Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002672.1 Hibiscus syriacus cultivar Beakdansim tig00005488_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: 55143
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:5981 original size:22 final size:22
Alignment explanation
Indices: 5935--5977 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
5925 TTTTTTAAAT
5935 TTTTTTTATAAAATGAATTATA
1 TTTTTTTATAAAATGAATTATA
*
5957 TTTTTTTA-AAAA-GAATGATA
1 TTTTTTTATAAAATGAATTATA
5977 T
1 T
5978 ATTTAGAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 4 0.20
22 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTTTTTATAAAATGAATTATA
Found at i:6204 original size:31 final size:28
Alignment explanation
Indices: 6098--6204 Score: 83
Period size: 29 Copynumber: 3.7 Consensus size: 28
6088 TATTATTTTT
* *
6098 AAAATATTAAAATAATTTATTTATT-AT-
1 AAAATATTAAAATTATAT-TTTATTAATA
* ***
6125 TAAATATTATTTTTATAATTTTATTAATA
1 AAAATATTAAAATTAT-ATTTTATTAATA
*
6154 AAAATATTAATATTGATATTTTATTGAAATA
1 AAAATATTAAAATT-ATATTTTATT--AATA
6185 AAAATATTATAAATTATATT
1 AAAATATTA-AAATTATATT
6205 AATTATTTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
27 17 0.27
28 3 0.05
29 19 0.30
30 2 0.03
31 18 0.29
32 4 0.06
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
AAAATATTAAAATTATATTTTATTAATA
Found at i:6319 original size:27 final size:27
Alignment explanation
Indices: 6284--6367 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
6274 ATATTATTAT
6284 ATATATATTACTATTAAATATATAAATA
1 ATAT-TATTACTATTAAATATATAAATA
* *
6312 ATATTATTCATTATT-AATA-ATTTAATA
1 ATATTATT-ACTATTAAATATA-TAAATA
* *
6339 ATATTATTTCTATGAAAT-TAATAAATA
1 ATATTATTACTATTAAATAT-ATAAATA
6366 AT
1 AT
6368 TTAAATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
26 4 0.09
27 31 0.69
28 10 0.22
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (27 bp):
ATATTATTACTATTAAATATATAAATA
Found at i:6459 original size:27 final size:25
Alignment explanation
Indices: 6421--6474 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
6411 TAATATCTTA
* *
6421 TTTATATTATTAAATATAATTGATTAT
1 TTTATAATATTAAAAATAA-T-ATTAT
6448 TTTATAATATTAAAAATAATATTAT
1 TTTATAATATTAAAAATAATATTAT
6473 TT
1 TT
6475 ATTAGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.28
26 1 0.04
27 17 0.68
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TTTATAATATTAAAAATAATATTAT
Found at i:9490 original size:2 final size:2
Alignment explanation
Indices: 9479--9510 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9469 GTTTACCCAA
9479 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9511 CACTATTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10284 original size:29 final size:29
Alignment explanation
Indices: 10251--10313 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
10241 GATGCTAAAA
* *
10251 TACTTTAA-AAAATTATGAGCCAAAATGAT
1 TACTTTAACAAAA-CATGAGCCAAAATGAC
10280 TAC-TTAATCAAAACATGAGCCAAAATGAC
1 TACTTTAA-CAAAACATGAGCCAAAATGAC
10309 TACTT
1 TACTT
10314 GATCAAACGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
28 4 0.14
29 20 0.69
30 5 0.17
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.29
Consensus pattern (29 bp):
TACTTTAACAAAACATGAGCCAAAATGAC
Found at i:10318 original size:29 final size:29
Alignment explanation
Indices: 10265--10320 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
10255 TTAAAAAATT
*
10265 ATGAGCCAAAATGATTACTTAATCAAAAC
1 ATGAGCCAAAATGACTACTTAATCAAAAC
*
10294 ATGAGCCAAAATGACTACTTGATCAAA
1 ATGAGCCAAAATGACTACTTAATCAAA
10321 CGTTAGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.23
Consensus pattern (29 bp):
ATGAGCCAAAATGACTACTTAATCAAAAC
Found at i:10881 original size:2 final size:2
Alignment explanation
Indices: 10874--10907 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10864 TTAAATAGTT
10874 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10908 AAAAAATCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16156 original size:18 final size:18
Alignment explanation
Indices: 16133--16176 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
16123 TAAATATAAT
16133 AAAATATTATATTTTTAA
1 AAAATATTATATTTTTAA
* * *
16151 AAAATATTGTTTTTTTAG
1 AAAATATTATATTTTTAA
16169 AAAATATT
1 AAAATATT
16177 TTCAGTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
AAAATATTATATTTTTAA
Found at i:16979 original size:183 final size:183
Alignment explanation
Indices: 16614--16999 Score: 591
Period size: 183 Copynumber: 2.1 Consensus size: 183
16604 ATTAAATTTT
* *
16614 AAATATTAAATATATTATATATAACATATGGGCTCAACCAAAATCATTAAAAATCTAATTAATAC
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCAAAACCATTAAAAATCTAATTAATAA
* * *
16679 TTTAAGATCCAATAATTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
66 TTTAAAATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
* * *
16744 TATTTTATAATTATATATTATTTAAATTAATTGTAAATTGTTTTTTAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTGAATTAAA
* *
16797 AAATATTAAATATATTATATATAACATATGGGCT-AAGCCCAAACCATTTAAAA-CTCAATTAAT
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCAAAACCATTAAAAATCT-AATTAAT
*
16860 AATTTAAAATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAAT
64 AATTTAAAATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAA-TTATATAAAAT
*
16925 TTTTATTTTATAATTATTTATTATTTAAATTAATTATAAACT-TTTTTGAATTAAA
128 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTGAATTAAA
* *
16980 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
17000 AATTAGAAAA
Statistics
Matches: 186, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
182 12 0.06
183 126 0.68
184 48 0.26
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCAAAACCATTAAAAATCTAATTAATAA
TTTAAAATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTGAATTAAA
Found at i:21451 original size:23 final size:24
Alignment explanation
Indices: 21368--21453 Score: 104
Period size: 23 Copynumber: 3.7 Consensus size: 24
21358 TGAATTTTGT
* *
21368 TATGATACCTGACCTGGATTCTGA
1 TATGATACTTGACTTGGATTCTGA
* *
21392 TCTGATA-TTGACATGGATTCTGA
1 TATGATACTTGACTTGGATTCTGA
* *
21415 TCTGATACATGACTTGGATT-TGA
1 TATGATACTTGACTTGGATTCTGA
21438 TATGATACTTGACTTG
1 TATGATACTTGACTTG
21454 AATTATGTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 38 0.70
24 16 0.30
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TATGATACTTGACTTGGATTCTGA
Found at i:22488 original size:112 final size:112
Alignment explanation
Indices: 22290--22975 Score: 1126
Period size: 112 Copynumber: 6.1 Consensus size: 112
22280 GATACTTATA
* * * *
22290 ATAAAGTATCGACACTATCAACACATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
*
22355 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
22402 ATAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACTTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
22467 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
22514 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTTTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
*
22579 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
22625 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
* *
22690 TTTATCATTTTTTGACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
22737 ATAAAGTATAGACACTTTCAATATATCCGATAGCGCTTTATC-TGTTTTGTCATTTATAGACCGG
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTA-CATGTTTTGTCATTTATAGACCGG
22801 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
65 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
22849 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTT-TCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
* * **
22913 TTTATCATTTTTTTACCTGTTATATTGTTATGGATCAATATTTTTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATA-CATTTTT
*
22961 ATAAAATATCGACAC
1 ATAAAGTATCGACAC
22976 AAACCGACAA
Statistics
Matches: 541, Mismatches: 29, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
111 161 0.30
112 379 0.70
113 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:22673 original size:223 final size:224
Alignment explanation
Indices: 22290--22975 Score: 1151
Period size: 223 Copynumber: 3.1 Consensus size: 224
22280 GATACTTATA
* * * * *
22290 ATAAAGTATCGACACTATCAACACATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
22355 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* * *
22420 CAATATATCCGGTAGCACTTTACTTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
131 CAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTACCT
22485 GTTATATTGTTATGGATCGATACATTTTT
196 GTTATATTGTTATGGATCGATACATTTTT
* *
22514 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTTTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
22579 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATATATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* *
22643 CAATATATTCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTGACCT
131 CAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTACCT
22708 GTTATATTGTTATGGATCGATACATTTTT
196 GTTATATTGTTATGGATCGATACATTTTT
* *
22737 ATAAAGTATAGACACTTTCAATATATCCGATAGCGCTTTATCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
22802 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* *
22867 CAATATATCCGATAGCGCTTTACCTGTTTT-TCATTTATAGACCGGTTTTATCATTTTTTTACCT
131 CAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTACCT
* **
22931 GTTATATTGTTATGGATCAATATTTTTTTT
196 GTTATATTGTTATGGATCGATA-CATTTTT
*
22961 ATAAAATATCGACAC
1 ATAAAGTATCGACAC
22976 AAACCGACAA
Statistics
Matches: 432, Mismatches: 28, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
223 266 0.62
224 166 0.38
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (224 bp):
ATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
CAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGTTTTATCATTTTTTTACCT
GTTATATTGTTATGGATCGATACATTTTT
Found at i:22927 original size:335 final size:336
Alignment explanation
Indices: 22290--22975 Score: 1180
Period size: 335 Copynumber: 2.0 Consensus size: 336
22280 GATACTTATA
22290 ATAAAGTATCGACACTATCAACACATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTATCAACACATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGAT
* * *
22355 TTTGTCATTTTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
66 TTTATCATTTTTTGACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATAGACACTTT
*
22420 CAATATATCCGGTAGCACTTTACTTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
131 CAATATATCCGATAGCACTTTACTTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
*
22485 GTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTAGCGC
196 GTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCGC
* *
22550 TTTACCTGTTTTTTCATTTATAGACCGGTTTTGTCATTTTTTACCTGTTATATTGTTATGGATCG
261 TTTACCTGTTTTTTCATTTATAGACCGGTTTTATCATTTTTTACCTGTTATATTGTTATGGATCA
22615 ATA-TATTTTT
326 ATATTATTTTT
* * * * * *
22625 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACACATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGAT
*
22690 TTTATCATTTTTTGACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATAGACACTTT
66 TTTATCATTTTTTGACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATAGACACTTT
*
22755 CAATATATCCGATAGCGCTTTA-TCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACC
131 CAATATATCCGATAGCACTTTACT-TGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACC
22819 TGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCG
195 TGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCG
22884 CTTTACCTG-TTTTTCATTTATAGACCGGTTTTATCATTTTTTTACCTGTTATATTGTTATGGAT
260 CTTTACCTGTTTTTTCATTTATAGACCGGTTTTATCA-TTTTTTACCTGTTATATTGTTATGGAT
*
22948 CAATATTTTTTTT
324 CAATATTATTTTT
*
22961 ATAAAATATCGACAC
1 ATAAAGTATCGACAC
22976 AAACCGACAA
Statistics
Matches: 331, Mismatches: 17, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
334 27 0.08
335 284 0.86
336 20 0.06
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (336 bp):
ATAAAGTATCGACACTATCAACACATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGAT
TTTATCATTTTTTGACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATAGACACTTT
CAATATATCCGATAGCACTTTACTTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
GTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCGC
TTTACCTGTTTTTTCATTTATAGACCGGTTTTATCATTTTTTACCTGTTATATTGTTATGGATCA
ATATTATTTTT
Found at i:23834 original size:18 final size:18
Alignment explanation
Indices: 23697--23834 Score: 94
Period size: 18 Copynumber: 7.9 Consensus size: 18
23687 AATTTATTCT
*
23697 AACTATATAATATATATA
1 AACTATATAGTATATATA
*
23715 AACTGTATAGTATATATA
1 AACTATATAGTATATATA
*
23733 AAGTATATA-TATAGT-T-
1 AACTATATAGTATA-TATA
*
23749 --C-AT-TAGTATATGTA
1 AACTATATAGTATATATA
* *
23763 AACTATATAATATATGTA
1 AACTATATAGTATATATA
* *
23781 AATTATATGGTATATTATA
1 AACTATATAGTATA-TATA
*
23800 TAATTCAT-TAGTATATATA
1 -AACT-ATATAGTATATATA
*
23819 AACTATATATTATATA
1 AACTATATAGTATATA
23835 GTTCTTTAAT
Statistics
Matches: 95, Mismatches: 13, Indels: 24
0.72 0.10 0.18
Matches are distributed among these distances:
12 3 0.03
13 7 0.07
16 1 0.01
17 9 0.09
18 56 0.59
19 7 0.07
20 10 0.11
21 2 0.02
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (18 bp):
AACTATATAGTATATATA
Found at i:24017 original size:13 final size:14
Alignment explanation
Indices: 23989--24018 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
23979 ATAACACAAG
23989 AATCATAATATAAA
1 AATCATAATATAAA
24003 AATCATAAT-TAAA
1 AATCATAATATAAA
24016 AAT
1 AAT
24019 TAAGTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
AATCATAATATAAA
Found at i:24068 original size:20 final size:20
Alignment explanation
Indices: 24030--24087 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
24020 AAGTATATTA
*
24030 ATTTAATTATTATAATTAAT
1 ATTTAATTATAATAATTAAT
* * *
24050 ATTTTATTATAATATTTAAA
1 ATTTAATTATAATAATTAAT
* * *
24070 AATTAATCATATTAATTA
1 ATTTAATTATAATAATTA
24088 GTATGATTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTAATTATAATAATTAAT
Found at i:36868 original size:46 final size:46
Alignment explanation
Indices: 36798--37149 Score: 588
Period size: 46 Copynumber: 7.8 Consensus size: 46
36788 TTCAAAATAT
* *
36798 TTACCATTTA-TCCCATAAGCTCGTAAGCTTATTTTACTAACATAC
1 TTACCATTTATTCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
36843 TTACCATTTATTCCTATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
36889 TTACCATTTATTCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
* * *
36935 TTACCATTTAATCCCATAAACGCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
36981 TTACCATTTATTCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
**
37027 TTGTCA-TTATT-CCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
37071 TTACCATTTATTCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTTATTCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
37117 TTGCCA-TTATT-CCATAAGCTCGTAAGCTTATTT
1 TTACCATTTATTCCCATAAGCTCGTAAGCTTATTT
37150 GCATGCTTAC
Statistics
Matches: 289, Mismatches: 15, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
44 59 0.20
45 25 0.09
46 205 0.71
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.39
Consensus pattern (46 bp):
TTACCATTTATTCCCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:37291 original size:40 final size:40
Alignment explanation
Indices: 37247--37368 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
37237 ACCGTAGTGC
*
37247 TACACATAAGATCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
37287 TACACATAAGGTCGTGCCCACCATATACACCGAAATGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
37327 TACACATAAGGTCGTGCTCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
37367 TA
1 TA
37369 TAAACCTGCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:39494 original size:13 final size:14
Alignment explanation
Indices: 39476--39510 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
39466 TATAATAGAG
39476 TATTATTTAATT-A
1 TATTATTTAATTAA
*
39489 TATTATTTATTTAA
1 TATTATTTAATTAA
39503 TATTATTT
1 TATTATTT
39511 TAAATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTTAATTAA
Found at i:44966 original size:21 final size:23
Alignment explanation
Indices: 44927--44968 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
44917 TTGCAATCAC
*
44927 AACAATAAAAATGAGTCATAATA
1 AACAATAAAAATGAATCATAATA
44950 AACAA-AAAAAT-AATCATAA
1 AACAATAAAAATGAATCATAA
44969 ATGAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.67, C:0.10, G:0.05, T:0.19
Consensus pattern (23 bp):
AACAATAAAAATGAATCATAATA
Found at i:48267 original size:17 final size:17
Alignment explanation
Indices: 48245--48284 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
48235 GGCAATGACT
48245 AAATTATAAAGTAAATA
1 AAATTATAAAGTAAATA
*
48262 AAATTATAAAGTATATA
1 AAATTATAAAGTAAATA
48279 AAATTA
1 AAATTA
48285 AACGACCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
AAATTATAAAGTAAATA
Found at i:49246 original size:3 final size:3
Alignment explanation
Indices: 49240--49279 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
49230 TTTTTTTATT
* * *
49240 TAA TAA TAA TAA TAA TAT TTA TAA TTA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
49280 TTTAAAATGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:49269 original size:18 final size:19
Alignment explanation
Indices: 49236--49274 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
49226 TATATTTTTT
49236 TATTTAATAATAATAATAA
1 TATTTAATAATAATAATAA
*
49255 TATTT-ATAATTATAATAA
1 TATTTAATAATAATAATAA
49273 TA
1 TA
49275 ATAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTTAATAATAATAATAA
Found at i:49688 original size:44 final size:44
Alignment explanation
Indices: 49587--50106 Score: 619
Period size: 44 Copynumber: 12.0 Consensus size: 44
49577 ATTTGAAAAT
* ** *
49587 ATCCTGCA-TGAAGGTCTTATGGATGGCCCGAAGGA-TTT-AAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
* * *
49628 ATCTTGCACTGGAGGTCTTACAAATGACCCGAATGATTTTAAAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
**
49672 ATCCTGCACTGGAGGTCTTATGGATGACCCGAAGGA-TTT-AAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
*
49714 ATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
** *
49758 ATCCTGCACTGGAGGTCTTATGGATGACCCGGAGGA-TTT-AAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
** *
49800 ATATTGCACTGGAGGTCTTACATATGACCCGAAGGA-TTT-AAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
* *
49842 ATCTTGTACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
** *
49886 ATCCTGCACTGGAGGTCTTATGGATGACCCGGAGGATTTTAAAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
* *
49930 ATCCTACACTGGAGGTCTTACAAATGACCCGAAGGATTTTAAAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
* * ** *
49974 ATCATGCACTGTAGGTCTTATGGATGACCCGGAGGATTTTAAAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
* * * *
50018 ATCCTACACTGGAGGTCTTACAAATGACCCAAAAGAATTTTAAAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCC-GAAGGATTTTAAAC
* * **
50063 ATCATGCACTGTAGGTCTTATGGATGACCC-AGAGGATTTATAAA
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGA-AGGATTT-TAAA
50107 TTTGAGAAAT
Statistics
Matches: 408, Mismatches: 61, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
41 7 0.02
42 129 0.32
43 16 0.04
44 217 0.53
45 39 0.10
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (44 bp):
ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAAC
Found at i:49743 original size:86 final size:88
Alignment explanation
Indices: 49587--50106 Score: 637
Period size: 86 Copynumber: 6.0 Consensus size: 88
49577 ATTTGAAAAT
* ** *
49587 ATCCTGCA-TGAAGGTCTTATGGATGGCCCGAAGGA-TTT-AACATCTTGCACTGGAGGTCTTAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCTTGCACTGGAGGTCTTAC
* *
49649 AAATGACCCGAATGATTTTAAAC
66 AGATGACCCGAAGGATTTTAAAC
**
49672 ATCCTGCACTGGAGGTCTTATGGATGACCCGAAGGA-TTT-AACATCTTGCACTGGAGGTCTTAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCTTGCACTGGAGGTCTTAC
49735 AGATGACCCGAAGGATTTTAAAC
66 AGATGACCCGAAGGATTTTAAAC
** * *
49758 ATCCTGCACTGGAGGTCTTATGGATGACCCGGAGGA-TTT-AACATATTGCACTGGAGGTCTTAC
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCTTGCACTGGAGGTCTTAC
*
49821 ATATGACCCGAAGGA-TTT-AAC
66 AGATGACCCGAAGGATTTTAAAC
* * * *
49842 ATCTTGTACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCTTAT
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCTTGCACTGGAGGTCTTAC
* *
49907 GGATGACCCGGAGGATTTTAAAC
66 AGATGACCCGAAGGATTTTAAAC
* * * * *
49930 ATCCTACACTGGAGGTCTTACAAATGACCCGAAGGATTTTAAACATCATGCACTGTAGGTCTTAT
1 ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCTTGCACTGGAGGTCTTAC
* *
49995 GGATGACCCGGAGGATTTTAAAC
66 AGATGACCCGAAGGATTTTAAAC
* * * * * *
50018 ATCCTACACTGGAGGTCTTACAAATGACCCAAAAGAATTTTAAACATCATGCACTGTAGGTCTTA
1 ATCCTGCACTGGAGGTCTTACAGATGACCC-GAAGGATTTTAAACATCTTGCACTGGAGGTCTTA
**
50083 TGGATGACCC-AGAGGATTTATAAA
65 CAGATGACCCGA-AGGATTT-TAAA
50107 TTTGAGAAAT
Statistics
Matches: 400, Mismatches: 27, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
84 34 0.09
85 14 0.04
86 181 0.45
87 3 0.01
88 115 0.29
89 49 0.12
90 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (88 bp):
ATCCTGCACTGGAGGTCTTACAGATGACCCGAAGGATTTTAAACATCTTGCACTGGAGGTCTTAC
AGATGACCCGAAGGATTTTAAAC
Found at i:49827 original size:128 final size:130
Alignment explanation
Indices: 49598--50082 Score: 636
Period size: 128 Copynumber: 3.7 Consensus size: 130
49588 TCCTGCATGA
** * * *** *
49598 AGGTCTTATGGATGGCCCGAAGGA-TTT-AACATCTTGCACTGGAGGTCTTACAAATGACCCGAA
1 AGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCTTATGGATGACCCGGA
* ***
49661 TGATTTTAAACATCCTGCACTGGAGGTCTTATGGATGACCCGAAGGATTTAACATCTTGCACTGG
66 GGATTTTAAACATCCTGCACTGGAGGTCTTACAAATGACCCGAAGGATTTAACATCTTGCACTGG
49726 AGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCTTATGGATGACCCGGA
1 AGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCTTATGGATGACCCGGA
** * *
49791 GGA-TTT-AACATATTGCACTGGAGGTCTTACATATGACCCGAAGGATTTAACATCTTGTACTGG
66 GGATTTTAAACATCCTGCACTGGAGGTCTTACAAATGACCCGAAGGATTTAACATCTTGCACTGG
49854 AGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCTTATGGATGACCCGGA
1 AGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCTTATGGATGACCCGGA
* *
49919 GGATTTTAAACATCCTACACTGGAGGTCTTACAAATGACCCGAAGGATTTTAAACATCATGCACT
66 GGATTTTAAACATCCTGCACTGGAGGTCTTACAAATGACCCGAAGGA-TTT-AACATCTTGCACT
*
49984 GT
129 GG
** * * *** **
49986 AGGTCTTATGGATGACCCGGAGGATTTTAAACATCCTACACTGGAGGTCTTACAAATGACCCAAA
1 AGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCTTATGGATGACCC-GG
* * *
50051 AGAATTTTAAACATCATGCACTGTAGGTCTTA
65 AGGATTTTAAACATCCTGCACTGGAGGTCTTA
50083 TGGATGACCC
Statistics
Matches: 315, Mismatches: 35, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
128 140 0.44
129 9 0.03
130 68 0.22
131 3 0.01
132 67 0.21
133 28 0.09
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (130 bp):
AGGTCTTACAGATGACCCGAAGGATTTTAAACATCCTGCACTGGAGGTCTTATGGATGACCCGGA
GGATTTTAAACATCCTGCACTGGAGGTCTTACAAATGACCCGAAGGATTTAACATCTTGCACTGG
Found at i:49843 original size:21 final size:21
Alignment explanation
Indices: 49781--49843 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
49771 GGTCTTATGG
49781 ATGACCCGGAGGATTTAACAT
1 ATGACCCGGAGGATTTAACAT
*
49802 ATTG-CACTGGAGG-TCTT-ACAT
1 A-TGAC-CCGGAGGAT-TTAACAT
*
49823 ATGACCCGAAGGATTTAACAT
1 ATGACCCGGAGGATTTAACAT
49844 CTTGTACTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
20 9 0.27
21 14 0.42
22 10 0.30
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (21 bp):
ATGACCCGGAGGATTTAACAT
Found at i:50779 original size:22 final size:22
Alignment explanation
Indices: 50754--50828 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
50744 AATAAAGCTT
50754 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
50776 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
50798 TCATCTTTG--AAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
50818 TCATCTTTGAA
1 TCATCTTTGAA
50829 GAATGTAGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 19 0.39
22 30 0.61
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:51740 original size:118 final size:118
Alignment explanation
Indices: 51614--51848 Score: 373
Period size: 118 Copynumber: 2.0 Consensus size: 118
51604 CAAAATGCTT
*
51614 CAACATTTTCTTCCTGATGATATGAGCTTTCAAAAATGCCCAAATATTCATACTGACATGGG-TC
1 CAACATTTTCTTCCTGATAATATGAGCTTTCAAAAATGCCCAAATATTCATACTGACATGGGCT-
* *
51678 TTCAAAATTCCCTACATGGATCATTTCTGTCTGAAATGGGCTTTCGAGATGCCC
65 TTCAAAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCTTTCGAGATGCCC
* * * ** *
51732 CAACATTTTCTTCTTGCTAATATGAGCTTTCAAAATTTTCCAAATATTCATACTGACGTGGGCTT
1 CAACATTTTCTTCCTGATAATATGAGCTTTCAAAAATGCCCAAATATTCATACTGACATGGGCTT
51797 TCAAAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCTTTCGAGATGCC
66 TCAAAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCTTTCGAGATGCC
51849 TCAATATTCT
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
118 106 0.99
119 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (118 bp):
CAACATTTTCTTCCTGATAATATGAGCTTTCAAAAATGCCCAAATATTCATACTGACATGGGCTT
TCAAAATGCCCCACATGGATCATTTCTGTCTGAAATGGGCTTTCGAGATGCCC
Found at i:52225 original size:12 final size:12
Alignment explanation
Indices: 52208--52232 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52198 CTCTCGGACC
52208 ACTTGCCTTCAA
1 ACTTGCCTTCAA
52220 ACTTGCCTTCAA
1 ACTTGCCTTCAA
52232 A
1 A
52233 TAATGTGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.08, T:0.32
Consensus pattern (12 bp):
ACTTGCCTTCAA
Done.