Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold418
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: 251372
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
File 2 of 2
Found at i:167863 original size:104 final size:102
Alignment explanation
Indices: 167693--167984 Score: 286
Period size: 104 Copynumber: 2.8 Consensus size: 102
167683 GAAGAGTGCT
* * * * *
167693 AATGTGCTGATTCACGACTAGTGACATTAGACTTGAAGATGAGAAGAATGCTAATGTGTTGATTC
1 AATGTGCTGATTCAAGGCTAGTGACATTAGACTT-AAGATGAAAAAAATGCCAATGTGTTGATTC
*
167758 AAGGCTAGCGACATTGGACTTAAAAATTTGA-AGAA-TACC
65 AAAGCTAGCGACATTGGACTTAAAAA--TGACA-AAGTACC
* * * * *
167797 AATGTGCTGATTCAAGGCTAGTGACATTGGGCTTAGGATTGATAAAAATGCCAATATGTTGATTC
1 AATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAGA-TGAAAAAAATGCCAATGTGTTGATTC
* * * * * * *
167862 AAAGTTAGTGATATCGAACTTAAAGATGACAAAGGTGCC
65 AAAGCTAGCGACATTGGACTTAAAAATGACAAA-GTACC
* * * * *
167901 AATATGTTGATTCAAGGCTAGCGATATTAGACTTAAGA--AAAAAAATGCCAATGTGCTGATTCA
1 AATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAGATGAAAAAAATGCCAATGTGTTGATTCA
*
167964 ATGCTAGCGACATTGGACTTA
66 AAGCTAGCGACATTGGACTTA
167985 GAAAGAGATA
Statistics
Matches: 151, Mismatches: 33, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
101 37 0.25
102 5 0.03
103 4 0.03
104 105 0.70
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (102 bp):
AATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAGATGAAAAAAATGCCAATGTGTTGATTCA
AAGCTAGCGACATTGGACTTAAAAATGACAAAGTACC
Found at i:168089 original size:33 final size:33
Alignment explanation
Indices: 168036--168278 Score: 198
Period size: 34 Copynumber: 7.5 Consensus size: 33
168026 CCAACGACAT
* *
168036 TGGG-TTTA-AAAGGAGATGCCATCGACTTGTG
1 TGGGCTTTAGAAAGGGGTTGCCATCGACTTGTG
* * *
168067 TGGGTTTTTGAAAGGGGTTGCCATCGATTTGTG
1 TGGGCTTTAGAAAGGGGTTGCCATCGACTTGTG
* * * * *
168100 TGAGCTTTAGAAAAAGGGTTACCACCGACTTGTA
1 TGGGCTTTAG-AAAGGGGTTGCCATCGACTTGTG
* * *
168134 TGGGCTTTAGAAAAGGGGTTACCACCGACTTGTA
1 TGGGCTTTAG-AAAGGGGTTGCCATCGACTTGTG
* *
168168 TGGGCTTTAG--AGGGATTGACA-CAGACTTGTG
1 TGGGCTTTAGAAAGGGGTTGCCATC-GACTTGTG
*
168199 TGGGCTTTAG-AA-GAGTTG-CA-CTGACTTGTG
1 TGGGCTTTAGAAAGGGGTTGCCATC-GACTTGTG
* * *
168229 TTGGCTTTTGAAAGGGGTTACCATCGACTTGTG
1 TGGGCTTTAGAAAGGGGTTGCCATCGACTTGTG
*
168262 AGGGCTTTAGAGAAGGG
1 TGGGCTTTAGA-AAGGG
168279 TGCCATGAAG
Statistics
Matches: 174, Mismatches: 28, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
30 20 0.11
31 35 0.20
32 8 0.05
33 45 0.26
34 66 0.38
ACGTcount: A:0.23, C:0.14, G:0.33, T:0.30
Consensus pattern (33 bp):
TGGGCTTTAGAAAGGGGTTGCCATCGACTTGTG
Found at i:168227 original size:30 final size:31
Alignment explanation
Indices: 168160--168236 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
168150 GGTTACCACC
* *
168160 GACTTGTATGGGCTTTAGAGGGATTGACACA
1 GACTTGTGTGGGCTTTAGAGAGATTGACACA
*
168191 GACTTGTGTGGGCTTTAGA-AGAGTTG-CACT
1 GACTTGTGTGGGCTTTAGAGAGA-TTGACACA
*
168221 GACTTGTGTTGGCTTT
1 GACTTGTGTGGGCTTT
168237 TGAAAGGGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
30 20 0.49
31 21 0.51
ACGTcount: A:0.19, C:0.13, G:0.32, T:0.35
Consensus pattern (31 bp):
GACTTGTGTGGGCTTTAGAGAGATTGACACA
Found at i:168380 original size:32 final size:33
Alignment explanation
Indices: 168331--168401 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
168321 TTGTGGACTT
* *
168331 AAAAAA-GTGCCACGGAGTTATGGGCTTTGAA-
1 AAAAAAGGTGCCACGGAGTTATAGACTTTGAAG
* *
168362 AAAAAAGGTGTCATGGAGTTATAGACTTTGAAG
1 AAAAAAGGTGCCACGGAGTTATAGACTTTGAAG
168395 AAAAAAG
1 AAAAAAG
168402 CCACTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 6 0.18
32 21 0.62
33 7 0.21
ACGTcount: A:0.42, C:0.08, G:0.27, T:0.23
Consensus pattern (33 bp):
AAAAAAGGTGCCACGGAGTTATAGACTTTGAAG
Found at i:168464 original size:30 final size:31
Alignment explanation
Indices: 168413--168645 Score: 273
Period size: 30 Copynumber: 7.7 Consensus size: 31
168403 CACTAAAAAG
* * * *
168413 GATGTCACTGAGTCGTAGAC-TTGAATAAGA
1 GATGCCACTAAGTCGTGGACTTTGAAGAAGA
* * *
168443 GATGCCATTGAGTCATGGACTTTGAAGAAGA
1 GATGCCACTAAGTCGTGGACTTTGAAGAAGA
* *
168474 -ATGCCACTAAGTCATGGAC-TTGGAGAAGA
1 GATGCCACTAAGTCGTGGACTTTGAAGAAGA
* * *
168503 AATGCCACTAAGTCGTGGACTTTAAAGAACA
1 GATGCCACTAAGTCGTGGACTTTGAAGAAGA
*
168534 -ATGCCACTAAGTCGTAGACTTTGAAGAAG-
1 GATGCCACTAAGTCGTGGACTTTGAAGAAGA
*
168563 GATGCCACTAAGTCGTGGACTTGGAA-AAGA
1 GATGCCACTAAGTCGTGGACTTTGAAGAAGA
168593 GATGCCACTAAGTCGTGGACTTTGAAGAAG-
1 GATGCCACTAAGTCGTGGACTTTGAAGAAGA
* *
168623 GATGCCACTGAGTCGTGAACTTT
1 GATGCCACTAAGTCGTGGACTTT
168646 TAGAAGGTTA
Statistics
Matches: 177, Mismatches: 20, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
29 12 0.07
30 146 0.82
31 19 0.11
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.24
Consensus pattern (31 bp):
GATGCCACTAAGTCGTGGACTTTGAAGAAGA
Found at i:168645 original size:90 final size:90
Alignment explanation
Indices: 168408--168645 Score: 302
Period size: 90 Copynumber: 2.7 Consensus size: 90
168398 AAAGCCACTA
* * * * * * *
168408 AAAAG-GATGTCACTGAGTCGTAGAC-TTGAATAAGAGATGCCATTGAGTCATGGACTTTGAAGA
1 AAAAGAGATGCCACTAAGTCGTGGACTTTGAAGAAG-GATGCCACTGAGTCGTGAACTTTGAAGA
168471 AGAATGCCACTAAGTCATGGACTTGG
65 AGAATGCCACTAAGTCATGGACTTGG
* * * ** *
168497 AGAAGAAATGCCACTAAGTCGTGGACTTTAAAGAACAATGCCACTAAGTCGT-AGACTTTGAAGA
1 AAAAGAGATGCCACTAAGTCGTGGACTTTGAAGAAGGATGCCACTGAGTCGTGA-ACTTTGAAGA
* *
168561 AGGATGCCACTAAGTCGTGGACTTGG
65 AGAATGCCACTAAGTCATGGACTTGG
168587 AAAAGAGATGCCACTAAGTCGTGGACTTTGAAGAAGGATGCCACTGAGTCGTGAACTTT
1 AAAAGAGATGCCACTAAGTCGTGGACTTTGAAGAAGGATGCCACTGAGTCGTGAACTTT
168646 TAGAAGGTTA
Statistics
Matches: 124, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
89 4 0.03
90 113 0.91
91 7 0.06
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (90 bp):
AAAAGAGATGCCACTAAGTCGTGGACTTTGAAGAAGGATGCCACTGAGTCGTGAACTTTGAAGAA
GAATGCCACTAAGTCATGGACTTGG
Found at i:169502 original size:33 final size:33
Alignment explanation
Indices: 169454--169521 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
169444 CAAAAGGTCA
* * *
169454 TTTTGACCAGCAAGGTGATATGGTTTGGTTTAT
1 TTTTGACAAGAAAGGTGATATGATTTGGTTTAT
169487 TTTTGACAAGAAAGGTGATATGATTTGGTTTAT
1 TTTTGACAAGAAAGGTGATATGATTTGGTTTAT
169520 TT
1 TT
169522 CAAGAAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (33 bp):
TTTTGACAAGAAAGGTGATATGATTTGGTTTAT
Found at i:173364 original size:13 final size:13
Alignment explanation
Indices: 173346--173373 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
173336 CATTATCACC
173346 TATGTAACTATGA
1 TATGTAACTATGA
173359 TATGTAACTATGA
1 TATGTAACTATGA
173372 TA
1 TA
173374 CATGAGAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (13 bp):
TATGTAACTATGA
Found at i:177667 original size:16 final size:16
Alignment explanation
Indices: 177648--177693 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
177638 AAAATTATAT
177648 ATTTATATAAATTTTA
1 ATTTATATAAATTTTA
177664 ATTTATA-ATAA-TTT-
1 ATTTATATA-AATTTTA
*
177678 ATTTATATAGATTTTA
1 ATTTATATAAATTTTA
177694 TATGTTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
14 8 0.32
15 8 0.32
16 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
ATTTATATAAATTTTA
Found at i:177731 original size:20 final size:21
Alignment explanation
Indices: 177706--177763 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
177696 TGTTTGTATC
177706 TTTATGTTATATTTATTTA-T
1 TTTATGTTATATTTATTTATT
*
177726 TTTATGTCATATTTATTTATT
1 TTTATGTTATATTTATTTATT
*
177747 TTTAATATTATATTTAT
1 TTT-ATGTTATATTTAT
177764 ATAATTTAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 18 0.55
21 4 0.12
22 11 0.33
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTATGTTATATTTATTTATT
Found at i:181513 original size:17 final size:17
Alignment explanation
Indices: 181493--181530 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
181483 TGATACAATG
*
181493 AATAATGTATCGATACA
1 AATAATGTATCGAAACA
181510 AATAATGTATCGAAACA
1 AATAATGTATCGAAACA
181527 AATA
1 AATA
181531 GTAAATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (17 bp):
AATAATGTATCGAAACA
Found at i:181621 original size:20 final size:21
Alignment explanation
Indices: 181596--181648 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
181586 ATTTTAGGTG
*
181596 TGTATCAATACATTCACT-TA
1 TGTATCGATACATTCACTATA
* *
181616 TGTATCGATACATTTACTATT
1 TGTATCGATACATTCACTATA
181637 TGTATCGATACA
1 TGTATCGATACA
181649 AATTGTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCACTATA
Found at i:181642 original size:21 final size:21
Alignment explanation
Indices: 181573--181648 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
181563 GCAAGGTGAT
181573 TTTGTATCGATACATTT--TA
1 TTTGTATCGATACATTTACTA
* * *
181592 GGTGTGTATCAATACATTCACT-
1 --TTTGTATCGATACATTTACTA
*
181614 TATGTATCGATACATTTACTA
1 TTTGTATCGATACATTTACTA
181635 TTTGTATCGATACA
1 TTTGTATCGATACA
181649 AATTGTAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 17 0.38
21 27 0.60
23 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (21 bp):
TTTGTATCGATACATTTACTA
Found at i:182385 original size:52 final size:52
Alignment explanation
Indices: 182310--182440 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
182300 TTAAAGATAG
* * *
182310 TAAAGATGAGAAGGGTGCTAATGTGCTAATTCATAG-CCAGTGACATTAAACT
1 TAAAGATGAGAAGAGTGCCAATGTGCTAATTCA-AGACCAGCGACATTAAACT
* * ** *
182362 TAAAGATGAGAAGAATGCCAATGTGTTGGTTCAAGACCAGCGACATTAGACT
1 TAAAGATGAGAAGAGTGCCAATGTGCTAATTCAAGACCAGCGACATTAAACT
* *
182414 TAAAAATGACAA-AGGTGCCAATGTGCT
1 TAAAGATGAGAAGA-GTGCCAATGTGCT
182441 GATTTAAGGC
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
51 3 0.05
52 62 0.95
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (52 bp):
TAAAGATGAGAAGAGTGCCAATGTGCTAATTCAAGACCAGCGACATTAAACT
Found at i:182599 original size:52 final size:52
Alignment explanation
Indices: 182534--182846 Score: 172
Period size: 52 Copynumber: 6.1 Consensus size: 52
182524 ATAATAAGGG
* * * * * *
182534 TGAGAAGAGTGCTAACGTGCTGATTCACGACTAGTGACATTAGACTTGAAGA
1 TGAGAAGAATGCTAATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAAAA
* * * *
182586 TGAGAAGAATGCTAATGAGCTGATTCAAGGCCAGCGACATTGGACTTAAAAA
1 TGAGAAGAATGCTAATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAAAA
** * * * * ** *
182638 TTTGAAGAATACCAATGTGCTGATTCAAGGCTAGTGACATTGGGCTTAGGAT
1 TGAGAAGAATGCTAATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAAAA
** * * * * * * * * *
182690 TGTTAAAAATGCCAATATGTTGATTCAAAGTTAGTGATA-TCGAACTTAAAGA
1 TGAGAAGAATGCTAATGTGCTGATTCAAGGCTAGTGACATTAG-ACTTAAAAA
* * * * * * *
182742 TGACAA-AGGTGCCAATATGTTGATTCAAGGCTAGCGATATTAGACTTAAGAAA
1 TGAGAAGA-ATGCTAATGTGCTGATTCAAGGCTAGTGACATTAGACTTAA-AAA
* * * * *
182795 --A-AA-AATGCTAATGTGTTGATTCAATGCTAGCGACATTGGACTTAGAAA
1 TGAGAAGAATGCTAATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAAAA
182843 -GAGA
1 TGAGA
182847 TAGTTTAACA
Statistics
Matches: 204, Mismatches: 51, Indels: 14
0.76 0.19 0.05
Matches are distributed among these distances:
48 3 0.01
49 35 0.17
50 4 0.02
51 4 0.02
52 154 0.75
53 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (52 bp):
TGAGAAGAATGCTAATGTGCTGATTCAAGGCTAGTGACATTAGACTTAAAAA
Found at i:182983 original size:34 final size:34
Alignment explanation
Indices: 182945--183032 Score: 149
Period size: 34 Copynumber: 2.6 Consensus size: 34
182935 GGGTTGCTAT
* *
182945 CGACTTGTGTGAGCTTTAGAAAAAGGGTTACCAC
1 CGACTTGTATGGGCTTTAGAAAAAGGGTTACCAC
*
182979 CGACTTGTATGGGCTTTAGAAAAGGGGTTACCAC
1 CGACTTGTATGGGCTTTAGAAAAAGGGTTACCAC
183013 CGACTTGTATGGGCTTTAGA
1 CGACTTGTATGGGCTTTAGA
183033 GGGATTGACA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (34 bp):
CGACTTGTATGGGCTTTAGAAAAAGGGTTACCAC
Found at i:183081 original size:30 final size:31
Alignment explanation
Indices: 183014--183090 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
183004 GGTTACCACC
* *
183014 GACTTGTATGGGCTTTAGAGGGATTGACACA
1 GACTTGTGTGGGCTTTAGAGAGATTGACACA
*
183045 GACTTGTGTGGGCTTTAGA-AGAGTTG-CACT
1 GACTTGTGTGGGCTTTAGAGAGA-TTGACACA
*
183075 GACTTGTGTTGGCTTT
1 GACTTGTGTGGGCTTT
183091 TGAAAGGGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
30 20 0.49
31 21 0.51
ACGTcount: A:0.19, C:0.13, G:0.32, T:0.35
Consensus pattern (31 bp):
GACTTGTGTGGGCTTTAGAGAGATTGACACA
Found at i:183202 original size:27 final size:31
Alignment explanation
Indices: 183117--183254 Score: 97
Period size: 32 Copynumber: 4.5 Consensus size: 31
183107 CGACTTGTGA
* * *
183117 GGACTTT-AGAGAAGGGTGCCACGAAGTTGT
1 GGACTTTAAGAAAAAGGTGCCACGGAGTTGT
**
183147 GGACTTTAAAGAAAAAGGTGCCATAGAGTTGT
1 GGACTTT-AAGAAAAAGGTGCCACGGAGTTGT
*
183179 GGAC-TT-A-AAAAA-GTGCCACGGAGTTAT
1 GGACTTTAAGAAAAAGGTGCCACGGAGTTGT
* * * * *
183206 GGGCTTTGAAAAAAAAAGGTGTCATGGAGTTAT
1 GGACTTT--AAGAAAAAGGTGCCACGGAGTTGT
*
183239 AGACTTTGAAGAAAAA
1 GGACTTT-AAGAAAAA
183255 AGCCACTAAA
Statistics
Matches: 85, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
27 15 0.18
28 7 0.08
29 1 0.01
30 7 0.08
31 3 0.04
32 34 0.40
33 18 0.21
ACGTcount: A:0.37, C:0.10, G:0.29, T:0.24
Consensus pattern (31 bp):
GGACTTTAAGAAAAAGGTGCCACGGAGTTGT
Found at i:183235 original size:33 final size:33
Alignment explanation
Indices: 183185--183256 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
183175 TTGTGGACTT
* *
183185 AAAAAA-GTGCCACGGAGTTATGGGCTTTGAAA
1 AAAAAAGGTGCCACGGAGTTATAGACTTTGAAA
* * *
183217 AAAAAAGGTGTCATGGAGTTATAGACTTTGAAG
1 AAAAAAGGTGCCACGGAGTTATAGACTTTGAAA
183250 AAAAAAG
1 AAAAAAG
183257 CCACTAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.43, C:0.08, G:0.26, T:0.22
Consensus pattern (33 bp):
AAAAAAGGTGCCACGGAGTTATAGACTTTGAAA
Found at i:183244 original size:60 final size:59
Alignment explanation
Indices: 183132--183244 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 59
183122 TTAGAGAAGG
* * * *
183132 GTGCCACGAAGTTGTGGACTTTAAAGAAAAAGGTGCCATAGAGTTGTGGACTTAAAAAA
1 GTGCCACGAAGTTATGGACTTTAAAAAAAAAGGTGCCATAGAGTTATAGACTTAAAAAA
* * * *
183191 GTGCCACGGAGTTATGGGCTTTGAAAAAAAAAGGTGTCATGGAGTTATAGACTT
1 GTGCCACGAAGTTATGGACTTT-AAAAAAAAAGGTGCCATAGAGTTATAGACTT
183245 TGAAGAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 19 0.42
60 26 0.58
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.26
Consensus pattern (59 bp):
GTGCCACGAAGTTATGGACTTTAAAAAAAAAGGTGCCATAGAGTTATAGACTTAAAAAA
Found at i:183319 original size:30 final size:30
Alignment explanation
Indices: 183285--183499 Score: 222
Period size: 30 Copynumber: 7.2 Consensus size: 30
183275 CTGAGTTGTA
* * * *
183285 GACTTGAATAAGAGATGCCATTGAGTCATG
1 GACTTGAAGAAGAGATGCCACTAAGTCGTG
* *
183315 GACTTTGAAGAAGA-ATGCCACTGAGTCATG
1 GAC-TTGAAGAAGAGATGCCACTAAGTCGTG
* *
183345 GACTTGGAGAAGAAATGCCACTAAGTCGTG
1 GACTTGAAGAAGAGATGCCACTAAGTCGTG
* * * *
183375 GACTTTAA-AAAAGAATGCCACTAAGTTGTA
1 GACTTGAAGAAGAG-ATGCCACTAAGTCGTG
183405 GACTTTGAAGAAG-GATGCCACTAAGTCGTG
1 GAC-TTGAAGAAGAGATGCCACTAAGTCGTG
* *
183435 GACTTGGAGAAGAGATGCCACTAAGTCGTA
1 GACTTGAAGAAGAGATGCCACTAAGTCGTG
*
183465 GACTTTGAAGAAG-GATGCCACTGAGTCGTG
1 GAC-TTGAAGAAGAGATGCCACTAAGTCGTG
*
183495 AACTT
1 GACTT
183500 TTAGAAGGTT
Statistics
Matches: 157, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
29 22 0.14
30 111 0.71
31 22 0.14
32 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (30 bp):
GACTTGAAGAAGAGATGCCACTAAGTCGTG
Found at i:183377 original size:60 final size:60
Alignment explanation
Indices: 183273--183500 Score: 255
Period size: 60 Copynumber: 3.8 Consensus size: 60
183263 AAAAGGATGT
* * * * * *
183273 CACTGAGTTGTAGAC-TTGAATAAGAGATGCCATTGAGTCATGGACTTTGAAGAAGAATGC
1 CACTAAGTCGTAGACTTTGAAGAAG-GATGCCACTAAGTCGTGGACTTTGAAGAAGAATGC
* * * * * * *
183333 CACTGAGTCATGGAC-TTGGAGAAGAAATGCCACTAAGTCGTGGACTTTAAAAAAGAATGC
1 CACTAAGTCGTAGACTTTGAAGAAG-GATGCCACTAAGTCGTGGACTTTGAAGAAGAATGC
* *
183393 CACTAAGTTGTAGACTTTGAAGAAGGATGCCACTAAGTCGTGGAC-TTGGAGAAGAGATGC
1 CACTAAGTCGTAGACTTTGAAGAAGGATGCCACTAAGTCGTGGACTTTGAAGAAGA-ATGC
* *
183453 CACTAAGTCGTAGACTTTGAAGAAGGATGCCACTGAGTCGTGAACTTT
1 CACTAAGTCGTAGACTTTGAAGAAGGATGCCACTAAGTCGTGGACTTT
183501 TAGAAGGTTA
Statistics
Matches: 142, Mismatches: 23, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
59 7 0.05
60 125 0.88
61 10 0.07
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.25
Consensus pattern (60 bp):
CACTAAGTCGTAGACTTTGAAGAAGGATGCCACTAAGTCGTGGACTTTGAAGAAGAATGC
Found at i:183500 original size:90 final size:90
Alignment explanation
Indices: 183268--183500 Score: 281
Period size: 90 Copynumber: 2.6 Consensus size: 90
183258 CACTAAAAAG
* * * * * * *
183268 GATGTCACTGAGTTGTAGAC-TTGAATAAGAGATGCCATTGAGTCATGGACTTTGAAGAAGAATG
1 GATGCCACTAAGTCGTAGACTTTGAAAAAG-GATGCCACTGAGTCGTGAACTTTGAAGAAGAATG
*
183332 CCACTGAGTCATGGACTTGGAGAAGA
65 CCACTAAGTCATGGACTTGGAGAAGA
* * * * * * *
183358 AATGCCACTAAGTCGTGGACTTTAAAAAAGAATGCCACTAAGTTGT-AGACTTTGAAGAAGGATG
1 GATGCCACTAAGTCGTAGACTTTGAAAAAGGATGCCACTGAGTCGTGA-ACTTTGAAGAAGAATG
*
183422 CCACTAAGTCGTGGACTTGGAGAAGA
65 CCACTAAGTCATGGACTTGGAGAAGA
*
183448 GATGCCACTAAGTCGTAGACTTTGAAGAAGGATGCCACTGAGTCGTGAACTTT
1 GATGCCACTAAGTCGTAGACTTTGAAAAAGGATGCCACTGAGTCGTGAACTTT
183501 TAGAAGGTTA
Statistics
Matches: 117, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
90 109 0.93
91 8 0.07
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (90 bp):
GATGCCACTAAGTCGTAGACTTTGAAAAAGGATGCCACTGAGTCGTGAACTTTGAAGAAGAATGC
CACTAAGTCATGGACTTGGAGAAGA
Found at i:184357 original size:33 final size:33
Alignment explanation
Indices: 184311--184376 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
184301 AAAGGTCATC
* * *
184311 TTGACCAGCAAGGTGATATGGTTTGGTTTATTT
1 TTGACAAGAAAGGTGATATGATTTGGTTTATTT
184344 TTGACAAGAAAGGTGATATGATTTGGTTTATTT
1 TTGACAAGAAAGGTGATATGATTTGGTTTATTT
184377 CAAGAAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.26, C:0.06, G:0.26, T:0.42
Consensus pattern (33 bp):
TTGACAAGAAAGGTGATATGATTTGGTTTATTT
Found at i:184912 original size:16 final size:17
Alignment explanation
Indices: 184888--184925 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
184878 TTTTTTTTGC
*
184888 TTTTGTGTTT-GCATTT
1 TTTTGTGTTTCCCATTT
*
184904 TTTTTTGTTTCCCATTT
1 TTTTGTGTTTCCCATTT
184921 TTTTG
1 TTTTG
184926 GGCTTTTGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.05, C:0.11, G:0.13, T:0.71
Consensus pattern (17 bp):
TTTTGTGTTTCCCATTT
Found at i:188215 original size:13 final size:13
Alignment explanation
Indices: 188197--188224 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
188187 CATTATCACC
188197 TATGTAACTATGA
1 TATGTAACTATGA
188210 TATGTAACTATGA
1 TATGTAACTATGA
188223 TA
1 TA
188225 CATGAGAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (13 bp):
TATGTAACTATGA
Found at i:191466 original size:20 final size:21
Alignment explanation
Indices: 191443--191494 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
191433 CATTTCAGGC
191443 ATGTATCGATACATTCACT-T
1 ATGTATCGATACATTCACTAT
* *
191463 ATGTATTGATACATTTACTAT
1 ATGTATCGATACATTCACTAT
*
191484 TTGTATCGATA
1 ATGTATCGATA
191495 TAAATTGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATTCACTAT
Found at i:193944 original size:12 final size:12
Alignment explanation
Indices: 193913--193966 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
193903 GATTTTTAAT
193913 AGAAAAAAAGAG
1 AGAAAAAAAGAG
**
193925 AGCCAAAAAGAG
1 AGAAAAAAAGAG
*
193937 AGAAAAAAAGAAA
1 AGAAAAAAAG-AG
*
193950 AAAAAAAAAGAG
1 AGAAAAAAAGAG
193962 AGAAA
1 AGAAA
193967 GAGTGATAGC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
12 23 0.70
13 10 0.30
ACGTcount: A:0.76, C:0.04, G:0.20, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAGAG
Found at i:194026 original size:24 final size:24
Alignment explanation
Indices: 193999--194046 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
193989 GCTTAAAGTG
193999 TTTTCTTTTATC-TTCTACTTTTAT
1 TTTTCTTTTATCTTTCT-CTTTTAT
*
194023 TTTTCTTTTTTCTTTCTCTTTTAT
1 TTTTCTTTTATCTTTCTCTTTTAT
194047 AAGACCTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTCTTTTATCTTTCTCTTTTAT
Found at i:194825 original size:58 final size:57
Alignment explanation
Indices: 194719--194961 Score: 219
Period size: 58 Copynumber: 4.2 Consensus size: 57
194709 TTATGATTTA
* *
194719 TCATGCATTTTA--ATGGCATTTTAGTCATTTTTTACGATTCATA-GGTTATTATGTAATT
1 TCATGCATTTTAGCAT--CATTTTAGTCATTTTTCATGATT-A-AGGGTTATTATGTAATT
* * * *
194777 TCATGCATTTTAGCACCATTTTAGTCATTTTTCATAATTGAAGAGTTATTATATAATT
1 TCATGCATTTTAGCATCATTTTAGTCATTTTTCATGATT-AAGGGTTATTATGTAATT
* * * *
194835 TCATGCATTTTAACATTATTTTAGTCATTTCT-ATGATTTAAGGGTTATTATGCAATT
1 TCATGCATTTTAGCATCATTTTAGTCATTTTTCATGA-TTAAGGGTTATTATGTAATT
* * * * * *
194892 TTATACATTTTAAG-GTCATTCTAATAATTTTTCATGATTAAGGGTTATTATGTAATAT
1 TCATGCATTTT-AGCATCATTTTAGTCATTTTTCATGATTAAGGGTTATTATGTAAT-T
*
194950 T-ATGAATTTTAG
1 TCATGCATTTTAG
194962 AGTTATTTAG
Statistics
Matches: 151, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
56 2 0.01
57 65 0.43
58 83 0.55
60 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (57 bp):
TCATGCATTTTAGCATCATTTTAGTCATTTTTCATGATTAAGGGTTATTATGTAATT
Found at i:194947 original size:28 final size:28
Alignment explanation
Indices: 194862--194947 Score: 68
Period size: 29 Copynumber: 3.0 Consensus size: 28
194852 ATTTTAGTCA
*
194862 TTTCTATGATTTAAGGGTTATTATGCAATT
1 TTTC-ATGA-TTAAGGGTTATTATGTAATT
* * * *
194892 TTATACAT-TTTAA-GGTCATTCTAATAATT
1 TT-T-CATGATTAAGGGTTATTAT-GTAATT
194921 TTTCATGATTAAGGGTTATTATGTAAT
1 TTTCATGATTAAGGGTTATTATGTAAT
194948 ATTATGAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
27 3 0.07
28 16 0.38
29 17 0.40
30 2 0.05
31 3 0.07
32 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.49
Consensus pattern (28 bp):
TTTCATGATTAAGGGTTATTATGTAATT
Found at i:195036 original size:114 final size:115
Alignment explanation
Indices: 194764--195037 Score: 256
Period size: 114 Copynumber: 2.4 Consensus size: 115
194754 GATTCATAGG
** * *
194764 TTATTATGTAATTTCATGCATTTT-AGCACCATTTTAGTCATTTTTCATAATTGAAGAGTTATTA
1 TTATTATACAATTTCATACATTTTAAG-ACCATTCTAGTCATTTTTCATAATTGAAGAGTTATTA
* * **
194828 TATAATTTCATGCATTTTAACATTATTTTAGTCATTTCTATGATTTAAGGG
65 TATAATTTCATGAATTTTAACATTATTTTAGTAATTTCTATGATTTAAGCC
* * ** * * * *
194879 TTATTATGCAATTTTATACATTTTAAGGTCATTCTAATAATTTTTCATGATT-AAGGGTTATTAT
1 TTATTATACAATTTCATACATTTTAAGACCATTCTAGTCATTTTTCATAATTGAAGAGTTATTAT
* * * *
194943 GTAATATT-ATGAATTTTAGA-GTTA-TTTAGTAATTTGTCAT-ATTTTGAGACC
66 ATAAT-TTCATGAATTTTA-ACATTATTTTAGTAATTTCT-ATGA-TTTAAG-CC
*
194994 TT-TTATACAATTTCATACATTTTAAGACCATTGTAGTCATTTTT
1 TTATTATACAATTTCATACATTTTAAGACCATTCTAGTCATTTTT
195038 TTTCCTTTAA
Statistics
Matches: 128, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
113 12 0.09
114 69 0.54
115 45 0.35
116 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.49
Consensus pattern (115 bp):
TTATTATACAATTTCATACATTTTAAGACCATTCTAGTCATTTTTCATAATTGAAGAGTTATTAT
ATAATTTCATGAATTTTAACATTATTTTAGTAATTTCTATGATTTAAGCC
Found at i:197158 original size:67 final size:66
Alignment explanation
Indices: 197064--197256 Score: 305
Period size: 68 Copynumber: 2.9 Consensus size: 66
197054 CAACTTTTCT
* **
197064 TCCCCTTATCAAATTATCCTTCTTTTATAAAAACAACTTTTCTCCCCTTTATAAATTGTTAAGTA
1 TCCCCTTAACAAATTATCCCCCTTTTATAAAAACAACTTTTCTCCCCTTTATAAATTGTTAAGTA
197129 C
66 C
*
197130 TCCCTCTTAACAAATTATCCCCCTTTTATAAAAATAACTTTTCTCCCCTTTTATAAATTGTTAAG
1 TCCC-CTTAACAAATTATCCCCCTTTTATAAAAACAACTTTTCTCCCC-TTTATAAATTGTTAAG
197195 TAC
64 TAC
*
197198 TCCCCTTTAACAAATTATCCCCCTTTTATAAACACAACTTTTCTCCCCCTTTATAAATT
1 TCCCC-TTAACAAATTATCCCCCTTTTATAAAAACAACTTTTCT-CCCCTTTATAAATT
197257 TTCCACCTTT
Statistics
Matches: 117, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
66 4 0.03
67 40 0.34
68 69 0.59
69 4 0.03
ACGTcount: A:0.30, C:0.27, G:0.02, T:0.41
Consensus pattern (66 bp):
TCCCCTTAACAAATTATCCCCCTTTTATAAAAACAACTTTTCTCCCCTTTATAAATTGTTAAGTA
C
Found at i:199219 original size:20 final size:20
Alignment explanation
Indices: 199194--199241 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
199184 AGGTTTTTCA
*
199194 AATGTATCGATATATTGAAT
1 AATGTATCGATATATTAAAT
*
199214 AATGTATCGATTTATTAAAT
1 AATGTATCGATATATTAAAT
199234 AATGTATC
1 AATGTATC
199242 AATACATTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (20 bp):
AATGTATCGATATATTAAAT
Found at i:210494 original size:184 final size:184
Alignment explanation
Indices: 210185--210548 Score: 701
Period size: 184 Copynumber: 2.0 Consensus size: 184
210175 AGGAATGAGG
*
210185 TCTTATCTATGAAATATCCTTCAATCTAGGTAACTATTCCTAGCATGACTTATTTTAGTATCTTT
1 TCTTATCTATGAAATATCCTTCAATCTAGGTAACTATTCCTAGCATGACTTATGTTAGTATCTTT
210250 GGTGAACCCACTCGTAAAATTTATAGTTGATGGCGTGTAGTAATAGCATGGTGCAATGCATTTCA
66 GGTGAACCCACTCGTAAAATTTATAGTTGATGGCGTGTAGTAATAGCATGGTGCAATGCATTTCA
210315 TAGTGGAATGCTTTATTATAGTTCAATGGCAGATACGTTGTGTTTAATATGCTT
131 TAGTGGAATGCTTTATTATAGTTCAATGGCAGATACGTTGTGTTTAATATGCTT
*
210369 TCTTATCTATGAAATATCCTTCAATTTAGGTAACTATTCCTAGCATGACTTATGTTAGTATCTTT
1 TCTTATCTATGAAATATCCTTCAATCTAGGTAACTATTCCTAGCATGACTTATGTTAGTATCTTT
210434 GGTGAACCCACTCGTAAAATTTATAGTTGATGGCGTGTAGTAATAGCATGGTGCAATGCATTTCA
66 GGTGAACCCACTCGTAAAATTTATAGTTGATGGCGTGTAGTAATAGCATGGTGCAATGCATTTCA
*
210499 TAGTGGAATGCTTTATTATAGTTCAATGGCTGATACGTTGTGTTTAATAT
131 TAGTGGAATGCTTTATTATAGTTCAATGGCAGATACGTTGTGTTTAATAT
210549 ACTCCACTAG
Statistics
Matches: 177, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 177 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (184 bp):
TCTTATCTATGAAATATCCTTCAATCTAGGTAACTATTCCTAGCATGACTTATGTTAGTATCTTT
GGTGAACCCACTCGTAAAATTTATAGTTGATGGCGTGTAGTAATAGCATGGTGCAATGCATTTCA
TAGTGGAATGCTTTATTATAGTTCAATGGCAGATACGTTGTGTTTAATATGCTT
Found at i:215063 original size:2 final size:2
Alignment explanation
Indices: 215056--215090 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
215046 TGTAACTACT
215056 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
215091 GTGTGTCTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:215495 original size:21 final size:20
Alignment explanation
Indices: 215471--215581 Score: 82
Period size: 21 Copynumber: 5.5 Consensus size: 20
215461 TAACCATTGA
215471 TATAATTTTAATAATATTTTG
1 TATAATTTTAATAAT-TTTTG
* *
215492 TATAATTTTGATAATCTTTG
1 TATAATTTTAATAATTTTTG
* * *
215512 ATACAATTTTATTAATGTTTG
1 -TATAATTTTAATAATTTTTG
* ** *
215533 ATATAGTTTTTGTAATTTTTTA
1 -TATAATTTTAATAA-TTTTTG
*
215555 TATAATTTTAA-AA-TTTTA
1 TATAATTTTAATAATTTTTG
215573 TATAATTTT
1 TATAATTTT
215582 GATACCTTTT
Statistics
Matches: 73, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
18 14 0.19
20 6 0.08
21 49 0.67
22 4 0.05
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (20 bp):
TATAATTTTAATAATTTTTG
Found at i:215562 original size:42 final size:42
Alignment explanation
Indices: 215450--215585 Score: 129
Period size: 42 Copynumber: 3.3 Consensus size: 42
215440 TAATCCATGA
* * * *
215450 TATAAATTTGATAACCATTGATATAATTTTAATAATATTTTG
1 TATAATTTTGATAATCTTTGATATAATTTTAATAATAGTTTG
* *
215492 TATAATTTTGATAATCTTTGATACAATTTTATTAAT-GTTTG
1 TATAATTTTGATAATCTTTGATATAATTTTAATAATAGTTTG
* * * *
215533 ATATAGTTTTTG-TAATTTTTTATATAATTTTAA-AAT--TTTA
1 -TATA-ATTTTGATAATCTTTGATATAATTTTAATAATAGTTTG
215573 TATAATTTTGATA
1 TATAATTTTGATA
215586 CCTTTTAATA
Statistics
Matches: 78, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
38 5 0.06
39 6 0.08
40 3 0.04
41 7 0.09
42 52 0.67
43 5 0.06
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (42 bp):
TATAATTTTGATAATCTTTGATATAATTTTAATAATAGTTTG
Found at i:215619 original size:23 final size:21
Alignment explanation
Indices: 215568--215621 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
215558 AATTTTAAAA
*
215568 TTTTATATAATTTTGATACCT
1 TTTTATATAAATTTGATACCT
* *
215589 TTTAATATAAATTTGATAGCTGT
1 TTTTATATAAATTTGATA-C-CT
215612 TTTTATATAA
1 TTTTATATAA
215622 TACCTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 16 0.59
22 1 0.04
23 10 0.37
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTATATAAATTTGATACCT
Found at i:215858 original size:20 final size:21
Alignment explanation
Indices: 215816--215883 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
215806 TTTTGTCATA
* *
215816 TTGATAACATTTGATATAATT
1 TTGATAACCTTTAATATAATT
*
215837 TTGATAACCTTT-ATACAATT
1 TTGATAACCTTTAATATAATT
*
215857 TT-AGTGACCTTTAATATAATT
1 TTGA-TAACCTTTAATATAATT
215878 TTGATA
1 TTGATA
215884 TTATTTTGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.03
20 16 0.41
21 21 0.54
22 1 0.03
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (21 bp):
TTGATAACCTTTAATATAATT
Found at i:215882 original size:52 final size:52
Alignment explanation
Indices: 215825--215935 Score: 134
Period size: 52 Copynumber: 2.1 Consensus size: 52
215815 ATTGATAACA
* *
215825 TTTGATATAATTTTGATAA-CCTTTATACAATTTTAGTGACCTTTAATATAAT
1 TTTGATATAATTTTGATAATCCTTTAGACAATTTTAGTG-CATTTAATATAAT
* ** * * *
215877 TTTGATATTATTTTGATAATTTTTTAGATAATTTTGGTGCATTTGATATAAT
1 TTTGATATAATTTTGATAATCCTTTAGACAATTTTAGTGCATTTAATATAAT
215929 TTTGATA
1 TTTGATA
215936 GTATTTATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
52 36 0.72
53 14 0.28
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (52 bp):
TTTGATATAATTTTGATAATCCTTTAGACAATTTTAGTGCATTTAATATAAT
Found at i:216042 original size:63 final size:63
Alignment explanation
Indices: 215920--216042 Score: 176
Period size: 63 Copynumber: 2.0 Consensus size: 63
215910 TTGGTGCATT
* * * * *
215920 TGATATAATTTTGATAGTATTTATAATAGTTTTGTTAACCTTAGATATAATTATGGTAACTTG
1 TGATATAATTCTGATAATATTTATAATAGTTTTGGTAAACTTAGATATAATTATAGTAACTTG
*
215983 TGATATAATTCTGATAATCA-TTATAATAGTTTTGGTAAACTTAGATATAATTTTAGTAAC
1 TGATATAATTCTGATAAT-ATTTATAATAGTTTTGGTAAACTTAGATATAATTATAGTAAC
216043 ACTCGATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 52 0.98
64 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.46
Consensus pattern (63 bp):
TGATATAATTCTGATAATATTTATAATAGTTTTGGTAAACTTAGATATAATTATAGTAACTTG
Found at i:216051 original size:63 final size:63
Alignment explanation
Indices: 215921--216067 Score: 167
Period size: 63 Copynumber: 2.3 Consensus size: 63
215911 TGGTGCATTT
* * * * * * *
215921 GATATAATTTTGATAGTATTTATAATAGTTTTGTTAACCTTAGATATAATTATGGTAACTTGT
1 GATATAATTCTGATAATATTTATAATAGTTTTGGTAAACTTAGATATAATTATAGTAACCTGC
*
215984 GATATAATTCTGATAATCA-TTATAATAGTTTTGGTAAACTTAGATATAATTTTAGTAACACT-C
1 GATATAATTCTGATAAT-ATTTATAATAGTTTTGGTAAACTTAGATATAATTATAGTAAC-CTGC
216047 GATATAATT-TCGATAA-ATTTA
1 GATATAATTCT-GATAATATTTA
216068 ATATAATTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
61 1 0.01
62 4 0.06
63 65 0.90
64 2 0.03
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (63 bp):
GATATAATTCTGATAATATTTATAATAGTTTTGGTAAACTTAGATATAATTATAGTAACCTGC
Found at i:216083 original size:41 final size:42
Alignment explanation
Indices: 216018--216097 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 42
216008 ATAGTTTTGG
*
216018 TAAACTTAGATATAATTTTAGTAACACTCGATATAATTTCGA
1 TAAACTTAGATATAATTATAGTAACACTCGATATAATTTCGA
* * ** *
216060 TAAATTTA-ATATAATTATCGTAACTTTTGATATAATTT
1 TAAACTTAGATATAATTATAGTAACACTCGATATAATTT
216098 ATGAAGAACA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 25 0.78
42 7 0.22
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (42 bp):
TAAACTTAGATATAATTATAGTAACACTCGATATAATTTCGA
Found at i:216224 original size:21 final size:21
Alignment explanation
Indices: 216048--216248 Score: 85
Period size: 21 Copynumber: 9.5 Consensus size: 21
216038 GTAACACTCG
* *
216048 ATATAATTTCGATAA-ATTTA
1 ATATAATTTTGACAACATTTA
* * * *
216068 ATATAATTATCG-TAACTTTTG
1 ATATAATT-TTGACAACATTTA
* * *
216089 ATATAATTTATGAAGAACAATAA
1 ATATAATTT-TG-ACAACATTTA
* *
216112 ATATAATTATT-ACAACCTTTG
1 ATATAATT-TTGACAACATTTA
*
216133 ATATAATTTTGAAAATC-TTTA
1 ATATAATTTTGACAA-CATTTA
* *
216154 CA-AAAATTTTGATAACATTT-
1 -ATATAATTTTGACAACATTTA
* * *
216174 CTGATAATTTTGACAACTTTTG
1 AT-ATAATTTTGACAACATTTA
*
216196 ATACAATTTT-ACTAACATTTA
1 ATATAATTTTGAC-AACATTTA
*
216217 ATATAATTTCGACAAC-TTTCA
1 ATATAATTTTGACAACATTT-A
*
216238 ATATGATTTTG
1 ATATAATTTTG
216249 GCTATTCTTA
Statistics
Matches: 136, Mismatches: 29, Indels: 31
0.69 0.15 0.16
Matches are distributed among these distances:
20 20 0.15
21 97 0.71
22 5 0.04
23 13 0.10
24 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (21 bp):
ATATAATTTTGACAACATTTA
Found at i:216317 original size:20 final size:20
Alignment explanation
Indices: 216270--216346 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 20
216260 GATTTTAGTA
*
216270 ACATTTGATATAGTTTTGAT
1 ACATTTGATATAGTTTTCAT
216290 A-ATCTTGATATAG-TTTCATT
1 ACAT-TTGATATAGTTTTCA-T
* *
216310 ACATTTGATATAATTTTAAT
1 ACATTTGATATAGTTTTCAT
* *
216330 GACTTTTAATATAGTTT
1 -ACATTTGATATAGTTT
216347 CGGTGGTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 6 0.13
20 21 0.46
21 19 0.41
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.51
Consensus pattern (20 bp):
ACATTTGATATAGTTTTCAT
Found at i:216559 original size:21 final size:21
Alignment explanation
Indices: 216535--216585 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
216525 AATCTTTGGT
216535 ATAATTTTGATAACTTTTGAA
1 ATAATTTTGATAACTTTTGAA
*
216556 ATAATTTTGATAATTTTTGAA
1 ATAATTTTGATAACTTTTGAA
216577 ATAATTTTG
1 ATAATTTTG
216586 TACAATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (21 bp):
ATAATTTTGATAACTTTTGAA
Found at i:216582 original size:12 final size:12
Alignment explanation
Indices: 216544--216584 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
216534 TATAATTTTG
*
216544 ATAACTTTTGAA
1 ATAATTTTTGAA
216556 ATAA-TTTTG--
1 ATAATTTTTGAA
216565 ATAATTTTTGAA
1 ATAATTTTTGAA
216577 ATAATTTT
1 ATAATTTT
216585 GTACAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 4 0.15
10 5 0.19
11 5 0.19
12 12 0.46
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (12 bp):
ATAATTTTTGAA
Found at i:216594 original size:21 final size:21
Alignment explanation
Indices: 216535--216594 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
216525 AATCTTTGGT
*
216535 ATAATTTTGATAACTTTTGAA
1 ATAATTTTGATAAATTTTGAA
*
216556 ATAATTTTGATAATTTTTGAA
1 ATAATTTTGATAAATTTTGAA
216577 ATAATTTTG-TACAATTTT
1 ATAATTTTGATA-AATTTT
216595 AATAACATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 2 0.06
21 34 0.94
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52
Consensus pattern (21 bp):
ATAATTTTGATAAATTTTGAA
Found at i:221598 original size:20 final size:21
Alignment explanation
Indices: 221573--221626 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
221563 TATTTCAGAC
221573 ATGTATCGATACATTTACT-T
1 ATGTATCGATACATTTACTAT
*
221593 ATGTATCTATACATTTACTAT
1 ATGTATCGATACATTTACTAT
* *
221614 TTATATCGATACA
1 ATGTATCGATACA
221627 AATTGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATTTACTAT
Found at i:223945 original size:13 final size:13
Alignment explanation
Indices: 223927--223952 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
223917 TACAGCAAGT
223927 ATGTATCGATACA
1 ATGTATCGATACA
223940 ATGTATCGATACA
1 ATGTATCGATACA
223953 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:226209 original size:21 final size:21
Alignment explanation
Indices: 226171--226215 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
226161 TTGCAAGTTG
*
226171 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
226193 AAATAATGAA-TTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
226213 AAA
1 AAA
226216 ACGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 7 0.33
22 9 0.43
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:228039 original size:15 final size:15
Alignment explanation
Indices: 228019--228049 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
228009 TAAAAATGTC
*
228019 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
228034 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
228049 C
1 C
228050 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:230142 original size:20 final size:20
Alignment explanation
Indices: 230066--230142 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
230056 GTCCAAAATA
* *
230066 TATCGATACATGTTTCTGTG
1 TATCGATACATTTTTCTATG
*
230086 TATCGATACATCTGGAAATTCTATG
1 TATCGATACAT-T----TTTCTATG
*
230111 TATCGATACATTTTTCTTTG
1 TATCGATACATTTTTCTATG
230131 TATCGATACATT
1 TATCGATACATT
230143 GTATCGATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
20 29 0.62
24 1 0.02
25 17 0.36
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (20 bp):
TATCGATACATTTTTCTATG
Found at i:230146 original size:13 final size:13
Alignment explanation
Indices: 230128--230166 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
230118 ACATTTTTCT
230128 TTGTATCGATACA
1 TTGTATCGATACA
230141 TTGTATCGATACA
1 TTGTATCGATACA
*
230154 CTGTATCGATACA
1 TTGTATCGATACA
230167 GGATGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:230311 original size:21 final size:21
Alignment explanation
Indices: 230287--230333 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
230277 AAATCTTTTG
230287 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
230308 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
230328 CAAAAT
1 CAAAAT
230334 CAGCATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:230330 original size:20 final size:19
Alignment explanation
Indices: 230289--230331 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
230279 ATCTTTTGCA
230289 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
230309 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
230329 AAA
1 AAA
230332 ATCAGCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:232724 original size:13 final size:13
Alignment explanation
Indices: 232706--232731 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
232696 TACAGCAAGT
232706 ATGTATCGATACA
1 ATGTATCGATACA
232719 ATGTATCGATACA
1 ATGTATCGATACA
232732 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:235357 original size:15 final size:15
Alignment explanation
Indices: 235337--235392 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 15
235327 TTTTAGTTAT
235337 GTCATAATTTATTAC
1 GTCATAATTTATTAC
*
235352 GTCATATTTTTTTTAGTTAC
1 GTCATA----ATTTA-TTAC
235372 GTCATAATTTATTAC
1 GTCATAATTTATTAC
235387 GTCATA
1 GTCATA
235393 TTTTTTTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
15 16 0.47
16 4 0.12
19 4 0.12
20 10 0.29
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (15 bp):
GTCATAATTTATTAC
Found at i:235397 original size:34 final size:35
Alignment explanation
Indices: 235321--235411 Score: 157
Period size: 35 Copynumber: 2.6 Consensus size: 35
235311 AAAAAAGAAG
*
235321 TATTTTTTTTAGTTATGTCATAATTTATTACGTCA
1 TATTTTTTTTAGTTACGTCATAATTTATTACGTCA
235356 TATTTTTTTTAGTTACGTCATAATTTATTACGTCA
1 TATTTTTTTTAGTTACGTCATAATTTATTACGTCA
*
235391 TA-TTTTTTTAGTTACATCATA
1 TATTTTTTTTAGTTACGTCATA
235412 TTTTCCTATC
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
34 18 0.33
35 36 0.67
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (35 bp):
TATTTTTTTTAGTTACGTCATAATTTATTACGTCA
Found at i:236239 original size:14 final size:14
Alignment explanation
Indices: 236216--236261 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
236206 ATTTTTAATG
236216 TATTTTTATTTATT
1 TATTTTTATTTATT
*
236230 TATTTATA-TTA-T
1 TATTTTTATTTATT
236242 TATTTTTATTTGATT
1 TATTTTTATTT-ATT
236257 T-TTTT
1 TATTTT
236262 GTTTTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
12 8 0.30
13 5 0.19
14 12 0.44
15 2 0.07
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (14 bp):
TATTTTTATTTATT
Found at i:237653 original size:17 final size:16
Alignment explanation
Indices: 237620--237654 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
237610 TTTTAGTTGA
*
237620 TTATTTTATTCATTAT
1 TTATTTTATTAATTAT
237636 TTATTTTAATTAATTAT
1 TTATTTT-ATTAATTAT
237653 TT
1 TT
237655 GTTGTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTTTATTAATTAT
Found at i:237879 original size:50 final size:50
Alignment explanation
Indices: 237804--238062 Score: 421
Period size: 50 Copynumber: 5.2 Consensus size: 50
237794 AGTTGTTGCC
* *
237804 ATTGTTGACTA-TCTTTCACCAACCTTTGATAATAGAGAGAGGTGGTCATA
1 ATTGTTGACGATTC-TTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
* **
237854 ATTGTTGACGATTCTTCATCAACCTTTGACAATAGAGAGAGGTGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
* *
237904 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
*
237954 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAAGTGGTCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
*
238004 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAAAGGTGGTCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
238054 ATTGTTGAC
1 ATTGTTGAC
238063 TCTAAGTATA
Statistics
Matches: 195, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
50 193 0.99
51 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
Found at i:242528 original size:50 final size:50
Alignment explanation
Indices: 242467--242711 Score: 400
Period size: 50 Copynumber: 4.9 Consensus size: 50
242457 TTGACTAGCA
*
242467 TTCACCAACCTTTGACAATAGAGAGAGGTGGCTATAATTGTTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
* *
242517 TTCACCAACCTTTGACAATAGAGAAAGGTGGCCATAATTGTTGATGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
* * *
242567 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATTATTATTGACGATTT
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
*
242617 TTCACCAACCTTTGATAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
* * *
242667 TTCACCAACCTTTGACAATAGAGAAAGGCGGTCATAATTGTTGAC
1 TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGAC
242712 TCTAAGTATA
Statistics
Matches: 179, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 179 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (50 bp):
TTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACGATTC
Found at i:243512 original size:5 final size:5
Alignment explanation
Indices: 243502--243570 Score: 78
Period size: 5 Copynumber: 14.8 Consensus size: 5
243492 ACCCTCGTAA
*
243502 TTAAT TTAAT TTAAT TTAAT TGAAAT TTAAT TTAA- TTAA- TTAAT TT-AT
1 TTAAT TTAAT TTAAT TTAAT T-TAAT TTAAT TTAAT TTAAT TTAAT TTAAT
243550 TT--T TTAA- TTAAT TTAAT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAA
243571 CTGAAAGTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
3 3 0.05
4 16 0.28
5 34 0.60
6 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (5 bp):
TTAAT
Found at i:243556 original size:16 final size:18
Alignment explanation
Indices: 243499--243569 Score: 92
Period size: 16 Copynumber: 3.9 Consensus size: 18
243489 TTTACCCTCG
243499 TAATTAATTTAATTTAATT
1 TAATTAATTTAATTT-ATT
*
243518 TAATTGAAATTTAATTTAAT
1 TAATT--AATTTAATTTATT
243538 TAATTAATTT-ATTT-TT
1 TAATTAATTTAATTTATT
243554 TAATTAATTTAATTTA
1 TAATTAATTTAATTTA
243570 ACTGAAAGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
16 11 0.24
17 8 0.17
18 5 0.11
19 5 0.11
20 7 0.15
21 10 0.22
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (18 bp):
TAATTAATTTAATTTATT
Found at i:243781 original size:45 final size:45
Alignment explanation
Indices: 243544--243790 Score: 244
Period size: 44 Copynumber: 5.6 Consensus size: 45
243534 TAATTAATTA
* * * * *
243544 ATTTATTTTTTAATTAATTTAATTTAACTGAAAGT-AAATTTTTT
1 ATTTATTTCTTAATTAATTTAATTTAATTAAAAATAAAATTTTTC
* * * *
243588 ATTTATTTCTTAATTAATTTAATTTAACTAGAAATTAAATTTTTTT
1 ATTTATTTCTTAATTAATTTAATTTAATTA-AAAATAAAATTTTTC
243634 ATTTA--TCTT-A-TAA-TTAATTTAATTAAAAATAAAATTCTTTC
1 ATTTATTTCTTAATTAATTTAATTTAATTAAAAATAAAATT-TTTC
* * * * *
243675 ATTTATCTCTTGATTAATTTAAATTT-ATT--AGAGAAAATTTTTT
1 ATTTATTTCTTAATTAATTT-AATTTAATTAAAAATAAAATTTTTC
* *
243718 ATTTATCTT-TTGATTAATTTAATTTAATTAAAAATAAAAATTTTC
1 ATTTAT-TTCTTAATTAATTTAATTTAATTAAAAATAAAATTTTTC
243763 ATTTATTTCTTAATTAATTTAATTTAAT
1 ATTTATTTCTTAATTAATTTAATTTAAT
243791 CAGAGTCAAA
Statistics
Matches: 172, Mismatches: 17, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
40 9 0.05
41 19 0.11
42 8 0.05
43 28 0.16
44 44 0.26
45 41 0.24
46 18 0.10
47 5 0.03
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (45 bp):
ATTTATTTCTTAATTAATTTAATTTAATTAAAAATAAAATTTTTC
Found at i:249018 original size:3 final size:3
Alignment explanation
Indices: 249010--249036 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
249000 AGCAAGAATA
249010 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
249037 ATATGCTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:250508 original size:11 final size:11
Alignment explanation
Indices: 250494--250518 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
250484 TTTATAATTA
250494 TTTTATTCTAT
1 TTTTATTCTAT
250505 TTTTATTCTAT
1 TTTTATTCTAT
250516 TTT
1 TTT
250519 CATAAAATAA
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTATTCTAT
Found at i:250991 original size:18 final size:19
Alignment explanation
Indices: 250965--251002 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
250955 TATAATTAAT
250965 TTAAATAAAAATA-TATTC
1 TTAAATAAAAATATTATTC
* *
250983 TTAATTAAAATTATTATTC
1 TTAAATAAAAATATTATTC
251002 T
1 T
251003 AAACTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAATAAAAATATTATTC
Done.