Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_130.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8132550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 35170 characters in sequence are not A, C, G, or T
File 11 of 14
Found at i:5590540 original size:108 final size:111
Alignment explanation
Indices: 5590238--5590569 Score: 529
Period size: 112 Copynumber: 3.0 Consensus size: 111
5590228 AAAATATAAG
5590238 TTTAATATA-TTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAATATATTTTTAAT
1 TTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATTTCTTAATATATTTTTAAT
*
5590302 ATCATATATTTTATTTTTTATTTATTATTA-AATATTTTATATTTTATT
65 GTCATATATTTTA-TTTTTATTTATTATTATAATA-TTTATATTTTATT
5590350 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAATATATTTTTAATG
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAATATATTTTTAATG
5590415 TCATATATTTT-TATTTTATTTATTATTATAATATTTATATTTTATT
66 TCATATATTTTAT-TTTTATTTATTATTATAATATTTATATTTTATT
*
5590461 TTTAATATATTTATATTTATA-TATTAATTTTTA-AT-ATATCATATT-TTAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCAT-TTCTTAATATATTTTTAAT
5590522 GTCATATATTTTATTTTTATTTATTATTAT-A-ATTTATATATTTATT
65 GTCATATATTTTATTTTTATTTATTATTATAATATTTATAT-TTTATT
5590568 TT
1 TT
5590570 CATTCTTTAA
Statistics
Matches: 212, Mismatches: 2, Indels: 17
0.92 0.01 0.07
Matches are distributed among these distances:
106 8 0.04
107 9 0.04
108 51 0.24
109 5 0.02
110 13 0.06
111 48 0.23
112 73 0.34
113 5 0.02
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (111 bp):
TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATTTCTTAATATATTTTTAATG
TCATATATTTTATTTTTATTTATTATTATAATATTTATATTTTATT
Found at i:5590650 original size:24 final size:24
Alignment explanation
Indices: 5590621--5590668 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5590611 CTTGTTTATC
5590621 TATATTATATAAATATTAATTTTT
1 TATATTATATAAATATTAATTTTT
* ** *
5590645 TATATTTTATTTATTTTAATTTTT
1 TATATTATATAAATATTAATTTTT
5590669 ATTCTTATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TATATTATATAAATATTAATTTTT
Found at i:5590681 original size:23 final size:24
Alignment explanation
Indices: 5590636--5590681 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5590626 TATATAAATA
*
5590636 TTAATTTTTTATATTTTATTTATT
1 TTAATTTTTTATATCTTATTTATT
5590660 TTAA-TTTTTAT-TCTTATATTAT
1 TTAATTTTTTATATCTTAT-TTAT
5590682 ATATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 11 0.55
24 4 0.20
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (24 bp):
TTAATTTTTTATATCTTATTTATT
Found at i:5590704 original size:26 final size:27
Alignment explanation
Indices: 5590622--5590708 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 27
5590612 TTGTTTATCT
*
5590622 ATATTATATAAATATTAATTTT--TTAT-
1 ATATTATAT--ATTTTAATTTTAATTATA
* * * * *
5590648 ATTTTATTTATTTTAATTTTTATTCTT
1 ATATTATATATTTTAATTTTAATTATA
5590675 ATATTATATATTTT-ATTTTAATTATA
1 ATATTATATATTTTAATTTTAATTATA
5590701 ATATTATA
1 ATATTATA
5590709 AAATATTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 10 0.20
26 27 0.55
27 12 0.24
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (27 bp):
ATATTATATATTTTAATTTTAATTATA
Found at i:5592876 original size:16 final size:16
Alignment explanation
Indices: 5592855--5592886 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5592845 TATTTTGTTG
5592855 CAGCTTTTGAATCTTC
1 CAGCTTTTGAATCTTC
*
5592871 CAGCTTTTGATTCTTC
1 CAGCTTTTGAATCTTC
5592887 TTCTTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.25, G:0.12, T:0.47
Consensus pattern (16 bp):
CAGCTTTTGAATCTTC
Found at i:5624123 original size:78 final size:78
Alignment explanation
Indices: 5623890--5624123 Score: 351
Period size: 78 Copynumber: 3.0 Consensus size: 78
5623880 GGTTCATTAG
* * * * *
5623890 TTTTCATGATTGCACAAATGGAAGCAGATAATAATAGGGATTTCATTGATAAGGTGTAAAATGTG
1 TTTTCATGATTGCACAAATTGAAGCAGATACTGATAGGAATTTCATTGATAAGGTGTAAAAGGTG
*
5623955 ATATGCTAGCATG
66 ATATGCTAGCATA
* * * * *
5623968 TTTTCGTGATTGCACAAATTGAAGCAGACACCGATAGGAATTTCATTGATAAAGTGTTAAAGGTG
1 TTTTCATGATTGCACAAATTGAAGCAGATACTGATAGGAATTTCATTGATAAGGTGTAAAAGGTG
*
5624033 AAATGCTAGCATA
66 ATATGCTAGCATA
5624046 TTTTCATGATTGCACAAATTGAAGCAGATACTGATAGGAATTTCATTGATAAGGTGTAAAAGGTG
1 TTTTCATGATTGCACAAATTGAAGCAGATACTGATAGGAATTTCATTGATAAGGTGTAAAAGGTG
*
5624111 ATATGCCAGCATA
66 ATATGCTAGCATA
5624124 ACATATTAAA
Statistics
Matches: 137, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 137 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (78 bp):
TTTTCATGATTGCACAAATTGAAGCAGATACTGATAGGAATTTCATTGATAAGGTGTAAAAGGTG
ATATGCTAGCATA
Found at i:5638202 original size:2 final size:2
Alignment explanation
Indices: 5638195--5638219 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5638185 AGAAAAACAG
5638195 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
5638220 TTTATTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5652403 original size:25 final size:25
Alignment explanation
Indices: 5652374--5652427 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
5652364 ATGCTAGTTT
*
5652374 AATTAAAATT-ATACTATCCTAATCA
1 AATTAAAATTAAAACTATCCTAA-CA
*
5652399 AATTACAATTCAAAACTATCCTAACA
1 AATTAAAATT-AAAACTATCCTAACA
5652425 AAT
1 AAT
5652428 CTGAACCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.36
26 5 0.20
27 11 0.44
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (25 bp):
AATTAAAATTAAAACTATCCTAACA
Found at i:5664424 original size:2 final size:2
Alignment explanation
Indices: 5664411--5664452 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
5664401 TCAAAGATAC
*
5664411 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5664453 TCTGTTAGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5665489 original size:2 final size:2
Alignment explanation
Indices: 5665482--5665507 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5665472 TTCCGTAAAA
5665482 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5665508 TGTGTTCCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5670860 original size:2 final size:2
Alignment explanation
Indices: 5670855--5670880 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5670845 AAGGGAAAAA
5670855 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5670881 CAATAGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5673766 original size:37 final size:37
Alignment explanation
Indices: 5673700--5673771 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
5673690 AGACAAAATG
* * *
5673700 GAAGATGAAACTGTTATTAATACCCATTCATCATATT
1 GAAGATGAAACAGTTACTAATACACATTCATCATATT
* *
5673737 GAAGATGAAACAGTTACTGATACATATTCATCATA
1 GAAGATGAAACAGTTACTAATACACATTCATCATA
5673772 AGCTGGAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (37 bp):
GAAGATGAAACAGTTACTAATACACATTCATCATATT
Found at i:5673819 original size:12 final size:13
Alignment explanation
Indices: 5673792--5673821 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5673782 ACAAATTATG
5673792 ATACACATTGTTC
1 ATACACATTGTTC
5673805 ATACACATT-TTC
1 ATACACATTGTTC
5673817 ATACA
1 ATACA
5673822 AATTAATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (13 bp):
ATACACATTGTTC
Found at i:5678248 original size:61 final size:62
Alignment explanation
Indices: 5678179--5678306 Score: 249
Period size: 62 Copynumber: 2.1 Consensus size: 62
5678169 GGTAGCAAAT
5678179 TTTCAG-TTTTTTAGCCTAATTCTTTGGTACATGTCCTAAGAAACTTGATTTCGAAGACGAG
1 TTTCAGTTTTTTTAGCCTAATTCTTTGGTACATGTCCTAAGAAACTTGATTTCGAAGACGAG
5678240 TTTCAGTTTTTTTAGCCTAATTCTTTGGTACATGTCCTAAGAAACTTGATTTCGAAGACGAG
1 TTTCAGTTTTTTTAGCCTAATTCTTTGGTACATGTCCTAAGAAACTTGATTTCGAAGACGAG
5678302 TTTCA
1 TTTCA
5678307 AGGGAAGAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
61 6 0.09
62 60 0.91
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (62 bp):
TTTCAGTTTTTTTAGCCTAATTCTTTGGTACATGTCCTAAGAAACTTGATTTCGAAGACGAG
Found at i:5681822 original size:2 final size:2
Alignment explanation
Indices: 5681806--5681844 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
5681796 ATTGTGTCAA
*
5681806 AT AT -T AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5681845 TTGTCTTGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5682350 original size:27 final size:27
Alignment explanation
Indices: 5682305--5682375 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
5682295 ATAAGGTGGC
* *
5682305 TCATACACCGGAGGTTTCTTAGGAGGT
1 TCATACACCGGTGGCTTCTTAGGAGGT
* *
5682332 TCATACACTGGTGGCTTCTTTGGAGGT
1 TCATACACCGGTGGCTTCTTAGGAGGT
* *
5682359 TCGTAAACCGGTGGCTT
1 TCATACACCGGTGGCTT
5682376 GGGCTCTGGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (27 bp):
TCATACACCGGTGGCTTCTTAGGAGGT
Found at i:5682464 original size:27 final size:27
Alignment explanation
Indices: 5682434--5682504 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
5682424 TGGCTTAGGT
* *
5682434 TCATATACTGGTGGTTTCTTTGGTGGC
1 TCATAAACTGGTGGTTTCTTTGGAGGC
* * * *
5682461 TCATACACCGGAGGCTTCTTTGGAGGC
1 TCATAAACTGGTGGTTTCTTTGGAGGC
5682488 TCATAAACTGGTGGTTT
1 TCATAAACTGGTGGTTT
5682505 GGGTTCTGGC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.17, C:0.18, G:0.28, T:0.37
Consensus pattern (27 bp):
TCATAAACTGGTGGTTTCTTTGGAGGC
Found at i:5682480 original size:129 final size:133
Alignment explanation
Indices: 5682317--5682563 Score: 340
Period size: 129 Copynumber: 1.9 Consensus size: 133
5682307 ATACACCGGA
* * * * *
5682317 GGTTTCTTAGGAGGTTCATACACTGGTGGCTTCTTTGGAGGTTCGTAAACCGGTGGCTTGGGCTC
1 GGTTTCTTAGGAGGCTCATACACCGGAGGCTTCTTTGGAGGCTCATAAACCGGTGGCTTGGGCTC
* *
5682382 TGGCTTCTCTTTC-TT-G-GG-AGGTTCATACACTGGTGGTTTTGGTGGCTTAGGTTCATATACT
66 TGGCTTCTCTTTCTTTGGTGGTAGGTTCATAAACTGGTGGCTTTGGTGGCTTAGGTTCATATACT
5682443 GGT
131 GGT
* * * * *
5682446 GGTTTCTTTGGTGGCTCATACACCGGAGGCTTCTTTGGAGGCTCATAAACTGGTGGTTTGGGTTC
1 GGTTTCTTAGGAGGCTCATACACCGGAGGCTTCTTTGGAGGCTCATAAACCGGTGGCTTGGGCTC
5682511 TGGCTTCTCTTTCTTTGGTGGCTTAGGTTCATAAACTGGTGGCTTTGGTGGCT
66 TGGCTTCTCTTTCTTTGGTGG--TAGGTTCATAAACTGGTGGCTTTGGTGGCT
5682564 NNNNNNNNNN
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
129 68 0.68
130 2 0.02
131 1 0.01
132 2 0.02
135 27 0.27
ACGTcount: A:0.13, C:0.17, G:0.32, T:0.38
Consensus pattern (133 bp):
GGTTTCTTAGGAGGCTCATACACCGGAGGCTTCTTTGGAGGCTCATAAACCGGTGGCTTGGGCTC
TGGCTTCTCTTTCTTTGGTGGTAGGTTCATAAACTGGTGGCTTTGGTGGCTTAGGTTCATATACT
GGT
Found at i:5682743 original size:24 final size:24
Alignment explanation
Indices: 5682716--5682781 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
5682706 CGGTTGGTCA
* **
5682716 GGAGGCTGGTGGGGTGGTTCACGC
1 GGAGGCTCGTGGGGTGGCCCACGC
* *
5682740 GGAGGCACGTGGGGTGGCCCACGT
1 GGAGGCTCGTGGGGTGGCCCACGC
* *
5682764 GGAGGCTCCTGAGGTGGC
1 GGAGGCTCGTGGGGTGGC
5682782 TCTTGTGGAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.11, C:0.21, G:0.52, T:0.17
Consensus pattern (24 bp):
GGAGGCTCGTGGGGTGGCCCACGC
Found at i:5683812 original size:26 final size:26
Alignment explanation
Indices: 5683735--5683824 Score: 67
Period size: 31 Copynumber: 3.3 Consensus size: 26
5683725 TATAATAGTT
* *
5683735 GAAAATAATGTTACACGCCATGTTGA
1 GAAAATATTGTTACACGCTATGTTGA
* **
5683761 GAAAAAATATTGTTGTTAAATTCTATGTTGA
1 G--AAAATA---TTGTTACACGCTATGTTGA
*
5683792 GAAAATATTGTTACACGCTATATT-A
1 GAAAATATTGTTACACGCTATGTTGA
5683817 -AAAATATT
1 GAAAATATT
5683825 TTATTACACT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
24 8 0.16
25 1 0.02
26 14 0.28
28 6 0.12
29 6 0.12
31 15 0.30
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (26 bp):
GAAAATATTGTTACACGCTATGTTGA
Found at i:5686762 original size:201 final size:201
Alignment explanation
Indices: 5686417--5687125 Score: 1005
Period size: 201 Copynumber: 3.5 Consensus size: 201
5686407 TTGTGCTCAA
* * *
5686417 GTGGAGGCGTCTCCCCCTTACCCTTGGGTGGTTTACCACCGGAAAATATTGGTGGCTTGTGCGAG
1 GTGGAGGCGTCTCTCCCTTGCCCTTGGGTGGTTTACCACCGGAAAATCTTGGTGGCTTGTGCGAG
*
5686482 TCCTCAACGTCCTCACCTAGGAGGCGTCTGTGAGGAGGTTTGTGGTCATGGGGTGGCTCCTTTCC
66 TCCTCAACATCCTCACCTAGGAGGCGTCTGTGAGGAGGTTTGTGGTCATGGGGTGGCTCCTTTCC
5686547 CTCACCCTTAGGCGGTTTGTCACCTGGGAATGGCTTCTTGGGTTCTTTACCATTTGGCAATTCAT
131 CTCACCCTTAGGCGGTTTGTCACCTGGGAATGGCTTCTTGGGTTCTTTACCATTTGGCAATTCAT
5686612 GTCCAT
196 GTCCAT
* * *
5686618 GTGGAGGCTTCTCTCCCTTGCCCTTGGGTGGTTTACCACCTGAAAATCTGGGTGGCTTGT-CGGA
1 GTGGAGGCGTCTCTCCCTTGCCCTTGGGTGGTTTACCACCGGAAAATCTTGGTGGCTTGTGC-GA
5686682 GTCCTCAACATCCTCACCTAGGAGGCGTCTGTGAGGAGGTTTGTGGTCATGGGGTGGCTCCTTTC
65 GTCCTCAACATCCTCACCTAGGAGGCGTCTGTGAGGAGGTTTGTGGTCATGGGGTGGCTCCTTTC
*
5686747 CCTCA-CCTGTAGGCGGTTTGTCACCTGGGAATGGCTTCTTGGGTTCTTTACCGTTTGGCAATTC
130 CCTCACCCT-TAGGCGGTTTGTCACCTGGGAATGGCTTCTTGGGTTCTTTACCATTTGGCAATTC
5686811 ATGTCCAT
194 ATGTCCAT
* * *
5686819 GTGGAGGCGTCTCTCCCTTGCCCTTGGGTGGTTTACCCCCGGAAAATCTTGGTGGCTCGTGGGAG
1 GTGGAGGCGTCTCTCCCTTGCCCTTGGGTGGTTTACCACCGGAAAATCTTGGTGGCTTGTGCGAG
* * * * *
5686884 TCCTCAGCATTCTCTCCTAAGAGGCGTCTGTGAGGAGGTTTGTGGTCATGGGGTGGCTCCTTGCC
66 TCCTCAACATCCTCACCTAGGAGGCGTCTGTGAGGAGGTTTGTGGTCATGGGGTGGCTCCTTTCC
* * ** ** * *
5686949 CTTACCCTTAGGCGGTTTGTCACCAGGGAATGGCTTCTTGGGTGGTTTACCATGGGGGAGTTCAT
131 CTCACCCTTAGGCGGTTTGTCACCTGGGAATGGCTTCTTGGGTTCTTTACCATTTGGCAATTCAT
* *
5687014 TTTCAT
196 GTCCAT
* * *** * * * *
5687020 GTGGAGGCTTCTCTCCCTTAG-CCTTGGGTGGTTTACCGCCTGG-GGTTTTTGGAGGTTTGTGTG
1 GTGGAGGCGTCTCTCCCTT-GCCCTTGGGTGGTTTACCACC-GGAAAATCTTGGTGGCTTGTGCG
* *
5687083 TGTCCTCAACATCCTCA-CTCAGGAGGTGTCTGTGAGGAGGTTT
64 AGTCCTCAACATCCTCACCT-AGGAGGCGTCTGTGAGGAGGTTT
5687126 TTCCCCATGT
Statistics
Matches: 455, Mismatches: 46, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
200 6 0.01
201 443 0.97
202 6 0.01
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.32
Consensus pattern (201 bp):
GTGGAGGCGTCTCTCCCTTGCCCTTGGGTGGTTTACCACCGGAAAATCTTGGTGGCTTGTGCGAG
TCCTCAACATCCTCACCTAGGAGGCGTCTGTGAGGAGGTTTGTGGTCATGGGGTGGCTCCTTTCC
CTCACCCTTAGGCGGTTTGTCACCTGGGAATGGCTTCTTGGGTTCTTTACCATTTGGCAATTCAT
GTCCAT
Found at i:5691576 original size:2 final size:2
Alignment explanation
Indices: 5691569--5691593 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5691559 TTTGAAACTT
5691569 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5691594 TAAAATCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5695496 original size:19 final size:19
Alignment explanation
Indices: 5695469--5695515 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
5695459 ATCTTCTTGG
5695469 CTTTC-TGTTATTCTTCTT
1 CTTTCTTGTTATTCTTCTT
*
5695487 CTTTCTTGTTTCTTCTTCTT
1 CTTTCTTG-TTATTCTTCTT
5695507 -TTTCTTGTT
1 CTTTCTTGTT
5695516 TGGTCCAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 7 0.27
19 9 0.35
20 10 0.38
ACGTcount: A:0.02, C:0.21, G:0.06, T:0.70
Consensus pattern (19 bp):
CTTTCTTGTTATTCTTCTT
Found at i:5722732 original size:25 final size:25
Alignment explanation
Indices: 5722703--5722763 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
5722693 GTTTGTTTTT
5722703 GTCAATATGATATATGACTAGGCAA
1 GTCAATATGATATATGACTAGGCAA
5722728 GTCAATATGATATATGACTAGGCAA
1 GTCAATATGATATATGACTAGGCAA
*
5722753 GTCGATATGAT
1 GTCAATATGAT
5722764 CACATGATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (25 bp):
GTCAATATGATATATGACTAGGCAA
Found at i:5733755 original size:23 final size:22
Alignment explanation
Indices: 5733729--5733799 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 22
5733719 TAAACAAACC
5733729 AATCCAACATAATTTAAAAGCCT
1 AATCCAACATAA-TTAAAAGCCT
5733752 AATCCAGTAGCA-AA--AAAA-CC-
1 AATCCA--A-CATAATTAAAAGCCT
5733772 AATCCAACATAATTCAAAAGCCT
1 AATCCAACATAATT-AAAAGCCT
5733795 AATCC
1 AATCC
5733800 TGGTTCCAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 18
0.68 0.00 0.32
Matches are distributed among these distances:
17 2 0.05
18 3 0.08
20 6 0.15
21 6 0.15
22 6 0.15
23 11 0.28
25 3 0.08
26 2 0.05
ACGTcount: A:0.49, C:0.25, G:0.06, T:0.20
Consensus pattern (22 bp):
AATCCAACATAATTAAAAGCCT
Found at i:5741369 original size:2 final size:2
Alignment explanation
Indices: 5741362--5741400 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5741352 ATAATCTATG
*
5741362 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5741401 TTCGTGACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5743382 original size:18 final size:16
Alignment explanation
Indices: 5743333--5743399 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 16
5743323 AACAGCTATG
5743333 AATTTAAAATTTTATAT
1 AATTTAAAA-TTTATAT
5743350 AA---AAAATCATTATAT
1 AATTTAAAAT--TTATAT
5743365 AATATTATAAATTTATAT
1 AAT-TTA-AAATTTATAT
*
5743383 AATTTAAATTTTATAT
1 AATTTAAAATTTATAT
5743399 A
1 A
5743400 TAATAATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
13 1 0.02
14 4 0.10
15 8 0.19
16 10 0.24
17 5 0.12
18 9 0.21
19 1 0.02
20 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTTAAAATTTATAT
Found at i:5748787 original size:2 final size:2
Alignment explanation
Indices: 5748780--5748804 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5748770 TCACTTTCAT
5748780 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5748805 CCGAAACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5750998 original size:13 final size:14
Alignment explanation
Indices: 5750970--5751002 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
5750960 TTTCTTTTGT
*
5750970 TCTTCCCACTTTTA
1 TCTTCTCACTTTTA
5750984 TCTTCTCAC-TTTA
1 TCTTCTCACTTTTA
5750997 TCTTCT
1 TCTTCT
5751003 TCTTATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.12, C:0.33, G:0.00, T:0.55
Consensus pattern (14 bp):
TCTTCTCACTTTTA
Found at i:5755551 original size:14 final size:15
Alignment explanation
Indices: 5755528--5755562 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
5755518 TATTTTTAAC
*
5755528 TTTAAATTAAA-TTT
1 TTTAATTTAAAGTTT
5755542 TTTAATTTAAAGTTT
1 TTTAATTTAAAGTTT
5755557 TTTAAT
1 TTTAAT
5755563 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTTAATTTAAAGTTT
Found at i:5759668 original size:24 final size:24
Alignment explanation
Indices: 5759641--5759689 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5759631 TTGAATTTGG
5759641 AAGGATATTTCAGGAATATGATTT
1 AAGGATATTTCAGGAATATGATTT
*
5759665 AAGGATGTTTCAGGAATATGATTT
1 AAGGATATTTCAGGAATATGATTT
5759689 A
1 A
5759690 CATATCCGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (24 bp):
AAGGATATTTCAGGAATATGATTT
Found at i:5766317 original size:34 final size:34
Alignment explanation
Indices: 5766270--5766354 Score: 154
Period size: 34 Copynumber: 2.5 Consensus size: 34
5766260 AACACAGATT
5766270 TTGA-TCATGCATGACGTTGGTTTCTTCTCAGGA
1 TTGAGTCATGCATGACGTTGGTTTCTTCTCAGGA
5766303 TTGAGTCATGCATGACGTTGGTTTCTTCTCAGGA
1 TTGAGTCATGCATGACGTTGGTTTCTTCTCAGGA
*
5766337 TTGAGTCATGCATAACGT
1 TTGAGTCATGCATGACGT
5766355 AATAACCTTC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 4 0.08
34 46 0.92
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (34 bp):
TTGAGTCATGCATGACGTTGGTTTCTTCTCAGGA
Found at i:5766365 original size:34 final size:34
Alignment explanation
Indices: 5766293--5766365 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
5766283 ACGTTGGTTT
* ** **
5766293 CTTCTCAGGATTGAGTCATGCATGACGTTGGTTT
1 CTTCTCAGGATTGAGTCATGCATAACGTTAATAC
5766327 CTTCTCAGGATTGAGTCATGCATAACG-TAATAAC
1 CTTCTCAGGATTGAGTCATGCATAACGTTAAT-AC
5766361 CTTCT
1 CTTCT
5766366 ACTTAATTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 2 0.06
34 31 0.94
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (34 bp):
CTTCTCAGGATTGAGTCATGCATAACGTTAATAC
Found at i:5769813 original size:26 final size:26
Alignment explanation
Indices: 5769777--5769831 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
5769767 GTGGATGGCT
5769777 GGGAATCTAGACCTGCTAGTATTGTA
1 GGGAATCTAGACCTGCTAGTATTGTA
5769803 GGGAATCTAGACCTGCTAGTATTGTA
1 GGGAATCTAGACCTGCTAGTATTGTA
5769829 GGG
1 GGG
5769832 TGCTACTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.29
Consensus pattern (26 bp):
GGGAATCTAGACCTGCTAGTATTGTA
Found at i:5772943 original size:27 final size:27
Alignment explanation
Indices: 5772898--5772952 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5772888 CAAGCCTTTT
5772898 AATCATTCATCAGGCTTGCACGTGAGG
1 AATCATTCATCAGGCTTGCACGTGAGG
* * * *
5772925 AATCGTTCATCCGGTTTGCATGTGAGG
1 AATCATTCATCAGGCTTGCACGTGAGG
5772952 A
1 A
5772953 GGCATGTTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (27 bp):
AATCATTCATCAGGCTTGCACGTGAGG
Found at i:5780152 original size:45 final size:45
Alignment explanation
Indices: 5780101--5780197 Score: 160
Period size: 45 Copynumber: 2.2 Consensus size: 45
5780091 CTATTACAAG
*
5780101 AGAGGCTGCACCTCAACAAAGCTCACAAATCGAATCAA-GTGCGTC
1 AGAGGCTGCACCTCAACAAAGCTCACAAATAGAATCAAGGT-CGTC
*
5780146 AGAGGCTGCACCTCAACAAAGCTCACAATTAGAATCAAGGTCGTC
1 AGAGGCTGCACCTCAACAAAGCTCACAAATAGAATCAAGGTCGTC
5780191 AGAGGCT
1 AGAGGCT
5780198 TCAGCAATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 47 0.96
46 2 0.04
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (45 bp):
AGAGGCTGCACCTCAACAAAGCTCACAAATAGAATCAAGGTCGTC
Found at i:5780726 original size:30 final size:30
Alignment explanation
Indices: 5780680--5780754 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 30
5780670 AATTAAGATT
*
5780680 TAATA-ATATAATATAAAT-TGTATAAAT-TA
1 TAATATATATTATATAAATAT-TA-AAATATA
5780709 -AATTATATATTATATAAATATTAAAATATA
1 TAA-TATATATTATATAAATATTAAAATATA
5780739 TAATATATATTATATA
1 TAATATATATTATATA
5780755 TTTAATATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
28 2 0.05
29 6 0.15
30 29 0.73
31 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (30 bp):
TAATATATATTATATAAATATTAAAATATA
Found at i:5780950 original size:24 final size:24
Alignment explanation
Indices: 5780922--5780967 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5780912 AGCATACATG
*
5780922 CATACACACATAGGCACAAACACC
1 CATACACACATAGACACAAACACC
**
5780946 CATACATGCATAGACACAAACA
1 CATACACACATAGACACAAACA
5780968 TACACACACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.33, G:0.09, T:0.11
Consensus pattern (24 bp):
CATACACACATAGACACAAACACC
Found at i:5786647 original size:41 final size:41
Alignment explanation
Indices: 5786590--5786675 Score: 145
Period size: 41 Copynumber: 2.1 Consensus size: 41
5786580 GCAAAAGGAA
*
5786590 AATTATGAATAGATCCCAACTCGAAACTATCATGAAATTCC
1 AATTATGAATAGATCCCAACTCGAAACTAACATGAAATTCC
* *
5786631 AATTATGAATAGATCCCAACTCGAAATTAACTTGAAATTCC
1 AATTATGAATAGATCCCAACTCGAAACTAACATGAAATTCC
5786672 AATT
1 AATT
5786676 TCATGACCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (41 bp):
AATTATGAATAGATCCCAACTCGAAACTAACATGAAATTCC
Found at i:5789355 original size:2 final size:2
Alignment explanation
Indices: 5789348--5789381 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5789338 ATACAGAAAC
5789348 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5789382 TCTCACTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5795902 original size:21 final size:21
Alignment explanation
Indices: 5795878--5795951 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
5795868 TCTTAAATTA
*
5795878 GTTTTAGGGTTTTTTTATTCG
1 GTTTTAGGGTTTTTTAATTCG
* * *
5795899 GTTTGA-GGTTTGATGAA-TCG
1 GTTTTAGGGTTT-TTTAATTCG
*
5795919 ATTTTAGGGTTTTTTAAATT-G
1 GTTTTAGGGTTTTTT-AATTCG
*
5795940 GTTTTAGAGTTT
1 GTTTTAGGGTTT
5795952 AAAGAATCAA
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
20 13 0.33
21 25 0.64
22 1 0.03
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.54
Consensus pattern (21 bp):
GTTTTAGGGTTTTTTAATTCG
Found at i:5795943 original size:41 final size:41
Alignment explanation
Indices: 5795879--5795971 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
5795869 CTTAAATTAG
* * *
5795879 TTTTAGGGTTTTTTTATTCGGTTTGAG-GTTTGATGAATCGA
1 TTTTAGGGTTTTTTAATTCGGTTTGAGAGTTTAAAGAATC-A
*
5795920 TTTTAGGGTTTTTTAAATT-GGTTTTAGAGTTTAAAGAATCA
1 TTTTAGGGTTTTTT-AATTCGGTTTGAGAGTTTAAAGAATCA
*
5795961 ATTTAGGGTTT
1 TTTTAGGGTTT
5795972 AATCAATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
41 32 0.71
42 13 0.29
ACGTcount: A:0.23, C:0.03, G:0.24, T:0.51
Consensus pattern (41 bp):
TTTTAGGGTTTTTTAATTCGGTTTGAGAGTTTAAAGAATCA
Found at i:5795980 original size:41 final size:41
Alignment explanation
Indices: 5795921--5796027 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
5795911 ATGAATCGAT
** * *
5795921 TTTAGGGTTTTTTAAATTGGTTTTAGAGTTTAAAGAATCAA-
1 TTTAGGGTTTAATAAATTGATTTTAGA-CTTAAAGAATCAAG
* **
5795962 TTTAGGGTTTAATCAATTGATTTTAGACTTGCAGAATCAAG
1 TTTAGGGTTTAATAAATTGATTTTAGACTTAAAGAATCAAG
** *
5796003 TTTAGGGTTTCTTGAATTGATTTTA
1 TTTAGGGTTTAATAAATTGATTTTA
5796028 AGGTTTAATG
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 10 0.18
41 45 0.82
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.46
Consensus pattern (41 bp):
TTTAGGGTTTAATAAATTGATTTTAGACTTAAAGAATCAAG
Found at i:5796027 original size:21 final size:21
Alignment explanation
Indices: 5796003--5796113 Score: 62
Period size: 21 Copynumber: 5.3 Consensus size: 21
5795993 CAGAATCAAG
*
5796003 TTTAGGGTTTCTTGAATTGAT
1 TTTAGGGTTTCGTGAATTGAT
* ** *
5796024 TTTAAGGTTTAATGAATCGAT
1 TTTAGGGTTTCGTGAATTGAT
* * * *
5796045 TCTAGTGTTTGGTGAACT-AGT
1 TTTAGGGTTTCGTGAATTGA-T
* ** *
5796066 TTTAGAGTTTTTTGGATTGAT
1 TTTAGGGTTTCGTGAATTGAT
* * *
5796087 TTTAAGGTTTCGTGAATCGAG
1 TTTAGGGTTTCGTGAATTGAT
5796108 TTTAGG
1 TTTAGG
5796114 ATTTTCAATC
Statistics
Matches: 63, Mismatches: 25, Indels: 4
0.68 0.27 0.04
Matches are distributed among these distances:
20 1 0.02
21 61 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.05, G:0.25, T:0.47
Consensus pattern (21 bp):
TTTAGGGTTTCGTGAATTGAT
Found at i:5797165 original size:2 final size:2
Alignment explanation
Indices: 5797158--5797198 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5797148 ATGTTACATC
5797158 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5797199 CATGCACAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5801834 original size:7 final size:7
Alignment explanation
Indices: 5801820--5801857 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
5801810 AAAAAGGGGC
5801820 TGCAACT
1 TGCAACT
*
5801827 TTCAACT
1 TGCAACT
5801834 TGCAACT
1 TGCAACT
5801841 TGCAACT
1 TGCAACT
5801848 TGCAACT
1 TGCAACT
5801855 TGC
1 TGC
5801858 TGAGTACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (7 bp):
TGCAACT
Found at i:5828433 original size:5 final size:5
Alignment explanation
Indices: 5828425--5828449 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5828415 AATAAAACCT
5828425 GGTTG GGTTG GGTTG GGTTG GGTTG
1 GGTTG GGTTG GGTTG GGTTG GGTTG
5828450 TGTAGGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
GGTTG
Found at i:5828823 original size:2 final size:2
Alignment explanation
Indices: 5828818--5828843 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5828808 TATATATAGG
5828818 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
5828844 ACAAAGGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5848040 original size:15 final size:14
Alignment explanation
Indices: 5847999--5848049 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
5847989 TATTTAAATT
5847999 TAAAATATTAAAT-A
1 TAAAATA-TAAATAA
5848013 TAAAAT-TATAATACA
1 TAAAATATA-AATA-A
5848028 TAAAATATAAATAA
1 TAAAATATAAATAA
*
5848042 TTAAATAT
1 TAAAATAT
5848050 GATATATAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
12 2 0.06
13 3 0.09
14 14 0.44
15 11 0.34
16 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAATATAAATAA
Found at i:5850689 original size:20 final size:21
Alignment explanation
Indices: 5850657--5850707 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
5850647 TTTATGTCAC
*
5850657 ATGACAT-ATTGATATGTCATA
1 ATGACATGA-TGATATGACATA
*
5850678 ATGA-ATGATGATGTGACATA
1 ATGACATGATGATATGACATA
5850698 ATGACATGAT
1 ATGACATGAT
5850708 TATGTTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (21 bp):
ATGACATGATGATATGACATA
Found at i:5850712 original size:21 final size:21
Alignment explanation
Indices: 5850657--5850717 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
5850647 TTTATGTCAC
* *
5850657 ATGACAT-ATTGATATGTCATA
1 ATGACATGATT-ATGTGACATA
*
5850678 ATGA-ATGATGATGTGACATA
1 ATGACATGATTATGTGACATA
*
5850698 ATGACATGATTATGTTACAT
1 ATGACATGATTATGTGACAT
5850718 TTTTCACTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (21 bp):
ATGACATGATTATGTGACATA
Found at i:5869544 original size:2 final size:2
Alignment explanation
Indices: 5869539--5869564 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5869529 CAAATTTATC
5869539 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5869565 TCAAAGGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5869976 original size:21 final size:23
Alignment explanation
Indices: 5869950--5869993 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
5869940 TGACATGGAC
5869950 AAAATCAA-AAATT-TTAAAAAG
1 AAAATCAATAAATTGTTAAAAAG
5869971 AAAATCAATTAAATTGTTAAAAA
1 AAAATCAA-TAAATTGTTAAAAA
5869994 TGAATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
23 5 0.25
24 7 0.35
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (23 bp):
AAAATCAATAAATTGTTAAAAAG
Found at i:5876866 original size:24 final size:24
Alignment explanation
Indices: 5876837--5876905 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 24
5876827 GTTATAATTA
5876837 AAATAAAAAATATCAAAATAAAAT
1 AAATAAAAAATATCAAAATAAAAT
* *
5876861 ATATAATAAGA-ATCAAAAATTAAAAT
1 AAATAA-AAAATATC-AAAA-TAAAAT
* *
5876887 AAATATATAATAT-AAAATA
1 AAATAAAAAATATCAAAATA
5876906 TATAAAGATT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
23 2 0.06
24 12 0.34
25 9 0.26
26 12 0.34
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (24 bp):
AAATAAAAAATATCAAAATAAAAT
Found at i:5876893 original size:30 final size:32
Alignment explanation
Indices: 5876829--5876898 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
5876819 TTTGTAATGT
5876829 TATAATTAAAATAAAAAATATCAAAATAAAATA
1 TATAA-TAAAATAAAAAATATCAAAATAAAATA
*
5876862 TATAATAAGAATCAAAAAT-T-AAAAT-AAATA
1 TATAATAA-AATAAAAAATATCAAAATAAAATA
5876892 TATAATA
1 TATAATA
5876899 TAAAATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
30 12 0.34
31 5 0.14
32 4 0.11
33 14 0.40
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (32 bp):
TATAATAAAATAAAAAATATCAAAATAAAATA
Found at i:5892042 original size:24 final size:25
Alignment explanation
Indices: 5892010--5892057 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5892000 TAATATAAAA
5892010 TCATAATAA-TAAAAGATTTAATTT
1 TCATAATAATTAAAAGATTTAATTT
* *
5892034 TCATGATAATTAAAAGGTTTAATT
1 TCATAATAATTAAAAGATTTAATT
5892058 AATTTTATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (25 bp):
TCATAATAATTAAAAGATTTAATTT
Found at i:5895749 original size:15 final size:17
Alignment explanation
Indices: 5895724--5895760 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
5895714 TTATACTAAG
5895724 TTTAA-GAATA-TAA-A
1 TTTAATGAATATTAATA
5895738 TTTAATGAATATTAATA
1 TTTAATGAATATTAATA
5895755 TTTAAT
1 TTTAAT
5895761 TTGAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 5 0.25
16 3 0.15
17 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (17 bp):
TTTAATGAATATTAATA
Found at i:5895897 original size:18 final size:17
Alignment explanation
Indices: 5895871--5895904 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5895861 AAATATTTTT
5895871 TAATAAAATTATTTATTG
1 TAATAAAATT-TTTATTG
*
5895889 TAATTAAATTTTTATT
1 TAATAAAATTTTTATT
5895905 TTTAAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TAATAAAATTTTTATTG
Found at i:5895904 original size:17 final size:18
Alignment explanation
Indices: 5895859--5895904 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
5895849 ATTAAAATTA
*
5895859 AAAAATATTT-TT-TAAT
1 AAAATTATTTATTGTAAT
5895875 AAAATTATTTATTGTAAT
1 AAAATTATTTATTGTAAT
*
5895893 TAAATT-TTTATT
1 AAAATTATTTATT
5895905 TTTAAATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 9 0.35
17 8 0.31
18 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
AAAATTATTTATTGTAAT
Found at i:5909972 original size:12 final size:12
Alignment explanation
Indices: 5909954--5909987 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5909944 CTCCCCTGAC
5909954 AAAAAGAAAAGG
1 AAAAAGAAAAGG
*
5909966 CAAAAGAAAAGG
1 AAAAAGAAAAGG
5909978 AACAAAGAAA
1 AA-AAAGAAA
5909988 CAAACAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.74, C:0.06, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGG
Found at i:5927991 original size:12 final size:12
Alignment explanation
Indices: 5927974--5928014 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
5927964 GTTTATATAT
5927974 AGAGAAAAAGAG
1 AGAGAAAAAGAG
5927986 AGAGAAAAAGAG
1 AGAGAAAAAGAG
* *
5927998 AAAGAAAGAGAG
1 AGAGAAAAAGAG
5928010 AGAGA
1 AGAGA
5928015 GAGCCGTGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
AGAGAAAAAGAG
Found at i:5929428 original size:34 final size:34
Alignment explanation
Indices: 5929385--5929456 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
5929375 CGCCTTAGTT
5929385 CAAGATAGTGCGAACATTACAAACATGAAAATTG
1 CAAGATAGTGCGAACATTACAAACATGAAAATTG
5929419 CAAGATAGTGCGAACATTACAAACATGAAAATTG
1 CAAGATAGTGCGAACATTACAAACATGAAAATTG
5929453 CAAG
1 CAAG
5929457 CGCACATGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.19
Consensus pattern (34 bp):
CAAGATAGTGCGAACATTACAAACATGAAAATTG
Found at i:5933092 original size:18 final size:18
Alignment explanation
Indices: 5933060--5933094 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5933050 TTAGCAAAAT
**
5933060 ATCATTTACTTTCCAATG
1 ATCATTTACCGTCCAATG
5933078 ATCATTTACCGTCCAAT
1 ATCATTTACCGTCCAAT
5933095 TAATTCCTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.40
Consensus pattern (18 bp):
ATCATTTACCGTCCAATG
Found at i:5933605 original size:2 final size:2
Alignment explanation
Indices: 5933598--5933634 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5933588 GTTTTGCTTT
5933598 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5933635 GTTTTCATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5935390 original size:24 final size:23
Alignment explanation
Indices: 5935353--5935408 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
5935343 ACAATAATTT
5935353 TTTTTTTCAATATGGCGTGTAACA
1 TTTTTTT-AATATGGCGTGTAACA
* *
5935377 TTTTTTTAACTATGGTGTGTAGCA
1 TTTTTTTAA-TATGGCGTGTAACA
*
5935401 TGTTTTTA
1 TTTTTTTA
5935409 TGTATAGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.21, C:0.09, G:0.18, T:0.52
Consensus pattern (23 bp):
TTTTTTTAATATGGCGTGTAACA
Found at i:5935490 original size:24 final size:24
Alignment explanation
Indices: 5935462--5935576 Score: 83
Period size: 24 Copynumber: 4.6 Consensus size: 24
5935452 AACAATCTAA
*
5935462 CCATGACATATAACATATTTTTGT
1 CCATGACGTATAACATATTTTTGT
*
5935486 CCATGACGTGTAATAACAGTATTTTTTTT
1 CCATGAC--GT-ATAACA-TA-TTTTTGT
* * **
5935515 CAACATGACGTTTAACA-A--TCTAA
1 C--CATGACGTATAACATATTTTTGT
*
5935538 CCATGACATATAACATATTTTTGT
1 CCATGACGTATAACATATTTTTGT
5935562 CCATGACGTATAACA
1 CCATGACGTATAACA
5935577 ACAATATTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
21 12 0.17
22 1 0.01
23 3 0.04
24 23 0.33
26 2 0.03
27 6 0.09
28 7 0.10
29 9 0.13
31 6 0.09
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (24 bp):
CCATGACGTATAACATATTTTTGT
Found at i:5935505 original size:76 final size:76
Alignment explanation
Indices: 5935418--5935599 Score: 337
Period size: 76 Copynumber: 2.4 Consensus size: 76
5935408 ATGTATAGCA
5935418 TGTAACAACAGTATTTTTTTTCAACATGACGTTTAACAATCTAACCATGACATATAACATATTTT
1 TGTAACAACAGTATTTTTTTTCAACATGACGTTTAACAATCTAACCATGACATATAACATATTTT
5935483 TGTCCATGACG
66 TGTCCATGACG
*
5935494 TGTAATAACAGTATTTTTTTTCAACATGACGTTTAACAATCTAACCATGACATATAACATATTTT
1 TGTAACAACAGTATTTTTTTTCAACATGACGTTTAACAATCTAACCATGACATATAACATATTTT
5935559 TGTCCATGACG
66 TGTCCATGACG
* *
5935570 TATAACAACAATATTTTTTTTCAACATGAC
1 TGTAACAACAGTATTTTTTTTCAACATGAC
5935600 ATGTAACATG
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 102 1.00
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (76 bp):
TGTAACAACAGTATTTTTTTTCAACATGACGTTTAACAATCTAACCATGACATATAACATATTTT
TGTCCATGACG
Found at i:5954201 original size:14 final size:13
Alignment explanation
Indices: 5954182--5954229 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
5954172 TTTATTTTTA
5954182 AAAATTATAAATTT
1 AAAATTATAAA-TT
5954196 AAAATTATACAATT
1 AAAATTATA-AATT
* *
5954210 AATATTTTAAATT
1 AAAATTATAAATT
5954223 AAAATTA
1 AAAATTA
5954230 AAAAATATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 9 0.31
14 18 0.62
15 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAATTATAAATT
Found at i:5954216 original size:21 final size:19
Alignment explanation
Indices: 5954182--5954230 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
5954172 TTTATTTTTA
*
5954182 AAAATTATAAATTTAAAATT
1 AAAATTA-ATATTTAAAATT
*
5954202 ATACAATTAATATTTTAAATT
1 A-A-AATTAATATTTAAAATT
5954223 AAAATTAA
1 AAAATTAA
5954231 AAAATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 6 0.24
20 2 0.08
21 12 0.48
22 5 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTAATATTTAAAATT
Found at i:5954268 original size:30 final size:29
Alignment explanation
Indices: 5954207--5954289 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 29
5954197 AAATTATACA
5954207 ATTAATATTTTAAATTAAAATTAAAAAAT
1 ATTAATATTTTAAATTAAAATTAAAAAAT
* ** * *
5954236 ATTAATATTTTCATATTTTAATTATAATAT
1 ATTAATATTTT-AAATTAAAATTAAAAAAT
* * *
5954266 ATTTATATTGTAAATAAAAATTAA
1 ATTAATATTTTAAATTAAAATTAA
5954290 TATTTTAAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
29 19 0.46
30 22 0.54
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
ATTAATATTTTAAATTAAAATTAAAAAAT
Found at i:5954310 original size:15 final size:15
Alignment explanation
Indices: 5954280--5954313 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5954270 ATATTGTAAA
5954280 TAAAAATTAATATTT
1 TAAAAATTAATATTT
5954295 TAAAATATTAAT-TTT
1 TAAAA-ATTAATATTT
5954310 TAAA
1 TAAA
5954314 TTGCTAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAAATTAATATTT
Found at i:5954644 original size:22 final size:22
Alignment explanation
Indices: 5954577--5954697 Score: 99
Period size: 22 Copynumber: 5.5 Consensus size: 22
5954567 TTTAAATTAT
*
5954577 AAATAAAATACTAATATTTCAAA
1 AAATAAAATATTAATATTT-AAA
*
5954600 AAATAATA-ATT-A-ATTT--A
1 AAATAAAATATTAATATTTAAA
5954617 AAATAAAATATTAATATTTAAA
1 AAATAAAATATTAATATTTAAA
** * *
5954639 TGATAAATTATTAATGTTATAAA
1 AAATAAAATATTAATATT-TAAA
5954662 TAAGATATAAATTATTAATATTTAAA
1 -AA-ATA-AAA-TATTAATATTTAAA
5954688 AAATAAAATA
1 AAATAAAATA
5954698 AAATAAAATA
Statistics
Matches: 77, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
17 8 0.10
18 3 0.04
19 1 0.01
20 8 0.10
21 1 0.01
22 19 0.25
23 14 0.18
24 3 0.04
25 5 0.06
26 6 0.08
27 9 0.12
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
AAATAAAATATTAATATTTAAA
Found at i:5954645 original size:66 final size:64
Alignment explanation
Indices: 5954515--5954646 Score: 160
Period size: 66 Copynumber: 2.0 Consensus size: 64
5954505 TAAATCAATT
* * *
5954515 ATAAATTACTAATATTTAAAAAATAAAATAAAAACAAATAATCATAATAATATTTAAATTATAA
1 ATAAAATACTAATATTTAAAAAATAAAATAAAAACAAATAATAATAATAATATTTAAATGATAA
** *
5954579 ATAAAATACTAATATTTCAAAAAATAATAATTAATTTA-AAATAA-AATATTAATATTTAAATGA
1 ATAAAATACTAATATTT-AAAAAATAA-AA-TAA-AAACAAATAATAATAATAATATTTAAATGA
5954642 TAA
62 TAA
5954645 AT
1 AT
5954647 TATTAATGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
64 16 0.28
65 9 0.16
66 23 0.40
67 9 0.16
68 1 0.02
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.35
Consensus pattern (64 bp):
ATAAAATACTAATATTTAAAAAATAAAATAAAAACAAATAATAATAATAATATTTAAATGATAA
Found at i:5954652 original size:40 final size:41
Alignment explanation
Indices: 5954560--5954669 Score: 125
Period size: 40 Copynumber: 2.7 Consensus size: 41
5954550 AAATAATCAT
* * *
5954560 AATAATATTTAAATTATAAATAAAATACTAATATTTCAAAA
1 AATAATAATTAATTTATAAATAAAATATTAATATTTCAAAA
*
5954601 AATAATAATTAATTTA-AAATAAAATATTAATATTT-AAAT
1 AATAATAATTAATTTATAAATAAAATATTAATATTTCAAAA
* * *
5954640 GATAAATTATTAATGTTATAAATAAGATAT
1 AAT-AATAATTAAT-TTATAAATAAAATAT
5954670 AAATTATTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
39 5 0.08
40 27 0.46
41 17 0.29
42 10 0.17
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (41 bp):
AATAATAATTAATTTATAAATAAAATATTAATATTTCAAAA
Found at i:5954834 original size:158 final size:152
Alignment explanation
Indices: 5954480--5954846 Score: 429
Period size: 158 Copynumber: 2.4 Consensus size: 152
5954470 TAAATTATCA
* * *
5954480 ATTTAATTATCAATTATTAATATTTT-AAATCAATTATAAATTACTAATATTTAAAAAATAAAAT
1 ATTTAAATATCAATTATTAAT-TTTTAAAATAAATTATAAATTATTAATATTTAAAAAATAAAAT
*
5954544 AAAAACAAATAATCATAATAATATTTAAATTATAAATAAAATACTAATATTTCAAAAAATAATAA
65 AAAAACAAATAATCATAATAACATTTAAATTATAAATAAAATACTAATATTTCAAAAAATAATAA
**
5954609 TTAATTTAAAATAAAATATTAAT
130 TTAAAATAAAATAAAATATTAAT
* *
5954632 ATTTAAATGATAAATTATTAA-TGTTATAAATAAGA-TATAAATTATTAATATTTAAAAAATAAA
1 ATTTAAAT-ATCAATTATTAATTTTTA-AAATAA-ATTATAAATTATTAATATTTAAAAAATAAA
** * * ** *
5954695 ATAAAATA-AAATAAATATTCATAATAACATTTAAATTATAAATTCAATATTATTATTTTTAATA
63 ATAAAA-ACAAAT--A-A-TCATAATAACATTTAAATTATAAATAAAATACTAATATTTCAAAAA
* *
5954759 TTAATTATTAAAATATAAATAAAATATTAAT
123 ATAATAATTAAAATA-AAATAAAATATTAAT
*
5954790 ATTTAAACTATCAATT-TTAAATTTTTAAAATAAATTATACATTATTAATATTTAAAA
1 ATTTAAA-TATCAATTATT-AATTTTTAAAATAAATTATAAATTATTAATATTTAAAA
5954847 TCATAATAAC
Statistics
Matches: 181, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
151 3 0.02
152 7 0.04
153 53 0.29
154 2 0.01
155 1 0.01
156 1 0.01
157 52 0.29
158 57 0.31
159 5 0.03
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.41
Consensus pattern (152 bp):
ATTTAAATATCAATTATTAATTTTTAAAATAAATTATAAATTATTAATATTTAAAAAATAAAATA
AAAACAAATAATCATAATAACATTTAAATTATAAATAAAATACTAATATTTCAAAAAATAATAAT
TAAAATAAAATAAAATATTAAT
Found at i:5963306 original size:9 final size:9
Alignment explanation
Indices: 5963292--5963347 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
5963282 GTCTGGTTTT
5963292 GGTGGTGGA
1 GGTGGTGGA
*
5963301 GCTGGTGGA
1 GGTGGTGGA
*
5963310 GGTGGTGGTTTT
1 GGTGGTGG---A
5963322 GGTGGTGGA
1 GGTGGTGGA
*
5963331 GCTGGTGGA
1 GGTGGTGGA
5963340 GGTGGTGG
1 GGTGGTGG
5963348 TTTTGGTGNN
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 30 0.79
12 8 0.21
ACGTcount: A:0.07, C:0.04, G:0.61, T:0.29
Consensus pattern (9 bp):
GGTGGTGGA
Found at i:5963321 original size:30 final size:30
Alignment explanation
Indices: 5963285--5963355 Score: 142
Period size: 30 Copynumber: 2.4 Consensus size: 30
5963275 GAGGTGGGTC
5963285 TGGTTTTGGTGGTGGAGCTGGTGGAGGTGG
1 TGGTTTTGGTGGTGGAGCTGGTGGAGGTGG
5963315 TGGTTTTGGTGGTGGAGCTGGTGGAGGTGG
1 TGGTTTTGGTGGTGGAGCTGGTGGAGGTGG
5963345 TGGTTTTGGTG
1 TGGTTTTGGTG
5963356 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.06, C:0.03, G:0.55, T:0.37
Consensus pattern (30 bp):
TGGTTTTGGTGGTGGAGCTGGTGGAGGTGG
Found at i:5963343 original size:18 final size:18
Alignment explanation
Indices: 5963294--5963347 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
5963284 CTGGTTTTGG
* *
5963294 TGGTGGAGCTGGTGGAGG
1 TGGTGGAGGTGGTGGAGC
*
5963312 TGGTGGTTTTGGTGGTGGAGC
1 TGGTGG---AGGTGGTGGAGC
5963333 TGGTGGAGGTGGTGG
1 TGGTGGAGGTGGTGG
5963348 TTTTGGTGNN
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 14 0.48
21 15 0.52
ACGTcount: A:0.07, C:0.04, G:0.59, T:0.30
Consensus pattern (18 bp):
TGGTGGAGGTGGTGGAGC
Found at i:5963345 original size:21 final size:21
Alignment explanation
Indices: 5963303--5963348 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5963293 GTGGTGGAGC
* ***
5963303 TGGTGGAGGTGGTGGTTTTGG
1 TGGTGGAGCTGGTGGAGGTGG
5963324 TGGTGGAGCTGGTGGAGGTGG
1 TGGTGGAGCTGGTGGAGGTGG
5963345 TGGT
1 TGGT
5963349 TTTGGTGNNN
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.02, G:0.59, T:0.33
Consensus pattern (21 bp):
TGGTGGAGCTGGTGGAGGTGG
Found at i:5964638 original size:18 final size:18
Alignment explanation
Indices: 5964611--5964645 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5964601 AGGTGGGGGT
5964611 GGTGGATTTGGAGGTGGC
1 GGTGGATTTGGAGGTGGC
*
5964629 GGTGGTTTTGGAGGTGG
1 GGTGGATTTGGAGGTGG
5964646 ACACCACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.03, G:0.57, T:0.31
Consensus pattern (18 bp):
GGTGGATTTGGAGGTGGC
Found at i:5980514 original size:24 final size:24
Alignment explanation
Indices: 5980487--5980532 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
5980477 CAAGACTTCG
5980487 ATATGTCCAGCAACACATCACACC
1 ATATGTCCAGCAACACATCACACC
5980511 ATATGTCCAGCAACACATCACA
1 ATATGTCCAGCAACACATCACA
5980533 AAAGTTAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.35, G:0.09, T:0.17
Consensus pattern (24 bp):
ATATGTCCAGCAACACATCACACC
Found at i:5981500 original size:201 final size:201
Alignment explanation
Indices: 5980971--5981653 Score: 1010
Period size: 202 Copynumber: 3.4 Consensus size: 201
5980961 ATGCCATGAA
* * * * * *
5980971 AGAGGCATTTCATGTAAGTCCATTAGCATTCAAAACGAAACTTTGCCTATAAGACATTTTAGCTT
1 AGAGACATTTGATGTAAGTCCATTAGCATTCAAAACTAAACATTGCATAAAAGACATTTTAGCTT
* * * *
5981036 TGCCAAGATGGACTACATGCCTAAGCAAAACACTCCAAGCAAGAACTTGGCCCACTTTTATTGGT
66 TGCCAAGATGGACTAAATGCCTAAGTAAAATACTCCAAACAAGAACTTGGCCCACTTTTATTGGT
* *
5981101 GCAAACCATATACTAATTTCTCCTCCCCACTGATCTGAGCTCCTCGTAGAATAAGAAGCACAAAG
131 GCAAACCATATACTAATGTCTCCTCCCCACTGATCTGAGCTCCTAGTAGAATAAGAAGCACAAAG
5981166 CTGTGAG
196 C-GTGAG
* * * * *
5981173 AGAGACATTTAATGTAAGTGCACTAGCATTCAAAACTAAACATTGCCTAAAAAACATTTTAGCTT
1 AGAGACATTTGATGTAAGTCCATTAGCATTCAAAACTAAACATTGCATAAAAGACATTTTAGCTT
5981238 TGCCAAGATGGACTAAATGCCTAAGTAAAATACTCCAAACAAGAACTTGGCCCAC-TTTATTGGT
66 TGCCAAGATGGACTAAATGCCTAAGTAAAATACTCCAAACAAGAACTTGGCCCACTTTTATTGGT
* * *
5981302 GCAAACCATATACTAACGTCTCCTCCCCACTGATTTGAACTCCTAGTAGAATAAGAAGCACAAAG
131 GCAAACCATATACTAATGTCTCCTCCCCACTGATCTGAGCTCCTAGTAGAATAAGAAGCACAAAG
5981367 CGTGAG
196 CGTGAG
* **
5981373 AGAGACATTTGATGTAAGTCCATTAGCATTCAAAACTAAACATTGCATAAAAGACGTTACAGCTT
1 AGAGACATTTGATGTAAGTCCATTAGCATTCAAAACTAAACATTGCATAAAAGACATTTTAGCTT
* * * *
5981438 TGCCAAGATGGACTAAATGCCCAAGTAAAATACTGCAAACAATAACTTGGCCGACTTTTATTGGT
66 TGCCAAGATGGACTAAATGCCTAAGTAAAATACTCCAAACAAGAACTTGGCCCACTTTTATTGGT
* * * *
5981503 GCAAGCCATATACTAATGTCTCCTCCCCACTGATCTGAGCTCCTACTACAATAAGAAGCCCAAAG
131 GCAAACCATATACTAATGTCTCCTCCCCACTGATCTGAGCTCCTAGTAGAATAAGAAGCACAAAG
5981568 CCGTGAG
196 -CGTGAG
* * * * *
5981575 AGAGAAATTTGATATAAGTCCATTAGCATTCAAAACTAATCATTGCATATAAGGC-TTTTAGCTT
1 AGAGACATTTGATGTAAGTCCATTAGCATTCAAAACTAAACATTGCATAAAAGACATTTTAGCTT
5981639 TGCCAAGATGGACTA
66 TGCCAAGATGGACTA
5981654 GCATGTTCTC
Statistics
Matches: 436, Mismatches: 43, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
200 113 0.26
201 159 0.36
202 164 0.38
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (201 bp):
AGAGACATTTGATGTAAGTCCATTAGCATTCAAAACTAAACATTGCATAAAAGACATTTTAGCTT
TGCCAAGATGGACTAAATGCCTAAGTAAAATACTCCAAACAAGAACTTGGCCCACTTTTATTGGT
GCAAACCATATACTAATGTCTCCTCCCCACTGATCTGAGCTCCTAGTAGAATAAGAAGCACAAAG
CGTGAG
Found at i:5986357 original size:2 final size:2
Alignment explanation
Indices: 5986352--5986376 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5986342 TGCCTGTGTG
5986352 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5986377 TTCTAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5990265 original size:3 final size:3
Alignment explanation
Indices: 5990257--5990286 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5990247 ACTATACTTC
5990257 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5990287 ATGTTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6000949 original size:28 final size:30
Alignment explanation
Indices: 6000894--6000961 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 30
6000884 TATAAATTTT
* *
6000894 AAATCAAAATTACAAAGTAGAAATTATTAA
1 AAATAAAAATTACAAAGTAGAAAATATTAA
*
6000924 ATAA-AAAAATTA-AAATTA-AAAATATTAA
1 A-AATAAAAATTACAAAGTAGAAAATATTAA
6000952 AAATAAAAAT
1 AAATAAAAAT
6000962 AAGTAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 2 0.06
28 16 0.48
29 5 0.15
30 8 0.24
31 2 0.06
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATAAAAATTACAAAGTAGAAAATATTAA
Found at i:6000961 original size:15 final size:15
Alignment explanation
Indices: 6000922--6000962 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
6000912 AGAAATTATT
*
6000922 AAATAAAAAAATTAA
1 AAATAAAAATATTAA
*
6000937 AATTAAAAATATTAA
1 AAATAAAAATATTAA
6000952 AAATAAAAATA
1 AAATAAAAATA
6000963 AGTAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAAAATATTAA
Found at i:6016686 original size:9 final size:9
Alignment explanation
Indices: 6016672--6016698 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
6016662 GATAAGGCTA
6016672 ATGTTAGGC
1 ATGTTAGGC
6016681 ATGTTAGGC
1 ATGTTAGGC
6016690 ATGTTAGGC
1 ATGTTAGGC
6016699 CAAGTCCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.33, T:0.33
Consensus pattern (9 bp):
ATGTTAGGC
Found at i:6019193 original size:29 final size:28
Alignment explanation
Indices: 6019161--6019432 Score: 129
Period size: 29 Copynumber: 9.8 Consensus size: 28
6019151 TGTAACAAAA
6019161 TTTTTTAAACATGACGTGTAATAATAAT
1 TTTTTTAAACATGACGTGTAATAATAAT
* * *
6019189 ATTTTTTCAACATGGCATGTAATAATAACATT
1 -TTTTTTAAACATGACGTGTAATAAT-A-A-T
* * *
6019221 TTTTTTCAACAT-A-ATGT-GTAAT-AT
1 TTTTTTAAACATGACGTGTAATAATAAT
* * * * * *
6019245 GTTTTTATATATAATGTGTAACAATAATTT
1 TTTTTTAAACATGACGTGTAATAATAA--T
* * *
6019275 TTTTTTTAACATGACGCGTAACAAT-AT
1 TTTTTTAAACATGACGTGTAATAATAAT
* *
6019302 TTTTTT-AACAATGACGTG---CAA-CAT
1 TTTTTTAAAC-ATGACGTGTAATAATAAT
* * *
6019326 GTTTTTATATATGACGTGTAATAATAAT
1 TTTTTTAAACATGACGTGTAATAATAAT
* *
6019354 TTTTTTGAAATATGAAGTG--A-AATAACT
1 TTTTTT-AAACATGACGTGTAATAATAA-T
* *
6019381 TTTTTTAATCATGACATGTAATAATAAT
1 TTTTTTAAACATGACGTGTAATAATAAT
* *
6019409 ATTTTTTTAACATGATGTGTAATA
1 -TTTTTTAAACATGACGTGTAATA
6019433 TCATGTGCGC
Statistics
Matches: 185, Mismatches: 36, Indels: 44
0.70 0.14 0.17
Matches are distributed among these distances:
24 27 0.15
25 3 0.02
26 19 0.10
27 27 0.15
28 14 0.08
29 61 0.33
30 20 0.11
31 13 0.07
32 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (28 bp):
TTTTTTAAACATGACGTGTAATAATAAT
Found at i:6019330 original size:25 final size:26
Alignment explanation
Indices: 6019276--6019331 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
6019266 CAATAATTTT
* *
6019276 TTTTTTAACATGACGCGTAACAATAT
1 TTTTTTAACATGACGCGCAACAATAG
*
6019302 TTTTTTAACAATGACGTGCAAC-AT-G
1 TTTTTTAAC-ATGACGCGCAACAATAG
6019327 TTTTT
1 TTTTT
6019332 ATATATGACG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 11 0.42
27 10 0.38
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (26 bp):
TTTTTTAACATGACGCGCAACAATAG
Found at i:6019331 original size:27 final size:26
Alignment explanation
Indices: 6019273--6019324 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
6019263 TAACAATAAT
*
6019273 TTTTTTTTTAACATGACGCGTAACAA
1 TTTTTTTTTAACATGACGCGCAACAA
* *
6019299 TATTTTTTTAACAATGACGTGCAACA
1 TTTTTTTTTAAC-ATGACGCGCAACA
6019325 TGTTTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (26 bp):
TTTTTTTTTAACATGACGCGCAACAA
Found at i:6019386 original size:81 final size:80
Alignment explanation
Indices: 6019162--6019386 Score: 177
Period size: 81 Copynumber: 2.8 Consensus size: 80
6019152 GTAACAAAAT
* * * * *
6019162 TTTTTAAACATGACGTGTAATAATAATATTTTTTCAACAT-GGCATGTAATAATAACATTTTTTT
1 TTTTTATATATGACGTGTAATAATAAT-TTTTTTCAA-ATATG-AAGTGA-AATAAC-TTTTTTT
* * *
6019226 TCAACATAATGTGTAATATG
61 TCAACATAACGTGCAACATG
* * * ** * * * * *
6019246 TTTTTATATATAATGTGTAACAATAATTTTTTTTTTAACATGACGCGTAACAA-TATTTTTTT-A
1 TTTTTATATATGACGTGTAATAATAA-TTTTTTTCAAATATGAAGTGAAATAACT-TTTTTTTCA
*
6019309 ACAATGACGTGCAACATG
64 AC-ATAACGTGCAACATG
*
6019327 TTTTTATATATGACGTGTAATAATAATTTTTTTGAAATATGAAGTGAAATAACTTTTTTT
1 TTTTTATATATGACGTGTAATAATAATTTTTTTCAAATATGAAGTGAAATAACTTTTTTT
6019387 AATCATGACA
Statistics
Matches: 108, Mismatches: 28, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
80 29 0.27
81 42 0.39
82 4 0.04
83 3 0.03
84 29 0.27
85 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (80 bp):
TTTTTATATATGACGTGTAATAATAATTTTTTTCAAATATGAAGTGAAATAACTTTTTTTTCAAC
ATAACGTGCAACATG
Found at i:6019537 original size:69 final size:69
Alignment explanation
Indices: 6019449--6019610 Score: 234
Period size: 69 Copynumber: 2.3 Consensus size: 69
6019439 GCGCGACATA
* * ** *
6019449 TAACATCATGTGTATTTGATATAAAAAAGTTTAGAACATAGTGTGAAATATATTTTTATATATGA
1 TAACATCATGTGCACTTGATATAAAAAAGTTTAGAACATAAAGTGAAATATATTTTTATATATAA
6019514 CGTG
66 CGTG
* * *
6019518 TAACATCATGTGCACTTGATATAAAAAGGTTTAGTACATAAAGTGAAATGTATTTTTATATATAA
1 TAACATCATGTGCACTTGATATAAAAAAGTTTAGAACATAAAGTGAAATATATTTTTATATATAA
*
6019583 CTTG
66 CGTG
*
6019587 TAACATCATGTGCACTTAATATAA
1 TAACATCATGTGCACTTGATATAA
6019611 GAAGGGTTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 83 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (69 bp):
TAACATCATGTGCACTTGATATAAAAAAGTTTAGAACATAAAGTGAAATATATTTTTATATATAA
CGTG
Found at i:6031175 original size:8 final size:9
Alignment explanation
Indices: 6031160--6031212 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 9
6031150 CGCCTCCTCA
6031160 ATAATTTTT
1 ATAATTTTT
6031169 A-AATTTTT
1 ATAATTTTT
6031177 ATAATTTATTT
1 ATAA-TT-TTT
*
6031188 ATATTTTTT
1 ATAATTTTT
6031197 AATAA-TTTT
1 -ATAATTTTT
6031206 ATAATTT
1 ATAATTT
6031213 CATCCCTCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 12 0.32
9 12 0.32
10 7 0.19
11 6 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:6031315 original size:62 final size:62
Alignment explanation
Indices: 6031165--6031342 Score: 214
Period size: 62 Copynumber: 2.9 Consensus size: 62
6031155 CCTCAATAAT
** * * * *
6031165 TTTTAAATTTTTATAATTTATTTATATTTTTTAATAATTTTATAATTTCATCCCTCTAATAAT
1 TTTTAAATTTTTATAACATATTTTTATTTTTTAAAAATTTTATAATTTCA-CCCTCTAAAAAA
* ** *
6031228 TTTTAAATTTTTATAACCTGCTTTTATTTTTTAAAAATTTTATAATTTC-GCCTCTACAAAAA
1 TTTTAAATTTTTATAACATATTTTTATTTTTTAAAAATTTTATAATTTCACCCTCTA-AAAAA
* * *
6031290 TTTTAAATTTTTTTCACATATTTTTATTTTTTAAAAATTTTATAATTTTACCC
1 TTTTAAATTTTTATAACATATTTTTATTTTTTAAAAATTTTATAATTTCACCC
6031343 CTACTATAAT
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
61 6 0.06
62 46 0.47
63 45 0.46
ACGTcount: A:0.33, C:0.10, G:0.01, T:0.56
Consensus pattern (62 bp):
TTTTAAATTTTTATAACATATTTTTATTTTTTAAAAATTTTATAATTTCACCCTCTAAAAAA
Found at i:6031354 original size:62 final size:63
Alignment explanation
Indices: 6031160--6031356 Score: 236
Period size: 63 Copynumber: 3.1 Consensus size: 63
6031150 CGCCTCCTCA
** * * *
6031160 ATAATTTTTAAATTTTTATAATTTATTTATATTTTTTAATAATTTTATAATTTCATCCCT-CT
1 ATAATTTTTAAATTTTTATAACATATTTTTATTTTTTAAAAATTTTATAATTTCACCCCTACT
* ** * *
6031222 AATAATTTTTAAATTTTTATAACCTGCTTTTATTTTTTAAAAATTTTATAATTTCGCCTCTAC-
1 -ATAATTTTTAAATTTTTATAACATATTTTTATTTTTTAAAAATTTTATAATTTCACCCCTACT
* * * * *
6031285 AAAAATTTTAAATTTTTTTCACATATTTTTATTTTTTAAAAATTTTATAATTTTACCCCTACT
1 ATAATTTTTAAATTTTTATAACATATTTTTATTTTTTAAAAATTTTATAATTTCACCCCTACT
6031348 ATAATTTTT
1 ATAATTTTT
6031357 TATTTAGTGA
Statistics
Matches: 111, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
62 52 0.47
63 58 0.52
64 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.01, T:0.56
Consensus pattern (63 bp):
ATAATTTTTAAATTTTTATAACATATTTTTATTTTTTAAAAATTTTATAATTTCACCCCTACT
Found at i:6033031 original size:12 final size:12
Alignment explanation
Indices: 6033014--6033040 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6033004 CAATTTACTG
6033014 TTTGTTCTTCAA
1 TTTGTTCTTCAA
6033026 TTTGTTCTTCAA
1 TTTGTTCTTCAA
6033038 TTT
1 TTT
6033041 ATTTCTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (12 bp):
TTTGTTCTTCAA
Found at i:6035478 original size:18 final size:17
Alignment explanation
Indices: 6035447--6035486 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
6035437 CAGTAAGGCA
6035447 AAGAACAAAACAAACTT
1 AAGAACAAAACAAACTT
* *
6035464 AAGAAGCAAAGCAAAGTT
1 AAGAA-CAAAACAAACTT
6035482 AAGAA
1 AAGAA
6035487 ATAGATAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.62, C:0.12, G:0.15, T:0.10
Consensus pattern (17 bp):
AAGAACAAAACAAACTT
Found at i:6048937 original size:16 final size:16
Alignment explanation
Indices: 6048901--6048931 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6048891 CAATCCTCTG
6048901 CTGAACAAACCCCACA
1 CTGAACAAACCCCACA
*
6048917 CTGAACAACCCCCAC
1 CTGAACAAACCCCAC
6048932 CATGAAGCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.48, G:0.06, T:0.06
Consensus pattern (16 bp):
CTGAACAAACCCCACA
Found at i:6051619 original size:3 final size:3
Alignment explanation
Indices: 6051613--6051649 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
6051603 CCCCTTTACC
6051613 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
6051650 TCCTCTCTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:6054282 original size:28 final size:27
Alignment explanation
Indices: 6054249--6054302 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
6054239 ATTAGAACAA
* *
6054249 ATTTAAATAAATTTTTATTTTTTATTAT
1 ATTTAAATAAAATTTTA-TATTTATTAT
*
6054277 ATTTAATTAAAATTTTATATTTATTA
1 ATTTAAATAAAATTTTATATTTATTA
6054303 GATAGATCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTTAAATAAAATTTTATATTTATTAT
Found at i:6055043 original size:74 final size:73
Alignment explanation
Indices: 6054917--6055186 Score: 336
Period size: 74 Copynumber: 3.7 Consensus size: 73
6054907 AGTACAACCT
* *
6054917 GAAAAATCAACCAGACAAGGTTGATCTCAACTTGGTAGAGTAAGTTTTTGTGCCCCGTTTGAAAT
1 GAAAAACCAACCAGACAAGGTTAATCTCAACTTGGTAGAGTAAGTTTTTGTGCCCCGTTTGAAAT
6054982 GAACAAGTG
66 G-ACAAGTG
* * * * *
6054991 GAAAAACCGACCAGACAAGGTTAATCTCAACTTGGTAGATTAAGTTTCTGTGCCCTGTCTGAAAT
1 GAAAAACCAACCAGACAAGGTTAATCTCAACTTGGTAGAGTAAGTTTTTGTGCCCCGTTTGAAAT
6055056 GTAC-AGCTG
66 G-ACAAG-TG
* * *
6055065 GAAAAACCAAGCAGACAAGGTTAATCTCAGCTTGGTAGAGTAAGTTTTTGTGCCACG-TTG---T
1 GAAAAACCAACCAGACAAGGTTAATCTCAACTTGGTAGAGTAAGTTTTTGTGCCCCGTTTGAAAT
*
6055126 -ACAAATG
66 GACAAGTG
** * *
6055133 GAAAAACCAAGAAGACAAGGTTAATCTCAAGTTGGTAGAGTAAGTATTTGTGCC
1 GAAAAACCAACCAGACAAGGTTAATCTCAACTTGGTAGAGTAAGTTTTTGTGCC
6055187 ATGTCTACAA
Statistics
Matches: 173, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
68 54 0.31
69 1 0.01
70 1 0.01
73 4 0.02
74 113 0.65
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (73 bp):
GAAAAACCAACCAGACAAGGTTAATCTCAACTTGGTAGAGTAAGTTTTTGTGCCCCGTTTGAAAT
GACAAGTG
Found at i:6055473 original size:7 final size:7
Alignment explanation
Indices: 6055461--6055507 Score: 94
Period size: 7 Copynumber: 6.7 Consensus size: 7
6055451 CGTTTCTCTT
6055461 GCTTTGA
1 GCTTTGA
6055468 GCTTTGA
1 GCTTTGA
6055475 GCTTTGA
1 GCTTTGA
6055482 GCTTTGA
1 GCTTTGA
6055489 GCTTTGA
1 GCTTTGA
6055496 GCTTTGA
1 GCTTTGA
6055503 GCTTT
1 GCTTT
6055508 TTGTAATATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.13, C:0.15, G:0.28, T:0.45
Consensus pattern (7 bp):
GCTTTGA
Found at i:6056300 original size:21 final size:22
Alignment explanation
Indices: 6056274--6056322 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
6056264 ATCCAGAAGG
*
6056274 TGATGATTGTTATGATGAT-GA
1 TGATGATTATTATGATGATGGA
*
6056295 TGATGATTATTATTATGATGGA
1 TGATGATTATTATGATGATGGA
6056317 -GATGAT
1 TGATGAT
6056323 AGTGATGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.43
Consensus pattern (22 bp):
TGATGATTATTATGATGATGGA
Found at i:6056301 original size:24 final size:24
Alignment explanation
Indices: 6056274--6056322 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
6056264 ATCCAGAAGG
*
6056274 TGATGATTGTTATGAT-GATGATGA
1 TGATGATTATTATGATGGA-GATGA
*
6056298 TGATTATTATTATGATGGAGATGA
1 TGATGATTATTATGATGGAGATGA
6056322 T
1 T
6056323 AGTGATGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.43
Consensus pattern (24 bp):
TGATGATTATTATGATGGAGATGA
Found at i:6061358 original size:21 final size:21
Alignment explanation
Indices: 6061334--6061373 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
6061324 TGTCCTATCT
6061334 AATTA-AAATTTTAAATTTAAA
1 AATTATAAATTTT-AATTTAAA
*
6061355 AATTATTAATTTTAATTTA
1 AATTATAAATTTTAATTTA
6061374 TTTATATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTATAAATTTTAATTTAAA
Found at i:6078361 original size:19 final size:19
Alignment explanation
Indices: 6078324--6078361 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
6078314 ATGTGAGGTT
6078324 TTTGATTTGAGATTGTCTTG
1 TTTGATTTGAGA-TGTCTTG
6078344 TTTGATTTTGAG-TGTCTT
1 TTTGA-TTTGAGATGTCTT
6078362 TTATTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.13, C:0.05, G:0.24, T:0.58
Consensus pattern (19 bp):
TTTGATTTGAGATGTCTTG
Found at i:6079250 original size:13 final size:13
Alignment explanation
Indices: 6079232--6079258 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6079222 AAATTGAAAT
6079232 AAAATTTATTTTA
1 AAAATTTATTTTA
6079245 AAAATTTATTTTA
1 AAAATTTATTTTA
6079258 A
1 A
6079259 TTTAAGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAATTTATTTTA
Found at i:6082860 original size:2 final size:2
Alignment explanation
Indices: 6082848--6082887 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
6082838 GATTTCCTGG
6082848 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6082888 GACCAAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:6085454 original size:21 final size:21
Alignment explanation
Indices: 6085430--6085471 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6085420 GATTTAAAAA
*
6085430 TAAAAAATTTTAAAATTTTTT
1 TAAAAAATTTAAAAATTTTTT
*
6085451 TAAATAATTTAAAAATTTTTT
1 TAAAAAATTTAAAAATTTTTT
6085472 AAATATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAAAAATTTAAAAATTTTTT
Found at i:6085463 original size:20 final size:19
Alignment explanation
Indices: 6085439--6085505 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
6085429 ATAAAAAATT
6085439 TTAAAATTTTTTTAAATAA
1 TTAAAATTTTTTTAAATAA
*
6085458 TTTAAAAATTTTTTAAAT-A
1 -TTAAAATTTTTTTAAATAA
** *
6085477 TTATAAATTTAATTAATTAA
1 TTA-AAATTTTTTTAAATAA
6085497 TTAAAATTT
1 TTAAAATTT
6085506 AATTATAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 3 0.08
19 17 0.43
20 20 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAAAATTTTTTTAAATAA
Found at i:6087055 original size:2 final size:2
Alignment explanation
Indices: 6087050--6087081 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6087040 TCTTTTTTTG
*
6087050 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6087082 CTTTTGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:6110131 original size:4 final size:4
Alignment explanation
Indices: 6110122--6110154 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
6110112 TGCTTTAAAC
6110122 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
6110155 ATTGCAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:6119946 original size:30 final size:31
Alignment explanation
Indices: 6119903--6119969 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 31
6119893 ATTGCATGGA
6119903 AAAT-CAT-TCAACATCAGCTAAAGCAAACC
1 AAATCCATGTCAACATCAGCTAAAGCAAACC
* *
6119932 AAA-CCATGTCAACATCAGCTCAAGCAAACT
1 AAATCCATGTCAACATCAGCTAAAGCAAACC
6119962 AAATCCAT
1 AAATCCAT
6119970 ATCTTTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 6 0.18
30 23 0.70
31 4 0.12
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.18
Consensus pattern (31 bp):
AAATCCATGTCAACATCAGCTAAAGCAAACC
Found at i:6128815 original size:2 final size:2
Alignment explanation
Indices: 6128808--6128848 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
6128798 GTATGATGAT
*
6128808 TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6128849 TTTCTTTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:6136991 original size:76 final size:76
Alignment explanation
Indices: 6136863--6137014 Score: 277
Period size: 76 Copynumber: 2.0 Consensus size: 76
6136853 TGCTTTCTCC
* *
6136863 CATTTAAACGTATAAGACACAAAGTTGACCACACCCCGGTGAATCTTGGCAACATCGAAAAACCA
1 CATTTAAACGTATAAGACACAAAGTTGACCAAACCCCGGTGAATCTTAGCAACATCGAAAAACCA
*
6136928 GGTTGTTTCAA
66 AGTTGTTTCAA
6136939 CATTTAAACGTATAAGACACAAAGTTGACCAAACCCCGGTGAATCTTAGCAACATCGAAAAACCA
1 CATTTAAACGTATAAGACACAAAGTTGACCAAACCCCGGTGAATCTTAGCAACATCGAAAAACCA
6137004 AGTTGTTTCAA
66 AGTTGTTTCAA
6137015 ACTTCTTTTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (76 bp):
CATTTAAACGTATAAGACACAAAGTTGACCAAACCCCGGTGAATCTTAGCAACATCGAAAAACCA
AGTTGTTTCAA
Found at i:6138393 original size:19 final size:19
Alignment explanation
Indices: 6138369--6138408 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
6138359 TATGGCTCTG
*
6138369 TGGCTACAGGAAACATTTA
1 TGGCTACAAGAAACATTTA
6138388 TGGCTACAAGAAACATTTA
1 TGGCTACAAGAAACATTTA
6138407 TG
1 TG
6138409 TTGTATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (19 bp):
TGGCTACAAGAAACATTTA
Found at i:6146446 original size:15 final size:15
Alignment explanation
Indices: 6146426--6146459 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
6146416 TATTTTAAAA
*
6146426 ATAATGAATACATAT
1 ATAATGAATAAATAT
*
6146441 ATAATGATTAAATAT
1 ATAATGAATAAATAT
6146456 ATAA
1 ATAA
6146460 ATATGCTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (15 bp):
ATAATGAATAAATAT
Found at i:6148236 original size:17 final size:17
Alignment explanation
Indices: 6148214--6148248 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6148204 ATTTTTTCCA
6148214 TATTTTATAAATTTTTT
1 TATTTTATAAATTTTTT
* *
6148231 TATTTTTTATATTTTTT
1 TATTTTATAAATTTTTT
6148248 T
1 T
6148249 TAGTTTCCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (17 bp):
TATTTTATAAATTTTTT
Found at i:6148238 original size:19 final size:19
Alignment explanation
Indices: 6148196--6148250 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
6148186 AAGCTCAAAA
*
6148196 TTTTTA-AAATTTTTTCCAT
1 TTTTTATAAATTTTTT-TAT
*
6148215 ATTTTATAAATTTTTTTAT
1 TTTTTATAAATTTTTTTAT
*
6148234 TTTTTAT-ATTTTTTTTA
1 TTTTTATAAATTTTTTTA
6148251 GTTTCCTCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 9 0.29
19 13 0.42
20 9 0.29
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTATAAATTTTTTTAT
Found at i:6153897 original size:80 final size:76
Alignment explanation
Indices: 6153691--6153900 Score: 215
Period size: 78 Copynumber: 2.7 Consensus size: 76
6153681 TCTCTTCAAT
* * * *
6153691 AATTTTTTTCTCTTAATAGGAATATCAAATTTTATGTAATTGTTGATTTTTTTTTTTCATATTTC
1 AATTTATTTCTCTTAATAAGAATATCAAATTTTATGTAATTGTTGA--TTTTTTGTCCATATTTC
* *
6153756 TTATCTGTCCCTT
64 ATATCTGTCCCTG
* ** * * **
6153769 AATTTATTTCCCTCCATAATAGTATCAAATTTTATGTAATTACTGATTTTTTGTCCATACTTGCT
1 AATTTATTTCTCTTAATAAGAATATCAAATTTTATGTAATTGTTGATTTTTTGTCCATA--T--T
6153834 TCATATCTGTCCCTG
62 TCATATCTGTCCCTG
* *
6153849 AATTTA-TTCTCTTAATAAGAATTTCAAATTTTATGTAACTGTTGGATTTTTT
1 AATTTATTTCTCTTAATAAGAATATCAAATTTTATGTAATTGTT-GATTTTTT
6153901 TTTTCATATT
Statistics
Matches: 105, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
76 11 0.10
78 38 0.36
79 28 0.27
80 28 0.27
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.52
Consensus pattern (76 bp):
AATTTATTTCTCTTAATAAGAATATCAAATTTTATGTAATTGTTGATTTTTTGTCCATATTTCAT
ATCTGTCCCTG
Done.