Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005583.1 Hibiscus syriacus cultivar Beakdansim tig00012961_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: 87619
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:2773 original size:18 final size:18
Alignment explanation
Indices: 2752--2789 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2742 CCTTACACAC
2752 TTTGCCACAACAACACCA
1 TTTGCCACAACAACACCA
* *
2770 TTTGCCACGACAACGCCA
1 TTTGCCACAACAACACCA
2788 TT
1 TT
2790 CATACTTCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.37, G:0.11, T:0.21
Consensus pattern (18 bp):
TTTGCCACAACAACACCA
Found at i:6374 original size:23 final size:23
Alignment explanation
Indices: 6305--6385 Score: 96
Period size: 23 Copynumber: 3.7 Consensus size: 23
6295 ACACCTAACA
*
6305 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
6327 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
6348 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
6371 GTGCATCGATGCACA
1 GTGCATCGATGCACA
6386 AGGCCGTGCA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.32
22 10 0.21
23 21 0.45
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:6402 original size:43 final size:43
Alignment explanation
Indices: 6305--6403 Score: 110
Period size: 43 Copynumber: 2.3 Consensus size: 43
6295 ACACCTAACA
* * *
6305 GTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGAAG
1 GTGCATCGATGCAGCCTTGAATGTGCATCGATACACCAAGAAC
* * **
6348 GTGCACCGATGCACGCCTTGAATGTGCATCGATGCA-CAAGGCC
1 GTGCATCGATGCA-GCCTTGAATGTGCATCGATACACCAAGAAC
*
6391 GTGCATTGATGCA
1 GTGCATCGATGCA
6404 TCCATCGGGT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
43 26 0.57
44 20 0.43
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.23
Consensus pattern (43 bp):
GTGCATCGATGCAGCCTTGAATGTGCATCGATACACCAAGAAC
Found at i:8324 original size:14 final size:15
Alignment explanation
Indices: 8299--8328 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
8289 TTGATTTTGA
8299 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
8314 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
8328 T
1 T
8329 AATGTTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.07, C:0.03, G:0.27, T:0.63
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:8381 original size:2 final size:2
Alignment explanation
Indices: 8374--8417 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
8364 TTTGAACTTA
8374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8416 AT
1 AT
8418 TTGGTTTGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9248 original size:43 final size:43
Alignment explanation
Indices: 9195--9545 Score: 256
Period size: 43 Copynumber: 8.2 Consensus size: 43
9185 TGAGAACAAA
* *
9195 AAACGCCGCAATAGGTCAATATATATTA-CGGCGTTTTTTGAAC
1 AAACGCCGCAAAAGGTCAATATATA-TAGCGGCGTTTTTGGAAC
* * *
9238 AAACGTCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCAATATATATAGCGGCGTTTTTGGAAC
* * * * * *
9281 AAACGCCACAAAAAGT-TATGATATATAGCGGCGTTTCT-AAAA
1 AAACGCCGCAAAAGGTCAAT-ATATATAGCGGCGTTTTTGGAAC
* *
9323 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAATATATATAGCGGCGTTTTTGGA-AC
* * ** * *
9366 AAATGCCGCAAAAGAG-C-AGACCTATA-CTGGCATTTTTAGAAC
1 AAACGCCGCAAAAG-GTCAATATATATAGC-GGCGTTTTTGGAAC
* **
9408 AAACGCCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAATATATATAGCGGCGTTTTTGGA-AC
* * ** **
9451 GAACGCTGCAAAAGGTCAGACCTATA-A-CGGCGTTTTTAAACAC
1 AAACGCCGCAAAAGGTCA-ATATATATAGCGGCGTTTTTGGA-AC
* * **
9494 AAACGCCGCAAAAAGTC-AGACCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAATATATATAGCGGCGTTTTTGGA-AC
9537 AAACGCCGC
1 AAACGCCGC
9546 TAATTACCTT
Statistics
Matches: 249, Mismatches: 45, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
41 20 0.08
42 59 0.24
43 165 0.66
44 2 0.01
45 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAATATATATAGCGGCGTTTTTGGAAC
Found at i:9330 original size:128 final size:127
Alignment explanation
Indices: 9192--9543 Score: 372
Period size: 128 Copynumber: 2.7 Consensus size: 127
9182 GTTTGAGAAC
* * * *
9192 AAAAAACGCCGCAATAGGTCA-ATATATATTACGGCGTTTTTTGA-ACAAACGTCGCAAAAGGTC
1 AAAAAACGCCGCAAAAGGTCAGATCTATA--ACGGCGTTTTTAGACACAAACGCCGCAAAAGGTC
* * * *
9255 GATATCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAAGTTATGATATATAGCGGCGTTTCT-
64 -AGACCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAAGTCA-GACATATAGCGGCGTTTCTG
9319 A
127 A
* * * *
9320 AAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAATGCCGCAAAAGAG-CA
1 AAAAAACGCCGCAAAAGGTCAGATCTATAACGGCGTTTTTAGACACAAACGCCGCAAAAG-GTCA
* * * * * *
9384 GACCTATA-CTGGCATTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGA
65 GACCTATAGC-GGCGTTTTTGGAACAAACGCCACAAAAAGTCAGACATATAGCGGCGTTTCT-GA
* ** * * * *
9448 CACGAACGCTGCAAAAGGTCAGACCTATAACGGCGTTTTTAAACACAAACGCCGCAAAAAGTCAG
1 AAAAAACGCCGCAAAAGGTCAGATCTATAACGGCGTTTTTAGACACAAACGCCGCAAAAGGTCAG
9513 ACCTATAGCGGCGTTTTTGGATACAAACGCC
66 ACCTATAGCGGCGTTTTTGGA-ACAAACGCC
9544 GCTAATTACC
Statistics
Matches: 186, Mismatches: 29, Indels: 17
0.80 0.12 0.07
Matches are distributed among these distances:
126 17 0.09
127 47 0.25
128 105 0.56
129 17 0.09
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (127 bp):
AAAAAACGCCGCAAAAGGTCAGATCTATAACGGCGTTTTTAGACACAAACGCCGCAAAAGGTCAG
ACCTATAGCGGCGTTTTTGGAACAAACGCCACAAAAAGTCAGACATATAGCGGCGTTTCTGA
Found at i:9368 original size:85 final size:83
Alignment explanation
Indices: 9221--9545 Score: 375
Period size: 85 Copynumber: 3.8 Consensus size: 83
9211 CAATATATAT
* * * * *
9221 TACGGCGTTTTTTGAACAAACGTCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGA-ACAAAC
1 TACGGCG-TTTTTAAAAAAACGCCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTGGATACAAAC
* * **
9285 GCCACAAAAAGTTATGATATA
64 GCCGCAAAAAGTCA-GACCTA
* * *
9306 TAGCGGCGTTTCTAAAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAATG
1 TA-CGGCGTTTTTAAAAAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAACG
9371 CCGCAAAAGAG-CAGACCTA
65 CCGCAAAA-AGTCAGACCTA
* * * *
9390 TACTGGCATTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACGAAC
1 TAC-GGCGTTTTTA-AAAAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAAC
* *
9455 GCTGCAAAAGGTCAGACCTA
64 GCCGCAAAAAGTCAGACCTA
*
9475 TAACGGCGTTTTTAAACACAAACGCCGCAAAAAGTCAGACCTATAGCGGCGTTTTTGGATACAAA
1 T-ACGGCGTTTTTAAA-A-AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAA
9540 CGCCGC
63 CGCCGC
9546 TAATTACCTT
Statistics
Matches: 206, Mismatches: 25, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
83 1 0.00
84 39 0.19
85 109 0.53
86 57 0.28
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (83 bp):
TACGGCGTTTTTAAAAAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGATACAAACGC
CGCAAAAAGTCAGACCTA
Found at i:13026 original size:41 final size:42
Alignment explanation
Indices: 12955--13316 Score: 378
Period size: 41 Copynumber: 8.8 Consensus size: 42
12945 TATGACAATT
* *
12955 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGGTATAAAAACGCCACAAAAGTACGAGTCTATA
* * *
12997 GCAGCGTTTGGT-TTAAAACGCCACAAAAGTACGTGTCTATA
1 GCGGCGTTTGGTATAAAAACGCCACAAAAGTACGAGTCTATA
* * *
13038 GCGGCGTTT-GTGTAAAAACGCCACTAAAGTACGAATCTATA
1 GCGGCGTTTGGTATAAAAACGCCACAAAAGTACGAGTCTATA
* * **
13079 GCGGCGTTTGGTATTAAAATGCCACAAAAGTACTTGTCTATA
1 GCGGCGTTTGGTATAAAAACGCCACAAAAGTACGAGTCTATA
* *
13121 GCGGCGTTT-GTATAAAAATGCCACTAAAGTACGAGTCTATA
1 GCGGCGTTTGGTATAAAAACGCCACAAAAGTACGAGTCTATA
* * * * *
13162 GCGGCGTTTGGTATTAAAACGCAACAAAAGAATGTGTCTATA
1 GCGGCGTTTGGTATAAAAACGCCACAAAAGTACGAGTCTATA
* * * *
13204 GCGGCGTTT-GAATAAAAACGCCAGTAAAA-TACTAGTTTATA
1 GCGGCGTTTGGTATAAAAACGCCA-CAAAAGTACGAGTCTATA
* * * * *
13245 GCGGCGTTT-GTATAAAAACGCCACTACATTACGATTCTTTA
1 GCGGCGTTTGGTATAAAAACGCCACAAAAGTACGAGTCTATA
* * * *
13286 GCGGCGTTT-TTATACAAACGTCACTAAAGTA
1 GCGGCGTTTGGTATAAAAACGCCACAAAAGTA
13317 TAGTATTTTG
Statistics
Matches: 267, Mismatches: 48, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
40 4 0.01
41 180 0.67
42 83 0.31
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (42 bp):
GCGGCGTTTGGTATAAAAACGCCACAAAAGTACGAGTCTATA
Found at i:13045 original size:83 final size:83
Alignment explanation
Indices: 12955--13316 Score: 478
Period size: 83 Copynumber: 4.4 Consensus size: 83
12945 TATGACAATT
* *
12955 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATAGCAGCGTTTGGT-TTAAAACGCC
1 GCGGCGTTT-GTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCC
13019 ACAAAAGTACGTGTCTATA
65 ACAAAAGTACGTGTCTATA
* * *
13038 GCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATAGCGGCGTTTGGTATTAAAATGCCA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
*
13103 CAAAAGTACTTGTCTATA
66 CAAAAGTACGTGTCTATA
* *
13121 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCAA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
* *
13186 CAAAAGAATGTGTCTATA
66 CAAAAGTACGTGTCTATA
* * * * * *
13204 GCGGCGTTTGAATAAAAACGCCAGTAAAATACTAGTTTATAGCGGCGTTT-GTATAAAAACGCCA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
* * * *
13268 CTACATTACGAT-TCTTTA
66 CAAAAGTACG-TGTCTATA
* * *
13286 GCGGCGTTTTTATACAAACGTCACTAAAGTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTA
13317 TAGTATTTTG
Statistics
Matches: 243, Mismatches: 34, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
82 87 0.36
83 156 0.64
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (83 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCA
CAAAAGTACGTGTCTATA
Found at i:13150 original size:124 final size:124
Alignment explanation
Indices: 12955--13316 Score: 410
Period size: 124 Copynumber: 2.9 Consensus size: 124
12945 TATGACAATT
* * * *
12955 GCGGCGTTTGGTATTAAAACGCCACTAAAGTACGAGTCTATAGCAGCGTTTGGT-TTAAAACGCC
1 GCGGCGTTTGGTATTAAAACGCCACAAAAGTACTAGTCTATAGCGGCGTTT-GTATAAAAACGCC
*
13019 ACAAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
65 ACTAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
* * *
13079 GCGGCGTTTGGTATTAAAATGCCACAAAAGTACTTGTCTATAGCGGCGTTTGTATAAAAATGCCA
1 GCGGCGTTTGGTATTAAAACGCCACAAAAGTACTAGTCTATAGCGGCGTTTGTATAAAAACGCCA
* * * * * **
13144 CTAAAGTACGAGTCTATAGCGGCGTTTG-GTATTAAAACGCAACAAAAGAATGTGTCTATA
66 CTAAAGTACGTGTCTATAGCGGCGTTTGTGTA--AAAACGCCACTAAAGTACGAATCTATA
* * * *
13204 GCGGCGTTT-GAATAAAAACGCCAGTAAAA-TACTAGTTTATAGCGGCGTTTGTATAAAAACGCC
1 GCGGCGTTTGGTATTAAAACGCCA-CAAAAGTACTAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * * * * * *
13267 ACTACATTACGAT-TCTTTAGCGGCGTTTTTATACAAACGTCACTAAAGTA
65 ACTAAAGTACG-TGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTA
13317 TAGTATTTTG
Statistics
Matches: 199, Mismatches: 33, Indels: 13
0.81 0.13 0.05
Matches are distributed among these distances:
123 17 0.09
124 146 0.73
125 36 0.18
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (124 bp):
GCGGCGTTTGGTATTAAAACGCCACAAAAGTACTAGTCTATAGCGGCGTTTGTATAAAAACGCCA
CTAAAGTACGTGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAGTACGAATCTATA
Found at i:13536 original size:65 final size:64
Alignment explanation
Indices: 13450--13609 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 64
13440 AATTAAATTG
* * *
13450 AACATCGAATGCATTTCATGCATCGATGC-TCATACAATGCATCGATGCACTGAGGAT-TTTATA
1 AACATCGAATGCATTTGATGCATCGATGCACCA-ACAATGCATCGATGCACTCAGGATATTT-T-
13513 AA
63 AA
* * * * * *
13515 AACATCGAATGCATTTGATGCATCGATGCACCAGCTATGCATTGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACCAACAATGCATCGATGCACTCAGGATATTTTAA
*
13579 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
13610 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 31 0.37
65 47 0.57
66 5 0.06
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACCAACAATGCATCGATGCACTCAGGATATTTTAA
Found at i:13609 original size:17 final size:19
Alignment explanation
Indices: 13581--13629 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
13571 TATTTTGAAA
13581 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
13599 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
13618 CACCGATGCACT
1 CATCGATGCACT
13630 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:13858 original size:11 final size:11
Alignment explanation
Indices: 13842--13871 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
13832 ACAATCAACT
13842 AGAATCAAGAG
1 AGAATCAAGAG
13853 AGAATCAAGAG
1 AGAATCAAGAG
13864 AGAATCAA
1 AGAATCAA
13872 ATAGAAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.10, G:0.23, T:0.10
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:16085 original size:22 final size:22
Alignment explanation
Indices: 16059--16111 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
16049 TTATAAATTT
16059 TTATAAAAGT-TATATGAAACTA
1 TTATAAAAGTATATATGAAA-TA
* *
16081 TTATAAAAAGTATATTTGTAATA
1 TTAT-AAAAGTATATATGAAATA
16104 TTATAAAA
1 TTATAAAA
16112 TATTTATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.30
23 12 0.44
24 7 0.26
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (22 bp):
TTATAAAAGTATATATGAAATA
Found at i:16335 original size:22 final size:23
Alignment explanation
Indices: 16250--16344 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 23
16240 GGTTTCATAC
* * *
16250 AATATTATTTAAAATAATTAATT
1 AATATGATTTTAAATAATTAAAT
* * * *
16273 AATATTACTTCAAATAAATAAAT
1 AATATGATTTTAAATAATTAAAT
16296 AATATGATTTTAAA-AATTAAAT
1 AATATGATTTTAAATAATTAAAT
**
16318 AA-AT-ATTTTAATATAATTTCAT
1 AATATGATTTTAA-ATAATTAAAT
16340 AATAT
1 AATAT
16345 TATAAATATA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
20 7 0.12
21 3 0.05
22 17 0.29
23 32 0.54
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (23 bp):
AATATGATTTTAAATAATTAAAT
Found at i:16382 original size:22 final size:21
Alignment explanation
Indices: 16319--16383 Score: 53
Period size: 23 Copynumber: 3.0 Consensus size: 21
16309 AAATTAAATA
* *
16319 AATATTTTAATATA-ATTTCAT
1 AATA-TTTAATATATATTTTAG
16340 AATATTATAA-ATATACTTTTTAG
1 AATATT-TAATATATA--TTTTAG
16363 AATGATTTAATATATATTTTA
1 AAT-ATTTAATATATATTTTA
16384 TAAATATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
20 5 0.14
21 8 0.22
22 5 0.14
23 10 0.28
24 8 0.22
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (21 bp):
AATATTTAATATATATTTTAG
Found at i:21626 original size:24 final size:21
Alignment explanation
Indices: 21579--21652 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 21
21569 TAAATTGTGT
*
21579 ATCGATGCA-TGGTAG--TGC
1 ATCGATGCACTTGTAGAATGC
21597 ATCGATGCACTTGTTAAAGAATGC
1 ATCGATGCACTTG-T--AGAATGC
21621 ATCGATGCAC-TGTAGAATGC
1 ATCGATGCACTTGTAGAATGC
*
21641 ACCGATGCACTT
1 ATCGATGCACTT
21653 CAATGGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
18 9 0.19
19 2 0.04
20 17 0.36
21 1 0.02
22 3 0.06
23 2 0.04
24 13 0.28
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (21 bp):
ATCGATGCACTTGTAGAATGC
Found at i:25861 original size:24 final size:21
Alignment explanation
Indices: 25829--25885 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 21
25819 TGCATGGTAG
25829 TGCATCGATGCACCTGTTAAGGAA
1 TGCATCGATGCACCTG-T-A-GAA
*
25853 TGCATCGATGTA-CTGTAGAA
1 TGCATCGATGCACCTGTAGAA
*
25873 TGCACCGATGCAC
1 TGCATCGATGCAC
25886 TTCAATGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 13 0.45
21 1 0.03
22 1 0.03
23 3 0.10
24 11 0.38
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
TGCATCGATGCACCTGTAGAA
Found at i:31803 original size:3 final size:3
Alignment explanation
Indices: 31795--31832 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
31785 TCATTGCTTC
31795 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31833 ATATGTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:32436 original size:2 final size:2
Alignment explanation
Indices: 32429--32489 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
32419 CAATCATTCA
32429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32471 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
32490 AACACTAGAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34063 original size:16 final size:16
Alignment explanation
Indices: 34042--34074 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
34032 CATTAGGTAA
34042 TCCCGATGATCTTTCC
1 TCCCGATGATCTTTCC
34058 TCCCGATGATCTTTCC
1 TCCCGATGATCTTTCC
34074 T
1 T
34075 GTCGGTAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.36, G:0.12, T:0.39
Consensus pattern (16 bp):
TCCCGATGATCTTTCC
Found at i:34929 original size:13 final size:13
Alignment explanation
Indices: 34911--34936 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34901 ATAAACTAAT
34911 AATAAAAAAATTA
1 AATAAAAAAATTA
34924 AATAAAAAAATTA
1 AATAAAAAAATTA
34937 TTAATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAAAAAATTA
Found at i:39049 original size:12 final size:13
Alignment explanation
Indices: 39028--39056 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
39018 TATGTTACTG
39028 AATATGAAACCTT
1 AATATGAAACCTT
39041 AATAT-AAACCTT
1 AATATGAAACCTT
39053 AATA
1 AATA
39057 ATACGTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.14, G:0.03, T:0.31
Consensus pattern (13 bp):
AATATGAAACCTT
Found at i:40368 original size:32 final size:32
Alignment explanation
Indices: 40331--40402 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
40321 AAGTGTCATG
*
40331 CGACACCAATGGCTC-ACGCATGGACTGCCATA
1 CGACACCAATGGC-CAACACATGGACTGCCATA
* * *
40363 TGACACCCATGGCCAACACATGGACTGCCATG
1 CGACACCAATGGCCAACACATGGACTGCCATA
40395 CGACACCA
1 CGACACCA
40403 TTGCATGCCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 1 0.03
32 32 0.97
ACGTcount: A:0.29, C:0.36, G:0.21, T:0.14
Consensus pattern (32 bp):
CGACACCAATGGCCAACACATGGACTGCCATA
Found at i:40761 original size:28 final size:28
Alignment explanation
Indices: 40721--40781 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
40711 CAGGTAATTT
40721 ATTTTATTCATATATTAGGGTTCAAAAA
1 ATTTTATTCATATATTAGGGTTCAAAAA
* *
40749 ATTTTATTCATATATTAGGGTTCGAATA
1 ATTTTATTCATATATTAGGGTTCAAAAA
40777 ATTTT
1 ATTTT
40782 CGAATAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (28 bp):
ATTTTATTCATATATTAGGGTTCAAAAA
Found at i:44090 original size:2 final size:2
Alignment explanation
Indices: 44048--44075 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44038 TACATATCAA
44048 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
44076 CAACTCTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57094 original size:36 final size:37
Alignment explanation
Indices: 57037--57107 Score: 117
Period size: 36 Copynumber: 1.9 Consensus size: 37
57027 TATATATTAG
*
57037 AAATATAAATTTTTAAAAAATTATATTAAAATTTTTA
1 AAATACAAATTTTTAAAAAATTATATTAAAATTTTTA
*
57074 AAATACAAA-TTTTAAGAAATTATATTAAAATTTT
1 AAATACAAATTTTTAAAAAATTATATTAAAATTTT
57108 AGAAGATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 24 0.75
37 8 0.25
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (37 bp):
AAATACAAATTTTTAAAAAATTATATTAAAATTTTTA
Found at i:60454 original size:2 final size:2
Alignment explanation
Indices: 60447--60504 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
60437 CCATACATAC
* *
60447 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60489 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
60505 TGCAGTGTGT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:61901 original size:14 final size:14
Alignment explanation
Indices: 61882--61914 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
61872 TTTGATGCAG
61882 GTGATGTTG-ATGA
1 GTGATGTTGCATGA
61895 TGTGATGTTGCATGA
1 -GTGATGTTGCATGA
61910 GTGAT
1 GTGAT
61915 CTCACCTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.21, C:0.03, G:0.36, T:0.39
Consensus pattern (14 bp):
GTGATGTTGCATGA
Found at i:63413 original size:23 final size:21
Alignment explanation
Indices: 63364--63415 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
63354 AAAATTATAA
* *
63364 TTTAAAATTTGATATTATTTT
1 TTTAAAATTTAAAATTATTTT
63385 TATTAAAATTTTAAAATTATTATT
1 T-TTAAAA-TTTAAAATTATT-TT
63409 TTTAAAA
1 TTTAAAA
63416 CGTGAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 6 0.23
23 16 0.62
24 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTAAAATTTAAAATTATTTT
Found at i:63877 original size:50 final size:50
Alignment explanation
Indices: 63773--63877 Score: 147
Period size: 50 Copynumber: 2.1 Consensus size: 50
63763 TGAATCGTGT
* * * *
63773 TATACGCTGATTTGGCGCCACGTGGGTATAGCGCGCCCCCTGCCCCGCGA
1 TATACGCTGATCTGGCGCCACGTGGGTATAGCGCGCCCCCAGACCCACGA
* * *
63823 TATACGTTGATCTGGCGCCACGTGGGTATAGCGCGCCCCCAGATCCACGC
1 TATACGCTGATCTGGCGCCACGTGGGTATAGCGCGCCCCCAGACCCACGA
63873 TATAC
1 TATAC
63878 CTGGGTATCT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.17, C:0.34, G:0.28, T:0.21
Consensus pattern (50 bp):
TATACGCTGATCTGGCGCCACGTGGGTATAGCGCGCCCCCAGACCCACGA
Found at i:64004 original size:10 final size:10
Alignment explanation
Indices: 63989--64029 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
63979 TTTTATCACA
63989 TCAAATTCTC
1 TCAAATTCTC
63999 TCAAATTCTC
1 TCAAATTCTC
64009 T-AAATTTCTC
1 TCAAA-TTCTC
*
64019 TCAAATACTC
1 TCAAATTCTC
64029 T
1 T
64030 ATCTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:64350 original size:111 final size:111
Alignment explanation
Indices: 64156--64488 Score: 594
Period size: 111 Copynumber: 3.0 Consensus size: 111
64146 TAAAAATCAT
* *
64156 ATATCTCTACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * * *
64221 TATTTAATTGATTTATTTAATGCATAATTATTTGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
64267 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
64332 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
64378 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATATAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
64443 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
64489 TTTTTGTAAT
Statistics
Matches: 214, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 214 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:67476 original size:12 final size:12
Alignment explanation
Indices: 67459--67496 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
67449 ATTTATAAGA
67459 GAGGAGAGATGC
1 GAGGAGAGATGC
*
67471 GA-G-GAGATGT
1 GAGGAGAGATGC
67481 GAGGAGAGATGC
1 GAGGAGAGATGC
67493 GAGG
1 GAGG
67497 TATTTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.36
11 2 0.09
12 12 0.55
ACGTcount: A:0.32, C:0.05, G:0.53, T:0.11
Consensus pattern (12 bp):
GAGGAGAGATGC
Found at i:67755 original size:51 final size:51
Alignment explanation
Indices: 67637--67768 Score: 131
Period size: 51 Copynumber: 2.6 Consensus size: 51
67627 CTACGTGGCG
* * * * * * *
67637 TATAGCGCGG-AGCAAGGGGCGCGCTATACCCCACGTGTAACCCAGTCAGCG
1 TATAGCGCGGTA-CAGGGGGCGCGCTATACTCCACGTGGAACCAAATCAACA
* * **
67688 TATACCGTGGTACAGGGGGCGCGCTATACTCCACGTGGCGCCAAATCAACA
1 TATAGCGCGGTACAGGGGGCGCGCTATACTCCACGTGGAACCAAATCAACA
* *
67739 TATAGCGCGGTTCAGGGGGCGCGCTTTACT
1 TATAGCGCGGTACAGGGGGCGCGCTATACT
67769 GCTACGGGTG
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
51 64 0.98
52 1 0.02
ACGTcount: A:0.22, C:0.29, G:0.31, T:0.18
Consensus pattern (51 bp):
TATAGCGCGGTACAGGGGGCGCGCTATACTCCACGTGGAACCAAATCAACA
Found at i:68035 original size:15 final size:16
Alignment explanation
Indices: 68007--68037 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
67997 GTGGGAATAA
68007 AAGATTATCAGGGAAT
1 AAGATTATCAGGGAAT
68023 AAGATTA-CAGGGAAT
1 AAGATTATCAGGGAAT
68038 GTTACATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (16 bp):
AAGATTATCAGGGAAT
Found at i:73156 original size:12 final size:12
Alignment explanation
Indices: 73127--73167 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
73117 GATACTGAAA
*
73127 TGATATTATTTT
1 TGATAATATTTT
*
73139 T-TTAATATTTT
1 TGATAATATTTT
73150 TGATAATATTTT
1 TGATAATATTTT
73162 TGATAA
1 TGATAA
73168 AAAATTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (12 bp):
TGATAATATTTT
Found at i:75295 original size:113 final size:113
Alignment explanation
Indices: 75170--75404 Score: 362
Period size: 113 Copynumber: 2.1 Consensus size: 113
75160 TATTCATTTC
* * * * *
75170 AATAAAAAATATCAATTTAATTTATGTCGGGACAATGATTCTGTTGAAAATTTTGTTCAACTTTA
1 AATAAAAAATATCAATTTAATTTATGACGAGACAATGATTCTGTCGAAAATTCTGTTAAACTTTA
* * *
75235 ATTAAAATATACTAATTTAATTTGTGATGGAATAATCATTCCATCGGA
66 ATTAAAATATACCAATTTAATTTATGATAGAATAATCATTCCATCGGA
*
75283 AATAAAAAATATCAATTTAATTTATGACGAGACAATGATTCTGTCGAAAATTCTGTTAAATTTTA
1 AATAAAAAATATCAATTTAATTTATGACGAGACAATGATTCTGTCGAAAATTCTGTTAAACTTTA
* * *
75348 ATTAAAATCTACCAATTTAATTTATGATAGAATAGTCATTCCGTCGGA
66 ATTAAAATATACCAATTTAATTTATGATAGAATAATCATTCCATCGGA
75396 AATAAAAAA
1 AATAAAAAA
75405 AAACTACATT
Statistics
Matches: 110, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
113 110 1.00
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (113 bp):
AATAAAAAATATCAATTTAATTTATGACGAGACAATGATTCTGTCGAAAATTCTGTTAAACTTTA
ATTAAAATATACCAATTTAATTTATGATAGAATAATCATTCCATCGGA
Found at i:75670 original size:41 final size:41
Alignment explanation
Indices: 75613--75694 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
75603 CACTAGAAAT
75613 TCACTCTTCCAAATCTTCTCTACAGGACCACACCAACAAAG
1 TCACTCTTCCAAATCTTCTCTACAGGACCACACCAACAAAG
* *** *
75654 TCACTCTTCTAAATCTTCTCTGTGGGATCACACCAACAAAG
1 TCACTCTTCCAAATCTTCTCTACAGGACCACACCAACAAAG
75695 CCACACCAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.32, C:0.33, G:0.10, T:0.26
Consensus pattern (41 bp):
TCACTCTTCCAAATCTTCTCTACAGGACCACACCAACAAAG
Found at i:83042 original size:31 final size:31
Alignment explanation
Indices: 83007--83065 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
82997 TGATGGGATG
* *
83007 TGTGGACCCATCAGAAATTTGTGACAGAATA
1 TGTGGACCCATCACAAATTTATGACAGAATA
* *
83038 TGTGGATCCGTCACAAATTTATGACAGA
1 TGTGGACCCATCACAAATTTATGACAGA
83066 TTCACCTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (31 bp):
TGTGGACCCATCACAAATTTATGACAGAATA
Found at i:87471 original size:26 final size:25
Alignment explanation
Indices: 87420--87472 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
87410 TAGGACTAAA
*
87420 TTAAATGAAAATTAAACTTTATAAT
1 TTAAATGAAAATTAAACTTTAGAAT
*
87445 TTAAATTAAGAATTAAA-TTATAGAAT
1 TTAAATGAA-AATTAAACTT-TAGAAT
87471 TT
1 TT
87473 TAAAAAGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.42
Consensus pattern (25 bp):
TTAAATGAAAATTAAACTTTAGAAT
Done.