Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007484.1 Hibiscus syriacus cultivar Beakdansim tig00020655_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: 96278
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:6258 original size:24 final size:21
Alignment explanation
Indices: 6224--6266 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
6214 TGCACAAGTT
*
6224 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
6246 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
6267 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:8021 original size:26 final size:26
Alignment explanation
Indices: 7978--8045 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
7968 CCCTAGAACA
* * ***
7978 CCCATGTGCTTTGCATATGATTGGCC
1 CCCATGTGCCTTGTATATGACCAGCC
*
8004 CCCATGTGCCTTGTATATTACCAGCC
1 CCCATGTGCCTTGTATATGACCAGCC
*
8030 CCCATGAGCCTTGTAT
1 CCCATGTGCCTTGTAT
8046 GTGGTTCATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.18, C:0.31, G:0.19, T:0.32
Consensus pattern (26 bp):
CCCATGTGCCTTGTATATGACCAGCC
Found at i:10132 original size:2 final size:2
Alignment explanation
Indices: 10114--10164 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
10104 TATCATAATA
*
10114 AT AT AG AT AT A- 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
10155 AT AT AT AT AT
1 AT AT AT AT AT
10165 GAAAATAACT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12932 original size:15 final size:15
Alignment explanation
Indices: 12864--12934 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 15
12854 TATGAAATAA
*
12864 GAAATGGAAGAAGAATG
1 GAAATGG-A-AAGAAAG
12881 GAAAT-GATAAGAAAG
1 GAAATGGA-AAGAAAG
12896 GAAATGGAAAGAAA-
1 GAAATGGAAAGAAAG
*
12910 -AGAT---AAGAAAG
1 GAAATGGAAAGAAAG
12921 GAAATGGAAAGAAA
1 GAAATGGAAAGAAA
12935 TGATATCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
10 6 0.14
12 3 0.07
13 3 0.07
15 24 0.55
16 3 0.07
17 5 0.11
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.10
Consensus pattern (15 bp):
GAAATGGAAAGAAAG
Found at i:12945 original size:25 final size:25
Alignment explanation
Indices: 12881--12939 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
12871 AAGAAGAATG
12881 GAAATGATAAGAAAGGAAATGGAAA
1 GAAATGATAAGAAAGGAAATGGAAA
*
12906 GAAAAGATAAGAAAGGAAATGGAAA
1 GAAATGATAAGAAAGGAAATGGAAA
12931 GAAATGATA
1 GAAATGATA
12940 TCAAAGTAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (25 bp):
GAAATGATAAGAAAGGAAATGGAAA
Found at i:16562 original size:12 final size:13
Alignment explanation
Indices: 16545--16573 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16535 TTATATATTG
16545 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
16557 GAAATAAAGAAAT
1 GAAATAAAGAAAT
16570 GAAA
1 GAAA
16574 GGATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:19261 original size:11 final size:12
Alignment explanation
Indices: 19230--19263 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
19220 CTATTTTTTT
19230 CAAAAAAAAAGG
1 CAAAAAAAAAGG
19242 CAAAAAAAAAGG
1 CAAAAAAAAAGG
19254 -AAACAAAAAA
1 CAAA-AAAAAA
19264 CAAAAAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 3 0.14
12 18 0.86
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAGG
Found at i:23621 original size:30 final size:30
Alignment explanation
Indices: 23585--23641 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
23575 GTGCTGGCAC
23585 GCACATGGGTGCTGTTTTGTTCCAAATCAT
1 GCACATGGGTGCTGTTTTGTTCCAAATCAT
*
23615 GCACATGGGTGTTGTTTTGTTCCAAAT
1 GCACATGGGTGCTGTTTTGTTCCAAAT
23642 GGTGAGTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (30 bp):
GCACATGGGTGCTGTTTTGTTCCAAATCAT
Found at i:24740 original size:30 final size:30
Alignment explanation
Indices: 24704--24760 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
24694 GTGCTGGCAC
24704 GCACATGGGTGCTGTTTTGTTCCAAATCAT
1 GCACATGGGTGCTGTTTTGTTCCAAATCAT
*
24734 GCACATGGGTGTTGTTTTGTTCCAAAT
1 GCACATGGGTGCTGTTTTGTTCCAAAT
24761 GGTGAGTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (30 bp):
GCACATGGGTGCTGTTTTGTTCCAAATCAT
Found at i:30222 original size:16 final size:16
Alignment explanation
Indices: 30179--30229 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
30169 GATTTCTTTA
*
30179 TTATCTTATTTCATCTT
1 TTAT-TTATTTTATCTT
*
30196 TCATTTA-TTTATCTT
1 TTATTTATTTTATCTT
*
30211 TTGTTTATTTTATTCTT
1 TTATTTATTTTA-TCTT
30228 TT
1 TT
30230 CGTGTTGTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
16 7 0.25
17 9 0.32
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTATTTTATCTT
Found at i:30591 original size:20 final size:20
Alignment explanation
Indices: 30560--30616 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
30550 CTATTTTTTT
30560 CAAAAAAACAAAAAAAAAA-
1 CAAAAAAACAAAAAAAAAAG
*
30579 CAAAAAAGGCAAAAAAAAAAGG
1 CAAAAAA-ACAAAAAAAAAA-G
30601 CAAAAAAACAAAAAAA
1 CAAAAAAACAAAAAAA
30617 GAGCCAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.21
20 11 0.33
21 8 0.24
22 7 0.21
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (20 bp):
CAAAAAAACAAAAAAAAAAG
Found at i:30593 original size:21 final size:21
Alignment explanation
Indices: 30560--30634 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
30550 CTATTTTTTT
30560 CAAAAAA-AC-AAAAAAAAAA
1 CAAAAAAGACAAAAAAAAAAA
* *
30579 CAAAAAAGGCAAAAAAAAAAGG
1 CAAAAAAGACAAAAAAAAAA-A
* **
30601 CAAAAAA-ACAAAAAAAGAGC
1 CAAAAAAGACAAAAAAAAAAA
*
30621 CAAAAAAGCCAAAA
1 CAAAAAAGACAAAA
30635 TTTCAAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 7 0.16
20 8 0.18
21 23 0.51
22 7 0.16
ACGTcount: A:0.77, C:0.13, G:0.09, T:0.00
Consensus pattern (21 bp):
CAAAAAAGACAAAAAAAAAAA
Found at i:30595 original size:12 final size:13
Alignment explanation
Indices: 30575--30608 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
30565 AAACAAAAAA
30575 AAAACAAAAAAGGC
1 AAAA-AAAAAAGGC
30589 AAAAAAAAAAGGC
1 AAAAAAAAAAGGC
30602 AAAAAAA
1 AAAAAAA
30609 CAAAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGGC
Found at i:30616 original size:11 final size:11
Alignment explanation
Indices: 30561--30585 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
30551 TATTTTTTTC
30561 AAAAAAACAAA
1 AAAAAAACAAA
30572 AAAAAAACAAA
1 AAAAAAACAAA
30583 AAA
1 AAA
30586 GGCAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:30624 original size:20 final size:19
Alignment explanation
Indices: 30560--30627 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 19
30550 CTATTTTTTT
*
30560 CAAAAAAACAAAAAAAAAA
1 CAAAAAAACAAAAAAAAGA
* *
30579 CAAAAAAGGCAAAAAAAAAAGG
1 CAAAAAA---ACAAAAAAAAGA
*
30601 CAAAAAAACAAAAAAAGAGC
1 CAAAAAAACAAAAAAA-AGA
30621 CAAAAAA
1 CAAAAAA
30628 GCCAAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
19 15 0.38
20 9 0.22
22 16 0.40
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (19 bp):
CAAAAAAACAAAAAAAAGA
Found at i:30634 original size:20 final size:20
Alignment explanation
Indices: 30560--30627 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
30550 CTATTTTTTT
*
30560 CAAAAAAACAAAAAAAAA-A
1 CAAAAAAACAAAAAAAAAGC
* *
30579 CAAAAAAGGCAAAAAAAAAAGG
1 CAAAAAA-AC-AAAAAAAAAGC
*
30601 CAAAAAAACAAAAAAAGAGC
1 CAAAAAAACAAAAAAAAAGC
30621 CAAAAAA
1 CAAAAAA
30628 GCCAAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 7 0.17
20 17 0.41
21 10 0.24
22 7 0.17
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (20 bp):
CAAAAAAACAAAAAAAAAGC
Found at i:36210 original size:23 final size:24
Alignment explanation
Indices: 36183--36233 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
36173 TTTCTTTCTC
*
36183 TTTTAATTTTCAGAATT-TGTTTT
1 TTTTAATTTTCAGAATTCTCTTTT
*
36206 TTTTAATTTTCGGAATTCTCTTTT
1 TTTTAATTTTCAGAATTCTCTTTT
36230 TTTT
1 TTTT
36234 TCAAGATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.18, C:0.08, G:0.08, T:0.67
Consensus pattern (24 bp):
TTTTAATTTTCAGAATTCTCTTTT
Found at i:36975 original size:30 final size:30
Alignment explanation
Indices: 36939--36995 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
36929 GTGCTGGCAC
36939 GCACATGGGTGCTGTTTTGTTCCAAATCAT
1 GCACATGGGTGCTGTTTTGTTCCAAATCAT
*
36969 GCACATGGGTGTTGTTTTGTTCCAAAT
1 GCACATGGGTGCTGTTTTGTTCCAAAT
36996 GGTGAGTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (30 bp):
GCACATGGGTGCTGTTTTGTTCCAAATCAT
Found at i:46181 original size:15 final size:14
Alignment explanation
Indices: 46163--46197 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
46153 AGAAATCGTT
*
46163 TGAATTGAAAATAA
1 TGAATTGAAAAGAA
46177 GTGAATTGAAAAGAA
1 -TGAATTGAAAAGAA
46192 TGAATT
1 TGAATT
46198 TGGAGGAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (14 bp):
TGAATTGAAAAGAA
Found at i:50147 original size:19 final size:19
Alignment explanation
Indices: 50107--50156 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
50097 GAAACCCTTT
**
50107 TGAAAATACATGTTTTTTA
1 TGAAAATACATGTTTTAAA
50126 TGAAAATACAT-TATTTAAA
1 TGAAAATACATGT-TTTAAA
*
50145 TGAATATACATG
1 TGAAAATACATG
50157 CTCTTGGCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 25 0.96
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (19 bp):
TGAAAATACATGTTTTAAA
Found at i:51345 original size:13 final size:12
Alignment explanation
Indices: 51326--51411 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
51316 ATATAGGCGT
51326 GATATGGTGATG
1 GATATGGTGATG
51338 GAATATGGTGAT-
1 G-ATATGGTGATG
*
51350 GATATAGGCG-T-
1 GATAT-GGTGATG
51361 GATAATGGTGATG
1 GAT-ATGGTGATG
51374 GACTATGGTGAT-
1 GA-TATGGTGATG
*
51386 GATATAGGCG-T-
1 GATAT-GGTGATG
51397 GATAATGGTGATG
1 GAT-ATGGTGATG
51410 GA
1 GA
51412 CGATTGTATC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:51381 original size:36 final size:36
Alignment explanation
Indices: 51308--51412 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
51298 ATTTATAAGT
* *
51308 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
51343 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
51379 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
51413 GATTGTATCT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:51801 original size:19 final size:20
Alignment explanation
Indices: 51754--51804 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
51744 GAAACCCCTT
**
51754 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
51774 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
51793 TGAAGATACATG
1 TGAAAATACATG
51805 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:53900 original size:13 final size:12
Alignment explanation
Indices: 53881--53966 Score: 67
Period size: 11 Copynumber: 7.2 Consensus size: 12
53871 ATATAGGAGT
53881 GATATGGTGATG
1 GATATGGTGATG
53893 GAATATGGTGAT-
1 G-ATATGGTGATG
53905 GATATAGGTG-T-
1 GATAT-GGTGATG
53916 GATAATGGTGATG
1 GAT-ATGGTGATG
53929 GACTATGGTGAT-
1 GA-TATGGTGATG
*
53941 GATATAGGCG-T-
1 GATAT-GGTGATG
53952 GATAATGGTGATG
1 GAT-ATGGTGATG
53965 GA
1 GA
53967 CAGATTGTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 22 0.35
12 17 0.27
13 22 0.35
14 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:53918 original size:11 final size:12
Alignment explanation
Indices: 53864--53948 Score: 65
Period size: 11 Copynumber: 7.2 Consensus size: 12
53854 TTTATAAGTT
*
53864 GGTGATAATATA
1 GGTGATGATATA
*
53876 GGAG-TGATAT-
1 GGTGATGATATA
53886 GGTGATGGA-ATA
1 GGTGAT-GATATA
53898 TGGTGATGATATA
1 -GGTGATGATATA
53911 GGTG-TGATA-A
1 GGTGATGATATA
53921 TGGTGATGGACTAT-
1 -GGTGAT-GA-TATA
53935 GGTGATGATATA
1 GGTGATGATATA
53947 GG
1 GG
53949 CGTGATAATG
Statistics
Matches: 59, Mismatches: 3, Indels: 22
0.70 0.04 0.26
Matches are distributed among these distances:
10 4 0.07
11 20 0.34
12 16 0.27
13 17 0.29
14 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.36, T:0.32
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:53936 original size:36 final size:36
Alignment explanation
Indices: 53863--53967 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
53853 ATTTATAAGT
* *
53863 TGGTGATAATATAGGAGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGAGTGATAATGGTGATGGACTA
*
53898 TGGTGATGATATAGGTGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGAGTGATAATGGTGATGGACTA
*
53934 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGAGTGATAATGGTGATGGAC
53968 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGAGTGATAATGGTGATGGACTA
Found at i:54357 original size:19 final size:20
Alignment explanation
Indices: 54310--54360 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
54300 GAAACCCCTT
**
54310 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
54330 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
54349 TGAAGATACATG
1 TGAAAATACATG
54361 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:56474 original size:11 final size:12
Alignment explanation
Indices: 56420--56504 Score: 63
Period size: 13 Copynumber: 7.2 Consensus size: 12
56410 TTTATAAGTT
*
56420 GGTGATAATATA
1 GGTGATGATATA
*
56432 GGCG-TGATAT-
1 GGTGATGATATA
56442 GGTGATGGA-ATA
1 GGTGAT-GATATA
56454 TGGTGATGATATA
1 -GGTGATGATATA
56467 GGTG-TGATA-A
1 GGTGATGATATA
* *
56477 TGGTGATGCTCTA
1 -GGTGATGATATA
56490 TGGTGATGATATA
1 -GGTGATGATATA
56503 GG
1 GG
56505 CGTGATAATG
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
10 4 0.07
11 17 0.29
12 16 0.28
13 21 0.36
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:56492 original size:36 final size:36
Alignment explanation
Indices: 56419--56520 Score: 152
Period size: 36 Copynumber: 2.9 Consensus size: 36
56409 ATTTATAAGT
* *
56419 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGCAATA
* **
56454 TGGTGATGATATAGGTGTGATAATGGTGATGCTCTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGCAATA
56490 TGGTGATGATATAGGCGTGATAATGGTGATG
1 TGGTGATGATATAGGCGTGATAATGGTGATG
56521 GACAGATTGT
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 19 0.32
36 41 0.68
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGCAATA
Found at i:60851 original size:22 final size:23
Alignment explanation
Indices: 60823--60874 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
60813 ATTTATAAGT
60823 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
60845 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
60868 TGGTGAT
1 TGGTGAT
60875 GGACTATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:60866 original size:36 final size:38
Alignment explanation
Indices: 60825--60904 Score: 107
Period size: 36 Copynumber: 2.2 Consensus size: 38
60815 TTATAAGTTG
60825 GTGATAATATAGGCG-T-GA-TATGGTGATGATATAGGC
1 GTGATAATAT-GGCGATGGACTATGGTGATGATATAGGC
*
60861 GTGAT-A-ATGGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATATGGCGATGGACTATGGTGATGATATAGGC
60897 GTGATAAT
1 GTGATAAT
60905 GGTGATGGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
33 3 0.08
34 3 0.08
35 3 0.08
36 28 0.74
37 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (38 bp):
GTGATAATATGGCGATGGACTATGGTGATGATATAGGC
Found at i:60905 original size:36 final size:36
Alignment explanation
Indices: 60843--60914 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
60833 ATAGGCGTGA
60843 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
60879 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
60915 AGATTGTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.06, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:63996 original size:35 final size:34
Alignment explanation
Indices: 63949--64028 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 34
63939 ATTTATAAGT
*
63949 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGAT--AATA
63984 TGGTGATGATATAGGCGTGATAATGGTGATAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATAATA
64018 TAGGTG-TGATA
1 T-GGTGATGATA
64029 ATGGTGATGG
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
34 10 0.24
35 24 0.57
36 8 0.19
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.33
Consensus pattern (34 bp):
TGGTGATGATATAGGCGTGATAATGGTGATAATA
Found at i:64011 original size:23 final size:23
Alignment explanation
Indices: 63983--64037 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
63973 GTGATGGAAT
63983 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
* *
64006 ATGGTGATAATATAGGTGTGATA
1 ATGGTGATGATATAGGCGTGATA
64029 ATGGTGATG
1 ATGGTGATG
64038 GACAGATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.33
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:64428 original size:19 final size:20
Alignment explanation
Indices: 64381--64428 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
64371 TGAAACCCTT
**
64381 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
64401 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
64420 TGAAGATAC
1 TGAAAATAC
64429 GTGCTCTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:69512 original size:15 final size:15
Alignment explanation
Indices: 69477--69505 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
69467 GTGCTTCAAC
69477 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
69491 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
69506 CTTTTTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:74155 original size:23 final size:23
Alignment explanation
Indices: 74110--74155 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
74100 TTATACCTAT
*
74110 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
74133 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
74156 TATATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:78735 original size:23 final size:23
Alignment explanation
Indices: 78690--78735 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
78680 TTATACCTAT
*
78690 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
78713 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
78736 TATATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:86108 original size:5 final size:5
Alignment explanation
Indices: 86098--86133 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
86088 CTTCAACTTC
*
86098 TTTCT TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
86134 CTTTTTGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:90163 original size:16 final size:16
Alignment explanation
Indices: 90130--90178 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
90120 TAAGGTAATG
90130 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
90148 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
90164 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
90179 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:91949 original size:18 final size:19
Alignment explanation
Indices: 91908--91946 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
91898 TATCCTTTCT
91908 TTATTTCATTTCATTCTTA
1 TTATTTCATTTCATTCTTA
91927 TTATTT-ATTTCATTACTTA
1 TTATTTCATTTCATT-CTTA
91946 T
1 T
91947 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTCATTTCATTCTTA
Done.