Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006043.1 Hibiscus syriacus cultivar Beakdansim tig00014279_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: 63785
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1898 original size:20 final size:20
Alignment explanation
Indices: 1873--1996 Score: 86
Period size: 20 Copynumber: 5.6 Consensus size: 20
1863 ACTAAAATGA
*
1873 ATGAAATGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
*
1893 ATGAAAGGATGACATAACTAAAATGC
1 ATGAAAGGATG-CAT---T--AAGGC
**
1919 ATGAAATAATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
* *
1939 ATAAAAGGATGGCATAACTTAAATGC
1 ATGAAAGGAT-GC---A-TT-AAGGC
1965 ATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCATTAAGGC
1985 ATGAAAGGATGC
1 ATGAAAGGATGC
1997 CATAACTAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
20 37 0.46
21 7 0.09
22 2 0.02
24 2 0.02
25 7 0.09
26 26 0.32
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.22
Consensus pattern (20 bp):
ATGAAAGGATGCATTAAGGC
Found at i:1912 original size:46 final size:46
Alignment explanation
Indices: 1859--2190 Score: 379
Period size: 46 Copynumber: 7.3 Consensus size: 46
1849 AAACCGAATT
* *
1859 CATAACTAAAATGAATGAAATGATGCATTAAGGCATGAAAGGATGA
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGA
** * *
1905 CATAACTAAAATGCATGAAATAATGCATTAAGGCATAAAAGGATGG
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGA
* *
1951 CATAACTTAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGC
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGA
* *
1997 CATAACTAAAATGCATGAAAGTACT-CATTAAGGCATG-AAGGATGC
1 CATAACTAAAATGCATGAAAGGA-TGCATTAAGGCATGAAAGGATGA
* * ** *
2042 CATAAATAAAATGGATG-AAGGATGCATTAAGTTATGAAATGAT-A
1 CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGA
*
2086 CCATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG-
1 -CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGA
* * * * * *
2132 CTATGATTAAAATGCATGAACGGATGTATTAATGCATGAAAAGA-GA
1 C-ATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGA
*
2178 CCATAACTGAAAT
1 -CATAACTAAAAT
2191 TAATGAATAA
Statistics
Matches: 243, Mismatches: 34, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
43 1 0.00
44 14 0.06
45 45 0.19
46 181 0.74
47 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (46 bp):
CATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGA
Found at i:1971 original size:26 final size:26
Alignment explanation
Indices: 1891--2017 Score: 89
Period size: 26 Copynumber: 5.3 Consensus size: 26
1881 ATGCATTAAG
* *
1891 GCATGAAAGGATGACATAACTAAAAT
1 GCATGAAAGGATGGCATAACTTAAAT
** *
1917 GCATGAAATAAT-GC---A-TT-AAG
1 GCATGAAAGGATGGCATAACTTAAAT
*
1937 GCATAAAAGGATGGCATAACTTAAAT
1 GCATGAAAGGATGGCATAACTTAAAT
*
1963 GCATGAAAGGAT-GC---A-TT-AAG
1 GCATGAAAGGATGGCATAACTTAAAT
* *
1983 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGGCATAACTTAAAT
2009 GCATGAAAG
1 GCATGAAAG
2018 TACTCATTAA
Statistics
Matches: 75, Mismatches: 14, Indels: 24
0.66 0.12 0.21
Matches are distributed among these distances:
20 25 0.33
21 6 0.08
22 2 0.03
24 2 0.03
25 6 0.08
26 34 0.45
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (26 bp):
GCATGAAAGGATGGCATAACTTAAAT
Found at i:2112 original size:136 final size:138
Alignment explanation
Indices: 1859--2172 Score: 393
Period size: 136 Copynumber: 2.3 Consensus size: 138
1849 AAACCGAATT
* *
1859 CATAACTAAAATGAATGAAATGATGCATTAAGGCATGAAAGGATGACATAACTAAAATGCATGAA
1 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGACATAAATAAAATGCATGAA
* ** *
1924 ATAATGCATTAAGGCATAAAAGGATGGCATAACTTAAATGCATGAAAGGATGCATTAAGGCATGA
66 AGAATGCATTAAGGCATAAAAGGATACCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGA
1989 AAGGATGC
131 AAGGATGC
* *
1997 CATAACTAAAATGCATGAAA-GTACT-CATTAAGGCATG-AAGGATGCCATAAATAAAATGGATG
1 CATAACTAAAATGCATGAAATG-A-TGCATTAAGGCATGAAAGGATGACATAAATAAAATGCATG
* ** * * *
2059 -AAGGATGCATTAAGTTATGAAATGATACCATAACTAAAATGCATGAAATGATGCATTAAGGCAT
64 AAAGAATGCATTAAGGCATAAAAGGATACCATAACTAAAATGCATGAAAGGATGCATTAAGGCAT
2123 GAAAGGATGC
129 GAAAGGATGC
* * * ** * *
2133 TATGATTAAAATGCATGAACGGATGTATTAATGCATGAAA
1 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAA
2173 AGAGACCATA
Statistics
Matches: 151, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
135 1 0.01
136 91 0.60
137 26 0.17
138 32 0.21
139 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.24
Consensus pattern (138 bp):
CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGACATAAATAAAATGCATGAA
AGAATGCATTAAGGCATAAAAGGATACCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGA
AAGGATGC
Found at i:14495 original size:18 final size:19
Alignment explanation
Indices: 14472--14514 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
14462 CACTCTTAGC
14472 AACTT-AGAATCACTAGGT
1 AACTTAAGAATCACTAGGT
14490 AACTTAGAAGAATCACTAGGT
1 AACTT--AAGAATCACTAGGT
14511 AACT
1 AACT
14515 CACTTATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.23
21 17 0.77
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (19 bp):
AACTTAAGAATCACTAGGT
Found at i:18654 original size:20 final size:20
Alignment explanation
Indices: 18631--18680 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
18621 GGTATTTTCA
*
18631 TTAGGATTTATTT-CTTTATT
1 TTAGGATTTATTTACCTT-TT
*
18651 TTAGGATTATCTTTACCTTTT
1 TTAGGATT-TATTTACCTTTT
18672 TTAGGATTT
1 TTAGGATTT
18681 TGAAGGCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 9 0.35
21 14 0.54
22 3 0.12
ACGTcount: A:0.20, C:0.08, G:0.12, T:0.60
Consensus pattern (20 bp):
TTAGGATTTATTTACCTTTT
Found at i:25160 original size:5 final size:5
Alignment explanation
Indices: 25150--25194 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
25140 TTTCATTCAG
**
25150 TTTAT TTTAT TTTAT TTTAT CGTAT GCTTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT --TTTAT TTTAT TTTAT TTT
25195 TCTCTGAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
5 31 0.91
7 3 0.09
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:30032 original size:83 final size:80
Alignment explanation
Indices: 29926--30115 Score: 191
Period size: 82 Copynumber: 2.3 Consensus size: 80
29916 CATAATGGTA
** * *
29926 ACTTTAGCGGTGTTTTTATACAAACATTGCAATAAGATTAATATATAGAGGCGTTTATTCAACAA
1 ACTTTAGCGGCATTTTTATACAAAC-CT-CAATAAGATTAATATATAGAGGCATTT-TTCAACAA
29991 ATGTCGCAGCAAAGTAGT
63 ATGTCGCAGCAAAGTAGT
* * * * * * *
30009 ACTTTAGCGGCATTGTTAGACAAATGCCTCAATAGGTTTCATATATAGTGGCATTTTTCACCAAA
1 ACTTTAGCGGCATTTTTATACAAA--CCTCAATAAGATTAATATATAGAGGCATTTTTCAACAAA
* **
30074 TGTCGCATCGGAGTAGT
64 TGTCGCAGCAAAGTAGT
* *
30091 AATTTAGAGGCATTTTTATACAAAC
1 ACTTTAGCGGCATTTTTATACAAAC
30116 GCCGCAATAA
Statistics
Matches: 87, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
80 1 0.01
82 42 0.48
83 42 0.48
84 1 0.01
85 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (80 bp):
ACTTTAGCGGCATTTTTATACAAACCTCAATAAGATTAATATATAGAGGCATTTTTCAACAAATG
TCGCAGCAAAGTAGT
Found at i:30103 original size:82 final size:83
Alignment explanation
Indices: 29966--30124 Score: 203
Period size: 82 Copynumber: 1.9 Consensus size: 83
29956 AATAAGATTA
* * *
29966 ATATATAGAGGCGTTTATTCAACAAATGTCGCAGCAAAGTAGTACTTTAGCGGCATTGTTAGACA
1 ATATATAGAGGCATTTATTCAACAAATGTCGCAGCAAAGTAGTAATTTAGAGGCATTGTTAGACA
* *
30031 AATGCCTCAATAGGTTTC
66 AACGCCGCAATAGGTTTC
* * * ** * *
30049 ATATATAGTGGCATTT-TTCACCAAATGTCGCATCGGAGTAGTAATTTAGAGGCATTTTTATACA
1 ATATATAGAGGCATTTATTCAACAAATGTCGCAGCAAAGTAGTAATTTAGAGGCATTGTTAGACA
30113 AACGCCGCAATA
66 AACGCCGCAATA
30125 AGTAAAATTT
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
82 50 0.78
83 14 0.22
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (83 bp):
ATATATAGAGGCATTTATTCAACAAATGTCGCAGCAAAGTAGTAATTTAGAGGCATTGTTAGACA
AACGCCGCAATAGGTTTC
Found at i:32687 original size:43 final size:43
Alignment explanation
Indices: 32639--32841 Score: 210
Period size: 44 Copynumber: 4.6 Consensus size: 43
32629 TAAAAGTGGC
* *
32639 TATCACTTGTTGTTTAGTTATATTTGGATCGGCATAGAAGGGA
1 TATCACTTGTCGTTTAGTTATATTTGGATCGGCATAGATGGGA
*
32682 TATCACTTGTCGTTTAGTTGTATTTGGATCGGCCA-AGATGCGGA
1 TATCACTTGTCGTTTAGTTATATTTGGATCGG-CATAGATG-GGA
* * * * * *
32726 TATCACTTGTCATTTAGTTATATTTAGATTGCCTTAGATGGGG
1 TATCACTTGTCGTTTAGTTATATTTGGATCGGCATAGATGGGA
* * * *
32769 TTTGCACTTGTCGTTTAGTTATATTTGGACCGACTTAGATGGGAA
1 TAT-CACTTGTCGTTTAGTTATATTTGGATCGGCATAGATGGG-A
* * *
32814 AATCACTCGTTGTTTAGTTAATATTTGG
1 TATCACTTGTCGTTTAGTT-ATATTTGG
32842 GTTGACTTAG
Statistics
Matches: 133, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
43 39 0.29
44 85 0.64
45 9 0.07
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (43 bp):
TATCACTTGTCGTTTAGTTATATTTGGATCGGCATAGATGGGA
Found at i:32809 original size:88 final size:87
Alignment explanation
Indices: 32639--32859 Score: 239
Period size: 88 Copynumber: 2.5 Consensus size: 87
32629 TAAAAGTGGC
* * * * *
32639 TATCACTTGTTGTTTAGTTATATTTGGATCGGCATAGAAGGGATATCACTTGTCGTTTAGTTGTA
1 TATCACTTGTTGTTTAGTTATATTTGGATTGACTTAGATGGGATATCACTTGTCGTTTAGTTATA
* *
32704 TTTGGATCGGCCAAGATGCGG-A
66 TTTGGACCGACCAAGATG-GGAA
** * * * *
32726 TATCACTTGTCATTTAGTTATATTTAGATTGCCTTAGATGGGGTTTGCACTTGTCGTTTAGTTAT
1 TATCACTTGTTGTTTAGTTATATTTGGATTGACTTAGATGGGATAT-CACTTGTCGTTTAGTTAT
**
32791 ATTTGGACCGACTTAGATGGGAA
65 ATTTGGACCGACCAAGATGGGAA
* * *
32814 AATCACTCGTTGTTTAGTTAATATTTGGGTTGACTTAGAT-GGATAT
1 TATCACTTGTTGTTTAGTT-ATATTTGGATTGACTTAGATGGGATAT
32860 ATAATTTTGT
Statistics
Matches: 108, Mismatches: 23, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
87 39 0.36
88 52 0.48
89 17 0.16
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (87 bp):
TATCACTTGTTGTTTAGTTATATTTGGATTGACTTAGATGGGATATCACTTGTCGTTTAGTTATA
TTTGGACCGACCAAGATGGGAA
Found at i:33487 original size:45 final size:45
Alignment explanation
Indices: 33423--33508 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
33413 AAGGTTTATA
33423 AATAAATTATAGATCATATCTATACCAATATACAACTATAATGAT
1 AATAAATTATAGATCATATCTATACCAATATACAACTATAATGAT
*
33468 AATAAATTATTGATCATATCTATACCAATATACAACTATAA
1 AATAAATTATAGATCATATCTATACCAATATACAACTATAA
33509 ATAAATTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (45 bp):
AATAAATTATAGATCATATCTATACCAATATACAACTATAATGAT
Found at i:33519 original size:45 final size:43
Alignment explanation
Indices: 33420--33519 Score: 155
Period size: 45 Copynumber: 2.2 Consensus size: 43
33410 TAGAAGGTTT
33420 ATAAATAAATTATAGATCATATCTATACCAATATACAACTATA
1 ATAAATAAATTATAGATCATATCTATACCAATATACAACTATA
*
33463 ATGATAATAAATTATTGATCATATCTATACCAATATACAACTATAA
1 AT-A-AATAAATTATAGATCATATCTATACCAATATACAACTAT-A
33509 ATAAATTAAAT
1 ATAAA-TAAAT
33520 GGTATAAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
43 2 0.04
44 3 0.06
45 44 0.85
46 3 0.06
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (43 bp):
ATAAATAAATTATAGATCATATCTATACCAATATACAACTATA
Found at i:35792 original size:21 final size:21
Alignment explanation
Indices: 35767--35806 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35757 ATTATAATGT
35767 ATTTAAAGTTGGTTGTTATAG
1 ATTTAAAGTTGGTTGTTATAG
*
35788 ATTTAAAGTTTGTTGTTAT
1 ATTTAAAGTTGGTTGTTAT
35807 GGGTGTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.53
Consensus pattern (21 bp):
ATTTAAAGTTGGTTGTTATAG
Found at i:39933 original size:67 final size:65
Alignment explanation
Indices: 39822--39947 Score: 216
Period size: 67 Copynumber: 1.9 Consensus size: 65
39812 TTTGAAAAAA
39822 TGTTTTTGAAAATGCTCTCCATTTGAAAATAATAAAACAATTTGAGAATTTCTGAAAAATTTTAT
1 TGTTTTTGAAAATGCTCTCCATTTGAAAATAATAAAACAATTTGAGAATTTCTGAAAAATTTTAT
* *
39887 TGTTTTTGAAAAATGCTCTCCCTTTGAAAAATAATAAAACAATTTGAGAATTTGTGAAAAA
1 TGTTTTTG-AAAATGCTCTCCATTTG-AAAATAATAAAACAATTTGAGAATTTCTGAAAAA
39948 AGTTTAAGAT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
65 8 0.14
66 16 0.28
67 33 0.58
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (65 bp):
TGTTTTTGAAAATGCTCTCCATTTGAAAATAATAAAACAATTTGAGAATTTCTGAAAAATTTTAT
Found at i:40216 original size:27 final size:28
Alignment explanation
Indices: 40182--40244 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
40172 AGTCATAAAA
* *
40182 ATCCAAATAACCAAA-AAAATATCCAAG
1 ATCCAAATAACCAAATAAAACATCAAAG
40209 -TACCAAAT-ACCAAATAAAACATCAAAG
1 AT-CCAAATAACCAAATAAAACATCAAAG
40236 ATCCAAATA
1 ATCCAAATA
40245 TTATAAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
26 7 0.23
27 22 0.73
28 1 0.03
ACGTcount: A:0.59, C:0.22, G:0.03, T:0.16
Consensus pattern (28 bp):
ATCCAAATAACCAAATAAAACATCAAAG
Found at i:41414 original size:31 final size:31
Alignment explanation
Indices: 41373--41438 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
41363 GCAACTTGAG
*
41373 GGTTGCTTGAGGATTGTCCCTTTAAAGCCAT
1 GGTTGCTTGAGGATTATCCCTTTAAAGCCAT
*
41404 GGTTGTTTGAGGATTATCCCTTTAAAGCCAT
1 GGTTGCTTGAGGATTATCCCTTTAAAGCCAT
41435 GGTT
1 GGTT
41439 TTTCTTCTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.38
Consensus pattern (31 bp):
GGTTGCTTGAGGATTATCCCTTTAAAGCCAT
Found at i:43060 original size:20 final size:20
Alignment explanation
Indices: 43024--43061 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43014 TCTAAATCAT
*
43024 TTTTCAAAATTTTATTTTGA
1 TTTTCAAAATTTAATTTTGA
43044 TTTTC-AAATTCTAATTTT
1 TTTTCAAAATT-TAATTTT
43062 TCTTTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTCAAAATTTAATTTTGA
Found at i:44342 original size:20 final size:20
Alignment explanation
Indices: 44286--44342 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
44276 TTTAATGCAC
44286 AAGGGATCAATCCTTTGTTGA
1 AAGGGATCAATCCTTTG-TGA
* * * *
44307 AAAGGATCGATACTTTAG-GG
1 AAGGGATCAATCCTTT-GTGA
44327 AAGGGATCAATCCTTT
1 AAGGGATCAATCCTTT
44343 TCATCGAGGG
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
20 14 0.50
21 13 0.46
22 1 0.04
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (20 bp):
AAGGGATCAATCCTTTGTGA
Found at i:44355 original size:41 final size:41
Alignment explanation
Indices: 44310--44396 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
44300 TTGTTGAAAA
44310 GGATCGATACTTTAGG-GAAGGGATCAATCCTTTTCATCGAG
1 GGATCGATACTTTAGGAGAAGGGATCAAT-CTTTTCATCGAG
* * * * *
44351 GGATCGATCCTTTTGGAGAAGGGATTAATCTTTTCCTCGGG
1 GGATCGATACTTTAGGAGAAGGGATCAATCTTTTCATCGAG
44392 GGATC
1 GGATC
44397 AATCCAAAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 29 0.73
42 11 0.28
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (41 bp):
GGATCGATACTTTAGGAGAAGGGATCAATCTTTTCATCGAG
Found at i:44373 original size:21 final size:21
Alignment explanation
Indices: 44286--44384 Score: 64
Period size: 21 Copynumber: 4.8 Consensus size: 21
44276 TTTAATGCAC
*
44286 AAGGGATCAATCCTTTGTTGA-
1 AAGGGATCAATCCTTT-TGGAG
* * * *
44307 AAAGGATCGATACTTTAGG-G
1 AAGGGATCAATCCTTTTGGAG
*
44327 AAGGGATCAATCCTTTT-CATCG
1 AAGGGATCAATCCTTTTGGA--G
*
44349 -AGGGATCGATCCTTTTGGAG
1 AAGGGATCAATCCTTTTGGAG
*
44369 AAGGGATTAAT-CTTTT
1 AAGGGATCAATCCTTTT
44385 CCTCGGGGGA
Statistics
Matches: 58, Mismatches: 14, Indels: 13
0.68 0.16 0.15
Matches are distributed among these distances:
20 20 0.34
21 36 0.62
22 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.32
Consensus pattern (21 bp):
AAGGGATCAATCCTTTTGGAG
Found at i:49555 original size:17 final size:18
Alignment explanation
Indices: 49506--49558 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
49496 CGTTGCAGCC
*
49506 AGGGGGTATAGATACCCT
1 AGGGGGTATAGATACCAT
*
49524 AGGAGGTATCA-ATACCAT
1 AGGGGGTAT-AGATACCAT
49542 -GGGGGTATAGATACCAT
1 AGGGGGTATAGATACCAT
49559 CCGAGCAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 1 0.03
17 14 0.47
18 14 0.47
19 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGGGGTATAGATACCAT
Found at i:53046 original size:17 final size:17
Alignment explanation
Indices: 52990--53055 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
52980 TTGTAGTCAA
*
52990 GGGGTATAGATACCCTAG
1 GGGGTATAGATACCAT-G
* * *
53008 GTGGTATCGATATCAT-
1 GGGGTATAGATACCATG
*
53024 -GGGTATCGATACCATG
1 GGGGTATAGATACCATG
53040 GGGGTATAGATACCAT
1 GGGGTATAGATACCAT
53056 CCGAGCAATC
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 13 0.33
17 14 0.36
18 12 0.31
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (17 bp):
GGGGTATAGATACCATG
Found at i:53211 original size:30 final size:30
Alignment explanation
Indices: 53172--53237 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
53162 ATTATTTTTG
* **
53172 AAACCTTTTG-AAACTTCAATTTTAGTCCAA
1 AAACATTTTGTAAA-TTCAATTCAAGTCCAA
*
53202 AAACATTTTGTAAATTTAATTCAAGTCCAA
1 AAACATTTTGTAAATTCAATTCAAGTCCAA
53232 AAACAT
1 AAACAT
53238 GTTGCCTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (30 bp):
AAACATTTTGTAAATTCAATTCAAGTCCAA
Found at i:59670 original size:21 final size:21
Alignment explanation
Indices: 59644--59683 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59634 CCCCCTTTGA
*
59644 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
59665 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
59684 TGGGGTTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Done.