Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 110 of 208
Found at i:33270181 original size:17 final size:17
Alignment explanation
Indices: 33270161--33270215 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
33270151 AATTTTTTTA
33270161 AAAATTAAAAAAATTAT
1 AAAATTAAAAAAATTAT
* *
33270178 AAAATTATTAAAAACTAT
1 AAAATTA-AAAAAATTAT
*
33270196 AAAATTTTAAAAAATT-T
1 AAAA-TTAAAAAAATTAT
33270213 AAA
1 AAA
33270216 TTTATAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 11 0.35
18 18 0.58
19 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTAAAAAAATTAT
Found at i:33270198 original size:9 final size:9
Alignment explanation
Indices: 33270159--33270208 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
33270149 TTAATTTTTT
33270159 TAAAAATTA
1 TAAAAATTA
*
33270168 AAAAAATTA
1 TAAAAATTA
33270177 T-AAAATTA
1 TAAAAATTA
*
33270185 TTAAAAACTA
1 -TAAAAATTA
*
33270195 T-AAAATTT
1 TAAAAATTA
33270203 TAAAAA
1 TAAAAA
33270209 ATTTAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
8 13 0.39
9 14 0.42
10 6 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (9 bp):
TAAAAATTA
Found at i:33270223 original size:17 final size:17
Alignment explanation
Indices: 33270168--33270229 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
33270158 TTAAAAATTA
*
33270168 AAAAAATTATAAAATTATT
1 AAAAAATT-TAAATTTA-T
* *
33270187 AAAAACTATAAAATTT-T
1 AAAAAAT-TTAAATTTAT
33270204 AAAAAATTTAAATTTAT
1 AAAAAATTTAAATTTAT
*
33270221 AAAGAATTT
1 AAAAAATTT
33270230 GTGATATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 7 0.20
17 16 0.46
19 11 0.31
20 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AAAAAATTTAAATTTAT
Found at i:33273961 original size:20 final size:21
Alignment explanation
Indices: 33273927--33273966 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
33273917 ATAGTAGTAC
33273927 ATTATATGTTAATTATTATAT
1 ATTATATGTTAATTATTATAT
*
33273948 ATTAT-TGTTTATTATTATA
1 ATTATATGTTAATTATTATA
33273967 GTAGTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (21 bp):
ATTATATGTTAATTATTATAT
Found at i:33283704 original size:30 final size:30
Alignment explanation
Indices: 33283668--33283724 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
33283658 TGTGAATGAA
*
33283668 ACCATGACTATTGAACTAGGAAACCAACCC
1 ACCATGACTATTGAACTAGCAAACCAACCC
*
33283698 ACCATGATTATTGAACTAGCAAACCAA
1 ACCATGACTATTGAACTAGCAAACCAA
33283725 ACCAAGCCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.19
Consensus pattern (30 bp):
ACCATGACTATTGAACTAGCAAACCAACCC
Found at i:33290716 original size:30 final size:30
Alignment explanation
Indices: 33290680--33290736 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
33290670 TGTGAATGAA
** *
33290680 ACCATGATTGTTGTACCAGTAAACCAACCT
1 ACCATGATTGTTAAACCAGCAAACCAACCT
33290710 ACCATGATTGTTAAACCAGCAAACCAA
1 ACCATGATTGTTAAACCAGCAAACCAA
33290737 TCCGACCCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.23
Consensus pattern (30 bp):
ACCATGATTGTTAAACCAGCAAACCAACCT
Found at i:33295433 original size:46 final size:46
Alignment explanation
Indices: 33295348--33295440 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
33295338 AGTTTAAAAG
* * *
33295348 ACCTTGACCCACTATCAAGAATGATATGAACATTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACATTAGTATATGATGA
* *
33295394 ACCTCGACCCACTATCAAGGATGATAGGAACCTTAGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACATTAGTATATGATGA
33295440 A
1 A
33295441 TGCCACACTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAATGATAGGAACATTAGTATATGATGA
Found at i:33299399 original size:13 final size:14
Alignment explanation
Indices: 33299380--33299415 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
33299370 AAAACTAACT
33299380 TTTTTTTTCAAGAA
1 TTTTTTTTCAAGAA
*
33299394 TTTTTTTTCACGAA
1 TTTTTTTTCAAGAA
33299408 TTTTTTTT
1 TTTTTTTT
33299416 ACAACTTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (14 bp):
TTTTTTTTCAAGAA
Found at i:33299816 original size:46 final size:46
Alignment explanation
Indices: 33299746--33299839 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
33299736 GGTTTAAAAG
*
33299746 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGATATATGATGA
*
33299792 ACCTCGACCCACTATCAAGGATGATAGGAACCTTGATATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGATATATGATGA
33299838 AC
1 AC
33299840 GCTACACTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAATGATAGGAACCTTGATATATGATGA
Found at i:33301148 original size:20 final size:20
Alignment explanation
Indices: 33301091--33301159 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
33301081 TTCAACTATG
33301091 ATTAAACTTAATCACTTTAAT
1 ATTAAA-TTAATCACTTTAAT
*
33301112 ATGAAATTAA--A-TTTAAT
1 ATTAAATTAATCACTTTAAT
33301129 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAATCACTTTAAT
33301149 ATTAAATTAAT
1 ATTAAATTAAT
33301160 AAAATACTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 13 0.32
18 2 0.05
19 2 0.05
20 19 0.46
21 5 0.12
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTAAATTAATCACTTTAAT
Found at i:33301200 original size:17 final size:17
Alignment explanation
Indices: 33301106--33301203 Score: 62
Period size: 17 Copynumber: 5.8 Consensus size: 17
33301096 ACTTAATCAC
*
33301106 TTTAATATGAAATTAAA
1 TTTAATATTAAATTAAA
33301123 TTTAATATTAAGA-TAATCA
1 TTTAATATTAA-ATTAA--A
33301142 CTTTAATATTAAATT-AA
1 -TTTAATATTAAATTAAA
** *
33301159 TAAAATACT--ATTAAGA
1 TTTAATATTAAATTAA-A
* *
33301175 -TAAAAATTAAATTAAA
1 TTTAATATTAAATTAAA
33301191 TTTAATATTAAAT
1 TTTAATATTAAAT
33301204 CTATTAAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
14 3 0.05
15 6 0.10
16 8 0.13
17 29 0.47
18 1 0.02
19 3 0.05
20 12 0.19
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (17 bp):
TTTAATATTAAATTAAA
Found at i:33306320 original size:23 final size:23
Alignment explanation
Indices: 33306243--33306321 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 23
33306233 ATACAGTGAG
*
33306243 CAATGGAAATTGTCTGCTGTTTT
1 CAATGGAAATTGTCTGCTATTTT
* * * * *
33306266 CAATTCAGACAGTTTTTTGATATTGTT
1 CAA-T-GGA-AATTGTCTGCTATT-TT
33306293 GCAATGGAAATTGTCTGCTATTTT
1 -CAATGGAAATTGTCTGCTATTTT
33306317 CAATG
1 CAATG
33306322 AAACTGGAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
23 8 0.20
24 3 0.08
25 12 0.30
26 11 0.28
27 3 0.08
28 3 0.08
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (23 bp):
CAATGGAAATTGTCTGCTATTTT
Found at i:33306366 original size:22 final size:22
Alignment explanation
Indices: 33306325--33306413 Score: 69
Period size: 23 Copynumber: 4.0 Consensus size: 22
33306315 TTCAATGAAA
33306325 CTGGAAATTG--TTGCATTTGTT
1 CTGGAAATTGTTTTG-ATTTGTT
* *
33306346 -TTGATATTGTTCTTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
*
33306368 CTGGAAATTGTTTTGA-TAGTCT
1 CTGGAAATTGTTTTGATTTGT-T
*
33306390 GCTGGAACTTGTTCTTGATTTGTT
1 -CTGGAAATTGTT-TTGATTTGTT
33306414 AGTGAGTAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
20 7 0.13
21 3 0.06
22 12 0.23
23 23 0.43
24 5 0.09
25 3 0.06
ACGTcount: A:0.17, C:0.09, G:0.22, T:0.52
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:33306473 original size:22 final size:22
Alignment explanation
Indices: 33306432--33306520 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 22
33306422 GAAGATGAAA
33306432 CTGGAAATTG--TTGCATTTGTT
1 CTGGAAATTGTTTTG-ATTTGTT
* *
33306453 -TTGATATTGTTCTTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
*
33306475 CTGGAAATTGTTTTGA-TAGTCT
1 CTGGAAATTGTTTTGATTTGT-T
33306497 GCTGGAAATTGTTCTTGATTTGTT
1 -CTGGAAATTGTT-TTGATTTGTT
33306521 AGTGAGTAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
20 7 0.13
21 3 0.06
22 12 0.22
23 24 0.44
24 5 0.09
25 3 0.06
ACGTcount: A:0.18, C:0.08, G:0.22, T:0.52
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:33306509 original size:107 final size:107
Alignment explanation
Indices: 33306319--33306576 Score: 507
Period size: 107 Copynumber: 2.4 Consensus size: 107
33306309 GCTATTTTCA
33306319 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
1 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
*
33306384 TAGTCTGCTGGAACTTGTTCTTGATTTGTTAGTGAGTAGAAG
66 TAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTGAGTAGAAG
33306426 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
1 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
33306491 TAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTGAGTAGAAG
66 TAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTGAGTAGAAG
33306533 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGAT
1 ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGAT
33306577 NNNNNNNNNN
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 150 1.00
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (107 bp):
ATGAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGATTTGTTCTGGAAATTGTTTTGA
TAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTGAGTAGAAG
Found at i:33310681 original size:47 final size:47
Alignment explanation
Indices: 33310628--33310767 Score: 157
Period size: 47 Copynumber: 3.0 Consensus size: 47
33310618 TCATATAAGA
33310628 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
* ** *
33310675 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATT-AT-TAA-ATT
* *
33310719 AAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
33310766 AT
1 AT
33310768 GTATAATATT
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
43 3 0.04
44 24 0.33
45 8 0.11
46 8 0.11
47 27 0.37
48 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (47 bp):
ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
Found at i:33310725 original size:44 final size:44
Alignment explanation
Indices: 33310677--33310815 Score: 140
Period size: 44 Copynumber: 3.1 Consensus size: 44
33310667 ATTAAATTAT
33310677 ATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAA
1 ATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAA
* * ** * **
33310721 ATTTATTATCAAGAATTTTATGAAATTATATATCATT-AT-TAA-ATT
1 ATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGAAA
33310766 ATGTATAATATTAATTATTTTAAATTATATAAATTCATATAAGAAA
1 AT-T-TAATATTAATTATTTTAAATTATATAAATTCATATAAGAAA
33310812 ATTT
1 ATTT
33310816 TTATGAAATT
Statistics
Matches: 72, Mismatches: 14, Indels: 18
0.69 0.13 0.17
Matches are distributed among these distances:
43 3 0.04
44 24 0.33
45 11 0.15
46 11 0.15
47 20 0.28
48 3 0.04
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (44 bp):
ATTTAATATTAATTATTTTAAATTATATAAATTCATATAAGAAA
Found at i:33310786 original size:47 final size:45
Alignment explanation
Indices: 33310629--33310787 Score: 137
Period size: 47 Copynumber: 3.5 Consensus size: 45
33310619 CATATAAGAA
* **
33310629 TATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 TATTTAATATTAATTATTTTATGAAATTATATATCATTATTAAA-T
* *
33310675 ATATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGAA
1 -TATTTAATATTAATTATTTTATGAAATTATATATCATT-AT-TAA-AT
* * * **
33310720 AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAAT
1 TATTTAATATTAATTATTTTATGAAATTATATATCATTATTAAAT
33310765 TATGTATAATATTAATTATTTTA
1 TAT-T-TAATATTAATTATTTTA
33310788 AATTATATAA
Statistics
Matches: 86, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
43 3 0.03
44 23 0.27
45 10 0.12
46 9 0.10
47 38 0.44
48 3 0.03
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (45 bp):
TATTTAATATTAATTATTTTATGAAATTATATATCATTATTAAAT
Found at i:33310826 original size:44 final size:44
Alignment explanation
Indices: 33310613--33310922 Score: 133
Period size: 44 Copynumber: 7.1 Consensus size: 44
33310603 ATGATTTTAG
* *
33310613 TAAATTCATATAAGAATATTTATTATTAAGAATT-TTATGAAATTATA
1 TAAATTCATATAAGAAAATTTATTA-T-A-AATTATT-TTAAATTATA
* * * *
33310660 TATCATT-AT-TAA-ATTATATTTAATATTAATTATTTTAAATTATA
1 TA-AATTCATATAAGA--AAATTTATTATAAATTATTTTAAATTATA
*
33310704 TAAATTCATATAAGAAAATTTATTATCAAGAATT-TTATGAAATTATA
1 TAAATTCATATAAGAAAATTTATTAT--A-AATTATT-TTAAATTATA
* ** * *
33310751 TATCATT-AT-TAA-ATTATGTATAATATTAATTATTTTAAATTATA
1 TA-AATTCATATAAGAAAAT-T-TATTATAAATTATTTTAAATTATA
*
33310795 TAAATTCATATAAGAAAATTT-TTATGAAATTA---TATATTAT-
1 TAAATTCATATAAGAAAATTTATTAT-AAATTATTTTAAATTATA
* * *
33310835 TAAATT-ATAT-------TTAATAAT-AATTATATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATAAATTATTTTAAATTATA
* *
33310870 CAAATTCATATAAGAAAATTTATTACTAATAATTATTTTAAATTTTA
1 TAAATTCATATAAGAAAATTTATTA-T-A-AATTATTTTAAATTATA
33310917 TTAAAT
1 -TAAAT
33310923 AATATATTTT
Statistics
Matches: 196, Mismatches: 30, Indels: 73
0.66 0.10 0.24
Matches are distributed among these distances:
31 5 0.03
32 2 0.01
33 3 0.02
34 7 0.04
35 5 0.03
36 4 0.02
39 4 0.02
40 6 0.03
41 7 0.04
43 14 0.07
44 50 0.26
45 15 0.08
46 14 0.07
47 50 0.26
48 10 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (44 bp):
TAAATTCATATAAGAAAATTTATTATAAATTATTTTAAATTATA
Found at i:33310836 original size:75 final size:78
Alignment explanation
Indices: 33310736--33310890 Score: 244
Period size: 75 Copynumber: 2.0 Consensus size: 78
33310726 TTATCAAGAA
* * * *
33310736 TTTTATGAAATTATATATCATTATTAAATTATGTATAATATTAATTATTTTAAATTATATAAATT
1 TTTTATGAAATTATATATCATTATTAAATTATATATAATAATAATTATATTAAATTATACAAATT
33310801 CATATAAGAAAAT
66 CATATAAGAAAAT
*
33310814 TTTTATGAAA-T-TATAT-ATTATTAAATTATATTTAATAATAATTATATTAAATTATACAAATT
1 TTTTATGAAATTATATATCATTATTAAATTATATATAATAATAATTATATTAAATTATACAAATT
33310876 CATATAAGAAAAT
66 CATATAAGAAAAT
33310889 TT
1 TT
33310891 ATTACTAATA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
75 56 0.78
76 5 0.07
77 1 0.01
78 10 0.14
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (78 bp):
TTTTATGAAATTATATATCATTATTAAATTATATATAATAATAATTATATTAAATTATACAAATT
CATATAAGAAAAT
Found at i:33310839 original size:15 final size:15
Alignment explanation
Indices: 33310816--33310869 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
33310806 AAGAAAATTT
*
33310816 TTATGAAATTATATA
1 TTATTAAATTATATA
33310831 TTATTAAATTATAT-
1 TTATTAAATTATATA
* *
33310845 TTAAT-AATAAT-TA
1 TTATTAAATTATATA
33310858 -TATTAAATTATA
1 TTATTAAATTATA
33310870 CAAATTCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
12 4 0.13
13 10 0.32
14 4 0.13
15 13 0.42
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TTATTAAATTATATA
Found at i:33310844 original size:91 final size:91
Alignment explanation
Indices: 33310613--33310819 Score: 371
Period size: 91 Copynumber: 2.3 Consensus size: 91
33310603 ATGATTTTAG
* *
33310613 TAAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
33310678 TTTAATATTAATTATTTTAAATTATA
66 TATAATATTAATTATTTTAAATTATA
*
33310704 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATG
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
33310769 TATAATATTAATTATTTTAAATTATA
66 TATAATATTAATTATTTTAAATTATA
33310795 TAAATTCATATAAGAAAATTT-TTAT
1 TAAATTCATATAAGAAAATTTATTAT
33310820 GAAATTATAT
Statistics
Matches: 112, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
90 4 0.04
91 108 0.96
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TATAATATTAATTATTTTAAATTATA
Found at i:33310936 original size:23 final size:24
Alignment explanation
Indices: 33310888--33310934 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
33310878 TATAAGAAAA
33310888 TTTATTACTAATAATTATTTTAAAT
1 TTTATTAC-AATAATTATTTTAAAT
33310913 TTTATTA-AATAATATATTTTAA
1 TTTATTACAATAAT-TATTTTAA
33310935 TTAAAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTATTACAATAATTATTTTAAAT
Found at i:33310938 original size:75 final size:74
Alignment explanation
Indices: 33310736--33310944 Score: 219
Period size: 75 Copynumber: 2.7 Consensus size: 74
33310726 TTATCAAGAA
* * * *
33310736 TTTTATGAAATTATATATCATTATTAAATTAT-GTATAATATTAATTATTTTAAATTATATAAAT
1 TTTTAT-AAA-TA-ATAT-ATTATTAAATTATATTA-AATAATAATTATATTAAATTATACAAAT
33310800 TCATATAAGAAAAT
61 TCATATAAGAAAAT
* *
33310814 TTTTATGAAATTATATATTATTAAATTATATTTAATAATAATTATATTAAATTATACAAATTCAT
1 TTTTAT-AAATAATATATTATTAAATTATATTAAATAATAATTATATTAAATTATACAAATTCAT
33310879 ATAAGAAAAT
65 ATAAGAAAAT
* * *
33310889 TTATTACT-AATAAT-TATT-TTAAATTTTATTAAATAATATATTTTAATTAAAATATA
1 TT-TTA-TAAATAATATATTATTAAATTATATTAAATAATA-ATTAT-ATTAAATTATA
33310945 TTTAATAATA
Statistics
Matches: 115, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
73 18 0.16
74 8 0.07
75 69 0.60
76 8 0.07
77 2 0.02
78 10 0.09
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (74 bp):
TTTTATAAATAATATATTATTAAATTATATTAAATAATAATTATATTAAATTATACAAATTCATA
TAAGAAAAT
Found at i:33311184 original size:17 final size:17
Alignment explanation
Indices: 33311152--33311184 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
33311142 TTATTAAGAG
33311152 TTTTATTAAATCATATA
1 TTTTATTAAATCATATA
33311169 TTTTAATTAAAT-ATAT
1 TTTT-ATTAAATCATAT
33311185 TTAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTATTAAATCATATA
Found at i:33311225 original size:25 final size:25
Alignment explanation
Indices: 33311174--33311225 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
33311164 ATATATTTTA
*
33311174 ATTAAATATATTTAATAATAATTAT
1 ATTAAATATATTTAATAATAATCAT
* *
33311199 ATTAAATTATATTTTATAGT-ATCAT
1 ATTAAA-TATATTTAATAATAATCAT
33311224 AT
1 AT
33311226 ATTATGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (25 bp):
ATTAAATATATTTAATAATAATCAT
Found at i:33311332 original size:239 final size:239
Alignment explanation
Indices: 33310910--33311444 Score: 912
Period size: 239 Copynumber: 2.2 Consensus size: 239
33310900 AATTATTTTA
33310910 AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAATAATTATTT-AAATTATATTTT
*
33310975 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTA
65 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTA
*
33311040 AAGCATATAATTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCAT
130 AAGCATATAATTTAATTAAAATATATTTAATAATAATTATTTCAAAATATATTTTATAGTATCAT
*
33311105 ATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
195 ATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
33311150 AGTTTTATTAAATCATATATTTTAATT-AAATATATTTAATAATAATTATATTAAATTATATTTT
1 AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAATAATTAT-TTAAATTATATTTT
*
33311214 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTG
65 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTA
*** *
33311279 AATTGTATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAAATATATTTTATAGTATCA
130 AAGCATATAATTTAATTAAAATATATTTAATAATAATTAT-TTCAAAATATATTTTATAGTATCA
33311343 TATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
194 TATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
33311389 AATTTTATTAAATTATATGTTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAATAATTAT-TTAAA
33311445 ATGTGATTAA
Statistics
Matches: 278, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
239 222 0.80
240 56 0.20
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (239 bp):
AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAATAATTATTTAAATTATATTTTA
TAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
AGCATATAATTTAATTAAAATATATTTAATAATAATTATTTCAAAATATATTTTATAGTATCATA
TATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:33311418 original size:18 final size:17
Alignment explanation
Indices: 33311391--33311424 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
33311381 TTATTAAGAA
*
33311391 TTTTATTAAATTATATG
1 TTTTATTAAAATATATG
33311408 TTTTAATTAAAATATAT
1 TTTT-ATTAAAATATAT
33311425 TTAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTATTAAAATATATG
Found at i:33311446 original size:120 final size:119
Alignment explanation
Indices: 33310910--33311444 Score: 910
Period size: 120 Copynumber: 4.5 Consensus size: 119
33310900 AATTATTTTA
*
33310910 AATTTTATTAAATAATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTT-AAATTATATTTT
*
33310975 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
65 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
33311030 AATTTTATTAAAGCATATAATTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTT-AAATTATATTTT
*
33311095 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
65 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
33311150 AGTTTTATTAAATCATATATTTTAATT-AAATATATTTAATAATAATTATATTAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTAAATTATATTTT
33311214 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
65 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* ** *
33311269 AATTTTATTGAATTGTATATTTTAATTAAAATATATTTAATAATAATTATGTTAAAATATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTAAATTATATTTT
33311334 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
65 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
33311389 AATTTTATTAAATTATATGTTTTAATTAAAATATATTTAATAATAATTATGTTAAA
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTAAA
33311445 ATGTGATTAA
Statistics
Matches: 397, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
119 111 0.28
120 286 0.72
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (119 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTAAATTATATTTTA
TAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:33312638 original size:35 final size:34
Alignment explanation
Indices: 33312599--33312665 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
33312589 AAAATGGATT
* *
33312599 CAAGGGAGAATAAGAAGAAAGAGAAAA-TAGAAATC
1 CAAGGGAGAAGAA-AAAAAAGA-AAAAGTAGAAATC
33312634 CAAGGGAGAAGAAAAAAAAGAAAAAGTAGAAA
1 CAAGGGAGAAGAAAAAAAAGAAAAAGTAGAAA
33312666 ATAAAAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 4 0.14
34 13 0.45
35 12 0.41
ACGTcount: A:0.64, C:0.04, G:0.25, T:0.06
Consensus pattern (34 bp):
CAAGGGAGAAGAAAAAAAAGAAAAAGTAGAAATC
Found at i:33314059 original size:24 final size:24
Alignment explanation
Indices: 33314013--33314059 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
33314003 ATTATAATTA
* * *
33314013 TAATAAAAGAAATGAATGCAAAAT
1 TAATAAAAGAAAAGAAAGAAAAAT
*
33314037 TAATCAAAGAAAAGAAAGAAAAA
1 TAATAAAAGAAAAGAAAGAAAAA
33314060 GAAAGAAAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.68, C:0.04, G:0.13, T:0.15
Consensus pattern (24 bp):
TAATAAAAGAAAAGAAAGAAAAAT
Found at i:33314064 original size:14 final size:14
Alignment explanation
Indices: 33314042--33314077 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
33314032 AAAATTAATC
33314042 AAAGAAAAGAAAGAA
1 AAAG-AAAGAAAGAA
33314057 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
33314071 AAA-AAAG
1 AAAGAAAG
33314078 CAAGGGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 13 0.62
15 4 0.19
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:33333604 original size:43 final size:43
Alignment explanation
Indices: 33333544--33333664 Score: 170
Period size: 43 Copynumber: 2.8 Consensus size: 43
33333534 TAACTAGAAT
* * * * *
33333544 CACCGCAAAAGACCATGTTCTTTAGTGGCGTTTGTAGTAAAGG
1 CACCGCTAAAGAACATGTTCTATAGTGACGTTTGTAGTAAAAG
* *
33333587 CACCGCTAAAGATCATGTTCTGTAGTGACGTTTGTAGTAAAAG
1 CACCGCTAAAGAACATGTTCTATAGTGACGTTTGTAGTAAAAG
*
33333630 CACCGCTAAAGAACATGTTCTATAGCGACGTTTGT
1 CACCGCTAAAGAACATGTTCTATAGTGACGTTTGT
33333665 GAGAAAACGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (43 bp):
CACCGCTAAAGAACATGTTCTATAGTGACGTTTGTAGTAAAAG
Found at i:33345592 original size:19 final size:19
Alignment explanation
Indices: 33345568--33345625 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
33345558 ATGCTATGTT
33345568 TATGTTAATGTATGAGATG
1 TATGTTAATGTATGAGATG
*
33345587 TATG-T--TGCTAT--G-TT
1 TATGTTAATG-TATGAGATG
33345601 TATGTTAATGTATGAGATG
1 TATGTTAATGTATGAGATG
33345620 TATGTT
1 TATGTT
33345626 TCAAAGTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 2 0.07
16 5 0.17
17 5 0.17
18 2 0.07
19 11 0.37
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (19 bp):
TATGTTAATGTATGAGATG
Found at i:33345596 original size:33 final size:33
Alignment explanation
Indices: 33345559--33345625 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
33345549 GAATGATTTA
33345559 TGCTATGTTTATGTTAATGTATGAGATGTATGT
1 TGCTATGTTTATGTTAATGTATGAGATGTATGT
33345592 TGCTATGTTTATGTTAATGTATGAGATGTATGT
1 TGCTATGTTTATGTTAATGTATGAGATGTATGT
33345625 T
1 T
33345626 TCAAAGTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.49
Consensus pattern (33 bp):
TGCTATGTTTATGTTAATGTATGAGATGTATGT
Found at i:33349008 original size:27 final size:27
Alignment explanation
Indices: 33348978--33349092 Score: 90
Period size: 27 Copynumber: 4.3 Consensus size: 27
33348968 TTTTAAGGTG
*
33348978 AACTCTAAAAGAAAAGTCATTGTGGCA
1 AACTCTAAAAGAAAAGCCATTGTGGCA
** *
33349005 AACT-TTGAAGAAAGAGCCATTGTGGCG
1 AACTCTAAAAGAAA-AGCCATTGTGGCA
* * *
33349032 AACTC-AGAAGGAAGAGCCTTTGTGGCA
1 AACTCTA-AAAGAAAAGCCATTGTGGCA
* * * * *
33349059 AACTCTAAAGGAAGAGTCTTTGTGGAA
1 AACTCTAAAAGAAAAGCCATTGTGGCA
33349086 AACTCTA
1 AACTCTA
33349093 GATGGACTGT
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
26 7 0.10
27 60 0.83
28 5 0.07
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (27 bp):
AACTCTAAAAGAAAAGCCATTGTGGCA
Found at i:33354327 original size:19 final size:19
Alignment explanation
Indices: 33354305--33354342 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
33354295 TCATCGTCAC
*
33354305 CCACCGTAATCAAATTTGT
1 CCACCATAATCAAATTTGT
*
33354324 CCACTATAATCAAATTTGT
1 CCACCATAATCAAATTTGT
33354343 TATTGACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (19 bp):
CCACCATAATCAAATTTGT
Found at i:33354951 original size:30 final size:31
Alignment explanation
Indices: 33354905--33354967 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
33354895 GGGAGTAGGA
33354905 TGGGAGGGGAGCAAAAGTTAT-GGAGGGAAAG
1 TGGGAGGGGAGCAAAAGTTATGGGA-GGAAAG
* *
33354936 TGGGA-GGGAGTAAAAGTTTTGGGAGGAAAG
1 TGGGAGGGGAGCAAAAGTTATGGGAGGAAAG
33354966 TG
1 TG
33354968 AAGAGGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.33, C:0.02, G:0.48, T:0.17
Consensus pattern (31 bp):
TGGGAGGGGAGCAAAAGTTATGGGAGGAAAG
Found at i:33355039 original size:18 final size:18
Alignment explanation
Indices: 33355016--33355052 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
33355006 TATAGTTTGA
*
33355016 TATTCGATTTATTCAAAT
1 TATTCGAGTTATTCAAAT
*
33355034 TATTCGAGTTATTCGAAT
1 TATTCGAGTTATTCAAAT
33355052 T
1 T
33355053 CGAAAACCAA
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:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (18 bp):
TATTCGAGTTATTCAAAT
Found at i:33358185 original size:47 final size:48
Alignment explanation
Indices: 33358078--33358192 Score: 205
Period size: 48 Copynumber: 2.4 Consensus size: 48
33358068 AGAAATGAAA
*
33358078 GAAAAAGAAAACAAAATTGAAAAAGAGATTGAGAGTGAAAAAGAATGT
1 GAAAAAGAAAAGAAAATTGAAAAAGAGATTGAGAGTGAAAAAGAATGT
*
33358126 GAAAAACAAAAGAAAATTGAAAAAGAGATTGAGAGTG-AAAAGAATGT
1 GAAAAAGAAAAGAAAATTGAAAAAGAGATTGAGAGTGAAAAAGAATGT
33358173 GAAAAAGAAAAGAAAATTGA
1 GAAAAAGAAAAGAAAATTGA
33358193 TGTAAAAAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
47 29 0.45
48 35 0.55
ACGTcount: A:0.62, C:0.02, G:0.23, T:0.14
Consensus pattern (48 bp):
GAAAAAGAAAAGAAAATTGAAAAAGAGATTGAGAGTGAAAAAGAATGT
Found at i:33364546 original size:424 final size:424
Alignment explanation
Indices: 33363743--33364752 Score: 1776
Period size: 424 Copynumber: 2.4 Consensus size: 424
33363733 TAGATCAAGA
* *
33363743 TTGAATTCATCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAGT
1 TTGAATCCTTCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAGT
*
33363808 TATCATTTTGCTAGGTAAGTATATACAATATGAACATTATTTAACATTCTTTCCTTTTTGTTCTT
66 TATCATTTTGCCAGGTAAGTATATACAATATGAACATTATTTAACATTCTTTCCTTTTTGTTCTT
*
33363873 AAATTGTATAACTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAATG
131 AAATTGTATAATTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAATG
* * *
33363938 ATGAACTATATTACGAAGGAATATGAGTAAAATTACAAAAAGAAAGTGTCCTGATAAACTTAGTA
196 ATAAACTATATTACAAAGGAATATGAGTAAAATTACAAAAAGAAAGTGTCCTGATAAACTCAGTA
*
33364003 AAAGACTCAAACAATGGTTACATGTTATTTCTTGATGATTCTGAGATCCAGCATTTGTTGCAGAC
261 AAAGACTCAAACAATGGTTACATGTTATTTCATGATGATTCTGAGATCCAGCATTTGTTGCAGAC
33364068 TCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTCGATGCTGTTTTAAAGCTTTAGT
326 TCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTCGATGCTGTTTTAAAGCTTTAGT
* *
33364133 CTGGACTAGTAACCTTACATGTATATATTGCCAT
391 CTGGACTAATAACCTTACATGTATATATAGCCAT
33364167 TTGAATCCTTCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAGT
1 TTGAATCCTTCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAGT
33364232 TATCATTTTGCCAGGTAAGTATATACAATATGAACATTATTTAACATTCTTTCCTTTTTGTTCTT
66 TATCATTTTGCCAGGTAAGTATATACAATATGAACATTATTTAACATTCTTTCCTTTTTGTTCTT
33364297 AAATTGTATAATTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAAT-
131 AAATTGTATAATTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAATG
*
33364361 ACTAAACTATATTACAAAGGAATGTGAGTAAAATTA-AAAAATGAAAGTGT-CTCGATAAACTCA
196 A-TAAACTATATTACAAAGGAATATGAGTAAAATTACAAAAA-GAAAGTGTCCT-GATAAACTCA
* * *
33364424 GTAAATGACTCAAATAATGGTTACATGTTATTTCATGATGATTCTGAGATCCATCATTTGTTGC-
258 GTAAAAGACTCAAACAATGGTTACATGTTATTTCATGATGATTCTGAGATCCAGCATTTGTTGCA
* *
33364488 GAACTCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTCGATGTTGTTTTAAAGGTT
323 G-ACTCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTCGATGCTGTTTTAAAGCTT
33364553 TAGTCTGGACTAATAACCTTACATGTATATATAGCCAT
387 TAGTCTGGACTAATAACCTTACATGTATATATAGCCAT
33364591 TTGAATCCTTCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAGT
1 TTGAATCCTTCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAGT
* * *
33364656 TATCATTTTGCCAGGTAAGTATATACAATATGAACATTATTTAACTTTCTTTCCTTTATGCTCTT
66 TATCATTTTGCCAGGTAAGTATATACAATATGAACATTATTTAACATTCTTTCCTTTTTGTTCTT
*
33364721 AAATTGTATAATTGAAAATTTGGCAAGTTAGA
131 AAATTGTATAATTGAAAATTTGGTAAGTTAGA
33364753 ACTTAGTAAA
Statistics
Matches: 562, Mismatches: 20, Indels: 8
0.95 0.03 0.01
Matches are distributed among these distances:
423 9 0.02
424 553 0.98
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (424 bp):
TTGAATCCTTCAAGAGAAGATCGTGGGAAAGGAAAAGTTTTTGAGTAGACTCTATTGTGGCGAGT
TATCATTTTGCCAGGTAAGTATATACAATATGAACATTATTTAACATTCTTTCCTTTTTGTTCTT
AAATTGTATAATTGAAAATTTGGTAAGTTAGATTTGGGTTGTTAAATATATAGAGGAGAGAAATG
ATAAACTATATTACAAAGGAATATGAGTAAAATTACAAAAAGAAAGTGTCCTGATAAACTCAGTA
AAAGACTCAAACAATGGTTACATGTTATTTCATGATGATTCTGAGATCCAGCATTTGTTGCAGAC
TCAAAGATACATGTGGCACAGATTTAGCCTGGACTGGTAATTCGATGCTGTTTTAAAGCTTTAGT
CTGGACTAATAACCTTACATGTATATATAGCCAT
Found at i:33370459 original size:16 final size:15
Alignment explanation
Indices: 33370438--33370483 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
33370428 TCTCATGCAT
33370438 TGAATTGAAATTTTAA
1 TGAATTGAAA-TTTAA
*
33370454 TGAATTTAAATTTAA
1 TGAATTGAAATTTAA
*
33370469 TAAATTG-AATTTAA
1 TGAATTGAAATTTAA
33370483 T
1 T
33370484 TAATATATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 8 0.30
15 10 0.37
16 9 0.33
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (15 bp):
TGAATTGAAATTTAA
Found at i:33370968 original size:20 final size:20
Alignment explanation
Indices: 33370939--33371024 Score: 81
Period size: 20 Copynumber: 4.4 Consensus size: 20
33370929 CTTGTACGAG
*
33370939 GTTT-CACTTCGGTGCCTTT
1 GTTTGCACTTCGGTGCCTCT
*
33370958 GTTTGCACTTCGATGCCTCT
1 GTTTGCACTTCGGTGCCTCT
*
33370978 GTTTGTACGTT-GGTGCCTCT
1 GTTTGCAC-TTCGGTGCCTCT
*
33370998 GATTGCACATT--GTGCCTCT
1 GTTTGCAC-TTCGGTGCCTCT
*
33371017 ATTTGCAC
1 GTTTGCAC
33371025 CTCAGTTCTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.32
20 36 0.64
21 2 0.04
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.42
Consensus pattern (20 bp):
GTTTGCACTTCGGTGCCTCT
Found at i:33374177 original size:11 final size:12
Alignment explanation
Indices: 33374161--33374195 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
33374151 CATGCAAAAT
33374161 AAAAGAAAGAA-
1 AAAAGAAAGAAG
33374172 AAAAGAAAGAAG
1 AAAAGAAAGAAG
*
33374184 AAAAGAAGGAAG
1 AAAAGAAAGAAG
33374196 GACGCACTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAAG
Found at i:33384128 original size:24 final size:24
Alignment explanation
Indices: 33384095--33384147 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
33384085 CATCTTTTTG
*
33384095 GGCTCTTCAACAGCA-TGTTGAGTA
1 GGCTCCTCAACAGCAGT-TTGAGTA
*
33384119 GGCTCCTCAACAGCAGTTTGAGTG
1 GGCTCCTCAACAGCAGTTTGAGTA
33384143 GGCTC
1 GGCTC
33384148 TTCGGCAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (24 bp):
GGCTCCTCAACAGCAGTTTGAGTA
Found at i:33398206 original size:29 final size:29
Alignment explanation
Indices: 33398174--33398265 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
33398164 TATTAATAAA
33398174 TTCAATGATCTAAATTAAGTATTGCACTT
1 TTCAATGATCTAAATTAAGTATTGCACTT
* * * * * * **
33398203 TTCAATTAT-GAACCTCAACT-TAGTCAGGT
1 TTCAATGATCTAA-ATTAAGTATTG-CACTT
33398232 TT-AATGATCTAAATTAAGTATTGCACTT
1 TTCAATGATCTAAATTAAGTATTGCACTT
33398260 TTCAAT
1 TTCAAT
33398266 TATGTGTCTA
Statistics
Matches: 42, Mismatches: 16, Indels: 10
0.62 0.24 0.15
Matches are distributed among these distances:
28 18 0.43
29 24 0.57
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (29 bp):
TTCAATGATCTAAATTAAGTATTGCACTT
Found at i:33403264 original size:39 final size:39
Alignment explanation
Indices: 33403157--33403281 Score: 209
Period size: 38 Copynumber: 3.3 Consensus size: 39
33403147 GAATTAAGAC
* *
33403157 ACATAATTAAA-ACACATATTAATGGTGTTCAAAATAAG
1 ACATAATTAAAGTCACATATTAATGATGTTCAAAATAAG
33403195 ACATAATTAAAGTCA-ATATTAATGATGTTCAAAATAAG
1 ACATAATTAAAGTCACATATTAATGATGTTCAAAATAAG
*
33403233 ACATAATTAAAGTCACATATTAATGATGTTCAAACTAAG
1 ACATAATTAAAGTCACATATTAATGATGTTCAAAATAAG
33403272 ACATAATTAA
1 ACATAATTAA
33403282 GACTCAAACT
Statistics
Matches: 82, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
38 48 0.59
39 34 0.41
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (39 bp):
ACATAATTAAAGTCACATATTAATGATGTTCAAAATAAG
Found at i:33409290 original size:27 final size:28
Alignment explanation
Indices: 33409235--33409290 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
33409225 CTCTATAAAG
* *
33409235 TATGTGTTTAGTGAGTGGTAAGAGTTGT
1 TATGGGTTTAGTGAGTGGTAAGAGATGT
33409263 TATGGGTTT-GTGAGTGGTAA-AGGATGT
1 TATGGGTTTAGTGAGTGGTAAGA-GATGT
33409290 T
1 T
33409291 GCCAAGATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 1 0.04
27 16 0.64
28 8 0.32
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (28 bp):
TATGGGTTTAGTGAGTGGTAAGAGATGT
Found at i:33415027 original size:28 final size:28
Alignment explanation
Indices: 33414985--33415079 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 28
33414975 AAAAGAAATG
* * *
33414985 CCTTTGTGGCAATTTCTTTACGAGATAA
1 CCTTTATGGCTATTTCTTTACGAGAAAA
* * *
33415013 CCTTTATGGCTATTT-TTGA--ATGACAG
1 CCTTTATGGCTATTTCTTTACGA-GAAAA
* *
33415039 CCTTTGTGGCTATTTCCTTACGAGAAAA
1 CCTTTATGGCTATTTCTTTACGAGAAAA
33415067 CCTTTATGGCTAT
1 CCTTTATGGCTAT
33415080 ATCTGAATGG
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
25 1 0.02
26 17 0.33
27 5 0.10
28 28 0.54
29 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (28 bp):
CCTTTATGGCTATTTCTTTACGAGAAAA
Found at i:33415102 original size:26 final size:27
Alignment explanation
Indices: 33415067--33415128 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 27
33415057 TACGAGAAAA
*
33415067 CCTTTATGGCTATATCTGAATGGAAG-
1 CCTTTGTGGCTATATCTGAATGGAAGT
*
33415093 CCTTTGTGGCTATCTCTGAATGGAAGT
1 CCTTTGTGGCTATATCTGAATGGAAGT
33415120 CC-TTGTGGC
1 CCTTTGTGGC
33415129 GACCTCTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 31 0.94
27 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (27 bp):
CCTTTGTGGCTATATCTGAATGGAAGT
Found at i:33415103 original size:54 final size:54
Alignment explanation
Indices: 33414984--33415105 Score: 183
Period size: 54 Copynumber: 2.3 Consensus size: 54
33414974 TAAAAGAAAT
* * * * *
33414984 GCCTTTGTGGCAATTTCTTTACGAGATAACCTTTATGGCTATTTTTGAATGACA
1 GCCTTTGTGGCTATTTCCTTACGAGAAAACCTTTATGGCTATATCTGAATGACA
33415038 GCCTTTGTGGCTATTTCCTTACGAGAAAACCTTTATGGCTATATCTGAATGGA-A
1 GCCTTTGTGGCTATTTCCTTACGAGAAAACCTTTATGGCTATATCTGAAT-GACA
33415092 GCCTTTGTGGCTAT
1 GCCTTTGTGGCTAT
33415106 CTCTGAATGG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 60 0.97
55 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (54 bp):
GCCTTTGTGGCTATTTCCTTACGAGAAAACCTTTATGGCTATATCTGAATGACA
Found at i:33415135 original size:26 final size:26
Alignment explanation
Indices: 33415081--33415135 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
33415071 TATGGCTATA
* *
33415081 TCTGAATGGAAGCCTTTGTGGCTATC
1 TCTGAATGGAAGCCTTTGTGGCGACC
33415107 TCTGAATGGAAGTCC-TTGTGGCGACC
1 TCTGAATGGAAG-CCTTTGTGGCGACC
33415133 TCT
1 TCT
33415136 ATTAAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (26 bp):
TCTGAATGGAAGCCTTTGTGGCGACC
Found at i:33417096 original size:33 final size:32
Alignment explanation
Indices: 33417059--33417148 Score: 89
Period size: 28 Copynumber: 2.8 Consensus size: 32
33417049 AATCAGTCTA
*
33417059 GGCCTGAGCCCAATACAGTATCAGTACAGTGTG
1 GGCCTTAGCCCAATACAGTATCA-TACAGTGTG
* *
33417092 GGCCTTAGCCCATTAGAG--T-A-ACAGTGTG
1 GGCCTTAGCCCAATACAGTATCATACAGTGTG
*
33417120 GGTCTTAGCCCAATACAGTAATCAATACA
1 GGCCTTAGCCCAATACAGT-ATC-ATACA
33417149 ATGCAATGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
28 23 0.51
30 1 0.02
31 2 0.04
33 16 0.36
34 3 0.07
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (32 bp):
GGCCTTAGCCCAATACAGTATCATACAGTGTG
Found at i:33417285 original size:26 final size:26
Alignment explanation
Indices: 33417255--33417354 Score: 112
Period size: 26 Copynumber: 3.8 Consensus size: 26
33417245 CTAATATCGC
* *
33417255 AGCAAAGCTACCAGTAATAGTGATGT
1 AGCAAAGCTACCAGTAACAGTAATGT
* *
33417281 AGCAAAGCTGCCAGTAACAGTAATGC
1 AGCAAAGCTACCAGTAACAGTAATGT
* *
33417307 AGCAAACCTGCCAGTAACAGTATATGT
1 AGCAAAGCTACCAGTAACAGTA-ATGT
* *
33417334 GGCAAAGCCACCAGT-ACAGTA
1 AGCAAAGCTACCAGTAACAGTA
33417355 TACTTCCCCT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
26 49 0.78
27 14 0.22
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
AGCAAAGCTACCAGTAACAGTAATGT
Found at i:33417353 original size:52 final size:52
Alignment explanation
Indices: 33417253--33417354 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 52
33417243 CACTAATATC
* * **
33417253 GCAGCAAAGCTACCAGTAATAGTGATGTAGCAAAGCTGCCAGTAACAGTAAT
1 GCAGCAAACCTACCAGTAACAGTGATGTAGCAAAGCCACCAGTAACAGTAAT
* * *
33417305 GCAGCAAACCTGCCAGTAACAGTATATGTGGCAAAGCCACCAGT-ACAGTA
1 GCAGCAAACCTACCAGTAACAGT-GATGTAGCAAAGCCACCAGTAACAGTA
33417355 TACTTCCCCT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 26 0.62
53 16 0.38
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.18
Consensus pattern (52 bp):
GCAGCAAACCTACCAGTAACAGTGATGTAGCAAAGCCACCAGTAACAGTAAT
Found at i:33417551 original size:27 final size:27
Alignment explanation
Indices: 33417504--33417699 Score: 184
Period size: 27 Copynumber: 7.3 Consensus size: 27
33417494 GGGTATAACA
* * *
33417504 GTCATTTTATCCTAT-GGGGGTATTTCG
1 GTCATTTTACCCT-TCGAGGGTAATTCG
*
33417531 GTCATTTTACCCTTCGAGGGTAATTCA
1 GTCATTTTACCCTTCGAGGGTAATTCG
* * * *
33417558 GTTATCTTACCCTTCAAGGGTAATTCA
1 GTCATTTTACCCTTCGAGGGTAATTCG
*
33417585 GTCATTTTACCTTTCG-GGGTTAATTCG
1 GTCATTTTACCCTTCGAGGG-TAATTCG
* **
33417612 TTCATTTTA-CCTTTTAGGGGTAATTCG
1 GTCATTTTACCCTTCGA-GGGTAATTCG
*
33417639 GTCATTTTACCCTTC-AGAAGTAATTCG
1 GTCATTTTACCCTTCGAG-GGTAATTCG
**
33417666 AACATTTTACCCTTCGAGGGTAATTCG
1 GTCATTTTACCCTTCGAGGGTAATTCG
*
33417693 GTTATTT
1 GTCATTT
33417700 GCCTATGATT
Statistics
Matches: 137, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
26 8 0.06
27 120 0.88
28 9 0.07
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTTCGAGGGTAATTCG
Found at i:33417633 original size:81 final size:80
Alignment explanation
Indices: 33417502--33417699 Score: 204
Period size: 81 Copynumber: 2.4 Consensus size: 80
33417492 AGGGGTATAA
* * * * *
33417502 CAGTCATTTTATCCTATGGGGGTATTTCGGTCATTTTACCCTTCGAGGGTAATTCAGTTATCTTA
1 CAGTCATTTTA-CCTTTCGGGGTAATTCGGTCATTTTACCCTTAGAGGGTAATTCAGTCATCTTA
*
33417567 CCCTTCA-AGGGTAATT
65 CCCTTCAGA-AGTAATT
* * * *
33417583 CAGTCATTTTACCTTTCGGGGTTAATTCGTTCATTTTACCTTTTAG-GGGTAATTCGGTCATTTT
1 CAGTCATTTTACCTTTCGGGG-TAATTCGGTCATTTTACC-CTTAGAGGGTAATTCAGTCATCTT
33417647 ACCCTTCAGAAGTAATT
64 ACCCTTCAGAAGTAATT
* * *
33417664 C-GAACATTTTACCCTTCGAGGGTAATTCGGTTATTT
1 CAG-TCATTTTACCTTTCG-GGGTAATTCGGTCATTT
33417700 GCCTATGATT
Statistics
Matches: 98, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
80 9 0.09
81 82 0.84
82 7 0.07
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (80 bp):
CAGTCATTTTACCTTTCGGGGTAATTCGGTCATTTTACCCTTAGAGGGTAATTCAGTCATCTTAC
CCTTCAGAAGTAATT
Found at i:33418491 original size:9 final size:9
Alignment explanation
Indices: 33418479--33418505 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
33418469 AAAGTAGGAG
33418479 TACGACACC
1 TACGACACC
33418488 TACGACACC
1 TACGACACC
33418497 TACGACACC
1 TACGACACC
33418506 CACACAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.44, G:0.11, T:0.11
Consensus pattern (9 bp):
TACGACACC
Found at i:33423275 original size:28 final size:28
Alignment explanation
Indices: 33423236--33423296 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
33423226 TATACAGTAT
** * *
33423236 CAGT-ACAGTGTGGGCCTTAGCCCATTA
1 CAGTAACAGTGTGAACCTTAACCCAATA
33423263 CAGTAACAGTGTGAACCTTAACCCAATA
1 CAGTAACAGTGTGAACCTTAACCCAATA
33423291 CAGTAA
1 CAGTAA
33423297 TCAATACAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (28 bp):
CAGTAACAGTGTGAACCTTAACCCAATA
Found at i:33423437 original size:26 final size:26
Alignment explanation
Indices: 33423408--33423482 Score: 123
Period size: 26 Copynumber: 2.9 Consensus size: 26
33423398 CACCAAATCA
33423408 CAGCAAAGCTGCCAGTAATAGTGATG
1 CAGCAAAGCTGCCAGTAATAGTGATG
*
33423434 CAGCAAAGCTGCCAGTAATAGTAATG
1 CAGCAAAGCTGCCAGTAATAGTGATG
* *
33423460 CAGCAAAACTGCCAGTAACAGTG
1 CAGCAAAGCTGCCAGTAATAGTG
33423483 TATGTGGCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.17
Consensus pattern (26 bp):
CAGCAAAGCTGCCAGTAATAGTGATG
Found at i:33424402 original size:15 final size:14
Alignment explanation
Indices: 33424365--33424402 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
33424355 GTTCGACACC
*
33424365 AAAAGAAAAAGGAG
1 AAAACAAAAAGGAG
33424379 AAAACAAAAAGGAG
1 AAAACAAAAAGGAG
33424393 AAAACAAAAA
1 AAAACAAAAA
33424403 TGTTCACCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAACAAAAAGGAG
Found at i:33431706 original size:30 final size:30
Alignment explanation
Indices: 33431672--33431734 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
33431662 ACTTAACAAG
33431672 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
33431702 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
33431732 CAA
1 CAA
33431735 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:33434554 original size:56 final size:51
Alignment explanation
Indices: 33434288--33434584 Score: 282
Period size: 50 Copynumber: 5.8 Consensus size: 51
33434278 AATAATAACA
* * ** ** *
33434288 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATGT-TTTATATAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCT-CGG
* * * * ** *
33434337 TACCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTC-ATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCGG
* * * **
33434387 TTCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTC-ATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCGG
* *
33434437 TGTCAATGCCATGTCCCAGACATGGTCTTACATAGGACCTCTCG-TCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCGG
*
33434487 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--GATCTC--GG
* *
33434542 ATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
33434585 TTACCAAAAT
Statistics
Matches: 205, Mismatches: 33, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
48 1 0.00
49 36 0.18
50 122 0.60
52 1 0.00
53 4 0.02
55 2 0.01
56 39 0.19
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCGG
Found at i:33437385 original size:30 final size:31
Alignment explanation
Indices: 33437349--33437433 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 31
33437339 AAAATGATAA
*
33437349 AATAAAAATA-AATAAAAATTATTAAATTTT
1 AATAAAAATATAATAAAAATTATAAAATTTT
* *
33437379 AATAAAAA-ATATTAAAAATTGTAAAATTTT
1 AATAAAAATATAATAAAAATTATAAAATTTT
*
33437409 -ATAAAAAT-T-GTAAAAATATATAAAA
1 AATAAAAATATAATAAAAAT-TATAAAA
33437434 CATATAGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 7 0.15
29 15 0.32
30 25 0.53
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (31 bp):
AATAAAAATATAATAAAAATTATAAAATTTT
Found at i:33437403 original size:19 final size:19
Alignment explanation
Indices: 33437383--33437433 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
33437373 AATTTTAATA
33437383 AAAAATAT-TAAAAATTGT
1 AAAAATATATAAAAATTGT
* *
33437401 AAAATTTTATAAAAATTGT
1 AAAAATATATAAAAATTGT
33437420 AAAAATATATAAAA
1 AAAAATATATAAAA
33437434 CATATAGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAAATATATAAAAATTGT
Found at i:33437432 original size:10 final size:10
Alignment explanation
Indices: 33437350--33437495 Score: 54
Period size: 10 Copynumber: 14.7 Consensus size: 10
33437340 AAATGATAAA
*
33437350 ATAAAAATAA
1 ATAAAAATAT
33437360 ATAAAAAT-T
1 ATAAAAATAT
* * *
33437369 ATTAAATTTT
1 ATAAAAATAT
33437379 AATAAAAA-AT
1 -ATAAAAATAT
33437389 ATTAAAAAT-T
1 A-TAAAAATAT
* * *
33437399 GTAAAATTTT
1 ATAAAAATAT
33437409 ATAAAAAT-T
1 ATAAAAATAT
*
33437418 GTAAAAATAT
1 ATAAAAATAT
*
33437428 AT-AAAACAT
1 ATAAAAATAT
*
33437437 ATAGAAATAT
1 ATAAAAATAT
* *
33437447 AGGAGAAAAAATT
1 A-TA-AAAATA-T
*
33437460 ATAAAAAAAT
1 ATAAAAATAT
*
33437470 GTAAAGAA-AT
1 ATAAA-AATAT
*
33437480 AT-AAAATTT
1 ATAAAAATAT
33437489 ATAAAAA
1 ATAAAAA
33437496 AAACTATAAA
Statistics
Matches: 101, Mismatches: 22, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
8 2 0.02
9 34 0.34
10 44 0.44
11 14 0.14
12 5 0.05
13 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:33437547 original size:11 final size:11
Alignment explanation
Indices: 33437531--33437572 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
33437521 AGAAGCATTT
33437531 TATAATTTTTC
1 TATAATTTTTC
33437542 TATAATTTTTC
1 TATAATTTTTC
* *
33437553 TATAACTTTTA
1 TATAATTTTTC
33437564 T-TAATTTTT
1 TATAATTTTT
33437573 ATTTTTTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 7 0.25
11 21 0.75
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (11 bp):
TATAATTTTTC
Found at i:33437714 original size:20 final size:20
Alignment explanation
Indices: 33437680--33437774 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 20
33437670 TTAAAGGGCC
33437680 TTTTTTATGCA-TTTTATAAT
1 TTTTTTATG-ATTTTTATAAT
*
33437700 TTTTTTATGATTTTTTTTAA-
1 TTTTTTATGA-TTTTTATAAT
** **
33437720 AATTTTACAATTTTTATAAT
1 TTTTTTATGATTTTTATAAT
* *
33437740 ATTTTTACGATTTTTAT-AT
1 TTTTTTATGATTTTTATAAT
* *
33437759 TTTTTTCTAATTTTTA
1 TTTTTTATGATTTTTA
33437775 GTAAAATTTA
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
19 23 0.38
20 30 0.50
21 7 0.12
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.66
Consensus pattern (20 bp):
TTTTTTATGATTTTTATAAT
Found at i:33437792 original size:28 final size:28
Alignment explanation
Indices: 33437761--33437831 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
33437751 TTTTATATTT
*
33437761 TTTTCTAATTTTTAGTAAAATTTAA-ATA
1 TTTT-TAATTTTTAGTAAAATTTAATAAA
*
33437789 TTTTTACATTTTTATTAAAATTTAATAAA
1 TTTTTA-ATTTTTAGTAAAATTTAATAAA
*
33437818 TTTTATAACTTTTA
1 TTTT-TAATTTTTA
33437832 TATATTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.05
28 21 0.57
29 12 0.32
30 2 0.05
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (28 bp):
TTTTTAATTTTTAGTAAAATTTAATAAA
Found at i:33437855 original size:9 final size:9
Alignment explanation
Indices: 33437713--33437856 Score: 66
Period size: 9 Copynumber: 15.6 Consensus size: 9
33437703 TTTATGATTT
33437713 TTTTTA-AA
1 TTTTTATAA
* *
33437721 ATTTTACAA
1 TTTTTATAA
33437730 TTTTTATAA
1 TTTTTATAA
33437739 TATTTT-TACGA
1 T-TTTTATA--A
*
33437750 TTTTTATATT
1 TTTTTATA-A
*
33437760 TTTTTCTAA
1 TTTTTATAA
33437769 TTTTTAGTAA
1 TTTTTA-TAA
**
33437779 AATTTA-AA
1 TTTTTATAA
33437787 TATTTT-TACA
1 T-TTTTATA-A
33437797 TTTTTATTAAA
1 TTTTTA-T-AA
* *
33437808 ATTTAATAA
1 TTTTTATAA
*
33437817 ATTTTATAA
1 TTTTTATAA
*
33437826 CTTTTATATA
1 TTTTTATA-A
33437836 TTTTTAT--
1 TTTTTATAA
33437843 TTTTTATAA
1 TTTTTATAA
33437852 TTTTT
1 TTTTT
33437857 TTCTACATGT
Statistics
Matches: 104, Mismatches: 17, Indels: 29
0.69 0.11 0.19
Matches are distributed among these distances:
7 7 0.07
8 7 0.07
9 47 0.45
10 32 0.31
11 10 0.10
12 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:33438182 original size:88 final size:88
Alignment explanation
Indices: 33437969--33438237 Score: 339
Period size: 91 Copynumber: 3.0 Consensus size: 88
33437959 GCCTTTTTGA
* * * * *
33437969 TGATGCATTTGACAA-TTCAAGTACCCAATTGAGTG-AGAAAAAAGTAGGGGCTTAATTGTTTTT
1 TGATGCATTTTAAAAGTTCAAGTACCCAATTGAGTGCA-AAAAAAGCAAGGGCTTAATTG---CT
*
33438032 TCTTTTTGAAAAAGTTTGAAGG-CTTTT
62 T-TTTTTGAAAAAGTTTGAGGGTCTTTT
* * * *
33438059 TGATGCATTTTGATAGTTCAAGTACCCAATTGAGTGCAAAAAAGGCAAGGACTTAATTGCTTTTT
1 TGATGCATTTTAAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAGCAAGGGCTTAATTGCTTTTT
33438124 TTGAAAAAGTTTGAGGGTCTTTT
66 TTGAAAAAGTTTGAGGGTCTTTT
33438147 TGATGCATTTTAAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAAAAGCAAGGGCTTAATTGCTT
1 TGATGCATTTTAAAAGTTCAAGTACCCAATTGAGTGC---AAAAAAAGCAAGGGCTTAATTGCTT
*
33438212 TTTTTGAAAAATTTTGAGGGT-TTTT
63 TTTTTGAAAAAGTTTGAGGGTCTTTT
33438237 T
1 T
33438238 ACATACTTAA
Statistics
Matches: 158, Mismatches: 15, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
87 19 0.12
88 42 0.27
90 16 0.10
91 80 0.51
92 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.37
Consensus pattern (88 bp):
TGATGCATTTTAAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAGCAAGGGCTTAATTGCTTTTT
TTGAAAAAGTTTGAGGGTCTTTT
Found at i:33438663 original size:2 final size:2
Alignment explanation
Indices: 33438656--33438687 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33438646 ATATTATGAA
33438656 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
33438688 TCAATGGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33442398 original size:18 final size:17
Alignment explanation
Indices: 33442375--33442408 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
33442365 CAATAGATTA
33442375 ACTTAATGGTTTACATTG
1 ACTTAATGGTTT-CATTG
33442393 ACTTAATGGTTTCATT
1 ACTTAATGGTTTCATT
33442409 ATCAATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (17 bp):
ACTTAATGGTTTCATTG
Found at i:33451886 original size:15 final size:15
Alignment explanation
Indices: 33451866--33451910 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
33451856 AAACTGAAAA
33451866 TAGAAAACAAAAATT
1 TAGAAAACAAAAATT
*
33451881 TAGAAAACAACAATT
1 TAGAAAACAAAAATT
*
33451896 TAGAAAAGAAAAATT
1 TAGAAAACAAAAATT
33451911 GGAGAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.64, C:0.07, G:0.09, T:0.20
Consensus pattern (15 bp):
TAGAAAACAAAAATT
Found at i:33453723 original size:80 final size:80
Alignment explanation
Indices: 33453568--33453759 Score: 232
Period size: 80 Copynumber: 2.4 Consensus size: 80
33453558 AATTTTTGTC
* *
33453568 TAAAACTCAAATACCATTATTTATTTCACTGACGCGGTGAAGCAACTATTTAAGTTTCCTTTATT
1 TAAAACTCAAATACCATTATTTACTTCACTGAAGCGGTGAAGCAACTATTTAAGTTTCCTTTATT
33453633 TATTTATTTTTAT-TT
66 TATTTATTTTT-TCTT
* * * * * * *
33453648 TAAAACTCAAACATCGTTATTTACTTCACTGAAGCGGTGCAGCTAACTTTTTAAGTTTCTTTTGC
1 TAAAACTCAAATACCATTATTTACTTCACTGAAGCGGTGAAGC-AACTATTTAAGTTTCCTTT-A
33453713 TTT-TTT-TTTTTTCTT
64 TTTATTTATTTTTTCTT
*
33453728 T--AACTCAAATACCATTATTTCCTTCACTGAAG
1 TAAAACTCAAATACCATTATTTACTTCACTGAAG
33453760 TAGCGAAACT
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
78 27 0.28
79 1 0.01
80 45 0.47
81 20 0.21
82 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (80 bp):
TAAAACTCAAATACCATTATTTACTTCACTGAAGCGGTGAAGCAACTATTTAAGTTTCCTTTATT
TATTTATTTTTTCTT
Found at i:33454540 original size:2 final size:2
Alignment explanation
Indices: 33454533--33454560 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33454523 GCATCCAAGG
33454533 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
33454561 ATATCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:33457171 original size:21 final size:21
Alignment explanation
Indices: 33457133--33457173 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
33457123 ATTTTTCAAT
*
33457133 AAAAATACATAAAAATATTTA
1 AAAAATAAATAAAAATATTTA
* *
33457154 AAAAATAAATTAATATATTT
1 AAAAATAAATAAAAATATTT
33457174 TTAGCATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAATAAATAAAAATATTTA
Found at i:33462530 original size:12 final size:12
Alignment explanation
Indices: 33462505--33462543 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
33462495 ACTCGCGTCT
* *
33462505 TTACTTACTCAC
1 TTACTTGCTTAC
*
33462517 TTACTTGTTTAC
1 TTACTTGCTTAC
33462529 TTACTTGCTTAC
1 TTACTTGCTTAC
33462541 TTA
1 TTA
33462544 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:33462860 original size:50 final size:50
Alignment explanation
Indices: 33462792--33462988 Score: 236
Period size: 50 Copynumber: 4.0 Consensus size: 50
33462782 TATTCTGTAC
* * * * ** * *
33462792 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * **
33462842 TGCCCATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
33462892 TGCCAACGCCATGTCCCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
33462942 TGCCAACGTCATGTCCCAGA-ATGGTCTTACATGGGG-GCTCTCATCTC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACA-GGGGACCTCTCATCTC
33462989 AATGATGTTA
Statistics
Matches: 128, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
49 21 0.16
50 107 0.84
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:33466003 original size:43 final size:43
Alignment explanation
Indices: 33465950--33466224 Score: 363
Period size: 43 Copynumber: 6.4 Consensus size: 43
33465940 TTATGTGAAA
* *
33465950 GCTTTTATCACAAACGCTGCTAAAGATCATGGCCTTTAGCGGC
1 GCTTTTATCACAAACGCCGCTAAAGATCATGACCTTTAGCGGC
*
33465993 GCTTCTATCACAAACGCCGCTAAAGATCATGACCTTTAGCGGC
1 GCTTTTATCACAAACGCCGCTAAAGATCATGACCTTTAGCGGC
* * **
33466036 GCTTCTATTACAAACGCCGCTAAAGATCATGACCTTTAATGGC
1 GCTTTTATCACAAACGCCGCTAAAGATCATGACCTTTAGCGGC
* * *
33466079 GCTTTTGTCACAAATGCCGCTAAATG-TCATGACCTTTAGCGAC
1 GCTTTTATCACAAACGCCGCTAAA-GATCATGACCTTTAGCGGC
* * * * *
33466122 GCTTTTGTCAAAAACGCCACTAAAAAACATGACCTTTAGCGGC
1 GCTTTTATCACAAACGCCGCTAAAGATCATGACCTTTAGCGGC
* * *
33466165 ACTTTTATCACAAACGCCGCTAAAAAACATGACCTTTAGCGGC
1 GCTTTTATCACAAACGCCGCTAAAGATCATGACCTTTAGCGGC
33466208 GCTTTTTATCACAAACG
1 GC-TTTTATCACAAACG
33466225 GCACTATAAA
Statistics
Matches: 205, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
43 190 0.93
44 15 0.07
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (43 bp):
GCTTTTATCACAAACGCCGCTAAAGATCATGACCTTTAGCGGC
Found at i:33466243 original size:43 final size:43
Alignment explanation
Indices: 33465951--33466287 Score: 291
Period size: 43 Copynumber: 7.9 Consensus size: 43
33465941 TATGTGAAAG
** * * * *
33465951 CTTTTATCACAAACGCTGCTAAAGATCATGGCCTTTAGCGGCG
1 CTTTTATCACAAACGCCACTAAAAAACATGACCTTTAGCGGCA
* * * * *
33465994 CTTCTATCACAAACGCCGCTAAAGATCATGACCTTTAGCGGCG
1 CTTTTATCACAAACGCCACTAAAAAACATGACCTTTAGCGGCA
* * * * * ** *
33466037 CTTCTATTACAAACGCCGCTAAAGATCATGACCTTTAATGGCG
1 CTTTTATCACAAACGCCACTAAAAAACATGACCTTTAGCGGCA
* * * *** * *
33466080 CTTTTGTCACAAATGCCGCTAAATGTCATGACCTTTAGCGACG
1 CTTTTATCACAAACGCCACTAAAAAACATGACCTTTAGCGGCA
* *
33466123 CTTTTGTCAAAAACGCCACTAAAAAACATGACCTTTAGCGGCA
1 CTTTTATCACAAACGCCACTAAAAAACATGACCTTTAGCGGCA
* *
33466166 CTTTTATCACAAACGCCGCTAAAAAACATGACCTTTAGCGGCG
1 CTTTTATCACAAACGCCACTAAAAAACATGACCTTTAGCGGCA
* * *
33466209 CTTTTTATCACAAACGGCACTATAAAACA-AACCTTTAGCGGCA
1 C-TTTTATCACAAACGCCACTAAAAAACATGACCTTTAGCGGCA
** * * * *
33466252 CTTTTCGCAAAAACACCGCT-AAAAACATAACCTTTA
1 CTTTTATCACAAACGCCACTAAAAAACATGACCTTTA
33466288 AAAAATATAT
Statistics
Matches: 253, Mismatches: 39, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
41 6 0.02
42 21 0.08
43 202 0.80
44 24 0.09
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (43 bp):
CTTTTATCACAAACGCCACTAAAAAACATGACCTTTAGCGGCA
Found at i:33466243 original size:86 final size:85
Alignment explanation
Indices: 33465950--33466287 Score: 347
Period size: 86 Copynumber: 3.9 Consensus size: 85
33465940 TTATGTGAAA
** * * * *
33465950 GCTTTTATCACAAACGCTGCTAAAGATCATGGCCTTTAGCGGCGCTTCTATCACAAACGCCGCTA
1 GCTTTTATCACAAACGCCACTAAA-AACATGACCTTTAGCGGCACTTTTATCACAAACGCCGCTA
* *
33466015 AAGATCATGACCTTTAGCGGC
65 AAAAACATGACCTTTAGCGGC
* * * * ** * * *
33466036 GCTTCTATTACAAACGCCGCTAAAGATCATGACCTTTAATGGCGCTTTTGTCACAAATGCCGCTA
1 GCTTTTATCACAAACGCCACTAAA-AACATGACCTTTAGCGGCACTTTTATCACAAACGCCGCTA
*** *
33466101 AATGTCATGACCTTTAGCGAC
65 AAAAACATGACCTTTAGCGGC
* *
33466122 GCTTTTGTCAAAAACGCCACTAAAAAACATGACCTTTAGCGGCACTTTTATCACAAACGCCGCTA
1 GCTTTTATCACAAACGCCACT-AAAAACATGACCTTTAGCGGCACTTTTATCACAAACGCCGCTA
33466187 AAAAACATGACCTTTAGCGGC
65 AAAAACATGACCTTTAGCGGC
* * ** * *
33466208 GCTTTTTATCACAAACGGCACTATAAAACA-AACCTTTAGCGGCACTTTTCGCAAAAACACCGCT
1 GC-TTTTATCACAAACGCCACTA-AAAACATGACCTTTAGCGGCACTTTTATCACAAACGCCGCT
*
33466272 -AAAAACATAACCTTTA
64 AAAAAACATGACCTTTA
33466288 AAAAATATAT
Statistics
Matches: 213, Mismatches: 36, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
85 15 0.07
86 173 0.81
87 25 0.12
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (85 bp):
GCTTTTATCACAAACGCCACTAAAAACATGACCTTTAGCGGCACTTTTATCACAAACGCCGCTAA
AAAACATGACCTTTAGCGGC
Found at i:33466243 original size:129 final size:129
Alignment explanation
Indices: 33465950--33466287 Score: 351
Period size: 129 Copynumber: 2.6 Consensus size: 129
33465940 TTATGTGAAA
** * * ** * * *
33465950 GCTTTTATCACAAACGCTGCTAAAGATCATGGCCTTTAGCGGCGCTTCTATCACAAACGCCGCTA
1 GCTTTTATCACAAACGCCACTAAATAACATAACCTTTAGCGGCGCTTTTGTCAAAAACGCCGCTA
* * * * * * *
33466015 AAGATCATGACCTTTAGCGGCGCTTCTATTACAAACGCCGCTAAAGATCATGACCTTTAATGGC
66 AAAAACATGACCTTTAGCGGCACTTCTATCACAAACGCCGCTAAAAAACATGACCTTTAACGGC
* * * ** * * *
33466079 GCTTTTGTCACAAATGCCGCTAAATGTCATGACCTTTAGCGACGCTTTTGTCAAAAACGCCACTA
1 GCTTTTATCACAAACGCCACTAAATAACATAACCTTTAGCGGCGCTTTTGTCAAAAACGCCGCTA
* *
33466144 AAAAACATGACCTTTAGCGGCACTTTTATCACAAACGCCGCTAAAAAACATGACCTTTAGCGGC
66 AAAAACATGACCTTTAGCGGCACTTCTATCACAAACGCCGCTAAAAAACATGACCTTTAACGGC
* * *
33466208 GCTTTTTATCACAAACGGCACTATAA-AACA-AACCTTTAGCGGCACTTTTCG-CAAAAACACCG
1 GC-TTTTATCACAAACGCCACTA-AATAACATAACCTTTAGCGGCGCTTTT-GTCAAAAACGCCG
*
33466270 CT-AAAAACATAACCTTTA
63 CTAAAAAACATGACCTTTA
33466288 AAAAATATAT
Statistics
Matches: 174, Mismatches: 32, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
128 15 0.09
129 138 0.79
130 19 0.11
131 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (129 bp):
GCTTTTATCACAAACGCCACTAAATAACATAACCTTTAGCGGCGCTTTTGTCAAAAACGCCGCTA
AAAAACATGACCTTTAGCGGCACTTCTATCACAAACGCCGCTAAAAAACATGACCTTTAACGGC
Found at i:33467311 original size:15 final size:15
Alignment explanation
Indices: 33467291--33467321 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33467281 ACTATCTTAA
*
33467291 GGTTTATGGATTATG
1 GGTTTAGGGATTATG
33467306 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
33467321 G
1 G
33467322 TTATGGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.39, T:0.42
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:33467381 original size:7 final size:7
Alignment explanation
Indices: 33467291--33467411 Score: 59
Period size: 7 Copynumber: 17.0 Consensus size: 7
33467281 ACTATCTTAA
*
33467291 GGTTTAT
1 GGTTTAG
*
33467298 GGATTATG
1 GGTTTA-G
33467306 GGTTTAG
1 GGTTTAG
* *
33467313 GGATTAT
1 GGTTTAG
*
33467320 GG-TTAT
1 GGTTTAG
33467326 GGTTTAAG
1 GGTTT-AG
*
33467334 GG-TTGG
1 GGTTTAG
*
33467340 GGTTTAA
1 GGTTTAG
*
33467347 GATTTAAG
1 GGTTT-AG
33467355 GG-TTAG
1 GGTTTAG
*
33467361 GAGTTTAT
1 G-GTTTAG
*
33467369 GATTTAG
1 GGTTTAG
33467376 GGTTTAG
1 GGTTTAG
*
33467383 GGATTAGG
1 GGTTTA-G
* *
33467391 GGTTAAA
1 GGTTTAG
33467398 GGTTTAG
1 GGTTTAG
33467405 GGTTTAG
1 GGTTTAG
33467412 ATTAATTAGT
Statistics
Matches: 84, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
6 12 0.14
7 53 0.63
8 19 0.23
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:33467381 original size:29 final size:30
Alignment explanation
Indices: 33467349--33467410 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
33467339 GGGTTTAAGA
* *
33467349 TTTAAGGG-TTAGGAGTTTATGATTTAGGG
1 TTTAAGGGATTAGGAGTTAAAGATTTAGGG
* *
33467378 TTT-AGGGATTAGGGGTTAAAGGTTTAGGG
1 TTTAAGGGATTAGGAGTTAAAGATTTAGGG
33467407 TTTA
1 TTTA
33467411 GATTAATTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.40
Consensus pattern (30 bp):
TTTAAGGGATTAGGAGTTAAAGATTTAGGG
Found at i:33467383 original size:22 final size:22
Alignment explanation
Indices: 33467328--33467379 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
33467318 ATGGTTATGG
*
33467328 TTTAAGGGTT-GGGGTTTAAGA
1 TTTAAGGGTTAGGAGTTTAAGA
*
33467349 TTTAAGGGTTAGGAGTTTATGA
1 TTTAAGGGTTAGGAGTTTAAGA
33467371 TTT-AGGGTT
1 TTTAAGGGTT
33467380 TAGGGATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.23, C:0.00, G:0.35, T:0.42
Consensus pattern (22 bp):
TTTAAGGGTTAGGAGTTTAAGA
Found at i:33467389 original size:14 final size:14
Alignment explanation
Indices: 33467291--33467411 Score: 52
Period size: 15 Copynumber: 8.5 Consensus size: 14
33467281 ACTATCTTAA
*
33467291 GGTTTATGGATTATG
1 GGTTTAGGGATTA-G
*
33467306 GGTTTAGGGATTAT
1 GGTTTAGGGATTAG
* *
33467320 GG-TTATGGTTTAAG
1 GGTTTAGGGATT-AG
* * *
33467334 GG-TTGGGGTTTAA
1 GGTTTAGGGATTAG
*
33467347 GATTTAAGGG-TTAG
1 GGTTT-AGGGATTAG
*
33467361 GAGTTTA-TGATTTAG
1 G-GTTTAGGGA-TTAG
33467376 GGTTTAGGGATTAGG
1 GGTTTAGGGATTA-G
* * *
33467391 GGTTAAAGGTTTAG
1 GGTTTAGGGATTAG
33467405 GGTTTAG
1 GGTTTAG
33467412 ATTAATTAGT
Statistics
Matches: 79, Mismatches: 19, Indels: 17
0.69 0.17 0.15
Matches are distributed among these distances:
13 10 0.13
14 33 0.42
15 36 0.46
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.40
Consensus pattern (14 bp):
GGTTTAGGGATTAG
Found at i:33469172 original size:37 final size:37
Alignment explanation
Indices: 33469121--33469212 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
33469111 AGTGTCGAGG
* * *
33469121 CGTGTTATTAGTTGGATTAACTCTTATGAGCATTTGA
1 CGTGTTATTGGTTGGATTAACTCTCATGAGAATTTGA
* * *
33469158 CGTGTTATCGGTTGGATTAGCTCTCATGAGAATTTGG
1 CGTGTTATTGGTTGGATTAACTCTCATGAGAATTTGA
*
33469195 TGTGTT-TTGGTTGGATTA
1 CGTGTTATTGGTTGGATTA
33469213 CTTATGTACT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 11 0.23
37 36 0.77
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (37 bp):
CGTGTTATTGGTTGGATTAACTCTCATGAGAATTTGA
Found at i:33469832 original size:20 final size:20
Alignment explanation
Indices: 33469796--33469833 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33469786 ATGTTATAAT
*
33469796 AATAAATAAAATTAAAGTAA
1 AATAAATAAAATGAAAGTAA
33469816 AATAAATGAAAA-GAAAGT
1 AATAAAT-AAAATGAAAGT
33469834 GGGAAAGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (20 bp):
AATAAATAAAATGAAAGTAA
Found at i:33469881 original size:13 final size:13
Alignment explanation
Indices: 33469863--33469900 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
33469853 CAAGCAAAAT
33469863 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
33469876 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
*
33469889 GAAAGAAGAGAA
1 AAAAGAA-AGAA
33469901 GTGTTAGACG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:33474151 original size:37 final size:38
Alignment explanation
Indices: 33474055--33474193 Score: 100
Period size: 40 Copynumber: 3.6 Consensus size: 38
33474045 ACACACCAGT
* **
33474055 TTGGCACCCAGTGCCTCATCGGATAATTCGAAGTAATAAA
1 TTGGCACCCAATGCCTCATCGGATAAACCGAAG--ATAAA
** * ** *
33474095 TTAACACCTAATGTGTCATCGGCTAAACCGAAG-TAAA
1 TTGGCACCCAATGCCTCATCGGATAAACCGAAGATAAA
* *
33474132 TTGGCACCCAATGCCTCATCGAATTAATCCGAAGTAGTAAA
1 TTGGCACCCAATGCCTCATCGGA-TAAACCGAAG-A-TAAA
* * *
33474173 TTGACACCCAGTGTCTCATCG
1 TTGGCACCCAATGCCTCATCG
33474194 TCTAGAAGTC
Statistics
Matches: 75, Mismatches: 20, Indels: 7
0.74 0.20 0.07
Matches are distributed among these distances:
37 20 0.27
38 9 0.12
40 24 0.32
41 22 0.29
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (38 bp):
TTGGCACCCAATGCCTCATCGGATAAACCGAAGATAAA
Found at i:33474666 original size:85 final size:84
Alignment explanation
Indices: 33474544--33474705 Score: 234
Period size: 85 Copynumber: 1.9 Consensus size: 84
33474534 TTAAAATAAC
* * ****
33474544 TAAAATTCATCAATACAACTAATTCAATCTTATATTTAATATTTCAAATTTTTTTTACTCAACAT
1 TAAAATTCATCAACACAACCAATTCAATCTTATATTTAATATTTCAAAAAAATTTTACTCAACAT
33474609 TTGCCCAAATTCAAACAAT
66 TTGCCCAAATTCAAACAAT
* *
33474628 TAAAATTCATCAACACAACACAATTCAATCTTATATTTAATATTTTAAAAAAATTTTACTCAATA
1 TAAAATTCATCAACACAAC-CAATTCAATCTTATATTTAATATTTCAAAAAAATTTTACTCAACA
*
33474693 TTTGCCTAAATTC
65 TTTGCCCAAATTC
33474706 GAATTTAGTC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 18 0.26
85 50 0.74
ACGTcount: A:0.42, C:0.17, G:0.01, T:0.40
Consensus pattern (84 bp):
TAAAATTCATCAACACAACCAATTCAATCTTATATTTAATATTTCAAAAAAATTTTACTCAACAT
TTGCCCAAATTCAAACAAT
Found at i:33475139 original size:10 final size:10
Alignment explanation
Indices: 33475124--33475186 Score: 54
Period size: 10 Copynumber: 5.8 Consensus size: 10
33475114 TCTTTCTCTT
33475124 TTTCTTTTTC
1 TTTCTTTTTC
33475134 TTTCTTTTTC
1 TTTCTTTTTC
* *
33475144 ATTCTATTTC
1 TTTCTTTTTC
33475154 GTTTAGCTTTCTGTC
1 -TTT--CTTT-T-TC
*
33475169 TTTCTTTTTG
1 TTTCTTTTTC
33475179 TTTCTTTT
1 TTTCTTTT
33475187 ATTTATTATA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
10 27 0.63
11 3 0.07
12 4 0.09
13 3 0.07
14 4 0.09
15 2 0.05
ACGTcount: A:0.05, C:0.17, G:0.06, T:0.71
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:33480795 original size:14 final size:14
Alignment explanation
Indices: 33480776--33480806 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
33480766 AGCTTGGCAA
33480776 TTGGGAACTATTTG
1 TTGGGAACTATTTG
33480790 TTGGGAACTATTTG
1 TTGGGAACTATTTG
33480804 TTG
1 TTG
33480807 TTAATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.06, G:0.29, T:0.45
Consensus pattern (14 bp):
TTGGGAACTATTTG
Found at i:33481088 original size:12 final size:12
Alignment explanation
Indices: 33481068--33481097 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33481058 TATGGTTAAT
*
33481068 TTCTTTAGCAGC
1 TTCTGTAGCAGC
33481080 TTCTGTAGCAGC
1 TTCTGTAGCAGC
33481092 TTCTGT
1 TTCTGT
33481098 TGTTTGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (12 bp):
TTCTGTAGCAGC
Found at i:33485257 original size:121 final size:121
Alignment explanation
Indices: 33484999--33485623 Score: 1144
Period size: 121 Copynumber: 5.2 Consensus size: 121
33484989 TCAAGTTATA
33484999 TATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAA
1 TATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAA
* * * *
33485064 TAT-AATAATATTAATTATTAAGAATTTTATTAAATTATATTGTTCAATTAAAATA
66 TATAAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAAATT
* *
33485119 TATTTAATCATATATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTA
1 TATTTAATAATA-ATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTA
33485184 ATATAAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAAATT
65 ATATAAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAAATT
33485241 TATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAA
1 TATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAA
33485306 TATAAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAAATT
66 TATAAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAAATT
33485362 TATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAA
1 TATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAA
33485427 TATAAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAAATT
66 TATAAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAAATT
*
33485483 TATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAA
1 TATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAA
* * *
33485548 TATAAAGAATATTAATTATTAAGAATTTTTTTAAATTATATATTTTAATTAAAATA
66 TATAAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAAATT
33485604 TATTTAATAATAATTATGTT
1 TATTTAATAATAATTATGTT
33485624 TAAATATGAT
Statistics
Matches: 491, Mismatches: 12, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
120 11 0.02
121 421 0.86
122 59 0.12
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.48
Consensus pattern (121 bp):
TATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAA
TATAAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAAATT
Found at i:33485875 original size:17 final size:16
Alignment explanation
Indices: 33485841--33485893 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
33485831 GATTAGCTAT
33485841 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
33485857 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
33485874 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
33485890 TACA
1 TACA
33485894 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:33488856 original size:41 final size:40
Alignment explanation
Indices: 33488743--33488879 Score: 131
Period size: 41 Copynumber: 3.5 Consensus size: 40
33488733 ACCAGTTTGG
* * * *
33488743 CACCCAGTGCCTCATCGGA-TAATTCGAAGTAAATAAATTAA
1 CACCCAGTGTCTCATCGAATTAA-TCGAAGT-AGTAAATTGA
* * *
33488784 CACCCAGTGTCTCATC-AGCTAAATCG-A--AGTAAATTGG
1 CACCCAGTGTCTCATCGA-ATTAATCGAAGTAGTAAATTGA
*
33488821 CACCCAGTGGCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGTCTCATCGAATTAAT-CGAAGTAGTAAATTGA
33488862 CACCCAGTGTCTCATCGA
1 CACCCAGTGTCTCATCGA
33488880 CTCGAAGTCG
Statistics
Matches: 77, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
37 26 0.34
38 3 0.04
39 1 0.01
40 1 0.01
41 44 0.57
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (40 bp):
CACCCAGTGTCTCATCGAATTAATCGAAGTAGTAAATTGA
Found at i:33489308 original size:16 final size:16
Alignment explanation
Indices: 33489287--33489339 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
33489277 TTGGTTCACT
33489287 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
33489303 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
33489319 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
33489335 GTAAT
1 GTAAT
33489340 AGGTAATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.38, C:0.06, G:0.34, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:33489408 original size:44 final size:46
Alignment explanation
Indices: 33489321--33489413 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 46
33489311 ATAGATGCGT
*
33489321 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
33489367 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
33489411 AAT
1 AAT
33489414 AGAGGTGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 24 0.52
45 3 0.07
46 19 0.41
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:33489409 original size:39 final size:44
Alignment explanation
Indices: 33489321--33489426 Score: 141
Period size: 39 Copynumber: 2.5 Consensus size: 44
33489311 ATAGATGCGT
*
33489321 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGG
33489367 AATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
*
33489406 AATGGAATAGAGGTGTAATAG
1 AATGGAATAGAGGCGTAATAG
33489427 CATAAGTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
39 19 0.33
40 2 0.04
43 1 0.02
44 13 0.23
45 3 0.05
46 19 0.33
ACGTcount: A:0.29, C:0.04, G:0.32, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:33489728 original size:10 final size:10
Alignment explanation
Indices: 33489666--33489738 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
33489656 AATACTATAA
33489666 AATATAATTT
1 AATATAATTT
*
33489676 AAAATAA-TT
1 AATATAATTT
*
33489685 -AT-T-ATTA
1 AATATAATTT
33489692 AATATAATTT
1 AATATAATTT
**
33489702 AATA-AAAAT
1 AATATAATTT
33489711 -ATATAATTT
1 AATATAATTT
* *
33489720 AATAAAATTC
1 AATATAATTT
33489730 AATATAATT
1 AATATAATT
33489739 ATTCTTATAC
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 6 0.13
9 9 0.20
10 28 0.61
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATAATTT
Found at i:33489785 original size:117 final size:119
Alignment explanation
Indices: 33489553--33489788 Score: 390
Period size: 120 Copynumber: 2.0 Consensus size: 119
33489543 TTAATCATAT
* *
33489553 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-TAATATT
*
33489618 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 AAATATTCTTATACGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
33489673 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTC-AATA-TA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
* *
33489736 ATTATTCTTATACGAATTTACTAAAATCATATTATATAAT-CTATAAAA-ATAA
66 AATATTCTTATACGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
33489788 T
1 T
33489789 ATATAATCTA
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
115 5 0.05
116 8 0.07
117 39 0.35
118 3 0.03
120 56 0.50
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (119 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTAATATTA
AATATTCTTATACGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:33491590 original size:4 final size:4
Alignment explanation
Indices: 33491581--33491611 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
33491571 GATGTTCATA
*
33491581 TATG TATG TATG TATG TATG CATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
33491612 TTGGTTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:33495264 original size:6 final size:6
Alignment explanation
Indices: 33495253--33495293 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
33495243 AGCAATCACA
33495253 TATATG TATATG TATATG TATATATG TATATG TATATG TAT
1 TATATG TATATG TATATG --TATATG TATATG TATATG TAT
33495294 TAGTGTATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 27 0.82
8 6 0.18
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:33495276 original size:14 final size:14
Alignment explanation
Indices: 33495259--33495289 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
33495249 CACATATATG
33495259 TATATGTATATGTA
1 TATATGTATATGTA
33495273 TATATGTATATGTA
1 TATATGTATATGTA
33495287 TAT
1 TAT
33495290 GTATTAGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (14 bp):
TATATGTATATGTA
Found at i:33495300 original size:14 final size:13
Alignment explanation
Indices: 33495253--33495301 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
33495243 AGCAATCACA
33495253 TATA-TGTATATG
1 TATAGTGTATATG
*
33495265 TATATGTATATATG
1 TATA-GTGTATATG
33495279 TATA-TGTATATG
1 TATAGTGTATATG
33495291 TATTAGTGTAT
1 TA-TAGTGTAT
33495302 TGAACTCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 13 0.42
13 2 0.06
14 16 0.52
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (13 bp):
TATAGTGTATATG
Found at i:33495301 original size:20 final size:20
Alignment explanation
Indices: 33495252--33495293 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
33495242 AAGCAATCAC
33495252 ATATATGTATATGTATATGT
1 ATATATGTATATGTATATGT
33495272 ATATATGTATATGTATATGT
1 ATATATGTATATGTATATGT
33495292 AT
1 AT
33495294 TAGTGTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (20 bp):
ATATATGTATATGTATATGT
Found at i:33498388 original size:15 final size:16
Alignment explanation
Indices: 33498370--33498399 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33498360 ATACTTTAAA
33498370 TTTCTTTC-TTTTTTT
1 TTTCTTTCATTTTTTT
33498385 TTTCTTTCATTTTTT
1 TTTCTTTCATTTTTT
33498400 CATTCTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTCTTTCATTTTTTT
Found at i:33498980 original size:12 final size:13
Alignment explanation
Indices: 33498963--33498992 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
33498953 CTAATAAGAG
33498963 ATGAAAAATT-AA
1 ATGAAAAATTAAA
33498975 ATGAAAAATTAAA
1 ATGAAAAATTAAA
33498988 ATGAA
1 ATGAA
33498993 TTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (13 bp):
ATGAAAAATTAAA
Found at i:33500955 original size:20 final size:21
Alignment explanation
Indices: 33500913--33500957 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
33500903 TTTTTAATAC
*
33500913 ATTTTATAATATATTTGTCAA
1 ATTTTATAATATAATTGTCAA
* *
33500934 ATTTTA-AATTTAATTGTGAA
1 ATTTTATAATATAATTGTCAA
33500954 ATTT
1 ATTT
33500958 AAAAACTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (21 bp):
ATTTTATAATATAATTGTCAA
Found at i:33504046 original size:15 final size:14
Alignment explanation
Indices: 33504013--33504043 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
33504003 CTACTCCTGC
33504013 AAAA-ACAGAAGCA
1 AAAAGACAGAAGCA
33504026 AAAAGACAGAAGCA
1 AAAAGACAGAAGCA
33504040 AAAA
1 AAAA
33504044 AGAGAGGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.71, C:0.13, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAGACAGAAGCA
Found at i:33504978 original size:3 final size:3
Alignment explanation
Indices: 33504972--33505022 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
33504962 TATTCAACTA
33504972 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
33505020 ATT
1 ATT
33505023 GTTGTTGTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:33505027 original size:3 final size:3
Alignment explanation
Indices: 33505021--33505063 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
33505011 ATTATTATTA
33505021 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
33505064 ATTTATTATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:33509709 original size:18 final size:17
Alignment explanation
Indices: 33509677--33509710 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
33509667 AATCAAAATC
*
33509677 AAAATAAAGAAATCAAG
1 AAAATAAAAAAATCAAG
33509694 AAAATAAAAAAAATCAA
1 AAAAT-AAAAAAATCAA
33509711 AGTCAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAATAAAAAAATCAAG
Found at i:33509734 original size:7 final size:7
Alignment explanation
Indices: 33509722--33509755 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
33509712 GTCAAAATAG
33509722 GAAAAAA
1 GAAAAAA
33509729 GAAAAATA
1 GAAAAA-A
33509737 -AAAAAA
1 GAAAAAA
33509743 GAAAAAA
1 GAAAAAA
33509750 GAAAAA
1 GAAAAA
33509756 GGAGAGGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.04
7 23 0.92
8 1 0.04
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (7 bp):
GAAAAAA
Found at i:33509735 original size:37 final size:38
Alignment explanation
Indices: 33509661--33509742 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
33509651 TTCAGACTAA
*
33509661 AAAAAAAATCAAAATCAAAATAAAGAAATCAAGAAAAT
1 AAAAAAAATCAAAATCAAAATAAAGAAATAAAGAAAAT
* *
33509699 AAAAAAAATCAAAGTCAAAAT-AGGAAA-AAAGAAAAAT
1 AAAAAAAATCAAAATCAAAATAAAGAAATAAAG-AAAAT
33509736 AAAAAAA
1 AAAAAAA
33509743 GAAAAAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
36 3 0.08
37 17 0.43
38 20 0.50
ACGTcount: A:0.76, C:0.06, G:0.07, T:0.11
Consensus pattern (38 bp):
AAAAAAAATCAAAATCAAAATAAAGAAATAAAGAAAAT
Found at i:33509754 original size:14 final size:15
Alignment explanation
Indices: 33509715--33509755 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
33509705 AATCAAAGTC
33509715 AAAATAGGAAAAAAGA
1 AAAATA-GAAAAAAGA
33509731 AAAATA-AAAAAAGA
1 AAAATAGAAAAAAGA
33509745 AAAA-AGAAAAA
1 AAAATAGAAAAA
33509756 GGAGAGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.04
14 17 0.71
16 6 0.25
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (15 bp):
AAAATAGAAAAAAGA
Found at i:33510551 original size:9 final size:9
Alignment explanation
Indices: 33510537--33510575 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
33510527 TGAGTCAAAC
33510537 AAAAAAATG
1 AAAAAAATG
33510546 AAAAAAATG
1 AAAAAAATG
33510555 --AAAAATG
1 AAAAAAATG
33510562 AAAAAAATG
1 AAAAAAATG
33510571 AAAAA
1 AAAAA
33510576 TTAAAAATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 7 0.25
9 21 0.75
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Done.