Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001754.1 Hibiscus syriacus cultivar Beakdansim tig00003548_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: 66067
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:10442 original size:40 final size:40
Alignment explanation
Indices: 10387--10469 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
10377 TTATTCCCTC
*
10387 TGCCAAAACCATGTTCGTTAATCTTGATATTGTATACCTT
1 TGCCAAAACCATGTTCGTTAATCCTGATATTGTATACCTT
* *
10427 TGCCAAAATCATGTTCGTTAGTCCTGATATTGTATACCTT
1 TGCCAAAACCATGTTCGTTAATCCTGATATTGTATACCTT
10467 TGC
1 TGC
10470 AAGCATACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.40
Consensus pattern (40 bp):
TGCCAAAACCATGTTCGTTAATCCTGATATTGTATACCTT
Found at i:13704 original size:21 final size:21
Alignment explanation
Indices: 13663--13705 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
13653 AAAATATTTC
*
13663 TTTATTCTAAAAAATATAACT
1 TTTATTCTAAAAAATAAAACT
*
13684 TTTA-TCTAAAATAGTAAAACT
1 TTTATTCTAAAA-AATAAAACT
13705 T
1 T
13706 AGATTCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTATTCTAAAAAATAAAACT
Found at i:16895 original size:15 final size:15
Alignment explanation
Indices: 16875--16905 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16865 TTGATTTCTC
16875 TTCATAATTAACATA
1 TTCATAATTAACATA
16890 TTCATAATTAACATA
1 TTCATAATTAACATA
16905 T
1 T
16906 ACACTTTTCT
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:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (15 bp):
TTCATAATTAACATA
Found at i:19250 original size:31 final size:31
Alignment explanation
Indices: 19172--19286 Score: 101
Period size: 31 Copynumber: 3.7 Consensus size: 31
19162 ATTTTTATCA
* * * * * *
19172 TAACTTTGAAAAATATATCTCATTTTTATTT
1 TAACTTTTAAAAATATATTTTATTATAATTG
* *
19203 TAAC--TTAAAAACATATTTTATTCTAATATG
1 TAACTTTTAAAAATATATTTTATTATAAT-TG
*
19233 -AACTTTTAAAAATATATTTTATTATCATTG
1 TAACTTTTAAAAATATATTTTATTATAATTG
*
19263 TACCTTTTAAAAATATAATTTTAT
1 TAACTTTTAAAAATAT-ATTTTAT
19287 CTTAATTTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 9
0.77 0.12 0.10
Matches are distributed among these distances:
29 20 0.29
30 3 0.04
31 38 0.56
32 7 0.10
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.49
Consensus pattern (31 bp):
TAACTTTTAAAAATATATTTTATTATAATTG
Found at i:19372 original size:31 final size:32
Alignment explanation
Indices: 19334--19400 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
19324 ATTTTAAAGA
*
19334 TTTTTAAAA-TAAAATAAAAATAAAATATATT
1 TTTTTAAAATTAAAATAAAAATAAAATATAAT
* *
19365 TTTTTAAAATTTAAGATATAAATAAAATATAAT
1 TTTTTAAAA-TTAAAATAAAAATAAAATATAAT
19398 TTT
1 TTT
19401 AAGTTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 9 0.29
33 22 0.71
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (32 bp):
TTTTTAAAATTAAAATAAAAATAAAATATAAT
Found at i:19378 original size:38 final size:40
Alignment explanation
Indices: 19312--19396 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 40
19302 ATATTGTAAG
19312 AATAAAATATATATTTTAAAGATTTTTAAAATA-AAATAAA
1 AATAAAATATATATTTTAAAGA-TTTTAAAATATAAATAAA
* *
19352 AATAAAATATATTTTTTTAAA-A-TTTAAGATATAAATAAA
1 AATAAAATATA-TATTTTAAAGATTTTAAAATATAAATAAA
19391 ATATAA
1 A-ATAA
19397 TTTTAAGTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
38 8 0.20
39 8 0.20
40 16 0.40
41 8 0.20
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (40 bp):
AATAAAATATATATTTTAAAGATTTTAAAATATAAATAAA
Found at i:19401 original size:31 final size:30
Alignment explanation
Indices: 19335--19430 Score: 81
Period size: 28 Copynumber: 3.2 Consensus size: 30
19325 TTTTAAAGAT
*
19335 TTTTAAAATAAAATAAAAATAAAATATATTT
1 TTTTAAAATAAAATAAAAATAAAATATA-TA
* *
19366 TTTTAAAATTTAAGATATAAATAAAATATA-A
1 TTTTAAAA--TAAAATAAAAATAAAATATATA
* * * *
19397 TTTT-AAGTTAAATAAGAATAAAATATGT-
1 TTTTAAAATAAAATAAAAATAAAATATATA
19425 TTTTAA
1 TTTTAA
19431 GTTAAGATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
28 19 0.37
29 1 0.02
30 2 0.04
31 12 0.23
33 18 0.35
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (30 bp):
TTTTAAAATAAAATAAAAATAAAATATATA
Found at i:19418 original size:28 final size:29
Alignment explanation
Indices: 19375--19440 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
19365 TTTTTAAAAT
19375 TTAAGATATA-AATAAAATATAATTTTAAG
1 TTAAGATA-AGAATAAAATATAATTTTAAG
**
19404 TTAA-ATAAGAATAAAATATGTTTTTAAG
1 TTAAGATAAGAATAAAATATAATTTTAAG
19432 TTAAGATAA
1 TTAAGATAA
19441 TATGTGTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 1 0.03
28 24 0.73
29 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (29 bp):
TTAAGATAAGAATAAAATATAATTTTAAG
Found at i:19999 original size:68 final size:69
Alignment explanation
Indices: 19879--20010 Score: 194
Period size: 68 Copynumber: 1.9 Consensus size: 69
19869 TTTTAAATGG
* * *
19879 CTCAACGTATAATTATAAATTATTTAAAAATCTAAAGGTAATTTATTTAAAATAAAATATTAATG
1 CTCAACGTATAATTATAAATTATGTAAAAATCTAAAGGTAAATTATTCAAAATAAAATATTAATG
19944 TAGA
66 TAGA
* * * *
19948 CTCAACGTATAATTATAAATTA-GTCAAAATTTTAAGGTAAATTATTCAAAATAAAATGTTAAT
1 CTCAACGTATAATTATAAATTATGTAAAAATCTAAAGGTAAATTATTCAAAATAAAATATTAAT
20011 TATTTTATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
68 34 0.61
69 22 0.39
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (69 bp):
CTCAACGTATAATTATAAATTATGTAAAAATCTAAAGGTAAATTATTCAAAATAAAATATTAATG
TAGA
Found at i:23947 original size:54 final size:55
Alignment explanation
Indices: 23803--23971 Score: 234
Period size: 54 Copynumber: 3.1 Consensus size: 55
23793 GACACTAAGG
* *
23803 GTGCAAAAACTTAAGAAATCCATACTAAGTGTATGAATTT-TGGTATGGGCACTTTGT
1 GTGC-AAAAC-TAAGAAATCCATACTAAGTGTATGAATTTCT-GTATGGGCACTATAT
* *
23860 GTGCAAAACTAAGAAATTCATACCAAGTGTATGAATTTCTGTATGGGCACTATAT
1 GTGCAAAACTAAGAAATCCATACTAAGTGTATGAATTTCTGTATGGGCACTATAT
* * *
23915 GTGC-AAACTAAGAAATCCATACTAACTGTATGAATTTCTGTATGGGAAATATAT
1 GTGCAAAACTAAGAAATCCATACTAAGTGTATGAATTTCTGTATGGGCACTATAT
23969 GTG
1 GTG
23972 AAATTATCAG
Statistics
Matches: 102, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
54 48 0.47
55 44 0.43
56 6 0.06
57 4 0.04
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.32
Consensus pattern (55 bp):
GTGCAAAACTAAGAAATCCATACTAAGTGTATGAATTTCTGTATGGGCACTATAT
Found at i:24785 original size:81 final size:81
Alignment explanation
Indices: 24243--24809 Score: 626
Period size: 81 Copynumber: 7.0 Consensus size: 81
24233 CTTTGAGGCC
** * * *
24243 TAGCTGTGCATTTGATAGAAATGTGTCAATTATGCTAGTTAGACGAACAATTAAAGACCGTTGAG
1 TAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAG
**
24308 TAAAAGATAAATAACA
66 TAAAAGATAAAGGACA
* * * * *
24324 TAGTTGTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCATTT
1 TAG--CTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTG
* *
24389 AGTAAAAAATAAATGGTC-
64 AGTAAAAGATAAA-GGACA
* *
24407 TAGCTATGCATTTGGCAGAAA-GCTGTCAATTATGCCAGTTAG-TCGAACGATTAAACACCGTTG
1 TAGCTGTGCATTTGGCAGAAATG-TGTCAATTATGCCAGTTAGAT-GAACGATTAAAGACCGTTG
* *
24470 AGTAAAAGATAATTGG-CC
64 AGTAAAAGATAA-AGGACA
* * * * * * *
24488 TAGCTGTGCATTTGGCAGAAAGGTGTCAATTATTCTAGTTAGATAAACGGTTAAAGACCGCTAAG
1 TAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAG
* * * *
24553 TAAAATATAAATGTCC
66 TAAAAGATAAAGGACA
* **
24569 TAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGGTCGTTGAG
1 TAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAG
*
24634 TAAAAGATAAATGACA
66 TAAAAGATAAAGGACA
* * *
24650 TAGTTGTGCATTTTGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACTGTTGAG
1 TAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAG
24715 TAAAAGATAAAGGACA
66 TAAAAGATAAAGGACA
* * * * * *
24731 TAGTTGTGCATTTGGCAGAAAAGTGTCAATCATG-CACGTTAGATGAAAGGTTAAATG-CCTTTG
1 TAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCA-GTTAGATGAACGATTAAA-GACCGTTG
24794 -GTAAAAGACTAAAGGA
64 AGTAAAAGA-TAAAGGA
24810 ATTATAATGC
Statistics
Matches: 417, Mismatches: 56, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
80 14 0.03
81 332 0.80
82 3 0.01
83 67 0.16
84 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (81 bp):
TAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAG
TAAAAGATAAAGGACA
Found at i:29511 original size:54 final size:55
Alignment explanation
Indices: 29357--29514 Score: 221
Period size: 55 Copynumber: 2.9 Consensus size: 55
29347 ATTACGAAAT
* **
29357 GGCACTAAGTGTGCAAAAACATAAGAAATTCATACTAAGTGTATGAATTTTGGTATG
1 GGCACTATGTGTGC-AAAAC-TAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* *
29414 GGCACTTTGTGTGCAAAACTAAGAAATTCATACTATGTGTATGAATTTCCGTATG
1 GGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
*
29469 GGCAGC-ATGTGTGC-AAACTAAGAAATCCATACTAAGTGTATGAATT
1 GGCA-CTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATT
29515 GTTGTATGAG
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
54 30 0.33
55 44 0.48
56 6 0.07
57 12 0.13
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30
Consensus pattern (55 bp):
GGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
Found at i:29953 original size:81 final size:81
Alignment explanation
Indices: 29805--30435 Score: 848
Period size: 81 Copynumber: 7.7 Consensus size: 81
29795 GTGCCTTTGA
* * * * *
29805 GGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGATCGTTTAAACACCAT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
29870 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * ***
29886 GGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGTCAGTCAGATGAACGGTTAGAGATTAT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
*
29951 TGAGTAAAAGATAAGT
66 TGAGTAAAAGATAAAT
* **
29967 GGTCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGATTTG
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGA-CCG
*
30032 TTGAGTAAAAGATAACT
65 TTGAGTAAAAGATAAAT
* * * *
30049 GGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATTGTGCCAATTAGATGAACGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
30114 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * * *
30130 GGCCTAGTTGTGCATTTGGCAAAAATGTGTTAATTATACCAGTTAGATGAACAGTTAAAGACAGT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
30195 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* *
30211 GGCCTCGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
30276 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * * *
30292 AGCCTAGTTATGTATTTGGCAGAAATATGTCAATTATGCCAGTTAGATAGATGAACAGTTAAAGA
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAG-T---TAGATGAACGGTTAAAGA
30357 CCGTTGAGTAAAAGATAAAT
62 CCGTTGAGTAAAAGATAAAT
* * * * * *
30377 GACCTAGCTGTGCATTTGGCAAAAAAGTGTCAATCATGCAAGTTAGATGAAAGGTTAAA
1 GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAA
30436 TGTCTTTGGG
Statistics
Matches: 482, Mismatches: 63, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
81 338 0.70
82 75 0.16
84 1 0.00
85 68 0.14
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (81 bp):
GGCCTAGCTGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGT
TGAGTAAAAGATAAAT
Found at i:30234 original size:244 final size:243
Alignment explanation
Indices: 29805--30457 Score: 855
Period size: 244 Copynumber: 2.7 Consensus size: 243
29795 GTGCCTTTGA
* * * * *
29805 GGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGATCGTTTAAACACCAT
1 GGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAATTAGATGAACGGTTAAAGACCGT
* * * *
29870 TGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGTCAGTCAGATG
66 TGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAAAAAAGTGTCAATTATGCCAGTTAGATG
* * * * *
29935 AACGGTTAGAGATTATTGAGTAAAAGATAAGTGGTCTAGCTGTGCATTTGGCAGAAATGTGTCAA
131 AACAGTTAAAGATCATTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAA
* ** *
30000 TTATGCCAGTTAGATGAACGGTTAAAGATTTGTTGAGTAAAAGATAACT
196 TTATGCCAGTTAGATGAAAGGTTAAAGA-CCGTTGAGTAAAAGATAAAT
* * *
30049 GGCCTAGCTGTGCATTTGGAAGAAAGGTGTCAATTGTGCCAATTAGATGAACGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAATTAGATGAACGGTTAAAGACCGT
* * * *
30114 TGAGTAAAAGATAAATGGCCTAGTTGTGCATTTGGCAAAAATGTGTTAATTATACCAGTTAGATG
66 TGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAAAAAAGTGTCAATTATGCCAGTTAGATG
*
30179 AACAGTTAAAGA-CAGTTGAGTAAAAGATAAATGGCCTCGCTGTGCATTTGGCAGAAATGTGTCA
131 AACAGTTAAAGATCA-TTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCA
30243 ATTATGCCAGTTAGATGAAAGGTTAAAGACCGTTGAGTAAAAGATAAAT
195 ATTATGCCAGTTAGATGAAAGGTTAAAGACCGTTGAGTAAAAGATAAAT
* * * * * *
30292 AGCCTAGTTATGTATTTGGCAGAAATA-TGTCAATTATGCCAGTTAGATAGATGAACAGTTAAAG
1 GGCCTAGCTGTGCATTTGGCAGAAA-AGTGTCAATTATGCCA---A-TTAGATGAACGGTTAAAG
* * *
30356 ACCGTTGAGTAAAAGATAAATGACCTAGCTGTGCATTTGGCAAAAAAGTGTCAATCATGCAAGTT
61 ACCGTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAAAAAAGTGTCAATTATGCCAGTT
* *
30421 AGATGAA-AGGTTAAATG-TCTTTGGGTAAAAGACTAAA
126 AGATGAACA-GTTAAA-GATCATTGAGTAAAAGA-TAAA
30458 GGAATTATAA
Statistics
Matches: 356, Mismatches: 43, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
243 51 0.14
244 199 0.56
246 2 0.01
247 98 0.28
248 6 0.02
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (243 bp):
GGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAATTAGATGAACGGTTAAAGACCGT
TGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAAAAAAGTGTCAATTATGCCAGTTAGATG
AACAGTTAAAGATCATTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAATGTGTCAA
TTATGCCAGTTAGATGAAAGGTTAAAGACCGTTGAGTAAAAGATAAAT
Found at i:42421 original size:11 final size:11
Alignment explanation
Indices: 42405--42429 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42395 ATAAAAAATA
42405 CCCCTTAGCAG
1 CCCCTTAGCAG
42416 CCCCTTAGCAG
1 CCCCTTAGCAG
42427 CCC
1 CCC
42430 ATGTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (11 bp):
CCCCTTAGCAG
Found at i:46500 original size:16 final size:16
Alignment explanation
Indices: 46476--46508 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
46466 TATCGCCGAC
*
46476 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
46492 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
46508 C
1 C
46509 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:50776 original size:20 final size:19
Alignment explanation
Indices: 50753--50799 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
50743 CAAAGAACAT
50753 TATCAATA-TTGTTCTTTCAG
1 TATCAATACTT-TT-TTTCAG
* *
50773 TATCGATACTTTTTTTTAG
1 TATCAATACTTTTTTTCAG
50792 TATCAATA
1 TATCAATA
50800 ATCATGACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (19 bp):
TATCAATACTTTTTTTCAG
Found at i:51416 original size:21 final size:20
Alignment explanation
Indices: 51392--51433 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
51382 GGTATTGATA
51392 TCAAGCCTTTGGTATGAATAC
1 TCAA-CCTTTGGTATGAATAC
* *
51413 TCAATCTTTGGTATGGATAC
1 TCAACCTTTGGTATGAATAC
51433 T
1 T
51434 AGTCCTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (20 bp):
TCAACCTTTGGTATGAATAC
Found at i:51468 original size:20 final size:20
Alignment explanation
Indices: 51445--51513 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
51435 GTCCTCTAAT
*
51445 ATGGAGACCAATTTTTCAGG
1 ATGGAGACCAATTTTTCTGG
51465 ATGGAGACC-ATTTATT-TGG
1 ATGGAGACCAATTT-TTCTGG
*
51484 TATGGAGA-CAAGTTTTTCTGT
1 -ATGGAGACCAA-TTTTTCTGG
51505 ATGGAGACC
1 ATGGAGACC
51514 CAGTGATCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
19 7 0.17
20 28 0.68
21 6 0.15
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (20 bp):
ATGGAGACCAATTTTTCTGG
Found at i:51651 original size:26 final size:26
Alignment explanation
Indices: 51606--51655 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
51596 GGAGGTACCG
*
51606 ATACCTATACTCTAGCATCGATACTT
1 ATACCTATACTCCAGCATCGATACTT
**
51632 ATACCTATACTCCATTATCGATAC
1 ATACCTATACTCCAGCATCGATAC
51656 CGAAGCCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (26 bp):
ATACCTATACTCCAGCATCGATACTT
Found at i:57045 original size:20 final size:20
Alignment explanation
Indices: 57022--57089 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
57012 TCCTCCAGTT
57022 TGGAGACCAGTTTTTCGGTA
1 TGGAGACCAGTTTTTCGGTA
* * *
57042 TGGAGACCA-TTCCTCCGGTT
1 TGGAGACCAGTT-TTTCGGTA
** *
57062 TGGAGATAAGTTTTTCAGTA
1 TGGAGACCAGTTTTTCGGTA
57082 TGGAGACC
1 TGGAGACC
57090 CAGTGGTCTC
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (20 bp):
TGGAGACCAGTTTTTCGGTA
Found at i:57056 original size:40 final size:40
Alignment explanation
Indices: 56998--57089 Score: 130
Period size: 40 Copynumber: 2.3 Consensus size: 40
56988 TCAAGCCTTT
* *
56998 GGTATGGATACCAGTCCTCCAGTTTGGAGACCAGTTTTTC
1 GGTATGGAGACCAGTCCTCCAGTTTGGAGACAAGTTTTTC
* * *
57038 GGTATGGAGACCATTCCTCCGGTTTGGAGATAAGTTTTTC
1 GGTATGGAGACCAGTCCTCCAGTTTGGAGACAAGTTTTTC
*
57078 AGTATGGAGACC
1 GGTATGGAGACC
57090 CAGTGGTCTC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.32
Consensus pattern (40 bp):
GGTATGGAGACCAGTCCTCCAGTTTGGAGACAAGTTTTTC
Done.