Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 127 of 135
Found at i:45844556 original size:2 final size:2
Alignment explanation
Indices: 45844549--45844573 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45844539 ATCTAGACCA
45844549 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 A
45844574 GCCTTCATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45856311 original size:16 final size:16
Alignment explanation
Indices: 45856292--45856322 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45856282 ATATTAATGT
*
45856292 TATTTAATTTTAAAAA
1 TATTTAATATTAAAAA
45856308 TATTTAATATTAAAA
1 TATTTAATATTAAAA
45856323 TAATACAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAATATTAAAAA
Found at i:45859405 original size:22 final size:21
Alignment explanation
Indices: 45859374--45859429 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
45859364 TTTTTATTTT
*
45859374 TTTATTATATTGTTAATACTG
1 TTTATTATATTATTAATACTG
*
45859395 TTTATTTATATTATTATTAC--
1 TTTA-TTATATTATTAATACTG
45859415 TTTATTATTATTATT
1 TTTATTA-TATTATT
45859430 TTATTATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 3 0.10
20 11 0.35
21 4 0.13
22 13 0.42
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTATTATATTATTAATACTG
Found at i:45859411 original size:3 final size:3
Alignment explanation
Indices: 45859403--45859466 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
45859393 TGTTTATTTA
*
45859403 TAT TAT TAT TAC T-T TAT TAT TAT TAT T-T TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
45859448 TAT CTAT TAT AAT TAT TAT
1 TAT -TAT TAT TAT TAT TAT
45859467 GCTTATTTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.09
3 45 0.85
4 3 0.06
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:45859425 original size:17 final size:16
Alignment explanation
Indices: 45859396--45859464 Score: 81
Period size: 14 Copynumber: 4.3 Consensus size: 16
45859386 TTAATACTGT
45859396 TTATTTA-TATTATTA
1 TTATTTATTATTATTA
45859411 TTACTTTATTATTATTA
1 TTA-TTTATTATTATTA
45859428 -T-TTTATTATTATTA
1 TTATTTATTATTATTA
*
45859442 TTATATTATCTATTATAA
1 TTAT-TTAT-TATTATTA
45859460 TTATT
1 TTATT
45859465 ATGCTTATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 13 0.28
15 4 0.09
16 6 0.13
17 13 0.28
18 11 0.23
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTATTATTATTA
Found at i:45867064 original size:23 final size:23
Alignment explanation
Indices: 45867012--45867065 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
45867002 CTTTTTTGAG
* *
45867012 TAATTATTCTTTTATTCTTTTTC
1 TAATCATTCTTTTATTCTATTTC
45867035 TACATCATTCTTTTATTC-ATTTC
1 TA-ATCATTCTTTTATTCTATTTC
45867058 ATAATCAT
1 -TAATCAT
45867066 ATTTTGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (23 bp):
TAATCATTCTTTTATTCTATTTC
Found at i:45871928 original size:89 final size:89
Alignment explanation
Indices: 45871797--45872132 Score: 271
Period size: 89 Copynumber: 3.8 Consensus size: 89
45871787 TCCCTGAGCA
** * * * *
45871797 GCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTTACAGTGAAGCAGATCGAAGA
1 GCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGA
*
45871862 C-CTTAACCTTGCCTCCCCGAGTTT
66 CAC-CAACCTTGCCTCCCCGAGTTT
*
45871886 GCAGTAGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGA
1 GCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGA
* ** *
45871951 CACCAGCCTTGCCTCCTTGGGTTT
66 CACCAACCTTGCCTCCCCGAGTTT
* ** * * * *** * **
45871975 ACAGTGGAACAGACTGTAGATAGCAGATCTTGTCTTCCTGTATTGGTAACGAAGTAGATCGAAGA
1 GCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGA
* * * ** *
45872040 TACCAGCCTTGTCTCCCTAAG-TA
66 CACCAACCTTGCCTCCCCGAGTTT
* ** * * * * *** * *
45872063 GTAGTGGAGTAGGTTAAAAATAGCAGATTTTGCCTTCTTGTACTGGTAGTGAAGCAGATCGAAGA
1 GCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGA
45872128 CACCA
66 CACCA
45872133 GTCTTATCGC
Statistics
Matches: 198, Mismatches: 48, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
88 54 0.27
89 143 0.72
90 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (89 bp):
GCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAACAGCGAAACAGATCGAAGA
CACCAACCTTGCCTCCCCGAGTTT
Found at i:45873934 original size:22 final size:21
Alignment explanation
Indices: 45873883--45873934 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
45873873 TTTTTAGTTT
*
45873883 TTTATTATATTGTTAATACTG
1 TTTATTATATTATTAATACTG
* *
45873904 TTTATTTATATTATTATTGCTG
1 TTTA-TTATATTATTAATACTG
45873926 TATTATTAT
1 T-TTATTAT
45873935 TAGTTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 19 0.73
23 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.62
Consensus pattern (21 bp):
TTTATTATATTATTAATACTG
Found at i:45873967 original size:21 final size:23
Alignment explanation
Indices: 45873941--45873984 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
45873931 TTATTAGTTT
45873941 ATTATTATA-TTATATAT-TATA
1 ATTATTATACTTATATATATATA
*
45873962 ATTATTATACTTATTTATATATA
1 ATTATTATACTTATATATATATA
45873985 CGTATATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTATTATACTTATATATATATA
Found at i:45876016 original size:16 final size:16
Alignment explanation
Indices: 45875995--45876036 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
45875985 AATAATTTGA
*
45875995 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
45876011 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
45876027 TAGTTTTAAT
1 TAATTTTAAT
45876037 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:45876020 original size:22 final size:22
Alignment explanation
Indices: 45876010--45876070 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
45876000 TTACTAACAA
* * *
45876010 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
45876032 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
45876054 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
45876071 CGGGCCGGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:45876829 original size:19 final size:19
Alignment explanation
Indices: 45876805--45876841 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
45876795 ATAATAATAC
45876805 AAATAATAATATAATTAAT
1 AAATAATAATATAATTAAT
*
45876824 AAATAATAATATTATTAA
1 AAATAATAATATAATTAA
45876842 ATTAATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATAATAATATAATTAAT
Found at i:45880643 original size:156 final size:154
Alignment explanation
Indices: 45880470--45880820 Score: 501
Period size: 156 Copynumber: 2.3 Consensus size: 154
45880460 GGAAATTAAA
*
45880470 AGTAAAATAAAAATCGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTATTTT
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAACTTATTTT
* * * *
45880535 ATTTCCAAAAA-AAGTAAATTAAAAAACATTTCGAAATTTATTCCCGCCATTCAATGATTTTATT
66 ATTTCCAAAAACAAGTAAAATAAAAAACATTTCGAAATTGATTCCCGCCATTAAATAATTTTATT
*
45880599 CCAAATTTATTTTATTTCTAAAAAATG
131 -CAAATTT-TTTTATTTCT-AAAAACG
* *
45880626 AGTAAAATAAAAATCGTTTCGGGATTGATT-CCGCTGTTCAACGATTTTATTCCAAACTTGTTTT
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAACTTATTTT
* * * **
45880690 ATTTCCAAAAACGAGTAAAATAAAAATCGTTTCGGGATTGATTCCCGCCATTAAATAATTTTATT
66 ATTTCCAAAAACAAGTAAAATAAAAAACATTTCGAAATTGATTCCCGCCATTAAATAATTTTATT
*
45880755 CTAATTTTTTTATTTCTAAAAACG
131 CAAATTTTTTTATTTCTAAAAACG
* *
45880779 AGTAACAT-AAAATCCGTTTCAGGATTGATTCCCGCCGTTCAA
1 AGTAAAATAAAAAT-CGTTTCGGGATTGATTCCCGCCGTTCAA
45880821 TTGATTTATT
Statistics
Matches: 175, Mismatches: 17, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
152 5 0.03
153 28 0.16
154 20 0.11
155 48 0.27
156 74 0.42
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (154 bp):
AGTAAAATAAAAATCGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAACTTATTTT
ATTTCCAAAAACAAGTAAAATAAAAAACATTTCGAAATTGATTCCCGCCATTAAATAATTTTATT
CAAATTTTTTTATTTCTAAAAACG
Found at i:45880830 original size:76 final size:78
Alignment explanation
Indices: 45880470--45880827 Score: 456
Period size: 77 Copynumber: 4.6 Consensus size: 78
45880460 GGAAATTAAA
*
45880470 AGTAAAATAAAAATCGTTTCGGGATTGATTCCCGCCGTTCAACGATTTTATTCCAAATTTATTTT
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCCCGCCGTTCAATGATTTTATTCCAAATTTATTTT
*
45880535 ATTTCCAAAAA-A
66 ATTTCCAAAAACG
* * * ** * *
45880547 AGTAAATTAAAAAACATTTCGAAATTTATTCCCGCCATTCAATGATTTTATTCCAAATTTATTTT
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCCCGCCGTTCAATGATTTTATTCCAAATTTATTTT
* *
45880612 ATTTCTAAAAAATG
66 ATTTC-CAAAAACG
* * * *
45880626 AGTAAAATAAAAATCGTTTCGGGATTGATT-CCGCTGTTCAACGATTTTATTCCAAACTTGTTTT
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCCCGCCGTTCAATGATTTTATTCCAAATTTATTTT
45880690 ATTTCCAAAAACG
66 ATTTCCAAAAACG
* * * *
45880703 AGTAAAATAAAAATCGTTTCGGGATTGATTCCCGCCATTAAATAATTTTATT-CTAATTT-TTTT
1 AGTAAAATAAAAATCGTTTCGGGATTGATTCCCGCCGTTCAATGATTTTATTCCAAATTTATTTT
*
45880766 ATTTCTAAAAACG
66 ATTTCCAAAAACG
* *
45880779 AGTAACAT-AAAATCCGTTTCAGGATTGATTCCCGCCGTTCAATTGATTT
1 AGTAAAATAAAAAT-CGTTTCGGGATTGATTCCCGCCGTTCAA-TGATTT
45880828 ATTACTTTTT
Statistics
Matches: 240, Mismatches: 36, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
75 5 0.02
76 48 0.20
77 108 0.45
78 55 0.23
79 24 0.10
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (78 bp):
AGTAAAATAAAAATCGTTTCGGGATTGATTCCCGCCGTTCAATGATTTTATTCCAAATTTATTTT
ATTTCCAAAAACG
Found at i:45880963 original size:83 final size:84
Alignment explanation
Indices: 45880863--45881018 Score: 235
Period size: 84 Copynumber: 1.9 Consensus size: 84
45880853 AACAATAAAT
* * * *
45880863 TAAATTAAATAAAATTTGTTTC-GGATTTATTCCCGCC-ACTTAACAAGATTTTATTTGATTTTA
1 TAAATTAAATAAAATTTGTTTCGGGATTTATTCCCACCGA-TTAACAAGATTTTAATCGATATTA
45880926 TTTTGTTTCTAAATTTGAAC
65 TTTTGTTTCTAAATTTGAAC
* *
45880946 TAAATTAAATAAAATTTGTTTCGGGATTTATTCCCACCGATTAACAATATTTTAATCGATATTGT
1 TAAATTAAATAAAATTTGTTTCGGGATTTATTCCCACCGATTAACAAGATTTTAATCGATATTAT
45881011 TTTGTTTC
66 TTTGTTTC
45881019 CAAACAAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
83 22 0.34
84 42 0.65
85 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.46
Consensus pattern (84 bp):
TAAATTAAATAAAATTTGTTTCGGGATTTATTCCCACCGATTAACAAGATTTTAATCGATATTAT
TTTGTTTCTAAATTTGAAC
Found at i:45881040 original size:84 final size:83
Alignment explanation
Indices: 45880852--45881041 Score: 204
Period size: 84 Copynumber: 2.3 Consensus size: 83
45880842 TTTTTTCCAA
* * * *
45880852 AAACAATAAATTAAATTAAATAAAATTTGTTTCGGATTTATTCCCGCCACTTAACAAGATTTTAT
1 AAACAA-AAACTAAATCAAATAAAATTTGTTTCGGATTTATTCCCACCACTTAACAAGATTTTAA
* * *
45880917 TTGATTTTATTTTGTTTCT
65 TCGATATTATTTTGTTTCC
**** * *
45880936 AAATTTGAACTAAATTAAATAAAATTTGTTTCGGGATTTATTCCCACCGA-TTAACAATATTTTA
1 AAACAAAAACTAAATCAAATAAAATTTGTTTC-GGATTTATTCCCACC-ACTTAACAAGATTTTA
*
45881000 ATCGATATTGTTTTGTTTCC
64 ATCGATATTATTTTGTTTCC
45881020 AAACAAAAACGT-AATCAAATAA
1 AAACAAAAAC-TAAATCAAATAA
45881042 GTCTATTTTG
Statistics
Matches: 86, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
83 24 0.28
84 60 0.70
85 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.41
Consensus pattern (83 bp):
AAACAAAAACTAAATCAAATAAAATTTGTTTCGGATTTATTCCCACCACTTAACAAGATTTTAAT
CGATATTATTTTGTTTCC
Found at i:45883516 original size:12 final size:13
Alignment explanation
Indices: 45883496--45883528 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
45883486 TAAATAATTC
*
45883496 TATTCATATTTTA
1 TATTTATATTTTA
45883509 T-TTTATATTTTA
1 TATTTATATTTTA
45883521 TATTTATA
1 TATTTATA
45883529 ATTAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTATATTTTA
Found at i:45884300 original size:16 final size:16
Alignment explanation
Indices: 45884275--45884310 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
45884265 ATATCTCAAT
45884275 TATATGTATATAAAAA
1 TATATGTATATAAAAA
*
45884291 TATATTTATATAAAAA
1 TATATGTATATAAAAA
45884307 TATA
1 TATA
45884311 AATGTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TATATGTATATAAAAA
Found at i:45884399 original size:15 final size:14
Alignment explanation
Indices: 45884366--45884404 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
45884356 ATATTTTTTA
*
45884366 AAAAATAAAATGAT
1 AAAAATAAAATAAT
45884380 AAAAATAAATATAAT
1 AAAAATAAA-ATAAT
*
45884395 TAAAATAAAA
1 AAAAATAAAA
45884405 ATTTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAAATAAAATAAT
Found at i:45884947 original size:26 final size:24
Alignment explanation
Indices: 45884918--45884969 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
45884908 AAAAAGTAAA
*
45884918 AATTAAAAAGTTTTCCATTTTTTTTT
1 AATTAAAAAG-TTT-AATTTTTTTTT
**
45884944 AATTTGAAAGTTTAATTTTTTTTT
1 AATTAAAAAGTTTAATTTTTTTTT
45884968 AA
1 AA
45884970 AAATCATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 12 0.52
25 3 0.13
26 8 0.35
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (24 bp):
AATTAAAAAGTTTAATTTTTTTTT
Found at i:45885880 original size:24 final size:24
Alignment explanation
Indices: 45885834--45885880 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
45885824 GGGACAGAGA
*
45885834 AAAAAGAAAAAGAAAACTAGATAG
1 AAAAAGAAAAAGAAAAATAGATAG
*
45885858 AAAAAGAAAGAGATAAAAT-GATA
1 AAAAAGAAAAAGA-AAAATAGATA
45885881 TTAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.70, C:0.02, G:0.17, T:0.11
Consensus pattern (24 bp):
AAAAAGAAAAAGAAAAATAGATAG
Found at i:45894509 original size:6 final size:6
Alignment explanation
Indices: 45894500--45894528 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
45894490 CAACAAAACA
45894500 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
45894529 GAAACAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:45895062 original size:6 final size:7
Alignment explanation
Indices: 45895034--45895079 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
45895024 TAAATGAATG
45895034 AAATGAA
1 AAATGAA
45895041 AAATGAA
1 AAATGAA
45895048 AAATG-A
1 AAATGAA
*
45895054 AAATAAAA
1 AAAT-GAA
45895062 AAATGAA
1 AAATGAA
45895069 AAATGGAA
1 AAAT-GAA
45895077 AAA
1 AAA
45895080 GTAAAATGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 5 0.15
7 18 0.53
8 11 0.32
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAATGAA
Found at i:45896306 original size:27 final size:27
Alignment explanation
Indices: 45896276--45896354 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
45896266 GCATAATTAG
45896276 GTTCATAAAATGGATTATACAGGTCAT
1 GTTCATAAAATGGATTATACAGGTCAT
* * *
45896303 GTTCCT----TAGA-TA-ACAGATCA-
1 GTTCATAAAATGGATTATACAGGTCAT
45896323 GTTTCATAAAATGGATTATACAGGTCAT
1 G-TTCATAAAATGGATTATACAGGTCAT
45896351 GTTC
1 GTTC
45896355 CCTAGAGAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
20 1 0.03
21 11 0.29
22 2 0.05
23 3 0.08
25 3 0.08
26 2 0.05
27 15 0.39
28 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (27 bp):
GTTCATAAAATGGATTATACAGGTCAT
Found at i:45896333 original size:48 final size:48
Alignment explanation
Indices: 45896277--45896372 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
45896267 CATAATTAGG
* *
45896277 TTCATAAAATGGATTATACAGGTCATGTTCCTTAGATAACAGATCAGT
1 TTCATAAAATGGATTATACAGGTCATGTTCCCTAGAGAACAGATCAGT
45896325 TTCATAAAATGGATTATACAGGTCATGTTCCCTAGAGAACAGATCAGT
1 TTCATAAAATGGATTATACAGGTCATGTTCCCTAGAGAACAGATCAGT
45896373 GAAGATAGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (48 bp):
TTCATAAAATGGATTATACAGGTCATGTTCCCTAGAGAACAGATCAGT
Found at i:45896523 original size:89 final size:88
Alignment explanation
Indices: 45896372--45897143 Score: 889
Period size: 89 Copynumber: 8.7 Consensus size: 88
45896362 AACAGATCAG
* *
45896372 TGAAGATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAAATCGAAGACACCAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
45896437 CCCTGGTTTTGCAACGGAGCAGAC
66 CCCTGG-TTTGCAGCGGAGCAGAC
* * * *
45896461 TGAAGATAGCAGATTTTACCTTCCTGTACTGACAGCAAAGCAGATCGAAGACACTAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* ** *
45896526 CCTTGGGTTTGCATTGGAGTAGAC
66 CCCT-GGTTTGCAGCGGAGCAGAC
* * * * * * * *
45896550 TGAAGATGGTAAATCTTGCCTTCCTATATTGATAGCGAAGCAGATCAAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* *
45896615 ACCTAGGTTTGCAGCGGAACAGAC
66 CCCT-GGTTTGCAGCGGAGCAGAC
*
45896639 TGAAGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
45896704 CCCTGGTTTTGTAGCGGAGCAGAC
66 CCCTGG-TTTGCAGCGGAGCAGAC
* *
45896728 TGAAGATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACAAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* * * ** *
45896793 CCTTCAGTTTACAGTAGAGTAGAC
66 CCCT-GGTTTGCAGCGGAGCAGAC
* * *
45896817 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAATATACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* *
45896882 CTCTGGGTTTGCAGTGGAGCAGAC
66 CCCT-GGTTTGCAGCGGAGCAGAC
* * *
45896906 TGAAGATAGCAGATCTTGCCTTCCTATACTGATAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
*
45896971 CCCTAGGTTTGCAACGGAGCAGAC
66 CCCT-GGTTTGCAGCGGAGCAGAC
** * * * * * **
45896995 TGAAGATAGCAGATCTTGCCTTATTGTACTGACAACGAAGCAAATAGAAGACATCAGCCTTATCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* **** ** * **
45897060 CCTTGAACAGCAGTAGAGTAGGT
66 CCCTGGTTTGCAGCGGAGCAGAC
* * * * *
45897083 TGAAAATAGCAGATCTTGCCTTCCTGTACT-AGCAGAGAAGCAGATTGAGGATACCAGTCTT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGA-CAGCGAAGCAGATCGAAGACACCAGTCTT
45897144 ATCGCCTTAA
Statistics
Matches: 576, Mismatches: 103, Indels: 9
0.84 0.15 0.01
Matches are distributed among these distances:
87 1 0.00
88 59 0.10
89 513 0.89
90 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (88 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
CCCTGGTTTGCAGCGGAGCAGAC
Found at i:45896856 original size:267 final size:264
Alignment explanation
Indices: 45896372--45897127 Score: 1014
Period size: 267 Copynumber: 2.8 Consensus size: 264
45896362 AACAGATCAG
* *
45896372 TGAAGATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAAATCGAAGACACCAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* * *
45896437 CCCTGGTTTTGCAACGGAGCAGACTGAAGATAGCAGATTTTACCTTCCTGTACTGACAGCAAAGC
66 CCCTGGTTTTGCAACGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGC
* * * * * *
45896502 AGATCGAAGACACTAGTCTTGCCTCCTTGGGTTTGCATTGGAGTAGACTGAAGATGGTAAATCTT
131 AGATCGAAGACAC-AGTCTTGCCTCCTT--GTTTACAGTAGAGTAGACTGAAGATAGCAGATCTT
* * *
45896567 GCCTTCCTATATTGATAGCGAAGCAGATCAAAGACACCAGCCTTGCCTAC-CTAGGTTTGCAGCG
193 GCCTTCCTGTACTGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCT-CTCTAGGTTTGCAGCG
45896631 GAACAGAC
257 GAACAGAC
*
45896639 TGAAGATAGCAGATATTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
* * *
45896704 CCCTGGTTTTGTAGCGGAGCAGACTGAAGATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGC
66 CCCTGGTTTTGCAACGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGC
45896769 AGATCGAAGACACAAGTCTTGCCTCCTTCAGTTTACAGTAGAGTAGACTGAAGATAGCAGATCTT
131 AGATCGAAGACAC-AGTCTTGCCTCCTT--GTTTACAGTAGAGTAGACTGAAGATAGCAGATCTT
* * * * *
45896834 GCCTTCCTGTACTGACAGCGAAGCAGATCGAATATACCAGCCTTGCCTCTCTGGGTTTGCAGTGG
193 GCCTTCCTGTACTGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCTCTAGGTTTGCAGCGG
*
45896899 AGCAGAC
258 AACAGAC
* * *
45896906 TGAAGATAGCAGATCTTGCCTTCCTATACTGATAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
** *
45896971 CCCTAGG-TTTGCAACGGAGCAGACTGAAGATAGCAGATCTTGCCTTATTGTACTGACAACGAAG
66 CCCT-GGTTTTGCAACGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAG
* * * ** *** ** *
45897035 CAAATAGAAGACATCAGCCTTATCTCCTTGAACAGCAGTAGAGTAGGTTGAAAATAGCAGATCTT
130 CAGATCGAAGACA-CAGTCTTGCCTCCTTGTTTA-CAGTAGAGTAGACTGAAGATAGCAGATCTT
*
45897100 GCCTTCCTGTACT-AGCAGAGAAGCAGAT
193 GCCTTCCTGTACTGA-CAGCGAAGCAGAT
45897128 TGAGGATACC
Statistics
Matches: 435, Mismatches: 49, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
265 3 0.01
266 53 0.12
267 376 0.86
268 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (264 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCT
CCCTGGTTTTGCAACGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGC
AGATCGAAGACACAGTCTTGCCTCCTTGTTTACAGTAGAGTAGACTGAAGATAGCAGATCTTGCC
TTCCTGTACTGACAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCTCTAGGTTTGCAGCGGAAC
AGAC
Found at i:45897437 original size:50 final size:51
Alignment explanation
Indices: 45897383--45897545 Score: 161
Period size: 50 Copynumber: 3.3 Consensus size: 51
45897373 ATTACAGTTA
45897383 AACAGATTGAAGCCACAACGA-CGAATCTTACTTCCCTGGCAGTGTAGTGG
1 AACAGATTGAAGCCACAACGAGCGAATCTTACTTCCCTGGCAGTGTAGTGG
* * * * ** ** * * **
45897433 AACAGATTGAAGCTAC-GCCAGTGAATCTTGTTTCCCCAGCATTGTAATTT
1 AACAGATTGAAGCCACAACGAGCGAATCTTACTTCCCTGGCAGTGTAGTGG
* * *
45897483 AATAGATTGAAGCCATAAC-AGCGAATCTTACTTCCCTGGCGGTGTAGTGG
1 AACAGATTGAAGCCACAACGAGCGAATCTTACTTCCCTGGCAGTGTAGTGG
*
45897533 AACAGATTAAAGC
1 AACAGATTGAAGC
45897546 TACGACGACA
Statistics
Matches: 83, Mismatches: 28, Indels: 4
0.72 0.24 0.03
Matches are distributed among these distances:
49 2 0.02
50 80 0.96
51 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (51 bp):
AACAGATTGAAGCCACAACGAGCGAATCTTACTTCCCTGGCAGTGTAGTGG
Found at i:45897490 original size:100 final size:100
Alignment explanation
Indices: 45897328--45897590 Score: 316
Period size: 100 Copynumber: 2.6 Consensus size: 100
45897318 TTGGCATTAC
* * *
45897328 AGTGGAATAGATTGAAGCTACGACGGAAAATCTTATTTCCCCGACATTACAGTTAAACAGATTGA
1 AGTGGAACAGATTGAAGCTACGACAGAAAATCTTATTTCCCCGACATTACAATTAAACAGATTGA
45897393 AGCCACAAC-GACGAATCTTACTTCCCTGGCAGTGT
66 AGCCACAACAG-CGAATCTTACTTCCCTGGCAGTGT
* ** * ** * *
45897428 AGTGGAACAGATTGAAGCTACGCCAGTGAATCTTGTTTCCCC-AGCATTGTAATTTAATAGATTG
1 AGTGGAACAGATTGAAGCTACGACAGAAAATCTTATTTCCCCGA-CATTACAATTAAACAGATTG
* *
45897492 AAGCCATAACAGCGAATCTTACTTCCCTGGCGGTGT
65 AAGCCACAACAGCGAATCTTACTTCCCTGGCAGTGT
* * * * *
45897528 AGTGGAACAGATTAAAGCTACGAC-GACAAATCTTGTTTCCCCGACATTGCAGTTAAATAGATT
1 AGTGGAACAGATTGAAGCTACGACAGA-AAATCTTATTTCCCCGACATTACAATTAAACAGATT
45897591 TAAGATGACA
Statistics
Matches: 139, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
99 2 0.01
100 135 0.97
101 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (100 bp):
AGTGGAACAGATTGAAGCTACGACAGAAAATCTTATTTCCCCGACATTACAATTAAACAGATTGA
AGCCACAACAGCGAATCTTACTTCCCTGGCAGTGT
Found at i:45897656 original size:44 final size:44
Alignment explanation
Indices: 45897603--45897977 Score: 200
Period size: 44 Copynumber: 8.6 Consensus size: 44
45897593 AGATGACAAG
45897603 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCAATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCAATAA
* * * ** * * *
45897647 TCCTATCTCCCTGAAGTTACAGTCGAGTGGATTAAAGTTGC-A-AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAG--CCAATAA
** **
45897691 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG-AAGATAGCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAAAGCCAATAA
* * * * * ****
45897735 GTCTTATCCCCCTAAAGTTACAGTGGGGTAGACTG-AAGATGGTGAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAAAGCCAAT-AA
* * * * *
45897781 TTTTATCTCCCTAAAGTTACAGTGGAGTAGATTAAAGCCAATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCAATAA
* * * ** *
45897825 TCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATC-A-GA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCAATAA
* * * * *
45897867 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCG-CATCC---AG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-GAAAGCCAATAA
* *
45897908 TCTTA-CTCCCTGAAGTTGCAGTGGAGCAGA-CAGAAG-AAACTAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGA-AAGCCAA-TAA
* * *
45897951 TCCTATTTCCCTGAAGTTACAGTGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
45897978 TGGATCGAAG
Statistics
Matches: 255, Mismatches: 60, Indels: 32
0.73 0.17 0.09
Matches are distributed among these distances:
40 24 0.09
41 5 0.02
42 31 0.12
43 6 0.02
44 117 0.46
45 69 0.27
46 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCAATAA
Found at i:45898491 original size:10 final size:10
Alignment explanation
Indices: 45898471--45898501 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
45898461 AAGATATAAG
45898471 ATTATTTATTT
1 ATTA-TTATTT
45898482 ATTATTATTT
1 ATTATTATTT
45898492 ATTATTATTT
1 ATTATTATTT
45898502 TTTGGTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTATTATTT
Found at i:45899321 original size:2 final size:2
Alignment explanation
Indices: 45899314--45899349 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
45899304 TAAACATACC
45899314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45899350 TCTTTCCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:45901429 original size:165 final size:166
Alignment explanation
Indices: 45901247--45901578 Score: 657
Period size: 165 Copynumber: 2.0 Consensus size: 166
45901237 ATACAATTTT
45901247 AAAAAAATACATATGGATTATAAAATTTGAACCAAAAACCTTAAAACTCCTTTTTCACTCAATTT
1 AAAAAAATACATATGGATTATAAAATTTGAACCAAAAACCTTAAAACTCCTTTTTCACTCAATTT
45901312 TATCATTTTGATCAAAATCACATTTTGCATTCATATAATTGTTTTTTATAGATTAATTTGTTACA
66 TATCATTTTGATCAAAATCACATTTTGCATTCATATAATTGTTTTTTATAGATTAATTTGTTACA
45901377 TAAAATTTTTTACTTTGAACATGCCATAATCTAAAA
131 TAAAATTTTTTACTTTGAACATGCCATAATCTAAAA
45901413 AAAAAAATAC-TATGGATTATAAAATTTGAACCAAAAACCTTAAAACTCCTTTTTCACTCAATTT
1 AAAAAAATACATATGGATTATAAAATTTGAACCAAAAACCTTAAAACTCCTTTTTCACTCAATTT
45901477 TATCATTTTGATCAAAATCACATTTTGCATTCATATAATTGTTTTTTATAGATTAATTTGTTACA
66 TATCATTTTGATCAAAATCACATTTTGCATTCATATAATTGTTTTTTATAGATTAATTTGTTACA
45901542 TAAAATTTTTTACTTTGAACATGCCATAATCTAAAA
131 TAAAATTTTTTACTTTGAACATGCCATAATCTAAAA
45901578 A
1 A
45901579 TTATAAAAGA
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
165 156 0.94
166 10 0.06
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (166 bp):
AAAAAAATACATATGGATTATAAAATTTGAACCAAAAACCTTAAAACTCCTTTTTCACTCAATTT
TATCATTTTGATCAAAATCACATTTTGCATTCATATAATTGTTTTTTATAGATTAATTTGTTACA
TAAAATTTTTTACTTTGAACATGCCATAATCTAAAA
Found at i:45902587 original size:42 final size:42
Alignment explanation
Indices: 45902527--45902616 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
45902517 TGTCTCAGCC
** *
45902527 CGTGTCCTTGCCCATGTAACTCA-CTGACTTGAGACACACGGT
1 CGTGTCCCAGCCCATGTAACT-ATCTAACTTGAGACACACGGT
* * **
45902569 CGTGTCCCAGCCCGTGTAACTATCTAACTTGGGTTACACGGT
1 CGTGTCCCAGCCCATGTAACTATCTAACTTGAGACACACGGT
45902611 CGTGTC
1 CGTGTC
45902617 ACAAACCGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.03
42 39 0.98
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (42 bp):
CGTGTCCCAGCCCATGTAACTATCTAACTTGAGACACACGGT
Found at i:45903258 original size:21 final size:21
Alignment explanation
Indices: 45903229--45903270 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
45903219 ACTATAATTT
45903229 AAAATGTAC-CTGAGTATAAC
1 AAAATGTACGCTGAGTATAAC
45903249 AAAATTGTACGCTGAGTATAAC
1 AAAA-TGTACGCTGAGTATAAC
45903271 TCAGAGATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 5 0.25
22 11 0.55
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (21 bp):
AAAATGTACGCTGAGTATAAC
Found at i:45906431 original size:17 final size:17
Alignment explanation
Indices: 45906383--45906446 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 17
45906373 GTTCAAGTAC
45906383 ATTTTGTTTTCTTCATGTTT
1 ATTTTGTTTT-TT-A-GTTT
*
45906403 ATTTTTTATTTTTAGTTT
1 ATTTTGT-TTTTTAGTTT
45906421 ATTTTGTTTTTT-GTTTT
1 ATTTTGTTTTTTAG-TTT
*
45906438 GTTTTGTTT
1 ATTTTGTTT
45906447 GCTTGAGGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 1 0.03
17 16 0.41
18 10 0.26
19 1 0.03
20 8 0.21
21 3 0.08
ACGTcount: A:0.09, C:0.03, G:0.11, T:0.77
Consensus pattern (17 bp):
ATTTTGTTTTTTAGTTT
Found at i:45906432 original size:18 final size:19
Alignment explanation
Indices: 45906383--45906432 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
45906373 GTTCAAGTAC
45906383 ATTTTGTTTTCTTCATGTTT
1 ATTTTGTTTT-TTCATGTTT
*
45906403 ATTTT-TTATTTTTA-GTTT
1 ATTTTGTT-TTTTCATGTTT
45906421 ATTTTGTTTTTT
1 ATTTTGTTTTTT
45906433 GTTTTGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 13 0.48
19 7 0.26
20 7 0.26
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.76
Consensus pattern (19 bp):
ATTTTGTTTTTTCATGTTT
Found at i:45914990 original size:11 final size:11
Alignment explanation
Indices: 45914974--45915004 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
45914964 TTTTAATAAG
45914974 GTATCGATATA
1 GTATCGATATA
45914985 GTATCGATATA
1 GTATCGATATA
45914996 GTATCGATA
1 GTATCGATA
45915005 CCTAACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (11 bp):
GTATCGATATA
Found at i:45918807 original size:3 final size:3
Alignment explanation
Indices: 45918799--45918865 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
45918789 TGCTCTACAT
45918799 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
45918847 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
45918866 CATCTCAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:45925082 original size:21 final size:21
Alignment explanation
Indices: 45925048--45925087 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
45925038 GGACTGAATC
* *
45925048 GAAAACATATAAAAGTTTTGA
1 GAAAACATAGAAAAATTTTGA
*
45925069 GAAAACTTAGAAAAATTTT
1 GAAAACATAGAAAAATTTT
45925088 CCAATAAGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (21 bp):
GAAAACATAGAAAAATTTTGA
Found at i:45926179 original size:26 final size:24
Alignment explanation
Indices: 45926146--45926214 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
45926136 AGCCATGATC
*
45926146 GGTAAGCTCATTTCGAGCTGAAGAAA
1 GGTAAGCTCATATCGAGCTG-A-AAA
*
45926172 GGTAAGCTC-TATCGAGCTGAAAT
1 GGTAAGCTCATATCGAGCTGAAAA
*
45926195 GGTAAGCTCATA-AGAGCTGA
1 GGTAAGCTCATATCGAGCTGA
45926215 TATTCGGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 18 0.46
24 3 0.08
25 9 0.23
26 9 0.23
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (24 bp):
GGTAAGCTCATATCGAGCTGAAAA
Found at i:45926211 original size:23 final size:24
Alignment explanation
Indices: 45926146--45926231 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
45926136 AGCCATGATC
* * *
45926146 GGTAAGCTCATTTCGAGCTGAAGAAA
1 GGTAAGCTCATATAGAGCTG-A-AAT
*
45926172 GGTAAGCTC-TATCGAGCTGAAAT
1 GGTAAGCTCATATAGAGCTGAAAT
*
45926195 GGTAAGCTCATA-AGAGCTGATATT
1 GGTAAGCTCATATAGAGCTGA-AAT
45926219 CGGTAAGCTCATA
1 -GGTAAGCTCATA
45926232 CGAGTTGTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
23 18 0.34
24 5 0.09
25 21 0.40
26 9 0.17
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (24 bp):
GGTAAGCTCATATAGAGCTGAAAT
Found at i:45936414 original size:26 final size:24
Alignment explanation
Indices: 45936381--45936449 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
45936371 AGCCATGATC
*
45936381 GGTAAGCTCATTTCGAGCTGAAGAAA
1 GGTAAGCTCATATCGAGCTG-A-AAA
*
45936407 GGTAAGCTC-TATCGAGCTGAAAT
1 GGTAAGCTCATATCGAGCTGAAAA
*
45936430 GGTAAGCTCATA-AGAGCTGA
1 GGTAAGCTCATATCGAGCTGA
45936450 TATTCGGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 18 0.46
24 3 0.08
25 9 0.23
26 9 0.23
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (24 bp):
GGTAAGCTCATATCGAGCTGAAAA
Found at i:45936446 original size:23 final size:24
Alignment explanation
Indices: 45936381--45936466 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
45936371 AGCCATGATC
* * *
45936381 GGTAAGCTCATTTCGAGCTGAAGAAA
1 GGTAAGCTCATATAGAGCTG-A-AAT
*
45936407 GGTAAGCTC-TATCGAGCTGAAAT
1 GGTAAGCTCATATAGAGCTGAAAT
*
45936430 GGTAAGCTCATA-AGAGCTGATATT
1 GGTAAGCTCATATAGAGCTGA-AAT
45936454 CGGTAAGCTCATA
1 -GGTAAGCTCATA
45936467 CGAGTTGTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
23 18 0.34
24 5 0.09
25 21 0.40
26 9 0.17
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (24 bp):
GGTAAGCTCATATAGAGCTGAAAT
Found at i:45939808 original size:34 final size:34
Alignment explanation
Indices: 45939752--45939843 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 34
45939742 TGATCTGATT
* * * *
45939752 TAATATGACATTTTAATCTGATATATGTTTTTGG
1 TAATATGACATTCTGATATGATATATGATTTTGG
* *
45939786 -AATTATGATATTCTGATGTGATATATGATTTTGG
1 TAA-TATGACATTCTGATATGATATATGATTTTGG
45939820 TAATATGACATTCTGATATGATAT
1 TAATATGACATTCTGATATGATAT
45939844 TTGTATAAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
33 2 0.04
34 45 0.92
35 2 0.04
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (34 bp):
TAATATGACATTCTGATATGATATATGATTTTGG
Found at i:45940790 original size:18 final size:17
Alignment explanation
Indices: 45940767--45940800 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
45940757 ATGTTTCTAG
*
45940767 AATAAATATTATTTATTT
1 AATAAAT-TTAATTATTT
45940785 AATAAATTTAATTATT
1 AATAAATTTAATTATT
45940801 ACAATTAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATAAATTTAATTATTT
Found at i:45945300 original size:39 final size:38
Alignment explanation
Indices: 45945238--45945368 Score: 163
Period size: 39 Copynumber: 3.4 Consensus size: 38
45945228 GACACAAAGT
* * *
45945238 TGCGATCAGGGGTACTGAAGTACAACAGGGGCATGTAAG
1 TGCGATCAGGGGTAC-CAAGTACAATAGGGGCACGTAAG
*
45945277 TGCGATCAGTGGTACCAACGTACAATAGGGGCACGTAAG
1 TGCGATCAGGGGTACCAA-GTACAATAGGGGCACGTAAG
* **
45945316 TGCAATTTGGGGTACCGAAGTACAATAGGGGCACGTAAG
1 TGCGATCAGGGGTACC-AAGTACAATAGGGGCACGTAAG
*
45945355 TGCTATCAGGGGTA
1 TGCGATCAGGGGTA
45945369 TGATTATATA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
38 2 0.03
39 75 0.95
40 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.34, T:0.20
Consensus pattern (38 bp):
TGCGATCAGGGGTACCAAGTACAATAGGGGCACGTAAG
Found at i:45945355 original size:19 final size:19
Alignment explanation
Indices: 45945296--45945355 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
45945286 TGGTACCAAC
45945296 GTACAATAGGGGCACGTAA
1 GTACAATAGGGGCACGTAA
* * *
45945315 GTGCAATTTGGGGTACCG-AA
1 GTACAA-TAGGGGCA-CGTAA
45945335 GTACAATAGGGGCACGTAA
1 GTACAATAGGGGCACGTAA
45945354 GT
1 GT
45945356 GCTATCAGGG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
18 2 0.06
19 15 0.47
20 13 0.41
21 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.33, T:0.20
Consensus pattern (19 bp):
GTACAATAGGGGCACGTAA
Found at i:45946960 original size:10 final size:10
Alignment explanation
Indices: 45946945--45946973 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
45946935 GGTTGGCGGA
45946945 GGAGTTCCAT
1 GGAGTTCCAT
45946955 GGAGTTCCAT
1 GGAGTTCCAT
45946965 GGAGTTCCA
1 GGAGTTCCA
45946974 ATGACATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.28
Consensus pattern (10 bp):
GGAGTTCCAT
Found at i:45947447 original size:26 final size:26
Alignment explanation
Indices: 45947418--45947495 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 26
45947408 CTTAATTTTT
45947418 TAAATTATCTATGCATTTTTAGGAAA
1 TAAATTATCTATGCATTTTTAGGAAA
** *
45947444 TAAATTAGGTAT-TATTTTT------
1 TAAATTATCTATGCATTTTTAGGAAA
45947463 TAAATTATCTATGCATTTTTAGGAAA
1 TAAATTATCTATGCATTTTTAGGAAA
45947489 TAAATTA
1 TAAATTA
45947496 GGTATTGGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
19 10 0.26
20 6 0.15
25 6 0.15
26 17 0.44
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (26 bp):
TAAATTATCTATGCATTTTTAGGAAA
Found at i:45947476 original size:45 final size:45
Alignment explanation
Indices: 45947412--45947501 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
45947402 TCATGCCTTA
45947412 ATTTTTTAAATTATCTATGCATTTTTAGGAAATAAATTAGGTATT
1 ATTTTTTAAATTATCTATGCATTTTTAGGAAATAAATTAGGTATT
45947457 ATTTTTTAAATTATCTATGCATTTTTAGGAAATAAATTAGGTATT
1 ATTTTTTAAATTATCTATGCATTTTTAGGAAATAAATTAGGTATT
45947502 GGTTTGTTGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (45 bp):
ATTTTTTAAATTATCTATGCATTTTTAGGAAATAAATTAGGTATT
Found at i:45949107 original size:29 final size:29
Alignment explanation
Indices: 45949056--45949114 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
45949046 TGAATAGTGT
* *
45949056 ATGTATATATATGTATATTATAAAAATAA
1 ATGTATATATATGTAAATAATAAAAATAA
*
45949085 ATGTATATATAT-TGAAATAATAATAATAA
1 ATGTATATATATGT-AAATAATAAAAATAA
45949114 A
1 A
45949115 AATAATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
ATGTATATATATGTAAATAATAAAAATAA
Found at i:45949119 original size:15 final size:15
Alignment explanation
Indices: 45949099--45949137 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
45949089 ATATATATTG
45949099 AAATAATAATAATAA
1 AAATAATAATAATAA
* *
45949114 AAATAATAGTAATTA
1 AAATAATAATAATAA
*
45949129 ATATAATAA
1 AAATAATAA
45949138 AATTAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAATAATAATAATAA
Found at i:45949120 original size:12 final size:12
Alignment explanation
Indices: 45949103--45949153 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
45949093 ATATTGAAAT
45949103 AATAATAATAAA
1 AATAATAATAAA
* *
45949115 AATAATAGTAATT
1 AATAATAATAA-A
45949128 AAT-ATAATAAA
1 AATAATAATAAA
*
45949139 ATTAATAATATAA
1 AATAATAATA-AA
45949152 AA
1 AA
45949154 GGAACTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
11 2 0.07
12 22 0.73
13 6 0.20
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:45950702 original size:41 final size:41
Alignment explanation
Indices: 45950644--45950789 Score: 141
Period size: 41 Copynumber: 3.5 Consensus size: 41
45950634 ATCTGTTCCA
* * *
45950644 CTGCAACTTCAGGGAGATAAGAATGGACATGATCCGCTCTT
1 CTGCAACTTCAGAGAGATAAGAATAGATATGATCCGCTCTT
* * * **
45950685 CTGCAACTTCAGAGAGATAAG-ATCTGATTTTAATCCGCTCAA
1 CTGCAACTTCAGAGAGATAAGAAT-AGA-TATGATCCGCTCTT
* * ** *
45950727 CTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTT
1 CTGCAACTTCAGAGAGATAAGAATAGATATGATCCGCTCTT
*
45950768 CTGTAACTTCAGAGAGATAAGA
1 CTGCAACTTCAGAGAGATAAGA
45950790 TCTGATTTTA
Statistics
Matches: 84, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
40 2 0.02
41 50 0.60
42 31 0.37
43 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (41 bp):
CTGCAACTTCAGAGAGATAAGAATAGATATGATCCGCTCTT
Found at i:45950766 original size:83 final size:81
Alignment explanation
Indices: 45950403--45950828 Score: 345
Period size: 83 Copynumber: 5.1 Consensus size: 81
45950393 ACAACTTTAA
* * * * *
45950403 AGATAAGTCTGATACGATCTGCTCTACTGCAACCGT-AGAGAGATGAGATCTATCATTTTGATCT
1 AGATAAGACTGATACGATCTGCTCTTCTGCAA-CTTCAGAGAGATAAGATC--T-ATTTTAATCT
* ** *
45950467 GCTTCACTATAACTTTAGGG
62 GCTCCACTGCAACTTCAGGG
** * *
45950487 AGATAAGACTGGACGCGATCTGCTCTTCTGCAACTTCAGGGAGATAGGAT-TATTTTCTTCAATC
1 AGATAAGACT-GATACGATCTGCTCTTCTGCAACTTCAGAGAGATAAGATCTA--TT-TT-AATC
* *
45950551 TGCTCCACTGCAACTTTAGAG
61 TGCTCCACTGCAACTTCAGGG
*** * * * * * *
45950572 AGATAAGATCTGATTTTAATCCGCTCCAT-TGCAACTTCAGGGAGATAGGAGTATTTTCTTCAAT
1 AGATAAGA-CTGA-TACGATCTGCT-CTTCTGCAACTTCAGAGAGATAAGA-TCTATT-TT-AAT
*
45950636 CTGTTCCACTGCAACTTCAGGG
60 CTGCTCCACTGCAACTTCAGGG
* * * * *
45950658 AGATAAGAATGGACATGATCCGCTCTTCTGCAACTTCAGAGAGATAAGATCTGATTTTAATCCGC
1 AGATAAGACT-GATACGATCTGCTCTTCTGCAACTTCAGAGAGATAAGATCT-ATTTTAATCTGC
*
45950723 TCAACTGCAACTTCAGGG
64 TCCACTGCAACTTCAGGG
* * **
45950741 AGATAAGACTAGATGCGATCTGCTCTTCTGTAACTTCAGAGAGATAAGATCTGATTTTAATCCAC
1 AGATAAGACT-GATACGATCTGCTCTTCTGCAACTTCAGAGAGATAAGATCT-ATTTTAATCTGC
45950806 TCCACTGCAACTTCAGGG
64 TCCACTGCAACTTCAGGG
45950824 AGATA
1 AGATA
45950829 GGATTATTTT
Statistics
Matches: 284, Mismatches: 44, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
81 1 0.00
82 1 0.00
83 103 0.36
84 19 0.07
85 89 0.31
86 67 0.24
87 3 0.01
88 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (81 bp):
AGATAAGACTGATACGATCTGCTCTTCTGCAACTTCAGAGAGATAAGATCTATTTTAATCTGCTC
CACTGCAACTTCAGGG
Found at i:45952416 original size:140 final size:141
Alignment explanation
Indices: 45952153--45952435 Score: 550
Period size: 140 Copynumber: 2.0 Consensus size: 141
45952143 CCCAATTTGG
45952153 CATCCCTCTAAAATCCCTTTGTATAGGAAGGATCTTTTTCAACACCAGCTCCCCTTCATAAAATT
1 CATCCCTCT-AAATCCCTTTGTATAGGAAGGATCTTTTTCAACACCAGCTCCCCTTCATAAAATT
45952218 CTCTAGGAAAAACCTTTTTGTTGTAGGCTCGCATCATTCGTTTTTGATACATCTAACCATGCTGA
65 CTCTAGGAAAAACCTTTTTGTTGTAGGCTCGCATCATTCGTTTTTGATACATCTAACCATGCTGA
45952283 ATAACCCTTAGC
130 ATAACCCTTAGC
45952295 CATCCCTCT-AATCCCTTTGTATAGGAAGGATCTTTTTCAACACCAGCTCCCCTTCATAAAATTC
1 CATCCCTCTAAATCCCTTTGTATAGGAAGGATCTTTTTCAACACCAGCTCCCCTTCATAAAATTC
45952359 TCTAGGAAAAACCTTTTTGTTGTAGGCTCGCATCATTCGTTTTTGATACATCTAACCATGCTGAA
66 TCTAGGAAAAACCTTTTTGTTGTAGGCTCGCATCATTCGTTTTTGATACATCTAACCATGCTGAA
45952424 TAACCCTTAGC
131 TAACCCTTAGC
45952435 C
1 C
45952436 TTTTCCCTTC
Statistics
Matches: 141, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
140 132 0.94
142 9 0.06
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.34
Consensus pattern (141 bp):
CATCCCTCTAAATCCCTTTGTATAGGAAGGATCTTTTTCAACACCAGCTCCCCTTCATAAAATTC
TCTAGGAAAAACCTTTTTGTTGTAGGCTCGCATCATTCGTTTTTGATACATCTAACCATGCTGAA
TAACCCTTAGC
Found at i:45968035 original size:2 final size:2
Alignment explanation
Indices: 45968028--45968065 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
45968018 AAAACCATTC
* *
45968028 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45968066 CAAAAGTACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45978707 original size:46 final size:46
Alignment explanation
Indices: 45978640--45978732 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
45978630 ATAGTCTAAA
45978640 TTAAGGAAAGATTGTTTTCAGCATACTGTGCGGACCAAAGTAACTT
1 TTAAGGAAAGATTGTTTTCAGCATACTGTGCGGACCAAAGTAACTT
45978686 TTAAGGAAAGATTGTTTTCAGCATACTGTGCGGACCAAAGTAACTT
1 TTAAGGAAAGATTGTTTTCAGCATACTGTGCGGACCAAAGTAACTT
45978732 T
1 T
45978733 CGTTGCATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (46 bp):
TTAAGGAAAGATTGTTTTCAGCATACTGTGCGGACCAAAGTAACTT
Found at i:45980398 original size:3 final size:3
Alignment explanation
Indices: 45980390--45980424 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
45980380 ACCTAAGGCA
45980390 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
45980425 ATGGCATTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:45983389 original size:23 final size:23
Alignment explanation
Indices: 45983354--45983408 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
45983344 ATAATTTTTT
*
45983354 TATAAATA-AAAATATAAAAATAA
1 TATAAATATTAAAT-TAAAAATAA
* *
45983377 T-TAGATATTAAATTAAAATTAA
1 TATAAATATTAAATTAAAAATAA
45983399 TATAAATATT
1 TATAAATATT
45983409 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
TATAAATATTAAATTAAAAATAA
Found at i:45983453 original size:110 final size:108
Alignment explanation
Indices: 45983320--45983531 Score: 338
Period size: 110 Copynumber: 1.9 Consensus size: 108
45983310 ATGTAAACAT
45983320 TAAAAAATGTTAAAATGACTAAATATAATTTTTTTATAAATA-AAAATATA-AAAATAATTAGAT
1 TAAAAAATGTTAAAATGACT-AA-ATAATTTTTTTATAAATAGAAAATATATAAAATAATTAGAT
45983383 ATTAAATTAAAATTAATATAAATATTTTAAAAAATAATATGTATAAC
64 ATTAAATTAAAATTAATAT--ATATTTTAAAAAATAATATGTATAAC
* * *
45983430 TAAAAAATTTTAAGATGACTAAATAATTTTTTTATAAATAGAAAATATATAAAATAGTTAGATAT
1 TAAAAAATGTTAAAATGACTAAATAATTTTTTTATAAATAGAAAATATATAAAATAATTAGATAT
*
45983495 TAAATTAAAATTAATATATATTTTTAAAAATAATATG
66 TAAATTAAAATTAATATATATTTTAAAAAATAATATG
45983532 GGTAGACTTA
Statistics
Matches: 96, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
108 37 0.39
109 10 0.10
110 49 0.51
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (108 bp):
TAAAAAATGTTAAAATGACTAAATAATTTTTTTATAAATAGAAAATATATAAAATAATTAGATAT
TAAATTAAAATTAATATATATTTTAAAAAATAATATGTATAAC
Found at i:45984225 original size:30 final size:30
Alignment explanation
Indices: 45984184--45984240 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
45984174 TTATAACTTG
*
45984184 TTGTTAATATTTTAATATATAAAATATAAA
1 TTGTAAATATTTTAATATATAAAATATAAA
45984214 TTGTAAATATTTTAATATATAAAATAT
1 TTGTAAATATTTTAATATATAAAATAT
45984241 TTTAAGCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (30 bp):
TTGTAAATATTTTAATATATAAAATATAAA
Found at i:45984240 original size:17 final size:17
Alignment explanation
Indices: 45984189--45984245 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
45984179 ACTTGTTGTT
45984189 AATATTTTAATATATAA
1 AATATTTTAATATATAA
* *
45984206 AATA--TAAAT-TGT-A
1 AATATTTTAATATATAA
45984219 AATATTTTAATATATAA
1 AATATTTTAATATATAA
45984236 AATATTTTAA
1 AATATTTTAA
45984246 GCAATAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 5 0.16
14 2 0.06
15 8 0.25
16 2 0.06
17 15 0.47
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AATATTTTAATATATAA
Found at i:45984352 original size:23 final size:23
Alignment explanation
Indices: 45984317--45984371 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
45984307 ATAATTTTTT
*
45984317 TATAAATA-AAAATATAAAAATAA
1 TATAAATATTAAAT-TAAAAATAA
* *
45984340 T-TAGATATTAAATTAAAATTAA
1 TATAAATATTAAATTAAAAATAA
45984362 TATAAATATT
1 TATAAATATT
45984372 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
TATAAATATTAAATTAAAAATAA
Found at i:45984380 original size:108 final size:109
Alignment explanation
Indices: 45984298--45984494 Score: 301
Period size: 110 Copynumber: 1.8 Consensus size: 109
45984288 AAACTATATT
45984298 TGACTAAATATAATTTTTTTATAAATA-AAAATATA-AAAATAATTAGATATTAAATTAAAATTA
1 TGACT-AA-ATAATTTTTTTATAAATAGAAAATATATAAAATAATTAGATATTAAATTAAAATTA
* * *
45984361 ATATAAATATTTTAAAAAATAATATGTATAACTAAAAAATTTTAAGA
64 ATATAAAT-TTTTAAAAAATAATATGTAGAACTAAAAAACTATAAGA
*
45984408 TGACTAAATAATTTTTTTATAAATAGAAAATATATAAAATAGTTAGATATTAAATTAAAATTAAT
1 TGACTAAATAATTTTTTTATAAATAGAAAATATATAAAATAATTAGATATTAAATTAAAATTAAT
*
45984473 ATATATTTTT-AAAAATAATATG
66 ATAAATTTTTAAAAAATAATATG
45984495 GGTAGACTTA
Statistics
Matches: 83, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
108 30 0.36
109 14 0.17
110 39 0.47
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.40
Consensus pattern (109 bp):
TGACTAAATAATTTTTTTATAAATAGAAAATATATAAAATAATTAGATATTAAATTAAAATTAAT
ATAAATTTTTAAAAAATAATATGTAGAACTAAAAAACTATAAGA
Found at i:45984456 original size:110 final size:108
Alignment explanation
Indices: 45984298--45984494 Score: 326
Period size: 108 Copynumber: 1.8 Consensus size: 108
45984288 AAACTATATT
45984298 TGACTAAATATAATTTTTTTATAAATAAAAATATAAAAATAATTAGATATTAAATTAAAATTAAT
1 TGACTAAATATAATTTTTTTATAAATAAAAATATAAAAATAATTAGATATTAAATTAAAATTAAT
45984363 ATAAATATTTTAAAAAATAATATGTATAACTAAAAAATTTTAAGA
66 AT--ATATTTTAAAAAATAATATGTATAACTAAAAAATTTTAAGA
*
45984408 TGACT-AA-ATAATTTTTTTATAAATAGAAAATATATAAAATAGTTAGATATTAAATTAAAATTA
1 TGACTAAATATAATTTTTTTATAAATA-AAAATATA-AAAATAATTAGATATTAAATTAAAATTA
*
45984471 ATATATATTTTTAAAAATAATATG
64 ATATATATTTTAAAAAATAATATG
45984495 GGTAGACTTA
Statistics
Matches: 83, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
108 37 0.45
109 10 0.12
110 36 0.43
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.40
Consensus pattern (108 bp):
TGACTAAATATAATTTTTTTATAAATAAAAATATAAAAATAATTAGATATTAAATTAAAATTAAT
ATATATTTTAAAAAATAATATGTATAACTAAAAAATTTTAAGA
Found at i:45985188 original size:30 final size:30
Alignment explanation
Indices: 45985147--45985203 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
45985137 TTATAACTTG
*
45985147 TTGTTAATATTTTAATATATAAAATATAAA
1 TTGTAAATATTTTAATATATAAAATATAAA
45985177 TTGTAAATATTTTAATATATAAAATAT
1 TTGTAAATATTTTAATATATAAAATAT
45985204 TTTAAGCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (30 bp):
TTGTAAATATTTTAATATATAAAATATAAA
Found at i:45985201 original size:963 final size:963
Alignment explanation
Indices: 45983335--45985261 Score: 3854
Period size: 963 Copynumber: 2.0 Consensus size: 963
45983325 AATGTTAAAA
45983335 TGACTAAATATAATTTTTTTATAAATAAAAATATAAAAATAATTAGATATTAAATTAAAATTAAT
1 TGACTAAATATAATTTTTTTATAAATAAAAATATAAAAATAATTAGATATTAAATTAAAATTAAT
45983400 ATAAATATTTTAAAAAATAATATGTATAACTAAAAAATTTTAAGATGACTAAATAATTTTTTTAT
66 ATAAATATTTTAAAAAATAATATGTATAACTAAAAAATTTTAAGATGACTAAATAATTTTTTTAT
45983465 AAATAGAAAATATATAAAATAGTTAGATATTAAATTAAAATTAATATATATTTTTAAAAATAATA
131 AAATAGAAAATATATAAAATAGTTAGATATTAAATTAAAATTAATATATATTTTTAAAAATAATA
45983530 TGGGTAGACTTAAAATGTGCTTAGATTAGATATTTACATATATGGGCAAAATTGCACAAAATTTT
196 TGGGTAGACTTAAAATGTGCTTAGATTAGATATTTACATATATGGGCAAAATTGCACAAAATTTT
45983595 AAATTCATATTTTGAATTAAGTCGGACTTAGGCAAGTATAAAGTATATCAATGTCATGCTTAGGC
261 AAATTCATATTTTGAATTAAGTCGGACTTAGGCAAGTATAAAGTATATCAATGTCATGCTTAGGC
45983660 TCGACTCAAACTTGACCTAACCCATGAACAACCCTATCCTCAATTCTATCGAGAGACTTACAGGT
326 TCGACTCAAACTTGACCTAACCCATGAACAACCCTATCCTCAATTCTATCGAGAGACTTACAGGT
45983725 TCATAGGTTGAGGGGTACTTCAACAAGTCAATATTGTTCTATGGTCAAAGTTTTGTCTCCAAAAT
391 TCATAGGTTGAGGGGTACTTCAACAAGTCAATATTGTTCTATGGTCAAAGTTTTGTCTCCAAAAT
45983790 TTGTTGAAAGCCCTAACAAGTTCACAAAATAGAACCACATTGTATCAACAGGAGGATTCATGACA
456 TTGTTGAAAGCCCTAACAAGTTCACAAAATAGAACCACATTGTATCAACAGGAGGATTCATGACA
45983855 AACGGAAGAGTTTGCGCATAATCTTACTTGACTCCGTGACTTATGACATGTAGGCCATTGATGTG
521 AACGGAAGAGTTTGCGCATAATCTTACTTGACTCCGTGACTTATGACATGTAGGCCATTGATGTG
45983920 AAAGCATATTAGTACTTGAGTTAGTTTGACTCTTAACAAATATTTAGGGCAATTTCTTCGTTGCT
586 AAAGCATATTAGTACTTGAGTTAGTTTGACTCTTAACAAATATTTAGGGCAATTTCTTCGTTGCT
45983985 TTTGAAAAGTACTTTTAAAAAATGTCAAGTTTAGTTTAAAATTTGAGTGTTTAGTATTGTTATCA
651 TTTGAAAAGTACTTTTAAAAAATGTCAAGTTTAGTTTAAAATTTGAGTGTTTAGTATTGTTATCA
45984050 AAAAGTGCTTTTGAGAAATAAAATGTCCATTTTAGACATGTTATTATCAAGTAACAAATATGTAT
716 AAAAGTGCTTTTGAGAAATAAAATGTCCATTTTAGACATGTTATTATCAAGTAACAAATATGTAT
45984115 TTAAATAATATTTAAATTAGTTAATATTATTATATTTTAGTAATAATATAAAAAAATTATTATAA
781 TTAAATAATATTTAAATTAGTTAATATTATTATATTTTAGTAATAATATAAAAAAATTATTATAA
45984180 CTTGTTGTTAATATTTTAATATATAAAATATAAATTGTAAATATTTTAATATATAAAATATTTTA
846 CTTGTTGTTAATATTTTAATATATAAAATATAAATTGTAAATATTTTAATATATAAAATATTTTA
45984245 AGCAATAAATATTAATTATTTATAAAATTTAATTAGAATATATAAACTATATT
911 AGCAATAAATATTAATTATTTATAAAATTTAATTAGAATATATAAACTATATT
45984298 TGACTAAATATAATTTTTTTATAAATAAAAATATAAAAATAATTAGATATTAAATTAAAATTAAT
1 TGACTAAATATAATTTTTTTATAAATAAAAATATAAAAATAATTAGATATTAAATTAAAATTAAT
45984363 ATAAATATTTTAAAAAATAATATGTATAACTAAAAAATTTTAAGATGACTAAATAATTTTTTTAT
66 ATAAATATTTTAAAAAATAATATGTATAACTAAAAAATTTTAAGATGACTAAATAATTTTTTTAT
45984428 AAATAGAAAATATATAAAATAGTTAGATATTAAATTAAAATTAATATATATTTTTAAAAATAATA
131 AAATAGAAAATATATAAAATAGTTAGATATTAAATTAAAATTAATATATATTTTTAAAAATAATA
45984493 TGGGTAGACTTAAAATGTGCTTAGATTAGATATTTACATATATGGGCAAAATTGCACAAAATTTT
196 TGGGTAGACTTAAAATGTGCTTAGATTAGATATTTACATATATGGGCAAAATTGCACAAAATTTT
45984558 AAATTCATATTTTGAATTAAGTCGGACTTAGGCAAGTATAAAGTATATCAATGTCATGCTTAGGC
261 AAATTCATATTTTGAATTAAGTCGGACTTAGGCAAGTATAAAGTATATCAATGTCATGCTTAGGC
45984623 TCGACTCAAACTTGACCTAACCCATGAACAACCCTATCCTCAATTCTATCGAGAGACTTACAGGT
326 TCGACTCAAACTTGACCTAACCCATGAACAACCCTATCCTCAATTCTATCGAGAGACTTACAGGT
45984688 TCATAGGTTGAGGGGTACTTCAACAAGTCAATATTGTTCTATGGTCAAAGTTTTGTCTCCAAAAT
391 TCATAGGTTGAGGGGTACTTCAACAAGTCAATATTGTTCTATGGTCAAAGTTTTGTCTCCAAAAT
45984753 TTGTTGAAAGCCCTAACAAGTTCACAAAATAGAACCACATTGTATCAACAGGAGGATTCATGACA
456 TTGTTGAAAGCCCTAACAAGTTCACAAAATAGAACCACATTGTATCAACAGGAGGATTCATGACA
45984818 AACGGAAGAGTTTGCGCATAATCTTACTTGACTCCGTGACTTATGACATGTAGGCCATTGATGTG
521 AACGGAAGAGTTTGCGCATAATCTTACTTGACTCCGTGACTTATGACATGTAGGCCATTGATGTG
45984883 AAAGCATATTAGTACTTGAGTTAGTTTGACTCTTAACAAATATTTAGGGCAATTTCTTCGTTGCT
586 AAAGCATATTAGTACTTGAGTTAGTTTGACTCTTAACAAATATTTAGGGCAATTTCTTCGTTGCT
45984948 TTTGAAAAGTACTTTTAAAAAATGTCAAGTTTAGTTTAAAATTTGAGTGTTTAGTATTGTTATCA
651 TTTGAAAAGTACTTTTAAAAAATGTCAAGTTTAGTTTAAAATTTGAGTGTTTAGTATTGTTATCA
45985013 AAAAGTGCTTTTGAGAAATAAAATGTCCATTTTAGACATGTTATTATCAAGTAACAAATATGTAT
716 AAAAGTGCTTTTGAGAAATAAAATGTCCATTTTAGACATGTTATTATCAAGTAACAAATATGTAT
45985078 TTAAATAATATTTAAATTAGTTAATATTATTATATTTTAGTAATAATATAAAAAAATTATTATAA
781 TTAAATAATATTTAAATTAGTTAATATTATTATATTTTAGTAATAATATAAAAAAATTATTATAA
45985143 CTTGTTGTTAATATTTTAATATATAAAATATAAATTGTAAATATTTTAATATATAAAATATTTTA
846 CTTGTTGTTAATATTTTAATATATAAAATATAAATTGTAAATATTTTAATATATAAAATATTTTA
45985208 AGCAATAAATATTAATTATTTATAAAATTTAATTAGAATATATAAACTATATT
911 AGCAATAAATATTAATTATTTATAAAATTTAATTAGAATATATAAACTATATT
45985261 T
1 T
45985262 TAATTAAGCA
Statistics
Matches: 964, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
963 964 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (963 bp):
TGACTAAATATAATTTTTTTATAAATAAAAATATAAAAATAATTAGATATTAAATTAAAATTAAT
ATAAATATTTTAAAAAATAATATGTATAACTAAAAAATTTTAAGATGACTAAATAATTTTTTTAT
AAATAGAAAATATATAAAATAGTTAGATATTAAATTAAAATTAATATATATTTTTAAAAATAATA
TGGGTAGACTTAAAATGTGCTTAGATTAGATATTTACATATATGGGCAAAATTGCACAAAATTTT
AAATTCATATTTTGAATTAAGTCGGACTTAGGCAAGTATAAAGTATATCAATGTCATGCTTAGGC
TCGACTCAAACTTGACCTAACCCATGAACAACCCTATCCTCAATTCTATCGAGAGACTTACAGGT
TCATAGGTTGAGGGGTACTTCAACAAGTCAATATTGTTCTATGGTCAAAGTTTTGTCTCCAAAAT
TTGTTGAAAGCCCTAACAAGTTCACAAAATAGAACCACATTGTATCAACAGGAGGATTCATGACA
AACGGAAGAGTTTGCGCATAATCTTACTTGACTCCGTGACTTATGACATGTAGGCCATTGATGTG
AAAGCATATTAGTACTTGAGTTAGTTTGACTCTTAACAAATATTTAGGGCAATTTCTTCGTTGCT
TTTGAAAAGTACTTTTAAAAAATGTCAAGTTTAGTTTAAAATTTGAGTGTTTAGTATTGTTATCA
AAAAGTGCTTTTGAGAAATAAAATGTCCATTTTAGACATGTTATTATCAAGTAACAAATATGTAT
TTAAATAATATTTAAATTAGTTAATATTATTATATTTTAGTAATAATATAAAAAAATTATTATAA
CTTGTTGTTAATATTTTAATATATAAAATATAAATTGTAAATATTTTAATATATAAAATATTTTA
AGCAATAAATATTAATTATTTATAAAATTTAATTAGAATATATAAACTATATT
Found at i:45985203 original size:17 final size:17
Alignment explanation
Indices: 45985152--45985208 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 17
45985142 ACTTGTTGTT
45985152 AATATTTTAATATATAA
1 AATATTTTAATATATAA
* *
45985169 AATA--TAAAT-TGT-A
1 AATATTTTAATATATAA
45985182 AATATTTTAATATATAA
1 AATATTTTAATATATAA
45985199 AATATTTTAA
1 AATATTTTAA
45985209 GCAATAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 5 0.16
14 2 0.06
15 8 0.25
16 2 0.06
17 15 0.47
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AATATTTTAATATATAA
Found at i:45985354 original size:12 final size:12
Alignment explanation
Indices: 45985329--45985362 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
45985319 TTTTCAGCTC
45985329 CTTTTCAGAAGTG
1 CTTTTCA-AAGTG
45985342 CTTTTCAAAGTG
1 CTTTTCAAAGTG
45985354 CTTTTCAAA
1 CTTTTCAAA
45985363 AGTACTTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (12 bp):
CTTTTCAAAGTG
Found at i:45985376 original size:25 final size:25
Alignment explanation
Indices: 45985329--45985376 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
45985319 TTTTCAGCTC
* * *
45985329 CTTTTCAGAAGTGCTTTTCAAAGTG
1 CTTTTCAAAAGTACTTCTCAAAGTG
*
45985354 CTTTTCAAAAGTACTTCTGAAAG
1 CTTTTCAAAAGTACTTCTCAAAG
45985377 CTAAAAATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (25 bp):
CTTTTCAAAAGTACTTCTCAAAGTG
Found at i:45985415 original size:14 final size:14
Alignment explanation
Indices: 45985396--45985435 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
45985386 TCAGCCAAAA
45985396 GCAGCTTGTTCTTC
1 GCAGCTTGTTCTTC
45985410 GCAGCTTGTTCTTC
1 GCAGCTTGTTCTTC
*
45985424 ACAGCTT-TTCTT
1 GCAGCTTGTTCTT
45985436 TCAAAAGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 5 0.20
14 20 0.80
ACGTcount: A:0.10, C:0.28, G:0.17, T:0.45
Consensus pattern (14 bp):
GCAGCTTGTTCTTC
Found at i:45989469 original size:14 final size:13
Alignment explanation
Indices: 45989434--45989497 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 13
45989424 CATTTTTCCT
*
45989434 TCCTAAATTCTCAA
1 TCCTCAATT-TCAA
45989448 CTCC-CAATCTTCAA
1 -TCCTCAAT-TTCAA
45989462 TCCTCAATTTCCAA
1 TCCTCAATTT-CAA
*
45989476 T-TTCCAATTTCAA
1 TCCT-CAATTTCAA
45989489 TCCTCAATT
1 TCCTCAATT
45989498 ATTTTTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
13 15 0.37
14 22 0.54
15 4 0.10
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.38
Consensus pattern (13 bp):
TCCTCAATTTCAA
Found at i:45990385 original size:18 final size:18
Alignment explanation
Indices: 45990362--45990396 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45990352 CCTTCGTCCT
* *
45990362 CTAAGGGGAAGCAGAAAG
1 CTAAGGGAAAGAAGAAAG
45990380 CTAAGGGAAAGAAGAAA
1 CTAAGGGAAAGAAGAAA
45990397 CCGACTAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.34, T:0.06
Consensus pattern (18 bp):
CTAAGGGAAAGAAGAAAG
Found at i:46009037 original size:28 final size:28
Alignment explanation
Indices: 46009006--46009075 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
46008996 TTCCCGGGAC
* *
46009006 ATTTTTCAAAACCCATCTCGTCAAAATT
1 ATTTTTCAAAACCCATATCATCAAAATT
*
46009034 ATTTTTCAGAACCCATATCATCAAAATT
1 ATTTTTCAAAACCCATATCATCAAAATT
*
46009062 ATTTTTAAAAACCC
1 ATTTTTCAAAACCC
46009076 CTAAACTCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.36
Consensus pattern (28 bp):
ATTTTTCAAAACCCATATCATCAAAATT
Found at i:46009351 original size:29 final size:29
Alignment explanation
Indices: 46009300--46009357 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
46009290 TGACCTAGAC
**
46009300 GCGTTTTTCTTTAGTGTGCTGACATGGAT
1 GCGTTTTTCTTTAGCCTGCTGACATGGAT
* *
46009329 GCGTTTTTCTTTAGCCTGTTGACCTGGAT
1 GCGTTTTTCTTTAGCCTGCTGACATGGAT
46009358 ATGTTTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (29 bp):
GCGTTTTTCTTTAGCCTGCTGACATGGAT
Found at i:46009363 original size:29 final size:29
Alignment explanation
Indices: 46009301--46009364 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
46009291 GACCTAGACG
** *
46009301 CGTTTTTCTTTAGTGTGCTGACATGGATG
1 CGTTTTTCTTTAGCCTGCTGACATGGATA
* *
46009330 CGTTTTTCTTTAGCCTGTTGACCTGGATA
1 CGTTTTTCTTTAGCCTGCTGACATGGATA
*
46009359 TGTTTT
1 CGTTTT
46009365 ATTGGTCAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.12, C:0.16, G:0.23, T:0.48
Consensus pattern (29 bp):
CGTTTTTCTTTAGCCTGCTGACATGGATA
Found at i:46009785 original size:14 final size:14
Alignment explanation
Indices: 46009766--46009801 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
46009756 AAATAAAATT
46009766 TCGAGTTAATCGAA
1 TCGAGTTAATCGAA
*
46009780 TCGAGTTAATTGAA
1 TCGAGTTAATCGAA
*
46009794 TCAAGTTA
1 TCGAGTTA
46009802 TTCAAGTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (14 bp):
TCGAGTTAATCGAA
Found at i:46010017 original size:19 final size:20
Alignment explanation
Indices: 46009974--46010034 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 20
46009964 CAAAAATTAC
46009974 AAAAAATTCAAAATAATTTTT
1 AAAAAATTCAAAAT-ATTTTT
46009995 --AAAATTCAAAAT-TTTTT
1 AAAAAATTCAAAATATTTTT
* *
46010012 AAAAAATT-ATAATAGTTTT
1 AAAAAATTCAAAATATTTTT
46010031 AAAA
1 AAAA
46010035 TTTTTTCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 5 0.14
18 4 0.11
19 26 0.74
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTTT
Found at i:46013571 original size:28 final size:30
Alignment explanation
Indices: 46013545--46013612 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
46013535 GGGTAACCTA
46013545 ATATAAT-TCAACTTGTGTGAGCAACCTTG
1 ATATAATGTCAACTTGTGTGAGCAACCTTG
* * *
46013574 ATATAATGTTAGCTTGTGTGAGTAACCTTG
1 ATATAATGTCAACTTGTGTGAGCAACCTTG
46013604 ATATAATGT
1 ATATAATGT
46013613 TAGCCTGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 7 0.20
30 28 0.80
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (30 bp):
ATATAATGTCAACTTGTGTGAGCAACCTTG
Found at i:46013592 original size:30 final size:30
Alignment explanation
Indices: 46013556--46013629 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
46013546 TATAATTCAA
46013556 CTTGTGTGAGCAACCTTGATATAATGTTAG
1 CTTGTGTGAGCAACCTTGATATAATGTTAG
*
46013586 CTTGTGTGAGTAACCTTGATATAATGTTAG
1 CTTGTGTGAGCAACCTTGATATAATGTTAG
* *
46013616 CCTGTATGAGCAAC
1 CTTGTGTGAGCAAC
46013630 TTAATCACCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (30 bp):
CTTGTGTGAGCAACCTTGATATAATGTTAG
Found at i:46016461 original size:25 final size:26
Alignment explanation
Indices: 46016410--46016462 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
46016400 TTAGAATTTT
* *
46016410 ATATTTTCAAAATGTATATCATTTATC
1 ATATTTTCAAAATATATAACA-TTATC
46016437 ATATTTTCAAAATATATAACA-TATC
1 ATATTTTCAAAATATATAACATTATC
46016462 A
1 A
46016463 GAATAAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
27 19 0.79
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (26 bp):
ATATTTTCAAAATATATAACATTATC
Found at i:46017469 original size:14 final size:15
Alignment explanation
Indices: 46017438--46017471 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
46017428 AAACTTCATA
46017438 AAAAGAAACAAGAAG
1 AAAAGAAACAAGAAG
46017453 AAAAGAAACAA-AAG
1 AAAAGAAACAAGAAG
46017467 AAAAG
1 AAAAG
46017472 GAAGAATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAGAAACAAGAAG
Found at i:46031313 original size:50 final size:50
Alignment explanation
Indices: 46031235--46031333 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
46031225 AAGCAGCGTC
*
46031235 TTTATGCTCATCATTTGCAGGAAGGTGCATCTGTGCACGAACACTTAACA
1 TTTATGCTCATCATTTGAAGGAAGGTGCATCTGTGCACGAACACTTAACA
* *
46031285 TTTATGCTCATCGTTTGAAGGAATGTGCATCTGTGCACGAACACTTAAC
1 TTTATGCTCATCATTTGAAGGAAGGTGCATCTGTGCACGAACACTTAAC
46031334 TGTGCACGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (50 bp):
TTTATGCTCATCATTTGAAGGAAGGTGCATCTGTGCACGAACACTTAACA
Found at i:46031338 original size:18 final size:18
Alignment explanation
Indices: 46031315--46031349 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
46031305 GAATGTGCAT
46031315 CTGTGCACGAACACTTAA
1 CTGTGCACGAACACTTAA
46031333 CTGTGCACGAACACTTA
1 CTGTGCACGAACACTTA
46031350 CTTCGTTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (18 bp):
CTGTGCACGAACACTTAA
Found at i:46036530 original size:20 final size:19
Alignment explanation
Indices: 46036487--46036544 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
46036477 NNNNNNNNNN
*
46036487 GTTTTACAATTTTTATAAA
1 GTTTTACAATTTTTATATA
*
46036506 ATTTTACAAATTTTTATATA
1 GTTTTAC-AATTTTTATATA
*
46036526 GTTTTTACAGTTTTTATAT
1 G-TTTTACAATTTTTATAT
46036545 TTTTTTCTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 6 0.18
20 21 0.64
21 6 0.18
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (19 bp):
GTTTTACAATTTTTATATA
Found at i:46036796 original size:87 final size:89
Alignment explanation
Indices: 46036674--46036869 Score: 238
Period size: 87 Copynumber: 2.2 Consensus size: 89
46036664 GCTTGTTTTG
* * *
46036674 AAAAAGTTTAAAGGC-CTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTG-CAAAAAA
1 AAAAAGTTTAAGGGCTTTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGACAAAAAA
* *
46036737 AGT-AGAGGCTTAATT-TTTTTAAA
66 AATAAGA-ACTTAATTATTTTTAAA
* * *
46036760 AAAAAGTTTAAGGGCTTTTTTTTATGTATTTTGAAAGTTCAAGTACCCAAATGAGTGATAAAAAA
1 AAAAAGTTTAAGGGCTTTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGACAAAAAA
***
46036825 AATAAGAACTTAATTACTTTTTTTG
66 AATAAGAACTTAATTA-TTTTTAAA
*
46036850 AAAAAGTTTGAGGGCTTTTT
1 AAAAAGTTTAAGGGCTTTTT
46036870 GTACTGTAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
86 14 0.15
87 37 0.40
88 15 0.16
89 3 0.03
90 24 0.26
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.37
Consensus pattern (89 bp):
AAAAAGTTTAAGGGCTTTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAATGAGTGACAAAAAA
AATAAGAACTTAATTATTTTTAAA
Found at i:46037683 original size:26 final size:26
Alignment explanation
Indices: 46037654--46037705 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
46037644 CCTTCCCTTT
*
46037654 CTTCTT-TTGATTCTTCTTTCTTTTTC
1 CTTCTTCTTCATTCTTC-TTCTTTTTC
*
46037680 CTTCTTCTTCATTTTTCTTCTTTTTC
1 CTTCTTCTTCATTCTTCTTCTTTTTC
46037706 ATCTTTCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.04, C:0.25, G:0.02, T:0.69
Consensus pattern (26 bp):
CTTCTTCTTCATTCTTCTTCTTTTTC
Found at i:46037694 original size:16 final size:16
Alignment explanation
Indices: 46037664--46037712 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
46037654 CTTCTTTTGA
*
46037664 TTCTTCTTTCTTTTTCC
1 TTCTTC-TTCATTTTCC
*
46037681 TTCTTCTTCATTTTTC
1 TTCTTCTTCATTTTCC
*
46037697 TTCTTTTTCATCTTTC
1 TTCTTCTTCAT-TTTC
46037713 AAGTGAGTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCTTCTTCATTTTCC
Found at i:46038502 original size:62 final size:63
Alignment explanation
Indices: 46038369--46038563 Score: 151
Period size: 62 Copynumber: 3.1 Consensus size: 63
46038359 GTGAGTCTAG
* * * ** * ** * * * *
46038369 GCCGTGTAACTCATTGTTTATTGTCTTGGTGCCACACGGGCA-ATAACACGGGCTTGTGTCTAG
1 GCCGTGTAACTCACTGTTTA-TGACTTAGAACCACACGGCCAGAGGACATGGGCATGTGTCCAA
* * * * *
46038432 GCCATGTAACTCTCTGTTTGTGACTTAGGACCACACGGCCAG-GGACATGGGCGTGTGTCCAA
1 GCCGTGTAACTCACTGTTTATGACTTAGAACCACACGGCCAGAGGACATGGGCATGTGTCCAA
** ** * * *
46038494 GCCGTGTAACTCACTGTTTATGTTTTAGAACCACACGGGTAGAGGACATAGGTAAGTGTCCAA
1 GCCGTGTAACTCACTGTTTATGACTTAGAACCACACGGCCAGAGGACATGGGCATGTGTCCAA
46038557 GCCGTGT
1 GCCGTGT
46038564 GTGTAACACC
Statistics
Matches: 103, Mismatches: 27, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
62 64 0.62
63 39 0.38
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (63 bp):
GCCGTGTAACTCACTGTTTATGACTTAGAACCACACGGCCAGAGGACATGGGCATGTGTCCAA
Found at i:46039797 original size:23 final size:23
Alignment explanation
Indices: 46039768--46039889 Score: 167
Period size: 23 Copynumber: 5.3 Consensus size: 23
46039758 ATAAGTGCCA
*
46039768 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
46039791 CACTGATATGTAGCC-ATAGCTAC
1 CACTGATATGTAGCCGA-AGCTAC
*
46039814 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
46039837 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
46039860 CACTGA-ATTGTAGCTGAAGCTAT
1 CACTGATA-TGTAGCCGAAGCTAC
46039883 CACTGAT
1 CACTGAT
46039890 CAATAACACT
Statistics
Matches: 89, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
22 2 0.02
23 86 0.97
24 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:46039835 original size:46 final size:46
Alignment explanation
Indices: 46039768--46039889 Score: 190
Period size: 46 Copynumber: 2.7 Consensus size: 46
46039758 ATAAGTGCCA
* *
46039768 CACTGATATGTAGCCAAAGCTACCACTGATATGTAGCCATAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
*
46039814 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
* * *
46039860 CACTGAATTGTAGCTGAAGCTATCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
46039890 CAATAACACT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCATAGCTAC
Found at i:46041257 original size:42 final size:42
Alignment explanation
Indices: 46041210--46041289 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
46041200 GGATATCATA
46041210 GTGTGAACCACAC-GAGCAAGGACACGAGCGTGTGTCCAGGCT
1 GTGTGAACCACACAG-GCAAGGACACGAGCGTGTGTCCAGGCT
*
46041252 GTGTGAACCACACAGGCAAGGACACGAGTGTGTGTCCA
1 GTGTGAACCACACAGGCAAGGACACGAGCGTGTGTCCA
46041290 AGCCATGTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.33, T:0.15
Consensus pattern (42 bp):
GTGTGAACCACACAGGCAAGGACACGAGCGTGTGTCCAGGCT
Found at i:46043752 original size:7 final size:7
Alignment explanation
Indices: 46043739--46043789 Score: 75
Period size: 7 Copynumber: 7.3 Consensus size: 7
46043729 ATATCAGAAT
46043739 CAGATAA
1 CAGATAA
*
46043746 TAGATAA
1 CAGATAA
*
46043753 TAGATAA
1 CAGATAA
46043760 CAGATAA
1 CAGATAA
*
46043767 CAGATTA
1 CAGATAA
46043774 CAGATAA
1 CAGATAA
46043781 CAGATAA
1 CAGATAA
46043788 CA
1 CA
46043790 TATCAAACGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.55, C:0.12, G:0.14, T:0.20
Consensus pattern (7 bp):
CAGATAA
Found at i:46050048 original size:25 final size:25
Alignment explanation
Indices: 46050016--46050068 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
46050006 CTAAGTACAA
* *
46050016 TTTTAGAAAGTACTAGCTACAGTGT
1 TTTTAGAAAGTACTAACTACAATGT
*
46050041 TTTTAGAAAGTTCTAACTACAATGT
1 TTTTAGAAAGTACTAACTACAATGT
46050066 TTT
1 TTT
46050069 CTAAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (25 bp):
TTTTAGAAAGTACTAACTACAATGT
Found at i:46072053 original size:23 final size:24
Alignment explanation
Indices: 46072022--46072066 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
46072012 TTAATGATGG
* *
46072022 TTATATATATATTTATATGTTAAC
1 TTATATATATATATACATGTTAAC
46072046 TTAT-TATATATATACATGTTA
1 TTATATATATATATACATGTTA
46072067 TATGTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (24 bp):
TTATATATATATATACATGTTAAC
Found at i:46072124 original size:15 final size:16
Alignment explanation
Indices: 46072106--46072153 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 16
46072096 ATTTATATGT
46072106 ATAAGTTATAA-AATA
1 ATAAGTTATAATAATA
*
46072121 ATAATACTTATAATAATA
1 AT-A-AGTTATAATAATA
46072139 AT-AGTTATAATAATA
1 ATAAGTTATAATAATA
46072154 GAATAGTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 14 0.50
16 1 0.04
17 7 0.25
18 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (16 bp):
ATAAGTTATAATAATA
Found at i:46072207 original size:23 final size:23
Alignment explanation
Indices: 46072181--46072233 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
46072171 ATGCAAAATT
46072181 AAGAGAAAGAA-GAAAGAAAAGAA
1 AAGAGAAAGAAGGAAAG-AAAGAA
* * *
46072204 AAGAAAAATAAGGAAAGAAAGGA
1 AAGAGAAAGAAGGAAAGAAAGAA
46072227 AAGAGAA
1 AAGAGAA
46072234 CGCACGGGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (23 bp):
AAGAGAAAGAAGGAAAGAAAGAA
Found at i:46072397 original size:16 final size:16
Alignment explanation
Indices: 46072376--46072410 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
46072366 GATTAAGATT
46072376 TTAAAT-GTTGTTAGTA
1 TTAAATAGTT-TTAGTA
46072392 TTAAATAGTTTTAGTA
1 TTAAATAGTTTTAGTA
46072408 TTA
1 TTA
46072411 GGGATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (16 bp):
TTAAATAGTTTTAGTA
Found at i:46072994 original size:16 final size:16
Alignment explanation
Indices: 46072975--46073008 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
46072965 AAATTAATAT
* *
46072975 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
46072991 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
46073007 AT
1 AT
46073009 TGGATATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:46078945 original size:20 final size:20
Alignment explanation
Indices: 46078920--46079043 Score: 131
Period size: 20 Copynumber: 6.2 Consensus size: 20
46078910 TGTACGGGAC
*
46078920 TGCACTTCGGTGCCTCTATT
1 TGCACTTCGGTGCCTCTGTT
*
46078940 TGCACTTTGGTGCCTCTGTT
1 TGCACTTCGGTGCCTCTGTT
* ** *
46078960 TCCACTTTAGTGCCTCTGTC
1 TGCACTTCGGTGCCTCTGTT
* *
46078980 TACACTTTGGTGCCTCTGTT
1 TGCACTTCGGTGCCTCTGTT
* * *
46079000 TCCACTTCAGTGCCTCTGTC
1 TGCACTTCGGTGCCTCTGTT
* *
46079020 GGCACTTCGGTGCCTCTGCT
1 TGCACTTCGGTGCCTCTGTT
46079040 TGCA
1 TGCA
46079044 TTTTAATGCT
Statistics
Matches: 86, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.09, C:0.31, G:0.21, T:0.39
Consensus pattern (20 bp):
TGCACTTCGGTGCCTCTGTT
Found at i:46078986 original size:40 final size:40
Alignment explanation
Indices: 46078942--46079037 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
46078932 CCTCTATTTG
* *
46078942 CACTTTGGTGCCTCTGTTTCCACTTTAGTGCCTCTGTCTA
1 CACTTTGGTGCCTCTGTTTCCACTTCAGTGCCTCTGTCGA
*
46078982 CACTTTGGTGCCTCTGTTTCCACTTCAGTGCCTCTGTCGG
1 CACTTTGGTGCCTCTGTTTCCACTTCAGTGCCTCTGTCGA
*
46079022 CACTTCGGTGCCTCTG
1 CACTTTGGTGCCTCTG
46079038 CTTGCATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.08, C:0.32, G:0.21, T:0.39
Consensus pattern (40 bp):
CACTTTGGTGCCTCTGTTTCCACTTCAGTGCCTCTGTCGA
Found at i:46084595 original size:31 final size:31
Alignment explanation
Indices: 46084557--46084624 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
46084547 ACGGATTAAT
46084557 TTGAAATGCTAGAATGGTGAATTAATTTTCA
1 TTGAAATGCTAGAATGGTGAATTAATTTTCA
46084588 TTGAAATGCTAGAATGGTGAATTAATTTTCA
1 TTGAAATGCTAGAATGGTGAATTAATTTTCA
46084619 TT-AAAT
1 TTGAAAT
46084625 ATGTTATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 33 0.89
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.40
Consensus pattern (31 bp):
TTGAAATGCTAGAATGGTGAATTAATTTTCA
Found at i:46087263 original size:10 final size:11
Alignment explanation
Indices: 46087248--46087285 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
46087238 TTATTCTTTA
46087248 AAAAAAACAG-
1 AAAAAAACAGC
*
46087258 AAAAAAAAAGC
1 AAAAAAACAGC
46087269 AAAAAAAC-GC
1 AAAAAAACAGC
46087279 AAAAAAA
1 AAAAAAA
46087286 GAAGAAGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.82, C:0.11, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAACAGC
Found at i:46087284 original size:23 final size:22
Alignment explanation
Indices: 46087258--46087334 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 22
46087248 AAAAAAACAG
*
46087258 AAAAAAAAAGCAAAAAAACGCAA
1 AAAAAAAAAGC-AAAAAGCGCAA
46087281 AAAAAGAAGAAGCAAAAAGCGCAA
1 AAAAA-AA-AAGCAAAAAGCGCAA
46087305 AAAAGAAAAAGCAAAAAGCGCAA
1 AAAA-AAAAAGCAAAAAGCGCAA
46087328 AAAAAAA
1 AAAAAAA
46087335 GTTGCCTACC
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
22 3 0.06
23 24 0.48
24 18 0.36
25 5 0.10
ACGTcount: A:0.74, C:0.12, G:0.14, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAGCAAAAAGCGCAA
Found at i:46093956 original size:32 final size:32
Alignment explanation
Indices: 46093911--46094230 Score: 601
Period size: 32 Copynumber: 10.1 Consensus size: 32
46093901 CTTAGATAAT
46093911 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
46093942 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
*
46093974 TTGAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
46094005 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
46094037 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
46094069 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
46094101 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
46094133 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
46094165 TTTAAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTT-AAAGAGTTTTTATTAGGATTCAATTACTC
46094197 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
46094229 TT
1 TT
46094231 GTAATTTGCC
Statistics
Matches: 283, Mismatches: 2, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
31 45 0.16
32 232 0.82
33 6 0.02
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:46105291 original size:37 final size:38
Alignment explanation
Indices: 46105236--46105315 Score: 126
Period size: 37 Copynumber: 2.1 Consensus size: 38
46105226 GAGAAAGTAA
46105236 AAGGAAATAAAAAGGCATTAGTGAATG-AAAACTATAC
1 AAGGAAATAAAAAGGCATTAGTGAATGAAAAACTATAC
* * *
46105273 AAGGTAATAAAGAGGCATTAGTGAATGAAAAAGTATAC
1 AAGGAAATAAAAAGGCATTAGTGAATGAAAAACTATAC
46105311 AAGGA
1 AAGGA
46105316 GCATGATGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 25 0.66
38 13 0.34
ACGTcount: A:0.53, C:0.06, G:0.23, T:0.19
Consensus pattern (38 bp):
AAGGAAATAAAAAGGCATTAGTGAATGAAAAACTATAC
Found at i:46106648 original size:25 final size:25
Alignment explanation
Indices: 46106619--46106667 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
46106609 AAAGAAGAAG
46106619 CGAATTTG-ACACTCACCAAAACAAA
1 CGAATTTGCA-ACTCACCAAAACAAA
*
46106644 CGAATTTGCAAGTCACCAAAACAA
1 CGAATTTGCAACTCACCAAAACAA
46106668 TGGAGACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.47, C:0.27, G:0.10, T:0.16
Consensus pattern (25 bp):
CGAATTTGCAACTCACCAAAACAAA
Found at i:46109530 original size:15 final size:15
Alignment explanation
Indices: 46109510--46109542 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
46109500 CTAAACTAAT
46109510 AAAATTAAACTACGA
1 AAAATTAAACTACGA
*
46109525 AAAATTAAATTACGA
1 AAAATTAAACTACGA
46109540 AAA
1 AAA
46109543 CAAACCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.09, G:0.06, T:0.21
Consensus pattern (15 bp):
AAAATTAAACTACGA
Found at i:46136896 original size:7 final size:7
Alignment explanation
Indices: 46136886--46136930 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
46136876 ATTTTAAGGT
*
46136886 TTATAGA
1 TTATGGA
46136893 TTATGGAA
1 TTATGG-A
*
46136901 TTAGGGA
1 TTATGGA
46136908 TTATGGA
1 TTATGGA
46136915 TTATGGA
1 TTATGGA
*
46136922 TTAGGGA
1 TTATGGA
46136929 TT
1 TT
46136931 CTGGTTTAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
7 27 0.82
8 6 0.18
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (7 bp):
TTATGGA
Found at i:46136911 original size:22 final size:21
Alignment explanation
Indices: 46136886--46136930 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
46136876 ATTTTAAGGT
46136886 TTATAGATTATGGAATTAGGGA
1 TTATAGATTATGG-ATTAGGGA
*
46136908 TTATGGATTATGGATTAGGGA
1 TTATAGATTATGGATTAGGGA
46136929 TT
1 TT
46136931 CTGGTTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (21 bp):
TTATAGATTATGGATTAGGGA
Found at i:46137259 original size:33 final size:35
Alignment explanation
Indices: 46137166--46137260 Score: 99
Period size: 34 Copynumber: 2.8 Consensus size: 35
46137156 GGGGTTAGTA
* *
46137166 GTTAAGGGTTTAGGGTTTGGGGTTT-G-GATTAGAG
1 GTTAAGAG-TTAGGGTTTAGGGTTTAGAGATTAGAG
* *
46137200 GTTAAGAGTTAGTGATTTAGGGTTTAGAGATTCGAG
1 GTTAAGAGTTAG-GGTTTAGGGTTTAGAGATTAGAG
*
46137236 GTT-AG-GTTAGGGTTTAAGGTTTAGA
1 GTTAAGAGTTAGGGTTTAGGGTTTAGA
46137261 TTAATTAGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
33 17 0.33
34 22 0.42
35 3 0.06
36 10 0.19
ACGTcount: A:0.23, C:0.01, G:0.38, T:0.38
Consensus pattern (35 bp):
GTTAAGAGTTAGGGTTTAGGGTTTAGAGATTAGAG
Found at i:46141675 original size:43 final size:43
Alignment explanation
Indices: 46141626--46141810 Score: 280
Period size: 43 Copynumber: 4.3 Consensus size: 43
46141616 AGGTTATGTT
* * * *
46141626 TTTAGCGGCGTTTTTGCGAAAAGCGTCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
46141669 TTTAGCGGCGTTTGTGGGAAAGGCGCCCCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
46141712 TTTAGCGGCGTTTGTGGGAGAAGTGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
46141755 TTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
46141798 TTTAGCAGCGTTT
1 TTTAGCGGCGTTT
46141811 TTTTCTAAAA
Statistics
Matches: 128, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 128 1.00
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:46142478 original size:20 final size:20
Alignment explanation
Indices: 46142435--46142479 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
46142425 ATGCTAGGCG
*
46142435 GTGTGGAGGTCTACACGCCC
1 GTGTGGAGGTCTACACACCC
* *
46142455 GTGTGGTGGTCTACACACCT
1 GTGTGGAGGTCTACACACCC
46142475 GTGTG
1 GTGTG
46142480 CAAGTTTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.24, G:0.36, T:0.27
Consensus pattern (20 bp):
GTGTGGAGGTCTACACACCC
Found at i:46153030 original size:50 final size:50
Alignment explanation
Indices: 46152947--46153078 Score: 158
Period size: 50 Copynumber: 2.6 Consensus size: 50
46152937 ATGACATATT
* * * * *
46152947 CTGTGAAGCCCTTATGGCCAACTATCTGTAAAGCCTTTGTGGCGAACTCA
1 CTGTGAAGCCTTTGTGGCAAACTCTCTGTAAAGCCTTTGTGGCAAACTCA
*
46152997 CTGTGCAA-CCTTTGTGGCAAACTCTCTGTAAAGCCTTTGTGGCAAACTCT
1 CTGTG-AAGCCTTTGTGGCAAACTCTCTGTAAAGCCTTTGTGGCAAACTCA
* ** *
46153047 TTGTGAAGCCTTTGTGGTGAACTCTCTATAAA
1 CTGTGAAGCCTTTGTGGCAAACTCTCTGTAAA
46153079 ATCTTCTTGG
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 2 0.03
50 66 0.94
51 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (50 bp):
CTGTGAAGCCTTTGTGGCAAACTCTCTGTAAAGCCTTTGTGGCAAACTCA
Found at i:46153069 original size:25 final size:25
Alignment explanation
Indices: 46152946--46153073 Score: 141
Period size: 25 Copynumber: 5.1 Consensus size: 25
46152936 CATGACATAT
* * * *
46152946 TCTGTGAAGCCCTTATGGCCAACTA
1 TCTGTGAAGCCTTTGTGGCAAACTC
* *
46152971 TCTGTAAAGCCTTTGTGGCGAACTC
1 TCTGTGAAGCCTTTGTGGCAAACTC
*
46152996 ACTGTGCAA-CCTTTGTGGCAAACTC
1 TCTGTG-AAGCCTTTGTGGCAAACTC
*
46153021 TCTGTAAAGCCTTTGTGGCAAACTC
1 TCTGTGAAGCCTTTGTGGCAAACTC
* **
46153046 TTTGTGAAGCCTTTGTGGTGAACTC
1 TCTGTGAAGCCTTTGTGGCAAACTC
46153071 TCT
1 TCT
46153074 ATAAAATCTT
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
24 2 0.02
25 82 0.95
26 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (25 bp):
TCTGTGAAGCCTTTGTGGCAAACTC
Found at i:46162979 original size:21 final size:20
Alignment explanation
Indices: 46162955--46162994 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
46162945 TAGATTAAAT
*
46162955 TAATTTCTTGGAATTATTATC
1 TAATTTATTGGAATT-TTATC
*
46162976 TAATTTATTGTAATTTTAT
1 TAATTTATTGGAATTTTAT
46162995 AATTAAAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (20 bp):
TAATTTATTGGAATTTTATC
Found at i:46163185 original size:28 final size:28
Alignment explanation
Indices: 46163132--46163185 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
46163122 GAGAAAATAA
* *
46163132 TTTAATTAAGTGAATTAATTAAATTTAT
1 TTTAATTAAGTGAAATAAATAAATTTAT
*
46163160 TTTAATTAA-TTAAATAAATAATATTT
1 TTTAATTAAGTGAAATAAATAA-ATTT
46163186 TTGGAATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
TTTAATTAAGTGAAATAAATAAATTTAT
Found at i:46166464 original size:73 final size:74
Alignment explanation
Indices: 46166366--46166513 Score: 289
Period size: 73 Copynumber: 2.0 Consensus size: 74
46166356 TTAATGTATT
46166366 ATATATAAAAAAAATTAATACGGGTGGGCCGGGTTGAGTTCGGATTTTAGCTTTATTATTCGGGA
1 ATATATAAAAAAAATTAATACGGGTGGGCCGGGTTGAGTTCGGATTTTAGCTTTATTATTCGGGA
46166431 TGAGTTTGA
66 TGAGTTTGA
46166440 ATATAT-AAAAAAATTAATACGGGTGGGCCGGGTTGAGTTCGGATTTTAGCTTTATTATTCGGGA
1 ATATATAAAAAAAATTAATACGGGTGGGCCGGGTTGAGTTCGGATTTTAGCTTTATTATTCGGGA
46166504 TGAGTTTGA
66 TGAGTTTGA
46166513 A
1 A
46166514 CAAAATTTTA
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 68 0.92
74 6 0.08
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (74 bp):
ATATATAAAAAAAATTAATACGGGTGGGCCGGGTTGAGTTCGGATTTTAGCTTTATTATTCGGGA
TGAGTTTGA
Done.