Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 64 of 135
Found at i:21386420 original size:23 final size:23
Alignment explanation
Indices: 21386390--21386510 Score: 206
Period size: 23 Copynumber: 5.3 Consensus size: 23
21386380 TCATAGGTCC
21386390 ATTTAAGCATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
* *
21386413 ATTTAAGCATAAATCATATTAAC
1 ATTTAAGCATAAATCACATTAAT
21386436 ATTTAAGCATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
* *
21386459 ATTTAAGCATAAATTATATTAAT
1 ATTTAAGCATAAATCACATTAAT
21386482 ATTTAAGCATAAATCACATTAAT
1 ATTTAAGCATAAATCACATTAAT
21386505 ATTTAA
1 ATTTAA
21386511 CACATTTAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 90 1.00
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (23 bp):
ATTTAAGCATAAATCACATTAAT
Found at i:21386958 original size:36 final size:36
Alignment explanation
Indices: 21386905--21387090 Score: 264
Period size: 36 Copynumber: 5.2 Consensus size: 36
21386895 TTAGCACAAT
* *
21386905 ATATTCACTGTCACATGGCATGAATAACATACCTAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
21386941 ATATTTATTGTCTCATGGCATGAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* *
21386977 ATATTTACTGTCACATGACATTAATAACATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* * *
21387013 ATATTTATTGTCACATGGCATGAAAAACATACCAAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
* * *
21387049 ATATTTACTATCACATGGCTTGAATAATATACCCAC
1 ATATTTACTGTCACATGGCATGAATAACATACCCAC
21387085 ATATTT
1 ATATTT
21387091 TTTTGCACAA
Statistics
Matches: 131, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 131 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.32
Consensus pattern (36 bp):
ATATTTACTGTCACATGGCATGAATAACATACCCAC
Found at i:21393174 original size:13 final size:13
Alignment explanation
Indices: 21393158--21393185 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21393148 AGTTAAAACA
21393158 GATAAGAAAGAAG
1 GATAAGAAAGAAG
21393171 GATAAGAAAGAAG
1 GATAAGAAAGAAG
21393184 GA
1 GA
21393186 GCGAAGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.07
Consensus pattern (13 bp):
GATAAGAAAGAAG
Found at i:21400808 original size:23 final size:23
Alignment explanation
Indices: 21400773--21401240 Score: 614
Period size: 23 Copynumber: 20.4 Consensus size: 23
21400763 ATCTCAATTG
*
21400773 TTTAACCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
21400796 TTTAATCATAAATCATATAAATA
1 TTTAAGCACAAATCACATTAATA
21400819 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
21400842 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
21400865 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
21400888 TTTAAGTACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
***
21400911 TTTAAATGCAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
21400934 TTTAAGCATAAATTA-ATTAATA
1 TTTAAGCACAAATCACATTAATA
*
21400956 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
21400979 TTTGAGCACAAATTATATTAATA
1 TTTAAGCACAAATCACATTAATA
**
21401002 TTTAAGCACAAATTGCATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
21401025 TTTGAGCACAAATTATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
21401048 TTTAAGAATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
21401071 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
21401094 TTTAAGCACAAATTACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
21401117 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
21401140 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
21401163 CTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
21401186 CTTAAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
21401209 TTTAATCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
21401232 TTTAAGCAC
1 TTTAAGCAC
21401241 GGATATAAGA
Statistics
Matches: 387, Mismatches: 57, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
22 21 0.05
23 366 0.95
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:21414042 original size:72 final size:72
Alignment explanation
Indices: 21413840--21414017 Score: 284
Period size: 72 Copynumber: 2.5 Consensus size: 72
21413830 TTTTATATTC
* * * * *
21413840 AAAATCAAATATAAACAATTATTGATAAAACTAAATTACACATAAATAAGTATAACATAAATTCA
1 AAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCA
21413905 ATATCCA
66 ATATCCA
*
21413912 AAAACCAAACATAAACAACTATTGATAAAATTAGATTACACATAAATAAGTAGAACATAAATTCA
1 AAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCA
21413977 ATATCCA
66 ATATCCA
* *
21413984 AAATCCAAAGATAAACAACTATTGATAAAACTAG
1 AAAACCAAACATAAACAACTATTGATAAAACTAG
21414018 TTTAGCATTG
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 97 1.00
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (72 bp):
AAAACCAAACATAAACAACTATTGATAAAACTAGATTACACATAAATAAGTAGAACATAAATTCA
ATATCCA
Found at i:21417091 original size:12 final size:12
Alignment explanation
Indices: 21417066--21417099 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
21417056 ACTTTTGAAG
21417066 AAAATGG-A-AA
1 AAAATGGAAGAA
21417076 AAAATGGAAGAA
1 AAAATGGAAGAA
21417088 AAAATGGAAGAA
1 AAAATGGAAGAA
21417100 GGGAAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.32
11 1 0.05
12 14 0.64
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.09
Consensus pattern (12 bp):
AAAATGGAAGAA
Found at i:21418889 original size:17 final size:16
Alignment explanation
Indices: 21418867--21418898 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
21418857 GCTCTTTAGC
21418867 CTTCCATTCCATTTTCT
1 CTTCCATTCC-TTTTCT
21418884 CTTCCATTCCTTTTC
1 CTTCCATTCCTTTTC
21418899 CGATTTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.09, C:0.38, G:0.00, T:0.53
Consensus pattern (16 bp):
CTTCCATTCCTTTTCT
Found at i:21421990 original size:49 final size:49
Alignment explanation
Indices: 21421908--21422088 Score: 143
Period size: 49 Copynumber: 3.7 Consensus size: 49
21421898 TTGAATCTAT
* * **
21421908 CCCTCTCCATCTTTAGGGTATAAGATTCCCCTTTGCGGCTTCAATATGC
1 CCCTCTTCATCTTTAGGATATAAGATTCCCCTTTGCAACTTCAATATGC
* ** * *
21421957 CCTTCTTCATCTTTAGGATATTAA-ATTTGCCTTTGCAATTTCAATCTGC
1 CCCTCTTCATCTTTAGGATA-TAAGATTCCCCTTTGCAACTTCAATATGC
* * ** **
21422006 CCCTCTTCATATTTA-GAGTATGAGATTCGACTTTGCTGCTTCAA-ATTGC
1 CCCTCTTCATCTTTAGGA-TATAAGATTCCCCTTTGCAACTTCAATA-TGC
* * * *
21422055 CTCACTTCATCTTTAGGGTATAAGATTCACCTTT
1 CCCTCTTCATCTTTAGGATATAAGATTCCCCTTT
21422089 AAGGCCTCAA
Statistics
Matches: 102, Mismatches: 25, Indels: 10
0.74 0.18 0.07
Matches are distributed among these distances:
48 4 0.04
49 94 0.92
50 4 0.04
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (49 bp):
CCCTCTTCATCTTTAGGATATAAGATTCCCCTTTGCAACTTCAATATGC
Found at i:21422088 original size:98 final size:98
Alignment explanation
Indices: 21421908--21422088 Score: 215
Period size: 98 Copynumber: 1.8 Consensus size: 98
21421898 TTGAATCTAT
* * * *
21421908 CCCTCTCCATCTTTAGGGTATAAGATTCCCCTTTGCGGCTTCAATATGCCCTTCTTCATCTTTAG
1 CCCTCTCCATATTTAGAGTATAAGATTCCACTTTGCGGCTTCAATATGCCCTACTTCATCTTTAG
**
21421973 GATATTAAATTTGCCTTTGCAATTTCAATCTGC
66 GATATTAAATTCACCTTTGCAATTTCAATCTGC
* * * *
21422006 CCCTCTTCATATTTAGAGTATGAGATTCGACTTTGCTGCTTCAA-ATTG-CCTCACTTCATCTTT
1 CCCTCTCCATATTTAGAGTATAAGATTCCACTTTGCGGCTTCAATA-TGCCCT-ACTTCATCTTT
*
21422069 AGGGTA-TAAGATTCACCTTT
64 AGGATATTAA-ATTCACCTTT
21422089 AAGGCCTCAA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
97 7 0.10
98 62 0.90
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (98 bp):
CCCTCTCCATATTTAGAGTATAAGATTCCACTTTGCGGCTTCAATATGCCCTACTTCATCTTTAG
GATATTAAATTCACCTTTGCAATTTCAATCTGC
Found at i:21422115 original size:49 final size:49
Alignment explanation
Indices: 21422062--21422889 Score: 833
Period size: 49 Copynumber: 17.1 Consensus size: 49
21422052 TGCCTCACTT
* ** * *
21422062 CATCTTTAGGGTATAAGATTCACCTTTAAGGCCTCAATCTTTCCCTCTA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCTTCAATCTTTCCCTCCA
* ** * ** *
21422111 CATCTCTAAGGTATAAGATTTTCCTTTGAGGCCACAATCTTTCCCTTCA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCTTCAATCTTTCCCTCCA
* * * *
21422160 CATCTCTAGGG--T---ATTCGCCTTTGCGACTTCAGTCTTTCCCTTCA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCTTCAATCTTTCCCTCCA
* * * *
21422204 CATCTCTA-GGTATAAGATTCGCCCTTACGGCTTCAATCTTTCCCTTCA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCTTCAATCTTTCCCTCCA
* *** * *
21422252 CATCTTTAGGGTATAAGATTTGTCTTTTCGACTTCAATCTTTCCCTCCA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCTTCAATCTTTCCCTCCA
* * ** * *
21422301 TATCTCTAGGCTATAAGATTTTCCTTTGCAGCTTTAATC-TT---TCCA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCTTCAATCTTTCCCTCCA
* * *
21422346 CATCTCAAGGGTATAAGATTCGCCTTTGCGGCTTCAATCTTTACCTCCA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCTTCAATCTTTCCCTCCA
*** * *
21422395 CATCTCTAGGGTATAAGATTTGTCTTTGCGGCCTCAGTCTTTCCCTCCA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCTTCAATCTTTCCCTCCA
* ** *
21422444 CATCTCTAGGGTATAAGATTCGCCCGTGCAG-TCTCAATCTTTCCCTCCA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCT-TCAATCTTTCCCTCCA
* * * * *
21422493 CATCTCTAAGGTATAAGATTCACCTTTGAGGCTTCAATATTTACCTACA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCTTCAATCTTTCCCTCCA
* * * *
21422542 CATCTCTATGGTATAAAATTCAACC-TTACGGCTTTAATCTTTCCCTCCA
1 CATCTCTAGGGTATAAGATTC-ACCTTTGCGGCTTCAATCTTTCCCTCCA
* *
21422591 CATCTCTAGGGTATAAGATTAGACC-TTGTGGCTTCAATCTTTCCCTCCA
1 CATCTCTAGGGTATAAGATT-CACCTTTGCGGCTTCAATCTTTCCCTCCA
* *
21422640 CATCTCTAGGCTATAAGATTCA-CTATTGCGGCTTCAATATTTCCCTCCA
1 CATCTCTAGGGTATAAGATTCACCT-TTGCGGCTTCAATCTTTCCCTCCA
* *
21422689 CATCTCTAAGGTACAAGATTCACCTTTGCGG-TCTCAATCTTTCCCTCCA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCT-TCAATCTTTCCCTCCA
* * *
21422738 CATCTCTAGGGTATAAGATTCACCCTAGCGGTTTCAATCTTTCCCTCCA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCTTCAATCTTTCCCTCCA
* ** *
21422787 CATCTCTAAGGTATAAGATTCGTGC-TAGCGGCTTCAATCTTTCCCTCCA
1 CATCTCTAGGGTATAAGATTC-ACCTTTGCGGCTTCAATCTTTCCCTCCA
* * ** * * *
21422836 CATATCTAAGGTATAAGATTTGCCCTAGTGGCTTCAATCTTTCCCTCCA
1 CATCTCTAGGGTATAAGATTCACCTTTGCGGCTTCAATCTTTCCCTCCA
21422885 CATCT
1 CATCT
21422890 GTAATGACCC
Statistics
Matches: 657, Mismatches: 101, Indels: 42
0.82 0.13 0.05
Matches are distributed among these distances:
43 2 0.00
44 33 0.05
45 37 0.06
46 2 0.00
47 2 0.00
48 40 0.06
49 533 0.81
50 8 0.01
ACGTcount: A:0.22, C:0.28, G:0.14, T:0.36
Consensus pattern (49 bp):
CATCTCTAGGGTATAAGATTCACCTTTGCGGCTTCAATCTTTCCCTCCA
Found at i:21422197 original size:44 final size:44
Alignment explanation
Indices: 21422145--21422265 Score: 152
Period size: 48 Copynumber: 2.7 Consensus size: 44
21422135 TTTGAGGCCA
* *
21422145 CAATCTTTCCCTTCACATCTCTAGGGTATTCGCCTTTGCGACTT
1 CAATCTTTCCCTTCACATCTCTAGGGTATTCGCCCTTACGACTT
* * *
21422189 CAGTCTTTCCCTTCACATCTCTAGGTATAAGATTCGCCCTTACGGCTT
1 CAATCTTTCCCTTCACATCTCTAGG-GT---ATTCGCCCTTACGACTT
*
21422237 CAATCTTTCCCTTCACATCTTTAGGGTAT
1 CAATCTTTCCCTTCACATCTCTAGGGTAT
21422266 AAGATTTGTC
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
44 26 0.40
45 1 0.02
47 1 0.02
48 37 0.57
ACGTcount: A:0.18, C:0.31, G:0.13, T:0.38
Consensus pattern (44 bp):
CAATCTTTCCCTTCACATCTCTAGGGTATTCGCCCTTACGACTT
Found at i:21424087 original size:26 final size:26
Alignment explanation
Indices: 21424054--21424289 Score: 212
Period size: 26 Copynumber: 9.0 Consensus size: 26
21424044 AAACAAGTAT
*
21424054 ATAGTAGGCCTTGAGCCGGTGAATAA
1 ATAGCAGGCCTTGAGCCGGTGAATAA
**
21424080 ATA-CTAGG-CTTCGAGAGTTGGTGAATAA
1 ATAGC-AGGCCTT---GAGCCGGTGAATAA
* * *
21424108 TTAGCAGG-CTTCGAGCCGGTGAGTAT
1 ATAGCAGGCCTT-GAGCCGGTGAATAA
*
21424134 ATAGTAGGCCTTGAGCCGGTGAATAA
1 ATAGCAGGCCTTGAGCCGGTGAATAA
* * *
21424160 ATAGCAAG-CTTCGAGCAGGTGAATAT
1 ATAGCAGGCCTT-GAGCCGGTGAATAA
* *
21424186 ATAGCATGCCTTGAGCTGGTGAATAA
1 ATAGCAGGCCTTGAGCCGGTGAATAA
* * * *
21424212 TTAACAGGCCTTGAGCTGATGAATAA
1 ATAGCAGGCCTTGAGCCGGTGAATAA
21424238 ATAGCAGG-CTTCGAGCCGGTGAATAA
1 ATAGCAGGCCTT-GAGCCGGTGAATAA
* *
21424264 ATAGCAGGCTTTAAGCCGGTGAATAA
1 ATAGCAGGCCTTGAGCCGGTGAATAA
21424290 TTATATAGCA
Statistics
Matches: 170, Mismatches: 30, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
25 9 0.05
26 132 0.78
27 8 0.05
28 20 0.12
29 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.25
Consensus pattern (26 bp):
ATAGCAGGCCTTGAGCCGGTGAATAA
Found at i:21424235 original size:78 final size:78
Alignment explanation
Indices: 21424059--21424292 Score: 242
Period size: 78 Copynumber: 3.0 Consensus size: 78
21424049 AGTATATAGT
* * * *
21424059 AGGCCTTGAGCCGGTGAATAAATA-CTAGGCTTCGAG-AGTTGGTGAATAATTAGCAGG-CTTCG
1 AGGCCTTGAGCCGATGAATAAATAGC-AAGCTTCGAGCA---GGTGAATAAATAGCAGGCCTT-A
* **
21424121 AGCCGGTGAGT-ATATAGT
61 AGCCGGTGAATAAT-TAAC
* * * * *
21424139 AGGCCTTGAGCCGGTGAATAAATAGCAAGCTTCGAGCAGGTGAATATATAGCATGCCTTGAGCTG
1 AGGCCTTGAGCCGATGAATAAATAGCAAGCTTCGAGCAGGTGAATAAATAGCAGGCCTTAAGCCG
21424204 GTGAATAATTAAC
66 GTGAATAATTAAC
* * * *
21424217 AGGCCTTGAGCTGATGAATAAATAGCAGGCTTCGAGCCGGTGAATAAATAGCAGGCTTTAAGCCG
1 AGGCCTTGAGCCGATGAATAAATAGCAAGCTTCGAGCAGGTGAATAAATAGCAGGCCTTAAGCCG
21424282 GTGAATAATTA
66 GTGAATAATTA
21424293 TATAGCAAGC
Statistics
Matches: 133, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
78 93 0.70
79 5 0.04
80 33 0.25
81 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.25
Consensus pattern (78 bp):
AGGCCTTGAGCCGATGAATAAATAGCAAGCTTCGAGCAGGTGAATAAATAGCAGGCCTTAAGCCG
GTGAATAATTAAC
Found at i:21426405 original size:13 final size:11
Alignment explanation
Indices: 21426383--21426439 Score: 66
Period size: 10 Copynumber: 5.5 Consensus size: 11
21426373 TGACCTTTCC
21426383 TTTTTCT-TTT
1 TTTTTCTCTTT
* *
21426393 TCTTTCTCGTT
1 TTTTTCTCTTT
21426404 TTTTTCTCTTT
1 TTTTTCTCTTT
*
21426415 TTTTTCTC-AT
1 TTTTTCTCTTT
21426425 TTTTTCT-TTT
1 TTTTTCTCTTT
21426435 TTTTT
1 TTTTT
21426440 ATTTTGCATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 20 0.51
11 19 0.49
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTTTCTCTTT
Found at i:21426409 original size:11 final size:11
Alignment explanation
Indices: 21426390--21426429 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
21426380 TCCTTTTTCT
*
21426390 TTTTCTTTCTCG
1 TTTT-TTTCTCA
*
21426402 TTTTTTTCTCT
1 TTTTTTTCTCA
21426413 TTTTTTTCTCA
1 TTTTTTTCTCA
21426424 TTTTTT
1 TTTTTT
21426430 CTTTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 22 0.85
12 4 0.15
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78
Consensus pattern (11 bp):
TTTTTTTCTCA
Found at i:21426437 original size:22 final size:22
Alignment explanation
Indices: 21426383--21426439 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
21426373 TGACCTTTCC
* *
21426383 TTTTTC-TTTTTCTTTCTCGTT
1 TTTTTCTTTTTTTTTTCTCATT
*
21426404 TTTTTCTCTTTTTTTTCTCA-T
1 TTTTTCTTTTTTTTTTCTCATT
21426425 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTTT
21426440 ATTTTGCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 21 0.68
22 10 0.32
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTTTTTTTTCTCATT
Found at i:21427354 original size:66 final size:68
Alignment explanation
Indices: 21427236--21427383 Score: 180
Period size: 66 Copynumber: 2.2 Consensus size: 68
21427226 TTTTTCTTTC
* *
21427236 TTTTTTCTTTTTTTCCTTCTGGGTTTTAGGATGACCTTTGTGAGTTTTCATCTCGA-CTCTTTTT
1 TTTTTTCTTTTTTTCCTTCTGGGTTTCAGGATGACCTTTGTGAGTTTCCATCTCGACCTCTTTTT
*
21427300 CGT
66 CCT
* *
21427303 TTTTTTCTTTTCTTT-CTT-TGGGTTTCAGGATGCCCTTTGCTG-GTTTCCATCTTGACCCTCTT
1 TTTTTTCTTTT-TTTCCTTCTGGGTTTCAGGATGACCTTTG-TGAGTTTCCATCTCGA-CCTCTT
21427365 TTTCCT
63 TTTCCT
*
21427371 TTTTCT-TTTTTTT
1 TTTTTTCTTTTTTT
21427384 AAGATAGCAC
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
66 33 0.46
67 20 0.28
68 18 0.25
ACGTcount: A:0.07, C:0.20, G:0.14, T:0.59
Consensus pattern (68 bp):
TTTTTTCTTTTTTTCCTTCTGGGTTTCAGGATGACCTTTGTGAGTTTCCATCTCGACCTCTTTTT
CCT
Found at i:21437502 original size:60 final size:60
Alignment explanation
Indices: 21437364--21437751 Score: 528
Period size: 60 Copynumber: 6.4 Consensus size: 60
21437354 GCATTTGGTA
* * * * *
21437364 ACTCATGATGACACAAAGTCATCGGACC-TTTAATCCATAATAGGATTCTTTTCTCATTTAAT
1 ACTCACGATGACACATAGTCATCGAACCATATAATCCATAA-AGGATTC-ATT-TCATTTAAT
* * * *
21437426 ACTCACGATGACACATAGT-ATTTGGACCTTATAATCCATAAAAGATTCATTTCATTTAAT
1 ACTCACGATGACACATAGTCA-TCGAACCATATAATCCATAAAGGATTCATTTCATTTAAT
* * *
21437486 ACTCATGATAACACATAGTAATCGAACCATATAATCCATAAAGGATTCATTTCATTTAAT
1 ACTCACGATGACACATAGTCATCGAACCATATAATCCATAAAGGATTCATTTCATTTAAT
* * ** *
21437546 ACTCACAATGACACATAGTCATCGGACCATATAATCTGTAAAGGATTCATTTCATTGAAT
1 ACTCACGATGACACATAGTCATCGAACCATATAATCCATAAAGGATTCATTTCATTTAAT
*
21437606 ACTCACGATGACACATAGTCATCGAACCATATAATCCGTAAAGGATTCATTTCATTTAAT
1 ACTCACGATGACACATAGTCATCGAACCATATAATCCATAAAGGATTCATTTCATTTAAT
**
21437666 ACTCACGATGACACATAGTCATCGAACCATATAATCTGTAAAGGATTCATTTCATTTAAT
1 ACTCACGATGACACATAGTCATCGAACCATATAATCCATAAAGGATTCATTTCATTTAAT
* *
21437726 ACTCATGATGACACATAATCATCGAA
1 ACTCACGATGACACATAGTCATCGAA
21437752 GCTTTTTGCA
Statistics
Matches: 296, Mismatches: 27, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
60 252 0.85
61 4 0.01
62 29 0.10
63 11 0.04
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (60 bp):
ACTCACGATGACACATAGTCATCGAACCATATAATCCATAAAGGATTCATTTCATTTAAT
Found at i:21456496 original size:56 final size:57
Alignment explanation
Indices: 21456430--21456541 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 57
21456420 TCATTTTCAT
* *
21456430 TTTTCTTTTTCATTTTGGAGAAAACCACATTCA-TTTCAAAATGATT-TCATTTCTCC
1 TTTTCATTTTCATTTTGGAGAAAACCACAATCATTTTC-AAATGATTCTCATTTCTCC
* *
21456486 TTTTCATTTTCATTTTGGAGAAAACCATAATCATTTTCAAATGTTTCTCATTTCTC
1 TTTTCATTTTCATTTTGGAGAAAACCACAATCATTTTCAAATGATTCTCATTTCTC
21456542 AATTTCACCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 37 0.74
57 13 0.26
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (57 bp):
TTTTCATTTTCATTTTGGAGAAAACCACAATCATTTTCAAATGATTCTCATTTCTCC
Found at i:21458219 original size:16 final size:17
Alignment explanation
Indices: 21458182--21458221 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
21458172 TGTTATGCTC
*
21458182 AAGTGGATCCCACTTGAA
1 AAGT-GATCACACTTGAA
21458200 AAGTGATCACACTT-AA
1 AAGTGATCACACTTGAA
21458216 AAGTGA
1 AAGTGA
21458222 GTGCCTAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 9 0.43
18 4 0.19
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (17 bp):
AAGTGATCACACTTGAA
Found at i:21460541 original size:18 final size:18
Alignment explanation
Indices: 21460504--21460545 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
21460494 ATAACTGATA
*
21460504 TGGAGGATACATTTGAGG
1 TGGAGGATACATTCGAGG
21460522 TGGAGGATACA-TCGACGG
1 TGGAGGATACATTCGA-GG
21460540 TGGAGG
1 TGGAGG
21460546 TGGGTGATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.26, C:0.10, G:0.43, T:0.21
Consensus pattern (18 bp):
TGGAGGATACATTCGAGG
Found at i:21464168 original size:17 final size:19
Alignment explanation
Indices: 21464146--21464180 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
21464136 TATCATGAAA
21464146 ATAAAAA-TAA-AAATAAT
1 ATAAAAATTAACAAATAAT
21464163 ATAAAAATTAACAAATAA
1 ATAAAAATTAACAAATAA
21464181 AAAATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (19 bp):
ATAAAAATTAACAAATAAT
Found at i:21464179 original size:25 final size:25
Alignment explanation
Indices: 21464143--21464200 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
21464133 ATTTATCATG
21464143 AAAA-TAA-AAAT-AAAAATAATATA
1 AAAATTAACAAATAAAAAAT-ATATA
*
21464166 AAAATTAACAAATAAAAAATTTATA
1 AAAATTAACAAATAAAAAATATATA
21464191 AAACATTAAC
1 AAA-ATTAAC
21464201 CAATTATCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.13
24 3 0.10
25 11 0.37
26 12 0.40
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAATTAACAAATAAAAAATATATA
Found at i:21467486 original size:56 final size:55
Alignment explanation
Indices: 21467422--21467564 Score: 195
Period size: 57 Copynumber: 2.6 Consensus size: 55
21467412 TGTGCAATTT
21467422 TTAA-ATCAAAATTTTAATGTTGAAAAAAAAAGTTTTTT-AAAGTTTGAATAAAAAA
1 TTAATATCAAAATTTTAATGTTGAAAAAAAAAGTTTTTTAAAAGTTTGAAT--AAAA
21467477 TTAATATCAAAATTTTAATGTTGAAAAACAAAAAAAGTTTTTTAAAAGTTTGAATAAAA
1 TTAATATCAAAATTTTAATGTTG---AA-AAAAAAAGTTTTTTAAAAGTTTGAATAAAA
*
21467536 --AATATCAAAATTTTAAAGTTGAAAAAAAA
1 TTAATATCAAAATTTTAATGTTGAAAAAAAA
21467565 CAATGTTTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 14
0.84 0.01 0.15
Matches are distributed among these distances:
53 6 0.07
54 2 0.02
55 4 0.05
56 18 0.22
57 20 0.25
59 6 0.07
60 14 0.17
61 11 0.14
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (55 bp):
TTAATATCAAAATTTTAATGTTGAAAAAAAAAGTTTTTTAAAAGTTTGAATAAAA
Found at i:21467575 original size:57 final size:55
Alignment explanation
Indices: 21467426--21467576 Score: 200
Period size: 56 Copynumber: 2.7 Consensus size: 55
21467416 CAATTTTTAA
21467426 ATCAAAATTTTAATGTTG-AAAAAAAAAGTTTTTTAAAGTTTGAATAAAAAATTAAT
1 ATCAAAATTTTAATGTTGAAAAAAAAAAGTTTTTTAAAGTTTGAAT-AAAAA-TAAT
21467482 ATCAAAATTTTAATGTTGAAAAACAAAAAAAGTTTTTTAAAAGTTTGAAT-AAAA-AAT
1 ATCAAAATTTTAATGTTG--AAA-AAAAAAAGTTTTTT-AAAGTTTGAATAAAAATAAT
*
21467539 ATCAAAATTTTAAAGTTGAAAAAAAACAATGTTTTTTA
1 ATCAAAATTTTAATGTTGAAAAAAAA-AA-GTTTTTTA
21467577 TTAGTATTAA
Statistics
Matches: 87, Mismatches: 1, Indels: 15
0.84 0.01 0.15
Matches are distributed among these distances:
54 5 0.06
55 6 0.07
56 25 0.29
57 20 0.23
59 6 0.07
60 14 0.16
61 11 0.13
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (55 bp):
ATCAAAATTTTAATGTTGAAAAAAAAAAGTTTTTTAAAGTTTGAATAAAAATAAT
Found at i:21471326 original size:26 final size:25
Alignment explanation
Indices: 21471297--21471379 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 25
21471287 TAAGTATTAT
21471297 TTAAAAGAGTTTTAGATAAATAATAA
1 TTAAAAGAGTTTTA-ATAAATAATAA
* * * *
21471323 TTAAAATAGAATTTT-AT-TATTATTA
1 TT-AAA-AGAGTTTTAATAAATAATAA
*
21471348 TCTAAAAGAGTTTTAAATAAAAAATAA
1 T-TAAAAGAGTTTT-AATAAATAATAA
21471375 TTAAA
1 TTAAA
21471380 TAGAAATTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
24 7 0.17
25 9 0.21
26 11 0.26
27 8 0.19
28 7 0.17
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (25 bp):
TTAAAAGAGTTTTAATAAATAATAA
Found at i:21471361 original size:52 final size:51
Alignment explanation
Indices: 21471291--21471389 Score: 153
Period size: 52 Copynumber: 1.9 Consensus size: 51
21471281 AGAATTTAAG
* * * *
21471291 TATTATTTAAAAGAGTTTTAGATAAATAATAATTAAAATAGAATTTTATTAT
1 TATTATCTAAAAGAGTTTTAAATAAAAAATAATT-AAATAGAAATTTATTAT
21471343 TATTATCTAAAAGAGTTTTAAATAAAAAATAATTAAATAGAAATTTA
1 TATTATCTAAAAGAGTTTTAAATAAAAAATAATTAAATAGAAATTTA
21471390 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 12 0.28
52 31 0.72
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (51 bp):
TATTATCTAAAAGAGTTTTAAATAAAAAATAATTAAATAGAAATTTATTAT
Found at i:21471469 original size:38 final size:38
Alignment explanation
Indices: 21471350--21471470 Score: 118
Period size: 38 Copynumber: 3.1 Consensus size: 38
21471340 TATTATTATC
* *
21471350 TAAAAGAGTTTTAAATAAAAAATAATTAAATAGAAATTTAAT
1 TAAAAGAGTTTTAGATAAATAATAATTAAATAGAAA--T--T
* * * **
21471392 TAAAAGAGTTTTAGATAAATAAAAATTATATTGTTATT
1 TAAAAGAGTTTTAGATAAATAATAATTAAATAGAAATT
*
21471430 TAAAAGAGTTATAGATAAATAATAATTAAAATAG-AATT
1 TAAAAGAGTTTTAGATAAATAATAATT-AAATAGAAATT
21471468 TAA
1 TAA
21471471 TTATTAGTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
38 32 0.48
39 4 0.06
40 1 0.02
42 29 0.44
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (38 bp):
TAAAAGAGTTTTAGATAAATAATAATTAAATAGAAATT
Found at i:21471487 original size:49 final size:47
Alignment explanation
Indices: 21471420--21471522 Score: 118
Period size: 49 Copynumber: 2.1 Consensus size: 47
21471410 ATAAAAATTA
* * * *
21471420 TATTGTTATTTAAAAGAGTTATAGATAAATA-ATAATTAAAATAGAATT
1 TATTATTAGTTAAAAGAGTTATAAATAAA-AGATAATT-AAATAGAAAT
* *
21471468 TAATTATTAGTTAAAAGAGTTTTAAATAAAAGATAATTTAATAGAAAT
1 T-ATTATTAGTTAAAAGAGTTATAAATAAAAGATAATTAAATAGAAAT
21471516 TATTATT
1 TATTATT
21471523 GAAAAGAGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
47 6 0.13
48 11 0.23
49 30 0.64
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.41
Consensus pattern (47 bp):
TATTATTAGTTAAAAGAGTTATAAATAAAAGATAATTAAATAGAAAT
Found at i:21471536 original size:132 final size:131
Alignment explanation
Indices: 21471293--21471534 Score: 391
Period size: 129 Copynumber: 1.8 Consensus size: 131
21471283 AATTTAAGTA
*
21471293 TTATTTAAAAGAGTTTTAGATAAATAATAATTAAAATAGAATTTTATTATTATTATCTAAAAGAG
1 TTATTTAAAAGAGTTATAGATAAATAATAATTAAAATAGAATTTTA-TATTATTATCTAAAAGAG
21471358 TTTTAAATAAAAAATAATTAAATAGAAATTTAATTAAAAGAGTTTTAGATAAATAAAAATTATAT
65 TTTTAAATAAAAAATAATTAAATAGAAATTTAATTAAAAGAGTTTTAGATAAATAAAAATTATAT
21471423 TG
130 TG
21471425 TTATTTAAAAGAGTTATAGATAAATAATAATTAAAATAGAA-TTTA-ATTATTAGT-TAAAAGAG
1 TTATTTAAAAGAGTTATAGATAAATAATAATTAAAATAGAATTTTATATTATTA-TCTAAAAGAG
* * *
21471487 TTTTAAATAAAAGATAATTTAATAGAAATTATTATTGAAAAGAGTTTT
65 TTTTAAATAAAAAATAATTAAATAGAAATT-TAATT-AAAAGAGTTTT
21471535 TAAAATTCAA
Statistics
Matches: 103, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
129 43 0.42
130 5 0.05
131 15 0.15
132 40 0.39
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (131 bp):
TTATTTAAAAGAGTTATAGATAAATAATAATTAAAATAGAATTTTATATTATTATCTAAAAGAGT
TTTAAATAAAAAATAATTAAATAGAAATTTAATTAAAAGAGTTTTAGATAAATAAAAATTATATT
G
Found at i:21471658 original size:2 final size:2
Alignment explanation
Indices: 21471653--21471682 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21471643 ACCCTATATA
21471653 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
21471683 ATATATACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:21472320 original size:25 final size:26
Alignment explanation
Indices: 21472276--21472335 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
21472266 ATATACGAAA
*
21472276 AAAATTGAAGAAAAAATAATACAGACT
1 AAAATTG-AGAAAAAATAATACAGACC
21472303 AAAATTGA-AAAAAATAATACAGACC
1 AAAATTGAGAAAAAATAATACAGACC
21472328 AAAATTGA
1 AAAATTGA
21472336 TTTACATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 24 0.75
26 1 0.03
27 7 0.22
ACGTcount: A:0.63, C:0.08, G:0.10, T:0.18
Consensus pattern (26 bp):
AAAATTGAGAAAAAATAATACAGACC
Found at i:21472336 original size:109 final size:109
Alignment explanation
Indices: 21472201--21472419 Score: 305
Period size: 109 Copynumber: 2.0 Consensus size: 109
21472191 AAAATTCGAA
** * * * ** *
21472201 AAAAAAATAATATGGACCAAATTTGATTTAGAGATTCAAAAAAATACGAACATTGTAGTCATTTG
1 AAAAAAATAATACAGACCAAAATTGATTTACAGATACAAAAAAATACGAACATTGTAGTCAACTA
*
21472266 ATATACGAAAAAAATT-GAAGAAAAAATAATACAGACTAAAATTG
66 AT-TACGAAAAAAATTCGAAGAAAAAATAATACAGACCAAAATTG
*
21472310 AAAAAAATAATACAGACCAAAATTGATTTACATATACAAAAAAATACGAACATTGTAGTCAACTA
1 AAAAAAATAATACAGACCAAAATTGATTTACAGATACAAAAAAATACGAACATTGTAGTCAACTA
* * *
21472375 ATTACGAAAAAAATTCGAAGAAAAATTAATGCGGACCAAAATTG
66 ATTACGAAAAAAATTCGAAGAAAAAATAATACAGACCAAAATTG
21472419 A
1 A
21472420 TTTACGGATA
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
108 13 0.14
109 83 0.86
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.24
Consensus pattern (109 bp):
AAAAAAATAATACAGACCAAAATTGATTTACAGATACAAAAAAATACGAACATTGTAGTCAACTA
ATTACGAAAAAAATTCGAAGAAAAAATAATACAGACCAAAATTG
Found at i:21472399 original size:85 final size:85
Alignment explanation
Indices: 21472311--21472593 Score: 310
Period size: 84 Copynumber: 3.4 Consensus size: 85
21472301 CTAAAATTGA
*
21472311 AAAAAATAATACAGACCAAAATTGATTTACATATACAAAAAAATACGAACATTGTAGTCAACTAA
1 AAAAAATAATACAGACCAAAATTGATTTACATATACAAAAAAATACAAACATTGTAGTCAACTAA
21472376 T-TACGAAAAAAATTCGAAG
66 TATACGAAAAAAATTCGAAG
* * * ** * * * * *
21472395 AAAAATTAATGCGGACCAAAATTGATTTACGGATACAAAAAAATAAAAATATCGTAGTCAATTGA
1 AAAAAATAATACAGACCAAAATTGATTTACATATACAAAAAAATACAAACATTGTAGTCAACTAA
21472460 TATACG-AAAAAA-TCGAAG
66 TATACGAAAAAAATTCGAAG
* ** *
21472478 AAAAATTAATATGGACCAGAATTGATTTACATATAC-AAAAAATACAAACATTGTAGT--ACTAA
1 AAAAAATAATACAGACCAAAATTGATTTACATATACAAAAAAATACAAACATTGTAGTCAACTAA
* *
21472540 TATACCAAAAAACAATTTCGAAC
66 TATA-CGAAAAA-AA-TTCGAAG
* *
21472563 AAAAAATAATA-AGGAACAAAATTGAATTACA
1 AAAAAATAATACA-GACCAAAATTGATTTACA
21472594 GAGAAAAAAA
Statistics
Matches: 164, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
80 7 0.04
81 1 0.01
82 22 0.13
83 39 0.24
84 61 0.37
85 34 0.21
ACGTcount: A:0.54, C:0.12, G:0.11, T:0.23
Consensus pattern (85 bp):
AAAAAATAATACAGACCAAAATTGATTTACATATACAAAAAAATACAAACATTGTAGTCAACTAA
TATACGAAAAAAATTCGAAG
Found at i:21472507 original size:167 final size:166
Alignment explanation
Indices: 21472303--21472606 Score: 400
Period size: 168 Copynumber: 1.8 Consensus size: 166
21472293 AATACAGACT
* *
21472303 AAAATTGAAAAAAATAATACAGACCAAAATTGATTTACATATACAAAAAAATACGAACATTGTAG
1 AAAATCGAAAAAAATAATACAGACCAAAATTGATTTACATATAC-AAAAAATACAAACATTGTAG
* * * ** * * * *
21472368 TCAACTAAT-TA-CGAAAAA-AA-TTCGAAGAAAAATTAATGCGGACCAAAATTGATTTACGGAT
65 T--ACTAATATACCAAAAAACAATTTCGAACAAAAAATAATAAGGAACAAAATTGAATTACAGAG
*
21472429 ACAAAAAAATAAAAATATCGTAGTCAATTGATATACGAA
128 AAAAAAAAATAAAAATATCGTAGTCAATTGATATACGAA
** *
21472468 AAAATCGAAGAAAAATTAATATGGACCAGAATTGATTTACATATACAAAAAATACAAACATTGTA
1 AAAATCGAA-AAAAA-TAATACAGACCAAAATTGATTTACATATACAAAAAATACAAACATTGTA
21472533 GTACTAATATACCAAAAAACAATTTCGAACAAAAAATAATAAGGAACAAAATTGAATTACAGAGA
64 GTACTAATATACCAAAAAACAATTTCGAACAAAAAATAATAAGGAACAAAATTGAATTACAGAGA
21472598 AAAAAAAAT
129 AAAAAAAAT
21472607 GATTTATGAA
Statistics
Matches: 118, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
164 6 0.05
165 10 0.08
166 31 0.26
167 29 0.25
168 42 0.36
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (166 bp):
AAAATCGAAAAAAATAATACAGACCAAAATTGATTTACATATACAAAAAATACAAACATTGTAGT
ACTAATATACCAAAAAACAATTTCGAACAAAAAATAATAAGGAACAAAATTGAATTACAGAGAAA
AAAAAATAAAAATATCGTAGTCAATTGATATACGAA
Found at i:21473772 original size:39 final size:39
Alignment explanation
Indices: 21473719--21473840 Score: 97
Period size: 39 Copynumber: 3.2 Consensus size: 39
21473709 TTTTTTTAAA
* *
21473719 AAAATACAAACTGATAAATTTTGAAAAAAGATTAATAAT
1 AAAATACGATCTGATAAATTTTGAAAAAAGATTAATAAT
* * **
21473758 AAAATACGATCTGATGATTTTTGAAAACAA-ATTTTTAA-
1 AAAATACGATCTGATAAATTTTGAAAA-AAGATTAATAAT
* * ** * *
21473796 AAAATATGAAT-TGATAAGTTTTTCAAAGAGATTAAAAAT
1 AAAATACG-ATCTGATAAATTTTGAAAAAAGATTAATAAT
21473835 AAAATA
1 AAAATA
21473841 TGATATGAAC
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
37 1 0.02
38 24 0.38
39 37 0.58
40 2 0.03
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (39 bp):
AAAATACGATCTGATAAATTTTGAAAAAAGATTAATAAT
Found at i:21473800 original size:38 final size:38
Alignment explanation
Indices: 21473577--21473801 Score: 96
Period size: 36 Copynumber: 6.1 Consensus size: 38
21473567 TAAATATCAT
* * * **
21473577 ATACGAACAGATAAATTTTGAAAAAAAATTAAT-AAAA
1 ATACAAACTGATAAATTTTGAAAAAAGATTTTTAAAAA
** *
21473614 A-AGGAACTGA-AATTTTTTG-AAAAAGA--TTTAAAAA
1 ATACAAACTGATAA-ATTTTGAAAAAAGATTTTTAAAAA
* * * * *
21473648 ATA-AGAATTAAAAAATTTCGAAAAAATA-TTTTAAAAA
1 ATACA-AACTGATAAATTTTGAAAAAAGATTTTTAAAAA
* * ***
21473685 ATTACATACTAATAAATTTTG---AATTTTTTTTAAAAAA
1 A-TACAAACTGATAAATTTTGAAAAAAGATTTTT-AAAAA
**
21473722 ATACAAACTGATAAATTTTGAAAAAAGATTAATAATAAA
1 ATACAAACTGATAAATTTTGAAAAAAGATTTTTAA-AAA
* * * *
21473761 ATACGATCTGATGATTTTTGAAAACAA-ATTTTTAAAAA
1 ATACAAACTGATAAATTTTGAAAA-AAGATTTTTAAAAA
21473799 ATA
1 ATA
21473802 TGAATTGATA
Statistics
Matches: 141, Mismatches: 31, Indels: 31
0.69 0.15 0.15
Matches are distributed among these distances:
33 1 0.01
34 5 0.04
35 20 0.14
36 41 0.29
37 16 0.11
38 21 0.15
39 35 0.25
40 2 0.01
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (38 bp):
ATACAAACTGATAAATTTTGAAAAAAGATTTTTAAAAA
Found at i:21479152 original size:28 final size:28
Alignment explanation
Indices: 21479094--21479153 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
21479084 TAATTTTTTT
* *
21479094 ACCCTAAACTCTAAATTTAAAATCTCAA
1 ACCCTAAACTATAAATCTAAAATCTCAA
21479122 ACCCTAAACTATAAA-CTAATAAT-TCATA
1 ACCCTAAACTATAAATCTAA-AATCTCA-A
21479150 ACCC
1 ACCC
21479154 CAAAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.21
28 22 0.79
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (28 bp):
ACCCTAAACTATAAATCTAAAATCTCAA
Found at i:21479194 original size:13 final size:14
Alignment explanation
Indices: 21479170--21479198 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21479160 TTTAAACCTT
21479170 AAACCTTAAATTCA
1 AAACCTTAAATTCA
21479184 AAACC-TAAATTCA
1 AAACCTTAAATTCA
21479197 AA
1 AA
21479199 CCCTGAACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCTTAAATTCA
Found at i:21480863 original size:6 final size:6
Alignment explanation
Indices: 21480852--21480887 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
21480842 TTGCAAGTTT
* *
21480852 ATAAAC ATAAAC ATAAAA ATAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
21480888 GATACAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:21486196 original size:12 final size:12
Alignment explanation
Indices: 21486181--21486206 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21486171 AATTAAAGAA
21486181 ATAATAGCATTC
1 ATAATAGCATTC
21486193 ATAATAGCATTC
1 ATAATAGCATTC
21486205 AT
1 AT
21486207 CATGATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:21489778 original size:120 final size:120
Alignment explanation
Indices: 21489583--21489841 Score: 358
Period size: 120 Copynumber: 2.2 Consensus size: 120
21489573 CCGATACTCT
*
21489583 AGCCATCGATACGGTATCTTATAATCCCAAATTTCATTCTCATGTCTGTATCAACTCTGTTACCA
1 AGCCATAGATACGGTATCTTATAATCCCAAATTTCATTCTCATGTCTGTATCAACTCTGTTACCA
* * * * * *
21489648 GTATACGATGCTGCTCATACGAGCTGTCGATGACTCGCAATATATGCGGTACCCC
66 GTATACGATGCTGCTCACACGAGCTATCAAGGACTCGCAACATATGCAGTACCCC
* * * *
21489703 AGCCATTGATATGGTATGC-TATAATCTCGAATTTCATTCTCATGTCTGTATCAACTCTGTTACC
1 AGCCATAGATACGGTAT-CTTATAATCCCAAATTTCATTCTCATGTCTGTATCAACTCTGTTACC
* * *
21489767 AGTATATGATGCTGCTCACACGAGCTATCAAGGACTCGTAACATTTGCAGTACCCC
65 AGTATACGATGCTGCTCACACGAGCTATCAAGGACTCGCAACATATGCAGTACCCC
* *
21489823 AACCATAGATACGATATCT
1 AGCCATAGATACGGTATCT
21489842 GTACATATAA
Statistics
Matches: 120, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
119 1 0.01
120 118 0.98
121 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.31
Consensus pattern (120 bp):
AGCCATAGATACGGTATCTTATAATCCCAAATTTCATTCTCATGTCTGTATCAACTCTGTTACCA
GTATACGATGCTGCTCACACGAGCTATCAAGGACTCGCAACATATGCAGTACCCC
Found at i:21498093 original size:17 final size:17
Alignment explanation
Indices: 21498071--21498105 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
21498061 CAATATCAAA
21498071 TAACACAAACTTCATCT
1 TAACACAAACTTCATCT
*
21498088 TAACACAAACTTTATCT
1 TAACACAAACTTCATCT
21498105 T
1 T
21498106 GTCTTTCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (17 bp):
TAACACAAACTTCATCT
Found at i:21500219 original size:27 final size:27
Alignment explanation
Indices: 21500189--21500243 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
21500179 TCACAATCTG
*
21500189 AGGGACTTCTACCGGTACCTGTTGGAC
1 AGGGACTTCTACCGATACCTGTTGGAC
21500216 AGGGACTTCTACCGATACCTGTTGGAC
1 AGGGACTTCTACCGATACCTGTTGGAC
21500243 A
1 A
21500244 AGTATCGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.25, G:0.27, T:0.25
Consensus pattern (27 bp):
AGGGACTTCTACCGATACCTGTTGGAC
Found at i:21501265 original size:120 final size:120
Alignment explanation
Indices: 21501052--21501416 Score: 516
Period size: 120 Copynumber: 3.0 Consensus size: 120
21501042 GCTTCCATAA
** * * * *
21501052 GCTATAATCTAAAATTTCATCCTAATGTCTGTATCAACTCTTTTACCAGTATACGATGCTGTTCA
1 GCTATAATCTTGAATTTCATTCTCATGTCTGTATCAACTCTGTTACCAGTATACGATGCTGCTCA
* * *
21501117 CACGAGCTATCAAGGACTCATAACATATGCGGTACCCCAACCATCGATACAGTAT
66 CACGAGCTGTCGAGGACTCGTAACATATGCGGTACCCCAACCATCGATACAGTAT
21501172 GCTATAATCTTGAATTTCATTCTCATGTCTGTATCAACTCTGTTACCAGTATACGATGCTGCTCA
1 GCTATAATCTTGAATTTCATTCTCATGTCTGTATCAACTCTGTTACCAGTATACGATGCTGCTCA
* * * *
21501237 CACGAGCTGTCGAGGACTCGCAACATATGCGATACCCCAGCCATCGATACGGTAT
66 CACGAGCTGTCGAGGACTCGTAACATATGCGGTACCCCAACCATCGATACAGTAT
* * * * * *
21501292 GCTATAATCCTGAATTTCATTATCATGTTTGTATAAACTCTGTTACCAATATACGATGCTACTCA
1 GCTATAATCTTGAATTTCATTCTCATGTCTGTATCAACTCTGTTACCAGTATACGATGCTGCTCA
* * * *
21501357 CACAAGCTGTCGAGGACTCGTAACATATGGGGTACCCCATCCATCGATACAATAT
66 CACGAGCTGTCGAGGACTCGTAACATATGCGGTACCCCAACCATCGATACAGTAT
21501412 -CTATA
1 GCTATA
21501417 CATATAATTG
Statistics
Matches: 219, Mismatches: 26, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
119 5 0.02
120 214 0.98
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (120 bp):
GCTATAATCTTGAATTTCATTCTCATGTCTGTATCAACTCTGTTACCAGTATACGATGCTGCTCA
CACGAGCTGTCGAGGACTCGTAACATATGCGGTACCCCAACCATCGATACAGTAT
Found at i:21502955 original size:39 final size:40
Alignment explanation
Indices: 21502894--21502974 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
21502884 ATTTAGTTAA
* *
21502894 AAAACTTTTTTTCAATTTAGTCCTAAACTAATTAGGACTG
1 AAAACTTGTTTTCAATTTAGTCCTAAACTAATTAAGACTG
*
21502934 AAAACTTGTTTTGAA-TTAGTCCTAAACTAATTAAGACTG
1 AAAACTTGTTTTCAATTTAGTCCTAAACTAATTAAGACTG
21502973 AA
1 AA
21502975 TGAATAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 25 0.66
40 13 0.34
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (40 bp):
AAAACTTGTTTTCAATTTAGTCCTAAACTAATTAAGACTG
Found at i:21513825 original size:6 final size:6
Alignment explanation
Indices: 21513814--21513848 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
21513804 ATTGTGAATG
21513814 AGAAAA AG-AAA AGAAAA AGAGAAA AGAAAA AGAAA
1 AGAAAA AGAAAA AGAAAA AGA-AAA AGAAAA AGAAA
21513849 TATTGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:21513838 original size:13 final size:13
Alignment explanation
Indices: 21513816--21513846 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
21513806 TGTGAATGAG
21513816 AAAA-AGAAAAGA
1 AAAAGAGAAAAGA
21513828 AAAAGAGAAAAGA
1 AAAAGAGAAAAGA
21513841 AAAAGA
1 AAAAGA
21513847 AATATTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAGAGAAAAGA
Found at i:21520890 original size:29 final size:30
Alignment explanation
Indices: 21520815--21520894 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 30
21520805 TTTTGTTCTG
* * * * *
21520815 TGATATTACTCT-TTGTTGAGTTATTTGTG
1 TGATATTATTCTGATGTTGTGTTATTAGTA
21520844 TGATATTATTCTGA-GTTGTGTTATTAGTA
1 TGATATTATTCTGATGTTGTGTTATTAGTA
*
21520873 TGATCTTATTCT-ATGTTGTGTT
1 TGATATTATTCTGATGTTGTGTT
21520895 GTCGCATGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.02
29 42 0.98
ACGTcount: A:0.19, C:0.06, G:0.20, T:0.55
Consensus pattern (30 bp):
TGATATTATTCTGATGTTGTGTTATTAGTA
Found at i:21522572 original size:21 final size:21
Alignment explanation
Indices: 21522543--21522593 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
21522533 GTTACATGCA
* *
21522543 TATGTGAACTCTTTTATATGT
1 TATGCGAACTCTTTTAGATGT
*
21522564 TATGCGAACTTTTTTAGATGT
1 TATGCGAACTCTTTTAGATGT
*
21522585 TGTGCGAAC
1 TATGCGAAC
21522594 AGTTTTACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.45
Consensus pattern (21 bp):
TATGCGAACTCTTTTAGATGT
Found at i:21522599 original size:21 final size:21
Alignment explanation
Indices: 21522554--21522609 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
21522544 ATGTGAACTC
* * **
21522554 TTTTATATGTTATGCGAACTT
1 TTTTACATGTTGTGCGAACAG
*
21522575 TTTTAGATGTTGTGCGAACAG
1 TTTTACATGTTGTGCGAACAG
21522596 TTTTACATGTTGTG
1 TTTTACATGTTGTG
21522610 TGAGCTCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.48
Consensus pattern (21 bp):
TTTTACATGTTGTGCGAACAG
Found at i:21523266 original size:31 final size:31
Alignment explanation
Indices: 21523229--21523303 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
21523219 TGTGATAAAC
*
21523229 CATCATTGTCGGACAATCCGAGGTGGTAGGT
1 CATCATTGTCGGAAAATCCGAGGTGGTAGGT
* *
21523260 CATCATTGTCGAAAAATTCGAGGTGGTAGGT
1 CATCATTGTCGGAAAATCCGAGGTGGTAGGT
*
21523291 TATCATTGCTCGG
1 CATCATTG-TCGG
21523304 TAACCTAGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 35 0.92
32 3 0.08
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (31 bp):
CATCATTGTCGGAAAATCCGAGGTGGTAGGT
Found at i:21523429 original size:75 final size:76
Alignment explanation
Indices: 21523278--21523451 Score: 199
Period size: 75 Copynumber: 2.3 Consensus size: 76
21523268 TCGAAAAATT
** * * * * **
21523278 CGAGGTGGTAGGTTATCATTGCTCGGTAACCTAGGATGATAAATTTGATTTGATAAACCATCGTT
1 CGAGGTGGTAGGCCATCATTGCTAGGCAATCTGGGATGATAAATTTGATTCAATAAACCATCGTT
* *
21523343 ACTGAGGAATC
66 ACGGAGCAATC
* * *
21523354 CGA-TTGGTAGGCCATCGTTGCTAGGCAATCTGGGATGATAGATTTGATTCAATAAACCATCGTT
1 CGAGGTGGTAGGCCATCATTGCTAGGCAATCTGGGATGATAAATTTGATTCAATAAACCATCGTT
21523418 ACCGGA-CAATC
66 A-CGGAGCAATC
*
21523429 CGAGGTGGTAGGTCATCATTGCT
1 CGAGGTGGTAGGCCATCATTGCT
21523452 TGGTGATCCG
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
75 58 0.73
76 22 0.28
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (76 bp):
CGAGGTGGTAGGCCATCATTGCTAGGCAATCTGGGATGATAAATTTGATTCAATAAACCATCGTT
ACGGAGCAATC
Found at i:21523564 original size:43 final size:43
Alignment explanation
Indices: 21523503--21523605 Score: 145
Period size: 43 Copynumber: 2.4 Consensus size: 43
21523493 TTGGTGTGAG
**
21523503 CATTCGTGCTGCACTTACAAGCAGTGTTTTC-AGAGAGTGCGAA
1 CATTCGTGCTGCACTTACAAGCAGTGCATTCGA-AGAGTGCGAA
* *
21523546 CATTCGTGCTGCACTTACAGGCAGTGCATTCGAAGAGTGCGAG
1 CATTCGTGCTGCACTTACAAGCAGTGCATTCGAAGAGTGCGAA
*
21523589 CATTCGTACTGCACTTA
1 CATTCGTGCTGCACTTA
21523606 TATGGCGATT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
43 53 0.98
44 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.27
Consensus pattern (43 bp):
CATTCGTGCTGCACTTACAAGCAGTGCATTCGAAGAGTGCGAA
Found at i:21523787 original size:29 final size:29
Alignment explanation
Indices: 21523742--21523914 Score: 213
Period size: 29 Copynumber: 5.9 Consensus size: 29
21523732 TTTGCTTATA
*
21523742 TGTATGCAAACTGTTTATATGTGAACTAT
1 TGTATGCGAACTGTTTATATGTGAACTAT
*
21523771 TGTATGCGAACTATTTATATGTGAACTAT
1 TGTATGCGAACTGTTTATATGTGAACTAT
* *
21523800 TGTATGCGAACTGTTTATTTGTGAATTATT
1 TGTATGCGAACTGTTTATATGTGAACTA-T
21523830 TGTATGCGAACTGTTTATATGTGAACTAT
1 TGTATGCGAACTGTTTATATGTGAACTAT
* * * * *
21523859 TTTATGCAAACTATTTATGTGTGAACTGT
1 TGTATGCGAACTGTTTATATGTGAACTAT
* * *
21523888 TCATGTGAGAACTG-TTATATGTGAACT
1 T-GTATGCGAACTGTTTATATGTGAACT
21523915 GTTCGTAAAC
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
29 90 0.73
30 34 0.27
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (29 bp):
TGTATGCGAACTGTTTATATGTGAACTAT
Found at i:21523852 original size:59 final size:59
Alignment explanation
Indices: 21523742--21523914 Score: 224
Period size: 59 Copynumber: 3.0 Consensus size: 59
21523732 TTTGCTTATA
*
21523742 TGTATGCAAACTGTTTATATGTGAACTA-TTGTATGCGAACTATTTATATGTGAACTAT
1 TGTATGCAAACTGTTTATATGTGAACTATTTGTATGCGAACTGTTTATATGTGAACTAT
* * *
21523800 TGTATGCGAACTGTTTATTTGTGAATTATTTGTATGCGAACTGTTTATATGTGAACTAT
1 TGTATGCAAACTGTTTATATGTGAACTATTTGTATGCGAACTGTTTATATGTGAACTAT
* * * * ** * *
21523859 TTTATGCAAACTATTTATGTGTGAACTGTTCATGTGAGAACTG-TTATATGTGAACT
1 TGTATGCAAACTGTTTATATGTGAACTATTTGTATGCGAACTGTTTATATGTGAACT
21523915 GTTCGTAAAC
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
58 38 0.38
59 62 0.62
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (59 bp):
TGTATGCAAACTGTTTATATGTGAACTATTTGTATGCGAACTGTTTATATGTGAACTAT
Found at i:21523911 original size:88 final size:88
Alignment explanation
Indices: 21523737--21523912 Score: 246
Period size: 88 Copynumber: 2.0 Consensus size: 88
21523727 ACTGTTTTGC
* *
21523737 TTATATGTATGCAAACTGTTTATATGTGAACTATTGTATGCGAACTATTTATATGTGAACTATTG
1 TTATATGTATGCAAACTGTTTATATGTGAACTATTGTATGCAAACTATTTATATGTGAACTATTA
* *
21523802 TATGCGAACTGTTTATTTGTGAA
66 TATGAGAACTGTTTATATGTGAA
* * * * *
21523825 TTATTTGTATGCGAACTGTTTATATGTGAACTATTTTATGCAAACTATTTATGTGTGAACTGTTC
1 TTATATGTATGCAAACTGTTTATATGTGAACTATTGTATGCAAACTATTTATATGTGAACTATT-
*
21523890 ATGTGAGAACTG-TTATATGTGAA
65 ATATGAGAACTGTTTATATGTGAA
21523913 CTGTTCGTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
88 68 0.88
89 9 0.12
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (88 bp):
TTATATGTATGCAAACTGTTTATATGTGAACTATTGTATGCAAACTATTTATATGTGAACTATTA
TATGAGAACTGTTTATATGTGAA
Found at i:21523932 original size:88 final size:88
Alignment explanation
Indices: 21523750--21523933 Score: 226
Period size: 88 Copynumber: 2.1 Consensus size: 88
21523740 TATGTATGCA
* * *
21523750 AACTGTTTATATGTGAACTATTGTATGCGAACTATTTATATGTGAACTATTGTATGCGAACTGTT
1 AACTGTTTATATGTGAACTATTGTATGCAAACTATTTATATGTGAACTATTATATGAGAACTGTT
* * * **
21523815 TATTTGTGAATTATTTGTATGCG
66 TATATGTGAACTATTCGTAAACG
* * * *
21523838 AACTGTTTATATGTGAACTATTTTATGCAAACTATTTATGTGTGAACTGTTCATGTGAGAACTG-
1 AACTGTTTATATGTGAACTATTGTATGCAAACTATTTATATGTGAACTATT-ATATGAGAACTGT
*
21523902 TTATATGTGAACTGTTCGTAAACG
65 TTATATGTGAACTATTCGTAAACG
*
21523926 AGCTGTTT
1 AACTGTTT
21523934 GGTATGAAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
88 72 0.89
89 9 0.11
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (88 bp):
AACTGTTTATATGTGAACTATTGTATGCAAACTATTTATATGTGAACTATTATATGAGAACTGTT
TATATGTGAACTATTCGTAAACG
Found at i:21529729 original size:6 final size:7
Alignment explanation
Indices: 21529712--21529739 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
21529702 TTGTGTGATA
21529712 AAAAAAT
1 AAAAAAT
21529719 AAAAAAT
1 AAAAAAT
21529726 AAAAAAT
1 AAAAAAT
21529733 AAAAAAT
1 AAAAAAT
21529740 TAGCTTCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:21531756 original size:50 final size:50
Alignment explanation
Indices: 21531698--21531804 Score: 214
Period size: 50 Copynumber: 2.1 Consensus size: 50
21531688 AATTTCAAAC
21531698 CATTCTAGATAATGTTGAAGAAATCAATAAAATATAACCAAGCTTTGATA
1 CATTCTAGATAATGTTGAAGAAATCAATAAAATATAACCAAGCTTTGATA
21531748 CATTCTAGATAATGTTGAAGAAATCAATAAAATATAACCAAGCTTTGATA
1 CATTCTAGATAATGTTGAAGAAATCAATAAAATATAACCAAGCTTTGATA
21531798 CATTCTA
1 CATTCTA
21531805 ATCTCTAAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (50 bp):
CATTCTAGATAATGTTGAAGAAATCAATAAAATATAACCAAGCTTTGATA
Found at i:21540063 original size:41 final size:41
Alignment explanation
Indices: 21540006--21540099 Score: 152
Period size: 41 Copynumber: 2.3 Consensus size: 41
21539996 GATTTTTATT
*
21540006 TTAACAAGAATTCTAGTCACCCAATTCTAACAATTTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
* *
21540047 TTAACAAGATTTCTAGTCACCCAATTCTAATAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
21540088 TTGACAAGAATT
1 TTAACAAGAATT
21540100 TTCTACGAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:21543709 original size:23 final size:24
Alignment explanation
Indices: 21543672--21543725 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
21543662 CCATGAATTG
*
21543672 TTTAGGGTTGTCGAAATTGAGGAT
1 TTTAGGGTGGTCGAAATTGAGGAT
* *
21543696 TTTA-GGTGGTCGAATTTGGGGAT
1 TTTAGGGTGGTCGAAATTGAGGAT
21543719 TTT-GGGT
1 TTTAGGGT
21543726 AAGGGTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.19, C:0.04, G:0.37, T:0.41
Consensus pattern (24 bp):
TTTAGGGTGGTCGAAATTGAGGAT
Found at i:21544412 original size:37 final size:38
Alignment explanation
Indices: 21544371--21544467 Score: 153
Period size: 37 Copynumber: 2.6 Consensus size: 38
21544361 AAATAGATTT
*
21544371 TAATATAATGATTTTAATAATTTTATATTTCAAAAT-A
1 TAATATAATAATTTTAATAATTTTATATTTCAAAATAA
21544408 TAATATAATAATTTTAATAATTTTATATTTCAAAATAA
1 TAATATAATAATTTTAATAATTTTATATTTCAAAATAA
*
21544446 TAATTTTAATAATTTTAA-AATT
1 TAA-TATAATAATTTTAATAATT
21544468 ATTTGTTCAC
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
37 35 0.62
38 8 0.14
39 13 0.23
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (38 bp):
TAATATAATAATTTTAATAATTTTATATTTCAAAATAA
Found at i:21544427 original size:9 final size:9
Alignment explanation
Indices: 21544413--21544467 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 9
21544403 AAATATAATA
21544413 TAATAATTT
1 TAATAATTT
21544422 TAATAATTT
1 TAATAATTT
21544431 T-AT-ATTT
1 TAATAATTT
*
21544438 CAA-AA---
1 TAATAATTT
21544443 TAATAATTT
1 TAATAATTT
21544452 TAATAATTT
1 TAATAATTT
21544461 TAA-AATT
1 TAATAATT
21544468 ATTTGTTCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
5 2 0.05
6 2 0.05
7 4 0.11
8 8 0.21
9 22 0.58
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (9 bp):
TAATAATTT
Found at i:21552727 original size:22 final size:20
Alignment explanation
Indices: 21552702--21552754 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
21552692 TATGAAAGCA
*
21552702 ATATGTATATGATATGTATAAG
1 ATATGTATATGATACGTAT--G
* *
21552724 ATATTTCTATGATACGTATG
1 ATATGTATATGATACGTATG
*
21552744 AAATGTATATG
1 ATATGTATATG
21552755 TTTGGGGTAG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 9 0.36
22 16 0.64
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.42
Consensus pattern (20 bp):
ATATGTATATGATACGTATG
Found at i:21553013 original size:14 final size:15
Alignment explanation
Indices: 21552981--21553013 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
21552971 ATTATGTACG
21552981 TATGTTATGATTCAA
1 TATGTTATGATTCAA
*
21552996 TATGTTATG-TTCAT
1 TATGTTATGATTCAA
21553010 TATG
1 TATG
21553014 ATTTAGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (15 bp):
TATGTTATGATTCAA
Found at i:21565533 original size:55 final size:55
Alignment explanation
Indices: 21565460--21565570 Score: 159
Period size: 55 Copynumber: 2.0 Consensus size: 55
21565450 ACTAATGTTA
* * * *
21565460 CTGCATGAGCATATCCAGAATTGCGCCCAAAATTGTCACCACATCTAATAGTTGT
1 CTGCATGAGCATATCCAGAACTACACCCAAAATTGTCACCACATCTAACAGTTGT
* * *
21565515 CTGCATGAGCATATCCAGAACTACACCTAGAATTGTCACCACATCTGACAGTTGT
1 CTGCATGAGCATATCCAGAACTACACCCAAAATTGTCACCACATCTAACAGTTGT
21565570 C
1 C
21565571 CGGATAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (55 bp):
CTGCATGAGCATATCCAGAACTACACCCAAAATTGTCACCACATCTAACAGTTGT
Found at i:21567058 original size:23 final size:23
Alignment explanation
Indices: 21567031--21567079 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
21567021 TGTTAATCTA
21567031 ACTTGTCACAGCACCTTCCAGTG
1 ACTTGTCACAGCACCTTCCAGTG
* *
21567054 ACTTGTCACCGCATCTTCCAGTG
1 ACTTGTCACAGCACCTTCCAGTG
21567077 ACT
1 ACT
21567080 GTGACTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.20, C:0.35, G:0.16, T:0.29
Consensus pattern (23 bp):
ACTTGTCACAGCACCTTCCAGTG
Found at i:21568952 original size:18 final size:19
Alignment explanation
Indices: 21568929--21568974 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
21568919 TAGAACAAAT
21568929 AAAATGCAGA-GACAA-TAA
1 AAAATGCA-ATGACAATTAA
21568947 AAAATGCAATGACAATTAA
1 AAAATGCAATGACAATTAA
21568966 AGAAATGCA
1 A-AAATGCA
21568975 TTCAAGTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.04
18 13 0.52
19 4 0.16
20 7 0.28
ACGTcount: A:0.59, C:0.11, G:0.15, T:0.15
Consensus pattern (19 bp):
AAAATGCAATGACAATTAA
Found at i:21571196 original size:24 final size:25
Alignment explanation
Indices: 21571146--21571197 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
21571136 TTCCTGCATA
* *
21571146 AAACTAAAGGAAACAAATTAAAAAT
1 AAACAAAAGGAAACAAAGTAAAAAT
* *
21571171 AAACAAAAGGCAA-AAAGTAAATAT
1 AAACAAAAGGAAACAAAGTAAAAAT
21571195 AAA
1 AAA
21571198 AAATTGCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.69, C:0.08, G:0.10, T:0.13
Consensus pattern (25 bp):
AAACAAAAGGAAACAAAGTAAAAAT
Found at i:21575086 original size:18 final size:18
Alignment explanation
Indices: 21575065--21575113 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
21575055 GTTATAACCG
* *
21575065 GTTGTGTCGACATGGGTA
1 GTTGCGTCGACATGGGCA
21575083 GTTGCGTCGACATGGGCA
1 GTTGCGTCGACATGGGCA
*
21575101 GTTGCATCGACAT
1 GTTGCGTCGACAT
21575114 CTTTTTAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (18 bp):
GTTGCGTCGACATGGGCA
Found at i:21592138 original size:124 final size:124
Alignment explanation
Indices: 21591918--21592166 Score: 498
Period size: 124 Copynumber: 2.0 Consensus size: 124
21591908 CATCATGTTC
21591918 GATCGTCTCGACAAAAGAGTTAGTCCTATTCCGGTAATTTTAGCCAAGACTTTCAGATCGTTGAA
1 GATCGTCTCGACAAAAGAGTTAGTCCTATTCCGGTAATTTTAGCCAAGACTTTCAGATCGTTGAA
21591983 CGCCTGCCAAAGAGAAAGAGAGGGAAGATTGATCGGTTGCACAAAGTTATTGTTGGTAT
66 CGCCTGCCAAAGAGAAAGAGAGGGAAGATTGATCGGTTGCACAAAGTTATTGTTGGTAT
21592042 GATCGTCTCGACAAAAGAGTTAGTCCTATTCCGGTAATTTTAGCCAAGACTTTCAGATCGTTGAA
1 GATCGTCTCGACAAAAGAGTTAGTCCTATTCCGGTAATTTTAGCCAAGACTTTCAGATCGTTGAA
21592107 CGCCTGCCAAAGAGAAAGAGAGGGAAGATTGATCGGTTGCACAAAGTTATTGTTGGTAT
66 CGCCTGCCAAAGAGAAAGAGAGGGAAGATTGATCGGTTGCACAAAGTTATTGTTGGTAT
21592166 G
1 G
21592167 GTTTCATAGC
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 125 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (124 bp):
GATCGTCTCGACAAAAGAGTTAGTCCTATTCCGGTAATTTTAGCCAAGACTTTCAGATCGTTGAA
CGCCTGCCAAAGAGAAAGAGAGGGAAGATTGATCGGTTGCACAAAGTTATTGTTGGTAT
Found at i:21613781 original size:189 final size:188
Alignment explanation
Indices: 21613419--21613941 Score: 624
Period size: 189 Copynumber: 2.8 Consensus size: 188
21613409 AATGGTCCAA
* * * ** * *
21613419 GAAGCACCAAATCCTATA-CCCTGAA-TTACAGTGGATCGGATTAAAATAATGAAGTAGATCTCA
1 GAAGTACCAAATCCTATACCCCT-AAGTTGCAGTGGGTCAAATAAAAATAACGAAGTAGATCTCA
* * * * * *
21613482 ATGTCCCTGAGGATACAGTGGAGTGGAGTGAAACTTCAAATCTCATCTTCCTAGTAAGGTATAGA
65 ACGTCCATGAGGATACAATGGAGTGGAGTGAGACTTCAAATCTCATCTTCCTAGTAAGGTACAAA
* * *
21613547 GAAATGTGTCAAAACAAAGCAGATCTTAACGCCCCTGAGGTTATAGTGGA-A-TGGAGT
130 GAAATGGGTCAAAACAAAGCAGATCTCAACACCCCTGAGGTTATAGTGGAGAGTGGAGT
* ** * *
21613604 GAAGTACCAAATCCTATACCCCCTAAGTTGTAGTGGGTTGGATTAAAAAATAACAAAGTAGATCT
1 GAAGTACCAAATCCTATA-CCCCTAAGTTGCAGTGGG-TCAAAT-AAAAATAACGAAGTAGATCT
* * * * *
21613669 CAACGTCCTTGAGGATACAATGGAGTGGAGTGAGACTTCAAATCCCATTTTCCTGGTGAGGTACA
63 CAACGTCCATGAGGATACAATGGAGTGGAGTGAGACTTCAAATCTCATCTTCCTAGTAAGGTACA
* *
21613734 AATAAATGGGTCAAAACAAAG-AGAATCTCAACATCCCTGAGGTTATAGTGGAGTGGAGTGGAGT
128 AAGAAATGGGTCAAAACAAAGCAG-ATCTCAACACCCCTGAGGTTATAGTGGA---GAGTGGAGT
* *
21613798 GAAGTACCAAATTCTATACCCCTGAGTTGCAGTGGGTCAAATAAAAATAACGAAGTAGATCTCAA
1 GAAGTACCAAATCCTATACCCCTAAGTTGCAGTGGGTCAAATAAAAATAACGAAGTAGATCTCAA
* ** *
21613863 CATCCAAAAGGATACAATGGAGTGGAGTGAGACTTCAAATCTCATCTTCCTAGTAATGTACAAAG
66 CGTCCATGAGGATACAATGGAGTGGAGTGAGACTTCAAATCTCATCTTCCTAGTAAGGTACAAAG
*
21613928 AAGTGGGTCAAAAC
131 AAATGGGTCAAAAC
21613942 GGTGTTCAAT
Statistics
Matches: 284, Mismatches: 43, Indels: 16
0.83 0.13 0.05
Matches are distributed among these distances:
185 17 0.06
186 2 0.01
187 11 0.04
188 5 0.02
189 116 0.41
191 90 0.32
192 3 0.01
193 17 0.06
194 23 0.08
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (188 bp):
GAAGTACCAAATCCTATACCCCTAAGTTGCAGTGGGTCAAATAAAAATAACGAAGTAGATCTCAA
CGTCCATGAGGATACAATGGAGTGGAGTGAGACTTCAAATCTCATCTTCCTAGTAAGGTACAAAG
AAATGGGTCAAAACAAAGCAGATCTCAACACCCCTGAGGTTATAGTGGAGAGTGGAGT
Found at i:21614670 original size:2 final size:2
Alignment explanation
Indices: 21614663--21614695 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21614653 GCATTCGCAT
21614663 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
21614696 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:21632442 original size:10 final size:10
Alignment explanation
Indices: 21632427--21632452 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
21632417 ATTAAATTAA
21632427 TTTTTATCAT
1 TTTTTATCAT
21632437 TTTTTATCAT
1 TTTTTATCAT
21632447 TTTTTA
1 TTTTTA
21632453 AGAGTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTATCAT
Found at i:21634428 original size:42 final size:42
Alignment explanation
Indices: 21634369--21634454 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
21634359 ATAAATAATA
*
21634369 AATGAAACACGTGACAATTTTTTAACTCTACTTGTAAAGGGT
1 AATGAAACACGTGACAATTTTTTAACTCTACTTGTAAAAGGT
21634411 AATGAAACACGTGACAATTTTTTAACTCTACTTGTAAAAGGT
1 AATGAAACACGTGACAATTTTTTAACTCTACTTGTAAAAGGT
21634453 AA
1 AA
21634455 AAAAGTACAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (42 bp):
AATGAAACACGTGACAATTTTTTAACTCTACTTGTAAAAGGT
Found at i:21634960 original size:19 final size:19
Alignment explanation
Indices: 21634936--21634972 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21634926 AAGCAAATAT
21634936 ACTGGCAAACATAGTGCAC
1 ACTGGCAAACATAGTGCAC
* *
21634955 ACTGGCACATATAGTGCA
1 ACTGGCAAACATAGTGCA
21634973 TACTAGAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (19 bp):
ACTGGCAAACATAGTGCAC
Found at i:21634983 original size:19 final size:19
Alignment explanation
Indices: 21634946--21634992 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
21634936 ACTGGCAAAC
* * *
21634946 ATAGTGCACACTGGCACAT
1 ATAGTGCATACTAGAACAT
21634965 ATAGTGCATACTAGAACAT
1 ATAGTGCATACTAGAACAT
21634984 ATAGTGCAT
1 ATAGTGCAT
21634993 CATTGGATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (19 bp):
ATAGTGCATACTAGAACAT
Found at i:21635274 original size:21 final size:20
Alignment explanation
Indices: 21635239--21635277 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
21635229 ATATCGTGTT
21635239 CATTTCAACTCAATTCACCA
1 CATTTCAACTCAATTCACCA
*
21635259 CATTTCATCATCAATTCAC
1 CATTTCAAC-TCAATTCAC
21635278 ATCACATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (20 bp):
CATTTCAACTCAATTCACCA
Found at i:21640137 original size:17 final size:16
Alignment explanation
Indices: 21640115--21640148 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
21640105 TCTGTATGGA
21640115 AATTAAAATTAAAGTCT
1 AATTAAAATTAAA-TCT
21640132 AATTAAAATTAAATCT
1 AATTAAAATTAAATCT
21640148 A
1 A
21640149 CTAACTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (16 bp):
AATTAAAATTAAATCT
Found at i:21641185 original size:20 final size:20
Alignment explanation
Indices: 21641160--21641213 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
21641150 TTGGGGGTTT
** *
21641160 GGGGGAAGTAAACTTTTTGA
1 GGGGGAAGTAAAAGTTTTAA
21641180 GGGGGAAGTAAAAGTTTTAA
1 GGGGGAAGTAAAAGTTTTAA
*
21641200 GGGGAAAGTAAAAG
1 GGGGGAAGTAAAAG
21641214 GAAAAAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.02, G:0.37, T:0.22
Consensus pattern (20 bp):
GGGGGAAGTAAAAGTTTTAA
Found at i:21641233 original size:74 final size:70
Alignment explanation
Indices: 21641110--21641264 Score: 220
Period size: 74 Copynumber: 2.2 Consensus size: 70
21641100 GAGGTTTGAT
* * *
21641110 GGAAGTAAAAGTTTTGAGGGAAAGCAAAAGGAAAAAAATTTTGGGGGTTTGGGGGAAGTAAACTT
1 GGAAGTAAAAGTTTTAAGGGAAAGCAAAAGGAAAAAAATTTTGGAGGTTT--GGGAAGTAAAATT
21641175 TTTGAGGG
64 TTTG-GGG
* *
21641183 GGAAGTAAAAGTTTTAAGGGGAAAGTAAAAGGAAAAAAGTTTTGGAGGTTTGGGAAGTAAAATTT
1 GGAAGTAAAAGTTTTAA-GGGAAAGCAAAAGGAAAAAAATTTTGGAGGTTTGGGAAGTAAAATTT
*
21641248 TTGGGT
65 TTGGGG
21641254 GGAAGTAAAAG
1 GGAAGTAAAAG
21641265 GGTCGGGGGT
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
71 13 0.17
72 16 0.21
73 16 0.21
74 30 0.40
ACGTcount: A:0.39, C:0.01, G:0.34, T:0.25
Consensus pattern (70 bp):
GGAAGTAAAAGTTTTAAGGGAAAGCAAAAGGAAAAAAATTTTGGAGGTTTGGGAAGTAAAATTTT
TGGGG
Found at i:21642450 original size:19 final size:18
Alignment explanation
Indices: 21642409--21642455 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
21642399 ATATATATTA
*
21642409 AAAAAT-TAAATTTTTTT
1 AAAAATATAAATTATTTT
21642426 AGAAAATATAAATTAATTTT
1 A-AAAATATAAATT-ATTTT
21642446 AAAAAGTATA
1 AAAAA-TATA
21642456 TTTTTTGGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 5 0.20
19 10 0.40
20 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
AAAAATATAAATTATTTT
Found at i:21644595 original size:20 final size:21
Alignment explanation
Indices: 21644549--21644598 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
21644539 TTTAAATGTG
21644549 TTAGAAA-TTTTATATTGAAA
1 TTAGAAATTTTTATATTGAAA
21644569 TTA-AAATTTTTA-ATAT-AAA
1 TTAGAAATTTTTATAT-TGAAA
21644588 TTAGAAATTTT
1 TTAGAAATTTT
21644599 GATGTAGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (21 bp):
TTAGAAATTTTTATATTGAAA
Found at i:21644647 original size:15 final size:16
Alignment explanation
Indices: 21644627--21644656 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21644617 AATGATTCTC
21644627 AAAAA-TATTTTTGAA
1 AAAAATTATTTTTGAA
21644642 AAAAATTATTTTTGA
1 AAAAATTATTTTTGA
21644657 GGAAAAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (16 bp):
AAAAATTATTTTTGAA
Found at i:21644784 original size:17 final size:17
Alignment explanation
Indices: 21644750--21644794 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
21644740 CAATTTATTT
21644750 AAATATTTTTT-CCCAA
1 AAATATTTTTTACCCAA
*
21644766 AAATATTTTTTACCTAA
1 AAATATTTTTTACCCAA
*
21644783 AAATGTTTTTTA
1 AAATATTTTTTA
21644795 AAAATAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATATTTTTTACCCAA
Found at i:21649703 original size:2 final size:2
Alignment explanation
Indices: 21649691--21649729 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
21649681 TATGAAATTT
*
21649691 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21649730 GAAGGTCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:21659843 original size:10 final size:10
Alignment explanation
Indices: 21659828--21659858 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
21659818 TTAATCTGAG
21659828 ATTATGTGAA
1 ATTATGTGAA
21659838 ATTATGTTGAA
1 ATTATG-TGAA
21659849 ATTATGTGAA
1 ATTATGTGAA
21659859 TTTTGCTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (10 bp):
ATTATGTGAA
Found at i:21660174 original size:31 final size:31
Alignment explanation
Indices: 21660133--21660211 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
21660123 CCAATGGCTA
*
21660133 ATATATTATTTAAATAAGTTCTTAAATTATT
1 ATATTTTATTTAAATAAGTTCTTAAATTATT
21660164 ATATTTTATTTAAATAAGTTCTTAAATTATT
1 ATATTTTATTTAAATAAGTTCTTAAATTATT
* *
21660195 -T-TTGTAGTTAAATAAGT
1 ATATTTTATTTAAATAAGT
21660212 ACCTATGTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 14 0.31
30 1 0.02
31 30 0.67
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (31 bp):
ATATTTTATTTAAATAAGTTCTTAAATTATT
Found at i:21663492 original size:58 final size:58
Alignment explanation
Indices: 21663404--21663549 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 58
21663394 ATATATTATA
* * *
21663404 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAA-AT-GTT-ATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATAATTAAATAAATTA-AT
* *
21663461 ATTATTTTATTAAATTTTATTTAATAATAATTATGTTAAAATATAATTAAATAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
21663521 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
21663550 CATTAAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
57 1 0.01
58 48 0.62
59 11 0.14
60 9 0.12
61 8 0.10
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
Found at i:21663740 original size:16 final size:16
Alignment explanation
Indices: 21663719--21663790 Score: 117
Period size: 16 Copynumber: 4.5 Consensus size: 16
21663709 TGAATTACTG
*
21663719 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
21663735 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
21663751 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
21663767 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
21663783 ATTACAGC
1 ATTACAGC
21663791 GAACCAAACG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:21663760 original size:32 final size:32
Alignment explanation
Indices: 21663719--21663789 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
21663709 TGAATTACTG
*
21663719 ATTACAGTTCTATTCCATTACAGCTCTATTCC
1 ATTACAGTTCTATTCCATTACACCTCTATTCC
21663751 ATTACAGTTCTATTCCATTACACCTCTATTCC
1 ATTACAGTTCTATTCCATTACACCTCTATTCC
21663783 ATTACAG
1 ATTACAG
21663790 CGAACCAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.27, C:0.28, G:0.06, T:0.39
Consensus pattern (32 bp):
ATTACAGTTCTATTCCATTACACCTCTATTCC
Found at i:21664035 original size:10 final size:10
Alignment explanation
Indices: 21664020--21664046 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
21664010 TTTTTTATTT
21664020 AAATTTTTAA
1 AAATTTTTAA
21664030 AAATTTTTAA
1 AAATTTTTAA
21664040 AAATTTT
1 AAATTTT
21664047 AAATTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AAATTTTTAA
Found at i:21664117 original size:30 final size:30
Alignment explanation
Indices: 21664059--21664117 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
21664049 ATTAATAAAA
* ** *
21664059 ATAAAATTATATTTTAATTTTTTTAAAATG
1 ATAAAATTATAATTTAATCATTTAAAAATG
*
21664089 ATAAAATTTTAATTTAATCATTTAAAAAT
1 ATAAAATTATAATTTAATCATTTAAAAAT
21664118 TACATTTTCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (30 bp):
ATAAAATTATAATTTAATCATTTAAAAATG
Found at i:21665659 original size:33 final size:33
Alignment explanation
Indices: 21665591--21665659 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
21665581 TTTTGATATA
* ***
21665591 AAAAAGTTGTCCTAATTTTATTTATCGATTTTT
1 AAAAAGTTGTCCTAATTTTATTGATCGAAAATT
*
21665624 AAAAAGTTGTGCTAATTTTATTGAT-GTAAAATT
1 AAAAAGTTGTCCTAATTTTATTGATCG-AAAATT
21665657 AAA
1 AAA
21665660 TTATTACTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.45
Consensus pattern (33 bp):
AAAAAGTTGTCCTAATTTTATTGATCGAAAATT
Found at i:21666021 original size:10 final size:10
Alignment explanation
Indices: 21666006--21666031 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
21665996 GAATATTAAA
21666006 CACATGAAAT
1 CACATGAAAT
21666016 CACATGAAAT
1 CACATGAAAT
21666026 CACATG
1 CACATG
21666032 CAATGTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.23, G:0.12, T:0.19
Consensus pattern (10 bp):
CACATGAAAT
Found at i:21666479 original size:18 final size:18
Alignment explanation
Indices: 21666458--21666494 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
21666448 ATTTTTTACA
*
21666458 AAATAAATCAACTTAAAT
1 AAATAAATCAACTCAAAT
*
21666476 AAATAAATGAACTCAAAT
1 AAATAAATCAACTCAAAT
21666494 A
1 A
21666495 TTTTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.11, G:0.03, T:0.24
Consensus pattern (18 bp):
AAATAAATCAACTCAAAT
Found at i:21672024 original size:257 final size:257
Alignment explanation
Indices: 21671529--21672049 Score: 936
Period size: 257 Copynumber: 2.0 Consensus size: 257
21671519 ATGAAGTAAT
*
21671529 AAAAATAAAAATTTATAATATTAGAAAAGTAATATATAGTCTATTTTATTACTTTTAAACTACAA
1 AAAAATAAAAATTTATAATATTAGAAAAATAATATATAGTCTATTTTATTACTTTTAAACTACAA
21671594 TGCATTTTAATGTGCTAGAATATCATTAGCGAAACAAAAAATTTAATTATCCTCTAAATTAAAAA
66 TGCATTTTAATGTGCTAGAATATCATTAGCGAAACAAAAAATTTAATTATCCTCTAAATTAAAAA
* * *
21671659 GCAAAATATTAGGGTACTAAATAACTTGAGAATTATATTTTACATCCAAACATAATGTTCATACG
131 GCAAAATATTAGAGTAATAAATAACTTGAGAATTATATTTTACATCCAAACATAATGTTCATACA
* * *
21671724 TTAACAAAAAATTACATGATGTCCGTCGAAAAGTTTTTTTTTGGAACAGAAAAAGGGTCTCG
196 TTAACAAAAAATTACATGATGTCCGTCGAAAAGTTTCTTTTTGGAAAAGAAAAAGGGTATCG
21671786 AAAAATAAAAATTTATAATATTAGAAAAATAATATATAGTCTATTTTATTACTTTTAAACTACAA
1 AAAAATAAAAATTTATAATATTAGAAAAATAATATATAGTCTATTTTATTACTTTTAAACTACAA
21671851 TGCATTTTAATGTGCTAGAATATCATTAGCGAAACAAAAAATTTAATTATCCTCTAAATTAAAAA
66 TGCATTTTAATGTGCTAGAATATCATTAGCGAAACAAAAAATTTAATTATCCTCTAAATTAAAAA
*
21671916 GCAAAATATTAGAAGTAATAAATAACTTGAGAATTATATTTTTCATCCAAACATAATGTTCATAC
131 GCAAAATATTAG-AGTAATAAATAACTTGAGAATTATATTTTACATCCAAACATAATGTTCATAC
* *
21671981 ATTAACAAAAAATTACATGATGTCCGTCGAAATG-TTCTTTTTGGAAAATAAAAAGGGTATCG
195 ATTAACAAAAAATTACATGATGTCCGTCGAAAAGTTTCTTTTTGGAAAAGAAAAAGGGTATCG
21672043 AAAAATA
1 AAAAATA
21672050 TTTTTATTGA
Statistics
Matches: 253, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
257 172 0.68
258 81 0.32
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (257 bp):
AAAAATAAAAATTTATAATATTAGAAAAATAATATATAGTCTATTTTATTACTTTTAAACTACAA
TGCATTTTAATGTGCTAGAATATCATTAGCGAAACAAAAAATTTAATTATCCTCTAAATTAAAAA
GCAAAATATTAGAGTAATAAATAACTTGAGAATTATATTTTACATCCAAACATAATGTTCATACA
TTAACAAAAAATTACATGATGTCCGTCGAAAAGTTTCTTTTTGGAAAAGAAAAAGGGTATCG
Found at i:21672632 original size:19 final size:19
Alignment explanation
Indices: 21672594--21672632 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
21672584 ATTTTAATTT
*
21672594 AATTAAAAATGAGTGCGTA
1 AATTAAAAATGAATGCGTA
* *
21672613 AATTAAATATGAATGTGTA
1 AATTAAAAATGAATGCGTA
21672632 A
1 A
21672633 TTTATTGGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.31
Consensus pattern (19 bp):
AATTAAAAATGAATGCGTA
Found at i:21672848 original size:84 final size:85
Alignment explanation
Indices: 21672750--21672934 Score: 282
Period size: 92 Copynumber: 2.1 Consensus size: 85
21672740 AATCAAAATC
21672750 ATTGAAAAACAAGATTAACTTAAAATACGACGAG-AAATAATTAAATTTTATGTACAAAAAAATC
1 ATTGAAAAACAAGATTAACTTAAAATACGACGAGAAAATAATTAAATTTTATGTACAAAAAAATC
21672814 GAAGAAAAATAAAAAAAGGG
66 GAAGAAAAATAAAAAAAGGG
21672834 ATTGAAAAACAAGATTAACTTAAAATACGACGAGAAATAATTAAATAATTAAATTTTATGTACAA
1 ATTGAAAAACAAGATTAACTTAAAATACGACGAG-----A--AAATAATTAAATTTTATGTACAA
*
21672899 AAAAATTGAAGAAAAATAAAAAAAGGG
59 AAAAATCGAAGAAAAATAAAAAAAGGG
*
21672926 GTTGAAAAA
1 ATTGAAAAA
21672935 TGAAGTTTAG
Statistics
Matches: 91, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
84 34 0.37
92 57 0.63
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23
Consensus pattern (85 bp):
ATTGAAAAACAAGATTAACTTAAAATACGACGAGAAAATAATTAAATTTTATGTACAAAAAAATC
GAAGAAAAATAAAAAAAGGG
Found at i:21673015 original size:29 final size:29
Alignment explanation
Indices: 21672953--21673176 Score: 166
Period size: 29 Copynumber: 7.6 Consensus size: 29
21672943 AGGATAATTT
* *
21672953 GGGGTCAAAATGCAATTTTGAAAAATTTA
1 GGGGTCAAAATGTAATTTTGAAAAGTTTA
*
21672982 AGGGTCAAAATGTAATTTTAGAAAAGTTT-
1 GGGGTCAAAATGTAATTTT-GAAAAGTTTA
* * * *
21673011 GGGGTTAAAATATGATTTTGGAAACGTTT-
1 GGGGTCAAAATGTAATTTT-GAAAAGTTTA
* * **
21673040 GTGGGTCAAAAAGTGATTTTGGGAAGTTT-
1 G-GGGTCAAAATGTAATTTTGAAAAGTTTA
* * ** *
21673069 GGGTGTCAAAAAGTGATTTTGGGAAGTTTG
1 GGG-GTCAAAATGTAATTTTGAAAAGTTTA
* * *
21673099 GGGGTTAAAATATAATTTTTGAAAAATTTA
1 GGGGTCAAAATGTAA-TTTTGAAAAGTTTA
*
21673129 GGGGTTAAAATGTAATTTTAGAAAAGTTTA
1 GGGGTCAAAATGTAATTTT-GAAAAGTTTA
* * *
21673159 GGGTTTAAAAAGTAATTT
1 GGGGTCAAAATGTAATTT
21673177 AAAAAAATTT
Statistics
Matches: 162, Mismatches: 27, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
28 2 0.01
29 85 0.52
30 75 0.46
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTGAAAAGTTTA
Found at i:21673133 original size:30 final size:30
Alignment explanation
Indices: 21673099--21673206 Score: 130
Period size: 30 Copynumber: 3.6 Consensus size: 30
21673089 GGGAAGTTTG
*
21673099 GGGGTTAAAATATAATTTTTGAAAAATTTA
1 GGGGTTAAAATATAATTTTAGAAAAATTTA
* *
21673129 GGGGTTAAAATGTAATTTTAGAAAAGTTTA
1 GGGGTTAAAATATAATTTTAGAAAAATTTA
* *
21673159 GGGTTTAAAA-AGTAA-TTTAAAAAAATTTA
1 GGGGTTAAAATA-TAATTTTAGAAAAATTTA
* *
21673188 AGGGTTAAAATATGATTTT
1 GGGGTTAAAATATAATTTT
21673207 TAAATAAAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
29 22 0.34
30 43 0.66
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (30 bp):
GGGGTTAAAATATAATTTTAGAAAAATTTA
Found at i:21673147 original size:59 final size:57
Alignment explanation
Indices: 21672948--21673198 Score: 173
Period size: 59 Copynumber: 4.3 Consensus size: 57
21672938 AGTTTAGGAT
* * * * *
21672948 AATTTGGGGTCAAAATGCAATTTTGAAAAATTTAAGGGTCAAAATGTAATTTTAGAAA
1 AATTTGGGGTTAAAATGTAATTTTGAAAAGTTTAGGGGTCAAAAAGTAA-TTTAGAAA
* * * * * * **
21673006 AGTTTGGGGTTAAAATATGATTTTGGAAACGTTT-GTGGGTCAAAAAGTGATTTTGGGA
1 AATTTGGGGTTAAAATGTAATTTT-GAAAAGTTTAG-GGGTCAAAAAGTAATTTAGAAA
* * * * ** * * *
21673064 AGTTTGGGTGTCAAAAAGTGATTTTGGGAAGTTTGGGGGTTAAAATA-TAATTTTTGAAA
1 AATTTGGG-GTTAAAATGTAATTTTGAAAAGTTTAGGGGTCAAAA-AGTAA-TTTAGAAA
* * *
21673123 AATTTAGGGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTTAAAAAGTAATTTAAAAA
1 AATTT-GGGGTTAAAATGTAATTTT-GAAAAGTTTAGGGGTCAAAAAGTAATTTAGAAA
*
21673182 AATTTAAGGGTTAAAAT
1 AATTT-GGGGTTAAAAT
21673199 ATGATTTTTA
Statistics
Matches: 150, Mismatches: 34, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
58 48 0.32
59 80 0.53
60 22 0.15
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (57 bp):
AATTTGGGGTTAAAATGTAATTTTGAAAAGTTTAGGGGTCAAAAAGTAATTTAGAAA
Found at i:21673177 original size:29 final size:30
Alignment explanation
Indices: 21672922--21673197 Score: 142
Period size: 29 Copynumber: 9.4 Consensus size: 30
21672912 AAATAAAAAA
* * *
21672922 AGGGGTTGAAAAA-TGAAGTTTAGGATAATTT
1 AGGGGTT-AAAAAGT-AATTTTAGAAAAATTT
* * *
21672953 -GGGGTCAAAATGCAATTTT-GAAAAATTT
1 AGGGGTTAAAAAGTAATTTTAGAAAAATTT
* * * *
21672981 AAGGGTCAAAATGTAATTTTAGAAAAGTTT
1 AGGGGTTAAAAAGTAATTTTAGAAAAATTT
* * **
21673011 -GGGGTTAAAATA-TGATTTTGGAAACGTTT
1 AGGGGTTAAAA-AGTAATTTTAGAAAAATTT
* * ** *
21673040 -GTGGGTCAAAAAGTGATTTT-GGGAAGTTT
1 AG-GGGTTAAAAAGTAATTTTAGAAAAATTT
* * ** *
21673069 -GGGTGTCAAAAAGTGATTTT-GGGAAGTTT
1 AGGG-GTTAAAAAGTAATTTTAGAAAAATTT
* *
21673098 GGGGGTTAAAATA-TAATTTTTGAAAAATTT
1 AGGGGTTAAAA-AGTAATTTTAGAAAAATTT
* *
21673128 AGGGGTTAAAATGTAATTTTAGAAAAGTTT
1 AGGGGTTAAAAAGTAATTTTAGAAAAATTT
* *
21673158 AGGGTTTAAAAAGTAA-TTTAAAAAAATTT
1 AGGGGTTAAAAAGTAATTTTAGAAAAATTT
*
21673187 AAGGGTTAAAA
1 AGGGGTTAAAA
21673198 TATGATTTTT
Statistics
Matches: 200, Mismatches: 34, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
28 9 0.05
29 114 0.57
30 77 0.38
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.34
Consensus pattern (30 bp):
AGGGGTTAAAAAGTAATTTTAGAAAAATTT
Found at i:21675222 original size:85 final size:85
Alignment explanation
Indices: 21675079--21675242 Score: 238
Period size: 85 Copynumber: 1.9 Consensus size: 85
21675069 AACTTCATCT
* ** *
21675079 TTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGACCACTTCATTGTTTTAATCCACTTCTCTG
1 TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTACTTTAACCCACTTCTCTG
*
21675144 TATCTCATTAGGAAGACAGA
66 CATCTCATTAGGAAGACAGA
* * * * *
21675164 TTTGGTCCACTTCTCTGTATCTCATCAGGAAGATTACCTCTTTATTACTTTGACCCACTTCTCTG
1 TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTACTTTAACCCACTTCTCTG
21675229 CATCTCATTAGGAA
66 CATCTCATTAGGAA
21675243 TAAAGGGATT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 69 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.38
Consensus pattern (85 bp):
TTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCACTTCATTACTTTAACCCACTTCTCTG
CATCTCATTAGGAAGACAGA
Found at i:21675433 original size:85 final size:85
Alignment explanation
Indices: 21675287--21675452 Score: 233
Period size: 85 Copynumber: 2.0 Consensus size: 85
21675277 TGCTTCTTTG
* * * *
21675287 ATTTGATCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCT
1 ATTTGATCCACTTCTCTATATCTCATCAGGAAGATGACCACTTCAGTGATTTAACCCACTTCTCT
21675352 GTATCTCATCAGGAAGGCGA
66 GTATCTCATCAGGAAGGCGA
* * * * * * *
21675372 ATTTGGTCCACTTTTCTGTATCTCATCAGGAAGATGATCACTTTAGTGCTTTGACCCACTTCTCT
1 ATTTGATCCACTTCTCTATATCTCATCAGGAAGATGACCACTTCAGTGATTTAACCCACTTCTCT
21675437 GTATCTCATCAGGAAG
66 GTATCTCATCAGGAAG
21675453 ATAAAGGTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (85 bp):
ATTTGATCCACTTCTCTATATCTCATCAGGAAGATGACCACTTCAGTGATTTAACCCACTTCTCT
GTATCTCATCAGGAAGGCGA
Found at i:21675466 original size:209 final size:209
Alignment explanation
Indices: 21675087--21675616 Score: 789
Period size: 209 Copynumber: 2.5 Consensus size: 209
21675077 CTTTTGGTCC
* * * *
21675087 ACTTCTTTGTATCTCATCAAGAAGATGACCACTTCATTGTTTTAATCCACTTCTCTGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCAT
* * * * *
21675152 TAGGAAGAC-AGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATTACCTCTTTATTACTTTG
66 CAGGAAGGCGA-ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTAGTACTTTG
* *
21675216 ACCCACTTCTCTGCATCTCATTAGGAATAAAGGGATTTGAAGTTTCACTCATATTGAGCTTTGCT
130 ACCCACTTCTCTGCATCTCATCAGGAATAAAGGGATTTGAAGTTTCACTCACATTGAGCTTTGCT
21675281 TCT-TTGATTTGATCT
195 T-TATTGATTTGATCT
*
21675296 ACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCAT
* * *
21675361 CAGGAAGGCGAATTTGGTCCACTTTTCTGTATCTCATCAGGAAGATGATCACTTTAGTGCTTTGA
66 CAGGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTAGTACTTTGA
*
21675426 CCCACTTCTCTGTATCTCATCAGGAAGATAAA-GG-TTTGAAGTTTCACTCACATTGAGCTTTGC
131 CCCACTTCTCTGCATCTCATCAGG-A-ATAAAGGGATTTGAAGTTTCACTCACATTGAGCTTTGC
*
21675489 TTTATTGATTTGGTCT
194 TTTATTGATTTGATCT
* * * *
21675505 ACTTTTCTGTATCTCATCAGGAAGATGACCGCTTTATTGATTTAATCCACTTTTTTGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCAT
* *
21675570 CAGGAAGGCGGATTTGGTCAACTTCTCTGTATCTCATCAGGAAGATG
66 CAGGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATG
21675617 GGGGGTTTGA
Statistics
Matches: 292, Mismatches: 25, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
208 1 0.00
209 282 0.97
210 4 0.01
211 5 0.02
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.38
Consensus pattern (209 bp):
ACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCAT
CAGGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTAGTACTTTGA
CCCACTTCTCTGCATCTCATCAGGAATAAAGGGATTTGAAGTTTCACTCACATTGAGCTTTGCTT
TATTGATTTGATCT
Found at i:21675665 original size:162 final size:162
Alignment explanation
Indices: 21675429--21675779 Score: 544
Period size: 162 Copynumber: 2.2 Consensus size: 162
21675419 GCTTTGACCC
*
21675429 ACTTCTCTGTATCTCATCAGGAAGAT-AAAGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTTA
1 ACTTCTCTGTATCTCATCAGGAAGATGAAAGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
* * * *
21675493 TTGATTTGGTCTACTTTTCTGTATCTCATCAGGAAGATGACCG-CTTTATTGATTTAATCCACTT
66 TTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCGTC-TCATTGATTTAATCCACTT
* * * * *
21675557 TTTTGTATCTCATCAGGAAGGCGGATTTGGTCA
130 CTCTGTATCTAATCAGAAAGGCAGATTTGGTCA
***
21675590 ACTTCTCTGTATCTCATCAGGAAGATGGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
1 ACTTCTCTGTATCTCATCAGGAAGATGAAAGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
*
21675655 TTGATTTGGTCTACTTCTCTATATCTCATTAAGAAGATGACCGTCTCATTGATTTAATCCACTTC
66 TTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCGTCTCATTGATTTAATCCACTTC
*
21675720 TCTGTATCTAATCAGAAAGGCAGATTTGGTCC
131 TCTGTATCTAATCAGAAAGGCAGATTTGGTCA
21675752 ACTTCTCTGTATCTCATCAGGAAGATGA
1 ACTTCTCTGTATCTCATCAGGAAGATGA
21675780 CCGCTTTATT
Statistics
Matches: 172, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
161 26 0.15
162 145 0.84
163 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (162 bp):
ACTTCTCTGTATCTCATCAGGAAGATGAAAGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
TTGATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCGTCTCATTGATTTAATCCACTTC
TCTGTATCTAATCAGAAAGGCAGATTTGGTCA
Found at i:21675802 original size:85 final size:85
Alignment explanation
Indices: 21675657--21675819 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 85
21675647 TTGCTTCATT
* * *
21675657 GATTTGGTCTACTTCTCTATATCTCATTAAGAAGATGACCGTCTCATTGATTTAATCCACTTCTC
1 GATTTGGTCCACTTCTCTATATCTCATCAAGAAGATGACCGTCTCATTGATTTAACCCACTTCTC
21675722 TGTATCTAATCAGAAAGGCA
66 TGTATCTAATCAGAAAGGCA
* * * *
21675742 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCG-CTTTATT-ACTTTGACCCACTTC
1 GATTTGGTCCACTTCTCTATATCTCATCAAGAAGATGACCGTC-TCATTGA-TTTAACCCACTTC
* *
21675805 TTTGTATCTCATCAG
64 TCTGTATCTAATCAG
21675820 GAAGATGAGG
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 2 0.03
85 65 0.97
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (85 bp):
GATTTGGTCCACTTCTCTATATCTCATCAAGAAGATGACCGTCTCATTGATTTAACCCACTTCTC
TGTATCTAATCAGAAAGGCA
Found at i:21676167 original size:209 final size:208
Alignment explanation
Indices: 21675590--21676246 Score: 992
Period size: 210 Copynumber: 3.1 Consensus size: 208
21675580 GATTTGGTCA
* *
21675590 ACTTCTCTGTATCTCATCAGGAAGATGGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
1 ACTTCTCTGTATCTCATCAGAAAGAT--GAGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
* * *
21675655 TTGATTTGGTCTACTTCTCTATATCTCATTAAGAAGATGACCG-TCTCATTGATTTAATCCACTT
64 TTGATTTGATCTACTTCTCTATATCTCATTAGGAAGATGACTGCT-TCATTGATTTAATCCACTT
* *
21675719 CTCTGTATCTAATCAGAAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGC
128 CTCTGTATCTAATCAGGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGACCGC
21675784 TTTATTACTTTGACCC
193 TTTATTACTTTGACCC
* *
21675800 ACTTCTTTGTATCTCATCAGGAAGATGAGGGCTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
1 ACTTCTCTGTATCTCATCAGAAAGATGA-GG-TTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
* * * * * *
21675865 TTGATTTGTTCTACTTCTTTTTATCTCATAAGGAAGATGACTACCTCATTGATTTAATCCACTTC
64 TTGATTTGATCTACTTCTCTATATCTCATTAGGAAGATGACTGCTTCATTGATTTAATCCACTTC
* * * *
21675930 TCTGTACCTAATCAAGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGGCGGCT
129 TCTGTATCTAATCAGGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGACCGCT
21675995 TTATTACTTTGACCC
194 TTATTACTTTGACCC
* * *
21676010 ACTTCTCTATATCTCATAAGAAAGATGTAGGTTTGAAGTTTCACTCACATTGAACTTTGCTTCAT
1 ACTTCTCTGTATCTCATCAGAAAGATG-AGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCAT
*
21676075 TGATTTGATCTACATCTCTATATCTCATTAGGAAGATGACTGCTTCATTGATTTAATCCACTTCT
65 TGATTTGATCTACTTCTCTATATCTCATTAGGAAGATGACTGCTTCATTGATTTAATCCACTTCT
* * * *
21676140 CTGTATCTCATCAGGAAGGCGGATTTGGTCAACTTCTCTGTATCTCATCAGAAAGATGACCACTT
130 CTGTATCTAATCAGGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGACCGCTT
*
21676205 TATTGCTTTGACCC
195 TATTACTTTGACCC
*
21676219 AGTTCTCTGTATCTCATCAGAAAGATGA
1 ACTTCTCTGTATCTCATCAGAAAGATGA
21676247 CCACTTTATT
Statistics
Matches: 403, Mismatches: 40, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
208 2 0.00
209 187 0.46
210 213 0.53
211 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (208 bp):
ACTTCTCTGTATCTCATCAGAAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATT
GATTTGATCTACTTCTCTATATCTCATTAGGAAGATGACTGCTTCATTGATTTAATCCACTTCTC
TGTATCTAATCAGGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGACCGCTTT
ATTACTTTGACCC
Found at i:21676181 original size:581 final size:580
Alignment explanation
Indices: 21675079--21676197 Score: 1704
Period size: 581 Copynumber: 1.9 Consensus size: 580
21675069 AACTTCATCT
* * *
21675079 TTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGACCACTTCATTGTTTTAATCCACTTCTCTG
1 TTTGGTCCACTTCTCTATATCTCATCAAGAAGATGACCACTTCATTGATTTAATCCACTTCTCTG
* * * * *
21675144 TATCTCATTAGGAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATTACCTCTTTAT
66 TATCTAATCAGAAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTAT
* * *
21675209 TACTTTGACCCACTTCTCTGCATCTCATTAGGAATAAAGGGATTTGAAGTTTCACTCATATTGAG
131 TACTTTGACCCACTTCTCTGCATCTCATCAGGAAGAAAGGGATTTGAAGTTTCACTCACATTGAG
* * * *
21675274 CTTTGCTTCTTTGATTTGATCTACTTCTCTATATCTCATCAGGAAGATGACCGCTTCATTGATTT
196 CTTTGCTTCATTGATTTGATCTACTTCTCTATATCTCATAAGGAAGATGACCACCTCATTGATTT
* * * * *
21675339 AATCCACTTCTCTGTATCTCATCAGGAAGGCGAATTTGGTCCACTTTTCTGTATCTCATCAGGAA
261 AATCCACTTCTCTGTACCTAATCAAGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGAAA
* * * * *
21675404 GATGATCACTTTAGTGCTTTGACCCACTTCTCTGTATCTCATCAGGAAGATAAAGGTTTGAAGTT
326 GATGAGCACTTTAGTACTTTGACCCACTTCTCTATATCTCATAAGAAAGATAAAGGTTTGAAGTT
* * * * * *
21675469 TCACTCACATTGAGCTTTGCTTTATTGATTTGGTCTACTTTTCTGTATCTCATCAGGAAGATGAC
391 TCACTCACATTGAACTTTGCTTCATTGATTTGATCTACATCTCTATATCTCATCAGGAAGATGAC
* * *
21675534 CGCTTTATTGATTTAATCCACTTTTTTGTATCTCATCAGGAAGGCGGATTTGGTCAACTTCTCTG
456 CGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGGATTTGGTCAACTTCTCTG
*
21675599 TATCTCATCAGGAAGATGGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGA
521 TATCTCATCAGAAAGATGGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGA
* * *
21675659 TTTGGTCTACTTCTCTATATCTCATTAAGAAGATGACC-GTCTCATTGATTTAATCCACTTCTCT
1 TTTGGTCCACTTCTCTATATCTCATCAAGAAGATGACCACT-TCATTGATTTAATCCACTTCTCT
*
21675723 GTATCTAATCAGAAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTA
65 GTATCTAATCAGAAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTA
* * * *
21675788 TTACTTTGACCCACTTCTTTGTATCTCATCAGGAAGATGAGGGCTTTGAAGTTTCACTCACATTG
130 TTACTTTGACCCACTTCTCTGCATCTCATCAGGAAGA-AAGGGATTTGAAGTTTCACTCACATTG
* * * *
21675853 AGCTTTGCTTCATTGATTTGTTCTACTTCTTTTTATCTCATAAGGAAGATGACTACCTCATTGAT
194 AGCTTTGCTTCATTGATTTGATCTACTTCTCTATATCTCATAAGGAAGATGACCACCTCATTGAT
21675918 TTAATCCACTTCTCTGTACCTAATCAAGAAGGC-AGATTTGGTCCACTTCTCTGTATCTCATCAG
259 TTAATCCACTTCTCTGTACCTAATCAAGAAGGCGA-ATTTGGTCCACTTCTCTGTATCTCATCAG
* * **
21675982 AAAGATG-GCGGCTTTATTACTTTGACCCACTTCTCTATATCTCATAAGAAAGATGTAGGTTTGA
323 AAAGATGAGC-ACTTTAGTACTTTGACCCACTTCTCTATATCTCATAAGAAAGATAAAGGTTTGA
*
21676046 AGTTTCACTCACATTGAACTTTGCTTCATTGATTTGATCTACATCTCTATATCTCATTAGGAAGA
387 AGTTTCACTCACATTGAACTTTGCTTCATTGATTTGATCTACATCTCTATATCTCATCAGGAAGA
*
21676111 TGACTGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGGATTTGGTCAACTTC
452 TGACCGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGGATTTGGTCAACTTC
21676176 TCTGTATCTCATCAGAAAGATG
517 TCTGTATCTCATCAGAAAGATG
21676198 ACCACTTTAT
Statistics
Matches: 482, Mismatches: 53, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
579 1 0.00
580 150 0.31
581 331 0.69
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (580 bp):
TTTGGTCCACTTCTCTATATCTCATCAAGAAGATGACCACTTCATTGATTTAATCCACTTCTCTG
TATCTAATCAGAAAGACAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGCTTTAT
TACTTTGACCCACTTCTCTGCATCTCATCAGGAAGAAAGGGATTTGAAGTTTCACTCACATTGAG
CTTTGCTTCATTGATTTGATCTACTTCTCTATATCTCATAAGGAAGATGACCACCTCATTGATTT
AATCCACTTCTCTGTACCTAATCAAGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGAAA
GATGAGCACTTTAGTACTTTGACCCACTTCTCTATATCTCATAAGAAAGATAAAGGTTTGAAGTT
TCACTCACATTGAACTTTGCTTCATTGATTTGATCTACATCTCTATATCTCATCAGGAAGATGAC
CGCTTCATTGATTTAATCCACTTCTCTGTATCTCATCAGGAAGGCGGATTTGGTCAACTTCTCTG
TATCTCATCAGAAAGATGGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTGA
Found at i:21676244 original size:48 final size:48
Alignment explanation
Indices: 21676173--21676293 Score: 215
Period size: 48 Copynumber: 2.5 Consensus size: 48
21676163 TTTGGTCAAC
21676173 TTCTCTGTATCTCATCAGAAAGATGACCACTTTATTGCTTTGACCCAG
1 TTCTCTGTATCTCATCAGAAAGATGACCACTTTATTGCTTTGACCCAG
* * *
21676221 TTCTCTGTATCTCATCAGAAAGATGACCACTTTATTGCTTTGGCTCAT
1 TTCTCTGTATCTCATCAGAAAGATGACCACTTTATTGCTTTGACCCAG
21676269 TTCTCTGTATCTCATCAGAAAGATG
1 TTCTCTGTATCTCATCAGAAAGATG
21676294 GGGGTTTGAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (48 bp):
TTCTCTGTATCTCATCAGAAAGATGACCACTTTATTGCTTTGACCCAG
Found at i:21676497 original size:161 final size:161
Alignment explanation
Indices: 21676221--21676523 Score: 480
Period size: 161 Copynumber: 1.9 Consensus size: 161
21676211 TTTGACCCAG
* * * * * *
21676221 TTCTCTGTATCTCATCAGAAAGATGACCACTTTATTGCTTTGGCTCATTTCTCTGTATCTCATCA
1 TTCTCTGTATCTCATAAGAAAGATGACCACTTTATTCCTTGGGCCCACTTCTCCGTATCTCATCA
21676286 GAAAGATGGGGGTTTGAAGTTTCACTCACATTGAGATTTGCTTAATTGATTTGGTCTACTTCTCT
66 GAAAGATGGGGGTTTGAAGTTTCACTCACATTGAGATTTGCTTAATTGATTTGGTCTACTTCTCT
21676351 GTATCTCATCAGAAAGGCGGATTTGGTCAAC
131 GTATCTCATCAGAAAGGCGGATTTGGTCAAC
* *
21676382 TTCTCTGTATCTCATAAGGAAGATGACCACTTTATTCCTTGGGCCCACTTCTCCGTATCTCATTA
1 TTCTCTGTATCTCATAAGAAAGATGACCACTTTATTCCTTGGGCCCACTTCTCCGTATCTCATCA
* ** * * *
21676447 GGAAGATTTGGGTTTGAAGTTTCACTCACATTGAGCTTTTCTTCATTGATTTGGTCTACTTCTCT
66 GAAAGATGGGGGTTTGAAGTTTCACTCACATTGAGATTTGCTTAATTGATTTGGTCTACTTCTCT
21676512 GTATCTCATCAG
131 GTATCTCATCAG
21676524 GAAGATAACC
Statistics
Matches: 128, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
161 128 1.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (161 bp):
TTCTCTGTATCTCATAAGAAAGATGACCACTTTATTCCTTGGGCCCACTTCTCCGTATCTCATCA
GAAAGATGGGGGTTTGAAGTTTCACTCACATTGAGATTTGCTTAATTGATTTGGTCTACTTCTCT
GTATCTCATCAGAAAGGCGGATTTGGTCAAC
Found at i:21676565 original size:209 final size:208
Alignment explanation
Indices: 21675590--21676571 Score: 995
Period size: 209 Copynumber: 4.7 Consensus size: 208
21675580 GATTTGGTCA
*
21675590 ACTTCTCTGTATCTCATCAGGAAGATGGGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
1 ACTTCTCTGTATCTCATCAGGAAGAT-GTGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
* *
21675655 TTGATTTGGTCTACTTCTCTATATCTCATTAAGAAGATGAC-CGTCTCATTGATTTAATCCACTT
65 TTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACTC-T-TCATTGATTTAATCCACTT
* * * *
21675719 CTCTGTATCTAATCAGAAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCGC
128 CTCTGTATCTCATCAGAAAGGCAGATTTGGTCAACTTCTCTGTATCTCATCAGAAAGATGACCAC
21675784 TTTATTACTTTGACCC
193 TTTATTACTTTGACCC
* *
21675800 ACTTCTTTGTATCTCATCAGGAAGATGAGGGCTTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
1 ACTTCTCTGTATCTCATCAGGAAGATGTGGG-TTTGAAGTTTCACTCACATTGAGCTTTGCTTCA
* * * * *
21675865 TTGATTTGTTCTACTTCTTTTTATCTCATAAGGAAGATGACTACCTCATTGATTTAATCCACTTC
65 TTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACT-CTTCATTGATTTAATCCACTTC
* * * * **
21675930 TCTGTACCTAATCA-AGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGAAAGATGGCGGC
129 TCTGTATCTCATCAGA-AAGGCAGATTTGGTCAACTTCTCTGTATCTCATCAGAAAGATGACCAC
21675994 TTTATTACTTTGACCC
193 TTTATTACTTTGACCC
* * * * *
21676010 ACTTCTCTATATCTCATAAGAAAGATGTAGGTTTGAAGTTTCACTCACATTGAACTTTGCTTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGTGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCAT
* * *
21676075 TGATTTGATCTACATCTCTATATCTCATTAGGAAGATGACTGCTTCATTGATTTAATCCACTTCT
66 TGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACT-CTTCATTGATTTAATCCACTTCT
* *
21676140 CTGTATCTCATCAGGAAGGCGGATTTGGTCAACTTCTCTGTATCTCATCAGAAAGATGACCACTT
130 CTGTATCTCATCAGAAAGGCAGATTTGGTCAACTTCTCTGTATCTCATCAGAAAGATGACCACTT
*
21676205 TATTGCTTTGACCC
195 TATTACTTTGACCC
* * **** * ** ***
21676219 AGTTCTCTGTATCTCATCAGAAAGATGACCACTTT-ATTGCTTTGGCT--CATTTCTCTGTAT-C
1 ACTTCTCTGTATCTCATCAGGAAGATG-TGGGTTTGA-AG-TTTCACTCACATTGAGCT-T-TGC
** ** * * * * *
21676280 TCATCAGAAAGATGGGGGTTTGAAGTT-TC---A-CTCA-CATTG-AGAT--TTGCTTAATTGAT
61 T--TC--ATTGAT-TTGGTCT--ACTTCTCTATATCTCATCA-GGAAGATGACT-CTTCATTGAT
** * * * *
21676336 TTGGTCTACTTCTCTGTATCTCATCAGAAAGGCGGATTTGGTCAACTTCTCTGTATCTCATAAGG
117 TTAATCCACTTCTCTGTATCTCATCAGAAAGGCAGATTTGGTCAACTTCTCTGTATCTCATCAGA
* * *
21676401 AAGATGACCACTTTATTCCTTGGGCCC
182 AAGATGACCACTTTATTACTTTGACCC
* * * *
21676428 ACTTCTCCGTATCTCATTAGGAAGATTTGGGTTTGAAGTTTCACTCACATTGAGCTTTTCTTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATGTGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCAT
* * * * * ** *
21676493 TGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATAACCTTTTTATTGCTTCGACCCACTTCT
66 TGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGA-CTCTTCATTGATTTAATCCACTTCT
*
21676558 TTGTATCTCATCAG
130 CTGTATCTCATCAG
21676572 GAAGATGGGG
Statistics
Matches: 640, Mismatches: 100, Indels: 65
0.80 0.12 0.08
Matches are distributed among these distances:
201 3 0.00
202 2 0.00
203 4 0.01
204 4 0.01
205 1 0.00
206 7 0.01
207 12 0.02
208 7 0.01
209 348 0.54
210 221 0.35
211 11 0.02
212 8 0.01
213 1 0.00
214 4 0.01
215 3 0.00
216 2 0.00
217 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (208 bp):
ACTTCTCTGTATCTCATCAGGAAGATGTGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCAT
TGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACTCTTCATTGATTTAATCCACTTCTC
TGTATCTCATCAGAAAGGCAGATTTGGTCAACTTCTCTGTATCTCATCAGAAAGATGACCACTTT
ATTACTTTGACCC
Found at i:21676590 original size:124 final size:124
Alignment explanation
Indices: 21676370--21676654 Score: 428
Period size: 124 Copynumber: 2.3 Consensus size: 124
21676360 CAGAAAGGCG
* * * *
21676370 GATTTGGTCAACTTCTCTGTATCTCATAAGGAAGATGACCACTTTATTCCTTGGGCCCACTTCTC
1 GATTTGGTCTACTTCTCTGTATCTCATAAGGAAGATAACCACTTTATTCCTTCGACCCACTTCTC
* **
21676435 CGTATCTCATTAGGAAGATTTGGGTTTGAAGTTTCACTCACATTGAGCTTTT-CTTCATT
66 CGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAG-TTTTGCTTCATT
* ** * *
21676494 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATAACCTTTTTATTGCTTCGACCCACTTCTT
1 GATTTGGTCTACTTCTCTGTATCTCATAAGGAAGATAACCACTTTATTCCTTCGACCCACTTCTC
*
21676559 TGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGTTTTGCTTCATT
66 CGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGTTTTGCTTCATT
21676618 GATTTGGTCTTACTTCTCTGTATCTCATAAGGAAGAT
1 GATTTGGTC-TACTTCTCTGTATCTCATAAGGAAGAT
21676655 GACCGCTTCA
Statistics
Matches: 145, Mismatches: 14, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
123 4 0.03
124 115 0.79
125 26 0.18
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (124 bp):
GATTTGGTCTACTTCTCTGTATCTCATAAGGAAGATAACCACTTTATTCCTTCGACCCACTTCTC
CGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGTTTTGCTTCATT
Found at i:21678293 original size:11 final size:11
Alignment explanation
Indices: 21678277--21678301 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21678267 ATCTTATCTC
21678277 CATAGATCTGG
1 CATAGATCTGG
21678288 CATAGATCTGG
1 CATAGATCTGG
21678299 CAT
1 CAT
21678302 TTATGATACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (11 bp):
CATAGATCTGG
Found at i:21686673 original size:25 final size:24
Alignment explanation
Indices: 21686640--21686702 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
21686630 AAATAATTAG
*
21686640 ATAAGAAGATTGAATTTAAAAAAGA
1 ATAAAAAGA-TGAATTTAAAAAAGA
* * *
21686665 ATAAAAAGAAG-ATTTTAAAAAGT
1 ATAAAAAGATGAATTTAAAAAAGA
*
21686688 ATAAAAAAATGAATT
1 ATAAAAAGATGAATT
21686703 AATTTAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 19 0.61
24 4 0.13
25 8 0.26
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.25
Consensus pattern (24 bp):
ATAAAAAGATGAATTTAAAAAAGA
Found at i:21687881 original size:23 final size:23
Alignment explanation
Indices: 21687849--21687895 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
21687839 TTATCTATTG
*
21687849 TCTCTATCTTGGTTCTCTATTTC
1 TCTCTATCTTGGCTCTCTATTTC
* *
21687872 TCTCTGTCTTGGCTCTCTGTTTC
1 TCTCTATCTTGGCTCTCTATTTC
21687895 T
1 T
21687896 TCTTTTTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.04, C:0.28, G:0.13, T:0.55
Consensus pattern (23 bp):
TCTCTATCTTGGCTCTCTATTTC
Found at i:21688700 original size:14 final size:14
Alignment explanation
Indices: 21688681--21688714 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
21688671 AATACATAAC
21688681 AATGAATTACCAAA
1 AATGAATTACCAAA
21688695 AATGAATTACCAAA
1 AATGAATTACCAAA
21688709 AATGAA
1 AATGAA
21688715 CATTTTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.12, G:0.09, T:0.21
Consensus pattern (14 bp):
AATGAATTACCAAA
Found at i:21689921 original size:30 final size:30
Alignment explanation
Indices: 21689846--21689921 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 30
21689836 AGTTTCGGAG
21689846 AATTT-AGGGTCAAAATGTAATCTTGGAAA
1 AATTTAAGGGTCAAAATGTAATCTTGGAAA
* * **
21689875 AATTTAGGGGTTAAAATGTAAT-TTTTAAA
1 AATTTAAGGGTCAAAATGTAATCTTGGAAA
21689904 AAGTTTAAGGGTCAAAAT
1 AA-TTTAAGGGTCAAAAT
21689922 AGATTTTTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
29 12 0.31
30 27 0.69
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (30 bp):
AATTTAAGGGTCAAAATGTAATCTTGGAAA
Done.