Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000042.1 Hibiscus syriacus cultivar Beakdansim tig00000064_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: 66021
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:185 original size:21 final size:21
Alignment explanation
Indices: 161--201 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
151 TCACTTGATT
161 TTATGACTTGTTTTGAATATG
1 TTATGACTTGTTTTGAATATG
182 TTATGACTTGTTTTGAATAT
1 TTATGACTTGTTTTGAATAT
202 AACTTGTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.05, G:0.17, T:0.54
Consensus pattern (21 bp):
TTATGACTTGTTTTGAATATG
Found at i:7341 original size:23 final size:23
Alignment explanation
Indices: 7289--7341 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
7279 AAGTCCGATG
*
7289 TATTTA-ATTCGTGTCGGCTACA
1 TATTTATATTCGTGTCGGATACA
** *
7311 TAAATATATTTGTGTCGGATACA
1 TATTTATATTCGTGTCGGATACA
7334 TATTTATA
1 TATTTATA
7342 CATACCATTG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (23 bp):
TATTTATATTCGTGTCGGATACA
Found at i:9190 original size:60 final size:60
Alignment explanation
Indices: 9078--9190 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 60
9068 ACTATAACTC
* ** * * **
9078 TCATTTTAAATTAGTCCTTAAACTTTTGAACATTCTAATTTTATCCTTAAATTAATAAAA
1 TCATTTTAAACTAGTCCCCAAACTTTTGAACATTCCAATTTCATCCCCAAATTAATAAAA
* **
9138 TCATTTTAAACTGGTCCCCAAACTTTTGAATGTTCCAATTTCATCCCCAAATT
1 TCATTTTAAACTAGTCCCCAAACTTTTGAACATTCCAATTTCATCCCCAAATT
9191 CATCCAAATA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 43 1.00
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (60 bp):
TCATTTTAAACTAGTCCCCAAACTTTTGAACATTCCAATTTCATCCCCAAATTAATAAAA
Found at i:17433 original size:23 final size:23
Alignment explanation
Indices: 17403--17452 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
17393 TCTCAGATTT
* *
17403 AACTTGGTTGAAGCTTAAATTCG
1 AACTTGGTTCAAGCTTAAACTCG
*
17426 AACTTGGTTCAAGTTTAAACTCG
1 AACTTGGTTCAAGCTTAAACTCG
17449 AACT
1 AACT
17453 CAAACATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (23 bp):
AACTTGGTTCAAGCTTAAACTCG
Found at i:19069 original size:50 final size:51
Alignment explanation
Indices: 18956--19069 Score: 117
Period size: 50 Copynumber: 2.3 Consensus size: 51
18946 GATTTGGCGT
* * * * *
18956 CACGTGGGGTATAGCGCGCCCCTTGCATCGCGCTATACGCTAGCTGGGTTA
1 CACGTGGGGTATAGCACGCCCCCTGCATCGCGCTATACGCTAGCTAGCTGA
* ** *
19007 CACGT-GGCTATAGCACGCCCCCTGC-TCCGCGCTATAC-CTATTTATCTGA
1 CACGTGGGGTATAGCACGCCCCCTGCAT-CGCGCTATACGCTAGCTAGCTGA
19056 CACGTGGGGTATAG
1 CACGTGGGGTATAG
19070 AGCGGTGCAG
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
49 12 0.24
50 34 0.67
51 5 0.10
ACGTcount: A:0.18, C:0.31, G:0.27, T:0.25
Consensus pattern (51 bp):
CACGTGGGGTATAGCACGCCCCCTGCATCGCGCTATACGCTAGCTAGCTGA
Found at i:19272 original size:17 final size:18
Alignment explanation
Indices: 19235--19275 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
19225 ATGTTATGTA
*
19235 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
19253 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
19270 TTTACT
1 TTTACT
19276 AATATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:19998 original size:26 final size:25
Alignment explanation
Indices: 19912--19998 Score: 74
Period size: 25 Copynumber: 3.5 Consensus size: 25
19902 AGATTTTTTT
* * *
19912 TTTTATTATATTTGTATTTACTTTA
1 TTTTGTTAAATTTATATTTACTTTA
19937 TTTTGTTAAATTGTA-ATTT--TTTA
1 TTTTGTTAAATT-TATATTTACTTTA
**
19960 TTATT-TTTCATTTAATATTTACTTTA
1 TT-TTGTTAAATTT-ATATTTACTTTA
19986 TTTTGTTAAATTT
1 TTTTGTTAAATTT
19999 GTTGGACTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
22 1 0.02
23 12 0.25
24 6 0.12
25 16 0.33
26 13 0.27
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.67
Consensus pattern (25 bp):
TTTTGTTAAATTTATATTTACTTTA
Found at i:21397 original size:20 final size:21
Alignment explanation
Indices: 21372--21411 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
21362 AATTTAACAG
*
21372 GATACTTTAATTT-ATAATAT
1 GATACTTCAATTTAATAATAT
21392 GATACTTCAATTTAATAATA
1 GATACTTCAATTTAATAATA
21412 AAATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (21 bp):
GATACTTCAATTTAATAATAT
Found at i:23022 original size:2 final size:2
Alignment explanation
Indices: 23015--23044 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
23005 CTTTACAATA
23015 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23045 AATTTAGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23723 original size:30 final size:30
Alignment explanation
Indices: 23687--23759 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
23677 TTCGAATGAC
23687 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
23717 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
23747 CTATACATAGGTC
1 CTATCCAGAGGTC
23760 CCGAAAAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:24933 original size:19 final size:19
Alignment explanation
Indices: 24909--24955 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
24899 TAGCATGTGT
24909 ATCGATGCAGTACCCGTGC
1 ATCGATGCAGTACCCGTGC
24928 ATCGATGCAGTACCCGTGC
1 ATCGATGCAGTACCCGTGC
24947 ATCGATGCA
1 ATCGATGCA
24956 CAAATCACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (19 bp):
ATCGATGCAGTACCCGTGC
Found at i:25012 original size:64 final size:63
Alignment explanation
Indices: 24944--25063 Score: 168
Period size: 64 Copynumber: 1.9 Consensus size: 63
24934 GCAGTACCCG
* * *
24944 TGCATCGATGCACAAATCACCTTCGATGTTTTCATTTTAAGGGGATGCATCGATGCACTCCTTA
1 TGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAGG-TGCATCGATGCACTCCTTA
* ** *
25008 TGCATCGATGCACCAATTGCATTCGATGTTTCCATTTTAATAGGTGCATCGATGCA
1 TGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAGGTGCATCGATGCA
25064 TTTCCTGTGC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 12 0.24
64 37 0.76
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (63 bp):
TGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAGGTGCATCGATGCACTCCTTA
Found at i:31321 original size:26 final size:26
Alignment explanation
Indices: 31292--31341 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
31282 AGTGCATATG
**
31292 GTGGGCATGACCTTATGTGTATTATT
1 GTGGGCACAACCTTATGTGTATTATT
31318 GTGGGCACAACCTTATGTGTATTA
1 GTGGGCACAACCTTATGTGTATTA
31342 GCACTTCGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (26 bp):
GTGGGCACAACCTTATGTGTATTATT
Found at i:35777 original size:21 final size:22
Alignment explanation
Indices: 35752--35794 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
35742 ATTATTTGTT
*
35752 AAAATAAATTTAAA-AAATAAA
1 AAAATAAATATAAACAAATAAA
35773 AAAATAAATATAAACAAATAAA
1 AAAATAAATATAAACAAATAAA
35795 TTAGAGAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAATAAATATAAACAAATAAA
Found at i:35839 original size:98 final size:98
Alignment explanation
Indices: 35727--35911 Score: 300
Period size: 98 Copynumber: 1.9 Consensus size: 98
35717 ATGGATAGAA
* *
35727 AATTATTAGTAGAATATTA-TTTGTTAAAATAAATTTAAAAAATAAAAAAATAAATATAAACAAA
1 AATTATCAGTAGAATATTATTTTGTTAAAATAAATTTAAAAAAT-AAAAAAGAAATATAAACAAA
*
35791 TAAATTAGAGAGTATGGATAGAATAAAAATATTC
65 GAAATTAGAGAGTATGGATAGAATAAAAATATTC
* * *
35825 AATTATCAGTAGAATATTATTTTTTTTAAATAAATTTAAAAAATAAAAAAGAAATCTAAACAAAG
1 AATTATCAGTAGAATATTATTTTGTTAAAATAAATTTAAAAAATAAAAAAGAAATATAAACAAAG
35890 AAATTAGAGAGTATGGATAGAA
66 AAATTAGAGAGTATGGATAGAA
35912 CATTAATAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
98 58 0.73
99 22 0.28
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (98 bp):
AATTATCAGTAGAATATTATTTTGTTAAAATAAATTTAAAAAATAAAAAAGAAATATAAACAAAG
AAATTAGAGAGTATGGATAGAATAAAAATATTC
Found at i:40287 original size:16 final size:17
Alignment explanation
Indices: 40228--40287 Score: 52
Period size: 19 Copynumber: 3.4 Consensus size: 17
40218 ATAAGAATTA
*
40228 TATAACTATTTTTATAAT
1 TATAA-TATTTATATAAT
*
40246 TATAATGATTTTTTATAAT
1 TATAAT-A-TTTATATAAT
40265 TGA-AATA-TTATATAAT
1 T-ATAATATTTATATAAT
40281 TATAATA
1 TATAATA
40288 GCAATGTTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
15 1 0.03
16 13 0.35
17 1 0.03
18 7 0.19
19 14 0.38
20 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
TATAATATTTATATAAT
Found at i:45615 original size:5 final size:5
Alignment explanation
Indices: 45605--45636 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
45595 TAGGGGTGTA
45605 TTCGG TTCGG TTCGG TTCGG TTCGG TTCGG TT
1 TTCGG TTCGG TTCGG TTCGG TTCGG TTCGG TT
45637 TTTTACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.00, C:0.19, G:0.38, T:0.44
Consensus pattern (5 bp):
TTCGG
Found at i:45791 original size:18 final size:18
Alignment explanation
Indices: 45734--45799 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
45724 ACCGAAACCA
45734 GTTTTATCGGTTCGGTTCG
1 GTTTT-TCGGTTCGGTTCG
45753 GTTTTT---TTAACGGTTCAG
1 GTTTTTCGGTT--CGGTTC-G
45771 GTTTTTCGGTTCGGTTCG
1 GTTTTTCGGTTCGGTTCG
*
45789 GTTTTTTGGTT
1 GTTTTTCGGTT
45800 TTTCAATGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
15 2 0.05
17 6 0.15
18 19 0.47
19 11 0.28
21 2 0.05
ACGTcount: A:0.06, C:0.12, G:0.29, T:0.53
Consensus pattern (18 bp):
GTTTTTCGGTTCGGTTCG
Found at i:47171 original size:79 final size:80
Alignment explanation
Indices: 47013--47173 Score: 216
Period size: 79 Copynumber: 2.0 Consensus size: 80
47003 ATTAATATTT
* * * ** **
47013 TTTAATATTTCTGGTAAAGCGCTACCTAAAACATTATTTTTTTCTACTTAAAATGTTAATATCGG
1 TTTAACATTTCTGGTAAAGCGATACCTAAAACATTATCTTTTTCTACCGAAAATGTTAATATCAA
* *
47078 GCTCTACCTAAAATG
66 ACGCTACCTAAAATG
* *
47093 TTTAACATTTCTGGTAAAGCGATACCTAAAATATTA-CTTTTTCTACCGGAAATGTTAATATCAA
1 TTTAACATTTCTGGTAAAGCGATACCTAAAACATTATCTTTTTCTACCGAAAATGTTAATATCAA
47157 ACGCTACCTAAAATG
66 ACGCTACCTAAAATG
47172 TT
1 TT
47174 ATTTTTTCTA
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
79 37 0.53
80 33 0.47
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (80 bp):
TTTAACATTTCTGGTAAAGCGATACCTAAAACATTATCTTTTTCTACCGAAAATGTTAATATCAA
ACGCTACCTAAAATG
Found at i:49961 original size:11 final size:11
Alignment explanation
Indices: 49945--49970 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
49935 TTTAGCCATC
49945 TTGATATCTGT
1 TTGATATCTGT
49956 TTGATATCTGT
1 TTGATATCTGT
49967 TTGA
1 TTGA
49971 AAACCCATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (11 bp):
TTGATATCTGT
Found at i:51009 original size:19 final size:19
Alignment explanation
Indices: 50981--51018 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
50971 TGATAAATTA
*
50981 TTATTTAAAATATTATTTT
1 TTATTAAAAATATTATTTT
51000 TTATTAAAAATATTATTTT
1 TTATTAAAAATATTATTTT
51019 CGCTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTAAAAATATTATTTT
Found at i:51109 original size:77 final size:77
Alignment explanation
Indices: 51037--51182 Score: 192
Period size: 79 Copynumber: 1.9 Consensus size: 77
51027 AATTTTTGGT
*
51037 ATAA-CTCAATATTAATA-TTTTCAGTAAAAAAAAT-TATTTTAAATA-ACACTTTATCGAAAAT
1 ATAATCTCAATATTAACATTTTTCA-TAAAAAAAATATATTTTAAATATA-ACTTTATCGAAAAT
51098 ATTAAATATTTTAG
64 ATTAAATATTTTAG
* *
51112 ATAATTCTTAATATTAACATTTTTTATAAAAAAAATAATATTTTAAATATAACTTTATCGAAAAT
1 ATAA-TCTCAATATTAACATTTTTCATAAAAAAAAT-ATATTTTAAATATAACTTTATCGAAAAT
*
51177 GTTAAA
64 ATTAAA
51183 AAAATAATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
75 4 0.07
77 21 0.34
78 5 0.08
79 30 0.49
80 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (77 bp):
ATAATCTCAATATTAACATTTTTCATAAAAAAAATATATTTTAAATATAACTTTATCGAAAATAT
TAAATATTTTAG
Found at i:54160 original size:16 final size:16
Alignment explanation
Indices: 54106--54158 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
54096 GATATTACTC
54106 GACCTATTTTCAACCT
1 GACCTATTTTCAACCT
* * *
54122 GACCTATTATGAACCC
1 GACCTATTTTCAACCT
*
54138 GACCTGTTTTCAACCT
1 GACCTATTTTCAACCT
54154 GACCT
1 GACCT
54159 GTAAATGATT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.25, C:0.32, G:0.11, T:0.32
Consensus pattern (16 bp):
GACCTATTTTCAACCT
Found at i:54339 original size:40 final size:40
Alignment explanation
Indices: 54268--54465 Score: 131
Period size: 40 Copynumber: 5.0 Consensus size: 40
54258 AAAATTGAGT
* * *
54268 TTATAATAAACCATACTAATTAAT-ATGATTAAATTTTAAATG
1 TTATAATAAA--ATATTAATT-ATGATAATTAAATTATAAATG
54310 TTATAATAAAATATTAATTATGATAATTAAATTGATAAAT-
1 TTATAATAAAATATTAATTATGATAATTAAATT-ATAAATG
* * ** ** * * * *
54350 ATAT-TTATTATATTAATTATGATTCTTATATTATGATTC
1 TTATAATAAAATATTAATTATGATAATTAAATTATAAATG
** * *
54389 TTATGTTATAAATCTTAA-TATG---ATTAAATTTTAAATG
1 TTATAATA-AAATATTAATTATGATAATTAAATTATAAATG
*
54426 TTATAAAAAAATATTAATTATGATAATTAAATTGATAAAT
1 TTATAATAAAATATTAATTATGATAATTAAATT-ATAAAT
54466 AGATTTATTA
Statistics
Matches: 119, Mismatches: 27, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
36 8 0.07
37 18 0.15
38 4 0.03
39 27 0.23
40 36 0.30
41 16 0.13
42 10 0.08
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (40 bp):
TTATAATAAAATATTAATTATGATAATTAAATTATAAATG
Found at i:54369 original size:39 final size:40
Alignment explanation
Indices: 54295--54488 Score: 107
Period size: 39 Copynumber: 5.0 Consensus size: 40
54285 AATTAATATG
* ** * *
54295 ATTAAATTTTAAATGTTATAATAAAATATTAATTATGATA
1 ATTAAATTATAAATCATATATTATAATATTAATTATGATA
* *
54335 ATTAAATTGATAAAT-ATAT-TTATTATATTAATTATGATT
1 ATTAAATT-ATAAATCATATATTATAATATTAATTATGATA
* * * * * * *
54374 CTTATATTATGATTCTTATGTTATAAATCTTAA-TATG---
1 ATTAAATTATAAATCATATATTAT-AATATTAATTATGATA
* ** ** *
54411 ATTAAATTTTAAATGTTATAAAAAAATATTAATTATGATA
1 ATTAAATTATAAATCATATATTATAATATTAATTATGATA
* *
54451 ATTAAATTGATAAAT-AGAT-TTATTATATTAATTATGAT
1 ATTAAATT-ATAAATCATATATTATAATATTAATTATGAT
54489 TCTTATATTC
Statistics
Matches: 114, Mismatches: 31, Indels: 19
0.70 0.19 0.12
Matches are distributed among these distances:
36 7 0.06
37 18 0.16
38 4 0.04
39 40 0.35
40 29 0.25
41 16 0.14
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (40 bp):
ATTAAATTATAAATCATATATTATAATATTAATTATGATA
Found at i:54384 original size:14 final size:14
Alignment explanation
Indices: 54365--54397 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
54355 TATTATATTA
54365 ATTATGATTCTTAT
1 ATTATGATTCTTAT
54379 ATTATGATTCTTAT
1 ATTATGATTCTTAT
*
54393 GTTAT
1 ATTAT
54398 AAATCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (14 bp):
ATTATGATTCTTAT
Found at i:54432 original size:16 final size:17
Alignment explanation
Indices: 54390--54432 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
54380 TTATGATTCT
54390 TATGTTATAAATCTTAA
1 TATGTTATAAATCTTAA
* *
54407 TATGAT-TAAATTTTAA
1 TATGTTATAAATCTTAA
54423 -ATGTTATAAA
1 TATGTTATAAA
54433 AAAATATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 4 0.18
16 13 0.59
17 5 0.23
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (17 bp):
TATGTTATAAATCTTAA
Found at i:54452 original size:116 final size:116
Alignment explanation
Indices: 54287--54520 Score: 441
Period size: 116 Copynumber: 2.0 Consensus size: 116
54277 ACCATACTAA
* *
54287 TTAATATGATTAAATTTTAAATGTTATAATAAAATATTAATTATGATAATTAAATTGATAAATAT
1 TTAATATGATTAAATTTTAAATGTTATAAAAAAATATTAATTATGATAATTAAATTGATAAATAG
54352 ATTTATTATATTAATTATGATTCTTATATTATGATTCTTATGTTATAAATC
66 ATTTATTATATTAATTATGATTCTTATATTATGATTCTTATGTTATAAATC
54403 TTAATATGATTAAATTTTAAATGTTATAAAAAAATATTAATTATGATAATTAAATTGATAAATAG
1 TTAATATGATTAAATTTTAAATGTTATAAAAAAATATTAATTATGATAATTAAATTGATAAATAG
*
54468 ATTTATTATATTAATTATGATTCTTATATTCTGATTCTTATGTTATAAATC
66 ATTTATTATATTAATTATGATTCTTATATTATGATTCTTATGTTATAAATC
54519 TT
1 TT
54521 CGATATAATC
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (116 bp):
TTAATATGATTAAATTTTAAATGTTATAAAAAAATATTAATTATGATAATTAAATTGATAAATAG
ATTTATTATATTAATTATGATTCTTATATTATGATTCTTATGTTATAAATC
Found at i:54770 original size:12 final size:12
Alignment explanation
Indices: 54753--54787 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
54743 GATAATGTAA
54753 ATAAAATTTGAT
1 ATAAAATTTGAT
54765 ATAAAATTTGA-
1 ATAAAATTTGAT
*
54776 ATAACATTTGAT
1 ATAAAATTTGAT
54788 TTATTACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.40
Consensus pattern (12 bp):
ATAAAATTTGAT
Found at i:54784 original size:11 final size:11
Alignment explanation
Indices: 54752--54786 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
54742 TGATAATGTA
54752 AATAAAATTTG
1 AATAAAATTTG
54763 ATATAAAATTTG
1 A-ATAAAATTTG
*
54775 AATAACATTTG
1 AATAAAATTTG
54786 A
1 A
54787 TTTATTACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (11 bp):
AATAAAATTTG
Found at i:62942 original size:40 final size:40
Alignment explanation
Indices: 62886--62962 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
62876 AATAAATGCA
* * *
62886 TACGAATTAGAGATCATG-TGTTAGGTTTGTTTTTAAAAAG
1 TACGAATTAAAGATCATGCGGTTAGGATT-TTTTTAAAAAG
*
62926 TACGAATTAAATATCATGCGGTTAGGATTTTTTTAAA
1 TACGAATTAAAGATCATGCGGTTAGGATTTTTTTAAA
62963 TGACAAAGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 24 0.75
41 8 0.25
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (40 bp):
TACGAATTAAAGATCATGCGGTTAGGATTTTTTTAAAAAG
Done.