Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000106.1 Hibiscus syriacus cultivar Beakdansim tig00000190_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: 82320
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:11889 original size:2 final size:2
Alignment explanation
Indices: 11882--11935 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
11872 GCTAAAATCC
11882 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11923 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
11936 TTATTTTATT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14753 original size:33 final size:33
Alignment explanation
Indices: 14714--14803 Score: 171
Period size: 33 Copynumber: 2.7 Consensus size: 33
14704 ATGTGGTTTG
14714 TTTATTTTCTATTTGTCTATTCCTGATTCTTGA
1 TTTATTTTCTATTTGTCTATTCCTGATTCTTGA
*
14747 TTTATTTTCTATTTCTCTATTCCTGATTCTTGA
1 TTTATTTTCTATTTGTCTATTCCTGATTCTTGA
14780 TTTATTTTCTATTTGTCTATTCCT
1 TTTATTTTCTATTTGTCTATTCCT
14804 TCTCTGAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.14, C:0.17, G:0.07, T:0.62
Consensus pattern (33 bp):
TTTATTTTCTATTTGTCTATTCCTGATTCTTGA
Found at i:14768 original size:26 final size:26
Alignment explanation
Indices: 14723--14774 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
14713 GTTTATTTTC
*
14723 TATTTGTCTATTCCTGATTCTTGATT
1 TATTTGTCTATTCCTGATTCCTGATT
14749 TATTT-TCTATTTCTCT-ATTCCTGATT
1 TATTTGTCTA-TTC-CTGATTCCTGATT
14775 CTTGATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 4 0.17
26 17 0.74
27 2 0.09
ACGTcount: A:0.15, C:0.17, G:0.08, T:0.60
Consensus pattern (26 bp):
TATTTGTCTATTCCTGATTCCTGATT
Found at i:19067 original size:20 final size:21
Alignment explanation
Indices: 19044--19088 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
19034 TGGGTACCGA
* *
19044 ATACTATAA-GGTCGGTATCG
1 ATACTAAAATGGTCAGTATCG
*
19064 ATACTAAAATGGTTAGTATCG
1 ATACTAAAATGGTCAGTATCG
19085 ATAC
1 ATAC
19089 CATCGTACTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (21 bp):
ATACTAAAATGGTCAGTATCG
Found at i:20767 original size:19 final size:19
Alignment explanation
Indices: 20743--20779 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
20733 GCAGCAACAG
20743 TTTTTCTTCTTCTTCCTTC
1 TTTTTCTTCTTCTTCCTTC
20762 TTTTTCTTCTTCTTCCTT
1 TTTTTCTTCTTCTTCCTT
20780 GTTCCTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTCTTCTTCTTCCTTC
Found at i:22566 original size:11 final size:11
Alignment explanation
Indices: 22550--22588 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
22540 TCGGTTGTGA
22550 GAAGAAGGAAG
1 GAAGAAGGAAG
22561 GAAGAAGGAAG
1 GAAGAAGGAAG
* *
22572 AAAGGAGGAA-
1 GAAGAAGGAAG
22582 GAAGAAG
1 GAAGAAG
22589 AAGAAACTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 5 0.21
11 19 0.79
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (11 bp):
GAAGAAGGAAG
Found at i:22923 original size:16 final size:17
Alignment explanation
Indices: 22902--22935 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
22892 TTTTATTATT
*
22902 ATTTAATATA-AAAATA
1 ATTTAAAATATAAAATA
22918 ATTTAAAATATAAAATA
1 ATTTAAAATATAAAATA
22935 A
1 A
22936 AAATAAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATATAAAATA
Found at i:31035 original size:20 final size:19
Alignment explanation
Indices: 31012--31053 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
31002 AAGTGTAGAA
31012 TAATTTA-AATACTATATTTT
1 TAATTTACAATA-TA-ATTTT
31032 TAATTTACAATATAATTTT
1 TAATTTACAATATAATTTT
31051 TAA
1 TAA
31054 AATGAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 9 0.43
21 4 0.19
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATTTACAATATAATTTT
Found at i:31114 original size:19 final size:19
Alignment explanation
Indices: 31090--31127 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31080 AACGCAATCT
31090 CAACTAGCTAAATTTTAAA
1 CAACTAGCTAAATTTTAAA
31109 CAACTAGCTAAATTTTAAA
1 CAACTAGCTAAATTTTAAA
31128 TTATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (19 bp):
CAACTAGCTAAATTTTAAA
Found at i:36035 original size:13 final size:13
Alignment explanation
Indices: 36017--36041 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36007 TCAATTCGTC
36017 ACACGTATGTATA
1 ACACGTATGTATA
36030 ACACGTATGTAT
1 ACACGTATGTAT
36042 TTTAAGAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ACACGTATGTATA
Found at i:37668 original size:39 final size:39
Alignment explanation
Indices: 37625--37746 Score: 208
Period size: 39 Copynumber: 3.1 Consensus size: 39
37615 CTCATGATTT
**
37625 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAGTCATGATAAACAATATCATACATAATAGTCA
37664 TATCAAAGTCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAGTCATGATAAACAATATCATACATAATAGTCA
* *
37703 TATCAAAGTCATGATAAACATTATCATAAATAATAGTCA
1 TATCAAAGTCATGATAAACAATATCATACATAATAGTCA
37742 TATCA
1 TATCA
37747 TATACTTTTT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.29
Consensus pattern (39 bp):
TATCAAAGTCATGATAAACAATATCATACATAATAGTCA
Found at i:37931 original size:19 final size:20
Alignment explanation
Indices: 37891--37944 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
37881 GTTTCCAAAC
*
37891 TCATAA-TTTATTTCAGATT
1 TCATAACTTAATTTCAGATT
*
37910 TCATAACTTAATTTCATA-T
1 TCATAACTTAATTTCAGATT
* *
37929 TCATAGCTTATTTTCA
1 TCATAACTTAATTTCA
37945 AGTTCATAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (20 bp):
TCATAACTTAATTTCAGATT
Found at i:37950 original size:19 final size:19
Alignment explanation
Indices: 37909--37954 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
37899 TATTTCAGAT
*
37909 TTCATAACTTAATTTCATA
1 TTCATAGCTTAATTTCATA
*
37928 TTCATAGCTTATTTTCA-A
1 TTCATAGCTTAATTTCATA
37946 GTTCATAGC
1 -TTCATAGC
37955 CCAATGCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.46
Consensus pattern (19 bp):
TTCATAGCTTAATTTCATA
Found at i:45038 original size:23 final size:24
Alignment explanation
Indices: 45007--45069 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
44997 TTTATTTCTC
45007 TATTTATTTATTTATTTCAAAT-T
1 TATTTATTTATTTATTTCAAATCT
* *
45030 TATTGATTTATTTATTTCGAATCT
1 TATTTATTTATTTATTTCAAATCT
*
45054 T-TTTATTTAATTATTT
1 TATTTATTTATTTATTT
45070 GAAGGGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 33 0.94
24 2 0.06
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (24 bp):
TATTTATTTATTTATTTCAAATCT
Found at i:45062 original size:4 final size:4
Alignment explanation
Indices: 44930--45046 Score: 58
Period size: 4 Copynumber: 27.8 Consensus size: 4
44920 GGAGGTAATT
* * *
44930 TTTA TTTA TTTA TTTA CTTTGAA TTT- TTT- TTTAA TTTT TTTGA GTAA
1 TTTA TTTA TTTA TTTA -TTT--A TTTA TTTA TTT-A TTTA TTT-A TTTA
* * * * * *
44977 TTTA TTTA TTTC TGTA ATAA TTTA TTTC TCTA TTTA TTTA TTTA TTTCAAA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT---A
*
45028 TTTA TTGA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTT
45047 CGAATCTTTT
Statistics
Matches: 84, Mismatches: 20, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
3 6 0.07
4 63 0.75
5 7 0.08
6 3 0.04
7 5 0.06
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:47250 original size:28 final size:27
Alignment explanation
Indices: 47192--47251 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
47182 AAATTTGTAA
*
47192 TTTTTTAGTTAATCAAACTCTATTTTC
1 TTTTTTAGTTAATCAAACTCCATTTTC
**
47219 TTTTTTAGTTAATTGAACTCCATTTTC
1 TTTTTTAGTTAATCAAACTCCATTTTC
47246 TTTTTT
1 TTTTTT
47252 TAAATAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.22, C:0.13, G:0.05, T:0.60
Consensus pattern (27 bp):
TTTTTTAGTTAATCAAACTCCATTTTC
Found at i:47336 original size:17 final size:17
Alignment explanation
Indices: 47290--47375 Score: 118
Period size: 18 Copynumber: 4.9 Consensus size: 17
47280 CTTTTTTTAA
47290 AATTTGTTTAAATTATT
1 AATTTGTTTAAATTATT
**
47307 AATTAACTTTAAATTATT
1 AATT-TGTTTAAATTATT
47325 AATTTGTTTAAATTATT
1 AATTTGTTTAAATTATT
*
47342 AATTAAGTTTAAATTATT
1 AATT-TGTTTAAATTATT
*
47360 AATTTGTTTAAGTTAT
1 AATTTGTTTAAATTAT
47376 CCTTGAACAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
17 29 0.48
18 31 0.52
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (17 bp):
AATTTGTTTAAATTATT
Found at i:47336 original size:35 final size:35
Alignment explanation
Indices: 47290--47375 Score: 154
Period size: 35 Copynumber: 2.5 Consensus size: 35
47280 CTTTTTTTAA
47290 AATTTGTTTAAATTATTAATTAACTTTAAATTATT
1 AATTTGTTTAAATTATTAATTAACTTTAAATTATT
*
47325 AATTTGTTTAAATTATTAATTAAGTTTAAATTATT
1 AATTTGTTTAAATTATTAATTAACTTTAAATTATT
*
47360 AATTTGTTTAAGTTAT
1 AATTTGTTTAAATTAT
47376 CCTTGAACAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (35 bp):
AATTTGTTTAAATTATTAATTAACTTTAAATTATT
Found at i:59084 original size:21 final size:21
Alignment explanation
Indices: 59059--59111 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
59049 GGAGAGGCAT
*
59059 TATCGATACTCTTCCCCTCAA
1 TATCGATACTCTCCCCCTCAA
59080 TATCGATACTCTCCCCCTCAA
1 TATCGATACTCTCCCCCTCAA
*
59101 TATTGATACTC
1 TATCGATACTC
59112 CCTACTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.36, G:0.06, T:0.34
Consensus pattern (21 bp):
TATCGATACTCTCCCCCTCAA
Found at i:60195 original size:20 final size:20
Alignment explanation
Indices: 60170--60245 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
60160 TTTAGTTCAT
60170 GGAATATAAGATTATCGGTG
1 GGAATATAAGATTATCGGTG
60190 GGAATATAAGATTATCGGTG
1 GGAATATAAGATTATCGGTG
*
60210 GGAATATAAGATTATCTGTG
1 GGAATATAAGATTATCGGTG
* *
60230 GGAATGTAAAATTATC
1 GGAATATAAGATTATC
60246 ATGAAATAGG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (20 bp):
GGAATATAAGATTATCGGTG
Found at i:60753 original size:21 final size:21
Alignment explanation
Indices: 60729--60789 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
60719 TATTCGCATT
60729 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
60750 GCGAATTTGAAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
* *
60771 GCGAA-TACGTAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
60790 TGTAAATACG
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
20 10 0.30
21 23 0.70
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:60786 original size:20 final size:20
Alignment explanation
Indices: 60761--60816 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
60751 CGAATTTGAA
60761 AAATCGCAATGCGAATACGT
1 AAATCGCAATGCGAATACGT
**
60781 AAATCGCAATGTAAATACGT
1 AAATCGCAATGCGAATACGT
60801 AAATCGCAATGCGAAT
1 AAATCGCAATGCGAAT
60817 CTGGCTATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (20 bp):
AAATCGCAATGCGAATACGT
Found at i:61039 original size:22 final size:22
Alignment explanation
Indices: 61014--61077 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
61004 GGCGACATCC
61014 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
61036 GTCCTCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
*
61058 GTCTCCATCTCCGACGAAAT
1 GTCCCCATCTCCGACGAAAT
61078 TATTTACGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:61278 original size:20 final size:20
Alignment explanation
Indices: 61252--61319 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
61242 GAAATTCAGT
*
61252 ATTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGAATCAC
* * *
61272 GTTGCGATAGCCAGATTCAC
1 ATTGCGATAGTCAGAATCAC
* *
61292 ATTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGAATCAC
61312 ATTGCGAT
1 ATTGCGAT
61320 TTACATATTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (20 bp):
ATTGCGATAGTCAGAATCAC
Found at i:61329 original size:20 final size:20
Alignment explanation
Indices: 61306--61438 Score: 212
Period size: 20 Copynumber: 6.7 Consensus size: 20
61296 CGATAGTCAG
*
61306 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
61326 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
61346 ATTCGCATTGCGATTTAGGT
1 ATTCGCATTGCGATTTACGT
*
61366 AATCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
61386 ATTCGCATTGCGAATTAGGT
1 ATTCGCATTGCGATTTACGT
*
61406 AATCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
61426 ATTCGCATTGCGA
1 ATTCGCATTGCGA
61439 ATTAGAAAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 102 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:61337 original size:60 final size:59
Alignment explanation
Indices: 61273--61438 Score: 144
Period size: 60 Copynumber: 2.8 Consensus size: 59
61263 CAGAATCTCG
*
61273 TTGCGATAGCCAG-ATTCACATTGCGA-TA-GTCAGATTCGCATTGCGATTTACATATTCGCA
1 TTGCGATAGAC-GTATTCACATTGCGATTAGGT-A-A-TCGCATTGCGATTTACATATTCGCA
** * *
61333 TTGCGATTTACGTATTCGCATTGCGATTTAGGTAATCGCATTGCGATTTACGTATTCGCA
1 TTGCGATAGACGTATTCACATTGCGA-TTAGGTAATCGCATTGCGATTTACATATTCGCA
* * * *
61393 TTGCGAATTAG--GTAATCGCATTGCGATTTACGTATTCGCATTGCGA
1 TTGCG-A-TAGACGTATTCACATTGCGA-TTAGGTAATCGCATTGCGA
61439 ATTAGAAAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
59 1 0.01
60 81 0.90
61 2 0.02
62 4 0.04
63 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (59 bp):
TTGCGATAGACGTATTCACATTGCGATTAGGTAATCGCATTGCGATTTACATATTCGCA
Found at i:61459 original size:21 final size:21
Alignment explanation
Indices: 61435--61489 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
61425 TATTCGCATT
61435 GCGAATTAGAAAAATCGCAAC
1 GCGAATTAGAAAAATCGCAAC
* * *
61456 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGAAAAATCGCAAC
61477 GCGATAGTTAGAA
1 GCGA-A-TTAGAA
61490 TCGCGTTGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.81
22 1 0.04
23 4 0.15
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.20
Consensus pattern (21 bp):
GCGAATTAGAAAAATCGCAAC
Found at i:61559 original size:19 final size:19
Alignment explanation
Indices: 61535--61578 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
61525 GGAGATTACG
61535 TTGCGAATTATCGATCGCA
1 TTGCGAATTATCGATCGCA
61554 TTGCGAATTATCGATCGCA
1 TTGCGAATTATCGATCGCA
61573 TTGCGA
1 TTGCGA
61579 TTTAGTTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (19 bp):
TTGCGAATTATCGATCGCA
Found at i:68385 original size:60 final size:60
Alignment explanation
Indices: 68308--68460 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
68298 AAAGTTCAAA
* * * *
68308 AAGGATCAATTTAGAATGAAGGTCATAGTTTGGGGATGAAATTGAAATATTCAAAATTTT
1 AAGGATCAATTTAGAATGAAGGTCATAATTTGAGGATGAAATTAAAATATTCAAAAGTTT
* * * *
68368 AAGGACCAATTTAGAATGATA-GTCAAAATTTAAGGATGAAATTAAAATATTTAAAAGTTT
1 AAGGATCAATTTAGAATGA-AGGTCATAATTTGAGGATGAAATTAAAATATTCAAAAGTTT
* * * *
68428 AGGGATTAATTTA-AAGTGAAGGTAATATTTTGA
1 AAGGATCAATTTAGAA-TGAAGGTCATAATTTGA
68461 AGAATGTGAT
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
59 3 0.04
60 71 0.95
61 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (60 bp):
AAGGATCAATTTAGAATGAAGGTCATAATTTGAGGATGAAATTAAAATATTCAAAAGTTT
Found at i:68766 original size:14 final size:12
Alignment explanation
Indices: 68747--68827 Score: 66
Period size: 14 Copynumber: 6.8 Consensus size: 12
68737 TGAATGTTCG
68747 GTTATGTTCGTAC
1 GTTATGTTCGT-C
68760 AGTTATGTTCGT-
1 -GTTATGTTCGTC
68772 -TTATGTTCGTTC
1 GTTATGTTCG-TC
68784 GGTTATGTTCGT-
1 -GTTATGTTCGTC
68796 -TTATGTTCGTTC
1 GTTATGTTCG-TC
68808 GGTTATGTTCGT-
1 -GTTATGTTCGTC
68820 -TTATGTTC
1 GTTATGTTC
68828 ATTCATTTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 20
0.75 0.00 0.25
Matches are distributed among these distances:
10 26 0.44
11 2 0.03
13 2 0.03
14 29 0.49
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.53
Consensus pattern (12 bp):
GTTATGTTCGTC
Found at i:68767 original size:24 final size:24
Alignment explanation
Indices: 68740--68827 Score: 149
Period size: 24 Copynumber: 3.7 Consensus size: 24
68730 ACGTTCGTGA
* * *
68740 ATGTTCGGTTATGTTCGTACAGTT
1 ATGTTCGTTTATGTTCGTTCGGTT
68764 ATGTTCGTTTATGTTCGTTCGGTT
1 ATGTTCGTTTATGTTCGTTCGGTT
68788 ATGTTCGTTTATGTTCGTTCGGTT
1 ATGTTCGTTTATGTTCGTTCGGTT
68812 ATGTTCGTTTATGTTC
1 ATGTTCGTTTATGTTC
68828 ATTCATTTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.11, C:0.12, G:0.24, T:0.52
Consensus pattern (24 bp):
ATGTTCGTTTATGTTCGTTCGGTT
Found at i:68783 original size:48 final size:48
Alignment explanation
Indices: 68718--68827 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 48
68708 CATAGGTCTC
*
68718 GTTCGTTCAT-TTACGTTC-GTGAATGTTCGGTTATGTTCGTACAGTTAT
1 GTTCGTTTATGTT-CGTTCGGT-AATGTTCGGTTATGTTCGTACAGTTAT
* * * *
68766 GTTCGTTTATGTTCGTTCGGTTATGTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTAATGTTCGGTTATGTTCGTACAGTTAT
68814 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
68828 ATTCATTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 51 0.93
49 4 0.07
ACGTcount: A:0.12, C:0.14, G:0.24, T:0.51
Consensus pattern (48 bp):
GTTCGTTTATGTTCGTTCGGTAATGTTCGGTTATGTTCGTACAGTTAT
Found at i:68837 original size:24 final size:24
Alignment explanation
Indices: 68740--68840 Score: 148
Period size: 24 Copynumber: 4.2 Consensus size: 24
68730 ACGTTCGTGA
* *
68740 ATGTTCGGTTATGTTCGTACAGTT
1 ATGTTCGTTTATGTTCGTTCAGTT
*
68764 ATGTTCGTTTATGTTCGTTCGGTT
1 ATGTTCGTTTATGTTCGTTCAGTT
*
68788 ATGTTCGTTTATGTTCGTTCGGTT
1 ATGTTCGTTTATGTTCGTTCAGTT
* *
68812 ATGTTCGTTTATGTTCATTCATTT
1 ATGTTCGTTTATGTTCGTTCAGTT
68836 ATGTT
1 ATGTT
68841 TAACCCAATC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.13, C:0.12, G:0.22, T:0.53
Consensus pattern (24 bp):
ATGTTCGTTTATGTTCGTTCAGTT
Found at i:69798 original size:16 final size:17
Alignment explanation
Indices: 69779--69819 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
69769 TTCGTTTATG
69779 TTTATGTTC-ATGTTCA
1 TTTATGTTCTATGTTCA
* *
69795 TTTATG-TCTGTGTTCG
1 TTTATGTTCTATGTTCA
69811 TTTATGTTC
1 TTTATGTTC
69820 GTTTATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 2 0.10
16 17 0.81
17 2 0.10
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (17 bp):
TTTATGTTCTATGTTCA
Found at i:69808 original size:22 final size:22
Alignment explanation
Indices: 69766--69809 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
69756 TCCAACGTTT
* *
69766 ATGTTCGTTTATGTTTATGTTC
1 ATGTTCATTTATGTCTATGTTC
*
69788 ATGTTCATTTATGTCTGTGTTC
1 ATGTTCATTTATGTCTATGTTC
69810 GTTTATGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.57
Consensus pattern (22 bp):
ATGTTCATTTATGTCTATGTTC
Found at i:69911 original size:16 final size:16
Alignment explanation
Indices: 69890--69922 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
69880 AAAAAAAAAT
69890 TGTTCGTTTATATTCG
1 TGTTCGTTTATATTCG
*
69906 TGTTCGTTTATGTTCG
1 TGTTCGTTTATATTCG
69922 T
1 T
69923 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATATTCG
Found at i:71438 original size:21 final size:21
Alignment explanation
Indices: 71413--71456 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
71403 TTTCAGCATT
71413 TTTCAAAGCCAATATCGAGAA
1 TTTCAAAGCCAATATCGAGAA
71434 TTTCAAAGCCAATATCGAGAA
1 TTTCAAAGCCAATATCGAGAA
71455 TT
1 TT
71457 AATTTGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (21 bp):
TTTCAAAGCCAATATCGAGAA
Done.