Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006714.1 Hibiscus syriacus cultivar Beakdansim tig00016763_pilon, 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: 138598
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4366 original size:37 final size:37
Alignment explanation
Indices: 4316--4389 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
4306 AACTCAATCC
*
4316 GATTCAATCGAATCTAAACTCAAACTCAAATTGCCAA
1 GATTCAATCGAATCTAAACTCAAACTCAAAATGCCAA
* *
4353 GATTCAATTGAATCTAATCTCAAACTCAAAATGCCAA
1 GATTCAATCGAATCTAAACTCAAACTCAAAATGCCAA
4390 CAATCTAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (37 bp):
GATTCAATCGAATCTAAACTCAAACTCAAAATGCCAA
Found at i:6838 original size:129 final size:128
Alignment explanation
Indices: 6609--6862 Score: 463
Period size: 129 Copynumber: 2.0 Consensus size: 128
6599 GAAAAGGTGC
* *
6609 AAATAGTTATTTTCATAAAGTAGTAGCAATAATATCATTCCGTAATCTCCTTTTTCTCGGTGAGT
1 AAATAGTTATTTTCATAAAGCAGTAGCAATAATATCATTCCGTAATCTCCTTTTTCTCGGAGAGT
6674 TTTCTTGATGTTCAAAGTGATGAACTCACTGATATTAAACTAACTAGCAACTCAAGCAGTAGA
66 TTTCTTGATGTTCAAAGTGATGAACTCACTGATATTAAACTAACTAGCAACTCAAGCAGTAGA
6737 AAATAGTTATTTTCATAAAGCAGTAGCAATAAATATCATTCCGTAATCTCCTTTTTCTCGGAGAG
1 AAATAGTTATTTTCATAAAGCAGTAGCAAT-AATATCATTCCGTAATCTCCTTTTTCTCGGAGAG
* *
6802 TTTTCTTGATGTTCAAAGTGATGAACTCACTGATATTGAACTAACTAGCAACTCAATCAGT
65 TTTTCTTGATGTTCAAAGTGATGAACTCACTGATATTAAACTAACTAGCAACTCAAGCAGT
6863 GCCACTGCTC
Statistics
Matches: 121, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
128 29 0.24
129 92 0.76
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (128 bp):
AAATAGTTATTTTCATAAAGCAGTAGCAATAATATCATTCCGTAATCTCCTTTTTCTCGGAGAGT
TTTCTTGATGTTCAAAGTGATGAACTCACTGATATTAAACTAACTAGCAACTCAAGCAGTAGA
Found at i:13988 original size:21 final size:21
Alignment explanation
Indices: 13939--13985 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
13929 ACCAATCATT
*
13939 GATTTTGTCTAGGTTGTGCAC
1 GATTTTGTATAGGTTGTGCAC
13960 TGA-TTTGTATAGGTTGTGCA-
1 -GATTTTGTATAGGTTGTGCAC
13980 GATTTT
1 GATTTT
13986 TGTTTGGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 2 0.09
20 3 0.13
21 16 0.70
22 2 0.09
ACGTcount: A:0.17, C:0.09, G:0.28, T:0.47
Consensus pattern (21 bp):
GATTTTGTATAGGTTGTGCAC
Found at i:16124 original size:51 final size:51
Alignment explanation
Indices: 16044--16140 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
16034 GACTAATGAA
* * * *
16044 TAAAAATAATGTTTTGATTCTATCATAATTCCTAATAAGATAATAATAAAC
1 TAAAAATAATGTTTTAACTCAATCATAATTCCTAATAAAATAATAATAAAC
*
16095 TAAAAATAATGTTTTAACTCAATCTTAATTCCTAATAAAATAATAA
1 TAAAAATAATGTTTTAACTCAATCATAATTCCTAATAAAATAATAA
16141 ATCTAATACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.37
Consensus pattern (51 bp):
TAAAAATAATGTTTTAACTCAATCATAATTCCTAATAAAATAATAATAAAC
Found at i:27862 original size:21 final size:21
Alignment explanation
Indices: 27838--27879 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
27828 TCAGCACCAC
27838 AAGCGCTCAACGGAACACCTT
1 AAGCGCTCAACGGAACACCTT
*
27859 AAGCGCTCCACGGAACACCTT
1 AAGCGCTCAACGGAACACCTT
27880 CATGATTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.36, G:0.19, T:0.14
Consensus pattern (21 bp):
AAGCGCTCAACGGAACACCTT
Found at i:33394 original size:20 final size:20
Alignment explanation
Indices: 33369--33440 Score: 144
Period size: 20 Copynumber: 3.6 Consensus size: 20
33359 AATGACCAAC
33369 AAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGGTCAAAAG
33389 AAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGGTCAAAAG
33409 AAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGGTCAAAAG
33429 AAAATCGCAACG
1 AAAATCGCAACG
33441 CGATCTTCCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.50, C:0.21, G:0.19, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGGTCAAAAG
Found at i:33459 original size:22 final size:21
Alignment explanation
Indices: 33431--33533 Score: 99
Period size: 20 Copynumber: 5.0 Consensus size: 21
33421 GTCAAAAGAA
33431 AATCGCAACGCGATCTTCCA-AG
1 AATCGCAACGCGAT-TT-CAGAG
* *
33453 AATCGCAATGCGA-TTAAGAG
1 AATCGCAACGCGATTTCAGAG
33473 AATCGCAACGCGATCTTCCA-AG
1 AATCGCAACGCGAT-TT-CAGAG
* *
33495 AATCGCAATGCG-TTTCAGAA
1 AATCGCAACGCGATTTCAGAG
33515 AATCGCAACGCGA-TTCAGA
1 AATCGCAACGCGATTTCAGA
33534 AAATGAGTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
19 3 0.04
20 36 0.53
21 1 0.01
22 27 0.40
23 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19
Consensus pattern (21 bp):
AATCGCAACGCGATTTCAGAG
Found at i:33477 original size:42 final size:42
Alignment explanation
Indices: 33426--33528 Score: 179
Period size: 42 Copynumber: 2.5 Consensus size: 42
33416 CAACGGTCAA
33426 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT
* *
33468 AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAATGCGTTT
1 AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT
*
33510 CAGAAAATCGCAACGCGAT
1 AAGAAAATCGCAACGCGAT
33529 TCAGAAAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGATT
Found at i:33692 original size:84 final size:84
Alignment explanation
Indices: 33551--33720 Score: 340
Period size: 84 Copynumber: 2.0 Consensus size: 84
33541 TAAATTCTTT
33551 CAAAAGCTGTTGCATTTGTTTATTTCTTAAGAATTTTCTCTAAAAAGATAGTATCCGCGCGGACG
1 CAAAAGCTGTTGCATTTGTTTATTTCTTAAGAATTTTCTCTAAAAAGATAGTATCCGCGCGGACG
33616 TGTCGAAGACACGTATTAC
66 TGTCGAAGACACGTATTAC
33635 CAAAAGCTGTTGCATTTGTTTATTTCTTAAGAATTTTCTCTAAAAAGATAGTATCCGCGCGGACG
1 CAAAAGCTGTTGCATTTGTTTATTTCTTAAGAATTTTCTCTAAAAAGATAGTATCCGCGCGGACG
33700 TGTCGAAGACACGTATTAC
66 TGTCGAAGACACGTATTAC
33719 CA
1 CA
33721 CGACCACGAC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (84 bp):
CAAAAGCTGTTGCATTTGTTTATTTCTTAAGAATTTTCTCTAAAAAGATAGTATCCGCGCGGACG
TGTCGAAGACACGTATTAC
Found at i:33728 original size:6 final size:6
Alignment explanation
Indices: 33717--33868 Score: 297
Period size: 6 Copynumber: 25.5 Consensus size: 6
33707 GACACGTATT
33717 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
33765 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
33813 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
33861 A-CACG ACC
1 ACCACG ACC
33869 CGAGACGAGA
Statistics
Matches: 145, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.03
6 140 0.97
ACGTcount: A:0.34, C:0.50, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:34370 original size:5 final size:5
Alignment explanation
Indices: 34366--34471 Score: 113
Period size: 5 Copynumber: 20.2 Consensus size: 5
34356 CTCGTCTCGG
* * *
34366 GTCGG GTCGG GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GGTCTT
1 GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT GTCGT -GTCGT
* * *
34417 GGTCTT GGTCTT GTCGT GGTCTT GGTCGT GTCGT GTCGT GTCGT GTCGT
1 -GTCGT -GTCGT GTCGT -GTCGT -GTCGT GTCGT GTCGT GTCGT GTCGT
34466 GTCGT G
1 GTCGT G
34472 GTCTTGGTCG
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
5 69 0.73
6 25 0.27
ACGTcount: A:0.00, C:0.19, G:0.42, T:0.40
Consensus pattern (5 bp):
GTCGT
Found at i:34421 original size:6 final size:6
Alignment explanation
Indices: 34410--34443 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
34400 TGTCGTGTCG
*
34410 TGGTCT TGGTCT TGGTCT T-GTCG TGGTCT TGGTC
1 TGGTCT TGGTCT TGGTCT TGGTCT TGGTCT TGGTC
34444 GTGTCGTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.00, C:0.18, G:0.35, T:0.47
Consensus pattern (6 bp):
TGGTCT
Found at i:34444 original size:12 final size:12
Alignment explanation
Indices: 34406--34503 Score: 87
Period size: 12 Copynumber: 8.2 Consensus size: 12
34396 GTCGTGTCGT
34406 GTCGTGGTCTTG
1 GTCGTGGTCTTG
*
34418 GTCTTGGTCTT-
1 GTCGTGGTCTTG
34429 GTCGTGGTCTTG
1 GTCGTGGTCTTG
*
34441 GTCGT-GTCGT-
1 GTCGTGGTCTTG
34451 GTCGT-GTCGTGTCG
1 GTCGTGGTC-T-T-G
34465 TGTCGTGGTCTTG
1 -GTCGTGGTCTTG
*
34478 GTCGTGGTCGTG
1 GTCGTGGTCTTG
* *
34490 GTTGTGGTCGTG
1 GTCGTGGTCTTG
34502 GT
1 GT
34504 AATACGTGTC
Statistics
Matches: 73, Mismatches: 6, Indels: 14
0.78 0.06 0.15
Matches are distributed among these distances:
10 8 0.11
11 14 0.19
12 40 0.55
13 1 0.01
14 1 0.01
15 6 0.08
16 3 0.04
ACGTcount: A:0.00, C:0.16, G:0.42, T:0.42
Consensus pattern (12 bp):
GTCGTGGTCTTG
Found at i:34458 original size:55 final size:55
Alignment explanation
Indices: 34370--34501 Score: 184
Period size: 55 Copynumber: 2.5 Consensus size: 55
34360 TCTCGGGTCG
* *
34370 GGTCG-GGTCGT-GTCGT-GTCGTGTCGTGTCGTGTCGTGTCGTGGTCTTGGTCTT
1 GGTCGTGGTCGTGGTTGTGGTCGTGTCGTGTCGTGTCGTGTCGT-GTCGTGGTCTT
*
34423 GGTC-TTGTCGTGGTCT-TGGTCGTGTCGTGTCGTGTCGTGTCGTGTCGTGGTCTT
1 GGTCGTGGTCGTGGT-TGTGGTCGTGTCGTGTCGTGTCGTGTCGTGTCGTGGTCTT
34477 GGTCGTGGTCGTGGTTGTGGTCGTG
1 GGTCGTGGTCGTGGTTGTGGTCGTG
34502 GTAATACGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
53 9 0.13
54 18 0.26
55 42 0.61
ACGTcount: A:0.00, C:0.17, G:0.42, T:0.40
Consensus pattern (55 bp):
GGTCGTGGTCGTGGTTGTGGTCGTGTCGTGTCGTGTCGTGTCGTGTCGTGGTCTT
Found at i:34512 original size:60 final size:60
Alignment explanation
Indices: 34388--34513 Score: 173
Period size: 60 Copynumber: 2.1 Consensus size: 60
34378 CGTGTCGTGT
* * * ** *
34388 CGTGTCGTGTCGTGTCGTGTCGTGGTCTTGGTCTTGGTCTTGTCGTGGTCTTGGTCGTGT
1 CGTGTCGTGTCGTGTCGTGTCGTGGTCTTGGTCGTGGTCTGGTCGTGGTCGTGGTAATGA
*
34448 CGTGTCGTGTCGTGTCGTGTCGTGGTCTTGGTCGTGGTCGTGGTTGTGGTCGTGGTAAT-A
1 CGTGTCGTGTCGTGTCGTGTCGTGGTCTTGGTCGTGGTC-TGGTCGTGGTCGTGGTAATGA
34508 CGTGTC
1 CGTGTC
34514 TTCGACACGT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 44 0.76
61 14 0.24
ACGTcount: A:0.02, C:0.17, G:0.40, T:0.40
Consensus pattern (60 bp):
CGTGTCGTGTCGTGTCGTGTCGTGGTCTTGGTCGTGGTCTGGTCGTGGTCGTGGTAATGA
Found at i:34631 original size:20 final size:20
Alignment explanation
Indices: 34606--34804 Score: 212
Period size: 20 Copynumber: 9.8 Consensus size: 20
34596 CTCATTTTCT
34606 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
34626 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
34647 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
34666 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
34687 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
34706 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
34726 GAAGATCGCGTTGCGATT-TTAT
1 G-A-ATCGCGTTGCGATTCTT-G
* *
34748 GAATCGCATTGCGATT-TTAT
1 GAATCGCGTTGCGATTCTT-G
* *
34768 GAATCGCTTTGCGATACTTAG
1 GAATCGCGTTGCGATTCTT-G
*
34789 AAGATCGCGTTGCGAT
1 GA-ATCGCGTTGCGAT
34805 CTTCTTCTCA
Statistics
Matches: 159, Mismatches: 7, Indels: 24
0.84 0.04 0.13
Matches are distributed among these distances:
18 10 0.06
20 104 0.65
21 8 0.05
22 37 0.23
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:34654 original size:40 final size:40
Alignment explanation
Indices: 34599--34810 Score: 264
Period size: 40 Copynumber: 5.2 Consensus size: 40
34589 AAATTTACTC
*
34599 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
34639 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
34679 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*** * *
34719 ATTCTTGGAAGATCGCGTTGCGATT-TTATGAATCGCATTGCG
1 ATT-TTCTTA-ATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
* * * * *
34761 ATTTTATGAATCGCTTTGCGATACTTAGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTT-GGA-ATCGCGTTGCG
*
34803 ATCTTCTT
1 ATTTTCTT
34811 CTCAACGTTG
Statistics
Matches: 150, Mismatches: 17, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
40 94 0.63
41 12 0.08
42 44 0.29
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.39
Consensus pattern (40 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:34744 original size:62 final size:61
Alignment explanation
Indices: 34608--34866 Score: 248
Period size: 62 Copynumber: 4.3 Consensus size: 61
34598 CATTTTCTGA
34608 ATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATTTTCTT-AATCGCGTTGCGATTCTTGG-A-
1 ATCGCGTTGCGATTTTCTT--AATCGCGTTGCGA--TTCTTGAATCGCGTTGCGATTCTTGGAAG
34668 ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTT-GAATCGCGTTGCGATTCTTGGAAG
* * * * * * *
34730 ATCGCGTTGCGATTTTATGAATCGCATTGCGATTTTATGAATCGCTTTGCGATACTTAGAAG
1 ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCT-TGAATCGCGTTGCGATTCTTGGAAG
* * * * * * * *
34792 ATCGCGTTGCGATCTTCTT-CTCAACGTTGCGCTTTTCTAAATCGCGTTGCGGTTC-T-G-AT
1 ATCGCGTTGCGATTTTCTTAATC-GCGTTGCGATTCT-TGAATCGCGTTGCGATTCTTGGAAG
34851 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
34867 GTTGGTCATT
Statistics
Matches: 170, Mismatches: 21, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
58 5 0.03
59 16 0.09
60 46 0.27
61 4 0.02
62 98 0.58
63 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (61 bp):
ATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTGAATCGCGTTGCGATTCTTGGAAG
Found at i:34839 original size:20 final size:20
Alignment explanation
Indices: 34816--34866 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
34806 TTCTTCTCAA
* *
34816 CGTTGCGCTTTTCTAAATCG
1 CGTTGCGATTTTCTGAATCG
*
34836 CGTTGCG--GTTCTGATATCG
1 CGTTGCGATTTTCTGA-ATCG
34855 CGTTGCGATTTT
1 CGTTGCGATTTT
34867 GTTGGTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 5 0.20
19 11 0.44
20 7 0.28
21 2 0.08
ACGTcount: A:0.12, C:0.22, G:0.25, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTTTCTGAATCG
Found at i:37417 original size:23 final size:22
Alignment explanation
Indices: 37387--37429 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
37377 GCATCAAATA
37387 TCTCGGTCCGGTGAGTCTTTATT
1 TCTCGGTCCGGT-AGTCTTTATT
*
37410 TCTCGGTCCGGTAGTGTTTA
1 TCTCGGTCCGGTAGTCTTTA
37430 GGTGCACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
TCTCGGTCCGGTAGTCTTTATT
Found at i:60758 original size:22 final size:22
Alignment explanation
Indices: 60717--60797 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
60707 CTCGTATAAA
60717 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
60740 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
60762 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
60784 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
60798 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:60793 original size:13 final size:13
Alignment explanation
Indices: 60731--60793 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
60721 CCGAAGTGCC
60731 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
60744 CC---GAAGTGC-
1 CCGTAGAATTGCA
60753 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
60766 CC---GAAGTGC-
1 CCGTAGAATTGCA
60775 CCGTAGAATTGCA
1 CCGTAGAATTGCA
60788 CCGTAG
1 CCGTAG
60794 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:62505 original size:21 final size:21
Alignment explanation
Indices: 62481--62525 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
62471 TCTTGTTCGT
* *
62481 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
62502 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
62523 TTG
1 TTG
62526 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:65735 original size:22 final size:22
Alignment explanation
Indices: 65694--65774 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
65684 CTCGTATAAA
65694 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
*
65717 TGCATCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
65739 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
65761 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
65775 ATATAATGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 44 0.80
23 11 0.20
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:67482 original size:21 final size:21
Alignment explanation
Indices: 67458--67502 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
67448 TCTTGTTCGT
* *
67458 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
67479 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
67500 TTG
1 TTG
67503 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:69755 original size:75 final size:77
Alignment explanation
Indices: 69628--69838 Score: 309
Period size: 81 Copynumber: 2.7 Consensus size: 77
69618 AGGAACAAAG
* *
69628 GAAATCATTTCGGAAGTTGACTCCGACAATGCAAGTAATACGTACATACATACATCCAC-AC-AT
1 GAAATCATTTCGGAAGTTGACTCCGACAATGTAAGTAATACATACATACATACATCCACAACAAT
*
69691 ACATATACGTAT
66 ACATATACATAT
*
69703 GAAATCATTTCGGAAGTTGACTCCGACAATGTAAGTAATACATACATTCATACATCCACATATAC
1 GAAATCATTTCGGAAGTTGACTCCGACAATGTAAGTAATACATACATACATACATCCAC--A-AC
69768 ATATACATATACATAT
63 A-ATACATATACATAT
* * *
69784 GAAATCATTTCGGAAGTTGACTCCGACAATGTAATTAATACATCCACACATACAT
1 GAAATCATTTCGGAAGTTGACTCCGACAATGTAAGTAATACATACATACATACAT
69839 ATACGTATGT
Statistics
Matches: 122, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
75 56 0.46
79 2 0.02
81 64 0.52
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.27
Consensus pattern (77 bp):
GAAATCATTTCGGAAGTTGACTCCGACAATGTAAGTAATACATACATACATACATCCACAACAAT
ACATATACATAT
Found at i:72019 original size:12 final size:12
Alignment explanation
Indices: 72002--72026 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
71992 AATTTTTAAA
72002 AGTTTATAACAT
1 AGTTTATAACAT
72014 AGTTTATAACAT
1 AGTTTATAACAT
72026 A
1 A
72027 TTCACTATTA
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
AGTTTATAACAT
Found at i:72071 original size:21 final size:22
Alignment explanation
Indices: 72047--72099 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
72037 AATGTATAAA
72047 ATTTAAACTTGTTATA-TATAT
1 ATTTAAACTTGTTATACTATAT
* * *
72068 ATTTGAGCATGTTATACTATAT
1 ATTTAAACTTGTTATACTATAT
72090 A-TTAAA-TTGT
1 ATTTAAACTTGT
72100 ATCAAATTGG
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
20 3 0.12
21 16 0.64
22 6 0.24
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTTAAACTTGTTATACTATAT
Found at i:73268 original size:18 final size:18
Alignment explanation
Indices: 73245--73282 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
73235 ATTCATTCTT
73245 TTTAGAAACAAAAAGGGA
1 TTTAGAAACAAAAAGGGA
*
73263 TTTAGAAATAAAAAGGGA
1 TTTAGAAACAAAAAGGGA
73281 TT
1 TT
73283 CGTGGTCGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.21, T:0.24
Consensus pattern (18 bp):
TTTAGAAACAAAAAGGGA
Found at i:73703 original size:134 final size:133
Alignment explanation
Indices: 73450--73690 Score: 319
Period size: 134 Copynumber: 1.8 Consensus size: 133
73440 TAAACATAAA
* *
73450 TAAGATATTTACTTATTTAGAAATATCAGAAAAGGACTTCTAGGTACCTTAAGACAGCTCTTTTC
1 TAAGATATTTACTTATTTAAAAATATCAAAAAAGGACTTCTAGGTACCTTAAGACAGCTCTTTTC
* ** *
73515 TTCGATATTAAAGAATAAATAAATTACTAAAAAATTTCTTGAGATAAAAAAAATTTATTTTAATA
66 TTCGATATTAAAGAATAAATAAATTACTAAAAAATATAATAAGATAAAAAAAATTTATTTTAATA
73580 TAG
131 TAG
* * *
73583 TAAGATATTTATTTATTTAAAAATATCAAAAAAATGG-CTTCTAGGTACCTTAAGATAGTTCTTT
1 TAAGATATTTACTTATTTAAAAATATC-AAAAAA-GGACTTCTAGGTACCTTAAGACAGCTCTTT
*
73647 TCTTCGATATTAATA-AATAAAAATAAA-TA-TTAAAAATATAATAA
64 TCTTCGATATTAA-AGAAT--AAATAAATTACTAAAAAATATAATAA
73691 TTTAAATAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
133 25 0.27
134 56 0.60
135 5 0.05
136 7 0.08
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (133 bp):
TAAGATATTTACTTATTTAAAAATATCAAAAAAGGACTTCTAGGTACCTTAAGACAGCTCTTTTC
TTCGATATTAAAGAATAAATAAATTACTAAAAAATATAATAAGATAAAAAAAATTTATTTTAATA
TAG
Found at i:73740 original size:134 final size:132
Alignment explanation
Indices: 73450--73741 Score: 306
Period size: 134 Copynumber: 2.2 Consensus size: 132
73440 TAAACATAAA
* *
73450 TAAGATATTTACTTATTTAGAAATATCAGAAAAGGACTTCTAGGTACCTTAAGACAGCTCTTTTC
1 TAAGATATTTAATTATTTA-AAATATCAAAAAAGGACTTCTAGGTACCTTAAGACAGCTCTTTTC
* ** * * *
73515 TTCGATATTAAAGAATAAATAAATTACTAAAAAATTTCTTGAGATAAAAAAAATTTATTTTAATA
65 TTCGATATTAAAGAATAAATAAATTACTAAAAAATATAATAAGATAAAAAAAATTAATTATAATA
73580 TAG
130 TAG
* * *
73583 TAAGATATTTATTTATTTAAAAATATCAAAAAAATGG-CTTCTAGGTACCTTAAGATAGTTCTTT
1 TAAGATATTTAATTATTT-AAAATATC-AAAAAA-GGACTTCTAGGTACCTTAAGACAGCTCTTT
* ** *
73647 TCTTCGATATTAATA-AATAAAAATAAA-TA-TTAAAAATATAATAATTTAAATAAAATTAAATT
63 TCTTCGATATTAA-AGAAT--AAATAAATTACTAAAAAATATAATAAGATAAAAAAAATT-AATT
* **
73709 ATAATTTTT
124 ATAATATAG
73718 TATA-ATATTTAATTATTTAAAATA
1 TA-AGATATTTAATTATTTAAAATA
73742 CCAGAATAGA
Statistics
Matches: 133, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
133 24 0.18
134 73 0.55
135 28 0.21
136 8 0.06
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (132 bp):
TAAGATATTTAATTATTTAAAATATCAAAAAAGGACTTCTAGGTACCTTAAGACAGCTCTTTTCT
TCGATATTAAAGAATAAATAAATTACTAAAAAATATAATAAGATAAAAAAAATTAATTATAATAT
AG
Found at i:73826 original size:2 final size:2
Alignment explanation
Indices: 73819--73856 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
73809 ATTATTTAAA
73819 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
73857 GTGACTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73882 original size:17 final size:17
Alignment explanation
Indices: 73862--73895 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
73852 TATATGTGAC
73862 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
73879 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
73896 AAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:73919 original size:16 final size:16
Alignment explanation
Indices: 73893--73933 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
73883 ATAAAAGTAA
73893 TAAAA-AAATAATATT
1 TAAAATAAATAATATT
73908 TAAAATAAATAATATT
1 TAAAATAAATAATATT
73924 TAAAATAAAT
1 TAAAATAAAT
73934 TTAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAATAAATAATATT
Found at i:73920 original size:27 final size:27
Alignment explanation
Indices: 73890--73949 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
73880 AATATAAAAG
73890 TAATA-AAAAAATAATATTTAAAATAAA
1 TAATATAAAAAATAA-ATTTAAAATAAA
**
73917 TAATATTTAAAATAAATTTAAAATAAA
1 TAATATAAAAAATAAATTTAAAATAAA
73944 TAATAT
1 TAATAT
73950 TAAATTGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 23 0.77
28 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
TAATATAAAAAATAAATTTAAAATAAA
Found at i:73935 original size:11 final size:11
Alignment explanation
Indices: 73914--73944 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
73904 TATTTAAAAT
73914 AAATAATATTTA
1 AAATAA-ATTTA
73926 AAATAAATTTA
1 AAATAAATTTA
73937 AAATAAAT
1 AAATAAAT
73945 AATATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATAAATTTA
Found at i:73950 original size:27 final size:28
Alignment explanation
Indices: 73897--73950 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
73887 AAGTAATAAA
73897 AAAATAATATTTAAAATAAATAATATTT
1 AAAATAATATTTAAAATAAATAATATTT
73925 AAAATAA-ATTTAAAATAAATAATATT
1 AAAATAATATTTAAAATAAATAATATT
73951 AAATTGCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAATAATATTTAAAATAAATAATATTT
Found at i:75364 original size:3 final size:3
Alignment explanation
Indices: 75358--75427 Score: 79
Period size: 3 Copynumber: 23.0 Consensus size: 3
75348 ATTTTTTTTT
* **
75358 TAA TAA TAA TAA TAA TAA TATA TAA TACA TAA TAA TAA TGA TAA TTT
1 TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA TAA TAA
*
75405 TAA TAA TAA TAA -AA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
75428 AATTGATGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 2 0.04
3 49 0.86
4 6 0.11
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:75943 original size:73 final size:73
Alignment explanation
Indices: 75819--76316 Score: 867
Period size: 73 Copynumber: 6.8 Consensus size: 73
75809 AACTCGAAAT
* *
75819 AACTGTCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAAT-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
**
75884 TTAAAGTGA
65 TTCGAGTGA
* * * *
75893 AACAGTCTCAAGCGAGACAAAATTTATTTTAAGAAAAATAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
75958 TCGAGTGA
66 TCGAGTGA
*
75966 AACTGTCTCAAGCGAAAC-AATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
76030 TCGAGTGA
66 TCGAGTGA
76038 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
76103 TCGAGTGA
66 TCGAGTGA
76111 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
76176 TCGAGTGA
66 TCGAGTGA
76184 AACTGTCTCAAGCGAGACAAA-TTTGTTTTAAGAAAAA-AATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
76247 TCGAGTGA
66 TCGAGTGA
* *
76255 AACAGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCT
76317 ATGAAAACAT
Statistics
Matches: 405, Mismatches: 16, Indels: 7
0.95 0.04 0.02
Matches are distributed among these distances:
71 54 0.13
72 100 0.25
73 231 0.57
74 20 0.05
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (73 bp):
AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
TCGAGTGA
Found at i:76105 original size:145 final size:144
Alignment explanation
Indices: 75819--76316 Score: 863
Period size: 145 Copynumber: 3.4 Consensus size: 144
75809 AACTCGAAAT
* *
75819 AACTGTCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAAT-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGT
** * *
75884 TTAAAGTGAAACAGTCTCAAGCGAGACAAAATTTATTTTAAGAAAAATAATCTCAAGTGAGATAA
65 TTCGAGTGAAACTGTCTCAAGCGAGAC-AAATTTGTTTTAAGAAAAA-AATCTCAAGTGAGATAA
75949 AGTTCTGTTTCGAGTGA
128 AGTTCTGTTTCGAGTGA
*
75966 AACTGTCTCAAGCGAAAC-AATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
76030 TCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
66 TCGAGTGAAACTGTCTCAAGCGAGACAAA-TTTGTTTTAAGAAAAA-AATCTCAAGTGAGATAAA
76095 GTTCTGTTTCGAGTGA
129 GTTCTGTTTCGAGTGA
76111 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
76176 TCGAGTGAAACTGTCTCAAGCGAGACAAATTTGTTTTAAGAAAAAAATCTCAAGTGAGATAAAGT
66 TCGAGTGAAACTGTCTCAAGCGAGACAAATTTGTTTTAAGAAAAAAATCTCAAGTGAGATAAAGT
76241 TCTGTTTCGAGTGA
131 TCTGTTTCGAGTGA
* *
76255 AACAGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCT
76317 ATGAAAACAT
Statistics
Matches: 338, Mismatches: 11, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
144 97 0.29
145 146 0.43
146 78 0.23
147 17 0.05
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (144 bp):
AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
TCGAGTGAAACTGTCTCAAGCGAGACAAATTTGTTTTAAGAAAAAAATCTCAAGTGAGATAAAGT
TCTGTTTCGAGTGA
Found at i:76198 original size:218 final size:217
Alignment explanation
Indices: 75819--76316 Score: 879
Period size: 218 Copynumber: 2.3 Consensus size: 217
75809 AACTCGAAAT
*
75819 AACTGTCTCAAGCGAGACAAATCTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTTTGT
1 AACTGTCTCAAGCGAGACAAAT-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGT
*
75884 TTAAAGTGAAACAGTCTCAAGCGAGACAAAATTTATTTTAAGAAAAATAATCTCAAGTGAGATAA
65 TTAAAGTGAAACAGTCTCAAGCGAGACAAAATTTATTTTAAGAAAAACAATCTCAAGTGAGATAA
*
75949 AGTTCTGTTTCGAGTGAAACTGTCTCAAGCGAAACAATTTTGTTTTAAGAAAAACAATCTCAAGT
130 AGTTCTGTTTCGAGTGAAACTGTCTCAAGCGAAACAAATTTGTTTTAAGAAAAA-AATCTCAAGT
76014 GAGATAAAGTTCTGTTTCGAGTGA
194 GAGATAAAGTTCTGTTTCGAGTGA
*
76038 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAGTTCTGTT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGTT
** * * *
76103 TCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
66 TAAAGTGAAACAGTCTCAAGCGAGACAAAATTTATTTTAAGAAAAACAATCTCAAGTGAGATAAA
*
76168 GTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTGTTTTAAGAAAAAAATCTCAAGTGA
131 GTTCTGTTTCGAGTGAAACTGTCTCAAGCGAAACAAATTTGTTTTAAGAAAAAAATCTCAAGTGA
76233 GATAAAGTTCTGTTTCGAGTGA
196 GATAAAGTTCTGTTTCGAGTGA
*
76255 AACAGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCT
1 AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCT
76317 ATGAAAACAT
Statistics
Matches: 267, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
217 94 0.35
218 151 0.57
219 22 0.08
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (217 bp):
AACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTTCTGTT
TAAAGTGAAACAGTCTCAAGCGAGACAAAATTTATTTTAAGAAAAACAATCTCAAGTGAGATAAA
GTTCTGTTTCGAGTGAAACTGTCTCAAGCGAAACAAATTTGTTTTAAGAAAAAAATCTCAAGTGA
GATAAAGTTCTGTTTCGAGTGA
Found at i:76600 original size:165 final size:165
Alignment explanation
Indices: 76353--76679 Score: 539
Period size: 165 Copynumber: 2.0 Consensus size: 165
76343 TATGGATGTG
* * * *
76353 GGAAATAGTTTACTAAGTAAGATACTATGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
1 GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
**
76418 AGAAAAGATTGAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTGAT
66 AGAAAAGATAAAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTGAT
*
76483 TGGGTAACATGCCCCAATCTCAAGATAATGCTGTT
131 TGGGTAACATGACCCAATCTCAAGATAATGCTGTT
76518 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGT-AAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
** * *
76583 C-GAAAAGATAAAATGAGAAACTATGGGAATCGTTTTCTCATTATTTTTCAAAATATCATGTTGA
65 CAGAAAAGATAAAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTGA
76647 TTGGGTAACATGACCCAATCTCAAGATAATGCT
130 TTGGGTAACATGACCCAATCTCAAGATAATGCT
76680 CATTCTTGTG
Statistics
Matches: 150, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
165 107 0.71
166 43 0.29
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (165 bp):
GGAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTC
AGAAAAGATAAAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTGAT
TGGGTAACATGACCCAATCTCAAGATAATGCTGTT
Found at i:77217 original size:22 final size:22
Alignment explanation
Indices: 77192--77246 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
77182 AATAAAGCTT
77192 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
77214 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
77236 TCATCTTTGAA
1 TCATCTTTGAA
77247 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:81620 original size:10 final size:8
Alignment explanation
Indices: 81585--81639 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
81575 ATTTCTCCCA
81585 TTTTT-CT
1 TTTTTCCT
*
81592 TTTTCCCT
1 TTTTTCCT
81600 TTTTTCCT
1 TTTTTCCT
*
81608 TTTTTCTCA
1 TTTTTC-CT
81617 TTTTT-CT
1 TTTTTCCT
81624 TTTTTCATCT
1 TTTTTC--CT
81634 TTTTTC
1 TTTTTC
81640 TTCTTATTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
7 10 0.26
8 15 0.38
9 6 0.15
10 8 0.21
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTCCT
Found at i:81640 original size:17 final size:16
Alignment explanation
Indices: 81585--81641 Score: 71
Period size: 17 Copynumber: 3.5 Consensus size: 16
81575 ATTTCTCCCA
*
81585 TTTTTC-TTTTTCCCT
1 TTTTTCTTTTTTCTCT
*
81600 TTTTTCCTTTTTTCTCA
1 TTTTT-CTTTTTTCTCT
81617 TTTTTCTTTTTTCATCT
1 TTTTTCTTTTTTC-TCT
81634 TTTTTCTT
1 TTTTTCTT
81642 CTTATTCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 5 0.14
16 9 0.25
17 22 0.61
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTCTTTTTTCTCT
Found at i:81649 original size:26 final size:24
Alignment explanation
Indices: 81598--81651 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
81588 TTCTTTTTCC
*
81598 CTTTTTTCCTTTTTTCTCATTTTT
1 CTTTTTTCCTTTTTTCTCATTATT
81622 CTTTTTTCATCTTTTTTCTTC-TTATT
1 CTTTTTTC--CTTTTTTC-TCATTATT
81648 CTTT
1 CTTT
81652 CTTTGCTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 8 0.31
26 16 0.62
27 2 0.08
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (24 bp):
CTTTTTTCCTTTTTTCTCATTATT
Found at i:86912 original size:18 final size:17
Alignment explanation
Indices: 86889--86941 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 17
86879 TTAATAGCTG
86889 AATAAAATAAAAAAAATT
1 AATAAAATAAAAAAAA-T
86907 AATAAAATAATATAAAAAT
1 AATAAAATAA-A-AAAAAT
86926 AATAAGTAATAAAAAA
1 AATAA--AATAAAAAA
86942 TTTGAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 10 0.32
19 10 0.32
20 6 0.19
21 5 0.16
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (17 bp):
AATAAAATAAAAAAAAT
Found at i:87865 original size:17 final size:17
Alignment explanation
Indices: 87845--87878 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
87835 TATGTGTGAC
87845 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
87862 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
87879 CAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:87900 original size:16 final size:15
Alignment explanation
Indices: 87881--87915 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
87871 AGTAATAACA
87881 AAATAATATTATAAAT
1 AAATAATATT-TAAAT
87897 AAATAATATTTAAAT
1 AAATAATATTTAAAT
87912 AAAT
1 AAAT
87916 TTAAAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATAATATTTAAAT
Found at i:89352 original size:3 final size:3
Alignment explanation
Indices: 89344--89406 Score: 72
Period size: 3 Copynumber: 20.0 Consensus size: 3
89334 TTTTATTTTT
* **
89344 TAA TAA TAA TAA TAA TATA TATA TAA TACA TAA TAA TAA TGA TAA TTT
1 TAA TAA TAA TAA TAA TA-A TA-A TAA TA-A TAA TAA TAA TAA TAA TAA
89392 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
89407 AATGAAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
3 42 0.81
4 10 0.19
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:93764 original size:14 final size:14
Alignment explanation
Indices: 93745--93771 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
93735 GTTGTTTACG
93745 ATAATATTAATAAT
1 ATAATATTAATAAT
93759 ATAATATTAATAA
1 ATAATATTAATAA
93772 ATTATTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATATTAATAAT
Found at i:100336 original size:133 final size:134
Alignment explanation
Indices: 100109--100356 Score: 399
Period size: 133 Copynumber: 1.9 Consensus size: 134
100099 AAAATAAGGG
* * * *
100109 TTTTTCATCTTAAAATGAAATGTTGGAAGCTAAAATGCTAAAGAATAAAAGATTAAGTGTCAAAA
1 TTTTTCACCCTAAAATAAAATGTTGGAAGCTAAAATGCTAAAGAATAAAAGATAAAGTGTCAAAA
* *
100174 CGACTATTTAATCAAATGTTATAAATATTTCCCTCCTAAAATGAGACATAATGTTCTAAAATAGG
66 CAACTATTTAATCAAATGTTATAAATATTTCCCCCCTAAAATGAGACATAATGTTCTAAAATAGG
100239 GGTT
131 GGTT
* * *
100243 TTTTTCACCCTAAAATAAAATGTTGGAATCTAAAATGCTATATAATAAAAGA-AAAGTGTCAAAA
1 TTTTTCACCCTAAAATAAAATGTTGGAAGCTAAAATGCTAAAGAATAAAAGATAAAGTGTCAAAA
*
100307 TAACTATTTAATCAAATGTTATAAATATTTCCCCCCTAAAATGAGACATA
66 CAACTATTTAATCAAATGTTATAAATATTTCCCCCCTAAAATGAGACATA
100357 GAAAGCAAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
133 58 0.56
134 46 0.44
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (134 bp):
TTTTTCACCCTAAAATAAAATGTTGGAAGCTAAAATGCTAAAGAATAAAAGATAAAGTGTCAAAA
CAACTATTTAATCAAATGTTATAAATATTTCCCCCCTAAAATGAGACATAATGTTCTAAAATAGG
GGTT
Found at i:102479 original size:14 final size:13
Alignment explanation
Indices: 102428--102491 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 13
102418 GATTTAATTT
*
102428 TTTAAAGATTTAAG
1 TTTAAA-ATTTAAA
*
102442 TTGTAAATTTTAAA
1 TT-TAAAATTTAAA
* *
102456 CTTTAGAATTTAGA
1 -TTTAAAATTTAAA
102470 TATTAAAATTTAAA
1 T-TTAAAATTTAAA
102484 TTTAAAAT
1 TTTAAAAT
102492 AAATATTTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
13 8 0.20
14 26 0.65
15 6 0.15
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (13 bp):
TTTAAAATTTAAA
Found at i:103367 original size:18 final size:18
Alignment explanation
Indices: 103344--103381 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
103334 CCAATAACAT
103344 ATTTGGCGGAAATCCCTG
1 ATTTGGCGGAAATCCCTG
103362 ATTTGGCGGAAATCCCTG
1 ATTTGGCGGAAATCCCTG
103380 AT
1 AT
103382 ATCTATCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (18 bp):
ATTTGGCGGAAATCCCTG
Found at i:110285 original size:55 final size:55
Alignment explanation
Indices: 110201--110358 Score: 248
Period size: 55 Copynumber: 2.9 Consensus size: 55
110191 ATTAGTAGTG
*
110201 CCAACCTGAGAAGTCCAAACCAATTATTGGGAACCCTTTGCTTCGTTTAATAGCA
1 CCAACCTGAGAAGTCCAAACCAATTATTGGGAACCCTTCGCTTCGTTTAATAGCA
**
110256 CCAA-CTAGAGAAGTCCAAACCAATTATTGGGAACCCTTCGCTTCGTTTAATAGTG
1 CCAACCT-GAGAAGTCCAAACCAATTATTGGGAACCCTTCGCTTCGTTTAATAGCA
* *
110311 CCAACCTGAGAAGTCCAAACCAATTTTTGGGAACCCTTC-ATTCGTTTA
1 CCAACCTGAGAAGTCCAAACCAATTATTGGGAACCCTTCGCTTCGTTTA
110359 CTGTTTAAAA
Statistics
Matches: 96, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
54 10 0.10
55 84 0.88
56 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (55 bp):
CCAACCTGAGAAGTCCAAACCAATTATTGGGAACCCTTCGCTTCGTTTAATAGCA
Found at i:116265 original size:20 final size:19
Alignment explanation
Indices: 116240--116289 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
116230 AATAAAACTT
*
116240 TAAAAATATATAATCAATCC
1 TAAAAATATATAATCAA-CA
*
116260 TAAAAATAATACAATCAACA
1 TAAAAAT-ATATAATCAACA
116280 TAAAAA-ATAT
1 TAAAAATATAT
116290 TATAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 3 0.12
20 14 0.54
21 9 0.35
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAAATATATAATCAACA
Found at i:118887 original size:2 final size:2
Alignment explanation
Indices: 118880--118913 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
118870 ATTCTAGCTT
118880 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
118914 GATTGATGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:121276 original size:21 final size:20
Alignment explanation
Indices: 121237--121299 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 20
121227 GTCGAGGTTT
121237 TCATAGGTCATTCGAGACAAC
1 TCATAGGTCATTCG-GACAAC
* *
121258 TCATAGGTCTTTCAGGACATAT
1 TCATAGGTCATTC-GGACA-AC
* *
121280 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCATTC-GGACAA
121300 ACTTCATATG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.27
Consensus pattern (20 bp):
TCATAGGTCATTCGGACAAC
Found at i:121906 original size:21 final size:21
Alignment explanation
Indices: 121880--121921 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
121870 CGAAGTTTTT
121880 ATGCATCAATGCACTGTAGCA
1 ATGCATCAATGCACTGTAGCA
*
121901 ATGCATCGATGCACTGTAGCA
1 ATGCATCAATGCACTGTAGCA
121922 TTGTACACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
ATGCATCAATGCACTGTAGCA
Found at i:121935 original size:7 final size:7
Alignment explanation
Indices: 121912--121946 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
121902 TGCATCGATG
121912 CACTGTA
1 CACTGTA
*
121919 GCATTGTA
1 -CACTGTA
121927 CACTGTA
1 CACTGTA
121934 CACTGTA
1 CACTGTA
121941 CACTGT
1 CACTGT
121947 TCATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (7 bp):
CACTGTA
Found at i:122500 original size:21 final size:21
Alignment explanation
Indices: 122447--122503 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
122437 AAAATTTAAA
*
122447 TTTTTTAATAAA-AAGTGAAT
1 TTTTTTAATAAAGAAGTCAAT
*
122467 TTTATGTAA-AAAGATA-TCAAT
1 TTT-TTTAATAAAGA-AGTCAAT
122488 TTTTTTAATAAAGAAG
1 TTTTTTAATAAAGAAG
122504 AGAAACCAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
20 11 0.38
21 17 0.59
22 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.42
Consensus pattern (21 bp):
TTTTTTAATAAAGAAGTCAAT
Found at i:123236 original size:29 final size:31
Alignment explanation
Indices: 123193--123252 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
123183 ATAAAATGAT
**
123193 TTAATTGTACTTTTA-TGA-AATATAGTGAC
1 TTAATTGTAAATTTACTGATAATATAGTGAC
*
123222 TTAATTGTAAATTTACTTATAATATAGTGAC
1 TTAATTGTAAATTTACTGATAATATAGTGAC
123253 ATATGTTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 2 0.08
31 11 0.42
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.45
Consensus pattern (31 bp):
TTAATTGTAAATTTACTGATAATATAGTGAC
Found at i:123555 original size:59 final size:60
Alignment explanation
Indices: 123473--123595 Score: 140
Period size: 59 Copynumber: 2.1 Consensus size: 60
123463 GTTCCTAAAT
* * * * * *
123473 TTTTGAACATTCTAATTTTATCCCAAAACTATGATCATAATTCTAAATTGGTCCC-AAAC
1 TTTTAAACATTCCAAATTCATCCCAAAACTATGACCATAATTCTAAATTGATCCCAAAAC
* * * * *
123532 TTTTAAACATTCCAAATTCATCCCCAAACTATTACCCTCATTCTATATTGATCCCAAAAC
1 TTTTAAACATTCCAAATTCATCCCAAAACTATGACCATAATTCTAAATTGATCCCAAAAC
123592 TTTT
1 TTTT
123596 GAATTCTCTA
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
59 44 0.85
60 8 0.15
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.37
Consensus pattern (60 bp):
TTTTAAACATTCCAAATTCATCCCAAAACTATGACCATAATTCTAAATTGATCCCAAAAC
Found at i:123615 original size:29 final size:29
Alignment explanation
Indices: 123573--123628 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
123563 TTACCCTCAT
*
123573 TCTATATTGATCCCAAAACTTTTGAATTC
1 TCTATATTCATCCCAAAACTTTTGAATTC
* *
123602 TCTATTTTCATCCCTAAACTTTTGAAT
1 TCTATATTCATCCCAAAACTTTTGAAT
123629 GATTAAGGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (29 bp):
TCTATATTCATCCCAAAACTTTTGAATTC
Found at i:123750 original size:59 final size:60
Alignment explanation
Indices: 123645--123816 Score: 181
Period size: 59 Copynumber: 2.9 Consensus size: 60
123635 GGGGAATGTT
* ** * * * *
123645 ATTGGAATGTTCAAATCTTTAGGGACCAAATTAGAATGAGAGTCATAGTTTGAGTATGAA
1 ATTGGGATGTTCAAAAGTTTAAGGACAAAATTAGAATGAGAGTCATAATTTGAGAATGAA
* *
123705 ATTGGGATGTTCAAAAGTTTAAGGA-AAAATTATAATGTGAGTCATAATTTGAGAATGAA
1 ATTGGGATGTTCAAAAGTTTAAGGACAAAATTAGAATGAGAGTCATAATTTGAGAATGAA
* * * *
123764 ATT-GGAAGTTTAAAAGTTTAATGATC-AATTTAGAATGAGAGTTC-TAATTTGAG
1 ATTGGGATGTTCAAAAGTTTAAGGA-CAAAATTAGAATGAGAG-TCATAATTTGAG
123817 GATGTATGAT
Statistics
Matches: 94, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
58 18 0.19
59 53 0.56
60 23 0.24
ACGTcount: A:0.39, C:0.05, G:0.22, T:0.34
Consensus pattern (60 bp):
ATTGGGATGTTCAAAAGTTTAAGGACAAAATTAGAATGAGAGTCATAATTTGAGAATGAA
Found at i:124279 original size:20 final size:21
Alignment explanation
Indices: 124256--124307 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
124246 ATTTCCCAAT
*
124256 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
124276 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
124297 TCGCAATGCGA
1 TCGCAATGCGA
124308 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:124321 original size:20 final size:20
Alignment explanation
Indices: 124296--124409 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
124286 AATTGGGAAA
*
124296 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
124316 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
124336 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
124357 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
124377 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
124397 TTCGCAACGCGAT
1 ATCGCAACGCGAT
124410 TTACATAGCG
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 65 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:124340 original size:61 final size:61
Alignment explanation
Indices: 124293--124409 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
124283 GCGAATTGGG
* * * *
124293 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
124354 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
124410 TTACATAGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:124971 original size:19 final size:19
Alignment explanation
Indices: 124926--124973 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
124916 TTCAAGAATG
*
124926 AAAATCGCAACGCGGAAAT
1 AAAATCGCAACGCGGAAAC
*
124945 AACTATCGCAACGC-GAAACC
1 AA-AATCGCAACGCGGAAA-C
124965 AAAATCGCA
1 AAAATCGCA
124974 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.46, C:0.27, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGGAAAC
Found at i:124991 original size:19 final size:19
Alignment explanation
Indices: 124969--125153 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
124959 GAAACCAAAA
*
124969 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
124988 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
125007 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
125026 TCGCAGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
125046 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
125062 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
125079 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
125093 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
125112 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
125132 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
125152 TC
1 TC
125154 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:125046 original size:39 final size:38
Alignment explanation
Indices: 124969--125153 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
124959 GAAACCAAAA
*
124969 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
125007 TCGCGTTGCGATTTTTATTTCGCAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
125046 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
125079 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
125112 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
125152 TC
1 TC
125154 AACCAAAAGA
Statistics
Matches: 124, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:125130 original size:20 final size:20
Alignment explanation
Indices: 125096--125153 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
125086 GCGATTCTCT
**
125096 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
125116 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
125136 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
125154 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:127215 original size:42 final size:42
Alignment explanation
Indices: 127135--127227 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
127125 GCCCGACTCA
* *
127135 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCC
* * *
127177 CCTATCATTCCTCGAGAGTCCCCTTCC-ACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCAC-TCCTACCGTTCAAGAGGCC
* *
127219 ACTGTCATC
1 CCTATCATC
127228 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.25
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCC
Found at i:128010 original size:14 final size:14
Alignment explanation
Indices: 127991--128026 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
127981 TTTGTTTAAT
127991 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
128005 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
128019 TGATTTGT
1 TGATTTGT
128027 TTTATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:128157 original size:19 final size:19
Alignment explanation
Indices: 128133--128199 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
128123 AAAAAGTACT
128133 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
128152 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
128166 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
128185 ATCGCAACGCGAAAT
1 ATCGCAATGCGAAAT
128200 TAAATTCGCG
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 9 0.24
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:128297 original size:65 final size:65
Alignment explanation
Indices: 128201--128331 Score: 228
Period size: 65 Copynumber: 2.0 Consensus size: 65
128191 ACGCGAAATT
*
128201 AAATTCGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGA-TTTCATTTCGCATTGCG
1 AAATTAGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
*
128265 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGA-TTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
128330 G
65 G
128331 A
1 A
128332 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 14 0.22
65 31 0.49
66 18 0.29
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (65 bp):
AAATTAGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:128332 original size:33 final size:32
Alignment explanation
Indices: 128208--128332 Score: 180
Period size: 33 Copynumber: 3.8 Consensus size: 32
128198 ATTAAATTCG
*
128208 CGTTGCGATTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTCATTTCGCATTGCGATTCTCT
* **
128240 CGTTGCGATTTCATTTCGCATTGCGAAAT-TAG
1 CGTTGCGATTTCATTTCGCATTGCG-ATTCTCT
128272 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGA-TTTCATTTCGCATTGCGATTCTCT
128305 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGA-TTTCATTTCGCATTGCGAT
128333 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
32 35 0.42
33 48 0.58
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTCATTTCGCATTGCGATTCTCT
Found at i:131950 original size:20 final size:20
Alignment explanation
Indices: 131925--131982 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
131915 ATTCATTTGA
131925 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
131945 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
131965 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
131983 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:132042 original size:19 final size:19
Alignment explanation
Indices: 132001--132067 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
131991 GAAATGAAAA
132001 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
132017 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
132034 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
132052 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
132068 TTGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:132203 original size:14 final size:14
Alignment explanation
Indices: 132184--132220 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
132174 CATCAATTAA
132184 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
132198 ACAAATCATCTTTT
1 ACAAATCAACATTT
132212 ACAAATCAA
1 ACAAATCAA
132221 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:134110 original size:19 final size:18
Alignment explanation
Indices: 134066--134188 Score: 92
Period size: 20 Copynumber: 6.7 Consensus size: 18
134056 TAGTTTACTT
* *
134066 TCGCAACACGAAACTTAAA
1 TCGCAACGCGAAA-TGAAA
*
134085 TTCGCAACGCGAAATGACTA
1 -TCGCAACGCGAAATGA-AA
* **
134105 TCGCAATGCGGAAATGGCTA
1 TCGCAACGC-GAAAT-GAAA
*
134125 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATG-AAA
*
134144 TCGCAA--CGACA--AAA
1 TCGCAACGCGAAATGAAA
134158 TCGCAACGCGAAATGAAA
1 TCGCAACGCGAAATGAAA
134176 TCGCAACGCGAAA
1 TCGCAACGCGAAA
134189 CACAAATCGC
Statistics
Matches: 86, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
14 9 0.10
16 4 0.05
17 4 0.05
18 17 0.20
19 22 0.26
20 29 0.34
21 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (18 bp):
TCGCAACGCGAAATGAAA
Found at i:134197 original size:19 final size:18
Alignment explanation
Indices: 134155--134199 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
134145 CGCAACGACA
**
134155 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAAAC
134173 AAATCGCAACGCGAAACAC
1 AAATCGCAACGCGAAA-AC
134192 AAATCGCA
1 AAATCGCA
134200 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (18 bp):
AAATCGCAACGCGAAAAC
Found at i:134236 original size:14 final size:14
Alignment explanation
Indices: 134217--134274 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
134207 TTTCATTTCG
134217 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
134231 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
134247 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
134263 CGTTGCGATTTT
1 CGTTGCGATTTT
134275 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:134281 original size:33 final size:33
Alignment explanation
Indices: 134200--134290 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
134190 ACAAATCGCA
*
134200 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
134233 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
134265 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
134291 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:134309 original size:20 final size:19
Alignment explanation
Indices: 134275--134329 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
134265 TTGCGATTTT
*
134275 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
134294 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
134314 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
134330 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:134838 original size:18 final size:18
Alignment explanation
Indices: 134812--134856 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
134802 GTCGATCAGA
*
134812 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
134830 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
134848 TGATGGCTC
1 TGATGGCTC
134857 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Done.