Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011983.1 Corchorus olitorius cultivar O-4 contig12016, 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: 27514
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:4351 original size:45 final size:46
Alignment explanation
Indices: 4285--4386 Score: 131
Period size: 46 Copynumber: 2.3 Consensus size: 46
4275 TTATTATTAC
4285 CTTTTACTT-TTTAGCTTAATTAACCT-T-A-CTACTGATTACTCTTG
1 CTTTTACTTCTTTAGCTTAATT-A-CTATAATCTACTGATTACTCTTG
** *
4329 CTTTTACTTCTTTAGCTTAATTACTATAATCTTTTGATTACTCTTT
1 CTTTTACTTCTTTAGCTTAATTACTATAATCTACTGATTACTCTTG
4375 CTTTTACTTCTT
1 CTTTTACTTCTT
4387 ATTACTCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
43 2 0.04
44 11 0.22
45 13 0.25
46 25 0.49
ACGTcount: A:0.21, C:0.20, G:0.05, T:0.55
Consensus pattern (46 bp):
CTTTTACTTCTTTAGCTTAATTACTATAATCTACTGATTACTCTTG
Found at i:4390 original size:22 final size:22
Alignment explanation
Indices: 4363--4464 Score: 134
Period size: 22 Copynumber: 4.7 Consensus size: 22
4353 TATAATCTTT
4363 TGATTACTCTTTCTTTTACTTC
1 TGATTACTCTTTCTTTTACTTC
* * *
4385 TTATTACTCTTTCTTCTGCTTC
1 TGATTACTCTTTCTTTTACTTC
* *
4407 TGATTACTCTTTCTTTTGCTTT
1 TGATTACTCTTTCTTTTACTTC
* *
4429 TGGTTACTCTTCCTTTTAC-TC
1 TGATTACTCTTTCTTTTACTTC
4450 TGATTACTCTTTCTT
1 TGATTACTCTTTCTT
4465 CTTAGCTTGA
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
21 14 0.21
22 54 0.79
ACGTcount: A:0.11, C:0.24, G:0.07, T:0.59
Consensus pattern (22 bp):
TGATTACTCTTTCTTTTACTTC
Found at i:4525 original size:47 final size:47
Alignment explanation
Indices: 4474--5299 Score: 793
Period size: 47 Copynumber: 17.4 Consensus size: 47
4464 TCTTAGCTTG
* * *
4474 ATTACCCAGAATCAAACTGTTTTATTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * * * * *
4521 ATTACCCGGAATTAAGCTCTTTTCTTTTTCTTTTACTTTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
*
4568 ATTACCCAGAATTAAACTAGCCTCTGTTTACTTCTTCTTTTACTCTTTAGTTTA
1 ATTACCCAGAATTAAACT-G----T-TTT-CTTCTTCTCTTACTCTTTAGTTTA
* * *
4622 ATTACCAAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTCAATTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * * * *
4669 ATTACCCCGAATTAAACTTTTTTCTTCTTCTGTTGCTTTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
4716 ATTACCCAGAATTAAACTAG----------C-C-T-CTCTTTAGTTTA
1 ATTACCCAGAATTAAACT-GTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * *
4751 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTAATTTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * *
4798 ATTACCCATAATTAAACTGTTTTCTTCTTCTCTTACTCTTCAATTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * * *
4845 ATTACCCCGAATTAAACTTTTTTCTTCTTCTCTTTCTTTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
*
4892 ATTACCCAGAATTAAACTAGCCTCTGTTTACTTCTTCTTTTACTCTTTAGTTTA
1 ATTACCCAGAATTAAACT-G----T-TTT-CTTCTTCTCTTACTCTTTAGTTTA
* * * *
4946 ATTTCCTAGAATTAAACTGTTTTCTTCTTCTTTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* * * *
4993 ATTACCCAGAATTAAACTCTTTTTTTCTCCTCTTACTTTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* *
5040 ATTACCCAGAATTAAACTAACCTCTGTTACTTCTTCTTTTACTCTTTAGTTTA
1 ATTACCCAGAATTAAACT---GT-T-TT-CTTCTTCTCTTACTCTTTAGTTTA
* * * *
5093 GTTACCAAGAATTAAACTGTTTTTTTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTG-TTTTCTTCTTCTCTTACTCTTTAGTTTA
* * * *
5141 ATTACCCAAAATTAAACTTTTTTCTTCTTCTCTTGCTTTTTAGTTTA
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
* ** * *
5188 ATTACCCTGAATTAAACTAG-CCTCTTCTTCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACT-GTTTTCTTCTTCTCTTACTCTTTAGTTTA
* ** * *
5235 ATT-CCCCGAAATTAAACTAATCTCTTCTTCTTTTACTAC-TTAGTTTA
1 ATTACCCAG-AATTAAACTGTTTTCTTCTTCTCTTACT-CTTTAGTTTA
*
5282 ATTACCCTGAATTAAACT
1 ATTACCCAGAATTAAACT
5300 AATCTTTTCT
Statistics
Matches: 648, Mismatches: 91, Indels: 80
0.79 0.11 0.10
Matches are distributed among these distances:
35 29 0.04
36 1 0.00
38 1 0.00
44 1 0.00
45 1 0.00
46 5 0.01
47 431 0.67
48 46 0.07
49 4 0.01
50 3 0.00
51 2 0.00
52 4 0.01
53 44 0.07
54 76 0.12
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.49
Consensus pattern (47 bp):
ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTA
Found at i:4639 original size:148 final size:148
Alignment explanation
Indices: 4474--4745 Score: 427
Period size: 148 Copynumber: 1.8 Consensus size: 148
4464 TCTTAGCTTG
* * * * * *
4474 ATTACCCAGAATCAAACTGTTTTATTCTTCTCTTGCTCTTTAGTTTAATTACCCGGAATTAAGCT
1 ATTACCAAGAATCAAACTGTTTTATTCTTCTCTTACTCTTCAATTTAATTACCCCGAATTAAACT
* * *
4539 CTTTTCTTTTTCTTTTACTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTGTTTACTTCTT
66 CTTTTCTTCTTCTGTTACTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTCTTTACTTCTT
4604 CTTTTACTCTTTAGTTTA
131 CTTTTACTCTTTAGTTTA
* *
4622 ATTACCAAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTCAATTTAATTACCCCGAATTAAACT
1 ATTACCAAGAATCAAACTGTTTTATTCTTCTCTTACTCTTCAATTTAATTACCCCGAATTAAACT
* *
4687 TTTTTCTTCTTCTGTTGCTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTCTTTA
66 CTTTTCTTCTTCTGTTACTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTCTTTA
4746 GTTTAATTAC
Statistics
Matches: 111, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
148 111 1.00
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (148 bp):
ATTACCAAGAATCAAACTGTTTTATTCTTCTCTTACTCTTCAATTTAATTACCCCGAATTAAACT
CTTTTCTTCTTCTGTTACTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTCTTTACTTCTT
CTTTTACTCTTTAGTTTA
Found at i:4819 original size:176 final size:181
Alignment explanation
Indices: 4559--4921 Score: 601
Period size: 176 Copynumber: 2.0 Consensus size: 181
4549 TCTTTTACTT
* *
4559 TTTAGTTTAATTACCCAGAATTAAACTAGCCTCTGTTTACTTCTTCTTTTACTCTTTAGTTTAAT
1 TTTAGTTTAATTACCCAGAATTAAAC-A-CCTCTGTTTACTTCTTCTCTTAATCTTTAGTTTAAT
4624 TACCAAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTCAATTTAATTACCCCGAATTAAACTTT
64 TACCAAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTCAATTTAATTACCCCGAATTAAACTTT
*
4689 TTTCTTCTTCTGTTGCTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTC
129 TTTCTTCTTCTCTTGCTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTC
*
4742 TTTAGTTTAATTACCCAGAATT-AA-A-CTCT-TTT-CTTCTTCTCTTAATTTTTAGTTTAATTA
1 TTTAGTTTAATTACCCAGAATTAAACACCTCTGTTTACTTCTTCTCTTAATCTTTAGTTTAATTA
* *
4802 CCCATAATTAAACTGTTTTCTTCTTCTCTTACTCTTCAATTTAATTACCCCGAATTAAACTTTTT
66 CCAAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTCAATTTAATTACCCCGAATTAAACTTTTT
* *
4867 TCTTCTTCTCTTTCTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTG
131 TCTTCTTCTCTTGCTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTC
4918 TTTA
1 TTTA
4922 CTTCTTCTTT
Statistics
Matches: 172, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
176 140 0.81
177 3 0.02
178 4 0.02
180 1 0.01
182 2 0.01
183 22 0.13
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.48
Consensus pattern (181 bp):
TTTAGTTTAATTACCCAGAATTAAACACCTCTGTTTACTTCTTCTCTTAATCTTTAGTTTAATTA
CCAAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTCAATTTAATTACCCCGAATTAAACTTTTT
TCTTCTTCTCTTGCTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTC
Found at i:5005 original size:148 final size:144
Alignment explanation
Indices: 4742--5299 Score: 702
Period size: 148 Copynumber: 3.9 Consensus size: 144
4732 CTAGCCTCTC
* * *
4742 TTTAGTTTAATTACCCAGAATTAAACT--CT-TTTCTTCTTCTCTTAATTTTTAGTTTAATTACC
1 TTTAGTTTAATTACCCAGAATTAAACTAGCTCTTTCTTCTTCTTTTACTCTTTAGTTTAATTACC
* * * *
4804 CATAATTAAACTGTTTTCTTCTTCTCTTACTCTTCAATTTAATTACCCCGAATTAAACTTTTTTC
66 CAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTAATTACCCAGAATTAAACTTTTTTC
*
4869 TTCTTCTCTTTCTT
131 TTCTTCTCTTACTT
4883 TTTAGTTTAATTACCCAGAATTAAACTAGCCTCTGTTTACTTCTTCTTTTACTCTTTAGTTTAAT
1 TTTAGTTTAATTACCCAGAATTAAACTAG-CTC--TTT-CTTCTTCTTTTACTCTTTAGTTTAAT
* * * *
4948 TTCCTAGAATTAAACTGTTTTCTTCTTCTTTTGCTCTTTAGTTTAATTACCCAGAATTAAACTCT
62 TACCCAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTAATTACCCAGAATTAAACT-T
*
5013 TTTT-TTCTCCTCTTACTT
126 TTTTCTTCTTCTCTTACTT
* *
5031 TTTAGTTTAATTACCCAGAATTAAACTAACCTCTGTTACTTCTTCTTTTACTCTTTAGTTTAGTT
1 TTTAGTTTAATTACCCAGAATTAAACT-AGCTCT-TT-CTTCTTCTTTTACTCTTTAGTTTAATT
* * * *
5096 ACCAAGAATTAAACTGTTTTTTTTCTTCTCTTGCTCTTTAGTTTAATTACCCAAAATTAAACTTT
63 ACCCAGAATTAAACTG-TTTTCTTCTTCTCTTACTCTTTAGTTTAATTACCCAGAATTAAACTTT
*
5161 TTTCTTCTTCTCTTGCTT
127 TTTCTTCTTCTCTTACTT
* *
5179 TTTAGTTTAATTACCCTGAATTAAACTAGC-C--TCTTCTTCTTTTACTATTTAGTTTAATT-CC
1 TTTAGTTTAATTACCCAGAATTAAACTAGCTCTTTCTTCTTCTTTTACTCTTTAGTTTAATTACC
* ** * * *
5240 CCGAAATTAAACTAATCTCTTCTTCTTTTACTAC-TTAGTTTAATTACCCTGAATTAAACT
66 CAG-AATTAAACTGTTTTCTTCTTCTCTTACT-CTTTAGTTTAATTACCCAGAATTAAACT
5300 AATCTTTTCT
Statistics
Matches: 367, Mismatches: 36, Indels: 28
0.85 0.08 0.06
Matches are distributed among these distances:
141 67 0.18
142 35 0.10
143 1 0.00
144 2 0.01
146 2 0.01
147 53 0.14
148 201 0.55
149 6 0.02
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.50
Consensus pattern (144 bp):
TTTAGTTTAATTACCCAGAATTAAACTAGCTCTTTCTTCTTCTTTTACTCTTTAGTTTAATTACC
CAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTTAGTTTAATTACCCAGAATTAAACTTTTTTC
TTCTTCTCTTACTT
Found at i:5079 original size:195 final size:190
Alignment explanation
Indices: 4498--5333 Score: 741
Period size: 195 Copynumber: 4.4 Consensus size: 190
4488 AACTGTTTTA
* * * * * * *
4498 TTCTTC-TCTTGCTCTTTAGTTTAATTACCCGGAATTAAGCT--CTTTTCTTTTTCTTTTACTTT
1 TTCTTCTTCTT-CTTTTTAGTTTAATTACCCAGAATTAAACTAGTTTTTCTTCTTCTCTTACTCT
* * *
4560 TTAGTTTAATTACCCAGAATTAAACTAGCCTCTGTTTACTTCTTCTTTTACTCTTTAGTTTAATT
65 TTAGTTTAATTACCCAGAATT-AA--A--CTCT-TTT-CTTCTTCTCTTGCTTTTTAGTTTAATT
* * * * * **
4625 ACCAAGAATTAAACTGTTTTCTTCTTCTCTTACTCTTCAATTTAATTACCCCGAATTAAACTTTT
123 ACCCAGAATTAAACTATTTTCTTCTTCTCTTACTATTTAGTTTAATTACCCCGAATTAAACTAAT
*
4690 TTC
188 CTC
*
4693 TTCTTCTGT-TGCTTTTTAGTTTAATTACCCAGAATTAAACTAG-----------C-C-T-CTCT
1 TTCTTCT-TCTTCTTTTTAGTTTAATTACCCAGAATTAAACTAGTTTTTCTTCTTCTCTTACTCT
** *
4743 TTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTAATTTTTAGTTTAATTACCCATA
65 TTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTTTTTAGTTTAATTACCCAGA
* * * * ** *
4808 ATTAAACTGTTTTCTTCTTCTCTTACTCTTCAATTTAATTACCCCGAATTAAACTTTTTTC
130 ATTAAACTATTTTCTTCTTCTCTTACTATTTAGTTTAATTACCCCGAATTAAACTAATCTC
*
4869 TTCTTC-TCTTTCTTTTTAGTTTAATTACCCAGAATTAAACTAGCCTCTGTTTACTTCTTCTTTT
1 TTCTTCTTC-TTCTTTTTAGTTTAATTACCCAGAATTAAACTAG--T-T-TTT-CTTCTTCTCTT
* * * * *
4933 ACTCTTTAGTTTAATTTCCTAGAATTAAACTGTTTTCTTCTTCTTTTGCTCTTTAGTTTAATTAC
60 ACTCTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTTTTTAGTTTAATTAC
* * * * *
4998 CCAGAATTAAACTCTTTTTTTCTCCTCTTACTTTTTAGTTTAATTACCCAGAATTAAACTAACCT
125 CCAGAATTAAACTATTTTCTTCTTCTCTTACTATTTAGTTTAATTACCCCGAATTAAACTAA--T
*
5063 CTG
188 CTC
* * * * *
5066 TTACTTCTTCTTTTACTCTTTAGTTTAGTTACCAAGAATTAAACT-GTTTTTTTTCTTCTCTTGC
1 TT-CTTCTTC--TT-CTTTTTAGTTTAATTACCCAGAATTAAACTAGTTTTTCTTCTTCTCTTAC
* *
5130 TCTTTAGTTTAATTACCCAAAATTAAACTTTTTTCTTCTTCTCTTGCTTTTTAGTTTAATTACCC
62 TCTTTAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTTTTTAGTTTAATTACCC
* *** *
5195 TGAATTAAACTAGCCTCTTCTTCTTTTACTATTTAGTTTAATT-CCCCGAAATTAAACTAATCTC
127 AGAATTAAACTATTTTCTTCTTCTCTTACTATTTAGTTTAATTACCCCG-AATTAAACTAATCTC
** * * * *
5259 TTCTTCTT-TTACTACTTAGTTTAATTACCCTGAATTAAACTAATCTTTTC-TC--CTTTTACTA
1 TTCTTCTTCTT-CTTTTTAGTTTAATTACCCAGAATTAAACTAGT-TTTTCTTCTTCTCTTACTC
*
5320 TTCAGTTTAATTAC
64 TTTAGTTTAATTAC
5334 TCTTCTAATT
Statistics
Matches: 541, Mismatches: 66, Indels: 75
0.79 0.10 0.11
Matches are distributed among these distances:
174 1 0.00
176 129 0.24
177 3 0.01
178 4 0.01
180 1 0.00
182 2 0.00
183 24 0.04
184 1 0.00
186 1 0.00
188 19 0.04
189 28 0.05
190 3 0.01
191 4 0.01
192 7 0.01
193 5 0.01
194 5 0.01
195 256 0.47
196 4 0.01
197 6 0.01
198 5 0.01
199 2 0.00
200 4 0.01
201 27 0.05
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.50
Consensus pattern (190 bp):
TTCTTCTTCTTCTTTTTAGTTTAATTACCCAGAATTAAACTAGTTTTTCTTCTTCTCTTACTCTT
TAGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTTTTTAGTTTAATTACCCAGAA
TTAAACTATTTTCTTCTTCTCTTACTATTTAGTTTAATTACCCCGAATTAAACTAATCTC
Found at i:12254 original size:338 final size:339
Alignment explanation
Indices: 11633--12254 Score: 795
Period size: 338 Copynumber: 1.8 Consensus size: 339
11623 TGAGGTTTTC
11633 ATTGATTATCTTAACTTCATTGTTCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGT
1 ATTGATTATCTTAACTTCATTGTTCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGT
* * * *
11698 CCTAGCAAACAATTAAGTTGTATTGCTTGATTGTTTGTGAATGTTGTGATCTTAGGTGTTCAATT
66 CCTAGCAAACAATTAAGTTGTATTGATTAATTGTTTGTGAATGTTGTGATCATAGGTGATCAATT
** * *
11763 GCAGGTCAAATTGAAGGTCTAAGGCCAACGAAAGAAGAAGATTGCTTAGTGAAGATCATCGACAA
131 GCAGGTCAAATTGAACATCTAAGGCCAACGAAAGAAGAAGATAGCTTAGGGAAGATCATCGACAA
* * * *
11828 ACACATCTAGAAGTTGAAGTTGTTCAAGTTGATTCTTGGCGGGTCACAAGGATAGATTTGAATCT
196 ACAAATCTAAAAGTTGAAGTTGTTCAAGTTGATTCTTGGAGGATCACAAGGATAGATTTGAATCT
*
11893 AAAAACAACTAGATTCGTATCAATCCCCCCCTTTGTAAACCAAGTTAAGTTTTCAATAAAGTTGA
261 AAAAACAACTAGATTCATATCAATCCCCCCCTTTGTAAACCAAGTTAAGTTTTCAATAAAGTTGA
11958 GGTTTATTCACCCT
326 GGTTTATTCACCCT
* *
11972 ATTGATTAT-TTAGCTTCATTGTTCTAGTTTGAGC-ATACTTAGGGTTCTTCAATCTTGTAGAGT
1 ATTGATTATCTTAACTTCATTGTTCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGT
* * *
12035 CCTAGCAAACAATTAGGTTGTGATTGATTAATTGTTTGTGAATTTTGTGATCATAGATTGAT-AA
66 CCTAGCAAACAATTAAGTTGT-ATTGATTAATTGTTTGTGAATGTTGTGATCATAG-GTGATCAA
* * *
12099 TTGCAGGTCTAATT-ATCCATCTAGAGG-CGACGAACA-AAGAAGATAAGCTAGCTAGGGAA-AT
129 TTGCAGGTCAAATTGA-ACATCTA-AGGCCAACGAA-AGAAGAAGAT-AGCT---TAGGGAAGAT
** * *
12160 CGATCTTC-ATCAAATCTAAAAGTTGAAG-T-TTCAAGTTGA-TCTTTGGAGGAAT-TCAA-GAG
187 C-ATCGACAAACAAATCTAAAAGTTGAAGTTGTTCAAGTTGATTC-TTGGAGG-ATCACAAGGA-
*
12219 TAGATTTGAATCT-AACACAACTAGATTCATATCAAT
248 TAGATTTGAATCTAAAAACAACTAGATTCATATCAAT
12255 TGGTATCAGA
Statistics
Matches: 244, Mismatches: 26, Indels: 27
0.82 0.09 0.09
Matches are distributed among these distances:
337 49 0.20
338 112 0.46
339 51 0.21
340 2 0.01
341 20 0.08
342 10 0.04
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (339 bp):
ATTGATTATCTTAACTTCATTGTTCTAGTTTGAGCAAAACTTAGGGTTCTTCAATCTTGTAGAGT
CCTAGCAAACAATTAAGTTGTATTGATTAATTGTTTGTGAATGTTGTGATCATAGGTGATCAATT
GCAGGTCAAATTGAACATCTAAGGCCAACGAAAGAAGAAGATAGCTTAGGGAAGATCATCGACAA
ACAAATCTAAAAGTTGAAGTTGTTCAAGTTGATTCTTGGAGGATCACAAGGATAGATTTGAATCT
AAAAACAACTAGATTCATATCAATCCCCCCCTTTGTAAACCAAGTTAAGTTTTCAATAAAGTTGA
GGTTTATTCACCCT
Found at i:18362 original size:15 final size:14
Alignment explanation
Indices: 18336--18365 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
18326 AACTAGGAAA
18336 AATAAAAAACAAGG
1 AATAAAAAACAAGG
18350 AATAAATAAACAAGG
1 AATAAA-AAACAAGG
18365 A
1 A
18366 TTGGACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.70, C:0.07, G:0.13, T:0.10
Consensus pattern (14 bp):
AATAAAAAACAAGG
Found at i:26825 original size:16 final size:16
Alignment explanation
Indices: 26807--26882 Score: 100
Period size: 16 Copynumber: 4.8 Consensus size: 16
26797 AATTTTGGGT
*
26807 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAATG
*
26823 ACCCGAATCC-AAATG
1 ACCCGAACCCGAAATG
26838 ACCCGAACCCGAAAATG
1 ACCCGAACCCG-AAATG
* *
26855 ACCCAAACCCAAAATG
1 ACCCGAACCCGAAATG
26871 ACCCGAACCCGA
1 ACCCGAACCCGA
26883 TCAACCCGAC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
15 13 0.25
16 24 0.47
17 14 0.27
ACGTcount: A:0.41, C:0.38, G:0.13, T:0.08
Consensus pattern (16 bp):
ACCCGAACCCGAAATG
Done.