Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 178 of 240
Found at i:55029898 original size:5 final size:5
Alignment explanation
Indices: 55029882--55029911 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
55029872 TTCTATTCTA
55029882 AAAAT AAGAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AA-AAT AAAAT AAAAT AAAAT AAAA
55029912 GAGAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:55030939 original size:23 final size:22
Alignment explanation
Indices: 55030890--55030946 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
55030880 AGGACATTGC
*
55030890 CTTTCTCCATCTTCCATCAAAT
1 CTTTTTCCATCTTCCATCAAAT
55030912 CTTTTTCCATCTCTCCAT-AATAT
1 CTTTTTCCATCT-TCCATCAA-AT
*
55030935 -TTTTTCTATCTT
1 CTTTTTCCATCTT
55030947 GATTATGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.03
22 23 0.74
23 7 0.23
ACGTcount: A:0.19, C:0.30, G:0.00, T:0.51
Consensus pattern (22 bp):
CTTTTTCCATCTTCCATCAAAT
Found at i:55037364 original size:24 final size:24
Alignment explanation
Indices: 55037310--55037369 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
55037300 TTAAAATATC
* *
55037310 ATTTAAAATCTATTTATCTGAATT
1 ATTTAAAATCTATTTAACTAAATT
* *
55037334 CTGTAAAATCTATTTAACTAAATT
1 ATTTAAAATCTATTTAACTAAATT
55037358 ATTTAAATATCT
1 ATTTAAA-ATCT
55037370 TATATAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (24 bp):
ATTTAAAATCTATTTAACTAAATT
Found at i:55040208 original size:21 final size:21
Alignment explanation
Indices: 55040172--55040225 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
55040162 ATCATATATT
55040172 CCAAGATTGC--ATATCATAC
1 CCAAGATTGCATATATCATAC
*
55040191 CCAAGATTGCATATATCATAT
1 CCAAGATTGCATATATCATAC
* *
55040212 CTAAGATTGTATAT
1 CCAAGATTGCATAT
55040226 CCTTGAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 10 0.33
21 20 0.67
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
CCAAGATTGCATATATCATAC
Found at i:55040652 original size:44 final size:44
Alignment explanation
Indices: 55040599--55041029 Score: 535
Period size: 44 Copynumber: 9.8 Consensus size: 44
55040589 ACCAGAATGG
* * * *
55040599 GAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGAA-AAAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC-AATACAT
* * *
55040643 GAAGACAAGATCTGTTTTCTTCGATCTACTT--CGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* * * * * ***
55040685 GAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCA-CGCCAATACAT
** *
55040730 GAAGACAAGATCTATTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
55040774 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
*
55040818 GAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* * * * * ***
55040862 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTC-ACGCCAATACAT
* *
55040907 GAAGACAATATCTGCTATCTTTGATCTACTTCATGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
55040951 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
* *
55040995 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACG
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACG
55041030 ACAACCCAGG
Statistics
Matches: 334, Mismatches: 48, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
41 2 0.01
42 35 0.10
44 225 0.67
45 72 0.22
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
Found at i:55040905 original size:177 final size:177
Alignment explanation
Indices: 55040599--55041029 Score: 697
Period size: 177 Copynumber: 2.4 Consensus size: 177
55040589 ACCAGAATGG
* * * * *
55040599 GAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGAA-AAATGAAGACAAGATCTGTTTTCT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCC-AATACATGAAGACAAGATCTGCTTTCT
55040663 TCGATCTACTT--CGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGT
65 TCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGT
*
55040726 ATGGGAAGACAAGATCTATTATCTTCGATCTACTTCACGCCAATACAT
130 ATGGGAAGACAAGATCTACTATCTTCGATCTACTTCACGCCAATACAT
* *
55040774 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATATT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
* * *
55040839 TGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTA
66 CGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTA
* * * *
55040904 TGGGAAGACAATATCTGCTATCTTTGATCTACTTCATGCCAATACAT
131 TGGGAAGACAAGATCTACTATCTTCGATCTACTTCACGCCAATACAT
55040951 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
55041016 CGATCTACTTCACG
66 CGATCTACTTCACG
55041030 ACAACCCAGG
Statistics
Matches: 235, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
174 2 0.01
175 64 0.27
177 169 0.72
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (177 bp):
GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
CGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTA
TGGGAAGACAAGATCTACTATCTTCGATCTACTTCACGCCAATACAT
Found at i:55040911 original size:133 final size:132
Alignment explanation
Indices: 55040599--55041103 Score: 538
Period size: 133 Copynumber: 3.8 Consensus size: 132
55040589 ACCAGAATGG
** * * ** * * * *
55040599 GAAGACAAGATCTGCTACCTTTGATCTATTTCATGCCGAA-AAATGAAGACAAGATCTGTTTTCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACACC-AATACAGGAAGACAAGATCTGCTATCT
* * * * * *
55040663 TCGATCTACTT--CGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGT
65 TTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCA-CGCCAAT
***
55040726 ATGG
129 ACAT
* * *
55040730 GAAGACAAGATCT-ATTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCT
1 GAAGACAAGATCTGCTT-TCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATCT
*
55040794 TTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATATTTGATCTACTTCACGCCAATA
65 TTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATA
55040859 CAT
130 CAT
* * ** *
55040862 GAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAATATCTGCTATCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTC-ACACCAATACAGGAAGACAAGATCTGCTATCT
*
55040927 TTGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATA
65 TTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATA
55040992 CAT
130 CAT
** * * * *
55040995 GAAGACAAGATCTGCTTTCTTCGATCTACTTCACGA-CAACCCAGGGAGGCAAG-GCTGGTATCT
1 GAAGACAAGATCTGCTTTCTTCGATCTACTTCAC-ACCAATACAGGAAGACAAGATCTGCTATCT
* * ** *
55041058 TTGATCTGCTTCACTGTCGGTACAGGAA-AGCAAGATCTGCTATCTT
65 TTGATCTACTTCAC-GCCAATACATGAAGA-CAAGATCTGCTATCTT
55041104 CAACCTGCTC
Statistics
Matches: 319, Mismatches: 46, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
130 3 0.01
131 81 0.25
132 69 0.22
133 166 0.52
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (132 bp):
GAAGACAAGATCTGCTTTCTTCGATCTACTTCACACCAATACAGGAAGACAAGATCTGCTATCTT
TGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATAC
AT
Found at i:55041092 original size:88 final size:88
Alignment explanation
Indices: 55040966--55041753 Score: 1030
Period size: 88 Copynumber: 9.0 Consensus size: 88
55040956 CAAGATCTGC
* * * * * * * * * * * *
55040966 TATCTTTGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCACG
1 TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
55041030 ACAACCCAGGGAGGCAAGGCTGG
66 ACAACCCAGGGAGGCAAGGCTGG
* * *
55041053 TATCTTTGATCTGCTTCACTGTCGGTACAGGAAAGCAAGATCTGCTATCTTCAACCTGCTCCACT
1 TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
55041118 ACAACCCAGGGAGGCAAGGCTGA
66 ACAACCCAGGGAGGCAAGGCTGG
* * * *
55041141 TATTTTCGATTTGTTTCACTGTC-AGTACAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
1 TATCTTCGATCTGCTTCACTGTCGA-TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
*
55041205 TACGACCCAGGGAGGCAAGGCTGG
65 TACAACCCAGGGAGGCAAGGCTGG
* * * *
55041229 TATCTTCGATCTGCTTCGCTGTCAATACAGGAAGACAAGATCTGTTATCTTCAACCTGCTCCACT
1 TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
55041294 ACAACCTAGGGAGGCAAGGCTGG
66 ACAACCCAGGGAGGCAAGGCTGG
* *
55041317 TAT-TTCGATCTGCTTCACTGTCGATGCAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
1 TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
55041381 ACAACCCAGGGAGACAAGGCTGG
66 ACAACCCAGGGAGGCAAGGCTGG
* * * * **
55041404 TATATTCGATCAGCTACGCTGTCGATGTAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
1 TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
55041469 ACAACCCAGAGAGGCAAGGCTGG
66 ACAACCCAGGGAGGCAAGGCTGG
* * * * *
55041492 TATCTTCGATCTGCTTCGCTGTCGATGCAAGAAGGCAAGATTTGCTATTTTCAACCTGCTCCACT
1 TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
55041557 ACAACCCAGAGAGGCAAGGCTGG
66 ACAACCCAGGGAGGCAAGGCTGG
* *
55041580 TATCTTCGATCTGCTTCGA-TGTCGATGCAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCAC
1 TATCTTCGATCTGCTTC-ACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
* *
55041644 TACAACCCAGAGAGGCAAGGCTAG
65 TACAACCCAGGGAGGCAAGGCTGG
* * *
55041668 TATCTTCGATCTGCTTCA-TCGTC-AGTACAGGAAGGCAAGATCTGTTATTTTCAACCTGCTCCG
1 TATCTTCGATCTGCTTCACT-GTCGA-TACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCA
* * *
55041731 CTGCAAACCAGGAAGGCAAGGCT
64 CTACAACCCAGGGAGGCAAGGCT
55041754 TTGTGATTTC
Statistics
Matches: 625, Mismatches: 69, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
87 100 0.16
88 524 0.84
89 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (88 bp):
TATCTTCGATCTGCTTCACTGTCGATACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
ACAACCCAGGGAGGCAAGGCTGG
Found at i:55041643 original size:351 final size:352
Alignment explanation
Indices: 55040966--55041753 Score: 1057
Period size: 351 Copynumber: 2.2 Consensus size: 352
55040956 CAAGATCTGC
* * * * * * * * * *
55040966 TATCTTTGATCTACTTCA-CGCCAATACATG-AAGACAAGATCTGCTTTCTTCGATCTACTTCAC
1 TATCTTCGATCTGCTTCATCGTCAGTACA-GAAAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
* * * * * *
55041029 GACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCTGCTTCACTGTCGGTACAGGAAAGCAAGAT
65 TACAACCCAGGGAGGCAAGGCTGGTATATTCGATCAGCTACACTGTCGATACAGGAAAGCAAGAT
* * * *
55041094 CTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGATATTTTCGATTTGTTTCA
130 CTGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCAAGGCTGATATCTTCGATCTGCTTCA
* *
55041159 CTGTCAGTACAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCAGGGAGGCAAG
195 CTGTCAGTACAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCAAG
* *
55041224 GCTGGTATCTTCGATCTGCTTCGCTGTCAATACAGGAAGACAAGATCTGTTATCTTCAACCTGCT
260 GCTGGTATCTTCGATCTGCTTCGATGTCAATACAGGAAGACAAGATCTGCTATCTTCAACCTGCT
* * *
55041289 CCACTACAACCTAGGGAGGCAAGGCTGG
325 CCACTACAACCCAGAGAGGCAAGGCTAG
*
55041317 TAT-TTCGATCTGCTTCA-CTGTC-GATGCAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCA
1 TATCTTCGATCTGCTTCATC-GTCAG-TACAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCA
* * ** *
55041379 CTACAACCCAGGGAGACAAGGCTGGTATATTCGATCAGCTACGCTGTCGATGTAGGAAGGCAAGA
64 CTACAACCCAGGGAGGCAAGGCTGGTATATTCGATCAGCTACACTGTCGATACAGGAAAGCAAGA
*
55041444 TCTGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCAAGGCTGGTATCTTCGATCTGCTTC
129 TCTGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCAAGGCTGATATCTTCGATCTGCTTC
* * * *
55041509 GCTGTC-GATGCAAGAAGGCAAGATTTGCTATTTTCAACCTGCTCCACTACAACCCAGAGAGGCA
194 ACTGTCAG-TACAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCA
* * * *
55041573 AGGCTGGTATCTTCGATCTGCTTCGATGTCGATGCAGGAAGGCAAGATCTGCTATCTTTAACCTG
258 AGGCTGGTATCTTCGATCTGCTTCGATGTCAATACAGGAAGACAAGATCTGCTATCTTCAACCTG
55041638 CTCCACTACAACCCAGAGAGGCAAGGCTAG
323 CTCCACTACAACCCAGAGAGGCAAGGCTAG
* * * *
55041668 TATCTTCGATCTGCTTCATCGTCAGTACAGGAAGGCAAGATCTGTTATTTTCAACCTGCTCCGCT
1 TATCTTCGATCTGCTTCATCGTCAGTACAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
* * *
55041733 GCAAACCAGGAAGGCAAGGCT
66 ACAACCCAGGGAGGCAAGGCT
55041754 TTGTGATTTC
Statistics
Matches: 379, Mismatches: 51, Indels: 13
0.86 0.12 0.03
Matches are distributed among these distances:
350 15 0.04
351 293 0.77
352 69 0.18
353 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (352 bp):
TATCTTCGATCTGCTTCATCGTCAGTACAGAAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
ACAACCCAGGGAGGCAAGGCTGGTATATTCGATCAGCTACACTGTCGATACAGGAAAGCAAGATC
TGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCAAGGCTGATATCTTCGATCTGCTTCAC
TGTCAGTACAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGAGAGGCAAGG
CTGGTATCTTCGATCTGCTTCGATGTCAATACAGGAAGACAAGATCTGCTATCTTCAACCTGCTC
CACTACAACCCAGAGAGGCAAGGCTAG
Found at i:55043375 original size:10 final size:9
Alignment explanation
Indices: 55043350--55043374 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55043340 CCTGGAAGAG
55043350 TTTTTTTCT
1 TTTTTTTCT
55043359 TTTTTTTCT
1 TTTTTTTCT
55043368 TTTTTTT
1 TTTTTTT
55043375 TGCACCATCC
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:55048628 original size:21 final size:21
Alignment explanation
Indices: 55048602--55048653 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
55048592 CATATCTTCC
55048602 AAGATTGCATATATCATATCT
1 AAGATTGCATATATCATATCT
*
55048623 AAGATTGC--ATGTCATATCT
1 AAGATTGCATATATCATATCT
*
55048642 AAAATTGCATAT
1 AAGATTGCATAT
55048654 CTTTGAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 17 0.63
21 10 0.37
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (21 bp):
AAGATTGCATATATCATATCT
Found at i:55049783 original size:57 final size:57
Alignment explanation
Indices: 55049674--55049785 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 57
55049664 AAAAAAAAAG
* * *
55049674 AAAAAAAATTTGGGTGTTGGCCTATCAATGGCCGGCACCCAGTACGAAAAAAAGGAA
1 AAAAAAAATTTAGGTGCTGGCCTATCAATGGCCGGCACCCAGCACGAAAAAAAGGAA
* * *
55049731 AAAAAAAATTTAGGTGCTGGCCTGTTAATGGTCGGCACCCAGCACAGTAAAAAAA
1 AAAAAAAATTTAGGTGCTGGCCTATCAATGGCCGGCACCCAGCAC-G-AAAAAAA
55049786 TTTATTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 39 0.83
58 1 0.02
59 7 0.15
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (57 bp):
AAAAAAAATTTAGGTGCTGGCCTATCAATGGCCGGCACCCAGCACGAAAAAAAGGAA
Found at i:55050073 original size:212 final size:211
Alignment explanation
Indices: 55049716--55050118 Score: 657
Period size: 212 Copynumber: 1.9 Consensus size: 211
55049706 CGGCACCCAG
* *
55049716 TACGAAAAAAAGGAAAAAAAAAATTTAGGTGCTGGCCTGTTAATGGTCGGCACCCAGCACAGTAA
1 TACGAAAAAAAGGAAAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAA
* * *
55049781 AAAAATTTATTTTTTTTCGTGTCAGTATCAGGTATCAGTATACGAAAAAAGTAATAAAAAAAAAT
66 AAAAATTTATCTTTTTTCATGTCAGTATCAAGTATCAGTATACGAAAAAAGTAATAAAAAAAAAT
*
55049846 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAAAAAAATTATTTTTTTCGTGTC
131 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT-AAAAAAAATTACTTTTTTCGTGTC
55049911 AGTATCAGGTATCAGTA
195 AGTATCAGGTATCAGTA
* *
55049928 TACGAAAAAAAGGAAGAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCATAGT
1 TACGAAAAAAAGGAA-AAAAAAAA-TTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
* *
55049993 AAAAAAATTTA-CTTTTTTCATGTCAGTATCAAGTATCAGTATACG-AAAAAGTAATAAAAATAT
64 AAAAAAATTTATCTTTTTTCATGTCAGTATCAAGTATCAGTATACGAAAAAAGTAATAAAAAAAA
* *
55050056 TTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAAAAAATTACTTTTTTCGT
129 ATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAAAAAATTACTTTTTTCGT
55050119 ATACTGATAC
Statistics
Matches: 177, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
211 20 0.11
212 71 0.40
213 39 0.22
214 47 0.27
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (211 bp):
TACGAAAAAAAGGAAAAAAAAAATTTAGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAA
AAAAATTTATCTTTTTTCATGTCAGTATCAAGTATCAGTATACGAAAAAAGTAATAAAAAAAAAT
TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTAAAAAAAATTACTTTTTTCGTGTCA
GTATCAGGTATCAGTA
Found at i:55050083 original size:105 final size:105
Alignment explanation
Indices: 55049716--55050118 Score: 587
Period size: 107 Copynumber: 3.8 Consensus size: 105
55049706 CGGCACCCAG
* * * *
55049716 TACGAAAAAAAGGAA-AAAAAAAA-TTTAGGTGCTGGCCTGTTAATGGTCGGCACCCAGCACAGT
1 TACG-AAAAAAGTAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
* *
55049779 AAAAAAATTTATTTTTTTTCGTGTCAGTATCAGGTATCAGTA
65 AAAAAAAATTA-CTTTTTTCGTGTCAGTATCAGGTATCAGTA
55049821 TACGAAAAAAGTAATAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
1 TACGAAAAAAGTAAT-AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
*
55049886 AAAAAAAAATTATTTTTTTCGTGTCAGTATCAGGTATCAGTA
65 -AAAAAAAATTACTTTTTTCGTGTCAGTATCAGGTATCAGTA
* * *
55049928 TACGAAAAAAAGGAAGAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCATAGT
1 TACG-AAAAAAGTAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
* * *
55049993 AAAAAAATTTACTTTTTTCATGTCAGTATCAAGTATCAGTA
65 AAAAAAAATTACTTTTTTCGTGTCAGTATCAGGTATCAGTA
** *
55050034 TACG-AAAAAGTAATAAAAATATTTTTTTGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
1 TACGAAAAAAGTAATAAAAA-AAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGT
55050098 AAAAAAAATTACTTTTTTCGT
65 AAAAAAAATTACTTTTTTCGT
55050119 ATACTGATAC
Statistics
Matches: 272, Mismatches: 20, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
104 22 0.08
105 63 0.23
106 49 0.18
107 119 0.44
108 19 0.07
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (105 bp):
TACGAAAAAAGTAATAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGCACAGTA
AAAAAAATTACTTTTTTCGTGTCAGTATCAGGTATCAGTA
Found at i:55053937 original size:3 final size:3
Alignment explanation
Indices: 55053929--55053967 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
55053919 TACTTCAAAA
*
55053929 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
55053968 GTTGGGGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:55064501 original size:13 final size:11
Alignment explanation
Indices: 55064470--55064498 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
55064460 CCATTGTACT
55064470 TTAAAAAGCAG
1 TTAAAAAGCAG
55064481 TTAAAAAGCAG
1 TTAAAAAGCAG
55064492 TTAAAAA
1 TTAAAAA
55064499 AAGTGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.21
Consensus pattern (11 bp):
TTAAAAAGCAG
Found at i:55065137 original size:15 final size:16
Alignment explanation
Indices: 55065110--55065140 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
55065100 AAACCAAATA
55065110 GGACAAGAAAAGAAAC
1 GGACAAGAAAAGAAAC
55065126 GGACAA-AAAAGAAAC
1 GGACAAGAAAAGAAAC
55065141 AGAAATAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.65, C:0.13, G:0.23, T:0.00
Consensus pattern (16 bp):
GGACAAGAAAAGAAAC
Found at i:55065461 original size:12 final size:12
Alignment explanation
Indices: 55065444--55065468 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55065434 TGCTGGTGAG
55065444 AAAGGAAGGAAA
1 AAAGGAAGGAAA
55065456 AAAGGAAGGAAA
1 AAAGGAAGGAAA
55065468 A
1 A
55065469 TACTGAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (12 bp):
AAAGGAAGGAAA
Found at i:55066767 original size:51 final size:52
Alignment explanation
Indices: 55066692--55066793 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 52
55066682 AGAGCCAATG
* **
55066692 AATGAAAATGAATAAAAATGATAAAGTAAC-AAAAATAGATCACACAAATCC
1 AATGAAAATAAATAAAAACAATAAAGTAACAAAAAATAGATCACACAAATCC
*
55066743 AATGGAAATAAATAAAAACAATAAAGTAACAAAAAATAGATCACACAAATC
1 AATGAAAATAAATAAAAACAATAAAGTAACAAAAAATAGATCACACAAATC
55066794 ACTATCCACA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
51 26 0.57
52 20 0.43
ACGTcount: A:0.63, C:0.12, G:0.09, T:0.17
Consensus pattern (52 bp):
AATGAAAATAAATAAAAACAATAAAGTAACAAAAAATAGATCACACAAATCC
Found at i:55066983 original size:16 final size:18
Alignment explanation
Indices: 55066956--55066988 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55066946 TAGAATTTGG
55066956 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
55066973 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
55066989 GTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:55068219 original size:9 final size:9
Alignment explanation
Indices: 55068201--55068251 Score: 75
Period size: 9 Copynumber: 5.4 Consensus size: 9
55068191 TTTGGTTAAA
55068201 AATTACCCG
1 AATTACCCG
*
55068210 AATTAACCG
1 AATTACCCG
55068219 AATTACCCG
1 AATTACCCG
55068228 AAAATTACCCG
1 --AATTACCCG
55068239 AATTACCCG
1 AATTACCCG
55068248 AATT
1 AATT
55068252 GAATCACATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
9 29 0.76
11 9 0.24
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:55068239 original size:20 final size:20
Alignment explanation
Indices: 55068201--55068249 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
55068191 TTTGGTTAAA
55068201 AATTACCCG--AATTAACCG
1 AATTACCCGAAAATTAACCG
*
55068219 AATTACCCGAAAATTACCCG
1 AATTACCCGAAAATTAACCG
55068239 AATTACCCGAA
1 AATTACCCGAA
55068250 TTGAATCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 9 0.32
20 19 0.68
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (20 bp):
AATTACCCGAAAATTAACCG
Found at i:55072462 original size:28 final size:25
Alignment explanation
Indices: 55072395--55072446 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
55072385 AAAATTGGTA
55072395 AGACATTTTCCATTCTTCTCTAAGC
1 AGACATTTTCCATTCTTCTCTAAGC
55072420 AGACATTTTCCATTC-TCTTCTAAGC
1 AGACATTTTCCATTCTTC-TCTAAGC
55072445 AG
1 AG
55072447 CAAACATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (25 bp):
AGACATTTTCCATTCTTCTCTAAGC
Found at i:55074938 original size:14 final size:14
Alignment explanation
Indices: 55074921--55074948 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55074911 AATATATATT
55074921 AATATATATTAATA
1 AATATATATTAATA
55074935 AATATATATTAATA
1 AATATATATTAATA
55074949 TATGTGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:55074951 original size:10 final size:10
Alignment explanation
Indices: 55074907--55074939 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
55074897 AAAAACAATT
55074907 TATTAATATA
1 TATTAATATA
55074917 TATTAATATA
1 TATTAATATA
*
55074927 TATTAATAAA
1 TATTAATATA
55074937 TAT
1 TAT
55074940 ATATTAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TATTAATATA
Found at i:55075006 original size:32 final size:33
Alignment explanation
Indices: 55074970--55075054 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
55074960 AACTTTTCTG
* * *
55074970 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
55075002 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
55075034 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
55075055 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:55075093 original size:34 final size:34
Alignment explanation
Indices: 55075035--55075100 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
55075025 CAAACACCAG
* *
55075035 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTACCAGTAAATCATTTTAC-GAAAAGT
*
55075070 AAAACATTTACCAG-AAATTATTTTACGAAAA
1 AAAACATTTACCAGTAAATCATTTTACGAAAA
55075101 ACATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.18
34 11 0.39
35 12 0.43
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (34 bp):
AAAACATTTACCAGTAAATCATTTTACGAAAAGT
Found at i:55078293 original size:39 final size:39
Alignment explanation
Indices: 55078217--55078375 Score: 183
Period size: 39 Copynumber: 4.1 Consensus size: 39
55078207 ACTTCCAATA
* * * * **
55078217 CACCGACACACAGCATGTTAGGCACAAAGCCCAAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
** *
55078256 CATTGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
* * * * *
55078295 CACCAGCACAAAACCTGTTAGGCACTTAACCCGAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
*
55078334 CACCGGCACAAAGCCTGCTAGGCGCTTAGCCCAAATAAT
1 CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
55078373 CAC
1 CAC
55078376 AGTATTTCTA
Statistics
Matches: 99, Mismatches: 21, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
39 99 1.00
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.16
Consensus pattern (39 bp):
CACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAAT
Found at i:55078362 original size:78 final size:78
Alignment explanation
Indices: 55078232--55078375 Score: 218
Period size: 78 Copynumber: 1.8 Consensus size: 78
55078222 ACACACAGCA
** *
55078232 TGTTAGGCACAAAGCCCAAATAATCATTGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAATCA
1 TGTTAGGCACAAAGCCCAAATAATCACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAATCA
55078297 CCAGCACAAAACC
66 CCAGCACAAAACC
* * *
55078310 TGTTAGGCACTTAA-CCCGAATAATCACCGGCACAAAGCCTGCTAGGCGCTTAGCCCAAATAATC
1 TGTTAGGCAC-AAAGCCCAAATAATCACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAATC
55078374 AC
65 AC
55078376 AGTATTTCTA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
78 57 0.97
79 2 0.03
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (78 bp):
TGTTAGGCACAAAGCCCAAATAATCACCGGCACAAAGCCTGCTAGGCACTTAGCCCAAATAATCA
CCAGCACAAAACC
Found at i:55089620 original size:14 final size:15
Alignment explanation
Indices: 55089603--55089631 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55089593 ATTAGAAGTA
55089603 TTAAGAG-ATTTTAT
1 TTAAGAGTATTTTAT
55089617 TTAAGAGTATTTTAT
1 TTAAGAGTATTTTAT
55089632 GTCTTTAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
TTAAGAGTATTTTAT
Found at i:55093909 original size:30 final size:29
Alignment explanation
Indices: 55093883--55093962 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
55093873 TTGTTCTGGG
55093883 AAAAATAATTTTGACAAGATGGGTTCTGA
1 AAAAATAATTTTGACAAGATGGGTTCTGA
* * * *
55093912 AAAAATAAATTTAACATGATGTGTTCTGA
1 AAAAATAATTTTGACAAGATGGGTTCTGA
* *
55093941 AAAAATTATTTTGACGAGATGG
1 AAAAATAATTTTGACAAGATGG
55093963 ATTTTGTTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (29 bp):
AAAAATAATTTTGACAAGATGGGTTCTGA
Found at i:55093961 original size:29 final size:28
Alignment explanation
Indices: 55093874--55093961 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 28
55093864 TGCTAAGTAT
*
55093874 TGTTCTGGGAAAAATAATTTTGACAAGATG
1 TGTTCT-GAAAAAATAATTTTGAC-AGATG
* * *
55093904 GGTTCTGAAAAAATAAATTTAACATGATG
1 TGTTCTGAAAAAATAATTTTGACA-GATG
*
55093933 TGTTCTGAAAAAATTATTTTGACGAGATG
1 TGTTCTGAAAAAATAATTTTGAC-AGATG
55093962 GATTTTGTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.02
29 41 0.85
30 6 0.12
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (28 bp):
TGTTCTGAAAAAATAATTTTGACAGATG
Found at i:55096419 original size:16 final size:16
Alignment explanation
Indices: 55096398--55096437 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
55096388 ACCATTGGTA
*
55096398 TTGTCTAAGGTACGTT
1 TTGTCTAAGGTACATT
55096414 TTGTCTAAGGTACATT
1 TTGTCTAAGGTACATT
55096430 TTGTCTAA
1 TTGTCTAA
55096438 CTACTACGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (16 bp):
TTGTCTAAGGTACATT
Found at i:55097502 original size:59 final size:59
Alignment explanation
Indices: 55097407--55097643 Score: 388
Period size: 59 Copynumber: 4.0 Consensus size: 59
55097397 CCACATCGAG
* *
55097407 AGAACTTCTAATTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAA
1 AGAACTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAAA
*
55097466 AGAACTTTTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAAA
1 AGAACTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAAA
*
55097525 AGAATTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATT-AACA
1 AGAACTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAA-A
* *
55097584 ACAACTTCTATTTTATTAAATGAAACAAT-CTAAAATTAATTTGTACAAAAATATTCAAA
1 AGAACTTCTATTTTATTAAATGAAACAATATTAAAA-TAATTTGTACAAAAATATTCAAA
55097643 A
1 A
55097644 ATAAATCACT
Statistics
Matches: 167, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
58 7 0.04
59 158 0.95
60 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (59 bp):
AGAACTTCTATTTTATTAAATGAAACAATATTAAAATAATTTGTACAAAAATATTCAAA
Found at i:55098043 original size:18 final size:18
Alignment explanation
Indices: 55098020--55098063 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
55098010 GTGGAAAAAA
* *
55098020 GATACATATAAGGGTTAG
1 GATACACATAAGAGTTAG
55098038 GATACACATAAGAGTTAG
1 GATACACATAAGAGTTAG
55098056 GATACACA
1 GATACACA
55098064 CCTTGTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (18 bp):
GATACACATAAGAGTTAG
Found at i:55102017 original size:3 final size:3
Alignment explanation
Indices: 55101996--55102058 Score: 54
Period size: 3 Copynumber: 21.0 Consensus size: 3
55101986 TTTAAGATTT
* * * ** * * *
55101996 TTA TTA TTG TTA TTG TTA TTA TTA ATA CCA TCA TCA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55102044 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
55102059 AATTGTTTTA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:55106203 original size:6 final size:6
Alignment explanation
Indices: 55106192--55106218 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
55106182 AGTGACTTTT
55106192 TTATAA TTATAA TTATAA TTATAA TTA
1 TTATAA TTATAA TTATAA TTATAA TTA
55106219 CTATGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTATAA
Found at i:55120311 original size:14 final size:14
Alignment explanation
Indices: 55120292--55120318 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55120282 AAAATAATAC
55120292 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
55120306 AAAAAAATAAAAA
1 AAAAAAATAAAAA
55120319 AAGGTGCAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:55120452 original size:4 final size:4
Alignment explanation
Indices: 55120435--55120478 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
55120425 GAATGAGAGG
*
55120435 GAAA G-AA G-AA GAAA GAAA GAAA GAAA G-AA -AAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
55120479 ATGAAAGGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 10 0.29
4 25 0.71
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:55120460 original size:22 final size:22
Alignment explanation
Indices: 55120435--55120514 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
55120425 GAATGAGAGG
55120435 GAAAGAAGAAGAAAGAAAGAAA
1 GAAAGAAGAAGAAAGAAAGAAA
* *
55120457 GAAAGAAAAAGAAGGAAAGAAAA
1 GAAAGAAGAAGAAAGAAAG-AAA
* * *
55120480 TGAAAGGAGAAGAGAAAAAAAAAA
1 -GAAAGAAGAAGA-AAGAAAGAAA
*
55120504 G-AAGTAGAAGA
1 GAAAGAAGAAGA
55120515 GGGGAGGAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 26 0.55
23 4 0.09
24 13 0.28
25 4 0.09
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.03
Consensus pattern (22 bp):
GAAAGAAGAAGAAAGAAAGAAA
Found at i:55120478 original size:18 final size:19
Alignment explanation
Indices: 55120434--55120478 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
55120424 AGAATGAGAG
55120434 GGAAAG-AAGAAGAAAGAA
1 GGAAAGAAAGAAGAAAGAA
*
55120452 AGAAAGAAAGAA-AAAGAA
1 GGAAAGAAAGAAGAAAGAA
55120470 GGAAAGAAA
1 GGAAAGAAA
55120479 ATGAAAGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (19 bp):
GGAAAGAAAGAAGAAAGAA
Found at i:55120479 original size:14 final size:14
Alignment explanation
Indices: 55120450--55120506 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
55120440 AAGAAGAAAG
55120450 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
*
55120464 AAAGAAGGAAAGAA
1 AAAGAAAGAAAGAA
*
55120478 AATGAAAGGAGAAGAGA
1 AAAGAAA-GA-AAGA-A
55120495 AAA-AAA-AAAGAA
1 AAAGAAAGAAAGAA
55120507 GTAGAAGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 1 0.03
13 4 0.11
14 19 0.53
15 2 0.06
16 7 0.19
17 3 0.08
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:55120485 original size:18 final size:17
Alignment explanation
Indices: 55120434--55120485 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
55120424 AGAATGAGAG
55120434 GGAAAGAAGAAGAAAGAA
1 GGAAAGAA-AAGAAAGAA
* *
55120452 AGAAAGAAAGAAAAAGAA
1 GGAAAGAAA-AGAAAGAA
55120470 GGAAAGAAAATGAAAG
1 GGAAAGAAAA-GAAAG
55120486 GAGAAGAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (17 bp):
GGAAAGAAAAGAAAGAA
Found at i:55121427 original size:284 final size:285
Alignment explanation
Indices: 55120914--55121580 Score: 1158
Period size: 284 Copynumber: 2.3 Consensus size: 285
55120904 AAAGTAAAAA
* *
55120914 TATAAAATTAGAAATTATGAAATTTTTTAAAGTAATAAAATACGGAGAAAAAAATACGAAGAAAT
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
* *
55120979 GGCCG-AGATAAGAGTGTTTTACAAAATTTTTTAAAAATTCAGAAATAATTAATACAAATATTTC
66 GGCCGAAG-TAAGAGTGTTTTACTAACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTC
* *
55121043 AAACAAAATGTACCGAAATAATATAAAATAATAAAATACAAAAATAATTTTTTTATTGAAAGTAA
130 AAACAAAATGTACCGAAATAATATAAAATAAAAAAATAAAAAAATAATTTTTTTATTGAAAGTAA
* *
55121108 TAAAATTCGGGAAAATAATACGAGCAAATGGCAGGAATAAGC-ATTTTTTTACACTAAATTAATT
195 TAAAATTCGGGAAAATAATACAAGCAAACGGCAGGAATAAGCGATTTTTTTACACTAAATTAATT
55121172 TAAAAAACACACTAAATTAATAAATT
260 TAAAAAACACACTAAATTAATAAATT
* *
55121198 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAACGCGGAGAAAAAAATAAGAAGAAAT
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
55121263 GGCCGAAGTAAGAGTGTTTTACTAACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCA
66 GGCCGAAGTAAGAGTGTTTTACTAACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCA
*
55121328 AACAAAATGTACTGAAATAATATAAAATAAAAAAATAAAAAAATAATTTTTTTATTGAAAGTAAT
131 AACAAAATGTACCGAAATAATATAAAATAAAAAAATAAAAAAATAATTTTTTTATTGAAAGTAAT
*
55121393 AAAATTCGGGAAAATAATACAAGCAAACGGCAGGAATAAGCGCTTTTTTTACACTAAATTAATTT
196 AAAATTCGGGAAAATAATACAAGCAAACGGCAGGAATAAGCGATTTTTTTACACTAAATTAATTT
55121458 AAAAAACACACTAAATTAATAAATT
261 AAAAAACACACTAAATTAATAAATT
* *
55121483 TATAAAATTAGAAATTATGATATTTTTTTAAGTAATAAAATGCGGAGAAAAGAATACGAAGAAAT
1 TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
* *
55121548 GACTGAAGTAAGAGTGTTTTACTAACTATTTTT
66 GGCCGAAGTAAGAGTGTTTTACTAACT-TTTTT
55121581 TCAACATGCA
Statistics
Matches: 362, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
284 222 0.61
285 135 0.37
286 5 0.01
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (285 bp):
TATAAAATTAGAAATTATGATATTTTTTAAAGTAATAAAATGCGGAGAAAAAAATACGAAGAAAT
GGCCGAAGTAAGAGTGTTTTACTAACTTTTTTAAAAATTCAGAAATAATTAATACAAATATTTCA
AACAAAATGTACCGAAATAATATAAAATAAAAAAATAAAAAAATAATTTTTTTATTGAAAGTAAT
AAAATTCGGGAAAATAATACAAGCAAACGGCAGGAATAAGCGATTTTTTTACACTAAATTAATTT
AAAAAACACACTAAATTAATAAATT
Found at i:55126746 original size:9 final size:9
Alignment explanation
Indices: 55126732--55126757 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55126722 ATGAAAACCA
55126732 TAATAATAT
1 TAATAATAT
55126741 TAATAATAT
1 TAATAATAT
55126750 TAATAATA
1 TAATAATA
55126758 ATTTTATACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAATAATAT
Found at i:55126790 original size:16 final size:18
Alignment explanation
Indices: 55126769--55126815 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
55126759 TTTTATACTC
55126769 AAAATAATACTAA-C-TA
1 AAAATAATACTAACCATA
55126785 AAAATAATAACTAACCATA
1 AAAATAAT-ACTAACCATA
*
55126804 ATAATAATACTA
1 AAAATAATACTA
55126816 GTTTTTTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 8 0.30
17 5 0.19
18 5 0.19
19 9 0.33
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATAATACTAACCATA
Found at i:55127097 original size:10 final size:10
Alignment explanation
Indices: 55127069--55127106 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
55127059 AAAATACCAT
55127069 TTTTTCTCTTC
1 TTTTTCTC-TC
*
55127080 TCTTTCTCTC
1 TTTTTCTCTC
55127090 TTTTTCTCTC
1 TTTTTCTCTC
55127100 TTTTTCT
1 TTTTTCT
55127107 GCAACAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:55127215 original size:27 final size:27
Alignment explanation
Indices: 55127177--55127241 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
55127167 AACAAGACTA
*
55127177 GTGCCGCCCATGGGAAGGGCACCATTG
1 GTGCCGCCCATGGGAAGGGCACCATCG
*
55127204 GTGCCGCCCATGGGAATGGCACCATCG
1 GTGCCGCCCATGGGAAGGGCACCATCG
55127231 GTGCCGCCCAT
1 GTGCCGCCCAT
55127242 TAGTTAGGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.17, C:0.34, G:0.34, T:0.15
Consensus pattern (27 bp):
GTGCCGCCCATGGGAAGGGCACCATCG
Found at i:55127734 original size:20 final size:20
Alignment explanation
Indices: 55127706--55127744 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55127696 CAAAAAATGC
*
55127706 AAAAGTATAAAAAATATTAT
1 AAAAATATAAAAAATATTAT
* *
55127726 AAAAATATATAAGATATTA
1 AAAAATATAAAAAATATTA
55127745 AATTTTAAAT
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:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
AAAAATATAAAAAATATTAT
Found at i:55127752 original size:7 final size:7
Alignment explanation
Indices: 55127742--55127768 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
55127732 ATATAAGATA
55127742 TTAAATT
1 TTAAATT
55127749 TTAAATT
1 TTAAATT
55127756 TTAAATT
1 TTAAATT
55127763 TTAAAT
1 TTAAAT
55127769 ATATATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:55128764 original size:21 final size:20
Alignment explanation
Indices: 55128740--55128779 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
55128730 TGGTTATAAA
*
55128740 AAAATATTAATATTTAAATTT
1 AAAATAATAA-ATTTAAATTT
*
55128761 AAAATAATAAATTTTAATT
1 AAAATAATAAATTTAAATT
55128780 ATTTTTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATAATAAATTTAAATTT
Found at i:55128772 original size:28 final size:27
Alignment explanation
Indices: 55128714--55128783 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
55128704 TGTATAAATT
*
55128714 AATATTAATATTTAAATGGTTATAAAAA
1 AATATTAATATTTAAAT-GTTAAAAAAA
55128742 AATATTAATATTTAAAT-TTAAAATAATA
1 AATATTAATATTTAAATGTTAAAA-AA-A
*
55128770 AATTTTAATTATTT
1 AATATTAA-TATTT
55128784 TTTTGGTGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 5 0.14
27 2 0.05
28 25 0.68
29 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (27 bp):
AATATTAATATTTAAATGTTAAAAAAA
Found at i:55132587 original size:19 final size:18
Alignment explanation
Indices: 55132538--55132589 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
55132528 AAAATTTTGT
55132538 TTTTTAAATTAATTTTCA
1 TTTTTAAATTAATTTTCA
**
55132556 TTATTTATTTTAA-TTTCTA
1 TT-TTTAAATTAATTTTC-A
55132575 TATTTTAAATTAATT
1 T-TTTTAAATTAATT
55132590 CATATTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
18 6 0.23
19 18 0.69
20 2 0.08
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTAAATTAATTTTCA
Found at i:55132711 original size:14 final size:15
Alignment explanation
Indices: 55132688--55132717 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55132678 ATGAATTAAA
55132688 TGTTT-TTTTTATTT
1 TGTTTATTTTTATTT
55132702 TGTTTATTTTTATTT
1 TGTTTATTTTTATTT
55132717 T
1 T
55132718 TTATAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (15 bp):
TGTTTATTTTTATTT
Found at i:55132971 original size:9 final size:9
Alignment explanation
Indices: 55132952--55132988 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55132942 TGAGCTTTCG
*
55132952 AATTTGAAT
1 AATTCGAAT
*
55132961 AACTCGAAT
1 AATTCGAAT
55132970 AATTCGAAT
1 AATTCGAAT
55132979 AATTCGAAT
1 AATTCGAAT
55132988 A
1 A
55132989 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:55140334 original size:102 final size:102
Alignment explanation
Indices: 55140216--55140415 Score: 319
Period size: 102 Copynumber: 2.0 Consensus size: 102
55140206 CCAGTGATTC
* * * *
55140216 GGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATTAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
*
55140281 CCAATGATTCAGGGAATCAACACTTAGCAACCCATCG
66 CCAATGAGTCAGGGAATCAACACTTAGCAACCCATCG
*
55140318 GGGGAATCATCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
* * *
55140383 CCAATGAGTCGGGGAATTAGCACTTAGCAACCC
66 CCAATGAGTCAGGGAATCAACACTTAGCAACCC
55140416 CTTTCACAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 89 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.21
Consensus pattern (102 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
CCAATGAGTCAGGGAATCAACACTTAGCAACCCATCG
Found at i:55140379 original size:42 final size:40
Alignment explanation
Indices: 55140320--55140456 Score: 117
Period size: 42 Copynumber: 3.5 Consensus size: 40
55140310 ACCCATCGGG
*
55140320 GGAATCATCACTTAGCAACCCCCTTCACATTTAAGATACGAT
1 GGAATCAGCACTTAGCAACCCCCTTCACA-TTAAGATACG-T
* * *
55140362 GGAATCAGCACTTAGCAA-CCAC--CA-A-TGAG-T-CGG
1 GGAATCAGCACTTAGCAACCCCCTTCACATTAAGATACGT
* *
55140395 GGAATTAGCACTTAGCAACCCCTTTCACAATTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCAC-ATTAAGATAC-GT
* *
55140437 GGGATCAACACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
55140457 ACCAATGAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
33 17 0.23
34 4 0.05
35 1 0.01
36 5 0.07
38 2 0.03
39 5 0.07
40 1 0.01
41 4 0.05
42 35 0.47
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (40 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTAAGATACGT
Found at i:55140414 original size:75 final size:75
Alignment explanation
Indices: 55140318--55140490 Score: 265
Period size: 75 Copynumber: 2.3 Consensus size: 75
55140308 CAACCCATCG
* * *
55140318 GGGGAATCATCACTTAGCAACCCCCTTCACATTTAAGATACGATGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACAATTAAGATACGATGGAATCAACACTTAGCAACCA
* *
55140383 CCAATGAGTC
66 CCAATGAATA
* * * *
55140393 GGGGAATTAGCACTTAGCAACCCCTTTCACAATTAAGATACGGTGGGATCAACACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACAATTAAGATACGATGGAATCAACACTTAGCAACCA
55140458 CCAATGAATA
66 CCAATGAATA
55140468 GGGGAATCAGCACTTAGCAACCC
1 GGGGAATCAGCACTTAGCAACCC
55140491 TTTGGAGGAA
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (75 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACAATTAAGATACGATGGAATCAACACTTAGCAACCA
CCAATGAATA
Found at i:55140485 original size:177 final size:177
Alignment explanation
Indices: 55140184--55140521 Score: 543
Period size: 177 Copynumber: 1.9 Consensus size: 177
55140174 CTGTTATCAG
* * * *
55140184 TGGATTCAGCACTTAGCAACCACCAGTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCACATT
1 TGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACAAT
* * *
55140249 TAAGATACGGTGGGATTAGCACTTAGCAACCACCAATGATTCAGGGAATCAACACTTAGCAACCC
66 TAAGATACGGTGGGATCAACACTTAGCAACCACCAATGAATCAGGGAATCAACACTTAGCAACCC
* *
55140314 ATCGGGGGAATCATCACTTAGCAACCCCCTTCACATTTAAGATACGA
131 ATCGGAGGAATCAACACTTAGCAACCCCCTTCACATTTAAGATACGA
*
55140361 TGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATTAGCACTTAGCAACCCCTTTCACAAT
1 TGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACAAT
*
55140426 TAAGATACGGTGGGATCAACACTTAGCAACCACCAATGAAT-AGGGGAATCAGCACTTAGCAACC
66 TAAGATACGGTGGGATCAACACTTAGCAACCACCAATGAATCA-GGGAATCAACACTTAGCAACC
* *
55140490 CTTTGGAGGAATCAACACTTAGCAACCCCCTT
130 CATCGGAGGAATCAACACTTAGCAACCCCCTT
55140522 TATATTCAAT
Statistics
Matches: 147, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
176 1 0.01
177 146 0.99
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.22
Consensus pattern (177 bp):
TGGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTTCACAAT
TAAGATACGGTGGGATCAACACTTAGCAACCACCAATGAATCAGGGAATCAACACTTAGCAACCC
ATCGGAGGAATCAACACTTAGCAACCCCCTTCACATTTAAGATACGA
Found at i:55140487 original size:33 final size:33
Alignment explanation
Indices: 55140362--55140489 Score: 112
Period size: 33 Copynumber: 3.6 Consensus size: 33
55140352 AAGATACGAT
* *
55140362 GGAATCAGCACTTAGCAACCACCAATGAGTCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATAGG
* * *
55140395 GGAATTAGCACTTAGCAACCCCTTTCACAATTAAGATACGG
1 GGAATCAGCACTTAGCAA--CC--AC-CAA-TGA-ATA-GG
* *
55140436 TGGGATCAACACTTAGCAACCACCAATGAATAGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATAGG
55140470 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
55140490 CTTTGGAGGA
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
33 35 0.47
34 2 0.03
35 5 0.07
36 2 0.03
37 4 0.05
38 4 0.05
39 2 0.03
40 3 0.04
41 2 0.03
42 15 0.20
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATAGG
Found at i:55149045 original size:127 final size:127
Alignment explanation
Indices: 55148819--55149135 Score: 415
Period size: 127 Copynumber: 2.5 Consensus size: 127
55148809 TTTTATAACC
* * * *
55148819 AATTTTAGTATACCAAAATCATGTTATCCAAGACTTTACCAAGATTTCTAACGAAATACTAAAAA
1 AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAACGAAATACTAAAAA
* * * * *
55148884 TTTTAAGTGCATATCTTAAGATATTTTGGTATATACCATAATTTTTATGGAATCTCGTTAAA
66 TTTTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
* * *
55148946 AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAATGAAATTC-CAAAA
1 AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAACGAAATACTAAAAA
55149010 TTTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
66 TTT-TAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
* * * * * *
55149073 AATTTTTGGCATACCAAAATCCA-GATT-TACAAGCCTATACCAATATTTTTAACAAAATGCTAA
1 AA-TTTTGGTATACCAAAAT-CATG-TTATCCAAGCCTTTACCAATATTTATAACGAAATACTAA
55149136 TTGTCTAATA
Statistics
Matches: 165, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
126 7 0.04
127 109 0.66
128 44 0.27
129 5 0.03
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.36
Consensus pattern (127 bp):
AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAACGAAATACTAAAAA
TTTTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
Found at i:55149143 original size:127 final size:127
Alignment explanation
Indices: 55148819--55149175 Score: 370
Period size: 127 Copynumber: 2.8 Consensus size: 127
55148809 TTTTATAACC
* * * * * * * * *
55148819 AATTTTAGTATACCAAAATCATGTTATCCAAGACTTTACCAAGATTTCTAA-CGAAATACTAAAA
1 AATTTTGGCATACCAAAATCATGTTATACAAGCCTATACCAATATTTATAATCAAAAT-C-CAAA
* * * * *
55148883 ATTT-TAAGTGCATATCTTAAGATATTTTGGTATATACCATAATTTTTATGGAATCTCGTTAAA
64 ATTTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
* * * * *
55148946 AATTTTGGTATACCAAAATCATGTTATCCAAGCCTTTACCAATATTTATAATGAAATTCCAAAAT
1 AATTTTGGCATACCAAAATCATGTTATACAAGCCTATACCAATATTTATAATCAAAATCCAAAAT
55149011 TTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
66 TTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
* * *
55149073 AATTTTTGGCATACCAAAATCCA-GATT-TACAAGCCTATACCAATATTTTTAA-CAAAATGC-T
1 AA-TTTTGGCATACCAAAAT-CATG-TTATACAAGCCTATACCAATATTTATAATCAAAATCCAA
* *
55149134 AATTGTCTAA-TAGCACATCCTCAA-ATATTTTGGTATATACCA
63 AATT-TCTAAGTA-CATAT-CTTAAGATATTTTGGTATATACCA
55149176 ACATTTACAA
Statistics
Matches: 199, Mismatches: 23, Indels: 16
0.84 0.10 0.07
Matches are distributed among these distances:
126 13 0.07
127 136 0.68
128 46 0.23
129 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (127 bp):
AATTTTGGCATACCAAAATCATGTTATACAAGCCTATACCAATATTTATAATCAAAATCCAAAAT
TTCTAAGTACATATCTTAAGATATTTTGGTATATACCACAATTTTTAAGAAACCTCGTTAAA
Found at i:55156781 original size:61 final size:63
Alignment explanation
Indices: 55156633--55156781 Score: 169
Period size: 63 Copynumber: 2.4 Consensus size: 63
55156623 AATATCCCTC
* * * * * *
55156633 ACACGGCCTGGACACACGCTCGTGTCTCTGGCCCTTGTGACTTTAAATCTAAAATAGTGAGTT
1 ACACGGCCTGGACACACGCTCGTGTCCCTGGCCCATGTGACTCTAAATCTAAAACAATGAGTA
* *
55156696 ACACGGCCTGGACACACGCCCGTGTCCCTGGCCCAT-TGACTCTAACT-TCAAAACAATGAGTA
1 ACACGGCCTGGACACACGCTCGTGTCCCTGGCCCATGTGACTCTAAATCT-AAAACAATGAGTA
* * *
55156758 ACATGG-CTTGACACACGGTCGTGT
1 ACACGGCCTGGACACACGCTCGTGT
55156782 GACCCACATG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
61 16 0.22
62 24 0.33
63 33 0.45
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (63 bp):
ACACGGCCTGGACACACGCTCGTGTCCCTGGCCCATGTGACTCTAAATCTAAAACAATGAGTA
Found at i:55157371 original size:22 final size:23
Alignment explanation
Indices: 55157326--55157376 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
55157316 AAAATATGAT
55157326 AGAAAGAAAAATGAACAAAAAAG
1 AGAAAGAAAAATGAACAAAAAAG
* *
55157349 AGAAGGAAGAATGAAC-AAAAAG
1 AGAAAGAAAAATGAACAAAAAAG
55157371 A-AAAGA
1 AGAAAGA
55157377 GGAGGAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 4 0.16
22 7 0.28
23 14 0.56
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.04
Consensus pattern (23 bp):
AGAAAGAAAAATGAACAAAAAAG
Found at i:55161353 original size:28 final size:28
Alignment explanation
Indices: 55161274--55161353 Score: 115
Period size: 28 Copynumber: 2.9 Consensus size: 28
55161264 AATTTTGGAC
* * *
55161274 AAAATTATAAAATATAAAAAATAAGGGA
1 AAAACTATAAAATCTAAAAAATAGGGGA
*
55161302 AAAACTATAAAATCTAAAAAATAGGGGC
1 AAAACTATAAAATCTAAAAAATAGGGGA
*
55161330 AAAACTGTAAAATCTAAAAAATAG
1 AAAACTATAAAATCTAAAAAATAG
55161354 TGGACATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.20
Consensus pattern (28 bp):
AAAACTATAAAATCTAAAAAATAGGGGA
Found at i:55164915 original size:16 final size:16
Alignment explanation
Indices: 55164889--55164928 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
55164879 TAACAGATCA
55164889 ACATCATACACATATAT
1 ACAT-ATACACATATAT
55164906 ACATATACACATATAT
1 ACATATACACATATAT
55164922 ATCATAT
1 A-CATAT
55164929 TAGAATTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (16 bp):
ACATATACACATATAT
Found at i:55166893 original size:3 final size:3
Alignment explanation
Indices: 55166879--55166933 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
55166869 AATTAAACAC
* * * *
55166879 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TGA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55166927 TAA TAA T
1 TAA TAA T
55166934 GAAATGTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55176322 original size:98 final size:98
Alignment explanation
Indices: 55176153--55176344 Score: 339
Period size: 98 Copynumber: 2.0 Consensus size: 98
55176143 ATACAATAAA
* *
55176153 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTTGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
55176218 CCTTTAGAATCCCAAACTCGGAATATTTCATTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCATTT
* *
55176251 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
55176316 CCTTTAGAATCTCAAACTCGGAATATTTC
66 CCTTTAGAATCCCAAACTCGGAATATTTC
55176345 CTTCATGATT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCATTT
Found at i:55176645 original size:15 final size:15
Alignment explanation
Indices: 55176627--55176659 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
55176617 CAAATGCTAT
55176627 AATAATAAATACAAC
1 AATAATAAATACAAC
*
55176642 AATAATAAATACATC
1 AATAATAAATACAAC
55176657 AAT
1 AAT
55176660 GACATATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:55177148 original size:3 final size:3
Alignment explanation
Indices: 55177112--55177139 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
55177102 GCGCATGAAT
55177112 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
55177140 CGATAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:55177760 original size:6 final size:6
Alignment explanation
Indices: 55177749--55177783 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
55177739 TTTGTTTGTA
55177749 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAA
55177784 GCTGTAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:55178834 original size:19 final size:19
Alignment explanation
Indices: 55178810--55178860 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
55178800 TCTTGAAAAA
*
55178810 TAAAAAATTAAAT-ATTATT
1 TAAAAAATTAAATAACT-TT
*
55178829 TAAAAATTTAAATAACTTT
1 TAAAAAATTAAATAACTTT
*
55178848 TAAATAATTAAAT
1 TAAAAAATTAAAT
55178861 TATTTGTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 25 0.93
20 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAAAATTAAATAACTTT
Found at i:55178892 original size:30 final size:30
Alignment explanation
Indices: 55178847--55178923 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
55178837 TAAATAACTT
* *
55178847 TTAAATAATTAAATTATTTGTTAAATCTTAAA
1 TTAAAT-A-TAAATTACTTGTGAAATCTTAAA
*
55178879 TTAAATATAAATTACTTGTGAAATTTTAAA
1 TTAAATATAAATTACTTGTGAAATCTTAAA
*
55178909 TTAAA-ATAATTTACT
1 TTAAATATAAATTACT
55178924 AATTAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 9 0.22
30 25 0.61
31 1 0.02
32 6 0.15
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (30 bp):
TTAAATATAAATTACTTGTGAAATCTTAAA
Found at i:55178931 original size:29 final size:30
Alignment explanation
Indices: 55178867--55178933 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
55178857 AAATTATTTG
* **
55178867 TTAAATCTTAAATTAAATATAAATTACTTG
1 TTAAATTTTAAATTAAATATAAATTACTAA
* *
55178897 TGAAATTTTAAATTAAA-ATAATTTACTAA
1 TTAAATTTTAAATTAAATATAAATTACTAA
55178926 TTAAATTT
1 TTAAATTT
55178934 AATAAATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (30 bp):
TTAAATTTTAAATTAAATATAAATTACTAA
Found at i:55179549 original size:24 final size:25
Alignment explanation
Indices: 55179500--55179553 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
55179490 TTAAATTTTA
*
55179500 TATTTAATGTATCATTACATTAAAT
1 TATTTAATATATCATTACATTAAAT
*
55179525 TATTTAA-ATATCATATA-ATTTAAT
1 TATTTAATATATCAT-TACATTAAAT
55179549 TATTT
1 TATTT
55179554 TTAGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.52
Consensus pattern (25 bp):
TATTTAATATATCATTACATTAAAT
Found at i:55182179 original size:46 final size:46
Alignment explanation
Indices: 55182112--55182204 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 46
55182102 GAGTTTGCCC
* ** *
55182112 AGGTTCCAAGCTCTTGCATATGTAGTGGACTCTAGAATACATGAAT
1 AGGTTCCAAGCTCCTGCATATGTAGCAGACTCAAGAATACATGAAT
* *
55182158 AGGTTCCGAGCTCCTGCATATGTTGCAGACTCAAGAATACATGAAT
1 AGGTTCCAAGCTCCTGCATATGTAGCAGACTCAAGAATACATGAAT
55182204 A
1 A
55182205 TTAAGCCCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (46 bp):
AGGTTCCAAGCTCCTGCATATGTAGCAGACTCAAGAATACATGAAT
Found at i:55187712 original size:15 final size:17
Alignment explanation
Indices: 55187681--55187714 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
55187671 TTAAAGTGTA
55187681 AATTTACTTTAATTTAT
1 AATTTACTTTAATTTAT
55187698 AATTT-CTTT-ATTTAT
1 AATTTACTTTAATTTAT
55187713 AA
1 AA
55187715 GAGATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTACTTTAATTTAT
Found at i:55195598 original size:20 final size:20
Alignment explanation
Indices: 55195573--55195618 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
55195563 CATTGGATGG
*
55195573 AAAATGAATGTATGAAATGA
1 AAAATGAATATATGAAATGA
**
55195593 AAAATGGTTATATGAAATGA
1 AAAATGAATATATGAAATGA
55195613 AAAATG
1 AAAATG
55195619 GTTGGAGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (20 bp):
AAAATGAATATATGAAATGA
Found at i:55195619 original size:20 final size:20
Alignment explanation
Indices: 55195583--55195621 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
55195573 AAAATGAATG
55195583 TATGAAATGAAAAATGGTTA
1 TATGAAATGAAAAATGGTTA
55195603 TATGAAATGAAAAATGGTT
1 TATGAAATGAAAAATGGTT
55195622 GGAGATGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.31
Consensus pattern (20 bp):
TATGAAATGAAAAATGGTTA
Found at i:55199659 original size:28 final size:28
Alignment explanation
Indices: 55199594--55199682 Score: 106
Period size: 28 Copynumber: 3.1 Consensus size: 28
55199584 ATACAATTCT
*
55199594 GGGTAAAATTATAAAAATTTAAAAAATAG
1 GGGTAAAATTAT-AAAATTTAAAAAATAA
* * *
55199623 GGGTAAAAACTATAAAATCTAAAAACTAA
1 GGGT-AAAATTATAAAATTTAAAAAATAA
* *
55199652 TGGTAAAATTGTAAAATTTAAAAAATAA
1 GGGTAAAATTATAAAATTTAAAAAATAA
55199680 GGG
1 GGG
55199683 ACACACGGCC
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
28 22 0.45
29 20 0.41
30 7 0.14
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (28 bp):
GGGTAAAATTATAAAATTTAAAAAATAA
Found at i:55203475 original size:50 final size:50
Alignment explanation
Indices: 55203349--55203646 Score: 262
Period size: 50 Copynumber: 5.9 Consensus size: 50
55203339 CATTTGGGTA
* *
55203349 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA-T
* * * *
55203403 ATGACAGGTCCCATGTAAGACCATGTTTAGGACATGGCGTTGGCACCGAGAT
1 A--AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
*
55203455 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * * * *
55203505 GAGAGGTCCCCCGTAGGACCATGTCTGGGACATGGCATGGGCACCAATAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
* ** * * * * *
55203555 GAGAACTCCCATGTAAGGCCATATATGGGATATGGCATTGGCAGTAC-AGGA-
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCGA-GAT
* * *
55203606 AACA--TCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
55203647 TGTTATTATC
Statistics
Matches: 202, Mismatches: 37, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
49 31 0.15
50 121 0.60
51 3 0.01
52 4 0.02
53 4 0.02
54 1 0.00
55 1 0.00
56 37 0.18
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGAT
Found at i:55209489 original size:16 final size:16
Alignment explanation
Indices: 55209470--55209500 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55209460 AAGCTATTTT
*
55209470 ATTATTTATTTTTAAA
1 ATTATTAATTTTTAAA
55209486 ATTATTAATTTTTAA
1 ATTATTAATTTTTAA
55209501 TGTCACATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATTAATTTTTAAA
Found at i:55209580 original size:6 final size:6
Alignment explanation
Indices: 55209569--55209633 Score: 62
Period size: 6 Copynumber: 10.5 Consensus size: 6
55209559 ATTTTTAATT
* *
55209569 ATTATA ATTATA ATTATA ATTATA ATTTATT ATTCA-A ATTATTA AATATA
1 ATTATA ATTATA ATTATA ATTATA A-TTATA ATT-ATA ATTA-TA ATTATA
55209619 ATT-TA ATTAATA ATT
1 ATTATA ATT-ATA ATT
55209634 CAAATATAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
5 6 0.12
6 28 0.57
7 15 0.31
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTATA
Found at i:55209609 original size:31 final size:30
Alignment explanation
Indices: 55209563--55209643 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
55209553 GAATATATTT
55209563 TTAATTATT-ATAATTATAATTATAATTATAA
1 TTAATTATTCA-AATTATAATTATAATT-TAA
* *
55209594 TTTATTATTCAAATTATTAAATATAATTTAA
1 TTAATTATTCAAATTA-TAATTATAATTTAA
*
55209625 TTAATAATTCAAA-TATAAT
1 TTAATTATTCAAATTATAAT
55209644 AAGACGAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 3 0.07
30 2 0.05
31 27 0.63
32 11 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
TTAATTATTCAAATTATAATTATAATTTAA
Found at i:55228164 original size:18 final size:18
Alignment explanation
Indices: 55228124--55228166 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
55228114 AATTAGAATG
*
55228124 TAAAAATTAAACTAAAAA
1 TAAAAATTAAAATAAAAA
*
55228142 CAAAAATATAAAAT-AAAA
1 TAAAAAT-TAAAATAAAAA
55228160 TAAAAAT
1 TAAAAAT
55228167 GGATAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (18 bp):
TAAAAATTAAAATAAAAA
Found at i:55246912 original size:26 final size:26
Alignment explanation
Indices: 55246876--55246927 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
55246866 GTTGCACAAA
55246876 CCTACGTGTTACACATATCATCCATT
1 CCTACGTGTTACACATATCATCCATT
55246902 CCTACGTGTTACACATATCATCCATT
1 CCTACGTGTTACACATATCATCCATT
55246928 ATATGTTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.35
Consensus pattern (26 bp):
CCTACGTGTTACACATATCATCCATT
Found at i:55247241 original size:33 final size:35
Alignment explanation
Indices: 55247204--55247271 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
55247194 CCATTTTTGA
* *
55247204 CACTG-TACTGAGAAGGGCTAAGGCTCAA-ACTGT
1 CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
*
55247237 CACTGATACTGAAAAGGGCTTAGGCCCAAGACTGT
1 CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
55247272 TCAACTGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.21
Consensus pattern (35 bp):
CACTGATACTGAAAAGGGCTAAGGCCCAAGACTGT
Found at i:55248875 original size:5 final size:5
Alignment explanation
Indices: 55248865--55248893 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
55248855 TCATATGTAC
55248865 ACATA ACATA ACATA ACATA ACATA ACAT
1 ACATA ACATA ACATA ACATA ACATA ACAT
55248894 TATAAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (5 bp):
ACATA
Found at i:55249591 original size:12 final size:12
Alignment explanation
Indices: 55249574--55249603 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
55249564 CCTCACACGC
55249574 CCGTGTGCTAGG
1 CCGTGTGCTAGG
55249586 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
55249598 CTGTGT
1 CCGTGT
55249604 AGCTTCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.23, G:0.40, T:0.30
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:55255333 original size:18 final size:18
Alignment explanation
Indices: 55255310--55255364 Score: 110
Period size: 18 Copynumber: 3.1 Consensus size: 18
55255300 TAATTTGGAG
55255310 AAAGAATTATGCTAGGTT
1 AAAGAATTATGCTAGGTT
55255328 AAAGAATTATGCTAGGTT
1 AAAGAATTATGCTAGGTT
55255346 AAAGAATTATGCTAGGTT
1 AAAGAATTATGCTAGGTT
55255364 A
1 A
55255365 TAACTTATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (18 bp):
AAAGAATTATGCTAGGTT
Found at i:55270632 original size:18 final size:18
Alignment explanation
Indices: 55270609--55270698 Score: 126
Period size: 18 Copynumber: 5.0 Consensus size: 18
55270599 CCCAACTACT
*
55270609 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
55270627 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
* * *
55270645 ATATATGTGAATAGTATC
1 GTATACGTGAATAGTACC
*
55270663 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
55270681 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
55270699 ATAAACGGTC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:55270666 original size:36 final size:36
Alignment explanation
Indices: 55270610--55270698 Score: 142
Period size: 36 Copynumber: 2.5 Consensus size: 36
55270600 CCAACTACTG
*
55270610 TATACGTGAACAGTACCGTATACGTGAATAGTGCCA
1 TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
* * *
55270646 TATATGTGAATAGTATCGTATACGTGAATAGTGCCG
1 TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
55270682 TATACGTGAATAGTACC
1 TATACGTGAATAGTACC
55270699 ATAAACGGTC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (36 bp):
TATACGTGAATAGTACCGTATACGTGAATAGTGCCA
Found at i:55273459 original size:22 final size:22
Alignment explanation
Indices: 55273411--55273507 Score: 65
Period size: 22 Copynumber: 4.4 Consensus size: 22
55273401 TTTATGAAAG
* *
55273411 GATAAATAA-ATTTAAATATTAA
1 GATAAATAATATTTATAT-TTAT
* *
55273433 AATAAATAATATTTATTTTTAT
1 GATAAATAATATTTATATTTAT
*
55273455 GATAATTAAATGATATT-TATTTAT
1 GATAAAT-AAT-AT-TTATATTTAT
* *
55273479 TAT-AATAATATTTATCTTTAT
1 GATAAATAATATTTATATTTAT
*
55273500 GAAAAATA
1 GATAAATA
55273508 TTAAAAATAA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
20 2 0.04
21 9 0.16
22 23 0.40
23 11 0.19
24 10 0.18
25 2 0.04
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (22 bp):
GATAAATAATATTTATATTTAT
Found at i:55273464 original size:26 final size:27
Alignment explanation
Indices: 55273435--55273487 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
55273425 AATATTAAAA
*
55273435 TAAATAATATTTATTT-TTATGATAAT
1 TAAATAATATTTATTTATTATAATAAT
*
55273461 TAAATGATATTTATTTATTATAATAAT
1 TAAATAATATTTATTTATTATAATAAT
55273488 ATTTATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (27 bp):
TAAATAATATTTATTTATTATAATAAT
Found at i:55273507 original size:19 final size:19
Alignment explanation
Indices: 55273467--55273509 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
55273457 TAATTAAATG
* *
55273467 ATATTTATTTATTATAATA
1 ATATTTATCTATTATAAAA
55273486 ATATTTATCT-TTATGAAAA
1 ATATTTATCTATTAT-AAAA
55273505 ATATT
1 ATATT
55273510 AAAAATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
ATATTTATCTATTATAAAA
Found at i:55275571 original size:13 final size:13
Alignment explanation
Indices: 55275553--55275624 Score: 58
Period size: 13 Copynumber: 5.3 Consensus size: 13
55275543 AACATGAAAG
55275553 TAAAAATAAAAAA
1 TAAAAATAAAAAA
55275566 TAAAAAGTAAAAATA
1 TAAAAA-TAAAAA-A
* *
55275581 AAGAAAATAAATAA
1 TA-AAAATAAAAAA
55275595 T-AAAATAAAGAAA
1 TAAAAATAAA-AAA
*
55275608 -ATAAATAAATAAA
1 TAAAAATAAA-AAA
55275621 TAAA
1 TAAA
55275625 TAAAACTTGG
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
12 8 0.17
13 18 0.39
14 9 0.20
15 7 0.15
16 4 0.09
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:55275574 original size:20 final size:20
Alignment explanation
Indices: 55275549--55275603 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
55275539 TATTAACATG
55275549 AAAGTAAAAATAAAAAATAA
1 AAAGTAAAAATAAAAAATAA
55275569 AAAGTAAAAATAAAGAAAATAA
1 AAAGTAAAAAT-AA-AAAATAA
55275591 ATAA-T-AAAATAAA
1 A-AAGTAAAAATAAA
55275604 GAAAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
21 7 0.22
22 9 0.28
23 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (20 bp):
AAAGTAAAAATAAAAAATAA
Found at i:55275587 original size:29 final size:29
Alignment explanation
Indices: 55275554--55275629 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
55275544 ACATGAAAGT
*
55275554 AAAAATAAAAAATAAAA-AGTA-AAAATAA
1 AAAAATAAAAAATAAAATA-AAGAAAATAA
*
55275582 AGAAAATAAATAATAAAATAAAGAAAATAA
1 A-AAAATAAAAAATAAAATAAAGAAAATAA
*
55275612 ATAAATAAATAAATAAAA
1 AAAAATAAA-AAATAAAA
55275630 CTTGGGTTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.03
29 23 0.57
30 16 0.40
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (29 bp):
AAAAATAAAAAATAAAATAAAGAAAATAA
Found at i:55275594 original size:4 final size:4
Alignment explanation
Indices: 55275556--55275628 Score: 57
Period size: 4 Copynumber: 18.8 Consensus size: 4
55275546 ATGAAAGTAA
* *
55275556 AAAT AAA- AAAT AAA- AAGT -AA- AAAT AAAGA AAAT AAAT -AAT AAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT -AAAT
*
55275601 AAAGA AAAT AAAT AAAT AAAT AAAT AAA
1 AAA-T AAAT AAAT AAAT AAAT AAAT AAA
55275629 ACTTGGGTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
3 11 0.20
4 35 0.64
5 9 0.16
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:55277539 original size:25 final size:25
Alignment explanation
Indices: 55277491--55277539 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
55277481 CATAATTGAA
* * *
55277491 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
55277516 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
55277540 GTGTATTGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:55280340 original size:39 final size:39
Alignment explanation
Indices: 55280278--55280356 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
55280268 TAGGAAACTC
* ** *
55280278 ATCCCTTATAAGAGTGTTGTCATAGGGTGTTTTTAACCT
1 ATCCCTTATAAGAGAGTCATCATAGGGTGTTTGTAACCT
*
55280317 ATCCTTTATAAGAGAGTCATCATAGGGTGTTTGTAACCT
1 ATCCCTTATAAGAGAGTCATCATAGGGTGTTTGTAACCT
55280356 A
1 A
55280357 CTCAAGTGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (39 bp):
ATCCCTTATAAGAGAGTCATCATAGGGTGTTTGTAACCT
Found at i:55290078 original size:12 final size:12
Alignment explanation
Indices: 55290061--55290085 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55290051 ATCATTTCTA
55290061 TTCATTTAGTTC
1 TTCATTTAGTTC
55290073 TTCATTTAGTTC
1 TTCATTTAGTTC
55290085 T
1 T
55290086 GCATGCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (12 bp):
TTCATTTAGTTC
Found at i:55295903 original size:17 final size:16
Alignment explanation
Indices: 55295869--55295913 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
55295859 TTGGCAACTT
*
55295869 GTAAGCTCTCAAGTTTG
1 GTAAGCTCGC-AGTTTG
55295886 GTAAGCTCGCAGTCTTG
1 GTAAGCTCGCAGT-TTG
*
55295903 GTGAGCTCGCA
1 GTAAGCTCGCA
55295914 CAATTTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (16 bp):
GTAAGCTCGCAGTTTG
Found at i:55301888 original size:12 final size:12
Alignment explanation
Indices: 55301854--55301901 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
55301844 GGCCTCTCAT
55301854 TTTTCTTTTTTC
1 TTTTCTTTTTTC
*
55301866 -GTTCTTCTTTTC
1 TTTTCTT-TTTTC
55301878 TTTTCTTTTTTC
1 TTTTCTTTTTTC
55301890 TTTTCATTTTTT
1 TTTTC-TTTTTT
55301902 TCAAGTGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 5 0.16
12 15 0.48
13 11 0.35
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:55302362 original size:25 final size:23
Alignment explanation
Indices: 55302329--55302375 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
55302319 CGGTAGAGGG
*
55302329 TTTTTTTTATTTTTTTGTTTTTTA
1 TTTTTTTTA-TTTTGTGTTTTTTA
55302353 TTTTCTTTTATTTTGTGTTTTTT
1 TTTT-TTTTATTTTGTGTTTTTT
55302376 TGTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.06, C:0.02, G:0.06, T:0.85
Consensus pattern (23 bp):
TTTTTTTTATTTTGTGTTTTTTA
Found at i:55302376 original size:25 final size:24
Alignment explanation
Indices: 55302329--55302386 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 24
55302319 CGGTAGAGGG
*
55302329 TTTTTTTTATTTTTTTGTTTTTTA
1 TTTTTTTTATTTTTGTGTTTTTTA
*
55302353 TTTTCTTTTATTTTGTGTTTTTTTGTA
1 TTTT-TTTTATTTT-TGTGTTTTT-TA
55302380 TTTTTTT
1 TTTTTTT
55302387 ACTATACTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.14
25 9 0.31
26 10 0.34
27 6 0.21
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.84
Consensus pattern (24 bp):
TTTTTTTTATTTTTGTGTTTTTTA
Found at i:55302387 original size:25 final size:24
Alignment explanation
Indices: 55302329--55302386 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 24
55302319 CGGTAGAGGG
55302329 TTTTTTTTATTTTTTTGTTTTTTA
1 TTTTTTTTATTTTTTTGTTTTTTA
55302353 TTTTCTTTTATTTTGTGTT-TTTTTGTA
1 TTTT-TTTTATTTT-T-TTGTTTTT-TA
55302380 TTTTTTT
1 TTTTTTT
55302387 ACTATACTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 4 0.13
25 9 0.30
26 9 0.30
27 8 0.27
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.84
Consensus pattern (24 bp):
TTTTTTTTATTTTTTTGTTTTTTA
Found at i:55306824 original size:14 final size:15
Alignment explanation
Indices: 55306805--55306833 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55306795 AAATACGATC
55306805 CTTGTATAAA-AAAA
1 CTTGTATAAATAAAA
55306819 CTTGTATAAATAAAA
1 CTTGTATAAATAAAA
55306834 TTAGTCGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (15 bp):
CTTGTATAAATAAAA
Found at i:55307454 original size:3 final size:3
Alignment explanation
Indices: 55307439--55307518 Score: 54
Period size: 3 Copynumber: 25.7 Consensus size: 3
55307429 TGAATGAGTA
* * *
55307439 AAT AAT TAT AAT AAT AAGGT AAGT AAT AAT AAG AA- ATAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AA--T AA-T AAT AAT AAT AAT A-AT AAT AAT AAT
* * * *
55307487 AAT AAA AAT AAT AAT AGT AAA AAT AAT GAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55307519 CACTATTAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
2 1 0.02
3 52 0.85
4 5 0.08
5 3 0.05
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:55307496 original size:15 final size:15
Alignment explanation
Indices: 55307478--55307518 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
55307468 TAAGAAATAC
55307478 AATAATAATAATAAA
1 AATAATAATAATAAA
*
55307493 AATAATAATAGTAAA
1 AATAATAATAATAAA
*
55307508 AATAATGATAA
1 AATAATAATAA
55307519 CACTATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:55311399 original size:17 final size:18
Alignment explanation
Indices: 55311360--55311401 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
55311350 TTTCAAATGT
55311360 ATTTTTTGATTTCACTTA
1 ATTTTTTGATTTCACTTA
* * *
55311378 TTTTTTTG-TTTGATTTA
1 ATTTTTTGATTTCACTTA
55311395 ATTTTTT
1 ATTTTTT
55311402 TAAAAGAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.17, C:0.05, G:0.07, T:0.71
Consensus pattern (18 bp):
ATTTTTTGATTTCACTTA
Found at i:55311874 original size:31 final size:32
Alignment explanation
Indices: 55311811--55311875 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
55311801 GGCAAATTAC
*
55311811 AAGAGTAATTGAATCTTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
*
55311843 AAGAGTAATTGAATCCTAAT-AAAACTTTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
55311874 AA
1 AA
55311876 ATTATCTAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.34
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:55318050 original size:31 final size:32
Alignment explanation
Indices: 55317991--55318055 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
55317981 GGCAAATTAC
55317991 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
*
55318023 AAGAGTACTTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
55318054 AA
1 AA
55318056 ATTATCTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.41
32 19 0.59
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:55319177 original size:58 final size:58
Alignment explanation
Indices: 55319104--55319214 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
55319094 TGATTATTTC
* * *
55319104 TATTTGATTTATTTA-TCATTCTCTTACT-TTCAAAATATTTAAATTTAATATTAGGTAT
1 TATTTGATCTATTTATTCATT-TCTTACTCTT-AAAATATTTAAACTTAACATTAGGTAT
* * *
55319162 TATTTTATCTATTTATTTATTTTTTACTCTTAAAATATTTAAACTTAACATTA
1 TATTTGATCTATTTATTCATTTCTTACTCTTAAAATATTTAAACTTAACATTA
55319215 TGTAAACATA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 39 0.87
59 6 0.13
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (58 bp):
TATTTGATCTATTTATTCATTTCTTACTCTTAAAATATTTAAACTTAACATTAGGTAT
Found at i:55319259 original size:3 final size:3
Alignment explanation
Indices: 55319251--55319306 Score: 103
Period size: 3 Copynumber: 18.3 Consensus size: 3
55319241 TTCTATCTTC
55319251 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55319299 TAT GTAT T
1 TAT -TAT T
55319307 TATTCACAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:55319376 original size:13 final size:13
Alignment explanation
Indices: 55319358--55319382 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55319348 GAACTGTATC
55319358 ATTTATTTATTTT
1 ATTTATTTATTTT
55319371 ATTTATTTATTT
1 ATTTATTTATTT
55319383 AGTTTCAAAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTATTTATTTT
Found at i:55321957 original size:24 final size:24
Alignment explanation
Indices: 55321930--55321976 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
55321920 TTTATATTTT
55321930 TAATACTTTTTAATTTTTTAAAAA
1 TAATACTTTTTAATTTTTTAAAAA
**
55321954 TAATTTTTTTTAATTTTTTAAAA
1 TAATACTTTTTAATTTTTTAAAA
55321977 TATTTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATACTTTTTAATTTTTTAAAAA
Found at i:55322454 original size:27 final size:25
Alignment explanation
Indices: 55322423--55322479 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
55322413 AAAGTATACA
*
55322423 ATTTTTT-TTCAGAAAACAAGATTCAC
1 ATTTTTTATTCACAAAA-AA-ATTCAC
*
55322449 ATTTTTTATTCACAAGAAAATTCAC
1 ATTTTTTATTCACAAAAAAATTCAC
55322474 ATTTTT
1 ATTTTT
55322480 GTATAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 12 0.43
26 9 0.32
27 7 0.25
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (25 bp):
ATTTTTTATTCACAAAAAAATTCAC
Found at i:55322779 original size:13 final size:13
Alignment explanation
Indices: 55322763--55322787 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55322753 ATTAAGATTC
55322763 TTTTAGTTGGGTT
1 TTTTAGTTGGGTT
55322776 TTTTAGTTGGGT
1 TTTTAGTTGGGT
55322788 CATTTTAAGT
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:0.00, G:0.32, T:0.60
Consensus pattern (13 bp):
TTTTAGTTGGGTT
Found at i:55325386 original size:3 final size:3
Alignment explanation
Indices: 55325378--55325454 Score: 86
Period size: 3 Copynumber: 25.3 Consensus size: 3
55325368 GTATTATCAT
55325378 TTA TTA TTA TTA TTA TTA TTA TTA TT- TCTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* * *
55325423 TGTA -TA TTA CTG TTA CTTA TCA TTA TTA TTA T
1 T-TA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
55325455 GTGATAGCTT
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
2 3 0.05
3 54 0.86
4 6 0.10
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Done.