAA
1 ATATTTTATGTAGCATTATATTCAA
*
42005144 ATATTTTGTGTAGCATTATATTCAA
1 ATATTTTATGTAGCATTATATTCAA
*
42005169 TTATTT
1 ATATTT
42005175 AAATATCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.55
Consensus pattern (25 bp):
ATATTTTATGTAGCATTATATTCAA
Found at i:42006536 original size:12 final size:12
Alignment explanation
Indices: 42006519--42006548 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42006509 GCCACACGGG
42006519 CGTGTGGTTGCC
1 CGTGTGGTTGCC
42006531 CGTGTGGTTGCC
1 CGTGTGGTTGCC
*
42006543 CATGTG
1 CGTGTG
42006549 CCATAACACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.03, C:0.23, G:0.40, T:0.33
Consensus pattern (12 bp):
CGTGTGGTTGCC
Found at i:42007332 original size:34 final size:34
Alignment explanation
Indices: 42007273--42007340 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
42007263 GCATATCTGA
*
42007273 TACTAAAACTGAAAAGGGCTAAGGCCCAGATTGC
1 TACTAAAACTGAAAAGGACTAAGGCCCAGATTGC
* * *
42007307 TACTGAAACTGAAATGGACTTAGGCCCAGATTGC
1 TACTAAAACTGAAAAGGACTAAGGCCCAGATTGC
42007341 ATTTGGCTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21
Consensus pattern (34 bp):
TACTAAAACTGAAAAGGACTAAGGCCCAGATTGC
Found at i:42008297 original size:22 final size:22
Alignment explanation
Indices: 42008269--42008335 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
42008259 ACACTTTTAA
42008269 CGTTGATCGGCTATTGACCAAT
1 CGTTGATCGGCTATTGACCAAT
42008291 CGTTGATCGGCTATTGACCAAT
1 CGTTGATCGGCTATTGACCAAT
42008313 CGTTGATCGGCTATTGACCAAT
1 CGTTGATCGGCTATTGACCAAT
42008335 C
1 C
42008336 ATGTGGCGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.31
Consensus pattern (22 bp):
CGTTGATCGGCTATTGACCAAT
Found at i:42008691 original size:14 final size:13
Alignment explanation
Indices: 42008659--42008696 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
42008649 AGTAATTTCT
42008659 TAAATTTTTTTTG
1 TAAATTTTTTTTG
42008672 TAAATTTTATTTT-
1 TAAATTTT-TTTTG
42008685 TATAATTTTTTT
1 TA-AATTTTTTT
42008697 ACAATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
TAAATTTTTTTTG
Found at i:42008726 original size:21 final size:20
Alignment explanation
Indices: 42008701--42008744 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
42008691 TTTTTTACAA
42008701 TTTATATGT-TTTGTTCTAGAT
1 TTTATATGTATTT-TTCTAG-T
42008722 TTTATATGTATTTTTCTAGT
1 TTTATATGTATTTTTCTAGT
42008742 TTT
1 TTT
42008745 CTTTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.18
21 15 0.68
22 3 0.14
ACGTcount: A:0.18, C:0.05, G:0.11, T:0.66
Consensus pattern (20 bp):
TTTATATGTATTTTTCTAGT
Found at i:42009673 original size:9 final size:11
Alignment explanation
Indices: 42009640--42009672 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
42009630 TAAATTGAAA
*
42009640 ATAA-TAATTT
1 ATAATTAATAT
42009650 ATAATTAATAT
1 ATAATTAATAT
42009661 ATAATTAATAT
1 ATAATTAATAT
42009672 A
1 A
42009673 AATATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
ATAATTAATAT
Found at i:42009676 original size:17 final size:18
Alignment explanation
Indices: 42009638--42009679 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
42009628 ATTAAATTGA
*
42009638 AAATA-ATAATTTATAAT
1 AAATATATAATTAATAAT
*
42009655 TAATATATAATTAAT-AT
1 AAATATATAATTAATAAT
42009672 AAATATAT
1 AAATATAT
42009680 TATATTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATATAATTAATAAT
Found at i:42010206 original size:24 final size:24
Alignment explanation
Indices: 42010162--42010207 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
42010152 ACCCTTTAAG
* *
42010162 ATATAGTATAGGATTATATAATAT
1 ATATAGTATAGGACTAAATAATAT
42010186 ATATAGTTATA-GACTAAATAAT
1 ATATAG-TATAGGACTAAATAAT
42010208 GGATGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (24 bp):
ATATAGTATAGGACTAAATAATAT
Found at i:42010324 original size:3 final size:3
Alignment explanation
Indices: 42010318--42010363 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
42010308 CTAAAAGAAG
42010318 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
42010364 AGGAGTTTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42016707 original size:40 final size:40
Alignment explanation
Indices: 42016652--42016861 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
42016642 AACATTGAAA
42016652 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
42016692 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
42016732 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
42016772 ATATATCCGGGCTAAGACCCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
42016811 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
42016852 CTATATCCGG
1 ATATATCCGG
42016862 TTAAATCCCG
Statistics
Matches: 151, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 149 0.99
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:42018901 original size:46 final size:45
Alignment explanation
Indices: 42018845--42019010 Score: 156
Period size: 46 Copynumber: 3.6 Consensus size: 45
42018835 TCTCATAGCT
42018845 GATGCATGTCCCAGACATGTCTTACATTGGCTTACGTCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACATTGGCTT-CGTCTCGAGGCC
* * * * * *
42018891 GAAGCATGTCCTAGACATGTCTTAC-TCTAGCATTTGTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACAT-TGGC-TTCGTCTCGAGGCC
* * * *
42018937 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACATTGGCT-TCGT-CTCGAGGCC
*
42018985 GATGCATGTCCTAGACATGTCTTACA
1 GATGCATGTCCCAGACATGTCTTACA
42019011 CTAGCTCACA
Statistics
Matches: 96, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
45 1 0.01
46 46 0.48
47 29 0.30
48 19 0.20
49 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACATTGGCTTCGTCTCGAGGCC
Found at i:42018985 original size:94 final size:92
Alignment explanation
Indices: 42018845--42019015 Score: 238
Period size: 94 Copynumber: 1.8 Consensus size: 92
42018835 TCTCATAGCT
* * *
42018845 GATGCATGTCCCAGACATGTCTTACATTGGCTTACGTCTCGAGGCCGAAGCATGTCCTAGACATG
1 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATATCGAGGCCGAAGCATGTCCTAGACATG
*
42018910 TCTTACTCTAGCATTTGTCTCAATGCC
66 TCTTACACTAGCATTTGTCTCAATGCC
* *
42018937 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGCCGATGCATGTCCTAGA
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-ATCGAGGCCGAAGCATGTCCTAGA
42019000 CATGTCTTACACTAGC
62 CATGTCTTACACTAGC
42019016 TCACACAAGT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
92 4 0.06
93 14 0.20
94 49 0.71
95 2 0.03
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.29
Consensus pattern (92 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTTACATATCGAGGCCGAAGCATGTCCTAGACATG
TCTTACACTAGCATTTGTCTCAATGCC
Found at i:42020430 original size:42 final size:42
Alignment explanation
Indices: 42020383--42020496 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 42
42020373 TACCATTCCA
* * *
42020383 ATGCCATATCCCAGATATGGCCTTACATG-GGATCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAG-TCTCATATCG
* * *
42020425 ATGCCAATAGT-CCAGCTATGGTTTTACACGAAGTCTCATATTG
1 ATGCC-ATA-TCCCAGATATGGTCTTACACGAAGTCTCATATCG
*
42020468 ATGCCATATCCCAGATATAGTCTTACACG
1 ATGCCATATCCCAGATATGGTCTTACACG
42020497 TAATCTTAGT
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
41 1 0.02
42 24 0.41
43 32 0.54
44 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
Found at i:42022195 original size:46 final size:44
Alignment explanation
Indices: 42022091--42022198 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
42022081 TGTCTTTGAC
** * * *
42022091 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
42022135 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
42022181 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
42022199 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:42023982 original size:44 final size:45
Alignment explanation
Indices: 42023892--42024020 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
42023882 GACAGAACGA
*
42023892 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
42023938 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
42023982 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
42024021 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:42031377 original size:42 final size:42
Alignment explanation
Indices: 42031300--42031426 Score: 152
Period size: 42 Copynumber: 3.0 Consensus size: 42
42031290 ATATTTGATC
* * * *
42031300 CATTTTATTCGATGATGCACTTATGTTCCAGTATAATTGCTT
1 CATTATATTCGATGATGCACTTAAGTGCCAATATAATTGCTT
*
42031342 CATTATATTCAATGATGCACTTAAGTGCCAATATAATTGCTT
1 CATTATATTCGATGATGCACTTAAGTGCCAATATAATTGCTT
*
42031384 CGA-TATA-TCTGATGATGCACTTACA-TGCCAATATATTTGCTT
1 C-ATTATATTC-GATGATGCACTTA-AGTGCCAATATAATTGCTT
42031426 C
1 C
42031427 GGTACATCCA
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 2 0.03
42 71 0.95
43 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
CATTATATTCGATGATGCACTTAAGTGCCAATATAATTGCTT
Found at i:42031441 original size:42 final size:42
Alignment explanation
Indices: 42031311--42031455 Score: 132
Period size: 42 Copynumber: 3.5 Consensus size: 42
42031301 ATTTTATTCG
** * * * *
42031311 ATGATGCACTTATGTTCCAGTATAATTGCTTC-ATTATATTCA
1 ATGATGCACTTACATGCCAATATAATTGCTTCGA-TACATCCA
* **
42031353 ATGATGCACTTA-AGTGCCAATATAATTGCTTCGATATATCTG
1 ATGATGCACTTACA-TGCCAATATAATTGCTTCGATACATCCA
* *
42031395 ATGATGCACTTACATGCCAATATATTTGCTTCGGTACATCCA
1 ATGATGCACTTACATGCCAATATAATTGCTTCGATACATCCA
* * *
42031437 ATGATACATTTACTTGCCA
1 ATGATGCACTTACATGCCA
42031456 GCATGATTGC
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 84 0.98
43 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (42 bp):
ATGATGCACTTACATGCCAATATAATTGCTTCGATACATCCA
Found at i:42036425 original size:42 final size:42
Alignment explanation
Indices: 42036278--42036445 Score: 156
Period size: 42 Copynumber: 3.9 Consensus size: 42
42036268 AGTAAGATGC
* **
42036278 CAATGCCATATCCCAGATATGGTCTTACATGGGATCACATATAT
1 CAATGCCATATCCCAGATATGGTCTTACACGAAATCAC--ATAT
* * * * ** * *
42036322 CGATGCCGATAGCCTAGCTATGGTCTTACACGATGTCTCGTAT
1 CAATGCC-ATATCCCAGATATGGTCTTACACGAAATCACATAT
* * *
42036365 CGATGCCATGTCCCAGATATGGTCTTACGCGAAATCACATAT
1 CAATGCCATATCCCAGATATGGTCTTACACGAAATCACATAT
* * *
42036407 CAATTCCATATCCTAGATATGGTCTTACATGAAATCACA
1 CAATGCCATATCCCAGATATGGTCTTACACGAAATCACA
42036446 CAACCCTAGT
Statistics
Matches: 98, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
42 59 0.60
43 10 0.10
44 6 0.06
45 23 0.23
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (42 bp):
CAATGCCATATCCCAGATATGGTCTTACACGAAATCACATAT
Found at i:42036977 original size:21 final size:22
Alignment explanation
Indices: 42036947--42036987 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
42036937 TAGTAAAAGT
42036947 CATTTCTCTAACCA-TAAACATG
1 CATTTCTCT-ACCATTAAACATG
42036969 CATTT-TCTACCATTAAACA
1 CATTTCTCTACCATTAAACA
42036988 CAAAACTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (22 bp):
CATTTCTCTACCATTAAACATG
Found at i:42040676 original size:27 final size:29
Alignment explanation
Indices: 42040646--42040760 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 29
42040636 ACGCAAGAGC
*
42040646 ATATA-GTGAATC-CGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
* **
42040673 ATATATTTTCAGCTCGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
* **
42040702 ATATAATTTTCAGCTCGCACACTTAGTGCT
1 ATAT-ATGTGAAGCTCGCACACTTAGTGCT
* ** *
42040732 ATATATTTTCAGTTCGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
42040761 GTACAATTTT
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
27 5 0.06
28 3 0.04
29 43 0.54
30 29 0.36
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (29 bp):
ATATATGTGAAGCTCGCACACTTAGTGCT
Found at i:42040713 original size:30 final size:29
Alignment explanation
Indices: 42040658--42040760 Score: 188
Period size: 29 Copynumber: 3.5 Consensus size: 29
42040648 ATAGTGAATC
42040658 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATATATTTTCAGCT
42040687 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATAT-ATTTTCAGCT
*
42040717 CGCACACTTAGTGCTATATATTTTCAGTT
1 CGCACACTTAGTGCTATATATTTTCAGCT
42040746 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42040761 GTACAATTTT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 43 0.60
30 29 0.40
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATATTTTCAGCT
Found at i:42040750 original size:59 final size:60
Alignment explanation
Indices: 42040657--42040790 Score: 207
Period size: 59 Copynumber: 2.2 Consensus size: 60
42040647 TATAGTGAAT
* * *
42040657 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA-TTTTCAGC
1 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATACAATTTTTAAAC
* * *
42040716 TCGCACACTTAGTGCTATATATTTTCAGTTCGCACACTTAGTGCTGTACAATTTTTAAAC
1 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATACAATTTTTAAAC
42040776 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
42040791 CAATCTTGTC
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
59 47 0.70
60 20 0.30
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35
Consensus pattern (60 bp):
CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATACAATTTTTAAAC
Found at i:42042083 original size:19 final size:18
Alignment explanation
Indices: 42042059--42042094 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42042049 CCCCCTTTTT
*
42042059 CTTTTCTTATTTTATTCCC
1 CTTTTCTT-TTTAATTCCC
42042078 CTTTTCTTTTTAATTCC
1 CTTTTCTTTTTAATTCC
42042095 TTTCTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.11, C:0.25, G:0.00, T:0.64
Consensus pattern (18 bp):
CTTTTCTTTTTAATTCCC
Found at i:42046501 original size:40 final size:40
Alignment explanation
Indices: 42046435--42046601 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
42046425 AAATTGAATG
* * *
42046435 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
42046474 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
42046514 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
42046554 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
42046594 ATATCCGG
1 ATATCCGG
42046602 TTATATTCCG
Statistics
Matches: 103, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
39 16 0.16
40 85 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:42054562 original size:40 final size:37
Alignment explanation
Indices: 42054461--42054567 Score: 119
Period size: 38 Copynumber: 2.8 Consensus size: 37
42054451 CTGGAAATTA
* *
42054461 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGGC
**
42054499 TATCCGGGCT-A-ACCCGAAGGCATTCGTGCGAGTTATTC
1 TATCCGGGCTAAGACCCGAAGGCATT-GTGCGAG-T-GGC
42054537 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCA-TTGTGC
42054568 ACGTGATTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
35 3 0.05
36 16 0.27
37 2 0.03
38 20 0.34
39 1 0.02
40 15 0.25
41 2 0.03
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.24
Consensus pattern (37 bp):
TATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGGC
Found at i:42054581 original size:40 final size:40
Alignment explanation
Indices: 42054421--42054583 Score: 144
Period size: 40 Copynumber: 4.2 Consensus size: 40
42054411 AAATTGAATG
* * **
42054421 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTG-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTGATT
* * *
42054460 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG--G
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATT
* *
42054498 CTATCCGGGCT-A-ACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGATT
* *
42054536 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGA-GTGATT
42054576 ATATCCGG
1 ATATCCGG
42054584 TTATATTCCG
Statistics
Matches: 100, Mismatches: 15, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
35 3 0.03
36 17 0.17
37 1 0.01
38 20 0.20
39 15 0.15
40 42 0.42
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGATT
Found at i:42056128 original size:38 final size:38
Alignment explanation
Indices: 42056081--42056318 Score: 404
Period size: 38 Copynumber: 6.3 Consensus size: 38
42056071 GGCTCAAAGG
* * *
42056081 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
42056119 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
42056157 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
42056195 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTTA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
42056233 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
42056271 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
42056309 CCCAGATATA
1 CCCGGATATA
42056319 CATCGAATAT
Statistics
Matches: 191, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 191 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:42058654 original size:40 final size:39
Alignment explanation
Indices: 42058609--42058816 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 39
42058599 CGGAATACAA
*
42058609 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42058649 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42058689 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
42058729 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
42058769 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
42058809 CCGGATAT
1 CCGGATAT
42058817 CATTCAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:42058749 original size:80 final size:81
Alignment explanation
Indices: 42058609--42058814 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
42058599 CGGAATACAA
* * *
42058609 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
42058673 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
42058689 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTAGCACAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTAGCACAAA
*
42058752 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
** * ** * *
42058769 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
42058815 ATCATTCAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
80 104 0.96
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (81 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:42066798 original size:40 final size:39
Alignment explanation
Indices: 42066753--42066959 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 39
42066743 CGGAATACAA
*
42066753 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42066793 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
42066833 CCGGATTTAACAACTTGCACGAATGCCTTC-GGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
42066872 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
42066912 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
42066952 CCGGATAT
1 CCGGATAT
42066960 CATTCAATTG
Statistics
Matches: 140, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
38 1 0.01
39 30 0.21
40 109 0.78
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:42066892 original size:79 final size:80
Alignment explanation
Indices: 42066753--42066958 Score: 231
Period size: 79 Copynumber: 2.6 Consensus size: 80
42066743 CGGAATACAA
* *
42066753 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTTGCACAAATG
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATG
*
42066818 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
* * * *
42066833 CCGGATTTAACAACTTGCACGAATGCCTTC-GGTCTTAGCCCGGAT-GTA-GTCACTAGCACAAT
1 CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACG--ACTAGCACAAA
*
42066895 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
** ** * *
42066912 CCGGATATAATTAC-TAGCATAAATGTCTTCGGGACTTAGCCCGGATA
1 CCGGATATAACAACAT-GCACGAATGCCTTCGGGTCTTAGCCCGGATA
42066959 TCATTCAATT
Statistics
Matches: 106, Mismatches: 15, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
77 1 0.01
78 3 0.03
79 61 0.58
80 41 0.39
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (80 bp):
CCGGATATAACAACATGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:42070296 original size:20 final size:20
Alignment explanation
Indices: 42070271--42070313 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
42070261 ATAAAGGGGA
*
42070271 AGAAGAAAAGGAAAATAAAG
1 AGAAGAAAAGGAAAAAAAAG
* *
42070291 AGAAGATAATGAAAAAAAAG
1 AGAAGAAAAGGAAAAAAAAG
42070311 AGA
1 AGA
42070314 GAGGAAAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (20 bp):
AGAAGAAAAGGAAAAAAAAG
Found at i:42072242 original size:19 final size:19
Alignment explanation
Indices: 42072218--42072263 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
42072208 AAAATGATAA
42072218 AAAATAATT-AAATTTTAAT
1 AAAAT-ATTAAAATTTTAAT
*
42072237 AAAATATTAAAATTTTATT
1 AAAATATTAAAATTTTAAT
42072256 AAAA-ATTA
1 AAAATATTA
42072264 TAAAAATCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATATTAAAATTTTAAT
Found at i:42072279 original size:20 final size:19
Alignment explanation
Indices: 42072256--42072384 Score: 66
Period size: 20 Copynumber: 6.6 Consensus size: 19
42072246 AAATTTTATT
*
42072256 AAAAATTATAAAAATCGTAA
1 AAAAATTATAAAAAT-ATAA
*
42072276 AAAAATTAT-AAAATATAT
1 AAAAATTATAAAAATATAA
* * *
42072294 AGAAA-TATAGAAAAGAATTA
1 AAAAATTATA-AAAA-TATAA
* *
42072314 TAAAATTTTATAAAATCATAA
1 AAAAATTATA-AAAAT-ATAA
* *
42072335 GAAAATTATAAAAATGTAA
1 AAAAATTATAAAAATATAA
* * *
42072354 AGAAA-TATAAAATTTGTAA
1 AAAAATTATAAAA-ATATAA
*
42072373 AAAAAATATAAA
1 AAAAATTATAAA
42072385 TTATCGTAGT
Statistics
Matches: 83, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
17 3 0.04
18 13 0.16
19 24 0.29
20 25 0.30
21 18 0.22
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (19 bp):
AAAAATTATAAAAATATAA
Found at i:42072315 original size:30 final size:28
Alignment explanation
Indices: 42072273--42072365 Score: 98
Period size: 30 Copynumber: 3.2 Consensus size: 28
42072263 ATAAAAATCG
42072273 TAAAAAAATTATAAAATATATAGAAATA
1 TAAAAAAATTATAAAATATATAGAAATA
*
42072301 TAGAAAAGAATTATAAAATTTTATA-AAATCA
1 TA-AAAA-AATTATAAAA-TATATAGAAAT-A
* * *
42072332 TAAGAAAATTATAAAAATGTAAAGAAATA
1 TAAAAAAATTAT-AAAATATATAGAAATA
42072361 TAAAA
1 TAAAA
42072366 TTTGTAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
28 2 0.04
29 19 0.35
30 25 0.46
31 8 0.15
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (28 bp):
TAAAAAAATTATAAAATATATAGAAATA
Found at i:42072548 original size:10 final size:10
Alignment explanation
Indices: 42072535--42072594 Score: 74
Period size: 10 Copynumber: 6.3 Consensus size: 10
42072525 TTTTGATGCA
42072535 TTTTATAATT
1 TTTTATAATT
*
42072545 TTTTATGATT
1 TTTTATAATT
42072555 TTTTA-AA-T
1 TTTTATAATT
42072563 TTTTA-AATT
1 TTTTATAATT
42072572 TTTTATAATT
1 TTTTATAATT
42072582 CTTTTAT-ATT
1 -TTTTATAATT
42072592 TTT
1 TTT
42072595 ATTTTATAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
8 8 0.18
9 10 0.22
10 21 0.47
11 6 0.13
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTTATAATT
Found at i:42072555 original size:18 final size:17
Alignment explanation
Indices: 42072534--42072624 Score: 64
Period size: 18 Copynumber: 5.3 Consensus size: 17
42072524 TTTTTGATGC
42072534 ATTTTATAATTTTTTAT
1 ATTTTATAATTTTTTAT
* *
42072551 GATTTTTTAAATTTTTAAAT
1 -ATTTTAT-AATTTTT-TAT
*
42072571 TTTTTATAATTCTTTTAT
1 ATTTTATAATT-TTTTAT
*
42072589 ATTTT-T-ATTTTATA-
1 ATTTTATAATTTTTTAT
*
42072603 ATTTT-TAATGTTTTAAT
1 ATTTTATAAT-TTTTTAT
42072620 ATTTT
1 ATTTT
42072625 TTATTAAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
14 6 0.10
15 6 0.10
16 7 0.12
17 6 0.10
18 16 0.28
19 15 0.26
20 2 0.03
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (17 bp):
ATTTTATAATTTTTTAT
Found at i:42072557 original size:19 final size:18
Alignment explanation
Indices: 42072535--42072596 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 18
42072525 TTTTGATGCA
42072535 TTTTATAATTTTTTATGAT
1 TTTTATAATTTTTTAT-AT
* *
42072554 TTTT-TAAATTTTTAAATT
1 TTTTATAATTTTTTATA-T
42072572 TTTTATAATTCTTTTATAT
1 TTTTATAATT-TTTTATAT
42072591 TTTTAT
1 TTTTAT
42072597 TTTATAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 1 0.03
18 14 0.39
19 15 0.42
20 6 0.17
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTATAATTTTTTATAT
Found at i:42072984 original size:84 final size:85
Alignment explanation
Indices: 42072780--42073007 Score: 266
Period size: 84 Copynumber: 2.7 Consensus size: 85
42072770 TTTTGATACA
* * *
42072780 TTTGACAGTTTAAGTACCCAATTGAGTGCAAAAAAAAAAATAGGGACTTAATTTTTTTTTTAAAT
1 TTTGAAAGTTCAAGTACCCAATTGAGTGC--AAAAAAAAACAGGGACTTAATTTTTTTTTTAAAT
42072845 TTTGAGGGCCTTTATGATGAAT
64 TTTGAGGGCCTTTATGATGAAT
** * *
42072867 TTTGAAAGTTCAAGTACCCAATTTTGTGC-AAAAAATACAGGGGCTTAATTTTTTTTTTTAAA-T
1 TTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAACAGGGACTTAA-TTTTTTTTTTAAATT
*
42072930 TTGAGGGCCTTT-TGATGCAT
65 TTGAGGGCCTTTATGATGAAT
* * * ** *
42072950 TTT-AAATGTTCAAGTACCTAATTGAATGCAAAAAAAAATACAGACTTAATTATTTTTT
1 TTTGAAA-GTTCAAGTACCCAATTGAGTGCAAAAAAAAACAGGGACTTAATTTTTTTTT
42073008 AAAAAATTTT
Statistics
Matches: 120, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
82 3 0.03
83 36 0.30
84 43 0.36
85 13 0.11
87 25 0.21
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (85 bp):
TTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAACAGGGACTTAATTTTTTTTTTAAATTT
TGAGGGCCTTTATGATGAAT
Found at i:42073006 original size:83 final size:85
Alignment explanation
Indices: 42072780--42073007 Score: 261
Period size: 83 Copynumber: 2.7 Consensus size: 85
42072770 TTTTGATACA
* * **
42072780 TTTGACAGTTTAAGTACCCAATTGAGTGCAAAAAAAAAAATAGGGACTTAATTTTTTTTTTAAAT
1 TTTGAAAGTTCAAGTACCCAATTGAGTGC--AAAAAAAAATACAGACTTAATTTTTTTTTTAAAT
42072845 TTTGAGGGCCTTTATGATGAAT
64 TTTGAGGGCCTTTATGATGAAT
** *
42072867 TTTGAAAGTTCAAGTACCCAATTTTGTGC---AAAAAATACAGGGGCTTAATTTTTTTTTTTAAA
1 TTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAATACA--GACTTAA-TTTTTTTTTTAAA
*
42072929 -TTTGAGGGCCTTT-TGATGCAT
63 TTTTGAGGGCCTTTATGATGAAT
* * *
42072950 TTT-AAATGTTCAAGTACCTAATTGAATGCAAAAAAAAATACAGACTTAATTATTTTTT
1 TTTGAAA-GTTCAAGTACCCAATTGAGTGCAAAAAAAAATACAGACTTAATTTTTTTTT
42073008 AAAAAATTTT
Statistics
Matches: 120, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
82 11 0.09
83 36 0.30
84 25 0.21
85 13 0.11
86 10 0.08
87 25 0.21
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (85 bp):
TTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAATACAGACTTAATTTTTTTTTTAAATTT
TGAGGGCCTTTATGATGAAT
Found at i:42074743 original size:23 final size:24
Alignment explanation
Indices: 42074717--42074767 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
42074707 TATTTTTTAA
* *
42074717 AAAATTAAAATTT-TTGAAATTTT
1 AAAATTAAAATTTATTAAAATTAT
*
42074740 AAAATTAGAATTTATTAAAATTAT
1 AAAATTAAAATTTATTAAAATTAT
42074764 AAAA
1 AAAA
42074768 AAATCATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
AAAATTAAAATTTATTAAAATTAT
Done.