Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005573.1 Hibiscus syriacus cultivar Beakdansim tig00012931_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: 151023
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:1641 original size:27 final size:28
Alignment explanation
Indices: 1583--1646 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
1573 TTAAACAAAA
** * *
1583 TAAAATTTTTGATTAAATTATAAGAATT
1 TAAAATTTTCAATTAAATAATAAGAATC
*
1611 TAAAATTTTCAATTAAATAATATGAA-C
1 TAAAATTTTCAATTAAATAATAAGAATC
1638 TAAATATTT
1 TAAA-ATTT
1647 AATATACAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 4 0.13
28 26 0.87
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (28 bp):
TAAAATTTTCAATTAAATAATAAGAATC
Found at i:1737 original size:14 final size:14
Alignment explanation
Indices: 1718--1748 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1708 TCAAAAGTTA
*
1718 AAAAATATAAGATT
1 AAAAATATAAGAGT
1732 AAAAATATAAGAGT
1 AAAAATATAAGAGT
1746 AAA
1 AAA
1749 GTACTATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (14 bp):
AAAAATATAAGAGT
Found at i:8866 original size:144 final size:144
Alignment explanation
Indices: 8606--8895 Score: 571
Period size: 144 Copynumber: 2.0 Consensus size: 144
8596 GACCATTCAT
8606 TGACATCCGTTGTCACGTTGGACGCAGTAGCAGACATATTTCTCCGTGTTAGATCGATCAACTCG
1 TGACATCCGTTGTCACGTTGGACGCAGTAGCAGACATATTTCTCCGTGTTAGATCGATCAACTCG
8671 GGACTTAACTGAGTTACAAATATTGTAACTCTTTATTGCAATCATTGCTTCCTCCTTCGATGCGA
66 GGACTTAACTGAGTTACAAATATTGTAACTCTTTATTGCAATCATTGCTTCCTCCTTCGATGCGA
8736 ACTCCATTCCAATA
131 ACTCCATTCCAATA
8750 TGACATCCGTTGTCACGTTGGACGCAGTAGCAGACATATTTCTCCGTGTTAGATCGATCAACTCG
1 TGACATCCGTTGTCACGTTGGACGCAGTAGCAGACATATTTCTCCGTGTTAGATCGATCAACTCG
*
8815 GGACTTAACTGAGTTACAAATATTGTAACTCTTTATTGCCATCATTGCTTCCTCCTTCGATGCGA
66 GGACTTAACTGAGTTACAAATATTGTAACTCTTTATTGCAATCATTGCTTCCTCCTTCGATGCGA
8880 ACTCCATTCCAATA
131 ACTCCATTCCAATA
8894 TG
1 TG
8896 TAAATTACCG
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 145 1.00
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (144 bp):
TGACATCCGTTGTCACGTTGGACGCAGTAGCAGACATATTTCTCCGTGTTAGATCGATCAACTCG
GGACTTAACTGAGTTACAAATATTGTAACTCTTTATTGCAATCATTGCTTCCTCCTTCGATGCGA
ACTCCATTCCAATA
Found at i:9891 original size:8 final size:8
Alignment explanation
Indices: 9878--9918 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
9868 CTCATTTTCA
9878 GAGAATTT
1 GAGAATTT
9886 GAGAATTT
1 GAGAATTT
*
9894 -AGAGTTT
1 GAGAATTT
*
9901 GGGAATTT
1 GAGAATTT
9909 GAGAATTT
1 GAGAATTT
9917 GA
1 GA
9919 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:10220 original size:128 final size:128
Alignment explanation
Indices: 9989--10488 Score: 896
Period size: 128 Copynumber: 3.9 Consensus size: 128
9979 TAATCGGAGT
* *
9989 ACTATTCACATGAAGGCGCGTTCTTGGGGACGCGCCTTCCATTATTTTGTCA-AGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
10053 CATTGCCCTATTATGTCACTCATGTCCCTTGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
10116 ACTATTCATATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGATAT
1 ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
10181 CATTGCTCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
10244 ACTATTCATATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
10309 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
10372 ACTATTCACATGAAGGCGCGATCCCGGGGGCGCGCCTTCCATTAATTTT-TCAGAGAATATGTTA
1 ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATT-ATTTTGTCAGAGAATATGTTA
10436 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
10489 AATGATTTTC
Statistics
Matches: 360, Mismatches: 11, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
127 49 0.14
128 306 0.85
129 5 0.01
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:11132 original size:34 final size:34
Alignment explanation
Indices: 11094--11194 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 34
11084 AAATTTATTG
* *
11094 TTAAACTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
11128 TTAAATTTCGAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
11162 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
11195 AACATTTATC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:11743 original size:21 final size:20
Alignment explanation
Indices: 11716--11785 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
11706 GGTATAAAAC
*
11716 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
*
11736 CCTGGCGGACTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
11757 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
11778 CCCTGCGG
1 -CCTGCGG
11786 AGATGGCATA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:11815 original size:21 final size:21
Alignment explanation
Indices: 11789--11836 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
11779 CCTGCGGAGA
*
11789 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
11810 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
11831 GGGCAT
1 TGGCAT
11837 GTACCCATGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:13599 original size:34 final size:31
Alignment explanation
Indices: 13556--13644 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
13546 TTAATAATTC
*
13556 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
13590 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* * *
13621 TATAAAATATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
13645 AAAATACTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 6 0.13
32 16 0.35
33 2 0.04
34 22 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:13621 original size:31 final size:33
Alignment explanation
Indices: 13556--13635 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
13546 TTAATAATTC
* *
13556 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
13590 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
13621 TATAAAATATAATAA
1 TA-AAAAAATAATAA
13636 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:15968 original size:5 final size:5
Alignment explanation
Indices: 15958--15984 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
15948 ATAGTTATAA
15958 AGATT AGATT AGATT AGATT AGATT AG
1 AGATT AGATT AGATT AGATT AGATT AG
15985 GAGGGAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (5 bp):
AGATT
Found at i:19235 original size:2 final size:2
Alignment explanation
Indices: 19228--19260 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
19218 GACTACCATA
*
19228 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19261 ACCAACAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20972 original size:21 final size:20
Alignment explanation
Indices: 20932--20973 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
20922 TCAACTTACA
*
20932 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
20952 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
20973 A
1 A
20974 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:23531 original size:23 final size:23
Alignment explanation
Indices: 23505--23549 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
23495 CACCACAGCT
*
23505 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
23528 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
23550 TATAATAATG
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:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:23766 original size:149 final size:148
Alignment explanation
Indices: 23517--23830 Score: 576
Period size: 149 Copynumber: 2.1 Consensus size: 148
23507 TATAATTGCA
23517 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCTATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCTATAATAATGTCCATAAGGACCACATATTAT
23581 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
65 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
* *
23646 CACAGAATATATATATATC
130 CAAAGAATATACATATATC
23665 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCC-TATAATAATGTCCATAAGGACCACATATTAT
23730 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
65 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
23795 CAAAGAATATACATATGTC
130 CAAAGAATATACATATATC
23814 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
23831 CCCTCGACTC
Statistics
Matches: 161, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
147 1 0.01
148 31 0.19
149 129 0.80
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (148 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCTATAATAATGTCCATAAGGACCACATATTATT
CCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCC
AAAGAATATACATATATC
Found at i:25416 original size:21 final size:21
Alignment explanation
Indices: 25386--25430 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
25376 TTTTGTTTGT
* *
25386 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
25407 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
25428 TTG
1 TTG
25431 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:28701 original size:23 final size:23
Alignment explanation
Indices: 28675--28719 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
28665 CACCACAGCT
*
28675 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
28698 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
28720 ATATAATAAT
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:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:28937 original size:149 final size:149
Alignment explanation
Indices: 28687--29001 Score: 587
Period size: 149 Copynumber: 2.1 Consensus size: 149
28677 TATAATTGCA
28687 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
28751 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* *
28816 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
28836 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
28901 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
28966 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
28985 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
29002 CCCTCGACTC
Statistics
Matches: 162, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 161 0.99
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:34107 original size:20 final size:21
Alignment explanation
Indices: 34082--34120 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
34072 TATTAGCTGT
34082 ATGACAACTAATA-ATTTTGC
1 ATGACAACTAATACATTTTGC
34102 ATGACAACTAATACATTTT
1 ATGACAACTAATACATTTT
34121 TCTTTACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (21 bp):
ATGACAACTAATACATTTTGC
Found at i:34782 original size:29 final size:29
Alignment explanation
Indices: 34703--34782 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 29
34693 TTATGTATCC
*
34703 TAAAATTTTATAAATTCAAGTTTATCTCT
1 TAAAATTTTATAAATTCAAATTTATCTCT
* * * * *
34732 TAAAATTTTATAAGTACGAATTTATTTTT
1 TAAAATTTTATAAATTCAAATTTATCTCT
*
34761 TAAAATTTTATAAATTTAAATT
1 TAAAATTTTATAAATTCAAATT
34783 CGCCTTTAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (29 bp):
TAAAATTTTATAAATTCAAATTTATCTCT
Found at i:40652 original size:2 final size:2
Alignment explanation
Indices: 40645--40675 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40635 ATAAATTTAG
40645 AT AT 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 A
40676 AAATTTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43276 original size:15 final size:16
Alignment explanation
Indices: 43240--43289 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
43230 ACTTTCATTG
43240 ATGTATGTATTAATGC
1 ATGTATGTATTAATGC
* *
43256 ATGTATGT-TTGATGT
1 ATGTATGTATTAATGC
*
43271 ATGTATATATTAATGC
1 ATGTATGTATTAATGC
43287 ATG
1 ATG
43290 ATGGATGTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (16 bp):
ATGTATGTATTAATGC
Found at i:43296 original size:27 final size:29
Alignment explanation
Indices: 43240--43297 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
43230 ACTTTCATTG
*
43240 ATGTATGTATTAATGCATGTATGTTTGATGT
1 ATGTATATATTAATGCATGTATG--TGATGT
43271 ATGTATATATTAATGCATG-ATG-GATGT
1 ATGTATATATTAATGCATGTATGTGATGT
43298 TGGGGATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 5 0.19
30 3 0.12
31 18 0.69
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.45
Consensus pattern (29 bp):
ATGTATATATTAATGCATGTATGTGATGT
Found at i:49214 original size:239 final size:236
Alignment explanation
Indices: 48789--49264 Score: 884
Period size: 239 Copynumber: 2.0 Consensus size: 236
48779 TCAAGGCAAC
48789 CTGATTTTATACCCATCGAAAAACCAAACCAAATCGAAGTCTTACGCTTAACAAACTGTTCCAAA
1 CTGATTTTATACCCATCGAAAAACCAAACCAAATCGAAGTCTTACGCTTAACAAACTGTTCCAAA
48854 TACGATTTAAAGGGATACGGAATCATGCTCTACCCACAATACATGGTGTACATACTTCAAACATA
66 TACGATTTAAAGGGATACGGAATCATGCTCTACCCACAATACATGGTGTACATACTTCAAACATA
48919 AAGGGGTAATATGCGCTTAGGCTTACCGTAACTTGCTACAACGGCTGGCCTGGTTA-TCTATGTG
131 AAGGGGTAATATGCGCTTAGGCTTACCGTAACTTGCTACAACGGCTGGCCTGGTTATTCTATGTG
48983 TTACCGACACGCCATTAACGAAACCTCAACTCATACAACAA
196 TTACCGACACGCCATTAACGAAACCTCAACTCATACAACAA
49024 CTGATTTTTATACCCATCGAAAAACCAAAACCAAAATCGAAGTCTTACGCTTAAC-AACTGTTCC
1 CTGA-TTTTATACCCATCGAAAAACC-AAACC-AAATCGAAGTCTTACGCTTAACAAACTGTTCC
*
49088 AAATACGATTTAAAGGGATACTGAATCATGCTCTACCCACAAATACATGGTGTACATACTTCAAA
63 AAATACGATTTAAAGGGATACGGAATCATGCTCTACCCAC-AATACATGGTGTACATACTTCAAA
49153 CATAAAAGGGGTAATATGCGCTTAGGCTTACCGTAACTTGCTACAACGGCTGGCCTGGTTATTCT
127 CAT-AAAGGGGTAATATGCGCTTAGGCTTACCGTAACTTGCTACAACGGCTGGCCTGGTTATTCT
49218 ATGTGTTACCGACACGCCATTAACGAAACCTCAACTCATACAACAA
191 ATGTGTTACCGACACGCCATTAACGAAACCTCAACTCATACAACAA
49264 C
1 C
49265 GGTGACGGAA
Statistics
Matches: 234, Mismatches: 1, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
235 4 0.02
236 21 0.09
237 53 0.23
238 49 0.21
239 57 0.24
240 50 0.21
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (236 bp):
CTGATTTTATACCCATCGAAAAACCAAACCAAATCGAAGTCTTACGCTTAACAAACTGTTCCAAA
TACGATTTAAAGGGATACGGAATCATGCTCTACCCACAATACATGGTGTACATACTTCAAACATA
AAGGGGTAATATGCGCTTAGGCTTACCGTAACTTGCTACAACGGCTGGCCTGGTTATTCTATGTG
TTACCGACACGCCATTAACGAAACCTCAACTCATACAACAA
Found at i:52624 original size:23 final size:23
Alignment explanation
Indices: 52598--52644 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
52588 GTCACCACAG
*
52598 CTCGTATAAATGCACCGAAGTGC
1 CTCGTAGAAATGCACCGAAGTGC
* *
52621 CTCGTAGAATTGCACCGTAGTGC
1 CTCGTAGAAATGCACCGAAGTGC
52644 C
1 C
52645 ATATAATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (23 bp):
CTCGTAGAAATGCACCGAAGTGC
Found at i:52893 original size:149 final size:149
Alignment explanation
Indices: 52623--52927 Score: 583
Period size: 149 Copynumber: 2.0 Consensus size: 149
52613 CGAAGTGCCT
* *
52623 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
52688 CATATACATATGCTAGGGATCAAGTATGTATCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTATCTTTCCAGACTTCACACATGTTCCAAAGAATATA
52753 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
52772 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
52837 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTATCTTTCCAGACTTCACACATGTTCCAAAGAATATA
52902 CATATGTCCCTAAGAACCG
131 CATATGTCCCTAAGAACCG
52921 CGTAGAC
1 CGTAGAC
52928 CCTCGACTCT
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGACTTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTATCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCTAAGAACCG
Found at i:53535 original size:2 final size:2
Alignment explanation
Indices: 53528--53561 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
53518 TCAGTTTCAC
*
53528 AT AT AT AT AT AT AT AT AT AT AT AT AC AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53562 GCACATACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:54024 original size:21 final size:21
Alignment explanation
Indices: 54000--54044 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
53990 TCTTGTTCGT
* *
54000 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
54021 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
54042 TTG
1 TTG
54045 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:56305 original size:20 final size:20
Alignment explanation
Indices: 56280--56317 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
56270 TTAACCTTAT
56280 AGTATCGATATTGTTCTTTC
1 AGTATCGATATTGTTCTTTC
56300 AGTATCGATATTGTTCTT
1 AGTATCGATATTGTTCTT
56318 CTTGTACCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (20 bp):
AGTATCGATATTGTTCTTTC
Found at i:58201 original size:6 final size:7
Alignment explanation
Indices: 58185--58210 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
58175 GAAGTAATGT
58185 AAAAACA
1 AAAAACA
58192 AAAAACA
1 AAAAACA
58199 AAAAACA
1 AAAAACA
58206 AAAAA
1 AAAAA
58211 TTTAGGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:61419 original size:19 final size:19
Alignment explanation
Indices: 61395--61433 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
61385 ATTATTTTAA
61395 TTTAAAATTTT-GATATATT
1 TTTAAAATTTTAGATA-ATT
*
61414 TTTAAATTTTTAGATAATT
1 TTTAAAATTTTAGATAATT
61433 T
1 T
61434 AAATCAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTAAAATTTTAGATAATT
Found at i:61747 original size:13 final size:13
Alignment explanation
Indices: 61731--61756 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61721 TAAATATATT
61731 TAATAAAAGTATA
1 TAATAAAAGTATA
61744 TAATAAAAGTATA
1 TAATAAAAGTATA
61757 AATTCATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
TAATAAAAGTATA
Found at i:65303 original size:47 final size:48
Alignment explanation
Indices: 65233--65325 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
65223 ACTATGATTA
* *
65233 TCATTTTAAATTAGTCCTCAAAC-TTTTCAACATTTTAGTTTCATCCT
1 TCATTCTAAATTAGTCCTCAAACTTTTTCAACATTTTAATTTCATCCT
*
65280 TCATTCTAAATTGGTCC-CTAAACTTTTTCAACATTTTAATTTCATC
1 TCATTCTAAATTAGTCCTC-AAACTTTTTCAACATTTTAATTTCATC
65326 TCAAACTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
46 1 0.02
47 19 0.46
48 21 0.51
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.46
Consensus pattern (48 bp):
TCATTCTAAATTAGTCCTCAAACTTTTTCAACATTTTAATTTCATCCT
Found at i:67000 original size:4 final size:4
Alignment explanation
Indices: 66991--67532 Score: 922
Period size: 4 Copynumber: 135.0 Consensus size: 4
66981 CTCTTATGGT
66991 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
67039 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
67087 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
67135 CATATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 --TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
67185 TATG TATG TATG TATG TATG TATA TATG TATG CATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
67233 CATG CATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * * *
67281 TATG TATG TATG TATG CATG CATG CATG CATG CATG CATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
67329 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
67377 TATG TATG TATG TATG TATG TATG TATG TATG CATG CATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
67425 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
67473 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
67521 TATG TATG TATG
1 TATG TATG TATG
67533 CATGCATGTG
Statistics
Matches: 524, Mismatches: 12, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
4 521 0.99
6 3 0.01
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:71436 original size:60 final size:61
Alignment explanation
Indices: 71359--71507 Score: 237
Period size: 60 Copynumber: 2.4 Consensus size: 61
71349 GTTAATAGGA
*
71359 GCCTAATATTTTCGTATATACTCAAATGAAGACTTAATCTTTC-AAAAGAGTTGAATAAGG
1 GCCTAATATTTTTGTATATACTCAAATGAAGACTTAATCTTTCAAAAAGAGTTGAATAAGG
* *
71419 GCCTAATATTTTTGTATATACTCAAATGAGGACTTAATCTTTCAAAAAGAGTTTAATAAGG
1 GCCTAATATTTTTGTATATACTCAAATGAAGACTTAATCTTTCAAAAAGAGTTGAATAAGG
* *
71480 GCCTAATATTTTTTTAATATACTTAAAT
1 GCCTAATATTTTTGT-ATATACTCAAAT
71508 AAAGTTCTAA
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
60 41 0.50
61 30 0.37
62 11 0.13
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38
Consensus pattern (61 bp):
GCCTAATATTTTTGTATATACTCAAATGAAGACTTAATCTTTCAAAAAGAGTTGAATAAGG
Found at i:72137 original size:23 final size:25
Alignment explanation
Indices: 72085--72140 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 25
72075 TAATGACTCC
72085 GAATCATTCAAAATGTACTTCTGTGCT
1 GAATCATTCAAAATGTA-TTCTGT-CT
72112 GAATCATTCAAAACTGT-TT-TGT-T
1 GAATCATTCAAAA-TGTATTCTGTCT
72135 GAATCA
1 GAATCA
72141 GTCAGCACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 7 0.25
25 3 0.11
26 2 0.07
27 13 0.46
28 3 0.11
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (25 bp):
GAATCATTCAAAATGTATTCTGTCT
Found at i:81570 original size:40 final size:40
Alignment explanation
Indices: 81513--81592 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
81503 TCATAATACA
81513 CACATCATGCGAATTTAAAGCATTCAACTTACAATATTTT
1 CACATCATGCGAATTTAAAGCATTCAACTTACAATATTTT
* *
81553 CACATCATGTGAGTTTAAAGCATTCAACTTACAATATTTT
1 CACATCATGCGAATTTAAAGCATTCAACTTACAATATTTT
81593 AACAGTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (40 bp):
CACATCATGCGAATTTAAAGCATTCAACTTACAATATTTT
Found at i:89627 original size:16 final size:17
Alignment explanation
Indices: 89606--89638 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
89596 TTTCTATAAC
89606 TACAAAAATA-TTATTT
1 TACAAAAATATTTATTT
*
89622 TACAAATATATTTATTT
1 TACAAAAATATTTATTT
89639 GAATATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
TACAAAAATATTTATTT
Found at i:90797 original size:31 final size:31
Alignment explanation
Indices: 90759--90945 Score: 322
Period size: 31 Copynumber: 6.0 Consensus size: 31
90749 CCCGAAGGAC
* * *
90759 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
90790 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
90821 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
90852 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
90883 CAGTCCATATGTCCCGAATAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
90914 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
90945 C
1 C
90946 CCTCGACCCT
Statistics
Matches: 150, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 149 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:92953 original size:172 final size:171
Alignment explanation
Indices: 92529--93011 Score: 761
Period size: 171 Copynumber: 2.8 Consensus size: 171
92519 GGATGTTACA
92529 TATGTATAAATGAATAGATAATTTGAAGGTGATTGACTACTTCGATTCAGACTTTAAGTATTCAT
1 TATGTATAAATGAATAGATAATTTGAAGGTGATTGACTACTTCGATTCAGACTTTAAGTATTCAT
* * * * * * *
92594 GGTCATTACAAACTGAATGAAAAATTTTTGGCAGTTTTCTTTAGTGGTACGTGAGTGGCTAAACA
66 GGTCATTACAAACTGAGTGAAAAAATATTGGCAGTTTCCTTAAGTGGTACGTGAGTGGCTGATCA
*
92659 ATTGGTGCTCGCACACCTAAAAGGGACAAAAGCTACATGCT
131 ACTGGTGCTCGCACACCTAAAAGGGACAAAAGCTACATGCT
92700 TATGTATAAATGAATAGATAATTTGAAGGTGATTGACTACTTCGATTCAGACTTTAAGTATTCAT
1 TATGTATAAATGAATAGATAATTTGAAGGTGATTGACTACTTCGATTCAGACTTTAAGTATTCAT
*
92765 GGTCATTACAAACTGAGTGAAAAAATATTGGCAGTTTCCTTAAGTGGTACGTGAGTGGTTGATCA
66 GGTCATTACAAACTGAGTGAAAAAATATTGGCAGTTTCCTTAAGTGGTACGTGAGTGGCTGATCA
* * *
92830 ACTGGTGCTCGTATACCTAAAAGGGACAAAGGACTACATGCT
131 ACTGGTGCTCGCACACCTAAAAGGGACAAAAG-CTACATGCT
* * *
92872 TATTTATAAATGAATAGATAATTTGAAGGTGATTGATTACTTCGATTCAAACTTTAAGTATTCAT
1 TATGTATAAATGAATAGATAATTTGAAGGTGATTGACTACTTCGATTCAGACTTTAAGTATTCAT
* * * *
92937 GGTCATTACGAACTGAGTGAGAAAATATTGACAGTTTCCTTCAA-TGGTTCGTGAGTGGCTGATC
66 GGTCATTACAAACTGAGTGAAAAAATATTGGCAGTTTCCTT-AAGTGGTACGTGAGTGGCTGATC
*
93001 AACTGCTGCTC
130 AACTGGTGCTC
93012 ATGAAAGTTA
Statistics
Matches: 289, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
171 150 0.52
172 137 0.47
173 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (171 bp):
TATGTATAAATGAATAGATAATTTGAAGGTGATTGACTACTTCGATTCAGACTTTAAGTATTCAT
GGTCATTACAAACTGAGTGAAAAAATATTGGCAGTTTCCTTAAGTGGTACGTGAGTGGCTGATCA
ACTGGTGCTCGCACACCTAAAAGGGACAAAAGCTACATGCT
Found at i:93939 original size:17 final size:17
Alignment explanation
Indices: 93919--93953 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
93909 AATACATAAC
93919 AAGATAAACT-TGAACAA
1 AAGATAAA-TATGAACAA
93936 AAGATAAATATGAACAA
1 AAGATAAATATGAACAA
93953 A
1 A
93954 TCTGATTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.17
Consensus pattern (17 bp):
AAGATAAATATGAACAA
Found at i:94590 original size:13 final size:13
Alignment explanation
Indices: 94572--94601 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
94562 TTCCTTTAAA
*
94572 AAAATCATTTTTC
1 AAAATCACTTTTC
94585 AAAATCACTTTTC
1 AAAATCACTTTTC
94598 AAAA
1 AAAA
94602 ATAATATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATCACTTTTC
Found at i:111033 original size:24 final size:24
Alignment explanation
Indices: 110999--111044 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
110989 TAATAGCTTC
110999 CTAACAAACTCATGCACAACAACT
1 CTAACAAACTCATGCACAACAACT
*
111023 CTAACAGACTCATGCACAACAA
1 CTAACAAACTCATGCACAACAA
111045 GCAATGTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.33, G:0.07, T:0.15
Consensus pattern (24 bp):
CTAACAAACTCATGCACAACAACT
Found at i:111654 original size:35 final size:35
Alignment explanation
Indices: 111580--111654 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
111570 ATTTAAACAT
* **
111580 TTAAAAATTCGAATTACATAATTGAAACATAAAGT
1 TTAAAAATTCAAATTACATAATTGAAACATAAAAC
* *
111615 TTAAAAATTCAAATTGCATAATCT-AAATATAAAAC
1 TTAAAAATTCAAATTACATAAT-TGAAACATAAAAC
111650 TTAAA
1 TTAAA
111655 TATTAAAAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 33 0.97
36 1 0.03
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.32
Consensus pattern (35 bp):
TTAAAAATTCAAATTACATAATTGAAACATAAAAC
Found at i:113600 original size:31 final size:31
Alignment explanation
Indices: 113562--113717 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
113552 CCCGAAGGAC
* * *
113562 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
113593 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
113624 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
113655 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
113686 CAATCCCTATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
113717 C
1 C
113718 CCTCGACCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 117 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:114281 original size:20 final size:22
Alignment explanation
Indices: 114247--114304 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
114237 CCTATTCATA
114247 ATCA-CATATTCATATAGTTTAT
1 ATCATCATA-TCATATAGTTTAT
*
114269 -T-ATCATATCATATGGTTTAT
1 ATCATCATATCATATAGTTTAT
*
114289 ATCATCATAACATATA
1 ATCATCATATCATATA
114305 CATATTCACA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 13 0.43
21 6 0.20
22 11 0.37
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (22 bp):
ATCATCATATCATATAGTTTAT
Found at i:114755 original size:21 final size:21
Alignment explanation
Indices: 114731--114775 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
114721 TTTTGTTCGT
114731 TTGAAGGGGTATCAG-TTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
* *
114752 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
114773 TTG
1 TTG
114776 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:118131 original size:31 final size:31
Alignment explanation
Indices: 118093--118248 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
118083 CCCGAAGGAC
* * *
118093 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
118124 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
118155 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
118186 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
118217 CAGTCCCTATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
118248 C
1 C
118249 CCTCGACCCT
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:118824 original size:19 final size:21
Alignment explanation
Indices: 118782--118824 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
118772 TTCATAATCA
118782 CATATTCATATAGTTTATTAT
1 CATATTCATATAGTTTATTAT
*
118803 CATA-TCATATGGTTTA-TAT
1 CATATTCATATAGTTTATTAT
118822 CAT
1 CAT
118825 CATAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 11 0.52
21 4 0.19
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (21 bp):
CATATTCATATAGTTTATTAT
Found at i:118833 original size:22 final size:20
Alignment explanation
Indices: 118788--118834 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
118778 ATCACATATT
*
118788 CATATAGTTTATTATCATAT
1 CATATAGTTTATTATCATAA
*
118808 CATATGGTTTATATCATCATAA
1 CATATAGTTTAT-T-ATCATAA
118830 CATAT
1 CATAT
118835 CACATATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 1 0.04
22 11 0.48
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (20 bp):
CATATAGTTTATTATCATAA
Found at i:119288 original size:21 final size:21
Alignment explanation
Indices: 119264--119304 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
119254 TTTTGTTCGT
* *
119264 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
119285 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
119305 TTTGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:121951 original size:100 final size:100
Alignment explanation
Indices: 121771--121952 Score: 258
Period size: 100 Copynumber: 1.8 Consensus size: 100
121761 AGCAATGGGC
* * *
121771 ATCGATACCATGGTAAGGGTATCGATACCAGTAAACATCGAATCTAATTTTGGTATCGATACCTA
1 ATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAAGCTAATTTTGGTATCGATACATA
*
121836 GAGGGAGTATTGATACCATAGCATAGCATAGGGGT
66 GAGGGAGTATCGATACCATAGCATAGCATAGGGGT
* ** * *
121871 ATCGATACCATGGTGAGGGTATCGATACCAGGCTATATCGAAGCTAATTTTGGTATTGATACAT-
1 ATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAAGCTAATTTTGGTATCGATACATA
*
121935 GAAGGGGGTATCGATACC
66 G-AGGGAGTATCGATACC
121953 CTAATAGGGT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 1 0.01
100 70 0.99
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (100 bp):
ATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAAGCTAATTTTGGTATCGATACATA
GAGGGAGTATCGATACCATAGCATAGCATAGGGGT
Found at i:121970 original size:22 final size:21
Alignment explanation
Indices: 121939--121996 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
121929 ATACATGAAG
* *
121939 GGGGTATCGATACCCTAA-TA
1 GGGGTATCGATACCATAAGCA
121959 GGGTAGTATCGATACCATAAGCA
1 GGG--GTATCGATACCATAAGCA
121982 GGGGTATCGATACCA
1 GGGGTATCGATACCA
121997 AAGGGGCCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 3 0.09
21 12 0.36
22 14 0.42
23 4 0.12
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (21 bp):
GGGGTATCGATACCATAAGCA
Found at i:122638 original size:134 final size:135
Alignment explanation
Indices: 122435--122692 Score: 401
Period size: 134 Copynumber: 1.9 Consensus size: 135
122425 AGGATGCCCT
* *
122435 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAACATAATTTGGTTGAAATGCATATAAGTG
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAACATAATATGGTTGAAATGCATATAAGTA
* * * *
122500 CATTATCAAC-AGAAAGTATGCTAGAGTTGAAATGCATATGGGTGCATTATCAACAGAAGAGCAT
66 CATTATCAACAAAAAAGCATACTAGAGTTGAAATGCATATGGGTACATTATCAACAGAAGAGCAT
122564 GCTAA
131 GCTAA
* * * **
122569 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAATATACTATGGTTGAAATGTATATGGGTA
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAACATAATATGGTTGAAATGCATATAAGTA
*
122634 CATTATCAACAAAAAAGCATACTATAGTTGAAATGCATATGGGTACATTATCAACAGAA
66 CATTATCAACAAAAAAGCATACTAGAGTTGAAATGCATATGGGTACATTATCAACAGAA
122693 AAGATGTTAT
Statistics
Matches: 111, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
134 68 0.61
135 43 0.39
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.28
Consensus pattern (135 bp):
AGTTGAAATGTATATGGGTACATTATCAACAGAAAAACATAATATGGTTGAAATGCATATAAGTA
CATTATCAACAAAAAAGCATACTAGAGTTGAAATGCATATGGGTACATTATCAACAGAAGAGCAT
GCTAA
Found at i:122695 original size:45 final size:45
Alignment explanation
Indices: 122434--122695 Score: 328
Period size: 45 Copynumber: 5.8 Consensus size: 45
122424 AAGGATGCCC
* * * *
122434 TAGTTGAAATGTATATGGGTACATTATCAACAGAAAAACATAATT
1 TAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGCATACTA
* ** * * *
122479 TGGTTGAAATGCATATAAGTGCATTATCAACAG-AAAGTATGCTA
1 TAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGCATACTA
* * * *
122523 GAGTTGAAATGCATATGGGTGCATTATCAACAGAAGAGCATGCTA
1 TAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGCATACTA
* * **
122568 AAGTTGAAATGTATATGGGTACATTATCAACAGAAAAATATACTA
1 TAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGCATACTA
* * *
122613 TGGTTGAAATGTATATGGGTACATTATCAACAAAAAAGCATACTA
1 TAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGCATACTA
122658 TAGTTGAAATGCATATGGGTACATTATCAACAGAAAAG
1 TAGTTGAAATGCATATGGGTACATTATCAACAGAAAAG
122696 ATGTTATAAC
Statistics
Matches: 185, Mismatches: 31, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
44 35 0.19
45 150 0.81
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (45 bp):
TAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGCATACTA
Found at i:122729 original size:90 final size:89
Alignment explanation
Indices: 122435--122734 Score: 235
Period size: 90 Copynumber: 3.3 Consensus size: 89
122425 AGGATGCCCT
* * * **
122435 AGTTGAAATGT-ATATGG-GTACATTATCAACAGAAAAA-CATAATTTGGTTGAAATGCATATAA
1 AGTTGAAA-GTCATATGGTGT--ATTATCAACA-AAAAAGCATACTATAGTTGAAATGCATATGG
* * *
122497 GTGCATTATCAACAG-AAAGTATGCTA-G
62 GTACATTATCAACAGAAAAG-ATGATATA
* * * * * *
122524 AGTTGAAA-TGCATATGGGTGCATTATCAACAGAAGAGCATGCTAAAGTTGAAATGTATATGGGT
1 AGTTGAAAGT-CATAT-GGTGTATTATCAACAAAAAAGCATACTATAGTTGAAATGCATATGGGT
122588 ACATTATCAACAGAAAA-AT-ATACTA
64 ACATTATCAACAGAAAAGATGATA-TA
*
122613 TGGTTGAAATGT-ATATGG-GTACATTATCAACAAAAAAGCATACTATAGTTGAAATGCATATGG
1 -AGTTGAAA-GTCATATGGTGT--ATTATCAACAAAAAAGCATACTATAGTTGAAATGCATATGG
*
122676 GTACATTATCAACAGAAAAGATGTTATA
62 GTACATTATCAACAGAAAAGATGATATA
* *
122704 ACTT-AAAGTACATAATGGTGTATTATAAACA
1 AGTTGAAAGT-CAT-ATGGTGTATTATCAACA
122735 TAAATGAATG
Statistics
Matches: 167, Mismatches: 25, Indels: 37
0.73 0.11 0.16
Matches are distributed among these distances:
87 3 0.02
88 8 0.05
89 58 0.35
90 84 0.50
91 9 0.05
92 5 0.03
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (89 bp):
AGTTGAAAGTCATATGGTGTATTATCAACAAAAAAGCATACTATAGTTGAAATGCATATGGGTAC
ATTATCAACAGAAAAGATGATATA
Found at i:123589 original size:183 final size:182
Alignment explanation
Indices: 123238--123587 Score: 494
Period size: 182 Copynumber: 1.9 Consensus size: 182
123228 GAACACTAAC
* * *
123238 TTACACAGTGTAAAATTCTTTAGTTTTACACAGATTTAGGATTGTTGAATGAGTGAAAATAGATG
1 TTACACAATGTAAAACTCTTTAGTTTTACACAGATTTAGGATTGTTGAATGAGTGAAAATAGATA
* * * *
123303 GTTGAGATTGACTCATTGTTTTTTTTGTTTCCATTGAATATTTTCTCATTTTCTACTATTAATTT
66 GTTGAGATTGACTCATTGTTTTTTTTATTTCCAATGAATATTTTCTCATTTCCTACTATTAATCT
* *
123368 CAGTCATCTATTTTCACTCATCCAATGGTCCATATATATGGAATGGGATCTG
131 CAATCATCTATTTTCACTCATCCAATGCTCCATATATATGGAATGGGATCTG
* *
123420 TTACACAATGTAGAACTCTTTTAGTTTTACACAGATTTAGGATTGTTGGATGAGTGAAAATAGAT
1 TTACACAATGTAAAACTC-TTTAGTTTTACACAGATTTAGGATTGTTGAATGAGTGAAAATAGAT
*
123485 AGTTGAGATTGACTCCTTG-TTTTTTTATTTCCAATGAATATCTTT-TCATTTCCTA-TAGTTAA
65 AGTTGAGATTGACTCATTGTTTTTTTTATTTCCAATGAATAT-TTTCTCATTTCCTACTA-TTAA
* * *
123547 TCTCAATTATCTA-TTTCTATTTATCCAATGCT-CATATATAT
128 TCTCAATCATCTATTTTC-ACTCATCCAATGCTCCATATATAT
123588 ATATATATAT
Statistics
Matches: 149, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
181 15 0.10
182 69 0.46
183 65 0.44
ACGTcount: A:0.28, C:0.13, G:0.14, T:0.44
Consensus pattern (182 bp):
TTACACAATGTAAAACTCTTTAGTTTTACACAGATTTAGGATTGTTGAATGAGTGAAAATAGATA
GTTGAGATTGACTCATTGTTTTTTTTATTTCCAATGAATATTTTCTCATTTCCTACTATTAATCT
CAATCATCTATTTTCACTCATCCAATGCTCCATATATATGGAATGGGATCTG
Found at i:123971 original size:2 final size:2
Alignment explanation
Indices: 123959--123995 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
123949 AATATAAAAT
*
123959 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
123996 AATGATGGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:126205 original size:2 final size:2
Alignment explanation
Indices: 126198--126230 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
126188 CAAGTAATTC
126198 AT AT AT 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
126231 CACTTACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:130765 original size:30 final size:31
Alignment explanation
Indices: 130731--130800 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
130721 AAAACATAAT
** *
130731 ATTTGGT-AATTTTGTTTTTATTTAGTTAAG
1 ATTTGGTCAATTTCATTTTTATTTAATTAAG
* *
130761 ATTTGGTCACTTTCATTTTTATTTAATTAAT
1 ATTTGGTCAATTTCATTTTTATTTAATTAAG
*
130792 ATGTGGTCA
1 ATTTGGTCA
130801 CTGAGGGTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.24, C:0.06, G:0.14, T:0.56
Consensus pattern (31 bp):
ATTTGGTCAATTTCATTTTTATTTAATTAAG
Found at i:132172 original size:18 final size:17
Alignment explanation
Indices: 132118--132166 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
132108 TTGGATCCTT
* *
132118 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
132136 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
132154 AGTGCATTCGATG
1 AGTGCA-TCGATG
132167 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:132275 original size:64 final size:64
Alignment explanation
Indices: 132139--132276 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 64
132129 GCACTAAGAG
* * * ***
132139 TGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAATGCATCGATGCATGGCAAA
* *
132203 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAATGCATCGATGCAT-G-AA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAATGCATCGATGCATGGCAA
132265 A
64 A
132266 TGCATTCGATG
1 TGCA-TCGATG
132277 TTCAATTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
63 4 0.06
64 34 0.54
65 22 0.35
66 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAATGCATCGATGCATGGCAAA
Found at i:132717 original size:16 final size:16
Alignment explanation
Indices: 132670--132717 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
132660 CCTTACTACA
*
132670 ACACTTCTCCCCTTTA
1 ACACTTCTCCCCTTTT
* * *
132686 ACACTTTTACACTTTT
1 ACACTTCTCCCCTTTT
132702 ACACTTCTCCCCTTTT
1 ACACTTCTCCCCTTTT
132718 TGTTAAATCA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.19, C:0.38, G:0.00, T:0.44
Consensus pattern (16 bp):
ACACTTCTCCCCTTTT
Found at i:135037 original size:20 final size:21
Alignment explanation
Indices: 134949--135040 Score: 71
Period size: 21 Copynumber: 4.3 Consensus size: 21
134939 CTTGTGCATT
* *
134949 GATGCATATTCAAGGCGTGCATC
1 GATGCACATTCAA-G-GTGTATC
* * *
134972 GGTGCACCTTCATGGTGTATC
1 GATGCACATTCAAGGTGTATC
*
134993 GATGCACATTCAAGGATGCATC
1 GATGCACATTCAAGG-TGTATC
*
135015 GATGCAC-TGT-TAGGTGTATC
1 GATGCACAT-TCAAGGTGTATC
135035 GATGCA
1 GATGCA
135041 TGAAGCACAA
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
20 11 0.20
21 22 0.39
22 14 0.25
23 9 0.16
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (21 bp):
GATGCACATTCAAGGTGTATC
Found at i:135040 original size:42 final size:44
Alignment explanation
Indices: 134949--135040 Score: 118
Period size: 42 Copynumber: 2.1 Consensus size: 44
134939 CTTGTGCATT
* * *
134949 GATGCATATTCAAGGCGTGCATCGGTGCACCTTCATGGTGTATC
1 GATGCACATTCAAGGCATGCATCGATGCACCTTCATGGTGTATC
*
134993 GATGCACATTCAAGG-ATGCATCGATGCA-CTGTTA-GGTGTATC
1 GATGCACATTCAAGGCATGCATCGATGCACCT-TCATGGTGTATC
135035 GATGCA
1 GATGCA
135041 TGAAGCACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 16 0.37
43 13 0.30
44 14 0.33
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (44 bp):
GATGCACATTCAAGGCATGCATCGATGCACCTTCATGGTGTATC
Found at i:140007 original size:17 final size:17
Alignment explanation
Indices: 139985--140022 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
139975 TTGACGGGCA
139985 TCGAATCGAGACCGGAG
1 TCGAATCGAGACCGGAG
140002 TCGAATCGAGACCGGAG
1 TCGAATCGAGACCGGAG
140019 TCGA
1 TCGA
140023 CATTTGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.34, T:0.13
Consensus pattern (17 bp):
TCGAATCGAGACCGGAG
Found at i:140882 original size:18 final size:17
Alignment explanation
Indices: 140828--140876 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
140818 TTGGACCCTT
* *
140828 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
140846 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
140864 AGTGCATTCGATG
1 AGTGCA-TCGATG
140877 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:140945 original size:46 final size:45
Alignment explanation
Indices: 140847--140952 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 45
140837 GTGCACTAAG
* *
140847 AGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* * *
140892 AGTGCATCGATGGATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
140938 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
140953 GGTATGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
45 28 0.53
46 22 0.42
47 3 0.06
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:144084 original size:9 final size:9
Alignment explanation
Indices: 144070--144121 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
144060 TTTATAATTA
144070 TTTATTTAT
1 TTTATTTAT
*
144079 TTTATTAAT
1 TTTATTTAT
*
144088 TTTATTTAC
1 TTTATTTAT
**
144097 TTTA-AAAT
1 TTTATTTAT
144105 TTTATTTAT
1 TTTATTTAT
144114 ATTTATTT
1 -TTTATTT
144122 TATAATATTA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
8 5 0.15
9 21 0.64
10 7 0.21
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATTTAT
Found at i:144091 original size:18 final size:18
Alignment explanation
Indices: 144070--144120 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
144060 TTTATAATTA
144070 TTTATTTATTTTATTAAT
1 TTTATTTATTTTATTAAT
* *
144088 TTTATTTACTTTA-AAAT
1 TTTATTTATTTTATTAAT
144105 TTTATTTATATTTATT
1 TTTATTTAT-TTTATT
144121 TTATAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTATTTTATTAAT
Found at i:144105 original size:17 final size:18
Alignment explanation
Indices: 144060--144112 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
144050 TGTGAATTTT
* *
144060 TTTATAATTATTTATTTAT
1 TTTATAAAT-TTTATTTAC
*
144079 TTTATTAATTTTATTTAC
1 TTTATAAATTTTATTTAC
144097 TTTA-AAATTTTATTTA
1 TTTATAAATTTTATTTA
144113 TATTTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 11 0.37
18 12 0.40
19 7 0.23
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTATAAATTTTATTTAC
Found at i:144116 original size:23 final size:23
Alignment explanation
Indices: 144081--144138 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
144071 TTATTTATTT
144081 TATTAATTT-TATTTACTTTAAAA
1 TATT-ATTTATATTTACTTTAAAA
* * *
144104 TTTTATTTATATTTATTTTATAA
1 TATTATTTATATTTACTTTAAAA
*
144127 TATTATTAATAT
1 TATTATTTATAT
144139 ATGTATGTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTATTTATATTTACTTTAAAA
Done.