Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 195 of 226
Found at i:62008266 original size:23 final size:22
Alignment explanation
Indices: 62008240--62008292 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
62008230 TATTTTTAAA
62008240 TTTTGGGCTTTTAGGT-TTTGGGC
1 TTTTGGG-TTTT-GGTATTTGGGC
*
62008263 TTTTAGGGTTTTTGTATTTGGGC
1 TTTT-GGGTTTTGGTATTTGGGC
62008286 TATTTGG
1 T-TTTGG
62008293 CTTATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 2 0.08
23 18 0.69
24 6 0.23
ACGTcount: A:0.08, C:0.06, G:0.32, T:0.55
Consensus pattern (22 bp):
TTTTGGGTTTTGGTATTTGGGC
Found at i:62008622 original size:50 final size:49
Alignment explanation
Indices: 62008568--62008696 Score: 154
Period size: 50 Copynumber: 2.6 Consensus size: 49
62008558 TTAGTGTTAC
* * *
62008568 AGTTTCATCTTG-CTCCATTGCAACTTCGA-GAAGATAAGATTTGTTGTTGT
1 AGTTTCATC-TGAC-CCACTGCAACTTCAATGAA-ATAAGATTTGTTATTGT
*
62008618 AGTTTCAATCTGACCCACTGCAACTTCAATTAAATAAGATTTGTTATTGT
1 AGTTTC-ATCTGACCCACTGCAACTTCAATGAAATAAGATTTGTTATTGT
*
62008668 AGTTTCAATCCGACCCACTGCAACTTCAA
1 AGTTTC-ATCTGACCCACTGCAACTTCAA
62008697 GGGTATAGGA
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
50 65 0.92
51 6 0.08
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.36
Consensus pattern (49 bp):
AGTTTCATCTGACCCACTGCAACTTCAATGAAATAAGATTTGTTATTGT
Found at i:62008711 original size:50 final size:50
Alignment explanation
Indices: 62008586--62008698 Score: 165
Period size: 50 Copynumber: 2.3 Consensus size: 50
62008576 CTTGCTCCAT
* * *
62008586 TGCAACTTCGA-GAAGATAAGATTTGTTGTTGTAGTTTCAATCTGACCCAC
1 TGCAACTTCAAGGAA-ATAAGATTTGTTATTGTAGTTTCAATCCGACCCAC
**
62008636 TGCAACTTCAATTAAATAAGATTTGTTATTGTAGTTTCAATCCGACCCAC
1 TGCAACTTCAAGGAAATAAGATTTGTTATTGTAGTTTCAATCCGACCCAC
62008686 TGCAACTTCAAGG
1 TGCAACTTCAAGG
62008699 GTATAGGATT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 54 0.96
51 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (50 bp):
TGCAACTTCAAGGAAATAAGATTTGTTATTGTAGTTTCAATCCGACCCAC
Found at i:62008755 original size:94 final size:94
Alignment explanation
Indices: 62008651--62008831 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 94
62008641 CTTCAATTAA
** * *
62008651 ATAAGATTTGTTATTG-TAGTTTCAATCCGACCCACTGCAACTTCAAGGG-TATAGGATTTGTAA
1 ATAAGATTTGTTA-TGATAACTTCAATCCGACCCACTACAAATTC-AGGGATATAGGATTTGTAA
* *
62008714 CTTCATCTGGCTCCACTGCAACTTTAGAGAG
64 CTTCATCTGACTCCACTACAACTTTAGAGAG
* *
62008745 ATAAGATTTGTTATGATAACTTCAATCCGACCCATTACAAATTCAGGGATATAGGATTTGTAGCT
1 ATAAGATTTGTTATGATAACTTCAATCCGACCCACTACAAATTCAGGGATATAGGATTTGTAACT
*
62008810 TCATCTTACTCCACTACAACTT
66 TCATCTGACTCCACTACAACTT
62008832 CAGGGGTATA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
93 6 0.08
94 70 0.92
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (94 bp):
ATAAGATTTGTTATGATAACTTCAATCCGACCCACTACAAATTCAGGGATATAGGATTTGTAACT
TCATCTGACTCCACTACAACTTTAGAGAG
Found at i:62008848 original size:94 final size:94
Alignment explanation
Indices: 62008625--62008834 Score: 248
Period size: 94 Copynumber: 2.2 Consensus size: 94
62008615 TGTAGTTTCA
* * * **
62008625 ATCTGAC-CCACTGCAACTTCA-ATTAAATAAGATTTGTTATTG-TAGTTTCAATCCGACCCACT
1 ATCTGACTCCACTACAACTTCAGA-GAGATAAGATTTGTTA-TGATAACTTCAATCCGACCCACT
* *
62008687 GCAACTTCAAGGGTATAGGATTTGTAACTTC
64 ACAAATTCAAGGGTATAGGATTTGTAACTTC
* * * *
62008718 ATCTGGCTCCACTGCAACTTTAGAGAGATAAGATTTGTTATGATAACTTCAATCCGACCCATTAC
1 ATCTGACTCCACTACAACTTCAGAGAGATAAGATTTGTTATGATAACTTCAATCCGACCCACTAC
*
62008783 AAATTC-AGGGATATAGGATTTGTAGCTTC
66 AAATTCAAGGG-TATAGGATTTGTAACTTC
*
62008812 ATCTTACTCCACTACAACTTCAG
1 ATCTGACTCCACTACAACTTCAG
62008835 GGGTATAGGA
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
93 12 0.12
94 86 0.87
95 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.32
Consensus pattern (94 bp):
ATCTGACTCCACTACAACTTCAGAGAGATAAGATTTGTTATGATAACTTCAATCCGACCCACTAC
AAATTCAAGGGTATAGGATTTGTAACTTC
Found at i:62008867 original size:138 final size:137
Alignment explanation
Indices: 62008682--62008961 Score: 382
Period size: 138 Copynumber: 2.0 Consensus size: 137
62008672 TCAATCCGAC
* * *
62008682 CCACTGCAACTTCAAGGGTATAGGATTTGTAACTTCATCTGGCTCCACTGCAACTTT-AGAGAGA
1 CCACTACAACTTCAAGGGTATAGGATTTGGAACTTCATCTGGCTCCACTACAACTTTAAG-GAGA
* * * *
62008746 TAAGATTTGTTATGATAACTTCAATCCGACCCATTACAAATTCAGGGATATAGGATTTGTAGCTT
65 TAAGATTTGCTATGATAACTTAAATCCGA-CCACTACAAATTCAGGGACATAGGATTTGTAGCTT
62008811 CATCTTACT
129 CATCTTACT
* * *
62008820 CCACTACAACTTCAGGGGTATAGGATTTGGAGCTTCATCTTGCTCCACTACAACTTTAAGGAGAT
1 CCACTACAACTTCAAGGGTATAGGATTTGGAACTTCATCTGGCTCCACTACAACTTTAAGGAGAT
* * * * * *
62008885 AAGATTTGCTATGGTAACTTAAATCTGACCACTGCAACTTTAGGGGCATAGGATTTGTAGCTTCA
66 AAGATTTGCTATGATAACTTAAATCCGACCACTACAAATTCAGGGACATAGGATTTGTAGCTTCA
*
62008950 TCTTGCT
131 TCTTACT
62008957 CCACT
1 CCACT
62008962 GCAAATTTAG
Statistics
Matches: 124, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
137 42 0.34
138 80 0.65
139 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (137 bp):
CCACTACAACTTCAAGGGTATAGGATTTGGAACTTCATCTGGCTCCACTACAACTTTAAGGAGAT
AAGATTTGCTATGATAACTTAAATCCGACCACTACAAATTCAGGGACATAGGATTTGTAGCTTCA
TCTTACT
Found at i:62009054 original size:94 final size:94
Alignment explanation
Indices: 62008820--62009310 Score: 549
Period size: 94 Copynumber: 5.2 Consensus size: 94
62008810 TCATCTTACT
* * * * * *
62008820 CCACTACAACTTCAGGGGTATAGGATTTGGAGCTTCATCTTGCTCCACTACAACTTTAAGGAGAT
1 CCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
* * *
62008885 AAGATTTGCTATGGTAACTTAAATCTGA-
66 AAGATTCGCTATGGTAACTTCATTCTGAC
* * *
62008913 CCACTGCAACTTTAGGGGCATAGGATTTGTAGCTTCATCTTGCTCCACTGCAAATTTAGGGAGAT
1 CCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
*
62008978 AAGATTCAGC-ATAGTAACTTCATTCTGAC
66 AAGATTC-GCTATGGTAACTTCATTCTGAC
* * * * * *
62009007 CCATTACAGCTTTAGGGGCATAGGATTTGTAGCTTCATCTTGCTCCACTGTAACTTCAGGTA-AC
1 CCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGA-
*
62009071 TAAGATTCGCTATGGTAACTTCAATGC-GAC
65 TAAGATTCGCTATGGTAACTTC-ATTCTGAC
** * * * *
62009101 CTGCTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTACTCCATTGCAACTTCAAGGAGAT
1 CCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
* * *
62009166 AAGATTCGCTATGGTAGCTTCAATCTAAC
66 AAGATTCGCTATGGTAACTTCATTCTGAC
* * * * *
62009195 CCACTGCAACTTTAGGGGTATAGGATTTATAACTTCATCTTACTCCATTGTAACTTCAGGGAGAT
1 CCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
* * * ** *
62009260 AAGATTCACCATTGTAGTTTCATTCTAAC
66 AAGATTCGCTATGGTAACTTCATTCTGAC
* *
62009289 CTACTGCAACTTCAGGGGTATA
1 CCACTGCAACTTTAGGGGTATA
62009311 AAAACTGTAG
Statistics
Matches: 341, Mismatches: 50, Indels: 13
0.84 0.12 0.03
Matches are distributed among these distances:
93 84 0.25
94 253 0.74
95 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (94 bp):
CCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGGGAGAT
AAGATTCGCTATGGTAACTTCATTCTGAC
Found at i:62009155 original size:44 final size:44
Alignment explanation
Indices: 62008682--62009255 Score: 220
Period size: 44 Copynumber: 12.4 Consensus size: 44
62008672 TCAATCCGAC
* * **
62008682 CCACTGCAACTTCAAGGGTATAGGATTTGTAACTTCATCTGGCT
1 CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTACT
* * * **
62008726 CCACTGCAACTTTAGAGAG-ATAAGATTTGTTATGATAACTTCAATCCGAC-
1 CCACTGCAACTTCAG-GGGTATAGGATTTG-TA-G----CTTC-ATCTTACT
* * * *
62008776 CCATTACAAATTCAGGGATATAGGATTTGTAGCTTCATCTTACT
1 CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTACT
* * *
62008820 CCACTACAACTTCAGGGGTATAGGATTTGGAGCTTCATCTTGCT
1 CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTACT
* * * * * *
62008864 CCACTACAACTTTAAGGAG-ATAAGATTTGCTATG-GT-AACTTAAATCT
1 CCACTGCAAC-TTCAGGGGTATAGGATTTG-TA-GCTTCATCTT--A-CT
* * *
62008911 GACCACTGCAACTTTAGGGGCATAGGATTTGTAGCTTCATCTTGCT
1 --CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTACT
* * * * *
62008957 CCACTGCAAATTTAGGGAG-ATAAGATTCAGCATAGTAACTTCATTCTGAC-
1 CCACTGCAACTTCAGGG-GTATAGGATT-----T-GTAGCTTCA-TCTTACT
* * * * * *
62009007 CCATTACAGCTTTAGGGGCATAGGATTTGTAGCTTCATCTTGCT
1 CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTACT
* * * *
62009051 CCACTGTAACTTCA--GGTAACTAAGATTCGCTATGGTAACTTCAATGC-GAC-
1 CCACTGCAACTTCAGGGGT-A-TAGGA-T---T-T-GTAGCTTC-AT-CTTACT
**
62009101 CTGCTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTACT
1 CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTACT
* * * *
62009145 CCATTGCAACTTCAAGGAG-ATAAGATTCGCTATGGTAGCTTCAATCTAAC-
1 CCACTGCAACTTC-AGGGGTATAGGA-T---T-T-GTAGCTTC-ATCTTACT
* * *
62009195 CCACTGCAACTTTAGGGGTATAGGATTTATAACTTCATCTTACT
1 CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTACT
* *
62009239 CCATTGTAACTTCAGGG
1 CCACTGCAACTTCAGGG
62009256 AGATAAGATT
Statistics
Matches: 395, Mismatches: 80, Indels: 110
0.68 0.14 0.19
Matches are distributed among these distances:
42 3 0.01
43 20 0.05
44 174 0.44
45 22 0.06
46 5 0.01
47 3 0.01
48 12 0.03
49 35 0.09
50 98 0.25
51 19 0.05
52 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGGTATAGGATTTGTAGCTTCATCTTACT
Found at i:62027969 original size:12 final size:12
Alignment explanation
Indices: 62027952--62027978 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
62027942 ACGAAAGTAC
62027952 CTTTAGTTTAAG
1 CTTTAGTTTAAG
62027964 CTTTAGTTTAAG
1 CTTTAGTTTAAG
62027976 CTT
1 CTT
62027979 AGGCTGTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (12 bp):
CTTTAGTTTAAG
Found at i:62032130 original size:19 final size:19
Alignment explanation
Indices: 62032096--62032133 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
62032086 TCAATTATCC
62032096 CTCATCTCATCATCTCTCA
1 CTCATCTCATCATCTCTCA
62032115 CTCAT-TCATCATTCTCTCA
1 CTCATCTCATCA-TCTCTCA
62032134 ACTTTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.39
Consensus pattern (19 bp):
CTCATCTCATCATCTCTCA
Found at i:62037453 original size:56 final size:50
Alignment explanation
Indices: 62037387--62037629 Score: 161
Period size: 50 Copynumber: 4.8 Consensus size: 50
62037377 GGGAATAAGA
* *
62037387 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTAGGGTTAGGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGC---A-TAGAG--AGGAGAGG
* * *
62037443 TCCCACGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATAGAGAGGAGAGG
* * * * **
62037493 TCCCCCGTAAGACCATGTCTGGGACATGACA-TGGACA-ACGATATGAGAAA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGG-CATA-GAGAGGAGAGG
* * * * * * * * **
62037543 TCTCATGTAAGACCATATCTAGGATATGGCATTTGC--AGTACAGGAAACA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATAG-AGAGGAGAGG
* * *
62037592 TCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCAT
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCAT
62037630 GTTATTATCA
Statistics
Matches: 152, Mismatches: 29, Indels: 17
0.77 0.15 0.09
Matches are distributed among these distances:
48 1 0.01
49 41 0.27
50 70 0.46
51 2 0.01
52 3 0.02
53 1 0.01
56 34 0.22
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATAGAGAGGAGAGG
Found at i:62037814 original size:26 final size:27
Alignment explanation
Indices: 62037785--62037837 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
62037775 TCAGTTGAGA
62037785 AAGAAATTTTAGCAAGGGAGGA-TAAG
1 AAGAAATTTTAGCAAGGGAGGAGTAAG
62037811 AAGAAATTTTAGCAAGGGAGGAGTAAG
1 AAGAAATTTTAGCAAGGGAGGAGTAAG
62037838 TTATAATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.45, C:0.04, G:0.32, T:0.19
Consensus pattern (27 bp):
AAGAAATTTTAGCAAGGGAGGAGTAAG
Found at i:62037882 original size:20 final size:20
Alignment explanation
Indices: 62037857--62037905 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
62037847 TGAGTTATTT
*
62037857 AAGTAAGCAAGTAAGTGAAC
1 AAGTAAGCAAGTAAGTAAAC
*
62037877 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
62037897 AAG-AAGCAA
1 AAGTAAGCAA
62037906 AGACCATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.55, C:0.06, G:0.27, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:62044279 original size:19 final size:19
Alignment explanation
Indices: 62044257--62044294 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
62044247 TCAATCATCC
62044257 CTCATCTCATCA-TCTCTCA
1 CTCAT-TCATCATTCTCTCA
62044276 CTCATTCATCATTCTCTCA
1 CTCATTCATCATTCTCTCA
62044295 ACTTTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.39
Consensus pattern (19 bp):
CTCATTCATCATTCTCTCA
Found at i:62047169 original size:16 final size:16
Alignment explanation
Indices: 62047148--62047182 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
62047138 AACCCCAACC
62047148 TCTATTCTTCTGAACT
1 TCTATTCTTCTGAACT
*
62047164 TCTATTTTTCTGAACT
1 TCTATTCTTCTGAACT
62047180 TCT
1 TCT
62047183 TCAATTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.06, T:0.54
Consensus pattern (16 bp):
TCTATTCTTCTGAACT
Found at i:62048922 original size:20 final size:20
Alignment explanation
Indices: 62048894--62048968 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
62048884 AAGACTATGA
*
62048894 ACCACTCCATTTACTTACTT
1 ACCATTCCATTTACTTACTT
62048914 ACCATTCCATTTACTTACTTT
1 ACCATTCCATTTACTTAC-TT
*
62048935 A-CATGT-CATTAACTTACCTT
1 ACCAT-TCCATTTACTTA-CTT
62048955 -CCATTCCATTTACT
1 ACCATTCCATTTACT
62048969 GAGCATAAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 1 0.02
20 41 0.87
21 5 0.11
ACGTcount: A:0.25, C:0.31, G:0.01, T:0.43
Consensus pattern (20 bp):
ACCATTCCATTTACTTACTT
Found at i:62051292 original size:28 final size:29
Alignment explanation
Indices: 62051228--62051292 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
62051218 TACAAAACTC
* * *
62051228 AACCCATCTCGTCAAAATTATTTCTTCAG
1 AACCCATCCCCTCAAAACTATTTCTTCAG
62051257 AACCCATCCCCTCAAAACTATTT-TTCAG
1 AACCCATCCCCTCAAAACTATTTCTTCAG
62051285 AACCCATC
1 AACCCATC
62051293 ATGTACAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (29 bp):
AACCCATCCCCTCAAAACTATTTCTTCAG
Found at i:62051301 original size:29 final size:28
Alignment explanation
Indices: 62051228--62051301 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
62051218 TACAAAACTC
*
62051228 AACCCATCTCGTCAAAATTATTTCTTCAG
1 AACCCATCT-GTCAAAACTATTTCTTCAG
**
62051257 AACCCATCCCCTCAAAACTATTT-TTCAG
1 AACCCAT-CTGTCAAAACTATTTCTTCAG
62051285 AACCCATCATGTACAAA
1 AACCCATC-TGT-CAAA
62051302 TTATATTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
27 1 0.03
28 13 0.35
29 22 0.59
30 1 0.03
ACGTcount: A:0.35, C:0.31, G:0.05, T:0.28
Consensus pattern (28 bp):
AACCCATCTGTCAAAACTATTTCTTCAG
Found at i:62055302 original size:25 final size:25
Alignment explanation
Indices: 62055274--62055323 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
62055264 GACCATATGG
62055274 GGTAAACAAATTTAACCTAAAGAGA
1 GGTAAACAAATTTAACCTAAAGAGA
*
62055299 GGTAAACAAATTTAACTTAAAGAGA
1 GGTAAACAAATTTAACCTAAAGAGA
62055324 TATTTAGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (25 bp):
GGTAAACAAATTTAACCTAAAGAGA
Found at i:62060235 original size:11 final size:11
Alignment explanation
Indices: 62060219--62060276 Score: 80
Period size: 11 Copynumber: 5.3 Consensus size: 11
62060209 TCAATTATTT
62060219 TCTCAATTTCC
1 TCTCAATTTCC
*
62060230 TCTCAATTACC
1 TCTCAATTTCC
*
62060241 TCTCAATTTGC
1 TCTCAATTTCC
* *
62060252 TCTCAAATTGC
1 TCTCAATTTCC
62060263 TCTCAATTTCC
1 TCTCAATTTCC
62060274 TCT
1 TCT
62060277 TAAATTTCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.21, C:0.33, G:0.03, T:0.43
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:62060247 original size:22 final size:22
Alignment explanation
Indices: 62060219--62060287 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
62060209 TCAATTATTT
62060219 TCTCAATTTCCTCTC-AATTACC
1 TCTCAATTTCCTCTCAAATT-CC
* *
62060241 TCTCAATTTGCTCTCAAATTGC
1 TCTCAATTTCCTCTCAAATTCC
* *
62060263 TCTCAATTTCCTCTTAAATTTC
1 TCTCAATTTCCTCTCAAATTCC
62060285 TCT
1 TCT
62060288 TAAATCCCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
22 37 0.90
23 4 0.10
ACGTcount: A:0.22, C:0.30, G:0.03, T:0.45
Consensus pattern (22 bp):
TCTCAATTTCCTCTCAAATTCC
Found at i:62061454 original size:7 final size:7
Alignment explanation
Indices: 62061442--62061467 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
62061432 TAGTCGATTG
62061442 GTATTTA
1 GTATTTA
62061449 GTATTTA
1 GTATTTA
62061456 GTATTTA
1 GTATTTA
62061463 GTATT
1 GTATT
62061468 ATGTATATAA
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:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:62062145 original size:18 final size:18
Alignment explanation
Indices: 62062118--62062157 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
62062108 CAGGTGCATT
* *
62062118 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
62062136 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
62062154 TCCT
1 TCCT
62062158 TTTCTGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:62062714 original size:22 final size:22
Alignment explanation
Indices: 62062698--62062776 Score: 115
Period size: 22 Copynumber: 3.6 Consensus size: 22
62062688 TTTAATTGAC
*
62062698 AAACCCTAAATCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
62062720 AAAACCT-AACCCTTAAGTTAA
1 AAACCCTAAACCCTTAACTTAA
62062741 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
62062763 AAACCTTAAACCCT
1 AAACCCTAAACCCT
62062777 AAACCCTAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
21 18 0.36
22 32 0.64
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:62062735 original size:21 final size:22
Alignment explanation
Indices: 62062702--62062776 Score: 100
Period size: 21 Copynumber: 3.5 Consensus size: 22
62062692 ATTGACAAAC
*
62062702 CCTAAATCCTTAACTTAAAAAA
1 CCTAAACCCTTAACTTAAAAAA
* *
62062724 CCT-AACCCTTAAGTTAAAAAC
1 CCTAAACCCTTAACTTAAAAAA
62062745 CCTAAACCCTTAACTT-AAAAA
1 CCTAAACCCTTAACTTAAAAAA
62062766 CCTTAAACCCT
1 CC-TAAACCCT
62062777 AAACCCTAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 24 0.52
22 22 0.48
ACGTcount: A:0.44, C:0.29, G:0.01, T:0.25
Consensus pattern (22 bp):
CCTAAACCCTTAACTTAAAAAA
Found at i:62062746 original size:43 final size:43
Alignment explanation
Indices: 62062689--62062832 Score: 148
Period size: 43 Copynumber: 3.5 Consensus size: 43
62062679 AATGTATAAT
* *
62062689 TTAATTGACAAACCCTAAATCCTTAACTTAAAAAACCT-AACCC
1 TTAATT-AAAAACCCTAAACCCTTAACTTAAAAAACCTAAACCC
62062732 TTAAGTTAAAAACCCTAAACCCTTAACTT-AAAAACCTTAAACCC
1 TTAA-TTAAAAACCCTAAACCCTTAACTTAAAAAACC-TAAACCC
*
62062776 -----T--AAACCCT-AACCCTTAACTTAAAAACCCTAAACCC
1 TTAATTAAAAACCCTAAACCCTTAACTTAAAAAACCTAAACCC
62062811 TTAACTTAAAAACCCT-AACCCT
1 TTAA-TTAAAAACCCTAAACCCT
62062833 AACCCTAACC
Statistics
Matches: 86, Mismatches: 3, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
35 19 0.22
36 13 0.15
38 1 0.01
41 1 0.01
42 7 0.08
43 38 0.44
44 7 0.08
ACGTcount: A:0.44, C:0.31, G:0.01, T:0.24
Consensus pattern (43 bp):
TTAATTAAAAACCCTAAACCCTTAACTTAAAAAACCTAAACCC
Found at i:62062785 original size:57 final size:55
Alignment explanation
Indices: 62062724--62062845 Score: 208
Period size: 57 Copynumber: 2.2 Consensus size: 55
62062714 ACTTAAAAAA
* *
62062724 CCTAACCCTTAAGTTAAAAACCCTAAACCCTTAACTTAAAAACCTTAAACCCTAAAC
1 CCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCT-AACCCT-AAC
62062781 CCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAAC
1 CCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAAC
62062836 CCTAACCCTT
1 CCTAACCCTT
62062846 GACTGGTACT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
55 13 0.21
56 6 0.10
57 44 0.70
ACGTcount: A:0.41, C:0.35, G:0.01, T:0.23
Consensus pattern (55 bp):
CCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTAAC
Found at i:62062795 original size:35 final size:36
Alignment explanation
Indices: 62062741--62062811 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
62062731 CTTAAGTTAA
*
62062741 AAACCCTAAACCCTTAACTTAAAAACCTTAAACCCT
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCT
62062777 AAACCCT-AACCCTTAACTTAAAAACCCTAAACCCT
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCT
62062812 TAACTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 27 0.79
36 7 0.21
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (36 bp):
AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCT
Found at i:62062812 original size:22 final size:21
Alignment explanation
Indices: 62062777--62062832 Score: 103
Period size: 22 Copynumber: 2.6 Consensus size: 21
62062767 CTTAAACCCT
62062777 AAACCCTAACCCTTAACTTAA
1 AAACCCTAACCCTTAACTTAA
62062798 AAACCCTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTAA
62062820 AAACCCTAACCCT
1 AAACCCTAACCCT
62062833 AACCCTAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 13 0.38
22 21 0.62
ACGTcount: A:0.43, C:0.36, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACCCTAACCCTTAACTTAA
Found at i:62066192 original size:126 final size:125
Alignment explanation
Indices: 62065934--62066251 Score: 487
Period size: 126 Copynumber: 2.5 Consensus size: 125
62065924 CCCAAACATG
* * * * *
62065934 CTACTGTAGCAAAAAG-GCGTCCACGTGGGCGCGATTTCACAAATTTTTCTGATAAAGCATCATG
1 CTACTGTAGC-AAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTG
62065998 CTTGAAGCGTTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCCAGGAC
65 CTTGAAGCGTTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCCAGGAC
* * * *
62066059 CTGCTGTAGCAAAAGCACGTTCACGAGGACACGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
*
62066124 TTGAAGCGTTTTTTATACTATTTTCTCAGAAATGTCAACTCGAAATTATTTTTTCCAGGAC
66 TTGAAGCG-TTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCCAGGAC
* *
62066185 CTACTGTAGCAAAAGCGCG-TCTACGAGGGCGCGATTTCACATATTCTTCTCAGAAAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTTC-ACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTG
62066249 CTT
65 CTT
62066252 TGATTTTATC
Statistics
Matches: 174, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
124 5 0.03
125 60 0.34
126 109 0.63
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTTCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCGTTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCCAGGAC
Found at i:62066382 original size:21 final size:22
Alignment explanation
Indices: 62066342--62066384 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
62066332 CCCTAAAAAT
* *
62066342 CCTAAAAACCCTAAACCCTAAC
1 CCTAAAAACCCAAAAACCTAAC
62066364 CCTAAAAA-CCAAAAACCTAAC
1 CCTAAAAACCCAAAAACCTAAC
62066385 GTGGGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (22 bp):
CCTAAAAACCCAAAAACCTAAC
Found at i:62072236 original size:12 final size:12
Alignment explanation
Indices: 62072219--62072243 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
62072209 TTTGAAAATC
62072219 TAAAAAATTAAA
1 TAAAAAATTAAA
62072231 TAAAAAATTAAA
1 TAAAAAATTAAA
62072243 T
1 T
62072244 TCTTAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAAAAATTAAA
Found at i:62072250 original size:28 final size:28
Alignment explanation
Indices: 62072219--62072277 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
62072209 TTTGAAAATC
*
62072219 TAAAAAATTAAA-TAAAAAATTAAATTCT
1 TAAAAAATAAAAGTAAAAAATTAAATT-T
*
62072247 T-AAAAATAAAAGTAAAATATTAAATTT
1 TAAAAAATAAAAGTAAAAAATTAAATTT
62072274 TAAA
1 TAAA
62072278 TTTATGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (28 bp):
TAAAAAATAAAAGTAAAAAATTAAATTT
Found at i:62072269 original size:20 final size:20
Alignment explanation
Indices: 62072219--62072271 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
62072209 TTTGAAAATC
* *
62072219 TAAAAAATTAAATAAAAAAT
1 TAAAATATTAAATAAAAAAG
* *
62072239 TAAATTCTTAAA-AATAAAAG
1 TAAAATATTAAATAA-AAAAG
62072259 TAAAATATTAAAT
1 TAAAATATTAAAT
62072272 TTTAAATTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
TAAAATATTAAATAAAAAAG
Found at i:62074427 original size:25 final size:25
Alignment explanation
Indices: 62074358--62074470 Score: 95
Period size: 25 Copynumber: 4.5 Consensus size: 25
62074348 GAAGCTACAT
*
62074358 GTTAT-TGGCTCGCATGAGCTTCCC
1 GTTATATGGCTCACATGAGCTTCCC
** * * *
62074382 GTTATACAGCCCAGATAAGCTTCCC
1 GTTATATGGCTCACATGAGCTTCCC
* *
62074407 ATTACATGGCTCACATGAGCTTCCC
1 GTTATATGGCTCACATGAGCTTCCC
* *
62074432 GTTATATGGCTTGAGA-GAGGGCTTCCC
1 GTTATATGGC-TCACATGA--GCTTCCC
62074459 GTTATATGGCTC
1 GTTATATGGCTC
62074471 GAGAGAGGAC
Statistics
Matches: 67, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
24 5 0.07
25 41 0.61
26 4 0.06
27 17 0.25
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (25 bp):
GTTATATGGCTCACATGAGCTTCCC
Found at i:62074457 original size:27 final size:27
Alignment explanation
Indices: 62074425--62074491 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
62074415 GCTCACATGA
*
62074425 GCTTCCCGTTATATGGCTTGAGAGAGG
1 GCTTCCCGTTATATGGCTCGAGAGAGG
62074452 GCTTCCCGTTATATGGCTCGAGAGAGG
1 GCTTCCCGTTATATGGCTCGAGAGAGG
*
62074479 ACTTCCCGATTAT
1 GCTTCCCG-TTAT
62074492 GTGCTCTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 33 0.89
28 4 0.11
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.30
Consensus pattern (27 bp):
GCTTCCCGTTATATGGCTCGAGAGAGG
Found at i:62084166 original size:22 final size:22
Alignment explanation
Indices: 62084141--62084188 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
62084131 GTACAATTGA
62084141 ACTGCAAGTAAACCATAAATTT
1 ACTGCAAGTAAACCATAAATTT
62084163 ACTGCAAGTAAACCATAAATTT
1 ACTGCAAGTAAACCATAAATTT
62084185 ACTG
1 ACTG
62084189 ATACAAATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (22 bp):
ACTGCAAGTAAACCATAAATTT
Found at i:62086294 original size:37 final size:37
Alignment explanation
Indices: 62086253--62086362 Score: 211
Period size: 37 Copynumber: 3.0 Consensus size: 37
62086243 AATTAATGAA
62086253 TGATTAATAGATAATTGAAGTGAATGTGATACTGAGT
1 TGATTAATAGATAATTGAAGTGAATGTGATACTGAGT
62086290 TGATTAATAGATAATTGAAGTGAATGTGATACTGAGT
1 TGATTAATAGATAATTGAAGTGAATGTGATACTGAGT
*
62086327 TGATTAATAGATAATTGAAGTGAATGTGATATTGAG
1 TGATTAATAGATAATTGAAGTGAATGTGATACTGAG
62086363 ATTATGAAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (37 bp):
TGATTAATAGATAATTGAAGTGAATGTGATACTGAGT
Found at i:62086468 original size:35 final size:34
Alignment explanation
Indices: 62086417--62086514 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 34
62086407 TTGTTGGTTC
*
62086417 ATTTGACTAGCACTGGGCGCAACTTTTGTCAGTTT
1 ATTTGACTAGCACTGGGCACAA-TTTTGTCAGTTT
* * *
62086452 ATTTGACTAGCGCTGGGCAC-ATATTCGTCGGTTT
1 ATTTGACTAGCACTGGGCACAAT-TTTGTCAGTTT
*
62086486 ATCTGACTAGCACTGGGCACAAATTTTGT
1 ATTTGACTAGCACTGGGCAC-AATTTTGT
62086515 TGGTTTATCC
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
33 1 0.02
34 28 0.53
35 22 0.42
36 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (34 bp):
ATTTGACTAGCACTGGGCACAATTTTGTCAGTTT
Found at i:62086530 original size:35 final size:35
Alignment explanation
Indices: 62086422--62086713 Score: 142
Period size: 35 Copynumber: 8.1 Consensus size: 35
62086412 GGTTCATTTG
* * * ***
62086422 ACTAGCACTGGGCGCAACTTTTGTCAGTTTATTTG
1 ACTAGCACTGGGCACAAATTTTGTCGGTTTATCCA
* * * **
62086457 ACTAGCGCTGGGCACATA-TTCGTCGGTTTATCTG
1 ACTAGCACTGGGCACAAATTTTGTCGGTTTATCCA
*
62086491 ACTAGCACTGGGCACAAATTTTGTTGGTTTATCCA
1 ACTAGCACTGGGCACAAATTTTGTCGGTTTATCCA
* * *
62086526 ACTAG-AGCTAGGCTCACCATTTATTTTGTTGGTTTATCCA
1 ACTAGCA-CT-GG-GCA-CA--AATTTTGTCGGTTTATCCA
* *** * *
62086566 AATAGCACTGGGCACAAATAACGTTGCTTTATCCA
1 ACTAGCACTGGGCACAAATTTTGTCGGTTTATCCA
* * * *
62086601 ACTAG-AGCTGCGCTAACTAATTATTCGTCTGTTTATCCG
1 ACTAGCA-CTGGGC--ACAAATT-TT-GTCGGTTTATCCA
* * * * **
62086640 ACTAGCACTGGGCGCAACTTCTGTCAGTTTATCTG
1 ACTAGCACTGGGCACAAATTTTGTCGGTTTATCCA
*** *
62086675 ACTAGTGTTGGGCACACA-TTTGTCGGTTTATCCA
1 ACTAGCACTGGGCACAAATTTTGTCGGTTTATCCA
62086709 ACTAG
1 ACTAG
62086714 TGCTGGGTGC
Statistics
Matches: 194, Mismatches: 49, Indels: 29
0.71 0.18 0.11
Matches are distributed among these distances:
34 48 0.25
35 79 0.41
36 3 0.02
37 13 0.07
38 4 0.02
39 21 0.11
40 25 0.13
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (35 bp):
ACTAGCACTGGGCACAAATTTTGTCGGTTTATCCA
Found at i:62086625 original size:75 final size:74
Alignment explanation
Indices: 62086473--62086652 Score: 193
Period size: 75 Copynumber: 2.4 Consensus size: 74
62086463 GCTGGGCACA
* ** * *** *
62086473 TATTCGTCGGTTTATCTGACTAGCACTGGGCACAAATTTTGTTGGTTTATCCAACTAGAGCTAGG
1 TATTCGTCTGTTTATCCAAATAGCACTGGGCACAAATAACGTTGCTTTATCCAACTAGAGCTAGG
* *
62086538 CTCACCATT
66 CTAACCAAT
*
62086547 TATTTTGT-TGGTTTATCCAAATAGCACTGGGCACAAATAACGTTGCTTTATCCAACTAGAGCT-
1 TA-TTCGTCT-GTTTATCCAAATAGCACTGGGCACAAATAACGTTGCTTTATCCAACTAGAGCTA
*
62086610 GCGCTAACTAAT
64 G-GCTAACCAAT
* *
62086622 TATTCGTCTGTTTATCCGACTAGCACTGGGC
1 TATTCGTCTGTTTATCCAAATAGCACTGGGC
62086653 GCAACTTCTG
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
74 27 0.31
75 60 0.69
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (74 bp):
TATTCGTCTGTTTATCCAAATAGCACTGGGCACAAATAACGTTGCTTTATCCAACTAGAGCTAGG
CTAACCAAT
Found at i:62091133 original size:27 final size:27
Alignment explanation
Indices: 62091096--62091180 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 27
62091086 GAGGCTATCC
* *
62091096 TTCATAGTTCGCCATAAAGGCTTTTCT
1 TTCATAATTCGCCAAAAAGGCTTTTCT
* *
62091123 TTCATGATTCGCTAAAAAGGCTTTTCT
1 TTCATAATTCGCCAAAAAGGCTTTTCT
** *
62091150 TTCATAATTTTCCACAAAGGCTTTTCCT
1 TTCATAATTCGCCAAAAAGGCTTTT-CT
62091178 TTC
1 TTC
62091181 TTGACATGCT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
27 43 0.90
28 5 0.10
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (27 bp):
TTCATAATTCGCCAAAAAGGCTTTTCT
Found at i:62095146 original size:8 final size:8
Alignment explanation
Indices: 62095133--62095157 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
62095123 GCTTAGTAGT
62095133 GGTGTTTA
1 GGTGTTTA
62095141 GGTGTTTA
1 GGTGTTTA
62095149 GGTGTTTA
1 GGTGTTTA
62095157 G
1 G
62095158 TAAGGTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (8 bp):
GGTGTTTA
Found at i:62096695 original size:27 final size:27
Alignment explanation
Indices: 62096672--62096900 Score: 236
Period size: 27 Copynumber: 8.5 Consensus size: 27
62096662 AGGGGTATAA
* *
62096672 CAGTCATTTTAACCTATGATGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
*
62096699 C-GATCATTTTACCCTATGGGGGTATTT
1 CAG-TCATTTTACCCTATGAGGGTATTT
*
62096726 C-GATCATTTTACCTTATG-GTGGTATTT
1 CAG-TCATTTTACCCTATGAG-GGTATTT
62096753 CAGTCATTTTACCCTAT-AGGGGTATTT
1 CAGTCATTTTACCCTATGA-GGGTATTT
*
62096780 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
*
62096807 C-GATCATTTTACCCTATGAGAGTATTT
1 CAG-TCATTTTACCCTATGAGGGTATTT
* * * *
62096834 CGGTCATTTTACCTTCTGGGGGTATTT
1 CAGTCATTTTACCCTATGAGGGTATTT
* *
62096861 C-GTTTATTTTACCCTATGGGGGTATTT
1 CAG-TCATTTTACCCTATGAGGGTATTT
* *
62096888 CGGTCAGTTTACC
1 CAGTCATTTTACC
62096901 TATTTTAGGG
Statistics
Matches: 175, Mismatches: 17, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
26 4 0.02
27 167 0.95
28 4 0.02
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.43
Consensus pattern (27 bp):
CAGTCATTTTACCCTATGAGGGTATTT
Found at i:62096721 original size:54 final size:54
Alignment explanation
Indices: 62096663--62096901 Score: 295
Period size: 54 Copynumber: 4.4 Consensus size: 54
62096653 TCATCTCCTA
** **
62096663 GGGGTATAACAGTCATTTTAACC-TATGATGGTATTTCGATCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTT-ACCTTATGGGGGTATTTCGATCATTTTACCCTATG
* *
62096717 GGGGTATTTC-GATCATTTTACCTTATGGTGGTATTTC-AGTCATTTTACCCTATA
1 GGGGTATTTCAG-TCATTTTACCTTATGGGGGTATTTCGA-TCATTTTACCCTATG
*
62096771 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCTTATGGGGGTATTTCGATCATTTTACCCTATG
* * * * * *
62096825 AGAGTATTTCGGTCATTTTACCTTCTGGGGGTATTTCGTTTATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCTTATGGGGGTATTTCGATCATTTTACCCTATG
* *
62096879 GGGGTATTTCGGTCAGTTTACCT
1 GGGGTATTTCAGTCATTTTACCT
62096902 ATTTTAGGGT
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
53 5 0.03
54 156 0.96
55 2 0.01
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (54 bp):
GGGGTATTTCAGTCATTTTACCTTATGGGGGTATTTCGATCATTTTACCCTATG
Found at i:62096787 original size:81 final size:80
Alignment explanation
Indices: 62096672--62096901 Score: 302
Period size: 81 Copynumber: 2.8 Consensus size: 80
62096662 AGGGGTATAA
* *
62096672 CAGTCATTTTAACCTATGATGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGATCATTTTA
1 CAGTCATTTTACCCTATG-GGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGATCATTTTA
*
62096737 CCTTATG-GTGGTATTT
65 CCTTATGAG-AGTATTT
62096753 CAGTCATTTTACCCTATAGGGGTATTTC-AGTCATTTTACCCTATGGGGGTATTTCGATCATTTT
1 CAGTCATTTTACCCTAT-GGGGTATTTCGA-TCATTTTACCCTATGGGGGTATTTCGATCATTTT
*
62096817 ACCCTATGAGAGTATTT
64 ACCTTATGAGAGTATTT
* * * * * * *
62096834 CGGTCATTTTACCTTCTGGGGGTATTTCGTTTATTTTACCCTATGGGGGTATTTCGGTCAGTTTA
1 CAGTCATTTTACCCTAT-GGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGATCATTTTA
62096899 CCT
65 CCT
62096902 ATTTTAGGGT
Statistics
Matches: 132, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
80 1 0.01
81 129 0.98
82 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.43
Consensus pattern (80 bp):
CAGTCATTTTACCCTATGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGATCATTTTAC
CTTATGAGAGTATTT
Found at i:62106962 original size:25 final size:26
Alignment explanation
Indices: 62106916--62106984 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 26
62106906 TCCTGTATAT
* * *
62106916 GTATGCTCACACAAGTTGTG-AATCG
1 GTATGCTCACACGAGCTATGAAATCG
*
62106941 GTATGCTCACACGAGCTATGAAAATGG
1 GTATGCTCACACGAGCTATG-AAATCG
62106968 GCT-TGCTCACACGAGCT
1 G-TATGCTCACACGAGCT
62106985 GTGGGTCGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 17 0.46
27 19 0.51
28 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (26 bp):
GTATGCTCACACGAGCTATGAAATCG
Found at i:62114846 original size:43 final size:43
Alignment explanation
Indices: 62114789--62114905 Score: 171
Period size: 43 Copynumber: 2.7 Consensus size: 43
62114779 GAATCATATA
62114789 CGATGCCAATGTCCTAGACATGGTCTTACACATTTTCTCACTT
1 CGATGCCAATGTCCTAGACATGGTCTTACACATTTTCTCACTT
* * **
62114832 CGATGCCAACGTCCTAGACATGGTTTTACATGTTTTCTCACTT
1 CGATGCCAATGTCCTAGACATGGTCTTACACATTTTCTCACTT
* * *
62114875 CGATGCCGATGTCCCAAACATGGTCTTACAC
1 CGATGCCAATGTCCTAGACATGGTCTTACAC
62114906 GAAATCACAC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.32
Consensus pattern (43 bp):
CGATGCCAATGTCCTAGACATGGTCTTACACATTTTCTCACTT
Found at i:62115075 original size:31 final size:31
Alignment explanation
Indices: 62115035--62115168 Score: 108
Period size: 31 Copynumber: 4.3 Consensus size: 31
62115025 TGCTCAAACC
* **
62115035 AATTTGGCAACATATATCAATATATGAATCA
1 AATTCGGCAACATATATCAATATACAAATCA
** **
62115066 AATTCGGCAATGTATATCTCTATACAAATCA
1 AATTCGGCAACATATATCAATATACAAATCA
* *
62115097 AATTCGGCAATGA-ATATCCATATACAAATCA
1 AATTCGGCAA-CATATATCAATATACAAATCA
* * ** * *
62115128 AATTTGACAATGTATAACCATATACAAATCA
1 AATTCGGCAACATATATCAATATACAAATCA
*
62115159 AATTTGGCAA
1 AATTCGGCAA
62115169 TGTATAAAAC
Statistics
Matches: 84, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
31 84 1.00
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (31 bp):
AATTCGGCAACATATATCAATATACAAATCA
Found at i:62115114 original size:62 final size:62
Alignment explanation
Indices: 62115048--62115170 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 62
62115038 TTGGCAACAT
** * *
62115048 ATATCAATATATGAATCAAATTCGGCAATGTATATCTC-TATACAAATCAAATTCGGCAATGA
1 ATATCAATATACAAATCAAATTCGACAATGTATAAC-CATATACAAATCAAATTCGGCAATGA
* * *
62115110 ATATCCATATACAAATCAAATTTGACAATGTATAACCATATACAAATCAAATTTGGCAATG
1 ATATCAATATACAAATCAAATTCGACAATGTATAACCATATACAAATCAAATTCGGCAATG
62115171 TATAAAACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
61 1 0.02
62 52 0.98
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (62 bp):
ATATCAATATACAAATCAAATTCGACAATGTATAACCATATACAAATCAAATTCGGCAATGA
Found at i:62115170 original size:31 final size:31
Alignment explanation
Indices: 62115061--62115185 Score: 162
Period size: 31 Copynumber: 4.0 Consensus size: 31
62115051 TCAATATATG
*
62115061 AATCAAATTCGGCAATGTATATCTC-TATACA
1 AATCAAATTCGGCAATGTATAAC-CATATACA
* *
62115092 AATCAAATTCGGCAATGAATATCCATATACA
1 AATCAAATTCGGCAATGTATAACCATATACA
* *
62115123 AATCAAATTTGACAATGTATAACCATATACA
1 AATCAAATTCGGCAATGTATAACCATATACA
* *
62115154 AATCAAATTTGGCAATGTATAAAACATATACA
1 AATCAAATTCGGCAATGTAT-AACCATATACA
62115186 TTTAAATTAA
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
30 1 0.01
31 74 0.87
32 10 0.12
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (31 bp):
AATCAAATTCGGCAATGTATAACCATATACA
Found at i:62118202 original size:31 final size:31
Alignment explanation
Indices: 62118164--62118278 Score: 124
Period size: 31 Copynumber: 3.7 Consensus size: 31
62118154 TACAGTGTAA
** *
62118164 AGGGTATGAAAATGAAAACGTGAATGATTAT
1 AGGGTATGAAAATGAAAATATGAATGATTAC
* * **
62118195 AGGGTATG-ATATGTAAATATGAATGAAGAC
1 AGGGTATGAAAATGAAAATATGAATGATTAC
*
62118225 AGGGTATGAATATGAAAATATGAATGATTAC
1 AGGGTATGAAAATGAAAATATGAATGATTAC
* * *
62118256 AGAGTATGATAATGCAAATATGA
1 AGGGTATGAAAATGAAAATATGA
62118279 GTATTTGATG
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
30 23 0.33
31 46 0.67
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.27
Consensus pattern (31 bp):
AGGGTATGAAAATGAAAATATGAATGATTAC
Found at i:62120728 original size:15 final size:15
Alignment explanation
Indices: 62120708--62120740 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
62120698 GATTTCTTGT
62120708 TTTTCATTTATTTAC
1 TTTTCATTTATTTAC
*
62120723 TTTTCATTTATTTCC
1 TTTTCATTTATTTAC
62120738 TTT
1 TTT
62120741 CTTATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCATTTATTTAC
Found at i:62128546 original size:22 final size:22
Alignment explanation
Indices: 62128518--62128560 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
62128508 GGTATTCATA
62128518 GTTAAGGGTAATTAACAACTTT
1 GTTAAGGGTAATTAACAACTTT
*
62128540 GTTAAGGGTAATTAACGACTT
1 GTTAAGGGTAATTAACAACTT
62128561 AGTTGATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (22 bp):
GTTAAGGGTAATTAACAACTTT
Found at i:62134006 original size:6 final size:6
Alignment explanation
Indices: 62133995--62134027 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
62133985 CATTTCTGAT
62133995 CATTGC CATTGC CATTGC CATTGC CATTGC CAT
1 CATTGC CATTGC CATTGC CATTGC CATTGC CAT
62134028 GGCTACAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.33
Consensus pattern (6 bp):
CATTGC
Found at i:62135659 original size:23 final size:23
Alignment explanation
Indices: 62135633--62135679 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
62135623 TAATGGAAAC
* *
62135633 TATGGAACCT-CATCCATTGTCAT
1 TATGCAACCTCCA-CCATTCTCAT
62135656 TATGCAACCTCCACCATTCTCAT
1 TATGCAACCTCCACCATTCTCAT
62135679 T
1 T
62135680 GATAACTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.34
Consensus pattern (23 bp):
TATGCAACCTCCACCATTCTCAT
Found at i:62135710 original size:13 final size:13
Alignment explanation
Indices: 62135692--62135716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62135682 TAACTATGAT
62135692 TTTTTAAAAATTA
1 TTTTTAAAAATTA
62135705 TTTTTAAAAATT
1 TTTTTAAAAATT
62135717 TTGATGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTAAAAATTA
Found at i:62145518 original size:17 final size:18
Alignment explanation
Indices: 62145498--62145536 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
62145488 TTTAGAAATG
*
62145498 TATTTGATTTAATA-ATT
1 TATTTGATTTAAGATATT
*
62145515 TATTTTATTTAAGATATT
1 TATTTGATTTAAGATATT
62145533 TATT
1 TATT
62145537 AAGTTCAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTTGATTTAAGATATT
Found at i:62146697 original size:20 final size:20
Alignment explanation
Indices: 62146674--62146818 Score: 75
Period size: 20 Copynumber: 7.2 Consensus size: 20
62146664 CACTTACATG
*
62146674 CCCCTGTTTGTACTTCGGTA
1 CCCCTATTTGTACTTCGGTA
* * *
62146694 CCCCT-TATTGCATTTAC-GTG
1 CCCCTAT-TTGTACTT-CGGTA
* *
62146714 CCCCTATTTGTTCTTTGGTA
1 CCCCTATTTGTACTTCGGTA
* * * * *
62146734 CCCCTAATGGCACTTAC-ATG
1 CCCCTATTTGTACTT-CGGTA
* * *
62146754 CCCTTGTTTGTACTTTGGTA
1 CCCCTATTTGTACTTCGGTA
*
62146774 CCCCT-TATTGTACTTAC-GTG
1 CCCCTAT-TTGTACTT-CGGTA
62146794 CCCCTATTTGTACTTCGGTA
1 CCCCTATTTGTACTTCGGTA
62146814 CCCCT
1 CCCCT
62146819 GAATGCACAT
Statistics
Matches: 88, Mismatches: 27, Indels: 20
0.65 0.20 0.15
Matches are distributed among these distances:
19 3 0.03
20 82 0.93
21 3 0.03
ACGTcount: A:0.14, C:0.30, G:0.16, T:0.40
Consensus pattern (20 bp):
CCCCTATTTGTACTTCGGTA
Found at i:62146716 original size:40 final size:40
Alignment explanation
Indices: 62146658--62146852 Score: 212
Period size: 40 Copynumber: 4.9 Consensus size: 40
62146648 AATTATTAAA
* *
62146658 TTATTACACTTACATGCCCCTGTTTGTACTTCGGTACCCC
1 TTATTGCACTTACATGCCCCTATTTGTACTTCGGTACCCC
* * * *
62146698 TTATTGCATTTACGTGCCCCTATTTGTTCTTTGGTACCCC
1 TTATTGCACTTACATGCCCCTATTTGTACTTCGGTACCCC
* * * * *
62146738 TAATGGCACTTACATGCCCTTGTTTGTACTTTGGTACCCC
1 TTATTGCACTTACATGCCCCTATTTGTACTTCGGTACCCC
* *
62146778 TTATTGTACTTACGTGCCCCTATTTGTACTTCGGTACCCC
1 TTATTGCACTTACATGCCCCTATTTGTACTTCGGTACCCC
* * * * *
62146818 TGAATGCACAT-CTGTGCCCCTATTTGCACTTCGGT
1 TTATTGCACTTAC-ATGCCCCTATTTGTACTTCGGT
62146853 GCCTCTAATC
Statistics
Matches: 129, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
39 1 0.01
40 128 0.99
ACGTcount: A:0.16, C:0.29, G:0.16, T:0.39
Consensus pattern (40 bp):
TTATTGCACTTACATGCCCCTATTTGTACTTCGGTACCCC
Found at i:62146797 original size:80 final size:81
Alignment explanation
Indices: 62146664--62146823 Score: 259
Period size: 80 Copynumber: 2.0 Consensus size: 81
62146654 TAAATTATTA
* *
62146664 CACTTACATGCCCCTGTTTGTACTTCGGTACCCCTTATTGCATTTACGTGCCCCTATTTGTTCTT
1 CACTTACATGCCCCTGTTTGTACTTCGGTACCCCTTATTGCACTTACGTGCCCCTATTTGTACTT
*
62146729 TGGTACCCCT-AATGG
66 CGGTACCCCTGAATGG
* * *
62146744 CACTTACATGCCCTTGTTTGTACTTTGGTACCCCTTATTGTACTTACGTGCCCCTATTTGTACTT
1 CACTTACATGCCCCTGTTTGTACTTCGGTACCCCTTATTGCACTTACGTGCCCCTATTTGTACTT
62146809 CGGTACCCCTGAATG
66 CGGTACCCCTGAATG
62146824 CACATCTGTG
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 69 0.95
81 4 0.05
ACGTcount: A:0.16, C:0.29, G:0.16, T:0.39
Consensus pattern (81 bp):
CACTTACATGCCCCTGTTTGTACTTCGGTACCCCTTATTGCACTTACGTGCCCCTATTTGTACTT
CGGTACCCCTGAATGG
Found at i:62146836 original size:80 final size:80
Alignment explanation
Indices: 62146668--62146852 Score: 248
Period size: 80 Copynumber: 2.3 Consensus size: 80
62146658 TTATTACACT
* * *
62146668 TACATGCCCCTGTTTGTACTTCGGTACCCCTTATTGCATTTACGTGCCCCTATTTGTTCTTTGGT
1 TACATGCCCCTGTTTGTACTTCGGTACCCCTTATTGCACTTACGTGCCCCTATTTGTACTTCGGT
*
62146733 ACCCCTAATGGCACT
66 ACCCCTAATGGCACA
* * *
62146748 TACATGCCCTTGTTTGTACTTTGGTACCCCTTATTGTACTTACGTGCCCCTATTTGTACTTCGGT
1 TACATGCCCCTGTTTGTACTTCGGTACCCCTTATTGCACTTACGTGCCCCTATTTGTACTTCGGT
62146813 ACCCCTGAAT-GCACA
66 ACCCCT-AATGGCACA
* * *
62146828 T-CTGTGCCCCTATTTGCACTTCGGT
1 TAC-ATGCCCCTGTTTGTACTTCGGT
62146853 GCCTCTAATC
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
79 1 0.01
80 87 0.96
81 3 0.03
ACGTcount: A:0.15, C:0.30, G:0.17, T:0.38
Consensus pattern (80 bp):
TACATGCCCCTGTTTGTACTTCGGTACCCCTTATTGCACTTACGTGCCCCTATTTGTACTTCGGT
ACCCCTAATGGCACA
Found at i:62146845 original size:20 final size:20
Alignment explanation
Indices: 62146791--62146855 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
62146781 TTGTACTTAC
* *
62146791 GTGCCCCTATTTGTACTTCG
1 GTGCCCCTATTTGCACATCG
* * *
62146811 GTACCCCTGA-ATGCACATCT
1 GTGCCCCT-ATTTGCACATCG
*
62146831 GTGCCCCTATTTGCACTTCG
1 GTGCCCCTATTTGCACATCG
62146851 GTGCC
1 GTGCC
62146856 TCTAATCCCA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.34, G:0.20, T:0.32
Consensus pattern (20 bp):
GTGCCCCTATTTGCACATCG
Found at i:62146868 original size:40 final size:40
Alignment explanation
Indices: 62146791--62146898 Score: 121
Period size: 40 Copynumber: 2.7 Consensus size: 40
62146781 TTGTACTTAC
* * *
62146791 GTGCCCCTATTTGTACTTCGGTACCCCTGAATGCACATCT
1 GTGCCCCTATTTGCACTTCGGTGCCCCTGAATCCACATCT
* *
62146831 GTGCCCCTATTTGCACTTCGGTGCCTCT-AATCCCACATTT
1 GTGCCCCTATTTGCACTTCGGTGCCCCTGAAT-CCACATCT
* *
62146871 GTGCTCCT-TATTGCACTTTGGTGCCCCT
1 GTGCCCCTAT-TTGCACTTCGGTGCCCCT
62146899 ATTATGCATC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 4 0.07
40 54 0.93
ACGTcount: A:0.14, C:0.33, G:0.18, T:0.35
Consensus pattern (40 bp):
GTGCCCCTATTTGCACTTCGGTGCCCCTGAATCCACATCT
Found at i:62154913 original size:10 final size:10
Alignment explanation
Indices: 62154882--62154926 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
62154872 TTTTATTTTT
62154882 AAAATCATTAA
1 AAAATCATT-A
*
62154893 AAAACCA-TA
1 AAAATCATTA
62154902 AAAATCATTA
1 AAAATCATTA
*
62154912 AAAATTATTA
1 AAAATCATTA
62154922 AAAAT
1 AAAAT
62154927 AATATAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
9 7 0.23
10 17 0.57
11 6 0.20
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATCATTA
Found at i:62154923 original size:20 final size:20
Alignment explanation
Indices: 62154882--62154946 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
62154872 TTTTATTTTT
**
62154882 AAAATCATTAAAAAACCA-TA
1 AAAATCATT-AAAAATTATTA
62154902 AAAATCATTAAAAATTATTA
1 AAAATCATTAAAAATTATTA
* *
62154922 AAAAT-AATATAAAATTATAA
1 AAAATCATTA-AAAATTATTA
62154942 AAAAT
1 AAAAT
62154947 ACTTCTAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.23
20 30 0.77
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATCATTAAAAATTATTA
Found at i:62154947 original size:20 final size:21
Alignment explanation
Indices: 62154912--62154968 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
62154902 AAAATCATTA
*
62154912 AAAATTATTAAAAATA-ATAT
1 AAAATTATAAAAAATACATAT
* *
62154932 AAAATTATAAAAAATACTTCT
1 AAAATTATAAAAAATACATAT
62154953 AAGAATTATAAAAAAT
1 AA-AATTATAAAAAAT
62154969 TAAGGTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 15 0.47
21 4 0.12
22 13 0.41
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (21 bp):
AAAATTATAAAAAATACATAT
Found at i:62155054 original size:25 final size:22
Alignment explanation
Indices: 62155008--62155058 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 22
62154998 TTTATAAAAC
62155008 AAATTATAAATGAAAAAATATA
1 AAATTATAAATGAAAAAATATA
62155030 AAATTATGAAAATGTAAAAAATATA
1 AAATTAT--AAATG-AAAAAATATA
62155055 AAAT
1 AAAT
62155059 AATTATTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 7 0.27
24 5 0.19
25 14 0.54
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (22 bp):
AAATTATAAATGAAAAAATATA
Found at i:62155214 original size:29 final size:27
Alignment explanation
Indices: 62155136--62155237 Score: 91
Period size: 28 Copynumber: 3.6 Consensus size: 27
62155126 AAAAATGTCT
* *
62155136 AAAATACCAAAAAATTTTAAATATTATA
1 AAAATA-CAAAAAATATTAAAAATTATA
* *
62155164 AAAATACAGAAAAGTGA-AAAAAATTATA
1 AAAATACA-AAAAAT-ATTAAAAATTATA
62155192 GAAAATTACAAAAAATATTAAAAATTATA
1 -AAAA-TACAAAAAATATTAAAAATTATA
62155221 TAAAAGTA-AAAAAATAT
1 -AAAA-TACAAAAAATAT
62155238 AATTTTTTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
27 2 0.03
28 30 0.49
29 25 0.41
30 4 0.07
ACGTcount: A:0.66, C:0.04, G:0.05, T:0.25
Consensus pattern (27 bp):
AAAATACAAAAAATATTAAAAATTATA
Found at i:62155585 original size:17 final size:18
Alignment explanation
Indices: 62155565--62155601 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
62155555 TTAAAAATTC
*
62155565 ATAATTTTTA-CATTTTT
1 ATAATTTATATCATTTTT
62155582 ATAATTTATATCATTTTT
1 ATAATTTATATCATTTTT
62155600 AT
1 AT
62155602 TTTTAATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (18 bp):
ATAATTTATATCATTTTT
Found at i:62155657 original size:19 final size:18
Alignment explanation
Indices: 62155631--62155681 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
62155621 TTTTATCAAT
62155631 TTTA-AATTATTTTTAT-A
1 TTTATAATTATTTTT-TCA
62155648 GTTTATAATT-TTTTTTCA
1 -TTTATAATTATTTTTTCA
*
62155666 TTTATAATAATTTTTT
1 TTTATAATTATTTTTT
62155682 TATAAATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 9 0.31
18 16 0.55
19 4 0.14
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATAATTATTTTTTCA
Found at i:62155690 original size:22 final size:19
Alignment explanation
Indices: 62155651--62155752 Score: 57
Period size: 20 Copynumber: 5.2 Consensus size: 19
62155641 TTTTATAGTT
*
62155651 TATAATTTTTTTTCATTTA
1 TATAATTTTTTTTAATTTA
*
62155670 TAATAATTTTTTTATAAATTTC
1 T-ATAATTTTTTT-T-AATTTA
** *
62155692 TATATATTTTTTGCACTTTA
1 TATA-ATTTTTTTTAATTTA
62155712 -AT-ATTTTTTTATAATTT-
1 TATAATTTTTTT-TAATTTA
* * *
62155729 TAAAATTTCTTTATAATTTT
1 TATAATTT-TTTTTAATTTA
62155749 TATA
1 TATA
62155753 TAAACTTTAT
Statistics
Matches: 62, Mismatches: 12, Indels: 17
0.68 0.13 0.19
Matches are distributed among these distances:
17 7 0.11
18 5 0.08
19 13 0.21
20 21 0.34
21 4 0.06
22 12 0.19
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (19 bp):
TATAATTTTTTTTAATTTA
Found at i:62155730 original size:19 final size:19
Alignment explanation
Indices: 62155610--62155792 Score: 92
Period size: 19 Copynumber: 9.4 Consensus size: 19
62155600 ATTTTTAATG
*
62155610 ATTTTAATA-TGTTTTATCA
1 ATTTTAATATTTTTTTAT-A
62155629 ATTTTAA-ATTATTTTTATA
1 ATTTTAATATT-TTTTTATA
*
62155648 GTTTATAAT-TTTTTTTCAT-
1 ATTT-TAATATTTTTTT-ATA
*
62155667 -TTATAATAATTTTTTTATAA
1 ATTTTAAT-ATTTTTTTAT-A
**
62155687 ATTTCT-ATATATTTTTT-GC
1 ATTT-TAATAT-TTTTTTATA
*
62155706 ACTTTAATATTTTTTTATA
1 ATTTTAATATTTTTTTATA
* *
62155725 ATTTTAAAATTTCTTTATA
1 ATTTTAATATTTTTTTATA
* *** *
62155744 ATTTTTATATAAACTTTATG
1 ATTTTAATAT-TTTTTTATA
*
62155764 ATTTTGTATAATTTTTTTATA
1 ATTTT-AAT-ATTTTTTTATA
62155785 ATTTTAAT
1 ATTTTAAT
62155793 TATAAAATAC
Statistics
Matches: 125, Mismatches: 22, Indels: 33
0.69 0.12 0.18
Matches are distributed among these distances:
17 4 0.03
18 12 0.10
19 55 0.44
20 28 0.22
21 23 0.18
22 3 0.02
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTTTAATATTTTTTTATA
Found at i:62155748 original size:30 final size:29
Alignment explanation
Indices: 62155714--62155791 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
62155704 GCACTTTAAT
*
62155714 ATTTTTTTATAATTTTAAAATTTCTTTATA
1 ATTTTTTTATAATTTTAAAATTT-TGTATA
* * **
62155744 ATTTTTATATAAACTTTATGATTTTGTATA
1 ATTTTTTTAT-AATTTTAAAATTTTGTATA
62155774 ATTTTTTTATAATTTTAA
1 ATTTTTTTATAATTTTAA
62155792 TTATAAAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 6 0.15
30 23 0.59
31 10 0.26
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (29 bp):
ATTTTTTTATAATTTTAAAATTTTGTATA
Found at i:62160849 original size:32 final size:33
Alignment explanation
Indices: 62160811--62160873 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
62160801 TAGATTGCTC
* * *
62160811 CCCCTTA-ATAAAATTCATTTTCGATTTAAGCT
1 CCCCTTATATAAAAATAATTTTCAATTTAAGCT
62160843 CCCCTTATATAAAAATAATTTTCAATTTAAG
1 CCCCTTATATAAAAATAATTTTCAATTTAAG
62160874 GCATAAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 7 0.26
33 20 0.74
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (33 bp):
CCCCTTATATAAAAATAATTTTCAATTTAAGCT
Found at i:62161528 original size:36 final size:36
Alignment explanation
Indices: 62161488--62161572 Score: 152
Period size: 36 Copynumber: 2.3 Consensus size: 36
62161478 GAAGTCTAAT
62161488 TTTTTTTCTTTTCAAAGTCATTATTAATTTCTTGCA
1 TTTTTTTCTTTTCAAAGTCATTATTAATTTCTTGCA
62161524 TTTTTTTCTTTTCAAAGTCATTATTAATTTCTTGCA
1 TTTTTTTCTTTTCAAAGTCATTATTAATTTCTTGCA
62161560 TTTTGTTTACTTT
1 TTTT-TTT-CTTT
62161573 CTCTCCAAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
36 40 0.85
37 3 0.06
38 4 0.09
ACGTcount: A:0.20, C:0.13, G:0.06, T:0.61
Consensus pattern (36 bp):
TTTTTTTCTTTTCAAAGTCATTATTAATTTCTTGCA
Found at i:62165556 original size:20 final size:19
Alignment explanation
Indices: 62165531--62165570 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
62165521 ATTTTGTTTA
62165531 TAATTTAATAAAAACATAAT
1 TAATTTAATAAAAA-ATAAT
**
62165551 TAATTTTTTAAAAAATAAT
1 TAATTTAATAAAAAATAAT
62165570 T
1 T
62165571 TAAGAAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATTTAATAAAAAATAAT
Found at i:62172338 original size:16 final size:15
Alignment explanation
Indices: 62172317--62172353 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
62172307 TTTATTATAC
62172317 TTATAAAAATGATTT
1 TTATAAAAATGATTT
62172332 TT-TATAAAATGATTT
1 TTATA-AAAATGATTT
62172347 TTATAAA
1 TTATAAA
62172354 GAAAACTCGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.10
15 16 0.80
16 2 0.10
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
TTATAAAAATGATTT
Found at i:62172349 original size:14 final size:15
Alignment explanation
Indices: 62172317--62172353 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
62172307 TTTATTATAC
62172317 TTATAAAAATGATTTT
1 TTAT-AAAATGATTTT
62172333 TTATAAAATGA-TTT
1 TTATAAAATGATTTT
62172347 TTATAAA
1 TTATAAA
62172354 GAAAACTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.48
15 7 0.33
16 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (15 bp):
TTATAAAATGATTTT
Found at i:62179612 original size:16 final size:16
Alignment explanation
Indices: 62179592--62179644 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
62179582 TTGGTTCGCT
* *
62179592 GTAATTGAATAGAGGT
1 GTAATGGAATAGAGGC
*
62179608 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
62179624 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
62179640 GTAAT
1 GTAAT
62179645 AGGTAATTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.38, C:0.04, G:0.32, T:0.26
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:62179705 original size:44 final size:46
Alignment explanation
Indices: 62179626--62179718 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
62179616 ATAGATGCGT
* *
62179626 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTGAATGG
*
62179672 AATGGAATATAGGCATAAT-GGT-ATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTGAATGG
62179716 AAT
1 AAT
62179719 AGAGGTATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 24 0.55
45 3 0.07
46 17 0.39
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.38
Consensus pattern (46 bp):
AATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:62179715 original size:39 final size:44
Alignment explanation
Indices: 62179626--62179728 Score: 117
Period size: 39 Copynumber: 2.4 Consensus size: 44
62179616 ATAGATGCGT
* *
62179626 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTT--ATGG
*
62179672 AATGGAATATAGGCATAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTATGG
*
62179711 AATGGAATAGAGGTATAA
1 AATGGAATAGAGGCATAA
62179729 CATCATAAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 17 0.33
40 1 0.02
43 1 0.02
44 13 0.25
45 3 0.06
46 17 0.33
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (44 bp):
AATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:62179899 original size:18 final size:18
Alignment explanation
Indices: 62179876--62179927 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
62179866 TTATTATTAA
62179876 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
62179894 ATATAATTTAAT-AAAAT
1 ATATAATTTAATAAAAAT
*
62179911 ATATGAATTTACTAAAA
1 ATAT-AATTTAATAAAA
62179928 CCATAATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 9 0.29
18 19 0.61
19 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:62180096 original size:15 final size:16
Alignment explanation
Indices: 62180062--62180098 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
62180052 ATATATATAC
*
62180062 TATAAATATATTTAAA
1 TATAATTATATTTAAA
62180078 -ATAATTATA-TTAAA
1 TATAATTATATTTAAA
62180092 TATAATT
1 TATAATT
62180099 TATAATCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAATTATATTTAAA
Found at i:62193958 original size:6 final size:6
Alignment explanation
Indices: 62193947--62193976 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
62193937 CGTATTTGTT
*
62193947 TGAGTC TGAGTC TGAGTC TAAGTC TGAGTC
1 TGAGTC TGAGTC TGAGTC TGAGTC TGAGTC
62193977 ATGTTAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (6 bp):
TGAGTC
Found at i:62196277 original size:62 final size:62
Alignment explanation
Indices: 62196200--62196319 Score: 231
Period size: 62 Copynumber: 1.9 Consensus size: 62
62196190 GCTAAATAAG
62196200 TCAATTTCCATAAAGTCACTTAAATATAAACATAAAATTGAAACAAATACAATTCAAATTAT
1 TCAATTTCCATAAAGTCACTTAAATATAAACATAAAATTGAAACAAATACAATTCAAATTAT
*
62196262 TCAATTTCCATAAAGTCACTTAAATATAAACATAAAATTGAAACAAATGCAATTCAAA
1 TCAATTTCCATAAAGTCACTTAAATATAAACATAAAATTGAAACAAATACAATTCAAA
62196320 AAATAATTTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.29
Consensus pattern (62 bp):
TCAATTTCCATAAAGTCACTTAAATATAAACATAAAATTGAAACAAATACAATTCAAATTAT
Found at i:62197041 original size:11 final size:10
Alignment explanation
Indices: 62197027--62197073 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
62197017 TATACTTACT
62197027 TTAATTTTTAA
1 TTAA-TTTTAA
*
62197038 TTAATCTTAA
1 TTAATTTTAA
62197048 TTAA-TTTAA
1 TTAATTTTAA
*
62197057 TTAAAATTTAA
1 TT-AATTTTAA
62197068 TTAATT
1 TTAATT
62197074 AACCATAAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
9 6 0.19
10 14 0.45
11 11 0.35
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (10 bp):
TTAATTTTAA
Found at i:62197049 original size:10 final size:9
Alignment explanation
Indices: 62197033--62197073 Score: 55
Period size: 9 Copynumber: 4.2 Consensus size: 9
62197023 TACTTTAATT
62197033 TTTAATTAA
1 TTTAATTAA
62197042 TCTTAATTAA
1 T-TTAATTAA
62197052 TTTAATTAAAA
1 TTTAATT--AA
62197063 TTTAATTAA
1 TTTAATTAA
62197072 TT
1 TT
62197074 AACCATAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 11 0.38
10 9 0.31
11 9 0.31
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (9 bp):
TTTAATTAA
Found at i:62210978 original size:40 final size:40
Alignment explanation
Indices: 62210862--62210984 Score: 142
Period size: 40 Copynumber: 3.1 Consensus size: 40
62210852 GTTTGGACAA
* * * *
62210862 AAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTATA-C
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCG-TTTTTAGG
* * *
62210902 AAAACACCGCTAAAGATCGAGCATTAGCGACGTTTTTAGG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTAGG
* *
62210942 AAAAGGCCGCTAAAAAT-GAGCATTAGCGGCGTTTTTTGG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTAGG
62210981 AAAA
1 AAAA
62210985 ATGCCGCAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
39 29 0.41
40 41 0.59
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTTAGG
Found at i:62210996 original size:39 final size:39
Alignment explanation
Indices: 62210908--62210984 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
62210898 ATACAAAACA
*
62210908 CCGCTAAAGATCGAGCATTAGCGACGTTTTTAGGAAAAGG
1 CCGCTAAAAAT-GAGCATTAGCGACGTTTTTAGGAAAAGG
* *
62210948 CCGCTAAAAATGAGCATTAGCGGCGTTTTTTGGAAAA
1 CCGCTAAAAATGAGCATTAGCGACGTTTTTAGGAAAA
62210985 ATGCCGCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 24 0.71
40 10 0.29
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (39 bp):
CCGCTAAAAATGAGCATTAGCGACGTTTTTAGGAAAAGG
Found at i:62210997 original size:40 final size:39
Alignment explanation
Indices: 62210920--62210997 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
62210910 GCTAAAGATC
*
62210920 GAGCATTAGCGACGTTTTTAGGAAAAGGCCGCTAAAAAT
1 GAGCATTAGCGACGTTTTTAGGAAAAGGCCGCAAAAAAT
* * *
62210959 GAGCATTAGCGGCGTTTTTTGGAAAAATGCCGCAAAAAA
1 GAGCATTAGCGACGTTTTTAGG-AAAAGGCCGCAAAAAA
62210998 CCTAAGCCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 20 0.59
40 14 0.41
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (39 bp):
GAGCATTAGCGACGTTTTTAGGAAAAGGCCGCAAAAAAT
Found at i:62211092 original size:41 final size:41
Alignment explanation
Indices: 62211035--62211275 Score: 288
Period size: 41 Copynumber: 5.9 Consensus size: 41
62211025 CTTTCAGGGC
*
62211035 TTTAGCGGCGTTTCTAAAAAAGGGCCGCTAATGCTCAGAGA
1 TTTAGCGGCGTTTCTAAAAAAGCGCCGCTAATGCTCAGAGA
* *
62211076 TTTAGCGGCGTTTCTAAAAAAACGCCGCTAATGCTCAGAGC
1 TTTAGCGGCGTTTCTAAAAAAGCGCCGCTAATGCTCAGAGA
* *
62211117 TTTAGCGGTGTTTCTAAAAAAGCGCCGCTAATGCTCAGAGC
1 TTTAGCGGCGTTTCTAAAAAAGCGCCGCTAATGCTCAGAGA
* * * * *
62211158 TTTAGTGGCGTTTTTAAAAAAGCGCCGCTAATGCT-TGGGCT
1 TTTAGCGGCGTTTCTAAAAAAGCGCCGCTAATGCTCAGAG-A
* * * * *
62211199 TTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTC-GGGA
1 TTTAGCGGCGTTTCTAAAAAAGCGCCGCTAATGCTCAGAGA
* * *
62211239 TTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTC
1 -TTTAGCGGCGTTTCTAAAAAAGCGCCGCTAATGCTC
62211276 GGGCTTTTAG
Statistics
Matches: 180, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.01
41 178 0.99
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTCTAAAAAAGCGCCGCTAATGCTCAGAGA
Found at i:62211170 original size:82 final size:82
Alignment explanation
Indices: 62211028--62211282 Score: 345
Period size: 82 Copynumber: 3.1 Consensus size: 82
62211018 TCCTGAACTT
* * *
62211028 TCAGGGCTTTAGCGGCGTTTCTAAAAAAGGGCCGCTAATGCTCAGAGATTTAGCGGCGTTTCTAA
1 TCAGGGCTTTAGCGGTGTTTCTAAAAAAGCGCCGCTAATGCTCAGAGATTTAGCGGCGTTTTTAA
*
62211093 AAAAACGCCGCTAATGC
66 AAAAGCGCCGCTAATGC
* * *
62211110 TCAGAGCTTTAGCGGTGTTTCTAAAAAAGCGCCGCTAATGCTCAGAGCTTTAGTGGCGTTTTTAA
1 TCAGGGCTTTAGCGGTGTTTCTAAAAAAGCGCCGCTAATGCTCAGAGATTTAGCGGCGTTTTTAA
62211175 AAAAGCGCCGCTAATGC
66 AAAAGCGCCGCTAATGC
* * * * *
62211192 T-TGGGCTTTTAGCGGTGTTTTTGAGAAAGCGCCGCTAATGCTC-GGGATTTTAGCGGCGTTTTT
1 TCAGGGC-TTTAGCGGTGTTTCTAAAAAAGCGCCGCTAATGCTCAGAGA-TTTAGCGGCGTTTTT
* *
62211255 GAGAAAGCGCCGCTAATGC
64 AAAAAAGCGCCGCTAATGC
62211274 TC-GGGCTTT
1 TCAGGGCTTT
62211283 TAGCAGCATT
Statistics
Matches: 153, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
81 8 0.05
82 145 0.95
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (82 bp):
TCAGGGCTTTAGCGGTGTTTCTAAAAAAGCGCCGCTAATGCTCAGAGATTTAGCGGCGTTTTTAA
AAAAGCGCCGCTAATGC
Found at i:62211300 original size:29 final size:29
Alignment explanation
Indices: 62211267--62211324 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
62211257 GAAAGCGCCG
*
62211267 CTAATGCTCGGGCTTTTAGCAGCATTTTT
1 CTAATGCTCGAGCTTTTAGCAGCATTTTT
* *
62211296 CTAATGCTCGAGCTTTTAGCGGCGTTTTT
1 CTAATGCTCGAGCTTTTAGCAGCATTTTT
62211325 GAAAAAGCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (29 bp):
CTAATGCTCGAGCTTTTAGCAGCATTTTT
Found at i:62211694 original size:14 final size:14
Alignment explanation
Indices: 62211666--62211737 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
62211656 AACGTTTATA
62211666 GATTATGGAATTAGG
1 GATTATGG-ATTAGG
62211681 GATTATGGATTAGG
1 GATTATGGATTAGG
* *
62211695 GATTCTGGTTTAAGG
1 GATTATGGATT-AGG
*
62211710 G-TTGT-GATTTAGG
1 GATTATGGA-TTAGG
* *
62211723 CATTAGGGATTAGG
1 GATTATGGATTAGG
62211737 G
1 G
62211738 GTTAGAGATT
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
13 4 0.09
14 27 0.60
15 14 0.31
ACGTcount: A:0.25, C:0.03, G:0.36, T:0.36
Consensus pattern (14 bp):
GATTATGGATTAGG
Found at i:62211954 original size:85 final size:81
Alignment explanation
Indices: 62211784--62211956 Score: 195
Period size: 85 Copynumber: 2.1 Consensus size: 81
62211774 ATTCGGTGTC
* *
62211784 AGGTTAGGCTTTAGGGTTTAGATTAATTAGTGTATTTTAATTTTTATGAAATAAGGTTTAAGGGT
1 AGGTTAGGATTTAGGGTTTAGATTAATTAATGTATTTTAATTTTTATGAAATAAGGTTTAAGGGT
*
62211849 TGAGGATTAGGGATTT
66 TGAGGATTAGGGATTA
* * * * *
62211865 AGGTTAGGATTTAGGGTTTTGATTAATTAATATTTTTTTTAATTTATATATTAAATAAGGTTTAG
1 AGGTTAGGATTTAGGGTTTAGATTAATT-A-ATGTATTTTAATTT-T-TATGAAATAAGGTTTAA
* * *
62211930 GGGTT-AGTGGTTTGGGGTTA
62 GGGTTGAG-GATTAGGGATTA
62211950 AGGTTAG
1 AGGTTAG
62211957 AAGTTAAGAG
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
81 26 0.34
82 1 0.01
83 11 0.14
84 3 0.04
85 35 0.46
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.45
Consensus pattern (81 bp):
AGGTTAGGATTTAGGGTTTAGATTAATTAATGTATTTTAATTTTTATGAAATAAGGTTTAAGGGT
TGAGGATTAGGGATTA
Found at i:62212090 original size:7 final size:7
Alignment explanation
Indices: 62212075--62212117 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
62212065 ATTGTAAAAG
*
62212075 AGGGCTT
1 AGGGGTT
62212082 AGGGGTT
1 AGGGGTT
*
62212089 AGAGGTT
1 AGGGGTT
*
62212096 AGGGATT
1 AGGGGTT
62212103 AGGGGTT
1 AGGGGTT
62212110 AGGGGTT
1 AGGGGTT
62212117 A
1 A
62212118 AAGATTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.21, C:0.02, G:0.49, T:0.28
Consensus pattern (7 bp):
AGGGGTT
Found at i:62212104 original size:21 final size:21
Alignment explanation
Indices: 62212075--62212117 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
62212065 ATTGTAAAAG
*
62212075 AGGGCTTAGGGGTTAGAGGTT
1 AGGGATTAGGGGTTAGAGGTT
*
62212096 AGGGATTAGGGGTTAGGGGTT
1 AGGGATTAGGGGTTAGAGGTT
62212117 A
1 A
62212118 AAGATTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.02, G:0.49, T:0.28
Consensus pattern (21 bp):
AGGGATTAGGGGTTAGAGGTT
Found at i:62212123 original size:21 final size:21
Alignment explanation
Indices: 62212080--62212124 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
62212070 AAAAGAGGGC
**
62212080 TTAGGGGTTAGAGGTTAGGGA
1 TTAGGGGTTAGAGGTTAAAGA
*
62212101 TTAGGGGTTAGGGGTTAAAGA
1 TTAGGGGTTAGAGGTTAAAGA
62212122 TTA
1 TTA
62212125 ATTGTTTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.42, T:0.31
Consensus pattern (21 bp):
TTAGGGGTTAGAGGTTAAAGA
Found at i:62214351 original size:20 final size:20
Alignment explanation
Indices: 62214318--62214402 Score: 68
Period size: 21 Copynumber: 4.2 Consensus size: 20
62214308 TTGAGTTAAT
62214318 TTTTTTTGATAATTATGT-TTA
1 TTTTTTT-A-AATTATGTATTA
* *
62214339 TTTTCTTTAAATTAAGTGTTA
1 TTTT-TTTAAATTATGTATTA
*
62214360 TTTTTTTAATTTCATGTATTA
1 TTTTTTTAAATT-ATGTATTA
* *
62214381 TTTATTTAATTTAT-TATT-
1 TTTTTTTAAATTATGTATTA
62214399 TTTT
1 TTTT
62214403 ACATATACAT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
18 3 0.05
19 4 0.07
20 16 0.29
21 29 0.53
22 3 0.05
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (20 bp):
TTTTTTTAAATTATGTATTA
Found at i:62214360 original size:21 final size:19
Alignment explanation
Indices: 62214318--62214368 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
62214308 TTGAGTTAAT
*
62214318 TTTTTTTGATAATTATGTTTA
1 TTTTTTT-A-AATTAAGTTTA
62214339 TTTTCTTTAAATTAAGTGTTA
1 TTTT-TTTAAATTAAGT-TTA
62214360 TTTTTTTAA
1 TTTTTTTAA
62214369 TTTCATGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 12 0.44
21 12 0.44
22 3 0.11
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTTTTTAAATTAAGTTTA
Found at i:62215796 original size:43 final size:43
Alignment explanation
Indices: 62215675--62215937 Score: 216
Period size: 43 Copynumber: 6.2 Consensus size: 43
62215665 ATAATTTTTT
* * *
62215675 TAAAGGTTATGTT-TTTAGCGGCGTTTTTGTC-AGAAGCGCCGC
1 TAAAGGTTATATTCTTTAGCGGCGTTTGTGGCTA-AAGCGCCGC
* * ** * *
62215717 TAAAGGTT-TGTTCTTTAGCGGCGTTTTTAACAAAAGCGCCAC
1 TAAAGGTTATATTCTTTAGCGGCGTTTGTGGCTAAAGCGCCGC
*
62215759 TAAAGGTTATATTCTTTAGCGGCGTTTGCGGCTAAAGCGCCGC
1 TAAAGGTTATATTCTTTAGCGGCGTTTGTGGCTAAAGCGCCGC
* * * * *
62215802 TAAAGGTCACAATCTTTAGCGGCATTTGTGGCTATAGCGCCGC
1 TAAAGGTTATATTCTTTAGCGGCGTTTGTGGCTAAAGCGCCGC
* * * **
62215845 TAAAGGTTACGA-TCTTTAGCAGCGTTT-TAG-TCACAAATGCCGC
1 TAAAGGTTA-TATTCTTTAGCGGCGTTTGTGGCT-A-AAGCGCCGC
* * * *
62215888 TAAAGGTCACGA-TCTTTAGCGGCATTTGTGACTAAAGCGCCGC
1 TAAAGGTTA-TATTCTTTAGCGGCGTTTGTGGCTAAAGCGCCGC
62215931 TAAAGGT
1 TAAAGGT
62215938 CATGACCTTT
Statistics
Matches: 182, Mismatches: 31, Indels: 15
0.80 0.14 0.07
Matches are distributed among these distances:
41 5 0.03
42 43 0.24
43 130 0.71
44 3 0.02
45 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (43 bp):
TAAAGGTTATATTCTTTAGCGGCGTTTGTGGCTAAAGCGCCGC
Found at i:62215861 original size:86 final size:85
Alignment explanation
Indices: 62215728--62215957 Score: 255
Period size: 86 Copynumber: 2.7 Consensus size: 85
62215718 AAAGGTTTGT
* * * * * * *
62215728 TCTTTAGCGGCGTTTTTAACAAAAGCGCCACTAAAGGTTATATTCTTTAGCGGCGTTTGCGGCTA
1 TCTTTAGCGGCATTTGTGACTAAAGCGCCGCTAAAGGTTAGA-TCTTTAGCGGCGTTTGAGGC-A
*
62215793 -AAGCGCCGCTAAAGGTCACAA
64 CAAACGCCGCTAAAGGTCACAA
* * * * *
62215814 TCTTTAGCGGCATTTGTGGCTATAGCGCCGCTAAAGGTTACGATCTTTAGCAGCGTTTTAGTCAC
1 TCTTTAGCGGCATTTGTGACTAAAGCGCCGCTAAAGGTTA-GATCTTTAGCGGCGTTTGAGGCAC
* *
62215879 AAATGCCGCTAAAGGTCACGA
65 AAACGCCGCTAAAGGTCACAA
* * *
62215900 TCTTTAGCGGCATTTGTGACTAAAGCGCCGCTAAAGGTCATGACCTTTAGTGGCGTTT
1 TCTTTAGCGGCATTTGTGACTAAAGCGCCGCTAAAGGTTA-GATCTTTAGCGGCGTTT
62215958 TTCACATAAA
Statistics
Matches: 120, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
85 1 0.01
86 118 0.98
87 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (85 bp):
TCTTTAGCGGCATTTGTGACTAAAGCGCCGCTAAAGGTTAGATCTTTAGCGGCGTTTGAGGCACA
AACGCCGCTAAAGGTCACAA
Found at i:62215938 original size:43 final size:43
Alignment explanation
Indices: 62215708--62215949 Score: 222
Period size: 43 Copynumber: 5.7 Consensus size: 43
62215698 TTTTTGTCAG
** * * * * *
62215708 AAGCGCCGCTAAAGGT-TTGTTCTTTAGCGGCGTTTTTAACAA
1 AAGCGCCGCTAAAGGTCACGATCTTTAGCGGCATTTGTGACTA
* * * * * *
62215750 AAGCGCCACTAAAGGTTA-TATTCTTTAGCGGCGTTTGCGGCTA
1 AAGCGCCGCTAAAGGTCACGA-TCTTTAGCGGCATTTGTGACTA
* *
62215793 AAGCGCCGCTAAAGGTCACAATCTTTAGCGGCATTTGTGGCTA
1 AAGCGCCGCTAAAGGTCACGATCTTTAGCGGCATTTGTGACTA
* * * * *
62215836 TAGCGCCGCTAAAGGTTACGATCTTTAGCAGCGTTTTAGTCAC-A
1 AAGCGCCGCTAAAGGTCACGATCTTTAGCGGC-ATTT-GTGACTA
*
62215880 AA-TGCCGCTAAAGGTCACGATCTTTAGCGGCATTTGTGACTA
1 AAGCGCCGCTAAAGGTCACGATCTTTAGCGGCATTTGTGACTA
* *
62215922 AAGCGCCGCTAAAGGTCATGACCTTTAG
1 AAGCGCCGCTAAAGGTCACGATCTTTAG
62215950 TGGCGTTTTT
Statistics
Matches: 163, Mismatches: 30, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
41 4 0.02
42 21 0.13
43 129 0.79
44 6 0.04
45 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCACGATCTTTAGCGGCATTTGTGACTA
Found at i:62219707 original size:16 final size:17
Alignment explanation
Indices: 62219681--62219719 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
62219671 TTTCCTTTCT
*
62219681 TTCTCTCCCCA-TTCATC
1 TTCT-TCCCCATTTCATA
62219698 TTCTTCCCCATTTCATA
1 TTCTTCCCCATTTCATA
62219715 TTCTT
1 TTCTT
62219720 ATTTACTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.13, C:0.38, G:0.00, T:0.49
Consensus pattern (17 bp):
TTCTTCCCCATTTCATA
Found at i:62226504 original size:9 final size:9
Alignment explanation
Indices: 62226487--62226521 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
62226477 TGAGTTTTCG
62226487 AATTCGAAT
1 AATTCGAAT
*
62226496 AACTCGAAT
1 AATTCGAAT
62226505 AATTCGAAT
1 AATTCGAAT
62226514 AATTCGAA
1 AATTCGAA
62226522 CATCAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (9 bp):
AATTCGAAT
Found at i:62226682 original size:14 final size:14
Alignment explanation
Indices: 62226665--62226713 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
62226655 CATTTCCCAC
*
62226665 CAAAATTTTACTCT
1 CAAAATTTTTCTCT
* *
62226679 CAAATTTACTTTTTCT
1 CAAAATT--TTTCTCT
62226695 CAAAATTTTTCTCT
1 CAAAATTTTTCTCT
62226709 CAAAA
1 CAAAA
62226714 ACCCTCAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 17 0.61
16 11 0.39
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (14 bp):
CAAAATTTTTCTCT
Found at i:62226907 original size:17 final size:17
Alignment explanation
Indices: 62226881--62226913 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
62226871 ACTTTCCTTC
62226881 AAACTTTTA-TTCCCCA
1 AAACTTTTATTTCCCCA
62226897 AAACTTTTTATTTCCCC
1 AAAC-TTTTATTTCCCC
62226914 CCTAAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.42
Consensus pattern (17 bp):
AAACTTTTATTTCCCCA
Found at i:62227553 original size:5 final size:5
Alignment explanation
Indices: 62227543--62227568 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
62227533 CTCGAAAATT
62227543 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
62227569 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:62229691 original size:50 final size:52
Alignment explanation
Indices: 62229622--62229752 Score: 178
Period size: 50 Copynumber: 2.6 Consensus size: 52
62229612 ATGTGTTTTG
* * * *
62229622 CATTTAATAAAGTCATGCATTATGTAACTCTCATGTTAG-TTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCAT
*
62229673 CA-TAAATT-ATTACATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCAT
1 CATTAAATTAAGT-CATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCAT
*
62229724 CATTAAATTAAGTCATGCATTAAGTAACT
1 CATTAAATTAAGTCATGCATTATGTAACT
62229753 AATTTGCTCA
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
49 2 0.03
50 29 0.42
51 15 0.22
52 21 0.30
53 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (52 bp):
CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCAT
Found at i:62237347 original size:4 final size:4
Alignment explanation
Indices: 62237338--62237363 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
62237328 TTTGTACATT
62237338 ATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA AT
62237364 GATCATATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:62238307 original size:45 final size:45
Alignment explanation
Indices: 62238238--62238338 Score: 175
Period size: 45 Copynumber: 2.2 Consensus size: 45
62238228 GAAGTATTTG
62238238 TGATACAAATTTGCAAGACTATAATTGAACTCTCCTTGACAATTA
1 TGATACAAATTTGCAAGACTATAATTGAACTCTCCTTGACAATTA
* *
62238283 TGATTCAAATTTGCAAGACTATAATTGAACTCTCCTTGGCAATTA
1 TGATACAAATTTGCAAGACTATAATTGAACTCTCCTTGACAATTA
*
62238328 TGATAAAAATT
1 TGATACAAATT
62238339 CTAACTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (45 bp):
TGATACAAATTTGCAAGACTATAATTGAACTCTCCTTGACAATTA
Found at i:62241090 original size:27 final size:27
Alignment explanation
Indices: 62241060--62241116 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
62241050 AGTCTTTGTA
62241060 GCAAACTCTAAAAGGGAT-GCCTTAGTG
1 GCAAACTCT-AAAGGGATCGCCTTAGTG
* * *
62241087 GCAAATTCTGAATGGATCGCCTTAGTG
1 GCAAACTCTAAAGGGATCGCCTTAGTG
62241114 GCA
1 GCA
62241117 TAATCTATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (27 bp):
GCAAACTCTAAAGGGATCGCCTTAGTG
Found at i:62246181 original size:20 final size:20
Alignment explanation
Indices: 62246152--62246190 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
62246142 AGAGCATGAA
*
62246152 ATATCAATACCTTAGGAAAT
1 ATATCAATACCTTAAGAAAT
*
62246172 ATATCGATACCTTAAGAAA
1 ATATCAATACCTTAAGAAA
62246191 AGTACCGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.28
Consensus pattern (20 bp):
ATATCAATACCTTAAGAAAT
Found at i:62246199 original size:20 final size:20
Alignment explanation
Indices: 62246158--62246200 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
62246148 TGAAATATCA
* *
62246158 ATACCTTAGGAAATATATCG
1 ATACCTTAAGAAATATACCG
62246178 ATACCTTAAGAAA-AGTACCG
1 ATACCTTAAGAAATA-TACCG
62246198 ATA
1 ATA
62246201 TTGGATCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (20 bp):
ATACCTTAAGAAATATACCG
Found at i:62253404 original size:23 final size:23
Alignment explanation
Indices: 62253378--62253421 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
62253368 TTTAATAATT
* *
62253378 ATTTTATGTTTATTATGTTTACA
1 ATTTGATGTTTATTATCTTTACA
*
62253401 ATTTGATTTTTATTATCTTTA
1 ATTTGATGTTTATTATCTTTA
62253422 TTTAAATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.64
Consensus pattern (23 bp):
ATTTGATGTTTATTATCTTTACA
Found at i:62255639 original size:284 final size:285
Alignment explanation
Indices: 62255171--62255739 Score: 1104
Period size: 284 Copynumber: 2.0 Consensus size: 285
62255161 ATGGTTGACC
62255171 AACTTTCTTCTCACCCATTTTCGCTGGCATTCCCTTTCATTGCCGTCCCACCACTAGCTCTTCCC
1 AACTTTCTTCTCACCCATTTTCGCTGGCATTCCCTTTCATTGCCGTCCCACCACTAGCTCTTCCC
62255236 AAATCTCTCCCTTTTCCATATTTTTTTTCTCTCTTTCGGTTAGCCTTTATCCTCTTTTTACTTGC
66 AAATCTCTCCCTTTTCCATA-TTTTTTTCTCTCTTTCGGTTAGCCTTTATCCTCTTTTTACTTGC
62255301 TTTCCCACCTCCTCCACCATGACCAACCTTGCTCTTCCACCATCACACCACCGTGTCAACACCAT
130 TTTCCCACCTCCTCCACCATGACCAACCTTGCTCTTCCACCATCACACCACCGTGTCAACACCAT
62255366 AGCCTCATTCTCCTCCTTTTTTCTCCAAGCGTCGCCACCGCTGCCGCTGTGGAAACCACTGCGCG
195 AGCCTCATTCTCCTCCTTTTTTCTCCAAGCGTCGCCACCGCTGCCGCTGTGGAAACCACTGCGCG
62255431 CCACTGCAATTTCTCTTTTTTCCTCT
260 CCACTGCAATTTCTCTTTTTTCCTCT
62255457 AACTTTCTTCTCACCCATTTTCGCTGGCATTCCCTTTCATTGCCGTCCCACCACTAGCTCTTCCC
1 AACTTTCTTCTCACCCATTTTCGCTGGCATTCCCTTTCATTGCCGTCCCACCACTAGCTCTTCCC
62255522 AAATCTCTCCCTTTTCCATA-TTTTTTCTCTCTTTCGGTTAGCCTTTATCCTCTTTTTACTTGCT
66 AAATCTCTCCCTTTTCCATATTTTTTTCTCTCTTTCGGTTAGCCTTTATCCTCTTTTTACTTGCT
*
62255586 TTCCCACCTCCTCCACCATGACCAACCTTGCTCTTCCACCATCACACCACCGTGTCAATACCATA
131 TTCCCACCTCCTCCACCATGACCAACCTTGCTCTTCCACCATCACACCACCGTGTCAACACCATA
62255651 GCCTCATTCTCCTCCTTTTTTCTCCAAGCGTCGCCACCGCTGCCGCTGTGGAAACCACTGCGCGC
196 GCCTCATTCTCCTCCTTTTTTCTCCAAGCGTCGCCACCGCTGCCGCTGTGGAAACCACTGCGCGC
*
62255716 CACTGCGATTTCTCTTTTTTCCTC
261 CACTGCAATTTCTCTTTTTTCCTC
62255740 CACCCTTTCT
Statistics
Matches: 281, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
284 196 0.70
286 85 0.30
ACGTcount: A:0.15, C:0.39, G:0.10, T:0.36
Consensus pattern (285 bp):
AACTTTCTTCTCACCCATTTTCGCTGGCATTCCCTTTCATTGCCGTCCCACCACTAGCTCTTCCC
AAATCTCTCCCTTTTCCATATTTTTTTCTCTCTTTCGGTTAGCCTTTATCCTCTTTTTACTTGCT
TTCCCACCTCCTCCACCATGACCAACCTTGCTCTTCCACCATCACACCACCGTGTCAACACCATA
GCCTCATTCTCCTCCTTTTTTCTCCAAGCGTCGCCACCGCTGCCGCTGTGGAAACCACTGCGCGC
CACTGCAATTTCTCTTTTTTCCTCT
Found at i:62256489 original size:15 final size:15
Alignment explanation
Indices: 62256469--62256502 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
62256459 TATATTTTTT
62256469 ATTATTAAAATCATG
1 ATTATTAAAATCATG
* *
62256484 ATTATTTAAATTATG
1 ATTATTAAAATCATG
62256499 ATTA
1 ATTA
62256503 AATGTGGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (15 bp):
ATTATTAAAATCATG
Found at i:62259127 original size:7 final size:7
Alignment explanation
Indices: 62259107--62259140 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
62259097 TTAATTGAAT
62259107 TTTG-GG
1 TTTGTGG
*
62259113 TTTCTGG
1 TTTGTGG
62259120 TTTGTGG
1 TTTGTGG
62259127 TTTGTGG
1 TTTGTGG
62259134 TTTGTGG
1 TTTGTGG
62259141 ACTTTTGGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
6 3 0.12
7 22 0.88
ACGTcount: A:0.00, C:0.03, G:0.41, T:0.56
Consensus pattern (7 bp):
TTTGTGG
Found at i:62265245 original size:25 final size:25
Alignment explanation
Indices: 62265189--62265237 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
62265179 ATACTCAATG
** *
62265189 TAAATCATGTATTTCATGTAACTTA
1 TAAATCATGTAAATCATATAACTTA
62265214 TAAATCATGTAAATCATATAACTT
1 TAAATCATGTAAATCATATAACTT
62265238 TTATATCAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (25 bp):
TAAATCATGTAAATCATATAACTTA
Done.