Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 183 of 222
Found at i:58530133 original size:42 final size:42
Alignment explanation
Indices: 58530081--58530202 Score: 190
Period size: 42 Copynumber: 2.9 Consensus size: 42
58530071 GTTTACAGAA
*
58530081 AAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTAAAT
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAAT
**
58530123 AAAAACGCCGCTAAAGCCCATGTTCTTTAGCGGCGCTTAAAT
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAAT
* * *
58530165 AAAAATGCCGCTAAAGATCACGTTCTTTCGCGGCGCTT
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
58530203 GTTTCACAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAAT
Found at i:58530630 original size:12 final size:12
Alignment explanation
Indices: 58530613--58530691 Score: 71
Period size: 12 Copynumber: 7.1 Consensus size: 12
58530603 TGAACCTCTA
58530613 CTTCTCTCGCTG
1 CTTCTCTCGCTG
*
58530625 CTTCTCTAGCTG
1 CTTCTCTCGCTG
**
58530637 CAGCT-T--CTG
1 CTTCTCTCGCTG
58530646 CTTCTCTCGCTG
1 CTTCTCTCGCTG
58530658 CTTCTCTCGCTG
1 CTTCTCTCGCTG
**
58530670 CAGC-CT--CTG
1 CTTCTCTCGCTG
58530679 CTTCTCTCGCTG
1 CTTCTCTCGCTG
58530691 C
1 C
58530692 AGCCTCTGCT
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
9 11 0.21
10 3 0.06
11 3 0.06
12 35 0.67
ACGTcount: A:0.04, C:0.41, G:0.18, T:0.38
Consensus pattern (12 bp):
CTTCTCTCGCTG
Found at i:58530650 original size:33 final size:33
Alignment explanation
Indices: 58530607--58530691 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
58530597 TTCTTTTGAA
*
58530607 CCTCTACTTCTCTCGCTGCTTCTCTAGCTGCAG
1 CCTCTGCTTCTCTCGCTGCTTCTCTAGCTGCAG
* *
58530640 CTTCTGCTTCTCTCGCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCTCTCGCTGCTTCTCTAGCTGCAG
58530673 CCTCTGCTTCTCTCGCTGC
1 CCTCTGCTTCTCTCGCTGC
58530692 AGCCTCTGCT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.05, C:0.41, G:0.16, T:0.38
Consensus pattern (33 bp):
CCTCTGCTTCTCTCGCTGCTTCTCTAGCTGCAG
Found at i:58530681 original size:21 final size:21
Alignment explanation
Indices: 58530655--58530723 Score: 120
Period size: 21 Copynumber: 3.3 Consensus size: 21
58530645 GCTTCTCTCG
58530655 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
58530676 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
58530697 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
58530718 CTGCTT
1 CTGCTT
58530724 TAAGTAGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.03, C:0.45, G:0.19, T:0.33
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:58532428 original size:20 final size:20
Alignment explanation
Indices: 58532403--58532483 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
58532393 ATACGAAATT
*
58532403 TTATCTTAATATTATATAAC
1 TTATCTTAATATTATATAAG
58532423 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
* * *
58532443 TTAT-GT-A-ATTAGA-AATT
1 TTATCTTAATATTATATAA-G
58532460 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
58532480 TTAT
1 TTAT
58532484 GAAGTGTCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
16 2 0.04
17 9 0.18
18 2 0.04
19 2 0.04
20 32 0.65
21 2 0.04
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (20 bp):
TTATCTTAATATTATATAAG
Found at i:58534106 original size:27 final size:27
Alignment explanation
Indices: 58534076--58534158 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
58534066 GGTTACCGTA
58534076 TTAATACCTAAAAATGTTCTTACTTTC
1 TTAATACCTAAAAATGTTCTTACTTTC
* ** * ** *
58534103 TTAA-CCCT-AATTTGAAT-TTACCGTA
1 TTAATACCTAAAAATG-TTCTTACTTTC
58534128 TTAATACCTAAAAATGTTCTTACTTTC
1 TTAATACCTAAAAATGTTCTTACTTTC
58534155 TTAA
1 TTAA
58534159 CCCTAATTTG
Statistics
Matches: 38, Mismatches: 14, Indels: 8
0.63 0.23 0.13
Matches are distributed among these distances:
25 13 0.34
26 8 0.21
27 17 0.45
ACGTcount: A:0.34, C:0.18, G:0.05, T:0.43
Consensus pattern (27 bp):
TTAATACCTAAAAATGTTCTTACTTTC
Found at i:58534130 original size:52 final size:52
Alignment explanation
Indices: 58534068--58534173 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
58534058 ATGGTTAAGG
58534068 TTACCGTATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAAT
1 TTACCGTATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAAT
58534120 TTACCGTATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAAT
1 TTACCGTATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAAT
58534172 TT
1 TT
58534174 TCTTATTTCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (52 bp):
TTACCGTATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAAT
Found at i:58534163 original size:26 final size:26
Alignment explanation
Indices: 58534082--58534164 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 26
58534072 CGTATTAATA
58534082 CCTAAAAATGTTCTTACTTTCTTAAC
1 CCTAAAAATGTTCTTACTTTCTTAAC
** * ** * *
58534108 CCT-AATTTGAAT-TTACCGTATTAATA
1 CCTAAAAATG-TTCTTACTTTCTTAA-C
58534134 CCTAAAAATGTTCTTACTTTCTTAAC
1 CCTAAAAATGTTCTTACTTTCTTAAC
58534160 CCTAA
1 CCTAA
58534165 TTTGAATTTT
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
25 13 0.33
26 13 0.33
27 13 0.33
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.41
Consensus pattern (26 bp):
CCTAAAAATGTTCTTACTTTCTTAAC
Found at i:58535484 original size:11 final size:11
Alignment explanation
Indices: 58535468--58535492 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
58535458 ATTTGAAAGT
58535468 TTTAAATTAAA
1 TTTAAATTAAA
58535479 TTTAAATTAAA
1 TTTAAATTAAA
58535490 TTT
1 TTT
58535493 GTTCTATTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:58536041 original size:21 final size:21
Alignment explanation
Indices: 58535989--58536041 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
58535979 ACATAATCAC
*
58535989 TAAACCCATAATTCATAAACCT
1 TAAA-CCATAACTCATAAACCT
** * *
58536011 TAAATTATAACTCTTAAATCT
1 TAAACCATAACTCATAAACCT
58536032 TAAACCATAA
1 TAAACCATAA
58536042 ACCCTAAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAACCATAACTCATAAACCT
Found at i:58536055 original size:35 final size:35
Alignment explanation
Indices: 58536002--58536077 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
58535992 ACCCATAATT
* * * * *
58536002 CATAAACCTTAAATTATAACTCTTAAATCTTAAAC
1 CATAAACCCTAAAATATAACCCTTAAACCCTAAAC
58536037 CATAAACCCTAAAATATAACCCTTAAACCCTAAAC
1 CATAAACCCTAAAATATAACCCTTAAACCCTAAAC
58536072 CATAAA
1 CATAAA
58536078 AACCAAACCC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (35 bp):
CATAAACCCTAAAATATAACCCTTAAACCCTAAAC
Found at i:58536109 original size:21 final size:21
Alignment explanation
Indices: 58536085--58536172 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 21
58536075 AAAAACCAAA
*
58536085 CCCTAAATC-TATCCCCATAAC
1 CCCTAAATCATAACCCC-TAAC
*
58536106 CCCTTAAAGCATAACCCCTAAC
1 CCC-TAAATCATAACCCCTAAC
*
58536128 CCTTAAATC----CCCCTAAC
1 CCCTAAATCATAACCCCTAAC
* * *
58536145 CCTTAAAGCATAACACCTAAC
1 CCCTAAATCATAACCCCTAAC
*
58536166 CCTTAAA
1 CCCTAAA
58536173 CCACAAAACC
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
17 16 0.29
21 22 0.40
22 11 0.20
23 6 0.11
ACGTcount: A:0.36, C:0.40, G:0.02, T:0.22
Consensus pattern (21 bp):
CCCTAAATCATAACCCCTAAC
Found at i:58536155 original size:38 final size:39
Alignment explanation
Indices: 58536095--58536172 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
58536085 CCCTAAATCT
*
58536095 ATCCCCATAACCCCTTAAAGCATAACCCCTAACCCTTAA
1 ATCCCCATAACCCCTTAAAGCATAACACCTAACCCTTAA
*
58536134 ATCCCCCTAA-CCCTTAAAGCATAACACCTAACCCTTAA
1 ATCCCCATAACCCCTTAAAGCATAACACCTAACCCTTAA
58536172 A
1 A
58536173 CCACAAAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 28 0.76
39 9 0.24
ACGTcount: A:0.37, C:0.40, G:0.03, T:0.21
Consensus pattern (39 bp):
ATCCCCATAACCCCTTAAAGCATAACACCTAACCCTTAA
Found at i:58536191 original size:22 final size:22
Alignment explanation
Indices: 58536138--58536193 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
58536128 CCTTAAATCC
* * *
58536138 CCCTAACCCTTAAAGCATAACA
1 CCCTAACCCTTAAACCACAAAA
58536160 -CCTAACCCTTAAACCACAAAA
1 CCCTAACCCTTAAACCACAAAA
*
58536181 CCCTAAACCTTAA
1 CCCTAACCCTTAA
58536194 TCCCCAAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.43, C:0.38, G:0.02, T:0.18
Consensus pattern (22 bp):
CCCTAACCCTTAAACCACAAAA
Found at i:58536658 original size:113 final size:113
Alignment explanation
Indices: 58536390--58536730 Score: 472
Period size: 114 Copynumber: 3.0 Consensus size: 113
58536380 TAAATCCCTG
*
58536390 AGCATTAGCGGCGCTTTATTGAAAACACCGCTAAA-CCCCCGAAAGCTCAGAAAACAGCATCGTT
1 AGCATTAGCGGCGCTTTATTGAAAACACCGCTAAACCCCCCGAAAGCTCAGAAAACGGCATCGTT
* * * *
58536454 GGGCTTAAATTTTTTTGCGGCGCTTTC-TCAACAACGCCGCTAAAGGCCTC
66 GGG-TTTAATTTTTTTGCGGCGCTTTCAT-AAAAACACCGCTAAA-GCCCC
*
58536504 AGCATTAGCGGCGCTTTATTGAAAACACCGCTAAACTCCCCGAAAGCTCAGAAAACGGCATCGTT
1 AGCATTAGCGGCGCTTTATTGAAAACACCGCTAAACCCCCCGAAAGCTCAGAAAACGGCATCGTT
58536569 GGGTTTAATTTTTTTGCGGCGCTTTCATAAAAACACCGCTAAAGCCCC
66 GGGTTTAATTTTTTTGCGGCGCTTTCATAAAAACACCGCTAAAGCCCC
* * * * * *
58536617 AGCATTAGCGGCACATTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAATGGCGTCATT
1 AGCATTAGCGGCGCTTTATTGAAAACACCGCTAAACCCCCCGAAAGCTCAGAAAACGGCATCGTT
* * * *
58536682 GGGCTTAGTTTTTTTTGCGCCGCTTT-ATTAAAAACACCGCTAAACCCCC
66 GGGTTTA-ATTTTTTTGCGGCGCTTTCA-TAAAAACACCGCTAAAGCCCC
58536731 GAAAGCTAAG
Statistics
Matches: 206, Mismatches: 17, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
113 69 0.33
114 106 0.51
115 31 0.15
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (113 bp):
AGCATTAGCGGCGCTTTATTGAAAACACCGCTAAACCCCCCGAAAGCTCAGAAAACGGCATCGTT
GGGTTTAATTTTTTTGCGGCGCTTTCATAAAAACACCGCTAAAGCCCC
Found at i:58536768 original size:74 final size:74
Alignment explanation
Indices: 58536631--58536843 Score: 288
Period size: 72 Copynumber: 2.9 Consensus size: 74
58536621 TTAGCGGCAC
* * *
58536631 ATTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAATGGCGTCATTGGGCTTAGTTTTTT
1 ATTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAATTTTTT
58536696 TTGCGCCGCT
66 TTGCGCCG-T
* * * *
58536706 -TTATTAAAAACACCGCTAAA-CCCCCGAAAGCTAAGAAAACGG-GTCGTTGGGTTTAATTTTTT
1 ATTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAATTTTTT
*
58536768 TTGCGGCGT
66 TTGCGCCGT
* * *
58536777 ATTGTTGAAAACGCCGCTAAACCCCCCCGAAAGCTCAGAAAACGGTGTCGTTGGGCTTAGTTTTT
1 ATTATTGAAAACGCCGCTAAA-CCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAATTTTT
58536842 TT
65 TT
58536844 GTGGCGCTTG
Statistics
Matches: 120, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
71 1 0.01
72 41 0.34
73 20 0.17
74 39 0.32
75 19 0.16
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (74 bp):
ATTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAATTTTTT
TTGCGCCGT
Found at i:58536794 original size:72 final size:74
Alignment explanation
Indices: 58536632--58536871 Score: 301
Period size: 74 Copynumber: 3.3 Consensus size: 74
58536622 TAGCGGCACA
* *
58536632 TTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAATGGCGTCATTGGGCTTAGTTTTTTT
1 TTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTTTTT
58536697 TGCGCCGCT
66 TGCGCCGCT
* * * * *
58536706 TTATTAAAAACACCGCTAAA-CCCCCGAAAGCTAAGAAAACGG-GTCGTTGGGTTTAATTTTTTT
1 TTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTTTTT
*
58536769 TGCGGCG-T
66 TGCGCCGCT
* *
58536777 ATTGTTGAAAACGCCGCTAAACCCCCCCGAAAGCTCAGAAAACGGTGTCGTTGGGCTTAGTTTTT
1 -TTATTGAAAACGCCGCTAAA-CCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTTT
58536842 TTGTG-G-CGCT
64 TT-TGCGCCGCT
* **
58536852 TGATCAAAAACGCCGCTAAA
1 TTATTGAAAACGCCGCTAAA
58536872 GCCCTTAGCA
Statistics
Matches: 142, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
71 1 0.01
72 41 0.29
73 20 0.14
74 57 0.40
75 21 0.15
76 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (74 bp):
TTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGTTTTTTT
TGCGCCGCT
Found at i:58536796 original size:186 final size:185
Alignment explanation
Indices: 58536511--58537265 Score: 668
Period size: 186 Copynumber: 4.1 Consensus size: 185
58536501 CTCAGCATTA
* * *
58536511 GCGGCGCTTTATTGAAAACACCGCTAAACTCCCCGAAAGCTCAGAAAACGGCATCGTTGGGTTTA
1 GCGGCGCTTTATTAAAAACACCGCTAAAC-CCCCGAAAGCTAAGAAAACGGCGTCGTTGGGTTTA
* *
58536576 ATTTTTTTGCGGCGCTTTCATAAAAACACCGCTAAAGCCCCAGCATTAGCGGCACATTATTGAAA
65 ATTTTTTTGCGGCGCTTTCATAAAAACGCCGCTAAATCCCCAGCATTAGCGGCACATTATTGAAA
*
58536641 ACGCCGCTAAACCCCCCGAAAGCTCAGAAAATGGCGTCATTGGGCTTAGTTTTTTTT
130 ACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCATTGGGCTTAG-TTTTTTT
*
58536698 GCGCCGCTTTATTAAAAACACCGCTAAACCCCCGAAAGCTAAGAAAACGG-GTCGTTGGGTTTAA
1 GCGGCGCTTTATTAAAAACACCGCTAAACCCCCGAAAGCTAAGAAAACGGCGTCGTTGGGTTTAA
** * * * *** *
58536762 TTTTTTTTGCGGCG-TATTGTTGAAAACGCCGCTAAACCCCCCCGAAAGC-TCAG-AAAACGGTG
66 -TTTTTTTGCGGCGCT-TTCATAAAAACGCCGCTAAA--TCCCC---AGCATTAGCGGCAC-AT-
* ** *** * ******** *** * * ** ** **
58536824 TCGTTG--GGCTTAGTTTTTTTGTGGCGCTTGATCA-AAAACGCCG-CTAAAGCCCTTAG--CAT
122 T-ATTGAAAACGCCG-CTAAACCCCCCGAAAGCTCAGAAAACGGCGTC-ATTGGGCTTAGTTTTT
*
58536883 TA
184 TT
* * *
58536885 GCGGCGCTTTATTAAAAACGCCACTAAACCCCTGAAAGCTAAGAAAACGGCGTCGTTGGGTTTTA
1 GCGGCGCTTTATTAAAAACACCGCTAAACCCCCGAAAGCTAAGAAAACGGCGTCGTTGGG-TTTA
** *
58536950 ATTTTTTTGCGGCGCTTTCATAAAAACGCCGCTAAATCCCCAGCATTAGCGGCGTATTGTTGAAA
65 ATTTTTTTGCGGCGCTTTCATAAAAACGCCGCTAAATCCCCAGCATTAGCGGCACATTATTGAAA
* * *
58537015 ACTCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGACTTAGTTTTTTT
130 ACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCATTGGGCTTAGTTTTTTT
* * * * * * * *
58537071 GCGGCGCTTGATAAAAAACGCCGCTAAACCCCTGAAAGCTCAGTAAATGGCGTCGTTGGGTTGAA
1 GCGGCGCTTTATTAAAAACACCGCTAAACCCCCGAAAGCTAAGAAAACGGCGTCGTTGGGTTTAA
* * * * *
58537136 TTTTTTTACGGCGCTTTCATAAAAATGCCGCTAAATCCCTCAGAATTAGCGGCGCTTTATTGAAA
66 TTTTTTTGCGGCGCTTTCATAAAAACGCCGCTAAATCCC-CAGCATTAGCGGCACATTATTGAAA
* * * *
58537201 ACGCCGCTAAACCCCTCGAAAGCTCAGAAAACGGCGTCGTTTGGCTTA-ATTTTTT
130 ACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCATTGGGCTTAGTTTTTTT
58537256 GCGGCGCTTT
1 GCGGCGCTTT
58537266 TGAGAGCGCC
Statistics
Matches: 442, Mismatches: 102, Indels: 50
0.74 0.17 0.08
Matches are distributed among these distances:
182 4 0.01
183 11 0.02
184 21 0.05
185 71 0.16
186 174 0.39
187 75 0.17
188 43 0.10
189 9 0.02
190 20 0.05
191 11 0.02
192 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (185 bp):
GCGGCGCTTTATTAAAAACACCGCTAAACCCCCGAAAGCTAAGAAAACGGCGTCGTTGGGTTTAA
TTTTTTTGCGGCGCTTTCATAAAAACGCCGCTAAATCCCCAGCATTAGCGGCACATTATTGAAAA
CGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCATTGGGCTTAGTTTTTTT
Found at i:58537047 original size:114 final size:112
Alignment explanation
Indices: 58536770--58537102 Score: 456
Period size: 113 Copynumber: 2.9 Consensus size: 112
58536760 AATTTTTTTT
*
58536770 GCGGCGTATTGTTGAAAACGCCGCTAAACCCCCCCGAAAGCTCAGAAAACGGTGTCGTTGGGCTT
1 GCGGCGTATTGTTGAAAACGCCGCTAAA-CCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTT
* * *
58536835 AGTTTTTTTGTGGCGCTTGATCAAAAACGCCGCTAAAGCCCTTAGCATTA
65 AGTTTTTTTGCGGCGCTTGATAAAAAACGCCGCTAAA-CCC-CAGCATTA
* * * * * *
58536885 GCGGCGCT-TTATTAAAAACGCCACTAAA-CCCCTGAAAGCTAAGAAAACGGCGTCGTTGGGTTT
1 GCGGCG-TATTGTTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGG-CT
* *
58536948 TAATTTTTTTGCGGCGCTTTCAT-AAAAACGCCGCTAAATCCCCAGCATTA
64 TAGTTTTTTTGCGGCGC-TTGATAAAAAACGCCGCTAAA-CCCCAGCATTA
* *
58536998 GCGGCGTATTGTTGAAAACTCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGACTTA
1 GCGGCGTATTGTTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
58537063 GTTTTTTTGCGGCGCTTGATAAAAAACGCCGCTAAACCCC
66 GTTTTTTTGCGGCGCTTGATAAAAAACGCCGCTAAACCCC
58537103 TGAAAGCTCA
Statistics
Matches: 190, Mismatches: 22, Indels: 15
0.84 0.10 0.07
Matches are distributed among these distances:
112 9 0.05
113 90 0.47
114 63 0.33
115 27 0.14
116 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (112 bp):
GCGGCGTATTGTTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
GTTTTTTTGCGGCGCTTGATAAAAAACGCCGCTAAACCCCAGCATTA
Found at i:58537128 original size:374 final size:373
Alignment explanation
Indices: 58536408--58537142 Score: 1098
Period size: 374 Copynumber: 2.0 Consensus size: 373
58536398 CGGCGCTTTA
58536408 TTGAAAACACCGCTAAACCCCCGAAAGCTCAGAAAACAGCATCGTTGGGCTTAAATTTTTTTGCG
1 TTGAAAACACCGCTAAACCCCCGAAAGCTCAGAAAACAGCATCGTTGGGCTTAAATTTTTTTGCG
** * * * *
58536473 GCGCTTTCTCAACAACGCCGCTAAAGGCCTCAGCATTAGCGGCGCTTTATTGAAAACACCGCTAA
66 GCGCTTGATCAAAAACGCCGCTAAAGCCCTCAGCATTAGCGGCGCTTTATTAAAAACACCACTAA
*
58536538 ACTCCCCGAAAGCTCAGAAAACGGCATCGTTGGGTTTAATTTTTTTGCGGCGCTTTCATAAAAAC
131 ACTCCCCGAAAGCTAAGAAAACGGCATCGTTGGGTTTAATTTTTTTGCGGCGCTTTCATAAAAAC
58536603 ACCGCTAAAGCCCCAGCATTAGCGGCACATTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAG
196 ACCGCTAAAGCCCCAGCATTAGCGGCACATTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAG
* * * *
58536668 AAAATGGCGTCATTGGGCTTAGTTTTTTTTGCGCCGCTTTATTAAAAACACCGCTAAACCCCCGA
261 AAAACGGCGTCATTGGACTTAGTTTTTTTTGCGCCGCTTGATAAAAAACACCGCTAAACCCCCGA
*
58536733 AAGCTAAGAAAACGGGTCGTTGGGTTTAATTTTTTTTGCGGCGTATTG
326 AAGCTAAGAAAACGGGTCGTTGGGTTGAATTTTTTTTGCGGCGTATTG
* * ** *
58536781 TTGAAAACGCCGCTAAACCCCCCCGAAAGCTCAGAAAACGGTGTCGTTGGGCTT-AGTTTTTTTG
1 TTGAAAACACCGCTAAA--CCCCCGAAAGCTCAGAAAACAGCATCGTTGGGCTTAAATTTTTTTG
* * *
58536845 TGGCGCTTGATCAAAAACGCCGCTAAAGCCCTTAGCATTAGCGGCGCTTTATTAAAAACGCCACT
64 CGGCGCTTGATCAAAAACGCCGCTAAAGCCCTCAGCATTAGCGGCGCTTTATTAAAAACACCACT
* *
58536910 AAAC-CCCTGAAAGCTAAGAAAACGGCGTCGTTGGGTTTTAATTTTTTTGCGGCGCTTTCATAAA
129 AAACTCCCCGAAAGCTAAGAAAACGGCATCGTTGGG-TTTAATTTTTTTGCGGCGCTTTCATAAA
* * ** * *
58536974 AACGCCGCTAAATCCCCAGCATTAGCGGCGTATTGTTGAAAACTCCGCTAAACCCCCCGAAAGCT
193 AACACCGCTAAAGCCCCAGCATTAGCGGCACATTATTGAAAACGCCGCTAAACCCCCCGAAAGCT
* * *
58537039 CAGAAAACGGCGTCGTTGGACTTAG-TTTTTTTGCGGCGCTTGATAAAAAACGCCGCTAAACCCC
258 CAGAAAACGGCGTCATTGGACTTAGTTTTTTTTGCGCCGCTTGATAAAAAACACCGCTAAACCCC
* * * *
58537103 TGAAAGCTCAGTAAATGGCGTCGTTGGGTTGAATTTTTTT
323 CGAAAGCTAAGAAAACGG-GTCGTTGGGTTGAATTTTTTT
58537143 ACGGCGCTTT
Statistics
Matches: 323, Mismatches: 35, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
373 93 0.29
374 198 0.61
375 32 0.10
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (373 bp):
TTGAAAACACCGCTAAACCCCCGAAAGCTCAGAAAACAGCATCGTTGGGCTTAAATTTTTTTGCG
GCGCTTGATCAAAAACGCCGCTAAAGCCCTCAGCATTAGCGGCGCTTTATTAAAAACACCACTAA
ACTCCCCGAAAGCTAAGAAAACGGCATCGTTGGGTTTAATTTTTTTGCGGCGCTTTCATAAAAAC
ACCGCTAAAGCCCCAGCATTAGCGGCACATTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAG
AAAACGGCGTCATTGGACTTAGTTTTTTTTGCGCCGCTTGATAAAAAACACCGCTAAACCCCCGA
AAGCTAAGAAAACGGGTCGTTGGGTTGAATTTTTTTTGCGGCGTATTG
Found at i:58537140 original size:72 final size:72
Alignment explanation
Indices: 58537012--58537175 Score: 197
Period size: 72 Copynumber: 2.3 Consensus size: 72
58537002 CGTATTGTTG
* * * *
58537012 AAAACTCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTTGGACTTAGTTTTTTTGCGGCG
1 AAAACGCCGCTAAA-CCCCTGAAAGCTCAGAAAACGGCGTCGTTGGACTTAATTTTTTTACGGCG
*
58537077 C-TTGATAA
65 CTTTCAT-A
* * *
58537085 AAAACGCCGCTAAACCCCTGAAAGCTCAGTAAATGGCGTCGTTGG-GTTGAATTTTTTTACGGCG
1 AAAACGCCGCTAAACCCCTGAAAGCTCAGAAAACGGCGTCGTTGGACTT-AATTTTTTTACGGCG
58537149 CTTTCATA
65 CTTTCATA
* *
58537157 AAAATGCCGCTAAATCCCT
1 AAAACGCCGCTAAACCCCT
58537176 CAGAATTAGC
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
71 2 0.03
72 60 0.76
73 17 0.22
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (72 bp):
AAAACGCCGCTAAACCCCTGAAAGCTCAGAAAACGGCGTCGTTGGACTTAATTTTTTTACGGCGC
TTTCATA
Found at i:58556164 original size:17 final size:17
Alignment explanation
Indices: 58556138--58556281 Score: 130
Period size: 17 Copynumber: 8.4 Consensus size: 17
58556128 ACGATATTTT
58556138 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
*
58556156 TTTTCAAAACACCG-AAA
1 TTTTTAAAACA-CGAAAA
* **
58556173 TTTTTGAAAACAAGAGGA
1 TTTTT-AAAACACGAAAA
* *
58556191 TTTTTGAAATACGAAAAA
1 TTTTTAAAACACG-AAAA
*
58556209 TTTTGAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *
58556226 TTTTTGAAACACGGAAA
1 TTTTTAAAACACGAAAA
*
58556243 TTTTTGAAA-ACGAAAA
1 TTTTTAAAACACGAAAA
* *
58556259 TTTTTGAAACACAAAAA
1 TTTTTAAAACACGAAAA
58556276 TTTTTA
1 TTTTTA
58556282 GAAGACACTA
Statistics
Matches: 102, Mismatches: 19, Indels: 11
0.77 0.14 0.08
Matches are distributed among these distances:
16 15 0.15
17 57 0.56
18 30 0.29
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:58556166 original size:38 final size:37
Alignment explanation
Indices: 58556049--58556177 Score: 122
Period size: 35 Copynumber: 3.4 Consensus size: 37
58556039 GATCCGATTG
*
58556049 AAACACGAGAATTTCTTGTTTTGAAAACACGAGAATTTTA
1 AAACACGA-AATTT-TT-TTTTGAAAACACGAAAATTTTA
* * *
58556089 AGACA-TAATATTTTTTTTT-AAAAC-C-AAAATTTATG
1 AAACACGAA-ATTTTTTTTTGAAAACACGAAAATTT-TA
*
58556124 AAACACGATATTTTTTTTTGAAAACACGAAAATTTTCA
1 AAACACGAAATTTTTTTTTGAAAACACGAAAATTTT-A
58556162 AAACACCGAAATTTTT
1 AAACA-CGAAATTTTT
58556178 GAAAACAAGA
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
34 6 0.08
35 16 0.22
36 11 0.15
37 6 0.08
38 15 0.21
39 14 0.19
40 4 0.06
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (37 bp):
AAACACGAAATTTTTTTTTGAAAACACGAAAATTTTA
Found at i:58556184 original size:35 final size:35
Alignment explanation
Indices: 58556138--58556300 Score: 170
Period size: 35 Copynumber: 4.7 Consensus size: 35
58556128 ACGATATTTT
**
58556138 TTTTTGAAAACACGAAAATTTTCAAAACACCGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* ** *
58556173 TTTTTGAAAACAAGAGGATTTTTGAAATA-CGAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCG-AAA
* *
58556208 ATTTTGAAAACACGAAAATTTTTGAAACACGGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
**
58556243 TTTTTG-AAA-ACGAAAATTTTTGAAACACAAAAA
1 TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
* * *
58556276 TTTTTAGAAGACACTAAAAATTTTG
1 TTTTT-GAAAACACGAAAATTTTTG
58556301 GAAAATGGAT
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
33 27 0.26
34 6 0.06
35 60 0.57
36 12 0.11
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (35 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACCGAAA
Found at i:58556517 original size:20 final size:19
Alignment explanation
Indices: 58556479--58556525 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
58556469 AATATATTTT
58556479 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACACG-GAAAAA
*
58556499 TTTTTGAAGGCAC-GAAAAA
1 TTTTTGAA-ACACGGAAAAA
58556518 -TTTTGAAA
1 TTTTTGAAA
58556526 AATAGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 8 0.33
21 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (19 bp):
TTTTTGAAACACGGAAAAA
Found at i:58556910 original size:7 final size:7
Alignment explanation
Indices: 58556898--58556948 Score: 84
Period size: 7 Copynumber: 7.0 Consensus size: 7
58556888 CTTTTTCTTC
58556898 CTTTTTT
1 CTTTTTT
58556905 CTTTTTT
1 CTTTTTT
58556912 CTTTTTT
1 CTTTTTT
58556919 CCTTTTTT
1 -CTTTTTT
58556927 CTTTTTT
1 CTTTTTT
58556934 CTTTTTT
1 CTTTTTT
58556941 CTTCTTTT
1 CTT-TTTT
58556949 TCTTCCTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
7 31 0.74
8 11 0.26
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
CTTTTTT
Found at i:58556922 original size:22 final size:22
Alignment explanation
Indices: 58556890--58556952 Score: 99
Period size: 22 Copynumber: 2.8 Consensus size: 22
58556880 TGAACCCCCT
58556890 TTTTCTTCCTTTTTTCTTTTTTC
1 TTTT-TTCCTTTTTTCTTTTTTC
58556913 TTTTTTCCTTTTTTCTTTTTTC
1 TTTTTTCCTTTTTTCTTTTTTC
*
58556935 TTTTTTCTTCTTTTTCTT
1 TTTTTTCCT-TTTTTCTT
58556953 CCTTTTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 26 0.68
23 12 0.32
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTTCCTTTTTTCTTTTTTC
Found at i:58556960 original size:22 final size:22
Alignment explanation
Indices: 58556889--58556964 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 22
58556879 TTGAACCCCC
*
58556889 TTTTTCTTCCTTTT-TTCTTTT
1 TTTTTCTTCTTTTTCTTCTTTT
* *
58556910 TTCTTTTTTCCTTTTTTCTTTTTTCT
1 TT-TTTCTT-C-TTTTTCTTCTTT-T
*
58556936 TTTTTCTTCTTTTTCTTCCTTT
1 TTTTTCTTCTTTTTCTTCTTTT
58556958 TTTTTCT
1 TTTTTCT
58556965 GCTGGGCTGC
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 2 0.05
22 13 0.30
23 11 0.25
24 5 0.11
25 10 0.23
26 3 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTCTTCTTTTTCTTCTTTT
Found at i:58556962 original size:14 final size:14
Alignment explanation
Indices: 58556898--58556948 Score: 84
Period size: 15 Copynumber: 3.5 Consensus size: 14
58556888 CTTTTTCTTC
58556898 CTTTTTTCTTTTTT
1 CTTTTTTCTTTTTT
58556912 CTTTTTTCCTTTTTT
1 CTTTTTT-CTTTTTT
58556927 CTTTTTTCTTTTTT
1 CTTTTTTCTTTTTT
58556941 CTTCTTTT
1 CTT-TTTT
58556949 TCTTCCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
14 17 0.49
15 18 0.51
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
CTTTTTTCTTTTTT
Found at i:58557244 original size:3 final size:3
Alignment explanation
Indices: 58557238--58557296 Score: 73
Period size: 3 Copynumber: 18.0 Consensus size: 3
58557228 TTTCTTTTTT
58557238 TTC TTC TTTC TTC TTC TCTC TTTC TTTC TTC TTC TTC TTC TTCC TTC
1 TTC TTC -TTC TTC TTC T-TC -TTC -TTC TTC TTC TTC TTC TT-C TTC
58557285 TTC TTC TTC TTC
1 TTC TTC TTC TTC
58557297 AAATCCGAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
3 37 0.71
4 14 0.27
5 1 0.02
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:58557249 original size:16 final size:16
Alignment explanation
Indices: 58557228--58557295 Score: 91
Period size: 16 Copynumber: 4.1 Consensus size: 16
58557218 TAAAATTTTT
* *
58557228 TTTCTTTTTTTTCTTC
1 TTTCTTCTTCTTCTTC
58557244 TTTCTTCTTCTCTCTTTC
1 TTTCTTCTTCT-TC-TTC
58557262 TTTCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTC
*
58557278 TTCCTTCTTCTTCTTC
1 TTTCTTCTTCTTCTTC
58557294 TT
1 TT
58557296 CAAATCCGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
16 29 0.62
17 4 0.09
18 14 0.30
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCTTCTTCTTCTTC
Found at i:58557276 original size:34 final size:33
Alignment explanation
Indices: 58557228--58557292 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
58557218 TAAAATTTTT
* * *
58557228 TTTCTTTTTTTTCTTCTTTCTTCTTCTCTCTTTC
1 TTTCTTCTTCTTCTTCTTCCTTCTTCT-TCTTTC
58557262 TTTCTTCTTCTTCTTCTTCCTTCTTCTTCTT
1 TTTCTTCTTCTTCTTCTTCCTTCTTCTTCTT
58557293 CTTCAAATCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (33 bp):
TTTCTTCTTCTTCTTCTTCCTTCTTCTTCTTTC
Found at i:58557705 original size:30 final size:30
Alignment explanation
Indices: 58557650--58557766 Score: 139
Period size: 30 Copynumber: 3.9 Consensus size: 30
58557640 TGTAATTTTT
* *
58557650 AGAAAATTTA-GGGTTAAAATGAAATTTAA
1 AGAAAGTTTAGGGGTCAAAATGAAATTTAA
* * *
58557679 TGAAAGTTTAGGGGTCTAAGTGAAATTTAA
1 AGAAAGTTTAGGGGTCAAAATGAAATTTAA
*
58557709 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAGTTTAGGGGTCAAAATGAAATTTAA
* *
58557738 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AG-AAAGTTTAGGGGTCAAAATGAAATTT
58557767 TTATTTTTAA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.14
30 64 0.86
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.30
Consensus pattern (30 bp):
AGAAAGTTTAGGGGTCAAAATGAAATTTAA
Found at i:58557766 original size:60 final size:59
Alignment explanation
Indices: 58557650--58557766 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 59
58557640 TGTAATTTTT
* * * *
58557650 AGAAAATTTAGGGTTAAAATGAAATTTAATGAAAGTTTAGGGGTCTAAGTGAAATTTAA
1 AGAAAATTTAGGGTCAAAATGAAATTTAAGGAAAGTTTAGGGGTCAAAATGAAATTTAA
* *
58557709 AGAAAGTTTAAGGGTCAAAATGAAATTT-AGGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAATTT-AGGGTCAAAATGAAATTTAAGG-AAAGTTTAGGGGTCAAAATGAAATTT
58557767 TTATTTTTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 10 0.20
60 40 0.80
ACGTcount: A:0.44, C:0.03, G:0.23, T:0.30
Consensus pattern (59 bp):
AGAAAATTTAGGGTCAAAATGAAATTTAAGGAAAGTTTAGGGGTCAAAATGAAATTTAA
Found at i:58558510 original size:21 final size:21
Alignment explanation
Indices: 58558484--58558524 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58558474 TTTTGTCATA
* * *
58558484 AAAATTTTAAACAATTTAAAT
1 AAAATTATAAAAAATATAAAT
58558505 AAAATTATAAAAAATATAAA
1 AAAATTATAAAAAATATAAA
58558525 ATCATTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAATTATAAAAAATATAAAT
Found at i:58563035 original size:43 final size:43
Alignment explanation
Indices: 58562973--58563058 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
58562963 CCTTTTTTCT
*
58562973 TTTTTATTCTAATTCATATGTTTAAATACAAAGTATACATTTA
1 TTTTTATTCTAATTCATATGTTTAAATACAAAGTAAACATTTA
* *
58563016 TTTTTATT-TCAATTTATATGTTTACATACAAAGTAAACATTTA
1 TTTTTATTCT-AATTCATATGTTTAAATACAAAGTAAACATTTA
58563059 AATAGGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
42 1 0.03
43 38 0.97
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (43 bp):
TTTTTATTCTAATTCATATGTTTAAATACAAAGTAAACATTTA
Found at i:58563354 original size:15 final size:16
Alignment explanation
Indices: 58563321--58563354 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58563311 ACTATCCTCC
**
58563321 TTTTTGACTTGCACTT
1 TTTTTGACTTAAACTT
58563337 TTTTTGACTTAAACTT
1 TTTTTGACTTAAACTT
58563353 TT
1 TT
58563355 GGCTCGCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.59
Consensus pattern (16 bp):
TTTTTGACTTAAACTT
Found at i:58569688 original size:30 final size:30
Alignment explanation
Indices: 58569654--58569715 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
58569644 ATAATGAGGT
*
58569654 GTAAGGTTGTGATTACCAATATGAGTGACG
1 GTAAGGTTGTGATTACCAATAAGAGTGACG
58569684 GTAAGGTTGTGATTACCAATAAGAGTGACG
1 GTAAGGTTGTGATTACCAATAAGAGTGACG
58569714 GT
1 GT
58569716 GGCTGTGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (30 bp):
GTAAGGTTGTGATTACCAATAAGAGTGACG
Found at i:58574033 original size:44 final size:44
Alignment explanation
Indices: 58573983--58574070 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
58573973 ATTAACATAA
** **
58573983 AATAGAAGTTGTGATAATTATGCATTTAAAAATAATTATAATTT
1 AATAGAAGTTGCAATAATTACACATTTAAAAATAATTATAATTT
* *
58574027 AATAGAATTTGCAATAATTACACATTTAAAAATTATTATAATTT
1 AATAGAAGTTGCAATAATTACACATTTAAAAATAATTATAATTT
58574071 CATTTACATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.41
Consensus pattern (44 bp):
AATAGAAGTTGCAATAATTACACATTTAAAAATAATTATAATTT
Found at i:58575111 original size:20 final size:20
Alignment explanation
Indices: 58575086--58575147 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
58575076 TTAATTTAAT
58575086 TAAAAATTAGAAAAATATTA
1 TAAAAATTAGAAAAATATTA
58575106 TAAAAATCGTA-AAAAATA-TA
1 TAAAAAT--TAGAAAAATATTA
* *
58575126 -AAAAAATAG-AAAATTTTA
1 TAAAAATTAGAAAAATATTA
58575144 TAAA
1 TAAA
58575148 GTTGTAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
17 7 0.20
18 2 0.06
19 8 0.23
20 9 0.26
21 7 0.20
22 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (20 bp):
TAAAAATTAGAAAAATATTA
Found at i:58575160 original size:38 final size:40
Alignment explanation
Indices: 58575087--58575171 Score: 95
Period size: 39 Copynumber: 2.2 Consensus size: 40
58575077 TAATTTAATT
*
58575087 AAAAATTAGAAAAATATTATAAAAATCGTAAAAAAT-ATA
1 AAAAAATAGAAAAATATTATAAAAATCGTAAAAAATGATA
* * * *
58575126 AAAAAATAG-AAAATTTTAT-AAAGTTGTAAGAAAATGGTA
1 AAAAAATAGAAAAATATTATAAAAATCGTAA-AAAATGATA
58575165 AAAAAAT
1 AAAAAAT
58575172 GTAAAGGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
37 8 0.21
38 14 0.36
39 17 0.44
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (40 bp):
AAAAAATAGAAAAATATTATAAAAATCGTAAAAAATGATA
Found at i:58575395 original size:19 final size:19
Alignment explanation
Indices: 58575371--58575471 Score: 63
Period size: 19 Copynumber: 5.4 Consensus size: 19
58575361 TAAATGGTCT
58575371 TTTTTTATGCA-TTTTATAA
1 TTTTTTATG-ATTTTTATAA
58575390 TTTTTTATGATTTTTATAA
1 TTTTTTATGATTTTTATAA
**
58575409 AATTTTAT-ATATTTTATTAA
1 TTTTTTATGAT-TTTTA-TAA
** *
58575429 -AGTTTACTCATTTTTAT-A
1 TTTTTTA-TGATTTTTATAA
58575447 -TTTTTATTGATTTTT-T-A
1 TTTTTTA-TGATTTTTATAA
58575464 TTTTTTAT
1 TTTTTTAT
58575472 AACTTTTTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
17 3 0.04
18 21 0.30
19 34 0.49
20 9 0.13
21 2 0.03
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (19 bp):
TTTTTTATGATTTTTATAA
Found at i:58575478 original size:17 final size:19
Alignment explanation
Indices: 58575439--58575479 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
58575429 AGTTTACTCA
* *
58575439 TTTTTATATTTTTATTGAT
1 TTTTTATATTTTTATTAAC
58575458 TTTTTAT-TTTTTA-TAAC
1 TTTTTATATTTTTATTAAC
58575475 TTTTT
1 TTTTT
58575480 TGTCACATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 7 0.35
18 6 0.30
19 7 0.35
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTTATATTTTTATTAAC
Found at i:58575478 original size:18 final size:19
Alignment explanation
Indices: 58575439--58575480 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
58575429 AGTTTACTCA
*
58575439 TTTTTATATTTTTATTGAT
1 TTTTTATATTTTTATTAAT
58575458 TTTTTAT-TTTTTA-TAACT
1 TTTTTATATTTTTATTAA-T
58575476 TTTTT
1 TTTTT
58575481 GTCACATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 12 0.57
19 7 0.33
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTTATATTTTTATTAAT
Found at i:58577009 original size:8 final size:8
Alignment explanation
Indices: 58576996--58577031 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
58576986 TCACCTCAGT
58576996 ATTTTAAA
1 ATTTTAAA
58577004 ATTTTAAA
1 ATTTTAAA
*
58577012 A-TTAAAA
1 ATTTTAAA
58577019 ATTTTAAA
1 ATTTTAAA
58577027 ATTTT
1 ATTTT
58577032 TAGGAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATTTTAAA
Found at i:58577021 original size:15 final size:15
Alignment explanation
Indices: 58577001--58577029 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
58576991 TCAGTATTTT
58577001 AAAATTTTAAAATTA
1 AAAATTTTAAAATTA
58577016 AAAATTTTAAAATT
1 AAAATTTTAAAATT
58577030 TTTAGGAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTTTAAAATTA
Found at i:58577827 original size:66 final size:65
Alignment explanation
Indices: 58577695--58577828 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 65
58577685 ATTCTAAAGC
* * * * *
58577695 TGTAGCTGGAGTTCATCATATTTTCTGCTTGCCTCTGCTTCCCTCGCTGCTGCCTCCGCTTTAAG
1 TGTAGCTAGAGTTCATCAGATTTTCT-CTTGCCTCTGCTTCCCTCGATGCTGCCTCCACTTCAAG
58577760 T
65 T
* * *
58577761 TGTAGCTAGAGTTCTTCAGATTTTCT-TTGAGCCTCTGCTTCTCTCGATGCTGCCTCTACTTCAA
1 TGTAGCTAGAGTTCATCAGATTTTCTCTT--GCCTCTGCTTCCCTCGATGCTGCCTCCACTTCAA
58577825 GT
64 GT
58577827 TG
1 TG
58577829 AGCAATTTGC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 2 0.03
66 56 0.97
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.40
Consensus pattern (65 bp):
TGTAGCTAGAGTTCATCAGATTTTCTCTTGCCTCTGCTTCCCTCGATGCTGCCTCCACTTCAAGT
Found at i:58584117 original size:31 final size:35
Alignment explanation
Indices: 58584063--58584131 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 35
58584053 AGAAATGGAC
* *
58584063 AAAAAAAATCTCGATTAGTTGGGTGATC-AAATTA
1 AAAAAAAATCTCGATTAGCTGGGTGACCAAAATTA
58584097 AAAAAAAAT-T-GA-TAGCTGGGTGACCAAAATTA
1 AAAAAAAATCTCGATTAGCTGGGTGACCAAAATTA
58584129 AAA
1 AAA
58584132 GAGGTAATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 11 0.34
32 11 0.34
33 1 0.03
34 9 0.28
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.25
Consensus pattern (35 bp):
AAAAAAAATCTCGATTAGCTGGGTGACCAAAATTA
Found at i:58594472 original size:19 final size:19
Alignment explanation
Indices: 58594434--58594473 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
58594424 TTTAAATCTA
* * *
58594434 AAAATTATTAAAATATTAT
1 AAAATTATAAAAAAACTAT
58594453 AAAATTATAAAAAAACTAT
1 AAAATTATAAAAAAACTAT
58594472 AA
1 AA
58594474 TTTTAATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTATAAAAAAACTAT
Found at i:58594763 original size:19 final size:19
Alignment explanation
Indices: 58594741--58594811 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
58594731 AGAAATTACT
*
58594741 AAAATTTTATAAATTTATA
1 AAAATTATATAAATTTATA
*
58594760 AAAATTATAT-AAGTTATTA
1 AAAATTATATAAATTTA-TA
*
58594779 AAAACTAT-TAAATGTTATA
1 AAAATTATATAAAT-TTATA
58594798 AAAATT-TA-AAATTT
1 AAAATTATATAAATTT
58594812 TATTATTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
17 2 0.05
18 11 0.26
19 27 0.63
20 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (19 bp):
AAAATTATATAAATTTATA
Found at i:58595119 original size:29 final size:29
Alignment explanation
Indices: 58595087--58595180 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
58595077 TTAAATGTTT
* *
58595087 AATTTATTGCACTTTTTGACAAGGGGCTC
1 AATTAATTGCAATTTTTGACAAGGGGCTC
* * * * * *
58595116 AATTAATTACTAATTTTCGATTAA-AGGTTT
1 AATTAATTGC-AATTTTTGA-CAAGGGGCTC
* *
58595146 AATTGATTGCATTTTTTGACAAGGGGCTC
1 AATTAATTGCAATTTTTGACAAGGGGCTC
58595175 AATTAA
1 AATTAA
58595181 ATTTACAATT
Statistics
Matches: 45, Mismatches: 17, Indels: 6
0.66 0.25 0.09
Matches are distributed among these distances:
28 2 0.04
29 23 0.51
30 18 0.40
31 2 0.04
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (29 bp):
AATTAATTGCAATTTTTGACAAGGGGCTC
Found at i:58595146 original size:59 final size:60
Alignment explanation
Indices: 58595049--58595180 Score: 198
Period size: 59 Copynumber: 2.2 Consensus size: 60
58595039 ACCATATTAC
* * *
58595049 AGGGGCTCAATT-ATCTGCTAACTTTTGATTAAATGTTTAATTTATTGCACTTTTTGACA
1 AGGGGCTCAATTAATCTACTAACTTTTGATTAAAGGTTTAATTGATTGCACTTTTTGACA
*
58595108 AGGGGCTCAATTAAT-TACTAA-TTTTCGATTAAAGGTTTAATTGATTGCATTTTTTGACA
1 AGGGGCTCAATTAATCTACTAACTTTT-GATTAAAGGTTTAATTGATTGCACTTTTTGACA
58595167 AGGGGCTCAATTAA
1 AGGGGCTCAATTAA
58595181 ATTTACAATT
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
58 4 0.06
59 61 0.91
60 2 0.03
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (60 bp):
AGGGGCTCAATTAATCTACTAACTTTTGATTAAAGGTTTAATTGATTGCACTTTTTGACA
Found at i:58603034 original size:13 final size:13
Alignment explanation
Indices: 58603016--58603042 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58603006 GGTTTCAGAC
58603016 GGTTTGGCACATG
1 GGTTTGGCACATG
58603029 GGTTTGGCACATG
1 GGTTTGGCACATG
58603042 G
1 G
58603043 CCTGCGATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.41, T:0.30
Consensus pattern (13 bp):
GGTTTGGCACATG
Found at i:58612602 original size:14 final size:14
Alignment explanation
Indices: 58612583--58612609 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58612573 GTTGTTGTTA
58612583 TGAATATTTTATTT
1 TGAATATTTTATTT
58612597 TGAATATTTTATT
1 TGAATATTTTATT
58612610 GAAACCAAAA
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:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
TGAATATTTTATTT
Found at i:58613091 original size:16 final size:16
Alignment explanation
Indices: 58613070--58613108 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
58613060 GTTTGGTTCG
58613070 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAA
*
58613086 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAA
58613102 CTGTAAT
1 CTGTAAT
58613109 AGTAATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAGAA
Found at i:58613154 original size:45 final size:44
Alignment explanation
Indices: 58613090--58613182 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
58613080 ATAGAACTGT
*
58613090 AATGGAATAGAGCTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
58613135 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
58613179 AATG
1 AATG
58613183 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:58613191 original size:39 final size:41
Alignment explanation
Indices: 58613090--58613194 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 41
58613080 ATAGAACTGT
58613090 AATGGAATAGA-GCTGTAATAGTAATTCAATTGTTTGGTTG
1 AATGGAATAGATGCTGTAATAGTAATTCAATTGTTTGGTTG
* *
58613130 AATGGAATGGAATAGAACTGTAATAGT-ATTC-TTGTGTTTGGTTG
1 AATGGAATAG-AT-G--CTGTAATAGTAATTCAAT-TGTTTGGTTG
*
58613174 AATGGAAT-GATGTTGTAATAG
1 AATGGAATAGATGCTGTAATAG
58613195 CATAAGGAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 8 0.14
40 9 0.16
41 2 0.04
42 2 0.04
43 3 0.05
44 22 0.39
45 10 0.18
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (41 bp):
AATGGAATAGATGCTGTAATAGTAATTCAATTGTTTGGTTG
Found at i:58613365 original size:18 final size:18
Alignment explanation
Indices: 58613338--58613373 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
58613328 AATTATTATT
58613338 AAATACAATTTAATAAAA
1 AAATACAATTTAATAAAA
*
58613356 AAATATAATTTAATAAAA
1 AAATACAATTTAATAAAA
58613374 TTCTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATACAATTTAATAAAA
Found at i:58620469 original size:27 final size:27
Alignment explanation
Indices: 58620419--58620471 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
58620409 TGTCAACTTC
**
58620419 TCCCAGATTGGTACCTATGGTTTTTTG
1 TCCCAGATTGGTACCTATACTTTTTTG
58620446 TCCCAGATTGGTACCTGA-ACTTTTTT
1 TCCCAGATTGGTACCT-ATACTTTTTT
58620472 TCTGTCCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (27 bp):
TCCCAGATTGGTACCTATACTTTTTTG
Found at i:58622455 original size:17 final size:17
Alignment explanation
Indices: 58622433--58622480 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
58622423 CCAGATTTTG
58622433 ATACCCATATCTTTCTA
1 ATACCCATATCTTTCTA
*
58622450 ATACCCATATCTTTCTG
1 ATACCCATATCTTTCTA
58622467 ATACCCATATCTTT
1 ATACCCATATCTTT
58622481 GACTTTCTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.02, T:0.42
Consensus pattern (17 bp):
ATACCCATATCTTTCTA
Found at i:58628799 original size:4 final size:4
Alignment explanation
Indices: 58628790--58628818 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
58628780 CCTTTGATAA
58628790 AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT A
58628819 TTGAAAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:58629422 original size:26 final size:27
Alignment explanation
Indices: 58629374--58629424 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
58629364 ATTTGATTTG
*
58629374 AAAATTTAAATTTTGAAATAAAATATT
1 AAAATTTAAATTTTGAAAAAAAATATT
58629401 AAAATTT-AATTGTT-AAAAAAAATA
1 AAAATTTAAATT-TTGAAAAAAAATA
58629425 GGGAATAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
AAAATTTAAATTTTGAAAAAAAATATT
Found at i:58630629 original size:54 final size:54
Alignment explanation
Indices: 58630528--58630667 Score: 156
Period size: 54 Copynumber: 2.6 Consensus size: 54
58630518 CAATTTGAAT
* * * * * *
58630528 CAATTGCT-TAGTTTGATTGCTTTGGACTATGGACAACTTATATTACCTACCAATA
1 CAATTGCTCTA-TTTGATT-CCTTAGACTATGGACAACATAGACTACCTACCAAGA
*
58630583 CAATTGCTCTATTTGATTCCTTAGACTATGGACAACATAGACTACCTACTAAGA
1 CAATTGCTCTATTTGATTCCTTAGACTATGGACAACATAGACTACCTACCAAGA
* * *
58630637 CATTTGGTCAATTTGATTCCTTTAGACTATG
1 CAATTGCTCTATTTGATTCC-TTAGACTATG
58630668 TATTATGACT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
54 46 0.63
55 25 0.34
56 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (54 bp):
CAATTGCTCTATTTGATTCCTTAGACTATGGACAACATAGACTACCTACCAAGA
Found at i:58636887 original size:25 final size:25
Alignment explanation
Indices: 58636825--58636884 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
58636815 ATGATATTTT
* * *
58636825 TATTAAATAATAATTTAATAATTTA
1 TATTAAATAATATTTTAATAAGTAA
58636850 T-TTAAAATAATATTTTAATAAGTAA
1 TATT-AAATAATATTTTAATAAGTAA
58636875 TATTATAATA
1 TATTA-AATA
58636885 TATGTAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 2 0.07
25 21 0.72
26 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TATTAAATAATATTTTAATAAGTAA
Found at i:58639285 original size:24 final size:24
Alignment explanation
Indices: 58639258--58639307 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
58639248 AACGGAAAGT
*
58639258 TCTTGTGAGCCATAAATAGGAAGC
1 TCTTGTGAGCCATAAACAGGAAGC
58639282 TCTTGTGAGCCATAAACAGGAAGC
1 TCTTGTGAGCCATAAACAGGAAGC
58639306 TC
1 TC
58639308 AAGAGAGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (24 bp):
TCTTGTGAGCCATAAACAGGAAGC
Found at i:58639315 original size:24 final size:24
Alignment explanation
Indices: 58639264--58639317 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
58639254 AAGTTCTTGT
* ** *
58639264 GAGCCATAAATAGGAAGCTCTTGT
1 GAGCCATAAACAGGAAGCTCAAGA
58639288 GAGCCATAAACAGGAAGCTCAAGA
1 GAGCCATAAACAGGAAGCTCAAGA
58639312 GAGCCA
1 GAGCCA
58639318 AATTTGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (24 bp):
GAGCCATAAACAGGAAGCTCAAGA
Found at i:58639389 original size:25 final size:24
Alignment explanation
Indices: 58639276--58639413 Score: 100
Period size: 24 Copynumber: 5.7 Consensus size: 24
58639266 GCCATAAATA
* * * *
58639276 GGAAGCTCTTGTGAGCCATAAACA
1 GGAAGCTCATGAGAGCCATAATCG
* *
58639300 GGAAGCTCAAGAGAGCCA-AATTTG
1 GGAAGCTCATGAGAGCCATAA-TCG
* *
58639324 GGAAGCTCATGCGAGCCA-ATATTG
1 GGAAGCTCATGAGAGCCATA-ATCG
** *
58639348 GGAAGCTCCGGAAAGCCATTAATCG
1 GGAAGCTCATGAGAGCCA-TAATCG
*
58639373 GGAAGCTCATGAGAGCCATATATCC
1 GGAAGCTCATGAGAGCCATA-ATCG
* *
58639398 GGATGCTCATAAGAGC
1 GGAAGCTCATGAGAGC
58639414 TAAATAACAT
Statistics
Matches: 90, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
23 2 0.02
24 51 0.57
25 36 0.40
26 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.19
Consensus pattern (24 bp):
GGAAGCTCATGAGAGCCATAATCG
Found at i:58641736 original size:9 final size:9
Alignment explanation
Indices: 58641722--58641753 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
58641712 TAAAAGTCAT
58641722 TAAGCAAAA
1 TAAGCAAAA
58641731 TAAGCAAAA
1 TAAGCAAAA
58641740 TTAAGCAAAA
1 -TAAGCAAAA
58641750 TAAG
1 TAAG
58641754 TTATGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.16
Consensus pattern (9 bp):
TAAGCAAAA
Found at i:58641746 original size:10 final size:10
Alignment explanation
Indices: 58641720--58641750 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
58641710 AATAAAAGTC
58641720 ATTAAGCAAA
1 ATTAAGCAAA
58641730 A-TAAGCAAA
1 ATTAAGCAAA
58641739 ATTAAGCAAA
1 ATTAAGCAAA
58641749 AT
1 AT
58641751 AAGTTATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.19
Consensus pattern (10 bp):
ATTAAGCAAA
Found at i:58645287 original size:32 final size:32
Alignment explanation
Indices: 58645236--58645431 Score: 214
Period size: 32 Copynumber: 6.2 Consensus size: 32
58645226 GAATGGCTAC
* * * *
58645236 AAGCCATAAGTA-CAGTAATATGATTGGCATA
1 AAGCCATCAGTAGTAGTAATATGATCGGCACA
*
58645267 AAGCCATCAGTAGTAGTAATATAATCGGCACA
1 AAGCCATCAGTAGTAGTAATATGATCGGCACA
* * *
58645299 CAGCCATCAATAGTAGTAGTATGATCGGCACA
1 AAGCCATCAGTAGTAGTAATATGATCGGCACA
* *
58645331 AAGCCATCAGTAGTAATAATATGATCGGTACA
1 AAGCCATCAGTAGTAGTAATATGATCGGCACA
* * * *
58645363 CAGCCATCAGTAATGGTAATATGATTGGCACA
1 AAGCCATCAGTAGTAGTAATATGATCGGCACA
* * * * *
58645395 CAGCCATCAGTAATGGTATTATGATCGGTACA
1 AAGCCATCAGTAGTAGTAATATGATCGGCACA
58645427 AAGCC
1 AAGCC
58645432 CTCAATAGCA
Statistics
Matches: 140, Mismatches: 24, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
31 11 0.08
32 129 0.92
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.24
Consensus pattern (32 bp):
AAGCCATCAGTAGTAGTAATATGATCGGCACA
Found at i:58645334 original size:64 final size:64
Alignment explanation
Indices: 58645249--58645439 Score: 247
Period size: 64 Copynumber: 3.0 Consensus size: 64
58645239 CCATAAGTAC
* * *
58645249 AGTAATATGATTGGCATAAAGCCATCAGTAGTAGTAATATAATCGGCACACAGCCATCAATAGT
1 AGTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGTACACAGCCATCAATAGT
* * * * *
58645313 AGTAGTATGATCGGCACAAAGCCATCAGTAGTAATAATATGATCGGTACACAGCCATCAGTAAT
1 AGTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGTACACAGCCATCAATAGT
* * * * * * *
58645377 GGTAATATGATTGGCACACAGCCATCAGTAATGGTATTATGATCGGTACAAAGCCCTCAATAG
1 AGTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGTACACAGCCATCAATAG
58645440 CATCGCAACA
Statistics
Matches: 107, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 107 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (64 bp):
AGTAATATGATTGGCACAAAGCCATCAGTAGTAGTAATATGATCGGTACACAGCCATCAATAGT
Found at i:58645668 original size:24 final size:24
Alignment explanation
Indices: 58645610--58645692 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
58645600 CCATGCACGG
* *
58645610 AATCATTCATACAAATCACAAACA
1 AATCATTCATTCAAATCACAGACA
**
58645634 AATCAGCCATTCAAATCACAGACA
1 AATCATTCATTCAAATCACAGACA
* * * *
58645658 AATCATTCATTTACATCAAAGGCA
1 AATCATTCATTCAAATCACAGACA
*
58645682 AATCAATCATT
1 AATCATTCATT
58645693 TAACCCTGAG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.47, C:0.24, G:0.05, T:0.24
Consensus pattern (24 bp):
AATCATTCATTCAAATCACAGACA
Found at i:58645798 original size:81 final size:81
Alignment explanation
Indices: 58645713--58645873 Score: 227
Period size: 81 Copynumber: 2.0 Consensus size: 81
58645703 GGGAAAAATA
* * * *
58645713 GTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTAC-AGGCGCATGACGG-TCATTTTA
1 GTCATTTTACCCAACAGCGGCATTACAGTCATTTTACCCTACAAGG-GCATGACGGTTC-TCTTA
*
58645776 CCCTACAGGGGCATTACT
64 CCCTACAGAGGCATTACT
* *
58645794 GTCATTTTACCCAACAGCGGCATTACAGTCATTTTACCCTACAAGGGCGTTACGGTTCTCTTACC
1 GTCATTTTACCCAACAGCGGCATTACAGTCATTTTACCCTACAAGGGCATGACGGTTCTCTTACC
58645859 CTACAGAGGCATTAC
66 CTACAGAGGCATTAC
58645874 GACTATGCAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
81 66 0.93
82 5 0.07
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (81 bp):
GTCATTTTACCCAACAGCGGCATTACAGTCATTTTACCCTACAAGGGCATGACGGTTCTCTTACC
CTACAGAGGCATTACT
Found at i:58645846 original size:27 final size:27
Alignment explanation
Indices: 58645713--58645874 Score: 188
Period size: 27 Copynumber: 6.0 Consensus size: 27
58645703 GGGAAAAATA
*
58645713 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAAGGGCATTACG
*
58645740 GTCATTTTACCCTAC-AGGCGCATGACG
1 GTCATTTTACCCTACAAGG-GCATTACG
* *
58645767 GTCATTTTACCCTACAGGGGCATTACT
1 GTCATTTTACCCTACAAGGGCATTACG
* *
58645794 GTCATTTTACCCAAC-AGCGGCATTACA
1 GTCATTTTACCCTACAAG-GGCATTACG
*
58645821 GTCATTTTACCCTACAAGGGCGTTACG
1 GTCATTTTACCCTACAAGGGCATTACG
*
58645848 GTTC-TCTTACCCTAC-AGAGGCATTACG
1 G-TCATTTTACCCTACAAG-GGCATTACG
58645875 ACTATGCAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
26 5 0.04
27 105 0.91
28 6 0.05
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (27 bp):
GTCATTTTACCCTACAAGGGCATTACG
Found at i:58645870 original size:54 final size:53
Alignment explanation
Indices: 58645712--58645873 Score: 218
Period size: 54 Copynumber: 3.0 Consensus size: 53
58645702 GGGGAAAAAT
*
58645712 AGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGCGCATGAC
1 AGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGG-GCATTAC
* * *
58645766 GGTCATTTTACCCTACAGGGGCATTACTGTCATTTTACCCAACAGCGGCATTAC
1 AGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAG-GGCATTAC
* * *
58645820 AGTCATTTTACCCTACAAGGGCGTTACGGTTC-TCTTACCCTACAGAGGCATTAC
1 AGTCATTTTACCCTACAGGGGCATTACGG-TCATTTTACCCTACAG-GGCATTAC
58645874 GACTATGCAA
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
54 92 0.97
55 3 0.03
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (53 bp):
AGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAGGGCATTAC
Found at i:58650850 original size:15 final size:15
Alignment explanation
Indices: 58650830--58650859 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58650820 TTTTCGATCA
58650830 CCTTTGTGAACCATG
1 CCTTTGTGAACCATG
58650845 CCTTTGTGAACCATG
1 CCTTTGTGAACCATG
58650860 AAGTGACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (15 bp):
CCTTTGTGAACCATG
Found at i:58658268 original size:54 final size:54
Alignment explanation
Indices: 58658185--58658317 Score: 157
Period size: 54 Copynumber: 2.5 Consensus size: 54
58658175 TACGACCAAA
* * *
58658185 ATACCCTCATAGGGTAAAATGA-TCGAAATACTCC-CATAGGGTAAAATGACCGAT
1 ATACCCCCATAGGATAAAATGACT-AAAATAC-CCTCATAGGGTAAAATGACCGAT
* *
58658239 ATACCCCCATAGGATAAAATGACTAAAATACCCTCATAGGGTAAAATGTCCGTT
1 ATACCCCCATAGGATAAAATGACTAAAATACCCTCATAGGGTAAAATGACCGAT
58658293 ATA-CCCC-TAGGAGATAAAATGACTA
1 ATACCCCCATA-G-GATAAAATGACTA
58658318 TTATGGCCTT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
52 2 0.03
53 7 0.10
54 60 0.86
55 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (54 bp):
ATACCCCCATAGGATAAAATGACTAAAATACCCTCATAGGGTAAAATGACCGAT
Found at i:58658298 original size:27 final size:27
Alignment explanation
Indices: 58658178--58658286 Score: 139
Period size: 27 Copynumber: 4.0 Consensus size: 27
58658168 GTCGATATAC
*
58658178 GACCAAAATACCCTCATAGGGTAAAAT
1 GACCGAAATACCCTCATAGGGTAAAAT
*
58658205 GATCGAAATACTCC-CATAGGGTAAAAT
1 GACCGAAATAC-CCTCATAGGGTAAAAT
* * *
58658232 GACCGATATACCCCCATAGGATAAAAT
1 GACCGAAATACCCTCATAGGGTAAAAT
**
58658259 GACTAAAATACCCTCATAGGGTAAAAT
1 GACCGAAATACCCTCATAGGGTAAAAT
58658286 G
1 G
58658287 TCCGTTATAC
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 2 0.03
27 66 0.94
28 2 0.03
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (27 bp):
GACCGAAATACCCTCATAGGGTAAAAT
Found at i:58658321 original size:27 final size:28
Alignment explanation
Indices: 58658185--58658321 Score: 94
Period size: 27 Copynumber: 5.1 Consensus size: 28
58658175 TACGACCAAA
* *
58658185 ATACCCTCATAGGG-TAAAATGATCGA-A
1 ATACCCTCATAGGGATAAAATGA-CTATT
*
58658212 ATACTCC-CATAGGG-TAAAATGACCGA-T
1 ATAC-CCTCATAGGGATAAAATGA-CTATT
* **
58658239 ATACCCCCATA-GGATAAAATGACTAAA
1 ATACCCTCATAGGGATAAAATGACTATT
* **
58658266 ATACCCTCATAGGG-TAAAATGTCCGTT
1 ATACCCTCATAGGGATAAAATGACTATT
58658293 ATACCC-C-TAGGAGATAAAATGACTATT
1 ATACCCTCATAGG-GATAAAATGACTATT
58658320 AT
1 AT
58658322 GGCCTTATGT
Statistics
Matches: 90, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
25 4 0.04
26 8 0.09
27 74 0.82
28 4 0.04
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (28 bp):
ATACCCTCATAGGGATAAAATGACTATT
Found at i:58658761 original size:28 final size:28
Alignment explanation
Indices: 58658685--58658761 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
58658675 ACTGTAATGT
*
58658685 TACTATATTGGGCTAAGGCCCACACTGA
1 TACTATATTGGGCTAAGGCCTACACTGA
* *
58658713 TACTATATTGGGCTAAAGCCTACACTGC
1 TACTATATTGGGCTAAGGCCTACACTGA
58658741 TACTGA-ATTGGGCTAAGGCCT
1 TACT-ATATTGGGCTAAGGCCT
58658762 TCATTGTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 43 0.98
29 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (28 bp):
TACTATATTGGGCTAAGGCCTACACTGA
Found at i:58661281 original size:18 final size:17
Alignment explanation
Indices: 58661258--58661316 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
58661248 TGTTTGGTTA
58661258 CCCTTCTTCTCCCCTTTC
1 CCCTTCTTCTCCCC-TTC
**
58661276 CCCTTCCCCTTCCCCTTC
1 CCCTTCTTC-TCCCCTTC
58661294 CCCTTCCCTT-TCCCCTTC
1 CCCTT--CTTCTCCCCTTC
58661312 CCCTT
1 CCCTT
58661317 GGGTTGCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 28 0.82
19 5 0.15
20 1 0.03
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (17 bp):
CCCTTCTTCTCCCCTTC
Found at i:58661284 original size:6 final size:6
Alignment explanation
Indices: 58661267--58661316 Score: 82
Period size: 6 Copynumber: 8.2 Consensus size: 6
58661257 ACCCTTCTTC
*
58661267 TCCCCTT TCCCCT TCCCCT TCCCCT TCCCCT TCCCTT TCCCCT TCCCCT
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT
58661316 T
1 T
58661317 GGGTTGCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
6 36 0.88
7 5 0.12
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (6 bp):
TCCCCT
Found at i:58661378 original size:22 final size:23
Alignment explanation
Indices: 58661353--58661397 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
58661343 CCTCTTCCGG
58661353 TTCC-TCCTTCTTCCATTCTTTA
1 TTCCTTCCTTCTTCCATTCTTTA
*
58661375 TTCCTTTTTCTTCTTCCATTCTT
1 TTCC--TTCCTTCTTCCATTCTT
58661398 CATCTTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
25 15 0.79
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (23 bp):
TTCCTTCCTTCTTCCATTCTTTA
Found at i:58665060 original size:19 final size:21
Alignment explanation
Indices: 58665013--58665060 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
58665003 TATATTTATT
* *
58665013 TATAAATAAATCATTGTAATA
1 TATAAAAAAATCATTGTAAAA
*
58665034 TATGAAAAAAT-ATT-TAAAA
1 TATAAAAAAATCATTGTAAAA
58665053 TATAAAAA
1 TATAAAAA
58665061 TTTATTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 11 0.48
20 3 0.13
21 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
TATAAAAAAATCATTGTAAAA
Found at i:58665070 original size:16 final size:18
Alignment explanation
Indices: 58665047--58665098 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
58665037 GAAAAAATAT
* *
58665047 TTAAAATATAAAAATTTA
1 TTAATATATATAAATTTA
58665065 TTAATATGTATATAAATTTA
1 TTAATA--TATATAAATTTA
*
58665085 TTAATATATGTAAA
1 TTAATATATATAAA
58665099 AATAACTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 12 0.41
20 17 0.59
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
TTAATATATATAAATTTA
Found at i:58665093 original size:22 final size:20
Alignment explanation
Indices: 58665053--58665101 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
58665043 ATATTTAAAA
58665053 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
* *
58665073 TATATAAATTTATTAATATA
1 TATAAAAATTTATTAATATG
*
58665093 TGTAAAAAT
1 TATAAAAAT
58665102 AACTTTTTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:58665650 original size:21 final size:21
Alignment explanation
Indices: 58665603--58665657 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
58665593 ACCGCTATTT
* * *
58665603 CTAATCTTACTGCTACAGTAT
1 CTAATCTCACCGCTACAGTAA
*
58665624 CCAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAGTAA
58665645 CTAATCTCACCGC
1 CTAATCTCACCGC
58665658 CACCGCAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.35, G:0.09, T:0.27
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAA
Found at i:58667645 original size:2 final size:2
Alignment explanation
Indices: 58667638--58667699 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
58667628 TAGAACCCAT
*
58667638 CA CA CA CA CA CA CA CA CA CA CA CA CA CG CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
58667680 CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA
58667700 TATATGACTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.48, C:0.50, G:0.02, T:0.00
Consensus pattern (2 bp):
CA
Found at i:58672603 original size:46 final size:45
Alignment explanation
Indices: 58672536--58672752 Score: 245
Period size: 36 Copynumber: 5.2 Consensus size: 45
58672526 TTTGAGTACT
* *
58672536 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
58672582 TCTGATCAAGTGAAAAAGTGATAA---GT-G----G-TACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
58672618 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
58672664 TCTGATCAAGTGAAAAAGTGATAAGT-GT--C--A--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
58672700 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
58672745 TCTGATCA
1 TCTGATCA
58672753 GGGACAAATG
Statistics
Matches: 145, Mismatches: 7, Indels: 39
0.76 0.04 0.20
Matches are distributed among these distances:
36 60 0.41
37 3 0.02
38 1 0.01
39 3 0.02
40 2 0.01
41 1 0.01
42 1 0.01
43 4 0.03
45 16 0.11
46 54 0.37
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:58672673 original size:82 final size:82
Alignment explanation
Indices: 58672536--58672752 Score: 384
Period size: 82 Copynumber: 2.7 Consensus size: 82
58672526 TTTGAGTACT
*
58672536 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
58672601 GATAAGTGGT-ACACTTA
66 GATAAGT-GTCACACTTA
58672618 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
58672683 GATAAGTGTCATACTTA
66 GATAAGTGTCACACTTA
*
58672700 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCA
58672753 GGGACAAATG
Statistics
Matches: 131, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
81 23 0.18
82 108 0.82
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGTCACACTTA
Found at i:58674376 original size:43 final size:42
Alignment explanation
Indices: 58674297--58674452 Score: 188
Period size: 42 Copynumber: 3.7 Consensus size: 42
58674287 AGGCTAAACA
* ** *
58674297 GAAACCCATAAGGGTTGAACGGAAGCTCGTAAGAGCTGAATC
1 GAAACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTTAATC
*
58674339 GAAACCCATAAGGGATTAAACTGAAGCTCAAAAGAGCTTAA-C
1 GAAACCCATAAGGG-TTAAACGGAAGCTCAAAAGAGCTTAATC
* * * *
58674381 AGAAACCCATTAGGGTTAAACTGAAGCTAAAAAGAGCTTAATG
1 -GAAACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTTAATC
* *
58674424 GAAACCCATTAGGGTTAAACGGAAACTCA
1 GAAACCCATAAGGGTTAAACGGAAGCTCA
58674453 TATGACTTAA
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
42 66 0.66
43 34 0.34
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACGGAAGCTCAAAAGAGCTTAATC
Found at i:58676834 original size:3 final size:3
Alignment explanation
Indices: 58676826--58676868 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
58676816 CTTTGCTTAT
*
58676826 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
58676869 TAAAAAATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:58678080 original size:9 final size:9
Alignment explanation
Indices: 58678051--58678087 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
58678041 TGAGTTTTCG
58678051 AATTCGAAT
1 AATTCGAAT
*
58678060 AACTCGAAT
1 AATTCGAAT
58678069 AATTCGAAT
1 AATTCGAAT
*
58678078 AATTAGAAT
1 AATTCGAAT
58678087 A
1 A
58678088 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:58680926 original size:50 final size:50
Alignment explanation
Indices: 58680859--58681156 Score: 317
Period size: 50 Copynumber: 5.8 Consensus size: 50
58680849 TTTCTTGTAC
* * * * * ** * *
58680859 TGCCAATGCCATATCCCATATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * * *
58680909 TGCCCATGCCATGTCCCAGACATGGTCTTAAAGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* *
58680959 TGCTAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGA
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
58681009 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
58681059 TGCCAACGCCATGTACCAGACATGGTCTTACATGTGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTC---ATCTC---GG
** * *
58681115 TGCCAATTCCATGTCTCAAACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
58681157 TTACCCAAAT
Statistics
Matches: 210, Mismatches: 32, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
50 169 0.80
53 5 0.02
56 36 0.17
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:58682867 original size:43 final size:43
Alignment explanation
Indices: 58682819--58683461 Score: 651
Period size: 43 Copynumber: 14.9 Consensus size: 43
58682809 CCGGTACGTA
* * *
58682819 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
** * * * *
58682862 AGTGCATCATCAAATATATCGAAGCAAATATACTAGCACACAT
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * * * * * *
58682905 AGTGCATCATCAGATGAAACTGAAACTACTATATTGGCACACAT
1 AGTGCATCATCGGAT-AAACCGAAGCAAATATACTGGCACACAC
* * * * *
58682949 AGGGCATCATTGGATCAACCGAAGAAAATATATTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
** * * *
58682992 AGTGCATCATCAAATATATCGAAGCAAATATACTAGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * * * * ** *
58683035 AGTGCATCATCAGATGAAACTGAAACTACTATTTTGGCACACAT
1 AGTGCATCATCGGAT-AAACCGAAGCAAATATACTGGCACACAC
* * *
58683079 AGTGCATCATTGGATCAACCGAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * *
58683122 AGTGCATCATCGAATGAAACCGAAGCTACTATACTGGCACACAC
1 AGTGCATCATCGGAT-AAACCGAAGCAAATATACTGGCACACAC
* * * * *
58683166 AGTGCATCATTGTATAAATCAAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * * * *
58683209 AATGCATCATCGAATATATCGAAGCAAATATACTGGCACATAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * *
58683252 AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * *
58683295 GGTGCATCATCGGATATACCGAAGCAAATATACTAG--CACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * *
58683336 AGTGCATCATCAGATATACCAAAGCAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * * *
58683379 AGTGCTTAATCAGATATACCGAAGCAAATATACTGGCACACAC
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
* * *
58683422 AATGCATCATCGGATATACCGAAGCAAATATACAGGCACA
1 AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACA
58683462 TGTAGTACAT
Statistics
Matches: 493, Mismatches: 102, Indels: 10
0.81 0.17 0.02
Matches are distributed among these distances:
41 37 0.08
43 356 0.72
44 100 0.20
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (43 bp):
AGTGCATCATCGGATAAACCGAAGCAAATATACTGGCACACAC
Found at i:58682972 original size:130 final size:128
Alignment explanation
Indices: 58682819--58683488 Score: 691
Period size: 130 Copynumber: 5.2 Consensus size: 128
58682809 CCGGTACGTA
*
58682819 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
1 AGTGCATCATTGGAT-AACCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
* * * * *
58682884 AGCAAATATACTAGCACACATAGTGCATCATCAGATGAAACTGAAACTACTATATTGGCACACAT
65 AGCAAATATACTGGCACACACAGTGCATCATCAGAT-AAACTGAAACAAATATACTGGCACACAT
* *
58682949 AGGGCATCATTGGATCAACCGAAGAAAATATATTGGCACACACAGTGCATCATCAAATATATCGA
1 AGTGCATCATTGGAT-AACCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
* * * **
58683014 AGCAAATATACTAGCACACACAGTGCATCATCAGATGAAACTGAAACTACTATTTTGGCACACAT
65 AGCAAATATACTGGCACACACAGTGCATCATCAGAT-AAACTGAAACAAATATACTGGCACACAT
* * *
58683079 AGTGCATCATTGGATCAACCGAAGAAAATATACTGGCACACACAGTGCATCATCGAATGAAACCG
1 AGTGCATCATTGGAT-AACCGAAGAAAATATACTGGCACACACAGTGCATCATCAAAT-ATATCG
* * * * *
58683144 AAGCTACTATACTGGCACACACAGTGCATCAT-TGTATAAA-TCAAAGAAAATATACTGGCACAC
64 AAGCAAATATACTGGCACACACAGTGCATCATCAG-ATAAACTGAAA-CAAATATACTGGCACAC
*
58683207 AC
127 AT
* * * * * * ** * *
58683209 AATGCATCATCGAATATATCGAAGCAAATATACTGGCACATACAGTGCATCATCGGATAAATCAA
1 AGTGCATCATTGGATA-ACCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
* * * * * * *
58683274 AGAAAATATACTGGCACACACGGTGCATCATCGGATATACCGAAGCAAATATACTAGCACAC--
65 AGCAAATATACTGGCACACACAGTGCATCATCAGATAAACTGAAACAAATATACTGGCACACAT
** * * * * * *
58683336 AGTGCATCATCAGATATACCAAAGCAAATATACTGGCACACACAGTGCTTAATCAGATATACCGA
1 AGTGCATCATTGGATA-ACCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
* * * * * * **
58683401 AGCAAATATACTGGCACACACAATGCATCATCGGATATACCGAAGCAAATATACAGGCACATGT
65 AGCAAATATACTGGCACACACAGTGCATCATCAGATAAACTGAAACAAATATACTGGCACACAT
* * *
58683465 AGTACATCGTTAGATATACCGAAG
1 AGTGCATCATTGGATA-ACCGAAG
58683489 TATAACCTAT
Statistics
Matches: 468, Mismatches: 64, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
127 109 0.23
129 76 0.16
130 248 0.53
131 35 0.07
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (128 bp):
AGTGCATCATTGGATAACCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGAA
GCAAATATACTGGCACACACAGTGCATCATCAGATAAACTGAAACAAATATACTGGCACACAT
Found at i:58683480 original size:86 final size:86
Alignment explanation
Indices: 58682819--58683488 Score: 625
Period size: 87 Copynumber: 7.8 Consensus size: 86
58682809 CCGGTACGTA
* * * * * * *
58682819 AGTGCATCATTGGATAAATCGAAGAAAATATACTGGCACACACAGTGCATCATCAAATATATCGA
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACACAGTGCATCATCAGATATACCGA
* *
58682884 AGCAAATATACTAGCACACAT
66 AGCAAATATACTGGCACACAC
* * * * * * * * **
58682905 AGTGCATCATCAGATGAAACTGAAA-CTACTATATTGGCACACATAGGGCATCATTGGATCA-AC
1 AGTGCATCATCGGAT-ATAC-CAAAGCAAATATACTGGCACACACAGTGCATCATCAGAT-ATAC
* *
58682968 CGAAGAAAATATATTGGCACACAC
63 CGAAGCAAATATACTGGCACACAC
** * * * * *
58682992 AGTGCATCATCAAATATATCGAAGCAAATATACTAGCACACACAGTGCATCATCAGATGAAACTG
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACACAGTGCATCATCAGAT-ATACCG
* * * ** *
58683057 AAACTACTATTTTGGCACACAT
65 AAGCAAATATACTGGCACACAC
* * * *
58683079 AGTGCATCATTGGATCA-ACCGAAGAAAATATACTGGCACACACAGTGCATCATC-GAATGAAAC
1 AGTGCATCATCGGAT-ATACCAAAGCAAATATACTGGCACACACAGTGCATCATCAG-AT-ATAC
* *
58683142 CGAAGCTACTATACTGGCACACAC
63 CGAAGCAAATATACTGGCACACAC
* * * * * * *
58683166 AGTGCATCATTGTATAAATCAAAGAAAATATACTGGCACACACAATGCATCATC-GAATATATCG
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACACAGTGCATCATCAG-ATATACCG
*
58683230 AAGCAAATATACTGGCACATAC
65 AAGCAAATATACTGGCACACAC
* * * * *
58683252 AGTGCATCATCGGATAAATCAAAGAAAATATACTGGCACACACGGTGCATCATCGGATATACCGA
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACACAGTGCATCATCAGATATACCGA
*
58683317 AGCAAATATACTAG--CACAC
66 AGCAAATATACTGGCACACAC
* * *
58683336 AGTGCATCATCAGATATACCAAAGCAAATATACTGGCACACACAGTGCTTAATCAGATATACCGA
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACACAGTGCATCATCAGATATACCGA
58683401 AGCAAATATACTGGCACACAC
66 AGCAAATATACTGGCACACAC
* * * *** * * *
58683422 AATGCATCATCGGATATACCGAAGCAAATATACAGGCACATGTAGTACATCGTTAGATATACCGA
1 AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACACAGTGCATCATCAGATATACCGA
58683487 AG
66 AG
58683489 TATAACCTAT
Statistics
Matches: 485, Mismatches: 88, Indels: 22
0.82 0.15 0.04
Matches are distributed among these distances:
84 74 0.15
85 2 0.00
86 198 0.41
87 207 0.43
88 4 0.01
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (86 bp):
AGTGCATCATCGGATATACCAAAGCAAATATACTGGCACACACAGTGCATCATCAGATATACCGA
AGCAAATATACTGGCACACAC
Found at i:58684407 original size:13 final size:13
Alignment explanation
Indices: 58684389--58684416 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
58684379 CTAATTGTAT
58684389 ATAGAAAAATAAC
1 ATAGAAAAATAAC
58684402 ATAGAAAAATAAC
1 ATAGAAAAATAAC
58684415 AT
1 AT
58684417 TGACAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (13 bp):
ATAGAAAAATAAC
Found at i:58685815 original size:12 final size:12
Alignment explanation
Indices: 58685778--58685820 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
58685768 AATATTAATC
58685778 AAAA-TAATTAA
1 AAAATTAATTAA
*
58685789 AAATATT-ATTTA
1 AAA-ATTAATTAA
58685801 AAAATTAATTAA
1 AAAATTAATTAA
58685813 AAAATTAA
1 AAAATTAA
58685821 ATGTGTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 6 0.22
12 20 0.74
13 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAAATTAATTAA
Found at i:58694503 original size:33 final size:33
Alignment explanation
Indices: 58694464--58694539 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
58694454 CTGCTATGAC
* * *
58694464 AGTAAACACATAATAAAGATAGTCCGCTAGGAT
1 AGTAAACACATAATAAAGATAGTCCACCAGGAG
* * *
58694497 ATTAAACACGTAATAGAGATAGTCCACCAGGAG
1 AGTAAACACATAATAAAGATAGTCCACCAGGAG
58694530 AGTAAACACA
1 AGTAAACACA
58694540 GATAAAGTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.18
Consensus pattern (33 bp):
AGTAAACACATAATAAAGATAGTCCACCAGGAG
Found at i:58694575 original size:28 final size:28
Alignment explanation
Indices: 58694544--58694613 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
58694534 AACACAGATA
* * *
58694544 AAGTTTATCGAGACAGTAAATACGGGTT
1 AAGTTTATCAAGACAGTAAACACGGGGT
*
58694572 AAGTTCT-CCAAGACAGTAAACACGGGGT
1 AAGTT-TATCAAGACAGTAAACACGGGGT
*
58694600 AAGTCTATCAAGAC
1 AAGTTTATCAAGAC
58694614 GTGAGAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 1 0.03
28 32 0.94
29 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (28 bp):
AAGTTTATCAAGACAGTAAACACGGGGT
Found at i:58709611 original size:22 final size:22
Alignment explanation
Indices: 58709580--58709627 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
58709570 TGTCTTAAGG
58709580 CAAAAACTTGCATATCTCGAGA
1 CAAAAACTTGCATATCTCGAGA
* ** *
58709602 CAAAAGCTTGTTTGTCTCGAGA
1 CAAAAACTTGCATATCTCGAGA
58709624 CAAA
1 CAAA
58709628 GTTTGCCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (22 bp):
CAAAAACTTGCATATCTCGAGA
Found at i:58721263 original size:12 final size:12
Alignment explanation
Indices: 58721231--58721264 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
58721221 AGTTGTTAAA
58721231 TTGTTAG-TAGT
1 TTGTTAGTTAGT
58721242 TTGGTTAGTTAGT
1 TT-GTTAGTTAGT
58721255 TTGTTAGTTA
1 TTGTTAGTTA
58721265 TTTAAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 13 0.62
13 6 0.29
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (12 bp):
TTGTTAGTTAGT
Found at i:58725646 original size:24 final size:25
Alignment explanation
Indices: 58725588--58725650 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
58725578 CAAGAACCAT
*
58725588 ATAACGGGAA-GCTCGTGAGAGCCAA
1 ATAAC-GGAATGCTCATGAGAGCCAA
* * *
58725613 ATATCAGAATGCTCATGAGAG-CTA
1 ATAACGGAATGCTCATGAGAGCCAA
58725637 ATAACGGAATGCTC
1 ATAACGGAATGCTC
58725651 TTTCGAGCTG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 17 0.55
25 14 0.45
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (25 bp):
ATAACGGAATGCTCATGAGAGCCAA
Found at i:58729687 original size:46 final size:46
Alignment explanation
Indices: 58729614--58729798 Score: 300
Period size: 46 Copynumber: 4.0 Consensus size: 46
58729604 ACAAGGCTAT
*
58729614 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
*
58729660 AACTCAGTATGGTTTTCTTTACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* *
58729706 AACTCAGTATGGTTTTCTTTACCAAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
**
58729752 AACTCAGTATGGTTTTCTTCATTGAAATACCATACCTA-TGTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACT-TTTCAC
58729798 A
1 A
58729799 CTTTTCCATG
Statistics
Matches: 131, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
45 1 0.01
46 130 0.99
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
Found at i:58731047 original size:17 final size:17
Alignment explanation
Indices: 58731025--58731057 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
58731015 AAATTCTTTT
58731025 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
58731042 TAAATCACAAAATTCA
1 TAAATCACAAAATTCA
58731058 CTAATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:58739864 original size:25 final size:25
Alignment explanation
Indices: 58739836--58739974 Score: 161
Period size: 25 Copynumber: 5.6 Consensus size: 25
58739826 GTAAACTTGA
* *
58739836 GAATTCTCTGGAAAGCCTTTGTGGT
1 GAATTATCTGGAAAGCCTTTGTGGC
* ** *
58739861 GAATTCTCTAAAAAGCTTTTGTGGC
1 GAATTATCTGGAAAGCCTTTGTGGC
* * *
58739886 GTATCATTTGGAAAGCCTTTGTGGC
1 GAATTATCTGGAAAGCCTTTGTGGC
* *
58739911 GAATTATTTGGAAAGCCCTTGTGGC
1 GAATTATCTGGAAAGCCTTTGTGGC
* *
58739936 GTATTATTTGGAAAGCCTTTGTGGC
1 GAATTATCTGGAAAGCCTTTGTGGC
58739961 GAATTATCTGGAAA
1 GAATTATCTGGAAA
58739975 TTCATTATGG
Statistics
Matches: 96, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 96 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.35
Consensus pattern (25 bp):
GAATTATCTGGAAAGCCTTTGTGGC
Found at i:58739926 original size:50 final size:50
Alignment explanation
Indices: 58739844--58739974 Score: 190
Period size: 50 Copynumber: 2.6 Consensus size: 50
58739834 GAGAATTCTC
* * ** **
58739844 TGGAAAGCCTTTGTGGTGAATTCTCTAAAAAGCTTTTGTGGCGTATCATT
1 TGGAAAGCCTTTGTGGCGAATTATCTGGAAAGCCCTTGTGGCGTATCATT
* *
58739894 TGGAAAGCCTTTGTGGCGAATTATTTGGAAAGCCCTTGTGGCGTATTATT
1 TGGAAAGCCTTTGTGGCGAATTATCTGGAAAGCCCTTGTGGCGTATCATT
58739944 TGGAAAGCCTTTGTGGCGAATTATCTGGAAA
1 TGGAAAGCCTTTGTGGCGAATTATCTGGAAA
58739975 TTCATTATGG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (50 bp):
TGGAAAGCCTTTGTGGCGAATTATCTGGAAAGCCCTTGTGGCGTATCATT
Found at i:58748379 original size:42 final size:42
Alignment explanation
Indices: 58748332--58748443 Score: 188
Period size: 42 Copynumber: 2.6 Consensus size: 42
58748322 AACTACCTCC
58748332 ATTGCATCATAGAATAAATTCTGACATCTCCATTATCTCTTA
1 ATTGCATCATAGAATAAATTCTGACATCTCCATTATCTCTTA
58748374 ATTGCATCATAGAATAAATTCTGACATCTCCATTATCTCTTA
1 ATTGCATCATAGAATAAATTCTGACATCTCCATTATCTCTTA
* * *
58748416 ATTGCATTATATAAATAAATTTTGACAT
1 ATTGCATCATA-GAATAAATTCTGACAT
58748444 GAAAATTCTT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
42 52 0.79
43 14 0.21
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (42 bp):
ATTGCATCATAGAATAAATTCTGACATCTCCATTATCTCTTA
Found at i:58750091 original size:16 final size:16
Alignment explanation
Indices: 58750065--58750102 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
58750055 GTTTTTTATT
58750065 TTTTGGATTTAGGGTCA
1 TTTT-GATTTAGGGTCA
*
58750082 TTTTGATTTAGGGTTA
1 TTTTGATTTAGGGTCA
58750098 TTTTG
1 TTTTG
58750103 GGTTATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.16, C:0.03, G:0.26, T:0.55
Consensus pattern (16 bp):
TTTTGATTTAGGGTCA
Found at i:58750122 original size:6 final size:6
Alignment explanation
Indices: 58750107--58750141 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
58750097 ATTTTGGGTT
*
58750107 ATTTTG ATTTTA ATTTTG ATTTTG ATTTTGG ATTT
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTT-G ATTT
58750142 AGGGTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (6 bp):
ATTTTG
Found at i:58752408 original size:77 final size:77
Alignment explanation
Indices: 58752322--58752495 Score: 240
Period size: 77 Copynumber: 2.3 Consensus size: 77
58752312 TTAGTGAGTG
* * * *
58752322 TTTTTTAATATGCATGCAGTTTTTTTTAATTTATCTGTGTATGATTGTTGGTGGGGTTGGTCGCA
1 TTTTTTAATATGCATGCAGTGTTTTTTAATTTATCTGTGTATGATTGTTGGTGGGGATAGTCACA
58752387 TGCTATTGACTA
66 TGCTATTGACTA
* * * * *
58752399 TTTTTTAATATACATGTAGTGTTTTTTAATTTGTCTGTGTATGATTGTTGGTGGGGATAGTTATA
1 TTTTTTAATATGCATGCAGTGTTTTTTAATTTATCTGTGTATGATTGTTGGTGGGGATAGTCACA
* *
58752464 TGTTGTTGACTA
66 TGCTATTGACTA
*
58752476 TTTTTTAATATGCATACAGT
1 TTTTTTAATATGCATGCAGT
58752496 AACGTTTTTT
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
77 83 1.00
ACGTcount: A:0.21, C:0.07, G:0.22, T:0.51
Consensus pattern (77 bp):
TTTTTTAATATGCATGCAGTGTTTTTTAATTTATCTGTGTATGATTGTTGGTGGGGATAGTCACA
TGCTATTGACTA
Found at i:58753266 original size:21 final size:21
Alignment explanation
Indices: 58753182--58753272 Score: 96
Period size: 21 Copynumber: 4.3 Consensus size: 21
58753172 GTGGTTGCCT
*
58753182 CAACTCAACAACAG-GCTACCC
1 CAACTCAACAAGAGAG-TACCC
* **
58753203 CAAATCAGTAAGAGAGTACCC
1 CAACTCAACAAGAGAGTACCC
*
58753224 CAACTCAGCAAGAGAGTACCC
1 CAACTCAACAAGAGAGTACCC
*
58753245 CAACTCAACAAGAG-GCTGCCC
1 CAACTCAACAAGAGAG-TACCC
58753266 CAACTCA
1 CAACTCA
58753273 GTTACAAACT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 1 0.02
21 58 0.97
22 1 0.02
ACGTcount: A:0.38, C:0.35, G:0.15, T:0.11
Consensus pattern (21 bp):
CAACTCAACAAGAGAGTACCC
Found at i:58754091 original size:36 final size:36
Alignment explanation
Indices: 58754051--58754253 Score: 113
Period size: 36 Copynumber: 5.2 Consensus size: 36
58754041 CATGTATAAC
58754051 AACATAAGCAACAATATACCAACAACAATATTACAA
1 AACATAAGCAACAATATACCAACAACAATATTACAA
** * * * * *
58754087 AACATAAGCGGGTTCTCCATGTATACCAACAGCCATGTATA-AC
1 AACATAA----G--CAACA-ATATACCAACAACAATAT-TACAA
58754130 AACATAAGCAACAATATACCAACAACAATATTACAA
1 AACATAAGCAACAATATACCAACAACAATATTACAA
* * * * * *
58754166 AACATAAGCTGGTTAGCCATGTATACCAACAGCCATGTATA-AT
1 AACATAAGC-----A-ACA-ATATACCAACAACAATAT-TACAA
* *
58754209 AACATAAGAAACAATATACCAGCAACAATATTACAA
1 AACATAAGCAACAATATACCAACAACAATATTACAA
58754245 AACATAAGC
1 AACATAAGC
58754254 TAGTTTTCAG
Statistics
Matches: 120, Mismatches: 29, Indels: 36
0.65 0.16 0.19
Matches are distributed among these distances:
35 4 0.03
36 53 0.44
37 5 0.04
38 1 0.01
39 1 0.01
40 1 0.01
41 1 0.01
42 5 0.04
43 45 0.38
44 4 0.03
ACGTcount: A:0.49, C:0.22, G:0.09, T:0.20
Consensus pattern (36 bp):
AACATAAGCAACAATATACCAACAACAATATTACAA
Found at i:58754124 original size:16 final size:16
Alignment explanation
Indices: 58754103--58754133 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58754093 AGCGGGTTCT
*
58754103 CCATGTATACCAACAG
1 CCATGTATAACAACAG
58754119 CCATGTATAACAACA
1 CCATGTATAACAACA
58754134 TAAGCAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (16 bp):
CCATGTATAACAACAG
Found at i:58754254 original size:79 final size:79
Alignment explanation
Indices: 58754008--58754254 Score: 422
Period size: 79 Copynumber: 3.1 Consensus size: 79
58753998 TGTAAGCAAC
* *
58754008 AACATAAGCTAGTTAGCCATGTATACCAGCAGCCATGTATAACAACATAAGCAACAATATACCAA
1 AACATAAGCTGGTTAGCCATGTATACCAACAGCCATGTATAACAACATAAGCAACAATATACCAA
58754073 CAACAATATTACAA
66 CAACAATATTACAA
* **
58754087 AACATAAGCGGGTTCTCCATGTATACCAACAGCCATGTATAACAACATAAGCAACAATATACCAA
1 AACATAAGCTGGTTAGCCATGTATACCAACAGCCATGTATAACAACATAAGCAACAATATACCAA
58754152 CAACAATATTACAA
66 CAACAATATTACAA
* * *
58754166 AACATAAGCTGGTTAGCCATGTATACCAACAGCCATGTATAATAACATAAGAAACAATATACCAG
1 AACATAAGCTGGTTAGCCATGTATACCAACAGCCATGTATAACAACATAAGCAACAATATACCAA
58754231 CAACAATATTACAA
66 CAACAATATTACAA
58754245 AACATAAGCT
1 AACATAAGCT
58754255 AGTTTTCAGT
Statistics
Matches: 157, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 157 1.00
ACGTcount: A:0.47, C:0.22, G:0.11, T:0.21
Consensus pattern (79 bp):
AACATAAGCTGGTTAGCCATGTATACCAACAGCCATGTATAACAACATAAGCAACAATATACCAA
CAACAATATTACAA
Found at i:58755859 original size:25 final size:25
Alignment explanation
Indices: 58755821--58755909 Score: 62
Period size: 25 Copynumber: 3.6 Consensus size: 25
58755811 AATAACGGGT
*
58755821 AGCTCCGAAGAGCC-TTTAATCGAGA
1 AGCTCCGAAGAGCCATAT-ATCGAGA
* *
58755846 AGCTCCGGATAGCCATATATCGAGA
1 AGCTCCGAAGAGCCATATATCGAGA
* *
58755871 AG-TTC-AAGCGAGCCATAT-TAG-GA
1 AGCTCCGAA--GAGCCATATATCGAGA
*
58755894 AGCTCCGGAGAGCCAT
1 AGCTCCGAAGAGCCAT
58755910 TAATGGGAAG
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
23 12 0.24
24 6 0.12
25 30 0.60
26 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATATATCGAGA
Found at i:58755906 original size:23 final size:23
Alignment explanation
Indices: 58755844--58755932 Score: 61
Period size: 25 Copynumber: 3.7 Consensus size: 23
58755834 CTTTAATCGA
* * *
58755844 GAAGCTCCGGATAGCCATATATCG
1 GAAGCTCCAGAGAGCCATAT-TAG
* * *
58755868 AGAAGTTCAAGCGAGCCATATTAG
1 -GAAGCTCCAGAGAGCCATATTAG
* * *
58755892 GAAGCTCCGGAGAGCCATTAATGG
1 GAAGCTCCAGAGAGCCA-TATTAG
58755916 GAAGCTCACAGAGAGCC
1 GAAGCTC-CAGAGAGCC
58755933 TTTAATTGGG
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
23 13 0.27
24 13 0.27
25 23 0.47
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (23 bp):
GAAGCTCCAGAGAGCCATATTAG
Found at i:58755937 original size:25 final size:25
Alignment explanation
Indices: 58755891--58755944 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
58755881 AGCCATATTA
*
58755891 GGAAGCTCCGGAGAGCCATTAA-TG
1 GGAAGCTCCAGAGAGCCATTAATTG
*
58755915 GGAAGCTCACAGAGAGCCTTTAATTG
1 GGAAGCTC-CAGAGAGCCATTAATTG
58755941 GGAA
1 GGAA
58755945 ACTTACGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 8 0.31
25 12 0.46
26 6 0.23
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.19
Consensus pattern (25 bp):
GGAAGCTCCAGAGAGCCATTAATTG
Found at i:58755956 original size:26 final size:25
Alignment explanation
Indices: 58755901--58755960 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
58755891 GGAAGCTCCG
*
58755901 GAGAGCCATTAATGGGAAGCTCACA
1 GAGAGCCATTAATGGGAAACTCACA
* *
58755926 GAGAGCCTTTAATTGGGAAACTTAC-
1 GAGAGCCATTAA-TGGGAAACTCACA
58755951 GAAGAGCCAT
1 G-AGAGCCAT
58755961 ATAACGGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (25 bp):
GAGAGCCATTAATGGGAAACTCACA
Done.