Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004890.1 Hibiscus syriacus cultivar Beakdansim tig00011009_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: 64717
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5690 original size:17 final size:17
Alignment explanation
Indices: 5650--5683 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5640 CACTACTATA
5650 GGCTGGGCTCGAGGTGC
1 GGCTGGGCTCGAGGTGC
5667 GGCTGGGCTCGAGGTGC
1 GGCTGGGCTCGAGGTGC
5684 TGTTGGGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.53, T:0.18
Consensus pattern (17 bp):
GGCTGGGCTCGAGGTGC
Found at i:7007 original size:20 final size:20
Alignment explanation
Indices: 6982--7033 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
6972 AAGCTCCTCA
* *
6982 GTATCGATATTGACCTCTGG
1 GTATCGATACTAACCTCTGG
*
7002 GTATCGATACTAACCTTTGG
1 GTATCGATACTAACCTCTGG
*
7022 GTATCCATACTA
1 GTATCGATACTA
7034 TTAACTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (20 bp):
GTATCGATACTAACCTCTGG
Found at i:9288 original size:25 final size:25
Alignment explanation
Indices: 9260--9316 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
9250 TGAGGTTGAG
* *
9260 TTGGAAAGCTTAATCATAACTCGCC
1 TTGGAAAGCTTAACCATAACTCACC
*
9285 TTGGAAAGCTTAACCCTAACTCACC
1 TTGGAAAGCTTAACCATAACTCACC
9310 TTAGGAA
1 TT-GGAA
9317 TAAGAAAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 24 0.86
26 4 0.14
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (25 bp):
TTGGAAAGCTTAACCATAACTCACC
Found at i:11207 original size:29 final size:30
Alignment explanation
Indices: 11126--11221 Score: 96
Period size: 28 Copynumber: 3.4 Consensus size: 30
11116 TTTTTAAAAG
*
11126 ATTTATATCACAAATAAGTATTT-AGGTT-T
1 ATTTATATCA-AAATAAGTATTTAAAGTTAT
* **
11155 -TTTTTATCAAAATAAGTACATAAAGTTAT
1 ATTTATATCAAAATAAGTATTTAAAGTTAT
*
11184 ATTT-TATCAAAATAAATATTTAAAG-TAT
1 ATTTATATCAAAATAAGTATTTAAAGTTAT
11212 -TTTATATCAA
1 ATTTATATCAA
11222 GATAGGTGTA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
27 13 0.23
28 21 0.38
29 19 0.34
30 3 0.05
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (30 bp):
ATTTATATCAAAATAAGTATTTAAAGTTAT
Found at i:11409 original size:28 final size:30
Alignment explanation
Indices: 11349--11428 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 30
11339 GTTTTAATTA
* *
11349 AAAAAAATATTTTAAATACTTATTTTTACT
1 AAAAAAATAATTTAAATACTTATTTTGACT
*
11379 -AAAAAATAACTTTAAGTACTTA-TTTGA-T
1 AAAAAAATAA-TTTAAATACTTATTTTGACT
*
11407 AAAAAAATAATTTAATTACTTA
1 AAAAAAATAATTTAAATACTTA
11429 AATGAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 12 0.27
29 21 0.48
30 11 0.25
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (30 bp):
AAAAAAATAATTTAAATACTTATTTTGACT
Found at i:11438 original size:28 final size:29
Alignment explanation
Indices: 11379--11438 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
11369 TATTTTTACT
** *
11379 AAAAAATAACTTTAAGTACTTATTTGATA
1 AAAAAATAACTTTAAGTACTTAAATGAAA
*
11408 AAAAAATAA-TTTAATTACTTAAATGAAA
1 AAAAAATAACTTTAAGTACTTAAATGAAA
11436 AAA
1 AAA
11439 GAACATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAAAATAACTTTAAGTACTTAAATGAAA
Found at i:14855 original size:12 final size:12
Alignment explanation
Indices: 14838--14871 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
14828 AGAAGTGATG
14838 CATTGATGCACT
1 CATTGATGCACT
14850 CATTGATGCACT
1 CATTGATGCACT
14862 CATTGATGCA
1 CATTGATGCA
14872 TCGATGGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (12 bp):
CATTGATGCACT
Found at i:14923 original size:18 final size:18
Alignment explanation
Indices: 14902--14952 Score: 102
Period size: 18 Copynumber: 2.8 Consensus size: 18
14892 AATGCATTTT
14902 ATGCATCGATGCACTACC
1 ATGCATCGATGCACTACC
14920 ATGCATCGATGCACTACC
1 ATGCATCGATGCACTACC
14938 ATGCATCGATGCACT
1 ATGCATCGATGCACT
14953 CAGGTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (18 bp):
ATGCATCGATGCACTACC
Found at i:15044 original size:45 final size:45
Alignment explanation
Indices: 14938--15044 Score: 173
Period size: 45 Copynumber: 2.4 Consensus size: 45
14928 ATGCACTACC
*
14938 ATGCATCGATGCACTCAGGTTTTATGAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCTGGTTTTATGAAAACATCGAATGCATTTT
14983 ATGCATCGATGCACTCTGGCTTGTT-T-AAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCTGG-TT-TTATGAAAACATCGAATGCATTTT
15028 ATGCATCGATGCACTCT
1 ATGCATCGATGCACTCT
15045 TAATGCACCG
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
45 54 0.92
46 3 0.05
47 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.34
Consensus pattern (45 bp):
ATGCATCGATGCACTCTGGTTTTATGAAAACATCGAATGCATTTT
Found at i:20849 original size:21 final size:21
Alignment explanation
Indices: 20823--20879 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
20813 TGGTGCATAA
20823 TGCATCGATACACTATGAAAG
1 TGCATCGATACACTATGAAAG
* * *
20844 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGAT--A-CACTATGAAAG
20868 TGCATCGATACA
1 TGCATCGATACA
20880 TCATGAAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 10 0.34
22 1 0.03
23 1 0.03
24 17 0.59
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (21 bp):
TGCATCGATACACTATGAAAG
Found at i:20874 original size:45 final size:44
Alignment explanation
Indices: 20823--20920 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 44
20813 TGGTGCATAA
20823 TGCATCGATACA-CTATGAA-AGTGCA-TCGATGCATC-CCTTTGAATG
1 TGCATCGATACATC-ATGAAGA-TGCACT-GATGCA-CGCC-TTGAATG
*
20868 TGCATCGATACATCATGAAGATGTACTGATGCACGCCTTGAATG
1 TGCATCGATACATCATGAAGATGCACTGATGCACGCCTTGAATG
20912 TGCATCGAT
1 TGCATCGAT
20921 GCACAAGGCC
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
44 17 0.35
45 28 0.58
46 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
TGCATCGATACATCATGAAGATGCACTGATGCACGCCTTGAATG
Found at i:21119 original size:19 final size:20
Alignment explanation
Indices: 21097--21134 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
21087 CTACATCTCC
*
21097 AAATCCTGC-TAACATCATT
1 AAATCCTGCAAAACATCATT
*
21116 AAATCGTGCAAAACATCAT
1 AAATCCTGCAAAACATCAT
21135 CATATTCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.42, C:0.24, G:0.08, T:0.26
Consensus pattern (20 bp):
AAATCCTGCAAAACATCATT
Found at i:23104 original size:20 final size:20
Alignment explanation
Indices: 23079--23116 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23069 ATTGAGAAGG
23079 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
**
23099 GATGCATTGATGCACTCA
1 GATGCACCGATGCACTCA
23117 CCATATCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:23249 original size:64 final size:63
Alignment explanation
Indices: 23121--23271 Score: 207
Period size: 64 Copynumber: 2.4 Consensus size: 63
23111 CACTCACCAT
* *
23121 ATCGAATGCAATTTATGCATCGATGCACTACCATGCATCGATGCACTCAAGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATGCACTCAAGTTTTATGAAAAC
* **
23184 ATCGAATGCATTTTATGTATCGATGCACAGACCATGCATCGATGCACTCTGGCTTATT-T-AAAA
1 ATCGAATGCATTTTATGCATCGATGCAC-GACCATGCATCGATGCACTCAAG-TT-TTATGAAAA
23247 C
63 C
*
23248 ATCCAATGCATTTTATGCATCGAT
1 ATCGAATGCATTTTATGCATCGAT
23272 TCACTCTTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
63 26 0.33
64 47 0.60
65 3 0.04
66 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATGCACTCAAGTTTTATGAAAAC
Found at i:23286 original size:64 final size:62
Alignment explanation
Indices: 23125--23295 Score: 193
Period size: 64 Copynumber: 2.7 Consensus size: 62
23115 CACCATATCG
* *
23125 AATGCAATTTATGCATCGATGCACTACCATGCATCGATGCACTCAAGTTTTATGAAAACATCG
1 AATGCATTTTATGCATCGATGCACT-CCATGCATCGATGCACTCAAGTTTTATGAAAACATCC
* * **
23188 AATGCATTTTATGTATCGATGCACAGACCATGCATCGATGCACTCTGGCTTATT-T-AAAACATC
1 AATGCATTTTATGCATCGATGCAC--TCCATGCATCGATGCACTCAAG-TT-TTATGAAAACATC
23251 C
62 C
* *
23252 AATGCATTTTATGCATCGATTCACTCTTATTGCATCGATGCACT
1 AATGCATTTTATGCATCGATGCACTC-CA-TGCATCGATGCACT
23296 AAGGGTACAA
Statistics
Matches: 92, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 23 0.25
64 63 0.68
65 3 0.03
66 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (62 bp):
AATGCATTTTATGCATCGATGCACTCCATGCATCGATGCACTCAAGTTTTATGAAAACATCC
Found at i:28421 original size:20 final size:20
Alignment explanation
Indices: 28396--28433 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28386 ATTGAGAAGG
28396 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
**
28416 GATGCATTGATGCACTCA
1 GATGCACCGATGCACTCA
28434 CCATATCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:28566 original size:64 final size:63
Alignment explanation
Indices: 28438--28588 Score: 207
Period size: 64 Copynumber: 2.4 Consensus size: 63
28428 CACTCACCAT
* *
28438 ATCGAATGCAATTTATGCATCGATGCACTACCATGCATCGATGCACTCAAGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATGCACTCAAGTTTTATGAAAAC
* **
28501 ATCGAATGCATTTTATGTATCGATGCACAGACCATGCATCGATGCACTCTGGCTTATT-T-AAAA
1 ATCGAATGCATTTTATGCATCGATGCAC-GACCATGCATCGATGCACTCAAG-TT-TTATGAAAA
28564 C
63 C
*
28565 ATCCAATGCATTTTATGCATCGAT
1 ATCGAATGCATTTTATGCATCGAT
28589 TCACTCTTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
63 26 0.33
64 47 0.60
65 3 0.04
66 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATGCACTCAAGTTTTATGAAAAC
Found at i:28603 original size:64 final size:62
Alignment explanation
Indices: 28442--28612 Score: 193
Period size: 64 Copynumber: 2.7 Consensus size: 62
28432 CACCATATCG
* *
28442 AATGCAATTTATGCATCGATGCACTACCATGCATCGATGCACTCAAGTTTTATGAAAACATCG
1 AATGCATTTTATGCATCGATGCACT-CCATGCATCGATGCACTCAAGTTTTATGAAAACATCC
* * **
28505 AATGCATTTTATGTATCGATGCACAGACCATGCATCGATGCACTCTGGCTTATT-T-AAAACATC
1 AATGCATTTTATGCATCGATGCAC--TCCATGCATCGATGCACTCAAG-TT-TTATGAAAACATC
28568 C
62 C
* *
28569 AATGCATTTTATGCATCGATTCACTCTTATTGCATCGATGCACT
1 AATGCATTTTATGCATCGATGCACTC-CA-TGCATCGATGCACT
28613 AAGGGTACAA
Statistics
Matches: 92, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 23 0.25
64 63 0.68
65 3 0.03
66 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (62 bp):
AATGCATTTTATGCATCGATGCACTCCATGCATCGATGCACTCAAGTTTTATGAAAACATCC
Found at i:33736 original size:20 final size:20
Alignment explanation
Indices: 33711--33748 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
33701 ATTGAGAAGG
33711 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
**
33731 GATGCATTGATGCACTCA
1 GATGCACCGATGCACTCA
33749 CCATATCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:33881 original size:64 final size:63
Alignment explanation
Indices: 33753--33903 Score: 207
Period size: 64 Copynumber: 2.4 Consensus size: 63
33743 CACTCACCAT
* *
33753 ATCGAATGCAATTTATGCATCGATGCACTACCATGCATCGATGCACTCAAGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATGCACTCAAGTTTTATGAAAAC
* **
33816 ATCGAATGCATTTTATGTATCGATGCACAGACCATGCATCGATGCACTCTGGCTTATT-T-AAAA
1 ATCGAATGCATTTTATGCATCGATGCAC-GACCATGCATCGATGCACTCAAG-TT-TTATGAAAA
33879 C
63 C
*
33880 ATCCAATGCATTTTATGCATCGAT
1 ATCGAATGCATTTTATGCATCGAT
33904 TCACTCTTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
63 26 0.33
64 47 0.60
65 3 0.04
66 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATGCACTCAAGTTTTATGAAAAC
Found at i:33918 original size:64 final size:62
Alignment explanation
Indices: 33757--33927 Score: 193
Period size: 64 Copynumber: 2.7 Consensus size: 62
33747 CACCATATCG
* *
33757 AATGCAATTTATGCATCGATGCACTACCATGCATCGATGCACTCAAGTTTTATGAAAACATCG
1 AATGCATTTTATGCATCGATGCACT-CCATGCATCGATGCACTCAAGTTTTATGAAAACATCC
* * **
33820 AATGCATTTTATGTATCGATGCACAGACCATGCATCGATGCACTCTGGCTTATT-T-AAAACATC
1 AATGCATTTTATGCATCGATGCAC--TCCATGCATCGATGCACTCAAG-TT-TTATGAAAACATC
33883 C
62 C
* *
33884 AATGCATTTTATGCATCGATTCACTCTTATTGCATCGATGCACT
1 AATGCATTTTATGCATCGATGCACTC-CA-TGCATCGATGCACT
33928 AAGGGTACAA
Statistics
Matches: 92, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 23 0.25
64 63 0.68
65 3 0.03
66 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (62 bp):
AATGCATTTTATGCATCGATGCACTCCATGCATCGATGCACTCAAGTTTTATGAAAACATCC
Found at i:39048 original size:20 final size:20
Alignment explanation
Indices: 39023--39060 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39013 ATTGAGAAGG
39023 GATGCACCGATGCACTCATT
1 GATGCACCGATGCACTCATT
**
39043 GATGCATTGATGCACTCA
1 GATGCACCGATGCACTCA
39061 CCATATCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
GATGCACCGATGCACTCATT
Found at i:39193 original size:64 final size:63
Alignment explanation
Indices: 39065--39215 Score: 207
Period size: 64 Copynumber: 2.4 Consensus size: 63
39055 CACTCACCAT
* *
39065 ATCGAATGCAATTTATGCATCGATGCACTACCATGCATCGATGCACTCAAGTTTTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATGCACTCAAGTTTTATGAAAAC
* **
39128 ATCGAATGCATTTTATGTATCGATGCACAGACCATGCATCGATGCACTCTGGCTTATT-T-AAAA
1 ATCGAATGCATTTTATGCATCGATGCAC-GACCATGCATCGATGCACTCAAG-TT-TTATGAAAA
39191 C
63 C
*
39192 ATCCAATGCATTTTATGCATCGAT
1 ATCGAATGCATTTTATGCATCGAT
39216 TCACTCTTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
63 26 0.33
64 47 0.60
65 3 0.04
66 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATGCACTCAAGTTTTATGAAAAC
Found at i:39230 original size:64 final size:62
Alignment explanation
Indices: 39069--39239 Score: 193
Period size: 64 Copynumber: 2.7 Consensus size: 62
39059 CACCATATCG
* *
39069 AATGCAATTTATGCATCGATGCACTACCATGCATCGATGCACTCAAGTTTTATGAAAACATCG
1 AATGCATTTTATGCATCGATGCACT-CCATGCATCGATGCACTCAAGTTTTATGAAAACATCC
* * **
39132 AATGCATTTTATGTATCGATGCACAGACCATGCATCGATGCACTCTGGCTTATT-T-AAAACATC
1 AATGCATTTTATGCATCGATGCAC--TCCATGCATCGATGCACTCAAG-TT-TTATGAAAACATC
39195 C
62 C
* *
39196 AATGCATTTTATGCATCGATTCACTCTTATTGCATCGATGCACT
1 AATGCATTTTATGCATCGATGCACTC-CA-TGCATCGATGCACT
39240 AAGGGTACAA
Statistics
Matches: 92, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 23 0.25
64 63 0.68
65 3 0.03
66 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (62 bp):
AATGCATTTTATGCATCGATGCACTCCATGCATCGATGCACTCAAGTTTTATGAAAACATCC
Found at i:44336 original size:20 final size:20
Alignment explanation
Indices: 44311--44348 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
44301 ATTGGGAAGG
44311 GATGCATCGATGCACTCATT
1 GATGCATCGATGCACTCATT
*
44331 GATGCATTGATGCACTCA
1 GATGCATCGATGCACTCA
44349 CCATATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (20 bp):
GATGCATCGATGCACTCATT
Found at i:44397 original size:35 final size:37
Alignment explanation
Indices: 44312--44398 Score: 92
Period size: 35 Copynumber: 2.4 Consensus size: 37
44302 TTGGGAAGGG
*
44312 ATGCATCGATGCACTCATTGATGCATTGATGCACTCACC
1 ATGCATCGATGCA--CATTGATGCATCGATGCACTCACC
* *
44351 AT--ATCAAATGCA-ATTTATGCATCGATGCACT-ACC
1 ATGCATC-GATGCACATTGATGCATCGATGCACTCACC
44385 ATGCATCGATGCAC
1 ATGCATCGATGCAC
44399 TCAAGTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
34 5 0.12
35 22 0.55
36 3 0.08
37 3 0.08
38 5 0.12
39 2 0.05
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (37 bp):
ATGCATCGATGCACATTGATGCATCGATGCACTCACC
Found at i:44424 original size:63 final size:62
Alignment explanation
Indices: 44357--44508 Score: 191
Period size: 63 Copynumber: 2.4 Consensus size: 62
44347 CACCATATCA
* *
44357 AATGCAATTTATGCATCGATGCACTACCATGCATCGATGCACTCAAG-TT-TTATGAAAACATCG
1 AATGCATTTTATGCATCGATGCACTACCA-GCATCGATGCACTCAAGCTTGTT-T-AAAACATCC
* * * **
44420 AATGCATTTTATGTATCGATGCACAGACCAGTATCGATGCACTCTGGCTTGTTTAAAACATCC
1 AATGCATTTTATGCATCGATGCAC-TACCAGCATCGATGCACTCAAGCTTGTTTAAAACATCC
44483 AATGCATTTTATGCATCGATGCACTA
1 AATGCATTTTATGCATCGATGCACTA
44509 AGGGTACAAC
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
62 1 0.01
63 67 0.87
64 7 0.09
65 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (62 bp):
AATGCATTTTATGCATCGATGCACTACCAGCATCGATGCACTCAAGCTTGTTTAAAACATCC
Found at i:45254 original size:31 final size:31
Alignment explanation
Indices: 45219--45277 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
45209 ATAACTCTGC
*
45219 TAGGTTCAATCACTG-CTGGCAATTCCTTGTA
1 TAGGTTCAA-CACCGACTGGCAATTCCTTGTA
*
45250 TAGGTTCAACACCGACTGGTAATTCCTT
1 TAGGTTCAACACCGACTGGCAATTCCTT
45278 ATGGACCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (31 bp):
TAGGTTCAACACCGACTGGCAATTCCTTGTA
Found at i:52615 original size:5 final size:5
Alignment explanation
Indices: 52605--52659 Score: 76
Period size: 5 Copynumber: 10.8 Consensus size: 5
52595 AACGGTCAAC
*
52605 GGTCG GGTCG GGTCAG CGGTCG GGTCG GGTC- GGTCG AGTCG GGTCG GGTCG
1 GGTCG GGTCG GGTC-G -GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG
52656 GGTC
1 GGTC
52660 AAACCGGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
4 4 0.09
5 35 0.78
6 2 0.04
7 4 0.09
ACGTcount: A:0.04, C:0.22, G:0.55, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:52624 original size:17 final size:17
Alignment explanation
Indices: 52598--52654 Score: 78
Period size: 17 Copynumber: 3.2 Consensus size: 17
52588 CGCGGTCAAC
*
52598 GGTCAACGGTCGGGTCG
1 GGTCAGCGGTCGGGTCG
52615 GGTCAGCGGTCGGGTCG
1 GGTCAGCGGTCGGGTCG
*
52632 GGTCGGTCGAGTCGGGTCG
1 GGTCAG-CG-GTCGGGTCG
52651 GGTC
1 GGTC
52655 GGGTCAAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 21 0.58
18 2 0.06
19 13 0.36
ACGTcount: A:0.07, C:0.23, G:0.51, T:0.19
Consensus pattern (17 bp):
GGTCAGCGGTCGGGTCG
Found at i:52647 original size:19 final size:17
Alignment explanation
Indices: 52604--52656 Score: 79
Period size: 17 Copynumber: 3.0 Consensus size: 17
52594 CAACGGTCAA
*
52604 CGGTCGGGTCGGGTCAG
1 CGGTCGGGTCGGGTCGG
52621 CGGTCGGGTCGGGTCGG
1 CGGTCGGGTCGGGTCGG
52638 TCGAGTCGGGTCGGGTCGG
1 -CG-GTCGGGTCGGGTCGG
52657 GTCAAACCGG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 16 0.48
18 2 0.06
19 15 0.45
ACGTcount: A:0.04, C:0.23, G:0.55, T:0.19
Consensus pattern (17 bp):
CGGTCGGGTCGGGTCGG
Found at i:56613 original size:14 final size:14
Alignment explanation
Indices: 56590--56641 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
56580 TCTATCTATA
*
56590 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
56603 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
56618 TGCAGGGATTTATT
1 TGCAGGGATTTATT
*
56632 TACAGGGATT
1 TGCAGGGATT
56642 ACTTCCCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
13 1 0.03
14 31 0.89
15 3 0.09
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:61513 original size:21 final size:21
Alignment explanation
Indices: 61489--61540 Score: 95
Period size: 21 Copynumber: 2.4 Consensus size: 21
61479 TTTGCTTTTT
61489 GGTTTTGTTGTAGGGTTGTTG
1 GGTTTTGTTGTAGGGTTGTTG
61510 GGTTTTGTTGTAGGGTTGTTG
1 GGTTTTGTTGTAGGGTTGTTG
61531 GGTTTATGTT
1 GGTTT-TGTT
61541 CTGGTGGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.06, C:0.00, G:0.40, T:0.54
Consensus pattern (21 bp):
GGTTTTGTTGTAGGGTTGTTG
Done.