Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 17 of 20
Found at i:2675615 original size:27 final size:27
Alignment explanation
Indices: 2675581--2676317 Score: 1118
Period size: 27 Copynumber: 27.0 Consensus size: 27
2675571 GCTTTGAAAT
*
2675581 GGGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
2675608 GGATGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2675635 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
2675662 GGGTGCCACAGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2675689 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
2675717 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2675744 GGGTGCCGCGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2675771 GAGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
2675798 AGGTGCTACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2675825 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2675852 GGGTGCCACGGAGTTGTAGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2675879 GAGATGCCACGGAGTTGTGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
*
2675907 GGGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2675934 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2675961 GGGTGCCACGGAGTTGTGGACTTAAAGA
1 GGGTGCCACGGAGTTGTGGACTTAAA-A
2675989 GGGTGCC-CTGGAGTTGTGGACTTTAAAA
1 GGGTGCCAC-GGAGTTGTGGAC-TTAAAA
* * *
2676017 GAGCGCTACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2676044 GGGTGCCACGGAGTTGTGGACTTTGAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
2676072 -GGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2676098 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* * **
2676126 GAGTGCCACGGAGTTTTGGACTTTGAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2676153 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2676180 GGGTGCCATGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
2676208 GAGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
2676236 GAGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2676263 GGGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2676290 GGATGCCACGGAGTTGTGGACTTCAAAA
1 GGGTGCCACGGAGTTGTGGACTT-AAAA
2676318 AGAAATGCCA
Statistics
Matches: 649, Mismatches: 50, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.01
27 465 0.72
28 173 0.27
29 6 0.01
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:2675716 original size:82 final size:81
Alignment explanation
Indices: 2675581--2676317 Score: 1118
Period size: 82 Copynumber: 9.0 Consensus size: 81
2675571 GCTTTGAAAT
* * *
2675581 GGGTGCCACGGAGTTGTGGATTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
2675646 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* *
2675662 GGGTGCCACAGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
2675727 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* * * *
2675744 GGGTGCCGCGGAGTTGTGGACTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAAGGTGCTACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
2675809 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* * *
2675825 GGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTAGACTTAAAAGAGATGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACG
2675890 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
*
2675907 GGGTGCCACGGAGTTGTGGATTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
2675972 AGTTGTGGACTTAAAGA
66 AGTTGTGGACTTAAA-A
* * *
2675989 GGGTGCC-CTGGAGTTGTGGACTTTAAAAGAGCGCTACGGAGTTGTGGACTTAAAAGGGTGCCAC
1 GGGTGCCAC-GGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
*
2676053 GGAGTTGTGGACTTTGAAA
64 GGAGTTGTGGAC-TTAAAA
* *
2676072 -GGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACG
* **
2676136 GAGTTTTGGACTTTGAA
65 GAGTTGTGGACTTAAAA
* *
2676153 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTTAAAAGAGTGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACG
2676218 GAGTTGTGGACTTTAAAA
65 GAGTTGTGGAC-TTAAAA
* * * *
2676236 GAGTGCCACGGAGTTGTGGATTTAAAAGGGTGCCACGGAGTTGTGGATTTAAAAGGATGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
2676301 AGTTGTGGACTTCAAAA
66 AGTTGTGGACTT-AAAA
2676318 AGAAATGCCA
Statistics
Matches: 599, Mismatches: 46, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
81 180 0.30
82 314 0.52
83 101 0.17
84 4 0.01
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (81 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAA
Found at i:2683851 original size:21 final size:22
Alignment explanation
Indices: 2683825--2683878 Score: 101
Period size: 21 Copynumber: 2.5 Consensus size: 22
2683815 TGGACATGTT
2683825 AAAAATGCATGAAACATAAT-A
1 AAAAATGCATGAAACATAATAA
2683846 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
2683868 AAAAATGCATG
1 AAAAATGCATG
2683879 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:2684836 original size:20 final size:20
Alignment explanation
Indices: 2684789--2684863 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
2684779 AAAAAGACAT
*
2684789 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
2684808 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
2684829 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
2684849 AATGTATTGATACAT
1 AATGTATCGATACAT
2684864 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:2684861 original size:40 final size:39
Alignment explanation
Indices: 2684786--2684863 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
2684776 GGTAAAAAGA
* *
2684786 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* * *
2684825 CATACATGTATCGATATATTGAAAAATGTATTGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
2684864 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:2686675 original size:21 final size:22
Alignment explanation
Indices: 2686646--2686691 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2686636 TGTTCAGACA
** *
2686646 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2686668 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2686689 AGT
1 AGT
2686692 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2688605 original size:27 final size:28
Alignment explanation
Indices: 2688571--2688636 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 28
2688561 GCCACCCATT
2688571 TGTTTGTCAAAAATAGTGGTTAT-TTTG
1 TGTTTGTCAAAAATAGTGGTTATCTTTG
* *
2688598 TGTTTGTCAAAAATGGTGGTTTTCTTTG
1 TGTTTGTCAAAAATAGTGGTTATCTTTG
2688626 -GATTTGTCAAA
1 TG-TTTGTCAAA
2688637 TATGGAGGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 22 0.63
28 13 0.37
ACGTcount: A:0.24, C:0.06, G:0.23, T:0.47
Consensus pattern (28 bp):
TGTTTGTCAAAAATAGTGGTTATCTTTG
Found at i:2691723 original size:25 final size:24
Alignment explanation
Indices: 2691695--2691748 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2691685 CATTGCCATC
2691695 TTTATCTAGAATATGAATGAAAACT
1 TTTATCTAGAATAT-AATGAAAACT
* * * *
2691720 TTTATTTCGAATATAGTGAAAATT
1 TTTATCTAGAATATAATGAAAACT
2691744 TTTAT
1 TTTAT
2691749 TCATATTCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (24 bp):
TTTATCTAGAATATAATGAAAACT
Found at i:2691739 original size:24 final size:25
Alignment explanation
Indices: 2691703--2691749 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2691693 TCTTTATCTA
2691703 GAATATGAATGAAAACTTTTATTTC
1 GAATATGAATGAAAACTTTTATTTC
* *
2691728 GAATAT-AGTGAAAATTTTTATT
1 GAATATGAATGAAAACTTTTATT
2691750 CATATTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.43
Consensus pattern (25 bp):
GAATATGAATGAAAACTTTTATTTC
Found at i:2692257 original size:109 final size:109
Alignment explanation
Indices: 2692049--2692245 Score: 256
Period size: 109 Copynumber: 1.8 Consensus size: 109
2692039 TCTAATTTTA
* * *
2692049 TTTATATTAAAAATCAGATCATACATAATTTCATTAATTATTAATTATTTAACATTTACTTAAAT
1 TTTATATTAAAAATCAGATAATACATAATTTCACTAATTATTAATTATTTAACATTTACTTAAAG
*
2692114 TTAAACTAAGTTTTTAAATATTACAAACAAAAAATTTTTGAACT
66 GTAAACTAAGTTTTTAAATATTACAAACAAAAAATTTTTGAACT
* * * * *
2692158 TTTATATTAAAAATTAGATAATA-A-ATTTTTACTAATTATTAACTATATTTAATATTTATTTAA
1 TTTATATTAAAAATCAGATAATACATAATTTCACTAATTATTAA-T-TATTTAACATTTACTTAA
*
2692221 CGGTAAACATAA-TTTTTAAATATTA
64 AGGTAAAC-TAAGTTTTTAAATATTA
2692246 AGAATAAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
107 15 0.20
108 2 0.03
109 55 0.73
110 3 0.04
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (109 bp):
TTTATATTAAAAATCAGATAATACATAATTTCACTAATTATTAATTATTTAACATTTACTTAAAG
GTAAACTAAGTTTTTAAATATTACAAACAAAAAATTTTTGAACT
Found at i:2692675 original size:22 final size:23
Alignment explanation
Indices: 2692647--2692700 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
2692637 AAAATAAACT
*
2692647 TCCAAGTCTTCA-AGGATTCGCA
1 TCCAAGTCTTCAGAAGATTCGCA
*
2692669 TCCAAGTATTCAGAAGATTCGCA
1 TCCAAGTCTTCAGAAGATTCGCA
*
2692692 TCTAAGTCT
1 TCCAAGTCT
2692701 GCTTCCCTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (23 bp):
TCCAAGTCTTCAGAAGATTCGCA
Found at i:2695783 original size:3 final size:3
Alignment explanation
Indices: 2695775--2695800 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2695765 GTTGTCATTA
2695775 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2695801 CAATGCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2695814 original size:2 final size:2
Alignment explanation
Indices: 2695807--2695843 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2695797 ATAACAATGC
*
2695807 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2695844 GAATGATGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2696932 original size:12 final size:12
Alignment explanation
Indices: 2696904--2696939 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
2696894 GATGAAGAAG
2696904 AAGAAAGAAAGAAA
1 AAGAAA-AAA-AAA
2696918 AAGAAAAAAAAA
1 AAGAAAAAAAAA
2696930 AAGAAAAAAA
1 AAGAAAAAAA
2696940 TATGAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 13 0.59
13 3 0.14
14 6 0.27
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:2701758 original size:34 final size:34
Alignment explanation
Indices: 2701700--2701890 Score: 215
Period size: 34 Copynumber: 5.7 Consensus size: 34
2701690 AAGTGGGAGA
* *
2701700 ATTGTTGATTGAATG-GTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGAGTGATTTGGTAGCTTACC
** *
2701733 ATTGTTGATTAAATGAGTGATTTGGTAATTTGCC
1 ATTGTTGATTAAATGAGTGATTTGGTAGCTTACC
* * * *
2701767 ATTGTTGACTAAATGGGAGATTTGATAGCTTACC
1 ATTGTTGATTAAATGAGTGATTTGGTAGCTTACC
*
2701801 ATTGTTGATTAAATGAGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGAGTGATTTGGTAGCTTACC
* * * * * **
2701835 ATTGTTGACTAAATGGGAGATTTAGTAGGTTGTC
1 ATTGTTGATTAAATGAGTGATTTGGTAGCTTACC
2701869 ATTGTTGATTAAATGA-TGATTT
1 ATTGTTGATTAAATGAGTGATTT
2701891 TTACTAAACC
Statistics
Matches: 131, Mismatches: 26, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
33 19 0.15
34 112 0.85
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (34 bp):
ATTGTTGATTAAATGAGTGATTTGGTAGCTTACC
Found at i:2701802 original size:68 final size:68
Alignment explanation
Indices: 2701700--2701890 Score: 244
Period size: 68 Copynumber: 2.8 Consensus size: 68
2701690 AAGTGGGAGA
* * * * * *
2701700 ATTGTTGATTGAAT-GGTGATTTGGTAGTTTACCATTGTTGATTAAATGAGTGATTTGGTAATTT
1 ATTGTTGACTAAATGGGAGATTTGATAGCTTACCATTGTTGATTAAATGAGTGATTTGGTAACTT
*
2701764 GCC
66 ACC
**
2701767 ATTGTTGACTAAATGGGAGATTTGATAGCTTACCATTGTTGATTAAATGAGTGATTTGGTGGCTT
1 ATTGTTGACTAAATGGGAGATTTGATAGCTTACCATTGTTGATTAAATGAGTGATTTGGTAACTT
2701832 ACC
66 ACC
* **
2701835 ATTGTTGACTAAATGGGAGATTT-AGTAGGTTGTCATTGTTGATTAAATGA-TGATTT
1 ATTGTTGACTAAATGGGAGATTTGA-TAGCTTACCATTGTTGATTAAATGAGTGATTT
2701891 TTACTAAACC
Statistics
Matches: 110, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
67 19 0.17
68 91 0.83
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (68 bp):
ATTGTTGACTAAATGGGAGATTTGATAGCTTACCATTGTTGATTAAATGAGTGATTTGGTAACTT
ACC
Found at i:2702691 original size:25 final size:27
Alignment explanation
Indices: 2702650--2702700 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 27
2702640 CTATATGAAG
2702650 TATGGATGAAAACTTTT-AT-TTCAAA
1 TATGGATGAAAACTTTTCATATTCAAA
*
2702675 TATGG-TGAAGAATTTTTCATATTCAA
1 TATGGATGAA-AACTTTTCATATTCAA
2702701 TTTGTTATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 4 0.18
25 11 0.50
26 2 0.09
27 5 0.23
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (27 bp):
TATGGATGAAAACTTTTCATATTCAAA
Found at i:2706804 original size:3 final size:3
Alignment explanation
Indices: 2706796--2706831 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2706786 GTTGCCATTA
2706796 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2706832 GATGATGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2710842 original size:2 final size:2
Alignment explanation
Indices: 2710835--2710868 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2710825 AGACCCTATT
2710835 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2710869 AACCCTAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2711943 original size:17 final size:18
Alignment explanation
Indices: 2711923--2712004 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 18
2711913 TAATAAGATA
2711923 TAAATATATAA-ATTTAT
1 TAAATATATAATATTTAT
*
2711940 TAAAAATATATAATATTAAT
1 T--AAATATATAATATTTAT
*
2711960 TATTAAT-TAATAAAATTTATT
1 TA--AATAT-ATAATATTTA-T
2711981 TAAATATATAATATTT-T
1 TAAATATATAATATTTAT
2711998 T-AATATA
1 TAAATATA
2712005 ATTATAATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
16 6 0.11
17 3 0.06
18 1 0.02
19 22 0.42
20 18 0.34
21 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATATATAATATTTAT
Found at i:2712760 original size:2 final size:2
Alignment explanation
Indices: 2712755--2712792 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2712745 TTTCCTTTAA
* *
2712755 AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2712793 GCATAGGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2713601 original size:2 final size:2
Alignment explanation
Indices: 2713594--2713626 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2713584 GGATTAACTC
2713594 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 A
2713627 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2713631 original size:2 final size:2
Alignment explanation
Indices: 2713626--2713680 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
2713616 ATATATATAT
2713626 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2713668 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
2713681 TTTCAGAACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2724963 original size:13 final size:14
Alignment explanation
Indices: 2724945--2724976 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2724935 CTAAAATGGA
2724945 GAGAAGAAA-CAAT
1 GAGAAGAAATCAAT
2724958 GAGAAGAAATCAAT
1 GAGAAGAAATCAAT
2724972 G-GAAG
1 GAGAAG
2724977 GGAATGTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.56, C:0.06, G:0.28, T:0.09
Consensus pattern (14 bp):
GAGAAGAAATCAAT
Found at i:2726635 original size:24 final size:25
Alignment explanation
Indices: 2726608--2726659 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 25
2726598 AAAAAATTTT
2726608 AATAAAA-TTTTATTTCATAATTAA
1 AATAAAAGTTTTATTTCATAATTAA
2726632 AATAAAATGTGTTTTATTTCATAATTAA
1 AATAAAA---GTTTTATTTCATAATTAA
2726660 TAATTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 7 0.29
28 17 0.71
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (25 bp):
AATAAAAGTTTTATTTCATAATTAA
Found at i:2729071 original size:15 final size:15
Alignment explanation
Indices: 2729051--2729080 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2729041 AATAAAAATT
2729051 ATTAAATATATTAAA
1 ATTAAATATATTAAA
*
2729066 ATTAAATATGTTAAA
1 ATTAAATATATTAAA
2729081 TGTATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
ATTAAATATATTAAA
Found at i:2729707 original size:3 final size:3
Alignment explanation
Indices: 2729699--2729733 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2729689 CACGAAAGAG
2729699 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2729734 GGAATCGTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2731393 original size:22 final size:22
Alignment explanation
Indices: 2731363--2731414 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
2731353 ATATTTTATG
2731363 ATAATATTTAAA-ATATTAT-TAAT
1 ATAA-ATTTAAATAT-TTATAT-AT
*
2731386 ATAAATTTTAATATTTATATAT
1 ATAAATTTAAATATTTATATAT
2731408 ATAAATT
1 ATAAATT
2731415 ATATTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAATTTAAATATTTATATAT
Found at i:2732430 original size:2 final size:2
Alignment explanation
Indices: 2732423--2732454 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2732413 GCGTGCGTGC
*
2732423 GT GT GT GT GC GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2732455 ATTTGTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
GT
Found at i:2732434 original size:10 final size:10
Alignment explanation
Indices: 2732419--2732451 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
2732409 GTATGCGTGC
2732419 GTGCGTGTGT
1 GTGCGTGTGT
2732429 GTGCGTGTGT
1 GTGCGTGTGT
*
2732439 GTGTGTGTGT
1 GTGCGTGTGT
2732449 GTG
1 GTG
2732452 TGTATTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.00, C:0.06, G:0.52, T:0.42
Consensus pattern (10 bp):
GTGCGTGTGT
Found at i:2732434 original size:14 final size:14
Alignment explanation
Indices: 2732415--2732445 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2732405 GCCTGTATGC
2732415 GTGCGTGCGTGTGT
1 GTGCGTGCGTGTGT
*
2732429 GTGCGTGTGTGTGT
1 GTGCGTGCGTGTGT
2732443 GTG
1 GTG
2732446 TGTGTGTGTA
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:0.00, C:0.10, G:0.52, T:0.39
Consensus pattern (14 bp):
GTGCGTGCGTGTGT
Found at i:2734040 original size:2 final size:2
Alignment explanation
Indices: 2734033--2734057 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2734023 AAGCTTGCTT
2734033 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 T
2734058 TTTAAGGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2737710 original size:15 final size:15
Alignment explanation
Indices: 2737690--2737719 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2737680 CGGGGCAAAA
2737690 AAAAAAAAAAAAGAG
1 AAAAAAAAAAAAGAG
*
2737705 AAAAAAAACAAAGAG
1 AAAAAAAAAAAAGAG
2737720 GCTTACAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAG
Found at i:2740044 original size:11 final size:11
Alignment explanation
Indices: 2740028--2740053 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2740018 TCCAAATTGA
2740028 AAAGAAAAGAG
1 AAAGAAAAGAG
2740039 AAAGAAAAGAG
1 AAAGAAAAGAG
2740050 AAAG
1 AAAG
2740054 TAACATGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAG
Found at i:2740287 original size:2 final size:2
Alignment explanation
Indices: 2740280--2740321 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2740270 AGAAAGAAAA
2740280 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
2740322 GTTTTCCATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2743968 original size:39 final size:39
Alignment explanation
Indices: 2743925--2744009 Score: 109
Period size: 39 Copynumber: 2.2 Consensus size: 39
2743915 TTTAGGCCTC
**
2743925 TTGGGCTTTAACTCCCTCCCTTTCCTT-TTGTTATTTGTT
1 TTGGGCTTTAACTCCCTCCCTTTCCTTCTT-TTATTTACT
* * *
2743964 TTGGGCTTTAATTGCTTCCCTTTCCTTCTTTTATTTACT
1 TTGGGCTTTAACTCCCTCCCTTTCCTTCTTTTATTTACT
2744003 TTGGGCT
1 TTGGGCT
2744010 CTAATACTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 38 0.95
40 2 0.05
ACGTcount: A:0.08, C:0.24, G:0.14, T:0.54
Consensus pattern (39 bp):
TTGGGCTTTAACTCCCTCCCTTTCCTTCTTTTATTTACT
Found at i:2745197 original size:20 final size:19
Alignment explanation
Indices: 2745172--2745209 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2745162 ATGAACTTAA
2745172 ATTTTTAAAATATCTTTTTG
1 ATTTTTAAAATAT-TTTTTG
*
2745192 ATTTTTATAATATTTTTT
1 ATTTTTAAAATATTTTTT
2745210 AAAACTAATT
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:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (19 bp):
ATTTTTAAAATATTTTTTG
Found at i:2745324 original size:3 final size:3
Alignment explanation
Indices: 2745316--2745347 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2745306 TACTCTTAAC
*
2745316 AAT AAT AAT AAT AAT AAT AAA AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2745348 AACCACATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2749275 original size:28 final size:28
Alignment explanation
Indices: 2749217--2749281 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
2749207 ATATTATATT
*
2749217 TTTATATTA-TTTTAATTAATTAATTAA
1 TTTATATTATTTTTAATTAATTAAGTAA
* *
2749244 TTTATATTATTTTTTATATATTTAAGT-A
1 TTTATATTATTTTTAAT-TAATTAAGTAA
2749272 TTTATATTAT
1 TTTATATTAT
2749282 ATATATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.27
28 17 0.52
29 7 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTATATTATTTTTAATTAATTAAGTAA
Found at i:2749303 original size:11 final size:11
Alignment explanation
Indices: 2749207--2749305 Score: 58
Period size: 13 Copynumber: 9.6 Consensus size: 11
2749197 ATGTTTTAAG
2749207 ATATTATATTTTT
1 ATATTATA--TTT
2749220 ATATTAT-TTT
1 ATATTATATTT
2749230 A-ATTA-A-TT
1 ATATTATATTT
2749238 A-ATTA-ATTT
1 ATATTATATTT
2749247 ATATTAT-TTT
1 ATATTATATTT
*
2749257 TTA-TATATTT
1 ATATTATATTT
*
2749267 A-A--GTATTT
1 ATATTATATTT
2749275 ATATTATATATAT
1 ATATTATAT-T-T
2749288 ATATTATATTT
1 ATATTATATTT
*
2749299 CTATTAT
1 ATATTAT
2749306 GCGCCTCTTG
Statistics
Matches: 71, Mismatches: 5, Indels: 22
0.72 0.05 0.22
Matches are distributed among these distances:
8 14 0.20
9 12 0.17
10 16 0.23
11 10 0.14
12 2 0.03
13 17 0.24
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (11 bp):
ATATTATATTT
Found at i:2749805 original size:17 final size:16
Alignment explanation
Indices: 2749783--2749818 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2749773 CTTTTTTAAA
2749783 TTTTATTTTAAAAATAT
1 TTTTA-TTTAAAAATAT
*
2749800 TTTTATTTAATAATAT
1 TTTTATTTAAAAATAT
2749816 TTT
1 TTT
2749819 AACATTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTATTTAAAAATAT
Found at i:2749909 original size:11 final size:11
Alignment explanation
Indices: 2749888--2749937 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
2749878 TTAAAATATT
2749888 TATTATATTTAA
1 TATT-TATTTAA
2749900 TATTTATTTAA
1 TATTTATTTAA
*
2749911 TA-TTA--AAA
1 TATTTATTTAA
2749919 TTATTTATTTAA
1 -TATTTATTTAA
2749931 TATTTAT
1 TATTTAT
2749938 GTTTTTCAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 6 0.19
11 16 0.50
12 6 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTATTTAA
Found at i:2750605 original size:27 final size:27
Alignment explanation
Indices: 2750563--2750635 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
2750553 TTCATATTAT
2750563 ATTTATA-TTATAATTATATTTGAA-GTA
1 ATTTATATTTAT-ATTATATTTGAATG-A
*
2750590 ATTTATATTTATATTA-ATTTTAATGA
1 ATTTATATTTATATTATATTTGAATGA
* *
2750616 ATTAATAATTCATATTATAT
1 ATTTAT-ATTTATATTATAT
2750636 ATATTTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 12 0.31
27 21 0.54
28 6 0.15
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (27 bp):
ATTTATATTTATATTATATTTGAATGA
Found at i:2751376 original size:37 final size:37
Alignment explanation
Indices: 2751335--2751418 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
2751325 CGTAAAATGA
*
2751335 TTAAACTTGA-TAAATACAAATATTAAATCAAATTAAT
1 TTAAACTTAATTAAAT-CAAATATTAAATCAAATTAAT
* * **
2751372 TTAAACTTAATTAACTTAAATATTAAATTTAATTAAT
1 TTAAACTTAATTAAATCAAATATTAAATCAAATTAAT
2751409 TATAAA-TTAA
1 T-TAAACTTAA
2751419 AATAATTCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 32 0.80
38 8 0.20
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.40
Consensus pattern (37 bp):
TTAAACTTAATTAAATCAAATATTAAATCAAATTAAT
Found at i:2751414 original size:16 final size:17
Alignment explanation
Indices: 2751395--2751441 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
2751385 ACTTAAATAT
*
2751395 TAAATTTAATTAATT-A
1 TAAATTTAAATAATTCA
*
2751411 TAAATTAAAATAATTCA
1 TAAATTTAAATAATTCA
2751428 -AAATTTAAATAATT
1 TAAATTTAAATAATT
2751442 GCTTTGGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 26 0.96
17 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATAATTCA
Found at i:2751421 original size:22 final size:21
Alignment explanation
Indices: 2751372--2751419 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
2751362 TCAAATTAAT
*
2751372 TTAAACTTAATTAACTTAAATA
1 TTAAATTTAATTAACTTAAA-A
2751394 TTAAATTTAATTAA-TTATAAA
1 TTAAATTTAATTAACTTA-AAA
2751415 TTAAA
1 TTAAA
2751420 ATAATTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAATTTAATTAACTTAAAA
Found at i:2751798 original size:22 final size:21
Alignment explanation
Indices: 2751737--2751790 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
2751727 CATGTCAACA
*
2751737 TTTTTATTTTCAGAATTAAAAT
1 TTTTTATTTTCA-AATTTAAAT
**
2751759 TTGAGTATTTTCAAATTTAAAT
1 TT-TTTATTTTCAAATTTAAAT
2751781 TTTTTATTTT
1 TTTTTATTTT
2751791 GATAATTTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 6 0.23
22 12 0.46
23 8 0.31
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (21 bp):
TTTTTATTTTCAAATTTAAAT
Found at i:2752290 original size:2 final size:2
Alignment explanation
Indices: 2752278--2752308 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2752268 ATTTATTAAT
*
2752278 TA TA CA 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 T
2752309 GTTTTATCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2752669 original size:31 final size:32
Alignment explanation
Indices: 2752618--2752688 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
2752608 ATTTTGTTAT
**
2752618 TTTATATTTATATAAATTT-AATTAATTA-ATA
1 TTTATA-TTATATAAATTTAAAAAAATTATATA
2752649 TTTATATTATATAAATTTTAAAAAAATTATATA
1 TTTATATTATATAAA-TTTAAAAAAATTATATA
2752682 TTTATAT
1 TTTATAT
2752689 CATAATTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 9 0.26
31 9 0.26
32 7 0.20
33 10 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
TTTATATTATATAAATTTAAAAAAATTATATA
Found at i:2752738 original size:15 final size:14
Alignment explanation
Indices: 2752694--2752748 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
2752684 TATATCATAA
*
2752694 TTATATTATT-TTTA
1 TTATATT-TTATTTT
*
2752708 TTATATTTTA--TA
1 TTATATTTTATTTT
2752720 TTATATTTTAATTTT
1 TTATATTTT-ATTTT
2752735 TTATATTTTATTTT
1 TTATATTTTATTTT
2752749 ATATCATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
12 11 0.31
13 3 0.08
14 12 0.33
15 10 0.28
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATATTTTATTTT
Found at i:2761551 original size:13 final size:13
Alignment explanation
Indices: 2761516--2761551 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2761506 AATTTTTTTA
2761516 TATATTTAATATT
1 TATATTTAATATT
*
2761529 TGTATTTAATATT
1 TATATTTAATATT
*
2761542 TATATCTAAT
1 TATATTTAAT
2761552 TGTGATAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (13 bp):
TATATTTAATATT
Found at i:2762606 original size:21 final size:20
Alignment explanation
Indices: 2762580--2762773 Score: 107
Period size: 21 Copynumber: 9.3 Consensus size: 20
2762570 TTATTTGATA
2762580 TAAAATTATTACAAATATTAT
1 TAAAATTATTA-AAATATTAT
* * *
2762601 TAAAATTTTATTCAAATCTGAT
1 TAAAA--TTATTAAAATATTAT
* *
2762623 AAAAAATTATTACGAAT-TTAAT
1 -TAAAATTATTA-AAATATT-AT
2762645 T-AAATTATT-AAATATTTAT
1 TAAAATTATTAAAATA-TTAT
*
2762664 AAAATAATTATTTTAAAA-ATTAT
1 -TAA-AATTA--TTAAAATATTAT
* *
2762687 CAGAATTATATAAAA-A-TAT
1 TAAAATTAT-TAAAATATTAT
2762706 TAATAATTATTAAAAT-TATAT
1 TAA-AATTATTAAAATAT-TAT
*
2762727 TAAATATTA-TAAAAAATTAT
1 TAAA-ATTATTAAAATATTAT
2762747 TAAAATTATATAAAATATTAT
1 TAAAATTAT-TAAAATATTAT
2762768 TAAAAT
1 TAAAAT
2762774 GTATATCAAA
Statistics
Matches: 135, Mismatches: 16, Indels: 44
0.69 0.08 0.23
Matches are distributed among these distances:
18 3 0.02
19 16 0.12
20 35 0.26
21 44 0.33
22 18 0.13
23 13 0.10
24 3 0.02
25 3 0.02
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (20 bp):
TAAAATTATTAAAATATTAT
Found at i:2762611 original size:11 final size:11
Alignment explanation
Indices: 2762584--2762773 Score: 74
Period size: 11 Copynumber: 18.0 Consensus size: 11
2762574 TTGATATAAA
2762584 ATTATTACAAAT
1 ATTATTA-AAAT
2762596 ATTATTAAAAT
1 ATTATTAAAAT
* *
2762607 TTTATTCAAAT
1 ATTATTAAAAT
* * *
2762618 CTGA-TAAAAA
1 ATTATTAAAAT
*
2762628 ATTATTACGAAT
1 ATTATTA-AAAT
2762640 -TTAATT--AA-
1 ATT-ATTAAAAT
2762648 ATTATT-AAAT
1 ATTATTAAAAT
2762658 ATT-TATAAAAT
1 ATTAT-TAAAAT
2762669 AATTATTTTAAAA-
1 -ATTA--TTAAAAT
* *
2762682 ATTA-TCAGA-
1 ATTATTAAAAT
2762691 ATTATATAAAA-
1 ATTAT-TAAAAT
*
2762702 A-TATTAATA-
1 ATTATTAAAAT
2762711 ATTATTAAAAT
1 ATTATTAAAAT
2762722 -TATATT-AAAT
1 AT-TATTAAAAT
*
2762732 ATTA-TAAAAA
1 ATTATTAAAAT
2762742 ATTATT-AAA-
1 ATTATTAAAAT
2762751 ATTATATAAAAT
1 ATTAT-TAAAAT
2762763 ATTATTAAAAT
1 ATTATTAAAAT
2762774 GTATATCAAA
Statistics
Matches: 138, Mismatches: 17, Indels: 47
0.68 0.08 0.23
Matches are distributed among these distances:
8 3 0.02
9 25 0.18
10 38 0.28
11 42 0.30
12 24 0.17
14 5 0.04
15 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.43
Consensus pattern (11 bp):
ATTATTAAAAT
Found at i:2762684 original size:34 final size:35
Alignment explanation
Indices: 2762646--2762748 Score: 95
Period size: 34 Copynumber: 2.9 Consensus size: 35
2762636 GAATTTAATT
2762646 AAATTATTAAATATTTATAAAATAATTATT-TTAA
1 AAATTATTAAATATTTATAAAATAATTATTATTAA
* * * *
2762680 AAATTATCAGAATTATATAAAAATATTAATAATTATTAA
1 AAATTATTA-AA-TATTTATAAA-A-TAATTATTATTAA
*
2762719 AATTATATTAAATA-TTATAAAA-AATTATTA
1 AAAT-TATTAAATATTTATAAAATAATTATTA
2762749 AAATTATATA
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
34 15 0.28
35 2 0.04
36 9 0.17
37 6 0.11
38 9 0.17
39 9 0.17
40 4 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (35 bp):
AAATTATTAAATATTTATAAAATAATTATTATTAA
Found at i:2762724 original size:9 final size:9
Alignment explanation
Indices: 2762679--2762773 Score: 73
Period size: 10 Copynumber: 9.6 Consensus size: 9
2762669 AATTATTTTA
*
2762679 AAAATTATC
1 AAAATTATT
*
2762688 AGAATTATAT
1 AAAATTAT-T
*
2762698 AAAAATATT
1 AAAATTATT
2762707 AATAATTATT
1 AA-AATTATT
2762717 AAAATTATATT
1 AAAA-T-TATT
*
2762728 AAATATTATAA
1 AAA-ATTAT-T
2762739 AAAATTATT
1 AAAATTATT
2762748 AAAATTATAT
1 AAAATTAT-T
2762758 AAAATATTATT
1 -AAA-ATTATT
2762769 AAAAT
1 AAAAT
2762774 GTATATCAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
9 22 0.31
10 27 0.39
11 15 0.21
12 6 0.09
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (9 bp):
AAAATTATT
Found at i:2762736 original size:41 final size:40
Alignment explanation
Indices: 2762677--2762785 Score: 118
Period size: 41 Copynumber: 2.7 Consensus size: 40
2762667 ATAATTATTT
* *
2762677 TAAAA-ATTATCAGAATTATATAAAAATATTAATAATTAT-
1 TAAAATATTATTAAAATTATATAAAAATATTAA-AATTATA
2762716 TAAAAT-TATATTAAATATTATA-AAAAATTATTAAAATTATA
1 TAAAATAT-TATTAAA-ATTATATAAAAA-TATTAAAATTATA
*
2762757 TAAAATATTATTAAAATGTATATCAAAAT
1 TAAAATATTATTAAAAT-TATATAAAAAT
2762786 CTAACCCAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
39 6 0.10
40 18 0.31
41 30 0.51
42 5 0.08
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (40 bp):
TAAAATATTATTAAAATTATATAAAAATATTAAAATTATA
Found at i:2762748 original size:31 final size:31
Alignment explanation
Indices: 2762646--2762772 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
2762636 GAATTTAATT
2762646 AAATTATTAAATATT-TATAAAATAATTATTTTAA
1 AAATTATTAAA-ATTATATAAAAT-ATTA--TTAA
* *
2762680 AAATTATCAGAATTATATAAAA-A-TATTAA
1 AAATTATTAAAATTATATAAAATATTATTAA
* * *
2762709 TAATTATTAAAATTATATTAAATATTATAAA
1 AAATTATTAAAATTATATAAAATATTATTAA
2762740 AAATTATTAAAATTATATAAAATATTATTAA
1 AAATTATTAAAATTATATAAAATATTATTAA
2762771 AA
1 AA
2762773 TGTATATCAA
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
29 22 0.28
30 1 0.01
31 37 0.46
32 1 0.01
33 3 0.04
34 16 0.20
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (31 bp):
AAATTATTAAAATTATATAAAATATTATTAA
Found at i:2762784 original size:12 final size:10
Alignment explanation
Indices: 2762690--2762785 Score: 83
Period size: 10 Copynumber: 9.3 Consensus size: 10
2762680 AAATTATCAG
2762690 AATTATATAA
1 AATTATATAA
*
2762700 AAATAT-TAA
1 AATTATATAA
2762709 TAATTAT-TAA
1 -AATTATATAA
2762719 AATTATATTAA
1 AATTATA-TAA
*
2762730 ATATTATAAAA
1 A-ATTATATAA
2762741 AATTAT-TAA
1 AATTATATAA
2762750 AATTATATAA
1 AATTATATAA
2762760 AA-TATTATTAA
1 AATTA-TA-TAA
2762771 AATGTATATCAA
1 AAT-TATAT-AA
2762783 AAT
1 AAT
2762786 CTAACCCAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
9 19 0.26
10 25 0.35
11 13 0.18
12 13 0.18
13 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (10 bp):
AATTATATAA
Found at i:2763175 original size:21 final size:21
Alignment explanation
Indices: 2763151--2763198 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2763141 TTATGAATAT
*
2763151 AATATAAATTTTAAAAT-TTTA
1 AATATAAA-TATAAAATATTTA
*
2763172 AATATAAATATAATATATTTA
1 AATATAAATATAAAATATTTA
2763193 AATATA
1 AATATA
2763199 TTATATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATAAATATAAAATATTTA
Found at i:2763196 original size:15 final size:15
Alignment explanation
Indices: 2763176--2763205 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2763166 ATTTTAAATA
2763176 TAAATATAATATATT
1 TAAATATAATATATT
*
2763191 TAAATATATTATATT
1 TAAATATAATATATT
2763206 AATTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATATAATATATT
Found at i:2763219 original size:24 final size:27
Alignment explanation
Indices: 2763179--2763251 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 27
2763169 TTAAATATAA
2763179 ATATAATA--TATTTAAATATATTA-T
1 ATATAATATTTATTTAAATATATTATT
2763203 AT-TAAT-TTTATTTAAATATATTATT
1 ATATAATATTTATTTAAATATATTATT
*
2763228 ATATTATATTTA-TTAAATATATTA
1 ATATAATATTTATTTAAATATATTA
2763252 CGTATTATAT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
23 4 0.09
24 17 0.40
25 3 0.07
26 15 0.35
27 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATATAATATTTATTTAAATATATTATT
Found at i:2763262 original size:30 final size:27
Alignment explanation
Indices: 2763197--2763251 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
2763187 TATTTAAATA
2763197 TATTATATTAATTTTATTTAAATATAT
1 TATTATATTAATTTTATTTAAATATAT
2763224 TATTATATT-ATATTTA-TTAAATATAT
1 TATTATATTAAT-TTTATTTAAATATAT
2763250 TA
1 TA
2763252 CGTATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TATTATATTAATTTTATTTAAATATAT
Found at i:2765310 original size:27 final size:27
Alignment explanation
Indices: 2765276--2765332 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
2765266 TATTTATAAA
*
2765276 GATTCATTGTTGTATACAATTAGAGAT
1 GATTCATTGTTATATACAATTAGAGAT
2765303 GATTCATTGTTATATACAATTAGAGAT
1 GATTCATTGTTATATACAATTAGAGAT
2765330 GAT
1 GAT
2765333 CTTTTTTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (27 bp):
GATTCATTGTTATATACAATTAGAGAT
Found at i:2767807 original size:22 final size:22
Alignment explanation
Indices: 2767763--2767807 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2767753 ATATATTATC
* * * *
2767763 TATTATTATTTAAATAAATAAT
1 TATTAATATTGAAAAAAAAAAT
2767785 TATTAATATTGAAAAAAAAAAT
1 TATTAATATTGAAAAAAAAAAT
2767807 T
1 T
2767808 TACGTGAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TATTAATATTGAAAAAAAAAAT
Found at i:2770645 original size:2 final size:2
Alignment explanation
Indices: 2770638--2770666 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2770628 TGCTACTCAC
2770638 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2770667 CCCCCCCCAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2773509 original size:16 final size:16
Alignment explanation
Indices: 2773471--2773514 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2773461 CATTAGATTA
*
2773471 ATTTATTATTATAATT
1 ATTTTTTATTATAATT
*
2773487 ATTTTTTATTTTAATT
1 ATTTTTTATTATAATT
2773503 -TTATTTTATTAT
1 ATT-TTTTATTAT
2773515 CATAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 2 0.08
16 22 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
ATTTTTTATTATAATT
Found at i:2774052 original size:23 final size:23
Alignment explanation
Indices: 2774011--2774059 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2774001 TTCAGAACGT
* *
2774011 AAAATTAAATTTAATTTATTTTA
1 AAAATTAAATTTAAATTATTATA
2774034 AAAATT-AATTTAAAATTATTATA
1 AAAATTAAATTT-AAATTATTATA
2774057 AAA
1 AAA
2774060 TAAAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAATTAAATTTAAATTATTATA
Found at i:2774419 original size:20 final size:20
Alignment explanation
Indices: 2774377--2774421 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2774367 AATTGTTAAA
* *
2774377 TTTAATAATATAATTATATT
1 TTTAATAATATAATTAAAAT
* *
2774397 TTTAATAATTTATTTAAAAT
1 TTTAATAATATAATTAAAAT
2774417 TTTAA
1 TTTAA
2774422 ATTAATTTAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAATAATATAATTAAAAT
Found at i:2782534 original size:17 final size:17
Alignment explanation
Indices: 2782512--2782553 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
2782502 TTAAAATATG
*
2782512 ATATAATATGATATAAA
1 ATATAATATAATATAAA
*
2782529 ATATAACATAATATAAA
1 ATATAATATAATATAAA
*
2782546 AAATAATA
1 ATATAATA
2782554 ATGCAAATGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
ATATAATATAATATAAA
Found at i:2783494 original size:2 final size:2
Alignment explanation
Indices: 2783487--2783518 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2783477 TTACATGAAC
2783487 AT AT AT 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 AT AT AT
2783519 CTTTGTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2784453 original size:34 final size:34
Alignment explanation
Indices: 2784386--2784602 Score: 280
Period size: 34 Copynumber: 6.4 Consensus size: 34
2784376 TGATAAAAAA
*
2784386 TGTTGATTAAATGG-TGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGATGATTTGGTAGCTTACCAT
* * *
2784419 TGTTGATTAAATGGATGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGATGATTTGGTAGCTTACCAT
*
2784453 TGTTGACTAAATAGGA-GATTTGGTAGCTTACCAT
1 TGTTGATTAAAT-GGATGATTTGGTAGCTTACCAT
*
2784487 TGTTGATTAAATGAGA-AATTTGGTAGCTTACCAT
1 TGTTGATTAAATG-GATGATTTGGTAGCTTACCAT
* * *
2784521 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGATGATTTGGTAGCTTACCAT
* *
2784555 TGTTGACTAAATGG-TAGATTTGGTAGGTTACCAT
1 TGTTGATTAAATGGAT-GATTTGGTAGCTTACCAT
2784589 TGTTGATTAAATGG
1 TGTTGATTAAATGG
2784603 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
33 17 0.10
34 142 0.88
35 3 0.02
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGATGATTTGGTAGCTTACCAT
Found at i:2784578 original size:102 final size:101
Alignment explanation
Indices: 2784386--2784602 Score: 337
Period size: 102 Copynumber: 2.1 Consensus size: 101
2784376 TGATAAAAAA
** * * * *
2784386 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGATGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGATGATTTGGTGGCTTACC
2784451 ATTGTTGACTAAATAGGAGATTTGGTAGCTTACCAT
66 ATTGTTGACTAAATAGGAGATTTGGTAGCTTACCAT
*
2784487 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGATGATTTGGTGGCTTAC
*
2784552 CATTGTTGACTAAAT-GGTAGATTTGGTAGGTTACCAT
65 CATTGTTGACTAAATAGG-AGATTTGGTAGCTTACCAT
2784589 TGTTGATTAAATGG
1 TGTTGATTAAATGG
2784603 TGGTTTTTAC
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
101 16 0.15
102 90 0.85
ACGTcount: A:0.26, C:0.08, G:0.25, T:0.41
Consensus pattern (101 bp):
TGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGATGATTTGGTGGCTTACC
ATTGTTGACTAAATAGGAGATTTGGTAGCTTACCAT
Found at i:2789126 original size:34 final size:34
Alignment explanation
Indices: 2789018--2789230 Score: 235
Period size: 34 Copynumber: 6.5 Consensus size: 34
2789008 AAGTGGGAGA
* *
2789018 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
2789051 ATTGTTGATTAAAT-GGATGATTTGGT-G-GT---
1 ATTGTTGATTAAATGGGA-GATTTGGTAGCTTACC
* *
2789080 -TTGTTGACTAAATGGGAGATTTGGTAGCTTACT
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2789113 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2789147 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
2789181 ATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2789215 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2789231 TGGTTTTTAC
Statistics
Matches: 151, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
28 20 0.13
29 4 0.03
30 1 0.01
32 1 0.01
33 17 0.11
34 108 0.72
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2789228 original size:102 final size:95
Alignment explanation
Indices: 2789018--2789230 Score: 282
Period size: 102 Copynumber: 2.2 Consensus size: 95
2789008 AAGTGGGAGA
** * *
2789018 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGATGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGATGATTTGGTGGTTTG
*
2789083 TTGACTAAATGGGAGATTTGGTAGCTTACT
66 TTGACTAAATGGGAGATTTGGTAGCTTACC
*
2789113 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGATGATTTGGTGG--T
* * *
2789178 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
63 ----TTGTTGACTAAATGGGAGATTTGGTAGCTTACC
2789215 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2789231 TGGTTTTTAC
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
95 15 0.15
96 41 0.40
98 1 0.01
101 1 0.01
102 44 0.43
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (95 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGATGATTTGGTGGTTTG
TTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:2789861 original size:15 final size:15
Alignment explanation
Indices: 2789841--2789884 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
2789831 TTGTTCAGCT
2789841 GAAAAATGAAAAAAA
1 GAAAAATGAAAAAAA
* *
2789856 GAAAAAGGAAAAAGA
1 GAAAAATGAAAAAAA
*
2789871 -AAAAATTAAAAAAA
1 GAAAAATGAAAAAAA
2789885 AAATTTAAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (15 bp):
GAAAAATGAAAAAAA
Found at i:2789931 original size:23 final size:23
Alignment explanation
Indices: 2789904--2789971 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 23
2789894 GATCCGTATT
2789904 TTTATTATTTTTATATTTAA-AA
1 TTTATTATTTTTATATTTAATAA
2789926 TATTA-TATTTTTATATATTAATAA
1 T-TTATTATTTTTATAT-TTAATAA
2789950 TTTATTTTATTTTATATATTTA
1 TTTA--TTATTTT-TATATTTA
2789972 TATGTATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
22 12 0.31
23 10 0.26
24 3 0.08
26 9 0.23
27 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTATTATTTTTATATTTAATAA
Found at i:2789937 original size:22 final size:24
Alignment explanation
Indices: 2789909--2789971 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
2789899 GTATTTTTAT
2789909 TATTTTTATATTTAA-AA-TATTA
1 TATTTTTATATTTAATAATTATTA
*
2789931 TATTTTTATATATTAATAATTTATTT
1 TATTTTTATAT-TTAATAA-TTATTA
2789957 TATTTTATATATTTA
1 TATTTT-TATATTTA
2789972 TATGTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
22 11 0.31
23 4 0.11
24 2 0.06
26 13 0.37
27 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTTTTATATTTAATAATTATTA
Found at i:2790005 original size:3 final size:3
Alignment explanation
Indices: 2789997--2790068 Score: 53
Period size: 3 Copynumber: 23.3 Consensus size: 3
2789987 GTATTATGTG
*
2789997 TTA TTA TTA TTA TTG TT- TT- TTA TTA TCTA TTTA TT- TATA TCTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA T-TA T-TA TTA
2790042 TTTA TTA TTA TTA TTA TTA TTTA TTA T
1 -TTA TTA TTA TTA TTA TTA -TTA TTA T
2790069 CTATCTATCT
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
2 7 0.12
3 39 0.66
4 12 0.20
5 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2790045 original size:16 final size:17
Alignment explanation
Indices: 2790015--2790072 Score: 65
Period size: 16 Copynumber: 3.7 Consensus size: 17
2790005 ATTATTGTTT
2790015 TTTATTATC--TATTTA
1 TTTATTATCTATATTTA
2790030 TTTA-TATCTATATTTA
1 TTTATTATCTATATTTA
2790046 -TTATTAT-TAT-TATTA
1 TTTATTATCTATAT-TTA
2790061 TTTATTATCTAT
1 TTTATTATCTAT
2790073 CTATCTATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.14
15 13 0.35
16 16 0.43
17 3 0.08
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATTATCTATATTTA
Found at i:2790053 original size:46 final size:46
Alignment explanation
Indices: 2789997--2790086 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
2789987 GTATTATGTG
* * * * *
2789997 TTATTATTATTATTGTTTTTTATTATCTATTTATTTATATCTATAT
1 TTATTATTATTATTATTATTTATTATCTATCTATCTATACCTATAT
2790043 TTATTATTATTATTATTATTTATTATCTATCTATCTATACCTAT
1 TTATTATTATTATTATTATTTATTATCTATCTATCTATACCTAT
2790087 CTAACATGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (46 bp):
TTATTATTATTATTATTATTTATTATCTATCTATCTATACCTATAT
Found at i:2790054 original size:62 final size:60
Alignment explanation
Indices: 2789954--2790068 Score: 142
Period size: 62 Copynumber: 1.9 Consensus size: 60
2789944 TAATAATTTA
* * *
2789954 TTTTATTTTATATATTTATATGTATATATATTCGTATTATGTGTTA-TTATTATTATTGTT
1 TTTTATTTTATATATTTATATCTATATATATTAGTATTAT-TATTATTTATTATTATTGTT
* * *
2790014 TTTTATTATCTATTTATTTATATCTATATTTATTATTATTATTATTATTTATTAT
1 TTTTATT-T-TATATATTTATATCTATATATATTAGTATTATTATTATTTATTAT
2790069 CTATCTATCT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 7 0.15
61 5 0.11
62 34 0.74
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (60 bp):
TTTTATTTTATATATTTATATCTATATATATTAGTATTATTATTATTTATTATTATTGTT
Found at i:2790534 original size:2 final size:2
Alignment explanation
Indices: 2790527--2790553 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2790517 CATATAGATT
2790527 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 T
2790554 GCAAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2791163 original size:23 final size:23
Alignment explanation
Indices: 2791136--2791180 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2791126 AAAATTTACA
**
2791136 TATTTATGTTTTTTATTATTTAT
1 TATTTATAATTTTTATTATTTAT
2791159 TATTTATAATTTTTATTATTTA
1 TATTTATAATTTTTATTATTTA
2791181 AAATATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
TATTTATAATTTTTATTATTTAT
Found at i:2791238 original size:10 final size:10
Alignment explanation
Indices: 2791223--2791257 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
2791213 AATTTATGTT
2791223 TTTATATTTA
1 TTTATATTTA
2791233 TTTATATTTA
1 TTTATATTTA
2791243 TTTTTATATTTA
1 --TTTATATTTA
2791255 TTT
1 TTT
2791258 TAATTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.57
12 10 0.43
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTATATTTA
Found at i:2791249 original size:22 final size:22
Alignment explanation
Indices: 2791221--2791296 Score: 91
Period size: 22 Copynumber: 3.4 Consensus size: 22
2791211 AAAATTTATG
2791221 TTTTTATATTTATTTATATTTA
1 TTTTTATATTTATTTATATTTA
*
2791243 TTTTTATATTTATTT-TAATTA
1 TTTTTATATTTATTTATATTTA
* * *
2791264 ATTTTAAATATTATATATATGTTA
1 TTTTTATAT-TTATTTATAT-TTA
2791288 TTTTTATAT
1 TTTTTATAT
2791297 ATTTAAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 12 0.27
22 20 0.45
23 2 0.05
24 10 0.23
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (22 bp):
TTTTTATATTTATTTATATTTA
Found at i:2791250 original size:12 final size:12
Alignment explanation
Indices: 2791221--2791258 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
2791211 AAAATTTATG
2791221 TTTTTATATTTA
1 TTTTTATATTTA
2791233 --TTTATATTTA
1 TTTTTATATTTA
2791243 TTTTTATATTTA
1 TTTTTATATTTA
2791255 TTTT
1 TTTT
2791259 AATTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.42
12 14 0.58
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTATATTTA
Found at i:2791306 original size:33 final size:32
Alignment explanation
Indices: 2791247--2791309 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
2791237 TATTTATTTT
*
2791247 TATATTTATTTTAATTAATTTTAAATATTATA
1 TATATTTATTTTAATTAATTTAAAATATTATA
*
2791279 TATATGTTATTTTTA-TATATTTAAAATATTA
1 TATAT-TTATTTTAATTA-ATTTAAAATATTA
2791310 AAAATTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 7 0.26
33 20 0.74
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (32 bp):
TATATTTATTTTAATTAATTTAAAATATTATA
Found at i:2791363 original size:12 final size:12
Alignment explanation
Indices: 2791334--2791406 Score: 55
Period size: 12 Copynumber: 6.1 Consensus size: 12
2791324 TTTGTACATA
2791334 TTAAT-TATTTAT
1 TTAATATATTT-T
2791346 TT-ATATATTTT
1 TTAATATATTTT
2791357 TTAATATATTTAT
1 TTAATATATTT-T
* *
2791370 ATATTCATATTTT
1 TTAAT-ATATTTT
*
2791383 TT-ATATTATGTT
1 TTAATA-TATTTT
2791395 TTAAT-TATTTT
1 TTAATATATTTT
2791406 T
1 T
2791407 ATTTATATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
11 12 0.24
12 23 0.47
13 8 0.16
14 6 0.12
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (12 bp):
TTAATATATTTT
Found at i:2791386 original size:37 final size:35
Alignment explanation
Indices: 2791339--2791448 Score: 96
Period size: 37 Copynumber: 2.9 Consensus size: 35
2791329 ACATATTAAT
*
2791339 TATTTATTTATATATTTTTTAATATATTTATATATTCA
1 TATTTATTTATATATGTTTTAAT-TATTT-T-TATTCA
*
2791377 TATTT-TTTATATTATGTTTTAATTATTTTTATTTA
1 TATTTATTTATA-TATGTTTTAATTATTTTTATTCA
* * *
2791412 TATTATGTTTATATCGTGTCTTAATTTATTTTATATT
1 TATT-TATTTATAT-ATGTTTTAA-TTATTTT-TATT
2791449 TTTTTACATA
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
35 9 0.15
36 3 0.05
37 24 0.39
38 22 0.35
39 4 0.06
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (35 bp):
TATTTATTTATATATGTTTTAATTATTTTTATTCA
Found at i:2792344 original size:13 final size:13
Alignment explanation
Indices: 2792326--2792350 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2792316 AAAAACTTCA
2792326 TATTTTTTATTTG
1 TATTTTTTATTTG
2792339 TATTTTTTATTT
1 TATTTTTTATTT
2792351 TTTAATTTTA
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:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TATTTTTTATTTG
Found at i:2792365 original size:19 final size:20
Alignment explanation
Indices: 2792343--2792386 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2792333 TATTTGTATT
* *
2792343 TTTTATTTTTTAATTTTA-A
1 TTTTATTTTTAAATTATATA
2792362 TTTTATTTTTAAATTATATA
1 TTTTATTTTTAAATTATATA
2792382 TTTTA
1 TTTTA
2792387 ATGTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATTTTTAAATTATATA
Found at i:2792366 original size:32 final size:32
Alignment explanation
Indices: 2792330--2792396 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
2792320 ACTTCATATT
** * * *
2792330 TTTTATTTGTATTTTTTATTTTTTAATTTTAA
1 TTTTATTTGTAAATTATATATTTTAATGTTAA
*
2792362 TTTTATTTTTAAATTATATATTTTAATGTTAA
1 TTTTATTTGTAAATTATATATTTTAATGTTAA
2792394 TTT
1 TTT
2792397 GCATTGTCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (32 bp):
TTTTATTTGTAAATTATATATTTTAATGTTAA
Found at i:2793550 original size:27 final size:27
Alignment explanation
Indices: 2793520--2793572 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
2793510 TTTAAAATAA
2793520 AAATATAATATA-TATTTAATTATATTT
1 AAATATAATATATTATTT-ATTATATTT
**
2793547 AAATATTTTATATTATTTATTATATT
1 AAATATAATATATTATTTATTATATT
2793573 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
AAATATAATATATTATTTATTATATTT
Found at i:2793561 original size:20 final size:20
Alignment explanation
Indices: 2793529--2793595 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
2793519 AAAATATAAT
2793529 ATATATTTA-ATTATATTTAA
1 ATAT-TTTATATTATATTTAA
*
2793549 ATATTTTATATTATTTATTATA
1 ATATTTTATATTATAT-TTA-A
*
2793571 TTATTTTTATATT-TA-TTAA
1 ATA-TTTTATATTATATTTAA
2793590 ATATTT
1 ATATTT
2793596 CATCTCACGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
18 3 0.08
19 7 0.18
20 13 0.33
21 3 0.08
22 4 0.10
23 9 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATATTTTATATTATATTTAA
Found at i:2793587 original size:12 final size:11
Alignment explanation
Indices: 2793552--2793583 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
2793542 TATTTAAATA
2793552 TTTTATATTAT
1 TTTTATATTAT
2793563 TTATTATATTAT
1 TT-TTATATTAT
2793575 TTTTATATT
1 TTTTATATT
2793584 TATTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTATATTAT
Found at i:2794787 original size:22 final size:21
Alignment explanation
Indices: 2794757--2794801 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2794747 TTGCTTGCTC
2794757 ATTT-TAT-TTTTAT-ATTAA
1 ATTTATATATTTTATAATTAA
2794775 TATTTATATATTTTATAATTAA
1 -ATTTATATATTTTATAATTAA
2794797 ATTTA
1 ATTTA
2794802 AATTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.17
20 3 0.13
21 11 0.48
22 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTATATATTTTATAATTAA
Found at i:2795631 original size:21 final size:21
Alignment explanation
Indices: 2795607--2795655 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2795597 CAAATTATCC
2795607 TTAATAAA-TATCAATTTAATT
1 TTAATAAATTAT-AATTTAATT
*
2795628 TTAATTAAATTATATTTTAATT
1 TTAA-TAAATTATAATTTAATT
*
2795650 TAAATA
1 TTAATA
2795656 CACACGCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 15 0.62
23 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATAAATTATAATTTAATT
Found at i:2803888 original size:2 final size:2
Alignment explanation
Indices: 2803881--2803909 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2803871 GAATTCTACC
2803881 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
2803910 TTAAATAATT
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:2815328 original size:21 final size:21
Alignment explanation
Indices: 2815284--2815336 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2815274 AACGATAACA
* **
2815284 ATAAAATTAATTATTATAGTG
1 ATAAAATTAAATATTATAAAG
*
2815305 ATAAAATTAAATATTGTAAAG
1 ATAAAATTAAATATTATAAAG
*
2815326 ATAAGATTAAA
1 ATAAAATTAAA
2815337 AATAATGATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (21 bp):
ATAAAATTAAATATTATAAAG
Found at i:2817954 original size:21 final size:20
Alignment explanation
Indices: 2817930--2817993 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
2817920 TTAAATATAT
2817930 AATTTTTAAAATAATTAATTA
1 AATTTTTAAAAT-ATTAATTA
* *
2817951 AATTAAATT-AAATTTTAATTTA
1 AATT--TTTAAAATATTAA-TTA
*
2817973 CATTTTTAAAATATTAATTA
1 AATTTTTAAAATATTAATTA
2817993 A
1 A
2817994 GAATAATGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
20 5 0.15
21 16 0.48
22 10 0.30
23 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTTTTAAAATATTAATTA
Found at i:2817956 original size:44 final size:44
Alignment explanation
Indices: 2817875--2817993 Score: 124
Period size: 44 Copynumber: 2.7 Consensus size: 44
2817865 TTAAGTTTAA
*
2817875 TTTAAATTTAATTTTTAAATATAA--AATATGAATATTAAAAT-ATT
1 TTTAAATTTAATTTTTAAA-ATAATTAAT-T-AATATTAAAATAAAT
*
2817919 TTTAAATATATAATTTTTAAAATAATTAATTAA-ATTAAATTAAAT
1 TTTAAAT-T-TAATTTTTAAAATAATTAATTAATATTAAAATAAAT
2817964 TTT-AATTTACATTTTTAAAAT-ATTAATTAA
1 TTTAAATTTA-ATTTTTAAAATAATTAATTAA
2817994 GAATAATGTA
Statistics
Matches: 67, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
42 11 0.16
43 12 0.18
44 17 0.25
45 12 0.18
46 12 0.18
47 3 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (44 bp):
TTTAAATTTAATTTTTAAAATAATTAATTAATATTAAAATAAAT
Found at i:2818215 original size:32 final size:32
Alignment explanation
Indices: 2818165--2818316 Score: 118
Period size: 32 Copynumber: 4.7 Consensus size: 32
2818155 GAAGGTTATT
*
2818165 TAAAT-TAATTTTATTAATTTATT-TTTAATA
1 TAAATATAATTTTAATAATTTATTATTTAATA
2818195 TAAATATAATTTTTAATAATTTAATT-TTTAA-A
1 TAAATATAA-TTTTAATAATTT-ATTATTTAATA
* ** *
2818227 TTAAAAAATAATAATATGTAA-TTATTATTTAATA
1 -T-AAATATAATTTTA-ATAATTTATTATTTAATA
*
2818261 TTAATAT-ATTTTAATTTATATATTATTATTTAATA
1 TAAATATAATTTTAA--TA-AT-TTATTATTTAATA
*
2818296 TAAATATAATTTTACTAATTT
1 TAAATATAATTTTAATAATTT
2818317 TTAATTATTT
Statistics
Matches: 96, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
30 5 0.05
31 7 0.07
32 23 0.24
33 23 0.24
34 13 0.14
35 19 0.20
36 6 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (32 bp):
TAAATATAATTTTAATAATTTATTATTTAATA
Found at i:2818221 original size:15 final size:15
Alignment explanation
Indices: 2818169--2818225 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
2818159 GTTATTTAAA
*
2818169 TTAA-TTTTATTAAT
1 TTAATTTTTAATAAT
2818183 TT-ATTTTTAATATAAAT
1 TTAATTTTT-A-AT-AAT
*
2818200 ATAATTTTTAATAAT
1 TTAATTTTTAATAAT
2818215 TTAATTTTTAA
1 TTAATTTTTAA
2818226 ATTAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
13 1 0.03
14 6 0.17
15 14 0.40
16 3 0.09
17 5 0.14
18 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAATTTTTAATAAT
Found at i:2818324 original size:35 final size:35
Alignment explanation
Indices: 2818247--2818358 Score: 102
Period size: 35 Copynumber: 3.1 Consensus size: 35
2818237 ATAATATGTA
* * *
2818247 ATTATTATTTAATATTAATATATTTTAATTTATAT
1 ATTATTATTTAATATAAATATATTTTAACTAATAT
2818282 ATTATTATTTAATATAAATATAATTTT-ACTAAT-T
1 ATTATTATTTAATATAAATAT-ATTTTAACTAATAT
* * *
2818316 TTTAATTATTTATCATTATATAGATATTTTAATCTAATAT
1 ATT-ATTATTTA--A-TATAAATATATTTTAA-CTAATAT
2818356 ATT
1 ATT
2818359 TAATAATTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
34 3 0.05
35 32 0.52
36 5 0.08
37 6 0.10
38 8 0.13
39 5 0.08
40 3 0.05
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (35 bp):
ATTATTATTTAATATAAATATATTTTAACTAATAT
Found at i:2818883 original size:17 final size:19
Alignment explanation
Indices: 2818861--2818895 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2818851 AACATAACTC
2818861 TATTT-ATAAA-AAAAATA
1 TATTTAATAAATAAAAATA
2818878 TATTTAATAAATAAAAAT
1 TATTTAATAAATAAAAAT
2818896 TAAATTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TATTTAATAAATAAAAATA
Found at i:2819015 original size:25 final size:26
Alignment explanation
Indices: 2818977--2819030 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
2818967 TCATTTTTAC
* *
2818977 TATATGTATATTTTGTTATGTTATATA
1 TATATGTATATTTTATTATG-CATATA
2819004 TATAT-TAT-TTTTATTATGCATATA
1 TATATGTATATTTTATTATGCATATA
2819028 TAT
1 TAT
2819031 TGTTTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.32
25 9 0.36
26 3 0.12
27 5 0.20
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.59
Consensus pattern (26 bp):
TATATGTATATTTTATTATGCATATA
Found at i:2819028 original size:41 final size:41
Alignment explanation
Indices: 2818957--2819034 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
2818947 AGTATATATA
*
2818957 TATAAATATATCATTTTTACTATATGTATATTTTGTTATGT
1 TATAAATATATCATTTTTACTATATGTATATATTGTTATGT
* *
2818998 TATATATATATTATTTTTA-T-TATGCATATATATTGTT
1 TATAAATATATCATTTTTACTATATG--TATATATTGTT
2819035 TTCTTTAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 4 0.12
40 1 0.03
41 27 0.84
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (41 bp):
TATAAATATATCATTTTTACTATATGTATATATTGTTATGT
Found at i:2819169 original size:20 final size:20
Alignment explanation
Indices: 2819144--2819204 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
2819134 TTTGAAGTAC
2819144 ATATATGTATATATTTTATT
1 ATATATGTATATATTTTATT
** * * * *
2819164 ATATATACACATAGTTAACT
1 ATATATGTATATATTTTATT
2819184 ATATATGTATATTATTTTATT
1 ATATATGTATA-TATTTTATT
2819205 CAAAAGAATG
Statistics
Matches: 28, Mismatches: 12, Indels: 1
0.68 0.29 0.02
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (20 bp):
ATATATGTATATATTTTATT
Found at i:2820099 original size:17 final size:16
Alignment explanation
Indices: 2820068--2820104 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
2820058 ATTTAATTTA
2820068 ATAATTATTTATAAAT
1 ATAATTATTTATAAAT
*
2820084 ATAATATATTTTTAAAT
1 ATAAT-TATTTATAAAT
2820101 ATAA
1 ATAA
2820105 ATTAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAATTATTTATAAAT
Found at i:2820146 original size:14 final size:15
Alignment explanation
Indices: 2820129--2820159 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2820119 TTGATTTAAT
2820129 TAAT-TATTTTAAAA
1 TAATATATTTTAAAA
2820143 TAATATATTTTAAAA
1 TAATATATTTTAAAA
2820158 TA
1 TA
2820160 TTTCAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATATATTTTAAAA
Found at i:2820200 original size:17 final size:17
Alignment explanation
Indices: 2820180--2820245 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 17
2820170 AATATCTTAT
2820180 AATTAAAAATAAATTTA
1 AATTAAAAATAAATTTA
**
2820197 AATTAAATTTAAA---A
1 AATTAAAAATAAATTTA
*
2820211 AATTAACAACT-AATTTA
1 AATTAA-AAATAAATTTA
* *
2820228 ATTTATAAATAAATTTA
1 AATTAAAAATAAATTTA
2820245 A
1 A
2820246 TCATAAATAC
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
14 9 0.24
15 2 0.05
16 3 0.08
17 23 0.62
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTAAAAATAAATTTA
Found at i:2820253 original size:16 final size:17
Alignment explanation
Indices: 2820222--2820254 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2820212 ATTAACAACT
*
2820222 AATTTAATTTATAAATA
1 AATTTAATTCATAAATA
2820239 AATTTAA-TCATAAATA
1 AATTTAATTCATAAATA
2820255 CATATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAATTCATAAATA
Found at i:2820640 original size:13 final size:14
Alignment explanation
Indices: 2820594--2820691 Score: 55
Period size: 13 Copynumber: 7.1 Consensus size: 14
2820584 AATCTAACAA
2820594 AATATAAA-TATAT
1 AATATAAATTATAT
* *
2820607 ATTTTAAAATTTATAT
1 AATAT-AAA-TTATAT
2820623 AATATAAATTAT-T
1 AATATAAATTATAT
* *
2820636 AATAT-AATAAAAT
1 AATATAAATTATAT
* *
2820649 AATTTAAA-TATAA
1 AATATAAATTATAT
*
2820662 AATATAATTGTAATAT
1 AATATAAAT-T-ATAT
2820678 AATA-AAA-TATAT
1 AATATAAATTATAT
2820690 AA
1 AA
2820692 ATATTATATT
Statistics
Matches: 63, Mismatches: 14, Indels: 17
0.67 0.15 0.18
Matches are distributed among these distances:
12 10 0.16
13 23 0.37
14 9 0.14
15 6 0.10
16 15 0.24
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (14 bp):
AATATAAATTATAT
Found at i:2820640 original size:18 final size:18
Alignment explanation
Indices: 2820619--2820700 Score: 62
Period size: 18 Copynumber: 4.5 Consensus size: 18
2820609 TTTAAAATTT
2820619 ATATAATATAAATTATTA
1 ATATAATATAAATTATTA
*
2820637 ATATAATA-AAATAATTTAA
1 ATATAATATAAATTA-TT-A
* *
2820656 ATATAAAATATAATT-GTA
1 ATATAATATA-AATTATTA
*
2820674 ATATAATA-AAATATATAA
1 ATATAATATAAAT-TATTA
*
2820692 ATATTATAT
1 ATATAATAT
2820701 TACGTATTGC
Statistics
Matches: 49, Mismatches: 8, Indels: 13
0.70 0.11 0.19
Matches are distributed among these distances:
16 3 0.06
17 7 0.14
18 26 0.53
19 9 0.18
20 1 0.02
21 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (18 bp):
ATATAATATAAATTATTA
Found at i:2820683 original size:21 final size:20
Alignment explanation
Indices: 2820614--2820688 Score: 76
Period size: 18 Copynumber: 4.0 Consensus size: 20
2820604 TATATTTTAA
2820614 AATTT-ATATAATATAAAT-T
1 AATTTAATATAATA-AAATAT
2820633 -A-TTAATATAAT-AAA-AT
1 AATTTAATATAATAAAATAT
2820649 AATTTAA-AT-ATAAAATAT
1 AATTTAATATAATAAAATAT
2820667 AATTGTAATATAATAAAATAT
1 AATT-TAATATAATAAAATAT
2820688 A
1 A
2820689 TAAATATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
16 6 0.13
17 8 0.17
18 18 0.38
19 3 0.06
20 2 0.04
21 10 0.21
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (20 bp):
AATTTAATATAATAAAATAT
Found at i:2821071 original size:16 final size:16
Alignment explanation
Indices: 2821024--2821076 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
2821014 TTTATAAAAA
2821024 TTAATTTAA-ATTAAT
1 TTAATTTAATATTAAT
2821039 TT--TTT-ATATATATAT
1 TTAATTTAATAT-TA-AT
2821054 TTAATTTAATATTAAT
1 TTAATTTAATATTAAT
2821070 TTAATTT
1 TTAATTT
2821077 TAAAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
12 1 0.03
13 5 0.16
14 2 0.06
15 6 0.19
16 9 0.28
17 5 0.16
18 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAATTTAATATTAAT
Found at i:2821422 original size:20 final size:19
Alignment explanation
Indices: 2821391--2821428 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2821381 ATTTATAAAT
2821391 TATTTAATAATAAATAATA
1 TATTTAATAATAAATAATA
*
2821410 TATTTATATAATAATTAAT
1 TATTTA-ATAATAAATAAT
2821429 TAAAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TATTTAATAATAAATAATA
Found at i:2821444 original size:24 final size:23
Alignment explanation
Indices: 2821395--2821458 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
2821385 ATAAATTATT
* *
2821395 TAATAATAAATAATATATTTATA
1 TAATAATAAATAAAATATTTAAA
*
2821418 TAATAATTAATTAAAATATTTAAA
1 TAATAA-TAAATAAAATATTTAAA
*
2821442 T-A-AATATATAAAATATT
1 TAATAATAAATAAAATATT
2821459 CTATGATCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 11 0.31
22 2 0.06
23 7 0.20
24 15 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAATAAATAAAATATTTAAA
Found at i:2821629 original size:3 final size:3
Alignment explanation
Indices: 2821621--2821665 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2821611 GATAGCGTAT
2821621 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2821666 CTTTAGTTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2823163 original size:9 final size:9
Alignment explanation
Indices: 2823149--2823178 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2823139 TACATTTTTT
2823149 AAAAATTAA
1 AAAAATTAA
2823158 AAAAATTAA
1 AAAAATTAA
*
2823167 ACAAATTAA
1 AAAAATTAA
2823176 AAA
1 AAA
2823179 TAAATTCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATTAA
Done.