Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000323.1 Hibiscus syriacus cultivar Beakdansim tig00000605_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: 106496
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4028 original size:20 final size:20
Alignment explanation
Indices: 3998--4069 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
3988 TGCGATTTTT
3998 TAAATTCGCAACTCGAATCTG
1 TAAA-TCGCAACTCGAATCTG
4019 TAAATCGCAACTCGAATCTG
1 TAAATCGCAACTCGAATCTG
* * *
4039 TAAATAGCAACGCGAATTTG
1 TAAATCGCAACTCGAATCTG
4059 TAAATCGCAAC
1 TAAATCGCAAC
4070 ACAGAAGTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 43 0.91
21 4 0.09
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (20 bp):
TAAATCGCAACTCGAATCTG
Found at i:4086 original size:20 final size:20
Alignment explanation
Indices: 4063--4169 Score: 105
Period size: 20 Copynumber: 5.4 Consensus size: 20
4053 AATTTGTAAA
4063 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
4083 TCGCAAC-GAGAAAGTAAAAT
1 TCGCAACACAG-AAGTCAAAT
* *
4103 TCGTAACGC-GAAAGTCAAAT
1 TCGCAACACAG-AAGTCAAAT
* *
4123 TCACAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
4143 TCGCAACACA-AAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
4162 TCGCAACA
1 TCGCAACA
4170 AGTGTTAGTT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
19 19 0.26
20 55 0.74
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:4089 original size:40 final size:40
Alignment explanation
Indices: 4045--4168 Score: 130
Period size: 40 Copynumber: 3.1 Consensus size: 40
4035 TCTGTAAATA
*
4045 GCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAATTC
1 GCAACGCGAA-TAGTAAAATTCGCAACAC-GAAGTCAAATTC
* * *
4085 GCAACGAGAA-AGTAAAATTCGTAACGCGAAAGTCAAATTC
1 GCAACGCGAATAGTAAAATTCGCAACACG-AAGTCAAATTC
* * *
4125 ACAACGCG-ATAGTCAAATTCGCAACACAAAGTCAAATTC
1 GCAACGCGAATAGTAAAATTCGCAACACGAAGTCAAATTC
4164 GCAAC
1 GCAAC
4169 AAGTGTTAGT
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
38 2 0.03
39 20 0.29
40 47 0.68
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.18
Consensus pattern (40 bp):
GCAACGCGAATAGTAAAATTCGCAACACGAAGTCAAATTC
Found at i:4323 original size:14 final size:15
Alignment explanation
Indices: 4304--4341 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
4294 TCCCCATCTC
4304 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
4318 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
4334 TAATTTTT
1 TAATTTTT
4342 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:4914 original size:12 final size:12
Alignment explanation
Indices: 4893--4926 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4883 ACCACATTTC
*
4893 CAATACCAAACA
1 CAATATCAAACA
4905 CAATATCAAACA
1 CAATATCAAACA
*
4917 CAATCTCAAA
1 CAATATCAAA
4927 ACCTACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:5105 original size:24 final size:24
Alignment explanation
Indices: 5047--5093 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5037 AGTCAGTATT
*
5047 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
5071 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
5094 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:17656 original size:20 final size:21
Alignment explanation
Indices: 17631--17693 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 21
17621 TTTTGGTGCA
*
17631 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
17651 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
17672 GAAGGGGAACCGATTCCCCCCA
1 G-A-GGGAACCGATTCCCCCCA
17694 CAGGGAAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 10 0.29
21 8 0.23
22 1 0.03
23 16 0.46
ACGTcount: A:0.24, C:0.35, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:18122 original size:15 final size:16
Alignment explanation
Indices: 18102--18131 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18092 AAATTAAAAA
18102 AAATTATTGT-TTTTC
1 AAATTATTGTGTTTTC
18117 AAATTATTGTGTTTT
1 AAATTATTGTGTTTT
18132 GATTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (16 bp):
AAATTATTGTGTTTTC
Found at i:25901 original size:15 final size:15
Alignment explanation
Indices: 25860--25911 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
25850 TCTCCATCAT
25860 AAAAAA-TGTT-GAA
1 AAAAAACTGTTCGAA
*
25873 AAAAATAGCAGTTCGAA
1 AAAAA-A-CTGTTCGAA
25890 AAAAAACTGTTCGAA
1 AAAAAACTGTTCGAA
25905 AGAAAAA
1 A-AAAAA
25912 GAAAAAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 5 0.16
14 1 0.03
15 9 0.28
16 9 0.28
17 8 0.25
ACGTcount: A:0.60, C:0.08, G:0.15, T:0.17
Consensus pattern (15 bp):
AAAAAACTGTTCGAA
Found at i:27969 original size:18 final size:18
Alignment explanation
Indices: 27946--27981 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
27936 AAGCAAAAGG
*
27946 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
27964 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
27982 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:28323 original size:20 final size:20
Alignment explanation
Indices: 28297--28341 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
28287 CAAACCGAAA
28297 ATCGCGTTGCGAATTTGACT
1 ATCGCGTTGCGAATTTGACT
* *
28317 TTCGCGTTGTGAATTTGACT
1 ATCGCGTTGCGAATTTGACT
28337 ATCGC
1 ATCGC
28342 AACGCTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (20 bp):
ATCGCGTTGCGAATTTGACT
Found at i:28822 original size:18 final size:18
Alignment explanation
Indices: 28801--28837 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28791 ATAATTGAAG
28801 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
28819 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
28837 T
1 T
28838 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:28844 original size:24 final size:25
Alignment explanation
Indices: 28782--28845 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
28772 TTTCAAATTC
28782 ATTTC-ATATATAA-TTGAAGTTTGA
1 ATTTCAATATA-AATTTGAAGTTTGA
* * *
28806 ATTTAAATTTCAATTTG-AGTTTGA
1 ATTTCAATATAAATTTGAAGTTTGA
28830 ATTTCAATATAAATTT
1 ATTTCAATATAAATTT
28846 CGGCTCCACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 26 0.81
25 6 0.19
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (25 bp):
ATTTCAATATAAATTTGAAGTTTGA
Found at i:29191 original size:39 final size:39
Alignment explanation
Indices: 29147--29233 Score: 158
Period size: 39 Copynumber: 2.2 Consensus size: 39
29137 TCTGATGCTC
29147 ATCAAAATCCAAAGT-TCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAA-TCTCATATGGTGCCAAGCAAAAGGAA
29186 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
29225 ATCAAAATC
1 ATCAAAATC
29234 TACAAGTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 1 0.02
39 46 0.98
ACGTcount: A:0.47, C:0.20, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
Found at i:29647 original size:14 final size:14
Alignment explanation
Indices: 29630--29666 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
29620 ATCAAATTAA
29630 ACAAATCAACTTTT
1 ACAAATCAACTTTT
29644 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
29658 GCAAATCAA
1 ACAAATCAA
29667 TTAATCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:31153 original size:21 final size:21
Alignment explanation
Indices: 31072--31147 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
31062 GCGGGCGGGA
* *
31072 CCTCTTGAACGATGACATGGG
1 CCTCTTGAACGATGAGAGGGG
* *
31093 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
31114 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
31135 CCTCTTGAACGAT
1 CCTCTTGAACGAT
31148 AGGAGGCACA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 41 0.95
22 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.34, T:0.25
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:31168 original size:42 final size:42
Alignment explanation
Indices: 31074--31170 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
31064 GGGCGGGACC
* * * * ** *
31074 TCTTGAACGATGACATGGGCCTCTTGAACGGTGGGAGGGGCT
1 TCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCACA
*
31116 TCTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGCACA
1 TCTT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGCACA
31158 TCTTGAATGATGA
1 TCTTGAATGATGA
31171 TAGGTGCATC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.02
42 43 0.96
43 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.25
Consensus pattern (42 bp):
TCTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCACA
Found at i:33854 original size:20 final size:20
Alignment explanation
Indices: 33829--33977 Score: 226
Period size: 20 Copynumber: 7.5 Consensus size: 20
33819 GCGTAAAAAC
33829 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
33849 ATTTGACTTTCGCGTTGCGG
1 ATTTGACTTTCGCGTTGCGA
33869 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
33889 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
33909 ATTTGACTATCGCGTTACGA
1 ATTTGACTTTCGCGTTGCGA
* *
33929 ATTTGACTATCGCGTTGTGA
1 ATTTGACTTTCGCGTTGCGA
*
33949 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
33969 ATTTGACTT
1 ATTTGACTT
33978 CTGTGTTACG
Statistics
Matches: 117, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 117 1.00
ACGTcount: A:0.17, C:0.17, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:33894 original size:60 final size:60
Alignment explanation
Indices: 33829--34013 Score: 232
Period size: 60 Copynumber: 3.1 Consensus size: 60
33819 GCGTAAAAAC
* * *
33829 ATTTGACTTTCGCGTTGCGAATTTGACTTTCGCGTTGCGGATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGAATTTGACTTTCGCGTTACGAATTTGACTATCGCGTTGCGA
* * * *
33889 ATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTACGAATTTGACTATCGCGTTGTGA
1 ATTTGACTTTCGCGTTGCGAATTTGACTTTCGCGTTACGAATTTGACTATCGCGTTGCGA
* * *
33949 ATTTGACTATCGCGTTGCGAATTTGAC-TTCTGTGTTACG-ATTT-ACAGATTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGAATTTGACTTTC-GCGTTACGAATTTGAC-TA-TCGCGTTGCGA
34009 ATTTG
1 ATTTG
34014 GAAATTGGAG
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
58 2 0.02
59 7 0.06
60 99 0.92
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.41
Consensus pattern (60 bp):
ATTTGACTTTCGCGTTGCGAATTTGACTTTCGCGTTACGAATTTGACTATCGCGTTGCGA
Found at i:34002 original size:40 final size:41
Alignment explanation
Indices: 33829--34013 Score: 215
Period size: 40 Copynumber: 4.6 Consensus size: 41
33819 GCGTAAAAAC
*
33829 ATTTGACT-TTCGCGTTGCGAATTTGACTT-TCGCGTTGCGG
1 ATTTGACTATTCGCGTTGCGAATTTGACTTCT-GCGTTGCGA
* *
33869 ATTTGACT-TTCGCGTTGCGAATTTGACTTTTGTGTTGCGA
1 ATTTGACTATTCGCGTTGCGAATTTGACTTCTGCGTTGCGA
* *
33909 ATTTGACTA-TCGCGTTACGAATTTGACTATC-GCGTTGTGA
1 ATTTGACTATTCGCGTTGCGAATTTGACT-TCTGCGTTGCGA
* *
33949 ATTTGACTA-TCGCGTTGCGAATTTGACTTCTGTGTTACG-
1 ATTTGACTATTCGCGTTGCGAATTTGACTTCTGCGTTGCGA
*
33988 ATTT-ACAGATTCGCGTTGCGAATTTG
1 ATTTGAC-TATTCGCGTTGCGAATTTG
34014 GAAATTGGAG
Statistics
Matches: 128, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
38 2 0.02
39 7 0.05
40 117 0.91
41 2 0.02
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.41
Consensus pattern (41 bp):
ATTTGACTATTCGCGTTGCGAATTTGACTTCTGCGTTGCGA
Found at i:47782 original size:22 final size:22
Alignment explanation
Indices: 47737--47783 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
47727 GTAAATTTCG
*
47737 ATTTTTTTAAGAATTTCAATTA
1 ATTTTTTTAAGAATTTCAAATA
*
47759 ATTTTTTTAATAATTT-AAGATA
1 ATTTTTTTAAGAATTTCAA-ATA
47781 ATT
1 ATT
47784 AGAAGATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTTTTTTAAGAATTTCAAATA
Found at i:48252 original size:13 final size:13
Alignment explanation
Indices: 48236--48277 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
48226 TTAGTTAATT
48236 ATAAACTTAAATA
1 ATAAACTTAAATA
*
48249 ATAATA-TTTAATA
1 ATAA-ACTTAAATA
48262 A-AAACTTAAATA
1 ATAAACTTAAATA
48274 ATAA
1 ATAA
48278 TAGAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 1 0.04
12 9 0.38
13 13 0.54
14 1 0.04
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAAACTTAAATA
Found at i:49792 original size:6 final size:6
Alignment explanation
Indices: 49781--49806 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
49771 AAATTAGGAC
49781 AACAAT AACAAT AACAAT AACAAT AA
1 AACAAT AACAAT AACAAT AACAAT AA
49807 TTCGGTAATA
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:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AACAAT
Found at i:52449 original size:27 final size:27
Alignment explanation
Indices: 52417--52483 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
52407 CAAAACAATG
*
52417 CTGAATGATTTAACACAAAAATACATT
1 CTGAATGATTCAACACAAAAATACATT
*
52444 CTGAATGATTCAACACAAAAATATATT
1 CTGAATGATTCAACACAAAAATACATT
* *
52471 TTAAATGATTCAA
1 CTGAATGATTCAA
52484 AGTCGTTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (27 bp):
CTGAATGATTCAACACAAAAATACATT
Found at i:52916 original size:21 final size:21
Alignment explanation
Indices: 52876--52950 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
52866 GATTCTTGAC
52876 AATCGCAATGCGATAGTACA-
1 AATCGCAATGCGATAGTACAG
* **
52896 AATTCGCATTGCGATTTTACAG
1 AA-TCGCAATGCGATAGTACAG
*
52918 AATCGCAACGCGAATA-TGA-A-
1 AATCGCAATGCG-ATAGT-ACAG
52938 AATCGCAATGCGA
1 AATCGCAATGCGA
52951 ACACATAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 1 0.02
20 13 0.30
21 25 0.57
22 5 0.11
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (21 bp):
AATCGCAATGCGATAGTACAG
Found at i:52943 original size:20 final size:20
Alignment explanation
Indices: 52918--53029 Score: 104
Period size: 20 Copynumber: 5.6 Consensus size: 20
52908 GATTTTACAG
* *
52918 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
*
52938 AATCGCAATGCGAACACATA
1 AATCGCAACGCGAACACATA
52958 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
52978 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
52998 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
53018 AATCGCAACGCG
1 AATCGCAACGCG
53030 TATCCGTAAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
19 1 0.01
20 79 0.96
21 2 0.02
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:53001 original size:60 final size:60
Alignment explanation
Indices: 52918--53147 Score: 234
Period size: 60 Copynumber: 3.8 Consensus size: 60
52908 GATTTTACAG
** * * * * *
52918 AATCGCAACGCGAATATGAAAATCGCAATGCG-AACACATAAATCGCAACGCGAACACATA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAACGCGAACACGTA
* * *
52978 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACGTA
* * * **
53038 AATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAATCA-GTA
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CACGTA
* * *
53098 AATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTAAATCGCAACG
1 AATCGCAACGCGAATCCGTAAATCGCAACGCGT-ATCCGTAAATCGCAACG
53148 AGAATCTGTA
Statistics
Matches: 143, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
59 2 0.01
60 137 0.96
61 4 0.03
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTA
Found at i:53032 original size:20 final size:20
Alignment explanation
Indices: 52956--53166 Score: 239
Period size: 20 Copynumber: 10.6 Consensus size: 20
52946 TGCGAACACA
* *
52956 TAAATCGCAACGCG-AACACA
1 TAAATCGCAACGCGTATC-CG
52976 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
52996 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
53016 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
53036 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
53056 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
53076 TAAATCGCAACG-ATAATCAG
1 TAAATCGCAACGCGT-ATCCG
* * *
53096 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
53116 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
53136 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
53156 TAAATCACAAC
1 TAAATCGCAAC
53167 ACTGAAATTT
Statistics
Matches: 166, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.01
20 163 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:53898 original size:24 final size:24
Alignment explanation
Indices: 53859--53905 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
53849 AAATTTGGTC
53859 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
53883 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
53906 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:54097 original size:12 final size:12
Alignment explanation
Indices: 54080--54104 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54070 ATATAATCCT
54080 GAAGAAGAAAAA
1 GAAGAAGAAAAA
54092 GAAGAAGAAAAA
1 GAAGAAGAAAAA
54104 G
1 G
54105 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:56438 original size:33 final size:33
Alignment explanation
Indices: 56391--56633 Score: 276
Period size: 33 Copynumber: 7.1 Consensus size: 33
56381 AATTACAATT
56391 GCAACGAGAGAATCGCAATGCGAAATGAAAATC
1 GCAACGAGAGAATCGCAATGCGAAATGAAAATC
* * *
56424 CCAACAAGAAAATCGCAATGCGGAAATGAAAATC
1 GCAACGAGAGAATCGCAATGC-GAAATGAAAATC
* * * * *
56458 GCAATGCGA-AAT-GAAAAT-CGCAACGATAGAATC
1 GCAACGAGAGAATCG-CAATGCGAAATGA-A-AATC
*
56491 GCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATC
1 GCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATC
56530 GCAACGAGAGAATCGCAATGCGAAATGAAAATC
1 GCAACGAGAGAATCGCAATGCGAAATGAAAATC
*
56563 GCAACGAGAGAATCGTAATGCGAAATGAAAATC
1 GCAACGAGAGAATCGCAATGCGAAATGAAAATC
56596 GCAACGAGAGAATCGCAATGCGGAAATGAAAATC
1 GCAACGAGAGAATCGCAATGC-GAAATGAAAATC
56630 GCAA
1 GCAA
56634 TGCGAAATGA
Statistics
Matches: 178, Mismatches: 18, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
31 5 0.03
32 3 0.02
33 109 0.61
34 34 0.19
36 2 0.01
37 1 0.01
39 10 0.06
40 7 0.04
41 7 0.04
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
GCAACGAGAGAATCGCAATGCGAAATGAAAATC
Found at i:56464 original size:53 final size:53
Alignment explanation
Indices: 56401--56566 Score: 289
Period size: 53 Copynumber: 3.2 Consensus size: 53
56391 GCAACGAGAG
* * *
56401 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
56454 AATCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
56507 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
56559 AATCGCAA
1 AATCGCAA
56567 CGAGAGAATC
Statistics
Matches: 108, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 16 0.15
53 92 0.85
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:56544 original size:86 final size:85
Alignment explanation
Indices: 56391--56651 Score: 306
Period size: 86 Copynumber: 3.0 Consensus size: 85
56381 AATTACAATT
*
56391 GCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA-C--AA-GAAAATCGCAATGCGGAAATG
1 GCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAAATCGCAA--C-G--ATG
56452 AAAATCGCAATGCGAAATGAAAATC
61 AAAATCGCAATGCGAAATGAAAATC
* *
56477 GCAACGATAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA-GAGA
1 GCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAA-GCGAAATGAAAATCGCAACGATGAAA
56541 ATCGCAATGCGAAATGAAAATC
64 ATCGCAATGCGAAATGAAAATC
* *
56563 GCAACGAGAGAATCGTAATGCGAAATGAAAATCGCAA-CG--A-GAGAATCGCAATGCGGAAATG
1 GCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAAATCGCAA--C-G--ATG
56624 AAAATCGCAATGCGAAATGAAAATC
61 AAAATCGCAATGCGAAATGAAAATC
56649 GCA
1 GCA
56652 TTGCGATTCT
Statistics
Matches: 156, Mismatches: 7, Indels: 24
0.83 0.04 0.13
Matches are distributed among these distances:
80 10 0.06
81 1 0.01
82 1 0.01
83 3 0.02
85 17 0.11
86 92 0.59
87 16 0.10
89 2 0.01
90 1 0.01
91 2 0.01
92 11 0.07
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (85 bp):
GCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAAATCGCAACGATGAAAAT
CGCAATGCGAAATGAAAATC
Found at i:56545 original size:14 final size:14
Alignment explanation
Indices: 56526--56613 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
56516 GCGAAATGAA
56526 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
56540 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
56559 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
56573 AATCGTAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
56592 AATCGCAACGAGAG
1 AATCGCAACGAGAG
56606 AATCGCAA
1 AATCGCAA
56614 TGCGGAAATG
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 27 0.47
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 19 0.33
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:56691 original size:53 final size:52
Alignment explanation
Indices: 56628--56743 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
56618 GAAATGAAAA
*
56628 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
56680 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
56733 TCGCATTGCGA
1 TCGCATTGCGA
56744 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 11 0.20
53 45 0.80
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:56706 original size:19 final size:19
Alignment explanation
Indices: 56666--56753 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
56656 GATTCTCTCG
56666 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
56686 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
56705 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
56719 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
56738 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
56754 AACATAATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 26 0.43
20 15 0.25
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:56863 original size:14 final size:14
Alignment explanation
Indices: 56844--56880 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
56834 CATCAATTAC
56844 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
56858 ACAAATCATCTTTT
1 ACAAATCAACTTTT
56872 ACAAATCAA
1 ACAAATCAA
56881 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:58761 original size:19 final size:19
Alignment explanation
Indices: 58719--58872 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
58709 TAGTTTACTT
* *
58719 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
58739 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
58758 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
58777 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
58796 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
* *
58810 TCACAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
58829 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
58843 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
58862 TCGCAATGCGA
1 TCGCAACGCGA
58873 TTTTGGTTTC
Statistics
Matches: 107, Mismatches: 17, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
14 17 0.16
15 1 0.01
16 7 0.07
17 7 0.07
18 1 0.01
19 62 0.58
20 12 0.11
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:58826 original size:33 final size:33
Alignment explanation
Indices: 58737--58867 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 33
58727 CGAAACTTAA
* *
58737 AATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAAC--G--A-CAG
58775 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* * *
58808 AATCACAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
58841 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
58868 TGCGATTTTG
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 57 0.66
34 1 0.01
36 1 0.01
38 27 0.31
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:58869 original size:52 final size:51
Alignment explanation
Indices: 58736--58872 Score: 132
Period size: 52 Copynumber: 2.6 Consensus size: 51
58726 ACGAAACTTA
* * * *
58736 AAATCGCAACGCGAAATGAGAATCGCAACGAGAAACCAAAATCGCAACGCG
1 AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
* ** * * * **
58787 AAAT-GAAAATCGCAACGACAGAATCACAATGCGAAATGAAAATCGCAACGAG
1 AAATCGCAACGCGAAATGA-A-AATCGCAATGCGAAACCAAAATCGCAACGAG
58839 AGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 A-AATCGCAACGCGAAATGAAAATCGCAATGCGA
58873 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 18, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
50 9 0.14
51 4 0.06
52 38 0.59
53 4 0.06
54 9 0.14
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (51 bp):
AAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACGAG
Found at i:58884 original size:19 final size:18
Alignment explanation
Indices: 58862--58917 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
58852 GAAATGAAAA
58862 TCGCAATGCGATTTTGGTT
1 TCGC-ATGCGATTTTGGTT
*
58881 TCGCGTTGCGATTTT-G--
1 TCGC-ATGCGATTTTGGTT
58897 TCG-ATGCGATTTTGGTT
1 TCGCATGCGATTTTGGTT
58914 TCGC
1 TCGC
58918 GTTGCGATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
14 9 0.30
15 1 0.03
16 3 0.10
17 3 0.10
18 1 0.03
19 13 0.43
ACGTcount: A:0.11, C:0.18, G:0.29, T:0.43
Consensus pattern (18 bp):
TCGCATGCGATTTTGGTT
Found at i:58909 original size:33 final size:33
Alignment explanation
Indices: 58867--58991 Score: 169
Period size: 33 Copynumber: 3.8 Consensus size: 33
58857 GAAAATCGCA
*
58867 ATGCGATTTTGGTTTCGCGTTGCGATTTTGTCG
1 ATGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
58900 ATGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 ATGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
* ** *
58933 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 ATGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
* * *
58966 TTGCGATTTTAAGTTTCGTGTTGCGA
1 ATGCGATTTT-GGTTTCGCGTTGCGA
58992 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.10, C:0.18, G:0.27, T:0.45
Consensus pattern (33 bp):
ATGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
Found at i:58925 original size:19 final size:18
Alignment explanation
Indices: 58868--58959 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 18
58858 AAAATCGCAA
58868 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
58887 TGCGATTTTG--T--CGA
1 TGCGATTTTGTTTCGCGT
58901 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
58920 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
58934 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
58953 TGCGATT
1 TGCGATT
58960 CTCTCGTTGC
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 22 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 29 0.50
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:58936 original size:14 final size:14
Alignment explanation
Indices: 58917--58973 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
58907 TTTGGTTTCG
*
58917 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
58931 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
58950 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
58964 CGTTGCGATT
1 CGTTGCGATT
58974 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:59389 original size:91 final size:93
Alignment explanation
Indices: 59089--59402 Score: 596
Period size: 93 Copynumber: 3.4 Consensus size: 93
59079 TCAGGGTATT
59089 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
59154 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
59182 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
59247 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
59275 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACC-AAAGAC-AAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
59338 GACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
59366 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
59403 AAGCAATCTA
Statistics
Matches: 219, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
91 76 0.35
92 6 0.03
93 137 0.63
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:61119 original size:20 final size:20
Alignment explanation
Indices: 61088--61194 Score: 104
Period size: 19 Copynumber: 5.7 Consensus size: 20
61078 TTTTGGTTGA
61088 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
61108 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
61128 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
61147 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
61162 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
61181 AATGAAAATCGCAA
1 AATGAAAATCGCAA
61195 TTTTCATTTC
Statistics
Matches: 74, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 30 0.41
20 17 0.23
21 12 0.16
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:61140 original size:21 final size:21
Alignment explanation
Indices: 61086--61150 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
61076 TCTTTTGGTT
61086 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
61107 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
61127 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
61148 GAA
1 GAA
61151 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:61242 original size:21 final size:21
Alignment explanation
Indices: 61217--61290 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
61207 GTTGCGATTC
61217 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
61238 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
61259 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
61280 TCTCGTTGCGA
1 TCTCGTTGCGA
61291 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:61412 original size:33 final size:33
Alignment explanation
Indices: 61370--61440 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
61360 AATACTAACT
61370 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
61403 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
61436 TGAAA
1 TGAAA
61441 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:61846 original size:20 final size:20
Alignment explanation
Indices: 61821--62012 Score: 253
Period size: 20 Copynumber: 9.6 Consensus size: 20
61811 CTTTAAAAAT
61821 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
61841 CGCGTTGCGATTTACTGATTA
1 CGCGTTGCGATTTACGGA-TA
*
61862 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
61881 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
61901 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
61921 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
61941 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
61961 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
61981 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
62001 CGCGTTGCGATT
1 CGCGTTGCGATT
62013 CTTGAAAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.01
20 147 0.97
21 3 0.02
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:62030 original size:21 final size:21
Alignment explanation
Indices: 62006--62052 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
61996 ATATTCGCGT
62006 TGCGATTCTTGAAAATCGCAA
1 TGCGATTCTTGAAAATCGCAA
62027 TGCGATTCTTGAAAATCGCAA
1 TGCGATTCTTGAAAATCGCAA
62048 TGCGA
1 TGCGA
62053 ATTTGTACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (21 bp):
TGCGATTCTTGAAAATCGCAA
Found at i:64376 original size:20 final size:20
Alignment explanation
Indices: 64326--64379 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
64316 TTGGAACTTC
*
64326 AAATTTATTATATTATTATTT
1 AAATTTATTATA-TATAATTT
* *
64347 TAATTAATTATATA-AATTT
1 AAATTTATTATATATAATTT
64366 AAAATTTATTATAT
1 -AAATTTATTATAT
64380 TATTGTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 4 0.15
20 13 0.48
21 10 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AAATTTATTATATATAATTT
Found at i:72222 original size:6 final size:6
Alignment explanation
Indices: 72211--72362 Score: 304
Period size: 6 Copynumber: 25.3 Consensus size: 6
72201 GATAAAGGGT
72211 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
72259 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
72307 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
72355 TATGTG TA
1 TATGTG TA
72363 CACATATACA
Statistics
Matches: 146, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 146 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
TATGTG
Found at i:78820 original size:38 final size:38
Alignment explanation
Indices: 78778--78854 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
78768 AAGTTCATCA
*
78778 ACTATTATGAAATCAAGACTAATATAAGTAGAACTGAG
1 ACTATTATGAAATCAAGACTAATACAAGTAGAACTGAG
*
78816 ACTATTATGAAATCAAGATTAATACAAGTAGAACTGAG
1 ACTATTATGAAATCAAGACTAATACAAGTAGAACTGAG
78854 A
1 A
78855 TAAGCTGAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (38 bp):
ACTATTATGAAATCAAGACTAATACAAGTAGAACTGAG
Found at i:84499 original size:14 final size:14
Alignment explanation
Indices: 84480--84506 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
84470 GTTGTTCTCC
84480 CTTGAAGTCTTGGG
1 CTTGAAGTCTTGGG
84494 CTTGAAGTCTTGG
1 CTTGAAGTCTTGG
84507 ACCGTGGCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.37
Consensus pattern (14 bp):
CTTGAAGTCTTGGG
Found at i:94107 original size:22 final size:23
Alignment explanation
Indices: 94070--94126 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
94060 GTGGGGCGAT
* *
94070 GGCGGGGGAGGAGGTGGCGG-GG
1 GGCGGGGGCGGAGGTGGAGGCGG
94092 GG-GGGAGGCGGAGGTGGAGGCGG
1 GGCGGG-GGCGGAGGTGGAGGCGG
94115 GGCGGGGGCGGA
1 GGCGGGGGCGGA
94127 CTTATATTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 3 0.10
22 14 0.47
23 10 0.33
24 3 0.10
ACGTcount: A:0.11, C:0.11, G:0.75, T:0.04
Consensus pattern (23 bp):
GGCGGGGGCGGAGGTGGAGGCGG
Done.