Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 46 of 54
Found at i:18291318 original size:20 final size:20
Alignment explanation
Indices: 18291293--18291355 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
18291283 GGGAGTGCGC
18291293 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
18291313 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
18291333 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
18291352 ATGA
1 ATGA
18291356 TGGGTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:18292533 original size:54 final size:54
Alignment explanation
Indices: 18292467--18292837 Score: 526
Period size: 54 Copynumber: 6.9 Consensus size: 54
18292457 TGATACTATT
* * ** *
18292467 CGGCTATGTGCACAAAGTGAAGGGATGCACATGAGCTGGGTGAGTTGGGATGTC
1 CGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTC
* *
18292521 CAGCTATGTGCACTATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTC
1 CGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTC
* *
18292575 TGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGTTGGGATGTC
1 CGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTC
** * *
18292629 TAGCTATGTGCACGATGTGGTGGGATGCACATGACCTGGGTGAGATGGGATGCC
1 CGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTC
* * * *
18292683 CGGCTATCTGCACGATGTGGTGGGATGCACATGACCTGGGTGAGTTAGGATGTC
1 CGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTC
* * *
18292737 CGGCTATGTGCACCATGTGGTGGGATGCACATGAGCTAGGTGAGATGGGATGTT
1 CGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTC
* * * *
18292791 CTGCTATGTGCATGATGTGGTGGGATGCACATAAGCTGGTTGAGATG
1 CGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATG
18292838 CACATGATGA
Statistics
Matches: 284, Mismatches: 33, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 284 1.00
ACGTcount: A:0.20, C:0.15, G:0.39, T:0.26
Consensus pattern (54 bp):
CGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTC
Found at i:18297724 original size:12 final size:12
Alignment explanation
Indices: 18297707--18297731 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18297697 TTCGAATCAT
18297707 AAATCACTTATC
1 AAATCACTTATC
18297719 AAATCACTTATC
1 AAATCACTTATC
18297731 A
1 A
18297732 TTTTCTAGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATCACTTATC
Found at i:18300953 original size:43 final size:43
Alignment explanation
Indices: 18300883--18301001 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
18300873 GTAATTATGT
* *
18300883 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
18300926 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
18300969 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
18301002 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:18301011 original size:43 final size:43
Alignment explanation
Indices: 18300893--18301014 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
18300883 TGACTCGGCT
* **
18300893 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
18300936 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
18300979 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
18301015 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:18301025 original size:20 final size:20
Alignment explanation
Indices: 18301000--18301062 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
18300990 GGGAGTGCGC
18301000 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
18301020 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
18301040 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
18301059 ATGA
1 ATGA
18301063 TGGGTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:18310635 original size:38 final size:37
Alignment explanation
Indices: 18310592--18310697 Score: 124
Period size: 38 Copynumber: 2.8 Consensus size: 37
18310582 ATAGTGCCCG
18310592 TGTGCACGATGTGGGGGGATGTACATGATGGC-ACTGA
1 TGTGCACGATGTGGGGGGATGTACATGATGGCGACT-A
* * * *
18310629 TTGTGCAAGATGTGGGGGGATGCACGCGATGGTGTCGACTA
1 -TGTGCACGATGTGGGGGGATGTA--C-ATGATGGCGACTA
18310670 TGTGCACGATGTGGGGGGATGTACATGA
1 TGTGCACGATGTGGGGGGATGTACATGA
18310698 GCCAGGTGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
37 3 0.05
38 22 0.39
40 22 0.39
41 7 0.12
42 3 0.05
ACGTcount: A:0.21, C:0.13, G:0.42, T:0.25
Consensus pattern (37 bp):
TGTGCACGATGTGGGGGGATGTACATGATGGCGACTA
Found at i:18314827 original size:43 final size:42
Alignment explanation
Indices: 18314763--18314882 Score: 161
Period size: 43 Copynumber: 2.8 Consensus size: 42
18314753 ACTCGGCTAA
**
18314763 GTGCGAGTAGGGAGTGTGCATAAGCTGAG-GATGACCCAGTTAT
1 GTGCGAGTAGGGAGTGTGCAT-AGCTG-GTGATGACCCAGCCAT
* *
18314806 GTGCGAATAGGGAGTGCGCATAGCTCGGTGATGACCCAGCCAT
1 GTGCGAGTAGGGAGTGTGCATAGCT-GGTGATGACCCAGCCAT
18314849 GTGCGAGTAGGGAGTGTGCATGAGCTGGTGATGA
1 GTGCGAGTAGGGAGTGTGCAT-AGCTGGTGATGA
18314883 TGATGATGGG
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
42 5 0.07
43 59 0.87
44 4 0.06
ACGTcount: A:0.23, C:0.16, G:0.39, T:0.22
Consensus pattern (42 bp):
GTGCGAGTAGGGAGTGTGCATAGCTGGTGATGACCCAGCCAT
Found at i:18314905 original size:8 final size:8
Alignment explanation
Indices: 18314892--18314925 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
18314882 ATGATGATGG
18314892 GTATATAT
1 GTATATAT
18314900 GTATATAT
1 GTATATAT
*
18314908 ATATATAT
1 GTATATAT
*
18314916 GTAAATAT
1 GTATATAT
18314924 GT
1 GT
18314926 GTGTTATAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (8 bp):
GTATATAT
Found at i:18315328 original size:60 final size:61
Alignment explanation
Indices: 18315211--18315361 Score: 180
Period size: 60 Copynumber: 2.5 Consensus size: 61
18315201 ACACTGTAGC
* * * * *
18315211 ATCTCACTGCAGTGAGAAACTTTCTATTTTCTGGGTTGCAATTTTGCTGCAGCGAGATTCA
1 ATCTCGCTGCAGTGAGAAACATTCTGTTTTCTGGGTTGAAATTTCGCTGCAGCGAGATTCA
* * *
18315272 ATCTCGCTGTAGTGAGAAACATTCTGTTTT-TGGGTTGAAATTTCGCT-CTAGTGAGATTGA
1 ATCTCGCTGCAGTGAGAAACATTCTGTTTTCTGGGTTGAAATTTCGCTGC-AGCGAGATTCA
* * *
18315332 ATCTCGTTGCAGTGAAAAACCTTCTGTTTT
1 ATCTCGCTGCAGTGAGAAACATTCTGTTTT
18315362 AGTCTCCTAT
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.01
60 50 0.65
61 26 0.34
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (61 bp):
ATCTCGCTGCAGTGAGAAACATTCTGTTTTCTGGGTTGAAATTTCGCTGCAGCGAGATTCA
Found at i:18317171 original size:31 final size:31
Alignment explanation
Indices: 18317136--18317198 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
18317126 TGCTTAAGAA
18317136 AGAGAGATCTCAAGTTTAATTTAAAAATCTT
1 AGAGAGATCTCAAGTTTAATTTAAAAATCTT
18317167 AGAGAGATCTCAAGTTTAATTTAAAAATCTT
1 AGAGAGATCTCAAGTTTAATTTAAAAATCTT
18317198 A
1 A
18317199 CCTTTTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (31 bp):
AGAGAGATCTCAAGTTTAATTTAAAAATCTT
Found at i:18317227 original size:21 final size:20
Alignment explanation
Indices: 18317203--18317250 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
18317193 ATCTTACCTT
* *
18317203 TTTTTCACTTGTTTCCTTGAA
1 TTTTTCACTT-TTCCCTTAAA
*
18317224 TTTTCACACTTTTCCCTTAAA
1 TTTT-TCACTTTTCCCTTAAA
18317245 TTTTTC
1 TTTTTC
18317251 CACCTACGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.17, C:0.23, G:0.04, T:0.56
Consensus pattern (20 bp):
TTTTTCACTTTTCCCTTAAA
Found at i:18317295 original size:11 final size:11
Alignment explanation
Indices: 18317261--18317307 Score: 69
Period size: 11 Copynumber: 4.4 Consensus size: 11
18317251 CACCTACGGT
18317261 TTTGTTCTTCC
1 TTTGTTCTTCC
*
18317272 CTT-TTCTTCC
1 TTTGTTCTTCC
*
18317282 TTTGTTCTTAC
1 TTTGTTCTTCC
18317293 TTTGTTCTTCC
1 TTTGTTCTTCC
18317304 TTTG
1 TTTG
18317308 GCTGGCCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 9 0.29
11 22 0.71
ACGTcount: A:0.02, C:0.26, G:0.09, T:0.64
Consensus pattern (11 bp):
TTTGTTCTTCC
Found at i:18317303 original size:22 final size:21
Alignment explanation
Indices: 18317261--18317307 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
18317251 CACCTACGGT
*
18317261 TTTGTTCTTCCCTTTTCTTCC
1 TTTGTTCTTACCTTTTCTTCC
*
18317282 TTTGTTCTTACTTTGTTCTTCC
1 TTTGTTCTTACCTT-TTCTTCC
18317304 TTTG
1 TTTG
18317308 GCTGGCCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.02, C:0.26, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTGTTCTTACCTTTTCTTCC
Found at i:18339013 original size:37 final size:37
Alignment explanation
Indices: 18338943--18339015 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
18338933 TACCACCATA
** *
18338943 TGTGCACTCCCTACTCACACATTTCAATGTCATCATG
1 TGTGCACTCCCTACTCACACACCTCAATATCATCATG
* *
18338980 TGTGCACTCCCTACTCGCACACCTCATTATCATCAT
1 TGTGCACTCCCTACTCACACACCTCAATATCATCAT
18339016 ACAACATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.23, C:0.36, G:0.10, T:0.32
Consensus pattern (37 bp):
TGTGCACTCCCTACTCACACACCTCAATATCATCATG
Found at i:18345860 original size:40 final size:40
Alignment explanation
Indices: 18345786--18346009 Score: 232
Period size: 43 Copynumber: 5.4 Consensus size: 40
18345776 TGTGATAATT
*
18345786 ATGACCTAGCCATGTGTGGTGTAGGAGTGCACATGAGCTGATG
1 ATGACCCAGCCATGTGT-G-G-AGGAGTGCACATGAGCTGATG
* * *
18345829 ATGATCCAGCCATGTGTGGAGGAGTACACATGAGCTAATG
1 ATGACCCAGCCATGTGTGGAGGAGTGCACATGAGCTGATG
* * *
18345869 ATGACCCAGCTATGTGCGAGTAGGGAGTGCACATGAGATGATG
1 ATGACCCAGCCATGTGTG-G-A-GGAGTGCACATGAGCTGATG
* *
18345912 ATGACCCAGCCATGTGTGGAGAAGTACACATGAGCTGATG
1 ATGACCCAGCCATGTGTGGAGGAGTGCACATGAGCTGATG
* * * *
18345952 ATGACCCAACTATGTAAGAGTATGGAGTGCACATGAGCTGATG
1 ATGACCCAGCCATGT--GTGGA-GGAGTGCACATGAGCTGATG
* *
18345995 ATGACCTAGCTATGT
1 ATGACCCAGCCATGT
18346010 CGGTGTGGGA
Statistics
Matches: 152, Mismatches: 23, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
40 64 0.42
41 3 0.02
42 6 0.04
43 79 0.52
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (40 bp):
ATGACCCAGCCATGTGTGGAGGAGTGCACATGAGCTGATG
Found at i:18345896 original size:83 final size:83
Alignment explanation
Indices: 18345809--18346009 Score: 312
Period size: 83 Copynumber: 2.4 Consensus size: 83
18345799 GTGTGGTGTA
* *
18345809 GGAGTGCACATGAGCTGATGATGATCCAGCCATGTGTGGAGGAGTACACATGAGCTAATGATGAC
1 GGAGTGCACATGAGCTGATGATGACCCAGCCATGTGTGGAGAAGTACACATGAGCTAATGATGAC
* **
18345874 CCAGCTATGTGCGAGTAG
66 CCAACTATGTAAGAGTAG
* *
18345892 GGAGTGCACATGAGATGATGATGACCCAGCCATGTGTGGAGAAGTACACATGAGCTGATGATGAC
1 GGAGTGCACATGAGCTGATGATGACCCAGCCATGTGTGGAGAAGTACACATGAGCTAATGATGAC
*
18345957 CCAACTATGTAAGAGTAT
66 CCAACTATGTAAGAGTAG
* *
18345975 GGAGTGCACATGAGCTGATGATGACCTAGCTATGT
1 GGAGTGCACATGAGCTGATGATGACCCAGCCATGT
18346010 CGGTGTGGGA
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 107 1.00
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.22
Consensus pattern (83 bp):
GGAGTGCACATGAGCTGATGATGACCCAGCCATGTGTGGAGAAGTACACATGAGCTAATGATGAC
CCAACTATGTAAGAGTAG
Found at i:18349587 original size:41 final size:38
Alignment explanation
Indices: 18349504--18349578 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
18349494 GAGTGTGGAT
* *
18349504 GATGATATTGCTTGTGCATGATGTGGGGGGATGCACAC
1 GATGATATTGCTTGTGCACGATGTGGGAGGATGCACAC
18349542 GATGATATTGCTTGTGCACGATGTGGGAGGATGCACA
1 GATGATATTGCTTGTGCACGATGTGGGAGGATGCACA
18349579 TGCCGATGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.28
Consensus pattern (38 bp):
GATGATATTGCTTGTGCACGATGTGGGAGGATGCACAC
Found at i:18352161 original size:18 final size:18
Alignment explanation
Indices: 18352138--18352181 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
18352128 AGCCATTCAT
*
18352138 GCCATCACATTGTCATAA
1 GCCATCAAATTGTCATAA
18352156 GCCATCAAATTGTCATAA
1 GCCATCAAATTGTCATAA
18352174 GCCATCAA
1 GCCATCAA
18352182 TTCCAACCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.25
Consensus pattern (18 bp):
GCCATCAAATTGTCATAA
Found at i:18359770 original size:42 final size:43
Alignment explanation
Indices: 18359707--18359825 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
18359697 TGTTGATGTG
* * *
18359707 GACCCGGCTATGTGCGAGTA-GGAGTGAACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGGAGTGCACATAAGCCGATGAT
* *
18359749 GACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGAT
1 GACCCGGCTATGTGCGAGTAGGGAGTGCACATAAGCCGATGAT
**
18359792 GACCCGATTATGTGCGAGTAGGGAGTGCACATAA
1 GACCCGGCTATGTGCGAGTAGGGAGTGCACATAA
18359826 CTTGGTGATG
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 19 0.28
43 48 0.72
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.21
Consensus pattern (43 bp):
GACCCGGCTATGTGCGAGTAGGGAGTGCACATAAGCCGATGAT
Found at i:18359804 original size:43 final size:43
Alignment explanation
Indices: 18359707--18359892 Score: 160
Period size: 43 Copynumber: 4.1 Consensus size: 43
18359697 TGTTGATGTG
* * * *
18359707 GACCCGGCTATGTGCGAGTA-GGAGTGAACATAAGCCGTTGCT
1 GACCCGGTTATGTGCGAGTAGGGAGTGCACATAAGCCGATGAT
* * *
18359749 GACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGAT
1 GACCCGGTTATGTGCGAGTAGGGAGTGCACATAAGCCGATGAT
*
18359792 GACCCGATTATGTGCGAGTAGGGAGTGCACATAACTTGGTGATGACCCGATGAT
1 GACCCGGTTATGTGCGAGTAGGGAGTGCACAT-A-------A-G--CCGATGAT
* *
18359846 GACCCGGTTATGTGCGAGTAGGGAGTGCGCATAA-CCCAGTGAT
1 GACCCGGTTATGTGCGAGTAGGGAGTGCACATAAGCCGA-TGAT
18359889 GACC
1 GACC
18359893 TAGCCATGTG
Statistics
Matches: 119, Mismatches: 12, Indels: 25
0.76 0.08 0.16
Matches are distributed among these distances:
42 22 0.18
43 54 0.45
44 1 0.01
46 1 0.01
51 1 0.01
52 1 0.01
53 1 0.01
54 38 0.32
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (43 bp):
GACCCGGTTATGTGCGAGTAGGGAGTGCACATAAGCCGATGAT
Found at i:18359888 original size:54 final size:54
Alignment explanation
Indices: 18359784--18359892 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
18359774 TGCGCATAAG
***
18359784 CCGATGATGACCCGATTATGTGCGAGTAGGGAGTGCACATAACTTGGTGATGAC
1 CCGATGATGACCCGATTATGTGCGAGTAGGGAGTGCACATAACCCAGTGATGAC
* *
18359838 CCGATGATGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCAGTGATGAC
1 CCGATGATGACCCGATTATGTGCGAGTAGGGAGTGCACATAACCCAGTGATGAC
18359892 C
1 C
18359893 TAGCCATGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.22
Consensus pattern (54 bp):
CCGATGATGACCCGATTATGTGCGAGTAGGGAGTGCACATAACCCAGTGATGAC
Found at i:18362454 original size:27 final size:27
Alignment explanation
Indices: 18362403--18362454 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
18362393 ATGTCTTGAT
*
18362403 GGTGGAAAATTACAATTTTGCCCCTGG
1 GGTGGAAAATTACAATTTTGACCCTGG
*
18362430 GGTGGCAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
18362455 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTGG
Found at i:18362525 original size:20 final size:20
Alignment explanation
Indices: 18362500--18362545 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
18362490 CTTCTAAACC
18362500 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
18362520 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
18362540 TCAAAT
1 TCAAAT
18362546 GGGGTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:18370337 original size:27 final size:27
Alignment explanation
Indices: 18370286--18370337 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
18370276 ATGTCTTGAT
*
18370286 GGTGGAAAATTACAATTTTGCCCCTAG
1 GGTGGAAAATTACAATTTTGACCCTAG
*
18370313 GGTGGCAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
18370338 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTAG
Found at i:18370408 original size:20 final size:20
Alignment explanation
Indices: 18370383--18370428 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
18370373 CTTCTAAACC
18370383 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
18370403 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
18370423 TCAAAT
1 TCAAAT
18370429 GGGTCAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:18371013 original size:26 final size:26
Alignment explanation
Indices: 18370991--18371063 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
18370981 CTTTGATAGA
*
18370991 ATGGTGTGTATGATGATGATGATGGG
1 ATGGTGTGCATGATGATGATGATGGG
18371017 ATGGTGTGCATGATGATGATGATGGG
1 ATGGTGTGCATGATGATGATGATGGG
18371043 ATGGTGTGCATGATGATGATG
1 ATGGTGTGCATGATGATGATG
18371064 GGCATATGGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.23, C:0.03, G:0.41, T:0.33
Consensus pattern (26 bp):
ATGGTGTGCATGATGATGATGATGGG
Found at i:18372424 original size:38 final size:39
Alignment explanation
Indices: 18372373--18372475 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 39
18372363 ATGTTGTGCG
*
18372373 TGTGCACGATGTGGGGGGATGCACA-A-AATGGCA-CTAA
1 TGTGCACGATGTGGGGGGATGCACACATAATGCCAGCT-A
* * *
18372410 CTGTGCACGATGTGGGAGGATGCACACGATGATTCCAGCTA
1 -TGTGCACGATGTGGGGGGATGCACAC-ATAATGCCAGCTA
18372451 TGTGCACGATGTGGGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
18372476 TAAGCTGGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 24 0.43
40 25 0.45
41 5 0.09
42 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.20
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGGATGCACACATAATGCCAGCTA
Found at i:18382121 original size:43 final size:43
Alignment explanation
Indices: 18382072--18382195 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
18382062 ATTGACTCGA
*
18382072 CTATGTGCTAGTAGGGAGTGCGCATAAGCCGATGATGACCTGG
1 CTATGTGCTAGTAGGGAGTGCGCATAAGCCGATGATGACCTAG
* * * *
18382115 TTATGTGCGAGTAGGGAATGCGCATAAACCGATGATGACCTAG
1 CTATGTGCTAGTAGGGAGTGCGCATAAGCCGATGATGACCTAG
* * *
18382158 CCATGTG-TGAGTAGGGAGTG-GACATGAGCTGATGATGA
1 CTATGTGCT-AGTAGGGAGTGCG-CATAAGCCGATGATGA
18382196 TGGGATGGTG
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.01
43 66 0.99
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.23
Consensus pattern (43 bp):
CTATGTGCTAGTAGGGAGTGCGCATAAGCCGATGATGACCTAG
Found at i:18382506 original size:21 final size:21
Alignment explanation
Indices: 18382482--18382532 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
18382472 AGAAAACTCA
18382482 CTGCAGCGAAAATAAATCTCG
1 CTGCAGCGAAAATAAATCTCG
18382503 CTGCAGCGAAAATAAATCTCG
1 CTGCAGCGAAAATAAATCTCG
18382524 CTGCAGCGA
1 CTGCAGCGA
18382533 GAAACTCTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (21 bp):
CTGCAGCGAAAATAAATCTCG
Found at i:18397335 original size:11 final size:11
Alignment explanation
Indices: 18397316--18397361 Score: 76
Period size: 11 Copynumber: 4.3 Consensus size: 11
18397306 ATGGCCGACA
18397316 AAAGGAAGAAC
1 AAAGGAAGAAC
*
18397327 AAAGCAAGAAC
1 AAAGGAAGAAC
18397338 AAAGGAAGAA-
1 AAAGGAAGAAC
18397348 AAAGGAAGAAC
1 AAAGGAAGAAC
18397359 AAA
1 AAA
18397362 ACCCTAGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 10 0.31
11 22 0.69
ACGTcount: A:0.67, C:0.09, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAGGAAGAAC
Found at i:18397356 original size:21 final size:22
Alignment explanation
Indices: 18397316--18397361 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
18397306 ATGGCCGACA
18397316 AAAGGAAGAACAAAGCAAGAAC
1 AAAGGAAGAACAAAGCAAGAAC
*
18397338 AAAGGAAGAA-AAAGGAAGAAC
1 AAAGGAAGAACAAAGCAAGAAC
18397359 AAA
1 AAA
18397362 ACCCTAGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.67, C:0.09, G:0.24, T:0.00
Consensus pattern (22 bp):
AAAGGAAGAACAAAGCAAGAAC
Found at i:18399676 original size:463 final size:462
Alignment explanation
Indices: 18398801--18399723 Score: 1612
Period size: 463 Copynumber: 2.0 Consensus size: 462
18398791 TTGGGATATT
* * *
18398801 CCTCAATCAAGGTATCCCTGATAACTGGGTATGAGAATGATTTTGGTACGAGCCAAAGTTTTAAG
1 CCTCAATCAAGGTATCCCTGATAACTGGGTATGAGAATAATTTTGGCAAGAGCCAAAGTTTTAAG
* *
18398866 AAATTCATAAGCCATGTTGATTACTCGATTTATATGAATTGATTTTATTTGGTTGAAGCAAGTTG
66 AAATTCATAAGCCATGTTGATTACTCGATTTATATGAATTGATTTTATTTGGTTGAAACAAGTGG
18398931 AAAGGTGATGAATTACAGTATGTTAAACTATTTTATCTATCTCCATTTACTCAACTTTAGATATT
131 AAAGGTGATGAATTACAGTATGTTAAACTATTTTATCTATCTCCATTTACTCAACTTTAGATATT
* *
18398996 TTAGATGGTATTTGTTTACTCACTGGGATTATATAATCTCATCACCCTCATTTCCACGAATTTCA
196 TTAGATGGTATTTGTTTACTCACTGGGATTATATAATCTCACCACCCTCATTTCCACCAATTTCA
* * *
18399061 GGCTCAGAATAGGCTGTAGATAGCTGATTTCATTGAGGCTACCATTGGATTTGCATCCTCCAAAT
261 GGCTCAGAATAGGCTATAGATAGCTGATTTCATCGAGGCTACCATTGGATTTGCATCCTCCAAAA
* * **
18399126 TGTAGGTTCACAATCTTCCTTACTTTTAGTTATTTGGGGGCCCACTGGTTATTGTAAATTAAATT
326 TGTAAGTTCACAATCTTCCTTACTTTAAGTTATTCCGGGGCCCACTGGTTATTGTAAATTAAATT
* * *
18399191 AAATACTCTGGTTTACTGTATTACAATATGTATGAATTTATTTTGCTTTTACATTGCTATAAAAA
391 AAATACTCTGGCTTACTGTATTACAATATGTATGAATTTATTTTGCTTTTACACTGCTACAAAAA
18399256 AATTANGC
456 AATTA-GC
*
18399264 CCTCGATCAAGGTATCCCTGATAACTGGGTATGAGAATAATTTTGGCAAGAGCCAAAGTTTTAAG
1 CCTCAATCAAGGTATCCCTGATAACTGGGTATGAGAATAATTTTGGCAAGAGCCAAAGTTTTAAG
18399329 AAATTCATAAGCCATGTTGATTACTCGATTTATATGAATTGATTTTATTTGGTTGAAACAAGTGG
66 AAATTCATAAGCCATGTTGATTACTCGATTTATATGAATTGATTTTATTTGGTTGAAACAAGTGG
* *
18399394 AAATGTGATGAATTACAGTATGTTAAACTATTTTATCTGTCTCCATTTACTCAACTTTAGATATT
131 AAAGGTGATGAATTACAGTATGTTAAACTATTTTATCTATCTCCATTTACTCAACTTTAGATATT
* *
18399459 TTAGATGGTATTTGTTTACTCACTGGGATTATATAATCTCACCACCCTCCTTTCCACCCATTTCA
196 TTAGATGGTATTTGTTTACTCACTGGGATTATATAATCTCACCACCCTCATTTCCACCAATTTCA
*
18399524 GGCTCAGAATAGGCTATAGATAGCTGATTTCATCGAGGCTATCATTGGATTTGCATCCTCCAAAA
261 GGCTCAGAATAGGCTATAGATAGCTGATTTCATCGAGGCTACCATTGGATTTGCATCCTCCAAAA
*
18399589 TGTAAGTTCACAATCTTCCTTACTTTAAGTTATTCCGGGGCCCGCTGGTTATTGTAAATTAAATT
326 TGTAAGTTCACAATCTTCCTTACTTTAAGTTATTCCGGGGCCCACTGGTTATTGTAAATTAAATT
*
18399654 AAATACTCTGGCTTATTGTATTACAATATGTATGAATTTATTTTGCTTTTACACTGCTACAAAAA
391 AAATACTCTGGCTTACTGTATTACAATATGTATGAATTTATTTTGCTTTTACACTGCTACAAAAA
18399719 AATTA
456 AATTA
18399724 TTTACGTATA
Statistics
Matches: 435, Mismatches: 25, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
463 435 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (462 bp):
CCTCAATCAAGGTATCCCTGATAACTGGGTATGAGAATAATTTTGGCAAGAGCCAAAGTTTTAAG
AAATTCATAAGCCATGTTGATTACTCGATTTATATGAATTGATTTTATTTGGTTGAAACAAGTGG
AAAGGTGATGAATTACAGTATGTTAAACTATTTTATCTATCTCCATTTACTCAACTTTAGATATT
TTAGATGGTATTTGTTTACTCACTGGGATTATATAATCTCACCACCCTCATTTCCACCAATTTCA
GGCTCAGAATAGGCTATAGATAGCTGATTTCATCGAGGCTACCATTGGATTTGCATCCTCCAAAA
TGTAAGTTCACAATCTTCCTTACTTTAAGTTATTCCGGGGCCCACTGGTTATTGTAAATTAAATT
AAATACTCTGGCTTACTGTATTACAATATGTATGAATTTATTTTGCTTTTACACTGCTACAAAAA
AATTAGC
Found at i:18404743 original size:11 final size:11
Alignment explanation
Indices: 18404723--18404769 Score: 78
Period size: 11 Copynumber: 4.4 Consensus size: 11
18404713 TATGGCCGGC
18404723 CAAAGGAAGAA
1 CAAAGGAAGAA
*
18404734 CAAAGCAAGAA
1 CAAAGGAAGAA
18404745 CAAAGGAAGAA
1 CAAAGGAAGAA
18404756 -AAAGGAAGAA
1 CAAAGGAAGAA
18404766 CAAA
1 CAAA
18404770 ACCGTAGGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
10 10 0.30
11 23 0.70
ACGTcount: A:0.66, C:0.11, G:0.23, T:0.00
Consensus pattern (11 bp):
CAAAGGAAGAA
Found at i:18404751 original size:22 final size:21
Alignment explanation
Indices: 18404723--18404769 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
18404713 TATGGCCGGC
18404723 CAAAGGAAGAACAAAGCAAGAA
1 CAAAGGAAGAA-AAAGCAAGAA
*
18404745 CAAAGGAAGAAAAAGGAAGAA
1 CAAAGGAAGAAAAAGCAAGAA
18404766 CAAA
1 CAAA
18404770 ACCGTAGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.66, C:0.11, G:0.23, T:0.00
Consensus pattern (21 bp):
CAAAGGAAGAAAAAGCAAGAA
Found at i:18404806 original size:21 final size:22
Alignment explanation
Indices: 18404780--18404821 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
18404770 ACCGTAGGTG
*
18404780 GAAAATTCAAGGGAA-AAGTGT
1 GAAAATTCAAGGAAACAAGTGT
18404801 GAAAATTCAAGGAAACAAGTG
1 GAAAATTCAAGGAAACAAGTG
18404822 ACAAAAGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.50, C:0.07, G:0.26, T:0.17
Consensus pattern (22 bp):
GAAAATTCAAGGAAACAAGTGT
Found at i:18404827 original size:22 final size:21
Alignment explanation
Indices: 18404781--18404827 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
18404771 CCGTAGGTGG
* **
18404781 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGAAAAAGTGAC
18404802 AAAATTCAAGGAAACAAGTGAC
1 AAAATTCAAGGAAA-AAGTGAC
18404824 AAAA
1 AAAA
18404828 GGTAAGATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.55, C:0.09, G:0.21, T:0.15
Consensus pattern (21 bp):
AAAATTCAAGGAAAAAGTGAC
Found at i:18408493 original size:21 final size:22
Alignment explanation
Indices: 18408451--18408497 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
18408441 TATGGCCGGC
18408451 CAAAGGAAGAACAAAGCGAGAA
1 CAAAGGAAGAACAAAGCGAGAA
*
18408473 CAAAGGAATAA-AAAG-GAAGAA
1 CAAAGGAAGAACAAAGCG-AGAA
18408494 CAAA
1 CAAA
18408498 ACCCTAGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 10 0.43
ACGTcount: A:0.64, C:0.11, G:0.23, T:0.02
Consensus pattern (22 bp):
CAAAGGAAGAACAAAGCGAGAA
Found at i:18414254 original size:43 final size:43
Alignment explanation
Indices: 18414207--18414309 Score: 143
Period size: 43 Copynumber: 2.4 Consensus size: 43
18414197 GGCTATGTGT
* * * **
18414207 GAGTAGGGATTGCGCATAAGCCGATGATGACCTGATTATGTAC
1 GAGTAGGGAGTGCGCATAACCCGATGATGACCCGACCATGTAC
* *
18414250 GAGTAGGGAGTGCGCATAACCCGGTGATGACCCGACCATGTGC
1 GAGTAGGGAGTGCGCATAACCCGATGATGACCCGACCATGTAC
18414293 GAGTAGGGAGTGCGCAT
1 GAGTAGGGAGTGCGCAT
18414310 GAGTTGGTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.20
Consensus pattern (43 bp):
GAGTAGGGAGTGCGCATAACCCGATGATGACCCGACCATGTAC
Found at i:18415137 original size:28 final size:30
Alignment explanation
Indices: 18415106--18415163 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
18415096 TTTTCGAGCA
* *
18415106 TAGGGGTAAAATAGTCATTTT-C-CCACCC
1 TAGGGGAAAAATAGTAATTTTACACCACCC
*
18415134 TAGGGGAAAAATTGTAATTTTACACCACCC
1 TAGGGGAAAAATAGTAATTTTACACCACCC
18415164 AACACTTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 18 0.72
29 1 0.04
30 6 0.24
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (30 bp):
TAGGGGAAAAATAGTAATTTTACACCACCC
Found at i:18415388 original size:21 final size:19
Alignment explanation
Indices: 18415362--18415404 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
18415352 TATGGCCGGC
18415362 CAAAGGAAGAGCAAAAAAGAA
1 CAAAGGAAGA--AAAAAAGAA
*
18415383 CAAAGGAAGAAAAGAAGAA
1 CAAAGGAAGAAAAAAAGAA
18415402 CAA
1 CAA
18415405 GAACCCTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.23, T:0.00
Consensus pattern (19 bp):
CAAAGGAAGAAAAAAAGAA
Found at i:18419561 original size:43 final size:43
Alignment explanation
Indices: 18419504--18419635 Score: 156
Period size: 43 Copynumber: 3.1 Consensus size: 43
18419494 GTAATGATAT
* * * *
18419504 TGACTCGGCTATGTGCGAGCACGGAGTGCGCATAAGCCGATGA
1 TGACCCGGCTATGTGCGAGTAAGGAGTGCACATAAGCCGATGA
* * *
18419547 TGACCCGGTTATGTGCGAGTAAGGAGTGCACATAAACCGGTGA
1 TGACCCGGCTATGTGCGAGTAAGGAGTGCACATAAGCCGATGA
* * * * *
18419590 TGACCCAGCCATGTGCGAGTAGGGAGTGCACATGAGCTGATGA
1 TGACCCGGCTATGTGCGAGTAAGGAGTGCACATAAGCCGATGA
18419633 TGA
1 TGA
18419636 TGGGATAGTG
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.26, C:0.20, G:0.34, T:0.20
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAAGGAGTGCACATAAGCCGATGA
Found at i:18424257 original size:29 final size:29
Alignment explanation
Indices: 18424215--18424407 Score: 241
Period size: 29 Copynumber: 6.7 Consensus size: 29
18424205 TGGTAGCTTT
18424215 AACATGTTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTTGTCTTAATTTAGACAAGAA
*
18424244 AACATGTTATGTCTTAATTTAGACAAGAA
1 AACATGTTTTGTCTTAATTTAGACAAGAA
* * *
18424273 AACATGTTTTGTTTTAATTTAGATAATAA
1 AACATGTTTTGTCTTAATTTAGACAAGAA
* *
18424302 AACATG-TTTGCCTTAATATAAGACAAGAA
1 AACATGTTTTGTCTTAAT-TTAGACAAGAA
* *
18424331 AA-ATGTGTTTTGTCCTAATCTAGACAAGAA
1 AACA--TGTTTTGTCTTAATTTAGACAAGAA
*
18424361 AACATGTTTT-TCTCT-ATTTAGACAAGAT
1 AACATGTTTTGTCT-TAATTTAGACAAGAA
18424389 AACATGTTTTGTCTTAATT
1 AACATGTTTTGTCTTAATT
18424408 AAAAACAAGA
Statistics
Matches: 139, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
28 34 0.24
29 82 0.59
30 13 0.09
31 10 0.07
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (29 bp):
AACATGTTTTGTCTTAATTTAGACAAGAA
Found at i:18424416 original size:88 final size:88
Alignment explanation
Indices: 18424214--18424417 Score: 240
Period size: 88 Copynumber: 2.3 Consensus size: 88
18424204 ATGGTAGCTT
* * *
18424214 TAACATGTTTTGTCTTAATT-TAGACAAGAAAACATGTTATGTCTTAATTTAGACAAGAAAACAT
1 TAACATGTTTTGTCTTAATTAAAGACAAGAAAACATGTTATGTCCTAATCTAGACAAGAAAACAT
* * *
18424278 GTTTTGTTTTAATTTAGATAATA
66 GTTTTGTTCTAATTTAGACAAGA
* * *
18424301 AAACATG-TTTGCCTTAA-TATAAGACAAGAAAA-ATGTGTTTTGTCCTAATCTAGACAAGAAAA
1 TAACATGTTTTGTCTTAATTA-AAGACAAGAAAACA--TGTTATGTCCTAATCTAGACAAGAAAA
18424363 CATGTTTT-TCTCT-ATTTAGACAAGA
63 CATGTTTTGT-TCTAATTTAGACAAGA
*
18424388 TAACATGTTTTGTCTTAATTAAAAACAAGA
1 TAACATGTTTTGTCTTAATTAAAGACAAGA
18424418 CTTGTTTGAA
Statistics
Matches: 98, Mismatches: 12, Indels: 13
0.80 0.10 0.11
Matches are distributed among these distances:
85 1 0.01
86 10 0.10
87 34 0.35
88 51 0.52
89 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (88 bp):
TAACATGTTTTGTCTTAATTAAAGACAAGAAAACATGTTATGTCCTAATCTAGACAAGAAAACAT
GTTTTGTTCTAATTTAGACAAGA
Found at i:18430657 original size:19 final size:19
Alignment explanation
Indices: 18430633--18430670 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18430623 CTGCCAAACC
*
18430633 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
18430652 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
18430671 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:18431522 original size:16 final size:15
Alignment explanation
Indices: 18431475--18431525 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 15
18431465 TTTTCTTCAT
18431475 TTTCTTTTCCTTGT--
1 TTTCTTTTCCTT-TCC
18431489 TTTCTTTTCCTTTCC
1 TTTCTTTTCCTTTCC
18431504 TTTCTTTT-CTTACTCC
1 TTTCTTTTCCTT--TCC
18431520 TTTCTT
1 TTTCTT
18431526 CTCCAAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.03
14 15 0.45
15 8 0.24
16 9 0.27
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTCTTTTCCTTTCC
Found at i:18432440 original size:23 final size:23
Alignment explanation
Indices: 18432410--18432465 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
18432400 AGCTAATGAT
18432410 CGGTGGGGGATTCCAGCCGTGTG
1 CGGTGGGGGATTCCAGCCGTGTG
*
18432433 CGGTGGGGGATTCCAGCCGTTTG
1 CGGTGGGGGATTCCAGCCGTGTG
*
18432456 CGGTGTGGGA
1 CGGTGGGGGA
18432466 GTGCACATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.09, C:0.20, G:0.48, T:0.23
Consensus pattern (23 bp):
CGGTGGGGGATTCCAGCCGTGTG
Found at i:18434498 original size:43 final size:43
Alignment explanation
Indices: 18434428--18434589 Score: 182
Period size: 43 Copynumber: 3.8 Consensus size: 43
18434418 GTAATTATGT
* * **
18434428 TGACTTGGCTATGTGCGAGTAGGGAGTGCGCATAAGTCGAGGA
1 TGACCTGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGA
*
18434471 TGATCTGGTTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
1 TGACCTGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGAG-GA
* * * *
18434514 TGACCCGGTTATCTACGAGTAGGGAGTGCGCATAACCCGATGA
1 TGACCTGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGA
* ** * *
18434557 TGACCTAGCCATGTGCGAGTAGAGAGTGTGCAT
1 TGACCTGGTTATGTGCGAGTAGGGAGTGCGCAT
18434590 GAGCTGGTGA
Statistics
Matches: 99, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.01
43 98 0.99
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.23
Consensus pattern (43 bp):
TGACCTGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGAGGA
Found at i:18434605 original size:3 final size:3
Alignment explanation
Indices: 18434597--18434659 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
18434587 CATGAGCTGG
* * * * *
18434597 TGA TGA TGA TGA TGA TGA -GC TGG TGA TGA TGA TGA TG- GGT TGG TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
18434643 -GA TGA TGA TGA TAGA TG
1 TGA TGA TGA TGA T-GA TG
18434660 TATATGTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.27, C:0.02, G:0.40, T:0.32
Consensus pattern (3 bp):
TGA
Found at i:18434615 original size:23 final size:23
Alignment explanation
Indices: 18434588--18434654 Score: 97
Period size: 23 Copynumber: 3.1 Consensus size: 23
18434578 GAGAGTGTGC
18434588 ATGAGCTGGTGATGATGATGATG
1 ATGAGCTGGTGATGATGATGATG
18434611 ATGAGCTGGTGATGATGATGATG
1 ATGAGCTGGTGATGATGATGATG
*
18434634 --G-GTTGGTGA-GATGATGATG
1 ATGAGCTGGTGATGATGATGATG
18434653 AT
1 AT
18434655 AGATGTATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
19 10 0.24
20 7 0.17
21 1 0.02
23 23 0.56
ACGTcount: A:0.25, C:0.03, G:0.40, T:0.31
Consensus pattern (23 bp):
ATGAGCTGGTGATGATGATGATG
Found at i:18434623 original size:20 final size:20
Alignment explanation
Indices: 18434600--18434653 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
18434590 GAGCTGGTGA
18434600 TGATGATGATGATGAGCTGG
1 TGATGATGATGATGAGCTGG
* *
18434620 TGATGATGATGATGGGTTGG
1 TGATGATGATGATGAGCTGG
18434640 TGA-GATGATGATGA
1 TGATGATGATGATGA
18434654 TAGATGTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.26, C:0.02, G:0.41, T:0.31
Consensus pattern (20 bp):
TGATGATGATGATGAGCTGG
Found at i:18442529 original size:133 final size:133
Alignment explanation
Indices: 18442281--18442529 Score: 315
Period size: 133 Copynumber: 1.9 Consensus size: 133
18442271 TAAGTTGACC
** * *
18442281 AAAATAACCTTCTATACATTACTTAGGAATTAATCCCTATATACCCCCTCCCTTCTACCATACAG
1 AAAATAACCTTCTATACATTACAGAGAAATTAATCCCTATATACCCCCTCCCTTCTACCATACAA
** * *
18442346 ACAAATTAAATGCTCTCTCATCTCCGTCAGCTCTCTTAATTCCTTGAACTCTCTCAGCTTTCTCA
66 ACAAATTAAATGCTCTCTCATCTCAATCAGCTCTCTTAATTCCCTAAACTCTCTCAGCTTTCTCA
18442411 GCA
131 GCA
* * *
18442414 AAAATAACCTTC-ATTACATTACAGAGAAATTAATCCCTATATATCTCCTTCCCTTCT-GCATAC
1 AAAATAACCTTCTA-TACATTACAGAGAAATTAATCCCTATATA-CCCCCTCCCTTCTACCATAC
* * * *
18442477 AAACAAATTAAATGCTTTCTTATCTCAATCAGCTTTC-TCATCTCCCTAAACTC
64 AAACAAATTAAATGCTCTCTCATCTCAATCAGCTCTCTTAAT-TCCCTAAACTC
18442530 GTGCTGCTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
132 4 0.04
133 83 0.85
134 11 0.11
ACGTcount: A:0.31, C:0.30, G:0.06, T:0.34
Consensus pattern (133 bp):
AAAATAACCTTCTATACATTACAGAGAAATTAATCCCTATATACCCCCTCCCTTCTACCATACAA
ACAAATTAAATGCTCTCTCATCTCAATCAGCTCTCTTAATTCCCTAAACTCTCTCAGCTTTCTCA
GCA
Found at i:18445302 original size:35 final size:35
Alignment explanation
Indices: 18445228--18445311 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
18445218 AGTTGTGCCT
* * *
18445228 AATTAATTAAATTGTTTAATTAAATAATTGAGCAT
1 AATTAATTAAATTATTTAATTAAATAAGTGAGCAG
* * * *
18445263 AATTAATTAAATTATTTAATTAAGTCAGTGGGCCG
1 AATTAATTAAATTATTTAATTAAATAAGTGAGCAG
18445298 AATTAATTAAATTA
1 AATTAATTAAATTA
18445312 AACAATTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (35 bp):
AATTAATTAAATTATTTAATTAAATAAGTGAGCAG
Found at i:18445319 original size:35 final size:35
Alignment explanation
Indices: 18445263--18445357 Score: 118
Period size: 35 Copynumber: 2.7 Consensus size: 35
18445253 AATTGAGCAT
*** *
18445263 AATTAATTAAATTATTTAATTAAGTCAGTGGGCCG
1 AATTAATTAAATTAAACAATTAAGTAAGTGGGCCG
* * *
18445298 AATTAATTAAATTAAACAATTAAGTAATTGGGTCT
1 AATTAATTAAATTAAACAATTAAGTAAGTGGGCCG
*
18445333 AATTGATTAAATTAAACAATTAAGT
1 AATTAATTAAATTAAACAATTAAGT
18445358 TAACTGGACT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (35 bp):
AATTAATTAAATTAAACAATTAAGTAAGTGGGCCG
Found at i:18446335 original size:21 final size:22
Alignment explanation
Indices: 18446309--18446349 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18446299 CCTAGGTGAA
*
18446309 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
18446330 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
18446350 AAAAAAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:18446350 original size:20 final size:21
Alignment explanation
Indices: 18446309--18446353 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
18446299 CCTAGGTGAA
*
18446309 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
18446330 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
18446350 AAAA
1 AAAA
18446354 AAGGTAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:18446354 original size:21 final size:21
Alignment explanation
Indices: 18446308--18446355 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
18446298 CCCTAGGTGA
*
18446308 AAAAATTCAAGGGAAAAGTGT
1 AAAAATTCAAGGAAAAAGTGT
* *
18446329 GAAAATTCAAGGAAACAAGTGA
1 AAAAATTCAAGGAAA-AAGTGT
18446351 AAAAA
1 AAAAA
18446356 GGTAAGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.58, C:0.06, G:0.21, T:0.15
Consensus pattern (21 bp):
AAAAATTCAAGGAAAAAGTGT
Found at i:18449726 original size:179 final size:179
Alignment explanation
Indices: 18449426--18449772 Score: 515
Period size: 179 Copynumber: 1.9 Consensus size: 179
18449416 GTTCATGACT
18449426 AAATATGCTGATTTTAAGCAAGAAATTGGAGCAAAAGTGAAAGTAGTCCAGCTCACTGTTATGAC
1 AAATATGCTGATTTTAAGCAAGAAATTGGAGCAAAAGTGAAAGTAGTCCAGCTCACTGTTATGAC
* *
18449491 ATGAATTTCAGATTTAATTGACAAGAAAGTCTTGGAAATTAATTCTGAAAAATTCCAGAAAATTA
66 ATGAATTTCAGATTTAATTGACAAGAAACTCTTGAAAATTAATTCTGAAAAATTCCAGAAAATTA
* *
18449556 TCTTTATTAAAATGTTCAATAAGGATTGTTTCTGGAAAATATCATGGTC
131 TATTTATTAAAATGTTCAATAAGGATTATTTCTGGAAAATATCATGGTC
* * *
18449605 AAATATGCTG-TTTTCAAGCAAGAAAATTGGTGCAAATA-T-AAA-TCTGTCCAGTTCACTGTT-
1 AAATATGCTGATTTT-AAGCAAG-AAATTGGAGCAAA-AGTGAAAGT-AGTCCAGCTCACTGTTA
* * *
18449665 TAGGCATGAATTTCAGTTTTAATTGACAAGAAACTCTTGAAAATTAGTTCTGAAAAATTCCAGAA
62 T-GACATGAATTTCAGATTTAATTGACAAGAAACTCTTGAAAATTAATTCTGAAAAATTCCAGAA
*
18449730 AATTATATTTATTAAAATGTTCAATGAGGATTATTTCTGGAAA
126 AATTATATTTATTAAAATGTTCAATAAGGATTATTTCTGGAAA
18449773 TTTTCATAGC
Statistics
Matches: 152, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
178 6 0.04
179 132 0.87
180 13 0.09
181 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (179 bp):
AAATATGCTGATTTTAAGCAAGAAATTGGAGCAAAAGTGAAAGTAGTCCAGCTCACTGTTATGAC
ATGAATTTCAGATTTAATTGACAAGAAACTCTTGAAAATTAATTCTGAAAAATTCCAGAAAATTA
TATTTATTAAAATGTTCAATAAGGATTATTTCTGGAAAATATCATGGTC
Found at i:18451687 original size:32 final size:32
Alignment explanation
Indices: 18451651--18451714 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
18451641 ATAGAGATAA
*
18451651 ATTTGGCAAGCTCAGTTACCTACCTAATCCAC
1 ATTTGGCAAGCTCAATTACCTACCTAATCCAC
*
18451683 ATTTGGTAAGCTCAATTACCTACCTAATCCAC
1 ATTTGGCAAGCTCAATTACCTACCTAATCCAC
18451715 CTACAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.30
Consensus pattern (32 bp):
ATTTGGCAAGCTCAATTACCTACCTAATCCAC
Found at i:18452822 original size:35 final size:35
Alignment explanation
Indices: 18452766--18452871 Score: 106
Period size: 35 Copynumber: 3.1 Consensus size: 35
18452756 CACTCAGCCA
* *
18452766 ATGTGCACTCCCTACACGCACAAGGCAATATCATC
1 ATGTGCACTCCCTACTCGCACAAAGCAATATCATC
* * ***
18452801 ATGTGGACTCCCTACTGGCACATTTCAATATCATC
1 ATGTGCACTCCCTACTCGCACAAAGCAATATCATC
*** *
18452836 GCATGCACTCCTTACTCGCA-AAAGCAATATCATC
1 ATGTGCACTCCCTACTCGCACAAAGCAATATCATC
18452870 AT
1 AT
18452872 CCACACTTTC
Statistics
Matches: 54, Mismatches: 17, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
34 11 0.20
35 43 0.80
ACGTcount: A:0.30, C:0.31, G:0.13, T:0.25
Consensus pattern (35 bp):
ATGTGCACTCCCTACTCGCACAAAGCAATATCATC
Found at i:18464435 original size:42 final size:42
Alignment explanation
Indices: 18464376--18464499 Score: 212
Period size: 42 Copynumber: 3.0 Consensus size: 42
18464366 TGTTGATTTG
18464376 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* *
18464418 GACCCGACTATGTGCGAGTAGGAGTGCATATAAGCCGTTGCT
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
* *
18464460 GACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGTTG
1 GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTG
18464500 TTGCCCCCAT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.23
Consensus pattern (42 bp):
GACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCT
Found at i:18464795 original size:26 final size:26
Alignment explanation
Indices: 18464734--18464795 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
18464724 TTGCATATGA
*
18464734 GATGATGATAATGGGATGATGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
18464760 GATGATGATGATGGGATGGTGTGCAT
1 GATGATGATGATGGGATGATGTGCAT
*
18464786 GTTGATGATG
1 GATGATGATG
18464796 GGTATATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.26, C:0.03, G:0.39, T:0.32
Consensus pattern (26 bp):
GATGATGATGATGGGATGATGTGCAT
Found at i:18468564 original size:22 final size:22
Alignment explanation
Indices: 18468523--18468565 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
18468513 TTTAAAACAA
* *
18468523 CTTTAAAACCAAATGTTCTGAC
1 CTTTAAAACCAAAAGCTCTGAC
18468545 CTTTAAAACCAAAAGCTCTGA
1 CTTTAAAACCAAAAGCTCTGA
18468566 TACTAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (22 bp):
CTTTAAAACCAAAAGCTCTGAC
Found at i:18476469 original size:20 final size:20
Alignment explanation
Indices: 18476444--18476482 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
18476434 AAGGAGAAAA
*
18476444 AGAAGCTGCTGAAAGTTAGG
1 AGAAGCTGCTGAAAATTAGG
18476464 AGAAGCTGCTGAAAATTAG
1 AGAAGCTGCTGAAAATTAG
18476483 ATATTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (20 bp):
AGAAGCTGCTGAAAATTAGG
Found at i:18478414 original size:13 final size:13
Alignment explanation
Indices: 18478396--18478420 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18478386 TTTCATGTTT
18478396 GAATAATTATGTG
1 GAATAATTATGTG
18478409 GAATAATTATGT
1 GAATAATTATGT
18478421 CATATTTAAT
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:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (13 bp):
GAATAATTATGTG
Found at i:18489455 original size:28 final size:27
Alignment explanation
Indices: 18489417--18489469 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
18489407 TATCTTAGTG
*
18489417 GTGGAAAATTACAATTTTGCCCCTAGA
1 GTGGAAAATTACAATTTTACCCCTAGA
*
18489444 GTGGCAAAATTACCATTTTACCCCTA
1 GTGG-AAAATTACAATTTTACCCCTA
18489470 TACTCCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (27 bp):
GTGGAAAATTACAATTTTACCCCTAGA
Found at i:18489537 original size:20 final size:20
Alignment explanation
Indices: 18489512--18489557 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
18489502 CTTCTTAACC
18489512 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
18489532 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
18489552 TCAAAT
1 TCAAAT
18489558 GGGGACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:18501069 original size:20 final size:20
Alignment explanation
Indices: 18501041--18501085 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
18501031 AAACCGCGAA
*
18501041 TTTCCCTTTGAATTTTCTTG
1 TTTCTCTTTGAATTTTCTTG
** *
18501061 TTTCTCTTTGGTTTTTCTTT
1 TTTCTCTTTGAATTTTCTTG
18501081 TTTCT
1 TTTCT
18501086 TCCTTTCCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.04, C:0.18, G:0.09, T:0.69
Consensus pattern (20 bp):
TTTCTCTTTGAATTTTCTTG
Found at i:18502713 original size:35 final size:34
Alignment explanation
Indices: 18502585--18502722 Score: 141
Period size: 36 Copynumber: 3.9 Consensus size: 34
18502575 AAAATTAAAC
18502585 AATTAAGTTATTAGGCCTAATTTATTAAATATGTTT
1 AATTAAGTTATTAGGCCTAA-TTATTAAAT-TGTTT
* *
18502621 AATTAAGTCATTGGGCCTAATTGATTAAAATTGTTT
1 AATTAAGTTATTAGGCCTAATT-ATT-AAATTGTTT
* * * *
18502657 AATTAAATTGTTGGGTCTAATTACTTAAATTGTTT
1 AATTAAGTTATTAGGCCTAATTA-TTAAATTGTTT
* **
18502692 AATTAAGCTATTAGGTTTAATTATTTAAATT
1 AATTAAGTTATTAGGCCTAATTA-TTAAATT
18502723 AAACAATTAA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
35 37 0.43
36 46 0.53
37 4 0.05
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (34 bp):
AATTAAGTTATTAGGCCTAATTATTAAATTGTTT
Found at i:18506416 original size:59 final size:60
Alignment explanation
Indices: 18506352--18506469 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
18506342 AAACATCATC
** * *
18506352 CCTACTCATGGGAACTGTCCA-TCCACCATATATAAATCGAGGCTTCAGGTCCCCCTTTA
1 CCTACTCATGGGAACTACCCACGCCACCAAATATAAATCGAGGCTTCAGGTCCCCCTTTA
* * *
18506411 CCTACTCGTGGGATCTACCCACGCCACCAAATATAAATCGGGGCTTCAGGTCCCCCTTT
1 CCTACTCATGGGAACTACCCACGCCACCAAATATAAATCGAGGCTTCAGGTCCCCCTTT
18506470 TACAATCAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 17 0.33
60 34 0.67
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.25
Consensus pattern (60 bp):
CCTACTCATGGGAACTACCCACGCCACCAAATATAAATCGAGGCTTCAGGTCCCCCTTTA
Found at i:18507224 original size:62 final size:64
Alignment explanation
Indices: 18507158--18507318 Score: 202
Period size: 62 Copynumber: 2.5 Consensus size: 64
18507148 ATTCTCTCCT
18507158 TCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTTCTTCCCTCTT-TTCTTCTCCTT-TACCGTTGC
1 TCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTTCTTCCCTCTTCTTCTTCTCCTTATACCGTTGC
* * * *
18507220 TCTTTCTCTTTTTCTTTTTCTTTTTCATTTTTCTTCCTTCTTCTTCTTCTCCTTGAGATGCCGTT
1 TCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTTCTTCCCTCTTCTTCTTCTCCTT---ATACCGTT
18507285 GC
63 GC
*
18507287 TCCATTTTTCCTTTT-TTTTTCTTTTTTCTTTT
1 T-C-TTTTTCTTTTTCTTTTTC-TTTTTCTTTT
18507319 CTCTCACTCG
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
62 39 0.46
63 11 0.13
67 9 0.11
68 7 0.08
69 18 0.21
ACGTcount: A:0.03, C:0.25, G:0.04, T:0.67
Consensus pattern (64 bp):
TCTTTTTCTTTTTCTTTTTCTTTTTCTTTTTTCTTCCCTCTTCTTCTTCTCCTTATACCGTTGC
Found at i:18507227 original size:74 final size:76
Alignment explanation
Indices: 18507105--18507268 Score: 199
Period size: 74 Copynumber: 2.2 Consensus size: 76
18507095 CTTCTCTTTC
* *
18507105 TTTCTTCTTTCTTGCCTCATCTTCTTCTCCTCTATCGCTACTCATTCTCTCCTTCTTTTTCTTTT
1 TTTCTTCTTTCTTCCCTCATCTTCTTCTCCTCTACCGCTACTCATTCTCTCCTTCTTTTTCTTTT
18507170 TC-TTTTTCTT
66 TCATTTTTCTT
* * * * * * **
18507180 TTTCTTTTTTCTTCCCTC-TTTTCTTCTCCTTTACCGTTGCTCTTTCTCTTTTTCTTTTTCTTTT
1 TTTCTTCTTTCTTCCCTCATCTTCTTCTCCTCTACCGCTACTCATTCTCTCCTTCTTTTTCTTTT
18507244 TCATTTTTCTT
66 TCATTTTTCTT
*
18507255 CCTTCTTC-TTCTTC
1 -TTTCTTCTTTCTTC
18507269 TCCTTGAGAT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
74 40 0.53
75 30 0.40
76 5 0.07
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.63
Consensus pattern (76 bp):
TTTCTTCTTTCTTCCCTCATCTTCTTCTCCTCTACCGCTACTCATTCTCTCCTTCTTTTTCTTTT
TCATTTTTCTT
Found at i:18507269 original size:6 final size:6
Alignment explanation
Indices: 18507157--18507254 Score: 72
Period size: 6 Copynumber: 15.8 Consensus size: 6
18507147 CATTCTCTCC
** *
18507157 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT-TCTT CCCTCTT TTCTTC
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCT-TT TTCT-TT TTCTTT
* ** * * *
18507206 TCCTTT ACCGTTG CTCTTT CTCTTT TTCTTT TTCTTT TTCATTT TTCTT
1 TTCTTT TTC-TTT TTCTTT TTCTTT TTCTTT TTCTTT TTC-TTT TTCTT
18507255 CCTTCTTCTT
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
5 1 0.01
6 59 0.79
7 15 0.20
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (6 bp):
TTCTTT
Found at i:18508598 original size:86 final size:86
Alignment explanation
Indices: 18508453--18508633 Score: 326
Period size: 86 Copynumber: 2.1 Consensus size: 86
18508443 TACTATATAT
*
18508453 ATGGATTTATGTTAATAAACATTACTAGTCTTCGTAATTGCAATTGCGGATAGTATGAGCTGTTA
1 ATGGATTTATGTTAATAAACATTACTAGTCTTCGTAATTGCAATTGCGGATAGTATGAGCTGATA
*
18508518 GCCTTGATAGGCAATTTTAAA
66 CCCTTGATAGGCAATTTTAAA
* *
18508539 ATGGATTTATGTTAATAAACATTGCTAGTCTTCTTAATTGCAATTGCGGATAGTATGAGCTGATA
1 ATGGATTTATGTTAATAAACATTACTAGTCTTCGTAATTGCAATTGCGGATAGTATGAGCTGATA
18508604 CCCTTGATAGGCAATTTTAAA
66 CCCTTGATAGGCAATTTTAAA
18508625 ATGGATTTA
1 ATGGATTTA
18508634 CAATGATTTA
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 91 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (86 bp):
ATGGATTTATGTTAATAAACATTACTAGTCTTCGTAATTGCAATTGCGGATAGTATGAGCTGATA
CCCTTGATAGGCAATTTTAAA
Found at i:18511172 original size:19 final size:19
Alignment explanation
Indices: 18511148--18511185 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18511138 CCATTTAACT
*
18511148 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
18511167 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
18511186 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:18511392 original size:28 final size:29
Alignment explanation
Indices: 18511351--18511410 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
18511341 GTCTATGGGA
*
18511351 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* *
18511379 AATTTTTCACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
18511409 AA
1 AA
18511411 ATTTCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
30 14 0.52
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:18512616 original size:16 final size:16
Alignment explanation
Indices: 18512595--18512629 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
18512585 ATAAAATATT
*
18512595 ATGTTTTCTAATTAAA
1 ATGTTTTCTAATAAAA
*
18512611 ATGTTTTTTAATAAAA
1 ATGTTTTCTAATAAAA
18512627 ATG
1 ATG
18512630 AGATTTATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.49
Consensus pattern (16 bp):
ATGTTTTCTAATAAAA
Found at i:18513900 original size:15 final size:14
Alignment explanation
Indices: 18513851--18513901 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
18513841 TTTAAAGATC
18513851 AAAGATTTTGATTTT
1 AAAG-TTTTGATTTT
*
18513866 AAAGCTTTGAATTTT
1 AAAGTTTTG-ATTTT
18513881 AAAGTTTTCGATTTT
1 AAAGTTTT-GATTTT
18513896 AAAGTT
1 AAAGTT
18513902 GTTTTAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 4 0.12
15 27 0.84
16 1 0.03
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (14 bp):
AAAGTTTTGATTTT
Found at i:18515922 original size:19 final size:19
Alignment explanation
Indices: 18515894--18515931 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18515884 CCATTTAACT
*
18515894 TATTGCAGTATGATTTGAG
1 TATTGCAGTATAATTTGAG
*
18515913 TATTGGAGTATAATTTGAG
1 TATTGCAGTATAATTTGAG
18515932 GGTTTGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.42
Consensus pattern (19 bp):
TATTGCAGTATAATTTGAG
Found at i:18516138 original size:28 final size:29
Alignment explanation
Indices: 18516097--18516156 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
18516087 GTCTATGGGC
* *
18516097 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGGCAAAAATGT
* *
18516125 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-GGGGGCAAAAATGT
18516155 AA
1 AA
18516157 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.38
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGCAAAAATGT
Found at i:18520000 original size:61 final size:62
Alignment explanation
Indices: 18519898--18520014 Score: 191
Period size: 61 Copynumber: 1.9 Consensus size: 62
18519888 AGAAAAGAAA
* * * *
18519898 AGATGAGCTGAGGAGAAAAAGGGAAAAAAAAGAAAAGAAAAATAATTCCAAAATTTAGGCCT
1 AGATGAGCTAAGGAAAAAAAGAGAAAAAAAAGAAAAGAAAAAAAATTCCAAAATTTAGGCCT
18519960 AGATGAGCTAAGGAAAAAAAGAG-AAAAAAAGAAAAGAAAAAAAATTCCAAAATTT
1 AGATGAGCTAAGGAAAAAAAGAGAAAAAAAAGAAAAGAAAAAAAATTCCAAAATTT
18520015 GAGCTAAGGA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
61 31 0.61
62 20 0.39
ACGTcount: A:0.60, C:0.07, G:0.20, T:0.14
Consensus pattern (62 bp):
AGATGAGCTAAGGAAAAAAAGAGAAAAAAAAGAAAAGAAAAAAAATTCCAAAATTTAGGCCT
Found at i:18520037 original size:61 final size:61
Alignment explanation
Indices: 18519908--18520050 Score: 150
Period size: 61 Copynumber: 2.3 Consensus size: 61
18519898 AGATGAGCTG
* * * * ***
18519908 AGGAGAAAAAGGGAAAAAAAAGAAAAGAAAAATAATTCCAAAATTTAGGCCTAGATGAGCTA
1 AGGAAAAAAAGAG-AAAAAAAGAAAAGAAAAAAAATTCCAAAATTTAGGCCTAGAGGAAAAA
18519970 AGGAAAAAAAGAGAAAAAAAGAAAAGAAAAAAAATTCCAAAATTT-GAG-CTA-AGGAAAAAA
1 AGGAAAAAAAGAGAAAAAAAGAAAAGAAAAAAAATTCCAAAATTTAG-GCCTAGAGG-AAAAA
18520030 AGCGAAAAGAAAGA-AAAAAAA
1 AG-GAAAA-AAAGAGAAAAAAA
18520051 TAATTTCAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
59 2 0.03
60 8 0.11
61 44 0.63
62 16 0.23
ACGTcount: A:0.64, C:0.06, G:0.19, T:0.10
Consensus pattern (61 bp):
AGGAAAAAAAGAGAAAAAAAGAAAAGAAAAAAAATTCCAAAATTTAGGCCTAGAGGAAAAA
Found at i:18520061 original size:50 final size:51
Alignment explanation
Indices: 18519963--18520091 Score: 190
Period size: 51 Copynumber: 2.5 Consensus size: 51
18519953 TAGGCCTAGA
18519963 TGAGCTAAGGAAAAAAAGAGAAAAAAAGAAAAGAAAAAAAATTCCAAAATT
1 TGAGCTAAGGAAAAAAAGAGAAAAAAAGAAAAGAAAAAAAATTCCAAAATT
* * *
18520014 TGAGCTAAGGAAAAAAAGCGAAAAGAAAG-AAA-AAAAATAATTTCAAAATT
1 TGAGCTAAGGAAAAAAAGAGAAAA-AAAGAAAAGAAAAAAAATTCCAAAATT
*
18520064 TGAGCTAAGGGAAAAAAAAAGAAAAAAA
1 TGAGCTAA-GGAAAAAAAGAGAAAAAAA
18520092 ATTCAAAAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
50 27 0.38
51 40 0.56
52 4 0.06
ACGTcount: A:0.65, C:0.05, G:0.17, T:0.12
Consensus pattern (51 bp):
TGAGCTAAGGAAAAAAAGAGAAAAAAAGAAAAGAAAAAAAATTCCAAAATT
Found at i:18521372 original size:40 final size:40
Alignment explanation
Indices: 18521317--18521410 Score: 145
Period size: 40 Copynumber: 2.4 Consensus size: 40
18521307 CCAAATTGTT
18521317 TTCAAGATCAAGTTGTAGACCCTTGAAGCG-TGAAGAATCA
1 TTCAAGATCAAGTTGTAGACCCTTGAAG-GATGAAGAATCA
* **
18521357 TTCAAGATCAAGTTGTAGGCCCTTGAAGGATGAAGAATTG
1 TTCAAGATCAAGTTGTAGACCCTTGAAGGATGAAGAATCA
18521397 TTCAAGATCAAGTT
1 TTCAAGATCAAGTT
18521411 TTCAAGTCGT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
39 1 0.02
40 49 0.98
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (40 bp):
TTCAAGATCAAGTTGTAGACCCTTGAAGGATGAAGAATCA
Found at i:18521433 original size:49 final size:48
Alignment explanation
Indices: 18521379--18521506 Score: 152
Period size: 49 Copynumber: 2.6 Consensus size: 48
18521369 TTGTAGGCCC
* *
18521379 TTGAAGGATGAAGAATTGTTCAAGATCAAGTTTTCAAGTCGTTTGACCA
1 TTGAAGGATGAAGAATTGTTCAAGATCAAGTATTCAAGTC-ATTGACCA
* * *
18521428 TTGAAGCATGAAGAATCGTTCAAGATCAAGTATTCAAGTCATTGACCC
1 TTGAAGGATGAAGAATTGTTCAAGATCAAGTATTCAAGTCATTGACCA
* *
18521476 TTAAAGTG-TGAAGAA-TGATTGAAGATCAAGT
1 TTGAAG-GATGAAGAATTG-TTCAAGATCAAGT
18521507 CATGCAAAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.01
48 30 0.44
49 37 0.54
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (48 bp):
TTGAAGGATGAAGAATTGTTCAAGATCAAGTATTCAAGTCATTGACCA
Found at i:18521501 original size:48 final size:48
Alignment explanation
Indices: 18521386--18521506 Score: 145
Period size: 48 Copynumber: 2.5 Consensus size: 48
18521376 CCCTTGAAGG
* * *
18521386 ATGAAGAATTGTTCAAGATCAAGTTTTCAAGTCGTTTGACCATTGAAGC
1 ATGAAGAA-TGTTCAAGATCAAGTATTCAAGTCGATTGACCATTAAAGC
* *
18521435 ATGAAGAATCGTTCAAGATCAAGTATTCAAGTC-ATTGACCCTTAAAGT
1 ATGAAGAAT-GTTCAAGATCAAGTATTCAAGTCGATTGACCATTAAAGC
* *
18521483 GTGAAGAATGATTGAAGATCAAGT
1 ATGAAGAATG-TTCAAGATCAAGT
18521507 CATGCAAAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
47 1 0.02
48 32 0.51
49 30 0.48
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (48 bp):
ATGAAGAATGTTCAAGATCAAGTATTCAAGTCGATTGACCATTAAAGC
Found at i:18523685 original size:20 final size:20
Alignment explanation
Indices: 18523656--18523698 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
18523646 ATTAGGTTAC
18523656 TTTTAAGTTAGTT-ATTTTAA
1 TTTTAAGTTA-TTCATTTTAA
* *
18523676 TTTTATGTTATTCCTTTTAA
1 TTTTAAGTTATTCATTTTAA
18523696 TTT
1 TTT
18523699 GGTTATTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTAAGTTATTCATTTTAA
Found at i:18532942 original size:20 final size:20
Alignment explanation
Indices: 18532913--18532955 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
18532903 ATTAGGTTAC
18532913 TTTTAAGTTAGTT-ATTTTAA
1 TTTTAAGTTA-TTCATTTTAA
* *
18532933 TTTTATGTTATTCCTTTTAA
1 TTTTAAGTTATTCATTTTAA
18532953 TTT
1 TTT
18532956 GGTTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTAAGTTATTCATTTTAA
Found at i:18541072 original size:19 final size:19
Alignment explanation
Indices: 18541035--18541072 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18541025 GAGGTTTAGC
*
18541035 AAGAAACCCTTGGCCAGTT
1 AAGAAACCCTCGGCCAGTT
*
18541054 AAGAAACCCTCGGCTAGTT
1 AAGAAACCCTCGGCCAGTT
18541073 GATAATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (19 bp):
AAGAAACCCTCGGCCAGTT
Found at i:18543000 original size:19 final size:19
Alignment explanation
Indices: 18542963--18543000 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18542953 CCATATAACT
* *
18542963 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATCTGAG
18542982 TATTGGAGTATAATCTGAG
1 TATTGGAGTATAATCTGAG
18543001 GGTTTGGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.39
Consensus pattern (19 bp):
TATTGGAGTATAATCTGAG
Found at i:18549214 original size:13 final size:13
Alignment explanation
Indices: 18549196--18549220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18549186 AGAGAAATTG
18549196 TGATTTTATAAAA
1 TGATTTTATAAAA
18549209 TGATTTTATAAA
1 TGATTTTATAAA
18549221 TTTTCTACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:18550984 original size:29 final size:28
Alignment explanation
Indices: 18550940--18551109 Score: 214
Period size: 28 Copynumber: 5.9 Consensus size: 28
18550930 TGGCAACTTT
18550940 AACATGTTTTGTCTTAATTTAGACAAGAA
1 AACATG-TTTGTCTTAATTTAGACAAGAA
* *
18550969 AGCATGTTATGTCTTAATTTTGACAAGAA
1 AACATGTT-TGTCTTAATTTAGACAAGAA
*
18550998 AACATGTATGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
*
18551026 AATATGTTTGTCTTAATTTAAGACAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* *
18551056 AATATGTTTTGTCTTAATCTAGACAAGAA
1 AACATG-TTTGTCTTAATTTAGACAAGAA
* **
18551085 AACATATTTGTCCCAATTTAGACAA
1 AACATGTTTGTCTTAATTTAGACAA
18551110 CATATATTTA
Statistics
Matches: 124, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
28 54 0.44
29 43 0.35
30 15 0.12
31 12 0.10
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:18551033 original size:57 final size:59
Alignment explanation
Indices: 18550940--18551109 Score: 222
Period size: 59 Copynumber: 2.9 Consensus size: 59
18550930 TGGCAACTTT
* *
18550940 AACATGTTTTGTCTTAATTTAGACAAGAAAGCATGTTATGTCTTAATTT-TGACAAG-AA
1 AACATGTTTTGTCTTAATTTAGACAAGAAAACATGTT-TGTCTTAATTTAAGACAAGAAA
* *
18550998 AACATG-TATGTCTTAATTTAGACAAGAAAATATGTTTGTCTTAATTTAAGACAAGAAA
1 AACATGTTTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAAGACAAGAAA
* * * **
18551056 AATATGTTTTGTCTTAATCTAGACAAGAAAACATATTTGTCCCAATTT-AGACAA
1 AACATGTTTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAAGACAA
18551110 CATATATTTA
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
56 11 0.11
57 33 0.34
58 19 0.19
59 35 0.36
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (59 bp):
AACATGTTTTGTCTTAATTTAGACAAGAAAACATGTTTGTCTTAATTTAAGACAAGAAA
Found at i:18551088 original size:87 final size:85
Alignment explanation
Indices: 18550947--18551109 Score: 227
Period size: 87 Copynumber: 1.9 Consensus size: 85
18550937 TTTAACATGT
* * * * **
18550947 TTTGTCTTAATTTAGACAAGAAAGCATGTTATGTCTTAATTTTGACAAGAAAACATGTATGTCTT
1 TTTGTCTTAATTTAGACAAGAAAACATGTTATGTCTTAATCTAGACAAGAAAACATATATGTCCC
18551012 AATTTAGACAAGAAAATATG
66 AATTTAGACAAGAAAATATG
* * *
18551032 TTTGTCTTAATTTAAGACAAGAAAAATATGTTTTGTCTTAATCTAGACAAGAAAACATATTTGTC
1 TTTGTCTTAATTT-AGACAAG-AAAACATGTTATGTCTTAATCTAGACAAGAAAACATATATGTC
18551097 CCAATTTAGACAA
64 CCAATTTAGACAA
18551110 CATATATTTA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
85 13 0.19
86 7 0.10
87 47 0.70
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (85 bp):
TTTGTCTTAATTTAGACAAGAAAACATGTTATGTCTTAATCTAGACAAGAAAACATATATGTCCC
AATTTAGACAAGAAAATATG
Found at i:18560612 original size:26 final size:26
Alignment explanation
Indices: 18560552--18560613 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
18560542 ACCATATACC
*
18560552 CATCATCAACATGCACACCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
*
18560578 CATCATCATCATGCACATCATCCCAT
1 CATCATCATCATGCACACCATCCCAT
18560604 CATCATCATC
1 CATCATCATC
18560614 TCATATGCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.40, G:0.03, T:0.24
Consensus pattern (26 bp):
CATCATCATCATGCACACCATCCCAT
Found at i:18578114 original size:38 final size:40
Alignment explanation
Indices: 18578072--18578174 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 40
18578062 ATAGTGCCCG
18578072 TGTGCACGATGTGGGGGGATGTACACGATGGCAC-AGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGCACTAGATA
** ** ** * *
18578110 TGTGCATAATGTGGGGGGATCCACACGATGGTGCTGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGCACTAGATA
18578150 TGTGCACGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
18578175 TGAGTCGGGT
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
38 28 0.55
39 2 0.04
40 21 0.41
ACGTcount: A:0.21, C:0.16, G:0.40, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGCACTAGATA
Found at i:18580505 original size:20 final size:19
Alignment explanation
Indices: 18580477--18580514 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
18580467 TTTATAAATC
18580477 ATTTTGAAATTGAATAATG
1 ATTTTGAAATTGAATAATG
*
18580496 ATTTTAGAAATTGAGTAAT
1 ATTTT-GAAATTGAATAAT
18580515 TGGAGAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
ATTTTGAAATTGAATAATG
Found at i:18592371 original size:29 final size:28
Alignment explanation
Indices: 18592310--18592371 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
18592300 TGTCTCGCCC
* * *
18592310 ACTGTCCCAGCACACTGCCTGACTTGCA
1 ACTGACCCAGCACACTACCTGACTCGCA
*
18592338 ACTGACCCAGCAGCACTACCTGGCTCGCA
1 ACTGACCCAGCA-CACTACCTGACTCGCA
*
18592367 GCTGA
1 ACTGA
18592372 TGGCTCTGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.23, C:0.39, G:0.21, T:0.18
Consensus pattern (28 bp):
ACTGACCCAGCACACTACCTGACTCGCA
Found at i:18592618 original size:20 final size:20
Alignment explanation
Indices: 18592595--18592645 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
18592585 ACCCCTCACC
* * *
18592595 CGCAGACAGCACAGGCAGTA
1 CGCACACAGCACAGACAGCA
*
18592615 CGCACCCAGCACAGACAGCA
1 CGCACACAGCACAGACAGCA
*
18592635 CGCACCCAGCA
1 CGCACACAGCA
18592646 GAGGGTATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.41, G:0.24, T:0.02
Consensus pattern (20 bp):
CGCACACAGCACAGACAGCA
Found at i:18593091 original size:22 final size:23
Alignment explanation
Indices: 18593066--18593110 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
18593056 GCACAGATTA
*
18593066 TCTGTTTGG-GCTGTGCGGGCTG
1 TCTGTTTGGAGCTGTGAGGGCTG
18593088 TCTGTTTGGAGCTGTGAGGGCTG
1 TCTGTTTGGAGCTGTGAGGGCTG
18593111 GCTCGCCCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.04, C:0.16, G:0.44, T:0.36
Consensus pattern (23 bp):
TCTGTTTGGAGCTGTGAGGGCTG
Found at i:18596312 original size:40 final size:38
Alignment explanation
Indices: 18596214--18596319 Score: 124
Period size: 38 Copynumber: 2.7 Consensus size: 38
18596204 ATGATAGTGC
* * *
18596214 CCATGTGCACGATGTGAGGGGATGTACACGATGGCACTG
1 CCATGTGCACGATGTG-GGGGATGCACACGATGACACAG
* *
18596253 AC-TGTGCACGATGTGGGGGGATGCACACGATGACTCCAG
1 CCATGTGCACGATGT-GGGGGATGCACACGATGAC-ACAG
18596292 CCATGTGCACGATGTAGGGGGATGCACA
1 CCATGTGCACGATGT-GGGGGATGCACA
18596320 TGAGCTGGGG
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
38 28 0.49
39 5 0.09
40 24 0.42
ACGTcount: A:0.24, C:0.22, G:0.36, T:0.19
Consensus pattern (38 bp):
CCATGTGCACGATGTGGGGGATGCACACGATGACACAG
Found at i:18596813 original size:28 final size:30
Alignment explanation
Indices: 18596772--18596836 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
18596762 ATCTATGGGC
18596772 AATTTTTCAGTTTT-TT-GGGCAAAAATGT
1 AATTTTTCAGTTTTATTGGGGCAAAAATGT
*
18596800 AATTTTTC-GCTTTTATTGGGGCAAAAGTGT
1 AATTTTTCAG-TTTTATTGGGGCAAAAATGT
*
18596830 AAATTTT
1 AATTTTT
18596837 AAAAATTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 1 0.03
28 12 0.38
29 2 0.06
30 17 0.53
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (30 bp):
AATTTTTCAGTTTTATTGGGGCAAAAATGT
Found at i:18608495 original size:22 final size:20
Alignment explanation
Indices: 18608452--18608493 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
18608442 AAGCCAATTC
18608452 TTCATATATTATGAATCATT
1 TTCATATATTATGAATCATT
18608472 TTCATATATTATGAATCATT
1 TTCATATATTATGAATCATT
18608492 TT
1 TT
18608494 TTTCTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (20 bp):
TTCATATATTATGAATCATT
Found at i:18614073 original size:32 final size:32
Alignment explanation
Indices: 18614018--18614165 Score: 204
Period size: 32 Copynumber: 4.8 Consensus size: 32
18614008 CCACTGTGGA
* * *
18614018 CGGCGGAGAGAGAGGGGCAGACCCACTGGTGAG
1 CGGCTGAGAGAGAGGGGC-GACCCACGGGCGAG
18614051 CGGCTGAGAGAGAGGGGCGACCCACGGGCGAG
1 CGGCTGAGAGAGAGGGGCGACCCACGGGCGAG
18614083 CGGCTGAGAGAGAGGGGCGA--C-C---C-A-
1 CGGCTGAGAGAGAGGGGCGACCCACGGGCGAG
18614107 CGGCTGAGAGAGAGGGGCGACCCACGGGCGAG
1 CGGCTGAGAGAGAGGGGCGACCCACGGGCGAG
18614139 CGGCTGAGAGAGAGGGGCGACCCACGG
1 CGGCTGAGAGAGAGGGGCGACCCACGG
18614166 TTGAGAGAGA
Statistics
Matches: 104, Mismatches: 3, Indels: 17
0.84 0.02 0.14
Matches are distributed among these distances:
24 20 0.19
25 1 0.01
26 2 0.02
27 1 0.01
29 1 0.01
30 2 0.02
31 1 0.01
32 59 0.57
33 17 0.16
ACGTcount: A:0.23, C:0.24, G:0.49, T:0.04
Consensus pattern (32 bp):
CGGCTGAGAGAGAGGGGCGACCCACGGGCGAG
Found at i:18614112 original size:24 final size:24
Alignment explanation
Indices: 18614083--18614177 Score: 109
Period size: 24 Copynumber: 3.6 Consensus size: 24
18614073 CACGGGCGAG
18614083 CGGCTGAGAGAGAGGGGCGACCCA
1 CGGCTGAGAGAGAGGGGCGACCCA
18614107 CGGCTGAGAGAGAGGGGCGACCCACGGGCGA
1 CGGCTGAGAGAGAGGGGCGA--C-C---C-A
18614138 GCGGCTGAGAGAGAGGGGCGACCCA
1 -CGGCTGAGAGAGAGGGGCGACCCA
*
18614163 CGGTTGAGAGAGAGG
1 CGGCTGAGAGAGAGG
18614178 AAGATGACCA
Statistics
Matches: 62, Mismatches: 1, Indels: 16
0.78 0.01 0.20
Matches are distributed among these distances:
24 34 0.55
25 1 0.02
26 2 0.03
27 1 0.02
29 1 0.02
30 2 0.03
31 1 0.02
32 20 0.32
ACGTcount: A:0.24, C:0.22, G:0.48, T:0.05
Consensus pattern (24 bp):
CGGCTGAGAGAGAGGGGCGACCCA
Found at i:18614118 original size:56 final size:56
Alignment explanation
Indices: 18614051--18614177 Score: 245
Period size: 56 Copynumber: 2.3 Consensus size: 56
18614041 CACTGGTGAG
18614051 CGGCTGAGAGAGAGGGGCGACCCACGGGCGAGCGGCTGAGAGAGAGGGGCGACCCA
1 CGGCTGAGAGAGAGGGGCGACCCACGGGCGAGCGGCTGAGAGAGAGGGGCGACCCA
18614107 CGGCTGAGAGAGAGGGGCGACCCACGGGCGAGCGGCTGAGAGAGAGGGGCGACCCA
1 CGGCTGAGAGAGAGGGGCGACCCACGGGCGAGCGGCTGAGAGAGAGGGGCGACCCA
*
18614163 CGGTTGAGAGAGAGG
1 CGGCTGAGAGAGAGG
18614178 AAGATGACCA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 70 1.00
ACGTcount: A:0.24, C:0.23, G:0.49, T:0.05
Consensus pattern (56 bp):
CGGCTGAGAGAGAGGGGCGACCCACGGGCGAGCGGCTGAGAGAGAGGGGCGACCCA
Found at i:18617152 original size:21 final size:21
Alignment explanation
Indices: 18617128--18617197 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
18617118 ATGATATTAT
18617128 TTTAAATTTAAATAAATTAAA
1 TTTAAATTTAAATAAATTAAA
* * **
18617149 TTTAAATAT-AATTAATCTTTA
1 TTTAAATTTAAATAAAT-TAAA
*
18617170 TTTAAATTTAAAAAAATTAAA
1 TTTAAATTTAAATAAATTAAA
18617191 TTTAAAT
1 TTTAAAT
18617198 ATAATAGATA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
20 6 0.16
21 27 0.71
22 5 0.13
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAAATTTAAATAAATTAAA
Found at i:18619657 original size:10 final size:9
Alignment explanation
Indices: 18619633--18619668 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
18619623 TTTTATTAAT
18619633 TTATTTTTA
1 TTATTTTTA
18619642 TTATTTTTA
1 TTATTTTTA
18619651 TTAATTTTTA
1 TT-ATTTTTA
18619661 TT-TTTTTA
1 TTATTTTTA
18619669 AGGGTTTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 6 0.23
9 11 0.42
10 9 0.35
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTATTTTTA
Found at i:18620060 original size:18 final size:19
Alignment explanation
Indices: 18620025--18620061 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18620015 TGGATTTGGG
*
18620025 TATTTTTGAAAGGTTAGGA
1 TATTTTTGAAAGGCTAGGA
18620044 TATTTTTGAAA-GCTAGGA
1 TATTTTTGAAAGGCTAGGA
18620062 AATAATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.41
Consensus pattern (19 bp):
TATTTTTGAAAGGCTAGGA
Found at i:18623593 original size:55 final size:53
Alignment explanation
Indices: 18623496--18623606 Score: 204
Period size: 55 Copynumber: 2.1 Consensus size: 53
18623486 TACAAAGAAC
18623496 TTGAATGATTTTATACAACTTTTTCTTAAAACAAGTGCCTTGGGAACAAGCTT
1 TTGAATGATTTTATACAACTTTTTCTTAAAACAAGTGCCTTGGGAACAAGCTT
18623549 NTTGAATGATTTTATACAACTTTTTTCTTAAAACAAGTGCCTTGGGAACAAGCTT
1 -TTGAATGATTTTATACAAC-TTTTTCTTAAAACAAGTGCCTTGGGAACAAGCTT
18623604 TTG
1 TTG
18623607 CTAAATGGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
54 22 0.39
55 34 0.61
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (53 bp):
TTGAATGATTTTATACAACTTTTTCTTAAAACAAGTGCCTTGGGAACAAGCTT
Found at i:18623849 original size:38 final size:40
Alignment explanation
Indices: 18623806--18623909 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 40
18623796 ATAGTGCCCG
18623806 TGTGCACGATGTGGGGGGATGTACACGATGGCACT-GAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGGATA
* * * * * *
18623844 TGTGCACGAAGTGGGAGGATGCACATGATGGCGCTGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGCACTGGATA
18623884 TGTGCACGATGTAGGGGGGATGTACA
1 TGTGCACGATGT-GGGGGGATGTACA
18623910 TGAGTCGGGT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
38 30 0.56
39 2 0.04
40 11 0.20
41 11 0.20
ACGTcount: A:0.22, C:0.15, G:0.40, T:0.22
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGCACTGGATA
Found at i:18639348 original size:20 final size:20
Alignment explanation
Indices: 18639305--18639349 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
18639295 CCTAGGTGGA
*
18639305 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAA-GGAAAAGAGTG
18639326 AAAATTCAA-GAAAAGAAGTG
1 AAAATTCAAGGAAAAG-AGTG
18639346 AAAA
1 AAAA
18639350 AAAGGTCAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 7 0.32
21 9 0.41
ACGTcount: A:0.58, C:0.04, G:0.22, T:0.16
Consensus pattern (20 bp):
AAAATTCAAGGAAAAGAGTG
Found at i:18644392 original size:38 final size:40
Alignment explanation
Indices: 18644341--18644441 Score: 125
Period size: 38 Copynumber: 2.5 Consensus size: 40
18644331 ATAATGTCCG
* *
18644341 TGTGCACGATGTGGGGGGATGTACACGATGGC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGTAAACGATGGCGACGGATA
* * * *
18644379 TGTGCACGATGTGGGGGGATGCAAATGATGGCGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTAAACGATGGCGACGGATA
18644419 TGTGCACGATGTGGGGGGGATGT
1 TGTGCACGATGT-GGGGGGATGT
18644442 GCATGAGCCG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 29 0.55
39 3 0.06
40 12 0.23
41 9 0.17
ACGTcount: A:0.19, C:0.15, G:0.44, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTAAACGATGGCGACGGATA
Found at i:18663273 original size:19 final size:18
Alignment explanation
Indices: 18663244--18663279 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
18663234 TATATTGGAT
18663244 TTGGGTATTTTTGAAAGG
1 TTGGGTATTTTTGAAAGG
18663262 TTGGGATATTTTTGAAAG
1 TTGGG-TATTTTTGAAAG
18663280 CCAAGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (18 bp):
TTGGGTATTTTTGAAAGG
Found at i:18669231 original size:286 final size:286
Alignment explanation
Indices: 18668719--18669290 Score: 1128
Period size: 286 Copynumber: 2.0 Consensus size: 286
18668709 TTCCACTTTT
18668719 CTTTCACGTATGCTCTGCCTATCCATGGTGTAATAAATGGAGGACAGTTATATACTTTCTATGCT
1 CTTTCACGTATGCTCTGCCTATCCATGGTGTAATAAATGGAGGACAGTTATATACTTTCTATGCT
18668784 ACAAAACAATAAATATATGCATTATGAGTAAATGTTACACTATACTTGCTTATCTTATGCACTGT
66 ACAAAACAATAAATATATGCATTATGAGTAAATGTTACACTATACTTGCTTATCTTATGCACTGT
18668849 ATGAGTTGAAAGACTAAAATTTTTATATTTTTTTTATATTTGGAATGAAGAATTCAAATCTTACT
131 ATGAGTTGAAAGACTAAAATTTTTATATTTTTTTTATATTTGGAATGAAGAATTCAAATCTTACT
18668914 CTTTTTTAATAAAATATTATACACCAATCAATAAGTTAAATACTTAAATATTTTACTTAATTCTA
196 CTTTTTTAATAAAATATTATACACCAATCAATAAGTTAAATACTTAAATATTTTACTTAATTCTA
18668979 TTCGTTTTAATGATATATT-TATATA
261 TTCGTTTTAATGATATATTATATATA
18669004 NCTTTCACGTATGCTCTGCCTATCCATGGTGTAATAAATGGAGGACAGTTATATACTTTCTATGC
1 -CTTTCACGTATGCTCTGCCTATCCATGGTGTAATAAATGGAGGACAGTTATATACTTTCTATGC
18669069 TACAAAACAATAAATATATGCATTATGAGTAAATGTTACACTATACTTGCTTATCTTATGCACTG
65 TACAAAACAATAAATATATGCATTATGAGTAAATGTTACACTATACTTGCTTATCTTATGCACTG
18669134 TATGAGTTGAAAGACTAAAATTTTTATATTTTTTTTATATTTGGAATGAAGAATTCAAATCTTAC
130 TATGAGTTGAAAGACTAAAATTTTTATATTTTTTTTATATTTGGAATGAAGAATTCAAATCTTAC
18669199 TCTTTTTTAATAAAATATTATACACCAATCAATAAGTTAAATACTTAAATATTTTACTTAATTCT
195 TCTTTTTTAATAAAATATTATACACCAATCAATAAGTTAAATACTTAAATATTTTACTTAATTCT
18669264 ATTCGTTTTAATGATATATTATATATA
260 ATTCGTTTTAATGATATATTATATATA
18669291 TATATACATA
Statistics
Matches: 285, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
286 279 0.98
287 6 0.02
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (286 bp):
CTTTCACGTATGCTCTGCCTATCCATGGTGTAATAAATGGAGGACAGTTATATACTTTCTATGCT
ACAAAACAATAAATATATGCATTATGAGTAAATGTTACACTATACTTGCTTATCTTATGCACTGT
ATGAGTTGAAAGACTAAAATTTTTATATTTTTTTTATATTTGGAATGAAGAATTCAAATCTTACT
CTTTTTTAATAAAATATTATACACCAATCAATAAGTTAAATACTTAAATATTTTACTTAATTCTA
TTCGTTTTAATGATATATTATATATA
Found at i:18669288 original size:2 final size:2
Alignment explanation
Indices: 18669277--18669348 Score: 101
Period size: 2 Copynumber: 36.5 Consensus size: 2
18669267 CGTTTTAATG
* * *
18669277 AT AT AT -T AT AT AT AT AT AT AC AT AC AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
18669318 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18669349 ACTGAGGAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:18681709 original size:100 final size:101
Alignment explanation
Indices: 18681580--18681781 Score: 291
Period size: 101 Copynumber: 2.0 Consensus size: 101
18681570 TTAAATAGTA
* *
18681580 TCTAAATGCATTTTTAAATTTTAGA-TTTTTTTATCTTAATCTTTGTAAGAACACAAAAATTCTA
1 TCTAAACGCAGTTTTAAATTTTAGATTTTTTTTATCTTAATCTTTGTAAGAACA-AAAAATTCTA
* ** *
18681644 GA-TTTTGATATTCTGTTGTTGGGTCTTCTGTTTTTT
65 AATTTTTGATATTCCATTATTGGGTCTTCTGTTTTTT
* *
18681680 TCTAAACGCAGTTTTGAATTTTAGATTTTTTTTCTCTTAATCTTTGTAAGAACAAAAAATTCTAA
1 TCTAAACGCAGTTTTAAATTTTAGATTTTTTTTATCTTAATCTTTGTAAGAACAAAAAATTCTAA
* *
18681745 ATTTTTGATATTCCATTATTGGTTTTTCTGTTTTTT
66 ATTTTTGATATTCCATTATTGGGTCTTCTGTTTTTT
18681781 T
1 T
18681782 AGTAGTTTTT
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
100 33 0.37
101 57 0.63
ACGTcount: A:0.26, C:0.10, G:0.11, T:0.52
Consensus pattern (101 bp):
TCTAAACGCAGTTTTAAATTTTAGATTTTTTTTATCTTAATCTTTGTAAGAACAAAAAATTCTAA
ATTTTTGATATTCCATTATTGGGTCTTCTGTTTTTT
Found at i:18681976 original size:15 final size:16
Alignment explanation
Indices: 18681958--18681992 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
18681948 TAAGCTTTTT
18681958 TTTTGT-AAAAATTTA
1 TTTTGTAAAAAATTTA
*
18681973 TTTTTTAAAAAATTTA
1 TTTTGTAAAAAATTTA
18681989 TTTT
1 TTTT
18681993 TATTTAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTTGTAAAAAATTTA
Found at i:18694215 original size:14 final size:14
Alignment explanation
Indices: 18694193--18694223 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
18694183 TTCCGACGAA
18694193 AAAAATTTCGTTGG
1 AAAAATTTCGTTGG
*
18694207 AAAATTTTCGTTGG
1 AAAAATTTCGTTGG
18694221 AAA
1 AAA
18694224 GTTCCAATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (14 bp):
AAAAATTTCGTTGG
Found at i:18694532 original size:22 final size:23
Alignment explanation
Indices: 18694492--18694562 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 23
18694482 ATACTATTCT
**
18694492 TTAAATTTTTTATTTAAAATATA
1 TTAAATTTTTTATAGAAAATATA
*
18694515 TTAAGATTTTTTA-A-AAAATTTA
1 TTAA-ATTTTTTATAGAAAATATA
*
18694537 TT-AATTTTTTATAGGAAATATA
1 TTAAATTTTTTATAGAAAATATA
18694559 TTAA
1 TTAA
18694563 TAAAATAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 8 0.20
21 2 0.05
22 17 0.43
23 5 0.12
24 8 0.20
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (23 bp):
TTAAATTTTTTATAGAAAATATA
Done.