Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 35 of 106
Found at i:13464504 original size:63 final size:62
Alignment explanation
Indices: 13464400--13464561 Score: 225
Period size: 63 Copynumber: 2.6 Consensus size: 62
13464390 CACATCATAG
* * * *
13464400 TCGGCATGTGTACTGCCCACTCCACACATGCACGGTTGTAATTGTCACAACATTGTCATTCAA
1 TCGGCATGTGCACTG-CCACTCCGCACATGAACGGTCGTAATTGTCACAACATTGTCATTCAA
* *
13464463 TCGGCATGTGCATTGTCCACTCCGCACATGAATGGTCGTAATTGTCACAACATTGTCATTCAA
1 TCGGCATGTGCACTG-CCACTCCGCACATGAACGGTCGTAATTGTCACAACATTGTCATTCAA
* *
13464526 CCGGCATGTGCACTGCTCACTCCGCACATGCACGGT
1 TCGGCATGTGCACTGC-CACTCCGCACATGAACGGT
13464562 TATATCAATT
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
62 1 0.01
63 86 0.99
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (62 bp):
TCGGCATGTGCACTGCCACTCCGCACATGAACGGTCGTAATTGTCACAACATTGTCATTCAA
Found at i:13471948 original size:21 final size:21
Alignment explanation
Indices: 13471909--13471948 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13471899 GGAGAGCAAA
*
13471909 AGTATCAAGACATAGAAGAAG
1 AGTATCAAGACATACAAGAAG
* *
13471930 AGTATCGAGACATTCAAGA
1 AGTATCAAGACATACAAGA
13471949 CAGAAGCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.23, T:0.17
Consensus pattern (21 bp):
AGTATCAAGACATACAAGAAG
Found at i:13476537 original size:29 final size:31
Alignment explanation
Indices: 13476495--13476579 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 31
13476485 TAACAAAATG
* *
13476495 TTTTCGAATATAGCGTGTAACAATA-ATATTT
1 TTTTC-AACATAGCGTGTAACAACAGATATTT
*
13476526 TTTT-AACATAGCGTGTAACAACAGTATTTTT
1 TTTTCAACATAGCGTGTAACAACAG-ATATTT
*
13476557 TTTTCAACATAGCATGTAACAAC
1 TTTTCAACATAGCGTGTAACAAC
13476580 TTTTTTTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 17 0.36
31 13 0.28
32 17 0.36
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (31 bp):
TTTTCAACATAGCGTGTAACAACAGATATTT
Found at i:13476876 original size:16 final size:17
Alignment explanation
Indices: 13476855--13476892 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
13476845 GTTAAAATTA
*
13476855 TAAAAA-ATATTATTTT
1 TAAAAATATATTATCTT
*
13476871 TAAAAATATCTTATCTT
1 TAAAAATATATTATCTT
13476888 TAAAA
1 TAAAA
13476893 GTTATTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAAATATATTATCTT
Found at i:13479687 original size:72 final size:71
Alignment explanation
Indices: 13479539--13479675 Score: 211
Period size: 72 Copynumber: 1.9 Consensus size: 71
13479529 TGGTGTGCAG
* * * *
13479539 CAAAATCATTTCAACATTGCCAAAGTTGTTATACGCCATGCATGTAACATCTCTAATGCATATGG
1 CAAAATCATTACAACATTACCAAAGTTGTTACACGCCATGCATGTAACATCTCTAATGCACATGG
13479604 TGCTAA
66 TGCTAA
* *
13479610 CAAAATCATTAGAACATTACCTAGAGTTGTTACACGCCATGCATGTAACATCTCTAATGCACATG
1 CAAAATCATTACAACATTACC-AAAGTTGTTACACGCCATGCATGTAACATCTCTAATGCACATG
13479675 G
65 G
13479676 CGTGTAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
71 18 0.31
72 41 0.69
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (71 bp):
CAAAATCATTACAACATTACCAAAGTTGTTACACGCCATGCATGTAACATCTCTAATGCACATGG
TGCTAA
Found at i:13479730 original size:23 final size:24
Alignment explanation
Indices: 13479697--13479773 Score: 77
Period size: 23 Copynumber: 3.2 Consensus size: 24
13479687 TATATTGAAA
13479697 TAACATGTTTTAATACATGGCGTG
1 TAACATGTTTTAATACATGGCGTG
** *
13479721 TAACAT-TTTTTTTGAACATGGCATG
1 TAACATGTTTTAAT--ACATGGCGTG
* *
13479746 TAACATGTTGTCA-ACATGGCGTG
1 TAACATGTTTTAATACATGGCGTG
13479769 TAACA
1 TAACA
13479774 ATTTTTTTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
23 19 0.44
24 6 0.14
25 15 0.35
26 3 0.07
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (24 bp):
TAACATGTTTTAATACATGGCGTG
Found at i:13479769 original size:48 final size:49
Alignment explanation
Indices: 13479697--13479798 Score: 170
Period size: 48 Copynumber: 2.1 Consensus size: 49
13479687 TATATTGAAA
* *
13479697 TAACATGTTTTAATACATGGCGTGTAACATTTTTTTTGAACATGGCATG
1 TAACATGTTGTAATACATGGCGTGTAACAATTTTTTTGAACATGGCATG
*
13479746 TAACATGTTGTCA-ACATGGCGTGTAACAATTTTTTTGAACATGGCATG
1 TAACATGTTGTAATACATGGCGTGTAACAATTTTTTTGAACATGGCATG
13479794 TAACA
1 TAACA
13479799 AAAATTTTTC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
48 39 0.78
49 11 0.22
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (49 bp):
TAACATGTTGTAATACATGGCGTGTAACAATTTTTTTGAACATGGCATG
Found at i:13479799 original size:25 final size:25
Alignment explanation
Indices: 13479711--13479799 Score: 110
Period size: 25 Copynumber: 3.6 Consensus size: 25
13479701 ATGTTTTAAT
* *
13479711 ACATGGCGTGTAACATTTTTTTTGA
1 ACATGGCATGTAACAATTTTTTTGA
* * *
13479736 ACATGGCATGTAAC-A-TGTTGTCA
1 ACATGGCATGTAACAATTTTTTTGA
*
13479759 ACATGGCGTGTAACAATTTTTTTGA
1 ACATGGCATGTAACAATTTTTTTGA
13479784 ACATGGCATGTAACAA
1 ACATGGCATGTAACAA
13479800 AAATTTTTCA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
23 18 0.35
24 1 0.02
25 33 0.63
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (25 bp):
ACATGGCATGTAACAATTTTTTTGA
Found at i:13479813 original size:26 final size:25
Alignment explanation
Indices: 13479711--13479815 Score: 81
Period size: 25 Copynumber: 4.2 Consensus size: 25
13479701 ATGTTTTAAT
* *** *
13479711 ACATGGCGTGTAACATTTTTTTTGA
1 ACATGGCATGTAACAAAATTTTTCA
*
13479736 ACATGGCATGTAAC---ATGTTGTCA
1 ACATGGCATGTAACAAAAT-TTTTCA
* ** *
13479759 ACATGGCGTGTAACAATTTTTTTGA
1 ACATGGCATGTAACAAAATTTTTCA
13479784 ACATGGCATGTAACAAAAATTTTTCA
1 ACATGGCATGTAAC-AAAATTTTTCA
13479810 ACATGG
1 ACATGG
13479816 TGTGTTGTGT
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
22 1 0.02
23 17 0.27
25 30 0.48
26 15 0.24
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.35
Consensus pattern (25 bp):
ACATGGCATGTAACAAAATTTTTCA
Found at i:13480331 original size:33 final size:33
Alignment explanation
Indices: 13480294--13480364 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
13480284 AAAAGGAAAA
13480294 TGCAGGGATATCTCGTACATGTCTTATTCCAAG
1 TGCAGGGATATCTCGTACATGTCTTATTCCAAG
13480327 TGCAGGGATATCTCGTACATGTCTTATTCCAAG
1 TGCAGGGATATCTCGTACATGTCTTATTCCAAG
13480360 TGCAG
1 TGCAG
13480365 AAAGGTTCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (33 bp):
TGCAGGGATATCTCGTACATGTCTTATTCCAAG
Found at i:13482005 original size:37 final size:37
Alignment explanation
Indices: 13481929--13482008 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
13481919 TGCAATATCT
* *
13481929 TCATCATGTGTGCACTCCCTACTCGCACACTGTATCA
1 TCATCATGTGTACACTCCCTACTCGCACACTGTAACA
* *
13481966 TCATCATGTGTACACTCCCTACTCTCACTCT-TCAACA
1 TCATCATGTGTACACTCCCTACTCGCACACTGT-AACA
13482003 TCATCA
1 TCATCA
13482009 CACAACATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
36 1 0.03
37 37 0.97
ACGTcount: A:0.24, C:0.36, G:0.09, T:0.31
Consensus pattern (37 bp):
TCATCATGTGTACACTCCCTACTCGCACACTGTAACA
Found at i:13485495 original size:76 final size:76
Alignment explanation
Indices: 13485332--13486268 Score: 811
Period size: 76 Copynumber: 12.4 Consensus size: 76
13485322 GCTCCGCTTA
* * * * * *
13485332 TTAGATGTCATTGACATCGTATTGTGACACGCCATGTTGTTGAAGTATTATAGGGTTACA---CA
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGTAGTATTATAGGGTTACACGCCA
* **
13485394 --CTGCGTTTG
66 CGCTCCAATTG
* * * * *
13485403 TTAGATGTCTTTTACATATTGTCGTGATACGCCATGTCGTTGTAGCATTATAGGGTTACACGCCA
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGTAGTATTATAGGGTTACACGCCA
* *
13485468 CACTCGAATTG
66 CGCTCCAATTG
** * * ** *
13485479 TTAGATGTTGTTTACATCTTGTGGTGTCACGCCATGTCATTG-ACGTATTATATTGTTACACACC
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGTA-GTATTATAGGGTTACACGCC
*
13485543 ATGCTCCAATTG
65 ACGCTCCAATTG
* ** * * * * * *
13485555 TTAGATGTCCTTTACATCTTGTCGG-GACACGTTGA-GTCGTTGTAGTATTACAAGGTGAAATGT
1 TTAGATGTCATTTACATCTTGT-GGTGACACG-CCATGTCGTTGTAGTATTATAGGGTTACACGC
*
13485618 CACGCTTCAATTG
64 CACGCTCCAATTG
* * * * ** *
13485631 TTAGGTGTCATTTACATTTTGTCGTGACACTCCATGTCGTTG-ATGTATTATATTGTTACATGCC
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGTA-GTATTATAGGGTTACACGCC
*
13485695 ACGCTCGAATTG
65 ACGCTCCAATTG
* * ** *
13485707 TTAGATGTCGTTTACATCTTATGGTGACACGCCATGTCGTTACAGTATTATAGGATTACACGCCA
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGTAGTATTATAGGGTTACACGCCA
* *
13485772 CACTCGAATTG
66 CGCTCCAATTG
* **
13485783 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCATTGTAGTATTATATTGTTACACGCCA
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGTAGTATTATAGGGTTACACGCCA
*
13485848 TGCTCCAATTG
66 CGCTCCAATTG
** **** * * * *
13485859 TTAGATGTCATTTACATCTTGCCGTGACATATTGA-GTCGTTACT-CTATTATAGGGTGACACAC
1 TTAGATGTCATTTACATCTTGTGGTGACA-CGCCATGTCGTT-GTAGTATTATAGGGTTACACGC
* *
13485922 AACACTCCAATTG
64 CACGCTCCAATTG
* * * ** *
13485935 TTAGATGTCATTTTCATCTTGTGGTGATACGCCATGTCGTTG-ACATATTATATTGTTACGCGCC
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGTA-GTATTATAGGGTTACACGCC
* * *
13485999 ATGTTCAAATTG
65 ACGCTCCAATTG
* * * ** * *
13486011 TTAGATGTCGTTTACATTTTATGGTGACACATCATGTCATTGTAGTATTATAGGGTTACACGTCA
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGTAGTATTATAGGGTTACACGCCA
** *
13486076 TACTCAAATTG
66 CGCTCCAATTG
** ** *
13486087 TTAGATGTCATTTACATCTTGTGGTGACACATCATGTCGTTG-ACGTATTATATTGTTACACACC
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGTA-GTATTATAGGGTTACACGCC
* *
13486151 ATGCTCAAATTG
65 ACGCTCCAATTG
** * * * *
13486163 TTAGATGTTGTTTACATCTTGTGGTGACACGTCATGTCATTGCAGTATTATAGGGTTACACACCA
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGTAGTATTATAGGGTTACACGCCA
13486228 CGCTCCAATTG
66 CGCTCCAATTG
* * *
13486239 TTAGATGCCGTTTACATCTTGTCGTGACAC
1 TTAGATGTCATTTACATCTTGTGGTGACAC
13486269 ACTGATTCAT
Statistics
Matches: 692, Mismatches: 153, Indels: 37
0.78 0.17 0.04
Matches are distributed among these distances:
71 50 0.07
74 2 0.00
75 6 0.01
76 625 0.90
77 9 0.01
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (76 bp):
TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGTAGTATTATAGGGTTACACGCCA
CGCTCCAATTG
Found at i:13485704 original size:228 final size:229
Alignment explanation
Indices: 13485400--13486292 Score: 941
Period size: 228 Copynumber: 3.9 Consensus size: 229
13485390 CACACTGCGT
* * * * *
13485400 TTGTTAGATGTCTTTTACATATTGTCGTGATACGCCATGTCGTTG-TAGCATTATAGGGTTACAC
1 TTGTTAGATGTCATTTACATCTTGTCGTGACACTCCATGTCGTTGAT-GTATTATAGGGTTACAC
* * *
13485464 GCCACACTCGAATTGTTAGATGTTGTTTACATCTTGTGGTGTCACGCCATGTCATTGAC-GTATT
65 ACCACACTCGAATTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTGACAGTATT
* * *
13485528 ATATTGTTACACACCATGCTCCAATTGTTAGATGTCCTTTACATCTTGTCGG-GACACGTTGA-G
130 ATATGGTTACACACCACGCTCCAATTGTTAGATGTCCTTTACATCTTGT-GGTGACACG-TCATG
* * * * * *
13485591 TCGTTGTAGTATTACAAGGTGAAATGTCACGCTTCAA
193 TCATTGTAGTATTATAAGGTTACACGTCATGCTTCAA
* * ** **
13485628 TTGTTAGGTGTCATTTACATTTTGTCGTGACACTCCATGTCGTTGATGTATTATATTGTTACATG
1 TTGTTAGATGTCATTTACATCTTGTCGTGACACTCCATGTCGTTGATGTATTATAGGGTTACACA
* * *
13485693 CCACGCTCGAATTGTTAGATGTCGTTTACATCTTATGGTGACACGCCATGTCGTT-ACAGTATTA
66 CCACACTCGAATTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTGACAGTATTA
* * * * *
13485757 TA-GGATTACACGCCACACTCGAATTGTTAGATGTCATTTACATCTTGTGGTGACACGCCATGTC
131 TATGG-TTACACACCACGCTCCAATTGTTAGATGTCCTTTACATCTTGTGGTGACACGTCATGTC
** * *
13485821 ATTGTAGTATTATATTGTTACACGCCATGCTCCAA
195 ATTGTAGTATTATAAGGTTACACGTCATGCTTCAA
* * ** * *
13485856 TTGTTAGATGTCATTTACATCTTGCCGTGACATATTGA-GTCGTT-ACTCTATTATAGGGTGACA
1 TTGTTAGATGTCATTTACATCTTGTCGTGACA-CTCCATGTCGTTGA-TGTATTATAGGGTTACA
* * * * * *
13485919 CACAACACTCCAATTGTTAGATGTCATTTTCATCTTGTGGTGATACGCCATGTCGTTGACA-TAT
64 CACCACACTCGAATTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTGACAGTAT
* * * * * * * * * *
13485983 TATATTGTTACGCGCCATGTTCAAATTGTTAGATGTCGTTTACATTTTATGGTGACACATCATGT
129 TATATGGTTACACACCACGCTCCAATTGTTAGATGTCCTTTACATCTTGTGGTGACACGTCATGT
* *
13486048 CATTGTAGTATTATAGGGTTACACGTCATAC-TCAAA
194 CATTGTAGTATTATAAGGTTACACGTCATGCTTC-AA
* * **
13486084 TTGTTAGATGTCATTTACATCTTGTGGTGACACAT-CATGTCGTTGACGTATTATATTGTTACAC
1 TTGTTAGATGTCATTTACATCTTGTCGTGACAC-TCCATGTCGTTGATGTATTATAGGGTTACAC
** * * *
13486148 ACCATGCTCAAATTGTTAGATGTTGTTTACATCTTGTGGTGACACGTCATGTCATTG-CAGTATT
65 ACCACACTCGAATTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTGACAGTATT
* * * *
13486212 ATAGGGTTACACACCACGCTCCAATTGTTAGATG-CCGTTTACATCTTGTCGTGACACACTGAT-
130 ATATGGTTACACACCACGCTCCAATTGTTAGATGTCC-TTTACATCTTGTGGTGACAC-GTCATG
*
13486275 TCATTGCAGTATTATAAG
193 TCATTGTAGTATTATAAG
13486293 TTGACATGCC
Statistics
Matches: 548, Mismatches: 101, Indels: 32
0.80 0.15 0.05
Matches are distributed among these distances:
227 12 0.02
228 525 0.96
229 11 0.02
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (229 bp):
TTGTTAGATGTCATTTACATCTTGTCGTGACACTCCATGTCGTTGATGTATTATAGGGTTACACA
CCACACTCGAATTGTTAGATGTCGTTTACATCTTGTGGTGACACGCCATGTCATTGACAGTATTA
TATGGTTACACACCACGCTCCAATTGTTAGATGTCCTTTACATCTTGTGGTGACACGTCATGTCA
TTGTAGTATTATAAGGTTACACGTCATGCTTCAA
Found at i:13485757 original size:29 final size:31
Alignment explanation
Indices: 13485711--13485771 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 31
13485701 GAATTGTTAG
*
13485711 ATGTCGTTTACATCTTAT-GG-TGACACGCC
1 ATGTCGTTTACATATTATAGGATGACACGCC
*
13485740 ATGTCG-TTACAGTATTATAGGATTACACGCC
1 ATGTCGTTTACA-TATTATAGGATGACACGCC
13485771 A
1 A
13485772 CACTCGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 11 0.41
30 2 0.07
31 9 0.33
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (31 bp):
ATGTCGTTTACATATTATAGGATGACACGCC
Found at i:13486269 original size:152 final size:152
Alignment explanation
Indices: 13485332--13486268 Score: 1003
Period size: 152 Copynumber: 6.2 Consensus size: 152
13485322 GCTCCGCTTA
* * * * * * ** *
13485332 TTAGATGTCATTGACATCGTATTGTGACACGCCATGTTGTTGAAGTATTATAGGGTTACAC-AC-
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGACGTATTATATTGTTACACGCCA
* * * * * * *
13485395 TGCGT----TTGTTAGATGTCTTTTACATATTGTCGTGATACGCCATGTCGTTGTAGCATTATAG
66 TGC-TCAAATTGTTAGATGTCGTTTACATCTTGTGGTGACACGTCATGTCGTTGCAGTATTATAG
*
13485456 GGTTACACGCCACACTCGAATTG
130 GGTTACACGCCACACTCCAATTG
** * * *
13485479 TTAGATGTTGTTTACATCTTGTGGTGTCACGCCATGTCATTGACGTATTATATTGTTACACACCA
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGACGTATTATATTGTTACACGCCA
* * * * *
13485544 TGCTCCAATTGTTAGATGTCCTTTACATCTTGTCGG-GACACGTTGA-GTCGTTGTAGTATTACA
66 TGCTCAAATTGTTAGATGTCGTTTACATCTTGT-GGTGACACG-TCATGTCGTTGCAGTATTATA
* * * * * * *
13485607 AGGTGAAATGTCACGCTTCAATTG
129 GGGTTACACGCCACACTCCAATTG
* * * * * *
13485631 TTAGGTGTCATTTACATTTTGTCGTGACACTCCATGTCGTTGATGTATTATATTGTTACATGCCA
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGACGTATTATATTGTTACACGCCA
* * * * *
13485696 CGCTCGAATTGTTAGATGTCGTTTACATCTTATGGTGACACGCCATGTCGTTACAGTATTATAGG
66 TGCTCAAATTGTTAGATGTCGTTTACATCTTGTGGTGACACGTCATGTCGTTGCAGTATTATAGG
* *
13485761 ATTACACGCCACACTCGAATTG
131 GTTACACGCCACACTCCAATTG
*
13485783 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCATTGTA-GTATTATATTGTTACACGCC
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTG-ACGTATTATATTGTTACACGCC
* * ** ** * * **
13485847 ATGCTCCAATTGTTAGATGTCATTTACATCTTGCCGTGACATATTGA-GTCGTTACTCTATTATA
65 ATGCTCAAATTGTTAGATGTCGTTTACATCTTGTGGTGACA-CGTCATGTCGTTGCAGTATTATA
* * *
13485911 GGGTGACACACAACACTCCAATTG
129 GGGTTACACGCCACACTCCAATTG
* * * *
13485935 TTAGATGTCATTTTCATCTTGTGGTGATACGCCATGTCGTTGACATATTATATTGTTACGCGCCA
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGACGTATTATATTGTTACACGCCA
* * * * * *
13486000 TGTTCAAATTGTTAGATGTCGTTTACATTTTATGGTGACACATCATGTCATTGTAGTATTATAGG
66 TGCTCAAATTGTTAGATGTCGTTTACATCTTGTGGTGACACGTCATGTCGTTGCAGTATTATAGG
* * *
13486065 GTTACACGTCATACTCAAATTG
131 GTTACACGCCACACTCCAATTG
** *
13486087 TTAGATGTCATTTACATCTTGTGGTGACACATCATGTCGTTGACGTATTATATTGTTACACACCA
1 TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGACGTATTATATTGTTACACGCCA
* *
13486152 TGCTCAAATTGTTAGATGTTGTTTACATCTTGTGGTGACACGTCATGTCATTGCAGTATTATAGG
66 TGCTCAAATTGTTAGATGTCGTTTACATCTTGTGGTGACACGTCATGTCGTTGCAGTATTATAGG
* *
13486217 GTTACACACCACGCTCCAATTG
131 GTTACACGCCACACTCCAATTG
* * *
13486239 TTAGATGCCGTTTACATCTTGTCGTGACAC
1 TTAGATGTCATTTACATCTTGTGGTGACAC
13486269 ACTGATTCAT
Statistics
Matches: 648, Mismatches: 128, Indels: 23
0.81 0.16 0.03
Matches are distributed among these distances:
147 49 0.08
148 2 0.00
149 3 0.00
151 6 0.01
152 584 0.90
153 4 0.01
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (152 bp):
TTAGATGTCATTTACATCTTGTGGTGACACGCCATGTCGTTGACGTATTATATTGTTACACGCCA
TGCTCAAATTGTTAGATGTCGTTTACATCTTGTGGTGACACGTCATGTCGTTGCAGTATTATAGG
GTTACACGCCACACTCCAATTG
Found at i:13486709 original size:25 final size:25
Alignment explanation
Indices: 13486681--13486728 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
13486671 GTTGATGCAC
13486681 TGATGATTTTGACAAAAGAATTTTT
1 TGATGATTTTGACAAAAGAATTTTT
*
13486706 TGATGATTTTGACAAATGAATTT
1 TGATGATTTTGACAAAAGAATTT
13486729 CCAATGGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (25 bp):
TGATGATTTTGACAAAAGAATTTTT
Found at i:13487772 original size:81 final size:80
Alignment explanation
Indices: 13487637--13487900 Score: 296
Period size: 81 Copynumber: 3.3 Consensus size: 80
13487627 TTTAAGGTAT
* * * * * *
13487637 ATGGTCTCCTTCAGCCTTAACTGACTCAAAGTTCCCATCCCCTCCCATACCTGCATCGACAACAA
1 ATGGTCTCCTTCAGCATCAACTGATTC-AAGTTCACATCCCCTCCCACAACTGCATCGACAACAA
13487702 CATCGACATGAAGTAC
65 CATCGACATGAAGTAC
* * *
13487718 ATGGTCTCCTTTAGCATCAACTGATTCAAGGTTCTCATCCCCTCCCACAACTGCATCGACAACCA
1 ATGGTCTCCTTCAGCATCAACTGATTCAA-GTTCACATCCCCTCCCACAACTGCATCGACAACAA
*
13487783 CATCGACATGAGGTAC
65 CATCGACATGAAGTAC
* * * * ***
13487799 ATGGTCTTCTTCAGCATCAACTGATTGACAGTGCACATCCCCTCCCACAACTTCATCGACAATGT
1 ATGGTCTCCTTCAGCATCAACTGATTCA-AGTTCACATCCCCTCCCACAACTGCATCGACAACAA
13487864 CATCGACATG-AGTTAC
65 CATCGACATGAAG-TAC
** * *
13487880 ATTTTCTCCTTTAGCACCAAC
1 ATGGTCTCCTTCAGCATCAAC
13487901 CACGTTATGG
Statistics
Matches: 156, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
80 3 0.02
81 152 0.97
82 1 0.01
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.26
Consensus pattern (80 bp):
ATGGTCTCCTTCAGCATCAACTGATTCAAGTTCACATCCCCTCCCACAACTGCATCGACAACAAC
ATCGACATGAAGTAC
Found at i:13491281 original size:21 final size:23
Alignment explanation
Indices: 13491233--13491285 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
13491223 AAATTTATGT
13491233 CGTGTCACATATTCAATCCATGG
1 CGTGTCACATATTCAATCCATGG
* *
13491256 CGTGTCATATATTCCATCCATGG
1 CGTGTCACATATTCAATCCATGG
*
13491279 TGTGTCA
1 CGTGTCA
13491286 GGTGTGTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (23 bp):
CGTGTCACATATTCAATCCATGG
Found at i:13491341 original size:23 final size:23
Alignment explanation
Indices: 13491315--13491892 Score: 236
Period size: 23 Copynumber: 25.3 Consensus size: 23
13491305 TTATGTTGTC
13491315 TCACATATTCTCACCAT-ACTGTG
1 TCACATATTCTCACCATGAC-GTG
* * *
13491338 TCACATATTTTCACCTTGGCGTG
1 TCACATATTCTCACCATGACGTG
* * * *
13491361 TCACGTATTCTCACCATGTCATC
1 TCACATATTCTCACCATGACGTG
* ** *
13491384 TCACATATTCTCACCCTGTTGCG
1 TCACATATTCTCACCATGACGTG
* * *
13491407 T--C--ATTCTAACCCT-ATCGCG
1 TCACATATTCTCACCATGA-CGTG
* * *
13491426 ACACATATTCTCACCCTGTCGTG
1 TCACATATTCTCACCATGACGTG
* * *
13491449 TCACATACTCTCACCATGCCATG
1 TCACATATTCTCACCATGACGTG
* ** * * *
13491472 TCACATATTCCCTTCTTGCCGTA
1 TCACATATTCTCACCATGACGTG
* *
13491495 TCACATACTT-TCA-CATGCCATG
1 TCACATA-TTCTCACCATGACGTG
* * * * * *
13491517 TCACATATTCCCTCTATGGCTTA
1 TCACATATTCTCACCATGACGTG
* *
13491540 TCACATATTCTCACCATGCCATG
1 TCACATATTCTCACCATGACGTG
* * *
13491563 TCATATATTCCCACC-TTACCGTG
1 TCACATATTCTCACCATGA-CGTG
* * * * * *
13491586 TCATAAACCTT-ACACC-CGCCATG
1 TCACATA--TTCTCACCATGACGTG
*
13491609 TCACATATTCTCACCTTG-CTGTG
1 TCACATATTCTCACCATGAC-GTG
*
13491632 TCACATATTCTCACCATGTCGTG
1 TCACATATTCTCACCATGACGTG
* * *
13491655 TCATATATTCTCAACATGTCGTG
1 TCACATATTCTCACCATGACGTG
* * *
13491678 TCACA-AATCCCAAACCCT-ATCGTG
1 TCACATATTCTC--ACCATGA-CGTG
*
13491702 TCACATATTCTCACCATGAGGTG
1 TCACATATTCTCACCATGACGTG
* *
13491725 TCACATATT-TCATCCATGTCGTC
1 TCACATATTCTCA-CCATGACGTG
* ** *
13491748 TCACATATTCCCTTCATGGCGTG
1 TCACATATTCTCACCATGACGTG
* * * * *
13491771 TCATAT-TTATCACCTTGTCGTA
1 TCACATATTCTCACCATGACGTG
* *
13491793 TCACATATTCTCACCATGGCGTT
1 TCACATATTCTCACCATGACGTG
* * * *
13491816 TCCCATATTCTCAACATGCCATG
1 TCACATATTCTCACCATGACGTG
* * * * *
13491839 TCACATTTTCCCTCCATGATGTC
1 TCACATATTCTCACCATGACGTG
13491862 TCACATATTCTCACCAT-ATCGTG
1 TCACATATTCTCACCATGA-CGTG
*
13491885 TCAAATAT
1 TCACATAT
13491893 AGTTCTTACA
Statistics
Matches: 408, Mismatches: 121, Indels: 52
0.70 0.21 0.09
Matches are distributed among these distances:
19 13 0.03
21 6 0.01
22 42 0.10
23 319 0.78
24 22 0.05
25 6 0.01
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (23 bp):
TCACATATTCTCACCATGACGTG
Found at i:13491525 original size:45 final size:46
Alignment explanation
Indices: 13491449--13491574 Score: 177
Period size: 45 Copynumber: 2.8 Consensus size: 46
13491439 CCCTGTCGTG
*
13491449 TCACATACTCTCACCATGCCATGTCACATATTCCCTTCT-TGCCGTA
1 TCACATACTTTCACCATGCCATGTCACATATTCCC-TCTATGCCGTA
* *
13491495 TCACATACTTTCA-CATGCCATGTCACATATTCCCTCTATGGCTTA
1 TCACATACTTTCACCATGCCATGTCACATATTCCCTCTATGCCGTA
*
13491540 TCACATA-TTCTCACCATGCCATGTCATATATTCCC
1 TCACATACTT-TCACCATGCCATGTCACATATTCCC
13491575 ACCTTACCGT
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
44 5 0.07
45 36 0.49
46 32 0.44
ACGTcount: A:0.24, C:0.34, G:0.08, T:0.34
Consensus pattern (46 bp):
TCACATACTTTCACCATGCCATGTCACATATTCCCTCTATGCCGTA
Found at i:13491827 original size:276 final size:270
Alignment explanation
Indices: 13491336--13491850 Score: 588
Period size: 276 Copynumber: 1.9 Consensus size: 270
13491326 CACCATACTG
* * * *
13491336 TGTCACATATTTTCACCTTGGCGTGTCACGTATTCTCACCATGTCATCTCACATATTCTCACCCT
1 TGTCACATATTCTCACCTTGGCGTGTCACATATTCTCACCATGTCATCTCACATATTCTCAACAT
* * * * *
13491401 GTTGCGTCATTCTAACCCTATCGCGACACATATTCTCACCCTGTCGTGTCACATACTCTCACCAT
66 GTCGCGTCATCCAAACCCTATCGCGACACATATTCTCACCATGACGTGTCACATACTCTCACCAT
* * * *
13491466 GCCATGTCACATATTCCCTTCTTGCCGTATCACATACTTTCACATGCCATGTCACATATTCCCTC
131 GCCATCTCACATATTCCCTTCATGCCGTAT-ACATACTTTCACATGCCATATCACATATTCCCAC
* * *
13491531 TATGGCTTATCACATATTCTCACCATGCCATGTCATATATTCCCACCTTACCGTGTCATAAACCT
195 CATGGCTTATCACATATTCTCAACATGCCATGTCACATATTCCCACCTTACCGTGTCATAAACCT
13491596 TACACCCGCCA
260 TACACCCGCCA
* * *
13491607 TGTCACATATTCTCACCTT-GCTGTGTCACATATTCTCACCATGTCGTGTCATATATTCTCAACA
1 TGTCACATATTCTCACCTTGGC-GTGTCACATATTCTCACCATGTCATCTCACATATTCTCAACA
* * * * *
13491671 TGTCGTGTCACAAATCCCAAACCCTATCGTGTCACATATTCTCACCATGAGGTGTCACATA-TTT
65 TGTCGCGT--C--AT-CCAAACCCTATCGCGACACATATTCTCACCATGACGTGTCACATACTCT
* * * * * * * *
13491735 CATCCATGTCGTCTCACATATTCCCTTCATGGCGTGT-CATATTTATCACCTTGTCGTATCACAT
125 CA-CCATGCCATCTCACATATTCCCTTCATGCCGTATACATACTT-TCA-CATGCCATATCACAT
* * *
13491799 ATTCTCACCATGGCGTT-TCCCATATTCTCAACATGCCATGTCACATTTTCCC
187 ATTCCCACCATGGC-TTATCACATATTCTCAACATGCCATGTCACATATTCCC
13491851 TCCATGATGT
Statistics
Matches: 199, Mismatches: 35, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
270 2 0.01
271 60 0.30
273 1 0.01
274 6 0.03
275 9 0.05
276 119 0.60
277 2 0.01
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (270 bp):
TGTCACATATTCTCACCTTGGCGTGTCACATATTCTCACCATGTCATCTCACATATTCTCAACAT
GTCGCGTCATCCAAACCCTATCGCGACACATATTCTCACCATGACGTGTCACATACTCTCACCAT
GCCATCTCACATATTCCCTTCATGCCGTATACATACTTTCACATGCCATATCACATATTCCCACC
ATGGCTTATCACATATTCTCAACATGCCATGTCACATATTCCCACCTTACCGTGTCATAAACCTT
ACACCCGCCA
Found at i:13498526 original size:42 final size:42
Alignment explanation
Indices: 13498467--13498592 Score: 198
Period size: 42 Copynumber: 3.0 Consensus size: 42
13498457 AGCTCATATG
*
13498467 CAACGGCTTATGCGCACTCCTACTCGCACATAGCCGGGTCAA
1 CAACGGCTTATGCGCACTCCTACTCGCACATAGCCGAGTCAA
* * *
13498509 CAACGGCTTATGCGCACTCCCACTCGCACATAACCGAGTCAG
1 CAACGGCTTATGCGCACTCCTACTCGCACATAGCCGAGTCAA
* *
13498551 CAACAGCTTATGCGCACTCCTACTTGCACATAGCCGAGTCAA
1 CAACGGCTTATGCGCACTCCTACTCGCACATAGCCGAGTCAA
13498593 TATTATTACA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.19
Consensus pattern (42 bp):
CAACGGCTTATGCGCACTCCTACTCGCACATAGCCGAGTCAA
Found at i:13498622 original size:2 final size:2
Alignment explanation
Indices: 13498615--13498647 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13498605 ACATTATTCG
*
13498615 TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13498648 CAACATAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13499136 original size:164 final size:164
Alignment explanation
Indices: 13498861--13499191 Score: 646
Period size: 164 Copynumber: 2.0 Consensus size: 164
13498851 TCTAACTTTG
13498861 ATTATTACTTCAAACGGATATGTAAGGCCTTGTTGGAACCTATCACCCACAATATAACTATCAAA
1 ATTATTACTTCAAACGGATATGTAAGGCCTTGTTGGAACCTATCACCCACAATATAACTATCAAA
13498926 AATATAACAGCCCATAAATCAAATTTCTAGTCATCTCTAACATCTTAAAATCAAATTCTAACCCA
66 AATATAACAGCCCATAAATCAAATTTCTAGTCATCTCTAACATCTTAAAATCAAATTCTAACCCA
13498991 TTTCTCACCTTGGTGGTTTTTTTTTTGTAGTTGA
131 TTTCTCACCTTGGTGGTTTTTTTTTTGTAGTTGA
13499025 ATTNATTACTTCAAACGGATATGTAA-GCCTTGTTGGAACCTATCACCCACAATATAACTATCAA
1 ATT-ATTACTTCAAACGGATATGTAAGGCCTTGTTGGAACCTATCACCCACAATATAACTATCAA
13499089 AAATATAACAGCCCATAAATCAAATTTCTAGTCATCTCTAACATCTTAAAATCAAATTCTAACCC
65 AAATATAACAGCCCATAAATCAAATTTCTAGTCATCTCTAACATCTTAAAATCAAATTCTAACCC
13499154 ATTTCTCACCTTGGTGGTTTTTTTTTTGTAGTTGA
130 ATTTCTCACCTTGGTGGTTTTTTTTTTGTAGTTGA
13499189 ATT
1 ATT
13499192 GCTTTTCAAA
Statistics
Matches: 166, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
164 144 0.87
165 22 0.13
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.36
Consensus pattern (164 bp):
ATTATTACTTCAAACGGATATGTAAGGCCTTGTTGGAACCTATCACCCACAATATAACTATCAAA
AATATAACAGCCCATAAATCAAATTTCTAGTCATCTCTAACATCTTAAAATCAAATTCTAACCCA
TTTCTCACCTTGGTGGTTTTTTTTTTGTAGTTGA
Found at i:13504684 original size:15 final size:15
Alignment explanation
Indices: 13504664--13504693 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13504654 CAAAATATCC
13504664 AATATTAATTAATTA
1 AATATTAATTAATTA
*
13504679 AATATTTATTAATTA
1 AATATTAATTAATTA
13504694 TTCACAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTAATTAATTA
Found at i:13505357 original size:15 final size:15
Alignment explanation
Indices: 13505337--13505367 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13505327 ACACTTATCT
13505337 TGCTCTTGACTTTTC
1 TGCTCTTGACTTTTC
*
13505352 TGCTCTTGTCTTTTC
1 TGCTCTTGACTTTTC
13505367 T
1 T
13505368 TTAAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.03, C:0.26, G:0.13, T:0.58
Consensus pattern (15 bp):
TGCTCTTGACTTTTC
Found at i:13510722 original size:21 final size:21
Alignment explanation
Indices: 13510696--13510741 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
13510686 TGGTTGGCAA
13510696 CAAGCCCTTTATATAGGCTTC
1 CAAGCCCTTTATATAGGCTTC
13510717 CAAGCCCTTTATATAGGCTTC
1 CAAGCCCTTTATATAGGCTTC
13510738 CAAG
1 CAAG
13510742 TGTCTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (21 bp):
CAAGCCCTTTATATAGGCTTC
Found at i:13514326 original size:22 final size:23
Alignment explanation
Indices: 13514297--13514362 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 23
13514287 TTATTAGATT
13514297 TTTTAAATATTAATAATCTAGAA
1 TTTTAAATATTAATAATCTAGAA
* *
13514320 TTTAAATAAAATATTAATAATTTATAA
1 TTT---T-AAATATTAATAATCTAGAA
13514347 -TTTAAATATTAATAAT
1 TTTTAAATATTAATAAT
13514363 TTATTTAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
22 13 0.35
23 4 0.11
26 3 0.08
27 17 0.46
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTTAAATATTAATAATCTAGAA
Found at i:13514331 original size:27 final size:27
Alignment explanation
Indices: 13514301--13514354 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
13514291 TAGATTTTTT
13514301 AAATATTAATAATCTAGAATTTAAATA
1 AAATATTAATAATCTAGAATTTAAATA
* *
13514328 AAATATTAATAATTTATAATTTAAATA
1 AAATATTAATAATCTAGAATTTAAATA
13514355 TTAATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
AAATATTAATAATCTAGAATTTAAATA
Found at i:13514463 original size:27 final size:28
Alignment explanation
Indices: 13514409--13514461 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
13514399 TTATTTTATT
13514409 TTTAAAATATTATATAATTGATAATTTA
1 TTTAAAATATTATATAATTGATAATTTA
13514437 TTTAAAATATTA-ATAATTG-TAATTT
1 TTTAAAATATTATATAATTGATAATTT
13514462 TAATATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 6 0.24
27 7 0.28
28 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (28 bp):
TTTAAAATATTATATAATTGATAATTTA
Found at i:13514476 original size:40 final size:40
Alignment explanation
Indices: 13514432--13514522 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 40
13514422 ATAATTGATA
13514432 ATTTATTTAAAATATTAATAATTGTA-ATTTT-AATATTAAT
1 ATTTATTTAAAAT-TTAATAATT-TATATTTTAAATATTAAT
* *
13514472 ATTTATTT-ATATTTAATTATTTATATTTTAAAATATTAAT
1 ATTTATTTAAAATTTAATAATTTATATTTT-AAATATTAAT
13514512 ATTTTATTTAA
1 A-TTTATTTAA
13514523 TTTAAATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
37 2 0.05
38 13 0.30
39 3 0.07
40 18 0.41
41 7 0.16
42 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (40 bp):
ATTTATTTAAAATTTAATAATTTATATTTTAAATATTAAT
Found at i:13514485 original size:86 final size:93
Alignment explanation
Indices: 13514336--13514509 Score: 211
Period size: 89 Copynumber: 1.9 Consensus size: 93
13514326 TAAAATATTA
* * * *
13514336 ATAATTTATAATTTAAATATTAATAATTTATTTAATTAAATATTATTATGATTAATTTTTATTTT
1 ATAATTTAT-ATTAAAATATTAATAATTTAATT-ATTAAATATTA-TATGATTAATTTATATTTA
13514401 A-T-TTTAT-TTTTAAAATATTATATAATTG
63 ATTATTTATATTTTAAAATATTATATAATTG
*
13514429 ATAATTTAT-TTAAAATATTAATAATTGTAATT-TT-AATATTA-AT-ATTTATTTATATTTAAT
1 ATAATTTATATTAAAATATTAATAATT-TAATTATTAAATATTATATGATTAATTTATATTTAAT
13514489 TATTTATATTTTAAAATATTA
65 TATTTATATTTTAAAATATTA
13514510 ATATTTTATT
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
86 13 0.18
87 3 0.04
88 5 0.07
89 20 0.28
90 2 0.03
91 16 0.22
92 4 0.06
93 9 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (93 bp):
ATAATTTATATTAAAATATTAATAATTTAATTATTAAATATTATATGATTAATTTATATTTAATT
ATTTATATTTTAAAATATTATATAATTG
Found at i:13514487 original size:46 final size:41
Alignment explanation
Indices: 13514435--13514533 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 41
13514425 ATTGATAATT
13514435 TATTTAAAATATTAATAATTGTAATTTTAATATTAATA-TTTATTTA
1 TATTT-AAATATTAAT-ATTGTAA----AATATTAATATTTTATTTA
* * *
13514481 TATTTAATTATTTATATTTTAAAATATTAATATTTTATTTA
1 TATTTAAATATTAATATTGTAAAATATTAATATTTTATTTA
13514522 -ATTTAAATATTA
1 TATTTAAATATTA
13514534 TGATGNNNNN
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
40 20 0.43
41 8 0.17
44 6 0.13
45 8 0.17
46 5 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (41 bp):
TATTTAAATATTAATATTGTAAAATATTAATATTTTATTTA
Found at i:13516394 original size:6 final size:6
Alignment explanation
Indices: 13516383--13516414 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
13516373 AGAGTTTATA
13516383 CAGCCG CAGCCG CAGCCG CAGCCG CAGCCG CA
1 CAGCCG CAGCCG CAGCCG CAGCCG CAGCCG CA
13516415 AACGCAAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.50, G:0.31, T:0.00
Consensus pattern (6 bp):
CAGCCG
Found at i:13516420 original size:18 final size:18
Alignment explanation
Indices: 13516383--13516420 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13516373 AGAGTTTATA
**
13516383 CAGCCGCAGCCGCAGCCG
1 CAGCCGCAGCCGCAAACG
13516401 CAGCCGCAGCCGCAAACG
1 CAGCCGCAGCCGCAAACG
13516419 CA
1 CA
13516421 AACGCCGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.47, G:0.29, T:0.00
Consensus pattern (18 bp):
CAGCCGCAGCCGCAAACG
Found at i:13520096 original size:30 final size:30
Alignment explanation
Indices: 13520060--13520123 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
13520050 ATCCTCTTCA
*
13520060 TCATGATTTCTATGATCATTTTGAATCTCT
1 TCATGATTTCTATGATCATTTTGAATCCCT
13520090 TCATGATTTCTATGATCATTTTGAATCCCT
1 TCATGATTTCTATGATCATTTTGAATCCCT
13520120 TCAT
1 TCAT
13520124 TAACTTCTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.48
Consensus pattern (30 bp):
TCATGATTTCTATGATCATTTTGAATCCCT
Found at i:13520961 original size:17 final size:17
Alignment explanation
Indices: 13520931--13520973 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
13520921 TTTTATTAAT
* *
13520931 TATTTTTTACTTTTATA
1 TATTTTTAAATTTTATA
* *
13520948 TTTTTTTAAATTTTTTA
1 TATTTTTAAATTTTATA
13520965 TATTTTTAA
1 TATTTTTAA
13520974 TATAATTAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTTTTAAATTTTATA
Found at i:13520963 original size:27 final size:27
Alignment explanation
Indices: 13520920--13520972 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
13520910 AGAATAATTA
*
13520920 ATTTTATTAATTATTTTTTACTTTTAT
1 ATTTTATTAATTATTTTATACTTTTAT
* *
13520947 ATTTTTTTAAATT-TTTTATATTTTTA
1 ATTTTATT-AATTATTTTATACTTTTA
13520973 ATATAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (27 bp):
ATTTTATTAATTATTTTATACTTTTAT
Found at i:13523623 original size:32 final size:32
Alignment explanation
Indices: 13523576--13523639 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
13523566 ATTTTTAGAA
* *
13523576 TAACGTTATAGAATATGTTATCTTGATTTTTT
1 TAACGTTACAAAATATGTTATCTTGATTTTTT
* *
13523608 TAACGTTACAAAATATTTTATTTTGATTTTTT
1 TAACGTTACAAAATATGTTATCTTGATTTTTT
13523640 GCTTGATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (32 bp):
TAACGTTACAAAATATGTTATCTTGATTTTTT
Found at i:13529119 original size:2 final size:2
Alignment explanation
Indices: 13529056--13529100 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
13529046 NNNNNNNNNN
13529056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13529098 TA T
1 TA T
13529101 CCATGTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13539191 original size:34 final size:34
Alignment explanation
Indices: 13539125--13539192 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
13539115 AACCACTTTG
*
13539125 GGTTTTAGTTGAGCCCGTGAAAAACTAGTGTAAA
1 GGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAA
* ** * *
13539159 GGTTTTGGTTGAGCTTGTGAAAAGCCATTGTAAA
1 GGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAA
13539193 AGCTTGGTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.29, C:0.10, G:0.28, T:0.32
Consensus pattern (34 bp):
GGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAA
Found at i:13540579 original size:19 final size:19
Alignment explanation
Indices: 13540557--13540597 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
13540547 ACTTCAATAT
13540557 TCAAATTCAAAAGTGATAA
1 TCAAATTCAAAAGTGATAA
13540576 TCAAATTCAAAAGTGATAA
1 TCAAATTCAAAAGTGATAA
13540595 TCA
1 TCA
13540598 TAAAAACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (19 bp):
TCAAATTCAAAAGTGATAA
Found at i:13552543 original size:81 final size:83
Alignment explanation
Indices: 13552400--13552559 Score: 234
Period size: 81 Copynumber: 2.0 Consensus size: 83
13552390 TATGTTAACA
* * *
13552400 GAAAAAATGTGGAATTAATAAATCTTAAAAGACTATACTCCTATCACCTGATCTTCAGGTGTTAG
1 GAAAAAATGTGGAATTAATAAATCTTAAAAGACTATACTCCCATCACCTGATCTTCAAGTGTTAA
*
13552465 TCTTATCGCTAACCACAG
66 TCTTATCACTAACCACAG
** * *
13552483 GAAAAAA-GTGGGGTTAATAAA-CTTAAAAGACTGTACTCCCATCACTTGATCTTCAAGTGTTAA
1 GAAAAAATGTGGAATTAATAAATCTTAAAAGACTATACTCCCATCACCTGATCTTCAAGTGTTAA
13552546 TCTTATCACTAACC
66 TCTTATCACTAACC
13552560 CCAAATATCC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
81 50 0.72
82 12 0.17
83 7 0.10
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.30
Consensus pattern (83 bp):
GAAAAAATGTGGAATTAATAAATCTTAAAAGACTATACTCCCATCACCTGATCTTCAAGTGTTAA
TCTTATCACTAACCACAG
Found at i:13573872 original size:22 final size:22
Alignment explanation
Indices: 13573847--13573927 Score: 117
Period size: 22 Copynumber: 3.7 Consensus size: 22
13573837 TAATAGACAG
* *
13573847 ATTCTCGCTGAAGCGGAAAAGC
1 ATTCTCGCTGCAGCGGAAAGGC
**
13573869 ATTCTCATTGCAGCGGAAAGGC
1 ATTCTCGCTGCAGCGGAAAGGC
*
13573891 ATTCTCGCTGCAGCGGAAGGGC
1 ATTCTCGCTGCAGCGGAAAGGC
13573913 ATTCTCGCTGCAGCG
1 ATTCTCGCTGCAGCG
13573928 TATTTTAGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.23, C:0.26, G:0.30, T:0.21
Consensus pattern (22 bp):
ATTCTCGCTGCAGCGGAAAGGC
Found at i:13576082 original size:37 final size:37
Alignment explanation
Indices: 13575966--13576082 Score: 191
Period size: 37 Copynumber: 3.2 Consensus size: 37
13575956 AAGTTGTGTT
*
13575966 ATGATGTTGAAGTGTGCAAGTAGGGAGTGCACACATG
1 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATG
**
13576003 ATGATAAT-AGAGTGTGCGAGTAGGGAGTGCACACATG
1 ATGATGTTGA-AGTGTGCGAGTAGGGAGTGCACACATG
13576040 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATG
1 ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATG
13576077 ATGATG
1 ATGATG
13576083 GTATTGCATT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
36 1 0.01
37 71 0.97
38 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.36, T:0.24
Consensus pattern (37 bp):
ATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACATG
Found at i:13578822 original size:2 final size:2
Alignment explanation
Indices: 13578815--13578869 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
13578805 TAAACCCCAA
13578815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13578857 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
13578870 GCAAATTGGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13589436 original size:42 final size:42
Alignment explanation
Indices: 13589381--13589511 Score: 174
Period size: 42 Copynumber: 3.1 Consensus size: 42
13589371 TGTTGATGTG
* *
13589381 GACCCGGCTATGTGCGAGTAGGAGTGCGCATACGTCGATGAT
1 GACCCGACTATGTGCGAGTAGGAGTGCGCATAAGTCGATGAT
* *
13589423 GACCCGACTATGTGTGAGTAGGAGTGCACATAAGTCGATGAT
1 GACCCGACTATGTGCGAGTAGGAGTGCGCATAAGTCGATGAT
* * * *
13589465 GA-CCTAGCTATGTGCGAGTAGGAGTGTGCATAAGCCGATGCT
1 GACCCGA-CTATGTGCGAGTAGGAGTGCGCATAAGTCGATGAT
13589507 GACCC
1 GACCC
13589512 AGCCATGTAC
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
41 3 0.04
42 72 0.94
43 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.22
Consensus pattern (42 bp):
GACCCGACTATGTGCGAGTAGGAGTGCGCATAAGTCGATGAT
Found at i:13589582 original size:2 final size:2
Alignment explanation
Indices: 13589575--13589612 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
13589565 ATGATGATGG
* *
13589575 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13589613 GTTTGTCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13591110 original size:19 final size:19
Alignment explanation
Indices: 13591086--13591124 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
13591076 CCATAAAATA
13591086 TCTTGAATTTCTAGCAGCT
1 TCTTGAATTTCTAGCAGCT
*
13591105 TCTTGAATTTCTAGTAGCT
1 TCTTGAATTTCTAGCAGCT
13591124 T
1 T
13591125 GTCTTCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (19 bp):
TCTTGAATTTCTAGCAGCT
Found at i:13591961 original size:42 final size:42
Alignment explanation
Indices: 13591894--13592018 Score: 189
Period size: 42 Copynumber: 3.0 Consensus size: 42
13591884 TGTTGATGTG
* *
13591894 GACCTGGCTATGTGCGAGT-AGGAGTGCACATAAGCCGTTGTT
1 GACCCGGCTATGTGCGAGTGA-GAGTGCACATAAGCCGTTGCT
*
13591936 GACCCGGTTATGTGCGAGTGAGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTGAGAGTGCACATAAGCCGTTGCT
* *
13591978 GACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGCCGTTGC
1 GACCCGGCTATGTGCGAGTGAGAGTGCACATAAGCCGTTGC
13592019 ATATGAGATG
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
42 75 0.99
43 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.35, T:0.23
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTGAGAGTGCACATAAGCCGTTGCT
Found at i:13593098 original size:94 final size:93
Alignment explanation
Indices: 13592920--13593105 Score: 248
Period size: 94 Copynumber: 2.0 Consensus size: 93
13592910 GAGGTGACCT
* *
13592920 TGTAGACTTGTATCCATCTTTTGGTAAGTGTCTCGGCATTCAGTAACTGTACATTCGTCCGAGTC
1 TGTAGACTTGTATCCATCTTTTGATAAGTGTCTCGACATTCAGTAACTGTACATTCGTCCGAGTC
*
13592985 CCTCCATAGGAAGTCGAGTATTATTTTG
66 CCTCCATAGAAAGTCGAGTATTATTTTG
* * * * *
13593013 NTGTAGACTTGTATCTATTTTTTGATAGGTGTCTCGACATTCAGTAGCTGTATATTCGTCCGAGT
1 -TGTAGACTTGTATCCATCTTTTGATAAGTGTCTCGACATTCAGTAACTGTACATTCGTCCGAGT
* * *
13593078 CCCTCC-TCTGAAAGTTGAGTATTTTTTT
65 CCCTCCAT-AGAAAGTCGAGTATTATTTT
13593106 TTTGTGTATA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
93 1 0.01
94 79 0.99
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (93 bp):
TGTAGACTTGTATCCATCTTTTGATAAGTGTCTCGACATTCAGTAACTGTACATTCGTCCGAGTC
CCTCCATAGAAAGTCGAGTATTATTTTG
Found at i:13593539 original size:17 final size:19
Alignment explanation
Indices: 13593507--13593541 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
13593497 ATATTTACCC
13593507 TAACTAAATCTATTTTTTG
1 TAACTAAATCTATTTTTTG
13593526 TAACT-AAT-TATTTTTT
1 TAACTAAATCTATTTTTT
13593542 TATTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (19 bp):
TAACTAAATCTATTTTTTG
Found at i:13593713 original size:18 final size:17
Alignment explanation
Indices: 13593687--13593720 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13593677 TTCTAAATAT
*
13593687 TTTATCTTCCTTATTTA
1 TTTATCTTCCCTATTTA
13593704 TTTATGCTTCCCTATTT
1 TTTAT-CTTCCCTATTT
13593721 TAGTAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.21, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTATCTTCCCTATTTA
Found at i:13597811 original size:20 final size:20
Alignment explanation
Indices: 13597786--13597826 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
13597776 ATGAGCCTTG
*
13597786 TTGATTTTTATGAAATGAAA
1 TTGATTTATATGAAATGAAA
13597806 TTGATTTATATGAAATGAAA
1 TTGATTTATATGAAATGAAA
13597826 T
1 T
13597827 GAGATTCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGATTTATATGAAATGAAA
Found at i:13597842 original size:25 final size:25
Alignment explanation
Indices: 13597795--13597844 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
13597785 GTTGATTTTT
*
13597795 ATGAAATGAAATTGATTTATATGAA
1 ATGAAATGAAATTGATGTATATGAA
*
13597820 ATGAAATGAGATTCGATGT-TATGAA
1 ATGAAATGAAATT-GATGTATATGAA
13597845 TCATATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (25 bp):
ATGAAATGAAATTGATGTATATGAA
Found at i:13599439 original size:17 final size:17
Alignment explanation
Indices: 13599417--13599461 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
13599407 ATGGAAATTA
*
13599417 GTGACAAAATAAATTTC
1 GTGACATAATAAATTTC
13599434 GTGACATAATAAATTTC
1 GTGACATAATAAATTTC
13599451 GTGACATAATA
1 GTGACATAATA
13599462 TTGTGACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (17 bp):
GTGACATAATAAATTTC
Found at i:13600158 original size:34 final size:35
Alignment explanation
Indices: 13600058--13600160 Score: 84
Period size: 34 Copynumber: 3.0 Consensus size: 35
13600048 TTCAAAGGTA
* * * *
13600058 ACATTGTAGGGGTTATGCTTGCTTCTAT-AAAAGG
1 ACATTATAAGGGTTGTGCTTGCTCCTATAAAAAGG
* * ** * *
13600092 ACATTGTAAGGGTCGTGCTTGAGCCCAGAAAAAGG
1 ACATTATAAGGGTTGTGCTTGCTCCTATAAAAAGG
**
13600127 -CATTATGTGGGTTGTGCTTGCTCCTATAAAAAGG
1 ACATTATAAGGGTTGTGCTTGCTCCTATAAAAAGG
13600161 TATTGTAAAG
Statistics
Matches: 52, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
34 46 0.88
35 6 0.12
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (35 bp):
ACATTATAAGGGTTGTGCTTGCTCCTATAAAAAGG
Found at i:13600182 original size:68 final size:67
Alignment explanation
Indices: 13600067--13600197 Score: 156
Period size: 68 Copynumber: 1.9 Consensus size: 67
13600057 AACATTGTAG
* * *
13600067 GGGTTATGCTTGCTTCTATAAAAGGACATTGTAAGGGTCGTGCTTGAGCCCAGAAAAAGGCATTA
1 GGGTTATGCTTGCTCCTATAAAAGGACATTGTAAAGGTCATGCTTGAGCCCA-AAAAAGGCATTA
13600132 TGT
65 TGT
* * * * * *
13600135 GGGTTGTGCTTGCTCCTATAAAAAGG-TATTGTAAAGGTTATGGTTGAGCTCAAAAAATGCATT
1 GGGTTATGCTTGCTCCTAT-AAAAGGACATTGTAAAGGTCATGCTTGAGCCCAAAAAAGGCATT
13600198 GTGAAGGTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
67 10 0.19
68 37 0.70
69 6 0.11
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (67 bp):
GGGTTATGCTTGCTCCTATAAAAGGACATTGTAAAGGTCATGCTTGAGCCCAAAAAAGGCATTAT
GT
Found at i:13604140 original size:2 final size:2
Alignment explanation
Indices: 13604133--13604167 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13604123 ATTACTTTGT
13604133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13604168 GTATTTGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13604330 original size:2 final size:2
Alignment explanation
Indices: 13604323--13604359 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
13604313 GGCNCTTTTG
13604323 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13604360 GTATTTGAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13604361 original size:192 final size:190
Alignment explanation
Indices: 13604128--13604507 Score: 742
Period size: 192 Copynumber: 2.0 Consensus size: 190
13604118 TTCTTATTAC
13604128 TTTGTTATATATATATATATATATATATATATATATATATGTATTTGAGCTTTATTGTTTTTGCT
1 TTTGTTATATATATATATATATATATATATATATATATATGTATTTGAGCTTTATTGTTTTTGCT
13604193 TGATTGTGGAAAATTGTCTTGATAAAATTTTCTCATGTTTTGTGAAATTGACTTCATATTATTTG
66 TGATTGTGGAAAATTGTCTTGATAAAATTTTCTCATGTTTTGTGAAATTGACTTCATATTATTTG
13604258 TTTGAAGAAAGATGATTTAAAGCATAAAAGGTTTGATGTTGATGGCATGAGAAATGGCNCT
131 TTTGAAGAAAGATGATTTAAAGCATAAAAGGTTTGATGTTGATGGCATGAGAAATGGC-CT
13604319 TTTGTATATATATATATATATATATATATATATATATATATGTATTTGAGCTTTATTGTTTTTGC
1 TTTGT-TATATATATATATATATATATATATATATATATATGTATTTGAGCTTTATTGTTTTTGC
13604384 TTGATTGTGGAAAATTGTCTTGATAAAATTTTCTCATGTTTTGTGAAATTGACTTCATATTATTT
65 TTGATTGTGGAAAATTGTCTTGATAAAATTTTCTCATGTTTTGTGAAATTGACTTCATATTATTT
13604449 GTTTGAAGAAAGATGATTTAAAGCATAAAAGGTTTGATGTTGATGGCATGAGAAATGGC
130 GTTTGAAGAAAGATGATTTAAAGCATAAAAGGTTTGATGTTGATGGCATGAGAAATGGC
13604508 TAATGTGATT
Statistics
Matches: 188, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
191 5 0.03
192 183 0.97
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (190 bp):
TTTGTTATATATATATATATATATATATATATATATATATGTATTTGAGCTTTATTGTTTTTGCT
TGATTGTGGAAAATTGTCTTGATAAAATTTTCTCATGTTTTGTGAAATTGACTTCATATTATTTG
TTTGAAGAAAGATGATTTAAAGCATAAAAGGTTTGATGTTGATGGCATGAGAAATGGCCT
Found at i:13614316 original size:36 final size:36
Alignment explanation
Indices: 13614276--13614415 Score: 156
Period size: 36 Copynumber: 3.9 Consensus size: 36
13614266 AGTGGAGTGC
* *
13614276 ATGTACCATTAGATTATTTACCAATGAGTGGGGTAG
1 ATGTACCACTAGATTATTTGCCAATGAGTGGGGTAG
* * * *
13614312 ATGTACTACTAAATTATTTGCCAATGAGTGAGGTGG
1 ATGTACCACTAGATTATTTGCCAATGAGTGGGGTAG
* *
13614348 ATGTACCACTAGATTATTTGCCAATGAGTGGCG-AA
1 ATGTACCACTAGATTATTTGCCAATGAGTGGGGTAG
* ** * *
13614383 ACGTACTGCTAGATTGTTTGCCAATAAGTGGGG
1 ATGTACCACTAGATTATTTGCCAATGAGTGGGG
13614416 AGGAAATACC
Statistics
Matches: 86, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 27 0.31
36 59 0.69
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (36 bp):
ATGTACCACTAGATTATTTGCCAATGAGTGGGGTAG
Found at i:13615689 original size:21 final size:21
Alignment explanation
Indices: 13615663--13615734 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
13615653 GATACAATTC
*
13615663 TTTTTGTAACTAAAGTTTATA
1 TTTTTGTAACTAAAGTTCATA
* * *
13615684 TTTTTGTAAGTGAAGTTCATC
1 TTTTTGTAACTAAAGTTCATA
*
13615705 TTTTTGTAACTAAAGTTGATA
1 TTTTTGTAACTAAAGTTCATA
*
13615726 ATTTTGTAA
1 TTTTTGTAA
13615735 TTAGTTTGTA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (21 bp):
TTTTTGTAACTAAAGTTCATA
Found at i:13616285 original size:50 final size:49
Alignment explanation
Indices: 13616217--13616331 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 49
13616207 ACTATCAAGA
* **
13616217 ATTCTTGCTTTCTAATGGG-AAGTGATAACCCTTACACAATCCATAAAGGG
1 ATTCTTGCTTTTTAATGGGAAAGTGATAA-CCTT-CACAATCCATAAAAAG
* * *
13616267 ATTTTTGCTTTTTCATGGGATCAAGTGATAACCTTTACAATCCATAAAAAG
1 ATTCTTGCTTTTTAATGGGA--AAGTGATAACCTTCACAATCCATAAAAAG
13616318 ATTCTTGCTTTTTA
1 ATTCTTGCTTTTTA
13616332 CGAGATCTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 16 0.30
51 25 0.46
52 4 0.07
53 9 0.17
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (49 bp):
ATTCTTGCTTTTTAATGGGAAAGTGATAACCTTCACAATCCATAAAAAG
Found at i:13617100 original size:71 final size:72
Alignment explanation
Indices: 13616975--13617114 Score: 183
Period size: 71 Copynumber: 2.0 Consensus size: 72
13616965 GCCTCTTCTA
* * * * * * *
13616975 TAGTTGACTATAGCTGTTCTTCAACTTTATTTTCTTGGTCTTTTTGGAGCAAGGTAGACTATGCT
1 TAGTTGACTATAACTGTTCTTAAACTTGATTTTCTTGATCTTTCTAGAACAAGGTAGACTATGCT
13617040 TCCTTTG
66 TCCTTTG
* * *
13617047 TAGTTGACTATAATTGTTC-TAAACTTGATTTTCTTGATCTTTCTAGAACAAGGTCGACTGTGCT
1 TAGTTGACTATAACTGTTCTTAAACTTGATTTTCTTGATCTTTCTAGAACAAGGTAGACTATGCT
13617111 TCCT
66 TCCT
13617115 CTCTAGTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
71 41 0.71
72 17 0.29
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.44
Consensus pattern (72 bp):
TAGTTGACTATAACTGTTCTTAAACTTGATTTTCTTGATCTTTCTAGAACAAGGTAGACTATGCT
TCCTTTG
Found at i:13620027 original size:2 final size:2
Alignment explanation
Indices: 13620020--13620050 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13620010 GTGTATATGC
13620020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13620051 GGATGAAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13622680 original size:50 final size:50
Alignment explanation
Indices: 13622562--13622700 Score: 142
Period size: 50 Copynumber: 2.8 Consensus size: 50
13622552 AATGTGAGGC
* *
13622562 GATAACCTTTACACAATCCACAAAGGGATTTTTGTTTTTTCACTAGATAAGT
1 GATAACC--TACACAATCCACAAAAGGATTTTTGCTTTTTCACTAGATAAGT
**
13622614 GATAACCTTTACAATCCACAAAAGGATTTTTGCTTTTT-AC-AGGATCAAGT
1 GATAACCTACACAATCCACAAAAGGATTTTTGCTTTTTCACTA-GAT-AAGT
* * *
13622664 -AGTAACCTACATAATCCACAAGA-GATTCTTGCTTTTT
1 GA-TAACCTACACAATCCACAAAAGGATTTTTGCTTTTT
13622701 GGTAAAAGCG
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
48 1 0.01
49 19 0.25
50 48 0.64
52 7 0.09
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (50 bp):
GATAACCTACACAATCCACAAAAGGATTTTTGCTTTTTCACTAGATAAGT
Found at i:13623211 original size:21 final size:20
Alignment explanation
Indices: 13623185--13623223 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13623175 TTTATAGTCG
13623185 ACTATGCCTTTCTTAAAATCA
1 ACTATGCC-TTCTTAAAATCA
*
13623206 ACTATGGCTTCTTAAAAT
1 ACTATGCCTTCTTAAAAT
13623224 TGACTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (20 bp):
ACTATGCCTTCTTAAAATCA
Found at i:13624019 original size:31 final size:31
Alignment explanation
Indices: 13623981--13624056 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
13623971 GTACCCACAA
* *
13623981 AGTCCTTATATTGTAGAAATTTGTTCAATTT
1 AGTCCTTATACTATAGAAATTTGTTCAATTT
* *
13624012 AGTCCTTATACTATAGTATTTTGTTCAATTT
1 AGTCCTTATACTATAGAAATTTGTTCAATTT
*
13624043 AAT-CTCTATACTAT
1 AGTCCT-TATACTAT
13624057 TTAGTTCAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 2 0.05
31 37 0.95
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (31 bp):
AGTCCTTATACTATAGAAATTTGTTCAATTT
Found at i:13641593 original size:19 final size:19
Alignment explanation
Indices: 13641569--13641606 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13641559 CCATTTGACT
*
13641569 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
13641588 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
13641607 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:13648660 original size:19 final size:19
Alignment explanation
Indices: 13648636--13648673 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
13648626 CCATTTGACT
*
13648636 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
13648655 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
13648674 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:13657324 original size:12 final size:12
Alignment explanation
Indices: 13657308--13657347 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
13657298 TAGTAAATGT
*
13657308 GTATATATATAT
1 GTATATATATAC
13657320 GTATATATATAC
1 GTATATATATAC
13657332 GTATATATATAC
1 GTATATATATAC
13657344 GTAT
1 GTAT
13657348 TCTAATGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (12 bp):
GTATATATATAC
Found at i:13665251 original size:20 final size:19
Alignment explanation
Indices: 13665226--13665265 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
13665216 CGTGAATTCC
13665226 CCTTTGAATTTTCTACTTTT
1 CCTTTGAATTTTCT-CTTTT
**
13665246 CCTTTGGTTTTTCTCTTTT
1 CCTTTGAATTTTCTCTTTT
13665265 C
1 C
13665266 TTCCTTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.07, C:0.23, G:0.07, T:0.62
Consensus pattern (19 bp):
CCTTTGAATTTTCTCTTTT
Found at i:13669206 original size:116 final size:114
Alignment explanation
Indices: 13668994--13669623 Score: 522
Period size: 116 Copynumber: 5.5 Consensus size: 114
13668984 AACTTATAGT
* * * * * *
13668994 TATTTAAATTAATTAAGATTTTATTAAATTAATGAAATGATTTAACTAATTAAATGAAA-TAATG
1 TATTTAAATTAATTAAGGTGTTAATGAATTAATTAAATAATTTAACTAATT-AAT-AAAGTAATG
* * * **
13669058 TTTTGGTAATTAAGCAA-TAAATTAAATTAGTAATATTATTTAATTTAAAAAA
64 TGTTAGTAATTAAGCAATTAAA-TAAATAAGTAATATTATAAAATTT-AAAAA
* * ** *
13669110 TACTTAAATTAATTAAGGTGTTAATGAGTTAATTAAATAATTTAGTTAATTAACTAATGTAATGT
1 TATTTAAATTAATTAAGGTGTTAATGAATTAATTAAATAATTTAACTAATTAA-TAAAGTAATGT
* * ** **
13669175 GTTAGTAATTAAGCAATTAAATAAACAAGTAATATTCTAAAATATTTTATT
65 GTTAGTAATTAAGCAATTAAATAAATAAGTAATATTATAAAAT-TTAAAAA
* * * *
13669226 TATTTAAATTAATTAAGGT-TTAAGGGAATTATTTACATAATTTAACTAATTAA-AAAGAATTAT
1 TATTTAAATTAATTAAGGTGTTAA-TGAATTAATTAAATAATTTAACTAATTAATAAAG--TAAT
* * * * * *
13669289 GTATTAGTAATTAAGCTATTAATTAAA-ATAGTAA-ATATAGGAAAATTTATAAT
63 GTGTTAGTAATTAAGCAATTAAATAAATA-AGTAATAT-TA-TAAAATTTAAAAA
* * * * * **
13669342 TATTTAAATTAATTAAGGTTTTATTAAATTAATGAAATAATTTAACTAATCAAATAAAAAAATGT
1 TATTTAAATTAATTAAGGTGTTAATGAATTAATTAAATAATTTAACTAAT-TAATAAAGTAATGT
* ** * * **
13669407 TTTAGTAATTAAATAATTAATTAAATTAGTAATATTATTTAATTT-AAAA
65 GTTAGTAATTAAGCAATTAAATAAATAAGTAATATTATAAAATTTAAAAA
* ** *
13669456 TATTTAAATTAATTAAGGTGTTAATGAGTTAATTAAATAATTTAGTTAATTAAGTAATGTAATGT
1 TATTTAAATTAATTAAGGTGTTAATGAATTAATTAAATAATTTAACTAATTAA-TAAAGTAATGT
* * * **
13669521 GTTAGTACTTAAGCAATTAACTAAATAAGTAATATTATATAACATTT-TATT
65 GTTAGTAATTAAGCAATTAAATAAATAAGTAATATTATA-AA-ATTTAAAAA
* * *
13669572 TATTTAAATTAATTAA-GTTTTGAAGGAATTAATTACATAATTTAACTAATTA
1 TATTTAAATTAATTAAGGTGTT-AATGAATTAATTAAATAATTTAACTAATTA
13669624 CAAAGAATCA
Statistics
Matches: 409, Mismatches: 86, Indels: 38
0.77 0.16 0.07
Matches are distributed among these distances:
113 2 0.00
114 88 0.22
115 21 0.05
116 277 0.68
117 18 0.04
118 3 0.01
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (114 bp):
TATTTAAATTAATTAAGGTGTTAATGAATTAATTAAATAATTTAACTAATTAATAAAGTAATGTG
TTAGTAATTAAGCAATTAAATAAATAAGTAATATTATAAAATTTAAAAA
Found at i:13669631 original size:346 final size:347
Alignment explanation
Indices: 13668982--13669636 Score: 1071
Period size: 346 Copynumber: 1.9 Consensus size: 347
13668972 GTAATTAAGC
* * *
13668982 AAAACTTATAGTTATTTAAATTAATTAAGATTTTATTAAATTAATGAAATGATTTAACTAATTAA
1 AAAACTTATAATTATTTAAATTAATTAAGATTTTATTAAATTAATGAAATAATTTAACTAATCAA
* * * *
13669047 ATGAAATAATGTTTTGGTAATTAAGCAATAAATTAAATTAGTAATATTATTTAATTTAAAAAATA
66 ATAAAAAAATGTTTTAGTAATTAAACAATAAATTAAATTAGTAATATTATTTAATTT-AAAAATA
13669112 CTTAAATTAATTAAGGTGTTAATGAGTTAATTAAATAATTTAGTTAATTAACTAATGTAATGTGT
130 CTTAAATTAATTAAGGTGTTAATGAGTTAATTAAATAATTTAGTTAATTAACTAATGTAATGTGT
* *
13669177 TAGTAATTAAGCAATTAAATAAACAAGTAATATTCTAAAATATTTTATTTATTTAAATTAATTAA
195 TAGTAATTAAGCAATTAAATAAACAAGTAATATTATAAAACATTTTATTTATTTAAATTAATTAA
* *
13669242 GGTTTAAGGGAATTATTTACATAATTTAACTAATTAAAAAGAATTATGTATTAGTAATTAAGCTA
260 GGTTTAAGGGAATTAATTACATAATTTAACTAATTAAAAAGAATCATGTATTAGTAATTAAGCTA
13669307 TTAATTAAAATAGTAAATATAGG
325 TTAATTAAAATAGTAAATATAGG
* *
13669330 AAAATTTATAATTATTTAAATTAATTAAGGTTTTATTAAATTAATGAAATAATTTAACTAATCAA
1 AAAACTTATAATTATTTAAATTAATTAAGATTTTATTAAATTAATGAAATAATTTAACTAATCAA
* * *
13669395 ATAAAAAAATGTTTTAGTAATTAAATAATTAATTAAATTAGTAATATTATTTAATTT-AAAATAT
66 ATAAAAAAATGTTTTAGTAATTAAACAATAAATTAAATTAGTAATATTATTTAATTTAAAAATAC
*
13669459 TTAAATTAATTAAGGTGTTAATGAGTTAATTAAATAATTTAGTTAATTAAGTAATGTAATGTGTT
131 TTAAATTAATTAAGGTGTTAATGAGTTAATTAAATAATTTAGTTAATTAACTAATGTAATGTGTT
* * * *
13669524 AGTACTTAAGCAATTAACTAAATAAGTAATATTATATAACATTTTATTTATTTAAATTAATTAAG
196 AGTAATTAAGCAATTAAATAAACAAGTAATATTATAAAACATTTTATTTATTTAAATTAATTAAG
* *
13669589 TTTTGAA-GGAATTAATTACATAATTTAACTAATTACAAAGAATCATGT
261 GTTT-AAGGGAATTAATTACATAATTTAACTAATTAAAAAGAATCATGT
13669637 TGCTAACAGT
Statistics
Matches: 283, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
346 170 0.60
347 2 0.01
348 111 0.39
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (347 bp):
AAAACTTATAATTATTTAAATTAATTAAGATTTTATTAAATTAATGAAATAATTTAACTAATCAA
ATAAAAAAATGTTTTAGTAATTAAACAATAAATTAAATTAGTAATATTATTTAATTTAAAAATAC
TTAAATTAATTAAGGTGTTAATGAGTTAATTAAATAATTTAGTTAATTAACTAATGTAATGTGTT
AGTAATTAAGCAATTAAATAAACAAGTAATATTATAAAACATTTTATTTATTTAAATTAATTAAG
GTTTAAGGGAATTAATTACATAATTTAACTAATTAAAAAGAATCATGTATTAGTAATTAAGCTAT
TAATTAAAATAGTAAATATAGG
Found at i:13672312 original size:20 final size:20
Alignment explanation
Indices: 13672268--13672312 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
13672258 CAACACTTCA
13672268 TTCC-TTTTCTTCTTATTCT
1 TTCCTTTTTCTTCTTATTCT
* *
13672287 TCCCTTTTTCTTCTTATTTT
1 TTCCTTTTTCTTCTTATTCT
13672307 TTCCTT
1 TTCCTT
13672313 ATATCACACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (20 bp):
TTCCTTTTTCTTCTTATTCT
Found at i:13676121 original size:16 final size:16
Alignment explanation
Indices: 13676102--13676132 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13676092 GATTATATAG
*
13676102 AAATTCAATTAAAACT
1 AAATTCAATCAAAACT
13676118 AAATTCAATCAAAAC
1 AAATTCAATCAAAAC
13676133 ATTAGACTAA
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:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATTCAATCAAAACT
Found at i:13679607 original size:21 final size:21
Alignment explanation
Indices: 13679568--13679607 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
13679558 TAAAACCTTA
**
13679568 TGAATAAGGTATTGGTACCCT
1 TGAATAAGGTATTAATACCCT
13679589 TGAATAAGGTATTAATACC
1 TGAATAAGGTATTAATACC
13679608 TAACAAGTTA
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:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (21 bp):
TGAATAAGGTATTAATACCCT
Found at i:13699260 original size:26 final size:25
Alignment explanation
Indices: 13699188--13699278 Score: 137
Period size: 25 Copynumber: 3.5 Consensus size: 25
13699178 TATTTATTTT
*
13699188 TTTATTTTCTATTGGGCCATGCCCA
1 TTTATTTTCTATTGGGTCATGCCCA
*
13699213 CTTATTTTCTATTGGGTCATGCCCA
1 TTTATTTTCTATTGGGTCATGCCCA
13699238 TTTATTTTCTATTTGGGTCATGCCCA
1 TTTATTTTCTA-TTGGGTCATGCCCA
13699264 TTTTTATTTTCTATT
1 --TTTATTTTCTATT
13699279 TCTTTTCTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
25 33 0.55
26 14 0.23
27 2 0.03
28 11 0.18
ACGTcount: A:0.15, C:0.20, G:0.13, T:0.52
Consensus pattern (25 bp):
TTTATTTTCTATTGGGTCATGCCCA
Found at i:13699300 original size:11 final size:11
Alignment explanation
Indices: 13699264--13699302 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
13699254 GTCATGCCCA
*
13699264 TTTTTATTTTC
1 TTTTTCTTTTC
*
13699275 TATTTCTTTTC
1 TTTTTCTTTTC
13699286 TTTTTCTTTT-
1 TTTTTCTTTTC
13699296 TTTTTCT
1 TTTTTCT
13699303 CTCTTTCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:13699349 original size:22 final size:22
Alignment explanation
Indices: 13699321--13699368 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
13699311 CCGTCACTCC
*
13699321 CTTCACCACCATGTCTTCCTCT
1 CTTCACCACCATGGCTTCCTCT
13699343 CTTCACCACCATGGCTTCCTCT
1 CTTCACCACCATGGCTTCCTCT
13699365 CTTC
1 CTTC
13699369 CTTGGGTCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.12, C:0.46, G:0.06, T:0.35
Consensus pattern (22 bp):
CTTCACCACCATGGCTTCCTCT
Found at i:13699584 original size:47 final size:46
Alignment explanation
Indices: 13699505--13699601 Score: 167
Period size: 47 Copynumber: 2.1 Consensus size: 46
13699495 AAATTGGCAG
*
13699505 CAAACAGCTCCAATTTTTCTGCGCAAACAGCTCCAATTTTTCCTGCA
1 CAAACAGCTCCAATTTTTCTGCACAAACAGCTCCAATTTTT-CTGCA
*
13699552 CAAACAGCTCCAATTTTTCTGCACAAATAGCTCCAATTTTTCTGCA
1 CAAACAGCTCCAATTTTTCTGCACAAACAGCTCCAATTTTTCTGCA
13699598 CAAA
1 CAAA
13699602 TTGGCAGCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 9 0.19
47 39 0.81
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.30
Consensus pattern (46 bp):
CAAACAGCTCCAATTTTTCTGCACAAACAGCTCCAATTTTTCTGCA
Found at i:13699602 original size:23 final size:23
Alignment explanation
Indices: 13699505--13699601 Score: 167
Period size: 23 Copynumber: 4.2 Consensus size: 23
13699495 AAATTGGCAG
*
13699505 CAAACAGCTCCAATTTTTCTGCG
1 CAAACAGCTCCAATTTTTCTGCA
13699528 CAAACAGCTCCAATTTTTCCTGCA
1 CAAACAGCTCCAATTTTT-CTGCA
13699552 CAAACAGCTCCAATTTTTCTGCA
1 CAAACAGCTCCAATTTTTCTGCA
*
13699575 CAAATAGCTCCAATTTTTCTGCA
1 CAAACAGCTCCAATTTTTCTGCA
13699598 CAAA
1 CAAA
13699602 TTGGCAGCAA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
23 49 0.69
24 22 0.31
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.30
Consensus pattern (23 bp):
CAAACAGCTCCAATTTTTCTGCA
Found at i:13699618 original size:34 final size:34
Alignment explanation
Indices: 13699575--13699644 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
13699565 TTTTTCTGCA
*
13699575 CAAATAGCTCCAATTTTTCTGCACAAATTGGCAG
1 CAAATAGCTCCAATTTTTCTCCACAAATTGGCAG
13699609 CAAATAGCTCCAATTTTTCTCCACAAATTGGCAG
1 CAAATAGCTCCAATTTTTCTCCACAAATTGGCAG
13699643 CA
1 CA
13699645 CTTTGCTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.29
Consensus pattern (34 bp):
CAAATAGCTCCAATTTTTCTCCACAAATTGGCAG
Found at i:13704764 original size:102 final size:102
Alignment explanation
Indices: 13704588--13705096 Score: 1018
Period size: 102 Copynumber: 5.0 Consensus size: 102
13704578 CCTCTCCGTT
13704588 CGAGGTACATATATAACCGGATTTCGTGCCCTTCTAATAGGCTGGTCCACAGAATCTGCCCACTG
1 CGAGGTACATATATAACCGGATTTCGTGCCCTTCTAATAGGCTGGTCCACAGAATCTGCCCACTG
13704653 CAGCAAGCTAAACCCACCATGCAATAAAATTTACAAC
66 CAGCAAGCTAAACCCACCATGCAATAAAATTTACAAC
13704690 CGAGGTACATATATAACCGGATTTCGTGCCCTTCTAATAGGCTGGTCCACAGAATCTGCCCACTG
1 CGAGGTACATATATAACCGGATTTCGTGCCCTTCTAATAGGCTGGTCCACAGAATCTGCCCACTG
13704755 CAGCAAGCTAAACCCACCATGCAATAAAATTTACAAC
66 CAGCAAGCTAAACCCACCATGCAATAAAATTTACAAC
13704792 CGAGGTACATATATAACCGGATTTCGTGCCCTTCTAATAGGCTGGTCCACAGAATCTGCCCACTG
1 CGAGGTACATATATAACCGGATTTCGTGCCCTTCTAATAGGCTGGTCCACAGAATCTGCCCACTG
13704857 CAGCAAGCTAAACCCACCATGCAATAAAATTTACAAC
66 CAGCAAGCTAAACCCACCATGCAATAAAATTTACAAC
13704894 CGAGGTACATATATAACCGGATTTCGTGCCCTTCTAATAGGCTGGTCCACAGAATCTGCCCACTG
1 CGAGGTACATATATAACCGGATTTCGTGCCCTTCTAATAGGCTGGTCCACAGAATCTGCCCACTG
13704959 CAGCAAGCTAAACCCACCATGCAATAAAATTTACAAC
66 CAGCAAGCTAAACCCACCATGCAATAAAATTTACAAC
13704996 CGAGGTACATATATAACCGGATTTCGTGCCCTTCTAATAGGCTGGTCCACAGAATCTGCCCACTG
1 CGAGGTACATATATAACCGGATTTCGTGCCCTTCTAATAGGCTGGTCCACAGAATCTGCCCACTG
13705061 CAGCAAGCTAAACCCACCATGCAATAAAATTTACAA
66 CAGCAAGCTAAACCCACCATGCAATAAAATTTACAA
13705097 TAGCATGACA
Statistics
Matches: 407, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 407 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (102 bp):
CGAGGTACATATATAACCGGATTTCGTGCCCTTCTAATAGGCTGGTCCACAGAATCTGCCCACTG
CAGCAAGCTAAACCCACCATGCAATAAAATTTACAAC
Found at i:13708548 original size:26 final size:25
Alignment explanation
Indices: 13708476--13708566 Score: 137
Period size: 25 Copynumber: 3.5 Consensus size: 25
13708466 TATTTATTTT
*
13708476 TTTATTTTCTATTGGGCCATGCCCA
1 TTTATTTTCTATTGGGTCATGCCCA
*
13708501 CTTATTTTCTATTGGGTCATGCCCA
1 TTTATTTTCTATTGGGTCATGCCCA
13708526 TTTATTTTCTATTTGGGTCATGCCCA
1 TTTATTTTCTA-TTGGGTCATGCCCA
13708552 TTTTTATTTTCTATT
1 --TTTATTTTCTATT
13708567 TCTTTTCTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
25 33 0.55
26 14 0.23
27 2 0.03
28 11 0.18
ACGTcount: A:0.15, C:0.20, G:0.13, T:0.52
Consensus pattern (25 bp):
TTTATTTTCTATTGGGTCATGCCCA
Found at i:13708588 original size:11 final size:11
Alignment explanation
Indices: 13708552--13708590 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
13708542 GTCATGCCCA
*
13708552 TTTTTATTTTC
1 TTTTTCTTTTC
*
13708563 TATTTCTTTTC
1 TTTTTCTTTTC
13708574 TTTTTCTTTT-
1 TTTTTCTTTTC
13708584 TTTTTCT
1 TTTTTCT
13708591 CTCTTTCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:13708637 original size:22 final size:22
Alignment explanation
Indices: 13708609--13708656 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
13708599 CCGTCACTCC
*
13708609 CTTCACCACCATGTCTTCCTCT
1 CTTCACCACCATGGCTTCCTCT
*
13708631 CTTCACCACCGTGGCTTCCTCT
1 CTTCACCACCATGGCTTCCTCT
13708653 CTTC
1 CTTC
13708657 CTTGGGTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.10, C:0.46, G:0.08, T:0.35
Consensus pattern (22 bp):
CTTCACCACCATGGCTTCCTCT
Found at i:13708809 original size:24 final size:23
Alignment explanation
Indices: 13708767--13708855 Score: 133
Period size: 23 Copynumber: 3.8 Consensus size: 23
13708757 CACAATGCTG
13708767 TCCAATTTTTCTGCACAAACAGC
1 TCCAATTTTTCTGCACAAACAGC
* * *
13708790 TCTAATTTTTCTACAGCAAACAAC
1 TCCAATTTTTCTGCA-CAAACAGC
13708814 TCCAATTTTTTCTGCACAAACAGC
1 TCCAA-TTTTTCTGCACAAACAGC
13708838 TCCAATTTTTCTGCACAA
1 TCCAATTTTTCTGCACAA
13708856 TTTTTTTGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
23 26 0.45
24 23 0.40
25 9 0.16
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (23 bp):
TCCAATTTTTCTGCACAAACAGC
Found at i:13709058 original size:24 final size:26
Alignment explanation
Indices: 13709024--13709071 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
13709014 AAAAATCAGC
*
13709024 TTTCTTACCT-CAAAAATTTCAGCTT
1 TTTCTTACCTCCAAAAATTGCAGCTT
13709049 TTTCTT-CCTCCAAAAATTGCAGC
1 TTTCTTACCTCCAAAAATTGCAGC
13709072 AAAAAGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.40
Consensus pattern (26 bp):
TTTCTTACCTCCAAAAATTGCAGCTT
Found at i:13714317 original size:38 final size:37
Alignment explanation
Indices: 13714264--13714339 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 37
13714254 CTCAGCTCTA
*
13714264 GTGCACTCCCTACTCGCACATTTCAAAATCATCATCAT
1 GTGCACTCCCCACTCGCACATTTCAAAATCATCA-CAT
* *
13714302 GTGCACTCCCCACTCGTACATTTCAATATCATCACAT
1 GTGCACTCCCCACTCGCACATTTCAAAATCATCACAT
13714339 G
1 G
13714340 CACTCTCGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 4 0.11
38 31 0.89
ACGTcount: A:0.28, C:0.34, G:0.09, T:0.29
Consensus pattern (37 bp):
GTGCACTCCCCACTCGCACATTTCAAAATCATCACAT
Found at i:13716404 original size:20 final size:20
Alignment explanation
Indices: 13716379--13716416 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13716369 CTTCCTTCAA
*
13716379 CTTTAACAAATTGAAATGAG
1 CTTTAACAAATTAAAATGAG
*
13716399 CTTTAACCAATTAAAATG
1 CTTTAACAAATTAAAATG
13716417 TCTATAAATT
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:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (20 bp):
CTTTAACAAATTAAAATGAG
Found at i:13719151 original size:27 final size:27
Alignment explanation
Indices: 13719119--13719174 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
13719109 TTTATGGCTA
*
13719119 TTGGGCCATGCCCATTTTTCTTTATTG
1 TTGGGCCATGCCCATTTTCCTTTATTG
*
13719146 TTGGGCCATGCCCATTTTCCTTTCTTG
1 TTGGGCCATGCCCATTTTCCTTTATTG
13719173 TT
1 TT
13719175 ACTTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.09, C:0.25, G:0.18, T:0.48
Consensus pattern (27 bp):
TTGGGCCATGCCCATTTTCCTTTATTG
Found at i:13719185 original size:5 final size:5
Alignment explanation
Indices: 13719177--13719209 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
13719167 TTCTTGTTAC
13719177 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
13719210 ATTTCTTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:13719416 original size:33 final size:34
Alignment explanation
Indices: 13719351--13719460 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 34
13719341 CCTTCAATTT
*
13719351 TCAGCAGCTAAAGCTGCTCATATTGGCT--TC-AAAA
1 TCAGCAGCT-AAGCTGCTC-TATT-TCTCCTCAAAAA
13719385 TCAGCAGCTAAGCTGCTCTATTTCTCCTCAAAAAA
1 TCAGCAGCTAAGCTGCTCTATTTCTCCTC-AAAAA
* *
13719420 TCAGCAACTAAGCTACTCT-TTT-TCCTCTAAAAA
1 TCAGCAGCTAAGCTGCTCTATTTCTCCTC-AAAAA
*
13719453 TTAGCAGC
1 TCAGCAGC
13719461 CAAAACAACA
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
31 2 0.03
32 4 0.06
33 27 0.41
34 12 0.18
35 21 0.32
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (34 bp):
TCAGCAGCTAAGCTGCTCTATTTCTCCTCAAAAA
Found at i:13719431 original size:35 final size:33
Alignment explanation
Indices: 13719381--13719458 Score: 102
Period size: 35 Copynumber: 2.3 Consensus size: 33
13719371 TATTGGCTTC
* *
13719381 AAAATCAGCAGCTAAGCTGCTCTATTTCTCCTCAA
1 AAAATCAGCAACTAAGCTACTCT-TTT-TCCTCAA
*
13719416 AAAATCAGCAACTAAGCTACTCTTTTTCCTCTA
1 AAAATCAGCAACTAAGCTACTCTTTTTCCTCAA
*
13719449 AAAATTAGCA
1 AAAATCAGCA
13719459 GCCAAAACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 15 0.38
34 3 0.08
35 21 0.54
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.29
Consensus pattern (33 bp):
AAAATCAGCAACTAAGCTACTCTTTTTCCTCAA
Found at i:13722250 original size:52 final size:52
Alignment explanation
Indices: 13722160--13722258 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 52
13722150 ATAACATCAC
* * *
13722160 AAGCATTTGGTACCTATGCCTTAGTAATTGATTATGCTCAGAGGATAAAGAT
1 AAGCATTTGGTACCTATGCCTTAGCAATTGACTATGCTCAAAGGATAAAGAT
* * * *
13722212 AAGCATTTGGTACCTTTGCCTTAGCAGTTGGCTGTGCTCAAAGGATA
1 AAGCATTTGGTACCTATGCCTTAGCAATTGACTATGCTCAAAGGATA
13722259 GAAATGAGGA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 40 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.32
Consensus pattern (52 bp):
AAGCATTTGGTACCTATGCCTTAGCAATTGACTATGCTCAAAGGATAAAGAT
Found at i:13726198 original size:19 final size:15
Alignment explanation
Indices: 13726148--13726185 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
13726138 TAAAATAAAA
13726148 ATTAATATTTTAAATT
1 ATTAAT-TTTTAAATT
13726164 ATTAATTTTTAAATT
1 ATTAATTTTTAAATT
13726179 ATTAATT
1 ATTAATT
13726186 GAAATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTAATTTTTAAATT
Found at i:13726332 original size:51 final size:51
Alignment explanation
Indices: 13726271--13726373 Score: 122
Period size: 51 Copynumber: 2.0 Consensus size: 51
13726261 ATTATATATT
*
13726271 ATAAAATATTTTGAATTTAAAAATT-AATTA-AAAGTATTAATATTTT-AATC
1 ATAAAATA-TTT-AAATTAAAAATTAAATTACAAAGTATTAATATTTTCAATC
* * *
13726321 ATAATAATATTTAAATTATAAATTAAATTACCAATTATTAATATTTTCAATC
1 ATAA-AATATTTAAATTAAAAATTAAATTACAAAGTATTAATATTTTCAATC
13726373 A
1 A
13726374 ATTATAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
49 10 0.22
50 12 0.27
51 18 0.40
52 5 0.11
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (51 bp):
ATAAAATATTTAAATTAAAAATTAAATTACAAAGTATTAATATTTTCAATC
Found at i:13726341 original size:17 final size:17
Alignment explanation
Indices: 13726308--13726341 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13726298 TTAAAAGTAT
*
13726308 TAATATTTTAATCATAA
1 TAATATTTAAATCATAA
*
13726325 TAATATTTAAATTATAA
1 TAATATTTAAATCATAA
13726342 ATTAAATTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATTTAAATCATAA
Found at i:13726540 original size:23 final size:23
Alignment explanation
Indices: 13726483--13726556 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
13726473 TAAATTACAA
* * *
13726483 ATAAAATATTAATACTTAAATA-
1 ATAAATTATTAATATTTAAAAAT
* *
13726505 ATCAACTATTAATATTTAAAAAT
1 ATAAATTATTAATATTTAAAAAT
13726528 ATAAATTATTAATATTTAAAAGAT
1 ATAAATTATTAATATTTAAAA-AT
13726552 A-AAAT
1 ATAAAT
13726557 AAAATAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.41
23 23 0.52
24 3 0.07
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (23 bp):
ATAAATTATTAATATTTAAAAAT
Found at i:13726553 original size:22 final size:21
Alignment explanation
Indices: 13726481--13726557 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 21
13726471 ATTAAATTAC
*
13726481 AAATAAAATATTAATACTTAA
1 AAATAAAATATTAATATTTAA
* *
13726502 ATAATCAACTATTAATATTTAA
1 A-AATAAAATATTAATATTTAA
13726524 AAATATAAATTATTAATATTTAA
1 AAATA-AAA-TATTAATATTTAA
13726547 AAGATAAAATA
1 AA-ATAAAATA
13726558 AAATAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.09
22 22 0.47
23 18 0.38
24 3 0.06
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (21 bp):
AAATAAAATATTAATATTTAA
Found at i:13726596 original size:127 final size:130
Alignment explanation
Indices: 13726460--13726723 Score: 369
Period size: 127 Copynumber: 2.1 Consensus size: 130
13726450 TAGTATTTTA
*
13726460 TAATATTAATGATTAAATTACAAATAAAATATTAATACTTAAA-TAATCAACTATTAATA-TTT-
1 TAATATTAATGATTAAAGTACAAATAAAATATTAATACTTAAACT-ATCAACTATTAATATTTTA
13726522 AA-AAA-TATAAATTATTAATATTTAAAAGATAAAATAAAATAAAAATAAATAATCACAATAACA
65 AATAAATTATAAATTATTAATATTTAAAA-ATAAAATAAAATAAAAATAAATAATCACAATAACA
13726585 TT
129 TT
* * * *
13726587 TAATATTAATGATTAAAGTATAAATAAAATATTAATATTTAAACTATCAATTTTTAATATTTTAA
1 TAATATTAATGATTAAAGTACAAATAAAATATTAATACTTAAACTATCAACTATTAATATTTTAA
* * ** * *
13726652 ATAAATTATACATTATTAATGTTTAAAAATAAAATAATTTAAAAATAAATAATCATAATAATATT
66 ATAAATTATAAATTATTAATATTTAAAAATAAAATAAAATAAAAATAAATAATCACAATAACATT
13726717 TAA-ATTA
1 TAATATTA
13726724 TAAATAAAAT
Statistics
Matches: 121, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
127 52 0.43
128 4 0.03
129 6 0.05
130 39 0.32
131 20 0.17
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (130 bp):
TAATATTAATGATTAAAGTACAAATAAAATATTAATACTTAAACTATCAACTATTAATATTTTAA
ATAAATTATAAATTATTAATATTTAAAAATAAAATAAAATAAAAATAAATAATCACAATAACATT
Found at i:13726701 original size:15 final size:16
Alignment explanation
Indices: 13726673--13726704 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
13726663 ATTATTAATG
13726673 TTTAAAAATAAAATAA
1 TTTAAAAATAAAATAA
13726689 TTTAAAAAT-AAATAA
1 TTTAAAAATAAAATAA
13726704 T
1 T
13726705 CATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTTAAAAATAAAATAA
Found at i:13726717 original size:26 final size:27
Alignment explanation
Indices: 13726680--13726730 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
13726670 ATGTTTAAAA
13726680 ATAAAATAATTTAAA-AATAAATAATC
1 ATAAAATAATTTAAATAATAAATAATC
*
13726706 ATAATAAT-ATTTAAATTATAAATAA
1 ATAA-AATAATTTAAATAATAAATAA
13726731 AATATTAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (27 bp):
ATAAAATAATTTAAATAATAAATAATC
Found at i:13726734 original size:20 final size:19
Alignment explanation
Indices: 13726706--13726780 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 19
13726696 ATAAATAATC
13726706 ATAATAATATTTAAATTATAA
1 ATAA-AATA-TTAAATTATAA
* *
13726727 ATAAAATATTAGTATTTTATA
1 ATAAAATATTA-AATTATA-A
*
13726748 ATATTAATGATTAAATTATAA
1 ATA-AAAT-ATTAAATTATAA
13726769 ATAAAATATTAA
1 ATAAAATATTAA
13726781 TATTTTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 8 0.18
20 12 0.27
21 12 0.27
22 8 0.18
23 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
ATAAAATATTAAATTATAA
Found at i:13726793 original size:22 final size:22
Alignment explanation
Indices: 13726725--13726798 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
13726715 TTTAAATTAT
*
13726725 AAATAAAATATTAGTATTTT-A
1 AAATAAAATATTAATATTTTAA
* * *
13726746 TAATATTAATGATTAA-A--TTAT
1 AAATA-AAAT-ATTAATATTTTAA
13726767 AAATAAAATATTAATATTTTAA
1 AAATAAAATATTAATATTTTAA
13726789 AAATAAAATA
1 AAATAAAATA
13726799 AAATAAAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
19 5 0.12
20 6 0.15
21 8 0.20
22 17 0.43
23 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
AAATAAAATATTAATATTTTAA
Found at i:13736135 original size:3 final size:3
Alignment explanation
Indices: 13736127--13736162 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
13736117 TATGTCGTAC
*
13736127 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGG AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
13736163 GAGGGGGGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:13748471 original size:13 final size:13
Alignment explanation
Indices: 13748453--13748484 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
13748443 CAACAACCCC
13748453 TATTTTTTATTTA
1 TATTTTTTATTTA
13748466 TA--TTTTATTTA
1 TATTTTTTATTTA
13748477 TATTTTTT
1 TATTTTTT
13748485 TAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.65
13 6 0.35
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTTTTATTTA
Found at i:13748473 original size:11 final size:11
Alignment explanation
Indices: 13748457--13748491 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
13748447 AACCCCTATT
13748457 TTTTATTTATA
1 TTTTATTTATA
13748468 TTTTATTTATA
1 TTTTATTTATA
13748479 TTTT-TTTA-A
1 TTTTATTTATA
13748488 TTTT
1 TTTT
13748492 TTTTCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 5 0.21
10 4 0.17
11 15 0.62
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTATA
Found at i:13761724 original size:2 final size:2
Alignment explanation
Indices: 13761714--13761753 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
13761704 CATGACACAC
* *
13761714 AT AT CT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13761754 CCATCATCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13761869 original size:41 final size:41
Alignment explanation
Indices: 13761818--13761943 Score: 146
Period size: 41 Copynumber: 3.0 Consensus size: 41
13761808 CACATGGCTG
* *
13761818 GGTCAACATCGACTTATGCGCACTCCTACTCGGACATAACC
1 GGTCATCATCGACTTATGCGCACTCCTACTCGCACATAACC
* * * * *
13761859 GGTCATCATCGGCTTATGGGCACTCCTACTTGCACATAGTCG
1 GGTCATCATCGACTTATGCGCACTCCTACTCGCACATA-ACC
* *
13761901 GGTCATCATCAGA-GTATGCGCACTCCTACTCGCACATAGCC
1 GGTCATCATC-GACTTATGCGCACTCCTACTCGCACATAACC
13761942 GG
1 GG
13761944 GTCCACATCA
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 36 0.51
42 33 0.47
43 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (41 bp):
GGTCATCATCGACTTATGCGCACTCCTACTCGCACATAACC
Found at i:13761953 original size:42 final size:42
Alignment explanation
Indices: 13761832--13761946 Score: 151
Period size: 42 Copynumber: 2.8 Consensus size: 42
13761822 AACATCGACT
* * * **
13761832 TATGCGCACTCCTACTCGGACATAACC-GGTCATCATCGGCT
1 TATGCGCACTCCTACTCGCACATAGCCGGGTCATCATCAGAG
* * *
13761873 TATGGGCACTCCTACTTGCACATAGTCGGGTCATCATCAGAG
1 TATGCGCACTCCTACTCGCACATAGCCGGGTCATCATCAGAG
13761915 TATGCGCACTCCTACTCGCACATAGCCGGGTC
1 TATGCGCACTCCTACTCGCACATAGCCGGGTC
13761947 CACATCAACA
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 22 0.35
42 40 0.65
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (42 bp):
TATGCGCACTCCTACTCGCACATAGCCGGGTCATCATCAGAG
Found at i:13763847 original size:16 final size:16
Alignment explanation
Indices: 13763826--13763860 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
13763816 AGGTCTTATT
13763826 TTTTTATTT-TATTTTA
1 TTTTTATTTCTA-TTTA
13763842 TTTTTATTTCTATTTA
1 TTTTTATTTCTATTTA
13763858 TTT
1 TTT
13763861 ATTTATTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTATTTCTATTTA
Found at i:13766724 original size:237 final size:236
Alignment explanation
Indices: 13766309--13766783 Score: 916
Period size: 237 Copynumber: 2.0 Consensus size: 236
13766299 AGCCTAGTTG
13766309 TTTATTTGGTTGAAATGAGTTGAAAGGTAATGAAATTACAATATGATGACTTATTTTAATTCGTC
1 TTTATTTGGTTGAAATGAGTTGAAAGGTAATGAAATTACAATATGATGACTTATTTTAATTCGTC
*
13766374 TCCATTTACTCGCCTTTAGATAGTTTAGATGGTGTCTGTTTACTCACGGGATTTTATAATCTCAC
66 CCCATTTACTCGCCTTTAGATAGTTTAGATGGTGTCTGTTTACTCACGGGATTTTATAATCTCAC
13766439 CACCCTCATTTCAGAACATTTCAGGCTCGGGGAATTTCATAGTTAACTGACTTTGACAAGGACCT
131 CACCCTCATTTCAGAACATTTCAGGCTCGGGGAATTTCATAGTTAACTGACTTTGACAAGGACCT
13766504 TCATTTGGACTTGAATCCGCAAAAGCTGTAAGTTTTGAGCT
196 TCATTTGGACTTGAATCCGCAAAAGCTGTAAGTTTTGAGCT
13766545 NTTTATTTGGTTG-AATGAGTTGAAAAGGTAATGAAATTACAATATGATGACTTATTTTAATTCG
1 -TTTATTTGGTTGAAATGAGTTG-AAAGGTAATGAAATTACAATATGATGACTTATTTTAATTCG
13766609 TCCCCATTTACTCGCCTTTAGATAGTTTAGATGGTGTCTGTTTACTCACGGGATTTTATAATCTC
64 TCCCCATTTACTCGCCTTTAGATAGTTTAGATGGTGTCTGTTTACTCACGGGATTTTATAATCTC
13766674 ACCACCCTCATTTCAGAACATTTCAGGCTCGGGGAATTTCATAGTTAACTGACTTTGACAAGGAC
129 ACCACCCTCATTTCAGAACATTTCAGGCTCGGGGAATTTCATAGTTAACTGACTTTGACAAGGAC
13766739 CTTCATTTGGACTTGAATCCGCAAAAGCTGTAAGTTTTGAGCT
194 CTTCATTTGGACTTGAATCCGCAAAAGCTGTAAGTTTTGAGCT
13766782 TT
1 TT
13766784 CGATACATTT
Statistics
Matches: 236, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
236 11 0.05
237 225 0.95
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (236 bp):
TTTATTTGGTTGAAATGAGTTGAAAGGTAATGAAATTACAATATGATGACTTATTTTAATTCGTC
CCCATTTACTCGCCTTTAGATAGTTTAGATGGTGTCTGTTTACTCACGGGATTTTATAATCTCAC
CACCCTCATTTCAGAACATTTCAGGCTCGGGGAATTTCATAGTTAACTGACTTTGACAAGGACCT
TCATTTGGACTTGAATCCGCAAAAGCTGTAAGTTTTGAGCT
Found at i:13771428 original size:22 final size:21
Alignment explanation
Indices: 13771374--13771438 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
13771364 GCTTCTCTAT
* *
13771374 AGGAAGAATCGATCTCTTGAAA
1 AGGAAAAATTGAT-TCTTGAAA
13771396 AGGAAAAATTGATTCTATGAAA
1 AGGAAAAATTGATTCT-TGAAA
* * *
13771418 AGGAGATATTGGTTCTTGAAA
1 AGGAAAAATTGATTCTTGAAA
13771439 GATAGAAGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 8 0.22
22 29 0.78
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.28
Consensus pattern (21 bp):
AGGAAAAATTGATTCTTGAAA
Found at i:13772541 original size:30 final size:31
Alignment explanation
Indices: 13772489--13772559 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
13772479 CATTATTGTT
13772489 GGTTATACCTCCACATAAAAGGTAGTG-TAAA
1 GGTTATACCTCCACATAAAAGGTAGTGCT-AA
** *
13772520 GGTTATACCTCCTTA-AAAAGGTATTGCTAA
1 GGTTATACCTCCACATAAAAGGTAGTGCTAA
13772550 GGTTATACCT
1 GGTTATACCT
13772560 TCTTTGGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.61
31 14 0.39
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (31 bp):
GGTTATACCTCCACATAAAAGGTAGTGCTAA
Found at i:13772652 original size:30 final size:30
Alignment explanation
Indices: 13772550--13772652 Score: 75
Period size: 30 Copynumber: 3.4 Consensus size: 30
13772540 GTATTGCTAA
*
13772550 GGTTATACCTTCTTTGGAAAAAATAAG-ATT
1 GGTTATACCTTCTTTGGAAAAAGT-AGTATT
** * * **
13772580 GGTTATACCTTC-GAGCAAAATGTAGTGCAAA
1 GGTTATACCTTCTTTGGAAAAAGTAGT--ATT
* * *
13772611 GGATGTACCTTCTTTGGAAAAGGTAGTATT
1 GGTTATACCTTCTTTGGAAAAAGTAGTATT
13772641 GGTTATACCTTC
1 GGTTATACCTTC
13772653 GACCAAAAGG
Statistics
Matches: 52, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
28 2 0.04
29 6 0.12
30 23 0.44
31 11 0.21
32 10 0.19
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (30 bp):
GGTTATACCTTCTTTGGAAAAAGTAGTATT
Found at i:13773930 original size:21 final size:21
Alignment explanation
Indices: 13773901--13773962 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
13773891 ACCCGAGAGT
* *
13773901 TTCTCGCTGTAGCGAAAATGA
1 TTCTAGCTGCAGCGAAAATGA
13773922 TTCTAGCTGCAGCGAAAATGA
1 TTCTAGCTGCAGCGAAAATGA
**
13773943 TTCTATTTGCAGCGAGAAAT
1 TTCTAGCTGCAGCGA-AAAT
13773963 AGGGCACCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 32 0.89
22 4 0.11
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (21 bp):
TTCTAGCTGCAGCGAAAATGA
Found at i:13774216 original size:26 final size:23
Alignment explanation
Indices: 13774155--13774214 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
13774145 TATACGTATA
*
13774155 CCCATCATCATCATGCACACCAT
1 CCCATCATCATCATACACACCAT
13774178 CCCATCATCATCATACACACCAT
1 CCCATCATCATCATACACACCAT
*
13774201 CACATCATCATCAT
1 CCCATCATCATCAT
13774215 CACCAGCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.42, G:0.02, T:0.23
Consensus pattern (23 bp):
CCCATCATCATCATACACACCAT
Done.