Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 11 of 54
Found at i:5208633 original size:21 final size:21
Alignment explanation
Indices: 5208609--5208677 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
5208599 AAAAGATTCA
5208609 TATTTATATATTTAAGACACT
1 TATTTATATATTTAAGACACT
* ** *
5208630 TATTT-TTTA-CGAATGTGAGACT
1 TATTTATATATTTAA---GACACT
*
5208652 TTTTTATATATTTAAGACACT
1 TATTTATATATTTAAGACACT
5208673 TATTT
1 TATTT
5208678 TTTACGGATG
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 14 0.42
22 9 0.27
23 3 0.09
24 2 0.06
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.51
Consensus pattern (21 bp):
TATTTATATATTTAAGACACT
Found at i:5208650 original size:24 final size:24
Alignment explanation
Indices: 5208623--5208693 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 24
5208613 TATATATTTA
5208623 AGACACTTATTTTTTACGAATGTG
1 AGACACTTATTTTTTACGAATGTG
* * * *
5208647 AG--ACTT-TTTTATA--TATTTA
1 AGACACTTATTTTTTACGAATGTG
*
5208666 AGACACTTATTTTTTACGGATGTG
1 AGACACTTATTTTTTACGAATGTG
5208690 AGAC
1 AGAC
5208694 TTATGACATT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 5 0.15
21 10 0.29
22 10 0.29
24 9 0.26
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (24 bp):
AGACACTTATTTTTTACGAATGTG
Found at i:5208672 original size:43 final size:43
Alignment explanation
Indices: 5208611--5208695 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
5208601 AAGATTCATA
5208611 TTTATATATTTAAGACACTTATTTTTTACGAATGTGAGACTTT
1 TTTATATATTTAAGACACTTATTTTTTACGAATGTGAGACTTT
*
5208654 TTTATATATTTAAGACACTTATTTTTTACGGATGTGAGACTT
1 TTTATATATTTAAGACACTTATTTTTTACGAATGTGAGACTT
5208696 ATGACATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.48
Consensus pattern (43 bp):
TTTATATATTTAAGACACTTATTTTTTACGAATGTGAGACTTT
Found at i:5208695 original size:22 final size:22
Alignment explanation
Indices: 5208627--5208697 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
5208617 TATTTAAGAC
5208627 ACTTATTTTTTACGAATGTGAG
1 ACTTATTTTTTACGAATGTGAG
* * * *
5208649 ACTT-TTTTATA--TATTTAAGAC
1 ACTTATTTTTTACGAATGT--GAG
*
5208670 ACTTATTTTTTACGGATGTGAG
1 ACTTATTTTTTACGAATGTGAG
5208692 ACTTAT
1 ACTTAT
5208698 GACATTTTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
19 3 0.08
21 12 0.33
22 18 0.50
24 3 0.08
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.48
Consensus pattern (22 bp):
ACTTATTTTTTACGAATGTGAG
Found at i:5217819 original size:15 final size:15
Alignment explanation
Indices: 5217787--5217817 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5217777 ATCTTCTATA
5217787 TTAAATAATTTATTT
1 TTAAATAATTTATTT
5217802 TTAAA-AATTTATTT
1 TTAAATAATTTATTT
5217816 TT
1 TT
5217818 TATCGTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAAATAATTTATTT
Found at i:5220288 original size:3 final size:3
Alignment explanation
Indices: 5220280--5220308 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5220270 CTTGTTGCAC
5220280 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5220309 AATTTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5221219 original size:71 final size:73
Alignment explanation
Indices: 5221135--5221311 Score: 218
Period size: 71 Copynumber: 2.4 Consensus size: 73
5221125 TTTTTATAAA
* * *
5221135 TAGAGATACCCATTGAGCTAAAGTAGAAGAATTTAC-GGTTTTCAT-TTGTTTGTT-TAGTTATC
1 TAGAGATACCCATTAAGCTAAAGTAGAAGAATTTACAGGTTTTC-TGTTATTT-TTGTAGTAATC
5221197 TT-GTGTAAT
64 TTGGTGTAAT
* **
5221206 TAGAGATACCCATTAAGCTAAAGCAGAAGAATTTACATTTTTTCTGGTTATTTTTGTAGTAATCT
1 TAGAGATACCCATTAAGCTAAAGTAGAAGAATTTACAGGTTTTCT-GTTATTTTTGTAGTAATCT
5221271 TGGTGTAAT
65 TGGTGTAAT
* * *
5221280 TAGAGACACCAATTAAGCTAAATTAGAAGAAT
1 TAGAGATACCCATTAAGCTAAAGTAGAAGAAT
5221312 ATGATGAGCA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
71 35 0.38
72 7 0.08
73 14 0.15
74 35 0.38
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (73 bp):
TAGAGATACCCATTAAGCTAAAGTAGAAGAATTTACAGGTTTTCTGTTATTTTTGTAGTAATCTT
GGTGTAAT
Found at i:5241009 original size:42 final size:43
Alignment explanation
Indices: 5240922--5241021 Score: 132
Period size: 42 Copynumber: 2.3 Consensus size: 43
5240912 TGAATCCCTA
* *
5240922 TGGCATAAGTCATAATCATAATAGAAACCACAATTAACCCCAG
1 TGGCATAGGTCATAATCATAATAGAAACCACAATTAACCACAG
*
5240965 TGGCATAGGTCATAATCAT-AT-GAAAACCACAATTAACCATAG
1 TGGCATAGGTCATAATCATAATAG-AAACCACAATTAACCACAG
* *
5241007 TGGAATGGGTCATAA
1 TGGCATAGGTCATAA
5241022 GTATATCAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
41 1 0.02
42 32 0.63
43 18 0.35
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (43 bp):
TGGCATAGGTCATAATCATAATAGAAACCACAATTAACCACAG
Found at i:5254767 original size:2 final size:2
Alignment explanation
Indices: 5254760--5254787 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5254750 AGCATGCAAA
5254760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5254788 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5254803 original size:2 final size:2
Alignment explanation
Indices: 5254798--5254849 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
5254788 NNNNNNNNNN
5254798 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5254840 AT AT AT AT AT
1 AT AT AT AT AT
5254850 GACTTTCGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5255344 original size:43 final size:42
Alignment explanation
Indices: 5255246--5255337 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
5255236 TCTGATATAC
** *
5255246 TTATGACCCATGCCACTGGGATTAATTGTGGTTTCGATATGA
1 TTATGACCCATGCCACTGGGATTAATCATGATTTCGATATGA
* *
5255288 TTATAACCCATGCCACTGGGATTAATCATGATTTCTGTTATGA
1 TTATGACCCATGCCACTGGGATTAATCATGATTTC-GATATGA
5255331 TTATGAC
1 TTATGAC
5255338 TTATGCCGTA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 31 0.72
43 12 0.28
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (42 bp):
TTATGACCCATGCCACTGGGATTAATCATGATTTCGATATGA
Found at i:5259110 original size:17 final size:17
Alignment explanation
Indices: 5259080--5259123 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
5259070 TTTTATTAAT
* *
5259080 TATTTTTTACTTTTATA
1 TATTTTTAATTTTTATA
*
5259097 TTTTTTTAATTTTTATA
1 TATTTTTAATTTTTATA
5259114 TATTTTTAAT
1 TATTTTTAAT
5259124 ATAATTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TATTTTTAATTTTTATA
Found at i:5264542 original size:22 final size:23
Alignment explanation
Indices: 5264517--5264565 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
5264507 TATTGTATAT
5264517 TAAAAT-TTGAAT-TTTTTTAATA
1 TAAAATATT-AATATTTTTTAATA
5264539 T-AAATATTAATATTTTTTAATA
1 TAAAATATTAATATTTTTTAATA
*
5264561 CAAAA
1 TAAAA
5264566 AAGTAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 7 0.30
22 13 0.57
23 3 0.13
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAATATTAATATTTTTTAATA
Found at i:5272789 original size:199 final size:199
Alignment explanation
Indices: 5272277--5274221 Score: 1754
Period size: 199 Copynumber: 9.8 Consensus size: 199
5272267 GAAAGCAAGG
* * * *
5272277 GGAATGCACCATATACTAAGATTTCAAATTCACATAATGGCACCATTATATCGTAACGTATAATA
1 GGAATGCACCATATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATA
* * * ** *
5272342 GGAATGCCATATGCCCGCACCTTAA-AGGTTTTTTATTTCTATAAGCACCATTAAGCCATTATTG
66 GGAATGCCACATGCCCACACCTTAATTGG-TTTTTATTTCTATAAGCACCATTGTGCCATTATTA
* ** * * * * * *
5272406 CACCATAGGAATGCCGGGTCAAGTATTTTGAATATCTAATTCGCACTATTTTACATTCGATCAAA
130 CACAATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAA
*
5272471 CAATA
195 TAATA
* * * * * * * *
5272476 TGAATGCGCCATATGCTCAA-ATTTCAAATTCATATCTTGGCACCATTATAACATAATGTATAAC
1 GGAATGCACCATATACT-AAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAAT
** * * * * * * * ** *
5272540 ACAAATGCCACATACCCAAACCTTAA-AGTTTCTTTATGTCGATCAGCACCATTGTGCCAAAACT
65 AGGAATGCCACATGCCCACACCTTAATTGGTT-TTTATTTCTATAAGCACCATTGTGCCATTATT
* * * * * *
5272604 ACACAATAGGAAGGCCATGTCAAGTA-TTCGAAATATTTAATTTACTCCACTATACCTTCGATCA
129 ACACAATAGGAATGCCATGTCAAGTACTT-TAAATATCTAATTTGCACCATTATACCTTCGATCA
**
5272668 AGCAATA
193 AATAATA
* * ** * **
5272675 GGAACGCACCATACACTAAGATTTTC-AATTTGCATATTAGCACCATTATACCACAATGTATAAT
1 GGAATGCACCATATACTAAGA-TTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAAT
* * *
5272739 AGGAATGCCACATGCCCACACCTTGAATTGG-TTTTATTTCTATAAGCACCATTGTTCCATAATC
65 AGGAATGCCACATGCCCACACCTT-AATTGGTTTTTATTTCTATAAGCACCATTGTGCCATTATT
* * * * *
5272803 AAAC-ATAGTAATGCAATGTCAAGTACTTTAAATATCGAATTTGCACCATTATACTTTCGATCAA
129 ACACAATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAA
*
5272867 ATAAGA
194 ATAATA
* * * * * *
5272873 GAAATGCACCATATACTAAAATTTCAAATTAACGTATTAGTACCATTATACCTTAATGTATAATA
1 GGAATGCACCATATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATA
* ** * * * * ** * **
5272938 AGAATGCCACATGTTCACACAC--AAATGTTTTTTGTTTTTGCAAGCACCGTTGTGCTGTTATTA
66 GGAATGCCACATGCCCACAC-CTTAATTGGTTTTTATTTCTATAAGCACCATTGTGCCATTATTA
* * *
5273001 CACAATAGGAATGCCTTGTTAAGCACTTTAAATATCTAATTTGCACC-TT-TACTCTATCGATCA
130 CACAATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTATAC-CT-TCGATCA
5273064 AATAATA
193 AATAATA
*
5273071 GGAATGCACCATATAC-AATGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAAA
1 GGAATGCACCATATACTAA-GATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAAT
* ** *
5273135 ACGAATGCCACATGCCTGCACCTTAA-AGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATT
65 AGGAATGCCACATGCCCACACCTTAATTGG-TTTTTATTTCTATAAGCACCATTGTGCCATTATT
* * * * * * * *
5273199 GCATAATATGAATGCCTTGTTAAGCACTTCAAATAT-TTATTTGCACCATTACT-CCTTCGATCA
129 ACACAATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTA-TACCTTCGATCA
5273262 AATAATA
193 AATAATA
* * *
5273269 GGAGTGCACCATATAC-AATGATTTCAAATTCACATATTGGCACCATTATGCCTTAATATATAAT
1 GGAATGCACCATATACTAA-GATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAAT
*** * ** * * *
5273333 AGGAATGCCACATGCTTGCCCCTTAAAGGGTTTTTGTTTTTGTAAGCACCATTGTGCCATTATTA
65 AGGAATGCCACATGCCCACACCTTAATTGGTTTTTATTTCTATAAGCACCATTGTGCCATTATTA
* * * * * * *
5273398 CACAATAGAAATGTC-TCGTTAAGCACTTTAAATATCTATTTTGCACCTTTACT-CCTTTGATCA
130 CACAATAGGAATGCCAT-GTCAAGTACTTTAAATATCTAATTTGCACCATTA-TACCTTCGATCA
5273461 AATAATA
193 AATAATA
* * * *
5273468 GGAATGCACCGTACACTACA-ATTTCAAATTCACATATTGGCACCATTATACCTTAAAGTATAAC
1 GGAATGCACCATATACTA-AGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAAT
* * *
5273532 AGAAATGCCACATGCTCC-CACCTTGATAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTAT
65 AGGAATGCCACATGC-CCACACCTTAATTGG-TTTTTATTTCTATAAGCACCATTGTGCCATTAT
* * * * * *
5273596 TGCACAATAGGAATACCATGTCAAGTACTTTAAATATCTAATTTGCACCTTTACACTTTCCATCA
128 TACACAATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCA
5273661 AATAATA
193 AATAATA
** * * ** * * * * * *
5273668 GGAAACCACCAAATGCTCGGATTCCAAATTCATAAATTGGCACCATCATACCGTAATGTATGATA
1 GGAATGCACCATATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATA
* * * * *
5273733 GGAATGCCACATGCTCACGCACTTAAAATT--TTTTTGTTTCTATAAGCACCATTATGCCAATAT
66 GGAATGCCACATGCCCACAC-CTT--AATTGGTTTTTATTTCTATAAGCACCATTGTGCCATTAT
* * * * *
5273796 TACACAATACGAATGCCACGTCAAGCACTTTAAATAT-TGAATTTGCA-C-TTTTACTTGTTCGA
128 TACACAATAGGAATGCCATGTCAAGTACTTTAAATATCT-AATTTGCACCATTATAC--CTTCGA
*
5273858 TCGAATAATA
190 TCAAATAATA
* * * * * * *
5273868 GGAACGCATCATATACTAAGATTTCATATTCACATATAGGCACCATTCTACTTTAATGCATAATA
1 GGAATGCACCATATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATA
*
5273933 GGAATGCCACATGCCCACACCTTAA--GGTTTTATTATTTTTATAAGCACCATTGTGCCATTATT
66 GGAATGCCACATGCCCACACCTTAATTGG-TTT-TTATTTCTATAAGCACCATTGTGCCATTATT
* * * * * * * * * *
5273996 AAACAATAGGAATGCCACGTCAGGTATTTTAAATATCTAATTTGCATCATCACACGTTCAATCAG
129 ACACAATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAA
*
5274061 TTAATA
194 ATAATA
* * * * *
5274067 GGAATGCATCATATGCTAAGATTTCATATTCACATATAGGCACCATTATACCTTAGTGTATAATA
1 GGAATGCACCATATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATA
** *** * **
5274132 GGAATGCCACATTTCCACACGACAGTT--TTATTT-TTTCTATAAGCACCACCGTGCCATTATTA
66 GGAATGCCACATGCCCACACCTTAATTGGTT-TTTATTTCTATAAGCACCATTGTGCCATTATTA
* *
5274194 CACAATAGGAGTGCCAAGTCAAGTACTT
130 CACAATAGGAATGCCATGTCAAGTACTT
5274222 CAAGTAGAAA
Statistics
Matches: 1418, Mismatches: 280, Indels: 98
0.79 0.16 0.05
Matches are distributed among these distances:
196 7 0.00
197 88 0.06
198 421 0.30
199 578 0.41
200 312 0.22
201 10 0.01
203 2 0.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (199 bp):
GGAATGCACCATATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATA
GGAATGCCACATGCCCACACCTTAATTGGTTTTTATTTCTATAAGCACCATTGTGCCATTATTAC
ACAATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAAT
AATA
Found at i:5273541 original size:397 final size:397
Alignment explanation
Indices: 5272277--5274208 Score: 1877
Period size: 397 Copynumber: 4.9 Consensus size: 397
5272267 GAAAGCAAGG
* * * *
5272277 GGAATGCACCATATACTAAGATTTCAAATTCACATAATGGCACCATTATATCGTAACGTATAATA
1 GGAATGCACCATATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATA
* * **
5272342 GGAATGCCATATGCCCGCACCTTAAAGGTTTTTTATTTCTATAAGCACCATTAAGCCATTATTGC
66 GGAATGCCACATGCCCACACCTTAAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTGC
* ** * * * * * *
5272407 ACCATAGGAATGCCGGGTCAAGTATTTTGAATATCTAATTCGCACTATT-TTACATTCGATCAAA
131 ACAATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTACT-CTTTCGATCAAA
* * * * * * * *
5272471 CAATATGAATGCGCCATATGCTCAA-ATTTCAAATTCATATCTTGGCACCATTATAACATAATGT
195 TAATAGGAATGCACCATAT--ACAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGT
* ** * * * * * *
5272535 ATAACACAAATGCCACATACCCAAAC-CTTAAA-GTTTCTT-TATGTCGATCAGCACCATTGTGC
258 ATAATAGGAATGCCACATGCTCACACACTTAAAGGTTT-TTGT-TTTTG-TAAGCACCATTGTGC
* * * * * * * * **
5272597 CAAAACTACACAATAGGAAGGCCAT-GTCAAGTA-TTCGAAATATTTAATTTACTCCACTA-TAC
320 CAATATTACACAATAGGAATGCC-TCGTCAAGCACTT-TAAATATCTAATTTGCACCTTTACT-C
**
5272659 CTTCGATCAAGCAATA
382 CTTCGATCAAATAATA
* * ** * **
5272675 GGAACGCACCATACACTAAGATTTTC-AATTTGCATATTAGCACCATTATACCACAATGTATAAT
1 GGAATGCACCATATACTAAGA-TTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAAT
* * *
5272739 AGGAATGCCACATGCCCACACCTTGAA--TTGGTTTTATTTCTATAAGCACCATTGTTCCA-TAA
65 AGGAATGCCACATGCCCACACCTTAAAGGTT--TTTTATTTCTATAAGCACCATTGTGCCATTAT
* * * *
5272801 T-CAAACATAGTAATGCAATGTCAAGTACTTTAAATATCGAATTTGCACCATTA-TACTTTCGAT
128 TGCACA-ATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTACT-CTTTCGAT
* * * * * * *
5272864 CAAATAAGAGAAATGCACCATATACTAAAATTTCAAATTAACGTATTAGTACCATTATACCTTAA
191 CAAATAATAGGAATGCACCATATAC-AAGATTTCAAATTCACATATTGGCACCATTATACCTTAA
* * * * *
5272929 TGTATAATAAGAATGCCACATGTTCACACAC--AAATGTTTTTTGTTTTTGCAAGCACCGTTGTG
255 TGTATAATAGGAATGCCACATGCTCACACACTTAAA-GGTTTTTGTTTTTGTAAGCACCATTGTG
*** * *
5272992 CTGTTATTACACAATAGGAATGCCTTGTTAAGCACTTTAAATATCTAATTTGCACCTTTACT-CT
319 CCAATATTACACAATAGGAATGCCTCGTCAAGCACTTTAAATATCTAATTTGCACCTTTACTCCT
5273056 ATCGATCAAATAATA
384 -TCGATCAAATAATA
*
5273071 GGAATGCACCATATAC-AATGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAAA
1 GGAATGCACCATATACTAA-GATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAAT
* **
5273135 ACGAATGCCACATGCCTGCACCTTAAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTG
65 AGGAATGCCACATGCCCACACCTTAAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTG
* * * * * * * *
5273200 CATAATATGAATGCCTTGTTAAGCACTTCAAATAT-TTATTTGCACCATTACTCCTTCGATCAAA
130 CACAATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTACTCTTTCGATCAAA
* * *
5273264 TAATAGGAGTGCACCATATACAATGATTTCAAATTCACATATTGGCACCATTATGCCTTAATATA
195 TAATAGGAATGCACCATATACAA-GATTTCAAATTCACATATTGGCACCATTATACCTTAATGTA
** * *
5273329 TAATAGGAATGCCACATGCTTGC-CCCTTAAAGGGTTTTTGTTTTTGTAAGCACCATTGTGCCAT
259 TAATAGGAATGCCACATGCTCACACACTTAAA-GGTTTTTGTTTTTGTAAGCACCATTGTGCCAA
* * * * *
5273393 TATTACACAATAGAAATGTCTCGTTAAGCACTTTAAATATCTATTTTGCACCTTTACTCCTTTGA
323 TATTACACAATAGGAATGCCTCGTCAAGCACTTTAAATATCTAATTTGCACCTTTACTCCTTCGA
5273458 TCAAATAATA
388 TCAAATAATA
* * * *
5273468 GGAATGCACCGTACACTACA-ATTTCAAATTCACATATTGGCACCATTATACCTTAAAGTATAAC
1 GGAATGCACCATATACTA-AGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAAT
* *
5273532 AGAAATGCCACATGCTCC-CACCTTGATAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTAT
65 AGGAATGCCACATGC-CCACACCTT-AAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTAT
* * * *
5273596 TGCACAATAGGAATACCATGTCAAGTACTTTAAATATCTAATTTGCACCTTTACACTTTCCATCA
128 TGCACAATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTACTCTTTCGATCA
** * * ** * * * * *
5273661 AATAATAGGAAACCACCAAATGCTCGGATTCCAAATTCATAAATTGGCACCATCATACCGTAATG
193 AATAATAGGAATGCACCATATAC-AAGATTTCAAATTCACATATTGGCACCATTATACCTTAATG
* * ** * * *
5273726 TATGATAGGAATGCCACATGCTCACGCACTTAAAATTTTTTTGTTTCTATAAGCACCATTATGCC
257 TATAATAGGAATGCCACATGCTCACACACTT-AAAGGTTTTTGTTTTTGTAAGCACCATTGTGCC
* * * **
5273791 AATATTACACAATACGAATGCCACGTCAAGCACTTTAAATAT-TGAATTTGCACTTTTACTTGTT
321 AATATTACACAATAGGAATGCCTCGTCAAGCACTTTAAATATCT-AATTTGCACCTTTACTCCTT
*
5273855 CGATCGAATAATA
385 CGATCAAATAATA
* * * * * * *
5273868 GGAACGCATCATATACTAAGATTTCATATTCACATATAGGCACCATTCTACTTTAATGCATAATA
1 GGAATGCACCATATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATA
* *
5273933 GGAATGCCACATGCCCACACCTT-AAGGTTTTATTATTTTTATAAGCACCATTGTGCCATTATTA
66 GGAATGCCACATGCCCACACCTTAAAGGTTTT-TTATTTCTATAAGCACCATTGTGCCATTATTG
* * * * * * * * * **
5273997 AACAATAGGAATGCCACGTCAGGTATTTTAAATATCTAATTTGCATCATCACACGTTCAATCAGT
130 CACAATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTACTCTTTCGATCAAA
* * * * *
5274062 TAATAGGAATGCATCATATGCTAAGATTTCATATTCACATATAGGCACCATTATACCTTAGTGTA
195 TAATAGGAATGCACCATATAC-AAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTA
* * * * * **
5274127 TAATAGGAATGCCACAT-TTC-CACAC-GACA-GTTTTATTTTTTCTATAAGCACCACCGTGCCA
259 TAATAGGAATGCCACATGCTCACACACTTAAAGGTTTT-TGTTTT-TGTAAGCACCATTGTGCCA
* *
5274188 TTATTACACAATAGGAGTGCC
322 ATATTACACAATAGGAATGCC
5274209 AAGTCAAGTA
Statistics
Matches: 1261, Mismatches: 233, Indels: 82
0.80 0.15 0.05
Matches are distributed among these distances:
394 4 0.00
395 20 0.02
396 300 0.24
397 329 0.26
398 189 0.15
399 253 0.20
400 163 0.13
401 3 0.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (397 bp):
GGAATGCACCATATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATA
GGAATGCCACATGCCCACACCTTAAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTGC
ACAATAGGAATGCCATGTCAAGTACTTTAAATATCTAATTTGCACCATTACTCTTTCGATCAAAT
AATAGGAATGCACCATATACAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATA
ATAGGAATGCCACATGCTCACACACTTAAAGGTTTTTGTTTTTGTAAGCACCATTGTGCCAATAT
TACACAATAGGAATGCCTCGTCAAGCACTTTAAATATCTAATTTGCACCTTTACTCCTTCGATCA
AATAATA
Found at i:5274349 original size:161 final size:161
Alignment explanation
Indices: 5274069--5274360 Score: 394
Period size: 161 Copynumber: 1.8 Consensus size: 161
5274059 AGTTAATAGG
* * * *
5274069 AATGCATCATATGCTAAGATTTCATATTCACATATAGGCACCATTATACCTTAGTGTATAATAGG
1 AATGCACCATATGCTAAGATTTCAAATTCACATATAGGCACCATTATACCTTAATGAATAATAGG
* * * * *
5274134 AATGCCACATTTCCACACGACAGTTTTATTTTTTCTATAAGCACCACCGTGCCATTATTACACAA
66 AATGCCACATATCCACACGACACTTGTATTTTTTCTATAAACACCACCGTGCCATTATTAAACAA
5274199 TAGGAGTGCCAAGTCAAGTACTTCAAGTAGA
131 TAGGAGTGCCAAGTCAAGTACTTCAAGTAGA
*
5274230 AATGCACCATATGCTAAGATTTCAAATTCACATATCGGCACCATTATACCTTAATGAATAATAGG
1 AATGCACCATATGCTAAGATTTCAAATTCACATATAGGCACCATTATACCTTAATGAATAATAGG
* * **
5274295 AATGCCA-A-ATGCACAC-AC-CTTAACGTATTTATTTCTATAAACACTATTGTGCCATTATTAA
66 AATGCCACATATCCACACGACACTT---GTATTT-TTTCTATAAACACCACCGTGCCATTATTAA
5274356 ACAAT
127 ACAAT
5274361 GGACATGTTA
Statistics
Matches: 113, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
157 2 0.02
158 2 0.02
159 6 0.05
160 6 0.05
161 97 0.86
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (161 bp):
AATGCACCATATGCTAAGATTTCAAATTCACATATAGGCACCATTATACCTTAATGAATAATAGG
AATGCCACATATCCACACGACACTTGTATTTTTTCTATAAACACCACCGTGCCATTATTAAACAA
TAGGAGTGCCAAGTCAAGTACTTCAAGTAGA
Found at i:5276336 original size:199 final size:198
Alignment explanation
Indices: 5275954--5277503 Score: 1577
Period size: 199 Copynumber: 7.8 Consensus size: 198
5275944 AGCAAGGGAT
* * *
5275954 ATGCACCGTATGCTGAA-ATTTTAAATTCACATATTAGCACCATTATACCTTAATGTATAATAGG
1 ATGCACCATATGCT-AAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGG
* * * * ** *
5276018 AATGCCATATGGCCGCACCTTAAAAGTTTTTTATTTCTATAGGCACCATCATGCCATTATTGCAC
65 AATGCCACATGCCCACACCTT-AAAGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTACAC
* * ** * *
5276083 AATAGAAATGTCGGGTCAAGTACTTTAAATATCTAATTTGCACCATTTTACCTTCGATCAAACAA
129 AATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAATAA
*
5276148 TATGA
194 TAGGA
** * * * * *
5276153 ATGTGCCATATGCTCAGATTTCAAGTTCATATATTGGCACCATTATACCGTAATATATAATAGGA
1 ATGCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGA
* * * * * * **
5276218 ATGCCAAATACCCAAACCTTAAAGTTTCTTCATGTCTATGAGCACCATTGTGCCAGAATTACACA
66 ATGCCACATGCCCACACCTTAAAGTTT-TTTATTTCTATAAGCACCATTGTGCCATTATTACACA
* * * * *
5276283 ATAGGAATGCCATGTCAAGTA-TTTGAAATATCTAATTTACTCCATGATACCTTCGATCAAGTAA
130 ATAGGAATGCCACGTCAAGTACTTT-AAATATCTAATTTGCACCATTATACCTTCGATCAAATAA
5276347 TAGGA
194 TAGGA
* * * * *
5276352 ACGGACCATATGCTAAGATTTCAAATTCACATATTAGCACCATTATACCGTAACGTATAATAGGA
1 ATGCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGA
* * * * * *
5276417 ATGCCACATGCCCACACCTTAAATTGTTTTTATTTCTATGAGCACCATTGTTCCATAATCAAACA
66 ATGCCACATGCCCACACCTTAAAGT-TTTTTATTTCTATAAGCACCATTGTGCCATTATTACACA
* * * * *
5276482 ATAGGAATGCAATGTCAAGCACTTTCAATATCAAATTTGCACCATTATACCTTCGATCAAATAAT
130 ATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAATAAT
5276547 AGGA
195 AGGA
* * * * *
5276551 ATGCACCATATACTAAGATGTCAAATTCACATACTGGCACCATTATATCTTAATGCATAATAGGA
1 ATGCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGA
** * * * * * * * **
5276616 ATGCCACATGTTCACACATACAAAGTTTCTTTCTTTTTGTAAGAACCATTGTACTGTTATTACAC
66 ATGCCACATGCCCACACCT-TAAAGTTT-TTTATTTCTATAAGCACCATTGTGCCATTATTACAC
* * * ** * * *
5276681 AATAGGAATGCCTCATCAAGCACTTTAAATATCTGGTTTGCACCTTTACACCCTCGATCAAATAA
129 AATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAATAA
5276746 TAAGG-
194 T-AGGA
* * * *
5276751 ATGCACCGTATACTAACATTTCAAATTCACATATTGGCACCATTACACCTTAATGTATAATAGGA
1 ATGCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGA
* *
5276816 ATGCCACATGCCCGCA-CTGTGAAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTGCA
66 ATGCCACATGCCCACACCT-T-AAA-GTTTTTTATTTCTATAAGCACCATTGTGCCATTATTACA
* * * * * *
5276880 CAATAGGAATGCCACGTCAAGTACTTTCAATATCTAATTTTCACCTTTACATCTTCCATCAAATA
128 CAATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAATA
5276945 ATAGGA
193 ATAGGA
* * ** * * * * * *
5276951 ATCCACAATATGCTCGGATTCCAAATTCATACATTGGCACCATCATACCATAATGTATGATAGGA
1 ATGCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGA
* * * * *
5277016 ATGCCACATGCCCACATACTTAAAGTTTTTTTGTTTCTGTAAGCACCATTGTTCCAATATTACAC
66 ATGCCACATGCCCACA-CCTTAAAG-TTTTTTATTTCTATAAGCACCATTGTGCCATTATTACAC
* * * *
5277081 AATAGGAATGCCACGTCAAGCACTTTAAATATCGAATTTGCACC-TT-TACTTGTTCGATCGAAT
129 AATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTATAC--CTTCGATCAAAT
5277144 AATAGGA
192 AATAGGA
* * * * * * *
5277151 ATGCATCATATACTAAGATTTCATATTCATATATAGGCACCATTAAACCTTAATGCATAATAGGA
1 ATGCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGA
* * * * *
5277216 ATGCCACATGCCCACACTTTCAAGTTTTATTATTTTTATAAGCACCATTGGGCCATTATTAAACA
66 ATGCCACATGCCCACACCTTAAAGTTTT-TTATTTCTATAAGCACCATTGTGCCATTATTACACA
* * * * * * * **
5277281 ATAGGAATGGCACGTTAGGTA-TTTGAAATATCTAATTTGCATCATCACACGTTCGATCAGTTAA
130 ATAGGAATGCCACGTCAAGTACTTT-AAATATCTAATTTGCACCATTATACCTTCGATCAAATAA
5277345 TAGGA
194 TAGGA
* * * * *
5277350 ATGCATCATATGCTAAGATATCATATTCACATATAGGCACCATTATACCTTAGTGTATAATAGGA
1 ATGCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGA
** ** * ** *
5277415 ATGCCACATTTCCAC-CCGACAAAGTTTTATTTTTTCTATAAGCACCACCGTGCTATTATTACAC
66 ATGCCACATGCCCACACC-TTAAAGTTTT-TTATTTCTATAAGCACCATTGTGCCATTATTACAC
* *
5277479 AATAGGAGTGCCAAGTCAAGTACTT
129 AATAGGAATGCCACGTCAAGTACTT
5277504 CAAGTAGAAA
Statistics
Matches: 1110, Mismatches: 219, Indels: 43
0.81 0.16 0.03
Matches are distributed among these distances:
198 20 0.02
199 603 0.54
200 475 0.43
201 10 0.01
202 2 0.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (198 bp):
ATGCACCATATGCTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGA
ATGCCACATGCCCACACCTTAAAGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTACACAA
TAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAATAATA
GGA
Found at i:5277043 original size:400 final size:396
Alignment explanation
Indices: 5275954--5277423 Score: 1548
Period size: 400 Copynumber: 3.7 Consensus size: 396
5275944 AGCAAGGGAT
* * *
5275954 ATGCACCGTATGCTGAA-ATTTTAAATTCACATATTAGCACCATTATACCTTAATGTATAATAGG
1 ATGCACCATATACT-AAGATTTCAAATTCACATATTAGCACCATTATACCTTAATGTATAATAGG
* * * * ** **
5276018 AATGCCATATGGCCGCACCTTAAAAGTTTTTTATTTCTATAGGCACCATCATGCCATTATTGCAC
65 AATGCCACATGCCCACACCTT-AAAGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTAAAC
* * ** *
5276083 AATAGAAATGTCGGGTCAAGTACTTTAAATATCTAATTTGCACCATTTTAC-CTTCGATCAAACA
129 AATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCA--TTACACTTCGATCAAATA
* ** * * * * * *
5276147 ATATGAATGTGCCATATGCTCAGATTTCAAGTTCATATATTGGCACCATTATACCGTAATATATA
192 ATAGGAATGCACCATATGCTAAGATATCAAATTCACATATTGGCACCATTATACCTTAATGTATA
* * * * * *
5276212 ATAGGAATGCCAAATACCCA-A-ACCTTAAAGTTTC-TTCATGTCTATGAGCACCATTGTGCCAG
257 ATAGGAATGCCACATGCCCACATA-CTTAAAGTTTCTTTC-TTTCTGTAAGCACCATTGT-ACAG
* * * * * * * *
5276274 AATTACACAATAGGAATGCCAT-GTCAAGTA-TTTGAAATATCTAATTTACTCCATGATACCTTC
319 TATTACACAATAGGAATGCC-TCGTCAAGCACTTT-AAATATCTGATTTGCACCTTTACACCTTC
*
5276337 GATCAAGTAATAGGA
382 GATCAAATAATAGGA
* * * * *
5276352 ACGGACCATATGCTAAGATTTCAAATTCACATATTAGCACCATTATACCGTAACGTATAATAGGA
1 ATGCACCATATACTAAGATTTCAAATTCACATATTAGCACCATTATACCTTAATGTATAATAGGA
* * * * *
5276417 ATGCCACATGCCCACACCTTAAATTGTTTTTATTTCTATGAGCACCATTGTTCCATAATCAAACA
66 ATGCCACATGCCCACACCTTAAAGT-TTTTTATTTCTATAAGCACCATTGTGCCATTATTAAACA
* * * * * *
5276482 ATAGGAATGCAATGTCAAGCACTTTCAATATCAAATTTGCACCATTATACCTTCGATCAAATAAT
130 ATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTACA-CTTCGATCAAATAAT
* * * * *
5276547 AGGAATGCACCATATACTAAGATGTCAAATTCACATACTGGCACCATTATATCTTAATGCATAAT
194 AGGAATGCACCATATGCTAAGATATCAAATTCACATATTGGCACCATTATACCTTAATGTATAAT
* * * *
5276612 AGGAATGCCACATGTTCACACATAC--AAAGTTTCTTTCTTTTTGTAAGAACCATTGTACTGTTA
259 AGGAATGCCACATG--CCCACATACTTAAAGTTTCTTTCTTTCTGTAAGCACCATTGTACAG-TA
* * *
5276675 TTACACAATAGGAATGCCTCATCAAGCACTTTAAATATCTGGTTTGCACCTTTACACCCTCGATC
321 TTACACAATAGGAATGCCTCGTCAAGCACTTTAAATATCTGATTTGCACCTTTACACCTTCGATC
5276740 AAATAATAAGG-
386 AAATAAT-AGGA
* * * *
5276751 ATGCACCGTATACTAACATTTCAAATTCACATATTGGCACCATTACACCTTAATGTATAATAGGA
1 ATGCACCATATACTAAGATTTCAAATTCACATATTAGCACCATTATACCTTAATGTATAATAGGA
* **
5276816 ATGCCACATGCCCGCA-CTGTGAAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTGCA
66 ATGCCACATGCCCACACCT-T-AAA-GTTTTTTATTTCTATAAGCACCATTGTGCCATTATTAAA
* * * *
5276880 CAATAGGAATGCCACGTCAAGTACTTTCAATATCTAATTTTCACCTTTACATCTTCCATCAAATA
128 CAATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTACA-CTTCGATCAAATA
* * ** * * * *
5276945 ATAGGAATCCACAATATGCTCGGAT-TCCAAATTCATACATTGGCACCATCATACCATAATGTAT
192 ATAGGAATGCACCATATGCTAAGATAT-CAAATTCACATATTGGCACCATTATACCTTAATGTAT
* * * * *
5277009 GATAGGAATGCCACATGCCCACATACTTAAAGTTTTTTTGTTTCTGTAAGCACCATTGTTCCAAT
256 AATAGGAATGCCACATGCCCACATACTTAAAGTTTCTTTCTTTCTGTAAGCACCATTG-TACAGT
* ***
5277074 ATTACACAATAGGAATGCCACGTCAAGCACTTTAAATATC-GAATTTGCACCTTTACTTGTTCGA
320 ATTACACAATAGGAATGCCTCGTCAAGCACTTTAAATATCTG-ATTTGCACCTTTACACCTTCGA
*
5277138 TCGAATAATAGGA
384 TCAAATAATAGGA
* * * * *
5277151 ATGCATCATATACTAAGATTTCATATTCATATA-TAGGCACCATTAAACCTTAATGCATAATAGG
1 ATGCACCATATACTAAGATTTCAAATTCACATATTA-GCACCATTATACCTTAATGTATAATAGG
* * * *
5277215 AATGCCACATGCCCACACTTTCAAGTTTTATTATTTTTATAAGCACCATTGGGCCATTATTAAAC
65 AATGCCACATGCCCACACCTTAAAGTTTT-TTATTTCTATAAGCACCATTGTGCCATTATTAAAC
* * * * * **
5277280 AATAGGAATGGCACGTTAGGTA-TTTGAAATATCTAATTTGCATCATCACACGTTCGATCAGTTA
129 AATAGGAATGCCACGTCAAGTACTTT-AAATATCTAATTTGCACCATTACAC-TTCGATCAAATA
* * * *
5277344 ATAGGAATGCATCATATGCTAAGATATCATATTCACATATAGGCACCATTATACCTTAGTGTATA
192 ATAGGAATGCACCATATGCTAAGATATCAAATTCACATATTGGCACCATTATACCTTAATGTATA
5277409 ATAGGAATGCCACAT
257 ATAGGAATGCCACAT
5277424 TTCCACCCGA
Statistics
Matches: 886, Mismatches: 158, Indels: 55
0.81 0.14 0.05
Matches are distributed among these distances:
396 3 0.00
397 6 0.01
398 239 0.27
399 301 0.34
400 330 0.37
401 6 0.01
402 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (396 bp):
ATGCACCATATACTAAGATTTCAAATTCACATATTAGCACCATTATACCTTAATGTATAATAGGA
ATGCCACATGCCCACACCTTAAAGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTAAACAA
TAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCATTACACTTCGATCAAATAATAG
GAATGCACCATATGCTAAGATATCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAG
GAATGCCACATGCCCACATACTTAAAGTTTCTTTCTTTCTGTAAGCACCATTGTACAGTATTACA
CAATAGGAATGCCTCGTCAAGCACTTTAAATATCTGATTTGCACCTTTACACCTTCGATCAAATA
ATAGGA
Found at i:5279892 original size:199 final size:198
Alignment explanation
Indices: 5279252--5280978 Score: 1422
Period size: 200 Copynumber: 8.7 Consensus size: 198
5279242 GTATATTGAA
* * * * *
5279252 ATTTTAAATTCACATATTGACACCATTATACCTTAATGTATAATAGGAATGTCATATGGCC-GCA
1 ATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACAT-GCCTACA
* * * * **
5279316 CCTTAAAGGTT-TTTTTATTTTTATAGGCACCATTGTGCCATTTTTGCACAATAGCAATGCCGGG
65 CCTTAAA--TTGTTTTTATTTTTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACG
* * *
5279380 TCAAGTACTTTAAATATCTAATTTGCACCATTTTACCTTCGATCAAACAATATGAAGGTGC-CAT
128 TCAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAATAATAGGAA--TGCACAT
* *
5279444 ATGCTCAG
191 ATACTAAG
* * * * * * * *
5279452 ATTTCAAGTTCATATATTGGCACCATTATACCGTAATGTATAATAAGAACGCCACATACCCAAAC
1 ATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCTACAC
* * * ** ** *
5279517 CTTAAA--GTTTCTTCATGTCTATGAGCACCATTGTGTTAGAATTACACAATAGGAATGCCATGT
66 CTTAAATTGTTT-TT-ATTTTTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACGT
* * * ** * * ** * *
5279580 AAAGTA-TTCGAAATATCTAATTTACTTCGTGATACCTT-GATCAAGCAATAGGAACGGACCATA
129 CAAGTACTT-TAAATATCTAATTTGCACCATTATACCTTCGATCAAATAATAGGAATGCA-CATA
*
5279643 TACGAAG
192 TACTAAG
* * *
5279650 ATTTCAAATTCACATATTAGCACCATTATACCGTAACGTATAATAGGAATGCCACATGCCTACAC
1 ATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCTACAC
* * * * * * * *
5279715 CTTAAATTGTTTTTATTTCTATAAGCACTATTGTTCCATAATCAAACAATAGGAATGCAATGTCA
66 CTTAAATTGTTTTTATTTTTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACGTCA
* * * * *
5279780 AGCACTTTCAATATCAAATTTGCACCATTATACCTTCAATCAAATAATAGGAATGCACGATACAC
131 AGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAATAATAGGAATGCAC-ATATAC
5279845 TAAG
195 TAAG
* * * * * * * *
5279849 ATGTCAAATTCACGTACTGGCACCATTATATCTTATTGTATAATAGGAATACCAGATG-TTCACA
1 ATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCT-ACA
* * * * * * * *
5279913 CATACAAAGTT-TCTTTGTTTTTGTAAGCACCATTGTGCCGTTATTACACAATAGGAATGCCTCA
65 CCT-TAAA-TTGTTTTTATTTTTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACG
* * * * * *
5279977 TCAAGCACTTTAAATATCTAGTTTGCACCTTTACT-CCCTCGATCAAATAATAGGGATGCATCGT
128 TCAAGTACTTTAAATATCTAATTTGCACCATTA-TACCTTCGATCAAATAATAGGAATGCA-CAT
*
5280041 ATACTAAC
191 ATACTAAG
* *
5280049 ATTTCAAATTCACATATTGGCATCATTATACCTTAATGTATAATAGGAACGCCACATGCCCT-CA
1 ATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACATG-CCTACA
* * * * *
5280113 CCGTGAAA-GGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTGCATAATAGGAATGCCACG
65 CC-TTAAATTG-TTTTTATTTTTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACG
* * * * * *
5280177 TCAAGTACTTTCAATATCTAATTTTCACCTTTACACCTTCCATCAAATAATAGGAATCCACAATA
128 TCAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAATAATAGGAATGCAC-ATA
* **
5280242 TGCTCGG
192 TACTAAG
* * * * * * *
5280249 ATTCCAAATTCATACATTGGCACCATCATACCGTAATGTATGATAGGAATGCCATATG-CTCACA
1 ATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCT-ACA
* * * *
5280313 TGCTTAAA--GTTTTT-TTGTT-T---NACCATTGTGCCATTATTGCACAATAGGAATGCCACGT
65 -CCTTAAATTGTTTTTATTTTTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACGT
* * * * * *
5280371 CAAGTACTTTCAATATCTAATTTTCACCTTTACACCTTCCATCAAATAATAGGAATCCACAATAT
129 CAAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAATAATAGGAATGCAC-ATAT
* **
5280436 GCTCGG
193 ACTAAG
* * * * * * *
5280442 ATTCCAAATTCATACATTGGCACCATCATACCGTAATGTATGATAGGAATGCCATATG-CTCACA
1 ATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCT-ACA
* * * * * *
5280506 TGCTTAAAGTTTTTTTTGTTTTTGTAAGCACCATTGTTCCAATATTACACAATAGGAATGCCACG
65 -CCTTAAA-TTGTTTTTATTTTTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACG
* * * * * *
5280571 TCAAGCACTTTAAATATCGAATTTGCACC-TT-TACTTGTTCAATCGAATAATAGGAATGCATTA
128 TCAAGTACTTTAAATATCTAATTTGCACCATTATAC--CTTCGATCAAATAATAGGAATGCA-CA
*
5280634 TACACTAAG
190 TATACTAAG
* * * * *
5280643 ATTTCATATTCACATATAGGCACCATTATACCTTAATGCATAATAGGAATGCCACATGCCCATAC
1 ATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCTACAC
* * *
5280708 CTTAAGGTT-TTATTATTTTTATAAGCACCATTGTGCCATTATTATACAATAGGAATGCCACGTC
66 CTTAA-ATTGTTTTTATTTTTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACGTC
* * * ** * * ** *
5280772 AGGTATTTTAAATATCTAATTTGCATCACCACACGTTCGATCAGTTAATAGGAATGCATCATATG
130 AAGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAATAATAGGAATGCA-CATATA
5280837 CTAAG
194 CTAAG
* * * *
5280842 ATTTCATATTCACATATAGGCACCATTATACCTTAGTGTATAATAGGAATGCCACATTTCC-ACA
1 ATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACA-TGCCTACA
*** ** * * * *
5280906 CGACAAA--GTTTAATT-TTTTCTATAAGCACCACCGTGCCATTATTACACAATAAGAGTGTCAA
65 CCTTAAATTGTTT--TTATTTT-TATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCAC
5280968 GTCAAGTACTT
127 GTCAAGTACTT
5280979 CAAGTAGAAA
Statistics
Matches: 1243, Mismatches: 237, Indels: 95
0.79 0.15 0.06
Matches are distributed among these distances:
193 179 0.14
196 7 0.01
197 12 0.01
198 166 0.13
199 354 0.28
200 381 0.31
201 142 0.11
202 2 0.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (198 bp):
ATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCTACAC
CTTAAATTGTTTTTATTTTTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACGTCA
AGTACTTTAAATATCTAATTTGCACCATTATACCTTCGATCAAATAATAGGAATGCACATATACT
AAG
Found at i:5283308 original size:212 final size:211
Alignment explanation
Indices: 5282929--5283344 Score: 491
Period size: 212 Copynumber: 2.0 Consensus size: 211
5282919 CCATATGCTC
* * *
5282929 AGATTTCAAGTTCATATATTGGTACCATTATACCGTAATGTATAATAGGAACGCCACAAACCCAA
1 AGATTTCAAATTCACATATTGGCACCATTATACCGTAATGTATAATAGGAACGCCACAAACCCAA
* *
5282994 ACCTTAAAGTTTCTTCATGTCTATGAGCACAATTGTGTCATAAGTACACAATAGGAATGCCATGT
66 ACCTTAAAGTTTCTTCATGTCTATGAGCACAATTGTGTCATAAGTAAACAATAGGAATGCAATGT
* * * ** * * *
5283059 CAAGTATTCGAAATATCTAATTTACTCCATGATACCTTTTATCAAGTAATAGGAACAGACCATAT
131 CAAGCATTCGAAATATCAAATTTACACCATGATACCTTCAATCAAATAATAGAAACACACCATAT
5283124 ACCAAGATTTCNTACTA
196 ACCAAGATTTC-TACTA
* * * * ** * *
5283141 AGATTTCAAATTCACATATTGGCATCATTATACCTTAATTTATAATAGGAATGCCACATGCCTAC
1 AGATTTCAAATTCACATATTGGCACCATTATACCGTAATGTATAATAGGAACGCCACAAACCCAA
* *
5283206 ACCTTAAATTGTTT-TT-ATTTCTATGAGCACCATTGT-TCCATAA-TCAAACAATAGGAATGCA
66 ACCTTAAA--GTTTCTTCATGTCTATGAGCACAATTGTGT-CATAAGT-AAACAATAGGAATGCA
* * * *
5283267 ATGTCAAGCACTTC-CAATATCAAATTTGCACCATTATACCTTCAATCAAATAATAGAAATACAC
127 ATGTCAAGCA-TTCGAAATATCAAATTTACACCATGATACCTTCAATCAAATAATAGAAACACAC
*
5283331 CATATACTAAGATT
191 CATATACCAAGATT
5283345 CAAATTCACG
Statistics
Matches: 171, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
211 2 0.01
212 160 0.94
213 5 0.03
214 4 0.02
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (211 bp):
AGATTTCAAATTCACATATTGGCACCATTATACCGTAATGTATAATAGGAACGCCACAAACCCAA
ACCTTAAAGTTTCTTCATGTCTATGAGCACAATTGTGTCATAAGTAAACAATAGGAATGCAATGT
CAAGCATTCGAAATATCAAATTTACACCATGATACCTTCAATCAAATAATAGAAACACACCATAT
ACCAAGATTTCTACTA
Found at i:5283664 original size:200 final size:198
Alignment explanation
Indices: 5282732--5284658 Score: 1625
Period size: 200 Copynumber: 9.6 Consensus size: 198
5282722 GTATGCTGAA
* * * * * * * *
5282732 ATTTCAAATTCACATATTGGCACCATTATAACTTATTGTATTATAGAAATGCCATATGGCCGCAC
1 ATTTCAAATTCACATATCGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCCACAC
* * * * *
5282797 CTTAAAGGTTTTTTATTTCCATAGGCACCATCGTGCCATTATTGCACAATAGGAATGCCGA-GTC
66 CTCAAAGG-TTTTTATTTCTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCC-ACGTC
* * * * **
5282861 AAGTACTTTAAATATCTAATTTGCACCATTT--TACCTTCGATCAAACAATATGAATGTGCCATA
129 AAGCACTTTAAATATCTAATTTGCACC-TTTACT-CCTTCAATCAAATAATAGGAATGCACCATA
* *
5282924 TGCTCAG
192 TACTAAG
* * * * * * ** *
5282931 ATTTCAAGTTCATATATTGGTACCATTATACCGTAATGTATAATAGGAACGCCACAAACCCAAAC
1 ATTTCAAATTCACATATCGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCCACAC
* * * * * * * *
5282996 CTTAAA-GTTTCTTCATGTCTATGAGCACAATTGTGTCATAAGTACACAATAGGAATGCCATGTC
66 CTCAAAGGTTT-TT-ATTTCTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACGTC
* * * * * * ** * *
5283060 AAGTA-TTCGAAATATCTAATTTACTCCATGA-TACCTTTTATCAAGTAATAGGAACAGACCATA
129 AAGCACTT-TAAATATCTAATTTGCACCTTTACT-CCTTCAATCAAATAATAGGAA-TG--C---
*
5283123 TACCAAGATTTCNTACTAAG
186 -ACC---A--T-ATACTAAG
* * * *
5283143 ATTTCAAATTCACATATTGGCATCATTATACCTTAATTTATAATAGGAATGCCACATGCCTACAC
1 ATTTCAAATTCACATATCGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCCACAC
* * * * * * * * *
5283208 CTTAAATTGTTTTTATTTCTATGAGCACCATTGTTCCATAATCAAACAATAGGAATGCAATGTCA
66 CTCAAA-GGTTTTTATTTCTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACGTCA
** * * * *
5283273 AGCACTTCCAATATCAAATTTGCACCATTA-TACCTTCAATCAAATAATAGAAATACACCATATA
130 AGCACTTTAAATATCTAATTTGCACCTTTACT-CCTTCAATCAAATAATAGGAATGCACCATATA
5283337 CTAAG
194 CTAAG
* * * * * **
5283342 A-TTCAAATTCACGTA-CTGGCACCATTATATCTTATTGTATAATAGGAATACCAGATGTTCACA
1 ATTTCAAATTCACATATC-GGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCCACA
* * * * * * * * *
5283405 CATACAAAGTTTCTTTGTTTTTGTAAGCACCATTGTGCCGTTATTACAGAATAGGAATGCCTCAT
65 CCT-CAAAGGTT-TTTATTTCTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACGT
* * * * * *
5283470 CAAGCACTTTAAATATCTAGTTTGCTCCTTTACTCCCTCAATCAAAGAATAGGGATGCACCGTAT
128 CAAGCACTTTAAATATCTAATTTGCACCTTTACTCCTTCAATCAAATAATAGGAATGCACCATAT
*
5283535 ACTAAC
193 ACTAAG
* * * *
5283541 ATTTCAAAATTCACATATCGTG-ATCATTATACCTTAATGTATAATCGGAACGCCACATGCCCGC
1 ATTTC-AAATTCACATATCG-GCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCCAC
* *
5283605 ACCGTGAAAGGTTTTTATTTCTATAAGCACCATTGTGCCATTATTGCACAATAGGAATGCCGA-G
64 ACC-TCAAAGGTTTTTATTTCTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCC-ACG
* * *
5283669 TCAAGTACTTTAAATATCTAATTTGCACCTTTACTTCTTCGATCAAATAATAGGAATGCACCATA
127 TCAAGCACTTTAAATATCTAATTTGCACCTTTACTCCTTCAATCAAATAATAGGAATGCACCATA
5283734 TACTAAG
192 TACTAAG
** * * **
5283741 AGGTCAAATTCACGTA-CTGGCACCATTATATCTTAATGTATAATAGGAATGCCACATGTTCACA
1 ATTTCAAATTCACATATC-GGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCCACA
* * * * * ** * * * *
5283805 CATACAAAGTTTCTTTGTTTTTGTAAGCACCATCATGTCGTTATTACACAATAGGAATGCCTCAT
65 CCT-CAAAGGTT-TTTATTTCTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACGT
* * * * * *
5283870 CAAGCACTTTAAATATCTAGTTTGCACTTTTACTCCCTCAATCAAATAATAGGGATGCATCGTAT
128 CAAGCACTTTAAATATCTAATTTGCACCTTTACTCCTTCAATCAAATAATAGGAATGCACCATAT
*
5283935 ACTAAC
193 ACTAAG
* * * * * *
5283941 ATTTCAAATTCACATGTTGGCATCATTATACCTTAATGTATAATCGGAACGCCACATGCCCGCAC
1 ATTTCAAATTCACATATCGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCCACAC
* *
5284006 CGTGAAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTGCACAATAGGAATGCCACGTC
66 C-TCAAAGG-TTTTTATTTCTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACGTC
* * * * * * * *
5284071 AAGTACTTTCAATATCTAATTTTCACCTTTACACCTTCCATCAAATAATAGGAATCCACAATATG
129 AAGCACTTTAAATATCTAATTTGCACCTTTACTCCTTCAATCAAATAATAGGAATGCACCATATA
*
5284136 CT-CG
194 CTAAG
* * * * * * *
5284140 AATTTCAAATTCATACATTGGCACCATCATACCGTAATGTATGATAGGAATGCCACATGCTCACA
1 -ATTTCAAATTCACATATCGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCCACA
* * * ** * *
5284205 TACTTAAA-GTTTTTATGTTTCTGTAAGCACCATTGTTTCAATATTACACAATTGGAATGCCACG
65 -CCTCAAAGGTTTTTA--TTTCTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACG
* ** * *
5284269 TCAAGCACTTTAAATATCGAATTTGCACCTTTACTTGTTCAATCGAATAATAGGAATGCATCATA
127 TCAAGCACTTTAAATATCTAATTTGCACCTTTACTCCTTCAATCAAATAATAGGAATGCACCATA
5284334 TACTAAG
192 TACTAAG
* ** *
5284341 ATTTCATATTCACATATAAGCACCATTATACCTTAATGCATAATAGGAATGCCACATGCCCACAC
1 ATTTCAAATTCACATATCGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCCACAC
* * *
5284406 CT-TAAGGTTTTATTATTTTTATAAGTACCATTGTGCCATTATTACACAATAGGAATGCCACGTC
66 CTCAAAGG-TTT-TTATTTCTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACGTC
* * * * * * * * * * *
5284470 AAGTATTTTAAATATCTAATTTGCATCATCACACGTTCGATCAATTAATAGGAATGCATCATATG
129 AAGCACTTTAAATATCTAATTTGCACCTTTACTCCTTCAATCAAATAATAGGAATGCACCATATA
5284535 CTAAG
194 CTAAG
* * ** * * * **
5284540 ATTTTATATTCACATATAAGCACCATTATAACTTAGTGTATAATAGGAATGCCACTTTTCCACAC
1 ATTTCAAATTCACATATCGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCCACAC
** * * ***
5284605 GACAAAGTTTTATTTTTTCTATAAGCACCACCATGCCATTATTACACAATAGGA
66 CTCAAAGGTTT-TTATTTCTATAAGCACCATTGTGCCATTATTACACAATAGGA
5284659 GTGTCAAGTC
Statistics
Matches: 1377, Mismatches: 303, Indels: 96
0.78 0.17 0.05
Matches are distributed among these distances:
197 3 0.00
198 72 0.05
199 495 0.36
200 581 0.42
201 59 0.04
202 4 0.00
205 3 0.00
206 2 0.00
209 2 0.00
211 1 0.00
212 147 0.11
213 4 0.00
214 4 0.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (198 bp):
ATTTCAAATTCACATATCGGCACCATTATACCTTAATGTATAATAGGAATGCCACATGCCCACAC
CTCAAAGGTTTTTATTTCTATAAGCACCATTGTGCCATTATTACACAATAGGAATGCCACGTCAA
GCACTTTAAATATCTAATTTGCACCTTTACTCCTTCAATCAAATAATAGGAATGCACCATATACT
AAG
Found at i:5283887 original size:400 final size:397
Alignment explanation
Indices: 5282711--5284658 Score: 1910
Period size: 400 Copynumber: 4.8 Consensus size: 397
5282701 AGAAAGCAAG
* * * * *
5282711 GGGAGTGCACCGTATGCTGAA-ATTTCAAATTCACATATTGGCACCATTATAACTTATTGTATTA
1 GGGA-TGCACCGTATACT-AACATTTCAAATTCACATATTGGCATCATTATACCTTAATGTATAA
* * * * * * *
5282775 TAGAAATGCCATATGGCCGCACCTTAAAGGTTTTTTATTTCCATAGGCACCATCGTGCCATTATT
64 TAGGAATGCCACATGCCCGCACCTGAAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATT
5282840 GCACAATAGGAATGCCGA-GTCAAGTACTTTAAATATCTAATTTGCACCATTTTACCTTCGATCA
129 GCACAATAGGAATGCC-ACGTCAAGTACTTTAAATATCTAATTTGCACC--TTTACCTTCGATCA
* * ** * * * * * *
5282904 AACAATATGAATGTGCCATATGCTCAGATTTCAAGTTCATATATTGGTACCATTATACCGTAATG
191 AATAATAGGAATGCACCATATGCTAAGATTTCAAATTCACATACTGGCACCATTATACCTTAATG
* **** * * * * * *
5282969 TATAATAGGAACGCCACAAACCCAAACCT-TAAAGTTTCTTCATGTCTATG--AGCACAATTGTG
256 TATAATAGGAATGCCACATGTTCACACATACAAAGTTTCTT--TGTTTTTGTAAGCACCATTGTG
* * * * * * * * *
5283031 TCATAAGTACACAATAGGAATGCCAT-GTCAAGTA-TTCGAAATATCTAATTTACTCCATGA-TA
319 TCATTATTACACAATAGGAATGCC-TCATCAAGCACTT-TAAATATCTAATTTGCACCTTTACT-
* **
5283093 CCTTTTATC-AAGTAATA
381 CCCTCAATCAAAG-AATA
** * *
5283110 GGAACAGACCATATACCAAGATTTCNTACTAAGATTTCAAATTCACATATTGGCATCATTATACC
1 GG----G---ATGCACC--G---T-ATACTAACATTTCAAATTCACATATTGGCATCATTATACC
* ** * * *
5283175 TTAATTTATAATAGGAATGCCACATGCCTACACCTTAAA-TTGTTTTTATTTCTATGAGCACCAT
53 TTAATGTATAATAGGAATGCCACATGCCCGCACCTGAAAGGT-TTTTTATTTCTATAAGCACCAT
* * *** * * * ** *
5283239 TGTTCCATAATCAAACAATAGGAATGCAATGTCAAGCACTTCCAATATCAAATTTGCACCATTAT
117 TGTGCCATTATTGCACAATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACC-TT-T
* * * * *
5283304 ACCTTCAATCAAATAATAGAAATACACCATATACTAAGA-TTCAAATTCACGTACTGGCACCATT
180 ACCTTCGATCAAATAATAGGAATGCACCATATGCTAAGATTTCAAATTCACATACTGGCACCATT
* * * *
5283368 ATATCTTATTGTATAATAGGAATACCAGATGTTCACACATACAAAGTTTCTTTGTTTTTGTAAGC
245 ATACCTTAATGTATAATAGGAATGCCACATGTTCACACATACAAAGTTTCTTTGTTTTTGTAAGC
* * * * *
5283433 ACCATTGTGCCGTTATTACAGAATAGGAATGCCTCATCAAGCACTTTAAATATCTAGTTTGCTCC
310 ACCATTGTGTCATTATTACACAATAGGAATGCCTCATCAAGCACTTTAAATATCTAATTTGCACC
5283498 TTTACTCCCTCAATCAAAGAATA
375 TTTACTCCCTCAATCAAAGAATA
*
5283521 GGGATGCACCGTATACTAACATTTCAAAATTCACATATCGTG-ATCATTATACCTTAATGTATAA
1 GGGATGCACCGTATACTAACATTTC-AAATTCACATATTG-GCATCATTATACCTTAATGTATAA
* *
5283585 TCGGAACGCCACATGCCCGCACCGTGAAAGG-TTTTTATTTCTATAAGCACCATTGTGCCATTAT
64 TAGGAATGCCACATGCCCGCACC-TGAAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTAT
5283649 TGCACAATAGGAATGCCGA-GTCAAGTACTTTAAATATCTAATTTGCACCTTTACTTCTTCGATC
128 TGCACAATAGGAATGCC-ACGTCAAGTACTTTAAATATCTAATTTGCACCTTTAC--CTTCGATC
* ** * *
5283713 AAATAATAGGAATGCACCATATACTAAGAGGTCAAATTCACGTACTGGCACCATTATATCTTAAT
190 AAATAATAGGAATGCACCATATGCTAAGATTTCAAATTCACATACTGGCACCATTATACCTTAAT
**
5283778 GTATAATAGGAATGCCACATGTTCACACATACAAAGTTTCTTTGTTTTTGTAAGCACCATCATGT
255 GTATAATAGGAATGCCACATGTTCACACATACAAAGTTTCTTTGTTTTTGTAAGCACCATTGTGT
* * *
5283843 CGTTATTACACAATAGGAATGCCTCATCAAGCACTTTAAATATCTAGTTTGCACTTTTACTCCCT
320 CATTATTACACAATAGGAATGCCTCATCAAGCACTTTAAATATCTAATTTGCACCTTTACTCCCT
*
5283908 CAATCAAATAATA
385 CAATCAAAGAATA
* * *
5283921 GGGATGCATCGTATACTAACATTTCAAATTCACATGTTGGCATCATTATACCTTAATGTATAATC
1 GGGATGCACCGTATACTAACATTTCAAATTCACATATTGGCATCATTATACCTTAATGTATAATA
*
5283986 GGAACGCCACATGCCCGCACCGTGAAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTG
66 GGAATGCCACATGCCCGCACC-TGAAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTG
* * *
5284051 CACAATAGGAATGCCACGTCAAGTACTTTCAATATCTAATTTTCACCTTTACACCTTCCATCAAA
130 CACAATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCTTT--ACCTTCGATCAAA
* * * * * * * *
5284116 TAATAGGAATCCACAATATGCT-CGAATTTCAAATTCATACATTGGCACCATCATACCGTAATGT
193 TAATAGGAATGCACCATATGCTAAG-ATTTCAAATTCACATACTGGCACCATTATACCTTAATGT
* * * *
5284180 ATGATAGGAATGCCACATG--CTCACATACTTAAAGTTT-TTATGTTTCTGTAAGCACCATTGTT
257 ATAATAGGAATGCCACATGTTCACACATAC--AAAGTTTCTT-TGTTTTTGTAAGCACCATTGTG
* * * * * ***
5284242 TCAATATTACACAATTGGAATGCCACGTCAAGCACTTTAAATATCGAATTTGCACCTTTACTTGT
319 TCATTATTACACAATAGGAATGCCTCATCAAGCACTTTAAATATCTAATTTGCACCTTTACTCCC
* *
5284307 TCAATCGAATAATA
384 TCAATCAAAGAATA
* * * * * ** * *
5284321 GGAATGCATCATATACTAAGATTTCATATTCACATATAAGCACCATTATACCTTAATGCATAATA
1 GGGATGCACCGTATACTAACATTTCAAATTCACATATTGGCATCATTATACCTTAATGTATAATA
* * * * *
5284386 GGAATGCCACATGCCCACACCT-TAAGGTTTTATTATTTTTATAAGTACCATTGTGCCATTATTA
66 GGAATGCCACATGCCCGCACCTGAAAGGTTTT-TTATTTCTATAAGCACCATTGTGCCATTATTG
* * * * *
5284450 CACAATAGGAATGCCACGTCAAGTATTTTAAATATCTAATTTGCATCATCACACGTTCGATCAAT
130 CACAATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCTTTAC-C-TTCGATCAAA
* * * * * *
5284515 TAATAGGAATGCATCATATGCTAAGATTTTATATTCACATA-TAAGCACCATTATAACTTAGTGT
193 TAATAGGAATGCACCATATGCTAAGATTTCAAATTCACATACT-GGCACCATTATACCTTAATGT
* * * ***
5284579 ATAATAGGAATGCCAC-TTTTC-CACACGACAAAGTTT-TATT-TTTTCTATAAGCACCACCATG
257 ATAATAGGAATGCCACATGTTCACACA-TACAAAGTTTCT-TTGTTTT-TGTAAGCACCATTGTG
*
5284640 CCATTATTACACAATAGGA
319 TCATTATTACACAATAGGA
5284659 GTGTCAAGTC
Statistics
Matches: 1300, Mismatches: 198, Indels: 103
0.81 0.12 0.06
Matches are distributed among these distances:
397 8 0.01
398 69 0.05
399 377 0.29
400 525 0.40
402 3 0.00
403 1 0.00
404 5 0.00
405 4 0.00
406 1 0.00
407 2 0.00
409 6 0.00
410 56 0.04
411 237 0.18
412 6 0.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (397 bp):
GGGATGCACCGTATACTAACATTTCAAATTCACATATTGGCATCATTATACCTTAATGTATAATA
GGAATGCCACATGCCCGCACCTGAAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTGC
ACAATAGGAATGCCACGTCAAGTACTTTAAATATCTAATTTGCACCTTTACCTTCGATCAAATAA
TAGGAATGCACCATATGCTAAGATTTCAAATTCACATACTGGCACCATTATACCTTAATGTATAA
TAGGAATGCCACATGTTCACACATACAAAGTTTCTTTGTTTTTGTAAGCACCATTGTGTCATTAT
TACACAATAGGAATGCCTCATCAAGCACTTTAAATATCTAATTTGCACCTTTACTCCCTCAATCA
AAGAATA
Found at i:5286890 original size:197 final size:197
Alignment explanation
Indices: 5286369--5287422 Score: 1064
Period size: 197 Copynumber: 5.3 Consensus size: 197
5286359 GAGTGCACTG
* * * *
5286369 TATACTGAGATCTCAAATTCACATATTGGCACCATTATACTTTAATGTATAATAGGAATACCACA
1 TATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACA
* * * * * * *
5286434 TGCCCTCACCTTAAAGGTTTTTTATTTCTATAGGCACCATCGTGCCATTACTGCACAATAAGAAT
66 TGCCCACACCTTAAAGG-TTTTTATTTCTATAAGCACCATTGTGCCATAATTACACAATAGGAAT
* * * * *
5286499 GCCAGGTCAAGTACTTTAAATATCTAATTTGCACCATTTTACCTTCGATCAAACCATATGAATGC
130 GCCATGTCAAGCACTTTAAATATCTAATTTGCACCATTATACCTT-GATCAAACAATAGGAATGC
*
5286564 GCCA
194 ACCA
* ** * * * ** *
5286568 TATGCTCGGATTTCAAATTCATATATTGGCACCATTATATCATAATGTATAATAGGAACACCACG
1 TATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACA
* * * * ** *
5286633 TACCCAAACCTTAAA-GTTTCTTCATGTCTGTGGGCACCATTGTGCCAGAATTACACAATAGGAA
66 TGCCCACACCTTAAAGGTTT-TT-ATTTCTATAAGCACCATTGTGCCATAATTACACAATAGGAA
* * * * * * *
5286697 TGCCATGTCAAGTA-TTCGAAATATCTAATTTACTCCATGATACCTTGATCAAGCAATAGGAACG
129 TGCCATGTCAAGCACTT-TAAATATCTAATTTGCACCATTATACCTTGATCAAACAATAGGAATG
5286761 CACCA
193 CACCA
* * * *
5286766 TATACTAAGATTTTAAATTCACATATTAGCACCATTATACCGTAA-GTATAATAGGAATGCCATA
1 TATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACA
* * * * *
5286830 TGCCCACACCTTAAATTGTTTTTATTTCTATGAGCACCATTGTTCCATAATCAAACAATAGGAAT
66 TGCCCACACCTTAAA-GGTTTTTATTTCTATAAGCACCATTGTGCCATAATTACACAATAGGAAT
* * ** * *
5286895 GCAATGTCAAGCACTTTAAATATCGAATTTGCACCATTATACCTCCAATCAAATAAAAGGAATGC
130 GCCATGTCAAGCACTTTAAATATCTAATTTGCACCATTATACCT-TGATCAAACAATAGGAATGC
5286960 ACCA
194 ACCA
**
5286964 TATACTAAGATTTCAAATTCACATATTGGTTCCATTATACCTTAATGTATAATAGGAATGCCACA
1 TATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACA
** * * * * * * * * *
5287029 TGGTCACACATACAAAGTTTCTTTGTTTTTGTAAGCACCATTGTGCCGTTATTACACAATACGAA
66 TGCCCACACCT-TAAAGGTT-TTTATTTCTATAAGCACCATTGTGCCATAATTACACAATAGGAA
* * * *
5287094 TGCC-TCATCAAGCACTTTAAATATCTAGTTTGCACC-TT-TACTCCT-ATCAAATAATAGGAAT
129 TGCCAT-GTCAAGCACTTTAAATATCTAATTTGCACCATTATAC-CTTGATCAAACAATAGGAAT
*
5287155 GCACCG
192 GCACCA
* * *
5287161 TACACTAACATTTCAAATTCACATATTGGCACCATTATATCTTAATGTATAATAGGAATGCCACA
1 TATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACA
* * * *
5287226 TGCCCGCACCTTGAAAGGTTTTTTATTTCTATAAGCATCATTGTGCCATTATTGCACAATAGGAA
66 TGCCCACACCTT-AAAGG-TTTTTATTTCTATAAGCACCATTGTGCCATAATTACACAATAGGAA
** * * *
5287291 TGCCCCGTCAAG-ATCTTTAAATATCTAATTTGCACCTTTACACCTTCCATCAAATC-ATAGGAA
129 TGCCATGTCAAGCA-CTTTAAATATCTAATTTGCACCATTATACCTT-GATCAAA-CAATAGGAA
*
5287354 TCCACCA
191 TGCACCA
* * * * * * *
5287361 CATACCAAGATTTCATATGCACATATAGGCACCATTATACCCTATTGTATAATAGGAATGCC
1 TATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCC
5287423 GTATACCAAC
Statistics
Matches: 701, Mismatches: 133, Indels: 41
0.80 0.15 0.05
Matches are distributed among these distances:
196 1 0.00
197 258 0.37
198 131 0.19
199 174 0.25
200 137 0.20
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (197 bp):
TATACTAAGATTTCAAATTCACATATTGGCACCATTATACCTTAATGTATAATAGGAATGCCACA
TGCCCACACCTTAAAGGTTTTTATTTCTATAAGCACCATTGTGCCATAATTACACAATAGGAATG
CCATGTCAAGCACTTTAAATATCTAATTTGCACCATTATACCTTGATCAAACAATAGGAATGCAC
CA
Found at i:5287314 original size:397 final size:395
Alignment explanation
Indices: 5286381--5287422 Score: 1159
Period size: 397 Copynumber: 2.6 Consensus size: 395
5286371 TACTGAGATC
* *
5286381 TCAAATTCACATATTGGCACCATTATACTTTAATGTATAATAGGAATACCACATGCCCTCACCTT
1 TCAAATTCACATATTGGCACCATTATAC-TTAATGTATAATAGGAATGCCACATGCCCACACCTT
* * * * *
5286446 AAAGGTTTTTTATTTCTATAGGCACCATCGTGCCATTACTGCACAATAAGAATGCCAGGTCAAG-
65 AAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTGCACAATAGGAATGCCACGTCAAGA
* * * * * * *
5286510 TACTTTAAATATCTAATTTGCACCATTTTACCTTCGATCAAACCATATGAATGCGCCATATGCTC
130 T-CTTTAAATATCTAATTTGCACCATTATACC-TCCATCAAATCATAGGAATGCACCATATACTA
* * * ** *
5286575 GGATTTCAAATTCATATATTGGCACCATTATATCATAATGTATAATAGGAACACCACGTACCCAA
193 AGATTTCAAATTCACATATTGGCACCATTATACCATAATGTATAATAGGAATGCCACATACCCAA
* * ** * *
5286640 ACCTTAAAGTTTCTTCATGTCTGTGGGCACCATTGTGCCAGAATTACACAATAGGAATGCCATGT
258 ACATCAAAGTTTCTTCATGTCTGTAAGCACCATTGTGCCAGAATTACACAATACGAATGCCATAT
* * * * *
5286705 CAAGTATTCGAAATATCTAATTTACTCCATGATACCTTGATCAAGCAATAGGAACGCACCATATA
323 CAAGCATTCGAAATATCTAATTTACACCATGATACCCTGATCAAACAATAGGAACGCACCATACA
*
5286770 CTAAGATT
388 CTAACATT
* * * *
5286778 TTAAATTCACATATTAGCACCATTATACCGTAA-GTATAATAGGAATGCCATATGCCCACACCTT
1 TCAAATTCACATATTGGCACCATTATA-CTTAATGTATAATAGGAATGCCACATGCCCACACCTT
* * * * *** * *
5286842 AAA-TTGTTTTTATTTCTATGAGCACCATTGTTCCATAATCAAACAATAGGAATGCAATGTCAAG
65 AAAGGT-TTTTTATTTCTATAAGCACCATTGTGCCATTATTGCACAATAGGAATGCCACGTCAAG
* * *
5286906 CA-CTTTAAATATCGAATTTGCACCATTATACCTCCAATCAAATAAAAGGAATGCACCATATACT
129 -ATCTTTAAATATCTAATTTGCACCATTATACCTCC-ATCAAATCATAGGAATGCACCATATACT
** * ***
5286970 AAGATTTCAAATTCACATATTGGTTCCATTATACCTTAATGTATAATAGGAATGCCACATGGTCA
192 AAGATTTCAAATTCACATATTGGCACCATTATACCATAATGTATAATAGGAATGCCACATACCCA
* ** * * *
5287035 CACATACAAAGTTTCTTTGTTTTTGTAAGCACCATTGTGCC-GTTATTACACAATACGAATGCC-
257 AACAT-CAAAGTTTCTTCATGTCTGTAAGCACCATTGTGCCAG-AATTACACAATACGAATGCCA
* * * * * *
5287098 TCATCAAGCACTT-TAAATATCTAGTTTGCACC-T-TTACTCCT-ATCAAATAATAGGAATGCAC
320 T-ATCAAGCA-TTCGAAATATCTAATTTACACCATGATAC-CCTGATCAAACAATAGGAACGCAC
*
5287159 CGTACACTAACATT
382 CATACACTAACATT
*
5287173 TCAAATTCACATATTGGCACCATTATATCTTAATGTATAATAGGAATGCCACATGCCCGCACCTT
1 TCAAATTCACATATTGGCACCATTATA-CTTAATGTATAATAGGAATGCCACATGCCCACACCTT
* *
5287238 GAAAGGTTTTTTATTTCTATAAGCATCATTGTGCCATTATTGCACAATAGGAATGCCCCGTCAAG
65 -AAAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTGCACAATAGGAATGCCACGTCAAG
* * * * *
5287303 ATCTTTAAATATCTAATTTGCACCTTTACACCTTCCATCAAATCATAGGAATCCACCACATACCA
129 ATCTTTAAATATCTAATTTGCACCATTATACC-TCCATCAAATCATAGGAATGCACCATATACTA
* * * * *
5287368 AGATTTCATATGCACATATAGGCACCATTATACCCTATTGTATAATAGGAATGCC
193 AGATTTCAAATTCACATATTGGCACCATTATACCATAATGTATAATAGGAATGCC
5287423 GTATACCAAC
Statistics
Matches: 532, Mismatches: 98, Indels: 30
0.81 0.15 0.05
Matches are distributed among these distances:
395 63 0.12
396 217 0.41
397 245 0.46
398 7 0.01
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (395 bp):
TCAAATTCACATATTGGCACCATTATACTTAATGTATAATAGGAATGCCACATGCCCACACCTTA
AAGGTTTTTTATTTCTATAAGCACCATTGTGCCATTATTGCACAATAGGAATGCCACGTCAAGAT
CTTTAAATATCTAATTTGCACCATTATACCTCCATCAAATCATAGGAATGCACCATATACTAAGA
TTTCAAATTCACATATTGGCACCATTATACCATAATGTATAATAGGAATGCCACATACCCAAACA
TCAAAGTTTCTTCATGTCTGTAAGCACCATTGTGCCAGAATTACACAATACGAATGCCATATCAA
GCATTCGAAATATCTAATTTACACCATGATACCCTGATCAAACAATAGGAACGCACCATACACTA
ACATT
Found at i:5293814 original size:30 final size:29
Alignment explanation
Indices: 5293780--5293839 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
5293770 TTAGCTCTTT
* *
5293780 TATGAGATAAATTTGAAAAGAATATTATTA
1 TATGAGATAAATCTCAAAAGAATATT-TTA
* *
5293810 TATGAGATTAATCTCAAAAGGATATTTTA
1 TATGAGATAAATCTCAAAAGAATATTTTA
5293839 T
1 T
5293840 TGTTTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.38
Consensus pattern (29 bp):
TATGAGATAAATCTCAAAAGAATATTTTA
Found at i:5298207 original size:4 final size:4
Alignment explanation
Indices: 5298190--5298322 Score: 149
Period size: 4 Copynumber: 33.2 Consensus size: 4
5298180 TGCACACCAC
* * * *
5298190 ATAT ATAT AAAT ATAT ATGT ATAT ATAT ATAT GTAT GTAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * *
5298238 GTAT GTAT ATAT ATAT ATGT ATGT ATAT ATAT ATGT ATGT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
5298286 ATGT ATGT ATAT ATAT ATGT ATAT ATAT ATAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
5298323 CACCACTAAA
Statistics
Matches: 113, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 113 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:5298214 original size:16 final size:16
Alignment explanation
Indices: 5298191--5298319 Score: 177
Period size: 16 Copynumber: 7.9 Consensus size: 16
5298181 GCACACCACA
* *
5298191 TATATATAAATATATA
1 TATATATATATATATG
*
5298207 TGTATATATATATATG
1 TATATATATATATATG
*
5298223 TATGTATATATATATG
1 TATATATATATATATG
5298239 TATGTATATATATATATG
1 TA--TATATATATATATG
*
5298257 TATGTATATATATATG
1 TATATATATATATATG
*
5298273 TATGTATATATATATG
1 TATATATATATATATG
*
5298289 TATGTATATATATATG
1 TATATATATATATATG
5298305 TATATATATATATAT
1 TATATATATATATAT
5298320 ATACACCACT
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
16 88 0.85
18 15 0.15
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
TATATATATATATATG
Found at i:5298231 original size:34 final size:34
Alignment explanation
Indices: 5298193--5298321 Score: 217
Period size: 34 Copynumber: 3.9 Consensus size: 34
5298183 ACACCACATA
* *
5298193 TATATAAATATATATGTATATATATATATGTATG
1 TATATATATATGTATGTATATATATATATGTATG
5298227 TATATATATATGTATGTATATATATATATGTATG
1 TATATATATATGTATGTATATATATATATGTATG
5298261 TATATATATATGTATG--TATATATATATGTATG
1 TATATATATATGTATGTATATATATATATGTATG
*
5298293 TATATATATATGTATATATATATATATAT
1 TATATATATATGTATGTATATATATATAT
5298322 ACACCACTAA
Statistics
Matches: 90, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
32 31 0.34
34 59 0.66
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (34 bp):
TATATATATATGTATGTATATATATATATGTATG
Found at i:5299179 original size:20 final size:20
Alignment explanation
Indices: 5299156--5299193 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5299146 AGAAAAAAGT
*
5299156 TGCTGGAAGCTTGAAGAAAC
1 TGCTGGAAACTTGAAGAAAC
*
5299176 TGCTGGAAATTTGAAGAA
1 TGCTGGAAACTTGAAGAA
5299194 GTCACTAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
TGCTGGAAACTTGAAGAAAC
Found at i:5304248 original size:11 final size:11
Alignment explanation
Indices: 5304232--5304256 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5304222 TAACAGATGC
5304232 TAATTAAGGTT
1 TAATTAAGGTT
5304243 TAATTAAGGTT
1 TAATTAAGGTT
5304254 TAA
1 TAA
5304257 CAGATACTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (11 bp):
TAATTAAGGTT
Found at i:5310387 original size:19 final size:19
Alignment explanation
Indices: 5310363--5310401 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5310353 AAAGACAAAA
5310363 CATAGTTCATTGTTTTGCT
1 CATAGTTCATTGTTTTGCT
5310382 CATAGTTCATTGTTTTGCT
1 CATAGTTCATTGTTTTGCT
5310401 C
1 C
5310402 TTTTAAAATA
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:0.15, C:0.18, G:0.15, T:0.51
Consensus pattern (19 bp):
CATAGTTCATTGTTTTGCT
Found at i:5315628 original size:17 final size:18
Alignment explanation
Indices: 5315606--5315640 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5315596 TAGGCATGTG
*
5315606 TTCTTATTTCTT-TTATT
1 TTCTTATTGCTTGTTATT
5315623 TTCTTATTGCTTGTTATT
1 TTCTTATTGCTTGTTATT
5315641 ATCCTCTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.71
Consensus pattern (18 bp):
TTCTTATTGCTTGTTATT
Found at i:5318041 original size:53 final size:54
Alignment explanation
Indices: 5317984--5318112 Score: 122
Period size: 53 Copynumber: 2.4 Consensus size: 54
5317974 AATTTTGTTA
* * *
5317984 GAAATTTTCAACAGAATTTCCTTTGGAAAAGCATTTCCGATG-AA-ATTTCATTG
1 GAAATTTTCAACAGAATTTCCATTGG-AAAGCATTTCCAACGAAATATTTCATTG
* * *
5318037 GAAA-TTTCTTAC-GAAATTTCCATTGGAAAGCATTTGCAACGAAATATTTCGTTG
1 GAAATTTTC-AACAG-AATTTCCATTGGAAAGCATTTCCAACGAAATATTTCATTG
* *
5318091 GTAATTTCCAACAGAATGTTCC
1 GAAATTTTCAACAGAAT-TTCC
5318113 GTCGATAATG
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
52 17 0.28
53 19 0.32
54 16 0.27
55 8 0.13
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (54 bp):
GAAATTTTCAACAGAATTTCCATTGGAAAGCATTTCCAACGAAATATTTCATTG
Found at i:5318079 original size:28 final size:27
Alignment explanation
Indices: 5317989--5318081 Score: 70
Period size: 28 Copynumber: 3.4 Consensus size: 27
5317979 TGTTAGAAAT
*
5317989 TTTCAAC-AGAATTTCCTTTGGAAAAGCA
1 TTTCAACGA-AATTTCCATTGG-AAAGCA
* *
5318017 TTTCCGATGAAATTT-CATTGG-AA--A
1 TTT-CAACGAAATTTCCATTGGAAAGCA
*
5318041 TTTCTTACGAAATTTCCATTGGAAAGCA
1 TTTC-AACGAAATTTCCATTGGAAAGCA
5318069 TTTGCAACGAAAT
1 TTT-CAACGAAAT
5318082 ATTTCGTTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
23 1 0.02
24 12 0.24
25 6 0.12
26 4 0.08
28 19 0.37
29 8 0.16
30 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (27 bp):
TTTCAACGAAATTTCCATTGGAAAGCA
Found at i:5320755 original size:10 final size:10
Alignment explanation
Indices: 5320716--5320785 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
5320706 AATATCTTTA
5320716 AATATTCATAT
1 AATATT-ATAT
* *
5320727 TATATTATAC
1 AATATTATAT
* *
5320737 ATTAATATAT
1 AATATTATAT
5320747 AATATTATAT
1 AATATTATAT
* *
5320757 AATATTGTAA
1 AATATTATAT
5320767 AATATTA-AT
1 AATATTATAT
*
5320776 TAT-TTATAT
1 AATATTATAT
5320785 A
1 A
5320786 TCAATAAATA
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
8 3 0.07
9 5 0.11
10 31 0.70
11 5 0.11
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (10 bp):
AATATTATAT
Found at i:5322212 original size:29 final size:29
Alignment explanation
Indices: 5322177--5322235 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
5322167 ATCGACTATA
5322177 ACCTCTGTCAAAAGTAATAGACCTATATG
1 ACCTCTGTCAAAAGTAATAGACCTATATG
5322206 ACCTCTGTCAAAAGTAATAGACCTATATG
1 ACCTCTGTCAAAAGTAATAGACCTATATG
5322235 A
1 A
5322236 GTTGTAGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (29 bp):
ACCTCTGTCAAAAGTAATAGACCTATATG
Found at i:5329096 original size:16 final size:16
Alignment explanation
Indices: 5329075--5329106 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5329065 TGTTACACAC
5329075 AGAAAATAAAATGAAA
1 AGAAAATAAAATGAAA
*
5329091 AGAAAATAAGATGAAA
1 AGAAAATAAAATGAAA
5329107 CCAGATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (16 bp):
AGAAAATAAAATGAAA
Found at i:5329513 original size:27 final size:27
Alignment explanation
Indices: 5329477--5329584 Score: 180
Period size: 27 Copynumber: 4.0 Consensus size: 27
5329467 ATGACATTGT
5329477 TTTTTGTACTCTTTCCTTCTTTCTCTG
1 TTTTTGTACTCTTTCCTTCTTTCTCTG
* *
5329504 TTTTTGTACTCTTTCCTCCTTTCCCTG
1 TTTTTGTACTCTTTCCTTCTTTCTCTG
* *
5329531 TTTTTGCACTCTTTTCTTCTTTCTCTG
1 TTTTTGTACTCTTTCCTTCTTTCTCTG
5329558 TTTTTGTACTCTTTCCTTCTTTCTCTG
1 TTTTTGTACTCTTTCCTTCTTTCTCTG
5329585 ATGCTATTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.04, C:0.28, G:0.07, T:0.61
Consensus pattern (27 bp):
TTTTTGTACTCTTTCCTTCTTTCTCTG
Found at i:5336558 original size:13 final size:13
Alignment explanation
Indices: 5336540--5336564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5336530 TTCTAGAAAA
5336540 TTTATAAAATCAT
1 TTTATAAAATCAT
5336553 TTTATAAAATCA
1 TTTATAAAATCA
5336565 CAATTTCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:5340818 original size:28 final size:29
Alignment explanation
Indices: 5340787--5340841 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
5340777 ATTTTAAAAA
*
5340787 ATTTAAATAATTTTTTAT-TTTTTATTAC
1 ATTTAAATAAATTTTTATATTTTTATTAC
*
5340815 ATTTAATTAAATTTTTATATTTTTATT
1 ATTTAAATAAATTTTTATATTTTTATT
5340842 TTGAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (29 bp):
ATTTAAATAAATTTTTATATTTTTATTAC
Found at i:5340860 original size:30 final size:29
Alignment explanation
Indices: 5340789--5340863 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 29
5340779 TTTAAAAAAT
* *
5340789 TTAAATAATTTTTTAT-TTTTTATTACAT
1 TTAAATAAATTTTTATATTTTTATTACAA
* **
5340817 TTAATTAAATTTTTATATTTTTATTTTGAA
1 TTAAATAAATTTTTATATTTTTA-TTACAA
*
5340847 TTAAATAAGTTTTTATA
1 TTAAATAAATTTTTATA
5340864 ATTCATAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 14 0.37
29 6 0.16
30 18 0.47
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (29 bp):
TTAAATAAATTTTTATATTTTTATTACAA
Found at i:5354265 original size:3 final size:3
Alignment explanation
Indices: 5354257--5354293 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5354247 TTCTTCCTGC
5354257 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T-G TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
5354294 TTCTATCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:5371816 original size:120 final size:116
Alignment explanation
Indices: 5371575--5371958 Score: 417
Period size: 120 Copynumber: 3.3 Consensus size: 116
5371565 ATATTGATGT
* * * *
5371575 TTTATTTATAAT-CTAATAATT-AACATTATAAAATACTAATATTTTATTTATAATTTAAATGT-
1 TTTATTTAAAATATTAATAATTGATCATT-T-AAATATTAATATTTTATTTATAATTTAAAT-TA
* ** * * *
5371637 TATTATGATTGTTTATTTTTAAATTAA-TTTATTTTTAAACATTAATAATGTATAA
63 TATTATGATTATTTATGATT-ATTTAATTTTATTTTTAAATATTAATAATTTAT-A
* *
5371692 TTTATTTAAAATATTAAAAATTGAT-AGTTTAAATATTAATATTTTATTTATACTTTAATCATTA
1 TTTATTTAAAATATTAATAATTGATCA-TTTAAATATTAATATTTTATTTATAATTTAA--ATT-
*
5371756 ATATTAAATG-TTA-TTATGATTATTTATTTTTATTTTTAAATATTAATAATTTATA
62 ATATT--ATGATTATTTATGATTATTTAATTTTATTTTTAAATATTAATAATTTATA
* * *
5371811 TTTTATTTATAATATTAATAATTTATCATTTAAATATTAATATTTTATTTATAATTTAAATTTTA
1 -TTTATTTAAAATATTAATAATTGATCATTTAAATATTAATATTTTATTTATAATTTAAATTATA
**
5371876 TTATGATTATTTATTTTTATTTAATTTTATCTTTTAAATATTAATAATTTATA
65 TTATGATTATTTATGATTATTTAATTTTAT-TTTTAAATATTAATAATTTATA
*
5371929 TTT-TTT-AAATATTAATAATTGATTATTTAA
1 TTTATTTAAAATATTAATAATTGATCATTTAA
5371959 GTNNNNNNNN
Statistics
Matches: 228, Mismatches: 24, Indels: 32
0.80 0.08 0.11
Matches are distributed among these distances:
115 24 0.11
116 6 0.03
117 61 0.27
118 35 0.15
119 10 0.04
120 86 0.38
121 3 0.01
122 3 0.01
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (116 bp):
TTTATTTAAAATATTAATAATTGATCATTTAAATATTAATATTTTATTTATAATTTAAATTATAT
TATGATTATTTATGATTATTTAATTTTATTTTTAAATATTAATAATTTATA
Found at i:5371841 original size:28 final size:28
Alignment explanation
Indices: 5371777--5371948 Score: 108
Period size: 27 Copynumber: 6.1 Consensus size: 28
5371767 TATTATGATT
*
5371777 ATTTAT-TTTTATTTTTAAATATTAATA
1 ATTTATATTTTATTTATAAATATTAATA
5371804 ATTTATATTTTATTTAT-AATATTAATA
1 ATTTATATTTTATTTATAAATATTAATA
* ** *
5371831 ATTTATCATTTAAATATTAATATTTTATTTATA
1 ATTTAT-ATTT---TATTTATA-AATATTAATA
* * * *
5371864 ATTTAAATTTTA-TTATGATTATTTAT-
1 ATTTATATTTTATTTATAAATATTAATA
* *
5371890 TTTTATTTAATTTTATCTTTTAAATATTAATA
1 ATTTA--T-ATTTTAT-TTATAAATATTAATA
5371922 ATTTATA--TT-TTT-TAAATATTAATA
1 ATTTATATTTTATTTATAAATATTAATA
5371946 ATT
1 ATT
5371949 GATTATTTAA
Statistics
Matches: 116, Mismatches: 16, Indels: 29
0.72 0.10 0.18
Matches are distributed among these distances:
24 15 0.13
25 2 0.02
26 5 0.04
27 32 0.28
28 16 0.14
29 9 0.08
30 1 0.01
31 16 0.14
32 8 0.07
33 12 0.10
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (28 bp):
ATTTATATTTTATTTATAAATATTAATA
Found at i:5371952 original size:69 final size:71
Alignment explanation
Indices: 5371788--5371957 Score: 190
Period size: 69 Copynumber: 2.4 Consensus size: 71
5371778 TTTATTTTTA
*
5371788 TTTTTAAATATTAATAATTTA-TATTTTATTTATAATATTAATAATTTATCATTTAAATATTAAT
1 TTTTTAAATATTAATAATTGATTA-TTTATTTATAATATTAAT-ATTTATCATTTAAATATTAAT
*
5371852 ATTTTATT
64 AATTTATT
* * * *
5371860 TATAATTTAAAT-TTTATTA-TGATTATTTATTT-TTAT-TTAAT-TTTATCTTTTAAATATTAA
1 T-T--TTTAAATATTAATAATTGATTATTTATTTATAATATTAATATTTATCATTTAAATATTAA
5371920 TAATTTATAT
63 TAATTTAT-T
5371930 TTTTTAAATATTAATAATTGATTATTTA
1 TTTTTAAATATTAATAATTGATTATTTA
5371958 AGTNNNNNNN
Statistics
Matches: 83, Mismatches: 8, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
67 7 0.08
68 5 0.06
69 36 0.43
70 2 0.02
71 5 0.06
72 4 0.05
73 10 0.12
74 7 0.08
75 7 0.08
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (71 bp):
TTTTTAAATATTAATAATTGATTATTTATTTATAATATTAATATTTATCATTTAAATATTAATAA
TTTATT
Found at i:5372678 original size:31 final size:31
Alignment explanation
Indices: 5372642--5372813 Score: 134
Period size: 31 Copynumber: 5.5 Consensus size: 31
5372632 TCTCCTAAAG
* *
5372642 GGTTTTTTAAATTGAATTAAATTGGTTTTAA
1 GGTTTTTTGAATTGAATTGAATTGGTTTTAA
* *
5372673 GGTTTTATGAATTAAATTGAATTGGTTTT-A
1 GGTTTTTTGAATTGAATTGAATTGGTTTTAA
* *
5372703 GAGTTTTGTGAATTGGATTGAATTGG-TTTAA
1 G-GTTTTTTGAATTGAATTGAATTGGTTTTAA
***
5372734 GGGTTTTTGTGAATTAGAA-TGAATCAATTTTGAA
1 -GGTTTTT-TGAATT-GAATTGAATTGGTTTT-AA
* ** * * *
5372768 GGTTTTGTGAATCAAATGGAATTAGTTTTTA
1 GGTTTTTTGAATTGAATTGAATTGGTTTTAA
5372799 GGTTTTTGTGAATTG
1 GGTTTTT-TGAATTG
5372814 GACCAAATCG
Statistics
Matches: 110, Mismatches: 22, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
30 5 0.05
31 61 0.55
32 31 0.28
33 11 0.10
34 2 0.02
ACGTcount: A:0.28, C:0.01, G:0.23, T:0.47
Consensus pattern (31 bp):
GGTTTTTTGAATTGAATTGAATTGGTTTTAA
Found at i:5372806 original size:32 final size:33
Alignment explanation
Indices: 5372735--5372811 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
5372725 TTGGTTTAAG
*
5372735 GGTTTTTGTGAATTAGAATGAATCAATTTTGAA
1 GGTTTTTGTGAATCAGAATGAATCAATTTTGAA
* * *
5372768 GG-TTTTGTGAATCA-AATGGAATTAGTTTT-TA
1 GGTTTTTGTGAATCAGAAT-GAATCAATTTTGAA
5372799 GGTTTTTGTGAAT
1 GGTTTTTGTGAAT
5372812 TGGACCAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
31 6 0.16
32 30 0.79
33 2 0.05
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.45
Consensus pattern (33 bp):
GGTTTTTGTGAATCAGAATGAATCAATTTTGAA
Found at i:5372977 original size:31 final size:31
Alignment explanation
Indices: 5372938--5373034 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
5372928 AATAGGATCA
* *
5372938 AATCGGTTTGATGGTTTTATGAACCAAATCG
1 AATCGGTTTGAAGGTTTTATGAATCAAATCG
* * *
5372969 AATTGGTTTGAAGGTTTTGTGAATCAAATTG
1 AATCGGTTTGAAGGTTTTATGAATCAAATCG
* * *
5373000 AATCGATCTGAGGGTTTTATGAATCAAATCG
1 AATCGGTTTGAAGGTTTTATGAATCAAATCG
5373031 AATC
1 AATC
5373035 ATATTAAGGT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (31 bp):
AATCGGTTTGAAGGTTTTATGAATCAAATCG
Found at i:5373054 original size:31 final size:30
Alignment explanation
Indices: 5372950--5373054 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 30
5372940 TCGGTTTGAT
* * * * *
5372950 GGTTTTATGAACCAAATCGAATTGGTTTGAA
1 GGTTTTGTGAATCAAATCGAATCGATCT-AA
* *
5372981 GGTTTTGTGAATCAAATTGAATCGATCTGAG
1 GGTTTTGTGAATCAAATCGAATCGATCT-AA
* *
5373012 GGTTTTATGAATCAAATCGAATC-ATATTAA
1 GGTTTTGTGAATCAAATCGAATCGAT-CTAA
5373042 GGTTTTTGTGAAT
1 GG-TTTTGTGAAT
5373055 TGAGCTAAAT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
30 5 0.08
31 55 0.92
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (30 bp):
GGTTTTGTGAATCAAATCGAATCGATCTAA
Found at i:5387968 original size:8 final size:8
Alignment explanation
Indices: 5387955--5387982 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5387945 ACAATGATTT
5387955 TTTTTTTG
1 TTTTTTTG
5387963 TTTTTTTG
1 TTTTTTTG
5387971 TTTTTTTG
1 TTTTTTTG
5387979 TTTT
1 TTTT
5387983 CTCTCTCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTTTG
Found at i:5389972 original size:26 final size:26
Alignment explanation
Indices: 5389918--5389972 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
5389908 ACTTGAATCT
* ***
5389918 TATTATTTGATAAGGTACTTTAACCC
1 TATTATTTGATAAAGTACCCGAACCC
*
5389944 TATTATTTGATAAAGTACCCGAACTC
1 TATTATTTGATAAAGTACCCGAACCC
5389970 TAT
1 TAT
5389973 AAATACTCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (26 bp):
TATTATTTGATAAAGTACCCGAACCC
Found at i:5391540 original size:156 final size:156
Alignment explanation
Indices: 5391321--5391635 Score: 479
Period size: 156 Copynumber: 2.0 Consensus size: 156
5391311 GTCCTAGAGA
*
5391321 TGGAGAAATATGGGAAGATGGTGCTGGCGTTGGAGATGATTCACTGGGAGATTCAGCAACAGGGG
1 TGGAGAAATATGGGAAGATGGTGCTGGCGTTGGAGATAATTCACTGGGAGATTCAGCAACAGGGG
* * * * *
5391386 AAGGGGATGTGGGAGCCAAAGCTGGCCCTGGAGATGATGCTTTGGGGGGTTTTGCAACAGGGCCA
66 AAGGAGATGTAGGAGCCAAAGCTGGACCTGGAGATGATGCTTTAGGAGGTTTTGCAACAGGGCCA
* *
5391451 TGATGCTTGGGAGAGTTTGCTGGCCC
131 TGATGCTTGGGAGACTGTGCTGGCCC
* * * * *
5391477 TGGATAAATGTGGGAAGATGGTGCTGGTGTTGGAGATAATTC-TTGGGGAGGTTCAGCAACAGGG
1 TGGAGAAATATGGGAAGATGGTGCTGGCGTTGGAGATAATTCACT-GGGAGATTCAGCAACAGGG
**
5391541 GTTGGAGATGTAGGAGCCAAAGCTGGACCTGGAGATGATGCTTTAGGAGGTTTTGCAACAGGGCC
65 GAAGGAGATGTAGGAGCCAAAGCTGGACCTGGAGATGATGCTTTAGGAGGTTTTGCAACAGGGCC
5391606 ATGATGCTTGGGAGACTGTGCTGGCCC
130 ATGATGCTTGGGAGACTGTGCTGGCCC
5391633 TGG
1 TGG
5391636 TGATGAATAT
Statistics
Matches: 143, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
155 1 0.01
156 142 0.99
ACGTcount: A:0.23, C:0.14, G:0.40, T:0.24
Consensus pattern (156 bp):
TGGAGAAATATGGGAAGATGGTGCTGGCGTTGGAGATAATTCACTGGGAGATTCAGCAACAGGGG
AAGGAGATGTAGGAGCCAAAGCTGGACCTGGAGATGATGCTTTAGGAGGTTTTGCAACAGGGCCA
TGATGCTTGGGAGACTGTGCTGGCCC
Found at i:5396404 original size:16 final size:16
Alignment explanation
Indices: 5396383--5396413 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5396373 AAATTTTTAA
5396383 TAAAATATTAATATTT
1 TAAAATATTAATATTT
5396399 TAAAATATTAATATT
1 TAAAATATTAATATT
5396414 AAATTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:5396442 original size:19 final size:19
Alignment explanation
Indices: 5396381--5396443 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 19
5396371 TCAAATTTTT
5396381 AATAAAATATTAATATTTTAA
1 AATAAAATATTAATA-TTT-A
*
5396402 AATATTAATATTAA-ATTATA
1 AATA-AAATATTAATATT-TA
5396422 AATAAAATATTAATATTTA
1 AATAAAATATTAATATTTA
5396441 AAT
1 AAT
5396444 TATCAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 13 0.35
20 10 0.27
21 6 0.16
22 8 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATAAAATATTAATATTTA
Found at i:5396558 original size:19 final size:21
Alignment explanation
Indices: 5396536--5396582 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
5396526 TAAATTATAT
5396536 ATAAAA-TATTAATA-ATTAA
1 ATAAAATTATTAATATATTAA
*
5396555 ATAATCAATTATTAATATTTTAA
1 ATAA--AATTATTAATATATTAA
5396578 ATAAA
1 ATAAA
5396583 TTANNNNNNN
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 4 0.17
21 3 0.13
22 8 0.35
23 8 0.35
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAAAATTATTAATATATTAA
Found at i:5396923 original size:22 final size:21
Alignment explanation
Indices: 5396898--5396963 Score: 53
Period size: 24 Copynumber: 3.0 Consensus size: 21
5396888 AATTAATCAT
5396898 AATAATATTTTAAATTAAATAA
1 AATAATATTTTAAATTAAAT-A
* *
5396920 AATATTAATATTTAAATTATTAATT
1 AATAAT-AT-TTTAAATTA--AATA
*
5396945 ATTAATATTTT-AATTAAAT
1 AATAATATTTTAAATTAAAT
5396964 TCTAGATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
20 3 0.08
22 10 0.28
23 5 0.14
24 11 0.31
25 4 0.11
26 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATAATATTTTAAATTAAATA
Found at i:5396940 original size:15 final size:15
Alignment explanation
Indices: 5396917--5396984 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 15
5396907 TTAAATTAAA
*
5396917 TAAAATATTAATATT
1 TAAATTATTAATATT
5396932 TAAATTATTAAT-TAT
1 TAAATTATTAATAT-T
5396947 TAATATT-TTAATTAAATT
1 TAA-ATTATTAA-T--ATT
*
5396965 CTAGATTATTAATATT
1 -TAAATTATTAATATT
5396981 TAAA
1 TAAA
5396985 AAATCTAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
14 1 0.02
15 22 0.52
16 7 0.17
18 5 0.12
19 7 0.17
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (15 bp):
TAAATTATTAATATT
Found at i:5396984 original size:22 final size:22
Alignment explanation
Indices: 5396922--5396984 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 22
5396912 TTAAATAAAA
*
5396922 TATTAATATTTAAATTATTAAT
1 TATTAATATTTAAATTACTAAT
*
5396944 TATTAATATTTTAATTAAATTCTAGAT
1 TATTAATATTTAAATT--A--CTA-AT
5396971 TATTAATATTTAAA
1 TATTAATATTTAAA
5396985 AAATCTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 15 0.45
24 1 0.03
26 2 0.06
27 15 0.45
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTAATATTTAAATTACTAAT
Found at i:5409265 original size:12 final size:12
Alignment explanation
Indices: 5409217--5409267 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
5409207 GAGTAATACT
5409217 TTCCGTTGAAAA
1 TTCCGTTGAAAA
5409229 TT-CGTTGAAAA
1 TTCCGTTGAAAA
**
5409240 TTTCCAAT-AGAAA
1 -TTCCGTTGA-AAA
5409253 TTCCGTTGAAAA
1 TTCCGTTGAAAA
5409265 TTC
1 TTC
5409268 ATTGCAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
11 9 0.29
12 16 0.52
13 6 0.19
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (12 bp):
TTCCGTTGAAAA
Found at i:5411086 original size:9 final size:9
Alignment explanation
Indices: 5411072--5411100 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
5411062 TGTATATATT
5411072 AAAATTAAA
1 AAAATTAAA
5411081 AAAATTAAA
1 AAAATTAAA
5411090 AAAATTAAA
1 AAAATTAAA
5411099 AA
1 AA
5411101 TTGAGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATTAAA
Found at i:5411870 original size:6 final size:6
Alignment explanation
Indices: 5411859--5411908 Score: 73
Period size: 6 Copynumber: 8.3 Consensus size: 6
5411849 GCTCCACATG
* * *
5411859 ATCTTC ATCTTC ATATTC ATTTTC ATCTTC ATCTTC ATCATC ATCTTC
1 ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC ATCTTC
5411907 AT
1 AT
5411909 TATCTTCTCC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.22, C:0.28, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTTC
Found at i:5416331 original size:16 final size:16
Alignment explanation
Indices: 5416310--5416344 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5416300 CCCTAACCCT
5416310 ATTAACTACTTGAATA
1 ATTAACTACTTGAATA
5416326 ATTAACTACTTGAATA
1 ATTAACTACTTGAATA
5416342 ATT
1 ATT
5416345 TTAAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTAACTACTTGAATA
Found at i:5416580 original size:20 final size:22
Alignment explanation
Indices: 5416551--5416610 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
5416541 TCTTCCACAA
*
5416551 AAATATTAAAATTAAA-AT-TT
1 AAATAATAAAATTAAATATCTT
*
5416571 AAATAATAAAAAATAAATATCTT
1 AAATAAT-AAAATTAAATATCTT
*
5416594 AAA-CATAAAATTAAATA
1 AAATAATAAAATTAAATA
5416611 ACTAAAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 6 0.18
21 18 0.55
22 4 0.12
23 5 0.15
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATAATAAAATTAAATATCTT
Found at i:5417826 original size:89 final size:89
Alignment explanation
Indices: 5417705--5417887 Score: 249
Period size: 89 Copynumber: 2.1 Consensus size: 89
5417695 TGCCGCAGGC
* * * *
5417705 AAAAGGAAGAAGCGAGAGAGAGAAGATCTGGGTTCATGTGCCGCCGGTTCTAGAGAGAGCTGGGG
1 AAAAGGAAGAAGCGAGAGAGACAAGATCTGGGTTCATGTGCAGCCGATTCTAAAGAGAGCTGGGG
* *
5417770 CTTCGGGCTTGTGTCATCGGCTGG
66 CTTCGAGCTTGTGTCATCGACTGG
* * * * *
5417794 AAAATGAAGAAGCGAGAGAGACAATATGTGGGTTCCTGTGCAGCCGATTCTAAAGAGAGTTGGGG
1 AAAAGGAAGAAGCGAGAGAGACAAGATCTGGGTTCATGTGCAGCCGATTCTAAAGAGAGCTGGGG
**
5417859 CTTCGAGCTTGTGTTGTCGACTGG
66 CTTCGAGCTTGTGTCATCGACTGG
5417883 AAAAG
1 AAAAG
5417888 AAAGGGGTTG
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.27, C:0.15, G:0.36, T:0.22
Consensus pattern (89 bp):
AAAAGGAAGAAGCGAGAGAGACAAGATCTGGGTTCATGTGCAGCCGATTCTAAAGAGAGCTGGGG
CTTCGAGCTTGTGTCATCGACTGG
Found at i:5431706 original size:11 final size:11
Alignment explanation
Indices: 5431675--5431708 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5431665 ATTTCATTGT
*
5431675 ATTTCCAACAG
1 ATTTCCAACGG
*
5431686 ATTTGCAACGG
1 ATTTCCAACGG
5431697 ATTTCCAACGG
1 ATTTCCAACGG
5431708 A
1 A
5431709 GTTTAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (11 bp):
ATTTCCAACGG
Found at i:5432006 original size:26 final size:26
Alignment explanation
Indices: 5431968--5432017 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
5431958 TTACAGTTTT
* * *
5431968 CAACGGAATTTTTCGTTGGAAATTTC
1 CAACAGAAATTTTCGTTGAAAATTTC
5431994 CAACAGAAATTTTCGTTGAAAATT
1 CAACAGAAATTTTCGTTGAAAATT
5432018 CATTGAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (26 bp):
CAACAGAAATTTTCGTTGAAAATTTC
Found at i:5432234 original size:13 final size:12
Alignment explanation
Indices: 5432205--5432230 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5432195 TACTATTTAC
5432205 AATTTCCAACGA
1 AATTTCCAACGA
5432217 AATTTCCAACGA
1 AATTTCCAACGA
5432229 AA
1 AA
5432231 ATTTTCGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (12 bp):
AATTTCCAACGA
Found at i:5433039 original size:2 final size:2
Alignment explanation
Indices: 5433032--5433076 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
5433022 GCTATAGAAA
*
5433032 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5433074 AT A
1 AT A
5433077 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5436972 original size:13 final size:13
Alignment explanation
Indices: 5436954--5436978 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5436944 TACAAGATAA
5436954 TTAAAGAGAGAAT
1 TTAAAGAGAGAAT
5436967 TTAAAGAGAGAA
1 TTAAAGAGAGAA
5436979 GCTCTCAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (13 bp):
TTAAAGAGAGAAT
Found at i:5437266 original size:29 final size:29
Alignment explanation
Indices: 5437204--5437283 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 29
5437194 GAGATGTATA
*
5437204 AGAATAGGTACAAGAGAAGAAGCTGTACG
1 AGAATAGGTACAAGAGAATAAGCTGTACG
5437233 AGAATAGGTACAAGAGAATAAGCTGTAC-
1 AGAATAGGTACAAGAGAATAAGCTGTACG
* * *
5437261 ATGAATAAGTATACGAGAATAAG
1 A-GAATAGGTACAAGAGAATAAG
5437284 GTAAGAGGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 1 0.02
29 45 0.98
ACGTcount: A:0.47, C:0.09, G:0.26, T:0.17
Consensus pattern (29 bp):
AGAATAGGTACAAGAGAATAAGCTGTACG
Found at i:5437555 original size:35 final size:35
Alignment explanation
Indices: 5437549--5437653 Score: 174
Period size: 35 Copynumber: 3.0 Consensus size: 35
5437539 GTAGCACTTC
*
5437549 ACTTATTCTGCGTGAAGTAGCATTTCACTTGTTCT
1 ACTTATTCTGCGTGAAGTAGCACTTCACTTGTTCT
* *
5437584 ACTTATTCTGCGTGAAGTAGCACTTCAGTTGTTTT
1 ACTTATTCTGCGTGAAGTAGCACTTCACTTGTTCT
*
5437619 ACTTATTCTACGTGAAGTAGCACTTCACTTGTTCT
1 ACTTATTCTGCGTGAAGTAGCACTTCACTTGTTCT
5437654 GGTTGTTCTC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (35 bp):
ACTTATTCTGCGTGAAGTAGCACTTCACTTGTTCT
Found at i:5437561 original size:26 final size:26
Alignment explanation
Indices: 5437525--5437583 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
5437515 TTTATTCTAG
*
5437525 TTATTCTGCGTTAAGTAGCACTTCAC
1 TTATTCTGCGTGAAGTAGCACTTCAC
*
5437551 TTATTCTGCGTGAAGTAGCATTTCAC
1 TTATTCTGCGTGAAGTAGCACTTCAC
*
5437577 TTGTTCT
1 TTATTCT
5437584 ACTTATTCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.42
Consensus pattern (26 bp):
TTATTCTGCGTGAAGTAGCACTTCAC
Found at i:5437897 original size:15 final size:15
Alignment explanation
Indices: 5437856--5437890 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
5437846 GCAGTATTGT
*
5437856 TTTAGACAGTAACAC
1 TTTAGCCAGTAACAC
*
5437871 TTTAGCCAGTAATAC
1 TTTAGCCAGTAACAC
5437886 TTTAG
1 TTTAG
5437891 GTAGTAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (15 bp):
TTTAGCCAGTAACAC
Found at i:5438080 original size:41 final size:41
Alignment explanation
Indices: 5437948--5438080 Score: 162
Period size: 41 Copynumber: 3.2 Consensus size: 41
5437938 TTGTAATGTC
5437948 AATATCTTTTTGTAATATTTGATTGATTATGCAATAATATTT
1 AATATC-TTTTGTAATATTTGATTGATTATGCAATAATATTT
* * **** *
5437990 AATGTCTTTCGTAATATTTGATTGCATT-TTTTTTAAT-TTC
1 AATATCTTTTGTAATATTTGATTG-ATTATGCAATAATATTT
*
5438030 AATATCTTTTGTAATATTTTATTGATTATGCAATAATATTT
1 AATATCTTTTGTAATATTTGATTGATTATGCAATAATATTT
5438071 AATATCTTTT
1 AATATCTTTT
5438081 TCATAAAAAT
Statistics
Matches: 73, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
39 3 0.04
40 28 0.38
41 34 0.47
42 8 0.11
ACGTcount: A:0.30, C:0.07, G:0.08, T:0.55
Consensus pattern (41 bp):
AATATCTTTTGTAATATTTGATTGATTATGCAATAATATTT
Found at i:5438108 original size:64 final size:64
Alignment explanation
Indices: 5438037--5438165 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
5438027 TTCAATATCT
* * *
5438037 TTTGTAATATTTTATTGATTATGCAATAATATTTAATATCTTTTTCATAAAAATCTTGATTCTA
1 TTTGTAATATTTTATTAATTATGCAATAATATTTAATATCTTTTCCATAAAAACCTTGATTCTA
5438101 TTTGTAATATTTTATTAATTATGCAATAATATTTAATATCTTTTCCATAAAAACCTTGATTCTA
1 TTTGTAATATTTTATTAATTATGCAATAATATTTAATATCTTTTCCATAAAAACCTTGATTCTA
5438165 T
1 T
5438166 GTGGCTTATA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.50
Consensus pattern (64 bp):
TTTGTAATATTTTATTAATTATGCAATAATATTTAATATCTTTTCCATAAAAACCTTGATTCTA
Found at i:5439146 original size:2 final size:2
Alignment explanation
Indices: 5439139--5439164 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5439129 TGCAGTAGTT
5439139 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5439165 GAAAGGGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5439996 original size:3 final size:3
Alignment explanation
Indices: 5439988--5440044 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
5439978 ATGCCGTAAG
* *
5439988 TTA TTA TTA TTA TTA TT- TTA TTA TT- TTA TAA TTT TTAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
5440032 -TA TTA TTT TTA TT
1 TTA TTA TTA TTA TT
5440045 TAAAGTTATA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 6 0.14
3 36 0.82
4 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:5440010 original size:8 final size:8
Alignment explanation
Indices: 5439988--5440040 Score: 61
Period size: 8 Copynumber: 6.2 Consensus size: 8
5439978 ATGCCGTAAG
5439988 TTATTATT
1 TTATTATT
5439996 ATTATTATT
1 -TTATTATT
5440005 TTATTATT
1 TTATTATT
*
5440013 TTATAATTT
1 TTATTA-TT
5440022 TTAATTATT
1 TT-ATTATT
*
5440031 ATATTATT
1 TTATTATT
5440039 TT
1 TT
5440041 TATTTAAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
8 20 0.53
9 15 0.39
10 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTATTATT
Found at i:5440030 original size:18 final size:18
Alignment explanation
Indices: 5439988--5440042 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
5439978 ATGCCGTAAG
*
5439988 TTATTATTATTATTATTTTA
1 TTATT-TTATTATT-TTTAA
*
5440008 TTATTTTATAATTTTTAA
1 TTATTTTATTATTTTTAA
*
5440026 TTATTATATTATTTTTA
1 TTATTTTATTATTTTTA
5440043 TTTAAAGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 19 0.61
19 7 0.23
20 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTTATTATTTTTAA
Found at i:5443580 original size:102 final size:101
Alignment explanation
Indices: 5443455--5443703 Score: 250
Period size: 102 Copynumber: 2.4 Consensus size: 101
5443445 CCAATAGCAT
* * * * *
5443455 AACATCATTACAACCAAATTATGAGCGATAAAGCTAGC-AGTTGGAATGT-GAATAATAAATTGT
1 AACATCATTACAGCCAAAATATGAGCGATAAAGCTAGCGA-CT-GAA-GTAGAATAATAAACTAT
*
5443518 GGTCAAAGAATAAACGATAAAACTTGTGACCAAAAGAAG
63 GGTCAAAGAATAAACGATAAAACTTGCGACCAAAAGAAG
* * * * * * *
5443557 AATATCATTGCAGCCAAAATATGAGCGGTAAAGTTTGCGACTGAAGTAAGAATGATGAACTATGG
1 AACATCATTACAGCCAAAATATGAGCGATAAAGCTAGCGACTGAAGT-AGAATAATAAACTATGG
* * * * *
5443622 TCAAAGAATAAGCGATAAAGCTTGCGACCAATAGTAT
65 TCAAAGAATAAACGATAAAACTTGCGACCAAAAGAAG
* * * *
5443659 AACATAATTACAGCCTAAATATAAGCGATAAAGCTAGCGGCTGAA
1 AACATCATTACAGCCAAAATATGAGCGATAAAGCTAGCGACTGAA
5443704 TATGAATTTT
Statistics
Matches: 117, Mismatches: 27, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
100 2 0.02
101 3 0.03
102 111 0.95
103 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (101 bp):
AACATCATTACAGCCAAAATATGAGCGATAAAGCTAGCGACTGAAGTAGAATAATAAACTATGGT
CAAAGAATAAACGATAAAACTTGCGACCAAAAGAAG
Found at i:5445350 original size:26 final size:26
Alignment explanation
Indices: 5445307--5445357 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
5445297 CTAGTTATTA
*
5445307 TGCGTTAAGCAGCACTTCACTTGTTT
1 TGCGTGAAGCAGCACTTCACTTGTTT
* *
5445333 TGCGTGAAGTAGCGCTTCACTTGTT
1 TGCGTGAAGCAGCACTTCACTTGTT
5445358 CTACTTATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.37
Consensus pattern (26 bp):
TGCGTGAAGCAGCACTTCACTTGTTT
Found at i:5445372 original size:35 final size:35
Alignment explanation
Indices: 5445333--5445429 Score: 158
Period size: 35 Copynumber: 2.8 Consensus size: 35
5445323 TCACTTGTTT
*
5445333 TGCGTGAAGTAGCGCTTCACTTGTTCTACTTATTC
1 TGCGTGAAGTAGCACTTCACTTGTTCTACTTATTC
* *
5445368 TGCGTGAAGTAGCATTTCACTTGTTTTACTTATTC
1 TGCGTGAAGTAGCACTTCACTTGTTCTACTTATTC
*
5445403 TGCGTGAAGTAACACTTCACTTGTTCT
1 TGCGTGAAGTAGCACTTCACTTGTTCT
5445430 GATTGTTCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.41
Consensus pattern (35 bp):
TGCGTGAAGTAGCACTTCACTTGTTCTACTTATTC
Found at i:5450304 original size:2 final size:2
Alignment explanation
Indices: 5450297--5450331 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5450287 TAATCCTAGG
5450297 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5450332 TTTAAACTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5478395 original size:30 final size:30
Alignment explanation
Indices: 5478361--5478418 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
5478351 GTTAACGAAA
5478361 AGATTCAAAATGATCATAGAAATCATGAAG
1 AGATTCAAAATGATCATAGAAATCATGAAG
*
5478391 AGATTCAAAATGATCATAGAAATTATGA
1 AGATTCAAAATGATCATAGAAATCATGA
5478419 TGAAGAGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.26
Consensus pattern (30 bp):
AGATTCAAAATGATCATAGAAATCATGAAG
Found at i:5483611 original size:60 final size:59
Alignment explanation
Indices: 5483539--5483715 Score: 230
Period size: 60 Copynumber: 2.9 Consensus size: 59
5483529 TCAGACATCA
* **
5483539 TCACCTACTCGTGAGAACTGCCCAATCCACCATATATAAATCGAGGCTTCAGGT-CCTCTT
1 TCACCTACTCGTGGGAACTGCCCACGCCACCA-ATATAAATCGAGGCTTCAGGTCCCTC-T
* * *
5483599 TTACCTATTCGTGGGAACTGCCCACGCCACTCAATATAAATCGAGGCTTCAAGTCCCTCT
1 TCACCTACTCGTGGGAACTGCCCACGCCAC-CAATATAAATCGAGGCTTCAGGTCCCTCT
* * *
5483659 TCACCTACTCGTGGGAACTGCTCACGCCACCCAATATGAATCGGGGCTTCAGGTCCC
1 TCACCTACTCGTGGGAACTGCCCACGCCA-CCAATATAAATCGAGGCTTCAGGTCCC
5483716 CCTTTTTACA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
60 95 0.93
61 7 0.07
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (59 bp):
TCACCTACTCGTGGGAACTGCCCACGCCACCAATATAAATCGAGGCTTCAGGTCCCTCT
Found at i:5484770 original size:16 final size:18
Alignment explanation
Indices: 5484741--5484773 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5484731 TATGTAAATA
5484741 AATTCCTTCGACAATAAT
1 AATTCCTTCGACAATAAT
5484759 AATTCC-TC-ACAATAA
1 AATTCCTTCGACAATAA
5484774 ACAATTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.42, C:0.24, G:0.03, T:0.30
Consensus pattern (18 bp):
AATTCCTTCGACAATAAT
Found at i:5485315 original size:28 final size:29
Alignment explanation
Indices: 5485280--5485352 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
5485270 TCCCCTTTTT
5485280 CTCTTTCTTTCTTTCTTTTTCAGCT-TTC
1 CTCTTTCTTTCTTTCTTTTTCAGCTCTTC
**
5485308 CTCTTTCTCTT-TTT-TTTTTTTGCTCTTC
1 CTCTTTCT-TTCTTTCTTTTTCAGCTCTTC
* *
5485336 TTCTTTCTCTCTTTCTT
1 CTCTTTCTTTCTTTCTT
5485353 CCTTGGGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
27 9 0.24
28 24 0.65
29 4 0.11
ACGTcount: A:0.01, C:0.27, G:0.03, T:0.68
Consensus pattern (29 bp):
CTCTTTCTTTCTTTCTTTTTCAGCTCTTC
Found at i:5485389 original size:4 final size:4
Alignment explanation
Indices: 5485380--5485427 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
5485370 TCCCTTTTTC
*
5485380 TCTT TCTT TCTT TCTT TCTT T-TT TAGCTT TC-C TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT T--CTT TCTT TCTT TCTT TCTT TCTT
5485428 CTTCGGCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 5 0.13
4 30 0.79
6 3 0.08
ACGTcount: A:0.02, C:0.25, G:0.02, T:0.71
Consensus pattern (4 bp):
TCTT
Found at i:5485436 original size:28 final size:28
Alignment explanation
Indices: 5485384--5485439 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
5485374 TTTTTCTCTT
* *
5485384 TCTTTCTTTCTTTCTTTTTTAGCTTTCC
1 TCTTTCTTTCTTTCTTCTTCAGCTTTCC
*
5485412 TCTTTCTTTCTTTCTTCTTCGGCTTTCC
1 TCTTTCTTTCTTTCTTCTTCAGCTTTCC
5485440 CCTTGCTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.02, C:0.29, G:0.05, T:0.64
Consensus pattern (28 bp):
TCTTTCTTTCTTTCTTCTTCAGCTTTCC
Found at i:5485502 original size:18 final size:18
Alignment explanation
Indices: 5485479--5485547 Score: 75
Period size: 18 Copynumber: 3.6 Consensus size: 18
5485469 CGAAACCTTT
5485479 CTTTTCTTTTTTTTCTCC
1 CTTTTCTTTTTTTTCTCC
*
5485497 CTTTTCTTTTCCTTTTNCTAC
1 CTTTTCTTTT--TTTT-CTCC
*
5485518 TTACTTTCTTTTTTTTCTCC
1 CT--TTTCTTTTTTTTCTCC
5485538 CTTTTCTTTT
1 CTTTTCTTTT
5485548 CCTTTTATTC
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 18 0.43
20 8 0.19
21 8 0.19
23 8 0.19
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.70
Consensus pattern (18 bp):
CTTTTCTTTTTTTTCTCC
Found at i:5485505 original size:23 final size:23
Alignment explanation
Indices: 5485476--5485553 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 23
5485466 GCTCGAAACC
5485476 TTTCTTTTCTTTTTTTTCTCCCT
1 TTTCTTTTCTTTTTTTTCTCCCT
* * *
5485499 TTTCTTTTC--CTTTTNCT-AC-
1 TTTCTTTTCTTTTTTTTCTCCCT
*
5485518 TTAC-TTTCTTTTTTTTCTCCCT
1 TTTCTTTTCTTTTTTTTCTCCCT
*
5485540 TTTCTTTTCCTTTT
1 TTTCTTTTCTTTTT
5485554 ATTCAAGTGG
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
18 4 0.10
19 3 0.07
20 7 0.17
21 7 0.17
22 3 0.07
23 17 0.41
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTCTTTTCTTTTTTTTCTCCCT
Found at i:5487472 original size:15 final size:15
Alignment explanation
Indices: 5487452--5487481 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5487442 TCCATTACCA
5487452 TTGAAAGAAAGAAAT
1 TTGAAAGAAAGAAAT
*
5487467 TTGAAAGAATGAAAT
1 TTGAAAGAAAGAAAT
5487482 AGAGTTTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (15 bp):
TTGAAAGAAAGAAAT
Found at i:5488792 original size:21 final size:20
Alignment explanation
Indices: 5488759--5488801 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
5488749 TTTATTCTAT
5488759 AATGGCAGAAAGTGATTTTG
1 AATGGCAGAAAGTGATTTTG
* *
5488779 AATGGGAGCAAAGTGGTTTTG
1 AATGGCAG-AAAGTGATTTTG
5488800 AA
1 AA
5488802 ATTCACGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.35, C:0.05, G:0.33, T:0.28
Consensus pattern (20 bp):
AATGGCAGAAAGTGATTTTG
Found at i:5496692 original size:69 final size:71
Alignment explanation
Indices: 5496590--5496723 Score: 186
Period size: 68 Copynumber: 1.9 Consensus size: 71
5496580 ATATATAGGA
* * *
5496590 AAAAAATAGCTGTTGGAAATATTAAACATATATTA-TGTTAGTTGATTG-AAATAGG-GAAATAG
1 AAAAAATAGCTCTTGGAAATATTAAACAGATATTATTGTTAATTGATTGAAAATAGGAGAAATAG
5496652 GTGGGG
66 GTGGGG
*
5496658 AAAAAATAGCTCTT-GAAGATCATTAAATAGATATTATTGTTAATTGATTGAAAATAGGAGAAAT
1 AAAAAATAGCTCTTGGAA-AT-ATTAAACAGATATTATTGTTAATTGATTGAAAATAGGAGAAAT
5496722 AG
64 AG
5496724 TTGAGAATTA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
67 3 0.05
68 15 0.26
69 13 0.23
70 12 0.21
71 7 0.12
72 7 0.12
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (71 bp):
AAAAAATAGCTCTTGGAAATATTAAACAGATATTATTGTTAATTGATTGAAAATAGGAGAAATAG
GTGGGG
Found at i:5499537 original size:35 final size:35
Alignment explanation
Indices: 5499491--5499565 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
5499481 TACATTTAAC
5499491 TTGATTTTATAAATCCACTTGACACCTATAATGTG
1 TTGATTTTATAAATCCACTTGACACCTATAATGTG
*
5499526 TTGATTTTATAAATCCATTTGACACCTATAATGTG
1 TTGATTTTATAAATCCACTTGACACCTATAATGTG
5499561 TTGAT
1 TTGAT
5499566 CAACAGGCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (35 bp):
TTGATTTTATAAATCCACTTGACACCTATAATGTG
Found at i:5518120 original size:19 final size:17
Alignment explanation
Indices: 5518087--5518130 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
5518077 CATAATGATA
*
5518087 AATTAAATAAAACATTC
1 AATTAAATAAAACATAC
5518104 AATTAACATATAAACATAC
1 AATTAA-ATA-AAACATAC
*
5518123 AATGAAAT
1 AATTAAAT
5518131 TTTTCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 6 0.26
18 5 0.22
19 12 0.52
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (17 bp):
AATTAAATAAAACATAC
Found at i:5522049 original size:20 final size:20
Alignment explanation
Indices: 5522010--5522049 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5522000 CAAACTAACG
*
5522010 TTGGGATGTTGTAAAGACAC
1 TTGGGATGTTGTAAAAACAC
5522030 TTGGG-TGTTGTGAAAAACAC
1 TTGGGATGTTGT-AAAAACAC
5522050 CAATCGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (20 bp):
TTGGGATGTTGTAAAAACAC
Found at i:5523468 original size:35 final size:35
Alignment explanation
Indices: 5523376--5523469 Score: 125
Period size: 35 Copynumber: 2.7 Consensus size: 35
5523366 GTAAATAATG
*
5523376 AGAACAACTAGAACAAGTGAAGCACTACTTCACGC
1 AGAACAACTAGAACAAGTGAAGTACTACTTCACGC
* * * *
5523411 ATAACAACTAGAATAAATGAAGTACTACTTCACGT
1 AGAACAACTAGAACAAGTGAAGTACTACTTCACGC
* *
5523446 AGAACAAGTAAAACAAGTGAAGTA
1 AGAACAACTAGAACAAGTGAAGTA
5523470 TTGCATCATG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.18
Consensus pattern (35 bp):
AGAACAACTAGAACAAGTGAAGTACTACTTCACGC
Found at i:5525889 original size:26 final size:26
Alignment explanation
Indices: 5525824--5525896 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 26
5525814 ATTAGGTGCC
5525824 TGAATATTTGTTGAGCATTGCGTGAG
1 TGAATATTTGTTGAGCATTGCGTGAG
* * * *
5525850 T---TCTTTATAG-GCATTACGTGAG
1 TGAATATTTGTTGAGCATTGCGTGAG
5525872 TGAATATTTGTTGAGCATTGCGTGA
1 TGAATATTTGTTGAGCATTGCGTGA
5525897 CAGGTATTAC
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
22 12 0.34
23 6 0.17
25 6 0.17
26 11 0.31
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (26 bp):
TGAATATTTGTTGAGCATTGCGTGAG
Found at i:5525940 original size:15 final size:15
Alignment explanation
Indices: 5525901--5525934 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5525891 GCGTGACAGG
*
5525901 TATTACGTGACTGAA
1 TATTACTTGACTGAA
5525916 TATTACTTGACTGAA
1 TATTACTTGACTGAA
5525931 TATT
1 TATT
5525935 TGTTGAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (15 bp):
TATTACTTGACTGAA
Found at i:5526022 original size:48 final size:48
Alignment explanation
Indices: 5525917--5526023 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 48
5525907 GTGACTGAAT
* * * **
5525917 ATTACTTGACTGAATATTTGTTGAGTATTGCTTGAGTTCTTTATAGGC
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACCTCTTTATAGGC
* * *
5525965 ATTATGTGACTGAATATTTGTTGAGCATTGCGTGACCTGTTTGTAGGC
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACCTCTTTATAGGC
*
5526013 ATTGCGTGACT
1 ATTACGTGACT
5526024 TTAGCTACCT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.42
Consensus pattern (48 bp):
ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACCTCTTTATAGGC
Found at i:5527577 original size:22 final size:22
Alignment explanation
Indices: 5527552--5527599 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
5527542 TTTTGTAAGC
* *
5527552 TTGCATGA-CTGATTTTTATTTA
1 TTGCATGACCTG-TTGTTATGTA
*
5527574 TTGCGTGACCTGTTGTTATGTA
1 TTGCATGACCTGTTGTTATGTA
5527596 TTGC
1 TTGC
5527600 GAGAGTGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.17, C:0.12, G:0.21, T:0.50
Consensus pattern (22 bp):
TTGCATGACCTGTTGTTATGTA
Found at i:5527876 original size:118 final size:118
Alignment explanation
Indices: 5527482--5527866 Score: 511
Period size: 118 Copynumber: 3.3 Consensus size: 118
5527472 CTATTGTAGT
* *
5527482 GAGAGTGGTGGCGCGTGACTTGTGCAATTCATGTGTTGTTTTG-AGACTTTTGTTCAGTAGTTTT
1 GAGAGTGGTGGCACGTGACTTGTGCAATTCATGTGTTGTTTTGAAG-CTTTTGTTTAGTAGTTTT
* * * * *
5527546 GTAAGCTTGCATGACTGATTTTTATTTATTGCGTGACCTGTTGTTATGTATTGC
65 TTAGGCTTGCGTGACTGGTTTTTATATATTGCGTGACCTGTTGTTATGTATTGC
* * * * *
5527600 GAGAGTGGTGGCACGTGACTTGTGTAATTCTTGTGTTGTCTTGAGGCTTTTGTTTAATAGTTTTT
1 GAGAGTGGTGGCACGTGACTTGTGCAATTCATGTGTTGTTTTGAAGCTTTTGTTTAGTAGTTTTT
* * * * * *
5527665 TAGCCCTACGTGACTAGTTTTTATATATTGCATGACATGTTGTTATGTATTGC
66 TAGGCTTGCGTGACTGGTTTTTATATATTGCGTGACCTGTTGTTATGTATTGC
* *
5527718 GAGAGTGGTGGCACGTGACTTTTGCATTTCATGTGTTGTTTTGAAGCTTTTGTTTAGTAGTTTTT
1 GAGAGTGGTGGCACGTGACTTGTGCAATTCATGTGTTGTTTTGAAGCTTTTGTTTAGTAGTTTTT
* * * *
5527783 TAGGCTTGCGTGACTGGTTTTTATATATTACGTGACCTATTGTTATATATTGT
66 TAGGCTTGCGTGACTGGTTTTTATATATTGCGTGACCTGTTGTTATGTATTGC
* * *
5527836 GAGAGCGATGGCACGTGACTTGTGTAATTCA
1 GAGAGTGGTGGCACGTGACTTGTGCAATTCA
5527867 CCTCTTGTTT
Statistics
Matches: 226, Mismatches: 40, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
118 225 1.00
119 1 0.00
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.44
Consensus pattern (118 bp):
GAGAGTGGTGGCACGTGACTTGTGCAATTCATGTGTTGTTTTGAAGCTTTTGTTTAGTAGTTTTT
TAGGCTTGCGTGACTGGTTTTTATATATTGCGTGACCTGTTGTTATGTATTGC
Found at i:5533506 original size:23 final size:23
Alignment explanation
Indices: 5533476--5533532 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
5533466 AAAATAGATG
*
5533476 AGTCACACGATGCAAGATCAACT
1 AGTCACACGATCCAAGATCAACT
* * *
5533499 AGTCACACGATCCCATATCATCT
1 AGTCACACGATCCAAGATCAACT
*
5533522 AGTCACGCGAT
1 AGTCACACGAT
5533533 TCAATAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (23 bp):
AGTCACACGATCCAAGATCAACT
Found at i:5533678 original size:23 final size:23
Alignment explanation
Indices: 5533652--5533712 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
5533642 GCGATTTTAG
*
5533652 AATAAATACTCACGCCATTCCAT
1 AATAAATACTCACGCCACTCCAT
* * *
5533675 AATAACTAGTAACGCCACTCCAT
1 AATAAATACTCACGCCACTCCAT
*
5533698 -ATATATTACTCACGC
1 AATA-AATACTCACGC
5533713 GAGTCAATAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.38, C:0.30, G:0.07, T:0.26
Consensus pattern (23 bp):
AATAAATACTCACGCCACTCCAT
Found at i:5533876 original size:70 final size:70
Alignment explanation
Indices: 5533791--5533942 Score: 250
Period size: 70 Copynumber: 2.2 Consensus size: 70
5533781 ACGCCACTCT
* *
5533791 ATATTTACTACTAACGGGAGTCAATATCAAATACTCACGCGATTCTAAATCTTAATGGTTCACGC
1 ATATTTACTACTAACGGGAGTCAATATCAAATACTCACGCAATTCTAAATCTTAATAGTTCACGC
5533856 AATCC
66 AATCC
* *
5533861 ATATTTACTACTAACGGGAGTCAATATCAAATACTCATGTAATTCTAAATCTTAATAGTTCACGC
1 ATATTTACTACTAACGGGAGTCAATATCAAATACTCACGCAATTCTAAATCTTAATAGTTCACGC
*
5533926 GATCC
66 AATCC
*
5533931 ATATTTGCTACT
1 ATATTTACTACT
5533943 CACACGATTC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 76 1.00
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (70 bp):
ATATTTACTACTAACGGGAGTCAATATCAAATACTCACGCAATTCTAAATCTTAATAGTTCACGC
AATCC
Found at i:5536145 original size:21 final size:21
Alignment explanation
Indices: 5536120--5536178 Score: 55
Period size: 26 Copynumber: 2.6 Consensus size: 21
5536110 ATGAATGAAT
*
5536120 ATACAGAATAATATATAAATG
1 ATACAGAATAATATAGAAATG
*
5536141 ATACAACAAAGAATAATATGGAAATG
1 AT---AC--AGAATAATATAGAAATG
5536167 ATACAGAATAAT
1 ATACAGAATAAT
5536179 GTTAATGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
21 10 0.32
23 2 0.06
24 2 0.06
26 17 0.55
ACGTcount: A:0.58, C:0.07, G:0.12, T:0.24
Consensus pattern (21 bp):
ATACAGAATAATATAGAAATG
Found at i:5537772 original size:24 final size:24
Alignment explanation
Indices: 5537745--5537790 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
5537735 TGCATCGACC
5537745 GTTGAATCTCCAACTGCATTGATT
1 GTTGAATCTCCAACTGCATTGATT
*
5537769 GTTGGATCTCCAACTGCATTGA
1 GTTGAATCTCCAACTGCATTGA
5537791 CTGCATCTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (24 bp):
GTTGAATCTCCAACTGCATTGATT
Found at i:5537842 original size:24 final size:24
Alignment explanation
Indices: 5537750--5537843 Score: 77
Period size: 24 Copynumber: 4.0 Consensus size: 24
5537740 CGACCGTTGA
* **
5537750 ATCTCCAACTGCATTGATTGTTGG
1 ATCTCCAACTGCATTGACTACTGG
*
5537774 ATCTCCAACTGCATTG---ACTGC
1 ATCTCCAACTGCATTGACTACTGG
* * * * **
5537795 ATCTGCATCTGCATCGTCCGCTGG
1 ATCTCCAACTGCATTGACTACTGG
5537819 ATCTCCAACTGCATTGACTACTGG
1 ATCTCCAACTGCATTGACTACTGG
5537843 A
1 A
5537844 ACTCTAATTT
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
21 15 0.28
24 38 0.72
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (24 bp):
ATCTCCAACTGCATTGACTACTGG
Found at i:5537858 original size:69 final size:69
Alignment explanation
Indices: 5537727--5537877 Score: 185
Period size: 69 Copynumber: 2.2 Consensus size: 69
5537717 AGTGACTTCG
* * ** *
5537727 TCTGCATCTGCATCGACCGTTGAATCTCCAACTGCATTGATTGTTGGATCTCCAACTGCATTGAC
1 TCTGCATCTGCATCGACCGCTGAATCTCCAACTGCATTGACTACTGGAACTCCAACTGCATTGAC
5537792 TGCA
66 TGCA
* * * * * *
5537796 TCTGCATCTGCATCGTCCGCTGGATCTCCAACTGCATTGACTACTGGAACTCTAATTTCATTGAT
1 TCTGCATCTGCATCGACCGCTGAATCTCCAACTGCATTGACTACTGGAACTCCAACTGCATTGAC
*
5537861 TGTA
66 TGCA
*
5537865 TCTGCATTTGCAT
1 TCTGCATCTGCAT
5537878 ATTCGTTTGT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (69 bp):
TCTGCATCTGCATCGACCGCTGAATCTCCAACTGCATTGACTACTGGAACTCCAACTGCATTGAC
TGCA
Found at i:5538020 original size:24 final size:24
Alignment explanation
Indices: 5537991--5538050 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
5537981 GACTCTGCAT
* *
5537991 GAGGGGCAGCACTTGAAGCAAGAG
1 GAGGGGCAGCAATAGAAGCAAGAG
* *
5538015 GAGGGGCAACAATAGAAGCAGGAG
1 GAGGGGCAGCAATAGAAGCAAGAG
* *
5538039 AAGGAGCAGCAA
1 GAGGGGCAGCAA
5538051 GAGTAGCAGC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.40, T:0.05
Consensus pattern (24 bp):
GAGGGGCAGCAATAGAAGCAAGAG
Found at i:5538087 original size:24 final size:24
Alignment explanation
Indices: 5538042--5538088 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5538032 GCAGGAGAAG
*
5538042 GAGCAGCAAGAGTAGCAGCATGAT
1 GAGCAGCAAGAGTAGCACCATGAT
*
5538066 GAGCAGCAGGAG-ATGCACCATGA
1 GAGCAGCAAGAGTA-GCACCATGA
5538089 AGAGTTGTAG
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:0.36, C:0.19, G:0.34, T:0.11
Consensus pattern (24 bp):
GAGCAGCAAGAGTAGCACCATGAT
Found at i:5539939 original size:23 final size:23
Alignment explanation
Indices: 5539907--5539952 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5539897 CAATATTCAT
5539907 GCAATAACCTAGAAATCAGTCAC
1 GCAATAACCTAGAAATCAGTCAC
* * *
5539930 GCAATGACCTATAAATTAGTCAC
1 GCAATAACCTAGAAATCAGTCAC
5539953 ACTAAGTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.24, G:0.13, T:0.22
Consensus pattern (23 bp):
GCAATAACCTAGAAATCAGTCAC
Found at i:5547162 original size:34 final size:34
Alignment explanation
Indices: 5547124--5547227 Score: 199
Period size: 34 Copynumber: 3.1 Consensus size: 34
5547114 CTTCAGCAGG
*
5547124 CAGCTTCCATCATACATTTGTTACTCTTCAAAAT
1 CAGCTTCCATCATACATTTGTTACACTTCAAAAT
5547158 CAGCTTCCATCATACATTTGTTACACTTCAAAAT
1 CAGCTTCCATCATACATTTGTTACACTTCAAAAT
5547192 CAGCTTCCATCATACATTTGTTACACTTCAAAAT
1 CAGCTTCCATCATACATTTGTTACACTTCAAAAT
5547226 CA
1 CA
5547228 CTCTACTCTC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.36
Consensus pattern (34 bp):
CAGCTTCCATCATACATTTGTTACACTTCAAAAT
Found at i:5561142 original size:41 final size:41
Alignment explanation
Indices: 5561085--5561170 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 41
5561075 ACACCAACCC
5561085 TTATAAGGTATTATCCACCTTAA-CTTACTGACCCCACGGTT
1 TTATAAGGTATTATCCACCTTAATC-TACTGACCCCACGGTT
* * *
5561126 TTATAAGGTATTATCCACCTTAATCTGCTGATCTCACGGTT
1 TTATAAGGTATTATCCACCTTAATCTACTGACCCCACGGTT
5561167 TTAT
1 TTAT
5561171 CCCATAAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 40 0.98
42 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (41 bp):
TTATAAGGTATTATCCACCTTAATCTACTGACCCCACGGTT
Found at i:5561635 original size:282 final size:282
Alignment explanation
Indices: 5561165--5561677 Score: 692
Period size: 282 Copynumber: 1.8 Consensus size: 282
5561155 GATCTCACGG
* * * *
5561165 TTTTATCCCATAAAAGGTACATCATAGATTGAAGGTGGTGTGAACCTTTATATTTCCAATACCAC
1 TTTTATCCCACAAAAGGGACATCAAAGATTAAAGGTGGTGTGAACCTTTATATTTCCAATACCAC
*
5561230 TCTAGTACAAAGCCGATGTGGGATTCATGGCTCCCATCTCTAAAGCCATGACATCTTCCCTTACT
66 TCTAGTACAAAGCCAATGTGGGATTCATGGCTCCCATCTCTAAAGCCATGACATCTTCCCTTACT
** * * * *
5561295 CCTCGTTGGGAGTTTTTCTTCGGTGTGGGACTTCGTAGCTCAACTCGTTAGGAGTATTATCTT-A
131 CCTCACTAGGAGTTTCTCTTCGATGTAGGACTTCGTAGCTCAACTCGTTAGGAGTATTAT-TTCA
5561359 ACAATGTGAGATTCACGTCCACGCGAGGACTGTGACACCACACCACCCCCTATGAGGTATTGTCC
195 ACAATGTGAGATTCACGTCCACGCGAGGACTGTGACACCACACCACCCCCTATGAGGTATTGTCC
5561424 GCTTTAGCCCGCTAGCCTCACAA
260 GCTTTAGCCCGCTAGCCTCACAA
* ** * *
5561447 TTTTATCCCACAAAAGGGACTTCACAAG-TTAAAGGTGGTGTGAACCTTTATATTTTTAGTATCA
1 TTTTATCCCACAAAAGGGACATCA-AAGATTAAAGGTGGTGTGAACCTTTATATTTCCAATACCA
* * *
5561511 CTCTAGTACATAGCCAATGTGGGATTCATGGCTCCCTTCTCT-AAGACCATGACATCTTCTCTTA
65 CTCTAGTACAAAGCCAATGTGGGATTCATGGCTCCCATCTCTAAAG-CCATGACATCTTCCCTTA
* ** * ** * *
5561575 TTTTTCACTAGGAGTTTCTCTTCGATGTAGGACTTTGT-GACTTTACTTGTTGGGAGTATTATTT
129 CTCCTCACTAGGAGTTTCTCTTCGATGTAGGACTTCGTAG-CTCAACTCGTTAGGAGTATTATTT
* * *
5561639 CGACGATGTGGGATTCACGTCCACGCGAGGACTGTGACA
193 CAACAATGTGAGATTCACGTCCACGCGAGGACTGTGACA
5561678 TCCTCCCCTA
Statistics
Matches: 197, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
281 6 0.03
282 189 0.96
283 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.32
Consensus pattern (282 bp):
TTTTATCCCACAAAAGGGACATCAAAGATTAAAGGTGGTGTGAACCTTTATATTTCCAATACCAC
TCTAGTACAAAGCCAATGTGGGATTCATGGCTCCCATCTCTAAAGCCATGACATCTTCCCTTACT
CCTCACTAGGAGTTTCTCTTCGATGTAGGACTTCGTAGCTCAACTCGTTAGGAGTATTATTTCAA
CAATGTGAGATTCACGTCCACGCGAGGACTGTGACACCACACCACCCCCTATGAGGTATTGTCCG
CTTTAGCCCGCTAGCCTCACAA
Found at i:5563014 original size:52 final size:50
Alignment explanation
Indices: 5562958--5563082 Score: 130
Period size: 52 Copynumber: 2.4 Consensus size: 50
5562948 AAAAAGAGAG
* *
5562958 AAAGAGA-AAAGAAAAGTTG-AAAAAAAAGAGATGAGGAGGGAAAGAAAGCCGA
1 AAAGAGAGAAAGAAAAG--GAAAAAAAAAGA-AAG-GGACGGAAAGAAAGCCGA
* *
5563010 AAAGAGAGAGAGAAAGAAGGAAAAAAAAAGAAAGGGACGGAAGGAAAGCCGA
1 AAAGAGAGAAAG-AA-AAGGAAAAAAAAAGAAAGGGACGGAAAGAAAGCCGA
5563062 AAAGAGAGAGAAG-AAAGGAAA
1 AAAGAGAGA-AAGAAAAGGAAA
5563083 GGAAGAGAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
50 7 0.11
51 1 0.02
52 32 0.51
53 8 0.13
54 12 0.19
55 3 0.05
ACGTcount: A:0.61, C:0.04, G:0.33, T:0.02
Consensus pattern (50 bp):
AAAGAGAGAAAGAAAAGGAAAAAAAAAGAAAGGGACGGAAAGAAAGCCGA
Found at i:5563113 original size:33 final size:33
Alignment explanation
Indices: 5563066--5563153 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 33
5563056 AGCCGAAAAG
* *
5563066 AGAGAGAAGAAAGGAAAGGAAGAG-AAAAAACAA
1 AGAGAGAGGGAAGG-AAGGAAGAGTAAAAAACAA
* * *
5563099 AGAGAGAGGGAAGGAAGCAA-AGTTGAAAAAGAA
1 AGAGAGAGGGAAGGAAGGAAGAG-TAAAAAACAA
*
5563132 AGAGAGAGAGAAGGAAGGAAGA
1 AGAGAGAGGGAAGGAAGGAAGA
5563154 AAAGTAGAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
31 2 0.04
32 5 0.11
33 37 0.82
34 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.36, T:0.02
Consensus pattern (33 bp):
AGAGAGAGGGAAGGAAGGAAGAGTAAAAAACAA
Found at i:5563113 original size:59 final size:54
Alignment explanation
Indices: 5562976--5563114 Score: 158
Period size: 52 Copynumber: 2.5 Consensus size: 54
5562966 AAGAAAAGTT
*
5562976 GAAAAAAAAGAGATGAGGAGGGAAAGAAAGCCGAAAAGAGAGAGAGAAAGAAGGAAA
1 GAAAAAAAA-AGA-GA-GAGGGAAGGAAAGCCGAAAAGAGAGAGAGAAAGAAGGAAA
*
5563033 -AAAAAAGAAAG-G-GACGGAAGGAAAGCCGAAAAGAGAGAGAAGAAAGGAAAGGAAGA
1 GAAAAAA-AAAGAGAGAGGGAAGGAAAGCCGAAAAGAGAGAG-AGAAA-G-AAGGAA-A
5563089 GAAAAAACAAAGAGAGAGGGAAGGAA
1 GAAAAAA-AAAGAGAGAGGGAAGGAA
5563115 GCAAAGTTGA
Statistics
Matches: 70, Mismatches: 4, Indels: 14
0.80 0.05 0.16
Matches are distributed among these distances:
52 25 0.36
53 5 0.07
54 2 0.03
55 6 0.09
56 9 0.13
57 12 0.17
58 1 0.01
59 10 0.14
ACGTcount: A:0.60, C:0.04, G:0.35, T:0.01
Consensus pattern (54 bp):
GAAAAAAAAAGAGAGAGGGAAGGAAAGCCGAAAAGAGAGAGAGAAAGAAGGAAA
Found at i:5563140 original size:37 final size:37
Alignment explanation
Indices: 5563060--5563176 Score: 115
Period size: 37 Copynumber: 3.3 Consensus size: 37
5563050 AAGGAAAGCC
* *
5563060 GAAA-AGAGAGAGAAGAAAGGAA-AGGAAG-AGAAAAA
1 GAAAGAGAGAGAGAAGGAAGGAAGA-AAAGTAGAAAAA
* *
5563095 -ACAA-AGAGAGAG--GGAAGGAAGCAAAGTTGAAAAA
1 GA-AAGAGAGAGAGAAGGAAGGAAGAAAAGTAGAAAAA
5563129 GAAAGAGAGAGAGAAGGAAGGAAGAAAAGTAGAAAAA
1 GAAAGAGAGAGAGAAGGAAGGAAGAAAAGTAGAAAAA
*
5563166 GAGAGAG-GAGA
1 GAAAGAGAGAGA
5563177 TAGAAAAAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
33 10 0.15
34 9 0.13
35 19 0.28
36 4 0.06
37 26 0.38
ACGTcount: A:0.60, C:0.02, G:0.36, T:0.03
Consensus pattern (37 bp):
GAAAGAGAGAGAGAAGGAAGGAAGAAAAGTAGAAAAA
Done.