Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004495.1 Hibiscus syriacus cultivar Beakdansim tig00009913_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: 78804
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:7974 original size:64 final size:65
Alignment explanation
Indices: 7841--7995 Score: 167
Period size: 64 Copynumber: 2.4 Consensus size: 65
7831 GAAGGTGTAT
* * ** *
7841 CGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAAAATAAAAACATCGAATGCAATTAGTGCAT
1 CGATGCACAAGCAGTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCAATTAGTGCAC
* * *
7905 TGATGCATAAGGCA-TGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATTTTA-TG
1 CGATGCACAA-GCAGTGCATCGATGCATCTCCATTAA-AATAAAAACATCGAATGCA-ATTAGTG
7966 CAC
63 CAC
*
7969 CGATGCACAAGTAGTGCATCGATGCAT
1 CGATGCACAAGCAGTGCATCGATGCAT
7996 ACCTTCATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
63 2 0.03
64 64 0.85
65 9 0.12
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (65 bp):
CGATGCACAAGCAGTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCAATTAGTGCAC
Found at i:8411 original size:29 final size:29
Alignment explanation
Indices: 8372--8452 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
8362 TATGTGATAT
8372 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
8402 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
8431 GAGAAACGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
8453 ACATATAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
28 7 0.15
29 36 0.75
30 5 0.10
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:15309 original size:29 final size:29
Alignment explanation
Indices: 15270--15350 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
15260 TATGTGATAT
15270 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
15300 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
15329 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
15351 ACATATAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 7 0.14
29 37 0.76
30 5 0.10
ACGTcount: A:0.46, C:0.16, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:17130 original size:34 final size:36
Alignment explanation
Indices: 17087--17161 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 36
17077 TGTTACAATC
17087 TAAATCTTACACTCT-AAATCT-AAGTAC-TAAATTT
1 TAAATCTTACACTCTAAAATCTAAAGT-CTTAAATTT
*
17121 TAAATCTTACACTCTAAAATTTAAAGTCTTAAATTT
1 TAAATCTTACACTCTAAAATCTAAAGTCTTAAATTT
17157 TAAAT
1 TAAAT
17162 GAGACATATG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
34 15 0.41
35 6 0.16
36 16 0.43
ACGTcount: A:0.43, C:0.15, G:0.03, T:0.40
Consensus pattern (36 bp):
TAAATCTTACACTCTAAAATCTAAAGTCTTAAATTT
Found at i:31495 original size:2 final size:2
Alignment explanation
Indices: 31435--31478 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
31425 AATTAAAGAT
* * * *
31435 TA TA TA TA TA TA TA TA TA AA TT TA TG CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31477 TA
1 TA
31479 AGAGATAAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:33172 original size:25 final size:24
Alignment explanation
Indices: 33144--33195 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
33134 CCATATTAAA
* * *
33144 ATAATTATTATAACATCCCTTATAT
1 ATAATTATTACAAAAT-CATTATAT
33169 ATAATTATTACAAAATCATTATAT
1 ATAATTATTACAAAATCATTATAT
33193 ATA
1 ATA
33196 GTCAATTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (24 bp):
ATAATTATTACAAAATCATTATAT
Found at i:34562 original size:18 final size:17
Alignment explanation
Indices: 34535--34573 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
34525 CTTTTTAAAA
34535 AATAGCTTATATAAATAT
1 AATAGCTTATAT-AATAT
* *
34553 AATAGTTTATATTATAT
1 AATAGCTTATATAATAT
34570 AATA
1 AATA
34574 TATTTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (17 bp):
AATAGCTTATATAATAT
Found at i:34766 original size:23 final size:23
Alignment explanation
Indices: 34732--34782 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
34722 TTATCATCTA
34732 TATTTTTATTATAAT-TTTTATT
1 TATTTTTATTATAATATTTTATT
* *
34754 GTATTTTTCTTATATTATTTTATT
1 -TATTTTTATTATAATATTTTATT
34778 TATTT
1 TATTT
34783 ATTAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (23 bp):
TATTTTTATTATAATATTTTATT
Found at i:38241 original size:15 final size:15
Alignment explanation
Indices: 38221--38257 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
38211 CTCTATACTT
38221 AATCTTCTACTGTTC
1 AATCTTCTACTGTTC
38236 AATCTTCTACTGTTC
1 AATCTTCTACTGTTC
38251 AATCTTC
1 AATCTTC
38258 ATGTAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.22, C:0.27, G:0.05, T:0.46
Consensus pattern (15 bp):
AATCTTCTACTGTTC
Found at i:39406 original size:37 final size:36
Alignment explanation
Indices: 39365--39625 Score: 213
Period size: 37 Copynumber: 6.9 Consensus size: 36
39355 TTGCAAACGG
* * *
39365 TTTTTGAAGATACATATATAATATATAGTTTCTAATTT
1 TTTTTGAA-A-ACATATATAATATATAGTTTTTAAATA
* *
39403 TTTTTTAAAA-ATGTATATAATATATAGTTTTTAAAACA
1 TTTTTGAAAACA--TATATAATATATAGTTTTT-AAATA
* *
39441 CTTTTGAAAAC-TATATAATATATAGTTTTTAAAACA
1 TTTTTGAAAACATATATAATATATAGTTTTT-AAATA
* *
39477 TTTTAGAAAATATATATAATATATAGTTTTTAAA-A
1 TTTTTGAAAACATATATAATATATAGTTTTTAAATA
*
39512 TCATTTTGAAAACTTATATAATATATAGTTTTTAAAAATA
1 T--TTTTGAAAACATATATAATATATAGTTTTT--AAATA
* *
39552 TTTTTTAAATAAACTTATATAATATATAGTTTTTGAAAATA
1 -TTTTT-GA-AAACATATATAATATATAGTTTTT--AAATA
* * *
39593 TTATTTTTAAAACTTATATAATATATAATTTTT
1 -T-TTTTGAAAACATATATAATATATAGTTTTT
39626 TTAAAAAACA
Statistics
Matches: 192, Mismatches: 17, Indels: 26
0.82 0.07 0.11
Matches are distributed among these distances:
35 3 0.02
36 37 0.19
37 65 0.34
38 17 0.09
39 7 0.04
40 25 0.13
41 34 0.18
42 4 0.02
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (36 bp):
TTTTTGAAAACATATATAATATATAGTTTTTAAATA
Found at i:39493 original size:73 final size:73
Alignment explanation
Indices: 39405--39652 Score: 286
Period size: 73 Copynumber: 3.2 Consensus size: 73
39395 TCTAATTTTT
39405 TTTTA-AAAATGTATATAATATATAGTTTTTAAAACACTTTTGAAAAC-TATATAATATATAGTT
1 TTTTAGAAAAT-TATATAATATATAGTTTTTAAAACA-TTTTGAAAACTTATATAATATATAGTT
39468 TTT-AAAACA
64 TTTAAAAACA
39477 TTTTAGAAAATATATATAATATATAGTTTTTAAAATCATTTTGAAAACTTATATAATATATAGTT
1 TTTTAGAAAAT-TATATAATATATAGTTTTTAAAA-CATTTTGAAAACTTATATAATATATAGTT
*
39542 TTTAAAAATA
64 TTTAAAAACA
* * *
39552 TTTTTTAAATAAACTTATATAATATATAGTTTTTGAAAATATTATTTTTAAAACTTATATAATAT
1 --TTTTAGA-AAA-TTATATAATATATAGTTTTT--AAA-A-CATTTTGAAAACTTATATAATAT
*
39617 ATAATTTTTTTAAAAAACA
58 AT-A-GTTTTT-AAAAACA
*
39636 TTTTGGAAAATTATATA
1 TTTTAGAAAATTATATA
39653 GTTTTCAAAA
Statistics
Matches: 153, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
72 5 0.03
73 38 0.25
74 21 0.14
75 5 0.03
77 6 0.04
78 22 0.14
79 1 0.01
80 10 0.07
81 28 0.18
82 6 0.04
83 5 0.03
84 6 0.04
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (73 bp):
TTTTAGAAAATTATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAGTTTT
TAAAAACA
Found at i:39716 original size:32 final size:30
Alignment explanation
Indices: 39624--39714 Score: 139
Period size: 30 Copynumber: 3.0 Consensus size: 30
39614 TATATAATTT
*
39624 TTTTAAAAAACATTTTGGAAAATTATATAG
1 TTTTAAAAAACATTTTTGAAAATTATATAG
39654 TTTTCAAAAAACATTTTTTGAAAATTATATAG
1 TTTT-AAAAAACA-TTTTTGAAAATTATATAG
39686 -TTTAAAAAACATTTTTGAAAATCTATATA
1 TTTTAAAAAACATTTTTGAAAAT-TATATA
39715 TAATATTGTT
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
29 11 0.19
30 18 0.32
31 11 0.19
32 17 0.30
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (30 bp):
TTTTAAAAAACATTTTTGAAAATTATATAG
Found at i:39739 original size:12 final size:12
Alignment explanation
Indices: 39722--39761 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
39712 ATATAATATT
*
39722 GTTTTTTAAAAC
1 GTTTTTAAAAAC
39734 GTTTTTAAAAAC
1 GTTTTTAAAAAC
*
39746 GTTTTTAAAAAA
1 GTTTTTAAAAAC
39758 GTTT
1 GTTT
39762 ATATTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (12 bp):
GTTTTTAAAAAC
Found at i:39816 original size:7 final size:8
Alignment explanation
Indices: 39786--39813 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
39776 AAAAAAAATA
39786 TTTTTATT
1 TTTTTATT
39794 TTTTTATT
1 TTTTTATT
39802 TTTTTATT
1 TTTTTATT
39810 TTTT
1 TTTT
39814 ATTACTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:39825 original size:2 final size:2
Alignment explanation
Indices: 39820--39852 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39810 TTTTATTACT
39820 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 T
39853 TCTTCAGGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41576 original size:16 final size:17
Alignment explanation
Indices: 41555--41586 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41545 CAAAATTTAA
41555 TATTTTTA-TTTATTTT
1 TATTTTTATTTTATTTT
41571 TATTTTTATTTTATTT
1 TATTTTTATTTTATTT
41587 CGTTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
TATTTTTATTTTATTTT
Found at i:41602 original size:26 final size:27
Alignment explanation
Indices: 41550--41621 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
41540 CCTTTCAAAA
* * *
41550 TTTAATATTTTTATTTATTTTTATTTT
1 TTTATTATTTTCATTTATTTTCATTTT
* *
41577 TATT-TTA-TTTCGTTTATTTTCCTTTT
1 T-TTATTATTTTCATTTATTTTCATTTT
41603 TTTATTATTTTCATTTATT
1 TTTATTATTTTCATTTATT
41622 AAATTTTAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
25 2 0.06
26 19 0.53
27 13 0.36
28 2 0.06
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.75
Consensus pattern (27 bp):
TTTATTATTTTCATTTATTTTCATTTT
Found at i:41780 original size:12 final size:12
Alignment explanation
Indices: 41763--41789 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41753 TCGGTTTTTT
41763 TTTAAATTCTAA
1 TTTAAATTCTAA
41775 TTTAAATTCTAA
1 TTTAAATTCTAA
41787 TTT
1 TTT
41790 TTGCAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTAAATTCTAA
Found at i:44266 original size:21 final size:21
Alignment explanation
Indices: 44242--44291 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
44232 GTAGAGAAAG
44242 AAGCAACAACAACACAGAGAA
1 AAGCAACAACAACACAGAGAA
* ** * *
44263 AAGCAGCGGCAGCACAGAGAG
1 AAGCAACAACAACACAGAGAA
44284 AAGCAACA
1 AAGCAACA
44292 TATCACAGAG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.24, G:0.24, T:0.00
Consensus pattern (21 bp):
AAGCAACAACAACACAGAGAA
Found at i:44734 original size:43 final size:41
Alignment explanation
Indices: 44687--44947 Score: 134
Period size: 43 Copynumber: 6.2 Consensus size: 41
44677 AACTTTACCA
* * *
44687 GCGTTTTTAGCAAAAATGCCGCAAAAAATCAATACATACTGCG
1 GCGTTTTTAG-AAAAACGCCGCAAAACATCAAAAC-TACTGCG
* *
44730 GCGTTTGTGAGAAAAACGCTGCAAAACATCAAAACCTACTGCG
1 GCGTTT-TTAGAAAAACGCCGCAAAACATCAAAA-CTACTGCG
* * * * *
44773 GCATTTGTGGAAAAAACGCCGCAAAACATCAACATCTATTGCG
1 GCGTTTTTAG-AAAAACGCCGCAAAACATCAA-AACTACTGCG
* * * * * * * *
44816 GCGTTTGTGGGAATACGTCGCTAAACATCAACACCTATTGCG
1 GCGTTTTTAGAAAAACGCCGCAAAACATCAA-AACTACTGCG
* * * * *
44858 GCATTTTAGAGAAAAACGCCGCTAAATATCATAAC--C-GCG
1 GCGTTTT-TAGAAAAACGCCGCAAAACATCAAAACTACTGCG
* * * * * *
44897 ACGTTTATCT-GAAAAACACCGCTAAATATCAACACCTATTGCG
1 GCGTTT-T-TAGAAAAACGCCGCAAAACATCAA-AACTACTGCG
44940 GCGTTTTT
1 GCGTTTTT
44948 GTTTAAAAAT
Statistics
Matches: 170, Mismatches: 38, Indels: 22
0.74 0.17 0.10
Matches are distributed among these distances:
39 27 0.16
40 3 0.02
41 1 0.01
42 36 0.21
43 98 0.58
44 5 0.03
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (41 bp):
GCGTTTTTAGAAAAACGCCGCAAAACATCAAAACTACTGCG
Found at i:44854 original size:42 final size:41
Alignment explanation
Indices: 44706--44876 Score: 164
Period size: 43 Copynumber: 4.0 Consensus size: 41
44696 GCAAAAATGC
* * * *
44706 CGCAAAAAATCAATACATACTGCGGCGTTTGTGAGAAAAACG
1 CGCAAAACATCAACACCTATTGCGGCGTTTGTG-GAAAAACG
* * *
44748 CTGCAAAACATCAAAACCTACTGCGGCATTTGTGGAAAAAACG
1 C-GCAAAACATCAACACCTATTGCGGCGTTTGTGG-AAAAACG
* * *
44791 CCGCAAAACATCAACATCTATTGCGGCGTTTGTGGGAATACG
1 -CGCAAAACATCAACACCTATTGCGGCGTTTGTGGAAAAACG
* *
44833 TCGCTAAACATCAACACCTATTGCGGCATTT-TAGAGAAAAACG
1 -CGCAAAACATCAACACCTATTGCGGCGTTTGT-G-GAAAAACG
44876 C
1 C
44877 CGCTAAATAT
Statistics
Matches: 108, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 36 0.33
43 70 0.65
44 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (41 bp):
CGCAAAACATCAACACCTATTGCGGCGTTTGTGGAAAAACG
Found at i:44877 original size:85 final size:86
Alignment explanation
Indices: 44698--44888 Score: 219
Period size: 85 Copynumber: 2.2 Consensus size: 86
44688 CGTTTTTAGC
* *
44698 AAAAATGCCGCAAAAAATCAATACATACTGCGGCGTTTGTGAGAAAAACGCTGCAAAACATCAAA
1 AAAAACGCCGCAAAAAATCAACACATACTGCGGCGTTTGTGAGAAAAACGCTGCAAAACATCAAA
*
44763 ACCTACTGCGGCATTTGTGGA
66 ACCTACTGCGGCATTTGTAGA
* * * * *
44784 AAAAACGCCGCAAAACATCAACATC-TATTGCGGCGTTTGTG-GGAATACG-TCGCTAAACATCA
1 AAAAACGCCGCAAAAAATCAACA-CATACTGCGGCGTTTGTGAGAAAAACGCT-GCAAAACATCA
* *
44846 ACACCTATTGCGGCATTT-TAGA
64 AAACCTACTGCGGCATTTGTAGA
* *
44868 GAAAAACGCCGCTAAATATCA
1 -AAAAACGCCGCAAAAAATCA
44889 TAACCGCGAC
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
84 4 0.04
85 50 0.56
86 35 0.39
87 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (86 bp):
AAAAACGCCGCAAAAAATCAACACATACTGCGGCGTTTGTGAGAAAAACGCTGCAAAACATCAAA
ACCTACTGCGGCATTTGTAGA
Found at i:45376 original size:28 final size:28
Alignment explanation
Indices: 45336--45391 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
45326 TAATAAGTCC
45336 CCAAGCTTCAAAAGTTAAAAAAACCCTT
1 CCAAGCTTCAAAAGTTAAAAAAACCCTT
45364 CCAAGCTTCAAAAGTTAAAAAAACCCTT
1 CCAAGCTTCAAAAGTTAAAAAAACCCTT
45392 AAATTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (28 bp):
CCAAGCTTCAAAAGTTAAAAAAACCCTT
Found at i:46774 original size:30 final size:30
Alignment explanation
Indices: 46740--46801 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
46730 AGTGAACATG
* *
46740 CGATTCAAACCGGTTTTACCGGTTTTCAAC
1 CGATTCAAACCGATTTTACCGATTTTCAAC
** *
46770 CGATTCACCCCGATTTTCCCGATTTTCAAC
1 CGATTCAAACCGATTTTACCGATTTTCAAC
46800 CG
1 CG
46802 GTTCTGTGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.21, C:0.32, G:0.15, T:0.32
Consensus pattern (30 bp):
CGATTCAAACCGATTTTACCGATTTTCAAC
Found at i:57602 original size:23 final size:23
Alignment explanation
Indices: 57569--57636 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
57559 AACCTTATAT
57569 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
57592 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
57615 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
57637 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:57971 original size:2 final size:2
Alignment explanation
Indices: 57964--57993 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
57954 ATATGTAATG
57964 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
57994 TGCATATGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63085 original size:23 final size:23
Alignment explanation
Indices: 63017--63085 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
63007 CAACCTTATA
*
63017 TGGCACTTCGGTGCATTTCTACA
1 TGGCACTTCGGTGCATTTCTACG
* * *
63040 CGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
63063 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
63086 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:71943 original size:33 final size:33
Alignment explanation
Indices: 71898--71964 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
71888 ATTCAAATTG
*
71898 TCAAGGTCTTATCTGCTGTTAGTTTCTTATATA
1 TCAAGGTATTATCTGCTGTTAGTTTCTTATATA
*
71931 TCAAGGTATTATCTGCTGTTGGTTTCTTATATA
1 TCAAGGTATTATCTGCTGTTAGTTTCTTATATA
71964 T
1 T
71965 TATTAAGGTA
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:0.21, C:0.13, G:0.16, T:0.49
Consensus pattern (33 bp):
TCAAGGTATTATCTGCTGTTAGTTTCTTATATA
Done.