Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 101 of 378
Found at i:27687439 original size:16 final size:16
Alignment explanation
Indices: 27687399--27687440 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
27687389 TAGCCAAACT
27687399 TTCAGCTTTTCGACAA
1 TTCAGCTTTTCGACAA
* *
27687415 TTCAACTTTTCGACAT
1 TTCAGCTTTTCGACAA
*
27687431 TTTAGCTTTT
1 TTCAGCTTTT
27687441 GCCGATCTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (16 bp):
TTCAGCTTTTCGACAA
Found at i:27688683 original size:16 final size:16
Alignment explanation
Indices: 27688657--27688694 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
27688647 AAAAGAAAAA
27688657 TTTGAGATTTCA-AGATT
1 TTTG-GATTTCAGA-ATT
27688674 TTTGGATTTCAGAATT
1 TTTGGATTTCAGAATT
27688690 TTTGG
1 TTTGG
27688695 GGCGTTACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.24, C:0.05, G:0.21, T:0.50
Consensus pattern (16 bp):
TTTGGATTTCAGAATT
Found at i:27689604 original size:11 final size:11
Alignment explanation
Indices: 27689584--27689614 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
27689574 ATTTTTTTAA
27689584 ATTA-TATTTT
1 ATTATTATTTT
27689594 ATTATTATTTT
1 ATTATTATTTT
27689605 ATTATTATTT
1 ATTATTATTT
27689615 CATGTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:27691041 original size:31 final size:31
Alignment explanation
Indices: 27691006--27691069 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
27690996 CCTTTTCATG
27691006 TTTCATATTCCATAACACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
* **
27691037 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTCCATAACACTGGGCCGAAGCCT
27691068 TT
1 TT
27691070 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATATTCCATAACACTGGGCCGAAGCCT
Found at i:27691312 original size:24 final size:24
Alignment explanation
Indices: 27691261--27691380 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
27691251 GCTTTATCAT
*
27691261 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
27691286 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
*
27691310 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
27691334 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
27691358 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
27691381 TCACTTCCTC
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
24 76 0.86
25 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:27691455 original size:20 final size:20
Alignment explanation
Indices: 27691430--27691490 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
27691420 TTATGATTAC
27691430 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
27691450 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
27691470 GTCATGTGCATCTCATACAT
1 ATCATGTGCATATCATACAT
27691490 A
1 A
27691491 CCATATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:27691565 original size:25 final size:25
Alignment explanation
Indices: 27691533--27691580 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
27691523 ATACATAAAC
* * *
27691533 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
27691558 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
27691581 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:27693570 original size:20 final size:22
Alignment explanation
Indices: 27693532--27693571 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
27693522 TTCAAATACG
*
27693532 ATAATATATATATATTTTCCTA
1 ATAATATATATATAATTTCCTA
27693554 ATAATA-AT-TATAATTTCC
1 ATAATATATATATAATTTCC
27693572 ATAAATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAATATATATATAATTTCCTA
Found at i:27698044 original size:44 final size:42
Alignment explanation
Indices: 27697980--27698139 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 42
27697970 ATATGTGTTA
* * ** * *
27697980 TCGTGTAAGATCACGTCTGGGATGTTGGCATCGATTTGTGATT
1 TCGTGTAAGACCATGTCTGGGACATTGGCAT-GATATATGATT
*
27698023 TACGTGTAAGACCATGTCTGGGACATTGGCATTATATATGATT
1 T-CGTGTAAGACCATGTCTGGGACATTGGCATGATATATGATT
* * *
27698066 TCGTGTAAGACCTTGTCTGGGACAATGGCATCGATA-ATTTATT
1 TCGTGTAAGACCATGTCTGGGACATTGGCAT-GATATA-TGATT
* * **
27698109 ACATGTAAGACCACCTCTGGGACATTGGCAT
1 TCGTGTAAGACCATGTCTGGGACATTGGCAT
27698140 TGTAAGAGCT
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
42 29 0.30
43 42 0.43
44 26 0.27
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
TCGTGTAAGACCATGTCTGGGACATTGGCATGATATATGATT
Found at i:27698075 original size:86 final size:84
Alignment explanation
Indices: 27697980--27698140 Score: 198
Period size: 85 Copynumber: 1.9 Consensus size: 84
27697970 ATATGTGTTA
* *** * **
27697980 TCGTGTAAGATCACGTCTGGGATGTTGGCATCGAT-TTGTGATTTACGTGTAAGACCATGTCTGG
1 TCGTGTAAGACCACGTCTGGGACAATGGCATCGATATT-T-A-TTACATGTAAGACCACCTCTGG
27698044 GACATTGGCATTATATATGATT
63 GACATTGGCATTATATATGATT
**
27698066 TCGTGTAAGACCTTGTCTGGGACAATGGCATCGATAATTTATTACATGTAAGACCACCTCTGGGA
1 TCGTGTAAGACCACGTCTGGGACAATGGCATCGAT-ATTTATTACATGTAAGACCACCTCTGGGA
27698131 CATTGGCATT
65 CATTGGCATT
27698141 GTAAGAGCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
85 31 0.48
86 30 0.47
87 1 0.02
88 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (84 bp):
TCGTGTAAGACCACGTCTGGGACAATGGCATCGATATTTATTACATGTAAGACCACCTCTGGGAC
ATTGGCATTATATATGATT
Found at i:27704716 original size:42 final size:43
Alignment explanation
Indices: 27704655--27704772 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 43
27704645 GATTTGTAAT
* *
27704655 TTACGTGTAAGACCATGTCTAGGACATTGGCATCG-T-ATACGA
1 TTACATGTAAGACCCTGTCTAGGACATTGGCATCGATAAT-CGA
* * * * *
27704697 TTTCATGTAAGACCCTGTCTGGGACAGTAGCATCGATAATTGA
1 TTACATGTAAGACCCTGTCTAGGACATTGGCATCGATAATCGA
**
27704740 TTACATGTAAGACCAC-GTCTAGGATGTTGGCAT
1 TTACATGTAAGACC-CTGTCTAGGACATTGGCAT
27704773 TATACAAGCT
Statistics
Matches: 60, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
42 29 0.48
43 28 0.47
44 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (43 bp):
TTACATGTAAGACCCTGTCTAGGACATTGGCATCGATAATCGA
Found at i:27704718 original size:86 final size:84
Alignment explanation
Indices: 27704616--27704772 Score: 194
Period size: 85 Copynumber: 1.8 Consensus size: 84
27704606 TGTGTTATCG
* * *
27704616 TGTAAGACCACGTCTGGGAC-GTTGGCATCGAT-TTGTAATTTACGTGTAAGACCATGTCTAGGA
1 TGTAAGACCACGTCTGGGACAG-TAGCATCGATATTG--A-TTACATGTAAGACCACGTCTAGGA
27704679 CATTGGCATCGTATACGATTTCA
62 CATTGGCATCGTATACGATTTCA
**
27704702 TGTAAGACC-CTGTCTGGGACAGTAGCATCGATAATTGATTACATGTAAGACCACGTCTAGGATG
1 TGTAAGACCAC-GTCTGGGACAGTAGCATCGAT-ATTGATTACATGTAAGACCACGTCTAGGACA
27704766 TTGGCAT
64 TTGGCAT
27704773 TATACAAGCT
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
85 30 0.48
86 28 0.45
87 1 0.02
88 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (84 bp):
TGTAAGACCACGTCTGGGACAGTAGCATCGATATTGATTACATGTAAGACCACGTCTAGGACATT
GGCATCGTATACGATTTCA
Found at i:27707455 original size:8 final size:8
Alignment explanation
Indices: 27707431--27707464 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
27707421 GTACAAAGAA
27707431 ATTTTGTG
1 ATTTTGTG
*
27707439 TACTTTGTG
1 -ATTTTGTG
27707448 ATTTTGTG
1 ATTTTGTG
27707456 ATTTTGTG
1 ATTTTGTG
27707464 A
1 A
27707465 ATTAAGGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.15, C:0.03, G:0.24, T:0.59
Consensus pattern (8 bp):
ATTTTGTG
Found at i:27707945 original size:42 final size:43
Alignment explanation
Indices: 27707874--27707989 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 43
27707864 ATATGTGTTA
*
27707874 TCGTGTAAGACCATGTTTGGAACGTTGGCATCG-TATTTGATT
1 TCGTGTAAGACCATGTTGGGAACGTTGGCATCGATATTTGATT
*
27707916 TCGTGTAAGACCCTGTCTGGGATA-G-TGGCATCGATATTTGATT
1 TCGTGTAAGACCATGT-TGGGA-ACGTTGGCATCGATATTTGATT
* * * *
27707959 ACATGTAATACCACGTTTGGG-ACGTTGGCAT
1 TCGTGTAAGACCATG-TTGGGAACGTTGGCAT
27707990 TGTACGAGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
41 1 0.02
42 24 0.39
43 34 0.56
44 2 0.03
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.34
Consensus pattern (43 bp):
TCGTGTAAGACCATGTTGGGAACGTTGGCATCGATATTTGATT
Found at i:27708760 original size:10 final size:10
Alignment explanation
Indices: 27708720--27708762 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
27708710 TATTGAAACA
*
27708720 TATGCTTTGG
1 TATGATTTGG
27708730 TATGATTTTGG
1 TATGA-TTTGG
*
27708741 TTTAGATTTGG
1 TAT-GATTTGG
27708752 TATGATTTGG
1 TATGATTTGG
27708762 T
1 T
27708763 TAGTGAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 12 0.43
11 14 0.50
12 2 0.07
ACGTcount: A:0.16, C:0.02, G:0.28, T:0.53
Consensus pattern (10 bp):
TATGATTTGG
Found at i:27711289 original size:40 final size:40
Alignment explanation
Indices: 27711244--27711431 Score: 270
Period size: 40 Copynumber: 4.7 Consensus size: 40
27711234 ATAACCACAA
* * *
27711244 GCACAATTGCCTTCGGGTCTTAACTCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
27711284 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
27711324 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
27711364 GCACAAATGCCTTCGGGTCTTAACCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTC
* * *
27711404 GCATAAATGCCTTCGGGGCTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAACCCGG
27711432 GTATCATTCA
Statistics
Matches: 135, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 133 0.99
41 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:27711329 original size:80 final size:79
Alignment explanation
Indices: 27711224--27711435 Score: 309
Period size: 80 Copynumber: 2.7 Consensus size: 79
27711214 TCTTCGGAAT
* * *
27711224 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACTCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
27711288 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* *
27711303 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCAC
1 TTAGCCCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
27711368 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* * * *
27711383 TTAACCCGGATATAATCACTAGCATAAATGCCTTCGGGGCTTAGCCCGGGTAT
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTAT
27711436 CATTCAATTG
Statistics
Matches: 119, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
79 5 0.04
80 113 0.95
81 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
TTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACA
AATGCCTTCGGGTC
Found at i:27719878 original size:15 final size:15
Alignment explanation
Indices: 27719858--27719918 Score: 70
Period size: 15 Copynumber: 4.0 Consensus size: 15
27719848 TGGTACGGTA
*
27719858 TTGTATATTGGATTT
1 TTGTATCTTGGATTT
27719873 TTGTATCTTGGATTT
1 TTGTATCTTGGATTT
*
27719888 CTT-CATCTTGGATTTT
1 -TTGTATCTTGGA-TTT
*
27719904 TTTTATCTTGGATTT
1 TTGTATCTTGGATTT
27719919 CTTTATTTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 27 0.68
16 13 0.32
ACGTcount: A:0.15, C:0.08, G:0.16, T:0.61
Consensus pattern (15 bp):
TTGTATCTTGGATTT
Found at i:27719913 original size:16 final size:15
Alignment explanation
Indices: 27719865--27719924 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
27719855 GTATTGTATA
*
27719865 TTGGATTTTTGTATC
1 TTGGATTTTTTTATC
* *
27719880 TTGGATTTCTTCATC
1 TTGGATTTTTTTATC
27719895 TTGGATTTTTTTTATC
1 TTGGA-TTTTTTTATC
*
27719911 TTGGATTTCTTTAT
1 TTGGATTTTTTTAT
27719925 TTCGGTCTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
15 25 0.66
16 13 0.34
ACGTcount: A:0.13, C:0.10, G:0.15, T:0.62
Consensus pattern (15 bp):
TTGGATTTTTTTATC
Found at i:27726581 original size:29 final size:29
Alignment explanation
Indices: 27726538--27726615 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
27726528 AACCATATTC
* *
27726538 ATATGGCCCCTTTAGGCCCAAATCACCTGT
1 ATATGG-CCCATTAGGCCCAAATCACATGT
* *
27726568 ATATGGCCCATTAGACCCAAATCACATTT
1 ATATGGCCCATTAGGCCCAAATCACATGT
*
27726597 ATATGGCCCGTTAGGCCCA
1 ATATGGCCCATTAGGCCCA
27726616 GTCACATTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 36 0.86
30 6 0.14
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACATGT
Found at i:27726611 original size:58 final size:58
Alignment explanation
Indices: 27726504--27726615 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 58
27726494 AAATTCACAT
* * * *
27726504 ACCTGTATTTGGCCTATTAAGCCCAACCATATTCATATGGCCCCTTTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAAGCCCAACCACATTCATATGGCCCCGTTAGGCCCAAATC
* *
27726562 ACCTGTATATGGCCCATT-AGACCCAAATCACATTTATATGG-CCCGTTAGGCCCA
1 ACCTGTATATGGCCCATTAAG-CCC-AACCACATTCATATGGCCCCGTTAGGCCCA
27726616 GTCACATTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 2 0.04
58 31 0.67
59 13 0.28
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (58 bp):
ACCTGTATATGGCCCATTAAGCCCAACCACATTCATATGGCCCCGTTAGGCCCAAATC
Found at i:27728827 original size:31 final size:31
Alignment explanation
Indices: 27728789--27728852 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
27728779 CCTTTTCATA
27728789 TTTCATATTTCATAACACTAGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
** * *
27728820 TTTCATATTTCATATTATTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTAGGCCGAAGCCT
27728851 TT
1 TT
27728853 ACTGTAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTAGGCCGAAGCCT
Found at i:27729114 original size:23 final size:24
Alignment explanation
Indices: 27729060--27729162 Score: 158
Period size: 23 Copynumber: 4.4 Consensus size: 24
27729050 CTAGAGGTCT
*
27729060 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
*
27729085 AGTCCTTTTAATAACT-GGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
27729108 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
27729131 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
27729154 AGCCCTTTT
1 AGCCCTTTT
27729163 TCACTTCCTC
Statistics
Matches: 73, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
22 10 0.14
23 45 0.62
24 15 0.21
25 3 0.04
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:27729237 original size:20 final size:20
Alignment explanation
Indices: 27729212--27729250 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
27729202 TATGATTACA
27729212 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
27729232 TCATGTGCATATCATACAT
1 TCATGTGCATATCATACAT
27729251 ACCATGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:27729256 original size:20 final size:20
Alignment explanation
Indices: 27729213--27729257 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
27729203 ATGATTACAT
**
27729213 CATGTGCATATCATACATGT
1 CATGTGCATATCATACATAC
27729233 CATGTGCATATCATACATAC
1 CATGTGCATATCATACATAC
27729253 CATGT
1 CATGT
27729258 TTATCAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTGCATATCATACATAC
Found at i:27729326 original size:25 final size:25
Alignment explanation
Indices: 27729294--27729341 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
27729284 ATACATAAAC
* *
27729294 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
27729319 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
27729342 CATGTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:27730384 original size:20 final size:21
Alignment explanation
Indices: 27730359--27730397 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27730349 AGTAGAGATA
27730359 AATGAA-AGAAATAATGGGTG
1 AATGAAGAGAAATAATGGGTG
*
27730379 AATGAAGGGAAATAATGGG
1 AATGAAGAGAAATAATGGG
27730398 CTGGTTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.49, C:0.00, G:0.33, T:0.18
Consensus pattern (21 bp):
AATGAAGAGAAATAATGGGTG
Found at i:27737290 original size:29 final size:29
Alignment explanation
Indices: 27737245--27737360 Score: 121
Period size: 29 Copynumber: 4.0 Consensus size: 29
27737235 TACCTGTATC
* *
27737245 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
27737273 TGGCCCCTTTAGGCCCAAATCACCTGT-ATA
1 TGG-CCCATTAGGCCCAAATCACAT-TCATA
* *
27737303 TGGCCCATTAGACCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* *
27737332 TGGCCCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
27737360 T
1 T
27737361 TCATGCTCAC
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
28 16 0.22
29 44 0.60
30 12 0.16
31 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:27737307 original size:58 final size:58
Alignment explanation
Indices: 27737236--27737347 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
27737226 AAATTCACAT
* * *
27737236 ACCTGTATCTGGCCCATTA-AGCCC-AATCATATTCATATGGCCCCTTTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAGA-CCCAAATCACATTCATATGG-CCCGTTAGGCCCAAATC
*
27737294 ACCTGTATATGGCCCATTAGACCCAAATCACATTTATATGGCCCGTTAGGCCCA
1 ACCTGTATATGGCCCATTAGACCCAAATCACATTCATATGGCCCGTTAGGCCCA
27737348 GTCACATTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 33 0.69
59 15 0.31
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (58 bp):
ACCTGTATATGGCCCATTAGACCCAAATCACATTCATATGGCCCGTTAGGCCCAAATC
Found at i:27741732 original size:20 final size:21
Alignment explanation
Indices: 27741707--27741754 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
27741697 TATTATGATT
27741707 TAATTG-ATTTTTTAGCTTGC
1 TAATTGAATTTTTTAGCTTGC
*
27741727 TAATTGGAATTTTTTAGCTTGG
1 TAATT-GAATTTTTTAGCTTGC
27741749 TAATTG
1 TAATTG
27741755 GACTTGGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 5 0.20
21 2 0.08
22 18 0.72
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (21 bp):
TAATTGAATTTTTTAGCTTGC
Found at i:27741741 original size:22 final size:22
Alignment explanation
Indices: 27741713--27741756 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27741703 GATTTAATTG
27741713 ATTTTTTAGCTTGCTAATTGGA
1 ATTTTTTAGCTTGCTAATTGGA
*
27741735 ATTTTTTAGCTTGGTAATTGGA
1 ATTTTTTAGCTTGCTAATTGGA
27741757 CTTGGCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.50
Consensus pattern (22 bp):
ATTTTTTAGCTTGCTAATTGGA
Found at i:27744527 original size:27 final size:28
Alignment explanation
Indices: 27744492--27744558 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 28
27744482 CAAATTAAAA
* *
27744492 ATATAAAAAATTATTTAATTTCAAA-TT
1 ATATTAAAAATTATTTAATTTAAAACTT
*
27744519 ATATTAAAAA-TATTTATTTTAAAACTT
1 ATATTAAAAATTATTTAATTTAAAACTT
* *
27744546 AAATTTAAAATTA
1 ATATTAAAAATTA
27744559 AAAAGGTTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 12 0.36
27 19 0.58
28 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATTAAAAATTATTTAATTTAAAACTT
Found at i:27744627 original size:18 final size:19
Alignment explanation
Indices: 27744591--27744628 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
27744581 TCTTAAAATA
27744591 AAAATATAAAATTTAATTT
1 AAAATATAAAATTTAATTT
* *
27744610 AAAA-ATAAATTTTCATTT
1 AAAATATAAAATTTAATTT
27744628 A
1 A
27744629 CCTAACTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATATAAAATTTAATTT
Found at i:27744942 original size:18 final size:18
Alignment explanation
Indices: 27744919--27744956 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
27744909 TTTTGTTACA
27744919 TATATAAATAACTTATAT
1 TATATAAATAACTTATAT
27744937 TATATAAATAACTTATAT
1 TATATAAATAACTTATAT
27744955 TA
1 TA
27744957 ATTAGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
TATATAAATAACTTATAT
Found at i:27746768 original size:19 final size:19
Alignment explanation
Indices: 27746744--27746782 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
27746734 ATTTTTTGAG
27746744 ATAGTTTTGGATAAAAGAA
1 ATAGTTTTGGATAAAAGAA
27746763 ATAGTTTTGGATAAAAGAA
1 ATAGTTTTGGATAAAAGAA
27746782 A
1 A
27746783 AATATGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.31
Consensus pattern (19 bp):
ATAGTTTTGGATAAAAGAA
Found at i:27747304 original size:30 final size:31
Alignment explanation
Indices: 27747248--27747306 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
27747238 ATTTTTTAAA
*
27747248 TTTTAAAAAATTCATAAAATTGTAAAATTAT
1 TTTTAAAAAATTCATAAAATTATAAAATTAT
*
27747279 TTTTAAAATATT-A-AAAATGTATAAAATT
1 TTTTAAAAAATTCATAAAAT-TATAAAATT
27747307 TATAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 9 0.36
31 11 0.44
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (31 bp):
TTTTAAAAAATTCATAAAATTATAAAATTAT
Found at i:27747313 original size:39 final size:40
Alignment explanation
Indices: 27747233--27747327 Score: 97
Period size: 39 Copynumber: 2.3 Consensus size: 40
27747223 GATAGCAATT
* * *
27747233 AATTAATTTTTTAAATTTTAAAAAATTCATAAAATTGT-AA
1 AATT-ATTTTTAAAATATTAAAAAATTCATAAAATTATAAA
27747273 AATTATTTTTAAAATATT-AAAAATGT-ATAAAATTTATAAAA
1 AATTATTTTTAAAATATTAAAAAAT-TCATAAAA-TTAT-AAA
27747314 AATATATTTTTAAA
1 AAT-TATTTTTAAA
27747328 TTTTTTAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
38 12 0.26
39 16 0.34
40 4 0.09
41 5 0.11
42 10 0.21
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (40 bp):
AATTATTTTTAAAATATTAAAAAATTCATAAAATTATAAA
Found at i:27747332 original size:9 final size:9
Alignment explanation
Indices: 27747320--27747345 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
27747310 AAAAAATATA
27747320 TTTTTAAAT
1 TTTTTAAAT
27747329 TTTTTAAAT
1 TTTTTAAAT
27747338 TTTTTAAA
1 TTTTTAAA
27747346 AAATGAATTA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:27748887 original size:8 final size:8
Alignment explanation
Indices: 27748874--27748907 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
27748864 AATATAATTT
27748874 AATTTACA
1 AATTTACA
27748882 AATTTACA
1 AATTTACA
27748890 AATTTACA
1 AATTTACA
27748898 AATTT-CA
1 AATTTACA
27748905 AAT
1 AAT
27748908 AATATAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.19
8 21 0.81
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
AATTTACA
Found at i:27749242 original size:23 final size:23
Alignment explanation
Indices: 27749216--27749261 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
27749206 AATAGACAAT
27749216 AAATAATATTA-ATATATATAATA
1 AAATAATATTACA-ATATATAATA
*
27749239 AAATAATCTTACAATATATAATA
1 AAATAATATTACAATATATAATA
27749262 TAAAAGCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
AAATAATATTACAATATATAATA
Found at i:27750935 original size:31 final size:29
Alignment explanation
Indices: 27750866--27750939 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
27750856 TTAGCTTGGA
* *
27750866 TTACATTTTAGCCACTTATGTTTAAAATG
1 TTACATTTTAGTCACTTACGTTTAAAATG
*
27750895 TTACATTTTAGTCACTTACG-TTAACATG
1 TTACATTTTAGTCACTTACGTTTAAAATG
27750923 TTGTAACATTTTAGTCA
1 -T-T-ACATTTTAGTCA
27750940 TTGAGCTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 7 0.18
29 19 0.49
30 1 0.03
31 12 0.31
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.45
Consensus pattern (29 bp):
TTACATTTTAGTCACTTACGTTTAAAATG
Found at i:27752706 original size:29 final size:27
Alignment explanation
Indices: 27752664--27752719 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 27
27752654 TGCGAGTTGT
*
27752664 ACCGATTTGGCTTCAGGCCGTGAATATCA
1 ACCGATTTGGCTTC-GGCCATG-ATATCA
27752693 ACCGATTTGGCTTCGGCCATGATATCA
1 ACCGATTTGGCTTCGGCCATGATATCA
27752720 GTACTTCGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 6 0.23
28 6 0.23
29 14 0.54
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (27 bp):
ACCGATTTGGCTTCGGCCATGATATCA
Found at i:27758559 original size:30 final size:30
Alignment explanation
Indices: 27758523--27758585 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
27758513 ACTCAATAAT
* *
27758523 CTATACTTGGGCAAAATGACCATTTTGCCC
1 CTATACTTGGGCAAAATAACCATTTTACCC
**
27758553 CTATACTTTTGCAAAATAACCATTTTACCC
1 CTATACTTGGGCAAAATAACCATTTTACCC
27758583 CTA
1 CTA
27758586 GGTCCGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (30 bp):
CTATACTTGGGCAAAATAACCATTTTACCC
Found at i:27761849 original size:68 final size:67
Alignment explanation
Indices: 27761777--27761927 Score: 182
Period size: 66 Copynumber: 2.3 Consensus size: 67
27761767 CATCATGTGT
* * * *
27761777 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGT-GTACACCAT
1 ACAAGAGAGCTACAAGACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGGTAGGACACCAT
27761841 GTAG
64 GTAG
** * *
27761845 ACAAGAGAGCTAC--GGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTAAGGACACCATG
1 ACAAGAGAGCTACAAGACATATATGTAGCTAGGTCGCATGCGTGATACCAGGT-AGGACACCATG
27761908 TAG
65 TAG
27761911 ACAAGAGAGCTACAAGA
1 ACAAGAGAGCTACAAGA
27761928 TAAATTGGCT
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
64 26 0.37
65 3 0.04
66 27 0.39
68 14 0.20
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACAAGACATATATGTAGCTAGGTCGCATGCGTGATACCAGGTAGGACACCATGT
AG
Found at i:27761882 original size:64 final size:63
Alignment explanation
Indices: 27761733--27761971 Score: 203
Period size: 68 Copynumber: 3.7 Consensus size: 63
27761723 TACAGAGAGT
* ** * * *
27761733 ATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGT-GTACAAGAGAGCTACAAGACAT
1 ATGTAGCTAGGTCGCATGGGTGGTACT-AGTGTACACCATGTAG-ACAAGAGAGCTACAAG--A-
*
27761797 TATG
61 TA-A
* ** *
27761801 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA-GTGTACACCATGTAGACAAGAGAGCTACAAGATAA
* * * *
27761865 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTAAGGACACCATGTAGACAAGAGAGCTACAAGATA
1 ATGTAGCTAGGTCGCATGGGTGGTACTA-GT--GTACACCATGTAGACAAGAGAGCTACAAGATA
27761930 A
63 A
* * *
27761931 AT-TGGCTAGGTCACATGGGTGGTACTGAGTGTTCACCATGT
1 ATGTAGCTAGGTCGCATGGGTGGTACT-AGTGTACACCATGT
27761972 GTGCAAGAGA
Statistics
Matches: 140, Mismatches: 26, Indels: 15
0.77 0.14 0.08
Matches are distributed among these distances:
63 9 0.06
64 26 0.19
65 23 0.16
66 33 0.24
67 1 0.01
68 47 0.34
69 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (63 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTAGTGTACACCATGTAGACAAGAGAGCTACAAGATAA
Found at i:27763901 original size:47 final size:47
Alignment explanation
Indices: 27763841--27764059 Score: 211
Period size: 47 Copynumber: 4.7 Consensus size: 47
27763831 TGTGAGAGCA
*
27763841 AGTGTAAGAACATGTCTGGGACATGGCATCGGCATCGAGACAAGTGCT
1 AGTGTAAG-ACATGTCTGGGACATGGCATCGGCATCGAGACAAGTGCC
* *
27763889 AGTGTAAGACATGTCTGGGACAT-GTATCGGCCTCGAGAC--GTAAGCC
1 AGTGTAAGACATGTCTGGGACATGGCATCGGCATCGAGACAAGT--GCC
* *
27763935 AGTGTAAGACATGTCTGGGACAT-GCATCGGCTACACGATGA-TAGT--C
1 AGTGTAAGACATGTCTGGGACATGGCATCGGC-A-TCGA-GACAAGTGCC
* * * * *
27763981 AGTGTAAGACCATGTCTGGGACATGGCATC-GAATTGAGATATGAGCC
1 AGTGTAAGA-CATGTCTGGGACATGGCATCGGCATCGAGACAAGTGCC
*
27764028 AGTGTGAGACCATGTCTGGGACATGGCATCGG
1 AGTGTAAGA-CATGTCTGGGACATGGCATCGG
27764060 TACTTTACTC
Statistics
Matches: 145, Mismatches: 13, Indels: 26
0.79 0.07 0.14
Matches are distributed among these distances:
44 4 0.03
45 3 0.02
46 57 0.39
47 60 0.41
48 17 0.12
49 2 0.01
50 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.22
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGGCATCGGCATCGAGACAAGTGCC
Found at i:27763939 original size:46 final size:46
Alignment explanation
Indices: 27763795--27764059 Score: 195
Period size: 47 Copynumber: 5.7 Consensus size: 46
27763785 ATTGTGAGCT
** * ** *
27763795 AGTGTAAGACATGTCTGGGACATGCATCAACCAC-A-TTGTGAGAGCA
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGT-A-AGCC
* *
27763841 AGTGTAAGAACATGTCTGGGACATGGCATCGGCATCGAGAC--AAGTGCT
1 AGTGTAAG-ACATGTCTGGGACAT-GCATCGGCCTCGAGACGTAA--GCC
*
27763889 AGTGTAAGACATGTCTGGGACATGTATCGGCCTCGAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTAAGCC
* *
27763935 AGTGTAAGACATGTCTGGGACATGCATCGG-CT--ACACGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-T-A-AGCC
** * ** *
27763981 AGTGTAAGACCATGTCTGGGACATGGCATC-GAATTGAGATATGAGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGACGTAAGCC
*
27764028 AGTGTGAGACCATGTCTGGGACATGGCATCGG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGG
27764060 TACTTTACTC
Statistics
Matches: 182, Mismatches: 20, Indels: 32
0.78 0.09 0.14
Matches are distributed among these distances:
43 4 0.02
44 1 0.01
45 3 0.02
46 66 0.36
47 78 0.43
48 26 0.14
49 2 0.01
50 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTAAGCC
Found at i:27764047 original size:140 final size:140
Alignment explanation
Indices: 27763795--27764052 Score: 351
Period size: 140 Copynumber: 1.8 Consensus size: 140
27763785 ATTGTGAGCT
*
27763795 AGTGTAAGACATGTCTGGGACATGCATCAACCACATTGTGAGAGCAAGTGTAAGAACATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAACCACATCGTGAGAGCAAGTGTAAGAACATGTCTGG
* * *
27763860 GACATGGCATCGGCATCGAGACAAGTGCTAGTGTAAGACATGTCTGGGACATGTATCGGCCTCGA
66 GACATGGCATCGGAATCGAGACAAGAGCCAGTGTAAGACATGTCTGGGACATGTATCGGCCTCGA
27763925 GACGTAAGCC
131 GACGTAAGCC
** * * *
27763935 AGTGTAAGACATGTCTGGGACATGCATCGGCTACA-CGATGATAGTC-AGTGTAAGACCATGTCT
1 AGTGTAAGACATGTCTGGGACATGCATCAACCACATCG-TGAGAG-CAAGTGTAAGAACATGTCT
* * * *
27763998 GGGACATGGCATC-GAATTGAGATATGAGCCAGTGTGAGACCATGTCTGGGACATG
64 GGGACATGGCATCGGAATCGAGACAAGAGCCAGTGTAAGA-CATGTCTGGGACATG
27764053 GCATCGGTAC
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
139 20 0.20
140 81 0.79
141 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (140 bp):
AGTGTAAGACATGTCTGGGACATGCATCAACCACATCGTGAGAGCAAGTGTAAGAACATGTCTGG
GACATGGCATCGGAATCGAGACAAGAGCCAGTGTAAGACATGTCTGGGACATGTATCGGCCTCGA
GACGTAAGCC
Found at i:27769461 original size:42 final size:42
Alignment explanation
Indices: 27769402--27769493 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
27769392 TGGCCCATAG
**
27769402 GCCCATTTCAATATCACAT-ATAATGTCAATGAAAGAATGCAA
1 GCCCATTTCAATATCACATGA-AATACCAATGAAAGAATGCAA
* *
27769444 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAAAGAATGCAA
*
27769486 ACCCATTT
1 GCCCATTT
27769494 GGGGAGACTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAAAGAATGCAA
Found at i:27769665 original size:23 final size:23
Alignment explanation
Indices: 27769635--27769800 Score: 251
Period size: 23 Copynumber: 7.1 Consensus size: 23
27769625 CCTTGCCTCT
*
27769635 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
* *
27769658 TTTAATAACTAGGGCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
* * *
27769681 TTTTGATCACTAGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
27769705 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
27769728 TTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
27769752 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
27769775 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
27769798 TTT
1 TTT
27769801 TGCACTTCCT
Statistics
Matches: 130, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
23 88 0.68
24 42 0.32
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:27769697 original size:47 final size:47
Alignment explanation
Indices: 27769633--27769800 Score: 266
Period size: 47 Copynumber: 3.6 Consensus size: 47
27769623 GGCCTTGCCT
* * * *
27769633 CTTTTAATAACTGGGGCAAAAGCCCTTTAATAACTAGGGCGTAAGCC
1 CTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
* *
27769680 CTTTTGATCACTAGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
1 CTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
27769727 CTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
1 CTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
*
27769774 C-TTTAATAACTGGGGCATAAGCCCTTT
1 CTTTTGATAACTGGGGCATAAGCCCTTT
27769801 TGCACTTCCT
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 25 0.22
47 87 0.78
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (47 bp):
CTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
Found at i:27769767 original size:70 final size:71
Alignment explanation
Indices: 27769635--27769802 Score: 259
Period size: 70 Copynumber: 2.4 Consensus size: 71
27769625 CCTTGCCTCT
* * * * *
27769635 TTTAATAACTGGGGCAAAAGCCC-TTTAATAACTAGGGCGTAAGCCCTTTTGATCACTAGGGCAT
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTAGGGCATAAGCCCTTTTAATAACTAGGGCAT
27769699 AAGCCC
66 AAGCCC
* *
27769705 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCAT
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTAGGGCATAAGCCCTTTTAATAACTAGGGCAT
27769769 AAGCCC
66 AAGCCC
27769775 TTTAATAACTGGGGCATAAGCCCTTTTG
1 TTTAATAACTGGGGCATAAGCCCTTTTG
27769803 CACTTCCTCC
Statistics
Matches: 90, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
70 70 0.78
71 20 0.22
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (71 bp):
TTTAATAACTGGGGCATAAGCCCTTTTGATAACTAGGGCATAAGCCCTTTTAATAACTAGGGCAT
AAGCCC
Found at i:27769873 original size:9 final size:9
Alignment explanation
Indices: 27769859--27769915 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
27769849 ATCTCATGTG
27769859 CATATCATA
1 CATATCATA
*
27769868 CATATCATGTG
1 CATATCA--TA
27769879 CATATCATA
1 CATATCATA
* *
27769888 CATGTCATGTG
1 CATATCA--TA
27769899 CATATCATA
1 CATATCATA
27769908 CATATCAT
1 CATATCAT
27769916 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:27769875 original size:20 final size:20
Alignment explanation
Indices: 27769847--27769917 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
27769837 GCATTTATGA
*
27769847 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
27769867 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
27769887 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
27769907 ACATATCATGT
1 ACATATCATGT
27769918 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:27769882 original size:11 final size:11
Alignment explanation
Indices: 27769852--27769906 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
27769842 TATGAACATC
27769852 TCATGTGCATA
1 TCATGTGCATA
*
27769863 TCA--TACATA
1 TCATGTGCATA
27769872 TCATGTGCATA
1 TCATGTGCATA
* *
27769883 TCA--TACATG
1 TCATGTGCATA
27769892 TCATGTGCATA
1 TCATGTGCATA
27769903 TCAT
1 TCAT
27769907 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:27769982 original size:25 final size:25
Alignment explanation
Indices: 27769954--27770001 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
27769944 ATATATAAAC
* *
27769954 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
27769979 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
27770002 CATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:27771221 original size:27 final size:27
Alignment explanation
Indices: 27771159--27771223 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
27771149 GGGCATATTC
27771159 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
27771186 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
*
27771213 GTCTTTTTACC
1 GTCATTTTACC
27771224 TAATAGGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:27771449 original size:27 final size:27
Alignment explanation
Indices: 27771281--27771532 Score: 125
Period size: 27 Copynumber: 9.3 Consensus size: 27
27771271 TCTACAAACT
* *
27771281 AAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTTAGTAATTTTGTAAATC
*
27771308 AATGGTATTTCTA-TAATTTT-TAGAAAGTC
1 AAGGGTATTT-TAGTAATTTTGT--AAA-TC
* *
27771337 AAGGGTATTTCT-GTAACTTTGTAAATT
1 AAGGGTATTT-TAGTAATTTTGTAAATC
* * ** *
27771364 AGGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTTAGTAATTTTGTAAATC
* * *** *
27771391 GAGGGT-TTTTCGGTAATTTCACAAACC
1 AAGGGTATTTT-AGTAATTTTGTAAATC
27771418 AAGGGTATTTTAGTAATTTTGTAAATC
1 AAGGGTATTTTAGTAATTTTGTAAATC
* **** *
27771445 GAGGGTAAAACAGTAATTCTGTAAATC
1 AAGGGTATTTTAGTAATTTTGTAAATC
**** * *
27771472 AAGGGTAAAACAGTAATTCTATAAATC
1 AAGGGTATTTTAGTAATTTTGTAAATC
*** * *
27771499 AAGGGTAAAATAGTAATTCTATAAATC
1 AAGGGTATTTTAGTAATTTTGTAAATC
27771526 AAGGGTA
1 AAGGGTA
27771533 AAACAGTAAT
Statistics
Matches: 186, Mismatches: 30, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
26 6 0.03
27 150 0.81
28 11 0.06
29 18 0.10
30 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (27 bp):
AAGGGTATTTTAGTAATTTTGTAAATC
Found at i:27771533 original size:27 final size:27
Alignment explanation
Indices: 27771430--27771910 Score: 541
Period size: 27 Copynumber: 17.8 Consensus size: 27
27771420 GGGTATTTTA
* * *
27771430 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCAAGGGTAAAACG
*
27771457 GTAATTCTGTAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCAAGGGTAAAACG
* **
27771484 GTAATTCTATAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCAAGGGTAAAACG
* *
27771511 GTAATTCTATAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCAAGGGTAAAACG
* *
27771538 GTAATTCAGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* *
27771565 GTAATTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * * *
27771592 ATAATTATGTAAATTAAAGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * * *
27771619 GTAATTATGTAAATTAGGGGTAAAACA
1 GTAATTCTGTAAATCAAGGGTAAAACG
* *
27771646 GTAATTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * *
27771673 ATAATTATGTAAATCAGGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* *
27771700 GTAATTATGTAAAT-TAGAGGTAAAACG
1 GTAATTCTGTAAATCAAG-GGTAAAACG
* *
27771727 GTAATTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * *
27771754 ATAATTATGTAAATCAGGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * *
27771781 GTAATTATGTAAATTAGGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* *
27771808 GTAATTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * * *
27771835 ATAATTATGTAAATCAGGGGTAAAATG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* *
27771862 GTAATTATGTAAATTAAGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
*
27771889 GTAATTCTGTAAATCGAGGGTA
1 GTAATTCTGTAAATCAAGGGTA
27771911 CTTTAGTAAT
Statistics
Matches: 389, Mismatches: 63, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
26 1 0.00
27 386 0.99
28 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.28
Consensus pattern (27 bp):
GTAATTCTGTAAATCAAGGGTAAAACG
Found at i:27771932 original size:27 final size:27
Alignment explanation
Indices: 27771899--27772005 Score: 119
Period size: 27 Copynumber: 4.0 Consensus size: 27
27771889 GTAATTCTGT
27771899 AAATCGAGGGTACTTT-AGTAATTTTAC
1 AAATCGAGGGTA-TTTCAGTAATTTTAC
* * * *
27771926 AAGTCGAAGGTATTTCGGTAAATTTAC
1 AAATCGAGGGTATTTCAGTAATTTTAC
*
27771953 AAATCGAGGGTATTTCAGTATTTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTAC
* *
27771980 AAA-CTAAGGGTATTTCGGTAATTTTA
1 AAATC-GAGGGTATTTCAGTAATTTTA
27772006 GTAAACTAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
26 4 0.06
27 62 0.94
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (27 bp):
AAATCGAGGGTATTTCAGTAATTTTAC
Found at i:27771945 original size:54 final size:53
Alignment explanation
Indices: 27771899--27772003 Score: 142
Period size: 54 Copynumber: 2.0 Consensus size: 53
27771889 GTAATTCTGT
*
27771899 AAATCGAGGGTACTTT-AGTAATTTTACAAGTCGAA-GGTATTTCGGTAAATTTAC
1 AAATCGAGGGTA-TTTCAGTAATTTTACAA-ACGAAGGGTATTTCGGT-AATTTAC
* *
27771953 AAATCGAGGGTATTTCAGTATTTTTACAAACTAAGGGTATTTCGGTAATTT
1 AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTTCGGTAATTT
27772004 TAGTAAACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
53 11 0.24
54 35 0.76
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.37
Consensus pattern (53 bp):
AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTTCGGTAATTTAC
Found at i:27771946 original size:81 final size:81
Alignment explanation
Indices: 27771431--27771910 Score: 689
Period size: 81 Copynumber: 5.9 Consensus size: 81
27771421 GGTATTTTAG
* * * * * *
27771431 TAATTTTGTAAATC-GAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACAGTAATTCTATA
1 TAATTATGTAAATCAG-GGGTAAAACGGTAATTATGTAAATTAAGGGTAAAACGGTAATTCTGTA
* * *
27771495 AATCAAGGGTAAAA-TA
65 AGTCGAGGGTAAAACGA
* * * * **
27771511 GTAATTCTATAAATCAAGGGTAAAACAGTAATTCA-GTAAATCGAGGGTAAAACGGTAATTCTGT
1 -TAATTATGTAAATCAGGGGTAAAACGGTAATT-ATGTAAATTAAGGGTAAAACGGTAATTCTGT
27771575 AAGTCGAGGGTAAAACGA
64 AAGTCGAGGGTAAAACGA
* ** * *
27771593 TAATTATGTAAATTAAAGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACAGTAATTCTGTAA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAAGGGTAAAACGGTAATTCTGTAA
27771658 GTCGAGGGTAAAACGA
66 GTCGAGGGTAAAACGA
27771674 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATT-AGAGGTAAAACGGTAATTCTGTA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAAG-GGTAAAACGGTAATTCTGTA
27771738 AGTCGAGGGTAAAACGA
65 AGTCGAGGGTAAAACGA
*
27771755 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAAGGGTAAAACGGTAATTCTGTAA
27771820 GTCGAGGGTAAAACGA
66 GTCGAGGGTAAAACGA
*
27771836 TAATTATGTAAATCAGGGGTAAAATGGTAATTATGTAAATTAAGGGTAAAACGGTAATTCTGTAA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAAGGGTAAAACGGTAATTCTGTAA
*
27771901 ATCGAGGGTA
66 GTCGAGGGTA
27771911 CTTTAGTAAT
Statistics
Matches: 365, Mismatches: 28, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
80 2 0.01
81 361 0.99
82 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.28
Consensus pattern (81 bp):
TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAAGGGTAAAACGGTAATTCTGTAA
GTCGAGGGTAAAACGA
Found at i:27772019 original size:27 final size:27
Alignment explanation
Indices: 27771915--27772020 Score: 74
Period size: 27 Copynumber: 3.9 Consensus size: 27
27771905 AGGGTACTTT
* *
27771915 AGTAATTTTACAAGTCGAAG-GTATTTC
1 AGTAATTTTACAA-ACTAAGAGTATTTC
* * * *
27771942 GGTAAATTTACAAA-TCGAGGGTATTTC
1 AGTAATTTTACAAACT-AAGAGTATTTC
* *
27771969 AGTATTTTTACAAACTAAGGGTATTTC
1 AGTAATTTTACAAACTAAGAGTATTTC
* *
27771996 GGTAATTTTAGTAAACTAA-AGTATT
1 AGTAATTTTA-CAAACTAAGAGTATT
27772021 CTAAACAGGG
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
26 2 0.03
27 52 0.84
28 8 0.13
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (27 bp):
AGTAATTTTACAAACTAAGAGTATTTC
Found at i:27774804 original size:42 final size:42
Alignment explanation
Indices: 27774745--27774836 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
27774735 TGGCCCATAG
**
27774745 GCCCATTTCAATATCACAT-ATAATGTCAATGAAAGAATGCAA
1 GCCCATTTCAATATCACATGA-AATACCAATGAAAGAATGCAA
* *
27774787 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAAAGAATGCAA
*
27774829 ACCCATTT
1 GCCCATTT
27774837 GGGGAGACTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.11, T:0.27
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAAAGAATGCAA
Found at i:27775008 original size:23 final size:23
Alignment explanation
Indices: 27774978--27775142 Score: 260
Period size: 23 Copynumber: 7.1 Consensus size: 23
27774968 CCTTGCCTCT
*
27774978 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
27775001 TTTAATAACT-GGGCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
* *
27775023 TTTTGATCACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
27775047 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
27775070 TTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
27775094 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
27775117 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
27775140 TTT
1 TTT
27775143 TGCACTTCCT
Statistics
Matches: 130, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
22 10 0.08
23 87 0.67
24 33 0.25
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:27775116 original size:70 final size:70
Alignment explanation
Indices: 27774978--27775144 Score: 266
Period size: 70 Copynumber: 2.4 Consensus size: 70
27774968 CCTTGCCTCT
* * * * *
27774978 TTTAATAACTGGGGCAAAAGCCC-TTTAATAACTGGGCGTAAGCCCTTTTGATCACTGGGGCATA
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGCATAAGCCCTTTTAATAACTGGGGCATA
27775042 AGCCC
66 AGCCC
27775047 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCAT
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACT-GGGCATAAGCCCTTTTAATAACTGGGGCAT
27775111 AAGCCC
65 AAGCCC
27775117 TTTAATAACTGGGGCATAAGCCCTTTTG
1 TTTAATAACTGGGGCATAAGCCCTTTTG
27775145 CACTTCCTCC
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
69 22 0.24
70 58 0.64
71 11 0.12
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (70 bp):
TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGCATAAGCCCTTTTAATAACTGGGGCATA
AGCCC
Found at i:27775215 original size:9 final size:9
Alignment explanation
Indices: 27775201--27775257 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
27775191 ATCTCATGTG
27775201 CATATCATA
1 CATATCATA
*
27775210 CATATCATGTG
1 CATATCA--TA
27775221 CATATCATA
1 CATATCATA
* *
27775230 CATGTCATGTG
1 CATATCA--TA
27775241 CATATCATA
1 CATATCATA
27775250 CATATCAT
1 CATATCAT
27775258 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:27775217 original size:20 final size:20
Alignment explanation
Indices: 27775189--27775259 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
27775179 GCATTTATGA
*
27775189 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
27775209 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
27775229 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
27775249 ACATATCATGT
1 ACATATCATGT
27775260 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:27775224 original size:11 final size:11
Alignment explanation
Indices: 27775194--27775248 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
27775184 TATGAACATC
27775194 TCATGTGCATA
1 TCATGTGCATA
*
27775205 TCA--TACATA
1 TCATGTGCATA
27775214 TCATGTGCATA
1 TCATGTGCATA
* *
27775225 TCA--TACATG
1 TCATGTGCATA
27775234 TCATGTGCATA
1 TCATGTGCATA
27775245 TCAT
1 TCAT
27775249 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:27775324 original size:25 final size:25
Alignment explanation
Indices: 27775296--27775343 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
27775286 ATATATAAAC
* *
27775296 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
27775321 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
27775344 CATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:27776566 original size:27 final size:27
Alignment explanation
Indices: 27776503--27776558 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
27776493 GGGCATATTC
27776503 GTCA-TTTACCATACAGGGGTATTACG
1 GTCACTTTACCATACAGGGGTATTACG
*
27776529 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCACTTTACCATACAGGGG-TATTACG
27776556 GTC
1 GTC
27776559 TTTTTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 4 0.15
27 22 0.81
28 1 0.04
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.30
Consensus pattern (27 bp):
GTCACTTTACCATACAGGGGTATTACG
Found at i:27776792 original size:27 final size:27
Alignment explanation
Indices: 27776625--27776794 Score: 107
Period size: 27 Copynumber: 6.3 Consensus size: 27
27776615 TCTACAAACT
* *
27776625 AAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTTAGTAATTTTGTAAATC
*
27776652 AATGGTATTTCTA-TAATTTT-TAGAAAGTC
1 AAGGGTATTT-TAGTAATTTTGT--AAA-TC
*
27776681 AAGGGTATTTCT-GTAACTTTGTAAAT-
1 AAGGGTATTT-TAGTAATTTTGTAAATC
* * ** *
27776707 TAGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTTTAGTAATTTTGTAAATC
* * *** *
27776734 GAGGGT-TTTTCGGTAATTTCACAAACC
1 AAGGGTATTTT-AGTAATTTTGTAAATC
27776761 AAGGGTATTTTAGTAATTTTGTAAATC
1 AAGGGTATTTTAGTAATTTTGTAAATC
*
27776788 GAGGGTA
1 AAGGGTA
27776795 AAACATAATT
Statistics
Matches: 113, Mismatches: 20, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
25 1 0.01
26 25 0.22
27 57 0.50
28 11 0.10
29 18 0.16
30 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
AAGGGTATTTTAGTAATTTTGTAAATC
Found at i:27777252 original size:27 final size:27
Alignment explanation
Indices: 27776773--27777245 Score: 525
Period size: 27 Copynumber: 17.6 Consensus size: 27
27776763 GGGTATTTTA
* *
27776773 GTAATTTTGTAAATCGAGGGTAAAAC-
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * *
27776799 ATAATTCTGTAAATCAATGGTAAAACA
1 GTAATTCTGTAAATCAAGGGTAAAACG
* **
27776826 GTAATTCTATAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * *
27776853 ATAATTCTATAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCAAGGGTAAAACG
* *
27776880 GTAATTCAGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* *
27776907 GTAATTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * * *
27776934 ATAATTATGTAAATTAAAGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * *
27776961 GTAATTATGTAAATTAGGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* *
27776988 GTAATTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * *
27777015 ATAATTATGTAAATCAGGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * *
27777042 GTAATTATGTAAATTAGGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* *
27777069 GTAATTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * *
27777096 ATAATTATGTAAATCAGGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * *
27777123 GTAATTATGTAAATTAGGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* *
27777150 GTAATTCTGTAAGTCGAGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * *
27777177 ATAATTATGTAAATCAGGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
* * *
27777204 GTAATTATGTAAATTAGGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAACG
27777231 GTAATTCTGTAAATC
1 GTAATTCTGTAAATC
27777246 GGGGGTACTT
Statistics
Matches: 382, Mismatches: 64, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
26 22 0.06
27 360 0.94
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (27 bp):
GTAATTCTGTAAATCAAGGGTAAAACG
Found at i:27777279 original size:27 final size:27
Alignment explanation
Indices: 27777249--27777347 Score: 103
Period size: 27 Copynumber: 3.7 Consensus size: 27
27777239 GTAAATCGGG
*
27777249 GGTACTTT-AGTAATTTTACAAGTCGAA
1 GGTA-TTTCAGTAATTTTACAAATCGAA
* * *
27777276 GGTATTTCGGTAAATTTACAAATCGAT
1 GGTATTTCAGTAATTTTACAAATCGAA
* *
27777303 GGTATTTCAGTATTTTTACAAA-CTAA
1 GGTATTTCAGTAATTTTACAAATCGAA
*
27777329 GGGTATTTCGGTAATTTTA
1 -GGTATTTCAGTAATTTTA
27777348 GTAAACTAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
26 5 0.08
27 54 0.92
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (27 bp):
GGTATTTCAGTAATTTTACAAATCGAA
Found at i:27777287 original size:54 final size:53
Alignment explanation
Indices: 27777241--27777345 Score: 124
Period size: 54 Copynumber: 2.0 Consensus size: 53
27777231 GTAATTCTGT
* *
27777241 AAATCGGGGGTACTTT-AGTAATTTTACAAGTCGAA-GGTATTTCGGTAAATTTAC
1 AAATCGAGGGTA-TTTCAGTAATTTTACAA-ACGAAGGGTATTTCGGT-AATTTAC
* * *
27777295 AAATCGATGGTATTTCAGTATTTTTACAAACTAAGGGTATTTCGGTAATTT
1 AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTTCGGTAATTT
27777346 TAGTAAACTA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
53 11 0.25
54 33 0.75
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.38
Consensus pattern (53 bp):
AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTTCGGTAATTTAC
Found at i:27777288 original size:81 final size:81
Alignment explanation
Indices: 27776774--27777252 Score: 705
Period size: 81 Copynumber: 5.9 Consensus size: 81
27776764 GGTATTTTAG
* * * * ** * *
27776774 TAATTTTGTAAATC-GAGGGTAAAAC-ATAATTCTGTAAATCAATGGTAAAACAGTAATTCTATA
1 TAATTATGTAAATCAG-GGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTA
* * **
27776837 AATCAAGGGTAAAATAA
65 AGTCGAGGGTAAAACGA
* * * * *
27776854 TAATTCTATAAATCAAGGGTAAAACAGTAATTCA-GTAAA-TCGAGGGTAAAACGGTAATTCTGT
1 TAATTATGTAAATCAGGGGTAAAACGGTAATT-ATGTAAATTAG-GGGTAAAACGGTAATTCTGT
27776917 AAGTCGAGGGTAAAACGA
64 AAGTCGAGGGTAAAACGA
* **
27776935 TAATTATGTAAATTAAAGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
27777000 GTCGAGGGTAAAACGA
66 GTCGAGGGTAAAACGA
27777016 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
27777081 GTCGAGGGTAAAACGA
66 GTCGAGGGTAAAACGA
27777097 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
27777162 GTCGAGGGTAAAACGA
66 GTCGAGGGTAAAACGA
27777178 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
* *
27777243 ATCGGGGGTA
66 GTCGAGGGTA
27777253 CTTTAGTAAT
Statistics
Matches: 367, Mismatches: 26, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
80 22 0.06
81 343 0.93
82 2 0.01
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (81 bp):
TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTGTAA
GTCGAGGGTAAAACGA
Found at i:27777361 original size:27 final size:27
Alignment explanation
Indices: 27777257--27777362 Score: 74
Period size: 27 Copynumber: 3.9 Consensus size: 27
27777247 GGGGTACTTT
* *
27777257 AGTAATTTTACAAGTCGAAG-GTATTTC
1 AGTAATTTTACAA-ACTAAGAGTATTTC
* * * *
27777284 GGTAAATTTACAAATCGATG-GTATTTC
1 AGTAATTTTACAAA-CTAAGAGTATTTC
* *
27777311 AGTATTTTTACAAACTAAGGGTATTTC
1 AGTAATTTTACAAACTAAGAGTATTTC
* *
27777338 GGTAATTTTAGTAAACTAA-AGTATT
1 AGTAATTTTA-CAAACTAAGAGTATT
27777363 CTAAACAGGG
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
26 3 0.05
27 53 0.84
28 7 0.11
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (27 bp):
AGTAATTTTACAAACTAAGAGTATTTC
Found at i:27780120 original size:42 final size:42
Alignment explanation
Indices: 27780049--27780139 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
27780039 GGCCCATAGG
**
27780049 CCCATTTCAATATCACATATAATGTCAATGAAAGAATGCAAA
1 CCCATTTCAATATCACATATAATACCAATGAAAGAATGCAAA
* * *
27780091 GCCATTTCAATATCACATGA-AATACCAATGAATGTATGCAAA
1 CCCATTTCAATATCACAT-ATAATACCAATGAAAGAATGCAAA
27780133 CCCATTT
1 CCCATTT
27780140 GGGGAGACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (42 bp):
CCCATTTCAATATCACATATAATACCAATGAAAGAATGCAAA
Found at i:27780310 original size:23 final size:23
Alignment explanation
Indices: 27780280--27780441 Score: 261
Period size: 23 Copynumber: 7.0 Consensus size: 23
27780270 CCTTGCCTCT
*
27780280 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
27780303 TTTAATAACTGGGGCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
* *
27780326 TTTTGATCACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
27780350 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
27780373 TTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
27780397 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
27780420 TTTAATAACTGGGGCATAAGCC
1 TTTAATAACTGGGGCATAAGCC
27780442 NTCATCACAC
Statistics
Matches: 128, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
23 86 0.67
24 42 0.33
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:27780338 original size:47 final size:47
Alignment explanation
Indices: 27780278--27780441 Score: 276
Period size: 47 Copynumber: 3.5 Consensus size: 47
27780268 GGCCTTGCCT
* *
27780278 CTTTTAATAACTGGGGCAAAAGCCCTTTAATAACTGGGGCGTAAGCC
1 CTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
* *
27780325 CTTTTGATCACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
*
27780372 CTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
27780419 C-TTTAATAACTGGGGCATAAGCC
1 CTTTTAATAACTGGGGCATAAGCC
27780442 NTCATCACAC
Statistics
Matches: 111, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
46 21 0.19
47 90 0.81
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (47 bp):
CTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCC
Found at i:27780363 original size:70 final size:70
Alignment explanation
Indices: 27780280--27780441 Score: 263
Period size: 70 Copynumber: 2.3 Consensus size: 70
27780270 CCTTGCCTCT
* * * *
27780280 TTTAATAACTGGGGCAAAAGCCC-TTTAATAACTGGGGCGTAAGCCCTTTTGATCACTGGGGCAT
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCAT
27780344 AAGCCC
65 AAGCCC
*
27780350 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATA
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATA
27780415 AGCCC
66 AGCCC
27780420 TTTAATAACTGGGGCATAAGCC
1 TTTAATAACTGGGGCATAAGCC
27780442 NTCATCACAC
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
70 65 0.76
71 21 0.24
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (70 bp):
TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATA
AGCCC
Found at i:27788559 original size:20 final size:20
Alignment explanation
Indices: 27788534--27788578 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
27788524 AGGGACTAAA
* *
27788534 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
27788554 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
27788574 ATGAA
1 ATGAA
27788579 TTTATGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:27789255 original size:57 final size:58
Alignment explanation
Indices: 27789120--27789275 Score: 153
Period size: 57 Copynumber: 2.7 Consensus size: 58
27789110 CATTGACCTT
* * *
27789120 GTTATAGAAAGGATTTAGCCCGGA-TAGGTAATCCTGATATAATACCTCTCGAGCATAT
1 GTTATATAAAGGATTTAGCCTGGACT-GGTAATCCTGATATAATACCTCTCGAGCATAC
* *
27789178 GTTATGGT-TAGGATTTAGCCTGGACTGGTAATCCT-A-ATCAAGCT-CCTCT-GAGCATAC
1 GTTAT-ATAAAGGATTTAGCCTGGACTGGTAATCCTGATAT-AA--TACCTCTCGAGCATAC
* * *
27789235 GTTATATAAAGGATTTAGCCTGGACTAGTAGTCCTGTTATA
1 GTTATATAAAGGATTTAGCCTGGACTGGTAATCCTGATATA
27789276 CAGTATGTGG
Statistics
Matches: 80, Mismatches: 10, Indels: 16
0.75 0.09 0.15
Matches are distributed among these distances:
56 3 0.04
57 39 0.49
58 34 0.43
59 4 0.05
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (58 bp):
GTTATATAAAGGATTTAGCCTGGACTGGTAATCCTGATATAATACCTCTCGAGCATAC
Found at i:27794928 original size:14 final size:15
Alignment explanation
Indices: 27794911--27794939 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27794901 GCACGAAAAT
27794911 TTCACACAT-ATAAA
1 TTCACACATAATAAA
27794925 TTCACACATAATAAA
1 TTCACACATAATAAA
27794940 CATAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:27795617 original size:43 final size:43
Alignment explanation
Indices: 27795484--27795650 Score: 135
Period size: 43 Copynumber: 3.9 Consensus size: 43
27795474 AAGCTCGTAC
* * * * *
27795484 AATGCC-ATATCCCAGATATGGTCTTACATGTTATCAC-CTAT
1 AATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATAT
* * * * *
27795525 CAATGCCACTGTCCTAGACAGGGTCTTACACGAAATCA-TATA-
1 -AATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATAT
* *
27795567 ACGATGCCAATGCCCCAGGCATGGTCTTACACGTAATCACAATAT
1 A--ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATAT
* * * *
27795612 AATGCCAATGTCACAGACACGTTCTTACATGTAATCACA
1 AATGCCAATGTCCCAGACATGGTCTTACACGTAATCACA
27795651 TCTCGGTAAT
Statistics
Matches: 97, Mismatches: 22, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
41 1 0.01
42 6 0.06
43 86 0.89
44 3 0.03
45 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (43 bp):
AATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATAT
Found at i:27799949 original size:13 final size:15
Alignment explanation
Indices: 27799931--27799962 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
27799921 CCTAACTAAA
27799931 ATTTATAG-AC-TAC
1 ATTTATAGCACATAC
27799944 ATTTATAGCACATAC
1 ATTTATAGCACATAC
27799959 ATTT
1 ATTT
27799963 CACAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 2 0.12
15 7 0.41
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.41
Consensus pattern (15 bp):
ATTTATAGCACATAC
Found at i:27827711 original size:52 final size:52
Alignment explanation
Indices: 27827633--27827734 Score: 168
Period size: 52 Copynumber: 2.0 Consensus size: 52
27827623 TATGATTCGG
*
27827633 TAGTACCTCGTACCCTGTTACAGCGACGGATACAGGTAAGGGGTGTTACATT
1 TAGTACCTCGTACCCTATTACAGCGACGGATACAGGTAAGGGGTGTTACATT
* * *
27827685 TAGTACCTCGTACCCTATTCCGGCGACGGATACGGGTAAGGGGTGTTACA
1 TAGTACCTCGTACCCTATTACAGCGACGGATACAGGTAAGGGGTGTTACA
27827735 GATCGAGCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (52 bp):
TAGTACCTCGTACCCTATTACAGCGACGGATACAGGTAAGGGGTGTTACATT
Found at i:27834177 original size:20 final size:20
Alignment explanation
Indices: 27834152--27834197 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
27834142 TATTACCTAG
27834152 GAAGAGAGGGAGAGATGGAA
1 GAAGAGAGGGAGAGATGGAA
27834172 GAAGAGAGGGAGAGATGGAA
1 GAAGAGAGGGAGAGATGGAA
*
27834192 GCAGAG
1 GAAGAG
27834198 TTGATCTCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.50, T:0.04
Consensus pattern (20 bp):
GAAGAGAGGGAGAGATGGAA
Found at i:27844550 original size:20 final size:20
Alignment explanation
Indices: 27844525--27844569 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
27844515 AGGGACTAAA
* *
27844525 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
27844545 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
27844565 ATGAA
1 ATGAA
27844570 TTTATGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:27845246 original size:57 final size:58
Alignment explanation
Indices: 27845111--27845266 Score: 153
Period size: 57 Copynumber: 2.7 Consensus size: 58
27845101 CATTGACCTT
* * *
27845111 GTTATAGAAAGGATTTAGCCCGGA-TAGGTAATCCTGATATAATACCTCTCGAGCATAT
1 GTTATATAAAGGATTTAGCCTGGACT-GGTAATCCTGATATAATACCTCTCGAGCATAC
* *
27845169 GTTATGGT-TAGGATTTAGCCTGGACTGGTAATCCT-A-ATCAAGCT-CCTCT-GAGCATAC
1 GTTAT-ATAAAGGATTTAGCCTGGACTGGTAATCCTGATAT-AA--TACCTCTCGAGCATAC
* * *
27845226 GTTATATAAAGGATTTAGCCTGGACTAGTAGTCCTGTTATA
1 GTTATATAAAGGATTTAGCCTGGACTGGTAATCCTGATATA
27845267 CAGTATGTGG
Statistics
Matches: 80, Mismatches: 10, Indels: 16
0.75 0.09 0.15
Matches are distributed among these distances:
56 3 0.04
57 39 0.49
58 34 0.43
59 4 0.05
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (58 bp):
GTTATATAAAGGATTTAGCCTGGACTGGTAATCCTGATATAATACCTCTCGAGCATAC
Found at i:27850919 original size:14 final size:15
Alignment explanation
Indices: 27850902--27850930 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27850892 GCACGAAAAT
27850902 TTCACACAT-ATAAA
1 TTCACACATAATAAA
27850916 TTCACACATAATAAA
1 TTCACACATAATAAA
27850931 CATAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:27851608 original size:43 final size:43
Alignment explanation
Indices: 27851475--27851641 Score: 135
Period size: 43 Copynumber: 3.9 Consensus size: 43
27851465 AAGCTCGTAC
* * * * *
27851475 AATGCC-ATATCCCAGATATGGTCTTACATGTTATCAC-CTAT
1 AATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATAT
* * * * *
27851516 CAATGCCACTGTCCTAGACAGGGTCTTACACGAAATCA-TATA-
1 -AATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATAT
* *
27851558 ACGATGCCAATGCCCCAGGCATGGTCTTACACGTAATCACAATAT
1 A--ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATAT
* * * *
27851603 AATGCCAATGTCACAGACACGTTCTTACATGTAATCACA
1 AATGCCAATGTCCCAGACATGGTCTTACACGTAATCACA
27851642 TCTCGGTAAT
Statistics
Matches: 97, Mismatches: 22, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
41 1 0.01
42 6 0.06
43 86 0.89
44 3 0.03
45 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (43 bp):
AATGCCAATGTCCCAGACATGGTCTTACACGTAATCACAATAT
Found at i:27853956 original size:68 final size:68
Alignment explanation
Indices: 27853842--27853970 Score: 165
Period size: 68 Copynumber: 1.9 Consensus size: 68
27853832 TAGATGGAGC
* *
27853842 GTAGCTAGGTCACATGTATGATGCCGAGTGCACATCATGTGTACAAGAAAGCTACGAGACACCCT
1 GTAGCTAGGTCACATGTATGATGACGAGTGCACACCATGTGTACAAGAAAGCTACGAGACACCCT
27853907 GTA
66 GTA
* * *
27853910 GTAGCTAGGTCACATGTGTGAT-ACGAGATGTATC-CCATGTAG-ACAAGAGAGCTACGAGACA
1 GTAGCTAGGTCACATGTATGATGACGAG-TGCA-CACCATGT-GTACAAGAAAGCTACGAGACA
27853971 AATCGGCTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
67 4 0.08
68 47 0.89
69 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (68 bp):
GTAGCTAGGTCACATGTATGATGACGAGTGCACACCATGTGTACAAGAAAGCTACGAGACACCCT
GTA
Found at i:27860686 original size:18 final size:17
Alignment explanation
Indices: 27860658--27860695 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
27860648 GTGTATTTTG
27860658 ATGTTTTATGATAGAAT
1 ATGTTTTATGATAGAAT
27860675 ATGTTATTATGATAGAAT
1 ATGTT-TTATGATAGAAT
27860693 ATG
1 ATG
27860696 AGGTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (17 bp):
ATGTTTTATGATAGAAT
Found at i:27861382 original size:68 final size:67
Alignment explanation
Indices: 27861261--27861388 Score: 170
Period size: 68 Copynumber: 1.9 Consensus size: 67
27861251 TAGATGGAGC
* *
27861261 GTAGCTAGGTCACATGTATGATGCGAGTGCACATCATGTGTACAAGAAAGCTACGAGACACCCTG
1 GTAGCTAGGTCACATGTATGATACGAGTGCACACCATGTGTACAAGAAAGCTACGAGACACCCTG
27861326 TA
66 TA
* * *
27861328 GTAGCTAGGTCACATGTGTGATACGAGATGTATC-CCATGTAG-ACAAGAGAGCTACGAGACA
1 GTAGCTAGGTCACATGTATGATACGAG-TGCA-CACCATGT-GTACAAGAAAGCTACGAGACA
27861389 AATCGGCTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
67 25 0.47
68 26 0.49
69 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (67 bp):
GTAGCTAGGTCACATGTATGATACGAGTGCACACCATGTGTACAAGAAAGCTACGAGACACCCTG
TA
Found at i:27865225 original size:30 final size:29
Alignment explanation
Indices: 27865131--27865232 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
27865121 TATAGTGAAT
* * *
27865131 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
27865160 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
27865188 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
27865218 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
27865233 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:27873097 original size:30 final size:29
Alignment explanation
Indices: 27873003--27873104 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 29
27872993 TATAGTGAAT
* * *
27873003 CCGCACACTTAGTGCTATATATTTTCAGC
1 CCGCACACTTAGTGCTATAAATTTTAAAC
* *
27873032 TCGCACACTTAGTGCTATAGAA--TCAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
* *
27873060 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATA-AATTTTAAAC
27873090 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
27873105 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 23 0.38
29 18 0.30
30 20 0.33
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATAAATTTTAAAC
Found at i:27880252 original size:43 final size:43
Alignment explanation
Indices: 27880205--27880307 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 43
27880195 CTAGACAGGG
* * * *
27880205 TCTTACACGAAATCA-TATAACGATGCCAATGTCCCAGGCATGA
1 TCTTACACGAAATCACAAT-ACAATGCCAATGTCACAGACATGA
* * *
27880248 TCTTACATGTAATCACAATACAATGCCAATGTCACAGACATGG
1 TCTTACACGAAATCACAATACAATGCCAATGTCACAGACATGA
* *
27880291 TCTTACATGTAATCACA
1 TCTTACACGAAATCACA
27880308 TCTTGTTAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
43 50 0.96
44 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (43 bp):
TCTTACACGAAATCACAATACAATGCCAATGTCACAGACATGA
Found at i:27882196 original size:18 final size:19
Alignment explanation
Indices: 27882155--27882196 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
27882145 ACTCATAATG
*
27882155 CTTTTCTATTGATTTTGTA
1 CTTTTCTATTGATTTTGCA
27882174 CTTTTCTACTTG-TTTT-CA
1 CTTTTCTA-TTGATTTTGCA
27882192 CTTTT
1 CTTTT
27882197 TCTGAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 12 0.57
20 3 0.14
ACGTcount: A:0.12, C:0.17, G:0.07, T:0.64
Consensus pattern (19 bp):
CTTTTCTATTGATTTTGCA
Found at i:27885363 original size:94 final size:92
Alignment explanation
Indices: 27885202--27885562 Score: 311
Period size: 94 Copynumber: 3.9 Consensus size: 92
27885192 TTTGTGCGCC
* * * * * *
27885202 AGTGTAAGACATGTCTGCGACATGCTTCGGCCACATTATGGGAGCCAGTGTAAGACATTGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACA-TGTCTGG
* * *
27885267 GACATGGCATTGGCATCCAGACGAGGGCT
65 GACATGGCATCGGCAT-CAGAAGAGTGCT
* *
27885296 AGTGTAAGACATGTTTGGGACATGCATCAGCCATACTATGACAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGA-CATGTCTGG
* * *
27885361 GACATAGCATCGGTA-CAGAGATGAGTGCC
65 GACATGGCATCGGCATCAGA-A-GAGTGCT
* * * * * **
27885390 AATGTAAGACATGTCTGGGACATGCATCGGCC-TCAACAAAGATAGCCAGTGTAAGATGTGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAT--ACTATGAGAGCCAGTGTAAGACATGTCTG
* * *
27885454 GGACA-CGCATCGGC-T-AAAAGTTGTGCT
64 GGACATGGCATCGGCATCAGAAG-AGTGCT
* * *
27885481 AGTGTAAGACACGTCTGGGACATGCATCATCACGCGTA-TATGAGAGCCAGTGTAAGACCATGTC
1 AGTGTAAGACATGTCTGGGACATGCATCA--GC-CATACTATGAGAGCCAGTGTAAGA-CATGTC
* *
27885545 AGAGACATGGCATCGGCA
62 TGGGACATGGCATCGGCA
27885563 ATATAACCCA
Statistics
Matches: 214, Mismatches: 39, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
90 1 0.00
91 31 0.14
92 22 0.10
93 19 0.09
94 120 0.56
95 21 0.10
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.22
Consensus pattern (92 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACATGTCTGGG
ACATGGCATCGGCATCAGAAGAGTGCT
Found at i:27885443 original size:47 final size:45
Alignment explanation
Indices: 27885199--27885508 Score: 211
Period size: 47 Copynumber: 6.7 Consensus size: 45
27885189 TGATTTGTGC
* * * **
27885199 GCCAGTGTAAGACATGTCTGCGACATGCTTCGGC-CACATTATGGGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTCACA--AAGATA
* * **
27885245 GCCAGTGTAAGACATTGTCTGGGACATGGCATTGGCATC-CAGACGAGG
1 GCCAGTGTAAGACA-TGTCTGGGACAT-GCATCGGC-TCACA-AAGATA
* * * * * *
27885293 GCTAGTGTAAGACATGTTTGGGACATGCATCAGC-CATACTATGACA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTC--ACAAAGATA
*
27885339 GCCAGTGTAAGACCATGTCTGGGACATAGCATCGG-T-ACAGAGATGA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTCACAAAGAT-A
*
27885385 GTGCCAATGTAAGACATGTCTGGGACATGCATCGGCCTCAACAAAGATA
1 --GCCAGTGTAAGACATGTCTGGGACATGCATCGG-CTC-ACAAAGATA
** * * *
27885434 GCCAGTGTAAGATGTGTCTGGGACACGCATCGGCT-A-AAAGTTGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTCACAAAGAT-A
* *
27885478 GCTAGTGTAAGACACGTCTGGGACATGCATC
1 GCCAGTGTAAGACATGTCTGGGACATGCATC
27885509 ATCACGCGTA
Statistics
Matches: 211, Mismatches: 35, Indels: 38
0.74 0.12 0.13
Matches are distributed among these distances:
43 5 0.02
44 28 0.13
45 4 0.02
46 44 0.21
47 79 0.37
48 40 0.19
49 3 0.01
50 8 0.04
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCTCACAAAGATA
Found at i:27887924 original size:68 final size:67
Alignment explanation
Indices: 27887878--27888035 Score: 244
Period size: 68 Copynumber: 2.3 Consensus size: 67
27887868 ATACTATATA
** *
27887878 GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGCAATGTATCCCATGCAGACAAGAGAGCTACG-GAGAGATA
27887943 AAT
65 AAT
*
27887946 GCAGCTAGGTCACATGTGTGATACGCAATGTATCCCATGCAGACAAGAGAGCTACGTGAGAGATA
1 GTAGCTAGGTCACATGTGTGATACGCAATGTATCCCATGCAGACAAGAGAGCTACG-GAGAGATA
27888011 AAT
65 AAT
* *
27888014 GTACCTAGGTCACATGAGTGAT
1 GTAGCTAGGTCACATGTGTGAT
27888036 TCCAAGTGAA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 83 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (67 bp):
GTAGCTAGGTCACATGTGTGATACGCAATGTATCCCATGCAGACAAGAGAGCTACGGAGAGATAA
AT
Found at i:27890193 original size:40 final size:40
Alignment explanation
Indices: 27890148--27890315 Score: 207
Period size: 40 Copynumber: 4.2 Consensus size: 40
27890138 CGGAATACAA
27890148 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* * * *
27890188 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* **
27890228 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* *
27890268 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTCTTAGC
27890308 CCGGATAT
1 CCGGATAT
27890316 CATTCAATTG
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 108 0.96
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
Found at i:27890288 original size:80 final size:80
Alignment explanation
Indices: 27890148--27890315 Score: 241
Period size: 80 Copynumber: 2.1 Consensus size: 80
27890138 CGGAATACAA
* *
27890148 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATG
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
*
27890213 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
** *
27890228 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA-AA-GTCACTAGCACAAT
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACG--ACTAGCACAAA
*
27890291 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
27890308 CCGGATAT
1 CCGGATAT
27890316 CATTCAATTG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
78 1 0.01
79 2 0.03
80 76 0.96
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (80 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:27895031 original size:48 final size:48
Alignment explanation
Indices: 27894929--27895085 Score: 174
Period size: 48 Copynumber: 3.5 Consensus size: 48
27894919 GTTTAACCAC
* *
27894929 GGTATATCCACTTAGCGCCACGTT-GATGAATCAATATATGTAACCGT
1 GGTATATCCACTTAGCACCACGTTACATGAATCAATATATGTAACCGT
* * * *
27894976 GGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATCGT
1 GGTATATCCACTTAGCACCACGTTACATGAATCAATATATGTAACCGT
*
27895024 GGTATATCCACTTAGCACCATGTTAC----A-C---ATA--TAACCGT
1 GGTATATCCACTTAGCACCACGTTACATGAATCAATATATGTAACCGT
27895062 GGTATATCCACTTAGCACCACGTT
1 GGTATATCCACTTAGCACCACGTT
27895086 TTTCCATTCC
Statistics
Matches: 98, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
38 29 0.30
40 2 0.02
43 1 0.01
44 1 0.01
47 22 0.22
48 43 0.44
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (48 bp):
GGTATATCCACTTAGCACCACGTTACATGAATCAATATATGTAACCGT
Found at i:27903971 original size:18 final size:18
Alignment explanation
Indices: 27903948--27903994 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
27903938 AAGGGCCTTG
27903948 ATGGGCCGTGTGGGCCCA
1 ATGGGCCGTGTGGGCCCA
*
27903966 ATGGGCCGTGTGGGCCTA
1 ATGGGCCGTGTGGGCCCA
27903984 ATGGGCTCGTG
1 ATGGGC-CGTG
27903995 GGCCCTGCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.11, C:0.23, G:0.45, T:0.21
Consensus pattern (18 bp):
ATGGGCCGTGTGGGCCCA
Found at i:27904561 original size:22 final size:22
Alignment explanation
Indices: 27904534--27904575 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
27904524 ACGGCCTTTA
27904534 GTCCTGCCTACGGCGTTGAGCC
1 GTCCTGCCTACGGCGTTGAGCC
* * *
27904556 GTCCTGTCTATGGTGTTGAG
1 GTCCTGCCTACGGCGTTGAG
27904576 TCGTTCTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.10, C:0.26, G:0.33, T:0.31
Consensus pattern (22 bp):
GTCCTGCCTACGGCGTTGAGCC
Found at i:27907694 original size:27 final size:27
Alignment explanation
Indices: 27907664--27907715 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
27907654 CCCAATATTG
* *
27907664 GTAAAATTACTGAAATACCCTTGTAGT
1 GTAAAATTACCGAAATACCCCTGTAGT
*
27907691 GTAAAATTACCGTAATACCCCTGTA
1 GTAAAATTACCGAAATACCCCTGTA
27907716 TGGTAGAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (27 bp):
GTAAAATTACCGAAATACCCCTGTAGT
Found at i:27908172 original size:27 final size:27
Alignment explanation
Indices: 27908142--27908194 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
27908132 GTATCTGATA
*
27908142 CTGATTCTG-TAATAGGTTTAGGCCCAC
1 CTGATTCTGTTAAT-GGTCTAGGCCCAC
27908169 CTGATTCTGTTAATGGTCTAGGCCCA
1 CTGATTCTGTTAATGGTCTAGGCCCA
27908195 ACTGTTACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.34
Consensus pattern (27 bp):
CTGATTCTGTTAATGGTCTAGGCCCAC
Found at i:27920866 original size:46 final size:46
Alignment explanation
Indices: 27920816--27920988 Score: 176
Period size: 46 Copynumber: 3.7 Consensus size: 46
27920806 TGGTTGAGCA
*
27920816 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATG
* * * * *
27920862 TCCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--AATGTA-ACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-AGA--ATG
*
27920907 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATG
* *
27920955 -CTCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
27920989 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
43 4 0.04
44 1 0.01
45 5 0.05
46 57 0.55
47 28 0.27
48 4 0.04
50 4 0.04
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATG
Found at i:27920972 original size:93 final size:93
Alignment explanation
Indices: 27920813--27920983 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
27920803 GGATGGTTGA
27920813 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCGAACTCGTTGAGT
27920878 TGAGTCTGAGTTCGTGAAATGTAACTAG
66 TGAGTCTGAGTTCGTGAAATGTAACTAG
* * *
27920906 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CTCGAGCTCGTTGAG
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTC-CGAACTCGTTGAG
27920970 TTGAGTCTGAGTTC
65 TTGAGTCTGAGTTC
27920984 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 1 0.01
93 73 0.99
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGAGAATGTCCGAACTCGTTGAGT
TGAGTCTGAGTTCGTGAAATGTAACTAG
Found at i:27923901 original size:46 final size:45
Alignment explanation
Indices: 27923851--27924023 Score: 215
Period size: 46 Copynumber: 3.8 Consensus size: 45
27923841 TGGTTGAGCA
27923851 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * * *
27923897 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAAATGTAACTACGCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-TGCGAAG
27923944 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
27923990 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
27924024 GGGGCGGGTT
Statistics
Matches: 108, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
44 4 0.04
45 2 0.02
46 64 0.59
47 32 0.30
48 2 0.02
49 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:27924007 original size:93 final size:93
Alignment explanation
Indices: 27923848--27924018 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
27923838 GGATGGTTGA
* *
27923848 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27923913 TGAGTCCGAGTTCGTGAAATGTAACTAC
66 TGAGTCCGAGTTCGTGAAATGTAACTAC
*
27923941 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
27924006 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
27924019 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAC
Found at i:27927587 original size:55 final size:55
Alignment explanation
Indices: 27927492--27927597 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
27927482 TAGGCCGACA
* * ** *
27927492 CCCGTGTTAATTTAACAGGTTCGACCACGGGTACTTGGCACGGGCATGTCGTATG
1 CCCGTGTTAATTTAACAGGTTAGACCACGAGTACCAGGCACCGGCATGTCGTATG
* * * *
27927547 CCCGTGTTAATTTGACAGGTTAGACCACGATTTCCAGGCACCTGCATGTCG
1 CCCGTGTTAATTTAACAGGTTAGACCACGAGTACCAGGCACCGGCATGTCG
27927598 CACGCTCGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 42 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.27
Consensus pattern (55 bp):
CCCGTGTTAATTTAACAGGTTAGACCACGAGTACCAGGCACCGGCATGTCGTATG
Found at i:27927608 original size:55 final size:55
Alignment explanation
Indices: 27927492--27927609 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 55
27927482 TAGGCCGACA
* * ** * * *
27927492 CCCGTGTTAATTTAACAGGTTCGACCACGGGTACTTGGCACGGGCATGTCGTATG
1 CCCGTGTTAATTTAACAGGTTAGACCACGAGTACCAGGCACCGGCATGTCGCACG
* * * *
27927547 CCCGTGTTAATTTGACAGGTTAGACCACGATTTCCAGGCACCTGCATGTCGCACG
1 CCCGTGTTAATTTAACAGGTTAGACCACGAGTACCAGGCACCGGCATGTCGCACG
*
27927602 CTCGTGTT
1 CCCGTGTT
27927610 GTTTTGGCAG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (55 bp):
CCCGTGTTAATTTAACAGGTTAGACCACGAGTACCAGGCACCGGCATGTCGCACG
Found at i:27933492 original size:29 final size:29
Alignment explanation
Indices: 27933453--27933531 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
27933443 CTTAATAATC
*
27933453 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
27933483 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
* *
27933512 AGCCCACACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
27933532 ATCTCACAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 3 0.07
29 37 0.86
30 3 0.07
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:27936694 original size:13 final size:13
Alignment explanation
Indices: 27936676--27936700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27936666 TGTGGATGCA
27936676 CACGGTCGTGTCG
1 CACGGTCGTGTCG
27936689 CACGGTCGTGTC
1 CACGGTCGTGTC
27936701 TGTCTTCGTT
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:0.08, C:0.32, G:0.36, T:0.24
Consensus pattern (13 bp):
CACGGTCGTGTCG
Found at i:27941572 original size:93 final size:93
Alignment explanation
Indices: 27941463--27941633 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
27941453 GCCCATAAGT
* * *
27941463 GAACTCGGACTCAACTCAATGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
27941528 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
27941556 GAACTCAGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
27941621 CGAGTTCGGATGC
66 CGAGCTCGGATGC
27941634 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:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:27941630 original size:46 final size:46
Alignment explanation
Indices: 27941455--27941630 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
27941445 CATGTAACGC
* *
27941455 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
27941501 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** * *
27941547 ACATCTCTCGAACTCAGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
27941594 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
27941631 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
46 68 0.62
47 31 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:27944000 original size:15 final size:15
Alignment explanation
Indices: 27943968--27944031 Score: 89
Period size: 15 Copynumber: 4.4 Consensus size: 15
27943958 CAAAGATAAC
27943968 AAGAAA-CC-GAATA
1 AAGAAATCCAGAATA
27943981 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
27943996 GAGAAATCCAGAATA
1 AAGAAATCCAGAATA
27944011 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
27944026 AAGAAA
1 AAGAAA
27944032 CCCAAGATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.13
14 3 0.07
15 35 0.78
16 1 0.02
ACGTcount: A:0.61, C:0.12, G:0.16, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Done.