Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005268.1 Hibiscus syriacus cultivar Beakdansim tig00011913_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: 47218
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:7937 original size:20 final size:20
Alignment explanation
Indices: 7872--7943 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
7862 TCATGTAGAG
*
7872 AGTATCGATACTGAGGGTTGG
1 AGTATCGATACTGAGGGTT-T
* ****
7893 AGTTTCGATACTGACCCCTT
1 AGTATCGATACTGAGGGTTT
*
7913 GGTATCGATACTGAGGGTTT
1 AGTATCGATACTGAGGGTTT
7933 AGTATCGATAC
1 AGTATCGATAC
7944 CCAATGCTCA
Statistics
Matches: 38, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
20 24 0.63
21 14 0.37
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.32
Consensus pattern (20 bp):
AGTATCGATACTGAGGGTTT
Found at i:8028 original size:20 final size:20
Alignment explanation
Indices: 7968--8038 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
7958 TGAGACCAGA
* * *
7968 TGGTTTCCATACCGAAGGAA
1 TGGTCTCCATACCAAAGGAC
* **
7988 TGGTCTTCATACCATTGGAC
1 TGGTCTCCATACCAAAGGAC
*
8008 TGGTCTCCATACCAAAAGAC
1 TGGTCTCCATACCAAAGGAC
*
8028 TGGTATCCATA
1 TGGTCTCCATA
8039 TCGAAGATTG
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (20 bp):
TGGTCTCCATACCAAAGGAC
Found at i:9145 original size:32 final size:32
Alignment explanation
Indices: 9097--9176 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
9087 TGGTCAAGTT
* * * *
9097 TGCATTCAGATGATGCATAGTATGTTCACGTG
1 TGCATTTAGATAATGCATAATATGTTCACGTC
*
9129 TGCATTTAGATAATGCATAATATGTTCAGGTC
1 TGCATTTAGATAATGCATAATATGTTCACGTC
**
9161 TATATTTAGATAATGC
1 TGCATTTAGATAATGC
9177 GTAGCAATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (32 bp):
TGCATTTAGATAATGCATAATATGTTCACGTC
Found at i:11171 original size:22 final size:22
Alignment explanation
Indices: 11139--11224 Score: 163
Period size: 22 Copynumber: 3.9 Consensus size: 22
11129 AGTCGAGGGT
*
11139 TACATAAGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
11161 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
11183 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
11205 TACATAGGTCCTTCGGGACA
1 TACATAGGTCCTTCGGGACA
11225 AATTTCATAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:13783 original size:21 final size:19
Alignment explanation
Indices: 13729--13798 Score: 50
Period size: 21 Copynumber: 3.4 Consensus size: 19
13719 TATATATATA
13729 TATTTTAAAATTTATTGATT
1 TATTTTAAAA-TTATTGATT
* * *
13749 AAATTTATATATTATGTGAGTT
1 TATTTTA-AAATTAT-TGA-TT
*
13771 TATTTTAAAATTAAATTGATA
1 TATTTTAAAATT--ATTGATT
13792 TATTTTA
1 TATTTTA
13799 TGATTATATG
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 9 0.24
21 17 0.45
22 10 0.26
23 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (19 bp):
TATTTTAAAATTATTGATT
Found at i:14371 original size:26 final size:27
Alignment explanation
Indices: 14332--14396 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
14322 TTTGATTCCT
*
14332 AAAAATTATAAAAATTAAAC-TCAAATTA
1 AAAAATT-T-AAAAGTAAACATCAAATTA
*
14360 AAAAATTTAAAAGTAAGCATCAAATTA
1 AAAAATTTAAAAGTAAACATCAAATTA
*
14387 AAAACTTTAA
1 AAAAATTTAA
14397 TTATATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.24
27 18 0.55
28 7 0.21
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (27 bp):
AAAAATTTAAAAGTAAACATCAAATTA
Found at i:14933 original size:2 final size:2
Alignment explanation
Indices: 14926--14990 Score: 76
Period size: 2 Copynumber: 32.0 Consensus size: 2
14916 GTTATTTTGT
* *
14926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TT TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
14969 TA TG TA TA CA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
14991 GTAATATAGG
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:15104 original size:37 final size:37
Alignment explanation
Indices: 15029--15308 Score: 237
Period size: 37 Copynumber: 7.5 Consensus size: 37
15019 CAAAATGTAA
* * * *
15029 TATATAATTTTCAGAAAACGATTTTCGAAAATTTATATAT
1 TATATAGTTTTTA-AAAAC-ATTTT-TAAAAATTATATAT
* * *
15069 TATATAGTTTTTAAAAATATTTTTAAAAAATATATAA
1 TATATAGTTTTTAAAAACATTTTTAAAAATTATATAT
* * * *
15106 TATATAG-TTTTGAAAATATTTTGAAAACATTTATATGT
1 TATATAGTTTTTAAAAACATTTTTAAAA-A-TTATATAT
* * *
15144 TATATAGTTTTT-AAAACATTTTGAAAACTTATATAA
1 TATATAGTTTTTAAAAACATTTTTAAAAATTATATAT
* * *
15180 TATATAGGTTTTAAAAGCATTTTTGAAAAATTATATAA
1 TATATAGTTTTTAAAAACATTTTT-AAAAATTATATAT
* * * *
15218 TGTATAG-TTTAAAAAACAGTTTTGAAAATTTATATAT
1 TATATAGTTTTTAAAAACA-TTTTTAAAAATTATATAT
*
15255 AATATATGTTTTTAAAAAACATTTTT-AAAATT-TATAT
1 TATATA-GTTTTT-AAAAACATTTTTAAAAATTATATAT
*
15292 TATATAGTTTTTTAAAA
1 TATATAGTTTTTAAAAA
15309 TATATTTATT
Statistics
Matches: 198, Mismatches: 33, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
35 4 0.02
36 41 0.21
37 61 0.31
38 59 0.30
39 15 0.08
40 18 0.09
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (37 bp):
TATATAGTTTTTAAAAACATTTTTAAAAATTATATAT
Found at i:15149 original size:38 final size:36
Alignment explanation
Indices: 15061--15271 Score: 178
Period size: 38 Copynumber: 5.6 Consensus size: 36
15051 TTTCGAAAAT
* *
15061 TTATATATTATATAGTTTTTAAAAATATTTTTAAAA-A
1 TTATATAATATATAG-TTTT-AAAATATTTTGAAAACA
*
15098 ATATATAATATATAGTTTTGAAAATATTTTGAAAACA
1 TTATATAATATATAGTTTT-AAAATATTTTGAAAACA
** *
15135 TTTATATGTTATATAGTTTTTAAAACATTTTGAAAAC-
1 -TTATATAATATATAG-TTTTAAAATATTTTGAAAACA
*
15172 TTATATAATATATAGGTTTTAAAAGCATTTTTGAAAA-A
1 TTATATAATATATA-GTTTTAAAA-TA-TTTTGAAAACA
* * * **
15210 TTATATAATGTATAGTTTAAAAAACAGTTTTGAAAATT
1 TTATATAATATATAGTTT-TAAAATA-TTTTGAAAACA
15248 TATATATAATATAT-GTTTTTAAAA
1 T-TATATAATATATAG-TTTTAAAA
15272 AACATTTTTA
Statistics
Matches: 147, Mismatches: 16, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
36 38 0.26
37 32 0.22
38 59 0.40
39 18 0.12
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (36 bp):
TTATATAATATATAGTTTTAAAATATTTTGAAAACA
Found at i:16494 original size:19 final size:18
Alignment explanation
Indices: 16468--16515 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
16458 TCCTTTAAAC
16468 TTTTTTTAGTTATTTTTT
1 TTTTTTTAGTTATTTTTT
16486 TTCTTTTTA---ATTTTTT
1 TT-TTTTTAGTTATTTTTT
*
16502 TTGTTTTAGTTATT
1 TTTTTTTAGTTATT
16516 CAATTTCCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
15 5 0.20
16 9 0.36
18 5 0.20
19 6 0.24
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.79
Consensus pattern (18 bp):
TTTTTTTAGTTATTTTTT
Found at i:16639 original size:29 final size:28
Alignment explanation
Indices: 16607--16709 Score: 73
Period size: 30 Copynumber: 3.4 Consensus size: 28
16597 TTTATTTTTC
16607 TTTTATTTTATTTCATTCATTTTTTATTA
1 TTTTATTTTATTTC-TTCATTTTTTATTA
** **
16636 TTTTTATTTT-TTTCTTTCCCTTTGGATTTA
1 -TTTTATTTTATTTC-TTCATTTTTTA-TTA
* *
16666 TTTAATGTTTTATTTTCTTCATTGTCTTATTA
1 TTT--TATTTTA-TTTCTTCATT-TTTTATTA
16698 TTTTATTTTATT
1 TTTTATTTTATT
16710 ATTATTTTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 13
0.69 0.15 0.16
Matches are distributed among these distances:
29 16 0.29
30 18 0.33
31 5 0.09
32 10 0.18
33 6 0.11
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.71
Consensus pattern (28 bp):
TTTTATTTTATTTCTTCATTTTTTATTA
Found at i:16644 original size:16 final size:15
Alignment explanation
Indices: 16596--16648 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 15
16586 AATTTTATTG
*
16596 TTTTATTTTTCTTTT
1 TTTTATTTTTATTTT
16611 ATTTTATTTCATTCATTTT
1 -TTTTATTT--TT-ATTTT
16630 TTATTATTTTTATTTT
1 TT-TTATTTTTATTTT
16646 TTT
1 TTT
16649 CTTTCCCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
15 1 0.03
16 15 0.47
17 2 0.06
18 4 0.12
19 10 0.31
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATTTTTATTTT
Found at i:16746 original size:2 final size:2
Alignment explanation
Indices: 16739--16773 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16729 TCCTCTCATT
16739 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16774 CCTCTAACGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18187 original size:14 final size:14
Alignment explanation
Indices: 18170--18201 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
18160 TACATCATCT
18170 TAAATCTTAAACCC
1 TAAATCTTAAACCC
*
18184 TAAATCTTAAATCC
1 TAAATCTTAAACCC
18198 TAAA
1 TAAA
18202 CCAAACTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATCTTAAACCC
Found at i:18228 original size:14 final size:14
Alignment explanation
Indices: 18211--18241 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
18201 ACCAAACTTA
18211 AACCCCTAAACTCT
1 AACCCCTAAACTCT
*
18225 AACCCCTAAATTCT
1 AACCCCTAAACTCT
18239 AAC
1 AAC
18242 TTAAAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.23
Consensus pattern (14 bp):
AACCCCTAAACTCT
Found at i:22363 original size:20 final size:22
Alignment explanation
Indices: 22335--22374 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
22325 CGAACACCTT
22335 CAAAAATAA-A-TAAAAAAACA
1 CAAAAATAATATTAAAAAAACA
*
22355 CAAACATAATATTAAAAAAA
1 CAAAAATAATATTAAAAAAA
22375 TATAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 1 0.06
22 8 0.47
ACGTcount: A:0.75, C:0.10, G:0.00, T:0.15
Consensus pattern (22 bp):
CAAAAATAATATTAAAAAAACA
Found at i:22381 original size:22 final size:21
Alignment explanation
Indices: 22345--22386 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
22335 CAAAAATAAA
22345 TAAAAAAACACAAACATAATAT
1 TAAAAAAACACAAACA-AATAT
* *
22367 TAAAAAAATATAAACAAATA
1 TAAAAAAACACAAACAAATA
22387 CGAACAGAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAAAAAACACAAACAAATAT
Found at i:23646 original size:20 final size:20
Alignment explanation
Indices: 23610--23647 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
23600 ATCCTATTCC
**
23610 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
23630 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
23648 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:24689 original size:19 final size:19
Alignment explanation
Indices: 24667--24703 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24657 TGACCGAGCC
24667 GAGCCATGTTAATCGAGTT
1 GAGCCATGTTAATCGAGTT
*
24686 GAGCCGTGTTAATCGAGT
1 GAGCCATGTTAATCGAGT
24704 CAAACCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (19 bp):
GAGCCATGTTAATCGAGTT
Found at i:25873 original size:20 final size:22
Alignment explanation
Indices: 25847--25891 Score: 69
Period size: 19 Copynumber: 2.2 Consensus size: 22
25837 GATTAATACG
25847 ATATTTTTA-TGATT-TTT-TA
1 ATATTTTTATTGATTATTTGTA
25866 ATATTTTTATTGATTATTTGTA
1 ATATTTTTATTGATTATTTGTA
25888 ATAT
1 ATAT
25892 AATTTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.39
20 5 0.22
21 3 0.13
22 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (22 bp):
ATATTTTTATTGATTATTTGTA
Found at i:26988 original size:22 final size:23
Alignment explanation
Indices: 26960--27039 Score: 94
Period size: 22 Copynumber: 3.6 Consensus size: 23
26950 TATTTATTTT
*
26960 TTTTAAA-ATCAAATATTTTAAA
1 TTTTAAATATAAAATATTTTAAA
26982 TTTTAAATATAAAATA-TTTAAA
1 TTTTAAATATAAAATATTTTAAA
**
27004 AATTAAATATAAAATA-TTTAAA
1 TTTTAAATATAAAATATTTTAAA
**
27026 AATTAAATATAAAA
1 TTTTAAATATAAAA
27040 ATACCATTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
22 47 0.87
23 7 0.13
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTTAAATATAAAATATTTTAAA
Found at i:27003 original size:15 final size:14
Alignment explanation
Indices: 26979--27039 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
26969 CAAATATTTT
*
26979 AAATTTTAAATATA
1 AAATATTAAATATA
* *
26993 AAATATTTAAAAATT
1 AAATA-TTAAATATA
*
27008 AAATATAAAATATTTA
1 AAATATTAAATA--TA
27024 AAA-ATTAAATATA
1 AAATATTAAATATA
27037 AAA
1 AAA
27040 ATACCATTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
13 5 0.14
14 9 0.24
15 19 0.51
16 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATATTAAATATA
Found at i:29353 original size:16 final size:15
Alignment explanation
Indices: 29325--29370 Score: 67
Period size: 14 Copynumber: 3.0 Consensus size: 15
29315 CCAATTAATC
29325 ATATTTTTATTTTTA
1 ATATTTTTATTTTTA
29340 AT-TTTTTATATTTTAA
1 ATATTTTTAT-TTTT-A
29356 ATATTTTTATTTTTA
1 ATATTTTTATTTTTA
29371 GAAAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 7 0.25
15 7 0.25
16 7 0.25
17 7 0.25
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
ATATTTTTATTTTTA
Found at i:31361 original size:21 final size:21
Alignment explanation
Indices: 31335--31375 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31325 TATCAATTAC
31335 AATAATACTA-TTATATATATA
1 AATAATA-TATTTATATATATA
*
31356 AATAATATATTTTTATATAT
1 AATAATATATTTATATATAT
31376 TATAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AATAATATATTTATATATATA
Found at i:32852 original size:14 final size:14
Alignment explanation
Indices: 32833--32859 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32823 CGAGTGACGT
32833 TTATTATATATATG
1 TTATTATATATATG
32847 TTATTATATATAT
1 TTATTATATATAT
32860 ATATAATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
TTATTATATATATG
Found at i:32860 original size:18 final size:18
Alignment explanation
Indices: 32833--32873 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
32823 CGAGTGACGT
**
32833 TTAT-TATATATATGTTA
1 TTATATATATATATAATA
32850 TTATATATATATATAATA
1 TTATATATATATATAATA
32868 TTATAT
1 TTATAT
32874 TATTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTATATATATATATAATA
Found at i:32872 original size:14 final size:14
Alignment explanation
Indices: 32833--32885 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
32823 CGAGTGACGT
*
32833 TTATT-ATATATATG
1 TTATTAATAT-TATA
32847 TTATT-ATA-TATA
1 TTATTAATATTATA
32859 -TATATAATATTATA
1 TTAT-TAATATTATA
32873 TTATTAATATTAT
1 TTATTAATATTAT
32886 TATTTACAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 3 0.09
12 4 0.12
13 3 0.09
14 21 0.62
15 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TTATTAATATTATA
Found at i:34242 original size:20 final size:21
Alignment explanation
Indices: 34203--34250 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
34193 TTTTTTATAT
*
34203 ATATAATTCGATAATTTAATTA
1 ATATAATTC-ATAATATAATTA
34225 ATATAATT-ATAATATAA-TA
1 ATATAATTCATAATATAATTA
*
34244 TTATAAT
1 ATATAAT
34251 AAAATACTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.33
20 8 0.33
22 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
ATATAATTCATAATATAATTA
Found at i:34455 original size:11 final size:11
Alignment explanation
Indices: 34439--34469 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
34429 ACCCGAGTTG
34439 TATTATTCTAA
1 TATTATTCTAA
34450 TATTATTCTAA
1 TATTATTCTAA
34461 TATTATTCT
1 TATTATTCT
34470 TAGGAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (11 bp):
TATTATTCTAA
Found at i:36244 original size:18 final size:17
Alignment explanation
Indices: 36190--36238 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
36180 TTGGACCCTT
* *
36190 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
36208 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
36226 AGTGCATTCGATG
1 AGTGCA-TCGATG
36239 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:36279 original size:19 final size:19
Alignment explanation
Indices: 36255--36306 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
36245 AATAGCCAGA
36255 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
36274 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
36293 GTGCATCGATGCAT
1 GTGCATCGATGCAT
36307 CAAATAGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.21, G:0.35, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTG
Found at i:36367 original size:84 final size:83
Alignment explanation
Indices: 36210--36372 Score: 215
Period size: 84 Copynumber: 2.0 Consensus size: 83
36200 TGCACTAAGA
* *
36210 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
36275 TGCATCGATGCATGGCTG
66 TGCATCGATGCATGGCTG
* *
36293 GTGCATCGATGCATCAAATAG-ATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGG-
1 GTGCATCGATGCATCAAAT-GCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGC
* *
36355 TATGTGGATCGATGCATG
63 T-GGTGCATCGATGCATG
36373 AAATGCATTC
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
83 27 0.39
84 40 0.57
85 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (83 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
TGCATCGATGCATGGCTG
Found at i:45696 original size:55 final size:55
Alignment explanation
Indices: 45212--45698 Score: 717
Period size: 55 Copynumber: 8.9 Consensus size: 55
45202 CTATACATAA
* * * *
45212 ATTCATCAACTCATGATAAATTCTGTGAATATGCACACAAAGTG-TATGTACGGTG
1 ATTCATCAACTTATGATGAATTCCGTGATTATGCACACAAAGTGCT-TGTACGGTG
** * * *
45267 ATTCATCAACTTATGATGAATTCTATGATTATGCACACAAAGTTCCTGTATGGTG
1 ATTCATCAACTTATGATGAATTCCGTGATTATGCACACAAAGTGCTTGTACGGTG
*
45322 ATTCATCAACTTATGATGAATTCTGTGATTATGCACACAAAGTG-TCTGTACGGTG
1 ATTCATCAACTTATGATGAATTCCGTGATTATGCACACAAAGTGCT-TGTACGGTG
* *
45377 ATTCATCAACTTATGATGAATTTCGTGATTATGCACACAAAGTGCTTGTACGATG
1 ATTCATCAACTTATGATGAATTCCGTGATTATGCACACAAAGTGCTTGTACGGTG
* * * *
45432 ATTCATTAACTTATGATGAATTCTGTGATTATGCACACGAAGTGCCTGTACGGTG
1 ATTCATCAACTTATGATGAATTCCGTGATTATGCACACAAAGTGCTTGTACGGTG
* * *
45487 ATTCATCAACTTATAATGAATTCCGTAATTATGCACACAAAGTGCATGTACGGTG
1 ATTCATCAACTTATGATGAATTCCGTGATTATGCACACAAAGTGCTTGTACGGTG
* *
45542 ATTCATCAACTTATGATGAATTCCGTGATTATGCACACAAAGTGCCTATACGGTG
1 ATTCATCAACTTATGATGAATTCCGTGATTATGCACACAAAGTGCTTGTACGGTG
* * *
45597 ATTCATCAACTTGTGATGAATTTCGTGATTATGCACACGAAGTGCTTGTACGGTG
1 ATTCATCAACTTATGATGAATTCCGTGATTATGCACACAAAGTGCTTGTACGGTG
*
45652 ATTTATCAACTTATGATGAATTCCGTGATTATGCACACAAAGTGCTT
1 ATTCATCAACTTATGATGAATTCCGTGATTATGCACACAAAGTGCTT
45699 ATAGTACACA
Statistics
Matches: 390, Mismatches: 39, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
55 389 1.00
56 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (55 bp):
ATTCATCAACTTATGATGAATTCCGTGATTATGCACACAAAGTGCTTGTACGGTG
Found at i:46264 original size:20 final size:19
Alignment explanation
Indices: 46218--46268 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
46208 TTCGATGTTT
*
46218 CTAGGTATCGATACCCTTA
1 CTAGGTATCGATACCCTCA
46237 CTATGGTATCGATACTACCTCA
1 CTA-GGTATCGATAC--CCTCA
46259 -TAGGTATCGA
1 CTAGGTATCGA
46269 CTGATTGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.11
20 19 0.68
21 2 0.07
22 4 0.14
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (19 bp):
CTAGGTATCGATACCCTCA
Done.