Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006008.1 Hibiscus syriacus cultivar Beakdansim tig00014174_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: 93771
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Found at i:9431 original size:61 final size:64
Alignment explanation
Indices: 9314--9448 Score: 170
Period size: 61 Copynumber: 2.2 Consensus size: 64
9304 GTAGTTTTAT
* * * * *
9314 ATTAGCACTAGTGTGTAAGGACACTAAGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCTGG
1 ATTAGCACTAGAGTGTAA-GACACTAAGTGCAGGTGATGGGCACAACCCTAAGTGTCATATCCGG
* *
9379 ATTAGCACTAGAGTGTAA-AC-CT-AGTGTAGGTGATGGGCACGACCCTAAGTGTCATATCCGG
1 ATTAGCACTAGAGTGTAAGACACTAAGTGCAGGTGATGGGCACAACCCTAAGTGTCATATCCGG
9440 -TTAGCACTA
1 ATTAGCACTA
9449 TAGCATAAGC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 9 0.14
61 33 0.52
62 2 0.03
63 2 0.03
65 17 0.27
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (64 bp):
ATTAGCACTAGAGTGTAAGACACTAAGTGCAGGTGATGGGCACAACCCTAAGTGTCATATCCGG
Found at i:26445 original size:20 final size:22
Alignment explanation
Indices: 26396--26449 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
26386 CAATTATGAG
*
26396 TATTCAATGTT-AATATTTAAT
1 TATTGAATGTTGAATATTTAAT
26417 TATTGAATGTTGAAT-TTTAAGT
1 TATTGAATGTTGAATATTTAA-T
26439 TA-T-AATGTTGA
1 TATTGAATGTTGA
26450 TTTGGGACCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 8 0.27
21 16 0.53
22 6 0.20
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (22 bp):
TATTGAATGTTGAATATTTAAT
Found at i:28694 original size:12 final size:12
Alignment explanation
Indices: 28677--28704 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28667 ACTTCTCCCT
28677 CCTCTGCCTCCA
1 CCTCTGCCTCCA
28689 CCTCTGCCTCCA
1 CCTCTGCCTCCA
28701 CCTC
1 CCTC
28705 CTCCGGCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.61, G:0.07, T:0.25
Consensus pattern (12 bp):
CCTCTGCCTCCA
Found at i:29367 original size:21 final size:21
Alignment explanation
Indices: 29338--29378 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29328 CAATTATGAG
29338 TATTCAATGTT-AATATTTAAT
1 TATTCAATGTTGAAT-TTTAAT
*
29359 TATTGAATGTTGAATTTTAA
1 TATTCAATGTTGAATTTTAA
29379 GTTAGAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (21 bp):
TATTCAATGTTGAATTTTAAT
Found at i:29765 original size:15 final size:15
Alignment explanation
Indices: 29745--29783 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
29735 ATCGATTTAG
* *
29745 TTATATTTTATAGAA
1 TTATATTATACAGAA
29760 TTATATTATACAGAA
1 TTATATTATACAGAA
*
29775 TTAGATTAT
1 TTATATTAT
29784 GTTTTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (15 bp):
TTATATTATACAGAA
Found at i:30248 original size:23 final size:24
Alignment explanation
Indices: 30201--30254 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
30191 GGGAACGTGC
* *
30201 CACAAGAGAATAGAAAAAGCGTGT
1 CACAAGAGAAGAGAAAAAGCATGT
*
30225 CACAAGAGCAGAG-AAAAGCATGT
1 CACAAGAGAAGAGAAAAAGCATGT
30248 CACAAGA
1 CACAAGA
30255 ACAAAGATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.50, C:0.17, G:0.24, T:0.09
Consensus pattern (24 bp):
CACAAGAGAAGAGAAAAAGCATGT
Found at i:43141 original size:77 final size:79
Alignment explanation
Indices: 43044--43195 Score: 200
Period size: 77 Copynumber: 1.9 Consensus size: 79
43034 AAAAAATTTA
* * **
43044 TTATTTAATTAATTCTAATTAAATATACATT-AAAGACATATAATCTGAATTACAATC-TTTAAT
1 TTATTTAATTAATTCGAATTAAATATAAATTCAAAGACATATAATCAAAATTACAATCTTTTAAT
*
43107 GTTTATTTAAAATC
66 GTTTACTTAAAATC
* ** * *
43121 TTATTTAATTATTTCGAATTAAATATAAATTCAAAGAGTTGTAATCAAAATTACATTCTTTTAAT
1 TTATTTAATTAATTCGAATTAAATATAAATTCAAAGACATATAATCAAAATTACAATCTTTTAAT
43186 GTTTACTTAA
66 GTTTACTTAA
43196 TATATTTGGG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 28 0.44
78 20 0.32
79 15 0.24
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (79 bp):
TTATTTAATTAATTCGAATTAAATATAAATTCAAAGACATATAATCAAAATTACAATCTTTTAAT
GTTTACTTAAAATC
Found at i:45613 original size:112 final size:111
Alignment explanation
Indices: 45412--45639 Score: 348
Period size: 112 Copynumber: 2.0 Consensus size: 111
45402 GTTATAAGTG
* * * * * *
45412 CATTTCGACATACTTTGTGTATGATGGTATTGATCGATTTTGTTTAATGCATAACGGTGCATTTT
1 CATTTCGACATACTTAGTGTATGAAGGTATCGATCAATTTTGCTTAATGCATAACAGTGCATTTT
* * *
45477 TGGCATAAAAGATGCCACCTATGGTATTCATAATGAGGTGGATTAC
66 CGGCATAAAAGATGCCACCCATGGTATTCATAATGAGGTGAATTAC
*
45523 CATTTCGACATACTTAGTGTATGAAAGTTATCGATCAATTTTGCTTAATGCATAACAGTGCATTT
1 CATTTCGACATACTTAGTGTATG-AAGGTATCGATCAATTTTGCTTAATGCATAACAGTGCATTT
*
45588 TCGGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
65 TCGGCATAAAAGATGCCACCCATGGTATTCATAATGAGGTGAATTAC
45635 CATTT
1 CATTT
45640 TGGCACTTCG
Statistics
Matches: 105, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
111 22 0.21
112 83 0.79
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (111 bp):
CATTTCGACATACTTAGTGTATGAAGGTATCGATCAATTTTGCTTAATGCATAACAGTGCATTTT
CGGCATAAAAGATGCCACCCATGGTATTCATAATGAGGTGAATTAC
Found at i:47673 original size:46 final size:46
Alignment explanation
Indices: 47496--47671 Score: 253
Period size: 46 Copynumber: 3.8 Consensus size: 46
47486 AATTATGTAA
* * * *
47496 TTTCAATTGTGGCATACTTTTAGGTAAATTATGCACTGATATACAT
1 TTTCATTTGTGGCATCCTTTCATGTAAATTATGCACTGATATACAT
* *
47542 TTTCATTTGTGGCATCCTTTCATGTAAATTATGAATTGATATACAT
1 TTTCATTTGTGGCATCCTTTCATGTAAATTATGCACTGATATACAT
* * *
47588 TTTCATTTGTTGCATCATTTCATGTAAATTATGCACTGTTATACAT
1 TTTCATTTGTGGCATCCTTTCATGTAAATTATGCACTGATATACAT
**
47634 TTTCATTTGTGGCATCCTTTCATGCCAATTATGCACTG
1 TTTCATTTGTGGCATCCTTTCATGTAAATTATGCACTG
47672 TTCTTCATCT
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 115 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (46 bp):
TTTCATTTGTGGCATCCTTTCATGTAAATTATGCACTGATATACAT
Found at i:47758 original size:49 final size:49
Alignment explanation
Indices: 47677--47774 Score: 115
Period size: 49 Copynumber: 2.0 Consensus size: 49
47667 CACTGTTCTT
* * * *
47677 CATCTAACTTGCATTAGTGACACCTTTCTGCCAGAAATGCACCATTAGG
1 CATCTAACTTGCATTAATGACACCTTTCTGCCAAAAAAGCACAATTAGG
* ** * *
47726 CATCTATCTTGCATTAATGGTACTTTTTTGCCAAAAAAGCACAATTAGG
1 CATCTAACTTGCATTAATGACACCTTTCTGCCAAAAAAGCACAATTAGG
47775 TATTTAGTCT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (49 bp):
CATCTAACTTGCATTAATGACACCTTTCTGCCAAAAAAGCACAATTAGG
Found at i:48082 original size:54 final size:54
Alignment explanation
Indices: 48024--48383 Score: 483
Period size: 54 Copynumber: 6.7 Consensus size: 54
48014 ACCAATACAA
*
48024 AAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCCATACTG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACTG
* * **
48078 AAATTTATAAAATTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACAA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACTG
* * * * *
48132 AAATTCGTAAACTTATTATAAATTTCTTAGTTTGCACATATGGTGCTCATA-TGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACT-G
* ** *
48186 AAATTCATAAACTTATTATGAGTTTCTTAGTTT-CACACATAGTGCTTATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACTG
* *
48239 AAATTCAAAAACTTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACAG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACTG
* * * *
48293 AAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACCTAGTGTCTATA-TAA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACT-G
* *
48347 AAATTCATAAGCTTTTTATGAATTTCTTAGTTTGCAC
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTGCAC
48384 GCTTAGTGTC
Statistics
Matches: 268, Mismatches: 34, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
53 46 0.17
54 222 0.83
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (54 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACTG
Found at i:48289 original size:161 final size:162
Alignment explanation
Indices: 48022--48383 Score: 541
Period size: 161 Copynumber: 2.2 Consensus size: 162
48012 CTACCAATAC
* *
48022 AAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCCATACTGAAATTTATA
1 AAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCCATACGGAAATTCATA
*
48087 AAATTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACAAAAATTCGTAAACTTATTATA
66 AAATTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACAAAAATTCATAAACTTATTATA
* *
48152 AATTTCTTAGTTTGCACATATGGTG-CTCATAT
131 AATTTCTTAGTTTGCACACATAGTGTCT-ATAT
** * * **
48184 GGAAATTCATAAACTTATTATGAGTTTCTTAGTTT-CACACATAGTGCTTATACGGAAATTCA-A
1 AAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCCATACGGAAATTCATA
*
48247 AAACTTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACAGAAATTCATAAACTTATTAT
66 AAA-TTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACAAAAATTCATAAACTTATTAT
* *
48312 GAATTTCTTAGTTTGCACACCTAGTGTCTATAT
130 AAATTTCTTAGTTTGCACACATAGTGTCTATAT
* *
48345 AAAAATTCATAAGCTTTTTATGAATTTCTTAGTTTGCAC
1 AAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCAC
48384 GCTTAGTGTC
Statistics
Matches: 178, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
160 4 0.02
161 137 0.77
162 37 0.21
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (162 bp):
AAAAATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCCATACGGAAATTCATA
AAATTATTATGAATTTCTTAGTTTGCACACATAGTGCCCATACAAAAATTCATAAACTTATTATA
AATTTCTTAGTTTGCACACATAGTGTCTATAT
Found at i:53822 original size:81 final size:81
Alignment explanation
Indices: 53685--54485 Score: 1122
Period size: 81 Copynumber: 9.9 Consensus size: 81
53675 CTGTTTTAAA
* * * * * *
53685 TAAAAGATTAATGGCCTCGCTGTGTATTTTACAGAAATGTGTCAATTATGCAAGTTAGATAAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
53750 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * * *
53766 TAAAATATTAATGGCCTAGCT-TGGCATTTTATAGAAATGAGTCAATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGT-GCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAA
53830 GGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
* * *
53847 TAAAAGATTAATGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATTCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
**
53912 AATAAATACCTTTGAG
66 GTTAAATACCTTTGAG
*
53928 TAAAAGATTAATGGCCTAGCTGTGCATTTGACATAAAGGTGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
53993 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
54009 TAAAAGATTAATGGCCTAGATGTGCATTTGACATAAAAGAGTCAATTATG-TGAGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCT-AGTTAGATGAAA
54073 GGTTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
* *
54090 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGTTGTCAATTATTCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
54155 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
54171 TAAAAGATTAATGGCCTAGCTATTCATTTGACAGAAAGATGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
* *
54236 GCTAAATACCTTTGCG
66 GTTAAATACCTTTGAG
* * * * ** * *
54252 TAAAAGATTAATGGCCTAGCTATGAATTTGATAAAAATATGTCAATTATACTAGTTGGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
*
54317 GTTAAATACCTTCGAG
66 GTTAAATACCTTTGAG
54333 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGAC-AGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATG-CTAGTTAGATGAAA
* *
54397 TGTTATATACCTTTGAG
65 GGTTAAATACCTTTGAG
* ** * * * *
54414 TAAAAGATTATTTACCTAGCTGTGCAATTGGCAGAAAAGTGTCAATTATGCAAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
*
54479 GCTAAAT
66 GTTAAAT
54486 GTGTTAGGGT
Statistics
Matches: 647, Mismatches: 67, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
80 3 0.00
81 641 0.99
82 3 0.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:61175 original size:41 final size:41
Alignment explanation
Indices: 61130--61223 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
61120 CATGTATTAA
* * *
61130 TTCACAATTCAATTCAATTCAATCA-TGACAACATGCAATAG
1 TTCACCATTCAATCCAATTCAATCATTG-CAACATGCAATAC
** *
61171 TTCACCATTTGATCCAATTCAATCATTGCAGCATGCAATAC
1 TTCACCATTCAATCCAATTCAATCATTGCAACATGCAATAC
61212 TTCACCATTCAA
1 TTCACCATTCAA
61224 CTTGTTTCGA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.31
Consensus pattern (41 bp):
TTCACCATTCAATCCAATTCAATCATTGCAACATGCAATAC
Found at i:70570 original size:10 final size:10
Alignment explanation
Indices: 70555--70590 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
70545 GTAACATCGT
70555 AAAAAAAGAA
1 AAAAAAAGAA
**
70565 AAAAAAAGTG
1 AAAAAAAGAA
70575 AAAAAAAGAA
1 AAAAAAAGAA
70585 AAAAAA
1 AAAAAA
70591 TGTGTAGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:73785 original size:17 final size:17
Alignment explanation
Indices: 73763--73807 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
73753 AGATTAAATT
*
73763 TAATAAATGGTAAAGTA
1 TAATAAATGATAAAGTA
73780 TAATAAATGATAAAGTA
1 TAATAAATGATAAAGTA
73797 TAATAAATGAT
1 TAATAAATGAT
73808 TTAGGAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (17 bp):
TAATAAATGATAAAGTA
Found at i:76554 original size:24 final size:24
Alignment explanation
Indices: 76522--76574 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
76512 GCTCCTAAGT
76522 TATGGGAGAAGAGGATGAAGGTCC
1 TATGGGAGAAGAGGATGAAGGTCC
*
76546 TATGGGAGAAGAGGATGAAGGTCT
1 TATGGGAGAAGAGGATGAAGGTCC
76570 TATGG
1 TATGG
76575 AAGATGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.32, C:0.06, G:0.42, T:0.21
Consensus pattern (24 bp):
TATGGGAGAAGAGGATGAAGGTCC
Found at i:85153 original size:41 final size:41
Alignment explanation
Indices: 85108--85205 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 41
85098 TTCACCACTA
* *
85108 AACTTGATTCGATCATGGTAGCATACATTAATTCAACATTC
1 AACTTGATTCGATCATGGTAGAATACAATAATTCAACATTC
* *
85149 AACTTGATTCGATCATTGTAGAATACAATAATTCACCATTC
1 AACTTGATTCGATCATGGTAGAATACAATAATTCAACATTC
*
85190 AACTTGATTCAATCAT
1 AACTTGATTCGATCAT
85206 AGTAACATGC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (41 bp):
AACTTGATTCGATCATGGTAGAATACAATAATTCAACATTC
Found at i:91006 original size:21 final size:21
Alignment explanation
Indices: 90989--91030 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
90979 CAACAATTTG
90989 TTCATTCAAGATTTCAATTCA
1 TTCATTCAAGATTTCAATTCA
91010 TTCATTCAAGATTTCAATTCA
1 TTCATTCAAGATTTCAATTCA
91031 ACTGAGTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (21 bp):
TTCATTCAAGATTTCAATTCA
Found at i:91101 original size:36 final size:36
Alignment explanation
Indices: 91061--91148 Score: 88
Period size: 40 Copynumber: 2.3 Consensus size: 36
91051 CATGTATTAA
*
91061 TTCACAATTCAATTCAATC-GTGACAACATGCAATAG
1 TTCACAATTCAATTCAATCAGTG-CAACATGCAATAC
* *
91097 TTCACCATTCGATCAATTCAATCATTGCAACATGCAATAC
1 TTCA-CAAT---TCAATTCAATCAGTGCAACATGCAATAC
*
91137 TTCACCATTCAA
1 TTCACAATTCAA
91149 CTTGTTTCGA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
36 8 0.19
37 3 0.07
39 2 0.05
40 27 0.64
41 2 0.05
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (36 bp):
TTCACAATTCAATTCAATCAGTGCAACATGCAATAC
Found at i:91113 original size:40 final size:40
Alignment explanation
Indices: 91069--91146 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
91059 AATTCACAAT
*
91069 TCAATTCAATC-GTGACAACATGCAATAGTTCACCATTCGA
1 TCAATTCAATCAGTG-CAACATGCAATACTTCACCATTCGA
*
91109 TCAATTCAATCATTGCAACATGCAATACTTCACCATTC
1 TCAATTCAATCAGTGCAACATGCAATACTTCACCATTC
91147 AACTTGTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 33 0.94
41 2 0.06
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.29
Consensus pattern (40 bp):
TCAATTCAATCAGTGCAACATGCAATACTTCACCATTCGA
Done.