Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 145 of 276
Found at i:47296782 original size:126 final size:126
Alignment explanation
Indices: 47296557--47296800 Score: 330
Period size: 126 Copynumber: 1.9 Consensus size: 126
47296547 GCTAACCTAG
* * * * * *
47296557 TTTATTTTACACAAGCACCACAACATGCACAATCATTCCCTGCATCAACACCTTCAACTCTAGTT
1 TTTATTTTACACAAACACCACAACATGCACAATCATTCCCTACATCAACACATTCAACACCAATT
* * *
47296622 TATTTTACACAAACACCATAGCACGCACAATCATTCCCCT-CATCAACACCTTCAGCTCCAA
66 TATTTTACACAAACACCATAACACCCACAATCATT-CCATGCATCAACACCTTCAGCTCCAA
* * * *
47296683 TTTATTTTACACAAACACCACAACATGTACAATCATTCCCTACATTAATACATTCAGCACCAATT
1 TTTATTTTACACAAACACCACAACATGCACAATCATTCCCTACATCAACACATTCAACACCAATT
*
47296748 TATTTTACACAAGA-ACCATAACACCCACAATCATTTCATGCATCAACACCTTC
66 TATTTTACACAA-ACACCATAACACCCACAATCATTCCATGCATCAACACCTTC
47296801 TCAATAGGTA
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
125 2 0.02
126 99 0.97
127 1 0.01
ACGTcount: A:0.36, C:0.32, G:0.05, T:0.27
Consensus pattern (126 bp):
TTTATTTTACACAAACACCACAACATGCACAATCATTCCCTACATCAACACATTCAACACCAATT
TATTTTACACAAACACCATAACACCCACAATCATTCCATGCATCAACACCTTCAGCTCCAA
Found at i:47300389 original size:5 final size:5
Alignment explanation
Indices: 47300379--47300409 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
47300369 TTTTCTTTAC
*
47300379 AATTT AATTT AATTT CATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT AATTT A
47300410 TTATTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:47300458 original size:26 final size:22
Alignment explanation
Indices: 47300410--47300455 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
47300400 ATTTAATTTA
47300410 TTATTTATTAATTTACTTTTTC
1 TTATTTATTAATTTACTTTTTC
47300432 TTATTTATTAATTTACTTTTTC
1 TTATTTATTAATTTACTTTTTC
47300454 TT
1 TT
47300456 TCTCTTGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTTATTAATTTACTTTTTC
Found at i:47302782 original size:55 final size:53
Alignment explanation
Indices: 47302659--47302801 Score: 142
Period size: 55 Copynumber: 2.6 Consensus size: 53
47302649 TGCGACATGG
* * * *
47302659 CCGTAGGCAAACCTGCCAAAACAACACGGGCGTGCGGCACGCCCGTGTCTAGAAC
1 CCGT-GGCAAACCTGTC-AAACAACACGGGCGTGCGACACGCCCGTGCCAAGAAC
* * ** *
47302714 CCGTGGCTGAACCTATCAAATCAACACGGGCGTTTGACACGCCCGTGCCAAGCAC
1 CCGTGGC-AAACCTGTCAAA-CAACACGGGCGTGCGACACGCCCGTGCCAAGAAC
*
47302769 CCGTGGTCAAACCTGTTAAACTAACACGGGCGT
1 CCGTGG-CAAACCTGTCAAAC-AACACGGGCGT
47302802 AGGCCTACAT
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
54 7 0.10
55 64 0.89
56 1 0.01
ACGTcount: A:0.27, C:0.33, G:0.25, T:0.15
Consensus pattern (53 bp):
CCGTGGCAAACCTGTCAAACAACACGGGCGTGCGACACGCCCGTGCCAAGAAC
Found at i:47308969 original size:23 final size:23
Alignment explanation
Indices: 47308936--47308979 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
47308926 ACTTTAACCA
47308936 TTTTTACTTTTA-TTTCAATTTAC
1 TTTTTACTTTTAGTTT-AATTTAC
*
47308959 TTTTTATTTTTAGTTTAATTT
1 TTTTTACTTTTAGTTTAATTT
47308980 TTTCTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTTACTTTTAGTTTAATTTAC
Found at i:47317211 original size:17 final size:17
Alignment explanation
Indices: 47317181--47317227 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
47317171 TTATTTTTAC
47317181 TTTATTTTGT-TTTTCCT
1 TTTATTTT-TATTTTCCT
* *
47317198 TTTGTTTTTATTTTTCT
1 TTTATTTTTATTTTCCT
47317215 TTTATTTTTATTT
1 TTTATTTTTATTT
47317228 CTATTTCCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 1 0.04
17 25 0.96
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (17 bp):
TTTATTTTTATTTTCCT
Found at i:47317223 original size:11 final size:11
Alignment explanation
Indices: 47317170--47317233 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
47317160 TTTGAGTCCA
*
47317170 TTTATTTTTAC
1 TTTATTTTTAT
47317181 TTTATTTTGT-T
1 TTTATTTT-TAT
*
47317192 TTTCCTTTTGT-T
1 TTT-ATTTT-TAT
*
47317204 TTTATTTTTCT
1 TTTATTTTTAT
47317215 TTTATTTTTAT
1 TTTATTTTTAT
47317226 TTCTATTT
1 TT-TATTT
47317234 CCAGTTTTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
10 1 0.02
11 28 0.62
12 16 0.36
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:47328734 original size:342 final size:342
Alignment explanation
Indices: 47328109--47328796 Score: 1340
Period size: 342 Copynumber: 2.0 Consensus size: 342
47328099 AATACTTTTA
47328109 GTCCTTGTGGATATGATATTTTCGGTCTCACCTTAACTATACTACTGTTCGATAGGTGAGCTTGC
1 GTCCTTGTGGATATGATATTTTCGGTCTCACCTTAACTATACTACTGTTCGATAGGTGAGCTTGC
47328174 CTTAGTAGAATTTTTAGTTAGTATAGCGATCATCAATGTAGCGATGAAGTTGACACTAAGTTGTA
66 CTTAGTAGAATTTTTAGTTAGTATAGCGATCATCAATGTAGCGATGAAGTTGACACTAAGTTGTA
47328239 TGTTATACCGCTTGATTGTAGCTACAAAAGAATATTTGGAGTCAAACTCTATCCCAACCTCTAAA
131 TGTTATACCGCTTGATTGTAGCTACAAAAGAATATTTGGAGTCAAACTCTATCCCAACCTCTAAA
47328304 TGGCCAAAATTTATTGCCGAAGTCGCATACCTTGGTATTTTATGAGGAAGGTCTAGGAATTTTAA
196 TGGCCAAAATTTATTGCCGAAGTCGCATACCTTGGTATTTTATGAGGAAGGTCTAGGAATTTTAA
47328369 ACCACCTTCACTGCAACATCGAGAATACGCATGTAGGGAGGGGATTCGTACACCGTGAACCCAGG
261 ACCACCTTCACTGCAACATCGAGAATACGCATGTAGGGAGGGGATTCGTACACCGTGAACCCAGG
47328434 TCATCCCATCAAGCAAT
326 TCATCCCATCAAGCAAT
47328451 GTCCTTGTGGATATGATATTTTCGGTCTCACCTTAACTATACTACTGTTCGATAGGTGAGCTTGC
1 GTCCTTGTGGATATGATATTTTCGGTCTCACCTTAACTATACTACTGTTCGATAGGTGAGCTTGC
47328516 CTTAGTAGAATTTTTAGTTAGTATAGCGATCATCAATGTAGCGATGAAGTTGACACTAAGTTGTA
66 CTTAGTAGAATTTTTAGTTAGTATAGCGATCATCAATGTAGCGATGAAGTTGACACTAAGTTGTA
47328581 TGTTATACCGCTTGATTGTAGCTACAAAAGAATATTTGGAGTCAAACTCTATCCCAACCTCTAAA
131 TGTTATACCGCTTGATTGTAGCTACAAAAGAATATTTGGAGTCAAACTCTATCCCAACCTCTAAA
*
47328646 TGGCCAAAATTTATTGTCGAAGTCGCATACCTTGGTATTTTATGAGGAAGGTCTAGGAATTTTAA
196 TGGCCAAAATTTATTGCCGAAGTCGCATACCTTGGTATTTTATGAGGAAGGTCTAGGAATTTTAA
* *
47328711 ACCACCTTCACTGCAACATCGAGAGTACGCATGTAGGGAGGGGATTCGTACGCCGTGAACCCAGG
261 ACCACCTTCACTGCAACATCGAGAATACGCATGTAGGGAGGGGATTCGTACACCGTGAACCCAGG
*
47328776 TTATCCCATCAAGCAAT
326 TCATCCCATCAAGCAAT
47328793 GTCC
1 GTCC
47328797 GAAGTTTGAC
Statistics
Matches: 342, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
342 342 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (342 bp):
GTCCTTGTGGATATGATATTTTCGGTCTCACCTTAACTATACTACTGTTCGATAGGTGAGCTTGC
CTTAGTAGAATTTTTAGTTAGTATAGCGATCATCAATGTAGCGATGAAGTTGACACTAAGTTGTA
TGTTATACCGCTTGATTGTAGCTACAAAAGAATATTTGGAGTCAAACTCTATCCCAACCTCTAAA
TGGCCAAAATTTATTGCCGAAGTCGCATACCTTGGTATTTTATGAGGAAGGTCTAGGAATTTTAA
ACCACCTTCACTGCAACATCGAGAATACGCATGTAGGGAGGGGATTCGTACACCGTGAACCCAGG
TCATCCCATCAAGCAAT
Found at i:47330487 original size:24 final size:21
Alignment explanation
Indices: 47330434--47330476 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
47330424 CTCAGTCTCC
*
47330434 TTTAAATTATTATTTTCTTTT
1 TTTAAATTATTATTTTATTTT
47330455 TTTAAATTATTATTTTATTTT
1 TTTAAATTATTATTTTATTTT
47330476 T
1 T
47330477 CTTGCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTAAATTATTATTTTATTTT
Found at i:47332598 original size:114 final size:114
Alignment explanation
Indices: 47332454--47332710 Score: 381
Period size: 114 Copynumber: 2.2 Consensus size: 114
47332444 TTTTTTTTTT
* * * *
47332454 GTTCTGGCCTTCTAATGGCCGGCACTAGGGACTTTTTTCGTGTCCCAACGCAATTTTTTTTTTAT
1 GTTCTGGCCTTCTAATGGTCGGCACCAGGGACTTTTTTCATGTCCCAACGCAA-TTTTTTTTTAC
*
47332519 TTTTGTACACTGATGGCCAGCACCAGACCAGTAA-TTTAAAAAAAAATTG
65 TTTTCTACACTGATGGCCAGCACCAGACCAGTAATTTTAAAAAAAAATTG
*
47332568 GTTCTGGCCTTCTAATGGTCGGCACCAGGGACTTTTTTCATGTCCCAATGCAATTTTTTTTTACT
1 GTTCTGGCCTTCTAATGGTCGGCACCAGGGACTTTTTTCATGTCCCAACGCAATTTTTTTTTACT
* *
47332633 TTTCTACACTGATGGTCGGCACCAGACCAGTAATTTTTAAAAAAAAATTG
66 TTTCTACACTGATGGCCAGCACCAGACCAGTAA-TTTTAAAAAAAAATTG
* * * *
47332683 GTTCTAGCCATGTAATGATCGGCACCAG
1 GTTCTGGCCTTCTAATGGTCGGCACCAG
47332711 AGTAAAAAAA
Statistics
Matches: 129, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
113 41 0.32
114 49 0.38
115 39 0.30
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (114 bp):
GTTCTGGCCTTCTAATGGTCGGCACCAGGGACTTTTTTCATGTCCCAACGCAATTTTTTTTTACT
TTTCTACACTGATGGCCAGCACCAGACCAGTAATTTTAAAAAAAAATTG
Found at i:47332740 original size:45 final size:43
Alignment explanation
Indices: 47332670--47332835 Score: 129
Period size: 46 Copynumber: 3.7 Consensus size: 43
47332660 CAGTAATTTT
* *
47332670 TAAAAAAAAA-TTGGTTCTAGCCATGTAATGATCGGCACCAGAG
1 TAAAAAAAAATTTGGTGCTGGCCATGTAATG-TCGGCACCAGAG
* * * * * *
47332713 TAAAAAAAAATTTGGGTGCTGGGCATGTATTGGCTGTCACCAAAAA
1 TAAAAAAAAATTT-GGTGCTGGCCATGTAATGTC-GGCACC-AGAG
* * * *
47332759 TAAAAAAAAATTGGGGTGTTGGGCA-GTTATTGGTCGGCACCAGAG
1 TAAAAAAAAATT-TGGTGCTGGCCATG-TAAT-GTCGGCACCAGAG
*
47332804 TAAAAAAAAAATTTGTTGCTGGCCATGTAATG
1 T-AAAAAAAAATTTGGTGCTGGCCATGTAATG
47332836 GCTGGCACTA
Statistics
Matches: 95, Mismatches: 19, Indels: 17
0.73 0.15 0.13
Matches are distributed among these distances:
43 10 0.11
44 4 0.04
45 34 0.36
46 45 0.47
47 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.26
Consensus pattern (43 bp):
TAAAAAAAAATTTGGTGCTGGCCATGTAATGTCGGCACCAGAG
Found at i:47332765 original size:46 final size:45
Alignment explanation
Indices: 47332703--47332843 Score: 135
Period size: 46 Copynumber: 3.1 Consensus size: 45
47332693 TGTAATGATC
* *
47332703 GGCACCAGAGTAAAAAAAAATTTGGGTGCTGGGCATGTATTGGCT
1 GGCACCAAAATAAAAAAAAATTTGGGTGCTGGGCATGTATTGGCT
* * *
47332748 GTCACCAAAAATAAAAAAAAATTGGGGTGTTGGGCA-GTTATTGG-T
1 GGCACC-AAAATAAAAAAAAATTTGGGTGCTGGGCATG-TATTGGCT
* * * * *
47332793 CGGCACCAGAGTAAAAAAAAAATTT-GTTGCTGGCCATGTAATGGCT
1 -GGCACCAAAAT-AAAAAAAAATTTGGGTGCTGGGCATGTATTGGCT
47332839 GGCAC
1 GGCAC
47332844 TAGAGAGAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
45 28 0.36
46 49 0.64
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (45 bp):
GGCACCAAAATAAAAAAAAATTTGGGTGCTGGGCATGTATTGGCT
Found at i:47332843 original size:45 final size:46
Alignment explanation
Indices: 47332671--47332848 Score: 145
Period size: 45 Copynumber: 4.0 Consensus size: 46
47332661 AGTAATTTTT
* * *
47332671 AAAAAAAAATT-GGTTCTAGCCATGTAAT-GATCGGCACCAGAGTA
1 AAAAAAAAATTGGGTGCTGGCCATGTAATGGCTCGGCACCAGAGTA
* * * * **
47332715 AAAAAAAATTTGGGTGCTGGGCATGTATTGGCT-GTCACCA-AAAA
1 AAAAAAAAATTGGGTGCTGGCCATGTAATGGCTCGGCACCAGAGTA
* * *
47332759 TAAAAAAAAATTGGGGTGTTGGGCA-GTTATTGG-TCGGCACCAGAGTA
1 -AAAAAAAAATT-GGGTGCTGGCCATG-TAATGGCTCGGCACCAGAGTA
* * *
47332806 AAAAAAAAATTTGTTGCTGGCCATGTAATGGCT-GGCACTAGAG
1 AAAAAAAAATTGGGTGCTGGCCATGTAATGGCTCGGCACCAGAG
47332849 AGAAAAATAT
Statistics
Matches: 105, Mismatches: 20, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
44 12 0.11
45 53 0.50
46 38 0.36
47 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (46 bp):
AAAAAAAAATTGGGTGCTGGCCATGTAATGGCTCGGCACCAGAGTA
Found at i:47333045 original size:27 final size:27
Alignment explanation
Indices: 47333007--47333072 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
47332997 ATCAAATGAT
*
47333007 TTTTTTGTAGTGGATTGTATATGGAAG
1 TTTTTTGTAGTGGATTGTAGATGGAAG
*
47333034 TTTTTTGTAGTGGATTGTAGATGGGAG
1 TTTTTTGTAGTGGATTGTAGATGGAAG
*
47333061 TTTTTCGTAGTG
1 TTTTTTGTAGTG
47333073 TATAACTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.18, C:0.02, G:0.32, T:0.48
Consensus pattern (27 bp):
TTTTTTGTAGTGGATTGTAGATGGAAG
Found at i:47333784 original size:22 final size:22
Alignment explanation
Indices: 47333741--47333782 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
47333731 ATTTAGTGCG
47333741 TATTATTTTTGTTTGAATTTTA
1 TATTATTTTTGTTTGAATTTTA
47333763 TATT-TTTTTGTATT-AATTTT
1 TATTATTTTTGT-TTGAATTTT
47333783 TAGAGTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (22 bp):
TATTATTTTTGTTTGAATTTTA
Found at i:47333784 original size:90 final size:88
Alignment explanation
Indices: 47333580--47333821 Score: 265
Period size: 90 Copynumber: 2.7 Consensus size: 88
47333570 AGGATTCATT
* *
47333580 TTTTATATTTTCTTGTATTAATTTCTTAGAATGTTTGTATTTTTTTGTATCTGTAAATTTAATTT
1 TTTTATATTTTCTTGTATTAATTT-TTACAATGTTTGTATTTTGTTGTATCTGTAAATTTAATTT
*
47333645 AGTCCGTATTATATGTAGTCTGCA
65 AGTCCGTATTATATGTAGTCTGAA
* * * * *
47333669 TTTAAAATTTTCGTGTATTAA-TTTTACCCATATGTTTGTATTTTGTTG-AGTGTTTAAATTTAA
1 TTTTATATTTTCTTGTATTAATTTTTA--CA-ATGTTTGTATTTTGTTGTA-TCTGTAAATTTAA
* * * *
47333732 TTTAGTGCGTATTAT-TTTTGTTTGAA
62 TTTAGTCCGTATTATATGTAGTCTGAA
* * * * *
47333758 TTTTATATTTTTTTGTATTAATTTTTAGAGTGTTTGTATTTTATTGTGTCTGTAAATTTAATTT
1 TTTTATATTTTCTTGTATTAATTTTTACAATGTTTGTATTTTGTTGTATCTGTAAATTTAATTT
47333822 GTCAATTTCT
Statistics
Matches: 125, Mismatches: 22, Indels: 14
0.78 0.14 0.09
Matches are distributed among these distances:
87 32 0.26
88 3 0.02
89 44 0.35
90 46 0.37
ACGTcount: A:0.24, C:0.05, G:0.13, T:0.58
Consensus pattern (88 bp):
TTTTATATTTTCTTGTATTAATTTTTACAATGTTTGTATTTTGTTGTATCTGTAAATTTAATTTA
GTCCGTATTATATGTAGTCTGAA
Found at i:47334392 original size:19 final size:19
Alignment explanation
Indices: 47334355--47334392 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
47334345 CTAATTAAGT
*
47334355 TTTAATTAAATGAATTTAG
1 TTTAATTAAATGAAATTAG
47334374 TTTAATTAAGA-GAAATTAG
1 TTTAATTAA-ATGAAATTAG
47334393 GAAAAACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (19 bp):
TTTAATTAAATGAAATTAG
Found at i:47334598 original size:29 final size:29
Alignment explanation
Indices: 47334544--47334600 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
47334534 TATTACGGTT
*
47334544 ATTATTTAATTATATTATAAATTAAATTG
1 ATTATTTAATTATATTAGAAATTAAATTG
47334573 ATTATATT-ATTATATTAGGAAA-TAAATT
1 ATTAT-TTAATTATATTA-GAAATTAAATT
47334601 AAGAAAAGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (29 bp):
ATTATTTAATTATATTAGAAATTAAATTG
Found at i:47334702 original size:33 final size:32
Alignment explanation
Indices: 47334659--47334730 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 32
47334649 AAATGAGTAC
47334659 ATTTGTATTATTTA-TATATAATTAGTAAAATGAT
1 ATTT-TATTATTTATTAT-TAATTAGTAAAA-GAT
47334693 ATTTTATTATTTATTATTAATTAGTAAAAGAT
1 ATTTTATTATTTATTATTAATTAGTAAAAGAT
47334725 -TTTTAT
1 ATTTTAT
47334731 ATGATAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.16
32 3 0.08
33 21 0.57
34 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (32 bp):
ATTTTATTATTTATTATTAATTAGTAAAAGAT
Found at i:47335738 original size:18 final size:18
Alignment explanation
Indices: 47335683--47335739 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
47335673 ATTACTGGAC
47335683 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
* * *
47335701 TG-AT--C-GTTTGATAC
1 TGAATAACTGATTGTTAT
47335715 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
47335733 TGAATAA
1 TGAATAA
47335740 AAATAATCAA
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 8 0.28
15 3 0.10
17 3 0.10
18 15 0.52
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (18 bp):
TGAATAACTGATTGTTAT
Found at i:47337012 original size:22 final size:22
Alignment explanation
Indices: 47336984--47337030 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
47336974 CCACAAGAAA
47336984 GCTTATTGTGTGTCATTTCTTT
1 GCTTATTGTGTGTCATTTCTTT
47337006 GCTTATTGTGTGTCATTTCTTT
1 GCTTATTGTGTGTCATTTCTTT
47337028 GCT
1 GCT
47337031 ATAAGGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.09, C:0.15, G:0.19, T:0.57
Consensus pattern (22 bp):
GCTTATTGTGTGTCATTTCTTT
Found at i:47343570 original size:19 final size:20
Alignment explanation
Indices: 47343546--47343591 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
47343536 CATCCAAACA
47343546 CCAGAAAAGTAAATCA-TTT
1 CCAGAAAAGTAAATCATTTT
*
47343565 CCAGAACAGTAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
47343585 CCAGAAA
1 CCAGAAA
47343592 TCATTTTCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.24
Consensus pattern (20 bp):
CCAGAAAAGTAAATCATTTT
Found at i:47343612 original size:14 final size:14
Alignment explanation
Indices: 47343575--47343605 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
47343565 CCAGAACAGT
47343575 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
47343589 AAATCATTTTCCGG
1 AAATCATTTTCCAG
47343603 AAA
1 AAA
47343606 ATATTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:47343772 original size:29 final size:29
Alignment explanation
Indices: 47343740--47343796 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
47343730 TATTATTGTT
* *
47343740 ATTATTTTATTATATTAT-AAATTAAATTG
1 ATTATATTATTATACTATGAAA-TAAATTG
47343769 ATTATATTATTATACTATGAAATAAATT
1 ATTATATTATTATACTATGAAATAAATT
47343797 AAGAAAAGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (29 bp):
ATTATATTATTATACTATGAAATAAATTG
Found at i:47343923 original size:30 final size:32
Alignment explanation
Indices: 47343855--47343917 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
47343845 AAATGAGTAC
*
47343855 ATTTGTATTATTTATATATAATTAGTAAAAATAT
1 ATTT-TATTATTTATATATAATTAGT-AAAATAG
47343889 ATTTTATTATTTAT-TATTAATTAGTAAAA
1 ATTTTATTATTTATATA-TAATTAGTAAAA
47343918 GATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 6 0.21
33 18 0.64
34 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (32 bp):
ATTTTATTATTTATATATAATTAGTAAAATAG
Found at i:47344209 original size:21 final size:20
Alignment explanation
Indices: 47344172--47344213 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
47344162 ATTTATTTAC
47344172 TTATTATTTAAGAAATAATAA
1 TTATTATTTAAGAAAT-ATAA
*
47344193 TTATTA-TTAAGTTAATATAA
1 TTATTATTTAAG-AAATATAA
47344213 T
1 T
47344214 AATACAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
TTATTATTTAAGAAATATAA
Found at i:47344266 original size:20 final size:20
Alignment explanation
Indices: 47344233--47344273 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
47344223 AACTAAAGTA
*
47344233 AAAATAAAAGATAAAACAAAC
1 AAAATAAAACATAAAA-AAAC
47344254 AAAA-AAAACATAAAAAAAC
1 AAAATAAAACATAAAAAAAC
47344273 A
1 A
47344274 GAACCATTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.80, C:0.10, G:0.02, T:0.07
Consensus pattern (20 bp):
AAAATAAAACATAAAAAAAC
Found at i:47347872 original size:28 final size:29
Alignment explanation
Indices: 47347840--47347915 Score: 111
Period size: 28 Copynumber: 2.7 Consensus size: 29
47347830 TTCATAATCA
* *
47347840 TCATTTCATTTTATATTCATTTA-ACATT
1 TCATTTCATTTCATATTCATTTACAAATT
*
47347868 TCATTTAATTTCATATTCA-TTACAAATT
1 TCATTTCATTTCATATTCATTTACAAATT
47347896 TCATTTCATTTCATATTCAT
1 TCATTTCATTTCATATTCAT
47347916 ATTTCATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 3 0.07
28 39 0.93
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (29 bp):
TCATTTCATTTCATATTCATTTACAAATT
Found at i:47347897 original size:18 final size:18
Alignment explanation
Indices: 47347874--47347923 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
47347864 CATTTCATTT
47347874 AATTTCATATTCATTACA
1 AATTTCATATTCATTACA
*
47347892 AATTTCAT-TTCATTTCA
1 AATTTCATATTCATTACA
*
47347909 TA-TTCATATTTCATT
1 AATTTCATA-TTCATT
47347924 TGATTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 14 0.50
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (18 bp):
AATTTCATATTCATTACA
Found at i:47347901 original size:23 final size:23
Alignment explanation
Indices: 47347870--47347924 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
47347860 TTAACATTTC
*
47347870 ATTTAATTTCATATTCAT-TACAA
1 ATTTCATTTCAT-TTCATATACAA
* *
47347893 ATTTCATTTCATTTCATATTCAT
1 ATTTCATTTCATTTCATATACAA
47347916 ATTTCATTT
1 ATTTCATTT
47347925 GATTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTTCATTTCATTTCATATACAA
Found at i:47347924 original size:5 final size:5
Alignment explanation
Indices: 47347840--47347915 Score: 62
Period size: 5 Copynumber: 13.8 Consensus size: 5
47347830 TTCATAATCA
* *
47347840 TCATT TCATT TTATAT TCATT TAACATT TCATT TAATT TCATAT TCATT
1 TCATT TCATT TCAT-T TCATT T--CATT TCATT TCATT TCAT-T TCATT
*
47347889 ACAAATT TCATT TCATT TCATAT TCAT
1 TC--ATT TCATT TCATT TCAT-T TCAT
47347916 ATTTCATTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
5 35 0.60
6 14 0.24
7 9 0.16
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (5 bp):
TCATT
Found at i:47347924 original size:28 final size:28
Alignment explanation
Indices: 47347840--47347924 Score: 95
Period size: 28 Copynumber: 3.0 Consensus size: 28
47347830 TTCATAATCA
*
47347840 TCATTTCATTTTATATTCAT-TTAACATT
1 TCATTTCATTTCATATTCATATT-ACATT
*
47347868 TCATTTAATTTCATATTC--ATTACAAATT
1 TCATTTCATTTCATATTCATATTAC--ATT
*
47347896 TCATTTCATTTCATATTCATATTTCATT
1 TCATTTCATTTCATATTCATATTACATT
47347924 T
1 T
47347925 GATTAAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
26 2 0.04
27 2 0.04
28 40 0.83
30 4 0.08
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.55
Consensus pattern (28 bp):
TCATTTCATTTCATATTCATATTACATT
Found at i:47348372 original size:17 final size:16
Alignment explanation
Indices: 47348312--47348372 Score: 70
Period size: 17 Copynumber: 3.7 Consensus size: 16
47348302 TTTTTTTTTA
47348312 TTTATTTCATT-TCAT
1 TTTATTTCATTCTCAT
* *
47348327 TTGATTCTTATTCTCAT
1 TTTATT-TCATTCTCAT
47348344 TTTATTTCCATTCTCAT
1 TTTATTT-CATTCTCAT
47348361 TTTCATTTCATT
1 TTT-ATTTCATT
47348373 TAAATTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
15 5 0.13
16 5 0.13
17 24 0.63
18 4 0.11
ACGTcount: A:0.18, C:0.18, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTATTTCATTCTCAT
Found at i:47348423 original size:43 final size:43
Alignment explanation
Indices: 47348363--47348523 Score: 180
Period size: 43 Copynumber: 3.6 Consensus size: 43
47348353 ATTCTCATTT
47348363 TCATTTCATTTAAATTATATTTTTTCAATTTAATTTTTTTTTC
1 TCATTTCATTTAAATTATATTTTTTCAATTTAATTTTTTTTTC
* * * * *
47348406 TCATTTCATTTATATTATTTTTTATTTAAATTAA-TTTTTTTCC
1 TCATTTCATTTAAATTATATTTT-TTCAATTTAATTTTTTTTTC
* *
47348449 TTATTTCATTTAAATTTATCTTTCTTTCAATTTTAATTAAATTTTTTTC
1 TCATTTCATTTAAA-TTATATTT-TTTCAA-TTTAATT---TTTTTTTC
*
47348498 TCATTTCATTTAAATTAAATTTTTTC
1 TCATTTCATTTAAATTATATTTTTTC
47348524 CTCATTTCAT
Statistics
Matches: 96, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
43 41 0.43
44 19 0.20
45 5 0.05
46 1 0.01
47 4 0.04
48 6 0.06
49 20 0.21
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (43 bp):
TCATTTCATTTAAATTATATTTTTTCAATTTAATTTTTTTTTC
Found at i:47348438 original size:16 final size:17
Alignment explanation
Indices: 47348413--47348445 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
47348403 TTCTCATTTC
*
47348413 ATTTATATT-ATTTTTT
1 ATTTAAATTAATTTTTT
47348429 ATTTAAATTAATTTTTT
1 ATTTAAATTAATTTTTT
47348446 TCCTTATTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTAAATTAATTTTTT
Found at i:47348461 original size:27 final size:26
Alignment explanation
Indices: 47348429--47348692 Score: 196
Period size: 27 Copynumber: 10.3 Consensus size: 26
47348419 ATTATTTTTT
*
47348429 ATTTAAATTAATTTTTTTCCTTATTTC
1 ATTTAAATTAATTTTTTT-CTCATTTC
* *
47348456 ATTTAAA-T--TTATCTT-TC-TTTC
1 ATTTAAATTAATTTTTTTCTCATTTC
*
47348477 AATTTTAATTAAATTTTTTTCTCATTTC
1 -ATTTAAATT-AATTTTTTTCTCATTTC
*
47348505 ATTTAAATTAAATTTTTTCCTCATTTC
1 ATTTAAATT-AATTTTTTTCTCATTTC
* * *
47348532 ATTTAAATTTATCTTTCTT-TCA-AT-
1 ATTTAAATTAAT-TTTTTTCTCATTTC
* *
47348556 -TTTAATTTAATTTTTTTCTAATTTC
1 ATTTAAATTAATTTTTTTCTCATTTC
*
47348581 ATTTAAATTAAATTTTTTCCTCATTTC
1 ATTTAAATT-AATTTTTTTCTCATTTC
* *
47348608 ATTTAAATTTATTTTTCTT-TCA-AT-
1 ATTTAAATTAATTTTT-TTCTCATTTC
*
47348632 -TTTAATTTTAA-TTTTTTCTCATTTC
1 ATTTAA-ATTAATTTTTTTCTCATTTC
* * *
47348657 TTTTAAATTAAAATTTTTCCTCATTTC
1 ATTTAAATT-AATTTTTTTCTCATTTC
47348684 ATTTAAATT
1 ATTTAAATT
47348693 TATCTTTCTT
Statistics
Matches: 187, Mismatches: 29, Indels: 42
0.72 0.11 0.16
Matches are distributed among these distances:
21 4 0.02
22 14 0.07
23 24 0.13
24 10 0.05
25 4 0.02
26 34 0.18
27 93 0.50
28 4 0.02
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTAAATTAATTTTTTTCTCATTTC
Found at i:47348467 original size:49 final size:48
Alignment explanation
Indices: 47348413--47348674 Score: 144
Period size: 49 Copynumber: 5.2 Consensus size: 48
47348403 TTCTCATTTC
*
47348413 ATTTATATTATTTTTTATTTAAATTAATTTTTTTCCTTATTTCATTTAA
1 ATTTATATT-TTTTTTATTTAAATTAATTTTTTTCCTCATTTCATTTAA
* ** *
47348462 ATTTATCTTTCTTTCAATTTTAATTAAATTTTTTT-CTCATTTCATTTAA
1 ATTTATATTT-TTTTTATTTAAATT-AATTTTTTTCCTCATTTCATTTAA
* * * * * *
47348511 A-TTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTTAATTT-A
1 ATTTATATTTTTT--TTATTTAAATT-AATTT-T-TTTC-CTC-A-TTTCATTTAA
* *
47348565 ATTT-T-TTTCTAATTTCATTTAAATTAAATTTTTTCCTCATTTCATTTAA
1 ATTTATATTT-T--TTTTATTTAAATTAATTTTTTTCCTCATTTCATTTAA
* * *
47348614 ATTTAT-TTTTCTTTCAATTTTAATTTTAA-TTTTTT-CTCATTTCTTTTAA
1 ATTTATATTTT-TTT-TA-TTTAA-ATTAATTTTTTTCCTCATTTCATTTAA
* *
47348663 ATTAAAATTTTT
1 ATTTATATTTTT
47348675 CCTCATTTCA
Statistics
Matches: 168, Mismatches: 25, Indels: 40
0.72 0.11 0.17
Matches are distributed among these distances:
47 3 0.02
48 17 0.10
49 72 0.43
50 31 0.18
51 11 0.07
52 1 0.01
53 9 0.05
54 13 0.08
55 9 0.05
56 2 0.01
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.62
Consensus pattern (48 bp):
ATTTATATTTTTTTTATTTAAATTAATTTTTTTCCTCATTTCATTTAA
Found at i:47348521 original size:76 final size:76
Alignment explanation
Indices: 47348429--47348704 Score: 473
Period size: 76 Copynumber: 3.6 Consensus size: 76
47348419 ATTATTTTTT
* * *
47348429 ATTTAAATTAATTTTTTTCCTTATTTCATTTAAATTTATCTTTCTTTCAATTTTAATTAAATTTT
1 ATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTTAATTTAATTTT
47348494 TTTCTCATTTC
66 TTTCTCATTTC
47348505 ATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTTAATTTAATTTT
1 ATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTTAATTTAATTTT
*
47348570 TTTCTAATTTC
66 TTTCTCATTTC
*
47348581 ATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATTTTTCTTTCAATTTTAATTTTAA-TT
1 ATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTTAA-TTTAATTT
47348645 TTTTCTCATTTC
65 TTTTCTCATTTC
* *
47348657 TTTTAAATTAAAATTTTTCCTCATTTCATTTAAATTTATCTTTCTTTC
1 ATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTC
47348705 CTTGTAAATT
Statistics
Matches: 190, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
76 185 0.97
77 5 0.03
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (76 bp):
ATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTTAATTTAATTTT
TTTCTCATTTC
Found at i:47348692 original size:21 final size:21
Alignment explanation
Indices: 47348667--47348786 Score: 62
Period size: 21 Copynumber: 5.2 Consensus size: 21
47348657 TTTTAAATTA
47348667 AAATTTTTCCTCATTTCATTT
1 AAATTTTTCCTCATTTCATTT
* * *
47348688 AAATTTATCTTTCTTTCCTTGTAAATTT
1 AAA--T-T-TTTC-CTCATT-TCA-TTT
* *
47348716 AAAATTTTCCTCAATTCATTT
1 AAATTTTTCCTCATTTCATTT
*
47348737 ATATTATTTTTGCTCATTTCAATTT
1 A-A--ATTTTTCCTCATTTC-ATTT
* *
47348762 -ATTTTTTTCTCATTTCATTT
1 AAATTTTTCCTCATTTCATTT
47348782 AAATT
1 AAATT
47348787 ATCTATCTTT
Statistics
Matches: 73, Mismatches: 14, Indels: 24
0.66 0.13 0.22
Matches are distributed among these distances:
20 4 0.05
21 23 0.32
22 3 0.04
23 5 0.07
24 17 0.23
25 9 0.12
26 4 0.05
27 2 0.03
28 6 0.08
ACGTcount: A:0.26, C:0.15, G:0.02, T:0.57
Consensus pattern (21 bp):
AAATTTTTCCTCATTTCATTT
Found at i:47348713 original size:49 final size:47
Alignment explanation
Indices: 47348501--47348798 Score: 167
Period size: 49 Copynumber: 6.1 Consensus size: 47
47348491 TTTTTTCTCA
* *
47348501 TTTCATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTC
1 TTTCCTTTAAATTAAAATTTTTCCTCATTTCATTTAAA-TTATCTTTC
* * * * * * **
47348549 TTTCAATTTTAATTTAATTTTTTTCTAATTTCATTTAAATTAAATTT-
1 TTTC-CTTTAAATTAAAATTTTTCCTCATTTCATTTAAATTATCTTTC
* * * * * *
47348596 TTTCCTCATTTCATTTAAATTTATTTTTCTTTCAATTTTAATTTTAATT-TTTTCTC
1 TTT-C-C-TTTAAATTAAA---ATTTTTC-CTC-A-TTTCATTTAAATTATCTT-TC
*
47348652 ATTTCTTTTAAATTAAAATTTTTCCTCATTTCATTTAAATTTATCTTTC
1 -TTTCCTTTAAATTAAAATTTTTCCTCATTTCATTTAAA-TTATCTTTC
* *
47348701 TTTCCTTGTAAATTTAAAA-TTTTCCTCAATTCATTTATATTAT-TTT-
1 TTTCCTT-TAAA-TTAAAATTTTTCCTCATTTCATTTAAATTATCTTTC
* * * * * * *
47348747 TGCTCATTTCAATT-TATTTTTTTCTCATTTCATTTAAATTATCTATC
1 T-TTCCTTTAAATTAAAATTTTTCCTCATTTCATTTAAATTATCTTTC
47348794 TTTCC
1 TTTCC
47348799 ATGTAATTTT
Statistics
Matches: 190, Mismatches: 40, Indels: 42
0.70 0.15 0.15
Matches are distributed among these distances:
44 1 0.01
45 23 0.12
46 8 0.04
47 11 0.06
48 30 0.16
49 65 0.34
50 11 0.06
51 7 0.04
52 5 0.03
53 1 0.01
54 12 0.06
55 12 0.06
56 1 0.01
57 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.01, T:0.59
Consensus pattern (47 bp):
TTTCCTTTAAATTAAAATTTTTCCTCATTTCATTTAAATTATCTTTC
Found at i:47348734 original size:152 final size:152
Alignment explanation
Indices: 47348429--47348762 Score: 473
Period size: 152 Copynumber: 2.2 Consensus size: 152
47348419 ATTATTTTTT
* *
47348429 ATTTAAATTAATTTTTTTCCTTATTTCATTTAAATTTATCTTTCTTTCAATTTTAATTAAATTTT
1 ATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTTAATTAAATTTT
* *
47348494 TTTCTCATTTCATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTT
66 TTTCTCATTTCATTTAAATTAAAATTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTA
** *
47348559 AATTTAATTTTTTTCTAATTTC
131 AATTTAAAATTTTCCTAATTTC
* *
47348581 ATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATTTTTCTTTCAATTTTAATTTTAA-TT
1 ATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTTAA-TTAAATTT
* *
47348645 TTTTCTCATTTCTTTTAAATTAAAATTTTTCCTCATTTCATTTAAATTTATCTTTCTTTC-CTTG
65 TTTTCTCATTTCATTTAAATTAAAATTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATT-
47348709 TAAATTTAAAATTTTCCTCAA-TTC
129 TAAATTTAAAATTTTCCT-AATTTC
* *
47348733 ATTTATATT--A-TTTTTGCTCATTTCAATTTA
1 ATTTAAATTAAATTTTTTCCTCATTTC-ATTTA
47348763 TTTTTTTCTC
Statistics
Matches: 165, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
149 13 0.08
150 6 0.04
151 2 0.01
152 138 0.84
153 6 0.04
ACGTcount: A:0.27, C:0.13, G:0.01, T:0.60
Consensus pattern (152 bp):
ATTTAAATTAAATTTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTTAATTAAATTTT
TTTCTCATTTCATTTAAATTAAAATTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCAATTTA
AATTTAAAATTTTCCTAATTTC
Found at i:47348765 original size:20 final size:20
Alignment explanation
Indices: 47348731--47348782 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
47348721 TTTCCTCAAT
47348731 TCATTT-ATATTA-TTTTTGC
1 TCATTTCAT-TTATTTTTTGC
*
47348750 TCATTTCAATTTATTTTTTTC
1 TCATTTC-ATTTATTTTTTGC
47348771 TCATTTCATTTA
1 TCATTTCATTTA
47348783 AATTATCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.21
20 8 0.28
21 15 0.52
ACGTcount: A:0.21, C:0.13, G:0.02, T:0.63
Consensus pattern (20 bp):
TCATTTCATTTATTTTTTGC
Found at i:47348829 original size:93 final size:94
Alignment explanation
Indices: 47348670--47348840 Score: 229
Period size: 93 Copynumber: 1.8 Consensus size: 94
47348660 TAAATTAAAA
* *
47348670 TTTTTCCTCATTTCATTTAAATTTATCTTTCTTTCCTTGTAAATTTAAAATTTTCCTCAATTCAT
1 TTTTTCCTCATTTCATTTAAATTTATCTATCTTTCCATGTAAATTTAAAATTTTCCTCAATTCAT
*
47348735 TTATATTATTTTTGCTCATTTCAATTTAT
66 TTATATAATTTTTGCTCATTTCAATTTAT
* * * ** *
47348764 TTTTTTCTCATTTCATTTAAA-TTATCTATCTTTCCATGTAATTTTCATTTTTTTCTC-ATTCCA
1 TTTTTCCTCATTTCATTTAAATTTATCTATCTTTCCATGTAAATTTAAAATTTTCCTCAATT-CA
*
47348827 TTTATCTAATTTTT
65 TTTATATAATTTTT
47348841 TATATATTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
92 3 0.05
93 43 0.65
94 20 0.30
ACGTcount: A:0.23, C:0.16, G:0.02, T:0.59
Consensus pattern (94 bp):
TTTTTCCTCATTTCATTTAAATTTATCTATCTTTCCATGTAAATTTAAAATTTTCCTCAATTCAT
TTATATAATTTTTGCTCATTTCAATTTAT
Found at i:47350899 original size:13 final size:14
Alignment explanation
Indices: 47350883--47350918 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
47350873 CAATCTCATA
47350883 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
47350896 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
47350909 TCTC-ATTTCA
1 TCTCAATTTCA
47350919 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:47350908 original size:18 final size:19
Alignment explanation
Indices: 47350870--47350910 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
47350860 TGGTTCATGT
47350870 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
47350889 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
47350907 TTTC
1 TTTC
47350911 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:47351100 original size:39 final size:38
Alignment explanation
Indices: 47351033--47351167 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
47351023 ACCAATATGG
* * *
47351033 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
47351072 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
47351110 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
47351151 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
47351168 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:47351433 original size:18 final size:19
Alignment explanation
Indices: 47351407--47351445 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
47351397 TTTCAATTCA
47351407 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
47351426 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
47351444 AT
1 AT
47351446 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:47352771 original size:5 final size:5
Alignment explanation
Indices: 47352761--47352817 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
47352751 TTACTTATTT
* *
47352761 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
47352809 ATAT- ATATA
1 ATATA ATATA
47352818 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:47352777 original size:12 final size:12
Alignment explanation
Indices: 47352760--47352815 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
47352750 TTTACTTATT
47352760 TATATAATATAA
1 TATATAATATAA
47352772 TATATAATATAATA
1 TATATAATAT-A-A
47352786 TACTATAATATAA
1 TA-TATAATATAA
*
47352799 TA-ATAATTTAA
1 TATATAATATAA
47352810 TATATA
1 TATATA
47352816 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:47352830 original size:26 final size:26
Alignment explanation
Indices: 47352762--47352817 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
47352752 TACTTATTTA
*
47352762 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
47352789 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
47352814 TATA
1 TATA
47352818 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:47355039 original size:118 final size:116
Alignment explanation
Indices: 47354736--47355414 Score: 522
Period size: 117 Copynumber: 5.9 Consensus size: 116
47354726 TTTTTATATC
* * * **
47354736 TCTGGTGCTGGCCATCAATGTAGAAAAGTAAAAAAATTTTGCATTGGGACACGAAAAAAGTCCTT
1 TCTGGTGCCGACCATCAGTGTAGAAAAGTAAAAAAAAATTGCATTGGGACACGAAAAAAGTCCTT
* * *
47354801 GGTTCTGGCCATTAGAAGGCTAGAACCAATTTTTTTTAAAAAAAAAATTACTGG
66 GGTGCTGGCCATTAGAAGGCCAAAACCAATTTTTTTT---AAAAAAATTACTGG
* * *
47354855 TTTGGTGCCGACCATCAGTGTAGAAAAGT--AAAAAAATTGCATTGGGACACGAAAAAAGCCCCT
1 TCTGGTGCCGACCATCAGTGTAGAAAAGTAAAAAAAAATTGCATTGGGACACGAAAAAAGTCCTT
* * * *
47354918 GGTGCTAGTCATTAGAAGGCCAAAACCAAATTTTTTTT-TAAAAATTATTGG
66 GGTGCTGGCCATTAGAAGGCCAAAACC-AATTTTTTTTAAAAAAATTACTGG
* * * *
47354969 TCTGGTGCCGACCATTAGTGTAGAAAAGTAAAAAAAAAAATTACATTGGAATACGAAAAAAGTCC
1 TCTGGTGCCGACCATCAGTGTAGAAAAGT--AAAAAAAAATTGCATTGGGACACGAAAAAAGTCC
* * ** ****** *
47355034 TTGGTGCCGGCCATTAGAAGGCCAGAATAAAAAAAAATT---AAAATTACTAG
64 TTGGTGCTGGCCATTAGAAGGCCAAAACCAATTTTTTTTAAAAAAATTACTGG
* * * *
47355084 TCTGGTGCC-AGCCAT-AGTGTAAAAAAGT-AAAAAAAATTGTATTGGGATACG----AA-TCTT
1 TCTGGTGCCGA-CCATCAGTGTAGAAAAGTAAAAAAAAATTGCATTGGGACACGAAAAAAGTCCT
** ** **** *
47355141 TGGTGCCT-GCCATTAGAAGGCCAGGATAAAAAAATTTTAAAACAATTACTGG
65 TGGTG-CTGGCCATTAGAAGGCCAAAACCAATTTTTTTTAAAAAAATTACTGG
* * * * *
47355193 TTTGGTGTCGGCCATCAGTGTAGAAAAATAAAAAAAAAATTGCATTGGGACACGAAAAAAGTCCA
1 TCTGGTGCCGACCATCAGTGTAGAAAAGT-AAAAAAAAATTGCATTGGGACACGAAAAAAGTCCT
* ** *
47355258 TGGTGCTGGCCATTAGAAGGCCAGAACCCAAAATTTTTT-------TTACCGG
65 TGGTGCTGGCCATTAGAAGGCCA-AAACCAATTTTTTTTAAAAAAATTACTGG
* * * * * *
47355304 TCTGGAGCTGGCCATCAGTGTAGAAAGGTAAAAAAAAAATTTGCGTTGGGACACTAAAAAAGTCC
1 TCTGGTGCCGACCATCAGTGTAGAAAAGT-AAAAAAAAA-TTGCATTGGGACACGAAAAAAGTCC
* * * * *
47355369 CTGGTGCTGGCCATTAAAAGGCTAGAACCAA-ATTTTTTAAAAAAAT
64 TTGGTGCTGGCCATTAGAAGGCCAAAACCAATTTTTTTTAAAAAAAT
47355415 ATTAATATTT
Statistics
Matches: 454, Mismatches: 77, Indels: 60
0.77 0.13 0.10
Matches are distributed among these distances:
106 35 0.08
107 3 0.01
109 20 0.04
110 18 0.04
111 64 0.14
112 65 0.14
114 51 0.11
115 22 0.05
116 4 0.01
117 79 0.17
118 68 0.15
119 25 0.06
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (116 bp):
TCTGGTGCCGACCATCAGTGTAGAAAAGTAAAAAAAAATTGCATTGGGACACGAAAAAAGTCCTT
GGTGCTGGCCATTAGAAGGCCAAAACCAATTTTTTTTAAAAAAATTACTGG
Found at i:47355106 original size:106 final size:110
Alignment explanation
Indices: 47354998--47355283 Score: 282
Period size: 106 Copynumber: 2.6 Consensus size: 110
47354988 GTAGAAAAGT
* *
47354998 AAAAAAAAAAATTACATTGGAATACGAAAAAAGTCCTTGGTGCCGGCCATTAGAAGGCCAGAATA
1 AAAAAAAAAAATTGCATTGGGATACGAAAAAAGTCCTTGGTGCCGGCCATTAGAAGGCCAGAATA
47355063 AAAAAAAATT-AA-AATTACTAGTCTGGTGCCAGCCAT-AGTGTAAA
66 AAAAAAAATTAAACAATTACTAGTCTGGTGCCAGCCATCAGTGT--A
* * * *
47355107 AAAGTAAAAAAAATTGTATTGGGATACG----AA-TCTTTGGTGCCTGCCATTAGAAGGCCAGGA
1 AAA--AAAAAAAATTGCATTGGGATACGAAAAAAGTCCTTGGTGCCGGCCATTAGAAGGCCAGAA
** * * * *
47355167 TAAAAAAATTTTAAAACAATTACTGGTTTGGTGTCGGCCATCAGTGTAGAAAA
64 TAAAAAAAAATT-AAACAATTACTAGTCTGGTGCCAGCCATCAGTGT-----A
* * *
47355220 ATAAAAAAAAAATTGCATTGGGACACGAAAAAAGTCCATGGTGCTGGCCATTAGAAGGCCAGAA
1 A-AAAAAAAAAATTGCATTGGGATACGAAAAAAGTCCTTGGTGCCGGCCATTAGAAGGCCAGAA
47355284 CCCAAAATTT
Statistics
Matches: 143, Mismatches: 19, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
106 37 0.26
107 2 0.01
108 2 0.01
109 23 0.16
110 5 0.03
111 20 0.14
112 21 0.15
113 4 0.03
114 2 0.01
116 2 0.01
117 25 0.17
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (110 bp):
AAAAAAAAAAATTGCATTGGGATACGAAAAAAGTCCTTGGTGCCGGCCATTAGAAGGCCAGAATA
AAAAAAAATTAAACAATTACTAGTCTGGTGCCAGCCATCAGTGTA
Found at i:47355327 original size:111 final size:110
Alignment explanation
Indices: 47355202--47355406 Score: 322
Period size: 112 Copynumber: 1.9 Consensus size: 110
47355192 GTTTGGTGTC
47355202 GGCCATCAGTGTAGAAAAATAAAAAAAAAA-TTGCATTGGGACACGAAAAAAGTCCATGGTGCTG
1 GGCCATCAGTGTAGAAAAATAAAAAAAAAATTTGCATTGGGACACGAAAAAAGTCCATGGTGCTG
*
47355266 GCCATTAGAAGGCCAGAACCCAAAATTTTTTTTACCGGTCTGGAGCT
66 GCCATTAAAAGGCCAGAA-CC-AAATTTTTTTTACCGGTCTGGAGCT
** * * *
47355313 GGCCATCAGTGTAGAAAGGTAAAAAAAAAATTTGCGTTGGGACACTAAAAAAGTCCCTGGTGCTG
1 GGCCATCAGTGTAGAAAAATAAAAAAAAAATTTGCATTGGGACACGAAAAAAGTCCATGGTGCTG
*
47355378 GCCATTAAAAGGCTAGAACCAAATTTTTT
66 GCCATTAAAAGGCCAGAACCAAATTTTTT
47355407 AAAAAAATAT
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
110 9 0.10
111 30 0.35
112 47 0.55
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (110 bp):
GGCCATCAGTGTAGAAAAATAAAAAAAAAATTTGCATTGGGACACGAAAAAAGTCCATGGTGCTG
GCCATTAAAAGGCCAGAACCAAATTTTTTTTACCGGTCTGGAGCT
Found at i:47358216 original size:20 final size:20
Alignment explanation
Indices: 47358191--47358229 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
47358181 CAATCGGTTT
47358191 TAATTACACCAAA-TATTACC
1 TAATTACA-CAAATTATTACC
47358211 TAATTACACAAATTATTAC
1 TAATTACACAAATTATTAC
47358230 AAATATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
TAATTACACAAATTATTACC
Found at i:47359368 original size:13 final size:13
Alignment explanation
Indices: 47359350--47359378 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
47359340 TATTGATGTC
47359350 ATTGAAATATAAT
1 ATTGAAATATAAT
47359363 ATTGAAATATAAT
1 ATTGAAATATAAT
47359376 ATT
1 ATT
47359379 TTGGTCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (13 bp):
ATTGAAATATAAT
Found at i:47362667 original size:18 final size:18
Alignment explanation
Indices: 47362644--47362685 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
47362634 TAAAAAAAAC
47362644 CAAGTCCGAATTATCTTG
1 CAAGTCCGAATTATCTTG
47362662 CAAGTCCGAATTATCTTG
1 CAAGTCCGAATTATCTTG
*
47362680 CTAGTC
1 CAAGTC
47362686 GGCCACCTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (18 bp):
CAAGTCCGAATTATCTTG
Found at i:47363500 original size:28 final size:29
Alignment explanation
Indices: 47363459--47363571 Score: 115
Period size: 29 Copynumber: 4.0 Consensus size: 29
47363449 CCTGTATCTA
* * *
47363459 GCCCATTAAGCCC-ATTCATATTCATATG
1 GCCCATTAGGCCCAAATCACATTCATATG
* *
47363487 ACCCATTAGGCCCAAATCACCTGT-ATATG
1 GCCCATTAGGCCCAAATCACAT-TCATATG
* *
47363516 GCCCATTAGGCCCAAATCATATTTATATG
1 GCCCATTAGGCCCAAATCACATTCATATG
* *
47363545 GCCCGTTAGGCCC-AGTCACATTCATAT
1 GCCCATTAGGCCCAAATCACATTCATAT
47363572 TCATGCTCAC
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
28 23 0.33
29 46 0.66
30 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.28
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCACATTCATATG
Found at i:47363558 original size:58 final size:57
Alignment explanation
Indices: 47363448--47363558 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 57
47363438 AAATTCACAT
* *
47363448 ACCTGTATCTAGCCCATTAAGCCCATTCATATTCATATGACCCATTAGGCCCAAATC
1 ACCTGTATATAGCCCATTAAGCCCAATCATATTCATATGACCCATTAGGCCCAAATC
* * * * *
47363505 ACCTGTATATGGCCCATTAGGCCCAAATCATATTTATATGGCCCGTTAGGCCCA
1 ACCTGTATATAGCCCATTAAGCCC-AATCATATTCATATGACCCATTAGGCCCA
47363559 GTCACATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 21 0.46
58 25 0.54
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (57 bp):
ACCTGTATATAGCCCATTAAGCCCAATCATATTCATATGACCCATTAGGCCCAAATC
Found at i:47367575 original size:392 final size:392
Alignment explanation
Indices: 47366851--47367634 Score: 1568
Period size: 392 Copynumber: 2.0 Consensus size: 392
47366841 CAAAGACTTG
47366851 AGCAAAGGAAGAATAGAGAATCGGCACAAGAAAAGAAAGAAGGAAGCAAGGGTTTTCGGCTTTTT
1 AGCAAAGGAAGAATAGAGAATCGGCACAAGAAAAGAAAGAAGGAAGCAAGGGTTTTCGGCTTTTT
47366916 GGATCTTGAAGAGAATAGGGTTTTCGGTAGCAAGGTGAAAAAAGATTTCGGCATTAGCCTGATAC
66 GGATCTTGAAGAGAATAGGGTTTTCGGTAGCAAGGTGAAAAAAGATTTCGGCATTAGCCTGATAC
47366981 CCTTGCATTCAACACCTATTTATAACCCTTATGGCCAAATTCCTCAAGCCCAAGTTCCCATTTCG
131 CCTTGCATTCAACACCTATTTATAACCCTTATGGCCAAATTCCTCAAGCCCAAGTTCCCATTTCG
47367046 GGTCCACTTGCTCCTCACTTCTCATCCCCTCATTTTTCTCCCTGATAACCCCTTGATCCTTTCCT
196 GGTCCACTTGCTCCTCACTTCTCATCCCCTCATTTTTCTCCCTGATAACCCCTTGATCCTTTCCT
47367111 CAAATTTCTCTTTTGATCACTCCCTTTGGAGTCCATCTTCATGCCACTTCCATCCTTCTAGAAGG
261 CAAATTTCTCTTTTGATCACTCCCTTTGGAGTCCATCTTCATGCCACTTCCATCCTTCTAGAAGG
47367176 CCAAAATTAAACTTCTAAAAGTACTAAACTAGGATTCAAACCTTGGATCCCCTTGCTAGCCACTA
326 CCAAAATTAAACTTCTAAAAGTACTAAACTAGGATTCAAACCTTGGATCCCCTTGCTAGCCACTA
47367241 AT
391 AT
47367243 AGCAAAGGAAGAATAGAGAATCGGCACAAGAAAAGAAAGAAGGAAGCAAGGGTTTTCGGCTTTTT
1 AGCAAAGGAAGAATAGAGAATCGGCACAAGAAAAGAAAGAAGGAAGCAAGGGTTTTCGGCTTTTT
47367308 GGATCTTGAAGAGAATAGGGTTTTCGGTAGCAAGGTGAAAAAAGATTTCGGCATTAGCCTGATAC
66 GGATCTTGAAGAGAATAGGGTTTTCGGTAGCAAGGTGAAAAAAGATTTCGGCATTAGCCTGATAC
47367373 CCTTGCATTCAACACCTATTTATAACCCTTATGGCCAAATTCCTCAAGCCCAAGTTCCCATTTCG
131 CCTTGCATTCAACACCTATTTATAACCCTTATGGCCAAATTCCTCAAGCCCAAGTTCCCATTTCG
47367438 GGTCCACTTGCTCCTCACTTCTCATCCCCTCATTTTTCTCCCTGATAACCCCTTGATCCTTTCCT
196 GGTCCACTTGCTCCTCACTTCTCATCCCCTCATTTTTCTCCCTGATAACCCCTTGATCCTTTCCT
47367503 CAAATTTCTCTTTTGATCACTCCCTTTGGAGTCCATCTTCATGCCACTTCCATCCTTCTAGAAGG
261 CAAATTTCTCTTTTGATCACTCCCTTTGGAGTCCATCTTCATGCCACTTCCATCCTTCTAGAAGG
47367568 CCAAAATTAAACTTCTAAAAGTACTAAACTAGGATTCAAACCTTGGATCCCCTTGCTAGCCACTA
326 CCAAAATTAAACTTCTAAAAGTACTAAACTAGGATTCAAACCTTGGATCCCCTTGCTAGCCACTA
47367633 AT
391 AT
47367635 GCCACCTCCC
Statistics
Matches: 392, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
392 392 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (392 bp):
AGCAAAGGAAGAATAGAGAATCGGCACAAGAAAAGAAAGAAGGAAGCAAGGGTTTTCGGCTTTTT
GGATCTTGAAGAGAATAGGGTTTTCGGTAGCAAGGTGAAAAAAGATTTCGGCATTAGCCTGATAC
CCTTGCATTCAACACCTATTTATAACCCTTATGGCCAAATTCCTCAAGCCCAAGTTCCCATTTCG
GGTCCACTTGCTCCTCACTTCTCATCCCCTCATTTTTCTCCCTGATAACCCCTTGATCCTTTCCT
CAAATTTCTCTTTTGATCACTCCCTTTGGAGTCCATCTTCATGCCACTTCCATCCTTCTAGAAGG
CCAAAATTAAACTTCTAAAAGTACTAAACTAGGATTCAAACCTTGGATCCCCTTGCTAGCCACTA
AT
Found at i:47367903 original size:16 final size:17
Alignment explanation
Indices: 47367875--47367913 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
47367865 ACAAAAAAAG
47367875 TTTGGGATTTCGAGATT
1 TTTGGGATTTCGAGATT
47367892 TTTGGG-TTTCGAGATT
1 TTTGGGATTTCGAGATT
47367908 TTTGGG
1 TTTGGG
47367914 GCATTACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.13, C:0.05, G:0.33, T:0.49
Consensus pattern (17 bp):
TTTGGGATTTCGAGATT
Found at i:47368223 original size:18 final size:19
Alignment explanation
Indices: 47368197--47368237 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
47368187 GGCCTCTCGA
47368197 CGGTAGCTG-ACCACC-CCT
1 CGGTAGCTGTA-CACCACCT
*
47368215 CGGTGGCTGTACACCACCT
1 CGGTAGCTGTACACCACCT
47368234 CGGT
1 CGGT
47368238 CCACGACTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.15, C:0.39, G:0.27, T:0.20
Consensus pattern (19 bp):
CGGTAGCTGTACACCACCT
Found at i:47381660 original size:46 final size:44
Alignment explanation
Indices: 47381601--47381715 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
47381591 ACAGGACAGA
* *
47381601 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
47381647 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
47381691 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
47381716 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:47381696 original size:44 final size:45
Alignment explanation
Indices: 47381601--47381734 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
47381591 ACAGGACAGA
* *
47381601 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
47381647 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
47381691 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
47381735 TAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:47399473 original size:31 final size:31
Alignment explanation
Indices: 47399438--47399498 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
47399428 CTGATCAGGC
47399438 AGAGGGGTTATCTAATATGATTTCAGTAATA
1 AGAGGGGTTATCTAATATGATTTCAGTAATA
* *
47399469 AGAGGGGTTATCTGATATGATTTCGGTAAT
1 AGAGGGGTTATCTAATATGATTTCAGTAAT
47399499 GCCAGCACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (31 bp):
AGAGGGGTTATCTAATATGATTTCAGTAATA
Found at i:47406762 original size:14 final size:14
Alignment explanation
Indices: 47406739--47406768 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
47406729 TTGAAAATAT
47406739 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
47406753 GTTGATTTGGATTG
1 GTTGAATTGGATTG
47406767 GT
1 GT
47406769 CTCGATATAA
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:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:47410173 original size:31 final size:31
Alignment explanation
Indices: 47410137--47410195 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
47410127 AAATGAAATG
*
47410137 TGAAAATATGAATAATTACAGGGTATGAAAA
1 TGAAAATATGAACAATTACAGGGTATGAAAA
* *
47410168 TGAAAATGTGACCAATTACAGGGTATGA
1 TGAAAATATGAACAATTACAGGGTATGA
47410196 TGAGCAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.25
Consensus pattern (31 bp):
TGAAAATATGAACAATTACAGGGTATGAAAA
Found at i:47416295 original size:26 final size:26
Alignment explanation
Indices: 47416252--47416302 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
47416242 GACTTGAGAA
** *
47416252 TTAATTAAATATTTTTAAATTATTAT
1 TTAATTAAATATAATTAAATAATTAT
*
47416278 TTAATTAATTATAATTAAATAATTA
1 TTAATTAAATATAATTAAATAATTA
47416303 AAATTCTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAATTAAATATAATTAAATAATTAT
Found at i:47417478 original size:17 final size:18
Alignment explanation
Indices: 47417456--47417489 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
47417446 GATAGATTAT
47417456 TAAACTTG-GTTGTTAAA
1 TAAACTTGTGTTGTTAAA
47417473 TAAACTTGTGTTGTTAA
1 TAAACTTGTGTTGTTAA
47417490 GTGTTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (18 bp):
TAAACTTGTGTTGTTAAA
Found at i:47425032 original size:37 final size:37
Alignment explanation
Indices: 47424969--47425040 Score: 85
Period size: 37 Copynumber: 1.9 Consensus size: 37
47424959 ATTATTATGG
*
47424969 TATTGAATTGAATAAAAATTTATGAATTATT-AGTGAT
1 TATTGAATTGAATAAAAATATATGAA-TATTGAGTGAT
* *
47425006 TATTGATATTGAAT-AGAATATGTGAATATTGAGTG
1 TATTGA-ATTGAATAAAAATATATGAATATTGAGTG
47425041 GAAAATTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 4 0.13
37 19 0.63
38 7 0.23
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (37 bp):
TATTGAATTGAATAAAAATATATGAATATTGAGTGAT
Found at i:47425380 original size:6 final size:6
Alignment explanation
Indices: 47425369--47425395 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
47425359 TGTGTACCGC
47425369 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
47425396 CCTTACAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:47431761 original size:48 final size:49
Alignment explanation
Indices: 47431595--47431824 Score: 188
Period size: 48 Copynumber: 4.8 Consensus size: 49
47431585 TCATTTGTAT
* * * **
47431595 GCTAGTGTAAGACATGTCTGGGACATGCATCGGC-CCCCAGATATTTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGC-GAGATGCAGA
* * * *
47431643 GCCAGTGTAAGACATGTCTGGGACATACATCAGCAT--TGAG-T-CGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGCGAGATGC-AGA
* * *
47431689 GCTAGTGTAAGACATGCCTAGGACATGCATCGGCCTCGCGAGATGCA-A
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGCGAGATGCAGA
* * * **
47431737 GCTAGTGTAAGACCTGTCTGGGACATGGCATCGACATTGATAGATG-AGA
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCATCGCGAGATGCAGA
* *
47431786 GCCAGTGTAAGACCATGTCTGGGACATGGCGTCGGCATC
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATC
47431825 TTAACCCATG
Statistics
Matches: 145, Mismatches: 27, Indels: 18
0.76 0.14 0.09
Matches are distributed among these distances:
45 2 0.01
46 33 0.23
48 59 0.41
49 28 0.19
50 23 0.16
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (49 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCGCGAGATGCAGA
Found at i:47439321 original size:46 final size:48
Alignment explanation
Indices: 47439212--47439440 Score: 186
Period size: 48 Copynumber: 4.8 Consensus size: 48
47439202 TCATTTGTAT
* * * * **
47439212 GCTAGTGTAAGACAGGACTGGGACAT-GCATCGGCCTCGAGATATTTA-A
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAG-TA-CGAGA
* *
47439260 GCCAGTGTAAGACATGTCTGAGACAT-GCATCGGCATTGAGT-CGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGTACGAGA
* * *
47439306 GCTAGTGTAAGACATGCCTGGGACAT-GCATCGGCCTCGCGAGATAC-A-A
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCAT--TGAG-TACGAGA
* * * *
47439354 GCTAGTGTAAGACCTGGCTGGGACATGGCATCGACATTGA-TAAATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGT--ACGAGA
*
47439403 GCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCAT
1 GCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGCAT
47439441 CTTAACCCAT
Statistics
Matches: 147, Mismatches: 23, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
45 2 0.01
46 33 0.22
47 4 0.03
48 63 0.43
49 23 0.16
50 22 0.15
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGAGTACGAGA
Found at i:47439379 original size:94 final size:95
Alignment explanation
Indices: 47439212--47439435 Score: 272
Period size: 94 Copynumber: 2.3 Consensus size: 95
47439202 TCATTTGTAT
* * ** *
47439212 GCTAGTGTAAGACAGGACTGGGACATGCATCGGCCTCGAGATATTTAAGCCAGTGTAAGACATGT
1 GCTAGTGTAAGACATGACTGGGACATGCATCGGCCTCGAGAGATACAAGCCAGTGTAAGACATGG
*
47439277 CTGAGACAT-GCATCGGCATTGAGT-CGAGA
66 CTGAGACATGGCATCGACATTGA-TACGAGA
* * * *
47439306 GCTAGTGTAAGACATGCCTGGGACATGCATCGGCCTCGCGAGATACAAGCTAGTGTAAGACCTGG
1 GCTAGTGTAAGACATGACTGGGACATGCATCGGCCTCGAGAGATACAAGCCAGTGTAAGACATGG
* *
47439371 CTGGGACATGGCATCGACATTGATAAATGAGA
66 CTGAGACATGGCATCGACATTGAT--ACGAGA
*
47439403 GCTAGTGTAAGACCATGTCTGGGACATGGCATC
1 GCTAGTGTAAGA-CATGACTGGGACAT-GCATC
47439436 AGCATCTTAA
Statistics
Matches: 111, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
94 65 0.59
95 12 0.11
97 16 0.14
98 13 0.12
99 5 0.05
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (95 bp):
GCTAGTGTAAGACATGACTGGGACATGCATCGGCCTCGAGAGATACAAGCCAGTGTAAGACATGG
CTGAGACATGGCATCGACATTGATACGAGA
Found at i:47442730 original size:20 final size:21
Alignment explanation
Indices: 47442702--47442750 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
47442692 CTCTTAAAAA
*
47442702 TTTTAAAAAATAATTCCA-ATT
1 TTTTAAAAAA-AATTCAAGATT
*
47442723 TTTTAAAAAAAATTTAAGATT
1 TTTTAAAAAAAATTCAAGATT
47442744 TTTTAAA
1 TTTTAAA
47442751 TTTTTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTTAAAAAAAATTCAAGATT
Found at i:47443330 original size:17 final size:17
Alignment explanation
Indices: 47443308--47443389 Score: 123
Period size: 17 Copynumber: 4.9 Consensus size: 17
47443298 ATTTATAAAA
*
47443308 ATTAAGAAATTAA-CTCT
1 ATTAAG-AATTAATTTCT
*
47443325 ATTAAGAATTAATTTCA
1 ATTAAGAATTAATTTCT
47443342 ATTAAGAATTAATTT-T
1 ATTAAGAATTAATTTCT
47443358 ATTAAGAATTAATTTCT
1 ATTAAGAATTAATTTCT
47443375 ATTAAGAATTAATTT
1 ATTAAGAATTAATTT
47443390 TTATAATAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
16 21 0.35
17 39 0.65
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (17 bp):
ATTAAGAATTAATTTCT
Found at i:47443361 original size:33 final size:33
Alignment explanation
Indices: 47443307--47443390 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
47443297 AATTTATAAA
* *
47443307 AATTAAGAAATTAACTCTATTAAGAATTAATTTC
1 AATTAAG-AATTAATTTTATTAAGAATTAATTTC
47443341 AATTAAGAATTAATTTTATTAAGAATTAATTTC
1 AATTAAGAATTAATTTTATTAAGAATTAATTTC
*
47443374 TATTAAGAATTAATTTT
1 AATTAAGAATTAATTTT
47443391 TATAATAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 40 0.85
34 7 0.15
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (33 bp):
AATTAAGAATTAATTTTATTAAGAATTAATTTC
Found at i:47449858 original size:23 final size:23
Alignment explanation
Indices: 47449814--47449865 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
47449804 TTAATATTTG
* *
47449814 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATAAAATTAAA
47449837 TGAACATGTTCG-TGAAAATTAAA
1 TGAACATGTTCGAT-AAAATTAAA
*
47449860 TAAACA
1 TGAACA
47449866 AACATAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (23 bp):
TGAACATGTTCGATAAAATTAAA
Found at i:47450361 original size:33 final size:35
Alignment explanation
Indices: 47450292--47450363 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 35
47450282 TATTTTTTTA
47450292 TTTAAAAAATAGTAAGTTAATCTTTATATATTAAAT
1 TTTAAAAAATAG-AAGTTAATCTTTATATATTAAAT
* *
47450328 TTTAAAAAATA-AA-TTAAT-TTTTTCTATTAAAAT
1 TTTAAAAAATAGAAGTTAATCTTTATATATT-AAAT
47450361 TTT
1 TTT
47450364 TATTTATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
32 8 0.24
33 12 0.36
34 2 0.06
36 11 0.33
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (35 bp):
TTTAAAAAATAGAAGTTAATCTTTATATATTAAAT
Found at i:47453516 original size:21 final size:22
Alignment explanation
Indices: 47453487--47453527 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
47453477 TCGTGTTACA
47453487 AAGGCACAC-GCCCGTGTGAAGT
1 AAGGCACACAG-CCGTGTGAAGT
47453509 AAGG-ACACAGCCGTGTGAA
1 AAGGCACACAGCCGTGTGAA
47453528 CAGGCCGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.32, C:0.24, G:0.32, T:0.12
Consensus pattern (22 bp):
AAGGCACACAGCCGTGTGAAGT
Found at i:47453781 original size:21 final size:21
Alignment explanation
Indices: 47453746--47453794 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
47453736 ACCTACATGC
* *
47453746 CCGTGAGCCCAAGGGACACAG
1 CCGTGTGCTCAAGGGACACAG
*
47453767 CTGTGTGCTCAAGGGACACAG
1 CCGTGTGCTCAAGGGACACAG
47453788 CCGTGTG
1 CCGTGTG
47453795 AATTCTAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.29, G:0.35, T:0.14
Consensus pattern (21 bp):
CCGTGTGCTCAAGGGACACAG
Found at i:47463244 original size:46 final size:46
Alignment explanation
Indices: 47463194--47463366 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
47463184 TGGTTGAGCA
47463194 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
47463240 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
47463285 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
47463333 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
47463367 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:47463350 original size:93 final size:93
Alignment explanation
Indices: 47463191--47463361 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
47463181 GGATGGTTGA
* *
47463191 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
47463256 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
47463284 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
47463349 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
47463362 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:47466517 original size:28 final size:30
Alignment explanation
Indices: 47466448--47466506 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
47466438 TATGAAATTC
**
47466448 TGTTAGACTGATTTGATTAGGATACTAATA
1 TGTTAGACTGATCAGATTAGGATACTAATA
47466478 TGTTAGACTGATCAGATTAGGATACTAAT
1 TGTTAGACTGATCAGATTAGGATACTAAT
47466507 GTGTGCCTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.37
Consensus pattern (30 bp):
TGTTAGACTGATCAGATTAGGATACTAATA
Found at i:47471831 original size:24 final size:24
Alignment explanation
Indices: 47471768--47471831 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
47471758 GAATTTTATA
*
47471768 TTTTTCTATTGTTTTTGGACTGCT
1 TTTTTCTATTGTTTTTGAACTGCT
* * * *
47471792 TTTTTCTGTTGATTTTGAATTGTT
1 TTTTTCTATTGTTTTTGAACTGCT
* *
47471816 TTTTTCTTTTCTTTTT
1 TTTTTCTATTGTTTTT
47471832 TATTAAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.08, C:0.09, G:0.12, T:0.70
Consensus pattern (24 bp):
TTTTTCTATTGTTTTTGAACTGCT
Found at i:47482815 original size:30 final size:31
Alignment explanation
Indices: 47482765--47482831 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
47482755 AAACTTATTT
*
47482765 TTTGATAATTTTTATTATTATTTTAAAGACA
1 TTTGCTAATTTTTATTATTATTTTAAAGACA
* * *
47482796 TTTGCTAA-TTTTGTTATTATTTTAGAGGCA
1 TTTGCTAATTTTTATTATTATTTTAAAGACA
47482826 TTTGCT
1 TTTGCT
47482832 TGTTAAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (31 bp):
TTTGCTAATTTTTATTATTATTTTAAAGACA
Found at i:47482974 original size:12 final size:12
Alignment explanation
Indices: 47482953--47482986 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
47482943 TATATATATT
*
47482953 AAAATTATATAA
1 AAAATAATATAA
47482965 AAAATAATATAA
1 AAAATAATATAA
*
47482977 AAATTAATAT
1 AAAATAATAT
47482987 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:47484080 original size:46 final size:48
Alignment explanation
Indices: 47484026--47484145 Score: 181
Period size: 46 Copynumber: 2.5 Consensus size: 48
47484016 TGATATGTGT
* *
47484026 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA-CGA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATAGACAA
* *
47484072 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATAGACAA
*
47484120 GCTAGTGTAAGACCTGTCTGGGACAT
1 GCTAGTGTAAGACATGTCTGGGACAT
47484146 AGCGTCAGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
46 40 0.60
47 1 0.01
48 26 0.39
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATAGACAA
Found at i:47484285 original size:142 final size:139
Alignment explanation
Indices: 47484020--47484338 Score: 340
Period size: 142 Copynumber: 2.2 Consensus size: 139
47484010 ATTGGGTGAT
* * ** *
47484020 ATGTGTGCTAGTGTAAGACATGTCTGGGACAT-GCATCGGCATTGAGACGAGAGCTAGTGTAAGA
1 ATGTGTGC-AGTGTAAGACCTGTCTGGGACATGGCATCGACACCGAGACGAGAGCTAATGTAAGA
* * * *
47484084 CATGTCTGGGACATGCATCGGCCTTGAGATATACAAGCTAGTGTAAGACCTGTCTGGGACATAGC
65 CATGTCTGGGACAAGCATCGGCCTCGACATATACAAGCTAGTGTAAGACCTATCTGGGACATAGC
* *
47484149 GTCAGC-TTG
130 ATCAACTTTG
* * *
47484158 TTGTGTGTCAGTGTAAGACCTGTCTAGGACATGGCATCGACACCGATAGATGAGAGCTAATGTAA
1 ATGTGTG-CAGTGTAAGACCTGTCTGGGACATGGCATCGACACCG--AGACGAGAGCTAATGTAA
* * *
47484223 GACCTGTTTGGGACACAGCATCGGCCTCGACATATGA-AAG-TCAGTGTAAGACCTATTTGGGAC
63 GACATGTCTGGGACA-AGCATCGGCCTCGACATAT-ACAAGCT-AGTGTAAGACCTATCTGGGAC
*
47484286 ATGGCATCAACTTTG
125 ATAGCATCAACTTTG
*
47484301 ATGTGCTAGCCAGTGTAAGACCATGTTTGGGACATGGC
1 ATGTG-T-G-CAGTGTAAGACC-TGTCTGGGACATGGC
47484339 GTCGGCATCT
Statistics
Matches: 148, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
138 27 0.18
139 10 0.07
141 30 0.20
142 46 0.31
143 8 0.05
144 1 0.01
145 13 0.09
146 13 0.09
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.26
Consensus pattern (139 bp):
ATGTGTGCAGTGTAAGACCTGTCTGGGACATGGCATCGACACCGAGACGAGAGCTAATGTAAGAC
ATGTCTGGGACAAGCATCGGCCTCGACATATACAAGCTAGTGTAAGACCTATCTGGGACATAGCA
TCAACTTTG
Found at i:47484293 original size:49 final size:49
Alignment explanation
Indices: 47484164--47484293 Score: 138
Period size: 49 Copynumber: 2.7 Consensus size: 49
47484154 CTTGTTGTGT
* * * *
47484164 GTCAGTGTAAGACCTGTCTAGGACATGGCATCGACACCGATAGATGAGA
1 GTCAGTGTAAGACCTGTTTGGGACATGGCATCGACACCGACAGATGAAA
* ** * *
47484213 G-CTAATGTAAGACCTGTTTGGGACACAGCATCGGC-CTCGACATATGAAA
1 GTC-AGTGTAAGACCTGTTTGGGACATGGCATCGACAC-CGACAGATGAAA
*
47484262 GTCAGTGTAAGACCTATTTGGGACATGGCATC
1 GTCAGTGTAAGACCTGTTTGGGACATGGCATC
47484294 AACTTTGATG
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
48 2 0.03
49 62 0.95
50 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (49 bp):
GTCAGTGTAAGACCTGTTTGGGACATGGCATCGACACCGACAGATGAAA
Found at i:47491069 original size:40 final size:40
Alignment explanation
Indices: 47491020--47491122 Score: 169
Period size: 40 Copynumber: 2.7 Consensus size: 40
47491010 TTTAATATGA
*
47491020 TTAAAAAATTCAATAATATAAATAGTACAAAATGTGAAAT
1 TTAATAAATTCAATAATATAAATAGTACAAAATGTGAAAT
47491060 TTAATAAATTCAATAATATAAATAGTACAAAATGTGAAAT
1 TTAATAAATTCAATAATATAAATAGTACAAAATGTGAAAT
47491100 TTAAT---TT-AATAATATAAATAGTA
1 TTAATAAATTCAATAATATAAATAGTA
47491123 GATATAGATA
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
36 16 0.26
37 2 0.03
40 44 0.71
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (40 bp):
TTAATAAATTCAATAATATAAATAGTACAAAATGTGAAAT
Found at i:47491891 original size:21 final size:21
Alignment explanation
Indices: 47491866--47491921 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
47491856 AAAGTTGATA
* *
47491866 AAAAATTCTAAAATTTATATT
1 AAAAATTTTAAAATTAATATT
*
47491887 AAAAATTTTAAAA-GAATATT
1 AAAAATTTTAAAATTAATATT
*
47491907 CAAAATTTTAAAATT
1 AAAAATTTTAAAATT
47491922 CTAAATATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATTTTAAAATTAATATT
Found at i:47493982 original size:43 final size:43
Alignment explanation
Indices: 47493921--47494007 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
47493911 CGTTTCCAAG
47493921 TCATCAAGACTTGGTAAAATTTAAAACTATTTCAGAACATATC
1 TCATCAAGACTTGGTAAAATTTAAAACTATTTCAGAACATATC
47493964 TCATCAAGACTTGGTAAAATTTAAAACTATTTCAGAACATATC
1 TCATCAAGACTTGGTAAAATTTAAAACTATTTCAGAACATATC
47494007 T
1 T
47494008 AAACTTCATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.33
Consensus pattern (43 bp):
TCATCAAGACTTGGTAAAATTTAAAACTATTTCAGAACATATC
Found at i:47494298 original size:28 final size:28
Alignment explanation
Indices: 47494248--47494302 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
47494238 GCAGTGATTT
*
47494248 TCACACGGCCTGACACACGCCCGTGTCCA
1 TCACACGACCTGACACAC-CCCGTGTCCA
47494277 TCACACGACCATGACACA-CCCGTGTC
1 TCACACGACC-TGACACACCCCGTGTC
47494303 TTAGCTCGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 9 0.38
30 7 0.29
ACGTcount: A:0.24, C:0.44, G:0.18, T:0.15
Consensus pattern (28 bp):
TCACACGACCTGACACACCCCGTGTCCA
Found at i:47495216 original size:139 final size:139
Alignment explanation
Indices: 47494966--47495227 Score: 497
Period size: 139 Copynumber: 1.9 Consensus size: 139
47494956 GCTTAGTAAG
*
47494966 CTCAATAGTTAAAGTAAAATAAAGTTTCATAAGCTTAATCTTCTTATACATACTCTTACCACAAG
1 CTCAATAGTTAAAGTAAAACAAAGTTTCATAAGCTTAATCTTCTTATACATACTCTTACCACAAG
47495031 TACTTAACATATTGAAATCTTTACTCAAGAGTTTTACATACATACCTATACTAACTCAATAATAA
66 TACTTAACATATTGAAATCTTTACTCAAGAGTTTTACATACATACCTATACTAACTCAATAATAA
47495096 ACAACATGA
131 ACAACATGA
47495105 CTCAATAGTTAAAGTAAAACAAAGTTTCATAAGCTTAATCTTCTTATACATACTCTTACCACAAG
1 CTCAATAGTTAAAGTAAAACAAAGTTTCATAAGCTTAATCTTCTTATACATACTCTTACCACAAG
* *
47495170 TACTTAACATATTGAAATCTTTACTCAAGAGTTTTACGTACATACCTGTACTAACTCA
66 TACTTAACATATTGAAATCTTTACTCAAGAGTTTTACATACATACCTATACTAACTCA
47495228 TAACATAATT
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
139 120 1.00
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (139 bp):
CTCAATAGTTAAAGTAAAACAAAGTTTCATAAGCTTAATCTTCTTATACATACTCTTACCACAAG
TACTTAACATATTGAAATCTTTACTCAAGAGTTTTACATACATACCTATACTAACTCAATAATAA
ACAACATGA
Found at i:47512125 original size:37 final size:37
Alignment explanation
Indices: 47512075--47512153 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
47512065 TTATTACGAA
* * *
47512075 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
47512112 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
47512149 GTCTT
1 GTCTT
47512154 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:47512379 original size:49 final size:49
Alignment explanation
Indices: 47512274--47512402 Score: 124
Period size: 49 Copynumber: 2.7 Consensus size: 49
47512264 CTTCGGGACT
* * * *
47512274 TATCACAT-T-TATGCACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC
* * * *
47512321 TGTCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC
* *
47512370 TATCTC--ATATATGCA-TGTTCACATCCATCACAT
1 TATCACATATATATACACT-TTCACATCCATCACAT
47512403 AGAATCCTAA
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
46 1 0.01
47 30 0.45
48 1 0.01
49 35 0.52
ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33
Consensus pattern (49 bp):
TATCACATATATATACACTTTCACATCCATCACATCGGCCACTAGGCCC
Found at i:47516403 original size:22 final size:22
Alignment explanation
Indices: 47516378--47516419 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
47516368 TCAGCCGACT
*
47516378 TTTTTCCTTGTCATGTAAGATA
1 TTTTTCCTTGCCATGTAAGATA
*
47516400 TTTTTCCTTGCCGTGTAAGA
1 TTTTTCCTTGCCATGTAAGA
47516420 CTTTTCAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (22 bp):
TTTTTCCTTGCCATGTAAGATA
Found at i:47517862 original size:34 final size:34
Alignment explanation
Indices: 47517819--47517888 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
47517809 AGCCTTATAG
47517819 TATCAATTCTGGCGACTGGGCAACTACTTCATCA
1 TATCAATTCTGGCGACTGGGCAACTACTTCATCA
*
47517853 TATCAATTCTGGCGACTGGGCAACTACTTTATCA
1 TATCAATTCTGGCGACTGGGCAACTACTTCATCA
47517887 TA
1 TA
47517889 GTCTACACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (34 bp):
TATCAATTCTGGCGACTGGGCAACTACTTCATCA
Found at i:47520764 original size:2 final size:2
Alignment explanation
Indices: 47520759--47520816 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
47520749 ACAATACACA
47520759 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
47520801 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
47520817 TTTTCTCTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:47520995 original size:21 final size:22
Alignment explanation
Indices: 47520950--47520996 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
47520940 TTAGCTGACT
*
47520950 TTTTTCCTTGCCGTGTAAGACC
1 TTTTTCCTTGCCATGTAAGACC
47520972 TTTTTCCTTGCCATGTAAGA-C
1 TTTTTCCTTGCCATGTAAGACC
47520993 TTTT
1 TTTT
47520997 CAATGTGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.47
Consensus pattern (22 bp):
TTTTTCCTTGCCATGTAAGACC
Found at i:47526664 original size:18 final size:20
Alignment explanation
Indices: 47526641--47526685 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
47526631 TTGTTTTTTG
47526641 AAAATTT-TAT-ATTATGTA
1 AAAATTTATATGATTATGTA
47526659 AAAATTTAATATGATTATGTA
1 AAAATTT-ATATGATTATGTA
47526680 AAAATT
1 AAAATT
47526686 AAATGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.29
20 3 0.12
21 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
AAAATTTATATGATTATGTA
Found at i:47530518 original size:38 final size:38
Alignment explanation
Indices: 47530445--47530518 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 38
47530435 TAATTTAACA
* * *
47530445 TTTTAATATAATTTTTAATAAATTTATATTTTTTTAAT
1 TTTTAAAATAATTTTTAATAAATTTATAATATTTTAAT
* *
47530483 TTTTAAAATAATTTTATAA-AATTTTGTAATATTTTA
1 TTTTAAAATAATTTT-TAATAAATTTATAATATTTTA
47530519 TAAATTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 27 0.90
39 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (38 bp):
TTTTAAAATAATTTTTAATAAATTTATAATATTTTAAT
Found at i:47530527 original size:20 final size:20
Alignment explanation
Indices: 47530470--47530527 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
47530460 TAATAAATTT
* *
47530470 ATATTTTTTTAATTTTTAAA
1 ATATTTTATAAATTTTTAAA
* **
47530490 ATAATTTTATAAAATTTTGTA
1 AT-ATTTTATAAATTTTTAAA
47530511 ATATTTTATAAATTTTT
1 ATATTTTATAAATTTTT
47530528 TGAAAATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATATTTTATAAATTTTTAAA
Found at i:47530536 original size:20 final size:20
Alignment explanation
Indices: 47530492--47530537 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
47530482 TTTTTAAAAT
47530492 AATTTTATAAAATTTTGTAA
1 AATTTTATAAAATTTTGTAA
* *
47530512 TATTTTAT-AAATTTTTTGAA
1 AATTTTATAAAATTTTGT-AA
47530532 AATTTT
1 AATTTT
47530538 GAAGATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
AATTTTATAAAATTTTGTAA
Found at i:47532970 original size:46 final size:46
Alignment explanation
Indices: 47532796--47533058 Score: 160
Period size: 46 Copynumber: 5.6 Consensus size: 46
47532786 GTGCCGATGC
* * ***
47532796 CATGTCCCAGACATGGTCTTACACTAGTTCAT-ATCTC-AAGTTGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTC-TCATCTCGAGGCCAATG
* * * *
47532842 TCATATCCCAAACATGGTCTTACACT-GACTATCATCTCGTA-GCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTAG-CTCTCATCTCG-AGGCCAATG
* * *
47532890 CATGTCCCAGACATATCTTACACTAGCAT-ACGTCTCGAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTAGC-TCTCATCTCGAGGCCAATG
* ** * **
47532936 CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTTAATGCCGAACC
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCGAGGCC-AATG
* * * * * * *
47532983 CATGTCCCACATATGGTCTTACACTGGCTCCCATAAT-GTGGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-CTCGAGGCCAATG
*
47533030 AATGTCCCAGACATGTCTTACACTAGCTC
1 CATGTCCCAGACATGTCTTACACTAGCTC
47533059 ACAAACAAAT
Statistics
Matches: 170, Mismatches: 35, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
45 2 0.01
46 73 0.43
47 69 0.41
48 24 0.14
49 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCGAGGCCAATG
Found at i:47534977 original size:46 final size:46
Alignment explanation
Indices: 47534803--47535065 Score: 160
Period size: 46 Copynumber: 5.6 Consensus size: 46
47534793 GTGCCGATGC
* * ***
47534803 CATGTCCCAGACATGGTCTTACACTAGTTCAT-ATCTC-AAGTTGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTC-TCATCTCGAGGCCAATG
* * * *
47534849 TCATATCCCAAACATGGTCTTACACT-GACTATCATCTCGTA-GCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTAG-CTCTCATCTCG-AGGCCAATG
* * *
47534897 CATGTCCCAGACATATCTTACACTAGCAT-ACGTCTCGAGGCCAATG
1 CATGTCCCAGACATGTCTTACACTAGC-TCTCATCTCGAGGCCAATG
* ** * **
47534943 CATGTCCCAGACATGTCTTACACTAGCTCTCGTCTTAATGCCGAACC
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCGAGGCC-AATG
* * * * * * *
47534990 CATGTCCCACATATGGTCTTACACTGGCTCCCATAAT-GTGGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-CTCGAGGCCAATG
*
47535037 AATGTCCCAGACATGTCTTACACTAGCTC
1 CATGTCCCAGACATGTCTTACACTAGCTC
47535066 ACAAACAAAT
Statistics
Matches: 170, Mismatches: 35, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
45 2 0.01
46 73 0.43
47 69 0.41
48 24 0.14
49 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATCTCGAGGCCAATG
Found at i:47540933 original size:3 final size:3
Alignment explanation
Indices: 47540920--47541423 Score: 219
Period size: 3 Copynumber: 167.7 Consensus size: 3
47540910 TAACAAAAAC
* * * * * * *
47540920 AAT AGT AAT AAT AAT ATT GAT AAT AAT AAT AGT AGT AGT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
47540968 AAT ACT AAT GAT AAT AAT AA- AAGT AAT AAT AAG AAT ATT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
* * * * * *
47541013 AAT ATT AGT ATT AAT AAT AAT GAT AAT AAT AAT AGAA AAT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* * * * *
47541059 AAA AAT AAT -AT AGT AAT AGT AAT AA- AAA AAG AA- AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
47541103 AGT AAT AAT -AC AAT AGT AAT AAT AAT AAA AAGGT -AT AGT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA--T AAT AAT AAT AAT
* * * * *
47541147 ATT AGAT AGT AA- AAA AAT AAT AAT AAT AAT AGT AAT AA- AAA AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
47541191 GAT AAT ACT GAT ATT AGT ATT AAT AAT AAT AGGA- AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A--AT AAT AAT AAT AAT
* * * * * *
47541237 ATAT ACT AAT AAC AAC AAT AAT -AT GAAA AAT AAGA AAT AAC AAT ACACT
1 A-AT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA-T AAT AAT AAT A-A-T
* * * *
47541286 AAT AAG AAT AGT AAT AGAT CACT AAT AAT AAT AGT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * * ** * * * *
47541334 -AT ATT ACT AAG GGT AAT GAT AAT AAA AAT AGT AAT -AT ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
47541380 AAT AAT AAT AAT AAT AAT AAT AAT GAA- AAT AAG AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
47541424 CATCTTGGAT
Statistics
Matches: 366, Mismatches: 104, Indels: 62
0.69 0.20 0.12
Matches are distributed among these distances:
2 27 0.07
3 312 0.85
4 23 0.06
5 4 0.01
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:47541117 original size:14 final size:14
Alignment explanation
Indices: 47541100--47541126 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47541090 AAAATATAAT
47541100 AATAGTAATAATAC
1 AATAGTAATAATAC
47541114 AATAGTAATAATA
1 AATAGTAATAATA
47541127 ATAAAAAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (14 bp):
AATAGTAATAATAC
Found at i:47541418 original size:68 final size:67
Alignment explanation
Indices: 47541285--47541423 Score: 158
Period size: 68 Copynumber: 2.0 Consensus size: 67
47541275 AACAATACAC
* * * * *
47541285 TAATAAGAATAGTAATAGATCACTAATAATAATAGTAAATAATAATAATATATTACTAAGGGTAA
1 TAATAAAAATAGTAATA-ATCACTAATAATAATAATAAATAATAATAATATATAAATAAGAGTAA
*
47541350 TGA
65 TAA
47541353 TAATAAAAATAGTAAT-AT-ACTAATAATAATAAT-AATAATAATAATAATAATGAAAATAAGAG
1 TAATAAAAATAGTAATAATCACTAATAATAATAATAAATAATAATAAT-AT-AT--AAATAAGAG
47541415 TAATAA
62 TAATAA
47541421 TAA
1 TAA
47541424 CATCTTGGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
64 12 0.20
65 16 0.26
66 4 0.07
68 29 0.48
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (67 bp):
TAATAAAAATAGTAATAATCACTAATAATAATAATAAATAATAATAATATATAAATAAGAGTAAT
AA
Found at i:47542081 original size:3 final size:3
Alignment explanation
Indices: 47542017--47542068 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
47542007 CAAAAAAGGG
*
47542017 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
47542064 T-T TAT
1 TAT TAT
47542069 ATGCTTTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:47543097 original size:44 final size:44
Alignment explanation
Indices: 47543049--47543366 Score: 200
Period size: 44 Copynumber: 7.3 Consensus size: 44
47543039 ATCTGCTGTA
*
47543049 CTACTGCTTAGGGAGATGAGATCTGTAATTTTCTGCCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCTGCCTGTTACC
* * * *
47543093 CTACTGCTTAGGG-GATCAAG-GCT-TACTATCTTC-GATCTGCT-CC
1 CTACTGCTTAGGGAGAT-AAGATCTGTA--ATTTTCTG-CCTGTTACC
* *
47543136 GCTACTGCTTAGGGAGATGAGATCTGTAATTTTCTGCCTGTTATC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATTTTCTGCCTGTTACC
* * * * ** *
47543181 CTATTGCTTAGGGGGTTAAG-GCTAGTGAATTTGAT--CTGTTTCC
1 CTACTGCTTAGGGAGATAAGATCT-GT-AATTTTCTGCCTGTTACC
*
47543224 CTACTGCTTAGGGTGATAAGATCTGTAATTTT-TAGCCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTGTAATTTTCT-GCCTGTTACC
* * * * * *
47543268 CTACTACTTAGGG-GGTCAAG-GCT-TACTGTCTTC-GATCTGCT-CC
1 CTACTGCTTAGGGAGAT-AAGATCTGTAAT-T-TTCTG-CCTGTTACC
* *
47543311 GCTACTGCTTAGGGAGACAAGATCTGTAA--TTCGGCCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGTAATTTTCTGCCTGTTACC
47543354 CTACTGCTTAGGG
1 CTACTGCTTAGGG
47543367 GGTTAAGGCT
Statistics
Matches: 208, Mismatches: 39, Indels: 56
0.69 0.13 0.18
Matches are distributed among these distances:
41 1 0.00
42 30 0.14
43 46 0.22
44 111 0.53
45 16 0.08
46 4 0.02
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (44 bp):
CTACTGCTTAGGGAGATAAGATCTGTAATTTTCTGCCTGTTACC
Found at i:47543385 original size:86 final size:86
Alignment explanation
Indices: 47542995--47543806 Score: 1011
Period size: 86 Copynumber: 9.4 Consensus size: 86
47542985 GTAATTTCTA
* * * **
47542995 GCCTGTTACCTTACTGCTTAAGGGGTTAAGGCT-AGCTC-TCTTTGATCTGCTGTACTACTGCTT
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCA-C-CGTCTTCGATCTGCTCCACTACTGCTT
** *
47543058 AGGGAGATGAGATCTGTAATTTTCT
64 AGGGAGACAAGATCTGTAA--TTCG
* * * ** *
47543083 GCCTGTTACCCTACTGCTTAGGGGATCAAGGCTTACTATCTTCGATCTGCTCCGCTACTGCTTAG
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAG
** *
47543148 GGAGATGAGATCTGTAATTTTCT
66 GGAGACAAGATCTGTAA--TTCG
* * ** ** * *
47543171 GCCTGTTATCCTATTGCTTAGGGGGTTAAGGCT-AGTGAATTTGATCTGTTTCC-CTACTGCTTA
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTG-CTCCACTACTGCTTA
* * **
47543234 GGGTGATAAGATCTGTAATTTTTA
65 GGGAGACAAGATCTGTAA--TTCG
* * * * *
47543258 GCCTGTTACCCTACTACTTAGGGGGTCAAGGCTTACTGTCTTCGATCTGCTCCGCTACTGCTTAG
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAG
47543323 GGAGACAAGATCTGTAATTCG
66 GGAGACAAGATCTGTAATTCG
*
47543344 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCTACTACTGCTTAG
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAG
*
47543409 GGAGACAATATCTGTAATTCG
66 GGAGACAAGATCTGTAATTCG
* * * * *
47543430 GCCTGTTACCCTACTACTTAAGGGGTTAAGGCTCACCATTTTCGATCTGCTCTACTACTGCTTAG
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAG
47543495 GGAGACAAGATCTGTAATTCG
66 GGAGACAAGATCTGTAATTCG
* * *
47543516 GCCTGTTACCCTACTGCTTAGGAGGTAAAGGCTTACCGTCTTCGATCTGCTCCACTACTGCTTAG
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAG
*
47543581 GGAGACAAGATCTGTAATTCA
66 GGAGACAAGATCTGTAATTCG
* * *
47543602 GCCTATTACACTACTGCTTAGGGGGTTAAGGCTCACTGTCTTCGATCTGCTCCACTACTGCTTAG
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAG
47543667 GGAGACAAGATCTGTAATTCG
66 GGAGACAAGATCTGTAATTCG
* * * * *
47543688 ACCTGTTACCCTACTGCTTAAGGGGTTAAGGCTCACCGTCTTTGATCTACTCCGCTACTGCTTAG
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAG
* *
47543753 GGAGATAAGATCTGTAATTCA
66 GGAGACAAGATCTGTAATTCG
*
47543774 GCCTGCTACCCTACTGCTTAGGGGGTTAAGGCT
1 GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCT
47543807 AGTAAATTCA
Statistics
Matches: 642, Mismatches: 77, Indels: 12
0.88 0.11 0.02
Matches are distributed among these distances:
86 424 0.66
87 72 0.11
88 145 0.23
89 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (86 bp):
GCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAG
GGAGACAAGATCTGTAATTCG
Found at i:47543973 original size:64 final size:64
Alignment explanation
Indices: 47543860--47543984 Score: 169
Period size: 64 Copynumber: 2.0 Consensus size: 64
47543850 CATGTATCTA
* * * *
47543860 CTTATGCCAAATAATTACGATACGATGATTGAAATGAATCAAATGCTCCTAACTAGATGTGCTG
1 CTTATGCCAAATAATTACGACACGATGATCGAAATAAATCAAATACTCCTAACTAGATGTGCTG
* * * * *
47543924 CTTATGTCAAATAATTAGGACGCTATGATCGAAATAAATCCAATACTCCTAACTAGATGTG
1 CTTATGCCAAATAATTACGACACGATGATCGAAATAAATCAAATACTCCTAACTAGATGTG
47543985 TCATGAATGA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (64 bp):
CTTATGCCAAATAATTACGACACGATGATCGAAATAAATCAAATACTCCTAACTAGATGTGCTG
Found at i:47545541 original size:9 final size:8
Alignment explanation
Indices: 47545527--47545594 Score: 52
Period size: 8 Copynumber: 8.5 Consensus size: 8
47545517 TGATCCTTAA
47545527 TTTGTTGTT
1 TTTGTT-TT
47545536 TTTGTTTT
1 TTTGTTTT
47545544 TTCT-TTTT
1 TT-TGTTTT
*
47545552 CTT-TTTT
1 TTTGTTTT
47545559 TTTG-TTT
1 TTTGTTTT
*
47545566 TTAGTTTT
1 TTTGTTTT
*
47545574 TTAGTTTT
1 TTTGTTTT
*
47545582 TGTTTTTTT
1 T-TTGTTTT
47545591 TTTG
1 TTTG
47545595 CAATATAGCG
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
7 13 0.27
8 23 0.47
9 13 0.27
ACGTcount: A:0.03, C:0.03, G:0.12, T:0.82
Consensus pattern (8 bp):
TTTGTTTT
Found at i:47545542 original size:6 final size:6
Alignment explanation
Indices: 47545531--47545594 Score: 55
Period size: 6 Copynumber: 10.5 Consensus size: 6
47545521 CCTTAATTTG
47545531 TTGTTT TTGTTT TT-TCTT TT-TCTT TT-TTT TTGTTT TTAGTTTT TTAGTTT
1 TTGTTT TTGTTT TTGT-TT TTGT-TT TTGTTT TTGTTT TT-G-TTT TT-GTTT
47545581 TTGTTT TT-TTT TTG
1 TTGTTT TTGTTT TTG
47545595 CAATATAGCG
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
5 10 0.19
6 30 0.57
7 6 0.11
8 7 0.13
ACGTcount: A:0.03, C:0.03, G:0.11, T:0.83
Consensus pattern (6 bp):
TTGTTT
Found at i:47545566 original size:7 final size:7
Alignment explanation
Indices: 47545534--47545593 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
47545524 TAATTTGTTG
47545534 TTTTTGT
1 TTTTTGT
*
47545541 TTTTTCTT
1 TTTTT-GT
*
47545549 TTTCTTTT
1 TTT-TTGT
47545557 TTTTTGT
1 TTTTTGT
*
47545564 TTTTAGT
1 TTTTTGT
47545571 TTTTTAG-
1 TTTTT-GT
47545578 TTTTTGT
1 TTTTTGT
47545585 TTTTT-T
1 TTTTTGT
47545591 TTT
1 TTT
47545594 GCAATATAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
6 5 0.11
7 28 0.62
8 10 0.22
9 2 0.04
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.85
Consensus pattern (7 bp):
TTTTTGT
Found at i:47545573 original size:15 final size:14
Alignment explanation
Indices: 47545531--47545590 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 14
47545521 CCTTAATTTG
47545531 TTGTTTTTGTTTTT
1 TTGTTTTTGTTTTT
*
47545545 TCT-TTTTCTTTTTTT
1 T-TGTTTT-TGTTTTT
47545560 TTGTTTTTAGTTTTT
1 TTGTTTTT-GTTTTT
*
47545575 TAGTTTTTGTTTTT
1 TTGTTTTTGTTTTT
47545589 TT
1 TT
47545591 TTTGCAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 14 0.37
15 24 0.63
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.83
Consensus pattern (14 bp):
TTGTTTTTGTTTTT
Found at i:47550585 original size:3 final size:3
Alignment explanation
Indices: 47550577--47550996 Score: 225
Period size: 3 Copynumber: 141.0 Consensus size: 3
47550567 AAAACGATAG
* * * * * *
47550577 TAA TAA TAA TAA TAT TGA TAA TAA TAA TAG TAG TAA AAA TAA TAA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
47550625 TAA TGA TAA TAA TAA -AA GTAA TAA TAA TTA TAT TAA TAT TAG TAT
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
47550670 TAA TAA TAA TGA TAA TAA TAA TAGA AAA TAA AAA TAA AAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* * * * *
47550715 TAG TAA TAG TAA TAA -AA AAA GAA -AA T-A TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
47550760 TAA T-A CAA TAG TAA TAA TAA TAA AAA GGT-A TAA TAA T-A TAT TAGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA --TAA TAA TAA TAA TAA TA-A
* * * * * * * * * *
47550805 CAG TAA AAA TAA TAA TAA TAA TAG TAA AAA AAA TGA TAA TAG TGA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
47550853 TAG TAG TAA TAA TAA TAA TAGGA -AA TAA TAA TAA TAG TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA--A TAA TAA TAA TAA TAA T-AA TAA TAA
* * *** * * * *
47550900 TAA TAA TAA T-A TAT TAC TAA GGG TAA TGA TAA TAA AAA CAG TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
47550946 TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TGAA -AA TAA GAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
47550991 TAA TAA
1 TAA TAA
47550997 CATCTTAGAT
Statistics
Matches: 310, Mismatches: 86, Indels: 42
0.71 0.20 0.10
Matches are distributed among these distances:
2 21 0.07
3 277 0.89
4 11 0.04
5 1 0.00
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:47550769 original size:14 final size:14
Alignment explanation
Indices: 47550738--47550778 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
47550728 AAAAAAAGAA
*
47550738 AATA-TAATAATAAT
1 AATAGTAATAAT-AC
47550752 AATAGTAATAATAC
1 AATAGTAATAATAC
47550766 AATAGTAATAATA
1 AATAGTAATAATA
47550779 ATAAAAAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (14 bp):
AATAGTAATAATAC
Found at i:47550881 original size:16 final size:16
Alignment explanation
Indices: 47550860--47550904 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
47550850 TATTAGTAGT
47550860 AATAATAATAATAGGA
1 AATAATAATAATAGGA
*
47550876 AATAATAATAATAGTA
1 AATAATAATAATAGGA
47550892 AATAATAATAATA
1 AATAATAATAATA
47550905 ATAATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (16 bp):
AATAATAATAATAGGA
Done.