Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007688.1 Hibiscus syriacus cultivar Beakdansim tig00109873_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: 73868
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:343 original size:12 final size:13
Alignment explanation
Indices: 326--354 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
316 TTTGGGGTAG
326 TTTATTTGTA-AT
1 TTTATTTGTACAT
338 TTTATTTGTACAT
1 TTTATTTGTACAT
351 TTTA
1 TTTA
355 GAAATTACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.24, C:0.03, G:0.07, T:0.66
Consensus pattern (13 bp):
TTTATTTGTACAT
Found at i:2246 original size:18 final size:18
Alignment explanation
Indices: 2225--2259 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2215 ATTTAGTCTT
2225 TAAACTTATTTTAATCTC
1 TAAACTTATTTTAATCTC
2243 TAAACTTATTTTAATCT
1 TAAACTTATTTTAATCT
2260 TCCTTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAACTTATTTTAATCTC
Found at i:3394 original size:30 final size:30
Alignment explanation
Indices: 3349--3503 Score: 213
Period size: 30 Copynumber: 5.2 Consensus size: 30
3339 TTGCTATAGT
*
3349 GACCACCATAGGTCTCCAGGAGCACACGAC
1 GACCTCCATAGGTCTCCAGGAGCACACGAC
* *
3379 GACCTCCATAAGTCTCCAGGAACACACGAC
1 GACCTCCATAGGTCTCCAGGAGCACACGAC
* *
3409 GACCTCCATAGGTCTCCAGGAGCATACGCC
1 GACCTCCATAGGTCTCCAGGAGCACACGAC
*
3439 GACCTCCATAGGTCTCCAGGAGCATAC-AGC
1 GACCTCCATAGGTCTCCAGGAGCACACGA-C
* * *
3469 GACCTCTATAGATCTCCAGGAGCACACGTC
1 GACCTCCATAGGTCTCCAGGAGCACACGAC
3499 GACCT
1 GACCT
3504 ATGGAGTTGC
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
30 111 1.00
ACGTcount: A:0.28, C:0.35, G:0.21, T:0.15
Consensus pattern (30 bp):
GACCTCCATAGGTCTCCAGGAGCACACGAC
Found at i:7008 original size:18 final size:19
Alignment explanation
Indices: 6964--7010 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
6954 TTTTTTCGGT
*
6964 GTTTCATCTTTAGATTCAA
1 GTTTCATTTTTAGATTCAA
* *
6983 -TTTAATTTTTTGATT-AA
1 GTTTCATTTTTAGATTCAA
7000 GTTTCATTTTT
1 GTTTCATTTTT
7011 GACGTTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (19 bp):
GTTTCATTTTTAGATTCAA
Found at i:13267 original size:20 final size:20
Alignment explanation
Indices: 13242--13371 Score: 172
Period size: 20 Copynumber: 6.5 Consensus size: 20
13232 GTTTCCAGAT
13242 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* **
13262 TCGCAACGTGATAAT-ACATAA
1 TCGCAACGCGATTCTGAC-T-A
13283 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
13303 TCGCAACTCAATTCTGACTA
1 TCGCAACGCGATTCTGACTA
13323 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
13343 ACGCAACGCGATTCTGACTG
1 TCGCAACGCGATTCTGACTA
13363 TCGCAACGC
1 TCGCAACGC
13372 TGAATTTCAA
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.02
20 76 0.81
21 14 0.15
22 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:13299 original size:41 final size:41
Alignment explanation
Indices: 13242--13350 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
13232 GTTTCCAGAT
*
13242 TCGCAACGCGATTCTGACTATCGCAACGT-GATAAT-ACATAA
1 TCGCAACGCGATTCTGACTATCGCAACGTCAATAATGAC-T-A
**
13283 TCGCAACGCGATTCTGACTATCGCAAC-TCAATTCTGACTA
1 TCGCAACGCGATTCTGACTATCGCAACGTCAATAATGACTA
*
13323 TCGCAACGCGATTCTGACTAACGCAACG
1 TCGCAACGCGATTCTGACTATCGCAACG
13351 CGATTCTGAC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
40 28 0.46
41 31 0.51
42 2 0.03
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAACGTCAATAATGACTA
Found at i:14757 original size:26 final size:27
Alignment explanation
Indices: 14691--14757 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
14681 AAAACAAGGT
14691 GTATGATTGACAAAAACTGTACGTGGC
1 GTATGATTGACAAAAACTGTACGTGGC
14718 GTATGATTGACAAAAACTGTACGTGGC
1 GTATGATTGACAAAAACTGTACGTGGC
14745 GTATGATTG-CAAA
1 GTATGATTGACAAA
14758 GAGGATAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 4 0.10
27 36 0.90
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.27
Consensus pattern (27 bp):
GTATGATTGACAAAAACTGTACGTGGC
Found at i:16552 original size:18 final size:18
Alignment explanation
Indices: 16529--16563 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16519 AGAAAAAGGC
*
16529 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
16547 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
16564 CAACCGGCTT
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:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:16872 original size:140 final size:140
Alignment explanation
Indices: 16620--17181 Score: 1018
Period size: 140 Copynumber: 4.0 Consensus size: 140
16610 GCAAACGTTG
16620 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
16685 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
16750 CGAATTTGAC
131 CGAATTTGAC
16760 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
16825 TTGAACATTACTATGATTTGTTCAGTTGTTATCACTTATTACACATTCA-TTGAATATCGCAACG
66 TTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
16889 CGAATTTGAC
131 CGAATTTGAC
*
16899 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* * *
16964 TTGAACTTTACTATGATCTGTTCAGTTTTTATCACTTATTACACATTCATTTGAATATCTCAACG
66 TTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
17029 CGAATTTGAT
131 CGAATTTGAC
*
17039 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTGGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
17104 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATAGCAACG
66 TTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
17169 CGAATTTGAC
131 CGAATTTGAC
17179 TAT
1 TAT
17182 CGAACCGCGA
Statistics
Matches: 405, Mismatches: 16, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
139 135 0.33
140 270 0.67
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:17120 original size:279 final size:280
Alignment explanation
Indices: 16620--17181 Score: 1018
Period size: 279 Copynumber: 2.0 Consensus size: 280
16610 GCAAACGTTG
*
16620 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
*
16685 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTACTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
16750 CGAATTTGACTATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAG
131 CGAATTTGACTATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAG
*
16815 TAACTTGAGTTTGAACATTACTATGATTTGTTCAGTTGTTATCACTTATTACACATTCA-TTGAA
196 TAACTTGAGTTTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAA
*
16879 TATCGCAACGCGAATTTGAC
261 TATAGCAACGCGAATTTGAC
16899 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
* * * *
16964 TTGAACTTTACTATGATCTGTTCAGTTTTTATCACTTATTACACATTCATTTGAATATCTCAACG
66 TTGAACATTACTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
* *
17029 CGAATTTGATTATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTGGGCATGTATTAG
131 CGAATTTGACTATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAG
*
17094 TAACTTGAGTTTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAA
196 TAACTTGAGTTTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAA
17159 TATAGCAACGCGAATTTGAC
261 TATAGCAACGCGAATTTGAC
17179 TAT
1 TAT
17182 CGAACCGCGA
Statistics
Matches: 271, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
279 244 0.90
280 27 0.10
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (280 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
TTGAACATTACTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGACTATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAG
TAACTTGAGTTTGAACATTACTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAA
TATAGCAACGCGAATTTGAC
Found at i:17177 original size:20 final size:20
Alignment explanation
Indices: 17152--17464 Score: 281
Period size: 20 Copynumber: 16.6 Consensus size: 20
17142 TTACACATTC
* *
17152 ATTTGAATATAGCAACGCGA
1 ATTTGACTATCGCAACGCGA
17172 ATTTGACTATCG-AACCGCGA
1 ATTTGACTATCGCAA-CGCGA
*
17192 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
17211 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
17225 ATTTGACTATAGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
17245 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
17265 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
17285 ATATGACTATCACAACGC-A
1 ATTTGACTATCGCAACGCGA
*
17304 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
17319 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
17339 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
17359 ATTTGACTATCGCAATGTGA
1 ATTTGACTATCGCAACGCGA
* *
17379 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
* *
17399 ATTTGACTATTGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
17419 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
17433 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
17453 A-TTGACTTTCGC
1 ATTTGACTATCGC
17465 GTTGCGATTT
Statistics
Matches: 241, Mismatches: 31, Indels: 43
0.77 0.10 0.14
Matches are distributed among these distances:
13 9 0.04
14 20 0.08
15 4 0.02
16 1 0.00
18 2 0.01
19 16 0.07
20 187 0.78
21 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:17335 original size:54 final size:54
Alignment explanation
Indices: 17253--17464 Score: 212
Period size: 54 Copynumber: 3.8 Consensus size: 54
17243 GAATTTGACT
* * * *
17253 ATCGCAACACGAATTTGACTATCACAACGCGAATATGACTATCACAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
* *
17307 ATCGCAACGCGAATTTGACTATCGCAACGTGAATTTGACTATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGC-AA----A-A
* * * * *
17367 ATCGCAATGTGAATTTGATTATCGCAACGGGAATTTGACTATTGCAACG-AGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCA-AAA
* * * *
17421 ATCGCAAAGCGTATTAGACTATCGCAACGCGAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGC
17465 GTTGCGATTT
Statistics
Matches: 131, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
53 9 0.07
54 72 0.55
55 3 0.02
58 1 0.01
59 2 0.02
60 44 0.34
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAA
Found at i:17395 original size:94 final size:93
Alignment explanation
Indices: 17152--17395 Score: 346
Period size: 94 Copynumber: 2.6 Consensus size: 93
17142 TTACACATTC
* * *
17152 ATTTGAATATAGCAACGCGAATTTGACTATCG-AACCGCGAATTTGACTATCGCAACTCAAAATC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAA-CGCGAATTTGACTATCGCAACGCAAAATC
17216 GCAACGCGAATTTGACTATAGCAACACGA
65 GCAACGCGAATTTGACTATAGCAACACGA
* * * *
17245 ATTTGACTATCGCAACACGAATTTGACTATCACAACGCGAATATGACTATCACAACGCAAAAATC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGC-AAAATC
* **
17310 GCAACGCGAATTTGACTATCGCAACGTGA
65 GCAACGCGAATTTGACTATAGCAACACGA
* * *
17339 ATTTGACTATCGCAACGCGAATTTGACTATCGCAATGTGAATTTGATTATCGCAACG
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
17396 GGAATTTGAC
Statistics
Matches: 132, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
93 48 0.36
94 84 0.64
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (93 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAATCG
CAACGCGAATTTGACTATAGCAACACGA
Found at i:17471 original size:19 final size:19
Alignment explanation
Indices: 17449--17513 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 19
17439 CTATCGCAAC
* *
17449 GCGAATTGACTTTCGCGTT
1 GCGATTTGACTTTCGCATT
*
17468 GCGATTTGGCTTTCGCATT
1 GCGATTTGACTTTCGCATT
17487 GCGATTTTGACTTTCGCATT
1 GCGA-TTTGACTTTCGCATT
17507 GCGATTT
1 GCGATTT
17514 TGAGTTTAGC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 23 0.56
20 18 0.44
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
GCGATTTGACTTTCGCATT
Found at i:17500 original size:20 final size:20
Alignment explanation
Indices: 17454--17530 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
17444 GCAACGCGAA
*
17454 TTGACTTTCGCGTTGCGA-T
1 TTGACTTTCGCATTGCGATT
*
17473 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
17493 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
17513 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
17531 AATTGTACCT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 16 0.31
20 35 0.69
ACGTcount: A:0.13, C:0.18, G:0.26, T:0.43
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:19034 original size:42 final size:42
Alignment explanation
Indices: 18975--19097 Score: 142
Period size: 42 Copynumber: 2.9 Consensus size: 42
18965 GTGAATCGAG
* *
18975 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAATGATGGGAGGGACCTCTTAAACGATGACAGGGGC
* * ** *
19017 CTCTTGAACGATGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAATGATGGGA-GGGACCTCTTAAACGATGACAGGGGC
*
19059 CTCTTGAATGATAGGAGAGG-CCTCTTAAACGATGACAGG
1 CTCTTGAATGATGGGAG-GGACCTCTTAAACGATGACAGG
19098 TGAGTCGGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.02
42 61 0.92
43 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAATGATGGGAGGGACCTCTTAAACGATGACAGGGGC
Found at i:19035 original size:21 final size:21
Alignment explanation
Indices: 18975--19092 Score: 101
Period size: 21 Copynumber: 5.6 Consensus size: 21
18965 GTGAATCGAG
* * *
18975 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGGGC
* **
18996 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
19017 CTCTTGAACGATGGGAGGGGA
1 CTCTTGAACGATGGGAGGGGC
** **
19038 CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* * *
19059 CTCTTGAATGATAGGAGAGGC
1 CTCTTGAACGATGGGAGGGGC
*
19080 CTCTTAAACGATG
1 CTCTTGAACGATG
19093 ACAGGTGAGT
Statistics
Matches: 73, Mismatches: 24, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:19615 original size:20 final size:20
Alignment explanation
Indices: 19572--19615 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
19562 AATAGTTTCT
*
19572 GAAACTTAAAATCGCAACAT
1 GAAACTTAAAATCGCAACAC
* *
19592 GAAACTTAAAATCGTAACGC
1 GAAACTTAAAATCGCAACAC
19612 GAAA
1 GAAA
19616 ATGACTATCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:19625 original size:20 final size:20
Alignment explanation
Indices: 19602--19649 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
19592 GAAACTTAAA
*
19602 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
19622 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
19642 ATCGCAAC
1 ATCGCAAC
19650 ATGATAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:20156 original size:21 final size:21
Alignment explanation
Indices: 20130--20170 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
20120 GTAAAGTACC
*
20130 GACCTCCTCACGCAAGGCATT
1 GACCTCATCACGCAAGGCATT
20151 GACCTCATCACGCAAGGCAT
1 GACCTCATCACGCAAGGCAT
20171 CTTTGTCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.37, G:0.20, T:0.17
Consensus pattern (21 bp):
GACCTCATCACGCAAGGCATT
Found at i:21727 original size:14 final size:14
Alignment explanation
Indices: 21708--21739 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
21698 AACGCGAAAT
21708 GAAAATCGCAATGA
1 GAAAATCGCAATGA
*
21722 GAAAATCGCAATGC
1 GAAAATCGCAATGA
21736 GAAA
1 GAAA
21740 CTAAAATCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAATGA
Found at i:22150 original size:22 final size:22
Alignment explanation
Indices: 22123--22173 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
22113 GATGGAGATA
22123 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
** *
22145 GACGGATTTCGTCGGAGATGTG
1 GACGGATTTCACCGGAGATGGG
22167 GACGGAT
1 GACGGAT
22174 GTCGTCGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.16, G:0.41, T:0.22
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:22178 original size:22 final size:22
Alignment explanation
Indices: 22135--22180 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
22125 CGGATTTCAC
*
22135 CGGAGATGGGGACGGATTTCGT
1 CGGAGATGGGGACGGATGTCGT
*
22157 CGGAGATGTGGACGGATGTCGT
1 CGGAGATGGGGACGGATGTCGT
22179 CG
1 CG
22181 TAGAGAGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.15, G:0.46, T:0.22
Consensus pattern (22 bp):
CGGAGATGGGGACGGATGTCGT
Found at i:22369 original size:20 final size:20
Alignment explanation
Indices: 22340--22411 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
22330 ATTATGTATT
* *
22340 ATCGCTTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAAA
* *
22360 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAAA
* **
22380 TTCGTATTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
22400 ATCGCGTTGCGA
1 ATCGCGTTGCGA
22412 ATCTGGAAAC
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
19 1 0.03
20 37 0.95
21 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAAA
Found at i:24956 original size:29 final size:29
Alignment explanation
Indices: 24913--24995 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
24903 CTCACCTAAC
24913 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
24943 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
24972 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
24996 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:29720 original size:29 final size:29
Alignment explanation
Indices: 29677--29759 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
29667 CTCACCTAAC
29677 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
29707 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
29736 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
29760 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:46478 original size:43 final size:42
Alignment explanation
Indices: 46431--46669 Score: 236
Period size: 43 Copynumber: 5.6 Consensus size: 42
46421 TCGAGACATA
** *
46431 TAGCGGCGTTTGTAAAGACAAACGCTGCTATTGACTGTGTATT
1 TAGCGGCGTTTGTATTGA-AAACGCCGCTATTGACTGTGTATT
* *
46474 TAGCGGCGTTTGTCTTTGAAAATGCCGCTATTGACTGTGTATT
1 TAGCGGCGTTTGT-ATTGAAAACGCCGCTATTGACTGTGTATT
* * *
46517 TAGCGTCGTTTG-ACTTTATAAACGCCGTTATTGACTGTGTATT
1 TAGCGGCGTTTGTA-TTGA-AAACGCCGCTATTGACTGTGTATT
* *
46560 TAGCGGCGTTTGTCTTTGAAAACGCCTCTATTGACTGTGTATT
1 TAGCGGCGTTTGT-ATTGAAAACGCCGCTATTGACTGTGTATT
* * *
46603 TAGCGGCG-TT-TA-TAAATAACACCGCTATTAACTGTGTATT
1 TAGCGGCGTTTGTATTGAA-AACGCCGCTATTGACTGTGTATT
* * *
46643 TAG-TGCATTTGTAATTAAAAACGCCGC
1 TAGCGGCGTTTGT-ATTGAAAACGCCGC
46670 AAATAAGCCC
Statistics
Matches: 163, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
39 5 0.03
40 25 0.15
41 2 0.01
42 13 0.08
43 113 0.69
44 5 0.03
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (42 bp):
TAGCGGCGTTTGTATTGAAAACGCCGCTATTGACTGTGTATT
Found at i:46540 original size:86 final size:83
Alignment explanation
Indices: 46431--46645 Score: 279
Period size: 86 Copynumber: 2.5 Consensus size: 83
46421 TCGAGACATA
* *
46431 TAGCGGCGTTTGTAAAGACAAACGCTGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTGAAAA
1 TAGCGGCGTTTAT-AA-ATAAACGC-GCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTGAAAA
*
46496 TGCCGCTATTGACTGTGTATT
63 CGCCGCTATTGACTGTGTATT
* ** *
46517 TAGCGTCGTTTGACTTTATAAACGCCGTTATTGACTGTGTATTTAGCGGCGTTTGTCTTTGAAAA
1 TAGCGGCGTTT-A-TAAATAAACG-CGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTGAAAA
*
46582 CGCCTCTATTGACTGTGTATT
63 CGCCGCTATTGACTGTGTATT
*
46603 TAGCGGCGTTTATAAATAACAC-CGCTATTAACTGTGTATTTAG
1 TAGCGGCGTTTATAAATAA-ACGCGCTATTGACTGTGTATTTAG
46646 TGCATTTGTA
Statistics
Matches: 112, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
83 19 0.17
84 5 0.04
85 3 0.03
86 83 0.74
87 1 0.01
88 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (83 bp):
TAGCGGCGTTTATAAATAAACGCGCTATTGACTGTGTATTTAGCGGCGTTTGTCTTTGAAAACGC
CGCTATTGACTGTGTATT
Found at i:50451 original size:125 final size:124
Alignment explanation
Indices: 50220--50472 Score: 337
Period size: 125 Copynumber: 2.0 Consensus size: 124
50210 CTATTGCGAT
* * * *
50220 GTTTGTCTTTGAAAACGCTGCTAAACTACTACTCTATTGCGGCGTTTATTAAAAACACCACTAAA
1 GTTTATCTTTGAAAACGCCGCTAAACTACTACTCTATTACGACGTTTATTAAAAACACCACTAAA
* *
50285 GATGGAATATATTACATCATTTTTATAAAAACGCCGCTAAAGTAAAACTCTGTTACGGC
66 GATGGAATATATTACAGCATTTTTATAAAAACGCCACTAAAGTAAAACTCTGTTACGGC
* *
50344 GTTTATCTTTGAAAACGCCGCTAAAGTACTACTTTATTACGACGTTTATTAAAAA-ATGCCACTA
1 GTTTATCTTTGAAAACGCCGCTAAACTACTACTCTATTACGACGTTTATTAAAAACA--CCACTA
* * * * * * * *
50408 AAGATGGAATCTATTGCGGCGTTTTTATAAAAACGCCATTAAAGTAATACTGTGTTGCGGC
64 AAGATGGAATATATTACAGCATTTTTATAAAAACGCCACTAAAGTAAAACTCTGTTACGGC
50469 GTTT
1 GTTT
50473 GTTGATAAAA
Statistics
Matches: 111, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
123 1 0.01
124 49 0.44
125 61 0.55
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (124 bp):
GTTTATCTTTGAAAACGCCGCTAAACTACTACTCTATTACGACGTTTATTAAAAACACCACTAAA
GATGGAATATATTACAGCATTTTTATAAAAACGCCACTAAAGTAAAACTCTGTTACGGC
Found at i:50466 original size:41 final size:42
Alignment explanation
Indices: 50307--50573 Score: 176
Period size: 41 Copynumber: 6.4 Consensus size: 42
50297 TACATCATTT
* * * * *
50307 TTATAAAAACGCCGCTAAAGTAAAACTCTGTTACGGCGTTTA
1 TTATAAAAACGCCACTAAAGTAATACTATGTTGCGGCGTTTG
* * * * * * * * *
50349 TCTTTGAAAACGCCGCTAAAGTACTACTTTATTACGACGTTTA
1 T-TATAAAAACGCCACTAAAGTAATACTATGTTGCGGCGTTTG
*
50392 TTA-AAAAATGCCACTAAAGATGGAAT-CTA--TTGCGGCGTTT-
1 TTATAAAAACGCCACTAAAG-T--AATACTATGTTGCGGCGTTTG
* *
50432 TTATAAAAACGCCATTAAAGTAATACTGTGTTGCGGCGTTTG
1 TTATAAAAACGCCACTAAAGTAATACTATGTTGCGGCGTTTG
* ** *
50474 TTGAT-AAAACGCCACTATAGATGAACCCTA--TTGCGTCGTTTG
1 TT-ATAAAAACGCCACTAAAG-T-AATACTATGTTGCGGCGTTTG
* * *
50516 -TGTAAAAACGCCGCTAAAGTACTACTATGTTGCGGCGTTTG
1 TTATAAAAACGCCACTAAAGTAATACTATGTTGCGGCGTTTG
50557 TTA-AAACAACGCCACTA
1 TTATAAA-AACGCCACTA
50574 TAGATGAACC
Statistics
Matches: 175, Mismatches: 33, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
38 3 0.02
39 6 0.03
40 6 0.03
41 75 0.43
42 39 0.22
43 40 0.23
44 6 0.03
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (42 bp):
TTATAAAAACGCCACTAAAGTAATACTATGTTGCGGCGTTTG
Found at i:50508 original size:42 final size:40
Alignment explanation
Indices: 50396--50609 Score: 132
Period size: 41 Copynumber: 5.2 Consensus size: 40
50386 CGTTTATTAA
* * * *
50396 AAAATGCCACTAAAGATGGAA-TCTATTGCGGCGTTTTTAT
1 AAAACGCCACTATAGAT-GAACCCTATTGCGGCGTTTGTAT
* * * ** *
50436 AAAAACGCCATTAAAG-TAATACTGTGTTGCGGCGTTTGTTGAT
1 -AAAACGCCACTATAGATGA-ACCCTATTGCGGCGTTTG-T-AT
* *
50479 AAAACGCCACTATAGATGAACCCTATTGCGTCGTTTGTGT
1 AAAACGCCACTATAGATGAACCCTATTGCGGCGTTTGTAT
* * * *
50519 AAAAACGCCGCTA-A-A-GTACTACTATGTTGCGGCGTTTGTTAA
1 -AAAACGCCACTATAGATGAAC-CCTA--TTGCGGCGTTTG-TAT
* *
50561 AACAACGCCACTATAGATGAACCCTACTGAGGCGTTTGTAT
1 AA-AACGCCACTATAGATGAACCCTATTGCGGCGTTTGTAT
50602 AAAACGCC
1 AAAACGCC
50610 GCTAAAGTTA
Statistics
Matches: 133, Mismatches: 26, Indels: 29
0.71 0.14 0.15
Matches are distributed among these distances:
38 3 0.02
39 5 0.04
40 10 0.08
41 55 0.41
42 48 0.36
43 5 0.04
44 4 0.03
45 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (40 bp):
AAAACGCCACTATAGATGAACCCTATTGCGGCGTTTGTAT
Found at i:50508 original size:83 final size:82
Alignment explanation
Indices: 50355--50637 Score: 304
Period size: 83 Copynumber: 3.5 Consensus size: 82
50345 TTTATCTTTG
* * * * * * * * * *
50355 AAAACGCCGCTAAAGTACTACTTTATTACGACGTTTATTAAAAAATGCCACTAAAGATGGAA-TC
1 AAAACGCCACTAAAGTAATACTATGTTGCGGCGTTTGTTAAAAAACGCCACTATAGAT-GAACCC
*
50419 TATTGCGGCGTTTTTATA
65 TATTGCGGCGTTTGTATA
* * *
50437 AAAACGCCATTAAAGTAATACTGTGTTGCGGCGTTTGTTGATAAAACGCCACTATAGATGAACCC
1 AAAACGCCACTAAAGTAATACTATGTTGCGGCGTTTGTT-AAAAAACGCCACTATAGATGAACCC
* *
50502 TATTGCGTCGTTTGTGTA
65 TATTGCGGCGTTTGTATA
* *
50520 AAAACGCCGCTAAAGTACTACTATGTTGCGGCGTTTGTTAAAACAACGCCACTATAGATGAACCC
1 AAAACGCCACTAAAGTAATACTATGTTGCGGCGTTTGTTAAAA-AACGCCACTATAGATGAACCC
* *
50585 TACTGAGGCGTTTGTAT-
65 TATTGCGGCGTTTGTATA
* * *
50602 AAAACGCCGCTAAAGT--TACAATTTTGCGGCGTTTGT
1 AAAACGCCACTAAAGTAATACTATGTTGCGGCGTTTGT
50638 GATGTAAACG
Statistics
Matches: 172, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 18 0.10
82 53 0.31
83 101 0.59
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (82 bp):
AAAACGCCACTAAAGTAATACTATGTTGCGGCGTTTGTTAAAAAACGCCACTATAGATGAACCCT
ATTGCGGCGTTTGTATA
Found at i:60002 original size:17 final size:18
Alignment explanation
Indices: 59980--60013 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
59970 GTATTACACA
*
59980 TATCTTGTCA-CATATCT
1 TATCTTATCATCATATCT
59997 TATCTTATCATCATATC
1 TATCTTATCATCATATC
60014 ATTACATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (18 bp):
TATCTTATCATCATATCT
Found at i:61011 original size:13 final size:13
Alignment explanation
Indices: 60993--61018 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60983 CACGGGATAG
60993 GAAGAAGAAAACT
1 GAAGAAGAAAACT
61006 GAAGAAGAAAACT
1 GAAGAAGAAAACT
61019 CTGGATACTT
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:0.62, C:0.08, G:0.23, T:0.08
Consensus pattern (13 bp):
GAAGAAGAAAACT
Found at i:63607 original size:31 final size:32
Alignment explanation
Indices: 63534--63614 Score: 92
Period size: 32 Copynumber: 2.6 Consensus size: 32
63524 CCCGAAGGAC
* * *
63534 CTATCCATATGTTCCGAAGAACATACGTAATC
1 CTATCCATATGTCCCGAAGAACATAAGTAATA
* * *
63566 CTATCTATATGTCCCGAAGGATATAAGTAA-A
1 CTATCCATATGTCCCGAAGAACATAAGTAATA
*
63597 CTATCCATATGTCTCGAA
1 CTATCCATATGTCCCGAA
63615 AGACATAGGT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 16 0.39
32 25 0.61
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (32 bp):
CTATCCATATGTCCCGAAGAACATAAGTAATA
Found at i:65704 original size:60 final size:60
Alignment explanation
Indices: 65610--65728 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
65600 AAGAATACCG
* *
65610 ATACTCCCTGTTCTAGGCAGTTTTATTTTTTAGAAAATTAATCCTCAACGGCTCCAAAAC
1 ATACTCCCTGTTCTAGGCAGTTTTATTTTGTAGAAAATTAATCCCCAACGGCTCCAAAAC
65670 ATACTCCCTGTTCTAGGCAGTTTTATTTTGTAGAAAATTAATCCCCAACGGCTCCAAAA
1 ATACTCCCTGTTCTAGGCAGTTTTATTTTGTAGAAAATTAATCCCCAACGGCTCCAAAA
65729 TATCCCCAAC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (60 bp):
ATACTCCCTGTTCTAGGCAGTTTTATTTTGTAGAAAATTAATCCCCAACGGCTCCAAAAC
Done.