Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 181 of 187
Found at i:54375739 original size:42 final size:42
Alignment explanation
Indices: 54375639--54375922 Score: 392
Period size: 42 Copynumber: 6.7 Consensus size: 42
54375629 GTTTACAAAC
54375639 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-AA
* *
54375682 AAAAACACCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
54375724 AAAAACGCCGCTAAAGACCATGTCCTTTAGCGGCGCTTATAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
54375766 TAAAAACGCCGCTAAAGACGATGTTCTTTAGCGGCGCTTAG-A
1 -AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* * *
54375808 AAAAACGCCACTAAAGAACATGGTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* ** * *
54375850 AAAGACGTTGCCAAAGACCATGTTCTTTAGCGGCGCTTTGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
54375892 AGAAACGCCGCTAAAGAGCAT-TGTCTTTAGC
1 AAAAACGCCGCTAAAGACCATGT-TCTTTAGC
54375923 AGCGTTTTTT
Statistics
Matches: 211, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
41 37 0.18
42 99 0.47
43 75 0.36
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:54375948 original size:126 final size:126
Alignment explanation
Indices: 54375639--54375971 Score: 386
Period size: 126 Copynumber: 2.6 Consensus size: 126
54375629 GTTTACAAAC
* * * *
54375639 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAACACCGCTAAAGACCATG
1 AAAAACGCCGCTAAAGACGATGTTCTTTAGCAGCGCTTAG--AAAAAACGCCGCTAAAGAACATG
* * *
54375704 TTCTTTAGCGGCACTTAGAAAAAAACGCCGCTAAAGACCATGTCCTTTAGCGGCGCTTATAAT
64 GTCTTTAGCGGCGCTTAGAAAAAAACGCCGCCAAAGACCATGTCCTTTAGCGGCGCTTATAAT
* *
54375767 AAAAACGCCGCTAAAGACGATGTTCTTTAGCGGCGCTTAGAAAAAACGCCACTAAAGAACATGGT
1 AAAAACGCCGCTAAAGACGATGTTCTTTAGCAGCGCTTAGAAAAAACGCCGCTAAAGAACATGGT
* ** *
54375832 CTTTAGCGGCGCTTAGAAAAAGACGTTGCCAAAGACCATGTTCTTTAGCGGCGCTT-TGAA-
66 CTTTAGCGGCGCTTAGAAAAAAACGCCGCCAAAGACCATGTCCTTTAGCGGCGCTTAT-AAT
* * ***** *
54375892 AGAAACGCCGCTAAAGA-GCAT-TGTCTTTAGCAGCGTTTTTTTCTAAGCGCCGCTAAAGAACAT
1 AAAAACGCCGCTAAAGACG-ATGT-TCTTTAGCAGCG-CTTAGAAAAAACGCCGCTAAAGAACAT
*
54375955 GGTCTTTAGTGGCGCTT
63 GGTCTTTAGCGGCGCTT
54375972 TTTCACAAAA
Statistics
Matches: 179, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
124 2 0.01
125 30 0.17
126 108 0.60
128 39 0.22
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (126 bp):
AAAAACGCCGCTAAAGACGATGTTCTTTAGCAGCGCTTAGAAAAAACGCCGCTAAAGAACATGGT
CTTTAGCGGCGCTTAGAAAAAAACGCCGCCAAAGACCATGTCCTTTAGCGGCGCTTATAAT
Found at i:54375950 original size:84 final size:83
Alignment explanation
Indices: 54375639--54375971 Score: 323
Period size: 84 Copynumber: 4.0 Consensus size: 83
54375629 GTTTACAAAC
* ** * * *
54375639 AAAAACGCCGCTAAAGACCA-TGTTCTTTAGCGGCGCTTAGAAAAAAAACACCGCTAAAGACCAT
1 AAAAACGCCGCTAAAGAACATTG-TCTTTAGCGGCG-TTTTAATAAAAGCGCCGCTAAAGACCAT
*
54375703 GTTCTTTAGCGGCACTTAGAA
64 GTTCTTTAGCGGCGCTTAG-A
* * * *
54375724 AAAAACGCCGCTAAAGACCA-TGTCCTTTAGCGGCGCTTATAATAAAAACGCCGCTAAAGACGAT
1 AAAAACGCCGCTAAAGAACATTGT-CTTTAGCGGCG-TTTTAATAAAAGCGCCGCTAAAGACCAT
54375788 GTTCTTTAGCGGCGCTTAGA
64 GTTCTTTAGCGGCGCTTAGA
* * * ** *
54375808 AAAAACGCCACTAAAGAACATGGTCTTTAGCGGCG-CTTAGA-AAAAGACGTTGCCAAAGACCAT
1 AAAAACGCCGCTAAAGAACATTGTCTTTAGCGGCGTTTTA-ATAAAAG-CGCCGCTAAAGACCAT
*
54375871 GTTCTTTAGCGGCGCTTTGA
64 GTTCTTTAGCGGCGCTTAGA
* * ** ** *
54375891 AAGAAACGCCGCTAAAGAGCATTGTCTTTAGCAGCGTTTTTTTCTAAGCGCCGCTAAAGAACATG
1 AA-AAACGCCGCTAAAGAACATTGTCTTTAGCGGCGTTTTAATAAAAGCGCCGCTAAAGACCATG
* *
54375956 GTCTTTAGTGGCGCTT
65 TTCTTTAGCGGCGCTT
54375972 TTTCACAAAA
Statistics
Matches: 210, Mismatches: 31, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
82 6 0.03
83 34 0.16
84 87 0.41
85 83 0.40
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (83 bp):
AAAAACGCCGCTAAAGAACATTGTCTTTAGCGGCGTTTTAATAAAAGCGCCGCTAAAGACCATGT
TCTTTAGCGGCGCTTAGA
Found at i:54376318 original size:21 final size:21
Alignment explanation
Indices: 54376292--54376339 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
54376282 TTTTGCTCTG
*
54376292 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
54376313 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
54376334 CGCTGC
1 CTCTGC
54376340 CGCCTCTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.04, C:0.46, G:0.21, T:0.29
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:54377069 original size:9 final size:9
Alignment explanation
Indices: 54377055--54377235 Score: 128
Period size: 9 Copynumber: 20.9 Consensus size: 9
54377045 GGCGTCCAAT
54377055 TTATGTAAG
1 TTATGTAAG
54377064 TTATGTAAG
1 TTATGTAAG
*
54377073 TTATGTAGG
1 TTATGTAAG
*
54377082 CTATGT-A-
1 TTATGTAAG
* *
54377089 TTATCTAAA
1 TTATGTAAG
*
54377098 TAATGTAAG
1 TTATGTAAG
* *
54377107 CTA-GGAAGG
1 TTATGTAA-G
54377116 TT-TGT-A-
1 TTATGTAAG
* *
54377122 TTATCTAAA
1 TTATGTAAG
*
54377131 TAATGTAAG
1 TTATGTAAG
* *
54377140 CTA-GGAAGG
1 TTATGTAA-G
54377149 TTATGT--G
1 TTATGTAAG
54377156 TTATGTAAG
1 TTATGTAAG
*
54377165 TTATTTAAG
1 TTATGTAAG
*
54377174 TTATGCAAG
1 TTATGTAAG
* *
54377183 TTATTTAAT
1 TTATGTAAG
54377192 TTATGTAAG
1 TTATGTAAG
54377201 TTATGTAAG
1 TTATGTAAG
*
54377210 TTATGTAAT
1 TTATGTAAG
54377219 TTATGTAAG
1 TTATGTAAG
54377228 TTATGTAA
1 TTATGTAA
54377236 TTAGAAATTT
Statistics
Matches: 129, Mismatches: 32, Indels: 22
0.70 0.17 0.12
Matches are distributed among these distances:
6 2 0.02
7 13 0.10
8 9 0.07
9 104 0.81
10 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (9 bp):
TTATGTAAG
Found at i:54377124 original size:33 final size:34
Alignment explanation
Indices: 54377083--54377159 Score: 138
Period size: 33 Copynumber: 2.3 Consensus size: 34
54377073 TTATGTAGGC
54377083 TATGTATTATCTAAATAATGTAAGCTAGGAAGGT
1 TATGTATTATCTAAATAATGTAAGCTAGGAAGGT
54377117 T-TGTATTATCTAAATAATGTAAGCTAGGAAGGT
1 TATGTATTATCTAAATAATGTAAGCTAGGAAGGT
*
54377150 TATGTGTTAT
1 TATGTATTAT
54377160 GTAAGTTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 33 0.80
34 8 0.20
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (34 bp):
TATGTATTATCTAAATAATGTAAGCTAGGAAGGT
Found at i:54377403 original size:112 final size:112
Alignment explanation
Indices: 54377206--54377555 Score: 578
Period size: 112 Copynumber: 3.1 Consensus size: 112
54377196 GTAAGTTATG
54377206 TAAGTTATGTAATTTATGTAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTAATCT
1 TAAGTTATGTAATTTATGTAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTAATCT
54377271 TAATATTGTATGAGTTATGTAATTCGAAATCTTACCTTAATATTGTA
66 TAATATTGTATGAGTTATGTAATTCGAAATCTTACCTTAATATTGTA
54377318 TAAGTTATGTAATTTATGTAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTAATCT
1 TAAGTTATGTAATTTATGTAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTAATCT
54377383 TAATATTGTATGAGTTATGTAATTCGAAATCTTACCTTAATATTGTA
66 TAATATTGTATGAGTTATGTAATTCGAAATCTTACCTTAATATTGTA
* * *
54377430 TAAGTTATGTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTTA-C
1 TAAGTTATGTAAT-TTATGTAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTAATC
** * * * * *
54377494 GGAAAATTATATAAGTTATGTAATTCGAAAT-TTGATCTTAATATTATA
65 TTAATATTGTATGAGTTATGTAATTCGAAATCTT-ACCTTAATATTGTA
54377542 TAAGTTATGTAATT
1 TAAGTTATGTAATT
54377556 CGAAATTTTA
Statistics
Matches: 226, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
111 3 0.01
112 177 0.78
113 46 0.20
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (112 bp):
TAAGTTATGTAATTTATGTAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTAATCT
TAATATTGTATGAGTTATGTAATTCGAAATCTTACCTTAATATTGTA
Found at i:54377464 original size:56 final size:56
Alignment explanation
Indices: 54377201--54377554 Score: 469
Period size: 56 Copynumber: 6.3 Consensus size: 56
54377191 TTTATGTAAG
* * *
54377201 TTATGTAAGTTATGTAAT-TTATGTAAGTTATGTAATTAGAAATTTTATCTTAATA
1 TTATATAAGTTATGTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATA
* * * * * *
54377256 TTATATAAGTAATCTTAATATTGTATGAGTTATGTAATTCGAAATCTTACCTTAATA
1 TTATATAAGTTAT-GTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATA
* * *
54377313 TTGTATAAGTTATGTAAT-TTATGTAAGTTATGTAATTAGAAATTTTATCTTAATA
1 TTATATAAGTTATGTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATA
* * * * * *
54377368 TTATATAAGTAATCTTAATATTGTATGAGTTATGTAATTCGAAATCTTACCTTAATA
1 TTATATAAGTTAT-GTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATA
*
54377425 TTGTATAAGTTATGTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATA
1 TTATATAAGTTATGTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATA
* * * *
54377481 TTATATAAGTTACGGAAAATTATATAAGTTATGTAATTCGAAATTTGATCTTAATA
1 TTATATAAGTTATGTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATA
54377537 TTATATAAGTTATGTAAT
1 TTATATAAGTTATGTAAT
54377555 TCGAAATTTT
Statistics
Matches: 253, Mismatches: 42, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
55 53 0.21
56 116 0.46
57 84 0.33
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.46
Consensus pattern (56 bp):
TTATATAAGTTATGTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATA
Found at i:54377549 original size:37 final size:37
Alignment explanation
Indices: 54377499--54377591 Score: 159
Period size: 37 Copynumber: 2.5 Consensus size: 37
54377489 GTTACGGAAA
54377499 ATTATATAAGTTATGTAATTCGAAATTTGATCTTAAT
1 ATTATATAAGTTATGTAATTCGAAATTTGATCTTAAT
*
54377536 ATTATATAAGTTATGTAATTCGAAATTTTATCTTAAT
1 ATTATATAAGTTATGTAATTCGAAATTTGATCTTAAT
* *
54377573 ATTGTGTAAGTTATGTAAT
1 ATTATATAAGTTATGTAAT
54377592 ATTATATAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (37 bp):
ATTATATAAGTTATGTAATTCGAAATTTGATCTTAAT
Found at i:54377592 original size:56 final size:56
Alignment explanation
Indices: 54377532--54377857 Score: 501
Period size: 56 Copynumber: 5.8 Consensus size: 56
54377522 AATTTGATCT
*
54377532 TAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTGTAAGTTATG
1 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTGTGTAAGTTATG
* ** * *
54377588 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAATCT
1 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTGTGTAAGTTAT-G
* *
54377645 TAATATTATATAAGTTATGTAATTCGGAATTTTATCTTAATATTGTGTAAGTTATG
1 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTGTGTAAGTTATG
* **
54377701 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAATAT-
1 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTGTGTAAGT--TATG
* *
54377758 TAATATTATATAAGTTATGTAATTCGGAATTTTATCTTAATATTGTGTAAGTTATG
1 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTGTGTAAGTTATG
54377814 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATT
1 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATT
54377858 ATAAAAGTAA
Statistics
Matches: 241, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
55 3 0.01
56 139 0.58
57 96 0.40
58 3 0.01
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (56 bp):
TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTGTGTAAGTTATG
Found at i:54377646 original size:20 final size:20
Alignment explanation
Indices: 54377621--54377659 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54377611 TCGAAATTTG
54377621 ATCTTAATATTATAAAAGTA
1 ATCTTAATATTATAAAAGTA
*
54377641 ATCTTAATATTATATAAGT
1 ATCTTAATATTATAAAAGT
54377660 TATGTAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
ATCTTAATATTATAAAAGTA
Found at i:54377676 original size:113 final size:113
Alignment explanation
Indices: 54377528--54377871 Score: 670
Period size: 113 Copynumber: 3.0 Consensus size: 113
54377518 TCGAAATTTG
*
54377528 ATCTTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTGTAAGTTATGTAATA
1 ATCTTAATATTATATAAGTTATGTAATTCGGAATTTTATCTTAATATTGTGTAAGTTATGTAATA
54377593 TTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTA
66 TTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTA
54377641 ATCTTAATATTATATAAGTTATGTAATTCGGAATTTTATCTTAATATTGTGTAAGTTATGTAATA
1 ATCTTAATATTATATAAGTTATGTAATTCGGAATTTTATCTTAATATTGTGTAAGTTATGTAATA
54377706 TTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTA
66 TTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTA
*
54377754 ATATTAATATTATATAAGTTATGTAATTCGGAATTTTATCTTAATATTGTGTAAGTTATGTAATA
1 ATCTTAATATTATATAAGTTATGTAATTCGGAATTTTATCTTAATATTGTGTAAGTTATGTAATA
54377819 TTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTA
66 TTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTA
54377867 ATCTT
1 ATCTT
54377872 NNNNNNNNNN
Statistics
Matches: 228, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 228 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.46
Consensus pattern (113 bp):
ATCTTAATATTATATAAGTTATGTAATTCGGAATTTTATCTTAATATTGTGTAAGTTATGTAATA
TTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTA
Found at i:54378046 original size:19 final size:19
Alignment explanation
Indices: 54378024--54378662 Score: 149
Period size: 20 Copynumber: 33.9 Consensus size: 19
54378014 AATTTTATCT
* *
54378024 TAATATTGTGTAAGTTATG
1 TAATATTATATAAGTTATG
54378043 TAATATTATATAAGTTATG
1 TAATATTATATAAGTTATG
** * *
54378062 T-A-ATTCGA-AATTTGATCT
1 TAATATTATATAAGTT-AT-G
* * *
54378080 TAATATTATAAAAGTAATCT
1 TAATATTATATAAGTTAT-G
54378100 TAATATTATATAAGTTAT-
1 TAATATTATATAAGTTATG
* *** * *
54378118 TTA-ATT-CGGAATTTGATCT
1 TAATATTATATAAGTT-AT-G
* * *
54378137 TAATATTATAAAAGTAATCT
1 TAATATTATATAAGTTAT-G
54378157 TAATATTATATAAGTTATG
1 TAATATTATATAAGTTATG
* ** *
54378176 TAAT-TCGA-A-ATTTTATCT
1 TAATAT-TATATAAGTTAT-G
* *
54378194 TAATATTGTGTAAGTTATG
1 TAATATTATATAAGTTATG
54378213 TAATATTATATAAGTTATG
1 TAATATTATATAAGTTATG
** * *
54378232 T-A-ATTCGA-AATTTGATCT
1 TAATATTATATAAGTT-AT-G
* * *
54378250 TAATATTATAAAAGTAATCT
1 TAATATTATATAAGTTAT-G
54378270 TAATATTATATAAGTTATG
1 TAATATTATATAAGTTATG
* ** *
54378289 TAAT-TCGA-A-ATTTTATCT
1 TAATAT-TATATAAGTTAT-G
* *
54378307 TAATATTGTGTAAGTTATG
1 TAATATTATATAAGTTATG
54378326 TAATATTATATAAGTTATG
1 TAATATTATATAAGTTATG
** * *
54378345 T-A-ATTCGA-AATTTGATCT
1 TAATATTATATAAGTT-AT-G
* * *
54378363 TAATATTATAAAAGTAATCT
1 TAATATTATATAAGTTAT-G
54378383 TAATATTATATAAGTTATG
1 TAATATTATATAAGTTATG
*** ** *
54378402 TAAT-TCGGA-ATTTTATCT
1 TAATATTATATAAGTTAT-G
* *
54378420 TAATATTGTGTAAGTTATG
1 TAATATTATATAAGTTATG
54378439 TAATATTATATAAGTTATG
1 TAATATTATATAAGTTATG
** * *
54378458 T-A-ATTCGA-AATTTGATCT
1 TAATATTATATAAGTT-AT-G
*
54378476 TAATATTATAAAAGTAATAT-
1 TAATATTATATAAGT--TATG
54378496 TAATATTATATAAGTTATG
1 TAATATTATATAAGTTATG
* * *
54378515 TAAT-TCA-A-AATTTTATCT
1 TAATATTATATAA-GTTAT-G
*
54378533 TAATATTGTATAAGTTATG
1 TAATATTATATAAGTTATG
* *
54378552 T-A-ATTAGA-AATTTTACCT-
1 TAATATTATATAA-GTTA--TG
*
54378570 TAATATTGTATAAGTTATG
1 TAATATTATATAAGTTATG
* ** *
54378589 TAAT-TCGAT-T-TTTTATCT
1 TAATAT-TATATAAGTTAT-G
*
54378607 TAACATTATATAAGTTATG
1 TAATATTATATAAGTTATG
*
54378626 TAATATTATATAAGTTATCT
1 TAATATTATATAAGTTAT-G
54378646 TAATATTATATAAGTTA
1 TAATATTATATAAGTTA
54378663 AGAAATTGTA
Statistics
Matches: 442, Mismatches: 119, Indels: 117
0.65 0.18 0.17
Matches are distributed among these distances:
16 24 0.05
17 60 0.14
18 47 0.11
19 128 0.29
20 161 0.36
21 19 0.04
22 2 0.00
23 1 0.00
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.46
Consensus pattern (19 bp):
TAATATTATATAAGTTATG
Found at i:54378104 original size:57 final size:57
Alignment explanation
Indices: 54377975--54378539 Score: 814
Period size: 57 Copynumber: 9.9 Consensus size: 57
54377965 NNNNNNNNNN
* * *
54377975 AAAGTAATCTTTAATATTATATAAGTTATGTAATTCGGAAATTTTATCTTAATATTGTG
1 AAAGTAATC-TTAATATTATATAAGTTATGTAATTC-GAAATTTGATCTTAATATTATA
* * *
54378034 TAAGTTAT-GTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
1 AAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
* *
54378090 AAAGTAATCTTAATATTATATAAGTTATTTAATTCGGAATTTGATCTTAATATTATA
1 AAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
* * *
54378147 AAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTG
1 AAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
* * *
54378204 TAAGTTAT-GTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
1 AAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
* * *
54378260 AAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTG
1 AAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
* * *
54378317 TAAGTTAT-GTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
1 AAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
* * * *
54378373 AAAGTAATCTTAATATTATATAAGTTATGTAATTCGGAATTTTATCTTAATATTGTG
1 AAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
* * *
54378430 TAAGTTAT-GTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
1 AAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
* * *
54378486 AAAGTAATATTAATATTATATAAGTTATGTAATTCAAAATTTTATCTTAATATT
1 AAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATT
54378540 GTATAAGTTA
Statistics
Matches: 449, Mismatches: 53, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
56 174 0.39
57 269 0.60
59 6 0.01
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.46
Consensus pattern (57 bp):
AAAGTAATCTTAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATA
Found at i:54378246 original size:113 final size:113
Alignment explanation
Indices: 54377986--54378555 Score: 953
Period size: 113 Copynumber: 5.0 Consensus size: 113
54377976 AAGTAATCTT
* * ** * *
54377986 TAATATTATATAAGTTATGTAATTCGGAAATTTTATCTTAATATTGTGTAAGTTAT-GTAATATT
1 TAATATTATATAAGTTATGTAATTC-GAAATTTGATCTTAATATTATAAAAGTAATCTTAATATT
* * ** * *
54378050 ATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAATCT
65 ATATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTGTAAGTTAT-G
* *
54378100 TAATATTATATAAGTTATTTAATTCGGAATTTGATCTTAATATTATAAAAGTAATCTTAATATTA
1 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAATCTTAATATTA
54378165 TATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTGTAAGTTATG
66 TATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTGTAAGTTATG
54378213 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAATCTTAATATTA
1 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAATCTTAATATTA
54378278 TATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTGTAAGTTATG
66 TATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTGTAAGTTATG
54378326 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAATCTTAATATTA
1 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAATCTTAATATTA
*
54378391 TATAAGTTATGTAATTCGGAATTTTATCTTAATATTGTGTAAGTTATG
66 TATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTGTAAGTTATG
*
54378439 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAATATTAATATTA
1 TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAATCTTAATATTA
* *
54378504 TATAAGTTATGTAATTCAAAATTTTATCTTAATATTGTATAAGTTATG
66 TATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTGTAAGTTATG
54378552 TAAT
1 TAAT
54378556 TAGAAATTTT
Statistics
Matches: 434, Mismatches: 21, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
113 360 0.83
114 74 0.17
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (113 bp):
TAATATTATATAAGTTATGTAATTCGAAATTTGATCTTAATATTATAAAAGTAATCTTAATATTA
TATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTGTAAGTTATG
Found at i:54378545 original size:37 final size:38
Alignment explanation
Indices: 54378495--54378662 Score: 209
Period size: 37 Copynumber: 4.5 Consensus size: 38
54378485 AAAAGTAATA
54378495 TTAATATTATATAAGTTATGTAATTCA-AAATTTTATC
1 TTAATATTATATAAGTTATGTAATTCAGAAATTTTATC
* *
54378532 TTAATATTGTATAAGTTATGTAATT-AGAAATTTTACC
1 TTAATATTATATAAGTTATGTAATTCAGAAATTTTATC
* **
54378569 TTAATATTGTATAAGTTATGTAATTC-GATTTTTTATC
1 TTAATATTATATAAGTTATGTAATTCAGAAATTTTATC
* * * *
54378606 TTAACATTATATAAGTTATGTAATATTATATAA-GTTATC
1 TTAATATTATATAAGTTATGTAAT-TCAGA-AATTTTATC
54378645 TTAATATTATATAAGTTA
1 TTAATATTATATAAGTTA
54378663 AGAAATTGTA
Statistics
Matches: 113, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
36 1 0.01
37 88 0.78
38 1 0.01
39 23 0.20
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (38 bp):
TTAATATTATATAAGTTATGTAATTCAGAAATTTTATC
Found at i:54378630 original size:150 final size:151
Alignment explanation
Indices: 54378268--54378662 Score: 362
Period size: 150 Copynumber: 2.6 Consensus size: 151
54378258 TAAAAGTAAT
* ** * *
54378268 CTTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTGTAAGTTATGTAATATT
1 CTTAATATTGTATAAGTTATGTAATTCGATTTTTTATCTTAA-ATTATATAAGTTATGTAATATT
** * * *
54378333 ATATAAGT-TATGT-A-ATTCGA-AATTTGATCTTAATATTATAAAAGTAATCTTAATATTATAT
65 ATATAAGTATAT-TAATATTATATAAGTT-ATCGTAATATCATAAAAGTAATCTTAATATTATAT
* * *
54378394 AAGTTATGTAATTCGGAATTTTAT
128 AAGTTATGTAATTAGAAATTTTAC
* * * ** ** * *
54378418 CTTAATATTGTGTAAGTTATGTAA-T--ATTATATAAGTTATGTAATTCGA-AATTTGATCTTAA
1 CTTAATATTGTATAAGTTATGTAATTCGATTTTTTATCTTA---AATTATATAAGTT-AT-GTAA
* ** * *
54378479 TATTATAAAAGTAATATTAATATTATATAAGTTAT-GTAAT-TCA-AAATTTTATCTTAATATTG
61 TATTATATAAGT-ATATTAATATTATATAAGTTATCGTAATATCATAAAAGTAATCTTAATATTA
54378541 TATAAGTTATGTAATTAGAAATTTTAC
125 TATAAGTTATGTAATTAGAAATTTTAC
54378568 CTTAATATTGTATAAGTTATGTAATTCGATTTTTTATCTTAACATTATATAAGTTATGTAATATT
1 CTTAATATTGTATAAGTTATGTAATTCGATTTTTTATCTTAA-ATTATATAAGTTATGTAATATT
*
54378633 ATATAAGTTATCTTAATATTATATAAGTTA
65 ATATAAG-TATATTAATATTATATAAGTTA
54378663 AGAAATTGTA
Statistics
Matches: 192, Mismatches: 37, Indels: 32
0.74 0.14 0.12
Matches are distributed among these distances:
147 7 0.04
148 4 0.02
149 6 0.03
150 133 0.69
151 11 0.06
152 12 0.06
153 15 0.08
154 4 0.02
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (151 bp):
CTTAATATTGTATAAGTTATGTAATTCGATTTTTTATCTTAAATTATATAAGTTATGTAATATTA
TATAAGTATATTAATATTATATAAGTTATCGTAATATCATAAAAGTAATCTTAATATTATATAAG
TTATGTAATTAGAAATTTTAC
Found at i:54380702 original size:19 final size:19
Alignment explanation
Indices: 54380678--54380719 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
54380668 GGACTACGTT
*
54380678 GGGGAACTGTTAGGGATTA
1 GGGGAAATGTTAGGGATTA
* *
54380697 GGGGAAATTTTAGGGATTT
1 GGGGAAATGTTAGGGATTA
54380716 GGGG
1 GGGG
54380720 GAGATGTCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.45, T:0.29
Consensus pattern (19 bp):
GGGGAAATGTTAGGGATTA
Found at i:54381416 original size:230 final size:230
Alignment explanation
Indices: 54381049--54381631 Score: 927
Period size: 231 Copynumber: 2.5 Consensus size: 230
54381039 TAATGCAAAT
*** * *
54381049 TTGCGGCG-TTTAATAAAAGCGCCACTAAAACCAACTAAGTAAACGGCGCCGTTTTCCGTAACAC
1 TTGCGGCGTTTTAATAAAA-CGCCACTAAATGTAA-TAAGAAAACGGCGCCGTTTTTCGTAACAC
*
54381113 CATTTCGATTTTGCGGCGTTTATATATAAGCGCCACTAAATATAAGGTCAAACGCAGTCGTTTAA
64 CATTTCGATTTTGCGGCGTTTATATATAAGTGCCACTAAATATAAGGTCAAACGCAGTCGTTTAA
* * **
54381178 AGCAAACTCCTGTAATCTTTAAAATATATTTGCGACGTTTTGGGTGTAACGCCACAAATATC-CT
129 AGCAAACTCCTGTAATCTTTAAAATATATTTGCGACGTTTCGGGTGTAACGCCACAAATAACAAA
* *
54381242 TGAAAACGACGCCGTTTCTGTAACAAAGAAAACATAC
194 GGAAAACGACGCCGTTTCCGTAACAAAGAAAACATAC
* *
54381279 TTGCGGCGTTTTAGATAAAACGCCACTAAATGTAATAAGAAAACGACGTCGTTTTTCGTAACACC
1 TTGCGGCGTTTTA-ATAAAACGCCACTAAATGTAATAAGAAAACGGCGCCGTTTTTCGTAACACC
* *
54381344 ATTTCGAGTTTGCGGCGTTTATATATAAGTGCCACTAAATATAAGGTCAAACGCAGTCGTTTAAC
65 ATTTCGATTTTGCGGCGTTTATATATAAGTGCCACTAAATATAAGGTCAAACGCAGTCGTTTAAA
* *
54381409 GCAAACTCCTGTAATCTTTAAAATATATTTGCGGCGTTTCGGGTGTAACGCCACTAATAACAAAG
130 GCAAACTCCTGTAATCTTTAAAATATATTTGCGACGTTTCGGGTGTAACGCCACAAATAACAAAG
54381474 GAAAACGACGCCGTTTCCGTAACAAAGAAAACATAC
195 GAAAACGACGCCGTTTCCGTAACAAAGAAAACATAC
* *
54381510 TTGCGGCGTTTTATCTAAAACGCCACTAAATGTAATAAAAAAACGGCGCCGTTTTTCGTAACACC
1 TTGCGGCGTTTTA-ATAAAACGCCACTAAATGTAATAAGAAAACGGCGCCGTTTTTCGTAACACC
*
54381575 ATTTCGATTTTGCGGCGTTTATATATAAGTGACACTAAATATAAGGTCAAACGCAGT
65 ATTTCGATTTTGCGGCGTTTATATATAAGTGCCACTAAATATAAGGTCAAACGCAGT
54381632 NNNNNNNNNN
Statistics
Matches: 325, Mismatches: 25, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
230 153 0.47
231 166 0.51
232 6 0.02
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (230 bp):
TTGCGGCGTTTTAATAAAACGCCACTAAATGTAATAAGAAAACGGCGCCGTTTTTCGTAACACCA
TTTCGATTTTGCGGCGTTTATATATAAGTGCCACTAAATATAAGGTCAAACGCAGTCGTTTAAAG
CAAACTCCTGTAATCTTTAAAATATATTTGCGACGTTTCGGGTGTAACGCCACAAATAACAAAGG
AAAACGACGCCGTTTCCGTAACAAAGAAAACATAC
Found at i:54382914 original size:18 final size:21
Alignment explanation
Indices: 54382891--54382939 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
54382881 ATTAATCACG
54382891 ATATTAATTTG-GTG-TTT-T
1 ATATTAATTTGTGTGATTTAT
* *
54382909 ATATTACTTTGTTTGATTTAT
1 ATATTAATTTGTGTGATTTAT
54382930 ATATTAATTT
1 ATATTAATTT
54382940 AGTCGAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 10 0.40
19 2 0.08
20 3 0.12
21 10 0.40
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (21 bp):
ATATTAATTTGTGTGATTTAT
Found at i:54383525 original size:112 final size:112
Alignment explanation
Indices: 54383276--54383508 Score: 296
Period size: 112 Copynumber: 2.1 Consensus size: 112
54383266 ATTACTATTA
* * * *
54383276 GCGGCGCTT-ACAGAAAAACGCCGCTAAAAAACA-TATCATTAGCGGCGTTTTTAAGAAAACGCC
1 GCGGCGCTTCTCAG-AAAACGCCGCT-AAAGACAGGAGCATTAGCGGCGTTTTTAAGAAAACGCC
54383339 GCTAAAGGCCCAAAAACAAAGAAAACGGGTCGTTGCCCTTAGGTTTTTT
64 GCTAAAGGCCCAAAAACAAAGAAAACGGGTCGTTGCCCTTAGGTTTTTT
54383388 GCGGCGCTTCTCAGAAAACGCCGCTAAAGACAGGAGCATTAGCGGCGCTTTTGT-A-AAAACGCC
1 GCGGCGCTTCTCAGAAAACGCCGCTAAAGACAGGAGCATTAGCGGCG-TTTT-TAAGAAAACGCC
* ** * * *
54383451 GCTAATGGCCCAAAAACTCAGTAAACGGCGTCGTTGGCCTTA-TTTTTTT
64 GCTAAAGGCCCAAAAACAAAGAAAACGG-GTCGTTGCCCTTAGGTTTTTT
54383500 GCGGCGCTT
1 GCGGCGCTT
54383509 TTTGTGAATC
Statistics
Matches: 106, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
111 6 0.06
112 79 0.75
113 20 0.19
114 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.23
Consensus pattern (112 bp):
GCGGCGCTTCTCAGAAAACGCCGCTAAAGACAGGAGCATTAGCGGCGTTTTTAAGAAAACGCCGC
TAAAGGCCCAAAAACAAAGAAAACGGGTCGTTGCCCTTAGGTTTTTT
Found at i:54395008 original size:35 final size:36
Alignment explanation
Indices: 54394964--54395035 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
54394954 TATTTAATAT
* * ** *
54394964 TAAATAATAATTATAGTTCTTCAAAAGAAACTATAA
1 TAAATAATAAATAAAGTGATTCAAAACAAACTATAA
54395000 TAAA-AATAAATAAAGTGATTCAAAACAAACTATAA
1 TAAATAATAAATAAAGTGATTCAAAACAAACTATAA
54395035 T
1 T
54395036 CTTAGAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 27 0.87
36 4 0.13
ACGTcount: A:0.57, C:0.08, G:0.06, T:0.29
Consensus pattern (36 bp):
TAAATAATAAATAAAGTGATTCAAAACAAACTATAA
Found at i:54396206 original size:18 final size:19
Alignment explanation
Indices: 54396183--54396219 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
54396173 AGTAAATTTT
54396183 GAATTT-TCATATTTTTAA
1 GAATTTGTCATATTTTTAA
*
54396201 GAATTTGTGATATTTTTAA
1 GAATTTGTCATATTTTTAA
54396220 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.54
Consensus pattern (19 bp):
GAATTTGTCATATTTTTAA
Found at i:54397491 original size:18 final size:17
Alignment explanation
Indices: 54397465--54397501 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
54397455 ATAAAATTTA
54397465 TAAAATTATTAAAAAAT
1 TAAAATTATTAAAAAAT
*
54397482 TAAAAGTTATTAAGAAAT
1 TAAAA-TTATTAAAAAAT
54397500 TA
1 TA
54397502 TAAAAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (17 bp):
TAAAATTATTAAAAAAT
Found at i:54397509 original size:29 final size:30
Alignment explanation
Indices: 54397467--54397524 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
54397457 AAAATTTATA
* *
54397467 AAATTATTAAAAAAT-TAAAAGTTATTAAG
1 AAATTATAAAAAAATCAAAAAGTTATTAAG
54397496 AAATTATAAAAAAATCAAAAAGTTATTAA
1 AAATTATAAAAAAATCAAAAAGTTATTAA
54397525 AATTATTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATTATAAAAAAATCAAAAAGTTATTAAG
Found at i:54397643 original size:10 final size:9
Alignment explanation
Indices: 54397625--54397707 Score: 61
Period size: 9 Copynumber: 9.7 Consensus size: 9
54397615 TTTTTTTTGC
54397625 AATTTTTAT
1 AATTTTTAT
54397634 AATTTCTTAT
1 AATTT-TTAT
*
54397644 -TTTTTTAT
1 AATTTTTAT
*
54397652 GATTTTTAGT
1 AATTTTTA-T
54397662 AA--TTT-T
1 AATTTTTAT
54397668 AATTTTTAT
1 AATTTTTAT
*
54397677 AATTTTAAT
1 AATTTTTAT
* *
54397686 -TTTTTTAC
1 AATTTTTAT
54397694 AATTTTTAT
1 AATTTTTAT
54397703 -ATTTT
1 AATTTT
54397708 AAAATATTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
6 3 0.05
8 20 0.34
9 29 0.50
10 6 0.10
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (9 bp):
AATTTTTAT
Found at i:54397673 original size:43 final size:40
Alignment explanation
Indices: 54397625--54397709 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 40
54397615 TTTTTTTTGC
* **
54397625 AATTTTTATAATTTCTTATTTTTTTATGATTTTTAGTAATTTT
1 AATTTTTATAATTT-TAATTTTTTTACAATTTTTA-T-ATTTT
54397668 AATTTTTATAATTTTAATTTTTTTACAATTTTTATATTTT
1 AATTTTTATAATTTTAATTTTTTTACAATTTTTATATTTT
54397708 AA
1 AA
54397710 AATATTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 7 0.18
41 1 0.03
42 17 0.44
43 14 0.36
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (40 bp):
AATTTTTATAATTTTAATTTTTTTACAATTTTTATATTTT
Found at i:54397679 original size:15 final size:16
Alignment explanation
Indices: 54397653--54397689 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
54397643 TTTTTTTATG
54397653 ATTTTTAGTAATTTTA
1 ATTTTTAGTAATTTTA
54397669 ATTTTTA-TAATTTTA
1 ATTTTTAGTAATTTTA
54397684 ATTTTT
1 ATTTTT
54397690 TTACAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTTTTAGTAATTTTA
Found at i:54397747 original size:15 final size:15
Alignment explanation
Indices: 54397723--54397752 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54397713 ATTTTTTACC
*
54397723 ATTTTTAATATTTTT
1 ATTTTAAATATTTTT
54397738 ATTTTAAATATTTTT
1 ATTTTAAATATTTTT
54397753 TTACAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTAAATATTTTT
Found at i:54409425 original size:22 final size:23
Alignment explanation
Indices: 54409400--54409445 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
54409390 TGATGATTTG
54409400 TTTTCATTTTAATAAT-CTCTTT
1 TTTTCATTTTAATAATACTCTTT
**
54409422 TTTTTTTTTTAATAATACTCTTT
1 TTTTCATTTTAATAATACTCTTT
54409445 T
1 T
54409446 AATTAACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTCATTTTAATAATACTCTTT
Found at i:54419560 original size:3 final size:3
Alignment explanation
Indices: 54419552--54419597 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
54419542 TATACACACA
54419552 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
54419598 GACTCATTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:54419950 original size:29 final size:25
Alignment explanation
Indices: 54419896--54419946 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 25
54419886 CACATTTGTG
*
54419896 TTTTTTTTATTTCATATTGTTTTAA
1 TTTTTTTTATTTCATAATGTTTTAA
54419921 TTTTTTTTATTTTCTATTAATGTTTT
1 TTTTTTTTA-TTTC-A-TAATGTTTT
54419947 TAATGCATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 4 0.18
27 1 0.05
28 8 0.36
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (25 bp):
TTTTTTTTATTTCATAATGTTTTAA
Found at i:54430766 original size:27 final size:25
Alignment explanation
Indices: 54430736--54430791 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
54430726 CATAATCAGC
54430736 AAGCACACTCTCGAGCCATATAACGGG
1 AAGCACA-TCT-GAGCCATATAACGGG
* * * *
54430763 AAGCTCATGTGATCCATGTAACGGG
1 AAGCACATCTGAGCCATATAACGGG
54430788 AAGC
1 AAGC
54430792 TTATCCGGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 17 0.68
26 2 0.08
27 6 0.24
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (25 bp):
AAGCACATCTGAGCCATATAACGGG
Found at i:54430972 original size:26 final size:26
Alignment explanation
Indices: 54430943--54430998 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
54430933 AAAGCTCTAG
54430943 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTCACAA
* * *
54430969 AGAGCCTTTAATTAGGAAGCTCACGA
1 AGAGCCATTAATCAGGAAGCTCACAA
54430995 AGAG
1 AGAG
54430999 TCATATAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (26 bp):
AGAGCCATTAATCAGGAAGCTCACAA
Found at i:54432555 original size:19 final size:21
Alignment explanation
Indices: 54432531--54432572 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
54432521 TGTTATGTGT
*
54432531 TACAAT-AA-ATATGTAATTA
1 TACAATGAATATATATAATTA
54432550 TACAATGAATATATATAATTA
1 TACAATGAATATATATAATTA
54432571 TA
1 TA
54432573 TATATCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 12 0.60
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (21 bp):
TACAATGAATATATATAATTA
Found at i:54435489 original size:43 final size:43
Alignment explanation
Indices: 54435403--54435489 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
54435393 ACATAGGATT
**
54435403 TCGATATGTGTTTTCGTGTAAGACCACGTCTGGGGTATCGGCA
1 TCGATATGTGTTTTCGTGTAAGACCACGTCTGGGACATCGGCA
* * *
54435446 TCGATTTGTGTTTAT-GTGTAAGACCATGTCTGGGACATTGGCA
1 TCGATATGTGTTT-TCGTGTAAGACCACGTCTGGGACATCGGCA
54435489 T
1 T
54435490 TGTACGAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
43 37 0.97
44 1 0.03
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.36
Consensus pattern (43 bp):
TCGATATGTGTTTTCGTGTAAGACCACGTCTGGGACATCGGCA
Found at i:54435921 original size:16 final size:18
Alignment explanation
Indices: 54435900--54435932 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
54435890 ATTTTTTTTT
54435900 GCTTAAG-A-CTTACTAA
1 GCTTAAGTAGCTTACTAA
54435916 GCTTAAGTAGCTTACTA
1 GCTTAAGTAGCTTACTA
54435933 TATGTGTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (18 bp):
GCTTAAGTAGCTTACTAA
Found at i:54437258 original size:28 final size:28
Alignment explanation
Indices: 54437226--54437282 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
54437216 TGCTTTGATG
54437226 TAAGTTCAAATTGAATTAATTGGAAATT
1 TAAGTTCAAATTGAATTAATTGGAAATT
54437254 TAAGTTCAAATTGAATTAATTGGAAATT
1 TAAGTTCAAATTGAATTAATTGGAAATT
54437282 T
1 T
54437283 TCAAAAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.40
Consensus pattern (28 bp):
TAAGTTCAAATTGAATTAATTGGAAATT
Found at i:54454955 original size:2 final size:2
Alignment explanation
Indices: 54454950--54454974 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54454940 AGTGAAATAC
54454950 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
54454975 AGAACACTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54463711 original size:39 final size:39
Alignment explanation
Indices: 54463668--54463757 Score: 146
Period size: 39 Copynumber: 2.3 Consensus size: 39
54463658 AACCCTAGTC
54463668 ATTTTGCTT-TTTAGGCAGTTTTCAATACAGTCCTGTTCT
1 ATTTT-CTTATTTAGGCAGTTTTCAATACAGTCCTGTTCT
*
54463707 ATTTTTTTATTTAGGCAGTTTTCAATACAGTCCTGTTCT
1 ATTTTCTTATTTAGGCAGTTTTCAATACAGTCCTGTTCT
*
54463746 ATTTTTTTATTT
1 ATTTTCTTATTT
54463758 TACCACTTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 2 0.04
39 47 0.96
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.54
Consensus pattern (39 bp):
ATTTTCTTATTTAGGCAGTTTTCAATACAGTCCTGTTCT
Found at i:54464780 original size:24 final size:24
Alignment explanation
Indices: 54464753--54464814 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
54464743 CAGCTCGAAA
*
54464753 GAGCATCCCGTTATTAGCTCTCAT-
1 GAGCATCCCGTTATTAGCCCTC-TC
*
54464777 GAGCATCACGTTATTAGCCCTCTC
1 GAGCATCCCGTTATTAGCCCTCTC
*
54464801 GAGCTTCCCGTTAT
1 GAGCATCCCGTTAT
54464815 ATGATTCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 1 0.03
24 32 0.97
ACGTcount: A:0.19, C:0.31, G:0.18, T:0.32
Consensus pattern (24 bp):
GAGCATCCCGTTATTAGCCCTCTC
Found at i:54464858 original size:24 final size:24
Alignment explanation
Indices: 54464752--54464859 Score: 71
Period size: 24 Copynumber: 4.5 Consensus size: 24
54464742 ACAGCTCGAA
*
54464752 AGAGCATCCCGTTATTAGC-TCTC
1 AGAGCATCCCGTTAATAGCTTCTC
* * *
54464775 ATGAGCATCACGTTATTAGCCCTCTC
1 A-GAGCATCCCGTTAATAG-CTTCTC
* *
54464801 -GAGCTTCCCGTT-ATATGATTCTTGC
1 AGAGCATCCCGTTAATA-GCTTC-T-C
* *
54464826 -GAGCTTCCCGTTAATAGCTTTTC
1 AGAGCATCCCGTTAATAGCTTCTC
54464849 AGAGCATCCCG
1 AGAGCATCCCG
54464860 ATTAGTTGTG
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
23 6 0.09
24 38 0.56
25 17 0.25
26 7 0.10
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.32
Consensus pattern (24 bp):
AGAGCATCCCGTTAATAGCTTCTC
Found at i:54464940 original size:26 final size:26
Alignment explanation
Indices: 54464898--54464979 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
54464888 ACACACCACA
*
54464898 GCTCTTA-TGAGCGTCCCGATATATG
1 GCTCTTAGTGAGCTTCCCGATATATG
* *
54464923 GCTCTTAGTGAGCTTCCCAAT-TAAAG
1 GCTCTTAGTGAGCTTCCCGATAT-ATG
* * *
54464949 GCTCTTTGTGAACTTCTCGATATATG
1 GCTCTTAGTGAGCTTCCCGATATATG
54464975 GCTCT
1 GCTCT
54464980 CCGGAGCTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
25 8 0.17
26 37 0.80
27 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (26 bp):
GCTCTTAGTGAGCTTCCCGATATATG
Found at i:54464995 original size:25 final size:26
Alignment explanation
Indices: 54464961--54465038 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 26
54464951 TCTTTGTGAA
54464961 CTTC-TCGATATATGGCTCTCCGGAG
1 CTTCTTCGATATATGGCTCTCCGGAG
* *** *
54464986 CTT-TTCGATAT-TGGCTCGCTTAAA
1 CTTCTTCGATATATGGCTCTCCGGAG
*
54465010 CTTCTT-GATATATGGCTATCCGGAG
1 CTTCTTCGATATATGGCTCTCCGGAG
54465035 CTTC
1 CTTC
54465039 CTGATTATTG
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
24 16 0.41
25 23 0.59
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (26 bp):
CTTCTTCGATATATGGCTCTCCGGAG
Found at i:54465073 original size:49 final size:48
Alignment explanation
Indices: 54464959--54465075 Score: 130
Period size: 49 Copynumber: 2.4 Consensus size: 48
54464949 GCTCTTTGTG
* * * *
54464959 AACTTCTCGATATATGGCTCTCCGGAGCTTTTCGATATTGGCTCGCTTA
1 AACTTCT-GATATATGGCTATCCGGAGCTTCTCGATATTGGCTCACTGA
54465008 AACTTCTTGATATATGGCTATCCGGAGCTTC-CTGATTATTGGCTCACGTGA
1 AACTTC-TGATATATGGCTATCCGGAGCTTCTC-GA-TATTGGCTCAC-TGA
*
54465059 AATTTCTGAT-TATGGCT
1 AACTTCTGATATATGGCT
54465076 CTTATGAGCT
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
48 1 0.02
49 36 0.61
50 15 0.25
51 7 0.12
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (48 bp):
AACTTCTGATATATGGCTATCCGGAGCTTCTCGATATTGGCTCACTGA
Found at i:54467217 original size:14 final size:14
Alignment explanation
Indices: 54467159--54467217 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 14
54467149 CTTATCTATT
*
54467159 TTATTATTATGATA
1 TTATTATTATAATA
*
54467173 TGATTA--ATAATA
1 TTATTATTATAATA
54467185 TTATTATTATTACATTA
1 TTATTATTA-TA-A-TA
*
54467202 TTGTTATTATAATA
1 TTATTATTATAATA
54467216 TT
1 TT
54467218 CCTTTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
12 10 0.28
14 10 0.28
15 3 0.08
16 3 0.08
17 10 0.28
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (14 bp):
TTATTATTATAATA
Found at i:54475476 original size:31 final size:30
Alignment explanation
Indices: 54475416--54475482 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
54475406 TTGTAGATTC
54475416 AGTCTCTATACTTTTTAAATTGATTAATTTT
1 AGTCTCTATACTTTTTAAATT-ATTAATTTT
* *
54475447 AGTCTCTATATTTTTTGAATT-TTAAAATTTT
1 AGTCTCTATACTTTTTAAATTATT--AATTTT
54475478 AGTCT
1 AGTCT
54475483 TGACCCAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 2 0.06
31 30 0.94
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.55
Consensus pattern (30 bp):
AGTCTCTATACTTTTTAAATTATTAATTTT
Found at i:54477136 original size:23 final size:22
Alignment explanation
Indices: 54477081--54477136 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 22
54477071 AGATATTTTG
54477081 AATA-ATTTAT-TTAATTAAAT
1 AATATATTTATATTAATTAAAT
*
54477101 AATATATTAATATTAATTAAATT
1 AATATATTTATATTAATTAAA-T
* *
54477124 AATTTTTTTATAT
1 AATATATTTATAT
54477137 ATTTTAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 4 0.14
21 5 0.17
22 9 0.31
23 11 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATATTTATATTAATTAAAT
Found at i:54482196 original size:100 final size:100
Alignment explanation
Indices: 54482055--54482287 Score: 233
Period size: 100 Copynumber: 2.3 Consensus size: 100
54482045 ATCTTACATG
* * * * * *
54482055 ATAAGATATTCATTTAGTAAGGCCTACACC-AAGTTCGATCAAGTGGCA-TCTTATTACATCTTA
1 ATAAGATA-TCATTTAGTAGGGTCTACACCAAAATTCGATCAAGTGACAGT-TTATCACATCTCA
* * *
54482118 A-TAAAGTT-TTCTATGACCTTACTTCAAACTTTACACA
64 ACCAAA-TTCTTC-ATGACCTTACTACAAACCTTACACA
* *
54482155 ATAAGATACTCATTAAGTAGGGTCTACACCAAAATT-TATCAAGTGACAGTTTATCACATCTCAA
1 ATAAGATA-TCATTTAGTAGGGTCTACACCAAAATTCGATCAAGTGACAGTTTATCACATCTCAA
* *
54482219 CCGAATTCTTCATGACCTTACTACAAACCTTACATA
65 CCAAATTCTTCATGACCTTACTACAAACCTTACACA
* * *
54482255 ATAAAATATCTATTTTGTGGGGTCTACACCAAA
1 ATAAGATATC-ATTTAGTAGGGTCTACACCAAA
54482288 CTCCATCAAA
Statistics
Matches: 110, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
99 2 0.02
100 98 0.89
101 10 0.09
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.33
Consensus pattern (100 bp):
ATAAGATATCATTTAGTAGGGTCTACACCAAAATTCGATCAAGTGACAGTTTATCACATCTCAAC
CAAATTCTTCATGACCTTACTACAAACCTTACACA
Found at i:54487942 original size:2 final size:2
Alignment explanation
Indices: 54487935--54487961 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54487925 TAACTTATTT
54487935 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 T
54487962 TAGTACTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54488172 original size:17 final size:17
Alignment explanation
Indices: 54488152--54488189 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
54488142 TTTTTTTTTT
*
54488152 TTTTGAGTTTTTCTAAG
1 TTTTGAATTTTTCTAAG
54488169 TTTTGAATTTTTCTAAG
1 TTTTGAATTTTTCTAAG
54488186 TTTT
1 TTTT
54488190 TTTTAATGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.13, T:0.63
Consensus pattern (17 bp):
TTTTGAATTTTTCTAAG
Found at i:54489076 original size:12 final size:12
Alignment explanation
Indices: 54489061--54489097 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
54489051 ATCATACCAA
54489061 TTAAGTTAAGAT
1 TTAAGTTAAGAT
54489073 TTAAGTTAAGAT
1 TTAAGTTAAGAT
*
54489085 TCAAGTTAAGAT
1 TTAAGTTAAGAT
54489097 T
1 T
54489098 CGATCAACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.41, C:0.03, G:0.16, T:0.41
Consensus pattern (12 bp):
TTAAGTTAAGAT
Found at i:54494988 original size:22 final size:22
Alignment explanation
Indices: 54494942--54494984 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
54494932 ATAAATTTAT
*
54494942 TAAATATTAAAATAATATAACA
1 TAAATATTAAAATAATATAAAA
54494964 TAAATATTTAAAA-AAT-TAAAA
1 TAAATA-TTAAAATAATATAAAA
54494985 ATAATATGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAATATTAAAATAATATAAAA
Found at i:54496534 original size:26 final size:25
Alignment explanation
Indices: 54496504--54496556 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
54496494 AAATTTTATT
*
54496504 AAATTTAAGTACCAAATTAGACAAAA
1 AAATTTAAATACCAAATTA-ACAAAA
* *
54496530 AAATTTAAATACTAAATTAAGAAAA
1 AAATTTAAATACCAAATTAACAAAA
54496555 AA
1 AA
54496557 TGTCGAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.25
Consensus pattern (25 bp):
AAATTTAAATACCAAATTAACAAAA
Found at i:54498762 original size:30 final size:30
Alignment explanation
Indices: 54498728--54498790 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
54498718 CCACCTCCCT
* *
54498728 TATGGAGGCGATGGAAATGGTCCTCATATA
1 TATGGAGGCAATGGAAATGGACCTCATATA
*
54498758 TATGGAGGCAATGGAAATGGACCTCATGTA
1 TATGGAGGCAATGGAAATGGACCTCATATA
54498788 TAT
1 TAT
54498791 ATACATATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.27
Consensus pattern (30 bp):
TATGGAGGCAATGGAAATGGACCTCATATA
Found at i:54502624 original size:10 final size:11
Alignment explanation
Indices: 54502611--54502647 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
54502601 ATTTTATGAT
54502611 ATTTTTTA-AA
1 ATTTTTTATAA
54502621 A-TTTTTATAA
1 ATTTTTTATAA
*
54502631 ACTTTTTATAA
1 ATTTTTTATAA
54502642 ATTTTT
1 ATTTTT
54502648 ATTACTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
9 6 0.25
10 4 0.17
11 14 0.58
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTTTTTATAA
Found at i:54502627 original size:21 final size:20
Alignment explanation
Indices: 54502602--54502658 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
54502592 TCCACATGTA
54502602 TTTTATGATATTTTTTAAAAT
1 TTTTAT-ATATTTTTTAAAAT
* *
54502623 TTTTATAAACTTTTTATAAAT
1 TTTTATATATTTTTTA-AAAT
54502644 TTTTAT-TACTTTTTT
1 TTTTATATA-TTTTTT
54502659 TAATATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 9 0.30
21 21 0.70
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTATATATTTTTTAAAAT
Found at i:54502648 original size:10 final size:10
Alignment explanation
Indices: 54502613--54502649 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
54502603 TTTATGATAT
54502613 TTTTTA-AAA
1 TTTTTATAAA
54502622 TTTTTATAAA
1 TTTTTATAAA
54502632 CTTTTTATAAA
1 -TTTTTATAAA
54502643 TTTTTAT
1 TTTTTAT
54502650 TACTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 6 0.23
10 10 0.38
11 10 0.38
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:54502666 original size:21 final size:21
Alignment explanation
Indices: 54502612--54502666 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
54502602 TTTTATGATA
*
54502612 TTTTTTAAAATTTTTATAAAC
1 TTTTTTTAAATTTTTATAAAC
* *
54502633 TTTTTATAAATTTTTAT-TAC
1 TTTTTTTAAATTTTTATAAAC
54502653 TTTTTTTAATATTT
1 TTTTTTTAA-ATTT
54502667 ATAGATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTTTAAATTTTTATAAAC
Found at i:54502667 original size:19 final size:20
Alignment explanation
Indices: 54502613--54502668 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
54502603 TTTATGATAT
* *
54502613 TTTTTA-AAATTTTTATAAAC
1 TTTTTATAAATATTTAT-TAC
*
54502633 TTTTTATAAATTTTTATTAC
1 TTTTTATAAATATTTATTAC
*
54502653 TTTTT-TTAATATTTAT
1 TTTTTATAAATATTTAT
54502669 AGATTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.28
20 13 0.41
21 10 0.31
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTATAAATATTTATTAC
Found at i:54508938 original size:146 final size:146
Alignment explanation
Indices: 54508674--54508972 Score: 553
Period size: 146 Copynumber: 2.0 Consensus size: 146
54508664 TACAAGTAGC
54508674 ATTTCCCTAATTGAAATGCACTTCCTAACTCCAAACCATCTCAACTAAATAAAATGCATATAAAA
1 ATTTCCCTAATTGAAATGCACTTCCTAACTCCAAACCATCTCAACTAAATAAAATGCATATAAAA
* *
54508739 TCTACCGATCATCGAATCAAGCATAAAAATTACCTACATTGCATCTACTAAAACCGAACGAATTT
66 TCTACCGATCATCGAATCAAGCATAAAAATTACCTACATTGCATCTACTAAAACCGAACAAATCT
54508804 AAGCTTAAAAACTCAA
131 AAGCTTAAAAACTCAA
*
54508820 ATTTCCCTAATTGAAATGCACTTCCTAACTCCGAACCATCTCAACTAAATAAAATGCATATAAAA
1 ATTTCCCTAATTGAAATGCACTTCCTAACTCCAAACCATCTCAACTAAATAAAATGCATATAAAA
* *
54508885 TCTACCGATCATCGAATTAAGCATAAAAATTACTTACATTGCATCTACTAAAACCGAACAAATCT
66 TCTACCGATCATCGAATCAAGCATAAAAATTACCTACATTGCATCTACTAAAACCGAACAAATCT
54508950 AAGCTTAAAAACTCAA
131 AAGCTTAAAAACTCAA
54508966 ATTTCCC
1 ATTTCCC
54508973 AGATCAAATT
Statistics
Matches: 148, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
146 148 1.00
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (146 bp):
ATTTCCCTAATTGAAATGCACTTCCTAACTCCAAACCATCTCAACTAAATAAAATGCATATAAAA
TCTACCGATCATCGAATCAAGCATAAAAATTACCTACATTGCATCTACTAAAACCGAACAAATCT
AAGCTTAAAAACTCAA
Found at i:54510512 original size:24 final size:24
Alignment explanation
Indices: 54510467--54510512 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
54510457 TAAAATCTAC
* *
54510467 TTTTTATTATTAATTATTAATTTA
1 TTTTTATTATTAAATATAAATTTA
54510491 TTTTTATT-TTAAATATGAAATT
1 TTTTTATTATTAAATAT-AAATT
54510513 AAATTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTTATTATTAAATATAAATTTA
Found at i:54511976 original size:21 final size:21
Alignment explanation
Indices: 54511950--54511994 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
54511940 CAAATCAAAG
54511950 TTTTTTTTTGACGCGTTTTGA
1 TTTTTTTTTGACGCGTTTTGA
54511971 TTTTTTTTTGACGCGTTTTGA
1 TTTTTTTTTGACGCGTTTTGA
54511992 TTT
1 TTT
54511995 GACATTGGGT
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:0.09, C:0.09, G:0.18, T:0.64
Consensus pattern (21 bp):
TTTTTTTTTGACGCGTTTTGA
Found at i:54515570 original size:39 final size:39
Alignment explanation
Indices: 54515516--54515593 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
54515506 CATAAACAGA
54515516 AAACCACTGATAAATGAGCAACTCGATCCTCCCTACCAT
1 AAACCACTGATAAATGAGCAACTCGATCCTCCCTACCAT
54515555 AAACCACTGATAAATGAGCAACTCGATCCTCCCTACCAT
1 AAACCACTGATAAATGAGCAACTCGATCCTCCCTACCAT
54515594 GAGTTATGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.33, G:0.10, T:0.21
Consensus pattern (39 bp):
AAACCACTGATAAATGAGCAACTCGATCCTCCCTACCAT
Found at i:54516169 original size:174 final size:180
Alignment explanation
Indices: 54515870--54516363 Score: 723
Period size: 174 Copynumber: 2.8 Consensus size: 180
54515860 AGTATGTGTG
** * * *
54515870 TGTGTGTTGAAAATATCTAACACACACAAAACCAACCCAGTCTAGAGTACATCGGAA-TATAATA
1 TGTGTGTTGAAAATATCTAACACACACAAAACCAGGCCAATCTAGAGTACATC-CAACTATAACA
* **
54515934 AAAGCCCCAATTAGTATAACTACTAATCTCATTTAAGTTCACCTTCTTTTCTCTGCTTTAGGGGC
65 AAAGCCCCAATTAGTATAACTACTAATCTCATTTAAGTTCATCTTCTTTTCTCCACTTTAGGGGC
54515999 AAAGCATGCAGCAT-AT-TATATA-TA-TATGCA-TACGTATATTATC-TC
130 AAAGCATGCAGCATAATATATATAGTAGTATGCAGTACGTATATTATCGTC
* *
54516044 TGTGCGTTGAAAATATCTAACACACACAAAACCAGGCAAATCTAGAGTACATCCAACTATAACAA
1 TGTGTGTTGAAAATATCTAACACACACAAAACCAGGCCAATCTAGAGTACATCCAACTATAACAA
*
54516109 AAGCCCCAATTAATATAACTACTAATCTCATTTAAGTTCATCTTCTTTTCTCCACTTTAGGGGCA
66 AAGCCCCAATTAGTATAACTACTAATCTCATTTAAGTTCATCTTCTTTTCTCCACTTTAGGGGCA
* * *
54516174 AAGCATGCAGCATAATATATATATGTATGTATGTATGTATGTATATTATCTGTG
131 AAGCATGCAGCATAATATATATA-GTA-GTATGCA-GTACGTATATTATC-GTC
* * *
54516228 TGTGTGTTGAAAGTATGTAACACACACAAAATCAGGCCAATCTAGAGTACATCCAACTATAACAA
1 TGTGTGTTGAAAATATCTAACACACACAAAACCAGGCCAATCTAGAGTACATCCAACTATAACAA
* *
54516293 AAGCCCCAATTAGTGTAACTACTAATCTCATTTAAGTTCATCTTCTTTTCTCCACTTTAGGGGAA
66 AAGCCCCAATTAGTATAACTACTAATCTCATTTAAGTTCATCTTCTTTTCTCCACTTTAGGGGCA
54516358 AAGCAT
131 AAGCAT
54516364 ACCTAATAGT
Statistics
Matches: 287, Mismatches: 22, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
173 2 0.01
174 129 0.45
175 2 0.01
176 6 0.02
178 2 0.01
180 5 0.02
182 12 0.04
184 129 0.45
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.31
Consensus pattern (180 bp):
TGTGTGTTGAAAATATCTAACACACACAAAACCAGGCCAATCTAGAGTACATCCAACTATAACAA
AAGCCCCAATTAGTATAACTACTAATCTCATTTAAGTTCATCTTCTTTTCTCCACTTTAGGGGCA
AAGCATGCAGCATAATATATATAGTAGTATGCAGTACGTATATTATCGTC
Found at i:54516999 original size:15 final size:15
Alignment explanation
Indices: 54516979--54517007 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54516969 AAGGTAAATA
54516979 ATTGTCTAATTAATT
1 ATTGTCTAATTAATT
54516994 ATTGTCTAATTAAT
1 ATTGTCTAATTAAT
54517008 CATTTAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (15 bp):
ATTGTCTAATTAATT
Found at i:54518344 original size:15 final size:15
Alignment explanation
Indices: 54518324--54518353 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
54518314 GGCTGTGTTT
54518324 TTGTCTGCAAGAAAA
1 TTGTCTGCAAGAAAA
54518339 TTGTCTGCAAGAAAA
1 TTGTCTGCAAGAAAA
54518354 CTGGATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
TTGTCTGCAAGAAAA
Found at i:54519953 original size:9 final size:9
Alignment explanation
Indices: 54519924--54519970 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
54519914 GACTTGTAAG
*
54519924 TTTTTTGGA
1 TTTTTAGGA
54519933 -TTTTAGG-
1 TTTTTAGGA
* *
54519940 GTTTTAGGG
1 TTTTTAGGA
54519949 TTTTTAGGA
1 TTTTTAGGA
54519958 TTTTTAGGA
1 TTTTTAGGA
54519967 TTTT
1 TTTT
54519971 GGAGAAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 13 0.39
9 20 0.61
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.60
Consensus pattern (9 bp):
TTTTTAGGA
Found at i:54519970 original size:17 final size:16
Alignment explanation
Indices: 54519923--54519970 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
54519913 GGACTTGTAA
*
54519923 GTTTTTTGGATTTTAG
1 GTTTTTAGGATTTTAG
* *
54519939 GGTTTTAGGGTTTTTAG
1 GTTTTTA-GGATTTTAG
54519956 GATTTTTAGGATTTT
1 G-TTTTTAGGATTTT
54519971 GGAGAAAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 5 0.20
17 15 0.60
18 5 0.20
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (16 bp):
GTTTTTAGGATTTTAG
Found at i:54533052 original size:55 final size:54
Alignment explanation
Indices: 54532966--54533091 Score: 198
Period size: 55 Copynumber: 2.3 Consensus size: 54
54532956 CTTTTTTTCA
* *
54532966 AAGCAAGGTTTCGGGTTCAAGTATTTGTGAGATGGTGAGGAATTTGGTACCTTT
1 AAGCAAGGTTTCGGGTTCAAGTAATTGTGAGATGGTCAGGAATTTGGTACCTTT
* *
54533020 AAGGCAAGGTTTCGGGTTCAAGTAATTGTGAGATGGTCAGGAGTTTGGTACTTTT
1 AA-GCAAGGTTTCGGGTTCAAGTAATTGTGAGATGGTCAGGAATTTGGTACCTTT
*
54533075 AAGCAAGGGTTCGGGTT
1 AAGCAAGGTTTCGGGTT
54533092 TGAGTGTTCT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 16 0.24
55 50 0.76
ACGTcount: A:0.24, C:0.10, G:0.33, T:0.33
Consensus pattern (54 bp):
AAGCAAGGTTTCGGGTTCAAGTAATTGTGAGATGGTCAGGAATTTGGTACCTTT
Found at i:54543102 original size:19 final size:19
Alignment explanation
Indices: 54543078--54543115 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
54543068 TGGCTAAGGT
54543078 AATAGTGATTCCTCTGTTA
1 AATAGTGATTCCTCTGTTA
54543097 AATAGTGATTCCTCTGTTA
1 AATAGTGATTCCTCTGTTA
54543116 TTTTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (19 bp):
AATAGTGATTCCTCTGTTA
Found at i:54545257 original size:47 final size:47
Alignment explanation
Indices: 54545203--54545296 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
54545193 AGTTAAATTG
*
54545203 ATACAAGATGTAAATATTAGAAAGCTAAAATTTTATCATTATGTCAT
1 ATACAAGATGTAAATATTAGAAAACTAAAATTTTATCATTATGTCAT
* *
54545250 ATACAAGATGTAAATATTAGAAAATTAAATTTTTATCATTATGTCAT
1 ATACAAGATGTAAATATTAGAAAACTAAAATTTTATCATTATGTCAT
54545297 TTTTAAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (47 bp):
ATACAAGATGTAAATATTAGAAAACTAAAATTTTATCATTATGTCAT
Found at i:54561490 original size:2 final size:2
Alignment explanation
Indices: 54561483--54561507 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54561473 GAAAAGCATG
54561483 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 T
54561508 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54561659 original size:2 final size:2
Alignment explanation
Indices: 54561652--54561681 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54561642 TTCTTTTAAA
54561652 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54561682 TNNNNNNNNN
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54561790 original size:2 final size:2
Alignment explanation
Indices: 54561783--54561819 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54561773 NNNNNNNNNN
54561783 TA TA TA 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 T
54561820 GTCAAAAATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54562757 original size:2 final size:2
Alignment explanation
Indices: 54562750--54562777 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54562740 GATACTATCA
54562750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54562778 CTTTGTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54567400 original size:22 final size:22
Alignment explanation
Indices: 54567326--54567389 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
54567316 ACCTGATGTT
* * *
54567326 TAACGAACTAAACCCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
54567348 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
54567370 TAACGTACTAAGCTCTCATG
1 TAACGTACTAAGCTCTCATG
54567390 TTTCACGTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGGC
Found at i:54570901 original size:23 final size:23
Alignment explanation
Indices: 54570871--54570914 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
54570861 ATTTTTTAAA
54570871 AATATTT-ATATTATCTTTAATTT
1 AATATTTAATATTAT-TTTAATTT
*
54570894 AATATTTAATTTTATTTTAAT
1 AATATTTAATATTATTTTAAT
54570915 AAAAATCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
AATATTTAATATTATTTTAATTT
Found at i:54570928 original size:23 final size:24
Alignment explanation
Indices: 54570866--54570928 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 24
54570856 TAAATATTTT
*
54570866 TTAAAAATATTTATATTATCTTTAA
1 TTAAAAAT-TTTATTTTATCTTTAA
* * *
54570891 TTTAATATTTAATTTTAT-TTTAA
1 TTAAAAATTTTATTTTATCTTTAA
54570914 -TAAAAATCTTTATTT
1 TTAAAAAT-TTTATTT
54570929 GTATAGTGAG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
22 5 0.17
23 11 0.37
24 8 0.27
25 6 0.20
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
TTAAAAATTTTATTTTATCTTTAA
Found at i:54589012 original size:2 final size:2
Alignment explanation
Indices: 54589005--54589029 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54588995 GTTTTAACCA
54589005 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
54589030 CATTTCGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54589718 original size:22 final size:22
Alignment explanation
Indices: 54589683--54589727 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
54589673 GGGCTCAATT
**
54589683 TTTATAATTTTTTAA-ATATTTG
1 TTTATAATACTTTAATA-ATTTG
54589705 TTTATAATACTTTAATAATTTG
1 TTTATAATACTTTAATAATTTG
54589727 T
1 T
54589728 ATTCTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (22 bp):
TTTATAATACTTTAATAATTTG
Found at i:54593981 original size:6 final size:5
Alignment explanation
Indices: 54593957--54594019 Score: 81
Period size: 5 Copynumber: 11.6 Consensus size: 5
54593947 AACCTTTTTT
54593957 TTTCA TTTCA TTTCA TTTCCA TTTCTA TTTCCA TTTCA TTTCA TTTACA
1 TTTCA TTTCA TTTCA TTT-CA TTTC-A TTT-CA TTTCA TTTCA TTT-CA
54594006 TTTCCA TTTCA TTT
1 TTT-CA TTTCA TTT
54594020 AAATTATTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
5 29 0.55
6 23 0.43
7 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (5 bp):
TTTCA
Found at i:54593991 original size:28 final size:27
Alignment explanation
Indices: 54593957--54594019 Score: 99
Period size: 28 Copynumber: 2.3 Consensus size: 27
54593947 AACCTTTTTT
* *
54593957 TTTCATTTCATTTCATTTCCATTTCTA
1 TTTCATTTCATTTCATTTACATTTCCA
54593984 TTTCCATTTCATTTCATTTACATTTCCA
1 TTT-CATTTCATTTCATTTACATTTCCA
54594012 TTTCATTT
1 TTTCATTT
54594020 AAATTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 8 0.24
28 25 0.76
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTCATTTCATTTCATTTACATTTCCA
Found at i:54594038 original size:24 final size:22
Alignment explanation
Indices: 54593965--54594062 Score: 72
Period size: 22 Copynumber: 4.3 Consensus size: 22
54593955 TTTTTCATTT
* * *
54593965 CATTTCATTTCCATTTCTATTTC
1 CATTTCATTT-AATTTTTTTTTC
* ***
54593988 CATTTCATTTCATTTACATTTC
1 CATTTCATTTAATTTTTTTTTC
54594010 CATTTCATTTAAATTATTTTTTTC
1 CATTTCATTT-AATT-TTTTTTTC
* *
54594034 CATTTAAATTTAATTTTTTTCT-
1 CATTT-CATTTAATTTTTTTTTC
54594056 CATTTCA
1 CATTTCA
54594063 ATTTTTGTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
21 1 0.02
22 25 0.40
23 19 0.30
24 14 0.22
25 4 0.06
ACGTcount: A:0.23, C:0.18, G:0.00, T:0.58
Consensus pattern (22 bp):
CATTTCATTTAATTTTTTTTTC
Found at i:54594059 original size:22 final size:21
Alignment explanation
Indices: 54594014--54594104 Score: 77
Period size: 19 Copynumber: 4.4 Consensus size: 21
54594004 CATTTCCATT
54594014 TCATTTAAA-TTATTTTTTTC
1 TCATTTAAATTTATTTTTTTC
54594034 -CATTTAAATTTAATTTTTTTC
1 TCATTTAAATTT-ATTTTTTTC
* *
54594055 TCATTTCAA-TT-TTTGTTT-
1 TCATTTAAATTTATTTTTTTC
*
54594073 TCATTTCAATTTATAATTTATTT-
1 TCATTTAAATTTAT--TTT-TTTC
54594096 TCATTTAAA
1 TCATTTAAA
54594105 CTTTCATTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
18 9 0.15
19 16 0.27
20 3 0.05
21 11 0.19
22 9 0.15
23 11 0.19
ACGTcount: A:0.27, C:0.10, G:0.01, T:0.62
Consensus pattern (21 bp):
TCATTTAAATTTATTTTTTTC
Found at i:54594059 original size:41 final size:41
Alignment explanation
Indices: 54594012--54594104 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
54594002 TACATTTCCA
*
54594012 TTTCATTTAAATTATTT-TTTTCCATTT-AAATT-TAATTTTT
1 TTTCATTTAAATT-TTTGTTTT-CATTTCAAATTATAATTTAT
* *
54594052 TTCTCATTTCAATTTTTGTTTTCATTTCAATTTATAATTTAT
1 TT-TCATTTAAATTTTTGTTTTCATTTCAAATTATAATTTAT
54594094 TTTCATTTAAA
1 TTTCATTTAAA
54594105 CTTTCATTCC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
40 10 0.22
41 26 0.58
42 9 0.20
ACGTcount: A:0.27, C:0.10, G:0.01, T:0.62
Consensus pattern (41 bp):
TTTCATTTAAATTTTTGTTTTCATTTCAAATTATAATTTAT
Found at i:54594068 original size:18 final size:18
Alignment explanation
Indices: 54594041--54594084 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
54594031 TTCCATTTAA
*
54594041 ATTT-AATTTTT-TTCTC
1 ATTTCAATTTTTGTTTTC
54594057 ATTTCAATTTTTGTTTTC
1 ATTTCAATTTTTGTTTTC
54594075 ATTTCAATTT
1 ATTTCAATTT
54594085 ATAATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 4 0.16
17 7 0.28
18 14 0.56
ACGTcount: A:0.20, C:0.11, G:0.02, T:0.66
Consensus pattern (18 bp):
ATTTCAATTTTTGTTTTC
Found at i:54594127 original size:28 final size:28
Alignment explanation
Indices: 54594095--54594201 Score: 119
Period size: 28 Copynumber: 3.8 Consensus size: 28
54594085 ATAATTTATT
*
54594095 TTCATTTAA-ACTTTCATTCCATTTCATA
1 TTCATTTAACA-TTTCATTTCATTTCATA
54594123 TTCATTTAACATTTCATTTCATTTCATA
1 TTCATTTAACATTTCATTTCATTTCATA
* * * * *
54594151 TCCA-TTACAAATTACATTACATTACATA
1 TTCATTTA-ACATTTCATTTCATTTCATA
*
54594179 TTTATTTAACATTTCATTTCATT
1 TTCATTTAACATTTCATTTCATT
54594202 AATTTTTTTC
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
27 3 0.05
28 58 0.89
29 4 0.06
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.50
Consensus pattern (28 bp):
TTCATTTAACATTTCATTTCATTTCATA
Found at i:54594142 original size:5 final size:5
Alignment explanation
Indices: 54594106--54594149 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
54594096 TCATTTAAAC
*
54594106 TTTCA TTCCA TTTCA TATTCA TTTAACA TTTCA TTTCA TTTCA T
1 TTTCA TTTCA TTTCA T-TTCA TTT--CA TTTCA TTTCA TTTCA T
54594150 ATCCATTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 24 0.71
6 5 0.15
7 5 0.15
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (5 bp):
TTTCA
Found at i:54594316 original size:15 final size:15
Alignment explanation
Indices: 54594273--54594316 Score: 61
Period size: 16 Copynumber: 2.9 Consensus size: 15
54594263 AGTAGTCTCA
* *
54594273 TTTCAATTTATCTTT
1 TTTCAATTCATTTTT
54594288 TTTCAATTCAATTTTT
1 TTTCAATTC-ATTTTT
54594304 TTTCAATTCATTT
1 TTTCAATTCATTT
54594317 CATATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTCAATTCATTTTT
Found at i:54594614 original size:5 final size:5
Alignment explanation
Indices: 54594606--54594706 Score: 69
Period size: 5 Copynumber: 18.6 Consensus size: 5
54594596 ATCTTTTTTT
*
54594606 TTTCA TTTCA TTTCTA TTTCTA TTTCA TTTTA TTTCA TATGT-A TTTTCA
1 TTTCA TTTCA TTTC-A TTTC-A TTTCA TTTCA TTTCA T-T-TCA -TTTCA
* * * *
54594655 TTTCA TTTCA TTTAA TTTGTA TTTGTA TTTCA TTTCTA TTTCTA TTTTA
1 TTTCA TTTCA TTTCA TTT-CA TTT-CA TTTCA TTTC-A TTTC-A TTTCA
54594704 TTT
1 TTT
54594707 AAATTACCTT
Statistics
Matches: 83, Mismatches: 6, Indels: 14
0.81 0.06 0.14
Matches are distributed among these distances:
5 46 0.55
6 35 0.42
7 2 0.02
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.65
Consensus pattern (5 bp):
TTTCA
Found at i:54594631 original size:22 final size:22
Alignment explanation
Indices: 54594606--54594706 Score: 87
Period size: 22 Copynumber: 4.4 Consensus size: 22
54594596 ATCTTTTTTT
54594606 TTTCATTTCATTTCTATTTCTA
1 TTTCATTTCATTTCTATTTCTA
* *
54594628 TTTCATTTTATTTCATATGTATTTTCA
1 TTTCATTTCATTTC-TA--T-TTCT-A
* *
54594655 TTTCATTTCATTT-AATTTGTA
1 TTTCATTTCATTTCTATTTCTA
*
54594676 TTTGTATTTCATTTCTATTTCTA
1 TTT-CATTTCATTTCTATTTCTA
*
54594699 TTTTATTT
1 TTTCATTT
54594707 AAATTACCTT
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
21 4 0.06
22 30 0.47
23 12 0.19
25 2 0.03
26 3 0.05
27 13 0.20
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.65
Consensus pattern (22 bp):
TTTCATTTCATTTCTATTTCTA
Found at i:54594650 original size:27 final size:26
Alignment explanation
Indices: 54594605--54594706 Score: 107
Period size: 27 Copynumber: 3.7 Consensus size: 26
54594595 CATCTTTTTT
*
54594605 TTTTCATTTCATTTCTATTTCTATTTCA
1 TTTT-ATTTCATTTGTATTT-TATTTCA
*
54594633 TTTTATTTCATATGTATTTTCATTTCA
1 TTTTATTTCATTTGTATTTT-ATTTCA
* *
54594660 TTTCATTTAATTTGTATTTGTATTTCA
1 TTTTATTTCATTTGTATTT-TATTTCA
54594687 TTTCTATTTCTATTT-TATTT
1 TTT-TATTTC-ATTTGTATTT
54594707 AAATTACCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
26 1 0.02
27 44 0.70
28 14 0.22
29 4 0.06
ACGTcount: A:0.20, C:0.12, G:0.03, T:0.66
Consensus pattern (26 bp):
TTTTATTTCATTTGTATTTTATTTCA
Found at i:54594824 original size:47 final size:47
Alignment explanation
Indices: 54594693--54595063 Score: 520
Period size: 47 Copynumber: 7.9 Consensus size: 47
54594683 TTCATTTCTA
* * *
54594693 TTTCT-ATTTTATTTAAATTACCTTTTTTTCATTTAAATTTAA-TTT
1 TTTCTCATTTCATTTAAATTATCTTTTTTCCATTTAAATTTAATTTT
*
54594738 TTTCTCATTTCATTTAAATTATCTTTTTTTTTCATTTAAATTTAATTTT
1 TTTCTCATTTCATTTAAATTATC--TTTTTTCCATTTAAATTTAATTTT
****
54594787 TTTCTCATTTCATTTAAATTAAAAATTTTCCATTTAAATTTAA-TTT
1 TTTCTCATTTCATTTAAATTATCTTTTTTCCATTTAAATTTAATTTT
54594833 TTTCTCATTTCATTTAAATTATCTTTCTTTCCATTTAAATTT-ATTTT
1 TTTCTCATTTCATTTAAATTATCTTT-TTTCCATTTAAATTTAATTTT
*
54594880 TTTCTCATTTCATTTAAATTATCTTTCTTTCCATTTAAATTTAATATT
1 TTTCTCATTTCATTTAAATTATCTTT-TTTCCATTTAAATTTAATTTT
*
54594928 TTTCTCATTTAATTTAAATTATCTTTTTTCCATTTAAATTTAATTTT
1 TTTCTCATTTCATTTAAATTATCTTTTTTCCATTTAAATTTAATTTT
* * *
54594975 TTTCTCATTTCATTTAAATTATATTTCTTTCTATTTTAATTTAA--TT
1 TTTCTCATTTCATTTAAATTATCTTT-TTTCCATTTAAATTTAATTTT
*
54595021 TTTCTCATTTCATTTAAATTATCTTTCTTTCCATTTTAATTTA
1 TTTCTCATTTCATTTAAATTATCTTT-TTTCCATTTAAATTTA
54595064 CGCTTTTTAT
Statistics
Matches: 298, Mismatches: 20, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
45 5 0.02
46 84 0.28
47 121 0.41
48 64 0.21
49 24 0.08
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (47 bp):
TTTCTCATTTCATTTAAATTATCTTTTTTCCATTTAAATTTAATTTT
Found at i:54594956 original size:74 final size:69
Alignment explanation
Indices: 54594719--54595063 Score: 234
Period size: 68 Copynumber: 4.9 Consensus size: 69
54594709 ATTACCTTTT
* * *
54594719 TTTC-ATTTAAATTTAATTTTTTCTCATTTCATTTAAATTATCTTTTTTTTTCATTTAAATTTAA
1 TTTCTATTTAAA-TTATTTTTTTCTCATTTCATTTAAATTATC-TTTCTTTCCATTTAAATTTAA
*
54594783 T-TTTT
64 TATTTC
*** * *
54594788 TTCTCATTTCATTTAAATTAAAAATTTTC-CATTTAAATTT-AATT-T-TTTCTCATTTCATTTA
1 TT-TC---T-ATTTAAATT-ATTTTTTTCTCATTT-CATTTAAATTATCTTTCT--TTCCATTTA
*
54594849 AA-TT-ATCTTTC
57 AATTTAATATTTC
*
54594860 TTTCCATTTAAATTTATTTTTTTCTCATTTCATTTAAATTATCTTTCTTTCCATTTAAATTTAAT
1 TTTCTATTTAAA-TTATTTTTTTCTCATTTCATTTAAATTATCTTTCTTTCCATTTAAATTTAAT
54594925 ATTT-
65 ATTTC
* * *
54594929 TTCTCATTTAATTTAAATTATCTTTTTTC-CATTTAAATTT-AATT-TTTTTCTCATTTCATTTA
1 TT-TC---T-ATTTAAATTAT-TTTTTTCTCATTT-CATTTAAATTATCTTTCT--TTCCATTTA
54594991 AA-TT-ATATTTC
57 AATTTAATATTTC
* * *
54595002 TTTCTATTTTAATT-TAATTTTTCTCATTTCATTTAAATTATCTTTCTTTCCATTTTAATTTA
1 TTTCTATTTAAATTAT-TTTTTTCTCATTTCATTTAAATTATCTTTCTTTCCATTTAAATTTA
54595064 CGCTTTTTAT
Statistics
Matches: 220, Mismatches: 23, Indels: 66
0.71 0.07 0.21
Matches are distributed among these distances:
67 37 0.17
68 40 0.18
69 14 0.06
70 14 0.06
71 8 0.04
72 21 0.10
73 29 0.13
74 39 0.18
75 18 0.08
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (69 bp):
TTTCTATTTAAATTATTTTTTTCTCATTTCATTTAAATTATCTTTCTTTCCATTTAAATTTAATA
TTTC
Found at i:54595061 original size:21 final size:21
Alignment explanation
Indices: 54594843--54595061 Score: 125
Period size: 21 Copynumber: 9.5 Consensus size: 21
54594833 TTTCTCATTT
54594843 CATTTAAATTATCTTTCTTTC
1 CATTTAAATTATCTTTCTTTC
* *
54594864 CATTTAAATTTATTTTTTTCTCATTT
1 CATTTAAA-TTA--TCTTTCT--TTC
54594890 CATTTAAATTATCTTTCTTTC
1 CATTTAAATTATCTTTCTTTC
* *
54594911 CATTTAAATTTAATATTTTTCTCATTT
1 CATTTAAA--T--TATCTTTCT--TTC
*
54594938 AATTTAAATTATCTTT-TTTC
1 CATTTAAATTATCTTTCTTTC
* *
54594958 CATTTAAATTTAATTTTTTTCTCATTT
1 CATTTAAA-TT-A--TCTTTCT--TTC
*
54594985 CATTTAAATTATATTTCTTTC
1 CATTTAAATTATCTTTCTTTC
* * * *
54595006 TATTTTAATTTAATTTTTCTCATTT
1 CA-TTTAAATT-ATCTTTCT--TTC
54595031 CATTTAAATTATCTTTCTTTC
1 CATTTAAATTATCTTTCTTTC
*
54595052 CATTTTAATT
1 CATTTAAATT
54595062 TACGCTTTTT
Statistics
Matches: 153, Mismatches: 23, Indels: 44
0.70 0.10 0.20
Matches are distributed among these distances:
20 9 0.06
21 34 0.22
22 12 0.08
23 33 0.22
24 17 0.11
25 17 0.11
26 12 0.08
27 19 0.12
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (21 bp):
CATTTAAATTATCTTTCTTTC
Found at i:54595071 original size:95 final size:95
Alignment explanation
Indices: 54594693--54595063 Score: 556
Period size: 95 Copynumber: 3.9 Consensus size: 95
54594683 TTCATTTCTA
* ** *
54594693 TTTCT-ATTTTATTTAAATTACCTTT-TTTTCATTTAAATTTAATTTTTTCTCATTTCATTTAAA
1 TTTCTCATTTCATTTAAATTATATTTCTTTCCATTTAAATTTAATTTTTTCTCATTTCATTTAAA
* *
54594756 TTATCTTTTTTTTTCATTTAAATTTAATTTT
66 TTATC-TTTCTTTCCATTTAAATTTAATTTT
* **
54594787 TTTCTCATTTCATTTAAATTAAAAAT-TTTCCATTTAAATTTAATTTTTTCTCATTTCATTTAAA
1 TTTCTCATTTCATTTAAATTATATTTCTTTCCATTTAAATTTAATTTTTTCTCATTTCATTTAAA
54594851 TTATCTTTCTTTCCATTTAAATTT-ATTTT
66 TTATCTTTCTTTCCATTTAAATTTAATTTT
* *
54594880 TTTCTCATTTCATTTAAATTATCTTTCTTTCCATTTAAATTTAATATTTTTCTCATTTAATTTAA
1 TTTCTCATTTCATTTAAATTATATTTCTTTCCATTTAAATTTAAT-TTTTTCTCATTTCATTTAA
54594945 ATTATCTTT-TTTCCATTTAAATTTAATTTT
65 ATTATCTTTCTTTCCATTTAAATTTAATTTT
* *
54594975 TTTCTCATTTCATTTAAATTATATTTCTTTCTATTTTAATTTAA-TTTTTCTCATTTCATTTAAA
1 TTTCTCATTTCATTTAAATTATATTTCTTTCCATTTAAATTTAATTTTTTCTCATTTCATTTAAA
*
54595039 TTATCTTTCTTTCCATTTTAATTTA
66 TTATCTTTCTTTCCATTTAAATTTA
54595064 CGCTTTTTAT
Statistics
Matches: 254, Mismatches: 18, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
93 54 0.21
94 70 0.28
95 130 0.51
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (95 bp):
TTTCTCATTTCATTTAAATTATATTTCTTTCCATTTAAATTTAATTTTTTCTCATTTCATTTAAA
TTATCTTTCTTTCCATTTAAATTTAATTTT
Found at i:54595135 original size:22 final size:22
Alignment explanation
Indices: 54595110--54595179 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
54595100 TTTTCATTTA
54595110 ATGTGTTTTAAAATAAATATGT
1 ATGTGTTTTAAAATAAATATGT
* **
54595132 ATGTATATTGTATTAT-AAT-T-T
1 ATGTGT-TT-TAAAATAAATATGT
54595153 AATGTGTTTTAAAATAAATATGT
1 -ATGTGTTTTAAAATAAATATGT
54595176 ATGT
1 ATGT
54595180 ATATTGTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 4 0.11
21 6 0.17
22 16 0.44
23 6 0.17
24 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.49
Consensus pattern (22 bp):
ATGTGTTTTAAAATAAATATGT
Found at i:54595256 original size:44 final size:44
Alignment explanation
Indices: 54595105--54595253 Score: 262
Period size: 44 Copynumber: 3.4 Consensus size: 44
54595095 TTTATTTTTC
54595105 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
54595149 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
* * *
54595193 ATTTAATGTGCTTTAAATTAAATATGCATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
*
54595237 ATTTAACGTGTTTTAAA
1 ATTTAATGTGTTTTAAA
54595254 TTAGGAATAA
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 100 1.00
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (44 bp):
ATTTAATGTGTTTTAAAATAAATATGTATGTATATTGTATTATA
Found at i:54596726 original size:46 final size:46
Alignment explanation
Indices: 54596652--54596882 Score: 399
Period size: 46 Copynumber: 5.0 Consensus size: 46
54596642 ACATTGCTAT
* * *
54596652 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
* * *
54596698 AACTCAGTATAGTTTTCTTTACCTAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
54596744 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
*
54596790 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTAAC
1 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
54596836 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
54596882 A
1 A
54596883 CTTTGCCATG
Statistics
Matches: 176, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 176 1.00
ACGTcount: A:0.29, C:0.27, G:0.08, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
Found at i:54601636 original size:111 final size:112
Alignment explanation
Indices: 54601477--54601679 Score: 313
Period size: 111 Copynumber: 1.8 Consensus size: 112
54601467 GGTGCCGTCC
54601477 ATCAGTGTCCCAAAGTAAAAAAAAAATTACCTTGGGACCCGAAAAATGTACCTGGTGCCAG-CCA
1 ATCAGTGTCCCAAAGT-AAAAAAAAATTACCTTGGGACCCGAAAAATGTACCTGGTG-CAGACCA
*
54601541 TCTACTGACCAGCACTC-AAATTTTTTTTAAATTGACATTGGTGTCGGCG
64 TCTACTGACCAACAC-CAAAATTTTTTTTAAATTGACATTGGTGTCGGCG
* * *
54601590 ATCAGTGTCCCAAAGT-AAAAAAAATTGCCTTGGGACCCGAAAAATGTACTTGGTGCTGACCATC
1 ATCAGTGTCCCAAAGTAAAAAAAAATTACCTTGGGACCCGAAAAATGTACCTGGTGCAGACCATC
*
54601654 TACTGGCCAACACCAAAATTTTTTTT
66 TACTGACCAACACCAAAATTTTTTTT
54601680 TTCAATGTGT
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
110 3 0.04
111 64 0.77
113 16 0.19
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (112 bp):
ATCAGTGTCCCAAAGTAAAAAAAAATTACCTTGGGACCCGAAAAATGTACCTGGTGCAGACCATC
TACTGACCAACACCAAAATTTTTTTTAAATTGACATTGGTGTCGGCG
Found at i:54602553 original size:18 final size:18
Alignment explanation
Indices: 54602530--54602566 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
54602520 TTGCTTATAT
54602530 AAAAT-AAAAATAATTTTA
1 AAAATAAAAAAT-ATTTTA
54602548 AAAATAAAAAATATTTTA
1 AAAATAAAAAATATTTTA
54602566 A
1 A
54602567 CTTTAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATAAAAAATATTTTA
Found at i:54624818 original size:2 final size:2
Alignment explanation
Indices: 54624811--54624835 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54624801 GATTTCCCTC
54624811 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
54624836 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:54631648 original size:19 final size:20
Alignment explanation
Indices: 54631626--54631663 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
54631616 TGAACTTTTT
54631626 ATTTTTTAA-TTTTAATTTG
1 ATTTTTTAATTTTTAATTTG
54631645 ATTTTTTAATTTTTAATTT
1 ATTTTTTAATTTTTAATTT
54631664 TTATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (20 bp):
ATTTTTTAATTTTTAATTTG
Found at i:54631670 original size:16 final size:16
Alignment explanation
Indices: 54631641--54631679 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
54631631 TTAATTTTAA
54631641 TTTG-ATTTTTTAATT
1 TTTGAATTTTTTAATT
54631656 TTT-AATTTTTATAATT
1 TTTGAATTTTT-TAATT
54631672 TTTGAATT
1 TTTGAATT
54631680 ATTTGTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.43
16 8 0.38
17 4 0.19
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTGAATTTTTTAATT
Found at i:54632331 original size:13 final size:13
Alignment explanation
Indices: 54632313--54632338 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54632303 TATTACTTTG
54632313 AACTCTTAGAAAA
1 AACTCTTAGAAAA
54632326 AACTCTTAGAAAA
1 AACTCTTAGAAAA
54632339 CTTTTGAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
AACTCTTAGAAAA
Found at i:54632382 original size:20 final size:19
Alignment explanation
Indices: 54632357--54632414 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
54632347 TCAACCTTTA
54632357 AATCAAATTAAAATAGTTTC
1 AATCAAATTAAAAT-GTTTC
* * *
54632377 AATCAAGTTAGAATTTTTC
1 AATCAAATTAAAATGTTTC
*
54632396 AATCAAAGTTAAATTGTTT
1 AATCAAA-TTAAAATGTTT
54632415 TTAAAACAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (19 bp):
AATCAAATTAAAATGTTTC
Found at i:54632397 original size:19 final size:19
Alignment explanation
Indices: 54632373--54632410 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
54632363 ATTAAAATAG
54632373 TTTCAATC-AAGTTAGAATT
1 TTTCAATCAAAGTTA-AATT
54632392 TTTCAATCAAAGTTAAATT
1 TTTCAATCAAAGTTAAATT
54632411 GTTTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (19 bp):
TTTCAATCAAAGTTAAATT
Found at i:54638152 original size:7 final size:7
Alignment explanation
Indices: 54638142--54638208 Score: 64
Period size: 7 Copynumber: 9.7 Consensus size: 7
54638132 CATAAATCTG
54638142 AAACTCA
1 AAACTCA
54638149 AAACTCA
1 AAACTCA
* **
54638156 AAAATTG
1 AAACTCA
54638163 AAACTCA
1 AAACTCA
* *
54638170 AAACCCT
1 AAACTCA
54638177 AAACTCA
1 AAACTCA
*
54638184 AAACTCC
1 AAACTCA
*
54638191 AAATTCA
1 AAACTCA
54638198 AAAC-CA
1 AAACTCA
54638204 AAACT
1 AAACT
54638209 TGAAGCCCTA
Statistics
Matches: 45, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
6 6 0.13
7 39 0.87
ACGTcount: A:0.55, C:0.27, G:0.01, T:0.16
Consensus pattern (7 bp):
AAACTCA
Found at i:54638187 original size:21 final size:21
Alignment explanation
Indices: 54638163--54638246 Score: 55
Period size: 21 Copynumber: 4.0 Consensus size: 21
54638153 TCAAAAATTG
54638163 AAACTCAAAACCCTAAACTCA
1 AAACTCAAAACCCTAAACTCA
* ** *
54638184 AAACTCCAAATTCAAAAC-CA
1 AAACTCAAAACCCTAAACTCA
** * *
54638204 AAACTTGAAGCCCTAAACCTTA
1 AAACTCAAAACCCTAAA-CTCA
* *
54638226 AACCT-AAAACCCTAAAATCA
1 AAACTCAAAACCCTAAACTCA
54638246 A
1 A
54638247 CCAAAAACCC
Statistics
Matches: 45, Mismatches: 16, Indels: 5
0.68 0.24 0.08
Matches are distributed among these distances:
20 16 0.36
21 24 0.53
22 5 0.11
ACGTcount: A:0.51, C:0.30, G:0.02, T:0.17
Consensus pattern (21 bp):
AAACTCAAAACCCTAAACTCA
Found at i:54638198 original size:28 final size:28
Alignment explanation
Indices: 54638149--54638202 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
54638139 CTGAAACTCA
**
54638149 AAACTCAAAAATTGAAACTCAAAACCCT
1 AAACTCAAAAATCCAAACTCAAAACCCT
* *
54638177 AAACTCAAAACTCCAAATTCAAAACC
1 AAACTCAAAAATCCAAACTCAAAACC
54638203 AAAACTTGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.54, C:0.28, G:0.02, T:0.17
Consensus pattern (28 bp):
AAACTCAAAAATCCAAACTCAAAACCCT
Found at i:54638291 original size:7 final size:7
Alignment explanation
Indices: 54638267--54638308 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
54638257 AAAACTTTAG
54638267 ACCATAA
1 ACCATAA
54638274 ACTC-T-A
1 AC-CATAA
54638280 ACCATAA
1 ACCATAA
54638287 ACCATAA
1 ACCATAA
*
54638294 ATCATAA
1 ACCATAA
54638301 ACCATAA
1 ACCATAA
54638308 A
1 A
54638309 ACTAAAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 1 0.03
6 4 0.13
7 24 0.80
8 1 0.03
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (7 bp):
ACCATAA
Found at i:54651933 original size:2 final size:2
Alignment explanation
Indices: 54651926--54651952 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54651916 AATATAGATT
54651926 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 T
54651953 TGTATTTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54653296 original size:10 final size:10
Alignment explanation
Indices: 54653283--54653309 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54653273 CAAACATACT
54653283 CAAAACATGC
1 CAAAACATGC
54653293 CAAAACATGC
1 CAAAACATGC
54653303 CAAAACA
1 CAAAACA
54653310 ATCATCTTAG
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:0.56, C:0.30, G:0.07, T:0.07
Consensus pattern (10 bp):
CAAAACATGC
Found at i:54655392 original size:2 final size:2
Alignment explanation
Indices: 54655385--54655417 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54655375 ATAACATATA
54655385 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
54655418 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:54657652 original size:44 final size:44
Alignment explanation
Indices: 54657597--54657680 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
54657587 ATTTAGCTAC
*
54657597 TATTTTAGAGGCATTTAATTGCTAAGTTGCAACTACTTTAGTGT
1 TATTTAAGAGGCATTTAATTGCTAAGTTGCAACTACTTTAGTGT
* * * *
54657641 TATTTAAGAGGCATTTACTTGTTAAGTTGCTACTATTTTA
1 TATTTAAGAGGCATTTAATTGCTAAGTTGCAACTACTTTA
54657681 ATTATTGCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.27, C:0.11, G:0.17, T:0.45
Consensus pattern (44 bp):
TATTTAAGAGGCATTTAATTGCTAAGTTGCAACTACTTTAGTGT
Found at i:54657691 original size:15 final size:16
Alignment explanation
Indices: 54657673--54657702 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54657663 TAAGTTGCTA
54657673 CTATTTTAAT-TATTG
1 CTATTTTAATGTATTG
54657688 CTATTTTAATGTATT
1 CTATTTTAATGTATT
54657703 TTCAATTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (16 bp):
CTATTTTAATGTATTG
Found at i:54658284 original size:21 final size:21
Alignment explanation
Indices: 54658241--54658316 Score: 80
Period size: 21 Copynumber: 3.4 Consensus size: 21
54658231 ATAAAGGATT
* *
54658241 CCCTTTAGTAGTATCACGGTATC
1 CCCTTTA--AGTATCGCGATATC
**
54658264 CCCTTTTGGTATCGCGATATC
1 CCCTTTAAGTATCGCGATATC
54658285 CCCTTTAAGTATCGCGATATC
1 CCCTTTAAGTATCGCGATATC
54658306 CACCTTCTAAG
1 C-CCTT-TAAG
54658317 GAAGACTTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 31 0.69
22 4 0.09
23 10 0.22
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (21 bp):
CCCTTTAAGTATCGCGATATC
Found at i:54673207 original size:21 final size:21
Alignment explanation
Indices: 54673183--54673222 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54673173 ATGTTCGAAA
* *
54673183 TTTAGTCTTTTTATTTTTATT
1 TTTAGTCTATTTACTTTTATT
54673204 TTTAGTCTATTTACTTTTA
1 TTTAGTCTATTTACTTTTA
54673223 AGATTTACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTAGTCTATTTACTTTTATT
Found at i:54673759 original size:19 final size:19
Alignment explanation
Indices: 54673747--54673834 Score: 72
Period size: 19 Copynumber: 4.5 Consensus size: 19
54673737 ATTTTTTAAA
54673747 TTTTAAAATATTTAAAATACT
1 TTTTAAAAT-TTTAAAATA-T
**
54673768 TTTTTTAATTTTAAAATAT
1 TTTTAAAATTTTAAAATAT
**
54673787 TTTTAAAATACTTT--TTTAT
1 TTTTAAAAT--TTTAAAATAT
**
54673806 TTTTTTAATTTTAAAATAT
1 TTTTAAAATTTTAAAATAT
54673825 TTTTAAAATT
1 TTTTAAAATT
54673835 ATTTTTAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
17 3 0.06
19 29 0.57
20 9 0.18
21 10 0.20
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAAATTTTAAAATAT
Done.