Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008559.1 Hibiscus syriacus cultivar Beakdansim tig00111466_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: 490547
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 3
Found at i:402718 original size:20 final size:20
Alignment explanation
Indices: 402693--402738 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
402683 CATTTCATTT
402693 TCATCCCCAAGCTATGATCA
1 TCATCCCCAAGCTATGATCA
*
402713 TCATCCCCAAGCTATGATCT
1 TCATCCCCAAGCTATGATCA
402733 TCATCC
1 TCATCC
402739 TAAATTGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.37, G:0.09, T:0.28
Consensus pattern (20 bp):
TCATCCCCAAGCTATGATCA
Found at i:406637 original size:18 final size:18
Alignment explanation
Indices: 406614--406673 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
406604 ACTTTATCCA
406614 TTTTCTTTCTTTTCCTTT
1 TTTTCTTTCTTTTCCTTT
*
406632 TTTTCTTTTTTTTCTCTTT
1 TTTTCTTTCTTTTC-CTTT
*
406651 TTTT-TCTCTTTT-C-TT
1 TTTTCTTTCTTTTCCTTT
406666 TTTTCTTT
1 TTTTCTTT
406674 GAGTTCTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 6 0.17
16 3 0.08
18 19 0.53
19 8 0.22
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCTTTCTTTTCCTTT
Found at i:406649 original size:11 final size:11
Alignment explanation
Indices: 406629--406673 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
406619 TTTCTTTTCC
406629 TTTTTT-TCTT
1 TTTTTTCTCTT
406639 TTTTTTCTCTT
1 TTTTTTCTCTT
406650 TTTTTTCTCTT
1 TTTTTTCTCTT
*
406661 TTCTTTTTTCTT
1 TT-TTTTCTCTT
406673 T
1 T
406674 GAGTTCTTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 6 0.19
11 17 0.53
12 9 0.28
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTCTCTT
Found at i:412505 original size:18 final size:18
Alignment explanation
Indices: 412480--412523 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
412470 AAAAGGTTTA
412480 AAAATAAATAATAATA-T
1 AAAATAAATAATAATAGT
*
412497 AATAATAAATAATAGTAGT
1 AA-AATAAATAATAATAGT
412516 AAAATAAA
1 AAAATAAA
412524 AAGGGGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 19 0.79
19 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAATAAATAATAATAGT
Found at i:412571 original size:18 final size:19
Alignment explanation
Indices: 412550--412593 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
412540 GTTATTTTTA
*
412550 AAATAAAAGATAA-GAATT
1 AAATAAAAGAAAATGAATT
*
412568 AAATAAAAGAAAATTAATT
1 AAATAAAAGAAAATGAATT
412587 AAATAAA
1 AAATAAA
412594 CAAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (19 bp):
AAATAAAAGAAAATGAATT
Found at i:413272 original size:71 final size:75
Alignment explanation
Indices: 413191--413376 Score: 265
Period size: 76 Copynumber: 2.5 Consensus size: 75
413181 AACATCTTAG
* * *
413191 ATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCT-AA-AAA-ATAATAT-TTAAAA
1 ATCCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAACAAATATAAAATATAAAAA
*
413251 TAATATTCTAA
65 TAATATCCTAA
413262 ATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAAAAA
1 ATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT-AAACAAATATAAAATATAAAAA
413327 TAATATCCTAA
65 TAATATCCTAA
* *
413338 AACTTAATTAAAATACTAAAACCTATTTAAACTAAAATA
1 ATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATA
413377 AAAAGATAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
70 5 0.05
71 35 0.34
73 2 0.02
74 3 0.03
75 6 0.06
76 52 0.50
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.30
Consensus pattern (75 bp):
ATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAACAAATATAAAATATAAAAAT
AATATCCTAA
Found at i:413286 original size:19 final size:19
Alignment explanation
Indices: 413258--413368 Score: 61
Period size: 19 Copynumber: 5.8 Consensus size: 19
413248 AAATAATATT
*
413258 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
* *
413277 CTAAAACCTATTTAAACTA
1 CTAAAACCTAATTAAAATA
*
413296 --AAATACCTAA-AACAAATA
1 CTAAA-ACCTAATTA-AAATA
** *
413314 -TAAAATATAA-AAATAATA
1 CTAAAACCTAATTAA-AATA
*
413332 TCCTAAAACTTAATTAAAATA
1 --CTAAAACCTAATTAAAATA
*
413353 CTAAAACCTATTTAAA
1 CTAAAACCTAATTAAA
413369 CTAAAATAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
17 5 0.07
18 19 0.27
19 33 0.46
21 12 0.17
22 2 0.03
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:413297 original size:24 final size:24
Alignment explanation
Indices: 413270--413376 Score: 74
Period size: 24 Copynumber: 4.3 Consensus size: 24
413260 AAATCCTAAT
413270 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
** * *
413294 TAAAATACCTAAAACAAATATAAAA
1 TAAAATA-CTAAAACCTATTTAAAC
* * * *
413319 TATAAA-AATAATATCCTAAAACTT-AAT
1 TA-AAATACTAA-AACCT---ATTTAAAC
413346 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
413370 TAAAATA
1 TAAAATA
413377 AAAAGATAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
23 3 0.05
24 19 0.32
25 18 0.30
26 10 0.17
27 8 0.13
28 2 0.03
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (24 bp):
TAAAATACTAAAACCTATTTAAAC
Found at i:413317 original size:25 final size:24
Alignment explanation
Indices: 413270--413317 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
413260 AAATCCTAAT
** *
413270 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
413294 TAAAATACCTAAAACAAATATAAA
1 TAAAATA-CTAAAACAAATATAAA
413318 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:413338 original size:32 final size:32
Alignment explanation
Indices: 413297--413358 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
413287 TTTAAACTAA
413297 AATACCTAAAAC-AAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
413328 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAA
413359 CCTATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:413401 original size:76 final size:73
Alignment explanation
Indices: 413193--413401 Score: 226
Period size: 76 Copynumber: 2.8 Consensus size: 73
413183 CATCTTAGAT
* ***
413193 CCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAA-TAATATTT-AAAATAAT
1 CCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATAAAAAAAAAATTAATATTTAAAAATAAT
* *
413255 ATTCTAAAT
65 ATCCTAAAA
* * * *
413264 CCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAAAAATA
1 CCTAATTAAAATACTAAAACCTATTTAAACTAAAATA--AAAAAAAAAT-TAATATTTAAAAATA
413329 ATATCCTAAAA
63 ATATCCTAAAA
* *
413340 CTTAATTAAAATACTAAAACCTATTTAAACTAAAATAAAAAGATAAAATCTAATGTTTAAAA
1 CCTAATTAAAATACTAAAACCTATTTAAACTAAAATAAAAA-A-AAAAT-TAATATTTAAAA
413402 TATTATTCTA
Statistics
Matches: 114, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
70 5 0.04
71 30 0.26
73 5 0.04
74 3 0.03
75 7 0.06
76 64 0.56
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (73 bp):
CCTAATTAAAATACTAAAACCTATTTAAACTAAAATAAAAAAAAAATTAATATTTAAAAATAATA
TCCTAAAA
Found at i:415112 original size:5 final size:5
Alignment explanation
Indices: 415102--415207 Score: 54
Period size: 5 Copynumber: 20.8 Consensus size: 5
415092 TTACAGAGAA
* * * *
415102 AAAAT AAAAT AAAAT -TAAT CAAAAT AAAAT -AAAT AGAAT GAAAT AAAGT
1 AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
**** * * *
415151 TCGCT AAAAAT AAAAT AAAAAT AAAAT GAACT AAAAAG AAAAT AAAAT
1 AAAAT -AAAAT AAAAT -AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT
*
415199 GAAAT AAAA
1 AAAAT AAAA
415208 ACAAAAATAT
Statistics
Matches: 72, Mismatches: 23, Indels: 12
0.67 0.21 0.11
Matches are distributed among these distances:
4 7 0.10
5 54 0.75
6 11 0.15
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:415185 original size:21 final size:20
Alignment explanation
Indices: 415158--415213 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 20
415148 AGTTCGCTAA
415158 AAATAAAATAAAAATAAAATG
1 AAATAAAA-AAAAATAAAATG
*
415179 AACTAAAAAGAAAATAAAATG
1 AAATAAAAA-AAAATAAAATG
415200 AAATAAAAACAAAA
1 AAATAAAAA-AAAA
415214 ATATAACGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.77, C:0.04, G:0.05, T:0.14
Consensus pattern (20 bp):
AAATAAAAAAAAATAAAATG
Found at i:420154 original size:19 final size:19
Alignment explanation
Indices: 420073--420160 Score: 56
Period size: 19 Copynumber: 4.5 Consensus size: 19
420063 TGCTCTTGTT
420073 CCTAATTAAAATACTTAAAA
1 CCTAATTAAAATAC-TAAAA
* *
420093 -CTATTTAAACTA--AAATA
1 CCTAATTAAAATACTAAA-A
** *
420110 CCTAAAAAATAATATTCTAAAT
1 CCTAATTAA-AATA--CTAAAA
420132 CCTAATTAAAATACTAAAA
1 CCTAATTAAAATACTAAAA
*
420151 CCTATTTAAA
1 CCTAATTAAA
420161 CTAAAATACC
Statistics
Matches: 50, Mismatches: 11, Indels: 15
0.66 0.14 0.20
Matches are distributed among these distances:
16 3 0.06
17 1 0.02
18 5 0.10
19 27 0.54
21 4 0.08
22 7 0.14
23 3 0.06
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (19 bp):
CCTAATTAAAATACTAAAA
Found at i:425547 original size:18 final size:18
Alignment explanation
Indices: 425524--425562 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
425514 GTGTTAAACG
425524 ACAGAGAAAAACCCTAAC
1 ACAGAGAAAAACCCTAAC
* *
425542 ACAGAGAGAACCCCTAAC
1 ACAGAGAAAAACCCTAAC
425560 ACA
1 ACA
425563 TAGAGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.31, G:0.13, T:0.05
Consensus pattern (18 bp):
ACAGAGAAAAACCCTAAC
Found at i:432005 original size:23 final size:23
Alignment explanation
Indices: 431979--432026 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
431969 ATAAAGTACA
* *
431979 ATAACATACTAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
432002 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
432025 AT
1 AT
432027 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:432430 original size:25 final size:25
Alignment explanation
Indices: 432373--432438 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
432363 ACTCAAAAAG
*
432373 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
432398 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
432423 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
432439 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:435213 original size:183 final size:182
Alignment explanation
Indices: 434905--435396 Score: 887
Period size: 183 Copynumber: 2.7 Consensus size: 182
434895 TTAAAATTAC
434905 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* * *
434970 ATTAGAAAGTGTCGATATATGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
435035 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
130 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
435088 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
435153 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
435218 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
130 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
* *
435271 CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCCATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTA-AATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
435336 ATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCG
435397 ATAGCATTGC
Statistics
Matches: 300, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
182 58 0.19
183 239 0.80
184 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (182 bp):
CGACACTTTTTTAAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
TATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
Found at i:435813 original size:23 final size:23
Alignment explanation
Indices: 435787--435844 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
435777 ATATAACCAC
435787 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
435810 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
435833 TACCTATTACAT
1 TACCTATTACAT
435845 CATACTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:436369 original size:24 final size:24
Alignment explanation
Indices: 436341--436403 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
436331 CAACAATCCT
436341 CAAATGTATATGTACACATAGAAG
1 CAAATGTATATGTACACATAGAAG
436365 CAAATGTATATGTACACATAGAAG
1 CAAATGTATATGTACACATAGAAG
436389 CAAATGTATAT-TACA
1 CAAATGTATATGTACA
436404 TTATACTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
23 4 0.10
24 35 0.90
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (24 bp):
CAAATGTATATGTACACATAGAAG
Found at i:436632 original size:198 final size:199
Alignment explanation
Indices: 436396--436878 Score: 905
Period size: 198 Copynumber: 2.4 Consensus size: 199
436386 AAGCAAATGT
436396 ATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACAC
1 ATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACAC
* *
436461 TTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAGTAAAA-AGTG
66 TTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAAATAGTG
436525 TCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAA
131 TCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAA
436590 TTAC
196 TTAC
*
436594 ATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCAACAC
1 ATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACAC
436659 TTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAAATAGTG
66 TTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAAATAGTG
436724 TCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAA
131 TCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAA
436789 TTAC
196 TTAC
*
436793 ATATTACATTATACTTTTGGTTTTCGATGTTTTTTGGGATCGACACTTTTTATATATGGATCGAC
1 ATATTACATTATACTTTTGG-GTTCGATG-TTTTTGGGATCGACACTTTTTATATATGGATCGAC
436858 ACTTTATGGTTGCACCCTGTT
64 ACTTTATGGTTGCACCCTGTT
436879 GGCCATATTG
Statistics
Matches: 277, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
198 122 0.44
199 93 0.34
200 7 0.03
201 55 0.20
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (199 bp):
ATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATATATGGATCGACAC
TTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAACAAAAATATCGACACAAACTAAAATAGTG
TCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAA
TTAC
Found at i:437043 original size:19 final size:19
Alignment explanation
Indices: 436997--437045 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
436987 TTATATTCAC
*
436997 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
437016 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
437035 ATACAAAATTA
1 ATACAAAATTA
437046 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:438881 original size:32 final size:32
Alignment explanation
Indices: 438839--438899 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
438829 TTAATATCAC
*
438839 CCCTTAACACCCCAACTTCTTTCACCACTTCA
1 CCCTCAACACCCCAACTTCTTTCACCACTTCA
* * *
438871 CCCTCAACACCTCTACTTCTTTTACCACT
1 CCCTCAACACCCCAACTTCTTTCACCACT
438900 CCATCTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.23, C:0.46, G:0.00, T:0.31
Consensus pattern (32 bp):
CCCTCAACACCCCAACTTCTTTCACCACTTCA
Found at i:438958 original size:21 final size:21
Alignment explanation
Indices: 438933--438976 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
438923 CCCCTTATGC
438933 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
438954 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
438975 CT
1 CT
438977 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:441209 original size:17 final size:18
Alignment explanation
Indices: 441187--441229 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
441177 ATATATCCGG
441187 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
441204 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
441224 TATCAT
1 TATCAT
441230 ATTTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:441463 original size:181 final size:182
Alignment explanation
Indices: 441159--441628 Score: 628
Period size: 181 Copynumber: 2.6 Consensus size: 182
441149 CGTACTTACG
* * *
441159 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTG-ATACCGGTT
1 AAAGTATCGACACTTTCAATAAATCCGGTAACGTTTTACCGGTTTTATCATTTTGTA-ACCGGTT
** * * *
441223 TTATCATATTTTTATTTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTA
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTA
*
441288 TAGGCGCTAAAAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 TAGGAGCTAAAAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
*
441340 AAAGTATCGACACTTTCAATAAATCCGGTAACGTTTTACCGGTTTTATCATTTTGTAACTGGTTT
1 AAAGTATCGACACTTTCAATAAATCCGGTAACGTTTTACCGGTTTTATCATTTTGTAACCGGTTT
* *
441405 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * * *
441470 AGGATTTAAAATTGTTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * * *
441522 AAAGTACCGACACTTTAAATGTAAT-AGGTAGCGCTTTACCGGTTTTATCATTCTAT-ACCGGTT
1 AAAGTATCGACACTTTCAAT-AAATCCGGTAACGTTTTACCGGTTTTATCATTTTGTAACCGGTT
* * *
441585 TTGTCATA-GTTTACCTGTTATATCG-TTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
441629 ATTTGGATCG
Statistics
Matches: 256, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
179 18 0.07
180 15 0.06
181 174 0.68
182 46 0.18
183 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATAAATCCGGTAACGTTTTACCGGTTTTATCATTTTGTAACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAAATGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:441599 original size:19 final size:19
Alignment explanation
Indices: 441555--441599 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
441545 ATAGGTAGCG
*
441555 CTTTACCGGTTTTATCATT
1 CTTTACCGGTTTTATCATA
* *
441574 CTATACCGGTTTTGTCATA
1 CTTTACCGGTTTTATCATA
*
441593 GTTTACC
1 CTTTACC
441600 TGTTATATCG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.47
Consensus pattern (19 bp):
CTTTACCGGTTTTATCATA
Found at i:442587 original size:13 final size:13
Alignment explanation
Indices: 442569--442594 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
442559 ACTTCTGCAC
442569 TAATCTAATTTAA
1 TAATCTAATTTAA
442582 TAATCTAATTTAA
1 TAATCTAATTTAA
442595 GGTTAAAGAA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATCTAATTTAA
Found at i:443201 original size:15 final size:15
Alignment explanation
Indices: 443183--443227 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
443173 AAAAAAAAGT
443183 AATAAAAATAAAGAA
1 AATAAAAATAAAGAA
*
443198 AATAAAAATAAATCAA
1 AATAAAAATAAA-GAA
*
443214 AGTAAAAATAAAGA
1 AATAAAAATAAAGA
443228 GGAAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.16
Consensus pattern (15 bp):
AATAAAAATAAAGAA
Found at i:443219 original size:16 final size:15
Alignment explanation
Indices: 443183--443225 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
443173 AAAAAAAAGT
*
443183 AATAAAAATAAAGAA
1 AATAAAAATAAACAA
443198 AATAAAAATAAATCAA
1 AATAAAAATAAA-CAA
*
443214 AGTAAAAATAAA
1 AATAAAAATAAA
443226 GAGGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (15 bp):
AATAAAAATAAACAA
Found at i:443309 original size:6 final size:6
Alignment explanation
Indices: 443285--443340 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
443275 ATAAATAATT
* *
443285 AAATAA AAACAA GAATAA AAATAA AAAT-- AAATAA AGAGATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A-A-ATAA AAATAA
*
443333 ATATAA AA
1 AAATAA AA
443341 GAAATAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
4 4 0.10
6 29 0.73
7 2 0.05
8 5 0.12
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:443312 original size:24 final size:24
Alignment explanation
Indices: 443285--443340 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
443275 ATAAATAATT
443285 AAATAAAAACAAGA-ATAAAAATAA
1 AAATAAAAA-AAGAGATAAAAATAA
*
443309 AAATAAATAAAGAGATAAAAATAA
1 AAATAAAAAAAGAGATAAAAATAA
*
443333 ATATAAAA
1 AAATAAAA
443341 GAAATAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (24 bp):
AAATAAAAAAAGAGATAAAAATAA
Found at i:443378 original size:30 final size:31
Alignment explanation
Indices: 443342--443407 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
443332 AATATAAAAG
* * * *
443342 AAATAAAAGTAAGATAAAGATAAAG-GAAAT
1 AAATAAAAATAAAATAAAGAAAAAGACAAAT
443372 AAATAAAAATAAAATAAAGAAAAAGACAAAT
1 AAATAAAAATAAAATAAAGAAAAAGACAAAT
443403 AAATA
1 AAATA
443408 TTTAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.15
Consensus pattern (31 bp):
AAATAAAAATAAAATAAAGAAAAAGACAAAT
Found at i:443637 original size:15 final size:15
Alignment explanation
Indices: 443580--443638 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
443570 AAAAAAGAAT
*
443580 AAAAATAGATATAT-
1 AAAAATAAATATATA
* * * *
443594 AACAATACATTTTTA
1 AAAAATAAATATATA
443609 AAAAAT-AATGATATA
1 AAAAATAAAT-ATATA
443624 AAAAATAAATATATA
1 AAAAATAAATATATA
443639 TTTATATTAG
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
14 12 0.35
15 19 0.56
16 3 0.09
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAAATAAATATATA
Found at i:446524 original size:3 final size:3
Alignment explanation
Indices: 446509--446593 Score: 70
Period size: 3 Copynumber: 29.7 Consensus size: 3
446499 TACATGATAT
* * * ** *
446509 TAA TAA TAC TAA TAA TTA TTA TAA T-A TAA TTG TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
446556 T-A TAA TAA TAA T-A TAA TAG TAA TAA TTA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
446594 TTTATAACCA
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
2 8 0.12
3 58 0.88
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:446538 original size:23 final size:23
Alignment explanation
Indices: 446511--446593 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 23
446501 CATGATATTA
* * *
446511 ATAATACTAATAATTATTATAAT
1 ATAATAATAATAATAATAATAAT
** *
446534 ATAATTGTTATAATAATAATAAT
1 ATAATAATAATAATAATAATAAT
*
446557 ATAATAATAAT-ATAATAGTAAT
1 ATAATAATAATAATAATAATAAT
*
446579 AATTATAAT-ATAATA
1 -ATAATAATAATAATA
446594 TTTATAACCA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
22 12 0.25
23 36 0.75
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAATAATAATAATAATAATAAT
Found at i:446562 original size:11 final size:11
Alignment explanation
Indices: 446546--446593 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
446536 AATTGTTATA
446546 ATAATAATAAT
1 ATAATAATAAT
446557 ATAATAATAAT
1 ATAATAATAAT
*
446568 ATAATAGT-A-
1 ATAATAATAAT
*
446577 ATAATTATAAT
1 ATAATAATAAT
446588 ATAATA
1 ATAATA
446594 TTTATAACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 23 0.74
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:446593 original size:14 final size:14
Alignment explanation
Indices: 446520--446600 Score: 80
Period size: 14 Copynumber: 5.9 Consensus size: 14
446510 AATAATACTA
*
446520 ATAATTATTATAAT
1 ATAATAATTATAAT
**
446534 ATAATTGTTATAAT
1 ATAATAATTATAAT
446548 AATAATAA-TAT-A-
1 -ATAATAATTATAAT
446560 ATAATAA-TATAAT
1 ATAATAATTATAAT
446573 AGTAATAATTATAAT
1 A-TAATAATTATAAT
*
446588 ATAATATTTATAA
1 ATAATAATTATAA
446601 CCAGGACAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
11 10 0.17
12 1 0.02
13 2 0.03
14 33 0.57
15 12 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
ATAATAATTATAAT
Found at i:446920 original size:52 final size:52
Alignment explanation
Indices: 446851--447403 Score: 935
Period size: 52 Copynumber: 10.6 Consensus size: 52
446841 TCGCTCTCTA
* *
446851 TTTCTTCAGGGAGTAGAACTCGAACGATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * *
446903 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGATATTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
*
446955 TTTCTTTAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* *
447007 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
447059 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * * *
447111 TTTCTTCAGGGACTAGAACTCGAATAAAAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * *
447163 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGTCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
447215 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
*
447267 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGAATGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
* * *
447319 TTTCTCCAGGGACTAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAAT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
447371 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
1 TTTCTTCAGGGACTAGAACTCGAACAATAATCT
447404 CCAACGATCG
Statistics
Matches: 471, Mismatches: 30, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 471 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (52 bp):
TTTCTTCAGGGACTAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAAT
Found at i:447508 original size:55 final size:55
Alignment explanation
Indices: 447399--447786 Score: 588
Period size: 55 Copynumber: 7.1 Consensus size: 55
447389 CTCGAACAAT
*
447399 AATCTCCAACGATCGCGTCTGCCCCCTA-TTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
447453 AATCTTCAACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
447508 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * * * *
447561 AATCTTTATCAATCGTGTCTGCCCCCTATTTCTTTAGAGAGTATAAGACTCGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
447616 AATCTTCAACGATCGCATCTGCCCCCCTATTTCTTCAGAGAGTATAAGA-TC-CAC
1 AATCTTCAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * *
447670 AATCTTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTAGAAT
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
447725 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
447780 AATCTTC
1 AATCTTC
447787 TTTTGCTTCA
Statistics
Matches: 297, Mismatches: 31, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
53 72 0.24
54 50 0.17
55 149 0.50
56 26 0.09
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (55 bp):
AATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:447527 original size:109 final size:108
Alignment explanation
Indices: 447396--447786 Score: 631
Period size: 109 Copynumber: 3.6 Consensus size: 108
447386 GAACTCGAAC
*
447396 AATAATCTCCAACGATCGCGTCTGCCCCCTA-TTCTTCAGAGAGTATAAGACTCGAACAATCTTC
1 AATAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-AACAATCTTC
* *
447460 AACAATCGCGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCG
64 ATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
* * *
447505 AACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGATCCACAATCTTTAT
1 AATAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGATCAACAATCTTCAT
* *
447570 CAATCGTGTCTGCCCCCTATTTCTTTAGAGAGTATAAGACTCG
66 CAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
* *
447613 AATAATCTTCAACGATCGCATCTGCCCCCCTATTTCTTCAGAGAGTATAAGATCCACAATCTTCA
1 AATAATCTTCAACGATCGCGTCTG-CCCCCTATTTCTTCAGAGAGTATAAGATCAACAATCTTCA
*
447678 TCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTAG
65 TCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
447722 AATAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC
1 AATAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGA-TC-AACAATCTTC
447787 TTTTGCTTCA
Statistics
Matches: 262, Mismatches: 16, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
108 98 0.37
109 136 0.52
110 28 0.11
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (108 bp):
AATAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGATCAACAATCTTCAT
CAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCG
Found at i:449083 original size:10 final size:10
Alignment explanation
Indices: 449068--449159 Score: 64
Period size: 10 Copynumber: 9.1 Consensus size: 10
449058 CCCCCTTTTA
*
449068 TTTTTTTT-G
1 TTTTTTTTCT
449077 TTTTTTTTCT
1 TTTTTTTTCT
449087 TTTTTTTTC-
1 TTTTTTTTCT
*
449096 TTTTTTTCCAT
1 TTTTTTTTC-T
*
449107 TTTTCTATT-T
1 TTTT-TTTTCT
* *
449117 TTCTATTTCAT
1 TTTTTTTTC-T
*
449128 TTTTTTTTTT
1 TTTTTTTTCT
449138 TTTTTTTTCAT
1 TTTTTTTTC-T
*
449149 TTTTTTATCT
1 TTTTTTTTCT
449159 T
1 T
449160 AAGCAAAACC
Statistics
Matches: 64, Mismatches: 12, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
9 18 0.28
10 24 0.38
11 20 0.31
12 2 0.03
ACGTcount: A:0.07, C:0.10, G:0.01, T:0.83
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:449089 original size:8 final size:8
Alignment explanation
Indices: 449062--449154 Score: 55
Period size: 8 Copynumber: 11.0 Consensus size: 8
449052 CTTGAACCCC
449062 CTTTTATTT
1 CTTTT-TTT
449071 -TTTTTGTT
1 CTTTTT-TT
449079 -TTTTTTCT
1 CTTTTTT-T
*
449087 TTTTTTTT
1 CTTTTTTT
449095 CTTTTTTT
1 CTTTTTTT
**
449103 CCATTTTT
1 CTTTTTTT
*
449111 CTATTTTT
1 CTTTTTTT
449119 CTATTTCATTT
1 CT-TTT--TTT
*
449130 TTTTTTTT
1 CTTTTTTT
*
449138 TTTTTTTT
1 CTTTTTTT
449146 CATTTTTTT
1 C-TTTTTTT
449155 ATCTTAAGCA
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
7 2 0.03
8 46 0.66
9 15 0.21
10 3 0.04
11 4 0.06
ACGTcount: A:0.06, C:0.10, G:0.01, T:0.83
Consensus pattern (8 bp):
CTTTTTTT
Found at i:449154 original size:16 final size:16
Alignment explanation
Indices: 449070--449140 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 16
449060 CCCTTTTATT
*
449070 TTTTTTGTTTTTTTTCTT
1 TTTTTT-TTTTTTTTC-A
449088 TTTTTTTCTTTTTTTCCA
1 TTTTTTT-TTTTTTT-CA
449106 TTTTTCTATTTTTCTATTTCA
1 -TTTT-T-TTTTT-T-TTTCA
449127 TTTTTTTTTTTTTT
1 TTTTTTTTTTTTTT
449141 TTTTTCATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 16
0.73 0.02 0.26
Matches are distributed among these distances:
16 3 0.07
17 2 0.04
18 18 0.40
19 6 0.13
20 8 0.18
21 5 0.11
22 3 0.07
ACGTcount: A:0.06, C:0.10, G:0.01, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTTTTTTCA
Found at i:457413 original size:3 final size:3
Alignment explanation
Indices: 457398--457482 Score: 70
Period size: 3 Copynumber: 29.7 Consensus size: 3
457388 TACCTGATAT
* * * ** *
457398 TAA TAA TAC TAA TAA TTA TTA TAA T-A TAA TTG TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
457445 T-A TAA TAA TAA T-A TAA TAG TAA TAA TTA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
457483 TTTATAACCA
Statistics
Matches: 66, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
2 8 0.12
3 58 0.88
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:457427 original size:23 final size:23
Alignment explanation
Indices: 457400--457482 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 23
457390 CCTGATATTA
* * *
457400 ATAATACTAATAATTATTATAAT
1 ATAATAATAATAATAATAATAAT
** *
457423 ATAATTGTTATAATAATAATAAT
1 ATAATAATAATAATAATAATAAT
*
457446 ATAATAATAAT-ATAATAGTAAT
1 ATAATAATAATAATAATAATAAT
*
457468 AATTATAAT-ATAATA
1 -ATAATAATAATAATA
457483 TTTATAACCA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
22 12 0.25
23 36 0.75
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAATAATAATAATAATAATAAT
Found at i:457451 original size:11 final size:11
Alignment explanation
Indices: 457435--457482 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
457425 AATTGTTATA
457435 ATAATAATAAT
1 ATAATAATAAT
457446 ATAATAATAAT
1 ATAATAATAAT
*
457457 ATAATAGT-A-
1 ATAATAATAAT
*
457466 ATAATTATAAT
1 ATAATAATAAT
457477 ATAATA
1 ATAATA
457483 TTTATAACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 6 0.19
10 2 0.06
11 23 0.74
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:457482 original size:14 final size:14
Alignment explanation
Indices: 457409--457489 Score: 80
Period size: 14 Copynumber: 5.9 Consensus size: 14
457399 AATAATACTA
*
457409 ATAATTATTATAAT
1 ATAATAATTATAAT
**
457423 ATAATTGTTATAAT
1 ATAATAATTATAAT
457437 AATAATAA-TAT-A-
1 -ATAATAATTATAAT
457449 ATAATAA-TATAAT
1 ATAATAATTATAAT
457462 AGTAATAATTATAAT
1 A-TAATAATTATAAT
*
457477 ATAATATTTATAA
1 ATAATAATTATAA
457490 CCAGGACAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
11 10 0.17
12 1 0.02
13 2 0.03
14 33 0.57
15 12 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (14 bp):
ATAATAATTATAAT
Found at i:462853 original size:4 final size:4
Alignment explanation
Indices: 462844--462889 Score: 58
Period size: 4 Copynumber: 11.2 Consensus size: 4
462834 TATCGAGAAA
*
462844 ACAT ACAT ACAT ACAT ACAT AAAT ACGCAT ACAT ACAT A-AT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A--CAT ACAT ACAT ACAT ACAT A
462890 AAATTTGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 3 0.08
4 31 0.84
6 3 0.08
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:463536 original size:103 final size:99
Alignment explanation
Indices: 463354--463575 Score: 254
Period size: 103 Copynumber: 2.2 Consensus size: 99
463344 AAACAATTGC
* * *
463354 GTCTCGCTTGAGACATTTTTCCTTTGAGATAAAATTTTGAATTTGATTCACTTAAAACAAAATTA
1 GTCTCGCTTGAGACATTTTCCCTTGGAGATAAAATTTCGAATTTGATTCACTTAAAACAAAATTA
*
463419 ATCTCACCTTAGATTGTTGTTTCTTTCAAAA-AAATTTT
66 ATCTCACCTTAGA---TTGTTTC--TCAAAACAAACTTT
* * * *
463457 GTCTCGCTTGAGACCTTTTCCCTTGGAGATCCAAATTTCGAATTTGTTTCACATT-AAAC-AAGT
1 GTCTCGCTTGAGACATTTTCCCTTGGAGAT-AAAATTTCGAATTTGATTCAC-TTAAAACAAAAT
*
463520 TGATCTCA-CTTGAGATTGTTTCTCAAAACAAACTTT
64 TAATCTCACCTT-AGATTGTTTCTCAAAACAAACTTT
*
463556 GTCTCGCTTGAGACAATTTC
1 GTCTCGCTTGAGACATTTTC
463576 TCTAAAAACA
Statistics
Matches: 104, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
98 6 0.06
99 24 0.23
100 7 0.07
102 3 0.03
103 40 0.38
104 22 0.21
105 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (99 bp):
GTCTCGCTTGAGACATTTTCCCTTGGAGATAAAATTTCGAATTTGATTCACTTAAAACAAAATTA
ATCTCACCTTAGATTGTTTCTCAAAACAAACTTT
Found at i:463568 original size:34 final size:33
Alignment explanation
Indices: 463523--463639 Score: 108
Period size: 34 Copynumber: 3.4 Consensus size: 33
463513 AACAAGTTGA
* *
463523 TCTCACTTGAGATTGTTTCTCAAAACAAACTTTG
1 TCTCACTTGAGACTATTTCTCAAAACAAA-TTTG
* *
463557 TCTCGCTTGAGACAATTTCTCTAAAAACAAATGTTG
1 TCTCACTTGAGACTATTTCTC--AAAACAAAT-TTG
* * * *
463593 TCTCATTTGAGACTATATCTTAAAGCAAATTTCG
1 TCTCACTTGAGACTATTTCTCAAAACAAATTT-G
*
463627 TCTCGCTTGAGAC
1 TCTCACTTGAGAC
463640 ATCATTTTCT
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
33 2 0.03
34 37 0.55
35 1 0.01
36 27 0.40
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (33 bp):
TCTCACTTGAGACTATTTCTCAAAACAAATTTG
Found at i:463594 original size:36 final size:33
Alignment explanation
Indices: 463544--463640 Score: 104
Period size: 36 Copynumber: 2.8 Consensus size: 33
463534 ATTGTTTCTC
*
463544 AAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAACAAA-TTTGTCTCGCTTGAGACAATATCT-T
** *
463579 AAAAACAAATGTTGTCTCATTTGAGACTATATCTT
1 -AAAACAAAT-TTGTCTCGCTTGAGACAATATCTT
*
463614 AAAGCAAATTTCGTCTCGCTTGAGACA
1 AAAACAAATTT-GTCTCGCTTGAGACA
463641 TCATTTTCTC
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
33 2 0.04
34 20 0.39
35 2 0.04
36 27 0.53
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (33 bp):
AAAACAAATTTGTCTCGCTTGAGACAATATCTT
Found at i:463971 original size:28 final size:26
Alignment explanation
Indices: 463886--463985 Score: 112
Period size: 28 Copynumber: 3.7 Consensus size: 26
463876 ACAGTTTCTC
463886 TTGAAAAAATCTTTGAGTTAGTTCCTT
1 TTGAAAAAATCTTTGAGTT-GTTCCTT
* *
463913 TTAAATAAAATCTTGGAGTTTGTTCCTT
1 TTGAA-AAAATCTTTGAG-TTGTTCCTT
*
463941 TTGAATAAATATCTTTGAGTTGTTTCTT
1 TTGAA-AAA-ATCTTTGAGTTGTTCCTT
*
463969 TTG-AAAAATCCTTGAGT
1 TTGAAAAAATCTTTGAGT
463986 CTATTTATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
25 9 0.14
26 3 0.05
27 5 0.08
28 37 0.58
29 10 0.16
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (26 bp):
TTGAAAAAATCTTTGAGTTGTTCCTT
Found at i:464124 original size:28 final size:28
Alignment explanation
Indices: 464081--464155 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 28
464071 CTTTAGACAA
464081 TTTTGTGAAAAAATCTTTGAGATTGTTTC
1 TTTTG-GAAAAAATCTTTGAGATTGTTTC
*
464110 TTTTGGAAAAAATCTTTGAGTTTGTTTC
1 TTTTGGAAAAAATCTTTGAGATTGTTTC
*
464138 TTTGGGAACAAAAT-TTTG
1 TTTTGGAA-AAAATCTTTG
464156 TCTCTCTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
28 33 0.77
29 10 0.23
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.47
Consensus pattern (28 bp):
TTTTGGAAAAAATCTTTGAGATTGTTTC
Found at i:464440 original size:63 final size:62
Alignment explanation
Indices: 464342--464459 Score: 168
Period size: 63 Copynumber: 1.9 Consensus size: 62
464332 GAAACAAAAC
*
464342 AAACATCTTTGAGATCATTTCCCTTTAAACGAATTTTGTCTCATTCGAGACAGTTTTCCTTT
1 AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTCGAGACAGTTTTCCTTT
* *
464404 AAACAATCTTTGAG-TCATTT-CCTTTGAAACAAAATTTTGTCTCTTTTGAGACAGTT
1 AAAC-ATCTTTGAGATCATTTCCCTTT-AAAC-AAATTTTGTCTCATTCGAGACAGTT
464460 GCTTTTGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
61 5 0.10
62 14 0.28
63 31 0.62
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.42
Consensus pattern (62 bp):
AAACATCTTTGAGATCATTTCCCTTTAAACAAATTTTGTCTCATTCGAGACAGTTTTCCTTT
Found at i:464786 original size:128 final size:128
Alignment explanation
Indices: 464537--465149 Score: 953
Period size: 128 Copynumber: 4.8 Consensus size: 128
464527 AACCATAACT
* * * * * *
464537 CCTTTAGATGACCAGATC-TCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCCTC
1 CCTTTAGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTC
* *
464601 ATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
64 ATCACGTATGAGCCGTGTC-ACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
464666 A
128 A
464667 CCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
1 CCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
*
464732 CACGTATGAGTCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
66 CACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
464795 CCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
1 CCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
*
464860 CACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
66 CACGTATGAGCCGTGTC-ACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
464924 CCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
1 CCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
*
464989 CACGTATGAGTCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
66 CACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
* * * *** * **
465052 CCTTTAGATAGCCAGAAC-TCTTCATTGCGTATGAGTCGTGTCATTCCCC-GACCAGATCTCTTC
1 CCTTTAGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTC
*
465115 ATCACGTATGAGCCGTGTCACCCTTAGATGACCAG
64 ATCACGTATGAGCCGTGTCACCC-TAGATAACCAG
465150 ACCTCTTCAT
Statistics
Matches: 454, Mismatches: 24, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
128 239 0.53
129 179 0.39
130 36 0.08
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (128 bp):
CCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
CACGTATGAGCCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
Found at i:464994 original size:257 final size:258
Alignment explanation
Indices: 464537--465149 Score: 1052
Period size: 257 Copynumber: 2.4 Consensus size: 258
464527 AACCATAACT
* * *
464537 CCTTTAGATGACCAGATCTCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCCTCA
1 CCTTTAGATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCA
*
464602 TCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
66 TCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
464667 CCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
131 CCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
464732 CACGTATGAGTCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
196 CACGTATGAGTCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
* * * *
464795 CCTTTAGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTC
1 CCTTTAGATGGCCAGAAC-TCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTC
464858 ATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
65 ATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
464923 ACCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCA
130 ACCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCA
464988 TCACGTATGAGTCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
195 TCACGTATGAGTCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
* * ** *
465052 CCTTTAGATAGCCAGAACTCTTCATTGCGTATGAGTCGTGTCATTCCCC-GACCAGATCTCTTCA
1 CCTTTAGATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCA
* * *
465116 TCACGTATGAGCCGTGTCACCCTTAGATGACCAG
66 TCACGTATGAGCCGTGTCAACCATAGATAACCAG
465150 ACCTCTTCAT
Statistics
Matches: 333, Mismatches: 19, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
257 291 0.87
258 42 0.13
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (258 bp):
CCTTTAGATGGCCAGAACTCCTCATCACGTATGAGCCGTGTCATTCCCCAGACCAGATCTCTTCA
TCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
CCTTTAGATGGCCAGCCGTCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCTTCAT
CACGTATGAGTCGTGTCACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCA
Found at i:465345 original size:3 final size:3
Alignment explanation
Indices: 465334--465394 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
465324 TTTTTTATCG
** *
465334 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
465379 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
465395 CATATTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:465389 original size:29 final size:30
Alignment explanation
Indices: 465327--465389 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 30
465317 TCCGGGTTTT
*
465327 TTTATCGTTATTTTATTATTATTATTATTA
1 TTTATCGTTATCTTATTATTATTATTATTA
465357 -TTATCGTTATCTTATTATT-TTATTATTA
1 TTTATCGTTATCTTATTATTATTATTATTA
465385 TTTAT
1 TTTAT
465390 TATTACATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (30 bp):
TTTATCGTTATCTTATTATTATTATTATTA
Found at i:465400 original size:28 final size:28
Alignment explanation
Indices: 465340--465405 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
465330 ATCGTTATTT
* *
465340 TATTATTATTATTATTATTATCGTTATCT
1 TATTATT-TTATTATTATTATCATTATCA
*
465369 TATTATTTTATTATTATTTATTATTA-CA
1 TATTATTTTATTATTA-TTATCATTATCA
*
465397 TATTTTTTT
1 TATTATTTT
465406 TGCAGGCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTTTATTATTATTATCATTATCA
Found at i:469420 original size:23 final size:23
Alignment explanation
Indices: 469377--469420 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
469367 AATTATCCTC
*
469377 AAAATATCAAATTGGATATAAAA
1 AAAATATCAAATTGAATATAAAA
*
469400 AAAAT-TCGAATTGAATCATAA
1 AAAATATCAAATTGAAT-ATAA
469421 GATAAACGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.27
Consensus pattern (23 bp):
AAAATATCAAATTGAATATAAAA
Found at i:472814 original size:22 final size:19
Alignment explanation
Indices: 472789--472831 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 19
472779 GAATCTCAAC
472789 CCTCTCTATTATTCATCTTCTT
1 CCTC-CTATTA-TCATC-TCTT
*
472811 CCTCGTATTATCATCTCTT
1 CCTCCTATTATCATCTCTT
472830 CC
1 CC
472832 CCTTTCACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
21 5 0.25
22 4 0.20
ACGTcount: A:0.14, C:0.35, G:0.02, T:0.49
Consensus pattern (19 bp):
CCTCCTATTATCATCTCTT
Found at i:475468 original size:144 final size:141
Alignment explanation
Indices: 475284--475810 Score: 616
Period size: 144 Copynumber: 3.7 Consensus size: 141
475274 GGGGGGGGGA
* * * * * *
475284 GGGGGGAGCGGGCCTCCGGCACCAAGGCTGGTGTCGGCCAGCCGATCTACCGAAACAAAGCTTAT
1 GGGGGGAGCCGGCCTCCGACACCAAGGCCGGTTTCGGCCAGCCAATCTACCGAAA-GAAGCTTAT
* * *
475349 TCATGAATAAAATTCCAGCATTCTTGGCAGGTCCAACTTCATAAAGATACATAAAGAAATACGAC
65 TCATGAATACAGTTCCAGCATTCTTGGCAGGTCCAACTTCATAAAGATACATAAATAAATACGAC
475414 CTAGTACGAGAGG
130 CTAGTA-GAGAGG
* *
475427 GGGGAGGAGCCGGCCTCCGACACCAATGCCAGTTTCGGCCAGCCAATCTACCGGAAAGAAGCTTA
1 GGGG-GGAGCCGGCCTCCGACACCAAGGCCGGTTTCGGCCAGCCAATCTACC-GAAAGAAGCTTA
* *
475492 TTCATGAATACAGTTCCAGCATTCTTGGCAGGTCCAACTTCGTAAAGATACATAAATAAATACAA
64 TTCATGAATACAGTTCCAGCATTCTTGGCAGGTCCAACTTCATAAAGATACATAAATAAATACGA
*
475557 CCTATTATGAGA-G
129 CCTAGTA-GAGAGG
* * * * *
475570 GAGGGGAGCCGGCCTCCGACACCAAGTCCGGTTTCAGCCATCCAATCTACCGGAATGAAGCTTAT
1 GGGGGGAGCCGGCCTCCGACACCAAGGCCGGTTTCGGCCAGCCAATCTACC-GAAAGAAGCTTAT
* * * *
475635 TCATGAA-ACAGTTTCAGCATTCTCGGCAGGTCCAACTTCATAAAG--ACACAAATAAATACGGC
65 TCATGAATACAGTTCCAGCATTCTTGGCAGGTCCAACTTCATAAAGATACATAAATAAATACGAC
*
475697 CTAGTA-AGAGAA
130 CTAGTAGAGAG-G
* * * * * * * * *
475709 GGGAGAAACCAGCCTCCGGCACCAGGGCTGGTGTT-GGTCAGCCGATCTACCGAAAGGAAGCTTA
1 GGGGGGAGCCGGCCTCCGACACCAAGGCCGGT-TTCGGCCAGCCAATCTACCGAAA-GAAGCTTA
* *
475773 TTCTTGAATACAGTTCCAGCATTCTTGGCAGTTCCAAC
64 TTCATGAATACAGTTCCAGCATTCTTGGCAGGTCCAAC
475811 ATGATAAGAT
Statistics
Matches: 329, Mismatches: 48, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
137 3 0.01
138 3 0.01
139 69 0.21
140 28 0.09
141 35 0.11
142 62 0.19
143 8 0.02
144 117 0.36
145 4 0.01
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.21
Consensus pattern (141 bp):
GGGGGGAGCCGGCCTCCGACACCAAGGCCGGTTTCGGCCAGCCAATCTACCGAAAGAAGCTTATT
CATGAATACAGTTCCAGCATTCTTGGCAGGTCCAACTTCATAAAGATACATAAATAAATACGACC
TAGTAGAGAGG
Found at i:475795 original size:281 final size:283
Alignment explanation
Indices: 475282--475810 Score: 690
Period size: 281 Copynumber: 1.9 Consensus size: 283
475272 GGGGGGGGGG
* * * * *
475282 GAGGGGGGAGCGGGCCTCCGGCACCAAGGCTGGTGTCGGCCAGCCGATCTACCGAAACAAAGCTT
1 GAGGGGGGAGCCGGCCTCCGACACCAAGGCCGGTGTCAGCCAGCCAATCTACCGAAACAAAGCTT
* *
475347 ATTCATGAATAAAATTCCAGCATTCTTGGCAGGTCCAACTTCATAAAGATACATAAAGAAATACG
66 ATTCATGAATAAAATTCCAGCATTCTCGGCAGGTCCAACTTCATAAAGA-ACACAAAGAAATACG
** * * * *
475412 ACCTAGTACGAGAGGGGGGAGGAGCCGGCCTCCGACACCAATGCCAGTTTCGGCCAGCCAATCTA
130 ACCTAGTAC-AGAGAAGGGAGAAACCAGCCTCCGACACCAAGGCCAGTTTCGGCCAGCCAATCTA
475477 CCGGAAAGAAGCTTATTCATGAATACAGTTCCAGCATTCTTGGCAGGTCCAACTTCGTAAAGATA
194 CCGGAAAGAAGCTTATTCATGAATACAGTTCCAGCATTCTTGGCAGGTCCAACTTCGTAAAGATA
475542 CATAAATAAATACAACCTATTATGA
259 CATAAATAAATACAACCTATTATGA
* * * * **
475567 GAGGAGGGGAGCCGGCCTCCGACACCAAGTCCGGTTTCAGCCATCCAATCTACCGGAATGAAGCT
1 GAGG-GGGGAGCCGGCCTCCGACACCAAGGCCGGTGTCAGCCAGCCAATCTACCGAAACAAAGCT
* * * *
475632 TATTCATGAA-ACAGTTTCAGCATTCTCGGCAGGTCCAACTTCATAAAG-ACACAAATAAATACG
65 TATTCATGAATAAAATTCCAGCATTCTCGGCAGGTCCAACTTCATAAAGAACACAAAGAAATACG
* * * ** * *
475695 GCCTAGTA-AGAGAAGGGAGAAACCAGCCTCCGGCACCAGGGCTGGTGTT-GGTCAGCCGATCTA
130 ACCTAGTACAGAGAAGGGAGAAACCAGCCTCCGACACCAAGGCCAGT-TTCGGCCAGCCAATCTA
* *
475758 CC-GAAAGGAAGCTTATTCTTGAATACAGTTCCAGCATTCTTGGCAGTTCCAAC
194 CCGGAAA-GAAGCTTATTCATGAATACAGTTCCAGCATTCTTGGCAGGTCCAAC
475811 ATGATAAGAT
Statistics
Matches: 209, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
280 4 0.02
281 86 0.41
282 2 0.01
283 20 0.10
285 38 0.18
286 59 0.28
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.21
Consensus pattern (283 bp):
GAGGGGGGAGCCGGCCTCCGACACCAAGGCCGGTGTCAGCCAGCCAATCTACCGAAACAAAGCTT
ATTCATGAATAAAATTCCAGCATTCTCGGCAGGTCCAACTTCATAAAGAACACAAAGAAATACGA
CCTAGTACAGAGAAGGGAGAAACCAGCCTCCGACACCAAGGCCAGTTTCGGCCAGCCAATCTACC
GGAAAGAAGCTTATTCATGAATACAGTTCCAGCATTCTTGGCAGGTCCAACTTCGTAAAGATACA
TAAATAAATACAACCTATTATGA
Found at i:479137 original size:15 final size:15
Alignment explanation
Indices: 479097--479141 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
479087 TTTTAATTAT
*
479097 ATATATATTTTTTAA
1 ATATATATATTTTAA
* *
479112 TTTTATA-ATTTTAA
1 ATATATATATTTTAA
479126 ATATATATATTTTAA
1 ATATATATATTTTAA
479141 A
1 A
479142 ATTGTCAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATATATATTTTAA
Found at i:480049 original size:2 final size:2
Alignment explanation
Indices: 480044--480077 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
480034 TATTTGACTA
*
480044 AT AT AT AT AT GT 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
480078 CAGATCGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Done.