Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_pilon, whole genome shotgun sequence
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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 24
Found at i:3077839 original size:47 final size:47
Alignment explanation
Indices: 3077787--3077878 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 47
3077777 AAAAAATCAG
* *
3077787 GAGCTCGATTAAAGCTCGAGACTCGAGCTCG-ATT-GAAGCTCGATTTT
1 GAGCTCGATTAAAGCTCGA-ACTCAAACTCGAATTAG-AGCTCGATTTT
*
3077834 GAGCTCGATTCAAGCTCGAACTCAAACTCGAATTAGAGCTCGATT
1 GAGCTCGATTAAAGCTCGAACTCAAACTCGAATTAGAGCTCGATT
3077879 CAAGCTCGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 9 0.22
47 30 0.75
48 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (47 bp):
GAGCTCGATTAAAGCTCGAACTCAAACTCGAATTAGAGCTCGATTTT
Found at i:3077858 original size:12 final size:12
Alignment explanation
Indices: 3077843--3077900 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
3077833 TGAGCTCGAT
3077843 TCAAGCTCGAAC
1 TCAAGCTCGAAC
*
3077855 TCAAACTCGAA-
1 TCAAGCTCGAAC
* *
3077866 TTAGAGCTCG-AT
1 TCA-AGCTCGAAC
3077878 TCAAGCTCGAAC
1 TCAAGCTCGAAC
*
3077890 TCAAACTCGAA
1 TCAAGCTCGAA
3077901 TTTGAACCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.24
12 28 0.76
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.21
Consensus pattern (12 bp):
TCAAGCTCGAAC
Found at i:3077863 original size:23 final size:23
Alignment explanation
Indices: 3077787--3077876 Score: 90
Period size: 24 Copynumber: 3.8 Consensus size: 23
3077777 AAAAAATCAG
3077787 GAGCTCGATTAAAGCTCGAGACTC
1 GAGCTCGATTAAAGCTCGA-ACTC
* ** *
3077811 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTAAAGCTCGAACTC
*
3077834 GAGCTCGATTCAAGCTCGAACTC
1 GAGCTCGATTAAAGCTCGAACTC
* * *
3077857 AAACTCGAATTAGAGCTCGA
1 GAGCTCG-ATTAAAGCTCGA
3077877 TTCAAGCTCG
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 25 0.47
24 28 0.53
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.24
Consensus pattern (23 bp):
GAGCTCGATTAAAGCTCGAACTC
Found at i:3077864 original size:35 final size:35
Alignment explanation
Indices: 3077825--3077905 Score: 144
Period size: 35 Copynumber: 2.3 Consensus size: 35
3077815 TCGATTGAAG
*
3077825 CTCGATTTTGAGCTCGATTCAAGCTCGAACTCAAA
1 CTCGAATTTGAGCTCGATTCAAGCTCGAACTCAAA
*
3077860 CTCGAATTAGAGCTCGATTCAAGCTCGAACTCAAA
1 CTCGAATTTGAGCTCGATTCAAGCTCGAACTCAAA
3077895 CTCGAATTTGA
1 CTCGAATTTGA
3077906 ACCTACAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (35 bp):
CTCGAATTTGAGCTCGATTCAAGCTCGAACTCAAA
Found at i:3078867 original size:32 final size:32
Alignment explanation
Indices: 3078799--3078900 Score: 79
Period size: 32 Copynumber: 3.3 Consensus size: 32
3078789 TTAAATAGTT
* * * * *
3078799 ATTATATTTTATATTAATATAAT-TATATAAA
1 ATTATTTTTTTTATTAAAATAATATTTATATA
3078830 TATTATTTTTTTTATTAAAATAATATTTATATA
1 -ATTATTTTTTTTATTAAAATAATATTTATATA
* * * *
3078863 ATTA--TTATTTATTTAAAT-TTATTAAT-TA
1 ATTATTTTTTTTATTAAAATAATATTTATATA
3078891 ATTATTTTTT
1 ATTATTTTTT
3078901 GTGCTAATTA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
28 6 0.11
29 6 0.11
30 15 0.26
32 24 0.42
33 6 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
ATTATTTTTTTTATTAAAATAATATTTATATA
Found at i:3080709 original size:21 final size:21
Alignment explanation
Indices: 3080683--3080752 Score: 115
Period size: 21 Copynumber: 3.3 Consensus size: 21
3080673 GTCATCTCCA
3080683 CAGGGTTACATTCCTAGCCCG
1 CAGGGTTACATTCCTAGCCCG
3080704 CAGGGTTACATTCCTAGCCCG
1 CAGGGTTACATTCCTAGCCCG
*
3080725 CCA-GGTTACATGCCTAGCCCG
1 -CAGGGTTACATTCCTAGCCCG
3080746 CAGGGTT
1 CAGGGTT
3080753 TTATACCATA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
20 2 0.04
21 42 0.91
22 2 0.04
ACGTcount: A:0.19, C:0.33, G:0.26, T:0.23
Consensus pattern (21 bp):
CAGGGTTACATTCCTAGCCCG
Found at i:3081317 original size:34 final size:34
Alignment explanation
Indices: 3081274--3081380 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
3081264 ATAAATGTTT
* *
3081274 TTAAAATACAGATTATAGCATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * *
3081308 TTAAAATACAAATAATATTATTCGAAATTTAAAT
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* *
3081342 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
3081376 TTAAA
1 TTAAA
3081381 TTCAAGTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:3082021 original size:127 final size:126
Alignment explanation
Indices: 3081795--3082197 Score: 716
Period size: 127 Copynumber: 3.2 Consensus size: 126
3081785 CCAGGAACGC
*
3081795 CCCCCGGAAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGAG
1 CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCG-G
3081860 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCG
65 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCG
* * * *
3081922 CCCCCAGGAACGCGCCTTCATGGTCCCCTAAGGAATAATAGGTATTGATATGAATAGTTCCCAGG
1 CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTC-GG
3081987 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCG
65 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCG
* *
3082049 TCCCCGGGAACGCGTCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGG
1 CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTC-GG
3082114 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCG
65 GGACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCG
3082176 CCCCCGGGAACGCGCCTTCACG
1 CCCCCGGGAACGCGCCTTCACG
3082198 TGAATAGTAC
Statistics
Matches: 261, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
127 260 1.00
128 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.22
Consensus pattern (126 bp):
CCCCCGGGAACGCGCCTTCACGGTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGG
GACATAAGTGACATAATAGGGTAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCG
Found at i:3087071 original size:11 final size:11
Alignment explanation
Indices: 3087055--3087090 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3087045 GTAAAATGTC
3087055 ATCATGACTCG
1 ATCATGACTCG
3087066 ATCATG-C-C-
1 ATCATGACTCG
3087074 ATCATGACTCG
1 ATCATGACTCG
3087085 ATCATG
1 ATCATG
3087091 CCATTCATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.27
9 2 0.09
10 2 0.09
11 12 0.55
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (11 bp):
ATCATGACTCG
Found at i:3087078 original size:19 final size:19
Alignment explanation
Indices: 3087054--3087099 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
3087044 AGTAAAATGT
3087054 CATCATGACTCGATCATGC
1 CATCATGACTCGATCATGC
3087073 CATCATGACTCGATCATGC
1 CATCATGACTCGATCATGC
3087092 CATTCATG
1 CA-TCATG
3087100 CAATTCAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.28
Consensus pattern (19 bp):
CATCATGACTCGATCATGC
Found at i:3088643 original size:14 final size:14
Alignment explanation
Indices: 3088573--3088650 Score: 51
Period size: 14 Copynumber: 5.8 Consensus size: 14
3088563 GTGTATAACT
3088573 TAAACCCTAAATCC
1 TAAACCCTAAATCC
3088587 TAATACCC--AATACC
1 TAA-ACCCTAAAT-CC
* *
3088601 TACACCATAAA-CC
1 TAAACCCTAAATCC
*
3088614 TTAAATCCT--A-CC
1 -TAAACCCTAAATCC
3088626 TAAACCCTAAATCC
1 TAAACCCTAAATCC
*
3088640 TAAACCATAAA
1 TAAACCCTAAA
3088651 CTCTATCACA
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
11 7 0.14
12 3 0.06
13 9 0.18
14 24 0.49
15 6 0.12
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAATCC
Found at i:3088752 original size:14 final size:14
Alignment explanation
Indices: 3088733--3088762 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3088723 TATAATTATC
*
3088733 AATAATGTATTTTT
1 AATAATGTAATTTT
3088747 AATAATGTAATTTT
1 AATAATGTAATTTT
3088761 AA
1 AA
3088763 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:3088876 original size:12 final size:11
Alignment explanation
Indices: 3088854--3088883 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
3088844 CGTTAAGAAA
3088854 TCGAGTCGAGC
1 TCGAGTCGAGC
3088865 TCGAGCTCGAGC
1 TCGAG-TCGAGC
3088877 TCGAGTC
1 TCGAGTC
3088884 CATTCAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.17, C:0.30, G:0.33, T:0.20
Consensus pattern (11 bp):
TCGAGTCGAGC
Found at i:3099770 original size:47 final size:47
Alignment explanation
Indices: 3099674--3099772 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 47
3099664 TCGAATAAAT
* * **
3099674 GCATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTCTCGAACAA
1 GCATGCGAACTAGAAATCATGCGGTTAGGATTATTTGTCAAGAACAA
* * * *
3099721 GCATGCGAATTAGATATCATGCGGTTAGGATT-TTTGTGAATAACAAA
1 GCATGCGAACTAGAAATCATGCGGTTAGGATTATTTGTCAAGAAC-AA
3099768 GCATG
1 GCATG
3099773 AGGTAGATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 7 0.16
47 36 0.84
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.31
Consensus pattern (47 bp):
GCATGCGAACTAGAAATCATGCGGTTAGGATTATTTGTCAAGAACAA
Found at i:3106542 original size:42 final size:42
Alignment explanation
Indices: 3106485--3106582 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
3106475 AGTAAACAAT
* * * * * * *
3106485 TTAAGTCCTTTGGGCCATCAGTAAGTCTTTCGGGTATGATGC
1 TTAAATCCTTAGGGCCATCAGTAAGTATTTCGAGCATAATGA
3106527 TTAAATCCTTAGGGCCATCAGTAAGTATTTCGAGCATAATGA
1 TTAAATCCTTAGGGCCATCAGTAAGTATTTCGAGCATAATGA
3106569 TTAAATCCTTAGGG
1 TTAAATCCTTAGGG
3106583 TAATTTGTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (42 bp):
TTAAATCCTTAGGGCCATCAGTAAGTATTTCGAGCATAATGA
Found at i:3106692 original size:42 final size:43
Alignment explanation
Indices: 3106633--3106716 Score: 125
Period size: 44 Copynumber: 2.0 Consensus size: 43
3106623 ATAAGTAAGT
* *
3106633 GCCATCAGTAAGTCTTTC-GAGCATGATGATGAAGTCCTTCGA
1 GCCATCAATAAGTCTTTCAGAGCATGATGATGAAATCCTTCGA
*
3106675 GCCATCAATAAGTCTTTCGAGAGCATGATGATTAAATCCTTC
1 GCCATCAATAAGTCTTTC-AGAGCATGATGATGAAATCCTTC
3106717 AGGAAATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 17 0.46
44 20 0.54
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (43 bp):
GCCATCAATAAGTCTTTCAGAGCATGATGATGAAATCCTTCGA
Found at i:3106693 original size:20 final size:20
Alignment explanation
Indices: 3106633--3106695 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
3106623 ATAAGTAAGT
*
3106633 GCCATCAGTAAGTCTTTCGA
1 GCCATCAATAAGTCTTTCGA
* *
3106653 G-CATGATGATGAAGTCCTTCGA
1 GCCATCA--AT-AAGTCTTTCGA
3106675 GCCATCAATAAGTCTTTCGA
1 GCCATCAATAAGTCTTTCGA
3106695 G
1 G
3106696 AGCATGATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 4 0.12
20 12 0.35
21 3 0.09
22 11 0.32
23 4 0.12
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (20 bp):
GCCATCAATAAGTCTTTCGA
Found at i:3106750 original size:137 final size:135
Alignment explanation
Indices: 3106498--3106769 Score: 384
Period size: 137 Copynumber: 2.0 Consensus size: 135
3106488 AGTCCTTTGG
* * * * * *
3106498 GCCATCAGTAAGTCTTTCGGGTATGATGCTTAAATCCTTAGGGCCATCAGTAAGTATTTCGAGCA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTAGAGCCATCAATAAGTATTTCGAGCA
* * *
3106563 TAATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACGGTAGAGTAGTGAAGCGAACCCATAAG
66 TAATGATTAAATCCTTAGGGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCATAAG
3106628 TAAGT
131 TAAGT
* * *
3106633 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGAGCCATCAATAAGTCTTTCGAGAG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTAGAGCCATCAATAAGTATTTC--GAG
*
3106698 CATGATGATTAAATCCTTCA-GGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCAT
64 CATAATGATTAAATCCTT-AGGGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCAT
*
3106762 CAGTAAGT
128 AAGTAAGT
3106770 CTTTCGAGCA
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
135 51 0.43
137 68 0.57
138 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.28
Consensus pattern (135 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTAGAGCCATCAATAAGTATTTCGAGCA
TAATGATTAAATCCTTAGGGAAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCATAAG
TAAGT
Found at i:3106886 original size:80 final size:80
Alignment explanation
Indices: 3106676--3106890 Score: 340
Period size: 80 Copynumber: 2.7 Consensus size: 80
3106666 GTCCTTCGAG
* * * *
3106676 CCATCAATAAGTCTTTCGAGAGCATGATGATTAAATCCTTCAGGAAATTTGTAAGCCTTCACGGA
1 CCATCAGTAAGTCTTTC--GAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGA
3106741 AGAGTAGTGAAGCAAAC
64 AGAGTAGTGAAGCAAAC
3106758 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
*
3106823 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAC
* * *
3106838 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTTGGGTTATTTGTAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAG
3106891 TCTTTCGAGC
Statistics
Matches: 125, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
80 109 0.87
82 16 0.13
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
AGTAGTGAAGCAAAC
Found at i:3107521 original size:55 final size:53
Alignment explanation
Indices: 3107315--3107607 Score: 338
Period size: 53 Copynumber: 5.5 Consensus size: 53
3107305 AGATTTTTTT
* * * *
3107315 GAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGGCAAAAGATAGTTC
1 GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTGTTC
* *
3107368 GAGTTCTACTCCCTGAAGCAAGAGGGAGAGAACCCGTAGGCAGAAGATTGTTC
1 GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTGTTC
*
3107421 GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAAGCAGAAGATTGTTC
1 GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTGTTC
* * * *
3107474 GAGTTCTACGCTCCATTAAGCAAGAGGGAGCGGACCCGTAAAG-AGAAGATCGTTC
1 GAGTTCTA--CTCCCTGAAGCAAGAGGGAGCGAACCCGT-AAGCAGAAGATTGTTC
* * * * **** *
3107529 GATTTCTACTCCCTGAAGAAATAGGGAGCGAACCCATTTTTAGAAGATTGTTT
1 GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTGTTC
*
3107582 GAGTTCCTTAATCCCTGAA-CAAGAGG
1 GAGTT-C-TACTCCCTGAAGCAAGAGG
3107608 AAACAGACCC
Statistics
Matches: 206, Mismatches: 28, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
53 144 0.70
54 6 0.03
55 53 0.26
56 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (53 bp):
GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGCAGAAGATTGTTC
Found at i:3107555 original size:108 final size:106
Alignment explanation
Indices: 3107315--3107565 Score: 342
Period size: 108 Copynumber: 2.3 Consensus size: 106
3107305 AGATTTTTTT
* * *
3107315 GAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGGCAAAAGATAGTTCGAGTTCTACTCC
1 GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAAGCAAAAGATAGTTCGAGTTCTACTCC
* * *
3107380 CTGAAGCAAGAGGGAGAGAACCCGTAGGCAGAAGATTGTTC
66 ATGAAGCAAGAGGGAGAGAACCCGTAAGCAGAAGATCGTTC
* *
3107421 GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAAGCAGAAGATTGTTCGAGTTCTACGCT
1 GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAAGCAAAAGATAGTTCGAGTTCTA--CT
* * *
3107486 CCATTAAGCAAGAGGGAGCGGACCCGTAAAG-AGAAGATCGTTC
64 CCATGAAGCAAGAGGGAGAGAACCCGT-AAGCAGAAGATCGTTC
* * *
3107529 GATTTCTACTCCCTGAAGAAATAGGGAGCGAACCCAT
1 GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCAT
3107566 TTTTAGAAGA
Statistics
Matches: 128, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
106 56 0.44
108 70 0.55
109 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (106 bp):
GAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCATAAGCAAAAGATAGTTCGAGTTCTACTCC
ATGAAGCAAGAGGGAGAGAACCCGTAAGCAGAAGATCGTTC
Found at i:3107992 original size:10 final size:10
Alignment explanation
Indices: 3107979--3108010 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
3107969 AAAGGGGCTC
3107979 TTTCATTTTT
1 TTTCATTTTT
3107989 TTTCATTTTTT
1 TTTCA-TTTTT
3108000 TTTCATTTTT
1 TTTCATTTTT
3108010 T
1 T
3108011 ACACAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCATTTTT
Found at i:3108000 original size:11 final size:11
Alignment explanation
Indices: 3107979--3108010 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
3107969 AAAGGGGCTC
3107979 TTTCA-TTTTT
1 TTTCATTTTTT
3107989 TTTCATTTTTT
1 TTTCATTTTTT
3108000 TTTCATTTTTT
1 TTTCATTTTTT
3108011 ACACAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTCATTTTTT
Found at i:3110918 original size:21 final size:22
Alignment explanation
Indices: 3110885--3110928 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3110875 TCACATTGTT
*
3110885 TTTATATAAATTTT-TAAAATA
1 TTTAAATAAATTTTCTAAAATA
* *
3110906 TTTAAATACATTTTCTTAAATA
1 TTTAAATAAATTTTCTAAAATA
3110928 T
1 T
3110929 GTATATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAAATAAATTTTCTAAAATA
Found at i:3113463 original size:24 final size:23
Alignment explanation
Indices: 3113426--3113471 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
3113416 CTAAATAATA
*
3113426 TAAAAAAATAAAATTAAAAATTC
1 TAAAAAAAAAAAATTAAAAATTC
*
3113449 TAAAAAAAAACAAATTTAAAATT
1 TAAAAAAAAA-AAATTAAAAATT
3113472 TTACTATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (23 bp):
TAAAAAAAAAAAATTAAAAATTC
Found at i:3115715 original size:2 final size:2
Alignment explanation
Indices: 3115710--3115740 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3115700 TCTTTCTTTA
3115710 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3115741 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3115745 original size:2 final size:2
Alignment explanation
Indices: 3115740--3115770 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3115730 TCTCTCTCTC
*
3115740 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3115771 GTAATGTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3116316 original size:21 final size:19
Alignment explanation
Indices: 3116271--3116310 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
3116261 TTTGACCAGA
3116271 AGTTTCGAAATTTCTACAAG
1 AGTTTCGAAATTTC-ACAAG
3116291 AGTTTCGAAACTTTC-CAAG
1 AGTTTCGAAA-TTTCACAAG
3116310 A
1 A
3116311 CAGTTTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (19 bp):
AGTTTCGAAATTTCACAAG
Found at i:3117449 original size:28 final size:28
Alignment explanation
Indices: 3117409--3117465 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
3117399 GGCTCGATAG
*
3117409 CTTAATGTTTTAAACATTGATTTGATGA
1 CTTAATGTTTTAAACATTGACTTGATGA
3117437 CTTAATGTTTTAAACATTGACTTGATGA
1 CTTAATGTTTTAAACATTGACTTGATGA
3117465 C
1 C
3117466 ATATGTAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (28 bp):
CTTAATGTTTTAAACATTGACTTGATGA
Found at i:3118967 original size:22 final size:22
Alignment explanation
Indices: 3118942--3119008 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
3118932 CCATTATATT
3118942 TTTTTATTTTTATAATTGAGTC
1 TTTTTATTTTTATAATTGAGTC
* *
3118964 -TTTTAGTTTTTAAAATTTTA-T-
1 TTTTTA-TTTTTATAA-TTGAGTC
*
3118985 TTTTTATCTTTATAATTGATGTC
1 TTTTTATTTTTATAATTGA-GTC
3119008 T
1 T
3119009 CTAATTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 11
0.68 0.10 0.22
Matches are distributed among these distances:
20 3 0.09
21 12 0.35
22 15 0.44
23 4 0.12
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.64
Consensus pattern (22 bp):
TTTTTATTTTTATAATTGAGTC
Found at i:3118988 original size:43 final size:43
Alignment explanation
Indices: 3118941--3119061 Score: 136
Period size: 43 Copynumber: 2.8 Consensus size: 43
3118931 TCCATTATAT
* * * **
3118941 TTTTTTATTTTTATAATTGAGTCTTTTAGTTTTTAAAATTTTA-
1 TTTTTTATCTTTATAATTGAGTC-TCTAATTTTTAAAATCCTAC
**
3118984 TTTTTTATCTTTATAATTGATGTCTCTAATTTTTGTAATCCTAC
1 TTTTTTATCTTTATAATTGA-GTCTCTAATTTTTAAAATCCTAC
*
3119028 TTTTTTATCTTTATAATTGAGGCTCTTAATTTTT
1 TTTTTTATCTTTATAATTGAGTCTC-TAATTTTT
3119062 TCAATATCAC
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
43 36 0.54
44 31 0.46
ACGTcount: A:0.23, C:0.08, G:0.07, T:0.61
Consensus pattern (43 bp):
TTTTTTATCTTTATAATTGAGTCTCTAATTTTTAAAATCCTAC
Found at i:3119076 original size:87 final size:86
Alignment explanation
Indices: 3118941--3119432 Score: 303
Period size: 87 Copynumber: 5.7 Consensus size: 86
3118931 TCCATTATAT
* * * * ** * * * *
3118941 TTTTTTATTTTTATAATTGAGTCTTTTAGTTTTTAAAATTTTATTTTTTATCTTTATAATTGATG
1 TTTTTTATCTTTATAATTGAGGCTCTTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGATG
* *
3119006 TCTCTAA-TTTTTGTAATCCTAC
66 TCCCTAACTTTTT-CAAT-CTAC
* * *
3119028 TTTTTTATCTTTATAATTGAGGCTCTTAATTTTTTCAATATCACTTTTTACATTTATAATTTATG
1 TTTTTTATCTTTATAATTGAGGCTCTTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGATG
* **
3119093 AT-CTTAAGGTTTTCAATCTCAC
66 -TCCCTAACTTTTTCAATCT-AC
* * * *
3119115 -TTTCTAGCTTTATAATTGA-GCTCCTAATTGTTTTTAATCTCA-TTTATCTACCTTTATAATTG
1 TTTTTTATCTTTATAATTGAGGCTCTTAATT-TTTTCAATCTCACTTT-T-TACCTTTATAATTG
*
3119177 ATG-CACCTAATTTTTTCAATCT-C
63 ATGTC-CCTAACTTTTTCAATCTAC
* * * ** * * * * * *
3119200 GTTTTCTAACTTTATAATCGATACCCCTAGTTTTTT-AGTCTCACTTTTTACCTTTATAATTAAG
1 -TTTTTTATCTTTATAATTGAGGCTCTTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAT
*
3119264 GCCCCTAACTTTTTCAATCCTA-
65 GTCCCTAACTTTTTCAAT-CTAC
* * * * *
3119286 TTTTTTA-CTTATATAATTTAGGCCCTTAACTTTTTCAATCTCACTTTTTACCTTTAAAATT-AG
1 TTTTTTATCTT-TATAATTGAGGCTCTTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAT
* * *
3119349 GACCCCTCA-TTTTTTAATCT-C
65 G-TCCCTAACTTTTTCAATCTAC
* * * * *
3119370 ATTTTTACCTTTATAATTGAGG-TCCCTAATATTTTTTAATCAT-ACTTTTTTACTTTTATAATT
1 TTTTTTATCTTTATAATTGAGGCT-CTTAAT-TTTTTCAATC-TCAC-TTTTTACCTTTATAATT
3119433 TAACCGTATA
Statistics
Matches: 326, Mismatches: 55, Indels: 49
0.76 0.13 0.11
Matches are distributed among these distances:
84 25 0.08
85 90 0.28
86 85 0.26
87 114 0.35
88 12 0.04
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.52
Consensus pattern (86 bp):
TTTTTTATCTTTATAATTGAGGCTCTTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGATG
TCCCTAACTTTTTCAATCTAC
Found at i:3119098 original size:43 final size:43
Alignment explanation
Indices: 3118985--3119432 Score: 232
Period size: 43 Copynumber: 10.4 Consensus size: 43
3118975 AAAATTTTAT
*
3118985 TTTTTATCTTTATAATTGATG-TCTCTAATTTTTGT-AATC-CTAC
1 TTTTTAGCTTTATAATTGATGATC-CTAATTTTT-TCAATCTC-AC
* * * * *
3119028 TTTTTTATCTTTATAATTGAGGCTCTTAATTTTTTCAATATCAC
1 -TTTTTAGCTTTATAATTGATGATCCTAATTTTTTCAATCTCAC
* * **
3119072 TTTTTA-CATTTATAATTTATGATCTTAAGGTTTTCAATCTCAC
1 TTTTTAGC-TTTATAATTGATGATCCTAATTTTTTCAATCTCAC
* * *
3119115 TTTCTAGCTTTATAATTGA-GCTCCTAATTGTTTTTAATCTCA-
1 TTTTTAGCTTTATAATTGATGATCCTAATT-TTTTCAATCTCAC
* *
3119157 TTTATCTACCTTTATAATTGATGCA-CCTAATTTTTTCAATCTC-G
1 TTT-T-TAGCTTTATAATTGATG-ATCCTAATTTTTTCAATCTCAC
* * * * *
3119201 TTTTCTAACTTTATAATCGAT-ACCCCTAGTTTTTT-AGTCTCAC
1 TTTT-TAGCTTTATAATTGATGA-TCCTAATTTTTTCAATCTCAC
* * * ** * *
3119244 TTTTTACCTTTATAATTAAGGCCCCTAACTTTTTCAATC-CTAT
1 TTTTTAGCTTTATAATTGATGATCCTAATTTTTTCAATCTC-AC
* ** *
3119287 TTTTTA-CTTATATAATTTA-GGCCCTTAACTTTTTCAATCTCAC
1 TTTTTAGCTT-TATAATTGATGATCC-TAATTTTTTCAATCTCAC
* * * * *
3119330 TTTTTACCTTTAAAATT-AGGACCCCTCATTTTTT-AATCTCA-
1 TTTTTAGCTTTATAATTGATGA-TCCTAATTTTTTCAATCTCAC
* * *
3119371 TTTTTACCTTTATAATTGA-GGTCCCTAATATTTTTTAATCAT-AC
1 TTTTTAGCTTTATAATTGATGAT-CCTAAT-TTTTTCAATC-TCAC
3119415 TTTTTTA-CTTTTATAATT
1 -TTTTTAGC-TTTATAATT
3119433 TAACCGTATA
Statistics
Matches: 328, Mismatches: 45, Indels: 61
0.76 0.10 0.14
Matches are distributed among these distances:
41 23 0.07
42 59 0.18
43 150 0.46
44 70 0.21
45 26 0.08
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (43 bp):
TTTTTAGCTTTATAATTGATGATCCTAATTTTTTCAATCTCAC
Found at i:3119406 original size:86 final size:84
Alignment explanation
Indices: 3119029--3119419 Score: 269
Period size: 86 Copynumber: 4.5 Consensus size: 84
3119019 TAATCCTACT
* * * * * * * *
3119029 TTTTTATCTTTATAATTGAGGCTCTTAATTTTTTCAATATCACTTTTTACATTTATAATTTATGA
1 TTTTTA-CTTTATAATTGAGGCCCTAAATTTTTT-AATCTCACTTTTTACCTTTAAAATTAAGGC
* * **
3119094 TCTTAAGGTTTTCAATCTCAC
64 CCCTAACTTTTTCAATCTCAC
* * * *
3119115 TTTCTAGCTTTATAATTGA-GCTCCTAATTGTTTTTAATCTCA-TTTATCTACCTTTATAATTGA
1 TTTTTA-CTTTATAATTGAGGC-CCTAAAT-TTTTTAATCTCACTTT-T-TACCTTTAAAATTAA
* * * *
3119178 TGCACCTAATTTTTTCAATCTC-G
61 GGCCCCTAACTTTTTCAATCTCAC
* ** * * *
3119201 TTTTCTAACTTTATAATCGATACCCCT-AGTTTTTTAGTCTCACTTTTTACCTTTATAATTAAGG
1 TTTT-T-ACTTTATAATTGA-GGCCCTAAATTTTTTAATCTCACTTTTTACCTTTAAAATTAAGG
*
3119265 CCCCTAACTTTTTCAATC-CTAT
63 CCCCTAACTTTTTCAATCTC-AC
* * *
3119287 TTTTTACTTATATAATTTAGGCCCTTAACTTTTTCAATCTCACTTTTTACCTTTAAAATT-AGGA
1 TTTTTACTT-TATAATTGAGGCCC-TAAATTTTTTAATCTCACTTTTTACCTTTAAAATTAAGG-
* *
3119351 CCCCTCA-TTTTTTAATCTCA-
63 CCCCTAACTTTTTCAATCTCAC
3119371 TTTTTACCTTTATAATTGAGGTCCCTAATATTTTTTAATCAT-ACTTTTT
1 TTTTTA-CTTTATAATTGAGG-CCCTAA-ATTTTTTAATC-TCACTTTTT
3119420 TACTTTTATA
Statistics
Matches: 248, Mismatches: 37, Indels: 41
0.76 0.11 0.13
Matches are distributed among these distances:
84 27 0.11
85 80 0.32
86 84 0.34
87 52 0.21
88 4 0.02
89 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (84 bp):
TTTTTACTTTATAATTGAGGCCCTAAATTTTTTAATCTCACTTTTTACCTTTAAAATTAAGGCCC
CTAACTTTTTCAATCTCAC
Found at i:3133102 original size:44 final size:44
Alignment explanation
Indices: 3133039--3133126 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
3133029 GAAAAACTAC
3133039 TCCATGAATTGTATATAAATAGACTTGTACTCATCATAATTTCA
1 TCCATGAATTGTATATAAATAGACTTGTACTCATCATAATTTCA
3133083 TCCATGAATTGTATATAAATAGACTTGTACTCATCATAATTTCA
1 TCCATGAATTGTATATAAATAGACTTGTACTCATCATAATTTCA
3133127 ATATAATTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (44 bp):
TCCATGAATTGTATATAAATAGACTTGTACTCATCATAATTTCA
Found at i:3133184 original size:19 final size:19
Alignment explanation
Indices: 3133160--3133196 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3133150 TCTTCAATAT
3133160 TCTCTAGCTTTCTTGGTAC
1 TCTCTAGCTTTCTTGGTAC
3133179 TCTCTAGCTTTCTTGGTA
1 TCTCTAGCTTTCTTGGTA
3133197 AACTACAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.24, G:0.16, T:0.49
Consensus pattern (19 bp):
TCTCTAGCTTTCTTGGTAC
Found at i:3135795 original size:17 final size:17
Alignment explanation
Indices: 3135773--3135816 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
3135763 ATGTAAAAAT
3135773 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
3135790 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
3135807 AAATATTTAA
1 AAATATTTAA
3135817 TCAAGTAGAG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:3143718 original size:21 final size:22
Alignment explanation
Indices: 3143693--3143738 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
3143683 TGAAAACATT
*
3143693 TCTCTTGAAAT-GAATTTTGTC
1 TCTCTTGAAATAAAATTTTGTC
3143714 TCTCTTGAAATAAAAATTTTGTC
1 TCTCTTGAAAT-AAAATTTTGTC
3143737 TC
1 TC
3143739 CATTGAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
23 11 0.50
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (22 bp):
TCTCTTGAAATAAAATTTTGTC
Found at i:3143819 original size:66 final size:67
Alignment explanation
Indices: 3143712--3143860 Score: 230
Period size: 66 Copynumber: 2.2 Consensus size: 67
3143702 ATGAATTTTG
3143712 TCTCTCTTGAAATAAAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
1 TCTCTCTTGAAATAAAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
3143777 CA
66 CA
* *
3143779 TCTCTCTTGGAA-CAAAATTTTGTCT-CACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
1 TCTCTCTTGAAATAAAAATTTTGTCTCCA-TTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
*
3143842 GCA
65 ACA
* *
3143845 TTTCCCTTGAAATAAA
1 TCTCTCTTGAAATAAA
3143861 TTGTATGAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 2 0.03
66 58 0.79
67 13 0.18
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (67 bp):
TCTCTCTTGAAATAAAAATTTTGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
CA
Found at i:3143909 original size:31 final size:31
Alignment explanation
Indices: 3143868--3143928 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
3143858 AAATTGTATG
* *
3143868 AAAACTTTTGAAAATGTTTCTCTTGAAACAC
1 AAAACCTTTGAAAATGTTTCCCTTGAAACAC
* *
3143899 AAAACCTTTGAGATTGTTTCCCTTGAAACA
1 AAAACCTTTGAAAATGTTTCCCTTGAAACA
3143929 AATTTCGTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (31 bp):
AAAACCTTTGAAAATGTTTCCCTTGAAACAC
Found at i:3143966 original size:67 final size:67
Alignment explanation
Indices: 3143883--3144069 Score: 230
Period size: 67 Copynumber: 2.7 Consensus size: 67
3143873 TTTTGAAAAT
* *
3143883 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGATA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
3143948 CA
66 CA
* * * *
3143950 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCCTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAG
* *
3144015 GCT
65 ACA
* * * * *
3144018 GTTTCTCATGAAACAACATATATCTTTAAGATCGTTTCCCTTGAAACGAATT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATT
3144070 CTGTCTTTTT
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
67 41 0.41
68 31 0.31
69 7 0.07
70 22 0.22
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
CA
Found at i:3144647 original size:107 final size:105
Alignment explanation
Indices: 3144385--3144647 Score: 325
Period size: 106 Copynumber: 2.5 Consensus size: 105
3144375 CAGGTTTTAG
* *
3144385 CTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
1 CTAGAGCCAATTTCAACTTCAC-ACGAAGGATATTGGACTCGAGACAGCACAAGTTCAACTTCAC
**
3144450 AACGAAGGGACAGCTGGTTGTCAACAAACAATTTCCCAATT
65 AACGAAGGGACAGCTGACTGTCAACAAACAATTTCCCAATT
* * **
3144491 -TCGGAGCCAATTTCAACTTCACATTGAAGGGCATTGGACTCGAGACAGCACAAGTTCAACTTCA
1 CT-AGAGCCAATTTCAACTTCACA-CGAAGGATATTGGACTCGAGACAGCACAAGTTCAACTTCA
* * *
3144555 CAACGAAGGGACGGCTGACTGTCAACAAAACAATTTCCGAGTT
64 CAACGAAGGGACAGCTGACTGTCAAC-AAACAATTTCCCAATT
* *
3144598 CTAGAACCAACTTCAACTTCACGACAGAA-GATATTGGACTCG-GAACAGCA
1 CTAGAGCCAATTTCAACTTCAC-AC-GAAGGATATTGGACTCGAG-ACAGCA
3144648 GGACCTGCAT
Statistics
Matches: 133, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
105 2 0.02
106 78 0.59
107 48 0.36
108 5 0.04
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (105 bp):
CTAGAGCCAATTTCAACTTCACACGAAGGATATTGGACTCGAGACAGCACAAGTTCAACTTCACA
ACGAAGGGACAGCTGACTGTCAACAAACAATTTCCCAATT
Found at i:3146039 original size:23 final size:22
Alignment explanation
Indices: 3145991--3146050 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
3145981 TTCGAATTAT
* *
3145991 TTATAT-TATATTATATTTTTTC
1 TTATATATATA-TATATTATGTC
3146013 TTATATATATATATATTATGTC
1 TTATATATATATATATTATGTC
* *
3146035 ATTATTTATATGTATA
1 -TTATATATATATATA
3146051 AGCAGAGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (22 bp):
TTATATATATATATATTATGTC
Found at i:3146159 original size:20 final size:21
Alignment explanation
Indices: 3146109--3146159 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
3146099 TTATATTTTG
*
3146109 TTCTATATGTTTCTATATATAT
1 TTCT-TATTTTTCTATATATAT
3146131 TTCTTATTTTTCTAT-TATTAT
1 TTCTTATTTTTCTATATA-TAT
3146152 TT-TTATTT
1 TTCTTATTT
3146160 AATACTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 15 0.56
22 4 0.15
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.69
Consensus pattern (21 bp):
TTCTTATTTTTCTATATATAT
Found at i:3155441 original size:36 final size:36
Alignment explanation
Indices: 3155394--3155469 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
3155384 AGAGAGAGAG
*
3155394 AGCTAAAAAGCTCTTTCTTTCTCTCTCTGTACAAGA
1 AGCTAAAAAGCTCTTTCTTTCTCTCTCTGTACAAAA
3155430 AGCTAAAAAGCTCTTTCTTTCTCTCTCTGTACAAAA
1 AGCTAAAAAGCTCTTTCTTTCTCTCTCTGTACAAAA
3155466 AGCT
1 AGCT
3155470 GAAAGTAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.36
Consensus pattern (36 bp):
AGCTAAAAAGCTCTTTCTTTCTCTCTCTGTACAAAA
Found at i:3156197 original size:43 final size:42
Alignment explanation
Indices: 3156136--3156243 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 42
3156126 TCCGACTTGA
* *
3156136 ATATATTAATATT-TTAAAATAATATATTTTATAATTATTTATT
1 ATATTTTAA-ATTATTAAAATAATATATTTTATAATAATTT-TT
*
3156179 ATATTTTAAATTATTAAAATAAAATATTTTATAATAATTTTT
1 ATATTTTAAATTATTAAAATAATATATTTTATAATAATTTTT
*
3156221 AT-TTTT-AATAATT-AAATAATATA
1 ATATTTTAAATTATTAAAATAATATA
3156244 ATTAAATAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
39 9 0.15
40 6 0.10
41 4 0.07
42 7 0.12
43 33 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (42 bp):
ATATTTTAAATTATTAAAATAATATATTTTATAATAATTTTT
Found at i:3156244 original size:13 final size:13
Alignment explanation
Indices: 3156228--3156257 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3156218 TTTATTTTTA
3156228 ATAATTAAATAAT
1 ATAATTAAATAAT
3156241 ATAATTAAATAAT
1 ATAATTAAATAAT
3156254 ATAA
1 ATAA
3156258 AAATAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATTAAATAAT
Found at i:3156253 original size:21 final size:21
Alignment explanation
Indices: 3156227--3156267 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3156217 TTTTATTTTT
*
3156227 AATAAT-TAAATAATATAATTA
1 AATAATATAAA-AATAAAATTA
3156248 AATAATATAAAAATAAAATT
1 AATAATATAAAAATAAAATT
3156268 TTAAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AATAATATAAAAATAAAATTA
Found at i:3156254 original size:40 final size:43
Alignment explanation
Indices: 3156149--3156243 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 43
3156139 TATTAATATT
* *
3156149 TTAAAATAATATATTTTATAATTATTTATTATATTTTAAATTA
1 TTAAAATAATATATTTTATAATAATTTATTATATTTTAAATAA
*
3156192 TTAAAATAAAATATTTTATAATAATTT-TTAT-TTTT-AATAA
1 TTAAAATAATATATTTTATAATAATTTATTATATTTTAAATAA
3156232 TT-AAATAATATA
1 TTAAAATAATATA
3156244 ATTAAATAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
39 9 0.19
40 6 0.12
41 4 0.08
42 4 0.08
43 25 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (43 bp):
TTAAAATAATATATTTTATAATAATTTATTATATTTTAAATAA
Found at i:3156842 original size:2 final size:2
Alignment explanation
Indices: 3156796--3156825 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3156786 TTATTTATCA
3156796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3156826 TTTAAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3157700 original size:18 final size:20
Alignment explanation
Indices: 3157660--3157703 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
3157650 ATGTAATTGC
3157660 AATTATATATGATATTCTCA
1 AATTATATATGATATTCTCA
* *
3157680 AATTATA-ATTATATT-TTA
1 AATTATATATGATATTCTCA
3157698 AATTAT
1 AATTAT
3157704 TTTTTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 7 0.32
20 7 0.32
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (20 bp):
AATTATATATGATATTCTCA
Found at i:3157747 original size:59 final size:59
Alignment explanation
Indices: 3157674--3157790 Score: 148
Period size: 59 Copynumber: 2.0 Consensus size: 59
3157664 ATATATGATA
* * * *
3157674 TTCTCAAATTATAATTATATTTTAAATTATTTTTTTAA-TTTTAAAATATTTTATATCAGT
1 TTCTCAAACTATAATTATATTCTAAATTA--ATTTTAATTTTTAAAATATTTTACATCAGT
*
3157734 TTCT-AAACTATAATTGTATTCTAAATTAATTTTAATTTTTTAAAATATTTTACATCA
1 TTCTCAAACTATAATTATATTCTAAATTAATTTTAA-TTTTTAAAATATTTTACATCA
3157791 ATACTTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
57 6 0.12
59 40 0.80
60 4 0.08
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.54
Consensus pattern (59 bp):
TTCTCAAACTATAATTATATTCTAAATTAATTTTAATTTTTAAAATATTTTACATCAGT
Found at i:3159182 original size:34 final size:33
Alignment explanation
Indices: 3159118--3159182 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
3159108 TAATTTTTTT
**
3159118 TAAAAAATTATTTATTATAAATGTTAAATATAA
1 TAAAAAATTATTTATTATAAAAATTAAATATAA
*
3159151 TAAAAATATTATTTATTATAAAAATTTAATAT
1 TAAAAA-ATTATTTATTATAAAAATTAAATAT
3159183 TATTATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 6 0.21
34 22 0.79
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (33 bp):
TAAAAAATTATTTATTATAAAAATTAAATATAA
Found at i:3159185 original size:19 final size:18
Alignment explanation
Indices: 3159118--3159188 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
3159108 TAATTTTTTT
3159118 TAAAAA-ATTATTTATTA
1 TAAAAATATTATTTATTA
* ** *
3159135 T--AAATGTTAAATATAA
1 TAAAAATATTATTTATTA
3159151 TAAAAATATTATTTATTA
1 TAAAAATATTATTTATTA
3159169 TAAAAAT-TTAATATTATTA
1 TAAAAATATT-AT-TTATTA
3159188 T
1 T
3159189 TATTTAAATA
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
15 3 0.07
16 8 0.20
17 3 0.07
18 20 0.49
19 7 0.17
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (18 bp):
TAAAAATATTATTTATTA
Found at i:3159263 original size:14 final size:14
Alignment explanation
Indices: 3159228--3159290 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
3159218 ATTATATGTC
3159228 AATATTATTATTAA
1 AATATTATTATTAA
*
3159242 AATATTATTTTTATA
1 AATATTATTATTA-A
* *
3159257 AAT-TTATAAATAAA
1 AATATTAT-TATTAA
**
3159271 AATATTAAAATTAA
1 AATATTATTATTAA
3159285 AATATT
1 AATATT
3159291 CTATTGAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
14 31 0.77
15 9 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:3159295 original size:19 final size:19
Alignment explanation
Indices: 3159272--3159315 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3159262 ATAAATAAAA
*
3159272 ATATTAAAATTAAAATATT
1 ATATTAAAATAAAAATATT
* *
3159291 CTATTGAAATAAAAATATT
1 ATATTAAAATAAAAATATT
3159310 ATATTA
1 ATATTA
3159316 TATTTTTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATTAAAATAAAAATATT
Found at i:3159572 original size:17 final size:17
Alignment explanation
Indices: 3159552--3159584 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3159542 TTAAAAATAT
3159552 TAATTAATATTTTTTAA
1 TAATTAATATTTTTTAA
3159569 TAATTAATATTTTTTA
1 TAATTAATATTTTTTA
3159585 TTAAAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTAATATTTTTTAA
Found at i:3160631 original size:20 final size:20
Alignment explanation
Indices: 3160601--3160652 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3160591 CTCTATAACT
* *
3160601 TAAACCTTAAATAAAATCTC
1 TAAACCCTAAATAAAACCTC
*
3160621 TAAACTCTAAATAAAACCTC
1 TAAACCCTAAATAAAACCTC
*
3160641 TCAACCCTAAAT
1 TAAACCCTAAAT
3160653 TTAACAGGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAACCCTAAATAAAACCTC
Found at i:3163979 original size:165 final size:166
Alignment explanation
Indices: 3163706--3164036 Score: 655
Period size: 165 Copynumber: 2.0 Consensus size: 166
3163696 TACATTAAGA
3163706 ACACGTCCTTTAACTCTTTCTTGAATCCCCATAAAGGGTAATCTTCAATAATGATTATCAACTCG
1 ACACGTCCTTTAACTCTTTCTTGAATCCCCATAAAGGGTAATCTTCAATAATGATTATCAACTCG
3163771 CAATTGAATTTAAACCTTATCCAAATTTGGATGTACGAAATACCTTAACCTCACATTGATAAGGT
66 CAATTGAATTTAAACCTTATCCAAATTTGGATGTACGAAATACCTTAACCTCACATTGATAAGGT
3163836 CATCATAAGTATCAGTTTTGTTCATGATTCTATCAC
131 CATCATAAGTATCAGTTTTGTTCATGATTCTATCAC
3163872 ACACGTCCTTTAACTCTTTCTTGAAT-CCCATAAAGGGTAATCTTCAATAATGATTATCAACTCG
1 ACACGTCCTTTAACTCTTTCTTGAATCCCCATAAAGGGTAATCTTCAATAATGATTATCAACTCG
3163936 CAATTGAATTTAAACCTTATCCAAATTTGGATGTACGAAATACCTTAACCTCACATTGATAAGGT
66 CAATTGAATTTAAACCTTATCCAAATTTGGATGTACGAAATACCTTAACCTCACATTGATAAGGT
3164001 CATCATAAGTATCAGTTTTGTTCATGATTCTATCAC
131 CATCATAAGTATCAGTTTTGTTCATGATTCTATCAC
3164037 CACAAGGAAT
Statistics
Matches: 165, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
165 139 0.84
166 26 0.16
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (166 bp):
ACACGTCCTTTAACTCTTTCTTGAATCCCCATAAAGGGTAATCTTCAATAATGATTATCAACTCG
CAATTGAATTTAAACCTTATCCAAATTTGGATGTACGAAATACCTTAACCTCACATTGATAAGGT
CATCATAAGTATCAGTTTTGTTCATGATTCTATCAC
Found at i:3165795 original size:111 final size:112
Alignment explanation
Indices: 3165444--3165855 Score: 630
Period size: 112 Copynumber: 3.7 Consensus size: 112
3165434 TTGTCGTTTT
** *
3165444 GTGTCGATACTTTATAAAAATATATTAATCCATAATAATATAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
*
3165509 CGATCTATAAATGA-AAAACAGGTAAAGCGCTACCGGATATATTGAAA
65 CGATCTATAAATGACAAAACAGGTAAAGCACTACCGGATATATTGAAA
*
3165556 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
3165621 GGTCTATAAATGACAAAACAAGTAAAGCACTACCAGATATATTGAAA
66 GATCTATAAATGACAAAACAGGTAAAGCACTACCGGATATATTGAAA
* * *
3165668 GTGTCGATACTATATAAAAATGTATTGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
3165732 GATCTATAAATGACAAAACAGGTAAACCTCTATCGGATATATTGAAA
66 GATCTATAAATGACAAAACAGGTAAAGCACTACCGGATATATTGAAA
* * * *
3165779 GTGTCAATACTTTATAAAAATATATCGATCCATAACAATATAATAGGTAAACAAATGACAAAACT
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
3165844 GGTCTATAAATG
66 GATCTATAAATG
3165856 TTGAACTTTG
Statistics
Matches: 272, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
111 127 0.47
112 145 0.53
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GATCTATAAATGACAAAACAGGTAAAGCACTACCGGATATATTGAAA
Found at i:3165837 original size:223 final size:223
Alignment explanation
Indices: 3165444--3165855 Score: 693
Period size: 223 Copynumber: 1.8 Consensus size: 223
3165434 TTGTCGTTTT
* *
3165444 GTGTCGATACTTTATAAAAATATATTAATCCATAATAATATAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTATATAAAAATATATTAATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
* *
3165509 CGATCTATAAATGAAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
65 CGATCTATAAATGAAAAACAGGTAAACCGCTACCGGATATATTGAAAGTGTCAATACTTTATAAA
3165574 AATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAA-TCGGTCTATAAATGACAAA
130 AATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACT-GGTCTATAAATGACAAA
3165638 ACAAGTAAAGCACTACCAGATATATTGAAA
194 ACAAGTAAAGCACTACCAGATATATTGAAA
* *
3165668 GTGTCGATACTATATAAAAATGTATTGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTATATAAAAATATATTAATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
3165732 GATCTATAAATGACAAAACAGGTAAACCTCTATCGGATATATTGAAAGTGTCAATACTTTATAAA
66 GATCTATAAATGA-AAAACAGGTAAACCGCTACCGGATATATTGAAAGTGTCAATACTTTATAAA
* *
3165797 AATATATCGATCCATAACAATATAATAGGTAAACAAATGACAAAACTGGTCTATAAATG
130 AATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACTGGTCTATAAATG
3165856 TTGAACTTTG
Statistics
Matches: 176, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
222 29 0.16
223 102 0.58
224 45 0.26
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (223 bp):
GTGTCGATACTATATAAAAATATATTAATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GATCTATAAATGAAAAACAGGTAAACCGCTACCGGATATATTGAAAGTGTCAATACTTTATAAAA
ATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACTGGTCTATAAATGACAAAAC
AAGTAAAGCACTACCAGATATATTGAAA
Found at i:3171009 original size:182 final size:182
Alignment explanation
Indices: 3170689--3171063 Score: 617
Period size: 182 Copynumber: 2.1 Consensus size: 182
3170679 AGTTAACAAT
* *
3170689 AAATGACAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTATTACAAGTATC
1 AAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTACAAGTATC
* ** * *
3170754 GACACTTTTGGAATTTAAAAAAGAAGAAGTTATAGTGCTAATAAAGTGTCGATACTTAATAAAAA
66 GACACTTTTGGAATTTAAAAAAGAAGAAGTTACAACGCCAATAAAGTGTCGATACTTAAGAAAAA
*
3170819 TATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCG
131 TATATCGATCCATAACAATATAACAAGTAAAAATATGACAAAATCGGTCTCG
* * *
3170871 AAATGACAAAACCGGTAAAGAGTTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATC
1 AAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTACAAGTATC
*
3170936 GACACTTTTGGAATTTAAAAGAA-AAGAAGTTACAACGCCAATAAAGTGTCGATACTTTAGAAAA
66 GACACTTTTGGAATTTAAAA-AAGAAGAAGTTACAACGCCAATAAAGTGTCGATACTTAAGAAAA
*
3171000 ATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAATCGGTCTCG
130 ATATATCGATCCATAACAATATAACAAGTAAAAATATGACAAAATCGGTCTCG
3171053 AAATGACAAAA
1 AAATGACAAAA
3171064 TCGATAGTAA
Statistics
Matches: 179, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
182 177 0.99
183 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (182 bp):
AAATGACAAAACAGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTACAAGTATC
GACACTTTTGGAATTTAAAAAAGAAGAAGTTACAACGCCAATAAAGTGTCGATACTTAAGAAAAA
TATATCGATCCATAACAATATAACAAGTAAAAATATGACAAAATCGGTCTCG
Found at i:3176303 original size:99 final size:99
Alignment explanation
Indices: 3176123--3176303 Score: 233
Period size: 99 Copynumber: 1.8 Consensus size: 99
3176113 TGCGCCTTGG
** * * *
3176123 TGTTATGTTAACTGGTTAAGTTATAGGGTAGAACCATATATATTATAAAAACTTAAAATAAACCT
1 TGTTATGTTAACTAATTAAGTTATAGGGTAGAACCATATATATTATAAAAACGTAAAACAAACAT
*
3176188 GATTTCCTAGATAACATTATATGTTGCACCTTTT
66 GATTTCCTAGAAAACATTATATGTTGCACCTTTT
* *
3176222 TGTTATGTTAACTAATTAAGTTATA-GGTTGAAACCATGTATATTATGAAAAA-GTAAAACAAAC
1 TGTTATGTTAACTAATTAAGTTATAGGGTAG-AACCATATATATTAT-AAAAACGTAAAACAAAC
*
3176285 ATGGTTTCCTA-ACAAACAT
64 ATGATTTCCTAGA-AAACAT
3176304 GGTTTCCTAG
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
98 5 0.07
99 60 0.86
100 5 0.07
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (99 bp):
TGTTATGTTAACTAATTAAGTTATAGGGTAGAACCATATATATTATAAAAACGTAAAACAAACAT
GATTTCCTAGAAAACATTATATGTTGCACCTTTT
Found at i:3176320 original size:17 final size:17
Alignment explanation
Indices: 3176278--3176312 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3176268 GAAAAAGTAA
3176278 AACAAACATGGTTTCCT
1 AACAAACATGGTTTCCT
3176295 AACAAACATGGTTTCCT
1 AACAAACATGGTTTCCT
3176312 A
1 A
3176313 GATAACATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (17 bp):
AACAAACATGGTTTCCT
Found at i:3178349 original size:101 final size:101
Alignment explanation
Indices: 3178189--3178379 Score: 242
Period size: 101 Copynumber: 1.9 Consensus size: 101
3178179 AAACCATTTT
* * * * *
3178189 TATTATGCAAAACTAAGGAAAAACATGTTTATATGTATAACTTTATAGGTAGCATCTTTTTTAAT
1 TATTATACAAAACTAAGGAAAAACATGTTTAAAAGTATAACATTATAGGTAGCACCTTTTTTAAT
* *
3178254 TATCAACCGTTTACG-TTATTTGTTTGGAACCTTCTA
66 TATCAACC-ATTAAGATTATTTGTTTGGAACCTTCTA
* * * *
3178290 TATTATACAAAAGTAA-GACAAAACATGTTTAAAAGTATATCATTGTAGGTTGCACCTTTTTTAA
1 TATTATACAAAACTAAGGA-AAAACATGTTTAAAAGTATAACATTATAGGTAGCACCTTTTTTAA
*
3178354 TTGTCAACCATTAAGATTATTTGTTT
65 TTATCAACCATTAAGATTATTTGTTT
3178380 CAAACTGTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
100 6 0.08
101 70 0.92
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (101 bp):
TATTATACAAAACTAAGGAAAAACATGTTTAAAAGTATAACATTATAGGTAGCACCTTTTTTAAT
TATCAACCATTAAGATTATTTGTTTGGAACCTTCTA
Found at i:3178395 original size:101 final size:101
Alignment explanation
Indices: 3178168--3178396 Score: 232
Period size: 101 Copynumber: 2.3 Consensus size: 101
3178158 AAAAATATGT
* * * * * *
3178168 TTATATGTTTG-AAACCATTTTTATTATGCAAAACTAAGGAAAAACATGTTTATATGTATAACTT
1 TTATTTGTTTGCAAA-CTTTTTTATTATACAAAACTAAGGAAAAACATGTTTAAAAGTATAACAT
* * *
3178232 TATAGGTAGCATCTTTTTTAATTATCAACCGTTTACG
65 TATAGGTAGCACCTTTTTTAATTATCAACCGATTAAG
* * * * * *
3178269 TTATTTGTTTGGAACCTTCTATATTATACAAAAGTAA-GACAAAACATGTTTAAAAGTATATCAT
1 TTATTTGTTTGCAAACTTTTTTATTATACAAAACTAAGGA-AAAACATGTTTAAAAGTATAACAT
* * *
3178333 TGTAGGTTGCACCTTTTTTAATTGTCAACC-ATTAAG
65 TATAGGTAGCACCTTTTTTAATTATCAACCGATTAAG
3178369 ATTATTTGTTT-CAAACTGTTTTTATTAT
1 -TTATTTGTTTGCAAACT-TTTTTATTAT
3178397 GTAACAATAA
Statistics
Matches: 103, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
100 10 0.10
101 91 0.88
102 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (101 bp):
TTATTTGTTTGCAAACTTTTTTATTATACAAAACTAAGGAAAAACATGTTTAAAAGTATAACATT
ATAGGTAGCACCTTTTTTAATTATCAACCGATTAAG
Found at i:3179906 original size:19 final size:17
Alignment explanation
Indices: 3179884--3179918 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
3179874 TATTATATAA
3179884 TAAAATTATAATATTAAAG
1 TAAAATTA-AA-ATTAAAG
3179903 TAAAATTAAAATTAAA
1 TAAAATTAAAATTAAA
3179919 TATAAACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
TAAAATTAAAATTAAAG
Found at i:3195710 original size:26 final size:25
Alignment explanation
Indices: 3195681--3195753 Score: 96
Period size: 24 Copynumber: 2.9 Consensus size: 25
3195671 TAAAATTCAT
3195681 AATATTTTATATATATTAACTTAAAA
1 AATATTTT-TATATATTAACTTAAAA
**
3195707 AATATTTTT-TATATTAACTTATTA
1 AATATTTTTATATATTAACTTAAAA
3195731 AATATATTTTAT-TATTAACTTAA
1 AATAT-TTTTATATATTAACTTAA
3195754 TTTAAAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
24 18 0.43
25 15 0.36
26 9 0.21
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (25 bp):
AATATTTTTATATATTAACTTAAAA
Found at i:3195763 original size:26 final size:25
Alignment explanation
Indices: 3195694--3195769 Score: 95
Period size: 26 Copynumber: 3.0 Consensus size: 25
3195684 ATTTTATATA
*
3195694 TATTAACTTAA--AAAATATTTTTT
1 TATTAACTTAATTAAAATATTTTAT
3195717 ATATTAACTT-ATTAAATATATTTTAT
1 -TATTAACTTAATTAAA-ATATTTTAT
3195743 TATTAACTTAATTTAAAATATTTTAT
1 TATTAACTTAA-TTAAAATATTTTAT
3195769 T
1 T
3195770 TTTATTTTCG
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
23 1 0.02
24 9 0.20
25 12 0.26
26 19 0.41
27 5 0.11
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTAACTTAATTAAAATATTTTAT
Found at i:3195995 original size:31 final size:31
Alignment explanation
Indices: 3195928--3195995 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
3195918 TGATGACCAC
* * *
3195928 ATCTTAATTAGATAAAAACAAAAGTGGCCAT
1 ATCTTAATTAAATAAAAACAAAAGTGACAAT
* **
3195959 GTCTTAATTAAATAAAAATGAAAGTGACAAT
1 ATCTTAATTAAATAAAAACAAAAGTGACAAT
3195990 ATCTTA
1 ATCTTA
3195996 TGTTTTTTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTGACAAT
Found at i:3199671 original size:39 final size:39
Alignment explanation
Indices: 3199628--3199894 Score: 207
Period size: 38 Copynumber: 7.3 Consensus size: 39
3199618 TACAAATGGT
* *
3199628 TTTTGAAAATACATATATAATATATAGTTTCTAAAAACA
1 TTTTGAAAATACTTATATAATATATAGTTTTTAAAAACA
* * *
3199667 TTTTGACAAT--GTATATAATGTATAGTTTTT-AAAACA
1 TTTTGAAAATACTTATATAATATATAGTTTTTAAAAACA
*
3199703 CTTTG-AAA-AC---TAT-ATA-ATAG--TTT-AAAACA
1 TTTTGAAAATACTTATATAATATATAGTTTTTAAAAACA
*
3199732 TTTT-AGAAATA--TATATAATATATAGTTTTTAAAATCA
1 TTTTGA-AAATACTTATATAATATATAGTTTTTAAAAACA
*
3199769 TTTTGAAAGAT--TTATATAATATATAGTTTTTGAAAACA
1 TTTTGAAA-ATACTTATATAATATATAGTTTTTAAAAACA
** * * *
3199807 TTTTTTTAAA-ACTTATATAATATATATTTTTTGAAAATA
1 -TTTTGAAAATACTTATATAATATATAGTTTTTAAAAACA
* *
3199846 TTTT-TAAA-ACTTATATAATATATAATTTTTTAAAAACA
1 TTTTGAAAATACTTATATAATATAT-AGTTTTTAAAAACA
3199884 TTTTAGAAAAT
1 TTTT-GAAAAT
3199895 TATATAGTTT
Statistics
Matches: 188, Mismatches: 18, Indels: 42
0.76 0.07 0.17
Matches are distributed among these distances:
29 12 0.06
30 3 0.02
31 5 0.03
32 5 0.03
33 6 0.03
34 4 0.02
35 2 0.01
36 13 0.07
37 47 0.25
38 48 0.26
39 40 0.21
40 3 0.02
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (39 bp):
TTTTGAAAATACTTATATAATATATAGTTTTTAAAAACA
Found at i:3199682 original size:37 final size:36
Alignment explanation
Indices: 3199641--3199900 Score: 241
Period size: 37 Copynumber: 7.2 Consensus size: 36
3199631 TGAAAATACA
* *
3199641 TATATAATATATAGTTTCTAAAAACATTTTGACAAT
1 TATATAATATATAGTTTTTAAAAACATTTTGAAAAT
* *
3199677 GTATATAATGTATAGTTTTT-AAAACACTTTGAAAA-
1 -TATATAATATATAGTTTTTAAAAACATTTTGAAAAT
*
3199712 -CTAT-ATA-ATAG--TTT-AAAACATTTT-AGAAAT
1 TATATAATATATAGTTTTTAAAAACATTTTGA-AAAT
*
3199742 ATATATAATATATAGTTTTTAAAATCATTTTGAAAGATT
1 -TATATAATATATAGTTTTTAAAAACATTTTGAAA-A-T
* *
3199781 TATATAATATATAGTTTTTGAAAACATTTTTTTAAAACT
1 TATATAATATATAGTTTTTAAAAACA--TTTTGAAAA-T
* * * *
3199820 TATATAATATATATTTTTTGAAAATATTTTTAAAACT
1 TATATAATATATAGTTTTTAAAAACATTTTGAAAA-T
*
3199857 TATATAATATATAATTTTTTAAAAACATTTTAGAAAAT
1 TATATAATATAT-AGTTTTTAAAAACATTTT-GAAAAT
3199895 TATATA
1 TATATA
3199901 GTTTTAAAAA
Statistics
Matches: 189, Mismatches: 18, Indels: 31
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.01
29 15 0.08
31 4 0.02
32 5 0.03
33 6 0.03
34 4 0.02
36 16 0.08
37 51 0.27
38 49 0.26
39 31 0.16
40 7 0.04
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAAACATTTTGAAAAT
Found at i:3199729 original size:29 final size:30
Alignment explanation
Indices: 3199694--3199751 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3199684 ATGTATAGTT
3199694 TTTAAAACACTTT-GAAA-ACTATATAATAG
1 TTTAAAACACTTTAGAAATA-TATATAATAG
*
3199723 TTTAAAACATTTTAGAAATATATATAATA
1 TTTAAAACACTTTAGAAATATATATAATA
3199752 TATAGTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.46
30 13 0.50
31 1 0.04
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (30 bp):
TTTAAAACACTTTAGAAATATATATAATAG
Found at i:3199953 original size:28 final size:30
Alignment explanation
Indices: 3199862--3199958 Score: 101
Period size: 31 Copynumber: 3.3 Consensus size: 30
3199852 AAACTTATAT
* ** *
3199862 AATATATAATTTTTTAAAAACATTTTAGAA
1 AATATATAGTTTTAAAAAAACATTTTTGAA
*
3199892 AATTATATAGTTTTAAAAAAACAAATTTTG-A
1 AA-TATATAGTTTTAAAAAAAC-ATTTTTGAA
3199923 AATATATAG-TTT-AAAAAACATTTTTGAA
1 AATATATAGTTTTAAAAAAACATTTTTGAA
*
3199951 AATTTATA
1 AATATATA
3199959 TACAATATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
27 6 0.11
28 15 0.26
29 3 0.05
30 9 0.16
31 19 0.33
32 5 0.09
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (30 bp):
AATATATAGTTTTAAAAAAACATTTTTGAA
Found at i:3199959 original size:30 final size:31
Alignment explanation
Indices: 3199877--3199960 Score: 104
Period size: 30 Copynumber: 2.8 Consensus size: 31
3199867 ATAATTTTTT
*
3199877 AAAAACATTTTAGAAAATTATATAGTTTTAA
1 AAAAACATTTTTGAAAATTATATAGTTTTAA
*
3199908 AAAAACAAATTTTG-AAA-TATATAG-TTT-A
1 AAAAAC-ATTTTTGAAAATTATATAGTTTTAA
3199936 AAAAACATTTTTGAAAATTTATATA
1 AAAAACATTTTTGAAAA-TTATATA
3199961 CAATATATAG
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 6 0.13
28 10 0.22
29 3 0.07
30 13 0.28
31 9 0.20
32 5 0.11
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (31 bp):
AAAAACATTTTTGAAAATTATATAGTTTTAA
Found at i:3199967 original size:39 final size:41
Alignment explanation
Indices: 3199923--3200018 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
3199913 CAAATTTTGA
3199923 AATATATAG-TTT-AAAAAACATTTTT-GAAAATTTATATAC
1 AATATATAGTTTTAAAAAAACATTTTTAG-AAATTTATATAC
3199962 AATATATAGTTTTAAAAAAACATTTTTAGAAATTTATAT--
1 AATATATAGTTTTAAAAAAACATTTTTAGAAATTTATATAC
3200001 --TATATAGTTTTAAAAAAA
1 AATATATAGTTTTAAAAAAA
3200019 ATACTTTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
37 18 0.33
39 9 0.17
40 3 0.06
41 23 0.43
42 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (41 bp):
AATATATAGTTTTAAAAAAACATTTTTAGAAATTTATATAC
Found at i:3201354 original size:13 final size:12
Alignment explanation
Indices: 3201328--3201372 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
3201318 ACATATATAT
3201328 TATTTATTTTTTA
1 TATTT-TTTTTTA
3201341 TATTTTTTTCTTA
1 TATTTTTTT-TTA
*
3201354 T-TATTTTTTTA
1 TATTTTTTTTTA
3201365 TATTTTTT
1 TATTTTTT
3201373 CTTTCAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 4 0.14
12 15 0.54
13 9 0.32
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (12 bp):
TATTTTTTTTTA
Found at i:3201360 original size:14 final size:13
Alignment explanation
Indices: 3201325--3201372 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
3201315 TATACATATA
3201325 TATTATTTATTTTT
1 TATTATTT-TTTTT
3201339 TA-TATTTTTTTCT
1 TATTATTTTTTT-T
*
3201352 TATTATTTTTTTA
1 TATTATTTTTTTT
3201365 TATT-TTTT
1 TATTATTTT
3201373 CTTTCAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 8 0.26
13 12 0.39
14 11 0.35
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (13 bp):
TATTATTTTTTTT
Found at i:3201433 original size:1 final size:1
Alignment explanation
Indices: 3201427--3201490 Score: 65
Period size: 1 Copynumber: 64.0 Consensus size: 1
3201417 TCTTTAATAG
* ** * * * *
3201427 TTTTTTTATTTTTCATTTTTTTTTTTTTTTTTTATTTTTTTTTCTGTTTTATTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3201491 ATATGTATTA
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.06, C:0.03, G:0.02, T:0.89
Consensus pattern (1 bp):
T
Found at i:3201451 original size:19 final size:17
Alignment explanation
Indices: 3201444--3201490 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
3201434 ATTTTTCATT
3201444 TTTTTTTTTTTTTTTTA
1 TTTTTTTTTTTTTTTTA
* *
3201461 TTTTTTTTTCTGTTTTA
1 TTTTTTTTTTTTTTTTA
3201478 TTTTTTTTTTTTT
1 TTTTTTTTTTTTT
3201491 ATATGTATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.04, C:0.02, G:0.02, T:0.91
Consensus pattern (17 bp):
TTTTTTTTTTTTTTTTA
Found at i:3201463 original size:26 final size:26
Alignment explanation
Indices: 3201427--3201490 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
3201417 TCTTTAATAG
*
3201427 TTTTTTTATTTTTCATTTT-T-TTTTTT
1 TTTTTTTATTTTT--TTTTCTGTTTTAT
3201453 TTTTTTTATTTTTTTTTCTGTTTTAT
1 TTTTTTTATTTTTTTTTCTGTTTTAT
3201479 TTTTTTT-TTTTT
1 TTTTTTTATTTTT
3201491 ATATGTATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 4 0.11
25 6 0.17
26 25 0.71
ACGTcount: A:0.06, C:0.03, G:0.02, T:0.89
Consensus pattern (26 bp):
TTTTTTTATTTTTTTTTCTGTTTTAT
Found at i:3201492 original size:31 final size:31
Alignment explanation
Indices: 3201430--3201488 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
3201420 TTAATAGTTT
* *
3201430 TTTTATTTTTCATTTTTTTTTTTTTTTTTTA
1 TTTTATTTTTCATGTTTTATTTTTTTTTTTA
3201461 TTTT-TTTTTC-TGTTTTATTTTTTTTTTT
1 TTTTATTTTTCATGTTTTATTTTTTTTTTT
3201489 TTATATGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 16 0.62
30 6 0.23
31 4 0.15
ACGTcount: A:0.07, C:0.03, G:0.02, T:0.88
Consensus pattern (31 bp):
TTTTATTTTTCATGTTTTATTTTTTTTTTTA
Found at i:3201499 original size:20 final size:19
Alignment explanation
Indices: 3201427--3201490 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
3201417 TCTTTAATAG
* *
3201427 TTTTTTTATTTTTCATTTT
1 TTTTTTTTTTTTTTATTTT
3201446 TTTTTTTTTTTTTTA--TT
1 TTTTTTTTTTTTTTATTTT
* *
3201463 TTTTTTTCTGTTTTATTTT
1 TTTTTTTTTTTTTTATTTT
3201482 TTTTTTTTT
1 TTTTTTTTT
3201491 ATATGTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
17 15 0.39
19 23 0.61
ACGTcount: A:0.06, C:0.03, G:0.02, T:0.89
Consensus pattern (19 bp):
TTTTTTTTTTTTTTATTTT
Found at i:3204110 original size:23 final size:23
Alignment explanation
Indices: 3204080--3204130 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
3204070 GCTCGTTAAA
*
3204080 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACATAGAAT
*
3204103 TGCACCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
3204126 TGCAC
1 TGCAC
3204131 TGTAGTACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:3204284 original size:101 final size:100
Alignment explanation
Indices: 3204156--3204367 Score: 329
Period size: 100 Copynumber: 2.1 Consensus size: 100
3204146 TAATGTCCAT
*
3204156 AAGGA-CACATATCATTCCTAAGAATCATATACATATGCCAAGGG-TCAAGTATGTGTCTCCAAA
1 AAGGACCACATATCATTCCTAAGAATCATATACATAT-ACAAGGGATCAAGTATGTGTCT-CAAA
3204219 AGACCTCACACATGTTCCAAAGAATACATATGTCCCG
64 AGACCTCACACATGTTCCAAAGAATACATATGTCCCG
* * **
3204256 AATGACCACATATCATTCCTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACTAG
1 AAGGACCACATATCATTCCTAAGAATCATATACATATACAAGGGATCAAGTATGTGTCTCAAAAG
* *
3204321 ACTTCACACATGTTCCAAAGAATACATATGTTCCG
66 ACCTCACACATGTTCCAAAGAATACATATGTCCCG
3204356 AAGGACCACATA
1 AAGGACCACATA
3204368 GACCCTCGAC
Statistics
Matches: 102, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
100 57 0.56
101 45 0.44
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (100 bp):
AAGGACCACATATCATTCCTAAGAATCATATACATATACAAGGGATCAAGTATGTGTCTCAAAAG
ACCTCACACATGTTCCAAAGAATACATATGTCCCG
Found at i:3208388 original size:84 final size:83
Alignment explanation
Indices: 3208233--3209607 Score: 1180
Period size: 84 Copynumber: 16.7 Consensus size: 83
3208223 TTTAAGACAA
* * * * *
3208233 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA-CAAAGACCTTCGAGTTCGACCAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTAC
3208297 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * * * *
3208316 CATTTGCAACATAGCTCAAGGCAAAAAGGGCTATTTTCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTT-CAACCAAAGACCTTCGAGTTCGACTAC
* *
3208381 GTTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * * * * *
3208400 AATTTGCAGCATAGCTTAAGTCGAGAAGGGATATC-T--GCCAAAGACCTTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
* *
3208462 CTCAGCTCAAAGGCACCAG
66 CTCAGCTCCAAGGCA-CAT
* * * * *
3208481 CATTTGCAGTATAACTTAAATCGAGAAGGGTTATCTGCCGACCAAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTAC
* * *
3208546 GCTCAACTCTAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * * * ** * **
3208565 CATTTGCAGTATAGCTTAAG--G-G-A----TATC-T--GCCAAAAACCCCCGAGTTCGATTAAA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
* * *
3208619 CTCAGCTTCGAGGGAACAT
66 CTCAGC-TCCAAGGCACAT
* * *
3208638 CATTTGCAGCATAACTTAAGTCAAGAAAGGTTATCTGACAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTAC
3208703 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* ** * * * *
3208722 CATTTGCAGCATAGCTTAAGTCGAGAAGGCCTATC-T--GCCAAAGACCCTCGAGTTTGACTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
* * *
3208784 TTCAACT-TATAGGGCACAT
66 CTCAGCTCCA-A-GGCACAT
* * * * *
3208803 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTAC
*
3208867 GCTCAGCTCCAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * *
3208886 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAATACCTTCGAGTACGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTT-CAACCAAAGACCTTCGAGTTCGACTAC
3208951 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * *
3208970 CATTTGCAGCATAACTTAAGTCGATAAGGGCTATC-T--GCCAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
* *
3209032 CTCAGCTTCGAGGACACAT
66 CTCAGCTCCAAGG-CACAT
* * * * * *
3209051 CATTTACAGCATAACTCAAGGCTAGAAGGGGTATCTGTC-ACCAAAAGACCTTCGAGTTCGACCA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACC-AAAGACCTTCGAGTTCGACTA
*
3209115 CGCTCAGCTCCAAGGCATAT
64 CGCTCAGCTCCAAGGCACAT
*
3209135 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTAC
*
3209200 GTTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * * * * *
3209219 CCTTTGCAGCATAGCTTAAGTTGAGAAGGGCTATC-T--GCCAAAGACCCTCAAGTTCGATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
* *
3209281 CTCAGCTTCAAGGACACAA
66 CTCAGCTCCAAGG-CACAT
* ** * * *
3209300 CATTTACAATATAACTCAAAG-CTAGAAGGGTTATCTGTC-ACCAAAGACCTTTGAGTTCGACTA
1 CATTTGCAGCATAACT-TAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTA
*
3209363 CGCTTAGCTCCAAGGCACAT
64 CGCTCAGCTCCAAGGCACAT
* ** * * * * * * *
3209383 AATTTGCAAAATATCTTAAGTCGAGAATGGCTATC-T--GCCAAAGACCTTCGAGTTCAATTACA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
*
3209445 CTCAGCTCCGGAGGCACAT
66 CTCAGCTCC-AAGGCACAT
* * * * * * * * *
3209464 CATTTACATCATAACTCAAGACTAAAAGGGTTATCTGCCAA-CAAAGACATTCGACTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCAACCAAAGACCTTCGAGTTCGACTAC
*
3209528 GCTCAGCTCAAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
** * * * *
3209547 CATTTGCAATATAGCTTAAGTCGAGGAGGGTTAT-TTGCCTACCAAAGACTTTCGAGTTCGA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTT--CAACCAAAGACCTTCGAGTTCGA
3209608 TTTCATTCAA
Statistics
Matches: 1026, Mismatches: 218, Indels: 95
0.77 0.16 0.07
Matches are distributed among these distances:
72 23 0.02
73 26 0.03
76 5 0.00
77 1 0.00
79 1 0.00
80 157 0.15
81 164 0.16
82 9 0.01
83 140 0.14
84 406 0.40
85 94 0.09
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (83 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACAT
Found at i:3208890 original size:164 final size:164
Alignment explanation
Indices: 3208233--3209609 Score: 1307
Period size: 164 Copynumber: 8.4 Consensus size: 164
3208223 TTTAAGACAA
* * * * * ** *
3208233 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACCACG
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCTTCGAGTTCGATTACA
* * * * * * * * *
3208298 CTCAGCTCCAA-GGCACATCATTTGCAACATAGCTCAAGGCAAAAAGGGCTATTTTCCAACCAAA
63 CTCAGCT-TAAGGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAA
* *
3208362 GACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCATAT
127 GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* *
3208400 AATTTGCAGCATAGCTTAAGTCGAGAAGGGATATCTGCCAAAGACCTTCGAGTTCGATTACACTC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTC
* * * * * * *
3208465 AGCTCAAAGGCACCAGCATTTGCAGTATAACTTAAATCGAGAAGGGTTATCTGCCGACCAAAGAC
66 AGCTTAAGGGCA-CATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGAC
* * * *
3208530 CTTCGAGTTTGACTACGCTCAACTCTAAGGCATAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * ** *
3208565 CATTTGCAGTATAGCTTAAG--G-G-A----TATCTGCCAAAAACCCCCGAGTTCGATTAAACTC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTC
* * * * * *
3208622 AGCTTCGAGGGAACATCATTTGCAGCATAACTTAAGTCAAGAAAGGTTATCTGACAACCAAAGAC
66 AGCTT-AAGGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGAC
3208687 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * * *
3208722 CATTTGCAGCATAGCTTAAGTCGAGAAGGCCTATCTGCCAAAGACCCTCGAGTTTGACTACATTC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTC
* * * * * *
3208787 AACTTATAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACAAAAGAC
66 AGCTTA-AGGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGAC
*
3208851 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * * * * *
3208886 CATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAATACCTTCGAGTACGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC-T---GCCAAAGACCTTCGAGTTCGATTAC
* * * * *
3208951 GCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCGATAAGGGCTATCTG----CCAA
62 ACTCAGCT-TAAGGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAA
* * * * *
3209011 AGACCCTCGAGTTCGATTACACTCAGCTTCGAGGACACAT
126 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG-CACAT
* * * * * * **
3209051 CATTTACAGCATAACTCAAGGCTAGAAGGGGTATCTGTCACCAAAAGACCTTCGAGTTCGACCAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CC-AAAGACCTTCGAGTTCGATTAC
* * * *
3209116 GCTCAGCTCCAA-GGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAA
62 ACTCAGCT-TAAGGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAA
*
3209180 AGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACAT
126 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * *
3209219 CCTTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTC
* * * ** * *
3209284 AGCTTCAAGGACACAACATTTACAATATAACTCAAAG-CTAGAAGGGTTATCTGTC-ACCAAAGA
66 AGCTT-AAGGGCACATCATTTGCAGCATAACTC-AAGTCGAGAAGGGTTATCTGCCAACCAAAGA
* *
3209347 CCTTTGAGTTCGACTACGCTTAGCTCCAAGGCACAT
129 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* ** * * *
3209383 AATTTGCAAAATATCTTAAGTCGAGAATGGCTATCTGCCAAAGACCTTCGAGTTCAATTACACTC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTC
*** * * * * *
3209448 AGCTCCGGAGGCACATCATTTACATCATAACTCAAGACTAAAAGGGTTATCTGCCAA-CAAAGAC
66 AGCTTAAG-GGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGAC
* * *
3209512 ATTCGACTTCGACTACGCTCAGCTCAAAGGCACAT
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
** * * * *
3209547 CATTTGCAATATAGCTTAAGTCGAGGAGGGTTATTTGCCTACCAAAGACTTTCGAGTTCGATT
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTA--T--CTGCCAAAGACCTTCGAGTTCGATT
3209610 TCATTCAACT
Statistics
Matches: 1007, Mismatches: 167, Indels: 71
0.81 0.13 0.06
Matches are distributed among these distances:
157 129 0.13
158 4 0.00
159 1 0.00
160 1 0.00
161 2 0.00
162 1 0.00
163 8 0.01
164 367 0.36
165 305 0.30
166 5 0.00
167 69 0.07
168 82 0.08
169 33 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (164 bp):
CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTC
AGCTTAAGGGCACATCATTTGCAGCATAACTCAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
Found at i:3209215 original size:249 final size:247
Alignment explanation
Indices: 3208233--3209551 Score: 1410
Period size: 248 Copynumber: 5.3 Consensus size: 247
3208223 TTTAAGACAA
* * * * * * *
3208233 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACCACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTCGAGTTCGACTACA
* * * * * * * *
3208298 CTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAAAAGGGCTAT-TTTCCAACC-AA
63 CTCAGCTTCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT-C-ACCAAA
* * *
3208361 AGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCATATAATTTGCAGCATAGCTTAAGTCGAGA
126 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGA
* * * * *
3208426 AGGGATATCTG---CCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACCAG
191 AGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CAT
* * * * *
3208481 CATTTGCAGTATAACTTAAATCGAGAAGGGTTATCTGCCGACCAAAGACCTTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCT---G-CCAAAGACCCTCGAGTTCGACTAC
* * * * * *
3208546 GCTCAAC-TCTAAGGCATATCATTTGCAG--T-A-T--A-GCT-TAAGGGATATCTG---CCAAA
62 ACTCAGCTTC-AAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAA
** * ** * * * * *
3208599 A-ACCCCCGAGTTCGATTAAACTCAGCTTCGAGGGAACATCATTTGCAGCATAACTTAAGTCAAG
126 AGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAG
*
3208663 AAAGGTTATCTGACAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
190 AAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * *
3208722 CATTTGCAGCATAGCTTAAGTCGAGAAGGCCTATCTGCCAAAGACCCTCGAGTTTGACTACATTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTC
*
3208787 AACTT-ATAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA-CAAAAGA
66 AGCTTCA-A-GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGA
*
3208850 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAGCATAACTTAAGTCGAGAAGG
129 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGG
* * *
3208915 GTTATCTTCCAACCAAATACCTTCGAGTACGACTACGCTCAGCTCCAAGGCACAT
194 GTTATC-TGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* *
3208970 CATTTGCAGCATAACTTAAGTCGATAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTC
* *
3209035 AGCTTCGAGGACACATCATTTACAGCATAACTCAAGGCTAGAAGGGGTATCTGTCACCAAAAGAC
66 AGCTTCAAGG-CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGAC
*
3209100 CTTCGAGTTCGACCACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
*
3209165 TTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACAT
195 TTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
* * * * *
3209219 CCTTTGCAGCATAGCTTAAGTTGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTC
* ** *
3209284 AGCTTCAAGGACACAACATTTACAATATAACTCAAAGCTAGAAGGGTTATCTGTCACC-AAAGAC
66 AGCTTCAAGG-CACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGAC
* * * * ** * *
3209348 CTTTGAGTTCGACTACGCTTAGCTCCAAGGCACATAATTTGCAAAATATCTTAAGTCGAGAATGG
130 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * * * *
3209413 CTATCTG---CCAAAGACCTTCGAGTTCAATTACACTCAGCTCCGGAGGCACAT
195 TTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCC-AAGGCACAT
* * * * * * * ** * *
3209464 CATTTACATCATAACTCAAGACTAAAAGGGTTATCTGCCAACAAAGACATTCGACTTCGACTACG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTCGAGTTCGACTACA
3209529 CTCAGC-TCAAAGGCACATCATTT
63 CTCAGCTTC-AAGGCACATCATTT
3209552 GCAATATAGC
Statistics
Matches: 914, Mismatches: 121, Indels: 73
0.82 0.11 0.07
Matches are distributed among these distances:
236 1 0.00
237 50 0.05
238 59 0.06
240 1 0.00
241 42 0.05
242 41 0.04
243 1 0.00
244 31 0.03
245 39 0.04
246 12 0.01
247 14 0.02
248 326 0.36
249 295 0.32
251 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (247 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGACTACACTC
AGCTTCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
TATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
Found at i:3210134 original size:38 final size:36
Alignment explanation
Indices: 3209996--3210400 Score: 312
Period size: 38 Copynumber: 10.9 Consensus size: 36
3209986 TGCAAATGGT
*
3209996 TTTTGAAAA-TACGTAT-ATATATAGTTTCTAAAAACA
1 TTTTGAAAATTA--TATAATATATAGTTTTTAAAAACA
* *
3210032 TTTTGACAATGTATATAATGTATAGTTTTT-AAAACA
1 TTTTGAAAAT-TATATAATATATAGTTTTTAAAAACA
* *
3210068 CTTTTGAAAACTATATAATATATCGTTTTTAAAAACA
1 -TTTTGAAAATTATATAATATATAGTTTTTAAAAACA
*
3210105 TTTTAGAAAATATATATAATATATAGTTTTTAAAATCA
1 TTTT-GAAAAT-TATATAATATATAGTTTTTAAAAACA
*
3210143 TTTTGAAAAATTTATATAATATATAGTTTTTGAAAACA
1 TTTTG-AAAA-TTATATAATATATAGTTTTTAAAAACA
* * * **
3210181 TTTTTTTAAAACTTATATAATATATATATTTTTGAAAATG
1 --TTTTGAAAA-TTATATAATATATA-GTTTTTAAAAACA
* *
3210221 TTTTTAAAACTTATATAATATATAATTTTTTAAAAACA
1 TTTTGAAAA-TTATATAATATAT-AGTTTTTAAAAACA
* *
3210259 TTTTAGAAAATTATATAGT-T-T--TTTTAAAAAAACAAA
1 TTTT-GAAAATTATATAATATATAGTTTT-TAAAAAC--A
* **
3210295 TTTTGAAAATTATATAGT-T-T--TTTAAAAAAACA
1 TTTTGAAAATTATATAATATATAGTTTTTAAAAACA
**
3210327 TTTTTGAAAATTTATATACAATATATAGTTTAAAAAAACA
1 -TTTTGAAAA-TTATAT--AATATATAGTTTTTAAAAACA
* *
3210367 TTTTTAGAAATT-TATATTATATAGTTTTTAAAAA
1 TTTTGA-AAATTATATAATATATAGTTTTTAAAAA
3210401 AAATACTTTT
Statistics
Matches: 313, Mismatches: 30, Indels: 52
0.79 0.08 0.13
Matches are distributed among these distances:
32 1 0.00
33 13 0.04
34 19 0.06
35 19 0.06
36 62 0.20
37 33 0.11
38 106 0.34
39 31 0.10
40 29 0.09
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TTTTGAAAATTATATAATATATAGTTTTTAAAAACA
Found at i:3210242 original size:77 final size:76
Alignment explanation
Indices: 3210012--3210275 Score: 276
Period size: 77 Copynumber: 3.5 Consensus size: 76
3210002 AAATACGTAT
* * * * * *
3210012 ATATATAGTTTCTAAAAACA-TTTT-GACAATGTATATAATGTATAGTTTTTAAAA-CACTTTTG
1 ATATATAGTTTTTAAAAACATTTTTAGAAAATATATATAATATATAATTTTTAAAATCA-TTTTA
3210074 AAAAC-TATATA
65 AAAACTTATATA
* *
3210085 ATATATCGTTTTTAAAAACA-TTTTAGAAAATATATATAATATATAGTTTTTAAAATCATTTTGA
1 ATATATAGTTTTTAAAAACATTTTTAGAAAATATATATAATATATAATTTTTAAAATCATTTT-A
*
3210149 AAAATTTATATA
65 AAAACTTATATA
* ** *
3210161 ATATATAGTTTTTGAAAACATTTTTTTAAAACT-TATATAATATATATATTTTTGAAAAT-GTTT
1 ATATATAGTTTTTAAAAACATTTTTAGAAAA-TATATATAATATATA-ATTTTT-AAAATCATTT
*
3210224 TTAAAACTTATATA
63 TAAAAACTTATATA
*
3210238 ATATATAATTTTTTAAAAACA-TTTTAGAAAAT-TATATA
1 ATATAT-AGTTTTTAAAAACATTTTTAGAAAATATATATA
3210276 GTTTTTTTAA
Statistics
Matches: 163, Mismatches: 19, Indels: 15
0.83 0.10 0.08
Matches are distributed among these distances:
73 22 0.13
74 31 0.19
75 6 0.04
76 31 0.19
77 46 0.28
78 22 0.13
79 5 0.03
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (76 bp):
ATATATAGTTTTTAAAAACATTTTTAGAAAATATATATAATATATAATTTTTAAAATCATTTTAA
AAACTTATATA
Found at i:3210316 original size:34 final size:33
Alignment explanation
Indices: 3210239--3210344 Score: 137
Period size: 34 Copynumber: 3.2 Consensus size: 33
3210229 ACTTATATAA
*
3210239 TATATAATTTTTT--AAAAAC-ATTTTAGAAAAT
1 TATATAGTTTTTTAAAAAAACAATTTT-GAAAAT
3210270 TATATAGTTTTTTTAAAAAAACAAATTTTGAAAAT
1 TATATAG-TTTTTTAAAAAAAC-AATTTTGAAAAT
*
3210305 TATATAGTTTTTTAAAAAAACATTTTTGAAAATT
1 TATATAGTTTTTTAAAAAAACAATTTTGAAAA-T
3210339 TATATA
1 TATATA
3210345 CAATATATAG
Statistics
Matches: 67, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
31 6 0.09
32 6 0.09
33 10 0.15
34 27 0.40
35 13 0.19
36 5 0.07
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (33 bp):
TATATAGTTTTTTAAAAAAACAATTTTGAAAAT
Found at i:3210412 original size:40 final size:39
Alignment explanation
Indices: 3210303--3210402 Score: 127
Period size: 40 Copynumber: 2.5 Consensus size: 39
3210293 AATTTTGAAA
3210303 ATTATATAGTTTTTTAAAAAAACATTTTT-GAAAATTTAT
1 ATTATATAG-TTTTTAAAAAAACATTTTTAGAAAATTTAT
3210342 ATACAATATATAG--TTTAAAAAAACATTTTTAG-AAATTTAT
1 AT----TATATAGTTTTTAAAAAAACATTTTTAGAAAATTTAT
3210382 ATTATATAGTTTTTAAAAAAA
1 ATTATATAGTTTTTAAAAAAA
3210403 ATACTTTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 15
0.78 0.00 0.22
Matches are distributed among these distances:
36 7 0.13
38 10 0.19
39 2 0.04
40 27 0.50
41 1 0.02
43 7 0.13
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (39 bp):
ATTATATAGTTTTTAAAAAAACATTTTTAGAAAATTTAT
Found at i:3210438 original size:13 final size:13
Alignment explanation
Indices: 3210420--3210449 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3210410 TTATATTTAT
3210420 TTATTTATTATTA
1 TTATTTATTATTA
3210433 TTATTTATTATTA
1 TTATTTATTATTA
3210446 TTAT
1 TTAT
3210450 CATTACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:3211780 original size:15 final size:15
Alignment explanation
Indices: 3211742--3211786 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
3211732 TATACATATA
3211742 TATTATTTATTTT-T
1 TATTATTTATTTTCT
3211756 TA-TA-TT-TTTTCT
1 TATTATTTATTTTCT
*
3211768 TATTATTTATTTTCA
1 TATTATTTATTTTCT
3211783 TATT
1 TATT
3211787 TTTTCTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
11 4 0.15
12 5 0.19
13 4 0.15
14 4 0.15
15 9 0.35
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTATTTATTTTCT
Found at i:3211786 original size:25 final size:26
Alignment explanation
Indices: 3211742--3211793 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
3211732 TATACATATA
*
3211742 TATTATTTATTTTTTATATTTTTTCT
1 TATTATTTATTTTTCATATTTTTTCT
3211768 TATTATTTA-TTTTCATATTTTTTCT
1 TATTATTTATTTTTCATATTTTTTCT
3211793 T
1 T
3211794 TCAAATTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 16 0.64
26 9 0.36
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (26 bp):
TATTATTTATTTTTCATATTTTTTCT
Found at i:3211788 original size:23 final size:25
Alignment explanation
Indices: 3211742--3211789 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
3211732 TATACATATA
*
3211742 TATTATTTATTTTTTATATTTTTTCT
1 TATTATTTATTTTTCATA-TTTTTCT
3211768 TATTATTTA-TTTTCATATTTTT
1 TATTATTTATTTTTCATATTTTT
3211790 TCTTTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 7 0.33
26 9 0.43
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (25 bp):
TATTATTTATTTTTCATATTTTTCT
Found at i:3211907 original size:12 final size:12
Alignment explanation
Indices: 3211880--3211947 Score: 54
Period size: 12 Copynumber: 5.6 Consensus size: 12
3211870 TTCTTTCGAC
3211880 TTATTATTATTA-
1 TTATTATT-TTAT
3211892 TTATTATTTTAT
1 TTATTATTTTAT
*
3211904 TTATTTATTCTGAT
1 TTA-TTATT-TTAT
3211918 TTATCT-TTTTAT
1 TTAT-TATTTTAT
3211930 TTATT-TATTTA-
1 TTATTAT-TTTAT
3211941 TTATTAT
1 TTATTAT
3211948 ATTTTTTTGT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
11 10 0.21
12 23 0.48
13 8 0.17
14 7 0.15
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (12 bp):
TTATTATTTTAT
Found at i:3211908 original size:4 final size:4
Alignment explanation
Indices: 3211899--3211951 Score: 56
Period size: 4 Copynumber: 12.8 Consensus size: 4
3211889 TTATTATTAT
3211899 TTTA TTTA TTTA TTCTGA TTTA TCTT- TTTA TTTA TTTA TTTA -TTA TTATA
1 TTTA TTTA TTTA TT-T-A TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TT-TA
3211949 TTT
1 TTT
3211952 TTTTGTCTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
3 5 0.12
4 27 0.63
5 8 0.19
6 3 0.07
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:3211947 original size:26 final size:25
Alignment explanation
Indices: 3211886--3211953 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 25
3211876 CGACTTATTA
3211886 TTATTATTATTATTTTATTTATTTAT
1 TTATTATTATT-TTTTATTTATTTAT
3211912 TCTGA-T-TTATCTTTTTATTTATTTAT
1 T-T-ATTATTAT-TTTTTATTTATTTAT
3211938 TTATTATTATATTTTT
1 TTATTATTAT-TTTTT
3211954 TTGTCTTACA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
24 1 0.03
25 2 0.06
26 29 0.81
27 3 0.08
28 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (25 bp):
TTATTATTATTTTTTATTTATTTAT
Found at i:3213319 original size:17 final size:18
Alignment explanation
Indices: 3213293--3213327 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3213283 AAAATGTTTT
*
3213293 CAATTCATTT-ATTTTAA
1 CAATTAATTTAATTTTAA
3213310 CAATTAATTTAATTTTAA
1 CAATTAATTTAATTTTAA
3213328 TAGTAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
CAATTAATTTAATTTTAA
Found at i:3213482 original size:56 final size:56
Alignment explanation
Indices: 3213419--3213532 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
3213409 AAAAAATTAC
3213419 ATATTATTTATAAATCGCCTTAAATTATTAAAAATAATTAATTTTATTTTGATTTG
1 ATATTATTTATAAATCGCCTTAAATTATTAAAAATAATTAATTTTATTTTGATTTG
3213475 ATATTATTTATAAATCGCCTTAAATTATTAAAAATAATTAATTTTATTTTGATTTG
1 ATATTATTTATAAATCGCCTTAAATTATTAAAAATAATTAATTTTATTTTGATTTG
3213531 AT
1 AT
3213533 TTTTTTAAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (56 bp):
ATATTATTTATAAATCGCCTTAAATTATTAAAAATAATTAATTTTATTTTGATTTG
Found at i:3214306 original size:29 final size:30
Alignment explanation
Indices: 3214273--3214329 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
3214263 TAATTTTTTC
* *
3214273 AGTTTAGTGTCTCACGTTT-ATTTCGTTCT
1 AGTTTAGTGTCTAACGTTTCATTCCGTTCT
*
3214302 AGTTTGGTGTCTAACGTTTCATTCCGTT
1 AGTTTAGTGTCTAACGTTTCATTCCGTT
3214330 ACTCAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.14, C:0.18, G:0.19, T:0.49
Consensus pattern (30 bp):
AGTTTAGTGTCTAACGTTTCATTCCGTTCT
Found at i:3214800 original size:29 final size:29
Alignment explanation
Indices: 3214768--3214826 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
3214758 CTTCACCTTC
*
3214768 AAGGAAGGTGTCATGGTTGCTATTGATTT
1 AAGGAAGGTGTCATGGTTGATATTGATTT
*
3214797 AAGGAAGGTGTCATGGTTGATGTTGATTT
1 AAGGAAGGTGTCATGGTTGATATTGATTT
3214826 A
1 A
3214827 GGGTTCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.05, G:0.32, T:0.37
Consensus pattern (29 bp):
AAGGAAGGTGTCATGGTTGATATTGATTT
Found at i:3215091 original size:29 final size:30
Alignment explanation
Indices: 3215049--3215116 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
3215039 CCATTTTGAG
*
3215049 TAACGAAATGAAACCTTAGGCACCAAACTA
1 TAACAAAATGAAACCTTAGGCACCAAACTA
* *
3215079 TAACAAAAT-AAACGTTAGGCACTAAACTA
1 TAACAAAATGAAACCTTAGGCACCAAACTA
*
3215108 GAA-AAAATG
1 TAACAAAATG
3215117 GCATAGGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.15
29 20 0.61
30 8 0.24
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (30 bp):
TAACAAAATGAAACCTTAGGCACCAAACTA
Found at i:3216705 original size:21 final size:21
Alignment explanation
Indices: 3216679--3216726 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
3216669 AAGGACTTCT
3216679 GAATTTCATAACAGAGAATCA
1 GAATTTCATAACAGAGAATCA
3216700 GAATTTCATAACAGAGAATCA
1 GAATTTCATAACAGAGAATCA
3216721 GAATTT
1 GAATTT
3216727 TATTAATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (21 bp):
GAATTTCATAACAGAGAATCA
Found at i:3220235 original size:3 final size:3
Alignment explanation
Indices: 3220227--3220251 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3220217 TTAAATATTC
3220227 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
3220252 CCTAGCAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3224899 original size:51 final size:51
Alignment explanation
Indices: 3224839--3224939 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
3224829 TCAAGGGGAG
*
3224839 AGTTACAAGGAATTTCAGCCTCTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGGAATTTCAACCTCTTCAAACCGATATTTCTTTACAGCCTATT
*
3224890 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTAT
1 AGTTACAAGGAATTTCAACCTCTTCAAACCGATATTTCTTTACAGCCTAT
3224940 CATTTCCTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACCTCTTCAAACCGATATTTCTTTACAGCCTATT
Found at i:3227182 original size:14 final size:14
Alignment explanation
Indices: 3227163--3227206 Score: 70
Period size: 14 Copynumber: 3.0 Consensus size: 14
3227153 TAACAGACTT
3227163 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
3227177 GTCTGTTTTCTACACA
1 GTCTGTTTTCT--ACA
3227193 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
3227207 ATATATACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.48
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:3227195 original size:16 final size:16
Alignment explanation
Indices: 3227163--3227206 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
3227153 TAACAGACTT
3227163 GTCTGTTTTCT--ACA
1 GTCTGTTTTCTACACA
3227177 GTCTGTTTTCTACACA
1 GTCTGTTTTCTACACA
3227193 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
3227207 ATATATACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 11 0.39
16 17 0.61
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.48
Consensus pattern (16 bp):
GTCTGTTTTCTACACA
Found at i:3232572 original size:43 final size:43
Alignment explanation
Indices: 3232523--3232605 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
3232513 GGACGGATGT
* *
3232523 AAACGAACATAAGCAAACACAATAAACAAATGTAAACGAATAC
1 AAACGAACATAAACAAACACAATAAACAAATATAAACGAATAC
* * * **
3232566 AAACGAACGTAAACGAACACAGTAAATGAATATAAACGAA
1 AAACGAACATAAACAAACACAATAAACAAATATAAACGAA
3232606 CGTATATGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.59, C:0.17, G:0.12, T:0.12
Consensus pattern (43 bp):
AAACGAACATAAACAAACACAATAAACAAATATAAACGAATAC
Found at i:3232807 original size:14 final size:14
Alignment explanation
Indices: 3232787--3232848 Score: 88
Period size: 14 Copynumber: 4.4 Consensus size: 14
3232777 AGATTGGCTA
3232787 AACATAAATGAACG
1 AACATAAATGAACG
* * *
3232801 CACATAAACGAATG
1 AACATAAATGAACG
3232815 AACATAAATGAACG
1 AACATAAATGAACG
*
3232829 AGCATAAATGAACG
1 AACATAAATGAACG
3232843 AACATA
1 AACATA
3232849 TTATCGAATG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.55, C:0.16, G:0.15, T:0.15
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:3234333 original size:8 final size:8
Alignment explanation
Indices: 3234320--3234350 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
3234310 GTACATGATG
3234320 TATGTATA
1 TATGTATA
3234328 TATGTATA
1 TATGTATA
3234336 TATGTATA
1 TATGTATA
3234344 TATGTAT
1 TATGTAT
3234351 GTATTTCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (8 bp):
TATGTATA
Found at i:3235330 original size:21 final size:22
Alignment explanation
Indices: 3235306--3235351 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
3235296 CTGTAAAGTT
3235306 TTATGTAAATCTCAATT-AATC
1 TTATGTAAATCTCAATTAAATC
3235327 TTATGTAAATCTCAATTAAATC
1 TTATGTAAATCTCAATTAAATC
3235349 TTA
1 TTA
3235352 AATATGATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (22 bp):
TTATGTAAATCTCAATTAAATC
Found at i:3236947 original size:19 final size:19
Alignment explanation
Indices: 3236920--3236957 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3236910 AACAAAAGCG
*
3236920 CAATGCGATCTCTAAATCA
1 CAATACGATCTCTAAATCA
3236939 CAATACGATCTCTAAATCA
1 CAATACGATCTCTAAATCA
3236958 TAACGCGATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.26, G:0.08, T:0.26
Consensus pattern (19 bp):
CAATACGATCTCTAAATCA
Found at i:3236966 original size:19 final size:19
Alignment explanation
Indices: 3236924--3236969 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3236914 AAAGCGCAAT
*
3236924 GCGATCTCTAAATCACAAT
1 GCGATCTCTAAATCACAAC
* *
3236943 ACGATCTCTAAATCATAAC
1 GCGATCTCTAAATCACAAC
3236962 GCGATCTC
1 GCGATCTC
3236970 CAGTATCGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (19 bp):
GCGATCTCTAAATCACAAC
Found at i:3238116 original size:14 final size:14
Alignment explanation
Indices: 3238087--3238123 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3238077 AGAAAAAGAA
3238087 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
3238102 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
3238116 GAAGAAAA
1 GAAGAAAA
3238124 TGTCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:3240364 original size:20 final size:20
Alignment explanation
Indices: 3240339--3240469 Score: 132
Period size: 20 Copynumber: 6.8 Consensus size: 20
3240329 TTACACATTC
*
3240339 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3240359 ATTTGACTATCGTAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
3240378 A----A-AATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
*
3240393 ATTTGATTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3240413 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
3240433 ATTTGATTATCGCAACAG-GA
1 ATTTGACTATCGCAAC-GCGA
*
3240453 ATTTGACTATCCCAACG
1 ATTTGACTATCGCAACG
3240470 AGAAAATCAC
Statistics
Matches: 92, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
14 8 0.09
15 3 0.03
19 4 0.04
20 76 0.83
21 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:3240500 original size:94 final size:93
Alignment explanation
Indices: 3240339--3240518 Score: 229
Period size: 94 Copynumber: 1.9 Consensus size: 93
3240329 TTACACATTC
** * * * *
3240339 ATTTGAATATCGCAACGCGAATTTGACTATCGTAACGCAAAAATCGCAATGCGAATTTGATTATC
1 ATTTGAATATCGCAACGCGAATTTGACTATCCCAACGCAAAAATCACAAAGCGAATTAGACTATC
3240404 GCAACGCGAATTTGACTATCGCAACGTGA
66 GCAACGCGAA-TTGACTATCGCAACGTGA
* * *
3240433 ATTTGATTATCGCAACAG-GAATTTGACTATCCCAACG-AGAAAATCACAAAGTGTATTAGACTA
1 ATTTGAATATCGCAAC-GCGAATTTGACTATCCCAACGCA-AAAATCACAAAGCGAATTAGACTA
*
3240496 TCGCAACGCGAATTGACTTTCGC
64 TCGCAACGCGAATTGACTATCGC
3240519 GTTGCGATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
93 11 0.15
94 62 0.84
95 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (93 bp):
ATTTGAATATCGCAACGCGAATTTGACTATCCCAACGCAAAAATCACAAAGCGAATTAGACTATC
GCAACGCGAATTGACTATCGCAACGTGA
Found at i:3240543 original size:20 final size:20
Alignment explanation
Indices: 3240520--3240571 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
3240510 GACTTTCGCG
*
3240520 TTGCGATTTTGGCTTT-TGTA
1 TTGCGATTTTGACTTTCT-TA
3240540 TTGCGATTTTGACTTTCTTA
1 TTGCGATTTTGACTTTCTTA
3240560 TTGCGATTTTGA
1 TTGCGATTTTGA
3240572 GTTTAGCGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.13, C:0.12, G:0.21, T:0.54
Consensus pattern (20 bp):
TTGCGATTTTGACTTTCTTA
Found at i:3240749 original size:67 final size:66
Alignment explanation
Indices: 3240637--3240806 Score: 177
Period size: 71 Copynumber: 2.5 Consensus size: 66
3240627 GATTGAAATC
*
3240637 AACAAATCAACTTTTACATTTCAATCAATTAAACAAGCACAAATAAGAA-TTA-TTTACACATCA
1 AACAAATCAACTTTTACA--T-AATCAATTAAACAAGCAAAAATAAGAATTTATTTTACACATCA
3240700 ATTA
63 ATTA
* * *
3240704 AACAAATCAACTTTTACA-AATCAATTAAACAAGCAAAAAATAATAATAATTCTTATTTTCCTCA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGC---AAA-AATAAGAA-T-TTATTTTACACA
3240768 TCAATTA
60 TCAATTA
* *
3240775 AACAAATCAACTTTTA-AGATTCAATTAAACAA
1 AACAAATCAACTTTTACATAATCAATTAAACAA
3240807 TAAAAAAAAG
Statistics
Matches: 89, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
63 16 0.18
66 2 0.02
67 25 0.28
70 4 0.04
71 42 0.47
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (66 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAATAAGAATTTATTTTACACATCAATT
A
Done.