Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009629.1 Hibiscus syriacus cultivar Beakdansim tig00117022_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: 453070
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:415579 original size:20 final size:21
Alignment explanation
Indices: 415554--415684 Score: 101
Period size: 20 Copynumber: 6.4 Consensus size: 21
415544 TTTTCCCAAT
*
415554 TCGCAATGCGAA-TAAGCAAA
1 TCGCAATGCGAATTAAGAAAA
* **
415574 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
415595 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
415615 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* **
415636 TCGCAATGCG-A-TACTGACTA
1 TCGCAATGCGAATTA-AGAAAA
*
415656 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCGA-ATTAAGAAAA
415677 TCGCAATG
1 TCGCAATG
415685 AGATACTTAC
Statistics
Matches: 85, Mismatches: 20, Indels: 11
0.73 0.17 0.09
Matches are distributed among these distances:
19 1 0.01
20 41 0.48
21 40 0.47
22 1 0.01
23 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:415597 original size:21 final size:21
Alignment explanation
Indices: 415571--415646 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
415561 GCGAATAAGC
415571 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
415592 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
415612 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
415633 AAATCGCAATGCGA
1 AAATCGCAACGCGA
415647 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:415599 original size:41 final size:41
Alignment explanation
Indices: 415554--415646 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
415544 TTTTCCCAAT
415554 TCGCAATGCGAATAAGCAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGCAAATCGCAACGCGAATTGGGAAAA
*
415595 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGCAAATCGCAACGCGAATTGGGAAAA
415636 TCGCAATGCGA
1 TCGCAATGCGA
415647 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (41 bp):
TCGCAATGCGAATAAGCAAATCGCAACGCGAATTGGGAAAA
Found at i:415659 original size:41 final size:41
Alignment explanation
Indices: 415573--415707 Score: 141
Period size: 41 Copynumber: 3.3 Consensus size: 41
415563 GAATAAGCAA
* *
415573 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
415614 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * *
415655 ATCGCAATGCGATAAT-AAAAAATCGCAATGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
415696 TTCGCAACGCGA
1 ATCGCAACGCGA
415708 TACTGACTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:415725 original size:20 final size:20
Alignment explanation
Indices: 415635--415728 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
415625 AATTGGGAAA
415635 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * **
415655 ATCGCAATGCGATAATAAAAA
1 ATCGCAATGCGATACT-GACT
* *
415676 ATCGCAATGAGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
415696 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
415716 TTCGCAACGCGAT
1 ATCGCAATGCGAT
415729 TTACATAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 45 0.75
21 15 0.25
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:416274 original size:20 final size:20
Alignment explanation
Indices: 416246--416301 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
416236 TTCGAGAATG
416246 AAAATCGCAACGCGAAAATA
1 AAAATCGCAACGCGAAAATA
**
416266 ACTATCGCAACGCG-AAATA
1 AAAATCGCAACGCGAAAATA
416285 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
416302 CCAAAATTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATA
Found at i:416335 original size:19 final size:19
Alignment explanation
Indices: 416313--416492 Score: 155
Period size: 19 Copynumber: 9.8 Consensus size: 19
416303 CAAAATTGCA
416313 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
416332 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
416351 TTGCGTTTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGC-G
*
416371 TTGCGATTTTCATTTCACG
1 TTGCGATTTTCATTTCGCG
*
416390 TTGCGATTGTC---T-G-G
1 TTGCGATTTTCATTTCGCG
* **
416404 TCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
416423 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
416437 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* *
416457 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
416477 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
416493 AACCAAAAGA
Statistics
Matches: 130, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 20 0.15
16 3 0.02
17 3 0.02
18 1 0.01
19 55 0.42
20 47 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:416382 original size:39 final size:38
Alignment explanation
Indices: 416313--416493 Score: 139
Period size: 33 Copynumber: 4.9 Consensus size: 38
416303 CAAAATTGCA
*
416313 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCACG
* *
416351 TTGCGTTTTTTATTTCGCGGTTGCGATTTTCATTTCACG
1 TTGCGATTTTCATTTCGC-GTTGCGATTTTCATTTCACG
* * ** *
416390 TTGCGATTGTC---T-G-GTCGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCACG
* ** *
416423 TTGCGA--TTC---TCTCGTTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTT-CACG
* *
416457 TTGCGATTCTCATTATCTCGTTGCGATTTTCATTTCA
1 TTGCGATTTTCATT-TCGCGTTGCGATTTTCATTTCA
416494 ACCAAAAGAC
Statistics
Matches: 116, Mismatches: 17, Indels: 19
0.76 0.11 0.12
Matches are distributed among these distances:
31 3 0.03
33 37 0.32
34 10 0.09
35 1 0.01
36 3 0.03
38 16 0.14
39 28 0.24
40 18 0.16
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (38 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCACG
Found at i:416469 original size:20 final size:20
Alignment explanation
Indices: 416435--416492 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
416425 GCGATTCTCT
**
416435 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
416455 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
416475 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
416493 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:418552 original size:42 final size:42
Alignment explanation
Indices: 418492--418614 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
418482 GCCCGACTCG
* * *
418492 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
418534 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
418576 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
418615 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:418572 original size:21 final size:21
Alignment explanation
Indices: 418548--418614 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
418538 TCATTCCTCG
418548 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
418569 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
418590 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
418611 AGAG
1 AGAG
418615 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:419978 original size:13 final size:14
Alignment explanation
Indices: 419970--420006 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
419960 GATTGTTTAA
419970 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
419984 GTGATTTGTAAAAG
1 TTGATTTGTAAAAG
419998 TTGATTTGT
1 TTGATTTGT
420007 TTAATTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:420211 original size:33 final size:32
Alignment explanation
Indices: 420169--420294 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
420159 ATTAAATTCG
420169 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
420202 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
420235 CGTTGCGA-TTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
420267 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
420295 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
30 3 0.04
32 25 0.30
33 53 0.63
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:420269 original size:65 final size:66
Alignment explanation
Indices: 420162--420293 Score: 239
Period size: 65 Copynumber: 2.0 Consensus size: 66
420152 ACGCGAAATT
*
420162 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
420227 G
66 G
*
420228 AAATTAGCGTTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
420292 G
66 G
420293 A
1 A
420294 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 50 0.78
66 14 0.22
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:422604 original size:12 final size:12
Alignment explanation
Indices: 422587--422611 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
422577 TCTTCGGGGA
422587 CTTTTTCTTCTT
1 CTTTTTCTTCTT
422599 CTTTTTCTTCTT
1 CTTTTTCTTCTT
422611 C
1 C
422612 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:422820 original size:24 final size:24
Alignment explanation
Indices: 422786--422839 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
422776 CTGAAACATC
* *
422786 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
422810 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
422834 ATCAAA
1 ATCAAA
422840 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:423924 original size:20 final size:20
Alignment explanation
Indices: 423899--423976 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
423889 ATTCATTTGA
423899 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
423919 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
423939 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
423959 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
423977 CGCAATGCAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:424019 original size:14 final size:14
Alignment explanation
Indices: 424000--424053 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
423990 GAAAATCGCA
424000 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
424014 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
424031 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
424047 TTGCGAT
1 TTGCGAT
424054 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:424037 original size:33 final size:33
Alignment explanation
Indices: 423995--424072 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
423985 AAAATGAAAA
***
423995 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
424028 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
424061 TCGCGTTGCGAT
1 TCGCATTGCGAT
424073 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:426097 original size:20 final size:19
Alignment explanation
Indices: 426062--426128 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
426052 GAAACTTAAA
426062 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
426081 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
426101 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
426120 ATCGCAACG
1 ATCGCAACG
426129 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:426195 original size:14 final size:14
Alignment explanation
Indices: 426176--426233 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
426166 TTGTGTTTCG
426176 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
426190 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
426206 CGCGTTTCGATTTTGT
1 --CGTTGCGATTTTGT
426222 CGTTGCGATTTT
1 CGTTGCGATTTT
426234 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.09, C:0.17, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:426210 original size:32 final size:33
Alignment explanation
Indices: 426171--426249 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
426161 GCGATTTGTG
426171 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
426203 TTTCGCGTTTCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
426236 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
426250 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 26 0.60
33 17 0.40
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:426268 original size:20 final size:19
Alignment explanation
Indices: 426234--426288 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
426224 TTGCGATTTT
*
426234 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
426253 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
426273 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
426289 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:426781 original size:18 final size:18
Alignment explanation
Indices: 426755--426799 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
426745 GTCGATCAGA
*
426755 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
426773 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
426791 TGATGGCTC
1 TGATGGCTC
426800 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:428143 original size:20 final size:20
Alignment explanation
Indices: 428118--428155 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
428108 AATAGTTTCT
428118 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
428138 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
428156 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:428437 original size:22 final size:22
Alignment explanation
Indices: 428412--428455 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
428402 GATTTAGATA
428412 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
428434 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
428456 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:428668 original size:20 final size:20
Alignment explanation
Indices: 428643--428695 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
428633 GATTATGTAT
*
428643 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
*
428663 TATCGCGTTGTGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
428683 TATCTCGTTGCGA
1 TATCGCGTTGCGA
428696 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:428708 original size:41 final size:41
Alignment explanation
Indices: 428663--428740 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
428653 CGAAAGTCAG
* * * *
428663 TATCGCGTTGTGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCACATTGCGATTTTTTAT
* *
428704 TATCGCATTGCGATAGTCAGTATCACATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCACATTGCGATTTT
428741 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCACATTGCGATTTTTTAT
Found at i:428756 original size:41 final size:41
Alignment explanation
Indices: 428726--428818 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
428716 ATAGTCAGTA
* *
428726 TCACATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCACATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
428767 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCACATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
*
428808 TCGCATTGCGA
1 TCACATTGCGA
428819 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (41 bp):
TCACATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:428757 original size:21 final size:21
Alignment explanation
Indices: 428731--428801 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
428721 CAGTATCACA
428731 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** *
428752 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCGCG
428772 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
428793 TTGCGATTT
1 TTGCGATTT
428802 ACTTATTCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:428770 original size:20 final size:20
Alignment explanation
Indices: 428745--428818 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
428735 GATTTTCCCA
*
428745 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
428765 ATTCGCATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
428786 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
428806 ATTCGCATTGCGA
1 ATTCGCATTGCGA
428819 ATTGGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:429162 original size:31 final size:30
Alignment explanation
Indices: 429113--429205 Score: 116
Period size: 31 Copynumber: 3.1 Consensus size: 30
429103 ACCTAAATTA
* *
429113 TTAC-TTTTATTCCGTTTTAATACTTAAAGT
1 TTACTTTTTATTTCATTTTAATACTTAAA-T
* *
429143 TTACTTTTTATTTCATTTTAGTACCTAATAT
1 TTACTTTTTATTTCATTTTAATACTTAA-AT
*
429174 TTATTTTTTATTTCATTTTAATACTTAAAT
1 TTACTTTTTATTTCATTTTAATACTTAAAT
429204 TT
1 TT
429206 TTAACGGCGG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
30 8 0.15
31 45 0.83
32 1 0.02
ACGTcount: A:0.27, C:0.11, G:0.03, T:0.59
Consensus pattern (30 bp):
TTACTTTTTATTTCATTTTAATACTTAAAT
Found at i:429545 original size:28 final size:27
Alignment explanation
Indices: 429499--429553 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
429489 TATTCTTAAA
429499 ATTTTTAAATTTTTATATAATTTAATT
1 ATTTTTAAATTTTTATATAATTTAATT
*
429526 ATTTTTATATTTTTATTATAATTTAATT
1 ATTTTTAAATTTTTA-TATAATTTAATT
429554 CTAATTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
ATTTTTAAATTTTTATATAATTTAATT
Found at i:436076 original size:25 final size:25
Alignment explanation
Indices: 436015--436069 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
436005 ATACATCATC
436015 AACAAGAAGGGAATCAATCACTAGT
1 AACAAGAAGGGAATCAATCACTAGT
436040 AACAAGAAGGGAATCAATCACTAGT
1 AACAAGAAGGGAATCAATCACTAGT
436065 AACAA
1 AACAA
436070 TTAGGGATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.15
Consensus pattern (25 bp):
AACAAGAAGGGAATCAATCACTAGT
Found at i:444980 original size:2 final size:2
Alignment explanation
Indices: 444973--445003 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
444963 TTTATACACC
444973 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
445004 TTGTGTGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.