Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001567.1 Hibiscus syriacus cultivar Beakdansim tig00003102_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: 67822
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2000 original size:18 final size:18
Alignment explanation
Indices: 1977--2018 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1967 TTCAAGCACA
1977 AGACACCACCTAACATGC
1 AGACACCACCTAACATGC
1995 AGACACCACCTAACATGC
1 AGACACCACCTAACATGC
*
2013 CGACAC
1 AGACAC
2019 TCAATTTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.40, G:0.12, T:0.10
Consensus pattern (18 bp):
AGACACCACCTAACATGC
Found at i:2248 original size:23 final size:22
Alignment explanation
Indices: 2221--2264 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
2211 TGATTATTTT
2221 ATTATA-ATTTTTAAATATTTATA
1 ATTATATA-TTTTAAA-ATTTATA
*
2244 ATTATTTATTTTAAAATTTAT
1 ATTATATATTTTAAAATTTAT
2265 TAAGCGGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 12 0.63
24 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTATATATTTTAAAATTTATA
Found at i:4387 original size:15 final size:16
Alignment explanation
Indices: 4321--4391 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 16
4311 TTATAAGGGA
*
4321 TTTTATTATATTTATT
1 TTTTAGTATATTTATT
4337 TTGTTAGTAT-TTTATT
1 TT-TTAGTATATTTATT
*
4353 TAATTATTGTATTATTTATT
1 T--TT-TAGTA-TATTTATT
4373 TTTTAGTAT-TTTATT
1 TTTTAGTATATTTATT
4388 TTTT
1 TTTT
4392 GCAGTTATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
15 10 0.22
16 10 0.22
17 11 0.24
18 7 0.15
19 1 0.02
20 7 0.15
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.72
Consensus pattern (16 bp):
TTTTAGTATATTTATT
Found at i:5984 original size:11 final size:11
Alignment explanation
Indices: 5968--6012 Score: 65
Period size: 11 Copynumber: 4.0 Consensus size: 11
5958 AGAATTTTGA
5968 AAAATATTTAT
1 AAAATATTTAT
5979 AAAATATTTAT
1 AAAATATTTAT
5990 -AAATATTTAT
1 AAAATATTTAT
6000 AACTAATATTTAT
1 AA--AATATTTAT
6013 TTTTCAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.32
11 12 0.39
13 9 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
AAAATATTTAT
Found at i:5993 original size:21 final size:22
Alignment explanation
Indices: 5969--6012 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
5959 GAATTTTGAA
5969 AAATATTTATAA-AATATTTAT
1 AAATATTTATAACAATATTTAT
5990 AAATATTTATAACTAATATTTAT
1 AAATATTTATAAC-AATATTTAT
6013 TTTTCAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.57
23 9 0.43
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATATTTATAACAATATTTAT
Found at i:5995 original size:10 final size:10
Alignment explanation
Indices: 5969--6001 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
5959 GAATTTTGAA
5969 AAATATTTAT
1 AAATATTTAT
5979 AAAATATTTAT
1 -AAATATTTAT
5990 AAATATTTAT
1 AAATATTTAT
6000 AA
1 AA
6002 CTAATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AAATATTTAT
Found at i:8682 original size:17 final size:16
Alignment explanation
Indices: 8644--8674 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8634 ATTTTATCCT
*
8644 TATAAAATTAGTATTA
1 TATAAAATTAATATTA
8660 TATAAAATTAATATT
1 TATAAAATTAATATT
8675 TGTATAAATC
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:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TATAAAATTAATATTA
Found at i:9577 original size:35 final size:37
Alignment explanation
Indices: 9506--9579 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 37
9496 CAAAAATTGA
9506 AGAAGAAAAGTTTGATGCTTTTCTATACATGTTTGGTG
1 AGAAGAAAAGTTTGATGCTTTTC-ATACATGTTTGGTG
9544 AGAAG-AAAGTTTGATGCTTTTC-TACATGTTTGGTG
1 AGAAGAAAAGTTTGATGCTTTTCATACATGTTTGGTG
9579 A
1 A
9580 TTTCTGGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 14 0.39
37 17 0.47
38 5 0.14
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.39
Consensus pattern (37 bp):
AGAAGAAAAGTTTGATGCTTTTCATACATGTTTGGTG
Found at i:16110 original size:4 final size:4
Alignment explanation
Indices: 16101--16127 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
16091 TAATGCATGT
16101 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
16128 CATCGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:18241 original size:60 final size:59
Alignment explanation
Indices: 18102--18263 Score: 143
Period size: 60 Copynumber: 2.7 Consensus size: 59
18092 GGAATGTTCA
** * * * *
18102 AAAAGTTTGGGGACCAATTTAGAATGAAGGTCATGGTTTGGGGATGAAATTGACATGTTC
1 AAAAGTTT-GGGACCAATTTAGAATGAAGGTCATAATTTAGAGATGAAATTGAAATATTC
* * * * *
18162 AAAAGGTTGATGACTAATTTAGAATGTTA-GTCATAATTTAGAGATGAAATTGAAATATTT
1 AAAAGTTTG-GGACCAATTTAGAATG-AAGGTCATAATTTAGAGATGAAATTGAAATATTC
*
18222 AAAAGTTTAGGGACCAATTTA-AATG-AGGATCAT-ATTTTGAGA
1 AAAAGTTT-GGGACCAATTTAGAATGAAGG-TCATAATTTAGAGA
18264 ACATATGATT
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
57 1 0.01
58 9 0.11
59 9 0.11
60 61 0.74
61 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (59 bp):
AAAAGTTTGGGACCAATTTAGAATGAAGGTCATAATTTAGAGATGAAATTGAAATATTC
Found at i:38043 original size:24 final size:24
Alignment explanation
Indices: 37994--38050 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
37984 ACACCGGTTA
* *
37994 AACCGTTGATAGTGAACCGACTAG
1 AACCGCTGATAGTGAACCGACCAG
*
38018 AACCGCTGATAGTGAACCGGCCAG
1 AACCGCTGATAGTGAACCGACCAG
*
38042 AACTGCTGA
1 AACCGCTGA
38051 ACCGTTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.18
Consensus pattern (24 bp):
AACCGCTGATAGTGAACCGACCAG
Found at i:39162 original size:5 final size:5
Alignment explanation
Indices: 39152--39181 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
39142 TAAAAGTAAG
39152 CTCAA CTCAA CTCAA CTCAA CTCAAA CTCA
1 CTCAA CTCAA CTCAA CTCAA CTC-AA CTCA
39182 CAAGCTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCAA
Found at i:40047 original size:25 final size:25
Alignment explanation
Indices: 40013--40076 Score: 128
Period size: 25 Copynumber: 2.6 Consensus size: 25
40003 CATCTGAAAA
40013 ATGTCAGGATGTAAATTAACATTTT
1 ATGTCAGGATGTAAATTAACATTTT
40038 ATGTCAGGATGTAAATTAACATTTT
1 ATGTCAGGATGTAAATTAACATTTT
40063 ATGTCAGGATGTAA
1 ATGTCAGGATGTAA
40077 TGATACGGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (25 bp):
ATGTCAGGATGTAAATTAACATTTT
Found at i:40628 original size:41 final size:41
Alignment explanation
Indices: 40583--40801 Score: 216
Period size: 41 Copynumber: 5.4 Consensus size: 41
40573 ATTTACGTTG
* *
40583 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
40624 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*** *
40665 CATTTCGCGTTGCGATAGTTG-AAATCGCAACGCGA-TCTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
** * * **
40704 CATCAACGCAAATT-CG-T-GTTGCATTTCGCGTTGCGATTTTC
1 CAT-TTCGC--GTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
40745 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
40786 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
40802 TTTCCATTTC
Statistics
Matches: 144, Mismatches: 25, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
38 2 0.01
39 12 0.08
40 27 0.19
41 100 0.69
42 3 0.02
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:40676 original size:61 final size:61
Alignment explanation
Indices: 40608--40974 Score: 275
Period size: 61 Copynumber: 6.0 Consensus size: 61
40598 TAGTTGAAAA
* **
40608 TCGCGTTGCGTTTTTCCATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTACAGATCGCGTTGCGATTTTCCATT
* * ** *** * * * * *
40669 TCGCGTTGCGATAGTT-GAAATCGCAACGCGAT-CTCCATCA-A-CGCAAATT-CG-TGTTGCAT
1 TCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGT-TA-CAGATCGC--GTTGCGATTTTCCAT
40728 T
61 T
40729 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG-TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TACAGATCGCGTTGCGATTTTCCATT
*
40790 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTACAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTACAGATCGCGTTGCGATTTTCCATT
* * ** * * ** ** * **
40851 TCGCGTTGCGATAGTTGCAAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTCTAAAG
1 TCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATAGTTACAGATCGCGTTGCGATTTTC-CATT
* * *
40913 TCGTGTTGCGCGATTTTCCGTTTCGCGTTGCGATAGTCTACAG-TTGTCGTTGCGATTTTCCA
1 TCGCGTT--GCGATTTTCCATTTCGCGTTGCGATAGT-TACAGATCG-CGTTGCGATTTTCCA
40975 AATTCGTTGC
Statistics
Matches: 233, Mismatches: 54, Indels: 35
0.72 0.17 0.11
Matches are distributed among these distances:
59 4 0.02
60 41 0.18
61 122 0.52
62 28 0.12
63 15 0.06
64 9 0.04
65 14 0.06
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (61 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTACAGATCGCGTTGCGATTTTCCATT
Found at i:40679 original size:20 final size:20
Alignment explanation
Indices: 40608--40680 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
40598 TAGTTGAAAA
*
40608 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
40628 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGAT-TTTCCATT
40649 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
40669 TCGCGTTGCGAT
1 TCGCGTTGCGAT
40681 AGTTGAAATC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.11, C:0.22, G:0.27, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:40692 original size:20 final size:21
Alignment explanation
Indices: 40587--40692 Score: 67
Period size: 20 Copynumber: 5.2 Consensus size: 21
40577 ACGTTGCATT
*
40587 TCGCATTGCGATAGTT-GAAAA
1 TCGCGTTGCGATAGTTCG-AAA
** * **
40608 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
* *
40628 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGATAGTTCGAAA
* * **
40649 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
40669 TCGCGTTGCGATAGTT-GAAA
1 TCGCGTTGCGATAGTTCGAAA
40689 TCGC
1 TCGC
40693 AACGCGATCT
Statistics
Matches: 61, Mismatches: 21, Indels: 7
0.69 0.24 0.08
Matches are distributed among these distances:
20 34 0.56
21 27 0.44
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTCGAAA
Found at i:40835 original size:41 final size:42
Alignment explanation
Indices: 40790--41015 Score: 286
Period size: 41 Copynumber: 5.4 Consensus size: 42
40780 ATTTTCCATT
*
40790 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TACAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAAG
* *
40831 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGCAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAAG
40872 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTA-AAG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAAG
* *
40913 TCGTGTTGCGCGATTTTCCGTTTCGCGTTGCGATAGTCTAC-AG
1 TCGCGTT--GCGATTTTCCATTTCGCGTTGCGATAGTCTACAAG
* *
40956 TTGTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTAC-AG
1 TCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAAG
*
40997 TTGTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
41016 AATTCGTTGT
Statistics
Matches: 170, Mismatches: 9, Indels: 13
0.89 0.05 0.07
Matches are distributed among these distances:
40 1 0.01
41 119 0.70
42 11 0.06
43 36 0.21
44 3 0.02
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (42 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAAG
Found at i:40887 original size:82 final size:83
Alignment explanation
Indices: 40790--41015 Score: 284
Period size: 84 Copynumber: 2.7 Consensus size: 83
40780 ATTTTCCATT
*
40790 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TACAAATCGCGTTGCGATTTTCCATTTCG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAAGTCGCGTTGCGATTTTCCATTTCG
*
40854 CGTTGCGATAGT-TGCAAA
66 CGTTGCGATAGTCTAC-AA
* *
40872 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTA-AAGTCGTGTTGCGCGATTTTCCGTTT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAAGTCGCGTT--GCGATTTTCCATTT
*
40936 CGCGTTGCGATAGTCTACAG
64 CGCGTTGCGATAGTCTACAA
* * *
40956 TTGTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTAC-AGTTGTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAAGTCG-CGTTGCGATTTTCCA
41016 AATTCGTTGT
Statistics
Matches: 126, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
82 43 0.34
83 12 0.10
84 49 0.39
85 19 0.15
86 3 0.02
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (83 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAAGTCGCGTTGCGATTTTCCATTTCG
CGTTGCGATAGTCTACAA
Found at i:40963 original size:22 final size:22
Alignment explanation
Indices: 40938--41009 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
40928 TTCCGTTTCG
40938 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
40960 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
40979 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
41001 CGTTGCGAT
1 CGTTGCGAT
41010 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:40983 original size:19 final size:19
Alignment explanation
Indices: 40959--41024 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
40949 TCTACAGTTG
40959 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
40978 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
40999 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
41019 TCGTTG
1 TCGTTG
41025 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:41024 original size:125 final size:122
Alignment explanation
Indices: 40797--41035 Score: 288
Period size: 125 Copynumber: 1.9 Consensus size: 122
40787 ATTTCGCGTT
*
40797 GCGATTTTCCATTTCGCGTTGCGATAGTTACAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGA
1 GCGATTTTCCATTTCGCGTTGCGATAGTTACAAATCGCGTTGCGATTTTCCAATTC-CGTTGCGA
* *
40862 TAGTTGCAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTAAAGTCGTGTTGC
65 TAGTTACAAATCGCGTTGCGATTTTCCAATTC-CGTTGCGATAGT-TAAAGTCGTGTTGC
* * *
40922 GCGATTTTCCGTTTCGCGTTGCGATAGTCTAC-AGTTGTCGTTGCGATTTTCCAAATT-CGTTGC
1 GCGATTTTCCATTTCGCGTTGCGATAGT-TACAAATCG-CGTTGCGATTTTCC-AATTCCGTTGC
* * *
40985 GATAGTCTAC-AGTTGTCGTTGCGATTTTCCAAATT-CGTTGTGATAGTTAAA
63 GATAGT-TACAAATCG-CGTTGCGATTTTCC-AATTCCGTTGCGATAGTTAAA
41036 AAAAAAGATT
Statistics
Matches: 99, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
124 4 0.04
125 56 0.57
126 33 0.33
127 6 0.06
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.38
Consensus pattern (122 bp):
GCGATTTTCCATTTCGCGTTGCGATAGTTACAAATCGCGTTGCGATTTTCCAATTCCGTTGCGAT
AGTTACAAATCGCGTTGCGATTTTCCAATTCCGTTGCGATAGTTAAAGTCGTGTTGC
Found at i:41141 original size:5 final size:5
Alignment explanation
Indices: 41113--41168 Score: 85
Period size: 5 Copynumber: 10.6 Consensus size: 5
41103 CGTATTACCA
41113 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGACC CGACC
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGACC CGACC
41161 CGACC CGA
1 CGACC CGA
41169 GACGAGACGA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 33 0.66
6 17 0.34
ACGTcount: A:0.25, C:0.55, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:41174 original size:5 final size:5
Alignment explanation
Indices: 41166--41196 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
41156 CGACCCGACC
41166 CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
41197 GCGGCGGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.35, C:0.23, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:41726 original size:6 final size:5
Alignment explanation
Indices: 41675--41725 Score: 75
Period size: 5 Copynumber: 9.6 Consensus size: 5
41665 CCGTCTCGTC
41675 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG
41723 TCG
1 TCG
41726 TACGTGTCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 28 0.62
6 17 0.38
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:41832 original size:19 final size:19
Alignment explanation
Indices: 41808--41873 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
41798 TTAACTATCA
*
41808 CAACGAATTTGGAAAATCG
1 CAACGAATTTAGAAAATCG
* **
41827 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTAGAAAATCG
*
41849 CAACGAATTTCGAAAATCG
1 CAACGAATTTAGAAAATCG
41868 CAACGA
1 CAACGA
41874 CAACTGTAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (19 bp):
CAACGAATTTAGAAAATCG
Found at i:41911 original size:20 final size:20
Alignment explanation
Indices: 41886--41958 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
41876 ACTGTAGACT
41886 ATCGCAACGCGAAACGGAAA
1 ATCGCAACGCGAAACGGAAA
**
41906 ATCGCAACGCG--ACTGTAGACT
1 ATCGCAACGCGAAAC-G--GAAA
*
41927 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAACGGAAA
41947 ATCGCAACGCGA
1 ATCGCAACGCGA
41959 CTGTAGACTA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
18 2 0.05
19 1 0.02
20 25 0.58
21 13 0.30
22 1 0.02
23 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.25, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAACGGAAA
Found at i:41977 original size:41 final size:42
Alignment explanation
Indices: 41817--41983 Score: 252
Period size: 41 Copynumber: 4.0 Consensus size: 42
41807 ACAACGAATT
*
41817 TGGAAAATCGCAACGACAACTGTAGACTATCGCAA--CGAATT
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAA-A
*
41858 TCGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
* *
41900 CGGAAAATCGCAACG-CGACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
*
41941 TGGAAAATCGCAACG-CGACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
41982 TG
1 TG
41984 CAACGCGAAT
Statistics
Matches: 118, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
41 101 0.86
42 13 0.11
43 4 0.03
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (42 bp):
TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
Found at i:42239 original size:37 final size:36
Alignment explanation
Indices: 42163--42239 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
42153 TTTTTATATT
*
42163 TTTAATTTTGTAAAAAAATTTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAA-TTATATAAATATTATCAA
* *
42200 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
42237 TTT
1 TTT
42240 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 18 0.51
38 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:46597 original size:24 final size:24
Alignment explanation
Indices: 46570--46618 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
46560 GAGTCTCAAT
46570 TATTAAACGTTATAAAATAGTCAC
1 TATTAAACGTTATAAAATAGTCAC
46594 TATTAAACGTTATAAAATAGTCAC
1 TATTAAACGTTATAAAATAGTCAC
46618 T
1 T
46619 CGATTGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (24 bp):
TATTAAACGTTATAAAATAGTCAC
Found at i:51755 original size:127 final size:126
Alignment explanation
Indices: 51529--51906 Score: 612
Period size: 127 Copynumber: 3.0 Consensus size: 126
51519 TATACACATG
* * * * **
51529 TATATATGATCATTTCCTTTTCATTACAATTCTCACAACTACTATAGGAGCCATTCAACAACACA
1 TATATATGATAATTTCCTTTTCATTACAATTCTCCCAACAACTAAAGGAAACATTCAACAACACA
*
51594 TCAGACATGCCATAGCATCATCCATCATCATCATAATAATACCAAAGCACATGAACTACACA
66 TCAGACATGACATAGCATCATCCATCATCATCAT-ATAATACCAAAGCACATGAACTACACA
*
51656 TATATATGATAATTTCCTTTTCATTACAATTCTCCCAACAACAAAAGGAAACATTCAACAACACA
1 TATATATGATAATTTCCTTTTCATTACAATTCTCCCAACAACTAAAGGAAACATTCAACAACACA
51721 TCAGACATGACATAGCATCATCCATCATCATCATATATATACCAAAGCACATGAACTACACA
66 TCAGACATGACATAGCATCATCCATCATCATCATATA-ATACCAAAGCACATGAACTACACA
* *
51783 TGTATATGATAATTTCCTTTTCATTACAATTCTCCCAACAGCTAAAGGAAACATTCAACAACACA
1 TATATATGATAATTTCCTTTTCATTACAATTCTCCCAACAACTAAAGGAAACATTCAACAACACA
* *
51848 TCAGACATGACATTGCATCATCAATCATCATCATCATAAATACCAAAGCACATGAACTA
66 TCAGACATGACATAGCATCATCCATCATCATCAT-AT-AATACCAAAGCACATGAACTA
51907 TACGGGAAGT
Statistics
Matches: 235, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
126 3 0.01
127 209 0.89
128 22 0.09
129 1 0.00
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.27
Consensus pattern (126 bp):
TATATATGATAATTTCCTTTTCATTACAATTCTCCCAACAACTAAAGGAAACATTCAACAACACA
TCAGACATGACATAGCATCATCCATCATCATCATATAATACCAAAGCACATGAACTACACA
Found at i:55538 original size:111 final size:110
Alignment explanation
Indices: 55345--55565 Score: 361
Period size: 111 Copynumber: 2.0 Consensus size: 110
55335 TAAGTTGTAA
55345 ACAAAATTAGCAAAAAATATGCATGCAGAACAAAAAAATATTGTAAGAGCATGAGAGAGTGTACT
1 ACAAAATTAGCAAAAAATATGCATGCAGAACAAAAAAATATTGTAAGAGCATGAGAGAGTGTACT
* *
55410 AGAATGCATCATGCCAGTAGCAGCAACAGATCCCACGGTATTCAG
66 AGAAGGCATCATGCCAGTAGCAGCAACAGATCCCACGCTATTCAG
** * *
55455 ACAAAATTAGCTTAAAATATGCATGCAAGAACAGAAAAATCTTGTAAGAGCATGAGAGAGTGTAC
1 ACAAAATTAGCAAAAAATATGCATGC-AGAACAAAAAAATATTGTAAGAGCATGAGAGAGTGTAC
* *
55520 TAGAAGGCATCATGCCAGTAGCAGCAACTGATCCCATGCTATTCAG
65 TAGAAGGCATCATGCCAGTAGCAGCAACAGATCCCACGCTATTCAG
55566 CAATTTCGGA
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
110 24 0.24
111 78 0.76
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (110 bp):
ACAAAATTAGCAAAAAATATGCATGCAGAACAAAAAAATATTGTAAGAGCATGAGAGAGTGTACT
AGAAGGCATCATGCCAGTAGCAGCAACAGATCCCACGCTATTCAG
Found at i:58676 original size:16 final size:16
Alignment explanation
Indices: 58655--58685 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
58645 TAATATTGAA
58655 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
58671 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
58686 AAATTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:67689 original size:26 final size:26
Alignment explanation
Indices: 67660--67715 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
67650 TTCCATGAAA
67660 CAACCAATACTTTCTATAGCACGATT
1 CAACCAATACTTTCTATAGCACGATT
67686 CAACCAATACTTTCTATAGCACGATT
1 CAACCAATACTTTCTATAGCACGATT
67712 CAAC
1 CAAC
67716 AATCCTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (26 bp):
CAACCAATACTTTCTATAGCACGATT
Done.