Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
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 11 of 425
Found at i:3069256 original size:21 final size:20
Alignment explanation
Indices: 3069232--3069271 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3069222 TTAGTTATCA
3069232 ATTTTCTATTCAGTTCAATCG
1 ATTTTCTATT-AGTTCAATCG
* *
3069253 ATTTTTTATTAGTTTAATC
1 ATTTTCTATTAGTTCAATC
3069272 TTTTTTCGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.55
Consensus pattern (20 bp):
ATTTTCTATTAGTTCAATCG
Found at i:3073470 original size:19 final size:21
Alignment explanation
Indices: 3073437--3073475 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
3073427 AATTAATTAA
3073437 TTAAGATTTTCATTAAAAATT
1 TTAAGATTTTCATTAAAAATT
*
3073458 TTAA-ATTTT-ATTAGAAAT
1 TTAAGATTTTCATTAAAAAT
3073476 ATATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 5 0.29
21 4 0.24
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (21 bp):
TTAAGATTTTCATTAAAAATT
Found at i:3076056 original size:18 final size:18
Alignment explanation
Indices: 3076029--3076064 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3076019 TTTTAAAAAA
3076029 TATAAAATTTAGAATTTT
1 TATAAAATTTAGAATTTT
* *
3076047 TATAATATTTTGAATTTT
1 TATAAAATTTAGAATTTT
3076065 AAAAATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TATAAAATTTAGAATTTT
Found at i:3076991 original size:30 final size:30
Alignment explanation
Indices: 3076957--3077080 Score: 196
Period size: 30 Copynumber: 4.2 Consensus size: 30
3076947 ATAAAAAAAA
*
3076957 CACCAACTCCACTAGCCACATTTGCTCCAC
1 CACCAACTCCACTAGCCACACTTGCTCCAC
3076987 CACCAACTCCACTAGCCACACTTGCTCCAC
1 CACCAACTCCACTAGCCACACTTGCTCCAC
* *
3077017 CACCTAC-CCACTAGCCACATTTGCTCCAC
1 CACCAACTCCACTAGCCACACTTGCTCCAC
* *
3077046 CACCTACTCCATTAGCCACACTTGCTCCAC
1 CACCAACTCCACTAGCCACACTTGCTCCAC
3077076 CACCA
1 CACCA
3077081 CTTGTACCTA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
29 28 0.32
30 59 0.68
ACGTcount: A:0.26, C:0.48, G:0.06, T:0.19
Consensus pattern (30 bp):
CACCAACTCCACTAGCCACACTTGCTCCAC
Found at i:3077062 original size:59 final size:59
Alignment explanation
Indices: 3076965--3077079 Score: 212
Period size: 59 Copynumber: 1.9 Consensus size: 59
3076955 AACACCAACT
3076965 CCACTAGCCACATTTGCTCCACCACCAACTCCACTAGCCACACTTGCTCCACCACCTAC
1 CCACTAGCCACATTTGCTCCACCACCAACTCCACTAGCCACACTTGCTCCACCACCTAC
* *
3077024 CCACTAGCCACATTTGCTCCACCACCTACTCCATTAGCCACACTTGCTCCACCACC
1 CCACTAGCCACATTTGCTCCACCACCAACTCCACTAGCCACACTTGCTCCACCACC
3077080 ACTTGTACCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.24, C:0.49, G:0.07, T:0.20
Consensus pattern (59 bp):
CCACTAGCCACATTTGCTCCACCACCAACTCCACTAGCCACACTTGCTCCACCACCTAC
Found at i:3077638 original size:27 final size:25
Alignment explanation
Indices: 3077546--3077741 Score: 102
Period size: 25 Copynumber: 7.9 Consensus size: 25
3077536 ATTATATTTC
*
3077546 TTAATATTATATTATGTATATAT-T
1 TTAATACTATATTATGTATATATAT
* * * *
3077570 TT-TTAATATATTAGGTATAT-T-C
1 TTAATACTATATTATGTATATATAT
* * *
3077592 TAAATTCTATATTACGTATATATAT
1 TTAATACTATATTATGTATATATAT
* *
3077617 ATT-ATACTATTTTATGTATATATCT
1 -TTAATACTATATTATGTATATATAT
* *
3077642 TTAATACTATATTATTTATATATTTTTT
1 TTAATACTATATTATGTATATA---TAT
** *
3077670 TCTACATGTTATCTTATGTATATAT-T
1 T-TA-ATACTATATTATGTATATATAT
* *
3077696 TTAAT--TATATTATGTATGTATTT
1 TTAATACTATATTATGTATATATAT
* * *
3077719 TTTACACTATATTATGTACATAT
1 TTAATACTATATTATGTATATAT
3077742 TTTTTTATAT
Statistics
Matches: 131, Mismatches: 28, Indels: 25
0.71 0.15 0.14
Matches are distributed among these distances:
22 16 0.12
23 33 0.25
24 7 0.05
25 51 0.39
26 3 0.02
27 1 0.01
28 3 0.02
29 2 0.02
30 15 0.11
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (25 bp):
TTAATACTATATTATGTATATATAT
Found at i:3077731 original size:77 final size:81
Alignment explanation
Indices: 3077610--3077780 Score: 197
Period size: 77 Copynumber: 2.2 Consensus size: 81
3077600 ATATTACGTA
* * * * * *
3077610 TATATATATTATACTATTTTATGTATATATCTTTAATACTATATTATTTATATATTTTTTTCTA-
1 TATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTATAT
*
3077674 C-ATGTTAT-CTTATG
66 CTATGTTATACATATG
* * * *
3077688 TATATATTTTA-ATTATATTATGTATGTATTTTTTACACTATATTATGTACATATTTTTTTATAT
1 TATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTATAT
*
3077752 CTATTTTATACATATG
66 CTATGTTATACATATG
*
3077768 TATATATTATATA
1 TATATATTTTATA
3077781 TATCTTAACA
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
77 43 0.57
78 11 0.14
79 6 0.08
80 15 0.20
81 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (81 bp):
TATATATTTTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATTTTTTTATAT
CTATGTTATACATATG
Found at i:3077755 original size:27 final size:25
Alignment explanation
Indices: 3077539--3077760 Score: 70
Period size: 25 Copynumber: 8.8 Consensus size: 25
3077529 TGTTATTATT
* * *
3077539 ATATTTCTTAATATTATATTATGTAT
1 ATATTTTTTAAT-CTATATTATGTAC
*
3077565 ATATTTTTTAA--TATATTAGGT--
1 ATATTTTTTAATCTATATTATGTAC
* * * *
3077586 ATA-TTCTAAATTCTATATTACGTAT
1 ATATTTTTTAA-TCTATATTATGTAC
* * * *
3077611 ATATATATT-ATACTATTTTATGTAT
1 ATATTTTTTAAT-CTATATTATGTAC
* * *
3077636 ATA-TCTTTAATACTATATTATTTAT
1 ATATTTTTTAAT-CTATATTATGTAC
* *
3077661 ATATTTTTTTCTACATGTTATCTTATGT--
1 ATA--TTTTT-TA-AT-CTATATTATGTAC
* *
3077689 ATATATTTTAAT-TATATTATGTAT
1 ATATTTTTTAATCTATATTATGTAC
*
3077713 GTATTTTTTACA-CTATATTATGTAC
1 ATATTTTTTA-ATCTATATTATGTAC
*
3077738 ATATTTTTTTATATCTATTTTAT
1 ATA-TTTTTTA-ATCTATATTAT
3077761 ACATATGTAT
Statistics
Matches: 149, Mismatches: 28, Indels: 37
0.70 0.13 0.17
Matches are distributed among these distances:
20 5 0.03
21 3 0.02
22 9 0.06
23 18 0.12
24 13 0.09
25 51 0.34
26 24 0.16
27 8 0.05
28 6 0.04
29 2 0.01
30 10 0.07
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.57
Consensus pattern (25 bp):
ATATTTTTTAATCTATATTATGTAC
Found at i:3077835 original size:25 final size:24
Alignment explanation
Indices: 3077807--3077872 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
3077797 GTTATATTTT
*
3077807 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
3077832 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
3077855 CACTATTACTATA-TATAT
1 CACTATTA-TATAGTATAT
3077873 ATATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
23 10 0.28
24 11 0.31
25 15 0.42
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:3077871 original size:2 final size:2
Alignment explanation
Indices: 3077864--3077888 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3077854 ACACTATTAC
3077864 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
3077889 TTACGTACAT
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:3084471 original size:14 final size:14
Alignment explanation
Indices: 3084454--3084482 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3084444 AAAAGATCTT
3084454 AAAAAAAAGAAAAG
1 AAAAAAAAGAAAAG
3084468 AAAAAAAAGAAAAG
1 AAAAAAAAGAAAAG
3084482 A
1 A
3084483 GAGAGGGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAG
Found at i:3085477 original size:89 final size:87
Alignment explanation
Indices: 3085343--3085777 Score: 375
Period size: 89 Copynumber: 4.7 Consensus size: 87
3085333 TATCTTTCAA
*
3085343 AAAAATCAACTCATATTGCGAGAGGTGAGTTG-GCCTCAGGTCACACGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GG-GACACGCTGAGGTATTTTCAATT
3085407 TCCGTTTTTTCAATTTATGCTTTTC
64 TCCG-TTTTTCAATTTATGCTTTTC
* *
3085432 AAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGCACAC-C-GAGGTATTTTTAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-ACACGCTGAGGTATTTTCAATTT
* *
3085495 CTGTTTTTCAATTTCTGCTTTT-
65 CCGTTTTTCAATTTATGCTTTTC
3085517 AATTTCTGTTTTTAAA-CAACTCATATTGCGAGAGGTGAGTTGAGCCT-GGG-CACGCT-AGGTA
1 AA-----------AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA
*
3085578 TTTTCAATTTCTGTTTTTCAATTTCCTTACTGCTTTTC
55 TTTTCAATTTCCGTTTTTCAA--T--TTA-TGCTTTTC
** *
3085616 AAATTCTGCTTTTCTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATT
1 AAA---------AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATT
* * *
3085681 TTCAATTTTCGTTTTTTTAATTTATG-TTTCTAA
57 TTCAATTTCCG-TTTTTCAATTTATGCTTT-T-C
* * * *
3085714 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGATACGCTGAGGTAATTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTT
3085778 TTGTTTGTCA
Statistics
Matches: 289, Mismatches: 20, Indels: 74
0.75 0.05 0.19
Matches are distributed among these distances:
85 2 0.01
86 18 0.06
87 17 0.06
88 2 0.01
89 93 0.32
90 5 0.02
92 3 0.01
93 26 0.09
94 3 0.01
95 31 0.11
96 6 0.02
97 5 0.02
98 44 0.15
99 4 0.01
100 7 0.02
101 16 0.06
102 7 0.02
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTATTTTCAATTTC
CGTTTTTCAATTTATGCTTTTC
Found at i:3085520 original size:13 final size:13
Alignment explanation
Indices: 3085485--3085531 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
3085475 CACCGAGGTA
3085485 TTTTTAATTTCTG
1 TTTTTAATTTCTG
3085498 TTTTTCAATTTCTG
1 TTTTT-AATTTCTG
*
3085512 CTTTTAATTTCTG
1 TTTTTAATTTCTG
3085525 TTTTTAA
1 TTTTTAA
3085532 ACAACTCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 19 0.61
14 12 0.39
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:3085651 original size:98 final size:94
Alignment explanation
Indices: 3085435--3085696 Score: 332
Period size: 98 Copynumber: 2.7 Consensus size: 94
3085425 GCTTTTCAAA
* * * *
3085435 AATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGCACACCGAGGTATTTTTAATTTCTGTT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCAC-GCTAGGTATTTTCAATTTCTGTT
* *
3085500 TTTCAATTTCTGCTTTTAATTTCTGTTTTT
65 TTTCAATTTCTGCTTTTAAATTCTGCTTTT
*
3085530 AAACAACTCATATTGCGAGAGGTGAGTTGAGCCT-GGGCACGCTAGGTATTTTCAATTTCTGTTT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTAGGTATTTTCAATTTCTGTTT
3085594 TTCAATTTCCTTACTGCTTTTCAAATTCTGCTTTT
66 TTCAA--T--TT-CTGCTTTT-AAATTCTGCTTTT
* *
3085629 -CTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTT-TCG
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACGCT-AGGTATTTTCAATTTCT-G
3085692 TTTTT
63 TTTTT
3085697 TTAATTTATG
Statistics
Matches: 147, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
93 26 0.18
94 6 0.04
95 33 0.22
97 2 0.01
98 39 0.27
99 11 0.07
100 9 0.06
101 21 0.14
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (94 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACGCTAGGTATTTTCAATTTCTGTTT
TTCAATTTCTGCTTTTAAATTCTGCTTTT
Found at i:3086043 original size:75 final size:73
Alignment explanation
Indices: 3085694--3086269 Score: 713
Period size: 75 Copynumber: 7.8 Consensus size: 73
3085684 AATTTTCGTT
* * * * *
3085694 TTTTTAATTTATGTTTCTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGATAC
1 TTTTCAATTTCTGTTT-TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
*
3085759 GCTGAGGTA
65 GTTGAGGTA
* * * * *
3085768 ATTTCAATTTTTGTTTGT-CAAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACAC
1 TTTTCAATTTCTGTTT-TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
3085832 GTTGAGG--
65 GTTGAGGTA
* *
3085839 TTTTCAATTTCT-TTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACAC
1 TTTTCAATTTCTGTTTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
*
3085903 GCTGAGGTA
65 GTTGAGGTA
* * *
3085912 ATTTCAATTTTTGTTTGT--CAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
1 TTTTCAATTTCTGTTT-TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
3085975 GTTGAGGTA
65 GTTGAGGTA
* * *
3085984 TTTTCAATTTCTGTCTTTAAAAAAAATCAGCGCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGT-TTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
3086049 CGTTGAGGTA
64 CGTTGAGGTA
* * *
3086059 TTTTCAATTTCTGTTTTTCAAAAAAATCAACACATATTGCGATAGGTGAGTTGAACCTCAAG--A
1 TTTTCAATTTCTG-TTTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
3086122 CGCTGAGGTAA
64 CGTTGAGGT-A
* *
3086133 TAATTTCAATTTTTGTTTGT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
1 T--TTTCAATTTCTGTTT-TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
3086197 ACGTTGAGGTA
63 ACGTTGAGGTA
* *
3086208 TTTTCAATTTCTGTCTTTAAAAAAATCAGCTCATA-TGCGAGAGGTGAGTTGAACCTCAAGAC
1 TTTTCAATTTCTGT-TTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
3086270 GCTGAGGTGT
Statistics
Matches: 437, Mismatches: 46, Indels: 39
0.84 0.09 0.07
Matches are distributed among these distances:
69 1 0.00
70 3 0.01
71 57 0.13
72 63 0.14
73 106 0.24
74 73 0.17
75 112 0.26
76 22 0.05
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (73 bp):
TTTTCAATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
TTGAGGTA
Found at i:3086056 original size:147 final size:145
Alignment explanation
Indices: 3085694--3086269 Score: 718
Period size: 147 Copynumber: 3.9 Consensus size: 145
3085684 AATTTTCGTT
* * * * *
3085694 TTTTTAATTTATGTTTCTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGATAC
1 TTTTCAATTTCTGTTT-TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
* * *
3085759 GCTGAGGTAATTTCAATTTTTGTTTGTCAAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCCT
65 GCTGAGGTAATTTCAATTTCTGTTTGTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAACCT
3085824 CAAGACACGTTGAGG--
129 CAAGACACGTTGAGGTA
* *
3085839 TTTTCAATTTCT-TTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACAC
1 TTTTCAATTTCTGTTTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
* *
3085903 GCTGAGGTAATTTCAATTTTTGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
65 GCTGAGGTAATTTCAATTTCTGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
3085968 AAGACACGTTGAGGTA
130 AAGACACGTTGAGGTA
* * *
3085984 TTTTCAATTTCTGTCTTTAAAAAAAATCAGCGCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGT-TTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * * * *
3086049 CGTTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACACATATTGCGATAGGTGAGTTGAA
64 CGCTGAGGTAATTTCAATTTCTGTTTGTC---AAAATCAACTCATATTGCGAGAGGTGAGTTGAA
*
3086114 CCTCAAG--ACGCTGAGGTAA
126 CCTCAAGACACGTTGAGGT-A
* *
3086133 TAATTTCAATTTTTGTTTGT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
1 T--TTTCAATTTCTGTTT-TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGAC
* * * *
3086197 ACGTTGAGGTATTTTCAATTTCTGTCTT-TAAAAAAATCAGCTCATA-TGCGAGAGGTGAGTTGA
63 ACGCTGAGGTAATTTCAATTTCTGT-TTGT--CAAAATCAACTCATATTGCGAGAGGTGAGTTGA
3086260 ACCTCAAGAC
125 ACCTCAAGAC
3086270 GCTGAGGTGT
Statistics
Matches: 385, Mismatches: 29, Indels: 30
0.87 0.07 0.07
Matches are distributed among these distances:
143 47 0.12
144 79 0.21
145 22 0.06
146 1 0.00
147 93 0.24
148 21 0.05
149 68 0.18
150 41 0.11
151 13 0.03
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (145 bp):
TTTTCAATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
CTGAGGTAATTTCAATTTCTGTTTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCA
AGACACGTTGAGGTA
Found at i:3086416 original size:91 final size:89
Alignment explanation
Indices: 3086268--3086741 Score: 439
Period size: 91 Copynumber: 5.3 Consensus size: 89
3086258 GAACCTCAAG
* * * * *
3086268 ACGCTGAGGTGTTTTCCATTT-TGTTCTTCAATTTTGTGTTTCAAAAAAATCAGCTCATATTGCG
1 ACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTTGTTTTTCAAAAAAATCAACTCATATTGCG
*
3086332 AGTGGTGAGTTGAGCCTTGACTCAC
66 AGAGGTGAGTTGAGCCTTGA-TCAC
* * *
3086357 ACGCTGAGGTATTTTCAAATTCTATTTTTCAAATTTTGTTTTTCTAAAAAATCAACTCATATT-C
1 ACGCTGAGGTATTTTCAATTTCTGTTTTTC-AATTTTGTTTTTCAAAAAAATCAACTCATATTGC
* * **
3086421 GAGAGGTGAGTTCAG-C-TCAGGAC
65 GAGAGGTGAGTTGAGCCTTGATCAC
* * *
3086444 ACGCTGAGATATTTTCAATTTCTTTTTTTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTG
1 ACGCTGAGGTATTTTCAATTTC-TGTTTTTCAATTT-TGTTTTTCAAAAAAATCAACTCATATTG
*
3086509 CGAGAGGTGAGTTGAGCCTCAGATCAC
64 CGAGAGGTGAGTTGAGCCT-TGATCAC
* * * * * *
3086536 ACGCCGAGGTATTTTCAATTGGTTTTTTTTTCAATTCATGCTTTGC--AAAAATCAACTCATATT
1 ACGCTGAGGTATTTTCAATT--TCTGTTTTTCAATT-TTGTTTTTCAAAAAAATCAACTCATATT
* * *
3086599 ACGAGAGGTGAGTTGAGCCTCGGGTCAC
63 GCGAGAGGTGAGTTGAGCCT-TGATCAC
** * ** *
3086627 ATACCGAGGTATTTTCAAAATCTGTTTTACAAATTTTG-TTTT---AAAAATCAACTCATATTGC
1 ACGCTGAGGTATTTTCAATTTCTGTTTTTC-AATTTTGTTTTTCAAAAAAATCAACTCATATTGC
* *
3086688 GA-AAGTGAGTTGAGCCTTGGCTCAC
65 GAGAGGTGAGTTGAGCCTT-GATCAC
** *
3086713 GTGCTGAGCTATTTTCAATTTCTGTTTTT
1 ACGCTGAGGTATTTTCAATTTCTGTTTTT
3086742 AATGTCTAGT
Statistics
Matches: 319, Mismatches: 53, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
86 41 0.13
87 47 0.15
88 37 0.12
89 43 0.13
90 25 0.08
91 87 0.27
92 21 0.07
93 17 0.05
94 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (89 bp):
ACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTTGTTTTTCAAAAAAATCAACTCATATTGCG
AGAGGTGAGTTGAGCCTTGATCAC
Found at i:3086522 original size:179 final size:175
Alignment explanation
Indices: 3086227--3086796 Score: 513
Period size: 179 Copynumber: 3.2 Consensus size: 175
3086217 TCTGTCTTTA
* * * * * *
3086227 AAAAAATCAGCTCATATGCGAGAGGTGAGTTGAACCTCA--AGACGCTGAGGTGTTTTCCATT-T
1 AAAAAATCAACTCATATTCGAGAGGTGAGTT-AAGCTCAGGACACGCTGAGGTATTTTCAATTCT
* * *
3086289 TGTTCTTCAATTTTGTGTTTCAAAAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCTTGACT
65 TGTTTTTCAATTTTGT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACT
* * * *
3086354 CACACGCTGAGGTATTTTCAAATTCTATTTTTCAAATT-TTGTTTTTC
129 CACACGCTGAGGTATTTTCAATTTCTATTTTTC-AATTCATGCTTTGC
* *
3086401 TAAAAAATCAACTCATATTCGAGAGGTGAGTTCAGCTCAGGACACGCTGAGATATTTTCAATTTC
1 -AAAAAATCAACTCATATTCGAGAGGTGAGTTAAGCTCAGGACACGCTGAGGTATTTTCAA-TTC
* *
3086466 TTTTTTTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
64 TTGTTTTTCAATTT-TGTTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-TG
* * *
3086531 A-TCACACGCCGAGGTATTTTCAATTGGTTTTTTTTTCAATTCATGCTTTGC
126 ACTCACACGCTGAGGTATTTTCAATT--TCTATTTTTCAATTCATGCTTTGC
* * ** *
3086582 -AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAAA
1 AAAAAATCAACTCATATT-CGAGAGGTGAGTTAAG-CTCAGG--ACACGCTGAGGTATTTTC-AA
* * *
3086646 ATC-TGTTTTACAAATTTTGTTTT---AAAAATCAACTCATATTGCGA-AAGTGAGTTGAGCCTT
61 TTCTTGTTTTTC-AATTTTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
* ** * * *
3086706 GGCTCACGTGCTGAGCTATTTTCAATTTCTGTTTTT-AATGTC-TAG-TTT-T
125 GACTCACACGCTGAGGTATTTTCAATTTCTATTTTTCAAT-TCAT-GCTTTGC
* * * **
3086755 AAAGAGTCAATTCATATTGCGAGAAATGAGTTAAGCTCAGGA
1 AAAAAATCAACTCATATT-CGAGAGGTGAGTTAAGCTCAGGA
3086797 TCACATGTCG
Statistics
Matches: 328, Mismatches: 47, Indels: 44
0.78 0.11 0.11
Matches are distributed among these distances:
171 1 0.00
173 5 0.02
174 39 0.12
175 39 0.12
176 17 0.05
177 36 0.11
178 35 0.11
179 81 0.25
180 21 0.06
181 20 0.06
182 11 0.03
183 21 0.06
184 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (175 bp):
AAAAAATCAACTCATATTCGAGAGGTGAGTTAAGCTCAGGACACGCTGAGGTATTTTCAATTCTT
GTTTTTCAATTTTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGACTCA
CACGCTGAGGTATTTTCAATTTCTATTTTTCAATTCATGCTTTGC
Found at i:3086880 original size:21 final size:21
Alignment explanation
Indices: 3086854--3086893 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3086844 TTTTATATCC
3086854 TTGAAGTTACAGTGAAGCTAA
1 TTGAAGTTACAGTGAAGCTAA
* *
3086875 TTGAAGTTGCAGTGGAGCT
1 TTGAAGTTACAGTGAAGCT
3086894 GATCGATGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (21 bp):
TTGAAGTTACAGTGAAGCTAA
Found at i:3087467 original size:30 final size:30
Alignment explanation
Indices: 3087422--3087550 Score: 168
Period size: 30 Copynumber: 4.3 Consensus size: 30
3087412 CTAGCCTTTG
3087422 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* * *
3087452 CCACCATCAATTCCACTAGCCACACTTGTT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
3087482 CCACCAACTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* * ** *
3087512 CTACCACCTACTTTATTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
3087542 CCACCACCA
1 CCACCACCA
3087551 CTTGTACCTA
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 85 1.00
ACGTcount: A:0.26, C:0.45, G:0.06, T:0.22
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:3088077 original size:24 final size:24
Alignment explanation
Indices: 3088029--3088110 Score: 71
Period size: 23 Copynumber: 3.5 Consensus size: 24
3088019 TTTTTTTTGT
*
3088029 TATTAT-TATATTTCTTAATATTA
1 TATTATGTATATTTCTTAATAATA
*
3088052 TATTATGTATATATTCTT-TTAATA
1 TATTATGTATAT-TTCTTAATAATA
* * **
3088076 TATTAGGTATA-TTCTAAATTCTA
1 TATTATGTATATTTCTTAATAATA
*
3088099 TATTACGTATAT
1 TATTATGTATAT
3088111 ATATATTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
22 4 0.09
23 19 0.40
24 19 0.40
25 5 0.11
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (24 bp):
TATTATGTATATTTCTTAATAATA
Found at i:3088206 original size:22 final size:22
Alignment explanation
Indices: 3088176--3088217 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3088166 TTTCTACATG
*
3088176 TTATCTTATGTATATATTTTAA
1 TTATATTATGTATATATTTTAA
*
3088198 TTATATTATGTATGTATTTT
1 TTATATTATGTATATATTTT
3088218 TTACGCTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (22 bp):
TTATATTATGTATATATTTTAA
Found at i:3088333 original size:25 final size:24
Alignment explanation
Indices: 3088305--3088360 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
3088295 GTTATATTTT
*
3088305 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
3088330 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
3088353 CACTATTA
1 CACTATTA
3088361 CTATTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:3088373 original size:2 final size:2
Alignment explanation
Indices: 3088366--3088392 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3088356 TATTACTATT
3088366 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
3088393 TACGTACATA
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:3090238 original size:4 final size:4
Alignment explanation
Indices: 3090229--3090259 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3090219 GGTCCATAAC
3090229 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
3090260 ATGAAGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:3091511 original size:197 final size:197
Alignment explanation
Indices: 3091301--3091816 Score: 870
Period size: 201 Copynumber: 2.6 Consensus size: 197
3091291 ACATATACAT
* *
3091301 ATACATACACACACACATATATATATATATATGCAAAATGATATTTAAGAAAAACCCAAAGAGGT
1 ATACATACACACACACATATATATATATATATGCAAAATGATATTTAAGGAAAACCCAAAGAGCT
* *
3091366 GATTAATGTAAAACTTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATA
66 GGTTAATGTAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATA
3091431 TCAAAGTAAAAAGGGTTATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGCCATACCTGC
131 TCAAAGTAAAAAGGGTTATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGCCATACCTGC
3091496 AA
196 AA
*
3091498 ATACATACACACACACACATATATATATATATCTAAGCAAAATGATATTTAAGGAAAACCCAAAG
1 ATACAT--ACACACACACATATATATATATA--TATGCAAAATGATATTTAAGGAAAACCCAAAG
* *
3091563 CGCTGGTTAATGTAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATTGCAGAAAGG
62 AGCTGGTTAATGTAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGG
3091628 AATATCAAAGTAAAAAGGGTTATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGCCATAC
127 AATATCAAAGTAAAAAGGGTTATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGCCATAC
3091693 CTGCAA
192 CTGCAA
* * * * ** *
3091699 ATACATACATATATATATATGCAAATATATATGCAAAATGATATTTAAGGAAAACCCAAAGAGCT
1 ATACATACACACACACATATATATATATATATGCAAAATGATATTTAAGGAAAACCCAAAGAGCT
3091764 GGTTAATGTAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATGG
66 GGTTAATGTAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATGG
3091817 AAGCAAGGTA
Statistics
Matches: 298, Mismatches: 17, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
197 92 0.31
199 39 0.13
201 167 0.56
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (197 bp):
ATACATACACACACACATATATATATATATATGCAAAATGATATTTAAGGAAAACCCAAAGAGCT
GGTTAATGTAAACCTTAAGACAGATCACAAATATCACTTAATAATTAAGATGGCAGAAAGGAATA
TCAAAGTAAAAAGGGTTATCAATGGCTGTCATGCAATGTGAGGCACATATTAAGGCCATACCTGC
AA
Found at i:3091742 original size:14 final size:12
Alignment explanation
Indices: 3091711--3091735 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3091701 ACATACATAT
3091711 ATATATATGCAA
1 ATATATATGCAA
3091723 ATATATATGCAA
1 ATATATATGCAA
3091735 A
1 A
3091736 ATGATATTTA
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
ATATATATGCAA
Found at i:3096880 original size:2 final size:2
Alignment explanation
Indices: 3096873--3096898 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3096863 TTACAAATCG
3096873 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
3096899 AATTTAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3099407 original size:5 final size:5
Alignment explanation
Indices: 3099397--3099423 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3099387 AAAATTTGTG
3099397 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
3099424 TCACAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:3099679 original size:33 final size:33
Alignment explanation
Indices: 3099634--3099699 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
3099624 GAAAAAGCGT
3099634 AAGGATCAAAAGACGTTAACACAATTACATCTG
1 AAGGATCAAAAGACGTTAACACAATTACATCTG
*
3099667 AAGGATCGAAAGACGTTAACACAATTACATCTG
1 AAGGATCAAAAGACGTTAACACAATTACATCTG
3099700 CATTTATCCA
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:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (33 bp):
AAGGATCAAAAGACGTTAACACAATTACATCTG
Found at i:3104912 original size:16 final size:18
Alignment explanation
Indices: 3104885--3104917 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3104875 TGAAAATAAG
3104885 TTTAATTAAAAT-ATTAT
1 TTTAATTAAAATGATTAT
3104902 TTTAA-TAAAATGATTA
1 TTTAATTAAAATGATTA
3104918 AATTCCACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (18 bp):
TTTAATTAAAATGATTAT
Found at i:3105132 original size:21 final size:21
Alignment explanation
Indices: 3105088--3105130 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3105078 TAATAACTAA
3105088 TGATAAATTAATTAATTAATT
1 TGATAAATTAATTAATTAATT
* *
3105109 TGATAACTTATATTTATTAATT
1 TGATAAATTA-ATTAATTAATT
3105131 GAACTTGTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
TGATAAATTAATTAATTAATT
Found at i:3109214 original size:6 final size:6
Alignment explanation
Indices: 3109203--3109227 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3109193 AATCAAAATT
3109203 ATTATA ATTATA ATTATA ATTATA A
1 ATTATA ATTATA ATTATA ATTATA A
3109228 AAATAATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTATA
Found at i:3113638 original size:27 final size:27
Alignment explanation
Indices: 3113600--3113664 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
3113590 AGGATAAATA
3113600 TTAAATTATACATAGAATTTAATTTTGT
1 TTAAA-TATACATAGAATTTAATTTTGT
3113628 TTAAATATACATAGAATTTAATTTTGT
1 TTAAATATACATAGAATTTAATTTTGT
3113655 TTAAATATAC
1 TTAAATATAC
3113665 TGTAGAAGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 32 0.86
28 5 0.14
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (27 bp):
TTAAATATACATAGAATTTAATTTTGT
Found at i:3114068 original size:31 final size:32
Alignment explanation
Indices: 3114002--3114072 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
3113992 TTACCATAAT
* *
3114002 TATACATATTAAACTTTGATTTTGGTTTAAATG
1 TATACATA-TAAACTTTGATTTTGATTCAAATG
**
3114035 TATACATA-AAACTTTGATTTTGATTCAGTTG
1 TATACATATAAACTTTGATTTTGATTCAAATG
3114066 TATACAT
1 TATACAT
3114073 TTATACATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 26 0.76
33 8 0.24
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.46
Consensus pattern (32 bp):
TATACATATAAACTTTGATTTTGATTCAAATG
Found at i:3114725 original size:10 final size:11
Alignment explanation
Indices: 3114713--3114754 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
3114703 GATTTTCTTT
3114713 ATTTTTTAAT-
1 ATTTTTTAATA
*
3114723 ATTTTTT-ATG
1 ATTTTTTAATA
3114733 ATTTTTTAATA
1 ATTTTTTAATA
3114744 ATTTATTTAAT
1 ATTT-TTTAAT
3114755 TAAACTGATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 2 0.07
10 14 0.50
11 6 0.21
12 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
ATTTTTTAATA
Found at i:3116185 original size:9 final size:9
Alignment explanation
Indices: 3116173--3116222 Score: 75
Period size: 9 Copynumber: 5.6 Consensus size: 9
3116163 AATAAATTTT
3116173 ATAATTCAA
1 ATAATTCAA
3116182 ATAATTCAA
1 ATAATTCAA
3116191 ATAACTT-AA
1 ATAA-TTCAA
*
3116200 ATACTTCAA
1 ATAATTCAA
3116209 ATAATTCAA
1 ATAATTCAA
3116218 ATAAT
1 ATAAT
3116223 AGATTGATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 2 0.05
9 33 0.89
10 2 0.05
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (9 bp):
ATAATTCAA
Found at i:3116192 original size:27 final size:27
Alignment explanation
Indices: 3116162--3116221 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
3116152 TCAATTTTTA
**
3116162 AAATAAATTTTATAATTCAAATAATTC
1 AAATAAATTAAATAATTCAAATAATTC
* *
3116189 AAATAACTTAAATACTTCAAATAATTC
1 AAATAAATTAAATAATTCAAATAATTC
3116216 AAATAA
1 AAATAA
3116222 TAGATTGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (27 bp):
AAATAAATTAAATAATTCAAATAATTC
Found at i:3121763 original size:26 final size:26
Alignment explanation
Indices: 3121733--3121785 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
3121723 TGACCAATGT
*
3121733 ACATGGACTGCATAGATAACTTATGC
1 ACATGGACTGCATACATAACTTATGC
3121759 ACATGGACTGCATACATAACTTATGC
1 ACATGGACTGCATACATAACTTATGC
3121785 A
1 A
3121786 TAGTGTAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (26 bp):
ACATGGACTGCATACATAACTTATGC
Found at i:3126003 original size:15 final size:15
Alignment explanation
Indices: 3125983--3126023 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
3125973 GAATTTGAGT
3125983 AAAAATATAAATTTA
1 AAAAATATAAATTTA
*
3125998 AAAAATAT-ATTTTA
1 AAAAATATAAATTTA
3126012 AAAAATA-AAATT
1 AAAAATATAAATT
3126024 CTTTTGAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATATAAATTTA
Found at i:3126109 original size:11 final size:11
Alignment explanation
Indices: 3126092--3126142 Score: 70
Period size: 11 Copynumber: 4.8 Consensus size: 11
3126082 GTTTTGTCGC
3126092 TATT-TTTT-T
1 TATTATTTTGT
3126101 TATTATTTTGT
1 TATTATTTTGT
3126112 TATTATTTTGT
1 TATTATTTTGT
* *
3126123 TATTATATCGT
1 TATTATTTTGT
3126134 TATTATTTT
1 TATTATTTT
3126143 ATTGTTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
9 4 0.11
10 4 0.11
11 28 0.78
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.73
Consensus pattern (11 bp):
TATTATTTTGT
Found at i:3126120 original size:22 final size:22
Alignment explanation
Indices: 3126092--3126151 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
3126082 GTTTTGTCGC
*
3126092 TATT-TTTT-TTATTATTTTGT
1 TATTATTTTATTATTATTTCGT
* *
3126112 TATTATTTTGTTATTATATCGT
1 TATTATTTTATTATTATTTCGT
*
3126134 TATTATTTTATTGTTATT
1 TATTATTTTATTATTATT
3126152 ATTTAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 4 0.12
21 4 0.12
22 25 0.76
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.72
Consensus pattern (22 bp):
TATTATTTTATTATTATTTCGT
Found at i:3126155 original size:14 final size:14
Alignment explanation
Indices: 3126122--3126155 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3126112 TATTATTTTG
*
3126122 TTATTATATCGTTA
1 TTATTTTATCGTTA
*
3126136 TTATTTTATTGTTA
1 TTATTTTATCGTTA
3126150 TTATTT
1 TTATTT
3126156 AAATTTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (14 bp):
TTATTTTATCGTTA
Found at i:3129462 original size:21 final size:22
Alignment explanation
Indices: 3129436--3129486 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
3129426 TATACAAAAC
*
3129436 AAAATATACACATAATATA-TT
1 AAAATATACACATAATATACGT
* *
3129457 AAAATATATACGTAATATACGT
1 AAAATATACACATAATATACGT
3129479 AAAATATA
1 AAAATATA
3129487 TGTAATGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.31
Consensus pattern (22 bp):
AAAATATACACATAATATACGT
Found at i:3131976 original size:86 final size:86
Alignment explanation
Indices: 3131780--3132067 Score: 384
Period size: 86 Copynumber: 3.3 Consensus size: 86
3131770 AATTTGGCTC
* * * ** * *
3131780 GTTACCCTACTGCTTAGGGGATTAAAGCTCAT-TATCTTTGATCTGTTTCC-CTACTGCTTAGGG
1 GTTACCCTACTGCTTAGGGGTTTAAGGTTC-TCCGTCTTCGATCTG-CTCCACTACTGCTTAGGG
*
3131843 TGATAAGATCTGTAAACTCAACCT
64 -GATAAGATCTGTAAATTCAACCT
3131867 GTTACCCTACTGCTTAGGGGTTTAAGGTTCTCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 GTTACCCTACTGCTTAGGGGTTTAAGGTTCTCCGTCTTCGATCTGCTCCACTACTGCTTAGGG-G
*
3131932 ATAAGATCTG-GAATTCAACCT
65 ATAAGATCTGTAAATTCAACCT
* * *
3131953 GTTACCCTACTGTTTAGGGGTTTAAGGTTCTTCGTCTTCGATCTGCTCCACTACTGCTTAGGGGT
1 GTTACCCTACTGCTTAGGGGTTTAAGGTTCTCCGTCTTCGATCTGCTCCACTACTGCTTAGGGGA
*
3132018 TAAGATCTGTAAATCTTCAGCCT
66 TAAGATCTGTAAA--TTCAACCT
3132041 GTTACCCTACTGCTTAGGGGTTTAAGG
1 GTTACCCTACTGCTTAGGGGTTTAAGG
3132068 CTTGTAAATT
Statistics
Matches: 180, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
85 10 0.06
86 76 0.42
87 61 0.34
88 33 0.18
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.35
Consensus pattern (86 bp):
GTTACCCTACTGCTTAGGGGTTTAAGGTTCTCCGTCTTCGATCTGCTCCACTACTGCTTAGGGGA
TAAGATCTGTAAATTCAACCT
Found at i:3132035 original size:44 final size:44
Alignment explanation
Indices: 3131738--3132198 Score: 264
Period size: 44 Copynumber: 10.5 Consensus size: 44
3131728 TTTTAGCCTA
* * * *
3131738 TTACCCTACTACTTAGGGGGTTAAGGTCTGTAAAT-TTGGCTC-G
1 TTACCCTACTGCTTA-GGGGTTAAGATCTGTAAATCTTCGATCTG
* *
3131781 TTACCCTACTGCTTAGGGGATTAAAGCTCAT-T--ATCTTTGATCTG
1 TTACCCTACTGCTTAGGGG-TT-AAGATC-TGTAAATCTTCGATCTG
* * * *
3131825 TTTCCCTACTGCTTAGGGTGATAAGATCTGTAAA-C-TCAACCTG
1 TTACCCTACTGCTTAGGG-GTTAAGATCTGTAAATCTTCGATCTG
* * ***
3131868 TTACCCTACTGCTTAGGGGTTTAAGGT-TCTCCGTCTTCGATCTG
1 TTACCCTACTGCTTAGGGG-TTAAGATCTGTAAATCTTCGATCTG
* * * * *
3131912 CT-CCACTACTGCTTAGGGAGATAAGATCTG-GAA--TTCAACCTG
1 TTACC-CTACTGCTTAGGG-GTTAAGATCTGTAAATCTTCGATCTG
* * **
3131954 TTACCCTACTGTTTAGGGGTTTAAGGTTCT-T-CGTCTTCGATCTG
1 TTACCCTACTGCTTAGGGG-TTAA-GATCTGTAAATCTTCGATCTG
* *
3131998 CT-CCACTACTGCTTAGGGGTTAAGATCTGTAAATCTTC-AGCCTG
1 TTACC-CTACTGCTTAGGGGTTAAGATCTGTAAATCTTCGA-TCTG
* * *
3132042 TTACCCTACTGCTTAGGGGTTTAAG-GCTTGTAAAT-TTAGCT-TG
1 TTACCCTACTGCTTAGGGG-TTAAGATC-TGTAAATCTTCGATCTG
* ** * *
3132085 TTACCCTACTGCTTAGGGGGTTAA-AGC-CCATCATCTTTGATCTG
1 TTACCCTACTGCTTA-GGGGTTAAGATCTGTA-AATCTTCGATCTG
* * *
3132129 TTTCCTTACTGCTTAGGGGGTTAAGATCTGTAAATCTTC-AGCCTG
1 TTACCCTACTGCTTA-GGGGTTAAGATCTGTAAATCTTCGA-TCTG
3132174 TTACCCTACTGCTTAGGGGGTTAAG
1 TTACCCTACTGCTTA-GGGGTTAAG
3132199 GCTTATGAAT
Statistics
Matches: 319, Mismatches: 62, Indels: 72
0.70 0.14 0.16
Matches are distributed among these distances:
41 2 0.01
42 39 0.12
43 98 0.31
44 127 0.40
45 52 0.16
46 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.36
Consensus pattern (44 bp):
TTACCCTACTGCTTAGGGGTTAAGATCTGTAAATCTTCGATCTG
Found at i:3144536 original size:21 final size:22
Alignment explanation
Indices: 3144510--3144560 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
3144500 TATACAAAAC
*
3144510 AAAATATACACATAATATA-TT
1 AAAATATACACATAATATACGT
* *
3144531 AAAATATATACGTAATATACGT
1 AAAATATACACATAATATACGT
3144553 AAAATATA
1 AAAATATA
3144561 TGTAATGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.31
Consensus pattern (22 bp):
AAAATATACACATAATATACGT
Found at i:3150764 original size:4 final size:4
Alignment explanation
Indices: 3150757--3150803 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
3150747 TTCATTATAC
3150757 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
3150804 AGTCATGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:3153941 original size:2 final size:2
Alignment explanation
Indices: 3153934--3153975 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3153924 TTAAATATTC
3153934 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
3153976 TTGTTGATTA
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:3154180 original size:22 final size:22
Alignment explanation
Indices: 3154148--3154197 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
3154138 ATTATAAATT
*
3154148 TTAATTTTTTTAAAAATT-TAA
1 TTAATTTTTTTTAAAATTCTAA
*
3154169 TTAATTTTTTTTAAAATTCTCA
1 TTAATTTTTTTTAAAATTCTAA
3154191 TTAATTT
1 TTAATTT
3154198 CACAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTAATTTTTTTTAAAATTCTAA
Found at i:3154675 original size:25 final size:28
Alignment explanation
Indices: 3154605--3154678 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 28
3154595 TCTTTTTAAT
* *
3154605 TAATAACTCTTTTATTTATATAAATAAAA
1 TAATAAATATTTTA-TTATATAAATAAAA
* *
3154634 TAATAAATATGTAATTATAT-AAT-AAA
1 TAATAAATATTTTATTATATAAATAAAA
*
3154660 -AATATATATTTTATTATAT
1 TAATAAATATTTTATTATAT
3154679 CATTATGTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 16 0.42
26 3 0.08
27 3 0.08
28 6 0.16
29 10 0.26
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (28 bp):
TAATAAATATTTTATTATATAAATAAAA
Found at i:3154783 original size:21 final size:18
Alignment explanation
Indices: 3154759--3154797 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
3154749 TATATGTTTT
3154759 TATATTTATCATTATTTTAAA
1 TATATTT-T-ATT-TTTTAAA
3154780 TATATTTTATTTTTTAAA
1 TATATTTTATTTTTTAAA
3154798 ACATCAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 1 0.06
21 7 0.39
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTTTATTTTTTAAA
Found at i:3155201 original size:19 final size:19
Alignment explanation
Indices: 3155164--3155209 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3155154 CATAATGATA
* *
3155164 TATATAA-TATATTTTTAT
1 TATATAATTACATATTTAT
3155182 TATATAATTACATATTTAT
1 TATATAATTACATATTTAT
*
3155201 TATTTAATT
1 TATATAATT
3155210 TTTATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATAATTACATATTTAT
Found at i:3161687 original size:6 final size:6
Alignment explanation
Indices: 3161673--3161708 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
3161663 TTATTTTATC
*
3161673 TTGAA- TTGAAA TTGAAG TTGAAG TTGAAG TTGAAG T
1 TTGAAG TTGAAG TTGAAG TTGAAG TTGAAG TTGAAG T
3161709 AGTAATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (6 bp):
TTGAAG
Found at i:3163874 original size:18 final size:19
Alignment explanation
Indices: 3163853--3163894 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 19
3163843 TTTACCCCAT
3163853 TTTTAATGAATTTATTTC-
1 TTTTAATGAATTTATTTCA
3163871 TTTTAATGAATTTATTTCA
1 TTTTAATGAATTTATTTCA
3163890 TTTTA
1 TTTTA
3163895 CCTAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTAATGAATTTATTTCA
Found at i:3167517 original size:76 final size:73
Alignment explanation
Indices: 3167332--3167522 Score: 197
Period size: 76 Copynumber: 2.5 Consensus size: 73
3167322 CATATCAAAG
* * * *
3167332 CATTAGAGTTATGATTTCACTTTAATTTTATTTTTTTTGGACCCTTTTATTTAAATCTTTTGATG
1 CATTAGAATTATGATTTCACTTGAATTTTTTTTTTTTTGGACCCTTTTATTTAAATCTTTAGATG
3167397 TTCAATAT
66 TTCAATAT
* ** * *
3167405 CATTAGAATTGTGGCTTCATTTCGACTTTATATTTTTTTTTGGACCCTTTTATTTAAATCCTTTA
1 CATTAGAATTATGATTTCACTT-GAATTT-T-TTTTTTTTTGGACCCTTTTATTTAAAT-CTTTA
*
3167470 G-TGTT-AGTAGT
62 GATGTTCAATA-T
3167481 CATTTCAGAATTATGATTTCACTTGAATTTTGTTTTTCTTTT
1 CA-TT-AGAATTATGATTTCACTTGAATTTT-TTTTT-TTTT
3167523 TTTCTTTTTT
Statistics
Matches: 94, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
73 17 0.18
74 4 0.04
75 4 0.04
76 39 0.41
77 16 0.17
78 14 0.15
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (73 bp):
CATTAGAATTATGATTTCACTTGAATTTTTTTTTTTTTGGACCCTTTTATTTAAATCTTTAGATG
TTCAATAT
Found at i:3167865 original size:31 final size:31
Alignment explanation
Indices: 3167830--3167892 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
3167820 ACGTTGAATT
3167830 CTTTCCCACTCAATTCGACAATAATTCAAAC
1 CTTTCCCACTCAATTCGACAATAATTCAAAC
3167861 CTTTCCCACTCAATTCGACAATAATTCAAAC
1 CTTTCCCACTCAATTCGACAATAATTCAAAC
3167892 C
1 C
3167893 CTTTTTAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.29
Consensus pattern (31 bp):
CTTTCCCACTCAATTCGACAATAATTCAAAC
Found at i:3168228 original size:14 final size:14
Alignment explanation
Indices: 3168209--3168240 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3168199 AACTTTCAAT
3168209 GTATATATCAACAA
1 GTATATATCAACAA
3168223 GTATATATCAACAA
1 GTATATATCAACAA
3168237 GTAT
1 GTAT
3168241 TGAGGTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (14 bp):
GTATATATCAACAA
Found at i:3168356 original size:5 final size:5
Alignment explanation
Indices: 3168346--3168373 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3168336 CCGTTGTTGA
3168346 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
3168374 TTACTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:3170107 original size:16 final size:16
Alignment explanation
Indices: 3170086--3170117 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3170076 GCAAACCCTT
*
3170086 TAAATACAAAAAAATC
1 TAAATAAAAAAAAATC
3170102 TAAATAAAAAAAAATC
1 TAAATAAAAAAAAATC
3170118 AACATACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAATAAAAAAAAATC
Found at i:3175169 original size:3 final size:3
Alignment explanation
Indices: 3175161--3175185 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3175151 TATATGAAAA
3175161 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
3175186 TTTATTGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3186026 original size:17 final size:17
Alignment explanation
Indices: 3186004--3186037 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3185994 ATCTCGGAAA
* *
3186004 CTAAAATTACCTTAAAC
1 CTAAAACTAACTTAAAC
3186021 CTAAAACTAACTTAAAC
1 CTAAAACTAACTTAAAC
3186038 AATTTAAAAC
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:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (17 bp):
CTAAAACTAACTTAAAC
Found at i:3195025 original size:26 final size:24
Alignment explanation
Indices: 3194982--3195039 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 24
3194972 TTATTTCATT
* *
3194982 AAATAAA-AAATTTTAAAATATAA
1 AAATAAATACATTTAAAAATATAA
3195005 TAAATCAAATACATTTAAAAATATAA
1 -AAAT-AAATACATTTAAAAATATAA
3195031 AAATAAATA
1 AAATAAATA
3195040 TTAAAACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.30
25 7 0.23
26 14 0.47
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAATACATTTAAAAATATAA
Found at i:3198418 original size:33 final size:31
Alignment explanation
Indices: 3198380--3198457 Score: 77
Period size: 34 Copynumber: 2.5 Consensus size: 31
3198370 TTTAATGTTT
**
3198380 ATATATATAAATTTAAATTTTATGAATTATAAA
1 ATATATATAAATTTAAATAATAT-AA-TATAAA
* * *
3198413 TTATATAATATATTAAAATAATATAATATAAA
1 ATATAT-ATAAATTTAAATAATATAATATAAA
3198445 ATAT-TATAAATTT
1 ATATATATAAATTT
3198458 TAAAAAAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
30 6 0.17
31 1 0.03
32 9 0.25
33 7 0.19
34 13 0.36
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (31 bp):
ATATATATAAATTTAAATAATATAATATAAA
Found at i:3198436 original size:18 final size:19
Alignment explanation
Indices: 3198405--3198442 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3198395 AATTTTATGA
*
3198405 ATTATAAATTATATAATAT
1 ATTATAAATAATATAATAT
3198424 ATTA-AAATAATATAATAT
1 ATTATAAATAATATAATAT
3198442 A
1 A
3198443 AAATATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTATAAATAATATAATAT
Found at i:3199564 original size:60 final size:59
Alignment explanation
Indices: 3199463--3199625 Score: 202
Period size: 60 Copynumber: 2.7 Consensus size: 59
3199453 TACACTACTC
* * * **
3199463 GTCACCCAACTATTAGTAAATTTCTCTTTTAGTCATATAACTATGAAAAGTTACAAAAT
1 GTCACCTAACTATTAGTAAATTTCTTTTTTGGTCACCTAACTATGAAAAGTTACAAAAT
* * * *
3199522 AGTCACCTAATTATTTGTAAATTTATTTTTTGGTCACCTAACTATGAAAAGTTATAAAAT
1 -GTCACCTAACTATTAGTAAATTTCTTTTTTGGTCACCTAACTATGAAAAGTTACAAAAT
* *
3199582 GATCACCTAACTATTAGTAAA-TTCTTTTTTGGTCGCCCAACTAT
1 G-TCACCTAACTATTAGTAAATTTCTTTTTTGGTCACCTAACTAT
3199626 CCTGAATTTT
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 21 0.24
60 67 0.76
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (59 bp):
GTCACCTAACTATTAGTAAATTTCTTTTTTGGTCACCTAACTATGAAAAGTTACAAAAT
Found at i:3202514 original size:43 final size:43
Alignment explanation
Indices: 3202453--3202537 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
3202443 GTCCTGTAAG
3202453 TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAATT
1 TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAATT
*
3202496 TTGTGAGTTTAGTCTTTGTTTTCCAATTTGATTATTTTTAAT
1 TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAAT
3202538 CATACTGCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.19, C:0.08, G:0.14, T:0.59
Consensus pattern (43 bp):
TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAATT
Found at i:3205106 original size:12 final size:12
Alignment explanation
Indices: 3205074--3205111 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3205064 CTTAAAATAA
3205074 TTTATATA-ATT
1 TTTATATATATT
3205085 TTT-T-TATATT
1 TTTATATATATT
3205095 TTTATATATATT
1 TTTATATATATT
3205107 TTTAT
1 TTTAT
3205112 TTTATTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 2 0.08
10 7 0.29
11 4 0.17
12 11 0.46
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATATATATT
Found at i:3206564 original size:24 final size:24
Alignment explanation
Indices: 3206523--3206570 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3206513 AAAATTAGAA
*
3206523 ATATTTTTAATACTAAATACATAAT
1 ATATTTTTAATAC-AAATAAATAAT
3206548 ATATTTTTAATGA-AAATAAATAA
1 ATATTTTTAAT-ACAAATAAATAA
3206571 ATTTAACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 11 0.52
26 1 0.05
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (24 bp):
ATATTTTTAATACAAATAAATAAT
Found at i:3207999 original size:23 final size:22
Alignment explanation
Indices: 3207953--3207999 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3207943 GATAAAAATT
*
3207953 AAACCCTAAAACTTGAAAATAA
1 AAACCCTAAAACTTGAAAACAA
3207975 AAACCCTCAAAACTT-AAATACAA
1 AAACCCT-AAAACTTGAAA-ACAA
3207998 AA
1 AA
3208000 TTCTCTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.60, C:0.21, G:0.02, T:0.17
Consensus pattern (22 bp):
AAACCCTAAAACTTGAAAACAA
Found at i:3209349 original size:14 final size:15
Alignment explanation
Indices: 3209327--3209365 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3209317 GGACAACAGT
3209327 AACAAAT-AATTTAA
1 AACAAATAAATTTAA
*
3209341 AACATATAAATTTAA
1 AACAAATAAATTTAA
*
3209356 AAAAAATAAA
1 AACAAATAAA
3209366 AATTGAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (15 bp):
AACAAATAAATTTAA
Found at i:3210736 original size:13 final size:13
Alignment explanation
Indices: 3210718--3210745 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3210708 AATATAAATC
3210718 TTATATCAAACCA
1 TTATATCAAACCA
3210731 TTATATCAAACCA
1 TTATATCAAACCA
3210744 TT
1 TT
3210746 GAACCATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (13 bp):
TTATATCAAACCA
Found at i:3211245 original size:21 final size:22
Alignment explanation
Indices: 3211211--3211268 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
3211201 AGTCGAATTT
3211211 AATCATAATTTTTTTATAA-AA
1 AATCATAATTTTTTTATAATAA
*
3211232 AATCA-AATTATTTTTTTAATAAA
1 AATCATAATT-TTTTTATAAT-AA
3211255 AAT-ATTAATTTTTT
1 AATCA-TAATTTTTT
3211269 AACATGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
20 4 0.13
21 13 0.42
22 1 0.03
23 9 0.29
24 4 0.13
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (22 bp):
AATCATAATTTTTTTATAATAA
Found at i:3211864 original size:26 final size:26
Alignment explanation
Indices: 3211835--3211889 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
3211825 TAAAATTTAG
* *
3211835 TTATTATATTTT-TATATTTAGAAATT
1 TTATTATATTTTGTAGATTT-CAAATT
*
3211861 TTATTTTATTTTGTAGATTTCAAATT
1 TTATTATATTTTGTAGATTTCAAATT
3211887 TTA
1 TTA
3211890 AGTTTAACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (26 bp):
TTATTATATTTTGTAGATTTCAAATT
Found at i:3213465 original size:42 final size:42
Alignment explanation
Indices: 3213405--3213493 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
3213395 GCCCTTAGCT
* * *
3213405 CGTGTGCAACACTGACTTTAAAACACGGCCATGACGCACGCC
1 CGTGTACAACACTAACTTTAAAACACGGCCATGACACACGCC
* * * *
3213447 CGTGTACAATACTAACTTTAATACACGGCCATGGCACACGTC
1 CGTGTACAACACTAACTTTAAAACACGGCCATGACACACGCC
3213489 CGTGT
1 CGTGT
3213494 GGCCTGCCCG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (42 bp):
CGTGTACAACACTAACTTTAAAACACGGCCATGACACACGCC
Found at i:3215706 original size:26 final size:26
Alignment explanation
Indices: 3215677--3215729 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3215667 ATTATGCTAG
3215677 TACACTAAAATATAAATAAAATAATT
1 TACACTAAAATATAAATAAAATAATT
3215703 TACACTAAAATATAAATAAAATAATT
1 TACACTAAAATATAAATAAAATAATT
3215729 T
1 T
3215730 TCTTAGCCTC
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (26 bp):
TACACTAAAATATAAATAAAATAATT
Found at i:3216666 original size:24 final size:24
Alignment explanation
Indices: 3216634--3216683 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3216624 AAAACATAGT
3216634 GTTTGAAATCTCCTATAGTCACAG
1 GTTTGAAATCTCCTATAGTCACAG
3216658 GTTTGAAATCTCCTATAGTCACAG
1 GTTTGAAATCTCCTATAGTCACAG
3216682 GT
1 GT
3216684 CCTTGTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (24 bp):
GTTTGAAATCTCCTATAGTCACAG
Found at i:3218033 original size:85 final size:86
Alignment explanation
Indices: 3217885--3218051 Score: 216
Period size: 85 Copynumber: 2.0 Consensus size: 86
3217875 GAGGATTCAC
* * *
3217885 TTTGACCATAGGTAAGGCAATGTCAAAGTTAATGTCTGAATCCAATTTCTGATAATCTTGTGACA
1 TTTGACCATAGGTAAGGCAATGTCAAAGATAATGTCTGAATCCAATTTCGGATAATCCTGTGACA
*
3217950 TACCTGCAATAACACAAATAT
66 TACCTGCAACAACACAAATAT
* * *
3217971 TTTG-CCATAGGTAAGGCAATGTCAGAGAT-ATGGT-TAGAATCTAATATT-GGATGATCCTGTG
1 TTTGACCATAGGTAAGGCAATGTCAAAGATAAT-GTCT-GAATCCAAT-TTCGGATAATCCTGTG
3218032 ACATACCTGCAACAACACAA
63 ACATACCTGCAACAACACAA
3218052 GTATGTGGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
84 3 0.04
85 62 0.87
86 6 0.08
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (86 bp):
TTTGACCATAGGTAAGGCAATGTCAAAGATAATGTCTGAATCCAATTTCGGATAATCCTGTGACA
TACCTGCAACAACACAAATAT
Found at i:3219804 original size:32 final size:32
Alignment explanation
Indices: 3219768--3219838 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
3219758 TATCGAGTTT
*
3219768 TCAGAATACTTTATCCCGAAATTTTTGGGTTC
1 TCAGAATACTTTATCCCGAAATTTTTGGCTTC
* ** * *
3219800 TCAGAAAACTTTATTGCGAGATTTTTGGCTTT
1 TCAGAATACTTTATCCCGAAATTTTTGGCTTC
3219832 TCAGAAT
1 TCAGAAT
3219839 TCAAGCTAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (32 bp):
TCAGAATACTTTATCCCGAAATTTTTGGCTTC
Found at i:3221335 original size:16 final size:16
Alignment explanation
Indices: 3221314--3221347 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3221304 GTATGCTTCC
*
3221314 CATAGCTCAGCTTCAA
1 CATAGCTAAGCTTCAA
3221330 CATAGCTAAGCTTCAA
1 CATAGCTAAGCTTCAA
3221346 CA
1 CA
3221348 GTTGAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (16 bp):
CATAGCTAAGCTTCAA
Found at i:3230502 original size:6 final size:6
Alignment explanation
Indices: 3230455--3230501 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
3230445 TGAAAATTTT
* *
3230455 TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCA TTGCCA TTGCC
1 TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCCG TTGCC
3230502 AATGCATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.04, C:0.34, G:0.28, T:0.34
Consensus pattern (6 bp):
TTGCCG
Found at i:3233538 original size:44 final size:44
Alignment explanation
Indices: 3233488--3233575 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
3233478 AATATTCCTG
3233488 AAATTTTTAAAAAGCATTGTAAGTAAATCTTTTATATGACTCCA
1 AAATTTTTAAAAAGCATTGTAAGTAAATCTTTTATATGACTCCA
3233532 AAATTTTTAAAAAGCATTGTAAGTAAATCTTTTATATGACTCCA
1 AAATTTTTAAAAAGCATTGTAAGTAAATCTTTTATATGACTCCA
3233576 TATTTTCATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (44 bp):
AAATTTTTAAAAAGCATTGTAAGTAAATCTTTTATATGACTCCA
Found at i:3233829 original size:22 final size:23
Alignment explanation
Indices: 3233804--3233849 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3233794 CAACCAAACC
3233804 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3233826 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3233849 A
1 A
3233850 CGTCATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3233855 original size:23 final size:22
Alignment explanation
Indices: 3233811--3233860 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
3233801 ACCAATTCAA
*
3233811 CATATTTTCAAGATAAATTCAT
1 CATATTTTCAAGATAAAGTCAT
*
3233833 GCATATTTAT-AAGATAACGTCAT
1 -CATATTT-TCAAGATAAAGTCAT
3233856 CATAT
1 CATAT
3233861 ACTCAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 18 0.75
24 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
CATATTTTCAAGATAAAGTCAT
Found at i:3238770 original size:20 final size:20
Alignment explanation
Indices: 3238708--3238776 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
3238698 ATATAGATAT
* *
3238708 TTATTATT-TATTATTATTA
1 TTATTATTAAATTATAATTA
*
3238727 TT-CTATTAAATTATAATT-
1 TTATTATTAAATTATAATTA
*
3238745 TATATTATTAAATTATGATTA
1 T-TATTATTAAATTATAATTA
3238766 TTATTATTAAA
1 TTATTATTAAA
3238777 AATAAATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
18 5 0.12
19 11 0.27
20 24 0.59
21 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (20 bp):
TTATTATTAAATTATAATTA
Found at i:3240154 original size:12 final size:12
Alignment explanation
Indices: 3240137--3240161 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3240127 GCTGACTATT
3240137 GTTACTGTTACC
1 GTTACTGTTACC
3240149 GTTACTGTTACC
1 GTTACTGTTACC
3240161 G
1 G
3240162 ATTCGACACT
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:3240189 original size:45 final size:45
Alignment explanation
Indices: 3240139--3240245 Score: 162
Period size: 45 Copynumber: 2.4 Consensus size: 45
3240129 TGACTATTGT
*
3240139 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAA
*
3240184 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
* *
3240229 TACTGCTACTGTTACTG
1 TACTGTTACCGTTACTG
3240246 CTACTGCTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
45 56 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.39
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
Found at i:3240252 original size:18 final size:18
Alignment explanation
Indices: 3240229--3240263 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3240219 GTGTGTTGAA
*
3240229 TACTGCTACTGTTACTGC
1 TACTGCTACCGTTACTGC
3240247 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
3240264 ATTACTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (18 bp):
TACTGCTACCGTTACTGC
Found at i:3242777 original size:22 final size:23
Alignment explanation
Indices: 3242752--3242797 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3242742 CAACCAAACC
3242752 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3242774 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3242797 A
1 A
3242798 CGTCATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3242803 original size:23 final size:22
Alignment explanation
Indices: 3242759--3242808 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
3242749 ACCAATTCAA
*
3242759 CATATTTTCAAGATAAATTCAT
1 CATATTTTCAAGATAAAGTCAT
*
3242781 GCATATTTAT-AAGATAACGTCAT
1 -CATATTT-TCAAGATAAAGTCAT
3242804 CATAT
1 CATAT
3242809 ACTCAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 18 0.75
24 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
CATATTTTCAAGATAAAGTCAT
Found at i:3247678 original size:20 final size:20
Alignment explanation
Indices: 3247645--3247701 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
3247635 TTTATTATTT
3247645 ATTATTATTCTATTAAATTATA
1 ATTATTA-T-TATTAAATTATA
*
3247667 ATT-TATATTATTAAATTATG
1 ATTAT-TATTATTAAATTATA
3247687 ATTATTATTATTAAA
1 ATTATTATTATTAAA
3247702 AATAAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 24 0.75
21 3 0.09
22 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTATTATTATTAAATTATA
Found at i:3247684 original size:25 final size:26
Alignment explanation
Indices: 3247636--3247684 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
3247626 ATATAGATAT
* **
3247636 TTATTATTTATTATTATTCTATTAAA
1 TTATAATTTATTATTATTAAATTAAA
3247662 TTATAATTTA-TATTATTAAATTA
1 TTATAATTTATTATTATTAAATTA
3247685 TGATTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TTATAATTTATTATTATTAAATTAAA
Found at i:3249094 original size:45 final size:45
Alignment explanation
Indices: 3249044--3249149 Score: 160
Period size: 45 Copynumber: 2.4 Consensus size: 45
3249034 GACTACTATC
*
3249044 ACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAAT
1 ACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAAT
*
3249089 ACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAAT
1 ACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAAT
* *
3249134 ACTGCTACTGTTACTG
1 ACTGTTACCGTTACTG
3249150 CTACTGCTAC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
45 55 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.39
Consensus pattern (45 bp):
ACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAAT
Found at i:3249156 original size:18 final size:18
Alignment explanation
Indices: 3249133--3249167 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3249123 GTGTGTTGAA
*
3249133 TACTGCTACTGTTACTGC
1 TACTGCTACCGTTACTGC
3249151 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
3249168 ATTACTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (18 bp):
TACTGCTACCGTTACTGC
Found at i:3253363 original size:22 final size:23
Alignment explanation
Indices: 3253338--3253383 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3253328 CAACCAAACC
3253338 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3253360 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3253383 A
1 A
3253384 TGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3262345 original size:12 final size:11
Alignment explanation
Indices: 3262328--3262365 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
3262318 AAAATATTAT
3262328 TTTATATTAATA
1 TTTATATTAA-A
3262340 TTTATA-TAAA
1 TTTATATTAAA
3262350 TTTATAATTAAA
1 TTTAT-ATTAAA
3262362 TTTA
1 TTTA
3262366 AATAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.25
11 4 0.17
12 14 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTATATTAAA
Found at i:3262346 original size:22 final size:22
Alignment explanation
Indices: 3262328--3262371 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3262318 AAAATATTAT
3262328 TTTAT-ATTAATATTTATATAAA
1 TTTATAATTAA-ATTTATATAAA
*
3262350 TTTATAATTAAATTTAAATAAA
1 TTTATAATTAAATTTATATAAA
3262372 AATATTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTATAATTAAATTTATATAAA
Found at i:3265569 original size:19 final size:18
Alignment explanation
Indices: 3265546--3265589 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3265536 TAAAATTTGA
3265546 AATTTTTATAAATATTTT
1 AATTTTTATAAATATTTT
*
3265564 ACA-TTTTAAAAAGTATTTT
1 A-ATTTTTATAAA-TATTTT
3265583 AATTTTT
1 AATTTTT
3265590 TGTTGAGAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
AATTTTTATAAATATTTT
Found at i:3265570 original size:18 final size:18
Alignment explanation
Indices: 3265549--3265588 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3265539 AATTTGAAAT
*
3265549 TTTTATAAA-TATTTTACA
1 TTTTAAAAAGTATTTTA-A
3265567 TTTTAAAAAGTATTTTAA
1 TTTTAAAAAGTATTTTAA
3265585 TTTT
1 TTTT
3265589 TTGTTGAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
TTTTAAAAAGTATTTTAA
Found at i:3267289 original size:16 final size:16
Alignment explanation
Indices: 3267268--3267316 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
3267258 TAATTTTTTT
3267268 ATATAAAAAATTAAAA
1 ATATAAAAAATTAAAA
* * *
3267284 ATATAATACATCAAAA
1 ATATAAAAAATTAAAA
3267300 ATACTAAAAACATTAAA
1 ATA-TAAAAA-ATTAAA
3267317 CTTAATACTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 16 0.64
17 4 0.16
18 5 0.20
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.24
Consensus pattern (16 bp):
ATATAAAAAATTAAAA
Found at i:3271109 original size:11 final size:11
Alignment explanation
Indices: 3271070--3271110 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
3271060 CTGCTCTCTC
3271070 TTTTTCTTTTAT
1 TTTTTCTTTT-T
3271082 TTTTTCTTTTT
1 TTTTTCTTTTT
**
3271093 AATTTCTTTTT
1 TTTTTCTTTTT
3271104 TTTTTCT
1 TTTTTCT
3271111 CGGGATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:3273680 original size:27 final size:27
Alignment explanation
Indices: 3273650--3273702 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3273640 AAAATGTCAA
* *
3273650 AAATGACTAAATTGAAGGGAATTATCT
1 AAATGAATAAATTGAAGGAAATTATCT
* *
3273677 AAATTAATAAATTGAATGAAATTATC
1 AAATGAATAAATTGAAGGAAATTATC
3273703 AATTTAAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (27 bp):
AAATGAATAAATTGAAGGAAATTATCT
Found at i:3275624 original size:17 final size:17
Alignment explanation
Indices: 3275604--3275642 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3275594 ATTAAAATAT
3275604 TTAAAATATATATTATA
1 TTAAAATATATATTATA
* *
3275621 TTAATATTTATATTATA
1 TTAAAATATATATTATA
3275638 TTAAA
1 TTAAA
3275643 TAAAATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAAATATATATTATA
Found at i:3275670 original size:21 final size:20
Alignment explanation
Indices: 3275578--3275667 Score: 68
Period size: 18 Copynumber: 4.5 Consensus size: 20
3275568 TTTATATTAC
3275578 TAAT-TTAAAA-AATTATAT
1 TAATATTAAAATAATTATAT
3275596 TAAAATATTTAAAAT-A-TATAT
1 T--AATA-TTAAAATAATTATAT
*
3275617 T-ATATTAATATTTATATTATAT
1 TAATATTAA-A-ATA-ATTATAT
3275639 TAA-A-TAAAATAATTATAT
1 TAATATTAAAATAATTATAT
3275657 TAATATTAAAA
1 TAATATTAAAA
3275668 ATATATATAT
Statistics
Matches: 57, Mismatches: 2, Indels: 24
0.69 0.02 0.29
Matches are distributed among these distances:
17 4 0.07
18 15 0.26
19 4 0.07
20 9 0.16
21 10 0.18
22 14 0.25
23 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAATATTAAAATAATTATAT
Found at i:3275672 original size:17 final size:17
Alignment explanation
Indices: 3275617--3275673 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
3275607 AAATATATAT
* * *
3275617 TATATTAATATTTATAT
1 TATATTAATATTAAAAA
*
3275634 TATATTAA-ATAAAATAA
1 TATATTAATATTAAA-AA
3275651 TTATATTAATATTAAAAA
1 -TATATTAATATTAAAAA
3275669 TATAT
1 TATAT
3275674 ATATCCTTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 3 0.09
17 14 0.44
18 10 0.31
19 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATTAATATTAAAAA
Found at i:3275673 original size:35 final size:33
Alignment explanation
Indices: 3275592--3275673 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 33
3275582 TTAAAAAATT
*
3275592 ATATTAAAATAT-TTAAAATATATATTATATTA
1 ATATTAAAATATATTAAAAAATATATTATATTA
* *
3275624 ATATTTATATTATATTAAATAAA-ATAATTATATTA
1 ATA-TTAAAATATATTAAA-AAATAT-ATTATATTA
3275659 ATATTAAAAATATAT
1 ATATT-AAAATATAT
3275674 ATATCCTTCC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
32 3 0.08
33 7 0.17
34 9 0.22
35 21 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
ATATTAAAATATATTAAAAAATATATTATATTA
Found at i:3276436 original size:16 final size:16
Alignment explanation
Indices: 3276415--3276447 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3276405 TTCATGCTAG
3276415 ATGTTTAAAGTGGAAA
1 ATGTTTAAAGTGGAAA
3276431 ATGTTTAAAGTGGAAA
1 ATGTTTAAAGTGGAAA
3276447 A
1 A
3276448 GATTGTATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (16 bp):
ATGTTTAAAGTGGAAA
Found at i:3279477 original size:24 final size:26
Alignment explanation
Indices: 3279431--3279485 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
3279421 TCAATATACT
*
3279431 AAAATATATAAATTTTTAATAAA-TGA
1 AAAAAATATAAA-TTTTAATAAATTGA
*
3279457 AAAAAATATAAA-TTTATTAAATTGA
1 AAAAAATATAAATTTTAATAAATTGA
3279482 AAAA
1 AAAA
3279486 TGAAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 8 0.31
25 7 0.27
26 11 0.42
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (26 bp):
AAAAAATATAAATTTTAATAAATTGA
Found at i:3279492 original size:23 final size:23
Alignment explanation
Indices: 3279458--3279501 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
3279448 AATAAATGAA
3279458 AAAAATATAAAT-TTATTAAATTG
1 AAAAATATAAATATTA-TAAATTG
3279481 AAAAATGA-AAATATTATAAAT
1 AAAAAT-ATAAATATTATAAAT
3279502 ATTTTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (23 bp):
AAAAATATAAATATTATAAATTG
Found at i:3280091 original size:15 final size:15
Alignment explanation
Indices: 3280071--3280103 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3280061 CCTAAAGAAA
3280071 GAAAAAGAAGAAATT
1 GAAAAAGAAGAAATT
3280086 GAAAAAGAAGAAATT
1 GAAAAAGAAGAAATT
3280101 GAA
1 GAA
3280104 GTTAAGGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (15 bp):
GAAAAAGAAGAAATT
Found at i:3282488 original size:43 final size:44
Alignment explanation
Indices: 3282422--3282505 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 44
3282412 ATCGAAATAT
* *
3282422 GATATTCGGGCTTCGGGCTTAGCAGGCTATAATGCCAGTGAGAC
1 GATATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCAGTGAGAC
* *
3282466 GATA-TCGGGCTTTGAGCCTAGCAGGCTATAATGCCGGTGA
1 GATATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCAGTGA
3282506 AATGAAATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 32 0.89
44 4 0.11
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (44 bp):
GATATTCGGGCTTCGAGCCTAGCAGGCTATAATGCCAGTGAGAC
Found at i:3282851 original size:38 final size:38
Alignment explanation
Indices: 3282801--3283059 Score: 358
Period size: 38 Copynumber: 6.8 Consensus size: 38
3282791 GGCTTAAAGA
*
3282801 CCCGCAGACTTCGTGCTGGTAATATATTCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATTCGGGTTAAAT
* *
3282839 CCCGTAGGCTTCGTGCTGGTAATATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATTCGGGTTAAAT
*
3282877 CCCGCAGGCTTCGTGCTGGTAATATATTCGGGCTTAAAGA
1 CCCGCAGGCTTCGTGCTGGTAATATATTCGGG-TTAAA-T
* * *
3282917 CCCGCAGGCTTTGTGCTGGTATTATATCCGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATTCGGGTTAAAT
* * *
3282955 CCCGCAGGCTTCATGCTGGTAATATATCCCGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATTCGGGTTAAAT
3282993 CCCGCAGGCTTCGTGCTGGTAATATA-TCTGGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTAATATATTC-GGGTTAAAT
* * * *
3283031 CCCGCAGGCCTAGTACTGGTATTATATTC
1 CCCGCAGGCTTCGTGCTGGTAATATATTC
3283060 AGGCCTTTGA
Statistics
Matches: 196, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
37 1 0.01
38 154 0.79
39 12 0.06
40 29 0.15
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTAATATATTCGGGTTAAAT
Found at i:3282993 original size:116 final size:115
Alignment explanation
Indices: 3282789--3283057 Score: 407
Period size: 116 Copynumber: 2.3 Consensus size: 115
3282779 GATGTGTATC
* * * * * *
3282789 CGGGCTTAAAGACCCGCAGACTTCGTGCTGGTAATATATTCGGGTTAAATCCCGTAGGCTTCGTG
1 CGGGCTTAAAGACCCGCAGGCTTAGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTCATG
*
3282854 CTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATATATT
66 CTGGTAATATATCCCGGTTAAATCCCGCAGGCTTCGTGCTGGTAATATA-T
*
3282905 CGGGCTTAAAGACCCGCAGGCTTTGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTCATG
1 CGGGCTTAAAGACCCGCAGGCTTAGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTCATG
3282970 CTGGTAATATATCCCGGTTAAATCCCGCAGGCTTCGTGCTGGTAATATAT
66 CTGGTAATATATCCCGGTTAAATCCCGCAGGCTTCGTGCTGGTAATATAT
* * *
3283020 CTGGG-TTAAA-TCCCGCAGGCCTAGTACTGGTATTATAT
1 C-GGGCTTAAAGACCCGCAGGCTTAGTGCTGGTATTATAT
3283058 TCAGGCCTTT
Statistics
Matches: 141, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
114 24 0.17
115 7 0.05
116 110 0.78
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.30
Consensus pattern (115 bp):
CGGGCTTAAAGACCCGCAGGCTTAGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTTCATG
CTGGTAATATATCCCGGTTAAATCCCGCAGGCTTCGTGCTGGTAATATAT
Found at i:3283119 original size:45 final size:45
Alignment explanation
Indices: 3283054--3283185 Score: 139
Period size: 45 Copynumber: 3.0 Consensus size: 45
3283044 TACTGGTATT
* * * *
3283054 ATATTCAGGCCTTTGAGCCTAGCAAGCTATTATGTCGGTGAGAT-
1 ATATTCGGGCCTTTGAGCCTAGCAAGCTATAATGCCGGTGACATG
* *
3283098 ACTATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGACATG
1 A-TATTCGGGCCTTTGAGCCTAGCAAGCTATAATGCCGGTGACATG
* * *
3283144 ATA-TCGAGCC-TTGAGCCTAGCAAGCGA-AATGCCAGTGA-ATG
1 ATATTCGGGCCTTTGAGCCTAGCAAGCTATAATGCCGGTGACATG
3283185 A
1 A
3283186 ATAAAAGTCT
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
41 4 0.05
42 10 0.13
43 14 0.19
44 7 0.09
45 39 0.52
46 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (45 bp):
ATATTCGGGCCTTTGAGCCTAGCAAGCTATAATGCCGGTGACATG
Found at i:3317418 original size:19 final size:19
Alignment explanation
Indices: 3317392--3317438 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3317382 ACCGGTCAAG
*
3317392 TTAAAAAATTATTAA-AAA
1 TTAAAAAATTAATAATAAA
*
3317410 TTCAAAAAAATAATAATAAA
1 TT-AAAAAATTAATAATAAA
3317430 TTAAAAAAT
1 TTAAAAAAT
3317439 CCAGTTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 17 0.71
20 5 0.21
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TTAAAAAATTAATAATAAA
Found at i:3322114 original size:36 final size:35
Alignment explanation
Indices: 3322012--3322114 Score: 133
Period size: 31 Copynumber: 3.0 Consensus size: 35
3322002 AGAAAGAAAG
*
3322012 AATAACAATCCATTAGATTAGATTCATT-AAAAAT
1 AATAACAATCCATTAGATTAAATTCATTAAAAAAT
3322046 AAT---AATCCATTAGATTAAATTCATTAAAAAAAT
1 AATAACAATCCATTAGATTAAATTCATT-AAAAAAT
* *
3322079 AATAACAATCCATAAAGATTAAATTCGTTAAAAAAT
1 AATAACAATCCAT-TAGATTAAATTCATTAAAAAAT
3322115 CGCAAAGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
31 21 0.35
33 9 0.15
34 3 0.05
36 14 0.23
37 13 0.22
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.31
Consensus pattern (35 bp):
AATAACAATCCATTAGATTAAATTCATTAAAAAAT
Found at i:3348467 original size:30 final size:30
Alignment explanation
Indices: 3348428--3348518 Score: 119
Period size: 30 Copynumber: 3.0 Consensus size: 30
3348418 ATAAGTTTGT
*
3348428 TTCTAATAATATTGCTTGTGATGAAAGAAA
1 TTCTGATAATATTGCTTGTGATGAAAGAAA
* * * *
3348458 TTTTGATAATATTGCTTTTGGTGAACGAAA
1 TTCTGATAATATTGCTTGTGATGAAAGAAA
* *
3348488 TTCTGATAATATTACTTGTGATGAAGGAAA
1 TTCTGATAATATTGCTTGTGATGAAAGAAA
3348518 T
1 T
3348519 GAGAAACAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.40
Consensus pattern (30 bp):
TTCTGATAATATTGCTTGTGATGAAAGAAA
Found at i:3352158 original size:19 final size:17
Alignment explanation
Indices: 3352134--3352170 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
3352124 TATTTAAATG
3352134 ATAAAATAATACAAAGAAA
1 ATAAAAT-ATA-AAAGAAA
3352153 ATAAAATATAAAAGAAA
1 ATAAAATATAAAAGAAA
3352170 A
1 A
3352171 ACAAAGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 3 0.17
19 7 0.39
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (17 bp):
ATAAAATATAAAAGAAA
Found at i:3352243 original size:9 final size:9
Alignment explanation
Indices: 3352220--3352253 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
3352210 CAGGGGAAGA
3352220 AAAAGAAAG
1 AAAAGAAAG
3352229 -AAAGAAAG
1 AAAAGAAAG
3352237 AAAAGAAAG
1 AAAAGAAAG
3352246 AAAAGAAA
1 AAAAGAAA
3352254 AAGGAAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:3352243 original size:13 final size:13
Alignment explanation
Indices: 3352220--3352253 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3352210 CAGGGGAAGA
3352220 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
3352233 -AAAGAAAAGAAAG
1 AAAAG-AAAGAAAG
3352246 AAAAGAAA
1 AAAAGAAA
3352254 AAGGAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.21
13 11 0.58
14 4 0.21
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Done.