Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002925.1 Hibiscus syriacus cultivar Beakdansim tig00006044_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: 65672
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:5832 original size:20 final size:20
Alignment explanation
Indices: 5807--5857 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
5797 CACTTAGGGA
*
5807 ACCGATTCCTCATAGGGGGT
1 ACCGATTCCCCATAGGGGGT
5827 ACCGATTCCCCATAGGGGGT
1 ACCGATTCCCCATAGGGGGT
5847 ACCGATTCCCC
1 ACCGATTCCCC
5858 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.22
Consensus pattern (20 bp):
ACCGATTCCCCATAGGGGGT
Found at i:11171 original size:22 final size:23
Alignment explanation
Indices: 11146--11208 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
11136 ATTTTGGTGC
*
11146 AGAGGGAATCGA-TCCCCCCTTG
1 AGAGGGAACCGATTCCCCCCTTG
*
11168 AGA--GAACCGATTCCCCCTTTG
1 AGAGGGAACCGATTCCCCCCTTG
11189 A-AGGGGAACCGATTCCCCCC
1 AGA-GGGAACCGATTCCCCCC
11209 CACAGGGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 7 0.21
21 10 0.29
22 3 0.09
23 14 0.41
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.17
Consensus pattern (23 bp):
AGAGGGAACCGATTCCCCCCTTG
Found at i:23545 original size:37 final size:37
Alignment explanation
Indices: 23469--23545 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
23459 TTTTTATATT
*
23469 TTTAATTTTGTAAAAAATATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAATATTATATAAATATTATCAA
* *
23506 TTTAATTTTTTAAAGAAA-A-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAATATTATATAAATATTAT-CAA
23543 TTT
1 TTT
23546 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 19 0.54
38 3 0.09
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAATATTATATAAATATTATCAA
Found at i:23726 original size:20 final size:20
Alignment explanation
Indices: 23690--23727 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23680 AATCATATTC
**
23690 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
23710 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
23728 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:24976 original size:12 final size:12
Alignment explanation
Indices: 24939--24976 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
24929 GTATCAGATT
24939 AGAATCCATGTC
1 AGAATCCATGTC
*
24951 AGATAT-CATATC
1 AGA-ATCCATGTC
24963 AGAATCCATGTC
1 AGAATCCATGTC
24975 AG
1 AG
24977 TATCAGATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 2 0.09
12 18 0.82
13 2 0.09
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (12 bp):
AGAATCCATGTC
Found at i:24992 original size:24 final size:24
Alignment explanation
Indices: 24876--24989 Score: 135
Period size: 24 Copynumber: 4.8 Consensus size: 24
24866 CATAAATCAG
* *
24876 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* *
24900 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
24924 GTCAAGTATCAGATTAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
24948 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
24972 GTC-AGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
24990 ATCAAATCGA
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
23 17 0.22
24 62 0.78
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:25180 original size:47 final size:47
Alignment explanation
Indices: 25111--25209 Score: 198
Period size: 47 Copynumber: 2.1 Consensus size: 47
25101 GTATACCGAT
25111 AGAATATCGGAATTCAGAATCACTATTGAAAGAGTTCAATAACTGAC
1 AGAATATCGGAATTCAGAATCACTATTGAAAGAGTTCAATAACTGAC
25158 AGAATATCGGAATTCAGAATCACTATTGAAAGAGTTCAATAACTGAC
1 AGAATATCGGAATTCAGAATCACTATTGAAAGAGTTCAATAACTGAC
25205 AGAAT
1 AGAAT
25210 CATCAGTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.25
Consensus pattern (47 bp):
AGAATATCGGAATTCAGAATCACTATTGAAAGAGTTCAATAACTGAC
Found at i:26154 original size:18 final size:18
Alignment explanation
Indices: 26133--26173 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
26123 CTTCCATCCG
*
26133 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
26151 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
*
26169 GTCTT
1 ATCTT
26174 TTCGAACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.02, T:0.54
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:27488 original size:15 final size:14
Alignment explanation
Indices: 27464--27507 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
27454 GGTCAACGTG
27464 GGTCACGGGTCAAC
1 GGTCACGGGTCAAC
27478 GGTCAACGGGTCAAC
1 GGTC-ACGGGTCAAC
27493 GGGT--CGGGTCAAC
1 -GGTCACGGGTCAAC
27506 GG
1 GG
27508 GTCGGGTCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.07
13 9 0.32
14 4 0.14
15 10 0.36
16 3 0.11
ACGTcount: A:0.20, C:0.25, G:0.41, T:0.14
Consensus pattern (14 bp):
GGTCACGGGTCAAC
Found at i:27489 original size:8 final size:8
Alignment explanation
Indices: 27444--27510 Score: 63
Period size: 8 Copynumber: 8.5 Consensus size: 8
27434 TCAAAGTTTT
27444 GGTCAACAG
1 GGTCAAC-G
27453 TGGTCAACGTG
1 -GGTCAAC--G
27464 GGTC-ACG
1 GGTCAACG
27471 GGTCAAC-
1 GGTCAACG
27478 GGTCAACG
1 GGTCAACG
27486 GGTCAACG
1 GGTCAACG
27494 GGT---CG
1 GGTCAACG
27499 GGTCAACG
1 GGTCAACG
27507 GGTC
1 GGTC
27511 GGGTCGGGTC
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
5 5 0.10
7 12 0.24
8 19 0.38
9 2 0.04
10 11 0.22
11 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.39, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:27502 original size:13 final size:13
Alignment explanation
Indices: 27484--27515 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
27474 CAACGGTCAA
27484 CGGGTCAACGGGT
1 CGGGTCAACGGGT
27497 CGGGTCAACGGGT
1 CGGGTCAACGGGT
27510 CGGGTC
1 CGGGTC
27516 GGGTCAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:27515 original size:18 final size:18
Alignment explanation
Indices: 27478--27563 Score: 92
Period size: 18 Copynumber: 4.9 Consensus size: 18
27468 ACGGGTCAAC
27478 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
27499 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
27517 GGTCAAC---T--GGTCG
1 GGTCAACGGGTCGGGTCG
*
27530 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
27548 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
27564 AAACGGTCGG
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
13 11 0.19
15 1 0.02
16 1 0.02
18 33 0.58
21 11 0.19
ACGTcount: A:0.15, C:0.21, G:0.45, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:27522 original size:31 final size:31
Alignment explanation
Indices: 27484--27581 Score: 171
Period size: 31 Copynumber: 3.2 Consensus size: 31
27474 CAACGGTCAA
* *
27484 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
27515 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
27546 CGGGTCAACTGGTCGGGTAAAC-GGTCGGGT
1 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
27576 CGGGTC
1 CGGGTC
27582 GGGTTATGAC
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 14 0.22
31 51 0.78
ACGTcount: A:0.14, C:0.21, G:0.46, T:0.18
Consensus pattern (31 bp):
CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
Found at i:27528 original size:13 final size:13
Alignment explanation
Indices: 27484--27576 Score: 62
Period size: 13 Copynumber: 6.5 Consensus size: 13
27474 CAACGGTCAA
*
27484 CGGGTCAACGGGT
1 CGGGTCAACTGGT
27497 CGGGTCAACGGGTCGGGT
1 CGGGTCAAC---T--GGT
27515 CGGGTCAACTGGT
1 CGGGTCAACTGGT
*
27528 CGGGTAAACGGGTCGGGT
1 CGGGTCAAC---T--GGT
27546 CGGGTCAACTGGT
1 CGGGTCAACTGGT
*
27559 CGGGTAAAC-GGT
1 CGGGTCAACTGGT
27571 CGGGTC
1 CGGGTC
27577 GGGTCGGGTT
Statistics
Matches: 65, Mismatches: 5, Indels: 21
0.71 0.05 0.23
Matches are distributed among these distances:
12 8 0.12
13 31 0.48
15 2 0.03
16 1 0.02
18 23 0.35
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACTGGT
Found at i:29781 original size:24 final size:24
Alignment explanation
Indices: 29758--29875 Score: 141
Period size: 24 Copynumber: 4.9 Consensus size: 24
29748 AAACATAAAT
*
29758 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
29782 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
29806 CAAGTCAAGTATCAGATTAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
29830 CATGTC-AGATATCATATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
29854 CATGTCAAGTATCAGATCAGAA
1 CAGGTCAAGTATCAGATCAGAA
29876 ATCAAATCGA
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.06
24 75 0.91
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:30068 original size:47 final size:47
Alignment explanation
Indices: 29999--30097 Score: 198
Period size: 47 Copynumber: 2.1 Consensus size: 47
29989 GTATACCGAT
29999 AGAATATCGGAATTCAGAATCACTATTGAAAGAGTTCAATAACTGAC
1 AGAATATCGGAATTCAGAATCACTATTGAAAGAGTTCAATAACTGAC
30046 AGAATATCGGAATTCAGAATCACTATTGAAAGAGTTCAATAACTGAC
1 AGAATATCGGAATTCAGAATCACTATTGAAAGAGTTCAATAACTGAC
30093 AGAAT
1 AGAAT
30098 CATCAGTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.25
Consensus pattern (47 bp):
AGAATATCGGAATTCAGAATCACTATTGAAAGAGTTCAATAACTGAC
Found at i:31044 original size:18 final size:18
Alignment explanation
Indices: 31023--31063 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
31013 CTTCCATCCG
*
31023 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
31041 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
*
31059 GTCTT
1 ATCTT
31064 TTCGAACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.17, G:0.02, T:0.54
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:32373 original size:7 final size:8
Alignment explanation
Indices: 32333--32400 Score: 72
Period size: 8 Copynumber: 8.5 Consensus size: 8
32323 TCAAAGTTTT
32333 GGTCAACAG
1 GGTCAAC-G
32342 TGGTCAACGTG
1 -GGTCAAC--G
32353 GGTCAACG
1 GGTCAACG
32361 GGTCAAC-
1 GGTCAACG
32368 GGTCAACG
1 GGTCAACG
32376 GGTCAACG
1 GGTCAACG
32384 GGT---CG
1 GGTCAACG
32389 GGTCAACG
1 GGTCAACG
32397 GGTC
1 GGTC
32401 GGGTCGGGTC
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
5 5 0.10
7 7 0.13
8 25 0.48
10 14 0.27
11 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.38, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:32373 original size:15 final size:15
Alignment explanation
Indices: 32353--32384 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
32343 GGTCAACGTG
32353 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
32368 GGTCAACGGGTCAAC
1 GGTCAACGGGTCAAC
32383 GG
1 GG
32385 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:32392 original size:13 final size:13
Alignment explanation
Indices: 32374--32405 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
32364 CAACGGTCAA
32374 CGGGTCAACGGGT
1 CGGGTCAACGGGT
32387 CGGGTCAACGGGT
1 CGGGTCAACGGGT
32400 CGGGTC
1 CGGGTC
32406 GGGTCAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:32405 original size:18 final size:18
Alignment explanation
Indices: 32368--32472 Score: 95
Period size: 18 Copynumber: 6.2 Consensus size: 18
32358 ACGGGTCAAC
32368 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
32389 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
32407 GGTCAAC---T--GGTCG
1 GGTCAACGGGTCGGGTCG
*
32420 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
32438 GGTCAAC---T--GGTCG
1 GGTCAACGGGTCGGGTCG
*
32451 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
32469 GGTC
1 GGTC
32473 GGGTTATGAC
Statistics
Matches: 70, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.31
15 2 0.03
16 2 0.03
18 33 0.47
21 11 0.16
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:32409 original size:31 final size:31
Alignment explanation
Indices: 32374--32472 Score: 180
Period size: 31 Copynumber: 3.2 Consensus size: 31
32364 CAACGGTCAA
* *
32374 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
32405 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
32436 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
32467 CGGGTC
1 CGGGTC
32473 GGGTTATGAC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.14, C:0.21, G:0.46, T:0.18
Consensus pattern (31 bp):
CGGGTCAACTGGTCGGGTAAACGGGTCGGGT
Found at i:32418 original size:13 final size:13
Alignment explanation
Indices: 32374--32467 Score: 62
Period size: 13 Copynumber: 6.5 Consensus size: 13
32364 CAACGGTCAA
*
32374 CGGGTCAACGGGT
1 CGGGTCAACTGGT
32387 CGGGTCAACGGGTCGGGT
1 CGGGTCAAC---T--GGT
32405 CGGGTCAACTGGT
1 CGGGTCAACTGGT
*
32418 CGGGTAAACGGGTCGGGT
1 CGGGTCAAC---T--GGT
32436 CGGGTCAACTGGT
1 CGGGTCAACTGGT
* *
32449 CGGGTAAACGGGT
1 CGGGTCAACTGGT
32462 CGGGTC
1 CGGGTC
32468 GGGTCGGGTT
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
13 39 0.60
15 2 0.03
16 1 0.02
18 23 0.35
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.18
Consensus pattern (13 bp):
CGGGTCAACTGGT
Found at i:38427 original size:20 final size:20
Alignment explanation
Indices: 38391--38428 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38381 ATATTTGAAT
*
38391 CTAGAAAATATTTCATCAAA
1 CTAGAAAATATTACATCAAA
38411 CTAGAAGAA-ATTACATCA
1 CTAGAA-AATATTACATCA
38429 GTAGTATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (20 bp):
CTAGAAAATATTACATCAAA
Found at i:43719 original size:85 final size:84
Alignment explanation
Indices: 43572--43741 Score: 209
Period size: 85 Copynumber: 2.0 Consensus size: 84
43562 ACAATCACGC
* * *
43572 CACACGAATGTGTGTCATCTTTTTAATGAAGTGTGCTTCAATGACACGCAATGTAAGTCATAAAT
1 CACACGAATGTGTGTCATCTTTTTAATGAAGGGGGCTTCAATGACACACAATGTAAGTCATAAAT
*
43637 GCGTGTCATAAATTTATGA
66 GCGCGTCATAAATTTATGA
* * ** *
43656 CACATGAATGTGTGTCATCTTCATTT-ATGACGGGGGCTTCAATGATGCACAATG-AGCGTCATA
1 CACACGAATGTGTGTCATCTT--TTTAATGAAGGGGGCTTCAATGACACACAATGTA-AGTCATA
*
43719 AATGTGCGTCATAAATTTATGA
63 AATGCGCGTCATAAATTTATGA
43741 C
1 C
43742 GCACAGTTAC
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 21 0.29
85 49 0.67
86 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (84 bp):
CACACGAATGTGTGTCATCTTTTTAATGAAGGGGGCTTCAATGACACACAATGTAAGTCATAAAT
GCGCGTCATAAATTTATGA
Found at i:46355 original size:13 final size:13
Alignment explanation
Indices: 46337--46362 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46327 AAAGGGAAAA
46337 TTTCAACTTTAAG
1 TTTCAACTTTAAG
46350 TTTCAACTTTAAG
1 TTTCAACTTTAAG
46363 CCCTACATGA
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:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TTTCAACTTTAAG
Found at i:46805 original size:20 final size:20
Alignment explanation
Indices: 46777--46821 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
46767 CTTGAGCTTA
*
46777 AAACCACCT-AAAACAAACCT
1 AAACTACCTGAAAAC-AACCT
*
46797 AAACTACCTGAAAACCACCT
1 AAACTACCTGAAAACAACCT
46817 AAACT
1 AAACT
46822 CTTCGGCTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.51, C:0.33, G:0.02, T:0.13
Consensus pattern (20 bp):
AAACTACCTGAAAACAACCT
Found at i:47348 original size:17 final size:17
Alignment explanation
Indices: 47326--47364 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
47316 TACAAGAGTT
47326 GCGTGGAGTGGAGCTTG
1 GCGTGGAGTGGAGCTTG
47343 GCGTGGAGTGGAGCTTG
1 GCGTGGAGTGGAGCTTG
47360 GCGTG
1 GCGTG
47365 CATGGAGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.10, C:0.13, G:0.54, T:0.23
Consensus pattern (17 bp):
GCGTGGAGTGGAGCTTG
Found at i:47517 original size:17 final size:17
Alignment explanation
Indices: 47473--47520 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
47463 TTCTGGCTTC
*
47473 CTGGTTGGGTTTTAGGT
1 CTGGTTGGGTTTTGGGT
* ** *
47490 TTAATTAGGTTTTGGGT
1 CTGGTTGGGTTTTGGGT
47507 CTGGTTGGGTTTTG
1 CTGGTTGGGTTTTG
47521 TTTTATTTTG
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.08, C:0.04, G:0.38, T:0.50
Consensus pattern (17 bp):
CTGGTTGGGTTTTGGGT
Found at i:47559 original size:22 final size:22
Alignment explanation
Indices: 47511--47552 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
47501 TTGGGTCTGG
**
47511 TTGGGTTTTGTTTTATTTTGTA
1 TTGGGTTGAGTTTTATTTTGTA
*
47533 ATGGGTTGAGTTTTATTTTG
1 TTGGGTTGAGTTTTATTTTG
47553 GTTTGGGCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.26, T:0.62
Consensus pattern (22 bp):
TTGGGTTGAGTTTTATTTTGTA
Found at i:61365 original size:12 final size:12
Alignment explanation
Indices: 61343--61375 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
61333 TTCCTCACAC
61343 TCTTCTTTTTTCT
1 TCTT-TTTTTTCT
61356 TCTTTTTTTTCT
1 TCTTTTTTTTCT
61368 TCTTTTTT
1 TCTTTTTT
61376 ATTTGGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TCTTTTTTTTCT
Found at i:61963 original size:22 final size:23
Alignment explanation
Indices: 61929--61972 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
61919 CCCAAGCTTG
61929 GTATCGATACCATAGC-TAGGGAA
1 GTATCGATACCATA-CATAGGGAA
61952 GTATCG-TACCATACATAGGGA
1 GTATCGATACCATACATAGGGA
61973 TACCGATACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.05
22 13 0.65
23 6 0.30
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (23 bp):
GTATCGATACCATACATAGGGAA
Found at i:62278 original size:15 final size:15
Alignment explanation
Indices: 62258--62306 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
62248 ATTCATGAAC
62258 ATGAGTATGT-TTGAT
1 ATGAGTATGTGTT-AT
62273 ATGAGTATGTGTTAT
1 ATGAGTATGTGTTAT
* * *
62288 ATGATTATATGTTAC
1 ATGAGTATGTGTTAT
62303 ATGA
1 ATGA
62307 TTGTGAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 28 0.93
16 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (15 bp):
ATGAGTATGTGTTAT
Found at i:62660 original size:31 final size:31
Alignment explanation
Indices: 62614--62678 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
62604 AAGAGTAGAG
*
62614 GGTTACTTATATCCTTCGAGACATATGGACA
1 GGTTACCTATATCCTTCGAGACATATGGACA
* * *
62645 GGTTACCTATTTCCTTCGGGACATATGGATA
1 GGTTACCTATATCCTTCGAGACATATGGACA
62676 GGT
1 GGT
62679 CCTTCGGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (31 bp):
GGTTACCTATATCCTTCGAGACATATGGACA
Found at i:63002 original size:13 final size:13
Alignment explanation
Indices: 62984--63010 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
62974 TTGTGATATT
62984 TGTATTAAGTTAA
1 TGTATTAAGTTAA
62997 TGTATTAAGTTAA
1 TGTATTAAGTTAA
63010 T
1 T
63011 AATTGAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TGTATTAAGTTAA
Done.