Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001199.1 Hibiscus syriacus cultivar Beakdansim tig00002373_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: 62197
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:10516 original size:256 final size:261
Alignment explanation
Indices: 9916--10518 Score: 944
Period size: 256 Copynumber: 2.4 Consensus size: 261
9906 CTTATTCATA
*
9916 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTTCTAATTC--ATA-----GT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTTGGGTCGGGTTTCTAATTCATATATTCGGGT
* * *
9974 CGGGTCGGGTGAAACTTTATTTTGGTCGGGTTGGGTCAGTGTTTTTAAGTGTGATATTCGGGTCG
66 CGGGTCGGGTGAAACTTTATTTTGGTCAGGTTCGGT-A-TGTTTTTAAGTGTGATATTCGGGTCA
* * * * *
10039 GGTTGAGTTCGGGTTTTGGGTGAAAAATACCCGACCCGACCCAAAAATATATATAATTTTACTTT
129 GGTCGAGTTCGGATTTAGGGTGAAAAATACCCAACCCGACCCAAAAATATATATAATTTTACGTT
*
10104 ATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATTAAGTCACTGT
194 ATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTATTTTTCAATTAAGTCACTGT
10169 TTT
259 TTT
**
10172 TATTGAATAAAAATATTTTTTTATTATTTCGGG-TCAGTCGGGTTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTTGGGTCGGGTTTCTAATTCATATATTCGGGT
* *
10236 CGGGTCGGGTGAAACTTTATTTTGGTCAGG-TCGGT-TTTTTTTAAGTTTGATATTCGGGTCAGG
66 CGGGTCGGGTGAAACTTTATTTTGGTCAGGTTCGGTATGTTTTTAAGTGTGATATTCGGGTCAGG
* *
10299 TCGGGTTCGGATTTAGGTTGAAAAATACCCAACCCGACCCAAAAA-ATATATAATTTTACGTTAT
131 TCGAGTTCGGATTTAGGGTGAAAAATACCCAACCCGACCCAAAAATATATATAATTTTACGTTAT
10363 ATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTATTTTT-AATTAAG-CACTGTTT
196 ATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTATTTTTCAATTAAGTCACTGTTT
10426 T
261 T
*
10427 TATTTAATAAAAATATTTTTTTATTATTTCGGGTTGGGTCGGGTTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTTGGGTCGGGTTTCTAATTCATATATTCGGGT
10492 CGGGTCGGGTGAAACTTTATTTTGGTC
66 CGGGTCGGGTGAAACTTTATTTTGGTC
10519 GGATCGGGTC
Statistics
Matches: 320, Mismatches: 19, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
255 57 0.18
256 96 0.30
257 68 0.21
258 64 0.20
261 4 0.01
262 31 0.10
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (261 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGGTTGGGTCGGGTTTCTAATTCATATATTCGGGT
CGGGTCGGGTGAAACTTTATTTTGGTCAGGTTCGGTATGTTTTTAAGTGTGATATTCGGGTCAGG
TCGAGTTCGGATTTAGGGTGAAAAATACCCAACCCGACCCAAAAATATATATAATTTTACGTTAT
ATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTATTTTTCAATTAAGTCACTGTTT
T
Found at i:10578 original size:42 final size:43
Alignment explanation
Indices: 10522--10604 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 43
10512 TTTGGTCGGA
*
10522 TCGGGTCTCTGATGGAGGTTCCCTT-TTCCGGGTCGGGTCGAG
1 TCGGGTCTCGGATGGAGGTTCCCTTGTTCCGGGTCGGGTCGAG
*
10564 TCGGGTCTCGGATGGAGGTTCCCTTGTTCTGGGTCGGGTCG
1 TCGGGTCTCGGATGGAGGTTCCCTTGTTCCGGGTCGGGTCG
10605 GGTGAACCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 24 0.63
43 14 0.37
ACGTcount: A:0.06, C:0.23, G:0.40, T:0.31
Consensus pattern (43 bp):
TCGGGTCTCGGATGGAGGTTCCCTTGTTCCGGGTCGGGTCGAG
Found at i:10957 original size:17 final size:17
Alignment explanation
Indices: 10923--10968 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
10913 TATGGAATTG
*
10923 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
10940 GATT-CAATTCCTTCACA
1 GATTCCAATTCC-TCACA
10957 GATTCCAATTCC
1 GATTCCAATTCC
10969 CTCAGAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.27
17 12 0.46
18 7 0.27
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:12980 original size:16 final size:16
Alignment explanation
Indices: 12959--12991 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12949 GGCATTCCTT
12959 CACGGTTTTACCGGTC
1 CACGGTTTTACCGGTC
12975 CACGGTTTTACCGGTC
1 CACGGTTTTACCGGTC
12991 C
1 C
12992 GTCAGGACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.33, G:0.24, T:0.30
Consensus pattern (16 bp):
CACGGTTTTACCGGTC
Found at i:24202 original size:22 final size:24
Alignment explanation
Indices: 24166--24213 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
24156 TGGTTGTTAC
*
24166 ATATGAATGTTTATCATGAAT-AT
1 ATATGAATATTTATCATGAATGAT
24189 ATATG-ATATTTATCATGAATGAT
1 ATATGAATATTTATCATGAATGAT
24212 AT
1 AT
24214 TTCGGGTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (24 bp):
ATATGAATATTTATCATGAATGAT
Found at i:27393 original size:6 final size:6
Alignment explanation
Indices: 27379--27415 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
27369 GACACGTATT
* *
27379 ACCACG ACCATG ACCACG ACCTCG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
27416 GCCGAACCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.32, C:0.46, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:33300 original size:6 final size:6
Alignment explanation
Indices: 33289--33332 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
33279 AGACACGTAT
33289 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GA
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GA
33333 GCCGAGCCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.34, C:0.48, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:38220 original size:29 final size:29
Alignment explanation
Indices: 38178--38264 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
38168 GTCCCGGGGG
*
38178 TAGGTCGCCATGCACGCCCGGCGACCTAC
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
**
38207 TAGGTCGCCATGCACGCCCAGCGACCTGG
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
* *
38236 TAGGTCGCCATGCATGCCCTGCGACCTAC
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
38265 CAGCACCTCC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.17, C:0.39, G:0.28, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAGCGACCTAC
Found at i:38280 original size:10 final size:10
Alignment explanation
Indices: 38273--38357 Score: 77
Period size: 10 Copynumber: 8.3 Consensus size: 10
38263 ACCAGCACCT
38273 CCATGCACGC
1 CCATGCACGC
38283 CCATGCACGC
1 CCATGCACGC
*
38293 CCA-ACGAC-C
1 CCATGC-ACGC
38302 TCCATGCACGC
1 -CCATGCACGC
38313 CCATGCACGC
1 CCATGCACGC
* *
38323 CCA-ACGACCTCC
1 CCATGC-A-C-GC
38335 CCATGCACGC
1 CCATGCACGC
38345 CCATGCACGC
1 CCATGCACGC
38355 CCA
1 CCA
38358 ACGACCTCCA
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
9 3 0.05
10 48 0.79
11 4 0.07
12 5 0.08
13 1 0.02
ACGTcount: A:0.22, C:0.52, G:0.16, T:0.09
Consensus pattern (10 bp):
CCATGCACGC
Found at i:38287 original size:40 final size:40
Alignment explanation
Indices: 38243--38325 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
38233 TGGTAGGTCG
* **
38243 CCATGCATGCCCTGCGACCTACCA-GCAC-CTCCATGCACGC
1 CCATGCACGCCCAACGACCT-CCATGCACGC-CCATGCACGC
38283 CCATGCACGCCCAACGACCTCCATGCACGCCCATGCACGC
1 CCATGCACGCCCAACGACCTCCATGCACGCCCATGCACGC
38323 CCA
1 CCA
38326 ACGACCTCCC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
39 3 0.08
40 34 0.89
41 1 0.03
ACGTcount: A:0.22, C:0.49, G:0.17, T:0.12
Consensus pattern (40 bp):
CCATGCACGCCCAACGACCTCCATGCACGCCCATGCACGC
Found at i:38303 original size:30 final size:30
Alignment explanation
Indices: 38269--38377 Score: 200
Period size: 30 Copynumber: 3.6 Consensus size: 30
38259 ACCTACCAGC
38269 ACCTCCATGCACGCCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
38299 ACCTCCATGCACGCCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
38329 ACCTCCCCATGCACGCCCATGCACGCCCAACG
1 ACCT--CCATGCACGCCCATGCACGCCCAACG
38361 ACCTCCATGCACGCCCA
1 ACCTCCATGCACGCCCA
38378 GCTCACCAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
30 47 0.61
32 30 0.39
ACGTcount: A:0.23, C:0.51, G:0.16, T:0.10
Consensus pattern (30 bp):
ACCTCCATGCACGCCCATGCACGCCCAACG
Found at i:39041 original size:21 final size:21
Alignment explanation
Indices: 39016--39059 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
39006 AATTTAGTTA
39016 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
39037 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
39058 AT
1 AT
39060 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:42158 original size:11 final size:11
Alignment explanation
Indices: 42142--42173 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
42132 GATTTTATAA
42142 TAATTATTTAG
1 TAATTATTTAG
*
42153 TTATTATTTAG
1 TAATTATTTAG
42164 TAATTATTTA
1 TAATTATTTA
42174 TAGTAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (11 bp):
TAATTATTTAG
Found at i:42196 original size:14 final size:14
Alignment explanation
Indices: 42164--43003 Score: 293
Period size: 14 Copynumber: 59.3 Consensus size: 14
42154 TATTATTTAG
* *
42164 TAATTATTT-ATAG
1 TAATGATTTAATAA
*
42177 TAATGATTTAATAC
1 TAATGATTTAATAA
42191 TAATGATTTAATAATTTA
1 TAATGATTTAAT-A---A
*
42209 GTAATGATTTAATAC
1 -TAATGATTTAATAA
42224 TAATGATTTAATAA
1 TAATGATTTAATAA
*
42238 TTTAGTGATGATTTAATAC
1 --TA---ATGATTTAATAA
42257 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
42268 TAATGATTTAATAC
1 TAATGATTTAATAA
42282 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
42293 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
42309 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
42328 TAATGATTTGATAA
1 TAATGATTTAATAA
*
42342 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
42354 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
42368 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
42380 T-ATTATTTAGTAA
1 TAATGATTTAATAA
42393 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
42403 TAATGATTTAATAC
1 TAATGATTTAATAA
42417 TAATGATTTAATAATTTA
1 TAATGATTTAAT-A---A
*
42435 GTAATGATTTAATAC
1 -TAATGATTTAATAA
42450 TAATGATTTAATAA
1 TAATGATTTAATAA
*
42464 TTTAGTGATGATTTAATAC
1 --TA---ATGATTTAATAA
42483 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
42494 TAATGATTTAATAC
1 TAATGATTTAATAA
42508 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
42519 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
42535 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
42554 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
42568 TAATTA-TT-ATAG
1 TAATGATTTAATAA
*
42580 TAATGATTTGATAA
1 TAATGATTTAATAA
*
42594 TAATCA-TT-ATAA
1 TAATGATTTAATAA
* * *
42606 AAATGATTTAGTAT
1 TAATGATTTAATAA
*
42620 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
42632 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
42643 TAATGATTTAAATATG
1 TAATGATTT-AATA-A
*
42659 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
42678 TAATGATTTGATAA
1 TAATGATTTAATAA
*
42692 TAATTA-TT-ATAA
1 TAATGATTTAATAA
*
42704 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
42718 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
42730 T-ATTATTTAGTAA
1 TAATGATTTAATAA
42743 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
42753 TAATGATTTAATAC
1 TAATGATTTAATAA
*
42767 TAATGATTTAATAT
1 TAATGATTTAATAA
42781 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
42792 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
42808 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
42827 TAATGATTTGATAA
1 TAATGATTTAATAA
*
42841 TAATTA-TT-ATAA
1 TAATGATTTAATAA
*
42853 TAATGATTTTATAA
1 TAATGATTTAATAA
* * *
42867 TAATTATTTAGTTAT
1 TAATGATTTA-ATAA
* *
42882 TATTTAGTAATT-ATAA
1 TA-AT-G-ATTTAATAA
*
42898 TAATGATTTAATAC
1 TAATGATTTAATAA
*
42912 TAATGATTTCATAATTTAG
1 TAATGA-TT--TAA--TAA
*
42931 TAATGATTTAATAC
1 TAATGATTTAATAA
42945 TAATGATTTAATAA
1 TAATGATTTAATAA
42959 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
42970 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
42986 TAATGATTTAATAC
1 TAATGATTTAATAA
43000 TAAT
1 TAAT
43004 AATAATGATT
Statistics
Matches: 641, Mismatches: 86, Indels: 199
0.69 0.09 0.21
Matches are distributed among these distances:
10 8 0.01
11 85 0.13
12 71 0.11
13 55 0.09
14 217 0.34
15 23 0.04
16 65 0.10
17 7 0.01
18 11 0.02
19 91 0.14
20 8 0.01
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:42215 original size:19 final size:19
Alignment explanation
Indices: 42191--42255 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
42181 GATTTAATAC
42191 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
42210 TAATGA-TT--TAA--TAC
1 TAATGATTTAATAATTTAG
42224 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
42243 TGATGATTTAATA
1 TAATGATTTAATA
42256 CTAATGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 8 0.21
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 20 0.53
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.46
Consensus pattern (19 bp):
TAATGATTTAATAATTTAG
Found at i:42216 original size:33 final size:33
Alignment explanation
Indices: 42174--42271 Score: 187
Period size: 33 Copynumber: 3.0 Consensus size: 33
42164 TAATTATTTA
42174 TAGTAATGATTTAATACTAATGATTTAATAATT
1 TAGTAATGATTTAATACTAATGATTTAATAATT
42207 TAGTAATGATTTAATACTAATGATTTAATAATT
1 TAGTAATGATTTAATACTAATGATTTAATAATT
*
42240 TAGTGATGATTTAATACTAATGATTTAATAAT
1 TAGTAATGATTTAATACTAATGATTTAATAAT
42272 GATTTAATAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (33 bp):
TAGTAATGATTTAATACTAATGATTTAATAATT
Found at i:42227 original size:25 final size:25
Alignment explanation
Indices: 42199--42529 Score: 112
Period size: 25 Copynumber: 12.9 Consensus size: 25
42189 ACTAATGATT
*
42199 TAATAATTTAGTAATGATTTAATAC
1 TAATAATTTAATAATGATTTAATAC
*
42224 TAATGATTTAATAATTTAGTGATGATTTAATAC
1 TAAT-AATT--TAA--TA---ATGATTTAATAC
*
42257 TAATGATTTAATAATGATTTAATAC
1 TAATAATTTAATAATGATTTAATAC
* *
42282 TAATGATTTAATAATGATTTAAATATT
1 TAATAATTTAATAATGATTT-AATA-C
* * * *
42309 TAATGA-TT--TGATGATTTAGTAA
1 TAATAATTTAATAATGATTTAATAC
* * *
42331 TGAT--TTGATAATAATCATTATAATAA
1 TAATAATT--TAATAATGATT-TAATAC
* * * *
42357 TGAT-TTTATAATAATTATTTAGT--
1 TAATAATT-TAATAATGATTTAATAC
* * * *
42380 T-ATTATTTAGTAATTATTT-ATAA
1 TAATAATTTAATAATGATTTAATAC
* * * * *
42403 TAATGATTTAATACT-A-ATGAT-T
1 TAATAATTTAATAATGATTTAATAC
*
42425 TAATAATTTAGTAATGATTTAATAC
1 TAATAATTTAATAATGATTTAATAC
*
42450 TAATGATTTAATAATTTAGTGATGATTTAATAC
1 TAAT-AATT--TAA--TA---ATGATTTAATAC
*
42483 TAATGATTTAATAATGATTTAATAC
1 TAATAATTTAATAATGATTTAATAC
*
42508 TAATGATTTAATAATGATTTAA
1 TAATAATTTAATAATGATTTAA
42530 ATATTTAATG
Statistics
Matches: 241, Mismatches: 32, Indels: 66
0.71 0.09 0.19
Matches are distributed among these distances:
21 2 0.01
22 29 0.12
23 12 0.05
24 21 0.09
25 83 0.34
26 32 0.13
27 8 0.03
28 8 0.03
30 10 0.04
32 4 0.02
33 32 0.13
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (25 bp):
TAATAATTTAATAATGATTTAATAC
Found at i:42441 original size:19 final size:19
Alignment explanation
Indices: 42417--42481 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
42407 GATTTAATAC
42417 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
42436 TAATGA-TT--TAA--TAC
1 TAATGATTTAATAATTTAG
42450 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
42469 TGATGATTTAATA
1 TAATGATTTAATA
42482 CTAATGATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 8 0.21
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 20 0.53
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.46
Consensus pattern (19 bp):
TAATGATTTAATAATTTAG
Found at i:42445 original size:33 final size:33
Alignment explanation
Indices: 42403--42497 Score: 181
Period size: 33 Copynumber: 2.9 Consensus size: 33
42393 TTATTTATAA
42403 TAATGATTTAATACTAATGATTTAATAATTTAG
1 TAATGATTTAATACTAATGATTTAATAATTTAG
42436 TAATGATTTAATACTAATGATTTAATAATTTAG
1 TAATGATTTAATACTAATGATTTAATAATTTAG
*
42469 TGATGATTTAATACTAATGATTTAATAAT
1 TAATGATTTAATACTAATGATTTAATAAT
42498 GATTTAATAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (33 bp):
TAATGATTTAATACTAATGATTTAATAATTTAG
Found at i:42510 original size:226 final size:226
Alignment explanation
Indices: 42116--42597 Score: 928
Period size: 226 Copynumber: 2.1 Consensus size: 226
42106 TCATCATTAG
*
42116 TAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAGTAAT
1 TAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAAT
42181 GATTTAATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTAATAATTTAGTGA
66 GATTTAATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTAATAATTTAGTGA
42246 TGATTTAATACTAATGATTTAATAATGATTTAATACTAATGATTTAATAATGATTTAAATATTTA
131 TGATTTAATACTAATGATTTAATAATGATTTAATACTAATGATTTAATAATGATTTAAATATTTA
42311 ATGATTTGATGATTTAGTAATGATTTGATAA
196 ATGATTTGATGATTTAGTAATGATTTGATAA
42342 TAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAAT
1 TAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAAT
42407 GATTTAATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTAATAATTTAGTGA
66 GATTTAATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTAATAATTTAGTGA
42472 TGATTTAATACTAATGATTTAATAATGATTTAATACTAATGATTTAATAATGATTTAAATATTTA
131 TGATTTAATACTAATGATTTAATAATGATTTAATACTAATGATTTAATAATGATTTAAATATTTA
42537 ATGATTTGATGATTTAGTAATGATTTGATAA
196 ATGATTTGATGATTTAGTAATGATTTGATAA
* * *
42568 TAATTATTATAGTAATGATTTGATAATAAT
1 TAATCATTATAATAATGATTTTATAATAAT
42598 CATTATAAAA
Statistics
Matches: 252, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
226 252 1.00
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (226 bp):
TAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAATAAT
GATTTAATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTAATAATTTAGTGA
TGATTTAATACTAATGATTTAATAATGATTTAATACTAATGATTTAATAATGATTTAAATATTTA
ATGATTTGATGATTTAGTAATGATTTGATAA
Found at i:42587 original size:26 final size:26
Alignment explanation
Indices: 42551--42878 Score: 178
Period size: 26 Copynumber: 13.2 Consensus size: 26
42541 TTTGATGATT
42551 TAGTAATGATTTGATAATAATTATTA
1 TAGTAATGATTTGATAATAATTATTA
*
42577 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATTATTA
** * *
42603 TAAAAATGATTT-AGTATTAATCATTA
1 TAGTAATGATTTGA-TAATAATTATTA
** * * *
42629 TAAAAATGATTTAATAATGATT-TAAA
1 TAGTAATGATTTGATAATAATTAT-TA
*
42655 TATGTAATGATTTG------ATGATT-
1 TA-GTAATGATTTGATAATAATTATTA
42675 TAGTAATGATTTGATAATAATTATTA
1 TAGTAATGATTTGATAATAATTATTA
* *
42701 TAATAATGATTTTATAATAATTATT-
1 TAGTAATGATTTGATAATAATTATTA
* * *
42726 TAGTTATTA-TT--TAGTAATTATTTA
1 TAGTAATGATTTGATAATAATTA-TTA
* * * *
42750 TAATAATGATTTAATACTAATGATTTAA
1 TAGTAATGATTTGATAATAATTA-TT-A
* *
42778 TATTAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATTATTA
* * * *
42800 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATTATTA
42824 TAGTAATGATTTGATAATAATTATTA
1 TAGTAATGATTTGATAATAATTATTA
* *
42850 TAATAATGATTTTATAATAATTATT-
1 TAGTAATGATTTGATAATAATTATTA
42875 TAGT
1 TAGT
42879 TATTATTTAG
Statistics
Matches: 239, Mismatches: 36, Indels: 55
0.72 0.11 0.17
Matches are distributed among these distances:
19 12 0.05
20 7 0.03
21 2 0.01
22 12 0.05
23 3 0.01
24 19 0.08
25 32 0.13
26 116 0.49
27 27 0.11
28 9 0.04
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATTATTA
Found at i:42778 original size:8 final size:8
Alignment explanation
Indices: 42753--42825 Score: 57
Period size: 8 Copynumber: 9.2 Consensus size: 8
42743 TTATTTATAA
42753 TAATGATT
1 TAATGATT
*
42761 TAAT-A-C
1 TAATGATT
42767 TAATGATT
1 TAATGATT
42775 TAAT-A-T
1 TAATGATT
42781 TAATGATTT
1 TAATGA-TT
42790 AATAATGATT
1 --TAATGATT
42800 TAAAT-ATT
1 T-AATGATT
42808 TAATGATT
1 TAATGATT
*
42816 TGATGATT
1 TAATGATT
42824 TA
1 TA
42826 GTAATGATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
6 9 0.17
7 7 0.13
8 24 0.46
9 4 0.08
10 2 0.04
11 6 0.12
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (8 bp):
TAATGATT
Found at i:42935 original size:33 final size:34
Alignment explanation
Indices: 42747--43022 Score: 175
Period size: 33 Copynumber: 7.7 Consensus size: 34
42737 TAGTAATTAT
42747 TTATAATAATGATTTAATACTAATGATTTAATATTAA
1 TTATAATAATGATTTAATACTAATGATTT-A-A-TAA
* * * *
42784 TGATTTAATAATGATTTAAATATTTAATGATTTGATGA
1 T--TATAATAATGATTT-AATA-CTAATGATTTAATAA
* * * *
42822 TT-TAGTAATGATTTGATAATAATTATTATAATAATGA
1 TTATAATAATGATTTAATACTAATGATT-TAAT-A--A
* * * *
42859 TTTTATAATAATTATTTAGT--T-ATTATTTAGTAA
1 --TTATAATAATGATTTAATACTAATGATTTAATAA
*
42892 TTATAATAATGATTTAATACTAATGATTTCATAA
1 TTATAATAATGATTTAATACTAATGATTTAATAA
*
42926 TT-TAGTAATGATTTAATACTAATGATTTAATAA
1 TTATAATAATGATTTAATACTAATGATTTAATAA
* *
42959 TAATGATTTAATAATGATTTAAATATTTAATGATTTAATAC
1 T--T-A--TAATAATGATTT-AATA-CTAATGATTTAATAA
* *
43000 TAATAATAATGATTTGATACTAA
1 TTATAATAATGATTTAATACTAA
43023 AAATCATTGT
Statistics
Matches: 189, Mismatches: 28, Indels: 47
0.72 0.11 0.18
Matches are distributed among these distances:
31 16 0.08
33 39 0.21
34 20 0.11
35 16 0.08
36 16 0.08
37 8 0.04
38 5 0.03
39 27 0.14
40 19 0.10
41 23 0.12
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (34 bp):
TTATAATAATGATTTAATACTAATGATTTAATAA
Found at i:43011 original size:20 final size:20
Alignment explanation
Indices: 42967--43022 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
42957 AATAATGATT
42967 TAATAATGATTTAA-A-T-A
1 TAATAATGATTTAATACTAA
*
42984 T-TTAATGATTTAATACTAA
1 TAATAATGATTTAATACTAA
*
43003 TAATAATGATTTGATACTAA
1 TAATAATGATTTAATACTAA
43023 AAATCATTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 11 0.34
17 2 0.06
18 1 0.03
19 2 0.06
20 16 0.50
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (20 bp):
TAATAATGATTTAATACTAA
Found at i:45184 original size:15 final size:15
Alignment explanation
Indices: 45157--45196 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
45147 TTTTCAACAC
45157 AAAACTT-TAATATA
1 AAAACTTATAATATA
*
45171 ATAACTTATAATATA
1 AAAACTTATAATATA
*
45186 AAAACTAATAA
1 AAAACTTATAA
45197 ACTAACAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAACTTATAATATA
Found at i:45322 original size:32 final size:34
Alignment explanation
Indices: 45247--45328 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
45237 ACCAAACCTT
* *
45247 AAAC-AACTAATAAAATATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
45280 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTTCA-TATAACTA
*
45313 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
45329 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 11 0.25
33 8 0.18
34 20 0.45
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTTTTTCATATAACTA
Found at i:45437 original size:42 final size:41
Alignment explanation
Indices: 45388--45498 Score: 118
Period size: 41 Copynumber: 2.6 Consensus size: 41
45378 AACTATTTAA
*
45388 CTAACAAAAACTAATTAAATAATTTTTTTA-TATAACTAACTAT
1 CTAACAAAAACTAATT-AATAATTTTTTAACTAT-A-TAACTAT
*
45431 -TAACAAACAAACTAATTAATTATTTTTTAACTATATAACTAT
1 CTAAC-AA-AAACTAATTAATAATTTTTTAACTATATAACTAT
* * *
45473 CAAACATATACTAATTAATAATTTTT
1 CTAACAAAAACTAATTAATAATTTTT
45499 AATTTATGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
41 17 0.29
42 12 0.21
43 17 0.29
44 12 0.21
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.41
Consensus pattern (41 bp):
CTAACAAAAACTAATTAATAATTTTTTAACTATATAACTAT
Found at i:45590 original size:16 final size:18
Alignment explanation
Indices: 45561--45599 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
45551 ACTAATTAAC
*
45561 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
45579 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
45595 ATTTA
1 ATTTA
45600 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:45959 original size:29 final size:29
Alignment explanation
Indices: 45917--46011 Score: 154
Period size: 29 Copynumber: 3.3 Consensus size: 29
45907 GTGACGCCGG
45917 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
45946 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
* ** *
45975 GGCAACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
46004 GGCGACCT
1 GGCGACCT
46012 CTCCATTGGC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 61 1.00
ACGTcount: A:0.24, C:0.33, G:0.29, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:46035 original size:32 final size:32
Alignment explanation
Indices: 45998--46079 Score: 164
Period size: 32 Copynumber: 2.6 Consensus size: 32
45988 GTCGCCCAGA
45998 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
46030 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
46062 CTGCATGGCGACCTCTCC
1 CTGCATGGCGACCTCTCC
46080 TCGTATAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.27
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:46157 original size:20 final size:18
Alignment explanation
Indices: 46134--46176 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 18
46124 TATATGGCTT
46134 GTATGGCTCGTATGTAACCC
1 GTATGGCTCGTATGT--CCC
46154 GTATGGCTCGTATGTCCC
1 GTATGGCTCGTATGTCCC
46172 GTATG
1 GTATG
46177 TCGCCTGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (18 bp):
GTATGGCTCGTATGTCCC
Found at i:46210 original size:29 final size:29
Alignment explanation
Indices: 46177--46265 Score: 169
Period size: 29 Copynumber: 3.1 Consensus size: 29
46167 GTCCCGTATG
46177 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
46206 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
*
46235 TCGCCTGGATTGCATGGCGTCCTACGAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
46264 TC
1 TC
46266 ACTGTAGAAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (29 bp):
TCGCCTGGATTGCATGGCGTCCTACAAGA
Found at i:53361 original size:48 final size:48
Alignment explanation
Indices: 53309--53419 Score: 116
Period size: 48 Copynumber: 2.3 Consensus size: 48
53299 CAATATTTTT
* * *
53309 TAATATTATTGATAAAATGTTCAATAATAACAAAATCAGTAGAAAAAA
1 TAATATTATTGATAAAACGTACAATAATAACAAAACCAGTAGAAAAAA
** * * * * *
53357 TAATAAAATCGGTTAAACGTACAATAATAATAAAACCAGTAGAAATAA
1 TAATATTATTGATAAAACGTACAATAATAACAAAACCAGTAGAAAAAA
53405 TAATATT-TTCGATAA
1 TAATATTATT-GATAA
53420 TTTTTGATCG
Statistics
Matches: 47, Mismatches: 15, Indels: 2
0.73 0.23 0.03
Matches are distributed among these distances:
47 1 0.02
48 46 0.98
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (48 bp):
TAATATTATTGATAAAACGTACAATAATAACAAAACCAGTAGAAAAAA
Done.