Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005311.1 Hibiscus syriacus cultivar Beakdansim tig00012019_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: 60909
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:4028 original size:34 final size:34
Alignment explanation
Indices: 3980--4150 Score: 279
Period size: 34 Copynumber: 5.0 Consensus size: 34
3970 TCAAGTGGGA
3980 GATTGTTGAAAATTCAACAAGGTAGGCGCCGAAT
1 GATTGTTGAAAATTCAACAAGGTAGGCGCCGAAT
*
4014 GATTATTGAAAATTCAACAAGGTAGGCGCCGAAT
1 GATTGTTGAAAATTCAACAAGGTAGGCGCCGAAT
4048 GATTGTTGAAAATTCAACAAGGTAGGCGCCGAAT
1 GATTGTTGAAAATTCAACAAGGTAGGCGCCGAAT
* * *
4082 GATTGCTGAAAATTCAACAAGGTAGGAGCCAAAT
1 GATTGTTGAAAATTCAACAAGGTAGGCGCCGAAT
* * *
4116 GATTATTGAAAAATCAACAAGGTAGGCACCGAAT
1 GATTGTTGAAAATTCAACAAGGTAGGCGCCGAAT
4150 G
1 G
4151 TGCAAGTAGT
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 126 1.00
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.22
Consensus pattern (34 bp):
GATTGTTGAAAATTCAACAAGGTAGGCGCCGAAT
Found at i:8050 original size:17 final size:17
Alignment explanation
Indices: 8028--8060 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
8018 CTAGTTAAAG
8028 AAGAAAGTTACTATTAA
1 AAGAAAGTTACTATTAA
8045 AAGAAAGTTACTATTA
1 AAGAAAGTTACTATTA
8061 TGTGAACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (17 bp):
AAGAAAGTTACTATTAA
Found at i:10357 original size:18 final size:16
Alignment explanation
Indices: 10336--10366 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10326 TTTTTAAATT
10336 TTTTTTGAGTTCAAGC
1 TTTTTTGAGTTCAAGC
10352 TTTTTTGAGTTCAAG
1 TTTTTTGAGTTCAAG
10367 TTTCAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (16 bp):
TTTTTTGAGTTCAAGC
Found at i:12767 original size:19 final size:20
Alignment explanation
Indices: 12732--12771 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12722 TTTATTTTAA
12732 TAATTTTTTTAATAAAACAC
1 TAATTTTTTTAATAAAACAC
*
12752 TAATTTTTTTTA-AAAACAC
1 TAATTTTTTTAATAAAACAC
12771 T
1 T
12772 TCAAATGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATTTTTTTAATAAAACAC
Found at i:14138 original size:52 final size:53
Alignment explanation
Indices: 14071--14176 Score: 187
Period size: 52 Copynumber: 2.0 Consensus size: 53
14061 TTGATACTTG
* *
14071 TGTTAAAAGTTAATTCGGTGGCCAGCTAACAATTGTTGAAGATTCAAA-CAAT
1 TGTTAAAAGTCAATTCGGTGGCCAGCCAACAATTGTTGAAGATTCAAAGCAAT
14123 TGTTAAAAGTCAATTCGGTGGCCAGCCAACAATTGTTGAAGATTCAAAGCAAT
1 TGTTAAAAGTCAATTCGGTGGCCAGCCAACAATTGTTGAAGATTCAAAGCAAT
14176 T
1 T
14177 TTCGGCGGGT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 46 0.90
53 5 0.10
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (53 bp):
TGTTAAAAGTCAATTCGGTGGCCAGCCAACAATTGTTGAAGATTCAAAGCAAT
Found at i:17909 original size:21 final size:21
Alignment explanation
Indices: 17885--17924 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
17875 TAATTAAAGG
17885 AAAAGG-TATATAGATAAGTAT
1 AAAAGGATAT-TAGATAAGTAT
17906 AAAAGGATATTAGATAAGT
1 AAAAGGATATTAGATAAGT
17925 GGTGCAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.28
Consensus pattern (21 bp):
AAAAGGATATTAGATAAGTAT
Found at i:18359 original size:20 final size:20
Alignment explanation
Indices: 18327--18400 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
18317 TTTTCCCAAT
*
18327 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
* * *
18347 TCGTAACGCGAATTAGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
18368 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
18388 TCGCAACGCGAAT
1 TCGCAACGCGAAT
18401 TGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:18370 original size:21 final size:21
Alignment explanation
Indices: 18327--18419 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
18317 TTTTCCCAAT
* * *
18327 TCGCAATGCGAA-TAAGTAAA
1 TCGCAACGCGAATTAGGAAAA
*
18347 TCGTAACGCGAATTAGGAAAA
1 TCGCAACGCGAATTAGGAAAA
* * *
18368 TCGCAATGCGAA-TAAGTAAA
1 TCGCAACGCGAATTAGGAAAA
*
18388 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAATTAGGAAAA
*
18409 TCGCAATGCGA
1 TCGCAACGCGA
18420 TACTGACTAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (21 bp):
TCGCAACGCGAATTAGGAAAA
Found at i:18372 original size:41 final size:41
Alignment explanation
Indices: 18327--18419 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
18317 TTTTCCCAAT
*
18327 TCGCAATGCGAATAAGTAAATCGTAACGCGAATTAGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTAGGAAAA
*
18368 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTAGGAAAA
18409 TCGCAATGCGA
1 TCGCAATGCGA
18420 TACTGACTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTAGGAAAA
Found at i:18435 original size:20 final size:20
Alignment explanation
Indices: 18410--18502 Score: 69
Period size: 20 Copynumber: 4.6 Consensus size: 20
18400 TTGGGAAAAT
*
18410 CGCAATGCGATACTGACTAA
1 CGCAACGCGATACTGACTAA
* * * **
18430 CGCAATGCGATAATAAAAAA
1 CGCAACGCGATACTGACTAA
* * **
18450 TCGCAACGAGATACTTACTTT
1 -CGCAACGCGATACTGACTAA
**
18471 CGCAACGCGATACTGACTTT
1 CGCAACGCGATACTGACTAA
18491 CGCAACGCGATA
1 CGCAACGCGATA
18503 ATACATAATC
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 46 0.79
21 12 0.21
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
CGCAACGCGATACTGACTAA
Found at i:18450 original size:41 final size:41
Alignment explanation
Indices: 18405--18482 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
18395 GCGAATTGGG
* * *
18405 AAAATCGCAATGCGATACTGACTAACGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTAACGCAACGCGATAATAA
* **
18446 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTAACGCAACGCGATA
18483 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTAACGCAACGCGATAATAA
Found at i:20775 original size:20 final size:19
Alignment explanation
Indices: 20730--20934 Score: 178
Period size: 20 Copynumber: 11.1 Consensus size: 19
20720 TCTTTTGGTT
*
20730 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
20749 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
20769 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
**
20789 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
20807 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** **
20823 GAAATGACTATCGTGAC-C
1 GAAATGAAAATCGCAACGC
*
20841 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
20856 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
20876 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
20895 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
20914 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
20933 GA
1 GA
20935 TTTTGGTTTC
Statistics
Matches: 156, Mismatches: 17, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
14 18 0.12
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 61 0.39
20 65 0.42
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:20832 original size:33 final size:33
Alignment explanation
Indices: 20779--20873 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 33
20769 GGAAATGACT
* *
20779 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAACGC-GAAATGACTATCGCAACCAGACA
**
20813 ATCGCAACGCGAAATGACTATCGTGACCAGACA
1 ATCGCAACGCGAAATGACTATCGCAACCAGACA
**
20846 ATCGCAACGCGAAATGAAAATCGCAACC
1 ATCGCAACGCGAAATGACTATCGCAACC
20874 GCGAAATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 43 0.81
34 10 0.19
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGACTATCGCAACCAGACA
Found at i:20869 original size:19 final size:19
Alignment explanation
Indices: 20845--20934 Score: 153
Period size: 19 Copynumber: 4.7 Consensus size: 19
20835 GTGACCAGAC
20845 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
20864 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
20884 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
20903 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
20922 AATCGCAATGCGA
1 AATCGCAACGCGA
20935 TTTTGGTTTC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 49 0.73
20 18 0.27
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:20899 original size:39 final size:38
Alignment explanation
Indices: 20845--20934 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
20835 GTGACCAGAC
20845 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
20884 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
20922 AATCGCAATGCGA
1 AATCGCAACGCGA
20935 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:20977 original size:20 final size:19
Alignment explanation
Indices: 20930--21015 Score: 127
Period size: 19 Copynumber: 4.5 Consensus size: 19
20920 AAAATCGCAA
**
20930 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
20949 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
20968 TGCGATTTTTATTTTGCGGT
1 TGCGATTTTTATTTCGC-GT
*
20988 TGCGATTTTCATTTCGCGT
1 TGCGATTTTTATTTCGCGT
21007 TGCGATTTT
1 TGCGATTTT
21016 CATTCTCAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 44 0.72
20 17 0.28
ACGTcount: A:0.09, C:0.15, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:20994 original size:39 final size:38
Alignment explanation
Indices: 20930--21015 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 38
20920 AAAATCGCAA
* *
20930 TGCGATTTTGGTTTCGCGTTGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGTTGCGATTTTCATTTCGCGT
* *
20968 TGCGATTTTTATTTTGCGGTTGCGATTTTCATTTCGCGT
1 TGCGATTTTGATTTCGC-GTTGCGATTTTCATTTCGCGT
21007 TGCGATTTT
1 TGCGATTTT
21016 CATTCTCAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 14 0.33
39 29 0.67
ACGTcount: A:0.09, C:0.15, G:0.24, T:0.51
Consensus pattern (38 bp):
TGCGATTTTGATTTCGCGTTGCGATTTTCATTTCGCGT
Found at i:21560 original size:20 final size:20
Alignment explanation
Indices: 21535--21587 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
21525 GCGCTATGTA
21535 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
21555 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
21575 TATCTCGTTGCGA
1 AATCGCGTTGCGA
21588 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:21621 original size:20 final size:20
Alignment explanation
Indices: 21596--21649 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
21586 GATTTTGTAT
*
21596 TATCGCATTGTGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
21616 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
21636 TATCGCATTGCGAT
1 TATCGCATTGCGAT
21650 TTTTCCCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:21761 original size:21 final size:21
Alignment explanation
Indices: 21721--21761 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21711 ATTGTATACC
**
21721 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
21742 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
21762 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:24457 original size:24 final size:24
Alignment explanation
Indices: 24391--24499 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
24381 ATGTTTTATC
* * *
24391 TGATTTCCGATTTGAATTATGTTT
1 TGATTTCTGATATGAATTCTGTTT
* * *
24415 TGATTTCTGGTCTGAATTCTGTTA
1 TGATTTCTGATATGAATTCTGTTT
*
24439 TGATTTCTGATATGGATTCT-TTT
1 TGATTTCTGATATGAATTCTGTTT
* * * * *
24462 CTAATATATGATCTGACTTCTGTTT
1 -TGATTTCTGATATGAATTCTGTTT
24487 TGATTTCTGATAT
1 TGATTTCTGATAT
24500 CTCCGTTTAC
Statistics
Matches: 64, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
23 2 0.03
24 59 0.92
25 3 0.05
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (24 bp):
TGATTTCTGATATGAATTCTGTTT
Found at i:29537 original size:52 final size:53
Alignment explanation
Indices: 29474--29581 Score: 173
Period size: 52 Copynumber: 2.1 Consensus size: 53
29464 GAAGTGGGAG
* * * *
29474 ATTGTTAAAAGTTAATTTGGTGGCCAGCCAACAATTGTTGAAGATTCAAA-CA
1 ATTGTTAAAAGTCAATTCGGTAGCCAACCAACAATTGTTGAAGATTCAAAGCA
29526 ATTGTTAAAAGTCAATTCGGTAGCCAACCAACAATTGTTGAAGATTCAAAGCA
1 ATTGTTAAAAGTCAATTCGGTAGCCAACCAACAATTGTTGAAGATTCAAAGCA
29579 ATT
1 ATT
29582 TTCGGTTGGT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
52 46 0.90
53 5 0.10
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (53 bp):
ATTGTTAAAAGTCAATTCGGTAGCCAACCAACAATTGTTGAAGATTCAAAGCA
Found at i:29676 original size:14 final size:14
Alignment explanation
Indices: 29657--29694 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
29647 TTGGGATTAT
29657 TGTACTTTAGTCTC
1 TGTACTTTAGTCTC
29671 TGTACTTTAGTCTC
1 TGTACTTTAGTCTC
*
29685 TATACTTTAG
1 TGTACTTTAG
29695 GGTATTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.50
Consensus pattern (14 bp):
TGTACTTTAGTCTC
Found at i:32423 original size:36 final size:37
Alignment explanation
Indices: 32374--32447 Score: 132
Period size: 36 Copynumber: 2.0 Consensus size: 37
32364 TGTCTTTGAA
32374 GTGTCTTTTCGCTTAATTTATTTACTCCCGAGTCCTT
1 GTGTCTTTTCGCTTAATTTATTTACTCCCGAGTCCTT
*
32411 GTGTC-TTTCGCTTAATTTATTTACTTCCGAGTCCTT
1 GTGTCTTTTCGCTTAATTTATTTACTCCCGAGTCCTT
32447 G
1 G
32448 CCTGTTCCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 31 0.86
37 5 0.14
ACGTcount: A:0.14, C:0.23, G:0.15, T:0.49
Consensus pattern (37 bp):
GTGTCTTTTCGCTTAATTTATTTACTCCCGAGTCCTT
Found at i:34810 original size:60 final size:59
Alignment explanation
Indices: 34698--34810 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
34688 GGTAAAGTAC
* * * *
34698 ACAAATAGTCCTTCGACTATAGGACATTATTTTGTTGAGTCTCTCGATTATTACAAGTT
1 ACAAATAGTCCTCCGACTATAGGACATTACTTTGTTGAATCTCTCGACTATTACAAGTT
* *
34757 ACAAATTGATCCTCCGACTATAGGACATTGCTTTGTTGAATCAT-TCGACTATTA
1 ACAAATAG-TCCTCCGACTATAGGACATTACTTTGTTGAATC-TCTCGACTATTA
34811 AAAATTATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
59 7 0.15
60 38 0.83
61 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (59 bp):
ACAAATAGTCCTCCGACTATAGGACATTACTTTGTTGAATCTCTCGACTATTACAAGTT
Found at i:34835 original size:60 final size:59
Alignment explanation
Indices: 34710--34837 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 59
34700 AAATAGTCCT
* * * * * *
34710 TCGACTATAGGACATTATTTTGTTGAGTCTCTCGATTATTACAAGTTACAAATTGATCC
1 TCGACTATAGGACATTACTTTGTTGAATCTCTCGACTATTAAAAATTACAAAATGATCC
* * *
34769 TCCGACTATAGGACATTGCTTTGTTGAATCAT-TCGACTATTAAAAATTATAAAATGGTCAC
1 T-CGACTATAGGACATTACTTTGTTGAATC-TCTCGACTATTAAAAATTACAAAATGATC-C
34830 TCGACTAT
1 TCGACTAT
34838 TTATATATTC
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
59 1 0.02
60 53 0.93
61 3 0.05
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (59 bp):
TCGACTATAGGACATTACTTTGTTGAATCTCTCGACTATTAAAAATTACAAAATGATCC
Found at i:35672 original size:31 final size:30
Alignment explanation
Indices: 35639--35697 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
35629 AAATCATCTA
35639 TTTGTGTCAT-TAACTTATTATTTAGTTTTTAT
1 TTTG-GTCATCTAA-TTATTA-TTAGTTTTTAT
*
35671 TTTGGTTATCTAATTATTATTAGTTTT
1 TTTGGTCATCTAATTATTATTAGTTTT
35698 AAAATCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 8 0.32
31 10 0.40
32 7 0.28
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (30 bp):
TTTGGTCATCTAATTATTATTAGTTTTTAT
Found at i:36986 original size:71 final size:71
Alignment explanation
Indices: 36896--37038 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 71
36886 TTCGTAACAT
*
36896 TTTCGATTGACAATCGAAAATAGTATATTATTCGTAACATTTTATATTCAACCGAAATATTAGTA
1 TTTCGATTGACAATCGAAAATAATATATTATTCGTAACATTTTATATTCAACCGAAATATTAGTA
36961 AAAATA
66 AAAATA
* *
36967 TTTCGATTGACAATTGAAAATAATATATTATTTGTAACATTTTATATTCAACCGAAATATTAGTA
1 TTTCGATTGACAATCGAAAATAATATATTATTCGTAACATTTTATATTCAACCGAAATATTAGTA
37032 AAAATA
66 AAAATA
37038 T
1 T
37039 AATATTTAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (71 bp):
TTTCGATTGACAATCGAAAATAATATATTATTCGTAACATTTTATATTCAACCGAAATATTAGTA
AAAATA
Found at i:48064 original size:29 final size:29
Alignment explanation
Indices: 48003--48066 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
47993 AGATGGATCT
* * *
48003 TAAACTTTTCTTTTGATCAAATTGACACT
1 TAAACTTTTCTTTAGATCAAATTAACACC
*
48032 TAAACTTTTCTTTCAG-TCAAATTAACCCC
1 TAAACTTTTCTTT-AGATCAAATTAACACC
48061 TAAACT
1 TAAACT
48067 CAACAAGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.41
Consensus pattern (29 bp):
TAAACTTTTCTTTAGATCAAATTAACACC
Found at i:48433 original size:41 final size:41
Alignment explanation
Indices: 48386--48497 Score: 215
Period size: 41 Copynumber: 2.7 Consensus size: 41
48376 GGTCCATACC
*
48386 AATTCAGTGGTGTTTGTCTTGCATAATGGTAGAGGGAGCCA
1 AATTCAGTGGTGTTTGTCTTGCATAATGGCAGAGGGAGCCA
48427 AATTCAGTGGTGTTTGTCTTGCATAATGGCAGAGGGAGCCA
1 AATTCAGTGGTGTTTGTCTTGCATAATGGCAGAGGGAGCCA
48468 AATTCAGTGGTGTTTGTCTTGCATAATGGC
1 AATTCAGTGGTGTTTGTCTTGCATAATGGC
48498 CTTATCGACG
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.33
Consensus pattern (41 bp):
AATTCAGTGGTGTTTGTCTTGCATAATGGCAGAGGGAGCCA
Done.