Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005310.1 Hibiscus syriacus cultivar Beakdansim tig00012016_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: 78971
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3537 original size:15 final size:14
Alignment explanation
Indices: 3517--3547 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3507 ATGTTAAAGT
3517 GTTTAAAGGGGAGAA
1 GTTTAAAGGGGA-AA
3532 GTTTAAAGGGGAAA
1 GTTTAAAGGGGAAA
3546 GT
1 GT
3548 GTTAGAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.23
Consensus pattern (14 bp):
GTTTAAAGGGGAAA
Found at i:5904 original size:23 final size:24
Alignment explanation
Indices: 5878--5924 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
5868 AAAAAATGTT
5878 ATATTTTTAAT-AATAATTTCAGC
1 ATATTTTTAATAAATAATTTCAGC
*
5901 ATATTTTTAATAAATATTTTCAGC
1 ATATTTTTAATAAATAATTTCAGC
5925 TACACCTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (24 bp):
ATATTTTTAATAAATAATTTCAGC
Found at i:11820 original size:116 final size:120
Alignment explanation
Indices: 11611--11840 Score: 326
Period size: 116 Copynumber: 1.9 Consensus size: 120
11601 TTCGTAAAGT
* ** ** *
11611 TTGTTTTGGTTAACTGATCCTGTTAATTAGATTGGCATTGGTATGGGTAAGCCTAAACCTATTGG
1 TTGTTTTGGTAAACTGATCCAATTAATTAGATTGGCATCAGTATGGGTAACCCTAAACCTA-TGG
*
11676 TTCACCTAAAAATCCAAATCAAATTCAAAGCAAATTTGATAAAAACTAGAACTAGA
65 TTCACCTAAAAATCCAAATCAAATTCAAAGCAAATCTGATAAAAACTAGAACTAGA
11732 TTGTTTTGGTAAACTGAT-CAATTAATTA-ATTTGGCATCAGTATGGGTAACCCTAAA-C-A-GG
1 TTGTTTTGGTAAACTGATCCAATTAATTAGA-TTGGCATCAGTATGGGTAACCCTAAACCTATGG
* *
11792 TTCACCTAAACATGCAAATCAAATTCAAAGCAAATCTGATAAAAACTAG
65 TTCACCTAAAAATCCAAATCAAATTCAAAGCAAATCTGATAAAAACTAG
11841 GAGTACAGCT
Statistics
Matches: 99, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
116 48 0.48
118 1 0.01
119 2 0.02
120 31 0.31
121 17 0.17
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (120 bp):
TTGTTTTGGTAAACTGATCCAATTAATTAGATTGGCATCAGTATGGGTAACCCTAAACCTATGGT
TCACCTAAAAATCCAAATCAAATTCAAAGCAAATCTGATAAAAACTAGAACTAGA
Found at i:17032 original size:2 final size:2
Alignment explanation
Indices: 17025--17056 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17015 TCTGCCCTAC
17025 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
17057 GTTTCTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:18236 original size:179 final size:179
Alignment explanation
Indices: 17934--18291 Score: 655
Period size: 179 Copynumber: 2.0 Consensus size: 179
17924 CGCATCTTAG
*
17934 GTGTAATTACACAACTACCCGACTTCAATACCTCCAAACCTCCCTATAAATACCTCCATCTTCAA
1 GTGTAATTACACAACTACCCGACTTCAATACCTCCAAACCTCCCTATAAATACCTCCATCCTCAA
*
17999 TTACTTTCATCACACCAAATTCTCTCAACTTCTCTCAAATACTCTTATAATCTCTTCTAAGGTAT
66 TTACTTTCATCACACCAAATTCTCTCAACTTCTCTCAAATACTCTTATAATATCTTCTAAGGTAT
18064 ATTTTATTATATTTTTAATATTTTGTATTTAATTTATTTAAGTATTTAA
131 ATTTTATTATATTTTTAATATTTTGTATTTAATTTATTTAAGTATTTAA
* *
18113 GTGTAATTACACAACTACCCGACTTCAATACC-CTTAAACCTCCCTATAAATACCTTCATCCTCA
1 GTGTAATTACACAACTACCCGACTTCAATACCTC-CAAACCTCCCTATAAATACCTCCATCCTCA
*
18177 ATTACTTTCATCACATCAAATTCTCTCAACTTCTCTCAAATACTCTTATAATATCTTCTAAGGTA
65 ATTACTTTCATCACACCAAATTCTCTCAACTTCTCTCAAATACTCTTATAATATCTTCTAAGGTA
18242 TATTTTATTATATTTTTAATATTTTGTATTTAATTTATTTAAGTATTTAA
130 TATTTTATTATATTTTTAATATTTTGTATTTAATTTATTTAAGTATTTAA
18292 TTTATTTAAT
Statistics
Matches: 173, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
178 1 0.01
179 172 0.99
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (179 bp):
GTGTAATTACACAACTACCCGACTTCAATACCTCCAAACCTCCCTATAAATACCTCCATCCTCAA
TTACTTTCATCACACCAAATTCTCTCAACTTCTCTCAAATACTCTTATAATATCTTCTAAGGTAT
ATTTTATTATATTTTTAATATTTTGTATTTAATTTATTTAAGTATTTAA
Found at i:18280 original size:9 final size:9
Alignment explanation
Indices: 18268--18319 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
18258 TAATATTTTG
18268 TATTTAATT
1 TATTTAATT
*
18277 TATTTAA-G
1 TATTTAATT
18285 TATTTAATT
1 TATTTAATT
18294 TATTTAA--
1 TATTTAATT
* *
18301 TATTTTACT
1 TATTTAATT
18310 TATTTAATT
1 TATTTAATT
18319 T
1 T
18320 TTTTCAGATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:18289 original size:17 final size:17
Alignment explanation
Indices: 18267--18316 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
18257 TTAATATTTT
18267 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
18284 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
* *
18301 -TATTTTACTTATTTAA
1 GTATTTAATTTATTTAA
18317 TTTTTTTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:18312 original size:16 final size:16
Alignment explanation
Indices: 18276--18321 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
18266 TGTATTTAAT
* *
18276 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
18293 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
18309 TTATTTAAT-TTTT
1 TTATTTAATATTTT
18322 TTCAGATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:24052 original size:55 final size:55
Alignment explanation
Indices: 23989--24109 Score: 188
Period size: 55 Copynumber: 2.2 Consensus size: 55
23979 AATGACGTCT
* * * **
23989 GATGAATGAAGAAATTTGAACCTGATTGAAGAACGATTCATAAAGATGGACATCC
1 GATGAATGAAGAAATCTGAAACTGATTGAAGAACGATCCATAAAGAAAGACATCC
*
24044 GATGAATGAAGAAATCTGAAACTGATTGAAGACCGATCCATAAAGAAAGACATCC
1 GATGAATGAAGAAATCTGAAACTGATTGAAGAACGATCCATAAAGAAAGACATCC
24099 GATGAATGAAG
1 GATGAATGAAG
24110 TTTGAAGTTG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (55 bp):
GATGAATGAAGAAATCTGAAACTGATTGAAGAACGATCCATAAAGAAAGACATCC
Found at i:24473 original size:6 final size:6
Alignment explanation
Indices: 24462--24498 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
24452 ATTAACACCT
24462 TTTGCA TTTGCA TTTAGCA TTTGCA TTTGCA -TTGCA T
1 TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA TTTGCA T
24499 GTATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
7 6 0.21
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (6 bp):
TTTGCA
Found at i:24483 original size:13 final size:12
Alignment explanation
Indices: 24462--24498 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
24452 ATTAACACCT
24462 TTTGCATTTGCA
1 TTTGCATTTGCA
24474 TTTAGCATTTGCA
1 TTT-GCATTTGCA
24487 TTTGCA-TTGCA
1 TTTGCATTTGCA
24498 T
1 T
24499 GTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 6 0.25
12 6 0.25
13 12 0.50
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (12 bp):
TTTGCATTTGCA
Found at i:27968 original size:125 final size:125
Alignment explanation
Indices: 27746--28007 Score: 357
Period size: 125 Copynumber: 2.1 Consensus size: 125
27736 AAGTTGTGAT
* * *
27746 ATGTTCGGGCACGACTGAACCCACATCACGTTGAGATGACAAGATTCAAACCAATGAGGTATGAA
1 ATGTTGGGGCACGACTGAACCCACATCACATTGAGATGACAAGATTCAAACCAATGAGGCATGAA
* * *
27811 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCTCGTACCAGTATAAGACA
66 GAATGAGCCTTACAATCTGAGATGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACA
* * * *
27871 ATGTTGGGGCACGACTGAACCCACATCATATTGAGATGATAAGATTTAGACCAA-GAAGGCATTG
1 ATGTTGGGGCACGACTGAACCCACATCACATTGAGATGACAAGATTCAAACCAATG-AGGCA-TG
* * *
27935 -AGAGTGAGCCTTACAATCTGAGATGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATA
64 AAGAATGAGCCTTACAATCTGAGATGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACA
* *
27996 ATATTGCGGCAC
1 ATGTTGGGGCAC
28008 TAGTGAAGGC
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
124 1 0.01
125 117 0.98
126 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (125 bp):
ATGTTGGGGCACGACTGAACCCACATCACATTGAGATGACAAGATTCAAACCAATGAGGCATGAA
GAATGAGCCTTACAATCTGAGATGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGACA
Found at i:29765 original size:55 final size:54
Alignment explanation
Indices: 29660--29766 Score: 160
Period size: 55 Copynumber: 2.0 Consensus size: 54
29650 AATGAAGATG
* * **
29660 TTCGAGTTCTATACTCCCTAAAAAAGAGGGAGTAAACCCGTTTGCGGAAGATTA
1 TTCGAATTCTATACTCCCTAAAAAAGAGGGAGCAAACCCGTTTGAAGAAGATTA
*
29714 TTCGAATTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGAT
1 TTCGAATTCTATACTCCCTAAA-AAAGAGGGAGCAAACCCGTTTGAAGAAGAT
29767 GTTCGAGTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 21 0.45
55 26 0.55
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (54 bp):
TTCGAATTCTATACTCCCTAAAAAAGAGGGAGCAAACCCGTTTGAAGAAGATTA
Found at i:29772 original size:54 final size:53
Alignment explanation
Indices: 29653--29772 Score: 168
Period size: 54 Copynumber: 2.2 Consensus size: 53
29643 TGAAGCAAAT
* * **
29653 GAAGATGTTCGAGTTCTATACTCCCTAAAAAAGAGGGAGTAAACCCGTTTGCG
1 GAAGATGTTCGAATTCTATACTCCCTAAAAAAGAGGGAGCAAACCCGTTTGAA
* *
29706 GAAGATTATTCGAATTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAA
1 GAAGA-TGTTCGAATTCTATACTCCCTAAA-AAAGAGGGAGCAAACCCGTTTGAA
29761 GAAGATGTTCGA
1 GAAGATGTTCGA
29773 GTCTTATACT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
53 5 0.09
54 28 0.48
55 25 0.43
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (53 bp):
GAAGATGTTCGAATTCTATACTCCCTAAAAAAGAGGGAGCAAACCCGTTTGAA
Found at i:29833 original size:55 final size:55
Alignment explanation
Indices: 29761--30404 Score: 893
Period size: 55 Copynumber: 11.8 Consensus size: 55
29751 CCCGTTTGAA
*
29761 GAAGA-TGTTCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
*
29815 GAAGATTGTTCGAGTCTTATACTCGCTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
** * *
29870 GAAGATTGTTCGAGTCTTATACTCTCTGAAACAATAGAGAGCATACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* * *
29925 GAATATTGTTCGATTCTTATACTCTCTGAAGGAATAGGGAGTAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* * *
29980 GAAGATTGTTCGAGTCTTATACTCTCTGAAAGAATAGAGAGCATACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* *
30035 GAATATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAACAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* * *
30090 GAAAATTGTTTGAGTCTTATACTCTCTGAAGGAATAGGGAGCAAACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* * * * * *
30145 GAAGGTTGTTCGAGTCTTATACTCTCTGAAGGAATATGGAGCAAACCCGTTTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* * *
30200 GAAGA-TGTTCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACAATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
*
30254 GAAGGTTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
* * * * * *
30309 GAAGATTATTCTAGTCATATACTTTCTGAAGTG-ATAGGGAGCAGACACGGTTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAG-GAATAGGGAGCAGACACGATTGTT
* * * * *
30364 AAAGA-TGTTCGAGT-TCTATACTCCCTAAAGAAAGAGGGAGC
1 GAAGATTGTTCGAGTCT-TATACTCTCTGAAGGAATAGGGAGC
30405 GAACCCATAA
Statistics
Matches: 520, Mismatches: 65, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
54 76 0.15
55 443 0.85
56 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTT
Found at i:30575 original size:54 final size:54
Alignment explanation
Indices: 30368--30595 Score: 341
Period size: 54 Copynumber: 4.2 Consensus size: 54
30358 GTTGATAAAG
*
30368 ATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATAAGAAGAAT
1 ATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAT
* * * *
30422 GTGTTCTAGTTTTATACTCCCTATAGAAAGAGGGAGCGAACCCGTAAGAAGAAT
1 ATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAT
* * *
30476 CTGTTCGAGTTCTATACTCCATAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAA
1 ATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAT
* *
30530 ATGTTTGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGCAA-AAG
1 ATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAG-AAGAAT
30584 ATTGTTCGAGTT
1 A-TGTTCGAGTT
30596 TCTACTCTCT
Statistics
Matches: 156, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
54 145 0.93
55 11 0.07
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.23
Consensus pattern (54 bp):
ATGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGAAGAAT
Found at i:39417 original size:15 final size:15
Alignment explanation
Indices: 39397--39445 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
39387 ATATTTAACT
*
39397 GGGCGGGCAGATGTG
1 GGGCGGGCAGATGCG
*
39412 GGGCGGGCGGATGCG
1 GGGCGGGCAGATGCG
**
39427 GGGCGGGTGGATGCG
1 GGGCGGGCAGATGCG
39442 GGGC
1 GGGC
39446 AGATGCGGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.08, C:0.16, G:0.65, T:0.10
Consensus pattern (15 bp):
GGGCGGGCAGATGCG
Found at i:43712 original size:30 final size:29
Alignment explanation
Indices: 43650--43712 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
43640 TACTGCTAAG
* *
43650 GGTGTTAGATCGGGAAATATAGTATGACC
1 GGTGTTAGATCAGGAAATATAGTATCACC
*
43679 GGTGTTAGATCAGTAAATATACCG-ATCACC
1 GGTGTTAGATCAGGAAATATA--GTATCACC
43709 GGTG
1 GGTG
43713 ATTTTTCGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 19 0.66
30 9 0.31
31 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (29 bp):
GGTGTTAGATCAGGAAATATAGTATCACC
Found at i:44318 original size:23 final size:23
Alignment explanation
Indices: 44292--44339 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
44282 ATAAAGTACA
*
44292 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
44315 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
44338 AT
1 AT
44340 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:44850 original size:23 final size:23
Alignment explanation
Indices: 44815--44887 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
44805 ATACTTTACA
*
44815 ATATAAGCACTACATATTACATT
1 ATATAAGCGCTACATATTACATT
*
44838 ATATAAACGCTACATATTACATT
1 ATATAAGCGCTACATATTACATT
* * *
44861 ATATAAGTGCTACCTATTACATC
1 ATATAAGCGCTACATATTACATT
44884 ATAT
1 ATAT
44888 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACATATTACATT
Found at i:45281 original size:23 final size:23
Alignment explanation
Indices: 45251--45323 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
45241 ATACTTTACA
*
45251 ATATAAACACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
45274 ATATAAACGCTATCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
45297 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
45320 ATAT
1 ATAT
45324 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:49342 original size:3 final size:3
Alignment explanation
Indices: 49334--49426 Score: 87
Period size: 3 Copynumber: 31.0 Consensus size: 3
49324 ACTTGTTTGG
* * * * *
49334 ATC ATC ATC ATC ATC ATC ATC GTC GTC ATC ATC TTC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * * *
49382 ATC GTC AGC TTC ATC ATC ATC ATC ATC GTC ATC TTC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
49427 TTTATCGTCA
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.23, C:0.33, G:0.08, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:49351 original size:12 final size:12
Alignment explanation
Indices: 49334--49449 Score: 115
Period size: 12 Copynumber: 9.7 Consensus size: 12
49324 ACTTGTTTGG
*
49334 ATCATCATCATC
1 ATCATCATCTTC
*
49346 ATCATCATCGTC
1 ATCATCATCTTC
*
49358 GTCATCATCTTC
1 ATCATCATCTTC
*
49370 ATCGTCATCTTC
1 ATCATCATCTTC
* *
49382 ATCGTCAGCTTC
1 ATCATCATCTTC
*
49394 ATCATCATCATC
1 ATCATCATCTTC
*
49406 ATCGTCATCTTC
1 ATCATCATCTTC
* *
49418 ATCGTCATCTTT
1 ATCATCATCTTC
* *
49430 ATCGTCAGCTTC
1 ATCATCATCTTC
*
49442 ATCTTCAT
1 ATCATCAT
49450 TGACCGCTTG
Statistics
Matches: 88, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 88 1.00
ACGTcount: A:0.22, C:0.32, G:0.08, T:0.39
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:49364 original size:18 final size:18
Alignment explanation
Indices: 49338--49426 Score: 106
Period size: 18 Copynumber: 4.9 Consensus size: 18
49328 GTTTGGATCA
49338 TCATCATCATCATCATCG
1 TCATCATCATCATCATCG
* *
49356 TCGTCATCATCTTCATCG
1 TCATCATCATCATCATCG
* * * *
49374 TCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCG
49392 TCATCATCATCATCATCG
1 TCATCATCATCATCATCG
* *
49410 TCATCTTCATCGTCATC
1 TCATCATCATCATCATC
49427 TTTATCGTCA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.37
Consensus pattern (18 bp):
TCATCATCATCATCATCG
Found at i:49449 original size:6 final size:6
Alignment explanation
Indices: 49338--49449 Score: 89
Period size: 6 Copynumber: 18.7 Consensus size: 6
49328 GTTTGGATCA
* * * * * * *
49338 TCATCA TCATCA TCATCG TCGTCA TCATCT TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * * * *
49386 TCAGCT TCATCA TCATCA TCATCG TCATCT TCATCG TCATCT TTATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
49434 TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCAT
49450 TGACCGCTTG
Statistics
Matches: 84, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 84 1.00
ACGTcount: A:0.21, C:0.32, G:0.08, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:51443 original size:200 final size:200
Alignment explanation
Indices: 50945--51709 Score: 1334
Period size: 200 Copynumber: 3.8 Consensus size: 200
50935 AATATTAAAC
* * *
50945 AGTGTCGATACA-TATTATATACCAATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
1 AGTGTCGACACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* * *
51009 AAAAATTACCTATTACATTATACTTATGGGTTTTGATGTTTATGGGATCGACACTTTTTATATAT
65 AAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
**
51074 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTACGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
*
51139 TAAAAAA
195 T-ACAAA
*
51146 AGTGTCGACACATTATTTAGACCTATTATCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
51211 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
51276 GATCGACACTTTACGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTACGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
51341 ACAAA
196 ACAAA
*
51346 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGG
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
51411 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
51476 GATCGACACTTTACGGTTGCACCCTGTTTACCATTCAATCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTACGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
51541 ACAAA
196 ACAAA
*
51546 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
51611 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * *
51676 GATCGACACTTTATGGTTACACCTTGTTTGCCAT
131 GATCGACACTTTACGGTTGCACCCTGTTTGCCAT
51710 ATTGTAAATT
Statistics
Matches: 541, Mismatches: 22, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
200 356 0.66
201 181 0.33
202 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTACGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:51833 original size:18 final size:18
Alignment explanation
Indices: 51810--51870 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
51800 TCTCATTCAT
*
51810 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
51828 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
51847 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
51866 AATTA
1 AATTA
51871 GCCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:51846 original size:19 final size:19
Alignment explanation
Indices: 51822--51870 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
51812 TTATATTCAC
51822 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
51841 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
51860 ATACAAAATTA
1 ATACAAAATTA
51871 GCCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:53702 original size:33 final size:33
Alignment explanation
Indices: 53665--53730 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
53655 CATCTTAATA
* *
53665 TCACCCCTTAACACCCCAACTTCTTTTACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
53698 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
53731 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:53789 original size:21 final size:21
Alignment explanation
Indices: 53764--53828 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
53754 CCCCTTATGC
* *
53764 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
53785 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
53806 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
53827 CT
1 CT
53829 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:56049 original size:17 final size:18
Alignment explanation
Indices: 56027--56069 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
56017 ATATATCCGG
56027 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
56044 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
56064 TATCAT
1 TATCAT
56070 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:56087 original size:20 final size:19
Alignment explanation
Indices: 56032--56078 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
56022 TCCGGTATCA
56032 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
56051 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
56072 TTTTACC
1 TTTTACC
56079 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:56248 original size:20 final size:20
Alignment explanation
Indices: 56214--56260 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
56204 TCCGGTAACG
* *
56214 TTTTATCGGTTTTATCAT-T
1 TTTTACCGGTGTTATCATAT
56233 TTGTTACCGGTGTTATCATAT
1 TT-TTACCGGTGTTATCATAT
56254 TTTTACC
1 TTTTACC
56261 TGGTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.17, C:0.15, G:0.13, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTGTTATCATAT
Found at i:56408 original size:182 final size:180
Alignment explanation
Indices: 55999--56472 Score: 660
Period size: 182 Copynumber: 2.6 Consensus size: 180
55989 CGTACTTACG
* * *
55999 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
56064 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTAAAGTATCGATACATTATA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATA
*
56129 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
56179 AAAGTATCGACACTTTCAATATATATCCGGTAACGTTTTATCGGTTTTATCATTTTGTTACCGGT
1 AAAGTATCGACACTTT-AA-ATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGT
* * *
56244 GTTATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTT
64 TTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTT-AAAGTATCGACACATT
** * *
56309 ATAGGATTTAAAACTTCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
128 ATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * **
56363 AAAGTACCGACACTTTAAATGTATCTGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * * *
56428 TGTCATAGTTTTACTTGTTATATCATTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
56473 AATTTGGATC
Statistics
Matches: 258, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
180 16 0.06
181 1 0.00
182 162 0.63
183 63 0.24
184 16 0.06
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (180 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:62769 original size:73 final size:73
Alignment explanation
Indices: 62685--62823 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 73
62675 TTTAGTGTAA
62685 TTAAAAAATTTG-AAAAATATTAAAAATATAAAAAAATTT-GAAGTTAAAAATAATATGAAACTT
1 TTAAAAAATTTGAAAAAATATT--AAATATAAAAAAATTTCGAAGTTAAAAATAATATGAAACTT
62748 TTAGAAATTT
64 TTAGAAATTT
* * *** *
62758 TTAATAAATTTGAAAAAATATTAAATTTTTTAAAATTTCGAAGTTAAAAATAATATGAAATTTTT
1 TTAAAAAATTTGAAAAAATATTAAATATAAAAAAATTTCGAAGTTAAAAATAATATGAAACTTTT
62823 A
66 A
62824 ACAAATTTGA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
72 12 0.21
73 37 0.64
74 9 0.16
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.38
Consensus pattern (73 bp):
TTAAAAAATTTGAAAAAATATTAAATATAAAAAAATTTCGAAGTTAAAAATAATATGAAACTTTT
AGAAATTT
Found at i:65234 original size:11 final size:11
Alignment explanation
Indices: 65218--65251 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
65208 ATCGTAAATA
65218 TTAATATTTTT
1 TTAATATTTTT
65229 TTAATATTTTTT
1 TTAATA-TTTTT
65241 TTAATATTTTT
1 TTAATATTTTT
65252 GATAGAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTAATATTTTT
Found at i:65241 original size:12 final size:12
Alignment explanation
Indices: 65218--65251 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
65208 ATCGTAAATA
65218 TTAATA-TTTTT
1 TTAATATTTTTT
65229 TTAATATTTTTT
1 TTAATATTTTTT
65241 TTAATATTTTT
1 TTAATATTTTT
65252 GATAGAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTAATATTTTTT
Found at i:65433 original size:23 final size:23
Alignment explanation
Indices: 65406--65450 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
65396 GAAAAGGTAG
*
65406 CAATTTTAAAAACACCATAAAAT
1 CAATTTTAAAAACACCAGAAAAT
*
65429 CAATTTTGAAAACACCAGAAAA
1 CAATTTTAAAAACACCAGAAAA
65451 GCTTGCAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.56, C:0.18, G:0.04, T:0.22
Consensus pattern (23 bp):
CAATTTTAAAAACACCAGAAAAT
Found at i:65559 original size:20 final size:20
Alignment explanation
Indices: 65534--65600 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
65524 CACGAAATGT
*
65534 AAGATTATCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
65554 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
65574 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
65594 AAGATTA
1 AAGATTA
65601 TCAGGGAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.22
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:67511 original size:32 final size:32
Alignment explanation
Indices: 67474--67553 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
67464 TGAAAGTAGG
*
67474 CATCTTTGGATTTAATATTGTAAACAAAACCC
1 CATCTTTGGATTCAATATTGTAAACAAAACCC
*
67506 CATCTTTGGCTTCAATATTGTAAACAAAACCC
1 CATCTTTGGATTCAATATTGTAAACAAAACCC
*
67538 CATCTTTGGCTTCAAT
1 CATCTTTGGATTCAAT
67554 TATGAACAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.35
Consensus pattern (32 bp):
CATCTTTGGATTCAATATTGTAAACAAAACCC
Found at i:69049 original size:24 final size:24
Alignment explanation
Indices: 69019--69086 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
69009 AACATAAATG
69019 AACGAACATAAATGAACGAACATA
1 AACGAACATAAATGAACGAACATA
* * *
69043 AATGAACGTAAATGAACGAATATA
1 AACGAACATAAATGAACGAACATA
69067 AACGAACATATAATCGAACG
1 AACGAACATA-AAT-GAACG
69087 TTCACGAGCG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 29 0.78
25 3 0.08
26 5 0.14
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.16
Consensus pattern (24 bp):
AACGAACATAAATGAACGAACATA
Found at i:69073 original size:14 final size:14
Alignment explanation
Indices: 69007--69050 Score: 88
Period size: 14 Copynumber: 3.1 Consensus size: 14
68997 GTCCTCTGTT
69007 CGAACATAAATGAA
1 CGAACATAAATGAA
69021 CGAACATAAATGAA
1 CGAACATAAATGAA
69035 CGAACATAAATGAA
1 CGAACATAAATGAA
69049 CG
1 CG
69051 TAAATGAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.14
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:70387 original size:5 final size:5
Alignment explanation
Indices: 70377--70407 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
70367 TTTTATTATT
*
70377 TCGGG TCGGG TCGGG TCAGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG T
70408 TTCTAATTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.19, G:0.55, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:70966 original size:268 final size:259
Alignment explanation
Indices: 70395--70987 Score: 818
Period size: 268 Copynumber: 2.3 Consensus size: 259
70385 GGTCGGGTCA
** *
70395 GGTCGGGTCGGGTTTCTAATTCATATA-T----TCGGGTCGGGTGAAACTTTATTTTGGTCTGGT
1 GGTCGGGTCAAGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGT
* * * * *
70455 CGGATCGATTTTTTTAAGTGTGATATTCGGGTTAGGTCGAGTTCGGGTTTAGGGTGAAAAATACC
66 CGGGTCGATTTTTTTAAGTGTAATATTCGGGTCAGGTCGAGGTCGGGTTTAAGGTGAAAAATACC
* * *
70520 CGACCCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCCA
131 CGACCCCCAAAAAATATAAAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCCA
* * *
70585 TATATAATTTTTTTCAATTAAATCATTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCG
196 TATATAATTTTTTTCAATTAAATCACTATTTTTATTGAATAAAAATAAATTTTTTATTATTTCG
**
70649 GGTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGT
1 GGTCGGGTCAAGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGT
* * * * * *
70714 CGGGTCGGTTTTTTTTTAAATTTTAATTTTCGGGTCGGGTCGGGGTCGGGTTTAAGGTGAAAAAT
66 CGGGTC-G-ATTTTTTT-AAGTGTAATATTCGGGTCAGGTCGAGGTCGGGTTTAAGGTGAAAAAT
* *
70779 ACCCGACCCGACCCAAAAAATATAAAATTTTACCTTGTATATTTAGGAATAATTATAATAATACC
128 ACCCGA-CC--CCCAAAAAATATAAAATTTTACCTTATATATTTAGGAATAATTACAATAATACC
* *
70844 CCTCTATATATAATTTTTTTTTCAATTAAGTCACTATTTTTATTGAATAAAAATAAAATTTTTTA
190 CCTCCATATATAA--TTTTTTTCAATTAAATCACTATTTTTATTGAATAAAAAT-AAATTTTTTA
70909 TTATTTCG
252 TTATTTCG
* *
70917 GGTTGGGTCAAGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGT
1 GGTCGGGTCAAGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGT
70982 CGGGTC
66 CGGGTC
70988 TCGGATGGAG
Statistics
Matches: 299, Mismatches: 26, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
254 27 0.09
255 1 0.00
259 36 0.12
260 1 0.00
261 7 0.02
262 44 0.15
263 2 0.01
265 61 0.20
267 36 0.12
268 84 0.28
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (259 bp):
GGTCGGGTCAAGTTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCAGGT
CGGGTCGATTTTTTTAAGTGTAATATTCGGGTCAGGTCGAGGTCGGGTTTAAGGTGAAAAATACC
CGACCCCCAAAAAATATAAAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCCA
TATATAATTTTTTTCAATTAAATCACTATTTTTATTGAATAAAAATAAATTTTTTATTATTTCG
Found at i:71338 original size:44 final size:44
Alignment explanation
Indices: 71275--71395 Score: 188
Period size: 44 Copynumber: 2.8 Consensus size: 44
71265 CATATTTGTG
* *
71275 AACCAAACATAATATGGAATTGGATTCCAATTTAATTTTCTGCC
1 AACCAAACAGAATATGGAATTGGATTCCAATTCAATTTTCTGCC
71319 AACCAAACAGAATATGGAATTGGATTCCAATTCAATTTTCTGCC
1 AACCAAACAGAATATGGAATTGGATTCCAATTCAATTTTCTGCC
** * *
71363 AACCAAACAGAATATATAATTAGATTTCAATTC
1 AACCAAACAGAATATGGAATTGGATTCCAATTC
71396 CTGACAAATT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (44 bp):
AACCAAACAGAATATGGAATTGGATTCCAATTCAATTTTCTGCC
Found at i:75087 original size:26 final size:27
Alignment explanation
Indices: 75040--75101 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
75030 CATATTGTAT
*
75040 GATAAAATTTTATAGTAAATAG-ATTA
1 GATAAAATTTTATAGTAAATAGAAATA
**
75066 GATAAAATTTT-TAGTTTCATAGTAAATA
1 GATAAAATTTTATAG-TAAATAG-AAATA
75094 GATAAAAT
1 GATAAAAT
75102 ACATATACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 3 0.10
26 16 0.53
28 11 0.37
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (27 bp):
GATAAAATTTTATAGTAAATAGAAATA
Found at i:75270 original size:16 final size:17
Alignment explanation
Indices: 75243--75278 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
75233 GATATGAGAA
75243 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
75260 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
75276 AAA
1 AAA
75279 ATAACGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:75424 original size:13 final size:13
Alignment explanation
Indices: 75406--75439 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
75396 GAACAATTCA
75406 TATGTAATTCATC
1 TATGTAATTCATC
75419 TATGTAATTCATC
1 TATGTAATTCATC
75432 TATGTAAT
1 TATGTAAT
75440 GTATAGCGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (13 bp):
TATGTAATTCATC
Done.