Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007422.1 Hibiscus syriacus cultivar Beakdansim tig00020088_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: 92531
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1424 original size:22 final size:21
Alignment explanation
Indices: 1382--1421 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1372 AAGACTGTTT
1382 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
1403 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
1422 ATAGAGTCTT
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:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:3445 original size:19 final size:20
Alignment explanation
Indices: 3421--3461 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
3411 AAACCATTCA
3421 GGGGGAATCGGTACCC-CTG
1 GGGGGAATCGGTACCCTCTG
*
3440 GGGGGAATCGGTTCCCTCTG
1 GGGGGAATCGGTACCCTCTG
3460 GG
1 GG
3462 CAATCTGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.12, C:0.24, G:0.44, T:0.20
Consensus pattern (20 bp):
GGGGGAATCGGTACCCTCTG
Found at i:3819 original size:29 final size:27
Alignment explanation
Indices: 3760--3824 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
3750 AAAAATATCA
* *
3760 AAAAGAAAATGAAAAAAGGACTAATTT
1 AAAAGAAAATGAAAAAAGGACAAACTT
**
3787 AAAAGAAAATGAAATTAGGGGACAAACTT
1 AAAAGAAAATGAAA--AAAGGACAAACTT
3816 AAAAGAAAA
1 AAAAGAAAA
3825 ATCAGGATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 14 0.44
29 18 0.56
ACGTcount: A:0.63, C:0.05, G:0.17, T:0.15
Consensus pattern (27 bp):
AAAAGAAAATGAAAAAAGGACAAACTT
Found at i:4776 original size:4 final size:4
Alignment explanation
Indices: 4767--4792 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4757 GCTAAAACAT
4767 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
4793 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:4899 original size:15 final size:15
Alignment explanation
Indices: 4853--4899 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
4843 TAAAATTTTT
4853 TTTTCAAAATAATATA
1 TTTTCAAAA-AATATA
*
4869 TTTTCAAAAAAAATA
1 TTTTCAAAAAATATA
* *
4884 TTTTTAAAAACTATA
1 TTTTCAAAAAATATA
4899 T
1 T
4900 ATTATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTTCAAAAAATATA
Found at i:4928 original size:38 final size:38
Alignment explanation
Indices: 4876--4982 Score: 144
Period size: 38 Copynumber: 2.8 Consensus size: 38
4866 ATATTTTCAA
*
4876 AAAAAATATTTTTAAAAACTATATATTATATATATATTC
1 AAAAAAT-GTTTTAAAAACTATATATTATATATATATTC
* * *
4915 AAAAAATGTTTTAAAAACTATATAATATATATGTTTTC
1 AAAAAATGTTTTAAAAACTATATATTATATATATATTC
*
4953 -AAAAATGTTTTCAAAACTTATATATTATAT
1 AAAAAATGTTTTAAAAAC-TATATATTATAT
4983 GTTTTCAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
37 16 0.26
38 38 0.62
39 7 0.11
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (38 bp):
AAAAAATGTTTTAAAAACTATATATTATATATATATTC
Found at i:4944 original size:36 final size:35
Alignment explanation
Indices: 4885--5197 Score: 187
Period size: 37 Copynumber: 8.7 Consensus size: 35
4875 AAAAAAATAT
4885 TTTTAAAAACTATATATTATATATATATTCAAAAAATG
1 TTTTAAAAACTATATA--ATATATATATTC-AAAAATG
*
4923 TTTTAAAAACTATATAATATATATGTTTTCAAAAATG
1 TTTTAAAAACTATATAATATATA--TATTCAAAAATG
* *
4960 TTTTCAAAACT-TAT-ATAT-TATA-T-----GT-
1 TTTTAAAAACTATATAATATATATATTCAAAAATG
* * * * *
4985 TTTCAAAAATTATATATTATATGTTTTCAAAAATG
1 TTTTAAAAACTATATAATATATATATTCAAAAATG
* * *
5020 TTTTAAAAAAACTATATATTATATAAGTTTTTAAAAATG
1 TTTT--AAAAACTATATAATATAT-A-TATTCAAAAATG
* * *
5059 ATTTTAAAACCCATATAATATATATATTTTCTAAAATG
1 -TTTTAAAAACTATATAATATATATA--TTCAAAAATG
* * * *
5097 TTTTCAAAACTATATATTATATAGTTTTCAAAAATA
1 TTTTAAAAACTATATAATATATA-TATTCAAAAATG
* **
5133 TTTTAAAAACTATATATTATATACGTATTTTCAAAAACC
1 TTTTAAAAACTATATA--ATATA--TATATTCAAAAATG
* **
5172 ATTTGCAAACTATATAATATATATAT
1 TTTTAAAAACTATATAATATATATAT
5198 GTATATATAT
Statistics
Matches: 215, Mismatches: 36, Indels: 51
0.71 0.12 0.17
Matches are distributed among these distances:
25 8 0.04
26 4 0.02
27 3 0.01
28 2 0.01
29 1 0.00
31 1 0.00
32 1 0.00
34 3 0.01
35 11 0.05
36 34 0.16
37 59 0.27
38 48 0.22
39 34 0.16
40 6 0.03
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (35 bp):
TTTTAAAAACTATATAATATATATATTCAAAAATG
Found at i:4989 original size:24 final size:24
Alignment explanation
Indices: 4957--5018 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
4947 GTTTTCAAAA
*
4957 ATGTTTTCAAAACTTATATATTAT
1 ATGTTTTCAAAAATTATATATTAT
4981 ATGTTTTCAAAAATTATATATTAT
1 ATGTTTTCAAAAATTATATATTAT
5005 ATGTTTTCAAAAAT
1 ATGTTTTCAAAAAT
5019 GTTTTAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.48
Consensus pattern (24 bp):
ATGTTTTCAAAAATTATATATTAT
Found at i:5182 original size:39 final size:36
Alignment explanation
Indices: 4984--5194 Score: 167
Period size: 39 Copynumber: 5.6 Consensus size: 36
4974 ATATTATATG
* **
4984 TTTTCAAAAATTATATATTATAT-GTTTTCAAAAATG
1 TTTT-AAAAACTATATATTATATAGTTTTCAAAAACA
* *
5020 TTTTAAAAAAACTATATATTATATAAGTTTTTAAAAATGA
1 TTTT--AAAAACTATATATTATAT-AGTTTTCAAAAA-CA
* * * **
5060 TTTTAAAACCCATATAATATATATA-TTTTCTAAAATG
1 TTTTAAAAACTATAT-AT-TATATAGTTTTCAAAAACA
* *
5097 TTTTCAAAACTATATATTATATAGTTTTCAAAAATA
1 TTTTAAAAACTATATATTATATAGTTTTCAAAAACA
5133 TTTTAAAAACTATATATTATATACGTATTTTCAAAAACCA
1 TTTTAAAAACTATATATTATATA-G--TTTTCAAAAA-CA
** *
5173 -TTTGCAAACTATATAATATATA
1 TTTTAAAAACTATATATTATATA
5195 TATGTATATA
Statistics
Matches: 143, Mismatches: 21, Indels: 19
0.78 0.11 0.10
Matches are distributed among these distances:
35 6 0.04
36 38 0.27
37 30 0.21
38 17 0.12
39 42 0.29
40 10 0.07
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (36 bp):
TTTTAAAAACTATATATTATATAGTTTTCAAAAACA
Found at i:5186 original size:73 final size:73
Alignment explanation
Indices: 5027--5194 Score: 178
Period size: 75 Copynumber: 2.2 Consensus size: 73
5017 ATGTTTTAAA
* * *
5027 AAAACTATATATTATATAAGTTTTTAAAAATGATTTTAAAACCCATATAATATATATATTTTCTA
1 AAAAC-ATATATTATAT-AGTTTTCAAAAATGATTTTAAAAACCATATAATATATATATTTTCAA
** *
5092 AAATGTTTTC
64 AAACATTTGC
* *
5102 AAAACTATATATTATATAGTTTTCAAAAAT-ATTTTAAAAACTATATATTATATACGTATTTTCA
1 AAAAC-ATATATTATATAGTTTTCAAAAATGATTTTAAAAACCATATAATATATA--TATTTTCA
5166 AAAACCATTTGC
63 AAAA-CATTTGC
*
5178 -AAACTATATAATATATA
1 AAAAC-ATATATTATATA
5195 TATGTATATA
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
73 21 0.26
74 12 0.15
75 44 0.54
76 4 0.05
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.42
Consensus pattern (73 bp):
AAAACATATATTATATAGTTTTCAAAAATGATTTTAAAAACCATATAATATATATATTTTCAAAA
ACATTTGC
Found at i:8654 original size:18 final size:18
Alignment explanation
Indices: 8633--8670 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
8623 GTGATATTGC
8633 AAAAAAATATGA-TACATT
1 AAAAAAA-ATGATTACATT
*
8651 AAAAAGAATGATTACATT
1 AAAAAAAATGATTACATT
8669 AA
1 AA
8671 TTTTGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (18 bp):
AAAAAAAATGATTACATT
Found at i:9481 original size:6 final size:6
Alignment explanation
Indices: 9467--9497 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
9457 TTTTCCAAAA
*
9467 CCTAAC CCTAGC CCTAAC CCTAAC CCTAAC C
1 CCTAAC CCTAAC CCTAAC CCTAAC CCTAAC C
9498 TATTTCTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.29, C:0.52, G:0.03, T:0.16
Consensus pattern (6 bp):
CCTAAC
Found at i:15953 original size:21 final size:21
Alignment explanation
Indices: 15927--15996 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
15917 ATATAATAAA
15927 AAAAAAACCAAAAATCAGAAG
1 AAAAAAACCAAAAATCAGAAG
* *
15948 AAAAAAATCCTCAACATTC--AA-
1 AAAAAAA--C-CAAAAATCAGAAG
*
15969 AAAAAAACCAAAAATTAGAAG
1 AAAAAAACCAAAAATCAGAAG
15990 AAAAAAA
1 AAAAAAA
15997 ATCCTCAACA
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
18 5 0.13
19 1 0.03
20 2 0.05
21 21 0.55
22 2 0.05
23 1 0.03
24 6 0.16
ACGTcount: A:0.70, C:0.14, G:0.06, T:0.10
Consensus pattern (21 bp):
AAAAAAACCAAAAATCAGAAG
Found at i:15989 original size:42 final size:43
Alignment explanation
Indices: 15924--16044 Score: 172
Period size: 42 Copynumber: 2.7 Consensus size: 43
15914 TACATATAAT
15924 AAAAAAAAAACCAAAAATCAGAAGAAAAAAATCCTCAACATTC
1 AAAAAAAAAACCAAAAATCAGAAGAAAAAAATCCTCAACATTC
*
15967 -AAAAAAAAACCAAAAATTAGAAGAAAAAAAATCCTCAACATTC
1 AAAAAAAAAACCAAAAATCAGAAG-AAAAAAATCCTCAACATTC
*
16010 AAATCATAAAAAAACCAAAAATCAAAAGAAAAAAA
1 -AA--A-AAAAAAACCAAAAATCAGAAGAAAAAAA
16045 AATTATAGCG
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
42 22 0.32
43 19 0.28
45 1 0.01
47 8 0.12
48 19 0.28
ACGTcount: A:0.69, C:0.16, G:0.04, T:0.12
Consensus pattern (43 bp):
AAAAAAAAAACCAAAAATCAGAAGAAAAAAATCCTCAACATTC
Found at i:15995 original size:43 final size:44
Alignment explanation
Indices: 15924--16045 Score: 176
Period size: 48 Copynumber: 2.7 Consensus size: 44
15914 TACATATAAT
15924 AAAAAAAAAACCAAAAATCAGAAG-AAAAAAATCCTCAACATTC
1 AAAAAAAAAACCAAAAATCAGAAGAAAAAAAATCCTCAACATTC
*
15967 -AAAAAAAAACCAAAAATTAGAAGAAAAAAAATCCTCAACATTC
1 AAAAAAAAAACCAAAAATCAGAAGAAAAAAAATCCTCAACATTC
*
16010 AAATCATAAAAAAACCAAAAATCAAAAGAAAAAAAA
1 -AA--A-AAAAAAACCAAAAATCAGAAGAAAAAAAA
16046 ATTATAGCGC
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
42 22 0.31
43 19 0.27
45 1 0.01
47 1 0.01
48 27 0.39
ACGTcount: A:0.69, C:0.16, G:0.04, T:0.11
Consensus pattern (44 bp):
AAAAAAAAAACCAAAAATCAGAAGAAAAAAAATCCTCAACATTC
Found at i:16043 original size:23 final size:23
Alignment explanation
Indices: 15967--16046 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
15957 CTCAACATTC
* *
15967 AAAAAAAAACCAAAAATTAGAAG
1 AAAAAAAAACCAAAAATCAAAAG
* * * **
15990 AAAAAAAATCCTCAACATTCAAATC
1 AAAAAAAA-AC-CAAAAATCAAAAG
*
16015 ATAAAAAAACCAAAAATCAAAAG
1 AAAAAAAAACCAAAAATCAAAAG
16038 AAAAAAAAA
1 AAAAAAAAA
16047 TTATAGCGCA
Statistics
Matches: 41, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
23 25 0.61
24 2 0.05
25 14 0.34
ACGTcount: A:0.71, C:0.14, G:0.04, T:0.11
Consensus pattern (23 bp):
AAAAAAAAACCAAAAATCAAAAG
Found at i:19111 original size:3 final size:3
Alignment explanation
Indices: 19103--19140 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
19093 ACCTAAAGAT
19103 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19141 TTAAATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19165 original size:25 final size:26
Alignment explanation
Indices: 19121--19188 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
19111 ATTATTATTA
* **
19121 TTATTATTAT-TATTATTATTTTAAAT
1 TTATT-TTATATATTTTTATTAAAAAT
19147 TT-TTTTATATATTTTTATTAAAAAT
1 TTATTTTATATATTTTTATTAAAAAT
19172 TTATTTT-TATCATTTTT
1 TTATTTTATAT-ATTTTT
19189 CAATCTTCGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 4 0.11
25 20 0.56
26 12 0.33
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (26 bp):
TTATTTTATATATTTTTATTAAAAAT
Found at i:26919 original size:63 final size:65
Alignment explanation
Indices: 26810--26971 Score: 181
Period size: 63 Copynumber: 2.5 Consensus size: 65
26800 ATCCCTTGAC
* *
26810 GGGTGCATCGATGCACTA-TCTATGCATCGATACA-TAAATCCTATTCGATGTTTGTA-TTTAAG
1 GGGTGCATCGATGCACTACT-TGTGCATCGATACACTAAATCCTATTCGATGTTTGTATTTTAAA
*
26872 G
65 A
* * *
26873 GGGTGCATCGATGCACTACTTGTGCATCGATACACT-GATGGC-ATTCGATGTTTTTATTTTAAA
1 GGGTGCATCGATGCACTACTTGTGCATCGATACACTAAAT-CCTATTCGATGTTTGTATTTTAAA
26936 A
65 A
** * *
26937 TAGTGCATCGATGCACTTCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTACTTGTGCATCGATACAC
26972 CTTGAACAGT
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 46 0.54
64 39 0.46
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (65 bp):
GGGTGCATCGATGCACTACTTGTGCATCGATACACTAAATCCTATTCGATGTTTGTATTTTAAAA
Found at i:33184 original size:86 final size:85
Alignment explanation
Indices: 32718--33177 Score: 407
Period size: 85 Copynumber: 5.4 Consensus size: 85
32708 AAGGTAATTA
** *
32718 GCGGCGTTTGTATCCAAAAA-GCCATTATAGATCTGACCTTTTGCGGCGA-TTG-TATCCAAAAA
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCAGACCTTTTGCGGC-ATTTGTTAT--AAAAA
*
32780 -GCCGCTATAGATCTCGACTTTTT
62 CGCCGCTATAGATCTCGACCTTTT
* * * ** * ** **
32803 GCGGCGTTTGTTCCAAAAACACCGCTATAGATCAGACCTTGTACGAAATTTATTCCAAAAATACC
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCAGACCTTTTGCGGCATTTGTTATAAAAACGCC
*
32868 GCTATAGATCTAGACCTTTT
66 GCTATAGATCTCGACCTTTT
* * **
32888 GCGGCGTTTGTTCCAAAAACGTCGCTATAGATCAAACCTTTTGTAG-AGTTTGTT-TAAAAAACG
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCAGACCTTTTGCGGCA-TTTGTTAT-AAAAACG
**
32951 CCGCTATAGATCTAAACCTTTT
64 CCGCTATAGATCTCGACCTTTT
* * * * ** *
32973 GCGACGTTTGTT-CAAAAAGCACCGCTATAGATATCA-ACCTTTTACGGCATTTATTCCAAAAAT
1 GCGGCGTTTGTTCCAAAAA-CGCCGCTATAG--ATCAGACCTTTTGCGGCATTTGTTATAAAAAC
* * *
33036 GTCGCTATCGATATCGACCTTTT
63 GCCGCTATAGATCTCGACCTTTT
* * * *
33059 GCGACGTTTGTTCCAAAAATGCCGCTATAGAT-ATCGACCTTTTGTGGCATTTGTTATAAAAACA
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCA--GACCTTTTGCGGCATTTGTTATAAAAACG
* *
33123 CCGCTATCGATATCGACCTTTT
64 CCGCTATAGATCTCGACCTTTT
* *
33145 GTGGCGTTTGTTCCAAAAACGCCGCTGTAGATC
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC
33178 TTGACCTATT
Statistics
Matches: 304, Mismatches: 55, Indels: 30
0.78 0.14 0.08
Matches are distributed among these distances:
83 1 0.00
84 23 0.08
85 141 0.46
86 128 0.42
87 11 0.04
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (85 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCAGACCTTTTGCGGCATTTGTTATAAAAACGCC
GCTATAGATCTCGACCTTTT
Found at i:33196 original size:43 final size:43
Alignment explanation
Indices: 32718--33184 Score: 424
Period size: 43 Copynumber: 10.9 Consensus size: 43
32708 AAGGTAATTA
**
32718 GCGGCGTTTGTATCCAAAAA-GCCATTATAGATCT-GACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTCGACCTTTT
* *
32760 GCGGCGATTGTATCCAAAAA-GCCGCTATAGATCTCGACTTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTCGACCTTTT
* * *
32803 GCGGCGTTTGTTCCAAAAACACCGCTATAGATC-AGACCTTGT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
* *** * ** *
32845 ACGAAATTTATTCCAAAAATACCGCTATAGATCTAGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
* **
32888 GCGGCGTTTGTTCCAAAAACGTCGCTATAGATC-AAACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
** * ** **
32930 GTAGAGTTTGTTTAAAAAACGCCGCTATAGATCTAAACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
* * * *
32973 GCGACGTTTGTT-CAAAAAGCACCGCTATAGATATCAACCTTTT
1 GCGGCGTTTGTTCCAAAAA-CGCCGCTATAGATCTCGACCTTTT
* * * * * * *
33016 ACGGCATTTATTCCAAAAATGTCGCTATCGATATCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
* * *
33059 GCGACGTTTGTTCCAAAAATGCCGCTATAGATATCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
* * ** * * *
33102 GTGGCATTTGTTATAAAAACACCGCTATCGATATCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
* * *
33145 GTGGCGTTTGTTCCAAAAACGCCGCTGTAGATCTTGACCT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCT
33185 ATTACAGCGT
Statistics
Matches: 349, Mismatches: 70, Indels: 11
0.81 0.16 0.03
Matches are distributed among these distances:
42 112 0.32
43 231 0.66
44 6 0.02
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (43 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTT
Found at i:39113 original size:6 final size:6
Alignment explanation
Indices: 39102--39165 Score: 110
Period size: 6 Copynumber: 10.7 Consensus size: 6
39092 AGAGAGTTCT
* *
39102 AGATCC AGATCC AGATCC AGATCC TGATCC TGATCC AGATCC AGATCC
1 AGATCC AGATCC AGATCC AGATCC AGATCC AGATCC AGATCC AGATCC
39150 AGATCC AGATCC AGAT
1 AGATCC AGATCC AGAT
39166 TCGGTTGCAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (6 bp):
AGATCC
Found at i:44622 original size:16 final size:16
Alignment explanation
Indices: 44601--44631 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44591 TACATATTCT
*
44601 TATATTCATATAGATA
1 TATATTCACATAGATA
44617 TATATTCACATAGAT
1 TATATTCACATAGAT
44632 CACTTTCACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (16 bp):
TATATTCACATAGATA
Found at i:49238 original size:20 final size:22
Alignment explanation
Indices: 49193--49246 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
49183 CTGTTGAAGA
*
49193 GGTATCGATA-CTGTAAGGGGT
1 GGTATCGATACCTGTAAGGGAT
49214 GGTATCGATACCTG-AA-GGAT
1 GGTATCGATACCTGTAAGGGAT
*
49234 GGTATTGATACCT
1 GGTATCGATACCT
49247 TGAAACATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 15 0.50
21 12 0.40
22 3 0.10
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Consensus pattern (22 bp):
GGTATCGATACCTGTAAGGGAT
Found at i:49298 original size:53 final size:54
Alignment explanation
Indices: 49234--49357 Score: 148
Period size: 53 Copynumber: 2.3 Consensus size: 54
49224 CCTGAAGGAT
* *
49234 GGTATTGATA-CCTTGAAACATCGAATG-TCATATTAGTATCGGTATC-TAGAAGA
1 GGTATCGATACCCTTGAAACATCGAATGAT-ATATTAGTATCGGTACCATAGAA-A
* * * *
49287 GGTTTCGATACCCTTG-AACATCGAATGATATTTTGGTATCGGTACCATGGAAA
1 GGTATCGATACCCTTGAAACATCGAATGATATATTAGTATCGGTACCATAGAAA
49340 GGTATCGATACCCTTGAA
1 GGTATCGATACCCTTGAA
49358 GGGGTAGTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
53 49 0.82
54 11 0.18
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (54 bp):
GGTATCGATACCCTTGAAACATCGAATGATATATTAGTATCGGTACCATAGAAA
Found at i:53369 original size:21 final size:20
Alignment explanation
Indices: 53333--53383 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
53323 TGTTGAAGAA
*
53333 GTATCGATACTGTAAGGGGTG
1 GTATCGATACTGTAA-GGATG
53354 GTATCGATACAT-TAAGGATG
1 GTATCGATAC-TGTAAGGATG
*
53374 ATATCGATAC
1 GTATCGATAC
53384 CTTGAAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 13 0.48
21 13 0.48
22 1 0.04
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (20 bp):
GTATCGATACTGTAAGGATG
Found at i:53452 original size:53 final size:53
Alignment explanation
Indices: 53352--53496 Score: 134
Period size: 53 Copynumber: 2.7 Consensus size: 53
53342 CTGTAAGGGG
* * * *
53352 TGGTATCGATACATTAAGGATGATATCGATA-CCTTGAAACATCGAATG-TCAGAT
1 TGGTATCGGTACCTTGAGGA-GGTATCGATACCCTTG-AACATCGAATGAT-AGAT
* * **
53406 TGGTATCGGTACCTTGAGGAGGTATCAATACCCTTGAACATTGAATGATATTT
1 TGGTATCGGTACCTTGAGGAGGTATCGATACCCTTGAACATCGAATGATAGAT
* * *
53459 TGGTATCGGTATCATG-GGAATGTATCGATACCCTTGAA
1 TGGTATCGGTACCTTGAGG-AGGTATCGATACCCTTGAA
53497 GGGTAGTATT
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
52 2 0.03
53 51 0.67
54 23 0.30
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (53 bp):
TGGTATCGGTACCTTGAGGAGGTATCGATACCCTTGAACATCGAATGATAGAT
Found at i:54154 original size:23 final size:23
Alignment explanation
Indices: 54125--54171 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
54115 AAAAGAATAC
*
54125 AAGTAAACTATGTGTCTAAGTGA
1 AAGTAAACTATGTGCCTAAGTGA
54148 AAGTAAACTATGTGCCTAAGTGA
1 AAGTAAACTATGTGCCTAAGTGA
54171 A
1 A
54172 TATGTGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (23 bp):
AAGTAAACTATGTGCCTAAGTGA
Found at i:61346 original size:2 final size:2
Alignment explanation
Indices: 61341--61380 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
61331 ATTTGAATTA
61341 AT AT AT AT AT 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 AT AT AT AT AT
61381 TTTGATATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61414 original size:21 final size:21
Alignment explanation
Indices: 61388--61430 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
61378 TATTTTGATA
*
61388 TTATGTTTGATATTTATAAAT
1 TTATGTTTGATATATATAAAT
*
61409 TTATGTTTGATATATATTAAT
1 TTATGTTTGATATATATAAAT
61430 T
1 T
61431 AATTCAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (21 bp):
TTATGTTTGATATATATAAAT
Found at i:62796 original size:21 final size:20
Alignment explanation
Indices: 62736--62798 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
62726 TTATTTTAGT
*
62736 ATAATTTTAATAAAATTATTA
1 ATAA-TTTAATAATATTATTA
* * * *
62757 ATTATTAAATTATATTTATTG
1 ATAATTTAATAATA-TTATTA
62778 ATAATCTTAATAATATTATTA
1 ATAAT-TTAATAATATTATTA
62799 TATTTTTGTG
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 7 0.23
21 17 0.55
22 7 0.23
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
ATAATTTAATAATATTATTA
Found at i:62924 original size:26 final size:27
Alignment explanation
Indices: 62864--62924 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 27
62854 ATATATAAAA
* * * *
62864 AATTATTAATAAAATTAATTTTATTAT
1 AATTATTTATAAAAATAATATTATTAG
*
62891 TATT-TTTATAAAAATAATATTA-TAG
1 AATTATTTATAAAAATAATATTATTAG
62916 AATTATTTA
1 AATTATTTA
62925 AATATTTAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
25 5 0.19
26 19 0.70
27 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
AATTATTTATAAAAATAATATTATTAG
Found at i:62993 original size:23 final size:23
Alignment explanation
Indices: 62955--63024 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
62945 TAAAATATAA
*
62955 TATAA-TATTCTTATTTTCA-TAT
1 TATAATTATTATTATTTT-ATTAT
*
62977 TATAATTTTTATTATTTTATTAT
1 TATAATTATTATTATTTTATTAT
*
63000 TATTATTATTATTATTATT-TTAT
1 TATAATTATTATTATT-TTATTAT
63023 TA
1 TA
63025 AGTAATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 6 0.15
23 33 0.80
24 2 0.05
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (23 bp):
TATAATTATTATTATTTTATTAT
Found at i:62999 original size:3 final size:3
Alignment explanation
Indices: 62974--63024 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
62964 CTTATTTTCA
* *
62974 TAT TAT AAT TTT TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
63020 TAT TA
1 TAT TA
63025 AGTAATTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:63003 original size:26 final size:26
Alignment explanation
Indices: 62974--63024 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
62964 CTTATTTTCA
*
62974 TATTATAATTTTTATTATTTTATTAT
1 TATTATAATTATTATTATTTTATTAT
*
63000 TATTATTATTATTATTATTTTATTA
1 TATTATAATTATTATTATTTTATTA
63025 AGTAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
TATTATAATTATTATTATTTTATTAT
Found at i:63084 original size:32 final size:32
Alignment explanation
Indices: 63008--63085 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
62998 ATTATTATTA
* *
63008 TTATTATTATTTTATTAAGTAATTAATATAAT
1 TTATTATTATTTTAATAAATAATTAATATAAT
* * *
63040 TAATTCTTATTTTAATAAATAATTAATATAGT
1 TTATTATTATTTTAATAAATAATTAATATAAT
*
63072 TTATTATAATTTTA
1 TTATTATTATTTTA
63086 TTTTAATAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (32 bp):
TTATTATTATTTTAATAAATAATTAATATAAT
Found at i:63193 original size:20 final size:19
Alignment explanation
Indices: 63170--63226 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
63160 CATATATTAA
63170 ATAAATTAATCTAATATTTT
1 ATAAATTAAT-TAATATTTT
* *
63190 ATAAATATTATTATTATTTT
1 ATAAAT-TAATTAATATTTT
* *
63210 GTAAATTAAATAATATT
1 ATAAATTAATTAATATT
63227 ATTTATTGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 8 0.27
20 19 0.63
21 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
ATAAATTAATTAATATTTT
Found at i:72848 original size:119 final size:119
Alignment explanation
Indices: 72637--72875 Score: 478
Period size: 119 Copynumber: 2.0 Consensus size: 119
72627 TCATTATCAA
72637 GAACCTACATGTTTGGGTATTCAAGATGTTGGATACCTAGTTTTTCGAGTACCAAAACAGTCGGT
1 GAACCTACATGTTTGGGTATTCAAGATGTTGGATACCTAGTTTTTCGAGTACCAAAACAGTCGGT
72702 TCGTGTCTCGACCTATGAAACTCGGGTACCTATAATTCGGGTCTTGCAAAACTT
66 TCGTGTCTCGACCTATGAAACTCGGGTACCTATAATTCGGGTCTTGCAAAACTT
72756 GAACCTACATGTTTGGGTATTCAAGATGTTGGATACCTAGTTTTTCGAGTACCAAAACAGTCGGT
1 GAACCTACATGTTTGGGTATTCAAGATGTTGGATACCTAGTTTTTCGAGTACCAAAACAGTCGGT
72821 TCGTGTCTCGACCTATGAAACTCGGGTACCTATAATTCGGGTCTTGCAAAACTT
66 TCGTGTCTCGACCTATGAAACTCGGGTACCTATAATTCGGGTCTTGCAAAACTT
72875 G
1 G
72876 GGTACTCGTT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 120 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (119 bp):
GAACCTACATGTTTGGGTATTCAAGATGTTGGATACCTAGTTTTTCGAGTACCAAAACAGTCGGT
TCGTGTCTCGACCTATGAAACTCGGGTACCTATAATTCGGGTCTTGCAAAACTT
Found at i:76034 original size:10 final size:10
Alignment explanation
Indices: 76019--76092 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
76009 CATTTAATAA
76019 ATAAACGAAC
1 ATAAACGAAC
76029 ATAAACGAAC
1 ATAAACGAAC
* *
76039 ACAAACATAAAC
1 ATAAAC--GAAC
*
76051 GA-ATACGAAC
1 -ATAAACGAAC
*
76061 ATAAATGAAC
1 ATAAACGAAC
76071 ----ACGAAC
1 ATAAACGAAC
76077 ATAAACGAAC
1 ATAAACGAAC
76087 ATAAAC
1 ATAAAC
76093 ATTGGAGACC
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 36 0.73
12 6 0.12
13 1 0.02
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:76047 original size:16 final size:16
Alignment explanation
Indices: 76026--76094 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
76016 TAAATAAACG
76026 AACATAAACGAACACA
1 AACATAAACGAACACA
* *
76042 AACATAAACGAATACG
1 AACATAAACGAACACA
* *
76058 AACATAAATGAACACG
1 AACATAAACGAACACA
*
76074 AACATAAACGAACATA
1 AACATAAACGAACACA
76090 AACAT
1 AACAT
76095 TGGAGACCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.12
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:76059 original size:32 final size:32
Alignment explanation
Indices: 76023--76085 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
76013 TAATAAATAA
76023 ACGAACATAAACGAACACAAACATAAACGAAT
1 ACGAACATAAACGAACACAAACATAAACGAAT
* *
76055 ACGAACATAAATGAACACGAACATAAACGAA
1 ACGAACATAAACGAACACAAACATAAACGAA
76086 CATAAACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.10
Consensus pattern (32 bp):
ACGAACATAAACGAACACAAACATAAACGAAT
Found at i:76757 original size:14 final size:14
Alignment explanation
Indices: 76731--76762 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
76721 AACAAACATA
76731 AACGAACATAACTG
1 AACGAACATAACTG
76745 AACGAACATAACTG
1 AACGAACATAACTG
76759 AACG
1 AACG
76763 TTCACGAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (14 bp):
AACGAACATAACTG
Found at i:76761 original size:24 final size:24
Alignment explanation
Indices: 76687--76755 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
76677 GATTAGCTTA
* *
76687 AACATAAATGAATGAACATAAACG
1 AACATAACTGAACGAACATAAACG
** *
76711 AACATAACCAAACAAACATAAACG
1 AACATAACTGAACGAACATAAACG
76735 AACATAACTGAACGAACATAA
1 AACATAACTGAACGAACATAA
76756 CTGAACGTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.59, C:0.19, G:0.09, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGAACATAAACG
Found at i:79784 original size:43 final size:43
Alignment explanation
Indices: 79734--79831 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 43
79724 CAATAGGTTA
* *
79734 AGATCTATAGCGGCGTTTTTGGAACAAACATCGCAAAAGGTCG
1 AGATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCG
* * * * * *
79777 ATATCTATAACGGCATTTTTTGAATAAACGCCGTAAAAGGTCG
1 AGATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCG
79820 AGATCTATAGCG
1 AGATCTATAGCG
79832 ACAAAATTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (43 bp):
AGATCTATAGCGGCATTTTTGGAACAAACACCGCAAAAGGTCG
Found at i:80514 original size:21 final size:21
Alignment explanation
Indices: 80490--80546 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
80480 CAACAATAAC
80490 CATGAATCAAATGCTCGAAAG
1 CATGAATCAAATGCTCGAAAG
80511 CATGAATCAAATGCTCGAAAG
1 CATGAATCAAATGCTCGAAAG
*
80532 CATGAATCGAATGCT
1 CATGAATCAAATGCT
80547 AAAAAACAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (21 bp):
CATGAATCAAATGCTCGAAAG
Found at i:82141 original size:41 final size:40
Alignment explanation
Indices: 82064--82142 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 40
82054 CGTTTACATG
* * * *
82064 AAAAAACGCCACTAATGTATGTGATTTTGTAGCGTTTTGC
1 AAAAAACGCCACTAATATATGGGATATCGTAGCGTTTTGC
82104 AAAAAACGCCACTATATATATGGGATATCGT-GACGTTTT
1 AAAAAACGCCACTA-ATATATGGGATATCGTAG-CGTTTT
82143 TTTTACATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 15 0.45
41 18 0.55
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (40 bp):
AAAAAACGCCACTAATATATGGGATATCGTAGCGTTTTGC
Found at i:83131 original size:15 final size:16
Alignment explanation
Indices: 83101--83138 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
83091 TGTGCAAATC
*
83101 CGGGTACCCGGATTTT
1 CGGGTAACCGGATTTT
83117 CGGGTAACC-GATTTT
1 CGGGTAACCGGATTTT
*
83132 CAGGTAA
1 CGGGTAA
83139 TCGAAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (16 bp):
CGGGTAACCGGATTTT
Found at i:83228 original size:17 final size:17
Alignment explanation
Indices: 83182--83232 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
83172 TGTCCCGACT
*
83182 CGGATGTTACGGGTACC
1 CGGATATTACGGGTACC
*
83199 CGG-TAAT-CGGGTACC
1 CGGATATTACGGGTACC
*
83214 CGGATTTTACGGGTACC
1 CGGATATTACGGGTACC
83231 CG
1 CG
83233 ATACCCGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 11 0.39
16 4 0.14
17 13 0.46
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.24
Consensus pattern (17 bp):
CGGATATTACGGGTACC
Found at i:83813 original size:26 final size:26
Alignment explanation
Indices: 83784--83839 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
83774 TTTTTTTCAT
83784 AATTT-TTTTATCTTTAAAATTTTATA
1 AATTTATTTTA-CTTTAAAATTTTATA
* * *
83810 AATTTATTTTAGTTTAAAGTTTTATT
1 AATTTATTTTACTTTAAAATTTTATA
83836 AATT
1 AATT
83840 CACTCTCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (26 bp):
AATTTATTTTACTTTAAAATTTTATA
Found at i:83936 original size:26 final size:26
Alignment explanation
Indices: 83907--83960 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
83897 ATCATTCTAG
* *
83907 TAGTTGGTTTGACCAACTAATTTGAT
1 TAGTTGATTTGACAAACTAATTTGAT
* *
83933 TAGTTGATTTGAGAAACTTATTTGAT
1 TAGTTGATTTGACAAACTAATTTGAT
83959 TA
1 TA
83961 ATTGTTTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (26 bp):
TAGTTGATTTGACAAACTAATTTGAT
Found at i:84747 original size:2 final size:2
Alignment explanation
Indices: 84740--84767 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
84730 AATTAAACAA
84740 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
84768 TGACTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86216 original size:3 final size:3
Alignment explanation
Indices: 86208--86252 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
86198 ATTTTATTTA
86208 AAT AAT AAT -AT AAT -AT ATAT AAT -AT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
86250 AAT
1 AAT
86253 TTTAATGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 8 0.22
3 26 0.70
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:86231 original size:14 final size:14
Alignment explanation
Indices: 86208--86252 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
86198 ATTTTATTTA
86208 AATAATAATATAAT
1 AATAATAATATAAT
86222 -ATATATAATATAAT
1 AATA-ATAATATAAT
*
86236 AATAATAATAAAAT
1 AATAATAATATAAT
86250 AAT
1 AAT
86253 TTTAATGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 3 0.11
14 22 0.79
15 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAATAATATAAT
Found at i:86501 original size:76 final size:76
Alignment explanation
Indices: 86401--87108 Score: 1185
Period size: 76 Copynumber: 9.4 Consensus size: 76
86391 GGTCCTAAGA
* * * *
86401 AAACATCATGCACTGAAGGGCTTACAAATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
86466 AGGCTTTTTGG
66 AGGCTTTTTGG
* ** * *
86477 AAACATCATGCATTATAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
86542 AGGCTTTTTGG
66 AGGCTTTTTGG
*
86553 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
86618 AGGCTTTTTGG
66 AGGCTTTTTGG
*
86629 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAATATC-AAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
86693 AGGCTTTTTGG
66 AGGCTTTTTGG
86704 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
86769 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
86780 AAACATCATGCACTGTAGGACTTACATATGACCCTAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
86844 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
86855 AAACATCATGTATTGCAGGACTTACAGAT---CCTAAGGCTTTG-AAACATCAAAAATCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
86916 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
86927 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
86992 AGGCTTTTTGG
66 AGGCTTTTTGG
*
87003 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGTTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
87068 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
87079 AAACATCATGCACTGCAAGACTTAAAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
87109 TGGGAAATAG
Statistics
Matches: 596, Mismatches: 30, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
71 7 0.01
72 60 0.10
75 134 0.22
76 395 0.66
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:86759 original size:151 final size:152
Alignment explanation
Indices: 86401--87108 Score: 1194
Period size: 151 Copynumber: 4.7 Consensus size: 152
86391 GGTCCTAAGA
* * * *
86401 AAACATCATGCACTGAAGGGCTTACAAATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* * * *
86466 AGGCTTTTTGGAAACATCATGCATTATAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
86531 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
*
86553 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* *
86618 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAATATC-A
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
86682 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
86704 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
86769 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACATATGACCCTAAGGCTTTGAAAACATC-A
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
86833 AAAGCTCCCGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
* * *
86855 AAACATCATGTATTGCAGGACTTACAGAT---CCTAAGGCTTTG-AAACATCAAAAATCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
86916 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
*
86981 AAAGCTCCTGAAGGCTTTTTGG
131 AAAGCTCCCGAAGGCTTTTTGG
*
87003 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGTTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* * *
87068 AGGCTTTTTGGAAACATCATGCACTGCAAGACTTAAAGATG
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
87109 TGGGAAATAG
Statistics
Matches: 525, Mismatches: 26, Indels: 10
0.94 0.05 0.02
Matches are distributed among these distances:
147 81 0.15
148 61 0.12
151 209 0.40
152 174 0.33
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (152 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGG
Found at i:87809 original size:22 final size:22
Alignment explanation
Indices: 87781--87857 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
87771 AATAAAGCTT
87781 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
87803 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
87825 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
87847 TCATCTTTGAA
1 TCATCTTTGAA
87858 GAGTGTAGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:92456 original size:16 final size:16
Alignment explanation
Indices: 92435--92493 Score: 84
Period size: 16 Copynumber: 3.7 Consensus size: 16
92425 CTTGATTCAA
92435 TTTTCCTTTTCTTTTT
1 TTTTCCTTTTCTTTTT
*
92451 TTTTCCTTTTTTTTTT
1 TTTTCCTTTTCTTTTT
92467 TTTTCCTTTT-TGTTTT
1 TTTTCCTTTTCT-TTTT
*
92483 TTTTCTTTTTC
1 TTTTCCTTTTC
92494 CTTCTCTTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
15 1 0.03
16 38 0.97
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTTCCTTTTCTTTTT
Found at i:92459 original size:11 final size:10
Alignment explanation
Indices: 92441--92492 Score: 54
Period size: 11 Copynumber: 5.0 Consensus size: 10
92431 TCAATTTTCC
92441 TTTTCTTTTT
1 TTTTCTTTTT
92451 TTTTCCTTTTT
1 TTTT-CTTTTT
92462 TTTT-TTTTT
1 TTTTCTTTTT
92471 CCTTTT-TGTTTT
1 --TTTTCT-TTTT
92483 TTTTCTTTTT
1 TTTTCTTTTT
92493 CCTTCTCTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.14
10 12 0.32
11 16 0.43
12 4 0.11
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.87
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:92493 original size:22 final size:22
Alignment explanation
Indices: 92441--92496 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
92431 TCAATTTTCC
92441 TTTTCTTTTT--TTTTCCTTTT
1 TTTTCTTTTTCCTTTTCCTTTT
* **
92461 TTTTTTTTTTCCTTTTTGTTTT
1 TTTTCTTTTTCCTTTTCCTTTT
92483 TTTTCTTTTTCCTT
1 TTTTCTTTTTCCTT
92497 CTCTTCTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 9 0.30
22 21 0.70
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (22 bp):
TTTTCTTTTTCCTTTTCCTTTT
Done.