Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 7 of 131
Found at i:2256489 original size:160 final size:161
Alignment explanation
Indices: 2256214--2256534 Score: 635
Period size: 160 Copynumber: 2.0 Consensus size: 161
2256204 GACAAAACCA
2256214 AAATATATTTCCCAAAAGTTATGTTTAAAGGTTCACGTACAAAATAGTACAAATACTTTAATTTA
1 AAATATATTTCCCAAAAGTTATGTTTAAAGGTTCACGTACAAAATAGTACAAATACTTTAATTTA
2256279 AAATGTACATGTGTATATATTTACAAAAAAAGAAAAAGTATAAGTACATGTATTGGTAAGTCATG
66 AAATGTACATGTGTATATATTTACAAAAAAAGAAAAAGTATAAGTACATGTATTGGTAAGTCATG
2256344 GAAATACGTATGTATTGAAATTTAAATACTT
131 GAAATACGTATGTATTGAAATTTAAATACTT
2256375 AAATATATTT-CCAAAAGTTATGTTTAAAGGTTCACGTACAAAATAGTACAAATACTTTAATTTA
1 AAATATATTTCCCAAAAGTTATGTTTAAAGGTTCACGTACAAAATAGTACAAATACTTTAATTTA
2256439 AAATGTACATGTGTATATATTTACAAAAAAAGAAAAAGTATAAGTACATGTATTGGTAAGTCATG
66 AAATGTACATGTGTATATATTTACAAAAAAAGAAAAAGTATAAGTACATGTATTGGTAAGTCATG
2256504 GAAATACGTATGTATTGAAATTTAAATACTT
131 GAAATACGTATGTATTGAAATTTAAATACTT
2256535 GTATATGCAC
Statistics
Matches: 160, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
160 150 0.94
161 10 0.06
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.34
Consensus pattern (161 bp):
AAATATATTTCCCAAAAGTTATGTTTAAAGGTTCACGTACAAAATAGTACAAATACTTTAATTTA
AAATGTACATGTGTATATATTTACAAAAAAAGAAAAAGTATAAGTACATGTATTGGTAAGTCATG
GAAATACGTATGTATTGAAATTTAAATACTT
Found at i:2266619 original size:3 final size:3
Alignment explanation
Indices: 2266611--2266668 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
2266601 ATAGTAATGG
* *
2266611 TAA TAA TAA CT-A TAG TAA GAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2266656 TAA TAA TATA TAA
1 TAA TAA TA-A TAA
2266669 CATAATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 1 0.02
3 43 0.90
4 4 0.08
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2267930 original size:19 final size:16
Alignment explanation
Indices: 2267900--2267947 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 16
2267890 AAAAAATCAT
2267900 ATATATATTATTAATAAA
1 ATATA-ATTATTAA-AAA
2267918 ATTATTAATTATTAAAAA
1 A-TA-TAATTATTAAAAA
2267936 ATATAATTATTA
1 ATATAATTATTA
2267948 CCAAAATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 9 0.32
17 2 0.07
18 5 0.18
19 10 0.36
20 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATAATTATTAAAAA
Found at i:2268593 original size:367 final size:368
Alignment explanation
Indices: 2267985--2268720 Score: 1456
Period size: 367 Copynumber: 2.0 Consensus size: 368
2267975 CATTCTTTTA
2267985 AAAATATTAAAATATTTAAAAAAATTCAAAAAGCTTTCTTTAGAGAATTGTTTAAAAAAATCTGG
1 AAAATATT-AAATATTTAAAAAAATTCAAAAAGCTTTCTTTAGAGAATTGTTTAAAAAAATCTGG
2268050 AAATACTAATGAACTTTAAAACGCATATTCGAAGTTTTATAATTTTTTTTTTGAATTTTTAAAAT
65 AAATACTAATGAACTTTAAAACGCATATTCGAAGTTTTATAATTTTTTTTTTGAATTTTTAAAAT
2268115 TCACCCAATCGAGAATGGCATGTGTATAGATGATTTTCACAATTATCATTTATTTACTTTATTTC
130 TCACCCAATCGAGAATGGCATGTGTATAGATGATTTTCACAATTATCATTTATTTACTTTATTTC
2268180 ATTACATAAACTTTTATAAATATTAATGGTGTTTTCAATTATTTTTATCTACTCACTTTTGAATA
195 ATTACATAAACTTTTATAAATATTAATGGTGTTTTCAATTATTTTTATCTACTCACTTTTGAATA
2268245 TTATAAAAATTAAATCATTATTAATAATAATTATTCAGTTAATATTAATATTAATTATTTTTTGG
260 TTATAAAAATTAAATCATTATTAATAATAATTATTCAGTTAATATTAATATTAATTATTTTTTGG
2268310 TGAAAAAGAATCCTTTCTGAGGGGATCTTCAATCAACGGTAAAT
325 TGAAAAAGAATCCTTTCTGAGGGGATCTTCAATCAACGGTAAAT
2268354 AAAATATT-AATATTTAAAAAAATTCAAAAAGCTTTCTTTAGAGAATTGTTTAAAAAAATCTGGA
1 AAAATATTAAATATTTAAAAAAATTCAAAAAGCTTTCTTTAGAGAATTGTTTAAAAAAATCTGGA
2268418 AATACTAATGAACTTTAAAACGCATATTCGAAGTTTTATAATTTTTTTTTTGAATTTTTAAAATT
66 AATACTAATGAACTTTAAAACGCATATTCGAAGTTTTATAATTTTTTTTTTGAATTTTTAAAATT
2268483 CACCCAATCGAGAATGGCATGTGTATAGATGATTTTCACAATTATCATTTATTTACTTTATTTCA
131 CACCCAATCGAGAATGGCATGTGTATAGATGATTTTCACAATTATCATTTATTTACTTTATTTCA
2268548 TTACATAAACTTTTATAAATATTAATGGTGTTTTCAATTATTTTTATCTACTCACTTTTGAATAT
196 TTACATAAACTTTTATAAATATTAATGGTGTTTTCAATTATTTTTATCTACTCACTTTTGAATAT
2268613 TATAAAAATTAAATCATTATTAATAATAATTATTCAGTTAATATTAATATTAATTATTTTTTGGT
261 TATAAAAATTAAATCATTATTAATAATAATTATTCAGTTAATATTAATATTAATTATTTTTTGGT
2268678 GAAAAAGAATCCTTTCTGAGGGGATCTTCAATCAACGGTAAAT
326 GAAAAAGAATCCTTTCTGAGGGGATCTTCAATCAACGGTAAAT
2268721 CAACTTTTCG
Statistics
Matches: 367, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
367 359 0.98
369 8 0.02
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.42
Consensus pattern (368 bp):
AAAATATTAAATATTTAAAAAAATTCAAAAAGCTTTCTTTAGAGAATTGTTTAAAAAAATCTGGA
AATACTAATGAACTTTAAAACGCATATTCGAAGTTTTATAATTTTTTTTTTGAATTTTTAAAATT
CACCCAATCGAGAATGGCATGTGTATAGATGATTTTCACAATTATCATTTATTTACTTTATTTCA
TTACATAAACTTTTATAAATATTAATGGTGTTTTCAATTATTTTTATCTACTCACTTTTGAATAT
TATAAAAATTAAATCATTATTAATAATAATTATTCAGTTAATATTAATATTAATTATTTTTTGGT
GAAAAAGAATCCTTTCTGAGGGGATCTTCAATCAACGGTAAAT
Found at i:2285995 original size:25 final size:25
Alignment explanation
Indices: 2285890--2285998 Score: 89
Period size: 25 Copynumber: 4.4 Consensus size: 25
2285880 TGGACACACC
* *
2285890 ACAGCTCGTATGAGCTT-CTCAATTT
1 ACAGCTCATATGAGCTTCCT-GATTT
* * *
2285915 ACAACTCATATAAGCTTCCCT-ATAT
1 ACAGCTCATATGAGCTT-CCTGATTT
2285940 ACAGCTCATATGAGCTTCCTGATTT
1 ACAGCTCATATGAGCTTCCTGATTT
** * *
2285965 GTAGCTCGTATGAGCTTTCTG-TTT
1 ACAGCTCATATGAGCTTCCTGATTT
2285989 CACAGCTCAT
1 -ACAGCTCAT
2285999 GAGAGCATAT
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
24 6 0.09
25 58 0.88
27 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.36
Consensus pattern (25 bp):
ACAGCTCATATGAGCTTCCTGATTT
Found at i:2286029 original size:25 final size:26
Alignment explanation
Indices: 2285966--2286032 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 26
2285956 TCCTGATTTG
* *
2285966 TAGCTCGTATGAGC-TTTCTGTTTCA
1 TAGCTCGTATGAGCATATCTGATTCA
* *
2285991 CAGCTCATGA-GAGCATAT-TGATTCA
1 TAGCTCGT-ATGAGCATATCTGATTCA
2286016 TAGCTCGTATGAGCATA
1 TAGCTCGTATGAGCATA
2286033 CATGAATATG
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
24 1 0.03
25 29 0.88
26 3 0.09
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (26 bp):
TAGCTCGTATGAGCATATCTGATTCA
Found at i:2291621 original size:59 final size:59
Alignment explanation
Indices: 2291529--2291647 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
2291519 ATATAATGAT
2291529 AGTTTTCAATCGAGCATAAAGATGGAACTGTATATGGCTCTGTATGGTCACAAATGTCG
1 AGTTTTCAATCGAGCATAAAGATGGAACTGTATATGGCTCTGTATGGTCACAAATGTCG
2291588 AGTTTTCAATCGAGCATAAAGATGGAACTGTATATGGCTCTGTATGGTCACAAATGTCG
1 AGTTTTCAATCGAGCATAAAGATGGAACTGTATATGGCTCTGTATGGTCACAAATGTCG
2291647 A
1 A
2291648 ACTCTATTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (59 bp):
AGTTTTCAATCGAGCATAAAGATGGAACTGTATATGGCTCTGTATGGTCACAAATGTCG
Found at i:2293331 original size:24 final size:24
Alignment explanation
Indices: 2293316--2293367 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
2293306 AATCAATGTC
2293316 AAATATATTATACTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
* *
2293340 AAATATATTATACTAATAAGTACT
1 AAATATATTATACTAATAAATGCT
2293364 AAAT
1 AAAT
2293368 CTTCTAGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:2295459 original size:2 final size:2
Alignment explanation
Indices: 2295454--2295479 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2295444 ATTAAGCCAT
2295454 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2295480 AATCATTCAC
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):
TA
Found at i:2308567 original size:15 final size:16
Alignment explanation
Indices: 2308547--2308581 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2308537 AGTCATTTCA
2308547 TATTTAAA-TAATTTT
1 TATTTAAATTAATTTT
2308562 TATTTAAATTAATTTT
1 TATTTAAATTAATTTT
2308578 TATT
1 TATT
2308582 CGAGTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTAAATTAATTTT
Found at i:2316463 original size:26 final size:25
Alignment explanation
Indices: 2316429--2316509 Score: 85
Period size: 26 Copynumber: 3.2 Consensus size: 25
2316419 TGGCTATCCA
2316429 GAGC-TCCTGATTAAAGGCTCTTCGT
1 GAGCTTCCTGATTAAAGGCTCTT-GT
* *
2316454 GAGCTTCCTGATTAAAAGTTCTTTGT
1 GAGCTTCCTGATTAAAGGCTC-TTGT
* * *
2316480 GAACTTCCTGATT-ATGGCTCTTAT
1 GAGCTTCCTGATTAAAGGCTCTTGT
2316504 GAGCTT
1 GAGCTT
2316510 TCTGTTATAT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
24 8 0.17
25 8 0.17
26 28 0.61
27 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (25 bp):
GAGCTTCCTGATTAAAGGCTCTTGT
Found at i:2318445 original size:43 final size:43
Alignment explanation
Indices: 2318397--2318510 Score: 165
Period size: 43 Copynumber: 2.7 Consensus size: 43
2318387 CAATGTCATA
* * * *
2318397 TCCCAGATATGGTCTTAGATGTTATCACATATCGATGCCAATG
1 TCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAATG
*
2318440 TCCCAGACATGGTCTTACACGTAATCTCATATCGATGCCAATG
1 TCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAATG
* *
2318483 TCCCAAACATGGTCTTACACGAAATCAC
1 TCCCAGACATGGTCTTACACGTAATCAC
2318511 TCCTTGAAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (43 bp):
TCCCAGACATGGTCTTACACGTAATCACATATCGATGCCAATG
Found at i:2322728 original size:23 final size:23
Alignment explanation
Indices: 2322702--2322872 Score: 166
Period size: 23 Copynumber: 7.5 Consensus size: 23
2322692 GTGTTATTGA
*
2322702 TCAGTGGTAGCTTCAGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
2322725 TCAGTGGTAGCTACGGCTACA-T
1 TCAGTGGTAGCTTCGGCTACATT
* * * *
2322747 ACTAGTGGTAGCTTTGGATATATT
1 TC-AGTGGTAGCTTCGGCTACATT
* * **
2322771 TCAGTGGTAGATACGGCTACACA
1 TCAGTGGTAGCTTCGGCTACATT
*
2322794 TCAGTGGTAGCTTCGGATACATT
1 TCAGTGGTAGCTTCGGCTACATT
* * * *
2322817 TCAGTGGTAGCTACCGCTACGTA
1 TCAGTGGTAGCTTCGGCTACATT
* *
2322840 TCAGTGGTAGCTTCGACTACATA
1 TCAGTGGTAGCTTCGGCTACATT
2322863 TCAGT-GTAGC
1 TCAGTGGTAGC
2322873 ACTTATGTGC
Statistics
Matches: 117, Mismatches: 29, Indels: 5
0.77 0.19 0.03
Matches are distributed among these distances:
22 7 0.06
23 108 0.92
24 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:2322757 original size:46 final size:46
Alignment explanation
Indices: 2322701--2322872 Score: 224
Period size: 46 Copynumber: 3.8 Consensus size: 46
2322691 AGTGTTATTG
* *
2322701 ATCAGTGGTAGCTTCAGCTACATTTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGATACATTTCAGTGGTAGCTACGGCTACAT
* * * *
2322747 A-CTAGTGGTAGCTTTGGATATATTTCAGTGGTAGATACGGCTACAC
1 ATC-AGTGGTAGCTTCGGATACATTTCAGTGGTAGCTACGGCTACAT
* *
2322793 ATCAGTGGTAGCTTCGGATACATTTCAGTGGTAGCTACCGCTACGT
1 ATCAGTGGTAGCTTCGGATACATTTCAGTGGTAGCTACGGCTACAT
*
2322839 ATCAGTGGTAGCTTC-GACTACATATCAGT-GTAGC
1 ATCAGTGGTAGCTTCGGA-TACATTTCAGTGGTAGC
2322873 ACTTATGTGC
Statistics
Matches: 110, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
45 8 0.07
46 101 0.92
47 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGATACATTTCAGTGGTAGCTACGGCTACAT
Found at i:2325861 original size:15 final size:16
Alignment explanation
Indices: 2325825--2325861 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2325815 TTTTAACTCG
*
2325825 ATCGGAGCTATTCTAT
1 ATCGGAGCTATTCGAT
2325841 AT-GGAGCTATT-GAT
1 ATCGGAGCTATTCGAT
2325855 ATCGGAG
1 ATCGGAG
2325862 TAGTTCTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 4 0.21
15 13 0.68
16 2 0.11
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (16 bp):
ATCGGAGCTATTCGAT
Found at i:2326128 original size:15 final size:16
Alignment explanation
Indices: 2326110--2326143 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2326100 CCAGATAATC
2326110 TCATTATTCTGA-ATT
1 TCATTATTCTGACATT
2326125 TCATTATTCTGACATT
1 TCATTATTCTGACATT
2326141 TCA
1 TCA
2326144 AATTGGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (16 bp):
TCATTATTCTGACATT
Found at i:2331211 original size:13 final size:13
Alignment explanation
Indices: 2331195--2331219 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2331185 ATAACAGTTA
2331195 CAGATATACAGAT
1 CAGATATACAGAT
2331208 CAGATATACAGA
1 CAGATATACAGA
2331220 ATCCTACCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (13 bp):
CAGATATACAGAT
Found at i:2332744 original size:2 final size:2
Alignment explanation
Indices: 2332737--2332761 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2332727 CTCATTTTGG
2332737 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
2332762 GGTAAATCAA
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:2340934 original size:28 final size:29
Alignment explanation
Indices: 2340877--2340935 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
2340867 GTTGGGAGGG
**
2340877 GAGTAAAAGTTTTTTGGGAAAAGTGGAAAA
1 GAGTAAAAGTTTTGAGGGAAAAGT-GAAAA
2340907 GAGTAAAAGTTTTGAGGGAAAAGT-AAAA
1 GAGTAAAAGTTTTGAGGGAAAAGTGAAAA
2340935 G
1 G
2340936 GGTTTGGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 5 0.19
30 22 0.81
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.24
Consensus pattern (29 bp):
GAGTAAAAGTTTTGAGGGAAAAGTGAAAA
Found at i:2345066 original size:42 final size:42
Alignment explanation
Indices: 2345007--2345095 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
2344997 CTGTTACAAC
* * *
2345007 CCAGGCCATGTGAGTCACACGGGCAAGGACACGGGTGTGTGT
1 CCAGGCCATGTGAGTCACACGAGCAAGGACACGAGCGTGTGT
*
2345049 CCAGGCCATGTGAGTCACACGAGCAGGGACACGAGCGTGTGT
1 CCAGGCCATGTGAGTCACACGAGCAAGGACACGAGCGTGTGT
2345091 CCAGG
1 CCAGG
2345096 TCGTGTAACT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.26, G:0.37, T:0.15
Consensus pattern (42 bp):
CCAGGCCATGTGAGTCACACGAGCAAGGACACGAGCGTGTGT
Found at i:2348518 original size:148 final size:149
Alignment explanation
Indices: 2348353--2348655 Score: 599
Period size: 148 Copynumber: 2.0 Consensus size: 149
2348343 ATAGTTAAAA
2348353 TTTTTAAATATATAAAATAAAACCATTAATTTAATTTATTCATAGCAATGGATAGATTATTAAAT
1 TTTTTAAATATATAAAATAAAACCATTAATTTAATTTATTCATAGCAATGGATAGATTATTAAAT
2348418 GAATAAGATTATTCAACGTTAATAATAAAAAAATTGTAAAAATTAAAAAATAATTAATTCCAATT
66 GAATAAGATTATTCAACGTTAATAATAAAAAAATTGTAAAAATTAAAAAATAATTAATTCCAATT
2348483 AAAAATAGTTAAAATTTAT
131 AAAAATAGTTAAAATTTAT
2348502 TTTTTAAATATA-AAAATAAAACCATTAATTTAATTTATTCATAGCAATGGATAGATTATTAAAT
1 TTTTTAAATATATAAAATAAAACCATTAATTTAATTTATTCATAGCAATGGATAGATTATTAAAT
2348566 GAATAAGATTATTCAACGTTAATAATAAAAAAATTGTAAAAATTAAAAAATAATTAATTCCAATT
66 GAATAAGATTATTCAACGTTAATAATAAAAAAATTGTAAAAATTAAAAAATAATTAATTCCAATT
2348631 AAAAATAGTTAAAATTTAT
131 AAAAATAGTTAAAATTTAT
2348650 TTTTTA
1 TTTTTA
2348656 CAGAAACAAA
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
148 142 0.92
149 12 0.08
ACGTcount: A:0.51, C:0.05, G:0.06, T:0.38
Consensus pattern (149 bp):
TTTTTAAATATATAAAATAAAACCATTAATTTAATTTATTCATAGCAATGGATAGATTATTAAAT
GAATAAGATTATTCAACGTTAATAATAAAAAAATTGTAAAAATTAAAAAATAATTAATTCCAATT
AAAAATAGTTAAAATTTAT
Found at i:2353056 original size:126 final size:126
Alignment explanation
Indices: 2352676--2353195 Score: 708
Period size: 125 Copynumber: 4.1 Consensus size: 126
2352666 TTTGTTTTTA
* * * * * *
2352676 TTTCTACACTAGTT-TCAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAAAA
1 TTTCTACAGTAGTTCT-TGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAAA
* * *
2352740 CGCTTCAAGTAGGATGCACTATCAGCAAAATTACTG-AAAATAGCTCCCACGTGAACGCTCTT
65 CGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAT-GCTCCCACGTGGACGCTCTT
* *
2352802 TTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTAAAAAAT
1 TTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAAAC
** * *
2352867 GCTTCAAGCAGGATGCA-TGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGGCACTCTT
66 GCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAATGCTCCCACGTGGACGCTCTT
* * *
2352927 TTTCTATAGTAGTTCTTGAAAAAATAATTTTGAGAAGGCAGTTCT-ATAAAAATAGTGTAAAAAA
1 TTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGA-AAAAATAGTGTAAAAAA
* * * *
2352991 CACTTCAAGTAGGATGCACTGTCAGCAAAATTACTGAAAAATGCTCCCATGTGGATGCTCTT
65 CGCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAATGCTCCCACGTGGACGCTCTT
* * * *
2353053 TTTCTACAATAGTTTTTGAAAAAATAATTTTGAGAAGATGGTTCTG-AAAAATAGTGTCAAAAAC
1 TTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAAAC
* * * *
2353117 GCTTCAAGCAGGATGCATTGTTAGCAAAATTACTGAAAAAGGCTCCCACGTGGATGCTCTT
66 GCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAATGCTCCCACGTGGACGCTCTT
2353178 TTTCTACAGTAGTTCTTG
1 TTTCTACAGTAGTTCTTG
2353196 CTTGGCCTTA
Statistics
Matches: 346, Mismatches: 43, Indels: 11
0.87 0.11 0.03
Matches are distributed among these distances:
124 1 0.00
125 193 0.56
126 151 0.44
127 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (126 bp):
TTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAAAC
GCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAATGCTCCCACGTGGACGCTCTT
Found at i:2353145 original size:251 final size:251
Alignment explanation
Indices: 2352676--2353195 Score: 742
Period size: 251 Copynumber: 2.1 Consensus size: 251
2352666 TTTGTTTTTA
* * * * * *
2352676 TTTCTACACTAGTT-TCAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAGATAATGTCAAAAA
1 TTTCTACAGTAGTTCT-TGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAATGTAAAAAA
*
2352740 CGCTTCAAGTAGGATGCACTATCAGCAAAATTACTGAAAATAGCTCCCACGTGAACGCTCTTTTT
65 CACTTCAAGTAGGATGCACTATCAGCAAAATTACTGAAAATAGCTCCCACGTGAACGCTCTTTTT
* *
2352805 CTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTAAAAAATGCT
130 CTACAATAGTTCTTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTAAAAAACGCT
*
2352870 TCAAGCAGGATGCATGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGGCACTCTT
195 TCAAGCAGGATGCATGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGACACTCTT
* * *
2352927 TTTCTATAGTAGTTCTTGAAAAAATAATTTTGAGAAGGCAGTTCT-ATAAAAATAGTGTAAAAAA
1 TTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTCTGA-AAAAATAATGTAAAAAA
* * * *
2352991 CACTTCAAGTAGGATGCACTGTCAGCAAAATTACTGAAAA-ATGCTCCCATGTGGATGCTCTTTT
65 CACTTCAAGTAGGATGCACTATCAGCAAAATTACTGAAAATA-GCTCCCACGTGAACGCTCTTTT
* * * *
2353055 TCTACAATAGTTTTTGAAAAAATAATTTTGAGAAGATGGTTCTG-AAAAATAGTGTCAAAAACGC
129 TCTACAATAGTTCTTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTAAAAAACGC
* ** **
2353119 TTCAAGCAGGATGCATTGTTAGCAAAATTACTGAAAAAGGCTCCCACGTGGATGCTCTT
194 TTCAAGCAGGATGCA-TGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGACACTCTT
2353178 TTTCTACAGTAGTTCTTG
1 TTTCTACAGTAGTTCTTG
2353196 CTTGGCCTTA
Statistics
Matches: 238, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
250 35 0.15
251 202 0.85
252 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (251 bp):
TTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAATGTAAAAAAC
ACTTCAAGTAGGATGCACTATCAGCAAAATTACTGAAAATAGCTCCCACGTGAACGCTCTTTTTC
TACAATAGTTCTTGAAAAAATAATTTTGAGAAGACGATTCTGAAAAAATAGTGTAAAAAACGCTT
CAAGCAGGATGCATGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGACACTCTT
Found at i:2356519 original size:18 final size:18
Alignment explanation
Indices: 2356498--2356534 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2356488 AAAAGGAAAT
* *
2356498 ATATAAGTGTTAGGATAC
1 ATATAAGGGCTAGGATAC
2356516 ATATAAGGGCTAGGATAC
1 ATATAAGGGCTAGGATAC
2356534 A
1 A
2356535 CACCTAGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (18 bp):
ATATAAGGGCTAGGATAC
Found at i:2358261 original size:15 final size:15
Alignment explanation
Indices: 2358218--2358261 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
2358208 ATATTTTTGA
2358218 AATTATAAAAAAAACT
1 AATT-TAAAAAAAACT
*
2358234 AATTTAGAAAAAACT
1 AATTTAAAAAAAACT
2358249 AATTTAAAAAAAA
1 AATTTAAAAAAAA
2358262 TTAAAGGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (15 bp):
AATTTAAAAAAAACT
Found at i:2359750 original size:156 final size:157
Alignment explanation
Indices: 2359456--2359768 Score: 619
Period size: 156 Copynumber: 2.0 Consensus size: 157
2359446 ATATTTTTAG
2359456 TTAAAAATATTAAAATATAATAATATAATTTTAAATTTTAACCTTAAAATGCAGCATATATTTAG
1 TTAAAAATATTAAAATATAATAATATAATTTTAAATTTTAACCTTAAAATGCAGCATATATTTAG
2359521 AATCATTATGTATTTGTTCAAGTATTTAGCTAAAAGAATGATCACCGAGTGCAATTATATCAATG
66 AATCATTATGTATTTGTTCAAGTATTTAGCTAAAAGAATGATCACCGAGTGCAATTATATCAATG
2359586 GCCATCCTTGAAACTTTCCCAAGCACA
131 GCCATCCTTGAAACTTTCCCAAGCACA
2359613 TTAAAAATA-TAAAATATAATAATATAATTTTAAATTTTAACCTTAAAATGCAGCATATATTTAG
1 TTAAAAATATTAAAATATAATAATATAATTTTAAATTTTAACCTTAAAATGCAGCATATATTTAG
2359677 AATCATTATGTATTTGTTCAAGTATTTAGCTAAAAGAATGATCACCGAGTGCAATTATATCAATG
66 AATCATTATGTATTTGTTCAAGTATTTAGCTAAAAGAATGATCACCGAGTGCAATTATATCAATG
2359742 GCCATCCTTGAAACTTTCCCAAGCACA
131 GCCATCCTTGAAACTTTCCCAAGCACA
2359769 ATTGCAAAGT
Statistics
Matches: 156, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
156 147 0.94
157 9 0.06
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (157 bp):
TTAAAAATATTAAAATATAATAATATAATTTTAAATTTTAACCTTAAAATGCAGCATATATTTAG
AATCATTATGTATTTGTTCAAGTATTTAGCTAAAAGAATGATCACCGAGTGCAATTATATCAATG
GCCATCCTTGAAACTTTCCCAAGCACA
Found at i:2360330 original size:20 final size:20
Alignment explanation
Indices: 2360305--2360389 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 20
2360295 GATTCGAGTT
*
2360305 AAACAACAAAGAATCAATTC
1 AAACAACAAACAATCAATTC
* *
2360325 AAACAATAAACAATCTATTC
1 AAACAACAAACAATCAATTC
* * * *
2360345 AAAGAATCAAAGAATCGATTTA
1 AAACAA-CAAACAATC-AATTC
*
2360367 AAACAACAAACAATCGATTC
1 AAACAACAAACAATCAATTC
2360387 AAA
1 AAA
2360390 GAAGCAACAA
Statistics
Matches: 49, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
20 27 0.55
21 15 0.31
22 7 0.14
ACGTcount: A:0.58, C:0.18, G:0.06, T:0.19
Consensus pattern (20 bp):
AAACAACAAACAATCAATTC
Found at i:2360376 original size:21 final size:21
Alignment explanation
Indices: 2360305--2360385 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
2360295 GATTCGAGTT
* * *
2360305 AAACAACAAAGAATC-AATTC
1 AAACAACAAACAATCGATTTA
* * *
2360325 AAACAATAAACAATCTATTCA
1 AAACAACAAACAATCGATTTA
* *
2360346 AAGA-ATCAAAGAATCGATTTA
1 AA-ACAACAAACAATCGATTTA
2360367 AAACAACAAACAATCGATT
1 AAACAACAAACAATCGATT
2360386 CAAAGAAGCA
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
20 14 0.30
21 31 0.67
22 1 0.02
ACGTcount: A:0.57, C:0.17, G:0.06, T:0.20
Consensus pattern (21 bp):
AAACAACAAACAATCGATTTA
Found at i:2360378 original size:42 final size:41
Alignment explanation
Indices: 2360311--2360392 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 41
2360301 AGTTAAACAA
* * *
2360311 CAAAGAATCAATTCAAACAATAAACAATCTATTCAAAGAAT
1 CAAAGAATCAATTAAAACAACAAACAATCGATTCAAAGAAT
*
2360352 CAAAGAATCGATTTAAAACAACAAACAATCGATTCAAAGAA
1 CAAAGAATC-AATTAAAACAACAAACAATCGATTCAAAGAA
2360393 GCAACAATGC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 9 0.25
42 27 0.75
ACGTcount: A:0.56, C:0.17, G:0.07, T:0.20
Consensus pattern (41 bp):
CAAAGAATCAATTAAAACAACAAACAATCGATTCAAAGAAT
Found at i:2361428 original size:24 final size:24
Alignment explanation
Indices: 2361407--2361463 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
2361397 AAGATTTAGT
*
2361407 ATTTATTAGTATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
* *
2361431 ATTTATTAGCATAATATATCTGAC
1 ATTTATTAGCATAATATATTTAAC
*
2361455 ATTGATTAG
1 ATTTATTAG
2361464 AATTAGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:2374529 original size:17 final size:17
Alignment explanation
Indices: 2374504--2374541 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2374494 TTATAATGAG
*
2374504 AATACCAATTTTATAAT
1 AATACCAATTTTATAAA
*
2374521 AATATCAATTTTATAAA
1 AATACCAATTTTATAAA
2374538 AATA
1 AATA
2374542 ATATTGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (17 bp):
AATACCAATTTTATAAA
Found at i:2374543 original size:20 final size:20
Alignment explanation
Indices: 2374518--2374555 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2374508 CCAATTTTAT
2374518 AATAATATCAATTTTATAAA
1 AATAATATCAATTTTATAAA
**
2374538 AATAATATTGATTTTATA
1 AATAATATCAATTTTATA
2374556 CTAATCACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
AATAATATCAATTTTATAAA
Found at i:2376783 original size:44 final size:44
Alignment explanation
Indices: 2376725--2377064 Score: 164
Period size: 44 Copynumber: 7.8 Consensus size: 44
2376715 ATCTACTTCG
* * * *
2376725 CTGCAACCTCAAGGAGATGAGATTTGTAGTTTTAATCAGCTCCA
1 CTGCAACTTCAAGGAGATAAGATTTATAGCTTTAATCAGCTCCA
* * *
2376769 CT-CTAACTTCAAGGAGATAAGATTTATGGCTTTAATCTGTTCCA
1 CTGC-AACTTCAAGGAGATAAGATTTATAGCTTTAATCAGCTCCA
* * * * *
2376813 CTGCAACTTTAAGGAGATATGGTTT-TA---AT-AT-A-CTCTA
1 CTGCAACTTCAAGGAGATAAGATTTATAGCTTTAATCAGCTCCA
* ** * ** *
2376850 CTACAACTTC-AGAGAGATAAGAGTTGCTATCTTCT-ATTTGTTCCA
1 CTGCAACTTCAAG-GAGATAAGA-TTTATAGCTT-TAATCAGCTCCA
* ** * * *
2376895 CTGCAACTTCAGGGAGATAAGATTTGCAGCTTCAATCTGCTCTA
1 CTGCAACTTCAAGGAGATAAGATTTATAGCTTTAATCAGCTCCA
* * * * * * *
2376939 TTGCAACTT-TAGAGAGATAAGATTTGCTATCTTCAATCTGCTCTA
1 CTGCAACTTCAAG-GAGATAAGATTT-ATAGCTTTAATCAGCTCCA
* * * * *
2376984 CTGCAACTTCAGGGAGATAAGATTTATTGCTTCAATCTGCTCTA
1 CTGCAACTTCAAGGAGATAAGATTTATAGCTTTAATCAGCTCCA
* * * *
2377028 TTGCAACTT-TAGAAAGATAAGATTTGTAGCTTTAATC
1 CTGCAACTTCAAG-GAGATAAGATTTATAGCTTTAATC
2377065 TACTCCAGTT
Statistics
Matches: 226, Mismatches: 53, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
36 2 0.01
37 18 0.08
38 2 0.01
39 4 0.02
40 1 0.00
43 7 0.03
44 132 0.58
45 58 0.26
46 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (44 bp):
CTGCAACTTCAAGGAGATAAGATTTATAGCTTTAATCAGCTCCA
Found at i:2376989 original size:45 final size:45
Alignment explanation
Indices: 2376845--2377053 Score: 253
Period size: 44 Copynumber: 4.7 Consensus size: 45
2376835 TTTTAATATA
* * * *
2376845 CTCTACTACAACTTCAGAGAGATAAGAGTTGCTATCTTCTATTTG
1 CTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTG
* * * *
2376890 TTCCACTGCAACTTCAGGGAGATAAGATTTGC-AGCTTCAATCTG
1 CTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTG
* *
2376934 CTCTATTGCAACTTTAGAGAGATAAGATTTGCTATCTTCAATCTG
1 CTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTG
* *
2376979 CTCTACTGCAACTTCAGGGAGATAAGATTT-AT-TGCTTCAATCTG
1 CTCTACTGCAACTTCAGAGAGATAAGATTTGCTAT-CTTCAATCTG
* * *
2377023 CTCTATTGCAACTTTAGAAAGATAAGATTTG
1 CTCTACTGCAACTTCAGAGAGATAAGATTTG
2377054 TAGCTTTAAT
Statistics
Matches: 139, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
43 1 0.01
44 73 0.53
45 65 0.47
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (45 bp):
CTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTG
Found at i:2376996 original size:89 final size:89
Alignment explanation
Indices: 2376853--2377071 Score: 314
Period size: 89 Copynumber: 2.5 Consensus size: 89
2376843 TACTCTACTA
* * * * *
2376853 CAACTTCAGAGAGATAAGAGTTGCTATCTTCTATTTGTTCCACTGCAACTTCAGGGAGATAAGAT
1 CAACTTTAGAGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*
2376918 TTGCAGCTTCAATCTGCTCTATTG
66 TTACAGCTTCAATCTGCTCTATTG
*
2376942 CAACTTTAGAGAGATAAGATTTGCTATCTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGAT
1 CAACTTTAGAGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
**
2377007 TTATTGCTTCAATCTGCTCTATTG
66 TTACAGCTTCAATCTGCTCTATTG
* * * *
2377031 CAACTTTAGAAAGATAAGATTTG-TAGCTTTAATCTACTCCA
1 CAACTTTAGAGAGATAAGATTTGCTATCTTCAATCTGCTCCA
2377072 GTTCAAGGAA
Statistics
Matches: 116, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
88 14 0.12
89 102 0.88
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (89 bp):
CAACTTTAGAGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
TTACAGCTTCAATCTGCTCTATTG
Found at i:2388810 original size:17 final size:14
Alignment explanation
Indices: 2388776--2388807 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2388766 TAATAATGAG
2388776 AATACCAATTTTAT
1 AATACCAATTTTAT
*
2388790 AATACCAATTATAT
1 AATACCAATTTTAT
2388804 AATA
1 AATA
2388808 ATAATATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (14 bp):
AATACCAATTTTAT
Found at i:2388825 original size:17 final size:17
Alignment explanation
Indices: 2388805--2388846 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
2388795 CAATTATATA
2388805 ATAATAATATCAATTTT
1 ATAATAATATCAATTTT
*
2388822 ATAATAATATCGATTTT
1 ATAATAATATCAATTTT
2388839 ATAATAAT
1 ATAATAAT
2388847 GGTACTAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (17 bp):
ATAATAATATCAATTTT
Found at i:2388845 original size:20 final size:19
Alignment explanation
Indices: 2388788--2388846 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
2388778 TACCAATTTT
*
2388788 ATAATACCAATTATATAATA
1 ATAATATCAATT-TATAATA
2388808 ATAATATCAATTT-T-ATA
1 ATAATATCAATTTATAATA
*
2388825 ATAATATCGATTTTATAATA
1 ATAATATC-AATTTATAATA
2388845 AT
1 AT
2388847 GGTACTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 11 0.32
18 5 0.15
19 2 0.06
20 16 0.47
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (19 bp):
ATAATATCAATTTATAATA
Found at i:2389213 original size:4 final size:4
Alignment explanation
Indices: 2389204--2389242 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
2389194 GCAAGGCAAT
** *
2389204 AATA AATA AATA AATA AATA AATA AGCA AATA AAAA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AAT
2389243 CATGAAAGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:2390579 original size:12 final size:12
Alignment explanation
Indices: 2390562--2390588 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2390552 TTATAAATGG
2390562 ATTGGACTGTTT
1 ATTGGACTGTTT
2390574 ATTGGACTGTTT
1 ATTGGACTGTTT
2390586 ATT
1 ATT
2390589 CATTTAGTTT
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:0.19, C:0.07, G:0.22, T:0.52
Consensus pattern (12 bp):
ATTGGACTGTTT
Found at i:2391573 original size:29 final size:28
Alignment explanation
Indices: 2391541--2391604 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
2391531 AAAAAGCCTT
2391541 TTTTTTGAAAATTTACCGAAATGGGCCGA
1 TTTTTTGAAAATTTACCGAAATGGGCC-A
* ** * *
2391570 TTTTTTTATTATTTACCGGAATGGTCCA
1 TTTTTTGAAAATTTACCGAAATGGGCCA
2391598 TTTTTTG
1 TTTTTTG
2391605 GGAAGTCGCG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (28 bp):
TTTTTTGAAAATTTACCGAAATGGGCCA
Found at i:2395147 original size:29 final size:29
Alignment explanation
Indices: 2395105--2395573 Score: 722
Period size: 29 Copynumber: 16.2 Consensus size: 29
2395095 NNNNNNNNNN
2395105 GGTTTTTAATTAAATTAGGTTAAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
* * *
2395134 GGTTTTAAATTAAATTAGGGTAGGGTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
* *
2395163 GGTCTTTAATTAAATTAGGTTAAGGTTAA
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
*
2395192 GGTTTTTAATTAAATTAGGTTAAGATTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
* *
2395221 GGTTTTTAATTAAATTAGGGTAGGGTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
2395250 GGTTTTTAATTAAATTAGGTTAAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
* * *
2395279 GGTTTTAAATTAAATTAGGGTAGGGTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
* *
2395308 GGTCTTTAATTAAATTAGGTTAAGGTTAA
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
*
2395337 GGTTTTTAATTAAATTAGGTTAAGATTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
* *
2395366 GGTTTTTAATTAAATTAGGGTAGGGTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
2395395 GGTTTTTAATTAAATTAGGTTAAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
* * *
2395424 GGTTTTAAATTAAATTAGGGTAGGGTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
* *
2395453 GGTCTTTAATTAAATTAGGTTAAGGTTAA
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
*
2395482 GGTTTTTAATTAAATTAGGTTAAGATTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
* *
2395511 GGTTTTTAATTAAATTAGGGTAGGGTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
2395540 GGTTTTTAATTAAATTAGGTTAAGGTTAG
1 GGTTTTTAATTAAATTAGGTTAAGGTTAG
2395569 GGTTT
1 GGTTT
2395574 AAAGGCCCGC
Statistics
Matches: 392, Mismatches: 48, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 392 1.00
ACGTcount: A:0.31, C:0.01, G:0.26, T:0.42
Consensus pattern (29 bp):
GGTTTTTAATTAAATTAGGTTAAGGTTAG
Found at i:2395368 original size:145 final size:145
Alignment explanation
Indices: 2395105--2395573 Score: 938
Period size: 145 Copynumber: 3.2 Consensus size: 145
2395095 NNNNNNNNNN
2395105 GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTAAATTAAATTAGGGTAGGGTTAGGGTCTTT
1 GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTAAATTAAATTAGGGTAGGGTTAGGGTCTTT
2395170 AATTAAATTAGGTTAAGGTTAAGGTTTTTAATTAAATTAGGTTAAGATTAGGGTTTTTAATTAAA
66 AATTAAATTAGGTTAAGGTTAAGGTTTTTAATTAAATTAGGTTAAGATTAGGGTTTTTAATTAAA
2395235 TTAGGGTAGGGTTAG
131 TTAGGGTAGGGTTAG
2395250 GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTAAATTAAATTAGGGTAGGGTTAGGGTCTTT
1 GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTAAATTAAATTAGGGTAGGGTTAGGGTCTTT
2395315 AATTAAATTAGGTTAAGGTTAAGGTTTTTAATTAAATTAGGTTAAGATTAGGGTTTTTAATTAAA
66 AATTAAATTAGGTTAAGGTTAAGGTTTTTAATTAAATTAGGTTAAGATTAGGGTTTTTAATTAAA
2395380 TTAGGGTAGGGTTAG
131 TTAGGGTAGGGTTAG
2395395 GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTAAATTAAATTAGGGTAGGGTTAGGGTCTTT
1 GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTAAATTAAATTAGGGTAGGGTTAGGGTCTTT
2395460 AATTAAATTAGGTTAAGGTTAAGGTTTTTAATTAAATTAGGTTAAGATTAGGGTTTTTAATTAAA
66 AATTAAATTAGGTTAAGGTTAAGGTTTTTAATTAAATTAGGTTAAGATTAGGGTTTTTAATTAAA
2395525 TTAGGGTAGGGTTAG
131 TTAGGGTAGGGTTAG
2395540 GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTT
1 GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTT
2395574 AAAGGCCCGC
Statistics
Matches: 324, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 324 1.00
ACGTcount: A:0.31, C:0.01, G:0.26, T:0.42
Consensus pattern (145 bp):
GGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTAAATTAAATTAGGGTAGGGTTAGGGTCTTT
AATTAAATTAGGTTAAGGTTAAGGTTTTTAATTAAATTAGGTTAAGATTAGGGTTTTTAATTAAA
TTAGGGTAGGGTTAG
Found at i:2397296 original size:31 final size:31
Alignment explanation
Indices: 2397261--2397325 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
2397251 GCCATTGATG
*
2397261 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTTAAA
*
2397292 AAAATATAAAAAAAATTATAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTTAAA
2397323 AAA
1 AAA
2397326 TAGATTTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (31 bp):
AAAATATAAAAAAAATTAAAATTATTTTAAA
Found at i:2397441 original size:26 final size:22
Alignment explanation
Indices: 2397382--2397426 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2397372 AGATATGGGT
2397382 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
2397404 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
2397426 T
1 T
2397427 ATTGAGATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:2400733 original size:94 final size:95
Alignment explanation
Indices: 2400624--2400902 Score: 348
Period size: 94 Copynumber: 3.0 Consensus size: 95
2400614 CAGTGAAACC
* * * *
2400624 ACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTGAAATC-ACCACAATAAATCTTATCTC
1 ACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTGAGATCTACCATAGTGAATCTTATCTC
2400688 CCTAAAGTTGCAGTGGAGCAGATCT-AAGCT
66 CCTAAAGTTGCAGTGGAGCAGAT-TGAAGCT
**
2400718 ACAAATCCTGCACCCCTGAAA-TTGCAGTGGGT--G---G-GATCTACCATAGTGAATCTTATCT
1 ACAAATCCTATACCCCT-AAAGTTGCAGTGGGTCAGATTGAGATCTACCATAGTGAATCTTATCT
2400776 CCC-AGAAGTTGCAGTGGAGCAGATTGAAGCT
65 CCCTA-AAGTTGCAGTGGAGCAGATTGAAGCT
* *
2400807 AAAAATCCTATACCCCTAAAGTTGCAGTAGGTCAGATT-AGATCTACCATAGTGAATCTTATCTC
1 ACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTGAGATCTACCATAGTGAATCTTATCTC
* *
2400871 CCTGAAGTTGCAGTGG-GTCAGATTGAATCT
66 CCTAAAGTTGCAGTGGAG-CAGATTGAAGCT
2400901 AC
1 AC
2400903 CATAGCGAAT
Statistics
Matches: 159, Mismatches: 13, Indels: 26
0.80 0.07 0.13
Matches are distributed among these distances:
88 8 0.05
89 68 0.43
91 1 0.01
92 1 0.01
93 1 0.01
94 77 0.48
95 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (95 bp):
ACAAATCCTATACCCCTAAAGTTGCAGTGGGTCAGATTGAGATCTACCATAGTGAATCTTATCTC
CCTAAAGTTGCAGTGGAGCAGATTGAAGCT
Found at i:2400901 original size:50 final size:50
Alignment explanation
Indices: 2400753--2400936 Score: 215
Period size: 50 Copynumber: 3.8 Consensus size: 50
2400743 AGTGGGTGGG
*
2400753 ATCTACCATAGTGAATCTTATCTCCCAGAAGTTGCAGTGGAG-CAGATTGA
1 ATCTACCATAGTGAATCTTATCTCCCTGAAGTTGCAGTGG-GTCAGATTGA
* * * *
2400803 AGCTA--A-A---AATCCTATAC-CCCTAAAGTTGCAGTAGGTCAGATT-A
1 ATCTACCATAGTGAATCTTAT-CTCCCTGAAGTTGCAGTGGGTCAGATTGA
2400846 GATCTACCATAGTGAATCTTATCTCCCTGAAGTTGCAGTGGGTCAGATTGA
1 -ATCTACCATAGTGAATCTTATCTCCCTGAAGTTGCAGTGGGTCAGATTGA
* *
2400897 ATCTACCATAGCGAATCTTATCTCTCTGAAGTTGCAGTGG
1 ATCTACCATAGTGAATCTTATCTCCCTGAAGTTGCAGTGG
2400937 AGCAAGATGA
Statistics
Matches: 112, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
43 2 0.02
44 31 0.28
45 1 0.01
46 1 0.01
47 2 0.02
48 1 0.01
49 1 0.01
50 72 0.64
51 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (50 bp):
ATCTACCATAGTGAATCTTATCTCCCTGAAGTTGCAGTGGGTCAGATTGA
Found at i:2401402 original size:15 final size:15
Alignment explanation
Indices: 2401379--2401424 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
2401369 GTCCGACCCG
*
2401379 AAACCAAAAATAAAT
1 AAACAAAAAATAAAT
2401394 AAACAAAAAAATAAA-
1 AAAC-AAAAAATAAAT
*
2401409 AACCAAAAAATAAAT
1 AAACAAAAAATAAAT
2401424 A
1 A
2401425 GTAAAACCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 10 0.37
15 8 0.30
16 9 0.33
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (15 bp):
AAACAAAAAATAAAT
Found at i:2402855 original size:3 final size:3
Alignment explanation
Indices: 2402847--2402918 Score: 119
Period size: 3 Copynumber: 24.3 Consensus size: 3
2402837 TATTATGTTC
2402847 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
2402895 TTA TTA TTA -AA TTA GTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2402919 AGTATTCTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 1 0.02
3 63 0.98
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2403900 original size:12 final size:12
Alignment explanation
Indices: 2403866--2403942 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 12
2403856 TTTTTATTCA
2403866 TTTATTATTATT
1 TTTATTATTATT
* **
2403878 GTCGTTATTATT
1 TTTATTATTATT
2403890 TTTA-T-TT-TT
1 TTTATTATTATT
*
2403899 ATTATTATTATT
1 TTTATTATTATT
* *
2403911 TTTCTTGTTA-T
1 TTTATTATTATT
2403922 TTTATTATT-TCT
1 TTTATTATTAT-T
2403934 TTTATTATT
1 TTTATTATT
2403943 TTTGGTACTT
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
9 5 0.10
10 3 0.06
11 11 0.23
12 29 0.60
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (12 bp):
TTTATTATTATT
Found at i:2403900 original size:15 final size:15
Alignment explanation
Indices: 2403866--2403945 Score: 63
Period size: 15 Copynumber: 5.2 Consensus size: 15
2403856 TTTTTATTCA
* *
2403866 TTTATTATTATTGTC
1 TTTATTATTATTATT
* *
2403881 GTTATTATTTTTATT
1 TTTATTATTATTATT
2403896 TTTATTATTATTATT
1 TTTATTATTATTATT
* *
2403911 TTTCTTGTTATTTTATT
1 TTTATTATTA--TTATT
*
2403928 ATTTCTT-TTATTATT
1 -TTTATTATTATTATT
2403943 TTT
1 TTT
2403946 GGTACTTTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 3 0.06
15 37 0.69
17 8 0.15
18 6 0.11
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (15 bp):
TTTATTATTATTATT
Found at i:2409826 original size:13 final size:13
Alignment explanation
Indices: 2409810--2409834 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2409800 TAATAATATT
2409810 AATTATTAATTAA
1 AATTATTAATTAA
2409823 AATTATTAATTA
1 AATTATTAATTA
2409835 TTCATATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATTATTAATTAA
Found at i:2416098 original size:266 final size:266
Alignment explanation
Indices: 2415617--2416098 Score: 732
Period size: 266 Copynumber: 1.8 Consensus size: 266
2415607 GACATGCTGA
* * *
2415617 ACATACAATCAGTAATACGGATGCAACAAGCATATATTATTCATATATCAAGCATATACAATAAT
1 ACATACAATCAGGAATACAGATGCAACAAGCATATATTATTCACATATCAAGCATATACAATAAT
* * * *
2415682 AATTCGGTCATTCAGATCATGCATTCCAATACTCATATTATCAGGGGTTCAATTGAAAGAAATAA
66 AATTCGGTCATTCAGATCATGCACTCCAATACTAATATTATCAAGGGTTCAATTAAAAGAAATAA
* * * * *
2415747 AACTCTAATAATAGTTTAGGGACTATTTAGAGACTAAACTGAACAAGTTATAAAATTCTGGGAAA
131 AACTCTAAAAATAGTTCAGGGACTATTTAGAGACTAAACTGAACAAATTATAAAAGTCTGGAAAA
* *
2415812 AATTATAAAATCTAAAAAATAGATGCCACACAGCCATGTCACCAAGTCGTTTAACAGACTGTGGC
196 AACTATAAAATATAAAAAATAGATGCCACACAGCCATGTCACCAAGTCGTTTAACAGACTGTGGC
2415877 CATATG
261 CATATG
* * *
2415883 ACATACAATCAGGAATACAGATGCAATATGCATATATTATTCACATATCATGCATATACAATAAT
1 ACATACAATCAGGAATACAGATGCAACAAGCATATATTATTCACATATCAAGCATATACAATAAT
*
2415948 AA-TCTGGTCATTCAGATCATGCACTCCAGTACTAATATTATCAAGGGTTCAATTAAAAGAAATA
66 AATTC-GGTCATTCAGATCATGCACTCCAATACTAATATTATCAAGGGTTCAATTAAAAGAAATA
* * * * *
2416012 AAACTCTAAAAATAGTTCGGGGGCTATTTAGGGAGTAAACTGAATAAATTATAAAAGTCTGGAAA
130 AAACTCTAAAAATAGTTCAGGGACTATTTAGAGACTAAACTGAACAAATTATAAAAGTCTGGAAA
*
2416077 AAACTATAAAATATGAAAAATA
195 AAACTATAAAATATAAAAAATA
2416099 AGGGTCACAC
Statistics
Matches: 191, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
265 2 0.01
266 189 0.99
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (266 bp):
ACATACAATCAGGAATACAGATGCAACAAGCATATATTATTCACATATCAAGCATATACAATAAT
AATTCGGTCATTCAGATCATGCACTCCAATACTAATATTATCAAGGGTTCAATTAAAAGAAATAA
AACTCTAAAAATAGTTCAGGGACTATTTAGAGACTAAACTGAACAAATTATAAAAGTCTGGAAAA
AACTATAAAATATAAAAAATAGATGCCACACAGCCATGTCACCAAGTCGTTTAACAGACTGTGGC
CATATG
Found at i:2420625 original size:42 final size:42
Alignment explanation
Indices: 2420522--2420719 Score: 255
Period size: 42 Copynumber: 4.8 Consensus size: 42
2420512 GTTTACAAAC
* *
2420522 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTCAGA
2420563 ---AAACGCCGCTAAAG-CACATGTTCTTTAGCGACGCTCAGA
1 AAAAAACGCCGCTAAAGAC-CATGTTCTTTAGCGACGCTCAGA
*
2420602 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTTAGA
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTCAGA
* * *
2420644 AGAAAATCGCCGCTAAAGACCATGTTCTTTAACGGCGCTTC-GA
1 A-AAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGC-TCAGA
* *
2420687 AAGAAACGCCACTAAAGACCATGTTCTTTAGCG
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCG
2420720 GCGTTTTTTT
Statistics
Matches: 138, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
37 1 0.01
38 34 0.25
42 65 0.47
43 37 0.27
44 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTCAGA
Found at i:2420709 original size:85 final size:80
Alignment explanation
Indices: 2420522--2420719 Score: 274
Period size: 85 Copynumber: 2.4 Consensus size: 80
2420512 GTTTACAAAC
*
2420522 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAACGCCGCTAAAGCACATGTTCT
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTTAGAAACGCCGCTAAAGCACATGTTCT
*
2420587 TTAGCGACGCTCAGA
66 TTAACGACGCTCAGA
2420602 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTTAGAAGAAAATCGCCGCTAAAG-ACCA
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTT---AG-AAA-CGCCGCTAAAGCA-CA
*
2420666 TGTTCTTTAACGGCGCTTC-GA
60 TGTTCTTTAACGACGC-TCAGA
* *
2420687 AAGAAACGCCACTAAAGACCATGTTCTTTAGCG
1 AAAAAACGCCGCTAAAGACCATGTTCTTTAGCG
2420720 GCGTTTTTTT
Statistics
Matches: 106, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
80 38 0.36
83 2 0.02
84 4 0.04
85 60 0.57
86 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (80 bp):
AAAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTTAGAAACGCCGCTAAAGCACATGTTCT
TTAACGACGCTCAGA
Found at i:2420784 original size:43 final size:42
Alignment explanation
Indices: 2420693--2420856 Score: 222
Period size: 44 Copynumber: 3.9 Consensus size: 42
2420683 TCGAAAGAAA
* * *
2420693 CGCCACTAAAGACCATGTTCTTTAGCGGCG-TTTTTTTTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTTTTAAG
* *
2420734 CGCCGCTAAAGAACATGGTCTTTAGTGGCGCTTTTTTTCAAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTTT-TAAG
* *
2420777 CGCCGCTAAAGAGCATGGTCTTTAGCGGCGTTTTTGTTTGTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTT-TTT-TAAG
*
2420821 CGCCGCTAAAGAACATGGTCTTTAGTGGCGCTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTT
2420857 CACAAAAACG
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
41 26 0.24
42 7 0.07
43 36 0.34
44 38 0.36
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTTTTTAAG
Found at i:2420831 original size:44 final size:42
Alignment explanation
Indices: 2420693--2420856 Score: 213
Period size: 43 Copynumber: 3.9 Consensus size: 42
2420683 TCGAAAGAAA
* * *
2420693 CGCCACTAAAGACCATGTTCTTTAGCGGCG-TTTTTTTTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTTAAG
* **
2420734 CGCCGCTAAAGAACATGGTCTTTAGTGGCGCTTTTTTTCAAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTTTTTAAG
*
2420777 CGCCGCTAAAGAGCATGGTCTTTAGCGGCGTTTTTGTTTGTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT-TTT-TAAG
* *
2420821 CGCCGCTAAAGAACATGGTCTTTAGTGGCGCTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT
2420857 CACAAAAACG
Statistics
Matches: 106, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
41 26 0.25
42 5 0.05
43 40 0.38
44 35 0.33
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTTAAG
Found at i:2420840 original size:87 final size:84
Alignment explanation
Indices: 2420693--2420856 Score: 274
Period size: 87 Copynumber: 1.9 Consensus size: 84
2420683 TCGAAAGAAA
*
2420693 CGCCACTAAAGACCATGTTCTTTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGGTCTTTA
1 CGCCACTAAAGACCATGGTCTTTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGGTCTTTA
2420758 GTGGCGCTTTTTTTCAAAG
66 GTGGCGCTTTTTTTCAAAG
* *
2420777 CGCCGCTAAAGAGCATGGTCTTTAGCGGCGTTTTTGTTTGTAAGCGCCGCTAAAGAACATGGTCT
1 CGCCACTAAAGACCATGGTCTTTAGCGGCG-TTTT-TTT-TAAGCGCCGCTAAAGAACATGGTCT
2420842 TTAGTGGCGCTTTTT
63 TTAGTGGCGCTTTTT
2420857 CACAAAAACG
Statistics
Matches: 74, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
84 27 0.36
85 4 0.05
86 3 0.04
87 40 0.54
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (84 bp):
CGCCACTAAAGACCATGGTCTTTAGCGGCGTTTTTTTTAAGCGCCGCTAAAGAACATGGTCTTTA
GTGGCGCTTTTTTTCAAAG
Found at i:2421583 original size:7 final size:7
Alignment explanation
Indices: 2421571--2421607 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
2421561 AACTTAAAAA
*
2421571 CCCAAAT
1 CCCAAAC
2421578 CCCAAAC
1 CCCAAAC
2421585 CCCAAAC
1 CCCAAAC
2421592 CCCAAAC
1 CCCAAAC
*
2421599 CACAAAC
1 CCCAAAC
2421606 CC
1 CC
2421608 TTACCCCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.43, C:0.54, G:0.00, T:0.03
Consensus pattern (7 bp):
CCCAAAC
Found at i:2421925 original size:15 final size:16
Alignment explanation
Indices: 2421897--2421927 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2421887 CCCTAACCCG
2421897 ACCCCTATAACCCTAA
1 ACCCCTATAACCCTAA
2421913 ACCCCTA-AACCCTAA
1 ACCCCTATAACCCTAA
2421928 GTCTTAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.16
Consensus pattern (16 bp):
ACCCCTATAACCCTAA
Found at i:2422208 original size:18 final size:21
Alignment explanation
Indices: 2422185--2422233 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
2422175 ATTAATCACG
2422185 ATATTAATTTG-GTG-TTT-T
1 ATATTAATTTGTGTGATTTAT
* *
2422203 ATATTACTTTGTTTGATTTAT
1 ATATTAATTTGTGTGATTTAT
2422224 ATATTAATTT
1 ATATTAATTT
2422234 AGTCGAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 10 0.40
19 2 0.08
20 3 0.12
21 10 0.40
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (21 bp):
ATATTAATTTGTGTGATTTAT
Found at i:2422930 original size:114 final size:111
Alignment explanation
Indices: 2422586--2422932 Score: 322
Period size: 113 Copynumber: 3.1 Consensus size: 111
2422576 TCCACAAAAA
* * * * * **
2422586 CGCCGCTAAAGA-ACAAATCATTAGCGGTGCTTTTAACAAAACACCGCTAAAGGCCCAAAAACAA
1 CGCCGCTAAAGACAC-GAGCATTAGCGGCGTTTTTAA-AAAACGCCGCTAAAGGCCCAAAAACTC
* * * ** *
2422650 AGAAAACGGCATCGTTGCCCTTAGGTTTTTTGCGGCACTTCTCAGAAAA
64 AGAAAACGGCGTCGTTGGCCTTAGGTTTTTTGCGGCGCTT-TTTGAAAT
* * * * * **
2422699 CGCCGCTAAAGACAGGAGCATTACCGGCGCTTTTCAAAAAGCGCCGCAAAAGGGACAAAAACTC-
1 CGCCGCTAAAGACACGAGCATTAGCGGCG-TTTTTAAAAAACGCCGCTAAAGGCCCAAAAACTCA
* * *
2422763 GGAAACGACGTCGTTGGCATTAGGTTTTTTGCGGCGCTTTTTAGAAAT
65 GAAAACGGCGTCGTTGGCCTTAGGTTTTTTGCGGCGCTTTTT-GAAAT
* * * *
2422811 TGCCGC-AAAGTCCCCCGAGCATTAGCGGCGTTTTTATAAAAACGCCGCTAATGGCCCAAAAACT
1 CGCCGCTAAAG--ACACGAGCATTAGCGGCGTTTTTA-AAAAACGCCGCTAAAGGCCCAAAAACT
* * *
2422875 CAGTAAACGGCGTCGTTGGCCTTATGTTTTTTGCGGCGCTTTTTGTGAAT
63 CAGAAAACGGCGTCGTTGGCCTTAGGTTTTTTGCGGCGCTTTTTG-AAAT
2422925 CGCCGCTA
1 CGCCGCTA
2422933 TTGCTTATTA
Statistics
Matches: 185, Mismatches: 40, Indels: 16
0.77 0.17 0.07
Matches are distributed among these distances:
111 5 0.03
112 47 0.25
113 80 0.43
114 52 0.28
115 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (111 bp):
CGCCGCTAAAGACACGAGCATTAGCGGCGTTTTTAAAAAACGCCGCTAAAGGCCCAAAAACTCAG
AAAACGGCGTCGTTGGCCTTAGGTTTTTTGCGGCGCTTTTTGAAAT
Found at i:2425350 original size:19 final size:20
Alignment explanation
Indices: 2425326--2425364 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2425316 CATTTGTACT
*
2425326 TTGGTTTT-TTTGTTTTCTA
1 TTGGTTTTATTTATTTTCTA
2425345 TTGGTTTTATTTATTTTCTA
1 TTGGTTTTATTTATTTTCTA
2425365 AAATTGGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.10, C:0.05, G:0.13, T:0.72
Consensus pattern (20 bp):
TTGGTTTTATTTATTTTCTA
Found at i:2426272 original size:23 final size:23
Alignment explanation
Indices: 2426225--2426301 Score: 59
Period size: 29 Copynumber: 3.1 Consensus size: 23
2426215 GTGTTATTCC
*
2426225 TGCAAACCCTACATGATTAT-T-TA
1 TGCAAACCCTATAT--TTATATATA
2426248 TGCAAACCCTATATTTATATATA
1 TGCAAACCCTATATTTATATATA
2426271 TGTGCATGCGAACCCTATATTTATATATA
1 --TGCA----AACCCTATATTTATATATA
2426300 TG
1 TG
2426302 TACATGCGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
21 4 0.09
22 1 0.02
23 15 0.33
25 4 0.09
27 2 0.04
29 19 0.42
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (23 bp):
TGCAAACCCTATATTTATATATA
Found at i:2426289 original size:29 final size:29
Alignment explanation
Indices: 2426247--2426316 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
2426237 ATGATTATTT
* *
2426247 ATGCAAACCCTATATTTATATATATGTGC
1 ATGCGAACCCTATATTTATATATATGTAC
2426276 ATGCGAACCCTATATTTATATATATGTAC
1 ATGCGAACCCTATATTTATATATATGTAC
2426305 ATGCGAACCCTA
1 ATGCGAACCCTA
2426317 GACGAGTAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (29 bp):
ATGCGAACCCTATATTTATATATATGTAC
Found at i:2428532 original size:28 final size:28
Alignment explanation
Indices: 2428478--2428532 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2428468 TGTTAGTATA
* *
2428478 TGATAAAATTATATTTTATTCTCTAAAT
1 TGATAAAATTATATTTAATCCTCTAAAT
* *
2428506 TGATAAAATTTTATTTAATCCTTTAAA
1 TGATAAAATTATATTTAATCCTCTAAA
2428533 AAGTTATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (28 bp):
TGATAAAATTATATTTAATCCTCTAAAT
Found at i:2429054 original size:22 final size:24
Alignment explanation
Indices: 2429018--2429063 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
2429008 ATTTATGCTT
* *
2429018 TTTTTTTTGCATTTT-TAAATTTA
1 TTTTTTTTACATTTTAAAAATTTA
2429041 TTTTTTTTAC-TTTTAAAAATTTA
1 TTTTTTTTACATTTTAAAAATTTA
2429064 ATCCATTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTTTTTACATTTTAAAAATTTA
Found at i:2430934 original size:30 final size:33
Alignment explanation
Indices: 2430874--2430939 Score: 93
Period size: 30 Copynumber: 2.1 Consensus size: 33
2430864 ACATGATTTT
*
2430874 TTTAAATAATTATAAAAATATTATAGAAAATTA
1 TTTAAATAACTATAAAAATATTATAGAAAATTA
*
2430907 TTTAAA-AACTATTAAAAT-TTA-AGAAAATTA
1 TTTAAATAACTATAAAAATATTATAGAAAATTA
2430937 TTT
1 TTT
2430940 GATACACTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 12 0.39
31 3 0.10
32 10 0.32
33 6 0.19
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (33 bp):
TTTAAATAACTATAAAAATATTATAGAAAATTA
Found at i:2433968 original size:47 final size:49
Alignment explanation
Indices: 2433909--2434015 Score: 182
Period size: 49 Copynumber: 2.2 Consensus size: 49
2433899 ACCACTGGTC
2433909 GTGCAGATAAACTGCTGACT-AAAA-ATTGGTGGATGAACCATCCATGG
1 GTGCAGATAAACTGCTGACTAAAAATATTGGTGGATGAACCATCCATGG
*
2433956 GTGCAAATAAACTGCTGACTAAAAATATTGGTGGATGAACCATCCATGG
1 GTGCAGATAAACTGCTGACTAAAAATATTGGTGGATGAACCATCCATGG
*
2434005 GTACAGATAAA
1 GTGCAGATAAA
2434016 AGCTACTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 19 0.35
48 4 0.07
49 32 0.58
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.23
Consensus pattern (49 bp):
GTGCAGATAAACTGCTGACTAAAAATATTGGTGGATGAACCATCCATGG
Found at i:2444671 original size:18 final size:18
Alignment explanation
Indices: 2444648--2444686 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2444638 TATTTATATA
2444648 AATCAAAATGTAGGTATT
1 AATCAAAATGTAGGTATT
2444666 AATCAAAATGTAGGTATT
1 AATCAAAATGTAGGTATT
2444684 AAT
1 AAT
2444687 TTTAAGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.33
Consensus pattern (18 bp):
AATCAAAATGTAGGTATT
Found at i:2444719 original size:13 final size:13
Alignment explanation
Indices: 2444701--2444735 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
2444691 AGTTATTCAC
2444701 TTTTATTTTATTT
1 TTTTATTTTATTT
2444714 TTTTA-TTTATTT
1 TTTTATTTTATTT
2444726 TATTTATTTT
1 T-TTTATTTT
2444736 TTTATAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 9 0.45
14 3 0.15
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:2444724 original size:17 final size:17
Alignment explanation
Indices: 2444701--2444740 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2444691 AGTTATTCAC
2444701 TTTTATTTTATTT-TTT
1 TTTTATTTTATTTATTT
2444717 TATTTATTTTATTTATTT
1 T-TTTATTTTATTTATTT
2444735 TTTTAT
1 TTTTAT
2444741 AAATCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 17 0.77
18 4 0.18
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTATTTTATTTATTT
Found at i:2444728 original size:9 final size:9
Alignment explanation
Indices: 2444702--2444740 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
2444692 GTTATTCACT
2444702 TTTATTTTA
1 TTTATTTTA
2444711 TTT-TTTTA
1 TTTATTTTA
2444719 TTTATTTTA
1 TTTATTTTA
2444728 TTTATTTT-
1 TTTATTTTA
2444736 TTTAT
1 TTTAT
2444741 AAATCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.45
9 16 0.55
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTATTTTA
Found at i:2452162 original size:26 final size:26
Alignment explanation
Indices: 2452108--2452169 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
2452098 TAATCCTACT
*
2452108 TTATTATATATTTTATTTATTTCAAA
1 TTATTATATATTTTATTTATATCAAA
*
2452134 TTATTAT-TATTATTATTATATAT-ATA
1 TTATTATATATT-TTATT-TATATCAAA
2452160 TTATT-TATAT
1 TTATTATATAT
2452170 CAAGTTGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
25 5 0.16
26 22 0.71
27 4 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (26 bp):
TTATTATATATTTTATTTATATCAAA
Found at i:2463471 original size:49 final size:49
Alignment explanation
Indices: 2463417--2463514 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
2463407 ATGGAAGCCA
2463417 TTTTACCCATTGAAGTGGAGATTCCTTCTCTT-GGGTATTAGCCTGAATT
1 TTTTACCCATTGAAGTGGAGATTCCTTCTCTTCGGGTATTAG-CTGAATT
2463466 TTTTACCCATTGAAGTGGAGATTCCTTCTCTTCGGGTATTAGCTGAATT
1 TTTTACCCATTGAAGTGGAGATTCCTTCTCTTCGGGTATTAGCTGAATT
2463515 GAAATTGGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 39 0.81
50 9 0.19
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (49 bp):
TTTTACCCATTGAAGTGGAGATTCCTTCTCTTCGGGTATTAGCTGAATT
Found at i:2464917 original size:41 final size:41
Alignment explanation
Indices: 2464768--2465545 Score: 225
Period size: 44 Copynumber: 17.9 Consensus size: 41
2464758 AGATGGTGAA
* ** * *
2464768 TCTTATCTCCCTGAGATTACAATGGAGCAGATTGAAGCCAGT
1 TCTTATCTCCCTGAGATTACAGTGGAATAGATCGAA-TCAGT
* * * ** * *
2464810 AATCCTATTTCCCTGAGATTACAGTGGAACAGATTAAAATAAAGGA
1 --TCTTATCTCCCTGAGATTACAGTGGAATAGA-TCGAAT-CA-GT
* * * * *
2464856 TCTTATCTCTCT-AAAGTTACAGTAGAGTAGATCGCATCAGT
1 TCTTATCTCCCTGAGA-TTACAGTGGAATAGATCGAATCAGT
* * *
2464897 TCTTATCTCCCTGATATTACAGTGGAATAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGATC---GAA-T-CAGT
* * * *
2464943 TCTTATCTCCCTGAGATTACAGCGG-ACAGATTGAAGCCAGT
1 TCTTATCTCCCTGAGATTACAGTGGAATAGATCGAA-TCAGT
* * * ** * *
2464984 AATCCTATTTCCCTGAGATTACAGTGGAACAGATTAAAATAAAGGA
1 --TCTTATCTCCCTGAGATTACAGTGGAATAGA-TCGAAT-CA-GT
* * * * *
2465030 TCTTATCTCTCT-AAAGTTACAGTAGAGTAGATCGCATCAGT
1 TCTTATCTCCCTGAGA-TTACAGTGGAATAGATCGAATCAGT
* * *
2465071 TCTTATCTCCCTGATATTACAGTGGAATAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGATC---GAA-T-CAGT
* ** * *
2465117 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGT
1 TCTTATCTCCCTGAGATTACAGTGGAATAGATCGAA-TCAGT
* * * * ** * *
2465159 AATCCTATTTCCCTGAGATTATAGTGGAATGGATTAAAATAAAGGA
1 --TCTTATCTCCCTGAGATTACAGTGGAATAGA-TCGAAT-CA-GT
* * * * * *
2465205 TCTTATCTCTCT-AAAGTTACAGTAGAGTAGATCGCATCAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAATAGATCGAATCAGT
* * * * * *
2465246 TCTTATCTCTCTGAGATTACAGTAGAACAGACCAAAAAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGATC---GAA-T-CAGT
* ** ** * *
2465292 TCTTATCTCCCAGAGATTACAGCAGAGCAGATTGAAGCCAGT
1 TCTTATCTCCCTGAGATTACAGTGGAATAGATCGAA-TCAGT
* * ** ** * *
2465334 AATCCTATTTCCCTGAGATTACAGTGGAACGGATTAAAATAAGGA
1 --TCTTATCTCCCTGAGATTACAGTGGAATAGA-TCGAATCA-GT
* * * * *
2465379 TCTTATCTCTCTGA-ATTTACAGTAGAGTAGATCGCATCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAATAGATCGAATCAGT
* *
2465420 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGATC---GAA-T-CAGT
* * ** * *
2465466 TATTATCTCCCTGAGATTACAGCGGAGCAGATTGAAACCAGT
1 TCTTATCTCCCTGAGATTACAGTGGAATAGATCG-AATCAGT
* *
2465508 AATCCTATTTCCCTGAGATTACAGTGGAATAGATCGAA
1 --TCTTATCTCCCTGAGATTACAGTGGAATAGATCGAA
2465546 GAATTTCAAA
Statistics
Matches: 528, Mismatches: 157, Indels: 99
0.67 0.20 0.13
Matches are distributed among these distances:
41 111 0.21
42 27 0.05
43 67 0.13
44 179 0.34
45 24 0.05
46 120 0.23
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
TCTTATCTCCCTGAGATTACAGTGGAATAGATCGAATCAGT
Found at i:2465267 original size:175 final size:175
Alignment explanation
Indices: 2464767--2465541 Score: 1338
Period size: 174 Copynumber: 4.4 Consensus size: 175
2464757 AAGATGGTGA
**
2464767 ATCTTATCTCCCTGAGATTACAATGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
2464832 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGT
66 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGT
*
2464897 TCTTATCTCCCTGATATTACAGTGGAATAGACCGAAGAATTACAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
2464942 ATCTTATCTCCCTGAGATTACAGCGGA-CAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
2465006 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGT
66 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGT
*
2465071 TCTTATCTCCCTGATATTACAGTGGAATAGACCGAAGAATTACAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
*
2465116 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAT
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
** *
2465181 AGTGGAATGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGA
66 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGT
* * * * *
2465246 TCTTATCTCTCTGAGATTACAGTAGAACAGACCAAAAAATTACAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
* *
2465291 ATCTTATCTCCCAGAGATTACAGCAGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
* * * *
2465356 AGTGGAACGGATTAAAAT-AAGGATCTTATCTCTCTGAATTTACAGTAGAGTAGATCGCATCAGG
66 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGT
2465420 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
* *
2465465 ATATTATCTCCCTGAGATTACAGCGGAGCAGATTGAAACCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
*
2465530 AGTGGAATAGAT
66 AGTGGAACAGAT
2465542 CGAAGAATTT
Statistics
Matches: 569, Mismatches: 30, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
174 328 0.58
175 241 0.42
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (175 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGT
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
Found at i:2465406 original size:349 final size:349
Alignment explanation
Indices: 2464767--2465541 Score: 1345
Period size: 349 Copynumber: 2.2 Consensus size: 349
2464757 AAGATGGTGA
**
2464767 ATCTTATCTCCCTGAGATTACAATGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
* *
2464832 AGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGT
66 AGTGGAATAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGA
* * * * * *
2464897 TCTTATCTCCCTGATATTACAGTGGAATAGACCGAAGAATTACAGATCTTATCTCCCTGAGATTA
131 TCTTATCTCCCTGAGATTACAGTAGAACAGACCAAAAAATTACAGATCTTATCTCCCAGAGATTA
*
2464962 CAGCGGACAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTACAGTGGAACAGATTAAAATAAA
196 CAGCAGACAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTACAGTGGAACAGATTAAAATAAA
* *
2465027 GGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGTTCTTATCTCCCTGATATTACA
261 GGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACA
2465092 GTGGAATAGACCGAAGAATTACAG
326 GTGGAATAGACCGAAGAATTACAG
*
2465116 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAT
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
*
2465181 AGTGGAATGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGA
66 AGTGGAATAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGA
*
2465246 TCTTATCTCTCTGAGATTACAGTAGAACAGACCAAAAAATTACAGATCTTATCTCCCAGAGATTA
131 TCTTATCTCCCTGAGATTACAGTAGAACAGACCAAAAAATTACAGATCTTATCTCCCAGAGATTA
*
2465311 CAGCAGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTACAGTGGAACGGATTAAAAT-A
196 CAGCAGA-CAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTACAGTGGAACAGATTAAAATAA
* *
2465375 AGGATCTTATCTCTCTGAATTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTAC
260 AGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTAC
2465440 AGTGGAATAGACCGAAGAATTACAG
325 AGTGGAATAGACCGAAGAATTACAG
* *
2465465 ATATTATCTCCCTGAGATTACAGCGGAGCAGATTGAAACCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
2465530 AGTGGAATAGAT
66 AGTGGAATAGAT
2465542 CGAAGAATTT
Statistics
Matches: 402, Mismatches: 23, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
349 348 0.87
350 54 0.13
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (349 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
AGTGGAATAGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGA
TCTTATCTCCCTGAGATTACAGTAGAACAGACCAAAAAATTACAGATCTTATCTCCCAGAGATTA
CAGCAGACAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTACAGTGGAACAGATTAAAATAAA
GGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACA
GTGGAATAGACCGAAGAATTACAG
Found at i:2465594 original size:90 final size:90
Alignment explanation
Indices: 2464904--2465595 Score: 250
Period size: 87 Copynumber: 7.9 Consensus size: 90
2464894 AGTTCTTATC
* * * * *
2464904 TCCCTGATATTACAGTGGAATAGACCGAAGAATTACAGATCTTATCTCCCTGAGATTACAGCGG-
1 TCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAAATATTATCTCCCAGAGAATACAGCGGA
* * *
2464968 ACAGATTGAAGCCAGTAATCCTATT
66 ACAGAGTAAAACCAGTAATCCTATT
* ** * * * * *
2464993 TCCCTGAGATTACAGTGGAACAGA-TTAA-AA-TA-AAGGATCTTATCTCTCTAAAG-TTACAGT
1 TCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAA--ATATTATCTC-CCAGAGAATACAGC
* ** *** * * *
2465053 AGAGTAGA-TCGCATCAGT--TCTTATC
63 GGAACAGAGTAAAACCAGTAATCCTATT
* * * * *
2465078 TCCCTGATATTACAGTGGAATAGACCGAAGAATTACAGATCTTATCTCCCTGAGATTACAGCGGA
1 TCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAAATATTATCTCCCAGAGAATACAGCGGA
* * * *
2465143 GCAGATTGAAGCCAGTAATCCTATT
66 ACAGAGTAAAACCAGTAATCCTATT
* * ** * * * * *
2465168 TCCCTGAGATTATAGTGGAATGGA-TTAA-AA-TA-AAGGATCTTATCTCTCTAAAG-TTACAGT
1 TCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAA--ATATTATCTC-CCAGAGAATACAGC
* ** *** * * *
2465228 AGAGTAGA-TCGCATCAG--ATCTTATC
63 GGAACAGAGTAAAACCAGTAATCCTATT
* * * * * * * * *
2465253 TCTCTGAGATTACAGTAGAACAGACCAAAAAATTACAGATCTTATCTCCCAGAGATTACAGCAGA
1 TCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAAATATTATCTCCCAGAGAATACAGCGGA
* * * *
2465318 GCAGATTGAAGCCAGTAATCCTATT
66 ACAGAGTAAAACCAGTAATCCTATT
** ** * * * * * **
2465343 TCCCTGAGATTACAGTGGAACGGA-TTAA-AA-TA-AGGATCTTATCTCTCTGA-ATTTACAGTA
1 TCCCTGAGATTACAGTGGAATAGACCGAAGAATTACA-AATATTATCTCCCAGAGA-ATACAGCG
** *** * * * *
2465403 GAGTAGA-TCGCATCAG--GTCTTATC
64 GAACAGAGTAAAACCAGTAATCCTATT
* * *
2465427 TCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAGATATTATCTCCCTGAGATTACAGCGGA
1 TCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAAATATTATCTCCCAGAGAATACAGCGGA
* * *
2465492 GCAGATTGAAACCAGTAATCCTATT
66 ACAGAGTAAAACCAGTAATCCTATT
* * * *
2465517 TCCCTGAGATTACAGTGGAATAGATCGAAGAATTTCAAATATTA-CTTCCCAG-GCAATGCAGTG
1 TCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAAATATTATC-TCCCAGAG-AATACAGCG
2465580 GAACAGAGTAAAACCA
64 GAACAGAGTAAAACCA
2465596 CATCGGTGAA
Statistics
Matches: 450, Mismatches: 118, Indels: 69
0.71 0.19 0.11
Matches are distributed among these distances:
84 27 0.06
85 55 0.12
86 22 0.05
87 136 0.30
88 54 0.12
89 33 0.07
90 123 0.27
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (90 bp):
TCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAAATATTATCTCCCAGAGAATACAGCGGA
ACAGAGTAAAACCAGTAATCCTATT
Found at i:2465709 original size:23 final size:23
Alignment explanation
Indices: 2465676--2465719 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2465666 CAGGCAGTAC
2465676 CGTGGAATAGATTAAAGCCACAT
1 CGTGGAATAGATTAAAGCCACAT
*
2465699 CGTGGACTAGATTAAAGCCAC
1 CGTGGAATAGATTAAAGCCAC
2465720 GACGGCGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTGGAATAGATTAAAGCCACAT
Found at i:2465796 original size:123 final size:123
Alignment explanation
Indices: 2465605--2466069 Score: 858
Period size: 123 Copynumber: 3.8 Consensus size: 123
2465595 ACATCGGTGA
2465605 ATCTTGCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCTACAACAGCGAATCTTACTTCCCAGG
1 ATCTTGCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCTACAACAGCGAATCTTACTTCCCAGG
2465670 CAGTACCGTGGAATAGATTAAAGCCACATCGTGGACTAGATTAAAGCCACGACGGCGT
66 CAGTACCGTGGAATAGATTAAAGCCACATCGTGGACTAGATTAAAGCCACGACGGCGT
2465728 ATCTTGCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCTACAACAGCGAATCTTACTTCCCAGG
1 ATCTTGCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCTACAACAGCGAATCTTACTTCCCAGG
2465793 CAGTACCGTGGAATAGATTAAAGCCACATCGTGGACTAGATTAAAGCCACGACGGCGT
66 CAGTACCGTGGAATAGATTAAAGCCACATCGTGGACTAGATTAAAGCCACGACGGCGT
2465851 ATCTTGCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCTACAACAGCGAATCTTACTTCCCAGG
1 ATCTTGCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCTACAACAGCGAATCTTACTTCCCAGG
2465916 CAGTACCGTGGAATAGATTAAAGCCACATCGTGGACTAGATTAAAGCCACGACGGCGT
66 CAGTACCGTGGAATAGATTAAAGCCACATCGTGGACTAGATTAAAGCCACGACGGCGT
* * *
2465974 ATCTTGCTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACAACAGCGAATCTTACTTCCTAGG
1 ATCTTGCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCTACAACAGCGAATCTTACTTCCCAGG
** * * *
2466039 TGGTGCAGTGGAACAGATTAAAGCCACATCG
66 CAGTACCGTGGAATAGATTAAAGCCACATCG
2466070 GTGAATTTTG
Statistics
Matches: 334, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 334 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (123 bp):
ATCTTGCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCTACAACAGCGAATCTTACTTCCCAGG
CAGTACCGTGGAATAGATTAAAGCCACATCGTGGACTAGATTAAAGCCACGACGGCGT
Found at i:2465832 original size:23 final size:23
Alignment explanation
Indices: 2465799--2465842 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2465789 CAGGCAGTAC
2465799 CGTGGAATAGATTAAAGCCACAT
1 CGTGGAATAGATTAAAGCCACAT
*
2465822 CGTGGACTAGATTAAAGCCAC
1 CGTGGAATAGATTAAAGCCAC
2465843 GACGGCGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTGGAATAGATTAAAGCCACAT
Found at i:2465955 original size:23 final size:23
Alignment explanation
Indices: 2465922--2465965 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2465912 CAGGCAGTAC
2465922 CGTGGAATAGATTAAAGCCACAT
1 CGTGGAATAGATTAAAGCCACAT
*
2465945 CGTGGACTAGATTAAAGCCAC
1 CGTGGAATAGATTAAAGCCAC
2465966 GACGGCGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTGGAATAGATTAAAGCCACAT
Found at i:2466028 original size:50 final size:50
Alignment explanation
Indices: 2465953--2466135 Score: 177
Period size: 50 Copynumber: 3.7 Consensus size: 50
2465943 ATCGTGGACT
* * * * *
2465953 AGATTAAAGCCACGACGGCGTATCTTGCTTCCCCGACATTGCAATTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* ** **** ** *
2466003 AGATTAAAGCTACAACAGCGAATCTTACTTCCTAGGTGGTGCAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * *
2466053 AGATTAAAGCCACATCGGTGAATTTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
*
2466103 AGATTAAAGCTACAACAGCGAATCTTACTTCCC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCC
2466136 AGGCAGTACC
Statistics
Matches: 97, Mismatches: 36, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
50 97 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (50 bp):
AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
Found at i:2466116 original size:223 final size:224
Alignment explanation
Indices: 2465830--2466235 Score: 717
Period size: 223 Copynumber: 1.8 Consensus size: 224
2465820 ATCGTGGACT
*
2465830 AGATTAAAGCCACGACGGCGTATCTTGCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCTACAA
1 AGATTAAAGCCACGACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCTACAA
*
2465895 CAGCGAATCTTACTTCCCAGGCAGTACCGTGGAATAGATTAAAGCCACATCGTGGACTAGATTAA
66 CAGCGAATCTTACTTCCCAGGCAGTACCGTGGAATAGATTAAAGCCACATCGTGGAATAGATTAA
**
2465960 AGCCACGACGGCGTATCTTGCTTCCCCGACATTGCAATTAAA-AAGATTAAAGCTACAACAGCGA
131 AGCCACGACGGCGTATCTTGCTTCCCCGACATCACAATTAAACAAGATTAAAGCTACAACAGCGA
2466024 ATCTTACTTCCTAGGTGGTGCAGTGGAAC
196 ATCTTACTTCCTAGGTGGTGCAGTGGAAC
* * *
2466053 AGATTAAAGCCAC-ATCGGTGAATTTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACA
1 AGATTAAAGCCACGA-CGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCTACA
2466117 ACAGCGAATCTTACTTCCCAGGCAGTACCGTGGAATAGATTAAAGCCACATCGTGGAATAGATTA
65 ACAGCGAATCTTACTTCCCAGGCAGTACCGTGGAATAGATTAAAGCCACATCGTGGAATAGATTA
*
2466182 AAGCCACGACGGCGTATCTTGCTTCCCCGACATCACAGTTAAACAAGATTAAAG
130 AAGCCACGACGGCGTATCTTGCTTCCCCGACATCACAATTAAACAAGATTAAAG
2466236 TTACGGGTTA
Statistics
Matches: 173, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
222 1 0.01
223 162 0.94
224 10 0.06
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (224 bp):
AGATTAAAGCCACGACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAGTAAAGCTACAA
CAGCGAATCTTACTTCCCAGGCAGTACCGTGGAATAGATTAAAGCCACATCGTGGAATAGATTAA
AGCCACGACGGCGTATCTTGCTTCCCCGACATCACAATTAAACAAGATTAAAGCTACAACAGCGA
ATCTTACTTCCTAGGTGGTGCAGTGGAAC
Found at i:2466119 original size:100 final size:100
Alignment explanation
Indices: 2465953--2466169 Score: 328
Period size: 100 Copynumber: 2.2 Consensus size: 100
2465943 ATCGTGGACT
*
2465953 AGATTAAAGCCACGA-CGGCGTATCTTGCTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACA
1 AGATTAAAGCCAC-ATCGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACA
* ** *
2466017 ACAGCGAATCTTACTTCCTAGGTGGTGCAGTGGAAC
65 ACAGCGAATCTTACTTCCCAGGCAGTACAGTGGAAC
* * *
2466053 AGATTAAAGCCACATCGGTGAATTTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGCTACAA
1 AGATTAAAGCCACATCGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACAA
* *
2466118 CAGCGAATCTTACTTCCCAGGCAGTACCGTGGAAT
66 CAGCGAATCTTACTTCCCAGGCAGTACAGTGGAAC
2466153 AGATTAAAGCCACATCG
1 AGATTAAAGCCACATCG
2466170 TGGAATAGAT
Statistics
Matches: 106, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 1 0.01
100 105 0.99
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (100 bp):
AGATTAAAGCCACATCGGCGAATCTTGCTTCCCCGACATTGCAATTAAAAAGATTAAAGCTACAA
CAGCGAATCTTACTTCCCAGGCAGTACAGTGGAAC
Found at i:2466157 original size:50 final size:50
Alignment explanation
Indices: 2466000--2466162 Score: 164
Period size: 50 Copynumber: 3.3 Consensus size: 50
2465990 ATTGCAATTA
* **
2466000 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCTAGGTGGTGCAGTGG
1 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTGCAGTGG
* * * * * * * * * * **
2466050 AACAGATTAAAGCCACATCGGTGAATTTTGCTTCCCCGACATTGCAGTTA
1 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTGCAGTGG
* *
2466100 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTACCGTGG
1 AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTGCAGTGG
*
2466150 AATAGATTAAAGC
1 AAAAGATTAAAGC
2466163 CACATCGTGG
Statistics
Matches: 83, Mismatches: 30, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
50 83 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (50 bp):
AAAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGGCAGTGCAGTGG
Found at i:2466175 original size:23 final size:23
Alignment explanation
Indices: 2466145--2466188 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
2466135 CAGGCAGTAC
2466145 CGTGGAATAGATTAAAGCCACAT
1 CGTGGAATAGATTAAAGCCACAT
2466168 CGTGGAATAGATTAAAGCCAC
1 CGTGGAATAGATTAAAGCCAC
2466189 GACGGCGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTGGAATAGATTAAAGCCACAT
Found at i:2471780 original size:8 final size:8
Alignment explanation
Indices: 2471767--2471806 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2471757 ACACATTTTA
2471767 ATAAAATT
1 ATAAAATT
2471775 ATAAAATT
1 ATAAAATT
*
2471783 ATAAAATA
1 ATAAAATT
* *
2471791 ATATAATA
1 ATAAAATT
2471799 ATAAAATT
1 ATAAAATT
2471807 GTATTTTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
ATAAAATT
Found at i:2476359 original size:129 final size:129
Alignment explanation
Indices: 2476129--2476391 Score: 517
Period size: 129 Copynumber: 2.0 Consensus size: 129
2476119 TTACTAATTC
*
2476129 GAAGCATAAAAATTTACTTTGAAAATTAATTTCACTGTTTATAGCAAACTTGTCCAATCGCGTAG
1 GAAGCATAAAAATTTACTTTGAAAATTAATTTCACTGTTTATAGCAAACTTGTCCAATCGCGCAG
2476194 CAGTTAATAAATTGATTATAACTTGAGCTACAGGACTCGAAATTTAATTATGTAAATTTTCCCT
66 CAGTTAATAAATTGATTATAACTTGAGCTACAGGACTCGAAATTTAATTATGTAAATTTTCCCT
2476258 GAAGCATAAAAATTTACTTTGAAAATTAATTTCACTGTTTATAGCAAACTTGTCCAATCGCGCAG
1 GAAGCATAAAAATTTACTTTGAAAATTAATTTCACTGTTTATAGCAAACTTGTCCAATCGCGCAG
2476323 CAGTTAATAAATTGATTATAACTTGAGCTACAGGACTCGAAATTTAATTATGTAAATTTTCCCT
66 CAGTTAATAAATTGATTATAACTTGAGCTACAGGACTCGAAATTTAATTATGTAAATTTTCCCT
2476387 GAAGC
1 GAAGC
2476392 TAGACTCATA
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 133 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (129 bp):
GAAGCATAAAAATTTACTTTGAAAATTAATTTCACTGTTTATAGCAAACTTGTCCAATCGCGCAG
CAGTTAATAAATTGATTATAACTTGAGCTACAGGACTCGAAATTTAATTATGTAAATTTTCCCT
Found at i:2477349 original size:50 final size:50
Alignment explanation
Indices: 2477238--2477529 Score: 361
Period size: 50 Copynumber: 5.7 Consensus size: 50
2477228 ACATGTCAAA
** * *
2477238 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATTGGTGTCC-AT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTG-CCAAT
***
2477289 GCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
**
2477339 TTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
* * * *
2477389 GCCATGTCCCACACATGGTCTTACATGAGACCTCTCATCTTGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
*
2477439 GCCATGTCCCAGACATGGTTTTACATGGGACCTCTCATGATCTCAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG-TGCCAAT
* *
2477495 TCCATGTCCCAGACATGGTTTTACATGGGACCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
2477530 TTACCCAAAT
Statistics
Matches: 210, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
49 2 0.01
50 135 0.64
51 27 0.13
53 4 0.02
55 2 0.01
56 40 0.19
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.29
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAT
Found at i:2487376 original size:18 final size:18
Alignment explanation
Indices: 2487342--2487376 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2487332 TATTGAAAAT
*
2487342 GGAAGTGGAGAGAGAAAG
1 GGAAGTGGAAAGAGAAAG
*
2487360 GGAAGTGGAAAGGGAAA
1 GGAAGTGGAAAGAGAAA
2487377 TACAATGGCT
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:0.46, C:0.00, G:0.49, T:0.06
Consensus pattern (18 bp):
GGAAGTGGAAAGAGAAAG
Found at i:2488517 original size:11 final size:10
Alignment explanation
Indices: 2488501--2488535 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 10
2488491 ACAAGGAAGG
2488501 AAAAAGAAGAA
1 AAAAAGAA-AA
2488512 AAAAAGAAAA
1 AAAAAGAAAA
2488522 ATAAAAGAAAA
1 A-AAAAGAAAA
2488533 AAA
1 AAA
2488536 TATAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:2488886 original size:25 final size:24
Alignment explanation
Indices: 2488858--2488909 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
2488848 CCCAACCGGC
* *
2488858 CAGCCCATTGCTCAGCAGCAGGCCT
1 CAGCCCAGTGCCCAGCAGCAGG-CT
*
2488883 CAGCCTAGTGCCCAGCAGCAGGCT
1 CAGCCCAGTGCCCAGCAGCAGGCT
2488907 CAG
1 CAG
2488910 AAGCACCCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.21, C:0.38, G:0.27, T:0.13
Consensus pattern (24 bp):
CAGCCCAGTGCCCAGCAGCAGGCT
Found at i:2488982 original size:16 final size:17
Alignment explanation
Indices: 2488961--2488993 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2488951 AGCCAACTGC
*
2488961 AGAAAA-AAAAGAAAAA
1 AGAAAAGAAAACAAAAA
2488977 AGAAAAGAAAACAAAAA
1 AGAAAAGAAAACAAAAA
2488994 GCTCGAGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (17 bp):
AGAAAAGAAAACAAAAA
Found at i:2492583 original size:3 final size:3
Alignment explanation
Indices: 2492577--2492635 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
2492567 AAAATAATAA
* * * *
2492577 ATT ATT ATC ATT ATC ATC ATTT GTT ATT ATT -TT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
2492622 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
2492636 CATCAGATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.94
4 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2492775 original size:8 final size:8
Alignment explanation
Indices: 2492762--2492787 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2492752 ATTTTGCTAT
2492762 ATATATAC
1 ATATATAC
2492770 ATATATAC
1 ATATATAC
2492778 ATATATAC
1 ATATATAC
2492786 AT
1 AT
2492788 GTTTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATAC
Found at i:2493538 original size:70 final size:70
Alignment explanation
Indices: 2493425--2493556 Score: 237
Period size: 70 Copynumber: 1.9 Consensus size: 70
2493415 CCTTTCAAAC
*
2493425 TCAAGTTTTAAACGATCTCGGGAATTAAGAGAAGATCGTGTCCTAACTTACTGGGCATGATCATC
1 TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCATC
2493490 TTTTT
66 TTTTT
* *
2493495 TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGTTTGTGTCCTAACTTACTGGGCATGATC
1 TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATC
2493557 CCTTTTCTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (70 bp):
TCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTGGGCATGATCATC
TTTTT
Found at i:2496313 original size:88 final size:88
Alignment explanation
Indices: 2496157--2496373 Score: 337
Period size: 88 Copynumber: 2.5 Consensus size: 88
2496147 CCGTTATCTA
* * * * * *
2496157 CAGTCTTAATGTCAGGGAGAGAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCGCTACAACGCTA
1 CAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCGCTACAACGCCA
2496222 GGGAAAAGAAGACTCGCTGTCTT
66 GGGAAAAGAAGACTCGCTGTCTT
*
2496245 CAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCGCTACAATGCCA
1 CAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCGCTACAACGCCA
2496310 GGGAAAAGAAGACTCGCTGTCTT
66 GGGAAAAGAAGACTCGCTGTCTT
* *
2496333 CAGTCTTAACGCCGGGGAGATAAGATTCACTG-CTTTCAGCT
1 CAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCTTT-AGCT
2496374 GCTTTGATCT
Statistics
Matches: 119, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
87 4 0.03
88 115 0.97
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.27
Consensus pattern (88 bp):
CAGTCTTAACGCCAGGGAGATAAGATTCGCTGCCTTTAGCTTTAATCTGCTCCGCTACAACGCCA
GGGAAAAGAAGACTCGCTGTCTT
Found at i:2497612 original size:1 final size:1
Alignment explanation
Indices: 2497597--2497667 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
2497587 TGGCCTCTCC
* * * * * * * * **
2497597 TTTTTCTTTTCTTTTTTTTCTTTTTTTATTTTTCTTTTCTTTTTTCTTTTTTCTTTTTTTCCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2497662 TTTTTT
1 TTTTTT
2497668 GAAATATTCT
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:2497616 original size:14 final size:14
Alignment explanation
Indices: 2497597--2497667 Score: 94
Period size: 14 Copynumber: 5.1 Consensus size: 14
2497587 TGGCCTCTCC
2497597 TTTTTCTTTTCTTT
1 TTTTTCTTTTCTTT
2497611 TTTTTCTTTT-TTT
1 TTTTTCTTTTCTTT
2497624 ATTTTTCTTTTCTTT
1 -TTTTTCTTTTCTTT
2497639 TTTCTT-TTTTCTTT
1 TTT-TTCTTTTCTTT
*
2497653 TTTTCCTTTT-TTT
1 TTTTTCTTTTCTTT
2497666 TT
1 TT
2497668 GAAATATTCT
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
13 9 0.17
14 38 0.73
15 5 0.10
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTCTTTTCTTT
Found at i:2497634 original size:19 final size:19
Alignment explanation
Indices: 2497597--2497653 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
2497587 TGGCCTCTCC
*
2497597 TTTTTCTTTTCTTTTTTTTCT
1 TTTTTC-TTT-TTTCTTTTCT
2497618 TTTTT-TATTTTTCTTTTCT
1 TTTTTCT-TTTTTCTTTTCT
2497637 TTTTTCTTTTTTCTTTT
1 TTTTTCTTTTTTCTTTT
2497654 TTTCCTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 25 0.76
20 3 0.09
21 5 0.15
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTTCTTTTTTCTTTTCT
Found at i:2497663 original size:7 final size:7
Alignment explanation
Indices: 2497597--2497655 Score: 72
Period size: 7 Copynumber: 8.7 Consensus size: 7
2497587 TGGCCTCTCC
2497597 TTTTTCT
1 TTTTTCT
2497604 TTTCTT-T
1 TTT-TTCT
2497611 TTTTTCT
1 TTTTTCT
2497618 TTTTT-T
1 TTTTTCT
2497624 ATTTTTC-
1 -TTTTTCT
2497631 -TTTTCT
1 TTTTTCT
2497637 TTTTTCT
1 TTTTTCT
2497644 TTTTTCT
1 TTTTTCT
2497651 TTTTT
1 TTTTT
2497656 TCCTTTTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
5 5 0.11
6 3 0.07
7 36 0.78
8 2 0.04
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:2499361 original size:9 final size:9
Alignment explanation
Indices: 2499347--2499440 Score: 102
Period size: 9 Copynumber: 10.4 Consensus size: 9
2499337 TTTGGTTAAA
*
2499347 AATTAACAG
1 AATTAACCG
2499356 AATTAACCG
1 AATTAACCG
2499365 AATT-ACCTG
1 AATTAACC-G
2499374 AATTAACCG
1 AATTAACCG
*
2499383 AATT-ACTTG
1 AATTAAC-CG
2499392 AATTAACCG
1 AATTAACCG
*
2499401 AATTACCCG
1 AATTAACCG
* *
2499410 AGTTACCCG
1 AATTAACCG
2499419 AATTAACCG
1 AATTAACCG
*
2499428 AATTAACCT
1 AATTAACCG
2499437 AATT
1 AATT
2499441 GAATCATACA
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
8 5 0.07
9 63 0.86
10 5 0.07
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:2499395 original size:36 final size:36
Alignment explanation
Indices: 2499347--2499440 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 36
2499337 TTTGGTTAAA
* *
2499347 AATTAACAGAATTAACCGAATTACCTGAATTAACCG
1 AATTAACCGAATTAACCGAATTACCCGAATTAACCG
* * *
2499383 AATT-ACTTGAATTAACCGAATTACCCGAGTTACCCG
1 AATTAAC-CGAATTAACCGAATTACCCGAATTAACCG
*
2499419 AATTAACCGAATTAACCTAATT
1 AATTAACCGAATTAACCGAATT
2499441 GAATCATACA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
35 2 0.04
36 46 0.92
37 2 0.04
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (36 bp):
AATTAACCGAATTAACCGAATTACCCGAATTAACCG
Found at i:2502970 original size:25 final size:25
Alignment explanation
Indices: 2502941--2503001 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
2502931 TATAAATTAT
*
2502941 AAAAATATATATATGT-ACATATAAG
1 AAAAATATATATATGTGA-ATAAAAG
*
2502966 AAAAATATATCTATGTGAATAAAAG
1 AAAAATATATATATGTGAATAAAAG
*
2502991 AAATATATATA
1 AAAAATATATA
2503002 AATATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.31
Consensus pattern (25 bp):
AAAAATATATATATGTGAATAAAAG
Found at i:2502987 original size:23 final size:24
Alignment explanation
Indices: 2502941--2503025 Score: 77
Period size: 23 Copynumber: 3.6 Consensus size: 24
2502931 TATAAATTAT
2502941 AAAAATATATATATGTACATATAA
1 AAAAATATATATATGTACATATAA
*
2502965 GAAAAATATATCTATGTGA-ATA-AA
1 -AAAAATATATATATGT-ACATATAA
* ** *
2502989 AGAAATATATATAAATATATAT-A
1 AAAAATATATATATGTACATATAA
*
2503012 AAAAATATACATAT
1 AAAAATATATATAT
2503026 TTTAAAATGT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
22 1 0.02
23 27 0.55
24 2 0.04
25 18 0.37
26 1 0.02
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.32
Consensus pattern (24 bp):
AAAAATATATATATGTACATATAA
Found at i:2504800 original size:27 final size:27
Alignment explanation
Indices: 2504732--2504794 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
2504722 AAAAAAAATA
**
2504732 ACCAAAATATTAT-AGCTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
2504758 ACCAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTATAAATTTTTTTATTT
2504785 ACCAAAATAT
1 ACCAAAATAT
2504795 ACTAAAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
26 13 0.38
27 21 0.62
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (27 bp):
ACCAAAATATTATAAATTTTTTTATTT
Found at i:2504971 original size:42 final size:41
Alignment explanation
Indices: 2504923--2505127 Score: 256
Period size: 42 Copynumber: 5.0 Consensus size: 41
2504913 AGGAGAGGGC
2504923 AAGAAAGAAAGAAAGAAAGGAA-AAGAAAGAAAAGGAAAGGAG
1 AAGAAAGAAAGAAAGAAA--AAGAAGAAAGAAAAGGAAAGGAG
*
2504965 AGGAAAGAAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAG
1 AAGAAAGAAAGAAAGAAAAAGAA-GAAAGAAAAGGAAAGGAG
*
2505007 AAGAAA-AAAGAAAGAAAAAGAGGAAAGAAAAGGAAAGGAG
1 AAGAAAGAAAGAAAGAAAAAGAAGAAAGAAAAGGAAAGGAG
* * *
2505047 AAGAAAAAAAGAAAGAAAACGAAGGAAAGAAAAGGAAATGAG
1 AAGAAAGAAAGAAAGAAAAAGAA-GAAAGAAAAGGAAAGGAG
* * * *
2505089 AAGAGAGAAA-AAAAAAGAAAGAAG-AAGAAGAGGGAAGGA
1 AAGAAAGAAAGAAAGAA-AAAGAAGAAAGAAAAGGAAAGGA
2505128 AGGAAAAAAA
Statistics
Matches: 145, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
40 38 0.26
41 37 0.26
42 70 0.48
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.00
Consensus pattern (41 bp):
AAGAAAGAAAGAAAGAAAAAGAAGAAAGAAAAGGAAAGGAG
Found at i:2505058 original size:82 final size:82
Alignment explanation
Indices: 2504923--2505138 Score: 280
Period size: 82 Copynumber: 2.6 Consensus size: 82
2504913 AGGAGAGGGC
*
2504923 AAGAAAGAAAGAAAGAAAGGAA-AAGAAAGAAAAGGAAAGGAGAGGAAAGAAAGAAAGAAAAAGA
1 AAGAAA-AAAGAAAGAAA--AAGAAGAAAGAAAAGGAAAGGAGAGGAAAAAAAGAAAGAAAAAGA
2504987 AGGAAAGAAAAGGAAAGGAG
63 AGGAAAGAAAAGGAAAGGAG
* * *
2505007 AAGAAAAAAGAAAGAAAAAGAGGAAAGAAAAGGAAAGGAGAAGAAAAAAAGAAAGAAAACGAAGG
1 AAGAAAAAAGAAAGAAAAAGAAGAAAGAAAAGGAAAGGAGAGGAAAAAAAGAAAGAAAAAGAAGG
*
2505072 AAAGAAAAGGAAATGAG
66 AAAGAAAAGGAAAGGAG
* *
2505089 AAGAGAGAAAA-AAA-AAGAAAGAAG-AAGAAGAGGGAAGGA-AGGAAAAAAAG
1 AAGA-A-AAAAGAAAGAA-AAAGAAGAAAGAAAAGGAAAGGAGAGGAAAAAAAG
2505139 GTAATTTTTA
Statistics
Matches: 119, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
81 12 0.10
82 76 0.64
83 21 0.18
84 10 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (82 bp):
AAGAAAAAAGAAAGAAAAAGAAGAAAGAAAAGGAAAGGAGAGGAAAAAAAGAAAGAAAAAGAAGG
AAAGAAAAGGAAAGGAG
Found at i:2505114 original size:24 final size:24
Alignment explanation
Indices: 2505044--2505116 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
2505034 AAAAGGAAAG
2505044 GAGAAGAAAAAAAGAAAGAA-AACGA
1 GAGAA-AAAAAAAGAAAGAAGAA-GA
* *
2505069 -AGGAAAGAAAAGGAAATG-AGAAGA
1 GA-GAAAAAAAAAGAAA-GAAGAAGA
2505093 GAGAAAAAAAAAGAAAGAAGAAGA
1 GAGAAAAAAAAAGAAAGAAGAAGA
2505117 AGAGGGAAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
23 1 0.03
24 31 0.79
25 7 0.18
ACGTcount: A:0.70, C:0.01, G:0.27, T:0.01
Consensus pattern (24 bp):
GAGAAAAAAAAAGAAAGAAGAAGA
Found at i:2505116 original size:10 final size:10
Alignment explanation
Indices: 2504923--2505117 Score: 85
Period size: 10 Copynumber: 19.5 Consensus size: 10
2504913 AGGAGAGGGC
2504923 AAGAAAGAAAG
1 AAGAAAG-AAG
2504934 AAAGAAAGGAA-
1 -AAGAAA-GAAG
2504945 AAGAAAGAA-
1 AAGAAAGAAG
*
2504954 AAGGAAAGGAG
1 AA-GAAAGAAG
*
2504965 AGGAAAGAAAG
1 AAGAAAG-AAG
2504976 AAAGAAA-AAG
1 -AAGAAAGAAG
2504986 AAGGAAAGAA-
1 AA-GAAAGAAG
*
2504996 AAGGAAAGGAG
1 AA-GAAAGAAG
*
2505007 AAGAAAAAAG
1 AAGAAAGAAG
2505017 AAAGAAA-AAG
1 -AAGAAAGAAG
*
2505027 AGGAAAGAA-
1 AAGAAAGAAG
*
2505036 AAGGAAAGGAG
1 AA-GAAAGAAG
2505047 AAGAAA-AA-
1 AAGAAAGAAG
2505055 AAGAAAGAA-
1 AAGAAAGAAG
*
2505064 AACGAAGGAAAG
1 AA-GAAAG-AAG
*
2505076 AA-AAGGAA-
1 AAGAAAGAAG
*
2505084 ATGAGAAGAGAG
1 AAGA-AAGA-AG
2505096 AA-AAA-AA-
1 AAGAAAGAAG
2505103 AAGAAAGAAG
1 AAGAAAGAAG
2505113 AAGAA
1 AAGAA
2505118 GAGGGAAGGA
Statistics
Matches: 145, Mismatches: 15, Indels: 48
0.70 0.07 0.23
Matches are distributed among these distances:
7 2 0.01
8 11 0.08
9 24 0.17
10 72 0.50
11 19 0.13
12 16 0.11
13 1 0.01
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.01
Consensus pattern (10 bp):
AAGAAAGAAG
Found at i:2508644 original size:11 final size:11
Alignment explanation
Indices: 2508628--2508654 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2508618 TTTATAACTT
2508628 AATTTGGATAC
1 AATTTGGATAC
2508639 AATTTGGATAC
1 AATTTGGATAC
2508650 AATTT
1 AATTT
2508655 AAGCATAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (11 bp):
AATTTGGATAC
Found at i:2510942 original size:18 final size:18
Alignment explanation
Indices: 2510919--2510956 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2510909 ATCCCAATGA
*
2510919 TCGCCATCACCTTCTTCT
1 TCGCCAGCACCTTCTTCT
2510937 TCGCCAGCACCTTCTTCT
1 TCGCCAGCACCTTCTTCT
2510955 TC
1 TC
2510957 ACCACCAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.45, G:0.08, T:0.37
Consensus pattern (18 bp):
TCGCCAGCACCTTCTTCT
Found at i:2512215 original size:27 final size:27
Alignment explanation
Indices: 2512177--2512281 Score: 147
Period size: 27 Copynumber: 3.9 Consensus size: 27
2512167 AACACGAGTA
* *
2512177 GTGCCGCCAATCAGTATGGCACCATTG
1 GTGCCGCCAATCACTTTGGCACCATTG
* * **
2512204 GTGCCGCCAATCTCCTTGGCACCAACG
1 GTGCCGCCAATCACTTTGGCACCATTG
*
2512231 GTGCCGCCAATCACTTTGGCACCTTTG
1 GTGCCGCCAATCACTTTGGCACCATTG
2512258 GTGCCGCCAATCACTTTGGCACCA
1 GTGCCGCCAATCACTTTGGCACCA
2512282 CCGGGTGTTG
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.19, C:0.35, G:0.23, T:0.23
Consensus pattern (27 bp):
GTGCCGCCAATCACTTTGGCACCATTG
Found at i:2512259 original size:54 final size:54
Alignment explanation
Indices: 2512177--2512281 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
2512167 AACACGAGTA
* *
2512177 GTGCCGCCAATCAGTATGGCACCATTGGTGCCGCCAATCTCCTTGGCACCAACG
1 GTGCCGCCAATCACTATGGCACCATTGGTGCCGCCAATCACCTTGGCACCAACG
* * *
2512231 GTGCCGCCAATCACTTTGGCACCTTTGGTGCCGCCAATCACTTTGGCACCA
1 GTGCCGCCAATCACTATGGCACCATTGGTGCCGCCAATCACCTTGGCACCA
2512282 CCGGGTGTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.19, C:0.35, G:0.23, T:0.23
Consensus pattern (54 bp):
GTGCCGCCAATCACTATGGCACCATTGGTGCCGCCAATCACCTTGGCACCAACG
Found at i:2512367 original size:27 final size:27
Alignment explanation
Indices: 2512337--2512400 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
2512327 TTTTTTTGGT
2512337 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
2512364 ATATTTTGGTAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
2512391 ATATTTTGGT
1 ATATTTTGGT
2512401 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:2514680 original size:26 final size:29
Alignment explanation
Indices: 2514637--2514692 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 29
2514627 CATAAAACCC
2514637 AATTACAACCCAAACCC-AAGACCCAACA
1 AATTACAACCCAAACCCAAAGACCCAACA
* *
2514665 AATTA-AA-CCAAGCCCAAATACCCAACA
1 AATTACAACCCAAACCCAAAGACCCAACA
2514692 A
1 A
2514693 GCCCAAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.28
27 13 0.52
28 5 0.20
ACGTcount: A:0.52, C:0.36, G:0.04, T:0.09
Consensus pattern (29 bp):
AATTACAACCCAAACCCAAAGACCCAACA
Found at i:2515998 original size:16 final size:15
Alignment explanation
Indices: 2515977--2516010 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2515967 TATATATATC
*
2515977 TTTTATGTTTTTTTAG
1 TTTTATATTTTTTT-G
2515993 TTTTATATTTTTTTG
1 TTTTATATTTTTTTG
2516008 TTT
1 TTT
2516011 ATTTCTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTTATATTTTTTTG
Found at i:2516620 original size:109 final size:109
Alignment explanation
Indices: 2516424--2516728 Score: 445
Period size: 109 Copynumber: 2.8 Consensus size: 109
2516414 TAAAATAATA
* * *
2516424 AAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTCTCGATTTTTC
1 AAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
*
2516489 TCGTTCAACCAAATAGCCAAATATCCTTTCAAAAATTCCAAAAT
66 TCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTCCAAAAT
* *
2516533 AAGGCAATGTTTTGCATTTGGGAATTCGAGAAAACATGCCCTAATGTGCTGGGTTTCGATTTTTC
1 AAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
* * *
2516598 TCGTTCAACCAAATGGCTAAATATCCTTCCAAAAATTTCAAAAT
66 TCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTCCAAAAT
* * * * *
2516642 AAGACAGTGTTTTGCATTTGGAAATTCGAG-GAACGTGCCCTAATGTGTTGGGTTCCGA--TTTC
1 AAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
* *
2516704 TCGTTTAACCAAATTGCCAAATATC
66 TCGTTCAACCAAATAGCCAAATATC
2516729 TTTTTGAATT
Statistics
Matches: 177, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
106 26 0.15
108 24 0.14
109 127 0.72
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (109 bp):
AAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
TCGTTCAACCAAATAGCCAAATATCCTTCCAAAAATTCCAAAAT
Done.