Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 110 of 171
Found at i:35336862 original size:14 final size:14
Alignment explanation
Indices: 35336809--35336867 Score: 68
Period size: 14 Copynumber: 4.4 Consensus size: 14
35336799 ATTGTTTCTA
* *
35336809 ATTTAGGGTTGAGG
1 ATTTAGAGTTTAGG
* *
35336823 -TTTAGGGTTTAAG
1 ATTTAGAGTTTAGG
35336836 ATTTAGAGTTTAGG
1 ATTTAGAGTTTAGG
35336850 ATTTAGAGTTTAGG
1 ATTTAGAGTTTAGG
35336864 -TTTA
1 ATTTA
35336868 TAGGTATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
13 15 0.38
14 25 0.62
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (14 bp):
ATTTAGAGTTTAGG
Found at i:35339140 original size:16 final size:16
Alignment explanation
Indices: 35339119--35339167 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
35339109 GGATGAGAAT
35339119 ATTATTTTGGTAATTA
1 ATTATTTTGGTAATTA
*
35339135 ATTATTTT-TTATATT-
1 ATTATTTTGGTA-ATTA
35339150 A-TATTTTGGTAATTA
1 ATTATTTTGGTAATTA
35339165 ATT
1 ATT
35339168 TAGAGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 12 0.44
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (16 bp):
ATTATTTTGGTAATTA
Found at i:35339814 original size:13 final size:13
Alignment explanation
Indices: 35339796--35339824 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35339786 ACAAATTAAA
35339796 AAATTTTAAAAAT
1 AAATTTTAAAAAT
35339809 AAA-TTTAAAAAT
1 AAATTTTAAAAAT
35339821 AAAT
1 AAAT
35339825 ACATTACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
12 12 0.80
13 3 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATTTTAAAAAT
Found at i:35339865 original size:23 final size:21
Alignment explanation
Indices: 35339834--35339917 Score: 79
Period size: 20 Copynumber: 4.1 Consensus size: 21
35339824 TACATTACTT
*
35339834 TTCTCTCTTTCTCTTTCTCCTTC
1 TTCTTTCTTT-TC-TTCTCCTTC
35339857 TTCTTTC-TTTCTTCTCCTTC
1 TTCTTTCTTTTCTTCTCCTTC
*
35339877 TTCTTT-TTTCCTTCT--TTC
1 TTCTTTCTTTTCTTCTCCTTC
*
35339895 TTTCTTTCTTTTCTT-TCTTTC
1 -TTCTTTCTTTTCTTCTCCTTC
35339916 TT
1 TT
35339918 TTTTTTCAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
18 3 0.06
19 7 0.13
20 30 0.57
21 5 0.09
22 2 0.04
23 6 0.11
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (21 bp):
TTCTTTCTTTTCTTCTCCTTC
Found at i:35339866 original size:4 final size:4
Alignment explanation
Indices: 35339857--35339918 Score: 74
Period size: 4 Copynumber: 15.5 Consensus size: 4
35339847 TTTCTCCTTC
* *
35339857 TTCT TTCT TTCT TCTCC TTC- TTCT TT-T TTCC TTCT TTCT TTCT TTCTT
1 TTCT TTCT TTCT T-TCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC-T
35339905 TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TT
35339919 TTTTTCAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
3 6 0.12
4 38 0.75
5 7 0.14
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TTCT
Found at i:35339867 original size:17 final size:18
Alignment explanation
Indices: 35339845--35339918 Score: 75
Period size: 17 Copynumber: 4.3 Consensus size: 18
35339835 TCTCTCTTTC
35339845 TCTTTCTCCTTC-TTCTT
1 TCTTTCTCCTTCTTTCTT
* *
35339862 TCTTTCTTC-TCCTTC-T
1 TCTTTCTCCTTCTTTCTT
*
35339878 TCTTTTTTCCTTCTTTCTT
1 TC-TTTCTCCTTCTTTCTT
*
35339897 TCTTTCT-TTTCTTTCTT
1 TCTTTCTCCTTCTTTCTT
35339914 TCTTT
1 TCTTT
35339919 TTTTTCAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
16 5 0.11
17 30 0.64
18 9 0.19
19 3 0.06
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TCTTTCTCCTTCTTTCTT
Found at i:35339871 original size:20 final size:20
Alignment explanation
Indices: 35339834--35339905 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
35339824 TACATTACTT
*
35339834 TTCTCTCTTTCTCT-TTCTCC
1 TTCT-TCTTTCTTTCTTCTCC
35339854 TTCTTCTTTCTTTCTTCTCC
1 TTCTTCTTTCTTTCTTCTCC
35339874 TTCTTCTTT-TTTCCTTCT--
1 TTCTTCTTTCTTT-CTTCTCC
35339892 TTCTTTCTTTCTTT
1 TTC-TTCTTTCTTT
35339906 TCTTTCTTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
18 3 0.06
19 17 0.36
20 27 0.57
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTTCTTTCTTTCTTCTCC
Found at i:35339903 original size:35 final size:35
Alignment explanation
Indices: 35339839--35339921 Score: 114
Period size: 35 Copynumber: 2.3 Consensus size: 35
35339829 TACTTTTCTC
*
35339839 TCTTTCTCTTTCTCCTTCTTCTTTCTTTCTTCTCCT
1 TCTTTCT-TTTTTCCTTCTTCTTTCTTTCTTCTCCT
* *
35339875 TC-TTCTTTTTTCCTTCTTTCTTTCTTTCTTTTCTT
1 TCTTTCTTTTTTCCTTC-TTCTTTCTTTCTTCTCCT
35339910 TCTTTCTTTTTT
1 TCTTTCTTTTTT
35339922 TTCAATACCA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 9 0.21
35 22 0.52
36 11 0.26
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (35 bp):
TCTTTCTTTTTTCCTTCTTCTTTCTTTCTTCTCCT
Found at i:35341138 original size:54 final size:54
Alignment explanation
Indices: 35341056--35341163 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
35341046 TGTTAAGCAG
35341056 CTTATACCACCACCTCTCTTTTTGTTGGCAAGGAAGAGTCAAATCCAACCAACA
1 CTTATACCACCACCTCTCTTTTTGTTGGCAAGGAAGAGTCAAATCCAACCAACA
35341110 CTTATACCACCACCTCTCTTTTTGTTGGCAAGGAAGAGTCAAATCCAACCAACA
1 CTTATACCACCACCTCTCTTTTTGTTGGCAAGGAAGAGTCAAATCCAACCAACA
35341164 ATAATGATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.26
Consensus pattern (54 bp):
CTTATACCACCACCTCTCTTTTTGTTGGCAAGGAAGAGTCAAATCCAACCAACA
Found at i:35341323 original size:10 final size:11
Alignment explanation
Indices: 35341308--35341336 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
35341298 TAGTTGATAG
35341308 TGGGTCAGG-T
1 TGGGTCAGGTT
35341318 TGGGTCAGGTT
1 TGGGTCAGGTT
35341329 TGGGTCAG
1 TGGGTCAG
35341337 ATTCGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.10, C:0.10, G:0.48, T:0.31
Consensus pattern (11 bp):
TGGGTCAGGTT
Found at i:35341757 original size:23 final size:23
Alignment explanation
Indices: 35341714--35341779 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 23
35341704 AGCATCCAAA
35341714 CAACAAAAGCAACAA-ACAAAATAG
1 CAACAAAA-CAACAACA-AAAATAG
*
35341738 -AAGCGAAACAACAACAAAAATAG
1 CAA-CAAAACAACAACAAAAATAG
*
35341761 CAACAAAAAAACAACAAAA
1 CAACAAAACAACAACAAAA
35341780 TTAACAGCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
23 29 0.81
24 7 0.19
ACGTcount: A:0.70, C:0.20, G:0.08, T:0.03
Consensus pattern (23 bp):
CAACAAAACAACAACAAAAATAG
Found at i:35341790 original size:23 final size:23
Alignment explanation
Indices: 35341747--35341791 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
35341737 GAAGCGAAAC
*
35341747 AACAACAAAAATAGCAACAAAAA
1 AACAACAAAAATAACAACAAAAA
* *
35341770 AACAACAAAATTAACAGCAAAA
1 AACAACAAAAATAACAACAAAA
35341792 GCAGCACCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.71, C:0.18, G:0.04, T:0.07
Consensus pattern (23 bp):
AACAACAAAAATAACAACAAAAA
Found at i:35341819 original size:20 final size:21
Alignment explanation
Indices: 35341796--35341836 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35341786 GCAAAAGCAG
*
35341796 CACC-AAAATAATAAAAAAAA
1 CACCAAAAACAATAAAAAAAA
35341816 CACCAAAAACAATAAAAAAAA
1 CACCAAAAACAATAAAAAAAA
35341837 AAATAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.76, C:0.17, G:0.00, T:0.07
Consensus pattern (21 bp):
CACCAAAAACAATAAAAAAAA
Found at i:35341847 original size:22 final size:21
Alignment explanation
Indices: 35341800--35341858 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
35341790 AAGCAGCACC
* * *
35341800 AAAATAATAAAAAAAACACCA
1 AAAACAATAAAAAAAAAAACA
*
35341821 AAAACAATAAAAAAAAAAATA
1 AAAACAATAAAAAAAAAAACA
**
35341842 AGAAACAGCAAAAAAAA
1 A-AAACAATAAAAAAAA
35341859 TAGCAATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.80, C:0.10, G:0.03, T:0.07
Consensus pattern (21 bp):
AAAACAATAAAAAAAAAAACA
Found at i:35343332 original size:86 final size:81
Alignment explanation
Indices: 35343214--35343398 Score: 228
Period size: 86 Copynumber: 2.2 Consensus size: 81
35343204 TAATCTTTTT
* * *
35343214 TTTTTAAAAAAAACAATAAAGCATTTTTTTTGCACTCATTTGAGTACTTGAACTTTTAAAATGCA
1 TTTTT-AAAAAAACAATTAAGCATTTTTTTTGCACTCAATTGAGTACTTAAACTTTTAAAATGCA
35343279 TCAAATAAACCCTCAAATC
65 TCAAA-AAACCCTCAAA-C
*
35343298 TTTTTAAAAAAACAATTAAGCCTCTATTTTTTTGCACTCAATTGAGTACTTAAACTTTTAAAATG
1 TTTTTAAAAAAACAATTAAG-C-AT-TTTTTTTGCACTCAATTGAGTACTTAAACTTTTAAAATG
* * * *
35343363 TATCAAAAGATCTTCAAAC
63 CATCAAAAAACCCTCAAAC
*
35343382 -ATTTAAAAAAACAATTA
1 TTTTTAAAAAAACAATTA
35343399 TGCCCCTAAT
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
83 30 0.34
84 7 0.08
85 9 0.10
86 43 0.48
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (81 bp):
TTTTTAAAAAAACAATTAAGCATTTTTTTTGCACTCAATTGAGTACTTAAACTTTTAAAATGCAT
CAAAAAACCCTCAAAC
Found at i:35343856 original size:17 final size:17
Alignment explanation
Indices: 35343834--35343867 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
35343824 AAAGAGAATT
35343834 TTTTTATGCATTT-TATA
1 TTTTTATG-ATTTCTATA
35343851 TTTTTATGATTTCTATA
1 TTTTTATGATTTCTATA
35343868 AAATTGTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTTATGATTTCTATA
Found at i:35343940 original size:10 final size:9
Alignment explanation
Indices: 35343921--35344008 Score: 56
Period size: 9 Copynumber: 9.7 Consensus size: 9
35343911 TTTTAATAAA
35343921 TTTAATTTT
1 TTTAATTTT
35343930 TTTATATTTT
1 TTTA-ATTTT
*
35343940 TATTAAAATTT
1 T-TT-AATTTT
**
35343951 AATAATTTT
1 TTTAATTTT
* *
35343960 TCTAAAGTTT
1 T-TTAATTTT
*
35343970 ATT-A-TTT
1 TTTAATTTT
*
35343977 TTTATTTTT
1 TTTAATTTT
35343986 TTTAA-TTT
1 TTTAATTTT
35343994 TTTAATTTT
1 TTTAATTTT
35344003 TTTAAT
1 TTTAAT
35344009 AAGAGAAAGG
Statistics
Matches: 59, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
7 5 0.08
8 9 0.15
9 26 0.44
10 12 0.20
11 6 0.10
12 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (9 bp):
TTTAATTTT
Found at i:35343959 original size:27 final size:26
Alignment explanation
Indices: 35343909--35343959 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
35343899 CAAAATTCTA
**
35343909 ATTTTTAATAAATTTAATTTTTTTAT
1 ATTTTTAATAAATTTAATAATTTTAT
*
35343935 ATTTTTATTAAAATTTAATAATTTT
1 ATTTTTAAT-AAATTTAATAATTTT
35343960 TCTAAAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATTTTTAATAAATTTAATAATTTTAT
Found at i:35343993 original size:17 final size:17
Alignment explanation
Indices: 35343973--35344008 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
35343963 AAAGTTTATT
*
35343973 ATTTTTTATTTTTTTTA
1 ATTTTTTAATTTTTTTA
35343990 ATTTTTTAATTTTTTTA
1 ATTTTTTAATTTTTTTA
35344007 AT
1 AT
35344009 AAGAGAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
ATTTTTTAATTTTTTTA
Found at i:35344116 original size:88 final size:90
Alignment explanation
Indices: 35344017--35344190 Score: 228
Period size: 89 Copynumber: 2.0 Consensus size: 90
35344007 ATAAGAGAAA
* *
35344017 GGGCTTAATTGCTTTTTTTGAAAAATTTTAAG-GGTCTTTGTAATGCATTTTGAAAGTTCAAGT-
1 GGGCTTAATTGCTTTTTTTGAAAAAGTTTAAGAGGTCTTTGTAATGCATTTTAAAAGTTCAAGTG
*
35344080 ATCCAATTGAATG-AAAAAAAAGCAG
66 CT-CAATTGAATGTAAAAAAAAGCAG
* * * * * *
35344105 GGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGAGTTTTTTTTGATGCATTTTAAAAGTTCAAGTG
1 GGGCTTAATTGCTTTTTTTGAAAAAGTTTAAGAGGTCTTTGTAATGCATTTTAAAAGTTCAAGTG
*
35344170 CTCAATTGAGTGTAAAAAAAA
66 CTCAATTGAATGTAAAAAAAA
35344191 ACTTAATTTA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
88 29 0.40
89 35 0.48
90 9 0.12
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (90 bp):
GGGCTTAATTGCTTTTTTTGAAAAAGTTTAAGAGGTCTTTGTAATGCATTTTAAAAGTTCAAGTG
CTCAATTGAATGTAAAAAAAAGCAG
Found at i:35346643 original size:20 final size:20
Alignment explanation
Indices: 35346604--35346643 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
35346594 TTTAGCTTTT
* * *
35346604 TTAAAAAAATTTAAATTCAA
1 TTAAAAAAACTGAAAATCAA
35346624 TTAAAAAAACTGAAAATCAA
1 TTAAAAAAACTGAAAATCAA
35346644 GAGAAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (20 bp):
TTAAAAAAACTGAAAATCAA
Found at i:35351339 original size:17 final size:17
Alignment explanation
Indices: 35351308--35351342 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
35351298 TATTTTTATT
**
35351308 TTTTAAATTTTTAAAAA
1 TTTTAAATTAATAAAAA
35351325 TTTTAAATTAATAAAAA
1 TTTTAAATTAATAAAAA
35351342 T
1 T
35351343 AAAATTATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAAATTAATAAAAA
Found at i:35351387 original size:30 final size:29
Alignment explanation
Indices: 35351340--35351398 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
35351330 AATTAATAAA
*
35351340 AATAAAATTATACTTTAATTTTTTTAAAAT
1 AATAAAATTATACTTTAA-TCTTTTAAAAT
*
35351370 AATAAAATTTTTA-TTTAATCTTTTAAAAT
1 AATAAAA-TTATACTTTAATCTTTTAAAAT
35351399 TATAGATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 10 0.38
30 12 0.46
31 4 0.15
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (29 bp):
AATAAAATTATACTTTAATCTTTTAAAAT
Found at i:35353523 original size:5 final size:5
Alignment explanation
Indices: 35353513--35353547 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
35353503 AGGGAAAAGA
*
35353513 AGAGG AGAGG AGAGG AGGGG AGAGG AGAGG AGAGG
1 AGAGG AGAGG AGAGG AGAGG AGAGG AGAGG AGAGG
35353548 CTAAAGAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (5 bp):
AGAGG
Found at i:35355883 original size:22 final size:24
Alignment explanation
Indices: 35355852--35355901 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
35355842 CGAATAAAAA
*
35355852 ATTAAAATTA-TTTA-TTT-TTTT
1 ATTAAAATTAGTTAATTTTGTTTT
35355873 ATTAATAATTAGTTAATTTTGTTTT
1 ATTAA-AATTAGTTAATTTTGTTTT
35355898 ATTA
1 ATTA
35355902 TTTTAGTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 5 0.21
23 3 0.12
24 3 0.12
25 8 0.33
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTAAAATTAGTTAATTTTGTTTT
Found at i:35356564 original size:103 final size:104
Alignment explanation
Indices: 35356433--35356627 Score: 347
Period size: 103 Copynumber: 1.9 Consensus size: 104
35356423 AAATGATAAA
* *
35356433 ATGGTAGAAATTTTTTTGGGTGTTTGGTTGATGAGAAAATGTAAGAAAATATAGTAAAAATTGTT
1 ATGGAAGAAATTTTTTTAGGTGTTTGGTTGATGAGAAAATGTAAGAAAATATAGTAAAAATTGTT
35356498 TGATGGGAAGAAAATATAAGAAAATGGATTCTCATCTTC
66 TGATGGGAAGAAAATATAAGAAAATGGATTCTCATCTTC
* *
35356537 ATGGAAGAAA-TTTTTTAGGTGTTTGGTTGATGAGAAAATGTAATAAAATATAGTTAAAATTGTT
1 ATGGAAGAAATTTTTTTAGGTGTTTGGTTGATGAGAAAATGTAAGAAAATATAGTAAAAATTGTT
35356601 TGATGGGAAGAAAATATAAGAAAATGG
66 TGATGGGAAGAAAATATAAGAAAATGG
35356628 GTAAAATAAA
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
103 78 0.90
104 9 0.10
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.34
Consensus pattern (104 bp):
ATGGAAGAAATTTTTTTAGGTGTTTGGTTGATGAGAAAATGTAAGAAAATATAGTAAAAATTGTT
TGATGGGAAGAAAATATAAGAAAATGGATTCTCATCTTC
Found at i:35360352 original size:87 final size:87
Alignment explanation
Indices: 35360224--35360396 Score: 238
Period size: 87 Copynumber: 2.0 Consensus size: 87
35360214 ACTGTCGACT
* * * * * *
35360224 TTGGAAAATTGAGTGGTCACTCTTGAAGAGTCCATATGGGACGTCAAGGAAAAGCTCGATGAAGT
1 TTGGAAAATGGAGTGGTCACTCTTAAAGAGTCCATAGGGGACGCCAAGGAAAAGCTCAATAAAGT
35360289 CGAGGAGGGACTCCCAAGTGGA
66 CGAGGAGGGACTCCCAAGTGGA
* * * *
35360311 TTGGAAAATGGAGTGGTCACTTTTAAAGAGTCTATGGGGGACGCCAAGGAGAAGCTCAATAAAGT
1 TTGGAAAATGGAGTGGTCACTCTTAAAGAGTCCATAGGGGACGCCAAGGAAAAGCTCAATAAAGT
* *
35360376 CTAGGAGGGACTCTCAAGTGG
66 CGAGGAGGGACTCCCAAGTGG
35360397 CTTGCAATCC
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.21
Consensus pattern (87 bp):
TTGGAAAATGGAGTGGTCACTCTTAAAGAGTCCATAGGGGACGCCAAGGAAAAGCTCAATAAAGT
CGAGGAGGGACTCCCAAGTGGA
Found at i:35364262 original size:30 final size:30
Alignment explanation
Indices: 35364228--35364288 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
35364218 AAAGAAGTAG
35364228 CCAAGGAGTGAAAAAAGAAGAAAAGGTTTT
1 CCAAGGAGTGAAAAAAGAAGAAAAGGTTTT
*
35364258 CCAAGGAGTGAAAAAAGAAGAAAATGTTTT
1 CCAAGGAGTGAAAAAAGAAGAAAAGGTTTT
35364288 C
1 C
35364289 TCCAAGTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.49, C:0.08, G:0.25, T:0.18
Consensus pattern (30 bp):
CCAAGGAGTGAAAAAAGAAGAAAAGGTTTT
Found at i:35364820 original size:24 final size:24
Alignment explanation
Indices: 35364789--35364877 Score: 99
Period size: 24 Copynumber: 3.7 Consensus size: 24
35364779 CAAATGAAAG
*
35364789 TGGCACTTCGATGCAATTGAAATG
1 TGGCACTTCGATGCAATTGAAATA
* * *
35364813 TGGCACTTTGGTGCAATTGAATTA
1 TGGCACTTCGATGCAATTGAAATA
35364837 TGGCACTTC-AGTGCAATTGAAATA
1 TGGCACTTCGA-TGCAATTGAAATA
** *
35364861 TAACACTTCGGTGCAAT
1 TGGCACTTCGATGCAAT
35364878 ACTGTGATTG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31
Consensus pattern (24 bp):
TGGCACTTCGATGCAATTGAAATA
Found at i:35369240 original size:10 final size:10
Alignment explanation
Indices: 35369211--35369246 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
35369201 TTCTTTTTCA
35369211 CTCAAATCTCT
1 CTCAAA-CTCT
35369222 CTC-AACTCT
1 CTCAAACTCT
35369231 CTCAAACTCT
1 CTCAAACTCT
35369241 CTCAAA
1 CTCAAA
35369247 TCCACTACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.29
10 14 0.58
11 3 0.12
ACGTcount: A:0.31, C:0.39, G:0.00, T:0.31
Consensus pattern (10 bp):
CTCAAACTCT
Found at i:35379086 original size:14 final size:14
Alignment explanation
Indices: 35379069--35379105 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
35379059 CTTTAACCTT
35379069 AAATCCAAAACCCA
1 AAATCCAAAACCCA
*
35379083 AAATCCAAAACTCA
1 AAATCCAAAACCCA
*
35379097 AAATTCAAA
1 AAATCCAAA
35379106 CCTCAAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (14 bp):
AAATCCAAAACCCA
Found at i:35379110 original size:14 final size:14
Alignment explanation
Indices: 35379069--35379112 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
35379059 CTTTAACCTT
35379069 AAATCCAAAACC-CA
1 AAATCC-AAACCTCA
*
35379083 AAATCCAAAACTCA
1 AAATCCAAACCTCA
*
35379097 AAATTCAAACCTCA
1 AAATCCAAACCTCA
35379111 AA
1 AA
35379113 CCTTAAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 4 0.15
14 22 0.85
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (14 bp):
AAATCCAAACCTCA
Found at i:35379143 original size:20 final size:20
Alignment explanation
Indices: 35379103--35379153 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
35379093 CTCAAAATTC
35379103 AAACCTCAAACCTTAAATCTT
1 AAACCT-AAACCTTAAATCTT
* *
35379124 AAACCTAAATCTTGAATCTT
1 AAACCTAAACCTTAAATCTT
35379144 AAACCCTAAA
1 AAA-CCTAAA
35379154 ATAGTTGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.27
Consensus pattern (20 bp):
AAACCTAAACCTTAAATCTT
Found at i:35380832 original size:107 final size:108
Alignment explanation
Indices: 35380701--35380905 Score: 297
Period size: 109 Copynumber: 1.9 Consensus size: 108
35380691 GATGAAGAGG
* * *
35380701 GACAAAGAATCTCTAAATCTGAAAACCAAAAACCTTGAC-AAGCCCACTGAAA-ATAGAATTAAA
1 GACAAAGAATCTCTAAATCTGAAAACCAAAAACCATGACAAAACCCACTGAAATATA-AAGTAAA
*
35380764 AAGAAGCATATATCTGAAACTAAAAACAGAGATAAAAACGAAAA
65 AAGAAGCATATATCTAAAACTAAAAACAGAGATAAAAACGAAAA
* * * *
35380808 GACAAAGGATCTTTAAATCTGAAAACCAAAAACCATGACAAAAACCCATTGAAATTTAAAGTAAA
1 GACAAAGAATCTCTAAATCTGAAAACCAAAAACCATGAC-AAAACCCACTGAAATATAAAGTAAA
*
35380873 AAGAAGCATATATCTAAAACTAAAAAGAGAGAT
65 AAGAAGCATATATCTAAAACTAAAAACAGAGAT
35380906 GGAAAGGAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 36 0.42
109 48 0.56
110 2 0.02
ACGTcount: A:0.55, C:0.16, G:0.12, T:0.18
Consensus pattern (108 bp):
GACAAAGAATCTCTAAATCTGAAAACCAAAAACCATGACAAAACCCACTGAAATATAAAGTAAAA
AGAAGCATATATCTAAAACTAAAAACAGAGATAAAAACGAAAA
Found at i:35381258 original size:22 final size:22
Alignment explanation
Indices: 35381223--35381268 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
35381213 TACTTTTTTA
**
35381223 TTTTTTTAAACCAATTGTCACT
1 TTTTTTTAAACCAACGGTCACT
* *
35381245 TTTTTTTTATCCAACGGTCACT
1 TTTTTTTAAACCAACGGTCACT
35381267 TT
1 TT
35381269 AAGGATACCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTTTTTAAACCAACGGTCACT
Found at i:35382483 original size:14 final size:15
Alignment explanation
Indices: 35382445--35382483 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
35382435 TAAAAACCCC
* *
35382445 AAACCCTAAATCTTT
1 AAACCCTAAATCATG
35382460 AAACCCTAAATCATG
1 AAACCCTAAATCATG
35382475 AAA-CCTAAA
1 AAACCCTAAA
35382484 ATCGTTGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.49, C:0.26, G:0.03, T:0.23
Consensus pattern (15 bp):
AAACCCTAAATCATG
Found at i:35384231 original size:109 final size:106
Alignment explanation
Indices: 35383984--35384254 Score: 361
Period size: 109 Copynumber: 2.5 Consensus size: 106
35383974 AATCCACTGA
* * *
35383984 AAAATTGAAATAAAAAGAAGGATATATCTGAAACTAAAAACAGAGATTAAAAG---GGATAAAGG
1 AAAATT-AAATAAAAAGAAGAATATATCTGAAACTAAAAACAGAGATGAAAAGAAAAGATAAAGG
* *
35384046 ATCTCTAACTCTAAAAACCAAAAAACTTGACAAAACCCATTG
65 ATCTCTAAATCTAAAAACCAAAAAACCTGACAAAACCCATTG
*
35384088 AAAA-TAGAATTAAAAAGAAGCATATATCTGAAACTAAAAACAGAGATGAAAACGAAAAGATAAA
1 AAAATTA-AA-TAAAAAGAAGAATATATCTGAAACTAAAAACAGAGATGAAAA-GAAAAGATAAA
* *
35384152 GGATCTCTAAATCTGAAAACCAAAAACCCTGACAAAAACCCATTG
63 GGATCTCTAAATCTAAAAACCAAAAAACCTGAC-AAAACCCATTG
* *
35384197 AAAATTAAAGTAAAAAGAAGAATATATCTAAAACTAAAAACAAAGATGAAAAGGAAAA
1 AAAATTAAA-TAAAAAGAAGAATATATCTGAAACTAAAAACAGAGATGAAAA-GAAAA
35384255 AGGCAACGTT
Statistics
Matches: 147, Mismatches: 12, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
102 1 0.01
103 3 0.02
104 44 0.30
105 1 0.01
108 35 0.24
109 61 0.41
110 2 0.01
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (106 bp):
AAAATTAAATAAAAAGAAGAATATATCTGAAACTAAAAACAGAGATGAAAAGAAAAGATAAAGGA
TCTCTAAATCTAAAAACCAAAAAACCTGACAAAACCCATTG
Found at i:35386779 original size:16 final size:16
Alignment explanation
Indices: 35386758--35386789 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
35386748 GTCCCTCAAC
35386758 AGGTCACTTTTCAGTG
1 AGGTCACTTTTCAGTG
35386774 AGGTCACTTTTCAGTG
1 AGGTCACTTTTCAGTG
35386790 CTCTCTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (16 bp):
AGGTCACTTTTCAGTG
Found at i:35388790 original size:52 final size:52
Alignment explanation
Indices: 35388722--35389021 Score: 460
Period size: 52 Copynumber: 5.8 Consensus size: 52
35388712 TAAACGGAAA
*
35388722 AGGTCCGATCACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
35388774 AGATCCGATGATTATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * *
35388826 AGGTTCGATGACTATGTGCCATCGTGAGTATATAAATCTTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
35388878 AGAAT-TGATGACTATG-GTCATCGTGAGTATATGAATCCTTTACGAATTATG
1 AG-GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
35388929 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
35388981 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTT
35389022 CGTGAGTATA
Statistics
Matches: 223, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
50 1 0.00
51 44 0.20
52 177 0.79
53 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:35388938 original size:103 final size:104
Alignment explanation
Indices: 35388722--35389021 Score: 478
Period size: 103 Copynumber: 2.9 Consensus size: 104
35388712 TAAACGGAAA
* * *
35388722 AGGTCCGATCACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGATCCGATGATT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGAGATCCGATGACT
* *
35388787 ATGTGTCATCATGAGTATATGAATCCTTTACGGATTATG
66 ATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
* * * * *
35388826 AGGTTCGATGACTATGTGCCATCGTGAGTATATAAATCTTTTACGAATTATGAGAAT-TGATGAC
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGAG-ATCCGATGAC
35388890 TATG-GTCATCGTGAGTATATGAATCCTTTACGAATTATG
65 TATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
*
35388929 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGAGGTCCGATGACT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGAGATCCGATGACT
35388994 ATGTGTCATCGTGAGTATATGAATCCTT
66 ATGTGTCATCGTGAGTATATGAATCCTT
35389022 CGTGAGTATA
Statistics
Matches: 177, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
102 1 0.01
103 93 0.53
104 81 0.46
105 2 0.01
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (104 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGAGATCCGATGACT
ATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
Found at i:35389026 original size:19 final size:19
Alignment explanation
Indices: 35389002--35389040 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
35388992 CTATGTGTCA
35389002 TCGTGAGTATATGAATCCT
1 TCGTGAGTATATGAATCCT
35389021 TCGTGAGTATATGAATCCT
1 TCGTGAGTATATGAATCCT
35389040 T
1 T
35389041 TACAAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (19 bp):
TCGTGAGTATATGAATCCT
Found at i:35389066 original size:71 final size:71
Alignment explanation
Indices: 35388950--35389089 Score: 217
Period size: 71 Copynumber: 2.0 Consensus size: 71
35388940 CTATGTGTCA
* ** * *
35388950 TCGTGAGTATATGAATCTTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATG
1 TCGTGAGTATATGAATCCTTTACAAATTATGAGATCCGATGACTATGTGTCATCATGAGTATATG
35389015 AATCCT
66 AATCCT
* *
35389021 TCGTGAGTATATGAATCCTTTACAAATTATGAGATTCGATGACTATGTGTCTTCATGAGTATATG
1 TCGTGAGTATATGAATCCTTTACAAATTATGAGATCCGATGACTATGTGTCATCATGAGTATATG
35389086 AATC
66 AATC
35389090 ATTTACGGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (71 bp):
TCGTGAGTATATGAATCCTTTACAAATTATGAGATCCGATGACTATGTGTCATCATGAGTATATG
AATCCT
Found at i:35389086 original size:52 final size:52
Alignment explanation
Indices: 35389021--35389238 Score: 294
Period size: 52 Copynumber: 4.2 Consensus size: 52
35389011 TATGAATCCT
** * *
35389021 TCGTGAGTATATGAATCCTTTACAAATTATGAGATTCGATGACTATGTGTCT
1 TCGTGAGTATATGAATCCTTTACGGATTATGAGGTTCGATGACTATGTGTCA
* * * * *
35389073 TCATGAGTATATGAATCATTTACGGATTATGAGGTCCGATGATTATGTCTCA
1 TCGTGAGTATATGAATCCTTTACGGATTATGAGGTTCGATGACTATGTGTCA
35389125 TCGTGAGTATATGAATCCTTTACGGATTATGAGGTTCGATGACTATGTGTCA
1 TCGTGAGTATATGAATCCTTTACGGATTATGAGGTTCGATGACTATGTGTCA
* * * * *
35389177 TCGTGAGCATATGAATCCTTTTTCGGATT-TAAGGTCCGATGACTTTGTGTCA
1 TCGTGAGTATATGAATCC-TTTACGGATTATGAGGTTCGATGACTATGTGTCA
35389229 TCGTGAGTAT
1 TCGTGAGTAT
35389239 TAAATGAGAA
Statistics
Matches: 145, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
52 136 0.94
53 9 0.06
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (52 bp):
TCGTGAGTATATGAATCCTTTACGGATTATGAGGTTCGATGACTATGTGTCA
Found at i:35389120 original size:123 final size:123
Alignment explanation
Indices: 35388898--35389144 Score: 422
Period size: 123 Copynumber: 2.0 Consensus size: 123
35388888 ACTATGGTCA
* * *
35388898 TCGTGAGTATATGAATCCTTTACGAATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATG
1 TCGTGAGTATATGAATCCTTTACAAATTATGAGATCCGATGACTATGTGTCATCATGAGTATATG
* *
35388963 AATCTTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCT
66 AATCATTTACGGATTATGAGGTCCGATGACTATGTCTCATCGTGAGTATATGAATCCT
* *
35389021 TCGTGAGTATATGAATCCTTTACAAATTATGAGATTCGATGACTATGTGTCTTCATGAGTATATG
1 TCGTGAGTATATGAATCCTTTACAAATTATGAGATCCGATGACTATGTGTCATCATGAGTATATG
*
35389086 AATCATTTACGGATTATGAGGTCCGATGATTATGTCTCATCGTGAGTATATGAATCCT
66 AATCATTTACGGATTATGAGGTCCGATGACTATGTCTCATCGTGAGTATATGAATCCT
35389144 T
1 T
35389145 TACGGATTAT
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 116 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (123 bp):
TCGTGAGTATATGAATCCTTTACAAATTATGAGATCCGATGACTATGTGTCATCATGAGTATATG
AATCATTTACGGATTATGAGGTCCGATGACTATGTCTCATCGTGAGTATATGAATCCT
Found at i:35389137 original size:175 final size:174
Alignment explanation
Indices: 35388847--35389196 Score: 567
Period size: 175 Copynumber: 2.0 Consensus size: 174
35388837 CTATGTGCCA
* * *
35388847 TCGTGAGTATATAAATCTTTTACGAATTATGAGAATTGATGACTATGGTCATCGTGAGTATATGA
1 TCGTGAGTATATAAATCCTTTACAAATTATGAGAATTGATGACTATGGTCATCATGAGTATATGA
* * *
35388912 ATCCTTTACGAATTATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGAT
66 ATCATTTACGAATTATGAGGTCCGATGACTATGTCTCATCGTGAGTATATGAATCCTTTACGGAT
*
35388977 TATGAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCT
131 TATGAGGTCCGATGACTATGTGTCATCGTGAGCATATGAATCCT
* *
35389021 TCGTGAGTATATGAATCCTTTACAAATTATGAG-ATTCGATGACTATGTGTCTTCATGAGTATAT
1 TCGTGAGTATATAAATCCTTTACAAATTATGAGAATT-GATGACTATG-GTCATCATGAGTATAT
* *
35389085 GAATCATTTACGGATTATGAGGTCCGATGATTATGTCTCATCGTGAGTATATGAATCCTTTACGG
64 GAATCATTTACGAATTATGAGGTCCGATGACTATGTCTCATCGTGAGTATATGAATCCTTTACGG
*
35389150 ATTATGAGGTTCGATGACTATGTGTCATCGTGAGCATATGAATCCT
129 ATTATGAGGTCCGATGACTATGTGTCATCGTGAGCATATGAATCCT
35389196 T
1 T
35389197 TTTCGGATTT
Statistics
Matches: 162, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
173 3 0.02
174 40 0.25
175 119 0.73
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (174 bp):
TCGTGAGTATATAAATCCTTTACAAATTATGAGAATTGATGACTATGGTCATCATGAGTATATGA
ATCATTTACGAATTATGAGGTCCGATGACTATGTCTCATCGTGAGTATATGAATCCTTTACGGAT
TATGAGGTCCGATGACTATGTGTCATCGTGAGCATATGAATCCT
Found at i:35393844 original size:52 final size:52
Alignment explanation
Indices: 35393766--35394103 Score: 455
Period size: 52 Copynumber: 6.5 Consensus size: 52
35393756 TAAACGGAAA
*
35393766 AGGTCCGATCACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
35393818 AGGTTCGATGACTATTTGTCGTCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * *
35393870 AGGTTCGATGACTATGTGCCATCGTGAGTATATAAATCTTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* ** *
35393922 AGATTTGATGACTATG-GTCATCGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
35393973 AGGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTACAGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * *
35394025 AGGTCCGATGACTATGTGTCATCATGAGCATATGAATCCTTTTTCAGATT-TA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTTACGGATTATG
*
35394077 AGGTCCGATGACTTTGTGTCATCGTGA
1 AGGTCCGATGACTATGTGTCATCGTGA
35394104 ATATTAAATG
Statistics
Matches: 256, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
51 43 0.17
52 204 0.80
53 9 0.04
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:35394087 original size:155 final size:156
Alignment explanation
Indices: 35393765--35394103 Score: 468
Period size: 155 Copynumber: 2.2 Consensus size: 156
35393755 ATAAACGGAA
* * *
35393765 AAGGTCCGATCACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTTCGATGAC
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATGAC
* * * * * *
35393830 TATTTGTCGTCGTGAGTATATGAATCCTTTACGGATTATGAGGTTCGATGACTATGTGCCATCGT
66 TATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAGGTCCGATGACTATGTGCCATCAT
*
35393895 GAGTATATAAATCTTTTACGAATTAT
131 GAGCATATAAATCTTTTACGAATTAT
* * **
35393921 GAGATTTGATGACTATG-GTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATGAC
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATGAC
* *
35393985 TATGTGTCATTGTGAGTATATGAATCCTTTACAGATTATAAGGTCCGATGACTATGTGTCATCAT
66 TATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAGGTCCGATGACTATGTGCCATCAT
* *
35394050 GAGCATATGAATCCTTTTTC-AGATT-T
131 GAGCATATAAAT-CTTTTACGA-ATTAT
*
35394076 AAGGTCCGATGACTTTGTGTCATCGTGA
1 AAGGTCCGATGACTATGTGTCATCGTGA
35394104 ATATTAAATG
Statistics
Matches: 157, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
155 126 0.80
156 31 0.20
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (156 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATGAC
TATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAGGTCCGATGACTATGTGCCATCAT
GAGCATATAAATCTTTTACGAATTAT
Found at i:35395955 original size:14 final size:14
Alignment explanation
Indices: 35395936--35395962 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35395926 GATCCTGGGA
35395936 AAACTAATTTGTTG
1 AAACTAATTTGTTG
35395950 AAACTAATTTGTT
1 AAACTAATTTGTT
35395963 TATATTCTCC
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:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (14 bp):
AAACTAATTTGTTG
Found at i:35401124 original size:29 final size:30
Alignment explanation
Indices: 35401057--35401125 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
35401047 AGCCTATATC
* * * *
35401057 TTTATAATTTTTAAAAGATTAAATTAAAAT
1 TTTATCATTTTTAAAAGATCAAAGTAAAAA
* *
35401087 TTTATCATTTTTAAAGGGTCAAAGTAAAAA
1 TTTATCATTTTTAAAAGATCAAAGTAAAAA
35401117 TTTA-CATTT
1 TTTATCATTT
35401126 ACTAATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (30 bp):
TTTATCATTTTTAAAAGATCAAAGTAAAAA
Found at i:35426016 original size:17 final size:17
Alignment explanation
Indices: 35425977--35426016 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
35425967 CTGTAGTATA
35425977 ATTGTCACTGCATTATT
1 ATTGTCACTGCATTATT
* * *
35425994 AATGTCATTGCATTTTT
1 ATTGTCACTGCATTATT
35426011 ATTGTC
1 ATTGTC
35426017 GATGCATCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (17 bp):
ATTGTCACTGCATTATT
Found at i:35431102 original size:14 final size:16
Alignment explanation
Indices: 35431085--35431116 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
35431075 GAATTAAAAA
35431085 ATTAT-AATATAA-AT
1 ATTATAAATATAATAT
35431099 ATTATAAATATAATAT
1 ATTATAAATATAATAT
35431115 AT
1 AT
35431117 AACCTACGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 7 0.44
16 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTATAAATATAATAT
Found at i:35438228 original size:12 final size:12
Alignment explanation
Indices: 35438211--35438243 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
35438201 CAACTTTTCG
35438211 TTTTATTTTCTA
1 TTTTATTTTCTA
35438223 TTTTATTTTCTA
1 TTTTATTTTCTA
35438235 TTTTATTTT
1 TTTTATTTT
35438244 ATGCTCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTCTA
Found at i:35445789 original size:12 final size:12
Alignment explanation
Indices: 35445772--35445806 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
35445762 CAACTTTTGC
35445772 TTTTATTTTATA
1 TTTTATTTTATA
*
35445784 TTTTATTTTATC
1 TTTTATTTTATA
*
35445796 TTTTAATTTAT
1 TTTTATTTTAT
35445807 GCTCTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTATTTTATA
Found at i:35450579 original size:15 final size:14
Alignment explanation
Indices: 35450559--35450598 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
35450549 TTTTCCCTTG
*
35450559 TTTATTTTATGTTAT
1 TTTATTTTATGAT-T
35450574 TTTATTTTATGATT
1 TTTATTTTATGATT
35450588 TTTATTGTTAT
1 TTTATT-TTAT
35450599 AAAACCCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
TTTATTTTATGATT
Found at i:35456414 original size:15 final size:14
Alignment explanation
Indices: 35456394--35456432 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 14
35456384 TTTCCCTTGA
35456394 TTATTTTATGATATT
1 TTATTTTATGAT-TT
35456409 TTATTTTATGATTT
1 TTATTTTATGATTT
35456423 TTATTATTAT
1 TTATT-TTAT
35456433 AAAACCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (14 bp):
TTATTTTATGATTT
Found at i:35470483 original size:17 final size:18
Alignment explanation
Indices: 35470446--35470491 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
35470436 TAGTCAAAGT
*
35470446 TGTCAATGCAATAAAAAA
1 TGTCAGTGCAATAAAAAA
*
35470464 TGTCAGTGCAA-AATAAA
1 TGTCAGTGCAATAAAAAA
*
35470481 TGTCAGAGCAA
1 TGTCAGTGCAA
35470492 CTGAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (18 bp):
TGTCAGTGCAATAAAAAA
Found at i:35479705 original size:73 final size:73
Alignment explanation
Indices: 35479594--35479740 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
35479584 GGGAAGGCGC
35479594 TGACAAATAGTGTTGTCCACTTTCCTTCACTACGGAATGTTTTGGCAGAAATTTGGCACCCTATA
1 TGACAAATAGTGTTGTCCACTTTCCTTCACTACGGAATGTTTTGGCAGAAATTTGGCACCCTATA
35479659 GAAGGAGT
66 GAAGGAGT
35479667 TGACAAATAGTGTTGTCCACTTTCCTTCACTACGGAATGTTTTGGCAGAAATTTGGCACCCTATA
1 TGACAAATAGTGTTGTCCACTTTCCTTCACTACGGAATGTTTTGGCAGAAATTTGGCACCCTATA
35479732 GAAGGAGT
66 GAAGGAGT
35479740 T
1 T
35479741 ACGATTTCTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (73 bp):
TGACAAATAGTGTTGTCCACTTTCCTTCACTACGGAATGTTTTGGCAGAAATTTGGCACCCTATA
GAAGGAGT
Found at i:35505357 original size:48 final size:48
Alignment explanation
Indices: 35505286--35505559 Score: 318
Period size: 48 Copynumber: 5.7 Consensus size: 48
35505276 CCATGAAGAC
* *
35505286 ATGAAGGGAAAGGTTTAAGCCGCAACGGCAAACCTTGTACCTCAGAAA
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAA
* * * * *
35505334 ATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACCAC-GAAG
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAA
* * *
35505381 ATGCAAAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAAA
1 ATG--AAGGGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAA
* * * *
35505431 ATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-GAAGA
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAA-A
** * * *
35505479 TACAAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAC
1 -ATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAA
*
35505528 ATGAAAGGAAAGATTTAAGCCGCAACGGCGAA
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAA
35505560 TTTGGTACCA
Statistics
Matches: 184, Mismatches: 36, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
47 9 0.05
48 98 0.53
49 68 0.37
50 9 0.05
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (48 bp):
ATGAAGGGAAAGATTTAAGCCGCAACGGCGAACCTTGTACCTCAGAAA
Found at i:35505440 original size:97 final size:97
Alignment explanation
Indices: 35505289--35505569 Score: 472
Period size: 97 Copynumber: 2.9 Consensus size: 97
35505279 TGAAGACATG
* *
35505289 AAGGGAAAGGTTTAAGCCGCAACGGCAAACCTTGTACCTCAGAAAATGAAGGGAAAGATTTAAGC
1 AAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAATGAAGGGAAAGATTTAAGC
* *
35505354 CGCAATGGCGAATCTAGTACCACGAAGATGCA
66 CGCAACGGCGAATCTAGTACCACGAAGATACA
*
35505386 AAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAAAATGAAGGGAAAGATTTAAGC
1 AAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAATGAAGGGAAAGATTTAAGC
*
35505451 CGCAACGACGAATCTAGTACCACGAAGATACA
66 CGCAACGGCGAATCTAGTACCACGAAGATACA
* *
35505483 AAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAACATGAAAGGAAAGATTTAAGC
1 AAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAATGAAGGGAAAGATTTAAGC
* *
35505548 CGCAACGGCGAATTTGGTACCA
66 CGCAACGGCGAATCTAGTACCA
35505570 TGCAGTCACG
Statistics
Matches: 172, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 172 1.00
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (97 bp):
AAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAAATGAAGGGAAAGATTTAAGC
CGCAACGGCGAATCTAGTACCACGAAGATACA
Found at i:35505618 original size:97 final size:97
Alignment explanation
Indices: 35505289--35505618 Score: 432
Period size: 97 Copynumber: 3.4 Consensus size: 97
35505279 TGAAGACATG
35505289 AAGGGAAAGGTTTAAGCCGCAACGGCAAACCTTGTACCTCAGAAAATGAAGGGAAAGATTTAAGC
1 AAGGGAAAGGTTTAAGCCGCAACGGCAAACCTTGTACCTCAGAAAATGAAGGGAAAGATTTAAGC
*
35505354 CGCAATGGCGAATCTAGTACCACGAAGATGCA-
66 CGCAACGGCGAATCTAGTACCACGAAGAT-CAC
* * *
35505386 AAGGGAAAGGTTTAAGTCACAACGGCGAACCTTGTACCTCAGAAAATGAAGGGAAAGATTTAAGC
1 AAGGGAAAGGTTTAAGCCGCAACGGCAAACCTTGTACCTCAGAAAATGAAGGGAAAGATTTAAGC
*
35505451 CGCAACGACGAATCTAGTACCACGAAGAT-AC
66 CGCAACGGCGAATCTAGTACCACGAAGATCAC
* * * *
35505482 AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAACATGAAAGGAAAGATTTAAG
1 -AAGGGAAAGGTTTAAGCCGCAACGGCAAACCTTGTACCTCAGAAAATGAAGGGAAAGATTTAAG
* * * *
35505547 CCGCAACGGCGAATTTGGTACCATGCAG-TCAC
65 CCGCAACGGCGAATCTAGTACCACGAAGATCAC
* ** * * * *
35505579 GAAGGGGAAGACTGAAGCCGCAACAGCAAATCTTATACCT
1 -AAGGGAAAGGTTTAAGCCGCAACGGCAAACCTTGTACCT
35505619 TAAAGCCGGA
Statistics
Matches: 207, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
95 1 0.00
96 1 0.00
97 205 0.99
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (97 bp):
AAGGGAAAGGTTTAAGCCGCAACGGCAAACCTTGTACCTCAGAAAATGAAGGGAAAGATTTAAGC
CGCAACGGCGAATCTAGTACCACGAAGATCAC
Found at i:35506044 original size:12 final size:13
Alignment explanation
Indices: 35506012--35506036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35506002 CAAAAATAAA
35506012 AAATTAAATTTTT
1 AAATTAAATTTTT
35506025 AAATTAAATTTT
1 AAATTAAATTTT
35506037 AATTTAAAAG
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:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATTAAATTTTT
Found at i:35509227 original size:166 final size:167
Alignment explanation
Indices: 35509017--35509544 Score: 517
Period size: 166 Copynumber: 3.1 Consensus size: 167
35509007 GATATAAATA
** * *
35509017 AACTATTAATATATTATTATACGACGTGATATAACAATATATAATATAGTTAGAGGGTTAACTTT
1 AACTATTAATATATTA-TATA-GATATGATATAACATTATATAATATAGTTAGAAGGTTAACTTT
* * * *
35509082 CAGATGTACGAAAAGTATAGGGACTTAGAGCATATTTCAACTAGTATAATAATAGACAATGATAT
64 CAAATGTACGAAAAGTATAGGGAATTAGAGCATATTTCAACTAGTATAATAATAAACAATAATAT
*
35509147 ATAATAATATGTAATATATAATGTACTTCTGTTATATAT
129 ATAATAATATGTAATATATAATGTACTTCTATTATATAT
35509186 AACTATTAATATATTATAT-GATATGATATAACATTATATAATATAG-TAGAAAGGTTAACTTTC
1 AACTATTAATATATTATATAGATATGATATAACATTATATAATATAGTTAG-AAGGTTAACTTTC
* * *
35509249 AAATGTACAAAAAGTATAAGGAATTAGAGCATATTTCAACT-GATATAATAATAAACAATAATAC
65 AAATGTACGAAAAGTATAGGGAATTAGAGCATATTTCAACTAG-TATAATAATAAACAATAATAT
35509313 ATAAT-A-AT-TAATATATAATGCATAACTTTTCTATTTAACTATTAT
129 ATAATAATATGTAATATATAATG--T-AC--TTCTA-TT-A-TA-TAT
* * * ** *
35509358 TA-TATT-ATATATTATAATAGAAGATAT-ATATCAACATGCATAT-ATATA-TTATAATATATT
1 AACTATTAATATATTAT-AT---AGATATGATAT-AACAT-TATATAATATAGTTAGAAGGT-TA
* * * * *
35509418 ACTTTCAAATGTACGAAAAGTATAGAGATTTGGAACACATTTCAGA-TAGTATAATAATAAACAA
59 ACTTTCAAATGTACGAAAAGTATAGGGAATTAGAGCATATTTCA-ACTAGTATAATAATAAACAA
* *
35509482 TAATATATAATATTGA-GTAATATATAATGTA-TTGCTATTGTATAT
123 TAATATATAATAAT-ATGTAATATATAATGTACTT-CTATTATATAT
*
35509527 AACTATTATTATATTATA
1 AACTATTAATATATTATA
35509545 GATTATAATT
Statistics
Matches: 300, Mismatches: 30, Indels: 57
0.78 0.08 0.15
Matches are distributed among these distances:
163 12 0.04
164 2 0.01
165 6 0.02
166 98 0.33
168 7 0.02
169 22 0.07
170 17 0.06
171 16 0.05
172 8 0.03
173 3 0.01
174 7 0.02
175 82 0.27
176 7 0.02
178 13 0.04
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.38
Consensus pattern (167 bp):
AACTATTAATATATTATATAGATATGATATAACATTATATAATATAGTTAGAAGGTTAACTTTCA
AATGTACGAAAAGTATAGGGAATTAGAGCATATTTCAACTAGTATAATAATAAACAATAATATAT
AATAATATGTAATATATAATGTACTTCTATTATATAT
Found at i:35509932 original size:27 final size:29
Alignment explanation
Indices: 35509859--35509933 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 29
35509849 TTAATATAAC
*
35509859 ATTTGATACTTGAACTTGATGGTTTTTCTTA
1 ATTTGATACTTGAACTT-AT-GTTTTACTTA
*
35509890 ATTTGATA-TCTAAACTT-T-TTTTACTTA
1 ATTTGATACT-TGAACTTATGTTTTACTTA
35509917 ATTTGATACTTGAACTT
1 ATTTGATACTTGAACTT
35509934 GACACTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 22 0.56
28 1 0.03
29 1 0.03
30 1 0.03
31 14 0.36
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.52
Consensus pattern (29 bp):
ATTTGATACTTGAACTTATGTTTTACTTA
Found at i:35509950 original size:58 final size:59
Alignment explanation
Indices: 35509859--35510030 Score: 204
Period size: 58 Copynumber: 2.9 Consensus size: 59
35509849 TTAATATAAC
*** * *
35509859 ATTTGATACTTGAACTTGATGGTTTTTCTTAATTTGATATCTAAACTTTTTTT-ACTTA
1 ATTTGATACTTGAACTTGACACTTTTTCCTAATTTGATATCTAAACTTTTTTTGACTCA
*
35509917 ATTTGATACTTGAACTTGACACTTTTTCCTAATTTGGTATCTAAACTTTTTTTGGACTCA
1 ATTTGATACTTGAACTTGACACTTTTTCCTAATTTGATATCTAAACTTTTTTT-GACTCA
* * * * *
35509977 ATTTGGTACCTGAACTTGACATTTTTTTCCTAGTTTGATA-CATAAGCTTTTTTT
1 ATTTGATACTTGAACTTGACA-CTTTTTCCTAATTTGATATC-TAAACTTTTTTT
35510031 TTAAGATTCA
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
58 48 0.49
60 24 0.24
61 26 0.27
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (59 bp):
ATTTGATACTTGAACTTGACACTTTTTCCTAATTTGATATCTAAACTTTTTTTGACTCA
Found at i:35510368 original size:89 final size:89
Alignment explanation
Indices: 35510217--35510384 Score: 196
Period size: 89 Copynumber: 1.9 Consensus size: 89
35510207 CCAAATCAGG
** * * *
35510217 AAAAAGAGTCAAGTTCAGGTACCAAATTAGACCTCAAAAAGTTTAAGTACCAACTTAAAAAAATT
1 AAAAAGAGTCAAGTTCAGGTACCAAATTAGACCAAAAAAAATTTAAGTACCAAATTAAAAAAAGT
*
35510282 GCCAAGTTTAGGTATCAAATTAAA
66 ACCAAGTTTAGGTATCAAATTAAA
* * * * *
35510306 AAAAAGTGTCAAGTT-TGAGTACCAAATTGGA-CAAAAAAAATTTAGGTACCAAATTAGTAAAAA
1 AAAAAGAGTCAAGTTCAG-GTACCAAATTAGACCAAAAAAAATTTAAGTACCAAATTA-AAAAAA
*
35510369 GTATCAAGTTTAGGTA
64 GTACCAAGTTTAGGTA
35510385 GCAACTGTTA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
88 21 0.32
89 44 0.68
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (89 bp):
AAAAAGAGTCAAGTTCAGGTACCAAATTAGACCAAAAAAAATTTAAGTACCAAATTAAAAAAAGT
ACCAAGTTTAGGTATCAAATTAAA
Found at i:35510384 original size:31 final size:31
Alignment explanation
Indices: 35510255--35510384 Score: 103
Period size: 31 Copynumber: 4.4 Consensus size: 31
35510245 AGACCTCAAA
* * * **
35510255 AAGTTTAAGTACCAACTTA-AAAAAATTGCC
1 AAGTTTAGGTACCAAATTAGAAAAAAGTATC
* * *
35510285 AAGTTTAGGTATCAAATTAAAAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAGAAAAAAGTATC
*
35510316 AAGTTT-GAGTACCAAATTGGACAAAAA--A--
1 AAGTTTAG-GTACCAAATTAGA-AAAAAGTATC
*
35510344 AA-TTTAGGTACCAAATTAGTAAAAAGTATC
1 AAGTTTAGGTACCAAATTAGAAAAAAGTATC
35510374 AAGTTTAGGTA
1 AAGTTTAGGTA
35510385 GCAACTGTTA
Statistics
Matches: 80, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
26 5 0.06
27 14 0.17
28 4 0.05
30 19 0.24
31 33 0.41
32 5 0.06
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (31 bp):
AAGTTTAGGTACCAAATTAGAAAAAAGTATC
Found at i:35514079 original size:12 final size:12
Alignment explanation
Indices: 35514032--35514079 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
35514022 AATAAAAAAA
*
35514032 TTTCTTCTTTTCT
1 TTTC-TCTTTTTT
*
35514045 TTTCTCTTTCTT
1 TTTCTCTTTTTT
*
35514057 TTTCTCATTTTT
1 TTTCTCTTTTTT
35514069 TTTCTCTTTTT
1 TTTCTCTTTTT
35514080 GAAGTGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 26 0.87
13 4 0.13
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTCTCTTTTTT
Found at i:35523055 original size:22 final size:23
Alignment explanation
Indices: 35523029--35523072 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
35523019 AAATTGTTAA
*
35523029 AATTGTCAATGTAA-TAAAAGTT
1 AATTGTCAATGCAACTAAAAGTT
35523051 AATTGTCAATGCAACTAAAAGT
1 AATTGTCAATGCAACTAAAAGT
35523073 AAATAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (23 bp):
AATTGTCAATGCAACTAAAAGTT
Found at i:35525284 original size:35 final size:35
Alignment explanation
Indices: 35525245--35525324 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
35525235 TTCTAGTCTC
* * **
35525245 CCAATGATTTAACTCATACGAGTTCTTCAAGATTT
1 CCAATAATTTAACTCAAACGAGCACTTCAAGATTT
*
35525280 CCAATAATTTAACTCAAACGAGCACTTCAAGATTC
1 CCAATAATTTAACTCAAACGAGCACTTCAAGATTT
*
35525315 CCAGTAATTT
1 CCAATAATTT
35525325 TTAGCTCTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.33
Consensus pattern (35 bp):
CCAATAATTTAACTCAAACGAGCACTTCAAGATTT
Found at i:35525366 original size:19 final size:19
Alignment explanation
Indices: 35525328--35525385 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
35525318 GTAATTTTTA
*
35525328 GCTCTTACGAGCCA--ATC
1 GCTCTTACAAGCCAGTATC
35525345 GCTCTTACAAGCCAGTATC
1 GCTCTTACAAGCCAGTATC
*
35525364 GCTCTTACAAGCTAGTATC
1 GCTCTTACAAGCCAGTATC
35525383 GCT
1 GCT
35525386 TCAAAGTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.35
19 24 0.65
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (19 bp):
GCTCTTACAAGCCAGTATC
Found at i:35530211 original size:20 final size:21
Alignment explanation
Indices: 35530186--35530232 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
35530176 TAAAATATTC
*
35530186 ATGTGATTAAATATAATTAA-
1 ATGTGACTAAATATAATTAAT
* *
35530206 ATGTGACTAAATGTGATTAAT
1 ATGTGACTAAATATAATTAAT
35530227 ATGTGA
1 ATGTGA
35530233 AGTGATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.38
Consensus pattern (21 bp):
ATGTGACTAAATATAATTAAT
Found at i:35530275 original size:48 final size:48
Alignment explanation
Indices: 35530206--35530327 Score: 192
Period size: 48 Copynumber: 2.5 Consensus size: 48
35530196 ATATAATTAA
*
35530206 ATGTGACTAAATGTGATTAATATGTGAAGTGATAAATGTTGAAATATTC
1 ATGTGAC-AAATGTGATTAATATGTGAAGTGATAAATGCTGAAATATTC
* *
35530255 ATGTGACCAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTC
1 ATGTGACAAATGTGATTAATATGTGAAGTGATAAATGCTGAAATATTC
*
35530303 ATGTGACTAATGTGATT-ATATGTGA
1 ATGTGACAAATGTGATTAATATGTGA
35530328 TTAAATGTGA
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 8 0.12
48 54 0.78
49 7 0.10
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.37
Consensus pattern (48 bp):
ATGTGACAAATGTGATTAATATGTGAAGTGATAAATGCTGAAATATTC
Found at i:35530279 original size:69 final size:68
Alignment explanation
Indices: 35530082--35530280 Score: 281
Period size: 69 Copynumber: 2.9 Consensus size: 68
35530072 CTAATATCTA
*
35530082 TGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGTCCAATGTGATTAAATGTGACTAA
1 TGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACCAATGTGATTAAATGTGACTAA
35530147 ATG
66 ATG
* * ** * ** * *
35530150 TGATTTATTTGTGATGTGATAAATACTAAAATATTCATGTGATTAAATATAATTAAATGTGACTA
1 TGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGA-CCAATGTGATTAAATGTGACTA
35530215 AATG
65 AATG
*
35530219 TGATTAATATGTGAAGTGATAAATGTTGAAATATTCATGTGACCAATGTGATTAATATGTGA
1 TGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACCAATGTGATTAA-ATGTGA
35530281 TGTGATAAAT
Statistics
Matches: 109, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
68 45 0.41
69 64 0.59
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.39
Consensus pattern (68 bp):
TGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACCAATGTGATTAAATGTGACTAA
ATG
Found at i:35530284 original size:117 final size:117
Alignment explanation
Indices: 35530137--35530347 Score: 316
Period size: 117 Copynumber: 1.8 Consensus size: 117
35530127 ATGTGATTAA
* * *
35530137 ATGTGACTAAATGTGATTTATTTGTGATGTGATAAATACTAAAATATTCATGTGATTAAATATAA
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATACTAAAATATTCATGTGACT-AATATAA
35530202 TTAAATGTGACTAAATGTGATTAATATGTGAAGTGATAAATGTTGAAATATTC
65 TTAAATGTGACTAAATGTGATTAATATGTGAAGTGATAAATGTTGAAATATTC
* * * * *
35530255 ATGTGAC-CAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGACTAATGTGAT
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATACTAAAATATTCATGTGACTAATATAAT
* *
35530319 TATATGTGATTAAATGTGATTAATATGTG
66 TAAATGTGACTAAATGTGATTAATATGTG
35530348 TTGTGTTAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
116 33 0.40
117 43 0.52
118 7 0.08
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (117 bp):
ATGTGACTAAATGTGATTAATATGTGATGTGATAAATACTAAAATATTCATGTGACTAATATAAT
TAAATGTGACTAAATGTGATTAATATGTGAAGTGATAAATGTTGAAATATTC
Found at i:35530323 original size:23 final size:25
Alignment explanation
Indices: 35530206--35530325 Score: 94
Period size: 23 Copynumber: 5.0 Consensus size: 25
35530196 ATATAATTAA
*
35530206 ATGTGACTAAATGTGATTAATATGTG
1 ATGTGACTAAATGTGATT-ATATGTC
* *
35530232 AAGTGA-TAAATGTTGA-AATAT-TC
1 ATGTGACTAAATG-TGATTATATGTC
* *
35530255 ATGTGAC-CAATGTGATTAATATGTG
1 ATGTGACTAAATGTGATT-ATATGTC
*
35530280 ATGTGA-TAAATGCTGA-AATAT-TC
1 ATGTGACTAAATG-TGATTATATGTC
35530303 ATGTGACT-AATGTGATTATATGT
1 ATGTGACTAAATGTGATTATATGT
35530326 GATTAAATGT
Statistics
Matches: 73, Mismatches: 11, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
22 6 0.08
23 25 0.34
24 14 0.19
25 17 0.23
26 11 0.15
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.38
Consensus pattern (25 bp):
ATGTGACTAAATGTGATTATATGTC
Found at i:35530327 original size:10 final size:10
Alignment explanation
Indices: 35530303--35530347 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
35530293 TGAAATATTC
*
35530303 ATGTGACTA-
1 ATGTGATTAT
35530312 ATGTGATTAT
1 ATGTGATTAT
*
35530322 ATGTGATTAA
1 ATGTGATTAT
35530332 ATGTGATTAAT
1 ATGTGATT-AT
35530343 ATGTG
1 ATGTG
35530348 TTGTGTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
9 8 0.26
10 17 0.55
11 6 0.19
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.42
Consensus pattern (10 bp):
ATGTGATTAT
Found at i:35530335 original size:68 final size:67
Alignment explanation
Indices: 35530263--35530392 Score: 181
Period size: 68 Copynumber: 1.9 Consensus size: 67
35530253 TCATGTGACC
* *
35530263 AATGTGATTAATATGTGATGTGATAAATGC-TGAAATATTCATGTGACTAATGTGATTATATGTG
1 AATGTGATTAATATGTGATGTGATAAATGCAT-AAATACTCATGTGACTAATGCGATTA-ATGTG
35530327 ATTA
64 ATTA
* * * *
35530331 AATGTGATTAATATGTGTTGTGTTAAATGCATAAGTACTCATGTGATTAATGCGATTAATGT
1 AATGTGATTAATATGTGATGTGATAAATGCATAAATACTCATGTGACTAATGCGATTAATGT
35530393 ATAAAAGAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 4 0.07
68 50 0.91
69 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (67 bp):
AATGTGATTAATATGTGATGTGATAAATGCATAAATACTCATGTGACTAATGCGATTAATGTGAT
TA
Found at i:35530375 original size:116 final size:117
Alignment explanation
Indices: 35530137--35530390 Score: 305
Period size: 116 Copynumber: 2.2 Consensus size: 117
35530127 ATGTGATTAA
* * *
35530137 ATGTGACTAAATGTGATTTATTTGTGATGTGATAAATACTAAAATATTCATGTGATTAAATATAA
1 ATGTGAC-AAATGTGATTAATATGTGATGTGATAAATACTAAAATATTCATGTGACTAAATATAA
* *
35530202 TTAAATGTGACTAAATGTGATTAATATGTGAAGTGATAAATGTTGAAATATTC
65 TTAAATGTGACTAAATGTGATTAATATGTGAAGTGATAAATGATGAAATACTC
* * * * *
35530255 ATGTGACCAATGTGATTAATATGTGATGTGATAAATGCTGAAATATTCATGTGACT-AATGTGAT
1 ATGTGACAAATGTGATTAATATGTGATGTGATAAATACTAAAATATTCATGTGACTAAATATAAT
* * ** * *
35530319 TATATGTGATTAAATGTGATTAATATGTGTTGTGTTAAATGCAT-AAGTACTC
66 TAAATGTGACTAAATGTGATTAATATGTGAAGTGATAAATG-ATGAAATACTC
** *
35530371 ATGTGATTAATGCGATTAAT
1 ATGTGACAAATGTGATTAAT
35530391 GTATAAAAGA
Statistics
Matches: 116, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
116 65 0.56
117 44 0.38
118 7 0.06
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.39
Consensus pattern (117 bp):
ATGTGACAAATGTGATTAATATGTGATGTGATAAATACTAAAATATTCATGTGACTAAATATAAT
TAAATGTGACTAAATGTGATTAATATGTGAAGTGATAAATGATGAAATACTC
Found at i:35531140 original size:23 final size:23
Alignment explanation
Indices: 35531111--35531293 Score: 289
Period size: 23 Copynumber: 8.0 Consensus size: 23
35531101 TCATGCATTA
35531111 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
35531134 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
35531157 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
35531180 TGTGCTT-AATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
35531202 TATGCTTAAATGTTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
35531225 TATTCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
35531248 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
35531271 TATG-TTGAAATATTCATGTGATT
1 TATGCTT-AAATATTAATGTGATT
35531294 AAATGTGATT
Statistics
Matches: 147, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
22 23 0.16
23 124 0.84
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:35531224 original size:91 final size:91
Alignment explanation
Indices: 35531111--35531293 Score: 287
Period size: 91 Copynumber: 2.0 Consensus size: 91
35531101 TCATGCATTA
* *
35531111 TATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATGT
1 TATGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATAT
*
35531176 GATTTGTGCTT-AATATTAATGTGATT
66 GATTTATG-TTAAATATTAATGTGATT
* *
35531202 TATGCTTAAATGTTAATATGATTTATTCTTAAATATTAATGTGATTTATGCTTAAATATTAATAT
1 TATGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATAT
*
35531267 GATTTATGTTGAAATATTCATGTGATT
66 GATTTATGTT-AAATATTAATGTGATT
35531294 AAATGTGATT
Statistics
Matches: 84, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
90 2 0.02
91 68 0.81
92 14 0.17
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (91 bp):
TATGCTTAAATATTAATATGATTTATGCTTAAATATTAATGTGATTTATGCTTAAATATTAATAT
GATTTATGTTAAATATTAATGTGATT
Found at i:35531301 original size:10 final size:10
Alignment explanation
Indices: 35531286--35531333 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
35531276 TGAAATATTC
35531286 ATGTGATTAA
1 ATGTGATTAA
35531296 ATGTGATTAA
1 ATGTGATTAA
*
35531306 ATGTGACTAA
1 ATGTGATTAA
*
35531316 ATGTGATTCAT
1 ATGTGATT-AA
35531327 ATGTGAT
1 ATGTGAT
35531334 GTGATAAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
10 26 0.76
11 8 0.24
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (10 bp):
ATGTGATTAA
Found at i:35533009 original size:21 final size:21
Alignment explanation
Indices: 35532983--35533023 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
35532973 CCCCCCCCAA
35532983 GCATAATTTGTGACATCCTTC
1 GCATAATTTGTGACATCCTTC
35533004 GCATAATTTGTGACATCCTT
1 GCATAATTTGTGACATCCTT
35533024 TGCTCTCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (21 bp):
GCATAATTTGTGACATCCTTC
Found at i:35535161 original size:21 final size:21
Alignment explanation
Indices: 35535132--35535270 Score: 84
Period size: 21 Copynumber: 6.1 Consensus size: 21
35535122 ATACGGAAAA
* *
35535132 AACAAAGAGTACCAAAGTACT
1 AACAGAGAGCACCAAAGTACT
*
35535153 AACAGAGAGCA-CATAAGTGCT
1 AACAGAGAGCACCA-AAGTACT
*
35535174 AGGCAACAGAGAGTACCAAAGTACT
1 ----AACAGAGAGCACCAAAGTACT
*
35535199 AACAGAGAGCA-CATAAGTGCT
1 AACAGAGAGCACCA-AAGTACT
*
35535220 AGGCAACAGAGAGTACACAAAGTACT
1 ----AACAGAGAGCAC-CAAAGTACT
*
35535246 AATCAGAGAGCACACAAAGTGCT
1 AA-CAGAGAGCAC-CAAAGTACT
35535269 AA
1 AA
35535271 TCAGGGAACA
Statistics
Matches: 93, Mismatches: 11, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
20 4 0.04
21 31 0.33
22 2 0.02
23 20 0.22
25 26 0.28
26 8 0.09
27 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (21 bp):
AACAGAGAGCACCAAAGTACT
Found at i:35535195 original size:25 final size:25
Alignment explanation
Indices: 35535153--35535232 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
35535143 CCAAAGTACT
35535153 AACAGAGAGCACATAAGTGCTAGGC
1 AACAGAGAGCACATAAGTGCTAGGC
* *
35535178 AACAGAGAGTACCA-AAGTACT----
1 AACAGAGAGCA-CATAAGTGCTAGGC
35535199 AACAGAGAGCACATAAGTGCTAGGC
1 AACAGAGAGCACATAAGTGCTAGGC
35535224 AACAGAGAG
1 AACAGAGAG
35535233 TACACAAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
20 2 0.04
21 16 0.36
25 25 0.56
26 2 0.04
ACGTcount: A:0.44, C:0.19, G:0.26, T:0.11
Consensus pattern (25 bp):
AACAGAGAGCACATAAGTGCTAGGC
Found at i:35535204 original size:46 final size:46
Alignment explanation
Indices: 35535132--35535269 Score: 231
Period size: 46 Copynumber: 2.9 Consensus size: 46
35535122 ATACGGAAAA
*
35535132 AACAAAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTAGGC
1 AACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTAGGC
35535178 AACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTAGGC
1 AACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTAGGC
*
35535224 AACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACA-TAAGTGCTA
35535270 ATCAGGGAAC
Statistics
Matches: 87, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
46 57 0.66
47 11 0.13
48 11 0.13
49 8 0.09
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (46 bp):
AACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTAGGC
Found at i:35535282 original size:23 final size:23
Alignment explanation
Indices: 35535234--35535294 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
35535224 AACAGAGAGT
* *
35535234 ACACAAAGTACTAATCAGAGAGC
1 ACACAAAGTGCTAATCAGAGAAC
*
35535257 ACACAAAGTGCTAATCAGGGAAC
1 ACACAAAGTGCTAATCAGAGAAC
*
35535280 ACACACAGTGCTAAT
1 ACACAAAGTGCTAAT
35535295 AACAGAGAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (23 bp):
ACACAAAGTGCTAATCAGAGAAC
Found at i:35537064 original size:58 final size:58
Alignment explanation
Indices: 35536970--35537172 Score: 282
Period size: 58 Copynumber: 3.5 Consensus size: 58
35536960 TTACAGATTA
* * *
35536970 AATGTGACTAAATGTGATTAACATCTGATGTGATAAATGTTGGAATATTCATGTGACC
1 AATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACC
* ** **
35537028 AATCTGACTAAATGTGATTAATATGTGATGTGATAAATACTGAAATATTCATGTGATTA
1 AATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGA-CC
* *
35537087 AATGTGACTAAATGTGATTAATATGTGATGTGGTAAATGTTAAAATATTCATGTGACC
1 AATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACC
* *
35537145 AATGTGATTAAATGTGACTAA-ATGTGAT
1 AATGTGACTAAATGTGATTAATATGTGAT
35537173 TAATAATTGA
Statistics
Matches: 127, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
57 7 0.06
58 69 0.54
59 51 0.40
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (58 bp):
AATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACC
Found at i:35537093 original size:10 final size:10
Alignment explanation
Indices: 35537078--35537115 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
35537068 TGAAATATTC
35537078 ATGTGATTAA
1 ATGTGATTAA
*
35537088 ATGTGACTAA
1 ATGTGATTAA
35537098 ATGTGATTAA
1 ATGTGATTAA
35537108 TATGTGAT
1 -ATGTGAT
35537116 GTGGTAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.39
Consensus pattern (10 bp):
ATGTGATTAA
Found at i:35537094 original size:68 final size:63
Alignment explanation
Indices: 35537032--35537219 Score: 199
Period size: 68 Copynumber: 3.0 Consensus size: 63
35537022 GTGACCAATC
**
35537032 TGACTAAATGTGATTAATATGTGATGTGATAAATACTGAAATATTCATGTG---AT-T-AAAT
1 TGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGATAATGTGAAAT
* * *
35537090 GTGACTAAATGTGATTAATATGTGATGTGGTAAATGTTAAAATATTCATGTGACCAATGTGATTA
1 -TGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGA-TAATGTG---A
35537155 AAT
61 AAT
* *
35537158 GTGACTAAATGTGATTAATAAT-TGATATGATAAATGTTGAAATAATCATGTGACTAATGTGA
1 -TGACTAAATGTGATTAAT-ATGTGATGTGATAAATGTTGAAATATTCATGTGA-TAATGTGA
35537220 TTATATGTGA
Statistics
Matches: 110, Mismatches: 9, Indels: 14
0.83 0.07 0.11
Matches are distributed among these distances:
59 47 0.43
63 2 0.02
64 1 0.01
65 1 0.01
68 57 0.52
69 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (63 bp):
TGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGATAATGTGAAAT
Found at i:35537160 original size:10 final size:10
Alignment explanation
Indices: 35537145--35537247 Score: 57
Period size: 10 Copynumber: 9.5 Consensus size: 10
35537135 TCATGTGACC
35537145 AATGTGATTA
1 AATGTGATTA
*
35537155 AATGTGACTA
1 AATGTGATTA
35537165 AATGTGATTAA
1 AATGTGATT-A
35537176 TAAT-TGATATGATA
1 -AATGTG--AT--TA
*
35537190 AATGTTGAAATA
1 AATG-TG-ATTA
*
35537202 ATCATGTGACT-
1 A--ATGTGATTA
35537213 AATGTGATTA
1 AATGTGATTA
*
35537223 TATGTGATTA
1 AATGTGATTA
*
35537233 AAGGTGATTA
1 AATGTGATTA
35537243 AATGT
1 AATGT
35537248 AAGTAATATG
Statistics
Matches: 72, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
9 7 0.10
10 38 0.53
11 4 0.06
12 8 0.11
13 7 0.10
14 5 0.07
15 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38
Consensus pattern (10 bp):
AATGTGATTA
Found at i:35537161 original size:19 final size:20
Alignment explanation
Indices: 35537145--35537247 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 20
35537135 TCATGTGACC
35537145 AATGTGATTAAATGTGACTA
1 AATGTGATTAAATGTGACTA
35537165 AATGTGATTAATAATTGATATGA-TA
1 AATGTGATT-A-AA-TG---TGACTA
*
35537190 AATGTTGAAATAATCATGTGACT-
1 AATG-TG-ATTAA--ATGTGACTA
* *
35537213 AATGTGATTATATGTGATTA
1 AATGTGATTAAATGTGACTA
*
35537233 AAGGTGATTAAATGT
1 AATGTGATTAAATGT
35537248 AAGTAATATG
Statistics
Matches: 65, Mismatches: 6, Indels: 24
0.68 0.06 0.25
Matches are distributed among these distances:
19 7 0.11
20 22 0.34
21 4 0.06
22 4 0.06
23 9 0.14
24 1 0.02
25 7 0.11
26 8 0.12
27 3 0.05
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38
Consensus pattern (20 bp):
AATGTGATTAAATGTGACTA
Found at i:35537209 original size:117 final size:116
Alignment explanation
Indices: 35536968--35537230 Score: 313
Period size: 117 Copynumber: 2.3 Consensus size: 116
35536958 TGTTACAGAT
* * **
35536968 TAAATGTGACTAAATGTGATTAACATCTGATGTGATAAATGTTGGAATATTCATGTGACCAATCT
1 TAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGTGACCAATCT
* * ** *
35537033 GACTAAATGTGATTAATATGTGATGTGATAAATACTGAAATATTCATGTGAT
66 GACTAAATGTGACTAATATGTGATGTAATAAATA-TGAAATATAAATGTGAA
* *
35537085 TAAATGTGACTAAATGTGATTAATATGTGATGTGGTAAATGTTAAAATATTCATGTGACCAATGT
1 TAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGTGACCAATCT
* *
35537150 GATTAAATGTGACTAA-ATGTGAT-TAAT-AAT-TGATATGATAAATGTTGAAA
66 GACTAAATGTGACTAATATGTGATGTAATAAATATGAAAT-ATAAATG-TG-AA
35537200 TAATCATGTGACT-AATGTGATT-ATATGTGAT
1 TAA--ATGTGACTAAATGTGATTAATATGTGAT
35537231 TAAAGGTGAT
Statistics
Matches: 128, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
112 5 0.04
113 5 0.04
114 5 0.04
115 16 0.12
116 16 0.12
117 81 0.63
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.37
Consensus pattern (116 bp):
TAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTAAAATATTCATGTGACCAATCT
GACTAAATGTGACTAATATGTGATGTAATAAATATGAAATATAAATGTGAA
Found at i:35537220 original size:68 final size:68
Alignment explanation
Indices: 35537078--35537247 Score: 245
Period size: 68 Copynumber: 2.5 Consensus size: 68
35537068 TGAAATATTC
* * *
35537078 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGGTAAATGTTAAAATATTCATGTGA
1 ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATATGATAAATGTTAAAATAATCATGTGA
35537143 CCA
66 CCA
*
35537146 ATGTGATTAAATGTGACTAAATGTGATTAATAAT-TGATATGATAAATGTTGAAATAATCATGTG
1 ATGTGATTAAATGTGACTAAATGTGATTAAT-ATGTGATATGATAAATGTTAAAATAATCATGTG
*
35537210 ACTA
65 ACCA
* * *
35537214 ATGTGATTATATGTGATTAAAGGTGATTAA-ATGT
1 ATGTGATTAAATGTGACTAAATGTGATTAATATGT
35537248 AAGTAATATG
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
66 2 0.02
67 1 0.01
68 87 0.95
69 2 0.02
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (68 bp):
ATGTGATTAAATGTGACTAAATGTGATTAATATGTGATATGATAAATGTTAAAATAATCATGTGA
CCA
Found at i:35538068 original size:23 final size:23
Alignment explanation
Indices: 35538036--35538197 Score: 218
Period size: 23 Copynumber: 7.0 Consensus size: 23
35538026 TCATGCGTTA
35538036 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
35538059 TGTGCTTAAATATTAATGTAATT
1 TATGCTTAAATATTAATGTGATT
*
35538082 TATGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
35538105 TATACTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
35538128 TAATGCTTAAATATTAATATGATT
1 T-ATGCTTAAATATTAATGTGATT
* * *
35538152 TATACTTAAATGTTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
35538175 TATG-TTGAAATATTCATGTGATT
1 TATGCTT-AAATATTAATGTGATT
35538198 AAATGTGATT
Statistics
Matches: 122, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
22 2 0.02
23 99 0.81
24 21 0.17
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:35538153 original size:70 final size:69
Alignment explanation
Indices: 35538040--35538202 Score: 229
Period size: 70 Copynumber: 2.3 Consensus size: 69
35538030 GCGTTATATG
* * *
35538040 CTTAAATATTAATGTGATTT-GTGCTTAAATATTAATGTAATTTATGCTTAAATATTAATATGAT
1 CTTAAATATTAATGTGATTTAATGCTTAAATATTAATATAATTTATACTTAAATATTAATATGAT
35538104 TTAT
66 TTAT
* *
35538108 ACTTAAATATTAATGTGATTTAATGCTTAAATATTAATATGATTTATACTTAAATGTTAATATGA
1 -CTTAAATATTAATGTGATTTAATGCTTAAATATTAATATAATTTATACTTAAATATTAATATGA
35538173 TTTAT
65 TTTAT
* * *
35538178 GTTGAAATATTCATGTGATTAAATG
1 CTT-AAATATTAATGTGATTTAATG
35538203 TGATTAAATG
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
69 22 0.26
70 62 0.74
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (69 bp):
CTTAAATATTAATGTGATTTAATGCTTAAATATTAATATAATTTATACTTAAATATTAATATGAT
TTAT
Found at i:35538205 original size:10 final size:10
Alignment explanation
Indices: 35538190--35538237 Score: 78
Period size: 10 Copynumber: 4.7 Consensus size: 10
35538180 TGAAATATTC
35538190 ATGTGATTAA
1 ATGTGATTAA
35538200 ATGTGATTAA
1 ATGTGATTAA
*
35538210 ATGTGACTAA
1 ATGTGATTAA
35538220 ATGTGATTAA
1 ATGTGATTAA
35538230 TATGTGAT
1 -ATGTGAT
35538238 GTGATAAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
10 28 0.80
11 7 0.20
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.40
Consensus pattern (10 bp):
ATGTGATTAA
Found at i:35539436 original size:12 final size:12
Alignment explanation
Indices: 35539421--35539458 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
35539411 AGAATGCAGT
35539421 AGAATAGAATTC
1 AGAATAGAATTC
*
35539433 AGAATAGAA--A
1 AGAATAGAATTC
35539443 AGAATAGAATTC
1 AGAATAGAATTC
35539455 AGAA
1 AGAA
35539459 AGTAAAAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.58, C:0.05, G:0.18, T:0.18
Consensus pattern (12 bp):
AGAATAGAATTC
Found at i:35539446 original size:22 final size:22
Alignment explanation
Indices: 35539421--35539466 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
35539411 AGAATGCAGT
35539421 AGAATAGAATTCAGAATAG-AAA
1 AGAATAGAATTCAGAA-AGTAAA
35539443 AGAATAGAATTCAGAAAGTAAA
1 AGAATAGAATTCAGAAAGTAAA
35539465 AG
1 AG
35539467 CCATGGTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.59, C:0.04, G:0.20, T:0.17
Consensus pattern (22 bp):
AGAATAGAATTCAGAAAGTAAA
Found at i:35543013 original size:41 final size:41
Alignment explanation
Indices: 35542968--35543061 Score: 134
Period size: 41 Copynumber: 2.2 Consensus size: 41
35542958 TGAATTCGAG
* *
35542968 GTTTAAGGTTTGAGGTTATGAGTTATAAGTTTGTGGTTTAA
1 GTTTAAGGTTTGAGGTTATGAGTTACAAGTTTGAGGTTTAA
* *
35543009 GTTTAAGGTTTGGGGTTATGAGTTACGAGTTTGAGGTTTAA
1 GTTTAAGGTTTGAGGTTATGAGTTACAAGTTTGAGGTTTAA
35543050 GATTTAAAGGTT
1 G-TTT-AAGGTT
35543062 CAATATTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
41 38 0.81
42 3 0.06
43 6 0.13
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.44
Consensus pattern (41 bp):
GTTTAAGGTTTGAGGTTATGAGTTACAAGTTTGAGGTTTAA
Found at i:35546888 original size:31 final size:31
Alignment explanation
Indices: 35546826--35546888 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
35546816 TTAAACAGGG
* *
35546826 TCTATTTCTCCCCTGATTTAAGCACATCAAA
1 TCTATTTCTCCCCTGATTTAAGCAAAACAAA
35546857 TCTATTTCTCCCCTGATTTAAGCAAAACAAA
1 TCTATTTCTCCCCTGATTTAAGCAAAACAAA
35546888 T
1 T
35546889 ATGGATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (31 bp):
TCTATTTCTCCCCTGATTTAAGCAAAACAAA
Found at i:35547892 original size:17 final size:17
Alignment explanation
Indices: 35547870--35547906 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
35547860 TATTTATTTA
35547870 TATCATTATCTAAACCG
1 TATCATTATCTAAACCG
35547887 TATCATTATCTAAACCG
1 TATCATTATCTAAACCG
35547904 TAT
1 TAT
35547907 TCAAACATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (17 bp):
TATCATTATCTAAACCG
Found at i:35557908 original size:26 final size:26
Alignment explanation
Indices: 35557872--35557924 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
35557862 TGTAAGGCGA
35557872 AAGGACTATTGTGAGCTTCTTGGAGT
1 AAGGACTATTGTGAGCTTCTTGGAGT
35557898 AAGGACTATTGTGAGCTTCTTGGAGT
1 AAGGACTATTGTGAGCTTCTTGGAGT
35557924 A
1 A
35557925 TTAATCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.34
Consensus pattern (26 bp):
AAGGACTATTGTGAGCTTCTTGGAGT
Found at i:35563255 original size:3 final size:3
Alignment explanation
Indices: 35563242--35563285 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
35563232 TTTACAACCC
35563242 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35563286 CCGAAGTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:35567144 original size:21 final size:21
Alignment explanation
Indices: 35567101--35567148 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
35567091 CCTATGACAG
* * *
35567101 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
*
35567122 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
35567143 TTCTAC
1 TTCTAC
35567149 TGGTACTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:35568339 original size:21 final size:20
Alignment explanation
Indices: 35568311--35568363 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
35568301 CTTCCCCTAT
35568311 TTCTTCTTTCATCTTCTTTA
1 TTCTTCTTTCATCTTCTTTA
* * *
35568331 TTCTGTCTTTCTTTTTCTTTC
1 TTCT-TCTTTCATCTTCTTTA
*
35568352 TTTTTC-TTCATC
1 TTCTTCTTTCATC
35568364 AATTATCCAC
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 4 0.15
20 6 0.23
21 16 0.62
ACGTcount: A:0.06, C:0.25, G:0.02, T:0.68
Consensus pattern (20 bp):
TTCTTCTTTCATCTTCTTTA
Found at i:35569865 original size:39 final size:39
Alignment explanation
Indices: 35569790--35569865 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
35569780 CTCTCCGTTA
* **
35569790 TCAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGTAC
1 TCAGCACTTCGTGTACTCTCTGATTAGCACAGTGTGTAC
* * *
35569829 TCAGTACTTTGTGTACTCTCTGTTTAGCACAGTGTGT
1 TCAGCACTTCGTGTACTCTCTGATTAGCACAGTGTGT
35569866 GCTCTCTGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (39 bp):
TCAGCACTTCGTGTACTCTCTGATTAGCACAGTGTGTAC
Found at i:35570202 original size:2 final size:2
Alignment explanation
Indices: 35570197--35570222 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35570187 TATATATATA
35570197 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
35570223 AAAGGTAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:35571163 original size:52 final size:52
Alignment explanation
Indices: 35571089--35571369 Score: 359
Period size: 52 Copynumber: 5.4 Consensus size: 52
35571079 GGGTGTTACA
* *
35571089 ATGACACATAGTCATTGGACCTCATAATTCGTAAAGGATTCGTATACTCACG
1 ATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCATATACTCACG
* * * * *
35571141 ATGACATATAGTCATCGAACCTCGTAATTCGTAAAAGATTCATACACTCACG
1 ATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCATATACTCACG
* *
35571193 ATGACACATAGTCAT-GGACCTCATAATCCATAAAGGATTCATATACTCACG
1 ATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCATATACTCACG
* ** * * * *
35571244 ATGACATATAGTCATCGGACCTTGTAA-TCTATAAAAGATTCATATACTTACA
1 ATGACACATAGTCATCGGACCTCATAATTC-GTAAAGGATTCATATACTCACG
** *
35571296 ATGACACATAGTCATCATACCTCATAATCCGTAAAGGATTCATATACTCACG
1 ATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCATATACTCACG
*
35571348 ATGACACAGAGTCATCGGACCT
1 ATGACACATAGTCATCGGACCT
35571370 TTTGCATTTA
Statistics
Matches: 192, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
51 45 0.23
52 146 0.76
53 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (52 bp):
ATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTCATATACTCACG
Found at i:35571271 original size:103 final size:103
Alignment explanation
Indices: 35571086--35571370 Score: 419
Period size: 103 Copynumber: 2.7 Consensus size: 103
35571076 TAAGGGTGTT
* *
35571086 ACAATGACACATAGTCATTGGACCTCATAATTCGTAAAGGATTCGTATACTCACGATGACATATA
1 ACAATGACACATAGTCA-TGGACCTCATAATCCGTAAAGGATTCATATACTCACGATGACATATA
* * *
35571151 GTCATCGAACCTCGTAAT-TCGTAAAAGATTCATACACTC
65 GTCATCGGACCTTGTAATCT-ATAAAAGATTCATACACTC
* *
35571190 ACGATGACACATAGTCATGGACCTCATAATCCATAAAGGATTCATATACTCACGATGACATATAG
1 ACAATGACACATAGTCATGGACCTCATAATCCGTAAAGGATTCATATACTCACGATGACATATAG
* *
35571255 TCATCGGACCTTGTAATCTATAAAAGATTCATATACTT
66 TCATCGGACCTTGTAATCTATAAAAGATTCATACACTC
** * *
35571293 ACAATGACACATAGTCATCATACCTCATAATCCGTAAAGGATTCATATACTCACGATGACACAGA
1 ACAATGACACATAGTCAT-GGACCTCATAATCCGTAAAGGATTCATATACTCACGATGACATATA
35571358 GTCATCGGACCTT
65 GTCATCGGACCTT
35571371 TTGCATTTAC
Statistics
Matches: 164, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
103 93 0.57
104 71 0.43
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.27
Consensus pattern (103 bp):
ACAATGACACATAGTCATGGACCTCATAATCCGTAAAGGATTCATATACTCACGATGACATATAG
TCATCGGACCTTGTAATCTATAAAAGATTCATACACTC
Found at i:35575580 original size:21 final size:21
Alignment explanation
Indices: 35575537--35575585 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
35575527 CCTATGACAG
* * *
35575537 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
*
35575558 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
*
35575579 TTTTACC
1 TTCTACC
35575586 AATACTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:35575699 original size:6 final size:6
Alignment explanation
Indices: 35575688--35575766 Score: 58
Period size: 6 Copynumber: 13.5 Consensus size: 6
35575678 GGCCCAACAG
* * * * *
35575688 AATTTA AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTGGA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATT-TA
*
35575735 AATTTA AATTT- -ATTATA AATTTG AATTTA AAT
1 AATTTA AATTTA AATT-TA AATTTA AATTTA AAT
35575767 ATATTTAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
4 3 0.05
5 9 0.16
6 36 0.64
7 8 0.14
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:35575716 original size:17 final size:17
Alignment explanation
Indices: 35575691--35575731 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
35575681 CCAACAGAAT
35575691 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
35575708 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAA
35575725 TTAAATT
1 TTAAATT
35575732 GGAAATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:35575756 original size:17 final size:17
Alignment explanation
Indices: 35575688--35575776 Score: 62
Period size: 17 Copynumber: 5.5 Consensus size: 17
35575678 GGCCCAACAG
*
35575688 AATTTAAATTTATTTTA
1 AATTTAAATTTATTATA
* * *
35575705 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTATA
**
35575722 AATTT-AA---ATTGGA
1 AATTTAAATTTATTATA
35575735 AATTTAAATTTATTATA
1 AATTTAAATTTATTATA
* *
35575752 AATTTGAATTTA-AATA
1 AATTTAAATTTATTATA
*
35575768 TATTTAAAT
1 AATTTAAAT
35575777 AATGTCCAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 9
0.73 0.16 0.12
Matches are distributed among these distances:
13 9 0.16
14 2 0.04
16 11 0.20
17 34 0.61
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:35577661 original size:29 final size:28
Alignment explanation
Indices: 35577624--35577850 Score: 115
Period size: 29 Copynumber: 7.8 Consensus size: 28
35577614 ACCCTCGAAC
* *
35577624 TTTCTAAAATTTCATTTTTGACCCTAATT
1 TTTCCAAAATTACATTTTT-ACCCTAATT
**
35577653 TTTCCAAAAATTACATTTTTACCCTCAAAC
1 TTTCC-AAAATTACATTTTTACCCT-AATT
* ** *
35577683 TTTCTAAAATCCCATTTTTGACCACT-ACT
1 TTTCCAAAATTACATTTTT-ACC-CTAATT
* *
35577712 TTTCCAAAAATTACATTTTTACCCCGAACT
1 TTTCC-AAAATTACATTTTTA-CCCTAATT
* *
35577742 TTT-CAAAA-TCCTATTTTTAACCCCAATT
1 TTTCCAAAATTAC-ATTTTT-ACCCTAATT
**
35577770 TTTCCAAAAATTACA-TTTTACCCTTAAAC
1 TTTCC-AAAATTACATTTTTACCC-TAATT
* * * *
35577799 TTACAAAAATTCCATTTTTGACCCCAA-T
1 TTTCCAAAATTACATTTTT-ACCCTAATT
*
35577827 TTTCTAAAAATTACCA-TTTTACCC
1 TTTC-CAAAATTA-CATTTTTACCC
35577851 CTAAACTTCC
Statistics
Matches: 154, Mismatches: 27, Indels: 35
0.71 0.12 0.16
Matches are distributed among these distances:
27 2 0.01
28 38 0.25
29 57 0.37
30 53 0.34
31 4 0.03
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.41
Consensus pattern (28 bp):
TTTCCAAAATTACATTTTTACCCTAATT
Found at i:35577687 original size:59 final size:58
Alignment explanation
Indices: 35577601--35577905 Score: 307
Period size: 58 Copynumber: 5.2 Consensus size: 58
35577591 AAACTGTCCT
* * * *
35577601 AAAATTGCATTTTACCCTCGAACTTTCTAAAATTTCATTTTTGACCCTAATTTTTCCA
1 AAAATTACATTTTACCCTCAAACTTTCTAAAATTCCATTTTTGACCCCAATTTTTCCA
* * * *
35577659 AAAATTACATTTTTACCCTCAAACTTTCTAAAATCCCATTTTTGACCACTACTTTTCCA
1 AAAATTACA-TTTTACCCTCAAACTTTCTAAAATTCCATTTTTGACCCCAATTTTTCCA
* *
35577718 AAAATTACATTTTTACCC-CGAACTTT-TCAAAA-TCCTATTTTTAACCCCAATTTTTCCA
1 AAAATTACA-TTTTACCCTCAAACTTTCT-AAAATTCC-ATTTTTGACCCCAATTTTTCCA
* * * *
35577776 AAAATTACATTTTACCCTTAAACTTACAAAAATTCCATTTTTGACCCCAA-TTTTCTA
1 AAAATTACATTTTACCCTCAAACTTTCTAAAATTCCATTTTTGACCCCAATTTTTCCA
* * * * * **
35577833 AAAATTACCATTTTACCC-CTAAACTTCCAAAAACTT-TATTTTTAATCCCAAACTTTCCA
1 AAAATTA-CATTTTACCCTC-AAACTTTCTAAAA-TTCCATTTTTGACCCCAATTTTTCCA
35577892 AAAATTATCATTTT
1 AAAATTA-CATTTT
35577906 GGCCCCGAGT
Statistics
Matches: 209, Mismatches: 28, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
57 24 0.11
58 102 0.49
59 83 0.40
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (58 bp):
AAAATTACATTTTACCCTCAAACTTTCTAAAATTCCATTTTTGACCCCAATTTTTCCA
Found at i:35577864 original size:29 final size:29
Alignment explanation
Indices: 35577771--35577865 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
35577761 ACCCCAATTT
*
35577771 TTCCAAAAATTA-CATTTTACCCTTAAAC
1 TTCCAAAAATTACCATTTTACCCCTAAAC
* **
35577799 TTACAAAAATT-CCATTTTTGACCCC-AATT
1 TTCCAAAAATTACCA-TTTT-ACCCCTAAAC
*
35577828 TTCTAAAAATTACCATTTTACCCCTAAAC
1 TTCCAAAAATTACCATTTTACCCCTAAAC
35577857 TTCCAAAAA
1 TTCCAAAAA
35577866 CTTTATTTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
28 17 0.32
29 29 0.55
30 7 0.13
ACGTcount: A:0.39, C:0.25, G:0.01, T:0.35
Consensus pattern (29 bp):
TTCCAAAAATTACCATTTTACCCCTAAAC
Found at i:35588957 original size:52 final size:52
Alignment explanation
Indices: 35588879--35589117 Score: 343
Period size: 52 Copynumber: 4.6 Consensus size: 52
35588869 TTCTCATTTA
* * *
35588879 ATACTCACGATGACACATAGTCATCGGTCCTCATAACCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAAGATTCAT
* * * *
35588931 ATACTCTCGATAACACATAGTCATCGGACCTCGTAATTCATAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAAGATTCAT
* *
35588983 ATACTCACGATGACACATAGTCATCGGACCTCGTAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAAGATTCAT
* * *
35589035 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAAGATTCAT
* * *
35589087 ATACTCATGATAACACAAAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
35589118 TTTGAATTTA
Statistics
Matches: 169, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 169 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAAGATTCAT
Found at i:35591143 original size:23 final size:23
Alignment explanation
Indices: 35591111--35591154 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
35591101 ACTACCATTT
35591111 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
35591134 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
35591155 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:35591147 original size:13 final size:11
Alignment explanation
Indices: 35591115--35591157 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
35591105 CCATTTTCTA
*
35591115 AATAAAATAAT
1 AATAAAATATT
35591126 AAT-AAATATCT
1 AATAAAATAT-T
35591137 AAGTAAAATATT
1 AA-TAAAATATT
35591149 AATAAAATA
1 AATAAAATA
35591158 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:35591160 original size:27 final size:27
Alignment explanation
Indices: 35591112--35591189 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 27
35591102 CTACCATTTT
35591112 CTAAATAA--AATAATAATAAATATCTAA
1 CTAAATAATTAATAA-AAT-AATATCTAA
* *
35591139 GTAAA-ATATTAATAAAATAATATTTAA
1 CTAAATA-ATTAATAAAATAATATCTAA
*
35591166 CTAATTAATTAATAAAA-AATATCT
1 CTAAATAATTAATAAAATAATATCT
35591190 CCAAAATATC
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
26 7 0.17
27 26 0.62
28 4 0.10
29 5 0.12
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (27 bp):
CTAAATAATTAATAAAATAATATCTAA
Done.