Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 84 of 279
Found at i:27869746 original size:43 final size:43
Alignment explanation
Indices: 27869682--27870070 Score: 213
Period size: 43 Copynumber: 8.9 Consensus size: 43
27869672 AGAATTAGTG
* * *
27869682 AATTCACCAGACCTTAACCCCCTAAGCAGTAGGGTAACATGTTA
1 AATTCA-CAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
*
27869726 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTG
1 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
* * * *
27869769 AATTCATAGATCTCAACCCCCTAAGCAGTAGGGAAATAGATTGA
1 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTT-A
* * ** * * *
27869813 AGATGAT-A-AG-CCTTAACCCTTTTATGCAGTAAGGTAACAGGCTAAA
1 A-AT--TCACAGATCTCAACCC-CCTAAGCAGTAGGGTAACAGG-T-TA
* * * * **
27869859 AATT-ACAGATCTTATCACCCTAAGCAGTAGGGAAACAGAGCGA
1 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAG-GTTA
* * * * * *
27869902 AGA-TGA-AGAACCTTAAACCCCTAAGTAGTAGGGTAACAGGTTG
1 A-ATTCACAG-ATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
* * * * *
27869945 AATTTACAGATCTCACCCCCCTAAGCAGTAGGGAAACAGATCGA
1 AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGT-TA
* * *
27869989 AGATGAT-A-AG-CCTTAA-CCCCTAAGCAGTAGGGTAACAGGTTG
1 A-AT--TCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
* * * *
27870031 AATTTATAGATCTTAACCCCCTTAAGCAGTAGGGAAACAG
1 AATTCACAGATCTCAACCCCC-TAAGCAGTAGGGTAACAG
27870071 ATCAGGAGTG
Statistics
Matches: 264, Mismatches: 57, Indels: 48
0.72 0.15 0.13
Matches are distributed among these distances:
39 1 0.00
40 1 0.00
41 4 0.02
42 7 0.03
43 133 0.50
44 80 0.30
45 31 0.12
46 5 0.02
47 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (43 bp):
AATTCACAGATCTCAACCCCCTAAGCAGTAGGGTAACAGGTTA
Found at i:27869924 original size:44 final size:45
Alignment explanation
Indices: 27869876--27870108 Score: 146
Period size: 43 Copynumber: 5.3 Consensus size: 45
27869866 GATCTTATCA
27869876 CCCTAAGCAGTAGGGAAACAGAGCGAAGATGA-AGAACCTTAAAC
1 CCCTAAGCAGTAGGGAAACAGAGCGAAGATGATAGAACCTTAAAC
* * * * * * * * **
27869920 CCCTAAGTAGTAGGGTAACAG-GTTGAA-TTTACAG-ATCTCACCC
1 CCCTAAGCAGTAGGGAAACAGAG-CGAAGATGATAGAACCTTAAAC
* *
27869963 CCCTAAGCAGTAGGGAAACAGATCGAAGATGATA-AGCCTT-AAC
1 CCCTAAGCAGTAGGGAAACAGAGCGAAGATGATAGAACCTTAAAC
* * * * * *
27870006 CCCTAAGCAGTAGGGTAACAG-GTTGAA-TTTATAG-ATCTTAACC
1 CCCTAAGCAGTAGGGAAACAGAG-CGAAGATGATAGAACCTTAAAC
* * *
27870049 CCCTTAAGCAGTAGGGAAACAGATC-AGGAGTGAT-GAGCCTTAAAC
1 CCC-TAAGCAGTAGGGAAACAGAGCGAAGA-TGATAGAACCTTAAAC
* *
27870094 CCATAAGCAATAGGG
1 CCCTAAGCAGTAGGG
27870109 TCACAGGCTG
Statistics
Matches: 136, Mismatches: 40, Indels: 26
0.67 0.20 0.13
Matches are distributed among these distances:
42 7 0.05
43 60 0.44
44 58 0.43
45 11 0.08
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (45 bp):
CCCTAAGCAGTAGGGAAACAGAGCGAAGATGATAGAACCTTAAAC
Found at i:27869982 original size:87 final size:86
Alignment explanation
Indices: 27869743--27870133 Score: 435
Period size: 87 Copynumber: 4.5 Consensus size: 86
27869733 AGATCTCAAC
* * * *
27869743 CCCCTAAGCAGTAGGGTAACAGGTTGAATTCATAGATCTCAACCCCCTAAGCAGTAGGGAAATAG
1 CCCCTAAGCAGTAGGGTAACAGGTTGAATTTACAGATCTCACCCCCCTAAGCAGTAGGGAAACAG
*
27869808 ATTGAAGATGATAAGCCTTAA
66 ATCGAAGATGATAAGCCTTAA
* * * ** * * * *
27869829 CCCTTTTATGCAGTAAGGTAACAGGCTAAAAATTACAGATCTTATCACCCTAAGCAGTAGGGAAA
1 CCC--CTAAGCAGTAGGGTAACAGG-TTGAATTTACAGATCTCACCCCCCTAAGCAGTAGGGAAA
* *
27869894 CAGAGCGAAGATGA-AGAACCTTAAA
63 CAGATCGAAGATGATA-AGCCTT-AA
*
27869919 CCCCTAAGTAGTAGGGTAACAGGTTGAATTTACAGATCTCACCCCCCTAAGCAGTAGGGAAACAG
1 CCCCTAAGCAGTAGGGTAACAGGTTGAATTTACAGATCTCACCCCCCTAAGCAGTAGGGAAACAG
27869984 ATCGAAGATGATAAGCCTTAA
66 ATCGAAGATGATAAGCCTTAA
* * *
27870005 CCCCTAAGCAGTAGGGTAACAGGTTGAATTTATAGATCTTAACCCCCTTAAGCAGTAGGGAAACA
1 CCCCTAAGCAGTAGGGTAACAGGTTGAATTTACAGATC-TCACCCCCCTAAGCAGTAGGGAAACA
* *
27870070 GATC-AGGAGTGATGAGCCTTAAA
65 GATCGAAGA-TGATAAGCCTT-AA
* * * * * *
27870093 CCCATAAGCAATAGGGTCACAGGCTGGAAATTACAAATCTC
1 CCCCTAAGCAGTAGGGTAACAGG-TTGAATTTACAGATCTC
27870134 TTCTCCCTGA
Statistics
Matches: 254, Mismatches: 41, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
86 44 0.17
87 89 0.35
88 58 0.23
89 58 0.23
90 5 0.02
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.21
Consensus pattern (86 bp):
CCCCTAAGCAGTAGGGTAACAGGTTGAATTTACAGATCTCACCCCCCTAAGCAGTAGGGAAACAG
ATCGAAGATGATAAGCCTTAA
Found at i:27871882 original size:27 final size:28
Alignment explanation
Indices: 27871837--27871890 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
27871827 TATATATATA
*
27871837 TTTTTATATTATGTCTATATTTTATGTTT
1 TTTTTATATTATG-CTATATATTATGTTT
27871866 TTTTTATATTATG-TATATATTATGT
1 TTTTTATATTATGCTATATATTATGT
27871891 ATATACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 11 0.46
29 13 0.54
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (28 bp):
TTTTTATATTATGCTATATATTATGTTT
Found at i:27871884 original size:11 final size:11
Alignment explanation
Indices: 27871870--27871895 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27871860 ATGTTTTTTT
27871870 TATATTATGTA
1 TATATTATGTA
27871881 TATATTATGTA
1 TATATTATGTA
27871892 TATA
1 TATA
27871896 CTTTTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (11 bp):
TATATTATGTA
Found at i:27871923 original size:23 final size:22
Alignment explanation
Indices: 27871880--27871929 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
27871870 TATATTATGT
*
27871880 ATATATTATGTATATACTTTTA
1 ATATATTATATATATACTTTTA
* *
27871902 ATATCATTATATATTTATTTTTA
1 ATAT-ATTATATATATACTTTTA
27871925 ATATA
1 ATATA
27871930 AACGTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATATTATATATATACTTTTA
Found at i:27872346 original size:13 final size:13
Alignment explanation
Indices: 27872328--27872352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27872318 ATTATTATTA
27872328 TATATATTTCTTT
1 TATATATTTCTTT
27872341 TATATATTTCTT
1 TATATATTTCTT
27872353 ATTACTTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TATATATTTCTTT
Found at i:27873431 original size:3 final size:3
Alignment explanation
Indices: 27873425--27873478 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
27873415 TGGTTACGAC
27873425 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
27873473 AAT AAT
1 AAT AAT
27873479 TGAAGTTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27879000 original size:53 final size:53
Alignment explanation
Indices: 27878938--27879155 Score: 436
Period size: 53 Copynumber: 4.1 Consensus size: 53
27878928 TCTTATTAAA
27878938 TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
1 TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
27878991 TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
1 TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
27879044 TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
1 TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
27879097 TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
1 TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
27879150 TTTTTT
1 TTTTTT
27879156 GTCTCGAAAA
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 165 1.00
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.50
Consensus pattern (53 bp):
TTTTTTATATAATTTTAAAAACTCTGTTTGCAATTTGATCTTAATGACATCAT
Found at i:27879466 original size:13 final size:13
Alignment explanation
Indices: 27879448--27879472 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27879438 GAGTGAAAAT
27879448 ATCATTAATTTTC
1 ATCATTAATTTTC
27879461 ATCATTAATTTT
1 ATCATTAATTTT
27879473 TTAAAATGAG
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:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
ATCATTAATTTTC
Found at i:27879981 original size:22 final size:23
Alignment explanation
Indices: 27879923--27879982 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
27879913 AGTGTTTGGG
27879923 AAATATTAAA-AT-AAATATATA
1 AAATATTAAATATAAAATATATA
* *
27879944 AAAAAGGT-AATGATAAAATAT-TA
1 AAATA-TTAAAT-ATAAAATATATA
27879967 AAATATTAAATATAAA
1 AAATATTAAATATAAA
27879983 TTACACTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
21 6 0.20
22 7 0.23
23 11 0.37
24 6 0.20
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (23 bp):
AAATATTAAATATAAAATATATA
Found at i:27885342 original size:21 final size:22
Alignment explanation
Indices: 27885291--27885342 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
27885281 GAAAGAAGAT
27885291 TAAAT-TT-AACTAAAAATAAA
1 TAAATATTAAACTAAAAATAAA
* * *
27885311 TAAAAACTAAACTAAAAA-ATA
1 TAAATATTAAACTAAAAATAAA
27885332 TAAATATTAAA
1 TAAATATTAAA
27885343 AGCTAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.16
21 12 0.48
22 9 0.36
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAATATTAAACTAAAAATAAA
Found at i:27887325 original size:43 final size:42
Alignment explanation
Indices: 27887255--27887436 Score: 165
Period size: 43 Copynumber: 4.3 Consensus size: 42
27887245 TTATGTGGAA
* * * * * *
27887255 AAACGCCGTTATAGAACATTACATTTAGCGACGCTTTTTCCAC
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGACGC-TTTCCCAC
*
27887298 AAACGCCGCTAAAGAACGTGACCTTTAGCGACGCTTTCCCCAT
1 AAACGCCGCTAAAGAACGTGACCTTTAGCGACGCTTT-CCCAC
*
27887341 AAACGCCACTAAAGAACGTGACCTTTAGCTG-CGCTTTCCCAC
1 AAACGCCGCTAAAGAACGTGACCTTTAGC-GACGCTTTCCCAC
** * *
27887383 AAACGTTGCTAAGAGAA--TGACCTTTAGC-AGCGCTTTTCTCAA
1 AAACGCCGCTAA-AGAACGTGACCTTTAGCGA-CGC-TTTCCCAC
*
27887425 AAACGCCACTAA
1 AAACGCCGCTAA
27887437 GGTCATGTTC
Statistics
Matches: 116, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
41 14 0.12
42 31 0.27
43 70 0.60
44 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACGTGACCTTTAGCGACGCTTTCCCAC
Found at i:27887519 original size:42 final size:42
Alignment explanation
Indices: 27887438--27887519 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
27887428 CGCCACTAAG
* * *
27887438 GTCATGTTCTTTAACGGCGTTTTAGTAAAAGCGCTGTTAAAA
1 GTCATGTTCTTTAACGGCGTTTTAGGAAAAACGCCGTTAAAA
**
27887480 GTCATGTTCTTTGGCGGCGTTTGT-GGAAAAACGCCGTTAA
1 GTCATGTTCTTTAACGGCGTTT-TAGGAAAAACGCCGTTAA
27887520 CTTTAGTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (42 bp):
GTCATGTTCTTTAACGGCGTTTTAGGAAAAACGCCGTTAAAA
Found at i:27887920 original size:66 final size:65
Alignment explanation
Indices: 27887792--27887925 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 65
27887782 ATTCTGAAGC
* * ***
27887792 TGTAGCTGGAGTTCGTCATATTTTCTGCTTGCCTCTGCTTCCCTCGCTGCTACCTTTGCTTTAAG
1 TGTAGCTGGAGTTCGTCATATTTTCT-CTTGCCTCTACTTCCCTCGATGCTACCTCCACTTTAAG
27887857 T
65 T
* * *
27887858 TGTAGCTGGAGTTCTTCATATTTTCT-TTGAGCCTCTACTTCTCTCGATGCTGCCTCCACTTTAA
1 TGTAGCTGGAGTTCGTCATATTTTCTCTT--GCCTCTACTTCCCTCGATGCTACCTCCACTTTAA
27887922 GT
64 GT
27887924 TG
1 TG
27887926 AGCAATTTGC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 2 0.03
66 56 0.97
ACGTcount: A:0.13, C:0.26, G:0.19, T:0.43
Consensus pattern (65 bp):
TGTAGCTGGAGTTCGTCATATTTTCTCTTGCCTCTACTTCCCTCGATGCTACCTCCACTTTAAGT
Found at i:27889704 original size:5 final size:5
Alignment explanation
Indices: 27889694--27889749 Score: 85
Period size: 5 Copynumber: 10.6 Consensus size: 5
27889684 TTAAGTATAT
27889694 TATTA TATTA TATTA TATTA TATTTA TATTTA TATTTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TA-TTA TA-TTA TA-TTA TATTA TATTA
27889742 TATTA TAT
1 TATTA TAT
27889750 ATAAAAGAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 33 0.66
6 17 0.34
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:27890473 original size:18 final size:18
Alignment explanation
Indices: 27890442--27890476 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27890432 GTGTGTTGAA
* *
27890442 TACTGTTACTGTTACTGC
1 TACTGCTACCGTTACTGC
27890460 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
27890477 ATTACTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (18 bp):
TACTGCTACCGTTACTGC
Found at i:27893695 original size:46 final size:46
Alignment explanation
Indices: 27893635--27893909 Score: 428
Period size: 46 Copynumber: 6.0 Consensus size: 46
27893625 TTTGACATGA
* * * * * *
27893635 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATG-T
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCA-GAC
*
27893681 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAC
27893727 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAC
*
27893773 TGCCATGGTATTTTTCAACCATGGTCTTACACATTTCATATCAGAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAC
*
27893819 TGCCATGGTATTTTTCAACCATGGTCTTACACATTTCATATCAGAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAC
*
27893865 TGCCATGGTATTTTTCAACCATGGTCTTACACATTTCATATCAGA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGA
27893910 AAGCACACTC
Statistics
Matches: 219, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
45 5 0.02
46 214 0.98
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGAC
Found at i:27895945 original size:14 final size:14
Alignment explanation
Indices: 27895909--27895954 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
27895899 GCTTTGTTTC
*
27895909 TTTATTTCTCTCC-T
1 TTTATTTC-CCCCTT
27895923 TTT-TTTCCCCCTT
1 TTTATTTCCCCCTT
*
27895936 TTTATTTCCCCTTT
1 TTTATTTCCCCCTT
27895950 TTTAT
1 TTTAT
27895955 ATATACACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 8 0.29
14 17 0.61
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATTTCCCCCTT
Found at i:27897696 original size:30 final size:30
Alignment explanation
Indices: 27897662--27897724 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
27897652 ACTTAAGAAG
27897662 CAAATG-CTTCTAAAATAATAAAAAAATTAA
1 CAAATGCCTT-TAAAATAATAAAAAAATTAA
*
27897692 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAATTAA
27897722 CAA
1 CAA
27897725 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAAAAAATTAA
Found at i:27901014 original size:5 final size:5
Alignment explanation
Indices: 27901004--27901046 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
27900994 AATAATTAAG
27901004 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT
27901047 ATAAAAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:27901695 original size:12 final size:12
Alignment explanation
Indices: 27901678--27901702 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27901668 GCCGACTACT
27901678 GTTACTGTTACC
1 GTTACTGTTACC
27901690 GTTACTGTTACC
1 GTTACTGTTACC
27901702 G
1 G
27901703 ATTCGACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:27901730 original size:45 final size:45
Alignment explanation
Indices: 27901680--27901786 Score: 135
Period size: 45 Copynumber: 2.4 Consensus size: 45
27901670 CGACTACTGT
*
27901680 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAA
* * * * *
27901725 TACTGTTACCGTTACTATTATAGATTCAGTATTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
*
27901770 TACTGTTACTGTTACTG
1 TACTGTTACCGTTACTG
27901787 CTATTGCTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 52 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
Found at i:27915707 original size:19 final size:20
Alignment explanation
Indices: 27915670--27915707 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
27915660 ATATGATTAA
27915670 TAAAATTTTCATGTGAAATT
1 TAAAATTTTCATGTGAAATT
27915690 TAAACATTTT-AT-TGAAAT
1 TAAA-ATTTTCATGTGAAAT
27915708 AATATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (20 bp):
TAAAATTTTCATGTGAAATT
Found at i:27919184 original size:22 final size:22
Alignment explanation
Indices: 27919156--27919205 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
27919146 AACTATTGTA
27919156 CATATTAGATGAATTCAATAAT
1 CATATTAGATGAATTCAATAAT
*
27919178 CATATTAGATGAATTCAATAGT
1 CATATTAGATGAATTCAATAAT
27919200 CATATT
1 CATATT
27919206 TGATTCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (22 bp):
CATATTAGATGAATTCAATAAT
Found at i:27921823 original size:15 final size:15
Alignment explanation
Indices: 27921803--27921832 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27921793 TTCATTCTTT
27921803 TATGTTTTCTTTGTA
1 TATGTTTTCTTTGTA
27921818 TATGTTTTCTTTGTA
1 TATGTTTTCTTTGTA
27921833 GTAAGTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (15 bp):
TATGTTTTCTTTGTA
Found at i:27921841 original size:15 final size:15
Alignment explanation
Indices: 27921806--27921840 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
27921796 ATTCTTTTAT
*
27921806 GTTTTCTTTGTATAT
1 GTTTTCTTTGTATAA
27921821 GTTTTCTTTGTAGTAA
1 GTTTTCTTTGTA-TAA
27921837 GTTT
1 GTTT
27921841 CATTGTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.14, C:0.06, G:0.17, T:0.63
Consensus pattern (15 bp):
GTTTTCTTTGTATAA
Found at i:27922173 original size:49 final size:51
Alignment explanation
Indices: 27922007--27922183 Score: 191
Period size: 52 Copynumber: 3.5 Consensus size: 51
27921997 GGATACTCGT
* * ** *
27922007 TGGCCTGCACATAGTACCACCCTTGT-AGTTAAAGCTA-CATTCTTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGA-CCAAAACTATC-TTCTTCACAAAG
*
27922058 TGGCCTTCACATAGTACTACACTTGTGACCAAAACTATCTTTCTTCACAAAG
1 TGGCCTTCACATAGTACCACACTTGTGACCAAAACTATC-TTCTTCACAAAG
** * * *
27922110 TGGCCTTCTTATAGTACCATACTTGTGACC-AAGCTATC-TCTTCTCAAAG
1 TGGCCTTCACATAGTACCACACTTGTGACCAAAACTATCTTCTTCACAAAG
*
27922159 TGGCCTTCACATAGTACCACGCTTG
1 TGGCCTTCACATAGTACCACACTTG
27922184 AGTCACTAGT
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
49 31 0.29
51 36 0.34
52 40 0.37
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (51 bp):
TGGCCTTCACATAGTACCACACTTGTGACCAAAACTATCTTCTTCACAAAG
Found at i:27936702 original size:26 final size:26
Alignment explanation
Indices: 27936666--27936749 Score: 159
Period size: 26 Copynumber: 3.2 Consensus size: 26
27936656 CATGAAATTC
27936666 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
27936692 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
27936718 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
27936744 TTATCA
1 TTATCA
27936750 ATTTGTATCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:27937562 original size:23 final size:23
Alignment explanation
Indices: 27937516--27937581 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 23
27937506 TTCTAATACT
* *
27937516 ATATCATATATACATATGCATTTTTC
1 ATAT-ATATATATATATG--TTTTTA
27937542 ATATATATATATATATGTTTTTA
1 ATATATATATATATATGTTTTTA
27937565 ATAT-TATAT-TATCATGT
1 ATATATATATATAT-ATGT
27937582 ATATGTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 3 0.08
22 9 0.24
23 9 0.24
25 12 0.32
26 4 0.11
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.52
Consensus pattern (23 bp):
ATATATATATATATATGTTTTTA
Found at i:27937568 original size:21 final size:24
Alignment explanation
Indices: 27937516--27937573 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
27937506 TTCTAATACT
*
27937516 ATATCATATATACATATGCATTTTTC
1 ATAT-ATATATATATATG-ATTTTTC
*
27937542 ATATATATATATATATG-TTTTTA
1 ATATATATATATATATGATTTTTC
27937565 ATAT-TATAT
1 ATATATATAT
27937574 TATCATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 5 0.17
23 9 0.30
25 12 0.40
26 4 0.13
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (24 bp):
ATATATATATATATATGATTTTTC
Found at i:27937573 original size:28 final size:27
Alignment explanation
Indices: 27937542--27937598 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
27937532 TGCATTTTTC
27937542 ATATATAT-ATATATATGTTTTTAATATT
1 ATAT-TATCATATATATG-TTTTAATATT
*
27937570 ATATTATCATGTATATGTTTTAATATT
1 ATATTATCATATATATGTTTTAATATT
27937597 AT
1 AT
27937599 TAGCTATCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (27 bp):
ATATTATCATATATATGTTTTAATATT
Found at i:27937782 original size:21 final size:21
Alignment explanation
Indices: 27937740--27937782 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
27937730 AATATAAATA
* *
27937740 TATATATACATCATATAGGTT
1 TATATACACATCATACAGGTT
* *
27937761 TATATACATATCATACATGTT
1 TATATACACATCATACAGGTT
27937782 T
1 T
27937783 CATTATTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (21 bp):
TATATACACATCATACAGGTT
Found at i:27943600 original size:45 final size:45
Alignment explanation
Indices: 27943549--27943651 Score: 127
Period size: 46 Copynumber: 2.3 Consensus size: 45
27943539 GAGTCATGGT
* * *
27943549 CGGTAAGCTCTTTCGAGCTG-AATAGTAAGCTCTATTGAGCTGAAA
1 CGGTAAGCTCTTT-GAGCTGAAACAGTAAGCTCCAATGAGCTGAAA
**
27943594 CGGTAAGCTCCAATGAGCTGAAACAGTAAGCTCCAATGAGCTGAAA
1 CGGTAAGCT-CTTTGAGCTGAAACAGTAAGCTCCAATGAGCTGAAA
*
27943640 CGATAAGCTCTT
1 CGGTAAGCTCTT
27943652 AAGAGCTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
45 16 0.33
46 32 0.67
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.24
Consensus pattern (45 bp):
CGGTAAGCTCTTTGAGCTGAAACAGTAAGCTCCAATGAGCTGAAA
Found at i:27943603 original size:23 final size:23
Alignment explanation
Indices: 27943549--27943658 Score: 111
Period size: 23 Copynumber: 4.8 Consensus size: 23
27943539 GAGTCATGGT
*
27943549 CGGTAAGCTCT-TTCGAGCTGAATA
1 CGGTAAGCTCTAAT-GAGCTGAA-A
*
27943573 --GTAAGCTCTATTGAGCTGAAA
1 CGGTAAGCTCTAATGAGCTGAAA
*
27943594 CGGTAAGCTCCAATGAGCTGAAA
1 CGGTAAGCTCTAATGAGCTGAAA
* *
27943617 CAGTAAGCTCCAATGAGCTGAAA
1 CGGTAAGCTCTAATGAGCTGAAA
*
27943640 CGATAAGCTCTTAA-GAGCT
1 CGGTAAGCTC-TAATGAGCT
27943659 ATGGTGAGTT
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
21 1 0.01
22 17 0.22
23 56 0.74
24 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (23 bp):
CGGTAAGCTCTAATGAGCTGAAA
Found at i:27943625 original size:46 final size:45
Alignment explanation
Indices: 27943563--27943649 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 45
27943553 AAGCTCTTTC
* * * *
27943563 GAGCTGAATAGTAAGCTCTATTGAGCTGAAACGGTAAGCTCCAAT
1 GAGCTGAACAGTAAGCTCCAATGAGCTGAAACGATAAGCTCCAAT
27943608 GAGCTGAAACAGTAAGCTCCAATGAGCTGAAACGATAAGCTC
1 GAGCTG-AACAGTAAGCTCCAATGAGCTGAAACGATAAGCTC
27943650 TTAAGAGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 6 0.16
46 31 0.84
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.21
Consensus pattern (45 bp):
GAGCTGAACAGTAAGCTCCAATGAGCTGAAACGATAAGCTCCAAT
Found at i:27946689 original size:28 final size:27
Alignment explanation
Indices: 27946645--27946698 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
27946635 AACATTTGAC
*
27946645 AAGTTTAGGTACAAAATTAGATAAAAAA
1 AAGTTCAGGTACAAAATTAGA-AAAAAA
*
27946673 AAGTTCAGGTATC-AAATTGGAAAAAA
1 AAGTTCAGGTA-CAAAATTAGAAAAAA
27946699 TGTTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 17 0.74
29 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.24
Consensus pattern (27 bp):
AAGTTCAGGTACAAAATTAGAAAAAAA
Found at i:27946770 original size:60 final size:58
Alignment explanation
Indices: 27946666--27946779 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 58
27946656 CAAAATTAGA
* * ** *
27946666 TAAAAAAAAGTTCAGGTATCAAATTGGAAAAAATGTTAAATTTAAATACCAAATTGTG
1 TAAAAAAAAGTTCAGATATCAAATTGAAAAAAAAATCAAATTTAAATACCAAATTGTG
* *
27946724 TAAAAAAATAGTTTAGATATCAAATTAGAAAAAAAAATCAAATTTAAATATCAAAT
1 TAAAAAAA-AGTTCAGATATCAAATT-GAAAAAAAAATCAAATTTAAATACCAAAT
27946780 GTTATGTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
58 8 0.17
59 15 0.32
60 24 0.51
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (58 bp):
TAAAAAAAAGTTCAGATATCAAATTGAAAAAAAAATCAAATTTAAATACCAAATTGTG
Found at i:27947294 original size:19 final size:19
Alignment explanation
Indices: 27947253--27947323 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
27947243 TAATTCTTAA
*
27947253 AAAAATATATAAAAAATTAT
1 AAAAATATAT-AAAAATTTT
* *
27947273 AAAAATACATAAATATTTT
1 AAAAATATATAAAAATTTT
* * *
27947292 AAAAAAAGATAAAAAATTT
1 AAAAATATATAAAAATTTT
*
27947311 AAATATATATAAA
1 AAAAATATATAAA
27947324 TTACATTGTA
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
19 32 0.78
20 9 0.22
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (19 bp):
AAAAATATATAAAAATTTT
Found at i:27948355 original size:24 final size:24
Alignment explanation
Indices: 27948328--27948379 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
27948318 TTAGTAAGTC
*
27948328 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
27948352 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
27948376 AAAT
1 AAAT
27948380 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:27950324 original size:24 final size:24
Alignment explanation
Indices: 27950297--27950348 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
27950287 TTAGTAAGTC
*
27950297 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
27950321 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
27950345 AAAT
1 AAAT
27950349 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:27954382 original size:25 final size:27
Alignment explanation
Indices: 27954345--27954397 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
27954335 TCAAACATGC
27954345 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
27954371 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
27954397 A
1 A
27954398 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:27955915 original size:26 final size:26
Alignment explanation
Indices: 27955884--27955991 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
27955874 TGAAATGCCC
*
27955884 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
27955910 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
27955936 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
27955962 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
27955988 ATCA
1 ATCA
27955992 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:27957417 original size:100 final size:100
Alignment explanation
Indices: 27957283--27957481 Score: 371
Period size: 100 Copynumber: 2.0 Consensus size: 100
27957273 CTTTTGCAGT
* *
27957283 GAGTAATCAGTACGAACTGGTATGAAATGGGCAGATTTTGTTAACCTATCCATCACTACCCACAC
1 GAGTAATCAGTACGAACTGGTATGAAATGAGCAGATTTTGTTAACCTATCCACCACTACCCACAC
27957348 AGAATCTTTCTTGGTGGGTGTCAAAGGTAGCCCAG
66 AGAATCTTTCTTGGTGGGTGTCAAAGGTAGCCCAG
*
27957383 GAGTAATCAGTACGAATTGGTATGAAATGAGCAGATTTTGTTAACCTATCCACCACTACCCACAC
1 GAGTAATCAGTACGAACTGGTATGAAATGAGCAGATTTTGTTAACCTATCCACCACTACCCACAC
27957448 AGAATCTTTCTTGGTGGGTGTCAAAGGTAGCCCA
66 AGAATCTTTCTTGGTGGGTGTCAAAGGTAGCCCA
27957482 CTCACAAAGT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (100 bp):
GAGTAATCAGTACGAACTGGTATGAAATGAGCAGATTTTGTTAACCTATCCACCACTACCCACAC
AGAATCTTTCTTGGTGGGTGTCAAAGGTAGCCCAG
Found at i:27962080 original size:25 final size:27
Alignment explanation
Indices: 27962043--27962095 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
27962033 TCAAACATGC
27962043 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
27962069 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
27962095 A
1 A
27962096 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:27963612 original size:26 final size:26
Alignment explanation
Indices: 27963582--27963637 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
27963572 TGAAATGCCC
27963582 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
27963608 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
27963634 ATCA
1 ATCA
27963638 ATTTTTACCA
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:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:27964556 original size:2 final size:2
Alignment explanation
Indices: 27964549--27964579 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27964539 TTTGTACCTT
27964549 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
27964580 AAGATGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27968085 original size:16 final size:15
Alignment explanation
Indices: 27968051--27968086 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
27968041 ATTTTTTTTT
27968051 AAAAAGTCGATTTCC
1 AAAAAGTCGATTTCC
27968066 AAAAAGTCGATTTCC
1 AAAAAGTCGATTTCC
27968081 AAAAAG
1 AAAAAG
27968087 GTTTTGACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (15 bp):
AAAAAGTCGATTTCC
Found at i:27970669 original size:36 final size:36
Alignment explanation
Indices: 27970621--27970693 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 36
27970611 AACTTTTGTC
**
27970621 TAAATTCTAATTTAGCCCCTAAATGGAGACTAACTT
1 TAAATTCTAATTTAGCCCCTAAACCGAGACTAACTT
27970657 TAAATT-TCAATTTAGCCCCTAAACCGAGACTAACTT
1 TAAATTCT-AATTTAGCCCCTAAACCGAGACTAACTT
27970693 T
1 T
27970694 TATTCTTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.33
Consensus pattern (36 bp):
TAAATTCTAATTTAGCCCCTAAACCGAGACTAACTT
Found at i:27971156 original size:20 final size:22
Alignment explanation
Indices: 27971118--27971157 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
27971108 TTTCGTTTGC
27971118 TTTGTTTCTCTTATTCATTTCT
1 TTTGTTTCTCTTATTCATTTCT
27971140 TTTGTTTC-CTT-TTCATTT
1 TTTGTTTCTCTTATTCATTT
27971158 ATTATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTGTTTCTCTTATTCATTTCT
Found at i:27971334 original size:14 final size:15
Alignment explanation
Indices: 27971310--27971355 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
27971300 ATAAATATCT
27971310 TATAATATAATTATAA
1 TATAAT-TAATTATAA
27971326 TA-AATTAATT-TAA
1 TATAATTAATTATAA
*
27971339 TATAATTTATTACTAA
1 TATAATTAATTA-TAA
27971355 T
1 T
27971356 TCGTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.19
14 12 0.46
15 3 0.12
16 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATTAATTATAA
Found at i:27976791 original size:26 final size:26
Alignment explanation
Indices: 27976755--27976864 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
27976745 CATGAAATTC
27976755 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
27976781 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
27976807 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
27976833 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
27976859 TTATCA
1 TTATCA
27976865 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:27980543 original size:27 final size:22
Alignment explanation
Indices: 27980506--27980564 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
27980496 TCCCCTGTTC
* *
27980506 TTCTCTGTTTCGTTTGC-TTTGT
1 TTCTCTTTTTCATTT-CTTTTGT
27980528 TTCTCTTTTTCATTTCTTTTGT
1 TTCTCTTTTTCATTTCTTTTGT
27980550 TTCTCTTTTTCATTT
1 TTCTCTTTTTCATTT
27980565 ATTATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.03, C:0.19, G:0.08, T:0.69
Consensus pattern (22 bp):
TTCTCTTTTTCATTTCTTTTGT
Found at i:27980741 original size:14 final size:15
Alignment explanation
Indices: 27980717--27980762 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
27980707 ATAAATATCT
27980717 TATAATATAATTATAA
1 TATAAT-TAATTATAA
27980733 TA-AATTAATT-TAA
1 TATAATTAATTATAA
*
27980746 TATAATTTATTACTAA
1 TATAATTAATTA-TAA
27980762 T
1 T
27980763 TCGTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.19
14 12 0.46
15 3 0.12
16 6 0.23
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATTAATTATAA
Found at i:27982511 original size:179 final size:179
Alignment explanation
Indices: 27982204--27982548 Score: 595
Period size: 179 Copynumber: 1.9 Consensus size: 179
27982194 AATAACCATT
* * *
27982204 TAGGTCGTCAAGTATTTTTTTAATATAAAACTCAATAGCGATTGGATTTTTACAATTTAGTCTCT
1 TAGGTCATCAAGTATTTTTCTAATATAAAACTCAATAGCAATTGGATTTTTACAATTTAGTCTCT
27982269 GAACTTTAATTAATAAATTTTTCGATTAAATTTCTGAACCAATCTTTAATATATTTTCATACTAA
66 GAACTTTAATTAATAAATTTTTCGATTAAATTTCTGAACCAATCTTTAATATATTTTCATACTAA
27982334 CTCCATAAAACCTCTTATTATAATCTCACGGACTTGATTAATTGCCAAC
131 CTCCATAAAACCTCTTATTATAATCTCACGGACTTGATTAATTGCCAAC
* *
27982383 TAGGTCATCAAGTA-TTTTCTAATATGAAACTCAATAGCAATTGGATTTTTATAATTTAGTCTCT
1 TAGGTCATCAAGTATTTTTCTAATATAAAACTCAATAGCAATTGGATTTTTACAATTTAGTCTCT
* *
27982447 GAACTTTAATTAACT-ATTTTTCTCGGTTAAATTTCTGAACCAATCTTTAATATATTTTCATACT
66 GAACTTTAATTAA-TAAATTTT-TCGATTAAATTTCTGAACCAATCTTTAATATATTTTCATACT
27982511 AACTCCATAAAACCTCTTATTATAATCTCACGGACTTG
129 AACTCCATAAAACCTCTTATTATAATCTCACGGACTTG
27982549 GTTTATAGAA
Statistics
Matches: 157, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
178 64 0.41
179 93 0.59
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (179 bp):
TAGGTCATCAAGTATTTTTCTAATATAAAACTCAATAGCAATTGGATTTTTACAATTTAGTCTCT
GAACTTTAATTAATAAATTTTTCGATTAAATTTCTGAACCAATCTTTAATATATTTTCATACTAA
CTCCATAAAACCTCTTATTATAATCTCACGGACTTGATTAATTGCCAAC
Found at i:27994645 original size:27 final size:26
Alignment explanation
Indices: 27994595--27994656 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
27994585 AGTGAAAAAT
27994595 AAATTAAAATTATAAAAATATTTAAA
1 AAATTAAAATTATAAAAATATTTAAA
*
27994621 AAATTCAAAATTATAAAAA-AGTTTATA
1 AAATT-AAAATTATAAAAATA-TTTAAA
*
27994648 AAACTAAAA
1 AAATTAAAA
27994657 AAATAAGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.31
27 22 0.69
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (26 bp):
AAATTAAAATTATAAAAATATTTAAA
Found at i:27997011 original size:12 final size:13
Alignment explanation
Indices: 27996994--27997030 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
27996984 GAACCGGACA
27996994 CGAACCGAA-CTC
1 CGAACCGAAGCTC
27997006 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
27997018 CGAACCGTAGCTC
1 CGAACCGAAGCTC
27997031 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:27997882 original size:21 final size:21
Alignment explanation
Indices: 27997853--27997892 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27997843 TTGCAACAAA
* *
27997853 CAGCTAAAATAACCCAATATT
1 CAGCAAAAAGAACCCAATATT
27997874 CAGCAAAAAGAACCCAATA
1 CAGCAAAAAGAACCCAATA
27997893 AATTTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.25, G:0.07, T:0.15
Consensus pattern (21 bp):
CAGCAAAAAGAACCCAATATT
Found at i:28001650 original size:69 final size:68
Alignment explanation
Indices: 28001560--28001688 Score: 163
Period size: 69 Copynumber: 1.9 Consensus size: 68
28001550 AGGTTTTATC
* * * *
28001560 GTTGTAATTGAGGTGCATAAATGTTGTTAATTG-TGATGT-TAAAGTGCTGCAAATTGAAGTATT
1 GTTGTAATTGAAGTGCATAAATGTTGTAAATTGAAG-TGTCT-AAGTACTGCAAATTGAAGTATT
28001623 AAAGT
64 AAAGT
**
28001628 GTTGTAAATTGAAGTGTTTAAATGTTGTAAATTGAAGTGTCTAAGTACTGCAAATTGAAGT
1 GTTGT-AATTGAAGTGCATAAATGTTGTAAATTGAAGTGTCTAAGTACTGCAAATTGAAGT
28001689 GTTTAGTTGC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
68 5 0.10
69 45 0.87
70 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (68 bp):
GTTGTAATTGAAGTGCATAAATGTTGTAAATTGAAGTGTCTAAGTACTGCAAATTGAAGTATTAA
AGT
Found at i:28001689 original size:23 final size:22
Alignment explanation
Indices: 28001596--28001708 Score: 93
Period size: 23 Copynumber: 4.9 Consensus size: 22
28001586 TTAATTGTGA
28001596 TGTTAAAGTGCTGCAAATTGAAG
1 TGTT-AAGTGCTGCAAATTGAAG
* * *
28001619 TATTAAAGTGTTGTAAATTGAAG
1 TGTT-AAGTGCTGCAAATTGAAG
* * *
28001642 TGTTTAAATGTTGTAAATTGAAG
1 TG-TTAAGTGCTGCAAATTGAAG
*
28001665 TGTCTAAGTACTGCAAATTGAAG
1 TGT-TAAGTGCTGCAAATTGAAG
*
28001688 TGTTTAGTTGCTAG-AAATTGA
1 TGTTAAG-TGCT-GCAAATTGA
28001709 GATATTTTGT
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
22 4 0.05
23 68 0.91
24 3 0.04
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (22 bp):
TGTTAAGTGCTGCAAATTGAAG
Found at i:28005041 original size:15 final size:16
Alignment explanation
Indices: 28005007--28005043 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
28004997 ATATACTAGA
*
28005007 ATAACAGATTATTCAG
1 ATAACAGATTAGTCAG
28005023 -TAACAGATT-GTCAG
1 ATAACAGATTAGTCAG
28005037 ATAACAG
1 ATAACAG
28005044 TTTCAATGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (16 bp):
ATAACAGATTAGTCAG
Found at i:28006424 original size:27 final size:28
Alignment explanation
Indices: 28006369--28006427 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
28006359 ATAACATTTG
*
28006369 AAAAGTTTAGGTACCAAATTAGATAAAA
1 AAAAGTTTAGGTACCAAATTAGAGAAAA
* * *
28006397 AAAAGTTTATGTATCAAATTAGGGAAAA
1 AAAAGTTTAGGTACCAAATTAGAGAAAA
28006425 AAA
1 AAA
28006428 TGTCAAGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.25
Consensus pattern (28 bp):
AAAAGTTTAGGTACCAAATTAGAGAAAA
Found at i:28006516 original size:28 final size:26
Alignment explanation
Indices: 28006476--28006530 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 26
28006466 AAAAAGTATC
*
28006476 AAGTTCAGGTACCAAATTAGGTAAAAAA
1 AAGTTCAGATACCAAATTA-G-AAAAAA
*
28006504 AAGTTTAGATACCAAATTAGAAAAAA
1 AAGTTCAGATACCAAATTAGAAAAAA
28006530 A
1 A
28006531 TGTCAAGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.28
27 1 0.04
28 17 0.68
ACGTcount: A:0.55, C:0.09, G:0.15, T:0.22
Consensus pattern (26 bp):
AAGTTCAGATACCAAATTAGAAAAAA
Found at i:28007868 original size:21 final size:22
Alignment explanation
Indices: 28007812--28007869 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
28007802 TGCCTTTTAC
**
28007812 ATTAAAATATTATTTTTTAATTT
1 ATTAAAATATTATTCATT-ATTT
** *
28007835 ATTAGTATTTTATTCATT-TTT
1 ATTAAAATATTATTCATTATTT
28007856 ATTAAAATATTATT
1 ATTAAAATATTATT
28007870 TTTATATTGA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
21 14 0.52
23 13 0.48
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTAAAATATTATTCATTATTT
Found at i:28008932 original size:43 final size:40
Alignment explanation
Indices: 28008849--28008936 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 40
28008839 AAAAAAAAGT
** *
28008849 TTAGGTATTAAATTAAAAAAAATCAAGTTCATGTATCAAA
1 TTAGGTATTAAATTAAAAAAAATCAAGTTCAAATACCAAA
* *
28008889 TTAGGTATTAAATTAAGAAAAAATGTTAAGTTTAAATACCAAA
1 TTAGGTATTAAATTAA-AAAAAA--TCAAGTTCAAATACCAAA
28008932 TTAGG
1 TTAGG
28008937 GGAAAAAAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
40 16 0.40
41 6 0.15
43 18 0.45
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (40 bp):
TTAGGTATTAAATTAAAAAAAATCAAGTTCAAATACCAAA
Found at i:28010825 original size:11 final size:11
Alignment explanation
Indices: 28010809--28010833 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28010799 TTATTTTGAA
28010809 TTTAATTTAAT
1 TTTAATTTAAT
28010820 TTTAATTTAAT
1 TTTAATTTAAT
28010831 TTT
1 TTT
28010834 TTATTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTAATTTAAT
Found at i:28010828 original size:16 final size:17
Alignment explanation
Indices: 28010801--28010832 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28010791 TGAGAGTATT
28010801 ATTTTGAATTTAATTTA
1 ATTTTGAATTTAATTTA
28010818 ATTTT-AATTTAATTT
1 ATTTTGAATTTAATTT
28010833 TTTATTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTTGAATTTAATTTA
Found at i:28012091 original size:24 final size:23
Alignment explanation
Indices: 28012034--28012093 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
28012024 TTTCATTTAC
28012034 TTATTGTT-TATTATTATTAGAT
1 TTATTGTTATATTATTATTAGAT
* * * *
28012056 TAAGTTGATATATTGTTATTATAT
1 TTA-TTGTTATATTATTATTAGAT
28012080 ATTATTGTTATATT
1 -TTATTGTTATATT
28012094 CCTATTTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 2 0.07
23 4 0.14
24 21 0.72
25 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (23 bp):
TTATTGTTATATTATTATTAGAT
Found at i:28012426 original size:3 final size:3
Alignment explanation
Indices: 28012413--28012524 Score: 113
Period size: 3 Copynumber: 37.7 Consensus size: 3
28012403 TGCTATTACC
* *
28012413 ATT ACT ATT ATT ATT ATT ATT ATT ACTT A-T ATT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
* * * * * *
28012458 ATC ATT ATG ATTT ATT ACT -TT ATT ATT ATC ATT ATT ACT ACT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28012503 A-T ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
28012525 ATTTTTACCC
Statistics
Matches: 90, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
2 5 0.06
3 80 0.89
4 5 0.06
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:28012507 original size:23 final size:23
Alignment explanation
Indices: 28012473--28012517 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28012463 TATGATTTAT
28012473 TACTTTATTATTATCATTATTAC
1 TACTTTATTATTATCATTATTAC
*
28012496 TACTATTA-TATTATTATTATTA
1 TACT-TTATTATTATCATTATTA
28012518 TTATTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (23 bp):
TACTTTATTATTATCATTATTAC
Found at i:28014809 original size:19 final size:19
Alignment explanation
Indices: 28014787--28014832 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
28014777 CTTCCTTTTT
*
28014787 TTTGCATT-CATTTCATGCA
1 TTTGCATTGCATTGCAT-CA
*
28014806 TTTGCATTGCATTGCATTA
1 TTTGCATTGCATTGCATCA
28014825 TTTGCATT
1 TTTGCATT
28014833 AGACTTTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (19 bp):
TTTGCATTGCATTGCATCA
Found at i:28017475 original size:3 final size:3
Alignment explanation
Indices: 28017469--28017508 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
28017459 CAAATCCTAA
28017469 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
28017509 TCATGGAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28019351 original size:66 final size:66
Alignment explanation
Indices: 28019231--28019362 Score: 210
Period size: 66 Copynumber: 2.0 Consensus size: 66
28019221 ATTCATATGT
* * * * *
28019231 CATTCATAACATATCTAATTAGGAGCATTTGATTCATTTCGATCATAGCCTCCTAATTATTTGAC
1 CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCAATCACAGCATCCTAATCATTTGAC
28019296 A
66 A
*
28019297 CATTCATAACACATCTAGTTAGGAGCATTTGATTCATTTCAATCACAGCATCCTAATCATTTGAC
1 CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCAATCACAGCATCCTAATCATTTGAC
28019362 A
66 A
28019363 TAAGCATAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (66 bp):
CATTCATAACACATCTAATTAGGAGCATTTGATTCATTTCAATCACAGCATCCTAATCATTTGAC
A
Found at i:28019603 original size:89 final size:88
Alignment explanation
Indices: 28019420--28019635 Score: 276
Period size: 89 Copynumber: 2.5 Consensus size: 88
28019410 CAGTGAATTC
* * *
28019420 ACAAGCCTTAACCCCCTAAGCAGTAGGGCAACAGGCTG-AATTGACAGATCTTAATCCTCTAAGC
1 ACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAATTGACAGATCTTAATCCCCTAAAC
* **
28019484 AGTAGGGAAACAGATCGAAGGTA
66 AGTAGGGAAACAGATCAAAGACA
* *
28019507 ACAAGCCTTGACCCCCTAAGCAGTAGGGTAACAGGCTGAAGATTTG-CAGATC-TCATCACCCTA
1 ACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAA-A-TTGACAGATCTTAATC-CCCTA
*
28019570 AACAGTAGGGAAACAGATCAAAGACG
63 AACAGTAGGGAAACAGATCAAAGACA
* * *
28019596 GCGAGCCTTAACCCCCTAAGCAGTAGAGTAACAGGCTGAA
1 ACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAA
28019636 TTACAAATCA
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
87 36 0.32
88 5 0.04
89 68 0.61
90 3 0.03
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (88 bp):
ACAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTGAAATTGACAGATCTTAATCCCCTAAAC
AGTAGGGAAACAGATCAAAGACA
Found at i:28019789 original size:45 final size:44
Alignment explanation
Indices: 28019690--28020209 Score: 232
Period size: 45 Copynumber: 11.5 Consensus size: 44
28019680 CCATAGCAGA
* * * * *
28019690 CTCCTTGAAGTTTCAGTGGAGTAGATTGAAAT-CACAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACT-AAATACACAAATCTTAT
*
28019734 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATATAGCAAATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACA-CAAATCTTAT
* * * * * *
28019779 TTCCTTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATCATAGATCTCAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACT-AA---ATACA-CA-A-ATCTTAT
* * * * *
28019830 CTCTCTGAAGTTGCAGTAGAGAAGA-T-CA-ACACAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACACAAATCTTAT
* * *
28019871 CTCCCTGAAGTTACAGTGGAGCAGACTAAAGATAGCAAATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACA-CAAATCTTAT
* * * * * *
28019916 TTCCCTGAAGTTGCAGTGGAACAAATTGAAGCTATAAACCATAGATCTCAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACT-AA---ATACA-CA-A-ATCTTAT
* * * * * *
28019967 CTCTCTGAAGATGTAGTAGAGCAGA-T-CA-ACACAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACACAAATCTTAT
* * * * * * *
28020008 CTCTCTAAAGTTGCAGTGGAGTAGACTAAAGAAAGAAAATTTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACA-CAAATCTTAT
* * * * * *
28020053 TTCACTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACT-AA---AT--A-CACAAATCTTAT
* * * * *
28020104 CTCTCTGAAGATGCAGTAGAGCAGA-T-CA-ACACAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACACAAATCTTAT
* * * *
28020145 CTCCCTGAAGTTGTAGTGGAGCAGACTAAAGAAAACAAGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGACTAAA-TACACAAATCTTAT
* *
28020190 TTCCCTGAAGTCGCAGTGGA
1 CTCCCTGAAGTTGCAGTGGA
28020210 ACATATTGAA
Statistics
Matches: 353, Mismatches: 90, Indels: 65
0.69 0.18 0.13
Matches are distributed among these distances:
41 81 0.23
42 6 0.02
43 11 0.03
44 32 0.09
45 123 0.35
46 6 0.02
49 12 0.03
50 5 0.01
51 76 0.22
52 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (44 bp):
CTCCCTGAAGTTGCAGTGGAGCAGACTAAATACACAAATCTTAT
Found at i:28019917 original size:137 final size:137
Alignment explanation
Indices: 28019722--28020270 Score: 846
Period size: 137 Copynumber: 4.0 Consensus size: 137
28019712 AGATTGAAAT
* * *
28019722 CACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATATAGCAAATCTTATTTCCTTGA
1 CACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCAAATCTTATTTCCCTGA
* * * *
28019787 AGTTGCAGTGGAACAGATTGAAGCTATAAATCATAGATCTCATCTCTCTGAAGTTGCAGTAGAGA
66 AGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGATGCAGTAGAGC
28019852 AGATCAA
131 AGATCAA
* *
28019859 CACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAAGATAGCAAATCTTATTTCCCTGA
1 CACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCAAATCTTATTTCCCTGA
* * *
28019924 AGTTGCAGTGGAACAAATTGAAGCTATAAACCATAGATCTCATCTCTCTGAAGATGTAGTAGAGC
66 AGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGATGCAGTAGAGC
28019989 AGATCAA
131 AGATCAA
* * * * * *
28019996 CACAAGTCTTATCTCTCTAAAGTTGCAGTGGAGTAGACTAAAGAAAGAAAATTTTATTTCACTGA
1 CACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCAAATCTTATTTCCCTGA
28020061 AGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGATGCAGTAGAGC
66 AGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGATGCAGTAGAGC
28020126 AGATCAA
131 AGATCAA
* * *
28020133 CACAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGAAAACAAGTCTTATTTCCCTGA
1 CACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCAAATCTTATTTCCCTGA
* * ** * *
28020198 AGTCGCAGTGGAACATATTGAAGCTATAAATAAACAGATCTTATCTCTCTGAAGTTGCAGTAGAG
66 AGTTGCAGTGGAACAGATTGAAGCTATAAA-CCACAGATCTCATCTCTCTGAAGATGCAGTAGAG
28020263 CAGATCAA
130 CAGATCAA
28020271 AATAAACTTT
Statistics
Matches: 377, Mismatches: 34, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
137 339 0.90
138 38 0.10
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (137 bp):
CACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAGCAAATCTTATTTCCCTGA
AGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGATGCAGTAGAGC
AGATCAA
Found at i:28021873 original size:3 final size:3
Alignment explanation
Indices: 28021860--28021962 Score: 95
Period size: 3 Copynumber: 34.7 Consensus size: 3
28021850 TGCTATTACC
* * *
28021860 ATT ACT ATT ATT ATT ATT ATT ACTT A-T ATT ATT ATC ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
* * * * *
28021905 ATT ATG ATTT ATT ACT -TT ATT ATT ATC ATT ATT ACT ACT ATT A-T
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28021949 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
28021963 ATTTTTACCC
Statistics
Matches: 81, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
2 5 0.06
3 71 0.88
4 5 0.06
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:28021951 original size:23 final size:23
Alignment explanation
Indices: 28021917--28021961 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
28021907 TATGATTTAT
28021917 TACTTTATTATTATCATTATTAC
1 TACTTTATTATTATCATTATTAC
*
28021940 TACTATTA-TATTATTATTATTA
1 TACT-TTATTATTATCATTATTA
28021962 TATTTTTACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (23 bp):
TACTTTATTATTATCATTATTAC
Found at i:28031159 original size:125 final size:125
Alignment explanation
Indices: 28030946--28031196 Score: 475
Period size: 125 Copynumber: 2.0 Consensus size: 125
28030936 TGATTTCATG
* *
28030946 ACTGGTGGAGGTGGGAGCCTTAATCGGCTAGTGATGTTCCAGCATGATGTTGAGTTTGGGGGTTG
1 ACTGGTGGAGGTGGGAGCCTCAATCGGCTAGTGATATTCCAGCATGATGTTGAGTTTGGGGGTTG
*
28031011 TAATACCATGGGAGTATTGATAAAATTGTTGATATGATTTGTACTGATAGGGATTTTGCT
66 TAATACCATGGGAGTATTGATAAAATTATTGATATGATTTGTACTGATAGGGATTTTGCT
28031071 ACTGGTGGAGGTGGGAGCCTCAATCGGCTAGTGATATTCCAGCATGATGTTGAGTTTGGGGGTTG
1 ACTGGTGGAGGTGGGAGCCTCAATCGGCTAGTGATATTCCAGCATGATGTTGAGTTTGGGGGTTG
28031136 TAATACCATGGGAGTATTGATAAAATTATTGATATGATTTGTACTGATAGGGATTTTGCT
66 TAATACCATGGGAGTATTGATAAAATTATTGATATGATTTGTACTGATAGGGATTTTGCT
28031196 A
1 A
28031197 GTTTTAAGGT
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 123 1.00
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.35
Consensus pattern (125 bp):
ACTGGTGGAGGTGGGAGCCTCAATCGGCTAGTGATATTCCAGCATGATGTTGAGTTTGGGGGTTG
TAATACCATGGGAGTATTGATAAAATTATTGATATGATTTGTACTGATAGGGATTTTGCT
Found at i:28036411 original size:24 final size:25
Alignment explanation
Indices: 28036352--28036416 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
28036342 TATATAATAT
*
28036352 AATAATATATAATAACA-TGATGTAA
1 AATAATATATAATAA-ATTGATGAAA
28036377 AATAATA-ATAATAAATTG-TGAAA
1 AATAATATATAATAAATTGATGAAA
*
28036400 AATAAGATATAATAAAT
1 AATAATATATAATAAAT
28036417 AATAATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 11 0.31
24 18 0.50
25 7 0.19
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (25 bp):
AATAATATATAATAAATTGATGAAA
Found at i:28036497 original size:15 final size:16
Alignment explanation
Indices: 28036468--28036507 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
28036458 AAAGTAAGGT
28036468 AAAAAATATCAATATAA
1 AAAAAATAT-AATATAA
*
28036485 AAAAAATAT-ATATAC
1 AAAAAATATAATATAA
28036500 AAAAAATA
1 AAAAAATA
28036508 AACATAGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.59
17 9 0.41
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAAATATAATATAA
Found at i:28038895 original size:205 final size:206
Alignment explanation
Indices: 28038449--28039650 Score: 1535
Period size: 205 Copynumber: 5.8 Consensus size: 206
28038439 CTACTTCTTT
* * * *
28038449 GATTTGTTCTCTGACAATACAGAGATGACAAATCGTCTTAGATTTGCTTCATCATAAGTACGTGA
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* *
28038514 AAGCCAAATCAGCTATGTCTTTGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
* * * *
28038579 CTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGA
131 CTTGCTTCAGTCTAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCTCTCCATCGAAGTGGAGA
* *
28038644 TGCCAGATTTT
196 TGCCAGACTTC
* * *
28038655 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGTTTCAAT-GTAAGCACGTG
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTC-ATCGTAAGCACGTG
* * * * *
28038719 AAAGCCAAATCAGCTATGTCTTCGATTTGCTCATTGTAAGCGCAAGGATGCCATACCATCTTGGA
65 AAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGA
* * * ** * **
28038784 TC-TACTTCAGTATAAACATCCGAAGGTTGGATCTGCTATGTGTCTGCCCTCTGTCGAAGTGGAG
130 TCTTGCTTCAGTCTAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCTCTCCATCGAAGTGGAG
28038848 ATGCCAGACTTC
195 ATGCCAGACTTC
* * *
28038860 -AGTTTGTTCTCTGATAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTG
1 GA-TTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTG
* * *
28038924 AAAACCAAATCAGCTATGTCTTCGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGT
65 AAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGA
* * * * *
28038989 TCTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTACTATGTATCTGCTCTCCATTGAAGTGGAG
130 TCTTGCTTCAGTCTAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCTCTCCATCGAAGTGGAG
* *
28039054 ATGCCAGATTTT
195 ATGCCAGACTTC
* * * *
28039066 AATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAACGTAAACACGTGA
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* * * *
28039131 AAGCCAAATCAGCTATGTCTTCTATTTGTTCCTTGTAAACACAAGGATACCAAACCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
* * * * * *
28039196 C-CGCTTCAG-CATAAACATCCGAAGG-CGAGATCTGCTATATGTCTGTTCTCTATCAAAGTGGA
131 CTTGCTTCAGTC-TAAACATCTGAAGGTC-AGATCTGCTATGTGTCTGCTCTCCATCGAAGTGGA
28039258 GATGCCAGACTTC
194 GATGCCAGACTTC
* * *
28039271 GATTTGTTCTCTAACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGG
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* * * ** * * **
28039336 AAGCCAAATCAGCTATATCTTCGATCTGCTCCCCGCTGAA-TACAGAGAGATAAGATC-TGTCAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTG-T-AAGCACA-AG-GAT--G-CCAAATCAT
* * *
28039399 CTAGGATC-TGCTTCAG-CGTAAACATCTGAAGGTGAGATCTGCTATGTGTCTGC-CTTCCATCA
124 CTTGGATCTTGCTTCAGTC-TAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCTC-TCCATCG
*
28039461 AAGTGGAAATGCCAGACTTC
187 AAGTGGAGATGCCAGACTTC
28039481 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
1 GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* *
28039546 AAGCCAAATCAGCTATGTCTTTGATTTGTTCCTTGTAAGCCCAAGGATGCCAAATCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
* *
28039611 CTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATG
131 CTTGCTTCAGTCTAAACATCTGAAGGTCAGATCTGCTATG
28039651 CTGCGGCCTA
Statistics
Matches: 855, Mismatches: 121, Indels: 40
0.84 0.12 0.04
Matches are distributed among these distances:
204 6 0.01
205 334 0.39
206 328 0.38
207 11 0.01
208 7 0.01
209 4 0.00
210 164 0.19
211 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (206 bp):
GATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
CTTGCTTCAGTCTAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCTCTCCATCGAAGTGGAGA
TGCCAGACTTC
Found at i:28039213 original size:411 final size:411
Alignment explanation
Indices: 28038449--28039620 Score: 1651
Period size: 411 Copynumber: 2.8 Consensus size: 411
28038439 CTACTTCTTT
* * *
28038449 GATTTGTTCTCTGACAATACAGAGATGACAAATCGTCTTAGATTTGCTTCATCATAAGTACGTGA
1 GATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
*
28038514 AAGCCAAATCAGCTATGTCTTTGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
66 AAGCCAAATCAGCTATGTCTTCGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
28038579 CTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGA
131 CTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGA
* * *
28038644 TGCCAGATTTTGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGTTTCAATG
196 TGCCAGATTTTGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAACG
* * * * *
28038709 TAAGCACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCATTGTAAGCGCAAGGATGCCATA
261 TAAGCACGTGAAAGCCAAATCAGCTATGTCTTCTATTTGTTCCTTGTAAGCACAAGGATGCCAAA
* * * * *
28038774 CCATCTTGGATCTACTTCAGTATAAACATCCGAAGGTTG-GATCTGCTATGTGTCTGCCCTCTGT
326 CCATCTTGGATCTGCTTCAGCATAAACATCCGAAGG-CGAGATCTGCTATATGTCTGCCCTCTAT
*
28038838 CGAAGTGGAGATGCCAGACTTC
390 CAAAGTGGAGATGCCAGACTTC
* *
28038860 -AGTTTGTTCTCTGATAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCACGTG
1 GA-TTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTG
* *
28038924 AAAACCAAATCAGCTATGTCTTCGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGT
65 AAAGCCAAATCAGCTATGTCTTCGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGA
*
28038989 TCTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTACTATGTATCTGCTCTCCATTGAAGTGGAG
130 TCTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAG
*
28039054 ATGCCAGATTTTAATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAAC
195 ATGCCAGATTTTGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAAC
* * *
28039119 GTAAACACGTGAAAGCCAAATCAGCTATGTCTTCTATTTGTTCCTTGTAAACACAAGGATACCAA
260 GTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCTATTTGTTCCTTGTAAGCACAAGGATGCCAA
* **
28039184 ACCATCTTGGATCCGCTTCAGCATAAACATCCGAAGGCGAGATCTGCTATATGTCTGTTCTCTAT
325 ACCATCTTGGATCTGCTTCAGCATAAACATCCGAAGGCGAGATCTGCTATATGTCTGCCCTCTAT
28039249 CAAAGTGGAGATGCCAGACTTC
390 CAAAGTGGAGATGCCAGACTTC
* * * *
28039271 GATTTGTTCTCTAACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACACGTGG
1 GATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
* * ** * * **
28039336 AAGCCAAATCAGCTATATCTTCGA-TCTGCTCCCCGCTGAA-TACAGAGAGATAAGATC-TGTCA
66 AAGCCAAATCAGCTATGTCTTCGACT-TGTTCCTTG-T-AAGCACA-AG-GAT--G-CCAAATCA
* * * * * *
28039398 TCTAGGATC-TGCTTCAG-CGTAAACATCTGAAGGTGAGATCTGCTATGTGTCTGC-CTTCCATC
123 TCTTGGATCTTGCTTCAGTC-TAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTC-TCCATT
* * * *
28039460 AAAGTGGAAATGCCAGACTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATT
186 GAAGTGGAGATGCCAGATTTTGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATT
* * *
28039525 TGCTTCATCGTAAGCACGTGAAAGCCAAATCAGCTATGTCTT-TGATTTGTTCCTTGTAAGCCCA
251 TGTTTCAACGTAAGCACGTGAAAGCCAAATCAGCTATGTCTTCT-ATTTGTTCCTTGTAAGCACA
*
28039589 AGGATGCCAAATCATCTTGGATCTTGCTTCAG
315 AGGATGCCAAACCATCTTGGATC-TGCTTCAG
28039621 TCTAATCGTC
Statistics
Matches: 680, Mismatches: 66, Indels: 25
0.88 0.09 0.03
Matches are distributed among these distances:
410 3 0.00
411 462 0.68
412 5 0.01
413 4 0.01
414 6 0.01
415 181 0.27
416 18 0.03
417 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (411 bp):
GATTTGTTCTCTGACAATACAGAGATGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGA
AAGCCAAATCAGCTATGTCTTCGACTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGAT
CTTGCTTCAGTCTAATCGTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGA
TGCCAGATTTTGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAACG
TAAGCACGTGAAAGCCAAATCAGCTATGTCTTCTATTTGTTCCTTGTAAGCACAAGGATGCCAAA
CCATCTTGGATCTGCTTCAGCATAAACATCCGAAGGCGAGATCTGCTATATGTCTGCCCTCTATC
AAAGTGGAGATGCCAGACTTC
Found at i:28043033 original size:28 final size:28
Alignment explanation
Indices: 28042993--28043048 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
28042983 TTGTCTGAGT
28042993 CAACTTCAATTCCTTTTTCACTTACTAC
1 CAACTTCAATTCCTTTTTCACTTACTAC
*
28043021 CAACTTCAATTCCTTTTTCGCTTACTAC
1 CAACTTCAATTCCTTTTTCACTTACTAC
28043049 GAAGCCTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.32, G:0.02, T:0.43
Consensus pattern (28 bp):
CAACTTCAATTCCTTTTTCACTTACTAC
Found at i:28047716 original size:15 final size:15
Alignment explanation
Indices: 28047674--28047716 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
28047664 GTAACTTTGA
*
28047674 ATGCAAATG-ATGTG
1 ATGCAAATGCATGAG
28047688 ATG-AAATGCTATGAG
1 ATGCAAATGC-ATGAG
28047703 ATGCAAATGCATGA
1 ATGCAAATGCATGA
28047717 ACGCAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.20
14 3 0.12
15 11 0.44
16 6 0.24
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:28048371 original size:13 final size:13
Alignment explanation
Indices: 28048339--28048363 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28048329 GATACTTGTG
28048339 CCCTTTTGTAATA
1 CCCTTTTGTAATA
28048352 CCCTTTTGTAAT
1 CCCTTTTGTAAT
28048364 GCTCTTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.48
Consensus pattern (13 bp):
CCCTTTTGTAATA
Found at i:28051775 original size:19 final size:19
Alignment explanation
Indices: 28051747--28051785 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28051737 ATATACATAA
28051747 AAAATAAAAA-ATATAGAAT
1 AAAATAAAAATATATA-AAT
*
28051766 AAAATGAAAATATATAAAT
1 AAAATAAAAATATATAAAT
28051785 A
1 A
28051786 TTATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAATAAAAATATATAAAT
Found at i:28051887 original size:25 final size:25
Alignment explanation
Indices: 28051865--28051941 Score: 70
Period size: 28 Copynumber: 3.0 Consensus size: 25
28051855 ACGTAATATG
28051865 TAAAAACAATATAT-ATATAAATAAT
1 TAAAAA-AATATATAATATAAATAAT
*
28051890 TAAATAAATATATAATAT-AATAAT
1 TAAAAAAATATATAATATAAATAAT
*
28051914 ATATAATAAAATTATATAAAAT-AATAAT
1 -TA-AA-AAAA-TATATAATATAAATAAT
28051942 AATAAATTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 13 0.30
25 11 0.25
26 2 0.05
27 3 0.07
28 15 0.34
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (25 bp):
TAAAAAAATATATAATATAAATAAT
Found at i:28051889 original size:28 final size:26
Alignment explanation
Indices: 28051858--28051939 Score: 75
Period size: 25 Copynumber: 3.2 Consensus size: 26
28051848 ATAATGGACG
28051858 TAATATGTAAAAACAATATATATATAAA
1 TAATAT-TAAAAA-AATATATATATAAA
*
28051886 T-A-ATTAAATAAATATATA-ATATAA
1 TAATATTAAAAAAATATATATATA-AA
*
28051910 TAATATATAATAAAAT-TATATA-AAA
1 TAATAT-TAAAAAAATATATATATAAA
28051935 TAATA
1 TAATA
28051940 ATAATAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
23 3 0.07
24 11 0.24
25 13 0.28
26 9 0.20
27 9 0.20
28 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (26 bp):
TAATATTAAAAAAATATATATATAAA
Found at i:28051920 original size:31 final size:30
Alignment explanation
Indices: 28051872--28051992 Score: 84
Period size: 31 Copynumber: 3.8 Consensus size: 30
28051862 ATGTAAAAAC
* *
28051872 AATAT-ATATATAAATAATTAAATAAATATAT
1 AATATAATA-ATAAATAATAAAAT-AATATAA
* *
28051903 AATATAATAATATATAATAAAATTATATAA
1 AATATAATAATAAATAATAAAATAATATAA
**
28051933 AATAATAATAATAAATTGTGAAAAATAAGATATAA
1 AAT-ATAATAATAAATAAT--AAAAT-A-ATATAA
28051968 TAA-ATAATAATATATATAATAAAAT
1 -AATATAATAATA-A-ATAATAAAAT
28051993 GATCTTATAA
Statistics
Matches: 71, Mismatches: 10, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
30 8 0.11
31 29 0.41
32 3 0.04
33 5 0.07
34 14 0.20
35 7 0.10
36 5 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (30 bp):
AATATAATAATAAATAATAAAATAATATAA
Found at i:28051967 original size:24 final size:24
Alignment explanation
Indices: 28051876--28051990 Score: 95
Period size: 24 Copynumber: 5.0 Consensus size: 24
28051866 AAAAACAATA
28051876 TATATATAAATAAT-TA-AATAAAT
1 TATATA-AAATAATATATAATAAAT
*
28051899 ATATAATATAATAATATATAATAAAAT
1 -TAT-ATAAAATAATATATAAT-AAAT
28051926 TATATAAAATAATA-ATAATAAAT
1 TATATAAAATAATATATAATAAAT
* *
28051949 TGTGA-AAAATAAGATATAATAAA-
1 TAT-ATAAAATAATATATAATAAAT
28051972 TA-AT--AAT-ATATATAATAAA
1 TATATAAAATAATATATAATAAA
28051991 ATGATCTTAT
Statistics
Matches: 78, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
19 11 0.14
20 3 0.04
21 1 0.01
23 15 0.19
24 23 0.29
25 15 0.19
26 6 0.08
27 4 0.05
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.35
Consensus pattern (24 bp):
TATATAAAATAATATATAATAAAT
Found at i:28052043 original size:15 final size:15
Alignment explanation
Indices: 28052023--28052060 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
28052013 AAAAGTAAGG
28052023 TAAAAAATATCA-ATA
1 TAAAAAATAT-ATATA
28052038 TAAAAAATATATATA
1 TAAAAAATATATATA
28052053 TACAAAAA
1 TA-AAAAA
28052061 ATAAACATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 15 0.71
16 5 0.24
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAAATATATATA
Found at i:28053564 original size:12 final size:12
Alignment explanation
Indices: 28053547--28053574 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28053537 TGTTCTTTTT
28053547 CTTTTTCAATGA
1 CTTTTTCAATGA
28053559 CTTTTTCAATGA
1 CTTTTTCAATGA
28053571 CTTT
1 CTTT
28053575 CTTGATCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.07, T:0.54
Consensus pattern (12 bp):
CTTTTTCAATGA
Found at i:28054260 original size:11 final size:11
Alignment explanation
Indices: 28054244--28054293 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
28054234 CATACTCATA
28054244 TTTTTTTGAAT
1 TTTTTTTGAAT
* *
28054255 TTTTTTCGTAT
1 TTTTTTTGAAT
28054266 TTTTTTTGAAACTT
1 TTTTTTTG-AA--T
28054280 TTTTTTTGAAT
1 TTTTTTTGAAT
28054291 TTT
1 TTT
28054294 ACTTGAGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
11 20 0.62
12 1 0.03
13 2 0.06
14 9 0.28
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.72
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:28064809 original size:22 final size:20
Alignment explanation
Indices: 28064769--28064817 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
28064759 CAATTTAAAA
28064769 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
28064789 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
28064809 TGTAAAAAT
1 TATAAAAAT
28064818 AACTTTTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:28064930 original size:20 final size:20
Alignment explanation
Indices: 28064905--28064944 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28064895 AAATATTTTC
28064905 AGTAAATCATTTTTCAGAAA
1 AGTAAATCATTTTTCAGAAA
28064925 AGTAAATCATTTTTCAGAAA
1 AGTAAATCATTTTTCAGAAA
28064945 TCATTTTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
AGTAAATCATTTTTCAGAAA
Found at i:28073193 original size:20 final size:20
Alignment explanation
Indices: 28073160--28073198 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28073150 TGTATCGCCA
* *
28073160 ATTATATTTTTTATGATTAC
1 ATTATATATATTATGATTAC
*
28073180 ATTATATATATTATTATTA
1 ATTATATATATTATGATTA
28073199 TTAAATCATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
ATTATATATATTATGATTAC
Found at i:28077689 original size:128 final size:128
Alignment explanation
Indices: 28077518--28077817 Score: 388
Period size: 128 Copynumber: 2.3 Consensus size: 128
28077508 CATGAAAAAC
* * * * * * * * *
28077518 CGAAACCCAACACAGTAGGGCACGATTCCTCGAATTTCTAAACATTGAAC-TTGCCTTGTTTTAG
1 CGAAACCCAGCACGGTAGGGCACGATTCCTCAAATCTCCAAACATCGAACATTACCTTGTTGTAA
* *
28077582 AATTTAAAAAAAACACGAGTGAAGTTCTAAAGGAATATTTGATTATTTTGAACAAA-AGGACAAT
66 AATTT-AAAAAAACACGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACAGGA-AAT
*
28077646 CGAAACCCAGTACGGTAGGGCACGATTCCTCAAATCTCCAAACATCGAACATTACCTTGTTGTAA
1 CGAAACCCAGCACGGTAGGGCACGATTCCTCAAATCTCCAAACATCGAACATTACCTTGTTGTAA
* * *
28077711 AATTTAGAAAAACATGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACGGGAAAT
66 AATTTAAAAAAACACGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACAGGAAAT
* * * * *
28077774 AGAAACCCAGCACGATAGGGCACTATTCCCCTAATCTCCAAACA
1 CGAAACCCAGCACGGTAGGGCACGATTCCTCAAATCTCCAAACA
28077818 CCAAATATTG
Statistics
Matches: 149, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
128 130 0.87
129 19 0.13
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (128 bp):
CGAAACCCAGCACGGTAGGGCACGATTCCTCAAATCTCCAAACATCGAACATTACCTTGTTGTAA
AATTTAAAAAAACACGAGTGAAATTCTAAAGGAATATTCGATTATTTTGAACAAACAGGAAAT
Found at i:28082695 original size:26 final size:26
Alignment explanation
Indices: 28082659--28082712 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
28082649 ACAGTTTTCG
28082659 TAAAATCAACCTATTCCCATAATTCT
1 TAAAATCAACCTATTCCCATAATTCT
28082685 TAAAATCAACCTATTCCCATAATTCT
1 TAAAATCAACCTATTCCCATAATTCT
28082711 TA
1 TA
28082713 CAAAAAAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAAATCAACCTATTCCCATAATTCT
Found at i:28083148 original size:13 final size:15
Alignment explanation
Indices: 28083119--28083153 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
28083109 CGTAAGAACA
28083119 ATTTTCAAGCTATAT
1 ATTTTCAAGCTATAT
28083134 ATTTTC-AGCATATAT
1 ATTTTCAAGC-TATAT
28083149 ATTTT
1 ATTTT
28083154 TTTTGCTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (15 bp):
ATTTTCAAGCTATAT
Found at i:28086059 original size:19 final size:19
Alignment explanation
Indices: 28086035--28086072 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
28086025 AAAATTACGT
28086035 ATTTAAAATATAA-ATATAA
1 ATTTAAAA-ATAATATATAA
28086054 ATTTAAAAATAATATATAA
1 ATTTAAAAATAATATATAA
28086073 TAAATAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATTTAAAAATAATATATAA
Found at i:28086346 original size:20 final size:17
Alignment explanation
Indices: 28086301--28086337 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
28086291 TTTAGTTTAG
28086301 TGATAAAATTAATAGAA
1 TGATAAAATTAATAGAA
*
28086318 TGATAAAATTAATAGCA
1 TGATAAAATTAATAGAA
28086335 TGA
1 TGA
28086338 GTTTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.30
Consensus pattern (17 bp):
TGATAAAATTAATAGAA
Found at i:28091402 original size:23 final size:22
Alignment explanation
Indices: 28091376--28091429 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
28091366 TGTATACGCG
28091376 TACATAATAAAAATATATACTAA
1 TACATAATAAAAATA-ATACTAA
* *
28091399 TACATAATAATAATAATAGTAA
1 TACATAATAAAAATAATACTAA
28091421 TAC-TAATAA
1 TACATAATAA
28091430 TACTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 6 0.21
22 9 0.31
23 14 0.48
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATAAAAATAATACTAA
Found at i:28091410 original size:3 final size:3
Alignment explanation
Indices: 28091379--28091449 Score: 63
Period size: 3 Copynumber: 23.3 Consensus size: 3
28091369 ATACGCGTAC
* * * *
28091379 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA ATA GTA ATA CTA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
28091426 ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
28091450 CGAGGATATT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 2 0.04
3 45 0.85
4 6 0.11
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:28091933 original size:13 final size:12
Alignment explanation
Indices: 28091915--28091950 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
28091905 AGAAAAAAAA
28091915 GAAGAGAGAGAGG
1 GAAGAGAGA-AGG
28091928 GAAGAGAGAAGG
1 GAAGAGAGAAGG
28091940 G-AGAGAGAAGG
1 GAAGAGAGAAGG
28091951 AAGGGGGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.43
12 4 0.17
13 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:28092087 original size:10 final size:9
Alignment explanation
Indices: 28092061--28092086 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28092051 GTAAAAAATA
28092061 TTTTTTTTC
1 TTTTTTTTC
28092070 TTTTTTTTC
1 TTTTTTTTC
28092079 TTTTTTTT
1 TTTTTTTT
28092087 TTGCTTAATA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:28092431 original size:157 final size:156
Alignment explanation
Indices: 28092146--28092457 Score: 597
Period size: 157 Copynumber: 2.0 Consensus size: 156
28092136 TATGTAAAAA
28092146 TAAACTCAAAACAGTAAAGAAAAAAAAAGAAAGAGTCACCTCAGGTTTTAGATTTGATTCTCCGA
1 TAAACTCAAAACAGTAAAGAAAAAAAAAGAAAGAGTCACCTCAGGTTTTAGATTTGATTCTCCGA
28092211 TTTGGTGTTAGAGCCCCTGATTGTATATATATTTTCGAATGGTTCTTGTATTGAATCTGTTAATA
66 TTTGGTGTTAGAGCCCCTGATTGTATATATATTTTCGAATGGTTCTTGTATTGAATCTGTTAATA
28092276 TTGAAAGAAAATCTTTTGTTTTCATG
131 TTGAAAGAAAATCTTTTGTTTTCATG
*
28092302 TAAACTCAAAACAGTAAAGAAAAAAAAAAGAAAGAGTCACCTTAGGTTTTAGATTTGATTCTCCG
1 TAAACTCAAAACAGTAAAG-AAAAAAAAAGAAAGAGTCACCTCAGGTTTTAGATTTGATTCTCCG
*
28092367 ATTTGGTGTTAGAGCCCCTGATTGTATATATATTTTTGAATGGTTCTTGTATTGAATCTGTTAAT
65 ATTTGGTGTTAGAGCCCCTGATTGTATATATATTTTCGAATGGTTCTTGTATTGAATCTGTTAAT
28092432 ATTGAAAGAAAATCTTTTGTTTTCAT
130 ATTGAAAGAAAATCTTTTGTTTTCAT
28092458 AGCAAAAAAT
Statistics
Matches: 153, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
156 19 0.12
157 134 0.88
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (156 bp):
TAAACTCAAAACAGTAAAGAAAAAAAAAGAAAGAGTCACCTCAGGTTTTAGATTTGATTCTCCGA
TTTGGTGTTAGAGCCCCTGATTGTATATATATTTTCGAATGGTTCTTGTATTGAATCTGTTAATA
TTGAAAGAAAATCTTTTGTTTTCATG
Found at i:28092617 original size:8 final size:8
Alignment explanation
Indices: 28092604--28092628 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28092594 GGTGTTCGGC
28092604 GCAAGTGG
1 GCAAGTGG
28092612 GCAAGTGG
1 GCAAGTGG
28092620 GCAAGTGG
1 GCAAGTGG
28092628 G
1 G
28092629 GGGTAGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.52, T:0.12
Consensus pattern (8 bp):
GCAAGTGG
Found at i:28093139 original size:44 final size:44
Alignment explanation
Indices: 28093091--28093188 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
28093081 AACTTCAGAG
* *
28093091 AGATAAGATCATTTAT-TTTAATCCACTCCACTGTAATCTCAGGC
1 AGATAAGATCA-CTATCTTCAATCCACTCCACTGTAATCTCAGGC
* * * * *
28093135 AGATAGGATTACTATCTTCAATCTACTCCGCTGTAATCTCAGGG
1 AGATAAGATCACTATCTTCAATCCACTCCACTGTAATCTCAGGC
28093179 AGATAAGATC
1 AGATAAGATC
28093189 TGAAATTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
43 3 0.07
44 41 0.93
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (44 bp):
AGATAAGATCACTATCTTCAATCCACTCCACTGTAATCTCAGGC
Found at i:28093182 original size:88 final size:87
Alignment explanation
Indices: 28093067--28093375 Score: 259
Period size: 88 Copynumber: 3.4 Consensus size: 87
28093057 GTCTGCTGTG
* *
28093067 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTGTAATCTCA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCA
*
28093132 GGCAGATAGGATTACTATCTTCA
66 GG-AGATAGGATTACTAGCTTCA
* * * *** * *
28093155 ATCTACTCCGCTGTAA-TCTCAGGGAGATAAGATCTGAAATT-TTTCGGTCTGTTCCACTGTAAT
1 ATCTACTCCACTGTAACT-TCAGAGAGATAAGATC---ATTTATTTTAATCCGCTCCACTGTAAT
* *
28093218 CTCAGGGAGATAAGATCT-CTGGCTTCA
62 CTCA-GGAGATAGGAT-TACTAGCTTCA
*
28093245 ATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCAC
1 ATC-----T-A-CT-C-C-ACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCAC
28093310 TGTAA-CTTCAGAGAGATAGGATTACTAGCTTCA
56 TGTAATC-TCAG-GAGATAGGATTACTAGCTTCA
* *
28093343 ATCTACTCCGCTGTAATCTT-AGGGAGATAAGAT
1 ATCTACTCCACTGTAA-CTTCAGAGAGATAAGAT
28093376 TACTATGGCT
Statistics
Matches: 173, Mismatches: 26, Indels: 44
0.71 0.11 0.18
Matches are distributed among these distances:
87 1 0.01
88 47 0.27
89 4 0.02
90 39 0.23
91 8 0.05
92 1 0.01
93 1 0.01
95 1 0.01
96 1 0.01
97 7 0.04
98 40 0.23
99 1 0.01
100 21 0.12
101 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (87 bp):
ATCTACTCCACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGCTCCACTGTAATCTCA
GGAGATAGGATTACTAGCTTCA
Found at i:28093331 original size:188 final size:187
Alignment explanation
Indices: 28093034--28093423 Score: 563
Period size: 188 Copynumber: 2.1 Consensus size: 187
28093024 CTAACTGCTT
* *** *
28093034 AGGGAGATAAGATCTGTGGTTTTGTCTGCTGTGATCTACTCTACTGTAACTTCAGAGAGATAAGA
1 AGGGAGATAAGATCTCTGGTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGA
*
28093099 TCATTTATTTTAATCCACTCCACTGTAATCTCAGGCAGATAGGATTACTATCTTCAATCTACTCC
66 TCATTTATTTTAATCCACTCCACTGTAATCTCAGGCAGATAGGATTACTAGCTTCAATCTACTCC
** ** * *
28093164 GCTGTAATCTCAGGGAGATAAGATCTGA-AAT-TTTTCGGTCTGTTCCACTGTAATCTC
131 GCTGTAATCTCAGGGAGATAAGAT-T-ACAATGGCTTCAATCTGCTCCACTGTAACCTC
28093221 AGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAG
1 AGGGAGATAAGATCTCTGG-TTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAG
* *
28093286 ATCCTTTATTTTAATCCGCTCCACTGTAA-CTTCAGAG-AGATAGGATTACTAGCTTCAATCTAC
65 ATCATTTATTTTAATCCACTCCACTGTAATC-TCAG-GCAGATAGGATTACTAGCTTCAATCTAC
* *
28093349 TCCGCTGTAATCTTAGGGAGATAAGATTACTATGGCTTCAATCTGCTCCACTGTAACCTC
128 TCCGCTGTAATCTCAGGGAGATAAGATTACAATGGCTTCAATCTGCTCCACTGTAACCTC
28093409 AGGGAGATAAGATCT
1 AGGGAGATAAGATCT
28093424 GAAATTCTTC
Statistics
Matches: 182, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
186 1 0.01
187 22 0.12
188 158 0.87
189 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (187 bp):
AGGGAGATAAGATCTCTGGTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAAGA
TCATTTATTTTAATCCACTCCACTGTAATCTCAGGCAGATAGGATTACTAGCTTCAATCTACTCC
GCTGTAATCTCAGGGAGATAAGATTACAATGGCTTCAATCTGCTCCACTGTAACCTC
Found at i:28093357 original size:44 final size:45
Alignment explanation
Indices: 28093255--28093596 Score: 168
Period size: 44 Copynumber: 7.7 Consensus size: 45
28093245 ATCTGATGTG
* * * **** *
28093255 ATCTACTCTACTGTAACTTCAGAGAGATAAGA-TCCTTTATTTTA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATTACTAGGCTTCA
** * *
28093299 ATCCGCTCCACTGTAACTTCAGAGAGATAGGATTACTA-GCTTCA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATTACTAGGCTTCA
*
28093343 ATCTACTCCGCTGTAATCTT-AGGGAGATAAGATTACTATGGCTTCA
1 ATCTACTCCACTGTAA-CTTCAGGGAGATAAGATTACTA-GGCTTCA
* * * ** *
28093389 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCG
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGAT-T-ACTAGGCTTCA
* * * * * * * *
28093435 GTCTACTCCACTATAACCTCAGGGTGATAAGA--CCT--GATACG
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATTACTAGGCTTCA
*** * * **** *
28093476 ATCTACTCTGTTGTAACTTCAGAGAGATAAGA-TCCTTTATTTTA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATTACTAGGCTTCA
** *
28093520 ATCCGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTA-GCTTCA
1 ATCTACTCCACTGTAACT-TCAGGGAGATAAGATTACTAGGCTTCA
**
28093564 ATCTACTCCGTTGTAA-TCTCAGGGAGATAAGAT
1 ATCTACTCCACTGTAACT-TCAGGGAGATAAGAT
28093597 CTGAAATTCT
Statistics
Matches: 225, Mismatches: 60, Indels: 26
0.72 0.19 0.08
Matches are distributed among these distances:
41 27 0.12
42 3 0.01
43 1 0.00
44 115 0.51
45 11 0.05
46 65 0.29
47 2 0.01
48 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (45 bp):
ATCTACTCCACTGTAACTTCAGGGAGATAAGATTACTAGGCTTCA
Found at i:28093403 original size:46 final size:43
Alignment explanation
Indices: 28093298--28093421 Score: 149
Period size: 46 Copynumber: 2.8 Consensus size: 43
28093288 CCTTTATTTT
* * *
28093298 AATCCGCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAACTT-AGGGAGATAAGATTACTAGCTTC
* *
28093342 AATCTACTCCGCTGTAATCTTAGGGAGATAAGATTACTATGGCTTC
1 AATCTGCTCCACTGTAA-CTTAGGGAGATAAGATTACTA--GCTTC
*
28093388 AATCTGCTCCACTGTAACCTCAGGGAGATAAGAT
1 AATCTGCTCCACTGTAA-CTTAGGGAGATAAGAT
28093422 CTGAAATTCT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 30 0.44
45 3 0.04
46 35 0.51
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (43 bp):
AATCTGCTCCACTGTAACTTAGGGAGATAAGATTACTAGCTTC
Found at i:28093444 original size:46 final size:45
Alignment explanation
Indices: 28093254--28093641 Score: 165
Period size: 44 Copynumber: 8.7 Consensus size: 45
28093244 AATCTGATGT
* * * **
28093254 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATT-TT-
1 GATCTACTCCACTGTAACCTCAGGGAGATAAGAT-CTGAATTCTTC
* ** * * * * *
28093298 AATCCGCTCCACTGTAACTTCAGAGAGATAGGAT-T-ACTAGCTTC
1 GATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGAAT-TCTTC
* * * * *
28093342 AATCTACTCCGCTGTAATCTTAGGGAGATAAGAT-T-ACTATGGCTTC
1 GATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGA--AT-TCTTC
* *
28093388 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTC
1 GATCTACTCCACTGTAACCTCAGGGAGATAAGATCTG-AATTCTTC
* * * * *
28093434 GGTCTACTCCACTATAACCTCAGGGTGATAAGACCTG-A---TAC
1 GATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTC
*** * * **
28093475 GATCTACTCTGTTGTAACTTCAGAGAGATAAGATCCTTTATT-TT-
1 GATCTACTCCACTGTAACCTCAGGGAGATAAGAT-CTGAATTCTTC
* ** * * * *
28093519 AATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACTAGCTTC
1 GATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGAAT-TCTTC
* ** * *
28093563 AATCTACTCCGTTGTAATCTCAGGGAGATAAGATCTGAAATTCTTT
1 GATCTACTCCACTGTAACCTCAGGGAGATAAGATCTG-AATTCTTC
* ** *
28093609 GGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 GATCTACTCCACTGTAACCTCAGGGAGATAAGA
28093642 CCTGTATAAT
Statistics
Matches: 258, Mismatches: 68, Indels: 34
0.72 0.19 0.09
Matches are distributed among these distances:
41 29 0.11
42 4 0.02
43 5 0.02
44 111 0.43
45 2 0.01
46 101 0.39
47 5 0.02
49 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (45 bp):
GATCTACTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTC
Found at i:28106047 original size:912 final size:912
Alignment explanation
Indices: 28104285--28106671 Score: 4693
Period size: 912 Copynumber: 2.6 Consensus size: 912
28104275 AACAATACAA
28104285 TAAAATAATAATATTTACGAACTCAAACATTAAAAATGGGGTTCCAAAATAGCCATTTTCAACAC
1 TAAAATAATAATATTTACGAACTCAAACATTAAAAATGGGGTTCCAAAATAGCCATTTTCAACAC
28104350 CACTGAAAACGGGTTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAATAGAACCA
66 CACTGAAAACGGGTTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAATAGAACCA
28104415 AGAAATCAATACAGTCAATATGTGATTGAACTATCAACAAAATCAATTTTCATTTTCATGTATCA
131 AGAAATCAATACAGTCAATATGTGATTGAACTATCAACAAAATCAATTTTCATTTTCATGTATCA
28104480 TATGTAAAATCTCATACCACATTTCATTAGGCGTGACATACATGAACATGTAATCGTATTTAACA
196 TATGTAAAATCTCATACCACATTTCATTAGGCGTGACATACATGAACATGTAATCGTATTTAACA
28104545 TTATATCAAATTTCATATGCATTTTAACATGTTACCAAGTTCATTTCATTTTCTCATTTCCATCT
261 TTATATCAAATTTCATATGCATTTTAACATGTTACCAAGTTCATTTCATTTTCTCATTTCCATCT
*
28104610 CGAATTCTCTTATTCGCTTTATATCCATATCGATCCTCAAGGCTTGTTTTATCTGGTTCGCATGA
326 CGAATTCTCTTATTCGCTTTATATCCATATCGATCCACAAGGCTTGTTTTATCTGGTTCGCATGA
28104675 TCTTTCACATGCCATCTTTTGTTACTCAATCACTAACATACCAAATTCATCATTAAATAATAGCT
391 TCTTTCACATGCCATCTTTTGTTACTCAATCACTAACATACCAAATTCATCATTAAATAATAGCT
28104740 TTTCATATAAAAAATCACATAGCATGATATATGTTTCATAACCCCTATTAATTGGACAGTGACCT
456 TTTCATATAAAAAATCACATAGCATGATATATGTTTCATAACCCCTATTAATTGGACAGTGACCT
28104805 AAGACGGGTACACGAATCATCCAACCATCATACCAATATATCTTGAAGAATCAATGAAGAGAAAA
521 AAGACGGGTACACGAATCATCCAACCATCATACCAATATATCTTGAAGAATCAATGAAGAGAAAA
28104870 TATGAAAGGAAAAATGGCATTAATTTCTTTTATTATTTTCTTTTATACTTGATTAATTTATAATT
586 TATGAAAGGAAAAATGGCATTAATTTCTTTTATTATTTTCTTTTATACTTGATTAATTTATAATT
28104935 AATCATAATTAACTTAATTAATCTTAATTAGTTAACCATAGGCATAATTTAACAGATTTGGTGGA
651 AATCATAATTAACTTAATTAATCTTAATTAGTTAACCATAGGCATAATTTAACAGATTTGGTGGA
28105000 TGACGAACGAATATCCACCACCGAACATCCATTTAAAAATGGATTAATTACTTAGTTGGTCCTCT
716 TGACGAACGAATATCCACCACCGAACATCCATTTAAAAATGGATTAATTACTTAGTTGGTCCTCT
28105065 AAATAATTAAAAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTTAAT
781 AAATAATTAAAAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTTAAT
28105130 TAACTATCCAATTAACAAAATTAAGGGATCGAACTTTAATTAACTTTTATTATAATATCGTAAAT
846 TAACTATCCAATTAACAAAATTAAGGGATCGAACTTTAATTAACTTTTATTATAATATCGTAAAT
28105195 AT
911 AT
28105197 TAAAATAATAATATTTACGAACTCAAACATTAAAAATGGGGTTCCAAAATAGCCATTTTCAACAC
1 TAAAATAATAATATTTACGAACTCAAACATTAAAAATGGGGTTCCAAAATAGCCATTTTCAACAC
28105262 CACTGAAAACGGGTTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAATAGAACCA
66 CACTGAAAACGGGTTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAATAGAACCA
28105327 AGAAATCAATACAGTCAATATGTGATTGAACTATCAACAAAATCAATTTTCATTTTCATGTATCA
131 AGAAATCAATACAGTCAATATGTGATTGAACTATCAACAAAATCAATTTTCATTTTCATGTATCA
28105392 TATGTAAAATCTCATACCACATTTCATTAGGCGTGACATACATGAACATGTAATCGTATTTAACA
196 TATGTAAAATCTCATACCACATTTCATTAGGCGTGACATACATGAACATGTAATCGTATTTAACA
28105457 TTATATCAAATTTCATATGCATTTTAACATGTTACCAAGTTCATTTCATTTTCTCATTTCCATCT
261 TTATATCAAATTTCATATGCATTTTAACATGTTACCAAGTTCATTTCATTTTCTCATTTCCATCT
28105522 CGAATTCTCTTATTCGCTTTATATCCATATCGATCCACAAGGCTTGTTTTATCTGGTTCGCATGA
326 CGAATTCTCTTATTCGCTTTATATCCATATCGATCCACAAGGCTTGTTTTATCTGGTTCGCATGA
* *
28105587 TCTTTCACATGCCATCTTTTGTTACTTAATCACTAACATACCAAATTAATCATTAAATAATAGCT
391 TCTTTCACATGCCATCTTTTGTTACTCAATCACTAACATACCAAATTCATCATTAAATAATAGCT
28105652 TTTCATATAAAAAATCACATAGCATGATATATGTTTCATAACCCCTATTAATTGGACAGTGACCT
456 TTTCATATAAAAAATCACATAGCATGATATATGTTTCATAACCCCTATTAATTGGACAGTGACCT
28105717 AAGACGGGTACACGAATCATCCAACCATCATACCAATATATCTTGAAGAATCAATGAAGAGAAAA
521 AAGACGGGTACACGAATCATCCAACCATCATACCAATATATCTTGAAGAATCAATGAAGAGAAAA
28105782 TATGAAAGGAAAAATGGCATTAATTTCTTTTATTATTTTCTTTTATACTTGATTAATTTATAATT
586 TATGAAAGGAAAAATGGCATTAATTTCTTTTATTATTTTCTTTTATACTTGATTAATTTATAATT
28105847 AATCATAATTAACTTAATTAATCTTAATTAGTTAACCATAGGCATAATTTAACAGATTTGGTGGA
651 AATCATAATTAACTTAATTAATCTTAATTAGTTAACCATAGGCATAATTTAACAGATTTGGTGGA
28105912 TGACGAACGAATATCCACCACCGAACATCCATTTAAAAATGGATTAATTACTTAGTTGGTCCTCT
716 TGACGAACGAATATCCACCACCGAACATCCATTTAAAAATGGATTAATTACTTAGTTGGTCCTCT
28105977 AAATAATTAAAAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTTAAT
781 AAATAATTAAAAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTTAAT
*
28106042 TAACTATCCAATTAACAAAATTAAGGGATTGAACTTTAATTAACTTTTATTATAATATCGTAAAT
846 TAACTATCCAATTAACAAAATTAAGGGATCGAACTTTAATTAACTTTTATTATAATATCGTAAAT
28106107 AT
911 AT
**
28106109 TAAAATAATAATATTTACGAACTCAAACATTAAAAATGGGGTTCCGTAATAGCCATTTTCAACAC
1 TAAAATAATAATATTTACGAACTCAAACATTAAAAATGGGGTTCCAAAATAGCCATTTTCAACAC
* * *
28106174 CACTGAAAATGGATTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAACAGAACCA
66 CACTGAAAACGGGTTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAATAGAACCA
28106239 AGAAATCAATACAGTCAATATGTGATTGAACTATCAACAAAATCAATTTTCATTTTCATGTATCA
131 AGAAATCAATACAGTCAATATGTGATTGAACTATCAACAAAATCAATTTTCATTTTCATGTATCA
28106304 TATGTAAAATCTCATACCACATTTCATTAGGCGTGACATACATGAACATGTAATCGTATTTAACA
196 TATGTAAAATCTCATACCACATTTCATTAGGCGTGACATACATGAACATGTAATCGTATTTAACA
28106369 TTATATCAAATTTCATATGCATTTTAACATGTTACCAAGTTCATTTCATTTTCTCATTTCCATCT
261 TTATATCAAATTTCATATGCATTTTAACATGTTACCAAGTTCATTTCATTTTCTCATTTCCATCT
28106434 CGAATTCTCTTATTCGCTTTATATCCATATCGATCCACAAGGCTTGTTTTATCTGGTTCGCATGA
326 CGAATTCTCTTATTCGCTTTATATCCATATCGATCCACAAGGCTTGTTTTATCTGGTTCGCATGA
28106499 TCTTTCACATGCCATCTTTTGTTACTCAATCACTAACATACCAAATTCATCATTAAATAATAGCT
391 TCTTTCACATGCCATCTTTTGTTACTCAATCACTAACATACCAAATTCATCATTAAATAATAGCT
28106564 TTTCATATAAAAAATCACATAGCATGATATATGTTTCATAACCCCTATTAATTGGACAGTGACCT
456 TTTCATATAAAAAATCACATAGCATGATATATGTTTCATAACCCCTATTAATTGGACAGTGACCT
28106629 AAGACGGGTACACGAATCATCCAACCATCATACCAATATATCT
521 AAGACGGGTACACGAATCATCCAACCATCATACCAATATATCT
28106672 GGCACCCAGT
Statistics
Matches: 1464, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
912 1464 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (912 bp):
TAAAATAATAATATTTACGAACTCAAACATTAAAAATGGGGTTCCAAAATAGCCATTTTCAACAC
CACTGAAAACGGGTTGTTATACTTCTTGGTACTTTCATGATTTAAATCAATAATCAATAGAACCA
AGAAATCAATACAGTCAATATGTGATTGAACTATCAACAAAATCAATTTTCATTTTCATGTATCA
TATGTAAAATCTCATACCACATTTCATTAGGCGTGACATACATGAACATGTAATCGTATTTAACA
TTATATCAAATTTCATATGCATTTTAACATGTTACCAAGTTCATTTCATTTTCTCATTTCCATCT
CGAATTCTCTTATTCGCTTTATATCCATATCGATCCACAAGGCTTGTTTTATCTGGTTCGCATGA
TCTTTCACATGCCATCTTTTGTTACTCAATCACTAACATACCAAATTCATCATTAAATAATAGCT
TTTCATATAAAAAATCACATAGCATGATATATGTTTCATAACCCCTATTAATTGGACAGTGACCT
AAGACGGGTACACGAATCATCCAACCATCATACCAATATATCTTGAAGAATCAATGAAGAGAAAA
TATGAAAGGAAAAATGGCATTAATTTCTTTTATTATTTTCTTTTATACTTGATTAATTTATAATT
AATCATAATTAACTTAATTAATCTTAATTAGTTAACCATAGGCATAATTTAACAGATTTGGTGGA
TGACGAACGAATATCCACCACCGAACATCCATTTAAAAATGGATTAATTACTTAGTTGGTCCTCT
AAATAATTAAAAATCAATAGCGATTAATTTTTACCAATTTTATAATTTAGTCATTGTACCTTAAT
TAACTATCCAATTAACAAAATTAAGGGATCGAACTTTAATTAACTTTTATTATAATATCGTAAAT
AT
Found at i:28107999 original size:142 final size:143
Alignment explanation
Indices: 28107830--28108107 Score: 459
Period size: 142 Copynumber: 2.0 Consensus size: 143
28107820 TAAATGACTG
* *
28107830 TCATCATTATCATCCATTATCTCATAAGAAACAATGAGTCAATAACCATTTAGGTCCCTTGGTTA
1 TCATCATTATCATCCACTATCTCATAAGAAACAATGAGTCAATAACCATTTAGGTCCCTTGATTA
* *
28107895 ATTACCAATTAGGTCATCAAACATTTTCCAATATAAAATTCAATAGCAATTGGAC-TTTACAATT
66 AATACCAATTAGGTCATCAAACATTTTCCAATATAAAATTCAATAACAATTGGACTTTTACAATT
28107959 TAGTCTCTAACTA
131 TAGTCTCTAACTA
* * *
28107972 TCATCATTATCATCCACTATCTTATAAGGAACAATGAGTTAATAACCATTTAGGTCCCTTGATTA
1 TCATCATTATCATCCACTATCTCATAAGAAACAATGAGTCAATAACCATTTAGGTCCCTTGATTA
* * *
28108037 AATACCAATTAGGTCATCAAGCATTTTCCACTATAAAATTTAATAACAATTGGACTTTTACAATT
66 AATACCAATTAGGTCATCAAACATTTTCCAATATAAAATTCAATAACAATTGGACTTTTACAATT
28108102 TAGTCT
131 TAGTCT
28108108 TTAAACTTTA
Statistics
Matches: 125, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
142 110 0.88
143 15 0.12
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (143 bp):
TCATCATTATCATCCACTATCTCATAAGAAACAATGAGTCAATAACCATTTAGGTCCCTTGATTA
AATACCAATTAGGTCATCAAACATTTTCCAATATAAAATTCAATAACAATTGGACTTTTACAATT
TAGTCTCTAACTA
Found at i:28110533 original size:14 final size:14
Alignment explanation
Indices: 28110514--28110540 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28110504 TTAGTGTAAG
28110514 AAAATAAATCCTTT
1 AAAATAAATCCTTT
28110528 AAAATAAATCCTT
1 AAAATAAATCCTT
28110541 GTTGTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATAAATCCTTT
Found at i:28113065 original size:21 final size:21
Alignment explanation
Indices: 28113039--28113087 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
28113029 CTAAAACATT
*
28113039 GGCATGTCCCATAGCCACACG
1 GGCATGTCCCATAGCCACACA
* *
28113060 GGCATGTCCCTTGGCCACACA
1 GGCATGTCCCATAGCCACACA
28113081 GGCATGT
1 GGCATGT
28113088 GACCCCTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.35, G:0.27, T:0.18
Consensus pattern (21 bp):
GGCATGTCCCATAGCCACACA
Found at i:28117698 original size:20 final size:18
Alignment explanation
Indices: 28117664--28117704 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
28117654 AATATATTCT
28117664 TAAAAAAAGAAAAAAAAA
1 TAAAAAAAGAAAAAAAAA
*
28117682 TAAAAACAAGTAAAAAATAA
1 TAAAAA-AAG-AAAAAAAAA
28117702 TAA
1 TAA
28117705 TAAAGAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 3 0.15
20 11 0.55
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.12
Consensus pattern (18 bp):
TAAAAAAAGAAAAAAAAA
Found at i:28119067 original size:21 final size:20
Alignment explanation
Indices: 28119043--28119082 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28119033 AATTATGTTT
* *
28119043 ATTTTTACAATTTCAATTTCA
1 ATTTATACAATGTC-ATTTCA
28119064 ATTTATACAATGTCATTTC
1 ATTTATACAATGTCATTTC
28119083 GTCCATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.50
Consensus pattern (20 bp):
ATTTATACAATGTCATTTCA
Done.