Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 92 of 221
Found at i:27853284 original size:20 final size:20
Alignment explanation
Indices: 27853238--27853284 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
27853228 AGCTTGTTTC
*
27853238 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
27853258 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
27853278 CAGCTCA
1 CAGCTCA
27853285 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:27856565 original size:13 final size:12
Alignment explanation
Indices: 27856536--27856583 Score: 69
Period size: 12 Copynumber: 3.8 Consensus size: 12
27856526 ATGCAATTTT
27856536 TTTTTCTTTTCAA
1 TTTTT-TTTTCAA
27856549 TTTTTTTTTCAA
1 TTTTTTTTTCAA
27856561 TTTTTTTTTCGAA
1 TTTTTTTTTC-AA
27856574 CTTTTTTTTT
1 -TTTTTTTTT
27856584 ACGTACCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
12 17 0.52
13 7 0.21
14 9 0.27
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:27861197 original size:23 final size:22
Alignment explanation
Indices: 27861146--27861197 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
27861136 CCTCGTCTTT
*
27861146 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
27861168 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
27861191 TTCTTTT
1 TTCTTTT
27861198 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:27862954 original size:11 final size:11
Alignment explanation
Indices: 27862938--27862976 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
27862928 TAGTTTCTCA
*
27862938 AAAAAAACTCG
1 AAAAAAATTCG
27862949 AAAAAAATTC-
1 AAAAAAATTCG
27862959 AAAAAAATTCG
1 AAAAAAATTCG
27862970 AAAAAAA
1 AAAAAAA
27862977 ACTAGTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.72, C:0.10, G:0.05, T:0.13
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:27863068 original size:15 final size:14
Alignment explanation
Indices: 27863015--27863069 Score: 92
Period size: 14 Copynumber: 3.9 Consensus size: 14
27863005 GGATATCAAG
27863015 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
*
27863029 TTTTGAAAAACAAAA
1 TTGTGAAAAA-AAAA
27863044 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
27863058 TTGTGAAAAAAA
1 TTGTGAAAAAAA
27863070 GAGAGCTAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.24
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:27864787 original size:33 final size:34
Alignment explanation
Indices: 27864739--27864804 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
27864729 ATCACTCTCC
*
27864739 CTCATTTAAATGCCG-TCCATTGCATGTGGAACAT
1 CTCATTTAAATGCCGTTCCA-TGCATGTAGAACAT
*
27864773 CTCA-TTAATTGCCGTTCCATGCATGTAGAACA
1 CTCATTTAAATGCCGTTCCATGCATGTAGAACA
27864805 ACATCTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (34 bp):
CTCATTTAAATGCCGTTCCATGCATGTAGAACAT
Found at i:27864815 original size:34 final size:33
Alignment explanation
Indices: 27864743--27864815 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
27864733 CTCTCCCTCA
* * *
27864743 TTTAAATGCCGTCCATTGCATGTGGAACATCTC
1 TTTAATTGCCGTCCATTGCATGTAGAACAACTC
*
27864776 ATTAATTGCCGTTCCA-TGCATGTAGAACAACATC
1 TTTAATTGCCG-TCCATTGCATGTAGAACAAC-TC
27864810 TTTAAT
1 TTTAAT
27864816 GCATGTCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
33 22 0.67
34 11 0.33
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (33 bp):
TTTAATTGCCGTCCATTGCATGTAGAACAACTC
Found at i:27867248 original size:12 final size:11
Alignment explanation
Indices: 27867215--27867247 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
27867205 TAGTAGTTTC
27867215 TTCAAAAAAAA
1 TTCAAAAAAAA
27867226 TTCAAAAAAAA
1 TTCAAAAAAAA
27867237 TTCAAAAAAAA
1 TTCAAAAAAAA
27867248 AAATTGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:27867310 original size:16 final size:16
Alignment explanation
Indices: 27867289--27867343 Score: 85
Period size: 15 Copynumber: 3.4 Consensus size: 16
27867279 GATATCAATT
27867289 TGAAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
27867305 TG-AAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
27867320 TGAAAAAAAAAATTTTCG
1 TGAAAAAAAAAA--TTCG
27867338 TGAAAA
1 TGAAAA
27867344 GAAGAAGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.42
16 11 0.31
18 10 0.28
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (16 bp):
TGAAAAAAAAAATTCG
Found at i:27867314 original size:18 final size:18
Alignment explanation
Indices: 27867291--27867343 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
27867281 TATCAATTTG
27867291 AAAAAAAAAATTCGTG--
1 AAAAAAAAAATTCGTGAA
27867307 -AAAAAAAAATTCGTGAA
1 AAAAAAAAAATTCGTGAA
**
27867324 AAAAAAAATTTTCGTGAA
1 AAAAAAAAAATTCGTGAA
27867342 AA
1 AA
27867344 GAAGAAGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 15 0.47
18 17 0.53
ACGTcount: A:0.62, C:0.06, G:0.11, T:0.21
Consensus pattern (18 bp):
AAAAAAAAAATTCGTGAA
Found at i:27867843 original size:22 final size:22
Alignment explanation
Indices: 27867813--27867856 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27867803 TTTGGTATTT
27867813 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
27867835 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
27867857 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:27868554 original size:20 final size:20
Alignment explanation
Indices: 27868508--27868554 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
27868498 AGCTCGTTTC
*
27868508 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
27868528 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
27868548 CAGCTCA
1 CAGCTCA
27868555 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:27869994 original size:13 final size:13
Alignment explanation
Indices: 27869976--27870000 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27869966 TCGAAACGTG
27869976 AAAAAAAAAAATC
1 AAAAAAAAAAATC
27869989 AAAAAAAAAAAT
1 AAAAAAAAAAAT
27870001 TTTTGAGTTG
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:0.88, C:0.04, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAAAAAAAAATC
Found at i:27870118 original size:14 final size:14
Alignment explanation
Indices: 27870071--27870122 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
27870061 CAAAAAAAAT
27870071 CAAAAAAAATTCGA-
1 CAAAAAAAATT-GAG
*
27870085 AAAAAAAAATTGATTG
1 CAAAAAAAATTGA--G
27870101 -AAAAAAAATTGAG
1 CAAAAAAAATTGAG
27870114 CAAAAAAAA
1 CAAAAAAAA
27870123 AAGGTGACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 3 0.09
14 18 0.55
15 12 0.36
ACGTcount: A:0.69, C:0.06, G:0.10, T:0.15
Consensus pattern (14 bp):
CAAAAAAAATTGAG
Found at i:27870119 original size:15 final size:13
Alignment explanation
Indices: 27870072--27870123 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 13
27870062 AAAAAAAATC
27870072 AAAAAAAATTCGAA
1 AAAAAAAATT-GAA
*
27870086 AAAAAAAATTGATTG
1 AAAAAAAATTGA--A
27870101 AAAAAAAATTGAGCA
1 AAAAAAAATTGA--A
27870116 AAAAAAAA
1 AAAAAAAA
27870124 AGGTGACCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 2 0.06
14 10 0.31
15 20 0.62
ACGTcount: A:0.71, C:0.04, G:0.10, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTGAA
Found at i:27873094 original size:20 final size:20
Alignment explanation
Indices: 27873048--27873094 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
27873038 AGCTCGTTTC
*
27873048 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
27873068 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
27873088 CAGCTCA
1 CAGCTCA
27873095 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:27881287 original size:16 final size:14
Alignment explanation
Indices: 27881264--27881325 Score: 67
Period size: 13 Copynumber: 4.5 Consensus size: 14
27881254 CCGTATGCAA
27881264 TTTTTTTTTCAAATT
1 TTTTTTTTTC-AATT
27881279 TTATTTTTTTCAA--
1 TT-TTTTTTTCAATT
*
27881292 TTTTTTTTTCGA-T
1 TTTTTTTTTCAATT
*
27881305 TTTTTTTTTCGATT
1 TTTTTTTTTCAATT
27881319 TTTTTTT
1 TTTTTTT
27881326 GAATCTACAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
12 9 0.21
13 14 0.33
14 8 0.19
15 4 0.09
16 8 0.19
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTTTTTTCAATT
Found at i:27881297 original size:12 final size:12
Alignment explanation
Indices: 27881261--27881325 Score: 67
Period size: 12 Copynumber: 5.0 Consensus size: 12
27881251 AGACCGTATG
27881261 CAATTTTTTTTT
1 CAATTTTTTTTT
27881273 CAAATTTTATTTTTTT
1 C-AA--TT-TTTTTTT
27881289 CAATTTTTTTTT
1 CAATTTTTTTTT
*
27881301 CGATTTTTTTTTT
1 C-AATTTTTTTTT
*
27881314 CGATTTTTTTTT
1 CAATTTTTTTTT
27881326 GAATCTACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 18 0.40
13 15 0.33
15 4 0.09
16 8 0.18
ACGTcount: A:0.15, C:0.08, G:0.03, T:0.74
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:27885986 original size:17 final size:17
Alignment explanation
Indices: 27885964--27886011 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
27885954 TTTCATTCTC
27885964 TTTTTTGAATTTTCCTT
1 TTTTTTGAATTTTCCTT
* *
27885981 TTTTTT-CATTTTTCTT
1 TTTTTTGAATTTTCCTT
*
27885997 TTCTTTTGTATTTTC
1 TT-TTTTGAATTTTC
27886012 GCTCTTTTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 10 0.40
17 10 0.40
18 5 0.20
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.75
Consensus pattern (17 bp):
TTTTTTGAATTTTCCTT
Found at i:27888564 original size:22 final size:22
Alignment explanation
Indices: 27888534--27888577 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27888524 TTTGGTATTT
27888534 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
27888556 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
27888578 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:27895889 original size:20 final size:20
Alignment explanation
Indices: 27895873--27895918 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
27895863 TTTTTCTTTT
27895873 ATTTCTTTTTCTTTTCTCTC
1 ATTTCTTTTTCTTTTCTCTC
27895893 ATTTCTTTTT-TTCTTCTCTC
1 ATTTCTTTTTCTT-TTCTCTC
27895913 AATTTC
1 -ATTTC
27895919 ATTCAAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 17 0.71
21 5 0.21
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTCTTTTTCTTTTCTCTC
Found at i:27900738 original size:20 final size:22
Alignment explanation
Indices: 27900715--27900762 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
27900705 TTTTTTATAC
27900715 TTCGATTTT-TTTT-AATTTTT
1 TTCGATTTTGTTTTAAATTTTT
27900735 TTCGATTTTGTTTTCAAATTTTT
1 TTCGATTTTGTTTT-AAATTTTT
27900758 TTCGA
1 TTCGA
27900763 ATTTCCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.36
21 4 0.16
23 12 0.48
ACGTcount: A:0.17, C:0.08, G:0.08, T:0.67
Consensus pattern (22 bp):
TTCGATTTTGTTTTAAATTTTT
Found at i:27900765 original size:11 final size:11
Alignment explanation
Indices: 27900715--27900766 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
27900705 TTTTTTATAC
27900715 TTCG-ATTTTT
1 TTCGAATTTTT
*
27900725 TT-TAATTTTT
1 TTCGAATTTTT
*
27900735 TTCGATTTTGTT
1 TTCGAATTT-TT
*
27900747 TTCAAATTTTT
1 TTCGAATTTTT
27900758 TTCGAATTT
1 TTCGAATTT
27900767 CCTCTTCTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
10 10 0.30
11 14 0.42
12 9 0.27
ACGTcount: A:0.17, C:0.08, G:0.08, T:0.67
Consensus pattern (11 bp):
TTCGAATTTTT
Found at i:27901929 original size:33 final size:34
Alignment explanation
Indices: 27901881--27901946 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
27901871 ATCACTCTCC
*
27901881 CTCATTTAAATGCCG-TCCATTGCATGTGGAACAT
1 CTCATTTAAATGCCGTTCCA-TGCATGTAGAACAT
*
27901915 CTCA-TTAATTGCCGTTCCATGCATGTAGAACA
1 CTCATTTAAATGCCGTTCCATGCATGTAGAACA
27901947 ACATCTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (34 bp):
CTCATTTAAATGCCGTTCCATGCATGTAGAACAT
Found at i:27901957 original size:34 final size:33
Alignment explanation
Indices: 27901885--27901957 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
27901875 CTCTCCCTCA
* * *
27901885 TTTAAATGCCGTCCATTGCATGTGGAACATCTC
1 TTTAATTGCCGTCCATTGCATGTAGAACAACTC
*
27901918 ATTAATTGCCGTTCCA-TGCATGTAGAACAACATC
1 TTTAATTGCCG-TCCATTGCATGTAGAACAAC-TC
27901952 TTTAAT
1 TTTAAT
27901958 GCATGTCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
33 22 0.67
34 11 0.33
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (33 bp):
TTTAATTGCCGTCCATTGCATGTAGAACAACTC
Found at i:27910085 original size:10 final size:10
Alignment explanation
Indices: 27910072--27910109 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
27910062 AAGAAGCTAA
27910072 ATTGAGCTCG
1 ATTGAGCTCG
27910082 ATTGAGCT-G
1 ATTGAGCTCG
27910091 ACTTGAGCTCG
1 A-TTGAGCTCG
*
27910102 AGTGAGCT
1 ATTGAGCT
27910110 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:27910096 original size:20 final size:20
Alignment explanation
Indices: 27910073--27910110 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
27910063 AGAAGCTAAA
*
27910073 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
27910093 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
27910111 GAAACGAGCT
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:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:27917728 original size:22 final size:22
Alignment explanation
Indices: 27917698--27917741 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
27917688 AATGGTATTT
27917698 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
* *
27917720 GGGATTTGGTACGGAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
27917742 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.39, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:27920986 original size:23 final size:21
Alignment explanation
Indices: 27920935--27920986 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 21
27920925 CCACATCTTT
*
27920935 TTCTTTTGTTTCTTTTTCTAA
1 TTCTTTTCTTTCTTTTTCTAA
27920956 TTCATTTTCTCTTCTTTCTTC-AA
1 TTC-TTTTCT-TTCTTT-TTCTAA
27920979 TGTCTTTT
1 T-TCTTTT
27920987 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 13 0.50
24 5 0.19
ACGTcount: A:0.10, C:0.19, G:0.04, T:0.67
Consensus pattern (21 bp):
TTCTTTTCTTTCTTTTTCTAA
Found at i:27928973 original size:23 final size:22
Alignment explanation
Indices: 27928921--27928973 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
27928911 TCCACGTCTT
*
27928921 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
27928943 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
27928966 TTTCTTTT
1 TTTCTTTT
27928974 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:27931597 original size:15 final size:14
Alignment explanation
Indices: 27931565--27931605 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
27931555 TTTTCACTCA
27931565 CTTTTTCTTTTCAT
1 CTTTTTCTTTTCAT
27931579 CTTTTTCTTTTC-T
1 CTTTTTCTTTTCAT
**
27931592 CGCTTTCTTTTCAT
1 CTTTTTCTTTTCAT
27931606 TTTCTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.05, C:0.24, G:0.02, T:0.68
Consensus pattern (14 bp):
CTTTTTCTTTTCAT
Found at i:27931598 original size:13 final size:14
Alignment explanation
Indices: 27931568--27931605 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
27931558 TCACTCACTT
**
27931568 TTTCTTTTCATCTT
1 TTTCTTTTCATCGC
27931582 TTTCTTTTC-TCGC
1 TTTCTTTTCATCGC
27931595 TTTCTTTTCAT
1 TTTCTTTTCAT
27931606 TTTCTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.05, C:0.24, G:0.03, T:0.68
Consensus pattern (14 bp):
TTTCTTTTCATCGC
Found at i:27931637 original size:19 final size:19
Alignment explanation
Indices: 27931594--27931655 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
27931584 TCTTTTCTCG
27931594 CTTTCTTTTC-ATTTTCTTT
1 CTTT-TTTTCAATTTTCTTT
*
27931613 -TTTTTTTGAATTTTCTTT
1 CTTTTTTTCAATTTTCTTT
*
27931631 CTTTTTTTCATTTTTCTTTT
1 CTTTTTTTCAATTTTC-TTT
27931651 CTTTT
1 CTTTT
27931656 GTATTTTCGC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.11
18 12 0.32
19 13 0.35
20 8 0.22
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (19 bp):
CTTTTTTTCAATTTTCTTT
Found at i:27931661 original size:18 final size:19
Alignment explanation
Indices: 27931599--27931677 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 19
27931589 TCTCGCTTTC
27931599 TTTTCA-TTTTCTTTT-TT
1 TTTTCATTTTTCTTTTCTT
* *
27931616 TTTTGAATTTTC-TTTCTTT
1 TTTTCATTTTTCTTTTC-TT
27931635 TTTTCATTTTTCTTTTCTT
1 TTTTCATTTTTCTTTTCTT
*
27931654 TTGT-ATTTTCGCTCTTTTCTT
1 TTTTCATTTT---TCTTTTCTT
27931675 TTT
1 TTT
27931678 CTCTCATTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
17 8 0.16
18 10 0.20
19 17 0.34
20 4 0.08
21 11 0.22
ACGTcount: A:0.06, C:0.14, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTTCATTTTTCTTTTCTT
Found at i:27931670 original size:36 final size:36
Alignment explanation
Indices: 27931566--27931671 Score: 106
Period size: 36 Copynumber: 2.9 Consensus size: 36
27931556 TTTCACTCAC
* * *
27931566 TTTTTCTTTTCATCTTTTTCTTTTCTCGCTTTCTTTTCA
1 TTTTTCTTTTC-T-TTTGTATTTTCTCTCTTT-TTTTCA
* * *
27931605 -TTTTCTTTTTTTTTTGAATTTTCTTTCTTTTTTTCA
1 TTTTTC-TTTTCTTTTGTATTTTCTCTCTTTTTTTCA
*
27931641 TTTTTCTTTTCTTTTGTATTTTCGCTCTTTT
1 TTTTTCTTTTCTTTTGTATTTTCTCTCTTTT
27931672 CTTTTTCTCT
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
36 27 0.49
37 18 0.33
38 6 0.11
39 4 0.07
ACGTcount: A:0.06, C:0.17, G:0.04, T:0.74
Consensus pattern (36 bp):
TTTTTCTTTTCTTTTGTATTTTCTCTCTTTTTTTCA
Found at i:27933879 original size:11 final size:11
Alignment explanation
Indices: 27933863--27933915 Score: 60
Period size: 10 Copynumber: 5.2 Consensus size: 11
27933853 AGACCGTATA
27933863 CAATTTTTTTT
1 CAATTTTTTTT
27933874 CAA-TTTTTTT
1 CAATTTTTTTT
*
27933884 -GA-TTTTTTT
1 CAATTTTTTTT
*
27933893 -GATTTTTTTT
1 CAATTTTTTTT
27933903 CAATTTTTTTT
1 CAATTTTTTTT
27933914 CA
1 CA
27933916 CGAATCTACT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
9 10 0.26
10 14 0.37
11 14 0.37
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.72
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:27933889 original size:8 final size:9
Alignment explanation
Indices: 27933876--27933901 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
27933866 TTTTTTTTCA
27933876 ATTTTTTTG
1 ATTTTTTTG
27933885 ATTTTTTTG
1 ATTTTTTTG
27933894 ATTTTTTT
1 ATTTTTTT
27933902 TCAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.81
Consensus pattern (9 bp):
ATTTTTTTG
Found at i:27935460 original size:20 final size:20
Alignment explanation
Indices: 27935437--27935483 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
27935427 GGGTTAAGAT
*
27935437 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
27935457 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
27935477 TGAGCTG
1 TGAGCTG
27935484 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:27938020 original size:20 final size:20
Alignment explanation
Indices: 27937973--27938020 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
27937963 AGTAAGCTCG
27937973 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
27937993 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
27938013 GTTGAGCT
1 GTTGAGCT
27938021 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:27939690 original size:11 final size:12
Alignment explanation
Indices: 27939660--27939691 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
27939650 TTTCACTCTT
27939660 CTCTTTTTCAAA
1 CTCTTTTTCAAA
27939672 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
27939684 TTCTTTTT
1 CTCTTTTT
27939692 TCGCTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:27939791 original size:18 final size:18
Alignment explanation
Indices: 27939695--27939796 Score: 91
Period size: 18 Copynumber: 5.6 Consensus size: 18
27939685 TCTTTTTTCG
27939695 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
*
27939714 CTTTTCTTCATTTTCATTTT
1 C-TTT-TTCTTTTTCATTTT
** *
27939734 CTTTCACTTTTTGA-TTT
1 CTTTTTCTTTTTCATTTT
* *
27939751 C-TTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
27939768 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
27939786 CTTTTTGTTTT
1 CTTTTTCTTTT
27939797 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
16 8 0.12
17 8 0.12
18 29 0.44
19 4 0.06
20 9 0.14
21 8 0.12
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.72
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:27939813 original size:6 final size:6
Alignment explanation
Indices: 27939695--27939800 Score: 56
Period size: 6 Copynumber: 17.7 Consensus size: 6
27939685 TCTTTTTTCG
* * * **
27939695 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CATTTT CTTTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
27939746 -GATTT C-TTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
27939792 -GTTTT CTTT
1 CTTTTT CTTT
27939801 CAATTTCTTT
Statistics
Matches: 73, Mismatches: 22, Indels: 10
0.70 0.21 0.10
Matches are distributed among these distances:
5 11 0.15
6 50 0.68
7 9 0.12
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:27940896 original size:12 final size:12
Alignment explanation
Indices: 27940871--27940906 Score: 51
Period size: 10 Copynumber: 3.2 Consensus size: 12
27940861 TTTTTTTTCC
27940871 TTTTTTTC-G-A
1 TTTTTTTCTGAA
27940881 TTTTTTT-TGAA
1 TTTTTTTCTGAA
27940892 TTTTTTTCTGAA
1 TTTTTTTCTGAA
27940904 TTT
1 TTT
27940907 CTTCTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 8 0.35
11 8 0.35
12 7 0.30
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (12 bp):
TTTTTTTCTGAA
Found at i:27942465 original size:20 final size:20
Alignment explanation
Indices: 27942418--27942465 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
27942408 AGTAAGCTCG
27942418 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
27942438 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
27942458 GTTGAGCT
1 GTTGAGCT
27942466 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:27943286 original size:48 final size:48
Alignment explanation
Indices: 27943231--27943336 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
27943221 TTGTCTTTTC
*
27943231 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
** *
27943279 TTTCTTTTTTGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
27943327 TTTCTTTTTC
1 TTTCTTTTTC
27943337 CATGACACTC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
48 38 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:27945950 original size:20 final size:20
Alignment explanation
Indices: 27945927--27945973 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
27945917 GGGTTAAGAT
*
27945927 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
27945947 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
27945967 TGAGCTG
1 TGAGCTG
27945974 CAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:27947698 original size:48 final size:48
Alignment explanation
Indices: 27947643--27947748 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
27947633 TTGTCTTTTC
*
27947643 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
** *
27947691 TTTCTTTTTTGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
27947739 TTTCTTTTTC
1 TTTCTTTTTC
27947749 CATGACACTC
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
48 38 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:27955216 original size:20 final size:20
Alignment explanation
Indices: 27955191--27955245 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
27955181 TGTGGTTCAA
* *
27955191 CTCATTCGAGCTCAAGTTAG
1 CTCATTCAAGCTCAAGTCAG
27955211 CTCATTCAAGCTCAAGTCAG
1 CTCATTCAAGCTCAAGTCAG
27955231 CTCATTCAAGCTCAA
1 CTCATTCAAGCTCAA
27955246 TTTAACTCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (20 bp):
CTCATTCAAGCTCAAGTCAG
Found at i:27956308 original size:13 final size:13
Alignment explanation
Indices: 27956290--27956323 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
27956280 GTAGTTTTCG
27956290 AAAAAAAATC-AA
1 AAAAAAAATCGAA
27956302 AAAAAAAATCGAA
1 AAAAAAAATCGAA
27956315 AAGAAAAAA
1 AA-AAAAAA
27956324 AATTGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 4 0.20
14 6 0.30
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (13 bp):
AAAAAAAATCGAA
Found at i:27956321 original size:16 final size:15
Alignment explanation
Indices: 27956300--27956336 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
27956290 AAAAAAAATC
27956300 AAAAAAAAAATCGAA
1 AAAAAAAAAATCGAA
*
27956315 AAGAAAAAAAATTGAA
1 AA-AAAAAAAATCGAA
27956331 AAAAAA
1 AAAAAA
27956337 TATATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.81, C:0.03, G:0.08, T:0.08
Consensus pattern (15 bp):
AAAAAAAAAATCGAA
Found at i:27960643 original size:30 final size:30
Alignment explanation
Indices: 27960609--27960704 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
27960599 GCTCACTCCC
27960609 AGCTCATA-TTTAGCTCACGAGCTAAACCTT
1 AGCTCA-ACTTTAGCTCACGAGCTAAACCTT
* * * * * * *
27960639 AGCTCAACTTCAGCTTAGGAGTTTAGCCTC
1 AGCTCAACTTTAGCTCACGAGCTAAACCTT
*
27960669 AGCTCAACTTTAGCTCACGAGCTAAAGCTT
1 AGCTCAACTTTAGCTCACGAGCTAAACCTT
27960699 AGCTCA
1 AGCTCA
27960705 TTTTAGTTTT
Statistics
Matches: 50, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 49 0.98
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (30 bp):
AGCTCAACTTTAGCTCACGAGCTAAACCTT
Found at i:27971851 original size:20 final size:20
Alignment explanation
Indices: 27971805--27971851 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
27971795 AGCTCGTTTC
*
27971805 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
27971825 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
27971845 CAGCTCA
1 CAGCTCA
27971852 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:27974470 original size:48 final size:49
Alignment explanation
Indices: 27974399--27974507 Score: 152
Period size: 48 Copynumber: 2.2 Consensus size: 49
27974389 CATTGAGCGA
* * *
27974399 GAAAAGGAGAAAGAGATTGAAAAAGAAATTGAGATTG-A-AAAAG-GATG
1 GAAAAAGAGAAAGAAATCGAAAAAGAAATTGAGATTGAACAAAAGTGA-G
27974446 TGAAAAAGAGAAAGAAATCGAAAAAGAAATTGAGATTGAACAAAAGTGAG
1 -GAAAAAGAGAAAGAAATCGAAAAAGAAATTGAGATTGAACAAAAGTGAG
27974496 GAAAAAGAGAAA
1 GAAAAAGAGAAA
27974508 ATTGAAAAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
48 34 0.62
49 13 0.24
50 6 0.11
51 2 0.04
ACGTcount: A:0.59, C:0.02, G:0.27, T:0.13
Consensus pattern (49 bp):
GAAAAAGAGAAAGAAATCGAAAAAGAAATTGAGATTGAACAAAAGTGAG
Found at i:27976237 original size:20 final size:20
Alignment explanation
Indices: 27976191--27976228 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27976181 AGCTCATTTC
*
27976191 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
*
27976211 CAACTCACTCAAGCTCAA
1 CAGCTCACTCAAGCTCAA
27976229 TTTAGCTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.37, G:0.13, T:0.18
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:27986641 original size:20 final size:19
Alignment explanation
Indices: 27986618--27986682 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
27986608 AAGCTCAAAC
27986618 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
27986638 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
27986658 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
27986678 GAGCT
1 GAGCT
27986683 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:27988494 original size:33 final size:33
Alignment explanation
Indices: 27988456--27988518 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
27988446 GATTACTCAC
27988456 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
27988489 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
27988519 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:27988545 original size:27 final size:27
Alignment explanation
Indices: 27988515--27988601 Score: 97
Period size: 27 Copynumber: 3.1 Consensus size: 27
27988505 TCAAGCTCTC
*
27988515 TTTCAATTTCTTTT-TTCGCTTTTTCTT
1 TTTCAATTTCTTTTCTTC-CATTTTCTT
* *
27988542 TTTCAATTTTTTTTCATTCTCAATTTCTT
1 TTTCAATTTCTTTTC-TTC-CATTTTCTT
27988571 TTTCAATTTTCTTTTCTT-CATTTTCTT
1 TTTCAA-TTTCTTTTCTTCCATTTTCTT
27988598 TTTC
1 TTTC
27988602 TCTCACTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
27 25 0.49
29 18 0.35
30 8 0.16
ACGTcount: A:0.11, C:0.18, G:0.01, T:0.69
Consensus pattern (27 bp):
TTTCAATTTCTTTTCTTCCATTTTCTT
Found at i:27988577 original size:29 final size:27
Alignment explanation
Indices: 27988536--27988601 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 27
27988526 TTTTTCGCTT
27988536 TTTCTTTTTCAATTTT-TTTTCATTCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
*
27988565 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
27988592 TTTCTTTTTC
1 TTTCTTTTTC
27988602 TCTCACTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 13 0.37
28 1 0.03
29 16 0.46
30 5 0.14
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:27988660 original size:18 final size:18
Alignment explanation
Indices: 27988533--27988682 Score: 80
Period size: 18 Copynumber: 8.4 Consensus size: 18
27988523 TCTTTTTTCG
27988533 CTTTTTCTTTTTCAATTT
1 CTTTTTCTTTTTCAATTT
* *
27988551 -TTTTTCATTCTCAATTT
1 CTTTTTCTTTTTCAATTT
*
27988568 CTTTTTCAATTTTC---TT
1 CTTTTTC-TTTTTCAATTT
* * **
27988584 -TTCTTCATTTTCTTTTT
1 CTTTTTCTTTTTCAATTT
* ** *
27988601 CTCTCACTTTTTCGATTT
1 CTTTTTCTTTTTCAATTT
*
27988619 -TCTTTTCTTTTGCAATTT
1 CT-TTTTCTTTTTCAATTT
27988637 CTTTTTCTTTTTC-ATTT
1 CTTTTTCTTTTTCAATTT
*
27988654 CCTTTTTGTTTTCTTTCAATTT
1 -C-TTTT-TCTT-TTTCAATTT
27988676 CTTTTTC
1 CTTTTTC
27988683 AATCTCTTTC
Statistics
Matches: 100, Mismatches: 19, Indels: 25
0.69 0.13 0.17
Matches are distributed among these distances:
14 6 0.06
15 5 0.05
16 2 0.02
17 22 0.22
18 38 0.38
19 11 0.11
20 7 0.07
21 5 0.05
22 4 0.04
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTTTCAATTT
Found at i:27988669 original size:11 final size:12
Alignment explanation
Indices: 27988565--27988683 Score: 70
Period size: 12 Copynumber: 9.9 Consensus size: 12
27988555 TCATTCTCAA
27988565 TTTCTTTTTCAAT
1 TTTCTTTTTC-AT
27988578 TTTCTTTTCTTCAT
1 TTTC-TTT-TTCAT
27988592 TTTCTTTTTC-T
1 TTTCTTTTTCAT
**
27988603 CTCACTTTTTCGAT
1 -TTTCTTTTTC-AT
27988617 TTTC-TTTTC-T
1 TTTCTTTTTCAT
** *
27988627 TTTGCAATTTCTT
1 TTT-CTTTTTCAT
27988640 TTTCTTTTTCAT
1 TTTCTTTTTCAT
* *
27988652 TTCCTTTTT-GT
1 TTTCTTTTTCAT
*
27988663 TTTC--TTTCAA
1 TTTCTTTTTCAT
27988673 TTTCTTTTTCA
1 TTTCTTTTTCA
27988684 ATCTCTTTCT
Statistics
Matches: 82, Mismatches: 13, Indels: 23
0.69 0.11 0.19
Matches are distributed among these distances:
9 3 0.04
10 8 0.10
11 6 0.07
12 39 0.48
13 13 0.16
14 10 0.12
15 3 0.04
ACGTcount: A:0.09, C:0.19, G:0.03, T:0.69
Consensus pattern (12 bp):
TTTCTTTTTCAT
Found at i:27992793 original size:20 final size:19
Alignment explanation
Indices: 27992770--27992834 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
27992760 AAGCTCAAAC
27992770 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
27992790 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
27992810 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
27992830 GAGCT
1 GAGCT
27992835 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:27994121 original size:17 final size:18
Alignment explanation
Indices: 27994099--27994132 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
27994089 ACAACACTCC
*
27994099 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
27994116 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
27994133 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:27994240 original size:15 final size:16
Alignment explanation
Indices: 27994215--27994246 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
27994205 TATCTCACAC
27994215 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
27994231 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
27994246 T
1 T
27994247 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:27995221 original size:12 final size:12
Alignment explanation
Indices: 27995206--27995274 Score: 68
Period size: 12 Copynumber: 5.5 Consensus size: 12
27995196 TTTTGCTCGA
*
27995206 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
27995218 TTTTTTTTGAAT
1 TTTTTTTTCAAT
27995230 TTTTTTTCAATCAAT
1 TTTTTTT---TCAAT
27995245 TTTTTTTTCGAAT
1 TTTTTTTTC-AAT
*
27995258 TTTTTTTT-GAT
1 TTTTTTTTCAAT
27995269 TTTTTT
1 TTTTTT
27995275 GTTACTCCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
11 8 0.16
12 19 0.39
13 11 0.22
15 11 0.22
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:27996896 original size:20 final size:19
Alignment explanation
Indices: 27996873--27996937 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
27996863 AAGCTCAAAC
27996873 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
27996893 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
27996913 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
27996933 GAGCT
1 GAGCT
27996938 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:28000586 original size:46 final size:46
Alignment explanation
Indices: 28000516--28000609 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
28000506 CAAAGAAAAG
*
28000516 ACCTCGACCCACTATCAATAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATAATGATAAGAACCTTGGTATATGATGA
*
28000562 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATAATGATAAGAACCTTGGTATATGATGA
28000608 AC
1 AC
28000610 GCCACACTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATAATGATAAGAACCTTGGTATATGATGA
Found at i:28001277 original size:21 final size:23
Alignment explanation
Indices: 28001232--28001278 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28001222 TCACTTGCAA
* *
28001232 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
28001255 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
28001276 TAA
1 TAA
28001279 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:28003435 original size:11 final size:10
Alignment explanation
Indices: 28003410--28003470 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
28003400 ACCAATAAAA
28003410 TAAA-TGAGC
1 TAAATTGAGC
*
28003419 TGAATTGTAGC
1 TAAATTG-AGC
28003430 TAAATTGAGC
1 TAAATTGAGC
**
28003440 TCGATTGAGC
1 TAAATTGAGC
28003450 TGAAA-TGAGC
1 T-AAATTGAGC
*
28003460 TCAATTGAGC
1 TAAATTGAGC
28003470 T
1 T
28003471 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:28003471 original size:20 final size:20
Alignment explanation
Indices: 28003411--28003471 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
28003401 CCAATAAAAT
*
28003411 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
28003431 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
28003452 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
28003472 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:28005653 original size:10 final size:10
Alignment explanation
Indices: 28005640--28005677 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
28005630 TTGTAGCTAA
28005640 ATTGAGCTCG
1 ATTGAGCTCG
28005650 ATTGAGCT-G
1 ATTGAGCTCG
28005659 ACTTGAGCTCG
1 A-TTGAGCTCG
*
28005670 AGTGAGCT
1 ATTGAGCT
28005678 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:28005657 original size:20 final size:20
Alignment explanation
Indices: 28005617--28005677 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
28005607 ACCAATAAAA
28005617 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
28005637 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
28005657 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
28005677 T
1 T
28005678 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:28005678 original size:20 final size:20
Alignment explanation
Indices: 28005641--28005678 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28005631 TGTAGCTAAA
*
28005641 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
28005661 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
28005679 GAAACGAGCT
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:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:28007380 original size:21 final size:22
Alignment explanation
Indices: 28007337--28007385 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
28007327 CTCTTTTTGA
28007337 TTTCTTTTCTTTTTCAATCTCTT
1 TTTCTTTTC-TTTTCAATCTCTT
* *
28007360 TTTCTTTTC-TTTCGATTTCTT
1 TTTCTTTTCTTTTCAATCTCTT
28007381 TTTCT
1 TTTCT
28007386 CGCTCGTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 15 0.62
23 9 0.38
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTCTTTTCTTTTCAATCTCTT
Found at i:28026111 original size:39 final size:38
Alignment explanation
Indices: 28026068--28026313 Score: 332
Period size: 39 Copynumber: 6.3 Consensus size: 38
28026058 GGACTAAGAT
* *
28026068 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGC
1 CCGAAGGCATTTGTGCGAGTTACTAA-TCCGGGTTAAGC
*
28026107 CCGAAGGCATTTGTGCGAGTTACTAATCCGGGTTAAGT
1 CCGAAGGCATTTGTGCGAGTTACTAATCCGGGTTAAGC
* *
28026145 CCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAGT
1 CCGAAGGCATTTGTGCGAGTTACT-AATCCGGGTTAAGC
28026184 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACT-AATCCGGGTTAAG-C
* *
28026224 CCGAAGGCATTTGTGTGAGTTACTAAT-CGGGTTAAGT
1 CCGAAGGCATTTGTGCGAGTTACTAATCCGGGTTAAGC
* * * *
28026261 CCGAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGTTACTA-ATCCGGGTTAAG-C
28026301 CCGAAGGCATTTG
1 CCGAAGGCATTTG
28026314 AACGAGAAGC
Statistics
Matches: 188, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
37 23 0.12
38 43 0.23
39 86 0.46
40 36 0.19
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (38 bp):
CCGAAGGCATTTGTGCGAGTTACTAATCCGGGTTAAGC
Found at i:28026176 original size:77 final size:78
Alignment explanation
Indices: 28026068--28026319 Score: 357
Period size: 77 Copynumber: 3.2 Consensus size: 78
28026058 GGACTAAGAT
* * * * *
28026068 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAA
28026133 TCCGGGTTAAGT-
66 TCCGGGTTAAGTC
28026145 CCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACT-A
28026210 ATCCGGGTTAAGTC
65 ATCCGGGTTAAGTC
** *
28026224 CCGAAGGCATTTGTGTGAGTTACT-AAT-CGGGTTAAGTCCGAAGGCATTTGTGCGAATTACTAT
1 CCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTA-
* * *
28026287 AACCGGGCTATGTC
65 ATCCGGGTTAAGTC
*
28026301 CCGAAGGCATTTGAACGAG
1 CCGAAGGCATTTGTACGAG
28026320 AAGCTATATC
Statistics
Matches: 158, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
76 1 0.01
77 118 0.75
78 17 0.11
79 22 0.14
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (78 bp):
CCGAAGGCATTTGTACGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAA
TCCGGGTTAAGTC
Found at i:28026255 original size:116 final size:116
Alignment explanation
Indices: 28026056--28026313 Score: 385
Period size: 116 Copynumber: 2.2 Consensus size: 116
28026046 GTGACAATAT
* *
28026056 CCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGT
1 CCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGT
*
28026121 GCGAGTTACTAATCCGGGTTAAGTCCGAAGGCATTTGTACGAGTTACTA-AA
65 GCGAGTTACTAATCCGGGTTAAGTCCGAAGGCATTTGTACGAATTACTATAA
* * *
28026172 TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 -CCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAG-CCCGAAGGCATTTG
* *
28026237 TGTGAGTTACTAAT-CGGGTTAAGTCCGAAGGCATTTGTGCGAATTACTATAA
64 TGCGAGTTACTAATCCGGGTTAAGTCCGAAGGCATTTGTACGAATTACTATAA
*
28026289 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGT-CCGAAGGCATTTG
28026314 AACGAGAAGC
Statistics
Matches: 128, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
116 78 0.61
117 50 0.39
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.27
Consensus pattern (116 bp):
CCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGGCTAAGCCCGAAGGCATTTGTG
CGAGTTACTAATCCGGGTTAAGTCCGAAGGCATTTGTACGAATTACTATAA
Found at i:28034154 original size:39 final size:39
Alignment explanation
Indices: 28034059--28034201 Score: 168
Period size: 39 Copynumber: 3.6 Consensus size: 39
28034049 TTCAATGCTG
*
28034059 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGA-T-ACTAAT
* *
28034097 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
*
28034138 TCTGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
*
28034177 TCCGGGCTAAGCCCAAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTTG
28034202 CACAAACTAG
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
39 68 0.75
40 11 0.12
41 11 0.12
42 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28035833 original size:29 final size:28
Alignment explanation
Indices: 28035797--28035874 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
28035787 TCATGAGATT
28035797 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
28035827 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
28035854 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
28035875 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:28036091 original size:173 final size:174
Alignment explanation
Indices: 28035827--28036153 Score: 584
Period size: 173 Copynumber: 1.9 Consensus size: 174
28035817 AAATTGTACA
*
28035827 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
28035892 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGAC-TTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
**
28035956 TTTTGGACATTGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
28036000 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
28036065 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
28036130 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
28036154 ACCTTGAGTT
Statistics
Matches: 146, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
173 113 0.77
174 33 0.23
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:28039428 original size:154 final size:156
Alignment explanation
Indices: 28039228--28039536 Score: 550
Period size: 154 Copynumber: 2.0 Consensus size: 156
28039218 TTTGTCATGA
*
28039228 TTAGTCTCTAGTTATATAATAAGCATGCTATACTAAAATAAATCATAGTGAAATTTACCTGAAAA
1 TTAGTCTCTAGTTATATAATAAGCATGCTATACTAAAATAAATCATAGTGAAATATACCTGAAAA
*
28039293 TCTTCAATATTTACAAAACAATTAGAATTTTCATGTACAATGCTTGAAAATTATTTGATACACAT
66 TCTTCAACATTTACAAAACAATTAGAATTTTCATGTACAATGCTTGAAAATTATTTGATACACAT
*
28039358 TGGACCAAATTTCAATGTCAATTATG
131 TGGACCAAATTTCAATGCCAATTATG
*
28039384 TTAGTCTCTAG-T-TATAATAAGCATGCTATACTAAAATATATCATAGTGAAATATACCTGAAAA
1 TTAGTCTCTAGTTATATAATAAGCATGCTATACTAAAATAAATCATAGTGAAATATACCTGAAAA
* *
28039447 TCTTTAACATTTACAAAACAATTAGAATTTTCATGTACAATGCTTGAAAGTTATTTGATACACAT
66 TCTTCAACATTTACAAAACAATTAGAATTTTCATGTACAATGCTTGAAAATTATTTGATACACAT
28039512 TGGACCAAATTTCAATGCCAATTAT
131 TGGACCAAATTTCAATGCCAATTAT
28039537 ATGTTATAGA
Statistics
Matches: 147, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
154 135 0.92
155 1 0.01
156 11 0.07
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (156 bp):
TTAGTCTCTAGTTATATAATAAGCATGCTATACTAAAATAAATCATAGTGAAATATACCTGAAAA
TCTTCAACATTTACAAAACAATTAGAATTTTCATGTACAATGCTTGAAAATTATTTGATACACAT
TGGACCAAATTTCAATGCCAATTATG
Found at i:28044226 original size:72 final size:72
Alignment explanation
Indices: 28044109--28044257 Score: 298
Period size: 72 Copynumber: 2.1 Consensus size: 72
28044099 CTGATTGCAC
28044109 TTGCAAAAAGGGAAGGAAATCTTATTGGGACAACGATGGGAAGAGGTAAAGTCCCAGTGTCTCAT
1 TTGCAAAAAGGGAAGGAAATCTTATTGGGACAACGATGGGAAGAGGTAAAGTCCCAGTGTCTCAT
28044174 TTGTTTT
66 TTGTTTT
28044181 TTGCAAAAAGGGAAGGAAATCTTATTGGGACAACGATGGGAAGAGGTAAAGTCCCAGTGTCTCAT
1 TTGCAAAAAGGGAAGGAAATCTTATTGGGACAACGATGGGAAGAGGTAAAGTCCCAGTGTCTCAT
28044246 TTGTTTT
66 TTGTTTT
28044253 TTGCA
1 TTGCA
28044258 GATGATAGTA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 77 1.00
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.28
Consensus pattern (72 bp):
TTGCAAAAAGGGAAGGAAATCTTATTGGGACAACGATGGGAAGAGGTAAAGTCCCAGTGTCTCAT
TTGTTTT
Found at i:28046749 original size:20 final size:20
Alignment explanation
Indices: 28046726--28046781 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
28046716 TATTAAAAAC
*
28046726 ATTTTCTAATATTTAATAAG
1 ATTTTCTAATATTTAATAAA
* * **
28046746 ATTTTATAATTTTTTCTAAA
1 ATTTTCTAATATTTAATAAA
*
28046766 ATTTTCCAATATTTAA
1 ATTTTCTAATATTTAA
28046782 ATAATTTAAA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTTTCTAATATTTAATAAA
Found at i:28049658 original size:29 final size:29
Alignment explanation
Indices: 28049616--28049678 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
28049606 TTGGATTGGA
28049616 AGACTGTTTCGAAGGGATTATATGCTTTG
1 AGACTGTTTCGAAGGGATTATATGCTTTG
28049645 AGACTGTTTCGAAGGGATTATATGCTTTG
1 AGACTGTTTCGAAGGGATTATATGCTTTG
28049674 AGACT
1 AGACT
28049679 CTCAATCCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (29 bp):
AGACTGTTTCGAAGGGATTATATGCTTTG
Found at i:28054187 original size:21 final size:20
Alignment explanation
Indices: 28054161--28054209 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
28054151 CTATAAACAT
*
28054161 TGTTTTCAAGATATGTGATTA
1 TGTTTTCAAGACATGT-ATTA
* *
28054182 TGTTTTGAAAGACATGTTTTA
1 TGTTTT-CAAGACATGTATTA
28054203 TGTTTTC
1 TGTTTTC
28054210 TTCTATGCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.51
Consensus pattern (20 bp):
TGTTTTCAAGACATGTATTA
Found at i:28054198 original size:22 final size:21
Alignment explanation
Indices: 28054168--28054208 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28054158 CATTGTTTTC
*
28054168 AAGATATGTGATTATGTTTTGA
1 AAGACATGT-ATTATGTTTTGA
*
28054190 AAGACATGTTTTATGTTTT
1 AAGACATGTATTATGTTTT
28054209 CTTCTATGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (21 bp):
AAGACATGTATTATGTTTTGA
Found at i:28057684 original size:40 final size:39
Alignment explanation
Indices: 28057653--28057862 Score: 215
Period size: 40 Copynumber: 5.3 Consensus size: 39
28057643 GGACTAAGAT
* *
28057653 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* * * *
28057693 CCGAAGGCCTTTGTGTGAGATACTAAATCTGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
28057733 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
28057773 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
28057813 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
28057852 CCGAAGGCATT
1 CCGAAGGCATT
28057863 TGAACGAGGA
Statistics
Matches: 149, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
39 33 0.22
40 113 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:28057882 original size:79 final size:80
Alignment explanation
Indices: 28057715--28057897 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
28057705 GTGTGAGATA
* * * *
28057715 CTAAATCTGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
28057780 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
28057795 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
28057859 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
28057874 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
28057898 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 26 0.30
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:28065254 original size:40 final size:39
Alignment explanation
Indices: 28065223--28065432 Score: 233
Period size: 40 Copynumber: 5.3 Consensus size: 39
28065213 GGACTAAGAT
* *
28065223 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
28065263 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
28065303 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
28065343 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
28065383 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
28065422 CCGAAGGCATT
1 CCGAAGGCATT
28065433 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
39 33 0.22
40 117 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:28065386 original size:120 final size:120
Alignment explanation
Indices: 28065170--28065432 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
28065160 TTGAATGCTG
* *
28065170 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
28065234 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
28065290 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * * * *
28065353 TCGTGCGAGTTGTTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
28065409 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28065433 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 38 0.32
120 73 0.61
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:28065452 original size:79 final size:80
Alignment explanation
Indices: 28065223--28065467 Score: 228
Period size: 80 Copynumber: 3.1 Consensus size: 80
28065213 GGACTAAGAT
* * * * * * * ** *
28065223 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGA-GATAC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
28065286 TAAATCCGGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
28065303 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
28065368 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
28065383 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
28065447 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
28065461 CCGAAGG
1 CCGAAGG
28065468 TACGTGATTT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 46 0.33
80 75 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:28083048 original size:21 final size:22
Alignment explanation
Indices: 28083010--28083054 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
28083000 ATTATGAATA
*
28083010 TTAATTCATAATATAATTAATT
1 TTAATTCATAATACAATTAATT
* *
28083032 TTAATTC-TAATCCAATTTATT
1 TTAATTCATAATACAATTAATT
28083053 TT
1 TT
28083055 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATTCATAATACAATTAATT
Found at i:28083703 original size:23 final size:23
Alignment explanation
Indices: 28083677--28083723 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
28083667 CTTTGGTAAT
28083677 ATGTTTGATTAAGTAAAACCATG
1 ATGTTTGATTAAGTAAAACCATG
28083700 ATGTTTGATTAAGTAAAACCATG
1 ATGTTTGATTAAGTAAAACCATG
28083723 A
1 A
28083724 CTAAGTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (23 bp):
ATGTTTGATTAAGTAAAACCATG
Found at i:28085284 original size:50 final size:51
Alignment explanation
Indices: 28085107--28085288 Score: 181
Period size: 51 Copynumber: 3.6 Consensus size: 51
28085097 AGCCTATAAA
* * * * * * *
28085107 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-GATA-GATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTATGTGAACCGGA-AGGCT-TTGAT
* * * *
28085158 CACATGTGTAGTACTATGTGCAGTCTACTATGTGTACCGGAAGGCTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTATGTGAACCGGAAGGCTTTGAT
* *
28085209 CACGTGTGTAGTACTATGTGCAGGCTACTATGTGAACTGGAATG-TTTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTATGTGAACCGGAAGGCTTTGAT
* * *
28085259 CACGTGTGTAGTGCTACGTGAAGGCTACTA
1 CACGTGTGTAGTACTATGTGCAGGCTACTA
28085289 CGTGTATCGA
Statistics
Matches: 113, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
50 32 0.28
51 77 0.68
52 4 0.04
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.31
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTATGTGAACCGGAAGGCTTTGAT
Found at i:28087584 original size:49 final size:50
Alignment explanation
Indices: 28087522--28087655 Score: 207
Period size: 50 Copynumber: 2.7 Consensus size: 50
28087512 TCATTCGATA
*
28087522 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AGTTTTAAAGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTAAAGCT
* * **
28087571 CACGTAGTAGCCTTCACATTGTACTACACATGTGATCAAGTTTTACGGCT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTAAAGCT
*
28087621 CACGTAGTAGCCTTCACATAGTACTACATACGTGA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGA
28087656 CCAAAGCTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
49 35 0.46
50 41 0.54
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTAAAGCT
Found at i:28087694 original size:51 final size:51
Alignment explanation
Indices: 28087520--28087858 Score: 239
Period size: 51 Copynumber: 6.7 Consensus size: 51
28087510 TATCATTCGA
* * * ***
28087520 TACACGTAGTAGCCTTCACATAGTACTACACACGTGATC--AGTTTTAAAG
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTCCGG
* * * * * * *
28087569 TTCACGTAGTAGCCTTCACATTGTACTACACATGTGATC-AAGTTTTACGG
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTCCGG
* *
28087619 CT-CACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTCCGG
1 -TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTCCGG
* * * * * *
28087670 TATC-CATAGTAGCCTTCACTTAGTACCACACATGTAACCATAG-TTTACCGA
1 TA-CACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTT-CCGG
* * * * * *
28087721 TACACGTAGTAGCTTTCGCACAATACTACACACGTG-CTCAAAAC-TTCTCGG
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGAC-CAAAGCTTTC-CGG
* * * * *
28087772 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTA--TTTATCGA
1 TACACATAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGCTTT-CCGG
* *
28087823 TACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 TACACATAGTAGCCTTCACATAGTACTACACACGTG
28087859 TTCATCGATA
Statistics
Matches: 231, Mismatches: 45, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
49 36 0.16
50 48 0.21
51 144 0.62
52 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (51 bp):
TACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTCCGG
Found at i:28087756 original size:102 final size:102
Alignment explanation
Indices: 28087517--28087858 Score: 371
Period size: 102 Copynumber: 3.4 Consensus size: 102
28087507 TTTTATCATT
* * * * ** * *
28087517 CGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC---AGTTTTAAAGTTCACGTAGT
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAAACTTCT-CGGTACACATAGT
*
28087579 AGCCTTCACATT-GTACTACACATGTGATCA-AGTTTTAC
65 AGCCTTCAC-TTAGTACTACACATGTGACCATAG-TTTAC
* * * * *
28087617 GGCT-CACGTAGTAGCCTTCACATAGTACTACATACGTGAC-CAAAGCTT-TCCGGTATC-CATA
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG-CTCAAAACTTCT-CGGTA-CACATA
* *
28087678 GTAGCCTTCACTTAGTACCACACATGTAACCATAGTTTAC
63 GTAGCCTTCACTTAGTACTACACATGTGACCATAGTTTAC
* * *
28087718 CGATACACGTAGTAGCTTTCGCACAATACTACACACGTGCTCAAAACTTCTCGGTACACATAGTA
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAAACTTCTCGGTACACATAGTA
*
28087783 GCCTTCACTTAGTACTACACATGTGACCATTA-TTTAT
66 GCCTTCACTTAGTACTACACATGTGACCA-TAGTTTAC
28087820 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
28087859 TTCATCGATA
Statistics
Matches: 202, Mismatches: 28, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
99 34 0.17
100 4 0.02
101 41 0.20
102 120 0.59
103 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (102 bp):
CGATACACGTAGTAGCCTTCACACAGTACTACACACGTGCTCAAAACTTCTCGGTACACATAGTA
GCCTTCACTTAGTACTACACATGTGACCATAGTTTAC
Found at i:28108689 original size:50 final size:50
Alignment explanation
Indices: 28108583--28108779 Score: 195
Period size: 50 Copynumber: 3.8 Consensus size: 50
28108573 ATTTGGGTAA
*
28108583 AAAGATCCCATGTAAGACCATGTCTACGACATGGCATTGGCATCATTGAGATTATG
1 AAAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA-C----AGA-TATG
* * *
28108639 AAAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACAGATATG
1 AAAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACAGATATG
* * * *
28108689 AAA-ACTCCCATGTAAGACCATATCTAGGATATGGCATTGG--CAGTACAAG
1 AAAGA-TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACAG-ATATG
* *
28108738 AAACATCCCATGTAAGACCATGTCTGGGACATGG-ATTTGGCA
1 AAAGATCCCATGTAAGACCATGTCTAGGACATGGCA-TTGGCA
28108780 TGTTATTATC
Statistics
Matches: 121, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
48 4 0.03
49 36 0.30
50 39 0.32
51 3 0.02
55 1 0.01
56 38 0.31
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.23
Consensus pattern (50 bp):
AAAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACAGATATG
Found at i:28108778 original size:49 final size:48
Alignment explanation
Indices: 28108644--28108779 Score: 159
Period size: 49 Copynumber: 2.8 Consensus size: 48
28108634 TTATGAAAGG
* * *
28108644 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACAGATATGAAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG--CAGACAAGAAAAC
* * *
28108694 TCCCATGTAAGACCATATCTAGGATATGGCATTGGCAGTACAAG-AAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAG-ACAAGAAAAC
28108742 ATCCCATGTAAGACCATGTCTGGGACATGG-ATTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGACATGGCA-TTGGCA
28108780 TGTTATTATC
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
48 8 0.11
49 35 0.47
50 31 0.42
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (48 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAGACAAGAAAAC
Found at i:28116266 original size:12 final size:12
Alignment explanation
Indices: 28116249--28116281 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
28116239 ACACATGGCT
28116249 GTGTCTCAGCCC
1 GTGTCTCAGCCC
*
28116261 GTGTCTCAGCCT
1 GTGTCTCAGCCC
28116273 GTGTCTCAG
1 GTGTCTCAG
28116282 TGTAAATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.33, G:0.27, T:0.30
Consensus pattern (12 bp):
GTGTCTCAGCCC
Found at i:28121035 original size:21 final size:21
Alignment explanation
Indices: 28120990--28121052 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
28120980 TTTGAACCAT
* *
28120990 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
28121012 TACCGTTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
28121033 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
28121053 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 23 0.66
22 12 0.34
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:28124806 original size:12 final size:12
Alignment explanation
Indices: 28124791--28124861 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 12
28124781 TCACTCTCAT
28124791 TTTCTTTTTCAA
1 TTTCTTTTTCAA
28124803 TTTCTTGTTTTC--
1 TTTC-T-TTTTCAA
* * *
28124815 TTTCATATTCAT
1 TTTCTTTTTCAA
28124827 TTTCTTTTTCAA
1 TTTCTTTTTCAA
***
28124839 TTTCTTTTTGTT
1 TTTCTTTTTCAA
28124851 TTTCTTTTTCA
1 TTTCTTTTTCA
28124862 CATGCTGTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
10 4 0.09
12 35 0.78
13 1 0.02
14 5 0.11
ACGTcount: A:0.11, C:0.15, G:0.03, T:0.70
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:28127124 original size:20 final size:20
Alignment explanation
Indices: 28127090--28127134 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
28127080 TAAATCTACA
28127090 TAATTAAAATAAGACAC-AAT
1 TAATTAAAATAAGAC-CTAAT
* *
28127110 TAATTAAATTCAGACCTAAT
1 TAATTAAAATAAGACCTAAT
28127130 TAATT
1 TAATT
28127135 CGGTTAGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.33
Consensus pattern (20 bp):
TAATTAAAATAAGACCTAAT
Found at i:28145055 original size:13 final size:13
Alignment explanation
Indices: 28144999--28145059 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
28144989 TTGGAGTAAC
28144999 AAAAAAAA-TC-A
1 AAAAAAAATTCAA
28145010 AAAAAAAATTCGAA
1 AAAAAAAATTC-AA
*
28145024 AAAAAAATTTGATTGAA
1 AAAAAAA----ATTCAA
28145041 AAAAAAAATTCAA
1 AAAAAAAATTCAA
28145054 AAAAAA
1 AAAAAA
28145060 GGTGAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
11 8 0.20
12 2 0.05
13 11 0.27
14 8 0.20
17 9 0.22
18 3 0.07
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:28146150 original size:12 final size:12
Alignment explanation
Indices: 28146138--28146255 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
28146128 GAAAGAGATT
*
28146138 GAAAAAGAAATT
1 GAAAAAGAAATA
28146150 G--AAAGAAA-A
1 GAAAAAGAAATA
*
28146159 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
28146170 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
28146183 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
28146195 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
28146207 GAAAAAGTGAGA
1 GAAAAAGAAATA
28146219 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
28146230 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
28146246 GAAAAAGAAA
1 GAAAAAGAAA
28146256 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:28146181 original size:18 final size:18
Alignment explanation
Indices: 28146155--28146258 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
28146145 AAATTGAAAG
*
28146155 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
28146173 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
28146191 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
28146209 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
28146227 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
28146248 AAAAGAAAAAG
1 AAAAGAAAAAG
28146259 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:28146183 original size:6 final size:6
Alignment explanation
Indices: 28146151--28146258 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
28146141 AAAGAAATTG
* * ** *
28146151 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
28146198 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
28146249 AAAGAA AAAG
1 AAAGAA AAAG
28146259 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:28146240 original size:14 final size:13
Alignment explanation
Indices: 28146219--28146256 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
28146209 AAAAGTGAGA
28146219 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
28146231 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
28146246 GAAAAAGAAAA
1 GAAAAAGAAAA
28146257 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:28146270 original size:21 final size:21
Alignment explanation
Indices: 28146220--28146270 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
28146210 AAAGTGAGAG
*
28146220 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
28146241 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
28146262 AAAAAGAAA
1 AAAAAGAAA
28146271 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:28146310 original size:33 final size:33
Alignment explanation
Indices: 28146273--28146335 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
28146263 AAAAGAAATT
28146273 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
28146306 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
28146336 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:28153407 original size:42 final size:42
Alignment explanation
Indices: 28153353--28153554 Score: 255
Period size: 42 Copynumber: 4.8 Consensus size: 42
28153343 TCATATACAG
28153353 TGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTTTAAA
1 TGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTTTAAA
* *
28153395 TTCAATGAAAAGTAAATGGACCTCCACACCT-GAGCCTCTAAA
1 TGCAATGAAAAGTAAATGGACCTCCACACCTAG-GCCTTTAAA
* * * **
28153437 TGCAAGGATAAGTAAATAGATGTCCACACCTAGGCCTTTAAA
1 TGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTTTAAA
* * *
28153479 TGCAATGAAAAATAAATGGGCCTCCACATCTAGG-CTATTAAA
1 TGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCT-TTAAA
* * *
28153521 TACAATGAAAAGTGAATGGACCTCCACATCTAGG
1 TGCAATGAAAAGTAAATGGACCTCCACACCTAGG
28153555 TCGTATTAAA
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
41 3 0.02
42 132 0.97
43 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (42 bp):
TGCAATGAAAAGTAAATGGACCTCCACACCTAGGCCTTTAAA
Found at i:28154159 original size:41 final size:41
Alignment explanation
Indices: 28154098--28154263 Score: 181
Period size: 41 Copynumber: 4.0 Consensus size: 41
28154088 AGAATAATGA
* *
28154098 TGAATTGCACATACGCGCCCCTATTTGTA-TTTCGGTACCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTT-GATACCCC
* *
28154139 TAAATTGCACATACGTGCCCCTATTTGTACTTTGATACACC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGATACCCC
* * * * **
28154180 TGAATTACTCATACATGCCCCTGTTTGTACTTTGATACCTT
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGATACCCC
* ** * *
28154221 TGAATTGCACAGACGTGCCTGTGTTTGTACTTCGATACCCC
1 TGAATTGCACATACGTGCCCCTATTTGTACTTTGATACCCC
28154262 TG
1 TG
28154264 GATGTATTTT
Statistics
Matches: 103, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
41 100 0.97
42 3 0.03
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.35
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTATTTGTACTTTGATACCCC
Found at i:28157066 original size:18 final size:20
Alignment explanation
Indices: 28157021--28157068 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
28157011 TGATTGTAAA
28157021 ATTATAAAAAATAAAGAATAT
1 ATTA-AAAAAATAAAGAATAT
**
28157042 ACAAAAAAAATAAA-AA-AT
1 ATTAAAAAAATAAAGAATAT
28157060 ATTAAAAAA
1 ATTAAAAAA
28157069 TATTATATGG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 9 0.39
19 2 0.09
20 10 0.43
21 2 0.09
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (20 bp):
ATTAAAAAAATAAAGAATAT
Found at i:28164651 original size:22 final size:20
Alignment explanation
Indices: 28164623--28164674 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
28164613 TTCCATGTGG
28164623 TATCGATACCACTTAAGGAAAA
1 TATCGATACC-CTTAA-GAAAA
* * *
28164645 TATCGATTCCCTTGAGACAA
1 TATCGATACCCTTAAGAAAA
28164665 TATCGATACC
1 TATCGATACC
28164675 TACATAACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 13 0.50
21 4 0.15
22 9 0.35
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (20 bp):
TATCGATACCCTTAAGAAAA
Found at i:28179735 original size:13 final size:13
Alignment explanation
Indices: 28179717--28179741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28179707 CTGTGATAAA
28179717 ACATGAAAATATC
1 ACATGAAAATATC
28179730 ACATGAAAATAT
1 ACATGAAAATAT
28179742 GTAGGTGTAA
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:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (13 bp):
ACATGAAAATATC
Found at i:28179824 original size:37 final size:37
Alignment explanation
Indices: 28179782--28179854 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
28179772 TTGCTATAGA
28179782 AATTTGGAAAACCATTTT-TAAAAGATCATTTTTGAGG
1 AATTTGGAAAACC-TTTTCTAAAAGATCATTTTTGAGG
*
28179819 AATTTGGAAAATCTTTTCTAAAAGATCATTTTTGAG
1 AATTTGGAAAACCTTTTCTAAAAGATCATTTTTGAG
28179855 TTTTGCGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (37 bp):
AATTTGGAAAACCTTTTCTAAAAGATCATTTTTGAGG
Found at i:28184793 original size:79 final size:80
Alignment explanation
Indices: 28184655--28184872 Score: 250
Period size: 79 Copynumber: 2.7 Consensus size: 80
28184645 ATGTCCGGGC
* * * * *
28184655 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGCATTTGTGCGAA-TTACTATAACCGGGCTAAG-TCCCGAAGGCATTTGTGCG
*
28184718 AGATACTAAATCTGGAT
64 AGATACTAAATCCGGAT
**
28184735 TAAGAT-CCGAAGGCATTTGTGCGAGA-TACTA-ATTTCGGGCTAAG-CCCGAAGGCATTTGTGC
1 TAAG-TCCCGAAGGCATTTGTGCGA-ATTACTATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGC
* *
28184796 GAGTTACTAAATCCGGGT
63 GAGATACTAAATCCGGAT
*
28184814 TAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCCCGAAGGCATTTG
1 TAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTTG
28184873 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 11, Indels: 18
0.80 0.07 0.12
Matches are distributed among these distances:
78 2 0.02
79 67 0.57
80 39 0.33
81 9 0.08
82 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (80 bp):
TAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
ATACTAAATCCGGAT
Found at i:28184836 original size:40 final size:40
Alignment explanation
Indices: 28184648--28184872 Score: 244
Period size: 40 Copynumber: 5.7 Consensus size: 40
28184638 TTGAATGATG
* * * *
28184648 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
28184688 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* ** * *
28184728 TCTGGATTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28184768 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
28184807 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
28184848 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28184873 AACGAGGAGC
Statistics
Matches: 160, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
39 34 0.21
40 116 0.73
41 10 0.06
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28184864 original size:119 final size:120
Alignment explanation
Indices: 28184650--28184872 Score: 269
Period size: 119 Copynumber: 1.9 Consensus size: 120
28184640 GAATGATGTC
*
28184650 CGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGT
* *
28184715 GCGAGATACTAAATCTGGATTAAGATCCGAAGGCATTTGTGCGAGATACTAATTT
66 GCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTT
* * * **
28184770 CGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTT
1 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATTT
* *
28184832 GTGCGA-ATTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTG
64 GTGCGAGA-TACTA-AATCCGGACTAAGAT-CCGAAGGCATTTG
28184873 AACGAGGAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
118 3 0.03
119 67 0.76
120 18 0.20
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
CGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGT
GCGAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTT
Found at i:28184894 original size:79 final size:78
Alignment explanation
Indices: 28184655--28184905 Score: 235
Period size: 79 Copynumber: 3.2 Consensus size: 78
28184645 ATGTCCGGGC
* * * *
28184655 TAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATTTGTGCG
1 TAAGTCCCGAAGGCATTTGTGCGAA-TTACTATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCG
* *
28184718 AGATACTAAATCTGGAT
64 AG-GACTAAATCCGG-T
*
28184735 TAAGAT-CCGAAGGCATTTGTGCGAGA-TACTA-ATTTCGGGCTAAG-CCCGAAGGCATTTGTGC
1 TAAG-TCCCGAAGGCATTTGTGCGA-ATTACTATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGC
*
28184796 GAGTTACTAAATCCGGGT
63 GAG-GACTAAATCC-GGT
* * **
28184814 TAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG
1 TAAGTCCCGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
*
28184879 GAGCTATATCCGGT
66 GA-CTAAATCCGGT
* *
28184893 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
28184906 TACGTGATTT
Statistics
Matches: 144, Mismatches: 16, Indels: 23
0.79 0.09 0.13
Matches are distributed among these distances:
78 2 0.01
79 80 0.56
80 52 0.36
81 9 0.06
82 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (78 bp):
TAAGTCCCGAAGGCATTTGTGCGAATTACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
GACTAAATCCGGT
Found at i:28191539 original size:79 final size:80
Alignment explanation
Indices: 28191363--28191587 Score: 271
Period size: 79 Copynumber: 2.8 Consensus size: 80
28191353 TTGAATGATG
* * * *
28191363 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTATATCCGGGCTAAGACCCGAAGGCATT
*
28191427 TGTGTGAGATACTAAA
65 TGTGCGAGATACTAAA
*
28191443 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTA-ATTCCGGGCTAAG-CCCGAAGGCA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTATA-TCCGGGCTAAGACCCGAAGGCA
*
28191504 TTTGTGCGAGTTACTAAA
63 TTTGTGCGAGATACTAAA
* * * * *
28191522 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTATATCCGGGCTAAGACCCGAAGGCATTT
28191587 G
66 G
28191588 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
78 1 0.01
79 66 0.53
80 49 0.39
81 9 0.07
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTATATCCGGGCTAAGACCCGAAGGCATTT
GTGCGAGATACTAAA
Done.