Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008961.1 Hibiscus syriacus cultivar Beakdansim tig00112295_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: 183149
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:154422 original size:33 final size:33
Alignment explanation
Indices: 154358--154482 Score: 182
Period size: 33 Copynumber: 3.8 Consensus size: 33
154348 AAAAATGACT
*
154358 ATCGCAACGCGAAATG--AATCGAAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
154389 ATCGCAACGCGAAATGAAAATCTCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
154422 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
**
154455 ATCGCAACGCGAAACCAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
154483 TGAAACTATA
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
31 16 0.19
33 69 0.81
ACGTcount: A:0.46, C:0.24, G:0.21, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:154554 original size:19 final size:19
Alignment explanation
Indices: 154530--154600 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
154520 GCGATTCTCT
154530 CGTTGCGATTTTCTTTTCG
1 CGTTGCGATTTTCTTTTCG
*
154549 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCTTTTCG
* ** *
154568 CCTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTC--TTTTCG
154589 CGTTGCGATTTT
1 CGTTGCGATTTT
154601 AAGTTCCAGA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 28 0.68
21 13 0.32
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.48
Consensus pattern (19 bp):
CGTTGCGATTTTCTTTTCG
Found at i:155061 original size:21 final size:21
Alignment explanation
Indices: 155037--155106 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
155027 CTATCATTCC
155037 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* * ** *
155058 TCAAGAGGCCACTGTCATCGT
1 TCAAGAGTCCCCTCCCACCGT
* *
155079 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCACCGT
155100 TCAAGAG
1 TCAAGAG
155107 CCCGATTCAC
Statistics
Matches: 35, Mismatches: 13, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:155064 original size:42 final size:42
Alignment explanation
Indices: 154988--155106 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
154978 AACTTGCCTG
* * * * * *
154988 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
155030 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
155072 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTC-CTCAAGA-GTCCCCTCCCACCGTTCAAGAG
155107 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.03
42 61 0.94
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:156470 original size:14 final size:14
Alignment explanation
Indices: 156451--156486 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
156441 ATTGTTTAAT
156451 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
156465 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
156479 TGATTTGT
1 TGATTTGT
156487 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:156678 original size:19 final size:19
Alignment explanation
Indices: 156625--156687 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
156615 ATAACGAGAG
*
156625 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
*
156644 AATCGCAACGTGAAACTAA
1 AATCGCAACGCGAAACTAA
156663 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
156682 ATTCGC
1 AATCGC
156688 GTTGCGATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 38 0.97
20 1 0.03
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.16
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:156730 original size:33 final size:33
Alignment explanation
Indices: 156687--156853 Score: 172
Period size: 33 Copynumber: 4.8 Consensus size: 33
156677 ACTAAATTCG
* *
156687 CGTTGCGATTTTCATTTCACTTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
156720 CGTTGTGATTTTCATTTCGCATTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---T-CT
* * * *
156759 CGTTGCGATATTCATATTCGCGTTGCGATTTTCA
1 CGTTGCGATTTTCAT-TTCGCATTGCGATTCTCT
* *
156793 CGCTGCGATTTTCATTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
156826 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
156854 AGACATTAAG
Statistics
Matches: 109, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
33 64 0.59
34 14 0.13
35 3 0.03
38 2 0.02
39 14 0.13
40 12 0.11
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:156792 original size:20 final size:19
Alignment explanation
Indices: 156683--156792 Score: 86
Period size: 20 Copynumber: 5.9 Consensus size: 19
156673 CGAAACTAAA
*
156683 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATATTCAT
* *
156702 TTCACTTTGCG--ATTC--
1 TTCGCGTTGCGATATTCAT
* * *
156717 -TCTCGTTGTGATTTTCAT
1 TTCGCGTTGCGATATTCAT
* *
156735 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATATTCAT
156754 TTCCGCGTTGCGATATTCAT
1 TT-CGCGTTGCGATATTCAT
*
156774 ATTCGCGTTGCGATTTTCA
1 -TTCGCGTTGCGATATTCA
156793 CGCTGCGATT
Statistics
Matches: 69, Mismatches: 15, Indels: 13
0.71 0.15 0.13
Matches are distributed among these distances:
14 7 0.10
16 3 0.04
17 3 0.04
19 24 0.35
20 30 0.43
21 2 0.03
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATATTCAT
Found at i:159403 original size:24 final size:24
Alignment explanation
Indices: 159369--159422 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
159359 CTGAAAAATC
159369 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
159393 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
159417 ATCAAA
1 ATCAAA
159423 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:159436 original size:24 final size:24
Alignment explanation
Indices: 159369--159436 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
159359 CTGAAAAATC
* * *
159369 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
159393 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
159417 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
159437 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:160308 original size:20 final size:20
Alignment explanation
Indices: 160285--160335 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
160275 GAATCTCGTT
160285 GCGATTTAC-TAAATCGCAAC
1 GCGA-TTACGTAAATCGCAAC
160305 GCGATTACGTAAATCGCAAC
1 GCGATTACGTAAATCGCAAC
*
160325 GCGAATACGTA
1 GCGATTACGTA
160336 TTCGCATTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 4 0.14
20 25 0.86
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (20 bp):
GCGATTACGTAAATCGCAAC
Found at i:160353 original size:20 final size:20
Alignment explanation
Indices: 160330--160470 Score: 122
Period size: 20 Copynumber: 7.0 Consensus size: 20
160320 GCAACGCGAA
*
160330 TACGTATTCGCATTGCGATT
1 TACGTATTCGCGTTGCGATT
* *
160350 TACGTATTCGCATTGTGATT
1 TACGTATTCGCGTTGCGATT
* *
160370 TACGGATACGCGTTGCGATT
1 TACGTATTCGCGTTGCGATT
* * *
160390 TACGGATACGCGTTTCGATTT
1 TACGTATTCGCGTTGCGA-TT
160411 TACGTATT-GTCGTTGCGATT
1 TACGTATTCG-CGTTGCGATT
* * *
160431 TACGAATACACGTTGCGATTT
1 TACGTATTCGCGTTGCGA-TT
* * *
160452 TACGAATACTCGTTGCGAT
1 TACGTATTCGCGTTGCGAT
160471 AGTCAGAATC
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
20 70 0.67
21 34 0.33
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
TACGTATTCGCGTTGCGATT
Found at i:160414 original size:21 final size:21
Alignment explanation
Indices: 160342--160492 Score: 118
Period size: 20 Copynumber: 7.4 Consensus size: 21
160332 CGTATTCGCA
* * *
160342 TTGCGA-TTTACGTATTCGCA
1 TTGCGATTTTACGAATACGCG
* *
160362 TTGTGA-TTTACGGATACGCG
1 TTGCGATTTTACGAATACGCG
*
160382 TTGCGA-TTTACGGATACGCG
1 TTGCGATTTTACGAATACGCG
* * *
160402 TTTCGATTTTACGTAT-TGTCG
1 TTGCGATTTTACGAATACG-CG
*
160423 TTGCGA-TTTACGAATACACG
1 TTGCGATTTTACGAATACGCG
*
160443 TTGCGATTTTACGAATACTCG
1 TTGCGATTTTACGAATACGCG
**
160464 TTGCGATAGT-CAGAAT-CGCG
1 TTGCGATTTTAC-GAATACGCG
160484 TTGCGATTT
1 TTGCGATTT
160493 ATATGTTCGC
Statistics
Matches: 108, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
20 68 0.63
21 40 0.37
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (21 bp):
TTGCGATTTTACGAATACGCG
Found at i:160425 original size:41 final size:41
Alignment explanation
Indices: 160342--160470 Score: 134
Period size: 41 Copynumber: 3.2 Consensus size: 41
160332 CGTATTCGCA
* * * * * * *
160342 TTGCGATTTACGTATTCGCATTGTGA-TTTACGGATACGCG
1 TTGCGATTTACGAATACACGTTGCGATTTTACGAATACTCG
* * * * **
160382 TTGCGATTTACGGATACGCGTTTCGATTTTACGTATTGTCG
1 TTGCGATTTACGAATACACGTTGCGATTTTACGAATACTCG
160423 TTGCGATTTACGAATACACGTTGCGATTTTACGAATACTCG
1 TTGCGATTTACGAATACACGTTGCGATTTTACGAATACTCG
160464 TTGCGAT
1 TTGCGAT
160471 AGTCAGAATC
Statistics
Matches: 73, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 21 0.29
41 52 0.71
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
TTGCGATTTACGAATACACGTTGCGATTTTACGAATACTCG
Found at i:160431 original size:61 final size:62
Alignment explanation
Indices: 160342--160470 Score: 165
Period size: 61 Copynumber: 2.1 Consensus size: 62
160332 CGTATTCGCA
* * * *
160342 TTGCGA-TTTACGTATTCGCATTGTGATTTACGGATACGCGTTGCGA-TTTACGGATACGCG
1 TTGCGATTTTACGTATTCGCATTGCGATTTACGAATACACGTTGCGATTTTACGAATACGCG
* * *
160402 TTTCGATTTTACGTATT-GTCGTTGCGATTTACGAATACACGTTGCGATTTTACGAATACTCG
1 TTGCGATTTTACGTATTCG-CATTGCGATTTACGAATACACGTTGCGATTTTACGAATACGCG
160464 TTGCGAT
1 TTGCGAT
160471 AGTCAGAATC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 6 0.10
61 34 0.59
62 18 0.31
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (62 bp):
TTGCGATTTTACGTATTCGCATTGCGATTTACGAATACACGTTGCGATTTTACGAATACGCG
Found at i:160486 original size:41 final size:41
Alignment explanation
Indices: 160342--160492 Score: 128
Period size: 41 Copynumber: 3.7 Consensus size: 41
160332 CGTATTCGCA
* * * * * * *
160342 TTGCGATTTACGTATTCGCATTGTGA-TTTACGGATACGCG
1 TTGCGATTCACGAATACGCGTTGCGATTTTACGAATACTCG
* * * * **
160382 TTGCGATTTACGGATACGCGTTTCGATTTTACGTATTGTCG
1 TTGCGATTCACGAATACGCGTTGCGATTTTACGAATACTCG
* *
160423 TTGCGATTTACGAATACACGTTGCGATTTTACGAATACTCG
1 TTGCGATTCACGAATACGCGTTGCGATTTTACGAATACTCG
160464 TTGCGATAGTCA-GAAT-CGCGTTGCGATTT
1 TTGCGAT--TCACGAATACGCGTTGCGATTT
160493 ATATGTTCGC
Statistics
Matches: 91, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
40 21 0.23
41 64 0.70
42 4 0.04
43 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (41 bp):
TTGCGATTCACGAATACGCGTTGCGATTTTACGAATACTCG
Found at i:160610 original size:20 final size:19
Alignment explanation
Indices: 160561--160614 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
160551 ATTCTTCATA
160561 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
160580 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
160601 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
160615 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:161331 original size:17 final size:18
Alignment explanation
Indices: 161289--161335 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
161279 TTGATTGAAG
161289 AATTTTTAAATTAATTTA
1 AATTTTTAAATTAATTTA
* *
161307 AATATTTAATTTAA-TTA
1 AATTTTTAAATTAATTTA
*
161324 ATTTTTTAAATT
1 AATTTTTAAATT
161336 GATAAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTTTAAATTAATTTA
Found at i:161335 original size:18 final size:19
Alignment explanation
Indices: 161289--161335 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
161279 TTGATTGAAG
161289 AATTTTTAAA-TTAATTTA
1 AATTTTTAAATTTAATTTA
*
161307 AATATTT-AATTTAA-TTA
1 AATTTTTAAATTTAATTTA
*
161324 ATTTTTTAAATT
1 AATTTTTAAATT
161336 GATAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTTTTAAATTTAATTTA
Found at i:168708 original size:18 final size:18
Alignment explanation
Indices: 168685--168725 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
168675 TTTTAAGTAA
168685 AACATACATGCGTGAAAG
1 AACATACATGCGTGAAAG
*
168703 AACATACCTGCGTGAAAG
1 AACATACATGCGTGAAAG
168721 AACAT
1 AACAT
168726 CATCCACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.17
Consensus pattern (18 bp):
AACATACATGCGTGAAAG
Found at i:168919 original size:16 final size:16
Alignment explanation
Indices: 168868--168910 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
168858 TGTGTATGAA
168868 AAATTCCCTTGCTGAC
1 AAATTCCCTTGCTGAC
168884 AAATTCCCTTGCTGAC
1 AAATTCCCTTGCTGAC
168900 AAATTCCCTTG
1 AAATTCCCTTG
168911 GTAACAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.33
Consensus pattern (16 bp):
AAATTCCCTTGCTGAC
Found at i:173613 original size:24 final size:24
Alignment explanation
Indices: 173586--173642 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
173576 CACCAAAGCT
173586 CATATAAATTGCACCGAAGTGCCA
1 CATATAAATTGCACCGAAGTGCCA
* * *
173610 CATAGAATTTGCACCGAAGTGCTA
1 CATATAAATTGCACCGAAGTGCCA
*
173634 CGTATAAAT
1 CATATAAAT
173643 GTCCCAAAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (24 bp):
CATATAAATTGCACCGAAGTGCCA
Found at i:173688 original size:23 final size:23
Alignment explanation
Indices: 173634--173709 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
173624 CGAAGTGCTA
* * *
173634 CGTATAAATGTCCCAAAGGACCA
1 CGTAGAAATGTCCCAAAAGACCG
* **
173657 CATTTAAATGTCCCAAAAGACCG
1 CGTAGAAATGTCCCAAAAGACCG
* * *
173680 TGTAGAAATTTCCCAAAGGACCG
1 CGTAGAAATGTCCCAAAAGACCG
173703 CGTAGAA
1 CGTAGAA
173710 CCCTCGACTC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGTCCCAAAAGACCG
Found at i:175483 original size:18 final size:18
Alignment explanation
Indices: 175456--175490 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
175446 ATCGACGTCT
*
175456 GTCAATGGTCAATGGTCG
1 GTCAACGGTCAATGGTCG
175474 GTCAACGGTCAATGGTC
1 GTCAACGGTCAATGGTC
175491 AACAGTGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (18 bp):
GTCAACGGTCAATGGTCG
Found at i:180028 original size:43 final size:41
Alignment explanation
Indices: 179961--180055 Score: 120
Period size: 43 Copynumber: 2.3 Consensus size: 41
179951 ATTTATTCTA
* *
179961 TAAATAAA-AATATAATTAATTGAAATAATGAGTAGAACCT
1 TAAATAAATAATATAATTAATTGAAATAATGAATAGAACAT
* *
180001 TAAATAAATAATAATAATTTAATTGAAATAGTGAATATAACAT
1 TAAATAAATAAT-ATAA-TTAATTGAAATAATGAATAGAACAT
*
180044 TAAATAAGTAAT
1 TAAATAAATAAT
180056 GAGTTTAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
40 8 0.17
41 3 0.06
42 4 0.09
43 32 0.68
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (41 bp):
TAAATAAATAATATAATTAATTGAAATAATGAATAGAACAT
Found at i:180707 original size:19 final size:18
Alignment explanation
Indices: 180671--180713 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
180661 TAACAAATAG
*
180671 AATAATTTAACAAAATTT
1 AATAATTGAACAAAATTT
* *
180689 CAATAATTGAATAATATTT
1 -AATAATTGAACAAAATTT
180708 AATAAT
1 AATAAT
180714 ATTTTAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (18 bp):
AATAATTGAACAAAATTT
Found at i:181068 original size:16 final size:16
Alignment explanation
Indices: 181049--181084 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
181039 GAATAGAAAC
181049 TTAAATAAATAA-TAAT
1 TTAAATAAA-AATTAAT
181065 TTAAATAAAAATTAAT
1 TTAAATAAAAATTAAT
181081 TTAA
1 TTAA
181085 GTGAAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 17 0.89
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAATAAAAATTAAT
Found at i:181278 original size:79 final size:78
Alignment explanation
Indices: 181160--181366 Score: 312
Period size: 79 Copynumber: 2.7 Consensus size: 78
181150 AAATAAATAA
*
181160 TATTTAAAT-AAAA-ATACGATTTAAGTAAAAGTAGTAAATAGAATTTAAATAAATACTAGTAAT
1 TATTTAAATAAAAAGATA-GATTAAAGTAAAAGTAGTAAATAGAATTTAAATAAATACTAGTAAT
181223 TTAAATCAAACTAT
65 TTAAATCAAACTAT
* * *
181237 TGA-TTAAATAAAAAGATGTGGTTAAAGTAAAAGTAGTAAATAGAATTTGAATAAATACTAGTAA
1 T-ATTTAAATAAAAAGAT-AGATTAAAGTAAAAGTAGTAAATAGAATTTAAATAAATACTAGTAA
181301 TTTAAATCAAACTAT
64 TTTAAATCAAACTAT
* *
181316 TATTTAAATAGAAAGATAGATTTAAGTAAAAGTAGTAAATAGAATTTAAAT
1 TATTTAAATAAAAAGATAGATTAAAGTAAAAGTAGTAAATAGAATTTAAAT
181367 CAAACAATAC
Statistics
Matches: 116, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
77 7 0.06
78 36 0.31
79 73 0.63
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (78 bp):
TATTTAAATAAAAAGATAGATTAAAGTAAAAGTAGTAAATAGAATTTAAATAAATACTAGTAATT
TAAATCAAACTAT
Done.