Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 42
Found at i:502699 original size:41 final size:41
Alignment explanation
Indices: 502608--502742 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
502598 AAAGTCAGTA
* * * ** *
502608 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
502648 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
502690 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
502731 TCGCGTTGCGAT
1 TCGCGTTGCGAT
502743 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:502713 original size:20 final size:20
Alignment explanation
Indices: 502669--502761 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
502659 ATAGTCAGTA
* **
502669 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
502690 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
502710 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
502731 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
502751 TCGCATTGCGA
1 TCGCATTGCGA
502762 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:502743 original size:41 final size:41
Alignment explanation
Indices: 502669--502764 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
502659 ATAGTCAGTA
*
502669 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
502710 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
502751 TCGCATTGCGAATT
1 TCGCATTGCGAATT
502765 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:509553 original size:19 final size:19
Alignment explanation
Indices: 509517--509552 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
509507 ATTTGTTCGT
*
509517 ATTTATTATATAATAAAAC
1 ATTTATTATAAAATAAAAC
509536 ATTTATT-TAAAATAAAA
1 ATTTATTATAAAATAAAA
509553 AATAAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTATTATAAAATAAAAC
Found at i:510726 original size:15 final size:15
Alignment explanation
Indices: 510706--510739 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
510696 TAAAAAAAAT
*
510706 TATAATATAAATATA
1 TATAATACAAATATA
510721 TATAATACAAATATA
1 TATAATACAAATATA
510736 TATA
1 TATA
510740 TAGTTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TATAATACAAATATA
Found at i:510947 original size:9 final size:9
Alignment explanation
Indices: 510933--510965 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
510923 GTGTAAACAA
*
510933 TATATAAAC
1 TATATAAAG
510942 TATATAAAG
1 TATATAAAG
510951 TAT-TAAAG
1 TATATAAAG
510959 TATATAA
1 TATATAA
510966 TTTATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (9 bp):
TATATAAAG
Found at i:511072 original size:14 final size:14
Alignment explanation
Indices: 511036--511081 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
511026 AACTATAATT
511036 TATATTATATAGA-TA
1 TATATTATA-A-ACTA
511051 TATA-TATAAACTA
1 TATATTATAAACTA
511064 TATATTATAAACTA
1 TATATTATAAACTA
511078 TATA
1 TATA
511082 AAGTGTATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.03
13 7 0.24
14 17 0.59
15 4 0.14
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (14 bp):
TATATTATAAACTA
Found at i:511494 original size:300 final size:303
Alignment explanation
Indices: 511150--511711 Score: 804
Period size: 300 Copynumber: 1.8 Consensus size: 303
511140 ATATATGTAA
*
511150 TCTATAGATTATATATATAAAGTAATAAAGTATATAGTTTATAGAAACACTATGCATAAACTATA
1 TCTATAGATTATATATATAAAGTAATAAAGTATATAGTTTATAGAAACACTATGCATAAA-TAAA
* * *
511215 -TAAGTTAAGTATATAA-TT-TAG-A-AACCTTAAAC-CCTAAAC-TATATGTATAGACACAGTT
65 GTAA-TAAAGTATATAATTTATAGAATAACCCTAAACACATAAACATATATGTATAGACACAGTT
*
511273 GATAATTCATATATAGTTATATAAAAAATAGTTTATATAAATTATATATGTAACCTTAACCTATA
129 GACAATTCA-ATATA-TTATATAAAAAATAGTTTATATAAA-T-TATATGTAACC-TAACCTATA
* * *
511338 GTC-TAAACGATGGTTAATATATGT-ACCTATAGT-TATGTATACATGTAAACTATATATGTAAC
189 GTCATAAACAATAGTTAATATATATAACCTATAGTATATGTATACATGTAAACTATATATGTAAC
511400 TTATAGTACATATAGCATAAACTATGTAGTATATATAACCTCTCTCTCTC
254 TTATAGTACATATAGCATAAACTATGTAGTATATATAACCTCTCTCTCTC
* * *
511450 TCTATATA-TATATATATTAAAGTAATAAAGTATATAGTTTATAGAAATACTATGCATATATAAA
1 TCTATAGATTATATATA-TAAAGTAATAAAGTATATAGTTTATAGAAACACTATGCATAAATAAA
*
511514 GTAATAAAGTATATAATTTATAGAAACATAACCCTAAACTATATAAACTATATATGTATAGACAC
65 GTAATAAAGTATATAATTTATAG--A-ATAACCCTAAAC-ACATAAAC-ATATATGTATAGACAC
*
511579 AGTTGACAATTCAATATATTATATAAACAATAGTTTATATAAATTATATGTAACCTAACCTATAG
125 AGTTGACAATTCAATATATTATATAAAAAATAGTTTATATAAATTATATGTAACCTAACCTATAG
511644 TCTATAAACAATAGTTAATATATATAACCTATAGTATATGTATACATGTAAACTATATATGTAAC
190 TC-ATAAACAATAGTTAATATATATAACCTATAGTATATGTATACATGTAAACTATATATGTAAC
511709 TTA
254 TTA
511712 ATGTATGTAT
Statistics
Matches: 232, Mismatches: 13, Indels: 25
0.86 0.05 0.09
Matches are distributed among these distances:
299 22 0.09
300 53 0.23
301 3 0.01
305 13 0.06
306 20 0.09
307 19 0.08
308 38 0.16
309 37 0.16
310 27 0.12
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (303 bp):
TCTATAGATTATATATATAAAGTAATAAAGTATATAGTTTATAGAAACACTATGCATAAATAAAG
TAATAAAGTATATAATTTATAGAATAACCCTAAACACATAAACATATATGTATAGACACAGTTGA
CAATTCAATATATTATATAAAAAATAGTTTATATAAATTATATGTAACCTAACCTATAGTCATAA
ACAATAGTTAATATATATAACCTATAGTATATGTATACATGTAAACTATATATGTAACTTATAGT
ACATATAGCATAAACTATGTAGTATATATAACCTCTCTCTCTC
Found at i:511732 original size:15 final size:15
Alignment explanation
Indices: 511712--511794 Score: 73
Period size: 14 Copynumber: 5.7 Consensus size: 15
511702 ATGTAACTTA
*
511712 ATGTATGTATAAACT
1 ATGTATATATAAACT
511727 ATGTATATATAAACT
1 ATGTATATATAAACT
* *
511742 ATATATATATATA-T
1 ATGTATATATAAACT
* *
511756 ATATATATATATA-T
1 ATGTATATATAAACT
* *
511770 ATATATATATATA-T
1 ATGTATATATAAACT
*
511784 ATATATATATA
1 ATGTATATATA
511795 TATATATACC
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
14 40 0.62
15 25 0.38
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (15 bp):
ATGTATATATAAACT
Found at i:511737 original size:2 final size:2
Alignment explanation
Indices: 511730--511823 Score: 134
Period size: 2 Copynumber: 46.0 Consensus size: 2
511720 ATAAACTATG
*
511730 TA TA TA TA AA CTA 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 TA TA TA TA TA
** *
511773 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CC TA TA GTA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
511816 TA TA TA TA
1 TA TA TA TA
511824 CAATCTATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
2 79 0.96
3 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:511871 original size:13 final size:13
Alignment explanation
Indices: 511853--511884 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
511843 ATATGTAACC
511853 TATATATATATTA
1 TATATATATATTA
*
511866 TGTATATATATTA
1 TATATATATATTA
511879 TATATA
1 TATATA
511885 CAATCTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
TATATATATATTA
Found at i:513353 original size:7 final size:7
Alignment explanation
Indices: 513343--513373 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
513333 TTTAAGTTTT
513343 GGTCAAC
1 GGTCAAC
513350 GGTCAAC
1 GGTCAAC
513357 GGTC-AC
1 GGTCAAC
513363 GGTCAAC
1 GGTCAAC
513370 GGTC
1 GGTC
513374 GGGTCGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (7 bp):
GGTCAAC
Found at i:513366 original size:13 final size:14
Alignment explanation
Indices: 513343--513373 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
513333 TTTAAGTTTT
513343 GGTCAACGGTCAAC
1 GGTCAACGGTCAAC
513357 GGTC-ACGGTCAAC
1 GGTCAACGGTCAAC
513370 GGTC
1 GGTC
513374 GGGTCGGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.23, C:0.29, G:0.32, T:0.16
Consensus pattern (14 bp):
GGTCAACGGTCAAC
Found at i:513427 original size:10 final size:9
Alignment explanation
Indices: 513390--513460 Score: 61
Period size: 9 Copynumber: 7.3 Consensus size: 9
513380 GGTTGGGTCG
*
513390 GGTCAGACC
1 GGTCAAACC
513399 GGTCAAACC
1 GGTCAAACC
*
513408 GGTTCGAACC
1 GG-TCAAACC
513418 GGTCGAAACC
1 GGTC-AAACC
*
513428 AGTCATAACC
1 GGTCA-AACC
*
513438 GGTTGAAAACC
1 GG-T-CAAACC
513449 GGTCAAACC
1 GGTCAAACC
513458 GGT
1 GGT
513461 TTCCAGCCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
9 21 0.42
10 21 0.42
11 7 0.14
12 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:513439 original size:30 final size:28
Alignment explanation
Indices: 513390--513457 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 28
513380 GGTTGGGTCG
* *
513390 GGTCAGACCGGTCAAACCGGTTCG-AACC
1 GGTCAAACCAGTCAAACCGGTT-GAAACC
513418 GGTCGAAACCAGTCATAACCGGTTGAAAACC
1 GGTC-AAACCAGTCA-AACCGGTTG-AAACC
513449 GGTCAAACC
1 GGTCAAACC
513458 GGTTTCCAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 4 0.12
29 9 0.26
30 13 0.38
31 8 0.24
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (28 bp):
GGTCAAACCAGTCAAACCGGTTGAAACC
Found at i:513461 original size:20 final size:19
Alignment explanation
Indices: 513390--513461 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
513380 GGTTGGGTCG
* *
513390 GGTCAGACCGG-TCAAACC
1 GGTCAAACCGGTTGAAACC
* *
513408 GGTTCGAACCGGTCGAAACC
1 GG-TCAAACCGGTTGAAACC
*
513428 AGTCATAACCGGTTGAAAACC
1 GGTCA-AACCGGTTG-AAACC
513449 GGTCAAACCGGTT
1 GGTCAAACCGGTT
513462 TCCAGCCCTC
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
18 2 0.05
19 9 0.21
20 22 0.52
21 9 0.21
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTGAAACC
Found at i:514222 original size:21 final size:21
Alignment explanation
Indices: 514193--514258 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
514183 TTTATATTAG
* * *
514193 TATACTATATAGTTTATAACC
1 TATAGTATATAATTTATAAAC
514214 TATAGTATATAATTTATAAAC
1 TATAGTATATAATTTATAAAC
* * *
514235 TATAGTTTAT-ATTAATATAC
1 TATAGTATATAATTTATAAAC
514255 TATA
1 TATA
514259 TAGTTTATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 12 0.31
21 27 0.69
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (21 bp):
TATAGTATATAATTTATAAAC
Found at i:514240 original size:57 final size:56
Alignment explanation
Indices: 514164--514329 Score: 196
Period size: 57 Copynumber: 3.0 Consensus size: 56
514154 GTATGTAACC
* * * *
514164 TATAGTTTATAAACAATAGTTTATATTAGTATACTATATAGTTTATAACCTATAGTA
1 TATAATTTATAAACTATAGTTTATATTAATATACTATATAGTTTATAA-CTATAATA
*
514221 TATAATTTATAAACTATAGTTTATATTAATATACTATATAGTTTAT-A-T-TAATG
1 TATAATTTATAAACTATAGTTTATATTAATATACTATATAGTTTATAACTATAATA
* * * *
514274 T-TAATTATCTTAACTATAATTTATATTAATATAGTATATAGTTTATAAACTATAAT
1 TATAATT-TATAAACTATAGTTTATATTAATATACTATATAGTTTAT-AACTATAAT
514330 TTGTATTAAT
Statistics
Matches: 95, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
52 5 0.05
53 39 0.41
54 1 0.01
55 1 0.01
56 2 0.02
57 47 0.49
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (56 bp):
TATAATTTATAAACTATAGTTTATATTAATATACTATATAGTTTATAACTATAATA
Found at i:514306 original size:15 final size:15
Alignment explanation
Indices: 514256--514306 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
514246 TTAATATACT
*
514256 ATATAGTTTATATTA
1 ATATAATTTATATTA
* *
514271 ATGTTAA-TTATCTTA
1 AT-ATAATTTATATTA
514286 ACTATAATTTATATTA
1 A-TATAATTTATATTA
514302 ATATA
1 ATATA
514307 GTATATAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:514325 original size:36 final size:36
Alignment explanation
Indices: 514285--514363 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
514275 TAATTATCTT
*
514285 AACTATAATTTATATTAATATAGTATATAGTTTATA
1 AACTATAATTTATATTAATATAGTAGATAGTTTATA
* *
514321 AACTATAATTTGTATTAATGTAGTAGATAGTTTATA
1 AACTATAATTTATATTAATATAGTAGATAGTTTATA
514357 AACTATA
1 AACTATA
514364 GTAACATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (36 bp):
AACTATAATTTATATTAATATAGTAGATAGTTTATA
Found at i:514421 original size:18 final size:15
Alignment explanation
Indices: 514381--514424 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 15
514371 TAATATTAAC
514381 ATATTAATTATAGTTT
1 ATATTAA-TATAGTTT
514397 ATATTAATATAGTATAT
1 ATATTAATATAGT-T-T
514414 AGTATTAATAT
1 A-TATTAATAT
514425 TAATTATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.24
16 8 0.32
17 2 0.08
18 9 0.36
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
ATATTAATATAGTTT
Found at i:514424 original size:24 final size:24
Alignment explanation
Indices: 514369--514439 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 24
514359 CTATAGTAAC
* *
514369 ATTAATATTAACATATTAATTATAGT
1 ATTAATATTAATATAGT-A-TATAGT
514395 -TT-ATATTAATATAGTATATAGT
1 ATTAATATTAATATAGTATATAGT
514417 ATTAATATTAATTATAGTATATA
1 ATTAATATTAA-TATAGTATATA
514440 AACCTTAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 6 0.15
23 3 0.08
24 18 0.45
25 13 0.32
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.48
Consensus pattern (24 bp):
ATTAATATTAATATAGTATATAGT
Found at i:514432 original size:18 final size:18
Alignment explanation
Indices: 514398--514436 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
514388 TTATAGTTTA
*
514398 TATTAATATAGTATATAG
1 TATTAATATAATATATAG
514416 TATTAATATTAAT-TATAG
1 TATTAATA-TAATATATAG
514434 TAT
1 TAT
514437 ATAAACCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (18 bp):
TATTAATATAATATATAG
Found at i:514549 original size:32 final size:31
Alignment explanation
Indices: 514499--514562 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
514489 TACTATATAA
514499 TTTATAAAATATAGTTTATATTTAATATCAAT
1 TTTATAAAATATAGTTTATA-TTAATATCAAT
* * * *
514531 TTTATAGACTATATTTTATATTAATATTAAT
1 TTTATAAAATATAGTTTATATTAATATCAAT
514562 T
1 T
514563 ACAAATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTATAAAATATAGTTTATATTAATATCAAT
Found at i:514589 original size:34 final size:34
Alignment explanation
Indices: 514532--514667 Score: 131
Period size: 34 Copynumber: 4.0 Consensus size: 34
514522 AATATCAATT
* *
514532 TTATAGACTATATTTTATATTAATATTAATTACAAA
1 TTATAAACTATA--TTATATTAATATTAATTATAAA
*
514568 TTATAAACTATATTATATTAATA-TAAGTTA-ATA
1 TTATAAACTATATTATATTAATATTAA-TTATAAA
* * *
514601 TTA-ATATTA-ATTATATTAATATTAA-TATTAA
1 TTATAAACTATATTATATTAATATTAATTATAAA
514632 TTATAATA-TATAATTATATTAATATTAATTATAAA
1 TTATAA-ACTAT-ATTATATTAATATTAATTATAAA
514667 T
1 T
514668 AGTTTATTAA
Statistics
Matches: 84, Mismatches: 8, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
30 2 0.02
31 16 0.19
32 10 0.12
33 9 0.11
34 30 0.36
35 6 0.07
36 11 0.13
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (34 bp):
TTATAAACTATATTATATTAATATTAATTATAAA
Found at i:514603 original size:16 final size:14
Alignment explanation
Indices: 514579--514664 Score: 73
Period size: 15 Copynumber: 5.4 Consensus size: 14
514569 TATAAACTAT
514579 ATTATATTAATATA
1 ATTATATTAATATA
514593 AGTTAATATTAATATTA
1 A-TT-ATATTAATA-TA
514610 ATTATATTAATATTAA
1 ATTATATTAATA-T-A
*
514626 TATTAATTATAATATATA
1 -ATT-A-TATTA-ATATA
514644 ATTATATTAATATTA
1 ATTATATTAATA-TA
514659 ATTATA
1 ATTATA
514665 AATAGTTTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 17
0.76 0.03 0.21
Matches are distributed among these distances:
14 4 0.07
15 25 0.41
16 13 0.21
17 9 0.15
18 2 0.03
19 5 0.08
20 3 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (14 bp):
ATTATATTAATATA
Found at i:514603 original size:21 final size:20
Alignment explanation
Indices: 514577--514662 Score: 86
Period size: 21 Copynumber: 4.0 Consensus size: 20
514567 ATTATAAACT
514577 ATATTATATTAATATAAGTTA
1 ATATTATATTAATATAA-TTA
514598 ATATTAATATTAAT-TATATTA
1 ATATT-ATATTAATATA-ATTA
514619 ATATTAATATTAATTATAA-TA
1 ATATT-ATATTAA-TATAATTA
514640 TATAATTATATTAATATTAATTA
1 -AT-ATTATATTAATA-TAATTA
514663 TAAATAGTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 14
0.80 0.00 0.20
Matches are distributed among these distances:
21 27 0.47
22 23 0.40
23 7 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (20 bp):
ATATTATATTAATATAATTA
Found at i:514604 original size:6 final size:6
Alignment explanation
Indices: 514577--514660 Score: 71
Period size: 6 Copynumber: 15.3 Consensus size: 6
514567 ATTATAAACT
*
514577 ATATT- ATATTA ATA-TA A-GTTA ATATTA ATATT- A-ATT- ATATTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
514619 ATATTA ATATTA AT-TATA ATA-T- ATAATT- ATATTA ATATTA AT
1 ATATTA ATATTA ATAT-TA ATATTA AT-ATTA ATATTA ATATTA AT
514661 TATAAATAGT
Statistics
Matches: 67, Mismatches: 2, Indels: 19
0.76 0.02 0.22
Matches are distributed among these distances:
4 6 0.09
5 21 0.31
6 40 0.60
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:514690 original size:49 final size:49
Alignment explanation
Indices: 514576--514678 Score: 121
Period size: 49 Copynumber: 2.2 Consensus size: 49
514566 AATTATAAAC
514576 TATATT-A-TATTA-ATATAAGTTAATATTAATATTAATTATATTAATAT
1 TATATTAATTATTATATATAAGTTAATATTAATATTAATTATA-TAATAT
*
514623 TAATATTAATTATAATATATAA-TT-ATATTAATATTAATTATA-AATAGT
1 T-ATATTAATTATTATATATAAGTTAATATTAATATTAATTATATAATA-T
514671 T-TATTAAT
1 TATATTAAT
514679 ATAAATTATA
Statistics
Matches: 50, Mismatches: 1, Indels: 11
0.81 0.02 0.18
Matches are distributed among these distances:
46 7 0.14
47 5 0.10
48 7 0.14
49 19 0.38
50 6 0.12
51 6 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (49 bp):
TATATTAATTATTATATATAAGTTAATATTAATATTAATTATATAATAT
Found at i:515378 original size:6 final size:6
Alignment explanation
Indices: 515367--515408 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
515357 CATCTTCTAT
*
515367 CCCAAA CCCAAA CCCAAA CCCAAA CTCAAA CCCAAA CCCAAA
1 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA
515409 TATGAACCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.50, C:0.48, G:0.00, T:0.02
Consensus pattern (6 bp):
CCCAAA
Found at i:515416 original size:18 final size:17
Alignment explanation
Indices: 515375--515428 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
515365 ATCCCAAACC
515375 CAAACCCAAACCCAAACT
1 CAAACCCAAACCCAAA-T
515393 CAAACCCAAACCCAAAT
1 CAAACCCAAACCCAAAT
*
515410 -ATGAACCCGAACCCAAAT
1 CA--AACCCAAACCCAAAT
515428 C
1 C
515429 TGATCCAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 1 0.03
17 1 0.03
18 30 0.94
ACGTcount: A:0.48, C:0.41, G:0.04, T:0.07
Consensus pattern (17 bp):
CAAACCCAAACCCAAAT
Found at i:515474 original size:18 final size:18
Alignment explanation
Indices: 515367--515480 Score: 63
Period size: 18 Copynumber: 6.1 Consensus size: 18
515357 CATCTTCTAT
* *
515367 CCCAAACCCAAACCCAAA
1 CCCAAATCCAAACCCGAA
*
515385 CCCAAA-CTCAAACCCAAA
1 CCCAAATC-CAAACCCGAA
***
515403 CCCAAATATGAACCCGAA
1 CCCAAATCCAAACCCGAA
515421 CCCAAATCTGATCCAAA-CCGAA
1 CCC-AA----ATCCAAACCCGAA
** *
515443 CCTGAA-CCTGAACCCGAA
1 CCCAAATCC-AAACCCGAA
515461 CCCAAATCCAAACCCGAA
1 CCCAAATCCAAACCCGAA
515479 CC
1 CC
515481 TAAAAAACCC
Statistics
Matches: 73, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
16 2 0.03
17 4 0.05
18 51 0.70
19 4 0.05
21 1 0.01
22 7 0.10
23 4 0.05
ACGTcount: A:0.43, C:0.42, G:0.07, T:0.08
Consensus pattern (18 bp):
CCCAAATCCAAACCCGAA
Found at i:515922 original size:39 final size:39
Alignment explanation
Indices: 515879--516004 Score: 105
Period size: 39 Copynumber: 3.2 Consensus size: 39
515869 TCGTTAGTTG
*
515879 CCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTCGTAGT
1 CCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTAGTAGT
* * * ** * *
515918 CCTTGTTTGTGTAGCTGA-TGGTTGTA-TAGGGTCGTTAGTTG-
1 CCTTG-TT-AGCAGCT-ACT-GTT-TATTTGTTTCCTTAGTAGT
*
515959 CCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTTGTAGT
1 CCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTAGTAGT
515998 CCTTGTT
1 CCTTGTT
516005 TGTGTAGCTG
Statistics
Matches: 63, Mismatches: 16, Indels: 16
0.66 0.17 0.17
Matches are distributed among these distances:
37 2 0.03
38 13 0.21
39 18 0.29
40 4 0.06
41 11 0.17
42 13 0.21
43 2 0.03
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (39 bp):
CCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTAGTAGT
Found at i:516022 original size:80 final size:80
Alignment explanation
Indices: 515855--516014 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
515845 TTCGTTGGGA
515855 ATGGTTGTATAGGGTCGTTAGTTGCCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTCGTAGTCC
1 ATGGTTGTATAGGGTCGTTAGTTGCCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTCGTAGTCC
515920 TTGTTTGTGTAGCTG
66 TTGTTTGTGTAGCTG
*
515935 ATGGTTGTATAGGGTCGTTAGTTGCCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTTGTAGTCC
1 ATGGTTGTATAGGGTCGTTAGTTGCCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTCGTAGTCC
516000 TTGTTTGTGTAGCTG
66 TTGTTTGTGTAGCTG
516015 TTTGTTGTTC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.47
Consensus pattern (80 bp):
ATGGTTGTATAGGGTCGTTAGTTGCCTTGTTAGCAGCTACTGTTTATTTGTTTCCTTCGTAGTCC
TTGTTTGTGTAGCTG
Found at i:516823 original size:21 final size:20
Alignment explanation
Indices: 516776--516823 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
516766 CTTTAAGTTT
*
516776 GTGAAAAAGATGACATGTGA
1 GTGAAAAAGATGACATGCGA
516796 GTGAAAAAGATGACATGCGA
1 GTGAAAAAGATGACATGCGA
516816 GTGAAAAA
1 GTGAAAAA
516824 AAGCATTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.48, C:0.06, G:0.29, T:0.17
Consensus pattern (20 bp):
GTGAAAAAGATGACATGCGA
Found at i:518499 original size:19 final size:19
Alignment explanation
Indices: 518475--518517 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
518465 TTCTGTAAGG
518475 GTTTGGTAAAGTCAGAAAT
1 GTTTGGTAAAGTCAGAAAT
518494 GTTTGGTAAAGTCAGAAAT
1 GTTTGGTAAAGTCAGAAAT
518513 GTTTG
1 GTTTG
518518 ACACTGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.35
Consensus pattern (19 bp):
GTTTGGTAAAGTCAGAAAT
Found at i:519196 original size:21 final size:21
Alignment explanation
Indices: 519170--519212 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
519160 TTATTTTGTA
*
519170 TTTACATAAATTAAATTATAT
1 TTTACATAAATTAAACTATAT
519191 TTTACATAAATTAAACTATAT
1 TTTACATAAATTAAACTATAT
519212 T
1 T
519213 AATTTACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTACATAAATTAAACTATAT
Found at i:519329 original size:30 final size:29
Alignment explanation
Indices: 519293--519360 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
519283 AATTTTATTA
519293 ATTTTATTAA-ATAATTTTAT-ATAATAAAT
1 ATTTTATTAATATAA--TTATCATAATAAAT
*
519322 ATATTTATTAATTTAATTATCATAATAAAT
1 AT-TTTATTAATATAATTATCATAATAAAT
519352 ATTTTATTA
1 ATTTTATTA
519361 TAACATTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 13 0.37
30 19 0.54
31 3 0.09
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTTTATTAATATAATTATCATAATAAAT
Found at i:519334 original size:48 final size:48
Alignment explanation
Indices: 519243--519340 Score: 112
Period size: 48 Copynumber: 2.0 Consensus size: 48
519233 TCAATGCCAA
* *
519243 TAATTTTATTAATCATATTTTATATAATTTACATTTAAATAATTTTAT
1 TAATTTTATTAATCATATTTTATATAATATACATTTAAATAATTTAAT
* *
519291 TAATTTTATTAA--ATAATTTTATATAATAAATATATTT-ATTAATTTAAT
1 TAATTTTATTAATCAT-ATTTTATATAAT--ATACATTTAAATAATTTAAT
519339 TA
1 TA
519341 TCATAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
46 2 0.05
47 12 0.28
48 23 0.53
49 6 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (48 bp):
TAATTTTATTAATCATATTTTATATAATATACATTTAAATAATTTAAT
Found at i:519501 original size:16 final size:16
Alignment explanation
Indices: 519454--519513 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
519444 CGTCCATGGT
*
519454 AATATACAATTCAGGTA
1 AATAT-CAAGTCAGGTA
* *
519471 AATGTCAAGTTAGGTA
1 AATATCAAGTCAGGTA
*
519487 AATATC-AGATCAGGTC
1 AATATCAAG-TCAGGTA
*
519503 AATAACAAGTC
1 AATATCAAGTC
519514 GGATCATTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 2 0.06
16 26 0.76
17 6 0.18
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (16 bp):
AATATCAAGTCAGGTA
Found at i:520601 original size:36 final size:36
Alignment explanation
Indices: 520516--520775 Score: 299
Period size: 36 Copynumber: 7.2 Consensus size: 36
520506 AAAGATGAAC
* *
520516 ACTTGAACCGGAAGTGCCGATGCTT-CCTCCCGTTC-
1 ACTTGAATCGGAAGTGCCGATGCTTCCCT-CCATTCG
* * *
520551 ACTTGAATCGGAAGTGCCGATGCTTACTTTCATTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCCTCCATTCG
* * *
520587 ATTTGAATCTGAAGTGCTGATGCTTCCCTCCATTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCCTCCATTCG
* * *
520623 ATTTGAATCGGAAGTGCCAATGCTTCCCTCCTTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCCTCCATTCG
* **
520659 ATTTGAATCGGAAGTGCCGATGCTTCCCTCTGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCCTCCATTCG
* * *
520695 ACTTGAATTGGAAGTGCCGATCCTTCCCTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCCTCCATTCG
* * * * *
520731 ACTTGAAACAGAAGTGTCGATGCTTACCTCTATTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCCTCCATTCG
520767 ACTTGAATC
1 ACTTGAATC
520776 AATGCAAACT
Statistics
Matches: 193, Mismatches: 30, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
35 28 0.15
36 165 0.85
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCCTCCATTCG
Found at i:531801 original size:15 final size:15
Alignment explanation
Indices: 531781--531849 Score: 78
Period size: 13 Copynumber: 5.0 Consensus size: 15
531771 TAATAAGGTT
531781 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
531796 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
531811 ATTTA--TTATAAT-
1 ATTTATTTTAAAATA
531823 -TTTATTTTAAAA-A
1 ATTTATTTTAAAATA
*
531836 A-TTATTATAAAATA
1 ATTTATTTTAAAATA
531850 TGAATTGATT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
11 4 0.09
13 21 0.46
14 1 0.02
15 20 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:531894 original size:32 final size:32
Alignment explanation
Indices: 531848--532228 Score: 199
Period size: 32 Copynumber: 12.7 Consensus size: 32
531838 TATTATAAAA
*
531848 TATGAATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
531880 TATGGATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
531902 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
531934 TATGAATTGATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
531956 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
**
531988 TATGGATTGATTTATTTTAAA-ATATGGATT-G
1 TATGGATTGATTTATTTTAAATA-ATTTATTAG
** * * *
532019 -ATTTATT-ATTGTAGTTGTATGGATTGATTTATT--
1 TATGGATTGATT-TA-TT-T-T-AAATAATTTATTAG
* * * * * * *
532052 T-T-AAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATT--T-T-AAATAATTTA--TT--AG
*
532090 TATGAATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
* *
532122 TAT--A--GATTTA-TTT--AT--TTTA-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAG
532144 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
532176 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
532208 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
532229 ATATGGATTG
Statistics
Matches: 277, Mismatches: 24, Indels: 96
0.70 0.06 0.24
Matches are distributed among these distances:
22 31 0.11
23 12 0.04
24 1 0.00
25 4 0.01
26 12 0.04
27 6 0.02
28 12 0.04
29 7 0.03
30 8 0.03
31 18 0.06
32 130 0.47
33 5 0.02
34 10 0.04
36 7 0.03
37 1 0.00
38 2 0.01
39 1 0.00
40 10 0.04
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:531895 original size:54 final size:54
Alignment explanation
Indices: 531837--532260 Score: 388
Period size: 54 Copynumber: 7.8 Consensus size: 54
531827 TTTTAAAAAA
* *
531837 TTATTATAAAATATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
*
531891 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
531945 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
*
531999 TTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGAT
** ** * ** * * * *
532047 TTATTTT-AAATAATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGAATTGAT
1 TTATTTTAAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGAT
** * * ** * * *
532101 TTATTTT-AAATAATTTATT-AGTATAGATTTATTTATTTTA-AAATATGGATTGAT
1 TTATTTTAAAAT-ATGGATTGA-TTTA-TTTTAAATAATTTATTAGTATGGATTGAT
532155 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTA-TTT---TAA---A--A-TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
532219 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
532261 TTGTAGTTGT
Statistics
Matches: 316, Mismatches: 28, Indels: 52
0.80 0.07 0.13
Matches are distributed among these distances:
47 4 0.01
48 27 0.09
49 3 0.01
50 5 0.02
51 2 0.01
52 4 0.01
53 1 0.00
54 217 0.69
55 7 0.02
57 1 0.00
58 1 0.00
59 1 0.00
60 3 0.01
62 1 0.00
63 13 0.04
64 24 0.08
65 2 0.01
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (54 bp):
TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
Found at i:531905 original size:22 final size:22
Alignment explanation
Indices: 531880--531922 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
531870 AATTTATTAG
531880 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
531902 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
531923 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:531959 original size:22 final size:22
Alignment explanation
Indices: 531934--531976 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
531924 AATTTATTAG
531934 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
531956 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
531977 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:532056 original size:80 final size:80
Alignment explanation
Indices: 531956--532105 Score: 291
Period size: 80 Copynumber: 1.9 Consensus size: 80
531946 TATTTTAAAA
*
531956 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
532021 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
532036 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
532101 TTATT
66 TTATT
532106 TTAAATAATT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
TTATTATTGTAGTTG
Found at i:532059 original size:188 final size:188
Alignment explanation
Indices: 531848--532196 Score: 655
Period size: 188 Copynumber: 1.9 Consensus size: 188
531838 TATTATAAAA
*
531848 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
531913 TTATTTTAAATAATTTATTAGTAT-GAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAA
66 TTATTTTAAATAATTTATTAGTATAG-ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAA
531977 TAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
130 TAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
*
532036 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
1 TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
*
532101 TTATTTTAAATAATTTATTAGTATAGATTTATTTATTTTAAAATATGGATTGATTTATTTTAAAT
66 TTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAT
532166 AATTTATTAGTATGGATTGATTTATTTTAAA
131 AATTTATTAGTATGGATTGATTTATTTTAAA
532197 TAATTTATTA
Statistics
Matches: 157, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
188 156 0.99
189 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (188 bp):
TATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
TTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAT
AATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
Found at i:532093 original size:22 final size:22
Alignment explanation
Indices: 532068--532164 Score: 77
Period size: 22 Copynumber: 4.0 Consensus size: 22
532058 AATTTATTAG
532068 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
532090 TATGAATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* *
532114 TTTATTAGTATAGATTTATTTATTTTAAAA
1 --TA-T-GGATTGATTTA----TTTTAAAA
532144 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
532165 TAATTTATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
22 24 0.40
23 2 0.03
24 2 0.03
26 11 0.18
27 2 0.03
28 11 0.18
30 2 0.03
31 2 0.03
32 4 0.07
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:532190 original size:18 final size:18
Alignment explanation
Indices: 532167--532223 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
532157 ATTTTAAATA
532167 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
* * *
532185 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGGATTG
532199 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
532217 ATTTATT
1 ATTTATT
532224 TTAAAATATG
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 9 0.31
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.55
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGGATTG
Found at i:532233 original size:22 final size:22
Alignment explanation
Indices: 532208--532250 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
532198 AATTTATTAG
532208 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
532230 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
532251 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:532310 original size:31 final size:31
Alignment explanation
Indices: 532275--532333 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
532265 AGTTGTATGG
532275 ATTATTTAAATTTCAATATTGTAAAACTAAA
1 ATTATTTAAATTTCAATATTGTAAAACTAAA
*
532306 ATTATTTAAATTTCAGTATTGTAAAACT
1 ATTATTTAAATTTCAATATTGTAAAACT
532334 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTGTAAAACTAAA
Found at i:534554 original size:37 final size:40
Alignment explanation
Indices: 534512--534588 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
534502 ATTAACTTTT
* *
534512 TAATATTTTCGG-TG-GAA-CAAAAATATTATGAAGAATG
1 TAATATTTTCGGTTGCCAACCAAAAATAGTATGAAGAATG
*
534549 TAATATTTTCGGTTGCCAACCAAAAATGGTATGAAGAATG
1 TAATATTTTCGGTTGCCAACCAAAAATAGTATGAAGAATG
534589 CATGCAACCG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 12 0.35
38 2 0.06
39 2 0.06
40 18 0.53
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (40 bp):
TAATATTTTCGGTTGCCAACCAAAAATAGTATGAAGAATG
Found at i:535027 original size:2 final size:2
Alignment explanation
Indices: 535015--535048 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
535005 CAATCCTTTT
*
535015 TA TA AA 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 TA
535049 AAGTTTTATT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:537472 original size:23 final size:22
Alignment explanation
Indices: 537405--537473 Score: 59
Period size: 26 Copynumber: 2.9 Consensus size: 22
537395 AATTTAACTT
537405 AAACAATTATCTTTTAATTTTAA
1 AAACAATTATC-TTTAATTTTAA
*
537428 AAA-AATATAATATTACATAATTTTAA
1 AAACAAT-T-ATCTT---TAATTTTAA
537454 AAACAATTATCTTTGAATTT
1 AAACAATTATCTTT-AATTT
537474 AACATAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
22 4 0.11
23 11 0.30
24 2 0.05
25 4 0.11
26 13 0.35
27 3 0.08
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.43
Consensus pattern (22 bp):
AAACAATTATCTTTAATTTTAA
Found at i:550118 original size:21 final size:21
Alignment explanation
Indices: 550093--550132 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
550083 GAGAAATTGT
550093 TTTCAAAATAT-AAAAATGATG
1 TTTCAAAAT-TGAAAAATGATG
550114 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
550133 AAATAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATG
Found at i:553950 original size:20 final size:19
Alignment explanation
Indices: 553925--553980 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
553915 TTTTGGTGCA
553925 GAGGGAATCGATACCCTCAT
1 GAGGGAATCGATACCC-CAT
* * *
553945 GAGGGAACCGATTCCCCCT
1 GAGGGAATCGATACCCCAT
553964 -AGGGGAATCGATACCCC
1 GA-GGGAATCGATACCCC
553981 CTGGGGTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.50
20 14 0.47
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
GAGGGAATCGATACCCCAT
Found at i:558278 original size:18 final size:18
Alignment explanation
Indices: 558246--558284 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
558236 GTCCTTCGAA
*
558246 ACATAGTGGTACTTCAGG
1 ACATAGTGATACTTCAGG
* *
558264 ACATAGTGATCCTTCGGG
1 ACATAGTGATACTTCAGG
558282 ACA
1 ACA
558285 AATATTCAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (18 bp):
ACATAGTGATACTTCAGG
Found at i:562966 original size:22 final size:22
Alignment explanation
Indices: 562941--562991 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
562931 CTACAGCAAC
*
562941 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATATCCGACGAA
*
562963 ATCCGTCCCCATATCCGGCGAA
1 ATCCGTCCCCATATCCGACGAA
562985 ATCCGTC
1 ATCCGTC
562992 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATATCCGACGAA
Found at i:563353 original size:20 final size:20
Alignment explanation
Indices: 563330--563373 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
563320 AAACTTAAAT
563330 TCGCAACACGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
**
563350 TCGCAATGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
563370 TCGC
1 TCGC
563374 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.14
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:565208 original size:42 final size:42
Alignment explanation
Indices: 565117--565208 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
565107 TGGTGCATGG
**
565117 CGTGATGACATACGGTCTTTACGTGGTGAGGTAGAGGTTTTA
1 CGTGATGACATACGGTCTTTACGTGGTGAGGTAGAGACTTTA
* * ***
565159 CGCGATGACA-ATGGTGCTTTACGTGGTGAGGTATCTACTTTA
1 CGTGATGACATACGGT-CTTTACGTGGTGAGGTAGAGACTTTA
565201 CGTGATGA
1 CGTGATGA
565209 GATAGCTGCT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 4 0.10
42 37 0.90
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.33
Consensus pattern (42 bp):
CGTGATGACATACGGTCTTTACGTGGTGAGGTAGAGACTTTA
Found at i:565513 original size:21 final size:21
Alignment explanation
Indices: 565487--565585 Score: 119
Period size: 21 Copynumber: 4.7 Consensus size: 21
565477 AATTCACTTG
*
565487 TCATCGTTCAAGAGGCCTCTCA
1 TCATCGTTCAAGAGGCCCCT-A
* *
565509 T-ATCGTTCAAGAGACCTCTA
1 TCATCGTTCAAGAGGCCCCTA
* *
565529 TCATCCTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* *
565550 CCATCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTA
565571 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
565586 TTCCTTCAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
20 2 0.03
21 64 0.96
22 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:565539 original size:42 final size:42
Alignment explanation
Indices: 565487--565585 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
565477 AATTCACTTG
* * *
565487 TCATCGTTCAAGAGGCCTCTCATATCGTTCAAGAGACCTCTA
1 TCATCGTTCAAGAGGCCCCTCACATCGTTCAAGAGACCCCTA
* * * *
565529 TCATCCTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTCACATCGTTCAAGAGACCCCTA
565571 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
565586 TTCCTTCAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.25
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCACATCGTTCAAGAGACCCCTA
Found at i:565600 original size:42 final size:40
Alignment explanation
Indices: 565485--565605 Score: 116
Period size: 42 Copynumber: 2.9 Consensus size: 40
565475 CCAATTCACT
*
565485 TGTCATCGTTCAAGAGGCCTCTCATATCGTTCAAGAGACCTC
1 TGTCATCGTTCAAGAGGCCT-TCA-ATCGTTCAAGAGACCCC
* * * * *
565527 TATCATCCTTCAAGAGGCCCCTCCCATCGTTCAAGAGGCCCC
1 TGTCATCGTTCAAGAGG--CCTTCAATCGTTCAAGAGACCCC
* *
565569 TGTCATCGTTCAAGAGGTTCCTTCAACCGTTCGAGAG
1 TGTCATCGTTCAAGAGG--CCTTCAATCGTTCAAGAG
565606 CCCAATTCAC
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 59 0.94
43 1 0.02
44 3 0.05
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.26
Consensus pattern (40 bp):
TGTCATCGTTCAAGAGGCCTTCAATCGTTCAAGAGACCCC
Found at i:567031 original size:64 final size:64
Alignment explanation
Indices: 566949--567097 Score: 235
Period size: 64 Copynumber: 2.3 Consensus size: 64
566939 AAATTGATGT
*
566949 ATTTGTAAAAGTTAATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
* * *** *
567013 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGTTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
567077 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
567098 GTTTTAAATT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 78 1.00
ACGTcount: A:0.30, C:0.01, G:0.17, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTG
Found at i:569824 original size:12 final size:12
Alignment explanation
Indices: 569803--569836 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
569793 GGTTGTGGGT
*
569803 TTTGAGATTGTG
1 TTTGATATTGTG
569815 TTTGATATTGTG
1 TTTGATATTGTG
*
569827 TTTGGTATTG
1 TTTGATATTG
569837 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:570634 original size:20 final size:19
Alignment explanation
Indices: 570590--570718 Score: 75
Period size: 20 Copynumber: 6.5 Consensus size: 19
570580 CAAAACATTT
*
570590 GTGTTGCGAAACTAAAA-C
1 GTGTTGCGAAATTAAAATC
*
570608 CTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAA-TC
570628 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATT--AAAATC
* **
570648 GAGTTGCGAAAACAAAATTC
1 GTGTTGCGAAATTAAAA-TC
**
570668 ACGTTGCG-AATTCAGAAATC
1 GTGTTGCGAAATT-A-AAATC
* * *
570688 GAGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATT-AAAATC
570708 AGTGTTGCGAA
1 -GTGTTGCGAA
570719 TTTGGAAATC
Statistics
Matches: 85, Mismatches: 16, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
18 15 0.18
19 10 0.12
20 38 0.45
21 22 0.26
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:570738 original size:20 final size:20
Alignment explanation
Indices: 570672--570786 Score: 101
Period size: 20 Copynumber: 5.7 Consensus size: 20
570662 AAATTCACGT
** * *
570672 TGCGAATTCAGAAATCGAGT
1 TGCGAATTTGGAAATCGCGC
* *
570692 TGCGAATTT-GAAATTCAGTGT
1 TGCGAATTTGGAAA-TC-GCGC
570713 TGCGAATTTGGAAATCGCGC
1 TGCGAATTTGGAAATCGCGC
*
570733 TGCGAATTTGGAAATCGCAAC
1 TGCGAATTTGGAAATCGC-GC
*
570754 -GCGAATTTGGAAATCGCAAC
1 TGCGAATTTGGAAATCGC-GC
570774 -GCGAATTTGGAAA
1 TGCGAATTTGGAAA
570787 ATCTTAATGC
Statistics
Matches: 86, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
19 4 0.05
20 63 0.73
21 15 0.17
22 4 0.05
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (20 bp):
TGCGAATTTGGAAATCGCGC
Found at i:570742 original size:41 final size:41
Alignment explanation
Indices: 570610--570738 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 41
570600 ACTAAAACCT
*
570610 GTTGCGAAATTAAAATTC-GTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAATTAAAATTCAGTGTTGCGAATTCGGAAATCGA
** * *
570650 GTTGCGAAAACAAAATTCA-CGTTGCGAATTCAGAAATCGA
1 GTTGCGAAATTAAAATTCAGTGTTGCGAATTCGGAAATCGA
* * * *
570690 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGGAAATCGC
1 GTTGCGAAATTAAAATTCAGTGTTGCGAATTCGGAAATCGA
*
570731 GCTGCGAA
1 GTTGCGAA
570739 TTTGGAAATC
Statistics
Matches: 73, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
40 49 0.67
41 24 0.33
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (41 bp):
GTTGCGAAATTAAAATTCAGTGTTGCGAATTCGGAAATCGA
Found at i:570798 original size:21 final size:20
Alignment explanation
Indices: 570714--570786 Score: 121
Period size: 20 Copynumber: 3.6 Consensus size: 20
570704 ATTCAGTGTT
*
570714 GCGAATTTGGAAATCGC-GC
1 GCGAATTTGGAAATCGCAAC
570733 TGCGAATTTGGAAATCGCAAC
1 -GCGAATTTGGAAATCGCAAC
570754 GCGAATTTGGAAATCGCAAC
1 GCGAATTTGGAAATCGCAAC
570774 GCGAATTTGGAAA
1 GCGAATTTGGAAA
570787 ATCTTAATGC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 50 0.98
21 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (20 bp):
GCGAATTTGGAAATCGCAAC
Found at i:574194 original size:2 final size:2
Alignment explanation
Indices: 574187--574213 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
574177 TTTGTCCGGG
574187 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
574214 GAATACATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:574318 original size:47 final size:46
Alignment explanation
Indices: 574249--574351 Score: 136
Period size: 47 Copynumber: 2.2 Consensus size: 46
574239 ATAGGTCTTA
*
574249 AATTGTAAATATTAAAGGTTATT-ATTTATGATTTCAAGTATGTTAGT
1 AATTGTGAATATTAAAGGTTATTAATTT-TG-TTTCAAGTATGTTAGT
* * *
574296 AATTGTGAATATTAAAGGTTATTAATTTTGTTTCGAGTGTTTTAGT
1 AATTGTGAATATTAAAGGTTATTAATTTTGTTTCAAGTATGTTAGT
*
574342 AATTGCGAAT
1 AATTGTGAAT
574352 GTTGATGTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
46 22 0.44
47 24 0.48
48 4 0.08
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (46 bp):
AATTGTGAATATTAAAGGTTATTAATTTTGTTTCAAGTATGTTAGT
Found at i:581730 original size:48 final size:48
Alignment explanation
Indices: 581641--581739 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 48
581631 GCGCCCGCCC
581641 AGGGCCCATAAAGTTTTATAATTTTTATAATATATATTTTTTAAGCAT
1 AGGGCCCATAAAGTTTTATAATTTTTATAATATATATTTTTTAAGCAT
*
581689 AGGGCCCATAAAAGTTTTATAATTTTTATACTATATATTTTTTAAGCAT
1 AGGGCCCAT-AAAGTTTTATAATTTTTATAATATATATTTTTTAAGCAT
581738 AG
1 AG
581740 ACACATCAGC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 9 0.18
49 40 0.82
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.44
Consensus pattern (48 bp):
AGGGCCCATAAAGTTTTATAATTTTTATAATATATATTTTTTAAGCAT
Found at i:582979 original size:2 final size:2
Alignment explanation
Indices: 582972--583005 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
582962 ATAATATACA
582972 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
583006 TTCTTCTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:583662 original size:2 final size:2
Alignment explanation
Indices: 583655--583696 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
583645 ACAAATTAAC
583655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GAT 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
583696 A
1 A
583697 ATAATAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 33 0.89
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:585487 original size:15 final size:15
Alignment explanation
Indices: 585467--585497 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
585457 AAATGTCCAA
585467 GCTATCAAGTCTACT
1 GCTATCAAGTCTACT
*
585482 GCTATCTAGTCTACT
1 GCTATCAAGTCTACT
585497 G
1 G
585498 GTTTGTTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (15 bp):
GCTATCAAGTCTACT
Found at i:586146 original size:20 final size:20
Alignment explanation
Indices: 586117--586172 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
586107 TATGACCCAA
*
586117 AGTTTTGATATTCTTGAAAG
1 AGTTTCGATATTCTTGAAAG
586137 AGTTTCGATATTCTTGAAAG
1 AGTTTCGATATTCTTGAAAG
* *
586157 AGTATCGATACTCTTG
1 AGTTTCGATATTCTTG
586173 CCCAGCAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.41
Consensus pattern (20 bp):
AGTTTCGATATTCTTGAAAG
Found at i:588241 original size:15 final size:15
Alignment explanation
Indices: 588223--588260 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
588213 AAGCTATCAA
588223 GTCTACTGTTA-TCTG
1 GTCTACTGTTATTC-G
*
588238 GTCTATTGTTATTCG
1 GTCTACTGTTATTCG
588253 GTCTACTG
1 GTCTACTG
588261 GTATGTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 18 0.90
16 2 0.10
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.47
Consensus pattern (15 bp):
GTCTACTGTTATTCG
Found at i:595787 original size:19 final size:21
Alignment explanation
Indices: 595749--595787 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
595739 ATTTTTATGA
*
595749 TTAAATAAAATATTATATTTC
1 TTAAATAAAATATTAAATTTC
595770 TTAAA-AAAAT-TTAAATTT
1 TTAAATAAAATATTAAATTT
595788 GAACAGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAAATAAAATATTAAATTTC
Found at i:598408 original size:21 final size:20
Alignment explanation
Indices: 598369--598414 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
598359 TAAAAATAAA
*
598369 ATTATAATTATTTTAAAATTT
1 ATTATAATTATTATAAAA-TT
598390 ATTATAATTATTA-ATAAATT
1 ATTATAATTATTATA-AAATT
598410 ATTAT
1 ATTAT
598415 GATAGATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTATAATTATTATAAAATT
Found at i:610128 original size:14 final size:14
Alignment explanation
Indices: 610109--610206 Score: 178
Period size: 14 Copynumber: 7.0 Consensus size: 14
610099 CAACAGACTT
610109 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
610123 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
*
610137 TTCTGTTTTCTACA
1 GTCTGTTTTCTACA
610151 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
*
610165 TTCTGTTTTCTACA
1 GTCTGTTTTCTACA
610179 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
610193 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
610207 TGGTATCAGG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 80 1.00
ACGTcount: A:0.14, C:0.21, G:0.12, T:0.52
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:611016 original size:34 final size:34
Alignment explanation
Indices: 610973--611048 Score: 152
Period size: 34 Copynumber: 2.2 Consensus size: 34
610963 CTGATGGTGC
610973 CACCAGTTTAGCGAACAGATGCTTCTGCACTTGT
1 CACCAGTTTAGCGAACAGATGCTTCTGCACTTGT
611007 CACCAGTTTAGCGAACAGATGCTTCTGCACTTGT
1 CACCAGTTTAGCGAACAGATGCTTCTGCACTTGT
611041 CACCAGTT
1 CACCAGTT
611049 CTACCTCTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.29
Consensus pattern (34 bp):
CACCAGTTTAGCGAACAGATGCTTCTGCACTTGT
Found at i:614973 original size:14 final size:14
Alignment explanation
Indices: 614954--615037 Score: 123
Period size: 14 Copynumber: 6.0 Consensus size: 14
614944 TAACAGACTT
614954 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
614968 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
* *
614982 TTATGTTTTCTACA
1 GTCTGTTTTCTACA
*
614996 ATCTGTTTTCTACA
1 GTCTGTTTTCTACA
* *
615010 TTCTGTTTTATACA
1 GTCTGTTTTCTACA
615024 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
615038 TGAAGAAAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 62 1.00
ACGTcount: A:0.18, C:0.19, G:0.11, T:0.52
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:615000 original size:28 final size:28
Alignment explanation
Indices: 614957--615038 Score: 137
Period size: 28 Copynumber: 2.9 Consensus size: 28
614947 CAGACTTGTC
614957 TGTTTTCTACAGTCTGTTTTCTACATTA
1 TGTTTTCTACAGTCTGTTTTCTACATTA
* *
614985 TGTTTTCTACAATCTGTTTTCTACATTC
1 TGTTTTCTACAGTCTGTTTTCTACATTA
*
615013 TGTTTTATACAGTCTGTTTTCTACAT
1 TGTTTTCTACAGTCTGTTTTCTACAT
615039 GAAGAAAACA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.18, C:0.18, G:0.10, T:0.54
Consensus pattern (28 bp):
TGTTTTCTACAGTCTGTTTTCTACATTA
Found at i:619403 original size:21 final size:21
Alignment explanation
Indices: 619364--619404 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
619354 AGGTCATTAG
619364 AGTAAAGTGAGTTTGAATTTC
1 AGTAAAGTGAGTTTGAATTTC
*
619385 AGTAAGAGTGTGTTT-AATTT
1 AGTAA-AGTGAGTTTGAATTT
619405 TTGTAGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.32, C:0.02, G:0.24, T:0.41
Consensus pattern (21 bp):
AGTAAAGTGAGTTTGAATTTC
Found at i:619705 original size:38 final size:38
Alignment explanation
Indices: 619622--619705 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 38
619612 AAAAAGTATT
* * *
619622 ATTTTATTTATTTAATATTTTAATATCATTTTAATAAA
1 ATTTTAATTATTAAATATTTTAATATCATTATAATAAA
** * *
619660 AAATTAATTATTAAA-ATATTTAATATTATTATAATATA
1 ATTTTAATTATTAAATAT-TTTAATATCATTATAATAAA
619698 ATTTTAAT
1 ATTTTAAT
619706 AATATTATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
37 2 0.06
38 34 0.94
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (38 bp):
ATTTTAATTATTAAATATTTTAATATCATTATAATAAA
Found at i:619741 original size:15 final size:13
Alignment explanation
Indices: 619701--619753 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
619691 TAATATAATT
619701 TTAATAATATTATA
1 TTAAT-ATATTATA
*
619715 TTAATAT-CTAT-
1 TTAATATATTATA
*
619726 TCAGATATATTATA
1 TTA-ATATATTATA
619740 TTAATATATTATA
1 TTAATATATTATA
619753 T
1 T
619754 GATATTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
11 2 0.06
12 7 0.22
13 16 0.50
14 7 0.22
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (13 bp):
TTAATATATTATA
Found at i:620233 original size:31 final size:30
Alignment explanation
Indices: 620153--620261 Score: 105
Period size: 31 Copynumber: 3.6 Consensus size: 30
620143 TCCAAAAAAT
* * * * *
620153 GTAATTCATTCTACGTAAAA-TAGTTTAAA
1 GTAATTTATTTTACGTAAAACAATTTTCAA
* *
620182 GTAATCTT-TTTTTCGTAAAACAATTTTCAT
1 GTAAT-TTATTTTACGTAAAACAATTTTCAA
620212 GTAATTTATTTTACGTGAAAACAATTTTCAA
1 GTAATTTATTTTACGT-AAAACAATTTTCAA
* *
620243 ATAATCTATTTTACGTAAA
1 GTAATTTATTTTACGTAAA
620262 TTATTTTTCA
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
29 17 0.26
30 21 0.32
31 27 0.42
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (30 bp):
GTAATTTATTTTACGTAAAACAATTTTCAA
Found at i:623842 original size:2 final size:2
Alignment explanation
Indices: 623835--623861 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
623825 CATAATGTAT
623835 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
623862 GTACATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:625748 original size:3 final size:3
Alignment explanation
Indices: 625740--625810 Score: 99
Period size: 3 Copynumber: 23.7 Consensus size: 3
625730 TAATTTATAT
* *
625740 TAA TAA TAA AAA TGAA -AA GAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
625785 TAA TAA TGA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
625811 TATAGAAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
2 2 0.03
3 57 0.93
4 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:627304 original size:24 final size:23
Alignment explanation
Indices: 627285--627330 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
627275 TTATTTATTT
627285 ATTTTT-TTCTTTTTTCATTTTTC
1 ATTTTTATT-TTTTTTCATTTTTC
627308 ATTTTTCATTTTTTTTCATTTTT
1 ATTTTT-ATTTTTTTTCATTTTT
627331 TTTCTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.29
24 13 0.62
25 2 0.10
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (23 bp):
ATTTTTATTTTTTTTCATTTTTC
Found at i:627324 original size:10 final size:10
Alignment explanation
Indices: 627309--627334 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
627299 TCATTTTTCA
627309 TTTTTCATTT
1 TTTTTCATTT
627319 TTTTTCATTT
1 TTTTTCATTT
627329 TTTTTC
1 TTTTTC
627335 TTCAAGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:627330 original size:7 final size:7
Alignment explanation
Indices: 627288--627320 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
627278 TTTATTTATT
*
627288 TTTTTCT
1 TTTTTCA
627295 TTTTTCA
1 TTTTTCA
627302 TTTTTCA
1 TTTTTCA
627309 TTTTTCA
1 TTTTTCA
627316 TTTTT
1 TTTTT
627321 TTTCATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTCA
Found at i:634000 original size:30 final size:29
Alignment explanation
Indices: 633966--634036 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
633956 TTAAATTTGA
**
633966 ATGCATATTATTGGTAATGTGTTATAAATG
1 ATGCAT-TTATTGGTAATGCATTATAAATG
*
633996 ATGCATTTTATTGGTGATGCATTATAAATG
1 ATGCA-TTTATTGGTAATGCATTATAAATG
*
634026 ATGAATTTATT
1 ATGCATTTATT
634037 TATGCAGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 6 0.17
30 29 0.81
31 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.45
Consensus pattern (29 bp):
ATGCATTTATTGGTAATGCATTATAAATG
Found at i:636714 original size:14 final size:13
Alignment explanation
Indices: 636691--636721 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
636681 ATGAATAAGG
636691 AAAAAAACAAAAC
1 AAAAAAACAAAAC
636704 AAAACAAACAAAAC
1 AAAA-AAACAAAAC
636718 AAAA
1 AAAA
636722 TAGTTAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:637723 original size:11 final size:11
Alignment explanation
Indices: 637707--637736 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
637697 AAAATTGATG
637707 ATTTGAAATTA
1 ATTTGAAATTA
637718 ATTTGAAATTA
1 ATTTGAAATTA
*
637729 AATTGAAA
1 ATTTGAAA
637737 AGAGTCGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (11 bp):
ATTTGAAATTA
Found at i:638652 original size:2 final size:2
Alignment explanation
Indices: 638645--638671 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
638635 ATGTATTTAT
638645 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
638672 GTACATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:640556 original size:3 final size:3
Alignment explanation
Indices: 640548--640612 Score: 96
Period size: 3 Copynumber: 21.7 Consensus size: 3
640538 TAATTTATAT
*
640548 TAA TAA TAA AAA TGAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
640593 TAA TGA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
640613 GATAGAAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.93
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:655282 original size:30 final size:29
Alignment explanation
Indices: 655248--655318 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
655238 TTAAATTTGA
**
655248 ATGCATATTATTGGTAATGTGTTATAAATG
1 ATGCAT-TTATTGGTAATGCATTATAAATG
*
655278 ATGCATTTTATTGGTGATGCATTATAAATG
1 ATGCA-TTTATTGGTAATGCATTATAAATG
*
655308 ATGAATTTATT
1 ATGCATTTATT
655319 TATGCAGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 6 0.17
30 29 0.81
31 1 0.03
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.45
Consensus pattern (29 bp):
ATGCATTTATTGGTAATGCATTATAAATG
Found at i:656276 original size:11 final size:10
Alignment explanation
Indices: 656255--656302 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
656245 TTTTATCTTC
656255 TGATTCATAT
1 TGATTCATAT
656265 TGATTGCATAT
1 TGATT-CATAT
**
656276 TGATTTTTAT
1 TGATTCATAT
656286 CTGATTGCATAT
1 -TGATT-CATAT
656298 TGATT
1 TGATT
656303 TTTATCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 8 0.26
11 20 0.65
12 3 0.10
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (10 bp):
TGATTCATAT
Found at i:656291 original size:22 final size:22
Alignment explanation
Indices: 656265--656309 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
656255 TGATTCATAT
656265 TGATTGCATATTGATTTTTATC
1 TGATTGCATATTGATTTTTATC
656287 TGATTGCATATTGATTTTTATC
1 TGATTGCATATTGATTTTTATC
656309 T
1 T
656310 TCTCCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.56
Consensus pattern (22 bp):
TGATTGCATATTGATTTTTATC
Found at i:656861 original size:3 final size:3
Alignment explanation
Indices: 656853--656885 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
656843 TAAAAATGAA
656853 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
656886 GAAAAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:657842 original size:21 final size:21
Alignment explanation
Indices: 657816--658172 Score: 143
Period size: 21 Copynumber: 17.6 Consensus size: 21
657806 GTTTCCAGAT
*
657816 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* *
657837 TCGCAATGCGAACTTCAAATA
1 TCGCAATGCGAACTTCGACTA
*
657858 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
657879 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* **
657899 TCGCATTGCG-A-TAGGACTA
1 TCGCAATGCGAACTTCGACTA
* * * *
657918 TCGCATTGCGAGCAATGCGAATA
1 TCGCAATGCGA--ACTTCGACTA
* *
657941 T----AT---AA-ATCG-CAA
1 TCGCAATGCGAACTTCGACTA
*
657953 TGCGGCAATGCGATA-GTCGACTA
1 T-C-GCAATGCGA-ACTTCGACTA
*
657976 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
657997 TCGTAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* *
658018 TCGCATTGCG-A-TT-TACATA
1 TCGCAATGCGAACTTCGAC-TA
* *
658037 TTCGCATTGCGATA-GTCGACTA
1 -TCGCAATGCGA-ACTTCGACTA
* *
658059 TCGCATTGCG-A-TT-TACATA
1 TCGCAATGCGAACTTCGAC-TA
* *
658078 TTCGCATTGCG-A--TAGTACTA
1 -TCGCAATGCGAACTTCG-ACTA
* *
658098 TTGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
658119 TCGCAACGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
658140 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
658161 TCGCAATGCGAA
1 TCGCAATGCGAA
658173 ATGTAAATCG
Statistics
Matches: 264, Mismatches: 40, Indels: 64
0.72 0.11 0.17
Matches are distributed among these distances:
12 2 0.01
13 2 0.01
14 1 0.00
16 1 0.00
18 7 0.03
19 32 0.12
20 38 0.14
21 158 0.60
22 12 0.05
23 11 0.04
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:657869 original size:42 final size:42
Alignment explanation
Indices: 657816--658172 Score: 162
Period size: 42 Copynumber: 8.3 Consensus size: 42
657806 GTTTCCAGAT
* *
657816 TCGCAACGCGAACTTCGACTATCGCAATGCGAACTTCAAATA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGAAATA
* *
657858 TCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTAA-A
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAACT-TGAAATA
* ** * * *
657899 TCGCATTGCG-A-TAGGACTATCGCATTGCGAGCAATGCGAATATATAAA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGA--ACT-TG-A-A-AT--A
* *
657947 TCGCAATGCGGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTA
1 TCGCAATGC-G-AA--C--T--TCGACTATCGCAATGCGAACTTGAAATA
* * * * *
657997 TCGTAACGCGAACTTCGACTATCGCATTGCG-A-TTTACATA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGAAATA
* * * * *
658037 TTCGCATTGCGATA-GTCGACTATCGCATTGCG-A-TTTACATA
1 -TCGCAATGCGA-ACTTCGACTATCGCAATGCGAACTTGAAATA
* * * * *
658078 TTCGCATTGCG-A--TAGTACTATTGCAATGCGAACTTGGACTA
1 -TCGCAATGCGAACTTCG-ACTATCGCAATGCGAACTTGAAATA
* * * *
658119 TCGCAACGCGAACTTGGACTATCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGAAATA
658161 TCGCAATGCGAA
1 TCGCAATGCGAA
658173 ATGTAAATCG
Statistics
Matches: 246, Mismatches: 41, Indels: 56
0.72 0.12 0.16
Matches are distributed among these distances:
38 2 0.01
39 30 0.12
40 14 0.06
41 63 0.26
42 88 0.36
43 2 0.01
44 2 0.01
45 1 0.00
46 1 0.00
48 11 0.04
49 2 0.01
50 8 0.03
51 1 0.00
52 1 0.00
53 1 0.00
55 1 0.00
56 3 0.01
58 15 0.06
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (42 bp):
TCGCAATGCGAACTTCGACTATCGCAATGCGAACTTGAAATA
Found at i:657978 original size:29 final size:29
Alignment explanation
Indices: 657905--657986 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
657895 TAAATCGCAT
*
657905 TGCGATAG-GACTATCGCATTGCGAGCAA
1 TGCGATAGTGACTATCGCAATGCGAGCAA
657933 TGCGAATA-T-A-TAAATCGCAATGCG-GCAA
1 TGCG-ATAGTGACT--ATCGCAATGCGAGCAA
657961 TGCGATAGTCGACTATCGCAATGCGA
1 TGCGATAGT-GACTATCGCAATGCGA
657987 ACTTGGACTA
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
27 4 0.09
28 14 0.32
29 24 0.55
30 1 0.02
31 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.22
Consensus pattern (29 bp):
TGCGATAGTGACTATCGCAATGCGAGCAA
Found at i:658043 original size:20 final size:20
Alignment explanation
Indices: 658018--658090 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
658008 ACTTCGACTA
658018 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
658038 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
658059 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
658079 TCGCATTGCGAT
1 TCGCATTGCGAT
658091 AGTACTATTG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.04
20 27 0.59
21 15 0.33
22 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:658064 original size:41 final size:41
Alignment explanation
Indices: 658011--658093 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
658001 AACGCGAACT
658011 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
658052 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
658093 T
1 T
658094 ACTATTGCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (41 bp):
TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
Found at i:658204 original size:122 final size:122
Alignment explanation
Indices: 657961--658216 Score: 283
Period size: 122 Copynumber: 2.1 Consensus size: 122
657951 AATGCGGCAA
* *
657961 TGCGATAGTCGACTATCGCAATGCGAACTTGGACTATCGTAACGCGAACTTCGACTATCGCATTG
1 TGCGATAGTC-ACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATG
* * * * * *
658026 CGATTTACATATTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCAT
65 CGATTGACATATTCGCAATGCGAAAGTC-ACAATCGCAATGCGATGTACATATTCGCAT
* *
658085 TGCGATAGT-ACTATTGCAATGCGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAATGC
1 TGCGATAGTCACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGC
*
658149 GAACTTGGAC-TA-TCGCAATGCGAAATGT-A-AATCGCAATGCGATAGT-CGA-AGTTCGCGT
66 G-A-TT-GACATATTCGCAATGCGAAA-GTCACAATCGCAATGCGAT-GTAC-ATA-TTCGCAT
658207 TGCGATAGTC
1 TGCGATAGTC
658217 CAAGTTCGCA
Statistics
Matches: 113, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
121 14 0.12
122 70 0.62
123 12 0.11
124 15 0.13
125 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (122 bp):
TGCGATAGTCACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGC
GATTGACATATTCGCAATGCGAAAGTCACAATCGCAATGCGATGTACATATTCGCAT
Found at i:658210 original size:21 final size:21
Alignment explanation
Indices: 658180--658316 Score: 154
Period size: 21 Copynumber: 6.6 Consensus size: 21
658170 GAAATGTAAA
* *
658180 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
658201 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
658222 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* * *
658242 ATCGCATTGCAAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
658263 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
658284 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
658305 TCGCGTTGCGAT
1 TCGCATTGCGAT
658317 TTATTCCAAA
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
20 16 0.16
21 81 0.83
22 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:658225 original size:143 final size:141
Alignment explanation
Indices: 657818--658236 Score: 417
Period size: 143 Copynumber: 3.0 Consensus size: 141
657808 TTCCAGATTC
* ** *
657818 GCAACGCGAACTTCGACTATCGCAATGCGAACTTCAAATATCGCAATGCGAACTTGGACTATCGC
1 GCAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGC
* *
657883 AATGCGAATATGTAAATCGCATTGCGATAG--GACTATCGCATTGCG--AG-CAATGCGAATATA
66 AATGCGAA-ATGTAAATCGCATTGCGATAGTCGACTATCGCATTGCGATAGTCAATTCGCAT-T-
*** * * *
657943 TAAATCGCAATGCG
128 GCGATAGTAATACG
* * * *
657957 GCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGTAACGCGAACTTCGACTATCG
1 GCAATGCGA-ACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCG
* * *
658021 CATTGCG--ATTTACATATTCGCATTGCGATAGTCGACTATCGCATTGCGAT-TTACATATTCGC
65 CAATGCGAAATGTA-A-A-TCGCATTGCGATAGTCGACTATCGCATTGCGATAGT-CA-ATTCGC
* **
658083 ATTGCGATAGTACTATT
125 ATTGCGATAGTAATACG
* *
658100 GCAATGCGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGC
1 GCAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGC
* * *
658165 AATGCGAAATGTAAATCGCAATGCGATAGTCGAAGT-TCGCGTTGCGATAGTCCAAGTTCGCATT
66 AATGCGAAATGTAAATCGCATTGCGATAGTCG-ACTATCGCATTGCGATAGT-CAA-TTCGCATT
658229 GCGATAGT
128 GCGATAGT
658237 CGACTATCGC
Statistics
Matches: 228, Mismatches: 35, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
136 4 0.02
137 1 0.00
138 1 0.00
139 74 0.32
140 1 0.00
141 15 0.07
142 29 0.13
143 89 0.39
144 4 0.02
145 10 0.04
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (141 bp):
GCAATGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATCGC
AATGCGAAATGTAAATCGCATTGCGATAGTCGACTATCGCATTGCGATAGTCAATTCGCATTGCG
ATAGTAATACG
Found at i:658471 original size:5 final size:6
Alignment explanation
Indices: 658432--658457 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
658422 GACACGTATT
658432 ACCACG ACCACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG AC
658458 TCGACCCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:659145 original size:21 final size:21
Alignment explanation
Indices: 659120--659227 Score: 105
Period size: 21 Copynumber: 5.2 Consensus size: 21
659110 AAATCACAAC
659120 GCGAAATTCGACTATCGCAAT
1 GCGAAATTCGACTATCGCAAT
*
659141 GCG-AATAT-GTA-AATCGCAAT
1 GCGAAAT-TCG-ACTATCGCAAT
* *
659161 GCGATAGTCGACTATCGCAAT
1 GCGAAATTCGACTATCGCAAT
* * *
659182 GCGAACTTGGACTATCGCAAC
1 GCGAAATTCGACTATCGCAAT
* *
659203 GCGAACTTCGACTATCGCATT
1 GCGAAATTCGACTATCGCAAT
659224 GCGA
1 GCGA
659228 TTTACATATT
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
20 17 0.24
21 53 0.76
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (21 bp):
GCGAAATTCGACTATCGCAAT
Found at i:659172 original size:41 final size:41
Alignment explanation
Indices: 659109--659227 Score: 123
Period size: 41 Copynumber: 2.9 Consensus size: 41
659099 AAATTTGGAA
*
659109 TAAATCACAACGCGAAATTCGACTATCGCAATGCGAATATG
1 TAAATCACAACGCGAAAGTCGACTATCGCAATGCGAATATG
* * *
659150 TAAATCGCAATGCGATAGTCGACTATCGCAATGCGAACT-TG
1 TAAATCACAACGCGAAAGTCGACTATCGCAATGCGAA-TATG
* * * ** *
659191 GACTATCGCAACGCGAACTTCGACTATCGCATTGCGA
1 TA-AATCACAACGCGAAAGTCGACTATCGCAATGCGA
659228 TTTACATATT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 36 0.55
42 29 0.45
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (41 bp):
TAAATCACAACGCGAAAGTCGACTATCGCAATGCGAATATG
Found at i:659288 original size:21 final size:21
Alignment explanation
Indices: 659262--659401 Score: 155
Period size: 21 Copynumber: 6.7 Consensus size: 21
659252 CCAAGTTTGC
659262 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
* *
659283 AAGTTCGCGTTGCGATAGTCC
1 AAGTTCGCATTGCGATAGTCG
*
659304 AAGTTCGCATTGCAATAGTCG
1 AAGTTCGCATTGCGATAGTCG
* *
659325 -ACTATCGCATTGCGAT-TTAC-
1 AAGT-TCGCATTGCGATAGT-CG
659345 ATA-TTCGCATTGCGATAGTTC-
1 A-AGTTCGCATTGCGATAG-TCG
659366 AAGTTCGCATTGCGATAGTCG
1 AAGTTCGCATTGCGATAGTCG
*
659387 AAGTTCGCGTTGCGA
1 AAGTTCGCATTGCGA
659402 ATCTTGAAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 16
0.80 0.08 0.13
Matches are distributed among these distances:
20 18 0.18
21 81 0.80
22 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (21 bp):
AAGTTCGCATTGCGATAGTCG
Found at i:662086 original size:27 final size:27
Alignment explanation
Indices: 662055--662122 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
662045 TCTATTTACA
662055 AAATCATATCTCTATAGCAATGGTAAC
1 AAATCATATCTCTATAGCAATGGTAAC
*
662082 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGCAATGGTAAC
662109 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
662123 ATTCCTACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 9 0.22
27 31 0.77
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGCAATGGTAAC
Found at i:668308 original size:22 final size:22
Alignment explanation
Indices: 668282--668335 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
668272 GTTTTGGTTC
668282 TGTTTTTCTGTTTTTGAAGGGG
1 TGTTTTTCTGTTTTTGAAGGGG
668304 TGTTTTTCTGTTTTTGAAGGGG
1 TGTTTTTCTGTTTTTGAAGGGG
668326 TGTTTTTCTG
1 TGTTTTTCTG
668336 GTTGTATCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.07, C:0.06, G:0.30, T:0.57
Consensus pattern (22 bp):
TGTTTTTCTGTTTTTGAAGGGG
Found at i:672894 original size:21 final size:20
Alignment explanation
Indices: 672868--672907 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
672858 TAAAAAATTG
672868 TTTTTTATTAAATGTTTTTAT
1 TTTTTTATTAAAT-TTTTTAT
*
672889 TTTTTTATTTAATTTTTTA
1 TTTTTTATTAAATTTTTTA
672908 AATAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (20 bp):
TTTTTTATTAAATTTTTTAT
Found at i:674771 original size:21 final size:21
Alignment explanation
Indices: 674718--674773 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
674708 TTCTGAAATG
* *
674718 TTGCTTCTGTCACTGCTCTCT
1 TTGCTTCTCTCGCTGCTCTCT
*
674739 CTGCTTCTCTCGCTGCTCTCT
1 TTGCTTCTCTCGCTGCTCTCT
674760 TTGCTTCTCTCGCT
1 TTGCTTCTCTCGCT
674774 TCAGCTTCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.02, C:0.38, G:0.14, T:0.46
Consensus pattern (21 bp):
TTGCTTCTCTCGCTGCTCTCT
Found at i:676102 original size:31 final size:31
Alignment explanation
Indices: 676056--676180 Score: 209
Period size: 31 Copynumber: 4.0 Consensus size: 31
676046 CCCGAAGGAC
676056 CAGTCCATA-GATCCCGAAGAATC-TAGGTAAA
1 CAGTCCATATG-TCCCGAAGAA-CATAGGTAAA
*
676087 CAGCCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
676118 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
676149 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
676180 C
1 C
676181 CCTCGACCCT
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
30 1 0.01
31 88 0.98
32 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:676932 original size:64 final size:63
Alignment explanation
Indices: 676824--676995 Score: 202
Period size: 64 Copynumber: 2.7 Consensus size: 63
676814 TAATGAAGGT
* * ** * * * **
676824 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTGCTGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTT-TCACTATTAATGAG
* *
676888 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCGATGTTTCACTATTAATGAG
676952 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTC
1 ATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTC
676996 TATTTCTTTA
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
63 3 0.03
64 90 0.97
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCGATGTTTCACTATTAATGAG
Done.