Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019240.1 Corchorus olitorius cultivar O-4 contig19273, whole genome shotgun sequence
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: 277473
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6241 original size:21 final size:21
Alignment explanation
Indices: 6193--6242 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
6183 TCCTGTGCAA
*
6193 TCTCCACCACCTCCCATACAC
1 TCTCCACCACCGCCCATACAC
* * * *
6214 TCCCCACCACCGCCCGTATAT
1 TCTCCACCACCGCCCATACAC
6235 TCTCCACC
1 TCTCCACC
6243 CCCACCACCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.56, G:0.04, T:0.20
Consensus pattern (21 bp):
TCTCCACCACCGCCCATACAC
Found at i:6878 original size:24 final size:24
Alignment explanation
Indices: 6851--6922 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
6841 TCCCCTCCAC
** *
6851 CACCTGTCTATTCTCCGCCACCAA
1 CACCTGTAAATTCTCCACCACCAA
* **
6875 CACCAGTAAATTCTCCACCACCGC
1 CACCTGTAAATTCTCCACCACCAA
* * *
6899 CACCTGTAAACTCTACTCCACCAA
1 CACCTGTAAATTCTCCACCACCAA
6923 TGCACTCTCC
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.28, C:0.44, G:0.07, T:0.21
Consensus pattern (24 bp):
CACCTGTAAATTCTCCACCACCAA
Found at i:7046 original size:24 final size:23
Alignment explanation
Indices: 7019--7095 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 23
7009 CCTGTACAAT
7019 CTCCACCACCTCCTATCTACTCCC
1 CTCCACCACCTCC-ATCTACTCCC
*
7043 CTCCACCA---CCAGTCTA-T-TC
1 CTCCACCACCTCCA-TCTACTCCC
*
7062 C-CCACCACCTCCAATCCACTCCC
1 CTCCACCACCTCC-ATCTACTCCC
7085 CTCCACCACCT
1 CTCCACCACCT
7096 GTCTATTCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
18 6 0.14
19 2 0.05
20 2 0.05
21 11 0.26
22 2 0.05
23 2 0.05
24 17 0.40
ACGTcount: A:0.19, C:0.58, G:0.01, T:0.21
Consensus pattern (23 bp):
CTCCACCACCTCCATCTACTCCC
Found at i:7058 original size:21 final size:21
Alignment explanation
Indices: 7034--7339 Score: 112
Period size: 21 Copynumber: 14.1 Consensus size: 21
7024 CCACCTCCTA
7034 TCTACTCCCCTCCACCACCAG
1 TCTACTCCCCTCCACCACCAG
* * * *
7055 TCTATTCCCCACCACCTCCAA
1 TCTACTCCCCTCCACCACCAG
* *
7076 TCCACTCCCCTCCACCACCTG
1 TCTACTCCCCTCCACCACCAG
* * * * *
7097 TCTATTCCCCACCCCCTCCTG
1 TCTACTCCCCTCCACCACCAG
*
7118 TCCACTCCCCTCCACCACCACCAG
1 TCTACTCCCCT---CCACCACCAG
** * * * *
7142 TAAACTCTCCGCCACCTCCAA
1 TCTACTCCCCTCCACCACCAG
* *
7163 TCCATTCCCCTCCACCACCACCAG
1 TCTACTCCCCT---CCACCACCAG
** * * *
7187 TAAACTCTCCGCCACCTCCAG
1 TCTACTCCCCTCCACCACCAG
* * * *
7208 TCCACTCACCGCCTCCACCAG
1 TCTACTCCCCTCCACCACCAG
* * *
7229 TATACTCTCCTCCTCCACCCATG
1 TCTACTCCCCTCCACCA-CCA-G
* * *
7252 CACT-CTCCACCACCGCCACCAG
1 -TCTACTCC-CCTCCACCACCAG
* *
7274 TGC-ATTCCCCGCCACCACCAG
1 T-CTACTCCCCTCCACCACCAG
* *
7295 TCCACTCCCCACCACCACCAG
1 TCTACTCCCCTCCACCACCAG
* * * *
7316 TTTCCTCACCTCCCCCACCAG
1 TCTACTCCCCTCCACCACCAG
7337 TCT
1 TCT
7340 TTTCACCACC
Statistics
Matches: 205, Mismatches: 67, Indels: 26
0.69 0.22 0.09
Matches are distributed among these distances:
20 1 0.00
21 153 0.75
22 8 0.04
23 7 0.03
24 36 0.18
ACGTcount: A:0.20, C:0.56, G:0.06, T:0.19
Consensus pattern (21 bp):
TCTACTCCCCTCCACCACCAG
Found at i:7083 original size:42 final size:42
Alignment explanation
Indices: 7021--7182 Score: 189
Period size: 42 Copynumber: 3.8 Consensus size: 42
7011 TGTACAATCT
* *
7021 CCACCACCTCCTATCTACTCCCCTCCACCACCAGTCTATTCC
1 CCACCACCTCCAATCCACTCCCCTCCACCACCAGTCTATTCC
*
7063 CCACCACCTCCAATCCACTCCCCTCCACCACCTGTCTATTCC
1 CCACCACCTCCAATCCACTCCCCTCCACCACCAGTCTATTCC
* ** ** * *
7105 CCACCCCCTCCTGTCCACTCCCCTCCACCACCACCAGTAAACTCT
1 CCACCACCTCCAATCCACTCCCCT---CCACCACCAGTCTATTCC
* *
7150 CCGCCACCTCCAATCCATTCCCCTCCACCACCA
1 CCACCACCTCCAATCCACTCCCCTCCACCACCA
7183 CCAGTAAACT
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 69 0.68
45 32 0.32
ACGTcount: A:0.20, C:0.57, G:0.03, T:0.20
Consensus pattern (42 bp):
CCACCACCTCCAATCCACTCCCCTCCACCACCAGTCTATTCC
Found at i:7091 original size:198 final size:194
Alignment explanation
Indices: 6338--7097 Score: 761
Period size: 198 Copynumber: 3.9 Consensus size: 194
6328 CCACCACCTA
* *
6338 CATTAAAACCTTCGGCCCCAGCACCATTAGACGATCCGCATAAGGAATCACCCATGACAAGGCTA
1 CATTAAAACCTTCGGCCCCAGCACCATTAGACGATCCCCATAAGGAATCACCCATGACAAGGCAA
* * * * * **
6403 C-GGTCGCCTCCTCCTGTACAATCTCCACCACCTGTCTATTCTTCACCACCACCATTACCAGTAA
66 CAGATCGCCTCCTCCTGTACAATCTCCACCACCT-CCTA-TCTACTCC-CCTCCACCACCAGTAA
* * * * *
6467 ATTCTCCGCCACCTCCAGTTCAGTCACCACCACCATCACCTGTATACTCTCCTCCACCAATGCAC
128 ATTCCCCACCACCTCCAG-TCA-TCTCCACCACCACCACCTGTAAACTCTCCTCCACCAATGCAC
6532 CCTC
191 CCTC
* * * * * * * *
6536 CATCAAAACCATT-GACCCCAGAACCATTGGACGATTCACATAAGGAATCACCCAAT-ATGAA-C
1 CATTAAAACC-TTCGGCCCCAGCACCATTAGACGATCCCCATAAGGAATCACCC-ATGA-CAAGG
* * * *
6598 CAA-AGATCGCCTCCTCCTGTACAATC-CTCGCCACCTCCAATCCATTCCCCTCCACCACCAACA
63 CAACAGATCGCCTCCTCCTGTACAATCTC-CACCACCTCCTATCTACTCCCCT---CCA-C--CA
* * *
6661 CCAGTAAATTCTCCTCCACCTCCAGT-TTACT-CACCACCACCACCTGTAAACTCTCCTCCACCA
121 CCAGTAAATTCCCCACCACCTCCAGTCAT-CTCCACCACCACCACCTGTAAACTCTCCTCCACCA
*
6724 ATGGACCCTC
185 ATGCACCCTC
* * *
6734 CATTAAAACCTTCGGCCCCAGCACCATTAGACGATTCCCATAAGGAATCACCTATAACAAGGCAA
1 CATTAAAACCTTCGGCCCCAGCACCATTAGACGATCCCCATAAGGAATCACCCATGACAAGGCAA
* * * * * * *
6799 C-GATTGCCTCCTCCTGTACAATCTCCATCACCTCATGTCTACTCCCCTCCACCACCTGTCTATT
66 CAGATCGCCTCCTCCTGTACAATCTCCACCACCTCCTATCTACTCCCCTCCACCACCAGT-AAAT
* * * * *
6863 CTCCGCCACCAACACCAGTAAATTCTCCACCACCGCCACCTGTAAACTCTACTCCACCAATGCAC
130 -TCC-CCACCACCTCCAGT-CA-TCTCCACCACCACCACCTGTAAACTCTCCTCCACCAATGCAC
*
6928 TCTC
191 CCTC
*
6932 CATTAAAACCTTCGGCCCCAGCACCAATAGACGATCCCCATAAGGAATCACCCATGACAAGGCAA
1 CATTAAAACCTTCGGCCCCAGCACCATTAGACGATCCCCATAAGGAATCACCCATGACAAGGCAA
* * **
6997 CAG-TCCCCTCCGCCTGTACAATCTCCACCACCTCCTATCTACTCCCCTCCACCACCAGTCTATT
66 CAGATCGCCTCCTCCTGTACAATCTCCACCACCTCCTATCTACTCCCCTCCACCACCAGTAAATT
* *
7061 CCCCACCACCTCCAATCCA-CTCC-CCTCCACCACCTGT
131 CCCCACCACCTCCAGT-CATCTCCACCACCACCACCTGT
7098 CTATTCCCCA
Statistics
Matches: 462, Mismatches: 75, Indels: 56
0.78 0.13 0.09
Matches are distributed among these distances:
192 18 0.04
193 6 0.01
194 3 0.01
195 28 0.06
196 7 0.02
197 12 0.03
198 353 0.76
199 9 0.02
200 1 0.00
201 25 0.05
ACGTcount: A:0.27, C:0.42, G:0.10, T:0.21
Consensus pattern (194 bp):
CATTAAAACCTTCGGCCCCAGCACCATTAGACGATCCCCATAAGGAATCACCCATGACAAGGCAA
CAGATCGCCTCCTCCTGTACAATCTCCACCACCTCCTATCTACTCCCCTCCACCACCAGTAAATT
CCCCACCACCTCCAGTCATCTCCACCACCACCACCTGTAAACTCTCCTCCACCAATGCACCCTC
Found at i:7094 original size:396 final size:392
Alignment explanation
Indices: 6338--7097 Score: 878
Period size: 396 Copynumber: 1.9 Consensus size: 392
6328 CCACCACCTA
* *
6338 CATTAAAACCTTCGGCCCCAGCACCATTAGACGATCCGCATAAGGAATCACCCATGACAAGGCTA
1 CATTAAAACCTTCGGCCCCAGCACCATTAGACGATCCGCATAAGGAATCACCCATAACAAGGCAA
* * **
6403 CGGTCGCCTCCTCCTGTACAATCTCCACCACCTGTCTATTCTTCACCACCACCATTACCAGTAAA
66 CGATCGCCTCCTCCTGTACAATCTCCACCACC-GTCTATTCTACACCACCACCACCACCAGTAAA
* ** * * *
6468 TTCTCCGCCACCTCCAGTTCAGTCACCACCACCATCACCTGTATACTCTCCTCCACCAATGCACC
130 TTCTCCGCCACCACCAGTAAAGTCACCACCACCACCACCTGTAAACTCTACTCCACCAATGCACC
* * * *
6533 CTCCATCAAAACCATTGACCCCAGAACCATTGGACGATTCACATAAGGAATCACCCAATATGAAC
195 CTCCATCAAAACCATTGACCCCAGAACCAATAGACGATCCACATAAGGAATCACCCAATATCAAC
* * * *
6598 CAAAGATCGCCTCCTCCTGTACAATCCTCGCCACCTCCAATCCATTCCCCTCCACCACCAACACC
260 CAAAGATCCCCTCCGCCTGTACAATCCTCACCACCTCCAATCCACTCCCCT-C-CCACC-ACACC
* * * *
6663 AGTAAATTCTCCTCCACCTCCAGTTTACTCACCACCACCACCTGTAAACTCTCCTCCACCAATGG
322 AGTAAATTCCCCACCACCTCCAATTCACTCACCACCACCACCTGTAAACTCTCCTCCACCAATGG
6728 ACCCTC
387 ACCCTC
*
6734 CATTAAAACCTTCGGCCCCAGCACCATTAGACGATTCC-CATAAGGAATCACCTATAACAAGGCA
1 CATTAAAACCTTCGGCCCCAGCACCATTAGACGA-TCCGCATAAGGAATCACCCATAACAAGGCA
* * * * * **
6798 ACGATTGCCTCCTCCTGTACAATCTCCATCACC-TC-ATGTCTACTCC-CCTCCACCACCTGTCT
65 ACGATCGCCTCCTCCTGTACAATCTCCACCACCGTCTAT-TCTACACCACCACCACCACCAGTAA
* * *
6860 ATTCTCCGCCACCAACACCAGTAAATTCTCCACCACCGCCACCTGTAAACTCTACTCCACCAATG
129 ATTCTCCGCCA-C--CACCAGTAAAGTCACCACCACCACCACCTGTAAACTCTACTCCACCAATG
* * * * *
6925 CACTCTCCATTAAAACC-TTCGGCCCCAGCACCAATAGACGATCCCCATAAGGAATCACCC-ATG
191 CACCCTCCATCAAAACCATT-GACCCCAGAACCAATAGACGATCCACATAAGGAATCACCCAAT-
* * *
6988 A-CAAGGCAACAG-TCCCCTCCGCCTGTACAAT-CTCCACCACCTCCTATCTACTCCCCT-CCA-
254 ATCAA-CCAA-AGATCCCCTCCGCCTGTACAATCCT-CACCACCTCCAATCCACTCCCCTCCCAC
** * * *
7048 C-CACCAGTCTATTCCCCACCACCTCCAATCCACTCCCCTCCACCACCTGT
316 CACACCAGTAAATTCCCCACCACCTCCAATTCACTCACCACCACCACCTGT
7098 CTATTCCCCA
Statistics
Matches: 306, Mismatches: 48, Indels: 26
0.81 0.13 0.07
Matches are distributed among these distances:
390 40 0.13
392 1 0.00
393 26 0.08
394 9 0.03
395 8 0.03
396 217 0.71
397 5 0.02
ACGTcount: A:0.27, C:0.42, G:0.10, T:0.21
Consensus pattern (392 bp):
CATTAAAACCTTCGGCCCCAGCACCATTAGACGATCCGCATAAGGAATCACCCATAACAAGGCAA
CGATCGCCTCCTCCTGTACAATCTCCACCACCGTCTATTCTACACCACCACCACCACCAGTAAAT
TCTCCGCCACCACCAGTAAAGTCACCACCACCACCACCTGTAAACTCTACTCCACCAATGCACCC
TCCATCAAAACCATTGACCCCAGAACCAATAGACGATCCACATAAGGAATCACCCAATATCAACC
AAAGATCCCCTCCGCCTGTACAATCCTCACCACCTCCAATCCACTCCCCTCCCACCACACCAGTA
AATTCCCCACCACCTCCAATTCACTCACCACCACCACCTGTAAACTCTCCTCCACCAATGGACCC
TC
Found at i:7148 original size:24 final size:24
Alignment explanation
Indices: 7121--7202 Score: 71
Period size: 24 Copynumber: 3.5 Consensus size: 24
7111 CCTCCTGTCC
7121 ACTCCCCTCCACCACCACCAGTAA
1 ACTCCCCTCCACCACCACCAGTAA
* * * **
7145 ACT---CTCCGCCACCTCCAATCC
1 ACTCCCCTCCACCACCACCAGTAA
*
7166 ATTCCCCTCCACCACCACCAGTAA
1 ACTCCCCTCCACCACCACCAGTAA
* *
7190 ACTCTCCGCCACC
1 ACTCCCCTCCACC
7203 TCCAGTCCAC
Statistics
Matches: 41, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
21 15 0.37
24 26 0.63
ACGTcount: A:0.24, C:0.55, G:0.05, T:0.16
Consensus pattern (24 bp):
ACTCCCCTCCACCACCACCAGTAA
Found at i:7185 original size:45 final size:45
Alignment explanation
Indices: 7018--7314 Score: 189
Period size: 45 Copynumber: 6.8 Consensus size: 45
7008 GCCTGTACAA
* * * ** *
7018 TCTCCACCACCTCCTATCTACTCCCCT---CCACCACCAGTCTAT
1 TCTCCGCCACCTCCAATCCACTCCCCTCCACCACCACCAGTAAAC
* * * ** *
7060 TCCCCACCACCTCCAATCCACTCCCCT---CCACCACCTGTCTAT
1 TCTCCGCCACCTCCAATCCACTCCCCTCCACCACCACCAGTAAAC
* * * **
7102 TCCCCACCCCCTCCTGTCCACTCCCCTCCACCACCACCAGTAAAC
1 TCTCCGCCACCTCCAATCCACTCCCCTCCACCACCACCAGTAAAC
*
7147 TCTCCGCCACCTCCAATCCATTCCCCTCCACCACCACCAGTAAAC
1 TCTCCGCCACCTCCAATCCACTCCCCTCCACCACCACCAGTAAAC
* * * * *
7192 TCTCCGCCACCTCCAGTCCACT---CACCGCCTCCACCAGTATAC
1 TCTCCGCCACCTCCAATCCACTCCCCTCCACCACCACCAGTAAAC
* * * * * * * * ** *
7234 TCTCCTCCTCCACCCATGCACTCTCCACCACCGCCACCAGTGCAT
1 TCTCCGCCACCTCCAATCCACTCCCCTCCACCACCACCAGTAAAC
* * * *
7279 TCCCCGCCACCACCAGTCCACTCCCCACCACCACCA
1 TCTCCGCCACCTCCAATCCACTCCCCTCCACCACCA
7315 GTTTCCTCAC
Statistics
Matches: 207, Mismatches: 42, Indels: 9
0.80 0.16 0.03
Matches are distributed among these distances:
42 94 0.45
45 113 0.55
ACGTcount: A:0.20, C:0.56, G:0.05, T:0.19
Consensus pattern (45 bp):
TCTCCGCCACCTCCAATCCACTCCCCTCCACCACCACCAGTAAAC
Found at i:7226 original size:87 final size:87
Alignment explanation
Indices: 7129--7316 Score: 214
Period size: 87 Copynumber: 2.2 Consensus size: 87
7119 CCACTCCCCT
* * *
7129 CCACCACCACCAGTAAACTCTCCGCCACCTCCAATCCATTCCCCTCCACCACCACCAGTAAACTC
1 CCACCACCACCAGTAAACTCTCCGCCACCACCAATCCACTCCCCACCACCACCACCAGTAAACTC
* *
7194 TCCGCCACCTCCAGTCCACTCA
66 CCCGCCACCACCAGTCCACTCA
* * * * * * * * * ** *
7216 CCGCCTCCACCAGTATACTCTCCTCCTCCACCCATGCACTCTCCACCACCGCCACCAGTGCATTC
1 CCACCACCACCAGTAAACTCTCCGCCACCACCAATCCACTCCCCACCACCACCACCAGTAAACTC
*
7281 CCCGCCACCACCAGTCCACTCC
66 CCCGCCACCACCAGTCCACTCA
7303 CCACCACCACCAGT
1 CCACCACCACCAGT
7317 TTCCTCACCT
Statistics
Matches: 81, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.22, C:0.54, G:0.07, T:0.16
Consensus pattern (87 bp):
CCACCACCACCAGTAAACTCTCCGCCACCACCAATCCACTCCCCACCACCACCACCAGTAAACTC
CCCGCCACCACCAGTCCACTCA
Found at i:28148 original size:88 final size:88
Alignment explanation
Indices: 28048--28223 Score: 334
Period size: 88 Copynumber: 2.0 Consensus size: 88
28038 ATTGTTTTTT
*
28048 TTTTTTTAAAAAGCAAGATTTATTAGAACCAAATATATGGGTATATAGAGGAGCCTCATTAAAAC
1 TTTTTTTAAAAAGCAAGATTTATTAGAACCAAATATATGAGTATATAGAGGAGCCTCATTAAAAC
28113 CTACAAGAGGAAAAACCCAATAG
66 CTACAAGAGGAAAAACCCAATAG
*
28136 TTTTTTTGAAAAGCAAGATTTATTAGAACCAAATATATGAGTATATAGAGGAGCCTCATTAAAAC
1 TTTTTTTAAAAAGCAAGATTTATTAGAACCAAATATATGAGTATATAGAGGAGCCTCATTAAAAC
28201 CTACAAGAGGAAAAACCCAATAG
66 CTACAAGAGGAAAAACCCAATAG
28224 AAAAAAATCC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (88 bp):
TTTTTTTAAAAAGCAAGATTTATTAGAACCAAATATATGAGTATATAGAGGAGCCTCATTAAAAC
CTACAAGAGGAAAAACCCAATAG
Found at i:31047 original size:3 final size:3
Alignment explanation
Indices: 31041--31075 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31031 ATGAAAACTT
31041 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
31076 TACAATTATA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:32513 original size:45 final size:45
Alignment explanation
Indices: 32422--32518 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 45
32412 AGCAACAATT
* * ** * *
32422 AATATTAACTTTATTTTGATGAATTATTTAAAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTAATGAATTACCTAAAGATGGAAGACTAG
* *
32467 AATATTAGTTTTATTTTAATGAATTACCTAAAGATGGAATACTAG
1 AATATTAGCTTTATTTTAATGAATTACCTAAAGATGGAAGACTAG
32512 AAT-TTAG
1 AATATTAG
32519 GCAATTAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 4 0.09
45 40 0.91
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.40
Consensus pattern (45 bp):
AATATTAGCTTTATTTTAATGAATTACCTAAAGATGGAAGACTAG
Found at i:40112 original size:5 final size:5
Alignment explanation
Indices: 40102--40130 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
40092 CTATTTACTG
40102 AAAGA AAAGA AAAGA AAAGA AAAGA AAAG
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAG
40131 GAGTGGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:42961 original size:20 final size:20
Alignment explanation
Indices: 42936--42975 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42926 TTAGGTTCAA
42936 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
42956 CTCTCACGGAATGTGAGTTT
1 CTCTCACGGAATGTGAGTTT
42976 GTTTGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (20 bp):
CTCTCACGGAATGTGAGTTT
Found at i:43243 original size:2 final size:2
Alignment explanation
Indices: 43238--43262 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43228 TCTCAAAAAA
43238 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
43263 AACAAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45990 original size:1 final size:1
Alignment explanation
Indices: 45984--46009 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
45974 ATGATAAGAG
45984 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
46010 GGTATCCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:47485 original size:23 final size:22
Alignment explanation
Indices: 47461--47504 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 22
47451 TTTTAGGGAT
47461 TAATTAATTAA-T-T-TTCATG
1 TAATTAATTAACTATGTTCATG
47480 TAATTAATTAACTATGTTCATG
1 TAATTAATTAACTATGTTCATG
47502 TAA
1 TAA
47505 AATCTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.50
20 1 0.05
21 1 0.05
22 9 0.41
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (22 bp):
TAATTAATTAACTATGTTCATG
Found at i:56792 original size:27 final size:27
Alignment explanation
Indices: 56752--56820 Score: 93
Period size: 27 Copynumber: 2.6 Consensus size: 27
56742 TTTGTGGAGT
* *
56752 ACTATGGATTTCTCTGTACCAAAAAAA
1 ACTATGGATGTCTCTCTACCAAAAAAA
* * *
56779 ATTATGGATGTCTCTCTTCCAGAAAAA
1 ACTATGGATGTCTCTCTACCAAAAAAA
56806 ACTATGGATGTCTCT
1 ACTATGGATGTCTCT
56821 AAAATTCTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (27 bp):
ACTATGGATGTCTCTCTACCAAAAAAA
Found at i:59448 original size:19 final size:21
Alignment explanation
Indices: 59413--59471 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
59403 GGAAATGTTG
* *
59413 TCACTATTTGATGTAATGAT-
1 TCACTATTAGGTGTAATGATA
*
59433 TC-CTTTTAGGTGTAATGATA
1 TCACTATTAGGTGTAATGATA
59453 TCACTATTAGGTGTAATGA
1 TCACTATTAGGTGTAATGA
59472 AGTTTCAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 14 0.42
20 4 0.12
21 15 0.45
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (21 bp):
TCACTATTAGGTGTAATGATA
Found at i:59881 original size:23 final size:23
Alignment explanation
Indices: 59861--59909 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
59851 ATGCCAAGGG
59861 AAAAGG-AAAAAAAATGGCAAGA
1 AAAAGGTAAAAAAAATGGCAAGA
* *
59883 AAAAGGTAAGAAAAATGGCAACA
1 AAAAGGTAAAAAAAATGGCAAGA
59906 AAAA
1 AAAA
59910 TGCTTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.67, C:0.06, G:0.20, T:0.06
Consensus pattern (23 bp):
AAAAGGTAAAAAAAATGGCAAGA
Found at i:59908 original size:12 final size:12
Alignment explanation
Indices: 59870--59911 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
59860 GAAAAGGAAA
59870 AAAAATGGCAAG
1 AAAAATGGCAAG
*
59882 AAAAA-GGTAAG
1 AAAAATGGCAAG
*
59893 AAAAATGGCAAC
1 AAAAATGGCAAG
59905 AAAAATG
1 AAAAATG
59912 CTTTGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.62, C:0.07, G:0.21, T:0.10
Consensus pattern (12 bp):
AAAAATGGCAAG
Found at i:61097 original size:47 final size:45
Alignment explanation
Indices: 61012--61099 Score: 149
Period size: 45 Copynumber: 1.9 Consensus size: 45
61002 GTGCGATCTG
*
61012 TTTTTTTTTTGTTTCTGGTGAATCTTTTGGAGACAAGTTGTTTTT
1 TTTTTTTTTTGTTTCTGGTGAATCTTTTGGAGAAAAGTTGTTTTT
61057 TTTTTTTTTTGTTTCTGGTGAATCTTTTGGAGAGAAAAGTTGT
1 TTTTTTTTTTGTTTCTGGTGAATCTTTT-G-GAGAAAAGTTGT
61100 AAGGCTTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 28 0.70
46 1 0.03
47 11 0.28
ACGTcount: A:0.16, C:0.06, G:0.22, T:0.57
Consensus pattern (45 bp):
TTTTTTTTTTGTTTCTGGTGAATCTTTTGGAGAAAAGTTGTTTTT
Found at i:65096 original size:21 final size:22
Alignment explanation
Indices: 65079--65124 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
65069 GGGTTTTAGA
*
65079 AAAAAAAATTATAATTTTAAAG
1 AAAAAAAGTTATAATTTTAAAG
65101 AAAAAAATGTTATAATTTTTAAAG
1 AAAAAAA-GTTATAA-TTTTAAAG
65125 GGTAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 6 0.29
24 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.35
Consensus pattern (22 bp):
AAAAAAAGTTATAATTTTAAAG
Found at i:65103 original size:23 final size:24
Alignment explanation
Indices: 65076--65124 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
65066 TTAGGGTTTT
65076 AGAAAAAAAAATTATAA-TTTTAA
1 AGAAAAAAAAATTATAATTTTTAA
**
65099 AGAAAAAAATGTTATAATTTTTAA
1 AGAAAAAAAAATTATAATTTTTAA
65123 AG
1 AG
65125 GGTAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (24 bp):
AGAAAAAAAAATTATAATTTTTAA
Found at i:74299 original size:16 final size:17
Alignment explanation
Indices: 74261--74301 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
74251 AAGGCCCAAA
*
74261 ATATATTAATTGTATTT
1 ATATATTAATTGTATCT
*
74278 AT-TATTTATT-TATCT
1 ATATATTAATTGTATCT
74293 ATATATTAA
1 ATATATTAA
74302 GCCTTGTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 6 0.30
16 12 0.60
17 2 0.10
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
ATATATTAATTGTATCT
Found at i:74957 original size:1 final size:1
Alignment explanation
Indices: 74951--74986 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
74941 CTTTCTACCG
74951 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
74987 CTATGGATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:93855 original size:30 final size:30
Alignment explanation
Indices: 93813--93891 Score: 149
Period size: 30 Copynumber: 2.6 Consensus size: 30
93803 TTCACTTTTT
93813 CACCCAAAAAAGATAACTTTTTTTTTGGTAC
1 CACCC-AAAAAGATAACTTTTTTTTTGGTAC
93844 CACCCAAAAAGATAACTTTTTTTTTGGTAC
1 CACCCAAAAAGATAACTTTTTTTTTGGTAC
93874 CACCCAAAAAGATAACTT
1 CACCCAAAAAGATAACTT
93892 CTAGCTCACT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 43 0.90
31 5 0.10
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.32
Consensus pattern (30 bp):
CACCCAAAAAGATAACTTTTTTTTTGGTAC
Found at i:113421 original size:100 final size:101
Alignment explanation
Indices: 113242--113430 Score: 285
Period size: 100 Copynumber: 1.9 Consensus size: 101
113232 AGTGCTCATG
*
113242 GTCATTTAGTGCTTAAATTGAACCCTGATTGTACAGGTGGCTTGATGGAGGAAAGTTTGACAAGA
1 GTCATTTAGTGCTTAAATTGAACCCTGATTGTACAAGTGGCTTGATGGA-GAAAGTTTGACAAGA
*
113307 TTCTAGTTACTCATAGATGAGGGAGGGAGAACTGATT
65 TTCTAGTTACTCATAAATGAGGGAGGGAGAACTGATT
*
113344 GTCATTTAGTTCTTAAA-TGAACCCTGATTGTACAAGTGG-TATGATGGCA-AAAGTTTGACAAG
1 GTCATTTAGTGCTTAAATTGAACCCTGATTGTACAAGTGGCT-TGATGG-AGAAAGTTTGACAAG
* *
113406 ATTCTTGTTATTCATAAATGAGGGA
64 ATTCTAGTTACTCATAAATGAGGGA
113431 AGGATAATTG
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
100 36 0.45
101 27 0.34
102 17 0.21
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.32
Consensus pattern (101 bp):
GTCATTTAGTGCTTAAATTGAACCCTGATTGTACAAGTGGCTTGATGGAGAAAGTTTGACAAGAT
TCTAGTTACTCATAAATGAGGGAGGGAGAACTGATT
Found at i:121451 original size:23 final size:23
Alignment explanation
Indices: 121421--121469 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
121411 AATTTAACAC
121421 TATCAAACTGGCTCTAGTGTCAT
1 TATCAAACTGGCTCTAGTGTCAT
121444 TATCAAACTGGCTCTAGTGTCAT
1 TATCAAACTGGCTCTAGTGTCAT
121467 TAT
1 TAT
121470 TGAGACCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (23 bp):
TATCAAACTGGCTCTAGTGTCAT
Found at i:133405 original size:12 final size:12
Alignment explanation
Indices: 133390--133414 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
133380 TCCTCTTCCT
133390 CATCCTAGCAGC
1 CATCCTAGCAGC
133402 CATCCTAGCAGC
1 CATCCTAGCAGC
133414 C
1 C
133415 CATGATCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.44, G:0.16, T:0.16
Consensus pattern (12 bp):
CATCCTAGCAGC
Found at i:133463 original size:18 final size:18
Alignment explanation
Indices: 133436--133478 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
133426 TTATTAATTG
*
133436 TCCCAACACCAACCCCAA
1 TCCCAGCACCAACCCCAA
*
133454 TCCCAGCACCAACTCCAA
1 TCCCAGCACCAACCCCAA
*
133472 CCCCAGC
1 TCCCAGC
133479 CACAACACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.56, G:0.05, T:0.07
Consensus pattern (18 bp):
TCCCAGCACCAACCCCAA
Found at i:133484 original size:18 final size:18
Alignment explanation
Indices: 133437--133489 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
133427 TATTAATTGT
* * *
133437 CCCAACACCAACCCCAAT
1 CCCAGCACCAACACCAAC
*
133455 CCCAGCACCAACTCCAAC
1 CCCAGCACCAACACCAAC
133473 CCCAGC-CACAACACCAA
1 CCCAGCAC-CAACACCAA
133490 GCAATCCTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 1 0.03
18 29 0.97
ACGTcount: A:0.38, C:0.55, G:0.04, T:0.04
Consensus pattern (18 bp):
CCCAGCACCAACACCAAC
Found at i:133487 original size:24 final size:24
Alignment explanation
Indices: 133438--133489 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
133428 ATTAATTGTC
* *
133438 CCAACACCAACCCCAATCCCAGCA
1 CCAACACCAACCCCAAGCCCAACA
*
133462 CCAACTCCAACCCC-AGCCACAACA
1 CCAACACCAACCCCAAGCC-CAACA
133486 CCAA
1 CCAA
133490 GCAATCCTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.38, C:0.54, G:0.04, T:0.04
Consensus pattern (24 bp):
CCAACACCAACCCCAAGCCCAACA
Found at i:134553 original size:31 final size:29
Alignment explanation
Indices: 134515--134622 Score: 103
Period size: 31 Copynumber: 3.6 Consensus size: 29
134505 AACTGACGCC
134515 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTT-GA-AACGTT
** * *
134546 AGGCCCTTATTTG-GTCAAATT-AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTGAAACG-TT
*
134575 AGGCCCTTATTTGAACATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTT-G-AAACGTT
134606 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
134623 ATTAGCCCCA
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
28 3 0.05
29 19 0.31
30 1 0.02
31 34 0.56
32 4 0.07
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (29 bp):
AGGCCCTTATTTGAGCATTTTGAAACGTT
Found at i:144994 original size:29 final size:29
Alignment explanation
Indices: 144961--145029 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
144951 CGCCAACAAT
* *
144961 CAAATAAGCCCTTGAACCT-CAATTTTGGC
1 CAAATAAGCCCCT-AAACTACAATTTTGGC
*
144990 CAAATAATCCCCTAAACTACCAATTTTGGC
1 CAAATAAGCCCCTAAACTA-CAATTTTGGC
*
145020 CAGATAAGCC
1 CAAATAAGCC
145030 ATTTTTCTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 4 0.12
29 11 0.33
30 18 0.55
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.25
Consensus pattern (29 bp):
CAAATAAGCCCCTAAACTACAATTTTGGC
Found at i:147799 original size:13 final size:13
Alignment explanation
Indices: 147781--147807 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
147771 TTTCACCATT
147781 TGTAAAATTCGAA
1 TGTAAAATTCGAA
147794 TGTAAAATTCGAA
1 TGTAAAATTCGAA
147807 T
1 T
147808 ATAAGATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTAAAATTCGAA
Found at i:162649 original size:13 final size:13
Alignment explanation
Indices: 162633--162661 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
162623 GGTACTATGT
162633 TGAGCAAAGAGGC
1 TGAGCAAAGAGGC
162646 TGAGCAAAGAGGC
1 TGAGCAAAGAGGC
162659 TGA
1 TGA
162662 TAAAGTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.38, T:0.10
Consensus pattern (13 bp):
TGAGCAAAGAGGC
Found at i:170925 original size:31 final size:32
Alignment explanation
Indices: 170854--170937 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 32
170844 ATAAGTGAAG
*
170854 AGATTTATAAGTTGTCTTTTTTTTTTTTGGGCATC
1 AGATTTATACGTTGTC---TTTTTTTTTGGGCATC
170889 GAGATTTATACGTTGTCTTTTTTTTT-GGCAAT-
1 -AGATTTATACGTTGTCTTTTTTTTTGGGC-ATC
170921 AGATTTATACGTTGTCT
1 AGATTTATACGTTGTCT
170938 AACTCACTAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 17 0.37
32 3 0.07
33 11 0.24
36 15 0.33
ACGTcount: A:0.19, C:0.10, G:0.18, T:0.54
Consensus pattern (32 bp):
AGATTTATACGTTGTCTTTTTTTTTGGGCATC
Found at i:171048 original size:20 final size:20
Alignment explanation
Indices: 171007--171048 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
170997 CTAGTAAATG
* * *
171007 ATTATTTATTTTAATTATTT
1 ATTATATATTTTAAGTACTT
171027 ATTATATATTTTAAGTACTT
1 ATTATATATTTTAAGTACTT
171047 AT
1 AT
171049 AGCCCTTCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTATATATTTTAAGTACTT
Found at i:172023 original size:4 final size:4
Alignment explanation
Indices: 172014--172038 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
172004 GATAATCTTT
172014 ACAA ACAA ACAA ACAA ACAA ACAA A
1 ACAA ACAA ACAA ACAA ACAA ACAA A
172039 TGAAAATCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
ACAA
Found at i:183786 original size:23 final size:24
Alignment explanation
Indices: 183750--183796 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
183740 CTTCTCTTCT
183750 CTCTCTTTTTTTTTTTAACTTATA
1 CTCTCTTTTTTTTTTTAACTTATA
183774 CTCTC-TTTTTTTTTTAACTTATA
1 CTCTCTTTTTTTTTTTAACTTATA
183797 TGAAGGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (24 bp):
CTCTCTTTTTTTTTTTAACTTATA
Found at i:183996 original size:19 final size:20
Alignment explanation
Indices: 183946--184003 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
183936 ACTGTTCTAA
*
183946 TAATCTCATATGTACAGTAC
1 TAATCTCATCTGTACAGTAC
* *
183966 TTAATCTAATCTGTACAGTGC
1 -TAATCTCATCTGTACAGTAC
183987 -AATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
184004 TGCTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTAC
Found at i:184189 original size:16 final size:16
Alignment explanation
Indices: 184168--184204 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
184158 TGGTGATATA
184168 TCTATGTTATTAGTAC
1 TCTATGTTATTAGTAC
184184 TCTATGTTATTAGTAC
1 TCTATGTTATTAGTAC
184200 TCTAT
1 TCTAT
184205 ATAAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (16 bp):
TCTATGTTATTAGTAC
Found at i:197951 original size:4 final size:4
Alignment explanation
Indices: 197944--197996 Score: 72
Period size: 4 Copynumber: 13.5 Consensus size: 4
197934 AAAAAAAACG
* *
197944 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA AAAA GAAA -AAA AAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
197991 GGAA GA
1 GAAA GA
197997 GCAACTATGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
3 3 0.07
4 40 0.93
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:213838 original size:38 final size:38
Alignment explanation
Indices: 213787--213861 Score: 150
Period size: 38 Copynumber: 2.0 Consensus size: 38
213777 AAACAGGACA
213787 TGGCCAGCCATGGATTAATGAAGGAAAAAGCATATATT
1 TGGCCAGCCATGGATTAATGAAGGAAAAAGCATATATT
213825 TGGCCAGCCATGGATTAATGAAGGAAAAAGCATATAT
1 TGGCCAGCCATGGATTAATGAAGGAAAAAGCATATAT
213862 ATATATATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (38 bp):
TGGCCAGCCATGGATTAATGAAGGAAAAAGCATATATT
Found at i:213883 original size:13 final size:12
Alignment explanation
Indices: 213858--213897 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 12
213848 GAAAAAGCAT
213858 ATATATATATATA
1 ATATA-ATATATA
213871 ATATAATAGTATA
1 ATATAATA-TATA
213884 ATATAATATTATA
1 ATATAATA-TATA
213897 A
1 A
213898 AATTTATAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 3 0.12
13 22 0.88
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
ATATAATATATA
Found at i:218584 original size:9 final size:9
Alignment explanation
Indices: 218562--218595 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
218552 ACATAGTAAG
*
218562 CATAATAGAG
1 CATAAT-GAA
218572 CATAATGAA
1 CATAATGAA
218581 CATAATGAA
1 CATAATGAA
218590 CATAAT
1 CATAAT
218596 AAGGTAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (9 bp):
CATAATGAA
Found at i:236204 original size:30 final size:28
Alignment explanation
Indices: 236170--236227 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
236160 AGGATAACAG
236170 CACAAGTTATTTATTGCCAAAAAAAAAAAA
1 CACAAGTTATTTA-T-CCAAAAAAAAAAAA
236200 CACAAGTTATTTATCCAAAAAAAAAAAA
1 CACAAGTTATTTATCCAAAAAAAAAAAA
236228 TAACACAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 14 0.50
29 1 0.04
30 13 0.46
ACGTcount: A:0.59, C:0.14, G:0.05, T:0.22
Consensus pattern (28 bp):
CACAAGTTATTTATCCAAAAAAAAAAAA
Found at i:250377 original size:69 final size:69
Alignment explanation
Indices: 250266--250401 Score: 263
Period size: 69 Copynumber: 2.0 Consensus size: 69
250256 CATGATTAGT
250266 TACAATACCGAAATGTTAATTTATGAGCCAACAAACCCCTTCCCCAACAAACAAACCCAGTGAAA
1 TACAATACCGAAATGTTAATTTATGAGCCAACAAACCCCTTCCCCAACAAACAAACCCAGTGAAA
250331 TCGC
66 TCGC
*
250335 TACAATACCGAAATGTTAATTTATGAGCCAACAAACCCCTTCCCCAACAAACAAAGCCAGTGAAA
1 TACAATACCGAAATGTTAATTTATGAGCCAACAAACCCCTTCCCCAACAAACAAACCCAGTGAAA
250400 TC
66 TC
250402 TCATTACAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.19
Consensus pattern (69 bp):
TACAATACCGAAATGTTAATTTATGAGCCAACAAACCCCTTCCCCAACAAACAAACCCAGTGAAA
TCGC
Found at i:254760 original size:124 final size:124
Alignment explanation
Indices: 254540--254789 Score: 491
Period size: 124 Copynumber: 2.0 Consensus size: 124
254530 ACATTGACTT
*
254540 CCCTATTTACAAATTTGAAATAGGGAAATCAAATAAGGTTGTCAGATCTCTAATATCATCTATCC
1 CCCTATTTACAAATTTGAAATAGGGAAATCAAATAAGGTTGCCAGATCTCTAATATCATCTATCC
254605 TAGAAACAAATACAAATAAATAATCAATTTCATTAATCAATGATTAGAGATTACAAACG
66 TAGAAACAAATACAAATAAATAATCAATTTCATTAATCAATGATTAGAGATTACAAACG
254664 CCCTATTTACAAATTTGAAATAGGGAAATCAAATAAGGTTGCCAGATCTCTAATATCATCTATCC
1 CCCTATTTACAAATTTGAAATAGGGAAATCAAATAAGGTTGCCAGATCTCTAATATCATCTATCC
254729 TAGAAACAAATACAAATAAATAATCAATTTCATTAATCAATGATTAGAGATTACAAACG
66 TAGAAACAAATACAAATAAATAATCAATTTCATTAATCAATGATTAGAGATTACAAACG
254788 CC
1 CC
254790 GGCAGAAATA
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 125 1.00
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.29
Consensus pattern (124 bp):
CCCTATTTACAAATTTGAAATAGGGAAATCAAATAAGGTTGCCAGATCTCTAATATCATCTATCC
TAGAAACAAATACAAATAAATAATCAATTTCATTAATCAATGATTAGAGATTACAAACG
Found at i:254862 original size:116 final size:116
Alignment explanation
Indices: 254732--254964 Score: 439
Period size: 116 Copynumber: 2.0 Consensus size: 116
254722 TCTATCCTAG
254732 AAACAAATACAAATAAATAATCAATTTCATTAATCAATGATTAGAGATTACAAACGCCGGCAGAA
1 AAACAAATACAAATAAATAATCAATTTCATTAATCAATGATTAGAGATTACAAACGCCGGCAGAA
* *
254797 ATAGTCTCGCACCACACGTTATCCAGCTCAATCTTTCATTAATCAATGATT
66 ATAGTCTCGCAACAAACGTTATCCAGCTCAATCTTTCATTAATCAATGATT
254848 AAACAAATACAAATAAATAATCAATTTCATTAATCAATGATTAGAGATTACAAACGCCGGCAGAA
1 AAACAAATACAAATAAATAATCAATTTCATTAATCAATGATTAGAGATTACAAACGCCGGCAGAA
*
254913 ATAGTCTCGCAACAAACGTTATCCGGCTCAATCTTTCATTAATCAATGATT
66 ATAGTCTCGCAACAAACGTTATCCAGCTCAATCTTTCATTAATCAATGATT
254964 A
1 A
254965 GAGATTACAA
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (116 bp):
AAACAAATACAAATAAATAATCAATTTCATTAATCAATGATTAGAGATTACAAACGCCGGCAGAA
ATAGTCTCGCAACAAACGTTATCCAGCTCAATCTTTCATTAATCAATGATT
Found at i:254970 original size:74 final size:74
Alignment explanation
Indices: 254872--255022 Score: 257
Period size: 74 Copynumber: 2.0 Consensus size: 74
254862 AAATAATCAA
254872 TTTCATTAATCAATGATTAGAGATTACAAACGCCGGCAGAAATAGTCTCGCAACAAACGTTATCC
1 TTTCATTAATCAATGATTAGAGATTACAAACGCCGGCAGAAATAGTCTCGCAACAAACGTTATCC
*
254937 GGCTCAATC
66 AGCTCAATC
* * * *
254946 TTTCATTAATCAATGATTAGAGATTACAAACGCTGGCAGAAATAGTCTCGCACCACACGTTATCT
1 TTTCATTAATCAATGATTAGAGATTACAAACGCCGGCAGAAATAGTCTCGCAACAAACGTTATCC
255011 AGCTCAATC
66 AGCTCAATC
255020 TTT
1 TTT
255023 AGCGAGAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (74 bp):
TTTCATTAATCAATGATTAGAGATTACAAACGCCGGCAGAAATAGTCTCGCAACAAACGTTATCC
AGCTCAATC
Found at i:255101 original size:132 final size:127
Alignment explanation
Indices: 254946--255594 Score: 605
Period size: 146 Copynumber: 4.7 Consensus size: 127
254936 CGGCTCAATC
*
254946 TTTCATTAATCAATGATTAGAGATTACAAACGCTGGCAGAAATAGTCTCGCACCACACGTTATCT
1 TTTCATTAATCAATGATTAGAGATTACAAACGCTGGCAGAAATAGTCTCGCACCACACGTTATCC
*
255011 AGCTCAATCTTTAGCGAGAGAATATGCAATTTCCTATTTACAAATTTGAAATACAGAAAATCTTC
66 AGCTCAATCTTTAGCTAGAGAATATGCAATTTCCTATTTACAAATTTGAAATAC-----ATCTTC
255076 AA
126 AA
255078 TTTCATTAATCAATGATTAGAGATTACAAACGCTACGCCGACAGAAATAGTCTCGCACCACACGT
1 TTTCATTAATCAATGATTAGAGATTACAAACGCT--G--G-CAGAAATAGTCTCGCACCACACGT
* *
255143 TATCCAGCTCAGTCTTTAGCTAGAGAATATGCAATTTCCTATTTACAATTTTGAAATACATCTTC
61 TATCCAGCTCAATCTTTAGCTAGAGAATATGCAATTTCCTATTTACAAATTTGAAATACATCTTC
255208 AA
126 AA
*
255210 TTTCATTAATCAATGATTAGAGATTACAAACGCCACGCCGGCAGAAATAGTCTCGCACCACACGT
1 TTTCATTAATCAATGATTAGAGATTAC-AA----ACGCTGGCAGAAATAGTCTCGCACCACACGT
* * * * * *
255275 TATCCAGCTCAATCTTTAGCTAGAGAATGTGTAGTCTCGCACCACACGTTATCCAGCTCAATCTT
61 TATCCAGCTCAATCTTTAGCTAGAGAATATGCAAT-T---TCC-TA--TT-T--A-C-AAAT-TT
* *
255340 TAGCATACATCTTCAA
113 GA-AATACATCTTCAA
* *
255356 TTTCATTAATCAATTATTAGAGATTACAAACGCCAGGCCGGCAGAAATAGTCTCGCACCACACGT
1 TTTCATTAATCAATGATTAGAGATTACAAA---C--GCTGGCAGAAATAGTCTCGCACCACACGT
* * * * * *
255421 TATCCAGCTCAATCTTTAGCTAGAGAATGTGTAGTCTCACACCACACGTTATCCAGCTCAATCTT
61 TATCCAGCTCAATCTTTAGCTAGAGAATATGCAAT-T---TCC-TA--TT-T--A-C-AAAT-TT
* *
255486 TAGCATACATCTTCAA
113 GA-AATACATCTTCAA
*
255502 TTTCATTAATCAATGATTAGAGATTACAAACGCCACACCGGCAGAAATAGTCTCGCACCACACGT
1 TTTCATTAATCAATGATTAGAGATTACAAACG-----CTGGCAGAAATAGTCTCGCACCACACGT
255567 TATCCAGCTCAATCTTTAGCTAGAGAAT
61 TATCCAGCTCAATCTTTAGCTAGAGAAT
255595 GTGTAGTCTC
Statistics
Matches: 465, Mismatches: 18, Indels: 54
0.87 0.03 0.10
Matches are distributed among these distances:
132 124 0.27
133 4 0.01
134 1 0.00
135 1 0.00
136 3 0.01
137 84 0.18
139 2 0.00
140 1 0.00
141 2 0.00
142 1 0.00
143 2 0.00
144 3 0.01
145 5 0.01
146 232 0.50
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (127 bp):
TTTCATTAATCAATGATTAGAGATTACAAACGCTGGCAGAAATAGTCTCGCACCACACGTTATCC
AGCTCAATCTTTAGCTAGAGAATATGCAATTTCCTATTTACAAATTTGAAATACATCTTCAA
Found at i:255464 original size:146 final size:146
Alignment explanation
Indices: 255198--255617 Score: 795
Period size: 146 Copynumber: 2.9 Consensus size: 146
255188 CAATTTTGAA
255198 ATACATCTTCAATTTCATTAATCAATGATTAGAGATTACAAACGCCACGCCGGCAGAAATAGTCT
1 ATACATCTTCAATTTCATTAATCAATGATTAGAGATTACAAACGCCACGCCGGCAGAAATAGTCT
255263 CGCACCACACGTTATCCAGCTCAATCTTTAGCTAGAGAATGTGTAGTCTCGCACCACACGTTATC
66 CGCACCACACGTTATCCAGCTCAATCTTTAGCTAGAGAATGTGTAGTCTCGCACCACACGTTATC
255328 CAGCTCAATCTTTAGC
131 CAGCTCAATCTTTAGC
* *
255344 ATACATCTTCAATTTCATTAATCAATTATTAGAGATTACAAACGCCAGGCCGGCAGAAATAGTCT
1 ATACATCTTCAATTTCATTAATCAATGATTAGAGATTACAAACGCCACGCCGGCAGAAATAGTCT
*
255409 CGCACCACACGTTATCCAGCTCAATCTTTAGCTAGAGAATGTGTAGTCTCACACCACACGTTATC
66 CGCACCACACGTTATCCAGCTCAATCTTTAGCTAGAGAATGTGTAGTCTCGCACCACACGTTATC
255474 CAGCTCAATCTTTAGC
131 CAGCTCAATCTTTAGC
*
255490 ATACATCTTCAATTTCATTAATCAATGATTAGAGATTACAAACGCCACACCGGCAGAAATAGTCT
1 ATACATCTTCAATTTCATTAATCAATGATTAGAGATTACAAACGCCACGCCGGCAGAAATAGTCT
*
255555 CGCACCACACGTTATCCAGCTCAATCTTTAGCTAGAGAATGTGTAGTCTCGTACCACACGTTA
66 CGCACCACACGTTATCCAGCTCAATCTTTAGCTAGAGAATGTGTAGTCTCGCACCACACGTTA
255618 GAATGTGCAA
Statistics
Matches: 266, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
146 266 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.28
Consensus pattern (146 bp):
ATACATCTTCAATTTCATTAATCAATGATTAGAGATTACAAACGCCACGCCGGCAGAAATAGTCT
CGCACCACACGTTATCCAGCTCAATCTTTAGCTAGAGAATGTGTAGTCTCGCACCACACGTTATC
CAGCTCAATCTTTAGC
Found at i:256042 original size:52 final size:52
Alignment explanation
Indices: 255964--256069 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
255954 GCTTGATAAA
255964 AAGGATTTTGAAGGTCGAATATAACTAATTGCAACTATCATGATGAGCTCTC
1 AAGGATTTTGAAGGTCGAATATAACTAATTGCAACTATCATGATGAGCTCTC
256016 AAGGATTTTGAAGGTCGAATATAACTAATTGCAACTATCATGATGAGCTCTC
1 AAGGATTTTGAAGGTCGAATATAACTAATTGCAACTATCATGATGAGCTCTC
256068 AA
1 AA
256070 AGGCTAAAGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (52 bp):
AAGGATTTTGAAGGTCGAATATAACTAATTGCAACTATCATGATGAGCTCTC
Found at i:258656 original size:10 final size:10
Alignment explanation
Indices: 258641--258676 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
258631 TTTCTAGGTA
258641 TATATATAGC
1 TATATATAGC
258651 TATATATA--
1 TATATATAGC
258659 TATATATAGC
1 TATATATAGC
258669 TATATATA
1 TATATATA
258677 TATACCTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
10 16 0.67
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (10 bp):
TATATATAGC
Found at i:258662 original size:18 final size:18
Alignment explanation
Indices: 258639--258680 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
258629 AATTTCTAGG
258639 TATATATATAGCTATATA
1 TATATATATAGCTATATA
258657 TATATATATAGCTATATA
1 TATATATATAGCTATATA
258675 TATATA
1 TATATA
258681 CCTGAAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
TATATATATAGCTATATA
Found at i:259971 original size:30 final size:31
Alignment explanation
Indices: 259935--259992 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
259925 GTTAGTAGGA
*
259935 CATTAAAATTTGAGGGTATAAG-AGAAAACT
1 CATTAAAATTTAAGGGTATAAGAAGAAAACT
*
259965 CATTAAAATTTAAGGGTGTAAGAAGAAA
1 CATTAAAATTTAAGGGTATAAGAAGAAA
259993 GTCAAGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.26
Consensus pattern (31 bp):
CATTAAAATTTAAGGGTATAAGAAGAAAACT
Found at i:264143 original size:42 final size:42
Alignment explanation
Indices: 264084--264163 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
264074 ATAGTGAATG
264084 ATGGAGGATACTTCATGCCAATGAAATCATTAGAGAATTTAT
1 ATGGAGGATACTTCATGCCAATGAAATCATTAGAGAATTTAT
* * *
264126 ATGGAGGATATTTCATGCCAATTAAATCATTCGAGAAT
1 ATGGAGGATACTTCATGCCAATGAAATCATTAGAGAAT
264164 GCTCTGCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (42 bp):
ATGGAGGATACTTCATGCCAATGAAATCATTAGAGAATTTAT
Found at i:267246 original size:60 final size:60
Alignment explanation
Indices: 267139--267297 Score: 194
Period size: 60 Copynumber: 2.6 Consensus size: 60
267129 TTATTGTTCG
* * * * **
267139 AATAAGGGCCTAACGTT-TGCTAAAATGCTTAAATAAGGGTCCAATCTTTTAATTTGGTCA
1 AATAAGGGCCTAACATTAT-CAAAAATGCTCAAATAAGGGTCCAATCTTCTAATTTGACCA
* * ** *
267199 AATCAGGGTCTAACATTATCAAAAATGCTCAAATAAGGGTCTGATCTTCTAATTTTACCA
1 AATAAGGGCCTAACATTATCAAAAATGCTCAAATAAGGGTCCAATCTTCTAATTTGACCA
*
267259 AATAAGGGCCTAACATTATCGAAAATGCTCAAATAAGGG
1 AATAAGGGCCTAACATTATCAAAAATGCTCAAATAAGGG
267298 CTTGGTGTCA
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 83 0.99
61 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (60 bp):
AATAAGGGCCTAACATTATCAAAAATGCTCAAATAAGGGTCCAATCTTCTAATTTGACCA
Found at i:267471 original size:60 final size:59
Alignment explanation
Indices: 267342--267502 Score: 207
Period size: 60 Copynumber: 2.7 Consensus size: 59
267332 CGACGCCAGA
* *
267342 TCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGG
1 TCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGG
* * * * * *
267401 GCCATCATTTGAACATTTTGGCAAATGCTAGACCCTTATTTGGCCAAATTAAAAGATCATG
1 TCC-TTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATC-GG
*
267462 TCCTTATTTGAGCATTTTAGCAAACGTTA-AGCCCTTATTTG
1 TCCTTATTTGAGCATTTTGGCAAACGTTAGA-CCCTTATTTG
267503 AGCAATTAAC
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
59 3 0.04
60 79 0.93
61 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (59 bp):
TCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGG
Found at i:268401 original size:101 final size:103
Alignment explanation
Indices: 268290--268491 Score: 363
Period size: 104 Copynumber: 2.0 Consensus size: 103
268280 AAAAACCATT
*
268290 TAACATTGAAACGGTGGAAGCATCTCCCACATAAAC-TT-AAGAGCCTGTTTGCATTAAAAATAT
1 TAACATTGAAACGGTGGAAGCACCTCCCACATAAACTTTAAAGAGCCTGTTTGCATTAAAAATAT
268353 CATATAAACCCACCTCACAGTGGCTAGTGGGTTATTTA
66 CATATAAACCCACCTCACAGTGGCTAGTGGGTTATTTA
268391 TAACATTGAAACGGTGGAAGCACCTCCCACATAAACTTTGAAAGAGCCTGTTTGCATTAAAAATA
1 TAACATTGAAACGGTGGAAGCACCTCCCACATAAACTTT-AAAGAGCCTGTTTGCATTAAAAATA
*
268456 TTATATAAACCCACCTCACAGTGGCTAGTGGGTTAT
65 TCATATAAACCCACCTCACAGTGGCTAGTGGGTTAT
268492 ATGGCCAAGT
Statistics
Matches: 96, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
101 35 0.36
102 2 0.02
104 59 0.61
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (103 bp):
TAACATTGAAACGGTGGAAGCACCTCCCACATAAACTTTAAAGAGCCTGTTTGCATTAAAAATAT
CATATAAACCCACCTCACAGTGGCTAGTGGGTTATTTA
Found at i:270169 original size:25 final size:26
Alignment explanation
Indices: 270119--270174 Score: 96
Period size: 25 Copynumber: 2.2 Consensus size: 26
270109 TAATAGGGCC
270119 TAATCAGTCCCATCATATATATGAAAA
1 TAATCAGTCCCATCA-ATATATGAAAA
270146 TAATCAGTCCCATC-ATATATGAAAA
1 TAATCAGTCCCATCAATATATGAAAA
270171 TAAT
1 TAAT
270175 ATATCGATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 15 0.52
27 14 0.48
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (26 bp):
TAATCAGTCCCATCAATATATGAAAA
Found at i:274675 original size:2 final size:2
Alignment explanation
Indices: 274668--274700 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
274658 TTCCAAATCC
274668 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
274701 CGTACCACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:276104 original size:33 final size:33
Alignment explanation
Indices: 276062--276130 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
276052 TCAGTGGATT
*
276062 ATGAATCAGCAGCATGTTTGGTACAAGTGTTTG
1 ATGAATCAGCAGCATGCTTGGTACAAGTGTTTG
276095 ATGAATCAGCAGCATGCTTGGTACAAGTGTTTG
1 ATGAATCAGCAGCATGCTTGGTACAAGTGTTTG
276128 ATG
1 ATG
276131 CTGTTATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (33 bp):
ATGAATCAGCAGCATGCTTGGTACAAGTGTTTG
Done.