Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004199.1 Hibiscus syriacus cultivar Beakdansim tig00009190_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: 65546
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:1720 original size:15 final size:16
Alignment explanation
Indices: 1696--1725 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1686 CAAAAAACAT
1696 AAAATATGACTTTTCA
1 AAAATATGACTTTTCA
1712 AAAAT-TGACTTTTC
1 AAAATATGACTTTTC
1726 GGTCAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (16 bp):
AAAATATGACTTTTCA
Found at i:1845 original size:17 final size:18
Alignment explanation
Indices: 1823--1856 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1813 CGAAAAACAT
1823 AAAA-TTTAACTTTTTCG
1 AAAATTTTAACTTTTTCG
*
1840 AAAATTTTGACTTTTTC
1 AAAATTTTAACTTTTTC
1857 AGTAAAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (18 bp):
AAAATTTTAACTTTTTCG
Found at i:4284 original size:16 final size:16
Alignment explanation
Indices: 4249--4303 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
4239 TAATTAGAGT
*
4249 AGTTGAGAGTGTTAAAG
1 AGTTGAGAGT-TTTAAG
4266 AGTTGAGAGTTTTAAG
1 AGTTGAGAGTTTTAAG
4282 AGTTGAGAGTTTTAAG
1 AGTTGAGAGTTTTAAG
4298 AGTTGA
1 AGTTGA
4304 ATTTATTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
16 27 0.73
17 10 0.27
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (16 bp):
AGTTGAGAGTTTTAAG
Found at i:5903 original size:2 final size:2
Alignment explanation
Indices: 5896--5969 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
5886 GATCATAACC
*
5896 AT AT AT AT AT AT AT AT AT AT AT AT AT AG 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
5938 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
5970 TCATTTAGAC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8745 original size:8 final size:8
Alignment explanation
Indices: 8732--8762 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
8722 ATTGTTATTC
8732 TTCATATA
1 TTCATATA
8740 TTCATATA
1 TTCATATA
*
8748 TTCATGTA
1 TTCATATA
8756 TTCATAT
1 TTCATAT
8763 CATTTCTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.52
Consensus pattern (8 bp):
TTCATATA
Found at i:15532 original size:22 final size:22
Alignment explanation
Indices: 15504--15567 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
15494 ATGTGAAATT
*
15504 TGTCCCGAAGGACCTATGTATA
1 TGTCCCGAAAGACCTATGTATA
* * *
15526 TGTCCCGAATGACCTCTTTATA
1 TGTCCCGAAAGACCTATGTATA
*
15548 TGTCCCAAAAGACCTATGTA
1 TGTCCCGAAAGACCTATGTA
15568 ACCCTCTACT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (22 bp):
TGTCCCGAAAGACCTATGTATA
Found at i:21786 original size:49 final size:49
Alignment explanation
Indices: 21669--22196 Score: 853
Period size: 49 Copynumber: 10.8 Consensus size: 49
21659 TGCACGGAAG
*
21669 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGTCACCTTTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACC-TTTTA
** * * *
21719 TATCGAAATGCATCGTTATGCATTTAACTTTCAGTAGTGACACCTTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
* *
21768 TGCCAAAATGCACCGTTATGCATTTAACTTTCATTAGTGGAACCTTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
* * * *
21817 TGCCTAAATG-ACTGTTATGCATTTAACTTTCATTAGTGACACATTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
21865 TGCCGAAAATGCACCGTTATGCATTT-ACTTTCATTAGTGGCACCTTTTA
1 TGCCG-AAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
21914 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
*
21963 TGCCGAAATGTACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
* *
22012 TGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGTCACCTTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
*
22061 TGCCGAAACGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
* *
22110 TGCTGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGTACCTTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
*
22159 TGCTGAAATGCACCGTTATGCATTTAACTTTCATTAGT
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGT
22197 TCATTTTAGA
Statistics
Matches: 444, Mismatches: 31, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
48 58 0.13
49 334 0.75
50 52 0.12
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (49 bp):
TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
Found at i:22648 original size:18 final size:18
Alignment explanation
Indices: 22625--22673 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
22615 TACCTTCCTC
22625 TTAGTATCGATACCCACA
1 TTAGTATCGATACCCACA
22643 TTAGTATCGATACCCACA
1 TTAGTATCGATACCCACA
*
22661 TCAGTATCGATAC
1 TTAGTATCGATAC
22674 TAATTGCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (18 bp):
TTAGTATCGATACCCACA
Found at i:23837 original size:18 final size:19
Alignment explanation
Indices: 23814--23853 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
23804 GCAACCAACA
23814 TCAAAACTGG-TGCCGCCG
1 TCAAAACTGGTTGCCGCCG
23832 TCAAAACTGGTTGCCGCCG
1 TCAAAACTGGTTGCCGCCG
23851 TCA
1 TCA
23854 GTTAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (19 bp):
TCAAAACTGGTTGCCGCCG
Found at i:26115 original size:32 final size:32
Alignment explanation
Indices: 26074--26138 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
26064 ATAGCTCCCA
26074 ACACTTCTAGGATATTTAACAGTGGATTCTGT
1 ACACTTCTAGGATATTTAACAGTGGATTCTGT
* *
26106 ACACTTCTAGGATATTTTACTGTGGATTCTGT
1 ACACTTCTAGGATATTTAACAGTGGATTCTGT
26138 A
1 A
26139 GTCCATGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.40
Consensus pattern (32 bp):
ACACTTCTAGGATATTTAACAGTGGATTCTGT
Found at i:27549 original size:87 final size:87
Alignment explanation
Indices: 27403--27577 Score: 332
Period size: 87 Copynumber: 2.0 Consensus size: 87
27393 ACAAGTTGAT
27403 AAACGAGCTTATTTGTGAATATAAACGAATTGAATACACTTATGTTCATGTTCATTTTTTCATTA
1 AAACGAGCTTATTTGTGAATATAAACGAATTGAATACACTTATGTTCATGTTCATTTTTTCATTA
27468 AATGAACATAAATGTATTTTTC
66 AATGAACATAAATGTATTTTTC
*
27490 AAACGAGCTTGTTTGTGAATATAAACGAATTGAATACACTTATGTTCATGTTCATTTTTTCATTA
1 AAACGAGCTTATTTGTGAATATAAACGAATTGAATACACTTATGTTCATGTTCATTTTTTCATTA
*
27555 AATGAACATAAATGTTTTTTTC
66 AATGAACATAAATGTATTTTTC
27577 A
1 A
27578 TACTCGTTTC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (87 bp):
AAACGAGCTTATTTGTGAATATAAACGAATTGAATACACTTATGTTCATGTTCATTTTTTCATTA
AATGAACATAAATGTATTTTTC
Found at i:33164 original size:24 final size:24
Alignment explanation
Indices: 33137--33248 Score: 145
Period size: 24 Copynumber: 4.7 Consensus size: 24
33127 ATTTGATTTA
*
33137 TGATCTGATACTTGACATGGATTC
1 TGATATGATACTTGACATGGATTC
*
33161 TGATTTGATA-TCTGACATGGATTC
1 TGATATGATACT-TGACATGGATTC
* * *
33185 TGATCTGATACTTGACTTGGATTT
1 TGATATGATACTTGACATGGATTC
* *
33209 TGATATGATACTTGACCTGGATTT
1 TGATATGATACTTGACATGGATTC
33233 TGATATGATACTTGAC
1 TGATATGATACTTGAC
33249 GTGAATTATG
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.01
24 78 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (24 bp):
TGATATGATACTTGACATGGATTC
Found at i:33197 original size:48 final size:48
Alignment explanation
Indices: 33137--33265 Score: 161
Period size: 48 Copynumber: 2.7 Consensus size: 48
33127 ATTTGATTTA
*
33137 TGATCTGATACTTGACATGGATTCTGATTTGATA-TCTGACATGGATTC
1 TGATCTGATACTTGACATGGATTATGATTTGATACT-TGACATGGATTC
* * * * *
33185 TGATCTGATACTTGACTTGGATTTTGATATGATACTTGACCTGGATTT
1 TGATCTGATACTTGACATGGATTATGATTTGATACTTGACATGGATTC
* * *
33233 TGATATGATACTTGACGTGAATTATGATTTGAT
1 TGATCTGATACTTGACATGGATTATGATTTGAT
33266 TTTTGATATA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
48 69 0.99
49 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.42
Consensus pattern (48 bp):
TGATCTGATACTTGACATGGATTATGATTTGATACTTGACATGGATTC
Found at i:33260 original size:24 final size:24
Alignment explanation
Indices: 33134--33265 Score: 140
Period size: 24 Copynumber: 5.5 Consensus size: 24
33124 TCGATTTGAT
*
33134 TTATGATCTGATACTTGACATGGA
1 TTATGATATGATACTTGACATGGA
* *
33158 TTCTGATTTGATA-TCTGACATGGA
1 TTATGATATGATACT-TGACATGGA
* * *
33182 TTCTGATCTGATACTTGACTTGGA
1 TTATGATATGATACTTGACATGGA
* *
33206 TTTTGATATGATACTTGACCTGGA
1 TTATGATATGATACTTGACATGGA
* * *
33230 TTTTGATATGATACTTGACGTGAA
1 TTATGATATGATACTTGACATGGA
*
33254 TTATGATTTGAT
1 TTATGATATGAT
33266 TTTTGATATA
Statistics
Matches: 95, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 93 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.42
Consensus pattern (24 bp):
TTATGATATGATACTTGACATGGA
Found at i:35350 original size:18 final size:18
Alignment explanation
Indices: 35327--35365 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
35317 ACCGGTCACA
35327 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
35345 ACCCGACCCGATCCGTTG
1 ACCCGACCCGACCCGTTG
35363 ACC
1 ACC
35366 ATTGACCGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.49, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:37890 original size:48 final size:48
Alignment explanation
Indices: 37836--37967 Score: 176
Period size: 48 Copynumber: 2.8 Consensus size: 48
37826 TCGATTTGAT
37836 TTCTGATCTGATACTTGACATGGATTCTGATTTGATATCTT-ACATGGA
1 TTCTGATCTGATACTTGACATGGATTCTGATTTGATA-CTTGACATGGA
* * *
37884 TTCTGATCTGATACTTGACTTGGATTCTGATCTGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGATTCTGATTTGATACTTGACATGGA
* * * * *
37932 TTTTGATATGATACTTGACGTGAATTATGATTTGAT
1 TTCTGATCTGATACTTGACATGGATTCTGATTTGAT
37968 TTTTGATATA
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
47 3 0.04
48 71 0.96
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (48 bp):
TTCTGATCTGATACTTGACATGGATTCTGATTTGATACTTGACATGGA
Found at i:37967 original size:24 final size:24
Alignment explanation
Indices: 37836--37950 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
37826 TCGATTTGAT
37836 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
*
37860 TTCTGATTTGATATCTT-ACATGGA
1 TTCTGATCTGATA-CTTGACATGGA
*
37884 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
*
37908 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
37932 TTTTGATATGATACTTGAC
1 TTCTGATCTGATACTTGAC
37951 GTGAATTATG
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 3 0.04
24 77 0.93
25 3 0.04
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:44478 original size:20 final size:20
Alignment explanation
Indices: 44435--44502 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
44425 TGCAAAAATG
* **
44435 GTATCGATACCGTAATAG-A
1 GTATCGATACCATGGTAGAA
44454 GTATCGATACCATGGTAGAA
1 GTATCGATACCATGGTAGAA
44474 GTATCGATACCATGGTAGAA
1 GTATCGATACCATGGTAGAA
44494 GTATCGATA
1 GTATCGATA
44503 TAATTGAGCC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 15 0.33
20 30 0.67
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (20 bp):
GTATCGATACCATGGTAGAA
Found at i:49507 original size:21 final size:22
Alignment explanation
Indices: 49464--49516 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
49454 ATAAATTGCA
49464 CCGAAGTG-CCATATAGAATGTC
1 CCGAAG-GACCATATAGAATGTC
*
49486 CTGAAGGACCATATAG-ATGTC
1 CCGAAGGACCATATAGAATGTC
49507 CCGAAGGACC
1 CCGAAGGACC
49517 GCGTAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (22 bp):
CCGAAGGACCATATAGAATGTC
Found at i:49537 original size:24 final size:24
Alignment explanation
Indices: 49505--49571 Score: 100
Period size: 23 Copynumber: 2.8 Consensus size: 24
49495 CATATAGATG
49505 TCCCGAAGGACCGCGTAGAAATTA
1 TCCCGAAGGACCGCGTAGAAATTA
*
49529 TCCCGAAGGACCACGTAG-AATTA
1 TCCCGAAGGACCGCGTAGAAATTA
* *
49552 TCCCGAATGAGCGCGTAGAA
1 TCCCGAAGGACCGCGTAGAA
49572 CCCTTGACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.16
Consensus pattern (24 bp):
TCCCGAAGGACCGCGTAGAAATTA
Found at i:49554 original size:23 final size:24
Alignment explanation
Indices: 49505--49558 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
49495 CATATAGATG
*
49505 TCCCGAAGGACCGCGTAGAAATTA
1 TCCCGAAGGACCACGTAGAAATTA
49529 TCCCGAAGGACCACGTAG-AATTA
1 TCCCGAAGGACCACGTAGAAATTA
49552 TCCCGAA
1 TCCCGAA
49559 TGAGCGCGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (24 bp):
TCCCGAAGGACCACGTAGAAATTA
Found at i:53772 original size:12 final size:12
Alignment explanation
Indices: 53755--53781 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53745 GGACCAAGGG
53755 AATAATTATACC
1 AATAATTATACC
53767 AATAATTATACC
1 AATAATTATACC
53779 AAT
1 AAT
53782 TTTCTTCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAATTATACC
Found at i:54576 original size:21 final size:21
Alignment explanation
Indices: 54526--54576 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
54516 GGTCTAGAAA
*
54526 TATTGATACTCCTTCATTGGG
1 TATTGATACTCCTTCATAGGG
** *
54547 TATCAATACT-CTTCGTAGGAG
1 TATTGATACTCCTTCATAGG-G
54568 TATTGATAC
1 TATTGATAC
54577 CTGGGTCACT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (21 bp):
TATTGATACTCCTTCATAGGG
Found at i:55935 original size:23 final size:22
Alignment explanation
Indices: 55874--55958 Score: 104
Period size: 23 Copynumber: 3.8 Consensus size: 22
55864 CAGCTCGTAA
*
55874 TTTGCACCAAAGTGCCACATAA
1 TTTGCACCAAAGTGCCACATAG
55896 TTAT-C-CCAAAG-GACCACATAGG
1 TT-TGCACCAAAGTG-CCACATA-G
55918 TTTGCACCAAAGTGCCACATAAG
1 TTTGCACCAAAGTGCCACAT-AG
55941 TTTGCACCAAAGTGCCAC
1 TTTGCACCAAAGTGCCAC
55959 CTAATTATCC
Statistics
Matches: 55, Mismatches: 1, Indels: 13
0.80 0.01 0.19
Matches are distributed among these distances:
20 1 0.02
21 14 0.25
22 6 0.11
23 32 0.58
24 2 0.04
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.21
Consensus pattern (22 bp):
TTTGCACCAAAGTGCCACATAG
Found at i:55992 original size:21 final size:21
Alignment explanation
Indices: 55955--56001 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
55945 CACCAAAGTG
*
55955 CCACCTAATTATCCCGAAAGA
1 CCACATAATTATCCCGAAAGA
* *
55976 CCACATAATTATTCCGAATGA
1 CCACATAATTATCCCGAAAGA
55997 CCACA
1 CCACA
56002 GAAAACCCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.32, G:0.09, T:0.21
Consensus pattern (21 bp):
CCACATAATTATCCCGAAAGA
Found at i:56230 original size:29 final size:30
Alignment explanation
Indices: 56170--56230 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
56160 TCATATAATC
* * **
56170 ATAAAACATAGCTTATATAATATAAATTGA
1 ATAAAACATAGCTAATATAACATAAAAGGA
*
56200 ATAAAACATTG-TAATATAACATAAAAGGA
1 ATAAAACATAGCTAATATAACATAAAAGGA
56229 AT
1 AT
56231 TATAAAGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.30
Consensus pattern (30 bp):
ATAAAACATAGCTAATATAACATAAAAGGA
Found at i:59938 original size:35 final size:35
Alignment explanation
Indices: 59899--60008 Score: 131
Period size: 35 Copynumber: 3.3 Consensus size: 35
59889 TATATAGTTT
59899 TTTTTAAAAATAGTTTTGAAAATGTATAATATATG
1 TTTTTAAAAATAGTTTTGAAAATGTATAATATATG
* * *
59934 TTTTTTAAAATGGTTTTGAAAACG--T-ATATA-G
1 TTTTTAAAAATAGTTTTGAAAATGTATAATATATG
*
59965 TTTTT-AAAATAGTTTTGAAAATATATAATATATAG
1 TTTTTAAAAATAGTTTTGAAAATGTATAATATAT-G
*
60000 TTTTGAAAA
1 TTTTTAAAA
60009 CCTATATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
30 15 0.24
31 6 0.10
32 6 0.10
33 6 0.10
35 26 0.42
36 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTTTAAAAATAGTTTTGAAAATGTATAATATATG
Found at i:59969 original size:30 final size:34
Alignment explanation
Indices: 59898--60003 Score: 112
Period size: 30 Copynumber: 3.1 Consensus size: 34
59888 ATATATAGTT
*
59898 TTTTTTAAAAATAGTTTTGAAAATGTATAATATATG
1 TTTTTT-AAAATAGTTTTGAAAACG-ATAATATATG
*
59934 TTTTTTAAAATGGTTTTGAAAACG-T-ATATA-G
1 TTTTTTAAAATAGTTTTGAAAACGATAATATATG
**
59965 -TTTTTAAAATAGTTTTGAAAATATATAATATATAG
1 TTTTTTAAAATAGTTTTGAAAA-CGATAATATAT-G
60000 TTTT
1 TTTT
60004 GAAAACCTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
30 20 0.34
31 1 0.02
32 6 0.10
33 6 0.10
35 17 0.29
36 9 0.15
ACGTcount: A:0.40, C:0.01, G:0.11, T:0.48
Consensus pattern (34 bp):
TTTTTTAAAATAGTTTTGAAAACGATAATATATG
Found at i:60014 original size:23 final size:25
Alignment explanation
Indices: 59973--60033 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 25
59963 AGTTTTTAAA
*
59973 ATAGTTTTGAAAATATATA-AT-AT
1 ATAGTTTTGAAAACATATATATAAT
*
59996 ATAGTTTTGAAAACCTATATATAAT
1 ATAGTTTTGAAAACATATATATAAT
* *
60021 ATTGTTTTTAAAA
1 ATAGTTTTGAAAA
60034 ATGGTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 17 0.53
24 2 0.06
25 13 0.41
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (25 bp):
ATAGTTTTGAAAACATATATATAAT
Found at i:60105 original size:29 final size:30
Alignment explanation
Indices: 60051--60115 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
60041 TTTAAAACGA
*
60051 TTTTTGAAAATATATTAATATATTATATAG
1 TTTTTGAAAATATAATAATATATTATATAG
* *
60081 TTTTTGGAAATATAAT-ATATGTTATATAG
1 TTTTTGAAAATATAATAATATATTATATAG
60110 TGTTTT
1 T-TTTT
60116 ATTATTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (30 bp):
TTTTTGAAAATATAATAATATATTATATAG
Found at i:60127 original size:9 final size:10
Alignment explanation
Indices: 60114--60168 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 10
60104 ATATAGTGTT
60114 TTATTATTTA
1 TTATTATTTA
60124 -TATTATTTA
1 TTATTATTTA
60133 TTATTATTTTA
1 TTATTA-TTTA
60144 GGTTACATTA-TTA
1 --TT--ATTATTTA
60157 TTATTATTTA
1 TTATTATTTA
60167 TT
1 TT
60169 GATTTATTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
9 13 0.34
10 10 0.26
11 6 0.16
13 5 0.13
15 4 0.11
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (10 bp):
TTATTATTTA
Found at i:62806 original size:18 final size:17
Alignment explanation
Indices: 62773--62806 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
62763 TTTTAAAAAA
*
62773 TATTTAAAAAATTAAAT
1 TATTTAAAAAACTAAAT
62790 TATTTAAAAAACCTAAA
1 TATTTAAAAAA-CTAAA
62807 AATTTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
TATTTAAAAAACTAAAT
Done.