Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009225.1 Hibiscus syriacus cultivar Beakdansim tig00112827_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: 59957
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:85 original size:33 final size:33
Alignment explanation
Indices: 44--125 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
34 ATCGCATGAG
*
44 AATGAAAATCGCAACGAGAGAATCGCAATGTGA
1 AATGAAAATCGCAACGAGAGAATCGCAATGCGA
*
77 AATGAAAATCGCAACGAGGGAATCGCAATGCGA
1 AATGAAAATCGCAACGAGAGAATCGCAATGCGA
110 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
126 CGAATTTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.13
Consensus pattern (33 bp):
AATGAAAATCGCAACGAGAGAATCGCAATGCGA
Found at i:121 original size:19 final size:19
Alignment explanation
Indices: 64--129 Score: 61
Period size: 19 Copynumber: 3.7 Consensus size: 19
54 GCAACGAGAG
*
64 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
**
83 AATCGCAA--CG--A-GGG
1 AATCGCAATGCGAAATGAA
97 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
116 AATCGCAACGCGAA
1 AATCGCAATGCGAA
130 TTTAATTTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
14 9 0.25
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 22 0.61
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:147 original size:19 final size:19
Alignment explanation
Indices: 125--185 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
115 AAATCGCAAC
125 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
*
144 GCG-ATTTCATTTTCGCGTT
1 GCGAATTT-AATTTCGCGTT
* * *
163 GCGATTTTCATTTCGCATT
1 GCGAATTTAATTTCGCGTT
182 GCGA
1 GCGA
186 TAGTACTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.11
19 28 0.80
20 3 0.09
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:186 original size:19 final size:19
Alignment explanation
Indices: 134--186 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
124 CGCGAATTTA
134 ATTTCGCGTTGCGA-TTTC
1 ATTTCGCGTTGCGATTTTC
152 ATTTTCGCGTTGCGATTTTC
1 A-TTTCGCGTTGCGATTTTC
*
172 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
187 AGTACTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 1 0.03
19 26 0.81
20 5 0.16
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:310 original size:14 final size:14
Alignment explanation
Indices: 291--326 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
281 CATCAATTAA
*
291 ACAAATCAACTTTT
1 ACAAATCAACCTTT
305 ACAAATC-ACCTTT
1 ACAAATCAACCTTT
318 ACAAATCAA
1 ACAAATCAA
327 TTAAACAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (14 bp):
ACAAATCAACCTTT
Found at i:1756 original size:42 final size:41
Alignment explanation
Indices: 1671--1792 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1661 GTGAATCGGG
* * * *
1671 CTCTTGAATGGTGGGA-GGGACCTCTTC-ACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1712 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1754 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
1793 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
40 2 0.03
41 20 0.29
42 44 0.65
43 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:3901 original size:19 final size:19
Alignment explanation
Indices: 3784--3967 Score: 165
Period size: 20 Copynumber: 10.1 Consensus size: 19
3774 GTCTTTGGTT
*
3784 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
3803 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3823 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
3841 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
3857 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
3875 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3890 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
3910 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3929 GAAATG-AAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3947 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3966 GA
1 GA
3968 TTTTGGTTTC
Statistics
Matches: 136, Mismatches: 15, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 22 0.16
19 42 0.31
20 45 0.33
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3922 original size:39 final size:37
Alignment explanation
Indices: 3784--3967 Score: 154
Period size: 33 Copynumber: 5.1 Consensus size: 37
3774 GTCTTTGGTT
* *
3784 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATG-AAATCGCAACGCGA-AATGAAAATCGCAACGC
* *
3823 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGA-AATCGCAACGCGAAATGAAAATCGCAACGC
* * *
3857 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGA-AATCGCAACGCGAAATGAAAATCGCAACGC
*
3890 GAAATGAAAATCGCAACCGCGAAATTAAAATCGCAACGC
1 GAAATG-AAATCGCAA-CGCGAAATGAAAATCGCAACGC
*
3929 GAAATGAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAATCGCAACGCGAAATGAAAATCGCAACGC
3966 GA
1 GA
3968 TTTTGGTTTC
Statistics
Matches: 125, Mismatches: 10, Indels: 21
0.80 0.06 0.13
Matches are distributed among these distances:
33 41 0.33
34 17 0.14
35 2 0.02
37 22 0.18
38 11 0.09
39 19 0.15
40 13 0.10
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (37 bp):
GAAATGAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:3996 original size:19 final size:19
Alignment explanation
Indices: 3963--4007 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3953 AAAATCGCAA
*
3963 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
3982 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
4001 TGCGATT
1 TGCGATT
4008 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:4644 original size:20 final size:20
Alignment explanation
Indices: 4559--4652 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
4549 CGCTAAGTAA
*
4559 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
4579 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
4599 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
4620 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
4640 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
4653 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:4671 original size:41 final size:41
Alignment explanation
Indices: 4641--4736 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
4631 ATAGTCAGTA
* * *
4641 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
4682 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
4723 TCGCATTGCGAATT
1 TCGCATTGCGAATT
4737 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:4685 original size:20 final size:20
Alignment explanation
Indices: 4641--4733 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
4631 ATAGTCAGTA
* **
4641 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
4662 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
4682 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
4703 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
4723 TCGCATTGCGA
1 TCGCATTGCGA
4734 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:8358 original size:5 final size:5
Alignment explanation
Indices: 8348--8374 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
8338 TACTTATGAA
8348 AGAAG AGAAG AGAAG AGAAG AGAAG AG
1 AGAAG AGAAG AGAAG AGAAG AGAAG AG
8375 GCAAAGAGAT
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:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:15740 original size:3 final size:3
Alignment explanation
Indices: 15722--15764 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
15712 TTTACAAAAA
*
15722 TAT TAT TAAT TA- TAT TAT TA- TGT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
15765 AAAAAATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 3 0.09
3 29 0.83
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:15749 original size:20 final size:20
Alignment explanation
Indices: 15724--15762 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
15714 TACAAAAATA
15724 TTATTAATTA-TATTATTATG
1 TTATT-ATTATTATTATTATG
15744 TTATTATTATTATTATTAT
1 TTATTATTATTATTATTAT
15763 TAAAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
TTATTATTATTATTATTATG
Found at i:16126 original size:3 final size:3
Alignment explanation
Indices: 16079--16111 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
16069 TTATATTAAA
*
16079 ATT A-T ATT ATT ATT ATT ATT AAT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
16112 ATGTTACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:24876 original size:8 final size:8
Alignment explanation
Indices: 24857--24941 Score: 74
Period size: 7 Copynumber: 10.8 Consensus size: 8
24847 TTAAAGATAA
24857 AAAAAATG
1 AAAAAATG
24865 -AAAAATG
1 AAAAAATG
24872 AAAAAAATG
1 -AAAAAATG
24881 AAAAAAATG
1 -AAAAAATG
24890 AAAAAATG
1 AAAAAATG
*
24898 -AAATA-G
1 AAAAAATG
24904 -AAAAATAG
1 AAAAAAT-G
24912 AAAAAATGG
1 AAAAAAT-G
24921 AAAAAAAT-
1 -AAAAAATG
24929 AAAAAAT-
1 AAAAAATG
24936 AAAAAA
1 AAAAAA
24942 AAGAAGAAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
6 5 0.07
7 24 0.35
8 9 0.13
9 23 0.34
10 7 0.10
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:24877 original size:9 final size:9
Alignment explanation
Indices: 24856--24952 Score: 73
Period size: 9 Copynumber: 10.8 Consensus size: 9
24846 CTTAAAGATA
24856 AAAAAAATG
1 AAAAAAATG
24865 --AAAAATG
1 AAAAAAATG
24872 AAAAAAATG
1 AAAAAAATG
24881 AAAAAAATG
1 AAAAAAATG
24890 -AAAAAATG
1 AAAAAAATG
24898 AAATAGAAAAAT-
1 --A-A-AAAAATG
24910 AGAAAAAATGG
1 A-AAAAAAT-G
24921 AAAAAAAT-
1 AAAAAAATG
24929 -AAAAAAT-
1 AAAAAAATG
*
24936 AAAAAAAAG
1 AAAAAAATG
24945 AAGAAAAA
1 AA-AAAAA
24953 AACAAAAAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 23
0.75 0.02 0.23
Matches are distributed among these distances:
7 14 0.19
8 14 0.19
9 24 0.32
10 14 0.19
11 1 0.01
12 1 0.01
13 6 0.08
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.10
Consensus pattern (9 bp):
AAAAAAATG
Found at i:24877 original size:17 final size:17
Alignment explanation
Indices: 24855--24943 Score: 66
Period size: 17 Copynumber: 5.5 Consensus size: 17
24845 GCTTAAAGAT
24855 AAAAAAAATGAAAAATG
1 AAAAAAAATGAAAAATG
24872 -AAAAAAATGAAAAA--
1 AAAAAAAATGAAAAATG
*
24886 AATGAAAAAATGAAATA-G
1 AA--AAAAAATGAAAAATG
*
24904 -AAAAATA-GAAAAAATG
1 AAAAAAAATG-AAAAATG
* *
24920 GAAAAAAATAAAAAAT-
1 AAAAAAAATGAAAAATG
24936 AAAAAAAA
1 AAAAAAAA
24944 GAAGAAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
14 1 0.02
15 10 0.17
16 22 0.38
17 25 0.43
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.11
Consensus pattern (17 bp):
AAAAAAAATGAAAAATG
Found at i:24901 original size:22 final size:22
Alignment explanation
Indices: 24876--24927 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
24866 AAAATGAAAA
24876 AAATGAAAAAAAT-GAAAAAATG
1 AAAT-AAAAAAATAGAAAAAATG
*
24898 AAATAGAAAAATAGAAAAAATG
1 AAATAAAAAAATAGAAAAAATG
*
24920 GAA-AAAAA
1 AAATAAAAA
24928 TAAAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (22 bp):
AAATAAAAAAATAGAAAAAATG
Found at i:24908 original size:39 final size:38
Alignment explanation
Indices: 24860--24935 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 38
24850 AAGATAAAAA
24860 AAATGAAAAAT-GAAAAAAAT-GAAAAAAATGAAAAAATG
1 AAATGAAAAATAG-AAAAAATGGAAAAAAAT-AAAAAATG
24898 AAATAGAAAAATAGAAAAAATGGAAAAAAATAAAAAAT
1 AAAT-GAAAAATAGAAAAAATGGAAAAAAATAAAAAAT
24936 AAAAAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
38 4 0.11
39 21 0.60
40 10 0.29
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.13
Consensus pattern (38 bp):
AAATGAAAAATAGAAAAAATGGAAAAAAATAAAAAATG
Found at i:24939 original size:6 final size:7
Alignment explanation
Indices: 24857--24966 Score: 53
Period size: 7 Copynumber: 14.6 Consensus size: 7
24847 TTAAAGATAA
24857 AAAAAAT
1 AAAAAAT
*
24864 GAAAAAT
1 AAAAAAT
24871 GAAAAAAAT
1 --AAAAAAT
24880 GAAAAAAAT
1 --AAAAAAT
24889 GAAAAAAT
1 -AAAAAAT
* * *
24897 GAAATAG
1 AAAAAAT
*
24904 AAAAATAG
1 AAAAA-AT
24912 AAAAAAT
1 AAAAAAT
24919 GGAAAAAAAT
1 ---AAAAAAT
24929 AAAAAAT
1 AAAAAAT
24936 AAAAAA-
1 AAAAAAT
*
24942 AAGAAGA-
1 AA-AAAAT
*
24949 AAAAAAC
1 AAAAAAT
24956 AAAAAAT
1 AAAAAAT
24963 AAAA
1 AAAA
24967 GGGGGGTTCA
Statistics
Matches: 83, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
6 5 0.06
7 42 0.51
8 14 0.17
9 15 0.18
10 7 0.08
ACGTcount: A:0.79, C:0.01, G:0.10, T:0.10
Consensus pattern (7 bp):
AAAAAAT
Found at i:24942 original size:8 final size:8
Alignment explanation
Indices: 24856--24966 Score: 61
Period size: 9 Copynumber: 13.5 Consensus size: 8
24846 CTTAAAGATA
24856 AAAAAAAT
1 AAAAAAAT
*
24864 -GAAAAAT
1 AAAAAAAT
24871 GAAAAAAAT
1 -AAAAAAAT
24880 GAAAAAAAT
1 -AAAAAAAT
*
24889 GAAAAAAT
1 AAAAAAAT
*
24897 ---GAAAT
1 AAAAAAAT
*
24902 AGAAAAAT
1 AAAAAAAT
24910 AGAAAAAAT
1 A-AAAAAAT
24919 GGAAAAAAAT
1 --AAAAAAAT
24929 -AAAAAAT
1 AAAAAAAT
*
24936 AAAAAAAAG
1 -AAAAAAAT
*
24945 AAGAAAAAA
1 AA-AAAAAT
24954 ACAAAAAAT
1 A-AAAAAAT
24963 AAAA
1 AAAA
24967 GGGGGGTTCA
Statistics
Matches: 82, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
5 4 0.05
7 13 0.16
8 17 0.21
9 39 0.48
10 8 0.10
11 1 0.01
ACGTcount: A:0.79, C:0.01, G:0.10, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:24951 original size:17 final size:16
Alignment explanation
Indices: 24853--24966 Score: 65
Period size: 17 Copynumber: 6.9 Consensus size: 16
24843 TTGCTTAAAG
24853 ATAAAAAAAATG-AAAA
1 ATAAAAAAAA-GAAAAA
*
24869 ATGAAAAAAATGAAAAAA
1 AT-AAAAAAAAG-AAAAA
* *
24887 ATGAAAAAATG---AA
1 ATAAAAAAAAGAAAAA
*
24900 ATAGAAAAATAGAAAAA
1 ATA-AAAAAAAGAAAAA
* *
24917 ATGGAAAAAAATAAAAA
1 AT-AAAAAAAAGAAAAA
24934 ATAAAAAAAAGAAGAAA
1 ATAAAAAAAAGAA-AAA
* *
24951 AAAACAAAAAATAAAA
1 ATAA-AAAAAAGAAAA
24967 GGGGGGTTCA
Statistics
Matches: 76, Mismatches: 12, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
13 4 0.05
14 6 0.08
16 12 0.16
17 40 0.53
18 14 0.18
ACGTcount: A:0.79, C:0.01, G:0.10, T:0.11
Consensus pattern (16 bp):
ATAAAAAAAAGAAAAA
Found at i:26330 original size:55 final size:55
Alignment explanation
Indices: 26246--26525 Score: 483
Period size: 55 Copynumber: 5.1 Consensus size: 55
26236 TGAAGCAAAA
26246 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
26301 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
26356 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
26409 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
26464 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
26519 GGAGATT
1 GAAGATT
26526 ATTGTTCGAG
Statistics
Matches: 210, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
53 47 0.22
54 6 0.03
55 157 0.75
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:26449 original size:108 final size:110
Alignment explanation
Indices: 26246--26528 Score: 507
Period size: 108 Copynumber: 2.6 Consensus size: 110
26236 TGAAGCAAAA
26246 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
26311 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
* *
26356 GAAGATTG-TGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
* *
26419 CGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
*
26464 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
26529 GTTCGAGTTC
Statistics
Matches: 164, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
108 101 0.62
109 6 0.04
110 57 0.35
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (110 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
Found at i:26581 original size:52 final size:52
Alignment explanation
Indices: 26521--26969 Score: 736
Period size: 52 Copynumber: 8.6 Consensus size: 52
26511 CGATCGTTGG
* *
26521 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
26573 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGTAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
26625 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
26677 AGATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * * * *
26729 AGTTTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
26781 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
26833 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
26885 AGATTATTGTTCAAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
26937 AGATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
26970 TAGAGAGCGA
Statistics
Matches: 375, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 375 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
Found at i:26782 original size:24 final size:24
Alignment explanation
Indices: 26755--26835 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
26745 TCTAGTCCCT
26755 GAAGAAAATTGGACAGTCTCGTAG
1 GAAGAAAATTGGACAGTCTCGTAG
** ** * **
26779 GAAGATTATTGTTCGAGTTCTAGTCCCT
1 GAAGAAAATTGGAC-AG-TCTCGT--AG
26807 GAAGAAAATTGGACAGTCTCGTAG
1 GAAGAAAATTGGACAGTCTCGTAG
26831 GAAGA
1 GAAGA
26836 TTATTGTTCG
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
24 15 0.38
25 2 0.05
26 10 0.26
27 2 0.05
28 10 0.26
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (24 bp):
GAAGAAAATTGGACAGTCTCGTAG
Found at i:27289 original size:3 final size:3
Alignment explanation
Indices: 27242--27274 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
27232 TTATATTAAA
*
27242 ATT A-T ATT ATT ATT ATT ATT AAT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
27275 ATGTTACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:34156 original size:24 final size:25
Alignment explanation
Indices: 34121--34175 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
34111 ACTTTGAGCC
*
34121 TCAA-TGATCACAACTTGTGGCACT
1 TCAAGTGATCACAACTTGTGGAACT
* *
34145 TCAAGTGA-CACAACTTTTTGAACT
1 TCAAGTGATCACAACTTGTGGAACT
34169 TCAAGTG
1 TCAAGTG
34176 GCATAACTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (25 bp):
TCAAGTGATCACAACTTGTGGAACT
Found at i:35489 original size:15 final size:15
Alignment explanation
Indices: 35454--35482 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35444 GTGCTTCAAC
35454 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
35468 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
35483 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:40124 original size:24 final size:24
Alignment explanation
Indices: 40096--40144 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
40086 TAGGATTATT
40096 TATATT-TATATTTATAGTATATAA
1 TATATTATATATTTATAGTA-ATAA
* *
40120 TATATTATGTATTTGTAGTAATAA
1 TATATTATATATTTATAGTAATAA
40144 T
1 T
40145 TTAGACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (24 bp):
TATATTATATATTTATAGTAATAA
Found at i:51559 original size:36 final size:36
Alignment explanation
Indices: 51507--51609 Score: 147
Period size: 36 Copynumber: 2.9 Consensus size: 36
51497 GTAGTAAAGC
* *
51507 AATTCAGCCTTTACAGAAGAGTAGTGAAGCAATACA
1 AATTCAGACTTCACAGAAGAGTAGTGAAGCAATACA
51543 AATTCAGACTTCACAGAAGAGTAGTGAAGCAATACA
1 AATTCAGACTTCACAGAAGAGTAGTGAAGCAATACA
*
51579 AATCCA-ACCTTCAC-GAAAGAGTAGTGAAGCA
1 AATTCAGA-CTTCACAG-AAGAGTAGTGAAGCA
51610 GGAAAAAATC
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
35 2 0.03
36 60 0.97
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (36 bp):
AATTCAGACTTCACAGAAGAGTAGTGAAGCAATACA
Found at i:51817 original size:3 final size:3
Alignment explanation
Indices: 51793--51834 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
51783 TCGTTATGTG
* *
51793 TAT TA- TAT TA- TAT TAT TTT TAT TAT TAG TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
51835 AGTTATTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:53592 original size:20 final size:20
Alignment explanation
Indices: 53556--53593 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53546 ATCCTATTCC
**
53556 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
53576 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
53594 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:53811 original size:6 final size:6
Alignment explanation
Indices: 53800--53825 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
53790 AACATAGGAT
53800 TATTTA TATTTA TATTTA TATTTA TA
1 TATTTA TATTTA TATTTA TATTTA TA
53826 GTATATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TATTTA
Found at i:53857 original size:24 final size:24
Alignment explanation
Indices: 53810--53858 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
53800 TATTTATATT
53810 TATATTTATATTTATAGTATATAA
1 TATATTTATATTTATAGTATATAA
* *
53834 TATATTATGTATTTGTAGTA-ATAA
1 TATATT-TATATTTATAGTATATAA
53858 T
1 T
53859 TTAGACATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (24 bp):
TATATTTATATTTATAGTATATAA
Found at i:57680 original size:16 final size:16
Alignment explanation
Indices: 57656--57697 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
57646 CAGATCGAAA
*
57656 AAACATACATCAATAC
1 AAACATACATCAACAC
*
57672 AAGCATACATCAACAC
1 AAACATACATCAACAC
57688 AAACATACAT
1 AAACATACAT
57698 GATATATGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.55, C:0.26, G:0.02, T:0.17
Consensus pattern (16 bp):
AAACATACATCAACAC
Found at i:58675 original size:70 final size:68
Alignment explanation
Indices: 58514--58732 Score: 212
Period size: 70 Copynumber: 3.2 Consensus size: 68
58504 TTTGAGTCTT
* * * * * * *
58514 TTTCTCTTAAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTTTTCAAACAAAACAATTTTTGAG
1 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTC-TTTGAAAAAAAACCATCTTTAAG
* *
58579 ATTA
65 TTTG
* *
58583 TTTCCCTTGAAACGAA-TTTTGTCTCTATTGAGATAGTTTCTATTGAAAAAAAAAACCATCTTTA
1 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCT-TTG--AAAAAAAACCATCTTTA
58647 AGTTTG
63 AGTTTG
* * * * *
58653 TTTCCTTTGAAAC-AAGTTTTGTCTCTCTTGAGACAGCTTCTCTTG--AAACAATCATCTTTAAG
1 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCT-TTGAAAAAAAACCATCTTTAAG
*
58715 TCTG
65 TTTG
58719 TTTCCCTTGAAACA
1 TTTCCCTTGAAACA
58733 TTATCCCTAT
Statistics
Matches: 125, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
66 30 0.24
67 1 0.01
68 25 0.20
69 15 0.12
70 54 0.43
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (68 bp):
TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTTTGAAAAAAAACCATCTTTAAGT
TTG
Done.