Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003860.1 Hibiscus syriacus cultivar Beakdansim tig00008298_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: 98264
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1314 original size:19 final size:20
Alignment explanation
Indices: 1271--1318 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1261 TCTAAATCCT
*
1271 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATATCATTTTGG
* *
1291 CTTTCAAAATAT-ATTTTTG
1 TTTTCAAAATATCATTTTGG
1310 TTTTCAAAA
1 TTTTCAAAA
1319 GAAAATTGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATATCATTTTGG
Found at i:2244 original size:30 final size:32
Alignment explanation
Indices: 2185--2245 Score: 81
Period size: 34 Copynumber: 1.9 Consensus size: 32
2175 GTTTTTTCGA
2185 GCTAAACTAGAACCTTTCCCTAGCTTTTACACGG
1 GCTAAACTAGAACCTTTCCC-A-CTTTTACACGG
*
2219 GCTAAGCTAGAACCTTT-CC-CTTTTACA
1 GCTAAACTAGAACCTTTCCCACTTTTACA
2246 AAACAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 8 0.31
33 2 0.08
34 16 0.62
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (32 bp):
GCTAAACTAGAACCTTTCCCACTTTTACACGG
Found at i:2611 original size:21 final size:21
Alignment explanation
Indices: 2586--2627 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2576 CCGTTAGACA
2586 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
**
2607 GGGGGAATTTGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
2628 ACATTTTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.26, G:0.40, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:5902 original size:14 final size:14
Alignment explanation
Indices: 5883--5910 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5873 GATCCATTAC
5883 TTGTATTTTAATAT
1 TTGTATTTTAATAT
5897 TTGTATTTTAATAT
1 TTGTATTTTAATAT
5911 AATTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
TTGTATTTTAATAT
Found at i:9843 original size:15 final size:15
Alignment explanation
Indices: 9823--9859 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
9813 GAAGTCAATC
9823 CTTTTAATTCCTCGT
1 CTTTTAATTCCTCGT
9838 CTTTTAATTCCTCGT
1 CTTTTAATTCCTCGT
*
9853 CGTTTAA
1 CTTTTAA
9860 GATTCCAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.51
Consensus pattern (15 bp):
CTTTTAATTCCTCGT
Found at i:10920 original size:126 final size:129
Alignment explanation
Indices: 10763--11018 Score: 410
Period size: 126 Copynumber: 2.0 Consensus size: 129
10753 AACCCAAAAT
10763 CATAAAACCACCGAGCGTAAAATCTTACACCGATGACTTAAATAGAAAAT-AAAAAATGATAAAA
1 CATAAAACCACCGAGCGTAAAATCTTACACCGATGACTTAAATAGAAAATAAAAAAATGATAAAA
* * * * *
10827 TGCAAGAAATCGT-A-TTTTTTTCGGATTGATTATGTCACGTAAAATAAAAATGAATCATATAC
66 TGCAAGAAATCATAATTTTTTTTCGAATTAATTATGTCACATAAAATAAAAACGAATCATATAC
10889 CATAAAACCACCGAGCGTAAAATCTTACACCGATGACTTAAATAGAAAATAAAAAAAATGATAAA
1 CATAAAACCACCGAGCGTAAAATCTTACACCGATGACTTAAATAGAAAAT-AAAAAAATGATAAA
* *
10954 ATGCAAGAAATCATAATTTTTTTTTCTAATTAATTATGTCACATAAAATAAAAACGTATCATATA
65 ATGCAAGAAATCATAA-TTTTTTTTCGAATTAATTATGTCACATAAAATAAAAACGAATCATATA
11019 GATCACGTTT
Statistics
Matches: 118, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
126 50 0.42
128 26 0.22
129 1 0.01
131 41 0.35
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.28
Consensus pattern (129 bp):
CATAAAACCACCGAGCGTAAAATCTTACACCGATGACTTAAATAGAAAATAAAAAAATGATAAAA
TGCAAGAAATCATAATTTTTTTTCGAATTAATTATGTCACATAAAATAAAAACGAATCATATAC
Found at i:13535 original size:17 final size:16
Alignment explanation
Indices: 13513--13546 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
13503 TGCTTAAATA
*
13513 AGAGTTTTTCTCGAAAG
1 AGAGTTTATCTC-AAAG
13530 AGAGTTTATCTCAAAG
1 AGAGTTTATCTCAAAG
13546 A
1 A
13547 AATGAAATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (16 bp):
AGAGTTTATCTCAAAG
Found at i:15444 original size:2 final size:2
Alignment explanation
Indices: 15437--15480 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
15427 ATTTTCAATA
15437 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15479 AT
1 AT
15481 CTGTGTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27611 original size:19 final size:20
Alignment explanation
Indices: 27589--27661 Score: 107
Period size: 19 Copynumber: 3.8 Consensus size: 20
27579 AAAATAGCCA
*
27589 GAGTGCATCAATGCATGGC-
1 GAGTGCATCGATGCATGGCT
27608 GAGTGCATCGATGCATGGCT
1 GAGTGCATCGATGCATGGCT
27628 G-GTGCATCGATGCATGGCT
1 GAGTGCATCGATGCATGGCT
*
27647 G-GTGCATTGATGCAT
1 GAGTGCATCGATGCAT
27662 CAAATGCATT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
19 50 0.98
20 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (20 bp):
GAGTGCATCGATGCATGGCT
Found at i:27782 original size:65 final size:65
Alignment explanation
Indices: 27627--27784 Score: 189
Period size: 65 Copynumber: 2.4 Consensus size: 65
27617 GATGCATGGC
* *
27627 TGGTGCATCGATGCATGGCTGGTGCATTGATGCATCAAATGCATTCGATGTTTTCATAAAATCCT
1 TGGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CT
27692 CA
64 CA
** * **
27694 --GTGCATCGATGCATGGTAAGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TC
1 TGGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTC
27755 A
65 A
27756 TGGTGCATCGATGCATGGATTGGTGCATC
1 TGGTGCATCGATGCATGG-TTGGTGCATC
27785 ACTCTGAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 21 0.27
65 51 0.65
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (65 bp):
TGGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCA
Found at i:42520 original size:65 final size:65
Alignment explanation
Indices: 42386--42546 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 65
42376 GTGCACTAAG
* * *
42386 AGTGCATCGATGCATCCAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
* * * *
42450 AGTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGC
42513 T
65 T
*
42514 AAGTGCATCGATGCATGAAATGCATTCGATGTT
1 -AGTGCATCGATGCATCAAATGCATTCGATGTT
42547 CAATTTAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 28 0.33
65 54 0.64
66 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (65 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCT
Found at i:42585 original size:65 final size:63
Alignment explanation
Indices: 42386--42596 Score: 205
Period size: 65 Copynumber: 3.3 Consensus size: 63
42376 GTGCACTAAG
* * * *
42386 AGTGCATCGATGCATCCAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGC
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGT
42449 T
63 T
* * *
42450 AGTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTA
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGTT
* **
42515 AGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGA
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-
42578 TT
62 TT
* *
42580 GGTGCATCGTTGCATCA
1 AGTGCATCGATGCATCA
42597 CTCTGAAAAA
Statistics
Matches: 123, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 47 0.38
65 65 0.53
66 4 0.03
67 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.30
Consensus pattern (63 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTT
Found at i:43066 original size:2 final size:2
Alignment explanation
Indices: 43059--43089 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43049 AATTGATTAA
43059 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
43090 GCTTTAGCTA
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:49202 original size:22 final size:21
Alignment explanation
Indices: 49160--49199 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49150 AGACTATTTT
49160 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
49181 TCATTTTTTTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
49200 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:51276 original size:65 final size:64
Alignment explanation
Indices: 51142--51299 Score: 194
Period size: 65 Copynumber: 2.5 Consensus size: 64
51132 GTGCACTAAG
* * *
51142 AGTGCATCGATGCATCCAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGCTGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGCTGCATGGCT
* * ** *
51206 AGTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAA-ATCTTCAGTGCATCGGTGCATGG-
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGCTGCATGGC
51269 T
64 T
*
51270 AAGTGCATCGATGCATGAAATGCATTCGAT
1 -AGTGCATCGATGCATCAAATGCATTCGAT
51300 ATTCAATTTA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
64 28 0.35
65 50 0.62
66 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGCTGCATGGCT
Found at i:54589 original size:65 final size:63
Alignment explanation
Indices: 54471--54633 Score: 161
Period size: 65 Copynumber: 2.5 Consensus size: 63
54461 TATTCAAAGG
*
54471 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAATTAATTGAACATCGAATGCATT
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC-ATGAATTAATTAAACATCGAATGCATT
54535 C
63 C
*
54536 CATGCACCGATGCACTCTCCATGCATCGATGCAGTC-TGAA-TATTTTCAAAACATCGAATGCAT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCATGAATTA-ATT--AAACATCGAATGCAT
*
54599 TT
62 TC
* * *** *
54601 GATGCATCGATGCACAAGCCATGTATCGATGCA
1 CATGCACCGATGCACTCTCCATGCATCGATGCA
54634 CCAGGCTATT
Statistics
Matches: 84, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
62 2 0.02
63 6 0.07
64 16 0.19
65 58 0.69
66 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCATGAATTAATTAAACATCGAATGCATTC
Found at i:54647 original size:65 final size:64
Alignment explanation
Indices: 54520--54680 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 64
54510 GAATTAATTG
* * *** * *
54520 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCAGTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCAGCCAGAATATTTTC-A
* * **
54585 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGTATCGATGCA-CCAGGCTATTTTTCA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCAGCCAGAATA-TTTTCA
* *
54649 AGCATCAAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
54681 CTTGGTGCAC
Statistics
Matches: 81, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 34 0.42
65 47 0.58
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCAGCCAGAATATTTTCA
Found at i:60313 original size:20 final size:21
Alignment explanation
Indices: 60284--60339 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
60274 TTTATGCTTC
*
60284 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
60304 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
60326 ATGCATCGATGCAT
1 ATGCATCGATGCAT
60340 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:61909 original size:21 final size:21
Alignment explanation
Indices: 61867--61910 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
61857 ACCCCGGGAG
*
61867 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
61888 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
61909 CT
1 CT
61911 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:63087 original size:64 final size:65
Alignment explanation
Indices: 62930--63090 Score: 193
Period size: 65 Copynumber: 2.5 Consensus size: 65
62920 GAATTAATTG
* * *** *
62930 AACATCGAATGCATTCCATGTA-CTGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AACATCGAATGCATTTCATGCATC-GATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCA
62994 A
65 A
* **
62995 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
63058 A
65 A
*
63059 AACGTCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
63091 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 35 0.42
65 47 0.57
66 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:64018 original size:43 final size:43
Alignment explanation
Indices: 63927--64010 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
63917 AAACGCCGCA
* * *
63927 AAAGATTAAGTTATTTAGTGGTGTTTATGAGACAAACACCACG
1 AAAGGTTAAGTCATTCAGTGGTGTTTATGAGACAAACACCACG
*
63970 AAAGGTTAAGTCATTCAGTGGTGTTTATGGGACAAACACCA
1 AAAGGTTAAGTCATTCAGTGGTGTTTATGAGACAAACACCA
64011 TTAAAGGTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.29
Consensus pattern (43 bp):
AAAGGTTAAGTCATTCAGTGGTGTTTATGAGACAAACACCACG
Found at i:64498 original size:37 final size:37
Alignment explanation
Indices: 64455--64528 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
64445 TCCTTTAAAG
*
64455 TTACAATTAAACCACTAAAATATAATAAAAATTTTAT
1 TTACAATTAAACCACTAAAATATAATAAAAATCTTAT
*
64492 TTACAATTAAACCCCTAAAATATAATAAAAATCTTAT
1 TTACAATTAAACCACTAAAATATAATAAAAATCTTAT
64529 ATATAACTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.34
Consensus pattern (37 bp):
TTACAATTAAACCACTAAAATATAATAAAAATCTTAT
Found at i:67052 original size:15 final size:15
Alignment explanation
Indices: 67017--67073 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
67007 TTAATGAAAG
*
67017 TAAATAAATAATAACAA
1 TAAATAAATAAT--GAA
*
67034 TAAATAAATATTGAA
1 TAAATAAATAATGAA
67049 TAAA-AAATAATGAGA
1 TAAATAAATAATGA-A
67064 -AAATAAATAA
1 TAAATAAATAA
67074 ATTTTCCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 11 0.31
15 13 0.37
17 11 0.31
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (15 bp):
TAAATAAATAATGAA
Found at i:68143 original size:3 final size:3
Alignment explanation
Indices: 68084--68132 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
68074 ATGATAGGTA
68084 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
68132 A
1 A
68133 TGCAATAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:68396 original size:35 final size:35
Alignment explanation
Indices: 68350--68420 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
68340 TACCGAACTG
68350 TTCTTGAGGTAATGATACCATAGGTGAGAGAAGTA
1 TTCTTGAGGTAATGATACCATAGGTGAGAGAAGTA
68385 TTCTTGAGGTAATGATACCATAGGTGAGAGAAGTA
1 TTCTTGAGGTAATGATACCATAGGTGAGAGAAGTA
68420 T
1 T
68421 CGATACTCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (35 bp):
TTCTTGAGGTAATGATACCATAGGTGAGAGAAGTA
Found at i:69586 original size:29 final size:29
Alignment explanation
Indices: 69554--69637 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 29
69544 TATAAACCCG
* *
69554 TGTAGAATGAGGATGGGGATATAATCACA
1 TGTAGAATCAGGACGGGGATATAATCACA
* * * *
69583 TGTAGATTCAAGACAGGGATATAATCCCA
1 TGTAGAATCAGGACGGGGATATAATCACA
* * *
69612 TGCAGAATTAGGACGAGGATATAATC
1 TGTAGAATCAGGACGGGGATATAATC
69638 CTATGTAAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (29 bp):
TGTAGAATCAGGACGGGGATATAATCACA
Found at i:73681 original size:12 final size:12
Alignment explanation
Indices: 73666--73704 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
73656 AATAGATCTG
73666 AAAATGAAAATAA
1 AAAAT-AAAATAA
73679 AAAATAAAATAA
1 AAAATAAAATAA
73691 AAAATAAAATAA
1 AAAATAAAATAA
73703 AA
1 AA
73705 TAAATAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:73699 original size:17 final size:17
Alignment explanation
Indices: 73666--73763 Score: 67
Period size: 17 Copynumber: 5.6 Consensus size: 17
73656 AATAGATCTG
73666 AAAATGAAAATAA-AAAAT
1 AAAAT-AAAA-AATAAAAT
73684 AAAATAAAAAATAAAAT
1 AAAATAAAAAATAAAAT
* *
73701 AAAATAAATAAGTGAAAT
1 AAAATAAA-AAATAAAAT
*
73719 -AAATAAATAATATAAAT
1 AAAATAAAAAATA-AAAT
* * *
73736 ATATATATATAATAAAA-
1 A-AAATAAAAAATAAAAT
73753 AACAATAAAAA
1 AA-AATAAAAA
73764 TTGTACATTT
Statistics
Matches: 64, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
16 5 0.08
17 34 0.53
18 15 0.23
19 10 0.16
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.22
Consensus pattern (17 bp):
AAAATAAAAAATAAAAT
Found at i:73711 original size:4 final size:4
Alignment explanation
Indices: 73673--73751 Score: 63
Period size: 4 Copynumber: 18.8 Consensus size: 4
73663 CTGAAAATGA
*
73673 AAAT AAA- AAAT AAAAT AAA- AAAT AAAAT AAAAT AAAT AAGT GAAAT
1 AAAT AAAT AAAT -AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT -AAAT
* *
73719 AAAT AAAT AATAT AAAT ATAT ATAT ATAAT AAA
1 AAAT AAAT AA-AT AAAT AAAT AAAT A-AAT AAA
73752 AAACAATAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
3 6 0.09
4 35 0.55
5 23 0.36
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:73919 original size:36 final size:36
Alignment explanation
Indices: 73770--74050 Score: 233
Period size: 36 Copynumber: 7.8 Consensus size: 36
73760 AAAATTGTAC
* *
73770 ATTTTC-AAAATCGCTTTT-AAAA-AATATATTATAT
1 ATTTTCAAAAATCG-TTTTCAAAACTATATAATATAT
* * *
73804 ATTTTC-AAAATCATTTTCGAAGCTATA-ATATATAT
1 ATTTTCAAAAATCGTTTTCAAAACTATATA-ATATAT
* **
73839 ATGTTTCCACAAATTATTTTTCAAAACTATAT-A-ATAT
1 AT-TTT-CA-AAAATCGTTTTCAAAACTATATAATATAT
73876 ATTTTCAAAAATCGTTTTCAAAACTATATAATATAT
1 ATTTTCAAAAATCGTTTTCAAAACTATATAATATAT
73912 ATTTTCAAAAATCGTTTTCAAAACTATAT-A-ATAT
1 ATTTTCAAAAATCGTTTTCAAAACTATATAATATAT
* * * *
73946 ATTTTCAAAAACCGATTTTTTAAAAAGTATATATTATAT
1 ATTTTCAAAAATCG---TTTTCAAAACTATATAATATAT
* *
73985 GA-TTTCAAAAACCGTTTTCTAAAAACTATATATTATAT
1 -ATTTTCAAAAATCGTTTTC--AAAACTATATAATATAT
* *
74023 TTTTTCAAAAAT-ATTTTCAAAAACTATA
1 ATTTTCAAAAATCGTTTTC-AAAACTATA
74051 CTATATTAAT
Statistics
Matches: 206, Mismatches: 22, Indels: 36
0.78 0.08 0.14
Matches are distributed among these distances:
33 4 0.02
34 51 0.25
35 14 0.07
36 53 0.26
37 25 0.12
38 26 0.13
39 32 0.16
40 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (36 bp):
ATTTTCAAAAATCGTTTTCAAAACTATATAATATAT
Found at i:87256 original size:123 final size:123
Alignment explanation
Indices: 87037--87284 Score: 487
Period size: 123 Copynumber: 2.0 Consensus size: 123
87027 TATGTTATTT
87037 ATAAATTTATGTTAATTTGGTTAACCGAACTTTGTTCAGTTAGATTAAAATTTAAAAAAATCAAT
1 ATAAATTTATGTTAATTTGGTTAACCGAACTTTGTTCAGTTAGATTAAAATTTAAAAAAATCAAT
87102 TTAGTCAACAATTAAAAAGAAAATCGGTTAACGATTTTTAGATAGTTCGGTTCAATTG
66 TTAGTCAACAATTAAAAAGAAAATCGGTTAACGATTTTTAGATAGTTCGGTTCAATTG
87160 ATAAATTTATGTTAATTTGGTTAACCGAACTTTGTTCAGTTAGATTAAAATTTAAAAAAATCAAT
1 ATAAATTTATGTTAATTTGGTTAACCGAACTTTGTTCAGTTAGATTAAAATTTAAAAAAATCAAT
*
87225 TTAGTCAACAATTAAAAAGGAAATCGGTTAACGATTTTTAGATAGTTCGGTTCAATTG
66 TTAGTCAACAATTAAAAAGAAAATCGGTTAACGATTTTTAGATAGTTCGGTTCAATTG
87283 AT
1 AT
87285 TAGCTGAACG
Statistics
Matches: 124, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
123 124 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (123 bp):
ATAAATTTATGTTAATTTGGTTAACCGAACTTTGTTCAGTTAGATTAAAATTTAAAAAAATCAAT
TTAGTCAACAATTAAAAAGAAAATCGGTTAACGATTTTTAGATAGTTCGGTTCAATTG
Found at i:91185 original size:22 final size:22
Alignment explanation
Indices: 91157--91216 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
91147 TTTTACACAC
*
91157 AGTGTACCGATACACCCTTGAG
1 AGTGTACCGATGCACCCTTGAG
91179 AGTGTACCGATGCACCCTTGAG
1 AGTGTACCGATGCACCCTTGAG
*
91201 AGTGTATCGATGCACC
1 AGTGTACCGATGCACC
91217 TACGCTCCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (22 bp):
AGTGTACCGATGCACCCTTGAG
Found at i:98031 original size:20 final size:21
Alignment explanation
Indices: 97979--98039 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
97969 ATTCCCCTGT
97979 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
98002 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
*
98022 GGGAGG-ATCGATTCCCTC
1 GGG-GGAATCGGTTCCCTC
98040 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 16 0.44
21 4 0.11
22 3 0.08
23 13 0.36
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Done.