Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007480.1 Hibiscus syriacus cultivar Beakdansim tig00020605_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: 83086
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:844 original size:3 final size:3
Alignment explanation
Indices: 831--929 Score: 109
Period size: 3 Copynumber: 34.3 Consensus size: 3
821 TGGGTTGTAT
*
831 ATA ATA A-A ATA AT- ATA ATA ATA ATA AT- ATA ATA TTA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* * * *
874 ATA ATA ATA ATA ATA GTA ATA AAA ATA AAA ATA AAA AT- ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
920 ATA ATA ATA A
1 ATA ATA ATA A
930 AACAAATGTA
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
2 10 0.12
3 67 0.84
4 3 0.04
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2344 original size:21 final size:21
Alignment explanation
Indices: 2320--2361 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2310 AGTTTATTTT
2320 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
2341 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
2362 AACTTGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:2424 original size:33 final size:33
Alignment explanation
Indices: 2356--2454 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
2346 TTTGTTTCAA
2356 TTATCGAACTTGGAAGTTTTTAAGTA-TTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
*
2388 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
2421 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2454 T
1 T
2455 ATCATAAACT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 25 0.41
33 36 0.59
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:2517 original size:15 final size:15
Alignment explanation
Indices: 2497--2527 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2487 AATTTTAATA
2497 TTATAATCGATTTTT
1 TTATAATCGATTTTT
*
2512 TTATAATCGGTTTTT
1 TTATAATCGATTTTT
2527 T
1 T
2528 AAAAAAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.10, T:0.61
Consensus pattern (15 bp):
TTATAATCGATTTTT
Found at i:7063 original size:16 final size:16
Alignment explanation
Indices: 7042--7090 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
7032 AAATATGCTT
7042 CCCTAATATTAATCTC
1 CCCTAATATTAATCTC
* *
7058 CCCTAATA-T--GCTT
1 CCCTAATATTAATCTC
7071 CCCTAATATTAATCTC
1 CCCTAATATTAATCTC
7087 CCCT
1 CCCT
7091 TATGTTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
15 1 0.04
16 14 0.54
ACGTcount: A:0.27, C:0.35, G:0.02, T:0.37
Consensus pattern (16 bp):
CCCTAATATTAATCTC
Found at i:7075 original size:29 final size:29
Alignment explanation
Indices: 7033--7090 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
7023 TGATGTAGAA
7033 AATATGCTTCCCTAATATTAATCTCCCCT
1 AATATGCTTCCCTAATATTAATCTCCCCT
7062 AATATGCTTCCCTAATATTAATCTCCCCT
1 AATATGCTTCCCTAATATTAATCTCCCCT
7091 TATGTTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.31, G:0.03, T:0.38
Consensus pattern (29 bp):
AATATGCTTCCCTAATATTAATCTCCCCT
Found at i:17011 original size:39 final size:40
Alignment explanation
Indices: 16937--17014 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 40
16927 CCAGCACCCA
*
16937 ACGTCCCCAGCACCCAATACCCCAACACAGGTCGCCATGC
1 ACGTCCCCAGCACCCAACACCCCAACACAGGTCGCCATGC
16977 ACGTCCCCAGCACCCAACA-CCCAACACAGGTCGCCATG
1 ACGTCCCCAGCACCCAACACCCCAACACAGGTCGCCATG
17015 TAGTCCCAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 19 0.51
40 18 0.49
ACGTcount: A:0.28, C:0.47, G:0.15, T:0.09
Consensus pattern (40 bp):
ACGTCCCCAGCACCCAACACCCCAACACAGGTCGCCATGC
Found at i:17050 original size:29 final size:29
Alignment explanation
Indices: 17004--17144 Score: 174
Period size: 29 Copynumber: 4.9 Consensus size: 29
16994 CACCCAACAC
* *
17004 AGGTCGCCATGTAGTCCCAGCGACCTACA
1 AGGTCGCCATGCACTCCCAGCGACCTACA
*
17033 AGGTCTCCATGCACTCCCAGCGACCTACA
1 AGGTCGCCATGCACTCCCAGCGACCTACA
*
17062 AGGTCGCCATGCACTCCCAGCGACCTACG
1 AGGTCGCCATGCACTCCCAGCGACCTACA
* * ***
17091 AGGTCACCATGCACTCCCATCGACCTTGT
1 AGGTCGCCATGCACTCCCAGCGACCTACA
* * *
17120 AGGTCGCCAAGCAATCCCGGCGACC
1 AGGTCGCCATGCACTCCCAGCGACC
17145 AAGCCTCGAC
Statistics
Matches: 97, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 97 1.00
ACGTcount: A:0.23, C:0.39, G:0.22, T:0.16
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCAGCGACCTACA
Found at i:17227 original size:45 final size:45
Alignment explanation
Indices: 17163--17252 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
17153 ACCTGCTGGC
17163 GACCAAACTTAACCCTGCTCCCTCGTGCATGGGCTGCATCCATAG
1 GACCAAACTTAACCCTGCTCCCTCGTGCATGGGCTGCATCCATAG
*
17208 GACCAAACTTAACCCTGCTCCCTCGTGCATGGGTTGCATCCATAG
1 GACCAAACTTAACCCTGCTCCCTCGTGCATGGGCTGCATCCATAG
17253 CTGGGAGATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.23
Consensus pattern (45 bp):
GACCAAACTTAACCCTGCTCCCTCGTGCATGGGCTGCATCCATAG
Found at i:17272 original size:23 final size:23
Alignment explanation
Indices: 17242--17285 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
17232 GTGCATGGGT
17242 TGCATCCATAGCTGGGAGATTCC
1 TGCATCCATAGCTGGGAGATTCC
17265 TGCATCCATAGCTGGGAGATT
1 TGCATCCATAGCTGGGAGATT
17286 GTAGCCAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (23 bp):
TGCATCCATAGCTGGGAGATTCC
Found at i:17751 original size:28 final size:30
Alignment explanation
Indices: 17710--17771 Score: 101
Period size: 28 Copynumber: 2.1 Consensus size: 30
17700 AATTTAGTTA
*
17710 ATTAGTTTGTTAGTTTAAGTTAT-T-TTAT
1 ATTAGTTTGCTAGTTTAAGTTATATATTAT
17738 ATTAGTTTGCTAGTTTAAGTTATATATTAT
1 ATTAGTTTGCTAGTTTAAGTTATATATTAT
17768 ATTA
1 ATTA
17772 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 22 0.71
29 1 0.03
30 8 0.26
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.56
Consensus pattern (30 bp):
ATTAGTTTGCTAGTTTAAGTTATATATTAT
Found at i:17834 original size:45 final size:49
Alignment explanation
Indices: 17738--17835 Score: 114
Period size: 50 Copynumber: 2.1 Consensus size: 49
17728 GTTATTTTAT
* **
17738 ATTAGTTTGCTAGTTTAAGTTATATATTATATTATATAAAAAATTCCTTA
1 ATTAGTTTGCTAGTTTAAGTTATATA-TATATTATAAAAAAAATTAATTA
**
17788 ATTAGTTTTTTAGTTTAAGTTAT-TA-A-A-TATAAAAAAAATTAATTA
1 ATTAGTTTGCTAGTTTAAGTTATATATATATTATAAAAAAAATTAATTA
17833 ATT
1 ATT
17836 TGTTAGTGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
45 18 0.42
46 1 0.02
47 1 0.02
49 2 0.05
50 21 0.49
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (49 bp):
ATTAGTTTGCTAGTTTAAGTTATATATATATTATAAAAAAAATTAATTA
Found at i:18109 original size:20 final size:21
Alignment explanation
Indices: 18065--18109 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
18055 AAATATTGTG
**
18065 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
18086 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
18106 TTTA
1 TTTA
18110 TATTATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:21345 original size:60 final size:60
Alignment explanation
Indices: 21272--21973 Score: 558
Period size: 60 Copynumber: 12.0 Consensus size: 60
21262 TTTATAAGAT
*
21272 TTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
1 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
* *
21332 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATTA
1 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
*
21392 TTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAG---T-A
1 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
*
21447 --A-TAATAAT----TTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGA
1 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
* * * ** * ** * * * *
21500 TTTGATAGTAATG-ATTTACGACTTGAACAATGAACAATG-TTTGGTTCAATTAATCATATTTTC
1 TTAG-TAATAATGAAATTATTA-TT-AA-TAT--TTAATGATTT-GAT--AGTAAT--GA-TTTA
* *
21563 GTTA-CA
54 GTAATGA
* * * * * * * *
21569 TAACTAGTAATGAAATTA-TAATAATGATTTAAT-A-ATGATTAGTAAT-A-AT-GAAATTA
1 TTAGTAATAATGAAATTATTATTAAT-ATTTAATGATTTGA-TAGTAATGATTTAGTAATGA
* ** * * *
21625 TTATTAAT-ATTTAATGA-T-TTGATA-TTAATGA-TT--TAGTAAAGA-TTAGTAAT-A
1 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
* * ** * * *
21676 AT-G-AA-ATTGTTATTAATATTTAATGATTTGAT-AGTAATGATTTAGTAATGA-TTAGTAATG
1 TTAGTAATAATGAAATTATTA-TTAAT-ATTTAATGA-T-TTGA--TAGTAATGATTTAGTAATG
21736 A
60 A
* *
21737 TTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTTGTAATGA
1 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
*
21797 TTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
1 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
* *
21857 TTAGTAATAATGAAATTATTATTAATACTTAATGATTTGATATTAATGATTTAGTAATGA
1 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
*
21917 TTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTAAT
1 TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAAT
21974 AATGAAATTA
Statistics
Matches: 519, Mismatches: 73, Indels: 101
0.75 0.11 0.15
Matches are distributed among these distances:
48 32 0.06
49 11 0.02
50 7 0.01
51 4 0.01
52 21 0.04
53 7 0.01
54 7 0.01
55 10 0.02
56 9 0.02
57 6 0.01
58 1 0.00
59 21 0.04
60 295 0.57
61 12 0.02
62 11 0.02
63 12 0.02
64 14 0.03
65 6 0.01
66 4 0.01
67 7 0.01
68 9 0.02
69 7 0.01
70 6 0.01
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.45
Consensus pattern (60 bp):
TTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
Found at i:21444 original size:109 final size:112
Alignment explanation
Indices: 21272--22182 Score: 547
Period size: 109 Copynumber: 7.9 Consensus size: 112
21262 TTTATAAGAT
*
21272 TTAGTAATGATGAAATTATTATTAAT-ATTTAATGATTTGATAGTAATGATTTAGTAATGATTAG
1 TTAGTAATAATGAAATTATTATTAATAATTT-A--A--TGAT--T-ATGA-TTAGTAATGATTAG
*
21336 TAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATTA
57 TAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATTA
*
21392 TTAGTAATAATGAAATTATTATTAAT-TTTTAATGATT-TGA-TAGTAATGATTAGTAATAAT-A
1 TTAGTAATAATGAAATTATTATTAATAATTTAATGATTATGATTAGTAATGATTAGTAATAATGA
* * *
21453 ATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGA
66 AATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATTA
* * * ** * ** * * *
21500 TTTGATAGTAATG-ATTTACGACTTGAACAATGAACAATG-TT-TGGTTCAATTAATCATATTTT
1 TTAG-TAATAATGAAATTATTA-TT-AATAAT--TTAATGATTATGATT--AGTAAT--GA--TT
* * * * *
21562 CGTTACATAACTAGTAATGA-AATT-ATA-ATAATGATTT-A-A-TAATGA-TTAGTAA-TA
55 AG-TA-ATAA-T-GAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATTA
* * * * * * * *
21616 AT-GAAATTAT--TATTAATATTTAATGATTTGAT-ATTAATGATTTAGTAAAGATTAGTAATAA
1 TTAGTAATAATGAAATTATTA-TTAATAATTTAATGATT-ATGA-TTAGTAATGATTAGTAATAA
*
21677 TGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATGA
63 TGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAG---T-A--A-T--T-A
* *
21737 TTAGTAATAATGAAATTGTTATTAAT-ATTTAATGATTTGATAGTAATGATTTTGTAATGATTAG
1 TTAGTAATAATGAAATTATTATTAATAATTT-A--A--TGAT--T-ATGA-TTAGTAATGATTAG
* *
21801 TAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGA
57 TAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATTA
* *
21857 TTAGTAATAATGAAATTATTATTAATACTTAATGATTTGATATTAATGATTTAGTAATGATTAGT
1 TTAGTAATAATGAAATTATTATTAATAATT--T-A-ATG--ATT-ATGA-TTAGTAATGATTAGT
*
21922 AATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTAA-TA
58 AATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATTA
* * * * * * *
21975 AT-GAAATTAT--TATTAATATTTAATGATTTGAT-ATTAATGATTTAGTAATGATTAGTAATAA
1 TTAGTAATAATGAAATTATTA-TTAATAATTTAATGATT-ATGA-TTAGTAATGATTAGTAATAA
*
22036 TGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA-TTAGTAA-TA
63 TGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATTA
* * * * * * * *
22084 AT-GAAATTAT--TATTAATATTTAATGATTTGAT-ATTAATGATTTAGTAATGATTAGTAGTAA
1 TTAGTAATAATGAAATTATTA-TTAATAATTTAATGATT-ATGA-TTAGTAATGATTAGTAATAA
*
22145 TGAAATTATTATTAATTTTTAATGATTTGATTAGTAAT
63 TGAAATTATTATTAATATTTAATGATTTGA-TAGTAAT
22183 AATAATTTAT
Statistics
Matches: 653, Mismatches: 80, Indels: 126
0.76 0.09 0.15
Matches are distributed among these distances:
103 4 0.01
104 4 0.01
105 7 0.01
106 11 0.02
107 4 0.01
108 55 0.08
109 199 0.30
110 17 0.03
111 8 0.01
112 11 0.02
113 15 0.02
114 6 0.01
115 16 0.02
116 10 0.02
117 15 0.02
118 8 0.01
119 12 0.02
120 123 0.19
121 17 0.03
122 16 0.02
123 11 0.02
124 9 0.01
125 1 0.00
126 1 0.00
127 2 0.00
128 2 0.00
130 69 0.11
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.46
Consensus pattern (112 bp):
TTAGTAATAATGAAATTATTATTAATAATTTAATGATTATGATTAGTAATGATTAGTAATAATGA
AATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATTA
Found at i:21457 original size:73 final size:72
Alignment explanation
Indices: 21361--21515 Score: 156
Period size: 73 Copynumber: 2.1 Consensus size: 72
21351 TATTAATATT
* * * *
21361 TAATGATTTGATATTAATGATTTAGTAATTATTAGTAATAATGAAATT-ATTATTAAT-TTT-TA
1 TAATGATTAGATAATAATAATTTA-TAATTAATA-T-ATAATG-AATTGA-TATTAATATTTATA
21423 ATGATTTGATAG
61 ATGATTTGATAG
* * *
21435 TAATGATTAG-TAATAATAATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATG
1 TAATGATTAGATAATAATAATTTATAATTAATATATAATGAATTGATATTAAT-ATTTA-TAATG
21499 ATTTGATAG
64 ATTTGATAG
21508 TAATGATT
1 TAATGATT
21516 TACGACTTGA
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
69 10 0.14
70 6 0.09
71 4 0.06
72 7 0.10
73 33 0.48
74 9 0.13
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (72 bp):
TAATGATTAGATAATAATAATTTATAATTAATATATAATGAATTGATATTAATATTTATAATGAT
TTGATAG
Found at i:21474 original size:48 final size:49
Alignment explanation
Indices: 21383--21497 Score: 178
Period size: 48 Copynumber: 2.3 Consensus size: 49
21373 ATTAATGATT
* *
21383 TAGTAATTATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
21432 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
21480 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
21498 GATTTGATAG
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 34 0.56
49 27 0.44
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:21485 original size:14 final size:14
Alignment explanation
Indices: 21469--21516 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
21459 TATTAATATT
*
21469 TAATGATTTGATAT
1 TAATGATTTGATAG
21483 TAATGA-TT--TAG
1 TAATGATTTGATAG
21494 TAATGATTTGATAG
1 TAATGATTTGATAG
21508 TAATGATTT
1 TAATGATTT
21517 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:21492 original size:130 final size:130
Alignment explanation
Indices: 21331--22018 Score: 492
Period size: 130 Copynumber: 5.2 Consensus size: 130
21321 TTTAGTAATG
* * *
21331 ATTAGTAATAATGAAATT-ATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATTATTA
1 ATTAATAATAATGAAATTGA-TATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTA
*
21395 GTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTAATAATAATTTAT
65 GTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATAATAATTTAT
21459 T
130 T
* * *
21460 ATTAATATTTAATG-ATTTGATATTAATGATTTAGTAATGATTTGATAGTAATGATTTACG-ACT
1 ATTAATA-ATAATGAAATTGATATTAAT-A-TT--TAATGATTTGATAGTAATGATTTA-GTA-A
** * * *** * * ** * ** * *
21523 TGAACAATGAACAATGTTTGGTTCAATTAATCATATTTTCGTTACATAACTAGTAATGAAATTA-
59 TGATTAGT-AATAATG--AAATT--ATTATTAATA-TTTAATGATTTGA-TAGTAATG-ATTTAG
*
21587 TAATAATGATTTAATAAT
116 TAATAATAATTT-AT--T
* * *
21605 GATTAGTAATAATGAAATT-ATTATTAATATTTAATGATTTGATATTAATGATTTAGTAAAGATT
1 -ATTAATAATAATGAAATTGA-TATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATT
* * * * *
21669 AGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAA
64 AGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATAATAATTTA
*
21734 TG
129 TT
* * *
21736 ATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTTGTAATGATTAG
1 ATTAATAATAATGAAATTGATATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAG
*
21801 TAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATA
66 TAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAAT-A--A-TAAT-
*
21866 ATGAAATT
126 -T--TATT
* * * *
21874 ATTATTAATACT-TAA-TGAT-TTGATA-TTAATGA-TT--TAGTAATGA--T--T-A------G
1 ATTAATAATAATGAAATTGATATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAG
* *
21921 TAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTAATAATGAAATTAT
66 TAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATAAT-AATTTAT
21985 T
130 T
* *
21986 ATTAATATTTAATG-ATTTGATATTAATGATTTA
1 ATTAATA-ATAATGAAATTGATATTAAT-ATTTA
22019 GTAATGATTA
Statistics
Matches: 445, Mismatches: 73, Indels: 94
0.73 0.12 0.15
Matches are distributed among these distances:
112 9 0.02
113 4 0.01
114 5 0.01
115 5 0.01
116 4 0.01
117 3 0.01
118 1 0.00
119 8 0.02
120 44 0.10
126 1 0.00
127 1 0.00
129 17 0.04
130 121 0.27
131 11 0.02
133 33 0.07
134 30 0.07
135 18 0.04
136 11 0.02
137 4 0.01
138 15 0.03
139 7 0.02
140 13 0.03
141 13 0.03
142 36 0.08
143 5 0.01
144 2 0.00
145 8 0.02
146 16 0.04
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.45
Consensus pattern (130 bp):
ATTAATAATAATGAAATTGATATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAG
TAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATAATAATTTATT
Found at i:21616 original size:13 final size:12
Alignment explanation
Indices: 21583--21619 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
21573 TAGTAATGAA
21583 ATTATAATAATG
1 ATTATAATAATG
21595 ATT-TAATAATG
1 ATTATAATAATG
21606 ATTAGTAATAATG
1 ATTA-TAATAATG
21619 A
1 A
21620 AATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 3 0.13
13 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (12 bp):
ATTATAATAATG
Found at i:21725 original size:25 final size:25
Alignment explanation
Indices: 21696--21798 Score: 78
Period size: 21 Copynumber: 4.3 Consensus size: 25
21686 TATTAATATT
21696 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
*
21721 TAATGA--T--TAGTAATGATTAGTAA
1 TAATGATTTGATAGTAATGATT--TAG
* * *
21744 TAATGAAATTGTTATTAAT-A-TT--
1 TAATG-ATTTGATAGTAATGATTTAG
*
21766 TAATGATTTGATAGTAATGATTTTG
1 TAATGATTTGATAGTAATGATTTAG
21791 TAATGATT
1 TAATGATT
21799 AGTAATAATG
Statistics
Matches: 62, Mismatches: 5, Indels: 22
0.70 0.06 0.25
Matches are distributed among these distances:
21 21 0.34
22 6 0.10
23 10 0.16
24 2 0.03
25 14 0.23
26 2 0.03
27 1 0.02
28 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.46
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:21732 original size:10 final size:10
Alignment explanation
Indices: 21707--21744 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
21697 AATGATTTGA
21707 TAGTAATGATT
1 TAGTAATGA-T
21718 TAGTAATGAT
1 TAGTAATGAT
21728 TAGTAATGAT
1 TAGTAATGAT
21738 TAGTAAT
1 TAGTAAT
21745 AATGAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:21739 original size:70 final size:70
Alignment explanation
Indices: 21650--21864 Score: 342
Period size: 70 Copynumber: 3.2 Consensus size: 70
21640 GATTTGATAT
*
21650 TAATGATTTAGTAAAGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATG
1 TAATGA-TTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATG
21715 ATTTAG
65 ATTTAG
21721 TAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATG-
1 TAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA
21785 ---A-
66 TTTAG
21786 T--T--TT-GTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA
1 TAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA
21846 TTTAG
66 TTTAG
21851 TAATGATTAGTAAT
1 TAATGATTAGTAAT
21865 AATGAAATTA
Statistics
Matches: 133, Mismatches: 1, Indels: 21
0.86 0.01 0.14
Matches are distributed among these distances:
60 55 0.41
61 2 0.02
63 1 0.01
64 1 0.01
65 2 0.02
66 1 0.01
67 1 0.01
69 2 0.02
70 62 0.47
71 6 0.05
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (70 bp):
TAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA
TTTAG
Found at i:21809 original size:190 final size:182
Alignment explanation
Indices: 21590--22175 Score: 735
Period size: 169 Copynumber: 3.3 Consensus size: 182
21580 GAAATTATAA
*
21590 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
1 TAATGATTT-GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
*
21655 ATTTAGTAAAGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTA
65 ATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGA-TTA
*
21720 GTAATGATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAG
129 GTAAT--TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGA-TT--T-G
* *
21780 TAATGATTTTGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATG
1 TAATGA-TTTGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG
* *
21845 ATTTAGTAATGATTAGTAATAATGAAATTATTATTAATACTTAATGATTTGATA-T--T-A--A-
65 ATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTAG
* *
21903 TGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG
130 TAATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG
21956 --AT-A---GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 TAATGATTTGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
22015 TTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTAGT
66 TTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTAGT
* * *
22080 AA--TAATGAA--ATTA-T--T-AT-TAA-TA-T-TTAATGA-TT--TGATAT-
131 AATTTAGT-AATGATTAGTAATAATGAAATTATTATTAAT-ATTTAATGATTTG
* *
22118 TAATGATTTAGTAATGATTAGTAGTAATGAAATTATTATTAATTTTTAATGATTTGAT
1 TAATGATTT-GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGAT
22176 TAGTAATAAT
Statistics
Matches: 359, Mismatches: 20, Indels: 55
0.83 0.05 0.13
Matches are distributed among these distances:
163 5 0.01
164 2 0.01
165 8 0.02
166 1 0.00
167 2 0.01
168 2 0.01
169 153 0.43
170 2 0.01
172 2 0.01
173 6 0.02
174 5 0.01
175 3 0.01
176 3 0.01
177 1 0.00
179 2 0.01
180 43 0.12
182 3 0.01
183 1 0.00
186 1 0.00
187 1 0.00
189 1 0.00
190 109 0.30
191 3 0.01
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (182 bp):
TAATGATTTGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
TTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTAGT
AATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG
Found at i:21843 original size:169 final size:168
Alignment explanation
Indices: 21668--22235 Score: 606
Period size: 169 Copynumber: 3.4 Consensus size: 168
21658 TAGTAAAGAT
* *
21668 TAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTA
1 TAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTA
*
21733 ATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTTGTAATGAT
66 ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA-TTTGTAATGAT
*
21798 TAGTAATAATGAAATTGTTATTAATATTTAATGATTTGA
130 TAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* * * * ** * * *
21837 TAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATACTTAATGATTTGATATTA
1 TAGTAAT-A-AT-GAAATTATTATTAAT-ATTTAATGA-T-TTGATA-TTAATGA-TT--TAGTA
*
21902 ATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGA-TT--T-G--AT-A-
56 ATGA-TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGAT
21959 --GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
120 TTGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
* * ** * * * * * * * * *
22006 TATTAATGATTTAGTAATGATTAGTA-ATAATGAAATTGTTATTAAT-ATTTAATGATTTGA-TA
1 TAGTAATAATGAAATTATTATTAATATTTAATG-ATTTGATATTAATGATTTAGT-A-ATGATTA
*
22068 GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAAT
63 GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT-GTAAT
* *
22133 GATTAGTAGTAATGAAATTATTATTAATTTTTAATGATTTGA
127 GATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
*
22175 TTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATT
1 -TAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATT
22236 TGATAGTAAT
Statistics
Matches: 323, Mismatches: 47, Indels: 58
0.75 0.11 0.14
Matches are distributed among these distances:
158 46 0.14
159 3 0.01
160 5 0.02
161 2 0.01
162 5 0.02
163 4 0.01
164 5 0.02
165 3 0.01
166 9 0.03
167 1 0.00
168 3 0.01
169 127 0.39
170 20 0.06
171 1 0.00
172 11 0.03
173 7 0.02
174 3 0.01
175 5 0.02
176 7 0.02
177 3 0.01
179 10 0.03
180 43 0.13
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46
Consensus pattern (168 bp):
TAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTA
ATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTGTAATGATT
AGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:22021 original size:60 final size:59
Alignment explanation
Indices: 21957--22082 Score: 225
Period size: 60 Copynumber: 2.1 Consensus size: 59
21947 AATGATTTGA
*
21957 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA-T
*
22017 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGAT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGAT
22076 TAGTAAT
1 TAGTAAT
22083 AATGAAATTA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 8 0.12
60 56 0.88
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.45
Consensus pattern (59 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGAT
Found at i:22193 original size:39 final size:40
Alignment explanation
Indices: 22132--22214 Score: 132
Period size: 39 Copynumber: 2.1 Consensus size: 40
22122 GATTTAGTAA
* *
22132 TGATTAGTAGTAATGAAATTATTATTAATTTTTAATGATT
1 TGATTAGTAATAATGAAATTATTATTAATATTTAATGATT
*
22172 TGATTAGTAATAAT-AATTTATTATTAATATTTAATGATT
1 TGATTAGTAATAATGAAATTATTATTAATATTTAATGATT
22211 TGAT
1 TGAT
22215 ATTAATGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 27 0.68
40 13 0.32
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.51
Consensus pattern (40 bp):
TGATTAGTAATAATGAAATTATTATTAATATTTAATGATT
Found at i:22219 original size:14 final size:14
Alignment explanation
Indices: 22203--22250 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
22193 TATTAATATT
*
22203 TAATGATTTGATAT
1 TAATGATTTGATAG
22217 TAATGA-TT--TAG
1 TAATGATTTGATAG
22228 TAATGATTTGATAG
1 TAATGATTTGATAG
22242 TAATGATTT
1 TAATGATTT
22251 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:24484 original size:15 final size:14
Alignment explanation
Indices: 24461--24491 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
24451 TACAACACTA
24461 AACTTTAATATAAT
1 AACTTTAATATAAT
24475 AACTTATAATATAAT
1 AACTT-TAATATAAT
24490 AA
1 AA
24492 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:24499 original size:16 final size:16
Alignment explanation
Indices: 24466--24512 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
24456 CACTAAACTT
*
24466 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
24481 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
24497 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
24513 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:24851 original size:22 final size:21
Alignment explanation
Indices: 24813--24853 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
24803 TTTATGTATA
*
24813 ATATAACTTAAACTAACAATC
1 ATATAACCTAAACTAACAATC
*
24834 ATATAACCCTAAATTAACAA
1 ATATAA-CCTAAACTAACAA
24854 ACTAATTAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.27
Consensus pattern (21 bp):
ATATAACCTAAACTAACAATC
Found at i:25014 original size:29 final size:27
Alignment explanation
Indices: 24981--25045 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
24971 TCTCCCCTTT
* *
24981 CTTTCTTTCTCGGCTGCAATTTCTTCTCC
1 CTTTCTTTCT--GCTACAATCTCTTCTCC
25010 CTTTC-TTCTGCTACAATCTCTTCTCC
1 CTTTCTTTCTGCTACAATCTCTTCTCC
*
25036 CTTTTTTTCT
1 CTTTCTTTCT
25046 TTTATGTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 19 0.59
27 4 0.12
28 4 0.12
29 5 0.16
ACGTcount: A:0.08, C:0.34, G:0.06, T:0.52
Consensus pattern (27 bp):
CTTTCTTTCTGCTACAATCTCTTCTCC
Found at i:25135 original size:33 final size:33
Alignment explanation
Indices: 25088--25154 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
25078 ATAATTTAGG
25088 TGTCACCGACTGCCTCAATTATTTCACCAATAA
1 TGTCACCGACTGCCTCAATTATTTCACCAATAA
**
25121 TGTCACCGGTTGCCTCAATTATTTCACCAATAA
1 TGTCACCGACTGCCTCAATTATTTCACCAATAA
25154 T
1 T
25155 TGTGCAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.33
Consensus pattern (33 bp):
TGTCACCGACTGCCTCAATTATTTCACCAATAA
Found at i:25306 original size:18 final size:19
Alignment explanation
Indices: 25275--25312 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
25265 GGCATGCAGA
25275 GGGAGCAGGAGGGGAGCAC
1 GGGAGCAGGAGGGGAGCAC
25294 GGGAGCA-GAGGGGAGCAC
1 GGGAGCAGGAGGGGAGCAC
25312 G
1 G
25313 TGAAGCTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.26, C:0.16, G:0.58, T:0.00
Consensus pattern (19 bp):
GGGAGCAGGAGGGGAGCAC
Found at i:25404 original size:29 final size:29
Alignment explanation
Indices: 25321--25409 Score: 115
Period size: 29 Copynumber: 3.1 Consensus size: 29
25311 CGTGAAGCTT
* * ***
25321 GGTCGCCGGGACTGCTTGGCGACCTACAA
1 GGTCGCTGGGAGTGCTTGGCGACCTTGTA
* *
25350 GGTCGCTGGGAGTGCATGGTGACCTTGTA
1 GGTCGCTGGGAGTGCTTGGCGACCTTGTA
25379 GGTCGCTGGGAGTGCTTGGCGACCTTGTA
1 GGTCGCTGGGAGTGCTTGGCGACCTTGTA
25408 GG
1 GG
25410 GGTGTTGGGG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.13, C:0.22, G:0.40, T:0.24
Consensus pattern (29 bp):
GGTCGCTGGGAGTGCTTGGCGACCTTGTA
Found at i:26629 original size:18 final size:18
Alignment explanation
Indices: 26606--26649 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
26596 GAAATCAATT
26606 GAAAATGTCACAACAAAA
1 GAAAATGTCACAACAAAA
26624 GAAAATGTCACAACAAAA
1 GAAAATGTCACAACAAAA
*
26642 CAAAATGT
1 GAAAATGT
26650 AAACACTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.59, C:0.16, G:0.11, T:0.14
Consensus pattern (18 bp):
GAAAATGTCACAACAAAA
Found at i:29128 original size:22 final size:23
Alignment explanation
Indices: 29072--29128 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 23
29062 ATAAACAAAC
* *
29072 GTTAAAAAATATATTTATGAACA
1 GTTAAATAATATATTTATGAAAA
*
29095 -TTAAAATGAATATATTT-TTAAAA
1 GTT-AAAT-AATATATTTATGAAAA
29118 GTTAAATAATA
1 GTTAAATAATA
29129 CGTTGTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 6 0.21
23 11 0.39
24 11 0.39
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.39
Consensus pattern (23 bp):
GTTAAATAATATATTTATGAAAA
Found at i:34639 original size:2 final size:2
Alignment explanation
Indices: 34583--34619 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
34573 ATAAATAAAT
34583 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34620 TTTAAAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:37636 original size:170 final size:165
Alignment explanation
Indices: 37338--37666 Score: 581
Period size: 170 Copynumber: 2.0 Consensus size: 165
37328 TATGACAATG
37338 AAGATAACATGCTTCAATCAGAGTTTATGCCGGTAAGTAGCCAATAGGTTTTCAAGAAGCTGTAT
1 AAGATAACATGCTTCAATCAGAGTTTATGCCGGTAAGTAGCCAATAGGTTTTCAAGAAGCTGTAT
37403 GTCGAAACAGATGAGCTTCTTAAAAGATCTGAATTGTAACTTACGACATTCTAACTCTATAATCA
66 GTCGAAACAGATGAGCTTCTTAAAAGATCTGAATTGTAACTTACGACATTCTAACTCTATAATCA
37468 TCGATTCAATGATACATACCTAGGATTAGGATTTCATGA
131 TCGATTCAATG----ATACCTAGGATTAGGATTTCATGA
37507 AAGATAACATGCTTCAATCAGAGTTTTATGCCGGTAAGTAGCCAATATGGTGTTTCAAGAAGCTG
1 AAGATAACATGCTTCAATCAGAG-TTTATGCCGGTAAGTAGCCAATA-GGT-TTTCAAGAAGCTG
37572 TATGTCGAAACAGATGAGCTTCTTAAAAGATCTGAA-T-TAACTTACGACATTCTAACTCTATAA
63 TATGTCGAAACAGATGAGCTTCTTAAAAGATCTGAATTGTAACTTACGACATTCTAACTCTATAA
37635 TCATCGATTCAATGATACCTAGGATTAGGATT
128 TCATCGATTCAATGATACCTAGGATTAGGATT
37667 CCTCGTACTA
Statistics
Matches: 157, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
166 18 0.11
169 23 0.15
170 63 0.40
171 4 0.03
172 49 0.31
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (165 bp):
AAGATAACATGCTTCAATCAGAGTTTATGCCGGTAAGTAGCCAATAGGTTTTCAAGAAGCTGTAT
GTCGAAACAGATGAGCTTCTTAAAAGATCTGAATTGTAACTTACGACATTCTAACTCTATAATCA
TCGATTCAATGATACCTAGGATTAGGATTTCATGA
Found at i:38416 original size:49 final size:48
Alignment explanation
Indices: 38358--38456 Score: 130
Period size: 49 Copynumber: 2.0 Consensus size: 48
38348 TAAAAAAACC
* *
38358 CAGATCCAAAATCGTTCATTTCCA-CGA-ATAGAGAAAAAAATCCAGTTTT
1 CAGATCCAAAATCGTTCATTTACACCAACATAG-GAAAAAAAT--AGTTTT
*
38407 CAGATCCAAAATCGTTCCTTTACACCAACATAGGAAAAAAATAGTTTT
1 CAGATCCAAAATCGTTCATTTACACCAACATAGGAAAAAAATAGTTTT
38455 CA
1 CA
38457 AATAGGAGAG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
48 8 0.18
49 22 0.49
50 11 0.24
51 4 0.09
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.26
Consensus pattern (48 bp):
CAGATCCAAAATCGTTCATTTACACCAACATAGGAAAAAAATAGTTTT
Found at i:48962 original size:26 final size:26
Alignment explanation
Indices: 48900--48969 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
48890 CACCGAAGGA
* *
48900 CGGTGGCTCACCGACGACATCACCAC
1 CGGTGGCTCATCGACAACATCACCAC
48926 CGGTGGCTCATCGACAACATCACCAC
1 CGGTGGCTCATCGACAACATCACCAC
* *
48952 CTGTGGCTCATTGACAAC
1 CGGTGGCTCATCGACAAC
48970 CTCATCGGCG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.24, C:0.37, G:0.21, T:0.17
Consensus pattern (26 bp):
CGGTGGCTCATCGACAACATCACCAC
Found at i:50653 original size:21 final size:21
Alignment explanation
Indices: 50629--50689 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
50619 AACTTTGAAA
50629 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
50650 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
50664 AAATGATTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
50685 AAATG
1 AAATG
50690 TTTCTTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 3 0.10
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.33
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:50666 original size:37 final size:37
Alignment explanation
Indices: 50621--50742 Score: 155
Period size: 35 Copynumber: 3.4 Consensus size: 37
50611 TCGTAACCAA
*
50621 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
50658 CTTTG--AAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* * *
50693 CTTT-AAAAAATAGTTTTTCAAAGTTTGATAGATGTTT
1 CTTTGAAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
50730 -GTTG-AAAAATGAT
1 CTTTGAAAAAATGAT
50743 AATGGAATAA
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
35 35 0.47
36 13 0.17
37 27 0.36
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.43
Consensus pattern (37 bp):
CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:55274 original size:35 final size:34
Alignment explanation
Indices: 55217--55309 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 34
55207 TGAAAGTATT
*
55217 AAAATGGTTTT-TAAGTTTGGTAA-CCAACTTTG
1 AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTG
****
55249 AAAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 --AAAATGGTTTTCAAAGTTTGGT-AATCCAACTTTG
55286 AAAATGGTTTTCAAAGTTTGGTAA
1 AAAATGGTTTTCAAAGTTTGGTAA
55310 ATGTTTCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
34 13 0.25
35 31 0.61
36 2 0.04
37 5 0.10
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.41
Consensus pattern (34 bp):
AAAATGGTTTTCAAAGTTTGGTAATCCAACTTTG
Found at i:55276 original size:21 final size:21
Alignment explanation
Indices: 55252--55312 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
55242 AACTTTGAAA
55252 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
55273 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
55287 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
55308 AAATG
1 AAATG
55313 TTTCTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:55310 original size:35 final size:35
Alignment explanation
Indices: 55251--55358 Score: 148
Period size: 35 Copynumber: 3.1 Consensus size: 35
55241 CAACTTTGAA
55251 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
55286 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTT-
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * * * *
55320 TAAATAGTTTTTCAAAGTTTGATAGATGTTT-GTTG
1 AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTTG
55355 AAAA
1 AAAA
55359 ATGATAATGG
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
34 6 0.09
35 59 0.91
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:60222 original size:21 final size:19
Alignment explanation
Indices: 60175--60295 Score: 134
Period size: 19 Copynumber: 5.9 Consensus size: 19
60165 ATTTTCTAAA
60175 TTCGTTGCGATAGTCCAAG
1 TTCGTTGCGATAGTCCAAG
*
60194 TTCGTTGCGATAGTCGAAG
1 TTCGTTGCGATAGTCCAAG
*
60213 TTCGCGTTGCGATTTATTCCAAG
1 TT--CGTTGCGA--TAGTCCAAG
*
60236 TTCGTTGCGATAGTCGAAG
1 TTCGTTGCGATAGTCCAAG
*
60255 TTCGCGTTGCGATTTATTCCAAG
1 TT--CGTTGCGA--TAGTCCAAG
60278 TTCGTTGCGATAGTCCAA
1 TTCGTTGCGATAGTCCAA
60296 AATCGTAACG
Statistics
Matches: 86, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
19 36 0.42
21 32 0.37
23 18 0.21
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (19 bp):
TTCGTTGCGATAGTCCAAG
Found at i:60238 original size:42 final size:42
Alignment explanation
Indices: 60188--60292 Score: 210
Period size: 42 Copynumber: 2.5 Consensus size: 42
60178 GTTGCGATAG
60188 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
60230 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
60272 TCCAAGTTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
60293 CAAAATCGTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:60409 original size:5 final size:5
Alignment explanation
Indices: 60387--60444 Score: 71
Period size: 5 Copynumber: 11.2 Consensus size: 5
60377 CACGTATTAT
* * *
60387 CACGA CCACGA CCACGA CACGA CACGA AACGA CACGA CCCGA GACGA CACGA
1 CACGA -CACGA -CACGA CACGA CACGA CACGA CACGA CACGA CACGA CACGA
60439 CACGA C
1 CACGA C
60445 CCGAGACGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
5 35 0.76
6 11 0.24
ACGTcount: A:0.38, C:0.41, G:0.21, T:0.00
Consensus pattern (5 bp):
CACGA
Found at i:60445 original size:20 final size:20
Alignment explanation
Indices: 60388--60452 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
60378 ACGTATTATC
* *
60388 ACGACCACGACCACGACACGAC
1 ACGA-CACGA-CACGACCCGAG
*
60410 ACGAAACGACACGACCCGAG
1 ACGACACGACACGACCCGAG
60430 ACGACACGACACGACCCGAG
1 ACGACACGACACGACCCGAG
60450 ACG
1 ACG
60453 GACGGCGGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 31 0.79
21 4 0.10
22 4 0.10
ACGTcount: A:0.37, C:0.40, G:0.23, T:0.00
Consensus pattern (20 bp):
ACGACACGACACGACCCGAG
Found at i:61238 original size:23 final size:23
Alignment explanation
Indices: 61210--61281 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 23
61200 ACTATTGCAA
61210 CGAACTTGGAATAAATCGCAACG
1 CGAACTTGGAATAAATCGCAACG
* *
61233 CGAACTTCGACT--ATCGCAA--
1 CGAACTTGGAATAAATCGCAACG
61252 CGAACTTGGAATAAATCGCAACG
1 CGAACTTGGAATAAATCGCAACG
61275 CGAACTT
1 CGAACTT
61282 CGACTATCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 10 0.24
21 14 0.34
23 17 0.41
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (23 bp):
CGAACTTGGAATAAATCGCAACG
Found at i:61257 original size:19 final size:19
Alignment explanation
Indices: 61196--61322 Score: 128
Period size: 19 Copynumber: 6.3 Consensus size: 19
61186 CGTTGCGATT
*
61196 TTGGACTATTGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
61215 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
61238 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
61257 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
61280 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
61299 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
61318 TTGGA
1 TTGGA
61323 AAATCGCATT
Statistics
Matches: 90, Mismatches: 10, Indels: 16
0.78 0.09 0.14
Matches are distributed among these distances:
19 43 0.48
21 27 0.30
23 20 0.22
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:61258 original size:42 final size:42
Alignment explanation
Indices: 61199--61303 Score: 201
Period size: 42 Copynumber: 2.5 Consensus size: 42
61189 TGCGATTTTG
*
61199 GACTATTGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
61241 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
61283 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
61304 CTATCGCAAC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:61355 original size:21 final size:21
Alignment explanation
Indices: 61326--61374 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
61316 ATTTGGAAAA
*
61326 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
61347 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
61368 TCGCGTT
1 TCGCGTT
61375 ACGAATCTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.31, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:66306 original size:15 final size:15
Alignment explanation
Indices: 66288--66318 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
66278 GAAAGAATGG
66288 TCACTTGAAGAAGGA
1 TCACTTGAAGAAGGA
66303 TCACTTGAAGAAGGA
1 TCACTTGAAGAAGGA
66318 T
1 T
66319 TGTTGGAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (15 bp):
TCACTTGAAGAAGGA
Found at i:72621 original size:15 final size:14
Alignment explanation
Indices: 72602--72635 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
72592 AATATATGTT
72602 TTTATAATATGATA
1 TTTATAATATGATA
*
72616 TATTATTATATGATA
1 T-TTATAATATGATA
72631 TTTAT
1 TTTAT
72636 TAAATTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (14 bp):
TTTATAATATGATA
Found at i:72631 original size:20 final size:20
Alignment explanation
Indices: 72577--72631 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
72567 TATTTAATTT
*
72577 TATTATTCTATG-TATAATA
1 TATTATTATATGATATAATA
* * *
72596 TATGT-TTTTATAATATGATA
1 TAT-TATTATATGATATAATA
72616 TATTATTATATGATAT
1 TATTATTATATGATAT
72632 TTATTAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (20 bp):
TATTATTATATGATATAATA
Found at i:75895 original size:52 final size:53
Alignment explanation
Indices: 75830--75936 Score: 171
Period size: 52 Copynumber: 2.0 Consensus size: 53
75820 CACAAGATGG
* *
75830 GGCACATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAA
1 GGCACATA-AAATAGGAAACTAGCCTAGAGTTAGGGAATTACAACTAATCACAA
*
75884 GGCACAT-AAATAGGAGACTAGCCTAGAGTTAGGGAATTACAACTAATCACAA
1 GGCACATAAAATAGGAAACTAGCCTAGAGTTAGGGAATTACAACTAATCACAA
75936 G
1 G
75937 AATATTATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
52 43 0.86
54 7 0.14
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (53 bp):
GGCACATAAAATAGGAAACTAGCCTAGAGTTAGGGAATTACAACTAATCACAA
Found at i:81375 original size:2 final size:2
Alignment explanation
Indices: 81368--81407 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
81358 TTTAAAGGTA
81368 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81408 TAGATTTGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81629 original size:2 final size:2
Alignment explanation
Indices: 81622--81654 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
81612 TGCATTTATT
81622 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
81655 AACCGGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.