Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000727.1 Hibiscus syriacus cultivar Beakdansim tig00001413_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: 104264
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:5026 original size:30 final size:30
Alignment explanation
Indices: 4992--5049 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
4982 CATTATAAGT
* *
4992 TTATAACATGGATTATCAGT-TAACAGTCAA
1 TTATAACAT-CATAATCAGTGTAACAGTCAA
*
5022 TTATATCATCATAATCAGTGTAACAGTC
1 TTATAACATCATAATCAGTGTAACAGTC
5050 TAACTACTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (30 bp):
TTATAACATCATAATCAGTGTAACAGTCAA
Found at i:5843 original size:31 final size:30
Alignment explanation
Indices: 5804--5866 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
5794 ACTATATCTA
* *
5804 ATTACTAATTATTAGTAAGATTATAAATAG
1 ATTACTAATTATTAATAAGATTACAAATAG
*
5834 ATTATCTAATTATTAATAAGATTACCAATAG
1 ATTA-CTAATTATTAATAAGATTACAAATAG
5865 AT
1 AT
5867 CATTCAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (30 bp):
ATTACTAATTATTAATAAGATTACAAATAG
Found at i:5917 original size:29 final size:28
Alignment explanation
Indices: 5860--5918 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 28
5850 TAAGATTACC
* *
5860 AATAGATCATTCAATTTTAAAAAGTTATA
1 AATAAATCACTCAATTTTAAAAAG-TATA
5889 AATAAATCACTCAATTAATTAAAAA-TATA
1 AATAAATCACTCAATT--TTAAAAAGTATA
5918 A
1 A
5919 TCTAAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 19 0.73
31 7 0.27
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (28 bp):
AATAAATCACTCAATTTTAAAAAGTATA
Found at i:15440 original size:30 final size:30
Alignment explanation
Indices: 15406--15469 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
15396 CAAATAAAAG
15406 CTATAATCGGACATCCCTTGATAATTTGTA
1 CTATAATCGGACATCCCTTGATAATTTGTA
15436 CTATAATCGGACATCCCTTGATAATTTGTA
1 CTATAATCGGACATCCCTTGATAATTTGTA
15466 CTAT
1 CTAT
15470 TATCCAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (30 bp):
CTATAATCGGACATCCCTTGATAATTTGTA
Found at i:22288 original size:23 final size:24
Alignment explanation
Indices: 22262--22306 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
22252 CTTTGTAGTC
22262 ATATATTAT-TT-GTAATTGTAATT
1 ATATATTATGTTAG-AATTGTAATT
22285 ATATATTATGTTAGAATTGTAA
1 ATATATTATGTTAGAATTGTAA
22307 ATATTAATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 10 0.50
25 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (24 bp):
ATATATTATGTTAGAATTGTAATT
Found at i:23282 original size:23 final size:24
Alignment explanation
Indices: 23238--23286 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
23228 AATCGACCAT
**
23238 ATCATTAATTTTTTATTCGATTAA
1 ATCATTAATTTTACATTCGATTAA
*
23262 ATCATTAATTTTACGTT-GATTAA
1 ATCATTAATTTTACATTCGATTAA
23285 AT
1 AT
23287 AAAAAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (24 bp):
ATCATTAATTTTACATTCGATTAA
Found at i:23943 original size:2 final size:2
Alignment explanation
Indices: 23936--23961 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23926 GCATAAATTC
23936 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
23962 CGATCCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24765 original size:21 final size:21
Alignment explanation
Indices: 24736--24777 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
24726 TGGGATTATC
24736 GGTGATGGTATCAGCGACATA
1 GGTGATGGTATCAGCGACATA
* *
24757 GGTGCTGGTATCAGCGGCATA
1 GGTGATGGTATCAGCGACATA
24778 ACTGCTGCTA
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:0.24, C:0.17, G:0.36, T:0.24
Consensus pattern (21 bp):
GGTGATGGTATCAGCGACATA
Found at i:24783 original size:21 final size:21
Alignment explanation
Indices: 24741--24784 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
24731 TTATCGGTGA
**
24741 TGGTATCAGCGACATAGGTGC
1 TGGTATCAGCGACATAACTGC
*
24762 TGGTATCAGCGGCATAACTGC
1 TGGTATCAGCGACATAACTGC
24783 TG
1 TG
24785 CTAAACAGTT
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:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (21 bp):
TGGTATCAGCGACATAACTGC
Found at i:32276 original size:28 final size:28
Alignment explanation
Indices: 32244--32302 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
32234 GCGTGCATGC
*
32244 TGCTACATACATTTTTGACATGAATGAG
1 TGCTACATACATTGTTGACATGAATGAG
* *
32272 TGCTACATACATTGTTGGCATGCATGAG
1 TGCTACATACATTGTTGACATGAATGAG
32300 TGC
1 TGC
32303 ATGCTGCTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (28 bp):
TGCTACATACATTGTTGACATGAATGAG
Found at i:38274 original size:14 final size:14
Alignment explanation
Indices: 38255--38281 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38245 TTTATTATTT
38255 ATTTATTTTCTTTG
1 ATTTATTTTCTTTG
38269 ATTTATTTTCTTT
1 ATTTATTTTCTTT
38282 TTTCTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (14 bp):
ATTTATTTTCTTTG
Found at i:38346 original size:52 final size:51
Alignment explanation
Indices: 38245--38443 Score: 142
Period size: 52 Copynumber: 3.8 Consensus size: 51
38235 ATTTATTATG
* * * *
38245 TTTATTATTTATTTATTTTCTTTGATTTATTTTCTTTTTTCTCTCTTTTTA
1 TTTATTATTTATTTATTTTCTTTGATTTATTTTATATTTTATCTATTTTTA
*
38296 TTTATTCTTTATCTT-TTTTCCTTTGATTTATTTTATCATTTTATC-ATTTTTA
1 TTTATTATTTAT-TTATTTT-CTTTGATTTATTTTAT-ATTTTATCTATTTTTA
* * *
38348 TTTTTTATTT-TTTACATTTTTTCTTCTGATTTATTTAATATATTAT-TA-TTTTA
1 TTTATTATTTATTT--A--TTTTCTT-TGATTTATTTTATATTTTATCTATTTTTA
* *
38401 TTT-TCCCT-TTTGATTTATTTTTTTTGATTTATTATTATTTTTT
1 TTTAT---TATTT-ATTTATTTTCTTTGATTTATT-TTATATTTT
38444 GTTTTCATTA
Statistics
Matches: 119, Mismatches: 13, Indels: 31
0.73 0.08 0.19
Matches are distributed among these distances:
50 2 0.02
51 25 0.21
52 44 0.37
53 14 0.12
54 14 0.12
55 17 0.14
56 3 0.03
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.72
Consensus pattern (51 bp):
TTTATTATTTATTTATTTTCTTTGATTTATTTTATATTTTATCTATTTTTA
Found at i:38350 original size:22 final size:22
Alignment explanation
Indices: 38322--38368 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
38312 TTTCCTTTGA
38322 TTTATTTTATCATTTTAT-CATT
1 TTTATTTT-TCATTTTATACATT
* *
38344 TTTATTTTTTATTTTTTACATT
1 TTTATTTTTCATTTTATACATT
38366 TTT
1 TTT
38369 TCTTCTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTTTCATTTTATACATT
Found at i:38350 original size:26 final size:26
Alignment explanation
Indices: 38288--38350 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
38278 CTTTTTTCTC
*
38288 TCTTTTTATTTATTCTTTATCTTTTT
1 TCTTTTTATTTATTCTTTATCTTTTA
* *
38314 TCCTTTGATTTA-T-TTTATCATTTTA
1 TCTTTTTATTTATTCTTTATC-TTTTA
38339 TCATTTTTATTT
1 TC-TTTTTATTT
38351 TTTATTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 6 0.20
25 7 0.23
26 17 0.57
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (26 bp):
TCTTTTTATTTATTCTTTATCTTTTA
Found at i:38380 original size:55 final size:53
Alignment explanation
Indices: 38296--38404 Score: 132
Period size: 55 Copynumber: 2.0 Consensus size: 53
38286 TCTCTTTTTA
* *
38296 TTTATTCTTTATCTTTTTTCCTTTGATTTATTTTATCATTTTATCATTTTTATTT
1 TTTATTCTTTATCTTTTTTCCTTTGATTTATTTAAT-ATATTATCA-TTTTATTT
* *
38351 TTTATTTTTTA-CATTTTTT-CTTCTGATTTATTTAATATATTATTATTTTATTT
1 TTTATTCTTTATC-TTTTTTCCTT-TGATTTATTTAATATATTATCATTTTATTT
38404 T
1 T
38405 CCCTTTTGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
53 9 0.19
54 11 0.23
55 28 0.58
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (53 bp):
TTTATTCTTTATCTTTTTTCCTTTGATTTATTTAATATATTATCATTTTATTT
Found at i:38441 original size:19 final size:20
Alignment explanation
Indices: 38419--38464 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
38409 TTTGATTTAT
38419 TTTTTTTGATTT-ATTATTA
1 TTTTTTTGATTTCATTATTA
*
38438 -TTTTTTGTTTTCATTATTA
1 TTTTTTTGATTTCATTATTA
38457 TGTTTTTT
1 T-TTTTTT
38465 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 10 0.43
19 7 0.30
21 6 0.26
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.76
Consensus pattern (20 bp):
TTTTTTTGATTTCATTATTA
Found at i:38568 original size:13 final size:13
Alignment explanation
Indices: 38550--38579 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38540 CTAATCGAGT
38550 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
38563 TTTTAATTTTTAA
1 TTTTAAATTTTAA
38576 TTTT
1 TTTT
38580 CACAATTAAG
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:39902 original size:23 final size:23
Alignment explanation
Indices: 39876--39927 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
39866 AGTAACCTTA
39876 CAATTCACTCAAGAATTATACCC
1 CAATTCACTCAAGAATTATACCC
*
39899 CAATTCCCTCAAGAATTATACCC
1 CAATTCACTCAAGAATTATACCC
39922 CAATTC
1 CAATTC
39928 TTAAACAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.27
Consensus pattern (23 bp):
CAATTCACTCAAGAATTATACCC
Found at i:40447 original size:64 final size:63
Alignment explanation
Indices: 40379--40586 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 63
40369 TGGACTAAGA
* *
40379 GTGCATCTATGCATAAAATGCACTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATA-CCAGAGTGCATCGATGCATGGTTG
* * *
40443 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAATACCTTA-ACTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATACC--AGAGTGCATCGATGCATGGT-
40507 T-
62 TG
* * *
40508 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTATTTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA--AATACCA-GAGTGCATCGATGCATGG-T
40571 TG
62 TG
*
40573 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
40587 CACTTTGAAA
Statistics
Matches: 123, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
63 5 0.04
64 44 0.36
65 72 0.59
66 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCAGAGTGCATCGATGCATGGTTG
Found at i:41953 original size:23 final size:24
Alignment explanation
Indices: 41903--41953 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
41893 ACAAATAAGT
*
41903 TCAAACATCCAATAACCATCAAAT
1 TCAAACATCCAATAACCATCAAAA
41927 TCAAACATCCAGA-AA-CATCAAAA
1 TCAAACATCCA-ATAACCATCAAAA
41950 TCAA
1 TCAA
41954 TCAAAGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 11 0.44
24 13 0.52
25 1 0.04
ACGTcount: A:0.53, C:0.27, G:0.02, T:0.18
Consensus pattern (24 bp):
TCAAACATCCAATAACCATCAAAA
Found at i:41973 original size:13 final size:13
Alignment explanation
Indices: 41952--41985 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
41942 CATCAAAATC
*
41952 AATCAAAGTTTGA
1 AATCTAAGTTTGA
41965 AATCTAAGTTTGA
1 AATCTAAGTTTGA
41978 AATCTAAG
1 AATCTAAG
41986 AAAGCATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (13 bp):
AATCTAAGTTTGA
Found at i:42729 original size:15 final size:15
Alignment explanation
Indices: 42706--42735 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42696 ATTTTCATTC
*
42706 TCATTATATAACCCA
1 TCATCATATAACCCA
42721 TCATCATATAACCCA
1 TCATCATATAACCCA
42736 AAACGGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (15 bp):
TCATCATATAACCCA
Found at i:43842 original size:23 final size:22
Alignment explanation
Indices: 43810--43886 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
43800 TGGCCTTGTA
43810 CATCGATGCACATTCAAGGCGTG
1 CATCGATGCACATTCAAGG-GTG
* * *
43833 CATCGGTGCACCTTC-ATGGTG
1 CATCGATGCACATTCAAGGGTG
* * *
43854 TATCGATGCACTTTCAAGGATG
1 CATCGATGCACATTCAAGGGTG
43876 CATCGATGCAC
1 CATCGATGCAC
43887 TGTTAGGTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 15 0.34
22 16 0.36
23 13 0.30
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGGTG
Found at i:43861 original size:44 final size:42
Alignment explanation
Indices: 43811--43905 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
43801 GGCCTTGTAC
* *
43811 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATGCA-CTGTCA-GGTGT
* *
43855 ATCGATGCACTTTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
43897 ATCGATGCA
1 ATCGATGCA
43906 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 16 0.35
43 13 0.28
44 17 0.37
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.28
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
Found at i:43863 original size:21 final size:20
Alignment explanation
Indices: 43810--43905 Score: 68
Period size: 21 Copynumber: 4.5 Consensus size: 20
43800 TGGCCTTGTA
*
43810 CATCGATGCACATTCAAGGCGTG
1 CATCGATGCACCTTC-A-G-GTG
*
43833 CATCGGTGCACCTTCATGGTG
1 CATCGATGCACCTTCA-GGTG
* *
43854 TATCGATGCACTTTCAAGGATG
1 CATCGATGCACCTTC-AGG-TG
*
43876 CATCGATGCA-CTGTTAGGTG
1 CATCGATGCACCT-TCAGGTG
*
43896 TATCGATGCA
1 CATCGATGCA
43906 TTAAGCACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
20 11 0.18
21 21 0.35
22 15 0.25
23 13 0.22
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (20 bp):
CATCGATGCACCTTCAGGTG
Found at i:43902 original size:20 final size:20
Alignment explanation
Indices: 43850--43905 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
43840 GCACCTTCAT
43850 GGTGTATCGATGCACTTTCAA
1 GGTGTATCGATGCACTTT-AA
*
43871 GGATGCATCGATGCACTGTT-A
1 GG-TGTATCGATGCACT-TTAA
43892 GGTGTATCGATGCA
1 GGTGTATCGATGCA
43906 TTAAGCACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 11 0.35
21 5 0.16
22 13 0.42
23 2 0.06
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (20 bp):
GGTGTATCGATGCACTTTAA
Found at i:51942 original size:16 final size:16
Alignment explanation
Indices: 51911--51953 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
51901 AATTTACTTT
* *
51911 CTTTTTATTAACTTAA
1 CTTTTTATCAAATTAA
51927 CTTTTTATCAAATTAA
1 CTTTTTATCAAATTAA
*
51943 TTGTTTTATCA
1 CT-TTTTATCA
51954 CATCTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.56
Consensus pattern (16 bp):
CTTTTTATCAAATTAA
Found at i:63873 original size:23 final size:24
Alignment explanation
Indices: 63823--63873 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
63813 ACAAATAAGT
*
63823 TCAAACATCCAATAACCATCAAAT
1 TCAAACATCCAATAACCATCAAAA
63847 TCAAACATCCAGA-AA-CATCAAAA
1 TCAAACATCCA-ATAACCATCAAAA
63870 TCAA
1 TCAA
63874 TCAAAGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 11 0.44
24 13 0.52
25 1 0.04
ACGTcount: A:0.53, C:0.27, G:0.02, T:0.18
Consensus pattern (24 bp):
TCAAACATCCAATAACCATCAAAA
Found at i:63893 original size:13 final size:13
Alignment explanation
Indices: 63872--63901 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
63862 CATCAAAATC
63872 AATCAAAGTTTGA
1 AATCAAAGTTTGA
*
63885 AATCCAAGTTTGA
1 AATCAAAGTTTGA
63898 AATC
1 AATC
63902 TAAGAAAGCA
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:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (13 bp):
AATCAAAGTTTGA
Found at i:64649 original size:15 final size:15
Alignment explanation
Indices: 64626--64655 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
64616 ATTTTCATTC
*
64626 TCATTATATAACCCA
1 TCATCATATAACCCA
64641 TCATCATATAACCCA
1 TCATCATATAACCCA
64656 AAACGGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.30, G:0.00, T:0.30
Consensus pattern (15 bp):
TCATCATATAACCCA
Found at i:65762 original size:23 final size:22
Alignment explanation
Indices: 65730--65806 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
65720 TGGCCTTGTA
65730 CATCGATGCACATTCAAGGCGTG
1 CATCGATGCACATTCAAGG-GTG
* * *
65753 CATCGGTGCACCTTC-ATGGTG
1 CATCGATGCACATTCAAGGGTG
* * *
65774 TATCGATGCACTTTCAAGGATG
1 CATCGATGCACATTCAAGGGTG
65796 CATCGATGCAC
1 CATCGATGCAC
65807 TGTTAGGTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 15 0.34
22 16 0.36
23 13 0.30
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGGTG
Found at i:65781 original size:44 final size:42
Alignment explanation
Indices: 65731--65825 Score: 120
Period size: 44 Copynumber: 2.2 Consensus size: 42
65721 GGCCTTGTAC
* *
65731 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCT-TCATGGTGT
1 ATCGATGCACATTCAAGG-ATGCATCGATGCA-CTGTCA-GGTGT
* *
65775 ATCGATGCACTTTCAAGGATGCATCGATGCACTGTTAGGTGT
1 ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
65817 ATCGATGCA
1 ATCGATGCA
65826 TTAAGCACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 16 0.35
43 13 0.28
44 17 0.37
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.28
Consensus pattern (42 bp):
ATCGATGCACATTCAAGGATGCATCGATGCACTGTCAGGTGT
Found at i:65783 original size:21 final size:20
Alignment explanation
Indices: 65730--65825 Score: 68
Period size: 21 Copynumber: 4.5 Consensus size: 20
65720 TGGCCTTGTA
*
65730 CATCGATGCACATTCAAGGCGTG
1 CATCGATGCACCTTC-A-G-GTG
*
65753 CATCGGTGCACCTTCATGGTG
1 CATCGATGCACCTTCA-GGTG
* *
65774 TATCGATGCACTTTCAAGGATG
1 CATCGATGCACCTTC-AGG-TG
*
65796 CATCGATGCA-CTGTTAGGTG
1 CATCGATGCACCT-TCAGGTG
*
65816 TATCGATGCA
1 CATCGATGCA
65826 TTAAGCACAA
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
20 11 0.18
21 21 0.35
22 15 0.25
23 13 0.22
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (20 bp):
CATCGATGCACCTTCAGGTG
Found at i:65822 original size:20 final size:20
Alignment explanation
Indices: 65770--65825 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
65760 GCACCTTCAT
65770 GGTGTATCGATGCACTTTCAA
1 GGTGTATCGATGCACTTT-AA
*
65791 GGATGCATCGATGCACTGTT-A
1 GG-TGTATCGATGCACT-TTAA
65812 GGTGTATCGATGCA
1 GGTGTATCGATGCA
65826 TTAAGCACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 11 0.35
21 5 0.16
22 13 0.42
23 2 0.06
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (20 bp):
GGTGTATCGATGCACTTTAA
Found at i:73861 original size:16 final size:16
Alignment explanation
Indices: 73830--73872 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
73820 AATTTACTTT
* *
73830 CTTTTTATTAACTTAA
1 CTTTTTATCAAATTAA
73846 CTTTTTATCAAATTAA
1 CTTTTTATCAAATTAA
*
73862 TTGTTTTATCA
1 CT-TTTTATCA
73873 CATCTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.56
Consensus pattern (16 bp):
CTTTTTATCAAATTAA
Found at i:75855 original size:14 final size:15
Alignment explanation
Indices: 75836--75864 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
75826 CTTTCTCTGC
75836 CAGCCTATGT-GATG
1 CAGCCTATGTCGATG
75850 CAGCCTATGTCGATG
1 CAGCCTATGTCGATG
75865 AAGGTGCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (15 bp):
CAGCCTATGTCGATG
Found at i:86147 original size:25 final size:25
Alignment explanation
Indices: 86095--86153 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
86085 TTTAATTTTT
* *
86095 TATAAAAAATAATAAATTATTTAAA
1 TATAAAATATAAAAAATTATTTAAA
86120 TATAAAATATAAAAAATTA-TTAAGA
1 TATAAAATATAAAAAATTATTTAA-A
*
86145 TATTAAATA
1 TATAAAATA
86154 CATTAAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
TATAAAATATAAAAAATTATTTAAA
Found at i:86161 original size:25 final size:25
Alignment explanation
Indices: 86095--86161 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 25
86085 TTTAATTTTT
* *
86095 TATAAAAAATAATAAATTATTTAAA
1 TATAAAATACAATAAATTATTTAAA
* *
86120 TATAAAATATAAAAAATTA-TTAAGA
1 TATAAAATACAATAAATTATTTAA-A
* *
86145 TATTAAATACATTAAAT
1 TATAAAATACAATAAAT
86162 GTAAAAATAC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
24 4 0.11
25 31 0.89
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (25 bp):
TATAAAATACAATAAATTATTTAAA
Found at i:90911 original size:30 final size:31
Alignment explanation
Indices: 90854--90913 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
90844 TATAAAGATT
*
90854 GGTGACTAGAATATAAAAGGGATAATAATTC
1 GGTGACTAGAATATAAAAGAGATAATAATTC
* *
90885 GGTGACTATAATATAAAA-ATATAATAATT
1 GGTGACTAGAATATAAAAGAGATAATAATT
90914 TGATGACCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (31 bp):
GGTGACTAGAATATAAAAGAGATAATAATTC
Found at i:100459 original size:64 final size:64
Alignment explanation
Indices: 100351--100511 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 64
100341 CAATGAATGT
* * ** *
100351 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTTAATGGGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAA-AAGC
* * *
100415 ATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTAAAATC
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATTTAAAAGC
* *
100479 ATGCATCGATGCACTGCATGTGCATCGATGCAT
1 ATGCATCGATGCACTACTTGTGCATCGATGCAT
100512 CTTAAACAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 5 0.06
64 72 0.86
65 7 0.08
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAAAGC
Found at i:102760 original size:60 final size:61
Alignment explanation
Indices: 102636--102764 Score: 188
Period size: 60 Copynumber: 2.1 Consensus size: 61
102626 GAGCACCATT
* * * *
102636 CGCGCCTTCGCGGGGTTTTATCCGATATGGCGCTACGTAAAGGAAGGCGCGGATCGACATC
1 CGCGCCTTCACGGGGTTTTATCCGAAATGGCACTACGTAAAAGAAGGCGCGGATCGACATC
* **
102697 CGCGCCTTCACGGGGTTTTGTCCGAAATGGCAC-ACGTAAAAGAAGGCGCGGATCGTTATC
1 CGCGCCTTCACGGGGTTTTATCCGAAATGGCACTACGTAAAAGAAGGCGCGGATCGACATC
102757 CGCGCCTT
1 CGCGCCTT
102765 AGTTGAACCT
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
60 32 0.52
61 29 0.48
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (61 bp):
CGCGCCTTCACGGGGTTTTATCCGAAATGGCACTACGTAAAAGAAGGCGCGGATCGACATC
Done.