Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008386.1 Hibiscus syriacus cultivar Beakdansim tig00111149_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: 339444
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:264192 original size:25 final size:23
Alignment explanation
Indices: 264139--264196 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
264129 TTGTAATTTT
264139 AAAAAATTTATTTAAAAATAAAA
1 AAAAAATTTATTTAAAAATAAAA
*
264162 ATAAAAATTATATTTTAAAAA-AACAC
1 A-AAAAATT-TA-TTTAAAAATAA-AA
264188 AAAAAATTT
1 AAAAAATTT
264197 GAAATAGCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.03
24 8 0.27
25 11 0.37
26 10 0.33
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAAAATTTATTTAAAAATAAAA
Found at i:269667 original size:60 final size:60
Alignment explanation
Indices: 269603--269716 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
269593 CTATGGCTAT
* * * *
269603 CATTCCAAATTAGTCCTC-AAGTTTTTGAACATTTTAATTTCATCACCAAACTATGAAACC
1 CATTCCAAATTAATCCCCAAACTTTTTGAACATTTCAATTTCATC-CCAAACTATGAAACC
* * *
269663 CATTCTAGATTAATCCCCAAACTTTTTGAATATTTCAATTTCATCCCAAACTAT
1 CATTCCAAATTAATCCCCAAACTTTTTGAACATTTCAATTTCATCCCAAACTAT
269717 ATTTATATAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 23 0.50
61 23 0.50
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (60 bp):
CATTCCAAATTAATCCCCAAACTTTTTGAACATTTCAATTTCATCCCAAACTATGAAACC
Found at i:270954 original size:17 final size:18
Alignment explanation
Indices: 270928--270968 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
270918 GACCCGAATT
270928 AATATATTTATTAAA-AA
1 AATATATTTATTAAATAA
*
270945 AATATTTTTATTAAATAA
1 AATATATTTATTAAATAA
270963 AA-ATAT
1 AATATAT
270969 GAATTTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATATATTTATTAAATAA
Found at i:274688 original size:37 final size:37
Alignment explanation
Indices: 274612--274688 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
274602 TTTTTATATT
*
274612 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * * *
274649 TTTATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
274686 TTT
1 TTT
274689 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 13 0.38
37 21 0.62
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:278344 original size:23 final size:20
Alignment explanation
Indices: 278317--278367 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 20
278307 TTTAATTTAG
278317 TTAAGTTTATTAATGTTTTGAGT
1 TTAAGTTTATTAA-G-TTTGA-T
*
278340 TTAAGTTTATTGAGTTTGAT
1 TTAAGTTTATTAAGTTTGAT
278360 TTAAGTTT
1 TTAAGTTT
278368 CAAATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.33
21 5 0.19
22 1 0.04
23 12 0.44
ACGTcount: A:0.25, C:0.00, G:0.18, T:0.57
Consensus pattern (20 bp):
TTAAGTTTATTAAGTTTGAT
Found at i:285235 original size:2 final size:2
Alignment explanation
Indices: 285228--285264 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
285218 GCTATTTTCA
285228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
285265 AAAAATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:305683 original size:20 final size:20
Alignment explanation
Indices: 305589--305957 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
305579 GATTTTCCAT
* ** *
305589 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
305609 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
305629 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
305649 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
305669 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
305689 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
305709 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
305729 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
305749 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
305769 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
305789 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
305809 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
305829 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
305849 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
305869 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
305889 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
305909 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
305929 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
305949 AATCACAAC
1 AATCGCAAC
305958 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:306877 original size:12 final size:12
Alignment explanation
Indices: 306860--306884 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
306850 ATATAATCCT
306860 GAAGAAGAAAAA
1 GAAGAAGAAAAA
306872 GAAGAAGAAAAA
1 GAAGAAGAAAAA
306884 G
1 G
306885 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:309187 original size:19 final size:19
Alignment explanation
Indices: 309165--309470 Score: 367
Period size: 19 Copynumber: 17.4 Consensus size: 19
309155 CGGAAAATAC
*
309165 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
309184 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
309198 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
309218 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
309232 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
309251 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
309270 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
309284 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
309303 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
309322 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
309336 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
309355 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
309374 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
309393 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
309411 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
309425 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
309444 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
309463 AATCGCAA
1 AATCGCAA
309471 CGAGATAATC
Statistics
Matches: 251, Mismatches: 10, Indels: 52
0.80 0.03 0.17
Matches are distributed among these distances:
14 48 0.19
15 3 0.01
16 20 0.08
17 9 0.04
18 12 0.05
19 146 0.58
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:309252 original size:33 final size:33
Alignment explanation
Indices: 309165--309492 Score: 264
Period size: 33 Copynumber: 9.5 Consensus size: 33
309155 CGGAAAATAC
* *
309165 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
309198 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
309232 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
309270 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
309303 AATCGCAATGCGAAATGAAAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
*
309336 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
309374 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAGA--A
309411 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
309444 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
309477 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
309493 TATAAACGCA
Statistics
Matches: 253, Mismatches: 15, Indels: 54
0.79 0.05 0.17
Matches are distributed among these distances:
32 12 0.05
33 109 0.43
34 34 0.13
35 19 0.08
36 8 0.03
37 12 0.05
38 59 0.23
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:309280 original size:52 final size:52
Alignment explanation
Indices: 309193--309470 Score: 379
Period size: 52 Copynumber: 5.2 Consensus size: 52
309183 AAATCCCAAC
309193 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
309246 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
309298 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
309350 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
309407 ATG-AAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
309458 ATGAAAATCGCAA
1 ATGAAAATCGCAA
309471 CGAGATAATC
Statistics
Matches: 214, Mismatches: 5, Indels: 13
0.92 0.02 0.06
Matches are distributed among these distances:
51 36 0.17
52 127 0.59
53 17 0.08
54 7 0.03
56 10 0.05
57 17 0.08
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:309316 original size:71 final size:70
Alignment explanation
Indices: 309232--309470 Score: 369
Period size: 71 Copynumber: 3.4 Consensus size: 70
309222 GCAACGAGAG
*
309232 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAACGAAAGAATCGCAATGCGA
309297 AATGAA
65 AATGAA
* *
309303 AATCGCAATGCGAAATGAAAATCGCAA--CGACA-G-AATCGCAATGCGAAATTAAAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAA--CG-AA--AGAATCGCAAT
309364 GCGAAATGAA
61 GCGAAATGAA
309374 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAA
309439 ATGAA
66 ATGAA
309444 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
309471 CGAGATAATC
Statistics
Matches: 154, Mismatches: 5, Indels: 19
0.87 0.03 0.11
Matches are distributed among these distances:
66 8 0.05
68 3 0.02
69 5 0.03
70 47 0.31
71 74 0.48
72 2 0.01
73 6 0.04
74 1 0.01
75 8 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (70 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAATCGCAACGAAAGAATCGCAATGCGAA
ATGAA
Found at i:309608 original size:19 final size:19
Alignment explanation
Indices: 309499--309600 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
309489 AAATTATAAA
309499 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
309518 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
309538 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
309554 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
309571 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
309590 CGCATTGCGAT
1 CGCATTGCGAT
309601 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:309726 original size:14 final size:14
Alignment explanation
Indices: 309707--309743 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
309697 CATCAATTAC
309707 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
309721 ACAAATCATCTTTT
1 ACAAATCAACTTTT
309735 ACAAATCAA
1 ACAAATCAA
309744 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:311686 original size:19 final size:19
Alignment explanation
Indices: 311646--311761 Score: 108
Period size: 19 Copynumber: 6.6 Consensus size: 19
311636 TAGTTTACTT
* *
311646 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
311666 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
311685 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
311699 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
311718 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
311732 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
311751 TCGCAATGCGA
1 TCGCAACGCGA
311762 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 5, Indels: 21
0.76 0.05 0.20
Matches are distributed among these distances:
14 16 0.20
16 11 0.14
17 11 0.14
19 31 0.38
20 12 0.15
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:311702 original size:14 final size:14
Alignment explanation
Indices: 311683--311739 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
311673 GCGAAATGAA
*
311683 AATCGCAACGACAG
1 AATCGCAACGAAAG
311697 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
311714 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
311730 AATCGCAACG
1 AATCGCAACG
311740 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:311710 original size:33 final size:33
Alignment explanation
Indices: 311664--311756 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
311654 CGAAACTTAA
*
311664 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
311697 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
311730 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
311757 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:311779 original size:19 final size:19
Alignment explanation
Indices: 311757--311885 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
311747 AAAATCGCAA
311757 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
311776 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
311790 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
311809 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
311823 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
311842 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
311861 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
311881 TGCGA
1 TGCGA
311886 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:311799 original size:33 final size:33
Alignment explanation
Indices: 311757--311848 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
311747 AAAATCGCAA
311757 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
311790 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
311823 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
311849 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:312088 original size:93 final size:93
Alignment explanation
Indices: 311929--312308 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
311919 TTGAATGGAT
311929 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
311994 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
312022 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
312087 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
312115 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
312179 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
312207 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
312272 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
312300 AAATTTACT
1 AAATTTACT
312309 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:312242 original size:185 final size:186
Alignment explanation
Indices: 311929--312308 Score: 744
Period size: 185 Copynumber: 2.0 Consensus size: 186
311919 TTGAATGGAT
311929 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
311994 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
312059 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
312115 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
312179 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
312244 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
312300 AAATTTACT
1 AAATTTACT
312309 AAGCAATCTA
Statistics
Matches: 193, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
185 154 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:314034 original size:14 final size:14
Alignment explanation
Indices: 314015--314104 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
314005 TTGAAATGAA
314015 AATCGCAACGAGAG
1 AATCGCAACGAGAG
314029 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
314046 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
314062 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
314081 AATCGCAACGAGAG
1 AATCGCAACGAGAG
314095 AATCGCAACG
1 AATCGCAACG
314105 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:314052 original size:33 final size:33
Alignment explanation
Indices: 314007--314121 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
313997 TCTTTTGGTT
314007 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
314040 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
314073 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
314106 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
314122 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:314053 original size:19 final size:18
Alignment explanation
Indices: 314014--314126 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
314004 GTTGAAATGA
314014 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
314029 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
314046 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
314062 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
314079 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
314095 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
314112 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
314127 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:314157 original size:14 final size:14
Alignment explanation
Indices: 314138--314192 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
314128 TTTGGTTTCG
314138 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
314152 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
314171 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
314185 CGTTGCGA
1 CGTTGCGA
314193 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:314170 original size:33 final size:33
Alignment explanation
Indices: 314122--314192 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
314112 AAAATCGCAA
**
314122 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
314155 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
314188 TGCGA
1 TGCGA
314193 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:314200 original size:33 final size:33
Alignment explanation
Indices: 314133--314214 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
314123 GCGATTTTGG
***
314133 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
314166 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
314199 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
314215 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:314219 original size:20 final size:20
Alignment explanation
Indices: 314145--314233 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
314135 TCGCGTTGCG
314145 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
314165 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
314178 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
314198 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
314218 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
314234 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:314355 original size:33 final size:33
Alignment explanation
Indices: 314313--314383 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
314303 AATACTAACT
*
314313 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
314346 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
314379 TGAAA
1 TGAAA
314384 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:314616 original size:22 final size:22
Alignment explanation
Indices: 314564--314618 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
314554 TGGTTGTGAG
**
314564 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
314586 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
314608 GGATTTCTTCG
1 GGATTTCTTCG
314619 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:314789 original size:20 final size:20
Alignment explanation
Indices: 314764--314956 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
314754 CTTTAAATAT
314764 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
314784 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
314806 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
314825 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
314845 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
314865 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
314885 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
314905 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
314925 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
314945 CGCGTTGCGATT
1 CGCGTTGCGATT
314957 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:314951 original size:60 final size:60
Alignment explanation
Indices: 314764--314956 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
314754 CTTTAAATAT
**
314764 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
314825 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
314885 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
314945 CGCGTTGCGATT
1 CGCGTTGCGATT
314957 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:315037 original size:20 final size:20
Alignment explanation
Indices: 315012--315063 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
315002 AAGAATCGCG
*
315012 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
315032 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
315052 TTGCGATTCTGG
1 TTGCGATTCTGG
315064 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:319633 original size:31 final size:31
Alignment explanation
Indices: 319590--319667 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
319580 GATAACATCT
319590 TAGTTTAGGTACTAAAATAGACCAAAATTGA
1 TAGTTTAGGTACTAAAATAGACCAAAATTGA
* *
319621 TAGTTTAAGTACTAAAATAGATCAAAATTGA
1 TAGTTTAGGTACTAAAATAGACCAAAATTGA
*
319652 TAGTTTAGGCACTAAA
1 TAGTTTAGGTACTAAA
319668 TGTATAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (31 bp):
TAGTTTAGGTACTAAAATAGACCAAAATTGA
Found at i:320060 original size:15 final size:15
Alignment explanation
Indices: 320015--320061 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
320005 GTCATCGGTT
320015 CGTTCGATTTTAGTC
1 CGTTCGATTTTAGTC
* *
320030 CCTAACG-TTATTAGTC
1 CGT-TCGATT-TTAGTC
320046 CGTTCGATTTTAGTC
1 CGTTCGATTTTAGTC
320061 C
1 C
320062 TTCAACCATG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (15 bp):
CGTTCGATTTTAGTC
Found at i:320255 original size:15 final size:15
Alignment explanation
Indices: 320232--320268 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
320222 GGACGGATGA
320232 CAACCTCTAAGATTT
1 CAACCTCTAAGATTT
*
320247 CAACTTCTAAGATTT
1 CAACCTCTAAGATTT
320262 CAACCTC
1 CAACCTC
320269 GGACCAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.32
Consensus pattern (15 bp):
CAACCTCTAAGATTT
Found at i:323100 original size:13 final size:14
Alignment explanation
Indices: 323073--323104 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
323063 ATAGTATCAT
323073 AATATTTTCTATAA
1 AATATTTTCTATAA
323087 AATATTTT-TATAA
1 AATATTTTCTATAA
323100 AATAT
1 AATAT
323105 AATTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
AATATTTTCTATAA
Found at i:327547 original size:51 final size:50
Alignment explanation
Indices: 327395--327563 Score: 232
Period size: 50 Copynumber: 3.3 Consensus size: 50
327385 CTTCCAATGA
* *
327395 CTGATCTATATTATATTGAACATTTTTTTCCCACGTTTGCTTTATTAGTTGG
1 CTGATTTATATTATA-TG-ACCTTTTTTTCCCACGTTTGCTTTATTAGTTGG
* * *
327447 CTGATTTATATTATATAGAGC-TTTTTCCCCACGTTTGCTTTCTTAGTTGG
1 CTGATTTATATTATAT-GACCTTTTTTTCCCACGTTTGCTTTATTAGTTGG
* *
327497 CTGATTTATATTATACTGACCTTTTTTTTCCACGTTTGCTTTATTGGTTGG
1 CTGATTTATATTATA-TGACCTTTTTTTCCCACGTTTGCTTTATTAGTTGG
327548 CTGATTTATATTATAT
1 CTGATTTATATTATAT
327564 TACTTTATTG
Statistics
Matches: 104, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
50 46 0.44
51 43 0.41
52 15 0.14
ACGTcount: A:0.20, C:0.15, G:0.14, T:0.51
Consensus pattern (50 bp):
CTGATTTATATTATATGACCTTTTTTTCCCACGTTTGCTTTATTAGTTGG
Found at i:329028 original size:26 final size:28
Alignment explanation
Indices: 328966--329028 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 28
328956 CGAGTATTGT
*
328966 TGAGCTCGACTCGACTCGAAAACTCTGAAA
1 TGAGCTCAACTCGACTCGAAAACTCTG--A
328996 TGAAGCTCAACTCGACTCGAAAACTC-G-
1 TG-AGCTCAACTCGACTCGAAAACTCTGA
329023 TGAGCT
1 TGAGCT
329029 TAAAGTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 2 0.06
30 3 0.10
31 22 0.71
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.21
Consensus pattern (28 bp):
TGAGCTCAACTCGACTCGAAAACTCTGA
Found at i:329794 original size:18 final size:20
Alignment explanation
Indices: 329750--329793 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
329740 CTAAAAAGAT
329750 AGTTTTAATTCAATAAGAGA
1 AGTTTTAATTCAATAAGAGA
*
329770 AGTTTTAATTCAATGAGAG-
1 AGTTTTAATTCAATAAGAGA
329789 AGTTT
1 AGTTT
329794 ATGTATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.39, C:0.05, G:0.18, T:0.39
Consensus pattern (20 bp):
AGTTTTAATTCAATAAGAGA
Found at i:330231 original size:21 final size:21
Alignment explanation
Indices: 330169--330225 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 21
330159 CACCGAAAAA
*
330169 CTAAGAAGAAAAAAGAATATTTT
1 CTAAGAAG-AAGAA-AATATTTT
*
330192 CTAAGAAGGAGAAAATATTTT
1 CTAAGAAGAAGAAAATATTTT
330213 -TAAG-AGAAGAAAA
1 CTAAGAAGAAGAAAA
330226 GTTATTGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 8 0.26
20 4 0.13
21 8 0.26
22 3 0.10
23 8 0.26
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.23
Consensus pattern (21 bp):
CTAAGAAGAAGAAAATATTTT
Found at i:330418 original size:44 final size:44
Alignment explanation
Indices: 330330--330439 Score: 122
Period size: 44 Copynumber: 2.5 Consensus size: 44
330320 TTCAAACTCT
330330 AAAAGAT-A-ATATA-TTTTAATTATCTTTTAATTTTAAATATTA
1 AAAAGATAATATATATTTTTAA-TATCTTTTAATTTTAAATATTA
*
330372 AAAAGATAATGATATATTTTTAATATC-TTTAATATTT-AATTTTA
1 AAAAGATAAT-ATATATTTTTAATATCTTTTAAT-TTTAAATATTA
* *
330416 AAAATATAATAAATATCTTTTAAT
1 AAAAGATAATATATAT-TTTTAAT
330440 TTAAAATATT
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
42 7 0.12
43 6 0.10
44 28 0.47
45 12 0.20
46 6 0.10
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (44 bp):
AAAAGATAATATATATTTTTAATATCTTTTAATTTTAAATATTA
Found at i:330510 original size:63 final size:63
Alignment explanation
Indices: 330435--330553 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 63
330425 TAAATATCTT
*
330435 TTAATTTAAAATATTCAAAA-TATATAAACT-TCTTTTACTATTCAAACTTAAATAGACATTATG
1 TTAATTTAAAATATTCAAAAGTATAT-AACTATCTTTTAATA-TCAAACTTAAATAGACATTATG
* * *
330498 TTAATTTGAAATATTCAAAAGTATATAATTATCTTTTAATATCAAAGTTAAATAGA
1 TTAATTTAAAATATTCAAAAGTATATAACTATCTTTTAATATCAAACTTAAATAGA
330554 TAATAAATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
63 36 0.72
64 14 0.28
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.41
Consensus pattern (63 bp):
TTAATTTAAAATATTCAAAAGTATATAACTATCTTTTAATATCAAACTTAAATAGACATTATG
Found at i:336712 original size:21 final size:21
Alignment explanation
Indices: 336686--336725 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
336676 ACAAACCCCA
*
336686 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
336707 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
336726 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Done.