Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020948.1 Corchorus olitorius cultivar O-4 contig20981, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5937
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Found at i:4865 original size:22 final size:20
Alignment explanation
Indices: 4840--4905 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
4830 ATTTCATTTT
4840 AATTTTCATTCTTTAATTACCA
1 AATTTTC-TT-TTTAATTACCA
* *
4862 AATTCT-TTTTTACTTTACCA
1 AATTTTCTTTTTA-ATTACCA
* *
4882 AAATTTCTTTTTTATTACCA
1 AATTTTCTTTTTAATTACCA
4902 AATT
1 AATT
4906 CTTTTTTAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 4 0.11
20 21 0.60
21 5 0.14
22 5 0.14
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTTCTTTTTAATTACCA
Found at i:4881 original size:20 final size:19
Alignment explanation
Indices: 4851--4966 Score: 89
Period size: 18 Copynumber: 6.2 Consensus size: 19
4841 ATTTTCATTC
*
4851 TTTAATTACCAAATTCTTT
1 TTTATTTACCAAATTCTTT
4870 TTTACTTTACCAAAATTTCTTT
1 TTTA-TTTACC-AAA-TTCTTT
4892 TTTA-TTACCAAATTCTTT
1 TTTATTTACCAAATTCTTT
* * *
4910 TTTAGTTATC-AATTC-CT
1 TTTATTTACCAAATTCTTT
** *
4927 TTTACTTTA-TTAATT-TTC
1 TTTA-TTTACCAAATTCTTT
*
4945 TTTAATTACCAAATTCTTT
1 TTTATTTACCAAATTCTTT
4964 TTT
1 TTT
4967 TACTTGCCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
17 8 0.10
18 30 0.39
19 16 0.21
20 10 0.13
21 3 0.04
22 10 0.13
ACGTcount: A:0.27, C:0.16, G:0.01, T:0.57
Consensus pattern (19 bp):
TTTATTTACCAAATTCTTT
Found at i:4936 original size:40 final size:40
Alignment explanation
Indices: 4848--4938 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 40
4838 TTAATTTTCA
* *
4848 TTCTTTAATTACCAAATTCTTTTTTACTTTACCAAAATTTCT
1 TTCTTT-ATTACCAAATTCTTTTTTACGTTACC-AAATTCCT
*
4890 TT-TTTATTACCAAATTCTTTTTTA-GTTATC-AATTCCTT
1 TTCTTTATTACCAAATTCTTTTTTACGTTACCAAATTCC-T
4928 TTACTTTATTA
1 TT-CTTTATTA
4939 ATTTTCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
37 5 0.12
38 3 0.07
39 4 0.09
40 26 0.60
41 3 0.07
42 2 0.05
ACGTcount: A:0.26, C:0.16, G:0.01, T:0.56
Consensus pattern (40 bp):
TTCTTTATTACCAAATTCTTTTTTACGTTACCAAATTCCT
Found at i:4993 original size:30 final size:30
Alignment explanation
Indices: 4959--5062 Score: 101
Period size: 30 Copynumber: 3.6 Consensus size: 30
4949 ATTACCAAAT
* *
4959 TCTTTTTTTACTTGCCAATTTTACTTTTAC
1 TCTTTTTTTAATTACCAATTTTACTTTTAC
* *
4989 TC---TTTTAATTACCAA-ATT-CTTTTTAA
1 TCTTTTTTTAATTACCAATTTTAC-TTTTAC
* *
5015 TTTTTTTTTAATTACCAATTTTACTTTTCC
1 TCTTTTTTTAATTACCAATTTTACTTTTAC
*
5045 TCTTTTTTTACTTACCAA
1 TCTTTTTTTAATTACCAA
5063 ATTCCTTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
25 1 0.02
26 8 0.14
27 11 0.19
29 13 0.22
30 24 0.41
31 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.01, T:0.59
Consensus pattern (30 bp):
TCTTTTTTTAATTACCAATTTTACTTTTAC
Found at i:5000 original size:47 final size:48
Alignment explanation
Indices: 4926--5686 Score: 743
Period size: 48 Copynumber: 15.6 Consensus size: 48
4916 TATCAATTCC
* * * *
4926 TTTTACTTTATTAATTTTCTTTAATTACCAAATTCTTTTTTTACTTGCCAA
1 TTTTAC-TT-TTACTTTT-TTTACTTACCAAATTCTTTTTTTAATTACCAA
* *
4977 TTTTACTTTTAC-TCTTTTAATTACCAAATTCTTTTTAATTTTTTTTTAATTACCAA
1 TTTTACTTTTACTTTTTTTACTTACCAAATTC---------TTTTTTTAATTACCAA
* *
5033 TTTTACTTTTCCTCTTTTTTTACTTACCAAATTCCTTTTTTAATTACCAA
1 TTTTACTTTT--ACTTTTTTTACTTACCAAATTCTTTTTTTAATTACCAA
*
5083 -TTT-CTTTTACCTTTTTTTACTTACCAAATTC--TTTTTACTTACCAA
1 TTTTACTTTTA-CTTTTTTTACTTACCAAATTCTTTTTTTAATTACCAA
*
5128 -TTT-CTTTTACCTTTTTTTATTTACCAAATTC-TTTTTTAATTACCAA
1 TTTTACTTTTA-CTTTTTTTACTTACCAAATTCTTTTTTTAATTACCAA
**
5174 TTTTA-----ACTTTTTTTTAAATACCAAATTCTCATTTTTTTAATTACCAA
1 TTTTACTTTTAC-TTTTTTTACTTACCAAA-T-TC-TTTTTTTAATTACCAA
5221 TTTTACTTTTACTTTTTTTTACTTACCAAATTCTTTTTTTTAATTACCAA
1 TTTTACTTTTAC-TTTTTTTACTTACCAAATTC-TTTTTTTAATTACCAA
***
5271 TTTTACTTTTACTTTTTTTCACTTACCAAATTAC--CAATT--TTA-C--
1 TTTTACTTTTACTTTTTTT-ACTTACCAAATT-CTTTTTTTAATTACCAA
* * **
5314 TTTT-GTTTT-TTTTACTT----ACCAAATTCGTTTTTTTTTAATTACCAA
1 TTTTACTTTTACTTTTTTTACTTACCAAATTC---TTTTTTTAATTACCAA
*
5359 TTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTAATTACAAA
1 TTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTAATTACCAA
* * *
5407 TTTTACTTTTACTTATTTTAATTACCAAATTC--TTTTTACTTACCAA
1 TTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTAATTACCAA
*
5453 TTTTACTTTTAC-TTTTTTACTTACCAAATTATTTTTTTTTAATTACCAA
1 TTTTACTTTTACTTTTTTTACTTACCAAA-T-TCTTTTTTTAATTACCAA
*
5502 TTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTCAATTACCAA
1 TTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTAATTACCAA
5550 TTTTACTTTTACTTCTTTTTTTTTACTTACCAAATTCTTTTTTTAATTACCAA
1 TTTTACTTTTA---C--TTTTTTTACTTACCAAATTCTTTTTTTAATTACCAA
5603 TTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTTTTAATTACCAA
1 TTTTACTTTTACTTTTTTTACTTACCAAATTC---TTTTTTTAATTACCAA
5654 TTTTACTTTTACTTTTTTTTTACTTACCAAATT
1 TTTTACTTTTAC--TTTTTTTACTTACCAAATT
5687 ACCAATTTTA
Statistics
Matches: 608, Mismatches: 43, Indels: 116
0.79 0.06 0.15
Matches are distributed among these distances:
35 1 0.00
36 8 0.01
40 2 0.00
41 5 0.01
42 8 0.01
43 21 0.03
44 1 0.00
45 64 0.11
46 45 0.07
47 66 0.11
48 101 0.17
49 39 0.06
50 76 0.12
51 46 0.08
52 18 0.03
53 65 0.11
56 24 0.04
58 1 0.00
59 17 0.03
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (48 bp):
TTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTAATTACCAA
Found at i:5040 original size:56 final size:60
Alignment explanation
Indices: 4956--5077 Score: 162
Period size: 56 Copynumber: 2.1 Consensus size: 60
4946 TTAATTACCA
* *
4956 AATTCTTTTTTTACTTGCCAATTTTACTTTTACTC-TTTTAATTACCAAATT-C-TTTTT
1 AATTCTTTTTTTAATTACCAATTTTACTTTTACTCTTTTTAATTACCAAATTCCTTTTTT
* *
5013 AATT-TTTTTTTAATTACCAATTTTACTTTTCCTCTTTTTTTACTTACCAAATTCCTTTTTT
1 AATTCTTTTTTTAATTACCAATTTTACTTTTACTC--TTTTTAATTACCAAATTCCTTTTTT
5074 AATT
1 AATT
5078 ACCAATTTCT
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
56 27 0.48
57 4 0.07
59 15 0.27
60 1 0.02
61 9 0.16
ACGTcount: A:0.23, C:0.17, G:0.01, T:0.59
Consensus pattern (60 bp):
AATTCTTTTTTTAATTACCAATTTTACTTTTACTCTTTTTAATTACCAAATTCCTTTTTT
Found at i:5070 original size:29 final size:29
Alignment explanation
Indices: 4991--5071 Score: 90
Period size: 30 Copynumber: 2.8 Consensus size: 29
4981 ACTTTTACTC
* *
4991 TTTTAATTACCAAATTCTTTTTAATTTTT
1 TTTTAATTACCAAATTCCTTTTAATCTTT
* * **
5020 TTTTAATTACCAATTTTACTTTTCCTCTTT
1 TTTTAATTACCAA-ATTCCTTTTAATCTTT
*
5050 TTTTACTTACCAAATTCCTTTT
1 TTTTAATTACCAAATTCCTTTT
5072 TTAATTACCA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 20 0.48
30 22 0.52
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTAATTACCAAATTCCTTTTAATCTTT
Found at i:5073 original size:20 final size:20
Alignment explanation
Indices: 5048--5127 Score: 65
Period size: 20 Copynumber: 3.8 Consensus size: 20
5038 CTTTTCCTCT
5048 TTTTTTACTTACCAAATTCC
1 TTTTTTACTTACCAAATTCC
* *
5068 TTTTTTAATTACCAATTTCTTTTACC
1 TTTTTTACTTACCAA-----ATT-CC
5094 TTTTTTTACTTACCAAATT-C
1 -TTTTTTACTTACCAAATTCC
5114 -TTTTTACTTACCAA
1 TTTTTTACTTACCAA
5128 TTTCTTTTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
18 14 0.29
20 15 0.31
22 2 0.04
25 2 0.04
26 2 0.04
27 14 0.29
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTTACTTACCAAATTCC
Found at i:5106 original size:27 final size:27
Alignment explanation
Indices: 5068--5162 Score: 91
Period size: 27 Copynumber: 3.9 Consensus size: 27
5058 ACCAAATTCC
*
5068 TTTTTTAATTACCAATTTCTTTTACCT
1 TTTTTTACTTACCAATTTCTTTTACCT
*
5095 TTTTTTACTTACCAA-----ATT--C-
1 TTTTTTACTTACCAATTTCTTTTACCT
5114 -TTTTTACTTACCAATTTCTTTTACCT
1 TTTTTTACTTACCAATTTCTTTTACCT
* *
5140 TTTTTTATTTACCAAATTCTTTT
1 TTTTTTACTTACCAATTTCTTTT
5163 TTAATTACCA
Statistics
Matches: 54, Mismatches: 5, Indels: 18
0.70 0.06 0.23
Matches are distributed among these distances:
18 14 0.26
20 1 0.02
22 2 0.04
23 2 0.04
25 1 0.02
27 34 0.63
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTTTACTTACCAATTTCTTTTACCT
Found at i:5137 original size:17 final size:18
Alignment explanation
Indices: 5096--5135 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
5086 CTTTTACCTT
5096 TTTTTACTTACCAAATTC
1 TTTTTACTTACCAAATTC
*
5114 TTTTTACTTACCAATTTC
1 TTTTTACTTACCAAATTC
5132 TTTT
1 TTTT
5136 ACCTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTACTTACCAAATTC
Found at i:5226 original size:244 final size:238
Alignment explanation
Indices: 4940--5663 Score: 820
Period size: 244 Copynumber: 3.0 Consensus size: 238
4930 ACTTTATTAA
* * * *
4940 TTTTCTTTAATTACCAAATTCTTTTTTTACTTGCCAATTTTACTTTTACTCTTTTAATTACCAAA
1 TTTTTTTTAATTACCAAATTCTTTTTTTACTTACCAATTTTACTTTTACTTTTTTACTTACCAAA
5005 TTCTTTTTAATTTTTTTTTAATTACCAATTTTACTTTTCCTCTTTTTTTACTTACCAAATTCCTT
66 TTC---TT-ATTTTTTTTTAATTACCAATTTTACTTTT-CTCTTTTTTTACTTACCAAATTCCTT
*
5070 TTTTAATTACCAATTTCTTTTACCTTTTTTTACTTACCAAATTC-TTTTTACTTACCAA-TTT-C
126 TTTTAATTACCAATTTCTTTTACCTTTTTTTACTTACCAAATTCTTTTTTAATTACCAATTTTAC
*
5132 TTTTACCTTTTTTTATTTACCAAATTC-TTTTTTAATTACCAATTTTAAC
191 TTTTA-CTTTTTTTACTTACCAAATTCTTTTTTTAATTACCAATTTT-AC
* *
5181 TTTTTTTTAAATACCAAATTCTCATTTTTTTAATTACCAATTTTACTTTTACTTTTTTTTACTTA
1 TTTTTTTTAATTACCAAA-T-TC-TTTTTTTACTTACCAATTTTACTTTTAC--TTTTTTACTTA
*
5246 CCAAATTC----TTTTTTTTAATTACCAATTTTACTTTTACT-TTTTTTCACTTACCAAATTACC
61 CCAAATTCTTATTTTTTTTTAATTACCAATTTTACTTTT-CTCTTTTTTTACTTACCAAATT-CC
* **
5306 ------AATT-----TTACTTTT-GTTTTTTTTACTTACCAAATTCGTTTTTTTTTAATTACCAA
124 TTTTTTAATTACCAATTTCTTTTACCTTTTTTTACTTACCAAATTC----TTTTTTAATTACCAA
*
5359 TTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTAATTACAAATTTTAC
185 TTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTAATTACCAATTTTAC
5413 TTTTACTTATTTTAATTACCAAATTC--TTTTTACTTACCAATTTTACTTTTACTTTTTTACTTA
1 --TT--TT-TTTTAATTACCAAATTCTTTTTTTACTTACCAATTTTACTTTTACTTTTTTACTTA
*
5476 CCAAA---TTATTTTTTTTTAATTACCAATTTTACTTTT-ACTTTTTTTACTTACCAAATT-CTT
61 CCAAATTCTTATTTTTTTTTAATTACCAATTTTACTTTTCTCTTTTTTTACTTACCAAATTCCTT
5536 TTTTCAATTACCAATTTTACTTTTACTTCTTTTTTTTTACTTACCAAATTCTTTTTTTAATTACC
126 TTTT-AATTACCAA-TTT-CTTTTAC--C--TTTTTTTACTTACCAAATTC-TTTTTTAATTACC
5601 AATTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTTTTAATTACCAATTTTAC
183 AATTTTACTTTTACTTTTTTTACTTACCAAATTC---TTTTTTTAATTACCAATTTTAC
5660 TTTT
1 TTTT
5664 ACTTTTTTTT
Statistics
Matches: 415, Mismatches: 22, Indels: 90
0.79 0.04 0.17
Matches are distributed among these distances:
226 20 0.05
227 7 0.02
228 1 0.00
230 34 0.08
231 40 0.10
232 54 0.13
233 24 0.06
234 2 0.00
235 6 0.01
236 3 0.01
237 31 0.07
238 31 0.07
241 18 0.04
242 6 0.01
243 4 0.01
244 74 0.18
245 2 0.00
246 17 0.04
247 41 0.10
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (238 bp):
TTTTTTTTAATTACCAAATTCTTTTTTTACTTACCAATTTTACTTTTACTTTTTTACTTACCAAA
TTCTTATTTTTTTTTAATTACCAATTTTACTTTTCTCTTTTTTTACTTACCAAATTCCTTTTTTA
ATTACCAATTTCTTTTACCTTTTTTTACTTACCAAATTCTTTTTTAATTACCAATTTTACTTTTA
CTTTTTTTACTTACCAAATTCTTTTTTTAATTACCAATTTTAC
Found at i:5331 original size:36 final size:37
Alignment explanation
Indices: 5262--5338 Score: 129
Period size: 36 Copynumber: 2.1 Consensus size: 37
5252 TCTTTTTTTT
5262 AATTACCAATTTTACTTTTACTTTTTTTCACTTACCA
1 AATTACCAATTTTACTTTTACTTTTTTTCACTTACCA
* *
5299 AATTACCAATTTTACTTTT-GTTTTTTTTACTTACCA
1 AATTACCAATTTTACTTTTACTTTTTTTCACTTACCA
5335 AATT
1 AATT
5339 CGTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 19 0.50
37 19 0.50
ACGTcount: A:0.27, C:0.18, G:0.01, T:0.53
Consensus pattern (37 bp):
AATTACCAATTTTACTTTTACTTTTTTTCACTTACCA
Found at i:5349 original size:23 final size:22
Alignment explanation
Indices: 5319--5397 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 22
5309 TTTACTTTTG
5319 TTTTTTTTACTTACCAAATTCGT
1 TTTTTTTTACTTACCAAATTC-T
* *
5342 TTTTTTTTAATTACCAATTTTACTTT
1 TTTTTTTTACTTACCAA-ATT-C--T
5368 TACTTTTTTTACTTACCAAATTCT
1 T--TTTTTTTACTTACCAAATTCT
5392 TTTTTT
1 TTTTTT
5398 AATTACAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
22 5 0.11
23 16 0.35
24 4 0.09
25 1 0.02
26 3 0.07
27 2 0.04
28 15 0.33
ACGTcount: A:0.22, C:0.15, G:0.01, T:0.62
Consensus pattern (22 bp):
TTTTTTTTACTTACCAAATTCT
Found at i:5395 original size:20 final size:19
Alignment explanation
Indices: 5370--5421 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
5360 TTTACTTTTA
5370 CTTTTTTTACTTACCAAATT
1 CTTTTTTTACTTA-CAAATT
*
5390 CTTTTTTTAATTACAAATT
1 CTTTTTTTACTTACAAATT
*
5409 -TTACTTTTACTTA
1 CTT-TTTTTACTTA
5422 TTTTAATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.07
19 14 0.50
20 12 0.43
ACGTcount: A:0.27, C:0.15, G:0.00, T:0.58
Consensus pattern (19 bp):
CTTTTTTTACTTACAAATT
Found at i:5406 original size:19 final size:20
Alignment explanation
Indices: 5370--5408 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5360 TTTACTTTTA
*
5370 CTTTTTTTACTTACCAAATT
1 CTTTTTTTAATTACCAAATT
5390 CTTTTTTTAATTA-CAAATT
1 CTTTTTTTAATTACCAAATT
5409 TTACTTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.56
Consensus pattern (20 bp):
CTTTTTTTAATTACCAAATT
Found at i:5515 original size:143 final size:147
Alignment explanation
Indices: 5013--5686 Score: 773
Period size: 143 Copynumber: 4.7 Consensus size: 147
5003 AATTCTTTTT
* * *
5013 AATTTTTTTTTAATTACCAATTTTACTTTTCCTCTTTTTTTACTTACCAAATTC---CTTTTTTA
1 AATTCTTTTTTAATTACCAATTTTACTTTT--AC-TTTTTTACTTACCAAATTCATTTTTTTTTA
* *
5075 ATTACCAA-TTT-CTTTTACCTTTTTTTACTTACCAAATTC-TTTTT-ACTTACCAA-TTT-CTT
63 ATTACCAATTTTACTTTTA-CTTTTTTTACTTACCAAATTCTTTTTTCAATTACAAATTTTACTT
* *
5134 TTACCTTT-TTTTATTTACCA
127 TTATCTTTATTTTAATTACCA
** *
5154 AATTCTTTTTTAATTACCAATTTTAAC--TT--TTTTTTAAATACCAAATTC-TCATTTTTTTAA
1 AATTCTTTTTTAATTACCAATTTT-ACTTTTACTTTTTTACTTACCAAATTCAT-TTTTTTTTAA
* *
5214 TTACCAATTTTACTTTTACTTTTTTTTACTTACCAAATTCTTTTTTTTAATTACCAATTTTACTT
64 TTACCAATTTTACTTTTAC-TTTTTTTACTTACCAAATTC-TTTTTTCAATTACAAATTTTACTT
*
5279 TTA-CTTT-TTTTCACTTACC-
127 TTATCTTTATTTT-AATTACCA
** *
5298 -A---------AATTACCAATTTTACTTTTGTTTTTTTTACTTACCAAATTCGTTTTTTTTTAAT
1 AATTCTTTTTTAATTACCAATTTTACTTTT-ACTTTTTTACTTACCAAATTCATTTTTTTTTAAT
*
5353 TACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTAATTACAAATTTTACTTTTA
65 TACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTCAATTACAAATTTTACTTTTA
5418 -C-TTATTTTAATTACCA
130 TCTTTATTTTAATTACCA
*
5434 AATTC-TTTTTACTTACCAATTTTACTTTTACTTTTTTACTTACCAAATT-ATTTTTTTTTAATT
1 AATTCTTTTTTAATTACCAATTTTACTTTTACTTTTTTACTTACCAAATTCATTTTTTTTTAATT
*
5497 ACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTCAATTACCAATTTTACTTTTAC
66 ACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTCAATTACAAATTTTACTTTTA-
* *
5562 TTCTTTTTTTTTACTTACCA
130 -TC-TTTATTTTAATTACCA
*
5582 AATTCTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTTTTAA
1 AATTC-TTTTTTAATTACCAATTTTACTTTTAC-TTTTTTACTTACCAAATTCATTTTTTTTTAA
5647 TTACCAATTTTACTTTTACTTTTTTTTTACTTACCAAATT
64 TTACCAATTTTACTTTTAC--TTTTTTTACTTACCAAATT
5687 ACCAATTTTA
Statistics
Matches: 471, Mismatches: 21, Indels: 69
0.84 0.04 0.12
Matches are distributed among these distances:
133 2 0.00
134 13 0.03
135 27 0.06
136 31 0.07
137 21 0.04
138 60 0.13
139 5 0.01
140 28 0.06
141 23 0.05
142 7 0.01
143 84 0.18
144 29 0.06
145 30 0.06
146 1 0.00
148 18 0.04
150 25 0.05
151 18 0.04
152 30 0.06
154 19 0.04
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (147 bp):
AATTCTTTTTTAATTACCAATTTTACTTTTACTTTTTTACTTACCAAATTCATTTTTTTTTAATT
ACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTCAATTACAAATTTTACTTTTAT
CTTTATTTTAATTACCA
Found at i:5538 original size:20 final size:20
Alignment explanation
Indices: 5513--5641 Score: 85
Period size: 20 Copynumber: 6.4 Consensus size: 20
5503 TTTACTTTTA
5513 CTTTTTTTACTTACCAAATT
1 CTTTTTTTACTTACCAAATT
* *
5533 CTTTTTTCAATTACC-AATT
1 CTTTTTTTACTTACCAAATT
*
5552 -TTACTTTTACTT--C---TT
1 CTT-TTTTTACTTACCAAATT
5567 -TTTTTTTACTTACCAAATT
1 CTTTTTTTACTTACCAAATT
*
5586 CTTTTTTTAATTACCAATTTTACTTTT
1 CTTTTTTTACTTACCAA----A---TT
5613 ACTTTTTTTACTTACCAAATT
1 -CTTTTTTTACTTACCAAATT
5634 CTTTTTTT
1 CTTTTTTT
5642 TTTAATTACC
Statistics
Matches: 86, Mismatches: 8, Indels: 30
0.69 0.06 0.24
Matches are distributed among these distances:
14 8 0.09
15 4 0.05
16 1 0.01
17 1 0.01
18 2 0.02
19 12 0.14
20 36 0.42
21 2 0.02
24 2 0.02
27 2 0.02
28 16 0.19
ACGTcount: A:0.22, C:0.18, G:0.00, T:0.60
Consensus pattern (20 bp):
CTTTTTTTACTTACCAAATT
Found at i:5672 original size:81 final size:80
Alignment explanation
Indices: 5588--5858 Score: 321
Period size: 81 Copynumber: 3.2 Consensus size: 80
5578 ACCAAATTCT
5588 TTTTTTAATTACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTTTTAATTACCA
1 TTTTTTAATTACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTTTTAATTACCA
*
5653 ATTTTACTTTTACTTTTT
66 ATTTTACTTTTAC---TC
**
5671 TTTTACTTACCAAATTACCAATTTTACTTTTGTTTTTTTTTTACTTACCAAATTCTTCTTTTTTA
1 TTTT--TT----AATTACCAATTTTAC-TTT-TACTTTTTTTACTTACCAAATTC-T-TTTTTT-
*
5736 ATTTAATTACCAATTTTACTTTTACCC
55 -TTTAATTACCAATTTTACTTTTACTC
*
5763 TTTTTTAATTACCAATTTTACTTTTACTTCTTTTTTTAATTACCAAATTC--TTTTTTTTAATTA
1 TTTTTTAATTACCAATTTTACTTTTA---CTTTTTTTACTTACCAAATTCTTTTTTTTTTAATTA
5826 CCAATTTTACTTTTACTC
63 CCAATTTTACTTTTACTC
5844 TTTTTTAATTACCAA
1 TTTTTTAATTACCAA
5859 ATTCTTTTTA
Statistics
Matches: 165, Mismatches: 8, Indels: 32
0.80 0.04 0.16
Matches are distributed among these distances:
81 40 0.24
83 9 0.05
84 1 0.01
85 5 0.03
86 15 0.09
87 19 0.12
89 15 0.09
90 5 0.03
91 21 0.13
92 5 0.03
93 6 0.04
95 24 0.15
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (80 bp):
TTTTTTAATTACCAATTTTACTTTTACTTTTTTTACTTACCAAATTCTTTTTTTTTTAATTACCA
ATTTTACTTTTACTC
Found at i:5690 original size:38 final size:38
Alignment explanation
Indices: 5645--5724 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
5635 TTTTTTTTTT
5645 AATTACCAATTTTACTTTTACTTTTTTTTTACTTACCA
1 AATTACCAATTTTACTTTTACTTTTTTTTTACTTACCA
**
5683 AATTACCAATTTTACTTTTGTTTTTTTTTTACTTACCA
1 AATTACCAATTTTACTTTTACTTTTTTTTTACTTACCA
5721 AATT
1 AATT
5725 CTTCTTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.26, C:0.16, G:0.01, T:0.56
Consensus pattern (38 bp):
AATTACCAATTTTACTTTTACTTTTTTTTTACTTACCA
Found at i:5796 original size:95 final size:91
Alignment explanation
Indices: 5615--5937 Score: 311
Period size: 95 Copynumber: 3.6 Consensus size: 91
5605 TTACTTTTAC
* *
5615 TTTTTTTACTTACCAAATTC-TTTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTTTACTT
1 TTTTTTTACTTACCAAATTCTTTTTTTTTTTAATTACCAATTTTACTTTTAC-TCTTTTTTAATT
*
5679 ACCAAATTACCAATTTTAC-T-TTTGTTT
65 ACCAAATTA-C-ATTTTACTTCTTTTTTT
*
5706 TTTTTTTACTTACCAAATTCTTCTTTTTTAATTTAATTACCAATTTTACTTTTACCCTTTTTTAA
1 TTTTTTTACTTACCAAATTCTT-TTTTTT--TTTAATTACCAATTTTACTTTTACTCTTTTTTAA
*
5771 TTACCAATTTTAC-TTTTACTTC-------
63 TTACCAA-ATTACATTTTACTTCTTTTTTT
*
5793 TTTTTTTAATTACCAAATTC---TTTTTTTTAATTACCAATTTTACTTTTACTCTTTTTTAATTA
1 TTTTTTTACTTACCAAATTCTTTTTTTTTTTAATTACCAATTTTACTTTTACTCTTTTTTAATTA
*
5855 CCAAATT-CTTTTTACTTACCAATTTTACTTT
66 CCAAATTACATTTTACTT--C--TTTT--TTT
* *
5886 TACTTTTTTACTTACCAAATTC--TTTTTTTTAAACTACCAATTTTACTTTTAC
1 T--TTTTTTACTTACCAAATTCTTTTTTTTTTTAATTACCAATTTTACTTTTAC
Statistics
Matches: 198, Mismatches: 10, Indels: 43
0.79 0.04 0.17
Matches are distributed among these distances:
79 1 0.01
80 10 0.05
81 40 0.20
82 1 0.01
83 5 0.03
87 19 0.10
91 20 0.10
92 7 0.04
93 8 0.04
94 15 0.08
95 45 0.23
96 27 0.14
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.58
Consensus pattern (91 bp):
TTTTTTTACTTACCAAATTCTTTTTTTTTTTAATTACCAATTTTACTTTTACTCTTTTTTAATTA
CCAAATTACATTTTACTTCTTTTTTT
Found at i:5829 original size:247 final size:242
Alignment explanation
Indices: 5319--5777 Score: 597
Period size: 247 Copynumber: 1.9 Consensus size: 242
5309 TTTACTTTTG
5319 TTTTTTTTACTTACCAAATTCGTTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTACTTAC
1 TTTTTTTTACTTACCAAATTC--TTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTACTTAC
***
5384 CAAATTCTTTTTTTAATTACAAATTTTACTTTTACTTATTTTAATTACCAAATTCTTTTTACTTA
64 CAAATTCTTTTTTTAATTACAAATTTTACTTTTACTTATTTTAATTACCAAATTCCAATTA-TTA
5449 CCAATTTTACTTTTACTTTTTTACTTACCAAATTATTTTTTTTTAATTACCAATTTTACTTTTAC
128 CC-ATTTTACTTTTA-TTTTTTACTTACCAAATTATTTTTTTTTAATTACCAATTTTACTTTTAC
* * * ** *
5514 TTTTTTTACTTACCAAATTCTTTTTTCAATTACCAATTTTACTTTTACTTCT
191 CTTTTTTAATTACCAAATTCTTTTTTCAATTACCAATTTTAATTCAAATTCT
5566 TTTTTTTTACTTACCAAATTC-TTTTTTTAATTACCAATTTTACTTTTACTTTTTTTACTTACCA
1 TTTTTTTTACTTACCAAATTCTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTACTTACCA
* * *
5630 AATTCTTTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTTTACTTACCAAATTACCAATT-
66 AATTC---TTTTTTTAATTACAAATTTTACTTTTAC--TTATTTTAATTACCAAATT-CCAATTA
* *
5694 TTA-C-TTTT-GTTTT-TTTTTTACTTACCAAATTCTTCTTTTTTAATTTAATTACCAATTTTAC
125 TTACCATTTTACTTTTATTTTTTACTTACCAAA---TTATTTTTT--TTTAATTACCAATTTTAC
5755 TTTTACCCTTTTTTAATTACCAA
185 TTTTA-CCTTTTTTAATTACCAA
5778 TTTTACTTTT
Statistics
Matches: 190, Mismatches: 10, Indels: 23
0.85 0.04 0.10
Matches are distributed among these distances:
242 16 0.08
244 52 0.27
245 12 0.06
247 72 0.38
248 18 0.09
249 17 0.09
250 3 0.02
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.58
Consensus pattern (242 bp):
TTTTTTTTACTTACCAAATTCTTTTTTTTAATTACCAATTTTACTTTTACTTTTTTTACTTACCA
AATTCTTTTTTTAATTACAAATTTTACTTTTACTTATTTTAATTACCAAATTCCAATTATTACCA
TTTTACTTTTATTTTTTACTTACCAAATTATTTTTTTTTAATTACCAATTTTACTTTTACCTTTT
TTAATTACCAAATTCTTTTTTCAATTACCAATTTTAATTCAAATTCT
Found at i:5839 original size:20 final size:21
Alignment explanation
Indices: 5790--5829 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5780 TTACTTTTAC
5790 TTCTT-TTTTTAATTACCAAA
1 TTCTTCTTTTTAATTACCAAA
*
5810 TTCTTTTTTTTAATTACCAA
1 TTCTTCTTTTTAATTACCAA
5830 TTTTACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (21 bp):
TTCTTCTTTTTAATTACCAAA
Found at i:5885 original size:47 final size:47
Alignment explanation
Indices: 5764--5937 Score: 226
Period size: 52 Copynumber: 3.6 Consensus size: 47
5754 CTTTTACCCT
5764 TTTTTAATTACCAATTTTACTTTTACTTCTTTTTTTAATTACCAAATTC
1 TTTTTAATTACCAATTTTACTTTTAC-TC-TTTTTTAATTACCAAATTC
5813 TTTTTTTTAATTACCAATTTTACTTTTACTCTTTTTTAATTACCAAATTC
1 ---TTTTTAATTACCAATTTTACTTTTACTCTTTTTTAATTACCAAATTC
* *
5863 TTTTTACTTACCAATTTTACTTTTA--CTTTTTTACTTACCAAATTC
1 TTTTTAATTACCAATTTTACTTTTACTCTTTTTTAATTACCAAATTC
*
5908 TTTTTTTTAAACTACCAATTTTACTTTTAC
1 ---TTTTT-AATTACCAATTTTACTTTTAC
Statistics
Matches: 113, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
45 19 0.17
47 24 0.21
48 5 0.04
49 18 0.16
50 19 0.17
51 2 0.02
52 26 0.23
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (47 bp):
TTTTTAATTACCAATTTTACTTTTACTCTTTTTTAATTACCAAATTC
Done.