Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006297.1 Hibiscus syriacus cultivar Beakdansim tig00015050_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: 54409
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:4867 original size:24 final size:24
Alignment explanation
Indices: 4840--4889 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
4830 ATAAAAAACC
4840 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
4864 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
4888 AA
1 AA
4890 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:6065 original size:22 final size:22
Alignment explanation
Indices: 6024--6067 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
6014 TCATTTAGTA
6024 CACTCTTTTCTTTTCTTTTTTT
1 CACTCTTTTCTTTTCTTTTTTT
6046 CACT-TTTTCCTTCTTCTTTTTT
1 CACTCTTTT-CTT-TTCTTTTTT
6068 AAGCTGCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.70
Consensus pattern (22 bp):
CACTCTTTTCTTTTCTTTTTTT
Found at i:10435 original size:24 final size:24
Alignment explanation
Indices: 10408--10457 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
10398 ATAAAGAACC
10408 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
10432 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
10456 AA
1 AA
10458 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:11702 original size:22 final size:22
Alignment explanation
Indices: 11676--11717 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11666 ACTTTTCGGA
* *
11676 TATTTTCTTTTATTAAATTTCT
1 TATTTTATTTCATTAAATTTCT
*
11698 TATTTTATTTCATTTAATTT
1 TATTTTATTTCATTAAATTT
11718 TCAGTATATT
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:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTTTATTTCATTAAATTTCT
Found at i:14811 original size:29 final size:29
Alignment explanation
Indices: 14749--14815 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
14739 CTTGTTCCAC
*
14749 GAAAAAAAATTGATCATTGTTTCGAACAG
1 GAAAAAAAATTGATCAATGTTTCGAACAG
* * *
14778 CAAAAAAAA-TGTTCAATGTTTCGAATAG
1 GAAAAAAAATTGATCAATGTTTCGAACAG
14806 AGAAAAAAAA
1 -GAAAAAAAA
14816 GAAAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 16 0.50
29 16 0.50
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (29 bp):
GAAAAAAAATTGATCAATGTTTCGAACAG
Found at i:16550 original size:4 final size:4
Alignment explanation
Indices: 16543--16576 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
16533 TTTTATCTCA
*
16543 ATTT ATTTT ATTT ATTT ATTT ATTT GTTT ATTT A
1 ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT A
16577 ATCTTTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:16744 original size:14 final size:13
Alignment explanation
Indices: 16630--16753 Score: 69
Period size: 13 Copynumber: 9.2 Consensus size: 13
16620 CATGTTATCT
*
16630 TTATTCTTATCTTA
1 TTATT-TTATTTTA
*
16644 TAATTATTA-TTTA
1 TTATT-TTATTTTA
16657 TT-TATTTATTTTA
1 TTAT-TTTATTTTA
*
16670 TTATTTTATCCTTA
1 TTATTTTAT-TTTA
**
16684 -TATTCCATTTTAAA
1 TTATTTTATTTT--A
*
16698 TGATTTATATTTTA
1 TTATTT-TATTTTA
16712 TTA-TTTATTTTA
1 TTATTTTATTTTA
16724 TTATTTTATTCTTA
1 TTATTTTATT-TTA
16738 TCT-TTTTATCTTTA
1 T-TATTTTAT-TTTA
16752 TT
1 TT
16754 TGAAATATCT
Statistics
Matches: 86, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
12 16 0.19
13 31 0.36
14 29 0.34
15 5 0.06
16 5 0.06
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:17317 original size:20 final size:20
Alignment explanation
Indices: 17292--17330 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17282 AAGATGGTAC
17292 ATGTGATTAGCATGAGTATT
1 ATGTGATTAGCATGAGTATT
*
17312 ATGTGATTGGCATGAGTAT
1 ATGTGATTAGCATGAGTAT
17331 AATATATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.38
Consensus pattern (20 bp):
ATGTGATTAGCATGAGTATT
Found at i:21379 original size:13 final size:13
Alignment explanation
Indices: 21361--21389 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
21351 ATTGCTCGTG
21361 GTGAAACATTTGT
1 GTGAAACATTTGT
21374 GTGAAACATTTGT
1 GTGAAACATTTGT
21387 GTG
1 GTG
21390 CAAAATTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.38
Consensus pattern (13 bp):
GTGAAACATTTGT
Found at i:23296 original size:17 final size:18
Alignment explanation
Indices: 23263--23299 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
23253 TTTAAGATTT
23263 TATATTCGATTCAAAATTA
1 TATATTCGATT-AAAATTA
23282 TATATTCGATT-AAATTA
1 TATATTCGATTAAAATTA
23299 T
1 T
23300 TCGAATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTAAAATTA
Found at i:25057 original size:18 final size:18
Alignment explanation
Indices: 25026--25068 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
25016 GTAGACCTCG
*
25026 AGAAGAAGAAGGAGATAA
1 AGAAGAAGAAGGAGAAAA
* *
25044 AGAAGGAGACGGAGAAAA
1 AGAAGAAGAAGGAGAAAA
25062 AGAAGAA
1 AGAAGAA
25069 TGTTGGAGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.35, T:0.02
Consensus pattern (18 bp):
AGAAGAAGAAGGAGAAAA
Found at i:27211 original size:58 final size:58
Alignment explanation
Indices: 27127--27260 Score: 196
Period size: 58 Copynumber: 2.3 Consensus size: 58
27117 TTTTTTTAAA
* * ** *
27127 TAATTACCAAAATAGCACCCTTTTCAAATTAATTCCCAAAATAGCACCAATTTCGAAT
1 TAATTCCCAGAATAGCACCCTTTTCAAAAAAATTACCAAAATAGCACCAATTTCGAAT
* *
27185 TAATTCCCAGAATATCACCTTTTTCAAAAAAATTACCAAAATAGCACCAATTTCGAAT
1 TAATTCCCAGAATAGCACCCTTTTCAAAAAAATTACCAAAATAGCACCAATTTCGAAT
*
27243 TAATTCCCCGAATAGCAC
1 TAATTCCCAGAATAGCAC
27261 TAAACTGAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 67 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (58 bp):
TAATTCCCAGAATAGCACCCTTTTCAAAAAAATTACCAAAATAGCACCAATTTCGAAT
Found at i:27225 original size:87 final size:86
Alignment explanation
Indices: 27108--27289 Score: 231
Period size: 87 Copynumber: 2.1 Consensus size: 86
27098 CATTTTACAC
** * **
27108 AAATAACA-CTTTTTTTAAATAATTACCAAAATAGCACCCTTTTCAAATTAATTCCCAAAATAGC
1 AAATAACACCTTTTTCAAAAAAATTACCAAAATAGCACCAATTTCAAATTAATTCCCAAAATAGC
**
27172 ACCAATTTCGAATTAATTCCCA
66 ACCAAACT-GAATTAATTCCCA
* * * **
27194 GAATATCACCTTTTTCAAAAAAATTACCAAAATAGCACCAATTTCGAATTAATTCCCCGAATAGC
1 AAATAACACCTTTTTCAAAAAAATTACCAAAATAGCACCAATTTCAAATTAATTCCCAAAATAGC
*
27259 ACTAAACTGAATTAATTCCCA
66 ACCAAACTGAATTAATTCCCA
27280 AAATAACACC
1 AAATAACACC
27290 GGTCAATAGT
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
86 27 0.34
87 53 0.66
ACGTcount: A:0.43, C:0.23, G:0.05, T:0.29
Consensus pattern (86 bp):
AAATAACACCTTTTTCAAAAAAATTACCAAAATAGCACCAATTTCAAATTAATTCCCAAAATAGC
ACCAAACTGAATTAATTCCCA
Found at i:27256 original size:29 final size:29
Alignment explanation
Indices: 27127--27289 Score: 157
Period size: 29 Copynumber: 5.7 Consensus size: 29
27117 TTTTTTTAAA
* ** *
27127 TAATTACCAAAATAGCACCCTTTTCAAAT
1 TAATTCCCAAAATAGCACCAATTTCGAAT
27156 TAATTCCCAAAATAGCACCAATTTCGAAT
1 TAATTCCCAAAATAGCACCAATTTCGAAT
* * ** * *
27185 TAATTCCCAGAATATCACCTTTTTCAAAA
1 TAATTCCCAAAATAGCACCAATTTCGAAT
* *
27214 AAATTACCAAAATAGCACCAATTTCGAAT
1 TAATTCCCAAAATAGCACCAATTTCGAAT
** * **
27243 TAATTCCCCGAATAGCACTAAACT-GAAT
1 TAATTCCCAAAATAGCACCAATTTCGAAT
*
27271 TAATTCCCAAAATAACACC
1 TAATTCCCAAAATAGCACC
27290 GGTCAATAGT
Statistics
Matches: 105, Mismatches: 29, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
28 19 0.18
29 86 0.82
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.28
Consensus pattern (29 bp):
TAATTCCCAAAATAGCACCAATTTCGAAT
Found at i:27326 original size:18 final size:18
Alignment explanation
Indices: 27303--27338 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
27293 CAATAGTCAA
27303 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
27321 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
27339 AAACGGGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:27338 original size:13 final size:13
Alignment explanation
Indices: 27298--27326 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
27288 CCGGTCAATA
27298 GTCAACGGGTCGG
1 GTCAACGGGTCGG
27311 GTCAACGGGTCGG
1 GTCAACGGGTCGG
27324 GTC
1 GTC
27327 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:27357 original size:26 final size:26
Alignment explanation
Indices: 27308--27359 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
27298 GTCAACGGGT
* * *
27308 CGGGTCAACGGGTCGGGTCGGGTCAA
1 CGGGTAAACGGGTCGGGACCGGTCAA
*
27334 CGGGTAAACGGGTCGTGACCGGTCAA
1 CGGGTAAACGGGTCGGGACCGGTCAA
27360 ACCGGTCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.15
Consensus pattern (26 bp):
CGGGTAAACGGGTCGGGACCGGTCAA
Found at i:34829 original size:21 final size:21
Alignment explanation
Indices: 34805--34844 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
34795 TTTATTTTAT
34805 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
34826 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
34845 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:34893 original size:33 final size:32
Alignment explanation
Indices: 34839--34937 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
34829 TTTGTTTCAA
34839 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
34871 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTG-AAGTTTTTAAGTATTTGAAT
* * *
34904 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
34937 T
1 T
34938 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 12 0.19
33 49 0.79
34 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:34966 original size:13 final size:13
Alignment explanation
Indices: 34923--34977 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
34913 TTGGAAGTAT
34923 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
34936 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
34950 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
34963 TTAAGTATTTGAA
1 TTAAGTATTTCAA
34976 TT
1 TT
34978 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:35199 original size:21 final size:21
Alignment explanation
Indices: 35173--35229 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
35163 TGGAGCGTGG
*
35173 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
35194 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
35215 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
35230 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:35399 original size:15 final size:15
Alignment explanation
Indices: 35374--35429 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
35364 ATCTGGAATA
*
35374 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
35389 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
35404 TTAAAAAATCGGTTTTT
1 TT--AAAACCGGTTTTT
35421 TTAAAACCG
1 TTAAAACCG
35430 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.46
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:35416 original size:17 final size:17
Alignment explanation
Indices: 35376--35426 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
35366 CTGGAATATT
35376 AAAATCGGTTTTTTT--
1 AAAATCGGTTTTTTTAA
* *
35391 ATAACCGGTTTTTTTAA
1 AAAATCGGTTTTTTTAA
35408 AAAATCGGTTTTTTTAA
1 AAAATCGGTTTTTTTAA
35425 AA
1 AA
35427 CCGAAACCGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 13 0.43
17 17 0.57
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (17 bp):
AAAATCGGTTTTTTTAA
Found at i:35546 original size:15 final size:17
Alignment explanation
Indices: 35520--35551 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
35510 TTCTATGGGA
35520 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
35536 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
35552 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:37582 original size:29 final size:29
Alignment explanation
Indices: 37532--37672 Score: 99
Period size: 29 Copynumber: 4.9 Consensus size: 29
37522 CATTTTACAC
* *
37532 AAATAGCA--CTTTTTTAAATAATTACCA
1 AAATAGCACCCTTTTTGAATTAATTACCA
37559 AAATAGCACCCTTTTTGAATTAATT-CCTA
1 AAATAGCACCCTTTTTGAATTAATTACC-A
** * *
37588 AAATAGCACCAATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATTACCA
* * * * ** *
37617 GAATATCACCTTTTTTCAAAAAAAAATACCA
1 AAATAGCACCCTTTTT--GAATTAATTACCA
* *
37648 AAATAGCACCCATTTCGAATTAATT
1 AAATAGCACCCTTTTTGAATTAATT
37673 CCCCGAATAG
Statistics
Matches: 84, Mismatches: 24, Indels: 10
0.71 0.20 0.08
Matches are distributed among these distances:
27 8 0.10
28 2 0.02
29 53 0.63
30 2 0.02
31 19 0.23
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.33
Consensus pattern (29 bp):
AAATAGCACCCTTTTTGAATTAATTACCA
Found at i:37754 original size:17 final size:17
Alignment explanation
Indices: 37722--37772 Score: 84
Period size: 17 Copynumber: 2.9 Consensus size: 17
37712 ACCGGTCAAC
37722 GGTCAACGGGTCGGGTCG
1 GGTCAAC-GGTCGGGTCG
*
37740 GGTCAACGATCGGGTCG
1 GGTCAACGGTCGGGTCG
37757 GGTCAACGGTCGGGTC
1 GGTCAACGGTCGGGTC
37773 AACGGGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 24 0.77
18 7 0.23
ACGTcount: A:0.14, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:37767 original size:12 final size:12
Alignment explanation
Indices: 37752--37777 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
37742 TCAACGATCG
37752 GGTCGGGTCAAC
1 GGTCGGGTCAAC
37764 GGTCGGGTCAAC
1 GGTCGGGTCAAC
37776 GG
1 GG
37778 GTAAACGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (12 bp):
GGTCGGGTCAAC
Found at i:42777 original size:17 final size:18
Alignment explanation
Indices: 42744--42780 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
42734 TTTAAGATTT
42744 TATATTCGATTCAAAATTA
1 TATATTCGATT-AAAATTA
42763 TATATTCGATT-AAATTA
1 TATATTCGATTAAAATTA
42780 T
1 T
42781 TCGAATATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTAAAATTA
Found at i:46933 original size:25 final size:25
Alignment explanation
Indices: 46905--46994 Score: 99
Period size: 25 Copynumber: 3.4 Consensus size: 25
46895 GTTTTTGGTT
*
46905 AGATGAAAGGAGTTTGTTGTGTAAGAG
1 AGATGAAAGGAGTGTGTTGTGT-A-AG
*
46932 ATTGAAGTGAAAAGAGTGTGTTGTGTAAG
1 A--G-A-TGAAAGGAGTGTGTTGTGTAAG
*
46961 AGATGAAAGGAGTGTGTTGTGTATG
1 AGATGAAAGGAGTGTGTTGTGTAAG
46986 AGATGAAAG
1 AGATGAAAG
46995 ATGATGTTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
25 29 0.53
26 1 0.02
27 2 0.04
29 4 0.07
30 2 0.04
31 17 0.31
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (25 bp):
AGATGAAAGGAGTGTGTTGTGTAAG
Found at i:48675 original size:3 final size:3
Alignment explanation
Indices: 48667--48699 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
48657 TTCTTGACAC
48667 AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AA
48700 AGGAAGAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:53128 original size:51 final size:52
Alignment explanation
Indices: 53051--53154 Score: 174
Period size: 51 Copynumber: 2.0 Consensus size: 52
53041 AAGTTGTTCG
*
53051 ACTTTGACTTGTAGGTTTTCATTGGTCTTTCAATAACTTAATC-ACTTTTGT
1 ACTTTGACTTGTAGGTTTTCAGTGGTCTTTCAATAACTTAATCGACTTTTGT
* *
53102 ACTTTGATTTGTGGGTTTTCAGTGGTCTTTCAATAACTTAATCGACTTTTGT
1 ACTTTGACTTGTAGGTTTTCAGTGGTCTTTCAATAACTTAATCGACTTTTGT
53154 A
1 A
53155 TTCGTTTGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 40 0.82
52 9 0.18
ACGTcount: A:0.21, C:0.14, G:0.16, T:0.48
Consensus pattern (52 bp):
ACTTTGACTTGTAGGTTTTCAGTGGTCTTTCAATAACTTAATCGACTTTTGT
Done.