Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, whole genome shotgun sequence
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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 101 of 109
Found at i:20216917 original size:17 final size:19
Alignment explanation
Indices: 20216883--20216923 Score: 59
Period size: 17 Copynumber: 2.2 Consensus size: 19
20216873 ACTTAAAAAA
20216883 TATATTTTTTTATTAATTTT
1 TATATTTTTTTA-TAATTTT
20216903 TATA-TTTTTTA-AATTTT
1 TATATTTTTTTATAATTTT
20216920 TATA
1 TATA
20216924 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.48
19 7 0.33
20 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TATATTTTTTTATAATTTT
Found at i:20217490 original size:16 final size:18
Alignment explanation
Indices: 20217450--20217495 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 18
20217440 TGACATTAAA
20217450 TTAAAATTTATATATAAT
1 TTAAAATTTATATATAAT
* *
20217468 ATAAAATTTA-A-ATTAT
1 TTAAAATTTATATATAAT
20217484 TTAAAATTTATA
1 TTAAAATTTATA
20217496 AAATTAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 13 0.54
17 2 0.08
18 9 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAAATTTATATATAAT
Found at i:20221781 original size:15 final size:14
Alignment explanation
Indices: 20221757--20221801 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 14
20221747 TTATTTTATT
*
20221757 AAATAGAATAATAAA
1 AAATAAAATAAT-AA
20221772 AAATAAAATAATAA
1 AAATAAAATAATAA
20221786 AAAT-AAA-AATAA
1 AAATAAAATAATAA
20221798 AAAT
1 AAAT
20221802 TTTGAGAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 9 0.31
13 3 0.10
14 6 0.21
15 11 0.38
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (14 bp):
AAATAAAATAATAA
Found at i:20221982 original size:18 final size:17
Alignment explanation
Indices: 20221951--20221984 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20221941 TTTCAAACAT
20221951 AAAAAAAATAAAAATGA
1 AAAAAAAATAAAAATGA
*
20221968 AAAAAATAATTAAAATG
1 AAAAAA-AATAAAAATG
20221985 TGGATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (17 bp):
AAAAAAAATAAAAATGA
Found at i:20228518 original size:17 final size:17
Alignment explanation
Indices: 20228498--20228581 Score: 75
Period size: 18 Copynumber: 4.8 Consensus size: 17
20228488 TGAAGGAAGC
*
20228498 AAAAAAATGAAAAAACG
1 AAAAAAATGAAAAAATG
20228515 AAAAAGAA-GAAAAAAATG
1 AAAAA-AATG-AAAAAATG
*
20228533 -AAAAAATAAAAAAAATG
1 AAAAAAAT-GAAAAAATG
20228550 AAGAAAGAATG-AAAAATG
1 AA-AAA-AATGAAAAAATG
20228568 AAAAAAAATGAAAA
1 -AAAAAAATGAAAA
20228582 TGAGAGAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
16 2 0.04
17 22 0.40
18 23 0.42
19 5 0.09
20 3 0.05
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.08
Consensus pattern (17 bp):
AAAAAAATGAAAAAATG
Found at i:20228533 original size:26 final size:25
Alignment explanation
Indices: 20228493--20228581 Score: 88
Period size: 28 Copynumber: 3.3 Consensus size: 25
20228483 ACGAATGAAG
20228493 GAAGCAAAAAAATGAAAAAACGAAAAA
1 GAAG-AAAAAAATGAAAAAA-GAAAAA
*
20228520 GAAGAAAAAAATGAAAAAATAAAAA
1 GAAGAAAAAAATGAAAAAAGAAAAA
* *
20228545 AAATGAAGAAAGAATGAAAAATGAAAAA
1 GAA-GAA-AAA-AATGAAAAAAGAAAAA
*
20228573 AAATGAAAA
1 GAA-GAAAA
20228582 TGAGAGAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
25 7 0.13
26 18 0.33
27 9 0.16
28 21 0.38
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.08
Consensus pattern (25 bp):
GAAGAAAAAAATGAAAAAAGAAAAA
Found at i:20228566 original size:18 final size:18
Alignment explanation
Indices: 20228526--20228591 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 18
20228516 AAAAGAAGAA
*
20228526 AAAAATGAA-AAAATAA-A
1 AAAAATGAAGAAAA-AATG
*
20228543 AAAAATGAAGAAAGAATG
1 AAAAATGAAGAAAAAATG
20228561 AAAAATGAA-AAAAAATG
1 AAAAATGAAGAAAAAATG
20228578 -AAAATGAGAGAAAA
1 AAAAATGA-AGAAAA
20228592 GGAATACTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
16 7 0.17
17 19 0.45
18 16 0.38
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (18 bp):
AAAAATGAAGAAAAAATG
Found at i:20228571 original size:28 final size:27
Alignment explanation
Indices: 20228498--20228581 Score: 111
Period size: 26 Copynumber: 3.1 Consensus size: 27
20228488 TGAAGGAAGC
* *
20228498 AAAAAAATGAAAAAACGAAAAAGAA-G
1 AAAAAAATGAAAAAATGAAAAAAAATG
20228524 AAAAAAATGAAAAAAT-AAAAAAAATG
1 AAAAAAATGAAAAAATGAAAAAAAATG
20228550 AAGAAAGAATG-AAAAATGAAAAAAAATG
1 AA-AAA-AATGAAAAAATGAAAAAAAATG
20228578 AAAA
1 AAAA
20228582 TGAGAGAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
25 7 0.13
26 18 0.35
27 11 0.21
28 16 0.31
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.08
Consensus pattern (27 bp):
AAAAAAATGAAAAAATGAAAAAAAATG
Found at i:20228581 original size:8 final size:8
Alignment explanation
Indices: 20228499--20228573 Score: 62
Period size: 8 Copynumber: 8.8 Consensus size: 8
20228489 GAAGGAAGCA
20228499 AAAAAATG
1 AAAAAATG
*
20228507 AAAAAACG
1 AAAAAATG
*
20228515 AAAAAGAAG
1 AAAAA-ATG
20228524 AAAAAAATG
1 -AAAAAATG
*
20228533 AAAAAATAA
1 AAAAAAT-G
20228542 AAAAAATG
1 AAAAAATG
20228550 AAGAAAGAATG
1 -A-AAA-AATG
20228561 -AAAAATG
1 AAAAAATG
20228568 AAAAAA
1 AAAAAA
20228574 AATGAAAATG
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
7 4 0.07
8 27 0.49
9 12 0.22
10 8 0.15
11 4 0.07
ACGTcount: A:0.77, C:0.01, G:0.13, T:0.08
Consensus pattern (8 bp):
AAAAAATG
Found at i:20228591 original size:17 final size:17
Alignment explanation
Indices: 20228543--20228591 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
20228533 AAAAAATAAA
20228543 AAAAATGAAGAAAGAATG
1 AAAAATGAAGAAA-AATG
*
20228561 AAAAATGAAAAAAAATG
1 AAAAATGAAGAAAAATG
20228578 -AAAATGAGAGAAAA
1 AAAAATGA-AGAAAA
20228592 GGAATACTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 7 0.25
17 9 0.32
18 12 0.43
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.10
Consensus pattern (17 bp):
AAAAATGAAGAAAAATG
Found at i:20230286 original size:43 final size:42
Alignment explanation
Indices: 20230213--20230424 Score: 182
Period size: 43 Copynumber: 5.0 Consensus size: 42
20230203 GATTGCCAAT
* *
20230213 GAGC-ATTTA-TTTTCAAAAGTAGTGGTTGCCTTTGTTTAGAG
1 GAGCAATTTATTTTTTAAAAGTCGTGG-TGCCTTTGTTTAGAG
*
20230254 GAGCAATTTATTTTTTAAAAGTCGTGGGTGCCTTTGTTTAGAA
1 GAGCAATTTATTTTTTAAAAGTCGT-GGTGCCTTTGTTTAGAG
* * * *
20230297 GAGCAATTTATTTTTCT-AAAGT-TTCGATGCCTCTGTTTAGAT
1 GAGCAATTTATTTTT-TAAAAGTCGT-GGTGCCTTTGTTTAGAG
** * * *
20230339 GAGCAATTTATTTTTCCAAAGTTGTGGTGCCTTTGTCTATAG
1 GAGCAATTTATTTTTTAAAAGTCGTGGTGCCTTTGTTTAGAG
* * * * *
20230381 GAGCTTTATTTA-TTTTTCAAAGTCGTTGAGCCTCTGTTTAGAG
1 GAGC--AATTTATTTTTTAAAAGTCGTGGTGCCTTTGTTTAGAG
20230424 G
1 G
20230425 TGTTTTGTTT
Statistics
Matches: 140, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
41 4 0.03
42 56 0.40
43 72 0.51
44 8 0.06
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (42 bp):
GAGCAATTTATTTTTTAAAAGTCGTGGTGCCTTTGTTTAGAG
Found at i:20230334 original size:42 final size:42
Alignment explanation
Indices: 20230239--20230374 Score: 159
Period size: 42 Copynumber: 3.2 Consensus size: 42
20230229 AAGTAGTGGT
* * * *
20230239 TGCCTTTGTTTAGAGGAGCAATTTATTTTT-TAAAAGTCGTGGG
1 TGCCTTTGTTTAGAAGAGCAATTTATTTTTCT-AAAGT-TTCGA
20230282 TGCCTTTGTTTAGAAGAGCAATTTATTTTTCTAAAGTTTCGA
1 TGCCTTTGTTTAGAAGAGCAATTTATTTTTCTAAAGTTTCGA
* * * *
20230324 TGCCTCTGTTTAGATGAGCAATTTATTTTTCCAAAGTTGT-GG
1 TGCCTTTGTTTAGAAGAGCAATTTATTTTTCTAAAGTT-TCGA
20230366 TGCCTTTGT
1 TGCCTTTGT
20230375 CTATAGGAGC
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
42 46 0.56
43 35 0.43
44 1 0.01
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.44
Consensus pattern (42 bp):
TGCCTTTGTTTAGAAGAGCAATTTATTTTTCTAAAGTTTCGA
Found at i:20230360 original size:85 final size:84
Alignment explanation
Indices: 20230239--20230424 Score: 225
Period size: 85 Copynumber: 2.2 Consensus size: 84
20230229 AAGTAGTGGT
* * *
20230239 TGCCTTTGTTTAGAGGAGCAATTTATTTTTTAAAAGTCGTGGGTGCCTTTGTTTAGAAGAGC-AA
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAGTCGT-GGTGCCTTTGTCTAGAAGAGCTAA
20230303 TTTATTTTTCTAAAGT-TTCGA
65 TTTATTTTTC-AAAGTCTT-GA
* * * * * *
20230324 TGCCTCTGTTTAGATGAGCAATTTATTTTTCCAAAGTTGTGGTGCCTTTGTCTATAGGAGCTTTA
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAGTCGTGGTGCCTTTGTCTAGAAGAGC-TAA
20230389 TTTATTTTTCAAAGTCGTTGA
65 TTTATTTTTCAAAGTC-TTGA
20230410 -GCCTCTGTTTAGAGG
1 TGCCTCTGTTTAGAGG
20230425 TGTTTTGTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
84 18 0.21
85 54 0.62
86 13 0.15
87 2 0.02
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.44
Consensus pattern (84 bp):
TGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAAGTCGTGGTGCCTTTGTCTAGAAGAGCTAAT
TTATTTTTCAAAGTCTTGA
Found at i:20230453 original size:44 final size:43
Alignment explanation
Indices: 20230303--20230570 Score: 184
Period size: 44 Copynumber: 6.2 Consensus size: 43
20230293 AGAAGAGCAA
* * * **
20230303 TTTATTTTTCTAAAGTT-TCGATGCCTCTGTTTAGATGAGC--AA
1 TTTA-TTTTCCAAAGTTGTTGA-GCCTCTGTTTAGAGGAGCTTTG
* * * * * *
20230345 TTTATTTTTCCAAAGTTGTGGTGCCTTTGTCTATAGGAGCTTTA
1 TTTA-TTTTCCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTG
* * * *
20230389 TTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGTGTTTTG
1 TTTATTTTCCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTG
***
20230432 TTTATTTGTCCAAAGTTGTTGAGCCTCAACTTAGAGGAGCTTTG
1 TTTATTT-TCCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTG
* * * * * * * *
20230476 TTTATCTTTCCAAAATCGTTGGGTCTCTATTTAGAAGAGCCTTA
1 TTTAT-TTTCCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTG
* * **
20230520 TTTATTTTTTCAAAGTTGTTAAATCTCTGTTTAGAGGAGCTTTG
1 TTTA-TTTTCCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTG
20230564 -TTATTTT
1 TTTATTTT
20230571 TTTTTAAATA
Statistics
Matches: 176, Mismatches: 44, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
42 34 0.19
43 41 0.23
44 98 0.56
45 3 0.02
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.46
Consensus pattern (43 bp):
TTTATTTTCCAAAGTTGTTGAGCCTCTGTTTAGAGGAGCTTTG
Found at i:20231821 original size:12 final size:13
Alignment explanation
Indices: 20231799--20231836 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
20231789 TTACTTGTGT
20231799 ATTCATTTATTTA
1 ATTCATTTATTTA
20231812 ATTC-TTTATTTA
1 ATTCATTTATTTA
* *
20231824 TTTTATTTATTTA
1 ATTCATTTATTTA
20231837 CTTATTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTCATTTATTTA
Found at i:20231836 original size:17 final size:17
Alignment explanation
Indices: 20231798--20231847 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
20231788 TTTACTTGTG
* *
20231798 TATTCATTTA-TTTAAT
1 TATTTATTTATTTTATT
*
20231814 TCTTTATTTATTTTATT
1 TATTTATTTATTTTATT
*
20231831 TATTTACTTATTTTATT
1 TATTTATTTATTTTATT
20231848 CAATAGAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 8 0.29
17 20 0.71
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTATTTATTTTATT
Found at i:20231886 original size:15 final size:15
Alignment explanation
Indices: 20231849--20231884 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
20231839 TATTTTATTC
*
20231849 AATAGAATAATAAAT
1 AATAAAATAATAAAT
20231864 AATAAAATAATAAA-
1 AATAAAATAATAAAT
20231878 AATAAAA
1 AATAAAA
20231885 ATTTTGAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:20234020 original size:6 final size:6
Alignment explanation
Indices: 20234011--20234064 Score: 54
Period size: 6 Copynumber: 8.3 Consensus size: 6
20234001 GGAATTTTTA
* *
20234011 TTTATT TTTATT TTAAATCT TTTATT TCATATT TATTATT TTTATT TTTATT
1 TTTATT TTTATT TT-TAT-T TTTATT T-TTATT T-TTATT TTTATT TTTATT
20234063 TT
1 TT
20234065 ATGGTTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
6 23 0.57
7 14 0.35
8 3 0.08
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:20234036 original size:20 final size:20
Alignment explanation
Indices: 20234011--20234066 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
20234001 GGAATTTTTA
20234011 TTTATTTTTATTTTA-AATCT
1 TTTATTTTTATTTTATAAT-T
* *
20234031 TTTA-TTTCATATTTATTATT
1 TTTATTTTTAT-TTTATAATT
20234051 TTTATTTTTATTTTAT
1 TTTATTTTTATTTTAT
20234067 GGTTTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.17
20 18 0.60
21 7 0.23
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATTTTTATTTTATAATT
Found at i:20235766 original size:3 final size:3
Alignment explanation
Indices: 20235760--20235799 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
20235750 TTTTTTTCAT
20235760 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
20235800 GATTAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20235910 original size:16 final size:15
Alignment explanation
Indices: 20235885--20235920 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
20235875 TTTCTAAAAT
20235885 AAAAAAATTTTTCAA
1 AAAAAAATTTTTCAA
*
20235900 AAAAAATATTTTTGAA
1 AAAAAA-ATTTTTCAA
20235916 AAAAA
1 AAAAA
20235921 GTTGAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAAAAATTTTTCAA
Found at i:20235986 original size:54 final size:54
Alignment explanation
Indices: 20235917--20236101 Score: 217
Period size: 54 Copynumber: 3.4 Consensus size: 54
20235907 ATTTTTGAAA
*
20235917 AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTAAAAAAATTTTAGC
1 AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTAAAAAAATTTTAGG
** * * * *** * *
20235971 AAAAGTTGAAAGTATCAATTTCCCTTGAAAATAAAATTTTCAAATGCTCTAAGG
1 AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTAAAAAAATTTTAGG
* * * *
20236025 AAAAGTTGAAAATATCAATTTTTCTTAAAAATAAAACTTCCAAAAATATTTTAGG
1 AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATT-TAAAAAAATTTTAGG
*
20236080 GAAAGTTGAAAGTATCAATTTT
1 AAAAGTTGAAAGTATCAATTTT
20236102 CTTTATATAA
Statistics
Matches: 105, Mismatches: 25, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
54 77 0.73
55 28 0.27
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (54 bp):
AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTTAAAAAAATTTTAGG
Found at i:20239758 original size:15 final size:15
Alignment explanation
Indices: 20239738--20239767 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20239728 TGATATGATA
20239738 ATTAAGTGCATAATT
1 ATTAAGTGCATAATT
20239753 ATTAAGTGCATAATT
1 ATTAAGTGCATAATT
20239768 TATTGGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
ATTAAGTGCATAATT
Found at i:20243704 original size:28 final size:27
Alignment explanation
Indices: 20243650--20243713 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
20243640 TTTTAATTTG
* *
20243650 AATTGAATTAAAAATACATCTATATATT
1 AATTAAATTAAAAATACATCTAAATA-T
*
20243678 AATTAAATTAAAAAATATAT-TAAATAT
1 AATTAAATT-AAAAATACATCTAAATAT
20243705 ATATTAAAT
1 A-ATTAAAT
20243714 GAGTATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 2 0.06
28 20 0.65
29 9 0.29
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (27 bp):
AATTAAATTAAAAATACATCTAAATAT
Found at i:20246054 original size:1 final size:1
Alignment explanation
Indices: 20246048--20246074 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
20246038 CGCAATTCAG
20246048 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
20246075 GCAAATGGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20249843 original size:19 final size:20
Alignment explanation
Indices: 20249814--20249864 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
20249804 TGATATTTTT
20249814 AAATA-TTTATA-TTTAAAA
1 AAATATTTTATATTTTAAAA
20249832 AAATATTTTATATTTTTAAAA
1 AAATATTTTATA-TTTTAAAA
20249853 ATAATATTTTAT
1 A-AATATTTTAT
20249865 TAATTTCGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.17
19 6 0.21
21 8 0.28
22 10 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATATTTTATATTTTAAAA
Found at i:20249865 original size:20 final size:19
Alignment explanation
Indices: 20249814--20249865 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
20249804 TGATATTTTT
*
20249814 AAATA-TTTATATTTAAAA
1 AAATATTTTATTTTTAAAA
20249832 AAATATTTTATATTTTTAAAA
1 AAATA-TTT-TATTTTTAAAA
20249853 ATAATATTTTATT
1 A-AATATTTTATT
20249866 AATTTCGAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 5 0.17
20 6 0.21
21 14 0.48
22 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATATTTTATTTTTAAAA
Found at i:20250534 original size:2 final size:2
Alignment explanation
Indices: 20250527--20250561 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20250517 AAACATCTTT
20250527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20250562 TATTCTACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20250695 original size:2 final size:2
Alignment explanation
Indices: 20250688--20250720 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20250678 ATATGAATTT
20250688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20250721 TCTTTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20251498 original size:2 final size:2
Alignment explanation
Indices: 20251491--20251520 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20251481 AGTTTTAGCC
20251491 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
20251521 CTAAGTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20251599 original size:23 final size:25
Alignment explanation
Indices: 20251546--20251599 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 25
20251536 TGTTATAGGA
20251546 AAAAATTTAGATGAAGCTTTTTAGTT
1 AAAAATTTA-ATGAAGCTTTTTAGTT
* *
20251572 -GAAATTT-ATGAAGTTTTTTA-TT
1 AAAAATTTAATGAAGCTTTTTAGTT
20251594 AAAAAT
1 AAAAAT
20251600 GATTAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 2 0.08
23 16 0.67
25 6 0.25
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.44
Consensus pattern (25 bp):
AAAAATTTAATGAAGCTTTTTAGTT
Found at i:20251689 original size:10 final size:11
Alignment explanation
Indices: 20251661--20251702 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
20251651 GATTAAGTGT
20251661 ATAAATTTTGA
1 ATAAATTTTGA
*
20251672 AAAAATTTT-A
1 ATAAATTTTGA
20251682 ATAAATTTTGA
1 ATAAATTTTGA
*
20251693 TATATATTTT
1 -ATAAATTTT
20251703 TAGGTAGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 9 0.35
11 9 0.35
12 8 0.31
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (11 bp):
ATAAATTTTGA
Found at i:20255768 original size:19 final size:19
Alignment explanation
Indices: 20255720--20255768 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
20255710 GCACAATAAG
* *
20255720 ATACGATTAACATGATTAT
1 ATACGATTAATATGATTAC
* * *
20255739 ATACAAATAATATGATTGC
1 ATACGATTAATATGATTAC
20255758 ATACGATTAAT
1 ATACGATTAAT
20255769 TCATTTATTA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (19 bp):
ATACGATTAATATGATTAC
Found at i:20263927 original size:21 final size:19
Alignment explanation
Indices: 20263900--20263948 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
20263890 AAATTTAATG
20263900 ATTAAAATTAAATATAAGATAT
1 ATTAAAATTAAATA-AA-A-AT
* *
20263922 ATAAAAATTAATTAAAAAT
1 ATTAAAATTAAATAAAAAT
20263941 ATTAAAAT
1 ATTAAAAT
20263949 AATTTAAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 9 0.38
20 1 0.04
21 2 0.08
22 12 0.50
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
ATTAAAATTAAATAAAAAT
Found at i:20265551 original size:17 final size:17
Alignment explanation
Indices: 20265516--20265555 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
20265506 GCATAAATAA
* *
20265516 TTTATAATTATTGGGAT
1 TTTAAAATTATTGGAAT
*
20265533 TTTAAAATTATTTGAAT
1 TTTAAAATTATTGGAAT
20265550 TTTAAA
1 TTTAAA
20265556 TGTTGTGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (17 bp):
TTTAAAATTATTGGAAT
Found at i:20272117 original size:21 final size:21
Alignment explanation
Indices: 20272075--20272117 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
20272065 TATTTATAAG
* *
20272075 TTATCAAAAATTAAATTTTAA
1 TTATCAAAAATTAAAATCTAA
20272096 TTAT-AAAAATTAAGAATCTAA
1 TTATCAAAAATTAA-AATCTAA
20272117 T
1 T
20272118 AATATATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (21 bp):
TTATCAAAAATTAAAATCTAA
Found at i:20297599 original size:34 final size:33
Alignment explanation
Indices: 20297520--20297601 Score: 94
Period size: 34 Copynumber: 2.5 Consensus size: 33
20297510 TTGAAAAATT
*
20297520 ATATAAATTTTT-GAAAATGGATTTCTAAAAAG
1 ATATAAATTTTTCTAAAATGGATTTCTAAAAAG
** * *
20297552 ATATAAACATTTCTAGAAATGGATTTTTAGAAAG
1 ATATAAATTTTTCTA-AAATGGATTTCTAAAAAG
*
20297586 TTATAAATTTTTCTAA
1 ATATAAATTTTTCTAA
20297602 GAATTCATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
32 10 0.25
33 2 0.05
34 28 0.70
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (33 bp):
ATATAAATTTTTCTAAAATGGATTTCTAAAAAG
Found at i:20297646 original size:33 final size:33
Alignment explanation
Indices: 20297574--20297679 Score: 110
Period size: 33 Copynumber: 3.2 Consensus size: 33
20297564 CTAGAAATGG
* *
20297574 ATTTTT-AGAAAGTTATA-AATTTTTCTAAGAATTC
1 ATTTTTGA-AAAGTTATATGATTTTT-TAA-AATTT
* *
20297608 ATTTTTGGAGAGGTT-TATGATTTTTTAAAATTT
1 ATTTTT-GAAAAGTTATATGATTTTTTAAAATTT
20297641 ATTTTTGAAAAGTTATATGATTTTTTAGAAATTT
1 ATTTTTGAAAAGTTATATGATTTTTTA-AAATTT
20297675 ATTTT
1 ATTTT
20297680 CAAAAAAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
32 6 0.10
33 22 0.36
34 22 0.36
35 10 0.16
36 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (33 bp):
ATTTTTGAAAAGTTATATGATTTTTTAAAATTT
Found at i:20304058 original size:6 final size:6
Alignment explanation
Indices: 20304049--20304075 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20304039 TGTTTGAAGA
20304049 AAAATG AAAATG AAAATG AAAATG AAA
1 AAAATG AAAATG AAAATG AAAATG AAA
20304076 TTAAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:20306998 original size:25 final size:23
Alignment explanation
Indices: 20306970--20307024 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
20306960 AGTATTTTAA
*
20306970 AAAATTATCAAATATATTGATAGTG
1 AAAATT-TCAAA-ATATTGATAATG
*
20306995 AAAATTTTAAAATATTGATAATG
1 AAAATTTCAAAATATTGATAATG
20307018 AAAATTT
1 AAAATTT
20307025 TAATTTCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 18 0.64
24 4 0.14
25 6 0.21
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (23 bp):
AAAATTTCAAAATATTGATAATG
Found at i:20307013 original size:23 final size:23
Alignment explanation
Indices: 20306983--20307027 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
20306973 ATTATCAAAT
*
20306983 ATATTGATAGTGAAAATTTTAAA
1 ATATTGATAATGAAAATTTTAAA
20307006 ATATTGATAATGAAAATTTTAA
1 ATATTGATAATGAAAATTTTAA
20307028 TTTCATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (23 bp):
ATATTGATAATGAAAATTTTAAA
Found at i:20312057 original size:26 final size:26
Alignment explanation
Indices: 20312028--20312079 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
20312018 TAGAAACTAG
* *
20312028 ATTGGATAATGACTATTTACTTATTC
1 ATTGGATAATAACTAATTACTTATTC
20312054 ATTGGATAATAACTAATTACTTATTC
1 ATTGGATAATAACTAATTACTTATTC
20312080 CATGGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (26 bp):
ATTGGATAATAACTAATTACTTATTC
Found at i:20313877 original size:6 final size:6
Alignment explanation
Indices: 20313869--20313904 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
20313859 GTTGATATAT
* *
20313869 ATTTAT ATTTAG ATTTAA ATTTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
20313905 GACAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:20317919 original size:26 final size:26
Alignment explanation
Indices: 20317890--20317943 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
20317880 CATTGTATCA
20317890 TTGAATATGATATTTAAACATTTTTT
1 TTGAATATGATATTTAAACATTTTTT
*
20317916 TTGAATATGATATTTAAACTTTTTTT
1 TTGAATATGATATTTAAACATTTTTT
20317942 TT
1 TT
20317944 TCAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.57
Consensus pattern (26 bp):
TTGAATATGATATTTAAACATTTTTT
Found at i:20327189 original size:25 final size:25
Alignment explanation
Indices: 20327160--20327208 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
20327150 ATAATAATAA
* *
20327160 AAATTATTTTAATTGCAATTGAAAG
1 AAATTACTATAATTGCAATTGAAAG
*
20327185 AAATTACTATAATTGTAATTGAAA
1 AAATTACTATAATTGCAATTGAAA
20327209 AAAAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (25 bp):
AAATTACTATAATTGCAATTGAAAG
Found at i:20329390 original size:12 final size:12
Alignment explanation
Indices: 20329361--20329394 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
20329351 ACTTTGGATT
20329361 GAGGCTGTTGGGG
1 GAGG-TGTTGGGG
20329374 G-GGTGTTGGGG
1 GAGGTGTTGGGG
20329385 GAGGTGTTGG
1 GAGGTGTTGG
20329395 AAGAGATGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 10 0.50
13 1 0.05
ACGTcount: A:0.06, C:0.03, G:0.65, T:0.26
Consensus pattern (12 bp):
GAGGTGTTGGGG
Found at i:20330367 original size:15 final size:15
Alignment explanation
Indices: 20330343--20330376 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
20330333 TCCTCACCTT
20330343 CTTGTCTGGTTGGCA
1 CTTGTCTGGTTGGCA
*
20330358 CTTGTTTGGTTGGCA
1 CTTGTCTGGTTGGCA
20330373 CTTG
1 CTTG
20330377 GCTCTAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.32, T:0.44
Consensus pattern (15 bp):
CTTGTCTGGTTGGCA
Found at i:20338728 original size:19 final size:20
Alignment explanation
Indices: 20338694--20338733 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
20338684 CCTTTTCATG
20338694 TTTTATCTTAATATTTCTAAA
1 TTTTATCTTAATATTT-TAAA
20338715 TTTTAT-TT-ATATTTTAAA
1 TTTTATCTTAATATTTTAAA
20338733 T
1 T
20338734 GTTTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 6 0.32
20 2 0.11
21 6 0.32
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTATCTTAATATTTTAAA
Found at i:20342039 original size:48 final size:48
Alignment explanation
Indices: 20341968--20342062 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
20341958 CCGACATAAT
20341968 CGACATGATTGAATCTTTCCAGATTCTTATCCTCAGCAAGATATTTTA
1 CGACATGATTGAATCTTTCCAGATTCTTATCCTCAGCAAGATATTTTA
20342016 CGACATGATTGAATCTTTCCAGATTCTTATCCTCAGCAAGATATTTT
1 CGACATGATTGAATCTTTCCAGATTCTTATCCTCAGCAAGATATTTT
20342063 GCTTCTTTAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (48 bp):
CGACATGATTGAATCTTTCCAGATTCTTATCCTCAGCAAGATATTTTA
Found at i:20342284 original size:22 final size:21
Alignment explanation
Indices: 20342259--20342306 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
20342249 TATATAATTC
*
20342259 AAAATTTTAATATAAATCAAA
1 AAAATTTTAATAAAAATCAAA
* *
20342280 TAAAAATTTAATAAAAATTAAA
1 -AAAATTTTAATAAAAATCAAA
20342302 AAAAT
1 AAAAT
20342307 ATATTTTATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATTTTAATAAAAATCAAA
Found at i:20347249 original size:16 final size:16
Alignment explanation
Indices: 20347223--20347268 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
20347213 TTCGTGAATA
20347223 ATTTGATTCATTTGTAT
1 ATTT-ATTCATTTGTAT
* *
20347240 TTTTATTCATTTTTAT
1 ATTTATTCATTTGTAT
20347256 ATTTATTCTATTT
1 ATTTATTC-ATTT
20347269 CAAGTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 18 0.72
17 7 0.28
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (16 bp):
ATTTATTCATTTGTAT
Found at i:20349568 original size:12 final size:12
Alignment explanation
Indices: 20349551--20349607 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
20349541 GATATAATTT
20349551 AAAATTTTAATA
1 AAAATTTTAATA
*
20349563 AAAATTTTATTA
1 AAAATTTTAATA
* * *
20349575 AACATATTAATT
1 AAAATTTTAATA
*
20349587 AAAATTTAAAATA
1 AAAATTT-TAATA
*
20349600 ATAATTTT
1 AAAATTTT
20349608 TTATATTATA
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
12 24 0.73
13 9 0.27
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (12 bp):
AAAATTTTAATA
Found at i:20349585 original size:24 final size:23
Alignment explanation
Indices: 20349549--20349593 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
20349539 TTGATATAAT
*
20349549 TTAAAATTTTAATAAAAATTTTA
1 TTAAAATATTAATAAAAATTTTA
*
20349572 TTAAACATATTAATTAAAATTT
1 TTAAA-ATATTAATAAAAATTT
20349594 AAAATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAAAATATTAATAAAAATTTTA
Found at i:20353105 original size:10 final size:10
Alignment explanation
Indices: 20353090--20353114 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20353080 ATGCCAATAC
20353090 ATAAAATTAA
1 ATAAAATTAA
20353100 ATAAAATTAA
1 ATAAAATTAA
20353110 ATAAA
1 ATAAA
20353115 TCGTTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAAATTAA
Found at i:20356795 original size:2 final size:2
Alignment explanation
Indices: 20356788--20356820 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20356778 ATGAATAGAC
20356788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20356821 AGCCAAAGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20357699 original size:23 final size:24
Alignment explanation
Indices: 20357655--20357718 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
20357645 GTTTTATTTC
*
20357655 TTGATTTTTAAAAT-TTAATTT-A
1 TTGATTTTTAATATATTAATTTAA
* *
20357677 TTGATTTTTTATATATTATTTTAA
1 TTGATTTTTAATATATTAATTTAA
*
20357701 TATAATTTTTAATATATT
1 T-TGATTTTTAATATATT
20357719 TAAATAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 12 0.35
23 6 0.18
24 2 0.06
25 14 0.41
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (24 bp):
TTGATTTTTAATATATTAATTTAA
Found at i:20358585 original size:28 final size:29
Alignment explanation
Indices: 20358536--20358595 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
20358526 AAATATAAAA
* **
20358536 TATAATTTTTTTATTTTATTAAATGTAT-T
1 TATAATTTTTTAAAATTATTAAAT-TATGT
20358565 TATAATTTTTTAAAATT-TTAAATTATGT
1 TATAATTTTTTAAAATTATTAAATTATGT
20358593 TAT
1 TAT
20358596 TTTTATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 3 0.11
28 10 0.37
29 14 0.52
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
TATAATTTTTTAAAATTATTAAATTATGT
Found at i:20358607 original size:24 final size:24
Alignment explanation
Indices: 20358571--20358627 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
20358561 TATTTATAAT
* * *
20358571 TTTTTAAAATTTTAAATTATGTTA
1 TTTTTATATTTTTAAATTATATTA
* *
20358595 TTTTTATATTTTTTATTTATATTA
1 TTTTTATATTTTTAAATTATATTA
20358619 TTTTTATAT
1 TTTTTATAT
20358628 GTATTTCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTTTATATTTTTAAATTATATTA
Found at i:20362845 original size:17 final size:17
Alignment explanation
Indices: 20362813--20362845 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20362803 TCGTCTTAAT
*
20362813 TTTTTTTATTCAAAAAG
1 TTTTTTTATTAAAAAAG
20362830 TTTTTTTATTAAAAAA
1 TTTTTTTATTAAAAAA
20362846 AATCCTAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTTTTTATTAAAAAAG
Found at i:20367635 original size:34 final size:34
Alignment explanation
Indices: 20367592--20367656 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
20367582 TACTGTCATC
* *
20367592 CACTAGCTAATTTATGCTAGGAAAATAAAAATTG
1 CACTAGCTAATCTATGCTAGGAAAAGAAAAATTG
*
20367626 CACTAGCTAATCTATGCTAGGGAAAGAAAAA
1 CACTAGCTAATCTATGCTAGGAAAAGAAAAA
20367657 CTATATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.25
Consensus pattern (34 bp):
CACTAGCTAATCTATGCTAGGAAAAGAAAAATTG
Found at i:20372101 original size:38 final size:38
Alignment explanation
Indices: 20372050--20372129 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
20372040 GATTATCAAG
* * * *
20372050 TCATCTTTTCAAATCTAATGAGCAATAAGTCTCCACGT
1 TCATCATTTCAAATCCAATGAACAATAAGTCTCCACGA
20372088 TCATCATTTCAAATCCAATGAACAATAAGTCTCCACGA
1 TCATCATTTCAAATCCAATGAACAATAAGTCTCCACGA
20372126 TCAT
1 TCAT
20372130 TTTTTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (38 bp):
TCATCATTTCAAATCCAATGAACAATAAGTCTCCACGA
Found at i:20373052 original size:17 final size:17
Alignment explanation
Indices: 20373030--20373063 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20373020 AATGTTACTC
*
20373030 ATATATAATAATAATAA
1 ATATATAACAATAATAA
20373047 ATATATAACAATAATAA
1 ATATATAACAATAATAA
20373064 GATCTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
ATATATAACAATAATAA
Found at i:20375239 original size:19 final size:19
Alignment explanation
Indices: 20375217--20375274 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
20375207 TTCCAAATAC
20375217 ATTTTCAAGAAATATTATG
1 ATTTTCAAGAAATATTATG
**
20375236 ATTTTTTA-AAA-A-TAT-
1 ATTTTCAAGAAATATTATG
*
20375251 ATTTTCAAGAAATGTTATG
1 ATTTTCAAGAAATATTATG
20375270 ATTTT
1 ATTTT
20375275 TCAAAAAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
15 6 0.20
16 6 0.20
17 1 0.03
18 6 0.20
19 11 0.37
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (19 bp):
ATTTTCAAGAAATATTATG
Found at i:20375241 original size:20 final size:20
Alignment explanation
Indices: 20375218--20375278 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
20375208 TCCAAATACA
20375218 TTTTCAAGAAATATTATGAT
1 TTTTCAAGAAATATTATGAT
*
20375238 TTTT-TA-AAA-A-TAT-A-
1 TTTTCAAGAAATATTATGAT
*
20375252 TTTTCAAGAAATGTTATGAT
1 TTTTCAAGAAATATTATGAT
20375272 TTTTCAA
1 TTTTCAA
20375279 AAAAGTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
14 4 0.12
15 2 0.06
16 6 0.19
17 1 0.03
18 6 0.19
19 2 0.06
20 11 0.34
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (20 bp):
TTTTCAAGAAATATTATGAT
Found at i:20375249 original size:34 final size:34
Alignment explanation
Indices: 20375211--20375357 Score: 172
Period size: 34 Copynumber: 4.3 Consensus size: 34
20375201 TCACTTTTCC
*
20375211 AAATACATTTTCAAGAAATATTATGATTTTTTAA
1 AAATATATTTTCAAGAAATATTATGATTTTTTAA
* *
20375245 AAATATATTTTCAAGAAATGTTATGATTTTTCAA
1 AAATATATTTTCAAGAAATATTATGATTTTTTAA
* *
20375279 AAA-AGTATTTTTAA-AAAGTATTATGATTTTTTGA
1 AAATA-TATTTTCAAGAAA-TATTATGATTTTTTAA
* * * *
20375313 AAATAAATTTTCAATAAGTATTATGATTTCTTAA
1 AAATATATTTTCAAGAAATATTATGATTTTTTAA
*
20375347 AAATTTATTTT
1 AAATATATTTT
20375358 TGAAAAATGT
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
33 4 0.04
34 88 0.93
35 3 0.03
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.46
Consensus pattern (34 bp):
AAATATATTTTCAAGAAATATTATGATTTTTTAA
Found at i:20375384 original size:68 final size:68
Alignment explanation
Indices: 20375229--20375384 Score: 156
Period size: 68 Copynumber: 2.3 Consensus size: 68
20375219 TTTCAAGAAA
* * * * *
20375229 TATTATGATTTTTTAAAAATATATTTTCAAGAAATGTTATGATTTTTCAAAAAAGTATTTTTAAA
1 TATTATAATTCTTTGAAAATAAATTTTCAAGAAATATTATGATTTTTCAAAAAAGTATTTTTAAA
20375294 AAG
66 AAG
* * * * **
20375297 TATTATGATTTTTTGAAAATAAATTTTCAATAAGTATTATGATTTCTT-AAAAATTTATTTTTGA
1 TATTATAATTCTTTGAAAATAAATTTTCAAGAAATATTATGATTT-TTCAAAAAAGTATTTTT-A
20375361 AAAA-
64 AAAAG
*
20375365 TGTTATAACTTCTTT-AAAAT
1 TATTATAA-TTCTTTGAAAAT
20375385 TATGAATATC
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
68 63 0.84
69 12 0.16
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (68 bp):
TATTATAATTCTTTGAAAATAAATTTTCAAGAAATATTATGATTTTTCAAAAAAGTATTTTTAAA
AAG
Found at i:20381918 original size:28 final size:28
Alignment explanation
Indices: 20381887--20381958 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
20381877 ATTATAATTT
* *
20381887 AATTACATATATAAATAATTTTTTATTA
1 AATTACATATATAAATAATATCTTATTA
*
20381915 AATTA-AAATATTAAATAATATCTTATTA
1 AATTACATATA-TAAATAATATCTTATTA
20381943 ATATAATACATATATA
1 A-AT--TACATATATA
20381959 TAAATATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
27 4 0.11
28 21 0.60
29 2 0.06
31 4 0.11
32 4 0.11
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (28 bp):
AATTACATATATAAATAATATCTTATTA
Found at i:20382814 original size:23 final size:22
Alignment explanation
Indices: 20382781--20382831 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
20382771 ATTAATTTTT
*
20382781 AAAAAAATTT-ATTTAATAAAAA
1 AAAAAAATTTAAATTAA-AAAAA
*
20382803 AATAAAATTTTAAATTAAAAAAA
1 AA-AAAAATTTAAATTAAAAAAA
20382826 AAAAAA
1 AAAAAA
20382832 GAATGAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 6 0.24
23 14 0.56
24 5 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAAAATTTAAATTAAAAAAA
Found at i:20390629 original size:23 final size:23
Alignment explanation
Indices: 20390599--20390646 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
20390589 GCAATTATCC
20390599 TTGATTGAGTTAGAATCATTTGA
1 TTGATTGAGTTAGAATCATTTGA
20390622 TTGATTGAGTTAGAATCATTTGA
1 TTGATTGAGTTAGAATCATTTGA
20390645 TT
1 TT
20390647 ATGATGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (23 bp):
TTGATTGAGTTAGAATCATTTGA
Found at i:20392038 original size:29 final size:29
Alignment explanation
Indices: 20392000--20392058 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
20391990 AACTATAGTT
* * * *
20392000 AAATATTTAATTTGATATTTGAATTTTAA
1 AAATATTTAATATAATATTTAAATTATAA
*
20392029 AAATTTTTAATATAATATTTAAATTATAA
1 AAATATTTAATATAATATTTAAATTATAA
20392058 A
1 A
20392059 CATGTTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (29 bp):
AAATATTTAATATAATATTTAAATTATAA
Found at i:20392108 original size:32 final size:34
Alignment explanation
Indices: 20392033--20392109 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 34
20392023 TTTTAAAAAT
*
20392033 TTTTAATATAATATTTAAATTATAAACATGTTAA
1 TTTTAATATAATATTCAAATTATAAACATGTTAA
*
20392067 --TTAATATAATATTCATATT-T-AACATGATTAA
1 TTTTAATATAATATTCAAATTATAAACATG-TTAA
20392098 TTTTAA-ATAATA
1 TTTTAATATAATA
20392110 ACATATTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 6 0.16
31 5 0.13
32 23 0.61
33 4 0.11
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (34 bp):
TTTTAATATAATATTCAAATTATAAACATGTTAA
Found at i:20393098 original size:14 final size:16
Alignment explanation
Indices: 20393081--20393118 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
20393071 TTTAAATTAT
20393081 ATAAATTT-TAAA-AA
1 ATAAATTTATAAATAA
20393095 ATAAATTTGATAAATAA
1 ATAAATTT-ATAAATAA
20393112 ATAAATT
1 ATAAATT
20393119 ATATTATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
16 4 0.19
17 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
ATAAATTTATAAATAA
Found at i:20395235 original size:29 final size:29
Alignment explanation
Indices: 20395182--20395237 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
20395172 TTAAAATTTT
* *
20395182 TAATTTCAATAAATATGATTTAATTTTGA
1 TAATTTCAATAAATATGAATGAATTTTGA
20395211 TAATTTCAATTAAATAT-AATGAATTTT
1 TAATTTCAA-TAAATATGAATGAATTTT
20395238 TACATATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (29 bp):
TAATTTCAATAAATATGAATGAATTTTGA
Found at i:20396473 original size:22 final size:22
Alignment explanation
Indices: 20396448--20396490 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20396438 TAAGAATAAA
*
20396448 AAATTGACTTAATTAATCAATT
1 AAATTGACTTAATTAACCAATT
* *
20396470 AAATTGATTTATTTAACCAAT
1 AAATTGACTTAATTAACCAAT
20396491 AATTATCGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (22 bp):
AAATTGACTTAATTAACCAATT
Found at i:20397324 original size:14 final size:15
Alignment explanation
Indices: 20397296--20397334 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
20397286 ATTTTAAAAA
20397296 TTAA-TCAATTAAAT
1 TTAATTCAATTAAAT
20397310 TTAATTCAATT-AAT
1 TTAATTCAATTAAAT
*
20397324 TTAATTAAATT
1 TTAATTCAATT
20397335 TTTTAGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAATTCAATTAAAT
Found at i:20397516 original size:20 final size:21
Alignment explanation
Indices: 20397493--20397540 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
20397483 ATCCATTTCA
20397493 TAAATTTTTTATTTTAT-ATT
1 TAAATTTTTTATTTTATGATT
*
20397513 TAAA-TTTTTATTTTTTGATT
1 TAAATTTTTTATTTTATGATT
*
20397533 AAAATTTT
1 TAAATTTT
20397541 GGTTAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.46
20 10 0.42
21 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TAAATTTTTTATTTTATGATT
Found at i:20397522 original size:19 final size:20
Alignment explanation
Indices: 20397493--20397540 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
20397483 ATCCATTTCA
20397493 TAAATTTTTTATTTTAT-ATT
1 TAAA-TTTTTATTTTATGATT
*
20397513 TAAATTTTTATTTTTTGATT
1 TAAATTTTTATTTTATGATT
*
20397533 AAAATTTT
1 TAAATTTT
20397541 GGTTAATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TAAATTTTTATTTTATGATT
Found at i:20402457 original size:2 final size:2
Alignment explanation
Indices: 20402450--20402478 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20402440 ATTATGAACT
20402450 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
20402479 GATACCCTAC
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:20402705 original size:14 final size:14
Alignment explanation
Indices: 20402688--20402728 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
20402678 AGTTTTTTAA
*
20402688 TAAATATATATTTT
1 TAAATAAATATTTT
20402702 TAAATAAATATTTT
1 TAAATAAATATTTT
*
20402716 TAATTAAAATATT
1 TAAAT-AAATATT
20402729 AATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAAATAAATATTTT
Found at i:20406506 original size:14 final size:13
Alignment explanation
Indices: 20406470--20406506 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
20406460 TTTAAGTAAA
*
20406470 ATTTATAAAATTT
1 ATTTATAAAATTG
20406483 ATTTATAAAATTG
1 ATTTATAAAATTG
20406496 ATTTAATAAAA
1 ATTT-ATAAAA
20406507 AAAATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (13 bp):
ATTTATAAAATTG
Found at i:20406640 original size:14 final size:13
Alignment explanation
Indices: 20406617--20406653 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
20406607 TATCACTATT
20406617 TTTATTAAAAATA
1 TTTATTAAAAATA
20406630 TTTATTTAAAAATA
1 TTTA-TTAAAAATA
*
20406644 TATATTAAAA
1 TTTATTAAAA
20406654 TTTTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATTAAAAATA
Found at i:20407557 original size:14 final size:14
Alignment explanation
Indices: 20407538--20407572 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
20407528 ACTCGAGAGC
**
20407538 TTATTTAATTTTTT
1 TTATTTAATTTAGT
20407552 TTATTTAATTTAGT
1 TTATTTAATTTAGT
20407566 TTATTTA
1 TTATTTA
20407573 TATAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTATTTAATTTAGT
Found at i:20412655 original size:24 final size:25
Alignment explanation
Indices: 20412610--20412666 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
20412600 TGGATAAAAT
*
20412610 TATAAAGATGATTATCATTTTTTTAA
1 TATAAA-ATGATTATAATTTTTTTAA
20412636 TATAAAATGATT-TAATTTTTTTAA
1 TATAAAATGATTATAATTTTTTTAA
*
20412660 AATAAAA
1 TATAAAA
20412667 AAATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 17 0.59
25 6 0.21
26 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (25 bp):
TATAAAATGATTATAATTTTTTTAA
Found at i:20412788 original size:38 final size:39
Alignment explanation
Indices: 20412699--20412788 Score: 103
Period size: 39 Copynumber: 2.3 Consensus size: 39
20412689 TAAGTTTATA
*
20412699 TATTTTATTATATTTTTAAAAATTATATCAATAATTTAAAT
1 TATTTTATT-T-TTTTAAAAAATTATATCAATAATTTAAAT
* * *
20412740 TATATAATTTTTTTAAAAAATT-TAATTAATAA-TTAAAT
1 TATTTTATTTTTTTAAAAAATTAT-ATCAATAATTTAAAT
20412778 TATTTTATTTT
1 TATTTTATTTT
20412789 AATTTTTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
38 16 0.38
39 18 0.43
40 1 0.02
41 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (39 bp):
TATTTTATTTTTTTAAAAAATTATATCAATAATTTAAAT
Found at i:20426971 original size:21 final size:22
Alignment explanation
Indices: 20426922--20426971 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
20426912 ACGGAATTAA
*
20426922 TTGAATTGATAAAATCTAATAT
1 TTGAATTTATAAAATCTAATAT
* *
20426944 TT-CATTTATAAAAT-TTATAT
1 TTGAATTTATAAAATCTAATAT
20426964 TTGAATTT
1 TTGAATTT
20426972 TGTTGTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 7 0.30
21 14 0.61
22 2 0.09
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (22 bp):
TTGAATTTATAAAATCTAATAT
Found at i:20427514 original size:15 final size:14
Alignment explanation
Indices: 20427495--20427527 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20427485 AATATCTTTG
*
20427495 GTTTTTTGGTTTTT
1 GTTTTTTTGTTTTT
20427509 GTTTTTTTGTTTTT
1 GTTTTTTTGTTTTT
20427523 -TTTTT
1 GTTTTT
20427528 AAATCTTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (14 bp):
GTTTTTTTGTTTTT
Found at i:20436301 original size:60 final size:58
Alignment explanation
Indices: 20436102--20436482 Score: 340
Period size: 60 Copynumber: 6.4 Consensus size: 58
20436092 CTATGCAAGG
* ** * * *
20436102 AAAATTGATACTTTCAACTTTTCCT-TAAAGCA--TTTTAAAATTTTTATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTATTTTTAAAA
* * * *
20436157 AAAATTGATACATTCAACTTTTCCTAAAAAATGTATTTTTTATTGAAA-TATTATTTTTTAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAA--TA--TTTT-TTGAAATTTTTATTTTTAAAA
* * * *
20436219 AAAATTGATACTTTTAAGTTTTCCTCAAAAATACTTTTCTTGAAATTTTTAATTTCAAAA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTT-TTGAAATTTTTATTTTTAAAA
* * *
20436279 AAAATTGATACTTTCAA-TTTTTCTCAAAAAATATATTTTTAAAAATTTTTATTTTAAAAA
1 AAAATTGATACTTTCAACTTTTCCTC-AAAAATAT-TTTTT-GAAATTTTTATTTTTAAAA
* * **
20436339 AAAATTAATACTTTCAACTTTTCTTCAAAAATACTTTTTTGAAAATTTTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTG-AAA-TTTTTATTTTTAAAA
* * * * *
20436400 AATATTGATAATTTTAACTTTTCCTCAAAAATATTTTTTCCAAATTTTGTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-GAAATTTT-TATTTTTAAAA
* *
20436460 AAAATTTATACTTTTAACTTTTC
1 AAAATTGATACTTTCAACTTTTC
20436483 TTTAAAATTT
Statistics
Matches: 267, Mismatches: 41, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
55 24 0.09
56 3 0.01
58 1 0.00
59 24 0.09
60 124 0.46
61 47 0.18
62 39 0.15
63 5 0.02
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAATTTTTATTTTTAAAA
Found at i:20436472 original size:121 final size:118
Alignment explanation
Indices: 20436134--20436518 Score: 390
Period size: 121 Copynumber: 3.2 Consensus size: 118
20436124 CCTTAAAGCA
*
20436134 TTTT-AAAATTTTTATTTTCAAGAAAAATTGATACA-TTCAACTTTTCCTAAAAAATGTATTTTT
1 TTTTGAAAATTTTTATTTTCAAGAAAAATTGATA-ATTTCAACTTTTCCTCAAAAA--TATTTTT
* * * * *
20436197 TATTGAAA-TATTATTTTTTAAAAAAATTGATACTTTTAAGTTTTCCTCAAAAATACTT
63 TA--AAAATTTTTA-TTTTTAAAAAAATTAATACTTTTAACTTTTCTTCAAAAATACTT
* * * *
20436255 TTCTTG-AAATTTTTAATTTCAAAAAAAATTGATACTTTCAA-TTTTTCTCAAAAAATATATTTT
1 TT-TTGAAAATTTTTATTTTCAAGAAAAATTGATAATTTCAACTTTTCCTC-AAAAATAT-TTTT
* *
20436318 TAAAAATTTTTATTTTAAAAAAAAATTAATACTTTCAACTTTTCTTCAAAAATACTT
63 TAAAAATTTTTATTTT-TAAAAAAATTAATACTTTTAACTTTTCTTCAAAAATACTT
* * * * *
20436375 TTTTGAAAATTTTTTATTTTTAAGGAATATTGATAATTTTAACTTTTCCTCAAAAATATTTTTTC
1 TTTTGAAAA-TTTTTATTTTCAAGAAAAATTGATAATTTCAACTTTTCCTCAAAAATATTTTTTA
* * *
20436440 CAAATTTTGTATTTTTAAGAAAAATTTATACTTTTAACTTTTCTT-TAAAAT--TT
65 AAAATTTT-TATTTTTAA-AAAAATTAATACTTTTAACTTTTCTTCAAAAATACTT
* * *
20436493 TTTTAAAAAATTTTATTTTCAGGAAA
1 TTTTGAAAATTTTTATTTTCAAGAAA
20436519 TCATTGAAAA
Statistics
Matches: 221, Mismatches: 31, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
117 13 0.06
118 10 0.05
119 10 0.05
120 66 0.30
121 77 0.35
122 45 0.20
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.49
Consensus pattern (118 bp):
TTTTGAAAATTTTTATTTTCAAGAAAAATTGATAATTTCAACTTTTCCTCAAAAATATTTTTTAA
AAATTTTTATTTTTAAAAAAATTAATACTTTTAACTTTTCTTCAAAAATACTT
Found at i:20436567 original size:22 final size:20
Alignment explanation
Indices: 20436534--20436581 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
20436524 GAAAATTTAA
20436534 AAATATTTAATTAAATAAAT
1 AAATATTTAATTAAATAAAT
* *
20436554 AAATGATTTCAATTTAATCAAT
1 AAAT-ATTT-AATTAAATAAAT
20436576 AAATAT
1 AAATAT
20436582 ATAAGCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.17
21 6 0.25
22 14 0.58
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (20 bp):
AAATATTTAATTAAATAAAT
Found at i:20437355 original size:8 final size:8
Alignment explanation
Indices: 20437342--20437371 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
20437332 TATTGATCCC
20437342 ATTTTTAA
1 ATTTTTAA
20437350 ATTTTTAA
1 ATTTTTAA
20437358 ATTTTTAA
1 ATTTTTAA
20437366 ATTTTT
1 ATTTTT
20437372 TATTTAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
ATTTTTAA
Found at i:20437860 original size:84 final size:85
Alignment explanation
Indices: 20437696--20437946 Score: 231
Period size: 84 Copynumber: 3.0 Consensus size: 85
20437686 CGTAATGATT
* **
20437696 TGGATCAAACTGAAATTTGAAATAAATAACTTTGACAGAACCAAAGAAAGATCTGACATAGGCCA
1 TGGATCAAACTGAAATCTGAAATAAATAACTTTGACAGAACCAAAGAAAGATCTGACATAGGAAA
20437761 AAATCCAAAACAAAATGACC
66 AAATCCAAAACAAAATGACC
* * * * * * * *
20437781 TGGATCAAATTGAAGTCTGAAATAAGTAAC-TTGACTGAACTAGAG-AAGAATTTGGCATAGGAA
1 TGGATCAAACTGAAATCTGAAATAAATAACTTTGACAGAACCAAAGAAAG-ATCTGACATAGGAA
20437844 AAAATCCAAAACAAAATGACC
65 AAAATCCAAAACAAAATGACC
* * * * * ** * * *
20437865 TGGA-CTGAACTGAAGTCT-AACATGAATAACTTAGACCGAGTCAAAGAATGATCTGGCATAGGC
1 TGGATC-AAACTGAAATCTGAA-ATAAATAACTTTGACAGAACCAAAGAAAGATCTGACATAGGA
* * *
20437928 CAAGATCTAAAACAAAATG
64 AAAAATCCAAAACAAAATG
20437947 GCTTGGACAG
Statistics
Matches: 134, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
83 6 0.04
84 64 0.48
85 62 0.46
86 2 0.01
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (85 bp):
TGGATCAAACTGAAATCTGAAATAAATAACTTTGACAGAACCAAAGAAAGATCTGACATAGGAAA
AAATCCAAAACAAAATGACC
Found at i:20438065 original size:170 final size:168
Alignment explanation
Indices: 20437844--20438293 Score: 537
Period size: 170 Copynumber: 2.6 Consensus size: 168
20437834 GGCATAGGAA
* *
20437844 AAAATCCAAAACAAAATGACCTGGACTGAACTGAAGTCTAACATGAATAACTTAGACCGAGTCAA
1 AAAATCCAAAACAAAATGACCTGGACTGAACTGAAGTCTAAAATGAATAACTTAGACTGAGTCAA
* * *
20437909 AGAATGATCTGGCATAGGCCAAGATCTAAAACAAAATGGCTTGGACAGAATCGAAGCCTGAAATG
66 AGAA-GATCTGGCATAGGCCAA-ATCTAAAACAAAATGACTTGGACAGAATCAAAGCCTAAAATG
* * *
20437974 AACAACTTAGATTGAGTTGAAAAAAGATCT-GATATAAGCC
129 AACAACTTAGACTGAGCTGAAAAAAGATCTAG-CATAAGCC
* *
20438014 AAAATCCAAAACAAAATGACCTGGACTGAA-TCGAAGTTTAAAATGAATAACTTAGATTGAGTCA
1 AAAATCCAAAACAAAATGACCTGGACTGAACT-GAAGTCTAAAATGAATAACTTAGACTGAGTCA
* * * * * * **
20438078 AAGAAAGATCTAGCATATGCTGAAATCTAAGATAAAATGACCTAAACAGAATCAAAGCCTAAAAT
65 AAG-AAGATCTGGCATAGGC-CAAATCTAAAACAAAATGACTTGGACAGAATCAAAGCCTAAAAT
* * *
20438143 GAACAACTTGGACTGAGCTGAAAAAGGATCTAGCATAAGCT
128 GAACAACTTAGACTGAGCTGAAAAAAGATCTAGCATAAGCC
* * * * * *
20438184 AAAATCCAAAATAAAATGATCTAGATTGAACTGAAGTCTGAAATGAACAACTTAGACTGAGTCGA
1 AAAATCCAAAACAAAATGACCTGGACTGAACTGAAGTCTAAAATGAATAACTTAGACTGAGTC-A
* *
20438249 AA-AAGAATTTGGCCTAGGCCAAAATCTAAAACAAAATGACTTGGA
65 AAGAAG-ATCTGGCATAGGCC-AAATCTAAAACAAAATGACTTGGA
20438294 TTGAACCAAA
Statistics
Matches: 233, Mismatches: 39, Indels: 16
0.81 0.14 0.06
Matches are distributed among these distances:
169 4 0.02
170 220 0.94
171 9 0.04
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (168 bp):
AAAATCCAAAACAAAATGACCTGGACTGAACTGAAGTCTAAAATGAATAACTTAGACTGAGTCAA
AGAAGATCTGGCATAGGCCAAATCTAAAACAAAATGACTTGGACAGAATCAAAGCCTAAAATGAA
CAACTTAGACTGAGCTGAAAAAAGATCTAGCATAAGCC
Found at i:20438321 original size:85 final size:85
Alignment explanation
Indices: 20437742--20438321 Score: 441
Period size: 85 Copynumber: 6.8 Consensus size: 85
20437732 AGAACCAAAG
* * *
20437742 AAAG-ATCTGACATAGGCCAAAATCCAAAACAAAATGACCTGGA-TCAAATTGAAGTCTGAAAT-
1 AAAGAATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTGGACT-GAATCGAAGTCTGAAATG
* *
20437804 AAGTAACTT-GACTGA-ACTAGA
65 AA-TAACTTAGACTGAGTCGA-A
* * **
20437825 GAAGAATTTGGCATAGGAAAAAATCCAAAACAAAATGACCTGGACTGAA-CTGAAGTCT-AACAT
1 AAAGAATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTGGACTGAATC-GAAGTCTGAA-AT
*
20437888 GAATAACTTAGACCGAGTC-AA
64 GAATAACTTAGACTGAGTCGAA
* * * * * *
20437909 AGAATG-ATCTGGCATAGGCCAAGATCTAAAACAAAATGGCTTGGACAGAATCGAAGCCTGAAAT
1 A-AA-GAATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTGGACTGAATCGAAGTCTGAAAT
* * *
20437973 GAACAACTTAGATTGAGTTGAA
64 GAATAACTTAGACTGAGTCGAA
** * * *
20437995 AAA-AGATCTGATATAAGCCAAAATCCAAAACAAAATGACCTGGACTGAATCGAAGTTTAAAATG
1 AAAGA-ATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTGGACTGAATCGAAGTCTGAAATG
* *
20438059 AATAACTTAGATTGAGTCAAA
65 AATAACTTAGACTGAGTCGAA
* * ** * * * ** * * * *
20438080 GAAAG-ATCTAGCATATGCTGAAATCTAAGATAAAATGACCTAAACAGAATCAAAGCCTAAAATG
1 -AAAGAATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTGGACTGAATCGAAGTCTGAAATG
* *
20438144 AACAACTTGGACTGAG-CTGAA
65 AATAACTTAGACTGAGTC-GAA
* * * * * * * *
20438165 AAAGGATCTAGCATAAGCTAAAATCCAAAATAAAATGATCTAGATTGAA-CTGAAGTCTGAAATG
1 AAAGAATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTGGACTGAATC-GAAGTCTGAAATG
*
20438229 AACAACTTAGACTGAGTCGAA
65 AATAACTTAGACTGAGTCGAA
* * * * * * *
20438250 AAAGAATTTGGCCTAGGCCAAAATCTAAAACAAAATGACTTGGATTGAACCAAAGTCTGAAAT-A
1 AAAGAATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTGGACTGAATCGAAGTCTGAAATGA
20438314 AGTAACTT
66 A-TAACTT
20438322 GATTAAACTA
Statistics
Matches: 394, Mismatches: 81, Indels: 42
0.76 0.16 0.08
Matches are distributed among these distances:
83 5 0.01
84 61 0.15
85 315 0.80
86 13 0.03
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (85 bp):
AAAGAATCTGGCATAGGCCAAAATCCAAAACAAAATGACCTGGACTGAATCGAAGTCTGAAATGA
ATAACTTAGACTGAGTCGAA
Found at i:20438630 original size:17 final size:17
Alignment explanation
Indices: 20438610--20438652 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
20438600 GAAGAATTGT
20438610 AAGATTTTCAA-ATTCGC
1 AAGA-TTTCAAGATTCGC
*
20438627 AAGATTTGAAGATTCGC
1 AAGATTTCAAGATTCGC
20438644 AAGAATTTC
1 AAG-ATTTC
20438653 TTATTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 13 0.59
18 4 0.18
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (17 bp):
AAGATTTCAAGATTCGC
Found at i:20438741 original size:17 final size:16
Alignment explanation
Indices: 20438721--20438765 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
20438711 AGAATCGGAG
*
20438721 ATTCACAAGAATTTCAT
1 ATTCACAAAAATTTC-T
*
20438738 ATTCAAAAAAATTTCT
1 ATTCACAAAAATTTCT
20438754 AGTTCACAAAAA
1 A-TTCACAAAAA
20438766 ATTTTAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 2 0.08
17 22 0.92
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.31
Consensus pattern (16 bp):
ATTCACAAAAATTTCT
Found at i:20438766 original size:18 final size:17
Alignment explanation
Indices: 20438730--20438769 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
20438720 GATTCACAAG
20438730 AATTTCATATTCAAAAA
1 AATTTCATATTCAAAAA
20438747 AATTTC-TAGTTCACAAAA
1 AATTTCATA-TTCA-AAAA
20438765 AATTT
1 AATTT
20438770 TAGATTTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.10
17 10 0.48
18 9 0.43
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (17 bp):
AATTTCATATTCAAAAA
Found at i:20440099 original size:8 final size:8
Alignment explanation
Indices: 20440086--20440123 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
20440076 AGTCTTCATT
20440086 TTTTTTTA
1 TTTTTTTA
20440094 TTTTTTTA
1 TTTTTTTA
*
20440102 TTTTTGT-
1 TTTTTTTA
*
20440109 TTTTTTCA
1 TTTTTTTA
20440117 TTTTTTT
1 TTTTTTT
20440124 TACTTCATCC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.08, C:0.03, G:0.03, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:20444293 original size:59 final size:60
Alignment explanation
Indices: 20444108--20444370 Score: 300
Period size: 60 Copynumber: 4.4 Consensus size: 60
20444098 TCTTAAAGCA
* * **
20444108 TTTTAAAAATTTTATCTTCAA-AGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTT
1 TTTTGAAAATTTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTCCTCAAAAATACCTT
* * * *
20444168 TTTTGAAAATTTTAATTTCAAGAAAAATTGATCCTTTCAACTTTTTCTCAAAAATACCTC
1 TTTTGAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATACCTT
* * **
20444228 TTTTGAAATTTTTATTTTCAAGAAAAATTAATACTTTCAACTTTTCCTTGAAAATA-CTT
1 TTTTGAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATACCTT
* * * * * *
20444287 TTTTGAAATTTTTTATTTT-AAAAAAAATTTATACTTTTAACTTTTTCTCAAAAATA-TTT
1 TTTTGAAA-ATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATACCTT
* *
20444346 TTTTTAAAATTTTATTTTCAGGAAA
1 TTTTGAAAATTTTATTTTCAAGAAA
20444371 TCATTGAAAA
Statistics
Matches: 173, Mismatches: 27, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
58 9 0.05
59 54 0.31
60 109 0.63
61 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (60 bp):
TTTTGAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATACCTT
Found at i:20444341 original size:119 final size:119
Alignment explanation
Indices: 20444074--20444370 Score: 336
Period size: 119 Copynumber: 2.5 Consensus size: 119
20444064 TTTTATGCAG
* * * * *
20444074 AAAAAATTGATACTTTTAACTTTTTCT--TAAA-GC-ATTTTAAAAATTTTATCTTCAA-AGAAA
1 AAAAAATTGATACTTTCAACTTTTTCTCAAAAATACTCTTTTAAAAATTTTATTTTCAAGA-AAA
* *
20444134 ATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAAATTTTAATTTCAA
65 ATTAATACTTTCAACTTTTCCTCAAAAATATCTTTTTTGAAAATTTTAATTTCAA
* * * *
20444189 GAAAAATTGATCCTTTCAACTTTTTCTCAAAAATACCTCTTTTGAAATTTTTATTTTCAAGAAAA
1 AAAAAATTGATACTTTCAACTTTTTCTCAAAAATA-CTCTTTTAAAAATTTTATTTTCAAGAAAA
** * * *
20444254 ATTAATACTTTCAACTTTTCCTTGAAAATA-CTTTTTTGAAATTTTTTATTTTAA
65 ATTAATACTTTCAACTTTTCCTCAAAAATATCTTTTTTGAAAATTTTAATTTCAA
* * * * * *
20444308 AAAAAATTTATACTTTTAACTTTTTCTCAAAAATATTTTTTTTAAAATTTTATTTTCAGGAAA
1 AAAAAATTGATACTTTCAACTTTTTCTCAAAAATACTCTTTTAAAAATTTTATTTTCAAGAAA
20444371 TCATTGAAAA
Statistics
Matches: 151, Mismatches: 25, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
115 24 0.16
117 3 0.02
118 23 0.15
119 52 0.34
120 48 0.32
121 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.47
Consensus pattern (119 bp):
AAAAAATTGATACTTTCAACTTTTTCTCAAAAATACTCTTTTAAAAATTTTATTTTCAAGAAAAA
TTAATACTTTCAACTTTTCCTCAAAAATATCTTTTTTGAAAATTTTAATTTCAA
Found at i:20446025 original size:23 final size:23
Alignment explanation
Indices: 20445975--20446018 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
20445965 AAAAAAAATA
* *
20445975 AAAATAGATAGTTAAATCTGTAT
1 AAAATAAATAGATAAATCTGTAT
*
20445998 AAAATAAATAGATAAGTCTGT
1 AAAATAAATAGATAAATCTGT
20446019 TCAAAATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.32
Consensus pattern (23 bp):
AAAATAAATAGATAAATCTGTAT
Found at i:20446341 original size:64 final size:65
Alignment explanation
Indices: 20446228--20446357 Score: 190
Period size: 64 Copynumber: 2.0 Consensus size: 65
20446218 AATTTTACAA
* * *
20446228 AAGTTCGGTGATCTTGTAATACGTCGGTGAATACTCAGTGGACTAATTTTGTATAATCAATCATT
1 AAGTTCGATGATCTAGTAATACGTCGATGAATACTCAGTGGACTAATTTTGTATAATCAATCATT
* * * *
20446293 AAGTTCGATGATCTAGTGATACGT-GATGAATATTCGGTGGACTAATTTTGTGTAATCAATCATT
1 AAGTTCGATGATCTAGTAATACGTCGATGAATACTCAGTGGACTAATTTTGTATAATCAATCATT
20446357 A
1 A
20446358 GGCTTCATTA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
64 37 0.64
65 21 0.36
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (65 bp):
AAGTTCGATGATCTAGTAATACGTCGATGAATACTCAGTGGACTAATTTTGTATAATCAATCATT
Found at i:20449816 original size:16 final size:15
Alignment explanation
Indices: 20449781--20449829 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
20449771 TTAAGATTTA
20449781 TGAAA-TAAATTTCAT
1 TGAAATTAAATTTC-T
*
20449796 T-AAATTTGAATTTCT
1 TGAAA-TTAAATTTCT
20449811 TGAAATTAAATTT-T
1 TGAAATTAAATTTCT
20449825 TGAAA
1 TGAAA
20449830 ATCTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 9 0.31
15 10 0.34
16 10 0.34
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (15 bp):
TGAAATTAAATTTCT
Found at i:20450425 original size:14 final size:12
Alignment explanation
Indices: 20450404--20450437 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
20450394 TTTTTTGTTT
20450404 ATATATATATAA
1 ATATATATATAA
20450416 TATAATATATATAA
1 -AT-ATATATATAA
20450430 ATATATAT
1 ATATATAT
20450438 TGTCCGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 4 0.20
14 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATATATATAA
Found at i:20450701 original size:2 final size:2
Alignment explanation
Indices: 20450696--20450722 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20450686 CTTGTGTGTG
20450696 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
20450723 GGAATGATAG
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:20458569 original size:22 final size:21
Alignment explanation
Indices: 20458528--20458570 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
20458518 AACAAACAAC
**
20458528 ATATTAAATAATAATTTTATT
1 ATATTAAATAATAAAATTATT
20458549 ATATTAAATTAATAAAATTATT
1 ATATTAAA-TAATAAAATTATT
20458571 TTATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTAAATAATAAAATTATT
Found at i:20459689 original size:22 final size:23
Alignment explanation
Indices: 20459655--20459700 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
20459645 TTTTTTGTTC
*
20459655 TTTATATATTATTTTAATATAATT
1 TTTATATATTATTTAAATA-AATT
20459679 TTTA-ATA-TATTTAAATAAATT
1 TTTATATATTATTTAAATAAATT
20459700 T
1 T
20459701 AAATATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 9 0.43
23 3 0.14
24 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTATATATTATTTAAATAAATT
Found at i:20459705 original size:20 final size:21
Alignment explanation
Indices: 20459667--20459707 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
20459657 TATATATTAT
* *
20459667 TTTAATATAATTTTTAATATA
1 TTTAATATAAATTTAAATATA
20459688 TTTAA-ATAAATTTAAATATA
1 TTTAATATAAATTTAAATATA
20459708 AAATAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATATAAATTTAAATATA
Found at i:20461571 original size:14 final size:14
Alignment explanation
Indices: 20461552--20461592 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
20461542 TTTAAAATAA
* *
20461552 ATAAAAAATAAATG
1 ATAAAAAACAAAAG
20461566 ATAAAAAACAAAAG
1 ATAAAAAACAAAAG
*
20461580 ATAAACAACAAAA
1 ATAAAAAACAAAA
20461593 AACAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.76, C:0.07, G:0.05, T:0.12
Consensus pattern (14 bp):
ATAAAAAACAAAAG
Found at i:20461583 original size:21 final size:21
Alignment explanation
Indices: 20461554--20461599 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
20461544 TAAAATAAAT
** *
20461554 AAAAAATAAATGATAAAAAAC
1 AAAAAATAAACAACAAAAAAC
*
20461575 AAAAGATAAACAACAAAAAAC
1 AAAAAATAAACAACAAAAAAC
20461596 AAAA
1 AAAA
20461600 TAATGAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.78, C:0.09, G:0.04, T:0.09
Consensus pattern (21 bp):
AAAAAATAAACAACAAAAAAC
Found at i:20461957 original size:22 final size:23
Alignment explanation
Indices: 20461920--20461981 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
20461910 AAATTATAAT
*
20461920 TTATT-TTTTTAAATATCTAAAA
1 TTATTATTTTTATATATCTAAAA
* * *
20461942 TTTTTATTTTT-TATATTTTTAAA
1 TTATTATTTTTATATA-TCTAAAA
20461965 TTATTATTTTTATATAT
1 TTATTATTTTTATATAT
20461982 TTTTTATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 7 0.22
23 21 0.66
24 4 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (23 bp):
TTATTATTTTTATATATCTAAAA
Found at i:20461965 original size:23 final size:24
Alignment explanation
Indices: 20461939--20461985 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
20461929 TAAATATCTA
*
20461939 AAATTTTTATTTTT-TATATTTTT
1 AAATTATTATTTTTATATATTTTT
20461962 AAATTATTATTTTTATATATTTTT
1 AAATTATTATTTTTATATATTTTT
20461986 TATTTTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
AAATTATTATTTTTATATATTTTT
Found at i:20462791 original size:27 final size:28
Alignment explanation
Indices: 20462749--20462812 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 28
20462739 ATTTTTATTT
20462749 ATTTATGTTTAATTTATTTAAA-T-AATAA
1 ATTTAT-TTTAATTTA-TTAAATTAAATAA
20462777 A-TTATTTTAATTTTATTAAATTAAATAA
1 ATTTATTTTAA-TTTATTAAATTAAATAA
20462805 ATTTATTT
1 ATTTATTT
20462813 GTAAATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
26 10 0.31
27 9 0.28
28 7 0.22
29 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
ATTTATTTTAATTTATTAAATTAAATAA
Found at i:20462829 original size:10 final size:10
Alignment explanation
Indices: 20462814--20462845 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
20462804 AATTTATTTG
20462814 TAAATATATA
1 TAAATATATA
20462824 TAAATATATA
1 TAAATATATA
*
20462834 TAAATAAATA
1 TAAATATATA
20462844 TA
1 TA
20462846 TTCACACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAATATATA
Found at i:20462840 original size:14 final size:14
Alignment explanation
Indices: 20462817--20462846 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20462807 TTATTTGTAA
*
20462817 ATATATATAAATAT
1 ATATAAATAAATAT
20462831 ATATAAATAAATAT
1 ATATAAATAAATAT
20462845 AT
1 AT
20462847 TCACACATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAAATAAATAT
Found at i:20462900 original size:21 final size:20
Alignment explanation
Indices: 20462857--20462901 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
20462847 TCACACATCC
*
20462857 TAAAAAAATCATAACTAAAA
1 TAAAAAAATCATAACGAAAA
* *
20462877 TAAAAAAATTATAAACGAATA
1 TAAAAAAATCAT-AACGAAAA
20462898 TAAA
1 TAAA
20462902 TGAATTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (20 bp):
TAAAAAAATCATAACGAAAA
Found at i:20464054 original size:14 final size:15
Alignment explanation
Indices: 20464032--20464066 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
20464022 TTTTTTACAC
*
20464032 TTTTCATTAAA-AAA
1 TTTTAATTAAATAAA
20464046 TTTTAATTAAATAAA
1 TTTTAATTAAATAAA
20464061 TTTTAA
1 TTTTAA
20464067 AAATAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAATTAAATAAA
Found at i:20471146 original size:2 final size:2
Alignment explanation
Indices: 20471139--20471171 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20471129 TTTTAATAAT
20471139 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
20471172 CATAGCCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20475865 original size:27 final size:25
Alignment explanation
Indices: 20475839--20475895 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
20475829 TATATATATA
20475839 ATATTTATTATTATTTATTTAATTAT
1 ATATTTATTA-TATTTATTTAATTAT
* *
20475865 ATA--TGTTATATTTATTTAATTTT
1 ATATTTATTATATTTATTTAATTAT
20475888 ATATTTAT
1 ATATTTAT
20475896 ATTTTAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 17 0.65
24 4 0.15
25 2 0.08
26 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
ATATTTATTATATTTATTTAATTAT
Found at i:20475896 original size:31 final size:33
Alignment explanation
Indices: 20475829--20475897 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
20475819 TTTGATTCGA
* *
20475829 TATATATATAATATTTATTATTATTTATTTAAT
1 TATATATATAATATTTATTATAATTTATATAAT
* * *
20475862 TATATATGTTATATTTATT-TAATTT-TATATT
1 TATATATATAATATTTATTATAATTTATATAAT
20475893 TATAT
1 TATAT
20475898 TTTAAAAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 9 0.29
32 5 0.16
33 17 0.55
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (33 bp):
TATATATATAATATTTATTATAATTTATATAAT
Found at i:20475901 original size:23 final size:23
Alignment explanation
Indices: 20475850--20475899 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
20475840 TATTTATTAT
20475850 TATTTATTTAATTATATATGTTA
1 TATTTATTTAATTATATATGTTA
*
20475873 TATTTATTTAATTTTATAT-TTA
1 TATTTATTTAATTATATATGTTA
20475895 TATTT
1 TATTT
20475900 TAAAAGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
TATTTATTTAATTATATATGTTA
Done.