Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 14 of 352
Found at i:4372462 original size:18 final size:19
Alignment explanation
Indices: 4372441--4372477 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
4372431 TATAAAAAAT
4372441 GAAAAA-TAATAAATTTTA
1 GAAAAATTAATAAATTTTA
*
4372459 GAAAAATTATTAAATTTTA
1 GAAAAATTAATAAATTTTA
4372478 ATAAGAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
GAAAAATTAATAAATTTTA
Found at i:4372845 original size:26 final size:26
Alignment explanation
Indices: 4372789--4372847 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
4372779 ACTTTATAAA
* **
4372789 ATTTTACAATTTTTATATTTCTATAT
1 ATTTTATAATTTTTATATTTAAATAT
4372815 ATTTTATAATTTTTAATATTTAAAT-T
1 ATTTTATAATTTTT-ATATTTAAATAT
*
4372841 TTTTTAT
1 ATTTTAT
4372848 TAAAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.64
Consensus pattern (26 bp):
ATTTTATAATTTTTATATTTAAATAT
Found at i:4375566 original size:6 final size:6
Alignment explanation
Indices: 4375528--4375579 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
4375518 TATCCAAAAG
* * * * * *
4375528 GATAAA GACAAA GACAAA GAAAAA AACAAA GATAAA GATAAA AATAAA
1 GATAAA GATAAA GATAAA GATAAA GATAAA GATAAA GATAAA GATAAA
4375576 GATA
1 GATA
4375580 GAGAGGTTGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.71, C:0.06, G:0.13, T:0.10
Consensus pattern (6 bp):
GATAAA
Found at i:4375578 original size:18 final size:18
Alignment explanation
Indices: 4375535--4375579 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
4375525 AAGGATAAAG
*
4375535 ACAAAGACAAAGAAAAAA
1 ACAAAGATAAAGAAAAAA
*
4375553 ACAAAGATAAAGATAAAA
1 ACAAAGATAAAGAAAAAA
*
4375571 ATAAAGATA
1 ACAAAGATA
4375580 GAGAGGTTGA
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:0.73, C:0.07, G:0.11, T:0.09
Consensus pattern (18 bp):
ACAAAGATAAAGAAAAAA
Found at i:4380899 original size:9 final size:8
Alignment explanation
Indices: 4380873--4380903 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
4380863 TTTATTGATA
4380873 TTTTT-AT
1 TTTTTAAT
4380880 TTTTTAAT
1 TTTTTAAT
4380888 TTTTTAAT
1 TTTTTAAT
4380896 TTTTTAAT
1 TTTTTAAT
4380904 AAATTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.22
8 18 0.78
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTAAT
Found at i:4385809 original size:13 final size:12
Alignment explanation
Indices: 4385791--4385820 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
4385781 CATAAACATT
4385791 TAAAAATAATATA
1 TAAAAATAATA-A
4385804 TAAAAATAATAA
1 TAAAAATAATAA
4385816 TAAAA
1 TAAAA
4385821 TGTAAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TAAAAATAATAA
Found at i:4392835 original size:22 final size:22
Alignment explanation
Indices: 4392810--4392866 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
4392800 ATATTGTTCG
4392810 ATACAGAGTTATATCAACAAAA
1 ATACAGAGTTATATCAACAAAA
* *
4392832 ATACTAGGGTTAGTATCGACAAAA
1 ATAC-AGAGTTA-TATCAACAAAA
*
4392856 AGA-AGAGTTAT
1 ATACAGAGTTAT
4392867 GATTTACTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 10 0.34
23 6 0.21
24 12 0.41
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.25
Consensus pattern (22 bp):
ATACAGAGTTATATCAACAAAA
Found at i:4393236 original size:27 final size:27
Alignment explanation
Indices: 4393198--4393257 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
4393188 ATTTTATACG
4393198 TATAATAACATAATATAAAAACTTTTC
1 TATAATAACATAATATAAAAACTTTTC
4393225 TATAATAACATAATATAAAAACTTTTC
1 TATAATAACATAATATAAAAACTTTTC
*
4393252 TTTAAT
1 TATAAT
4393258 TGATCAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (27 bp):
TATAATAACATAATATAAAAACTTTTC
Found at i:4409405 original size:3 final size:3
Alignment explanation
Indices: 4409397--4409432 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
4409387 GGTTCAAATC
*
4409397 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4409433 AACTTAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4413141 original size:19 final size:19
Alignment explanation
Indices: 4413117--4413153 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4413107 TAAAAATGAG
4413117 ATAAACAAACTAATGTAAC
1 ATAAACAAACTAATGTAAC
4413136 ATAAACAAACTAATGTAA
1 ATAAACAAACTAATGTAA
4413154 ATATATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.14, G:0.05, T:0.22
Consensus pattern (19 bp):
ATAAACAAACTAATGTAAC
Found at i:4418398 original size:19 final size:19
Alignment explanation
Indices: 4418346--4418401 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
4418336 AATTTTTTGA
*
4418346 AATTTTATTATAATTTTTAT
1 AATTTTA-TATAATTTTAAT
* *
4418366 AATTTT-TGTCATTTATAAT
1 AATTTTATATAATTT-TAAT
*
4418385 AATTTTATATATTTTTA
1 AATTTTATATAATTTTA
4418402 TACTTTAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
18 6 0.21
19 11 0.39
20 11 0.39
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
AATTTTATATAATTTTAAT
Found at i:4418400 original size:10 final size:9
Alignment explanation
Indices: 4418353--4418403 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
4418343 TGAAATTTTA
4418353 TTATAATTT
1 TTATAATTT
4418362 TTATAATTT
1 TTATAATTT
* *
4418371 TTGTCATTT
1 TTATAATTT
*
4418380 ATAATAA-TT
1 -TTATAATTT
4418389 TTATATATTT
1 TTATA-ATTT
4418399 TTATA
1 TTATA
4418404 CTTTAATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
8 4 0.12
9 19 0.58
10 10 0.30
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTATAATTT
Found at i:4418408 original size:28 final size:28
Alignment explanation
Indices: 4418324--4418408 Score: 70
Period size: 28 Copynumber: 3.0 Consensus size: 28
4418314 TTTTATTATG
* *
4418324 ATAATAAGTTTTA-AT-TTTTTGAAATTTT
1 ATAATAA-TTTTATATATTTTT-ATACTTT
* *
4418352 ATTATAATTTT-TATAATTTTTGT-CATTT
1 ATAATAATTTTATAT-ATTTTTATAC-TTT
4418380 ATAATAATTTTATATATTTTTATACTTT
1 ATAATAATTTTATATATTTTTATACTTT
4418408 A
1 A
4418409 ATATTCTATA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
27 6 0.13
28 30 0.67
29 9 0.20
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (28 bp):
ATAATAATTTTATATATTTTTATACTTT
Found at i:4419919 original size:29 final size:29
Alignment explanation
Indices: 4419865--4419920 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
4419855 TAAGTTTAAA
*
4419865 TAAAAAAATTATATAATAATATTAAAATG
1 TAAAAAAATTATATAATAATAATAAAATG
*
4419894 TAAAAAAATATATATATTAA-AATAAAA
1 TAAAAAAAT-TATATAATAATAATAAAA
4419921 ATTTAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (29 bp):
TAAAAAAATTATATAATAATAATAAAATG
Found at i:4419922 original size:30 final size:29
Alignment explanation
Indices: 4419865--4419922 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
4419855 TAAGTTTAAA
* *
4419865 TAAAAAAATTATATAATAATATTAAAATG
1 TAAAAAAATTATATAATAAAATAAAAATG
*
4419894 TAAAAAAATATATATATTAAAATAAAAAT
1 TAAAAAAAT-TATATAATAAAATAAAAAT
4419923 TTAATTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (29 bp):
TAAAAAAATTATATAATAAAATAAAAATG
Found at i:4420089 original size:11 final size:11
Alignment explanation
Indices: 4420073--4420117 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
4420063 TCATAAAACA
4420073 ATACTTAAATT
1 ATACTTAAATT
4420084 ATACTT-AATT
1 ATACTTAAATT
*
4420094 AT-C-TAAAGTG
1 ATACTTAAA-TT
4420104 ATACTTAAATT
1 ATACTTAAATT
4420115 ATA
1 ATA
4420118 TGATTTTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
8 1 0.04
9 3 0.11
10 9 0.32
11 11 0.39
12 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (11 bp):
ATACTTAAATT
Found at i:4421093 original size:16 final size:17
Alignment explanation
Indices: 4421063--4421096 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4421053 ATATATTATT
*
4421063 AAAATATTAATTATAAA
1 AAAATATTAAATATAAA
4421080 AAAATA-TAAATATAAA
1 AAAATATTAAATATAAA
4421096 A
1 A
4421097 TTACTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATATTAAATATAAA
Found at i:4422897 original size:20 final size:20
Alignment explanation
Indices: 4422874--4422912 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4422864 AATTTTATTT
* *
4422874 TATTTAACTTAATTTAAAAA
1 TATTTAAATTAAATTAAAAA
4422894 TATTTAAATTAAATTAAAA
1 TATTTAAATTAAATTAAAA
4422913 TAATAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTTAAATTAAATTAAAAA
Found at i:4427627 original size:20 final size:19
Alignment explanation
Indices: 4427599--4427664 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
4427589 ACAAAACAAA
*
4427599 TCAAGATAATTTTCATAAAT
1 TCAAAATAATTTTCA-AAAT
*
4427619 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTTCAAAAT
*
4427638 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTT-TCAAAAT
4427657 TCCAAAAT
1 T-CAAAAT
4427665 TTATAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
18 4 0.10
19 18 0.44
20 19 0.46
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (19 bp):
TCAAAATAATTTTCAAAAT
Found at i:4427637 original size:19 final size:19
Alignment explanation
Indices: 4427599--4427664 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
4427589 ACAAAACAAA
* *
4427599 TCAAGATAATTTTCATAAAT
1 TCAAAATAATTTT-AAAAAT
*
4427619 TCAAAATAATTTTTAAAAT
1 TCAAAATAATTTTAAAAAT
4427638 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTT-TAAAAAT
4427657 TCCAAAAT
1 T-CAAAAT
4427665 TTATAATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.10
19 18 0.45
20 18 0.45
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.38
Consensus pattern (19 bp):
TCAAAATAATTTTAAAAAT
Found at i:4427663 original size:27 final size:27
Alignment explanation
Indices: 4427633--4427690 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
4427623 AATAATTTTT
*
4427633 AAAATTCAAAATA-TTTATAAAAATTCC
1 AAAATTCAAAATATTTTA-AAAAATTAC
* *
4427660 AAAATTTATAATATTTTAAAAAATTAC
1 AAAATTCAAAATATTTTAAAAAATTAC
4427687 AAAA
1 AAAA
4427691 ATTTCAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (27 bp):
AAAATTCAAAATATTTTAAAAAATTAC
Found at i:4427666 original size:18 final size:19
Alignment explanation
Indices: 4427615--4427670 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
4427605 TAATTTTCAT
*
4427615 AAATTCAAAATAATTT-TTA
1 AAATTCAAAAT-ATTTATAA
4427634 AAATTCAAAATATTTATAA
1 AAATTCAAAATATTTATAA
*
4427653 AAATTCCAAA-ATTTATAA
1 AAATTCAAAATATTTATAA
4427671 TATTTTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 12 0.35
19 22 0.65
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATTCAAAATATTTATAA
Found at i:4432568 original size:46 final size:46
Alignment explanation
Indices: 4432516--4432606 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
4432506 TCTCATCCAT
4432516 AAGCCCAGTTATTTAGATAGTTGTAATTCCATTTTTATGATTCTAA
1 AAGCCCAGTTATTTAGATAGTTGTAATTCCATTTTTATGATTCTAA
4432562 AAGCCCAGTTATTTAGATAGTTGTAATTCCATTTTTATGATTCTA
1 AAGCCCAGTTATTTAGATAGTTGTAATTCCATTTTTATGATTCTA
4432607 TGTATGGTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (46 bp):
AAGCCCAGTTATTTAGATAGTTGTAATTCCATTTTTATGATTCTAA
Found at i:4433396 original size:17 final size:17
Alignment explanation
Indices: 4433374--4433408 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
4433364 GTGGGCCTGG
4433374 TTGGGCTCAATTTAGGC
1 TTGGGCTCAATTTAGGC
4433391 TTGGGCTCAATTTAGGC
1 TTGGGCTCAATTTAGGC
4433408 T
1 T
4433409 CTGTATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.37
Consensus pattern (17 bp):
TTGGGCTCAATTTAGGC
Found at i:4441581 original size:3 final size:3
Alignment explanation
Indices: 4441573--4441645 Score: 53
Period size: 3 Copynumber: 24.3 Consensus size: 3
4441563 TTAATTTATT
* * *
4441573 TAA TAA TAA TGA T-T TAA T-A TAA -AA TCA TAA TAA TAA TTAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
* *
4441616 TAA TAA TAA TTA TTA TATA TAA TATA TAA T
1 TAA TAA TAA TAA TAA TA-A TAA TA-A TAA T
4441646 CTAAGAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
2 5 0.09
3 43 0.75
4 9 0.16
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:4441615 original size:13 final size:13
Alignment explanation
Indices: 4441572--4441622 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
4441562 TTTAATTTAT
*
4441572 TTAATAATAATGAT
1 TTAATAATAAT-AA
4441586 TTAAT-ATAA-AA
1 TTAATAATAATAA
*
4441597 -TCATAATAATAA
1 TTAATAATAATAA
4441609 TTAATAATAATAA
1 TTAATAATAATAA
4441622 T
1 T
4441623 AATTATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
10 3 0.10
11 5 0.16
12 2 0.06
13 16 0.52
14 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
TTAATAATAATAA
Found at i:4443969 original size:16 final size:18
Alignment explanation
Indices: 4443950--4443987 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
4443940 TATTTTAAGA
4443950 ATAAGATATT-TAAT-AT
1 ATAAGATATTATAATAAT
*
4443966 ATAATATATTATAATAAT
1 ATAAGATATTATAATAAT
4443984 ATAA
1 ATAA
4443988 TAGAATAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 4 0.21
18 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
ATAAGATATTATAATAAT
Found at i:4444070 original size:12 final size:11
Alignment explanation
Indices: 4444052--4444087 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
4444042 AACGAAATAG
4444052 AAAGGAAAGAA
1 AAAGGAAAGAA
4444063 AAAGGGAAAGAA
1 AAA-GGAAAGAA
4444075 AAA-GAAAGAA
1 AAAGGAAAGAA
4444085 AAA
1 AAA
4444088 ATAGGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.42
11 3 0.12
12 11 0.46
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (11 bp):
AAAGGAAAGAA
Found at i:4450745 original size:12 final size:12
Alignment explanation
Indices: 4450728--4450758 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4450718 GAAGCAGGGG
4450728 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
4450740 AGAAAAAGGGAA
1 AGAAAAAGAGAA
4450752 AGAAAAA
1 AGAAAAA
4450759 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:4462304 original size:18 final size:17
Alignment explanation
Indices: 4462249--4462305 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 17
4462239 AATATTCTGC
4462249 CATAATAATCTATTTAA
1 CATAATAATCTATTTAA
4462266 -A-AA-AAGTCGTATTCTAA
1 CATAATAA-TC-TATT-TAA
4462283 CATAATAATCTATTTAA
1 CATAATAATCTATTTAA
4462300 GCATAA
1 -CATAA
4462306 AACTTATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 5 0.15
17 6 0.18
18 10 0.30
19 4 0.12
20 2 0.06
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (17 bp):
CATAATAATCTATTTAA
Found at i:4463491 original size:40 final size:40
Alignment explanation
Indices: 4463436--4463515 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
4463426 CTTTATGCGT
4463436 GGGAATAAAATATATATAATATTTTAATAGTTGTAAATGA
1 GGGAATAAAATATATATAATATTTTAATAGTTGTAAATGA
4463476 GGGAATAAAATATATATAATATTTTAATAGTTGTAAATGA
1 GGGAATAAAATATATATAATATTTTAATAGTTGTAAATGA
4463516 AAAGTTATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (40 bp):
GGGAATAAAATATATATAATATTTTAATAGTTGTAAATGA
Found at i:4463611 original size:17 final size:17
Alignment explanation
Indices: 4463585--4463625 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
4463575 CAAGTAGATA
4463585 TCTATTGAATAATTAT-
1 TCTATTGAATAATTATG
4463601 TCTACTTGAATAATTATG
1 TCTA-TTGAATAATTATG
4463619 TCTATTG
1 TCTATTG
4463626 CTAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.49
Consensus pattern (17 bp):
TCTATTGAATAATTATG
Found at i:4465815 original size:46 final size:47
Alignment explanation
Indices: 4465551--4465814 Score: 358
Period size: 46 Copynumber: 5.7 Consensus size: 47
4465541 TGTCATAGTG
* *
4465551 TCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTA
* * * *
4465597 TCTTTCAACCATGTTCTTATTCATTTTCCTGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTA
* * * *
4465644 TCTTTCAACCATGGTCTTATTCA-TTTCATGTCACGCTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTA
*
4465690 TCTTTCAACCATGGTCTTATTCATTTTC-TATCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTA
* *
4465736 TCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTA
* *
4465782 TCTTTCAACCATGGTCGTACACA-TTTCATATCA
1 TCTTTCAACCATGGTCTTACTCATTTTCATATCA
4465815 GAGAGCGCAC
Statistics
Matches: 201, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
45 4 0.02
46 153 0.76
47 44 0.22
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (47 bp):
TCTTTCAACCATGGTCTTACTCATTTTCATATCATGTTGCCATGGTA
Found at i:4467768 original size:19 final size:20
Alignment explanation
Indices: 4467733--4467774 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
4467723 ACACCTTTAA
4467733 TTTTCTCCTTTTCTTCTTTC
1 TTTTCTCCTTTTCTTCTTTC
*
4467753 TTTTCT-CTTTTTTTCTTTC
1 TTTTCTCCTTTTCTTCTTTC
4467772 TTT
1 TTT
4467775 CCGTCCCCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTCTCCTTTTCTTCTTTC
Found at i:4467849 original size:2 final size:2
Alignment explanation
Indices: 4467844--4467872 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4467834 TTCTTTTTTC
4467844 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 A
4467873 CATGTATTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4468000 original size:28 final size:29
Alignment explanation
Indices: 4467964--4468031 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
4467954 ACATTTGTCA
*
4467964 TTATTTAATATATTT-ATCATATAAA-ATC
1 TTATATAATATATTTAATCA-ATAAATATC
*
4467992 TTATATAAT-TATTTAATTAATAAATATC
1 TTATATAATATATTTAATCAATAAATATC
*
4468020 TTTTATAATATA
1 TTATATAATATA
4468032 ATAAATATCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 10 0.29
28 22 0.65
29 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (29 bp):
TTATATAATATATTTAATCAATAAATATC
Found at i:4468056 original size:22 final size:21
Alignment explanation
Indices: 4468005--4468046 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4467995 TATAATTATT
4468005 TAAT-TAATAAATATCTTTTA
1 TAATATAATAAATATCTTTTA
4468025 TAATATAATAAATATCTATTTA
1 TAATATAATAAATATCT-TTTA
4468047 ACATCTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATATAATAAATATCTTTTA
Found at i:4469119 original size:31 final size:31
Alignment explanation
Indices: 4469083--4469143 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
4469073 TTAAGGCGAA
*
4469083 TGACTTAAATAAAAACATTTAAATAGTTCAG
1 TGACTTAAATAAAAACATTTAAATAATTCAG
* *
4469114 TGACTTAAATGAAAACTTTTAAATAATTCA
1 TGACTTAAATAAAAACATTTAAATAATTCA
4469144 ATAATCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (31 bp):
TGACTTAAATAAAAACATTTAAATAATTCAG
Found at i:4470730 original size:5 final size:5
Alignment explanation
Indices: 4470720--4470751 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
4470710 TTGTGTGTTC
4470720 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
4470752 TCACAATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:4470734 original size:9 final size:9
Alignment explanation
Indices: 4470720--4470750 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
4470710 TTGTGTGTTC
4470720 TTTATTTTA
1 TTTATTTTA
4470729 TTTATTTTA
1 TTTATTTTA
4470738 TTTTATTTTA
1 -TTTATTTTA
4470748 TTT
1 TTT
4470751 TTCACAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:4478100 original size:2 final size:2
Alignment explanation
Indices: 4478093--4478129 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4478083 GTCTTTCAAG
4478093 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
4478130 TATATATATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4483414 original size:20 final size:20
Alignment explanation
Indices: 4483376--4483415 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4483366 TAGAAAGTTC
*
4483376 TACATAAAAATTTCTAAAAA
1 TACATAAAAATTTCAAAAAA
4483396 TACATAGAAAATTT-AAAAAA
1 TACATA-AAAATTTCAAAAAA
4483416 AAATAGATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (20 bp):
TACATAAAAATTTCAAAAAA
Found at i:4483415 original size:21 final size:20
Alignment explanation
Indices: 4483376--4483416 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
4483366 TAGAAAGTTC
**
4483376 TACATAAAAATTTCTAAAAA
1 TACATAAAAATTTAAAAAAA
4483396 TACATAGAAAATTTAAAAAAA
1 TACATA-AAAATTTAAAAAAA
4483417 AATAGATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.27
Consensus pattern (20 bp):
TACATAAAAATTTAAAAAAA
Found at i:4484849 original size:13 final size:13
Alignment explanation
Indices: 4484828--4484898 Score: 70
Period size: 13 Copynumber: 5.5 Consensus size: 13
4484818 AAATTTTTCT
4484828 AAAGCACTTCTCA
1 AAAGCACTTCTCA
*
4484841 AAAGTACTTCTCA
1 AAAGCACTTCTCA
* *
4484854 AAAGCACTTTTCC
1 AAAGCACTTCTCA
** * *
4484867 ACGGCACTTTTTA
1 AAAGCACTTCTCA
*
4484880 AAAGCACTTTTCA
1 AAAGCACTTCTCA
4484893 AAAGCA
1 AAAGCA
4484899 ATGAAGAACT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (13 bp):
AAAGCACTTCTCA
Found at i:4485537 original size:19 final size:19
Alignment explanation
Indices: 4485507--4485552 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
4485497 TAGTAAATAC
* *
4485507 ATGTATAAAAATAATATACAT
1 ATGTAT-AAATTAATA-AAAT
4485528 ATGTATAAATTAATAAAAT
1 ATGTATAAATTAATAAAAT
4485547 ATGTAT
1 ATGTAT
4485553 TACTTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 8 0.35
21 6 0.26
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (19 bp):
ATGTATAAATTAATAAAAT
Found at i:4485626 original size:16 final size:17
Alignment explanation
Indices: 4485600--4485633 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4485590 TTATATTATT
4485600 ATAATAATATTAAGTAA
1 ATAATAATATTAAGTAA
*
4485617 ATAA-AATATTAATTAA
1 ATAATAATATTAAGTAA
4485633 A
1 A
4485634 AACAAAACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
ATAATAATATTAAGTAA
Found at i:4485680 original size:20 final size:18
Alignment explanation
Indices: 4485645--4485700 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
4485635 ACAAAACGAA
*
4485645 ATAGAAAAAAACAGAAAG
1 ATAGAAAAAAAAAGAAAG
4485663 ATAGAACAAAACAAAGAAA-
1 ATAGAA-AAAA-AAAGAAAG
*
4485682 AAAGAAAGAAAAAA-AAAG
1 ATAGAAA-AAAAAAGAAAG
4485700 A
1 A
4485701 AAAGAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 3 0.09
18 11 0.34
19 12 0.38
20 6 0.19
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.04
Consensus pattern (18 bp):
ATAGAAAAAAAAAGAAAG
Found at i:4485689 original size:11 final size:11
Alignment explanation
Indices: 4485659--4485718 Score: 61
Period size: 10 Copynumber: 5.5 Consensus size: 11
4485649 AAAAAAACAG
*
4485659 AAAGATAGAACA
1 AAAGAAAGAA-A
*
4485671 AAACAAAGAAA
1 AAAGAAAGAAA
4485682 AAAGAAAGAAA
1 AAAGAAAGAAA
4485693 AAA-AAAGAAA
1 AAAGAAAGAAA
* *
4485703 AGA-AAAGAGA
1 AAAGAAAGAAA
4485713 AAAGAA
1 AAAGAA
4485719 GGAGAATTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
10 17 0.41
11 16 0.39
12 8 0.20
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:4485699 original size:21 final size:23
Alignment explanation
Indices: 4485659--4485703 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4485649 AAAAAAACAG
*
4485659 AAAGATAGAACAAAACAAAGAAA
1 AAAGAAAGAACAAAACAAAGAAA
4485682 AAAGAAAGAA-AAAA-AAAGAAA
1 AAAGAAAGAACAAAACAAAGAAA
4485703 A
1 A
4485704 GAAAAGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 4 0.19
23 9 0.43
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.02
Consensus pattern (23 bp):
AAAGAAAGAACAAAACAAAGAAA
Found at i:4485709 original size:20 final size:20
Alignment explanation
Indices: 4485631--4485715 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 20
4485621 AATATTAATT
*
4485631 AAAAACAAAACGAAATAGAAAA
1 AAAAAGAAAA-GAAA-AGAAAA
* *
4485653 AAACAG-AAAG-ATAGAACAA
1 AAAAAGAAAAGAAAAGAA-AA
*
4485672 AACAAAGAAAAAAGAAAGAAAA
1 AA-AAAGAAAAGA-AAAGAAAA
4485694 AAAAAGAAAAGAAAAGAGAAA
1 AAAAAGAAAAGAAAAGA-AAA
4485715 A
1 A
4485716 GAAGGAGAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
18 4 0.08
19 5 0.10
20 9 0.18
21 19 0.38
22 8 0.16
23 5 0.10
ACGTcount: A:0.78, C:0.06, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAGAAAA
Found at i:4486842 original size:38 final size:39
Alignment explanation
Indices: 4486758--4486892 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
4486748 ACCAATATGG
*
4486758 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
4486797 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
4486835 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
4486876 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
4486893 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:4488383 original size:16 final size:16
Alignment explanation
Indices: 4488364--4488394 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4488354 CTTATTTCCC
*
4488364 CTTTTCTTTCTTTCTT
1 CTTTCCTTTCTTTCTT
4488380 CTTTCCTTTCTTTCT
1 CTTTCCTTTCTTTCT
4488395 CCCCTGTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
CTTTCCTTTCTTTCTT
Found at i:4488472 original size:13 final size:14
Alignment explanation
Indices: 4488459--4488500 Score: 68
Period size: 13 Copynumber: 3.0 Consensus size: 14
4488449 TTTCTTTTAT
4488459 ATATAATAAATATA
1 ATATAATAAATATA
4488473 ATATAAT-AATATA
1 ATATAATAAATATA
4488486 ATATAATATAATATA
1 ATATAATA-AATATA
4488501 CTTAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.50
14 7 0.27
15 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATAATAAATATA
Found at i:4488477 original size:5 final size:5
Alignment explanation
Indices: 4488459--4488500 Score: 63
Period size: 5 Copynumber: 9.0 Consensus size: 5
4488449 TTTCTTTTAT
4488459 ATATA ATA-A ATATA ATAT- A-ATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
4488501 CTTAATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 2 0.06
4 6 0.18
5 26 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:4488488 original size:18 final size:17
Alignment explanation
Indices: 4488456--4488498 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 17
4488446 TTGTTTCTTT
4488456 TATATATAATAAATATAA
1 TATA-ATAATAAATATAA
4488474 TATAATAATATAATATAA
1 TATAATAATA-AATATAA
4488492 TATAATA
1 TATAATA
4488499 TACTTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATAATAATAAATATAA
Found at i:4494651 original size:38 final size:39
Alignment explanation
Indices: 4494567--4494701 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
4494557 ACCAATATGG
*
4494567 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
4494606 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
4494644 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
4494685 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
4494702 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:4496996 original size:40 final size:39
Alignment explanation
Indices: 4496877--4497008 Score: 126
Period size: 40 Copynumber: 3.4 Consensus size: 39
4496867 CCTCGAGTCG
* *
4496877 ATGAGACACTAGGTGTCAATCTATTACTTC-AGATTAATTCA
1 ATGAGACACTGGGTGTCAAT-TATTACTTCGA-ATT-ATCCA
* * ** *
4496918 ATGAGGCACTGGGTGCCAA-T-TTACTTCGGTTTAGCCA
1 ATGAGACACTGGGTGTCAATTATTACTTCGAATTATCCA
4496955 ATGAGACACTGGGTGTCAACTTATTACTTCGAATTATCCA
1 ATGAGACACTGGGTGTCAA-TTATTACTTCGAATTATCCA
**
4496995 ATGAGGTACTGGGT
1 ATGAGACACTGGGT
4497009 ACCAAACTGG
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
37 20 0.27
38 9 0.12
39 2 0.03
40 26 0.36
41 16 0.22
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (39 bp):
ATGAGACACTGGGTGTCAATTATTACTTCGAATTATCCA
Found at i:4497771 original size:24 final size:24
Alignment explanation
Indices: 4497736--4497782 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4497726 TAAAGGTATT
*
4497736 TGAATGTGTTTTGAATTGGTTGAA
1 TGAATGTGTTTTGAATTGCTTGAA
*
4497760 TGAATG-GTTTTTGAGTTGCTTGA
1 TGAATGTG-TTTTGAATTGCTTGA
4497783 TGTCTAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.21, C:0.02, G:0.30, T:0.47
Consensus pattern (24 bp):
TGAATGTGTTTTGAATTGCTTGAA
Found at i:4498387 original size:8 final size:8
Alignment explanation
Indices: 4498374--4498417 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
4498364 ACTTAAGTAT
4498374 ATAATATA
1 ATAATATA
4498382 ATAATATA
1 ATAATATA
*
4498390 TTAATATA
1 ATAATATA
*
4498398 ATAATTTA
1 ATAATATA
4498406 ATAATATA
1 ATAATATA
4498414 ATAA
1 ATAA
4498418 AACATAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATAATATA
Found at i:4500871 original size:47 final size:47
Alignment explanation
Indices: 4500764--4500954 Score: 186
Period size: 47 Copynumber: 3.9 Consensus size: 47
4500754 AATGTGATTT
* * * *
4500764 CCGTATAAGACCATAGCTGGGCTATGGCTTCGGACAAATGTGATATGTGCTT
1 CCGTATAAGACCATATCTGGGATATGGCATCGG-----TGTGATATGTGCTA
*
4500816 CCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTA
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* * * *
4500863 CTGTATAAGACCATATTTGGGATATGGCATCAGTGTGATATGTGAT-
1 CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
* ** * *
4500909 CCGTGTAAGACCATGGCTGGGTTATGGCCTCGGTATGTGATATGTG
1 CCGTATAAGACCATATCTGGGATATGGCATCGG--TGTGATATGTG
4500955 ACTATGTGCA
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 25 0.21
47 54 0.45
48 11 0.09
52 29 0.24
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (47 bp):
CCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGCTA
Found at i:4500987 original size:95 final size:93
Alignment explanation
Indices: 4500802--4500972 Score: 211
Period size: 93 Copynumber: 1.8 Consensus size: 93
4500792 TTCGGACAAA
* *
4500802 TGTGATATGTGCTTCCGTATAAGACCATATCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
1 TGTGATATGTGCATCCGTATAAGACCATAGCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
*
4500867 ATAAGACCATATTTGGGATATGGCATCAG
66 ACAAGACCATATTT-GGATATGGCATCAG
* * * * *
4500896 TGTGATATGTG-ATCCGTGTAAGACCATGGCTGGGTTATGGCCTCGGTATGTGATATGTGACTA-
1 TGTGATATGTGCATCCGTATAAGACCATAGCCGGGATATGGCATCGG--TGTGATATGTG-CTAC
*
4500959 TGTGCAAGACCATA
63 TGTACAAGACCATA
4500973 GTTTTACTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
93 28 0.43
94 11 0.17
95 23 0.35
96 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (93 bp):
TGTGATATGTGCATCCGTATAAGACCATAGCCGGGATATGGCATCGGTGTGATATGTGCTACTGT
ACAAGACCATATTTGGATATGGCATCAG
Found at i:4505636 original size:20 final size:20
Alignment explanation
Indices: 4505588--4505638 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
4505578 TTACGTCAAT
*
4505588 AAAAAAATT-TAAAAATAAA
1 AAAAAAATTAAAAAAATAAA
*
4505607 AAAATCAAATTAAAAAAATTAA
1 AAAA--AAATTAAAAAAATAAA
4505629 AAAAAAATTA
1 AAAAAAATTA
4505639 CATACCATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.15
20 6 0.22
21 5 0.19
22 12 0.44
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAAAAATTAAAAAAATAAA
Found at i:4509048 original size:22 final size:22
Alignment explanation
Indices: 4508993--4509056 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
4508983 TAATAATTTA
*
4508993 AAAATTATAAAGATATAGATTATT
1 AAAATTATAAA-AT-TATATTATT
* *
4509017 AAAATAATAAAATTATATTTTT
1 AAAATTATAAAATTATATTATT
* *
4509039 AATATTATAAAAATATAT
1 AAAATTATAAAATTATAT
4509057 AATTTAGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 22 0.65
23 2 0.06
24 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
AAAATTATAAAATTATATTATT
Found at i:4511529 original size:19 final size:19
Alignment explanation
Indices: 4511505--4511543 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
4511495 TTTAATTTAA
4511505 AAAAAATAGTTACTTGACT
1 AAAAAATAGTTACTTGACT
4511524 AAAAAATAGTTACTTGACT
1 AAAAAATAGTTACTTGACT
4511543 A
1 A
4511544 TGTTCATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (19 bp):
AAAAAATAGTTACTTGACT
Found at i:4513768 original size:88 final size:88
Alignment explanation
Indices: 4513611--4513774 Score: 231
Period size: 88 Copynumber: 1.9 Consensus size: 88
4513601 AACCCTAAAT
* * *
4513611 TCAAACCCCTTTGTCTCCATGGTCAAAGGCATTGGATTGAAGTTGTCTATCATGCTAATAAATTT
1 TCAAACCCCTATGTCTCCATGGTCAAAGACATTGGATTGAAGTTCTCTATCATGCTAATAAATTT
4513676 TTTTAATTTTTAATTTTCAAAAA
66 TTTTAATTTTTAATTTTCAAAAA
* * * * *
4513699 TCAAACCCCTATGTCTCTATGGTCAAAGACATT-GTTTGAAGTTCTGTATTATGCTAATAATTTT
1 TCAAACCCCTATGTCTCCATGGTCAAAGACATTGGATTGAAGTTCTCTATCATGCTAATAAATTT
*
4513763 ATTTTATTTTTT
66 -TTTTAATTTTT
4513775 CAAAATTTTC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
87 26 0.39
88 40 0.61
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (88 bp):
TCAAACCCCTATGTCTCCATGGTCAAAGACATTGGATTGAAGTTCTCTATCATGCTAATAAATTT
TTTTAATTTTTAATTTTCAAAAA
Found at i:4517384 original size:21 final size:22
Alignment explanation
Indices: 4517319--4517384 Score: 55
Period size: 24 Copynumber: 2.9 Consensus size: 22
4517309 ATAAATTAAA
* *
4517319 TTAAAAAATAAATTGTATTT-TT
1 TTAAAAAA-AAATTATCTTTATT
*
4517341 TATTAAAAAAAATTATCTATTTATT
1 T-TAAAAAAAAATTATC--TTTATT
4517366 TTAAAAAAAAATT-TCTTTA
1 TTAAAAAAAAATTATCTTTA
4517385 AAATATTGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
21 4 0.11
22 7 0.19
23 8 0.22
24 14 0.39
25 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAAAAAAAAATTATCTTTATT
Found at i:4533535 original size:19 final size:20
Alignment explanation
Indices: 4533489--4533535 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
4533479 AATTATAAAA
4533489 AATATTATCTAAAAATTATG
1 AATATTATCTAAAAATTATG
* *
4533509 AAGTTATTAT-TAAATATTATT
1 AA--TATTATCTAAAAATTATG
4533530 AATATT
1 AATATT
4533536 TAATTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 4 0.17
20 2 0.09
21 11 0.48
22 6 0.26
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (20 bp):
AATATTATCTAAAAATTATG
Found at i:4534172 original size:16 final size:17
Alignment explanation
Indices: 4534151--4534184 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4534141 CATTTGTATA
4534151 TATTTTTATAAT-ATTT
1 TATTTTTATAATAATTT
*
4534167 TATTTTTTTAATAATTT
1 TATTTTTATAATAATTT
4534184 T
1 T
4534185 TAATAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTTATAATAATTT
Found at i:4537307 original size:25 final size:27
Alignment explanation
Indices: 4537279--4537338 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
4537269 TTATTATAGT
*
4537279 CTTGTT-GTGTTGTTGTTA-TTGTTTA
1 CTTGTTCGTGTTGTTGTTATTTGTTCA
*
4537304 CTTGTACTCGTGTTGTTTTTATTTGTTCA
1 CTTGT--TCGTGTTGTTGTTATTTGTTCA
4537333 CTTGTT
1 CTTGTT
4537339 TCCTCCAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
25 5 0.17
27 2 0.07
28 11 0.38
29 11 0.38
ACGTcount: A:0.08, C:0.10, G:0.20, T:0.62
Consensus pattern (27 bp):
CTTGTTCGTGTTGTTGTTATTTGTTCA
Found at i:4542026 original size:18 final size:18
Alignment explanation
Indices: 4541935--4542027 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
4541925 CCCAACTACT
* *
4541935 GTATACGTGAACAGTACT
1 GTATACGTGAATAGTACC
*
4541953 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
* *
4541971 GTATACATAAATAGTACC
1 GTATACGTGAATAGTACC
* *
4541989 ATATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
4542007 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
4542025 GTA
1 GTA
4542028 AACGATCATA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:4549934 original size:558 final size:558
Alignment explanation
Indices: 4548880--4549984 Score: 2201
Period size: 558 Copynumber: 2.0 Consensus size: 558
4548870 GTGACGATCA
4548880 AAATCTTGTGATCTACTACCCAGCTAGCAAATCTGTACAAAAAACGAATTAATAATCAACAAACA
1 AAATCTTGTGATCTACTACCCAGCTAGCAAATCTGTACAAAAAACGAATTAATAATCAACAAACA
4548945 TATTGTCGGCGATGTAGACTAGAGGTGGAGAAAACCTGACATGCATGCAAGGATTGCTTTGGGTG
66 TATTGTCGGCGATGTAGACTAGAGGTGGAGAAAACCTGACATGCATGCAAGGATTGCTTTGGGTG
4549010 TTTAGACTGCTCTGGGTTTCATGTTTTGACCACTACAGTCGTCGGACACAAGGTGCTTGGTTGAC
131 TTTAGACTGCTCTGGGTTTCATGTTTTGACCACTACAGTCGTCGGACACAAGGTGCTTGGTTGAC
4549075 CTACTAGCTAGGCAAATAAGGTTAAACTTAGTTTGGGTCTTGCTTGTTTATAGAGTATCTAGTAT
196 CTACTAGCTAGGCAAATAAGGTTAAACTTAGTTTGGGTCTTGCTTGTTTATAGAGTATCTAGTAT
4549140 AATCGGAATCGAAAGTTTCATGAGGGATAGAGATTTGTATTGGTGATCAGTACCCCTCTGATCAA
261 AATCGGAATCGAAAGTTTCATGAGGGATAGAGATTTGTATTGGTGATCAGTACCCCTCTGATCAA
4549205 TGGAAATTTGCTTTAGCCCAAGTTATACTAGTGATGCTGCCTCAATTGATTAGGAAGACTTGATT
326 TGGAAATTTGCTTTAGCCCAAGTTATACTAGTGATGCTGCCTCAATTGATTAGGAAGACTTGATT
4549270 TCTACGAGACCTCCACTTTTAACGAAGAACTTTGGTGGAGCTCTAGCCAGTAATTAGTGCTTTGG
391 TCTACGAGACCTCCACTTTTAACGAAGAACTTTGGTGGAGCTCTAGCCAGTAATTAGTGCTTTGG
4549335 AGTGGTGGGCTTTATAGCAAGAAAGAATCTCGGGGAAACTATAACAGTAGGAGCGAATTGAGTCC
456 AGTGGTGGGCTTTATAGCAAGAAAGAATCTCGGGGAAACTATAACAGTAGGAGCGAATTGAGTCC
4549400 CTTTTGTTATTGATCGGGGTTTATGCTAGCCAGCTAGC
521 CTTTTGTTATTGATCGGGGTTTATGCTAGCCAGCTAGC
4549438 AAATCTTGTGATCTACTACCCAGCTAGCAAATCTGTACAAAAAACGAATTAATAATCAACAAACA
1 AAATCTTGTGATCTACTACCCAGCTAGCAAATCTGTACAAAAAACGAATTAATAATCAACAAACA
4549503 TATTGTCGGCGATGTAGACTAGAGGTGGAGAAAACCTGACATGCATGCAAGGATTGCTTTGGGTG
66 TATTGTCGGCGATGTAGACTAGAGGTGGAGAAAACCTGACATGCATGCAAGGATTGCTTTGGGTG
4549568 TTTAGACTGCTCTGGGTTTCATGTTTTGACCACTACAGTCGTCGGACACAAGGTGCTTGGTTGAC
131 TTTAGACTGCTCTGGGTTTCATGTTTTGACCACTACAGTCGTCGGACACAAGGTGCTTGGTTGAC
4549633 CTACTAGCTAGGCAAATAAGGTTAAACTTAGTTTGGGTCTTGCTTGTTTATAGAGTATCTAGTAT
196 CTACTAGCTAGGCAAATAAGGTTAAACTTAGTTTGGGTCTTGCTTGTTTATAGAGTATCTAGTAT
4549698 AATCGGAATCGAAAGTTTCATGAGGGATAGAGATTTGTATTGGTGATCAGTACCCCTCTGATCAA
261 AATCGGAATCGAAAGTTTCATGAGGGATAGAGATTTGTATTGGTGATCAGTACCCCTCTGATCAA
4549763 TGGAAATTTGCTTTAGCCCAAGTTATACTAGTGATGCTGCCTCAATTGATTAGGAAGACTTGATT
326 TGGAAATTTGCTTTAGCCCAAGTTATACTAGTGATGCTGCCTCAATTGATTAGGAAGACTTGATT
*
4549828 TCTACGAGACCTCCACTTTTAACGACGAACTTTGGTGGAGCTCTAGCCAGTAATTAGTGCTTTGG
391 TCTACGAGACCTCCACTTTTAACGAAGAACTTTGGTGGAGCTCTAGCCAGTAATTAGTGCTTTGG
4549893 AGTGGTGGGCTTTATAGCAAGAAAGAATCTCGGGGAAACTATAACAGTAGGAGCGAATTGAGTCC
456 AGTGGTGGGCTTTATAGCAAGAAAGAATCTCGGGGAAACTATAACAGTAGGAGCGAATTGAGTCC
4549958 CTTTTGTTATTGATCGGGGTTTATGCT
521 CTTTTGTTATTGATCGGGGTTTATGCT
4549985 TGTCGTTCAA
Statistics
Matches: 546, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
558 546 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (558 bp):
AAATCTTGTGATCTACTACCCAGCTAGCAAATCTGTACAAAAAACGAATTAATAATCAACAAACA
TATTGTCGGCGATGTAGACTAGAGGTGGAGAAAACCTGACATGCATGCAAGGATTGCTTTGGGTG
TTTAGACTGCTCTGGGTTTCATGTTTTGACCACTACAGTCGTCGGACACAAGGTGCTTGGTTGAC
CTACTAGCTAGGCAAATAAGGTTAAACTTAGTTTGGGTCTTGCTTGTTTATAGAGTATCTAGTAT
AATCGGAATCGAAAGTTTCATGAGGGATAGAGATTTGTATTGGTGATCAGTACCCCTCTGATCAA
TGGAAATTTGCTTTAGCCCAAGTTATACTAGTGATGCTGCCTCAATTGATTAGGAAGACTTGATT
TCTACGAGACCTCCACTTTTAACGAAGAACTTTGGTGGAGCTCTAGCCAGTAATTAGTGCTTTGG
AGTGGTGGGCTTTATAGCAAGAAAGAATCTCGGGGAAACTATAACAGTAGGAGCGAATTGAGTCC
CTTTTGTTATTGATCGGGGTTTATGCTAGCCAGCTAGC
Found at i:4555363 original size:16 final size:16
Alignment explanation
Indices: 4555342--4555384 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
4555332 GTGAAATTTA
* *
4555342 AATATTTTATTGAGAT
1 AATATTTTATTAAAAT
4555358 AATATTTTAATTAAAAT
1 AATATTTT-ATTAAAAT
4555375 AAT-TTTTATT
1 AATATTTTATT
4555385 TAATAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 12 0.50
17 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
AATATTTTATTAAAAT
Found at i:4562384 original size:33 final size:33
Alignment explanation
Indices: 4562342--4562410 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
4562332 GATTGTCAGG
4562342 TTTGAGTGTATTATGTAAGCCTCTTACTTTTTC
1 TTTGAGTGTATTATGTAAGCCTCTTACTTTTTC
4562375 TTTGAGTGTATTATGTAAGCCTCTTACTTTTTC
1 TTTGAGTGTATTATGTAAGCCTCTTACTTTTTC
4562408 TTT
1 TTT
4562411 CTCTGATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.54
Consensus pattern (33 bp):
TTTGAGTGTATTATGTAAGCCTCTTACTTTTTC
Found at i:4577549 original size:20 final size:20
Alignment explanation
Indices: 4577524--4577573 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
4577514 TGGCTTAAAA
4577524 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
4577544 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
4577561 GTGGTAGTGGATT
1 TTGGTAGTGGATT
4577574 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:4582186 original size:20 final size:20
Alignment explanation
Indices: 4582161--4582210 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
4582151 TGGCTTAAAA
4582161 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
4582181 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
4582198 GTGGTAGTGGATT
1 TTGGTAGTGGATT
4582211 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:4584222 original size:16 final size:16
Alignment explanation
Indices: 4584188--4584223 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4584178 GTATCATGGA
* *
4584188 TTAATTAGATATTAGT
1 TTAATTAGATAGTAAT
4584204 TTAATTAGATAGTAAT
1 TTAATTAGATAGTAAT
4584220 TTAA
1 TTAA
4584224 ATATTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (16 bp):
TTAATTAGATAGTAAT
Found at i:4587776 original size:30 final size:30
Alignment explanation
Indices: 4587740--4587797 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4587730 AGAAGCATTA
*
4587740 TAAACACCCTTATTAATTAATAAAAATATG
1 TAAACACCCCTATTAATTAATAAAAATATG
* *
4587770 TAAACACCCCTATTGATTGATAAAAATA
1 TAAACACCCCTATTAATTAATAAAAATA
4587798 CATATTCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (30 bp):
TAAACACCCCTATTAATTAATAAAAATATG
Found at i:4588277 original size:5 final size:5
Alignment explanation
Indices: 4588267--4588312 Score: 83
Period size: 5 Copynumber: 9.0 Consensus size: 5
4588257 AATAATTAAG
4588267 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT
4588313 ATAAAAGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 35 0.88
6 5 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:4588364 original size:31 final size:30
Alignment explanation
Indices: 4588329--4588389 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
4588319 GAAACAGAAT
*
4588329 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
4588360 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
4588390 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:4589963 original size:39 final size:39
Alignment explanation
Indices: 4589856--4589990 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
4589846 GACCTCGAGT
* * *
4589856 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
4589897 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
4589935 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
4589974 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
4589991 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:4592176 original size:131 final size:131
Alignment explanation
Indices: 4591800--4592186 Score: 447
Period size: 131 Copynumber: 2.9 Consensus size: 131
4591790 AAAACACGAG
* * * * * * * *
4591800 TGAAATTCCGAAGAGATATTCAATTATTTTGAACAAACGGGAGATTGCAACCCAGCACGATAGGG
1 TGAAATTTCGAAGAGATATTCGATTATTTTGAGCAAACGCGAAATTGTAACCCAACACGTTAGGG
* * * * ** *
4591865 CACTATTCCCCGAATTGCCAAACATCGAA-CATT-TCTTTCGTTTTAAAGAGTTTTTAGTAGATA
66 CACGATTCCGCGAATTGCCAAACATCGAATC-TTGTC-TTCGTTTTGAAGA-ATTTTAAAAGACA
4591928 TGAA
128 TGAA
* * *
4591932 TGAAATCTT-GAAGGGATACTCGATTATTTTGAGCAAACACGAAATTGTAACCCAACACGTTAGG
1 TGAAAT-TTCGAAGAGATATTCGATTATTTTGAGCAAACGCGAAATTGTAACCCAACACGTTAGG
* * * * * * * * *
4591996 GCACGATTCCGTGAATTACTAAATATCGAATGTCGTCCTCATTTGGAAGAATTTTAAAAGACATG
65 GCACGATTCCGCGAATTGCCAAACATCGAATCTTGTCTTCGTTTTGAAGAATTTTAAAAGACATG
4592061 AA
130 AA
*
4592063 TGAAATTTCGAAGCGATATTCGATTATTTTGAGCAAACGCGAAATTGTAACCCAACACGTTAGGG
1 TGAAATTTCGAAGAGATATTCGATTATTTTGAGCAAACGCGAAATTGTAACCCAACACGTTAGGG
* *
4592128 CACGATTCCGCGAATTGCCAAACATCAAATCTTGTCTTCGTTTTGAAGAATTTTTAAAG
66 CACGATTCCGCGAATTGCCAAACATCGAATCTTGTCTTCGTTTTGAAGAATTTTAAAAG
4592187 GAATACTTAT
Statistics
Matches: 210, Mismatches: 41, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
130 2 0.01
131 120 0.57
132 85 0.40
133 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (131 bp):
TGAAATTTCGAAGAGATATTCGATTATTTTGAGCAAACGCGAAATTGTAACCCAACACGTTAGGG
CACGATTCCGCGAATTGCCAAACATCGAATCTTGTCTTCGTTTTGAAGAATTTTAAAAGACATGA
A
Found at i:4598600 original size:33 final size:35
Alignment explanation
Indices: 4598553--4598625 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 35
4598543 TTATTTATAT
4598553 TATATATATATGTGTG-TTTTAAATATTAT-GTTA
1 TATATATATATGTGTGATTTTAAATATTATAGTTA
* *
4598586 TATATATATGTGTGTGTATTTTTAATATTATCAGTTA
1 TATATATATATGTGTG-ATTTTAAATATTAT-AGTTA
4598623 TAT
1 TAT
4598626 TTTCTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 15 0.44
35 12 0.35
37 7 0.21
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (35 bp):
TATATATATATGTGTGATTTTAAATATTATAGTTA
Found at i:4598602 original size:35 final size:35
Alignment explanation
Indices: 4598539--4598625 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
4598529 ATTATATATA
*
4598539 AAAT-TTAT-TTATATTATATATATATGTGTGTTTT
1 AAATATTATGTTATA-TATATATATATGTGTATTTT
* *
4598573 AAATATTATGTTATATATATATGTGTGTGTATTTT
1 AAATATTATGTTATATATATATATATGTGTATTTT
*
4598608 TAATATTATCAGTTATAT
1 AAATATTAT--GTTATAT
4598626 TTTCTTATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
34 4 0.09
35 29 0.64
36 5 0.11
37 7 0.16
ACGTcount: A:0.33, C:0.01, G:0.10, T:0.55
Consensus pattern (35 bp):
AAATATTATGTTATATATATATATATGTGTATTTT
Found at i:4600164 original size:8 final size:8
Alignment explanation
Indices: 4600151--4600180 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
4600141 ATTTAAGTAA
4600151 ATATTATT
1 ATATTATT
4600159 ATATTATT
1 ATATTATT
4600167 ATATTATT
1 ATATTATT
4600175 ATATTA
1 ATATTA
4600181 ATTAAATAAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATATTATT
Found at i:4600422 original size:17 final size:15
Alignment explanation
Indices: 4600400--4600433 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
4600390 AGGGGAGAAA
4600400 GAAAGAAAGGAAAAAGG
1 GAAAGAAA-G-AAAAGG
4600417 GAAAGAAAGAAAAGG
1 GAAAGAAAGAAAAGG
4600432 GA
1 GA
4600434 GAAATTGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 1 0.06
17 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGAAAAGG
Found at i:4600437 original size:17 final size:18
Alignment explanation
Indices: 4600399--4600437 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
4600389 CAGGGGAGAA
4600399 AGAAAGAAAGGAAAAAGG
1 AGAAAGAAAGGAAAAAGG
*
4600417 -GAAAGAAA-GAAAAGGG
1 AGAAAGAAAGGAAAAAGG
4600433 AGAAA
1 AGAAA
4600438 TTGGGGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGAAAGAAAGGAAAAAGG
Found at i:4601158 original size:26 final size:27
Alignment explanation
Indices: 4601125--4601175 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
4601115 ATATAGATGT
4601125 GAAATGAAAGAAATGATAC-ATGTTAA
1 GAAATGAAAGAAATGATACAATGTTAA
4601151 GAAATGAAAGAAATGATACAATGTT
1 GAAATGAAAGAAATGATACAATGTT
4601176 TGGAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.24
Consensus pattern (27 bp):
GAAATGAAAGAAATGATACAATGTTAA
Found at i:4601374 original size:39 final size:39
Alignment explanation
Indices: 4601319--4601426 Score: 146
Period size: 39 Copynumber: 2.7 Consensus size: 39
4601309 CCTTCTCGAG
4601319 AATTAAAAGTGAATAGGATTTATTCCTGATTCACTA-AAGA
1 AATT-AAAGTGAATAGGATTTATTCCTGATTCACTAGAA-A
4601359 AATTAAAGTGAATAGGATTTATTCCTGATTCACTAGAAA
1 AATTAAAGTGAATAGGATTTATTCCTGATTCACTAGAAA
* * * *
4601398 TATATAAAATGGATAGGATTTGTTCCTGA
1 AAT-TAAAGTGAATAGGATTTATTCCTGA
4601427 AATGGTAACT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
39 34 0.55
40 28 0.45
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (39 bp):
AATTAAAGTGAATAGGATTTATTCCTGATTCACTAGAAA
Found at i:4601425 original size:40 final size:39
Alignment explanation
Indices: 4601319--4601426 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 39
4601309 CCTTCTCGAG
4601319 AATTAAAAGTGAATAGGATTTATTCCTGATTCACTAAAGA
1 AATTAAAA-TGAATAGGATTTATTCCTGATTCACTAAAGA
*
4601359 AATTAAAGTGAATAGGATTTATTCCTGATTCACTAGAA-A
1 AATTAAAATGAATAGGATTTATTCCTGATTCACTA-AAGA
* * *
4601398 TATATAAAATGGATAGGATTTGTTCCTGA
1 AAT-TAAAATGAATAGGATTTATTCCTGA
4601427 AATGGTAACT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
39 30 0.49
40 31 0.51
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (39 bp):
AATTAAAATGAATAGGATTTATTCCTGATTCACTAAAGA
Found at i:4610934 original size:41 final size:43
Alignment explanation
Indices: 4610851--4610948 Score: 110
Period size: 41 Copynumber: 2.3 Consensus size: 43
4610841 ATCGGGTACC
* * * **
4610851 TAGTACCTCATCGGATTTAATCCGAAGCAATAAAACGGCAC-A
1 TAGTGCCTCATTGGAATTAATCCGAAGCAATAAAACAACACAA
**
4610893 TAGTGCCTCATTGGAATT-ATCCGAAGCAATATTACAACACATA
1 TAGTGCCTCATTGGAATTAATCCGAAGCAATAAAACAACACA-A
4610936 TAGTGCCTCATTG
1 TAGTGCCTCATTG
4610949 ACTCGAGGTC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 18 0.38
42 15 0.32
43 14 0.30
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (43 bp):
TAGTGCCTCATTGGAATTAATCCGAAGCAATAAAACAACACAA
Found at i:4615620 original size:52 final size:52
Alignment explanation
Indices: 4615563--4615678 Score: 189
Period size: 51 Copynumber: 2.2 Consensus size: 52
4615553 CTAAAAATAT
* * * *
4615563 AATTTTGTTATTTGAATGGTTTATTTTTATAATTTTTAGAAGATTAAATTAA
1 AATTTTATTATTTAAATAGATTATTTTTATAATTTTTAGAAGATTAAATTAA
4615615 AATTTTATT-TTTAAATAGATTATTTTTATAATTTTTAGAAGATTAAATTAA
1 AATTTTATTATTTAAATAGATTATTTTTATAATTTTTAGAAGATTAAATTAA
4615666 AATTTTATTATTT
1 AATTTTATTATTT
4615679 TTAAGAGAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
51 48 0.81
52 11 0.19
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (52 bp):
AATTTTATTATTTAAATAGATTATTTTTATAATTTTTAGAAGATTAAATTAA
Found at i:4615621 original size:30 final size:30
Alignment explanation
Indices: 4615587--4615681 Score: 100
Period size: 30 Copynumber: 3.5 Consensus size: 30
4615577 AATGGTTTAT
4615587 TTTTATAATTTTTAGAAGATTAAATTAAAA
1 TTTTATAATTTTTAGAAGATTAAATTAAAA
* *
4615617 -TTT-T-ATTTTT--AA-A-TAGATT--AT
1 TTTTATAATTTTTAGAAGATTAAATTAAAA
4615638 TTTTATAATTTTTAGAAGATTAAATTAAAA
1 TTTTATAATTTTTAGAAGATTAAATTAAAA
*
4615668 TTTTATTATTTTTA
1 TTTTATAATTTTTA
4615682 AGAGAAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
21 1 0.02
22 3 0.06
23 6 0.12
24 7 0.14
25 2 0.04
26 2 0.04
27 7 0.14
28 6 0.12
29 3 0.06
30 14 0.27
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (30 bp):
TTTTATAATTTTTAGAAGATTAAATTAAAA
Found at i:4615657 original size:23 final size:23
Alignment explanation
Indices: 4615583--4615659 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 23
4615573 TTTGAATGGT
4615583 TTATTTTTATAATTTTTAGAAGA
1 TTATTTTTATAATTTTTAGAAGA
*
4615606 TTAAATTAAAATTT-T-ATTTTTAAATAGA
1 TT--ATT----TTTATAATTTTTAGA-AGA
4615634 TTATTTTTATAATTTTTAGAAGA
1 TTATTTTTATAATTTTTAGAAGA
4615657 TTA
1 TTA
4615660 AATTAAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
22 3 0.07
23 9 0.21
24 8 0.19
25 3 0.07
26 3 0.07
27 8 0.19
28 6 0.14
29 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (23 bp):
TTATTTTTATAATTTTTAGAAGA
Found at i:4619102 original size:33 final size:33
Alignment explanation
Indices: 4619065--4619162 Score: 119
Period size: 33 Copynumber: 3.0 Consensus size: 33
4619055 ACACATTACA
* * *
4619065 TAGCTTGCACATTACACAACTCGCACATCATTG
1 TAGCTCGCACATTACACAGCTCACACATCATTG
*
4619098 TAGCTCACACATTACACAGCTCACACATCACTATG
1 TAGCTCGCACATTACACAGCTCACACATCA-T-TG
*
4619133 -A-CTCGCAAATTACACAGCTCACACATCATT
1 TAGCTCGCACATTACACAGCTCACACATCATT
4619163 ACGACTCGCA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
31 1 0.02
32 1 0.02
33 51 0.89
34 2 0.04
35 2 0.04
ACGTcount: A:0.34, C:0.33, G:0.09, T:0.24
Consensus pattern (33 bp):
TAGCTCGCACATTACACAGCTCACACATCATTG
Found at i:4619120 original size:16 final size:16
Alignment explanation
Indices: 4619047--4619158 Score: 66
Period size: 16 Copynumber: 6.9 Consensus size: 16
4619037 TGCATATTTT
*
4619047 CACAACTCACACATTA
1 CACAGCTCACACATTA
* **
4619063 CATAGCTTGCACATTA
1 CACAGCTCACACATTA
* * *
4619079 CACAACTCGCACATCA
1 CACAGCTCACACATTA
***
4619095 TTGTAGCTCACACATTA
1 -CACAGCTCACACATTA
4619112 CACAGCTCACACA-T-
1 CACAGCTCACACATTA
* *
4619126 CACTATGACTCGCAAATTA
1 CAC-A-G-CTCACACATTA
4619145 CACAGCTCACACAT
1 CACAGCTCACACAT
4619159 CATTACGACT
Statistics
Matches: 69, Mismatches: 21, Indels: 12
0.68 0.21 0.12
Matches are distributed among these distances:
14 3 0.04
15 2 0.03
16 42 0.61
17 17 0.25
18 2 0.03
19 3 0.04
ACGTcount: A:0.36, C:0.34, G:0.08, T:0.22
Consensus pattern (16 bp):
CACAGCTCACACATTA
Found at i:4619169 original size:33 final size:33
Alignment explanation
Indices: 4619108--4619172 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
4619098 TAGCTCACAC
*
4619108 ATTACACAGCTCACACATCACTATGACTCGCAA
1 ATTACACAGCTCACACATCACTACGACTCGCAA
*
4619141 ATTACACAGCTCACACATCATTACGACTCGCA
1 ATTACACAGCTCACACATCACTACGACTCGCA
4619173 CATTGATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.34, G:0.09, T:0.22
Consensus pattern (33 bp):
ATTACACAGCTCACACATCACTACGACTCGCAA
Found at i:4621346 original size:43 final size:44
Alignment explanation
Indices: 4621271--4621357 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
4621261 ATTGATACTT
* * *
4621271 TTATGTGGTGTAATATTTAGTTATGCACTTGGACAATGTTATTA
1 TTATGTGGTGTAATATCTAATTATGCACTTGGACAATATTATTA
* * *
4621315 TTATGTGGTGTACTA-CTAATTATGCATTTGGATAATATTATTA
1 TTATGTGGTGTAATATCTAATTATGCACTTGGACAATATTATTA
4621358 ATTTCTAGTA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 23 0.62
44 14 0.38
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.46
Consensus pattern (44 bp):
TTATGTGGTGTAATATCTAATTATGCACTTGGACAATATTATTA
Found at i:4621622 original size:22 final size:20
Alignment explanation
Indices: 4621579--4621617 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4621569 CAATTTAAAA
4621579 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
4621599 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
4621618 ATGTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:4621739 original size:20 final size:20
Alignment explanation
Indices: 4621714--4621754 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4621704 AAATATTTTC
4621714 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
*
4621734 AGTAAATCATTTTCCGGAAA
1 AGTAAATCATTTTCCAGAAA
4621754 A
1 A
4621755 CATTTTACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:4623699 original size:14 final size:14
Alignment explanation
Indices: 4623675--4623707 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4623665 TCCCTGCTTC
4623675 GTTTCTGTTTCTTTT
1 GTTTCTGTTTC-TTT
4623690 GTTT-TGTTTCTTT
1 GTTTCTGTTTCTTT
4623703 GTTTC
1 GTTTC
4623708 CTTAATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.73
Consensus pattern (14 bp):
GTTTCTGTTTCTTT
Found at i:4624040 original size:15 final size:14
Alignment explanation
Indices: 4624022--4624052 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4624012 TTAATTTATT
4624022 TAATAATAATGCTAA
1 TAATAATAAT-CTAA
4624037 TAATAATAATCTAA
1 TAATAATAATCTAA
4624051 TA
1 TA
4624053 TAAAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.35
Consensus pattern (14 bp):
TAATAATAATCTAA
Found at i:4624063 original size:21 final size:20
Alignment explanation
Indices: 4624039--4624107 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
4624029 AATGCTAATA
4624039 ATAATAATCTAATATAAAACC
1 ATAATAAT-TAATATAAAACC
* **
4624060 ATAAT-GTTAAT-TAATAATT
1 ATAATAATTAATATAA-AACC
4624079 ATAATAATTTAATATAAAACC
1 ATAATAA-TTAATATAAAACC
4624100 ATAATAAT
1 ATAATAAT
4624108 AATCATTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
18 3 0.08
19 11 0.29
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.36
Consensus pattern (20 bp):
ATAATAATTAATATAAAACC
Found at i:4633601 original size:20 final size:21
Alignment explanation
Indices: 4633572--4633610 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4633562 TTGAAACCTT
*
4633572 AAAATCATTTATGATTCACGA
1 AAAATCATTTATGACTCACGA
4633593 AAAAT-ATTTATGACTCAC
1 AAAATCATTTATGACTCAC
4633611 ATAGAGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (21 bp):
AAAATCATTTATGACTCACGA
Found at i:4633929 original size:19 final size:19
Alignment explanation
Indices: 4633907--4633949 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
4633897 TAATTTTTAT
4633907 TTTTTTAAAAAAAATAAGA
1 TTTTTTAAAAAAAATAAGA
***
4633926 TTTTTTATTTAAAATAAGA
1 TTTTTTAAAAAAAATAAGA
4633945 TTTTT
1 TTTTT
4633950 AGTTTTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTTTTAAAAAAAATAAGA
Found at i:4634690 original size:20 final size:20
Alignment explanation
Indices: 4634654--4634691 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4634644 AAGTTATAAC
*
4634654 AATATTTATATTAATTTATT
1 AATATTTATAATAATTTATT
4634674 AATATTTTATAAT-ATTTA
1 AATA-TTTATAATAATTTA
4634692 AAATTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTTATAATAATTTATT
Found at i:4643982 original size:3 final size:3
Alignment explanation
Indices: 4643974--4644000 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4643964 TATTTAACCC
4643974 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
4644001 CATCATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4651124 original size:15 final size:17
Alignment explanation
Indices: 4651084--4651125 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
4651074 ATTTTAGAAG
4651084 TATTTTTAAGATAAAAA
1 TATTTTTAAGATAAAAA
* *
4651101 TATTATTAA-AT-AATA
1 TATTTTTAAGATAAAAA
4651116 TATTTTTAAG
1 TATTTTTAAG
4651126 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 11 0.52
16 2 0.10
17 8 0.38
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (17 bp):
TATTTTTAAGATAAAAA
Found at i:4656217 original size:7 final size:7
Alignment explanation
Indices: 4656205--4656240 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
4656195 AGTGAAAGTG
4656205 AAAGTAA
1 AAAGTAA
4656212 AAAGTAA
1 AAAGTAA
4656219 AAAGTAA
1 AAAGTAA
4656226 AAAGT-A
1 AAAGTAA
4656232 AAAGTAA
1 AAAGTAA
4656239 AA
1 AA
4656241 GAAGAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAGTAA
Found at i:4656220 original size:6 final size:6
Alignment explanation
Indices: 4656186--4656241 Score: 58
Period size: 6 Copynumber: 8.8 Consensus size: 6
4656176 AACAAATAAG
* * *
4656186 AAAAAT AAAAGT GAAAGT GAAAGT AAAAAGT AAAAAGT AAAAAGT AAAAGT
1 AAAAGT AAAAGT AAAAGT AAAAGT -AAAAGT -AAAAGT -AAAAGT AAAAGT
4656237 AAAAG
1 AAAAG
4656242 AAGAAAAAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
6 27 0.59
7 19 0.41
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.14
Consensus pattern (6 bp):
AAAAGT
Found at i:4656224 original size:14 final size:13
Alignment explanation
Indices: 4656186--4656240 Score: 69
Period size: 13 Copynumber: 4.3 Consensus size: 13
4656176 AACAAATAAG
4656186 AAAAA-TAAAAGT
1 AAAAAGTAAAAGT
* *
4656198 -GAAAGTGAAAGT
1 AAAAAGTAAAAGT
4656210 AAAAAGTAAAAAGT
1 AAAAAGT-AAAAGT
4656224 AAAAAGTAAAAGT
1 AAAAAGTAAAAGT
4656237 AAAA
1 AAAA
4656241 GAAGAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 3 0.08
12 6 0.17
13 15 0.42
14 12 0.33
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.15
Consensus pattern (13 bp):
AAAAAGTAAAAGT
Found at i:4656255 original size:21 final size:21
Alignment explanation
Indices: 4656231--4656271 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4656221 AGTAAAAAGT
* *
4656231 AAAAGTAAAAGAAGAAAAAAC
1 AAAAGTAAAAAAAAAAAAAAC
*
4656252 AAAATTAAAAAAAAAAAAAA
1 AAAAGTAAAAAAAAAAAAAA
4656272 GATGCAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.83, C:0.02, G:0.07, T:0.07
Consensus pattern (21 bp):
AAAAGTAAAAAAAAAAAAAAC
Found at i:4658296 original size:6 final size:6
Alignment explanation
Indices: 4658285--4658309 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4658275 TAGAATACTA
4658285 TCACCT TCACCT TCACCT TCACCT T
1 TCACCT TCACCT TCACCT TCACCT T
4658310 TTATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.48, G:0.00, T:0.36
Consensus pattern (6 bp):
TCACCT
Found at i:4667407 original size:22 final size:21
Alignment explanation
Indices: 4667382--4667427 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
4667372 GATTTTTCCG
*
4667382 ATTTCTAGTTGAATAAATTAAA
1 ATTTC-AGTTAAATAAATTAAA
* *
4667404 ATTTCAGTTAAATTAGTTAAA
1 ATTTCAGTTAAATAAATTAAA
4667425 ATT
1 ATT
4667428 AATATCCGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (21 bp):
ATTTCAGTTAAATAAATTAAA
Found at i:4682105 original size:33 final size:31
Alignment explanation
Indices: 4682025--4682105 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 31
4682015 TGAAATATAA
*
4682025 ATTTTAAATATTTTTAATTAATAAATATTAATT
1 ATTTTAAATA--TTTAATTAATAAATATAAATT
4682058 ATTTATAAAT-TTTAATTAA-AATATATAAACTAT
1 ATTT-TAAATATTTAATTAATAA-ATATAAA-T-T
4682091 ATTTTAAATATTTAA
1 ATTTTAAATATTTAA
4682106 ATATAACTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
30 2 0.05
31 15 0.36
32 6 0.14
33 14 0.33
34 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
ATTTTAAATATTTAATTAATAAATATAAATT
Found at i:4684710 original size:22 final size:22
Alignment explanation
Indices: 4684650--4684710 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
4684640 AAATTGAACC
* *
4684650 TAAAAAAACTTAAATACTAAAT
1 TAAAAAAAATTAAGTACTAAAT
***
4684672 TAACAAATTGTTAAGTACTAAAT
1 TAA-AAAAAATTAAGTACTAAAT
4684695 TAAAAAAAATTAAGTA
1 TAAAAAAAATTAAGTA
4684711 TAGAAACTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (22 bp):
TAAAAAAAATTAAGTACTAAAT
Found at i:4687747 original size:44 final size:45
Alignment explanation
Indices: 4687694--4687793 Score: 130
Period size: 44 Copynumber: 2.2 Consensus size: 45
4687684 CTTTGACATA
* * *
4687694 GACTTACATGAATTATTCCTGTCTCCAATGCCATA-TATAATATG
1 GACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAATATG
** *
4687738 GACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAATATG
1 GACTTACATGAATCAATCCTGTCTCCAAAGCCATA-TTATAATATG
4687784 GACTTACATG
1 GACTTACATG
4687794 GCTCATTTCC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
44 30 0.62
46 18 0.38
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (45 bp):
GACTTACATGAATCAATCCTGTCTCCAAAGCCATATTATAATATG
Found at i:4687795 original size:46 final size:44
Alignment explanation
Indices: 4687710--4687798 Score: 142
Period size: 46 Copynumber: 2.0 Consensus size: 44
4687700 CATGAATTAT
*
4687710 TCCTGTCTCCAATGCCATATATAATATGGACTTACATGGCTCAA
1 TCCTGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAA
*
4687754 TCCTGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA
1 TCCTGTCTCCAAAGCCATA--TATAATATGGACTTACATGGCTCA
4687799 TTTCCGTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 18 0.44
46 23 0.56
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (44 bp):
TCCTGTCTCCAAAGCCATATATAATATGGACTTACATGGCTCAA
Found at i:4690488 original size:33 final size:33
Alignment explanation
Indices: 4690419--4690516 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
4690409 CTATACCCAT
* * *
4690419 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
4690456 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
4690489 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
4690517 ACATATCTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:4690776 original size:41 final size:41
Alignment explanation
Indices: 4690731--4690886 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
4690721 ACCGGCTCTT
*
4690731 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
4690772 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
4690813 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
4690854 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
4690887 TAACGATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 98 0.92
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:4691393 original size:21 final size:23
Alignment explanation
Indices: 4691369--4691416 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
4691359 AATATATATA
4691369 TATTTC-AC-TCATACTTTTAAT
1 TATTTCAACATCATACTTTTAAT
*
4691390 TATTTCAACTATCATATTTTTAAT
1 TATTTCAAC-ATCATACTTTTAAT
4691414 TAT
1 TAT
4691417 ATTTCATCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 2 0.09
24 15 0.65
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTCAACATCATACTTTTAAT
Done.