Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002369.1 Hibiscus syriacus cultivar Beakdansim tig00004841_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: 56557
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:1761 original size:2 final size:2
Alignment explanation
Indices: 1754--1825 Score: 130
Period size: 2 Copynumber: 37.0 Consensus size: 2
1744 TTTTCATTAA
1754 AT AT AT AT AT AT AT AT A- 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 AT AT AT AT AT
1795 AT AT AT AT -T 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
1826 TTGTGTGTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 66 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7461 original size:2 final size:2
Alignment explanation
Indices: 7454--7486 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7444 AGAACTAAAC
7454 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 T
7487 TTAAGAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8433 original size:31 final size:32
Alignment explanation
Indices: 8373--8449 Score: 111
Period size: 31 Copynumber: 2.4 Consensus size: 32
8363 TTTAAAGATA
*
8373 ATTTTGTAATAATTTGATAAATGTTAATGACT
1 ATTTTGTAATAATTTGATAAAGGTTAATGACT
* *
8405 ATTTTGTAATCATTTGA-AAAGGTTAATGATT
1 ATTTTGTAATAATTTGATAAAGGTTAATGACT
*
8436 ATTTTATAATAATT
1 ATTTTGTAATAATT
8450 GGAAGATTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 24 0.60
32 16 0.40
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.48
Consensus pattern (32 bp):
ATTTTGTAATAATTTGATAAAGGTTAATGACT
Found at i:11261 original size:5 final size:5
Alignment explanation
Indices: 11253--11281 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
11243 GAATGATATG
11253 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
11282 ATGAAGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:15181 original size:16 final size:17
Alignment explanation
Indices: 15146--15182 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
15136 TTATATGAGT
15146 ATATGTGTTGTATGTTG
1 ATATGTGTTGTATGTTG
*
15163 ATATGTTTTGTAT-TTG
1 ATATGTGTTGTATGTTG
15179 ATAT
1 ATAT
15183 ATGATGTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.57
Consensus pattern (17 bp):
ATATGTGTTGTATGTTG
Found at i:16298 original size:23 final size:22
Alignment explanation
Indices: 16268--16337 Score: 86
Period size: 23 Copynumber: 3.1 Consensus size: 22
16258 ATATTATATG
16268 GCACTACGGTGCATTTCTACGCA
1 GCACTACGGTGCATTTCTACG-A
* *
16291 GCACTACGGTGCAATTCTACGT
1 GCACTACGGTGCATTTCTACGA
* *
16313 GACACTTCGGTGCATTTATACGA
1 G-CACTACGGTGCATTTCTACGA
16336 GC
1 GC
16338 TGTGGTGACA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
22 2 0.05
23 38 0.95
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (22 bp):
GCACTACGGTGCATTTCTACGA
Found at i:18297 original size:21 final size:19
Alignment explanation
Indices: 18260--18301 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 19
18250 TGAAAGTTTA
18260 TATTTTTACAAGTTTATATG
1 TATTTTTACAAGTTTAT-TG
18280 TATTTTTACGAAAG-TTATTG
1 TATTTTTAC--AAGTTTATTG
18300 TA
1 TA
18302 GTAGTGCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 13 0.65
21 4 0.20
22 3 0.15
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (19 bp):
TATTTTTACAAGTTTATTG
Found at i:18382 original size:12 final size:12
Alignment explanation
Indices: 18341--18382 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
18331 AAATATTTCT
*
18341 CTGTTCACGGTA
1 CTGTTCATGGTA
18353 CTGTTCAT--TA
1 CTGTTCATGGTA
*
18363 TTGTTCATGGTA
1 CTGTTCATGGTA
18375 CTGTTCAT
1 CTGTTCAT
18383 ACCGTATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
10 9 0.36
12 16 0.64
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (12 bp):
CTGTTCATGGTA
Found at i:19887 original size:2 final size:2
Alignment explanation
Indices: 19880--19911 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19870 ACTGGAAAGA
19880 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
19912 GGATCGTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24097 original size:24 final size:24
Alignment explanation
Indices: 24027--24097 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
24017 CAATCTTATA
*
24027 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* * *
24050 CGGCACTTTGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
*
24074 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
24098 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 11 0.28
24 28 0.72
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:24726 original size:12 final size:12
Alignment explanation
Indices: 24709--24733 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24699 GAGTTTTGTA
24709 ATGGTACTGTTC
1 ATGGTACTGTTC
24721 ATGGTACTGTTC
1 ATGGTACTGTTC
24733 A
1 A
24734 CAGTATTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATGGTACTGTTC
Found at i:25290 original size:32 final size:30
Alignment explanation
Indices: 25235--25299 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 30
25225 ATCTTTGCAT
25235 ATTATTATTTTGTTTTCATTTATTCTCAG-A
1 ATTATTATTTTGTTTTCATTTATT-TCAGTA
25265 ATTATTATTTTGTTTTTTC-TGTTATTTCAGTA
1 ATTATTATTTTG--TTTTCAT-TTATTTCAGTA
25297 ATT
1 ATT
25300 TTCTGATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
30 12 0.39
31 5 0.16
32 14 0.45
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.63
Consensus pattern (30 bp):
ATTATTATTTTGTTTTCATTTATTTCAGTA
Found at i:28935 original size:23 final size:24
Alignment explanation
Indices: 28888--28940 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
28878 ATTTACAAAT
* *
28888 ATGTTAGTGTAAATGTTTGTTAAC
1 ATGTTCGTGTAAATGTTTGTAAAC
*
28912 ATGTTCGTGTAGA-GTTTGTAAAC
1 ATGTTCGTGTAAATGTTTGTAAAC
28935 ATGTTC
1 ATGTTC
28941 ATGTTGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.26, C:0.08, G:0.23, T:0.43
Consensus pattern (24 bp):
ATGTTCGTGTAAATGTTTGTAAAC
Found at i:29142 original size:76 final size:76
Alignment explanation
Indices: 29056--29203 Score: 278
Period size: 76 Copynumber: 1.9 Consensus size: 76
29046 TAAAATATAA
29056 AAAAAATGAAAAGAAGAACCGAATAAACAAGTTTTTAAACAAGTTTATTCGTGAACACAAACGAA
1 AAAAAATGAAAAGAAGAACCGAATAAACAAGTTTTTAAACAAGTTTATTCGTGAACACAAACGAA
29121 CTGAACAATAT
66 CTGAACAATAT
* *
29132 AAAAAATGAAAAGAAGAACCGAATAAACGAGTTTTTAAACAAGTTTATTCGTGAACACAAATGAA
1 AAAAAATGAAAAGAAGAACCGAATAAACAAGTTTTTAAACAAGTTTATTCGTGAACACAAACGAA
29197 CTGAACA
66 CTGAACA
29204 CACCTTTATT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.52, C:0.13, G:0.14, T:0.21
Consensus pattern (76 bp):
AAAAAATGAAAAGAAGAACCGAATAAACAAGTTTTTAAACAAGTTTATTCGTGAACACAAACGAA
CTGAACAATAT
Found at i:42741 original size:92 final size:92
Alignment explanation
Indices: 42633--42818 Score: 336
Period size: 92 Copynumber: 2.0 Consensus size: 92
42623 TGTACCAAAA
*
42633 TGAAACAAAAAATAAATCTTAGGTATGATTTTAAAAGAAATGAAAGTTTAAGTACTAAAACGAAA
1 TGAAACAAAAAATAAATCTTAGGTATGATTTTAAAACAAATGAAAGTTTAAGTACTAAAACGAAA
*
42698 CAAAACTAATAATTTAAGTACTAAATG
66 CAAAACTAATAATTTAAATACTAAATG
*
42725 TGAAACAAAAAGTAAATCTTAGGTATGATTTTAAAACAAATGAAAGTTTAAGTACTAAAACGAAA
1 TGAAACAAAAAATAAATCTTAGGTATGATTTTAAAACAAATGAAAGTTTAAGTACTAAAACGAAA
*
42790 CAAAACTAATAATTTAAATATTAAATG
66 CAAAACTAATAATTTAAATACTAAATG
42817 TG
1 TG
42819 TAATTTATCC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.53, C:0.08, G:0.12, T:0.28
Consensus pattern (92 bp):
TGAAACAAAAAATAAATCTTAGGTATGATTTTAAAACAAATGAAAGTTTAAGTACTAAAACGAAA
CAAAACTAATAATTTAAATACTAAATG
Found at i:45393 original size:20 final size:19
Alignment explanation
Indices: 45347--45417 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
45337 CGCGAACTCC
*
45347 AATTTCGCAACTCGATTTT
1 AATTTCGCAACACGATTTT
45366 CGAA-TTCGCAACACGAATTTT
1 --AATTTCGCAACACG-ATTTT
*
45387 AATTTCGCAACA-GGTTTT
1 AATTTCGCAACACGATTTT
*
45405 AGTTTCGCAACAC
1 AATTTCGCAACAC
45418 AAATGTTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
18 15 0.34
19 3 0.07
20 19 0.43
21 7 0.16
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (19 bp):
AATTTCGCAACACGATTTT
Found at i:46196 original size:24 final size:24
Alignment explanation
Indices: 46145--46198 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
46135 GTATTCGAAA
*
46145 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
46169 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
46193 TTTGAT
1 TTTGAT
46199 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:46378 original size:12 final size:12
Alignment explanation
Indices: 46361--46385 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46351 ATATAACCCT
46361 GAAGAAGAAAAA
1 GAAGAAGAAAAA
46373 GAAGAAGAAAAA
1 GAAGAAGAAAAA
46385 G
1 G
46386 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:48464 original size:18 final size:18
Alignment explanation
Indices: 48441--48476 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
48431 AAGCAAAAGG
*
48441 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
48459 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
48477 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:48779 original size:20 final size:20
Alignment explanation
Indices: 48747--48813 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
48737 GGAATCGCAA
*
48747 TGCGAATTTTGACTTTTGCAT
1 TGCGAA-TTTGACTTTTGCGT
*
48768 TGCGAATTTGACTTTCGCGT
1 TGCGAATTTGACTTTTGCGT
* *
48788 TACAAATTTGA-TTTTCGCGT
1 TGCGAATTTGACTTTT-GCGT
48808 TGCGAA
1 TGCGAA
48814 AGTGTACCTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 3 0.08
20 29 0.76
21 6 0.16
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (20 bp):
TGCGAATTTGACTTTTGCGT
Found at i:49011 original size:65 final size:64
Alignment explanation
Indices: 48876--49025 Score: 228
Period size: 65 Copynumber: 2.3 Consensus size: 64
48866 TTAAAACAAT
48876 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAAC
1 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAAC
* *** * *
48940 AAATCAACTTTTACAAATCAATTAAATAAGCAAAAAAATAATTCTTATTTCCTCATCAATTAAAC
1 AAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAAGAATTATTTACACATCAATTAAAC
*
49005 AAATCAACTTTTATAAATCAA
1 AAATCAACTTTTACAAATCAA
49026 CTTTTACAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 30 0.38
65 48 0.62
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (64 bp):
AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAAC
Found at i:49024 original size:14 final size:14
Alignment explanation
Indices: 49003--49039 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
48993 CATCAATTAA
49003 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
49017 ATAAATCAACTTTT
1 ACAAATCAACTTTT
49031 ACAAATCAA
1 ACAAATCAA
49040 TTAAACAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:50424 original size:21 final size:21
Alignment explanation
Indices: 50395--50470 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
50385 GTGAATCGGG
*
50395 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGGAC
* ** *
50416 CTTTTGAACGATGACAGGGGC
1 CTCTTGAACGATGGGAGGGAC
*
50437 CTCTTGAACGATGGGAGGGGC
1 CTCTTGAACGATGGGAGGGAC
* *
50458 TTCTTGAAGGATG
1 CTCTTGAACGATG
50471 ATAAGGGCCT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGAC
Found at i:50465 original size:42 final size:42
Alignment explanation
Indices: 50395--50480 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
50385 GTGAATCGGG
* *
50395 CTCTTGAACGGTGGGAGGGACCTTTTGAACGATGACAGGGGC
1 CTCTTGAACGATGGGAGGGACCTTTTGAACGATGACAAGGGC
* * *
50437 CTCTTGAACGATGGGAGGG-GCTTCTTGAAGGATGATAAGGGC
1 CTCTTGAACGATGGGAGGGACCTT-TTGAACGATGACAAGGGC
50479 CT
1 CT
50481 ATGGCCTCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 3 0.08
42 35 0.92
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGATGGGAGGGACCTTTTGAACGATGACAAGGGC
Found at i:50926 original size:63 final size:63
Alignment explanation
Indices: 50833--50953 Score: 142
Period size: 63 Copynumber: 1.9 Consensus size: 63
50823 CCACGTAAAT
* *
50833 CACCATTGTCATCGCGTAAAACCTCTACCTCAC-CACGTAAAG-ATCGTACCTCATCACGCCATG
1 CACCATTGTCATCACGTAAAACCTCTACCTC-CTCACGCAAAGCATCG-ACCTCATCACGCCATG
* *
50896 CACCATTGTCGTCACGTAAAGTACC-C-ACCTCCTCACGCAAAGCATTGACCTCATCACG
1 CACCATTGTCATCACGTAAA--ACCTCTACCTCCTCACGCAAAGCATCGACCTCATCACG
50954 TAACTCCCCT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
62 1 0.02
63 42 0.84
64 4 0.08
65 3 0.06
ACGTcount: A:0.28, C:0.37, G:0.13, T:0.21
Consensus pattern (63 bp):
CACCATTGTCATCACGTAAAACCTCTACCTCCTCACGCAAAGCATCGACCTCATCACGCCATG
Found at i:52875 original size:16 final size:16
Alignment explanation
Indices: 52831--52875 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
52821 TTTAAATATG
*
52831 AAAAATCTAATAATAAA
1 AAAAAT-TAAAAATAAA
*
52848 AAAAATTCAAAATAAA
1 AAAAATTAAAAATAAA
*
52864 AATAATTAAAAA
1 AAAAATTAAAAA
52876 AACTAACCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATTAAAAATAAA
Found at i:52978 original size:22 final size:22
Alignment explanation
Indices: 52951--53006 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
52941 ATGGAGATAC
*
52951 ACGGATTTCGTCGGAGATGGGG
1 ACGGATTTCGTCGAAGATGGGG
52973 ACGGATTTCGTCGAAGATGGGG
1 ACGGATTTCGTCGAAGATGGGG
*
52995 ACGGATGTCGTC
1 ACGGATTTCGTC
53007 TTAGAGAGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.20, C:0.16, G:0.41, T:0.23
Consensus pattern (22 bp):
ACGGATTTCGTCGAAGATGGGG
Found at i:53180 original size:20 final size:20
Alignment explanation
Indices: 53155--53237 Score: 130
Period size: 20 Copynumber: 4.2 Consensus size: 20
53145 TAAACGCGCT
* *
53155 TTGCGAATTACAAATTTGCG
1 TTGCGATTTACAGATTTGCG
53175 TTGCGATTTACAGATTTGCG
1 TTGCGATTTACAGATTTGCG
*
53195 TTGCGATTTACAGATTTACG
1 TTGCGATTTACAGATTTGCG
*
53215 TTGCGATTTACAGATTCGCG
1 TTGCGATTTACAGATTTGCG
53235 TTG
1 TTG
53238 TGAATTTGAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACAGATTTGCG
Found at i:54402 original size:92 final size:92
Alignment explanation
Indices: 54291--54665 Score: 562
Period size: 92 Copynumber: 4.1 Consensus size: 92
54281 TTATAATATG
* * * **
54291 ATTCGTTTATTGAAGAAATAAAATTGATAGAAAATAAAAACATGTATTAGAAGTTGAGGTTCTTA
1 ATTCGTTTATTGAAGAAATAAAATTGAGAGAAAATAAAGACATGTATTAGATGCGGAGGTTCTTA
*
54356 AATCCAGTTCGCACATAATATCCTCCT
66 GATCCAGTTCGCACATAATATCCTCCT
*
54383 ATTCATTTATTGAAGAAATAAAATTGAGAGAAAATAAAGACATGTATTAGATGCGGAGGTTCTTA
1 ATTCGTTTATTGAAGAAATAAAATTGAGAGAAAATAAAGACATGTATTAGATGCGGAGGTTCTTA
*
54448 GATCCGGTTCGCACATAATATCCTCCT
66 GATCCAGTTCGCACATAATATCCTCCT
* * *
54475 ATTCGTTTATCGAAGAAATAAAATTGTGAGAAAATAAAGACCTGTATTAGATGCGGAGGTTCTTA
1 ATTCGTTTATTGAAGAAATAAAATTGAGAGAAAATAAAGACATGTATTAGATGCGGAGGTTCTTA
*
54540 GATCCAGTTCGCACATACTA---T--T
66 GATCCAGTTCGCACATAATATCCTCCT
* ** *
54562 ATTCGTTTATTGAAGAAATAAAATTGAGAGAAAATAAAGACCTGTATTAGATGTAGAGGTTCTTC
1 ATTCGTTTATTGAAGAAATAAAATTGAGAGAAAATAAAGACATGTATTAGATGCGGAGGTTCTTA
*
54627 GATCCAGTTCGTACATAATATCCTCCT
66 GATCCAGTTCGCACATAATATCCTCCT
54654 ATTCGTTTATTG
1 ATTCGTTTATTG
54666 TGCGATCGTT
Statistics
Matches: 257, Mismatches: 21, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
87 79 0.31
89 1 0.00
90 1 0.00
92 176 0.68
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (92 bp):
ATTCGTTTATTGAAGAAATAAAATTGAGAGAAAATAAAGACATGTATTAGATGCGGAGGTTCTTA
GATCCAGTTCGCACATAATATCCTCCT
Found at i:54610 original size:179 final size:181
Alignment explanation
Indices: 54291--54663 Score: 554
Period size: 179 Copynumber: 2.1 Consensus size: 181
54281 TTATAATATG
* **
54291 ATTCGTTTATTGAAGAAATAAAATTGATAGAAAATAAAAACATGTATTAGAAGTTGAGGTTCTTA
1 ATTCGTTTATCGAAGAAATAAAATTGATAGAAAATAAAAACATGTATTAGAAGCGGAGGTTCTTA
54356 AATCCAGTTCGCACATAATATCCTCCTATTCATTTATTGAAGAAATAAAATTGAGAGAAAATAAA
66 AATCCAGTTCGCACATAATA--CT-CTATTCATTTATTGAAGAAATAAAATTGAGAGAAAATAAA
* *
54421 GACATGTATTAGATGCGGAGGTTCTTAGATCCGGTTCGCACATAATATCCTCCT
128 GACATGTATTAGATGCAGAGGTTCTTAGATCCAGTTCGCACATAATATCCTCCT
* * *
54475 ATTCGTTTATCGAAGAAATAAAATTG-TGAGAAAATAAAGACCTGTATTAGATGCGGAGGTTCTT
1 ATTCGTTTATCGAAGAAATAAAATTGAT-AGAAAATAAAAACATGTATTAGAAGCGGAGGTTCTT
* * *
54539 AGATCCAGTTCGCACATACTA-T-TATTCGTTTATTGAAGAAATAAAATTGAGAGAAAATAAAGA
65 AAATCCAGTTCGCACATAATACTCTATTCATTTATTGAAGAAATAAAATTGAGAGAAAATAAAGA
* * * *
54602 CCTGTATTAGATGTAGAGGTTCTTCGATCCAGTTCGTACATAATATCCTCCT
130 CATGTATTAGATGCAGAGGTTCTTAGATCCAGTTCGCACATAATATCCTCCT
54654 ATTCGTTTAT
1 ATTCGTTTAT
54664 TGTGCGATCG
Statistics
Matches: 173, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
179 96 0.55
181 1 0.01
183 1 0.01
184 75 0.43
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (181 bp):
ATTCGTTTATCGAAGAAATAAAATTGATAGAAAATAAAAACATGTATTAGAAGCGGAGGTTCTTA
AATCCAGTTCGCACATAATACTCTATTCATTTATTGAAGAAATAAAATTGAGAGAAAATAAAGAC
ATGTATTAGATGCAGAGGTTCTTAGATCCAGTTCGCACATAATATCCTCCT
Done.