Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006818.1 Hibiscus syriacus cultivar Beakdansim tig00017326_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: 71074
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:5498 original size:17 final size:17
Alignment explanation
Indices: 5464--5511 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
5454 TATTTCTTTA
*
5464 TTTTTTTATTATTATAG
1 TTTTTTCATTATTATAG
5481 TTATTTTCATTATT-TAG
1 TT-TTTTCATTATTATAG
5498 TTTTTTCTATTATT
1 TTTTTTC-ATTATT
5512 GTTATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 5 0.18
17 13 0.46
18 10 0.36
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTTTCATTATTATAG
Found at i:17599 original size:106 final size:105
Alignment explanation
Indices: 17027--17821 Score: 1301
Period size: 105 Copynumber: 7.7 Consensus size: 105
17017 AGGTTTTACC
*
17027 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
17092 ACGAAGGGACCGCTGGTTGTCAACAAAGATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
17132 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
17197 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
17237 CAGAGCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
17302 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
17342 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
17407 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
17447 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
17512 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* *
17553 CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
17618 GCGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* *
17659 CAGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
17724 ACGAAGGGACCGCTGGTTGTCAA-TAA-A-----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
17757 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTAC-C-AGTTCAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA--ACGCAAGTTCAACTTCA
17816 CGACGA
64 CGACGA
17822 GGATGTCATT
Statistics
Matches: 666, Mismatches: 21, Indels: 17
0.95 0.03 0.02
Matches are distributed among these distances:
94 57 0.09
95 1 0.00
96 2 0.00
98 7 0.01
103 1 0.00
105 403 0.61
106 195 0.29
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:19225 original size:2 final size:2
Alignment explanation
Indices: 19151--19208 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
19141 CATATTTAAT
19151 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19193 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
19209 CTATTAGCAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19361 original size:21 final size:19
Alignment explanation
Indices: 19337--19376 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
19327 TATGTATATA
19337 TTCTGTATTTTATCTTATTAT
1 TTCTGTATTTT-T-TTATTAT
*
19358 TTCTTTATTTTTTTATTAT
1 TTCTGTATTTTTTTATTAT
19377 AGTTATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (19 bp):
TTCTGTATTTTTTTATTAT
Found at i:21641 original size:60 final size:60
Alignment explanation
Indices: 21577--21695 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
21567 AGAAAGAGGG
* * ** *
21577 TCATAGTTT-AGGGATGAGATTAGAATGTTCAAGAGTTTAAAGACTAATTTAAAATGAGAT
1 TCATAGTTTGA-GGATGAAATTAAAATAATCAAAAGTTTAAAGACTAATTTAAAATGAGAT
* *
21637 TCATAGTTTGAGGATGAAATTAAAATAATCAAAAGTTTAAGGATTAATTTAAAATGAGA
1 TCATAGTTTGAGGATGAAATTAAAATAATCAAAAGTTTAAAGACTAATTTAAAATGAGA
21696 ATTAGTTGGA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 50 0.98
61 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (60 bp):
TCATAGTTTGAGGATGAAATTAAAATAATCAAAAGTTTAAAGACTAATTTAAAATGAGAT
Found at i:21645 original size:31 final size:30
Alignment explanation
Indices: 21605--21695 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 30
21595 ATTAGAATGT
* *
21605 TCAAGAGTTTAAAGACTAATTTAAAATGAGA
1 TCAAAAGTTTAAGGA-TAATTTAAAATGAGA
* * *
21636 TTC-ATAGTTTGAGGATGAAATTAAAAT-A-A
1 -TCAAAAGTTTAAGGAT-AATTTAAAATGAGA
21665 TCAAAAGTTTAAGGATTAATTTAAAATGAGA
1 TCAAAAGTTTAAGGA-TAATTTAAAATGAGA
21696 ATTAGTTGGA
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
28 2 0.04
29 20 0.43
30 4 0.09
31 19 0.40
32 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.32
Consensus pattern (30 bp):
TCAAAAGTTTAAGGATAATTTAAAATGAGA
Found at i:22665 original size:31 final size:31
Alignment explanation
Indices: 22623--22695 Score: 119
Period size: 31 Copynumber: 2.3 Consensus size: 31
22613 AGCTCAGCTT
*
22623 GAACTCGAAATATAATATTGAAACTCGACTC
1 GAACTCAAAATATAATATTGAAACTCGACTC
*
22654 GAACTCAAAATATAATATTGAAACTCGACTT
1 GAACTCAAAATATAATATTGAAACTCGACTC
22685 GAACTCGAAAA
1 GAACTC-AAAA
22696 GACTTGAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 35 0.90
32 4 0.10
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (31 bp):
GAACTCAAAATATAATATTGAAACTCGACTC
Found at i:22711 original size:16 final size:16
Alignment explanation
Indices: 22680--22711 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
22670 ATTGAAACTC
*
22680 GACTTGAACTCGAAAA
1 GACTTGAACTCAAAAA
22696 GACTTGAACTCAAAAA
1 GACTTGAACTCAAAAA
22712 AATTTCAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.19
Consensus pattern (16 bp):
GACTTGAACTCAAAAA
Found at i:22770 original size:17 final size:17
Alignment explanation
Indices: 22748--22780 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22738 ATTTTGAGCT
*
22748 CGATTCAATCTCGAACA
1 CGATTCAAGCTCGAACA
22765 CGATTCAAGCTCGAAC
1 CGATTCAAGCTCGAAC
22781 TCAAACTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.21
Consensus pattern (17 bp):
CGATTCAAGCTCGAACA
Found at i:36268 original size:82 final size:83
Alignment explanation
Indices: 36146--36329 Score: 203
Period size: 82 Copynumber: 2.2 Consensus size: 83
36136 ATGATTAATC
* *
36146 TATAGTGGCATTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGTAG-CGTTGTTATACAAA
1 TATAGTGGCATTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAG-AGACATTGTTATAAAAA
* *
36210 CACCGTAAT-GGGTTCATA
65 CACCGCAATAGGGTACATA
* * * * * * * * *
36228 TATAGTGGCGTTTATTT-TACAAACGCTGCACCATATTAGTAGTTTAGCGACATTTTTATAAAAA
1 TATAGTGGCATTT-TTTCAACAAACGCCGCAACAGAGTAGTACTTTAGAGACATTGTTATAAAAA
*
36292 CACCGCAATAGGGTACGTA
65 CACCGCAATAGGGTACATA
36311 TATAGTGGCATTTTTTCAA
1 TATAGTGGCATTTTTTCAA
36330 TAAATGCTAC
Statistics
Matches: 82, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
81 1 0.01
82 58 0.71
83 23 0.28
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (83 bp):
TATAGTGGCATTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGAGACATTGTTATAAAAAC
ACCGCAATAGGGTACATA
Found at i:36343 original size:42 final size:40
Alignment explanation
Indices: 36297--36391 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 40
36287 AAAAACACCG
*
36297 CAATAGGGTACGTATATAGTGGCATTTTTTCAATAAATGCT-A
1 CAATAGGGTACATATATAGTGGC-TTTTTTCAA-AAAT-CTCA
* *
36339 CAATAGGATTCATATATAGTGGCTTTTTTCAAAAATCTCCA
1 CAATAGGGTACATATATAGTGGCTTTTTTCAAAAATCT-CA
36380 CAATAGTGGTAC
1 CAATAG-GGTAC
36392 TTTAGCGGCG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
39 2 0.04
40 4 0.09
41 16 0.36
42 23 0.51
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (40 bp):
CAATAGGGTACATATATAGTGGCTTTTTTCAAAAATCTCA
Found at i:36571 original size:41 final size:41
Alignment explanation
Indices: 36522--36600 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
36512 TAAAACGCTG
** *
36522 CAAAAGACTCTTACGTTAGTGGTGTTTGTATT-CAAACGCCA
1 CAAAAGACTCAGACGTTAGTGGCGTTTGT-TTACAAACGCCA
*
36563 CAAAAGACTCAGACTTTAGTGGCGTTTGTTTACAAACG
1 CAAAAGACTCAGACGTTAGTGGCGTTTGTTTACAAACG
36601 TCGCTATAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.06
41 31 0.94
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (41 bp):
CAAAAGACTCAGACGTTAGTGGCGTTTGTTTACAAACGCCA
Found at i:36748 original size:40 final size:42
Alignment explanation
Indices: 36639--36767 Score: 111
Period size: 42 Copynumber: 3.1 Consensus size: 42
36629 TTGTTTTTTC
* * * *
36639 AAACTCCGCAATAGTCTTGTACTTTAGTGGTGTTTTTGTAAT
1 AAACGCCGCAATAGACATGTACTTTAGTGGCGTTTTTGTAAT
** *
36681 AAACGATGCAATA-ATCATGTAATTTAGTGGCG-TTTTG-AAT
1 AAACGCCGCAATAGA-CATGTACTTTAGTGGCGTTTTTGTAAT
* * * * * *
36721 AAATGCCGCAATAGACATGTACCTTAGTTGCATTTTTATTAT
1 AAACGCCGCAATAGACATGTACTTTAGTGGCGTTTTTGTAAT
36763 AAACG
1 AAACG
36768 TCGTGATTAT
Statistics
Matches: 66, Mismatches: 17, Indels: 8
0.73 0.19 0.09
Matches are distributed among these distances:
40 26 0.39
41 10 0.15
42 30 0.45
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (42 bp):
AAACGCCGCAATAGACATGTACTTTAGTGGCGTTTTTGTAAT
Found at i:44550 original size:28 final size:28
Alignment explanation
Indices: 44496--44569 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
44486 GGTGACATTT
* * *
44496 TGGTAATTATTTGGGAAATGGTGCTATTC
1 TGGTAATTATTT-TGAAAAGGAGCTATTC
*
44525 TGGTAATTATTTTGAAAAGGAGCTATTT
1 TGGTAATTATTTTGAAAAGGAGCTATTC
* *
44553 TTGTAATT-TTTTTAAAA
1 TGGTAATTATTTTGAAAA
44570 TATGACAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 8 0.21
28 19 0.49
29 12 0.31
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (28 bp):
TGGTAATTATTTTGAAAAGGAGCTATTC
Found at i:44619 original size:29 final size:28
Alignment explanation
Indices: 44492--44673 Score: 111
Period size: 29 Copynumber: 6.4 Consensus size: 28
44482 ATTGGGTGAC
* * * *
44492 ATTTTGGTAATTATTTGGGAAATGGTGCT
1 ATTTTAGTAATTATTT-TGAAAAGATGCT
* *
44521 ATTCTGGTAATTATTTTGAAAAGGA-GCT
1 ATTTTAGTAATTATTTTGAAAA-GATGCT
* * * *
44549 ATTTTTGTAATT-TTTTTAAAATATGACA
1 ATTTTAGTAATTATTTTGAAAAGATG-CT
* * * *
44577 ATTTCA-TAA-AATTTTTAAAAGAGTGAT
1 ATTTTAGTAATTATTTTGAAAAGA-TGCT
*
44604 ATTTTAGTAATTATTTTGAAAATGATGCC
1 ATTTTAGTAATTATTTTGAAAA-GATGCT
* * *
44633 ATTTTGGTAATTAATTTCAAAATGATGCT
1 ATTTTAGTAATTATTTTGAAAA-GATGCT
*
44662 ATTTTTGTAATT
1 ATTTTAGTAATT
44674 TTAAAAAAAA
Statistics
Matches: 120, Mismatches: 25, Indels: 16
0.75 0.16 0.10
Matches are distributed among these distances:
26 1 0.01
27 27 0.22
28 27 0.22
29 63 0.52
30 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (28 bp):
ATTTTAGTAATTATTTTGAAAAGATGCT
Found at i:44692 original size:112 final size:112
Alignment explanation
Indices: 44487--44700 Score: 268
Period size: 112 Copynumber: 1.9 Consensus size: 112
44477 CGTTGATTGG
* * * * * *
44487 GTGACATTTTGGTAATTATTTGGGAAATGGTGCTATTCTGGTAATTATTTTGAAAAGGAGCTATT
1 GTGACATTTTAGTAATTATTTGGAAAATGATGCCATTCTGGTAATTAATTTCAAAAGGAGCTATT
** *
44552 TTTGTAATTTTTTTAAAATATGACAATTTCATAAAATTTTTAAAAGA
66 TTTGTAATTTTTAAAAAAAATGACAATTTCATAAAATTTTTAAAAGA
* * * *
44599 GTGATATTTTAGTAATTATTTTGAAAATGATGCCATTTTGGTAATTAATTTCAAAATGATGCTAT
1 GTGACATTTTAGTAATTATTTGGAAAATGATGCCATTCTGGTAATTAATTTCAAAAGGA-GCTAT
** *
44664 TTTTGTAA-TTTTAAAAAAAATGTTAATTTCTTAAAAT
65 TTTTGTAATTTTTAAAAAAAATGACAATTTCATAAAAT
44701 GGTTGACTAC
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
112 72 0.85
113 13 0.15
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (112 bp):
GTGACATTTTAGTAATTATTTGGAAAATGATGCCATTCTGGTAATTAATTTCAAAAGGAGCTATT
TTTGTAATTTTTAAAAAAAATGACAATTTCATAAAATTTTTAAAAGA
Found at i:45825 original size:117 final size:117
Alignment explanation
Indices: 45614--45905 Score: 494
Period size: 117 Copynumber: 2.5 Consensus size: 117
45604 GGAAGTATTT
*
45614 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGT
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
*
45679 GGAACCTACACATTGTAGTGATTAGAGTGACTAGATGGGGAAGTTATTACTG
66 GGAACCTACACATTGTAGTGATTAGAGTGACTAGATGGGAAAGTTATTACTG
* *
45731 CAGGTTCCTTTACTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
* *
45796 GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGAAAGTTATTACTG
66 GGAACCTACACATTGTAGTGATTAGAGTGACTAGATGGGAAAGTTATTACTG
** * *
45848 CAGGCTCCTCGGCTTTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
45906 TTTCGGGAAA
Statistics
Matches: 163, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 163 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.33
Consensus pattern (117 bp):
CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
GGAACCTACACATTGTAGTGATTAGAGTGACTAGATGGGAAAGTTATTACTG
Found at i:46898 original size:20 final size:21
Alignment explanation
Indices: 46861--46899 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
46851 TTCATTTTAT
* *
46861 GTAGTAAAATTAATATTTTCG
1 GTAGTAAAAATAACATTTTCG
46882 GTAG-AAAAATAACATTTT
1 GTAGTAAAAATAACATTTT
46900 AAGTATTGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (21 bp):
GTAGTAAAAATAACATTTTCG
Found at i:54629 original size:13 final size:13
Alignment explanation
Indices: 54611--54643 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
54601 TAATTGTCTT
54611 TATTTCATTTCCA
1 TATTTCATTTCCA
54624 TATTTCATTTCCA
1 TATTTCATTTCCA
54637 TATTTCA
1 TATTTCA
54644 ACTATATCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTCATTTCCA
Found at i:66754 original size:242 final size:242
Alignment explanation
Indices: 66314--66799 Score: 827
Period size: 242 Copynumber: 2.0 Consensus size: 242
66304 AGTACACCCG
66314 TGACACAACTAAAAATTATCCAACAATCTCACCACTGATCCATGTATGAAAATTTGAATTCAATA
1 TGACACAACTAAAAATTATCCAACAATCTCACCACTGA-CCATGTATGAAAATTTGAATTCAATA
*
66379 ACAAGGGATTCGTGATATACCTTAGGTTATTAGAATAACAACAAATCAGCAGCAGTCATGAACAT
65 ACAAGGGATTCGTGATATACCTTAGGTTATTAGAATAACAACAAATCAGCAGCAATCATGAACAT
66444 TTCAATTCCTAAACTCCACGTAATTGTTCAGTCTCAACTAAGTTCGCCCAATTGAGAGCAATTTT
130 TTCAATTCCTAAACTCCACGTAATTGTTCAGTCTCAACTAAGTTCGCCCAATTGAGAGCAATTTT
66509 CTTTTCTCAAAACGGTTTTGAGAAATA-TCAAGAGGATTTAAACGGCTGC
195 CTTTTCTC-AAACGG-TTTGAGAAATATTCAAGAGGATTTAAACGGCTGC
*
66558 TGACAGAACTAAAAA-TATCCAAACAATCTCACCACTG-CCATGTATGAAAATTTGAATTCAATA
1 TGACACAACTAAAAATTATCC-AACAATCTCACCACTGACCATGTATGAAAATTTGAATTCAATA
* * *
66621 ACAAGGGATTCGTGATATACCTTAGTTTATTAGAATAATAGCAAATCAGCAGCAATCATGAACAT
65 ACAAGGGATTCGTGATATACCTTAGGTTATTAGAATAACAACAAATCAGCAGCAATCATGAACAT
66686 TTCAATTCCTAAACTCCACGTAATTGTTTCAGTCTCAACTAAGTTCGCCCAATTGAGAGCAA-TT
130 TTCAATTCCTAAACTCCACGTAATTG-TTCAGTCTCAACTAAGTTCGCCCAATTGAGAGCAATTT
*
66750 TCTTTTCTCAAATGGTTTGAGAAATATTGTCAAGAGGATTTAAACGGCTG
194 TCTTTTCTCAAACGGTTTGAGAAATA-T-TCAAGAGGATTTAAACGGCTG
66800 TTAGGGCATC
Statistics
Matches: 231, Mismatches: 6, Indels: 11
0.93 0.02 0.04
Matches are distributed among these distances:
240 11 0.05
241 5 0.02
242 124 0.54
243 61 0.26
244 30 0.13
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (242 bp):
TGACACAACTAAAAATTATCCAACAATCTCACCACTGACCATGTATGAAAATTTGAATTCAATAA
CAAGGGATTCGTGATATACCTTAGGTTATTAGAATAACAACAAATCAGCAGCAATCATGAACATT
TCAATTCCTAAACTCCACGTAATTGTTCAGTCTCAACTAAGTTCGCCCAATTGAGAGCAATTTTC
TTTTCTCAAACGGTTTGAGAAATATTCAAGAGGATTTAAACGGCTGC
Done.