Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 33 of 59
Found at i:12042334 original size:19 final size:20
Alignment explanation
Indices: 12042310--12042347 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12042300 CTATAAATAC
12042310 CTTGAA-TTTCTAGCAGCTT
1 CTTGAATTTTCTAGCAGCTT
12042329 CTTGAATTTTCTAGCAGCT
1 CTTGAATTTTCTAGCAGCT
12042348 GGTCTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (20 bp):
CTTGAATTTTCTAGCAGCTT
Found at i:12043190 original size:43 final size:43
Alignment explanation
Indices: 12043133--12043264 Score: 162
Period size: 43 Copynumber: 3.1 Consensus size: 43
12043123 ATAATTATAT
*
12043133 TGACTCAGCTATGTGCGAGTAGGGAGTGCGCATAAGC-CGAG-GA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAA-CTCG-GTGA
* * *
12043176 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACTTGGTGA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAACTCGGTGA
* *
12043219 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCATGAGCT-GGTGA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCGCAT-AACTCGGTGA
12043262 TGA
1 TGA
12043265 TGATGATGGG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
42 2 0.03
43 73 0.94
44 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (43 bp):
TGACCCAGCTATGTGCGAGTAGGGAGTGCGCATAACTCGGTGA
Found at i:12043309 original size:8 final size:8
Alignment explanation
Indices: 12043296--12043329 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
12043286 ATGATGATGG
12043296 GTATATAT
1 GTATATAT
12043304 GTATATAT
1 GTATATAT
*
12043312 ATATATAT
1 GTATATAT
*
12043320 GTAAATAT
1 GTATATAT
12043328 GT
1 GT
12043330 GGGTTATAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (8 bp):
GTATATAT
Found at i:12044769 original size:22 final size:22
Alignment explanation
Indices: 12044744--12044786 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
12044734 CCTTTTTCCC
*
12044744 TTTTCTTTTTGTTA-TTTCTTAG
1 TTTTCTTTCT-TTAGTTTCTTAG
*
12044766 TTTTGTTTCTTTAGTTTCTTA
1 TTTTCTTTCTTTAGTTTCTTA
12044787 TTAGACTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.72
Consensus pattern (22 bp):
TTTTCTTTCTTTAGTTTCTTAG
Found at i:12046628 original size:29 final size:29
Alignment explanation
Indices: 12046511--12046721 Score: 202
Period size: 29 Copynumber: 7.4 Consensus size: 29
12046501 TATGGTACCC
* **
12046511 ACAAAG-TCTAAAAGGTGCTAAGGTGCCTA
1 ACAAAGTTC-AAAAGGTGCAAAGGCACCTA
* *
12046540 ATAAAG-TCAAATGGTGCTAAA-GCACCTA
1 ACAAAGTTCAAAAGGTGC-AAAGGCACCTA
*
12046568 ACAAAGTTCAAAAGGT---AA-GCACCTT
1 ACAAAGTTCAAAAGGTGCAAAGGCACCTA
** * *
12046593 ACAAAGTTCCGAATGTGCCAAGGCACCTA
1 ACAAAGTTCAAAAGGTGCAAAGGCACCTA
* *
12046622 ACAAAGTTCAAAAGGTACTAAGGCACCTA
1 ACAAAGTTCAAAAGGTGCAAAGGCACCTA
* * *
12046651 ATAAAGTTTAAAAGGTGAAAAGGCACCTA
1 ACAAAGTTCAAAAGGTGCAAAGGCACCTA
*
12046680 ATAAAGTTCAAAAGGTGCAAAGGCACCTA
1 ACAAAGTTCAAAAGGTGCAAAGGCACCTA
*
12046709 ACAAGGTTCAAAA
1 ACAAAGTTCAAAA
12046722 ATGTGAAAAC
Statistics
Matches: 150, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
25 21 0.14
28 20 0.13
29 109 0.73
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (29 bp):
ACAAAGTTCAAAAGGTGCAAAGGCACCTA
Found at i:12048481 original size:55 final size:55
Alignment explanation
Indices: 12048395--12048548 Score: 227
Period size: 55 Copynumber: 2.8 Consensus size: 55
12048385 AACTACTAGC
**
12048395 TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCATCAACCTG
1 TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCATCAACCAA
* * * ** *
12048450 TCATCAACTCATGTGCACTCCCACACCGCACATAACTAAAATCATCATCCACCAA
1 TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCATCAACCAA
*
12048505 TCATCAGCTCATGTGCACTCCCACACTGCACATAGTTGGAATCA
1 TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCA
12048549 CACGTCATCA
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 85 1.00
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.23
Consensus pattern (55 bp):
TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCATCAACCAA
Found at i:12048618 original size:110 final size:109
Alignment explanation
Indices: 12048395--12048588 Score: 265
Period size: 110 Copynumber: 1.8 Consensus size: 109
12048385 AACTACTAGC
*
12048395 TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAATCATCATCAACCTGTCATCAACTC
1 TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAA-CATCATCAACCTGTCATCAACGC
* *
12048460 ATGTGCACTCCCACACCGCACATAACTAAAATCATCATCCACCAA
65 ATGTGCACTCCCACACCGCACACAACTAAAATCATCATCCAACAA
* *
12048505 TCATCAGCTCATGTGCACTCCCACACTGCACATAGTTGG-A-ATCA-C-A-C-GTCATCACCGGC
1 TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAACATCATCAACCTGTCATCAAC-GC
**
12048564 ATGTGCACTCCCACATTGCACACAA
65 ATGTGCACTCCCACACCGCACACAA
12048589 GCGGTTACAA
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
103 8 0.10
104 24 0.31
105 1 0.01
106 1 0.01
107 4 0.05
109 1 0.01
110 38 0.49
ACGTcount: A:0.30, C:0.36, G:0.12, T:0.22
Consensus pattern (109 bp):
TCATCAGCTCATGTGCACTCCCACACTGCACATAGCTGGAACATCATCAACCTGTCATCAACGCA
TGTGCACTCCCACACCGCACACAACTAAAATCATCATCCAACAA
Found at i:12057048 original size:2 final size:2
Alignment explanation
Indices: 12057041--12057074 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12057031 GGGTATTACA
*
12057041 GT GT GT GT AT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
12057075 TTGTATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
GT
Found at i:12072230 original size:24 final size:25
Alignment explanation
Indices: 12072203--12072261 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
12072193 GTCGTTGCAA
* *
12072203 CCACGTATATCAACT-GTGGCCTAG
1 CCACATATAACAACTCGTGGCCTAG
*
12072227 CCACATATAACAACTCGTGGCCTTG
1 CCACATATAACAACTCGTGGCCTAG
12072252 CCACATATAA
1 CCACATATAA
12072262 TCACGGACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 13 0.42
25 18 0.58
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.24
Consensus pattern (25 bp):
CCACATATAACAACTCGTGGCCTAG
Found at i:12075961 original size:58 final size:53
Alignment explanation
Indices: 12075824--12075979 Score: 170
Period size: 58 Copynumber: 2.8 Consensus size: 53
12075814 TGCAAAGGTG
*
12075824 CCTAATAAAG-TCAACGGTGCTAAGGCACCTAACAAAGTTCAAAAGGTACGCA
1 CCTAATAAAGTTCAAAGGTGCTAAGGCACCTAACAAAGTTCAAAAGGTACGCA
* * * *
12075876 CCTTACAAAGTTTCATAGGTGCTAAGGCACCTAACAAAGTTCTAAAGGTACTAACGCA
1 CCTAATAAAG-TTCAAAGGTGCTAAGGCACCTAACAAAGTTCAAAAGG---T-ACGCA
* * * *
12075934 CCTAATAAAGTTCAAAAGGTGCAAAGGCACTTAACAAGGTTAAAAA
1 CCTAATAAAGTTC-AAAGGTGCTAAGGCACCTAACAAAGTTCAAAA
12075980 ATGTGAAAAC
Statistics
Matches: 84, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
52 8 0.10
54 33 0.39
57 4 0.05
58 39 0.46
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (53 bp):
CCTAATAAAGTTCAAAGGTGCTAAGGCACCTAACAAAGTTCAAAAGGTACGCA
Found at i:12075979 original size:29 final size:29
Alignment explanation
Indices: 12075809--12075979 Score: 140
Period size: 29 Copynumber: 6.1 Consensus size: 29
12075799 TATAGAATCT
* ** *
12075809 AAAGGTGCAAAGGTGCCTAATAAAGT-C-
1 AAAGGTGCTAAGGCACCTAACAAAGTTCA
*
12075836 AACGGTGCTAAGGCACCTAACAAAGTTCA
1 AAAGGTGCTAAGGCACCTAACAAAGTTCA
* *
12075865 AAA-G-G-T-ACGCACCTTACAAAGTTTC-
1 AAAGGTGCTAAGGCACCTAACAAAG-TTCA
* *
12075890 ATAGGTGCTAAGGCACCTAACAAAGTTCT
1 AAAGGTGCTAAGGCACCTAACAAAGTTCA
* * *
12075919 AAAGGTACTAACGCACCTAATAAAGTTCA
1 AAAGGTGCTAAGGCACCTAACAAAGTTCA
* * * *
12075948 AAAGGTGCAAAGGCACTTAACAAGGTTAA
1 AAAGGTGCTAAGGCACCTAACAAAGTTCA
12075977 AAA
1 AAA
12075980 ATGTGAAAAC
Statistics
Matches: 113, Mismatches: 23, Indels: 14
0.75 0.15 0.09
Matches are distributed among these distances:
25 15 0.13
26 5 0.04
27 23 0.20
28 6 0.05
29 64 0.57
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (29 bp):
AAAGGTGCTAAGGCACCTAACAAAGTTCA
Found at i:12096338 original size:13 final size:13
Alignment explanation
Indices: 12096320--12096344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12096310 TTTCAGAAAA
12096320 TTTATAAAATCAT
1 TTTATAAAATCAT
12096333 TTTATAAAATCA
1 TTTATAAAATCA
12096345 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:12097504 original size:27 final size:28
Alignment explanation
Indices: 12097474--12097527 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
12097464 ATGTCCTGGT
*
12097474 GGTGG-AAAATTACAATTTTGCCCCTAG
1 GGTGGCAAAATTACAATTTTACCCCTAG
*
12097501 GGTGGCAAAATTACCATTTTACCCCTA
1 GGTGGCAAAATTACAATTTTACCCCTA
12097528 TGCTCCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (28 bp):
GGTGGCAAAATTACAATTTTACCCCTAG
Found at i:12098965 original size:37 final size:36
Alignment explanation
Indices: 12098924--12099037 Score: 156
Period size: 37 Copynumber: 3.1 Consensus size: 36
12098914 ATACATCGTA
*
12098924 ATCATGTGTGCACTCCCTACTCGCACAATCTATCATC
1 ATCATGTGTGCACTCCCTACTCGCACACTC-ATCATC
*
12098961 ATCATGTGTGCACTCCCTACCCGCACACTCCATCATC
1 ATCATGTGTGCACTCCCTACTCGCACACT-CATCATC
* * * *
12098998 ATCAAGTGTGCACTCCGTACTTGCACACTCAACATC
1 ATCATGTGTGCACTCCCTACTCGCACACTCATCATC
12099034 ATCA
1 ATCA
12099038 CCTAACATCA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 10 0.14
37 58 0.84
38 1 0.01
ACGTcount: A:0.25, C:0.37, G:0.11, T:0.26
Consensus pattern (36 bp):
ATCATGTGTGCACTCCCTACTCGCACACTCATCATC
Found at i:12099833 original size:3 final size:3
Alignment explanation
Indices: 12099825--12099864 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12099815 AACGTGAAAG
12099825 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
12099865 AAGCTGCTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12117273 original size:22 final size:22
Alignment explanation
Indices: 12117248--12117290 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
12117238 CCTTTTTCCT
*
12117248 TTTTCTTTTTGTTA-TTTCTTAG
1 TTTTCTTTCT-TTAGTTTCTTAG
*
12117270 TTTTGTTTCTTTAGTTTCTTA
1 TTTTCTTTCTTTAGTTTCTTA
12117291 TTGCACAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.72
Consensus pattern (22 bp):
TTTTCTTTCTTTAGTTTCTTAG
Found at i:12119049 original size:28 final size:26
Alignment explanation
Indices: 12118972--12119055 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 26
12118962 CAAAATCCAC
* *
12118972 AGGTGCTATGGCACCTACAAAGTCTAA
1 AGGTGCTAAGGCACCAACAAAGTC-AA
** *
12118999 AGGTGCTAAGGTGCCTAATAAAGTCAA
1 AGGTGCTAAGGCACC-AACAAAGTCAA
12119026 ACGGTGCTAAGGCACCGAACAAAGTTCAA
1 A-GGTGCTAAGGCACC-AACAAAG-TCAA
12119055 A
1 A
12119056 AGGTACGTAC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
27 15 0.33
28 25 0.56
29 5 0.11
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.19
Consensus pattern (26 bp):
AGGTGCTAAGGCACCAACAAAGTCAA
Found at i:12119132 original size:29 final size:29
Alignment explanation
Indices: 12118972--12119197 Score: 153
Period size: 29 Copynumber: 8.0 Consensus size: 29
12118962 CAAAATCCAC
* *
12118972 AGGTGCTATGGCACCT-ACAAAG-TCTAA
1 AGGTGCTAAGGCACCTAACAAAGTTCAAA
** *
12118999 AGGTGCTAAGGTGCCTAATAAAG-TCAAA
1 AGGTGCTAAGGCACCTAACAAAGTTCAAA
* *
12119027 CGGTGCTAAGGCACCGAACAAAGTTCAAA
1 AGGTGCTAAGGCACCTAACAAAGTTCAAA
* * * * *
12119056 A-G-G-T-ACGTACCTTACAAAGTTCTAG
1 AGGTGCTAAGGCACCTAACAAAGTTCAAA
** **
12119081 AGGTTTTAAGGCATGTAACAAAGTTCAAA
1 AGGTGCTAAGGCACCTAACAAAGTTCAAA
** * **
12119110 AGGTATTAAGGCACCTAATAAAGTTTGAA
1 AGGTGCTAAGGCACCTAACAAAGTTCAAA
* * *
12119139 AGGTGCAAAAGCACCTAATAAAGTTCAAA
1 AGGTGCTAAGGCACCTAACAAAGTTCAAA
* *
12119168 AGGTGC-AGAGGCACCTAACAAGGTTAAAA
1 AGGTGCTA-AGGCACCTAACAAAGTTCAAA
12119197 A
1 A
12119198 ATGTGAAAAC
Statistics
Matches: 151, Mismatches: 41, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
25 16 0.11
26 2 0.01
27 14 0.09
28 30 0.20
29 89 0.59
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (29 bp):
AGGTGCTAAGGCACCTAACAAAGTTCAAA
Found at i:12121276 original size:2 final size:2
Alignment explanation
Indices: 12121269--12121298 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12121259 GCAATGCCTT
12121269 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12121299 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:12121359 original size:2 final size:2
Alignment explanation
Indices: 12121352--12121399 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
12121342 TTGCCCTTTC
12121352 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12121394 CT CT CT
1 CT CT CT
12121400 ATGTTTAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12134509 original size:2 final size:2
Alignment explanation
Indices: 12134502--12134545 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12134492 TTAGCAATGC
12134502 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12134544 CT
1 CT
12134546 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12135970 original size:2 final size:2
Alignment explanation
Indices: 12135963--12136023 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
12135953 CAAATATTGC
12135963 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
12136005 CT CT CT TT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
12136024 CTTAATTACC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:12139908 original size:19 final size:20
Alignment explanation
Indices: 12139881--12139926 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
12139871 AGGAGACAAG
*
12139881 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
12139900 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
12139919 ATAATATT
1 ATAATATT
12139927 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:12141759 original size:13 final size:13
Alignment explanation
Indices: 12141741--12141765 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12141731 AGAGAAATTG
12141741 TGATTTTATAAAA
1 TGATTTTATAAAA
12141754 TGATTTTATAAA
1 TGATTTTATAAA
12141766 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:12146979 original size:81 final size:81
Alignment explanation
Indices: 12146844--12147005 Score: 315
Period size: 81 Copynumber: 2.0 Consensus size: 81
12146834 ACTCTCTCTC
12146844 CCTCTCTCTTTCTGTAAAGCCCGACCTTATAAAATACTAGTCATGACATACATGTGATGATAGCA
1 CCTCTCTCTTTCTGTAAAGCCCGACCTTATAAAATACTAGTCATGACATACATGTGATGATAGCA
12146909 TGATTGCATGCTAGAA
66 TGATTGCATGCTAGAA
*
12146925 CCTCTCTCTTTCTGTAAAGCCCGACCTTATAAAATATTAGTCATGACATACATGTGATGATAGCA
1 CCTCTCTCTTTCTGTAAAGCCCGACCTTATAAAATACTAGTCATGACATACATGTGATGATAGCA
12146990 TGATTGCATGCTAGAA
66 TGATTGCATGCTAGAA
12147006 GAGTCCCGAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (81 bp):
CCTCTCTCTTTCTGTAAAGCCCGACCTTATAAAATACTAGTCATGACATACATGTGATGATAGCA
TGATTGCATGCTAGAA
Found at i:12147383 original size:28 final size:27
Alignment explanation
Indices: 12147352--12147404 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
12147342 ATTTAGAGTA
*
12147352 TAGGGGTAAAATGGTAATTTTGCCACTC
1 TAGGGGCAAAATGGTAATTTT-CCACTC
12147380 TAGGGGCAAAATGGTAATTTTCCAC
1 TAGGGGCAAAATGGTAATTTTCCAC
12147405 CACCAGGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (27 bp):
TAGGGGCAAAATGGTAATTTTCCACTC
Found at i:12148742 original size:20 final size:20
Alignment explanation
Indices: 12148699--12148736 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12148689 TTTCGGTTCC
*
12148699 ATTTGACTTATTGGAGTATA
1 ATTTAACTTATTGGAGTATA
12148719 ATTTAACTTATTGGAGTA
1 ATTTAACTTATTGGAGTA
12148737 AGATTTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (20 bp):
ATTTAACTTATTGGAGTATA
Found at i:12148820 original size:27 final size:25
Alignment explanation
Indices: 12148790--12148848 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 25
12148780 TTGGAGTAAA
*
12148790 AGGGTAAAATGGTAATTTTGCCACCCC
1 AGGGT-AAATGGTAATTTT-CCACCAC
*
12148817 AGGGGCTAAATTGTAATTTTCCACCAC
1 A-GGG-TAAATGGTAATTTTCCACCAC
12148844 AGGGT
1 AGGGT
12148849 CTTCCTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
25 1 0.04
26 3 0.11
27 8 0.29
28 15 0.54
29 1 0.04
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (25 bp):
AGGGTAAATGGTAATTTTCCACCAC
Found at i:12157241 original size:13 final size:13
Alignment explanation
Indices: 12157223--12157247 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12157213 AGAGAAATTG
12157223 TGATTTTATAAAA
1 TGATTTTATAAAA
12157236 TGATTTTATAAA
1 TGATTTTATAAA
12157248 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:12161558 original size:13 final size:13
Alignment explanation
Indices: 12161540--12161564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12161530 TTTCAGAAAA
12161540 TTTATAAAATCAT
1 TTTATAAAATCAT
12161553 TTTATAAAATCA
1 TTTATAAAATCA
12161565 CAATTTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:12173643 original size:2 final size:2
Alignment explanation
Indices: 12173636--12173669 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
12173626 NNNNNNNNNN
*
12173636 CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12173670 TTAATTACCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:12173945 original size:23 final size:25
Alignment explanation
Indices: 12173900--12173947 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
12173890 TTTAATCAGT
*
12173900 TTTTTTGTCAAAAATGTTGTTGAAA
1 TTTTTTGTCAAAAATGTTATTGAAA
*
12173925 TTTTTTGT-TAAAA-GTTATTGAAA
1 TTTTTTGTCAAAAATGTTATTGAAA
12173948 AAATGATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 4 0.19
25 8 0.38
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (25 bp):
TTTTTTGTCAAAAATGTTATTGAAA
Found at i:12179792 original size:13 final size:13
Alignment explanation
Indices: 12179774--12179799 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12179764 GCGAGGTAAC
12179774 TAATTATTTGAAA
1 TAATTATTTGAAA
12179787 TAATTATTTGAAA
1 TAATTATTTGAAA
12179800 AAATGCAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TAATTATTTGAAA
Found at i:12184448 original size:27 final size:27
Alignment explanation
Indices: 12184418--12184499 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
12184408 GGCTCATGGC
* *
12184418 CAAAATCCATAGGTGCCATGGCACCTA
1 CAAAATCCAAAGGTGCCAAGGCACCTA
* *
12184445 CAAAGTCCAAAGGTGCTAAGGCACCTA
1 CAAAATCCAAAGGTGCCAAGGCACCTA
*
12184472 -ATAAAGT-CAAACGGTGCTAAGGCACCTA
1 CA-AAA-TCCAAA-GGTGCCAAGGCACCTA
12184500 ACGCAATTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.62
28 17 0.36
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.17
Consensus pattern (27 bp):
CAAAATCCAAAGGTGCCAAGGCACCTA
Found at i:12184567 original size:29 final size:28
Alignment explanation
Indices: 12184428--12184612 Score: 152
Period size: 29 Copynumber: 6.7 Consensus size: 28
12184418 CAAAATCCAT
* * *
12184428 AGGTGCCATGGCACCT-ACAAAGTCCAA
1 AGGTGCTAAGGCACCTAACAAAGTCAAA
*
12184455 AGGTGCTAAGGCACCTAATAAAGTCAAA
1 AGGTGCTAAGGCACCTAACAAAGTCAAA
* * * *
12184483 CGGTGCTAAGGCACCTAACGCAATTCAGA
1 AGGTGCTAAGGCACCTAAC-AAAGTCAAA
* * *
12184512 A-G-G-T---GCACCTTACAAAGCTCTAT
1 AGGTGCTAAGGCACCTAACAAAG-TCAAA
12184535 AGGTGCTAAGGCACCTAACAAAGATCAAA
1 AGGTGCTAAGGCACCTAACAAAG-TCAAA
*
12184564 AGGTGCAAAGGCACCTAACAAAGTTCAAA
1 AGGTGCTAAGGCACCTAACAAAG-TCAAA
*
12184593 AGGTTCTTAA-GCACCTAACA
1 AGGTGC-TAAGGCACCTAACA
12184613 GGGTTCAAAA
Statistics
Matches: 124, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
22 2 0.02
23 11 0.09
24 1 0.01
25 1 0.01
26 2 0.02
27 15 0.12
28 27 0.22
29 63 0.51
30 2 0.02
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.18
Consensus pattern (28 bp):
AGGTGCTAAGGCACCTAACAAAGTCAAA
Found at i:12184596 original size:81 final size:78
Alignment explanation
Indices: 12184438--12184596 Score: 212
Period size: 81 Copynumber: 2.0 Consensus size: 78
12184428 AGGTGCCATG
* * *
12184438 GCACCTACAAAGTCCAAAGGTGCTAAGGCACCTAATAAAGTCAAACGGTGCTAAGGCACCTAACG
1 GCACCTACAAAGTCCAAAGGTGCTAAGGCACCTAACAAAGTCAAAAGGTGCAAAGGCACCTAACG
* *
12184503 CAATTCAGAAGGT
66 AAATTCAAAAGGT
* *
12184516 GCACCTTACAAAGCTCTATAGGTGCTAAGGCACCTAACAAAGATCAAAAGGTGCAAAGGCACCTA
1 GCACC-TACAAAG-TCCAAAGGTGCTAAGGCACCTAACAAAG-TCAAAAGGTGCAAAGGCACCTA
12184581 AC-AAAGTTCAAAAGGT
63 ACGAAA-TTCAAAAGGT
12184597 TCTTAAGCAC
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
78 5 0.07
79 7 0.10
80 27 0.39
81 31 0.44
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (78 bp):
GCACCTACAAAGTCCAAAGGTGCTAAGGCACCTAACAAAGTCAAAAGGTGCAAAGGCACCTAACG
AAATTCAAAAGGT
Found at i:12187124 original size:25 final size:25
Alignment explanation
Indices: 12187096--12187205 Score: 121
Period size: 25 Copynumber: 4.4 Consensus size: 25
12187086 TAGTCTGTGA
*
12187096 TTATACGAGGCAAGGTCACGGGTTG
1 TTATACGTGGCAAGGTCACGGGTTG
* *
12187121 TTATGCGTGGCAAGGTCACGAGTTG
1 TTATACGTGGCAAGGTCACGGGTTG
* *
12187146 TTATGCGTGGCAAGGTCATGGGTTG
1 TTATACGTGGCAAGGTCACGGGTTG
* * * **
12187171 TTATACATGGCTAGGCCACTAGTTG
1 TTATACGTGGCAAGGTCACGGGTTG
*
12187196 ATATACGTGG
1 TTATACGTGG
12187206 TTGTGACCAC
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 71 1.00
ACGTcount: A:0.22, C:0.15, G:0.34, T:0.29
Consensus pattern (25 bp):
TTATACGTGGCAAGGTCACGGGTTG
Found at i:12187195 original size:50 final size:50
Alignment explanation
Indices: 12187097--12187205 Score: 137
Period size: 50 Copynumber: 2.2 Consensus size: 50
12187087 AGTCTGTGAT
* * * * *
12187097 TATACGAGGCAAGGTCACGGGTTGTTATGCGTGGCAAGGTCACGAGTTGT
1 TATACGTGGCAAGGTCACGGGTTGTTATACATGGCAAGGCCACGAGTTGA
* * * *
12187147 TATGCGTGGCAAGGTCATGGGTTGTTATACATGGCTAGGCCACTAGTTGA
1 TATACGTGGCAAGGTCACGGGTTGTTATACATGGCAAGGCCACGAGTTGA
12187197 TATACGTGG
1 TATACGTGG
12187206 TTGTGACCAC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.22, C:0.16, G:0.34, T:0.28
Consensus pattern (50 bp):
TATACGTGGCAAGGTCACGGGTTGTTATACATGGCAAGGCCACGAGTTGA
Found at i:12190905 original size:3 final size:3
Alignment explanation
Indices: 12190897--12190950 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
12190887 AAGTTTTCTC
* *
12190897 ATA ATA ATA ATA CTA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12190944 AT- ATA AT
1 ATA ATA AT
12190951 TTTAAATCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12204354 original size:2 final size:2
Alignment explanation
Indices: 12204347--12204378 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12204337 CATTATGTTG
12204347 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
12204379 GTTGTGCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12204940 original size:21 final size:20
Alignment explanation
Indices: 12204903--12204944 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
12204893 TTTGGCAGCC
*
12204903 ATAAACTTGCTGCAGCGAGA
1 ATAAACTCGCTGCAGCGAGA
*
12204923 ATAAATCTCGCTGTAGCGAGA
1 ATAAA-CTCGCTGCAGCGAGA
12204944 A
1 A
12204945 ACTCTCAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (20 bp):
ATAAACTCGCTGCAGCGAGA
Found at i:12205207 original size:21 final size:21
Alignment explanation
Indices: 12205178--12205218 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12205168 TTGGCCACCC
*
12205178 GAATCTCACTGCAGCGAGAAT
1 GAATCTCACTGAAGCGAGAAT
* *
12205199 GAATTTCACTGAAGTGAGAA
1 GAATCTCACTGAAGCGAGAA
12205219 ACTTGTTGCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (21 bp):
GAATCTCACTGAAGCGAGAAT
Found at i:12209205 original size:2 final size:2
Alignment explanation
Indices: 12209198--12209241 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12209188 GTGAATACAA
12209198 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
12209240 AT
1 AT
12209242 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12209246 original size:2 final size:2
Alignment explanation
Indices: 12209241--12209296 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
12209231 TATATATATA
12209241 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
12209283 TG -G TG CG TG TG TG T
1 TG TG TG TG TG TG TG T
12209297 ATTGAATAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.00, C:0.02, G:0.50, T:0.48
Consensus pattern (2 bp):
TG
Found at i:12217395 original size:19 final size:19
Alignment explanation
Indices: 12217367--12217433 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 19
12217357 CACTTGATTC
12217367 TAAT-TTTTAATAAAATAT
1 TAATATTTTAATAAAATAT
*
12217385 TAATATTTTAAAATATTAATAT
1 TAATATTTT--AATA-AAATAT
*
12217407 TAA-ATTATAAATAAAATAT
1 TAATATT-TTAATAAAATAT
12217426 TAATATTT
1 TAATATTT
12217434 AAACTATCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
18 4 0.10
19 13 0.32
20 7 0.17
21 7 0.17
22 9 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATATTTTAATAAAATAT
Found at i:12217398 original size:16 final size:16
Alignment explanation
Indices: 12217377--12217407 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12217367 TAATTTTTAA
12217377 TAAAATATTAATATTT
1 TAAAATATTAATATTT
12217393 TAAAATATTAATATT
1 TAAAATATTAATATT
12217408 AAATTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:12217407 original size:22 final size:22
Alignment explanation
Indices: 12217375--12217452 Score: 76
Period size: 22 Copynumber: 3.7 Consensus size: 22
12217365 TCTAATTTTT
12217375 AATA-AAATATTAATATTTTAA
1 AATATAAATATTAATATTTTAA
* *
12217396 AATATTAATATTAA-ATTAT-A
1 AATATAAATATTAATATTTTAA
12217416 AATA-AAATATTAATA-TTTAA
1 AATATAAATATTAATATTTTAA
* *
12217436 ACTATCAATTATTAATA
1 AATAT-AAATATTAATA
12217453 AAATAAATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 10 0.22
20 10 0.22
21 8 0.17
22 18 0.39
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (22 bp):
AATATAAATATTAATATTTTAA
Found at i:12219998 original size:14 final size:14
Alignment explanation
Indices: 12219979--12220005 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12219969 GATTAACTTC
12219979 ATATTTATATATAA
1 ATATTTATATATAA
12219993 ATATTTATATATA
1 ATATTTATATATA
12220006 TTTTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTTATATATAA
Found at i:12220908 original size:21 final size:21
Alignment explanation
Indices: 12220884--12220927 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
12220874 TTAAATTAAA
12220884 AATAT-TTTTTATTAATATTTT
1 AATATCTTTTTATT-ATATTTT
12220905 AATATCTTTTTATTATATTTT
1 AATATCTTTTTATTATATTTT
12220926 AA
1 AA
12220928 AATTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
AATATCTTTTTATTATATTTT
Found at i:12223023 original size:15 final size:15
Alignment explanation
Indices: 12223003--12223034 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12222993 TAATATTATA
12223003 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
12223018 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
12223033 AT
1 AT
12223035 AATATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:12223431 original size:15 final size:15
Alignment explanation
Indices: 12223411--12223453 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
12223401 TATGTTCCCG
* *
12223411 GCAATCATATTGCTT
1 GCAATCACATTACTT
12223426 GCAATCACATTACTT
1 GCAATCACATTACTT
12223441 GCAATCACATTAC
1 GCAATCACATTAC
12223454 CTGTAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.33
Consensus pattern (15 bp):
GCAATCACATTACTT
Found at i:12224771 original size:12 final size:12
Alignment explanation
Indices: 12224754--12224790 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
12224744 TTTCTGATAA
12224754 ACATGTATCGAT
1 ACATGTATCGAT
12224766 ACATGT-TC-AT
1 ACATGTATCGAT
12224776 A-ATGTATCGAT
1 ACATGTATCGAT
12224787 ACAT
1 ACAT
12224791 TTTCCCTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.18
10 5 0.23
11 5 0.23
12 8 0.36
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (12 bp):
ACATGTATCGAT
Found at i:12226008 original size:68 final size:67
Alignment explanation
Indices: 12225750--12226012 Score: 256
Period size: 68 Copynumber: 3.9 Consensus size: 67
12225740 CATGTTTGGT
* * * * * *
12225750 ATGATGAATGCCATAAGATTATGTATATGATGAAAATTCCATATACCATAAGAGATGATCAAGTA
1 ATGATGAATGCCATGAGATTACGCATATGATGTAAATTCCATATA-CATATGAGATGATTAAGTA
12225815 TGC
65 TGC
* * * * * ** * * *
12225818 GTGATGTATACTATGGGATTGTGCATATGATGTAGATTCCATATACAATATGAGGTAATTAAGTA
1 ATGATGAATGCCATGAGATTACGCATATGATGTAAATTCCATATAC-ATATGAGATGATTAAGTA
12225883 TGC
65 TGC
* * * * * *
12225886 ATGATTAATGCCATGAGAATTACGTATATGATGTAGATTCCATATACTACATGAGATGATTGAGC
1 ATGATGAATGCCATGAG-ATTACGCATATGATGTAAATTCCATATAC-ATATGAGATGATTAAGT
*
12225951 AAGC
64 ATGC
* *
12225955 ATGATAAATGCCATGAGATTACGCATATGATGTAAATTCCATATAACTTATGAGATGA
1 ATGATGAATGCCATGAGATTACGCATATGATGTAAATTCCATAT-ACATATGAGATGA
12226013 GGAAAGATGT
Statistics
Matches: 157, Mismatches: 35, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
67 1 0.01
68 97 0.62
69 59 0.38
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (67 bp):
ATGATGAATGCCATGAGATTACGCATATGATGTAAATTCCATATACATATGAGATGATTAAGTAT
GC
Found at i:12226728 original size:16 final size:15
Alignment explanation
Indices: 12226709--12226747 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
12226699 ATGATTAGGA
12226709 AGTTATGAATGGCATG
1 AGTTATGAAT-GCATG
*
12226725 AGTTATAAATGCATG
1 AGTTATGAATGCATG
12226740 -GTTATGAA
1 AGTTATGAA
12226748 ATACTCTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 7 0.33
15 5 0.24
16 9 0.43
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (15 bp):
AGTTATGAATGCATG
Found at i:12226749 original size:15 final size:17
Alignment explanation
Indices: 12226709--12226749 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
12226699 ATGATTAGGA
12226709 AGTTATG-AATGGCATG
1 AGTTATGAAATGGCATG
12226725 AGTTAT-AAAT-GCATG
1 AGTTATGAAATGGCATG
12226740 -GTTATGAAAT
1 AGTTATGAAAT
12226750 ACTCTTATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 9 0.39
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (17 bp):
AGTTATGAAATGGCATG
Found at i:12227137 original size:2 final size:2
Alignment explanation
Indices: 12227130--12227159 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12227120 GGCACTTTTC
*
12227130 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12227160 CAAATGCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12230696 original size:34 final size:33
Alignment explanation
Indices: 12230658--12230766 Score: 101
Period size: 34 Copynumber: 3.2 Consensus size: 33
12230648 AAGTTAGTGT
*
12230658 GGGTTATGGTTAAGCTTGGAAAGAGCCATTGTGA
1 GGGTTATGGTTGAGCTTGGAAA-AGCCATTGTGA
* ** * * ** *
12230692 GGGTTGTGGTTGCTCTTATGTAAAGTTATTGTAA
1 GGGTTATGGTTGAGCTT-GGAAAAGCCATTGTGA
*
12230726 GGGTTGTGGTTGAGCTTGGAAAAAGCCATTGTGA
1 GGGTTATGGTTGAGCTTGG-AAAAGCCATTGTGA
12230760 GGGTTAT
1 GGGTTAT
12230767 TGCTTGATTC
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
33 1 0.02
34 52 0.93
35 3 0.05
ACGTcount: A:0.23, C:0.07, G:0.35, T:0.35
Consensus pattern (33 bp):
GGGTTATGGTTGAGCTTGGAAAAGCCATTGTGA
Found at i:12231779 original size:63 final size:63
Alignment explanation
Indices: 12231705--12231823 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 63
12231695 ATAGAGATAA
* ** *
12231705 AAAGTTTCAGACTTTATGAAGAACTGACATCTCAGGA-AAGAAGAATCGATTCTCCAAAAGTAG
1 AAAGCTTCAGACTTTATGAAGAACCAACAACTCAGGATAA-AAGAATCGATTCTCCAAAAGTAG
* *
12231768 AAAGCTTCAGACTTTATGAAGAACCAACAACTCATGATTAAAGAATCGATTCTCCA
1 AAAGCTTCAGACTTTATGAAGAACCAACAACTCAGGATAAAAGAATCGATTCTCCA
12231824 TGTGTGACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
63 48 0.98
64 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (63 bp):
AAAGCTTCAGACTTTATGAAGAACCAACAACTCAGGATAAAAGAATCGATTCTCCAAAAGTAG
Found at i:12241607 original size:2 final size:2
Alignment explanation
Indices: 12241596--12241626 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12241586 ATTCATTATG
12241596 CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
12241627 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:12252279 original size:36 final size:36
Alignment explanation
Indices: 12252227--12252313 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
12252217 GCGATATGGA
* * * ***
12252227 GGGGAACACACAATGGCATTAGCTGTGTGTGATGTG
1 GGGGAGCACACGATGGCATTAGCTATGCACGATGTG
12252263 GGGGAGCACACGATGGCATTAGCTATGCACGATGTG
1 GGGGAGCACACGATGGCATTAGCTATGCACGATGTG
*
12252299 GGGGTGCACACGATG
1 GGGGAGCACACGATG
12252314 ACTCCGGCTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (36 bp):
GGGGAGCACACGATGGCATTAGCTATGCACGATGTG
Found at i:12259813 original size:40 final size:38
Alignment explanation
Indices: 12259722--12259820 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
12259712 ATAGTGCCCG
* *
12259722 TGTGCATGATGTGGGGGGATGCACACGATGGCACTAAT
1 TGTGCACGATGTGGGGGGATGCACACGATGGCACGAAT
* *
12259760 TGTGCACGATGTGGGGAGATGCACACGATGGTGC-CGATT
1 TGTGCACGATGTGGGGGGATGCACACGAT-G-GCACGAAT
12259799 ATGTGCACGATGTGGGGGGATG
1 -TGTGCACGATGTGGGGGGATG
12259821 TACATGAGCT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
38 27 0.51
39 4 0.08
40 22 0.42
ACGTcount: A:0.21, C:0.15, G:0.40, T:0.23
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGCACACGATGGCACGAAT
Found at i:12261344 original size:2 final size:2
Alignment explanation
Indices: 12261337--12261368 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12261327 ACATACATAC
12261337 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
12261369 GAAAATGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12265233 original size:4 final size:4
Alignment explanation
Indices: 12265224--12265258 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
12265214 AAATTGTAAT
12265224 ATTA ATTA ATTA ATTA A-TA ATTA ATTA ATTCA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT-A ATT
12265259 CCATAGACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
3 3 0.10
4 22 0.76
5 4 0.14
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (4 bp):
ATTA
Found at i:12267484 original size:7 final size:7
Alignment explanation
Indices: 12267461--12267499 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
12267451 GGATCATCAG
12267461 TTTCCCT
1 TTTCCCT
* *
12267468 TTTTCTT
1 TTTCCCT
12267475 TTTCCCT
1 TTTCCCT
12267482 TTTCCCT
1 TTTCCCT
12267489 TTTCCCT
1 TTTCCCT
12267496 TTTC
1 TTTC
12267500 AACAACTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTCCCT
Found at i:12273189 original size:43 final size:43
Alignment explanation
Indices: 12273126--12273209 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
12273116 TGTGATAATA
* * *
12273126 ATGACCCATCTATGTGCGGTGTGGGAGTGCATATGAGCTGATG
1 ATGACCCAACTATGTACGGTGTGGGAGTGCACATGAGCTGATG
12273169 ATGACCCAACTATGTACGGTGTGGGAGTGCACATGAGCTGA
1 ATGACCCAACTATGTACGGTGTGGGAGTGCACATGAGCTGA
12273210 GTGTGACGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (43 bp):
ATGACCCAACTATGTACGGTGTGGGAGTGCACATGAGCTGATG
Found at i:12273361 original size:23 final size:23
Alignment explanation
Indices: 12273318--12273364 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12273308 AATTACTCCC
* *
12273318 AAATTGCTTTTTATTTCAACAAG
1 AAATGGCTTTTTATGTCAACAAG
12273341 AAATGGCTTTTTGATGT-AACAAG
1 AAATGGCTTTTT-ATGTCAACAAG
12273364 A
1 A
12273365 CCCCTTCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (23 bp):
AAATGGCTTTTTATGTCAACAAG
Found at i:12273511 original size:18 final size:17
Alignment explanation
Indices: 12273459--12273512 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 17
12273449 TCCATGCTCT
12273459 GAATTTTGCTGCAGTGA
1 GAATTTTGCTGCAGTGA
12273476 GAATTGATTCTCGCTGCAGTGA
1 GAA-T--TT-T-GCTGCAGTGA
12273498 GGAATTTTGCTGCAG
1 -GAATTTTGCTGCAG
12273513 CAAAAATGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
17 3 0.10
18 8 0.26
19 1 0.03
20 4 0.13
21 1 0.03
22 11 0.35
23 3 0.10
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (17 bp):
GAATTTTGCTGCAGTGA
Found at i:12276002 original size:72 final size:73
Alignment explanation
Indices: 12275871--12276058 Score: 204
Period size: 73 Copynumber: 2.6 Consensus size: 73
12275861 ATATTGAGAA
* ** *
12275871 ACAGAACCAACTTAGTTGACCAAGGTGAGAGTTAGTCGACT-AAGAAGCTACTACCAAAATTTG-
1 ACAGAACCAACTTAGTCGACCAA-GAAAGAGTTAGTCGACTAAAGAAGCTACTACCAAAATCTGC
**
12275934 GACTTCAAG
65 GACCACAAG
* *
12275943 ACAGAACCAACTTAGTCGACCAAGAAATGAGTTAGTCGACTAAATG-ATCT-CTACTAAAATCTG
1 ACAGAACCAACTTAGTCGACCAAGAAA-GAGTTAGTCGACTAAA-GAAGCTACTACCAAAATCTG
*
12276006 CGACCAGAAG
64 CGACCACAAG
* * *
12276016 ACAGAACCAACTTAGTCAACCAAGAAGAAAGTTAGTCTACTAA
1 ACAGAACCAACTTAGTCGACCAAGAA-AGAGTTAGTCGACTAA
12276059 GAGCTTTTTG
Statistics
Matches: 99, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
71 2 0.02
72 46 0.46
73 49 0.49
74 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (73 bp):
ACAGAACCAACTTAGTCGACCAAGAAAGAGTTAGTCGACTAAAGAAGCTACTACCAAAATCTGCG
ACCACAAG
Found at i:12278623 original size:42 final size:42
Alignment explanation
Indices: 12278558--12278638 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
12278548 GTTGATTTGA
12278558 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
* *
12278600 ACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGTTG
1 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTG
12278639 TTGCCTCCGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.35, T:0.22
Consensus pattern (42 bp):
ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTG
Found at i:12278909 original size:26 final size:26
Alignment explanation
Indices: 12278873--12278934 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
12278863 TTGCATATGA
12278873 GATGATGATGATGGGATGATGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
12278899 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
12278925 GTTGATGATG
1 GATGATGATG
12278935 GGTATATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.24, C:0.03, G:0.40, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGATGTGCAT
Found at i:12284458 original size:20 final size:19
Alignment explanation
Indices: 12284428--12284465 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
12284418 CAAAACAGAA
*
12284428 TGAATTTAGTCGACTAAGG
1 TGAATTTAGTCAACTAAGG
12284447 TGAATCTTAGTCAACTAAG
1 TGAAT-TTAGTCAACTAAG
12284466 AGTGTTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (19 bp):
TGAATTTAGTCAACTAAGG
Found at i:12286906 original size:41 final size:41
Alignment explanation
Indices: 12286842--12286924 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
12286832 TGGAGGAACT
* * *
12286842 AGGAATTTAGGAAATAAATGAAGCAAAAATGAACCAGAGGC
1 AGGAACTTAGGAAAAAAAGGAAGCAAAAATGAACCAGAGGC
*
12286883 AGGAACTTAGGAAAAAAAGGAAGCAAAAATGAACTAGAGGC
1 AGGAACTTAGGAAAAAAAGGAAGCAAAAATGAACCAGAGGC
12286924 A
1 A
12286925 ATTTAGGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.53, C:0.10, G:0.25, T:0.12
Consensus pattern (41 bp):
AGGAACTTAGGAAAAAAAGGAAGCAAAAATGAACCAGAGGC
Found at i:12287064 original size:22 final size:22
Alignment explanation
Indices: 12287036--12287081 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
12287026 AAATGGGTGT
*
12287036 TAATATGTTTATGATATTTTGC
1 TAATATGTTTATGATATTTGGC
*
12287058 TAATATGTTTATGGTATTTGGC
1 TAATATGTTTATGATATTTGGC
12287080 TA
1 TA
12287082 CTGATGATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.52
Consensus pattern (22 bp):
TAATATGTTTATGATATTTGGC
Found at i:12287459 original size:17 final size:17
Alignment explanation
Indices: 12287434--12287470 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12287424 AGCAAAATAT
12287434 GCACACACTAAGGGGGA
1 GCACACACTAAGGGGGA
* *
12287451 GCACTCACTTAGGGGGA
1 GCACACACTAAGGGGGA
12287468 GCA
1 GCA
12287471 ATCCTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.35, T:0.11
Consensus pattern (17 bp):
GCACACACTAAGGGGGA
Found at i:12288495 original size:22 final size:20
Alignment explanation
Indices: 12288467--12288509 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
12288457 GTTTTGGTTG
12288467 AGCTTGGTAAAAGCCATTGTAA
1 AGCTTGGTAAAAG-C-TTGTAA
*
12288489 AGCTTGGTGAAAGCTTGTAA
1 AGCTTGGTAAAAGCTTGTAA
12288509 A
1 A
12288510 TTTCATCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 1 0.05
22 12 0.60
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.28
Consensus pattern (20 bp):
AGCTTGGTAAAAGCTTGTAA
Found at i:12293197 original size:43 final size:43
Alignment explanation
Indices: 12293136--12293262 Score: 193
Period size: 43 Copynumber: 3.0 Consensus size: 43
12293126 TGTGATAATA
*
12293136 ATGACCCAGCTATGTGCGGTATGGGAGTGCACATGACCTGATG
1 ATGACCCAGCTATGTGCGGTATGGGAGTGCACATGAGCTGATG
* *
12293179 ATGACCCAGCTATGTGCGGTGTAGGAGTGCACATGAGCTGATG
1 ATGACCCAGCTATGTGCGGTATGGGAGTGCACATGAGCTGATG
* *
12293222 ATGACCCGGCTATGTGAGAGTA-GGGAGTGCACATGAGCTGA
1 ATGACCCAGCTATGTGCG-GTATGGGAGTGCACATGAGCTGA
12293263 ATGAGGCGAG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
43 74 0.97
44 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (43 bp):
ATGACCCAGCTATGTGCGGTATGGGAGTGCACATGAGCTGATG
Found at i:12293551 original size:22 final size:22
Alignment explanation
Indices: 12293521--12293566 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
12293511 ATTTTTCTGT
*
12293521 AGCGCAAATGGATTCTCGCTGC
1 AGCGAAAATGGATTCTCGCTGC
*
12293543 AGCGAAAATGGATTCTCGTTGC
1 AGCGAAAATGGATTCTCGCTGC
12293565 AG
1 AG
12293567 TGAGAAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (22 bp):
AGCGAAAATGGATTCTCGCTGC
Found at i:12295338 original size:43 final size:43
Alignment explanation
Indices: 12295277--12295398 Score: 142
Period size: 43 Copynumber: 2.8 Consensus size: 43
12295267 TGACTCGGCG
* **
12295277 ATGTGCGAGTAGGGAGTGCGCATAAGC-CGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAA-CTCG-GTGATGACCCAGCC
*
12295320 ATGTGCGAGTAGGGAGTGCGCATAACTCGGTGATGACCTAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAACTCGGTGATGACCCAGCC
* *
12295363 CTGTGCGAGTAGGGAGTGCGCATGAGCT-GGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCAT-AACTCGGTGATGA
12295399 TGATGATGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
42 2 0.03
43 65 0.93
44 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAACTCGGTGATGACCCAGCC
Found at i:12295425 original size:23 final size:23
Alignment explanation
Indices: 12295395--12295454 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
12295385 TGAGCTGGTG
* * *
12295395 ATGATGATGATGTGATGGTGTGT
1 ATGATGATGATGGGATGATGTGC
12295418 ATGATGATGATGGGATGATGTGC
1 ATGATGATGATGGGATGATGTGC
*
12295441 ATGATAATGATGGG
1 ATGATGATGATGGG
12295455 TATATGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.02, G:0.38, T:0.33
Consensus pattern (23 bp):
ATGATGATGATGGGATGATGTGC
Found at i:12297535 original size:20 final size:20
Alignment explanation
Indices: 12297506--12297545 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12297496 TTTTCCAAAA
*
12297506 CCAAAAGTATTGATACATTT
1 CCAAAAGTATCGATACATTT
*
12297526 CCAAATGTATCGATACATTT
1 CCAAAAGTATCGATACATTT
12297546 AATCAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (20 bp):
CCAAAAGTATCGATACATTT
Found at i:12300227 original size:68 final size:68
Alignment explanation
Indices: 12300124--12300253 Score: 190
Period size: 68 Copynumber: 1.9 Consensus size: 68
12300114 GATGAATGCC
* *
12300124 ATAAGATTATGTATACGATGTAAATAACATATACCATATGAGATGATTAAGTATGCATGATGTAT
1 ATAAGATTACGCATACGATGTAAATAACATATACCATATGAGATGATTAAGTATGCATGATGTAT
12300189 ACT
66 ACT
* * * *
12300192 ATAAGATTACGCATATGATGTAAACT-CCATGTACCATATGAGGTGATTAAGTATGCATGATG
1 ATAAGATTACGCATACGATGTAAA-TAACATATACCATATGAGATGATTAAGTATGCATGATG
12300254 ACTGCCAAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 54 0.98
69 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (68 bp):
ATAAGATTACGCATACGATGTAAATAACATATACCATATGAGATGATTAAGTATGCATGATGTAT
ACT
Found at i:12300319 original size:68 final size:69
Alignment explanation
Indices: 12300206--12300378 Score: 165
Period size: 68 Copynumber: 2.5 Consensus size: 69
12300196 GATTACGCAT
* * * * * * ** * *
12300206 ATGATGTAAACTCCATGTACCATATGAGGTGATTAAGTATGCATGATGACTGCCAAGAAATTATA
1 ATGATGTATATTCCATATACTATATGAGATGATTAAGAAAACATGACGAATGCCAAGAAATTATA
12300271 TA-G
66 TATG
* * * *
12300274 ATGATGTATATTCCATATACTACATGAGATGATTAAGAAAACATGACGAATGCCATGAGATTATG
1 ATGATGTATATTCCATATACTATATGAGATGATTAAGAAAACATGACGAATGCCAAGAAATTATA
12300339 TATG
66 TATG
*
12300343 -TGATGTAT-TTCCCATATACCT-TATGAGATGAGTAAG
1 ATGATGTATATT-CCATATA-CTATATGAGATGATTAAG
12300379 CATGTATGTG
Statistics
Matches: 86, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
67 2 0.02
68 81 0.94
69 3 0.03
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (69 bp):
ATGATGTATATTCCATATACTATATGAGATGATTAAGAAAACATGACGAATGCCAAGAAATTATA
TATG
Found at i:12302061 original size:2 final size:2
Alignment explanation
Indices: 12302056--12302085 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12302046 TATATTTAGA
*
12302056 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12302086 GCGGATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12303491 original size:22 final size:22
Alignment explanation
Indices: 12303463--12303511 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
12303453 ATATCTAATC
* *
12303463 TCCAGCAACTTCTCTTTAGTTT
1 TCCAGCAACTTCTCTTCAATTT
12303485 TCCAGCAACTTCTCTTCAATTT
1 TCCAGCAACTTCTCTTCAATTT
12303507 TCCAG
1 TCCAG
12303512 TAGCTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.31, G:0.08, T:0.41
Consensus pattern (22 bp):
TCCAGCAACTTCTCTTCAATTT
Found at i:12303962 original size:2 final size:2
Alignment explanation
Indices: 12303955--12303996 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
12303945 TATAGGATGC
12303955 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
12303997 GTTGTGTATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12304780 original size:22 final size:22
Alignment explanation
Indices: 12304755--12304814 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
12304745 CAAAAATTCA
12304755 TTTTCGCTGTAGCGAGAATGCC
1 TTTTCGCTGTAGCGAGAATGCC
*
12304777 TTTTCGCTGTAGAGAGAATGCC
1 TTTTCGCTGTAGCGAGAATGCC
* *
12304799 TTTCCGCTGCAGCGAG
1 TTTTCGCTGTAGCGAG
12304815 GATTAGTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.30
Consensus pattern (22 bp):
TTTTCGCTGTAGCGAGAATGCC
Found at i:12312384 original size:20 final size:18
Alignment explanation
Indices: 12312351--12312389 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
12312341 CACCATTGCC
12312351 TTCTTTGATTTCTTATTT
1 TTCTTTGATTTCTTATTT
*
12312369 TTCTTTGGAGTTTCTTCTTT
1 TTCTTT-GA-TTTCTTATTT
12312389 T
1 T
12312390 AGCAAGGGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 2 0.11
20 10 0.56
ACGTcount: A:0.08, C:0.13, G:0.10, T:0.69
Consensus pattern (18 bp):
TTCTTTGATTTCTTATTT
Found at i:12328129 original size:28 final size:29
Alignment explanation
Indices: 12328088--12328147 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
12328078 GTCTATGGGC
*
12328088 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
12328116 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
12328146 AA
1 AA
12328148 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:12336785 original size:5 final size:5
Alignment explanation
Indices: 12336766--12336816 Score: 57
Period size: 5 Copynumber: 10.2 Consensus size: 5
12336756 CTATTCAACC
* * * * *
12336766 TAACC TAACT TAACT TAACT TGACT TGACT TAAGT TAGCT TAACT TAACT
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT
12336816 T
1 T
12336817 GGGCCACACT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (5 bp):
TAACT
Found at i:12336855 original size:11 final size:11
Alignment explanation
Indices: 12336839--12336866 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12336829 CACTGTAAAT
12336839 TTTAAAACAAC
1 TTTAAAACAAC
12336850 TTTAAAACAAC
1 TTTAAAACAAC
12336861 TTTAAA
1 TTTAAA
12336867 CCCAAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (11 bp):
TTTAAAACAAC
Found at i:12336903 original size:22 final size:22
Alignment explanation
Indices: 12336860--12336903 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12336850 TTTAAAACAA
* *
12336860 CTTTAAACCCAAAAACTGTAAT
1 CTTTAAAACCAAAAACTCTAAT
*
12336882 CTTTAAAACCAAAAGCTCTAAT
1 CTTTAAAACCAAAAACTCTAAT
12336904 ACCAATAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.27
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTAAT
Found at i:12345590 original size:20 final size:20
Alignment explanation
Indices: 12345542--12345599 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
12345532 ACAATTTACT
* *
12345542 AATGTATCGATACATTCTAG
1 AATGTATTGATACATTCAAG
* * *
12345562 AAAGCATTGATGCATTCAAG
1 AATGTATTGATACATTCAAG
*
12345582 AATGTATTGATATATTCA
1 AATGTATTGATACATTCA
12345600 TTGCAAAAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (20 bp):
AATGTATTGATACATTCAAG
Found at i:12351720 original size:22 final size:22
Alignment explanation
Indices: 12351685--12351736 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
12351675 CAAAAGTTAC
*
12351685 TCACTGCAGTGAGAATCCATTT
1 TCACTGCAGCGAGAATCCATTT
* * *
12351707 TCGCTGCAGCGAGAATTCTTTT
1 TCACTGCAGCGAGAATCCATTT
12351729 TCACTGCA
1 TCACTGCA
12351737 ACAAGAAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (22 bp):
TCACTGCAGCGAGAATCCATTT
Found at i:12352095 original size:43 final size:43
Alignment explanation
Indices: 12352006--12352098 Score: 125
Period size: 43 Copynumber: 2.2 Consensus size: 43
12351996 AGCCGGGTCA
* * * *
12352006 TCATCATCGGCTTATGCGAACTCCTTACTCGCACATAGCTGAG
1 TCATCATCGGCTAATGCGAACTCCCTACTCGCACATACCAGAG
*
12352049 TCATCATCGGCTAATGCGCACTCCCTACTCGCACATAACCAG-G
1 TCATCATCGGCTAATGCGAACTCCCTACTCGCACAT-ACCAGAG
12352092 TCATCAT
1 TCATCAT
12352099 TAGCTCATGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 41 0.93
44 3 0.07
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (43 bp):
TCATCATCGGCTAATGCGAACTCCCTACTCGCACATACCAGAG
Found at i:12354156 original size:25 final size:25
Alignment explanation
Indices: 12354111--12354159 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
12354101 AAAATCAAAT
*
12354111 TTTTTTTTCATTTTCTTTTCCTTCCC
1 TTTTTTTTCA-TTACTTTTCCTTCCC
12354137 TTTTTTTTC-TTACTTCTTCCTTC
1 TTTTTTTTCATTACTT-TTCCTTC
12354160 AGTTACCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 7 0.33
26 9 0.43
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTTTTCATTACTTTTCCTTCCC
Found at i:12355194 original size:71 final size:71
Alignment explanation
Indices: 12355111--12355276 Score: 226
Period size: 71 Copynumber: 2.3 Consensus size: 71
12355101 TACAAACGTG
* *
12355111 CGTGTGCAGTGTGGGAGTGCACATGACGGTGATGGTGAGCTGCGGTGTGGGAGTGCGCATGATGG
1 CGTGTGCGGTGTGGGAGTGCACATGACGGTGATGGTGAGCTGCGGTGTGGGACTGCGCATGAT-G
*
12355176 A-ATTGT
65 ATATTGC
* * * *
12355182 CGTGTGCGGTGTGAGAGTGCACATGATGGTGATGGTGAGGTGCGGTGTGGGACTGTGCATGATGA
1 CGTGTGCGGTGTGGGAGTGCACATGACGGTGATGGTGAGCTGCGGTGTGGGACTGCGCATGATGA
12355247 TATTGC
66 TATTGC
* * *
12355253 CATGTGTGGTGTGGAAGTGCACAT
1 CGTGTGCGGTGTGGGAGTGCACAT
12355277 AATGACATTA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
70 2 0.02
71 81 0.98
ACGTcount: A:0.17, C:0.12, G:0.43, T:0.27
Consensus pattern (71 bp):
CGTGTGCGGTGTGGGAGTGCACATGACGGTGATGGTGAGCTGCGGTGTGGGACTGCGCATGATGA
TATTGC
Found at i:12355245 original size:36 final size:36
Alignment explanation
Indices: 12355114--12355233 Score: 145
Period size: 36 Copynumber: 3.4 Consensus size: 36
12355104 AAACGTGCGT
* *
12355114 GTGCAGTGTGGGAGTGCACATGACGGTGATGGTGAG
1 GTGCGGTGTGGGAGTGCACATGATGGTGATGGTGAG
* * * * *
12355150 CTGCGGTGTGGGAGTGCGCATGATGG-AATTGTCG-T
1 GTGCGGTGTGGGAGTGCACATGATGGTGATGGT-GAG
*
12355185 GTGCGGTGTGAGAGTGCACATGATGGTGATGGTGAG
1 GTGCGGTGTGGGAGTGCACATGATGGTGATGGTGAG
12355221 GTGCGGTGTGGGA
1 GTGCGGTGTGGGA
12355234 CTGTGCATGA
Statistics
Matches: 67, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
35 28 0.42
36 39 0.58
ACGTcount: A:0.17, C:0.11, G:0.47, T:0.25
Consensus pattern (36 bp):
GTGCGGTGTGGGAGTGCACATGATGGTGATGGTGAG
Found at i:12355670 original size:62 final size:62
Alignment explanation
Indices: 12355570--12355689 Score: 186
Period size: 62 Copynumber: 1.9 Consensus size: 62
12355560 AACATCATTT
*
12355570 TCACCGCAGCCAAATTGATTTTCACCACGGCGAAAAACTTTCTACCTTAAGAGTTACTGTTC
1 TCACCGCAACCAAATTGATTTTCACCACGGCGAAAAACTTTCTACCTTAAGAGTTACTGTTC
* * * * *
12355632 TCACCGCAACCAAATTGATTTTCACCGCGGCTAGAAACTTTCTGCTTTAAGAGTTACT
1 TCACCGCAACCAAATTGATTTTCACCACGGCGAAAAACTTTCTACCTTAAGAGTTACT
12355690 ATCATGACCC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (62 bp):
TCACCGCAACCAAATTGATTTTCACCACGGCGAAAAACTTTCTACCTTAAGAGTTACTGTTC
Found at i:12361163 original size:19 final size:19
Alignment explanation
Indices: 12361067--12361166 Score: 58
Period size: 19 Copynumber: 5.1 Consensus size: 19
12361057 ACCCGACTCA
12361067 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
* * ** *
12361086 TGCACATAGCCGGCACCATCA
1 TGTACAT-CCCCCCA-CATCG
*
12361107 TGTGCATCCCCCCTACATCG
1 TGTACATCCCCCC-ACATCG
*****
12361127 TGTACAATTAGTGC-CATCG
1 TGTAC-ATCCCCCCACATCG
12361146 TGTACATCCCCCCACATCG
1 TGTACATCCCCCCACATCG
12361165 TG
1 TG
12361167 CACACGGGCA
Statistics
Matches: 54, Mismatches: 22, Indels: 10
0.63 0.26 0.12
Matches are distributed among these distances:
18 3 0.06
19 23 0.43
20 15 0.28
21 13 0.24
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.23
Consensus pattern (19 bp):
TGTACATCCCCCCACATCG
Found at i:12361293 original size:2 final size:2
Alignment explanation
Indices: 12361282--12361312 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12361272 ATTCATCATG
12361282 CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
12361313 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:12362867 original size:5 final size:5
Alignment explanation
Indices: 12362846--12362883 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
12362836 AGCATTTCAG
* *
12362846 TTTCT TTTC- CTTGT TTTCT TTTCT TTTCT TTTCT TTTC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
12362884 CTACTTCTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
4 2 0.07
5 26 0.93
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTCT
Found at i:12363857 original size:44 final size:44
Alignment explanation
Indices: 12363751--12363861 Score: 159
Period size: 44 Copynumber: 2.5 Consensus size: 44
12363741 TTATGCCCTA
* * *
12363751 TGCGGTGTGGGAGAACACATGGTGCTGATGATGACATTGTAATG
1 TGCGGTGTGGGAGAGCACATGATACTGATGATGACATTGTAATG
* *
12363795 TGTGGTGTGGGAGAGCACATGATACTGATGATGATATTGTAATG
1 TGCGGTGTGGGAGAGCACATGATACTGATGATGACATTGTAATG
* *
12363839 TGCGGTGTGGAAGGGCACATGAT
1 TGCGGTGTGGGAGAGCACATGAT
12363862 GACCTAGCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 59 1.00
ACGTcount: A:0.25, C:0.10, G:0.37, T:0.28
Consensus pattern (44 bp):
TGCGGTGTGGGAGAGCACATGATACTGATGATGACATTGTAATG
Found at i:12365468 original size:80 final size:80
Alignment explanation
Indices: 12365335--12365501 Score: 289
Period size: 80 Copynumber: 2.1 Consensus size: 80
12365325 GTCCTTTATA
* * *
12365335 ATATACACTATGGGCTAAGCTTGTAAGTGATTTATGAGGTTATGAAATGTATGCCATGAGATGTA
1 ATATACACTATGGGCTAAGCATGTAAGTGATTTATGAGGTTATCAAATATATGCCATGAGATGTA
*
12365400 TGTGTTGAGATAGTC
66 CGTGTTGAGATAGTC
*
12365415 ATATACACTATGGGCTAAGCATGTAAGTGATTTATGAGGTTATCAAATATATGCCGTGAGATGTA
1 ATATACACTATGGGCTAAGCATGTAAGTGATTTATGAGGTTATCAAATATATGCCATGAGATGTA
12365480 CGTGTTGAGATAGTC
66 CGTGTTGAGATAGTC
12365495 ATATACA
1 ATATACA
12365502 TTATAGGCAA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.34
Consensus pattern (80 bp):
ATATACACTATGGGCTAAGCATGTAAGTGATTTATGAGGTTATCAAATATATGCCATGAGATGTA
CGTGTTGAGATAGTC
Found at i:12365526 original size:80 final size:78
Alignment explanation
Indices: 12365335--12365530 Score: 232
Period size: 80 Copynumber: 2.4 Consensus size: 78
12365325 GTCCTTTATA
* * * * *
12365335 ATATACACTATGGGCTAAGCTTGTAAGTGATTTATGAGGTTATGAAATGTATGCCATGAGATGTA
1 ATATACACTATAGGCAAAGCATGT-A-TGATTTATGAGGTTATCAAATATATGCCATGAGATGTA
*
12365400 TGTGTTGAGATAGTC
64 CGTGTTGAGATAGTC
* * *
12365415 ATATACACTATGGGCTAAGCATGTAAGTGATTTATGAGGTTATCAAATATATGCCGTGAGATGTA
1 ATATACACTATAGGCAAAGCATGT-A-TGATTTATGAGGTTATCAAATATATGCCATGAGATGTA
12365480 CGTGTTGAGATAGTC
64 CGTGTTGAGATAGTC
*
12365495 ATATACATTATAGGCAAAGTACAATGT-TGATTTATG
1 ATATACACTATAGGCAAAG--C-ATGTATGATTTATG
12365531 TAAATGTTAT
Statistics
Matches: 105, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
80 100 0.95
82 1 0.01
83 4 0.04
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (78 bp):
ATATACACTATAGGCAAAGCATGTATGATTTATGAGGTTATCAAATATATGCCATGAGATGTACG
TGTTGAGATAGTC
Found at i:12366980 original size:34 final size:34
Alignment explanation
Indices: 12366935--12367028 Score: 100
Period size: 34 Copynumber: 2.7 Consensus size: 34
12366925 TTGGCTGCTG
*
12366935 AAAATTTGAGCTGTTTGCTGCCAATTTGTGCAAA
1 AAAATTGGAGCTGTTTGCTGCCAATTTGTGCAAA
** * **
12366969 AAAATTGGAGCTGTTTGCTGGTAGTTTGTGCAGG
1 AAAATTGGAGCTGTTTGCTGCCAATTTGTGCAAA
12367003 AAAATTGGACAGCT-TTGTGCTGCCAA
1 AAAATTGG--AGCTGTT-TGCTGCCAA
12367029 AATTGAGAAG
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
34 36 0.75
35 2 0.04
36 10 0.21
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.33
Consensus pattern (34 bp):
AAAATTGGAGCTGTTTGCTGCCAATTTGTGCAAA
Found at i:12367240 original size:10 final size:10
Alignment explanation
Indices: 12367222--12367284 Score: 62
Period size: 10 Copynumber: 6.6 Consensus size: 10
12367212 AGAAACGTGG
*
12367222 AAGAGAGAAA
1 AAGAAAGAAA
12367232 AAGAAAGAAA
1 AAGAAAGAAA
*
12367242 AAGAAAAAAA
1 AAGAAAGAAA
*
12367252 AACAAA-AAA
1 AAGAAAGAAA
12367261 AA-ATAA-AAA
1 AAGA-AAGAAA
12367270 AA-AAAGAAA
1 AAGAAAGAAA
12367279 AAGAAA
1 AAGAAA
12367285 AAGAAAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
8 3 0.06
9 18 0.38
10 26 0.55
ACGTcount: A:0.84, C:0.02, G:0.13, T:0.02
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:12367243 original size:1 final size:1
Alignment explanation
Indices: 12367229--12367291 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
12367219 TGGAAGAGAG
* * * * * * * *
12367229 AAAAAGAAAGAAAAAGAAAAAAAAACAAAAAAAAATAAAAAAAAAAGAAAAAGAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12367292 TAAATGGGCA
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.87, C:0.02, G:0.10, T:0.02
Consensus pattern (1 bp):
A
Found at i:12367244 original size:6 final size:6
Alignment explanation
Indices: 12367227--12367291 Score: 64
Period size: 6 Copynumber: 11.0 Consensus size: 6
12367217 CGTGGAAGAG
* * *
12367227 AGAAAA AG--AA AGAAAA AGAAAA A-AAAA CAAAAAA AAATAAA AAAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA -AGAAAA AGA-AAA AGAAAA
12367274 AGAAAA AGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA
12367292 TAAATGGGCA
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
4 4 0.08
5 4 0.08
6 35 0.66
7 10 0.19
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:12367318 original size:25 final size:25
Alignment explanation
Indices: 12367286--12367343 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
12367276 AAAAAGAAAA
12367286 AGAAAATAAATGGGCATGACCCAAT
1 AGAAAATAAATGGGCATGACCCAAT
* *
12367311 AGAAAATAAGTGGGCATGGCCCAAT
1 AGAAAATAAATGGGCATGACCCAAT
*
12367336 AGGAAATA
1 AGAAAATA
12367344 CAAATAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.47, C:0.14, G:0.24, T:0.16
Consensus pattern (25 bp):
AGAAAATAAATGGGCATGACCCAAT
Found at i:12374550 original size:21 final size:20
Alignment explanation
Indices: 12374503--12374575 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
12374493 TTCTATGTGA
*
12374503 AATGTATCTATACATTACC--
1 AATGTATCGATACATT-CCAT
* *
12374522 AATGGTATCGATAGATTCCTT
1 AAT-GTATCGATACATTCCAT
*
12374543 ACATGTATAGATACATTCCAT
1 A-ATGTATCGATACATTCCAT
12374564 AATGTATCGATA
1 AATGTATCGATA
12374576 AAATTGTTGC
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 5 0.11
20 21 0.48
21 16 0.36
22 2 0.05
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCCAT
Found at i:12378454 original size:35 final size:33
Alignment explanation
Indices: 12378415--12378521 Score: 117
Period size: 35 Copynumber: 3.2 Consensus size: 33
12378405 GATCTCGTGA
*
12378415 GAAAAACCATTGTTGTAGGTTATGGTTGAGCCTTT
1 GAAAAACCAAT-TTG-AGGTTATGGTTGAGCCTTT
* * * **
12378450 GAAAAACCACTTTG-GGTTTTGTTTGAGCCCGT
1 GAAAAACCAATTTGAGGTTATGGTTGAGCCTTT
12378482 GAAAAACCAATTTGAATGGTTATGGTTGAGCCTTT
1 GAAAAACCAATTTG-A-GGTTATGGTTGAGCCTTT
12378517 GAAAA
1 GAAAA
12378522 CCACTTTCGG
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
32 27 0.46
34 3 0.05
35 29 0.49
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (33 bp):
GAAAAACCAATTTGAGGTTATGGTTGAGCCTTT
Found at i:12378485 original size:32 final size:32
Alignment explanation
Indices: 12378432--12378541 Score: 114
Period size: 32 Copynumber: 3.4 Consensus size: 32
12378422 CATTGTTGTA
*
12378432 GGTTATGGTTGAGCCTTTGAAAAACCACTTTG
1 GGTTTTGGTTGAGCCTTTGAAAAACCACTTTG
* ** *
12378464 GGTTTTGTTTGAGCCCGTGAAAAACCAATTTG
1 GGTTTTGGTTGAGCCTTTGAAAAACCACTTTG
* *
12378496 AATGGTTATGGTTGAGCCTTTG-AAAACCACTTTC
1 ---GGTTTTGGTTGAGCCTTTGAAAAACCACTTTG
*
12378530 GGTTTTAGTTGA
1 GGTTTTGGTTGA
12378542 TCCCTGGTAA
Statistics
Matches: 62, Mismatches: 13, Indels: 7
0.76 0.16 0.09
Matches are distributed among these distances:
31 10 0.16
32 27 0.44
34 10 0.16
35 15 0.24
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (32 bp):
GGTTTTGGTTGAGCCTTTGAAAAACCACTTTG
Found at i:12378504 original size:67 final size:67
Alignment explanation
Indices: 12378392--12378541 Score: 196
Period size: 67 Copynumber: 2.2 Consensus size: 67
12378382 AAGTTAGTTG
* * * *
12378392 TTGGGTTTTGGTTGATCTCGTGAGAAAAACCATTGTTGTAGGTTATGGTTGAGCCTTTGAAAAAC
1 TTGGGTTTTGGTTGAGCCCGT-AGAAAAACCAATGTTGAAGGTTATGGTTGAGCCTTTG-AAAAC
12378457 CACT
64 CACT
*
12378461 TTGGGTTTTGTTTGAGCCCGT-GAAAAACCAAT-TTGAATGGTTATGGTTGAGCCTTTGAAAACC
1 TTGGGTTTTGGTTGAGCCCGTAGAAAAACCAATGTTGAA-GGTTATGGTTGAGCCTTTGAAAACC
12378524 ACT
65 ACT
* *
12378527 TTCGGTTTTAGTTGA
1 TTGGGTTTTGGTTGA
12378542 TCCCTGGTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
66 25 0.35
67 29 0.40
69 18 0.25
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.37
Consensus pattern (67 bp):
TTGGGTTTTGGTTGAGCCCGTAGAAAAACCAATGTTGAAGGTTATGGTTGAGCCTTTGAAAACCA
CT
Found at i:12398168 original size:36 final size:38
Alignment explanation
Indices: 12398100--12398235 Score: 118
Period size: 39 Copynumber: 3.6 Consensus size: 38
12398090 AACTTAGCTT
* *
12398100 ATGTGCACTCCCACATCGCACATAGC-TAATATC-C-TC
1 ATGTGCACTCCCACACCGCACATGGCAT-ATATCACATC
*
12398136 ATGTTCACTCCCACACCGCACATGGCATATATCATCATC
1 ATGTGCACTCCCACACCGCACATGGCATATATCA-CATC
* * **
12398175 ATGTGCTA-TCTCACACCACACATGGCATATATCATCGGC
1 ATGTGC-ACTCCCACACCGCACATGGCATATATCA-CATC
** *
12398214 ATGTGCTTTCTCACACCGCACA
1 ATGTGCACTCCCACACCGCACA
12398236 CTATCGGCAC
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
36 28 0.33
37 1 0.01
38 1 0.01
39 53 0.63
40 1 0.01
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.26
Consensus pattern (38 bp):
ATGTGCACTCCCACACCGCACATGGCATATATCACATC
Found at i:12398190 original size:39 final size:39
Alignment explanation
Indices: 12398147--12398235 Score: 142
Period size: 39 Copynumber: 2.3 Consensus size: 39
12398137 TGTTCACTCC
*
12398147 CACACCGCACATGGCATATATCATCATCATGTGCTATCT
1 CACACCGCACATGGCATATATCATCAGCATGTGCTATCT
* * *
12398186 CACACCACACATGGCATATATCATCGGCATGTGCTTTCT
1 CACACCGCACATGGCATATATCATCAGCATGTGCTATCT
12398225 CACACCGCACA
1 CACACCGCACA
12398236 CTATCGGCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.28, C:0.34, G:0.13, T:0.25
Consensus pattern (39 bp):
CACACCGCACATGGCATATATCATCAGCATGTGCTATCT
Found at i:12401996 original size:38 final size:39
Alignment explanation
Indices: 12401919--12402019 Score: 98
Period size: 38 Copynumber: 2.6 Consensus size: 39
12401909 TAGTGCCCGT
* * * *
12401919 GTGCACGATGT-GGGAGATGTACACGATGGCACTGACTA
1 GTGCACGATGTGGGGGGATGCACACGATGACACCGACTA
* *
12401957 -TGCACGATGTGGGGGGATGCACACGATGACTCCGGCTA
1 GTGCACGATGTGGGGGGATGCACACGATGACACCGACTA
** *
12401995 TGTGCATTATGTGGGGGAATGCACA
1 -GTGCACGATGTGGGGGGATGCACA
12402020 TGAGTTGGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
37 10 0.20
38 21 0.41
40 20 0.39
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.22
Consensus pattern (39 bp):
GTGCACGATGTGGGGGGATGCACACGATGACACCGACTA
Found at i:12405391 original size:2 final size:2
Alignment explanation
Indices: 12405386--12405419 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12405376 NNNNNNNNNN
12405386 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
12405420 AACACGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12413058 original size:15 final size:15
Alignment explanation
Indices: 12413038--12413088 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
12413028 TTCTTAAAAC
12413038 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
*
12413053 AACTTTAAAATCC-AT
1 AACTTTAAAA-CCAAA
*
12413068 ATCTTTAAAACCAAA
1 AACTTTAAAACCAAA
*
12413083 ATCTTT
1 AACTTT
12413089 GATCTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:12422846 original size:2 final size:2
Alignment explanation
Indices: 12422839--12422889 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
12422829 NNNNNNNNNN
12422839 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
*
12422881 TA TA CA TA T
1 TA TA TA TA T
12422890 GTAAATGTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12432156 original size:23 final size:23
Alignment explanation
Indices: 12432126--12432185 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
12432116 TATACGTATA
* * *
12432126 CCCATCATTATCATGCACATCAT
1 CCCATCATCATCATACACACCAT
12432149 CCCATCATCATCATACACACCAT
1 CCCATCATCATCATACACACCAT
*
12432172 CACATCATCATCAT
1 CCCATCATCATCAT
12432186 CACCAACTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.33, C:0.38, G:0.02, T:0.27
Consensus pattern (23 bp):
CCCATCATCATCATACACACCAT
Done.