Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 9 of 438
Found at i:2526611 original size:2 final size:2
Alignment explanation
Indices: 2526604--2526639 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2526594 AAGAGTCTAG
*
2526604 AT AT AT 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
2526640 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2528347 original size:19 final size:19
Alignment explanation
Indices: 2528319--2528388 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 19
2528309 AAAAATATAT
*
2528319 AAAT-TTTGAAATTTTTAT
1 AAATATTTGAAATTTTTAA
* *
2528337 GAATATTTG-AATTTTAAA
1 AAATATTTGAAATTTTTAA
*
2528355 AAATATTTTAAATTTTTAA
1 AAATATTTGAAATTTTTAA
*
2528374 AAATTATTTTAAATT
1 AAA-TATTTGAAATT
2528389 ATTTTGTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 17 0.40
19 15 0.35
20 11 0.26
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (19 bp):
AAATATTTGAAATTTTTAA
Found at i:2528373 original size:20 final size:20
Alignment explanation
Indices: 2528348--2528388 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2528338 AATATTTGAA
2528348 TTTTAAAAAATATTTTAAAT
1 TTTTAAAAAATATTTTAAAT
*
2528368 TTTTAAAAATTATTTTAAAT
1 TTTTAAAAAATATTTTAAAT
2528388 T
1 T
2528389 ATTTTGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTAAAAAATATTTTAAAT
Found at i:2532153 original size:72 final size:72
Alignment explanation
Indices: 2532031--2532300 Score: 325
Period size: 72 Copynumber: 3.8 Consensus size: 72
2532021 CACTTTGGAC
* * *
2532031 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTATGCAATATGAGTCAACTTAG-CG
1 GCATCTTATAACAATTTGAATGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGACG
2532095 -TTTGCTAT
66 TTTTG--AT
* * * * * * *
2532103 GCATTTTATAATAATTTCAATGGCCCAATACCAAATTGCTTATGCAATATGAGTCAACTAAGAGG
1 GCATCTTATAACAATTTGAATGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGACG
2532168 TTTTGAT
66 TTTTGAT
* *
2532175 GCATCTTATAACAATTTGAGTGGCTCAATTCCAAATTGCTT-GGACAATATGAGTCAACTT-GAC
1 GCATCTTATAACAATTTGAATGGCCCAATTCCAAATTGCTTAGG-CAATATGAGTCAACTTAGAC
2532238 AGTTTTGAT
65 -GTTTTGAT
* * *
2532247 GTATCTTATAACAATTT-AAGTGGCCCAATTCCAAATTGTTTGGGCAATATGAGT
1 GCATCTTATAACAATTTGAA-TGGCCCAATTCCAAATTGCTTAGGCAATATGAGT
2532301 GCTCTGATTT
Statistics
Matches: 171, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
71 4 0.02
72 160 0.94
73 3 0.02
74 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (72 bp):
GCATCTTATAACAATTTGAATGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGACG
TTTTGAT
Found at i:2532294 original size:144 final size:143
Alignment explanation
Indices: 2532031--2532300 Score: 368
Period size: 144 Copynumber: 1.9 Consensus size: 143
2532021 CACTTTGGAC
* *
2532031 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTATGCAATATGAGTCAACTTAGCGT
1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGCGT
* * *
2532096 TTGCTATGCATTTTATAATAATTTCAATGGCCCAATACCAAATTGCTTATGCAATATGAGTCAAC
66 TTGC-ATGCATCTTATAACAATTTCAATGGCCCAATACCAAATTGCTTAGGCAATATGAGTCAAC
2532161 TAAGAGGTTTTGAT
130 TAAGAGGTTTTGAT
*
2532175 GCATCTTATAACAATTTGAGTGGCTCAATTCCAAATTGCTT-GGACAATATGAGTCAACTT-GAC
1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGG-CAATATGAGTCAACTTAG-C
* * * *
2532238 AGTTTTG-ATGTATCTTATAACAATTT-AAGTGGCCCAATTCCAAATTGTTTGGGCAATATGAGT
64 -G-TTTGCATGCATCTTATAACAATTTCAA-TGGCCCAATACCAAATTGCTTAGGCAATATGAGT
2532301 GCTCTGATTT
Statistics
Matches: 111, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
143 4 0.04
144 102 0.92
145 1 0.01
146 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (143 bp):
GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGCGT
TTGCATGCATCTTATAACAATTTCAATGGCCCAATACCAAATTGCTTAGGCAATATGAGTCAACT
AAGAGGTTTTGAT
Found at i:2533834 original size:17 final size:17
Alignment explanation
Indices: 2533812--2533847 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2533802 TGCAGGACAT
*
2533812 GGAATGTCTAGTCAGGA
1 GGAATGTCCAGTCAGGA
2533829 GGAATGTCCAGTCAGGA
1 GGAATGTCCAGTCAGGA
2533846 GG
1 GG
2533848 TACGTTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.14, G:0.39, T:0.19
Consensus pattern (17 bp):
GGAATGTCCAGTCAGGA
Found at i:2535169 original size:29 final size:30
Alignment explanation
Indices: 2535115--2535173 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
2535105 ATCTCAAAAT
*
2535115 TATATATAAACTTTGATTTAATGTGTAATTG
1 TATATATAAACTTTGATTT-AGGTGTAATTG
2535146 TATATATAAACTTT-AGTTT-GGTGTAATT
1 TATATATAAACTTTGA-TTTAGGTGTAATT
2535174 ATACACGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 8 0.31
30 1 0.04
31 17 0.65
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (30 bp):
TATATATAAACTTTGATTTAGGTGTAATTG
Found at i:2537871 original size:26 final size:25
Alignment explanation
Indices: 2537835--2537970 Score: 200
Period size: 26 Copynumber: 5.2 Consensus size: 25
2537825 TGATACAAAT
*
2537835 TGATAATAGGTTAGGTAAATGTTCAA
1 TGATAATGGGTTAGGTAAATGTTC-A
*
2537861 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTT-CA
2537887 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATG-TTCA
*
2537913 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAAT-GTTCA
2537939 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATG-TTCA
2537965 TGATAA
1 TGATAA
2537971 GAATTACATG
Statistics
Matches: 103, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
26 100 0.97
27 3 0.03
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (25 bp):
TGATAATGGGTTAGGTAAATGTTCA
Found at i:2541726 original size:131 final size:129
Alignment explanation
Indices: 2541529--2541940 Score: 407
Period size: 131 Copynumber: 3.1 Consensus size: 129
2541519 TATTCATCCA
* * ** *
2541529 AAAATTCTTCAAAACAAAGATGAAATTTGATGTTCAGCGATTCGCGGAATCA-TGCCCTAACGTG
1 AAAATCCTT-AAAACGAAGATGAAATTTGATGTTTGGCAATTCGCGGAAT-AGTGCCCTAACGTG
* * * *
2541593 TTGGGTTGCAATTTCGTATTTGCTCAAAATAATCGAATTTCCCTTCGAAATTTCATTCATATCTT
64 TTGGGTTGCAATTTCG-ATTTGTTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATATCTT
2541658 TT
128 TT
* *
2541660 AAAAATCCCTT-AAATGAAGATGAGATTTGATGTTTGGCAATTCGCGGAATAGTGCCCTAACGTG
1 -AAAAT-CCTTAAAACGAAGATGAAATTTGATGTTTGGCAATTCGCGGAATAGTGCCCTAACGTG
* * * ** * *
2541724 TTGGGTTGCAATTTCGCATTTGTTCAAGATAATCGAATATCACTTTAAAATTTTGCTCGTGTCTT
64 TTGGGTTGCAATTTCG-ATTTGTTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATATCTT
2541789 TT
128 TT
* ** * * * * * *
2541791 AAAATCTTTAAAACGAAGGCGATATGTGATATTTGGCAATTCGCGGGATCGTGCCTTAACGTGTT
1 AAAATCCTTAAAACGAAGATGAAATTTGATGTTTGGCAATTCGCGGAATAGTGCCCTAACGTGTT
* * * ***
2541856 GGGTAGCAATTTCCCGA-TTGTTTAAAATAATCAAATATCCCTTCAAAATTTCACTCGGCTCTTC
66 GGGTTGCAATTT--CGATTTGTTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATATCTT-
*
2541920 TA
128 TT
2541922 AAAATCCTTTAAAACGAAG
1 AAAATCC-TTAAAACGAAG
2541941 GCAATACTCG
Statistics
Matches: 232, Mismatches: 41, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
129 3 0.01
130 100 0.43
131 108 0.47
132 18 0.08
133 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (129 bp):
AAAATCCTTAAAACGAAGATGAAATTTGATGTTTGGCAATTCGCGGAATAGTGCCCTAACGTGTT
GGGTTGCAATTTCGATTTGTTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATATCTTTT
Found at i:2541877 original size:130 final size:132
Alignment explanation
Indices: 2541568--2541942 Score: 384
Period size: 130 Copynumber: 2.9 Consensus size: 132
2541558 ATGTTCAGCG
* ** * * *
2541568 ATTCGCGGAATCA-TGCCCTAACGTGTTGGGTTGCAATTTCGTATTTGCTCAAAATAATCGAATT
1 ATTCGCGGAAT-AGTGCCCTAACGTGTTGGGTAGCAATTTCCCATTTGTTCAAAATAATCAAATA
* * * *** * * * ** * * *
2541632 TCCCTTCGAAATTTCATTCATATCTTTTAAAAATCCCTT-AAATGAAGATGAGATTTGATGTTTG
65 TCACTTCAAAATTTCACTCGGCTCTTCTAAAAATCCTTTAAAACGAAGGCGATATGTGATATTTG
2541696 GCA
130 GCA
* * * *
2541699 ATTCGCGGAATAGTGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGTTCAAGATAATCGAATAT
1 ATTCGCGGAATAGTGCCCTAACGTGTTGGGTAGCAATTTCCCATTTGTTCAAAATAATCAAATAT
* ** *
2541764 CACTTTAAAATTTTGCTCGTG-TCTT-TTAAAAT-CTTTAAAACGAAGGCGATATGTGATATTTG
66 CACTTCAAAATTTCACTCG-GCTCTTCTAAAAATCCTTTAAAACGAAGGCGATATGTGATATTTG
2541826 GCA
130 GCA
* * * *
2541829 ATTCGCGGGATCGTGCCTTAACGTGTTGGGTAGCAATTTCCCGA-TTGTTTAAAATAATCAAATA
1 ATTCGCGGAATAGTGCCCTAACGTGTTGGGTAGCAATTTCCC-ATTTGTTCAAAATAATCAAATA
*
2541893 TCCCTTCAAAATTTCACTCGGCTCTTCTAAAAATCCTTTAAAACGAAGGC
65 TCACTTCAAAATTTCACTCGGCTCTTCTAAAAATCCTTTAAAACGAAGGC
2541943 AATACTCGGT
Statistics
Matches: 204, Mismatches: 33, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
129 4 0.02
130 103 0.50
131 82 0.40
132 15 0.07
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (132 bp):
ATTCGCGGAATAGTGCCCTAACGTGTTGGGTAGCAATTTCCCATTTGTTCAAAATAATCAAATAT
CACTTCAAAATTTCACTCGGCTCTTCTAAAAATCCTTTAAAACGAAGGCGATATGTGATATTTGG
CA
Found at i:2546483 original size:13 final size:13
Alignment explanation
Indices: 2546465--2546490 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2546455 GCCATCAACA
2546465 CCGTGATTCCAGG
1 CCGTGATTCCAGG
2546478 CCGTGATTCCAGG
1 CCGTGATTCCAGG
2546491 TTTTGAATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
CCGTGATTCCAGG
Found at i:2547560 original size:28 final size:29
Alignment explanation
Indices: 2547511--2547565 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
2547501 TATTTCAATA
* *
2547511 TTTTGTATATATATATATTTATCTTAAAC
1 TTTTGTATATATATAGAATTATCTTAAAC
* *
2547540 TTTT-TATATATATCGAATTATTTTAA
1 TTTTGTATATATATAGAATTATCTTAA
2547566 TAATATTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 18 0.82
29 4 0.18
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (29 bp):
TTTTGTATATATATAGAATTATCTTAAAC
Found at i:2547740 original size:23 final size:23
Alignment explanation
Indices: 2547714--2547762 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
2547704 ACTTGTATGC
*
2547714 TATTGTCATATATTAT-TAGGTAT
1 TATT-TCATATATTATATACGTAT
* *
2547737 TATTTTATATTTTATATACGTAT
1 TATTTCATATATTATATACGTAT
2547760 TAT
1 TAT
2547763 ATGATATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (23 bp):
TATTTCATATATTATATACGTAT
Found at i:2555714 original size:20 final size:19
Alignment explanation
Indices: 2555689--2555726 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2555679 AAATTTAACC
*
2555689 CTATATTTATTTTTATTATT
1 CTATATATATTTTT-TTATT
2555709 CTATATATATTTTTTTAT
1 CTATATATATTTTTTTAT
2555727 ATATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
CTATATATATTTTTTTATT
Found at i:2555727 original size:14 final size:15
Alignment explanation
Indices: 2555710--2555739 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2555700 TTTATTATTC
2555710 TATATA-TATTTTTT
1 TATATATTATTTTTT
2555724 TATATATTATTTTTT
1 TATATATTATTTTTT
2555739 T
1 T
2555740 TACCCTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATATATTATTTTTT
Found at i:2555787 original size:13 final size:13
Alignment explanation
Indices: 2555771--2555916 Score: 50
Period size: 13 Copynumber: 11.5 Consensus size: 13
2555761 ATTATAAGAT
2555771 TATTTTATATATA
1 TATTTTATATATA
2555784 TATTATTATTATATA
1 TATT-TTA-TATATA
*
2555799 TTATTTT-TCACA-A
1 -TATTTTAT-ATATA
2555812 -ATTATTAT-TAT-
1 TATT-TTATATATA
*
2555823 TATTTTACATCAT-
1 TATTTTATAT-ATA
2555836 TATTTT-TATAT-
1 TATTTTATATATA
*
2555847 TATTATTATAT-TT
1 TATT-TTATATATA
*
2555860 TACTTGTAT-TATA
1 TA-TTTTATATATA
2555873 TA-TTTAT-TA-A
1 TATTTTATATATA
2555883 T-TATTTATATATA
1 TAT-TTTATATATA
*
2555896 TTATTCTTACATATA
1 -TATT-TTATATATA
2555911 TATTTT
1 TATTTT
2555917 CGTTATTTTG
Statistics
Matches: 103, Mismatches: 8, Indels: 44
0.66 0.05 0.28
Matches are distributed among these distances:
10 2 0.02
11 24 0.23
12 14 0.14
13 29 0.28
14 13 0.13
15 17 0.17
16 4 0.04
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.61
Consensus pattern (13 bp):
TATTTTATATATA
Found at i:2555791 original size:19 final size:19
Alignment explanation
Indices: 2555769--2555914 Score: 55
Period size: 19 Copynumber: 8.0 Consensus size: 19
2555759 ACATTATAAG
2555769 ATTATTTTATATATATATT
1 ATTATTTTATATATATATT
2555788 ATTA--TTATATAT-TATT
1 ATTATTTTATATATATATT
*** *
2555804 -TT-TCACAAAT-TATTATT
1 ATTATTTTATATATA-TATT
*
2555821 ATTATTTTACATCAT-TATT
1 ATTATTTTATAT-ATATATT
* *
2555840 TTTATATTAT-TATTATATT
1 ATTATTTTATATA-TATATT
*
2555859 -TTACTTGTAT-TATATATTT
1 ATTA-TTTTATATATATA-TT
* *
2555878 ATTA-ATTATTTATATA-T
1 ATTATTTTATATATATATT
*
2555895 ATTATTCTTACATATATATT
1 ATTATT-TTATATATATATT
2555915 TTCGTTATTT
Statistics
Matches: 93, Mismatches: 17, Indels: 33
0.65 0.12 0.23
Matches are distributed among these distances:
15 3 0.03
16 7 0.08
17 18 0.19
18 14 0.15
19 46 0.49
20 4 0.04
21 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (19 bp):
ATTATTTTATATATATATT
Found at i:2555900 original size:24 final size:24
Alignment explanation
Indices: 2555834--2555900 Score: 65
Period size: 23 Copynumber: 2.9 Consensus size: 24
2555824 ATTTTACATC
2555834 ATTATT-TTTATAT-TATTATTAT
1 ATTATTATTTATATATATTATTAT
2555856 ATT-TTACTTGTAT-TATA-TATT-T
1 ATTATTA-TT-TATATATATTATTAT
2555878 ATTAATTATTTATATATATTATT
1 ATT-ATTATTTATATATATTATT
2555901 CTTACATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
21 2 0.05
22 10 0.27
23 13 0.35
24 12 0.32
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (24 bp):
ATTATTATTTATATATATTATTAT
Found at i:2556205 original size:31 final size:32
Alignment explanation
Indices: 2556162--2556222 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
2556152 AATTATTAAT
2556162 TATTTATTTATTATGCATTATTTTA-AAATGA
1 TATTTATTTATTATGCATTATTTTATAAATGA
**
2556193 TATTT-TTATATTATGTGTTATTTTATAAAT
1 TATTTATT-TATTATGCATTATTTTATAAAT
2556223 TCTTTTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.08
31 20 0.77
32 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (32 bp):
TATTTATTTATTATGCATTATTTTATAAATGA
Found at i:2564864 original size:16 final size:17
Alignment explanation
Indices: 2564843--2564887 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 17
2564833 TGATAAAGAG
2564843 GAAAAAGAAAAGAACA-
1 GAAAAAGAAAAGAACAC
2564859 GAAAAAG--AAGAACAC
1 GAAAAAGAAAAGAACAC
2564874 GAAAAAGAGAAAGA
1 GAAAAAGA-AAAGA
2564888 GAAAGAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 7 0.28
15 7 0.28
16 7 0.28
18 4 0.16
ACGTcount: A:0.71, C:0.07, G:0.22, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAAAGAACAC
Found at i:2564877 original size:15 final size:14
Alignment explanation
Indices: 2564852--2564905 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
2564842 GGAAAAAGAA
2564852 AAGAACAGAAAAAG
1 AAGAACAGAAAAAG
2564866 AAGAACACGAAAAAG
1 AAGAACA-GAAAAAG
*
2564881 -AGAA-AGAGAAAG
1 AAGAACAGAAAAAG
*
2564893 AAAGAAAAGAAAA
1 -AAGAACAGAAAA
2564906 TGGAAAGGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
12 6 0.18
13 1 0.03
14 15 0.44
15 12 0.35
ACGTcount: A:0.72, C:0.06, G:0.22, T:0.00
Consensus pattern (14 bp):
AAGAACAGAAAAAG
Found at i:2564895 original size:33 final size:31
Alignment explanation
Indices: 2564843--2564903 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
2564833 TGATAAAGAG
*
2564843 GAAAAAGAAAAGAACAGAAA-AAGAAGAACAC
1 GAAAAAGAAAAGAAAAGAAAGAA-AAGAACAC
2564874 GAAAAAGAGAAAGAGAAAGAAAGAAAAGAA
1 GAAAAAGA-AAAGA-AAAGAAAGAAAAGAA
2564904 AATGGAAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 8 0.31
32 5 0.19
33 11 0.42
34 2 0.08
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (31 bp):
GAAAAAGAAAAGAAAAGAAAGAAAAGAACAC
Found at i:2564896 original size:10 final size:9
Alignment explanation
Indices: 2564846--2564904 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 9
2564836 TAAAGAGGAA
2564846 AAAGAAAAG
1 AAAGAAAAG
2564855 AACAGAAAA-
1 AA-AGAAAAG
*
2564864 AGAAGAACACG
1 A-AAGAA-AAG
*
2564875 AAA-AAGAG
1 AAAGAAAAG
2564883 AAAGAGAAAG
1 AAAGA-AAAG
2564893 AAAGAAAAG
1 AAAGAAAAG
2564902 AAA
1 AAA
2564905 ATGGAAAGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
8 4 0.10
9 17 0.43
10 18 0.45
11 1 0.03
ACGTcount: A:0.73, C:0.05, G:0.22, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:2574047 original size:18 final size:18
Alignment explanation
Indices: 2574010--2574102 Score: 78
Period size: 18 Copynumber: 5.2 Consensus size: 18
2574000 CCCAACTACT
* * *
2574010 GTATACGTGAACAGTACC
1 GTATACGTAAATAGTGCC
*
2574028 GTATTCGTAAATAGTGCC
1 GTATACGTAAATAGTGCC
* * *
2574046 GTATACATAAATAGTACT
1 GTATACGTAAATAGTGCC
* *
2574064 GTATACGTGAATAGTGCT
1 GTATACGTAAATAGTGCC
* * *
2574082 GTATACATGAATAGTACC
1 GTATACGTAAATAGTGCC
2574100 GTA
1 GTA
2574103 AACGGTCGTA
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (18 bp):
GTATACGTAAATAGTGCC
Found at i:2574062 original size:36 final size:36
Alignment explanation
Indices: 2574022--2574102 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
2574012 ATACGTGAAC
*
2574022 AGTACCGTATTCGTAAATAGTGCCGTATACATAAAT
1 AGTACCGTATACGTAAATAGTGCCGTATACATAAAT
* * * *
2574058 AGTACTGTATACGTGAATAGTGCTGTATACATGAAT
1 AGTACCGTATACGTAAATAGTGCCGTATACATAAAT
2574094 AGTACCGTA
1 AGTACCGTA
2574103 AACGGTCGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (36 bp):
AGTACCGTATACGTAAATAGTGCCGTATACATAAAT
Found at i:2575498 original size:72 final size:70
Alignment explanation
Indices: 2575378--2575575 Score: 202
Period size: 72 Copynumber: 2.7 Consensus size: 70
2575368 CATTTTTGTC
* * * *
2575378 GCATCTGATAACAATTTGAGTGGCCCAATTCCAAATTGGTT-ATGCAATATGAGTAAA-TTTAGC
1 GCATCTTATAACAATTT-AATGGCCCAATTCCAAATTGCTTGA--CAATATGAGTAAACTTGA-C
** *
2575441 GTTTTCTAT
62 ACTTTCGAT
* * *
2575450 GCATCTTATAATAATTTCAATGGCCCAATTCCAAATTGCTTGGACAATATGAGTCAGCTTGACAC
1 GCATCTTATAACAATTT-AATGGCCCAATTCCAAATTGCTT-GACAATATGAGTAAACTTGACAC
2575515 TTTCGAT
64 TTTCGAT
* *
2575522 GTATCTTATAACAATTTAAGTGGCCCAATTCCAAATTACTTGAGCAATATGAGT
1 GCATCTTATAACAATTTAA-TGGCCCAATTCCAAATTGCTTGA-CAATATGAGT
2575576 GCTCTGAGAT
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
71 4 0.04
72 99 0.93
73 3 0.03
74 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (70 bp):
GCATCTTATAACAATTTAATGGCCCAATTCCAAATTGCTTGACAATATGAGTAAACTTGACACTT
TCGAT
Found at i:2583177 original size:52 final size:52
Alignment explanation
Indices: 2583115--2583221 Score: 205
Period size: 52 Copynumber: 2.1 Consensus size: 52
2583105 TATAAGTTAA
2583115 TTTATTTATGGGTGCTATACCAAAGTTTAATTAAAAGATTTTAATGGCACAC
1 TTTATTTATGGGTGCTATACCAAAGTTTAATTAAAAGATTTTAATGGCACAC
*
2583167 TTTATTTATGGGTGCTATACCAAAGTTTAATTAAAAGATTTTAATGGTACAC
1 TTTATTTATGGGTGCTATACCAAAGTTTAATTAAAAGATTTTAATGGCACAC
2583219 TTT
1 TTT
2583222 TACATTTAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (52 bp):
TTTATTTATGGGTGCTATACCAAAGTTTAATTAAAAGATTTTAATGGCACAC
Found at i:2586038 original size:16 final size:17
Alignment explanation
Indices: 2586009--2586064 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
2585999 AATTTATGAT
2586009 AATTATACATTTAAAAA
1 AATTATACATTTAAAAA
*
2586026 AATTATA-ATTTAATAA
1 AATTATACATTTAAAAA
* *
2586042 AAGTACACATTTAAAAA
1 AATTATACATTTAAAAA
2586059 TAATTA
1 -AATTA
2586065 GAACTTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
16 13 0.41
17 15 0.47
18 4 0.12
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (17 bp):
AATTATACATTTAAAAA
Found at i:2591013 original size:2 final size:2
Alignment explanation
Indices: 2591006--2591040 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2590996 TTTTCCATAG
* *
2591006 AT AT AT AT AT AT AT AT CT AT AT AT AT AG AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2591041 GAATAAGGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2591432 original size:26 final size:26
Alignment explanation
Indices: 2591396--2591448 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2591386 CAAAACCAAA
2591396 ATTGTAGGGATTAGTTTTATAATTTT
1 ATTGTAGGGATTAGTTTTATAATTTT
2591422 ATTGTAGGGATTAGTTTTATAATTTT
1 ATTGTAGGGATTAGTTTTATAATTTT
2591448 A
1 A
2591449 CTTAAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (26 bp):
ATTGTAGGGATTAGTTTTATAATTTT
Found at i:2596651 original size:19 final size:21
Alignment explanation
Indices: 2596618--2596660 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
2596608 TTTGAAATTT
2596618 TTTTCAAAAAAATAT-TACAA
1 TTTTCAAAAAAATATGTACAA
*
2596638 TTTT-AAAAATATATGTACAA
1 TTTTCAAAAAAATATGTACAA
2596658 TTT
1 TTT
2596661 GAAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTTCAAAAAAATATGTACAA
Found at i:2596683 original size:20 final size:21
Alignment explanation
Indices: 2596658--2596705 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
2596648 ATATGTACAA
*
2596658 TTTGAAATTTTTATAAA-TAT
1 TTTGAAATTTTTAAAAATTAT
2596678 TTTGAAA--TTTAAAAATTAT
1 TTTGAAATTTTTAAAAATTAT
2596697 TTTGAAATT
1 TTTGAAATT
2596706 ATTTTGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 7 0.29
19 10 0.42
20 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (21 bp):
TTTGAAATTTTTAAAAATTAT
Found at i:2596857 original size:3 final size:3
Alignment explanation
Indices: 2596849--2596874 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2596839 ACTTCAAAAG
2596849 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2596875 TTATTATTAT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2596879 original size:3 final size:3
Alignment explanation
Indices: 2596873--2596911 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2596863 ATAATAATAA
2596873 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2596912 CCCTTGCTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2598995 original size:222 final size:222
Alignment explanation
Indices: 2598601--2599057 Score: 614
Period size: 222 Copynumber: 2.1 Consensus size: 222
2598591 ACCTTACTGA
* * * * *
2598601 ATTTCCAGAATTCATTAGAAGACAAGACAAGTTGGGTTCTCTAGATCTTTCTCACAACCATATCC
1 ATTTCCAGAGTTCATCAAAACACAAGACAAGTTGGGTTCTCTAGATCTTTCTAACAACCATATCC
** * *
2598666 ATGGTTTTGTGCCCAATTGGTTGTGGAAGAGCAAACTTTCATGGGTAGACCTTTCTTTCAATATG
66 ATGGAGTTGTGCCCAATTGGTTGTGGAAGAGCAAACTTTCAAGGGTAAACCTTTCTTTCAATATG
2598731 ATTGATTTCCCAAAACAGCTTCCCTTAAGTGATGCTAACTTCTCTTTCCCAATGTTGAAAGAATT
131 ATTGATTTCCCAAAACAGCTTCCCTTAAGTGATGCTAACTTCTCTTTCCCAATGTTGAAAGAATT
* ** *
2598796 ATATTTGGCCTCATGTAACATAAGTTC
196 ATATATGGAATCATGTAACATAAGCTC
*
2598823 ATTTCCAGAGTTCATCAAAACACAAGACAAGTT-GGTTGACT-TAGATCTTTCTAACAATCATAT
1 ATTTCCAGAGTTCATCAAAACACAAGACAAGTTGGGTT--CTCTAGATCTTTCTAACAACCATAT
* * ** *
2598886 CTATGGAGTTGTGCCTAATTGGTTGTGGAAGAGCAGCCTTTCAAGGGTAAACCTTTCTTTCAATG
64 CCATGGAGTTGTGCCCAATTGGTTGTGGAAGAGCAAACTTTCAAGGGTAAACCTTTCTTTCAATA
* * ** **
2598951 TGATTGATTTTCCAAAACAGCTTCCCTTAAGTGAT-TTAAACTTCTCTTTTTCAATGTTGAGGGA
129 TGATTGATTTCCCAAAACAGCTTCCCTTAAGTGATGCT-AACTTCTCTTTCCCAATGTTGAAAGA
* * *
2599015 ATTGTCTATGGAATCTTGTAACATAAGCTC
193 ATTATATATGGAATCATGTAACATAAGCTC
2599045 ATTTCCAGAGTTC
1 ATTTCCAGAGTTC
2599058 TTAAAGAGTC
Statistics
Matches: 204, Mismatches: 28, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
221 5 0.02
222 197 0.97
223 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (222 bp):
ATTTCCAGAGTTCATCAAAACACAAGACAAGTTGGGTTCTCTAGATCTTTCTAACAACCATATCC
ATGGAGTTGTGCCCAATTGGTTGTGGAAGAGCAAACTTTCAAGGGTAAACCTTTCTTTCAATATG
ATTGATTTCCCAAAACAGCTTCCCTTAAGTGATGCTAACTTCTCTTTCCCAATGTTGAAAGAATT
ATATATGGAATCATGTAACATAAGCTC
Found at i:2599137 original size:222 final size:222
Alignment explanation
Indices: 2598687--2599139 Score: 466
Period size: 222 Copynumber: 2.0 Consensus size: 222
2598677 CCCAATTGGT
* *
2598687 TGTGGAAGAGCAAACTTTCATGGGTAGACCTTTCTTTCAATATGATTGATTTCCCAAAACAGCTT
1 TGTGGAAGAGCAAACTTTCAAGGGTAAACCTTTCTTTCAATATGATTGATTTCCCAAAACAGCTT
* **
2598752 CCCTTAAGTGATGCTAACTTCTCTTTCCCAATGTTGAAAGAATTATATTTGGCCTCATGTAACAT
66 CCCTTAAGTGATGCTAACTTCTCTTTCCCAATGTTGAAAGAATTATATATGGAATCATGTAACAT
* * ** * * * *
2598817 AAGTTCATTTCCAGAGTTCATCAAAACACAAGACAAGTTGGTTGACTTAGATCTTTCTAACAATC
131 AAGCTCATTTCCAGAGTTCATCAAAACACAAGAAAAGTTGAATGACTCAGAACTTTCAAACAATA
* * *** * * * *
2598882 ATATCTATGGAGTTGTGCCTAATTGGT
196 AAATCAATGGAGCAATACCAAACTGGG
** * *
2598909 TGTGGAAGAGCAGCCTTTCAAGGGTAAACCTTTCTTTCAATGTGATTGATTTTCCAAAACAGCTT
1 TGTGGAAGAGCAAACTTTCAAGGGTAAACCTTTCTTTCAATATGATTGATTTCCCAAAACAGCTT
* ** ** * * *
2598974 CCCTTAAGTGAT-TTAAACTTCTCTTTTTCAATGTTGAGGGAATTGTCTATGGAATCTTGTAACA
66 CCCTTAAGTGATGCT-AACTTCTCTTTCCCAATGTTGAAAGAATTATATATGGAATCATGTAACA
* ** * *
2599038 TAAGCTCATTTCCAGAGTTC-TTAAAGAGTCAAGAAAATTTAGAAT-ATCTCA-AACTTTCAAAT
130 TAAGCTCATTTCCAGAGTTCATCAAA-ACACAAGAAAAGTT-GAATGA-CTCAGAACTTTCAAAC
*
2599100 AATAAAAT-AAGTGGTGCAATACCAAACTGGG
192 AATAAAATCAA-TGGAGCAATACCAAACTGGG
2599131 TGTGGAAGA
1 TGTGGAAGA
2599140 AAAGTTTGCG
Statistics
Matches: 186, Mismatches: 40, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
221 6 0.03
222 175 0.94
223 5 0.03
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (222 bp):
TGTGGAAGAGCAAACTTTCAAGGGTAAACCTTTCTTTCAATATGATTGATTTCCCAAAACAGCTT
CCCTTAAGTGATGCTAACTTCTCTTTCCCAATGTTGAAAGAATTATATATGGAATCATGTAACAT
AAGCTCATTTCCAGAGTTCATCAAAACACAAGAAAAGTTGAATGACTCAGAACTTTCAAACAATA
AAATCAATGGAGCAATACCAAACTGGG
Found at i:2599353 original size:72 final size:72
Alignment explanation
Indices: 2599244--2599513 Score: 373
Period size: 72 Copynumber: 3.8 Consensus size: 72
2599234 CTATTTCAAC
* *
2599244 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTATGCAATATGAGTCAACTTAGCAC
1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGCAC
2599309 TTTCTAT
66 TTTCTAT
* * * * * **
2599316 GCATCTTATAACAATTTCAATGGCCCAATACCAAATTGCTTATGTAATATGAGTCAACTTAGCGG
1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGCAC
2599381 TTT-TGAT
66 TTTCT-AT
* *
2599388 GCATCTTATAACAATTTGAGTGGCTCAATTCCAAATTGCTT-GGACAATATGAGTCAACTTGGCA
1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGG-CAATATGAGTCAACTTAGCA
*
2599452 CTTTCGAT
65 CTTTCTAT
* * *
2599460 GTATCTTATAACAATTTGAGTGGCCCAATTCCTAATTGCTTGGGCAATATGAGT
1 GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGT
2599514 GCTCTGAGTT
Statistics
Matches: 174, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
71 2 0.01
72 170 0.98
73 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (72 bp):
GCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTAGGCAATATGAGTCAACTTAGCAC
TTTCTAT
Found at i:2603172 original size:21 final size:21
Alignment explanation
Indices: 2603146--2603186 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2603136 AGACAAGCGA
* *
2603146 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2603167 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2603187 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2618890 original size:13 final size:13
Alignment explanation
Indices: 2618872--2618896 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2618862 TTGCTCGACC
2618872 AAAAATTCTAGAA
1 AAAAATTCTAGAA
2618885 AAAAATTCTAGA
1 AAAAATTCTAGA
2618897 TAGATATATG
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:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAATTCTAGAA
Found at i:2642587 original size:18 final size:18
Alignment explanation
Indices: 2642564--2642620 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
2642554 CCCAACTACT
*
2642564 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* * *
2642582 GTATACATGAATAGTGCT
1 GTATACGTGAATAGTACC
2642600 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
2642618 GTA
1 GTA
2642621 AACAGTCGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:2649982 original size:14 final size:14
Alignment explanation
Indices: 2649952--2649980 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2649942 CCAAGTGGGC
2649952 TTATTTTAAGAATT
1 TTATTTTAAGAATT
2649966 TTATTTTAA-AATT
1 TTATTTTAAGAATT
2649979 TT
1 TT
2649981 TAAATATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TTATTTTAAGAATT
Found at i:2653190 original size:6 final size:6
Alignment explanation
Indices: 2653181--2653229 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
2653171 TCTTTTTACA
* * *
2653181 TAGTTT TAGTTT TAGTTT TAGTTT TAGTTT TAATTT TAATTT TAATTT
1 TAGTTT TAGTTT TAGTTT TAGTTT TAGTTT TAGTTT TAGTTT TAGTTT
2653229 T
1 T
2653230 CATTTTCAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.67
Consensus pattern (6 bp):
TAGTTT
Found at i:2653204 original size:18 final size:18
Alignment explanation
Indices: 2653181--2653240 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
2653171 TCTTTTTACA
*
2653181 TAGTTTTAGTTTTAGTTT
1 TAGTTTTAGTTTTAATTT
2653199 TAGTTTTAGTTTTAATTT
1 TAGTTTTAGTTTTAATTT
* * *
2653217 TAATTTTAATTTTCATTT
1 TAGTTTTAGTTTTAATTT
2653235 TCAGTT
1 T-AGTT
2653241 AAGACTTAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
18 33 0.92
19 3 0.08
ACGTcount: A:0.22, C:0.03, G:0.10, T:0.65
Consensus pattern (18 bp):
TAGTTTTAGTTTTAATTT
Found at i:2653237 original size:6 final size:6
Alignment explanation
Indices: 2653184--2653235 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
2653174 TTTTACATAG
* * * * *
2653184 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAA TTTTAA TTTTAA TTTTCA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
2653232 TTTT
1 TTTT
2653236 CAGTTAAGAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:2656888 original size:193 final size:193
Alignment explanation
Indices: 2656354--2657037 Score: 1030
Period size: 193 Copynumber: 3.5 Consensus size: 193
2656344 GGTAGAAAAA
* * * *
2656354 TTAGGATTACTGACATGTTTAACTCAGTCCATATAATGTCTTTTTCAGGAGGT-AAAGAAAATGC
1 TTAGGATGACTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAAG-AAATGC
* * *
2656418 ATCTCACGTGCGCCAATTAGTGGGAATGAGAGGACTAACGTCTGATCCCCAAGGAAAAATGATCG
65 ATCTCACGTGCACCAATTAGTGGGAATGAGAGGACTAATGTCTGATCCCCAAGGACAAATGATCG
* * *
2656483 ATGCGGTAGAAAAATTACCCCAATCTATTGAGATATGGTTTGCAACAAGAAATGAATCTTAATT
130 ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATT
* * *
2656547 TTAGGATGATTGACCTGTTTAACCCAGTCAATATAATGTCTTTTT-AGGAGCTAAAGGAAATGCA
1 TTAGGATGACTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAAGAAATGCA
* * * *
2656611 TCTCACGTGCACCAATTAGTGGGAACGAAAGGATTAATGTCGGATCCCCAAGGACAAATGATCGA
66 TCTCACGTGCACCAATTAGTGGGAATGAGAGGACTAATGTCTGATCCCCAAGGACAAATGATCGA
* *
2656676 TGCGGTAGAAAAATTACGCCAATCTATTGAGATGTGGTTTGCGACAAGAAATTAATCCTAATT
131 TGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATT
* * * * *
2656739 TTAGGATGACTGACCTATTTAACCCACTACATATAATGTCTTTTTCACGAGCTAAAAGAAATGCG
1 TTAGGATGACTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAAGAAATGCA
* * *
2656804 TCTCATGTGCACCAATTAGTGGGAATGAGAGGACTAATGTCTGATCCCTAAGGACAAATGATCAA
66 TCTCACGTGCACCAATTAGTGGGAATGAGAGGACTAATGTCTGATCCCCAAGGACAAATGATCGA
* * *
2656869 TGCGATAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGATAAGAAATGAATCCTGATT
131 TGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATT
* *
2656932 TTAGGATGACTGACTTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCA
1 TTAGGATGACTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAAGAAATGCA
* * *
2656997 TCTCGCGTGCACCAATTAGTGGCAATGAGAGGATTAATGTC
66 TCTCACGTGCACCAATTAGTGGGAATGAGAGGACTAATGTC
2657038 GGATTGTGAT
Statistics
Matches: 439, Mismatches: 50, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
192 169 0.38
193 270 0.62
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (193 bp):
TTAGGATGACTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAAGAAATGCA
TCTCACGTGCACCAATTAGTGGGAATGAGAGGACTAATGTCTGATCCCCAAGGACAAATGATCGA
TGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCCTAATT
Found at i:2660856 original size:193 final size:193
Alignment explanation
Indices: 2660223--2660862 Score: 1007
Period size: 192 Copynumber: 3.3 Consensus size: 193
2660213 GGGAATGTAC
**
2660223 ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGTGACAAGAAATGAATCCTAATTT
1 ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCAACAAGAAATGAATCCTAATTT
* *
2660288 TAAGG-TTATTGACCTATTTAATCCAGTCCATA-AATGTCTTTTTCAGGAGCTAAAGGAAATGCA
66 T-AGGATTATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCA
* *
2660351 TCTCACGTGCGCCAATTAGTGGGAATAAGAGGATTAATGTCGGATCCCCAAGGACAAATGATCG
130 TCTCACGTGCACCAATTAGTGGGAATGAGAGGATTAATGTCGGATCCCCAAGGACAAATGATCG
* * *
2660415 ATACGGTAGAAAAATTATGCCAATCTAGTGAGATATGGTTTGCAACAAGAAATGAATCCTAATTT
1 ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCAACAAGAAATGAATCCTAATTT
* * *
2660480 TAGGATTATTGACATGTTTAACCCAGTCCATATAATATCTTTTTCAGGAGCTAAAGGAAATACAT
66 TAGGATTATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCAT
** * *
2660545 CTCACGTG-TGCAATTAGTGGGAATGAGAGTATTAATGTCAGATCCCCAAGGACAAATGATCG
131 CTCACGTGCACCAATTAGTGGGAATGAGAGGATTAATGTCGGATCCCCAAGGACAAATGATCG
* * *
2660607 ATGCGGTAGAAAATTTACGCCAATCTATTGAGATATGGTTTGCGACAAGAAATGAATCATAATTT
1 ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCAACAAGAAATGAATCCTAATTT
* * *
2660672 TAGGATGATTAACCTGTTTAACCCAGTCAATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCAT
66 TAGGATTATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCAT
* *
2660737 CTCACGTGCACCAATTAGTGGGAATGAGAGGATTAATATCGGATACCCAAGGACAAATGATCG
131 CTCACGTGCACCAATTAGTGGGAATGAGAGGATTAATGTCGGATCCCCAAGGACAAATGATCG
* * *
2660800 ATGCGGTAGAAAAATTACGTCAATCTATTGAAATGTGGTTTGCAACAAGAAATGAATCCTAAT
1 ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCAACAAGAAATGAATCCTAAT
2660863 GTCTTTTTCA
Statistics
Matches: 406, Mismatches: 39, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
191 3 0.01
192 260 0.64
193 143 0.35
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (193 bp):
ATGCGGTAGAAAAATTACGCCAATCTATTGAGATATGGTTTGCAACAAGAAATGAATCCTAATTT
TAGGATTATTGACCTGTTTAACCCAGTCCATATAATGTCTTTTTCAGGAGCTAAAGGAAATGCAT
CTCACGTGCACCAATTAGTGGGAATGAGAGGATTAATGTCGGATCCCCAAGGACAAATGATCG
Found at i:2662763 original size:27 final size:27
Alignment explanation
Indices: 2662725--2662779 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
2662715 AAAATTAAAA
2662725 AAATTGGATCTATGTCCAACATATCAC
1 AAATTGGATCTATGTCCAACATATCAC
2662752 AAATTGGATCTATGTCCAACATATCAC
1 AAATTGGATCTATGTCCAACATATCAC
2662779 A
1 A
2662780 CCTACCAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (27 bp):
AAATTGGATCTATGTCCAACATATCAC
Found at i:2664720 original size:2 final size:2
Alignment explanation
Indices: 2664713--2664738 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2664703 CCCCAGTAGA
2664713 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
2664739 GAAGTGCAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2668455 original size:13 final size:13
Alignment explanation
Indices: 2668405--2668460 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
2668395 GTACATATAT
*
2668405 TTCCATATGACCAA
1 TTCCATATAACC-A
*
2668419 TTCC-TATAAACA
1 TTCCATATAACCA
* * *
2668431 TTTCACACAACCA
1 TTCCATATAACCA
2668444 TTCCATATAACCA
1 TTCCATATAACCA
2668457 TTCC
1 TTCC
2668461 GTCTGATACA
Statistics
Matches: 32, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
12 4 0.12
13 24 0.75
14 4 0.12
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (13 bp):
TTCCATATAACCA
Found at i:2668615 original size:46 final size:46
Alignment explanation
Indices: 2668545--2668910 Score: 520
Period size: 46 Copynumber: 7.9 Consensus size: 46
2668535 TTCGACATGA
* * * * * *
2668545 TGCCATAGTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTC-ATTTCATATCACGT
* *** *
2668591 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATATCACGT
* *
2668638 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
2668684 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
2668730 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
2668776 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
*
2668822 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAC-T
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATC-ACGT
* *
2668868 TGCCATGGTATCTTTCAACCATGGTCTTACACATTCCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCA
2668911 GAGAGCACAT
Statistics
Matches: 301, Mismatches: 16, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
45 1 0.00
46 259 0.86
47 41 0.14
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATATCACGT
Found at i:2673391 original size:11 final size:12
Alignment explanation
Indices: 2673375--2673403 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2673365 CGCCACGTTC
2673375 TATCTTTCCA-T
1 TATCTTTCCATT
2673386 TATCTTTCCATT
1 TATCTTTCCATT
2673398 TATCTT
1 TATCTT
2673404 CTTTATTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TATCTTTCCATT
Found at i:2673821 original size:19 final size:19
Alignment explanation
Indices: 2673797--2673843 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
2673787 AAAAAAAGTG
* *
2673797 ATAAAAAAAGTACAAAAAA
1 ATAAAAAAAGAAAAAAAAA
* *
2673816 ATAAAATACGAAAAAAAAA
1 ATAAAAAAAGAAAAAAAAA
2673835 ATAAAAAAA
1 ATAAAAAAA
2673844 TTATGTGGGT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.11
Consensus pattern (19 bp):
ATAAAAAAAGAAAAAAAAA
Found at i:2682320 original size:16 final size:17
Alignment explanation
Indices: 2682299--2682330 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2682289 CTCTAATTCT
2682299 AAAAATTTTT-AAAAAG
1 AAAAATTTTTCAAAAAG
2682315 AAAAATTTTTCAAAAA
1 AAAAATTTTTCAAAAA
2682331 TTATTTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
AAAAATTTTTCAAAAAG
Found at i:2683034 original size:6 final size:6
Alignment explanation
Indices: 2683023--2683056 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
2683013 AAGTTAGCAT
2683023 TTTCAG TTTCAG TTTCAG TTTCAG TTTCAG TTTC
1 TTTCAG TTTCAG TTTCAG TTTCAG TTTCAG TTTC
2683057 CTTTTCCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.53
Consensus pattern (6 bp):
TTTCAG
Found at i:2683062 original size:18 final size:18
Alignment explanation
Indices: 2683020--2683062 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2683010 AAAAAGTTAG
2683020 CATTTTCAGTTTCAGTTT
1 CATTTTCAGTTTCAGTTT
*
2683038 CAGTTTCAGTTTCAGTTT
1 CATTTTCAGTTTCAGTTT
*
2683056 CCTTTTC
1 CATTTTC
2683063 CTTTGCTTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.21, G:0.12, T:0.53
Consensus pattern (18 bp):
CATTTTCAGTTTCAGTTT
Found at i:2686214 original size:14 final size:15
Alignment explanation
Indices: 2686195--2686224 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2686185 AAAAAATTAT
2686195 AAGTACTTA-ATGGG
1 AAGTACTTATATGGG
2686209 AAGTACTTATATGGG
1 AAGTACTTATATGGG
2686224 A
1 A
2686225 TACAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (15 bp):
AAGTACTTATATGGG
Found at i:2687624 original size:79 final size:79
Alignment explanation
Indices: 2687387--2687625 Score: 390
Period size: 79 Copynumber: 3.0 Consensus size: 79
2687377 TCAGGTTTCC
*
2687387 TAGTTGGAAAATTTTAATAGTGCAATGTTTTTAATATTATCCTCATAAAT-TTTCATATTTAATA
1 TAGTTGGAAAATTTTAATATTGCAATGTTTTTAATATTATCCTCATAAATATTT-ATATTTAATA
*
2687451 TTTACGGATTTGATT
65 TTTACGGACTTGATT
* * *
2687466 TAGTTGGAAAATGTTAATATTGCAACGTTTTTAATATTATCCTCATAAATATTCATATTTAATAT
1 TAGTTGGAAAATTTTAATATTGCAATGTTTTTAATATTATCCTCATAAATATTTATATTTAATAT
*
2687531 TTACGGACTAGATT
66 TTACGGACTTGATT
2687545 TAGTTGGAAAATTTTAATATTGCAATGTTTTTAATATTATCCTCATAAATATTTATATTTAATAT
1 TAGTTGGAAAATTTTAATATTGCAATGTTTTTAATATTATCCTCATAAATATTTATATTTAATAT
* *
2687610 TTATGAACTTGATT
66 TTACGGACTTGATT
2687624 TA
1 TA
2687626 CGAAAATGGG
Statistics
Matches: 147, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
79 145 0.99
80 2 0.01
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (79 bp):
TAGTTGGAAAATTTTAATATTGCAATGTTTTTAATATTATCCTCATAAATATTTATATTTAATAT
TTACGGACTTGATT
Found at i:2693467 original size:29 final size:29
Alignment explanation
Indices: 2693425--2693482 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2693415 ATTGATTAAT
2693425 CCAAATTATTTTTTATATTATTCAAGTAG
1 CCAAATTATTTTTTATATTATTCAAGTAG
2693454 CCAAATTATTTTTTATATTATTCAAGTAG
1 CCAAATTATTTTTTATATTATTCAAGTAG
2693483 AACACACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.48
Consensus pattern (29 bp):
CCAAATTATTTTTTATATTATTCAAGTAG
Found at i:2698622 original size:131 final size:130
Alignment explanation
Indices: 2698400--2698767 Score: 305
Period size: 131 Copynumber: 2.8 Consensus size: 130
2698390 GACGAGATTT
* * * * *
2698400 GATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGGTTGCAATTTCGCGTTTGCTCAAA
1 GATGTTTGGCAATTAG-GGAATCATGCCCTATCGTGTT-GGGTTG-AATTTCTCGTTTGTTCAAA
* * *
2698465 ATAATCGAATATCACTTCAAAATTTCACTCA-AGTCTT-CTAAAAATCCTTT-AAAACGAAGGTG
63 ACAATCGAATATCACTTCAAAATTTCACTCATA-T-TTACTAAAAA-CCTTTCAAAACAAAGGCG
2698527 ATACTC
125 ATACTC
* * *
2698533 GGTGTTTGACAATTAGGGAATCATGCCCTATCGTGTTGGGTTGTGATTTCTCGTTTGTTCAAAAC
1 GATGTTTGGCAATTAGGGAATCATGCCCTATCGTGTTGGGTTG-AATTTCTCGTTTGTTCAAAAC
* * *** * * **
2698598 AATTGAATATTC-CTTTAGGTTTTCATTCATATTTATTAAAAACCTTTCAAAACAAAGGCGATGT
65 AATCGAATA-TCACTTCAAAATTTCACTCATATTTACTAAAAACCTTTCAAAACAAAGGCGATAC
2698662 TC
129 TC
* * * * * * *
2698664 GATGTTTGGCGATTTGAGAATCGA-GCCCTATCGTGCTGGGTTGCACTTTTTCATTTGTTCAAAA
1 GATGTTTGGCAATTAGGGAATC-ATGCCCTATCGTGTTGGGTTG-AATTTCTCGTTTGTTCAAAA
* * ** * * *
2698728 CAATCGAAGATCCCTTCGGAATTTTACTCGTATTTTCTAA
64 CAATCGAATATCACTTCAAAATTTCACTCATATTTACTAA
2698768 GATGAGGTAA
Statistics
Matches: 186, Mismatches: 43, Indels: 14
0.77 0.18 0.06
Matches are distributed among these distances:
130 9 0.05
131 141 0.76
132 23 0.12
133 13 0.07
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (130 bp):
GATGTTTGGCAATTAGGGAATCATGCCCTATCGTGTTGGGTTGAATTTCTCGTTTGTTCAAAACA
ATCGAATATCACTTCAAAATTTCACTCATATTTACTAAAAACCTTTCAAAACAAAGGCGATACTC
Found at i:2705536 original size:28 final size:28
Alignment explanation
Indices: 2705472--2705536 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
2705462 TATTCTTATG
2705472 ATTTTAAAAATTATTTTAATATGTAATT
1 ATTTTAAAAATTATTTTAATATGTAATT
**
2705500 ATTCAAAAAATTATAATTT-ATATG-AATT
1 ATTTTAAAAATTAT--TTTAATATGTAATT
2705528 ATTTTAAAA
1 ATTTTAAAA
2705537 TGATAGAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 23 0.74
29 5 0.16
30 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (28 bp):
ATTTTAAAAATTATTTTAATATGTAATT
Found at i:2709873 original size:21 final size:22
Alignment explanation
Indices: 2709849--2709890 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2709839 CATATATCTA
*
2709849 GATTATTTTAAT-TCATATAAG
1 GATTATTTTAATCTAATATAAG
2709870 GATTATTTTAATCTAATATAA
1 GATTATTTTAATCTAATATAA
2709891 CAATTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (22 bp):
GATTATTTTAATCTAATATAAG
Found at i:2712908 original size:24 final size:24
Alignment explanation
Indices: 2712876--2712925 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
2712866 ACAAGTGAGC
*
2712876 ATTATTGTTAATCATTTATCGGAA
1 ATTATTGTTAATCATTCATCGGAA
2712900 ATTATTGTTAATCATTCATCGGAA
1 ATTATTGTTAATCATTCATCGGAA
2712924 AT
1 AT
2712926 AAACTAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (24 bp):
ATTATTGTTAATCATTCATCGGAA
Found at i:2715905 original size:25 final size:27
Alignment explanation
Indices: 2715876--2715936 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
2715866 TATTTATCTG
*
2715876 AATCAAATAATTTTT-TTCAATT-ATT
1 AATCAAATAATTTTTGTTAAATTAATT
* *
2715901 AATCAATTATTTTTTGTTAAATTAATT
1 AATCAAATAATTTTTGTTAAATTAATT
*
2715928 AATAAAATA
1 AATCAAATA
2715937 TAAAATAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 13 0.45
26 6 0.21
27 10 0.34
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (27 bp):
AATCAAATAATTTTTGTTAAATTAATT
Found at i:2716378 original size:22 final size:22
Alignment explanation
Indices: 2716314--2716378 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 22
2716304 TGCAGGTGAA
* *
2716314 GTAATCAAAAT-ATATATTAAT
1 GTAATAAAAATAATAAATTAAT
* **
2716335 GTAAATAGAAAAAAAT-GTTTAAT
1 GT-AATA-AAAATAATAAATTAAT
2716358 GTAATAAAAATAATAAATTAA
1 GTAATAAAAATAATAAATTAA
2716379 GGAAAATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
21 9 0.27
22 11 0.33
23 11 0.33
24 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (22 bp):
GTAATAAAAATAATAAATTAAT
Found at i:2717936 original size:103 final size:101
Alignment explanation
Indices: 2717751--2717957 Score: 342
Period size: 103 Copynumber: 2.0 Consensus size: 101
2717741 CAAATTGTAA
*
2717751 TTAAATTACAAAATTAATATATTAATAAAATTATATTTTAACTCTCAAATTTATCACTTTCAAGA
1 TTAAATTACAAAATTAATAAATTAATAAAATTATATTTTAACTCTCAAATTTATCACTTTCAAGA
2717816 AAAATTTTGACTCTCACTTCTACCAATACCCAAATCT
66 AAAATTTTGACTCTCACTTCTACCAATACCC-AATCT
* * * *
2717853 TTAAGATTACAAAATTAATAAATTAATAAATTTGTGTTTTAACTCTCAAATTTATCACTTTGAAG
1 TTAA-ATTACAAAATTAATAAATTAATAAAATTATATTTTAACTCTCAAATTTATCACTTTCAAG
*
2717918 AAAAATTTTGACTTTCACTTCTACCAATACCCAATCT
65 AAAAATTTTGACTCTCACTTCTACCAATACCCAATCT
2717955 TTA
1 TTA
2717958 CAGGGGGATT
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 12 0.12
103 86 0.88
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.39
Consensus pattern (101 bp):
TTAAATTACAAAATTAATAAATTAATAAAATTATATTTTAACTCTCAAATTTATCACTTTCAAGA
AAAATTTTGACTCTCACTTCTACCAATACCCAATCT
Found at i:2727118 original size:43 final size:43
Alignment explanation
Indices: 2727057--2727142 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
2727047 GTCATGATTA
*
2727057 ATATCAAATTTTTAAGCGAATGTTGCAATTGGTAAAGGTGTTG
1 ATATCAAATTTTTAAGCGAATGTTACAATTGGTAAAGGTGTTG
2727100 ATATCAAATTTTTAAGCGAATGTTACAATTGGTAAAGGTGTTG
1 ATATCAAATTTTTAAGCGAATGTTACAATTGGTAAAGGTGTTG
2727143 GTAAAGGTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (43 bp):
ATATCAAATTTTTAAGCGAATGTTACAATTGGTAAAGGTGTTG
Found at i:2727145 original size:12 final size:12
Alignment explanation
Indices: 2727128--2727154 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2727118 AATGTTACAA
2727128 TTGGTAAAGGTG
1 TTGGTAAAGGTG
2727140 TTGGTAAAGGTG
1 TTGGTAAAGGTG
2727152 TTG
1 TTG
2727155 AGTACACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.37
Consensus pattern (12 bp):
TTGGTAAAGGTG
Found at i:2729639 original size:15 final size:15
Alignment explanation
Indices: 2729616--2729645 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2729606 CGTATCTTCA
*
2729616 CATATTTTAATTTAT
1 CATAATTTAATTTAT
2729631 CATAATTTAATTTAT
1 CATAATTTAATTTAT
2729646 ATTTTACAAA
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:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
CATAATTTAATTTAT
Found at i:2735200 original size:38 final size:38
Alignment explanation
Indices: 2735080--2735217 Score: 186
Period size: 39 Copynumber: 3.6 Consensus size: 38
2735070 TTTTTATAAT
* * *
2735080 AATAAAACAAAATGGTATGAGGAAGTAGTTTTAATTAAC
1 AATAAAACAAAATAGCATG-GGGAGTAGTTTTAATTAAC
*
2735119 AATAAAACAAAATAGTATGGGGAAGTAGTTTTAATTAAC
1 AATAAAACAAAATAGCATGGGG-AGTAGTTTTAATTAAC
* * *
2735158 AATAAAACAAAATAGCATGGGGAGTGGTTTTGATTAAT
1 AATAAAACAAAATAGCATGGGGAGTAGTTTTAATTAAC
*
2735196 AATAAAACAAAGTAGCATGGGG
1 AATAAAACAAAATAGCATGGGG
2735218 GGAGTGGGAT
Statistics
Matches: 91, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 36 0.40
39 55 0.60
ACGTcount: A:0.47, C:0.06, G:0.21, T:0.26
Consensus pattern (38 bp):
AATAAAACAAAATAGCATGGGGAGTAGTTTTAATTAAC
Found at i:2747239 original size:24 final size:24
Alignment explanation
Indices: 2747207--2747254 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2747197 GAAGCATCAT
2747207 AAGCACTAAGGCAATAGGTTGACA
1 AAGCACTAAGGCAATAGGTTGACA
2747231 AAGCACTAAGGCAATAGGTTGACA
1 AAGCACTAAGGCAATAGGTTGACA
2747255 GACATCAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.17
Consensus pattern (24 bp):
AAGCACTAAGGCAATAGGTTGACA
Found at i:2749279 original size:11 final size:11
Alignment explanation
Indices: 2749242--2749303 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
2749232 AAAAAGTTAC
* *
2749242 TATTGTTTTTT
1 TATTATTTTGT
*
2749253 TATTGTTTT-T
1 TATTATTTTGT
2749263 TCATTATTTTGT
1 T-ATTATTTTGT
* *
2749275 TATTATATTAT
1 TATTATTTTGT
2749286 TATTATTTTGT
1 TATTATTTTGT
*
2749297 TGTTATT
1 TATTATT
2749304 GTTTAGATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
10 2 0.05
11 39 0.91
12 2 0.05
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.73
Consensus pattern (11 bp):
TATTATTTTGT
Found at i:2754899 original size:17 final size:18
Alignment explanation
Indices: 2754865--2754905 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2754855 ATCATTCAAC
2754865 TATTTAAAAAATATAATT
1 TATTTAAAAAATATAATT
* *
2754883 TTTTTAAATAA-ATAATT
1 TATTTAAAAAATATAATT
2754900 TATTTA
1 TATTTA
2754906 TATATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTAAAAAATATAATT
Found at i:2760999 original size:17 final size:17
Alignment explanation
Indices: 2760977--2761010 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2760967 TTTGTTGCTC
2760977 AGATTTATGATAACAAG
1 AGATTTATGATAACAAG
* *
2760994 AGATTTCTGATACCAAG
1 AGATTTATGATAACAAG
2761011 GTCTTAGCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (17 bp):
AGATTTATGATAACAAG
Found at i:2764096 original size:19 final size:19
Alignment explanation
Indices: 2764064--2764108 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
2764054 AAAGAAATTC
*
2764064 AAAAAATTTTAAAAT-TTT
1 AAAAAATTTGAAAATATTT
2764082 AAAATAATTTGAAAATATTT
1 AAAA-AATTTGAAAATATTT
2764102 ATAAAAA
1 A-AAAAA
2764109 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 10 0.43
20 6 0.26
21 3 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAAAATTTGAAAATATTT
Found at i:2765711 original size:2 final size:2
Alignment explanation
Indices: 2765704--2765732 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2765694 TAGATGTCAC
2765704 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
2765733 GGATATTCAT
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:2765769 original size:18 final size:18
Alignment explanation
Indices: 2765741--2765787 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2765731 ATGGATATTC
*
2765741 ATATAACTTTTAAATATA
1 ATATAATTTTTAAATATA
*
2765759 ATATAATTTTT-TATATA
1 ATATAATTTTTAAATATA
*
2765776 A-ATTATTTTTAA
1 ATATAATTTTTAA
2765788 TTCTGTCATG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 8 0.33
17 6 0.25
18 10 0.42
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATAATTTTTAAATATA
Found at i:2768493 original size:36 final size:36
Alignment explanation
Indices: 2768423--2768515 Score: 141
Period size: 36 Copynumber: 2.5 Consensus size: 36
2768413 TTTATTAAAT
* *
2768423 ATTAGAATTACAAAATTATCTAAATTTGAACATTTGTA
1 ATTAGAATTA-AAAA-AATATAAATTTGAACATTTGTA
*
2768461 ATTAGAATTAAAAAAATATAAATTTGAGCATTTGTA
1 ATTAGAATTAAAAAAATATAAATTTGAACATTTGTA
2768497 ATTAGAATTAAAAAAATAT
1 ATTAGAATTAAAAAAATAT
2768516 TTTAAGTTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
36 38 0.73
37 4 0.08
38 10 0.19
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.37
Consensus pattern (36 bp):
ATTAGAATTAAAAAAATATAAATTTGAACATTTGTA
Found at i:2769446 original size:33 final size:33
Alignment explanation
Indices: 2769404--2769469 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
2769394 AAGGAGAGAG
*
2769404 GCTTCCTCCTAAAGACTAATACTCGTGGCTTCT
1 GCTTCCTCCTAAAGACTAATACCCGTGGCTTCT
2769437 GCTTCCTCCTAAAGACTAATACCCGTGGCTTCT
1 GCTTCCTCCTAAAGACTAATACCCGTGGCTTCT
2769470 CTCTTTGGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.21, C:0.32, G:0.15, T:0.32
Consensus pattern (33 bp):
GCTTCCTCCTAAAGACTAATACCCGTGGCTTCT
Found at i:2771215 original size:23 final size:23
Alignment explanation
Indices: 2771171--2771214 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
2771161 TTTTCATAAC
2771171 ATATTAATATTATTCTTAATATA
1 ATATTAATATTATTCTTAATATA
*
2771194 ATATTAAT-TTA-TCTTTATATA
1 ATATTAATATTATTCTTAATATA
2771215 TTACATACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 3 0.15
23 8 0.40
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATTAATATTATTCTTAATATA
Found at i:2771260 original size:31 final size:29
Alignment explanation
Indices: 2771186--2771261 Score: 71
Period size: 31 Copynumber: 2.5 Consensus size: 29
2771176 AATATTATTC
* * * *
2771186 TTAATATAATATTAATTTATCTTTATATA
1 TTAATATAAAAATAATTTATATATATATA
* *
2771215 TTACATACACAAATAATTATATATATATATA
1 TTA-ATATAAAAATAATT-TATATATATATA
2771246 TTTAATATAAAAATAA
1 -TTAATATAAAAATAA
2771262 GTGAATGTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
29 3 0.08
30 10 0.28
31 20 0.56
32 3 0.08
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (29 bp):
TTAATATAAAAATAATTTATATATATATA
Found at i:2771788 original size:60 final size:58
Alignment explanation
Indices: 2771686--2771809 Score: 221
Period size: 60 Copynumber: 2.1 Consensus size: 58
2771676 CACTTATTTG
2771686 GCCCTTCAAATTTATAAAAAAAAAAATTTAGTCTTCTATTTGATTTTTCACATTCTTA
1 GCCCTTCAAATTTATAAAAAAAAAAATTTAGTCTTCTATTTGATTTTTCACATTCTTA
*
2771744 GCCCTTCAAATTTATAAAAAAAAATTATTTTAGTCTTCTATTTGATTTTTCACATTCTTA
1 GCCCTTCAAATTTATAAAAAAAAA--AATTTAGTCTTCTATTTGATTTTTCACATTCTTA
2771804 GCCCTT
1 GCCCTT
2771810 AAACTTACTT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 24 0.38
60 39 0.62
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (58 bp):
GCCCTTCAAATTTATAAAAAAAAAAATTTAGTCTTCTATTTGATTTTTCACATTCTTA
Found at i:2776135 original size:3 final size:3
Alignment explanation
Indices: 2776127--2776170 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2776117 TACTATGGCT
2776127 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2776171 CGGGTTGGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2778460 original size:2 final size:2
Alignment explanation
Indices: 2778453--2778481 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2778443 TCTTTCTTTT
2778453 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
2778482 TTGTGGGTTA
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:2781443 original size:2 final size:2
Alignment explanation
Indices: 2781436--2781461 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2781426 ACCTGCCTTG
2781436 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
2781462 TGTACATGTA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2797164 original size:13 final size:13
Alignment explanation
Indices: 2797127--2797166 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
2797117 AATTTAGTAA
2797127 TACTTTTGAAAAG
1 TACTTTTGAAAAG
*
2797140 TAC-TGTGAAAAAG
1 TACTTTTG-AAAAG
2797153 TACTTTTGAAAAG
1 TACTTTTGAAAAG
2797166 T
1 T
2797167 TTGATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 3 0.13
13 17 0.74
14 3 0.13
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.35
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:2800308 original size:18 final size:18
Alignment explanation
Indices: 2800285--2800320 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2800275 CAAAAATGAA
2800285 TGAACATATTTACTTTTG
1 TGAACATATTTACTTTTG
2800303 TGAACATATTTACTTTTG
1 TGAACATATTTACTTTTG
2800321 GGATAATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
TGAACATATTTACTTTTG
Found at i:2800608 original size:62 final size:62
Alignment explanation
Indices: 2800511--2800638 Score: 247
Period size: 62 Copynumber: 2.1 Consensus size: 62
2800501 AAAATATCAC
*
2800511 ATCATCACATGGACAAAAGTTGTGAAAAGTAAACAAATTCTAAGACTAATGGAACCAAAAAA
1 ATCATCACATGGACAAAAGTTGTGAAAAGTAAACAAATTCTAAGACTAATGGAACAAAAAAA
2800573 ATCATCACATGGACAAAAGTTGTGAAAAGTAAACAAATTCTAAGACTAATGGAACAAAAAAA
1 ATCATCACATGGACAAAAGTTGTGAAAAGTAAACAAATTCTAAGACTAATGGAACAAAAAAA
2800635 ATCA
1 ATCA
2800639 GGGACTAAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.20
Consensus pattern (62 bp):
ATCATCACATGGACAAAAGTTGTGAAAAGTAAACAAATTCTAAGACTAATGGAACAAAAAAA
Found at i:2806563 original size:29 final size:32
Alignment explanation
Indices: 2806521--2806584 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
2806511 TAGAAAAGAT
*
2806521 AAAATTATACTTTAGCCCCT-AAAAATAATAA
1 AAAATTATACTTTAACCCCTAAAAAATAATAA
* *
2806552 AAAATTA-A-TTTAATCCCTAAAAAATTATAA
1 AAAATTATACTTTAACCCCTAAAAAATAATAA
2806582 AAA
1 AAA
2806585 TAGAGGTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 8 0.28
30 14 0.48
31 7 0.24
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (32 bp):
AAAATTATACTTTAACCCCTAAAAAATAATAA
Found at i:2818683 original size:22 final size:21
Alignment explanation
Indices: 2818658--2818707 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
2818648 TAAAATTTTT
*
2818658 AAAAAAATTTTAAGAAGTGTA
1 AAAAAAAATTTAAGAAGTGTA
*
2818679 AAAAAAAA-TTAAGAAGTTTA
1 AAAAAAAATTTAAGAAGTGTA
*
2818699 AAAATAAAT
1 AAAAAAAAT
2818708 AAAAAATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (21 bp):
AAAAAAAATTTAAGAAGTGTA
Found at i:2826221 original size:17 final size:18
Alignment explanation
Indices: 2826188--2826222 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2826178 ATTATGTATA
*
2826188 TAAATATTTTAATTTTTT
1 TAAATAATTTAATTTTTT
2826206 TAAATAATTT-ATTTTTT
1 TAAATAATTTAATTTTTT
2826223 ATTGTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TAAATAATTTAATTTTTT
Found at i:2831411 original size:22 final size:22
Alignment explanation
Indices: 2831385--2831429 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2831375 TTTTAATAAA
2831385 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
2831407 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
2831429 A
1 A
2831430 CACTCCCCCT
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:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:2836008 original size:22 final size:22
Alignment explanation
Indices: 2835983--2836027 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2835973 TTTAATAAAA
2835983 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
2836005 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
2836027 A
1 A
2836028 CACCATTTAT
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:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:2836035 original size:22 final size:22
Alignment explanation
Indices: 2835991--2836036 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2835981 AAAAAATATC
*
2835991 TACAAAATATTCCTAAAATATT
1 TACAAAATATTCCTAAAACATT
* * *
2836013 TACAGAATATTCCTACACCATT
1 TACAAAATATTCCTAAAACATT
2836035 TA
1 TA
2836037 TTACTGAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (22 bp):
TACAAAATATTCCTAAAACATT
Found at i:2837019 original size:15 final size:16
Alignment explanation
Indices: 2836988--2837020 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2836978 GGACTAGTAC
*
2836988 AAAAGTGCTTTTAGAA
1 AAAAGTGCTGTTAGAA
2837004 AAAAGTGCTGTT-GAA
1 AAAAGTGCTGTTAGAA
2837019 AA
1 AA
2837021 GTGGTGTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.27
Consensus pattern (16 bp):
AAAAGTGCTGTTAGAA
Found at i:2837463 original size:19 final size:19
Alignment explanation
Indices: 2837439--2837481 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2837429 TGTTCTTCAT
*
2837439 CACTTCTGTAGTGGAAAAA
1 CACTTCTGCAGTGGAAAAA
*
2837458 CACTTCTGCAGTGTAAAAA
1 CACTTCTGCAGTGGAAAAA
*
2837477 TACTT
1 CACTT
2837482 TTAACCCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (19 bp):
CACTTCTGCAGTGGAAAAA
Found at i:2842687 original size:16 final size:17
Alignment explanation
Indices: 2842652--2842685 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
2842642 GGTCAGTAAC
2842652 TTATTTCTTTTAAATAT
1 TTATTTCTTTTAAATAT
2842669 TTATTT-TTTT-AATAT
1 TTATTTCTTTTAAATAT
2842684 TT
1 TT
2842686 TAATATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 4 0.24
17 6 0.35
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTCTTTTAAATAT
Found at i:2847223 original size:29 final size:30
Alignment explanation
Indices: 2847159--2847220 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
2847149 TTATTTACGT
2847159 AAATTCCTTAATGCAAAAACTCTTGGTGGA
1 AAATTCCTTAATGCAAAAACTCTTGGTGGA
2847189 AAATTCCTTAATGCAAAAACTCTTGGTGGA
1 AAATTCCTTAATGCAAAAACTCTTGGTGGA
2847219 AA
1 AA
2847221 TTCGTTAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (30 bp):
AAATTCCTTAATGCAAAAACTCTTGGTGGA
Found at i:2847399 original size:41 final size:41
Alignment explanation
Indices: 2847342--2847423 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
2847332 AATGATAAGT
2847342 TTTAAGTCATTTAAGTTTACATAATTTTAATCACTCATAAA
1 TTTAAGTCATTTAAGTTTACATAATTTTAATCACTCATAAA
2847383 TTTAAGTCATTTAAGTTTACATAATTTTAATCACTCATAAA
1 TTTAAGTCATTTAAGTTTACATAATTTTAATCACTCATAAA
2847424 AACAAGTCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (41 bp):
TTTAAGTCATTTAAGTTTACATAATTTTAATCACTCATAAA
Found at i:2847684 original size:35 final size:34
Alignment explanation
Indices: 2847645--2847754 Score: 98
Period size: 35 Copynumber: 3.2 Consensus size: 34
2847635 TTGACTTAGC
*
2847645 TTTATTAATGGAAAATTTAGGTCTTCATTTTTCGT
1 TTTATTAATGGAAAATTTAAGTCTTCA-TTTTCGT
* * * * *
2847680 TTTATTCATGGAAATTTTACA-TCTTTGATTATGGT
1 TTTATTAATGGAAAATTTA-AGTC-TTCATTTTCGT
* *
2847715 TTTATTAATGGAAACTTTAAGTCTTCAGTTT-GCT
1 TTTATTAATGGAAAATTTAAGTCTTCATTTTCG-T
2847749 TTTATT
1 TTTATT
2847755 CTTGCAAATT
Statistics
Matches: 60, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
33 1 0.02
34 13 0.22
35 43 0.72
36 3 0.05
ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52
Consensus pattern (34 bp):
TTTATTAATGGAAAATTTAAGTCTTCATTTTCGT
Found at i:2851617 original size:21 final size:21
Alignment explanation
Indices: 2851591--2851631 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2851581 AGACGAGCGA
* *
2851591 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2851612 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2851632 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2860804 original size:18 final size:18
Alignment explanation
Indices: 2860779--2860820 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2860769 ACAAATAATC
2860779 TTTG-GCTAACCAATAAA
1 TTTGAGCTAACCAATAAA
*
2860796 TTTGAGCTAACCAATAGA
1 TTTGAGCTAACCAATAAA
2860814 TTTGAGC
1 TTTGAGC
2860821 AATAGATAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (18 bp):
TTTGAGCTAACCAATAAA
Found at i:2861608 original size:26 final size:26
Alignment explanation
Indices: 2861571--2861654 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
2861561 TGAAACAAAT
* *
2861571 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2861597 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2861623 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
2861649 TGATAA
1 TGATAA
2861655 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:2863377 original size:27 final size:26
Alignment explanation
Indices: 2863273--2863387 Score: 115
Period size: 27 Copynumber: 4.3 Consensus size: 26
2863263 TGGAGGAAGC
* * *
2863273 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTAGTGGCTCTGCCAC-ATTATCT
* *
2863300 GATCTGGTGGCTCTGCCACATATATCT
1 GTTCTAGTGGCTCTGCCACAT-TATCT
2863327 GTTCT-GTTGGCTCTGCCACGATTATCT
1 GTTCTAG-TGGCTCTGCCAC-ATTATCT
* *
2863354 GTATCTAGTGACTCTGTCACATTATCT
1 GT-TCTAGTGGCTCTGCCACATTATCT
2863381 GTTCTAG
1 GTTCTAG
2863388 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
26 7 0.09
27 54 0.70
28 15 0.19
29 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.37
Consensus pattern (26 bp):
GTTCTAGTGGCTCTGCCACATTATCT
Found at i:2863380 original size:54 final size:54
Alignment explanation
Indices: 2863273--2863385 Score: 147
Period size: 54 Copynumber: 2.1 Consensus size: 54
2863263 TGGAGGAAGC
* *
2863273 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTAGTGACTCTGCCACATATATCT
* * * * *
2863327 GTTCTGTTGGCTCTGCCACGATTATCTGTATCTAGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTAGTGACTCTGCCACATATATCT
2863381 GTTCT
1 GTTCT
2863386 AGCAGCCATG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 34 0.67
55 17 0.33
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTAGTGACTCTGCCACATATATCT
Found at i:2864730 original size:32 final size:31
Alignment explanation
Indices: 2864671--2864730 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
2864661 GCTATGAAAT
* * *
2864671 CAAATTCAGGTACCAATTTAAATAAAAAAAC
1 CAAATTCAGATACCAATTGAAAGAAAAAAAC
*
2864702 CAAATTCAGATACCCAATTGAACGAAAAA
1 CAAATTCAGATA-CCAATTGAAAGAAAAA
2864731 TAATCTTGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 11 0.46
32 13 0.54
ACGTcount: A:0.53, C:0.18, G:0.08, T:0.20
Consensus pattern (31 bp):
CAAATTCAGATACCAATTGAAAGAAAAAAAC
Found at i:2866741 original size:4 final size:4
Alignment explanation
Indices: 2866732--2866793 Score: 85
Period size: 4 Copynumber: 15.8 Consensus size: 4
2866722 GTCCCGTTTC
2866732 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT- TTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
2866778 TTT- TATTA TTCTA TTT
1 TTTA T-TTA TT-TA TTT
2866794 TAATTTTAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
3 7 0.13
4 41 0.77
5 5 0.09
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2866936 original size:3 final size:3
Alignment explanation
Indices: 2866930--2867007 Score: 147
Period size: 3 Copynumber: 25.7 Consensus size: 3
2866920 ATAGCTTTAA
2866930 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2866978 TAT TAT TAT TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
2867008 GTGAATATTT
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 71 0.96
4 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2871308 original size:6 final size:6
Alignment explanation
Indices: 2871297--2871380 Score: 73
Period size: 6 Copynumber: 13.2 Consensus size: 6
2871287 CAACCCAATC
**
2871297 TTTATT TTTATT TTTATT TTTATT TTTATT TATTATT TTCCTT TATT-TCT
1 TTTATT TTTATT TTTATT TTTATT TTTATT T-TTATT TTTATT T-TTAT-T
2871347 TTTATT ATTTATT ATTTATAT TATTA-T TTTATT T
1 TTTATT -TTTATT -TTTAT-T T-TTATT TTTATT T
2871381 ATTTTATTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
5 3 0.04
6 37 0.55
7 23 0.34
8 4 0.06
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:2871314 original size:12 final size:13
Alignment explanation
Indices: 2871297--2871383 Score: 85
Period size: 12 Copynumber: 6.8 Consensus size: 13
2871287 CAACCCAATC
2871297 TTTATTT-TTATT
1 TTTATTTATTATT
2871309 TTTATTT-TTATT
1 TTTATTTATTATT
2871321 TTTATTTATTATT
1 TTTATTTATTATT
**
2871334 TTCCTTTATT-TCT
1 TTTATTTATTAT-T
2871347 TTTA-TTATTTATT
1 TTTATTTA-TTATT
2871360 ATTTATATTATTA-T
1 -TTTAT-TTATTATT
2871374 TTTATTTATT
1 TTTATTTATT
2871384 TTATTTTAGT
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
12 28 0.44
13 24 0.38
14 6 0.09
15 3 0.05
16 3 0.05
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATTATT
Found at i:2871350 original size:9 final size:9
Alignment explanation
Indices: 2871297--2871389 Score: 61
Period size: 9 Copynumber: 10.3 Consensus size: 9
2871287 CAACCCAATC
2871297 TTTATTTTTA
1 TTTA-TTTTA
2871307 TTT-TTATT-
1 TTTATT-TTA
2871315 TTTATTTTTA
1 TTTA-TTTTA
*
2871325 TTTATTAT-
1 TTTATTTTA
**
2871333 TTTCCTTTA
1 TTTATTTTA
*
2871342 TTTCTTTTA
1 TTTATTTTA
2871351 -TTATTTATTA
1 TTTA-TT-TTA
*
2871361 TTTATATTA
1 TTTATTTTA
2871370 -TTATTTTA
1 TTTATTTTA
2871378 TTTATTTTA
1 TTTATTTTA
2871387 TTT
1 TTT
2871390 TAGTTAAATA
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
8 19 0.29
9 31 0.47
10 13 0.20
11 3 0.05
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTTA
Found at i:2871355 original size:41 final size:40
Alignment explanation
Indices: 2871295--2871385 Score: 89
Period size: 41 Copynumber: 2.2 Consensus size: 40
2871285 GGCAACCCAA
* * *
2871295 TCTTTATTTTTATTTTTATTT-TTATTTTTATTTATTATTT
1 TCTTTATTTTTATTATTATTTATTA-TTATATTAATTATTT
2871335 TCCTTTATTTCTT-TTATTATTTATTATTTATATT-ATTATTT
1 T-CTTTATTT-TTATTATTATTTATTA-TTATATTAATTATTT
*
2871376 TATTTATTTT
1 TCTTTATTTT
2871386 ATTTTAGTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
39 1 0.02
40 8 0.18
41 24 0.53
42 12 0.27
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (40 bp):
TCTTTATTTTTATTATTATTTATTATTATATTAATTATTT
Found at i:2872462 original size:118 final size:118
Alignment explanation
Indices: 2872254--2872484 Score: 390
Period size: 118 Copynumber: 2.0 Consensus size: 118
2872244 TGTTTTCCAT
* *
2872254 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
2872319 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
**
2872372 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
****
2872437 CTACTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
2872485 ACCTGAAATA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 105 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:2872626 original size:1 final size:1
Alignment explanation
Indices: 2872610--2872662 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
2872600 AATAAAATTT
* * * * * *
2872610 AAAAAATAAAATAAAAAAAGAAAAAAAGAAAAAAAAAGAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2872663 TAAGTACTAA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.89, C:0.00, G:0.08, T:0.04
Consensus pattern (1 bp):
A
Found at i:2872634 original size:9 final size:9
Alignment explanation
Indices: 2872622--2872662 Score: 66
Period size: 9 Copynumber: 4.6 Consensus size: 9
2872612 AAAATAAAAT
2872622 AAAAAAAG-
1 AAAAAAAGA
2872630 AAAAAAAGAA
1 AAAAAAAG-A
2872640 AAAAAAAGA
1 AAAAAAAGA
2872649 AAAAAAAGA
1 AAAAAAAGA
2872658 AAAAA
1 AAAAA
2872663 TAAGTACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.26
9 15 0.48
10 8 0.26
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:2872643 original size:18 final size:19
Alignment explanation
Indices: 2872622--2872662 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
2872612 AAAATAAAAT
2872622 AAAAAAAG-AAAAAAAGAA
1 AAAAAAAGAAAAAAAAGAA
2872640 AAAAAAAGAAAAAAAAGAA
1 AAAAAAAGAAAAAAAAGAA
2872659 AAAA
1 AAAA
2872663 TAAGTACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAAGAA
Found at i:2874396 original size:12 final size:12
Alignment explanation
Indices: 2874379--2874403 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2874369 TATTATGTTT
2874379 TTTTTAATACCA
1 TTTTTAATACCA
2874391 TTTTTAATACCA
1 TTTTTAATACCA
2874403 T
1 T
2874404 GTATGTTGTG
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:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTTAATACCA
Found at i:2886574 original size:66 final size:66
Alignment explanation
Indices: 2886466--2886626 Score: 200
Period size: 66 Copynumber: 2.5 Consensus size: 66
2886456 CATACATCAC
* * * *
2886466 TCATAACACATCTAATTAGGAGCATTTGATTCATTTCAATCATAGCATTCTAGTTATTTGATTCA
1 TCATAACACATCTAATTAAGAGCATTTGATTCATTTCAATCATACCATCCTAATTATTTGATTCA
2886531 T
66 T
* * * **
2886532 TCATAACACGTTTAATTAAGAGCATTTGATTCATTTCGATCATACCATCCTAATTATTTGACACA
1 TCATAACACATCTAATTAAGAGCATTTGATTCATTTCAATCATACCATCCTAATTATTTGATTCA
2886597 T
66 T
* * *
2886598 CCAT--CACATCTAGTTAGGAGCATTTGATT
1 TCATAACACATCTAATTAAGAGCATTTGATT
2886627 TGACCATGGC
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 21 0.26
66 60 0.74
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.39
Consensus pattern (66 bp):
TCATAACACATCTAATTAAGAGCATTTGATTCATTTCAATCATACCATCCTAATTATTTGATTCA
T
Found at i:2886811 original size:45 final size:45
Alignment explanation
Indices: 2886760--2886874 Score: 203
Period size: 45 Copynumber: 2.6 Consensus size: 45
2886750 AAAATTACAG
**
2886760 ATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCAAATCCCGTGA
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCAAATCCCACGA
2886805 ATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCAAATCCCACGA
1 ATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCAAATCCCACGA
*
2886850 ATCTTGTCTTCCTGAAGTTGCAGTG
1 ATCTTGTCTCCCTGAAGTTGCAGTG
2886875 AAGTAGATTG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (45 bp):
ATCTTGTCTCCCTGAAGTTGCAGTGGAACAGATCAAATCCCACGA
Found at i:2887128 original size:43 final size:42
Alignment explanation
Indices: 2887080--2887272 Score: 169
Period size: 43 Copynumber: 4.5 Consensus size: 42
2887070 AGCCTTAACC
2887080 CCCTAAGCAGTAGGGAAACAGGCTAAACTTACAGATCTTATCA
1 CCCTAAGCAGTAGGGAAACAGGCTAAA-TTACAGATCTTATCA
* * * *
2887123 CCCTAAGCAGTAGGGAAACA-GATCAAGGA-TA-ATGAGCTTTAACC
1 CCCTAAGCAGTAGGGAAACAGGCT-AA--ATTACA-GATC-TTATCA
* * * * * *
2887167 CCCTAAGCAGTAGGGTAACAAGCTCAATTTACAGACCTCA-AA
1 CCCTAAGCAGTAGGGAAACAGGCT-AAATTACAGATCTTATCA
* * *
2887209 CCCCTAAGCAGTAGGGTAACAGGGTAAATTGCAGATCTTATCA
1 -CCCTAAGCAGTAGGGAAACAGGCTAAATTACAGATCTTATCA
2887252 CCCTAAGCAGTAGGGAAACAG
1 CCCTAAGCAGTAGGGAAACAG
2887273 ATCAAAGAAG
Statistics
Matches: 121, Mismatches: 19, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
42 34 0.28
43 52 0.43
44 28 0.23
45 7 0.06
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (42 bp):
CCCTAAGCAGTAGGGAAACAGGCTAAATTACAGATCTTATCA
Found at i:2887310 original size:129 final size:130
Alignment explanation
Indices: 2887079--2887313 Score: 377
Period size: 129 Copynumber: 1.8 Consensus size: 130
2887069 AAGCCTTAAC
2887079 CCCCTAAGCAGTAGGGAAACAGGCTAAACTTACAGATCTTATCACCCTAAGCAGTAGGGAAACAG
1 CCCCTAAGCAGTAGGGAAACAGGCTAAACTTACAGATCTTATCACCCTAAGCAGTAGGGAAACAG
* *
2887144 ATCAAGGATAATGAGCTTTAACCCCCTAAGCAGTAGGGTAACAAGCTCAATTTACAGACCTCAAA
66 ATCAAAGATAATGAGCCTTAACCCCCTAAGCAGTAGGGTAACAAGCTCAATTTACAGACCTCAAA
* * *
2887209 CCCCTAAGCAGTAGGGTAACAGGGTAAA-TTGCAGATCTTATCACCCTAAGCAGTAGGGAAACAG
1 CCCCTAAGCAGTAGGGAAACAGGCTAAACTTACAGATCTTATCACCCTAAGCAGTAGGGAAACAG
*
2887273 ATCAAAGA-AGATGGGCCTTAACCCCCTAAGC-GATAGGGTAA
66 ATCAAAGATA-ATGAGCCTTAACCCCCTAAGCAG-TAGGGTAA
2887314 TAGGCTGAAA
Statistics
Matches: 97, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
128 2 0.02
129 69 0.71
130 26 0.27
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.19
Consensus pattern (130 bp):
CCCCTAAGCAGTAGGGAAACAGGCTAAACTTACAGATCTTATCACCCTAAGCAGTAGGGAAACAG
ATCAAAGATAATGAGCCTTAACCCCCTAAGCAGTAGGGTAACAAGCTCAATTTACAGACCTCAAA
Done.