Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002288.1 Hibiscus syriacus cultivar Beakdansim tig00004655_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: 58307
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:2079 original size:93 final size:92
Alignment explanation
Indices: 1806--2167 Score: 632
Period size: 93 Copynumber: 4.0 Consensus size: 92
1796 TTCCAAAAGG
*
1806 TATATATATA-AAACATTTTGTTATCG--ATTCTTGTTTCA-TATAGTATTGTA-TTTCTTAGAT
1 TATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAGAT
1866 GAAAAATCTGAAAGAACATTCAGATTA
66 GAAAAATCTGAAAGAACATTCAGATTA
1893 TATATATTTATAAACATTTTGTTATCGATATTC-TG-TTCATTATAGTATTGTATTTTCTTAGAT
1 TATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAGAT
1956 GAAAAAATCTGAAAGAACATTCAGATTA
66 G-AAAAATCTGAAAGAACATTCAGATTA
1984 TATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTC-TAGAT
1 TATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAGAT
2048 GAAAAATCTGAAAGAACATTCAGATTATA
66 GAAAAATCTGAAAGAACATTCAGA-T-TA
2077 TATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAGAT
1 TATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAGAT
2142 GAAAAATCTGAAAGAACATTCAGATT
66 GAAAAATCTGAAAGAACATTCAGATT
2168 TGGAAAGTTG
Statistics
Matches: 263, Mismatches: 1, Indels: 17
0.94 0.00 0.06
Matches are distributed among these distances:
87 9 0.03
88 20 0.08
89 14 0.05
90 15 0.06
91 82 0.31
92 10 0.04
93 84 0.32
94 29 0.11
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (92 bp):
TATATATTTATAAACATTTTGTTATCGATATTCTTGTTTCATTATAGTATTGTATTTTCTTAGAT
GAAAAATCTGAAAGAACATTCAGATTA
Found at i:3880 original size:3 final size:3
Alignment explanation
Indices: 3872--3919 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
3862 CACCCATTTA
3872 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3920 GAGAAAAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:8197 original size:21 final size:21
Alignment explanation
Indices: 8173--8216 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
8163 TCATAAAACC
8173 CTACAGTGGCATATGAAACGA
1 CTACAGTGGCATATGAAACGA
* * * *
8194 CTACGGTGTCATCTGAACCGA
1 CTACAGTGGCATATGAAACGA
8215 CT
1 CT
8217 GTGTACCCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (21 bp):
CTACAGTGGCATATGAAACGA
Found at i:9855 original size:15 final size:15
Alignment explanation
Indices: 9835--9869 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9825 TGCAAAAAGT
* *
9835 AATAAAATTTAGTAA
1 AATAAAATATAATAA
9850 AATAAAATATAATAA
1 AATAAAATATAATAA
9865 AATAA
1 AATAA
9870 TAAACTCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
AATAAAATATAATAA
Found at i:10652 original size:39 final size:39
Alignment explanation
Indices: 10591--10696 Score: 153
Period size: 39 Copynumber: 2.7 Consensus size: 39
10581 TTATATTCAT
*
10591 TTATTT-ATTAAACG-AACGAACATGAGCAAGATTTTGTG
1 TTATTTAATTAAA-GAAACGAACATGAACAAGATTTTGTG
* *
10629 TTATTTAATTAAAGAAACAAACATGAACAAGATTTTTTG
1 TTATTTAATTAAAGAAACGAACATGAACAAGATTTTGTG
*
10668 TTATTTAATTAAAGAAACGAACACGAACA
1 TTATTTAATTAAAGAAACGAACATGAACA
10697 GAGGACTCAT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
38 7 0.11
39 54 0.89
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (39 bp):
TTATTTAATTAAAGAAACGAACATGAACAAGATTTTGTG
Found at i:10953 original size:10 final size:10
Alignment explanation
Indices: 10938--11013 Score: 62
Period size: 10 Copynumber: 6.9 Consensus size: 10
10928 AAAAAATATT
10938 TTCGTTTATG
1 TTCGTTTATG
**
10948 TTCGTTTACA
1 TTCGTTTATG
10958 TTCGTTTATG
1 TTCGTTTATG
*
10968 TTCATTTATTTTG
1 TTCGTTTA---TG
10981 TTCGTTTACATTCG
1 TTCGTTT--A-T-G
10995 TTCGTTTATG
1 TTCGTTTATG
11005 TTCGTTTAT
1 TTCGTTTAT
11014 TTGTGTTCGT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
10 33 0.61
11 1 0.02
12 1 0.02
13 10 0.19
14 8 0.15
15 1 0.02
ACGTcount: A:0.13, C:0.13, G:0.14, T:0.59
Consensus pattern (10 bp):
TTCGTTTATG
Found at i:10983 original size:33 final size:34
Alignment explanation
Indices: 10946--11031 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 34
10936 TTTTCGTTTA
10946 TGTTCGTTTACATTCGTTTATGTTCATTTATTT-
1 TGTTCGTTTACATTCGTTTATGTTCATTTATTTG
*
10979 TGTTCGTTTACATTCGTTCGTTTATGTTCGTTTATTTG
1 TGTTCGTTTACA----TTCGTTTATGTTCATTTATTTG
11017 TGTTCGTTTATCATT
1 TGTTCGTTTA-CATT
11032 TAAATGAACG
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
33 12 0.26
35 2 0.04
37 20 0.43
38 10 0.22
39 2 0.04
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.59
Consensus pattern (34 bp):
TGTTCGTTTACATTCGTTTATGTTCATTTATTTG
Found at i:11013 original size:37 final size:39
Alignment explanation
Indices: 10958--11031 Score: 125
Period size: 37 Copynumber: 1.9 Consensus size: 39
10948 TTCGTTTACA
10958 TTCGTTTATGTTCATTTATTT-TGTTCGTTTA-CATTCG
1 TTCGTTTATGTTCATTTATTTGTGTTCGTTTATCATTCG
*
10995 TTCGTTTATGTTCGTTTATTTGTGTTCGTTTATCATT
1 TTCGTTTATGTTCATTTATTTGTGTTCGTTTATCATT
11032 TAAATGAACG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 20 0.59
38 10 0.29
39 4 0.12
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.61
Consensus pattern (39 bp):
TTCGTTTATGTTCATTTATTTGTGTTCGTTTATCATTCG
Found at i:20003 original size:18 final size:18
Alignment explanation
Indices: 19974--20035 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
19964 GTACGTACCT
* *
19974 TCATTATCACCACCATGA
1 TCATCATCACCACCATCA
*
19992 TCATCA-CTACCACCACCA
1 TCATCATC-ACCACCATCA
*
20010 TCATCATCACCATCATCA
1 TCATCATCACCACCATCA
20028 TCATCATC
1 TCATCATC
20036 GTCACTTGAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 1 0.03
18 35 0.95
19 1 0.03
ACGTcount: A:0.32, C:0.40, G:0.02, T:0.26
Consensus pattern (18 bp):
TCATCATCACCACCATCA
Found at i:20022 original size:12 final size:12
Alignment explanation
Indices: 20005--20035 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19995 TCACTACCAC
20005 CACCATCATCAT
1 CACCATCATCAT
20017 CACCATCATCAT
1 CACCATCATCAT
*
20029 CATCATC
1 CACCATC
20036 GTCACTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.42, G:0.00, T:0.26
Consensus pattern (12 bp):
CACCATCATCAT
Found at i:25919 original size:20 final size:20
Alignment explanation
Indices: 25894--25934 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
25884 TAAGCATCCC
25894 TTAGAAGTTCTCCCGCATCT
1 TTAGAAGTTCTCCCGCATCT
*
25914 TTAGAAGTTCTCCTGCATCT
1 TTAGAAGTTCTCCCGCATCT
25934 T
1 T
25935 GTGACAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.39
Consensus pattern (20 bp):
TTAGAAGTTCTCCCGCATCT
Found at i:27015 original size:33 final size:33
Alignment explanation
Indices: 26978--27066 Score: 117
Period size: 33 Copynumber: 2.7 Consensus size: 33
26968 AGAAATCTAA
* * *
26978 CCATCACGAGAACCATGTACAGATGGA-ATCTGG
1 CCATCATGAGAACCATGCACAGATGGAGA-ATGG
*
27011 CCATCATGAGAACTATGCACAGATGGAGAATGG
1 CCATCATGAGAACCATGCACAGATGGAGAATGG
*
27044 CCATAATGAGAACCATGCACAGA
1 CCATCATGAGAACCATGCACAGA
27067 CAAAGACGAG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
33 48 0.98
34 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (33 bp):
CCATCATGAGAACCATGCACAGATGGAGAATGG
Found at i:30756 original size:13 final size:13
Alignment explanation
Indices: 30738--30762 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30728 TGGTGAAAAC
30738 GCTATGGAGGAAT
1 GCTATGGAGGAAT
30751 GCTATGGAGGAA
1 GCTATGGAGGAA
30763 CCATGGCGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.40, T:0.20
Consensus pattern (13 bp):
GCTATGGAGGAAT
Found at i:32031 original size:19 final size:19
Alignment explanation
Indices: 32020--32065 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
32010 TACACTATAT
32020 ATACATAAATACAAAATAC
1 ATACATAAATACAAAATAC
* *
32039 ATACATACATACATACATAC
1 ATACATAAATACA-AAATAC
32059 ATACATA
1 ATACATA
32066 CATGTCATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.24
Consensus pattern (19 bp):
ATACATAAATACAAAATAC
Found at i:32044 original size:4 final size:4
Alignment explanation
Indices: 32020--32068 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
32010 TACACTATAT
* *
32020 ATAC ATAA ATAC A-AA ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
32067 AT
1 AT
32069 GTCATTATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 2 0.05
4 38 0.95
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:32462 original size:18 final size:18
Alignment explanation
Indices: 32441--32506 Score: 87
Period size: 18 Copynumber: 3.6 Consensus size: 18
32431 ATTTGTCCTA
*
32441 AAGGATCACTATGTCCCG
1 AAGGACCACTATGTCCCG
*
32459 AAGGACCACTGATTGTTCCG
1 AAGGACCACT-A-TGTCCCG
*
32479 AAGAACCACTATGTCCCG
1 AAGGACCACTATGTCCCG
32497 AAGGACCACT
1 AAGGACCACT
32507 GATAATCACT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 24 0.59
19 2 0.05
20 15 0.37
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (18 bp):
AAGGACCACTATGTCCCG
Found at i:33478 original size:2 final size:2
Alignment explanation
Indices: 33471--33564 Score: 152
Period size: 2 Copynumber: 46.0 Consensus size: 2
33461 CGTGAATTAG
*
33471 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
33514 ACT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33557 AT AT AT AT
1 AT AT AT AT
33565 GATTACTACT
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
2 82 0.95
3 4 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34001 original size:64 final size:65
Alignment explanation
Indices: 33929--34053 Score: 166
Period size: 64 Copynumber: 1.9 Consensus size: 65
33919 ATCCCTTGAC
* *
33929 GGGTGCATCGATGCACT-ATCTATGCATCGGTGCA-TAAATCTCATTCGATGTT-TTTATTTTAA
1 GGGTGCATCGATGCACTCCT-TATGCATCGATGCACTAAATCT-ATTCGATGTTATTTATTTTAA
33991 GT
64 GT
* *
33993 GGGTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGTATTCGATGTTCATTTATTT
1 GGGTGCATCGATGCACTCCTTATGCATCGATGCACTAAATCTATTCGATGTT-ATTTATTT
34054 GAGAGTGCAT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
64 40 0.75
65 6 0.11
66 7 0.13
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (65 bp):
GGGTGCATCGATGCACTCCTTATGCATCGATGCACTAAATCTATTCGATGTTATTTATTTTAAGT
Found at i:37800 original size:18 final size:18
Alignment explanation
Indices: 37777--37849 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
37767 ACTGAATATT
* *
37777 TGTCCCAAATGACCACTA
1 TGTCCCGAAGGACCACTA
37795 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
37814 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
37833 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
37850 GTTTGTCCTG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 2 0.04
20 15 0.32
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:37824 original size:20 final size:20
Alignment explanation
Indices: 37776--37872 Score: 103
Period size: 20 Copynumber: 5.0 Consensus size: 20
37766 CACTGAATAT
* *
37776 TTGTCCCAAATGACCACT-A
1 TTGTCCCGAAGGACCACTGA
37795 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
37814 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
*
37833 -TGTCCCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACTGA
* *
37852 TTGTCCTGAATGACCACTGA
1 TTGTCCCGAAGGACCACTGA
37872 T
1 T
37873 AATCCCTCGA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
18 30 0.47
19 2 0.03
20 32 0.50
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:37868 original size:38 final size:37
Alignment explanation
Indices: 37775--37869 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 37
37765 GCACTGAATA
*
37775 TTTGTCCCAAATGACCACTATGTCCCGAAGGACCACTG
1 TTTGT-CCGAATGACCACTATGTCCCGAAGGACCACTG
*
37813 ATTGTTCCGAA-GAACCACTATGTCCCGAAGGACCACTG
1 TTTG-TCCGAATG-ACCACTATGTCCCGAAGGACCACTG
37851 TTTGTCCTGAATGACCACT
1 TTTGTCC-GAATGACCACT
37870 GATAATCCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
37 4 0.08
38 44 0.88
39 2 0.04
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (37 bp):
TTTGTCCGAATGACCACTATGTCCCGAAGGACCACTG
Found at i:40283 original size:105 final size:105
Alignment explanation
Indices: 40101--40309 Score: 418
Period size: 105 Copynumber: 2.0 Consensus size: 105
40091 ATGTTACAAC
40101 TATATCATATGTAAGTAATTTAGATGAAATGTAGTAGGTTGCATAAGTTTGAAGCATTCCCATGG
1 TATATCATATGTAAGTAATTTAGATGAAATGTAGTAGGTTGCATAAGTTTGAAGCATTCCCATGG
40166 TAGATGTCACGTTTTAGAGTTATAAACATGTTTAAAGTCA
66 TAGATGTCACGTTTTAGAGTTATAAACATGTTTAAAGTCA
40206 TATATCATATGTAAGTAATTTAGATGAAATGTAGTAGGTTGCATAAGTTTGAAGCATTCCCATGG
1 TATATCATATGTAAGTAATTTAGATGAAATGTAGTAGGTTGCATAAGTTTGAAGCATTCCCATGG
40271 TAGATGTCACGTTTTAGAGTTATAAACATGTTTAAAGTC
66 TAGATGTCACGTTTTAGAGTTATAAACATGTTTAAAGTC
40310 TTATTTATGC
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (105 bp):
TATATCATATGTAAGTAATTTAGATGAAATGTAGTAGGTTGCATAAGTTTGAAGCATTCCCATGG
TAGATGTCACGTTTTAGAGTTATAAACATGTTTAAAGTCA
Found at i:42327 original size:21 final size:21
Alignment explanation
Indices: 42285--42329 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
42275 AAAGAAAAAA
* *
42285 ATCTGATCCCGATATTTGGAT
1 ATCTGATCCCGAAATTTAGAT
42306 ATCTGAT-CCGAAATTTCAGAT
1 ATCTGATCCCGAAATTT-AGAT
42327 ATC
1 ATC
42330 CGAATTTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (21 bp):
ATCTGATCCCGAAATTTAGAT
Found at i:42352 original size:15 final size:16
Alignment explanation
Indices: 42311--42346 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42301 TGGATATCTG
*
42311 ATCCGAAATTTCAGAT
1 ATCCGAATTTTCAGAT
*
42327 ATCCGAATTTTCGGAT
1 ATCCGAATTTTCAGAT
42343 ATCC
1 ATCC
42347 TATTTTTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (16 bp):
ATCCGAATTTTCAGAT
Found at i:44890 original size:16 final size:17
Alignment explanation
Indices: 44863--44896 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
44853 ATTTTCATTC
44863 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
44880 TTTTG-AAAAGTCAATG
1 TTTTGTAAAAGTAAATG
44896 T
1 T
44897 GACATCTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:48663 original size:29 final size:29
Alignment explanation
Indices: 48628--48690 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
48618 TTTATAGGTT
48628 GATCTCTATAGTCGCATGGAGCACACGGC
1 GATCTCTATAGTCGCATGGAGCACACGGC
* * *
48657 GATCTCTATGGTCGTATGGAGCATACGGC
1 GATCTCTATAGTCGCATGGAGCACACGGC
48686 GATCT
1 GATCT
48691 ACCTAGCGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.22, C:0.24, G:0.29, T:0.25
Consensus pattern (29 bp):
GATCTCTATAGTCGCATGGAGCACACGGC
Found at i:49281 original size:21 final size:21
Alignment explanation
Indices: 49248--49445 Score: 203
Period size: 21 Copynumber: 9.5 Consensus size: 21
49238 ATTTCCAGAT
* *
49248 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
49269 TCACAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
49290 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
49311 TCGCAATGCG-ACTATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
49331 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
49352 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
49373 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
49393 TCGTAATGCGATAGTCT--ACTA
1 TCGCAATGCGA-ACT-TGGACTA
49414 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
49435 TCGCAATGCGA
1 TCGCAATGCGA
49446 TTTACATATT
Statistics
Matches: 147, Mismatches: 19, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.01
20 32 0.22
21 111 0.76
22 3 0.02
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:49401 original size:41 final size:43
Alignment explanation
Indices: 49265--49445 Score: 159
Period size: 41 Copynumber: 4.3 Consensus size: 43
49255 GCGAACTTCG
* *
49265 ACTATCACAATGCGAACT-TGGACTATCGCAATGCGAACT-TGG
1 ACTATCGCAATGCGAACTATGGACTATCGCAATGCGAA-TATGT
* *
49307 ACTATCGCAATGCG-ACTATGTA-AATCGCAATGCG-ATA-GT
1 ACTATCGCAATGCGAACTATGGACTATCGCAATGCGAATATGT
49346 CGACTATCGCAATGCGAACT-TGGACTATCGCAATGCGAATATGT
1 --ACTATCGCAATGCGAACTATGGACTATCGCAATGCGAATATGT
* * ** *
49390 A-AATCGTAATGCG-A-TAGTCTACTATCGCAATGCGAACT-TGG
1 ACTATCGCAATGCGAACTA-TGGACTATCGCAATGCGAA-TATGT
49431 ACTATCGCAATGCGA
1 ACTATCGCAATGCGA
49446 TTTACATATT
Statistics
Matches: 113, Mismatches: 13, Indels: 25
0.75 0.09 0.17
Matches are distributed among these distances:
39 3 0.03
40 2 0.02
41 61 0.54
42 42 0.37
43 3 0.03
44 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (43 bp):
ACTATCGCAATGCGAACTATGGACTATCGCAATGCGAATATGT
Found at i:49417 original size:83 final size:83
Alignment explanation
Indices: 49248--49445 Score: 242
Period size: 83 Copynumber: 2.4 Consensus size: 83
49238 ATTTCCAGAT
* * * *
49248 TCGCAACGCGAACTTCGACTATCACAATGCGAACTTGGACTATCGCAATGCGAACTTGGACTATC
1 TCGCAATGCGAACGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACAATC
*
49313 GCAATGCGACTATGTAAA
66 GCAATGCGACTATCTAAA
*
49331 TCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGA-ACGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACT-TGGACAA
* *
49393 TCGTAATGCGA-TAGTCTACTA
64 TCGCAATGCGACTA-TCTA-AA
* *
49414 TCGCAATGCGAACTTGGACTATCGCAATGCGA
1 TCGCAATGCGAACGTCGACTATCGCAATGCGA
49446 TTTACATATT
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
81 2 0.02
82 16 0.16
83 81 0.81
84 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (83 bp):
TCGCAATGCGAACGTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAACTTGGACAATC
GCAATGCGACTATCTAAA
Found at i:49470 original size:62 final size:61
Alignment explanation
Indices: 49285--49446 Score: 288
Period size: 62 Copynumber: 2.6 Consensus size: 61
49275 TGCGAACTTG
49285 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGACTATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGA-TATGTAAATCGCAATGCGATAGTC
*
49347 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGTAATGCGATAGTC
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCG-ATATGTAAATCGCAATGCGATAGTC
*
49409 TACTATCGCAATGCGAACTTGGACTATCGCAATGCGAT
1 GACTATCGCAATGCGAACTTGGACTATCGCAATGCGAT
49447 TTACATATTC
Statistics
Matches: 97, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
61 2 0.02
62 94 0.97
63 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (61 bp):
GACTATCGCAATGCGAACTTGGACTATCGCAATGCGATATGTAAATCGCAATGCGATAGTC
Found at i:49483 original size:21 final size:21
Alignment explanation
Indices: 49454--49494 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
49444 GATTTACATA
49454 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
49475 TTCGTATTGCGATAGTCCAA
1 TTCGCATTGCGATAGTCCAA
49495 AATTGCAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:50236 original size:21 final size:21
Alignment explanation
Indices: 50211--50355 Score: 163
Period size: 21 Copynumber: 6.8 Consensus size: 21
50201 ATTTTGGACT
50211 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
50232 ATCGCAATGCGAACTTTGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
50253 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
50274 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
50295 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
50316 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
50337 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
50356 CTATCGCAAT
Statistics
Matches: 104, Mismatches: 10, Indels: 18
0.79 0.08 0.14
Matches are distributed among these distances:
19 19 0.18
21 55 0.53
23 30 0.29
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:50310 original size:63 final size:63
Alignment explanation
Indices: 50211--50355 Score: 245
Period size: 63 Copynumber: 2.3 Consensus size: 63
50201 ATTTTGGACT
* * *
50211 ATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTTGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
50274 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
50337 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
50356 CTATCGCAAT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
63 67 0.87
65 10 0.13
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (63 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:50809 original size:15 final size:16
Alignment explanation
Indices: 50789--50819 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
50779 CCGAATTCAG
50789 TGCCCAATTTT-TTGA
1 TGCCCAATTTTGTTGA
50804 TGCCCAATTTTGTTGA
1 TGCCCAATTTTGTTGA
50820 AAATGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.45
Consensus pattern (16 bp):
TGCCCAATTTTGTTGA
Found at i:51911 original size:15 final size:15
Alignment explanation
Indices: 51887--51918 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
51877 TGACAGATCG
*
51887 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
51902 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
51917 AA
1 AA
51919 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:55230 original size:15 final size:15
Alignment explanation
Indices: 55210--55240 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
55200 GGGCACCGAA
55210 TTTGGTGCCCAATTT
1 TTTGGTGCCCAATTT
55225 TTTGGTGCCCAATTT
1 TTTGGTGCCCAATTT
55240 T
1 T
55241 GTTAAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (15 bp):
TTTGGTGCCCAATTT
Done.