Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 138 of 211
Found at i:43588848 original size:28 final size:31
Alignment explanation
Indices: 43588784--43588859 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
43588774 TATAAAATAT
43588784 ATAAAACTTATAAAAAAATTCATAATAAGTTCTA
1 ATAAAA-TTATAAAAAAATTCATAAT-A-TTCTA
*
43588818 AT-AAATTATAAAAAAATT-ATAAT-TTTTA
1 ATAAAATTATAAAAAAATTCATAATATTCTA
43588846 ATAAAATTATAAAA
1 ATAAAATTATAAAA
43588860 CATTATCGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
28 6 0.15
29 11 0.28
31 5 0.12
32 13 0.32
33 3 0.08
34 2 0.05
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (31 bp):
ATAAAATTATAAAAAAATTCATAATATTCTA
Found at i:43589716 original size:10 final size:9
Alignment explanation
Indices: 43589693--43589767 Score: 66
Period size: 9 Copynumber: 8.3 Consensus size: 9
43589683 TATGTTTCAT
43589693 TAATTTTTA
1 TAATTTTTA
43589702 TAATTTTTA
1 TAATTTTTA
43589711 TGAATTTTTA
1 T-AATTTTTA
**
43589721 TAA--TACA
1 TAATTTTTA
43589728 TAAGTTTTTA
1 TAA-TTTTTA
*
43589738 TGATTTTT-
1 TAATTTTTA
43589746 TATATTTTTA
1 TA-ATTTTTA
*
43589756 TACTTTTTA
1 TAATTTTTA
43589765 TAA
1 TAA
43589768 GTGTGAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
7 5 0.10
8 1 0.02
9 31 0.60
10 15 0.29
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (9 bp):
TAATTTTTA
Found at i:43589762 original size:27 final size:27
Alignment explanation
Indices: 43589695--43589765 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
43589685 TGTTTCATTA
43589695 ATTTTTATAATTTTTATGAATTTTTAT
1 ATTTTTATAATTTTTATGAATTTTTAT
* ** *
43589722 A-ATACATAAGTTTTTATGATTTTTTAT
1 ATTTTTATAA-TTTTTATGAATTTTTAT
*
43589749 ATTTTTATACTTTTTAT
1 ATTTTTATAATTTTTAT
43589766 AAGTGTGAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
26 5 0.15
27 25 0.74
28 4 0.12
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (27 bp):
ATTTTTATAATTTTTATGAATTTTTAT
Found at i:43591635 original size:18 final size:18
Alignment explanation
Indices: 43591612--43591665 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
43591602 AATTTTTATG
43591612 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGGTA
*
43591630 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGGTA
* *
43591648 CTTGGGTTTGGATTGGGT
1 ATTGGG-TTGGGTTGGGT
43591666 TTAGGTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 22 0.71
19 9 0.29
ACGTcount: A:0.11, C:0.02, G:0.46, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGGTA
Found at i:43593313 original size:16 final size:17
Alignment explanation
Indices: 43593292--43593329 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
43593282 AGCAACTCTA
43593292 TTCTTAAGTTCTTT-TT
1 TTCTTAAGTTCTTTCTT
*
43593308 TTCTTAATTTCTTTCTT
1 TTCTTAAGTTCTTTCTT
43593325 TTCTT
1 TTCTT
43593330 CCGTACTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.11, C:0.16, G:0.03, T:0.71
Consensus pattern (17 bp):
TTCTTAAGTTCTTTCTT
Found at i:43595491 original size:17 final size:16
Alignment explanation
Indices: 43595464--43595502 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
43595454 TTTATCCATT
*
43595464 TTTTATTTTAATTTTAA
1 TTTT-TTTTAAATTTAA
43595481 TATTTTTTTAAATTTAA
1 T-TTTTTTTAAATTTAA
43595498 TTTTT
1 TTTTT
43595503 ACATTCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 13 0.65
18 3 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTTTAAATTTAA
Found at i:43599014 original size:39 final size:39
Alignment explanation
Indices: 43598960--43599180 Score: 132
Period size: 39 Copynumber: 5.6 Consensus size: 39
43598950 AGAAACTTCT
* *
43598960 AATAGAATCATTAGGTATGGCTTGATAAAGCATAC-TTTC
1 AATAGAATTAGTAGGTATGGCTTGA-AAAGCATACATTTC
* * *
43598999 AATAGAATTAGTAGGTAAGGCTCG-ATAGCACATACATTTC
1 AATAGAATTAGTAGGTATGGCTTGAAAAG--CATACATTTC
* * ** * *
43599039 AGTGGAATCGGTAGGTATGG-TTCAAAAGCGCATACGTTTC
1 AATAGAATTAGTAGGTATGGCTTGAAAA--GCATACATTTC
* *
43599079 AGTAG-ATTCAGTAGGTATGGCTTGAAGCA-CATACATTTC
1 AATAGAATT-AGTAGGTATGGCTTGAA-AAGCATACATTTC
* * * *
43599118 AATAGATTTAGTAGCTATGG-TTCGAAAAGCACATACGTTTT
1 AATAGAATTAGTAGGTATGGCTT-GAAAAG--CATACATTTC
*
43599159 AGTAG-ATTCAGTAGGTATGGCT
1 AATAGAATT-AGTAGGTATGGCT
43599181 CAAAAGAATA
Statistics
Matches: 137, Mismatches: 29, Indels: 29
0.70 0.15 0.15
Matches are distributed among these distances:
37 3 0.02
38 3 0.02
39 54 0.39
40 48 0.35
41 26 0.19
42 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.31
Consensus pattern (39 bp):
AATAGAATTAGTAGGTATGGCTTGAAAAGCATACATTTC
Found at i:43599053 original size:40 final size:39
Alignment explanation
Indices: 43598962--43599222 Score: 175
Period size: 40 Copynumber: 6.6 Consensus size: 39
43598952 AAACTTCTAA
* * * *
43598962 TAGAATCATTAGGTATGGCTTGATA-AAGCATAC-TTTCAA
1 TAGAATCAGTAGGTATGGCTCGA-AGCA-CATACATTTCAG
* *
43599001 TAGAATTAGTAGGTAAGGCTCGATAGCACATACATTTCAG
1 TAGAATCAGTAGGTATGGCTCGA-AGCACATACATTTCAG
* * * * * *
43599041 TGGAATCGGTAGGTATGGTTCAAAAGCGCATACGTTTCAG
1 TAGAATCAGTAGGTATGGCTC-GAAGCACATACATTTCAG
* * *
43599081 TAGATTCAGTAGGTATGGCTTGAAGCACATACATTTCAA
1 TAGAATCAGTAGGTATGGCTCGAAGCACATACATTTCAG
* * * * * *
43599120 TAGATTTAGTAGCTATGGTTCGAAAAGCACATACGTTTTAG
1 TAGAATCAGTAGGTATGGCTCG--AAGCACATACATTTCAG
* * * * *
43599161 TAGATTCAGTAGGTATGGCTCAAAAGAATATACGTTTCAG
1 TAGAATCAGTAGGTATGGCTC-GAAGCACATACATTTCAG
* * * *
43599201 TAGATTCAATAGATATCGCTCG
1 TAGAATCAGTAGGTATGGCTCG
43599223 TCTGAGCACC
Statistics
Matches: 175, Mismatches: 41, Indels: 12
0.77 0.18 0.05
Matches are distributed among these distances:
39 58 0.33
40 84 0.48
41 33 0.19
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (39 bp):
TAGAATCAGTAGGTATGGCTCGAAGCACATACATTTCAG
Found at i:43599072 original size:79 final size:80
Alignment explanation
Indices: 43598960--43599181 Score: 249
Period size: 80 Copynumber: 2.8 Consensus size: 80
43598950 AGAAACTTCT
* * * *
43598960 AATAGAATCATTAGGTATGGCTT-GATAAA--GCATAC-TTTCAATAGAATT-AGTAGGTAAGGC
1 AATAGAATCAGTAGCTATGG-TTCGA-AAAGCGCATACGTTTCAGTAG-ATTCAGTAGGTATGGC
43599020 TCGATAGCACATACATTTC
63 TCGA-AGCACATACATTTC
* * * * *
43599039 AGTGGAATCGGTAGGTATGGTTC-AAAAGCGCATACGTTTCAGTAGATTCAGTAGGTATGGCTTG
1 AATAGAATCAGTAGCTATGGTTCGAAAAGCGCATACGTTTCAGTAGATTCAGTAGGTATGGCTCG
43599103 AAGCACATACATTTC
66 AAGCACATACATTTC
* * * *
43599118 AATAGATTTAGTAGCTATGGTTCGAAAAGCACATACGTTTTAGTAGATTCAGTAGGTATGGCTC
1 AATAGAATCAGTAGCTATGGTTCGAAAAGCGCATACGTTTCAGTAGATTCAGTAGGTATGGCTC
43599182 AAAAGAATAT
Statistics
Matches: 121, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
77 3 0.02
78 3 0.02
79 56 0.46
80 59 0.49
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (80 bp):
AATAGAATCAGTAGCTATGGTTCGAAAAGCGCATACGTTTCAGTAGATTCAGTAGGTATGGCTCG
AAGCACATACATTTC
Found at i:43605366 original size:40 final size:40
Alignment explanation
Indices: 43605203--43605510 Score: 268
Period size: 40 Copynumber: 7.7 Consensus size: 40
43605193 GTTTGAGCAA
* *
43605203 TTTCTAGTAGAATCATTAGGTATGGCTCGATAA--AGCATAC-
1 TTTC-AGTAGATTCAGTAGGTATGGCTCGA-AAGCA-CATACG
* * * * *
43605243 TTTTAGTAGAATT-AGTAGGTAAGGCTCGATAGCACATGCA
1 TTTCAGTAG-ATTCAGTAGGTATGGCTCGAAAGCACATACG
* * * * ** * *
43605283 TTTAAGTGGAATTGA-TATGTATCACTTGAAAGCGCATACG
1 TTTCAGTAG-ATTCAGTAGGTATGGCTCGAAAGCACATACG
*
43605323 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATATG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATACG
* ** *
43605363 TTTCAGTAGATTCGGTAGGGGTGGCTCGAAAGCACACACG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATACG
*
43605403 TTTCAGTAAATTCAGTAGGTATGGCTCGAAAGCACATACG
1 TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATACG
* ** *
43605443 TTTCAATAGGCTCTA-TAGGTATGGCTCGAAAGCACATAAG
1 TTTCAGTAGATTC-AGTAGGTATGGCTCGAAAGCACATACG
* * *
43605483 TTTCAGTAGATTCAATAGATATCGCTCG
1 TTTCAGTAGATTCAGTAGGTATGGCTCG
43605511 TCTGAGCACT
Statistics
Matches: 214, Mismatches: 46, Indels: 16
0.78 0.17 0.06
Matches are distributed among these distances:
38 1 0.00
39 28 0.13
40 183 0.86
41 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.30
Consensus pattern (40 bp):
TTTCAGTAGATTCAGTAGGTATGGCTCGAAAGCACATACG
Found at i:43607103 original size:17 final size:18
Alignment explanation
Indices: 43607075--43607108 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
43607065 TCATTAGTAT
43607075 TTTTACTTTTATTTTTTA
1 TTTTACTTTTATTTTTTA
43607093 TTTTA-TTTTATTTTTT
1 TTTTACTTTTATTTTTT
43607109 TCTTATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTACTTTTATTTTTTA
Found at i:43611083 original size:17 final size:16
Alignment explanation
Indices: 43611061--43611100 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
43611051 AATTAGTGAC
43611061 TTTATTTAGTTTTATGT
1 TTTATTTAGTTTTAT-T
**
43611078 TTTATTTTTTTTTATT
1 TTTATTTAGTTTTATT
43611094 TTTATTT
1 TTTATTT
43611101 TTATTTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.80
Consensus pattern (16 bp):
TTTATTTAGTTTTATT
Found at i:43611086 original size:6 final size:6
Alignment explanation
Indices: 43611065--43611120 Score: 62
Period size: 6 Copynumber: 9.5 Consensus size: 6
43611055 AGTGACTTTA
* * *
43611065 TTTAGT TTTATGT TTTA-T TTT-TT TTTATT TTTATT TTTATT TGTACT
1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
43611112 TTTATT TTT
1 TTTATT TTT
43611121 TGTTATGTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
7 5 0.12
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:43611166 original size:5 final size:5
Alignment explanation
Indices: 43611158--43611192 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
43611148 GACTTATATG
* *
43611158 TTTTG TTTTG TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
43611193 CATTTTACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:43614084 original size:3 final size:3
Alignment explanation
Indices: 43614076--43614112 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
43614066 TTGTCCTTAT
*
43614076 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
43614113 GGTACTAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:43615611 original size:29 final size:29
Alignment explanation
Indices: 43615569--43615630 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
43615559 TTAAAATTAG
** * *
43615569 TAATCACCTGATTATTAATAAATTTCT-TT
1 TAATCACCCAATTA-TAAAAAATTACTCTT
43615598 TAATCACCCAATTATAAAAAATTACTCTT
1 TAATCACCCAATTATAAAAAATTACTCTT
43615627 TAAT
1 TAAT
43615631 TTTATTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (29 bp):
TAATCACCCAATTATAAAAAATTACTCTT
Found at i:43619110 original size:24 final size:23
Alignment explanation
Indices: 43619061--43619133 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 23
43619051 ACCAAATTAT
* * **
43619061 AATTATATGAATTAACTTAACCG
1 AATTATATTAATTAAATTAATTG
43619084 AATTAATATTAATTAAATTAATTG
1 AATT-ATATTAATTAAATTAATTG
43619108 AA-TATATT--TTAATAGTTAATTG
1 AATTATATTAATTAA-A-TTAATTG
43619130 AATT
1 AATT
43619134 GAATTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
20 4 0.10
21 1 0.02
22 14 0.33
23 6 0.14
24 17 0.40
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (23 bp):
AATTATATTAATTAAATTAATTG
Found at i:43619134 original size:27 final size:26
Alignment explanation
Indices: 43619099--43619171 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
43619089 ATATTAATTA
**
43619099 AATT-AATTGAATATATTTTAATAGTT
1 AATTGAATTGAATATATTTTAA-AAAT
* *
43619125 AATTGAATTGAATTTTTTTTAAAAAT
1 AATTGAATTGAATATATTTTAAAAAT
43619151 AATTGAATTGAA-ATATTTTAA
1 AATTGAATTGAATATATTTTAA
43619172 CTAATTTCGT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 7 0.17
26 18 0.45
27 15 0.38
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (26 bp):
AATTGAATTGAATATATTTTAAAAAT
Found at i:43619822 original size:29 final size:29
Alignment explanation
Indices: 43619790--43619855 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
43619780 AATGTCGATA
* * *
43619790 TTTTTTAATATTTGTGGGAGTAGGTTGTT
1 TTTTTTAATATTTATGGAAGTAGGTCGTT
* *
43619819 TTTTTGAATATTTATGGAATTAGGTCGTT
1 TTTTTTAATATTTATGGAAGTAGGTCGTT
43619848 TTTTTTAA
1 TTTTTTAA
43619856 ACACGCTTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.21, C:0.02, G:0.21, T:0.56
Consensus pattern (29 bp):
TTTTTTAATATTTATGGAAGTAGGTCGTT
Found at i:43620008 original size:14 final size:14
Alignment explanation
Indices: 43619989--43620029 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
43619979 CCTGAACCAA
*
43619989 TTTAGGGTTTTTCT
1 TTTAGGGTTTTTAT
*
43620003 TTTAGGGTATTTAT
1 TTTAGGGTTTTTAT
*
43620017 TTTAGAGTTTTTA
1 TTTAGGGTTTTTA
43620030 GGGTTTTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.17, C:0.02, G:0.20, T:0.61
Consensus pattern (14 bp):
TTTAGGGTTTTTAT
Found at i:43626865 original size:41 final size:40
Alignment explanation
Indices: 43626790--43626882 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 40
43626780 ACCCGTTTAG
* * * * * *
43626790 CACCTAATGCCTCATCGGATAATTCGAAGTAGTAATTTGA
1 CACCCAATGTCTCATCGAATAATCCGAAGCAGTAAATTGA
*
43626830 CACCCAGTGTCTCATCGAATAAATCCGAAGCAGTAAATTGA
1 CACCCAATGTCTCATCGAAT-AATCCGAAGCAGTAAATTGA
*
43626871 CCCCCAATGTCT
1 CACCCAATGTCT
43626883 GATTGGTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
40 16 0.37
41 27 0.63
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (40 bp):
CACCCAATGTCTCATCGAATAATCCGAAGCAGTAAATTGA
Found at i:43629490 original size:18 final size:19
Alignment explanation
Indices: 43629469--43629504 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
43629459 TCTTTCTAGT
43629469 TTATTTTTATTT-ATTAAA
1 TTATTTTTATTTAATTAAA
*
43629487 TTATTTTTCTTTAATTAA
1 TTATTTTTATTTAATTAA
43629505 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTTATTTAATTAAA
Found at i:43629506 original size:18 final size:17
Alignment explanation
Indices: 43629469--43629528 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
43629459 TCTTTCTAGT
43629469 TTATTTTTATTT-ATTAAA
1 TTATTTTT-TTTAATT-AA
43629487 TTATTTTTCTTTAATTAA
1 TTATTTTT-TTTAATTAA
*
43629505 TT-TTTATTTTTAAATTTA
1 TTATTT-TTTTT-AATTAA
43629523 TTATTT
1 TTATTT
43629529 GTCATGATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
17 6 0.17
18 24 0.67
19 6 0.17
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTTTTTTTAATTAA
Found at i:43630414 original size:22 final size:23
Alignment explanation
Indices: 43630389--43630433 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
43630379 ATATACATTT
*
43630389 TTATGGATATTTTT-ATATATAA
1 TTATGGATATTTTTCACATATAA
*
43630411 TTATGTATATTTTTCACATATAA
1 TTATGGATATTTTTCACATATAA
43630434 AGTTGTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (23 bp):
TTATGGATATTTTTCACATATAA
Found at i:43631503 original size:24 final size:24
Alignment explanation
Indices: 43631471--43631516 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
43631461 TAAAAATTTT
43631471 TATGATTAAA-TTGTTGTTATTAAA
1 TATGATTAAACTTGTTG-TATTAAA
*
43631495 TATGCTTAAACTTGTTGTATTA
1 TATGATTAAACTTGTTGTATTA
43631517 TATCTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (24 bp):
TATGATTAAACTTGTTGTATTAAA
Found at i:43641005 original size:11 final size:10
Alignment explanation
Indices: 43640977--43641031 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
43640967 AATTAAAATG
43640977 TTAAAATAAA
1 TTAAAATAAA
*
43640987 TTTAAATAAA
1 TTAAAATAAA
43640997 TTAACAAT--A
1 TTAA-AATAAA
* *
43641006 TTGAAATAAG
1 TTAAAATAAA
*
43641016 TTGAAATAAA
1 TTAAAATAAA
43641026 TTAAAA
1 TTAAAA
43641032 ATGTTAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
8 3 0.08
9 4 0.11
10 26 0.72
11 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (10 bp):
TTAAAATAAA
Found at i:43641014 original size:29 final size:28
Alignment explanation
Indices: 43640967--43641042 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
43640957 ATAATATATG
* *
43640967 AATTAAAATGTTAAAATAAATTTAAATA
1 AATTAAAATATTAAAATAAATTGAAATA
* *
43640995 AATTAACAATATTGAAATAAGTTGAAATA
1 AATTAA-AATATTAAAATAAATTGAAATA
*
43641024 AATTAAAAATGTTAAAATA
1 AATT-AAAATATTAAAATA
43641043 TTTGAAAGAG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 6 0.15
29 32 0.80
30 2 0.05
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (28 bp):
AATTAAAATATTAAAATAAATTGAAATA
Found at i:43642170 original size:18 final size:18
Alignment explanation
Indices: 43642147--43642182 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
43642137 AGCTAATATT
43642147 GAAGAAACAGAAAAGAAA
1 GAAGAAACAGAAAAGAAA
**
43642165 GAAGAAATTGAAAAGAAA
1 GAAGAAACAGAAAAGAAA
43642183 TAAAAGAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.22, T:0.06
Consensus pattern (18 bp):
GAAGAAACAGAAAAGAAA
Found at i:43642989 original size:50 final size:49
Alignment explanation
Indices: 43642935--43643200 Score: 201
Period size: 50 Copynumber: 5.3 Consensus size: 49
43642925 TGTGATGTCG
* *
43642935 GGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTGTTCCACTGCACCGCCT
1 GGGAAGCAAGATTCGCCGTTGTGGCTT-AATCTGTTCAACTGCAACGCCT
* * * * * * * * *
43642985 GGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTTAAATGCAATGTCG
1 GGGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCAACTGCAACGCCT
* * *
43643035 GGGAAGCAAGATTCGCCGTTGTGGCATTAATCTGTTCCACTGCATCGCTT
1 GGGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCAACTGCAACGCCT
* * * * * * * * * * *
43643085 GAGAAGTAAGATTCGCTGTGGTAGCTTTAATCTTTTTAATTGTAATGTC-
1 GGGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCAACTGCAACGCCT
* * *
43643134 GGGAAAGCAAGATTCGCCGTTGTGGCGTTAATCTGTTCTACTGCACCGCTT
1 GGG-AAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCAACTGCAACGCCT
* *
43643185 GAGAAGTAAGATTCGC
1 GGGAAGCAAGATTCGC
43643201 TATTCTTAAT
Statistics
Matches: 157, Mismatches: 56, Indels: 6
0.72 0.26 0.03
Matches are distributed among these distances:
49 2 0.01
50 151 0.96
51 4 0.03
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (49 bp):
GGGAAGCAAGATTCGCCGTTGTGGCTTAATCTGTTCAACTGCAACGCCT
Found at i:43643091 original size:100 final size:99
Alignment explanation
Indices: 43642929--43643201 Score: 447
Period size: 100 Copynumber: 2.7 Consensus size: 99
43642919 CTTGACTGTG
* *
43642929 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTCAATCTGTTCCACTGCACCGCCTGGGAAGTAA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTT-AATCTGTTCCACTGCACCGCTTGAGAAGTAA
*
43642994 GATTCGCTGTTGTAGCTTTAATCTTTTTAAATGCA
65 GATTCGCTGTGGTAGCTTTAATCTTTTTAAATGCA
*
43643029 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCATTAATCTGTTCCACTGCATCGCTTGAGAAGTAA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACCGCTTGAGAAGTAA
* *
43643094 GATTCGCTGTGGTAGCTTTAATCTTTTTAATTGTA
65 GATTCGCTGTGGTAGCTTTAATCTTTTTAAATGCA
* *
43643129 ATGTCGGGAAAGCAAGATTCGCCGTTGTGGCGTTAATCTGTTCTACTGCACCGCTTGAGAAGTAA
1 ATGTCGGGGAAGCAAGATTCGCCGTTGTGGC-TTAATCTGTTCCACTGCACCGCTTGAGAAGTAA
43643194 GATTCGCT
65 GATTCGCT
43643202 ATTCTTAATC
Statistics
Matches: 162, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
100 160 0.99
101 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (99 bp):
ATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTAATCTGTTCCACTGCACCGCTTGAGAAGTAAG
ATTCGCTGTGGTAGCTTTAATCTTTTTAAATGCA
Found at i:43643615 original size:44 final size:44
Alignment explanation
Indices: 43643565--43643855 Score: 216
Period size: 44 Copynumber: 6.6 Consensus size: 44
43643555 CTTTGATCTG
* * *
43643565 TTCCACTACTGTTTGGGGAGAC-ATGATCTACAATCTTCAACCTA
1 TTCCACTACTGGTTAGGGAG-CTAGGATCTACAATCTTCAACCTA
* * *
43643609 TTCCACTGCTGGTTAGGGAGCTAGGATTTACAATCTTCTACCTA
1 TTCCACTACTGGTTAGGGAGCTAGGATCTACAATCTTCAACCTA
* * **
43643653 TTCCACTGCTGGTTAGGGAGCTAGGA-CTTATAATCTTCCTCCTA
1 TTCCACTACTGGTTAGGGAGCTAGGATC-TACAATCTTCAACCTA
* * * * *
43643697 TTCCACT-GTTGTTCAGGGAGCTAGGA-CTTTCAGTCTTCCACCTA
1 TTCCACTACTGGTT-AGGGAGCTAGGATC-TACAATCTTCAACCTA
* * * * **
43643741 TTCCACTACTGGTCAGGGATCTAGGATTTATAATCTTCCGCCTA
1 TTCCACTACTGGTTAGGGAGCTAGGATCTACAATCTTCAACCTA
* * * * * *
43643785 TTCCACTGCT-GTTCAGGGAGCTAGGA-CTTCCAGTCTGCCACTTA
1 TTCCACTACTGGTT-AGGGAGCTAGGATC-TACAATCTTCAACCTA
** *
43643829 TTCCACTGTTGGTCAGGGAGCTAGGAT
1 TTCCACTACTGGTTAGGGAGCTAGGAT
43643856 TTATAGTTTC
Statistics
Matches: 201, Mismatches: 37, Indels: 17
0.79 0.15 0.07
Matches are distributed among these distances:
43 7 0.03
44 189 0.94
45 5 0.02
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (44 bp):
TTCCACTACTGGTTAGGGAGCTAGGATCTACAATCTTCAACCTA
Found at i:43643715 original size:88 final size:87
Alignment explanation
Indices: 43643596--43643860 Score: 352
Period size: 88 Copynumber: 3.0 Consensus size: 87
43643586 CATGATCTAC
* * * *
43643596 AATCTTCAACCTATTCCACTGCTGGTT-AGGGAGCTAGGATTTACAATCTTCTACCTATTCCACT
1 AATCTTCCACCTATTCCACTG-TTGTTCAGGGAGCTAGGATTT-CAGTCTTCCACCTATTCCACT
* *
43643660 GCTGGTTAGGGAGCTAGGACTTAT
64 GCTGGTCAGGGAGCTAGGATTTAT
* *
43643684 AATCTTCCTCCTATTCCACTGTTGTTCAGGGAGCTAGGACTTTCAGTCTTCCACCTATTCCACTA
1 AATCTTCCACCTATTCCACTGTTGTTCAGGGAGCTAGGA-TTTCAGTCTTCCACCTATTCCACTG
*
43643749 CTGGTCAGGGATCTAGGATTTAT
65 CTGGTCAGGGAGCTAGGATTTAT
* * * * *
43643772 AATCTTCCGCCTATTCCACTGCTGTTCAGGGAGCTAGGACTTCCAGTCTGCCACTTATTCCACTG
1 AATCTTCCACCTATTCCACTGTTGTTCAGGGAGCTAGGA-TTTCAGTCTTCCACCTATTCCACTG
*
43643837 TTGGTCAGGGAGCTAGGATTTAT
65 CTGGTCAGGGAGCTAGGATTTAT
43643860 A
1 A
43643861 GTTTCACCGG
Statistics
Matches: 158, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
87 4 0.03
88 151 0.96
89 3 0.02
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (87 bp):
AATCTTCCACCTATTCCACTGTTGTTCAGGGAGCTAGGATTTCAGTCTTCCACCTATTCCACTGC
TGGTCAGGGAGCTAGGATTTAT
Found at i:43643744 original size:132 final size:132
Alignment explanation
Indices: 43643598--43643854 Score: 372
Period size: 132 Copynumber: 1.9 Consensus size: 132
43643588 TGATCTACAA
* * *
43643598 TCTTCAACCTATTCCACTGCTGGTTAGGGAGCTAGGATTTACAATCTTCTACCTATTCCACTGCT
1 TCTTCAACCTATTCCACTACTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCT
* * * *
43643663 GGTT-AGGGAGCTAGGACTTATAATCTTCCTCCTATTCCACTGTTGTTCAGGGAGCTAGGACTTT
66 -GTTCAGGGAGCTAGGACTTACAATCTGCCACCTATTCCACTGTTGGTCAGGGAGCTAGGACTTT
43643727 CAG
130 CAG
* * * *
43643730 TCTTCCACCTATTCCACTACTGGTCAGGGATCTAGGATTTATAATCTTCCGCCTATTCCACTGCT
1 TCTTCAACCTATTCCACTACTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCT
* * *
43643795 GTTCAGGGAGCTAGGACTTCCAGTCTGCCACTTATTCCACTGTTGGTCAGGGAGCTAGGA
66 GTTCAGGGAGCTAGGACTTACAATCTGCCACCTATTCCACTGTTGGTCAGGGAGCTAGGA
43643855 TTTATAGTTT
Statistics
Matches: 110, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
131 3 0.03
132 107 0.97
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (132 bp):
TCTTCAACCTATTCCACTACTGGTCAGGGAGCTAGGATTTACAATCTTCCACCTATTCCACTGCT
GTTCAGGGAGCTAGGACTTACAATCTGCCACCTATTCCACTGTTGGTCAGGGAGCTAGGACTTTC
AG
Found at i:43668945 original size:17 final size:18
Alignment explanation
Indices: 43668912--43668945 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
43668902 GTAGATCATC
*
43668912 AAACTATTTTTATGCTTG
1 AAACTATTTTGATGCTTG
43668930 AAACTA-TTTGATGCTT
1 AAACTATTTTGATGCTT
43668946 ACTATTCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (18 bp):
AAACTATTTTGATGCTTG
Found at i:43673002 original size:43 final size:43
Alignment explanation
Indices: 43672914--43673008 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 43
43672904 TTCGAATGCC
* * * **
43672914 CACACGGGCGTGTCTCTTGACCGTGTGAGTCACACGGCCTGAT
1 CACACGGGCATGTCTCTTGACCGTGTGAGCCACACAGCCAAAT
*
43672957 CACATGGGCATGTCTCTTGACCGTGTGAGCCACACAGCCAAAT
1 CACACGGGCATGTCTCTTGACCGTGTGAGCCACACAGCCAAAT
43673000 CACACGGGC
1 CACACGGGC
43673009 GTGTGTCCCC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.21, C:0.32, G:0.27, T:0.20
Consensus pattern (43 bp):
CACACGGGCATGTCTCTTGACCGTGTGAGCCACACAGCCAAAT
Found at i:43679293 original size:40 final size:40
Alignment explanation
Indices: 43679225--43679302 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
43679215 TACGTGGACA
* * *
43679225 CAAAGCGCGCTTACGAGGACTCGATTTGTTGTCACGTAAG
1 CAAAGCGCGCTGACGAGGACGCGATTTGTTGCCACGTAAG
* *
43679265 CAAAGCGCGCTGACGTGGACGCGTTTTGTTGCCACGTA
1 CAAAGCGCGCTGACGAGGACGCGATTTGTTGCCACGTA
43679303 GCGGGCCCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
CAAAGCGCGCTGACGAGGACGCGATTTGTTGCCACGTAAG
Found at i:43679808 original size:124 final size:125
Alignment explanation
Indices: 43679515--43679955 Score: 695
Period size: 125 Copynumber: 3.5 Consensus size: 125
43679505 GATAAAATCA
43679515 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * *
43679580 AGCTCCTGAAAAAATAATTTCGAGTTGACGATTCTAAGAAAATAGTATAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAAATGCTTC
* * * * * *
43679640 AAGCAGAATGCTTTATCAGTAGAATTTCTGAAATCACGCCCACGTGGACACGCTTTTGCTATAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* *
43679705 AGGTCCTAAAAAAATAATTTCGAGTTGACGTTTCTAAGCCAATAGTAT-AAAAATGCTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAAATGCTTC
43679764 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
*
43679829 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAATGCTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAAATGCTTC
* * ** ** *
43679889 AAGCAGGATGCTTTATCAGAAGAATTTATGAAATCGTACCCTTGTGGACGCGCTTTTGCTACGGT
1 AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
43679954 AG
66 AG
43679956 CATGTTTGGG
Statistics
Matches: 287, Mismatches: 28, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
124 114 0.40
125 173 0.60
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAAATGCTTC
Found at i:43683011 original size:35 final size:35
Alignment explanation
Indices: 43682972--43683140 Score: 97
Period size: 35 Copynumber: 4.6 Consensus size: 35
43682962 ATCTAACATT
* *
43682972 TTGTTAGTAAAATTATTAATTGTTAATTGTATTAA
1 TTGTTAGTAAAATTATAAATTGTTAAATGTATTAA
* *
43683007 TTGTTAATAAAATTATCAAATTATATCAAAT-TATTAA
1 TTGTTAGTAAAATTAT-AAATTGT-T-AAATGTATTAA
* * * * * * ** *
43683044 TTGTTAGTACCAGTCAAAACATTTTGTAAAATCTAACATT
1 TTGTTAGTA-AAATTATAA-A--TTGTTAAATGTATTA-A
* * *
43683084 TTGTTAGTCAAATTATTAATTGTTAATTGTATTAA
1 TTGTTAGTAAAATTATAAATTGTTAAATGTATTAA
*
43683119 TTGTTAGTAAATTTATCAAATT
1 TTGTTAGTAAAATTAT-AAATT
43683141 ATATCATATT
Statistics
Matches: 95, Mismatches: 29, Indels: 19
0.66 0.20 0.13
Matches are distributed among these distances:
35 29 0.31
36 19 0.20
37 17 0.18
38 12 0.13
39 7 0.07
40 11 0.12
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (35 bp):
TTGTTAGTAAAATTATAAATTGTTAAATGTATTAA
Found at i:43683135 original size:112 final size:112
Alignment explanation
Indices: 43682938--43683151 Score: 392
Period size: 112 Copynumber: 1.9 Consensus size: 112
43682928 ATATTTTTTT
43682938 GTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTA
1 GTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTA
43683003 TTAATTGTTAATAAAATTATCAAATTATATCAAATTATTAATTGTTA
66 TTAATTGTTAATAAAATTATCAAATTATATCAAATTATTAATTGTTA
*
43683050 GTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTAGTCAAATTATTAATTGTTAATTGTA
1 GTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTA
* * *
43683115 TTAATTGTTAGTAAATTTATCAAATTATATCATATTA
66 TTAATTGTTAATAAAATTATCAAATTATATCAAATTA
43683152 GGATTAGGTT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 98 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (112 bp):
GTACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTA
TTAATTGTTAATAAAATTATCAAATTATATCAAATTATTAATTGTTA
Found at i:43683249 original size:21 final size:21
Alignment explanation
Indices: 43683224--43683293 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
43683214 TAAGGGTTAC
*
43683224 GGTTAGGGTTTTTAAGTTTAG
1 GGTTAGGGTTTTTAAGTTAAG
*
43683245 GGTTAGGCTTTTTAAGTTAAG
1 GGTTAGGGTTTTTAAGTTAAG
* *
43683266 GGTTTAAGGTTTTTAAGTTAAA
1 GG-TTAGGGTTTTTAAGTTAAG
43683288 GGTTAG
1 GGTTAG
43683294 AGTTAGGGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 24 0.57
22 18 0.43
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.44
Consensus pattern (21 bp):
GGTTAGGGTTTTTAAGTTAAG
Found at i:43683278 original size:22 final size:21
Alignment explanation
Indices: 43683230--43683291 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
43683220 TTACGGTTAG
*
43683230 GGTTTTTAAGTTTAGGG-TTA
1 GGTTTTTAAGTTAAGGGTTTA
43683250 GGCTTTTTAAGTTAAGGGTTTAA
1 GG-TTTTTAAGTTAAGGGTTT-A
*
43683273 GGTTTTTAAGTTAAAGGTT
1 GGTTTTTAAGTTAAGGGTT
43683292 AGAGTTAGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.05
21 14 0.38
22 18 0.49
23 3 0.08
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (21 bp):
GGTTTTTAAGTTAAGGGTTTA
Found at i:43685766 original size:11 final size:11
Alignment explanation
Indices: 43685752--43685828 Score: 54
Period size: 11 Copynumber: 6.9 Consensus size: 11
43685742 TTAAATATGG
43685752 ATTTGAGAGAA
1 ATTTGAGAGAA
*
43685763 ATTTGAAAGGAA
1 ATTTGAGA-GAA
43685775 A-TTGAGAGCAA
1 ATTTGAGAG-AA
*
43685786 ATTGTGAG-CAA
1 ATT-TGAGAGAA
43685797 A-TTGAGAGAA
1 ATTTGAGAGAA
*
43685807 AATTGAGA-AA
1 ATTTGAGAGAA
43685817 ATAATTGAGAGA
1 AT--TTGAGAGA
43685829 GGATTAGTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
9 4 0.08
10 8 0.15
11 24 0.46
12 11 0.21
13 5 0.10
ACGTcount: A:0.48, C:0.03, G:0.26, T:0.23
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:43685779 original size:22 final size:21
Alignment explanation
Indices: 43685754--43685812 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
43685744 AAATATGGAT
*
43685754 TTGAGAGAAATTTGAAAGGAAA
1 TTGAGAGAAATTTG-AAGCAAA
43685776 TTGAGAGCAAATTGTG-AGCAAA
1 TTGAGAG-AAATT-TGAAGCAAA
*
43685798 TTGAGAGAAAATTGA
1 TTGAGAGAAATTTGA
43685813 GAAAATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 2 0.06
21 4 0.12
22 19 0.59
23 5 0.16
24 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.27, T:0.24
Consensus pattern (21 bp):
TTGAGAGAAATTTGAAGCAAA
Found at i:43692845 original size:15 final size:16
Alignment explanation
Indices: 43692825--43692857 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43692815 TTTATTAAAA
*
43692825 AAATTA-AATAATGTT
1 AAATTAGAATAAAGTT
43692840 AAATTAGAATAAAGTT
1 AAATTAGAATAAAGTT
43692856 AA
1 AA
43692858 TATTTAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (16 bp):
AAATTAGAATAAAGTT
Found at i:43697871 original size:19 final size:19
Alignment explanation
Indices: 43697824--43697880 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
43697814 TTTAACTTTT
* *
43697824 TTGTATGAATATTATAATTT
1 TTGTATGAATATTGTAA-TG
*
43697844 TTTTATGAATATTGTAATG
1 TTGTATGAATATTGTAATG
43697863 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
43697881 TATTTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (19 bp):
TTGTATGAATATTGTAATG
Found at i:43697959 original size:27 final size:25
Alignment explanation
Indices: 43697951--43698043 Score: 115
Period size: 23 Copynumber: 3.8 Consensus size: 25
43697941 TAATATTGTA
*
43697951 ATTTTGTATGAATATTATAAT-TTT
1 ATTTTGTATGAATATTGTAATATTT
43697975 -TTTTGTATGAATATTGTAATATTAT
1 ATTTTGTATGAATATTGTAATATT-T
*
43698000 AGTTTTGTATGAATATTGCAA-A-TT
1 A-TTTTGTATGAATATTGTAATATTT
43698024 -TTTTGTATGAATATTGTAAT
1 ATTTTGTATGAATATTGTAAT
43698044 TTTGTATGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
22 18 0.30
23 19 0.31
24 3 0.05
25 2 0.03
26 1 0.02
27 18 0.30
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (25 bp):
ATTTTGTATGAATATTGTAATATTT
Found at i:43697964 original size:19 final size:19
Alignment explanation
Indices: 43697942--43698133 Score: 110
Period size: 19 Copynumber: 10.6 Consensus size: 19
43697932 TGAATATTGT
43697942 AATATTGTAATTTTGTATG
1 AATATTGTAATTTTGTATG
* * *
43697961 AATATTATAATTTTTTTTG
1 AATATTGTAATTTTGTATG
*
43697980 --TA-TG-AATATTG--T-
1 AATATTGTAATTTTGTATG
* *
43697992 AATATTATAGTTTTGTATG
1 AATATTGTAATTTTGTATG
*
43698011 AATATTGCAAATTTTTTGTATG
1 AATATTG-TAA--TTTTGTATG
43698033 AATATTGTAATTTTGTATG
1 AATATTGTAATTTTGTATG
* *
43698052 AATATTAT-ATTTT-TTTG
1 AATATTGTAATTTTGTATG
*
43698069 --TA-TG-AATATTG--T-
1 AATATTGTAATTTTGTATG
*
43698081 AATATTATAATTTTGTATG
1 AATATTGTAATTTTGTATG
*
43698100 AATATTGCAATTTTTTTGTATG
1 AATATTGTAA---TTTTGTATG
43698122 AATATTGTAATT
1 AATATTGTAATT
43698134 ATTTTATAAT
Statistics
Matches: 129, Mismatches: 22, Indels: 44
0.66 0.11 0.23
Matches are distributed among these distances:
13 2 0.02
14 9 0.07
15 9 0.07
16 12 0.09
17 5 0.04
18 7 0.05
19 48 0.37
20 1 0.01
21 2 0.02
22 34 0.26
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (19 bp):
AATATTGTAATTTTGTATG
Found at i:43698047 original size:41 final size:41
Alignment explanation
Indices: 43697942--43698133 Score: 181
Period size: 49 Copynumber: 4.3 Consensus size: 41
43697932 TGAATATTGT
**
43697942 AATATTGTAATTTTGTATGAATATTATAATTTTTTTTGTATG
1 AATATTGTAATTTTGTATGAATATTGCAA-TTTTTTTGTATG
*
43697984 AATATTGTAATATTATAGTTTTGTATGAATATTGCAAATTTTTTGTATG
1 AATATTG------TA-A-TTTTGTATGAATATTGCAATTTTTTTGTATG
43698033 AATATTGTAATTTTGTATGAATATT--ATATTTTTTTGTATG
1 AATATTGTAATTTTGTATGAATATTGCA-ATTTTTTTGTATG
43698073 AATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATG
1 AATATTG--------TAATTTTGTATGAATATTGCAATTTTTTTGTATG
43698122 AATATTGTAATT
1 AATATTGTAATT
43698134 ATTTTATAAT
Statistics
Matches: 127, Mismatches: 4, Indels: 39
0.75 0.02 0.23
Matches are distributed among these distances:
39 1 0.01
40 19 0.15
41 20 0.16
42 8 0.06
43 2 0.02
48 20 0.16
49 39 0.31
50 18 0.14
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (41 bp):
AATATTGTAATTTTGTATGAATATTGCAATTTTTTTGTATG
Found at i:43698095 original size:89 final size:91
Alignment explanation
Indices: 43697942--43698133 Score: 352
Period size: 89 Copynumber: 2.1 Consensus size: 91
43697932 TGAATATTGT
*
43697942 AATATTGTAATTTTGTATGAATATTATAATTTTTTTTGTATGAATATTGTAATATTATAGTTTTG
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTTGTATGAATATTGTAATATTATAATTTTG
43698007 TATGAATATTGCAAATTTTTTGTATG
66 TATGAATATTGCAAATTTTTTGTATG
43698033 AATATTGTAATTTTGTATGAATATTAT-A-TTTTTTTGTATGAATATTGTAATATTATAATTTTG
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTTGTATGAATATTGTAATATTATAATTTTG
*
43698096 TATGAATATTGCAATTTTTTTGTATG
66 TATGAATATTGCAAATTTTTTGTATG
43698122 AATATTGTAATT
1 AATATTGTAATT
43698134 ATTTTATAAT
Statistics
Matches: 99, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
89 71 0.72
90 1 0.01
91 27 0.27
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54
Consensus pattern (91 bp):
AATATTGTAATTTTGTATGAATATTATAATTTTTTTTGTATGAATATTGTAATATTATAATTTTG
TATGAATATTGCAAATTTTTTGTATG
Found at i:43698102 original size:27 final size:23
Alignment explanation
Indices: 43697952--43698138 Score: 192
Period size: 27 Copynumber: 8.1 Consensus size: 23
43697942 AATATTGTAA
* *
43697952 TTTTGTATGAATATTATAATTTT
1 TTTTGTATGAATATTGTAATATT
43697975 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGTAATA-T-T
*
43698000 AGTTTTGTATGAATATTGCAA-ATT
1 --TTTTGTATGAATATTGTAATATT
43698024 TTTTGTATGAATATTGT-A-A--
1 TTTTGTATGAATATTGTAATATT
*
43698043 TTTTGTATGAATATTAT-AT-TT
1 TTTTGTATGAATATTGTAATATT
43698064 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGTAATA-T-T
*
43698089 AATTTTGTATGAATATTGCAAT-TT
1 --TTTTGTATGAATATTGTAATATT
43698113 TTTTGTATGAATATTGTAATTATT
1 TTTTGTATGAATATTGTAA-TATT
43698137 TT
1 TT
43698139 ATAATTAATT
Statistics
Matches: 141, Mismatches: 8, Indels: 29
0.79 0.04 0.16
Matches are distributed among these distances:
19 17 0.12
21 18 0.13
22 36 0.26
23 20 0.14
24 8 0.06
25 4 0.03
26 1 0.01
27 37 0.26
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (23 bp):
TTTTGTATGAATATTGTAATATT
Found at i:43698192 original size:59 final size:60
Alignment explanation
Indices: 43698126--43698246 Score: 165
Period size: 59 Copynumber: 2.0 Consensus size: 60
43698116 TGTATGAATA
* * * * *
43698126 TTGTAATTATTTTATAATTAATTTGTTAGTAATTT-GGAATTATGTTATAAATT-TTGTGT
1 TTGTAATTATTTAAAAATTAATTTATTAGTAATTTAGG-ATTAAGCTATAAATTGTTGTGT
*
43698185 TTGTAATTATTTAAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGT
1 TTGTAATTATTTAAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
43698245 TT
1 TT
43698247 AGTTTAGTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
59 44 0.81
60 10 0.19
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTAAAAATTAATTTATTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:43698325 original size:38 final size:38
Alignment explanation
Indices: 43698280--43698361 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
43698270 CATATAAAGT
43698280 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
* *
43698318 TTATAAAAAAATTAAAAATTATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
43698356 TTATAA
1 TTATAA
43698362 CTGACTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:43698439 original size:15 final size:15
Alignment explanation
Indices: 43698398--43698439 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
43698388 GTTAACTCAT
*
43698398 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
43698413 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
43698429 TTAAATTTTAT
1 TTAAATTTTAT
43698440 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:43700072 original size:6 final size:6
Alignment explanation
Indices: 43700063--43700109 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
43700053 GCATCATGCA
* *
43700063 CCAGAG CCAGAG CTAGAG CTAGAG CCAGAG CCAGAG CCAGAG CCAGA
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGA
43700110 ACTACATTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.34, C:0.30, G:0.32, T:0.04
Consensus pattern (6 bp):
CCAGAG
Found at i:43703468 original size:22 final size:22
Alignment explanation
Indices: 43703433--43703499 Score: 118
Period size: 22 Copynumber: 3.1 Consensus size: 22
43703423 TACCTAATTT
*
43703433 TTTTCTTCT-TTTCCTTCCTTC
1 TTTTCTTCTGCTTCCTTCCTTC
43703454 TTTTCTTCTGCTTCCTTCCTTC
1 TTTTCTTCTGCTTCCTTCCTTC
43703476 TTTTCTTCTGCTTCCTTCCTTC
1 TTTTCTTCTGCTTCCTTCCTTC
43703498 TT
1 TT
43703500 CTTTCTTCCG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 9 0.20
22 35 0.80
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.63
Consensus pattern (22 bp):
TTTTCTTCTGCTTCCTTCCTTC
Found at i:43703614 original size:27 final size:27
Alignment explanation
Indices: 43703565--43703666 Score: 143
Period size: 27 Copynumber: 3.8 Consensus size: 27
43703555 AAAATCACAG
**
43703565 CATTGGCGCCTTTCAG-TATGGCACCAC
1 CATTGGCGCCTCCCAGATA-GGCACCAC
43703592 CATTGGCGCCTCCCAGATAGGCACCAC
1 CATTGGCGCCTCCCAGATAGGCACCAC
* *
43703619 CATTGGCGCCTCCCAAATAGGCATCAC
1 CATTGGCGCCTCCCAGATAGGCACCAC
*
43703646 CATTGGCGCCTTCCAGATAGG
1 CATTGGCGCCTCCCAGATAGG
43703667 TGCCAATACT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 66 0.97
28 2 0.03
ACGTcount: A:0.22, C:0.35, G:0.23, T:0.21
Consensus pattern (27 bp):
CATTGGCGCCTCCCAGATAGGCACCAC
Found at i:43704303 original size:22 final size:24
Alignment explanation
Indices: 43704278--43704336 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
43704268 CAAGTCTCAA
* *
43704278 TTTTAATAT-TTATACTTTAATTT
1 TTTTAATATCTCATACTTCAATTT
43704301 TTTTATATAATCTCATACTTCAATTT
1 TTTTA-AT-ATCTCATACTTCAATTT
*
43704327 TTATAATATC
1 TTTTAATATC
43704337 ATTGTTAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 5 0.17
24 5 0.17
25 4 0.13
26 16 0.53
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (24 bp):
TTTTAATATCTCATACTTCAATTT
Found at i:43704578 original size:38 final size:38
Alignment explanation
Indices: 43704536--43704611 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
43704526 CTTTATTCTG
43704536 ATTAAAATGTTGGTTTAACATAATTTGGTACTTCAACT
1 ATTAAAATGTTGGTTTAACATAATTTGGTACTTCAACT
43704574 ATTAAAATGTTGGTTTAACATAATTTGGTACTTCAACT
1 ATTAAAATGTTGGTTTAACATAATTTGGTACTTCAACT
43704612 TTAGCCCCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (38 bp):
ATTAAAATGTTGGTTTAACATAATTTGGTACTTCAACT
Found at i:43705147 original size:17 final size:16
Alignment explanation
Indices: 43705106--43705147 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
43705096 AAAATATTTT
43705106 TAAAAATCAAAGATAA
1 TAAAAATCAAAGATAA
43705122 -AAATGAATCAAAAGATAA
1 TAAA--AATC-AAAGATAA
43705140 TAAAAATC
1 TAAAAATC
43705148 TTTTTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
15 3 0.14
17 8 0.36
18 8 0.36
19 3 0.14
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (16 bp):
TAAAAATCAAAGATAA
Found at i:43706322 original size:7 final size:7
Alignment explanation
Indices: 43706310--43706335 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43706300 CTTACAATAA
43706310 AAAATTT
1 AAAATTT
43706317 AAAATTT
1 AAAATTT
43706324 AAAATTT
1 AAAATTT
43706331 AAAAT
1 AAAAT
43706336 AGAATAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAAATTT
Found at i:43707861 original size:9 final size:9
Alignment explanation
Indices: 43707832--43707868 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
43707822 TGAGTTTTCG
43707832 AATTCGAAT
1 AATTCGAAT
*
43707841 AACTCGAAT
1 AATTCGAAT
43707850 AATTCGAAT
1 AATTCGAAT
*
43707859 AATTCAAAT
1 AATTCGAAT
43707868 A
1 A
43707869 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:43715287 original size:14 final size:14
Alignment explanation
Indices: 43715270--43715296 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43715260 CGTGTTTGGG
43715270 GTTTAAAGTTTAGA
1 GTTTAAAGTTTAGA
43715284 GTTTAAAGTTTAG
1 GTTTAAAGTTTAG
43715297 GATTCATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
GTTTAAAGTTTAGA
Found at i:43715418 original size:14 final size:14
Alignment explanation
Indices: 43715380--43715418 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
43715370 AATGTTTGGG
* *
43715380 GTTTAGGATTTAGA
1 GTTTAGGGTTTAAA
*
43715394 GTTTAGTGTTTAAA
1 GTTTAGGGTTTAAA
43715408 GTTTAGGGTTT
1 GTTTAGGGTTT
43715419 GAGTCTGGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
GTTTAGGGTTTAAA
Found at i:43722831 original size:27 final size:29
Alignment explanation
Indices: 43722790--43722861 Score: 112
Period size: 27 Copynumber: 2.6 Consensus size: 29
43722780 GACTACATTC
*
43722790 AACATTGCCTGGTGTCTTTGT-TAAAAAA
1 AACATTGCCTGGTGTCTTTGTAAAAAAAA
43722818 AA-ATTGCCTGGTGTCTTTGTAAAAAAAA
1 AACATTGCCTGGTGTCTTTGTAAAAAAAA
*
43722846 AACATTGCTTGGTGTC
1 AACATTGCCTGGTGTC
43722862 GGTAGCATTG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 18 0.45
28 10 0.25
29 12 0.30
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (29 bp):
AACATTGCCTGGTGTCTTTGTAAAAAAAA
Found at i:43728399 original size:20 final size:20
Alignment explanation
Indices: 43728361--43728399 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43728351 GATCATAAAT
* *
43728361 TGAGCCCAGGAGCCCAAAAC
1 TGAGACCAGGAGCCAAAAAC
*
43728381 TGAGACCAGGATCCAAAAA
1 TGAGACCAGGAGCCAAAAA
43728400 AGGTTAAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.28, G:0.23, T:0.08
Consensus pattern (20 bp):
TGAGACCAGGAGCCAAAAAC
Found at i:43730531 original size:24 final size:24
Alignment explanation
Indices: 43730504--43730554 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
43730494 ATGATTTAGT
*
43730504 ATTTATGAGTATAATATATTTAAC
1 ATTTATGAGCATAATATATTTAAC
* *
43730528 ATTTATTAGCATAATATATTTGAC
1 ATTTATGAGCATAATATATTTAAC
43730552 ATT
1 ATT
43730555 GATTAGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (24 bp):
ATTTATGAGCATAATATATTTAAC
Found at i:43730559 original size:24 final size:24
Alignment explanation
Indices: 43730514--43730560 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
43730504 ATTTATGAGT
*
43730514 ATAATATATTTAACATTTATTAGC
1 ATAATATATTTAACATTGATTAGC
*
43730538 ATAATATATTTGACATTGATTAG
1 ATAATATATTTAACATTGATTAG
43730561 AATTAGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (24 bp):
ATAATATATTTAACATTGATTAGC
Found at i:43734098 original size:18 final size:18
Alignment explanation
Indices: 43734075--43734109 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43734065 AGATACATAG
43734075 TGAATCTAGGTAAAGAAT
1 TGAATCTAGGTAAAGAAT
43734093 TGAATCTAGGTAAAGAA
1 TGAATCTAGGTAAAGAA
43734110 CATTGGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.26
Consensus pattern (18 bp):
TGAATCTAGGTAAAGAAT
Found at i:43734813 original size:24 final size:24
Alignment explanation
Indices: 43734750--43734801 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
43734740 TTTCTAAAAG
* * *
43734750 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
43734774 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
43734798 ATTT
1 ATTT
43734802 GACTTTGATT
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:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:43736561 original size:34 final size:33
Alignment explanation
Indices: 43736488--43736567 Score: 83
Period size: 34 Copynumber: 2.3 Consensus size: 33
43736478 GGTTCGAGTT
43736488 TTCAAGGTTTGAGGGTCAGGGTTTTGGATTTGAAG
1 TTCAAGGTTT-AGGGTCAGGG-TTTGGATTTGAAG
*
43736523 TTCAAGGTTTAGGGTTTAGGG-TTGGAGTTT-AGAG
1 TTCAAGGTTTAGGG-TCAGGGTTTGGA-TTTGA-AG
*
43736557 TTCAAGATTTA
1 TTCAAGGTTTA
43736568 AGTTTAAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
33 6 0.15
34 19 0.47
35 15 0.38
ACGTcount: A:0.23, C:0.05, G:0.34, T:0.39
Consensus pattern (33 bp):
TTCAAGGTTTAGGGTCAGGGTTTGGATTTGAAG
Found at i:43743448 original size:19 final size:19
Alignment explanation
Indices: 43743421--43743469 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
43743411 AAATGATAAG
*
43743421 GATGAGAAATGGAAAATGA
1 GATGTGAAATGGAAAATGA
* *
43743440 GATGTGAAATTGAATATGA
1 GATGTGAAATGGAAAATGA
*
43743459 AATGGTGAAAT
1 GAT-GTGAAAT
43743470 TGGTTGTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (19 bp):
GATGTGAAATGGAAAATGA
Found at i:43750112 original size:42 final size:42
Alignment explanation
Indices: 43750000--43750114 Score: 101
Period size: 42 Copynumber: 2.7 Consensus size: 42
43749990 AGCTTGTACA
* * *
43750000 ATGCC-ATCGTCCCAAACGTGGTCTTACATCTAATCAAATATCG
1 ATGCCAAT-GTCCCAGACATGGTCTTACA-CGAATCAAATATCG
* * * *
43750043 ATGCCACTGTCCCAGATA-GAGTTTTACACGAAGTCATATA-CG
1 ATGCCAATGTCCCAGACATG-GTCTTACACGAA-TCAAATATCG
*
43750085 GTGCCAATGTCCCAGACATGGTCTTACACG
1 ATGCCAATGTCCCAGACATGGTCTTACACG
43750115 TAAATCTCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
42 30 0.53
43 26 0.46
44 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAATCAAATATCG
Found at i:43760514 original size:29 final size:29
Alignment explanation
Indices: 43760459--43760520 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
43760449 TCTCTAATAT
* * *
43760459 ATGTGAGCCTTAGTGGTGAAATATGTTAC
1 ATGTGAGCCCTAGTGGTGAAACATGTTAA
* *
43760488 ATGTGAGCCCTAGTGGTGGAACCTGTTAA
1 ATGTGAGCCCTAGTGGTGAAACATGTTAA
43760517 ATGT
1 ATGT
43760521 TGAAGCCTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (29 bp):
ATGTGAGCCCTAGTGGTGAAACATGTTAA
Found at i:43761281 original size:72 final size:72
Alignment explanation
Indices: 43761164--43761334 Score: 279
Period size: 72 Copynumber: 2.4 Consensus size: 72
43761154 AAAATAAGCA
* * *
43761164 TTAGCAGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAAGCGAAACGACGTCGTTTCCCAAGCTTT
1 TTAGCGGCGTTTCTAAGAAAGCGCCGCAAAAAACCTAAGCGAAACGACGTCGTTTCCCAAGCTTT
*
43761229 CGGGGAT
66 CGAGGAT
*
43761236 TTAGCGGCGTTTCTAAGAAAGCGCCGCAAAAAACCTAAGCGAAACGACGTCGTTTCCCGAGCTTT
1 TTAGCGGCGTTTCTAAGAAAGCGCCGCAAAAAACCTAAGCGAAACGACGTCGTTTCCCAAGCTTT
*
43761301 TGAGGAT
66 CGAGGAT
*
43761308 TTAGCGGCGTTTCTAAGAAAACGCCGC
1 TTAGCGGCGTTTCTAAGAAAGCGCCGC
43761335 TAATGCTCAG
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 92 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (72 bp):
TTAGCGGCGTTTCTAAGAAAGCGCCGCAAAAAACCTAAGCGAAACGACGTCGTTTCCCAAGCTTT
CGAGGAT
Found at i:43761556 original size:113 final size:114
Alignment explanation
Indices: 43761235--43761559 Score: 406
Period size: 114 Copynumber: 2.9 Consensus size: 114
43761225 CTTTCGGGGA
* * ** * * *
43761235 TTTAGCGGCGTTTCT-AAGAAAGCGCCGC-AAAAAACCTAAGCGAAACGACGTCGTTTCCCGAGC
1 TTTAGCGGCGTTTTTGGA-AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC
* * * * *
43761298 TTTTGAGGATTTAGCGGCGTTTCTAAGAAAACGCCGCTAATGCTCAGGGC
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGC
** ** * *
43761348 TTTAGCTACGTTTTTCGG-AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGGTGTTTTTTGGGC
1 TTTAGCGGCGTTTTT-GGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC
43761412 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGC
65 TTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGC
43761462 TTTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAA-CCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * * *
43761526 GTCGGGGATTTAGCGGCATTTTTGACAAAGCGCC
66 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCC
43761560 GCAAAAAACC
Statistics
Matches: 181, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
113 74 0.41
114 107 0.59
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGC
Found at i:43761558 original size:186 final size:186
Alignment explanation
Indices: 43761366--43761744 Score: 609
Period size: 186 Copynumber: 2.0 Consensus size: 186
43761356 CGTTTTTCGG
** ** *
43761366 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGGTGTTTT-TTGGGCTTTCGGGGATTTAGCGGC
1 AAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCCCGAGCTTTCGGGGATTTAGCGGC
43761430 GTTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAA
65 GTTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGC-AAAA
* *
43761495 AACCTAA-CCCAACGACGCCGTTTTCTGAGCTGTCGGGGATTTAGCGGCATTTTTGAC
129 AACCTAAGCCCAACGACGCCGTTTTCTGAGCTGTCGAGGATTTAGCGGCATTTTTAAC
43761552 AAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCCCGAGCTTTCGGGGATTTAGCGGCG
1 AAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCCCGAGCTTTCGGGGATTTAGCGGCG
* *
43761617 TTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAA
66 TTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAA
* * * *
43761682 CCTAAGTCCAACGACGCCGTTTTCTGAGCTTTCGAGGATTTAGCGGCGTTTTTAAG
131 CCTAAGCCCAACGACGCCGTTTTCTGAGCTGTCGAGGATTTAGCGGCATTTTTAAC
43761738 AAAGCGC
1 AAAGCGC
43761745 TGCTAATGCT
Statistics
Matches: 178, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
185 38 0.21
186 140 0.79
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (186 bp):
AAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCCCGAGCTTTCGGGGATTTAGCGGCG
TTTTTAAGAAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAA
CCTAAGCCCAACGACGCCGTTTTCTGAGCTGTCGAGGATTTAGCGGCATTTTTAAC
Found at i:43761579 original size:72 final size:72
Alignment explanation
Indices: 43761462--43761634 Score: 260
Period size: 72 Copynumber: 2.4 Consensus size: 72
43761452 TGCTCAGGGC
*
43761462 TTTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAACCCAACGACGCCGTTTT-CTGAGCT
1 TTTAGCGGCGTTTTT-GAAAAGCGCCGCAAAAAAACCTAACCCAACGACGCCGTTTTCCCGAGCT
43761526 GTCGGGGA
65 GTCGGGGA
*
43761534 TTTAGCGGCATTTTTGACAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCCCGAGC
1 TTTAGCGGCGTTTTTGA-AAAGCGCCGCAAAAAAACCTAA-CCCAACGACGCCGTTTTCCCGAGC
*
43761598 TTTCGGGGA
64 TGTCGGGGA
*
43761607 TTTAGCGGCGTTTTTAAGAAAGCGCCGC
1 TTTAGCGGCGTTTTTGA-AAAGCGCCGC
43761635 TAATGCTCAG
Statistics
Matches: 92, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
71 13 0.14
72 41 0.45
73 38 0.41
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.23
Consensus pattern (72 bp):
TTTAGCGGCGTTTTTGAAAAGCGCCGCAAAAAAACCTAACCCAACGACGCCGTTTTCCCGAGCTG
TCGGGGA
Found at i:43761715 original size:299 final size:299
Alignment explanation
Indices: 43761164--43761867 Score: 1029
Period size: 299 Copynumber: 2.4 Consensus size: 299
43761154 AAAATAAGCA
* * ** * * **
43761164 TTAGCAGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAAGCGAAACGACGTCGTTTCCCAAGCTT
1 TTAGCGGCGTTTTTGACAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * *
43761228 TCGGGGATTTAGCGGCGTTTCTAAGAAAGCGCCGCAAAAAACCTAAGCGAAACGACGTCGTTTCC
66 TCGGGGATTTAGCGGCGTTTTTGA-AAAGCGCCGCAAAAAACCTAAGCCAAACGACGCCGTTTCC
* *
43761293 CGAGCTTTTGAGGATTTAGCGGCGTTTCTAAGAAAACGCCGCTAATGCTCAGGGCTTTAGCTACG
130 CGAGCTTTCGAGGATTTAGCGGCGTTTCTAAGAAAACGCCGCTAATGCTCAGGGCTTTAGCGACG
** * * *
43761358 TTTTTCGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGGTGTTTTTTGGGCTTTCGGGGATT
195 TTTTTCGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGAGGATT
43761423 TAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCT
260 TAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCT
43761463 TTAGCGGCGTTTTTGGA-AAAGCGCCGCAAAAAAACCTAA-CCCAACGACGCCGTTTTCTGAGCT
1 TTAGCGGCGTTTTT-GACAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
43761526 GTCGGGGATTTAGCGGCATTTTTGACAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTT
65 TTCGGGGATTTAGCGGCGTTTTTGA-AAAGCGCCGCAAAAAACCTAAGCCAAACGACGCCG-TTT
* * * *
43761591 CCCGAGCTTTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGG
128 CCCGAGCTTTCGAGGATTTAGCGGCGTTTCTAAGAAAACGCCGCTAATGCTCAGGGCTTTAGCGA
* *
43761656 CGTTTTTGGGAAAGCGCCGC-AAAAAACCTAAGTCCAACGACGCCGTTTTCTGAGCTTTCGAGGA
193 CGTTTTTCGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGAGGA
**
43761720 TTTAGCGGCGTTTTTAAGAAAGCGCTGCTAATGCTCAGGGCT
258 TTTAGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCT
* *
43761762 TTAGCGGCGTTTTTGACAAAGCGCCGCAAAAAAACCTAAGTCCAACGACACCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGACAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
43761827 TCGGGGATTTAGCGGCGTTTTTGGAAAATCACCGCAAAAAA
66 TCGGGGATTTAGCGGCGTTTTT-GAAAAGCGCCGCAAAAAA
43761868 TAATTTATCT
Statistics
Matches: 363, Mismatches: 36, Indels: 11
0.89 0.09 0.03
Matches are distributed among these distances:
298 2 0.01
299 208 0.57
300 151 0.42
301 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (299 bp):
TTAGCGGCGTTTTTGACAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTGAAAAGCGCCGCAAAAAACCTAAGCCAAACGACGCCGTTTCCC
GAGCTTTCGAGGATTTAGCGGCGTTTCTAAGAAAACGCCGCTAATGCTCAGGGCTTTAGCGACGT
TTTTCGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGAGGATTT
AGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGGCT
Found at i:43761757 original size:113 final size:113
Alignment explanation
Indices: 43761534--43761848 Score: 540
Period size: 114 Copynumber: 2.8 Consensus size: 113
43761524 CTGTCGGGGA
* * *
43761534 TTTAGCGGCATTTTTGACAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCCCGAGCT
1 TTTAGCGGCGTTTTTGACAAAGCGCCGCAAAAAACCTAAGTCCAACGACGCCGTTTT-CTGAGCT
43761599 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
65 TTCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
**
43761648 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGTCCAACGACGCCGTTTTCTGAGCTT
1 TTTAGCGGCGTTTTTGACAAAGCGCCGCAAAAAACCTAAGTCCAACGACGCCGTTTTCTGAGCTT
* *
43761713 TCGAGGATTTAGCGGCGTTTTTAAGAAAGCGCTGCTAATGCTCAGGGC
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
*
43761761 TTTAGCGGCGTTTTTGACAAAGCGCCGCAAAAAAACCTAAGTCCAACGACACCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGACAAAGCGCCGC-AAAAAACCTAAGTCCAACGACGCCGTTTTCTGAGCT
43761826 TTCGGGGATTTAGCGGCGTTTTT
65 TTCGGGGATTTAGCGGCGTTTTT
43761849 GGAAAATCAC
Statistics
Matches: 189, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
113 79 0.42
114 110 0.58
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (113 bp):
TTTAGCGGCGTTTTTGACAAAGCGCCGCAAAAAACCTAAGTCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGGC
Found at i:43762133 original size:15 final size:15
Alignment explanation
Indices: 43762113--43762143 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43762103 CATATTTTAA
43762113 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
43762128 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
43762143 G
1 G
43762144 ATTAGGGATT
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:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:43762150 original size:14 final size:15
Alignment explanation
Indices: 43762116--43762153 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
43762106 ATTTTAAGGT
* *
43762116 TTAGGGAGTATGGGT
1 TTAGGGATTATGGGA
43762131 TTAGGGATTAT-GGA
1 TTAGGGATTATGGGA
43762145 TTAGGGATT
1 TTAGGGATT
43762154 GGGATTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (15 bp):
TTAGGGATTATGGGA
Found at i:43762403 original size:14 final size:14
Alignment explanation
Indices: 43762386--43762420 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
43762376 AGGTTTAGGG
43762386 GTTAGGGGTT-AGA
1 GTTAGGGGTTAAGA
43762399 TGTTAGGGGTTAAGA
1 -GTTAGGGGTTAAGA
43762414 GTTAGGG
1 GTTAGGG
43762421 ATTTAAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.23, C:0.00, G:0.46, T:0.31
Consensus pattern (14 bp):
GTTAGGGGTTAAGA
Found at i:43763511 original size:29 final size:29
Alignment explanation
Indices: 43763453--43763518 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
43763443 GATTTCGCGG
*
43763453 AAAATAGCCCATTCCGGTAAATAATCAAA
1 AAAATGGCCCATTCCGGTAAATAATCAAA
* * ** *
43763482 AAATTGGCCCATTTCGGTAAATTTTGAAA
1 AAAATGGCCCATTCCGGTAAATAATCAAA
43763511 AAAATGGC
1 AAAATGGC
43763519 TTTTTTTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (29 bp):
AAAATGGCCCATTCCGGTAAATAATCAAA
Found at i:43768314 original size:43 final size:42
Alignment explanation
Indices: 43768265--43768511 Score: 293
Period size: 43 Copynumber: 5.8 Consensus size: 42
43768255 TACCAAAAAT
*
43768265 GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTAGAGAAAGC
1 GCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGT-GAGAAAGC
* * * *
43768308 GTCGCTAAAGAACATGATCTTTAGTGGCGTTTGTG-GCTAAAGC
1 GCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGAG--AAAGC
*
43768351 GCCGCTAAAGATCATGTTCTTTAGCGGTGTTTGTTG-GTAAAGC
1 GCCGCTAAAGATCATGTTCTTTAGCGGCGTTTG-TGAG-AAAGC
*
43768394 GCCGCTAAAGATCATGTTTTTTAGCGGCGTTTGTGAGTAAAGC
1 GCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGAG-AAAGC
* * *
43768437 GCCGCTAAAGATCATGTTCTGTAGCGGCGTTTGTGGGTAACA-T
1 GCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGAG-AA-AGC
* *
43768480 ACCGTTAAAGATCATGTTCTTTAGCGGCGTTT
1 GCCGCTAAAGATCATGTTCTTTAGCGGCGTTT
43768512 CAATCATAAA
Statistics
Matches: 180, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.01
42 3 0.02
43 172 0.96
44 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (42 bp):
GCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGAGAAAGC
Found at i:43768470 original size:129 final size:129
Alignment explanation
Indices: 43768265--43768511 Score: 354
Period size: 129 Copynumber: 1.9 Consensus size: 129
43768255 TACCAAAAAT
* * *
43768265 GCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTAGAGAAAGCGTCGCTAAAGAACATGATCTTT
1 GCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTAGAGAAAGCGCCGCTAAAGAACATGATCTGT
* * *
43768330 AGTGGCGTTTGTGGCTAA-AGCGCCGCTAAAGATCATGTTCTTTAGCGGTGTTTGTTGGTAAAGC
66 AGCGGCGTTTGTGGCTAACA-CACCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTTGGTAAAGC
* * *
43768394 GCCGCTAAAGATCATGTTTTTTAGCGGCGTTTGT-GAGTAAAGCGCCGCTAAAGATCATGTTCTG
1 GCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTAGAG-AAAGCGCCGCTAAAGAACATGATCTG
* * *
43768458 TAGCGGCGTTTGTGGGTAACATACCGTTAAAGATCATGTTCTTTAGCGGCGTTT
65 TAGCGGCGTTTGTGGCTAACACACCGCTAAAGATCATGTTCTTTAGCGGCGTTT
43768512 CAATCATAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
128 3 0.03
129 100 0.96
130 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (129 bp):
GCCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTAGAGAAAGCGCCGCTAAAGAACATGATCTGT
AGCGGCGTTTGTGGCTAACACACCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTTGGTAAAGC
Found at i:43772693 original size:11 final size:11
Alignment explanation
Indices: 43772674--43772703 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
43772664 AACAAAAGAC
*
43772674 TTGGGAAAAAA
1 TTGGAAAAAAA
43772685 TTGGAAAAAAA
1 TTGGAAAAAAA
43772696 TTGGAAAA
1 TTGGAAAA
43772704 CAGGGGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (11 bp):
TTGGAAAAAAA
Found at i:43773575 original size:37 final size:38
Alignment explanation
Indices: 43773520--43773677 Score: 162
Period size: 38 Copynumber: 4.2 Consensus size: 38
43773510 CATCAGCTCA
* * * *
43773520 AAGCCTGCTAAGCACTAAGTCTGATTAACACCGCATC-
1 AAGCCTGCTAGGCACTAAGCCTGAATAACACCGAATCT
* *
43773557 AAGCTTGCTAGGCACTAAGCCCGAATAACACCGAATCT
1 AAGCCTGCTAGGCACTAAGCCTGAATAACACCGAATCT
* *
43773595 AAGCCTACTAGGCACTAAGCCTGAATAACACTGACA-CT
1 AAGCCTGCTAGGCACTAAGCCTGAATAACACCGA-ATCT
* * *
43773633 AAGCCTACTAGGCACTTAG-CTAGAATAACACCAGCA-CT
1 AAGCCTGCTAGGCACTAAGCCT-GAATAACACC-GAATCT
43773671 AAGCCTG
1 AAGCCTG
43773678 AATAATACCC
Statistics
Matches: 103, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
37 33 0.32
38 68 0.66
39 2 0.02
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (38 bp):
AAGCCTGCTAGGCACTAAGCCTGAATAACACCGAATCT
Found at i:43773676 original size:76 final size:75
Alignment explanation
Indices: 43773520--43773664 Score: 175
Period size: 75 Copynumber: 1.9 Consensus size: 75
43773510 CATCAGCTCA
* * * * * *
43773520 AAGCCTGCTAAGCACTAAGTCTGATTAACACCGCATCAAGCTTGCTAGGCACTAAGCCCGAATAA
1 AAGCCTACTAAGCACTAAGCCTGAATAACACCGCATCAAGCCTACTAGGCACTAAGCCAGAATAA
43773585 CACCGAATCT
66 CACCGAATCT
* * * *
43773595 AAGCCTACTAGGCACTAAGCCTGAATAACACTGACA-CTAAGCCTACTAGGCACTTAGCTAGAAT
1 AAGCCTACTAAGCACTAAGCCTGAATAACACCG-CATC-AAGCCTACTAGGCACTAAGCCAGAAT
43773659 AACACC
64 AACACC
43773665 AGCACTAAGC
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
75 29 0.50
76 29 0.50
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (75 bp):
AAGCCTACTAAGCACTAAGCCTGAATAACACCGCATCAAGCCTACTAGGCACTAAGCCAGAATAA
CACCGAATCT
Found at i:43775547 original size:27 final size:27
Alignment explanation
Indices: 43775517--43775568 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
43775507 GCAGGGTCTG
43775517 CCATAGAAACTATCCCTTCATAATTTA
1 CCATAGAAACTATCCCTTCATAATTTA
* **
43775544 CCATATAGGCTATCCCTTCATAATT
1 CCATAGAAACTATCCCTTCATAATT
43775569 CGCCATAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.35
Consensus pattern (27 bp):
CCATAGAAACTATCCCTTCATAATTTA
Found at i:43775590 original size:27 final size:26
Alignment explanation
Indices: 43775560--43775778 Score: 161
Period size: 27 Copynumber: 8.1 Consensus size: 26
43775550 AGGCTATCCC
*
43775560 TTCATAATTCGCCATAAAGTCTTTTCT
1 TTCATAATTCGCCACAAAGT-TTTTCT
*
43775587 TTCATGATTCGCCACAAAGGTTTTTCT
1 TTCATAATTCGCCACAAA-GTTTTTCT
* * *
43775614 TTCAT-ATCTTGCCACAAAGACTTTTGT
1 TTCATAAT-TCGCCACAAAG-TTTTTCT
* * *
43775641 TTCATATTTCACCATAAAAGTTTTTCT
1 TTCATAATTCGCCA-CAAAGTTTTTCT
* *
43775668 TTCATGATTCGCCACAAAGGTTTTCCT
1 TTCATAATTCGCCACAAA-GTTTTTCT
* * * *
43775695 TTCGTATTTCGCCATAAAATTTTTCCT
1 TTCATAATTCGCCACAAAGTTTTT-CT
** * *
43775722 TTTGTATTTCGCCACAAAGGCTTTTCT
1 TTCATAATTCGCCACAAA-GTTTTTCT
* * *
43775749 TTCATGATTCACCACAAAGGCTTTTCT
1 TTCATAATTCGCCACAAA-GTTTTTCT
43775776 TTC
1 TTC
43775779 TTGACGTATT
Statistics
Matches: 153, Mismatches: 31, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
26 10 0.07
27 132 0.86
28 11 0.07
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.43
Consensus pattern (26 bp):
TTCATAATTCGCCACAAAGTTTTTCT
Found at i:43775618 original size:54 final size:54
Alignment explanation
Indices: 43775560--43775778 Score: 196
Period size: 54 Copynumber: 4.1 Consensus size: 54
43775550 AGGCTATCCC
* *
43775560 TTCATAATTCGCCATAAAGTCTTTTCTTTCATGA-TTCGCCACAAAGGTTTTTCT
1 TTCATAATTCGCCACAAAGTCTTTTCTTTCAT-ATTTCACCACAAAGGTTTTTCT
* * * * *
43775614 TTCAT-ATCTTGCCACAAAGACTTTTGTTTCATATTTCACCATAAAAGTTTTTCT
1 TTCATAAT-TCGCCACAAAGTCTTTTCTTTCATATTTCACCACAAAGGTTTTTCT
* * * * * *
43775668 TTCATGATTCGCCACAAAGGT-TTTCCTTTCGTATTTCGCCATAAA-ATTTTTCCT
1 TTCATAATTCGCCACAAA-GTCTTTTCTTTCATATTTCACCACAAAGGTTTTT-CT
** * * *
43775722 TTTGTATTTCGCCACAAAGGCTTTTCTTTCATGA-TTCACCACAAAGGCTTTTCT
1 TTCATAATTCGCCACAAAGTCTTTTCTTTCAT-ATTTCACCACAAAGGTTTTTCT
43775776 TTC
1 TTC
43775779 TTGACGTATT
Statistics
Matches: 131, Mismatches: 26, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
53 9 0.07
54 114 0.87
55 8 0.06
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.43
Consensus pattern (54 bp):
TTCATAATTCGCCACAAAGTCTTTTCTTTCATATTTCACCACAAAGGTTTTTCT
Found at i:43775668 original size:81 final size:81
Alignment explanation
Indices: 43775560--43775778 Score: 264
Period size: 81 Copynumber: 2.7 Consensus size: 81
43775550 AGGCTATCCC
*
43775560 TTCATAATTCGCCAT-AAAGTCTTTTCTTTCATGATTCGCCACAAAGGTTTTTCTTTCATATCTT
1 TTCATATTTCGCCATAAAAGT-TTTTCTTTCATGATTCGCCACAAAGGTTTTTCTTTCATAT-TT
*
43775624 -GCCACAAAGACTTTT-GT
64 CGCCACAAA-ACTTTTCCT
* * *
43775641 TTCATATTTCACCATAAAAGTTTTTCTTTCATGATTCGCCACAAAGGTTTTCCTTTCGTATTTCG
1 TTCATATTTCGCCATAAAAGTTTTTCTTTCATGATTCGCCACAAAGGTTTTTCTTTCATATTTCG
* *
43775706 CCATAAAATTTTTCCT
66 CCACAAAACTTTTCCT
** * * * * *
43775722 TTTGTATTTCGCCACAAAGGCTTTTCTTTCATGATTCACCACAAAGGCTTTTCTTTC
1 TTCATATTTCGCCATAAAAGTTTTTCTTTCATGATTCGCCACAAAGGTTTTTCTTTC
43775779 TTGACGTATT
Statistics
Matches: 119, Mismatches: 16, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
80 7 0.06
81 107 0.90
82 5 0.04
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.43
Consensus pattern (81 bp):
TTCATATTTCGCCATAAAAGTTTTTCTTTCATGATTCGCCACAAAGGTTTTTCTTTCATATTTCG
CCACAAAACTTTTCCT
Found at i:43777342 original size:25 final size:26
Alignment explanation
Indices: 43777306--43777405 Score: 136
Period size: 25 Copynumber: 4.0 Consensus size: 26
43777296 ACAATAAACA
*
43777306 CGAATT-TCT-AAAAAGTCTTTGTGG
1 CGAATTATCTGAAAAAGACTTTGTGG
43777330 CGAATTATCT-AAAAAGACTTTGTGG
1 CGAATTATCTGAAAAAGACTTTGTGG
*
43777355 CGAATTATCTGAAAAAGACTTTATGG
1 CGAATTATCTGAAAAAGACTTTGTGG
* *
43777381 CGAATTCTCTGAAAAA-CCTTTGTGG
1 CGAATTATCTGAAAAAGACTTTGTGG
43777406 TAAATTCTCT
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
24 6 0.09
25 34 0.49
26 29 0.42
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (26 bp):
CGAATTATCTGAAAAAGACTTTGTGG
Found at i:43777382 original size:51 final size:49
Alignment explanation
Indices: 43777306--43777405 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 49
43777296 ACAATAAACA
* *
43777306 CGAATTTCTAAAAAGTCTTTGTGGCGAATTATCT-AAAAAGACTTTGTGG
1 CGAATTTCTAAAAAGACTTTATGGCGAATTATCTGAAAAA-ACTTTGTGG
* *
43777355 CGAATTATCTGAAAAAGACTTTATGGCGAATTCTCTGAAAAACCTTTGTGG
1 CGAATT-TCT-AAAAAGACTTTATGGCGAATTATCTGAAAAAACTTTGTGG
43777406 TAAATTCTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
49 6 0.14
50 3 0.07
51 30 0.68
52 5 0.11
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (49 bp):
CGAATTTCTAAAAAGACTTTATGGCGAATTATCTGAAAAAACTTTGTGG
Found at i:43777411 original size:25 final size:25
Alignment explanation
Indices: 43777322--43777496 Score: 95
Period size: 25 Copynumber: 7.0 Consensus size: 25
43777312 TCTAAAAAGT
* * *
43777322 CTTTGTGGCGAATTATCT-AAAAAGA
1 CTTTGTGGTGAATTCTCTGAAAAA-C
* * *
43777347 CTTTGTGGCGAATTATCTGAAAAAGA
1 CTTTGTGGTGAATTCTCTGAAAAA-C
* *
43777373 CTTTATGGCGAATTCTCTGAAAAAC
1 CTTTGTGGTGAATTCTCTGAAAAAC
* * * *
43777398 CTTTGTGGTAAATTCTCTGGAACAT
1 CTTTGTGGTGAATTCTCTGAAAAAC
* * *
43777423 CTTTGCGGTAAATCCTCT-AAAAAGC
1 CTTTGTGGTGAATTCTCTGAAAAA-C
* * * * *
43777448 CTTTATAGTGAATTCTCAGGAAAGC
1 CTTTGTGGTGAATTCTCTGAAAAAC
* *
43777473 CTTTGCGGCT-AATTCTCTAAAAAA
1 CTTTGTGG-TGAATTCTCTGAAAAA
43777497 TTCATATAGT
Statistics
Matches: 117, Mismatches: 29, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
24 3 0.03
25 81 0.69
26 33 0.28
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (25 bp):
CTTTGTGGTGAATTCTCTGAAAAAC
Found at i:43778866 original size:28 final size:28
Alignment explanation
Indices: 43778825--43778906 Score: 121
Period size: 28 Copynumber: 3.0 Consensus size: 28
43778815 ACGCCAATGA
*
43778825 ATATGAAAATGGAAGCCTTTGTGGCAAT
1 ATATGATAATGGAAGCCTTTGTGGCAAT
* *
43778853 CTATGATAATGGAAGCCTTTGTGCCAAT
1 ATATGATAATGGAAGCCTTTGTGGCAAT
*
43778881 ATATGATAATAGAAG-CTTTGTGGCAA
1 ATATGATAATGGAAGCCTTTGTGGCAA
43778907 CCACATGAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 10 0.21
28 38 0.79
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.30
Consensus pattern (28 bp):
ATATGATAATGGAAGCCTTTGTGGCAAT
Found at i:43788367 original size:25 final size:25
Alignment explanation
Indices: 43788339--43788388 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
43788329 CAAGGAGGAG
*
43788339 TGATGAAGTTG-GCTAGCATGCTGCA
1 TGATGAAG-TGAGCCAGCATGCTGCA
*
43788364 TGATGATGTGAGCCAGCATGCTGCA
1 TGATGAAGTGAGCCAGCATGCTGCA
43788389 CCACCAGCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (25 bp):
TGATGAAGTGAGCCAGCATGCTGCA
Found at i:43792826 original size:13 final size:13
Alignment explanation
Indices: 43792808--43792833 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43792798 GAAGAAATTG
43792808 ATAAATTTAACAT
1 ATAAATTTAACAT
43792821 ATAAATTTAACAT
1 ATAAATTTAACAT
43792834 GGAAAAACCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAAATTTAACAT
Found at i:43795201 original size:3 final size:3
Alignment explanation
Indices: 43795193--43795227 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
43795183 TTAAAGGCAA
43795193 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
43795228 AATAACAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:43795833 original size:42 final size:42
Alignment explanation
Indices: 43795773--43795895 Score: 192
Period size: 42 Copynumber: 2.9 Consensus size: 42
43795763 AAATTTTTTT
* *
43795773 ACCGTTACAATATCAAATAATTATCCAAATTAAAAACTATTG
1 ACCGTTATAATACCAAATAATTATCCAAATTAAAAACTATTG
**
43795815 ATTGTTATAATACCAAATAATTATCCAAATTAAAAACTATTG
1 ACCGTTATAATACCAAATAATTATCCAAATTAAAAACTATTG
* *
43795857 ACCGTTATAATACCAAATAATTACCCTAATTAAAAACTA
1 ACCGTTATAATACCAAATAATTATCCAAATTAAAAACTA
43795896 CTAATATTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (42 bp):
ACCGTTATAATACCAAATAATTATCCAAATTAAAAACTATTG
Found at i:43798376 original size:24 final size:24
Alignment explanation
Indices: 43798349--43798395 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
43798339 ATTGAAATGG
43798349 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
43798373 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
43798396 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:43798675 original size:40 final size:40
Alignment explanation
Indices: 43798552--43798690 Score: 117
Period size: 40 Copynumber: 3.5 Consensus size: 40
43798542 GACTTCAAGT
* * * * *
43798552 CGATCAGACACT-GGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATT-ATC
* * * *
43798592 CGATGAGGCACTGGGTG-CCAA-T-TTACTTC-AGTTTAAC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGA-ATTATC
43798629 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
* * *
43798669 CAATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
43798691 CTAGTATGTT
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
37 17 0.22
38 11 0.14
39 2 0.03
40 42 0.55
41 5 0.06
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.29
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
Found at i:43803456 original size:9 final size:9
Alignment explanation
Indices: 43803442--43803478 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
43803432 TGAGTTTTCA
43803442 AATTCGAAT
1 AATTCGAAT
43803451 AATTCGAAT
1 AATTCGAAT
43803460 AATTCGAAT
1 AATTCGAAT
43803469 AATTCGAAT
1 AATTCGAAT
43803478 A
1 A
43803479 TCAAACTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:43803555 original size:21 final size:21
Alignment explanation
Indices: 43803514--43803555 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
43803504 ACCCCAAACT
* *
43803514 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTATTCC
43803535 CTCAAAAC-TTTTACTCATTCC
1 CTCAAAACTTTTTACT-ATTCC
43803556 GATTTTCCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.24, C:0.33, G:0.00, T:0.43
Consensus pattern (21 bp):
CTCAAAACTTTTTACTATTCC
Found at i:43805455 original size:25 final size:25
Alignment explanation
Indices: 43805410--43805473 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
43805400 TACAGCTCTT
* *
43805410 ATGAGCTTTTCGTTATTTGGCTCAC
1 ATGAGCTTCTCGTTATGTGGCTCAC
*
43805435 ATGAGCTTCTCGATTA-GTGGCTCTC
1 ATGAGCTTCTCG-TTATGTGGCTCAC
* *
43805460 TTGAGCTTCCCGTT
1 ATGAGCTTCTCGTT
43805474 TATATGCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 2 0.06
25 28 0.85
26 3 0.09
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.41
Consensus pattern (25 bp):
ATGAGCTTCTCGTTATGTGGCTCAC
Found at i:43819589 original size:17 final size:17
Alignment explanation
Indices: 43819567--43819599 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
43819557 CACTCAGCGT
43819567 CTTTCTTCCCAAACTTC
1 CTTTCTTCCCAAACTTC
*
43819584 CTTTCTTGCCAAACTT
1 CTTTCTTCCCAAACTT
43819600 TCTCCAATAA
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:0.18, C:0.36, G:0.03, T:0.42
Consensus pattern (17 bp):
CTTTCTTCCCAAACTTC
Found at i:43830799 original size:9 final size:9
Alignment explanation
Indices: 43830761--43830806 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
43830751 TGAGTTTTCG
43830761 AATTCGAAT
1 AATTCGAAT
*
43830770 AACTCGAAT
1 AATTCGAAT
*
43830779 AACTCGAAT
1 AATTCGAAT
43830788 AATTCGAAT
1 AATTCGAAT
*
43830797 AATTCAAAT
1 AATTCGAAT
43830806 A
1 A
43830807 TCAAACTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTCGAAT
Found at i:43831746 original size:15 final size:16
Alignment explanation
Indices: 43831726--43831755 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43831716 GAACAAATAT
43831726 ATTCGATTC-AATTCA
1 ATTCGATTCGAATTCA
43831741 ATTCGATTCGAATTC
1 ATTCGATTCGAATTC
43831756 CATCTCACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (16 bp):
ATTCGATTCGAATTCA
Found at i:43833559 original size:21 final size:21
Alignment explanation
Indices: 43833530--43833598 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
43833520 GAAGCTCGAA
43833530 AGCTGAACAGAAGCTCATAAG
1 AGCTGAACAGAAGCTCATAAG
* *
43833551 AGCTTAACAGAAGCTCGTAAG
1 AGCTGAACAGAAGCTCATAAG
*
43833572 GGCTGAACAGAAGCTCATAAG
1 AGCTGAACAGAAGCTCATAAG
43833593 AGCTGA
1 AGCTGA
43833599 TCCATCCAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (21 bp):
AGCTGAACAGAAGCTCATAAG
Found at i:43833581 original size:42 final size:40
Alignment explanation
Indices: 43833519--43833596 Score: 129
Period size: 42 Copynumber: 1.9 Consensus size: 40
43833509 ATAAGTCAAT
43833519 AGAAGCTCGAAAGCTGAACAGAAGCTCATAAGAGCTTAAC
1 AGAAGCTCGAAAGCTGAACAGAAGCTCATAAGAGCTTAAC
*
43833559 AGAAGCTCGTAAGGGCTGAACAGAAGCTCATAAGAGCT
1 AGAAGCTCG-AA-AGCTGAACAGAAGCTCATAAGAGCT
43833597 GATCCATCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
40 9 0.26
41 2 0.06
42 24 0.69
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (40 bp):
AGAAGCTCGAAAGCTGAACAGAAGCTCATAAGAGCTTAAC
Found at i:43834318 original size:24 final size:23
Alignment explanation
Indices: 43834282--43834339 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
43834272 TAAATCCATG
* * *
43834282 TTATTCATCAAAAACATCTAATAT
1 TTATTAAT-AAAAACATCCAAAAT
*
43834306 TTATTAATAAAAACTTCCAAAAT
1 TTATTAATAAAAACATCCAAAAT
43834329 TT-TTAATAAAA
1 TTATTAATAAAA
43834340 TAAAAAACGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 9 0.30
23 14 0.47
24 7 0.23
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (23 bp):
TTATTAATAAAAACATCCAAAAT
Found at i:43839861 original size:68 final size:71
Alignment explanation
Indices: 43839736--43839871 Score: 188
Period size: 68 Copynumber: 1.9 Consensus size: 71
43839726 AATTAAACCT
* * * * *
43839736 AATCATTTTAATATTAAATTTATATAATATTTATCTAAAAGATAAACATTAAATTAAATTTAATA
1 AATCACTTTAATATTAAATTAATAAAATATCTATCT-AAAGATAAACATTAAATTAAAGTTAATA
43839801 TTAAGAC
65 TTAAGAC
*
43839808 AATCACTTTAATATTAAATTAATAAAATA-CTAT-T-AAGATAAATATTAAATTAAAGTTAATAT
1 AATCACTTTAATATTAAATTAATAAAATATCTATCTAAAGATAAACATTAAATTAAAGTTAATAT
43839870 TA
66 TA
43839872 GATCTATTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
68 28 0.48
70 1 0.02
71 3 0.05
72 26 0.45
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.40
Consensus pattern (71 bp):
AATCACTTTAATATTAAATTAATAAAATATCTATCTAAAGATAAACATTAAATTAAAGTTAATAT
TAAGAC
Found at i:43844431 original size:9 final size:9
Alignment explanation
Indices: 43844414--43844450 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
43844404 TATAGTTTGA
*
43844414 TATTTGAAT
1 TATTCGAAT
43844423 TATTCGAAT
1 TATTCGAAT
*
43844432 TATTCGAGT
1 TATTCGAAT
43844441 TATTCGAAT
1 TATTCGAAT
43844450 T
1 T
43844451 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:43858857 original size:92 final size:92
Alignment explanation
Indices: 43858700--43858883 Score: 359
Period size: 92 Copynumber: 2.0 Consensus size: 92
43858690 CTTAATTGTC
*
43858700 ATTTTGTATTAAGCTTTTGTTGTATCAATGTTTGAATTTGACATCATCGCAATTTTAGTTGGAAC
1 ATTTTGTATTAAGCTTTTGTTGTATCAATGTTTGAATTTGACATCATCGCAATTGTAGTTGGAAC
43858765 TGAAGTTATATGATTCATGATCAACTG
66 TGAAGTTATATGATTCATGATCAACTG
43858792 ATTTTGTATTAAGCTTTTGTTGTATCAATGTTTGAATTTGACATCATCGCAATTGTAGTTGGAAC
1 ATTTTGTATTAAGCTTTTGTTGTATCAATGTTTGAATTTGACATCATCGCAATTGTAGTTGGAAC
43858857 TGAAGTTATATGATTCATGATCAACTG
66 TGAAGTTATATGATTCATGATCAACTG
43858884 GGTGAAGCTT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (92 bp):
ATTTTGTATTAAGCTTTTGTTGTATCAATGTTTGAATTTGACATCATCGCAATTGTAGTTGGAAC
TGAAGTTATATGATTCATGATCAACTG
Found at i:43864752 original size:24 final size:26
Alignment explanation
Indices: 43864725--43864775 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
43864715 CTACCAAGCT
43864725 TTAAGCTAAAC-A-CATACCAAAACA
1 TTAAGCTAAACTATCATACCAAAACA
*
43864749 TTAAGCTAAGCTATCATACCAAAACA
1 TTAAGCTAAACTATCATACCAAAACA
43864775 T
1 T
43864776 ATACAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
25 1 0.04
26 13 0.54
ACGTcount: A:0.49, C:0.24, G:0.06, T:0.22
Consensus pattern (26 bp):
TTAAGCTAAACTATCATACCAAAACA
Found at i:43867137 original size:17 final size:17
Alignment explanation
Indices: 43867115--43867148 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43867105 TAGACCAATT
43867115 TTATACAATTATATATA
1 TTATACAATTATATATA
*
43867132 TTATACAATTTTATATA
1 TTATACAATTATATATA
43867149 CAAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATACAATTATATATA
Found at i:43869936 original size:24 final size:24
Alignment explanation
Indices: 43869920--43870017 Score: 70
Period size: 24 Copynumber: 4.0 Consensus size: 24
43869910 AGCGTCCCAT
43869920 TATTAGCTCTCATGAGCATCCCGA
1 TATTAGCTCTCATGAGCATCCCGA
* * * * *
43869944 TATTGGCTCTCTTCAGCTTCCTGA
1 TATTAGCTCTCATGAGCATCCCGA
* * * *
43869968 TATATGGCTCTCACGAGCTTCCCGT
1 TAT-TAGCTCTCATGAGCATCCCGA
* ** *
43869993 TAATAGCTCTTTTGAGTATCCCGA
1 TATTAGCTCTCATGAGCATCCCGA
43870017 T
1 T
43870018 TGGTTGTGAT
Statistics
Matches: 55, Mismatches: 18, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
24 37 0.67
25 18 0.33
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (24 bp):
TATTAGCTCTCATGAGCATCCCGA
Found at i:43869986 original size:25 final size:24
Alignment explanation
Indices: 43869920--43869991 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
43869910 AGCGTCCCAT
* * *
43869920 TATTAGCTCTCATGAGCATCCCGA
1 TATTGGCTCTCACGAGCTTCCCGA
* *
43869944 TATTGGCTCTCTTC-AGCTTCCTGA
1 TATTGGCTCTC-ACGAGCTTCCCGA
43869968 TATATGGCTCTCACGAGCTTCCCG
1 TAT-TGGCTCTCACGAGCTTCCCG
43869992 TTAATAGCTC
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
24 22 0.58
25 16 0.42
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.33
Consensus pattern (24 bp):
TATTGGCTCTCACGAGCTTCCCGA
Found at i:43870106 original size:25 final size:25
Alignment explanation
Indices: 43870076--43870183 Score: 105
Period size: 25 Copynumber: 4.3 Consensus size: 25
43870066 GTCCCAATAT
*
43870076 ATGGCTCTTTGGAGCTTCCCGATTA
1 ATGGCTCTTTAGAGCTTCCCGATTA
*
43870101 AAGGCTCTTTCATGAGCTTCCCGATTA
1 ATGGCTCTTT-A-GAGCTTCCCGATTA
* *
43870128 ATGGCTCTTCAGAGCTACCCGA-TA
1 ATGGCTCTTTAGAGCTTCCCGATTA
**
43870152 ATGGCTC-ACATGAGCTTCCCG-TTA
1 ATGGCTCTTTA-GAGCTTCCCGATTA
43870176 TATGGCTC
1 -ATGGCTC
43870184 GAGAGAGAGC
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
23 2 0.03
24 20 0.28
25 26 0.37
26 1 0.01
27 22 0.31
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.31
Consensus pattern (25 bp):
ATGGCTCTTTAGAGCTTCCCGATTA
Found at i:43870121 original size:27 final size:26
Alignment explanation
Indices: 43870087--43870183 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 26
43870077 TGGCTCTTTG
*
43870087 GAGCTTCCCGATTAAAGGCTCTTTCAT
1 GAGCTTCCCGATTAATGGCTC-TTCAT
43870114 GAGCTTCCCGATTAATGGCTCTTCA-
1 GAGCTTCCCGATTAATGGCTCTTCAT
* *
43870139 GAGCTACCCGA-TAATGGCTC-ACAT
1 GAGCTTCCCGATTAATGGCTCTTCAT
43870163 GAGCTTCCCG-TTATATGGCTC
1 GAGCTTCCCGATTA-ATGGCTC
43870184 GAGAGAGAGC
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
23 2 0.03
24 20 0.32
25 17 0.27
26 4 0.06
27 20 0.32
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.30
Consensus pattern (26 bp):
GAGCTTCCCGATTAATGGCTCTTCAT
Done.