Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold504
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: 246700
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 2
Found at i:168029 original size:179 final size:171
Alignment explanation
Indices: 167678--168097 Score: 446
Period size: 179 Copynumber: 2.4 Consensus size: 171
167668 TCCTATCCTG
* * * ** * * *
167678 TAACATGTAAAATCAATCAAATTTTCTACTTATAAAAAGAAATTTGATTTTCCAATATAATTTAT
1 TAACATTTACAATCAATCAACTTTT-TTTTTATAAAAAG-AA-TTGA-TTTCAAATATAATTCAC
* *
167743 GTATTAGTCTAATCTTTACAGTCTGATATTTACAATCAATCAACTTTTTTTCTATAAAAAAGAAT
62 GCATTAATCTAATCTTTACAGTCTGATATTTACAATCAATCAACTTTTTTTCTATAAAAAAGAAT
* * * *
167808 GCAATTCTCTGATATAATTCATGCATTAGTCTAATTCTTGCAGTC
127 GCAATTCTCTGATATAACTCATGCATCAGTCTAATCCTTGCAGTA
*
167853 TGACATTTACAATCAATCAACTTTTTTTTTATAAAAAGAATCTGATTCTCAAATATAATTCACGC
1 TAACATTTACAATCAATCAACTTTTTTTTTATAAAAAGAAT-TGATT-TCAAATATAATTCACGC
* * * *
167918 ATTAATCTAATCTTTGCAGTTTGATATTTATACTCAATCAACTTTTCTTTTTTTTCTATAAAAAA
64 ATTAATCTAATCTTTACAGTCTGATATTTACAATCAATCAA-----C-TTTTTTTCTATAAAAAA
*
167983 GAAT-CTGATTCTCTGATATAACTCATGCATCAGTCTAATCCTTGCAGTA
123 GAATGC-AATTCTCTGATATAACTCATGCATCAGTCTAATCCTTGCAGTA
* * * *
168032 TAACATTTGCACTTAATCAACTTTTCTTTTTTTATTAAAAAAGAATTCGATTTCAGATATAATTC
1 TAACATTTACAATCAATCAAC--TT-TTTTTTTA-T-AAAAAGAATT-GATTTCAAATATAATTC
168097 A
60 A
168098 TGTATTAGTC
Statistics
Matches: 205, Mismatches: 25, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
172 3 0.01
173 54 0.26
174 11 0.05
175 21 0.10
178 2 0.01
179 76 0.37
181 2 0.01
182 8 0.04
183 15 0.07
184 13 0.06
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.41
Consensus pattern (171 bp):
TAACATTTACAATCAATCAACTTTTTTTTTATAAAAAGAATTGATTTCAAATATAATTCACGCAT
TAATCTAATCTTTACAGTCTGATATTTACAATCAATCAACTTTTTTTCTATAAAAAAGAATGCAA
TTCTCTGATATAACTCATGCATCAGTCTAATCCTTGCAGTA
Found at i:168163 original size:68 final size:68
Alignment explanation
Indices: 168054--168190 Score: 163
Period size: 68 Copynumber: 2.0 Consensus size: 68
168044 TTAATCAACT
* * * * *
168054 TTTCTTTTTTTATTAAAAAAGAATTCGATTTCAGATATAATTCATGTATTAGTCTCATACTTGCA
1 TTTCTTTTTTTATTAAAAAAGAATTCGATTTCAAATATAATTCATGCATTAATCTAATACTTACA
168119 GTC
66 GTC
* *
168122 TTTCTTTTTTT-CTATAAAAA-AA-TCTGATTCTCAAATATAATTCATGCATTAATCTAATCCTT
1 TTTCTTTTTTTATTA-AAAAAGAATTC-GATT-TCAAATATAATTCATGCATTAATCTAATACTT
168184 ACAGTC
63 ACAGTC
168190 T
1 T
168191 GACATTTACA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
66 2 0.03
67 8 0.14
68 49 0.83
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.45
Consensus pattern (68 bp):
TTTCTTTTTTTATTAAAAAAGAATTCGATTTCAAATATAATTCATGCATTAATCTAATACTTACA
GTC
Found at i:168225 original size:84 final size:85
Alignment explanation
Indices: 168125--168378 Score: 314
Period size: 84 Copynumber: 2.9 Consensus size: 85
168115 TGCAGTCTTT
* *
168125 CTTTTTTTCTATAAAAAAATCTGATTCTCAAATATAATTCATGCATTAATCTAATCCTTACAGTC
1 CTTTTTTTCTATAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTC
168190 TGACATTTACAA-CTAATCAA
66 TGACATTTACAATC-AATCAA
* * * *
168210 CTTTTTTT-AATAAAAAAATCTGATTCTTAGATATAATTCATGCATTAGTCTAATTCTTGCAGTC
1 CTTTTTTTCTATAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTC
* *
168274 TGACATTTACCATCAATTAA
66 TGACATTTACAATCAATCAA
* *
168294 CTTTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAGTCTTT
1 C---T-TTTTTTCTAT-AAAAA-AATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
* * *
168359 ATAATCTAACATTTACAATC
60 ACAGTCTGACATTTACAATC
168379 TATGCATTAT
Statistics
Matches: 143, Mismatches: 18, Indels: 10
0.84 0.11 0.06
Matches are distributed among these distances:
84 67 0.47
85 9 0.06
87 1 0.01
88 6 0.04
89 2 0.01
90 5 0.03
91 53 0.37
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (85 bp):
CTTTTTTTCTATAAAAAAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACAGTC
TGACATTTACAATCAATCAA
Found at i:170956 original size:21 final size:20
Alignment explanation
Indices: 170906--170957 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
170896 TTCTCTTGTA
170906 GATTTAGAAAAATCTAAACAG
1 GATTT-GAAAAATCTAAACAG
* * * *
170927 AATTAGAAAAATCTAATTCCG
1 GATTTGAAAAATCTAA-ACAG
170948 GATTTGAAAA
1 GATTTGAAAA
170958 GAGGAGGTCG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (20 bp):
GATTTGAAAAATCTAAACAG
Found at i:171140 original size:17 final size:15
Alignment explanation
Indices: 171120--171169 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
171110 TTAGGTAAAA
171120 AAGAAAGAAAGAAGACG
1 AAGAAAGAAAGAA-A-G
171137 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
*
171151 AA-AAAGAAA-AAAA
1 AAGAAAGAAAGAAAG
171164 AAGAAA
1 AAGAAA
171170 AAAATATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.17
14 12 0.40
15 1 0.03
16 9 0.30
17 3 0.10
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:171158 original size:10 final size:10
Alignment explanation
Indices: 171117--171173 Score: 62
Period size: 10 Copynumber: 5.4 Consensus size: 10
171107 AAGTTAGGTA
171117 AAAAAGAAAG
1 AAAAAGAAAG
171127 AAAGAAGACGAAG
1 AAA-AAGA--AAG
171140 AAGAAAGAAAG
1 AA-AAAGAAAG
*
171151 AAAAAGAAAA
1 AAAAAGAAAG
171161 AAAAAGAAA-
1 AAAAAGAAAG
171170 AAAA
1 AAAA
171174 TATGAAATGG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
9 4 0.10
10 19 0.45
11 9 0.21
13 9 0.21
14 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:171394 original size:69 final size:69
Alignment explanation
Indices: 171249--171454 Score: 378
Period size: 68 Copynumber: 3.0 Consensus size: 69
171239 TTTGCCACGT
*
171249 TCATTTTTTGGTTAAAAATTATCAAAAGAGTTATTTAACTTGTTTATTTTCTGGGTAATTGAAAA
1 TCATTTTTTGGTTAAGAATTATCAAAAGAGTTATTTAACTTGTTTATTTTCTGGGTAATTGAAAA
171314 ATTG
66 ATTG
* *
171318 TCATTTTTTGGTTAAGAATTATC-AACGAGTTATTTAACTTGTTTATTTTCTGGGTAATTAAAAA
1 TCATTTTTTGGTTAAGAATTATCAAAAGAGTTATTTAACTTGTTTATTTTCTGGGTAATTGAAAA
171382 ATTG
66 ATTG
171386 TCATTTTTTGGTTAAGAATTATCAAAAGAGTTATTTAACTTGTTTATTTTCTGGGTAATTGAAAA
1 TCATTTTTTGGTTAAGAATTATCAAAAGAGTTATTTAACTTGTTTATTTTCTGGGTAATTGAAAA
171451 ATTG
66 ATTG
171455 AAGTGGCTGG
Statistics
Matches: 131, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
68 66 0.50
69 65 0.50
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.47
Consensus pattern (69 bp):
TCATTTTTTGGTTAAGAATTATCAAAAGAGTTATTTAACTTGTTTATTTTCTGGGTAATTGAAAA
ATTG
Found at i:176742 original size:20 final size:19
Alignment explanation
Indices: 176703--176742 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
176693 ATTAAATTTA
* *
176703 AATAAAAATAATTTTTATT
1 AATAAAAATAATTCTAATT
176722 AATAAATAATAATTCTAATT
1 AATAAA-AATAATTCTAATT
176742 A
1 A
176743 GATCAAGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAAAAATAATTCTAATT
Found at i:177643 original size:26 final size:24
Alignment explanation
Indices: 177595--177643 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
177585 ATTAATTAAC
* *
177595 TATTTTTATATAAATGTATAAATT
1 TATTTTTATATAAATGAACAAATT
177619 TATTTATTATATTAAATGAACAAAT
1 TATTT-TTATA-TAAATGAACAAAT
177644 ATTTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 5 0.24
25 5 0.24
26 11 0.52
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (24 bp):
TATTTTTATATAAATGAACAAATT
Found at i:178298 original size:34 final size:34
Alignment explanation
Indices: 178252--178327 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
178242 AAATATAATG
* *
178252 TTAGGTGATGTGTTCGGTAAACATATTAGGTGTA
1 TTAGGTGATGTGTTAGATAAACATATTAGGTGTA
* * *
178286 TTAGGTGGTGTGTTAGATGAACATATTAGGTGTG
1 TTAGGTGATGTGTTAGATAAACATATTAGGTGTA
178320 TTAGGTGA
1 TTAGGTGA
178328 ACATATGATG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.25, C:0.04, G:0.33, T:0.38
Consensus pattern (34 bp):
TTAGGTGATGTGTTAGATAAACATATTAGGTGTA
Found at i:178320 original size:22 final size:22
Alignment explanation
Indices: 178292--178333 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
178282 TGTATTAGGT
178292 GGTGTGTTAGATGAACATATTA
1 GGTGTGTTAGATGAACATATTA
*
178314 GGTGTGTTAGGTGAACATAT
1 GGTGTGTTAGATGAACATAT
178334 GATGTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.31, T:0.36
Consensus pattern (22 bp):
GGTGTGTTAGATGAACATATTA
Found at i:178770 original size:34 final size:34
Alignment explanation
Indices: 178723--178796 Score: 103
Period size: 34 Copynumber: 2.2 Consensus size: 34
178713 TATGTTCACT
*
178723 TAACACACATAATATGCTCACCTAATACACCACC
1 TAACACACATAATATGCTCACCTAACACACCACC
* * *
178757 TAACACACCTAATATGTTTACCTAACACACCACC
1 TAACACACATAATATGCTCACCTAACACACCACC
*
178791 AAACAC
1 TAACAC
178797 TAAGTTCACC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.42, C:0.35, G:0.03, T:0.20
Consensus pattern (34 bp):
TAACACACATAATATGCTCACCTAACACACCACC
Found at i:178890 original size:34 final size:34
Alignment explanation
Indices: 178838--178903 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
178828 TTATTAGATG
* *
178838 GTGTGTTAGGTAAACATATTAAATGTGTTAAGTA
1 GTGTGTTAAGTAAACATATTAAATATGTTAAGTA
* * *
178872 GTGTGTTAAGTGAGCATATTAAGTATGTTAAG
1 GTGTGTTAAGTAAACATATTAAATATGTTAAG
178904 AACGCCTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.38
Consensus pattern (34 bp):
GTGTGTTAAGTAAACATATTAAATATGTTAAGTA
Found at i:179857 original size:3 final size:3
Alignment explanation
Indices: 179851--179886 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
179841 CAACAACAAC
179851 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
179887 TTATCTCCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:180863 original size:25 final size:25
Alignment explanation
Indices: 180829--180887 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
180819 AATTAACCTT
180829 TGCAAATGTTACATGGAATCAGACG
1 TGCAAATGTTACATGGAATCAGACG
180854 TGCAAATGTTACATGGAATCAGACG
1 TGCAAATGTTACATGGAATCAGACG
*
180879 TGTAAATGT
1 TGCAAATGT
180888 CAGACACGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.27
Consensus pattern (25 bp):
TGCAAATGTTACATGGAATCAGACG
Found at i:184805 original size:46 final size:43
Alignment explanation
Indices: 184739--184840 Score: 100
Period size: 44 Copynumber: 2.3 Consensus size: 43
184729 TAGTTTAAAC
* * *
184739 ATTTATATTTA-AAAAAATTA-TATAAATTTTTTAAAATATATTTT
1 ATTTTTATTTATAAAAAATTATTAT-AA--TTTTAAAATATAATTA
*
184783 ATTTTTATTTATAAAACTATTATTATAATTTTAAAATATAATTA
1 ATTTTTATTTATAAAA-AATTATTATAATTTTAAAATATAATTA
184827 ATTTTATAATTTAT
1 ATTTT-T-ATTTAT
184841 TATTATGATT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
44 29 0.59
45 5 0.10
46 12 0.24
47 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (43 bp):
ATTTTTATTTATAAAAAATTATTATAATTTTAAAATATAATTA
Found at i:185723 original size:23 final size:23
Alignment explanation
Indices: 185662--185738 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
185652 GTGTGCCTTG
*
185662 AATTATTGAGCTAGATCTTTCCT
1 AATTATTGAGCTAGATCTTTCCA
*
185685 AATTATTAAGCTAGATCTTTCCA
1 AATTATTGAGCTAGATCTTTCCA
* * **
185708 AATTATTGGGCCAGATCCCTCCA
1 AATTATTGAGCTAGATCTTTCCA
*
185731 AATAATTG
1 AATTATTG
185739 CTTAGAAAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (23 bp):
AATTATTGAGCTAGATCTTTCCA
Found at i:188996 original size:32 final size:31
Alignment explanation
Indices: 188939--189041 Score: 111
Period size: 32 Copynumber: 3.3 Consensus size: 31
188929 TCAAAAAATC
* *
188939 AAAAACCCAAATCTGAAATAA-CCCGAACCCG
1 AAAAACCCGAACCTGAAA-AAGCCCGAACCCG
*
188970 AAATAACCCGAACCT-AAGAAAGCCCGAACCTGG
1 AAA-AACCCGAACCTGAA-AAAGCCCGAACC-CG
* *
189003 GAAAGCCCGAACCTGAAAAAGCCCGAACCCG
1 AAAAACCCGAACCTGAAAAAGCCCGAACCCG
189034 AAAAACCC
1 AAAAACCC
189042 AAGCCCGAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
31 14 0.24
32 40 0.68
33 5 0.08
ACGTcount: A:0.45, C:0.33, G:0.16, T:0.07
Consensus pattern (31 bp):
AAAAACCCGAACCTGAAAAAGCCCGAACCCG
Found at i:189048 original size:15 final size:16
Alignment explanation
Indices: 188960--189051 Score: 84
Period size: 16 Copynumber: 5.8 Consensus size: 16
188950 TCTGAAATAA
188960 CCCGAACCCGAAATAA-
1 CCCGAACCCGAAA-AAG
*
188976 CCCGAA-CCTAAGAAAG
1 CCCGAACCCGAA-AAAG
* **
188992 CCCGAACCTGGGAAAG
1 CCCGAACCCGAAAAAG
*
189008 CCCGAACCTGAAAAAG
1 CCCGAACCCGAAAAAG
189024 CCCGAACCCGAAAAA-
1 CCCGAACCCGAAAAAG
189039 CCC-AAGCCCGAAA
1 CCCGAA-CCCGAAA
189052 GAATTCGAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
14 2 0.03
15 16 0.25
16 45 0.70
17 1 0.02
ACGTcount: A:0.41, C:0.36, G:0.18, T:0.04
Consensus pattern (16 bp):
CCCGAACCCGAAAAAG
Found at i:189078 original size:16 final size:15
Alignment explanation
Indices: 189028--189079 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
189018 AAAAAGCCCG
*
189028 AACCCGAAAAACCCA
1 AACCCGAAAAACTCA
* * *
189043 AGCCCGAAAGAATTCG
1 AACCCGAAA-AACTCA
189059 AACCCGAAATAACTCA
1 AACCCGAAA-AACTCA
189075 AACCC
1 AACCC
189080 AAGATTGACC
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.46, C:0.35, G:0.12, T:0.08
Consensus pattern (15 bp):
AACCCGAAAAACTCA
Found at i:192863 original size:4 final size:4
Alignment explanation
Indices: 192854--192880 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
192844 TAAAGTAATT
192854 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
192881 TTATAGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:193387 original size:73 final size:73
Alignment explanation
Indices: 193294--193449 Score: 267
Period size: 73 Copynumber: 2.1 Consensus size: 73
193284 TTAATTAATG
* * *
193294 ATTTTTTATTTGGTTGGATTATTATGTTCTTCATTAATTAATAATTTTTTATTTAGATTACAATA
1 ATTTTTTATTGGGTTAGATTATTATGTTCTTCATTAATTAATAATTTTTTATTTAGATTAAAATA
193359 TGAAATAA
66 TGAAATAA
* *
193367 ATTTCTTATTGGGTTAGATTATTATGTTCTTTATTAATTAATAATTTTTTATTTAGATTAAAATA
1 ATTTTTTATTGGGTTAGATTATTATGTTCTTCATTAATTAATAATTTTTTATTTAGATTAAAATA
193432 TGAAATAA
66 TGAAATAA
193440 ATTTTTTATT
1 ATTTTTTATT
193450 AAACTTGAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.54
Consensus pattern (73 bp):
ATTTTTTATTGGGTTAGATTATTATGTTCTTCATTAATTAATAATTTTTTATTTAGATTAAAATA
TGAAATAA
Found at i:193749 original size:31 final size:32
Alignment explanation
Indices: 193708--193778 Score: 108
Period size: 31 Copynumber: 2.2 Consensus size: 32
193698 CTCGAACCCG
* *
193708 AACCCGAATAAATCCGAAACTGAATGAGCTCA
1 AACCCGAATAAAACCGAAACCGAATGAGCTCA
*
193740 AACCC-AATAAAACCGAACCCGAATGAGCTCA
1 AACCCGAATAAAACCGAAACCGAATGAGCTCA
193771 AACCCGAA
1 AACCCGAA
193779 CCTAAACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 28 0.80
32 7 0.20
ACGTcount: A:0.45, C:0.30, G:0.14, T:0.11
Consensus pattern (32 bp):
AACCCGAATAAAACCGAAACCGAATGAGCTCA
Found at i:193776 original size:16 final size:16
Alignment explanation
Indices: 193729--193778 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
193719 ATCCGAAACT
193729 GAATGAGCTCAAACCC
1 GAATGAGCTCAAACCC
* * *
193745 -AATAAAAC-CGAACCC
1 GAAT-GAGCTCAAACCC
193760 GAATGAGCTCAAACCC
1 GAATGAGCTCAAACCC
193776 GAA
1 GAA
193779 CCTAAACAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.44, C:0.30, G:0.16, T:0.10
Consensus pattern (16 bp):
GAATGAGCTCAAACCC
Found at i:193811 original size:16 final size:16
Alignment explanation
Indices: 193792--193827 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
193782 AAACAAACTT
* *
193792 GAACCTGAACCTGCCC
1 GAACCCGAACCTACCC
193808 GAACCCGAACCTACCC
1 GAACCCGAACCTACCC
193824 GAAC
1 GAAC
193828 TCGCCCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.44, G:0.17, T:0.08
Consensus pattern (16 bp):
GAACCCGAACCTACCC
Found at i:196596 original size:25 final size:22
Alignment explanation
Indices: 196555--196600 Score: 56
Period size: 25 Copynumber: 2.0 Consensus size: 22
196545 GAAGACTTCA
196555 AATAAAATTTAAGAGTGATTTTT
1 AATAAAATTTAAGAGTG-TTTTT
*
196578 AATAAATATTTTAATAGTGTTTT
1 AATAAA-A-TTTAAGAGTGTTTT
196601 GATAAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
AATAAAATTTAAGAGTGTTTTT
Found at i:196678 original size:17 final size:19
Alignment explanation
Indices: 196660--196699 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
196650 CGTATTTTTT
196660 TCCTTTT-TTCTTTTCTTTC
1 TCCTTTTCTTCTTTTC-TTC
196679 TCCTTTTCTTCTTCTTCTTC
1 TCCTTTTCTTCTT-TTCTTC
196699 T
1 T
196700 TTAGTTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 9 0.47
21 3 0.16
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TCCTTTTCTTCTTTTCTTC
Found at i:197685 original size:16 final size:16
Alignment explanation
Indices: 197664--197698 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
197654 ATTGAATGTC
197664 AGAACAGATGTGCTCA
1 AGAACAGATGTGCTCA
197680 AGAACAGATGTGCTCA
1 AGAACAGATGTGCTCA
197696 AGA
1 AGA
197699 GAGGAGAGGA
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:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (16 bp):
AGAACAGATGTGCTCA
Found at i:198869 original size:13 final size:13
Alignment explanation
Indices: 198853--198877 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
198843 TATTTTTTAA
198853 TAATATTTATATC
1 TAATATTTATATC
198866 TAATATTTATAT
1 TAATATTTATAT
198878 GTTAATAAAA
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:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATATTTATATC
Found at i:199291 original size:39 final size:41
Alignment explanation
Indices: 199175--199291 Score: 109
Period size: 39 Copynumber: 2.8 Consensus size: 41
199165 TCTAATTTTA
*
199175 ATTAATATTTAAATAATAAAATAATTTTAAAATTAAAGATAGAT
1 ATTAAT-TTTAAATAATAAAATAATTTTTAAATT--AGATAGAT
* * *
199219 ATTAATATT-AAT-ATAAAAATAATTTTTTTAATTA-TTA-AT
1 ATTAATTTTAAATAAT-AAAATAA-TTTTTAAATTAGATAGAT
199258 ATT-ATTTTAAATAATAAAATTAATTTTTAAATTA
1 ATTAATTTTAAATAATAAAA-TAATTTTTAAATTA
199292 ATTTAAATCT
Statistics
Matches: 62, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
38 4 0.06
39 22 0.35
40 7 0.11
41 3 0.05
42 10 0.16
43 10 0.16
44 6 0.10
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (41 bp):
ATTAATTTTAAATAATAAAATAATTTTTAAATTAGATAGAT
Found at i:201023 original size:25 final size:25
Alignment explanation
Indices: 200977--201027 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 25
200967 ATTTTAATAT
200977 ATTTTTATATTAATATCATATTTATA
1 ATTTTTATATTAATATCATA-TTATA
*
201003 ATTTTT-TATT-ATACTCCTATTATA
1 ATTTTTATATTAATA-TCATATTATA
201027 A
1 A
201028 AATCATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 9 0.39
25 8 0.35
26 6 0.26
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTTTATATTAATATCATATTATA
Found at i:201308 original size:2 final size:2
Alignment explanation
Indices: 201301--201334 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
201291 AATTAATCAT
201301 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
201335 ACTAAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:201625 original size:16 final size:18
Alignment explanation
Indices: 201590--201628 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 18
201580 TTGAATGTAT
201590 TAAATATATTTATTAAATA
1 TAAATATATTTA-TAAATA
201609 TAAATAT-TTTA-AAATA
1 TAAATATATTTATAAATA
201625 TAAA
1 TAAA
201629 AAATAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
18 4 0.20
19 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATATATTTATAAATA
Found at i:201810 original size:109 final size:108
Alignment explanation
Indices: 201681--201898 Score: 280
Period size: 109 Copynumber: 2.0 Consensus size: 108
201671 TAATGTTGAC
* * * *
201681 TCCCTTTCGTCGGCTAAAAACATGTTAATACCCTCATTATTTTTTAAAAAATATATATAATTGT-
1 TCCCTTTCGCCGGCTAAAAACATATTAATACCCTCATTATTTTTT-AAAAAGA-ATATAATTATC
201745 CCTCTTAGGCTTTGACAATAGATGAGCTAGGTTTAT-ATATATATA
64 CCT-TTAGGCTTTGACAATAGATGAGCTAGGTTTATAATATATATA
***
201790 TCCCTTTCGCCGG-TCAAAAACATATTAATACCCTCATTATTTTTTTTTAAGAATATAATTATCC
1 TCCCTTTCGCCGGCT-AAAAACATATTAATACCCTCATTATTTTTTAAAAAGAATATAATTATCC
* * * *
201854 CTTTAGGTTTTGACGATGGATGAGCTAGGTTTTTAATATATATA
65 CTTTAGGCTTTGACAATAGATGAGCTAGGTTTATAATATATATA
201898 T
1 T
201899 ATATATATAT
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
107 37 0.39
108 17 0.18
109 41 0.43
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (108 bp):
TCCCTTTCGCCGGCTAAAAACATATTAATACCCTCATTATTTTTTAAAAAGAATATAATTATCCC
TTTAGGCTTTGACAATAGATGAGCTAGGTTTATAATATATATA
Found at i:201896 original size:2 final size:2
Alignment explanation
Indices: 201889--201918 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
201879 TAGGTTTTTA
201889 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
201919 CAAAAAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:202440 original size:22 final size:22
Alignment explanation
Indices: 202415--202457 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
202405 AAATTTTATT
202415 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
*
202437 TAAATATTAATATGAAAATAT
1 TAAATATTAATATAAAAATAT
202458 TTTTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:202796 original size:18 final size:19
Alignment explanation
Indices: 202773--202816 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
202763 TTTGTATTTA
202773 TAATTTTCT-TTATTTTTAG
1 TAATTTTCTCTTATTTTT-G
202792 T-ATTTT-TCTTATTTTTG
1 TAATTTTCTCTTATTTTTG
202809 TAATTTTC
1 TAATTTTC
202817 ATTTTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.14
18 18 0.82
19 1 0.05
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (19 bp):
TAATTTTCTCTTATTTTTG
Found at i:202800 original size:19 final size:17
Alignment explanation
Indices: 202773--202816 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
202763 TTTGTATTTA
202773 TAATTTTCTTTATTTTTAG
1 TAATTTTC-TTATTTTT-G
*
202792 TATTTTTCTTATTTTTG
1 TAATTTTCTTATTTTTG
202809 TAATTTTC
1 TAATTTTC
202817 ATTTTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 8 0.35
19 7 0.30
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (17 bp):
TAATTTTCTTATTTTTG
Found at i:203189 original size:2 final size:2
Alignment explanation
Indices: 203184--203208 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
203174 CTTTATTTCT
203184 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
203209 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:204861 original size:17 final size:17
Alignment explanation
Indices: 204841--204885 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
204831 TAATTTTTTA
* *
204841 AAAAAAAATTTAAATAT
1 AAAAAATATTTAAAAAT
204858 AAAAAATA-TTAAAAAT
1 AAAAAATATTTAAAAAT
*
204874 TAAAAATATTTA
1 AAAAAATATTTA
204886 TATCAACTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAAATATTTAAAAAT
Found at i:206149 original size:63 final size:63
Alignment explanation
Indices: 206049--206177 Score: 195
Period size: 63 Copynumber: 2.0 Consensus size: 63
206039 CAGCTTTCCA
* *
206049 GGCAATGCAGATGCTCCAAATCAAGGTGGCATAGCCATGGCACAACCTCAGTTCCCACCCCAG
1 GGCAATGCAGATGCTCCAAATCAAGGTGGCATAGCCATGCCACAACCTAAGTTCCCACCCCAG
* * * * *
206112 GGCAATGCAGCTGTTCCGAATCAAGGTGGCATGGCCATGCCATAACCTAAGTTCCCACCCCAG
1 GGCAATGCAGATGCTCCAAATCAAGGTGGCATAGCCATGCCACAACCTAAGTTCCCACCCCAG
206175 GGC
1 GGC
206178 TCTGTGAATC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (63 bp):
GGCAATGCAGATGCTCCAAATCAAGGTGGCATAGCCATGCCACAACCTAAGTTCCCACCCCAG
Found at i:206549 original size:31 final size:33
Alignment explanation
Indices: 206514--206585 Score: 112
Period size: 31 Copynumber: 2.2 Consensus size: 33
206504 GTATTTTATA
206514 ATTATATAAATTTCAATA-ATTAATA-ATTCAT
1 ATTATATAAATTTCAATATATTAATATATTCAT
* *
206545 ATTATATAAATTTTAATATATTTATATATTCAT
1 ATTATATAAATTTCAATATATTAATATATTCAT
206578 ATTATATA
1 ATTATATA
206586 TTATATCATG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 17 0.46
32 6 0.16
33 14 0.38
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (33 bp):
ATTATATAAATTTCAATATATTAATATATTCAT
Found at i:219814 original size:14 final size:13
Alignment explanation
Indices: 219782--219832 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
219772 TTTATCATAC
*
219782 ATTTTCATTTATTT
1 ATTTTTATTT-TTT
219796 A-TTTTATTATTTT
1 ATTTTTATT-TTTT
*
219809 ATTTTTATTTTTC
1 ATTTTTATTTTTT
219822 ATCTTTTATTT
1 AT-TTTTATTT
219833 ATTAAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 15 0.47
14 17 0.53
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.75
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:220127 original size:18 final size:20
Alignment explanation
Indices: 220090--220126 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
220080 TTTTCCTTTC
220090 AATTATTTTCTCACATTTTT
1 AATTATTTTCTCACATTTTT
220110 AATT-TTTT-TCAC-TTTTT
1 AATTATTTTCTCACATTTTT
220127 TCTTCCACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.29
18 4 0.24
19 4 0.24
20 4 0.24
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.65
Consensus pattern (20 bp):
AATTATTTTCTCACATTTTT
Found at i:221633 original size:18 final size:19
Alignment explanation
Indices: 221596--221633 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
221586 ATAAAGCATT
*
221596 AAAAAATTTTAATGTATTA
1 AAAAAATTTTAATATATTA
221615 AAAAAATTTTAATAT-TTA
1 AAAAAATTTTAATATATTA
221633 A
1 A
221634 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AAAAAATTTTAATATATTA
Found at i:223088 original size:29 final size:30
Alignment explanation
Indices: 223047--223103 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 30
223037 ACATCAAAAA
223047 GTTATATTGAAAGAACACAACATTTAAATTT
1 GTTATATTGAAAG-ACACAACATTTAAATTT
* *
223078 GTTATA-T-AAAGACATAGCATTTAAAT
1 GTTATATTGAAAGACACAACATTTAAAT
223104 AAAAACATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.54
29 4 0.17
30 1 0.04
31 6 0.25
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.35
Consensus pattern (30 bp):
GTTATATTGAAAGACACAACATTTAAATTT
Found at i:223103 original size:242 final size:238
Alignment explanation
Indices: 222653--223121 Score: 740
Period size: 242 Copynumber: 2.0 Consensus size: 238
222643 CTTAATAAGT
* * *
222653 TAGCAATTATTTAAAAGTCAAAGATGGGTACTTGGATACTTGAATACTTGGACTTAAATTTAGAG
1 TAGCAATTATTTAAAAGTAAAAAATGGGTACTTGGATACTTGAACACTTGGACTTAAATTTAGAG
*
222718 ATACAATTATATTTTAATTATATTATTTATTTATTTATTAATATTTAATTCGAAATATTTTATAT
66 ATACAATTATATTTTAATTATATTATTTATTTATTTATTAATATTTAATTCGAAATATTATATAT
* * * * * *
222783 ATATATTTTATTGCATCAAAAAGTTGTGTTTAAAGAATACAACATTTAAACTTGTTATTTAAAGA
131 ATATATTTTATTACATCAAAAAGTTATATTGAAAGAACACAACATTTAAACTTGTTATATAAAGA
* *
222848 TATAGCATTTAAATAAAGACATGTTGTGTAAAAACACAAACTG
196 CATAGCATTTAAATAAAAACATGTTGTGTAAAAACACAAACTG
* * *
222891 TAGCAATTATTTAAAAGTAAAAAATGGGTACTTGGGTATTTGAGCACTTGGACTTAAATTTAGAG
1 TAGCAATTATTTAAAAGTAAAAAATGGGTACTTGGATACTTGAACACTTGGACTTAAATTTAGAG
* *
222956 ATGCAATTATATTTTAATTATATTATTTATTTATTTATTTATTAATATTTAATTTGAAATATTAT
66 ATACAATTATATTTTAA-T-TA-TA-TTATTTATTTATTTATTAATATTTAATTCGAAATATTAT
*
223021 ATATATATATTTTATTACATCAAAAAGTTATATTGAAAGAACACAACATTTAAATTTGTTATATA
127 ATATATATATTTTATTACATCAAAAAGTTATATTGAAAGAACACAACATTTAAACTTGTTATATA
223086 AAGACATAGCATTTAAATAAAAACATGTTGTGTAAA
192 AAGACATAGCATTTAAATAAAAACATGTTGTGTAAA
223122 GACGTAACTA
Statistics
Matches: 209, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
238 75 0.36
239 1 0.00
240 2 0.01
241 2 0.01
242 129 0.62
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (238 bp):
TAGCAATTATTTAAAAGTAAAAAATGGGTACTTGGATACTTGAACACTTGGACTTAAATTTAGAG
ATACAATTATATTTTAATTATATTATTTATTTATTTATTAATATTTAATTCGAAATATTATATAT
ATATATTTTATTACATCAAAAAGTTATATTGAAAGAACACAACATTTAAACTTGTTATATAAAGA
CATAGCATTTAAATAAAAACATGTTGTGTAAAAACACAAACTG
Found at i:223722 original size:3 final size:3
Alignment explanation
Indices: 223714--223761 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
223704 AACGGACCGT
* *
223714 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
223760 TT
1 TT
223762 TTAGGAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.95
4 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:223886 original size:14 final size:15
Alignment explanation
Indices: 223856--223888 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
223846 TTGTAACCAG
223856 AAATTTAAAATTAAA
1 AAATTTAAAATTAAA
*
223871 AAATTTAAATTTAAA
1 AAATTTAAAATTAAA
223886 AAA
1 AAA
223889 AAAAAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTTAAAATTAAA
Found at i:226815 original size:126 final size:123
Alignment explanation
Indices: 226537--226937 Score: 613
Period size: 123 Copynumber: 3.2 Consensus size: 123
226527 AGTGACTAGT
* * *
226537 ATGGTCGATGAAGAAGTATTGGTTGATGTAGATGTAGCTGAAGCTGAAACAATCCATGTGAGTTC
1 ATGGT-GATGCAGAAGCATTGGTTGATGTAAATGTAGCTGAAGCTGAAACAATCCATGTGAGTTC
* * * *
226602 ATTCCAGAATGCTTCGCAATCTGTTCTGGATGATATCCCAGTTCACAAGATGGTAAATT
65 ATTCCACAATGCTTCCCAATCTGTTGTGGATGATATCCCAGTTCACAAGATGGTAAATG
* * *
226661 ATGTTGATGCAGAAGCATTGGTTGATGTAAATGTATCTGCAGCTGAAACAATCCATGTGAGTTCA
1 ATGGTGATGCAGAAGCATTGGTTGATGTAAATGTAGCTGAAGCTGAAACAATCCATGTGAGTTCA
* *
226726 TTCCACAATGCTTCCCAATCTGCTGTGGACGGTATTATCCCAGTTCACAAGATGGTAAATG
66 TTCCACAATGCTTCCCAATCTGTTGTGGA-TG-A-TATCCCAGTTCACAAGATGGTAAATG
* *
226787 ATGGTGATGCAGAAGCATTGGTTGATGTAAATGTGGCTGAAGCTGAAACAATCCATGTGAGCTCA
1 ATGGTGATGCAGAAGCATTGGTTGATGTAAATGTAGCTGAAGCTGAAACAATCCATGTGAGTTCA
226852 TTCCACAATGCTTCCCAATCTGTTGTGGATGATATCCCAGTTCACAAGATGGTAAATG
66 TTCCACAATGCTTCCCAATCTGTTGTGGATGATATCCCAGTTCACAAGATGGTAAATG
* * *
226910 AGGGTGATGCGGAAGCATTGATTGATGT
1 ATGGTGATGCAGAAGCATTGGTTGATGT
226938 CTGTGTAAAG
Statistics
Matches: 252, Mismatches: 22, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
123 131 0.52
124 6 0.02
125 2 0.01
126 113 0.45
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (123 bp):
ATGGTGATGCAGAAGCATTGGTTGATGTAAATGTAGCTGAAGCTGAAACAATCCATGTGAGTTCA
TTCCACAATGCTTCCCAATCTGTTGTGGATGATATCCCAGTTCACAAGATGGTAAATG
Found at i:230073 original size:2 final size:2
Alignment explanation
Indices: 230068--230123 Score: 75
Period size: 2 Copynumber: 30.0 Consensus size: 2
230058 TCTCTCTCTC
*
230068 TA TA TA TA TA -A AA TA TA -A TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
230107 -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
230124 AGGTTCTGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
1 4 0.08
2 45 0.92
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:230122 original size:22 final size:22
Alignment explanation
Indices: 230068--230124 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
230058 TCTCTCTCTC
*
230068 TATATATATAAAATATAATATA
1 TATATATATATAATATAATATA
230090 TATATATATATAATATAATATA
1 TATATATATATAATATAATATA
230112 TATATATATATAA
1 TATATATATATAA
230125 GGTTCTGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TATATATATATAATATAATATA
Found at i:234321 original size:16 final size:16
Alignment explanation
Indices: 234300--234331 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
234290 AACATTACAT
234300 TTATGCTTAGAATCCA
1 TTATGCTTAGAATCCA
234316 TTATGCTTAGAATCCA
1 TTATGCTTAGAATCCA
234332 ATATCTAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
TTATGCTTAGAATCCA
Found at i:237957 original size:3 final size:3
Alignment explanation
Indices: 237949--237996 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
237939 GGAAAAAATA
*
237949 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
237997 CATACCACCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:241751 original size:16 final size:16
Alignment explanation
Indices: 241732--241865 Score: 55
Period size: 16 Copynumber: 8.2 Consensus size: 16
241722 TAATAATTAA
241732 TATATTTTTAATATAT
1 TATATTTTTAATATAT
* *
241748 TATAATTTT-ATTTA-
1 TATATTTTTAATATAT
* *
241762 AAAATTTTT-ATAT-T
1 TATATTTTTAATATAT
241776 TATATAAATTTTAATATAT
1 TATAT---TTTTAATATAT
*
241795 TAATAATTTATAATATA-
1 T-AT-ATTTTTAATATAT
* *
241812 TAAATTTTAAAATATAT
1 TATATTTT-TAATATAT
241829 TATATTATATTTAAT-TAT
1 TATA-T-T-TTTAATATAT
* * *
241847 TTTATTTATATTATAT
1 TATATTTTTAATATAT
241863 TAT
1 TAT
241866 GTCGAATGAT
Statistics
Matches: 86, Mismatches: 18, Indels: 28
0.65 0.14 0.21
Matches are distributed among these distances:
14 12 0.14
15 12 0.14
16 21 0.24
17 9 0.10
18 20 0.23
19 6 0.07
20 4 0.05
21 2 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATTTTTAATATAT
Found at i:241786 original size:18 final size:18
Alignment explanation
Indices: 241763--241819 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
241753 TTTTATTTAA
241763 AAATTTTTATATTTATAT
1 AAATTTTTATATTTATAT
*
241781 AAATTTTAATATATTA-AT
1 AAATTTTTATAT-TTATAT
*
241799 -AA--TTTATA-ATATAT
1 AAATTTTTATATTTATAT
241813 AAATTTT
1 AAATTTT
241820 AAAATATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 11
0.69 0.07 0.24
Matches are distributed among these distances:
13 2 0.06
14 2 0.06
15 7 0.23
17 4 0.13
18 13 0.42
19 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATTTTTATATTTATAT
Found at i:241826 original size:14 final size:14
Alignment explanation
Indices: 241776--241827 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
241766 TTTTTATATT
241776 TATATAAATTTTAA
1 TATATAAATTTTAA
241790 TATATTAATAATTTATAA
1 TATA-T-A-AATTT-TAA
241808 TATATAAATTTTAA
1 TATATAAATTTTAA
*
241822 AATATA
1 TATATA
241828 TTATATTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 12 0.36
15 6 0.18
16 2 0.06
17 6 0.18
18 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:241834 original size:5 final size:5
Alignment explanation
Indices: 241824--241865 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
241814 AATTTTAAAA
*
241824 TATAT TATAT TATAT T-TAAT TATTT TAT-T TATAT TATAT TAT
1 TATAT TATAT TATAT TAT-AT TATAT TATAT TATAT TATAT TAT
241866 GTCGAATGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
4 5 0.15
5 27 0.82
6 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TATAT
Found at i:242132 original size:20 final size:19
Alignment explanation
Indices: 242109--242154 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
242099 AATAATATTA
242109 AAATATTTTAAATATTAAAT
1 AAATATTTT-AATATTAAAT
*
242129 AAATAATTTTAATGTTAAAT
1 AAAT-ATTTTAATATTAAAT
242149 AAATAT
1 AAATAT
242155 AATATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 17 0.71
21 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AAATATTTTAATATTAAAT
Found at i:242197 original size:19 final size:21
Alignment explanation
Indices: 242170--242210 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
242160 ATAATAAATA
242170 TTTAATAAA-AATAT-ATTTT
1 TTTAATAAATAATATGATTTT
*
242189 TTTATTAAATAATATGATTTT
1 TTTAATAAATAATATGATTTT
242210 T
1 T
242211 GAAAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTAATAAATAATATGATTTT
Found at i:244925 original size:32 final size:32
Alignment explanation
Indices: 244866--244941 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
244856 AAAATTTAAT
* *
244866 TTAAATAAATTTAAATTATTAATTTTTTTCAAA
1 TTAAATAAA-TTAAATTAATAATTTTTTTAAAA
*
244899 TTAAATTAATTAAATTTAATAA-TTTTTTAAAA
1 TTAAATAAATTAAA-TTAATAATTTTTTTAAAA
*
244931 TTTAATAAATT
1 TTAAATAAATT
244942 TTATTAACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 23 0.62
33 14 0.38
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TTAAATAAATTAAATTAATAATTTTTTTAAAA
Found at i:244933 original size:18 final size:20
Alignment explanation
Indices: 244910--244948 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
244900 TAAATTAATT
244910 AAATTTAAT-AATTTT-TTA
1 AAATTTAATAAATTTTATTA
244928 AAATTTAATAAATTTTATTA
1 AAATTTAATAAATTTTATTA
244948 A
1 A
244949 CTCGATCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 6 0.32
20 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATTTAATAAATTTTATTA
Found at i:245372 original size:20 final size:20
Alignment explanation
Indices: 245289--245372 Score: 54
Period size: 19 Copynumber: 4.3 Consensus size: 20
245279 ATTATGTGTT
*
245289 TATATTTATATTT-TTTTATT
1 TATATTTAT-TTTATTTTATA
* * *
245309 TA-AATTATTATAGTTTT-TG
1 TATATTTATTTTA-TTTTATA
*
245328 TATATTT-TTTATATATTA-A
1 TATATTTATTT-TATTTTATA
245347 TA-ATTTATTTTATTTTATA
1 TATATTTATTTTATTTTATA
245366 TATATTT
1 TATATTT
245373 TTATATATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
18 12 0.25
19 21 0.44
20 15 0.31
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
TATATTTATTTTATTTTATA
Found at i:245425 original size:14 final size:11
Alignment explanation
Indices: 245288--245417 Score: 67
Period size: 11 Copynumber: 11.7 Consensus size: 11
245278 CATTATGTGT
*
245288 TTATATTTATA
1 TTATTTTTATA
245299 TT-TTTTTAT-
1 TTATTTTTATA
*
245308 TTAAATTATTATA
1 TT--ATTTTTATA
*
245321 GTT-TTTGTATA
1 -TTATTTTTATA
245332 TT-TTTTATATA
1 TTATTTT-TATA
* *
245343 TTAATAATTTATT
1 TT-AT-TTTTATA
245356 TTA-TTTTATA
1 TTATTTTTATA
245366 TATATTTTTATA
1 T-TATTTTTATA
* *
245378 TATATATTTGTA
1 T-TATTTTTATA
*
245390 TTA--TATATA
1 TTATTTTTATA
245399 TTATTTTTATA
1 TTATTTTTATA
245410 TTATTTTT
1 TTATTTTT
245418 TAAATATTTT
Statistics
Matches: 92, Mismatches: 14, Indels: 26
0.70 0.11 0.20
Matches are distributed among these distances:
9 9 0.10
10 17 0.18
11 31 0.34
12 25 0.27
13 6 0.07
14 4 0.04
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
TTATTTTTATA
Done.