Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004862.1 Hibiscus syriacus cultivar Beakdansim tig00010968_pilon, 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: 2846896
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:188501 original size:17 final size:19
Alignment explanation
Indices: 188460--188501 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
188450 AATGCATTTT
* *
188460 ATGCATCGATGCACATACC
1 ATGCATCGATACACATACA
188479 ATGCATCGATACAC-T-CA
1 ATGCATCGATACACATACA
188496 ATGCAT
1 ATGCAT
188502 TTGATACATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 7 0.33
18 1 0.05
19 13 0.62
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (19 bp):
ATGCATCGATACACATACA
Found at i:190700 original size:47 final size:47
Alignment explanation
Indices: 190643--190857 Score: 367
Period size: 47 Copynumber: 4.6 Consensus size: 47
190633 TTATGGTTTA
*
190643 TTGATAAAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGTATG
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
*
190690 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATT
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
* *
190737 TTGATAAAACAAGCTTACGAGATTATGGAATTTAAATGGTAAGTATG
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
* *
190784 TTGATAAAATAAGCTTACGAGCTTATAGAATTTAAATGGTAAGTATT
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
*
190831 TTGGTAAAATAAGCTTACGAGCTTATG
1 TTGATAAAATAAGCTTACGAGCTTATG
190858 AGATAAATGA
Statistics
Matches: 157, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 157 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.35
Consensus pattern (47 bp):
TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
Found at i:195486 original size:47 final size:47
Alignment explanation
Indices: 195417--195632 Score: 342
Period size: 47 Copynumber: 4.6 Consensus size: 47
195407 TTATGGTTTA
* * *
195417 TTGATAAAATAAGCTTACGAGCTTATGGAATTTCAATAGTAAGCATG
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
* *
195464 TTGATAAAATAAGCTTACGAGCTTATGGAATTTTTAATGGTAAGTATT
1 TTGATAAAATAAGCTTACGAGCTTATGGAA-TTTAAATGGTAAGTATG
*
195512 TTGATAAAATAAGCTTACGAGATTATGGAATTTAAATGGTAAGTATG
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
* *
195559 TTGATAAAATAAGCTTACGAGCGTATGGAATTTAAATGGTAAGTATT
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
*
195606 TTGGTAAAATAAGCTTACGAGCTTATG
1 TTGATAAAATAAGCTTACGAGCTTATG
195633 AGATAAATGA
Statistics
Matches: 156, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
47 114 0.73
48 42 0.27
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (47 bp):
TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATG
Found at i:195580 original size:95 final size:94
Alignment explanation
Indices: 195417--195632 Score: 360
Period size: 95 Copynumber: 2.3 Consensus size: 94
195407 TTATGGTTTA
*
195417 TTGATAAAATAAGCTTACGAGCTTATGGAATTTCAATAGTAAGCATGTTGATAAAATAAGCTTAC
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATAGTAAGCATGTTGATAAAATAAGCTTAC
* *
195482 GAGCTTATGGAATTTTTAATGGTAAGTATT
66 GAGCGTATGGAA-TTTAAATGGTAAGTATT
* * *
195512 TTGATAAAATAAGCTTACGAGATTATGGAATTTAAATGGTAAGTATGTTGATAAAATAAGCTTAC
1 TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATAGTAAGCATGTTGATAAAATAAGCTTAC
195577 GAGCGTATGGAATTTAAATGGTAAGTATT
66 GAGCGTATGGAATTTAAATGGTAAGTATT
*
195606 TTGGTAAAATAAGCTTACGAGCTTATG
1 TTGATAAAATAAGCTTACGAGCTTATG
195633 AGATAAATGA
Statistics
Matches: 113, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
94 41 0.36
95 72 0.64
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (94 bp):
TTGATAAAATAAGCTTACGAGCTTATGGAATTTAAATAGTAAGCATGTTGATAAAATAAGCTTAC
GAGCGTATGGAATTTAAATGGTAAGTATT
Found at i:197211 original size:46 final size:46
Alignment explanation
Indices: 197123--197230 Score: 137
Period size: 46 Copynumber: 2.4 Consensus size: 46
197113 TAGAGTATGT
* *
197123 AAAATGCATGAAAGGATGCATTAAGGTATGAAAGGAAACCATAAAC
1 AAAATACATGAAAGGATGCATTAAGGCATGAAAGGAAACCATAAAC
* ** *
197169 AAAATACATGAAATGATGCATTAAGGCATGAAAGGATGCCAT-AAT
1 AAAATACATGAAAGGATGCATTAAGGCATGAAAGGAAACCATAAAC
* *
197214 TAAATGCATGAAAGGAT
1 AAAATACATGAAAGGAT
197231 CCCATAATTA
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 16 0.30
46 37 0.70
ACGTcount: A:0.48, C:0.10, G:0.21, T:0.20
Consensus pattern (46 bp):
AAAATACATGAAAGGATGCATTAAGGCATGAAAGGAAACCATAAAC
Found at i:197236 original size:71 final size:72
Alignment explanation
Indices: 197150--197302 Score: 254
Period size: 71 Copynumber: 2.1 Consensus size: 72
197140 GCATTAAGGT
*
197150 ATGAAAGGAAACCATAAACAAAATACATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATT
1 ATGAAAGGATACCATAAACAAAATACATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATT
197215 -AAATGC
66 AAAATGC
* ** *
197221 ATGAAAGGATCCCATAATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATT
1 ATGAAAGGATACCATAAACAAAATACATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATT
197286 AAAATGC
66 AAAATGC
197293 ATGAAAGGAT
1 ATGAAAGGAT
197303 GCATTAAGGC
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 60 0.79
72 16 0.21
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.22
Consensus pattern (72 bp):
ATGAAAGGATACCATAAACAAAATACATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATT
AAAATGC
Found at i:197251 original size:26 final size:25
Alignment explanation
Indices: 197194--197337 Score: 146
Period size: 26 Copynumber: 6.0 Consensus size: 25
197184 ATGCATTAAG
197194 GCATGAAAGGATGCCATAATTAAAT
1 GCATGAAAGGATGCCATAATTAAAT
*
197219 GCATGAAAGGATCCCATAATTAAAAT
1 GCATGAAAGGATGCCATAATT-AAAT
* *
197245 GCATGAAATGATG-C---ATT-AAG
1 GCATGAAAGGATGCCATAATTAAAT
197265 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGCCATAATT-AAAT
*
197291 GCATGAAAGGATG-C---ATT-AAG
1 GCATGAAAGGATGCCATAATTAAAT
*
197311 GCATGAAAGGATGGCATAATTTAAAT
1 GCATGAAAGGATGCCATAA-TTAAAT
197337 G
1 G
197338 TATAAATGGA
Statistics
Matches: 98, Mismatches: 8, Indels: 25
0.75 0.06 0.19
Matches are distributed among these distances:
20 29 0.30
21 2 0.02
22 6 0.06
24 4 0.04
25 24 0.24
26 33 0.34
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (25 bp):
GCATGAAAGGATGCCATAATTAAAT
Found at i:197270 original size:20 final size:20
Alignment explanation
Indices: 197245--197323 Score: 86
Period size: 20 Copynumber: 3.6 Consensus size: 20
197235 TAATTAAAAT
*
197245 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
197265 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
197291 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
197311 GCATGAAAGGATG
1 GCATGAAAGGATG
197324 GCATAATTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
20 27 0.54
21 1 0.02
22 3 0.06
24 3 0.06
25 1 0.02
26 15 0.30
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:197271 original size:46 final size:46
Alignment explanation
Indices: 197219--197345 Score: 202
Period size: 46 Copynumber: 2.8 Consensus size: 46
197209 ATAATTAAAT
*
197219 GCATGAAAGGATCCCATAATTAAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAATTAAAATGCATGAAATGATGCATTAAG
*
197265 GCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAATTAAAATGCATGAAATGATGCATTAAG
* * *
197311 GCATGAAAGGATGGCATAATTTAAATGTAT-AAATG
1 GCATGAAAGGATGCCATAATTAAAATGCATGAAATG
197346 GATATGTTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
45 4 0.05
46 71 0.95
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.24
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAATTAAAATGCATGAAATGATGCATTAAG
Found at i:197329 original size:117 final size:118
Alignment explanation
Indices: 197122--197337 Score: 344
Period size: 117 Copynumber: 1.8 Consensus size: 118
197112 TTAGAGTATG
* *
197122 TAAAATGCATGAAAGGATGCATTAAGGTATGAAAGGAAACCATAAACAAAATACATGAAATGATG
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAAACCATAAACAAAATACATGAAAGGATG
197187 CATTAAGGCATGAAAGGATGCCATAA-TTAAATGCATGAAAGGATCCCATAAT
66 CATTAAGGCATGAAAGGATGCCATAATTTAAATGCATGAAAGGATCCCATAAT
* ** ** *
197239 TAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAAAGGATG
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAAACCATAAACAAAATACATGAAAGGATG
*
197304 CATTAAGGCATGAAAGGATGGCATAATTTAAATG
66 CATTAAGGCATGAAAGGATGCCATAATTTAAATG
197338 TATAAATGGA
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
117 82 0.92
118 7 0.08
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (118 bp):
TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGAAACCATAAACAAAATACATGAAAGGATG
CATTAAGGCATGAAAGGATGCCATAATTTAAATGCATGAAAGGATCCCATAAT
Found at i:203641 original size:20 final size:20
Alignment explanation
Indices: 203613--203879 Score: 140
Period size: 20 Copynumber: 11.8 Consensus size: 20
203603 ACGTAAAATC
203613 CATGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
* *
203633 CATGTAAGGATGCCATAATTAAAATG
1 CATGAAAGGATG-C---ATT--AAGG
203659 CATGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
**
203679 CATGAAAGGATGCCATAATTAAAATC
1 CATGAAAGGATG-C---ATT--AAGG
*
203705 CATGAAAGGATGCACTAAGG
1 CATGAAAGGATGCATTAAGG
* *
203725 CATGAAATGATGGCATAATTAAAATG
1 CATGAAAGGAT-GC---ATT--AAGG
203751 CATGAAAGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
*
203771 CATGAAAGGATGCCACAATTAAAATG
1 CATGAAAGGATG---C-ATT--AAGG
*
203797 CATGAAATGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
* **
203817 CGTGAAAGGATGTCATAATTAAAATA
1 CATGAAAGGATG-C---ATT--AAGG
203843 CATGAAA-GATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
203862 CATGAAAGGATGCCATTA
1 CATGAAAGGATG-CATTA
203880 TTAAAATGCA
Statistics
Matches: 191, Mismatches: 24, Indels: 63
0.69 0.09 0.23
Matches are distributed among these distances:
19 9 0.05
20 70 0.37
21 13 0.07
22 11 0.06
23 2 0.01
24 15 0.08
25 8 0.04
26 63 0.33
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (20 bp):
CATGAAAGGATGCATTAAGG
Found at i:203662 original size:26 final size:25
Alignment explanation
Indices: 203632--203946 Score: 170
Period size: 26 Copynumber: 13.6 Consensus size: 25
203622 ATGCATTAAG
*
203632 GCATGTAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGCCA-AATTAAAAT
*
203658 GCATGAAAGGATG-C--ATT--AAG
1 GCATGAAAGGATGCCAAATTAAAAT
203678 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGCCA-AATTAAAAT
* * *
203704 CCATGAAAGGATG-C--ACT--AAG
1 GCATGAAAGGATGCCAAATTAAAAT
* *
203724 GCATGAAATGATGGCATAATTAAAAT
1 GCATGAAAGGATGCCA-AATTAAAAT
*
203750 GCATGAAAGGATG-C--ATT--AAG
1 GCATGAAAGGATGCCAAATTAAAAT
203770 GCATGAAAGGATGCCACAATTAAAAT
1 GCATGAAAGGATGCCA-AATTAAAAT
* *
203796 GCATGAAATGATG-C--ATT--AAG
1 GCATGAAAGGATGCCAAATTAAAAT
* *
203816 GCGTGAAAGGATGTCATAATTAAAAT
1 GCATGAAAGGATGCCA-AATTAAAAT
* *
203842 ACATGAAA-GATG-C--ATT--AAG
1 GCATGAAAGGATGCCAAATTAAAAT
*
203861 GCATGAAAGGATGCCATTATTAAAAT
1 GCATGAAAGGATGCCA-AATTAAAAT
*
203887 GCATTAAAGGATG-C--ATT--AAT
1 GCATGAAAGGATGCCAAATTAAAAT
* ** *
203907 GCTTGAAAATATGTCATAATTAAAAT
1 GCATGAAAGGATGCCA-AATTAAAAT
203933 GCATGAAAGGATGC
1 GCATGAAAGGATGC
203947 ATTAATGCAT
Statistics
Matches: 220, Mismatches: 32, Indels: 74
0.67 0.10 0.23
Matches are distributed among these distances:
19 9 0.04
20 72 0.33
21 9 0.04
22 14 0.06
24 18 0.08
25 9 0.04
26 89 0.40
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (25 bp):
GCATGAAAGGATGCCAAATTAAAAT
Found at i:203927 original size:183 final size:184
Alignment explanation
Indices: 203606--203987 Score: 563
Period size: 183 Copynumber: 2.1 Consensus size: 184
203596 TTAGAGTACG
* * * *
203606 TAAAATCCATGAAAGGATGCATTAAGGCATGTAAGGATGCCATAATTAAAATGCATGAAAGGATG
1 TAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATACATGAAAGGATG
203671 CATTAAGGCATGAAAGGATGCCATAATTAAAATCCATGAAAGGATGCACTAAGGCATGAAATGAT
66 CATTAAGGCATGAAAGGATGCCATAATTAAAATCCATGAAAGGATGCACTAAGGCATGAAATGAT
*
203736 GGCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCACAAT
131 GGCATAATTAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCACAAT
* *
203790 TAAAATGCATGAAATGATGCATTAAGGCGTGAAAGGATGTCATAATTAAAATACATGAAA-GATG
1 TAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATACATGAAAGGATG
* * * * * *
203854 CATTAAGGCATGAAAGGATGCCATTATTAAAATGCATTAAAGGATGCATTAATGCTTGAAAAT-A
66 CATTAAGGCATGAAAGGATGCCATAATTAAAATCCATGAAAGGATGCACTAAGGCATG-AAATGA
* * * *
203918 TGTCATAATTAAAATGCATGAAAGGATGCATTAATGCATAAAAGGATGTCATAAT
130 TGGCATAATTAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCACAAT
* *
203973 TTAAATGTAT-AAATG
1 TAAAATGCATGAAATG
203988 GATATATTAA
Statistics
Matches: 178, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
182 5 0.03
183 115 0.65
184 58 0.33
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.25
Consensus pattern (184 bp):
TAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATACATGAAAGGATG
CATTAAGGCATGAAAGGATGCCATAATTAAAATCCATGAAAGGATGCACTAAGGCATGAAATGAT
GGCATAATTAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATGCCACAAT
Found at i:203998 original size:46 final size:46
Alignment explanation
Indices: 203606--203979 Score: 543
Period size: 46 Copynumber: 8.2 Consensus size: 46
203596 TTAGAGTACG
* *
203606 TAAAATCCATGAAAGGATGCATTAAGGCATGTAAGGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
203652 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * * *
203698 TAAAATCCATGAAAGGATGCACTAAGGCATGAAATGATGGCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
*
203744 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCACAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * *
203790 TAAAATGCATGAAATGATGCATTAAGGCGTGAAAGGATGTCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* *
203836 TAAAATACATGAAA-GATGCATTAAGGCATGAAAGGATGCCATTAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * * ** *
203881 TAAAATGCATTAAAGGATGCATTAATGCTTGAAAATATGTCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
* * *
203927 TAAAATGCATGAAAGGATGCATTAATGCATAAAAGGATGTCATAAT
1 TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
*
203973 TTAAATG
1 TAAAATG
203980 TATAAATGGA
Statistics
Matches: 294, Mismatches: 33, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 40 0.14
46 254 0.86
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (46 bp):
TAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAAT
Found at i:207154 original size:40 final size:40
Alignment explanation
Indices: 207110--207185 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
207100 CAGTCTAGGG
207110 GTATCGATAC-CAACAGGTCAATATCGATACCGAAGGTTTA
1 GTATCGATACTCAA-AGGTCAATATCGATACCGAAGGTTTA
* * * *
207150 GTATCGATACTGAAGGGTCAATATCGGTACTGAAGG
1 GTATCGATACTCAAAGGTCAATATCGATACCGAAGG
207186 GTCAATATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 29 0.94
41 2 0.06
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (40 bp):
GTATCGATACTCAAAGGTCAATATCGATACCGAAGGTTTA
Found at i:207174 original size:20 final size:20
Alignment explanation
Indices: 207125--207194 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
207115 GATACCAACA
*
207125 GGTCAATATCGATACCGAAG
1 GGTCAATATCGATACTGAAG
* * *
207145 GTTTAGTATCGATACTGAAG
1 GGTCAATATCGATACTGAAG
*
207165 GGTCAATATCGGTACTGAAG
1 GGTCAATATCGATACTGAAG
207185 GGTCAATATC
1 GGTCAATATC
207195 AGTACCCATG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (20 bp):
GGTCAATATCGATACTGAAG
Found at i:207199 original size:20 final size:20
Alignment explanation
Indices: 207157--207199 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
207147 TTAGTATCGA
*
207157 TACTGAAGGGTCAATATCGG
1 TACTGAAGGGTCAATATCAG
207177 TACTGAAGGGTCAATATCAG
1 TACTGAAGGGTCAATATCAG
207197 TAC
1 TAC
207200 CCATGAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (20 bp):
TACTGAAGGGTCAATATCAG
Found at i:214916 original size:29 final size:31
Alignment explanation
Indices: 214828--214917 Score: 89
Period size: 32 Copynumber: 3.0 Consensus size: 31
214818 CAAAATATAT
* * *
214828 AACTTTTAAAAATTATAGTTTTGGTC-CTTG
1 AACTTTTAAAATTTATAGTTTTGATCACTAG
* *
214858 AACTTTTCCAAAGTTTATAGTTTAGA-CACTAG
1 AACTTTT--AAAATTTATAGTTTTGATCACTAG
214890 -ACTTTTAAAATTTATA-TTTTGATCACTA
1 AACTTTTAAAATTTATAGTTTTGATCACTA
214918 ACCAAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
28 5 0.10
29 14 0.29
30 7 0.14
31 7 0.14
32 16 0.33
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (31 bp):
AACTTTTAAAATTTATAGTTTTGATCACTAG
Found at i:219867 original size:26 final size:27
Alignment explanation
Indices: 219838--219894 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
219828 TAAATAAAAC
*
219838 AAAA-TAAAGTAAAAAATAAATATTA-T
1 AAAAGTAAAATAAAAAA-AAATATTATT
*
219864 AAAAGTAAAATAAAATAAAATATTATT
1 AAAAGTAAAATAAAAAAAAATATTATT
219891 AAAA
1 AAAA
219895 ATATAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (27 bp):
AAAAGTAAAATAAAAAAAAATATTATT
Found at i:219879 original size:5 final size:5
Alignment explanation
Indices: 219824--219885 Score: 52
Period size: 5 Copynumber: 12.0 Consensus size: 5
219814 GTTAGTACTG
* * * * **
219824 AAATT AAATA AAACA AAATA AAGTA AAAAA TAAATA TTATA AAAGTA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA -AAATA AAATA AAA-TA AAATA
219876 AAATA AAATA
1 AAATA AAATA
219886 TTATTAAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
5 35 0.80
6 9 0.20
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:219901 original size:29 final size:25
Alignment explanation
Indices: 219850--219905 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
219840 AATAAAGTAA
*
219850 AAAATAAATATTATAAAAGTAAAAT
1 AAAATAAATATTATAAAAATAAAAT
219875 AAAATAAAATATTATTAAAAATATAAA-
1 AAAAT-AAATATTA-TAAAAATA-AAAT
219902 AAAA
1 AAAA
219906 CGCTCTAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 5 0.19
26 8 0.30
27 11 0.41
28 3 0.11
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAATAAATATTATAAAAATAAAAT
Found at i:219904 original size:26 final size:24
Alignment explanation
Indices: 219847--219904 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 24
219837 CAAAATAAAG
*
219847 TAAAAAATAAATATTATAAAAGTA
1 TAAAAAATAAATATTATAAAAATA
*
219871 AAATAAAATAAAATATTATTAAAAATA
1 TAA-AAAAT-AAATATTA-TAAAAATA
219898 TAAAAAA
1 TAAAAAA
219905 ACGCTCTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 2 0.07
25 5 0.18
26 12 0.43
27 9 0.32
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (24 bp):
TAAAAAATAAATATTATAAAAATA
Found at i:220090 original size:2 final size:2
Alignment explanation
Indices: 220074--220111 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
220064 ATGAATTGAA
*
220074 AT AT AT AG AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
220112 AAGAACAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:221790 original size:3 final size:3
Alignment explanation
Indices: 221782--221892 Score: 107
Period size: 3 Copynumber: 35.7 Consensus size: 3
221772 TTTTACTTAC
* * *
221782 AAT AAT AAT AGTT AAT AAT AAT AATT AAT AAT AAT AAC AACT AAT AAC
1 AAT AAT AAT A-AT AAT AAT AAT AA-T AAT AAT AAT AAT AA-T AAT AAT
* * *
221830 AAT AAT AAT ATT AAT AATT AAT AAT AAT AAC AACT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AA-T AAT AAT AAT AAT
*
221877 AAT -AT TAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
221893 ATTTTGGACA
Statistics
Matches: 89, Mismatches: 13, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.02
3 75 0.84
4 12 0.13
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:221800 original size:13 final size:13
Alignment explanation
Indices: 221782--221892 Score: 92
Period size: 13 Copynumber: 8.8 Consensus size: 13
221772 TTTTACTTAC
*
221782 AATAATAATAGTT
1 AATAATAATAATT
221795 AATAATAATAATT
1 AATAATAATAATT
*
221808 AATAATAATAA-C
1 AATAATAATAATT
*
221820 AACTAATAACAA-T
1 AA-TAATAATAATT
*
221833 AATAATATTAA-T
1 AATAATAATAATT
221845 AATTAATAATAA-T
1 AA-TAATAATAATT
* *
221858 AACAACTAATAA-C
1 AATAA-TAATAATT
221871 AATAATAAT-ATT
1 AATAATAATAATT
221883 -ATAATAATAA
1 AATAATAATAA
221893 ATTTTGGACA
Statistics
Matches: 82, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
11 9 0.11
12 19 0.23
13 54 0.66
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (13 bp):
AATAATAATAATT
Found at i:221803 original size:16 final size:15
Alignment explanation
Indices: 221782--221892 Score: 107
Period size: 16 Copynumber: 7.1 Consensus size: 15
221772 TTTTACTTAC
*
221782 AATAATAATAGTTAAT
1 AATAATAATA-ATAAT
221798 AATAATAATTAATAAT
1 AATAATAA-TAATAAT
* *
221814 AATAACAACTAATAAC
1 AATAATAA-TAATAAT
*
221830 AATAATAATATTAAT
1 AATAATAATAATAAT
*
221845 AATTAATAATAATAAC
1 AA-TAATAATAATAAT
*
221861 AACTAATAACAATAAT
1 AA-TAATAATAATAAT
*
221877 AAT-ATTATAATAAT
1 AATAATAATAATAAT
221891 AA
1 AA
221893 ATTTTGGACA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
14 11 0.14
15 8 0.10
16 58 0.73
17 2 0.03
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (15 bp):
AATAATAATAATAAT
Found at i:221836 original size:22 final size:22
Alignment explanation
Indices: 221808--221880 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
221798 AATAATAATT
221808 AATAATAATAACAACTAATAAC
1 AATAATAATAACAACTAATAAC
** *
221830 AATAATAATATTAA-TAAT--T
1 AATAATAATAACAACTAATAAC
221849 AATAATAATAACAACTAATAAC
1 AATAATAATAACAACTAATAAC
221871 AATAATAATA
1 AATAATAATA
221881 TTATAATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 12 0.29
20 4 0.10
21 4 0.10
22 22 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (22 bp):
AATAATAATAACAACTAATAAC
Found at i:221845 original size:41 final size:41
Alignment explanation
Indices: 221794--221892 Score: 175
Period size: 41 Copynumber: 2.5 Consensus size: 41
221784 TAATAATAGT
*
221794 TAATAATAATAATTAATAATAATAACAACTAATAACAATAA
1 TAATATTAATAATTAATAATAATAACAACTAATAACAATAA
221835 TAATATTAATAATTAATAATAATAACAACTAATAACAATAA
1 TAATATTAATAATTAATAATAATAACAACTAATAACAATAA
221876 TAATATT-ATAA-TAATAA
1 TAATATTAATAATTAATAA
221893 ATTTTGGACA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
39 6 0.11
40 4 0.07
41 47 0.82
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (41 bp):
TAATATTAATAATTAATAATAATAACAACTAATAACAATAA
Found at i:229559 original size:27 final size:27
Alignment explanation
Indices: 229521--229574 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
229511 CGCTACCATT
229521 GTCCTTTCATTTATCAGATATCCAAAA
1 GTCCTTTCATTTATCAGATATCCAAAA
229548 GTCCTTTCATTTATCAGATATCCAAAA
1 GTCCTTTCATTTATCAGATATCCAAAA
229575 TTCTGTAGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (27 bp):
GTCCTTTCATTTATCAGATATCCAAAA
Found at i:237819 original size:21 final size:20
Alignment explanation
Indices: 237795--237852 Score: 59
Period size: 19 Copynumber: 3.0 Consensus size: 20
237785 CCGAAAATGA
237795 AGCAAGAAAAGCACAGAGAGC
1 AGCAAGAAAAGCA-AGAGAGC
237816 AGC-AGCAAAAG-AAGAGAGC
1 AGCAAG-AAAAGCAAGAGAGC
* *
237835 AGCAATAGAAGC-AGAGAG
1 AGCAAGAAAAGCAAGAGAG
237853 AAGTAGCGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 20 0.62
20 4 0.12
21 8 0.25
ACGTcount: A:0.52, C:0.16, G:0.31, T:0.02
Consensus pattern (20 bp):
AGCAAGAAAAGCAAGAGAGC
Found at i:237837 original size:16 final size:16
Alignment explanation
Indices: 237811--237850 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
237801 AAAAGCACAG
237811 AGAGCAGCAGCAAAAGA
1 AGAG-AGCAGCAAAAGA
*
237828 AGAGAGCAGCAATAGA
1 AGAGAGCAGCAAAAGA
237844 AGCAGAG
1 AG-AGAG
237851 AGAAGTAGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.50, C:0.15, G:0.33, T:0.03
Consensus pattern (16 bp):
AGAGAGCAGCAAAAGA
Found at i:239506 original size:33 final size:33
Alignment explanation
Indices: 239437--239506 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
239427 TCAATGCCCC
* ** *
239437 CTCGATCCTGGGTTCATCCTCTTCTCTGTATAA
1 CTCGATCCTGGGCTCATCCTCACCTCTGGATAA
*
239470 CTCGATCCTGGGCTCATCCATCACCT-TGGATGA
1 CTCGATCCTGGGCTCATCC-TCACCTCTGGATAA
239503 CTCG
1 CTCG
239507 GCTCCCCTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 27 0.87
34 4 0.13
ACGTcount: A:0.16, C:0.33, G:0.19, T:0.33
Consensus pattern (33 bp):
CTCGATCCTGGGCTCATCCTCACCTCTGGATAA
Found at i:249561 original size:5 final size:5
Alignment explanation
Indices: 249551--249576 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
249541 TGACTTAGAA
249551 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
249577 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:250076 original size:2 final size:2
Alignment explanation
Indices: 250069--250103 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
250059 ATAATATAAA
250069 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
250104 ACATGCAACA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:251865 original size:3 final size:3
Alignment explanation
Indices: 251857--251908 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
251847 ACAAATAGAG
* *
251857 ATA ATA ATA ATA ACA A-A AT- ATA ATA ATT ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
251903 ATA ATA
1 ATA ATA
251909 TGAAACTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:251872 original size:22 final size:22
Alignment explanation
Indices: 251844--251908 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
251834 AAAGCCTGAA
251844 AACACAAATAGAGATAATAATAAT
1 AACA-AAATAGA-ATAATAATAAT
* *
251868 AACAAAATATAATAATTATAAT
1 AACAAAATAGAATAATAATAAT
*
251890 AATAATAAT--AATAATAATA
1 AACAA-AATAGAATAATAATA
251909 TGAAACTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 9 0.25
22 14 0.39
23 9 0.25
24 4 0.11
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (22 bp):
AACAAAATAGAATAATAATAAT
Found at i:252329 original size:42 final size:41
Alignment explanation
Indices: 252236--252342 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
252226 GCTTAAAGGT
* *
252236 CTTATTGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATTGATGGCCCGAAAGACTTAGCATCTTGCTCGAAAGA
* ** *
252277 CGTACAGATGGCCCGAAAGATTTAAGCATCATT-CTCGAAAGA
1 CTTATTGATGGCCCGAAAGACTT-AGCATC-TTGCTCGAAAGA
* *
252319 CTTATTGATGGCACGAAGGACTTA
1 CTTATTGATGGCCCGAAAGACTTA
252343 CAAATTTTGG
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
41 19 0.37
42 31 0.60
43 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (41 bp):
CTTATTGATGGCCCGAAAGACTTAGCATCTTGCTCGAAAGA
Found at i:252807 original size:232 final size:232
Alignment explanation
Indices: 252063--253352 Score: 1666
Period size: 233 Copynumber: 5.6 Consensus size: 232
252053 GACCTGAAGA
* * * * * * *
252063 ATTTAAGCATCATGCTCGAAAGTCTTAATGATGGCCCAAAAGACTTACCAACTTTT-GAAATAGT
1 ATTTAAGCATCATGCTCGAAAGACTTACTGATGGCACGAAGGACTTA-TAAATTTTGGAAATAGT
* *
252127 TTACTAGATAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTAAAATGAGAAA-TC
65 TTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACT-
* *** *
252191 TTTCTCATTTTTCAAGAGACATGTGAAAACAT-CTAGCTTAAAGGTCTTATTGATGGCCCGAAGG
129 TTTCTCATTTTTCGAGAGACATGTGAAAACATCCT-GCCCGAAGGTCTTATGGATGGCCCGAAGG
* * *
252255 ACTTATCATCTTGCTCGAAAGACGTACAGATGGCCCGAAA-G
193 ACTTATCATCTT-TTCGAAAGACTTACAGATGACCC-AAAGG
* * *
252296 ATTTAAGCATCATTCTCGAAAGACTTATTGATGGCACGAAGGACTTACAAATTTTGGAAATAGTT
1 ATTTAAGCATCATGCTCGAAAGACTTACTGATGGCACGAAGGACTTATAAATTTTGGAAATAGTT
* * * *
252361 TACTAGGTAAGAAACCTTTCTCACTTTTCAAAAATTTCAAATTTCAAATTTAAATGAGAAATTTT
66 TACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTT
*** * * * *
252426 TCTCATTTTTTTTGAAATCACGTGAAAACATCCTGCCCGAATGTCTTA-GGAATGGCCCGAATGA
131 TCTCATTTTTCGAGAGA-CATGTGAAAACATCCTGCCCGAAGGTCTTATGG-ATGGCCCGAAGGA
*
252490 CTTATCATCTTTCTCGAAAGACTTACAGATTACCCAAAGG
194 CTTATCATCTTT-TCGAAAGACTTACAGATGACCCAAAGG
* * *
252530 ATTTAAGCATCACGCTCGAAAGACTTAGTGATGGCCCGAAGGACTTATAAATTTTGGAAATAGTT
1 ATTTAAGCATCATGCTCGAAAGACTTACTGATGGCACGAAGGACTTATAAATTTTGGAAATAGTT
* * * *
252595 TACTAGGTAAGAAACCTTTCTTATTTTTCAAAAATTTCATTTTTTAGATTTAAATGAGAAACCTT
66 TACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTT
* * * * *
252660 TCTCATTTTTTGAGAGACATGTGAAAA-ATCCTGCACGAAGGTCTTATGGATTGCTCGAATGACT
131 TCTCATTTTTCGAGAGACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACT
* *
252724 TATCATCTTGTTCGAAAGACTTACAAATGACCCCAAGG
196 TATCATCTT-TTCGAAAGACTTACAGATGACCCAAAGG
* *
252762 ATTTAAGCATCATGCTCGAAAGACTTACTGATGGCATGCAGGACTTATAAATTTTGGAAATAGTT
1 ATTTAAGCATCATGCTCGAAAGACTTACTGATGGCACGAAGGACTTATAAATTTTGGAAATAGTT
* * *
252827 TACTAGGTAAGAAACCTTTCTTACTTTTAAAAAATTTCAATTTTTAGATTTAAATGAGAAACGTT
66 TACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTT
* *
252892 TCTTATTTTTCGAGAGACATGTGAAAACATCTTGCCCGAAGGTCTTATGGATGGCCCGAAGGACT
131 TCTCATTTTTCGAGAGACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACT
252957 TATCATC--TT-----G-C-T-CTA-A--ACCCAAAGG
196 TATCATCTTTTCGAAAGACTTAC-AGATGACCCAAAGG
* * * *
252982 ATTTAAGCATCATGCTTGAATGACTTACTGATGGCTCGAAGGACTTATAAATTTGGGAAATAGTT
1 ATTTAAGCATCATGCTCGAAAGACTTACTGATGGCACGAAGGACTTATAAATTTTGGAAATAGTT
* * * *
253047 TACTAGGTAAGAAATCTTTATTACTTTTCAAAAATTTCAATTTTCAAATTTGAATGAGAAACTTT
66 TACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTT
** * * * *
253112 TCTCATTTTTCGAGAGACATGTGAAAACATCCTATCCAAAGGTCTTATAGATGACCCGTAGGACT
131 TCTCATTTTTCGAGAGACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACT
* ***
253177 TATCATCTTTCTCAAAAGACTTACAGATGACTTGAAGG
196 TATCATCTTT-TCGAAAGACTTACAGATGACCCAAAGG
*
253215 ATTTAAGCATCATGCTCGAAAGAATTACTGATGGC-CAGAAGGACTTATAAATTTTGGAAATAGT
1 ATTTAAGCATCATGCTCGAAAGACTTACTGATGGCAC-GAAGGACTTATAAATTTTGGAAATAGT
* *
253279 TTACTAGGTAAGAAATCTTTTTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTT
65 TTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTT
253344 TTCTCATTT
130 TTCTCATTT
253353 CTTAACTTAT
Statistics
Matches: 932, Mismatches: 99, Indels: 52
0.86 0.09 0.05
Matches are distributed among these distances:
220 189 0.20
222 3 0.00
223 3 0.00
224 1 0.00
225 1 0.00
228 1 0.00
229 1 0.00
230 4 0.00
231 2 0.00
232 217 0.23
233 311 0.33
234 197 0.21
235 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (232 bp):
ATTTAAGCATCATGCTCGAAAGACTTACTGATGGCACGAAGGACTTATAAATTTTGGAAATAGTT
TACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACTTT
TCTCATTTTTCGAGAGACATGTGAAAACATCCTGCCCGAAGGTCTTATGGATGGCCCGAAGGACT
TATCATCTTTTCGAAAGACTTACAGATGACCCAAAGG
Found at i:253140 original size:220 final size:222
Alignment explanation
Indices: 252521--253352 Score: 1019
Period size: 220 Copynumber: 3.7 Consensus size: 222
252511 CTTACAGATT
* * *
252521 ACCCAAAGGATTTAAGCATCACGCTCGAAAGACTTAGTGATGGCCCGAAGGACTTATAAATTTTG
1 ACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTATAAATTTTG
* * * * *
252586 GAAATAGTTTACTAGGTAAGAAACCTTTCTTATTTTTCAAAAATTTCATTTTTTAGATTTAAATG
66 GAAATAGTTTACTAGGTAAGAAATCTTTATTACTTTTCAAAAATTTCAATTTTCAGATTTAAATG
* * * * * *
252651 AGAAACCTTTCTCATTTTTTGAGAGACATGTGAAAA-ATCCTGCACGAAGGTCTTATGGATTG-C
131 AGAAACTTTTCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCAAAGGTCTTATAGA-TGAC
* * *
252714 TCGAATGACTTATCATCTTGTTCGAAAGACTTACAAATG
195 CCGAAGGACTTATCATC---TT-----G-C-T-CAAAAG
* *
252753 ACCCCAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCAT-GCAGGACTTATAAATTTT
1 ACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGC-TCGAAGGACTTATAAATTTT
* * * *
252817 GGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTAAAAAATTTCAATTTTTAGATTTAAAT
65 GGAAATAGTTTACTAGGTAAGAAATCTTTATTACTTTTCAAAAATTTCAATTTTCAGATTTAAAT
* * * * * * *
252882 GAGAAACGTTTCTTATTTTTCGAGAGACATGTGAAAACATCTTGCCCGAAGGTCTTATGGATGGC
130 GAGAAACTTTTCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCAAAGGTCTTATAGATGAC
*
252947 CCGAAGGACTTATCATCTTGCTC-TAA-
195 CCGAAGGACTTATCATCTTGCTCAAAAG
* * *
252973 ACCCAAAGGATTTAAGCATCATGCTTGAATGACTTACTGATGGCTCGAAGGACTTATAAATTTGG
1 ACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTATAAATTTTG
* *
253038 GAAATAGTTTACTAGGTAAGAAATCTTTATTACTTTTCAAAAATTTCAATTTTCAAATTTGAATG
66 GAAATAGTTTACTAGGTAAGAAATCTTTATTACTTTTCAAAAATTTCAATTTTCAGATTTAAATG
*
253103 AGAAACTTTTCTCATTTTTCGAGAGACATGTGAAAACATCCTATCCAAAGGTCTTATAGATGACC
131 AGAAACTTTTCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCAAAGGTCTTATAGATGACC
* *
253168 CGTAGGACTTATCATCTTTCTCAAAAG
196 CGAAGGACTTATCATCTTGCTCAAAAG
* *
253195 ACTTACAGATGACTTGAAGGATTTAAGCATCATGCTCGAAAGAATTACTGATGGC-CAGAAGGAC
1 AC---C------C--AAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTC-GAAGGAC
*
253259 TTATAAATTTTGGAAATAGTTTACTAGGTAAGAAATCTTTTTTACTTTTCAAAAATTTCAATTTT
54 TTATAAATTTTGGAAATAGTTTACTAGGTAAGAAATCTTTATTACTTTTCAAAAATTTCAATTTT
253324 CAGATTTAAATGAGAAACTTTTCTCATTT
119 CAGATTTAAATGAGAAACTTTTCTCATTT
253353 CTTAACTTAT
Statistics
Matches: 535, Mismatches: 47, Indels: 35
0.87 0.08 0.06
Matches are distributed among these distances:
219 1 0.00
220 194 0.36
221 3 0.01
222 3 0.01
223 1 0.00
224 1 0.00
225 2 0.00
230 2 0.00
231 1 0.00
232 157 0.29
233 170 0.32
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (222 bp):
ACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTATAAATTTTG
GAAATAGTTTACTAGGTAAGAAATCTTTATTACTTTTCAAAAATTTCAATTTTCAGATTTAAATG
AGAAACTTTTCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCAAAGGTCTTATAGATGACC
CGAAGGACTTATCATCTTGCTCAAAAG
Found at i:264415 original size:44 final size:43
Alignment explanation
Indices: 264365--264593 Score: 244
Period size: 44 Copynumber: 5.2 Consensus size: 43
264355 AAATGAATGA
*
264365 ATAAATGAAAATGCATAAGGTTGTATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAAGG-TGCATTATTGGCAGAAAGGTGCC
** * * *
264409 ATAAATGAAAATGCATAACAATGCATTATTGGCATAAATGTACC
1 ATAAATGAAAATGCATAA-GGTGCATTATTGGCAGAAAGGTGCC
*
264453 ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAA-GGTGCATTATTGGCAGAAAGGTGCC
* * ** *
264497 ATAAATAAAAATGTATAAAGGTGTGTTATTGGTAGAAAGGTGCC
1 ATAAATGAAAATGCAT-AAGGTGCATTATTGGCAGAAAGGTGCC
* * * *
264541 ATAAATGAAAATGCATGACGATGCATT-TTGGAAGGAAGGTGCC
1 ATAAATGAAAATGCAT-AAGGTGCATTATTGGCAGAAAGGTGCC
* *
264584 ACAAACGAAA
1 ATAAATGAAA
264594 CTTAAATGTA
Statistics
Matches: 153, Mismatches: 30, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
43 22 0.14
44 129 0.84
45 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (43 bp):
ATAAATGAAAATGCATAAGGTGCATTATTGGCAGAAAGGTGCC
Found at i:271221 original size:44 final size:43
Alignment explanation
Indices: 271171--271434 Score: 237
Period size: 44 Copynumber: 5.9 Consensus size: 43
271161 AAATGAATGA
271171 ATAAATGAAAATGCATAAGGTTGCATTATTGGCAGAAAGGTACC
1 ATAAATGAAAATGCATAAGG-TGCATTATTGGCAGAAAGGTACC
* *
271215 ATAAATGAGAATGCATAACAGTGCATTATTGGCAGAAAGGTACC
1 ATAAATGAAAATGCATAA-GGTGCATTATTGGCAGAAAGGTACC
* * * **
271259 ATAAATGAAAATACATAATGATGCATTATTGGCAGAAAGATGTC
1 ATAAATGAAAATGCATAA-GGTGCATTATTGGCAGAAAGGTACC
* * * * *
271303 ATAAATGAGAATGCATAACGGTGCGTTATTGGTATAAATG-AGCC
1 ATAAATGAAAATGCATAA-GGTGCATTATTGGCAGAAAGGTA-CC
* * * * *
271347 ATAAATGAAAATGCATTATGGTGTATT-TTGGCAGGAACGTGCC
1 ATAAATGAAAATGCA-TAAGGTGCATTATTGGCAGAAAGGTACC
*
271390 ATAAATGAAACTTAAATGCATAATGGTGTATT-TTGGCAGAAAGGT
1 ATAAATG--A---AAATGCATAA-GGTGCATTATTGGCAGAAAGGT
271435 GCCACTCTTG
Statistics
Matches: 177, Mismatches: 33, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
43 17 0.10
44 128 0.72
45 4 0.02
47 2 0.01
48 26 0.15
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (43 bp):
ATAAATGAAAATGCATAAGGTGCATTATTGGCAGAAAGGTACC
Found at i:271276 original size:88 final size:87
Alignment explanation
Indices: 271171--271397 Score: 278
Period size: 88 Copynumber: 2.6 Consensus size: 87
271161 AAATGAATGA
*
271171 ATAAATGAAAATGCATAAGGTTGCATTATTGGCAGAAAGGTACCATAAATGAGAATGCATAACAG
1 ATAAATGAAAATGCATAAGG-TGCATTATTGGCAGAAAGGTGCCATAAATGAGAATGCATAACAG
271236 TGCATTATTGGCAGAAAGGTA-CC
65 TGCATTATTGGCAGAAAGG-AGCC
* * * * *
271259 ATAAATGAAAATACATAATGATGCATTATTGGCAGAAAGATGTCATAAATGAGAATGCATAACGG
1 ATAAATGAAAATGCATAA-GGTGCATTATTGGCAGAAAGGTGCCATAAATGAGAATGCATAACAG
* * * *
271324 TGCGTTATTGGTATAAATGAGCC
65 TGCATTATTGGCAGAAAGGAGCC
* * * *
271347 ATAAATGAAAATGCATTATGGTGTATT-TTGGCAGGAACGTGCCATAAATGA
1 ATAAATGAAAATGCA-TAAGGTGCATTATTGGCAGAAAGGTGCCATAAATGA
271398 AACTTAAATG
Statistics
Matches: 118, Mismatches: 18, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
87 21 0.18
88 94 0.80
89 3 0.03
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.26
Consensus pattern (87 bp):
ATAAATGAAAATGCATAAGGTGCATTATTGGCAGAAAGGTGCCATAAATGAGAATGCATAACAGT
GCATTATTGGCAGAAAGGAGCC
Found at i:273193 original size:14 final size:14
Alignment explanation
Indices: 273174--273207 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
273164 ACAGCGTATT
273174 AGTGAGACTTATCA
1 AGTGAGACTTATCA
273188 AGTGAGACTTATCA
1 AGTGAGACTTATCA
*
273202 GGTGAG
1 AGTGAG
273208 TGCATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.26
Consensus pattern (14 bp):
AGTGAGACTTATCA
Found at i:273433 original size:44 final size:44
Alignment explanation
Indices: 273370--273523 Score: 220
Period size: 44 Copynumber: 3.5 Consensus size: 44
273360 AAATGAATGA
273370 ATAAATGAAAATGCATAACGGTACATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTACATTATTGGCAGAAAGGTGCC
* *
273414 ATAAAGGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTACATTATTGGCAGAAAGGTGCC
* * * * * *
273458 ATATACGAAAATGCATAACAG-AGCATTATTGGTAGAAATGTGTC
1 ATAAATGAAAATGCATAACGGTA-CATTATTGGCAGAAAGGTGCC
273502 ATAAATGAAAATGCATAACGGT
1 ATAAATGAAAATGCATAACGGT
273524 GTATTTTGGT
Statistics
Matches: 96, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
44 96 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTACATTATTGGCAGAAAGGTGCC
Found at i:276613 original size:23 final size:23
Alignment explanation
Indices: 276572--276639 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
276562 GTTGAGGGTT
* *
276572 CTATGTGGTCTTTCAGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
*
276595 CTATGTTGTCCTTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
* * *
276618 CTATATGGTCTTTTGGGACAAA
1 CTATGTGGTCCTTCGGGACAAA
276640 TATGTTGCAC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAC
Found at i:280240 original size:16 final size:17
Alignment explanation
Indices: 280215--280248 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
280205 TCGAGGTGTC
280215 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
280231 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
280248 A
1 A
280249 GAATGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:289903 original size:44 final size:46
Alignment explanation
Indices: 289783--289908 Score: 152
Period size: 47 Copynumber: 2.8 Consensus size: 46
289773 TATAAAATCT
* *
289783 CTTATCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
289828 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
289875 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTT-TTTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTT
289909 GTATAGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
43 4 0.06
44 19 0.26
45 9 0.12
46 2 0.03
47 38 0.53
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:292443 original size:23 final size:22
Alignment explanation
Indices: 292416--292472 Score: 80
Period size: 23 Copynumber: 2.6 Consensus size: 22
292406 ACATAGAATT
*
292416 TGTCCCGAAGGACTGCGTAGAAA
1 TGTCCCGAAGGACTACG-AGAAA
292439 TGTCCCGAAGGACTACGAGAAA
1 TGTCCCGAAGGACTACGAGAAA
*
292461 TAT-CCGAAGGAC
1 TGTCCCGAAGGAC
292473 CACATATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 9 0.28
22 7 0.22
23 16 0.50
ACGTcount: A:0.33, C:0.23, G:0.28, T:0.16
Consensus pattern (22 bp):
TGTCCCGAAGGACTACGAGAAA
Found at i:293392 original size:15 final size:15
Alignment explanation
Indices: 293368--293410 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
293358 ACCTCCCTAT
*
293368 TGGTATCGATACCCA
1 TGGTACCGATACCCA
*
293383 TGGTACCGATACACA
1 TGGTACCGATACCCA
293398 TGGTACCGATACC
1 TGGTACCGATACC
293411 ACCACTTCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (15 bp):
TGGTACCGATACCCA
Found at i:293506 original size:20 final size:20
Alignment explanation
Indices: 293462--293506 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
293452 CTTCCTTATG
*
293462 GTATCAATATTGTATGAATA
1 GTATCAATATTGTATGAACA
*
293482 ATATCAATATTGTATGAACA
1 GTATCAATATTGTATGAACA
293502 GTATC
1 GTATC
293507 GATACCCTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (20 bp):
GTATCAATATTGTATGAACA
Found at i:297228 original size:22 final size:22
Alignment explanation
Indices: 297201--297250 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
297191 ATGGATAAAC
*
297201 CTATGTGGTCCTTCGAGACAAA
1 CTATGTGGTCATTCGAGACAAA
* *
297223 CTATGTAGTCATTCGGGACAAA
1 CTATGTGGTCATTCGAGACAAA
297245 -TATGTG
1 CTATGTG
297251 ACACTTCGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (22 bp):
CTATGTGGTCATTCGAGACAAA
Found at i:297258 original size:21 final size:22
Alignment explanation
Indices: 297211--297273 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
297201 CTATGTGGTC
* *
297211 CTTCGAGACAAACTATGTAGTCA
1 CTTCGGGACAAACTATGT-GACA
297234 -TTCGGGACAAA-TATGTGACA
1 CTTCGGGACAAACTATGTGACA
*
297254 CTTCGGTG-CAAATTATGTGA
1 CTTCGG-GACAAACTATGTGA
297274 GCAATGGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
20 3 0.09
21 14 0.40
22 18 0.51
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (22 bp):
CTTCGGGACAAACTATGTGACA
Found at i:299386 original size:15 final size:16
Alignment explanation
Indices: 299366--299398 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
299356 GTTTGATAAC
299366 TAAAAAATATTTT-TT
1 TAAAAAATATTTTCTT
299381 TAAAAAATATTTTCTT
1 TAAAAAATATTTTCTT
299397 TA
1 TA
299399 TTTTTATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAAAAATATTTTCTT
Found at i:299998 original size:263 final size:262
Alignment explanation
Indices: 299496--300011 Score: 810
Period size: 263 Copynumber: 2.0 Consensus size: 262
299486 TTAATTAGTG
* * *
299496 TTTGATAGTTGTAATTGATTTTCCTAATATAATTATTTTTTTTAGTTCCTTTGTATTTTCTGTAA
1 TTTGATAGTTGTAATTGATTTTCCCAATATAATTATGTTTTCTAGTTCCTTTGTATTTTCTGTAA
*
299561 ATTATTTTATCATATAATTTTCCGTAAAATATTTTTCTAACTTTTGACTTCTTCATCATAATATA
66 ATTATTTTATCATATAATTTTCCGTAAAACATTTTTCTAACTTTTGACTTCTTCA-CATAATATA
* *
299626 AGCACTCAAAAAATATTATTTTATTTATTTAATATTAGATTAATATTTTATTATCATTTTAATAA
130 AGCACTCAAAAAATATTATTTTATTTATTTAATATTAGATTAATATTTTAATACCATTTTAATAA
299691 AAATATTAATTATTAAAATATTTAATATACATATAATATAATAATATTATATTAATATATTTTCA
195 AAATATTAATTATTAAAATATTTAATATACATATAATATAATAATATTATATTAATATATTTTCA
299756 TTA
260 TTA
*
299759 TTTGATAGTTGTAATTGATTTTCCCAATGTAATTCA-GTTTTCTAGTTCCTTTGTATTTTCTGTA
1 TTTGATAGTTGTAATTGATTTTCCCAATATAATT-ATGTTTTCTAGTTCCTTTGTATTTTCTGTA
* *
299823 AATTGTTTTATCATATAATTTTCCGTAAAACATTTTTCTAACTTTTTACTTCTTCA-A-AATATA
65 AATTATTTTATCATATAATTTTCCGTAAAACATTTTTCTAACTTTTGACTTCTTCACATAATATA
* *
299886 AGTACTC-AAAAAT-TTATTTTTATTTATTTAATATTATATTAATATTTTAATACCATTTTAAT-
130 AGCACTCAAAAAATATTA-TTTTATTTATTTAATATTAGATTAATATTTTAATACCATTTTAATA
*
299948 AAAATATTAATTGTTAAAATATTTAATATACATATAATACAATTTAATAATATTATATTAATAT
194 AAAATATTAATTATTAAAATATTTAATATACATATAAT---A--TAATAATATTATATTAATAT
300012 GTACTCAGAC
Statistics
Matches: 234, Mismatches: 12, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
258 40 0.17
259 48 0.21
260 12 0.05
261 2 0.01
263 131 0.56
264 1 0.00
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (262 bp):
TTTGATAGTTGTAATTGATTTTCCCAATATAATTATGTTTTCTAGTTCCTTTGTATTTTCTGTAA
ATTATTTTATCATATAATTTTCCGTAAAACATTTTTCTAACTTTTGACTTCTTCACATAATATAA
GCACTCAAAAAATATTATTTTATTTATTTAATATTAGATTAATATTTTAATACCATTTTAATAAA
AATATTAATTATTAAAATATTTAATATACATATAATATAATAATATTATATTAATATATTTTCAT
TA
Found at i:303212 original size:16 final size:16
Alignment explanation
Indices: 303191--303232 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
303181 AGAAGAGTTT
303191 GATTTGCAAATCTTTA
1 GATTTGCAAATCTTTA
303207 GATTTGCAAATCTTTA
1 GATTTGCAAATCTTTA
303223 GATTTGCAAA
1 GATTTGCAAA
303233 ATTTACTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (16 bp):
GATTTGCAAATCTTTA
Found at i:309800 original size:21 final size:21
Alignment explanation
Indices: 309772--309828 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
309762 TTTACACTTA
*
309772 GGGAACCGATTCCCTATGAGG
1 GGGAACCGATTCCCCATGAGG
*
309793 GGGGACCGATTCCCCATGAGG
1 GGGAACCGATTCCCCATGAGG
309814 GGGAACCGATTCCCC
1 GGGAACCGATTCCCC
309829 CCACGCTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (21 bp):
GGGAACCGATTCCCCATGAGG
Found at i:310507 original size:17 final size:15
Alignment explanation
Indices: 310477--310516 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
310467 TAATATACAT
310477 ATAATATAATTTTTA
1 ATAATATAATTTTTA
310492 ATAATATTATATTTTTA
1 ATAATA-TA-ATTTTTA
*
310509 ATATTATA
1 ATAATATA
310517 TAAATATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 6 0.27
16 4 0.18
17 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATATAATTTTTA
Found at i:311433 original size:16 final size:16
Alignment explanation
Indices: 311408--311445 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
311398 GGGTCTCAAT
*
311408 CAGGCTTCGTGAGACA
1 CAGGCCTCGTGAGACA
311424 CAGGCCTCGTGAGACA
1 CAGGCCTCGTGAGACA
311440 CAGGCC
1 CAGGCC
311446 AGGGGCGAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.32, G:0.32, T:0.13
Consensus pattern (16 bp):
CAGGCCTCGTGAGACA
Found at i:312027 original size:26 final size:24
Alignment explanation
Indices: 311966--312035 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
311956 TTTGGAAAAA
*
311966 TATCTCAAGAGAGATTGTAAAATT
1 TATCTAAAGAGAGATTGTAAAATT
311990 TATCTAAAGAGAGATTGTAAAATT
1 TATCTAAAGAGAGATTGTAAAATT
* *
312014 TATCTAAAGCGAGATTGGAAAA
1 TATCTAAAGAGAGATTGTAAAA
312036 AGGATCACGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (24 bp):
TATCTAAAGAGAGATTGTAAAATT
Found at i:316478 original size:2 final size:2
Alignment explanation
Indices: 316471--316502 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
316461 CCCTATTTGT
316471 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
316503 CGGTCGTCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:319073 original size:2 final size:2
Alignment explanation
Indices: 319066--319134 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
319056 ATAAATTACA
319066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
319108 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
319135 GATCTGCTTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:319358 original size:2 final size:2
Alignment explanation
Indices: 319351--319382 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
319341 ATAGTAACCC
319351 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
319383 TTGTTGAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:321497 original size:4 final size:4
Alignment explanation
Indices: 321488--321524 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
321478 GGGAAACACA
*
321488 ATAC ATAC ATAC ATAC AT-- ATAT ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
321525 TATATATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (4 bp):
ATAC
Found at i:321515 original size:18 final size:18
Alignment explanation
Indices: 321492--321530 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
321482 AACACAATAC
321492 ATACATACATACATATAT
1 ATACATACATACATATAT
321510 ATACATACATACATATAT
1 ATACATACATACATATAT
321528 ATA
1 ATA
321531 TATATAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.33
Consensus pattern (18 bp):
ATACATACATACATATAT
Found at i:322725 original size:2 final size:2
Alignment explanation
Indices: 322718--322787 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
322708 CTTGAACCCT
322718 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
322760 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
322788 CCTTGCGAGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:333850 original size:24 final size:24
Alignment explanation
Indices: 333823--333918 Score: 101
Period size: 23 Copynumber: 4.1 Consensus size: 24
333813 CTGCTCATAT
333823 AATTTG-CACCGAAGTG-CCACGTAG
1 AATTTGTC-CCGAAG-GACCACGTAG
*
333847 AATTTGTCCCGAAGGACCACGTAT
1 AATTTGTCCCGAAGGACCACGTAG
* * * *
333871 AA-TTGTCCCAAATGATCACATAG
1 AATTTGTCCCGAAGGACCACGTAG
333894 -ATTTGTCCCGAAGGACCACGTAG
1 AATTTGTCCCGAAGGACCACGTAG
333917 AA
1 AA
333919 CCCTCGACTC
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
22 1 0.02
23 34 0.59
24 22 0.38
25 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (24 bp):
AATTTGTCCCGAAGGACCACGTAG
Found at i:334619 original size:20 final size:21
Alignment explanation
Indices: 334596--334645 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
334586 CTTCCTCTTG
*
334596 GTATCGATACCTC-CATATCA
1 GTATCGATACCTCTCAAATCA
* *
334616 GTATC-ATACTTCTTAAATCA
1 GTATCGATACCTCTCAAATCA
334636 GTATCGATAC
1 GTATCGATAC
334646 AGTTTATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 6 0.24
20 15 0.60
21 4 0.16
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (21 bp):
GTATCGATACCTCTCAAATCA
Found at i:338563 original size:26 final size:26
Alignment explanation
Indices: 338533--338586 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
338523 CTTCGGTATG
338533 AGAAATAATTTATAAACATCTCACTA
1 AGAAATAATTTATAAACATCTCACTA
*
338559 AGAAATAATTTGTAAACATCTCACTA
1 AGAAATAATTTATAAACATCTCACTA
338585 AG
1 AG
338587 GTTTTGTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (26 bp):
AGAAATAATTTATAAACATCTCACTA
Found at i:347827 original size:54 final size:54
Alignment explanation
Indices: 347755--347976 Score: 336
Period size: 54 Copynumber: 4.1 Consensus size: 54
347745 GTGTATTATA
*
347755 GGCACTATGTGTGAAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC
1 GGCACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC
*
347809 GGCACTATGTATGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC
1 GGCACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC
** * * * *
347863 GATACTATGTGTGCAATCCACGGAATTCATAATGTGTTTGTGAATTATCATTTT
1 GGCACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC
* * *
347917 AGCACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTTAATTACCATGTC
1 GGCACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC
*
347971 GACACT
1 GGCACT
347977 TAGGTGCAAT
Statistics
Matches: 148, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 148 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (54 bp):
GGCACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC
Found at i:354524 original size:24 final size:24
Alignment explanation
Indices: 354496--354549 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
354486 AAAGTAGCAG
354496 AATAGTTGGACA-CTAATAAGGCAA
1 AATAGTTGGACATC-AATAAGGCAA
* *
354520 AATAGTTGGACATCATTAAGGCAT
1 AATAGTTGGACATCAATAAGGCAA
354544 AATAGT
1 AATAGT
354550 GAGGCATACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.26
Consensus pattern (24 bp):
AATAGTTGGACATCAATAAGGCAA
Found at i:360499 original size:26 final size:26
Alignment explanation
Indices: 360450--360499 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
360440 ACACCATTGA
* *
360450 AACATCCTTCATCATTCATTAAGGTC
1 AACATCCATCATCATACATTAAGGTC
360476 AACATCCATCATCA-ACATTGAAGG
1 AACATCCATCATCATACATT-AAGG
360500 CAGAATCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (26 bp):
AACATCCATCATCATACATTAAGGTC
Found at i:365118 original size:85 final size:85
Alignment explanation
Indices: 364975--365140 Score: 278
Period size: 85 Copynumber: 2.0 Consensus size: 85
364965 ATACAATCAC
* * * *
364975 GACACACGAATGTGTGTCATTTTCATTTATGACGGGGGCTTCAATGACATGTAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
*
365040 AATGCGTGTCATAAATTTAT
66 AATGCGCGTCATAAATTTAT
*
365060 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
365125 AATGCGCGTCATAAAT
66 AATGCGCGTCATAAAT
365141 GCGTGTCATA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 75 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTAAGTCATA
AATGCGCGTCATAAATTTAT
Found at i:365135 original size:13 final size:13
Alignment explanation
Indices: 365119--365166 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
365109 CGCAATGTAA
365119 GTCATAAATGCGC
1 GTCATAAATGCGC
*
365132 GTCATAAATGCGT
1 GTCATAAATGCGC
365145 GTCATAAATGCGC
1 GTCATAAATGCGC
365158 GTCATAAAT
1 GTCATAAAT
365167 TTATGACGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:365141 original size:26 final size:26
Alignment explanation
Indices: 365112--365166 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
365102 AATGACGCGC
*
365112 AATGTAAGTCATAAATGCGCGTCATA
1 AATGCAAGTCATAAATGCGCGTCATA
**
365138 AATGCGTGTCATAAATGCGCGTCATA
1 AATGCAAGTCATAAATGCGCGTCATA
365164 AAT
1 AAT
365167 TTATGACGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.27
Consensus pattern (26 bp):
AATGCAAGTCATAAATGCGCGTCATA
Found at i:365500 original size:53 final size:53
Alignment explanation
Indices: 365437--365653 Score: 300
Period size: 53 Copynumber: 4.1 Consensus size: 53
365427 TGTACTATCA
365437 GCACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC
1 GCACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC
*
365490 GCACTATGTGTGCAATCCATGGAATTCACAATGAGTTTGTGAATTACC-TGTT-
1 GCACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCAT-TTC
* * *
365542 -CAGTATTGTGTGTAATCCATGGAATTCATAATGAGTTTGTTAATTACCATTTC
1 GCACTA-TGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC
* *
365595 GACACTA--TGTGCAATTCATGGAATTCATAATGAGTTTTTTGAATTACCATTTC
1 G-CACTATGTGTGCAATCCATGGAATTCATAATGAG-TTTGTGAATTACCATTTC
365648 GGCACT
1 -GCACT
365654 TAGGTGCAAT
Statistics
Matches: 146, Mismatches: 10, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
51 4 0.03
52 67 0.46
53 70 0.48
54 1 0.01
55 4 0.03
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (53 bp):
GCACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTC
Found at i:365575 original size:52 final size:51
Alignment explanation
Indices: 365443--365648 Score: 279
Period size: 52 Copynumber: 3.9 Consensus size: 51
365433 ATCAGCACTA
365443 TGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGCACT
1 TGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGCA-T
* *
365495 ATGTGTGCAATCCATGGAATTCACAATGAGTTTGTGAATTACC-TGTTCAGTAT
1 -TGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCAT-TTC-GCAT
* * *
365548 TGTGTGTAATCCATGGAATTCATAATGAGTTTGTTAATTACCATTTCGACAC
1 TGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCG-CAT
* * *
365600 TATGTGCAATTCATGGAATTCATAATGAGTTTTTTGAATTACCATTTCG
1 TGTGTGCAATCCATGGAATTCATAATGAG-TTTGTGAATTACCATTTCG
365649 GCACTTAGGT
Statistics
Matches: 136, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
51 1 0.01
52 70 0.51
53 63 0.46
54 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (51 bp):
TGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGCAT
Found at i:365577 original size:105 final size:105
Alignment explanation
Indices: 365443--365642 Score: 323
Period size: 105 Copynumber: 1.9 Consensus size: 105
365433 ATCAGCACTA
365443 TGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCG-CACTATGTGTGCAATC
1 TGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGACACTA--TGTGCAATC
365507 CATGGAATTCACAATGAG-TTTGTGAATTACCTGTTCAGTAT
64 CATGGAATTCACAATGAGTTTTGTGAATTACCTGTTCAGTAT
* * *
365548 TGTGTGTAATCCATGGAATTCATAATGAGTTTGTTAATTACCATTTCGACACTATGTGCAATTCA
1 TGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGACACTATGTGCAATCCA
* *
365613 TGGAATTCATAATGAGTTTTTTGAATTACC
66 TGGAATTCACAATGAGTTTTGTGAATTACC
365643 ATTTCGGCAC
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
104 25 0.28
105 58 0.66
106 5 0.06
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (105 bp):
TGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTCGACACTATGTGCAATCCA
TGGAATTCACAATGAGTTTTGTGAATTACCTGTTCAGTAT
Found at i:370123 original size:18 final size:18
Alignment explanation
Indices: 370082--370126 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
370072 CTAGTGAATT
* *
370082 TTTATTTTATTTTTTAAA
1 TTTATATTATTTTTAAAA
*
370100 -TAATATTATTTTTAAAA
1 TTTATATTATTTTTAAAA
370117 TTTATATTAT
1 TTTATATTAT
370127 AAAAAAATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATATTATTTTTAAAA
Found at i:374201 original size:47 final size:43
Alignment explanation
Indices: 374150--374245 Score: 113
Period size: 47 Copynumber: 2.1 Consensus size: 43
374140 ATAAAATTCT
*
374150 TATATCCACATAACTGTCAATATCATATAAAATTTAAATATAGCAT-A
1 TATATACACATAACTGTC-A-AT-ATATAAAATTT--ATATAGCATGA
* *
374197 TATATATATATAACTGTCAATATATAAAATTTATATAGCATGA
1 TATATACACATAACTGTCAATATATAAAATTTATATAGCATGA
374240 TATATA
1 TATATA
374246 TATATATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
42 9 0.20
43 7 0.16
44 11 0.24
45 2 0.04
46 1 0.02
47 15 0.33
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (43 bp):
TATATACACATAACTGTCAATATATAAAATTTATATAGCATGA
Found at i:374244 original size:2 final size:2
Alignment explanation
Indices: 374239--374285 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
374229 ATATAGCATG
374239 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
374280 AT AT AT
1 AT AT AT
374286 TATGTAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:378932 original size:18 final size:17
Alignment explanation
Indices: 378895--378963 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
378885 GACCGGTCAC
**
378895 GACCCGACCCGATAGTT
1 GACCCGACCCGACCGTT
378912 GACCCGACCCGACCCGTT
1 GACCCGACCCGA-CCGTT
378930 GACCCGA--C--CCGTT
1 GACCCGACCCGACCGTT
378943 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
378960 GACC
1 GACC
378964 GTTGACCGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 12 0.27
15 1 0.02
16 1 0.02
17 21 0.47
18 10 0.22
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:378935 original size:13 final size:13
Alignment explanation
Indices: 378917--378953 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
378907 TAGTTGACCC
378917 GACCCGACCCGTT
1 GACCCGACCCGTT
378930 GACCCGACCCGTT
1 GACCCGACCCGTT
378943 GACCCGACCCG
1 GACCCGACCCG
378954 ACCGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:379013 original size:29 final size:29
Alignment explanation
Indices: 378971--379049 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
378961 ACCGTTGACC
* *
378971 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
379000 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
379029 GGTGCTATTCTGGT-AATAATT
1 GGTGCTATTCTGGTAAATAATT
379050 AGAAAAGGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.15
29 41 0.85
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.46
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAGTTTT
Found at i:386183 original size:18 final size:17
Alignment explanation
Indices: 386146--386214 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
386136 GACCGGTCAC
**
386146 GACCCGACCCGATAGTT
1 GACCCGACCCGACCGTT
386163 GACCCGACCCGACCCGTT
1 GACCCGACCCGA-CCGTT
386181 GACCCGA--C--CCGTT
1 GACCCGACCCGACCGTT
386194 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
386211 GACC
1 GACC
386215 GTTGACCGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 12 0.27
15 1 0.02
16 1 0.02
17 21 0.47
18 10 0.22
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:386186 original size:13 final size:13
Alignment explanation
Indices: 386168--386204 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
386158 TAGTTGACCC
386168 GACCCGACCCGTT
1 GACCCGACCCGTT
386181 GACCCGACCCGTT
1 GACCCGACCCGTT
386194 GACCCGACCCG
1 GACCCGACCCG
386205 ACCGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:386264 original size:29 final size:29
Alignment explanation
Indices: 386222--386300 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
386212 ACCGTTGACC
* *
386222 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
386251 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
386280 GGTGCTATTCT-GTAAATAATT
1 GGTGCTATTCTGGTAAATAATT
386301 AGAAAAAGGG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
28 10 0.21
29 38 0.79
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.46
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAGTTTT
Found at i:387895 original size:21 final size:21
Alignment explanation
Indices: 387834--387888 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
387824 TTTGGGTTGT
387834 GTGCATCGATGCATCTTCAAG
1 GTGCATCGATGCATCTTCAAG
387855 GTGCATCGATGCATCTTCAAG
1 GTGCATCGATGCATCTTCAAG
*
387876 GTGTATCGATGCA
1 GTGCATCGATGCA
387889 CTATCAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (21 bp):
GTGCATCGATGCATCTTCAAG
Found at i:388369 original size:10 final size:10
Alignment explanation
Indices: 388342--388375 Score: 54
Period size: 9 Copynumber: 3.6 Consensus size: 10
388332 GTGGTTGTTA
388342 TGATTATATG
1 TGATTATATG
388352 TG-TTATATG
1 TGATTATATG
388361 TGATTATATG
1 TGATTATATG
388371 T-ATTA
1 TGATTA
388376 CATTAATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.57
10 10 0.43
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (10 bp):
TGATTATATG
Found at i:389667 original size:23 final size:23
Alignment explanation
Indices: 389601--389667 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
389591 ACCTTATATA
* * *
389601 GCACTTCGGTGCATTTCTACACG
1 GCACTTCAGTGCATTTATACGCG
* * *
389624 GCACTACAGTGCAATTATACGTG
1 GCACTTCAGTGCATTTATACGCG
389647 GCACTTCAGTGCATTTATACG
1 GCACTTCAGTGCATTTATACG
389668 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (23 bp):
GCACTTCAGTGCATTTATACGCG
Found at i:390533 original size:32 final size:32
Alignment explanation
Indices: 390492--390559 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
390482 TGTCTCGGTG
* *
390492 TCTTTAGGGAAAGGGTTTAGGGTTTCTTAACA
1 TCTTTAGGGAAAGGGTATAGGGTTTCTCAACA
390524 TCTTTAGGGAAAGGGTATAGGGTTTCTCAACA
1 TCTTTAGGGAAAGGGTATAGGGTTTCTCAACA
390556 TCTT
1 TCTT
390560 CAGCTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (32 bp):
TCTTTAGGGAAAGGGTATAGGGTTTCTCAACA
Found at i:390627 original size:43 final size:43
Alignment explanation
Indices: 390579--390682 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 43
390569 TTGGTTCAAA
*
390579 GGATCTCTCGGCGTTTTCAACAAAAAAATTTCCATGCAAACTT
1 GGATCTCTCGGCGTCTTCAACAAAAAAATTTCCATGCAAACTT
* ** *
390622 GGATCTCTCGGTGTCTTCATTAAAAAATTTTCCATGCAAACTT
1 GGATCTCTCGGCGTCTTCAACAAAAAAATTTCCATGCAAACTT
*
390665 GGAT-TGCTCGACGTCTTC
1 GGATCT-CTCGGCGTCTTC
390683 TATGAAAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
42 1 0.02
43 52 0.98
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (43 bp):
GGATCTCTCGGCGTCTTCAACAAAAAAATTTCCATGCAAACTT
Found at i:392390 original size:21 final size:21
Alignment explanation
Indices: 392366--392405 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
392356 ACAAGACGCA
392366 GAGACATCTCACATGCAAGCC
1 GAGACATCTCACATGCAAGCC
392387 GAGACATCTCACATGCAAG
1 GAGACATCTCACATGCAAG
392406 ATGAAGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (21 bp):
GAGACATCTCACATGCAAGCC
Found at i:395139 original size:2 final size:2
Alignment explanation
Indices: 395128--395163 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
395118 AAAGAAAAAA
*
395128 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
395164 CAAAGTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:395417 original size:27 final size:27
Alignment explanation
Indices: 395354--395410 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
395344 GTTTTTTTTT
* *
395354 AAATAATAATATAATAATATGAATAAAA
1 AAATAATAA-AAAATAATATAAATAAAA
*
395382 AAATAATAAAAAATAATATAAATATAA
1 AAATAATAAAAAATAATATAAATAAAA
395409 AA
1 AA
395411 GTTATAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (27 bp):
AAATAATAAAAAATAATATAAATAAAA
Found at i:395624 original size:43 final size:45
Alignment explanation
Indices: 395533--395621 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 45
395523 AGATAATTAC
* ** * *
395533 AATATATATATAGTAATATTAGACTTATAAGTAAAATATTAAAGA
1 AATATATATATAGTAATAATAGAAATATAAGTAAAAAAATAAAGA
*
395578 AATATATATATA-TAATAATA-AAATAT-AGTAAAAAAATAATGA
1 AATATATATATAGTAATAATAGAAATATAAGTAAAAAAATAAAGA
395620 AA
1 AA
395622 ATAATTTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
42 15 0.39
43 4 0.11
44 7 0.18
45 12 0.32
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.33
Consensus pattern (45 bp):
AATATATATATAGTAATAATAGAAATATAAGTAAAAAAATAAAGA
Found at i:395676 original size:17 final size:16
Alignment explanation
Indices: 395654--395691 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
395644 ATATATACAT
*
395654 ATAATAATATAACATGA
1 ATAATAAAATAA-ATGA
395671 ATAATAAAATAAATGA
1 ATAATAAAATAAATGA
395687 A-AATA
1 ATAATA
395692 TCCATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 5 0.25
17 11 0.55
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (16 bp):
ATAATAAAATAAATGA
Found at i:396099 original size:37 final size:37
Alignment explanation
Indices: 396049--396153 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
396039 GTGCTTGTGG
* * * *
396049 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
396086 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
396123 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
396154 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:396992 original size:105 final size:105
Alignment explanation
Indices: 396696--397143 Score: 631
Period size: 105 Copynumber: 4.3 Consensus size: 105
396686 GCATTGTTCC
* * *
396696 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAATTG-TTGTTGACA
* * * * *
396760 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
396802 GAGTCCAATATCCTTCCCTGTGAAGTTGAAATTGACTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAG
* * *
396862 CAGCGGTCCCTTCATCGTGGAGTTGAACTTGCGTTATCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
396902 GAGTCCAATATCATTCGTTGTGAAGTTCAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAG
396967 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
397007 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAG
*
397072 CAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
397112 AAG-CCTAATATCATTCGTTGTGAAGTTGAAAT
1 GAGTCC-AATATCCTTCGTTGTGAAGTTGAAAT
397144 CTATTCTCGA
Statistics
Matches: 308, Mismatches: 27, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
100 79 0.26
101 1 0.00
102 7 0.02
104 8 0.03
105 178 0.58
106 35 0.11
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:397310 original size:36 final size:36
Alignment explanation
Indices: 397263--397338 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
397253 TGTTTGGAGA
* * *
397263 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
397299 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
397335 GAAA
1 GAAA
397339 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:397459 original size:105 final size:104
Alignment explanation
Indices: 397238--397556 Score: 509
Period size: 105 Copynumber: 3.1 Consensus size: 104
397228 TTCGTTAAAT
* ** *
397238 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
397300 AAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
397339 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
397404 AAACTATCTCAAGAGAGAAAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAG-AAAAAATTCATTTCAAGGGAAA
* *
397444 TGTTTTCAATGTTTATGTTTTAAGAGAAATTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
397509 AAACTATCTCAGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
397548 TGTTTTCAA
1 TGTTTTCAA
397557 GAGAAACTGT
Statistics
Matches: 202, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
101 46 0.23
103 3 0.01
104 54 0.27
105 99 0.49
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAAATTCATTTCAAGGGAAA
Found at i:397622 original size:90 final size:89
Alignment explanation
Indices: 397458--397623 Score: 280
Period size: 90 Copynumber: 1.9 Consensus size: 89
397448 TTCAATGTTT
* *
397458 ATGTTTTAAGAGAAATTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAGGA
1 ATGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAGCA
397523 GAGAAAAAATTAATTTCAAGGGAA
66 GAGAAAAAATTAATTTCAAGGGAA
397547 ATGTTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAAG
1 ATGTTTT-AAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTC-AG
*
397612 CA-AGATAAAATT
64 CAGAGAAAAAATT
397624 TTCTTAAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
89 7 0.10
90 62 0.86
91 3 0.04
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (89 bp):
ATGTTTTAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGGAAACTATCTCAGCA
GAGAAAAAATTAATTTCAAGGGAA
Found at i:397712 original size:36 final size:36
Alignment explanation
Indices: 397672--397785 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 36
397662 CTTTCGAGTG
* *
397672 AAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
* ** * * * * **
397708 AAAACAATCTTGAGTAAAATAAATCTTCTTTCGAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
*
397744 AAAACAGTCTCAAGTGAGACAAAGT-ATGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAA-TCTTGTTTTAAGA
397780 AAAACA
1 AAAACA
397786 AATTTGAGTG
Statistics
Matches: 56, Mismatches: 21, Indels: 2
0.71 0.27 0.03
Matches are distributed among these distances:
36 55 0.98
37 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (36 bp):
AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
Found at i:397763 original size:72 final size:75
Alignment explanation
Indices: 397627--397794 Score: 204
Period size: 72 Copynumber: 2.3 Consensus size: 75
397617 TAAAATTTTC
** * * *
397627 TTAA-AAAAACAGCCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTAAAATGAAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGA
*
397691 CAAA-TCTTGTT
65 CAAAGT-ATGTT
*
397702 TTAAGAAAAACAATCTTGAGTAAAAT-AAAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGAC
1 TTAAGAAAAACAATCTTGAGTAAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGAC
397764 AAAGTATGTT
66 AAAGTATGTT
397774 TTAAGAAAAACAAAT-TTGAGT
1 TTAAGAAAAAC-AATCTTGAGT
397795 GAGATAATCA
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
72 42 0.51
73 15 0.18
75 8 0.10
76 18 0.22
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (75 bp):
TTAAGAAAAACAATCTTGAGTAAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGAC
AAAGTATGTT
Found at i:399103 original size:183 final size:183
Alignment explanation
Indices: 398795--399148 Score: 629
Period size: 183 Copynumber: 1.9 Consensus size: 183
398785 ATCAGGTTTA
398795 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
398860 GCCAAGTGTCCGAGTAATGTCATGATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAATGTCATGATTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
398925 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* * *
398978 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
*
399043 GCCAAGTGTCCGAGCAGTGTCAT-AGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAATGTCATGA-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
399107 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
399149 CGGATTTAAT
Statistics
Matches: 163, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
182 1 0.01
183 162 0.99
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAATGTCATGATTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:402040 original size:15 final size:15
Alignment explanation
Indices: 402020--402052 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
402010 AGTAATAATA
402020 AAAAACAATAAA-AAC
1 AAAAAC-ATAAATAAC
402035 AAAAACATAAATAAC
1 AAAAACATAAATAAC
402050 AAA
1 AAA
402053 TAAAATAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAAACATAAATAAC
Found at i:406615 original size:14 final size:14
Alignment explanation
Indices: 406596--406628 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
406586 TGGGGAGTAA
*
406596 TCCCTGTAAATAAT
1 TCCCTGCAAATAAT
406610 TCCCTGCAAATAAT
1 TCCCTGCAAATAAT
406624 TCCCT
1 TCCCT
406629 ACATAGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (14 bp):
TCCCTGCAAATAAT
Found at i:410577 original size:26 final size:26
Alignment explanation
Indices: 410541--410596 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
410531 TGTTACCAAA
*
410541 GGAGATCTGAAAAGCGAAAGTGGAAT
1 GGAGATATGAAAAGCGAAAGTGGAAT
*
410567 GGAGATATGAAAAGCGAAAGTGGGAT
1 GGAGATATGAAAAGCGAAAGTGGAAT
410593 GGAG
1 GGAG
410597 GATTTCCCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.05, G:0.39, T:0.14
Consensus pattern (26 bp):
GGAGATATGAAAAGCGAAAGTGGAAT
Found at i:414596 original size:6 final size:6
Alignment explanation
Indices: 414585--414614 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
414575 CTTAATTACG
414585 AAAATT AAAATT AAAATT AAAATT AAAATT
1 AAAATT AAAATT AAAATT AAAATT AAAATT
414615 TAGAAGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAAATT
Found at i:414782 original size:23 final size:22
Alignment explanation
Indices: 414725--414789 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
414715 GATATGAATA
* *
414725 AAAAAATAATAAA-GTAAAAAT
1 AAAAAATAATAAATGTTAAATT
*
414746 AAAAAA-AAGAAAATGTTAAATT
1 AAAAAATAA-TAAATGTTAAATT
*
414768 AAAAAATATATAAATATTAAAT
1 AAAAAATA-ATAAATGTTAAAT
414790 AGGATTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 2 0.06
21 9 0.26
22 12 0.34
23 11 0.31
24 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.25
Consensus pattern (22 bp):
AAAAAATAATAAATGTTAAATT
Found at i:415940 original size:5 final size:5
Alignment explanation
Indices: 415930--416167 Score: 134
Period size: 5 Copynumber: 48.8 Consensus size: 5
415920 TAACTGAATA
* *
415930 ATAAT ATAAT ATAAT ATAAT AATACT ATAAT AT-AC ATAAT A-ATAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT
* ** *
415980 ATACAT -T-CT ATAAT AATAA- AT-AT ATGCT ATAAT A-AAA ATAAT ATAAT
1 ATA-AT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
*
416027 A-AAT ATAA- ATATAT ATACT AT-AT ACT-AT ATAAT ATAAAT ATAA-
1 ATAAT ATAAT ATA-AT ATAAT ATAAT A-TAAT ATAAT AT-AAT ATAAT
* *
416070 ATATAT ATAAT ATAA- AT-AT ATATT ATAAT ATTTAAT AT-AT AGAAT
1 ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT A--TAAT ATAAT ATAAT
* * *
416115 ATAAT ACT-AT ATAAT AT-AT GTTAT ATAAT ATAGT ATAAT ACT-AT ATAAT
1 ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT
416164 ATAA
1 ATAA
416168 AAAGAATCCC
Statistics
Matches: 182, Mismatches: 22, Indels: 58
0.69 0.08 0.22
Matches are distributed among these distances:
3 3 0.02
4 37 0.20
5 113 0.62
6 24 0.13
7 5 0.03
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:415940 original size:21 final size:20
Alignment explanation
Indices: 415911--416084 Score: 93
Period size: 21 Copynumber: 8.7 Consensus size: 20
415901 AAAAACATAT
415911 TAATA-AATATAACTGAATAA
1 TAATATAATATAACT-AATAA
*
415931 TAATATAATATAATATAATAA
1 TAATATAATATAA-CTAATAA
*
415952 TACTATAATAT-ACATAATAA
1 TAATATAATATAAC-TAATAA
415972 T-ATATAATATACATTCT-ATAA
1 TAATATAATATA-A--CTAATAA
*
415993 TAATA-AATATATGCT-ATAA
1 TAATATAATATA-ACTAATAA
*
416012 TAAAAATAATATAA-TAA-ATA
1 T-AATATAATATAACTAATA-A
*
416032 TAA-AT-ATATATACTATATAC
1 TAATATAATATA-ACTA-ATAA
*
416052 T-ATATAATATAAAT-ATAAA
1 TAATATAATATAACTAAT-AA
416071 TATATATAATATAA
1 TA-ATATAATATAA
416085 ATATATATTA
Statistics
Matches: 122, Mismatches: 11, Indels: 41
0.70 0.06 0.24
Matches are distributed among these distances:
17 5 0.04
18 5 0.04
19 24 0.20
20 25 0.20
21 57 0.47
22 5 0.04
23 1 0.01
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (20 bp):
TAATATAATATAACTAATAA
Found at i:415979 original size:19 final size:19
Alignment explanation
Indices: 415926--416166 Score: 159
Period size: 19 Copynumber: 12.8 Consensus size: 19
415916 AATATAACTG
415926 AATAATAATATAATATAATAT
1 AATAAT-ATATAATAT-ATAT
*
415947 AATAATACTATAATATACAT
1 AATAATA-TATAATATATAT
*
415967 AATAATATATAATATACATT
1 AATAATATATAATATATA-T
*
415987 CTATAATA-ATAA-ATATAT
1 -AATAATATATAATATATAT
* *
416005 GCTATAATA-AAAATA-ATAT
1 --AATAATATATAATATATAT
416024 AATAA-ATATAA-ATATAT
1 AATAATATATAATATATAT
* *
416041 -ATACTATATACTATATA-
1 AATAATATATAATATATAT
416058 ATATAA-ATATAA-ATATAT
1 A-ATAATATATAATATATAT
416076 -ATAATATA-AATATATAT
1 AATAATATATAATATATAT
* * *
416093 TATAATATTTAATATATAG
1 AATAATATATAATATATAT
*
416112 AAT-ATA-ATACTATATAAT
1 AATAATATATAATATAT-AT
**
416130 ATATGTTATATAATATAGTAT
1 A-ATAATATATAATATA-TAT
*
416151 AATACTATATAATATA
1 AATAATATATAATATA
416167 AAAAGAATCC
Statistics
Matches: 179, Mismatches: 20, Indels: 43
0.74 0.08 0.18
Matches are distributed among these distances:
16 11 0.06
17 37 0.21
18 23 0.13
19 45 0.25
20 32 0.18
21 30 0.17
22 1 0.01
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (19 bp):
AATAATATATAATATATAT
Found at i:416042 original size:2 final size:2
Alignment explanation
Indices: 416020--416166 Score: 86
Period size: 2 Copynumber: 77.5 Consensus size: 2
416010 AATAAAAATA
* *
416020 AT AT A- AT AA AT AT AA AT AT AT AT ACT AT AT ACT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT
* * *
416062 AA AT AT AA AT AT AT AT A- AT AT AA AT AT AT AT -T AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
416101 TT A- AT AT AT AG A- AT AT A- AT ACT AT AT A- AT AT AT GT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
416139 AT A- AT AT AGT AT A- AT ACT AT AT A- AT AT A
1 AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT A
416167 AAAAGAATCC
Statistics
Matches: 113, Mismatches: 14, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
1 13 0.12
2 90 0.80
3 10 0.09
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:416152 original size:34 final size:32
Alignment explanation
Indices: 416035--416166 Score: 117
Period size: 34 Copynumber: 3.9 Consensus size: 32
416025 ATAAATATAA
* *
416035 ATATATATACTAT-ATACTATATAATATAAATATAA
1 ATATATATAGTATAATACTATATAATAT--AT-T-T
* *
416070 ATATATATAATATAAATA-TATATTATAATATTT
1 ATATATATAGTAT-AATACTATATAAT-ATATTT
416103 A-ATATATAGAATATAATACTATATAATATATGTT
1 ATATATATAG--TATAATACTATATAATATAT-TT
416137 ATATAATATAGTATAATACTATATAATATA
1 ATAT-ATATAGTATAATACTATATAATATA
416167 AAAAGAATCC
Statistics
Matches: 83, Mismatches: 5, Indels: 19
0.78 0.05 0.18
Matches are distributed among these distances:
32 7 0.08
33 9 0.11
34 33 0.40
35 16 0.19
36 13 0.16
37 5 0.06
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.42
Consensus pattern (32 bp):
ATATATATAGTATAATACTATATAATATATTT
Found at i:417158 original size:24 final size:22
Alignment explanation
Indices: 417128--417172 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
417118 TGACGTCCTG
417128 TGATTCTTGCCAATCTTGATTTTC
1 TGATTCTTG--AATCTTGATTTTC
*
417152 TGATTCTTGATTCTTGATTTT
1 TGATTCTTGAATCTTGATTTT
417173 TTGGTCCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (22 bp):
TGATTCTTGAATCTTGATTTTC
Found at i:424762 original size:23 final size:23
Alignment explanation
Indices: 424732--424777 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
424722 CATTCATTTG
424732 ATTCAATACAGACAACCTTGCAA
1 ATTCAATACAGACAACCTTGCAA
424755 ATTCAATACAGACAACCTTGCAA
1 ATTCAATACAGACAACCTTGCAA
424778 TGATATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (23 bp):
ATTCAATACAGACAACCTTGCAA
Found at i:428534 original size:20 final size:20
Alignment explanation
Indices: 428494--428532 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
428484 CATTCTAGGA
*
428494 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
428514 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
428533 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:441572 original size:19 final size:19
Alignment explanation
Indices: 441548--441591 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
441538 ACAATGTATG
*
441548 AAACAGATGAAACAAACTA
1 AAACAGAGGAAACAAACTA
*
441567 AAACAGAGGAAACAAGCTA
1 AAACAGAGGAAACAAACTA
441586 AAACAG
1 AAACAG
441592 TAACTTTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.61, C:0.16, G:0.16, T:0.07
Consensus pattern (19 bp):
AAACAGAGGAAACAAACTA
Found at i:443314 original size:19 final size:19
Alignment explanation
Indices: 443292--443330 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
443282 TCACTATAAT
*
443292 TAAAATTTATAACTAAAAA
1 TAAAATTTATAACAAAAAA
*
443311 TAAAATTTATCACAAAAAA
1 TAAAATTTATAACAAAAAA
443330 T
1 T
443331 TGAATCTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAATTTATAACAAAAAA
Found at i:445682 original size:23 final size:22
Alignment explanation
Indices: 445639--445682 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
445629 GTTAAATTAA
** *
445639 AAATATAAAATATTATTAAAAT
1 AAATATAAAATAAAATAAAAAT
445661 AAATAGTAAAATAAAATAAAAA
1 AAATA-TAAAATAAAATAAAAA
445683 ATGTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
AAATATAAAATAAAATAAAAAT
Done.