Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001670.1 Hibiscus syriacus cultivar Beakdansim tig00003342_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: 79220
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:5042 original size:31 final size:31
Alignment explanation
Indices: 5007--5072 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
4997 GTCATAACCC
* *
5007 GACCCAAACCGACCCGTTTACCTGACCCGTT
1 GACCCAAACCGACCCGTTGACCCGACCCGTT
* * * *
5038 GACCCGACCCGACCTGTTGACCCGTCCCGTT
1 GACCCAAACCGACCCGTTGACCCGACCCGTT
5069 GACC
1 GACC
5073 GTTGACCGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.18, C:0.44, G:0.20, T:0.18
Consensus pattern (31 bp):
GACCCAAACCGACCCGTTGACCCGACCCGTT
Found at i:5056 original size:18 final size:18
Alignment explanation
Indices: 5030--5066 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5020 CCGTTTACCT
5030 GACCCGTTGACCCGACCC
1 GACCCGTTGACCCGACCC
* *
5048 GACCTGTTGACCCGTCCC
1 GACCCGTTGACCCGACCC
5066 G
1 G
5067 TTGACCGTTG
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:0.14, C:0.46, G:0.24, T:0.16
Consensus pattern (18 bp):
GACCCGTTGACCCGACCC
Found at i:5061 original size:13 final size:13
Alignment explanation
Indices: 5015--5048 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5005 CCGACCCAAA
*
5015 CCGACCCGTTTAC
1 CCGACCCGTTGAC
*
5028 CTGACCCGTTGAC
1 CCGACCCGTTGAC
5041 CCGACCCG
1 CCGACCCG
5049 ACCTGTTGAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.15, C:0.47, G:0.21, T:0.18
Consensus pattern (13 bp):
CCGACCCGTTGAC
Found at i:7573 original size:24 final size:24
Alignment explanation
Indices: 7546--7664 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
7536 TTCGATTTGA
*
7546 ATTCTGATATGATACTTGGCATGG
1 ATTCTGATATGATACTTGACATGG
* * *
7570 ATTCTGATCTGATA-TCGGATATGG
1 ATTCTGATATGATACT-TGACATGG
* * *
7594 ATTCTCATCTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
7618 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
7642 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
7665 AATTATGTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
23 1 0.01
24 78 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:7841 original size:43 final size:43
Alignment explanation
Indices: 7780--7874 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 43
7770 GGGCCTTACT
* * *
7780 TGGTGTATTGGTGGGTGTATGGTTTTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
7823 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
*
7866 TGATGTGTT
1 TGGTGTGTT
7875 CGGTTGGAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.18, C:0.09, G:0.35, T:0.38
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:10003 original size:13 final size:13
Alignment explanation
Indices: 9985--10016 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
9975 GTCATAACCT
9985 GACCCGTTGACCC
1 GACCCGTTGACCC
*
9998 GACCCGTTGACTC
1 GACCCGTTGACCC
10011 GACCCG
1 GACCCG
10017 ACCTATTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.44, G:0.25, T:0.16
Consensus pattern (13 bp):
GACCCGTTGACCC
Found at i:10016 original size:18 final size:18
Alignment explanation
Indices: 9993--10034 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
9983 CTGACCCGTT
* *
9993 GACCCGACCCGTTGACTC
1 GACCCGACCCATTGACCC
*
10011 GACCCGACCTATTGACCC
1 GACCCGACCCATTGACCC
10029 GACCCG
1 GACCCG
10035 TTAACCCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.45, G:0.21, T:0.14
Consensus pattern (18 bp):
GACCCGACCCATTGACCC
Found at i:12632 original size:24 final size:24
Alignment explanation
Indices: 12605--12723 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
12595 TTCGATTTGA
12605 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
12629 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
12653 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
12677 ATTCTGATATGATACTTAACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
12701 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
12724 AATTATGTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.01
24 84 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:12907 original size:43 final size:43
Alignment explanation
Indices: 12839--12933 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 43
12829 GGGCCTTACT
* * *
12839 TGGTGTATTGGTGGGTGTATGGTTCTGGGGAACCTACACATTT
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
*
12882 TGTTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
12925 TGGTGTGTT
1 TGGTGTGTT
12934 CGGTTGGAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.16, C:0.11, G:0.35, T:0.39
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:15072 original size:13 final size:13
Alignment explanation
Indices: 15054--15085 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
15044 GTCATAACCC
*
15054 GACCCGACCTGTT
1 GACCCGACCCGTT
15067 GACCCGACCCGTT
1 GACCCGACCCGTT
15080 GACCCG
1 GACCCG
15086 TTGACCATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.44, G:0.25, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:17676 original size:24 final size:24
Alignment explanation
Indices: 17649--17767 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
17639 TTCGATTTGA
17649 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
17673 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
17697 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
17721 ATTCTGATATGATACTTAACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
17745 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
17768 AATTATGTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.01
24 84 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:17960 original size:43 final size:43
Alignment explanation
Indices: 17883--17977 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 43
17873 GGGCCTTACT
* * * *
17883 TGGTGTATTGGTGGGTGTATGGTTGTGGGGAACCTACACATTT
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
*
17926 TGTTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
17969 TGGTGTGTT
1 TGGTGTGTT
17978 CGGTTGGAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.16, C:0.09, G:0.36, T:0.39
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:20057 original size:24 final size:24
Alignment explanation
Indices: 20023--20086 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
20013 AAACAGAGAT
*
20023 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATCCAG
* * * *
20047 ATCAGATATCATAACCGAATCCAT
1 ATCAGAAATCAAAACAGAATCCAG
*
20071 ATCAGAAATCAGAACA
1 ATCAGAAATCAAAACA
20087 AAAATCATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.50, C:0.20, G:0.11, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATCCAG
Found at i:21953 original size:19 final size:19
Alignment explanation
Indices: 21931--21970 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
21921 AGTCCAGGTG
*
21931 GCTCGACTTAGCTCAAACA
1 GCTCGACTCAGCTCAAACA
*
21950 GCTCGGCTCAGCTCAAACA
1 GCTCGACTCAGCTCAAACA
21969 GC
1 GC
21971 CCCCTTTGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.17
Consensus pattern (19 bp):
GCTCGACTCAGCTCAAACA
Found at i:23605 original size:19 final size:19
Alignment explanation
Indices: 23555--23607 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
23545 AGTTGACCTA
*
23555 GTGTATCGATAAACTTGGG
1 GTGTATCGATACACTTGGG
*
23574 GTGTATCGGTACACTTGGG
1 GTGTATCGATACACTTGGG
23593 GTGTATCGATACACT
1 GTGTATCGATACACT
23608 AATTGCATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (19 bp):
GTGTATCGATACACTTGGG
Found at i:24321 original size:19 final size:21
Alignment explanation
Indices: 24286--24329 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
24276 AATAAACATT
*
24286 AAATTTAAACTAATC-AAACC
1 AAATTCAAACTAATCAAAACC
24306 AAATTCAAAC-AATCAAAACC
1 AAATTCAAACTAATCAAAACC
24326 AAAT
1 AAAT
24330 ATATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.59, C:0.20, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATTCAAACTAATCAAAACC
Found at i:24335 original size:2 final size:2
Alignment explanation
Indices: 24328--24358 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24318 TCAAAACCAA
24328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24359 AGCGTTCAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41964 original size:49 final size:49
Alignment explanation
Indices: 41892--41988 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
41882 TAATCAAGAG
41892 GTTTGAGAAAAGGGCCTAATAACACCAGAACTTCACTAAATAACACTAT
1 GTTTGAGAAAAGGGCCTAATAACACCAGAACTTCACTAAATAACACTAT
*
41941 GTTTGAGAAAAGGGCTTAATAACACCAGAACTTCACTAAATAACACTA
1 GTTTGAGAAAAGGGCCTAATAACACCAGAACTTCACTAAATAACACTA
41989 CAAGTTAGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (49 bp):
GTTTGAGAAAAGGGCCTAATAACACCAGAACTTCACTAAATAACACTAT
Found at i:45061 original size:11 final size:12
Alignment explanation
Indices: 45034--45066 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
45024 GGTTACTAAG
45034 AGAAGATAAAGGA
1 AGAAGA-AAAGGA
45047 AGAAGAAAA-GA
1 AGAAGAAAAGGA
45058 AGAAGAAAA
1 AGAAGAAAA
45067 TATGAGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 3 0.15
13 6 0.30
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (12 bp):
AGAAGAAAAGGA
Found at i:49363 original size:20 final size:20
Alignment explanation
Indices: 49330--49382 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
49320 TATTGTTTAT
* * *
49330 TACTGTTCACACAGTATCGG
1 TACTATTCATACAGTACCGG
*
49350 TACTATTTATACAGTACCGG
1 TACTATTCATACAGTACCGG
49370 TACTATTCATACA
1 TACTATTCATACA
49383 ATAAAGTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (20 bp):
TACTATTCATACAGTACCGG
Found at i:49652 original size:18 final size:20
Alignment explanation
Indices: 49604--49657 Score: 76
Period size: 18 Copynumber: 2.8 Consensus size: 20
49594 TTTAATGTAG
49604 AAGATACCAATTGTTAACAA
1 AAGATACCAATTGTTAACAA
*
49624 AAGGATGCCAATTGTT-A-AA
1 AA-GATACCAATTGTTAACAA
49643 AAGATACCAATTGTT
1 AAGATACCAATTGTT
49658 GGAAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 12 0.39
19 4 0.13
20 3 0.10
21 12 0.39
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (20 bp):
AAGATACCAATTGTTAACAA
Found at i:51985 original size:22 final size:20
Alignment explanation
Indices: 51945--51985 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
51935 AGTCGTATAT
51945 AGCCGTTGGAGATGTTTTGG
1 AGCCGTTGGAGATGTTTTGG
*
51965 AGCCGTTTGGGGATTGTTTTG
1 AGCCG-TTGGAGA-TGTTTTG
51986 TCTACAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.12, C:0.10, G:0.39, T:0.39
Consensus pattern (20 bp):
AGCCGTTGGAGATGTTTTGG
Found at i:57956 original size:38 final size:38
Alignment explanation
Indices: 57901--57983 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 38
57891 CTTGAGCATA
*
57901 AAGTCTGTGAAAGAATTACT-AGCCCTCCTAACACATTT
1 AAGTCTGTGAAAGAATTA-TGAACCCTCCTAACACATTT
* * *
57939 AAGTCTGTGATATAATTATGAACCCTCTTAACACATTT
1 AAGTCTGTGAAAGAATTATGAACCCTCCTAACACATTT
57977 AAGTCTG
1 AAGTCTG
57984 CCTAATGAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 1 0.03
38 39 0.98
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (38 bp):
AAGTCTGTGAAAGAATTATGAACCCTCCTAACACATTT
Found at i:60456 original size:20 final size:20
Alignment explanation
Indices: 60423--60461 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
60413 TATCGATACA
*
60423 TGTTCTTTGAGTATCAATAT
1 TGTTCGTTGAGTATCAATAT
*
60443 TGTTCGTTGGGTATCAATA
1 TGTTCGTTGAGTATCAATA
60462 CTCAAGGGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.10, G:0.21, T:0.46
Consensus pattern (20 bp):
TGTTCGTTGAGTATCAATAT
Found at i:60642 original size:18 final size:18
Alignment explanation
Indices: 60619--60653 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
60609 AAGCAAATTT
* *
60619 TAGTATTGATACTCAAGA
1 TAGTATCGATACACAAGA
60637 TAGTATCGATACACAAG
1 TAGTATCGATACACAAG
60654 TTTAGGAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (18 bp):
TAGTATCGATACACAAGA
Found at i:64830 original size:19 final size:19
Alignment explanation
Indices: 64806--64857 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
64796 AATGCAATTG
64806 GTGCATCGATGCATAAGGA
1 GTGCATCGATGCATAAGGA
64825 GTGCATCGATGCATAAGGA
1 GTGCATCGATGCATAAGGA
64844 GTGCATCGATGCAT
1 GTGCATCGATGCAT
64858 CCCCTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (19 bp):
GTGCATCGATGCATAAGGA
Found at i:64954 original size:20 final size:21
Alignment explanation
Indices: 64909--64967 Score: 84
Period size: 20 Copynumber: 2.7 Consensus size: 21
64899 GCATGGGTAG
64909 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-T-TT-AAGAA
64933 TGCATCGATGCACTTT-AGAA
1 TGCATCGATGCACTTTAAGAA
64953 TGCATCGATGCACTT
1 TGCATCGATGCACTT
64968 CAAGGGGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 19 0.54
22 2 0.06
23 1 0.03
24 13 0.37
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACTTTAAGAA
Found at i:65978 original size:18 final size:18
Alignment explanation
Indices: 65785--65972 Score: 304
Period size: 18 Copynumber: 10.4 Consensus size: 18
65775 GAGGGTCTAC
*
65785 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
*
65803 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
65821 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
65839 GTGGTCTTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
65857 ATGGTCCTTCGGGAAATA
1 GTGGTCCTTCGGGACATA
65875 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
65893 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
*
65911 GTGTTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
65929 ATGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
65947 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
65965 GTGGTCCT
1 GTGGTCCT
65973 ATGGGATAAA
Statistics
Matches: 157, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 157 1.00
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.28
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:67788 original size:2 final size:2
Alignment explanation
Indices: 67781--67811 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
67771 TCTTTTTAAA
*
67781 AC AC AC AC AC GC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
67812 TATATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.48, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:68011 original size:24 final size:24
Alignment explanation
Indices: 67996--68102 Score: 128
Period size: 24 Copynumber: 4.5 Consensus size: 24
67986 CAGAAATTAA
*
67996 AACAGAATTTAGATCAAATATCAG
1 AACAGAATTCAGATCAAATATCAG
*
68020 AACAGAATTCAGATCAAATATCAT
1 AACAGAATTCAGATCAAATATCAG
* *
68044 AACAGAATCCATATCAGAA-ATCAG
1 AACAGAATTCAGATCA-AATATCAG
* *
68068 AACAGAATTCAGGT-AATGTATCAG
1 AACAGAATTCAGATCAA-ATATCAG
68092 AACAGAATTCA
1 AACAGAATTCA
68103 AGTCGAAAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 67 0.94
25 2 0.03
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (24 bp):
AACAGAATTCAGATCAAATATCAG
Found at i:68114 original size:24 final size:23
Alignment explanation
Indices: 67996--68116 Score: 88
Period size: 24 Copynumber: 5.0 Consensus size: 23
67986 CAGAAATTAA
*
67996 AACAGAATT-TAGATCAAATATCAG
1 AACAGAATTCAAG-TCAAA-ATCAG
*
68020 AACAGAATTC-AGATCAAATATCAT
1 AACAGAATTCAAG-TCAAA-ATCAG
*
68044 AACAGAATCCATA-TCAGAAATCAG
1 AACAGAATTCA-AGTCA-AAATCAG
* *
68068 AACAGAATTCAGGT-AATGTATCAG
1 AACAGAATTCAAGTCAA--AATCAG
68092 AACAGAATTCAAGTCGAAAATCAG
1 AACAGAATTCAAGTC-AAAATCAG
68116 A
1 A
68117 TAAAATATTT
Statistics
Matches: 80, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 73 0.91
25 2 0.03
26 3 0.04
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (23 bp):
AACAGAATTCAAGTCAAAATCAG
Found at i:75504 original size:20 final size:19
Alignment explanation
Indices: 75477--75514 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
75467 CGATACTAAA
*
75477 CCTTTGGTATTGATACCCT
1 CCTTTGGTATTAATACCCT
75496 CCTTCTGGTATTAATACCC
1 CCTT-TGGTATTAATACCC
75515 CCTAACTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.29, G:0.13, T:0.39
Consensus pattern (19 bp):
CCTTTGGTATTAATACCCT
Done.