Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 304 of 427
Found at i:88108634 original size:20 final size:21
Alignment explanation
Indices: 88108579--88108637 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
88108569 ATTCGACATT
88108579 TGTATATGTATAAG-TATATAA
1 TGTATATG-ATAAGATATATAA
* * *
88108600 TGT-TTTGATATGATAT-TTA
1 TGTATATGATAAGATATATAA
88108619 TGTATATGATAAGATATAT
1 TGTATATGATAAGATATAT
88108638 TTGTAATGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 9 0.30
20 17 0.57
21 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.47
Consensus pattern (21 bp):
TGTATATGATAAGATATATAA
Found at i:88108642 original size:20 final size:20
Alignment explanation
Indices: 88108576--88108642 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
88108566 ATGATTCGAC
88108576 ATTTGTATATGTATAAG-TAT
1 ATTTGTATATG-ATAAGATAT
* * *
88108596 ATAATGT-TTTGATATGATAT
1 AT-TTGTATATGATAAGATAT
88108616 -TTATGTATATGATAAGATAT
1 ATT-TGTATATGATAAGATAT
88108636 ATTTGTA
1 ATTTGTA
88108643 ATGTATTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
19 8 0.22
20 23 0.64
21 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
ATTTGTATATGATAAGATAT
Found at i:88110437 original size:29 final size:29
Alignment explanation
Indices: 88110395--88110499 Score: 131
Period size: 29 Copynumber: 3.6 Consensus size: 29
88110385 GTGACAAGAT
* **
88110395 TGGCACTAAGTGTGCGGGCTTGAAA-GGTA
1 TGGCACTAAGTGTGCGAGCTT-AAATCATA
* *
88110424 TGGCACTAAGTGTGCGAACTTAAATTATA
1 TGGCACTAAGTGTGCGAGCTTAAATCATA
* *
88110453 TGGCACTATGTGTGCGAGCTTAAATCACA
1 TGGCACTAAGTGTGCGAGCTTAAATCATA
88110482 TGGCACTAAGTGTGCGAG
1 TGGCACTAAGTGTGCGAG
88110500 ATCGATTATT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
28 3 0.05
29 63 0.95
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTAAATCATA
Found at i:88121915 original size:17 final size:17
Alignment explanation
Indices: 88121862--88121919 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
88121852 TCATATGCTG
88121862 ATCTAAAAAGAAAAGAT
1 ATCTAAAAAGAAAAGAT
*
88121879 ATC-AAATTTGCAACAAAAGAT
1 ATCTAAA-----AAGAAAAGAT
88121900 ATCTAAAAAGAAAAGAT
1 ATCTAAAAAGAAAAGAT
88121917 ATC
1 ATC
88121920 GAAAGTCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 3 0.09
17 15 0.45
21 12 0.36
22 3 0.09
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.21
Consensus pattern (17 bp):
ATCTAAAAAGAAAAGAT
Found at i:88123655 original size:18 final size:18
Alignment explanation
Indices: 88123609--88123642 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
88123599 TTAGTACCAG
*
88123609 TCAGTCAAT-AGTAATAA
1 TCAGTTAATCAGTAATAA
88123626 TCAGTTAATCAGTAATA
1 TCAGTTAATCAGTAATA
88123643 TTCATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (18 bp):
TCAGTTAATCAGTAATAA
Found at i:88123834 original size:6 final size:6
Alignment explanation
Indices: 88123825--88123850 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
88123815 CACCGTAAGG
88123825 GTAACA GTAACA GTAACA GTAACA GT
1 GTAACA GTAACA GTAACA GTAACA GT
88123851 CAGGTACGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:88124895 original size:13 final size:13
Alignment explanation
Indices: 88124879--88124903 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88124869 CTTTTTCCTT
88124879 TTTCTTTATTTCA
1 TTTCTTTATTTCA
88124892 TTTCTTTATTTC
1 TTTCTTTATTTC
88124904 TTTTATTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTTATTTCA
Found at i:88127002 original size:24 final size:23
Alignment explanation
Indices: 88126967--88127011 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
88126957 TTGATTATAA
* *
88126967 AATGATATTTTGTATTTGATATTG
1 AATGATACTTTGAATTT-ATATTG
88126991 AATGATACTTTGAATTTATAT
1 AATGATACTTTGAATTTATAT
88127012 AAATATGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.51
Consensus pattern (23 bp):
AATGATACTTTGAATTTATATTG
Found at i:88132467 original size:38 final size:38
Alignment explanation
Indices: 88132416--88132495 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
88132406 AAGAAAACAC
88132416 TTGATTTGTATTTAGATATGAAAACAAATCCACAAAGT
1 TTGATTTGTATTTAGATATGAAAACAAATCCACAAAGT
88132454 TTGATTTGTATTTAGATATGAAAACAAATCCACAAAGT
1 TTGATTTGTATTTAGATATGAAAACAAATCCACAAAGT
88132492 TTGA
1 TTGA
88132496 CAATCTCTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (38 bp):
TTGATTTGTATTTAGATATGAAAACAAATCCACAAAGT
Found at i:88139720 original size:10 final size:10
Alignment explanation
Indices: 88139705--88139739 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
88139695 TATATAAAAT
88139705 TAAAAAATTA
1 TAAAAAATTA
88139715 TAAAAAAATTA
1 T-AAAAAATTA
*
88139726 TAAAAAAGTA
1 TAAAAAATTA
88139736 TAAA
1 TAAA
88139740 TTATATAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:88139722 original size:11 final size:11
Alignment explanation
Indices: 88139706--88139732 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
88139696 ATATAAAATT
88139706 AAAAAATTATA
1 AAAAAATTATA
88139717 AAAAAATTATA
1 AAAAAATTATA
88139728 AAAAA
1 AAAAA
88139733 GTATAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:88145144 original size:40 final size:40
Alignment explanation
Indices: 88145074--88145291 Score: 271
Period size: 40 Copynumber: 5.5 Consensus size: 40
88145064 AAGCCAGGTA
** * *
88145074 CCTTCGGGAGGTAA-CCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAACCCGGATATAG-TAACTCGCACAAATG
* *
88145113 CCTTCGGGACATAACCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
* *
88145153 CCTTCGGGACTTAGCCCGGATATAGTAACTCGTACAAATG
1 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
*
88145193 CCTTCGGGACTTAACCCGGATATAGTAACACGCACAAATG
1 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
* * * *
88145233 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAACCCGGATA-TAGTAACTCGCACAAATG
*
88145273 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAACCCGG
88145292 TTATCATCCG
Statistics
Matches: 160, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 14 0.09
40 146 0.91
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
Found at i:88148026 original size:42 final size:42
Alignment explanation
Indices: 88147977--88148085 Score: 200
Period size: 42 Copynumber: 2.6 Consensus size: 42
88147967 AGTATTGGTC
88147977 TCGGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGA
1 TCGGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGA
*
88148019 TTGGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGA
1 TCGGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGA
*
88148061 TCGGCACTAAGTGTGCGGGTTTAAA
1 TCGGCACTAAGTGTGCGGGTATAAA
88148086 ATTTGTACAG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (42 bp):
TCGGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGA
Found at i:88148151 original size:27 final size:28
Alignment explanation
Indices: 88148094--88148162 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 28
88148084 AAATTTGTAC
**
88148094 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
88148122 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
88148149 AGCACTAAGTGTGC
1 AGCACTAAGTGTGC
88148163 AGACTCACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:88148174 original size:27 final size:27
Alignment explanation
Indices: 88148094--88148175 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
88148084 AAATTTGTAC
** * *
88148094 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCG-AGCTCACTATAT
* * *
88148122 AGCACTATGTGTGCGAGCTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
88148149 AGCACTAAGTGTGC-AGACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
88148176 GCTTTTGCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.04
27 31 0.66
28 14 0.30
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:88151112 original size:86 final size:82
Alignment explanation
Indices: 88150904--88151197 Score: 241
Period size: 86 Copynumber: 3.4 Consensus size: 82
88150894 TTTGGTTTAG
* * * * *
88150904 TCGATGATGCAGTATGAGTGCTAGTATATTTGCTTTGGTTTATCTGATGATGCACTATATGTGCT
1 TCGATGATGCACTATGTGTGCTAGTATAATTACTTCGGTTT-TC-GATGATGCAC-ATATGTGCT
* * **
88150969 AGTATGATTGCTTTGA-TTT
63 AGTATAATTACTTCAACTTT
* * * * *
88150988 ATCTGATGATGCATTATGTGTGCCAATACAATTACTTCGGTCTGTTCGATGATGCACACCATGTG
1 -TC-GATGATGCACTATGTGTGCTAGTATAATTACTTCGGT-T-TTCGATGATGCACA-TATGTG
88151053 CTAGTATAATTACTTCAACTTT
61 CTAGTATAATTACTTCAACTTT
* * * * *
88151075 CTCGATGATGCACTATGTGTGCTAGTATGATTGCTTCGATTTATCCGATGATGCATTATGTGTGC
1 -TCGATGATGCACTATGTGTGCTAGTATAATTACTTCGGTTT-T-CGATGATGCA-CATATGTGC
* * * *
88151140 CAATATAATTACTTCAGTCTAT
62 TAGTATAATTACTTCA-ACTTT
88151162 TCGATGATGCACT-TCGTGTGCTAGTATAATTACTTC
1 TCGATGATGCACTAT-GTGTGCTAGTATAATTACTTC
88151198 AACTTTCTCA
Statistics
Matches: 169, Mismatches: 30, Indels: 19
0.78 0.14 0.09
Matches are distributed among these distances:
84 1 0.01
85 6 0.04
86 149 0.88
87 12 0.07
88 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (82 bp):
TCGATGATGCACTATGTGTGCTAGTATAATTACTTCGGTTTTCGATGATGCACATATGTGCTAGT
ATAATTACTTCAACTTT
Found at i:88151134 original size:129 final size:129
Alignment explanation
Indices: 88150949--88151225 Score: 464
Period size: 129 Copynumber: 2.1 Consensus size: 129
88150939 TGGTTTATCT
* * *
88150949 GATGATGCACTATATGTGCTAGTATGATTGCTTTGATTTATCTGATGATGCATTATGTGTGCCAA
1 GATGATGCACTATGTGTGCTAGTATGATTGCTTCGATTTATCCGATGATGCATTATGTGTGCCAA
* *
88151014 TACAATTACTTCGGTCTGTTCGATGATGCACACCATGTGCTAGTATAATTACTTCAACTTTCTC
66 TACAATTACTTCAGTCTATTCGATGATGCACACCATGTGCTAGTATAATTACTTCAACTTTCTC
88151078 GATGATGCACTATGTGTGCTAGTATGATTGCTTCGATTTATCCGATGATGCATTATGTGTGCCAA
1 GATGATGCACTATGTGTGCTAGTATGATTGCTTCGATTTATCCGATGATGCATTATGTGTGCCAA
* ** *
88151143 TATAATTACTTCAGTCTATTCGATGATGCACTTCGTGTGCTAGTATAATTACTTCAACTTTCTC
66 TACAATTACTTCAGTCTATTCGATGATGCACACCATGTGCTAGTATAATTACTTCAACTTTCTC
*
88151207 AATGATGCACTATGTGTGC
1 GATGATGCACTATGTGTGC
88151226 CATTATATTT
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 138 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.39
Consensus pattern (129 bp):
GATGATGCACTATGTGTGCTAGTATGATTGCTTCGATTTATCCGATGATGCATTATGTGTGCCAA
TACAATTACTTCAGTCTATTCGATGATGCACACCATGTGCTAGTATAATTACTTCAACTTTCTC
Found at i:88151212 original size:86 final size:87
Alignment explanation
Indices: 88151057--88151256 Score: 230
Period size: 86 Copynumber: 2.3 Consensus size: 87
88151047 CATGTGCTAG
* * * * *
88151057 TATAATTACTTCA-ACTTTCTCGATGATGCACTATGTGTGCTAGTATGATTGCTTCGATTTATCC
1 TATAATTACTTCAGTCTATCTCGATGATGCACTATGTGTGCTAGTATAATTACTTCAATTTATCC
* *
88151121 GATGATGCATTATGTGTGCCAA
66 AATGATGCACTATGTGTGCCAA
*
88151143 TATAATTACTTCAGTCTAT-TCGATGATGCACT-TCGTGTGCTAGTATAATTACTTCAACTT-TC
1 TATAATTACTTCAGTCTATCTCGATGATGCACTAT-GTGTGCTAGTATAATTACTTCAATTTATC
*
88151205 TCAATGATGCACTATGTGTGCCAT
65 -CAATGATGCACTATGTGTGCCAA
* * * *
88151229 TATATTTTCTTCAGTTTATC-CAATGATG
1 TATAATTACTTCAGTCTATCTCGATGATG
88151257 TAGTAATATA
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
85 3 0.03
86 91 0.94
87 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (87 bp):
TATAATTACTTCAGTCTATCTCGATGATGCACTATGTGTGCTAGTATAATTACTTCAATTTATCC
AATGATGCACTATGTGTGCCAA
Found at i:88151253 original size:43 final size:43
Alignment explanation
Indices: 88150907--88151256 Score: 199
Period size: 43 Copynumber: 8.1 Consensus size: 43
88150897 GGTTTAGTCG
* * * * * ** **
88150907 ATGATGCAGTATGAGTGCTAGTATATTTGCTTTGGTTTATCTG
1 ATGATGCACTATGTGTGCCAGTATAATTACTTCAGTTTATCCA
* * * * * **
88150950 ATGATGCACTATATGTGCTAGTATGATTGCTT-TGATTTATCTG
1 ATGATGCACTATGTGTGCCAGTATAATTACTTCAG-TTTATCCA
* * * * * * * *
88150993 ATGATGCATTATGTGTGCCAATACAATTACTTCGGTCTGTTCG
1 ATGATGCACTATGTGTGCCAGTATAATTACTTCAGTTTATCCA
** * ** *
88151036 ATGATGCAC-ACCATGTGCTAGTATAATTACTTCAACTT-TCTCG
1 ATGATGCACTA-TGTGTGCCAGTATAATTACTTCAGTTTATC-CA
* * * *
88151079 ATGATGCACTATGTGTGCTAGTATGATTGCTTC-GATTTATCCG
1 ATGATGCACTATGTGTGCCAGTATAATTACTTCAG-TTTATCCA
* * * * *
88151122 ATGATGCATTATGTGTGCCAATATAATTACTTCAGTCTATTCG
1 ATGATGCACTATGTGTGCCAGTATAATTACTTCAGTTTATCCA
* **
88151165 ATGATGCACT-TCGTGTGCTAGTATAATTACTTCAACTT-TCTCA
1 ATGATGCACTAT-GTGTGCCAGTATAATTACTTCAGTTTATC-CA
* * *
88151208 ATGATGCACTATGTGTGCCATTATATTTTCTTCAGTTTATCCA
1 ATGATGCACTATGTGTGCCAGTATAATTACTTCAGTTTATCCA
88151251 ATGATG
1 ATGATG
88151257 TAGTAATATA
Statistics
Matches: 239, Mismatches: 56, Indels: 24
0.75 0.18 0.08
Matches are distributed among these distances:
42 5 0.02
43 226 0.95
44 8 0.03
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (43 bp):
ATGATGCACTATGTGTGCCAGTATAATTACTTCAGTTTATCCA
Found at i:88151255 original size:129 final size:129
Alignment explanation
Indices: 88150950--88151256 Score: 438
Period size: 129 Copynumber: 2.4 Consensus size: 129
88150940 GGTTTATCTG
* * * **
88150950 ATGATGCACTATATGTGCTAGTATGATTGCTTTGATTTATCTGATGATGCATTATGTGTGCCAAT
1 ATGATGCACTATGTGTGCCAGTATGATTGCTTCGATTTATCCAATGATGCATTATGTGTGCCAAT
* * *
88151015 ACAATTACTTCGGTCTGTTCGATGATGCACACCATGTGCTAGTATAATTACTTCAACTTTCTCG
66 ACAATTACTTCAGTCTATTCGATGATGCACACCATGTGCTAGTATAATTACTTCAACTTTCTCA
* *
88151079 ATGATGCACTATGTGTGCTAGTATGATTGCTTCGATTTATCCGATGATGCATTATGTGTGCCAAT
1 ATGATGCACTATGTGTGCCAGTATGATTGCTTCGATTTATCCAATGATGCATTATGTGTGCCAAT
* ** *
88151144 ATAATTACTTCAGTCTATTCGATGATGCACTTCGTGTGCTAGTATAATTACTTCAACTTTCTCA
66 ACAATTACTTCAGTCTATTCGATGATGCACACCATGTGCTAGTATAATTACTTCAACTTTCTCA
* *
88151208 ATGATGCACTATGTGTGCCATTAT-ATTTTCTTC-AGTTTATCCAATGATG
1 ATGATGCACTATGTGTGCCAGTATGA-TTGCTTCGA-TTTATCCAATGATG
88151257 TAGTAATATA
Statistics
Matches: 162, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
128 2 0.01
129 160 0.99
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.40
Consensus pattern (129 bp):
ATGATGCACTATGTGTGCCAGTATGATTGCTTCGATTTATCCAATGATGCATTATGTGTGCCAAT
ACAATTACTTCAGTCTATTCGATGATGCACACCATGTGCTAGTATAATTACTTCAACTTTCTCA
Found at i:88154733 original size:14 final size:14
Alignment explanation
Indices: 88154711--88154742 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
88154701 TAATTATATA
88154711 TAAAGAAATAAATT
1 TAAAGAAATAAATT
*
88154725 TAAATAAATAAATT
1 TAAAGAAATAAATT
88154739 TAAA
1 TAAA
88154743 AAGCATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
TAAAGAAATAAATT
Found at i:88158299 original size:13 final size:13
Alignment explanation
Indices: 88158281--88158305 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88158271 CACCCGTGTC
88158281 CCAGGCCGTGTGG
1 CCAGGCCGTGTGG
88158294 CCAGGCCGTGTG
1 CCAGGCCGTGTG
88158306 ACTCACACAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.44, T:0.16
Consensus pattern (13 bp):
CCAGGCCGTGTGG
Found at i:88160562 original size:40 final size:40
Alignment explanation
Indices: 88160517--88160684 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
88160507 CGGAATATAA
*
88160517 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-AGCACAAATGCCTTCGGGTCTTAGC
* ** * *
88160557 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
88160597 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
88160637 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
88160677 CCGGATAT
1 CCGGATAT
88160685 CATTCAATTT
Statistics
Matches: 105, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 104 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:88160667 original size:80 final size:80
Alignment explanation
Indices: 88160533--88160684 Score: 200
Period size: 80 Copynumber: 1.9 Consensus size: 80
88160523 ATAACCATGT
* *
88160533 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
88160598 CGGATATAGCCACTA
66 CGGATATAGCCACTA
* * ** * *
88160613 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
88160676 CCCGGATAT
64 CCCGGATAT
88160685 CATTCAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
79 3 0.05
80 59 0.95
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATATAGCCACTA
Found at i:88169073 original size:28 final size:28
Alignment explanation
Indices: 88169028--88169096 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
88169018 TTTAAAACCC
*
88169028 TAGGGGT-ATATCGGTAATTATGCTCTT
1 TAGGGGTAATTTCGGTAATTATGCTCTT
*
88169055 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTATGCTCTT
88169083 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
88169097 TGATCTACGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 7 0.18
28 32 0.82
ACGTcount: A:0.20, C:0.10, G:0.28, T:0.42
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTATGCTCTT
Found at i:88176691 original size:20 final size:20
Alignment explanation
Indices: 88176666--88176725 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
88176656 ATTAATGATT
*
88176666 ATAATAATATAATAAAAGAA
1 ATAATAAAATAATAAAAGAA
*
88176686 ATAATAAAAGAATAAAAGAA
1 ATAATAAAATAATAAAAGAA
* *
88176706 ATAA-AACATAAAAAAAGAA
1 ATAATAAAATAATAAAAGAA
88176725 A
1 A
88176726 GAAAGAAGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 13 0.37
20 22 0.63
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.17
Consensus pattern (20 bp):
ATAATAAAATAATAAAAGAA
Found at i:88176773 original size:16 final size:17
Alignment explanation
Indices: 88176745--88176788 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 17
88176735 CACGATTAGC
88176745 AGGGAAAGAAAGAAGGAAAA
1 AGGGAAAGAAA-AA-G-AAA
88176765 AGGGAAAGAAAAAGAAA
1 AGGGAAAGAAAAAGAAA
88176782 AGGGAAA
1 AGGGAAA
88176789 ATTAGGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.42
18 1 0.04
19 2 0.08
20 11 0.46
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
AGGGAAAGAAAAAGAAA
Found at i:88184805 original size:16 final size:16
Alignment explanation
Indices: 88184784--88184816 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
88184774 GAAGGAAGAC
88184784 TAACTTGCTTCATTGT
1 TAACTTGCTTCATTGT
*
88184800 TAACTTGCTTTATTGT
1 TAACTTGCTTCATTGT
88184816 T
1 T
88184817 CATTATTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.12, T:0.55
Consensus pattern (16 bp):
TAACTTGCTTCATTGT
Found at i:88186838 original size:32 final size:32
Alignment explanation
Indices: 88186802--88186862 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
88186792 CATATTTCAT
88186802 ATTTCATAACACTGGGCCGAAGCCTTTTCAAA
1 ATTTCATAACACTGGGCCGAAGCCTTTTCAAA
**
88186834 ATTTCATATTACTGGGCCGAAGCCTTTTC
1 ATTTCATAACACTGGGCCGAAGCCTTTTC
88186863 TATAAACGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (32 bp):
ATTTCATAACACTGGGCCGAAGCCTTTTCAAA
Found at i:88187183 original size:47 final size:47
Alignment explanation
Indices: 88187116--88187357 Score: 376
Period size: 47 Copynumber: 5.1 Consensus size: 47
88187106 GCCTTGCCTT
* * *
88187116 TTTTAATAACTGGGGCAAAAGCCCTTTAATAACTGGGGCGTAAGCCC
1 TTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
* * *
88187163 TTTTGATCACTGGGGCAAAAGCCCTTTAATAACTAGGGCATAAGCCC
1 TTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
*
88187210 TTTTGATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCGTAAGCCC
1 TTTTGATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCC
*
88187258 TTTTGATCACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
1 TTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
* *
88187305 TTTTGATAACTGGGGCATAAGCCTTTTTGATAACTGGGGCATAAGCCC
1 TTTTGATAACTGGGGCATAAGCC-CTTTAATAACTGGGGCATAAGCCC
88187353 TTTTG
1 TTTTG
88187358 CACTTCCTCC
Statistics
Matches: 180, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
47 109 0.61
48 71 0.39
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (47 bp):
TTTTGATAACTGGGGCATAAGCCCTTTAATAACTGGGGCATAAGCCC
Found at i:88187184 original size:24 final size:24
Alignment explanation
Indices: 88187116--88187357 Score: 346
Period size: 24 Copynumber: 10.2 Consensus size: 24
88187106 GCCTTGCCTT
* *
88187116 TTTTAATAACTGGGGCAAAAGCCC
1 TTTTGATAACTGGGGCATAAGCCC
* *
88187140 -TTTAATAACTGGGGCGTAAGCCC
1 TTTTGATAACTGGGGCATAAGCCC
* *
88187163 TTTTGATCACTGGGGCAAAAGCCC
1 TTTTGATAACTGGGGCATAAGCCC
* *
88187187 -TTTAATAACTAGGGCATAAGCCC
1 TTTTGATAACTGGGGCATAAGCCC
88187210 TTTTGATAACTGGGGCATAAGCCC
1 TTTTGATAACTGGGGCATAAGCCC
* *
88187234 TTTTAATAACTGGGGCGTAAGCCC
1 TTTTGATAACTGGGGCATAAGCCC
*
88187258 TTTTGATCACTGGGGCATAAGCCC
1 TTTTGATAACTGGGGCATAAGCCC
*
88187282 -TTTAATAACTGGGGCATAAGCCC
1 TTTTGATAACTGGGGCATAAGCCC
*
88187305 TTTTGATAACTGGGGCATAAGCCT
1 TTTTGATAACTGGGGCATAAGCCC
88187329 TTTTGATAACTGGGGCATAAGCCC
1 TTTTGATAACTGGGGCATAAGCCC
88187353 TTTTG
1 TTTTG
88187358 CACTTCCTCC
Statistics
Matches: 193, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
23 61 0.32
24 132 0.68
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (24 bp):
TTTTGATAACTGGGGCATAAGCCC
Found at i:88187283 original size:95 final size:95
Alignment explanation
Indices: 88187116--88187357 Score: 414
Period size: 95 Copynumber: 2.6 Consensus size: 95
88187106 GCCTTGCCTT
* *
88187116 TTTTAATAACTGGGGCAAAAGCCC-TTTAATAACTGGGGCGTAAGCCCTTTTGATCACTGGGGCA
1 TTTTGATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCGTAAGCCCTTTTGATCACTGGGGCA
88187180 AAAGCCCTTTAATAACTAGGGCATAAGCCC
66 AAAGCCCTTTAATAACTAGGGCATAAGCCC
88187210 TTTTGATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCGTAAGCCCTTTTGATCACTGGGGCA
1 TTTTGATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCGTAAGCCCTTTTGATCACTGGGGCA
* *
88187275 TAAGCCCTTTAATAACTGGGGCATAAGCCC
66 AAAGCCCTTTAATAACTAGGGCATAAGCCC
* * *
88187305 TTTTGATAACTGGGGCATAAGCCTTTTTGATAACTGGGGCATAAGCCCTTTTG
1 TTTTGATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCGTAAGCCCTTTTG
88187358 CACTTCCTCC
Statistics
Matches: 140, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
94 22 0.16
95 118 0.84
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (95 bp):
TTTTGATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCGTAAGCCCTTTTGATCACTGGGGCA
AAAGCCCTTTAATAACTAGGGCATAAGCCC
Found at i:88187428 original size:9 final size:9
Alignment explanation
Indices: 88187414--88187470 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
88187404 ATCTCATGTG
88187414 CATATCATA
1 CATATCATA
*
88187423 CATATCATGTG
1 CATATCA--TA
88187434 CATATCATA
1 CATATCATA
* *
88187443 CATGTCATGTG
1 CATATCA--TA
88187454 CATATCATA
1 CATATCATA
88187463 CATATCAT
1 CATATCAT
88187471 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:88187432 original size:20 final size:20
Alignment explanation
Indices: 88187407--88187472 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
88187397 TATGACCATC
88187407 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
88187427 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATA
88187447 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
88187467 TCATGT
1 TCATGT
88187473 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:88187437 original size:11 final size:11
Alignment explanation
Indices: 88187407--88187461 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
88187397 TATGACCATC
88187407 TCATGTGCATA
1 TCATGTGCATA
*
88187418 TCA--TACATA
1 TCATGTGCATA
88187427 TCATGTGCATA
1 TCATGTGCATA
* *
88187438 TCA--TACATG
1 TCATGTGCATA
88187447 TCATGTGCATA
1 TCATGTGCATA
88187458 TCAT
1 TCAT
88187462 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:88187550 original size:25 final size:24
Alignment explanation
Indices: 88187508--88187555 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
88187498 CATAATAAAC
* * *
88187508 CCTAGGGGTATAATGGTCACTTTTA
1 CCTAGGGGCAAAACGGTCA-TTTTA
88187533 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
88187556 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (24 bp):
CCTAGGGGCAAAACGGTCATTTTA
Found at i:88188859 original size:27 final size:27
Alignment explanation
Indices: 88188829--88188880 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
88188819 GTAAATCAAC
88188829 AAACCAAAGGTATTTC-AGTAATTTTGT
1 AAACCAAAGGTATTTCTA-TAATTTTGT
*
88188856 AAACCAATGGTATTTCTATAATTTT
1 AAACCAAAGGTATTTCTATAATTTT
88188881 TAGAAAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (27 bp):
AAACCAAAGGTATTTCTATAATTTTGT
Found at i:88188924 original size:56 final size:54
Alignment explanation
Indices: 88188827--88189072 Score: 194
Period size: 54 Copynumber: 4.5 Consensus size: 54
88188817 TGGTAAATCA
* * * *
88188827 ACAAACCAAAGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTTT
1 ACAAATCAAGGGTATTTCAGTAACTTTGTAAACCAAGGGTATTT-TGATAA-TTTT
* * * * *
88188882 AGAAAGTCAAGGGTATTTCTGTAACTTTGTAAATCAGGGGTATTTTGGTAATTTT
1 ACAAA-TCAAGGGTATTTCAGTAACTTTGTAAACCAAGGGTATTTTGATAATTTT
* * ** *
88188937 ACAAATTAAGGGTATTTCGGTAA-TTTCACAAACCAAGGGTATTTTGGTAATTTT
1 ACAAATCAAGGGTATTTCAGTAACTTT-GTAAACCAAGGGTATTTTGATAATTTT
** * ** * *
88188991 ACAAATTGAGGGTATTTCGGTAA-TTTCACAAACCAAGGATATTTTGGTAATTTT
1 ACAAATCAAGGGTATTTCAGTAACTTT-GTAAACCAAGGGTATTTTGATAATTTT
* * *
88189045 ACAAA-CTAGGGGTATTTTAGTAATTTTG
1 ACAAATC-AAGGGTATTTCAGTAACTTTG
88189073 CAAATCGAGG
Statistics
Matches: 162, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
53 3 0.02
54 108 0.67
55 16 0.10
56 35 0.22
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (54 bp):
ACAAATCAAGGGTATTTCAGTAACTTTGTAAACCAAGGGTATTTTGATAATTTT
Found at i:88188932 original size:27 final size:26
Alignment explanation
Indices: 88188879--88189085 Score: 166
Period size: 27 Copynumber: 7.7 Consensus size: 26
88188869 TTCTATAATT
*
88188879 TTTAGAAAGTCAAGGGTATTTCT-GTAA
1 TTTACAAA-TCAAGGGTATTT-TGGTAA
** *
88188906 CTTTGTAAATCAGGGGTATTTTGGTAA
1 -TTTACAAATCAAGGGTATTTTGGTAA
* *
88188933 TTTTACAAATTAAGGGTATTTCGGTAA
1 -TTTACAAATCAAGGGTATTTTGGTAA
*
88188960 TTTCACAAACCAAGGGTATTTTGGTAA
1 TTT-ACAAATCAAGGGTATTTTGGTAA
** *
88188987 TTTTACAAATTGAGGGTATTTCGGTAA
1 -TTTACAAATCAAGGGTATTTTGGTAA
* *
88189014 TTTCACAAACCAAGGATATTTTGGTAA
1 TTT-ACAAATCAAGGGTATTTTGGTAA
* *
88189041 TTTTACAAA-CTAGGGGTATTTTAGTAA
1 -TTTACAAATC-AAGGGTATTTTGGTAA
* *
88189068 TTTTGCAAATCGAGGGTA
1 -TTTACAAATCAAGGGTA
88189086 AAACAGTAAT
Statistics
Matches: 145, Mismatches: 27, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
26 8 0.06
27 124 0.86
28 13 0.09
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.38
Consensus pattern (26 bp):
TTTACAAATCAAGGGTATTTTGGTAA
Found at i:88188977 original size:54 final size:54
Alignment explanation
Indices: 88188919--88189070 Score: 250
Period size: 54 Copynumber: 2.8 Consensus size: 54
88188909 TGTAAATCAG
88188919 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAA
*
88188973 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAA
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAA
* * * **
88189027 GGATATTTTGGTAATTTTACAAACTAGGGGTATTTTAGTAATTT
1 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTT
88189071 TGCAAATCGA
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAA
Found at i:88189013 original size:81 final size:81
Alignment explanation
Indices: 88188889--88189085 Score: 227
Period size: 81 Copynumber: 2.4 Consensus size: 81
88188879 TTTAGAAAGT
* ** * * ** *
88188889 CAAGGGTATTTCT-GTAACTTTGTAAATC-AGGGGTATTTTGGTAATTTTACAAATTAAGGGTAT
1 CAAGGGTATTT-TAGTAATTTTACAAATCGA-GGGTATTTCGGTAATTTCACAAACCAAGGATAT
88188952 TTCGGTAATTTCACAAAC
64 TTCGGTAATTTCACAAAC
* *
88188970 CAAGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAAGGATATTT
1 CAAGGGTATTTTAGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAACCAAGGATATTT
* *
88189035 TGGTAATTTTACAAAC
66 CGGTAATTTCACAAAC
* * *
88189051 TAGGGGTATTTTAGTAATTTTGCAAATCGAGGGTA
1 CAAGGGTATTTTAGTAATTTTACAAATCGAGGGTA
88189086 AAACAGTAAT
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
80 1 0.01
81 96 0.98
82 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (81 bp):
CAAGGGTATTTTAGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAACCAAGGATATTT
CGGTAATTTCACAAAC
Found at i:88189093 original size:27 final size:27
Alignment explanation
Indices: 88189063--88189301 Score: 246
Period size: 27 Copynumber: 8.9 Consensus size: 27
88189053 GGGGTATTTT
* *
88189063 AGTAATTTTGCAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
88189090 AGTAATTCTGTAAATCAAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
88189117 AGTAATTCTATAAATCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
88189144 AGTAATTCAGTAAATTGAGGGTGAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
88189171 GGTAATTCTGTAAGTCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
88189198 -GATAATTATGTAAATCGGGGGTAAAAT
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * * *
88189225 GGTAATTATGTAAATCGGGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
88189252 GGTAATTCTGTAAATTGGGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
88189279 GGTAATTCTATAAATCGGGGGTA
1 AGTAATTCTGTAAATCGAGGGTA
88189302 CTTTGGTAAT
Statistics
Matches: 185, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 183 0.99
28 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:88189139 original size:81 final size:80
Alignment explanation
Indices: 88189062--88189328 Score: 255
Period size: 81 Copynumber: 3.3 Consensus size: 80
88189052 AGGGGTATTT
* *
88189062 TAGTAATTTTGCAAATCGAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTA
1 TAGTAATTTTGCAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA-AGTAATTCTA
**
88189127 TAAATCAAGGGTAAAA
65 TAAATCGGGGGTAAAA
* ** * * * * * * *
88189143 CAGTAATTCAGTAAATTGAGGGTGAAACGGTAATTCTGTAAGTCGAGGGTAAAACGATAATTATG
1 TAGTAATTTTGCAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAAG-TAATTCTA
88189208 TAAATCGGGGGTAAAA
65 TAAATCGGGGGTAAAA
* * * * * * * *
88189224 TGGTAATTATGTAAATCGGGGGTAAAATGGTAATTCTGTAAATTGGGGGTAAAACGGTAATTCTA
1 TAGTAATTTTGCAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAA-AGTAATTCTA
***
88189289 TAAATCGGGGGTACTT
65 TAAATCGGGGGTAAAA
* * *
88189305 TGGTAATTTTACAAGTCGAGGGTA
1 TAGTAATTTTGCAAATCGAGGGTA
88189329 TTTCAATAAT
Statistics
Matches: 148, Mismatches: 36, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
80 1 0.01
81 146 0.99
82 1 0.01
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.29
Consensus pattern (80 bp):
TAGTAATTTTGCAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAAAGTAATTCTAT
AAATCGGGGGTAAAA
Found at i:88193728 original size:26 final size:26
Alignment explanation
Indices: 88193697--88193749 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
88193687 GAGGCTTATC
88193697 AATGGTAGAAAACCATGGTTAGTGTG
1 AATGGTAGAAAACCATGGTTAGTGTG
88193723 AATGGTAGAAAACCATGGTTAGTGTG
1 AATGGTAGAAAACCATGGTTAGTGTG
88193749 A
1 A
88193750 CTCCTGAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.30, T:0.26
Consensus pattern (26 bp):
AATGGTAGAAAACCATGGTTAGTGTG
Found at i:88194980 original size:64 final size:64
Alignment explanation
Indices: 88194905--88195025 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 64
88194895 AAACAAATTG
* *
88194905 AATTGGTGAATAGAATAATTTCTACAGTGTCCACCA-GGAAAATGATTGTTCAGGGCGCAAACTA
1 AATTGGCGAATAGAATAATTTCTACAGTGTCCA-CATGGAAAATGATTATTCAGGGCGCAAACTA
* * *
88194969 AATTGGCGAATAGAATAATTTCTGCATTGTCCACATGGACAATGATTATTCAGGGCG
1 AATTGGCGAATAGAATAATTTCTACAGTGTCCACATGGAAAATGATTATTCAGGGCG
88195026 TAGATGCTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 2 0.04
64 49 0.96
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (64 bp):
AATTGGCGAATAGAATAATTTCTACAGTGTCCACATGGAAAATGATTATTCAGGGCGCAAACTA
Found at i:88198048 original size:40 final size:40
Alignment explanation
Indices: 88197993--88198140 Score: 217
Period size: 40 Copynumber: 3.7 Consensus size: 40
88197983 ATAACCACAA
* * *
88197993 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
88198033 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
88198073 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAAGC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT-AGCAACTC
* *
88198113 GCATAAATGCCTTCGGGACTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAGCCCGG
88198141 GTATCATTCA
Statistics
Matches: 99, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 97 0.98
41 2 0.02
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:88198121 original size:80 final size:80
Alignment explanation
Indices: 88197973--88198140 Score: 232
Period size: 80 Copynumber: 2.1 Consensus size: 80
88197963 TCTTTGGAAT
* * * *
88197973 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATATAACAACAAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTAGCAC
*
88198037 AAATGCCTTCGGGTC
66 AAATGCCTTCGGGAC
** *
88198052 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAAGC-ACTAGCA
1 TTAGCCCGGATATAACAACAAGCACAAATGCCTTCGGGTCTTAACCCGGATAT-AGCAACTAGCA
*
88198116 TAAATGCCTTCGGGAC
65 CAAATGCCTTCGGGAC
88198132 TTAGCCCGG
1 TTAGCCCGG
88198141 GTATCATTCA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
79 4 0.05
80 71 0.91
81 3 0.04
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (80 bp):
TTAGCCCGGATATAACAACAAGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTAGCAC
AAATGCCTTCGGGAC
Found at i:88206196 original size:40 final size:40
Alignment explanation
Indices: 88206131--88206298 Score: 223
Period size: 40 Copynumber: 4.2 Consensus size: 40
88206121 TCTTCGGAAT
* ** *
88206131 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * *
88206170 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
88206210 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * *
88206250 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAA-CAACTCGCACAAATGCCTTCGGGTC
88206290 TTAGCCCGG
1 TTAGCCCGG
88206299 GTATCATTCA
Statistics
Matches: 114, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 3 0.03
40 110 0.96
41 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
Found at i:88214561 original size:39 final size:39
Alignment explanation
Indices: 88214549--88214697 Score: 255
Period size: 39 Copynumber: 3.8 Consensus size: 39
88214539 TATGGTAGCC
* *
88214549 CGCACAA-TGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCATAACT
88214588 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
*
88214627 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
88214666 CGCACAATTGCCTTCGGGCTTAGCCCGGATAT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATAT
88214698 TACCCGAACA
Statistics
Matches: 106, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
39 96 0.91
40 10 0.09
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
Found at i:88218145 original size:48 final size:47
Alignment explanation
Indices: 88218061--88218193 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 47
88218051 TGCAAACATT
* ** *
88218061 ATAAA-TGAAAAAAAATCAAGCAATATTGAAATTTTAATTATAATT-GC
1 ATAAATTGAAAAAATATCAAATAGTATTGAAA-TTTAATTA-AATTGGC
*
88218108 ATAAA-TGAAGTAAATATCAAATAGTATTGTAAATTTAATTAAATTGGC
1 ATAAATTGAA-AAAATATCAAATAGTATTG-AAATTTAATTAAATTGGC
**
88218156 ATAAATTGAAAAAATATTGAATAGTATTGAAAATTTAA
1 ATAAATTGAAAAAATATCAAATAGTATTG-AAATTTAA
88218194 AATTATCACT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
47 13 0.18
48 53 0.73
49 7 0.10
ACGTcount: A:0.52, C:0.04, G:0.11, T:0.34
Consensus pattern (47 bp):
ATAAATTGAAAAAATATCAAATAGTATTGAAATTTAATTAAATTGGC
Found at i:88218347 original size:11 final size:11
Alignment explanation
Indices: 88218328--88218391 Score: 58
Period size: 11 Copynumber: 5.9 Consensus size: 11
88218318 TTTTAAACAA
*
88218328 AGAAATTTGAT
1 AGAATTTTGAT
88218339 AGAATTTTGAT
1 AGAATTTTGAT
*
88218350 AGAATTTTGAG
1 AGAATTTTGAT
* **
88218361 AAAATTTCAAT
1 AGAATTTTGAT
*
88218372 -GAAATTTGAT
1 AGAATTTTGAT
*
88218382 AGATTTTTGA
1 AGAATTTTGA
88218392 AGGGAATATT
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
10 6 0.15
11 34 0.85
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.41
Consensus pattern (11 bp):
AGAATTTTGAT
Found at i:88219521 original size:9 final size:9
Alignment explanation
Indices: 88219509--88219533 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
88219499 TTTTAAAATT
88219509 ATAAAATAA
1 ATAAAATAA
88219518 ATAAAATAA
1 ATAAAATAA
88219527 ATAAAAT
1 ATAAAAT
88219534 CTTTAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAAAATAA
Found at i:88222475 original size:2 final size:2
Alignment explanation
Indices: 88222468--88222494 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
88222458 CATGGGATAT
88222468 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 A
88222495 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:88237615 original size:39 final size:38
Alignment explanation
Indices: 88237529--88237684 Score: 186
Period size: 39 Copynumber: 4.0 Consensus size: 38
88237519 CAAATCCAAT
* * * *
88237529 CACCACCACAAAGCATGCAGGACTTTAAGCCCAGATATAA
1 CACCAGCACAAAGCCTGCGGGAC-TT-AGCCCGGATATAA
* *
88237569 TATCAGCACAAAGCCTGCGGGACTTTAGCCCGGATATAA
1 CACCAGCACAAAGCCTGCGGGAC-TTAGCCCGGATATAA
* *
88237608 CACCAGCACAATGCCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCACAAAGCCTGCGGGACTTAGCCCGGATATAA
* *
88237646 CACCAGCACGAATGCCTTCGGGACTTAGCCCGGATATAA
1 CACCAGCAC-AAAGCCTGCGGGACTTAGCCCGGATATAA
88237685 TTCTCCATTA
Statistics
Matches: 105, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
38 24 0.23
39 60 0.57
40 21 0.20
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (38 bp):
CACCAGCACAAAGCCTGCGGGACTTAGCCCGGATATAA
Found at i:88237644 original size:38 final size:38
Alignment explanation
Indices: 88237556--88237684 Score: 195
Period size: 39 Copynumber: 3.3 Consensus size: 38
88237546 CAGGACTTTA
* * * * *
88237556 AGCCCAGATATAATATCAGCACAAAGCCTGCGGGACTTT
1 AGCCCGGATATAACACCAGCACAATGCCTTCGGGAC-TT
88237595 AGCCCGGATATAACACCAGCACAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACAATGCCTTCGGGACTT
88237633 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCAC-AATGCCTTCGGGACTT
88237672 AGCCCGGATATAA
1 AGCCCGGATATAA
88237685 TTCTCCATTA
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
38 24 0.29
39 60 0.71
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.19
Consensus pattern (38 bp):
AGCCCGGATATAACACCAGCACAATGCCTTCGGGACTT
Found at i:88246789 original size:17 final size:17
Alignment explanation
Indices: 88246767--88246799 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
88246757 CATGAAACAT
88246767 TTAATGCACCCATATTC
1 TTAATGCACCCATATTC
88246784 TTAATGCACCCATATT
1 TTAATGCACCCATATT
88246800 ATTCGGGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.36
Consensus pattern (17 bp):
TTAATGCACCCATATTC
Found at i:88250234 original size:23 final size:23
Alignment explanation
Indices: 88250204--88250251 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
88250194 GAGAATAAGC
88250204 ATGTGTTAAAGTTTCATGAAGAA
1 ATGTGTTAAAGTTTCATGAAGAA
88250227 ATGTGTTAAAGTTTCATGAAGAA
1 ATGTGTTAAAGTTTCATGAAGAA
88250250 AT
1 AT
88250252 TCTATGTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (23 bp):
ATGTGTTAAAGTTTCATGAAGAA
Found at i:88252436 original size:19 final size:20
Alignment explanation
Indices: 88252400--88252450 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
88252390 CGGGTAAGGG
*
88252400 ACACGAGCGTGTCCCAATGC
1 ACACGGGCGTGTCCCAATGC
*
88252420 ACATGGGCGTG-CCCAATGC
1 ACACGGGCGTGTCCCAATGC
*
88252439 GCACGGGCGTGT
1 ACACGGGCGTGT
88252451 GCATTGCCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.20, C:0.31, G:0.33, T:0.16
Consensus pattern (20 bp):
ACACGGGCGTGTCCCAATGC
Found at i:88253802 original size:47 final size:47
Alignment explanation
Indices: 88253750--88253879 Score: 179
Period size: 47 Copynumber: 2.8 Consensus size: 47
88253740 TGCGAGTAAA
* * * * *
88253750 TACCTTGATTTGGCTACAGGCCATGGTATAGGTATTTTGTGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCTGGGAGAAGT
* * *
88253797 TACCTTGATTTGGCTACGGGTCATGGTATAGGTACTCTGGGATAATT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCTGGGAGAAGT
*
88253844 TACCTTGATTTGGCTACGGGCCATGATATAGGTACT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACT
88253880 TATCAATTGT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCTGGGAGAAGT
Found at i:88257521 original size:20 final size:19
Alignment explanation
Indices: 88257485--88257535 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
88257475 AAGGGCTATT
*
88257485 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
88257504 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
88257524 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
88257536 GTTGTTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:88260655 original size:19 final size:19
Alignment explanation
Indices: 88260631--88260674 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
88260621 GAAGCTAGCT
88260631 TGTTGTGAACTTGAGAATA
1 TGTTGTGAACTTGAGAATA
88260650 TGTTGTGAACTTGAGAATA
1 TGTTGTGAACTTGAGAATA
88260669 TGTTGT
1 TGTTGT
88260675 CAGGTTAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (19 bp):
TGTTGTGAACTTGAGAATA
Found at i:88273964 original size:55 final size:55
Alignment explanation
Indices: 88273827--88273964 Score: 125
Period size: 55 Copynumber: 2.5 Consensus size: 55
88273817 TGCGACATGG
* * * **
88273827 CCGTGGGTGAACCTGCCAAAAAAAATACAGGCGTGCGACACGCCCTTGCCTTGAAA
1 CCGTGGGCGAACCTGCC-AAAAAAACACAGGCGTGCGACACGCCCGTGCCAAGAAA
* ** ** * * *
88273883 CCGTGGCCGAACCTATCAAATTAACACAGGCAG-GTGACACGCCCGTGTCAAGCAA
1 CCGTGGGCGAACCTGCCAAAAAAACACAGGC-GTGCGACACGCCCGTGCCAAGAAA
*
88273938 CCGTGGGCGAACCTGCCAAAACAACAC
1 CCGTGGGCGAACCTGCCAAAAAAACAC
88273965 GGCCATGGAC
Statistics
Matches: 63, Mismatches: 18, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
55 49 0.78
56 14 0.22
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (55 bp):
CCGTGGGCGAACCTGCCAAAAAAACACAGGCGTGCGACACGCCCGTGCCAAGAAA
Found at i:88296824 original size:5 final size:5
Alignment explanation
Indices: 88296814--88296840 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
88296804 ACAGGACCTT
88296814 CAACA CAACA CAACA CAACA CAACA CA
1 CAACA CAACA CAACA CAACA CAACA CA
88296841 CCCTTCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (5 bp):
CAACA
Found at i:88319116 original size:46 final size:46
Alignment explanation
Indices: 88319063--88319238 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
88319053 TATTTGGGCA
88319063 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
88319109 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
88319156 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
88319202 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
88319239 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:88319218 original size:93 final size:93
Alignment explanation
Indices: 88319059--88319230 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
88319049 GGGATATTTG
* *
88319059 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
88319124 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
88319152 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
88319217 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
88319231 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:88322204 original size:15 final size:15
Alignment explanation
Indices: 88322184--88322252 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
88322174 GTATCTTGGG
88322184 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
88322199 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
88322214 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
88322229 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
88322244 TTTCTTTAT
1 TTTCTTTAT
88322253 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:88322253 original size:30 final size:30
Alignment explanation
Indices: 88322175--88322262 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
88322165 CATAGTATCG
* * * *
88322175 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
88322205 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
88322235 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
88322263 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:88324695 original size:46 final size:46
Alignment explanation
Indices: 88324645--88324820 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
88324635 TATTTGGGCA
88324645 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
88324691 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
88324738 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
88324784 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
88324821 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:88324800 original size:93 final size:93
Alignment explanation
Indices: 88324641--88324812 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
88324631 TGGATATTTG
* *
88324641 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
88324706 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
88324734 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
88324799 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
88324813 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:88338931 original size:27 final size:28
Alignment explanation
Indices: 88338901--88339006 Score: 121
Period size: 27 Copynumber: 3.9 Consensus size: 28
88338891 TAAGATGACC
*
88338901 GAAATAGCCCC-ATAGGGTAAAATGATT
1 GAAATATCCCCTATAGGGTAAAATGATT
* **
88338928 GAAATA-CCCCTATAGGGTAAAAAGACC
1 GAAATATCCCCTATAGGGTAAAATGATT
* *
88338955 GAAATAT-CCCTATAAGGTATAATGATT
1 GAAATATCCCCTATAGGGTAAAATGATT
*
88338982 GTAAT-TCCCCTATAGGGTAAAATGA
1 GAAATATCCCCTATAGGGTAAAATGA
88339007 CTTTTTTGCC
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
26 5 0.08
27 60 0.92
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (28 bp):
GAAATATCCCCTATAGGGTAAAATGATT
Found at i:88338980 original size:54 final size:54
Alignment explanation
Indices: 88338897--88339003 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 54
88338887 CGAGTAAGAT
*
88338897 GACCGAAATAGCCCCATAGGGTAAAATGATTGAAATACCCCTATAGGGTAAAAA
1 GACCGAAATAGCCCCATAAGGTAAAATGATTGAAATACCCCTATAGGGTAAAAA
* * * * *
88338951 GACCGAAATATCCCTATAAGGTATAATGATTGTAATTCCCCTATAGGGTAAAA
1 GACCGAAATAGCCCCATAAGGTAAAATGATTGAAATACCCCTATAGGGTAAAA
88339004 TGACTTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (54 bp):
GACCGAAATAGCCCCATAAGGTAAAATGATTGAAATACCCCTATAGGGTAAAAA
Found at i:88339803 original size:20 final size:22
Alignment explanation
Indices: 88339778--88339818 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
88339768 CCTTTCTAAA
88339778 TTTTATT-TCTT-AATTTATAC
1 TTTTATTGTCTTCAATTTATAC
*
88339798 TTTTATTGTTTTCAATTTATA
1 TTTTATTGTCTTCAATTTATA
88339819 ACTGGTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTTATTGTCTTCAATTTATAC
Found at i:88343393 original size:28 final size:29
Alignment explanation
Indices: 88343353--88343423 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
88343343 GACAAGATTG
*
88343353 GCACTAAGTGTGCGAGTTTG-AT-TATATA
1 GCACTAAGTGTGCGAG-CTGAATGTATATA
88343381 GCACTAAGTGTGCGAGCTGAATGTATATA
1 GCACTAAGTGTGCGAGCTGAATGTATATA
88343410 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
88343424 GATTCACTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 18 0.45
29 20 0.50
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTGAATGTATATA
Found at i:88349854 original size:28 final size:28
Alignment explanation
Indices: 88349785--88349885 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
88349775 GACAAGATTG
* * * *
88349785 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
88349815 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
88349843 GCACTAAGTGTGCGAG-CTGAATGTATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
88349872 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
88349886 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 24 0.38
29 20 0.31
30 18 0.28
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:88349879 original size:29 final size:28
Alignment explanation
Indices: 88349814--88349885 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 28
88349804 AAAATTGTAC
*
88349814 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGATTATAT
88349842 AGCACTAAGTGTGCGAG-CTGAATGTATAT
1 AGCACTAAGTGTGCGAGTCTG-AT-TATAT
88349871 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
88349886 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGATTATAT
Found at i:88352541 original size:20 final size:20
Alignment explanation
Indices: 88352512--88352558 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
88352502 TTGTGTGTTC
*
88352512 TTTATCTTTATTTT-TATTTA
1 TTTATTTTTATTTTAT-TTTA
88352532 TTTATTTTTATTTTATTTTA
1 TTTATTTTTATTTTATTTTA
88352552 TTT-TTTT
1 TTTATTTT
88352559 CTTAAATTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 20 0.80
21 1 0.04
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTATTTTTATTTTATTTTA
Found at i:88358774 original size:21 final size:21
Alignment explanation
Indices: 88358734--88358775 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
88358724 TGTGCTCTTT
*
88358734 TGGTAGAGATACCTTGATTTA
1 TGGTAGAGATACCTTCATTTA
88358755 TGGTAGAGATA-CTCTCATTTA
1 TGGTAGAGATACCT-TCATTTA
88358776 AAGATGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (21 bp):
TGGTAGAGATACCTTCATTTA
Found at i:88359392 original size:33 final size:33
Alignment explanation
Indices: 88359354--88359420 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
88359344 ACAAGATCTT
88359354 AGTGTTTGCAAAATTAAGCTCAATTACAATGAA
1 AGTGTTTGCAAAATTAAGCTCAATTACAATGAA
*
88359387 AGTGTTTGCAAAATTAAGCTTAATTACAATGAA
1 AGTGTTTGCAAAATTAAGCTCAATTACAATGAA
88359420 A
1 A
88359421 AACACTTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.31
Consensus pattern (33 bp):
AGTGTTTGCAAAATTAAGCTCAATTACAATGAA
Found at i:88370606 original size:14 final size:14
Alignment explanation
Indices: 88370587--88370630 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
88370577 TATGTGCTTA
88370587 TTATGTTTGAATTT
1 TTATGTTTGAATTT
*
88370601 TTATGTGTGAAATTT
1 TTATGTTTG-AATTT
* *
88370616 TTGTGTTTTAATTT
1 TTATGTTTGAATTT
88370630 T
1 T
88370631 GTCGTTTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (14 bp):
TTATGTTTGAATTT
Found at i:88371805 original size:27 final size:29
Alignment explanation
Indices: 88371740--88371807 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
88371730 ATAGGATTCC
*
88371740 GATATGTGATGTGCGAGTAAGACCATGGCATT
1 GATATATG-TGTGCGAGTAAGACCA--GCATT
88371772 GATATATGTGTGCGAGTAAGACCA-CATT
1 GATATATGTGTGCGAGTAAGACCAGCATT
*
88371800 -TTATATGT
1 GATATATGT
88371808 TGGCATCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 7 0.21
28 4 0.12
31 16 0.47
32 7 0.21
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (29 bp):
GATATATGTGTGCGAGTAAGACCAGCATT
Found at i:88371833 original size:56 final size:56
Alignment explanation
Indices: 88371772--88371906 Score: 220
Period size: 56 Copynumber: 2.4 Consensus size: 56
88371762 CCATGGCATT
88371772 GATATATGTGTGCGAGTAAGACCACA-TTTTATA-TGTTGGCATCAATATGTGACTCC
1 GATATATGTGTGCGAGTAAGACCA-AGTTTTATACT-TTGGCATCAATATGTGACTCC
* *
88371828 GATATATGTGTGTGAGTAAGACCAAGTTTTATACTTTGGCATCGATATGTGACTCC
1 GATATATGTGTGCGAGTAAGACCAAGTTTTATACTTTGGCATCAATATGTGACTCC
88371884 GATATATGTGTGCGAGTAAGACC
1 GATATATGTGTGCGAGTAAGACC
88371907 CTGTTTAGGA
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
55 1 0.01
56 72 0.97
57 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (56 bp):
GATATATGTGTGCGAGTAAGACCAAGTTTTATACTTTGGCATCAATATGTGACTCC
Found at i:88371924 original size:56 final size:55
Alignment explanation
Indices: 88371772--88371935 Score: 206
Period size: 56 Copynumber: 2.9 Consensus size: 55
88371762 CCATGGCATT
88371772 GATATATGTGTGCGAGTAAGACCACAT-TTTATA-TGTTGGCATCAATATGTGACTCC
1 GATATATGTGTGCGAGTAAGACC-C-TGTTTATACTG-TGGCATCAATATGTGACTCC
* ** * *
88371828 GATATATGTGTGTGAGTAAGACCAAGTTTTATACTTTGGCATCGATATGTGACTCC
1 GATATATGTGTGCGAGTAAGACCCTG-TTTATACTGTGGCATCAATATGTGACTCC
* *
88371884 GATATATGTGTGCGAGTAAGACCCTGTTTAGGACAGTGGCATCAATATGTGA
1 GATATATGTGTGCGAGTAAGACCCTGTTTA-TACTGTGGCATCAATATGTGA
88371936 TTACATGTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
55 4 0.04
56 87 0.95
57 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (55 bp):
GATATATGTGTGCGAGTAAGACCCTGTTTATACTGTGGCATCAATATGTGACTCC
Found at i:88384346 original size:39 final size:39
Alignment explanation
Indices: 88384292--88384548 Score: 383
Period size: 39 Copynumber: 6.5 Consensus size: 39
88384282 TAATGGAGAA
**
88384292 TTATATCCGGGCTAAGTCCCGAAGTTATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
88384331 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
88384370 TTATATCCGGGCTAAGTCCCGAAGGAATTCGTGCTGGTA
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
88384409 TTATATCTGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
**
88384448 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTTTTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
88384487 TTATATCCGGGCTAAAGTCCC-ACAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGA-AGGCATTCGTGCTGGTG
88384526 TTATATCCGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
88384549 CATGCTTTGT
Statistics
Matches: 200, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
39 180 0.90
40 20 0.10
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:88391781 original size:40 final size:40
Alignment explanation
Indices: 88391736--88391903 Score: 207
Period size: 40 Copynumber: 4.2 Consensus size: 40
88391726 CGGAATACAA
88391736 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* * * *
88391776 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* **
88391816 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
* *
88391856 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTCTTAGC
88391896 CCGGATAT
1 CCGGATAT
88391904 CATTCAATTG
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 108 0.96
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
Found at i:88391876 original size:80 final size:80
Alignment explanation
Indices: 88391736--88391903 Score: 241
Period size: 80 Copynumber: 2.1 Consensus size: 80
88391726 CGGAATACAA
* *
88391736 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATG
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
*
88391801 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
** *
88391816 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATA-AA-GTCACTAGCACAAT
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACG--ACTAGCACAAA
*
88391879 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
88391896 CCGGATAT
1 CCGGATAT
88391904 CATTCAATTG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
78 1 0.01
79 2 0.03
80 76 0.96
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (80 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:88401229 original size:30 final size:29
Alignment explanation
Indices: 88401157--88401221 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
88401147 TGACGAGATT
* *
88401157 GGCACTAAGTGTGCATGCTGGAAATATAT
1 GGCACTAAGTGTGCATGCTGGAAAAATAC
88401186 GGCACTAAGTGTGCATGCTGGAAAAAATAC
1 GGCACTAAGTGTGCATGCTGG-AAAAATAC
88401216 GGCACT
1 GGCACT
88401222 GGGTGTGCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
29 21 0.64
30 12 0.36
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (29 bp):
GGCACTAAGTGTGCATGCTGGAAAAATAC
Found at i:88404863 original size:20 final size:20
Alignment explanation
Indices: 88404838--88404881 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
88404828 TGTTTGTGAG
88404838 TTTTGAAACTCGAGATATAA
1 TTTTGAAACTCGAGATATAA
88404858 TTTTGAAACTCGAGATATAA
1 TTTTGAAACTCGAGATATAA
88404878 TTTT
1 TTTT
88404882 TAAGGGGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (20 bp):
TTTTGAAACTCGAGATATAA
Found at i:88407875 original size:13 final size:13
Alignment explanation
Indices: 88407857--88407882 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
88407847 AGGGGTTTAT
88407857 TTATCTAAACTAA
1 TTATCTAAACTAA
88407870 TTATCTAAACTAA
1 TTATCTAAACTAA
88407883 GGATGCACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:88410934 original size:39 final size:40
Alignment explanation
Indices: 88410854--88410938 Score: 100
Period size: 44 Copynumber: 2.0 Consensus size: 40
88410844 GGAACTATGT
* *
88410854 CATCTGAACTCATGAGTTGTGGTCTGAGTTCATGATATATGTGA
1 CATCTGAACTCATAAGTTGTGGTC---G-TCATAATATATGTGA
*
88410898 CATCTGAACTCATAAGTTGTGGTC-TCATAATTTATGTGA
1 CATCTGAACTCATAAGTTGTGGTCGTCATAATATATGTGA
88410937 CA
1 CA
88410939 CATTATATGG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
39 15 0.39
44 23 0.61
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (40 bp):
CATCTGAACTCATAAGTTGTGGTCGTCATAATATATGTGA
Found at i:88415336 original size:45 final size:45
Alignment explanation
Indices: 88415279--88415498 Score: 271
Period size: 45 Copynumber: 4.9 Consensus size: 45
88415269 GATTATCATT
* * * *
88415279 TCACCAGCATTATAGCCTGCTAGGCTCGAAA-GCTCGGATAGTATC
1 TCACCGGCATAATAGCCTGCTAGGCTC-AAAGGCCCGAATAGTATC
* * *
88415324 TCATCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATT
1 TCACCGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* * * * * *
88415369 TCACCAGCATCATAGCCTACTAGGCTCAAAGGCCCAAATAATGTC
1 TCACCGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* * * *
88415414 TCACCGACATAATAGCCTACTAGGCTCAAAGGCCAGAATAGTGTC
1 TCACCGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
88415459 TCACCGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATA
1 TCACCGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATA
88415499 TAATACCAGT
Statistics
Matches: 152, Mismatches: 22, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
44 3 0.02
45 149 0.98
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
TCACCGGCATAATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
Found at i:88415539 original size:38 final size:38
Alignment explanation
Indices: 88415491--88415614 Score: 203
Period size: 38 Copynumber: 3.3 Consensus size: 38
88415481 GGCTCAAAGG
* * * *
88415491 CCCGAATATAATACCAGTACTAGGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
*
88415529 CCTGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
88415567 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
88415605 CCCGGATATA
1 CCCGGATATA
88415615 CATCAAATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 80 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:88425463 original size:48 final size:48
Alignment explanation
Indices: 88425315--88425480 Score: 185
Period size: 48 Copynumber: 3.5 Consensus size: 48
88425305 TATGTATGCT
* *
88425315 AGTGTAAGACATGTCTGGGACATGCATCGACCAC-ATAT-TA-AGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATACA-AGCC
* * * * **
88425361 AGTGTAAGACATGTCTAGGATATGCATTGTCCTCGAGATATACCGGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATACAAGCC
* * *
88425409 AATGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATACAAGCC
* *
88425457 AGTGTAAGACCTGTTTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
88425481 GTGTCAGCTT
Statistics
Matches: 98, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
46 29 0.30
47 3 0.03
48 66 0.67
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACCTCGAGATATACAAGCC
Found at i:88427349 original size:20 final size:20
Alignment explanation
Indices: 88427311--88427349 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
88427301 ATCAAATTGA
* *
88427311 ATTGTCATTAAATGGATTTG
1 ATTGTAATTAAATGCATTTG
*
88427331 ATTGTAATTAGATGCATTT
1 ATTGTAATTAAATGCATTT
88427350 ATATAATTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (20 bp):
ATTGTAATTAAATGCATTTG
Found at i:88431756 original size:2 final size:2
Alignment explanation
Indices: 88431749--88431780 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
88431739 GTGAGACTCT
88431749 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
88431781 TGAAAACATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:88436623 original size:21 final size:21
Alignment explanation
Indices: 88436597--88436641 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
88436587 CATGCAATTA
88436597 CTATGTTGAAAAATTTCAAAT
1 CTATGTTGAAAAATTTCAAAT
88436618 CTATGTTGAAAAATTTCAAAT
1 CTATGTTGAAAAATTTCAAAT
88436639 CTA
1 CTA
88436642 CAGTGTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (21 bp):
CTATGTTGAAAAATTTCAAAT
Found at i:88446012 original size:30 final size:30
Alignment explanation
Indices: 88445977--88446034 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
88445967 CACAGCCATG
88445977 ACACACGGGCGTGTGG-TCTACCCGTGTGTC
1 ACACACGGGCGTGTGGATC-ACCCGTGTGTC
88446007 ACACACGGGCGTGTGGATCACCCGTGTG
1 ACACACGGGCGTGTGGATCACCCGTGTG
88446035 GAAGTGCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.21
Consensus pattern (30 bp):
ACACACGGGCGTGTGGATCACCCGTGTGTC
Found at i:88453005 original size:20 final size:20
Alignment explanation
Indices: 88452980--88453019 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
88452970 TGTTTCACGT
*
88452980 TCGACGTGGTTTTAAAGACA
1 TCGACGTGGTCTTAAAGACA
88453000 TCGACGTGGTCTTAAAGACA
1 TCGACGTGGTCTTAAAGACA
88453020 ATTAAGTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (20 bp):
TCGACGTGGTCTTAAAGACA
Found at i:88454546 original size:57 final size:58
Alignment explanation
Indices: 88454420--88454548 Score: 138
Period size: 58 Copynumber: 2.2 Consensus size: 58
88454410 ACCTCATTAC
* * *
88454420 AAAAAGGATTTAGCCCGGATGGGTAATCCTAATACAAATCCTCTCGAGCATATGTTAT
1 AAAAAGGATTTAGCCCGGACGGGTAATCCTAATACAAATCCTCTAGAGCATATGTCAT
* ** * * *
88454478 AGATTGGATTTAGTCTGGACGGGTAATCC-AGAT-CAAGCTCCT-TAGAGCATATGTCAT
1 AAAAAGGATTTAGCCCGGACGGGTAATCCTA-ATACAA-ATCCTCTAGAGCATATGTCAT
88454535 AAAAAGGATTTAGC
1 AAAAAGGATTTAGC
88454549 TTAGACTGGT
Statistics
Matches: 56, Mismatches: 13, Indels: 5
0.76 0.18 0.07
Matches are distributed among these distances:
57 27 0.48
58 29 0.52
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (58 bp):
AAAAAGGATTTAGCCCGGACGGGTAATCCTAATACAAATCCTCTAGAGCATATGTCAT
Found at i:88457475 original size:25 final size:25
Alignment explanation
Indices: 88457435--88457557 Score: 130
Period size: 25 Copynumber: 5.0 Consensus size: 25
88457425 TCATTAGGGA
*
88457435 TTACCGATTGT-AGCTCGTGAGAGC
1 TTACCGATTCTCAGCTCGTGAGAGC
*
88457459 TTATCGATTCTCAGCTCGT-ATGAGC
1 TTACCGATTCTCAGCTCGTGA-GAGC
*
88457484 TTACCGATT-GCAGCTCGTGAGAGC
1 TTACCGATTCTCAGCTCGTGAGAGC
* *
88457508 TTAGCGATTCTCAGCTCGT-ATGAAC
1 TTACCGATTCTCAGCTCGTGA-GAGC
*
88457533 TTACCGATT-TACAGCTTGTGAGAGC
1 TTACCGATTCT-CAGCTCGTGAGAGC
88457558 ATATTGATTC
Statistics
Matches: 82, Mismatches: 10, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
24 32 0.39
25 49 0.60
26 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (25 bp):
TTACCGATTCTCAGCTCGTGAGAGC
Found at i:88457507 original size:49 final size:49
Alignment explanation
Indices: 88457435--88457581 Score: 195
Period size: 49 Copynumber: 3.0 Consensus size: 49
88457425 TCATTAGGGA
*
88457435 TTACCGATTGTAGCTCGTGAGAGCTTATCGATTCTCAGCTCGTATGAGC
1 TTACCGATTGCAGCTCGTGAGAGCTTATCGATTCTCAGCTCGTATGAGC
* *
88457484 TTACCGATTGCAGCTCGTGAGAGCTTAGCGATTCTCAGCTCGTATGAAC
1 TTACCGATTGCAGCTCGTGAGAGCTTATCGATTCTCAGCTCGTATGAGC
* * * * ** *
88457533 TTACCGATTTACAGCTTGTGAGAGCATATTGATTCAAAACTCGTATGAG
1 TTACCGA-TTGCAGCTCGTGAGAGCTTATCGATTCTCAGCTCGTATGAG
88457582 TATACATGTA
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
49 53 0.62
50 32 0.38
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.31
Consensus pattern (49 bp):
TTACCGATTGCAGCTCGTGAGAGCTTATCGATTCTCAGCTCGTATGAGC
Found at i:88459488 original size:25 final size:25
Alignment explanation
Indices: 88459456--88459503 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
88459446 TTATAAGATG
88459456 AAAATGACTATTTTACCCCTAGGTA
1 AAAATGACTATTTTACCCCTAGGTA
88459481 AAAATGACTATTTTACCCCTAGG
1 AAAATGACTATTTTACCCCTAGG
88459504 GTTTAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.31
Consensus pattern (25 bp):
AAAATGACTATTTTACCCCTAGGTA
Found at i:88459636 original size:61 final size:61
Alignment explanation
Indices: 88459571--88459694 Score: 239
Period size: 61 Copynumber: 2.0 Consensus size: 61
88459561 GCACATGATA
*
88459571 TGTATGATATGCACATGATGTATTCATTATGCATGGGTTGGGTTTATATGGATGGAGGAAG
1 TGTATGATATGCACATGATGTATTCATTATGCATGGGTTGGGTTTATATGGATGGAGAAAG
88459632 TGTATGATATGCACATGATGTATTCATTATGCATGGGTTGGGTTTATATGGATGGAGAAAG
1 TGTATGATATGCACATGATGTATTCATTATGCATGGGTTGGGTTTATATGGATGGAGAAAG
88459693 TG
1 TG
88459695 CAAAAGGGCT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.27, C:0.06, G:0.31, T:0.36
Consensus pattern (61 bp):
TGTATGATATGCACATGATGTATTCATTATGCATGGGTTGGGTTTATATGGATGGAGAAAG
Found at i:88459789 original size:26 final size:25
Alignment explanation
Indices: 88459696--88459815 Score: 172
Period size: 24 Copynumber: 4.8 Consensus size: 25
88459686 GAGAAAGTGC
*
88459696 AAAAGGGCTATGCCCCAG-TTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
88459720 AAAAGGGCTTTGCCCCAG-TTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
88459744 AAAAGGGCTTTGCCCTAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* *
88459769 AAAAGGGCTTTTGCCCCAGTTTATCA
1 AAAAGGGC-TTTGCCCCAGTTTACCG
88459795 AAAAGGGCTTTTGCCCCAGTT
1 AAAAGGGC-TTTGCCCCAGTT
88459816 ATTAAAAGAG
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
24 40 0.45
25 14 0.16
26 35 0.39
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:88459828 original size:25 final size:26
Alignment explanation
Indices: 88459706--88459828 Score: 102
Period size: 24 Copynumber: 4.9 Consensus size: 26
88459696 AAAAGGGCTA
*
88459706 TGCCCCAG-TTACCGAAAAG-GGC-TT
1 TGCCCCAGTTTATC-AAAAGAGGCTTT
*
88459730 TGCCCCAG-TTACCGAAAAG-GGC-TT
1 TGCCCCAGTTTATC-AAAAGAGGCTTT
* *
88459754 TGCCCTAGTTTACCGAAAAG-GGCTTT
1 TGCCCCAGTTTATC-AAAAGAGGCTTT
88459780 TGCCCCAGTTTATCAAAA-AGGGCTTT
1 TGCCCCAGTTTATCAAAAGA-GGCTTT
*
88459806 TGCCCCAG-TTATTAAAAGAGGCT
1 TGCCCCAGTTTATCAAAAGAGGCT
88459829 GGGCCTCTAG
Statistics
Matches: 90, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
24 31 0.34
25 30 0.33
26 29 0.32
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (26 bp):
TGCCCCAGTTTATCAAAAGAGGCTTT
Found at i:88460073 original size:31 final size:31
Alignment explanation
Indices: 88460035--88460107 Score: 137
Period size: 31 Copynumber: 2.4 Consensus size: 31
88460025 TTGTTACAGT
88460035 AAAGGCTTCGGCCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
88460066 AAAGGCTTCGGCCCAGTGATATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
88460097 AAAGGCTTCGG
1 AAAGGCTTCGG
88460108 TGCAGTATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:88469101 original size:40 final size:40
Alignment explanation
Indices: 88469056--88469223 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
88469046 CGGAATATAA
88469056 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
88469096 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
88469136 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
88469176 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
88469216 CCGGATAT
1 CCGGATAT
88469224 CATTCAATTT
Statistics
Matches: 107, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 106 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:88478689 original size:40 final size:40
Alignment explanation
Indices: 88478644--88478810 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
88478634 CGGAATATAA
88478644 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
88478684 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
88478724 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
88478764 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
88478803 CCGGATAT
1 CCGGATAT
88478811 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:88480667 original size:25 final size:26
Alignment explanation
Indices: 88480615--88480710 Score: 135
Period size: 26 Copynumber: 3.8 Consensus size: 26
88480605 GAGGAAGTGC
*
88480615 AAAAGGGC-TATGCCCCAG-TTACCG
1 AAAAGGGCTTTTGCCCCAGTTTACCG
*
88480639 AAAAGGGC-TTTGCCCTAGTTTACCG
1 AAAAGGGCTTTTGCCCCAGTTTACCG
* *
88480664 AAAAGGGCTTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTTGCCCCAGTTTACCG
88480690 AAAAGGGCTTTTGCCCCAGTT
1 AAAAGGGCTTTTGCCCCAGTT
88480711 ATTAAAAGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 16 0.25
25 14 0.22
26 35 0.54
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCCAGTTTACCG
Found at i:88480723 original size:25 final size:26
Alignment explanation
Indices: 88480625--88480723 Score: 93
Period size: 25 Copynumber: 3.9 Consensus size: 26
88480615 AAAAGGGCTA
*
88480625 TGCCCCAG-TTACCGAAAAG-GGC-TT
1 TGCCCCAGTTTATC-AAAAGAGGCTTT
* *
88480649 TGCCCTAGTTTACCGAAAAG-GGCTTT
1 TGCCCCAGTTTATC-AAAAGAGGCTTT
88480675 TGCCCCAGTTTATCAAAA-AGGGCTTT
1 TGCCCCAGTTTATCAAAAGA-GGCTTT
*
88480701 TGCCCCAG-TTATTAAAAGAGGCT
1 TGCCCCAGTTTATCAAAAGAGGCT
88480724 AGTCCTCCAG
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
24 7 0.11
25 30 0.45
26 29 0.44
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.27
Consensus pattern (26 bp):
TGCCCCAGTTTATCAAAAGAGGCTTT
Found at i:88480970 original size:31 final size:31
Alignment explanation
Indices: 88480929--88481014 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
88480919 ATTGTTACAG
* *
88480929 TAAAGGCTTCGGCCTAGTGATATGAATAATGA
1 TAAAAGCTTCGGCCCAGTGATATGAATAAT-A
88480961 -AAAAGCTTCGGCCCAGTGATATGAATAATA
1 TAAAAGCTTCGGCCCAGTGATATGAATAATA
*
88480991 TAAAGGCTTCGGCCCAGTGATATG
1 TAAAAGCTTCGGCCCAGTGATATG
88481015 TTGAGATTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (31 bp):
TAAAAGCTTCGGCCCAGTGATATGAATAATA
Found at i:88482712 original size:29 final size:29
Alignment explanation
Indices: 88482679--88482735 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
88482669 CTCAACAGTG
* *
88482679 TGTGACACACGGCCAGGTGAGTGACCGTA
1 TGTGACACACGACCAGGTGAATGACCGTA
88482708 TGTGACACACGACCAGGTGAATGACCGT
1 TGTGACACACGACCAGGTGAATGACCGT
88482736 GTGTCCCCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.26, C:0.25, G:0.32, T:0.18
Consensus pattern (29 bp):
TGTGACACACGACCAGGTGAATGACCGTA
Found at i:88488521 original size:11 final size:11
Alignment explanation
Indices: 88488493--88488522 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
88488483 AGAAGAAGAA
88488493 AAAGAAAAACT
1 AAAGAAAAACT
88488504 AAGAGAAAAACT
1 AA-AGAAAAACT
88488516 AAAGAAA
1 AAAGAAA
88488523 CCTTGAGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.73, C:0.07, G:0.13, T:0.07
Consensus pattern (11 bp):
AAAGAAAAACT
Found at i:88489055 original size:13 final size:13
Alignment explanation
Indices: 88489039--88489067 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
88489029 CTTCAAGCAA
88489039 AATGTGGAAGCCT
1 AATGTGGAAGCCT
88489052 AATGTGGAAGCCT
1 AATGTGGAAGCCT
88489065 AAT
1 AAT
88489068 TTGCCATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (13 bp):
AATGTGGAAGCCT
Found at i:88489184 original size:20 final size:20
Alignment explanation
Indices: 88489159--88489198 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
88489149 ACGTGAAACA
88489159 CATTGCTGATGGAAATATAG
1 CATTGCTGATGGAAATATAG
88489179 CATTGCTGATGGAAATATAG
1 CATTGCTGATGGAAATATAG
88489199 AAAGGCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (20 bp):
CATTGCTGATGGAAATATAG
Found at i:88493857 original size:2 final size:2
Alignment explanation
Indices: 88493850--88493889 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
88493840 TGCATGTGAT
88493850 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
88493890 AACTTACTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:88497319 original size:30 final size:30
Alignment explanation
Indices: 88497283--88497376 Score: 163
Period size: 30 Copynumber: 3.1 Consensus size: 30
88497273 GCAATCCGTA
88497283 TGTCACACACGGCCTAGACAAACGCACGTG
1 TGTCACACACGGCCTAGACAAACGCACGTG
88497313 TGTCACACACGGCCTAGACACAA-GCACGTG
1 TGTCACACACGGCCTAGACA-AACGCACGTG
*
88497343 TGTCACACACGGCCTAGACACACGCACGTG
1 TGTCACACACGGCCTAGACAAACGCACGTG
88497373 TGTC
1 TGTC
88497377 TACCCGTGTG
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
29 1 0.02
30 58 0.95
31 2 0.03
ACGTcount: A:0.28, C:0.34, G:0.23, T:0.15
Consensus pattern (30 bp):
TGTCACACACGGCCTAGACAAACGCACGTG
Found at i:88504934 original size:47 final size:47
Alignment explanation
Indices: 88504880--88505010 Score: 172
Period size: 47 Copynumber: 2.8 Consensus size: 47
88504870 TACAATCGAT
* * *
88504880 AAGTACCTATACCATTGCCCGTAGCCAAATCAAGGTAACTTATCCCG
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCA
* * * *
88504927 GAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAGCTCCTCTCA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCA
* * *
88504974 AAATACCTATATCATGGCCTGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
88505011 TTATTCGCAC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCA
Found at i:88506177 original size:3 final size:3
Alignment explanation
Indices: 88506169--88506224 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
88506159 AATTTGGATG
88506169 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
88506217 TTA TTA TT
1 TTA TTA TT
88506225 TTGTATGTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:88508752 original size:20 final size:21
Alignment explanation
Indices: 88508709--88508754 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
88508699 ACTGTTTTGT
88508709 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
88508729 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
88508748 TATGGGC
1 TATGGGC
88508755 ATGCCCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:88516207 original size:54 final size:52
Alignment explanation
Indices: 88516146--88516272 Score: 139
Period size: 54 Copynumber: 2.4 Consensus size: 52
88516136 CCTCAATTTA
* * *
88516146 TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATT
1 TAAAATTACCAAAATACCCTCGATTTACAGAATTACAGTTTTACCCTCGATT
*** *
88516198 TACAGAATTA-CAGTTTTACCCTCGATTTACAGAATTATAGTTTTACCCTCGATT
1 TA-A-AATTACCA-AAATACCCTCGATTTACAGAATTACAGTTTTACCCTCGATT
88516252 AGTAAAATTACCAAAATACCC
1 --TAAAATTACCAAAATACCC
88516273 CTGGTTTGTA
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
52 2 0.03
53 3 0.05
54 50 0.83
55 3 0.05
56 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (52 bp):
TAAAATTACCAAAATACCCTCGATTTACAGAATTACAGTTTTACCCTCGATT
Done.