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 50 of 54
Found at i:19708160 original size:71 final size:70
Alignment explanation
Indices: 19708111--19708255 Score: 272
Period size: 71 Copynumber: 2.0 Consensus size: 70
19708101 CGTTCTATGT
19708111 CAATCCTCCTCTCTATAAATCACCCATTATCTATTATATTTATAAAAAATCGTTTTAAATATATA
1 CAATCCTCCTCTCTATAAATCACCCATTATCTATTATATTTATAAAAAATC-TTTTAAATATATA
19708176 ACAAAA
65 ACAAAA
19708182 CAATCCTCCTCTCTATAAATCACCCATTATCTATTATATTTATAAAAAATCGTTTTAAATATATA
1 CAATCCTCCTCTCTATAAATCACCCATTATCTATTATATTTATAAAAAATC-TTTTAAATATATA
19708247 ACAAAA
65 ACAAAA
19708253 CAA
1 CAA
19708256 AATTAACTTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.43, C:0.20, G:0.01, T:0.36
Consensus pattern (70 bp):
CAATCCTCCTCTCTATAAATCACCCATTATCTATTATATTTATAAAAAATCTTTTAAATATATAA
CAAAA
Found at i:19709410 original size:18 final size:18
Alignment explanation
Indices: 19709362--19709410 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
19709352 ATTAATTTTT
19709362 TTATTA-TAAATAAAAAAA
1 TTATTATTAAAT-AAAAAA
*
19709380 TTCATAATT-AATAAAAAA
1 TT-ATTATTAAATAAAAAA
19709398 TTATTATTAAATA
1 TTATTATTAAATA
19709411 TTTATAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 5 0.19
18 14 0.54
19 6 0.23
20 1 0.04
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TTATTATTAAATAAAAAA
Found at i:19715739 original size:23 final size:23
Alignment explanation
Indices: 19715663--19715772 Score: 94
Period size: 23 Copynumber: 4.8 Consensus size: 23
19715653 GTGTAGTTTG
*
19715663 TTGGAGTCATGGCGTGTAACATC
1 TTGGAGTCATGGCGTGTAACTTC
*
19715686 TTGTAGTCATGGCGTGTAACTTC
1 TTGGAGTCATGGCGTGTAACTTC
** * * * *
19715709 CAGCAGTCGTGGCGTGGAACTTG
1 TTGGAGTCATGGCGTGTAACTTC
* * * *
19715732 TTGGAGTCTTGGCATGTAGCTTG
1 TTGGAGTCATGGCGTGTAACTTC
* *
19715755 TTGAAGTTATGGCGTGTA
1 TTGGAGTCATGGCGTGTA
19715773 GTTTGCAACT
Statistics
Matches: 68, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.34
Consensus pattern (23 bp):
TTGGAGTCATGGCGTGTAACTTC
Found at i:19717311 original size:17 final size:17
Alignment explanation
Indices: 19717285--19717319 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19717275 CCAAATTCAA
19717285 AAAAAAAAAAATAATAAT
1 AAAAAAAAAAA-AATAAT
*
19717303 AAAAGAAAAAAAATAAT
1 AAAAAAAAAAAAATAAT
19717320 TAATTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAAAAAAAAAAATAAT
Found at i:19723069 original size:29 final size:29
Alignment explanation
Indices: 19723033--19723089 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
19723023 GGATATTCAA
* *
19723033 TATATCTTGCTTAGCTACTGTGGATATTG
1 TATATCTTACTTAGCTACTGTAGATATTG
* *
19723062 TATATCTTATTTAGCTATTGTAGATATT
1 TATATCTTACTTAGCTACTGTAGATATT
19723090 ATAAATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.49
Consensus pattern (29 bp):
TATATCTTACTTAGCTACTGTAGATATTG
Found at i:19726696 original size:38 final size:39
Alignment explanation
Indices: 19726654--19726756 Score: 145
Period size: 38 Copynumber: 2.6 Consensus size: 39
19726644 ATAGTGCATG
* * *
19726654 TGTGCACGATGTAGGGGGATGTACACGATGGCACTGGC-
1 TGTGCACGATGTGGGGGGATGCACACGATGACACTGGCA
* *
19726692 TGTGCACAATGTGGGGGGATGCACACGATGACTCTGGCTA
1 TGTGCACGATGTGGGGGGATGCACACGATGACACTGGC-A
19726732 TGTGCACGATGTGGGGGGATGCACA
1 TGTGCACGATGTGGGGGGATGCACA
19726757 TGAGCTGGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 33 0.58
40 24 0.42
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.21
Consensus pattern (39 bp):
TGTGCACGATGTGGGGGGATGCACACGATGACACTGGCA
Found at i:19731009 original size:20 final size:20
Alignment explanation
Indices: 19730986--19731028 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
19730976 CCATTTCTCT
19730986 TTTGGACTTTTCTTTTCTTA
1 TTTGGACTTTTCTTTTCTTA
19731006 TTTGGACTTTTCTTTTCTTA
1 TTTGGACTTTTCTTTTCTTA
19731026 TTT
1 TTT
19731029 CCATGGGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.14, G:0.09, T:0.67
Consensus pattern (20 bp):
TTTGGACTTTTCTTTTCTTA
Found at i:19731108 original size:22 final size:22
Alignment explanation
Indices: 19731076--19731134 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 22
19731066 CCACTCTTTT
*
19731076 TTTTTGTTTCTTTCTT-TTCCCG
1 TTTTT-TTTCTTTCTTCTGCCCG
*
19731098 TTTCTTTTTCTCTCTCTTCTGCTCG
1 TTT-TTTTTCT-T-TCTTCTGCCCG
19731123 TTTTTTTTCTTT
1 TTTTTTTTCTTT
19731135 TCCTTCCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 9 0.29
23 4 0.13
24 11 0.35
25 7 0.23
ACGTcount: A:0.00, C:0.24, G:0.07, T:0.69
Consensus pattern (22 bp):
TTTTTTTTCTTTCTTCTGCCCG
Found at i:19731385 original size:16 final size:16
Alignment explanation
Indices: 19731364--19731394 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19731354 TCACGTTCCT
19731364 TTTCTTCTTCTTTTTA
1 TTTCTTCTTCTTTTTA
*
19731380 TTTCTTTTTCTTTTT
1 TTTCTTCTTCTTTTT
19731395 CTTCTCTCCA
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:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTCTTCTTCTTTTTA
Found at i:19732264 original size:19 final size:18
Alignment explanation
Indices: 19732242--19732284 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
19732232 TTAATATTTT
19732242 AATATTATTTTATTCATAA
1 AATATTATTTTATTC-TAA
*
19732261 AATAATATTTTATTCTAA
1 AATATTATTTTATTCTAA
*
19732279 ATTATT
1 AATATT
19732285 TTTCTCATGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTATTTTATTCTAA
Found at i:19736166 original size:2 final size:2
Alignment explanation
Indices: 19736159--19736188 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19736149 ATTTGTGCCT
19736159 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19736189 AGAAAATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19737842 original size:35 final size:35
Alignment explanation
Indices: 19737767--19737849 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 35
19737757 TCTTCTCTAT
* *
19737767 TTCTCCCCTCAAAAACGGCTGCAACCATCCAAGGAA
1 TTCTCCCCTC-AAAACGGCTGCAACCACCCAAGAAA
* *
19737803 TTCTCTCCTCAAACCGGCTGCAACCACCCAA-AAA
1 TTCTCCCCTCAAAACGGCTGCAACCACCCAAGAAA
19737837 CTTCTCCCCTCAA
1 -TTCTCCCCTCAA
19737850 CCAGCGATAC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 2 0.05
35 30 0.73
36 9 0.22
ACGTcount: A:0.30, C:0.41, G:0.10, T:0.19
Consensus pattern (35 bp):
TTCTCCCCTCAAAACGGCTGCAACCACCCAAGAAA
Found at i:19739788 original size:19 final size:19
Alignment explanation
Indices: 19739764--19739801 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19739754 CTGCCAAACC
*
19739764 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
19739783 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
19739802 AGTCTAATAG
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:19740922 original size:6 final size:6
Alignment explanation
Indices: 19740911--19740945 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
19740901 GTCACCTTCA
19740911 TTTTCT TTTTC- TTTT-T TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T
19740946 CTCTCCATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 8 0.30
6 19 0.70
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:19740932 original size:16 final size:16
Alignment explanation
Indices: 19740911--19740942 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19740901 GTCACCTTCA
19740911 TTTTCTTTTTCTTTTT
1 TTTTCTTTTTCTTTTT
19740927 TTTTCTTTTTCTTTTT
1 TTTTCTTTTTCTTTTT
19740943 CTTCTCTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTT
Found at i:19741818 original size:19 final size:18
Alignment explanation
Indices: 19741796--19741838 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
19741786 TTAATATTTT
*
19741796 AATATTATTTTTTTCATAA
1 AATATTATTTTATTC-TAA
*
19741815 AATAATATTTTATTCTAA
1 AATATTATTTTATTCTAA
*
19741833 ATTATT
1 AATATT
19741839 TTTCTCACCC
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
AATATTATTTTATTCTAA
Found at i:19743658 original size:20 final size:20
Alignment explanation
Indices: 19743621--19743660 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
19743611 GCATAAATAT
**
19743621 CTCATTTCTCCAGTAGCTTC
1 CTCATTTCTCCAACAGCTTC
*
19743641 CTCATTTTTCCAACAGCTTC
1 CTCATTTCTCCAACAGCTTC
19743661 TTCTTCTTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.35, G:0.07, T:0.40
Consensus pattern (20 bp):
CTCATTTCTCCAACAGCTTC
Found at i:19744540 original size:35 final size:37
Alignment explanation
Indices: 19744517--19744587 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
19744507 AGTGTGAAGG
*
19744517 ATGACATT-GTTGTGCGCGATGTGGGGGTTGCACACA
1 ATGACATTGGTTGTGCGCGATGTGGGAGTTGCACACA
* * *
19744553 ATGGCATTGGTTGTGCGCGATGTGGGGGATGCACA
1 ATGACATTGGTTGTGCGCGATGTGGGAGTTGCACA
19744588 TGCCGGTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 7 0.22
37 25 0.78
ACGTcount: A:0.18, C:0.15, G:0.39, T:0.27
Consensus pattern (37 bp):
ATGACATTGGTTGTGCGCGATGTGGGAGTTGCACACA
Found at i:19744645 original size:104 final size:103
Alignment explanation
Indices: 19744461--19744796 Score: 503
Period size: 104 Copynumber: 3.3 Consensus size: 103
19744451 TAACTGTGCG
* * *
19744461 TGTGCACGATGTGGGGGATGCACATGTCGGTGATGACAGGTGTGGGAGTGTGAAGGATGACATTG
1 TGTGCGCGATGTGGGGGATGCACATGCCGGTGATGACAGGTGTGGGAGTGTGGAGGATGACATTG
*
19744526 TTGTGCGCGATGTGGGGGTTGCACACAATGGCATTGGT
66 TTGTGCGCGATGTGGGGGTTGCACACAATGGCATTAGT
*
19744564 TGTGCGCGATGTGGGGGATGCACATGCCGGTGATGACAGGGTGTGCGAGTGTGGAGGATGACATT
1 TGTGCGCGATGTGGGGGATGCACATGCCGGTGATGACA-GGTGTGGGAGTGTGGAGGATGACATT
* * * *
19744629 GTTGTGCGTGGTGTGGGGTTTGTACACAATGGCATTAGT
65 GTTGTGCGCGATGTGGGGGTTGCACACAATGGCATTAGT
* **
19744668 TGTGCGCGATGTGGGGGGTGCACATGCCGGTGATGACAAGGTGTGGGAGTGAAGAGGATGACATT
1 TGTGCGCGATGTGGGGGATGCACATGCCGGTGATGAC-AGGTGTGGGAGTGTGGAGGATGACATT
* *
19744733 ATTGTGTGCGATGTGGGGGTTGCACACAATGGCATTAGT
65 GTTGTGCGCGATGTGGGGGTTGCACACAATGGCATTAGT
* *
19744772 TGTGTGTGATGTGGGGG-TGCACATG
1 TGTGCGCGATGTGGGGGATGCACATG
19744797 ATGACTCCAG
Statistics
Matches: 210, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
103 44 0.21
104 165 0.79
105 1 0.00
ACGTcount: A:0.19, C:0.12, G:0.42, T:0.27
Consensus pattern (103 bp):
TGTGCGCGATGTGGGGGATGCACATGCCGGTGATGACAGGTGTGGGAGTGTGGAGGATGACATTG
TTGTGCGCGATGTGGGGGTTGCACACAATGGCATTAGT
Found at i:19744878 original size:2 final size:2
Alignment explanation
Indices: 19744871--19744899 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19744861 CATGTTTATG
19744871 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19744900 GGAAGTTCGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19748756 original size:28 final size:27
Alignment explanation
Indices: 19748720--19748772 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
19748710 ATATCCTGGT
*
19748720 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
19748747 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
19748773 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:19748842 original size:20 final size:20
Alignment explanation
Indices: 19748817--19748862 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
19748807 CTTCTAAACC
19748817 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
19748837 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
19748857 TCAAAT
1 TCAAAT
19748863 GGGGCCAAAA
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:19749632 original size:13 final size:13
Alignment explanation
Indices: 19749614--19749638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19749604 TTCCAGAAAA
19749614 TTTATAAAATCAT
1 TTTATAAAATCAT
19749627 TTTATAAAATCA
1 TTTATAAAATCA
19749639 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:19759518 original size:27 final size:28
Alignment explanation
Indices: 19759488--19759544 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
19759478 TTTCGAGGAT
* * *
19759488 AAGGGTAAAATAGTCATTTTGC-CACCC
1 AAGGGAAAAATAGTAATTTTACACACCC
*
19759515 AAGGGAAAAATTGTAATTTTACACACCC
1 AAGGGAAAAATAGTAATTTTACACACCC
19759543 AA
1 AA
19759545 CACTTGTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (28 bp):
AAGGGAAAAATAGTAATTTTACACACCC
Found at i:19762849 original size:20 final size:20
Alignment explanation
Indices: 19762824--19762863 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19762814 GCATAAATAT
19762824 CTCATTTCTCTAGCAACTTC
1 CTCATTTCTCTAGCAACTTC
* *
19762844 CTCATTTTTCTAGCAGCTTC
1 CTCATTTCTCTAGCAACTTC
19762864 TTCTTCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.33, G:0.07, T:0.42
Consensus pattern (20 bp):
CTCATTTCTCTAGCAACTTC
Found at i:19764037 original size:104 final size:104
Alignment explanation
Indices: 19763723--19764275 Score: 831
Period size: 104 Copynumber: 5.3 Consensus size: 104
19763713 GGGAGTGTGG
* *
19763723 ATGGCATTAGTTGTGCACGATGTGGGGGATGCATACGCCGGTGATGACAGGGTGTGGGAGTGTGG
1 ATGGCATTAGTTGTGCACGATGTGGGGGATGCACATGCCGGTGATGACAGGGTGTGGGAGTGTGG
*
19763788 AGGATGACATTGTTGTGTGCGATGTGGGGGTTACACACA
66 AGGATGACATTGTTGTGCGCGATGTGGGGGTTACACACA
* * *
19763827 ATGGCATTAGTTGTGCACGATGTGAGGGATGCATATGCCGGTGATGATAGGGTGT-GGAGTGTGG
1 ATGGCATTAGTTGTGCACGATGTGGGGGATGCACATGCCGGTGATGACAGGGTGTGGGAGTGTGG
*
19763891 AGGATGACATTGTTGTGCGCGATGTGGGGGTTACACATA
66 AGGATGACATTGTTGTGCGCGATGTGGGGGTTACACACA
* * * * *
19763930 ATGGCATTAGTTGTGCGCAATGTGGGGGATGCAAATGCAGGTGATGACAAGGTGTGGGAGTGTGG
1 ATGGCATTAGTTGTGCACGATGTGGGGGATGCACATGCCGGTGATGACAGGGTGTGGGAGTGTGG
* * *
19763995 AGGATGACATTGTTATGTGCGATATGGGGGTTACACACA
66 AGGATGACATTGTTGTGCGCGATGTGGGGGTTACACACA
* * * * *
19764034 ATGGCATTAGTTGTGTACGATGTGAGGGATGCACATGTCGGTGATGATAGGGTGTGGGAATGTGG
1 ATGGCATTAGTTGTGCACGATGTGGGGGATGCACATGCCGGTGATGACAGGGTGTGGGAGTGTGG
* *
19764099 AGGATGACATTGTTGTGCGTGATGTGGGGGTTGCACACA
66 AGGATGACATTGTTGTGCGCGATGTGGGGGTTACACACA
* * *
19764138 ATGGCATTAGCTGTGCATGATGTGGGGGATGCACATGCCGGTGATGACAGGGTGTGGGAGTGGGG
1 ATGGCATTAGTTGTGCACGATGTGGGGGATGCACATGCCGGTGATGACAGGGTGTGGGAGTGTGG
* * *
19764203 AGGATGACATTGTTGTGCGCTATGTGGGGGTTGCAAACA
66 AGGATGACATTGTTGTGCGCGATGTGGGGGTTACACACA
*
19764242 ATGGCATTAGTTGTGCGCGATGTGGGGG-TGCACA
1 ATGGCATTAGTTGTGCACGATGTGGGGGATGCACA
19764276 CAATGACTCC
Statistics
Matches: 403, Mismatches: 45, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
103 100 0.25
104 303 0.75
ACGTcount: A:0.21, C:0.11, G:0.41, T:0.27
Consensus pattern (104 bp):
ATGGCATTAGTTGTGCACGATGTGGGGGATGCACATGCCGGTGATGACAGGGTGTGGGAGTGTGG
AGGATGACATTGTTGTGCGCGATGTGGGGGTTACACACA
Found at i:19764078 original size:207 final size:208
Alignment explanation
Indices: 19763723--19764275 Score: 867
Period size: 207 Copynumber: 2.7 Consensus size: 208
19763713 GGGAGTGTGG
* *
19763723 ATGGCATTAGTTGTGCACGATGTGGGGGATGCATACGCCGGTGATGACAGGGTGTGGGAGTGTGG
1 ATGGCATTAGTTGTGCACGATGTGGGGGATGCAAATGCCGGTGATGACAGGGTGTGGGAGTGTGG
19763788 AGGATGACATTGTTGTGTGCGATGTGGGGGTTACACACAATGGCATTAGTTGTGCACGATGTGAG
66 AGGATGACATTGTTGTGTGCGATGTGGGGGTTACACACAATGGCATTAGTTGTGCACGATGTGAG
* *
19763853 GGATGCATATGCCGGTGATGATAGGGTGT-GGAGTGTGGAGGATGACATTGTTGTGCGCGATGTG
131 GGATGCACATGCCGGTGATGATAGGGTGTGGGAATGTGGAGGATGACATTGTTGTGCGCGATGTG
*
19763917 GGGGTTACACATA
196 GGGGTTACACACA
* * * *
19763930 ATGGCATTAGTTGTGCGCAATGTGGGGGATGCAAATGCAGGTGATGACAAGGTGTGGGAGTGTGG
1 ATGGCATTAGTTGTGCACGATGTGGGGGATGCAAATGCCGGTGATGACAGGGTGTGGGAGTGTGG
* * *
19763995 AGGATGACATTGTTATGTGCGATATGGGGGTTACACACAATGGCATTAGTTGTGTACGATGTGAG
66 AGGATGACATTGTTGTGTGCGATGTGGGGGTTACACACAATGGCATTAGTTGTGCACGATGTGAG
* *
19764060 GGATGCACATGTCGGTGATGATAGGGTGTGGGAATGTGGAGGATGACATTGTTGTGCGTGATGTG
131 GGATGCACATGCCGGTGATGATAGGGTGTGGGAATGTGGAGGATGACATTGTTGTGCGCGATGTG
*
19764125 GGGGTTGCACACA
196 GGGGTTACACACA
* * * *
19764138 ATGGCATTAGCTGTGCATGATGTGGGGGATGCACATGCCGGTGATGACAGGGTGTGGGAGTGGGG
1 ATGGCATTAGTTGTGCACGATGTGGGGGATGCAAATGCCGGTGATGACAGGGTGTGGGAGTGTGG
* * * * *
19764203 AGGATGACATTGTTGTGCGCTATGTGGGGGTTGCAAACAATGGCATTAGTTGTGCGCGATGTG-G
66 AGGATGACATTGTTGTGTGCGATGTGGGGGTTACACACAATGGCATTAGTTGTGCACGATGTGAG
*
19764267 GGGTGCACA
131 GGATGCACA
19764276 CAATGACTCC
Statistics
Matches: 313, Mismatches: 32, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
207 157 0.50
208 156 0.50
ACGTcount: A:0.21, C:0.11, G:0.41, T:0.27
Consensus pattern (208 bp):
ATGGCATTAGTTGTGCACGATGTGGGGGATGCAAATGCCGGTGATGACAGGGTGTGGGAGTGTGG
AGGATGACATTGTTGTGTGCGATGTGGGGGTTACACACAATGGCATTAGTTGTGCACGATGTGAG
GGATGCACATGCCGGTGATGATAGGGTGTGGGAATGTGGAGGATGACATTGTTGTGCGCGATGTG
GGGGTTACACACA
Found at i:19764256 original size:37 final size:35
Alignment explanation
Indices: 19764210--19764280 Score: 106
Period size: 37 Copynumber: 2.0 Consensus size: 35
19764200 GGGAGGATGA
*
19764210 CATTGTTGTGCGCTATGTGGGGGTTGCAAACAATGG
1 CATTGTTGTGCGCGATGTGGGGG-TGCAAACAATGG
*
19764246 CATTAGTTGTGCGCGATGTGGGGGTGCACACAATG
1 CATT-GTTGTGCGCGATGTGGGGGTGCAAACAATG
19764281 ACTCCAGCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 14 0.44
37 18 0.56
ACGTcount: A:0.20, C:0.15, G:0.37, T:0.28
Consensus pattern (35 bp):
CATTGTTGTGCGCGATGTGGGGGTGCAAACAATGG
Found at i:19764960 original size:19 final size:19
Alignment explanation
Indices: 19764936--19764973 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19764926 CCATTTGACT
*
19764936 TATTGGAGTATGATTTGAG
1 TATTGGAGAATGATTTGAG
19764955 TATTGGAGAATGATTTGAG
1 TATTGGAGAATGATTTGAG
19764974 GTTTAGAAGT
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:0.32, T:0.39
Consensus pattern (19 bp):
TATTGGAGAATGATTTGAG
Found at i:19767433 original size:15 final size:14
Alignment explanation
Indices: 19767413--19767465 Score: 70
Period size: 15 Copynumber: 3.6 Consensus size: 14
19767403 GGTTTAAAGA
19767413 TTAAAGATTTTGGTT
1 TTAAAG-TTTTGGTT
*
19767428 TTAAAGCTTTGGATT
1 TTAAAGTTTTGG-TT
19767443 TTAAAGTTTTTGGTT
1 TTAAAG-TTTTGGTT
19767458 TTAAAGTT
1 TTAAAGTT
19767466 GTTTTAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 7 0.21
15 22 0.65
16 5 0.15
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.53
Consensus pattern (14 bp):
TTAAAGTTTTGGTT
Found at i:19769525 original size:19 final size:19
Alignment explanation
Indices: 19769501--19769538 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19769491 CCATTTGACT
19769501 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
19769520 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
19769539 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:19770781 original size:13 final size:13
Alignment explanation
Indices: 19770763--19770787 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19770753 TGAGAAATTG
19770763 TGATTTTATAAAA
1 TGATTTTATAAAA
19770776 TGATTTTATAAA
1 TGATTTTATAAA
19770788 TTTTCTAGAA
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:19772381 original size:19 final size:19
Alignment explanation
Indices: 19772357--19772394 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19772347 CCATTTGACT
19772357 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
19772376 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
19772395 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:19773636 original size:13 final size:13
Alignment explanation
Indices: 19773618--19773642 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19773608 GGAGAAATTG
19773618 TGATTTTATAAAA
1 TGATTTTATAAAA
19773631 TGATTTTATAAA
1 TGATTTTATAAA
19773643 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:19776526 original size:15 final size:16
Alignment explanation
Indices: 19776506--19776549 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
19776496 TTTGTTTTCC
19776506 TTCCTTTCTTCTCTT-
1 TTCCTTTCTTCTCTTA
*
19776521 TTCCTTTCTTTTCTTA
1 TTCCTTTCTTCTCTTA
19776537 CTT-CTTTCTTCTC
1 -TTCCTTTCTTCTC
19776550 CTAACTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 14 0.56
16 9 0.36
17 2 0.08
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (16 bp):
TTCCTTTCTTCTCTTA
Found at i:19783850 original size:2 final size:2
Alignment explanation
Indices: 19783843--19783868 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19783833 TTCGATATGA
19783843 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19783869 TGCTCGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19784737 original size:16 final size:16
Alignment explanation
Indices: 19784716--19784751 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
19784706 TAAAACAAAA
19784716 TTTGGATTTTGATTCT
1 TTTGGATTTTGATTCT
*
19784732 TTTGGATTTTGATTTT
1 TTTGGATTTTGATTCT
19784748 TTTG
1 TTTG
19784752 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.03, G:0.19, T:0.67
Consensus pattern (16 bp):
TTTGGATTTTGATTCT
Found at i:19786110 original size:68 final size:68
Alignment explanation
Indices: 19785931--19786112 Score: 197
Period size: 68 Copynumber: 2.7 Consensus size: 68
19785921 CGTGTTTGGT
* *
19785931 ATGATGAATGCCATGAGATTATGTATATGATGTATATTTT-ATATTCTACAAAAGACGATTGAGA
1 ATGATGAATGCCATGAGATTATGTATATGATGTAT-TTTTCATGTACTACAAAAGACGATTGAGA
*
19785995 AAGC
65 AAAC
* * * * * ** * *
19785999 ATGATGAATGCCATAAGATAATGTACATGATAG-ATATTCCATGTACTACATGAGATGATTTAGA
1 ATGATGAATGCCATGAGATTATGTATATGAT-GTATTTTTCATGTACTACAAAAGACGATTGAGA
19786063 AAAC
65 AAAC
* * *
19786067 ATGAAGAATGCCTTGAGATTATGTATATAATGTATTTTTCATGTAC
1 ATGATGAATGCCATGAGATTATGTATATGATGTATTTTTCATGTAC
19786113 CTTATGAGAT
Statistics
Matches: 91, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
67 3 0.03
68 87 0.96
69 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (68 bp):
ATGATGAATGCCATGAGATTATGTATATGATGTATTTTTCATGTACTACAAAAGACGATTGAGAA
AAC
Found at i:19786669 original size:20 final size:20
Alignment explanation
Indices: 19786623--19786674 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 20
19786613 ACATTTTACT
**
19786623 AATGTATCGATAAATGCTTG
1 AATGTATCGATAAATGCAAG
* * *
19786643 AAAGTATCGATACATTCAAG
1 AATGTATCGATAAATGCAAG
*
19786663 AATGTATTGATA
1 AATGTATCGATA
19786675 GATTTGGTGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (20 bp):
AATGTATCGATAAATGCAAG
Found at i:19796739 original size:80 final size:80
Alignment explanation
Indices: 19796628--19796787 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
19796618 ACATATTGAT
*
19796628 AACCTCCTTATTTTTTATGGTCATAAAAACCACAATTTGCAAAACTAGCTTTCTATCACAAGTTT
1 AACCTCCATATTTTTTATGGTCATAAAAACCACAATTTGCAAAACTAGCTTTCTATCACAAGTTT
19796693 GCAATCGGAACATTA
66 GCAATCGGAACATTA
19796708 AACCTCCATATTTTTTATGGTCATAAAAACCACAATTTGCAAAACTAGCTTTCTATCACAAGTTT
1 AACCTCCATATTTTTTATGGTCATAAAAACCACAATTTGCAAAACTAGCTTTCTATCACAAGTTT
19796773 GCAATCGGAACATTA
66 GCAATCGGAACATTA
19796788 GTCTCAACAT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (80 bp):
AACCTCCATATTTTTTATGGTCATAAAAACCACAATTTGCAAAACTAGCTTTCTATCACAAGTTT
GCAATCGGAACATTA
Found at i:19800114 original size:15 final size:16
Alignment explanation
Indices: 19800086--19800115 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19800076 AAAAATGAGT
19800086 AAACAACTCAATAATA
1 AAACAACTCAATAATA
19800102 AAACAACTC-ATAAT
1 AAACAACTCAATAAT
19800116 CCCAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (16 bp):
AAACAACTCAATAATA
Found at i:19803231 original size:10 final size:10
Alignment explanation
Indices: 19803216--19803249 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
19803206 TTCAGTACCA
*
19803216 AGGAGACAAT
1 AGGAGACAAG
19803226 AGGAGACAAG
1 AGGAGACAAG
19803236 AGGAGACAAG
1 AGGAGACAAG
19803246 AGGA
1 AGGA
19803250 AATTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.50, C:0.09, G:0.38, T:0.03
Consensus pattern (10 bp):
AGGAGACAAG
Found at i:19804665 original size:35 final size:35
Alignment explanation
Indices: 19804618--19804760 Score: 189
Period size: 35 Copynumber: 4.1 Consensus size: 35
19804608 GTGTTGATAG
* * * *
19804618 TGATGTTTATGTGTGCGAGTAGGGAGTACATACGA
1 TGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGA
* * *
19804653 TGATGTTGATGTGTGCGAGTAGGGAGTGC-TACTA
1 TGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGA
* * *
19804687 TGATATTGAAGTGTGTGAGTGGGGAGTGCACACGA
1 TGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGA
19804722 TGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGA
1 TGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGA
19804757 TGAT
1 TGAT
19804761 ATTGCCTTCT
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
34 29 0.31
35 66 0.69
ACGTcount: A:0.24, C:0.09, G:0.38, T:0.29
Consensus pattern (35 bp):
TGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGA
Found at i:19804701 original size:69 final size:70
Alignment explanation
Indices: 19804628--19804764 Score: 204
Period size: 69 Copynumber: 2.0 Consensus size: 70
19804618 TGATGTTTAT
* * * *
19804628 GTGTGCGAGTAGGGAGTACATACGATGATGTTGATGTGTGCGAGTAGGGAGTGC-TACTATGATA
1 GTGTGCGAGTAGGGAGTACACACGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGATGATA
19804692 TTGAA
66 TTGAA
* * *
19804697 GTGTGTGAGTGGGGAGTGCACACGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGATGATA
1 GTGTGCGAGTAGGGAGTACACACGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGATGATA
19804762 TTG
66 TTG
19804765 CCTTCTGCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
69 49 0.82
70 11 0.18
ACGTcount: A:0.25, C:0.09, G:0.39, T:0.27
Consensus pattern (70 bp):
GTGTGCGAGTAGGGAGTACACACGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACGATGATA
TTGAA
Found at i:19804779 original size:35 final size:35
Alignment explanation
Indices: 19804631--19804788 Score: 156
Period size: 35 Copynumber: 4.5 Consensus size: 35
19804621 TGTTTATGTG
* * * * *
19804631 TGCGAGTAGGGAGTACATACGATGATGTTGATGTG
1 TGCGAGTAGGGAGTGCACACGATGATATTGAAGTC
* * *
19804666 TGCGAGTAGGGAGTGC-TACTATGATATTGAAGTG
1 TGCGAGTAGGGAGTGCACACGATGATATTGAAGTC
* * * *
19804700 TGTGAGTGGGGAGTGCACACGATGATGTTGAAGTG
1 TGCGAGTAGGGAGTGCACACGATGATATTGAAGTC
***
19804735 TGCGAGTAGGGAGTGCACACGATGATATTGCCTTC
1 TGCGAGTAGGGAGTGCACACGATGATATTGAAGTC
**
19804770 TGCTTGTAGGGAGTGCACA
1 TGCGAGTAGGGAGTGCACA
19804789 TTGGCTAAGT
Statistics
Matches: 104, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
34 29 0.28
35 75 0.72
ACGTcount: A:0.24, C:0.12, G:0.37, T:0.27
Consensus pattern (35 bp):
TGCGAGTAGGGAGTGCACACGATGATATTGAAGTC
Found at i:19807912 original size:28 final size:30
Alignment explanation
Indices: 19807871--19807930 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
19807861 GTCTATGGTC
* *
19807871 AATTTTTCAGTTTT-TG-GGGTAAAAATGT
1 AATTTTTCACTTTTACGAGGGTAAAAATGT
*
19807899 AATTTTTCACTTTTACGAGGGTAAAAGTGT
1 AATTTTTCACTTTTACGAGGGTAAAAATGT
19807929 AA
1 AA
19807931 ATTTCAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 13 0.48
29 1 0.04
30 13 0.48
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.42
Consensus pattern (30 bp):
AATTTTTCACTTTTACGAGGGTAAAAATGT
Found at i:19815444 original size:2 final size:2
Alignment explanation
Indices: 19815437--19815473 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19815427 ACTTTCTATA
19815437 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
19815474 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:19815573 original size:43 final size:43
Alignment explanation
Indices: 19815513--19815648 Score: 179
Period size: 43 Copynumber: 3.2 Consensus size: 43
19815503 ACCATCCCAC
*
19815513 CATCATCAGCTCATGTGCACTGCCCACTTGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTGCCCACTCGCACATAGCTGGGT
* **
19815556 CATCATCAGCTCATGTGCACT-CCCA-TACCGCACATACCAAGGT
1 CATCATCAGCTCATGTGCACTGCCCACT--CGCACATAGCTGGGT
* *
19815599 CATCATCAGCTCATGTGCACTG-CCACGCGCACATAGCTGTGT
1 CATCATCAGCTCATGTGCACTGCCCACTCGCACATAGCTGGGT
19815641 CATCATCA
1 CATCATCA
19815649 TCACACAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
41 1 0.01
42 23 0.29
43 56 0.70
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (43 bp):
CATCATCAGCTCATGTGCACTGCCCACTCGCACATAGCTGGGT
Found at i:19837416 original size:63 final size:63
Alignment explanation
Indices: 19837304--19837473 Score: 236
Period size: 63 Copynumber: 2.7 Consensus size: 63
19837294 AGCTCATATG
* **
19837304 CATCATT--ACCGGCATGTGCACTGCCCACTCCGCACATGCACGGTAGTAATAATCGCAACAT
1 CATCATTCAACCGGCATATGCACTGCCCACTCCGCACATGCACGGTAGTAATAATCAAAACAT
* * * * *
19837365 CGTCATTCAACCGGCATATGCACTGCCCACTCCGCACATGCATGGTTGTAATTATCAAAACCT
1 CATCATTCAACCGGCATATGCACTGCCCACTCCGCACATGCACGGTAGTAATAATCAAAACAT
* *
19837428 CATCATTCAACCGGCATATGCATTGCCCACTCTGCACATGCACGGT
1 CATCATTCAACCGGCATATGCACTGCCCACTCCGCACATGCACGGT
19837474 GACATCCATT
Statistics
Matches: 95, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
61 6 0.06
63 89 0.94
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.24
Consensus pattern (63 bp):
CATCATTCAACCGGCATATGCACTGCCCACTCCGCACATGCACGGTAGTAATAATCAAAACAT
Found at i:19838582 original size:13 final size:14
Alignment explanation
Indices: 19838537--19838586 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
19838527 ATGAAGAAGT
*
19838537 AAGAAAAGAAAAAGA
1 AAGAAAA-AGAAAGA
*
19838552 AATG-AAAAGAAAGG
1 AA-GAAAAAGAAAGA
19838566 AAGAAAAAG-AAGA
1 AAGAAAAAGAAAGA
19838579 AAGAAAAA
1 AAGAAAAA
19838587 AATTTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 12 0.40
14 12 0.40
15 5 0.17
16 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (14 bp):
AAGAAAAAGAAAGA
Found at i:19842616 original size:139 final size:139
Alignment explanation
Indices: 19842353--19842609 Score: 309
Period size: 139 Copynumber: 1.8 Consensus size: 139
19842343 TTATGCTTGT
* * * *
19842353 TAAAATGCCACATGACAAGGAAAATAACACACGATAATGAGACGTGTCAATCCTCATAGCTGATT
1 TAAAATGCCACACGACAAGGAAAATAACACACGATAATGAAACGTGCCAAGCCTCATAGCTGATT
*** ** *
19842418 ATGGGACCCGTTAACCCTAACATACAAATACACGACACGTCATACATGAACTGGCAAAATATAGG
66 ATGGGACCCACCAACCCTAACATACAAATACACGACACACCATACATGAAATGGCAAAATATAGG
19842483 TTGATATCG
131 TTGATATCG
* * * * *
19842492 TAAAATGCCACACGACAAGGAAAATAACACATGATAATGAAATGTGCCAGGCCTTATAGTTGATT
1 TAAAATGCCACACGACAAGGAAAATAACACACGATAATGAAACGTGCCAAGCCTCATAGCTGATT
* * ** **
19842557 ATGTGG-CCTACCAATCCTAACATACAAATACGTGACACACCATGGATGAAATG
66 ATG-GGACCCACCAACCCTAACATACAAATACACGACACACCATACATGAAATG
19842610 AGAAAATGGC
Statistics
Matches: 96, Mismatches: 21, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
139 94 0.98
140 2 0.02
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.22
Consensus pattern (139 bp):
TAAAATGCCACACGACAAGGAAAATAACACACGATAATGAAACGTGCCAAGCCTCATAGCTGATT
ATGGGACCCACCAACCCTAACATACAAATACACGACACACCATACATGAAATGGCAAAATATAGG
TTGATATCG
Found at i:19849865 original size:42 final size:42
Alignment explanation
Indices: 19849801--19849907 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
19849791 GACTCGACTA
* *
19849801 TGTGTGAGTAGGGAGTGCGCATAAGCCGAAGATGACCCGGTT
1 TGTGCGAGTAGGGAGTGCGCATAACCCGAAGATGACCCGGTT
* ** ***
19849843 TGTGCGAGTAGGGAGTGTGCATAACCCGGTGATGACCCAGCCA
1 TGTGCGAGTAGGGAGTGCGCATAACCCGAAGATGACCC-GGTT
* *
19849886 TGTGCAAGTAGGGTGTGCGCAT
1 TGTGCGAGTAGGGAGTGCGCAT
19849908 GAGCTGGTGA
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
42 33 0.62
43 20 0.38
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
TGTGCGAGTAGGGAGTGCGCATAACCCGAAGATGACCCGGTT
Found at i:19849953 original size:23 final size:23
Alignment explanation
Indices: 19849923--19849976 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
19849913 GGTGATGATA
* * *
19849923 ATGATGGGATGGTGTGTATCATG
1 ATGATGGGATGGTATGCATAATG
19849946 ATGATGGGATGGTATGCATAATG
1 ATGATGGGATGGTATGCATAATG
19849969 ATGATGGG
1 ATGATGGG
19849977 TATATACGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.26, C:0.04, G:0.39, T:0.31
Consensus pattern (23 bp):
ATGATGGGATGGTATGCATAATG
Found at i:19855055 original size:2 final size:2
Alignment explanation
Indices: 19854972--19855047 Score: 109
Period size: 2 Copynumber: 38.5 Consensus size: 2
19854962 ATTATGTTGG
*
19854972 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
19855013 TG TN TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19855048 GAATATATGT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19855088 original size:20 final size:21
Alignment explanation
Indices: 19855046--19855088 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
19855036 ATATATATAT
*
19855046 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTGCAATG
*
19855067 ATGAATA-ATGTTGTGTAATG
1 ATGAATATATGTTGTGCAATG
19855087 AT
1 AT
19855089 ATTGACCCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (21 bp):
ATGAATATATGTTGTGCAATG
Found at i:19855146 original size:42 final size:42
Alignment explanation
Indices: 19855091--19855219 Score: 136
Period size: 42 Copynumber: 3.1 Consensus size: 42
19855081 GTAATGATAT
* *
19855091 TGACCCGGCTATGTG-TGAGTAGGAGTGTGCATAAGCCGATGA
1 TGACCCGACTATGTGCT-AGTAGGAGTGCGCATAAGCCGATGA
* * *
19855133 TGACCCGACTATGTGCTAGTGGGTGTGCGCATAAGCCGATGC
1 TGACCCGACTATGTGCTAGTAGGAGTGCGCATAAGCCGATGA
* * * * *
19855175 TGACCC-AGCTATGTGCAAATGGGAGTGCACATAAGCCGATAA
1 TGACCCGA-CTATGTGCTAGTAGGAGTGCGCATAAGCCGATGA
19855217 TGA
1 TGA
19855220 TGATGACCTG
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 72 0.97
43 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (42 bp):
TGACCCGACTATGTGCTAGTAGGAGTGCGCATAAGCCGATGA
Found at i:19865523 original size:2 final size:2
Alignment explanation
Indices: 19865490--19865515 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19865480 TATTATGTTA
19865490 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19865516 GAATATATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19865556 original size:20 final size:21
Alignment explanation
Indices: 19865514--19865556 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
19865504 ATATATATAT
*
19865514 ATGAATATATGTTGTGCATTG
1 ATGAATATATGTTGTGCAATG
*
19865535 ATGAATA-ATGTTGTGTAATG
1 ATGAATATATGTTGTGCAATG
19865555 AT
1 AT
19865557 ATTGACCCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (21 bp):
ATGAATATATGTTGTGCAATG
Found at i:19865613 original size:42 final size:42
Alignment explanation
Indices: 19865566--19865688 Score: 183
Period size: 42 Copynumber: 2.9 Consensus size: 42
19865556 TATTGACCCA
* *
19865566 GCTATGTGCAAATAAGAGTGCGCATAAGCCGATGATGACTCG
1 GCTATGTGCAAGTAGGAGTGCGCATAAGCCGATGATGACTCG
* * *
19865608 GCTATGTGCAAGTGGGAGTGCGCATAAGCCGATGCTGACTTG
1 GCTATGTGCAAGTAGGAGTGCGCATAAGCCGATGATGACTCG
*
19865650 GCTATGTGCAAGTAGGGAGTGCGCATAAGCTGATGATGA
1 GCTATGTGCAAGTA-GGAGTGCGCATAAGCCGATGATGA
19865689 TGATGACCTG
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 50 0.69
43 22 0.31
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (42 bp):
GCTATGTGCAAGTAGGAGTGCGCATAAGCCGATGATGACTCG
Found at i:19865982 original size:21 final size:21
Alignment explanation
Indices: 19865957--19866008 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
19865947 AGCCCTGTTA
* *
19865957 CTCGCTGCAGCAAGAATGAAT
1 CTCGCTGCAGCAAAAATAAAT
19865978 CTCGCTGCAGCAAAAATAAAT
1 CTCGCTGCAGCAAAAATAAAT
*
19865999 CTAGCTGCAG
1 CTCGCTGCAG
19866009 TGAGAAACTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (21 bp):
CTCGCTGCAGCAAAAATAAAT
Found at i:19867889 original size:27 final size:27
Alignment explanation
Indices: 19867803--19867897 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 27
19867793 TTAGAATTCA
* * *
19867803 TATTTCGTTACAAGCCTTGCATAATTTT
1 TATTTTGTTACACGCCTTAC-TAATTTT
* *
19867831 TATTTTGTTACTCGCCCTTACTAATTTC
1 TATTTTGTTACACG-CCTTACTAATTTT
19867859 TATTTTGTTACACG-CTTGACTAATTTT
1 TATTTTGTTACACGCCTT-ACTAATTTT
19867886 TATTTTGTTACA
1 TATTTTGTTACA
19867898 TGCCATACCT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.05
27 20 0.34
28 30 0.52
29 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.09, T:0.51
Consensus pattern (27 bp):
TATTTTGTTACACGCCTTACTAATTTT
Found at i:19869434 original size:240 final size:239
Alignment explanation
Indices: 19868975--19869452 Score: 717
Period size: 240 Copynumber: 2.0 Consensus size: 239
19868965 TATTTTTGAA
* ** *
19868975 GCAATTTTTTCAAATGTGTGATTCGCCCTTCCTTGTGTGAAGTGCAAACGGACAAACGTTGTCCC
1 GCAATTTTTTCAAATGTGTCATTCGCCCTTCCTTGTGAAAAGTGAAAACGGACAAACGTTGTCCC
* * *
19869040 CTTTTGCTAGCACAAAAGCATAGCTAAAATCGCCCTCATTTGCTGAAGGTTCAATTGAAATCATG
66 CTTTTGCTAGCACAAAAGCATAGCTAAAATCACCCTCATTTACTGAAGGTTCAACTGAAATCATG
* * *
19869105 TGTAGTATAGTTAAAGGCCGAGAGATTGATTGGCTAGGATTCTTGCTTCTTATGGTGTTCGTAGG
131 TGTACTATAGTTAAAGGCCAAGAGATTGATTGGCTAGGATTCTTGCTTCTAATGGTGTTCGTAGG
*
19869170 TTGCATTGAGGAGATTGCTATTCCCATCAAAAGAATGTTGCCAT
196 TTACATTGAGGAGATTGCTATTCCCATCAAAAGAATGTTGCCAT
* * *
19869214 GCAATTTTTTCAAATTTGTCACTT-GCCCTTCCTTGTGAAAAGTGAAAAGGGACAAATGTTGTCC
1 GCAATTTTTTCAAATGTGTCA-TTCGCCCTTCCTTGTGAAAAGTGAAAACGGACAAACGTTGTCC
19869278 CCTTTTGCTAGCACAAAAGCATAGCTAAAATCACCCTCATTTACTGAAAGGTTCAACTGAAATCA
65 CCTTTTGCTAGCACAAAAGCATAGCTAAAATCACCCTCATTTACTG-AAGGTTCAACTGAAATCA
** * * *
19869343 TGTGTACTATAGTTGGAGTCCAAGAGCTTGATTGGCTAAGG-TTCTTGCTTCTAATGGTGTTTGT
129 TGTGTACTATAGTTAAAGGCCAAGAGATTGATTGGCT-AGGATTCTTGCTTCTAATGGTGTTCGT
* * *
19869407 AGGTTACATTGAGGAGATTGTTATTCCCATTAGAAGAATGTTGCCA
193 AGGTTACATTGAGGAGATTGCTATTCCCATCAAAAGAATGTTGCCA
19869453 AGGTTAGCTT
Statistics
Matches: 214, Mismatches: 22, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
239 98 0.46
240 113 0.53
241 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (239 bp):
GCAATTTTTTCAAATGTGTCATTCGCCCTTCCTTGTGAAAAGTGAAAACGGACAAACGTTGTCCC
CTTTTGCTAGCACAAAAGCATAGCTAAAATCACCCTCATTTACTGAAGGTTCAACTGAAATCATG
TGTACTATAGTTAAAGGCCAAGAGATTGATTGGCTAGGATTCTTGCTTCTAATGGTGTTCGTAGG
TTACATTGAGGAGATTGCTATTCCCATCAAAAGAATGTTGCCAT
Found at i:19873592 original size:23 final size:23
Alignment explanation
Indices: 19873562--19873610 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
19873552 GAAACATTCT
19873562 TTCCTTAAATGAATCCACACTAG
1 TTCCTTAAATGAATCCACACTAG
19873585 TTCCTTAAATGAATCCACACTAG
1 TTCCTTAAATGAATCCACACTAG
19873608 TTC
1 TTC
19873611 TCTTTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.08, T:0.33
Consensus pattern (23 bp):
TTCCTTAAATGAATCCACACTAG
Found at i:19878772 original size:2 final size:2
Alignment explanation
Indices: 19878767--19878795 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19878757 TTGTGTTATC
19878767 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19878796 GGTTTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19901499 original size:12 final size:12
Alignment explanation
Indices: 19901482--19901506 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19901472 AAGAAAATGG
19901482 AATATTTTATTT
1 AATATTTTATTT
19901494 AATATTTTATTT
1 AATATTTTATTT
19901506 A
1 A
19901507 GTTTGATTAG
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATATTTTATTT
Found at i:19902061 original size:17 final size:17
Alignment explanation
Indices: 19902039--19902075 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
19902029 ATGTTCTGAT
19902039 TTTGTTACTGCATTCTC
1 TTTGTTACTGCATTCTC
*
19902056 TTTGTTATTGCATTCTC
1 TTTGTTACTGCATTCTC
19902073 TTT
1 TTT
19902076 CTCATTGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.19, G:0.11, T:0.59
Consensus pattern (17 bp):
TTTGTTACTGCATTCTC
Found at i:19902082 original size:17 final size:17
Alignment explanation
Indices: 19902047--19902083 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19902037 ATTTTGTTAC
* *
19902047 TGCATTCTCTTTGTTAT
1 TGCATTCTCTTTCTCAT
19902064 TGCATTCTCTTTCTCAT
1 TGCATTCTCTTTCTCAT
19902081 TGC
1 TGC
19902084 CTTTTGAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.24, G:0.11, T:0.54
Consensus pattern (17 bp):
TGCATTCTCTTTCTCAT
Found at i:19902753 original size:40 final size:41
Alignment explanation
Indices: 19902692--19902771 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 41
19902682 TTGTGAAAGA
*
19902692 CACCAATCGTGGAGAAGGTTGAAAACCCTACTAAGGTGAAT
1 CACCAATCGTGGACAAGGTTGAAAACCCTACTAAGGTGAAT
* *
19902733 CACCAATCTTGG-CAAGGTTGAAAACGCTACTAAGGTGAA
1 CACCAATCGTGGACAAGGTTGAAAACCCTACTAAGGTGAA
19902772 AATAATAGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 25 0.69
41 11 0.31
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (41 bp):
CACCAATCGTGGACAAGGTTGAAAACCCTACTAAGGTGAAT
Found at i:19906355 original size:2 final size:2
Alignment explanation
Indices: 19906310--19906346 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
19906300 TATTATGTTG
19906310 AT AT AT AT AT AT AT 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 AT AT AT A
19906347 CGAATATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19906419 original size:42 final size:42
Alignment explanation
Indices: 19906360--19906457 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 42
19906350 ATATATGGTG
19906360 TGCATAAACCGATGCTGACCCGGCTATGTGCGAGTAGGAGTA
1 TGCATAAACCGATGCTGACCCGGCTATGTGCGAGTAGGAGTA
* *
19906402 TGCATAAACCGATGCTGACCCGGCTATGTGCGAGTGGGAGTG
1 TGCATAAACCGATGCTGACCCGGCTATGTGCGAGTAGGAGTA
* *
19906444 CGCATAAGCCGATG
1 TGCATAAACCGATG
19906458 ATGATGATGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.20
Consensus pattern (42 bp):
TGCATAAACCGATGCTGACCCGGCTATGTGCGAGTAGGAGTA
Found at i:19909434 original size:11 final size:11
Alignment explanation
Indices: 19909414--19909458 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
19909404 TATGGCTGGC
*
19909414 CAAAGCAAGAA
1 CAAAGGAAGAA
19909425 CAAAGGAAGAA
1 CAAAGGAAGAA
*
19909436 CAAGGGAAG-A
1 CAAAGGAAGAA
19909446 -AAA-GAAGAA
1 CAAAGGAAGAA
19909455 CAAA
1 CAAA
19909459 AACCCTAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
8 4 0.14
9 3 0.10
10 4 0.14
11 18 0.62
ACGTcount: A:0.64, C:0.11, G:0.24, T:0.00
Consensus pattern (11 bp):
CAAAGGAAGAA
Found at i:19910380 original size:15 final size:17
Alignment explanation
Indices: 19910351--19910392 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
19910341 AATTTTTAGG
**
19910351 TTTTATAAACAAAATG-
1 TTTTATAAATGAAATGA
19910367 TTTT-TAAATGAAATGA
1 TTTTATAAATGAAATGA
19910383 TTTTATAAAT
1 TTTTATAAAT
19910393 TGTCTTGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 9 0.41
16 8 0.36
17 5 0.23
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (17 bp):
TTTTATAAATGAAATGA
Found at i:19915973 original size:42 final size:42
Alignment explanation
Indices: 19915911--19916078 Score: 219
Period size: 42 Copynumber: 4.0 Consensus size: 42
19915901 GTAATAATAT
* *
19915911 TAACCCGGCTATGTGTGAGTAGGAGTGCGCATAAGCCTATGC
1 TAACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
*
19915953 TAACCCGGCTATGTGAGAGTAGGAGTGCGCATAAGCCGATGC
1 TAACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
** * * *
19915995 TAACTTGGCTATGTGCGAGTGGGAGTACGCGTAAGCCGATGC
1 TAACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
* ** *
19916037 TGACCTAGCTATGTGCGAGTAGGGAGTGCTCATAAGCCGATG
1 TAACCCGGCTATGTGCGAGTA-GGAGTGCGCATAAGCCGATG
19916079 ATGATGATGA
Statistics
Matches: 110, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 93 0.85
43 17 0.15
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (42 bp):
TAACCCGGCTATGTGCGAGTAGGAGTGCGCATAAGCCGATGC
Found at i:19921584 original size:42 final size:42
Alignment explanation
Indices: 19921486--19921615 Score: 170
Period size: 42 Copynumber: 3.1 Consensus size: 42
19921476 AGCCAGGTAA
* *
19921486 TCATCATCGGCTTATGCGCACTCCTTACTCACACATAGTCGGG
1 TCATCATCGGCTTATGCGCACTCC-TACTCGCACATAGCCGGG
* * * * *
19921529 TCAGCATCGGCTTATGCCCACTCCCACTTGCATATAGCCGGG
1 TCATCATCGGCTTATGCGCACTCCTACTCGCACATAGCCGGG
* *
19921571 TCATCATCTGCTTATGCGCACTCCTACTCGCACATTGCCGGG
1 TCATCATCGGCTTATGCGCACTCCTACTCGCACATAGCCGGG
19921613 TCA
1 TCA
19921616 ATATCATTAC
Statistics
Matches: 73, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
42 51 0.70
43 22 0.30
ACGTcount: A:0.19, C:0.35, G:0.19, T:0.27
Consensus pattern (42 bp):
TCATCATCGGCTTATGCGCACTCCTACTCGCACATAGCCGGG
Found at i:19924548 original size:21 final size:20
Alignment explanation
Indices: 19924517--19924564 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
19924507 AACCAAGCTT
*
19924517 TTTCTTCCTTTCTCTCTTTTTC
1 TTTC-TCCTTTCTCTC-TTTCC
*
19924539 TTTCTCCTTTCTTTCTTTCC
1 TTTCTCCTTTCTCTCTTTCC
19924559 TTTCTC
1 TTTCTC
19924565 ATCTATTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
21 10 0.42
22 4 0.17
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTCTCCTTTCTCTCTTTCC
Found at i:19931433 original size:175 final size:174
Alignment explanation
Indices: 19931139--19931490 Score: 632
Period size: 175 Copynumber: 2.0 Consensus size: 174
19931129 GTCGGCTAAT
*
19931139 TTGGTTGACTAAGTTGATTATGTTTCTGGTTTACAGATTTTGGTAGAGGGCACTTAATCGACTGA
1 TTGGTTGACTAAGTTGATTATGTTTCTGGTTTACAGATTTTGGCAGAGGGCACTTAATCGACTGA
* *
19931204 CTTGGTTGACTAAGTTGGTTCTGTTTCTCAAACTCTTCAGCCTGCCATTTCTCCAATTTGAAATT
66 CTTGGTTGACTAAGTGGGTTCTGTTTCTCAAACTCTTCAACCTGCCATTTCTCCAATTTGAAATT
19931269 TGGTCAACCAATGCTCTTCCTTTTTTAACCAACAAGCTTCCTCC
131 TGGTCAACCAATGCTCTTCCTTTTTTAACCAACAAGCTTCCTCC
* * * *
19931313 TTGNGTTGACTAAGTTGATTTTGTTTTTGGTTTGCAGATTTTGGCAGAGGGCATTTAATCGACTG
1 TTG-GTTGACTAAGTTGATTATGTTTCTGGTTTACAGATTTTGGCAGAGGGCACTTAATCGACTG
19931378 ACTTGGTTGACTAAGTGGGTTCTGTTTCTCAAACTCTTCAACCTGCCATTTCTCCAATTTGAAAT
65 ACTTGGTTGACTAAGTGGGTTCTGTTTCTCAAACTCTTCAACCTGCCATTTCTCCAATTTGAAAT
19931443 TTGGTCAACCAATGCTCTTCCTTTTTTAACCAACAAGCTTCCTCC
130 TTGGTCAACCAATGCTCTTCCTTTTTTAACCAACAAGCTTCCTCC
19931488 TTG
1 TTG
19931491 TTATTCAGTT
Statistics
Matches: 170, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
174 3 0.02
175 167 0.98
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (174 bp):
TTGGTTGACTAAGTTGATTATGTTTCTGGTTTACAGATTTTGGCAGAGGGCACTTAATCGACTGA
CTTGGTTGACTAAGTGGGTTCTGTTTCTCAAACTCTTCAACCTGCCATTTCTCCAATTTGAAATT
TGGTCAACCAATGCTCTTCCTTTTTTAACCAACAAGCTTCCTCC
Found at i:19949446 original size:43 final size:43
Alignment explanation
Indices: 19949362--19949446 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
19949352 ACCCCCTCAT
* * *
19949362 CATCAGCTCATGTGCACTCCTTACTCGCGCATAGCTAGGTCAG
1 CATCAGCTCATGTGCACTCCCTACTCGCACATAGCCAGGTCAG
* *
19949405 CATCAGCTTATGTGCACTCCCTACTCGCACATAGCCGGGTCA
1 CATCAGCTCATGTGCACTCCCTACTCGCACATAGCCAGGTCA
19949447 ATATCATCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (43 bp):
CATCAGCTCATGTGCACTCCCTACTCGCACATAGCCAGGTCAG
Found at i:19959534 original size:17 final size:18
Alignment explanation
Indices: 19959512--19959547 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
19959502 ATCTTGTGGC
*
19959512 CATCAT-CAACTTCATAT
1 CATCATCCAACCTCATAT
19959529 CATCATCCAACCTCATAT
1 CATCATCCAACCTCATAT
19959547 C
1 C
19959548 CGAAAGTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (18 bp):
CATCATCCAACCTCATAT
Found at i:19960371 original size:28 final size:29
Alignment explanation
Indices: 19960330--19960389 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
19960320 GTCTATGGGC
* *
19960330 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGGCAAAAATGT
*
19960358 AATTTTTCACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-GGGGGCAAAAATGT
19960388 AA
1 AA
19960390 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:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGCAAAAATGT
Found at i:19972081 original size:21 final size:22
Alignment explanation
Indices: 19972051--19972092 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
19972041 TAATGGTTAG
19972051 AAATGTTAGAGAGAAAATGGAA
1 AAATGTTAGAGAGAAAATGGAA
**
19972073 AAAT-TTAGAGCTAAAATGGA
1 AAATGTTAGAGAGAAAATGGA
19972093 GCGCGTTAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.52, C:0.02, G:0.24, T:0.21
Consensus pattern (22 bp):
AAATGTTAGAGAGAAAATGGAA
Found at i:19976821 original size:32 final size:31
Alignment explanation
Indices: 19976785--19976895 Score: 98
Period size: 32 Copynumber: 3.4 Consensus size: 31
19976775 TTTACCAGGA
*
19976785 TCAACTAAAACCCGAAGAGGTTTTTCAAAGGC
1 TCAACCAAAACCC-AAGAGGTTTTTCAAAGGC
* *
19976817 TCAACCACAACCTTTCATA-ATGGTTTTTCACAGGC
1 TCAACCAAAACC---CA-AGA-GGTTTTTCAAAGGC
* *
19976852 TTAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCC-AAGAGGTTTTTCAAAGGC
*
19976884 TCAACCACAACC
1 TCAACCAAAACC
19976896 TACAACAATG
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
32 35 0.56
33 1 0.02
34 2 0.03
35 25 0.40
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (31 bp):
TCAACCAAAACCCAAGAGGTTTTTCAAAGGC
Found at i:19976842 original size:35 final size:32
Alignment explanation
Indices: 19976803--19976913 Score: 125
Period size: 35 Copynumber: 3.3 Consensus size: 32
19976793 AACCCGAAGA
19976803 GGTTTTTCAAAGGCTCAACCACAACCTTTCATAAT
1 GGTTTTTCAAAGGCTCAACCACAACC--TCA-AAT
* * *
19976838 GGTTTTTCACAGGCTTAACCAAAACC-CAAAGT
1 GGTTTTTCAAAGGCTCAACCACAACCTCAAA-T
19976870 GGTTTTTCAAAGGCTCAACCACAACCTACAACAAT
1 GGTTTTTCAAAGGCTCAACCACAACCT-C-A-AAT
19976905 GGTTTTTCA
1 GGTTTTTCA
19976914 CGAGATCAAC
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
31 2 0.03
32 26 0.40
34 1 0.02
35 34 0.52
36 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (32 bp):
GGTTTTTCAAAGGCTCAACCACAACCTCAAAT
Found at i:19976864 original size:67 final size:67
Alignment explanation
Indices: 19976783--19976933 Score: 207
Period size: 67 Copynumber: 2.3 Consensus size: 67
19976773 TTTTTACCAG
* * * *
19976783 GATCAACTAAAACCCGAAGAGGTTTTTCAAAGGCTCAACCACAACCTTTC-ATAATGGTTTTTCA
1 GATCAACCAAAACCCAAAGAGGTTTTTCAAAGGCTCAACCACAACC-TACAACAATGGTTTTTCA
19976847 C-A
65 CGA
* * *
19976849 GGCTTAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACCACAACCTACAACAATGGTTTTTCA
1 -GATCAACCAAAACCCAAAGAGGTTTTTCAAAGGCTCAACCACAACCTACAACAATGGTTTTTCA
19976914 CGA
65 CGA
19976917 GATCAACCAAAACCCAA
1 GATCAACCAAAACCCAA
19976934 CAACTAACTT
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
66 2 0.03
67 70 0.96
68 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.23
Consensus pattern (67 bp):
GATCAACCAAAACCCAAAGAGGTTTTTCAAAGGCTCAACCACAACCTACAACAATGGTTTTTCAC
GA
Found at i:19979271 original size:252 final size:247
Alignment explanation
Indices: 19978484--19979271 Score: 772
Period size: 253 Copynumber: 3.1 Consensus size: 247
19978474 ACTAACATAA
* * *
19978484 TTTATAAATTTTAATTTATAAGCAAATAATAA-CAAAGACAAAAATAATTATAGAAAAAAATAAC
1 TTTATAAATTTTAATTTATAA--AAATAATAATCAAAGATAAAAATAATTATAG-TAAAAAT-AG
* * * *
19978548 AATTGAAAAACCTTGACGTAAACATGTAAGAATTAATGTAAAAAATAATAAAGGTGGAATAAGCA
62 AATTGAAAAA-CTTGACGTAAACATGTAAGAAATAATGTAAAAAATTATAAAGGTGGAACAAGGA
* ** * *
19978613 TTGTCAAAAAATTGACATAAATATGTGAGATTTAACGTAACAAGTCAATTAAGTCAAAATAAACA
126 TTGTCAAAATATTGATGTAAATGTGTGAGATTTAATGTAACAAGTCAATTAAGTCAAAATAAACA
* *
19978678 TAATTTTTGTGAAAATTAAAC-TTGTAAATTTATATTATCGAGTTAAAAGTATTTAACAA
191 TAATTTTTGAGAAAATTAAACATT-TAAATTTATA-TATCGAGTTAAAA-TATTTAACAG
* * * * *
19978737 TTTATAAATTTTAATTTAAAAAAGGATAATAAT-ACAGATAAAAATAATTATGGTGAAAACTAGC
1 TTTATAAATTTTAATTTATAAAA--ATAATAATCAAAGATAAAAATAATTATAGT-AAAAATAGA
* * * * *
19978801 ATCTGAAAAACATTGACATACACTTGTAAGAGCA-AATGTAAAAAATTATACAGGTGGAACAAGT
63 AT-TGAAAAAC-TTGACGTAAACATGTAAGA-AATAATGTAAAAAATTATAAAGGTGGAACAAG-
* * * *
19978865 G-TTG-CTGAAATATTGATGTAAACGTGTGAGATTTATTGTAACAAGTCAATTAAGTCAAAATCA
124 GATTGTC-AAAATATTGATGTAAATGTGTGAGATTTAATGTAACAAGTCAATTAAGTCAAAATAA
* * ** *
19978928 ATATAATTTTTGAGAAAATTAAGCATTTAAATTTATATGATTAAGGTAAAAATATTTAACAG
188 ACATAATTTTTGAGAAAATTAAACATTTAAATTTATAT-ATCGA-GTTAAAATATTTAACAG
* * * *
19978990 TTTATAAATTTTAATTTA-CAAATTAATAATCATAAGGATAAAAATAATTATACTAAAAGTTAGT
1 TTTATAAATTTTAATTTATAAAAATAATAATCA-AA-GATAAAAATAATTATAGTAAAA-ATAG-
* * * * *
19979054 AATTGAAAAATCTTGATGTAAACCTGTTAGAAATAATGT-AAAAATTATAAAAGTGGAAGAAGGA
62 AATTGAAAAA-CTTGACGTAAACATGTAAGAAATAATGTAAAAAATTATAAAGGTGGAACAAGGA
* * *
19979118 TTGTCAAAATATTGATGTAAATGTGTGAAATTTAATATAACAAGTTAATTAAGTC-AAATAAACA
126 TTGTCAAAATATTGATGTAAATGTGTGAGATTTAATGTAACAAGTCAATTAAGTCAAAATAAACA
* * ** * *
19979182 TAATTTGTTG-GGAAATTAAACACTTAAGCTTATATACTCGAGTTTAAATACTTATA-AG
191 TAATTT-TTGAGAAAATTAAACATTTAAATTTATATA-TCGAGTTAAAATATTTA-ACAG
*
19979240 TTTA-CAATTTTAATTTATAAAAGGATAATAAT
1 TTTATAAATTTTAATTTATAAAA--ATAATAAT
19979272 AATGAGAAAT
Statistics
Matches: 438, Mismatches: 70, Indels: 55
0.78 0.12 0.10
Matches are distributed among these distances:
249 12 0.03
250 27 0.06
251 40 0.09
252 92 0.21
253 256 0.58
254 11 0.03
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.33
Consensus pattern (247 bp):
TTTATAAATTTTAATTTATAAAAATAATAATCAAAGATAAAAATAATTATAGTAAAAATAGAATT
GAAAAACTTGACGTAAACATGTAAGAAATAATGTAAAAAATTATAAAGGTGGAACAAGGATTGTC
AAAATATTGATGTAAATGTGTGAGATTTAATGTAACAAGTCAATTAAGTCAAAATAAACATAATT
TTTGAGAAAATTAAACATTTAAATTTATATATCGAGTTAAAATATTTAACAG
Found at i:19985578 original size:28 final size:30
Alignment explanation
Indices: 19985520--19985579 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
19985510 TTTTTGAAAT
*
19985520 TTACACTTTTGCCCCTATAAAAGTCAAAAA
1 TTACACTTTTGCCCCTATAAAACTCAAAAA
* *
19985550 TTACATTTTTGCCCC-A-AAAACTGAAAAA
1 TTACACTTTTGCCCCTATAAAACTCAAAAA
19985578 TT
1 TT
19985580 GCCCATAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.44
29 1 0.04
30 14 0.52
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.32
Consensus pattern (30 bp):
TTACACTTTTGCCCCTATAAAACTCAAAAA
Found at i:19992071 original size:20 final size:20
Alignment explanation
Indices: 19992046--19992091 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
19992036 TTTTTACCCC
*
19992046 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGAAGTATA
*
19992066 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
19992086 ATTTGA
1 ATTTGA
19992092 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:19997520 original size:24 final size:24
Alignment explanation
Indices: 19997493--19997539 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
19997483 AAATGAAAAG
*
19997493 ACAAAATGATTAAATCGGAACAAA
1 ACAAAATGATTAAATCAGAACAAA
* * *
19997517 ACAACATTATTCAATCAGAACAA
1 ACAAAATGATTAAATCAGAACAA
19997540 GAGCATATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.55, C:0.17, G:0.09, T:0.19
Consensus pattern (24 bp):
ACAAAATGATTAAATCAGAACAAA
Found at i:20003035 original size:20 final size:20
Alignment explanation
Indices: 20002990--20003027 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
20002980 TTTTGGCTCC
20002990 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
20003010 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
20003028 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:20012797 original size:22 final size:22
Alignment explanation
Indices: 20012772--20012815 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20012762 TTTAAAATGA
*
20012772 CTTTAAAACTAAAAACTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
20012794 CTTTAAAACCAAAAACTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
20012816 ACCAATCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTGAT
Found at i:20018520 original size:55 final size:53
Alignment explanation
Indices: 20018457--20018564 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 53
20018447 AATTATAGAC
*
20018457 TTATTGTAGGGACAAAATTATAAAATTCTAAAAAAAATAAAGGTATGTTATAAAA
1 TTATTGTAGGGACAAAATTATAAAATT-TAAAAAAAATAAAAGT-TGTTATAAAA
* *
20018512 TTATTGTAGGGGCAAAATTATAAAATTTCAAAAAAATAAAAGTTGTTATAAAA
1 TTATTGTAGGGACAAAATTATAAAATTTAAAAAAAATAAAAGTTGTTATAAAA
20018565 ATTTCAAAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 10 0.20
54 14 0.28
55 26 0.52
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.31
Consensus pattern (53 bp):
TTATTGTAGGGACAAAATTATAAAATTTAAAAAAAATAAAAGTTGTTATAAAA
Found at i:20019364 original size:16 final size:17
Alignment explanation
Indices: 20019336--20019370 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
20019326 AAAACGTGTT
20019336 CATCAACCCAATTAATC
1 CATCAACCCAATTAATC
*
20019353 CATCAA-CCAATTAGTC
1 CATCAACCCAATTAATC
20019369 CA
1 CA
20019371 ATAATCCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.40, C:0.34, G:0.03, T:0.23
Consensus pattern (17 bp):
CATCAACCCAATTAATC
Found at i:20021500 original size:3 final size:3
Alignment explanation
Indices: 20021492--20021554 Score: 81
Period size: 3 Copynumber: 21.0 Consensus size: 3
20021482 TAAATATAGT
* * * *
20021492 TAC TAC TAC TAC TAC TAC TAC TGC TAC TAC TGC TGC TGC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
*
20021540 TAT TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC
20021555 CAGAGATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.27, C:0.32, G:0.06, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:20023448 original size:13 final size:13
Alignment explanation
Indices: 20023430--20023458 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
20023420 CTTTTTGAAC
20023430 TTTTTTTAAA-GT
1 TTTTTTTAAATGT
20023442 TTTTTTTAAATGT
1 TTTTTTTAAATGT
20023455 TTTT
1 TTTT
20023459 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (13 bp):
TTTTTTTAAATGT
Found at i:20023457 original size:22 final size:22
Alignment explanation
Indices: 20023432--20023476 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
20023422 TTTTGAACTT
20023432 TTTTTAAAGTTTTTTTTAAATG
1 TTTTTAAAGTTTTTTTTAAATG
* *
20023454 TTTTTGAATTTTTTTTTAAATG
1 TTTTTAAAGTTTTTTTTAAATG
20023476 T
1 T
20023477 ACTTGCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (22 bp):
TTTTTAAAGTTTTTTTTAAATG
Found at i:20023469 original size:11 final size:11
Alignment explanation
Indices: 20023407--20023469 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
20023397 GATTACCACC
*
20023407 TTTTTTTTTAA
1 TTTTTTTTGAA
*
20023418 TTCTTTTTGAA
1 TTTTTTTTGAA
* *
20023429 CTTTTTTTAAA
1 TTTTTTTTGAA
20023440 GTTTTTTTT-AA
1 -TTTTTTTTGAA
* *
20023451 ATGTTTTTGAA
1 TTTTTTTTGAA
20023462 TTTTTTTT
1 TTTTTTTT
20023470 TAAATGTACT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
10 6 0.15
11 27 0.68
12 7 0.17
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.71
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:20023532 original size:4 final size:5
Alignment explanation
Indices: 20023516--20023548 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
20023506 TCTAATAATA
20023516 AAAAT AAAA- ATAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAA
20023549 GTAAGTTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 1 0.04
5 24 0.92
6 1 0.04
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:20024973 original size:42 final size:42
Alignment explanation
Indices: 20024909--20024988 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
20024899 GTGAATGGAG
*
20024909 GCATCAGTCTTTATCATAAATGCATTAGTCTTTGTTATAAAT
1 GCATCAGTCTTTATCATAAATGCATCAGTCTTTGTTATAAAT
* *
20024951 GCATCAGTCTTTGTCATGAATGCATCAGTCTTTGTTAT
1 GCATCAGTCTTTATCATAAATGCATCAGTCTTTGTTAT
20024989 GAACGGTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.42
Consensus pattern (42 bp):
GCATCAGTCTTTATCATAAATGCATCAGTCTTTGTTATAAAT
Found at i:20024991 original size:21 final size:21
Alignment explanation
Indices: 20024909--20024985 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
20024899 GTGAATGGAG
*
20024909 GCATCAGTCTTTATCATAAAT
1 GCATCAGTCTTTGTCATAAAT
* *
20024930 GCATTAGTCTTTGTTATAAAT
1 GCATCAGTCTTTGTCATAAAT
*
20024951 GCATCAGTCTTTGTCATGAAT
1 GCATCAGTCTTTGTCATAAAT
20024972 GCATCAGTCTTTGT
1 GCATCAGTCTTTGT
20024986 TATGAACGGT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.42
Consensus pattern (21 bp):
GCATCAGTCTTTGTCATAAAT
Found at i:20033675 original size:15 final size:15
Alignment explanation
Indices: 20033655--20033699 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
20033645 AAAAATAGAA
20033655 GAAGAAAAGAGAAAG
1 GAAGAAAAGAGAAAG
*
20033670 GAAGAAAAAAGTAAAG
1 GAAGAAAAGAG-AAAG
*
20033686 AAAGAAAAAGAGAA
1 GAAG-AAAAGAGAA
20033700 GAGAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 10 0.40
16 9 0.36
17 6 0.24
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (15 bp):
GAAGAAAAGAGAAAG
Found at i:20033687 original size:27 final size:28
Alignment explanation
Indices: 20033656--20033716 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
20033646 AAAATAGAAG
*
20033656 AAGAAAAGAGAAAG-GAAGA-AAAAAGTA
1 AAGAAAAGAAAAAGAGAAGAGAAAAAG-A
20033683 AAG-AAAGAAAAAGAGAAGAGAAAAAGA
1 AAGAAAAGAAAAAGAGAAGAGAAAAAGA
*
20033710 AAAAAAA
1 AAGAAAA
20033717 TAAATACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
26 9 0.31
27 11 0.38
28 9 0.31
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (28 bp):
AAGAAAAGAAAAAGAGAAGAGAAAAAGA
Found at i:20033701 original size:15 final size:15
Alignment explanation
Indices: 20033653--20033709 Score: 59
Period size: 16 Copynumber: 3.9 Consensus size: 15
20033643 ATAAAAATAG
20033653 AAGAAG-AAAAGAGA
1 AAGAAGAAAAAGAGA
20033667 AAGGAAGAAAAA-AGTA
1 AA-GAAGAAAAAGAG-A
20033683 AAGAAAGAAAAAGAG-
1 AAG-AAGAAAAAGAGA
20033698 AAG-AGAAAAAGA
1 AAGAAGAAAAAGA
20033710 AAAAAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 10 0.26
16 15 0.39
17 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (15 bp):
AAGAAGAAAAAGAGA
Found at i:20033715 original size:37 final size:36
Alignment explanation
Indices: 20033642--20033720 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 36
20033632 AGTCAACAAT
* *
20033642 AATAAA-AATAGAAGAAGAAAAGAGAAAGGAAGAAAA
1 AATAAAGAA-AGAAAAAGAAAAGAGAAAAGAAGAAAA
*
20033678 AAGTAAAGAAAGAAAAAGAGAAGAGAAAAAGAA-AAAA
1 AA-TAAAGAAAGAAAAAGAAAAGAG-AAAAGAAGAAAA
20033715 AATAAA
1 AATAAA
20033721 TACAAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 6 0.16
37 23 0.62
38 8 0.22
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (36 bp):
AATAAAGAAAGAAAAAGAAAAGAGAAAAGAAGAAAA
Found at i:20038060 original size:24 final size:24
Alignment explanation
Indices: 20038028--20038082 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
20038018 TTTCAATAAA
20038028 CACATTATTCGTTATGTCATCCAC
1 CACATTATTCGTTATGTCATCCAC
20038052 CACATTATTCGTTATGTCATCCAC
1 CACATTATTCGTTATGTCATCCAC
20038076 CACATTA
1 CACATTA
20038083 ATTAAGAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.29, G:0.07, T:0.36
Consensus pattern (24 bp):
CACATTATTCGTTATGTCATCCAC
Found at i:20038851 original size:12 final size:12
Alignment explanation
Indices: 20038819--20038852 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20038809 TTTTCAACCA
20038819 CAATTTCTTTTT
1 CAATTTCTTTTT
* *
20038831 CAGTATCTTTTT
1 CAATTTCTTTTT
20038843 CAATTTCTTT
1 CAATTTCTTT
20038853 CTCATCAGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.03, T:0.62
Consensus pattern (12 bp):
CAATTTCTTTTT
Found at i:20042986 original size:7 final size:7
Alignment explanation
Indices: 20042976--20043000 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20042966 AATTAACAAT
20042976 TTCAACA
1 TTCAACA
20042983 TTCAACA
1 TTCAACA
20042990 TTCAACA
1 TTCAACA
20042997 TTCA
1 TTCA
20043001 TTGCAATCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (7 bp):
TTCAACA
Found at i:20044502 original size:24 final size:23
Alignment explanation
Indices: 20044475--20044529 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
20044465 CATTATTAAC
*
20044475 TTAAAATAAA-TATTTAAACATAAA
1 TTAAAATAAACTA-ATAAA-ATAAA
*
20044499 TTAAACTAAACTAATAAAATAAA
1 TTAAAATAAACTAATAAAATAAA
*
20044522 TAAAAATA
1 TTAAAATA
20044530 CCTAAATTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 11 0.42
24 13 0.50
25 2 0.08
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.29
Consensus pattern (23 bp):
TTAAAATAAACTAATAAAATAAA
Found at i:20045171 original size:18 final size:19
Alignment explanation
Indices: 20045148--20045183 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20045138 CATACATAAC
20045148 CATTTCAAAAG-AAAAGAT
1 CATTTCAAAAGCAAAAGAT
*
20045166 CATTTCTAAAGCAAAAGA
1 CATTTCAAAAGCAAAAGA
20045184 ACAAGAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.22
Consensus pattern (19 bp):
CATTTCAAAAGCAAAAGAT
Found at i:20049536 original size:20 final size:20
Alignment explanation
Indices: 20049502--20049541 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
20049492 GTGATCATAT
* *
20049502 CATTATACTACATCATCATC
1 CATTATAATACATCAACATC
*
20049522 CATTATAATATATCAACATC
1 CATTATAATACATCAACATC
20049542 ACATGATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (20 bp):
CATTATAATACATCAACATC
Found at i:20054798 original size:47 final size:47
Alignment explanation
Indices: 20054721--20055492 Score: 612
Period size: 47 Copynumber: 16.2 Consensus size: 47
20054711 AGGAAAATTC
* *
20054721 TCAATCTTTTTAAAGTTGTGTAGCCTCGTTTA-AGGATGAGGAGCTTTT
1 TCAATCATTTT-AAGTTGTGTAGCCTCATTTAGA-GATGAGGAGCTTTT
* * * * * * *
20054769 TAAATTATTTTAAGTTGCGTAACCTCGTTTAAAGAGGAGGAGCTTTT
1 TCAATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGAGGAGCTTTT
* * *
20054816 ACAATCATTTTAAGTTGTGTAGCCTCATTTAAAGAT--GGAGAATTTT
1 TCAATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGAGGAG-CTTTT
* *
20054862 TCTAATCATTTTTAAGTTGTGTAGCCTCATTTAGAGATAACGAGCTTTT
1 TC-AATCA-TTTTAAGTTGTGTAGCCTCATTTAGAGATGAGGAGCTTTT
* * ** * *
20054911 CCAATCATTCTAAGTTACGTAGCCTCATTTAGAGAGGAAGAGCTTTT
1 TCAATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGAGGAGCTTTT
* * * *
20054958 ACAATCATTTTAAGTTGTGTAGCTTGATTTAGAGAT-AGGGAGCCTTT
1 TCAATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGA-GGAGCTTTT
* * * *
20055005 CCAATCATTTTTAAAGTTGTATAGCCTCGTTTAGAGATGAAGAGCTTTT
1 TCAATCA-TTTT-AAGTTGTGTAGCCTCATTTAGAGATGAGGAGCTTTT
* * * * * * *
20055054 CCAATTATTTTAAGTTGTGCAACCTCATTTAGAGATGAAGAGC-CTA
1 TCAATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGAGGAGCTTTT
* **
20055100 CCTAATCATTTTAAGTTGCATAGCCTCATTTAGAGATGAGGAGCTTTT
1 TC-AATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGAGGAGCTTTT
* * * * * * *
20055148 CCCATCATTTTAAGTTGCGTAGCCTCGTTTAGAGGTG-GGAAACTATT
1 TCAATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGAGG-AGCTTTT
* * * * * *
20055195 CCAATCATTTTTAAGTTGCGTGGCCTTATTTTA-AGATAAGGAGCCTTT
1 TCAATCA-TTTTAAGTTGTGTAGCCTCA-TTTAGAGATGAGGAGCTTTT
* * * ** *
20055243 CCAATCATTTTAAAATTGGGTAGCCTTGTTTAGAGATGAGGA-CTGTT
1 TCAATCATTTT-AAGTTGTGTAGCCTCATTTAGAGATGAGGAGCTTTT
* * * * *
20055290 TCTAATCATTTTTAAGTTATGTAGCCTTATTTTGAGATGGGGGGCTTTT
1 TC-AATCA-TTTTAAGTTGTGTAGCCTCATTTAGAGATGAGGAGCTTTT
*
20055339 TTAATCATTTTAAAGTTAG-GTAGCCTCATTTAGAGATG-GAGAGCTTTT
1 TCAATCATTTT-AAGTT-GTGTAGCCTCATTTAGAGATGAG-GAGCTTTT
* * * * * *
20055387 CCAATCATTTTAAACTTGTGTAGTCTCGTTTAAAGATGAGAAGC-TTT
1 TCAATCATTTT-AAGTTGTGTAGCCTCATTTAGAGATGAGGAGCTTTT
* ** * *
20055434 TAAATCATTTTAAGTTACGTAGCCTCATTTAGAGCTGAGGAGTTTTTT
1 TCAATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGAGGAG-CTTTT
*
20055482 TCAATTATTTT
1 TCAATCATTTT
20055493 TAGAGTTGAG
Statistics
Matches: 584, Mismatches: 112, Indels: 56
0.78 0.15 0.07
Matches are distributed among these distances:
45 4 0.01
46 34 0.06
47 276 0.47
48 211 0.36
49 55 0.09
50 4 0.01
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (47 bp):
TCAATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGAGGAGCTTTT
Found at i:20055067 original size:96 final size:93
Alignment explanation
Indices: 20054722--20055467 Score: 599
Period size: 96 Copynumber: 7.9 Consensus size: 93
20054712 GGAAAATTCT
* * * ** *
20054722 CAATCTTTTTAAAGTTGTGTAGCCTCGTTTA-AGGATGAGGAGCTTTTTAAATTATTTTAAGTTG
1 CAATCATTTT-AAGTTGTGTAGCCTCATTTAGA-GATGAAGAGCTTTTCCAATCATTTTAAGTTG
* * * * * *
20054786 CGTAACCTCGTTTAAAGAGGAGGAGCTTTTA
64 CGTAGCCTCATTTAGAGATG-GGAGCCTTTC
* * ** * *
20054817 CAATCATTTTAAGTTGTGTAGCCTCATTTAAAGATGGAGAATTTTTCTAATCATTTTTAAGTTGT
1 CAATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGAAGAGCTTTTCCAATCA-TTTTAAGTTGC
** *
20054882 GTAGCCTCATTTAGAGATAACGAGCTTTTC
65 GTAGCCTCATTTAGAGAT-GGGAGCCTTTC
* ** * * *
20054912 CAATCATTCTAAGTTACGTAGCCTCATTTAGAGAGGAAGAGCTTTTACAATCATTTTAAGTTGTG
1 CAATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGAAGAGCTTTTCCAATCATTTTAAGTTGCG
* *
20054977 TAGCTTGATTTAGAGATAGGGAGCCTTTC
66 TAGCCTCATTTAGAGAT-GGGAGCCTTTC
* * *
20055006 CAATCATTTTTAAAGTTGTATAGCCTCGTTTAGAGATGAAGAGCTTTTCCAATTATTTTAAGTTG
1 CAATCA-TTTT-AAGTTGTGTAGCCTCATTTAGAGATGAAGAGCTTTTCCAATCATTTTAAGTTG
* * * * *
20055071 TGCAACCTCATTTAGAGATGAAGAGCC-TAC
64 CGTAGCCTCATTTAGAGATG-GGAGCCTTTC
** * *
20055101 CTAATCATTTTAAGTTGCATAGCCTCATTTAGAGATGAGGAGCTTTTCCCATCATTTTAAGTTGC
1 C-AATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGAAGAGCTTTTCCAATCATTTTAAGTTGC
* * **
20055166 GTAGCCTCGTTTAGAGGTGGGAAACTATTC
65 GTAGCCTCATTTAGAGATGGGAGCCT-TTC
* * * * *
20055196 CAATCATTTTTAAGTTGCGTGGCCTTATTTTA-AGAT-AAGGAGCCTTTCCAATCATTTTAAAAT
1 CAATCA-TTTTAAGTTGTGTAGCCTCA-TTTAGAGATGAA-GAGCTTTTCCAATCATTTT-AAGT
* ** *
20055259 TGGGTAGCCTTGTTTAGAGATGAGGA-CTGTTTC
62 TGCGTAGCCTCATTTAGAGATG-GGAGC-CTTTC
* * * * ** * **
20055292 TAATCATTTTTAAGTTATGTAGCCTTATTTTGAGATGGGGGGCTTTTTTAATCATTTTAAAGTTA
1 CAATCA-TTTTAAGTTGTGTAGCCTCATTTAGAGATGAAGAGCTTTTCCAATCATTTT-AAGTT-
*
20055357 G-GTAGCCTCATTTAGAGATGGAGAGCTTTTC
63 GCGTAGCCTCATTTAGAGATGG-GAGCCTTTC
* * * * * *
20055388 CAATCATTTTAAACTTGTGTAGTCTCGTTTAAAGATG-AGAAGCTTTT-AAATCATTTTAAGTTA
1 CAATCATTTT-AAGTTGTGTAGCCTCATTTAGAGATGAAG-AGCTTTTCCAATCATTTTAAGTTG
20055451 CGTAGCCTCATTTAGAG
64 CGTAGCCTCATTTAGAG
20055468 CTGAGGAGTT
Statistics
Matches: 529, Mismatches: 99, Indels: 47
0.78 0.15 0.07
Matches are distributed among these distances:
93 3 0.01
94 165 0.31
95 155 0.29
96 200 0.38
97 6 0.01
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (93 bp):
CAATCATTTTAAGTTGTGTAGCCTCATTTAGAGATGAAGAGCTTTTCCAATCATTTTAAGTTGCG
TAGCCTCATTTAGAGATGGGAGCCTTTC
Found at i:20055087 original size:143 final size:141
Alignment explanation
Indices: 20054722--20055492 Score: 636
Period size: 142 Copynumber: 5.4 Consensus size: 141
20054712 GGAAAATTCT
* **
20054722 CAATC-TTTTTAAAGTTGTGTAGCCTCGTTTA-AGGATGAGGAGCTTTTTAAATTATTTTAAGTT
1 CAATCATTTTT-AAGTTGTGTAGCCTCGTTTAGA-GATGAAGAGCTTTTCCAATTATTTTAAGTT
* * * *
20054785 GCGTAACCTCGTTTAAAGAGGAGGAGCTTTTACAATCATTTTAAGTTGTGTAGCCTCATTTAAAG
64 GCGTAACCTCATTTAGAGAGGAAGAGCTTTTACAATCATTTTAAGTTGTGTAGCCTCATTTAGAG
**
20054850 ATGGAGAATTTTTC
129 ATGG-GAGCTTTTC
* * * * *
20054864 TAATCATTTTTAAGTTGTGTAGCCTCATTTAGAGAT-AACGAGCTTTTCCAATCATTCTAAGTTA
1 CAATCATTTTTAAGTTGTGTAGCCTCGTTTAGAGATGAA-GAGCTTTTCCAATTATTTTAAGTTG
* * *
20054928 CGTAGCCTCATTTAGAGAGGAAGAGCTTTTACAATCATTTTAAGTTGTGTAGCTTGATTTAGAGA
65 CGTAACCTCATTTAGAGAGGAAGAGCTTTTACAATCATTTTAAGTTGTGTAGCCTCATTTAGAGA
*
20054993 TAGGGAGCCTTTC
130 T-GGGAGCTTTTC
*
20055006 CAATCATTTTTAAAGTTGTATAGCCTCGTTTAGAGATGAAGAGCTTTTCCAATTATTTTAAGTTG
1 CAATCATTTTT-AAGTTGTGTAGCCTCGTTTAGAGATGAAGAGCTTTTCCAATTATTTTAAGTTG
* * * * **
20055071 TGCAACCTCATTTAGAGATGAAGAGC--CTACCTAATCATTTTAAGTTGCATAGCCTCATTTAGA
65 CGTAACCTCATTTAGAGAGGAAGAGCTTTTA-C-AATCATTTTAAGTTGTGTAGCCTCATTTAGA
20055134 GATGAGGAGCTTTTC
128 GATG-GGAGCTTTTC
* * * * *
20055149 CCATCA-TTTTAAGTTGCGTAGCCTCGTTTAGAGGTGGGAA-A-CTATTCCAATCATTTTTAAGT
1 CAATCATTTTTAAGTTGTGTAGCCTCGTTTAGAGAT--GAAGAGCTTTTCCAATTA-TTTTAAGT
** * * * * * * **
20055211 TGCGTGGCCTTATTTTA-AGA-TAAGGAGCCTTTCCAATCATTTTAAAATTGGGTAGCCTTGTTT
63 TGCGTAACCTCA-TTTAGAGAGGAA-GAGCTTTTACAATCATTTT-AAGTTGTGTAGCCTCATTT
20055274 AGAGATGAGGA-CTGTTTC
125 AGAGATG-GGAGCT-TTTC
* * ** * ** * ** *
20055292 TAATCATTTTTAAGTTATGTAGCCTTATTTTGAGATGGGGGGCTTTTTTAATCATTTTAAAGTTA
1 CAATCATTTTTAAGTTGTGTAGCCTCGTTTAGAGATGAAGAGCTTTTCCAATTATTTT-AAGTT-
* * * * * *
20055357 G-GTAGCCTCATTTAGAGATGG-AGAGCTTTTCCAATCATTTTAAACTTGTGTAGTCTCGTTTAA
64 GCGTAACCTCATTTAGAGA-GGAAGAGCTTTTACAATCATTTT-AAGTTGTGTAGCCTCATTTAG
*
20055420 AGATGAGAAGCTTTT-
127 AGATG-GGAGCTTTTC
* ** * * * * *
20055435 AAATCA-TTTTAAGTTACGTAGCCTCATTTAGAGCTGAGGAGTTTTTTTCAATTATTTT
1 CAATCATTTTTAAGTTGTGTAGCCTCGTTTAGAGATGAAGAG-CTTTTCCAATTATTTT
20055493 TAGAGTTGAG
Statistics
Matches: 514, Mismatches: 87, Indels: 55
0.78 0.13 0.08
Matches are distributed among these distances:
141 37 0.07
142 191 0.37
143 186 0.36
144 96 0.19
145 4 0.01
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (141 bp):
CAATCATTTTTAAGTTGTGTAGCCTCGTTTAGAGATGAAGAGCTTTTCCAATTATTTTAAGTTGC
GTAACCTCATTTAGAGAGGAAGAGCTTTTACAATCATTTTAAGTTGTGTAGCCTCATTTAGAGAT
GGGAGCTTTTC
Found at i:20055713 original size:49 final size:49
Alignment explanation
Indices: 20055597--20055737 Score: 170
Period size: 49 Copynumber: 3.0 Consensus size: 49
20055587 TGTGCTATCC
* *
20055597 CAATTATTTTTAAAGTTGTGTAGCTTTG-TTAGAGATAAGGAG-TTTTT
1 CAATTATTTTTAAAGTTGTGTAGCCTCGTTTAGAGATAAGGAGCTTTTT
* *
20055644 ---TT-TTTTTAAA-TTGAGTAGCCTCGTTTAGAGATAAAGAGCTTTTT
1 CAATTATTTTTAAAGTTGTGTAGCCTCGTTTAGAGATAAGGAGCTTTTT
* * *
20055688 CAATTATTTTAAAAGTTGTGTAGCCTCGTTTAAAGATGAGGAGCTTTTT
1 CAATTATTTTTAAAGTTGTGTAGCCTCGTTTAGAGATAAGGAGCTTTTT
20055737 C
1 C
20055738 TTAATCCGTC
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
42 10 0.13
43 21 0.27
44 7 0.09
47 2 0.03
48 7 0.09
49 31 0.40
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.44
Consensus pattern (49 bp):
CAATTATTTTTAAAGTTGTGTAGCCTCGTTTAGAGATAAGGAGCTTTTT
Found at i:20063416 original size:40 final size:40
Alignment explanation
Indices: 20063358--20063436 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
20063348 ACGTGAAAGA
*
20063358 CACCAATCGTGGCGAGGTTGAAAAACCCACTAAGGTGAAT
1 CACCAATCGTGGCAAGGTTGAAAAACCCACTAAGGTGAAT
* *
20063398 CACCAATCTTGGCAAGGTTGAAAACCCCACTAAGGTGAA
1 CACCAATCGTGGCAAGGTTGAAAAACCCACTAAGGTGAA
20063437 AAATAGTCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (40 bp):
CACCAATCGTGGCAAGGTTGAAAAACCCACTAAGGTGAAT
Found at i:20066110 original size:40 final size:40
Alignment explanation
Indices: 20066055--20066132 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
20066045 TATGAAAGAC
20066055 ACCAATCATGGCAAGGTTAAAAACCCCACTAAAGTGAATA
1 ACCAATCATGGCAAGGTTAAAAACCCCACTAAAGTGAATA
* * *
20066095 ACCAATCTTGGCAAGGTTGAAAACCCCACTAAGGTGAA
1 ACCAATCATGGCAAGGTTAAAAACCCCACTAAAGTGAA
20066133 AAATAGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (40 bp):
ACCAATCATGGCAAGGTTAAAAACCCCACTAAAGTGAATA
Found at i:20074097 original size:2 final size:2
Alignment explanation
Indices: 20074090--20074181 Score: 114
Period size: 2 Copynumber: 44.0 Consensus size: 2
20074080 ATAAAAATGC
20074090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT ACT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T A-T
* *
20074133 ACT ACT AT A- AT AA AN AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20074176 AT AT AT
1 AT AT AT
20074182 CCAATACTCA
Statistics
Matches: 85, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
1 1 0.01
2 70 0.82
3 14 0.16
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:20092167 original size:52 final size:52
Alignment explanation
Indices: 20092105--20092224 Score: 231
Period size: 52 Copynumber: 2.3 Consensus size: 52
20092095 AAATAAGAGT
20092105 AATTTTTAACATATTAAGCTTAGTTCTTAAATCTAAATGCGACAATTGGAGC
1 AATTTTTAACATATTAAGCTTAGTTCTTAAATCTAAATGCGACAATTGGAGC
20092157 AATTTTTAACATATTAAGCTTAGTTCTTAAATCTAAATGCGACAATTGGAGC
1 AATTTTTAACATATTAAGCTTAGTTCTTAAATCTAAATGCGACAATTGGAGC
*
20092209 AATGTTTAACATATTA
1 AATTTTTAACATATTA
20092225 TGAATAGCTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (52 bp):
AATTTTTAACATATTAAGCTTAGTTCTTAAATCTAAATGCGACAATTGGAGC
Found at i:20095609 original size:31 final size:30
Alignment explanation
Indices: 20095574--20095697 Score: 98
Period size: 30 Copynumber: 4.2 Consensus size: 30
20095564 AAGACAACTT
*
20095574 TTGTCTGTA-ATTAAGATAAAAATATTTTATC
1 TTGTCT-TAGATTAAGAAAAAAATATTTT-TC
* * *
20095605 TTGTC-TAAATT--GAGACAAATATGTTTTC
1 TTGTCTTAGATTAAGAAAAAAATAT-TTTTC
* *
20095633 TTGTC-GAGATTAAGACAAAAAATAGTTTTC
1 TTGTCTTAGATTAAGA-AAAAAATATTTTTC
* *
20095663 TTGTCTTAGATTAAGACAAACATA-TTTTC
1 TTGTCTTAGATTAAGAAAAAAATATTTTTC
20095692 TTGTCT
1 TTGTCT
20095698 AAATTAACAC
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
28 20 0.26
29 16 0.21
30 21 0.27
31 20 0.26
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (30 bp):
TTGTCTTAGATTAAGAAAAAAATATTTTTC
Found at i:20095656 original size:59 final size:58
Alignment explanation
Indices: 20095582--20095745 Score: 197
Period size: 59 Copynumber: 2.8 Consensus size: 58
20095572 TTTTGTCTGT
* * * *
20095582 AATTAAGA-TAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCTTGTCGA
1 AATTAAGACAAAAAATAGTTT-TCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCGA
* * * *
20095640 GATTAAGACAAAAAATAGTTTTCTTGTCTTAGATTAAGACAAACATATTTTCTTGTCTA
1 AATTAAGACAAAAAATAGTTTTCTTGTC-TAAATTAAGACAAACATGTTTTCTTGTCGA
* * *
20095699 AATTAACACCAAACAT-GTTTTCTTGTCTAAATTAAGACAAACATGTT
1 AATTAAGACAAAAAATAGTTTTCTTGTCTAAATTAAGACAAACATGTT
20095746 AAAGCTGCCA
Statistics
Matches: 90, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
57 18 0.20
58 25 0.28
59 47 0.52
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.38
Consensus pattern (58 bp):
AATTAAGACAAAAAATAGTTTTCTTGTCTAAATTAAGACAAACATGTTTTCTTGTCGA
Found at i:20095711 original size:29 final size:28
Alignment explanation
Indices: 20095582--20095742 Score: 169
Period size: 29 Copynumber: 5.5 Consensus size: 28
20095572 TTTTGTCTGT
* *
20095582 AATTAAGATAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAACATA-TTT-TCTTGTCTA
* * * *
20095612 AATTGAGACAAATATGTTTTCTTGTCGA
1 AATTAAGACAAACATATTTTCTTGTCTA
* *
20095640 GATTAAGACAAAAAATAGTTTTCTTGTCTTA
1 AATTAAGAC-AAACATA-TTTTCTTGTC-TA
*
20095671 GATTAAGACAAACATATTTTCTTGTCTA
1 AATTAAGACAAACATATTTTCTTGTCTA
* *
20095699 AATTAACACCAAACATGTTTTCTTGTCTA
1 AATTAAGA-CAAACATATTTTCTTGTCTA
20095728 AATTAAGACAAACAT
1 AATTAAGACAAACAT
20095743 GTTAAAGCTG
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
28 30 0.27
29 44 0.39
30 28 0.25
31 10 0.09
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (28 bp):
AATTAAGACAAACATATTTTCTTGTCTA
Found at i:20098120 original size:42 final size:42
Alignment explanation
Indices: 20098068--20098219 Score: 184
Period size: 42 Copynumber: 3.6 Consensus size: 42
20098058 GTTGTGTAAT
*
20098068 GATGTTGACCCAGCTATGTGCGAGTGAAAGTGCACATAAGCC
1 GATGCTGACCCAGCTATGTGCGAGTGAAAGTGCACATAAGCC
* *
20098110 GATGCTGACCC-GACTATGTGCGAGTGGGAA-TGCACATAAGCT
1 GATGCTGACCCAG-CTATGTGCGAGT-GAAAGTGCACATAAGCC
* *
20098152 GATGCTAACCCAGCTATGTGCGAGT-AGAAGTGCACATAAGTC
1 GATGCTGACCCAGCTATGTGCGAGTGA-AAGTGCACATAAGCC
* * *
20098194 GATGATGACCCAGCCATGTGCTAGTG
1 GATGCTGACCCAGCTATGTGCGAGTG
20098220 GGGAGTGCAT
Statistics
Matches: 93, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
41 3 0.03
42 86 0.92
43 4 0.04
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.22
Consensus pattern (42 bp):
GATGCTGACCCAGCTATGTGCGAGTGAAAGTGCACATAAGCC
Done.