Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002077.1 Hibiscus syriacus cultivar Beakdansim tig00004246_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: 88592
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1333 original size:20 final size:22
Alignment explanation
Indices: 1282--1341 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
1272 CCGATACTCG
*
1282 GGGAAGTATTGATACCATAGGA
1 GGGAAGTATCGATACCATAGGA
1304 GGGAAGTATCGATATCCA-AGGA
1 GGGAAGTATCGATA-CCATAGGA
*
1326 -GG-AGTATCGGTACCAT
1 GGGAAGTATCGATACCAT
1342 CGTGAATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.09
20 9 0.26
21 2 0.06
22 17 0.50
23 3 0.09
ACGTcount: A:0.33, C:0.13, G:0.32, T:0.22
Consensus pattern (22 bp):
GGGAAGTATCGATACCATAGGA
Found at i:6280 original size:23 final size:23
Alignment explanation
Indices: 6230--6274 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
6220 ACCAAACGGG
6230 GGAATGTGAATTCCATTCCCATA
1 GGAATGTGAATTCCATTCCCATA
*
6253 GGAATGTGAATTTCATTCCCAT
1 GGAATGTGAATTCCATTCCCAT
6275 GAGAATCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (23 bp):
GGAATGTGAATTCCATTCCCATA
Found at i:12395 original size:14 final size:14
Alignment explanation
Indices: 12376--12426 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
12366 TATATGTTCG
12376 TTTATGTTCATTCA
1 TTTATGTTCATTCA
**
12390 TTTATGTTCGCTCA
1 TTTATGTTCATTCA
12404 TTTATGTTCATTCA
1 TTTATGTTCATTCA
12418 TTTATGTTC
1 TTTATGTTC
12427 GAACAAAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.57
Consensus pattern (14 bp):
TTTATGTTCATTCA
Found at i:12670 original size:10 final size:10
Alignment explanation
Indices: 12655--12680 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
12645 TATCATTTAA
12655 ATGAACGAAC
1 ATGAACGAAC
12665 ATGAACGAAC
1 ATGAACGAAC
12675 ATGAAC
1 ATGAAC
12681 AATCTATATT
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:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (10 bp):
ATGAACGAAC
Found at i:12861 original size:8 final size:8
Alignment explanation
Indices: 12829--12861 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
12819 TCTTTTTTAT
12829 ATTATAT-
1 ATTATATA
12836 ATATATATA
1 AT-TATATA
12845 ATTATATA
1 ATTATATA
12853 ATTATATA
1 ATTATATA
12861 A
1 A
12862 AGAAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 2 0.08
8 20 0.83
9 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTATATA
Found at i:13592 original size:27 final size:30
Alignment explanation
Indices: 13540--13603 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 30
13530 TTTGAGGGCC
* *
13540 TATTTAATCTTTTTAGAAAGTATAAGGTCT
1 TATTTAATCTTTTTAGAAAATATAAGGTAT
*
13570 TGTTTAAT-TTTTTA-AAAAT-TAAGGTAT
1 TATTTAATCTTTTTAGAAAATATAAGGTAT
13597 TATTTAA
1 TATTTAA
13604 ATGTAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 13 0.43
28 4 0.13
29 6 0.20
30 7 0.23
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.50
Consensus pattern (30 bp):
TATTTAATCTTTTTAGAAAATATAAGGTAT
Found at i:17142 original size:11 final size:12
Alignment explanation
Indices: 17118--17145 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
17108 TGATTTTTCG
17118 TTATAAATTTTT
1 TTATAAATTTTT
17130 TTATAAATTTTT
1 TTATAAATTTTT
17142 TTAT
1 TTAT
17146 TATACTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATAAATTTTT
Found at i:22838 original size:17 final size:18
Alignment explanation
Indices: 22818--22858 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
22808 AAATTATATT
22818 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
22835 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
22853 ATTAAA
1 AGTAAA
22859 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:24904 original size:24 final size:24
Alignment explanation
Indices: 24876--24932 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
24866 ATGGGATTGT
24876 GGTGAATTTTGTGAAGATCTTGAA
1 GGTGAATTTTGTGAAGATCTTGAA
24900 GGTGAATTTTGTGAAGATCTTGAA
1 GGTGAATTTTGTGAAGATCTTGAA
*
24924 GGTGGATTT
1 GGTGAATTT
24933 GAGGAGAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.04, G:0.32, T:0.39
Consensus pattern (24 bp):
GGTGAATTTTGTGAAGATCTTGAA
Found at i:32182 original size:21 final size:20
Alignment explanation
Indices: 32155--32252 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
32145 AATCAGTGTC
32155 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
32176 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
32196 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
32216 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
32237 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
32253 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 31 0.51
21 30 0.49
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:32205 original size:41 final size:41
Alignment explanation
Indices: 32096--32252 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
32086 AAATGACCAA
* **
32096 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
32135 CAGAATCGCAAATC-AGTGTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
32176 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
32217 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
32253 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:32262 original size:20 final size:20
Alignment explanation
Indices: 32239--32409 Score: 107
Period size: 20 Copynumber: 8.6 Consensus size: 20
32229 GCGAATATGA
32239 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* * *
32259 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
32279 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAACCAT
** *
32299 AAATCGCAACGCGTTTCCGT
1 AAATCGCAACGCGTAACCAT
* * *
32319 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* *
32339 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
* **
32359 AAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGTAA-CCAT
* *
32379 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGTAA-CCAT
32399 AAATCGCAACG
1 AAATCGCAACG
32410 AGAATCTGTA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.02
20 127 0.97
21 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:32304 original size:60 final size:58
Alignment explanation
Indices: 32219--32428 Score: 208
Period size: 60 Copynumber: 3.5 Consensus size: 58
32209 CGATTTTCCA
* ** * *
32219 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCGAAC-CGTAAATCGCAA-GCGTATCCGT
* ** *
32279 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTTTCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGTAAATCGCAACGCG-AACCGTAAATCGCAA-GCGTATCCGT
* *
32339 AAATCGCAACGAT-AATCCGTAAATCGCAACGAGAATCTGTAAATCGCAA-CGATAATCCGT
1 AAATCGCAACG-TGAATCCGTAAATCGCAACGCGAA-CCGTAAATCGCAAGCG-T-ATCCGT
* * *
32399 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGTGAATCCGTAAATCGCAAC
32429 ACTGAAATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
58 2 0.02
59 1 0.01
60 120 0.96
61 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (58 bp):
AAATCGCAACGTGAATCCGTAAATCGCAACGCGAACCGTAAATCGCAAGCGTATCCGT
Found at i:32410 original size:20 final size:20
Alignment explanation
Indices: 32273--32428 Score: 174
Period size: 20 Copynumber: 7.8 Consensus size: 20
32263 CGCAATGCGT
*
32273 ATCCGTAAATCGCAACG-TGT
1 ATCCGTAAATCGCAACGAT-A
*
32293 ATCCGTAAATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
* * *
32313 TTCCGTATATCGCAACGCGT-
1 ATCCGTAAATCGCAACG-ATA
32333 ATCCGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
32353 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
*
32373 ATCTGTAAATCGCAACGATA
1 ATCCGTAAATCGCAACGATA
*
32393 ATCCGTAAATCGCAACGAGA
1 ATCCGTAAATCGCAACGATA
* *
32413 ATCTGTAAATCACAAC
1 ATCCGTAAATCGCAAC
32429 ACTGAAATTT
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCCGTAAATCGCAACGATA
Found at i:32410 original size:40 final size:40
Alignment explanation
Indices: 32239--32428 Score: 208
Period size: 40 Copynumber: 4.8 Consensus size: 40
32229 GCGAATATGA
* *
32239 AAATCGCAACGCGAA-CACATAAATCGCAATGCG-T-ATCCGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAA--CGATAATCCGT
* * * *
32279 AAATCGCAACGTGTATCCGTAAATCGCAACGCGT-TTCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACG-ATAATCCGT
* * *
32319 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
*
32359 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
* *
32399 AAATCGCAACGAGAATCTGTAAATCACAAC
1 AAATCGCAACGAGAATCCGTAAATCGCAAC
32429 ACTGAAATTT
Statistics
Matches: 133, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 129 0.97
41 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (40 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGATAATCCGT
Found at i:33348 original size:12 final size:12
Alignment explanation
Indices: 33331--33355 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33321 ATATAATCCT
33331 GAAGAAGAAAAA
1 GAAGAAGAAAAA
33343 GAAGAAGAAAAA
1 GAAGAAGAAAAA
33355 G
1 G
33356 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:35660 original size:19 final size:19
Alignment explanation
Indices: 35638--35949 Score: 439
Period size: 19 Copynumber: 17.4 Consensus size: 19
35628 CGGAAATTAC
*
35638 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
35657 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
35671 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
35691 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
35705 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35724 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
35743 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
35757 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35776 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35795 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35814 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35833 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35852 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35871 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35890 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35909 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
35923 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
35942 AATCGCAA
1 AATCGCAA
35950 CGAGAGAATC
Statistics
Matches: 266, Mismatches: 6, Indels: 42
0.85 0.02 0.13
Matches are distributed among these distances:
14 40 0.15
15 2 0.01
16 11 0.04
17 10 0.04
18 3 0.01
19 187 0.70
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:35928 original size:14 final size:14
Alignment explanation
Indices: 35909--35963 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
35899 GCGAAATGAA
35909 AATCGCAACGAAAG
1 AATCGCAACGAAAG
35923 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
35940 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
35956 AATCGCAA
1 AATCGCAA
35964 TGCGAAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 5 0.14
19 8 0.23
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:36022 original size:19 final size:19
Alignment explanation
Indices: 35978--36075 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
35968 AAATTATAAA
35978 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
35997 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
36017 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
36033 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
36050 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
36069 CGCATTG
1 CGCATTG
36076 TGATAGCCAT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 32 0.45
20 19 0.27
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:36086 original size:19 final size:19
Alignment explanation
Indices: 36045--36087 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
36035 TTGCGATTTT
***
36045 CATTTCGCATTGCGATTTT
1 CATTTCGCATTGCGATAGC
*
36064 CATTTCGCATTGTGATAGC
1 CATTTCGCATTGCGATAGC
36083 CATTT
1 CATTT
36088 TTGCCTTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:36205 original size:14 final size:15
Alignment explanation
Indices: 36186--36223 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
36176 CATCAATTAC
36186 ACAAATCAA-CTTTT
1 ACAAATCAATCTTTT
36200 ACAAAT-AATCTTTT
1 ACAAATCAATCTTTT
36214 ACAAATCAAT
1 ACAAATCAAT
36224 TAAACAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 17 0.77
15 3 0.14
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAATCTTTT
Found at i:38215 original size:14 final size:14
Alignment explanation
Indices: 38196--38252 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
38186 GCGAAATGAA
*
38196 AATCGCAACGACAG
1 AATCGCAACGAAAG
38210 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
38227 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
38243 AATCGCAACG
1 AATCGCAACG
38253 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:38223 original size:33 final size:33
Alignment explanation
Indices: 38177--38269 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
38167 GCGAAACCAA
*
38177 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
38210 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
38243 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
38270 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:38234 original size:19 final size:19
Alignment explanation
Indices: 38140--38274 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
38130 TAGTTTACTT
* *
38140 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
38160 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
38179 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
38198 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
38212 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
38231 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
38245 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
38264 TCGCAATGCGA
1 TCGCAACGCGA
38275 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:38286 original size:19 final size:19
Alignment explanation
Indices: 38270--38382 Score: 111
Period size: 19 Copynumber: 6.5 Consensus size: 19
38260 AAAATCGCAA
38270 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
38289 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
38303 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
38322 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
38336 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
38355 TGCGATTTTGGTTTCGCAT
1 TGCGATTTTGGTTTCGCGT
38374 TGCGATTTT
1 TGCGATTTT
38383 AACTTTCGTG
Statistics
Matches: 76, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.29
15 1 0.01
16 2 0.03
17 2 0.03
18 2 0.03
19 47 0.62
ACGTcount: A:0.08, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:38312 original size:33 final size:33
Alignment explanation
Indices: 38270--38361 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
38260 AAAATCGCAA
38270 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
38303 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
38336 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
38362 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:38396 original size:20 final size:18
Alignment explanation
Indices: 38300--38398 Score: 71
Period size: 19 Copynumber: 5.4 Consensus size: 18
38290 GCGATCTTGT
*
38300 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTT-ATTTCG
* *
38319 CGTTGCGA--TTCTGT--
1 CGTTGCGATTTTATTTCG
38333 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTT-ATTTCG
*
38352 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTT-ATTTCG
*
38371 CATTGCGATTTTAACTTTCG
1 CGTTGCGATTTT-A-TTTCG
*
38391 TGTTGCGA
1 CGTTGCGA
38399 AAGTAAACTA
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
14 8 0.13
16 4 0.06
17 4 0.06
19 36 0.57
20 11 0.17
ACGTcount: A:0.10, C:0.18, G:0.26, T:0.45
Consensus pattern (18 bp):
CGTTGCGATTTTATTTCG
Found at i:38562 original size:93 final size:93
Alignment explanation
Indices: 38446--38914 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
38436 ATGGATTGCA
*
38446 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAAAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
38510 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
38538 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
38603 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
38631 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
38696 TAGCAGAATTGGTAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
38724 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
38789 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
38817 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
38882 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
38910 TTACT
1 TTACT
38915 AAGCAATCTA
Statistics
Matches: 372, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 368 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:40637 original size:14 final size:14
Alignment explanation
Indices: 40618--40674 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
40608 TTGAAATGAA
40618 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
40632 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
40651 AATCGCAACGAGAG
1 AATCGCAACGAGAG
40665 AATCGCAACG
1 AATCGCAACG
40675 CGAAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.42, C:0.25, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:40655 original size:33 final size:33
Alignment explanation
Indices: 40610--40691 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
40600 TCTTTTGGTT
40610 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
40643 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
40676 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
40692 TGCGATTTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:40656 original size:19 final size:19
Alignment explanation
Indices: 40632--40696 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
40622 GCAACGAGAG
*
40632 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
40651 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
40665 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
40684 AATCGCAATGCGA
1 AATCGCAACGCGA
40697 TTTTGGTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 10 0.27
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 21 0.57
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:40727 original size:14 final size:14
Alignment explanation
Indices: 40708--40764 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
40698 TTTGGTTTCG
40708 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
40722 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
40741 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
40755 CGTTGCGATT
1 CGTTGCGATT
40765 GTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:40746 original size:19 final size:19
Alignment explanation
Indices: 40722--40810 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 19
40712 GCGATTCTCT
40722 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
40741 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
40755 CGTTGCGATTGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*** *
40774 CGTTGCGACAGTCATTCTCT
1 CGTTGCGATTTTCATT-TCG
40794 CGTTGCGATTTTCATTT
1 CGTTGCGATTTTCATTT
40811 ATCTCGTTGC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 25 0.45
20 15 0.27
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:40802 original size:39 final size:33
Alignment explanation
Indices: 40692--40810 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 33
40682 AAAATCGCAA
**
40692 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
40725 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
40758 TGCGATTGTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT--G-C-G--ATTCTCTCGT
40797 TGCGATTTTCATTT
1 TGCGATTTTCATTT
40811 ATCTCGTTGC
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
33 50 0.66
35 1 0.01
36 1 0.01
37 1 0.01
39 23 0.30
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:40944 original size:33 final size:33
Alignment explanation
Indices: 40902--40972 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
40892 AATACTAACT
40902 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
40935 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
40968 TGAAA
1 TGAAA
40973 TCTAAGTGAA
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:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:41206 original size:22 final size:22
Alignment explanation
Indices: 41154--41208 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
41144 TGGTTGTGAG
**
41154 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
41176 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
41198 GGATTTCTTCG
1 GGATTTCTTCG
41209 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:41380 original size:20 final size:20
Alignment explanation
Indices: 41355--41548 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
41345 CTTTAAATAT
41355 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
41375 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
* *
41397 -TCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATA
*
41416 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
41436 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
41456 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
41476 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
41496 CGCATTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
41516 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
41536 CGCGTTGCGATTT
1 CGCGTTGCGATTT
41549 TGGAAAATCG
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:41542 original size:60 final size:60
Alignment explanation
Indices: 41355--41548 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
41345 CTTTAAATAT
* ** *
41355 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACCGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGA-TTTATGTATTCGCGTTGCGATTTACAGATA
* *** * *
41416 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
* * * * *
41476 CACGTTGCGATTTACGGATACGCATTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
41536 CGCGTTGCGATTT
1 CGCGTTGCGATTT
41549 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCATTGCGATTTATGTATTCGCGTTGCGATTTACAGATA
Found at i:41565 original size:21 final size:20
Alignment explanation
Indices: 41515--41612 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
41505 ATTTATGTGT
* * * *
41515 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
41535 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
41556 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
41576 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
41597 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
41613 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:41607 original size:41 final size:41
Alignment explanation
Indices: 41515--41612 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
41505 ATTTATGTGT
* * *
41515 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
41556 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
41597 TCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTG
41613 GAAACTGATT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.04
41 42 0.91
42 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Found at i:41906 original size:12 final size:13
Alignment explanation
Indices: 41880--41908 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41870 TCTATCAACC
41880 TCTTAAAAAATTA
1 TCTTAAAAAATTA
41893 TCTTAAAAAA-TA
1 TCTTAAAAAATTA
41905 TCTT
1 TCTT
41909 TTTTGAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (13 bp):
TCTTAAAAAATTA
Found at i:48776 original size:2 final size:2
Alignment explanation
Indices: 48769--48801 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
48759 GAATAAATAA
48769 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 A
48802 AAATTATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48953 original size:18 final size:16
Alignment explanation
Indices: 48927--48969 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
48917 TTTTTTCTAT
48927 TAAATTATAACTTATTATA
1 TAAA-TATAAC-TATTA-A
*
48946 TATATATAACTATTAA
1 TAAATATAACTATTAA
48962 TAAATATA
1 TAAATATA
48970 TTCAATATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 8 0.36
17 5 0.23
18 6 0.27
19 3 0.14
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATATAACTATTAA
Found at i:48970 original size:18 final size:18
Alignment explanation
Indices: 48927--48970 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
48917 TTTTTTCTAT
48927 TAAAT-TATAACTTATTA
1 TAAATATATAACTTATTA
*
48944 TATATATATAAC-TATTAA
1 TAAATATATAACTTATT-A
48962 TAAATATAT
1 TAAATATAT
48971 TCAATATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATATATAACTTATTA
Found at i:56216 original size:31 final size:30
Alignment explanation
Indices: 56176--56253 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
56166 TTAAAATATT
56176 GTAAGAATAAAATATAAATATTT-AAGTTAAA
1 GTAAGAATAAAATATAAAT-TTTAAAGTT-AA
* * *
56207 GTAAAAATAAAATTTATATTTTAAAGTTAA
1 GTAAGAATAAAATATAAATTTTAAAGTTAA
*
56237 GATAAGACTAAAATATA
1 G-TAAGAATAAAATATA
56254 TTTTTATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 6 0.15
31 33 0.85
ACGTcount: A:0.56, C:0.01, G:0.09, T:0.33
Consensus pattern (30 bp):
GTAAGAATAAAATATAAATTTTAAAGTTAA
Found at i:62858 original size:7 final size:7
Alignment explanation
Indices: 62846--62893 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
62836 AATTAACTGA
62846 AAATATT
1 AAATATT
62853 AAATATT
1 AAATATT
62860 AAATATT
1 AAATATT
*
62867 ATATATT
1 AAATATT
* *
62874 ATATAAAT
1 AAAT-ATT
*
62882 ATATATT
1 AAATATT
62889 AAATA
1 AAATA
62894 CATATTTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
7 30 0.83
8 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATATT
Found at i:62865 original size:14 final size:14
Alignment explanation
Indices: 62846--62893 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
62836 AATTAACTGA
*
62846 AAATATTAAATATT
1 AAATATTATATATT
62860 AAATATTATATATT
1 AAATATTATATATT
* *
62874 ATATAAATATATATT
1 AAAT-ATTATATATT
62889 AAATA
1 AAATA
62894 CATATTTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATATTATATATT
Found at i:62898 original size:15 final size:14
Alignment explanation
Indices: 62855--62898 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
62845 AAAATATTAA
*
62855 ATATTAAATATTAT
1 ATATTAAATAATAT
*
62869 ATATTATATAAATAT
1 ATATTAAAT-AATAT
62884 ATATTAAATACATAT
1 ATATTAAATA-ATAT
62899 TTCAAGCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATTAAATAATAT
Found at i:71102 original size:16 final size:17
Alignment explanation
Indices: 71067--71100 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
71057 ACAATTAAAA
71067 TAAGATAAAAACATCTT
1 TAAGATAAAAACATCTT
*
71084 TAAGATAAAACCATCTT
1 TAAGATAAAAACATCTT
71101 AAAGCAGCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (17 bp):
TAAGATAAAAACATCTT
Found at i:73283 original size:15 final size:15
Alignment explanation
Indices: 73265--73311 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 15
73255 TTAACGGCAT
73265 AATAATTAAATTAAA
1 AATAATTAAATTAAA
73280 AATAATTTAAAATTAAA
1 AATAA-TT-AAATTAAA
*
73297 TA-AATT-AATTAAA
1 AATAATTAAATTAAA
73310 AA
1 AA
73312 ATTTAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 8 0.29
15 7 0.25
16 4 0.14
17 9 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAATTAAATTAAA
Found at i:77338 original size:14 final size:15
Alignment explanation
Indices: 77309--77349 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
77299 TAAAATACGA
77309 TTTTGATCAAATTTT
1 TTTTGATCAAATTTT
77324 TTTTGATCAAATTTT
1 TTTTGATCAAATTTT
*
77339 TTTTGAACAAA
1 TTTTGATCAAA
77350 ATCGTAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (15 bp):
TTTTGATCAAATTTT
Found at i:77476 original size:20 final size:20
Alignment explanation
Indices: 77451--77495 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
77441 GAATATGTAA
77451 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
77471 ATCGCAACGTGATTCTGACT
1 ATCGCAACGCGATTCTGACT
77491 ATCGC
1 ATCGC
77496 GTTACGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:77694 original size:22 final size:22
Alignment explanation
Indices: 77669--77719 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
77659 CTACGGCGAC
*
77669 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCACATCTCCGACGAA
**
77691 ATCCGTCCACATCTCCGGTGAA
1 ATCCGTCCACATCTCCGACGAA
77713 ATCCGTC
1 ATCCGTC
77720 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCACATCTCCGACGAA
Found at i:78196 original size:58 final size:59
Alignment explanation
Indices: 78106--78219 Score: 212
Period size: 58 Copynumber: 1.9 Consensus size: 59
78096 GATAGTCAAA
78106 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCA-TTTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGCGTTGCGATTTTCAT
*
78164 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGTGTTGCGATTTT
1 TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGCGTTGCGATTTT
78220 AAGTTTCAGA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
58 38 0.70
59 16 0.30
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (59 bp):
TTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGCGTTGCGATTTTCAT
Found at i:78217 original size:20 final size:20
Alignment explanation
Indices: 78106--78219 Score: 151
Period size: 20 Copynumber: 5.8 Consensus size: 20
78096 GATAGTCAAA
**
78106 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCATT
*
78126 TTCGTGTTGCGATTTTCA-T
1 TTCGCGTTGCGATTTTCATT
78145 TTCGCGTTGCGATTTTCA-T
1 TTCGCGTTGCGATTTTCATT
**
78164 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCATT
*
78184 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
78204 TTCGTGTTGCGATTTT
1 TTCGCGTTGCGATTTT
78220 AAGTTTCAGA
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
19 35 0.42
20 49 0.58
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:79809 original size:42 final size:42
Alignment explanation
Indices: 79763--79870 Score: 162
Period size: 42 Copynumber: 2.6 Consensus size: 42
79753 TCAATGCCTT
* * *
79763 GCGTGAGGAGGTCGGTACTTTACGCGATGACAATGGTGCATG
1 GCGTGACGAGGTAGCTACTTTACGCGATGACAATGGTGCATG
*
79805 GCGTGACGAGGTATCTACTTTACGCGATGACAATGGTGCATG
1 GCGTGACGAGGTAGCTACTTTACGCGATGACAATGGTGCATG
* *
79847 GTGTGACGAGGTATCTACTTTACG
1 GCGTGACGAGGTAGCTACTTTACG
79871 TGGTGAGGTA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (42 bp):
GCGTGACGAGGTAGCTACTTTACGCGATGACAATGGTGCATG
Found at i:80206 original size:20 final size:20
Alignment explanation
Indices: 80178--80226 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
80168 AAACTTAAAA
*
80178 ATCGTAACGCGAAAATAACT
1 ATCGCAACGCGAAAATAACT
* ** *
80198 ATCGCAACGTGAATTTGACT
1 ATCGCAACGCGAAAATAACT
80218 ATCGCAACG
1 ATCGCAACG
80227 GGATAATCGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAACT
Found at i:80257 original size:33 final size:34
Alignment explanation
Indices: 80218--80297 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 34
80208 GAATTTGACT
* *
80218 ATCGCAACGGGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGCGAAAATCGCAATGCGAAAATAAAA
*
80251 ATCGCAACGCGAAAATCGCAATGCGAAAATGAAA
1 ATCGCAACGCGAAAATCGCAATGCGAAAATAAAA
*
80285 ATCGTAACGCGAA
1 ATCGCAACGCGAA
80298 TTTAGTTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 23 0.55
34 19 0.45
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAAAATCGCAATGCGAAAATAAAA
Found at i:80267 original size:14 final size:14
Alignment explanation
Indices: 80248--80280 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
80238 ATGCGAAATA
80248 AAAATCGCAACGCG
1 AAAATCGCAACGCG
*
80262 AAAATCGCAATGCG
1 AAAATCGCAACGCG
80276 AAAAT
1 AAAAT
80281 GAAAATCGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGCG
Found at i:80325 original size:19 final size:20
Alignment explanation
Indices: 80298--80336 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
80288 GTAACGCGAA
*
80298 TTTAGTTTCACGTTGCGATT
1 TTTAGTTTCACATTGCGATT
*
80318 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCACATTGCGATT
80337 ATCCCGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCACATTGCGATT
Found at i:80369 original size:20 final size:20
Alignment explanation
Indices: 80341--80389 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
80331 GCGATTATCC
80341 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
80361 CGTTTCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
80381 AGTTGCGAT
1 CGTTGCGAT
80390 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:80399 original size:20 final size:20
Alignment explanation
Indices: 80376--80419 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
80366 CGATAGTCAT
80376 TTTCGAGTTGCGATTTTAAG
1 TTTCGAGTTGCGATTTTAAG
* *
80396 TTTCGTGTTGTGATTTTAAG
1 TTTCGAGTTGCGATTTTAAG
80416 TTTC
1 TTTC
80420 AGAAACTATT
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:0.16, C:0.09, G:0.23, T:0.52
Consensus pattern (20 bp):
TTTCGAGTTGCGATTTTAAG
Found at i:83425 original size:24 final size:24
Alignment explanation
Indices: 83358--83417 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
83348 CTTAAACATC
83358 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
83382 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
83406 ATCAAATTTCGA
1 ATCAAAATTCGA
83418 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Done.