Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001141.1 Hibiscus syriacus cultivar Beakdansim tig00002277_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: 70707
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:7844 original size:14 final size:14
Alignment explanation
Indices: 7796--7852 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
7786 CATTCGTGAA
* *
7796 CGTTCGGTTATATT
1 CGTTTGGTTATGTT
*
7810 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
7824 CG--T--TTATGTT
1 CGTTTGGTTATGTT
7834 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
7848 CGTTT
1 CGTTT
7853 ATGTTCATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 9 0.24
12 1 0.03
14 27 0.73
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.54
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:7855 original size:24 final size:24
Alignment explanation
Indices: 7797--7858 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
7787 ATTCGTGAAC
* *
7797 GTTCGGTTATATTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
*
7821 GTTCGTTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
7845 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
7859 ATTCATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.10, C:0.11, G:0.24, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:7868 original size:24 final size:24
Alignment explanation
Indices: 7797--7871 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
7787 ATTCGTGAAC
* * * *
7797 GTTCGGTTATATTCGTTCGGTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
* **
7821 GTTCGTTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
*
7845 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
7869 GTT
1 GTT
7872 TAACCCAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.12, C:0.11, G:0.21, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCAGTTAT
Found at i:8818 original size:64 final size:64
Alignment explanation
Indices: 8714--8865 Score: 180
Period size: 64 Copynumber: 2.4 Consensus size: 64
8704 GAATAAATTG
* *** * * * * *
8714 AACATCGAATGCATTTCATGCATCGATGCAATCTCTATGCATCGATGCACT-TGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATACAAGAGCAATGCACCGATGCACTCAGGCTATT-TTAA
* *
8778 AACATCGAATGCATTTCATGCATCGATACACGAGCAATGCACCGATGCACTCAGGCTATTTTCA
1 AACATCGAATGCATTTCATGCATCGATACAAGAGCAATGCACCGATGCACTCAGGCTATTTTAA
*
8842 AACATCGAATGCATTTTATGCATC
1 AACATCGAATGCATTTCATGCATC
8866 AATGCACACT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
64 70 0.93
65 5 0.07
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATACAAGAGCAATGCACCGATGCACTCAGGCTATTTTAA
Found at i:17389 original size:45 final size:45
Alignment explanation
Indices: 17363--17483 Score: 242
Period size: 45 Copynumber: 2.7 Consensus size: 45
17353 GAATAAATTG
17363 AACATCGAATGCATTTCATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACTTGGGTTTTATTAA
17408 AACATCGAATGCATTTCATGCATCGATGCACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACTTGGGTTTTATTAA
17453 AACATCGAATGCATTTCATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
17484 AAGCAATGCA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (45 bp):
AACATCGAATGCATTTCATGCATCGATGCACTTGGGTTTTATTAA
Found at i:18641 original size:24 final size:24
Alignment explanation
Indices: 18568--18646 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 24
18558 GTTGAGCTTG
* *
18568 AATCGAGC-TCAAAATCGAATTTT
1 AATCGAGCTTCAGAATCGAGTTTT
* *
18591 AATCGAGC-TCAGAATCGAGATTC
1 AATCGAGCTTCAGAATCGAGTTTT
* **
18614 AATCGAGCTTGAGTCTCGAGTTTT
1 AATCGAGCTTCAGAATCGAGTTTT
18638 AATCGAGCT
1 AATCGAGCT
18647 CTTAAATTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 27 0.59
24 19 0.41
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (24 bp):
AATCGAGCTTCAGAATCGAGTTTT
Found at i:18868 original size:16 final size:16
Alignment explanation
Indices: 18847--18897 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
18837 GTCTCCAACG
*
18847 TTTATGTTTGTGTTCA
1 TTTATGTTCGTGTTCA
*
18863 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
18879 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
18893 TTTAT
1 TTTAT
18898 TAAATGAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 25 0.78
ACGTcount: A:0.12, C:0.08, G:0.18, T:0.63
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:18980 original size:16 final size:16
Alignment explanation
Indices: 18956--18986 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18946 ACAAAAAAAT
*
18956 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
18972 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
18987 ATTTATTTAT
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:0.06, C:0.10, G:0.23, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:21662 original size:28 final size:28
Alignment explanation
Indices: 21628--21684 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
21618 AAACTTTCCA
21628 GAAGTTT-AGAAAATTGGAAACTTCCCTT
1 GAAGTTTCA-AAAATTGGAAACTTCCCTT
* *
21656 GAAGTTTCAAAATTTGGAAACTTTCCTT
1 GAAGTTTCAAAAATTGGAAACTTCCCTT
21684 G
1 G
21685 CCACATTCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (28 bp):
GAAGTTTCAAAAATTGGAAACTTCCCTT
Found at i:25974 original size:3 final size:3
Alignment explanation
Indices: 25961--26018 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
25951 TTATCTATCA
* * *
25961 ATC ACC ATC ATC ATC ATC GA-C ATC ACC ATC GTC ATC ATC ATC GA-C
1 ATC ATC ATC ATC ATC ATC -ATC ATC ATC ATC ATC ATC ATC ATC -ATC
26006 ATC ATC ATC ATC A
1 ATC ATC ATC ATC A
26019 AATCACCATT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 2 0.04
3 41 0.91
4 2 0.04
ACGTcount: A:0.33, C:0.36, G:0.05, T:0.26
Consensus pattern (3 bp):
ATC
Found at i:25984 original size:12 final size:12
Alignment explanation
Indices: 25969--26014 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
25959 CAATCACCAT
25969 CATCATCATCGA
1 CATCATCATCGA
* *
25981 CATCACCATCGT
1 CATCATCATCGA
25993 CATCATCATCGA
1 CATCATCATCGA
26005 CATCATCATC
1 CATCATCATC
26015 ATCAAATCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.30, C:0.37, G:0.07, T:0.26
Consensus pattern (12 bp):
CATCATCATCGA
Found at i:26000 original size:24 final size:24
Alignment explanation
Indices: 25968--26014 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
25958 TCAATCACCA
25968 TCATCATCATCGACATCACCATCG
1 TCATCATCATCGACATCACCATCG
*
25992 TCATCATCATCGACATCATCATC
1 TCATCATCATCGACATCACCATC
26015 ATCAAATCAC
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:0.30, C:0.36, G:0.06, T:0.28
Consensus pattern (24 bp):
TCATCATCATCGACATCACCATCG
Found at i:27974 original size:10 final size:10
Alignment explanation
Indices: 27959--27999 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
27949 TTCATCACAC
27959 CAAATTCTCT
1 CAAATTCTCT
*
27969 CAAATTTTCT
1 CAAATTCTCT
*
27979 CAATTTCTCT
1 CAAATTCTCT
*
27989 CAAATACTCT
1 CAAATTCTCT
27999 C
1 C
28000 TCTCTGTTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:28080 original size:17 final size:18
Alignment explanation
Indices: 28043--28083 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
28033 ATATTATGTA
*
28043 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
28061 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
28078 TTTACT
1 TTTACT
28084 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:30359 original size:26 final size:24
Alignment explanation
Indices: 30288--30359 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
30278 TTATATTTGT
30288 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
30313 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
30335 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
30360 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:34336 original size:13 final size:13
Alignment explanation
Indices: 34315--34344 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34305 GCAACCTTAA
34315 TATTCTTTAAAAT
1 TATTCTTTAAAAT
*
34328 TATTGTTTAAAAT
1 TATTCTTTAAAAT
34341 TATT
1 TATT
34345 ATAATAGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (13 bp):
TATTCTTTAAAAT
Found at i:34757 original size:32 final size:32
Alignment explanation
Indices: 34685--34773 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
34675 CCAAAATATG
* * * * *
34685 ATCAGTTGGTGTTCGGGTCGGGTTAATCTCGG
1 ATCAGTTGGTGTTCGAGTCGGATCAATATCGA
* *
34717 ATCGGTTGGTGTTCGAGTCGGATCGATATCGA
1 ATCAGTTGGTGTTCGAGTCGGATCAATATCGA
*
34749 ATCAGTTGGT-TTCGACTCGGATCAA
1 ATCAGTTGGTGTTCGAGTCGGATCAA
34774 ACTTTAGATT
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 13 0.28
32 34 0.72
ACGTcount: A:0.18, C:0.17, G:0.33, T:0.33
Consensus pattern (32 bp):
ATCAGTTGGTGTTCGAGTCGGATCAATATCGA
Found at i:34825 original size:46 final size:45
Alignment explanation
Indices: 34750--34852 Score: 143
Period size: 46 Copynumber: 2.2 Consensus size: 45
34740 CGATATCGAA
*
34750 TCAGTTGGTTTCGACTCGGATCAAACTTTAGATTTTCGGGTCAAT
1 TCAGTTGGTTTCGACTCGGATCAAACTTTAGATTTTCAGGTCAAT
* * *
34795 TCAGATTGGTTTCGATTCGGATCAACCTTTAGATTTTTAGGTCAAT
1 TCAG-TTGGTTTCGACTCGGATCAAACTTTAGATTTTCAGGTCAAT
*
34841 TCGGGTTGGTTT
1 TC-AGTTGGTTT
34853 TGGTTTAGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
45 4 0.08
46 46 0.90
47 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (45 bp):
TCAGTTGGTTTCGACTCGGATCAAACTTTAGATTTTCAGGTCAAT
Found at i:34872 original size:46 final size:46
Alignment explanation
Indices: 34754--34898 Score: 141
Period size: 46 Copynumber: 3.2 Consensus size: 46
34744 ATCGAATCAG
* * * ** *
34754 TTGGTTTCGACTCGGATCAAACTTTAGATTTTCGGGTCAATTCAGA
1 TTGGTTTCGATTCAGATCAACCTTTAGATTTTTAGGTCAATTCGGA
* *
34800 TTGGTTTCGATTCGGATCAACCTTTAGATTTTTAGGTCAATTCGGG
1 TTGGTTTCGATTCAGATCAACCTTTAGATTTTTAGGTCAATTCGGA
* * * * * *
34846 TTGGTTTTGGTTTAGATTAACTTTTAGA-TTTTAGAGTTAATTCGGA
1 TTGGTTTCGATTCAGATCAACCTTTAGATTTTTAG-GTCAATTCGGA
34892 TT-GTTTC
1 TTGGTTTC
34899 TAGTTAGGTC
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
45 10 0.12
46 73 0.88
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.44
Consensus pattern (46 bp):
TTGGTTTCGATTCAGATCAACCTTTAGATTTTTAGGTCAATTCGGA
Found at i:37250 original size:64 final size:64
Alignment explanation
Indices: 37182--37406 Score: 267
Period size: 64 Copynumber: 3.5 Consensus size: 64
37172 TTGTTTGAAG
** **
37182 GTGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATT
37245 T
64 T
** *
37246 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTA
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTT
* * * * *
37310 GTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTT
1 GTGCATCGATGCATAA-GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTT
* * *
37374 ATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCAT
37407 ACCTTCATTA
Statistics
Matches: 138, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
63 2 0.01
64 129 0.93
65 7 0.05
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (64 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTT
Found at i:38251 original size:103 final size:103
Alignment explanation
Indices: 38018--38240 Score: 419
Period size: 103 Copynumber: 2.2 Consensus size: 103
38008 GTCGAGGGTC
*
38018 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
38083 TTGATCCCTAGTATATGTATATGATTCTTCAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
*
38121 TATGTGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
38186 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
38224 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
38241 CATTATTATA
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
103 117 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
Found at i:38285 original size:23 final size:23
Alignment explanation
Indices: 38252--38314 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
38242 ATTATTATAT
38252 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
38275 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
38298 GGCACTTCAGTGCAATT
1 GGCACTACGGTGCAATT
38315 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:42848 original size:64 final size:64
Alignment explanation
Indices: 42779--43000 Score: 202
Period size: 64 Copynumber: 3.5 Consensus size: 64
42769 ATTGTTTGAA
** *
42779 AGTGCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAAT
1 AGTGCATCGATGCATTGGTAGTGCATCGATGCATC-CCATTAATAAGAAA-ACATCGAATGCAAT
42842 T
64 T
* * * *
42843 TGTGCATCGATGC-TTAAGTAGTGCGTCGATGCATCCCATTAATAAGGAAACATCGAATGCAATT
1 AGTGCATCGATGCATT-GGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATT
* * * * * * *
42907 AGTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAATAATAATACAACATCGAATACATTT
1 AGTGCATCGATGCAT-TGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCA-AT
42971 T
64 T
* * **
42972 A-TGCACCGATGTATCAGTAGTGCATCGAT
1 AGTGCATCGATGCATTGGTAGTGCATCGAT
43001 ACATACCTTC
Statistics
Matches: 128, Mismatches: 23, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
63 4 0.03
64 113 0.88
65 11 0.09
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (64 bp):
AGTGCATCGATGCATTGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATT
Found at i:43881 original size:103 final size:103
Alignment explanation
Indices: 43756--43978 Score: 419
Period size: 103 Copynumber: 2.2 Consensus size: 103
43746 GTCGAGGGTC
* * *
43756 TATGTGGTACTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGCATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
43821 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
43859 TATGTGGTCCTTCGGGATATATATGCATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGCATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
43924 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
43962 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
43979 CATTATTATA
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
103 117 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGCATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
Found at i:44023 original size:23 final size:23
Alignment explanation
Indices: 43990--44052 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
43980 ATTATTATAT
43990 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
44013 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
44036 AGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
44053 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:59500 original size:83 final size:83
Alignment explanation
Indices: 59337--59500 Score: 224
Period size: 83 Copynumber: 2.0 Consensus size: 83
59327 GTGTATATCT
*
59337 GTTTAATATTTTAAAACTAAAAGATATTATTATCTATTTAAATTTATATATTAAAAGATATATGG
1 GTTTAATATTTTAAAACTAAAAGATATTATTATCTATTTAAATTTATATATTAAAAGAGATATGG
* *
59402 TTGATATAAATCTCTCAG
66 TTGAGATAAAACTCTCAG
** * * *
59420 GTTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGT-TATTAAAAGAGATTTT
1 GTTTAATATTTTAAAACTAAAAGATATTATTATCTATTTAAATTTA-TATATTAAAAGAGATATG
59484 GTTGGAGA-AAAACTCTC
65 GTT-GAGATAAAACTCTC
59501 TCGAAATTCC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
83 67 0.94
84 4 0.06
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.44
Consensus pattern (83 bp):
GTTTAATATTTTAAAACTAAAAGATATTATTATCTATTTAAATTTATATATTAAAAGAGATATGG
TTGAGATAAAACTCTCAG
Found at i:60545 original size:63 final size:63
Alignment explanation
Indices: 60474--60603 Score: 260
Period size: 63 Copynumber: 2.1 Consensus size: 63
60464 AGAATTCATA
60474 TTATATATGTCGTAATATAATACTAAATTGTCTTCAAGATTCATTATATCTGGTATATACTGG
1 TTATATATGTCGTAATATAATACTAAATTGTCTTCAAGATTCATTATATCTGGTATATACTGG
60537 TTATATATGTCGTAATATAATACTAAATTGTCTTCAAGATTCATTATATCTGGTATATACTGG
1 TTATATATGTCGTAATATAATACTAAATTGTCTTCAAGATTCATTATATCTGGTATATACTGG
60600 TTAT
1 TTAT
60604 GAAACATCAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (63 bp):
TTATATATGTCGTAATATAATACTAAATTGTCTTCAAGATTCATTATATCTGGTATATACTGG
Found at i:60952 original size:29 final size:28
Alignment explanation
Indices: 60919--61008 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 28
60909 AAATTTTAAC
60919 TAGTGACTAAAATATAATTTTTGAAAGTT
1 TAGTGACTAAAATATAA-TTTTGAAAGTT
** * * *
60948 TAGTGGTTGAAGTATAAAGTTTGAAAAGTT
1 TAGTGACTAAAATAT-AATTTTG-AAAGTT
* *
60978 TAGGGACTAGAAATATAATTTTGAAAATT
1 TAGTGACTA-AAATATAATTTTGAAAGTT
61007 TA
1 TA
61009 TAGATTTTAG
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
29 22 0.48
30 19 0.41
31 5 0.11
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.38
Consensus pattern (28 bp):
TAGTGACTAAAATATAATTTTGAAAGTT
Found at i:61001 original size:30 final size:31
Alignment explanation
Indices: 60919--61008 Score: 86
Period size: 30 Copynumber: 3.1 Consensus size: 31
60909 AAATTTTAAC
60919 TAGT-GACTA-AAATATAATTTTTG-AAAGTT
1 TAGTGGACTAGAAATATAA-TTTTGAAAAGTT
* * *
60948 TAGTGG--TTGAAGTATAAAGTTTGAAAAGTT
1 TAGTGGACTAGAAATAT-AATTTTGAAAAGTT
60978 TAG-GGACTAGAAATATAATTTTGAAAA-TT
1 TAGTGGACTAGAAATATAATTTTGAAAAGTT
61007 TA
1 TA
61009 TAGATTTTAG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
28 1 0.02
29 19 0.39
30 22 0.45
31 7 0.14
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.38
Consensus pattern (31 bp):
TAGTGGACTAGAAATATAATTTTGAAAAGTT
Found at i:63805 original size:18 final size:18
Alignment explanation
Indices: 63779--63817 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
63769 AATTCTAAAT
*
63779 ATTTATAGTTATCAGATA
1 ATTTATAGTTACCAGATA
*
63797 ATTTGTAGTTACCAGATA
1 ATTTATAGTTACCAGATA
63815 ATT
1 ATT
63818 ACAAAGATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (18 bp):
ATTTATAGTTACCAGATA
Found at i:65147 original size:16 final size:17
Alignment explanation
Indices: 65118--65150 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
65108 CTGGGAACTA
*
65118 AAGGTAGAATTTCCAAG
1 AAGGTAGAAATTCCAAG
65135 AAGG-AGAAATTCCAAG
1 AAGGTAGAAATTCCAAG
65151 GGAAGTGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.18
Consensus pattern (17 bp):
AAGGTAGAAATTCCAAG
Done.