Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 191 of 193
Found at i:59740150 original size:16 final size:16
Alignment explanation
Indices: 59740125--59740157 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59740115 ATTTAATCTG
59740125 ATTAATTTAAAA-AAA
1 ATTAATTTAAAAGAAA
59740140 ATTAGATTTAAAAGAAA
1 ATTA-ATTTAAAAGAAA
59740157 A
1 A
59740158 AAACAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
ATTAATTTAAAAGAAA
Found at i:59744121 original size:23 final size:23
Alignment explanation
Indices: 59744095--59744215 Score: 149
Period size: 23 Copynumber: 5.2 Consensus size: 23
59744085 ACACTAGCGC
59744095 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
59744118 GCTCTCT-ATTTAGCAC-GTCTCGT
1 GCTCTCTGA-TTAGCACTGTGT-GT
59744141 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
59744166 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
59744189 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
59744212 GCTC
1 GCTC
59744216 AGTACTTTGT
Statistics
Matches: 86, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
22 5 0.06
23 60 0.70
24 1 0.01
25 16 0.19
26 4 0.05
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:59744164 original size:48 final size:46
Alignment explanation
Indices: 59744095--59744215 Score: 165
Period size: 48 Copynumber: 2.6 Consensus size: 46
59744085 ACACTAGCGC
*
59744095 GCTCTCTGATTAGCACTGTGTGTGCTCT-CTATTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGA-TTAGCACGTCGT-GT
*
59744141 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
*
59744189 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
59744216 AGTACTTTGT
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
46 26 0.38
48 39 0.57
49 3 0.04
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:59744244 original size:39 final size:39
Alignment explanation
Indices: 59744180--59744254 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
59744170 TCCGATTAGC
*
59744180 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
59744219 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
59744255 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:59745426 original size:18 final size:18
Alignment explanation
Indices: 59745405--59746000 Score: 211
Period size: 18 Copynumber: 32.4 Consensus size: 18
59745395 TTAAAGTAAA
59745405 TAATTATATTTAATTATT
1 TAATTATATTTAATTATT
* **
59745423 TAATTATGTTTAATTAAA
1 TAATTATATTTAATTATT
* **
59745441 TATTTA-ATTATAAACAGTAT
1 TAATTATATT-TAATTA-T-T
*
59745461 TAGTTA-ATTTAA-TATT
1 TAATTATATTTAATTATT
*
59745477 TAATTTGAAAGATTTAATTATT
1 TAA-TT---ATATTTAATTATT
59745499 TAA-T-TATTTAATTATT
1 TAATTATATTTAATTATT
*
59745515 TAATTATGTTTAATTAAATATT
1 TAATTATATTTAA-T---TATT
59745537 TAATTATATTTAATTAAATAT
1 TAATTATATTTAATT--AT-T
59745558 TAATTAAATATTT-A--ATT
1 TAATT--ATATTTAATTATT
* * **
59745575 TAA-AATATTAAATTAAA
1 TAATTATATTTAATTATT
59745592 TAATTATATTTAATTATT
1 TAATTATATTTAATTATT
* * *
59745610 TAACTATGTTTAATTATA
1 TAATTATATTTAATTATT
* *
59745628 TATTTA-ATTATAAATAGTAT
1 TAATTATATT-TAATTA-T-T
* *
59745648 TAGTTA-A-TTAAATATT
1 TAATTATATTTAATTATT
*
59745664 TAATTTAAAAGATTTAATTATT
1 TAA-TT---ATATTTAATTATT
59745686 TAATTATATTTAATTATGTT
1 TAATTATATTTAATTA--TT
59745706 TAATTATATATTTAATTA--
1 TAA-T-TATATTTAATTATT
** * *
59745724 TAAACAGTA-TTAGTTAAT
1 TAATTA-TATTTAATTATT
59745742 TAA--ATATTT-A--ATT
1 TAATTATATTTAATTATT
* *
59745755 TAA-AAGATTTAATTATT
1 TAATTATATTTAATTATT
**
59745772 TAATTATATTTAATTAAA
1 TAATTATATTTAATTATT
*
59745790 TAATTATGTTTAATTATGTT
1 TAATTATATTTAATTA--TT
59745810 TAATTATATATTTAATTA-T
1 TAA-T-TATATTTAATTATT
* *
59745829 AAATAGTATCAATTAATTATT
1 TAAT--TAT-ATTTAATTATT
* * **
59745850 TAATTATATTAAAGTAAA
1 TAATTATATTTAATTATT
*
59745868 TAATTATATTAAATTATT
1 TAATTATATTTAATTATT
* *
59745886 TAATTATGTTTAATTATA
1 TAATTATATTTAATTATT
* * *
59745904 TATTTA-ATTATAAATA-G
1 TAATTATATT-TAATTATT
*
59745921 T-ATCA-A-TTAATTATT
1 TAATTATATTTAATTATT
* * **
59745936 TAATTATATTAAAGTAAA
1 TAATTATATTTAATTATT
*
59745954 TAATTATATTAAATTATT
1 TAATTATATTTAATTATT
*
59745972 TAATTATGTTTAATATATATT
1 TAATTATATTT-A-AT-TATT
59745993 TAATTATA
1 TAATTATA
59746001 AACAGTATCA
Statistics
Matches: 434, Mismatches: 83, Indels: 119
0.68 0.13 0.19
Matches are distributed among these distances:
13 5 0.01
14 15 0.03
15 6 0.01
16 36 0.08
17 31 0.07
18 191 0.44
19 16 0.04
20 37 0.09
21 33 0.08
22 58 0.13
23 6 0.01
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (18 bp):
TAATTATATTTAATTATT
Found at i:59745439 original size:22 final size:22
Alignment explanation
Indices: 59745414--59745998 Score: 149
Period size: 22 Copynumber: 26.1 Consensus size: 22
59745404 ATAATTATAT
* *
59745414 TTAATTATTTAATTATGTTTAA
1 TTAAATATTTAATTATATTTAA
*
59745436 TTAAATATTTAATTATA--AACA
1 TTAAATATTTAATTATATTTA-A
* * *
59745457 GT-ATTAGTTAATTTAATATTTAA
1 TTAAATATTTAA-TT-ATATTTAA
* * *
59745480 TTTGAAAGATTTAATTATTTAATTAT
1 -TT-AAATATTTAATTA--TATTTAA
* *
59745506 TTAATTATTTAATTATGTTTAA
1 TTAAATATTTAATTATATTTAA
59745528 TTAAATATTTAATTATATTTAA
1 TTAAATATTTAATTATATTTAA
59745550 TTAAATA-TTAATTAAATATTTAA
1 TTAAATATTTAATT--ATATTTAA
* *
59745573 TTTAAAATATTAAATTA-A-ATAA
1 -TT-AAATATTTAATTATATTTAA
59745595 TT--ATATTTAA-T-TATTTAA
1 TTAAATATTTAATTATATTTAA
* *
59745613 CT--ATGTTTAATTATATATTTAA
1 TTAAATATTTAA-T-TATATTTAA
* *
59745635 TTATAA-A--T-AGTATTAGTTAA
1 TTA-AATATTTAATTA-TATTTAA
**
59745655 TTAAATATTTAATT-TA-AAAGA
1 TTAAATATTTAATTATATTTA-A
*
59745676 TTTAATTATTTAATTATATTTAA
1 -TTAAATATTTAATTATATTTAA
* *
59745699 TT--ATGTTTAATTATA--TAT
1 TTAAATATTTAATTATATTTAA
* ** * *
59745717 TTAATTATAAACAGTATTAGTTAA
1 TTAAATATTTA-ATTA-TATTTAA
**
59745741 TTAAATATTTAATT-TA-AAAGA
1 TTAAATATTTAATTATATTTA-A
*
59745762 TTTAATTATTTAATTATATTTAA
1 -TTAAATATTTAATTATATTTAA
*
59745785 TT-AA-A--TAATTATGTTTAA
1 TTAAATATTTAATTATATTTAA
*
59745803 TT--ATGTTTAATTATATATTTAA
1 TTAAATATTTAA-T-TATATTTAA
*
59745825 TTATAAATAGTATCAATTAATTATTTAA
1 -T-TAAATA-T-TTAATT-A-TATTTAA
* * *
59745853 TT--ATATTAAAGTAAATAATTATA
1 TTAAATATTTAA-T-TATATTTA-A
*
59745876 TTAAATTATTTAATTATGTTTAA
1 TTAAA-TATTTAATTATATTTAA
*
59745899 TTATATATTTAATTATAAATAGTATCAA
1 TTAAATATTTAATTAT--AT--T-T-AA
* *
59745927 TTAATTATTTAATTATATTAAA
1 TTAAATATTTAATTATATTTAA
* *
59745949 GTAAATAATTATATTAAATTATTTAA
1 TTAAATATTTA-ATT--A-TATTTAA
*
59745975 TT--ATGTTTAATATATATTTAA
1 TTAAATATTTAAT-TATATTTAA
59745996 TTA
1 TTA
59745999 TAAACAGTAT
Statistics
Matches: 410, Mismatches: 79, Indels: 148
0.64 0.12 0.23
Matches are distributed among these distances:
17 3 0.01
18 36 0.09
19 4 0.01
20 38 0.09
21 34 0.08
22 132 0.32
23 37 0.09
24 46 0.11
25 13 0.03
26 36 0.09
27 5 0.01
28 26 0.06
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (22 bp):
TTAAATATTTAATTATATTTAA
Found at i:59745475 original size:32 final size:31
Alignment explanation
Indices: 59745432--59745702 Score: 168
Period size: 30 Copynumber: 8.6 Consensus size: 31
59745422 TTAATTATGT
59745432 TTAATTAAATATTTAATTATAAACAGTATTAG
1 TTAATTAAATATTTAATTATAAA-AGTATTAG
* * *
59745464 TTAATTTAATATTTAATT-TGAAAG-ATTTAA
1 TTAATTAAATATTTAATTATAAAAGTA-TTAG
* * ** *
59745494 TTATTTAATTATTTAATTATTTAATTA-T-G
1 TTAATTAAATATTTAATTATAAAAGTATTAG
* * *
59745523 TTTAATTAAATATTTAATTATATTTAATTAAATA-
1 -TTAATTAAATATTTAATTATA--AAAGT-ATTAG
*
59745557 TTAATTAAATATTTAATT-TAAAA-TATTAAA
1 TTAATTAAATATTTAATTATAAAAGTATT-AG
* ** *
59745587 TTAAATAATTATATTTAATTATTTAACTA-T-G
1 TTAATTAA--ATATTTAATTATAAAAGTATTAG
*
59745618 TTTAATTATATATTTAATTATAAATAGTATTAG
1 -TTAATTAAATATTTAATTATAAA-AGTATTAG
*
59745651 TTAATTAAATATTTAATT-TAAAAG-ATTTAA
1 TTAATTAAATATTTAATTATAAAAGTA-TTAG
*
59745681 TTATTTAATTATATTTAATTAT
1 TTAATTAA--ATATTTAATTAT
59745703 GTTTAATTAT
Statistics
Matches: 189, Mismatches: 27, Indels: 45
0.72 0.10 0.17
Matches are distributed among these distances:
28 2 0.01
29 4 0.02
30 73 0.39
31 13 0.07
32 69 0.37
33 25 0.13
34 3 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (31 bp):
TTAATTAAATATTTAATTATAAAAGTATTAG
Found at i:59745585 original size:13 final size:12
Alignment explanation
Indices: 59745524--59745609 Score: 65
Period size: 12 Copynumber: 7.2 Consensus size: 12
59745514 TTAATTATGT
59745524 TTAA-TTAAATA
1 TTAATTTAAATA
*
59745535 TTTAA-TTATAT-
1 -TTAATTTAAATA
59745546 TTAA-TTAAATA
1 TTAATTTAAATA
59745557 TTAA-TTAAATA
1 TTAATTTAAATA
59745568 TTTAATTTAAAATA
1 -TTAATTT-AAATA
*
59745582 TTAAATTAAATAA
1 TTAATTTAAAT-A
*
59745595 TTATATTTAATTA
1 TTA-ATTTAAATA
59745608 TT
1 TT
59745610 TAACTATGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
10 9 0.14
11 11 0.17
12 17 0.27
13 15 0.24
14 11 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTAATTTAAATA
Found at i:59745785 original size:86 final size:86
Alignment explanation
Indices: 59745598--59745787 Score: 348
Period size: 86 Copynumber: 2.2 Consensus size: 86
59745588 TAAATAATTA
* *
59745598 TATTTAA-T-TATTTAACTATGTTTAATTATATATTTAATTATAAATAGTATTAGTTAATTAAAT
1 TATTTAATTATATTTAATTATGTTTAATTATATATTTAATTATAAACAGTATTAGTTAATTAAAT
59745661 ATTTAATTTAAAAGATTTAAT
66 ATTTAATTTAAAAGATTTAAT
59745682 TATTTAATTATATTTAATTATGTTTAATTATATATTTAATTATAAACAGTATTAGTTAATTAAAT
1 TATTTAATTATATTTAATTATGTTTAATTATATATTTAATTATAAACAGTATTAGTTAATTAAAT
59745747 ATTTAATTTAAAAGATTTAAT
66 ATTTAATTTAAAAGATTTAAT
59745768 TATTTAATTATATTTAATTA
1 TATTTAATTATATTTAATTA
59745788 AATAATTATG
Statistics
Matches: 102, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
84 7 0.07
85 1 0.01
86 94 0.92
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (86 bp):
TATTTAATTATATTTAATTATGTTTAATTATATATTTAATTATAAACAGTATTAGTTAATTAAAT
ATTTAATTTAAAAGATTTAAT
Found at i:59745832 original size:86 final size:86
Alignment explanation
Indices: 59745798--59746032 Score: 454
Period size: 86 Copynumber: 2.7 Consensus size: 86
59745788 AATAATTATG
59745798 TTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAATTATTTAATTATATTAAA
1 TTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAATTATTTAATTATATTAAA
59745863 GTAAATAATTATATTAAATTA
66 GTAAATAATTATATTAAATTA
59745884 TTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAATTATTTAATTATATTAAA
1 TTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAATTATTTAATTATATTAAA
59745949 GTAAATAATTATATTAAATTA
66 GTAAATAATTATATTAAATTA
*
59745970 TTTAATTATGTTTAA-TATATATTTAATTATAAACAGTATCAATTAATTATTTAATTATATTAA
1 TTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAATTATTTAATTATATTAA
59746033 TTAACTATTT
Statistics
Matches: 148, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
85 47 0.32
86 101 0.68
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (86 bp):
TTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAATTATTTAATTATATTAAA
GTAAATAATTATATTAAATTA
Found at i:59745862 original size:104 final size:96
Alignment explanation
Indices: 59745679--59746000 Score: 378
Period size: 86 Copynumber: 3.4 Consensus size: 96
59745669 TAAAAGATTT
* * * *
59745679 AATTATTTAATTATATTTAATTATGTTTAATTATATATTTAATTATAAACAGTATTAGTTAATTA
1 AATTATTTAATTATGTTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAATTA
** * *
59745744 AATATTTA-ATTTAAAAGATTTAATTATTTAATTATATTT
66 TTTAATTATA-TT-AAAG---TAA--A--TAATTATATTA
**
59745783 AATTAAATAATTATGTTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAATTA
1 AATTATTTAATTATGTTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAATTA
59745848 TTTAATTATATTAAAGTAAATAA-T-TA-T-
66 TTTAATTATATTAAAGTAAATAATTATATTA
59745875 -ATTA---AATTA--TTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAATTA
1 AATTATTTAATTATGTTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAATTA
59745934 TTTAATTATATTAAAGTAAATAATTATATTA
66 TTTAATTATATTAAAGTAAATAATTATATTA
*
59745965 AATTATTTAATTATGTTTAATATATATTTAATTATA
1 AATTATTTAATTATGTTTAAT-TATGTTTAATTATA
59746001 AACAGTATCA
Statistics
Matches: 196, Mismatches: 10, Indels: 31
0.83 0.04 0.13
Matches are distributed among these distances:
86 73 0.37
87 1 0.01
88 7 0.04
89 1 0.01
91 8 0.04
93 1 0.01
94 7 0.04
95 1 0.01
96 9 0.05
97 13 0.07
98 1 0.01
100 3 0.02
103 4 0.02
104 66 0.34
105 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (96 bp):
AATTATTTAATTATGTTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAATTA
TTTAATTATATTAAAGTAAATAATTATATTA
Found at i:59745960 original size:190 final size:189
Alignment explanation
Indices: 59745405--59745978 Score: 481
Period size: 190 Copynumber: 3.0 Consensus size: 189
59745395 TTAAAGTAAA
* * *
59745405 TAATTATATTTAATTATTTAATTATGTTTAATTAAATATTTAATTATAAACAGTATTAGTTAATT
1 TAATTATATATAATTATTTAATTATGTTTAATTATATATTTAATTATAAATAGTATTAGTTAATT
* * * *
59745470 -TAATATTTAATTTGAAAGATTTAATTATTTAATTATTTAATTATTTAATTATGTTTAATTAAAT
66 AT-ATATTTAATTT-AAA-A-GTAATTAATT-A-TATTAAATTATTTAATTATGTTTAATTATAT
** * * * * * * **
59745534 ATTTAATTATATTTAATTAAATATTAATTAAATATTTA-ATTTAAAAT-ATTAAATTAAATAATT
125 ATTTAATTATAAAT-AGTATA-ATTAATT-ATTAATTATA-TTAAAGTAAAT-AATTATTTAATT
59745597 ATATT
185 ATATT
* * *
59745602 TAATTAT-T-TAACTATGT--TTA--ATT----ATATATTTAATTATAAATAGTATTAGTTAATT
1 TAATTATATATAATTATTTAATTATGTTTAATTATATATTTAATTATAAATAGTATTAGTTAATT
* * *
59745657 AAATATTTAATTTAAAAG-ATTTAATTAT-TTAATTATATTTAATTATGTTTAATTATATATTTA
66 ATATATTTAATTTAAAAGTAATTAATTATATTAAAT-TATTTAATTATGTTTAATTATATATTTA
* * * * **
59745720 ATTATAAACAGTATTAGTTAATTAAATATTTA-ATTTAAAAG-ATTTAATTATTTAATTATATT
130 ATTATAAATAGTA-TAATTAATT-ATTAATTATA-TT-AAAGTAAATAATTATTTAATTATATT
* *
59745782 TAATTA-A-ATAATTATGTTTAATTATGTTTAATTATATATTTAATTATAAATAGTATCAATTAA
1 TAATTATATATAATTA--TTTAATTATGTTTAATTATATATTTAATTATAAATAGTATTAGTTAA
* * *
59745845 TTATTTAATT-ATATT-AAAGTAAATAATTATATTAAATTATTTAATTATGTTTAATTATATATT
64 TTATATATTTAAT-TTAAAAGTAATTAATTATATTAAATTATTTAATTATGTTTAATTATATATT
*
59745908 TAATTATAAATAGTATCAATTAATTATTTAATTATATTAAAGTAAATAATTATATTAAAT-TATT
128 TAATTATAAATAGTAT-AATTAATTA-TTAATTATATTAAAGTAAATAATTAT-TTAATTATATT
59745972 TAATTAT
1 TAATTAT
59745979 GTTTAATATA
Statistics
Matches: 311, Mismatches: 40, Indels: 58
0.76 0.10 0.14
Matches are distributed among these distances:
180 52 0.17
181 40 0.13
182 3 0.01
183 6 0.02
184 3 0.01
185 1 0.00
186 5 0.02
187 41 0.13
189 12 0.04
190 117 0.38
191 13 0.04
193 3 0.01
195 7 0.02
196 1 0.00
197 7 0.02
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (189 bp):
TAATTATATATAATTATTTAATTATGTTTAATTATATATTTAATTATAAATAGTATTAGTTAATT
ATATATTTAATTTAAAAGTAATTAATTATATTAAATTATTTAATTATGTTTAATTATATATTTAA
TTATAAATAGTATAATTAATTATTAATTATATTAAAGTAAATAATTATTTAATTATATT
Found at i:59745996 original size:11 final size:10
Alignment explanation
Indices: 59745405--59746000 Score: 150
Period size: 10 Copynumber: 58.8 Consensus size: 10
59745395 TTAAAGTAAA
59745405 TAATTATATT
1 TAATTATATT
59745415 TAA-T-TATT
1 TAATTATATT
*
59745423 TAATTATGTT
1 TAATTATATT
59745433 TAATTAAATATT
1 TAATT--ATATT
59745445 TAATTATA--
1 TAATTATATT
* * *
59745453 AACAGTATTAGT
1 TA-ATTA-TATT
59745465 TAATTTAATATT
1 TAA-TT-ATATT
*
59745477 TAATTTGAAAGATT
1 TAA-TT---ATATT
59745491 TAA-T-TATT
1 TAATTATATT
59745499 TAA-T-TATT
1 TAATTATATT
59745507 TAA-T-TATT
1 TAATTATATT
*
59745515 TAATTATGTT
1 TAATTATATT
59745525 TAATTAAATATT
1 TAATT--ATATT
59745537 TAATTATATT
1 TAATTATATT
*
59745547 TAATTAAATAT
1 TAATTATAT-T
59745558 TAATTAAATATT
1 TAATT--ATATT
59745570 TAATTTAAAATATT
1 TAA-TT---ATATT
* *
59745584 AAATTA-A-A
1 TAATTATATT
59745592 TAATTATATT
1 TAATTATATT
59745602 TAA-T-TATT
1 TAATTATATT
* *
59745610 TAACTATGTT
1 TAATTATATT
59745620 TAATTATATATT
1 TAA-T-TATATT
**
59745632 TAATTATAAA
1 TAATTATATT
* *
59745642 T-AGTATTAGT
1 TAATTA-TATT
59745652 TAATTAAATATT
1 TAATT--ATATT
*
59745664 TAATTTAAAAGATT
1 TAA-TT---ATATT
59745678 TAA-T-TATT
1 TAATTATATT
59745686 TAATTATATT
1 TAATTATATT
*
59745696 TAATTATGTT
1 TAATTATATT
59745706 TAATTATATATT
1 TAA-T-TATATT
59745718 TAATTATA--
1 TAATTATATT
* * *
59745726 AACAGTATTAGT
1 TA-ATTA-TATT
59745738 TAATTAAATATT
1 TAATT--ATATT
*
59745750 TAATTTAAAAGATT
1 TAA-TT---ATATT
59745764 TAA-T-TATT
1 TAATTATATT
59745772 TAATTATATT
1 TAATTATATT
*
59745782 TAATTA-A-A
1 TAATTATATT
*
59745790 TAATTATGTT
1 TAATTATATT
*
59745800 TAATTATGTT
1 TAATTATATT
59745810 TAATTATATATT
1 TAA-T-TATATT
**
59745822 TAATTATAAA
1 TAATTATATT
* *
59745832 T-AGTATCAAT
1 TAATTAT-ATT
59745842 TAA-T-TATT
1 TAATTATATT
59745850 TAATTATATT
1 TAATTATATT
* * *
59745860 AAAGTA-A-A
1 TAATTATATT
59745868 TAATTATA-T
1 TAATTATATT
*
59745877 TAAAT-TATT
1 TAATTATATT
*
59745886 TAATTATGTT
1 TAATTATATT
59745896 TAATTATATATT
1 TAA-T-TATATT
**
59745908 TAATTATAAA
1 TAATTATATT
* *
59745918 T-AGTATCAAT
1 TAATTAT-ATT
59745928 TAA-T-TATT
1 TAATTATATT
59745936 TAATTATATT
1 TAATTATATT
* * *
59745946 AAAGTA-A-A
1 TAATTATATT
59745954 TAATTATA-T
1 TAATTATATT
*
59745963 TAAAT-TATT
1 TAATTATATT
*
59745972 TAATTATGTT
1 TAATTATATT
59745982 TAATATATATT
1 TAAT-TATATT
59745993 TAATTATA
1 TAATTATA
59746001 AACAGTATCA
Statistics
Matches: 446, Mismatches: 72, Indels: 136
0.68 0.11 0.21
Matches are distributed among these distances:
8 83 0.19
9 53 0.12
10 151 0.34
11 29 0.07
12 81 0.18
13 14 0.03
14 35 0.08
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (10 bp):
TAATTATATT
Found at i:59746022 original size:28 final size:27
Alignment explanation
Indices: 59745818--59746028 Score: 134
Period size: 28 Copynumber: 7.4 Consensus size: 27
59745808 TTTAATTATA
59745818 TATTTAATTATAAATAGTATCAATTAAT
1 TATTTAATTATAAATAGTATCAA-TAAT
59745846 TATTTAATTATATTAA-AGTA--AATAAT
1 TATTTAATTATA--AATAGTATCAATAAT
* * *
59745872 TATATTAAATTATTTAATTATGT-TTAATTAT
1 TAT-TT-AATTA--TAAATA-GTATCAATAAT
59745903 ATATTTAATTATAAATAGTATCAATTAAT
1 -TATTTAATTATAAATAGTATCAA-TAAT
59745932 TATTTAATTATATTAA-AGTA--AATAAT
1 TATTTAATTATA--AATAGTATCAATAAT
* *
59745958 TATATTAAATTATTTAATTATGT-TTAAT-AT
1 TAT-TT-AATTA--TAAATA-GTATCAATAAT
*
59745988 ATATTTAATTATAAACAGTATCAATTAAT
1 -TATTTAATTATAAATAGTATCAA-TAAT
59746017 TATTTAATTATA
1 TATTTAATTATA
59746029 TTAATTAACT
Statistics
Matches: 147, Mismatches: 9, Indels: 54
0.70 0.04 0.26
Matches are distributed among these distances:
26 16 0.11
27 17 0.12
28 57 0.39
29 20 0.14
30 21 0.14
31 13 0.09
32 3 0.02
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
TATTTAATTATAAATAGTATCAATAAT
Found at i:59746196 original size:33 final size:32
Alignment explanation
Indices: 59746158--59746224 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
59746148 CCAAATATTT
* *
59746158 AAGTAAAATGTTGTCACTAATATATATATTTTA
1 AAGTAAAATATCGTCACTAATATATAT-TTTTA
*
59746191 AAGTAAAATATCGTCATTAATATATATTTTTA
1 AAGTAAAATATCGTCACTAATATATATTTTTA
59746223 AA
1 AA
59746225 TTTAAATCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (32 bp):
AAGTAAAATATCGTCACTAATATATATTTTTA
Found at i:59751508 original size:21 final size:21
Alignment explanation
Indices: 59751482--59751534 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
59751472 AACTTAAAGT
*
59751482 GGAGGCAGTAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
59751503 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
* *
59751524 GAAGGAAGCAG
1 GGAGGCAGCAG
59751535 GGGCTACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.47, T:0.02
Consensus pattern (21 bp):
GGAGGCAGCAGCGAGGCAAGC
Found at i:59751761 original size:15 final size:14
Alignment explanation
Indices: 59751741--59751772 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
59751731 ATTTGAAGTT
59751741 ATTGGTTGGATTTGA
1 ATTGGTTGGA-TTGA
59751756 ATTGGTTGGATTGA
1 ATTGGTTGGATTGA
59751770 ATT
1 ATT
59751773 TACAGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (14 bp):
ATTGGTTGGATTGA
Found at i:59755083 original size:21 final size:21
Alignment explanation
Indices: 59755059--59755117 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 21
59755049 GATATATATT
*
59755059 TTAATAATATAAATAT-TAATA
1 TTAATAATATAAAAATATAA-A
59755080 TTAAT-ATA-AAAAATATAAA
1 TTAATAATATAAAAATATAAA
*
59755099 TTAA-AATATATTAAATATA
1 TTAATAATATA-AAAATATA
59755118 TTGAAACGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 13 0.41
20 7 0.22
21 12 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAATAATATAAAAATATAAA
Found at i:59755113 original size:15 final size:16
Alignment explanation
Indices: 59755076--59755117 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
59755066 TATAAATATT
59755076 AATATT-AATATAAAA
1 AATATTAAATATAAAA
59755091 AATA-TAAAT-TAAAA
1 AATATTAAATATAAAA
*
59755105 TATATTAAATATA
1 AATATTAAATATA
59755118 TTGAAACGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 9 0.39
15 12 0.52
16 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATTAAATATAAAA
Found at i:59757093 original size:11 final size:11
Alignment explanation
Indices: 59757072--59757102 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
59757062 GGCTGTTTGA
59757072 ATTATTATTATT
1 ATTA-TATTATT
59757084 ATTATATTATT
1 ATTATATTATT
59757095 ATTATATT
1 ATTATATT
59757103 GAAAGGTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTATATTATT
Found at i:59764218 original size:365 final size:366
Alignment explanation
Indices: 59763515--59764251 Score: 1174
Period size: 365 Copynumber: 2.0 Consensus size: 366
59763505 TCGTATTCTT
*
59763515 TCAAAACTCTTTTTAGACCAGTAGCTCCTTCCAAATTTGCTTTACTAAATAAATTGCAGTTATTT
1 TCAAAACTCTTTTTAGACCAGTAGCTCCTTCCAAATTTGCTTTACTAAATAAATTACAGTTATTT
* * *
59763580 GCAAACAGTAAATGGGATATCGTCGGACCATTCTTATAGGCTCTTCCACCAATTAGATGTCCCTT
66 GCAAACAGTAAATGGGATATCGACGGACCATTCTTATAGGCTCTTACACCAATTAGATGTCCCGT
* *
59763645 ACTAACAGTCAACCTCATTAAAGTTTGAAAGATTTTCACTCAAAATAATAAAAAGAAAAGGGTTG
131 ACTAACAGTCAACCTCATTAAAGTTCGAAAGACTTTCACTCAAAATAATAAAAAGAAAAGGGTTG
* * * *
59763710 AGGTGGTTACCTTGTCGAAGCCTTTTAGTAGGTTTGAACGTATCTCCCATTCTTCCATTCATATT
196 AGGGGGTCACCTTGTCGAAGCCCTCTAGTAGGTTTGAACGTATCTCCCATTCTTCCATTCATATT
* *
59763775 GATAAAGTAAGAGATTGTGGAGATACAATGCATTAACTTCCCCACCCATGCAATTGCAAATCCCA
261 GATAAAGTAAGAGATTGCGGAGATACAATGCATTAACTTCCCCAACCATGCAATTGCAAATCCCA
* * * *
59763840 TCTTAAACATCATTGCTTCCATTTAACTTCATTTTACTTTG
326 TCTTAAACATCATTACTTCCAATAAACTTCATTCTACTTTG
* ** *
59763881 TCAAACCTCTTTTTAGACTGGTAGCT-CTTACCAAATTTGTTTTACTAAATAAATTACAGTTATT
1 TCAAAACTCTTTTTAGACCAGTAGCTCCTT-CCAAATTTGCTTTACTAAATAAATTACAGTTATT
*
59763945 TGCAAACAGTAAATGGGATATCGACGGACCATTTTTATAGGCTCTTACACCAATCT-GATGTCCC
65 TGCAAACAGTAAATGGGATATCGACGGACCATTCTTATAGGCTCTTACACCAAT-TAGATGTCCC
**
59764009 GTACTAACAGTCAACCTCATTAAAG-TCGAAAGACTTTCACTGTAAATAATAAAAAGAAAAGGGT
129 GTACTAACAGTCAACCTCATTAAAGTTCGAAAGACTTTCACTCAAAATAATAAAAAGAAAAGGGT
* *
59764073 TGAGGGGGTCACTTTGTTGAAGCCCTCTAGTAGGTTTGAACGTATCTCCCATTCTTCCATTCATA
194 TGAGGGGGTCACCTTGTCGAAGCCCTCTAGTAGGTTTGAACGTATCTCCCATTCTTCCATTCATA
* *
59764138 TTGATAAAGTAAGAGATTGCGTAGATATAATGCATTAACTTCCCCAACCATGCAATTGCAAATCC
259 TTGATAAAGTAAGAGATTGCGGAGATACAATGCATTAACTTCCCCAACCATGCAATTGCAAATCC
* *
59764203 CATCTTAACCATCATTATTTCCAATAAACTTCATTCTACTTTG
324 CATCTTAAACATCATTACTTCCAATAAACTTCATTCTACTTTG
59764246 TCAAAA
1 TCAAAA
59764252 GCTTTACTCA
Statistics
Matches: 339, Mismatches: 30, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
365 200 0.59
366 138 0.41
367 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (366 bp):
TCAAAACTCTTTTTAGACCAGTAGCTCCTTCCAAATTTGCTTTACTAAATAAATTACAGTTATTT
GCAAACAGTAAATGGGATATCGACGGACCATTCTTATAGGCTCTTACACCAATTAGATGTCCCGT
ACTAACAGTCAACCTCATTAAAGTTCGAAAGACTTTCACTCAAAATAATAAAAAGAAAAGGGTTG
AGGGGGTCACCTTGTCGAAGCCCTCTAGTAGGTTTGAACGTATCTCCCATTCTTCCATTCATATT
GATAAAGTAAGAGATTGCGGAGATACAATGCATTAACTTCCCCAACCATGCAATTGCAAATCCCA
TCTTAAACATCATTACTTCCAATAAACTTCATTCTACTTTG
Found at i:59766734 original size:29 final size:29
Alignment explanation
Indices: 59766675--59766771 Score: 81
Period size: 29 Copynumber: 3.3 Consensus size: 29
59766665 TAAAAATAAT
* * * *
59766675 AATTAAAGTATATAGGAAATTAGAAAATA
1 AATTAAAATATATAAGAAATTACAAATTA
59766704 AATTAAAATATATAAGAAATTTA-AAATTAA
1 AATTAAAATATATAAGAAA-TTACAAATT-A
* * *
59766734 AATTTAAATA-AAAATAAAATTACAAATTA
1 AATTAAAATATATAA-GAAATTACAAATTA
59766763 AATTTAAAA
1 AA-TTAAAA
59766772 AGTAAAGTGA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
29 30 0.54
30 26 0.46
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (29 bp):
AATTAAAATATATAAGAAATTACAAATTA
Found at i:59766735 original size:6 final size:6
Alignment explanation
Indices: 59766724--59766771 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
59766714 TATAAGAAAT
* * *
59766724 TTAAAA TTAAAA TTTAAA -TAAAA ATAAAA TTACAAA TTAAAT TTAAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTA-AAA TTAAAA TTAAAA
59766772 AGTAAAGTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
5 4 0.11
6 25 0.71
7 6 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (6 bp):
TTAAAA
Found at i:59766743 original size:30 final size:30
Alignment explanation
Indices: 59766663--59766770 Score: 80
Period size: 29 Copynumber: 3.6 Consensus size: 30
59766653 ATATAATTTT
* *
59766663 TTTA-AAAATAATAATTAAAGTATATAGGAAA
1 TTTACAAAATAA-ATTTAAA-TATATAAGAAA
* *
59766694 -TTAGAAAATAAATTAAAATATATAAGAAA
1 TTTACAAAATAAATTTAAATATATAAGAAA
* * *
59766723 TTTA-AAATTAAAATTTAAATA-AAAATAAA
1 TTTACAAAAT-AAATTTAAATATATAAGAAA
* *
59766752 ATTACAAATTAAATTTAAA
1 TTTACAAAATAAATTTAAA
59766771 AAGTAAAGTG
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
29 32 0.49
30 26 0.40
31 7 0.11
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (30 bp):
TTTACAAAATAAATTTAAATATATAAGAAA
Found at i:59766755 original size:23 final size:23
Alignment explanation
Indices: 59766698--59766765 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
59766688 AGGAAATTAG
* *
59766698 AAAAT-AAATTAAAATATATAAGA
1 AAAATAAAATTAAAATTTA-AATA
**
59766721 AATTTAAAATTAAAATTTAAATA
1 AAAATAAAATTAAAATTTAAATA
59766744 AAAATAAAATTACAAA-TTAAAT
1 AAAATAAAATTA-AAATTTAAAT
59766766 TTAAAAAGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
23 22 0.59
24 15 0.41
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (23 bp):
AAAATAAAATTAAAATTTAAATA
Found at i:59770646 original size:30 final size:30
Alignment explanation
Indices: 59770612--59770680 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
59770602 ATTTTATTTT
*
59770612 TATTTTAA-ATTTCATTTTGAATTTCTTGTA
1 TATTTTAATATTTC-TTTTGAATTTCCTGTA
* * *
59770642 TATTTTAATTTTTCTTTTTAATTTCCTGTG
1 TATTTTAATATTTCTTTTGAATTTCCTGTA
*
59770672 TATTCTAAT
1 TATTTTAAT
59770681 TATTATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.23, C:0.09, G:0.06, T:0.62
Consensus pattern (30 bp):
TATTTTAATATTTCTTTTGAATTTCCTGTA
Found at i:59770681 original size:30 final size:30
Alignment explanation
Indices: 59770621--59770690 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
59770611 TTATTTTAAA
* * *
59770621 TTTCATTTTGAATTTCTTGTATATTTTAATT
1 TTTC-TTTTTAATTTCCTGTATATTCTAATT
*
59770652 TTTCTTTTTAATTTCCTGTGTATTCTAATT
1 TTTCTTTTTAATTTCCTGTATATTCTAATT
* *
59770682 ATTATTTTT
1 TTTCTTTTT
59770691 TAAAAAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.20, C:0.09, G:0.06, T:0.66
Consensus pattern (30 bp):
TTTCTTTTTAATTTCCTGTATATTCTAATT
Found at i:59777376 original size:15 final size:17
Alignment explanation
Indices: 59777344--59777380 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
59777334 TTTATCACAC
*
59777344 AAAATATTTTATATTAA
1 AAAATATGTTATATTAA
59777361 AAAATATGTTA-A-TAA
1 AAAATATGTTATATTAA
59777376 AAAAT
1 AAAAT
59777381 TATTAGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AAAATATGTTATATTAA
Found at i:59777755 original size:20 final size:20
Alignment explanation
Indices: 59777730--59777771 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
59777720 ATTGATAAGC
* *
59777730 AATAAATAATAAATTTTAAT
1 AATAAATAAAAAATTTAAAT
59777750 AATAAATAAAAAATTTAAAT
1 AATAAATAAAAAATTTAAAT
59777770 AA
1 AA
59777772 ATTCATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAATAAAAAATTTAAAT
Found at i:59781039 original size:39 final size:39
Alignment explanation
Indices: 59780991--59781169 Score: 157
Period size: 39 Copynumber: 4.6 Consensus size: 39
59780981 TAATTATTGT
*
59780991 ACTGGTAGTGACACTGTAAACACTGCAATGCTATACTAA
1 ACTGATAGTGACACTGTAAACACTGCAATGCTATACTAA
* * * * * *
59781030 ACTGATAGTGATACTATAAACACTGCGATGTTATATTGA
1 ACTGATAGTGACACTGTAAACACTGCAATGCTATACTAA
* ** *
59781069 ATTGGCAGTGACACTTTAAACACTGTC-ATGCTATACTAA
1 ACTGATAGTGACACTGTAAACACTG-CAATGCTATACTAA
* * * * *
59781108 ACTG-CAGTGACACTGTAAACATTACAATGCTATATTGA
1 ACTGATAGTGACACTGTAAACACTGCAATGCTATACTAA
* *
59781146 GCT-AGTAGTGACATTGTAAACACT
1 ACTGA-TAGTGACACTGTAAACACT
59781170 ATAAGACTAC
Statistics
Matches: 111, Mismatches: 25, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
37 1 0.01
38 29 0.26
39 80 0.72
40 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (39 bp):
ACTGATAGTGACACTGTAAACACTGCAATGCTATACTAA
Found at i:59781166 original size:77 final size:78
Alignment explanation
Indices: 59780985--59781169 Score: 205
Period size: 77 Copynumber: 2.4 Consensus size: 78
59780975 TGATAATAAT
* * * * *
59780985 TATTGTACTGGTAGTGACACTGTAAACACTGCAATGCTATACTAAACTGATAGTGATACTATAAA
1 TATTGAACTAGTAGTGACATTGTAAACACTGCAATGCTATACTAAACTGACAGTGACACTATAAA
* * *
59781050 CACTGCGATGTTA
66 CACTACAATGCTA
* * * *
59781063 TATTGAATTGGCAGTGACACTT-TAAACACTGTC-ATGCTATACTAAACTG-CAGTGACACTGTA
1 TATTGAACTAGTAGTGACA-TTGTAAACACTG-CAATGCTATACTAAACTGACAGTGACACTATA
*
59781125 AACATTACAATGCTA
64 AACACTACAATGCTA
*
59781140 TATTGAGCTAGTAGTGACATTGTAAACACT
1 TATTGAACTAGTAGTGACATTGTAAACACT
59781170 ATAAGACTAC
Statistics
Matches: 89, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
76 2 0.02
77 44 0.49
78 41 0.46
79 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (78 bp):
TATTGAACTAGTAGTGACATTGTAAACACTGCAATGCTATACTAAACTGACAGTGACACTATAAA
CACTACAATGCTA
Found at i:59788025 original size:18 final size:18
Alignment explanation
Indices: 59787986--59788025 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
59787976 AATTAATGAC
*
59787986 AAAAACAAAATGTCACAT
1 AAAAACAAAACGTCACAT
59788004 AAAAATCAAAACGTCACA-
1 AAAAA-CAAAACGTCACAT
59788022 AAAA
1 AAAA
59788026 TTCCAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.65, C:0.17, G:0.05, T:0.12
Consensus pattern (18 bp):
AAAAACAAAACGTCACAT
Found at i:59789367 original size:19 final size:20
Alignment explanation
Indices: 59789345--59789392 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
59789335 ATTATTATTC
59789345 ATTTAATA-AAAAA-AATCAT
1 ATTTAATAGAAAAATAAT-AT
*
59789364 ATTTAATTAGAAAAATAATTT
1 ATTTAA-TAGAAAAATAATAT
59789385 ATTTAATA
1 ATTTAATA
59789393 TCGTAAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.24
20 4 0.16
21 12 0.48
22 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTTAATAGAAAAATAATAT
Found at i:59792862 original size:16 final size:16
Alignment explanation
Indices: 59792831--59792864 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
59792821 TATATAAAAA
59792831 AATTTATACATAATAT
1 AATTTATACATAATAT
59792847 AATTTAATACAT-ATAT
1 AATTT-ATACATAATAT
59792863 AA
1 AA
59792865 AATTCTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTATACATAATAT
Found at i:59794130 original size:2 final size:2
Alignment explanation
Indices: 59794125--59794153 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
59794115 CGGTCGTTCA
59794125 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59794154 TTTAGATCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59798059 original size:40 final size:38
Alignment explanation
Indices: 59797991--59798125 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
59797981 ACCAGAATGG
* *
59797991 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
59798031 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
59798068 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
59798109 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
59798126 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:59798123 original size:41 final size:38
Alignment explanation
Indices: 59798023--59798126 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
59798013 TTCGAAGCAA
* *
59798023 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
59798060 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
59798098 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
59798127 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:59798969 original size:2 final size:2
Alignment explanation
Indices: 59798962--59799011 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
59798952 CTTTTATTTC
* *
59798962 AT AT AT AT AT AT AT AT AT GT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59799004 AT AT AT AT
1 AT AT AT AT
59799012 TAGTTAATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59805919 original size:10 final size:9
Alignment explanation
Indices: 59805870--59805967 Score: 83
Period size: 9 Copynumber: 10.4 Consensus size: 9
59805860 AATATCATAG
59805870 AAAATTATA
1 AAAATTATA
59805879 AAAATTAGTA
1 AAAATTA-TA
59805889 AAAA-TATGA
1 AAAATTAT-A
59805898 AAAATTAT-
1 AAAATTATA
59805906 AAAATTATA
1 AAAATTATA
*
59805915 AAAAATATA
1 AAAATTATA
* *
59805924 ACAATTATCG
1 AAAATTAT-A
*
59805934 ATAATTAATAA
1 AAAATT-AT-A
*
59805945 AAAATTCTA
1 AAAATTATA
59805954 ACAAATTATA
1 A-AAATTATA
59805964 AAAA
1 AAAA
59805968 CCATAAAGTG
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
8 9 0.12
9 33 0.46
10 23 0.32
11 7 0.10
ACGTcount: A:0.63, C:0.04, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:59806414 original size:21 final size:20
Alignment explanation
Indices: 59806390--59806429 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
59806380 AATAATTGCA
59806390 TTAAAAAATATTTTATATTTT
1 TTAAAAAATATTTTA-ATTTT
**
59806411 TTAAAATTTATTTTAATTT
1 TTAAAAAATATTTTAATTT
59806430 ATAATTTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTAAAAAATATTTTAATTTT
Found at i:59806463 original size:20 final size:21
Alignment explanation
Indices: 59806426--59806490 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 21
59806416 ATTTATTTTA
* *
59806426 ATTTATAATTTAA-CATAAAT
1 ATTTATAATGTAATTATAAAT
* *
59806446 ATTTATTAT-TATTTATAAA-
1 ATTTATAATGTAATTATAAAT
59806465 ATTT-TAATGTAATTATATAAT
1 ATTTATAATGTAATTATA-AAT
59806486 ATTTA
1 ATTTA
59806491 AATATATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
18 3 0.09
19 13 0.37
20 15 0.43
21 4 0.11
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTATAATGTAATTATAAAT
Found at i:59818329 original size:3 final size:3
Alignment explanation
Indices: 59818318--59818351 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
59818308 CGAAGACGAC
*
59818318 GAA GAAA GAA GAA CAA GAA GAA GAA GAA GAA GAA
1 GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA
59818352 AAGCGATCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:59820169 original size:12 final size:12
Alignment explanation
Indices: 59820149--59820189 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
59820139 AAGCCTCTCT
59820149 TCTTCATCTTAA
1 TCTTCATCTTAA
*
59820161 TCTTAATCTTAA
1 TCTTCATCTTAA
* *
59820173 TATTCATCTTCA
1 TCTTCATCTTAA
59820185 TCTTC
1 TCTTC
59820190 TTCTCTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (12 bp):
TCTTCATCTTAA
Found at i:59820911 original size:193 final size:192
Alignment explanation
Indices: 59820582--59820967 Score: 682
Period size: 193 Copynumber: 2.0 Consensus size: 192
59820572 AAAGGGCTTC
*
59820582 ACTTGCTCACAAATCTTGAATCTTTGGAACTTTCTCAGAACAAGCTAGAGGGTAGAATTCCATTG
1 ACTTGCTCACAAATCTTGAATCTTTGGAACTTTCTCAGAACAAGCTAGAGGGTAGAATTCCAGTG
* *
59820647 GAATTGATGTTTGAGACTGCATTAAGAAAAATAAAAAGAGAAGAAGATTAAGATGGAGAAGAGAG
66 GAATTGATGGTTGAGACTGCATTAAGAAAAATAAAAAGAGAAGAAGAGTAAGATGGAGAAGAGAG
*
59820712 GCTTGGAAATGAATTTAGAATTTTTTCATTTAAGGTTTAGGTTTTAAAATTTTTAATTAATTA
131 GCTTGGAAATGAATTTAGAATTTTTT-ATTTAAGGTTTAGGCTTTAAAATTTTTAATTAATTA
*
59820775 ACTTGCTCACAAATCTTGAATCTTTGGAACTTTCTTAGAACAAGCTAGAGGGTAGAATTCCAGTG
1 ACTTGCTCACAAATCTTGAATCTTTGGAACTTTCTCAGAACAAGCTAGAGGGTAGAATTCCAGTG
*
59820840 GAATTGATGGTTGAGACTGCATTGAGAAAAATAAAAAGAGAAGAAGAGTAAGATGGAGAAGAGAG
66 GAATTGATGGTTGAGACTGCATTAAGAAAAATAAAAAGAGAAGAAGAGTAAGATGGAGAAGAGAG
* **
59820905 GCTTGGAAATGAGTTTAGGGTTTTTTATTTAAGGTTTAGGCTTTAAAATTTTTAATTAATTA
131 GCTTGGAAATGAATTTAGAATTTTTTATTTAAGGTTTAGGCTTTAAAATTTTTAATTAATTA
59820967 A
1 A
59820968 ATTTATTTAA
Statistics
Matches: 184, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
192 36 0.20
193 148 0.80
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (192 bp):
ACTTGCTCACAAATCTTGAATCTTTGGAACTTTCTCAGAACAAGCTAGAGGGTAGAATTCCAGTG
GAATTGATGGTTGAGACTGCATTAAGAAAAATAAAAAGAGAAGAAGAGTAAGATGGAGAAGAGAG
GCTTGGAAATGAATTTAGAATTTTTTATTTAAGGTTTAGGCTTTAAAATTTTTAATTAATTA
Found at i:59820978 original size:18 final size:16
Alignment explanation
Indices: 59820955--59820990 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
59820945 CTTTAAAATT
59820955 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
59820973 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
59820989 TT
1 TT
59820991 ATCATCCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:59821477 original size:16 final size:16
Alignment explanation
Indices: 59821435--59821477 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
59821425 ACCTAAAATT
*
59821435 AACACTTAAATTTTTC
1 AACACTTAATTTTTTC
* *
59821451 AATA-TTTATTTTTTC
1 AACACTTAATTTTTTC
59821466 AACACTTAATTT
1 AACACTTAATTT
59821478 GTTAATTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (16 bp):
AACACTTAATTTTTTC
Found at i:59825539 original size:415 final size:416
Alignment explanation
Indices: 59824750--59825555 Score: 1424
Period size: 415 Copynumber: 1.9 Consensus size: 416
59824740 AATTCATTTT
* *
59824750 ACGTTAAGAGTGTTAATAAAAAAAAATTAGAGGCATATATCTAAAAACCTCCAAAATTTAAGGGC
1 ACGTTAAGAGTGTTAATAAAAAAAAATTAGAGACATATATCTAAAAACCTCCAAAATTTAAGAGC
*
59824815 TTTTTTTTACAATTTGCTTGTATGTTTTGGTTGTTCGGTTGGTTTGCTAAAATGGAGTTGAATTG
66 TTTTTTTTACAATTTGCTGGTATGTTTTGGTTGTTCGGTTGGTTTGCTAAAATGGAGTTGAATTG
* *
59824880 CTGGGTTGTTGTTGTTAAGTCAAGATTTTTTTTAACATATTGATGTTATTACATGATATTATCTA
131 CTGGG-TGTTGTTGTTAAGTCAAGATTTTTTTTAACATATTGATGTTATTAAATGATAGTATCTA
59824945 TTCATACTTTTTAATTCTTTGACAACGCACACATACTTTGCACACACAGGTGCTCCCTGAATCTC
195 TTCATACTTTTTAATTCTTTGACAACGCACACATACTTTGCACACACAGGTGCTCCCTGAATCTC
59825010 CTAGGATGAACATCATCCTCTTTTCCACTAGAGCCATTCGTTGAATTCTAAGTCAAGATTCTAAA
260 CTAGGATGAACATCATCCTCTTTTCCACTAGAGCCATTCGTTGAATTCTAAGTCAAGATTCTAAA
59825075 CATTAAAATTTGCTTAAACTTCAAGTAGTTCTAATCCTAAAACCAAACACCAGAATTTCAACCCC
325 CATTAAAATTTGCTTAAACTTCAAGTAGTTCTAATCCTAAAACCAAACACCAGAATTTCAACCCC
59825140 CCATTGAATTCATTTTTAAAAATTATA
390 CCATTGAATTCATTTTTAAAAATTATA
59825167 ACGTTAAGAGTGTTAATAAAAAAAAA-TAGAGACATATATCTAAAAACCTCCAAAATTTGAA-AG
1 ACGTTAAGAGTGTTAATAAAAAAAAATTAGAGACATATATCTAAAAACCTCCAAAATTT-AAGAG
59825230 C-TTTTTTTACAATTTGCTGGTATGTTTTGGTTGTTCGGTTGGTTTGCTAAAATGGAGTTGAATT
65 CTTTTTTTTACAATTTGCTGGTATGTTTTGGTTGTTCGGTTGGTTTGCTAAAATGGAGTTGAATT
*
59825294 G-TTGG-GTTGTTGTTAAGTCAAGATTTTTTTTTTAACATATTGATGTTATTAAATGATAGTATC
130 GCTGGGTGTTGTTGTTAAGTCAAGA--TTTTTTTTAACATATTGATGTTATTAAATGATAGTATC
* *
59825357 TATTCATTCTTTCTTAATTCTTTGACAACGCATACATACTTTGCACACACAGGTGCTCCCTGAAT
193 TATTCATACTTT-TTAATTCTTTGACAACGCACACATACTTTGCACACACAGGTGCTCCCTGAAT
*
59825422 CTCCTAGGATGAACATCATCCTCTTTTCCACTAGAGCCATTCGTTGGATTCTAAGTCAAGATTCT
257 CTCCTAGGATGAACATCATCCTCTTTTCCACTAGAGCCATTCGTTGAATTCTAAGTCAAGATTCT
* * *
59825487 AAACATTAAAATTTGCTTAAACTTTAAGTAGTTCTAATCTTAAAACCAAACACCAGAATTTCAGC
322 AAACATTAAAATTTGCTTAAACTTCAAGTAGTTCTAATCCTAAAACCAAACACCAGAATTTCAAC
59825552 CCCC
387 CCCC
59825556 TACATTCATA
Statistics
Matches: 373, Mismatches: 12, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
412 18 0.05
414 50 0.13
415 244 0.65
416 33 0.09
417 28 0.08
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (416 bp):
ACGTTAAGAGTGTTAATAAAAAAAAATTAGAGACATATATCTAAAAACCTCCAAAATTTAAGAGC
TTTTTTTTACAATTTGCTGGTATGTTTTGGTTGTTCGGTTGGTTTGCTAAAATGGAGTTGAATTG
CTGGGTGTTGTTGTTAAGTCAAGATTTTTTTTAACATATTGATGTTATTAAATGATAGTATCTAT
TCATACTTTTTAATTCTTTGACAACGCACACATACTTTGCACACACAGGTGCTCCCTGAATCTCC
TAGGATGAACATCATCCTCTTTTCCACTAGAGCCATTCGTTGAATTCTAAGTCAAGATTCTAAAC
ATTAAAATTTGCTTAAACTTCAAGTAGTTCTAATCCTAAAACCAAACACCAGAATTTCAACCCCC
CATTGAATTCATTTTTAAAAATTATA
Found at i:59847247 original size:24 final size:27
Alignment explanation
Indices: 59847218--59847266 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
59847208 AAAAATTTAA
59847218 AAATA-TCAAT-TAAA-ATTTATTATT
1 AAATATTCAATCTAAATATTTATTATT
*
59847242 AAATATTTAATCTAAATATTTATTA
1 AAATATTCAATCTAAATATTTATTA
59847267 AAAGTAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 4 0.19
26 4 0.19
27 8 0.38
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
AAATATTCAATCTAAATATTTATTATT
Found at i:59849931 original size:22 final size:21
Alignment explanation
Indices: 59849906--59849947 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
59849896 TATAAGCTTT
59849906 AAATATAATTATATAATATTTA
1 AAATATAATTATAT-ATATTTA
* *
59849928 AAATATATTTTTATATATTT
1 AAATATAATTATATATATTT
59849948 TAGATTGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAATATAATTATATATATTTA
Found at i:59854543 original size:24 final size:24
Alignment explanation
Indices: 59854493--59854544 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
59854483 TTCGTAGGTC
*
59854493 AAATAAATTATACTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
59854517 AAATATATTATACTAATAAATATA
1 AAATAAATTATACTAATAAATACA
59854541 AAAT
1 AAAT
59854545 CTTCAGAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:59862305 original size:2 final size:2
Alignment explanation
Indices: 59862298--59862323 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59862288 TGTATCAACA
59862298 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
59862324 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59864442 original size:3 final size:3
Alignment explanation
Indices: 59864434--59864459 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
59864424 AATGGCATGA
59864434 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
59864460 AGGATGGCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:59878422 original size:2 final size:2
Alignment explanation
Indices: 59878417--59878456 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
59878407 ATATACCTTT
59878417 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
59878457 ACATTTAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59883354 original size:10 final size:10
Alignment explanation
Indices: 59883336--59883389 Score: 65
Period size: 10 Copynumber: 5.4 Consensus size: 10
59883326 TATATAATTC
*
59883336 AAAATTTAAA
1 AAAAATTAAA
59883346 AAAAATTAAA
1 AAAAATTAAA
*
59883356 AAAAGTTACAA
1 AAAAATTA-AA
59883367 AAAAA-TAAA
1 AAAAATTAAA
*
59883376 AAAAATGAAA
1 AAAAATTAAA
59883386 AAAA
1 AAAA
59883390 GTAAAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 7 0.18
10 25 0.66
11 6 0.16
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.17
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:59883359 original size:9 final size:9
Alignment explanation
Indices: 59883344--59883395 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
59883334 TCAAAATTTA
59883344 AAAAAAATT
1 AAAAAAATT
59883353 AAAAAAAGTT
1 AAAAAAA-TT
*
59883363 ACAAAAAAATA
1 --AAAAAAATT
*
59883374 AAAAAAATG
1 AAAAAAATT
*
59883383 AAAAAAAGT
1 AAAAAAATT
59883392 AAAA
1 AAAA
59883396 TATTGTTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 26 0.72
10 2 0.06
11 1 0.03
12 7 0.19
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (9 bp):
AAAAAAATT
Found at i:59883359 original size:20 final size:21
Alignment explanation
Indices: 59883336--59883381 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
59883326 TATATAATTC
*
59883336 AAAATTTA-AAAAAAATTAAA
1 AAAATTTACAAAAAAATAAAA
*
59883356 AAAAGTTACAAAAAAATAAAA
1 AAAATTTACAAAAAAATAAAA
59883377 AAAAT
1 AAAAT
59883382 GAAAAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAATTTACAAAAAAATAAAA
Found at i:59883613 original size:29 final size:30
Alignment explanation
Indices: 59883581--59883639 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
59883571 TATAATTTCA
*
59883581 TGTGTAATTGTATACATG-AATTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
*
59883610 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
59883640 GATACAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAATTTTGATTT
Found at i:59883648 original size:30 final size:29
Alignment explanation
Indices: 59883586--59883648 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
59883576 TTTCATGTGT
*
59883586 AATTGTATACATGAATTTTGATTTTGTGC
1 AATTGTATACATGAATTTTGATTTTGTAC
*
59883615 AATTTTATACATGAAATTTTGA-TTTGATAC
1 AATTGTATACATG-AATTTTGATTTTG-TAC
59883645 AATT
1 AATT
59883649 CTTGTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (29 bp):
AATTGTATACATGAATTTTGATTTTGTAC
Found at i:59884966 original size:22 final size:22
Alignment explanation
Indices: 59884940--59884986 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
59884930 GACTTTCCTA
59884940 TTTTCTATTTCTTTCAATTCTG
1 TTTTCTATTTCTTTCAATTCTG
* * * *
59884962 TTTTCTTTTTTTTTTAATTTTG
1 TTTTCTATTTCTTTCAATTCTG
59884984 TTT
1 TTT
59884987 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTCTATTTCTTTCAATTCTG
Found at i:59886775 original size:35 final size:35
Alignment explanation
Indices: 59886680--59886775 Score: 88
Period size: 41 Copynumber: 2.6 Consensus size: 35
59886670 TCCCCTTTCC
59886680 TTTTTATTTATTTATTTACTTGTATTATTTTATTTA
1 TTTTTATTTATTTATTTA-TTGTATTATTTTATTTA
* *
59886716 TTTTGGTATTTAATTATTGTTTATT-TATTGCTTTTATCTTA
1 TTTT--TATTT-A-T-TTATTTATTGTATT-ATTTTAT-TTA
59886757 TTTTTATTTATTT-TTTATT
1 TTTTTATTTATTTATTTATT
59886776 ATTCTAATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
35 6 0.12
36 6 0.12
37 1 0.02
38 6 0.12
39 10 0.20
40 9 0.18
41 13 0.25
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (35 bp):
TTTTTATTTATTTATTTATTGTATTATTTTATTTA
Found at i:59886777 original size:20 final size:22
Alignment explanation
Indices: 59886728--59886778 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
59886718 TTGGTATTTA
59886728 ATTATTGTTTATTTATTGCTTTT
1 ATTATTGTTTATTTATT-CTTTT
59886751 ATCTTATT-TTTATTTATT-TTTT
1 A--TTATTGTTTATTTATTCTTTT
59886773 ATTATT
1 ATTATT
59886779 CTAATTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 5 0.19
22 5 0.19
23 1 0.04
24 10 0.38
25 5 0.19
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (22 bp):
ATTATTGTTTATTTATTCTTTT
Found at i:59886778 original size:10 final size:11
Alignment explanation
Indices: 59886680--59886775 Score: 68
Period size: 11 Copynumber: 7.7 Consensus size: 11
59886670 TCCCCTTTCC
59886680 TTTTTATTTAT
1 TTTTTATTTAT
59886691 TTATTTACTTGTAT
1 TT-TTTA-TT-TAT
59886705 TATTTTATTTAT
1 T-TTTTATTTAT
*
59886717 TTTGGTATTTAATT
1 TTT-TTATTT-A-T
59886731 ATTGTTTATTTAT
1 -TT-TTTATTTAT
59886744 TGCTTTTATCTTA-
1 T--TTTTAT-TTAT
59886757 TTTTTATTTAT
1 TTTTTATTTAT
59886768 TTTTTATT
1 TTTTTATT
59886776 ATTCTAATTT
Statistics
Matches: 70, Mismatches: 2, Indels: 26
0.71 0.02 0.27
Matches are distributed among these distances:
10 3 0.04
11 18 0.26
12 14 0.20
13 12 0.17
14 14 0.20
15 8 0.11
16 1 0.01
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:59890708 original size:23 final size:23
Alignment explanation
Indices: 59890678--59890723 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
59890668 GGTAGCGCGT
* *
59890678 TTACTGTTTTGCACTTCGTGTGC
1 TTACTGTTTCGCACCTCGTGTGC
59890701 TTACTGTTTCGCACCTCGTGTGC
1 TTACTGTTTCGCACCTCGTGTGC
59890724 CTATTGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.26, G:0.22, T:0.43
Consensus pattern (23 bp):
TTACTGTTTCGCACCTCGTGTGC
Found at i:59890782 original size:23 final size:22
Alignment explanation
Indices: 59890718--59890797 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
59890708 TTCGCACCTC
* *
59890718 GTGTGCCTATTGATTTGCGCTAT
1 GTGTGCCTATTGA-TTGCACTGT
* *
59890741 GTGCGCCTACTGATTGCACTGT
1 GTGTGCCTATTGATTGCACTGT
59890763 GTGTGCCTATTGGATTGCACTGT
1 GTGTGCCTATT-GATTGCACTGT
*
59890786 GTGTGCTTATTG
1 GTGTGCCTATTG
59890798 TTTCCCGAGC
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 17 0.35
23 32 0.65
ACGTcount: A:0.12, C:0.19, G:0.29, T:0.40
Consensus pattern (22 bp):
GTGTGCCTATTGATTGCACTGT
Found at i:59891298 original size:15 final size:14
Alignment explanation
Indices: 59891274--59891304 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
59891264 TTCAGGGGGT
59891274 TATACGTATATTAA
1 TATACGTATATTAA
59891288 TATATCGTATATTAA
1 TATA-CGTATATTAA
59891303 TA
1 TA
59891305 AAATATTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (14 bp):
TATACGTATATTAA
Found at i:59891727 original size:14 final size:15
Alignment explanation
Indices: 59891701--59891733 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
59891691 CACATCCTTG
59891701 TTTAGATGAATCAGA
1 TTTAGATGAATCAGA
59891716 TTTAGA-GAATCAGA
1 TTTAGATGAATCAGA
59891730 TTTA
1 TTTA
59891734 TATTATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (15 bp):
TTTAGATGAATCAGA
Found at i:59892716 original size:23 final size:23
Alignment explanation
Indices: 59892686--59892755 Score: 113
Period size: 23 Copynumber: 3.0 Consensus size: 23
59892676 ACGGTAGCGC
59892686 GTTTACTGTTTTGCACTTCGTGT
1 GTTTACTGTTTTGCACTTCGTGT
*
59892709 GTTTACTGTTTCGCACTTCGTGT
1 GTTTACTGTTTTGCACTTCGTGT
* *
59892732 GCTTATTGTTTTGCACTTCGTGT
1 GTTTACTGTTTTGCACTTCGTGT
59892755 G
1 G
59892756 CCTATTGATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.09, C:0.19, G:0.23, T:0.50
Consensus pattern (23 bp):
GTTTACTGTTTTGCACTTCGTGT
Found at i:59892756 original size:23 final size:23
Alignment explanation
Indices: 59892692--59892768 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
59892682 GCGCGTTTAC
* *
59892692 TGTTTTGCACTTCGTGTGTTTAC
1 TGTTTTGCACTTCGTGTGCTTAT
*
59892715 TGTTTCGCACTTCGTGTGCTTAT
1 TGTTTTGCACTTCGTGTGCTTAT
*
59892738 TGTTTTGCACTTCGTGTGCCTAT
1 TGTTTTGCACTTCGTGTGCTTAT
*
59892761 TGATTTGC
1 TGTTTTGC
59892769 GCTATGTGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.09, C:0.19, G:0.22, T:0.49
Consensus pattern (23 bp):
TGTTTTGCACTTCGTGTGCTTAT
Found at i:59893308 original size:15 final size:14
Alignment explanation
Indices: 59893284--59893313 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
59893274 TTCAGGGGGT
59893284 TATACGTATATTAA
1 TATACGTATATTAA
59893298 TATATCGTATATTAA
1 TATA-CGTATATTAA
59893313 T
1 T
59893314 GAAATATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
TATACGTATATTAA
Found at i:59893737 original size:14 final size:15
Alignment explanation
Indices: 59893711--59893743 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
59893701 CACATTCTTG
59893711 TTTAGATGAATCAGA
1 TTTAGATGAATCAGA
59893726 TTTAGA-GAATCAGA
1 TTTAGATGAATCAGA
59893740 TTTA
1 TTTA
59893744 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (15 bp):
TTTAGATGAATCAGA
Found at i:59901248 original size:22 final size:22
Alignment explanation
Indices: 59901186--59901248 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
59901176 AAATAAATTT
* * *
59901186 TATGATAAATAGTTTTTTTATTTT
1 TATGATAAAT-G-TTATTTATCTC
*
59901210 TATGAT-AATATTATTTATCTC
1 TATGATAAATGTTATTTATCTC
59901231 TATGATAAATGTTATTTA
1 TATGATAAATGTTATTTA
59901249 AATATTAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 14 0.42
22 10 0.30
23 3 0.09
24 6 0.18
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (22 bp):
TATGATAAATGTTATTTATCTC
Found at i:59901436 original size:49 final size:48
Alignment explanation
Indices: 59901369--59901472 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 48
59901359 TAAATTTTCT
*
59901369 ATGAAAATTTTAACTTTAAACTGAATATTCAAATTAATAAATTAATTA
1 ATGAAAATTTTAACTTTAAACTAAATATTCAAATTAATAAATTAATTA
*
59901417 ATGAAAATTTTTAACTTTAAACTAAATATTCAAATTAATATATTAATTA
1 ATGAAAA-TTTTAACTTTAAACTAAATATTCAAATTAATAAATTAATTA
59901466 ATGAAAA
1 ATGAAAA
59901473 AGTAGAATAG
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
48 7 0.13
49 46 0.87
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (48 bp):
ATGAAAATTTTAACTTTAAACTAAATATTCAAATTAATAAATTAATTA
Found at i:59907535 original size:12 final size:12
Alignment explanation
Indices: 59907520--59907544 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59907510 CCACTTTCGC
59907520 TATCACTTATGT
1 TATCACTTATGT
59907532 TATCACTTATGT
1 TATCACTTATGT
59907544 T
1 T
59907545 CATACTCTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TATCACTTATGT
Found at i:59908039 original size:52 final size:52
Alignment explanation
Indices: 59907967--59908071 Score: 140
Period size: 52 Copynumber: 2.0 Consensus size: 52
59907957 TTACAAATGG
* ** * *
59907967 TAAGAAAATGTTATTTAATTATTT-ATTTTTAATCTGTTAATTATTATGATGT
1 TAAGAAAATATTATCAAATTATTTAATTTTAAAT-AGTTAATTATTATGATGT
*
59908019 TAAGAAAATATTATCAAATTATTTAATTTTAAATAGTTAATTATTATGTTGT
1 TAAGAAAATATTATCAAATTATTTAATTTTAAATAGTTAATTATTATGATGT
59908071 T
1 T
59908072 CAGATTAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
52 38 0.83
53 8 0.17
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (52 bp):
TAAGAAAATATTATCAAATTATTTAATTTTAAATAGTTAATTATTATGATGT
Found at i:59909809 original size:63 final size:63
Alignment explanation
Indices: 59909652--59909826 Score: 228
Period size: 62 Copynumber: 2.8 Consensus size: 63
59909642 TTACAACACA
* * * * *
59909652 CACCAGTTTATTTTACACCAA-CACCACATCACGCGCATTCATTCCCTACACCAATACAGTCAT
1 CACCAATTTATTTTACA-CAAGCACCACAACACGCGCAATCATTCCCTACACCAACACAATCAT
* *
59909715 CACCAA-TTATTTTACACAAGCACCACAACACGCACAATCATTCCCTGCACCAACACAATCAT
1 CACCAATTTATTTTACACAAGCACCACAACACGCGCAATCATTCCCTACACCAACACAATCAT
* * * *
59909777 CACGAATTTATTTTACACAAGCACCATAACACGTGCAATCATTTCCTACA
1 CACCAATTTATTTTACACAAGCACCACAACACGCGCAATCATTCCCTACA
59909827 TTGATACCTT
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
61 3 0.03
62 51 0.53
63 43 0.44
ACGTcount: A:0.35, C:0.34, G:0.06, T:0.24
Consensus pattern (63 bp):
CACCAATTTATTTTACACAAGCACCACAACACGCGCAATCATTCCCTACACCAACACAATCAT
Found at i:59910107 original size:36 final size:36
Alignment explanation
Indices: 59910067--59910249 Score: 154
Period size: 36 Copynumber: 5.1 Consensus size: 36
59910057 GAGGTTACCA
* * *
59910067 ATCAACCTCAATGTGCACATGAAGATGAGGTTGAAG
1 ATCAACCCCAATGTGCACATGAAGACGAGGCTGAAG
* *
59910103 ATCAACCCCGATGTGTACATGAAGACGAGGCTGAAG
1 ATCAACCCCAATGTGCACATGAAGACGAGGCTGAAG
** ** * *
59910139 ATCAACCCTGACATGCACATGAAGACGAGGCCGGAG
1 ATCAACCCCAATGTGCACATGAAGACGAGGCTGAAG
* * * * * *
59910175 ATCCACCCCATTATGCATAT-AGAGACGAGACCGAAG
1 ATCAACCCCAATGTGCACATGA-AGACGAGGCTGAAG
* * *
59910211 ATCAACCCTAACT-TGCACATGAAGACAAGGCCGAAG
1 ATCAACCCCAA-TGTGCACATGAAGACGAGGCTGAAG
59910247 ATC
1 ATC
59910250 CAGTGGAGTC
Statistics
Matches: 119, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
35 1 0.01
36 116 0.97
37 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (36 bp):
ATCAACCCCAATGTGCACATGAAGACGAGGCTGAAG
Found at i:59918667 original size:48 final size:48
Alignment explanation
Indices: 59918611--59918706 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
59918601 ATGACAAGTT
59918611 GCGTAAAATTATCAAGGAAAGATCCATTCAAGTAACAATTTGCACTTG
1 GCGTAAAATTATCAAGGAAAGATCCATTCAAGTAACAATTTGCACTTG
59918659 GCGTAAAATTATCAAGGAAAGATCCATTCAAGTAACAATTTGCACTTG
1 GCGTAAAATTATCAAGGAAAGATCCATTCAAGTAACAATTTGCACTTG
59918707 AAGAACATAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (48 bp):
GCGTAAAATTATCAAGGAAAGATCCATTCAAGTAACAATTTGCACTTG
Found at i:59922969 original size:27 final size:27
Alignment explanation
Indices: 59922922--59923007 Score: 97
Period size: 26 Copynumber: 3.2 Consensus size: 27
59922912 TCTATAAATT
* * *
59922922 TTTTTAAAAATA-TATGAATTTTTGAA
1 TTTTTAAAAATATTTTGGATTTTTAAA
*
59922948 TTTTTATAAATATTTTGGA-TTTTAAA
1 TTTTTAAAAATATTTTGGATTTTTAAA
59922974 TTTTTAAAAATTATTTT-GATTTTTAAAA
1 TTTTTAAAAA-TATTTTGGATTTTT-AAA
59923002 TTTTTA
1 TTTTTA
59923008 TTAAGAGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
26 28 0.55
27 14 0.27
28 9 0.18
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (27 bp):
TTTTTAAAAATATTTTGGATTTTTAAA
Found at i:59929636 original size:4 final size:4
Alignment explanation
Indices: 59929627--59929652 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
59929617 ATCGAAACAA
59929627 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
59929653 AAAATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:59934902 original size:28 final size:27
Alignment explanation
Indices: 59934870--59934928 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 27
59934860 AAAAATTATA
59934870 AAAAC-ATTATACAAA-AAATAAAAAATTC
1 AAAACTATTAT-CAAATAAA-AAAAAA-TC
*
59934898 AAAACTATTATCAAATTAAAAAAAATC
1 AAAACTATTATCAAATAAAAAAAAATC
59934925 AAAA
1 AAAA
59934929 TTCTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 6 0.21
28 15 0.54
29 7 0.25
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.22
Consensus pattern (27 bp):
AAAACTATTATCAAATAAAAAAAAATC
Found at i:59936531 original size:30 final size:29
Alignment explanation
Indices: 59936482--59936551 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
59936472 GTTTAATTTG
* *
59936482 TAATTGTATACATAAATTTTGATTTTG-TT
1 TAATTTTATACATAAATTTT-AATTTGATT
*
59936511 TAATTTTATATATAAAATTTTAATTTGATT
1 TAATTTTATACAT-AAATTTTAATTTGATT
59936541 TAATTCTTATA
1 TAATT-TTATA
59936552 AATTATTAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.46
30 14 0.40
31 5 0.14
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (29 bp):
TAATTTTATACATAAATTTTAATTTGATT
Found at i:59936718 original size:31 final size:30
Alignment explanation
Indices: 59936674--59936742 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
59936664 GATTAAATCA
*
59936674 AAATTAAAGTTTCA-A-GTATATATTTGAACC
1 AAATTAAAATTTCACATGTATA-A-TTGAACC
59936704 ATAATTAAAATTTCACATGTATAATTGAACC
1 A-AATTAAAATTTCACATGTATAATTGAACC
59936735 AAATTAAA
1 AAATTAAA
59936743 GTTCATGTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
30 8 0.23
31 20 0.57
32 2 0.06
33 5 0.14
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.35
Consensus pattern (30 bp):
AAATTAAAATTTCACATGTATAATTGAACC
Found at i:59937193 original size:29 final size:29
Alignment explanation
Indices: 59937161--59937245 Score: 82
Period size: 31 Copynumber: 2.8 Consensus size: 29
59937151 TTTAATGTGT
*
59937161 AATTATATACATGAAATTTAATTTGGTGC
1 AATTATATACATGAAATTTAATTTAGTGC
* * *
59937190 AATTATACACATGAATTTCTAATTATAGTTC
1 AATTATATACATGAAATT-TAATT-TAGTGC
*
59937221 ACA-TGTATACATGAAACTTTAATTT
1 A-ATTATATACATGAAA-TTTAATTT
59937246 TGATTTAATC
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
29 16 0.36
30 6 0.13
31 20 0.44
32 3 0.07
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (29 bp):
AATTATATACATGAAATTTAATTTAGTGC
Found at i:59938543 original size:52 final size:52
Alignment explanation
Indices: 59938487--59938611 Score: 162
Period size: 52 Copynumber: 2.4 Consensus size: 52
59938477 TTTTGTGTTC
59938487 TAATGGATTGATGGGTTTTGTTTGTGATGTTAATTATATGGGTTTTGCATTA
1 TAATGGATTGATGGGTTTTGTTTGTGATGTTAATTATATGGGTTTTGCATTA
** * * *
59938539 TAAT-GATTTGATGGGAGTTGTTTGTGATGTTAATTTTCTGGGTTTTGCATTG
1 TAATGGA-TTGATGGGTTTTGTTTGTGATGTTAATTATATGGGTTTTGCATTA
* * *
59938591 TAGTGGAGTGATGAGTTTTGT
1 TAATGGATTGATGGGTTTTGT
59938612 GAATTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
51 2 0.03
52 57 0.93
53 2 0.03
ACGTcount: A:0.19, C:0.02, G:0.30, T:0.49
Consensus pattern (52 bp):
TAATGGATTGATGGGTTTTGTTTGTGATGTTAATTATATGGGTTTTGCATTA
Found at i:59947658 original size:38 final size:38
Alignment explanation
Indices: 59947615--59947712 Score: 126
Period size: 38 Copynumber: 2.6 Consensus size: 38
59947605 ATATAGGCTT
* *
59947615 ACATCCTATGACAAACCACTATCCTTAAAATTAGAGG-C
1 ACATCCCATGACAAACCACTATCCTTAAAACTAG-GGAC
* * * *
59947653 ACATCCCCTGACAAGCCACTACCCTTAAAACTAGGGAT
1 ACATCCCATGACAAACCACTATCCTTAAAACTAGGGAC
59947691 ACATCCCATGACAAACCACTAT
1 ACATCCCATGACAAACCACTAT
59947713 GCTAGAAAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 2 0.04
38 48 0.96
ACGTcount: A:0.38, C:0.32, G:0.10, T:0.20
Consensus pattern (38 bp):
ACATCCCATGACAAACCACTATCCTTAAAACTAGGGAC
Found at i:59951383 original size:21 final size:20
Alignment explanation
Indices: 59951320--59951385 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 20
59951310 TTAACTTCGT
59951320 CAACTAAGCCCACAATTTCTG
1 CAACTAAGCCCAC-ATTTCTG
* * * *
59951341 CAGCCAAGACTC-CATCTCCTG
1 CAACTAAG-CCCACAT-TTCTG
59951362 CAACTAAGCCCACAGTTTCTG
1 CAACTAAGCCCACA-TTTCTG
59951383 CAA
1 CAA
59951386 GATCCTCCAC
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
20 4 0.12
21 26 0.79
22 3 0.09
ACGTcount: A:0.30, C:0.36, G:0.12, T:0.21
Consensus pattern (20 bp):
CAACTAAGCCCACATTTCTG
Found at i:59953402 original size:6 final size:6
Alignment explanation
Indices: 59953391--59953419 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
59953381 ACAGTAATAG
59953391 AATCAC AATCAC AATCAC AATCAC AATCA
1 AATCAC AATCAC AATCAC AATCAC AATCA
59953420 TGATCCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17
Consensus pattern (6 bp):
AATCAC
Found at i:59971733 original size:19 final size:19
Alignment explanation
Indices: 59971709--59971757 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
59971699 AAAAATTACA
59971709 AAAAAATCAAAATAAATTT
1 AAAAAATCAAAATAAATTT
* *
59971728 AAAAAATTGAAAATAATTTT
1 AAAAAA-TCAAAATAAATTT
* *
59971748 TAAAATTCAA
1 AAAAAATCAA
59971758 GTTATTCGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAAAATCAAAATAAATTT
Found at i:59980986 original size:21 final size:22
Alignment explanation
Indices: 59980953--59980995 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
59980943 AAAAAATGTC
59980953 ATATGTATCTTTT-TATTTTAA
1 ATATGTATCTTTTATATTTTAA
* *
59980974 ATATTTATTTTTTAATATTTTA
1 ATATGTATCTTTT-ATATTTTA
59980996 CTATACTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
ATATGTATCTTTTATATTTTAA
Found at i:59992008 original size:2 final size:2
Alignment explanation
Indices: 59992001--59992037 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
59991991 AACAAACTTT
59992001 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59992038 TACTTTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59993335 original size:2 final size:2
Alignment explanation
Indices: 59993324--59993362 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
59993314 AGCGGTGCAG
59993324 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59993363 CCATTCGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:59994756 original size:22 final size:24
Alignment explanation
Indices: 59994718--59994768 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
59994708 TTTAACTAAA
59994718 TTTTTAAAAATTAAATTAT-A-AT
1 TTTTTAAAAATTAAATTATCACAT
*
59994740 TTTTTAAATA-TATAATTATCACAT
1 TTTTTAAAAATTA-AATTATCACAT
59994764 TTTTT
1 TTTTT
59994769 TTTAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 15 0.60
23 1 0.04
24 7 0.28
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTTTAAAAATTAAATTATCACAT
Found at i:59994794 original size:27 final size:27
Alignment explanation
Indices: 59994739--59994800 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
59994729 TAAATTATAA
* *
59994739 TTTTTTAAATATATAATTATCACATTT
1 TTTTTTAAATAAATAATTATCACACTT
59994766 TTTTTTAAATAAATAATTATCTA-ACTT
1 TTTTTTAAATAAATAATTATC-ACACTT
59994793 TTATTTTA
1 TT-TTTTA
59994801 GTTTAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTTTTAAATAAATAATTATCACACTT
Found at i:59998092 original size:19 final size:19
Alignment explanation
Indices: 59998068--59998106 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
59998058 ATGCCTCTCC
59998068 ACCTAAATAGGAAACAAAG
1 ACCTAAATAGGAAACAAAG
59998087 ACCTAAATAGGAAACAAAG
1 ACCTAAATAGGAAACAAAG
59998106 A
1 A
59998107 AGATGTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.10
Consensus pattern (19 bp):
ACCTAAATAGGAAACAAAG
Found at i:60004447 original size:24 final size:24
Alignment explanation
Indices: 60004420--60004490 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
60004410 TAATCAAGAC
*
60004420 TAAAAAAAGTTTGACTCAAACAAA
1 TAAAAAAAGTTTAACTCAAACAAA
* * *
60004444 TAAACAAAGTTTAATTGAAACAAA
1 TAAAAAAAGTTTAACTCAAACAAA
* *
60004468 TAAACAGAGTTTAACT-AAA-AAA
1 TAAAAAAAGTTTAACTCAAACAAA
60004490 T
1 T
60004491 TATTTCTCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.10
23 3 0.07
24 34 0.83
ACGTcount: A:0.58, C:0.10, G:0.08, T:0.24
Consensus pattern (24 bp):
TAAAAAAAGTTTAACTCAAACAAA
Found at i:60008614 original size:16 final size:17
Alignment explanation
Indices: 60008593--60008624 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
60008583 TATTTTTATT
60008593 AATTTAAA-ATTTAAAA
1 AATTTAAAGATTTAAAA
60008609 AATTTAAAGATTTAAA
1 AATTTAAAGATTTAAA
60008625 TGATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
AATTTAAAGATTTAAAA
Found at i:60009091 original size:90 final size:89
Alignment explanation
Indices: 60008918--60009102 Score: 205
Period size: 90 Copynumber: 2.1 Consensus size: 89
60008908 CAAATTTAAA
* * * * * * **
60008918 AAAAAAAGTAATTAAGTTTC-T-CTTTTTTTTGCATTCATTTGGGTATTTGAACTTTCAAAATGC
1 AAAAAAAGCAATTAAG-TCCATGCTTTTTTTTGCACTCAATTGGATACTTGAACTTTCAAAAAAC
* *
60008981 ATAAAAAAAAGTCTTCAACTTTTTC
65 ATAAAAAAAAGCCCTCAACTTTTTC
* *
60009006 AAGAAAAGCAATTAAGTCCATGCTTTTATTTTGCACTCAATTGGATACTTGAATTTTCAAAAAAC
1 AAAAAAAGCAATTAAGTCCATGCTTTT-TTTTGCACTCAATTGGATACTTGAACTTTCAAAAAAC
*
60009071 AT-AAAAAAGGCCCTCAAACTTTTTC
65 ATAAAAAAAAGCCCTC-AACTTTTTC
60009096 AAAAAAA
1 AAAAAAA
60009103 AAAAAGCAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
87 2 0.03
88 15 0.19
89 15 0.19
90 47 0.59
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (89 bp):
AAAAAAAGCAATTAAGTCCATGCTTTTTTTTGCACTCAATTGGATACTTGAACTTTCAAAAAACA
TAAAAAAAAGCCCTCAACTTTTTC
Found at i:60009312 original size:8 final size:9
Alignment explanation
Indices: 60009274--60009343 Score: 63
Period size: 10 Copynumber: 7.6 Consensus size: 9
60009264 CATGTGGGAA
60009274 AAAAATTAT
1 AAAAATTAT
60009283 AAAAA--AT
1 AAAAATTAT
*
60009290 AAAAATCAAT
1 AAAAAT-TAT
60009300 AAAAATTAT
1 AAAAATTAT
60009309 AAAAATTATT
1 AAAAATTA-T
**
60009319 AAATTTTAAT
1 AAAAATT-AT
60009329 AAAAATATAT
1 AAAAAT-TAT
60009339 AAAAA
1 AAAAA
60009344 AGAACTCAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
7 7 0.14
9 15 0.30
10 26 0.52
11 2 0.04
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:60009321 original size:19 final size:19
Alignment explanation
Indices: 60009274--60009343 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
60009264 CATGTGGGAA
60009274 AAAAATTA-TAAAAA--AT
1 AAAAATTATTAAAAATTAT
* *
60009290 AAAAATCAATAAAAATTAT
1 AAAAATTATTAAAAATTAT
**
60009309 AAAAATTATTAAATTTTAAT
1 AAAAATTATTAAAAATT-AT
60009329 AAAAA-TATATAAAAA
1 AAAAATTAT-TAAAAA
60009344 AGAACTCAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
16 7 0.17
17 6 0.14
19 18 0.43
20 11 0.26
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATTATTAAAAATTAT
Found at i:60013042 original size:23 final size:24
Alignment explanation
Indices: 60013002--60013053 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
60012992 ATTTAAAATT
*
60013002 TAATTTTTGTATTTTTA-TTTTAA
1 TAATTTATGTATTTTTATTTTTAA
60013025 TAATTTAT-TATTTATTATTTTTAA
1 TAATTTATGTATTT-TTATTTTTAA
60013049 -AATTT
1 TAATTT
60013054 TAAAATTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 5 0.19
23 15 0.58
24 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TAATTTATGTATTTTTATTTTTAA
Found at i:60013379 original size:30 final size:29
Alignment explanation
Indices: 60013343--60013399 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
60013333 TTTAAATTTT
*
60013343 ATTTTTT-TCTATATTTTATATTATCTAATA
1 ATTTTTTATCTAT-TTTAATATT-TCTAATA
60013373 ATTTTTTATCTATTTTAATATTTCTAA
1 ATTTTTTATCTATTTTAATATTTCTAA
60013400 AAAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 5 0.20
30 15 0.60
31 5 0.20
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (29 bp):
ATTTTTTATCTATTTTAATATTTCTAATA
Found at i:60013715 original size:17 final size:16
Alignment explanation
Indices: 60013693--60013724 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
60013683 ATTTTGGAAA
60013693 AATAAATTATTATATAT
1 AATAAATTA-TATATAT
60013710 AATAAATTATATATA
1 AATAAATTATATATA
60013725 CTACCAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATTATATATAT
Found at i:60023578 original size:2 final size:2
Alignment explanation
Indices: 60023571--60023604 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
60023561 TGTTAGCATT
60023571 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
60023605 GTTAAGTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:60033465 original size:5 final size:5
Alignment explanation
Indices: 60033444--60033488 Score: 65
Period size: 5 Copynumber: 9.0 Consensus size: 5
60033434 TGGCTTGTTA
*
60033444 GGATT GGAATT -GATT GGATT GGATT GGATT GAATT GGATT GGATT
1 GGATT GG-ATT GGATT GGATT GGATT GGATT GGATT GGATT GGATT
60033489 TAAATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
4 3 0.08
5 30 0.83
6 3 0.08
ACGTcount: A:0.24, C:0.00, G:0.36, T:0.40
Consensus pattern (5 bp):
GGATT
Found at i:60033898 original size:17 final size:17
Alignment explanation
Indices: 60033876--60033908 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
60033866 TAAATTGGTA
*
60033876 ATTTATTTTTTTATTTC
1 ATTTATTTATTTATTTC
60033893 ATTTATTTATTTATTT
1 ATTTATTTATTTATTT
60033909 TTGGGTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTATTTATTTATTTC
Found at i:60039883 original size:24 final size:23
Alignment explanation
Indices: 60039817--60039884 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 23
60039807 TAAATTATCA
*
60039817 ATTTGGGTTTTAAATATTAATGTGT
1 ATTTGGG-TTTAAAT-TTAATGGGT
**
60039842 A-TTGAATTTAAAATTTTAATGGGT
1 ATTTGGGTTT-AAA-TTTAATGGGT
60039866 ATTTGGGTTTAAAGTTTAA
1 ATTTGGGTTTAAA-TTTAA
60039885 ATTTGGGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
23 3 0.09
24 23 0.68
25 8 0.24
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (23 bp):
ATTTGGGTTTAAATTTAATGGGT
Found at i:60041004 original size:2 final size:2
Alignment explanation
Indices: 60040991--60041036 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
60040981 CAGGTTGATC
* * *
60040991 AG AG AT AG AG AG AG AC AG GG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
60041033 AG AG
1 AG AG
60041037 CATGTTTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Found at i:60044547 original size:6 final size:6
Alignment explanation
Indices: 60044536--60044560 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
60044526 GATTTTGAAG
60044536 GGATCT GGATCT GGATCT GGATCT G
1 GGATCT GGATCT GGATCT GGATCT G
60044561 CAGAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.36, T:0.32
Consensus pattern (6 bp):
GGATCT
Found at i:60047945 original size:18 final size:19
Alignment explanation
Indices: 60047908--60047946 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
60047898 TTAAAATTTC
*
60047908 AAATATAAATTTAAATCAT
1 AAATATAAATTTAAAGCAT
*
60047927 AAATA-AAATTTCAAGCAT
1 AAATATAAATTTAAAGCAT
60047945 AA
1 AA
60047947 TATTATACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (19 bp):
AAATATAAATTTAAAGCAT
Found at i:60059431 original size:29 final size:30
Alignment explanation
Indices: 60059399--60059481 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 30
60059389 TTTACAATAA
* *
60059399 TAAAAA-TAATTTATATTTTTATAATTTTT
1 TAAAAATTAAATTAAATTTTTATAATTTTT
*
60059428 TAAAAATTAAATTAAATTTTTATTA-TTTT
1 TAAAAATTAAATTAAATTTTTATAATTTTT
* *
60059457 TAACAGAATTAAAATATATTTTTAT
1 TAA-A-AATTAAATTAAATTTTTAT
60059482 TTTTATTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 13 0.28
30 16 0.35
31 17 0.37
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (30 bp):
TAAAAATTAAATTAAATTTTTATAATTTTT
Found at i:60059449 original size:30 final size:29
Alignment explanation
Indices: 60059356--60059481 Score: 98
Period size: 29 Copynumber: 4.3 Consensus size: 29
60059346 AAGTCAAAAA
** *
60059356 ATATTTTTA-AATGATT-AAAATTATATT
1 ATATTTTTATAATTTTTAAAAATTAAATT
* ** *
60059383 ATAATTTTTACAA-TAATAAAAA-TAATTT
1 AT-ATTTTTATAATTTTTAAAAATTAAATT
60059411 ATATTTTTATAATTTTTTAAAAATTAAATT
1 ATATTTTTATAA-TTTTTAAAAATTAAATT
* * *
60059441 AAATTTTTATTATTTTTAACAGAATTAAAAT
1 ATATTTTTATAATTTTTAA-A-AATTAAATT
60059472 ATATTTTTAT
1 ATATTTTTAT
60059482 TTTTATTAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
27 11 0.14
28 15 0.19
29 20 0.25
30 16 0.20
31 17 0.22
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
ATATTTTTATAATTTTTAAAAATTAAATT
Found at i:60059478 original size:31 final size:29
Alignment explanation
Indices: 60059410--60059490 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 29
60059400 AAAAATAATT
* *
60059410 TATATTTTTATAATTTTTTAAAAATTAAAT
1 TATATTTTTATTA-TTTTTAAAAATTAAAA
*
60059440 TAAATTTTTATTATTTTTAACAGAATTAAAA
1 TATATTTTTATTATTTTTAA-A-AATTAAAA
60059471 TATATTTTTATT-TTTATTAA
1 TATATTTTTATTATTT-TTAA
60059491 TTTAAATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 7 0.16
30 15 0.34
31 22 0.50
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (29 bp):
TATATTTTTATTATTTTTAAAAATTAAAA
Found at i:60061033 original size:20 final size:20
Alignment explanation
Indices: 60060987--60061033 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
60060977 TTTATATTTT
* *
60060987 TAAAGATATATAAAAATTTA
1 TAAATATATATAAAAAATTA
*
60061007 TATATATATATTAAAAAATTA
1 TAAATATATA-TAAAAAATTA
60061028 -AAATAT
1 TAAATAT
60061034 TTCTAGAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAATATATATAAAAAATTA
Found at i:60062146 original size:20 final size:21
Alignment explanation
Indices: 60062110--60062154 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
60062100 TTAGTTTAAT
*
60062110 ATTTTTTAATAATTTTTATGA
1 ATTTTTTAATAATTTTTAAGA
60062131 ATTTTTATAA-AA-TTTTAAGA
1 ATTTTT-TAATAATTTTTAAGA
60062151 ATTT
1 ATTT
60062155 ATGTACGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 8 0.36
22 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
ATTTTTTAATAATTTTTAAGA
Found at i:60071619 original size:59 final size:59
Alignment explanation
Indices: 60071523--60071638 Score: 153
Period size: 59 Copynumber: 2.0 Consensus size: 59
60071513 TTTTGGGAGC
*
60071523 TTGGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGTCAAAAACGGAATTTTTGGAAGTT
1 TTGGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGTCAAAAACGGAATTTTTAGAAGTT
* * * * * *
60071582 TTGGTGTCAAAAATGTAA-TTTTGGAAGTTTTAGGGTCAAAAATGTAATTTTTAGAAG
1 TTGGGGTCAAAAATGGAATTTTTGGAAG-TTCAAGGTCAAAAACGGAATTTTTAGAAG
60071639 ATCGAGGGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
58 9 0.18
59 40 0.82
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.35
Consensus pattern (59 bp):
TTGGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGTCAAAAACGGAATTTTTAGAAGTT
Found at i:60071729 original size:30 final size:29
Alignment explanation
Indices: 60071499--60071731 Score: 174
Period size: 29 Copynumber: 8.1 Consensus size: 29
60071489 GGATGCCCGA
* *
60071499 GGGC-AAAATGGTAA-TTTTGGGAGCTT-G
1 GGGCAAAAAT-GTAATTTTTGGAAGTTTAG
* * *
60071526 GGGTCAAAAATGGAATTTTTGGAAGTTCAA
1 GGG-CAAAAATGTAATTTTTGGAAGTTTAG
* * * *
60071556 GGTCAAAAACGGAATTTTTGGAAGTTTTG
1 GGGCAAAAATGTAATTTTTGGAAGTTTAG
*
60071585 GTGTCAAAAATGTAA-TTTTGGAAGTTTTAG
1 G-GGCAAAAATGTAATTTTTGGAAG-TTTAG
* * * *
60071615 GGTCAAAAATGTAATTTTTAGAAG-ATCG
1 GGGCAAAAATGTAATTTTTGGAAGTTTAG
* * * * *
60071643 AGGGAAAAAATATAGTTTTTAGAAGTTTCG
1 -GGGCAAAAATGTAATTTTTGGAAGTTTAG
**
60071673 GGG--TTAATGTAATTTTTGGAAGTTTAG
1 GGGCAAAAATGTAATTTTTGGAAGTTTAG
60071700 GGGCAAAAATGTAATTTTTGGATAGTTTAG
1 GGGCAAAAATGTAATTTTTGGA-AGTTTAG
60071730 GG
1 GG
60071732 ACTTTCAGGG
Statistics
Matches: 165, Mismatches: 29, Indels: 21
0.77 0.13 0.10
Matches are distributed among these distances:
27 24 0.15
28 6 0.04
29 97 0.59
30 38 0.23
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (29 bp):
GGGCAAAAATGTAATTTTTGGAAGTTTAG
Found at i:60073851 original size:59 final size:59
Alignment explanation
Indices: 60073787--60074085 Score: 322
Period size: 59 Copynumber: 5.1 Consensus size: 59
60073777 TGGGCTCTCG
* * * *
60073787 AGGGTAAAAATGTAATTTTTGAAAGTTTTTGGGTCAAAAATGGAATTTTTGGAAGTTTC
1 AGGGTAAAAATATAATTTTTGAAAGTTTTAGGGTCAAAAATGTAATTTTTGGAAGTTTT
* * * *
60073846 GGGGTAAAAACATAATTTTGGGAAGTTTTAGGGTCAAAAATGTAATTTTTGGAAGTTTT
1 AGGGTAAAAATATAATTTTTGAAAGTTTTAGGGTCAAAAATGTAATTTTTGGAAGTTTT
* * *
60073905 AGGGTTAAAATATAATTTTTGGAAGTTTTGGGGTC-AAAATGTAA-TTTTGAAGAAGTTTT
1 AGGGTAAAAATATAATTTTTGAAAGTTTTAGGGTCAAAAATGTAATTTTTG--GAAGTTTT
* * *
60073964 AGGGT-CAAATATAATTTTTGAAAGTTTTAAGGTCAAAAATGTAATTTTAGAGAAGTTTT
1 AGGGTAAAAATATAATTTTTGAAAGTTTTAGGGTCAAAAATGTAATTTTTG-GAAGTTTT
* * * * * *
60074023 -GAGGTTAAAATGTAATATTTGAGAAGTTTAAGGGT-TAAAATATAATTTTTGGATAG-TTT
1 AG-GGTAAAAATATAATTTTTGA-AAGTTTTAGGGTCAAAAATGTAATTTTTGGA-AGTTTT
60074082 AGGG
1 AGGG
60074086 ACGTCTAAGG
Statistics
Matches: 205, Mismatches: 26, Indels: 18
0.82 0.10 0.07
Matches are distributed among these distances:
57 5 0.02
58 35 0.17
59 122 0.60
60 33 0.16
61 10 0.05
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.39
Consensus pattern (59 bp):
AGGGTAAAAATATAATTTTTGAAAGTTTTAGGGTCAAAAATGTAATTTTTGGAAGTTTT
Found at i:60073895 original size:89 final size:87
Alignment explanation
Indices: 60073787--60074073 Score: 344
Period size: 89 Copynumber: 3.2 Consensus size: 87
60073777 TGGGCTCTCG
* * *
60073787 AGGGTAAAAATGTAATTTTTGAAAGTTTTTGGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTA
1 AGGGTAAAAATATAATTTTTGAAAGTTTTAGGGTCAAAAAT-GAATTTTTGGAAGTTTTGGGGTA
** *
60073852 AAAACATAATTTTGGGAAGTTTT
65 AAAATGTAATTTTGAGAAGTTTT
* * *
60073875 AGGGTCAAAAATGTAATTTTTGGAAGTTTTAGGGTTAAAATAT-AATTTTTGGAAGTTTTGGGGT
1 AGGGT-AAAAATATAATTTTTGAAAGTTTTAGGGTCAAAA-ATGAATTTTTGGAAGTTTTGGGGT
*
60073939 CAAAATGTAATTTTGAAGAAGTTTT
64 AAAAATGTAATTTTG-AGAAGTTTT
* * * *
60073964 AGGGT-CAAATATAATTTTTGAAAGTTTTAAGGTCAAAAATGTAATTTTAGAGAAGTTTTGAGGT
1 AGGGTAAAAATATAATTTTTGAAAGTTTTAGGGTCAAAAATG-AATTTTTG-GAAGTTTTGGGGT
* *
60074028 TAAAATGTAATATTTGAGAAGTTTA
64 AAAAATGTAAT-TTTGAGAAGTTTT
*
60074053 AGGGTTAAAATATAATTTTTG
1 AGGGTAAAAATATAATTTTTG
60074074 GATAGTTTAG
Statistics
Matches: 173, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
86 2 0.01
87 28 0.16
88 44 0.25
89 79 0.46
90 20 0.12
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (87 bp):
AGGGTAAAAATATAATTTTTGAAAGTTTTAGGGTCAAAAATGAATTTTTGGAAGTTTTGGGGTAA
AAATGTAATTTTGAGAAGTTTT
Found at i:60074081 original size:30 final size:29
Alignment explanation
Indices: 60073787--60074085 Score: 273
Period size: 30 Copynumber: 10.1 Consensus size: 29
60073777 TGGGCTCTCG
* *
60073787 AGGGTAAAAATGTAATTTTTGAAAGTTTT
1 AGGGTAAAAATATAATTTTTGGAAGTTTT
* ** *
60073816 TGGGTCAAAAATGGAATTTTTGGAAGTTTC
1 AGGGT-AAAAATATAATTTTTGGAAGTTTT
* * *
60073846 GGGGTAAAAACATAATTTTGGGAAGTTTT
1 AGGGTAAAAATATAATTTTTGGAAGTTTT
*
60073875 AGGGTCAAAAATGTAATTTTTGGAAGTTTT
1 AGGGT-AAAAATATAATTTTTGGAAGTTTT
*
60073905 AGGGTTAAAATATAATTTTTGGAAGTTTT
1 AGGGTAAAAATATAATTTTTGGAAGTTTT
* * *
60073934 GGGGTCAAAATGTAA-TTTTGAAGAAGTTTT
1 AGGGTAAAAATATAATTTTTG--GAAGTTTT
* *
60073964 AGGGT-CAAATATAATTTTTGAAAGTTTT
1 AGGGTAAAAATATAATTTTTGGAAGTTTT
* * *
60073992 AAGGTCAAAAATGTAATTTTAGAGAAGTTTT
1 AGGGT-AAAAATATAATTTTTG-GAAGTTTT
* * * *
60074023 -GAGGTTAAAATGTAATATTTGAGAAGTTTA
1 AG-GGTAAAAATATAATTTTTG-GAAGTTTT
*
60074053 AGGGTTAAAATATAATTTTTGGATAG-TTT
1 AGGGTAAAAATATAATTTTTGGA-AGTTTT
60074082 AGGG
1 AGGG
60074086 ACGTCTAAGG
Statistics
Matches: 223, Mismatches: 36, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
28 16 0.07
29 76 0.34
30 120 0.54
31 11 0.05
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.39
Consensus pattern (29 bp):
AGGGTAAAAATATAATTTTTGGAAGTTTT
Found at i:60074545 original size:36 final size:36
Alignment explanation
Indices: 60074498--60074588 Score: 146
Period size: 36 Copynumber: 2.5 Consensus size: 36
60074488 GTTAAACTCT
*
60074498 AAAACGGCGTCGTTTTGAGATTAAAACTCAACCCTC
1 AAAACGGCGTCGTTTTGAGACTAAAACTCAACCCTC
* * *
60074534 AAAACGGCGTCGTTTTGGGGCTAAAACTCAGCCCTC
1 AAAACGGCGTCGTTTTGAGACTAAAACTCAACCCTC
60074570 AAAACGGCGTCGTTTTGAG
1 AAAACGGCGTCGTTTTGAG
60074589 GGCTTATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (36 bp):
AAAACGGCGTCGTTTTGAGACTAAAACTCAACCCTC
Done.