Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 103 of 345
Found at i:27914723 original size:237 final size:225
Alignment explanation
Indices: 27914331--27915155 Score: 883
Period size: 237 Copynumber: 3.5 Consensus size: 225
27914321 TATATTTTTC
* * ** *
27914331 AAAAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAAT
1 AAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAAT
** * *
27914396 TTCTG-TTGTCAAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTG
66 TTCTGTTTGTC-----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
* * * **
27914460 AGGTATTTTCAATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCA
126 AGGTATTTTCAATTTATATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
* *
27914525 AGACATGCTGAGGTATTTTCAATTTTTGTCTTTCAA
191 GGACACGCTGAGGTATTTTCAATTTTTGT-TTTCAA
* * *
27914561 AAAAAAAATCAACTCATATTGTGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTAGTTTCAAT
1 AAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAAT
27914626 TTCTGCTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
66 TTCTG------TT-TG----TCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
*
27914691 ACGCTGAGGTATTTTCAATTTCTATTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGA
120 ACGCTGAGGTATTTTCAATTTATATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
* *
27914754 GCCTCGGGACACGCTGAGGTATTGTCAATTTTTGTGTTTCAA
185 GCCTCAGGACACGCTGAGGTATTTTCAATTTTTGT-TTTCAA
** * * *
27914796 TCTATTTTTCAAAAATCAACTTATATTACGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAA
1 ---A----AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAA
27914861 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGG-CACG
59 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACG
*
27914925 TTGAGGTAATTTCAATATCTGCTTTTCAATTTATATTTTTCAAAAAAATTCAACTCATATTGCGA
123 CTGAGG---------TA-----TTTTCAATTTATATTTTTCAAAAAAA-TCAACTCATATTGCGA
* * *
27914990 GAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTC--
173 GAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTTGTTTTCAA
* *
27915041 -AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAAT
1 AAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAAT
* * *
27915105 TTTTATCTT-TCAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCA
66 TTCTGT-TTGTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
27915156 AGGCAGGTTT
Statistics
Matches: 509, Mismatches: 47, Indels: 71
0.81 0.07 0.11
Matches are distributed among these distances:
230 62 0.12
231 49 0.10
232 3 0.01
235 70 0.14
236 2 0.00
237 131 0.26
238 42 0.08
240 2 0.00
242 63 0.12
245 18 0.04
247 8 0.02
248 59 0.12
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (225 bp):
AAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAAT
TTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
TTTTCAATTTATATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
CGCTGAGGTATTTTCAATTTTTGTTTTCAA
Found at i:27914806 original size:635 final size:633
Alignment explanation
Indices: 27913766--27915180 Score: 2469
Period size: 635 Copynumber: 2.2 Consensus size: 633
27913756 TTTATATTTT
* ** * * * *
27913766 TCAAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTA
1 TCAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTC
* **
27913831 AATTTCTGT-TGTAAAAAAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
66 AATTTTTGTCT-T-----TCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGAC
27913895 ATGCTGAGGTATTTTCAATTTTTGTCTTTCAAAAAAAAATCAACTCATATTGCGAGAAATAAGTT
125 ATGCTGAGGTATTTTCAATTTTTGTCTTTCAAAAAAAAATCAACTCATATTGCGAGAAATAAGTT
* *
27913960 GAGCCTCAAGACATGTTGAGGTAGTTTCAATTTCTGTTCAATTTATGTTTTTCAAAAATCAACTC
190 GAGCCTCAAGACACGTTGAGGTAGTTTCAATTTCTGCTCAATTTATGTTTTTCAAAAATCAACTC
*
27914025 ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTCTGTTTTTCAAAA
255 ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTCTATTTTTCAAAA
*
27914090 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTGTCAATTTTTGTG
320 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTGTCAATTTTTGTG
27914155 TTTCAATCTATTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCAGGACACGCTG
385 TTTCAATCTATTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCAGGACACGCTG
27914220 AGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG
450 AGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG
*
27914285 GCACGTTGAGGTAATTTCAATTTCTGCTTTTCAATTTATATTTTTCAAAAAAATTCAACTCATAT
515 GCACGTTGAGGTAATTTCAATATCTGCTTTTCAATTTATATTTTTCAAAAAAATTCAACTCATAT
27914350 TGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
580 TGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
27914404 TCAAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTT
1 TC-AAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTT
27914469 CAATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCT
65 CAATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCT
* *
27914534 GAGGTATTTTCAATTTTTGTCTTTCAAAAAAAAAATCAACTCATATTGTGAGAAATGAGTTGAGC
130 GAGGTATTTTCAATTTTTGTCTTTC-AAAAAAAAATCAACTCATATTGCGAGAAATAAGTTGAGC
27914599 CTCAAGACACGTTGAGGTAGTTTCAATTTCTGCTCAATTTATGTTTTTCAAAAATCAACTCATAT
194 CTCAAGACACGTTGAGGTAGTTTCAATTTCTGCTCAATTTATGTTTTTCAAAAATCAACTCATAT
*
27914664 TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTATTTTTCAAAAATCA
259 TGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTCTATTTTTCAAAAATCA
27914729 ACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTGTCAATTTTTGTGTTTC
324 ACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTGTCAATTTTTGTGTTTC
*
27914794 AATCTATTTTTCAAAAATCAACTTATATTACGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGT
389 AATCTATTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGT
27914859 AATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCAC
454 AATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCAC
*
27914924 GTTGAGGTAATTTCAATATCTGCTTTTCAATTTATATTTTTCAAAAAAATTCAACTCATATTGCG
519 GTTGAGGTAATTTCAATATCTGCTTTTCAATTTATATTTTTCAAAAAAATTCAACTCATATTGCA
27914989 AGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
584 AGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
27915039 TC--AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTC
1 TCAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTC
* * ** * * * *
27915102 AATTTTTATCTTTC-AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGGCAGGTTT
66 AATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTG
*
27915166 AGGTAATTTCAATTT
131 AGGTATTTTCAATTT
27915181 CTGCTTTTCA
Statistics
Matches: 745, Mismatches: 29, Indels: 13
0.95 0.04 0.02
Matches are distributed among these distances:
631 57 0.08
632 74 0.10
634 75 0.10
635 471 0.63
638 2 0.00
639 65 0.09
640 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (633 bp):
TCAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTC
AATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTG
AGGTATTTTCAATTTTTGTCTTTCAAAAAAAAATCAACTCATATTGCGAGAAATAAGTTGAGCCT
CAAGACACGTTGAGGTAGTTTCAATTTCTGCTCAATTTATGTTTTTCAAAAATCAACTCATATTG
CGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTCTATTTTTCAAAAATCAAC
TCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTGTCAATTTTTGTGTTTCAA
TCTATTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAA
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACGT
TGAGGTAATTTCAATATCTGCTTTTCAATTTATATTTTTCAAAAAAATTCAACTCATATTGCAAG
AGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
Found at i:27915190 original size:74 final size:74
Alignment explanation
Indices: 27914961--27915191 Score: 304
Period size: 74 Copynumber: 3.1 Consensus size: 74
27914951 CAATTTATAT
27914961 TTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTAAT
1 TTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGG-CACGCTGAGGTAAT
27915025 TTCAATTTCTG
64 TTCAATTTCTG
* ** * * *
27915036 TTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTT
1 TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTAATTT
* *
27915101 CAATTTTTA
66 CAATTTCTG
* * * *
27915110 TCTTTC-AAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGGCAGGTTTAGGTAATT
1 T-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTAATT
27915174 TCAATTTCTG
65 TCAATTTCTG
27915184 CTTTTCAA
1 -TTTTCAA
27915192 TTTATATTTT
Statistics
Matches: 133, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
74 115 0.86
75 18 0.14
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (74 bp):
TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTAATTT
CAATTTCTG
Found at i:27921849 original size:46 final size:46
Alignment explanation
Indices: 27921763--27921852 Score: 121
Period size: 46 Copynumber: 1.9 Consensus size: 46
27921753 TAATCTGCTA
27921763 AAAATCAAAATAAAACGAAAATGTAGGTCCACAAACTAAATAGCCCC
1 AAAATCAAAATAAAACGAAAATG-AGGTCCACAAACTAAATAGCCCC
* *
27921810 AAAATCAAAATGAAACATAAAATG-GG-CCTACAAACTAAATAGC
1 AAAATCAAAATAAAAC-GAAAATGAGGTCC-ACAAACTAAATAGC
27921853 TGGGCTGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 2 0.05
46 16 0.41
47 15 0.38
48 6 0.15
ACGTcount: A:0.54, C:0.19, G:0.11, T:0.16
Consensus pattern (46 bp):
AAAATCAAAATAAAACGAAAATGAGGTCCACAAACTAAATAGCCCC
Found at i:27922744 original size:35 final size:35
Alignment explanation
Indices: 27922705--27922772 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
27922695 TCCCAGCTAA
* *
27922705 CTTCGAGATTAACTATACAGGCTCGCAACATATAG
1 CTTCGAGATTAACAATACAGGCTCCCAACATATAG
27922740 CTTCGAGATTAACAATACAGGCTCCCAACATAT
1 CTTCGAGATTAACAATACAGGCTCCCAACATAT
27922773 CTTCTAGTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (35 bp):
CTTCGAGATTAACAATACAGGCTCCCAACATATAG
Found at i:27925048 original size:41 final size:40
Alignment explanation
Indices: 27924916--27925051 Score: 127
Period size: 41 Copynumber: 3.5 Consensus size: 40
27924906 ACCAGTTTGG
* *
27924916 CACCCAGTGCCTCATC-AGATAATTCGAAGTAATAATTTGA
1 CACCCAGTGCCTCATCGA-ATAATCCGAAGTAATAAATTGA
* * *** * *
27924956 CACCTAGTGTCTCATCGGCGAAACCGAAG---TAAATTGG
1 CACCCAGTGCCTCATCGAATAATCCGAAGTAATAAATTGA
*
27924993 CACCTAGTGCCTCATCGAATTAATCCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCCGAAGTAATAAATTGA
*
27925034 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
27925052 CTCGAAGTGG
Statistics
Matches: 74, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
37 22 0.30
38 8 0.11
40 21 0.28
41 23 0.31
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAATCCGAAGTAATAAATTGA
Found at i:27925936 original size:20 final size:20
Alignment explanation
Indices: 27925913--27925950 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27925903 GAAACCCTAA
27925913 CTTTCTCCTTCTTTCTTTCT
1 CTTTCTCCTTCTTTCTTTCT
* *
27925933 CTTTTTCTTTCTTTCTTT
1 CTTTCTCCTTCTTTCTTT
27925951 TTCCCCCTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (20 bp):
CTTTCTCCTTCTTTCTTTCT
Found at i:27925942 original size:16 final size:15
Alignment explanation
Indices: 27925921--27925952 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
27925911 AACTTTCTCC
27925921 TTCTTTCTTTCTCTTT
1 TTCTTTCTTTCT-TTT
27925937 TTCTTTCTTTCTTTT
1 TTCTTTCTTTCTTTT
27925952 T
1 T
27925953 CCCCCTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTCTTTCTTTCTTTT
Found at i:27926033 original size:3 final size:3
Alignment explanation
Indices: 27926025--27926071 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
27926015 TTGTTTTAAT
27926025 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
27926072 TATTTACTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27926116 original size:19 final size:20
Alignment explanation
Indices: 27926092--27926130 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
27926082 ATTAATAAGC
27926092 AATACATAT-TTTATTATTA
1 AATACATATGTTTATTATTA
27926111 AATACATATGTTTATTATTA
1 AATACATATGTTTATTATTA
27926131 CACATGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (20 bp):
AATACATATGTTTATTATTA
Found at i:27928223 original size:42 final size:43
Alignment explanation
Indices: 27928164--27928327 Score: 183
Period size: 42 Copynumber: 3.9 Consensus size: 43
27928154 TTAGGGTTAC
* *
27928164 TGAGACTAT-GTGTAAGACCATATCTGGGATATGGCATCAATA
1 TGAGACTATCGTGTAAGACCATATCTAGGATATGGCATCGATA
27928206 TGAGACT-TCGTGTAAGACCATATCTAGGATATGGCATCGATA
1 TGAGACTATCGTGTAAGACCATATCTAGGATATGGCATCGATA
* * * * *
27928248 TGAGACT-TTGTGTAAGACCATAGCTGGGCTATTAGCATCGATA
1 TGAGACTATCGTGTAAGACCATATCTAGGATA-TGGCATCGATA
* ** * *
27928291 CGAGA-TCCCATGTAAGACTATATCTAGGATATGGCAT
1 TGAGACTATCGTGTAAGACCATATCTAGGATATGGCAT
27928328 TGGTATGGTA
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.01
42 71 0.69
43 31 0.30
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (43 bp):
TGAGACTATCGTGTAAGACCATATCTAGGATATGGCATCGATA
Found at i:27928322 original size:85 final size:84
Alignment explanation
Indices: 27928164--27928327 Score: 222
Period size: 85 Copynumber: 1.9 Consensus size: 84
27928154 TTAGGGTTAC
* * * * *
27928164 TGAGACTATGTGTAAGACCATATCTGGGATATGGCATCAATATGAGACTTCGTGTAAGACCATAT
1 TGAGACTATGTGTAAGACCATAGCTGGGATATAGCATCAATACGAGACTCCATGTAAGACCATAT
27928229 CTAGGATATGGCATCGATA
66 CTAGGATATGGCATCGATA
* * * *
27928248 TGAGACTTTGTGTAAGACCATAGCTGGGCTATTAGCATCGATACGAGA-TCCCATGTAAGACTAT
1 TGAGACTATGTGTAAGACCATAGCTGGGATA-TAGCATCAATACGAGACT-CCATGTAAGACCAT
27928312 ATCTAGGATATGGCAT
64 ATCTAGGATATGGCAT
27928328 TGGTATGGTA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
84 29 0.42
85 40 0.58
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (84 bp):
TGAGACTATGTGTAAGACCATAGCTGGGATATAGCATCAATACGAGACTCCATGTAAGACCATAT
CTAGGATATGGCATCGATA
Found at i:27928346 original size:85 final size:84
Alignment explanation
Indices: 27928164--27928346 Score: 190
Period size: 85 Copynumber: 2.2 Consensus size: 84
27928154 TTAGGGTTAC
* * * * * * *
27928164 TGAGACTATGTGTAAGACCATATCTGGGATATGGCATCAATATGAGACTTCGTGTAAGACCATAT
1 TGAGACCAAGTGTAAGACCATAGCTGGGATATAGCATCAATACGAGACTCCATGTAAGACCATAT
27928229 CTAGGATATGGCATCGATA
66 CTAGGATATGGCATCGATA
*** * * *
27928248 TGAGACTTTGTGTAAGACCATAGCTGGGCTATTAGCATCGATACGAGA-TCCCATGTAAGACTAT
1 TGAGACCAAGTGTAAGACCATAGCTGGGATA-TAGCATCAATACGAGACT-CCATGTAAGACCAT
* *
27928312 ATCTAGGATATGGCATTGGTA
64 ATCTAGGATATGGCATCGATA
27928333 TG-GTACCAAGTGTA
1 TGAG-ACCAAGTGTA
27928347 TAGGACTCCC
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
84 30 0.37
85 52 0.63
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (84 bp):
TGAGACCAAGTGTAAGACCATAGCTGGGATATAGCATCAATACGAGACTCCATGTAAGACCATAT
CTAGGATATGGCATCGATA
Found at i:27933362 original size:18 final size:18
Alignment explanation
Indices: 27933339--27933376 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
27933329 TTCCATCAAA
27933339 TTTGCATGACCAATTCAG
1 TTTGCATGACCAATTCAG
*
27933357 TTTGCATGATCAATTCAG
1 TTTGCATGACCAATTCAG
27933375 TT
1 TT
27933377 CACTTACCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (18 bp):
TTTGCATGACCAATTCAG
Found at i:27933761 original size:19 final size:19
Alignment explanation
Indices: 27933734--27933770 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
27933724 AAAGCGTATA
27933734 CTGGAACATGAAGTGCATT
1 CTGGAACATGAAGTGCATT
*
27933753 CTGGCACATGAAGTGCAT
1 CTGGAACATGAAGTGCAT
27933771 CTTAGCGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (19 bp):
CTGGAACATGAAGTGCATT
Found at i:27935245 original size:15 final size:15
Alignment explanation
Indices: 27935227--27935276 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
27935217 TATTTATCAT
27935227 ATCAAAATTCATAAA
1 ATCAAAATTCATAAA
27935242 ATC-AAATT-A-AATA
1 ATCAAAATTCATAA-A
27935255 TATCAAAATTCATAAA
1 -ATCAAAATTCATAAA
27935271 ATCAAA
1 ATCAAA
27935277 TTAAATATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
12 2 0.07
13 2 0.07
14 8 0.27
15 14 0.47
16 2 0.07
17 2 0.07
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (15 bp):
ATCAAAATTCATAAA
Found at i:27935257 original size:29 final size:29
Alignment explanation
Indices: 27935225--27935284 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
27935215 CATATTTATC
27935225 ATATCAAAATTCATAAAATCAAATTAAAT
1 ATATCAAAATTCATAAAATCAAATTAAAT
27935254 ATATCAAAATTCATAAAATCAAATTAAAT
1 ATATCAAAATTCATAAAATCAAATTAAAT
27935283 AT
1 AT
27935285 TCACAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (29 bp):
ATATCAAAATTCATAAAATCAAATTAAAT
Found at i:27935624 original size:3 final size:3
Alignment explanation
Indices: 27935616--27935656 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
27935606 TTTATTACCT
27935616 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
27935657 GTTTAGTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:27939798 original size:55 final size:55
Alignment explanation
Indices: 27939734--27939851 Score: 227
Period size: 55 Copynumber: 2.1 Consensus size: 55
27939724 AAAATTCAAA
27939734 TAATTTATTATATTATTTAATTAATGTAGATCATTAACTAATTTTTAGTAATAAT
1 TAATTTATTATATTATTTAATTAATGTAGATCATTAACTAATTTTTAGTAATAAT
27939789 TAATTTATTATATTATTTAATTAATGTAGATCATTAACTAATTTTTAGTAATAAT
1 TAATTTATTATATTATTTAATTAATGTAGATCATTAACTAATTTTTAGTAATAAT
27939844 TGAATTTA
1 T-AATTTA
27939852 CGATAGAACT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 56 0.90
56 6 0.10
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (55 bp):
TAATTTATTATATTATTTAATTAATGTAGATCATTAACTAATTTTTAGTAATAAT
Found at i:27939865 original size:55 final size:55
Alignment explanation
Indices: 27939751--27939866 Score: 171
Period size: 55 Copynumber: 2.1 Consensus size: 55
27939741 TTATATTATT
** * **
27939751 TAATTAATGTAGATCATTAACTAATTTTTAGTAATAATTAATTTATTATATTATT
1 TAATTAATGTAGATCATTAACTAATTTTTAGTAATAATTAATTTACGATATGAAC
27939806 TAATTAATGTAGATCATTAACTAATTTTTAGTAATAATTGAATTTACGATA-GAAC
1 TAATTAATGTAGATCATTAACTAATTTTTAGTAATAATT-AATTTACGATATGAAC
27939861 TAATTA
1 TAATTA
27939867 TGAGTTATAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
55 46 0.84
56 9 0.16
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (55 bp):
TAATTAATGTAGATCATTAACTAATTTTTAGTAATAATTAATTTACGATATGAAC
Found at i:27945021 original size:11 final size:11
Alignment explanation
Indices: 27945002--27945046 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
27944992 CAGCTATTTA
27945002 TAATAAAATAT
1 TAATAAAATAT
*
27945013 TAGTAAAATAT
1 TAATAAAATAT
*
27945024 CTCATTAAAATAT
1 -T-AATAAAATAT
27945037 TAATAAAATA
1 TAATAAAATA
27945047 ATATTTATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 18 0.62
12 2 0.07
13 9 0.31
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:27948341 original size:22 final size:23
Alignment explanation
Indices: 27948311--27948356 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
27948301 AATATGGCAA
27948311 TGATAAAA-TT-CGAGCTTTAAAT
1 TGATAAAATTTACGAG-TTTAAAT
*
27948333 TGATGAAATTTACGAGTTTAAAT
1 TGATAAAATTTACGAGTTTAAAT
27948356 T
1 T
27948357 TTTTTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 10 0.48
24 4 0.19
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (23 bp):
TGATAAAATTTACGAGTTTAAAT
Found at i:27948570 original size:30 final size:30
Alignment explanation
Indices: 27948536--27948592 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
27948526 TTAGAAAGGT
* *
27948536 TTAATGAAACTTTTTAAAAAAAATTGTGGG
1 TTAATGAAAATTTTCAAAAAAAATTGTGGG
* *
27948566 TTAATTAAAATTTTCAAAGAAAATTGT
1 TTAATGAAAATTTTCAAAAAAAATTGT
27948593 AAAATTTTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.39
Consensus pattern (30 bp):
TTAATGAAAATTTTCAAAAAAAATTGTGGG
Found at i:27951448 original size:17 final size:16
Alignment explanation
Indices: 27951421--27951467 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
27951411 TCAAATAATG
*
27951421 AATATATATTCAATAT
1 AATATAAATTCAATAT
*
27951437 ATATATCAATTCAAT-T
1 A-ATATAAATTCAATAT
27951453 AATATAAATTCAATA
1 AATATAAATTCAATA
27951468 AATTCATCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 12 0.46
16 3 0.12
17 11 0.42
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATAAATTCAATAT
Found at i:27953334 original size:20 final size:21
Alignment explanation
Indices: 27953311--27953352 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
27953301 GTTATATACG
*
27953311 TATATAGTATGTGTATT-TTA
1 TATATAGTATGTATATTATTA
*
27953331 TATATATTATGTATATTATTA
1 TATATAGTATGTATATTATTA
27953352 T
1 T
27953353 TTTTACTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
TATATAGTATGTATATTATTA
Found at i:27953428 original size:10 final size:10
Alignment explanation
Indices: 27953402--27953440 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
27953392 ATTCATGTAT
27953402 TTTATTATATA
1 TTTA-TATATA
* *
27953413 TGTATATATC
1 TTTATATATA
27953423 TTTATATATA
1 TTTATATATA
27953433 TTTATATA
1 TTTATATA
27953441 AGTATATCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 21 0.88
11 3 0.12
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (10 bp):
TTTATATATA
Found at i:27953555 original size:109 final size:110
Alignment explanation
Indices: 27953388--27953613 Score: 420
Period size: 109 Copynumber: 2.1 Consensus size: 110
27953378 TTAAATATCA
27953388 TATTATTCATGTATTTTATTATATATGTATATATCTTTATATATATTTATATAAGTATATCTTCA
1 TATTATTCATGTATTTTATTATATATGTATATATCTTTATATATATTTATATAAGTATATCTTCA
27953453 TGTAATATTAGTATTATTATTAATGTTAATACACCTTTAACATCG
66 TGTAATATTAGTATTATTATTAATGTTAATACACCTTTAACATCG
27953498 TATTATTCATGTATTTATATTATATATGTATATATCTTTA-ATATA-TTATATAAGTATATCTTC
1 TATTATTCATGTATTT-TATTATATATGTATATATCTTTATATATATTTATATAAGTATATCTTC
27953561 ATGTAATATTAGTATTATTATTAATGTTAATACACCTTTAACATCG
65 ATGTAATATTAGTATTATTATTAATGTTAATACACCTTTAACATCG
27953607 TAATTAT
1 T-ATTAT
27953614 GTGTGTACAT
Statistics
Matches: 114, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
109 65 0.57
110 26 0.23
111 23 0.20
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.50
Consensus pattern (110 bp):
TATTATTCATGTATTTTATTATATATGTATATATCTTTATATATATTTATATAAGTATATCTTCA
TGTAATATTAGTATTATTATTAATGTTAATACACCTTTAACATCG
Found at i:27953649 original size:24 final size:25
Alignment explanation
Indices: 27953622--27953672 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
27953612 ATGTGTGTAC
27953622 ATATTATGTAAATATTTTA-ATATT
1 ATATTATGTAAATATTTTATATATT
** *
27953646 ATATTATGTGTATGTTTTATATATT
1 ATATTATGTAAATATTTTATATATT
27953671 AT
1 AT
27953673 GAACATGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (25 bp):
ATATTATGTAAATATTTTATATATT
Found at i:27965340 original size:15 final size:15
Alignment explanation
Indices: 27965320--27965356 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 15
27965310 TTTTTTTAAA
27965320 AAAAAAGAGAGAAAAAG
1 AAAAAAGA-A-AAAAAG
27965337 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
27965352 AAAAA
1 AAAAA
27965357 GGGGATCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 1 0.05
17 8 0.40
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:27965348 original size:8 final size:8
Alignment explanation
Indices: 27965319--27965356 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
27965309 TTTTTTTTAA
27965319 AAAAAAAG
1 AAAAAAAG
27965327 AGAGAAAAAG
1 A-A-AAAAAG
27965337 -AAAAAAG
1 AAAAAAAG
27965344 AAAAAAAG
1 AAAAAAAG
27965352 AAAAA
1 AAAAA
27965357 GGGGATCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 6 0.22
8 14 0.52
9 1 0.04
10 6 0.22
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:27966292 original size:14 final size:14
Alignment explanation
Indices: 27966273--27966307 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
27966263 CGCTGAGGTA
*
27966273 TTTTCAATTTCTGT
1 TTTTCAATTTCTGC
27966287 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
27966301 TTTTCAA
1 TTTTCAA
27966308 AAAAGTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:27966524 original size:54 final size:54
Alignment explanation
Indices: 27966367--27966525 Score: 246
Period size: 54 Copynumber: 2.9 Consensus size: 54
27966357 AGGTAATTTC
** ** *
27966367 AATTTCTGTTTGCCAAAAATTGACTCATATTGCGAGAGGTGAGTTGAGCATTTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
*
27966421 AATTTCTGTTTTTCAAAAATCAACTCACATTGCGAGAGGTGAGTTGAGCCTTTT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
* *
27966475 AATTTCTGTTTTTCAACAATCAACTCATATTGTGAGAGGTGAGTTGAGCCT
1 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
27966526 CAAGGCACGT
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (54 bp):
AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT
Found at i:27966562 original size:14 final size:14
Alignment explanation
Indices: 27966543--27966569 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27966533 CGTTGAGGTA
27966543 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
27966557 TTTTCAATTTCTG
1 TTTTCAATTTCTG
27966570 CTCTTCAAAA
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:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:27966680 original size:75 final size:74
Alignment explanation
Indices: 27966557--27966760 Score: 293
Period size: 75 Copynumber: 2.7 Consensus size: 74
27966547 CAATTTCTGT
* * *
27966557 TTTTCAATTTCTGCTCTTCAAAAAAGTTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
1 TTTTCAATTTCT-CTTTTCAAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
27966622 CGCTGAGGTA
65 CGCTGAGGTA
*
27966632 TTTTCAATTTCTACTTTTCAAAAAAGTCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCT-CTTTTCAAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
27966697 CGCTGAGGTA
65 CGCTGAGGTA
* * * * * *
27966707 ATTTCAATTTCTGTTTGCCAAAAA-TCGACTCATATTACGAGAGGTGAGTTGAGC
1 TTTTCAATTTCTCTTTTCAAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGC
27966761 ATTTTAATTT
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
73 27 0.23
74 9 0.08
75 81 0.69
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (74 bp):
TTTTCAATTTCTCTTTTCAAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTA
Found at i:27966794 original size:54 final size:54
Alignment explanation
Indices: 27966707--27966891 Score: 298
Period size: 54 Copynumber: 3.4 Consensus size: 54
27966697 CGCTGAGGTA
* ** * *
27966707 ATTTCAATTTCTGTTTGCCAAAAATCGACTCATATTACGAGAGGTGAGTTGAGC
1 ATTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
27966761 ATTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 ATTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
27966815 CTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 ATTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
**
27966869 CCTTTAATTTCTGTTTTTCAAAA
1 ATTTTAATTTCTGTTTTTCAAAA
27966892 TCTACTTTTC
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 124 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (54 bp):
ATTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:27968875 original size:24 final size:24
Alignment explanation
Indices: 27968848--27968897 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
27968838 CCCCACAACT
27968848 TTGTTTTTAGTTTAATTTTGATCC
1 TTGTTTTTAGTTTAATTTTGATCC
27968872 TTGTTTTTAGTTTAATTTTGATCC
1 TTGTTTTTAGTTTAATTTTGATCC
27968896 TT
1 TT
27968898 TCTTCGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.08, G:0.12, T:0.64
Consensus pattern (24 bp):
TTGTTTTTAGTTTAATTTTGATCC
Found at i:27969336 original size:21 final size:21
Alignment explanation
Indices: 27969307--27969346 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27969297 ATTCATGTAT
*
27969307 TTTATTATATATGTATATATC
1 TTTAATATATATGTATATATC
*
27969328 TTTAATATATATTTATATA
1 TTTAATATATATGTATATA
27969347 AGTATATCTT
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:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTAATATATATGTATATATC
Found at i:27969446 original size:24 final size:25
Alignment explanation
Indices: 27969419--27969469 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
27969409 ATGTGTGTAC
27969419 ATATTATGTAAATGTTTTA-ATATT
1 ATATTATGTAAATGTTTTATATATT
**
27969443 ATATTATGTGTATGTTTTATATATT
1 ATATTATGTAAATGTTTTATATATT
27969468 AT
1 AT
27969470 GAACATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (25 bp):
ATATTATGTAAATGTTTTATATATT
Found at i:27981437 original size:11 final size:11
Alignment explanation
Indices: 27981421--27981459 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
27981411 AAATCACTTA
27981421 TTTTTTT-GAT
1 TTTTTTTCGAT
27981431 TTTTTTTCGAAT
1 TTTTTTTCG-AT
*
27981443 TTTTTTTCAAT
1 TTTTTTTCGAT
27981454 TTTTTT
1 TTTTTT
27981460 AACTTGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 7 0.27
11 9 0.35
12 10 0.38
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (11 bp):
TTTTTTTCGAT
Found at i:27981444 original size:12 final size:12
Alignment explanation
Indices: 27981421--27981459 Score: 57
Period size: 11 Copynumber: 3.5 Consensus size: 12
27981411 AAATCACTTA
27981421 TTTTTTT-G-AT
1 TTTTTTTCGAAT
27981431 TTTTTTTCGAAT
1 TTTTTTTCGAAT
27981443 TTTTTTTC-AAT
1 TTTTTTTCGAAT
27981454 TTTTTT
1 TTTTTT
27981460 AACTTGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 7 0.26
11 10 0.37
12 10 0.37
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (12 bp):
TTTTTTTCGAAT
Found at i:27981825 original size:14 final size:14
Alignment explanation
Indices: 27981796--27981843 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
27981786 CAAAGTAGAA
*
27981796 AAAGGGATACGAACG
1 AAAGGG-TAGGAACG
*
27981811 AAATGGTAGGAACG
1 AAAGGGTAGGAACG
*
27981825 AAAGGGTAGGAACA
1 AAAGGGTAGGAACG
27981839 AAAGG
1 AAAGG
27981844 ATATGAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 24 0.83
15 5 0.17
ACGTcount: A:0.48, C:0.08, G:0.35, T:0.08
Consensus pattern (14 bp):
AAAGGGTAGGAACG
Found at i:27981851 original size:14 final size:14
Alignment explanation
Indices: 27981795--27981854 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
27981785 TCAAAGTAGA
*
27981795 AAAAGGGATACGAAC
1 AAAA-GGATAGGAAC
*
27981810 GAAATGG-TAGGAAC
1 -AAAAGGATAGGAAC
* *
27981824 GAAAGGGTAGGAAC
1 AAAAGGATAGGAAC
*
27981838 AAAAGGATATGAAC
1 AAAAGGATAGGAAC
27981852 AAA
1 AAA
27981855 TTGGTTGGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
13 4 0.11
14 27 0.75
15 2 0.06
16 3 0.08
ACGTcount: A:0.52, C:0.08, G:0.30, T:0.10
Consensus pattern (14 bp):
AAAAGGATAGGAAC
Found at i:27985127 original size:27 final size:26
Alignment explanation
Indices: 27985097--27985154 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
27985087 AATATTTTTT
* *
27985097 AAATATTCATATATATTATATACATAC
1 AAATATT-ACATATACTATATACATAC
* *
27985124 AAATA-TACCTATACTATATACATAT
1 AAATATTACATATACTATATACATAC
27985149 AAATAT
1 AAATAT
27985155 ATTTATAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 20 0.77
26 1 0.04
27 5 0.19
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATATTACATATACTATATACATAC
Found at i:27985161 original size:25 final size:25
Alignment explanation
Indices: 27985108--27985155 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
27985098 AATATTCATA
*
27985108 TATATTATATACATACAAATATACC
1 TATACTATATACATACAAATATACC
*
27985133 TATACTATATACATATAAATATA
1 TATACTATATACATACAAATATA
27985156 TTTATAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (25 bp):
TATACTATATACATACAAATATACC
Found at i:27987432 original size:15 final size:16
Alignment explanation
Indices: 27987400--27987441 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
27987390 AAATATTACT
*
27987400 AAAATAAAATATATAAA
1 AAAATAAAA-AGATAAA
27987417 AAAATAAAAAGA-AAA
1 AAAATAAAAAGATAAA
*
27987432 AAATTAAAAA
1 AAAATAAAAA
27987442 TTTTACCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 12 0.52
16 2 0.09
17 9 0.39
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAATAAAAAGATAAA
Found at i:27987576 original size:16 final size:17
Alignment explanation
Indices: 27987534--27987576 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
27987524 CCGGTAGCCC
27987534 CCTCTCTCCTTTCCCTT
1 CCTCTCTCCTTTCCCTT
* *
27987551 -CTCCCTCCTTTCTCTT
1 CCTCTCTCCTTTCCCTT
27987567 CCTCTC-CCTT
1 CCTCTCTCCTT
27987577 CTTCTCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (17 bp):
CCTCTCTCCTTTCCCTT
Found at i:27988019 original size:3 final size:3
Alignment explanation
Indices: 27988013--27988053 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
27988003 TTTTATATGT
* *
27988013 TTA TTA TTA TTA -TA TTA TTA CTA TTA TTC TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27988054 AGTATATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:27988517 original size:20 final size:20
Alignment explanation
Indices: 27988488--27988528 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
27988478 TTTTAATATG
*
27988488 TATTACATATATATGTATTT
1 TATTACATATATATATATTT
*
27988508 TATTATATATATATATATTT
1 TATTACATATATATATATTT
27988528 T
1 T
27988529 TCATATATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTACATATATATATATTT
Found at i:27991331 original size:53 final size:54
Alignment explanation
Indices: 27991273--27991377 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
27991263 ATGCAGCATG
* *
27991273 GCTGCCAGAACAGATA-ATGTGACAGAGTCACCAGAACAAATAATTGTGGCAGA
1 GCTGCCAGAACAGATATATGTGACAGAGCCACCAGAACAAATAAATGTGGCAGA
* * *
27991326 GCTGCCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAAATGTGGCA
1 GCTGCCAGAACAGATATATGTGACAGAGCCACCAGAACAAATAAATGTGGCA
27991378 TAGCCATCAG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 16 0.35
54 30 0.65
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (54 bp):
GCTGCCAGAACAGATATATGTGACAGAGCCACCAGAACAAATAAATGTGGCAGA
Found at i:27991382 original size:27 final size:27
Alignment explanation
Indices: 27991277--27991383 Score: 126
Period size: 27 Copynumber: 4.0 Consensus size: 27
27991267 AGCATGGCTG
* *
27991277 CCAGAACAGAT-AATGTGACAGAGTCA
1 CCAGAACAGATAAATGTGGCAGAGCCA
* * **
27991303 CCAGAACAAATAATTGTGGCAGAGCTG
1 CCAGAACAGATAAATGTGGCAGAGCCA
*
27991330 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATAAATGTGGCAGAGCCA
* *
27991357 CCAGATCAGATAAATGTGGCATAGCCA
1 CCAGAACAGATAAATGTGGCAGAGCCA
27991384 TCAGGACGCT
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
26 10 0.15
27 56 0.85
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATAAATGTGGCAGAGCCA
Found at i:27992851 original size:24 final size:25
Alignment explanation
Indices: 27992788--27992844 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
27992778 AACTCTTGCT
*
27992788 CCTTGATCAGCTCCTAAATCTTCTCC
1 CCTT-ATCAACTCCTAAATCTTCTCC
27992814 CCTTATCAACTCCTAAATCTTCT-C
1 CCTTATCAACTCCTAAATCTTCTCC
27992838 CCTTATC
1 CCTTATC
27992845 CCCTCCTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 8 0.27
25 18 0.60
26 4 0.13
ACGTcount: A:0.21, C:0.39, G:0.04, T:0.37
Consensus pattern (25 bp):
CCTTATCAACTCCTAAATCTTCTCC
Found at i:27995353 original size:38 final size:35
Alignment explanation
Indices: 27995292--27995409 Score: 126
Period size: 31 Copynumber: 3.5 Consensus size: 35
27995282 TCAATCATGC
*
27995292 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTT-AT--T
*
27995331 ACTGGGCCGAAGCATTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
27995362 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
27995393 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
27995410 ACTGTAAACG
Statistics
Matches: 76, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
31 48 0.63
33 2 0.03
34 1 0.01
36 1 0.01
38 13 0.17
39 11 0.14
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (35 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
Found at i:27995406 original size:31 final size:31
Alignment explanation
Indices: 27995315--27995409 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
27995305 CCTTTTCATA
* *
27995315 TTTCATATTTCATAATACTGGGCCGAAGCAT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
27995346 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
27995377 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
27995408 TT
1 TT
27995410 ACTGTAAACG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:27995652 original size:24 final size:24
Alignment explanation
Indices: 27995601--27995767 Score: 248
Period size: 24 Copynumber: 7.0 Consensus size: 24
27995591 GCTTTATCAT
* *
27995601 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* **
27995626 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTG
27995650 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTG
27995673 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
27995697 ATAATTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
27995721 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
27995745 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
27995768 TCACTTCCTC
Statistics
Matches: 133, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
23 23 0.17
24 98 0.74
25 12 0.09
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:27995706 original size:71 final size:71
Alignment explanation
Indices: 27995600--27995767 Score: 248
Period size: 71 Copynumber: 2.3 Consensus size: 71
27995590 TGCTTTATCA
*
27995600 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
27995664 AGCCCTTT
64 AGCCCTTT
* * * **
27995672 TATAACTGGGGCATAAGCCCTTTTGATAATTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAG
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAG
27995737 CCCTTT
66 CCCTTT
27995743 TGATAACTGGGGCATAAGCCCTTTT
1 T-ATAACTGGGGCATAAGCCCTTTT
27995768 TCACTTCCTC
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
71 52 0.59
72 36 0.41
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (71 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAAG
CCCTTT
Found at i:27995843 original size:20 final size:20
Alignment explanation
Indices: 27995818--27995877 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
27995808 TATGATTACC
27995818 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
* *
27995838 TCATGTGCATAGCATACATT
1 TCATGTGCATATCATACATA
27995858 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
27995878 CCATATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:27995952 original size:25 final size:25
Alignment explanation
Indices: 27995920--27995967 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
27995910 ATACATAAAC
* * *
27995920 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
27995945 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
27995968 CATGGTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:27997188 original size:27 final size:27
Alignment explanation
Indices: 27997126--27997190 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
27997116 GGGCATATTC
27997126 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
27997153 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
*
27997180 GTCTTTTTACC
1 GTCATTTTACC
27997191 TTTTAGGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:27997274 original size:27 final size:27
Alignment explanation
Indices: 27997252--27997418 Score: 131
Period size: 27 Copynumber: 6.1 Consensus size: 27
27997242 ACAAACCAAA
* *
27997252 GGTATTTCAGTAATTTTGTAAACCAAT
1 GGTATTTCAGTAATTTTGTAAATCAAG
*
27997279 GGTACTTCTA-TAATTTT-TAAAAGTCAAG
1 GGTATTTC-AGTAATTTTGT-AAA-TCAAG
* * *
27997307 GGTATTTCTGTAACTTTGTAAATCAGG
1 GGTATTTCAGTAATTTTGTAAATCAAG
** ** **
27997334 GGTATTTTGGTAATTTTACAAATTGAG
1 GGTATTTCAGTAATTTTGTAAATCAAG
* *
27997361 GGTATTTCGGTAATTTTGTAAATCGAG
1 GGTATTTCAGTAATTTTGTAAATCAAG
*** *
27997388 GGTAAAACAGTAATTCTGTAAATCAAG
1 GGTATTTCAGTAATTTTGTAAATCAAG
27997415 GGTA
1 GGTA
27997419 AAACGGTAAT
Statistics
Matches: 110, Mismatches: 25, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
26 1 0.01
27 88 0.80
28 20 0.18
29 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (27 bp):
GGTATTTCAGTAATTTTGTAAATCAAG
Found at i:27997419 original size:27 final size:27
Alignment explanation
Indices: 27997368--27997607 Score: 288
Period size: 27 Copynumber: 8.9 Consensus size: 27
27997358 GAGGGTATTT
*
27997368 CGGTAATTTTGTAAATCGAGGGTAAAA
1 CGGTAATTATGTAAATCGAGGGTAAAA
* * *
27997395 CAGTAATTCTGTAAATCAAGGGTAAAA
1 CGGTAATTATGTAAATCGAGGGTAAAA
* *
27997422 CGGTAATTCTGTAAGTCGAGGGTAAAA
1 CGGTAATTATGTAAATCGAGGGTAAAA
*
27997449 CGATAATTATGTAAATC-AGGGGTAAAA
1 CGGTAATTATGTAAATCGA-GGGTAAAA
* *
27997476 CGGTAATTATGTAAATTGTGGGTAAAA
1 CGGTAATTATGTAAATCGAGGGTAAAA
* *
27997503 CGGTAATTCTGTAAGTCGAGGGTAAAA
1 CGGTAATTATGTAAATCGAGGGTAAAA
* *
27997530 TGATAATTATGTAAATC-AGGGGTAAAA
1 CGGTAATTATGTAAATCGA-GGGTAAAA
*
27997557 CGGTAATTATGTAAAT-TAGGGGTAAAA
1 CGGTAATTATGTAAATCGA-GGGTAAAA
* *
27997584 CGGTAATTCTATAAATCGAGGGTA
1 CGGTAATTATGTAAATCGAGGGTA
27997608 CTTTGGTAAT
Statistics
Matches: 183, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.01
27 180 0.98
28 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.25, T:0.28
Consensus pattern (27 bp):
CGGTAATTATGTAAATCGAGGGTAAAA
Found at i:27997634 original size:81 final size:81
Alignment explanation
Indices: 27997371--27997607 Score: 352
Period size: 81 Copynumber: 2.9 Consensus size: 81
27997361 GGTATTTCGG
* * * * * *
27997371 TAATTTTGTAAATC-GAGGGTAAAACAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTGTA
1 TAATTATGTAAATCAG-GGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTATA
* *
27997435 AGTCGAGGGTAAAACGA
65 AATCGAGGGTAAAATGA
*
27997452 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATT-GTGGGTAAAACGGTAATTCTGTA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAG-GGGTAAAACGGTAATTCTATA
*
27997516 AGTCGAGGGTAAAATGA
65 AATCGAGGGTAAAATGA
27997533 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTATAA
1 TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTATAA
27997598 ATCGAGGGTA
66 ATCGAGGGTA
27997608 CTTTGGTAAT
Statistics
Matches: 145, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
81 143 0.99
82 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (81 bp):
TAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAAATTAGGGGTAAAACGGTAATTCTATAA
ATCGAGGGTAAAATGA
Found at i:27997644 original size:27 final size:27
Alignment explanation
Indices: 27997614--27997678 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
27997604 GGTACTTTGG
27997614 TAATTTTACAAGTCGAGGGTATTTCAA
1 TAATTTTACAAGTCGAGGGTATTTCAA
* *
27997641 TAATTTTACAGGTCGAGGGTATTTCAG
1 TAATTTTACAAGTCGAGGGTATTTCAA
*
27997668 TAATTTCACAA
1 TAATTTTACAA
27997679 ATTAGGGGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.37
Consensus pattern (27 bp):
TAATTTTACAAGTCGAGGGTATTTCAA
Found at i:27997687 original size:27 final size:27
Alignment explanation
Indices: 27997657--27997754 Score: 128
Period size: 27 Copynumber: 3.7 Consensus size: 27
27997647 TACAGGTCGA
* * *
27997657 GGGTATTTCAGTAATTTCACAAATTAG
1 GGGTATTTTAGTAATTTTACAAACTAG
*
27997684 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTAGTAATTTTACAAACTAG
27997711 GGGTATTTTAGTAATTTTACAAAGC-A-
1 GGGTATTTTAGTAATTTTACAAA-CTAG
*
27997737 GGGTATTTTGGTAATTTT
1 GGGTATTTTAGTAATTTT
27997755 GTAAACCAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.27
27 46 0.72
28 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.42
Consensus pattern (27 bp):
GGGTATTTTAGTAATTTTACAAACTAG
Found at i:28001154 original size:46 final size:46
Alignment explanation
Indices: 28001104--28001276 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
28001094 TGGTTGAGCA
*
28001104 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
28001150 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
28001197 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
28001243 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
28001277 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 61 0.57
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:28001260 original size:93 final size:93
Alignment explanation
Indices: 28001101--28001271 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
28001091 GGATGGTTGA
* *
28001101 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
28001166 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
28001194 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
28001259 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
28001272 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28011168 original size:27 final size:27
Alignment explanation
Indices: 28011114--28011224 Score: 145
Period size: 27 Copynumber: 4.1 Consensus size: 27
28011104 AGCATGGCTG
* *
28011114 CCAGAACAGATAA-TGTGACAGAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
28011140 CCAGAACAGATAATTGTGGCAGAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
28011167 CCAGAACAGAT-CTATGTGGCAGAGCCA
1 CCAGAACAGATAAT-TGTGGCAGAGCCA
* * *
28011194 CCAGATCAGATAAATGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
28011221 CCAG
1 CCAG
28011225 GACGCTTCCT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 14 0.19
27 61 0.81
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.15
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:28011372 original size:26 final size:27
Alignment explanation
Indices: 28011343--28011402 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
28011333 AGGTATAATG
* *
28011343 GTAATTT-TACACCTAGGGGTATAT-CA
1 GTAATTTCCACACATAGGGGTAT-TCCA
*
28011369 GTAATTTCCATACATAGGGGTATTCCA
1 GTAATTTCCACACATAGGGGTATTCCA
28011396 GTAATTT
1 GTAATTT
28011403 ATCTATTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (27 bp):
GTAATTTCCACACATAGGGGTATTCCA
Found at i:28012249 original size:16 final size:16
Alignment explanation
Indices: 28012228--28012268 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
28012218 AGCAGAAAAG
28012228 TTCGGCTACCACAAGA
1 TTCGGCTACCACAAGA
28012244 TTCGGCTACCACAAGA
1 TTCGGCTACCACAAGA
28012260 TTCGGCTAC
1 TTCGGCTAC
28012269 TGAGGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.22
Consensus pattern (16 bp):
TTCGGCTACCACAAGA
Found at i:28012687 original size:25 final size:25
Alignment explanation
Indices: 28012649--28012707 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
28012639 CCAACTCTTG
*
28012649 CTCCTTGATCAGCTCCTAAATCTTCT
1 CTCCTT-ATCAGCTCCTAAATATTCT
*
28012675 CTCCTTATTAGCTCCTAAATATTCT
1 CTCCTTATCAGCTCCTAAATATTCT
28012700 C-CCTTATC
1 CTCCTTATC
28012708 CCCTCCTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 6 0.20
25 18 0.60
26 6 0.20
ACGTcount: A:0.20, C:0.34, G:0.05, T:0.41
Consensus pattern (25 bp):
CTCCTTATCAGCTCCTAAATATTCT
Found at i:28012713 original size:24 final size:25
Alignment explanation
Indices: 28012649--28012714 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
28012639 CCAACTCTTG
* *
28012649 CTCCTTGATCAGCTCCTAAATCTTCT
1 CTCCTT-ATCACCTCCTAAATATTCT
* *
28012675 CTCCTTATTAGCTCCTAAATATTCT
1 CTCCTTATCACCTCCTAAATATTCT
*
28012700 C-CCTTATCCCCTCCT
1 CTCCTTATCACCTCCT
28012715 TACTCAATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 11 0.31
25 18 0.51
26 6 0.17
ACGTcount: A:0.18, C:0.38, G:0.05, T:0.39
Consensus pattern (25 bp):
CTCCTTATCACCTCCTAAATATTCT
Found at i:28022274 original size:153 final size:157
Alignment explanation
Indices: 28022030--28022417 Score: 430
Period size: 158 Copynumber: 2.5 Consensus size: 157
28022020 TTAATTTATG
* * * **
28022030 TTTCAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGTCATATGCCGAGGTATTTT
1 TTTC-AAAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTCAGGACA-A-GATGAGGTATTTT
* * ** * **
28022095 CAAATTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGTTCACATG-TC
63 CAATTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAAAC-TCGACTCACATGCT-
*
28022159 GAGGTATTTTCAAAATCT-TCTT-TT-AAG-T
126 GAGGTATTTCCAAAATCTGTCTTATTCAAGTT
* * * *
28022187 TTT-AGAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTCAGGACAAGATGAGGTATTTTCAA
* * *
28022251 TTTGTGTTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAAACTCGACTCGCATGCTGAGGT
66 TTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAAACTCGACTCACATGCTGAGGT
** * *
28022316 ATTTCCAATTTCTGTTTTAATTCACGTT
131 ATTTCCAAAATCTGTCTT-ATTCAAGTT
*
28022344 TTTCAAAAATCAACTCATATTGCA-AGAAGTGAGTTGAGCCTCAGGACAAGATGAGGTATTTTCA
1 TTTCAAAAATCAACTCATATTG-AGAGAGGTGAGTTGAGCCTCAGGACAAGATGAGGTATTTTCA
*
28022408 ATTTCTGTTT
65 ATTTATGTTT
28022418 TCAATTTATG
Statistics
Matches: 194, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
152 23 0.12
153 58 0.30
155 41 0.21
156 2 0.01
157 7 0.04
158 62 0.32
159 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (157 bp):
TTTCAAAAATCAACTCATATTGAGAGAGGTGAGTTGAGCCTCAGGACAAGATGAGGTATTTTCAA
TTTATGTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAAACTCGACTCACATGCTGAGGT
ATTTCCAAAATCTGTCTTATTCAAGTT
Found at i:28022420 original size:13 final size:13
Alignment explanation
Indices: 28022402--28022431 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28022392 AGATGAGGTA
*
28022402 TTTTCAATTTCTG
1 TTTTCAATTTATG
28022415 TTTTCAATTTATG
1 TTTTCAATTTATG
28022428 TTTT
1 TTTT
28022432 TCCAAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.67
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:28022451 original size:86 final size:85
Alignment explanation
Indices: 28022257--28022466 Score: 260
Period size: 86 Copynumber: 2.4 Consensus size: 85
28022247 TCAATTTGTG
* * * ** * * *
28022257 TTTCAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAAACTCGACTCG-CATGCTGAGGTATTTC
1 TTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTC-A--GGACAAGATGAGGTATTTC
28022321 CAATTTCTGTTTTAATTCACGTT
63 CAATTTCTGTTTTAATTCACGTT
*
28022344 TTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCAGGACAAGATGAGGTATTTTCAA
1 TTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCAGGACAAGATGAGGTATTTCCAA
* *
28022409 TTTCTGTTTTCAATTTATGTT
66 TTTCTGTTTT-AATTCACGTT
* *
28022430 TTTCCAAAATCAACTCATATTGCAAGAGGTGAGTTGA
1 TTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGA
28022467 ACCTTTTAAT
Statistics
Matches: 108, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
84 1 0.01
85 26 0.24
86 44 0.41
87 37 0.34
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (85 bp):
TTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCAGGACAAGATGAGGTATTTCCAA
TTTCTGTTTTAATTCACGTT
Found at i:28022605 original size:142 final size:140
Alignment explanation
Indices: 28022342--28022608 Score: 335
Period size: 142 Copynumber: 1.9 Consensus size: 140
28022332 TTAATTCACG
* *
28022342 TTTTTCAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCAGGACAAGATGAGGTATTTTC
1 TTTTTCAAAAATCAACTCATATCGCAAGAAGTGAGTTGAGCCTCAGGACAAGATGAGCTATTTTC
* **
28022407 AATTTCTGTTTTCAATTTATGTTTTTCCAAAATCAACTCATATTGCAAGAGGTGAGTTGAACCTT
66 AATTTCTGTTTTCAATGTATGTTTTTCCAAAATCAACTCATATTGCAAGAAATGAGTTGAACCTT
28022472 TTAATTTCTA
131 TTAATTTCTA
* * ** *
28022482 TTTTTCAAAAATCAACTCATATCGCGAA-AGGTGAGTTGAGCCT-TGGCTCACGTGCTGAGCTAT
1 TTTTTCAAAAATCAACTCATATCGC-AAGAAGTGAGTTGAGCCTCAGG---ACAAGATGAGCTAT
* * *
28022545 TTTCAATTTCTGTTTTTAATGTCTG-TTTT-CAAAGAGTCAATTCATATTGCAAGAAATGAGTTG
62 TTTCAATTTCTGTTTTCAATGTATGTTTTTCCAAA-A-TCAACTCATATTGCAAGAAATGAGTTG
28022608 A
125 A
28022609 GCTCAAGATC
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
139 2 0.02
140 42 0.39
141 7 0.06
142 57 0.53
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.37
Consensus pattern (140 bp):
TTTTTCAAAAATCAACTCATATCGCAAGAAGTGAGTTGAGCCTCAGGACAAGATGAGCTATTTTC
AATTTCTGTTTTCAATGTATGTTTTTCCAAAATCAACTCATATTGCAAGAAATGAGTTGAACCTT
TTAATTTCTA
Found at i:28022874 original size:21 final size:21
Alignment explanation
Indices: 28022849--28022898 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
28022839 CATATCCTTG
28022849 AAGCTACATAGAAGTAGATTA
1 AAGCTACATAGAAGTAGATTA
* *
28022870 AAGCTACATTGAAGTAGATTG
1 AAGCTACATAGAAGTAGATTA
28022891 AAGCTACA
1 AAGCTACA
28022899 AGGCGTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (21 bp):
AAGCTACATAGAAGTAGATTA
Found at i:28024433 original size:3 final size:3
Alignment explanation
Indices: 28024425--28024465 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
28024415 TTTTATATGT
* *
28024425 TTA TTA TTA TTA -TA TTA TTA CTA TTA TTC TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28024466 AGTATATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:28024924 original size:22 final size:22
Alignment explanation
Indices: 28024898--28024968 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
28024888 ATGTATTACA
28024898 TATATATGTATTTTTATTATAT
1 TATATATGTATTTTTATTATAT
*
28024920 TATATATATATTTTTCA-TATAT
1 TATATATGTATTTTT-ATTATAT
* * * *
28024942 CAATACATGTGTTTTT-TAATAT
1 -TATATATGTATTTTTATTATAT
28024964 TATAT
1 TATAT
28024969 TTATATATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
21 3 0.08
22 23 0.61
23 12 0.32
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (22 bp):
TATATATGTATTTTTATTATAT
Found at i:28030575 original size:23 final size:22
Alignment explanation
Indices: 28030503--28030590 Score: 92
Period size: 21 Copynumber: 4.1 Consensus size: 22
28030493 TACCTGATCA
*
28030503 GAATATGACACATAA-GTGCCT
1 GAATACGACACATAAGGTGCCT
*
28030524 GAA-ACGACACATGAGGTGCCT
1 GAATACGACACATAAGGTGCCT
* * *
28030545 G-CTGCGACACACAAGGTGCCT
1 GAATACGACACATAAGGTGCCT
*
28030566 GAAATACGACACATAAAGTGCCT
1 G-AATACGACACATAAGGTGCCT
28030589 GA
1 GA
28030591 TCAGTAAAGC
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
20 9 0.17
21 26 0.49
22 1 0.02
23 17 0.32
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (22 bp):
GAATACGACACATAAGGTGCCT
Found at i:28030587 original size:44 final size:41
Alignment explanation
Indices: 28030509--28030589 Score: 108
Period size: 44 Copynumber: 1.9 Consensus size: 41
28030499 ATCAGAATAT
* * *
28030509 GACACATAAGTGCCTGAAACGACACATGAGGTGCCTGCTGC
1 GACACACAAGTGCCTGAAACGACACATAAAGTGCCTGCTGC
28030550 GACACACAAGGTGCCTGAAATACGACACATAAAGTGCCTG
1 GACACACAA-GTGCCTG-AA-ACGACACATAAAGTGCCTG
28030590 ATCAGTAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 8 0.24
42 7 0.21
43 2 0.06
44 17 0.50
ACGTcount: A:0.33, C:0.26, G:0.25, T:0.16
Consensus pattern (41 bp):
GACACACAAGTGCCTGAAACGACACATAAAGTGCCTGCTGC
Found at i:28030835 original size:24 final size:22
Alignment explanation
Indices: 28030781--28030841 Score: 122
Period size: 22 Copynumber: 2.8 Consensus size: 22
28030771 AAATGTCCAA
28030781 CCAAAACACACCAGTATAATCT
1 CCAAAACACACCAGTATAATCT
28030803 CCAAAACACACCAGTATAATCT
1 CCAAAACACACCAGTATAATCT
28030825 CCAAAACACACCAGTAT
1 CCAAAACACACCAGTAT
28030842 CATATAATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.46, C:0.33, G:0.05, T:0.16
Consensus pattern (22 bp):
CCAAAACACACCAGTATAATCT
Found at i:28030898 original size:29 final size:28
Alignment explanation
Indices: 28030795--28030899 Score: 125
Period size: 28 Copynumber: 4.0 Consensus size: 28
28030785 AACACACCAG
28030795 TATAAT-CTCCAAAACACACCAG-----
1 TATAATCCTCCAAAACACACCAGAATAA
* *
28030817 TATAAT-CTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
28030844 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
28030872 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
28030900 GCACAAAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
22 22 0.31
27 6 0.08
28 26 0.36
29 18 0.25
ACGTcount: A:0.47, C:0.30, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:28034283 original size:6 final size:6
Alignment explanation
Indices: 28034260--28034294 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
28034250 AGGACTTAAG
* *
28034260 TCTGAA TCTGAG TTTGAA TCTGAA TCTGAA TCTGA
1 TCTGAA TCTGAA TCTGAA TCTGAA TCTGAA TCTGA
28034295 CTGTGTATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (6 bp):
TCTGAA
Found at i:28035519 original size:20 final size:21
Alignment explanation
Indices: 28035485--28035538 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
28035475 TGATGATATT
*
28035485 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
28035506 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
28035526 TTTTATTATTTTA
1 TTATATTATTTTA
28035539 TTATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:28035544 original size:11 final size:11
Alignment explanation
Indices: 28035528--28035555 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
28035518 ATGAGATATT
28035528 TTATTATTTTA
1 TTATTATTTTA
28035539 TTATTATTTTA
1 TTATTATTTTA
28035550 TTATTA
1 TTATTA
28035556 ATTATTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:28037733 original size:46 final size:46
Alignment explanation
Indices: 28037681--28038046 Score: 597
Period size: 46 Copynumber: 8.0 Consensus size: 46
28037671 AGTGTGCTCT
28037681 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
28037727 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
28037773 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
28037819 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
28037865 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
28037911 CTGATATGAAATGTGTAAGATCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ***
28037957 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * ** ** * * *
28038003 ATGACAAAAAATAAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
28038047 TCATGTCAAA
Statistics
Matches: 302, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 302 1.00
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:28041967 original size:18 final size:19
Alignment explanation
Indices: 28041944--28041981 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
28041934 TAAATAAATG
28041944 AATAAAGAAA-TAAAATAA
1 AATAAAGAAAGTAAAATAA
28041962 AATAAAGAAAGTAAAATAA
1 AATAAAGAAAGTAAAATAA
28041981 A
1 A
28041982 TGAAGAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (19 bp):
AATAAAGAAAGTAAAATAA
Found at i:28041982 original size:18 final size:17
Alignment explanation
Indices: 28041935--28041992 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
28041925 AACCAAAAAT
*
28041935 AAAT-AAATGAATAAAG
1 AAATAAAATAAATAAAG
28041951 AAATAAAATAAAATAAAG
1 AAATAAAAT-AAATAAAG
*
28041969 AAAGTAAAATAAATGAAG
1 AAA-TAAAATAAATAAAG
28041987 AGAATA
1 A-AATA
28041993 GGGGTAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 4 0.11
17 4 0.11
18 20 0.56
19 8 0.22
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (17 bp):
AAATAAAATAAATAAAG
Found at i:28042754 original size:10 final size:10
Alignment explanation
Indices: 28042732--28042763 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
28042722 TAAAGTGGGA
28042732 AAAATCAAGCC
1 AAAATC-AGCC
28042743 AAAATCAGCC
1 AAAATCAGCC
28042753 AAAATCAGCC
1 AAAATCAGCC
28042763 A
1 A
28042764 TTTTCTTCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.71
11 6 0.29
ACGTcount: A:0.53, C:0.28, G:0.09, T:0.09
Consensus pattern (10 bp):
AAAATCAGCC
Found at i:28052917 original size:28 final size:27
Alignment explanation
Indices: 28052854--28052923 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
28052844 ATAGTGAGTC
28052854 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
28052881 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
28052909 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28052924 GTACAAGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:28057418 original size:12 final size:12
Alignment explanation
Indices: 28057401--28057431 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28057391 CCTACACGGG
28057401 CGTGTGTTTGGC
1 CGTGTGTTTGGC
*
28057413 CGTGTGGTTGGC
1 CGTGTGTTTGGC
28057425 CGTGTGT
1 CGTGTGT
28057432 AAGACACGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.45, T:0.39
Consensus pattern (12 bp):
CGTGTGTTTGGC
Found at i:28057465 original size:40 final size:39
Alignment explanation
Indices: 28057421--28057509 Score: 88
Period size: 40 Copynumber: 2.3 Consensus size: 39
28057411 GCCGTGTGGT
* *
28057421 TGGCCGTGTGTAAGACACGACCGTATGGTTGATGAGGGTA
1 TGGCCGTGTGCAAGACACGACCGTATGG-TGATGAGAGTA
* ** * * * *
28057461 TGGCCATGCACAAGACACGATCGTGTGGTGGTGTGAGTA
1 TGGCCGTGTGCAAGACACGACCGTATGGTGATGAGAGTA
28057500 TGGCCGTGTG
1 TGGCCGTGTG
28057510 GGCTACACGG
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
39 15 0.41
40 22 0.59
ACGTcount: A:0.20, C:0.17, G:0.38, T:0.25
Consensus pattern (39 bp):
TGGCCGTGTGCAAGACACGACCGTATGGTGATGAGAGTA
Found at i:28057692 original size:103 final size:103
Alignment explanation
Indices: 28057506--28057723 Score: 267
Period size: 103 Copynumber: 2.1 Consensus size: 103
28057496 AGTATGGCCG
* * * * *
28057506 TGTGGGCTACACGGGCTAGTCCAAGTTGGACGTGTGGGCCCATACGAGCGTGTAGGTTTTTATCT
1 TGTGGGCCACACGGGCTAGGCCAAGTTGGACGTGTAGGCCCACACGAGCGTGTAGGTTTTTAGCT
*
28057571 AAACCGTGTGAAGAACACGGGTAAGGCCAAACTGGGCA
66 AAACCGTGTGAACAACACGGGTAAGGCCAAACTGGGCA
* * *
28057609 TGTGGGCCATACGGGCTAGGCCAAGTTGGGCTTGTAGGCCCACACGAGCGTGTAGG-TTTTAGGC
1 TGTGGGCCACACGGGCTAGGCCAAGTTGGACGTGTAGGCCCACACGAGCGTGTAGGTTTTTA-GC
** * * * *
28057673 TAGGCCGTTTGACCCACACGGGTAAGGCCAATCTGGGCA
65 TAAACCGTGTGAACAACACGGGTAAGGCCAAACTGGGCA
* *
28057712 TGTAGGCTACAC
1 TGTGGGCCACAC
28057724 AAGCACGTGG
Statistics
Matches: 96, Mismatches: 18, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
102 5 0.05
103 91 0.95
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (103 bp):
TGTGGGCCACACGGGCTAGGCCAAGTTGGACGTGTAGGCCCACACGAGCGTGTAGGTTTTTAGCT
AAACCGTGTGAACAACACGGGTAAGGCCAAACTGGGCA
Found at i:28057956 original size:2 final size:2
Alignment explanation
Indices: 28057949--28057974 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28057939 ATAATTTTCA
28057949 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
28057975 CTAATTCGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28062791 original size:11 final size:11
Alignment explanation
Indices: 28062775--28062799 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28062765 TTGGTGTATA
28062775 TATATATTGAT
1 TATATATTGAT
28062786 TATATATTGAT
1 TATATATTGAT
28062797 TAT
1 TAT
28062800 TTGAATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
TATATATTGAT
Found at i:28064556 original size:22 final size:22
Alignment explanation
Indices: 28064526--28064582 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
28064516 AAACAGGTTC
28064526 ACACGCCCGTGTGGACATAAGG
1 ACACGCCCGTGTGGACATAAGG
*
28064548 ACACACCCGTGTGGACATAAGG
1 ACACGCCCGTGTGGACATAAGG
28064570 ACACGCCCGTGTG
1 ACACGCCCGTGTG
28064583 CCTTTGGCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.14
Consensus pattern (22 bp):
ACACGCCCGTGTGGACATAAGG
Found at i:28066612 original size:49 final size:49
Alignment explanation
Indices: 28066551--28066816 Score: 284
Period size: 49 Copynumber: 5.6 Consensus size: 49
28066541 ACATCTAAGT
*
28066551 CGATGTCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGC
* *
28066600 CGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATATC-AGTGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAG-GC
* * * *
28066649 CAATGCCATGTCCCAGACAGGTCTTACACTGA----CACATGTC-AAGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGC
* * * * *
28066693 CGATGCCATGTCCCAGACAAGCCTTATACTGGCTTTCATATCTCGAGGC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGC
* * * *
28066742 CGATG-CATGTCCCAGACATGTCTTACACT-AGCTTCCATA-AT-GTGGA
1 CGATGCCATGTCCCAGACAGGTCTTACACTGA-CTTTCATATATCGAGGC
*
28066788 CGATG-CATGTCCCAGACATGTCTTACACT
1 CGATGCCATGTCCCAGACAGGTCTTACACT
28066817 AGCACACATA
Statistics
Matches: 186, Mismatches: 24, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
44 29 0.16
45 7 0.04
46 32 0.17
47 1 0.01
48 36 0.19
49 81 0.44
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGC
Found at i:28066725 original size:93 final size:94
Alignment explanation
Indices: 28066557--28066770 Score: 272
Period size: 93 Copynumber: 2.3 Consensus size: 94
28066547 AAGTCGATGT
* * * *
28066557 CATGTCCCAGACAGGTCTTACACTGACTTTCATATATCGAGGCCGATGCCATGTCCCAGACAGGT
1 CATGTCCCAGACAGGTCTTACACTGA---TCACATATCGAAGCCGATGCCATGTCCCAGACAAGC
28066622 CTTACACTGGCTCTCATATATC-AGTGCCAATG
63 CTTACACTGGCTCTCATATATCGAG-GCCAATG
*
28066654 CCATGTCCCAGACAGGTCTTACACTGA-CACATGTC-AAGCCGATGCCATGTCCCAGACAAGCCT
1 -CATGTCCCAGACAGGTCTTACACTGATCACATATCGAAGCCGATGCCATGTCCCAGACAAGCCT
* * * *
28066717 TATACTGGCTTTCATATCTCGAGGCCGATG
65 TACACTGGCTCTCATATATCGAGGCCAATG
*
28066747 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACAGGTCTTACACT
28066771 AGCTTCCATA
Statistics
Matches: 105, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
92 23 0.22
93 48 0.46
94 8 0.08
98 26 0.25
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (94 bp):
CATGTCCCAGACAGGTCTTACACTGATCACATATCGAAGCCGATGCCATGTCCCAGACAAGCCTT
ACACTGGCTCTCATATATCGAGGCCAATG
Found at i:28067505 original size:20 final size:20
Alignment explanation
Indices: 28067480--28067518 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28067470 ACAATTTCGA
28067480 TTATTTCAC-ACATTTACAAC
1 TTATTTCACAAC-TTTACAAC
*
28067500 TTATTTTACAACTTTACAA
1 TTATTTCACAACTTTACAA
28067519 AATAGCCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATTTCACAACTTTACAAC
Found at i:28072834 original size:15 final size:15
Alignment explanation
Indices: 28072772--28072843 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 15
28072762 ATGTAAAATG
28072772 TAATATATATTATAA
1 TAATATATATTATAA
* *
28072787 TAAAATATATT-TAC
1 TAATATATATTATAA
*
28072801 T--TA-ACATT-TAA
1 TAATATATATTATAA
28072812 GT-ATATATATTATAA
1 -TAATATATATTATAA
28072827 TAATATAT-TATATAA
1 TAATATATAT-TATAA
28072842 TA
1 TA
28072844 TAAAACAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
11 6 0.13
12 2 0.04
13 2 0.04
14 9 0.20
15 26 0.58
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (15 bp):
TAATATATATTATAA
Found at i:28073623 original size:15 final size:15
Alignment explanation
Indices: 28073603--28073654 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
28073593 TGATAAATTT
28073603 ATTGAATTTATATTG
1 ATTGAATTTATATTG
*
28073618 ATTGAATTGGTATATATAT
1 ATTGAATT--TATAT-T-G
*
28073637 ATTGAATATATATTG
1 ATTGAATTTATATTG
28073652 ATT
1 ATT
28073655 ATTTGAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 11 0.37
16 1 0.03
17 10 0.33
18 1 0.03
19 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:28073830 original size:41 final size:38
Alignment explanation
Indices: 28073783--28073882 Score: 94
Period size: 37 Copynumber: 2.6 Consensus size: 38
28073773 TTCGACTTCG
* *
28073783 AGTCGATGAGACACTTGGTGTCGATTTACTACTTCAGATTA
1 AGTCGATGAGACACTTGGTGTCCAATT--TACTTCAG-TTA
* * * * *
28073824 ATTCGATAAGGCACTTGGAG-CCAATTTACTTCAGTTT
1 AGTCGATGAGACACTTGGTGTCCAATTTACTTCAGTTA
*
28073861 AGTCGATGAGACACTGGGTGTC
1 AGTCGATGAGACACTTGGTGTC
28073883 AACCTATTAC
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
37 17 0.37
38 9 0.20
40 4 0.09
41 16 0.35
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (38 bp):
AGTCGATGAGACACTTGGTGTCCAATTTACTTCAGTTA
Found at i:28075502 original size:16 final size:16
Alignment explanation
Indices: 28075483--28075513 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28075473 CTTCTTCACT
28075483 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
28075499 TACTTACTTACTTAA
1 TACTCACTTACTTAA
28075514 TCAAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:28075519 original size:20 final size:20
Alignment explanation
Indices: 28075480--28075519 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28075470 AAACTTCTTC
* *
28075480 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
28075500 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
28075520 TTATTAATGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:28075835 original size:53 final size:54
Alignment explanation
Indices: 28075750--28075957 Score: 251
Period size: 55 Copynumber: 3.8 Consensus size: 54
28075740 GGTATTCTTT
* *
28075750 TGAAACTTACCATTGCCATGTC-TGGACATGGTCTTACATGGTATCATTGCCTTA
1 TGAAACTTACCAATGCCATGCCTTGG-CATGGTCTTACATGGTATCATTGCCTTA
* * * *
28075804 TG-AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTA
1 TGAAACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCATTGCCTTA
* * * * *
28075857 TAGAAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA
1 T-GAAACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCATTGCCTTA
*
28075912 -GAAACCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATC
1 TGAAA-CTTACCAA-TGCCATGCCTTGGCATGGTCTTACATGGTATC
28075958 CTTAAACCCT
Statistics
Matches: 130, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
53 46 0.35
54 13 0.10
55 71 0.55
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (54 bp):
TGAAACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGTATCATTGCCTTA
Found at i:28075896 original size:55 final size:54
Alignment explanation
Indices: 28075706--28075960 Score: 231
Period size: 55 Copynumber: 4.8 Consensus size: 54
28075696 ACACGGGTAC
* ** * * *
28075706 CTTACCATTGCCATGAATTGTCATGGTCTTACGTGGTA--TT--CTT-TTGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAAA
* * * *
28075755 CTTACCATTGCCATGTCTGGACATGGTCTTACATGGTATCATTGCCTTAT-G-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAAA
* * *
28075808 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAGAAA
* * *
28075863 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCC-T-TAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAAA
* *
28075916 CCTTACCAATTTCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTA-CCTT
28075961 AAACCCTAAT
Statistics
Matches: 171, Mismatches: 23, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
49 33 0.19
52 3 0.02
53 49 0.29
54 13 0.08
55 71 0.42
56 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAAA
Found at i:28075897 original size:108 final size:110
Alignment explanation
Indices: 28075751--28075953 Score: 313
Period size: 108 Copynumber: 1.9 Consensus size: 110
28075741 GTATTCTTTT
* *
28075751 GAAACTTACCATTGCCATGTCTGGACATGGTCTTACATGGTATCATTGCCTTATG-AA-CTCACC
1 GAAACTTACCAATGCCATGTCTGGACATGGTCTTACATGATATCATTGCCTTA-GAAACCTCACC
28075814 AA-TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
65 AATTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
* * * *
28075859 GAAACTTATCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTTACCA
1 GAAACTTACCAATGCCATGTCTGGACATGGTCTTACATGATATCATTGCCTTAGAAACCTCACCA
*
28075924 ATTTCCATGCCTTGGCATGGTCTTACATGG
66 ATTGCCATGCCTTGGCATGGTCTTACATGG
28075954 TATCCTTAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 50 0.59
109 7 0.08
110 27 0.32
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (110 bp):
GAAACTTACCAATGCCATGTCTGGACATGGTCTTACATGATATCATTGCCTTAGAAACCTCACCA
ATTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATA
Found at i:28077227 original size:27 final size:28
Alignment explanation
Indices: 28077197--28077296 Score: 100
Period size: 27 Copynumber: 3.7 Consensus size: 28
28077187 TTTAGTTTAC
28077197 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* ** *
28077224 TAAAAATACTAAAATACCC-TCGATTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
28077251 TAAAATTACTGAAATA-CCTTCGACTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
28077278 TAAAATTACC-AAAGTACCC
1 TAAAATTACCGAAA-TACCC
28077297 CCGATTTACA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
26 7 0.11
27 52 0.85
28 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (28 bp):
TAAAATTACCGAAATACCCTTAGATTTG
Found at i:28077256 original size:54 final size:54
Alignment explanation
Indices: 28077197--28077303 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
28077187 TTTAGTTTAC
* * *
28077197 TAAAATTACCGAAATACCCTTAG-TTTGTAAAAATACTAAAATACCCTCGATTTG
1 TAAAATTACCGAAATA-CCTTAGACTTGTAAAAATACCAAAATACCCCCGATTTG
* * * *
28077251 TAAAATTACTGAAATACCTTCGACTTGTAAAATTACCAAAGTACCCCCGATTT
1 TAAAATTACCGAAATACCTTAGACTTGTAAAAATACCAAAATACCCCCGATTT
28077304 ACAGAATTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 5 0.11
54 40 0.89
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (54 bp):
TAAAATTACCGAAATACCTTAGACTTGTAAAAATACCAAAATACCCCCGATTTG
Found at i:28077311 original size:27 final size:27
Alignment explanation
Indices: 28077281--28077341 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
28077271 CGACTTGTAA
28077281 AATTACCAAAGTACCCCCGATTTACAG
1 AATTACCAAAGTACCCCCGATTTACAG
* **** *
28077308 AATTATCGTTTTACCCCCGATTTACAT
1 AATTACCAAAGTACCCCCGATTTACAG
28077335 AATTACC
1 AATTACC
28077342 GTTTTACCCC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (27 bp):
AATTACCAAAGTACCCCCGATTTACAG
Found at i:28077344 original size:27 final size:27
Alignment explanation
Indices: 28077292--28077502 Score: 271
Period size: 27 Copynumber: 7.8 Consensus size: 27
28077282 ATTACCAAAG
* *
28077292 TACCCCCGATTTACAGAATTATCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
28077319 TACCCCCGATTTACATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
28077346 TACCC-CTAATTTACATAATTATCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* *
28077373 TACCCTCGACTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
28077400 TACCCTCGATTTACAGAATTACAGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
28077427 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
28077454 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
28077481 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
28077503 TAAAATACCC
Statistics
Matches: 164, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.01
27 162 0.99
28 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:28077515 original size:54 final size:54
Alignment explanation
Indices: 28077224--28077513 Score: 199
Period size: 54 Copynumber: 5.4 Consensus size: 54
28077214 CCTTAGTTTG
* * * ** * *** * * *
28077224 TAAAAATACTAAAATACCCTCGATTTGTAAAATTACTGAAATACCTTCGACTTG
1 TAAAATTACCAAATTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTA
* * *
28077278 TAAAATTACCAAAGTACCCCCGATTTACAGAATTA-TCGTTTTACCCCCGATTTA
1 TAAAATTACCAAATTACCCTCGATTTACAGAATTACT-GTTTTACCCTCGATTTA
* * *** * * *
28077332 CATAATTACCGTTTTACCC-CTAATTTACATAATTA-TCGTTTTACCCTCGACTTA
1 TAAAATTACCAAATTACCCTC-GATTTACAGAATTACT-GTTTTACCCTCGATTTA
* *** *
28077386 TAGAATTACCGTTTTACCCTCGATTTACAGAATTACAGTTTTACCCTCGATTTA
1 TAAAATTACCAAATTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTA
* **** *
28077440 TAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGTTTTACCCTCGATTTA
1 TAAAATTACCAAATTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTA
* * *
28077494 CAAAATTACTAAAATACCCT
1 TAAAATTACCAAATTACCCT
28077514 TGGTTTGTGA
Statistics
Matches: 193, Mismatches: 39, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
53 2 0.01
54 190 0.98
55 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (54 bp):
TAAAATTACCAAATTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTA
Found at i:28077529 original size:81 final size:81
Alignment explanation
Indices: 28077238--28077513 Score: 216
Period size: 81 Copynumber: 3.4 Consensus size: 81
28077228 AATACTAAAA
** * * * * * ***** * *
28077238 TACCCTCGATTTGTAAAATTACTGAAATACCTTCGACTTGTAAAATTACCAAAGTACCCCCGATT
1 TACCCTCGATTTACAAAATTACAGAAATACCCTCGATTTATAGAATTACTGTTTTACCCTCGACT
*
28077303 TACAGAATTATCGTTT
66 TACAGAATTACCGTTT
* * * *** * * *
28077319 TACCCCCGATTTACATAATTACCGTTTTACCC-CTAATTTACATAATTA-TCGTTTTACCCTCGA
1 TACCCTCGATTTACAAAATTACAGAAATACCCTC-GATTTATAGAATTACT-GTTTTACCCTCGA
*
28077382 CTTATAGAATTACCGTTT
64 CTTACAGAATTACCGTTT
* *** * *
28077400 TACCCTCGATTTACAGAATTACAGTTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGATT
1 TACCCTCGATTTACAAAATTACAGAAATACCCTCGATTTATAGAATTACTGTTTTACCCTCGACT
*
28077465 TACAGAATTACTGTTT
66 TACAGAATTACCGTTT
28077481 TACCCTCGATTTACAAAATTACTA-AAATACCCT
1 TACCCTCGATTTACAAAATTAC-AGAAATACCCT
28077514 TGGTTTGTGA
Statistics
Matches: 153, Mismatches: 37, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
80 1 0.01
81 149 0.97
82 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.37
Consensus pattern (81 bp):
TACCCTCGATTTACAAAATTACAGAAATACCCTCGATTTATAGAATTACTGTTTTACCCTCGACT
TACAGAATTACCGTTT
Found at i:28078771 original size:25 final size:25
Alignment explanation
Indices: 28078742--28078789 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28078732 TTATAATATG
* * *
28078742 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
28078767 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
28078790 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:28078890 original size:20 final size:20
Alignment explanation
Indices: 28078832--28078891 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
28078822 ATAAATATGG
*
28078832 TATGTATGATATGCACATAA
1 TATGTATGATATGCACATGA
*
28078852 AATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
28078872 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
28078892 GGTAATCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:28078996 original size:23 final size:24
Alignment explanation
Indices: 28078942--28079040 Score: 157
Period size: 23 Copynumber: 4.2 Consensus size: 24
28078932 GAGGAAGTGA
*
28078942 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
28078966 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
28078989 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
28079013 GAAAGGG-TTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
28079036 AAAAG
1 AAAAG
28079041 AAGCTAGGCC
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
23 41 0.59
24 29 0.41
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:28079011 original size:47 final size:47
Alignment explanation
Indices: 28078942--28079040 Score: 155
Period size: 47 Copynumber: 2.1 Consensus size: 47
28078932 GAGGAAGTGA
28078942 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGG-TTATGCCCCAGTTATT
** *
28078989 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGTTATGCCCCAGTTATT
28079036 AAAAG
1 AAAAG
28079041 AAGCTAGGCC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
46 13 0.27
47 35 0.73
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGTTATGCCCCAGTTATT
Found at i:28079286 original size:31 final size:31
Alignment explanation
Indices: 28079251--28079345 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
28079241 CGTTTACAGT
28079251 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
28079282 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
28079313 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
28079344 AA
1 AA
28079346 TATGAAAAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:28087240 original size:15 final size:16
Alignment explanation
Indices: 28087199--28087233 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28087189 GTATATTTAC
*
28087199 TTATTATATAAGTATA
1 TTATTAAATAAGTATA
28087215 TTATTAAATAA-TATA
1 TTATTAAATAAGTATA
28087230 TTAT
1 TTAT
28087234 ATAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTATTAAATAAGTATA
Found at i:28088298 original size:19 final size:20
Alignment explanation
Indices: 28088276--28088323 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
28088266 AATTATATTG
*
28088276 AATTGAAAAAAATAT-AGTT
1 AATTGAAAAAAATATGAATT
*
28088295 AATT-AATTAAAATATGAATT
1 AATTGAA-AAAAATATGAATT
28088315 AATTGAAAA
1 AATTGAAAA
28088324 TTGGAAAGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
18 2 0.09
19 11 0.48
20 8 0.35
21 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
AATTGAAAAAAATATGAATT
Found at i:28088566 original size:6 final size:6
Alignment explanation
Indices: 28088555--28088615 Score: 104
Period size: 6 Copynumber: 10.2 Consensus size: 6
28088545 CTGTGTACCG
*
28088555 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTAT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT
*
28088603 TACTGT TATTGT T
1 TACTGT TACTGT T
28088616 CCAGCTTCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (6 bp):
TACTGT
Done.