Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004689.1 Hibiscus syriacus cultivar Beakdansim tig00010523_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: 61392
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:19124 original size:11 final size:11
Alignment explanation
Indices: 19102--19219 Score: 66
Period size: 11 Copynumber: 10.7 Consensus size: 11
19092 CTCGAATAAA
19102 AAAATAAAAAAT
1 AAAAT-AAAAAT
19114 AAAATAAAAAT
1 AAAATAAAAAT
* *
19125 AAAA-AAGAGAG
1 AAAATAA-AAAT
* *
19136 AGAAAGAAAATT
1 A-AAATAAAAAT
19148 AAAATTAAAAA-
1 AAAA-TAAAAAT
* *
19159 AAAAGATAAA-
1 AAAATAAAAAT
*
19169 AAAATGAAAA-
1 AAAATAAAAAT
*
19179 AAGATAAAAAT
1 AAAATAAAAAT
19190 AAAATAAAAA-
1 AAAATAAAAAT
*
19200 AGAAAGAAAAAT
1 A-AAATAAAAAT
*
19212 AGAATAAA
1 AAAATAAA
19220 CAAAAGGGGA
Statistics
Matches: 81, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
10 22 0.27
11 42 0.52
12 15 0.19
13 2 0.02
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:19124 original size:18 final size:18
Alignment explanation
Indices: 19099--19200 Score: 73
Period size: 18 Copynumber: 5.4 Consensus size: 18
19089 TTGCTCGAAT
19099 AAAAAAATAAAAAATAAA
1 AAAAAAATAAAAAATAAA
* *
19117 ATAAAAATAAAAAAGAGAGA
1 AAAAAAATAAAAAATA-A-A
* *
19137 GAAAGAAAATTAAAATTAAA
1 -AAA-AAAATAAAAAATAAA
*
19157 AAAAAAGATAAAAAA-ATGA
1 AAAAAA-ATAAAAAATA-AA
*
19176 AAAAAGAT-AAAAATAAA
1 AAAAAAATAAAAAATAAA
19193 ATAAAAAA
1 A-AAAAAA
19201 GAAAGAAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
17 7 0.11
18 26 0.41
19 16 0.25
20 2 0.03
21 3 0.05
22 10 0.16
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAAAAATAAAAAATAAA
Found at i:19179 original size:28 final size:26
Alignment explanation
Indices: 19096--19179 Score: 73
Period size: 28 Copynumber: 3.1 Consensus size: 26
19086 ATTTTGCTCG
*
19096 AATAAAAAAATAA-AAAATAAAATAAA
1 AATAAAAAAA-AAGAAAAGAAAATAAA
*
19122 AATAAAAAAGAGAGAGAAAGAAAATTAAA
1 AATAAAAAA-AAAGA-AAAGAAAA-TAAA
*
19151 ATTAAAAAAAAAGATAAA-AAAATGAAA
1 AATAAAAAAAAAGA-AAAGAAAAT-AAA
19178 AA
1 AA
19180 AGATAAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
26 11 0.23
27 10 0.21
28 14 0.30
29 12 0.26
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (26 bp):
AATAAAAAAAAAGAAAAGAAAATAAA
Found at i:20426 original size:15 final size:15
Alignment explanation
Indices: 20406--20436 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20396 TTTATATTTG
20406 ATATTATTGAAGACA
1 ATATTATTGAAGACA
20421 ATATTATTGAAGACA
1 ATATTATTGAAGACA
20436 A
1 A
20437 GAAAACCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (15 bp):
ATATTATTGAAGACA
Found at i:20742 original size:134 final size:132
Alignment explanation
Indices: 20452--20751 Score: 386
Period size: 134 Copynumber: 2.2 Consensus size: 132
20442 CCAAATCGAA
* * * * * * *
20452 CTCGATTCAATATTCCCTGAGCAACAGTGGAATGAATCAACATCCTCAGATCTGATTTTTCTCTC
1 CTCGATTCAATCTTCCCTAAG-AACAGTGGAATGAATCAACATCCCCAGACCTGAATTTCCCCTC
* *
20517 AAGAAAGCGAAACAGGTCCATCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTC
65 AAGAAAGCGAAACAGATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTC
20582 TAC
130 TAC
* * * *
20585 ATTGATTCAATCTTCCTTGAAGAATAGTGGAATGAATCAACATCCCCAGACCT-AATTTCCCCTC
1 CTCGATTCAATCTTCCCT-AAGAACAGTGGAATGAATCAACATCCCCAGACCTGAATTTCCCCTC
* * * *
20649 AAGAAGAAGCGGAATAGATTCATCTCTTTCAAGATTTGATATTCCCTGAGTGACAGTGGAACAAG
65 AAG-A-AAGCGAAACAGATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
20714 TCTAC
128 TCTAC
*
20719 CTCGATTCAATCTTCCCTAAAGAACAGTAGAAT
1 CTCGATTCAATCTTCCCT-AAGAACAGTGGAAT
20752 AAGTCAATGT
Statistics
Matches: 141, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
132 11 0.08
133 43 0.30
134 87 0.62
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (132 bp):
CTCGATTCAATCTTCCCTAAGAACAGTGGAATGAATCAACATCCCCAGACCTGAATTTCCCCTCA
AGAAAGCGAAACAGATCCATCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
AC
Found at i:22837 original size:19 final size:18
Alignment explanation
Indices: 22807--22848 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
22797 AACGCATATC
22807 ATTTTTTATCTTTTAAAATT
1 ATTTTTTATC--TTAAAATT
22827 ATTTTTT-TCTTAAAATT
1 ATTTTTTATCTTAAAATT
22844 ATTTT
1 ATTTT
22849 AAAGGATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.59
19 2 0.09
20 7 0.32
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTTATCTTAAAATT
Found at i:32756 original size:45 final size:45
Alignment explanation
Indices: 32667--32800 Score: 218
Period size: 45 Copynumber: 3.0 Consensus size: 45
32657 GTAAGCATGC
* * * *
32667 AAATAAGCTTATGAGCTTATGGAAT-AATGGCAAATATATTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
32711 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
32756 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGT-TATTGGTA
1 AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
32800 A
1 A
32801 GAAAGTTGTA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
44 32 0.38
45 53 0.62
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGATTAAATGGTAAGTATATTGGTA
Found at i:38466 original size:14 final size:14
Alignment explanation
Indices: 38447--38491 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
38437 CTAGAAACGC
38447 ATATACTTATAGAT
1 ATATACTTATAGAT
38461 ATATACTTATAGAT
1 ATATACTTATAGAT
*
38475 ATATACTTATATAT
1 ATATACTTATAGAT
38489 ATA
1 ATA
38492 ATGAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
ATATACTTATAGAT
Found at i:42235 original size:29 final size:29
Alignment explanation
Indices: 42202--42378 Score: 246
Period size: 29 Copynumber: 6.1 Consensus size: 29
42192 AGTCCATTAT
**
42202 TCTTTTACTCAACAGTGTTTAATTGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
* *
42231 TCTTTTACTCAATAGTGCTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
* *
42260 TCTTTTACTCAATAGTGCTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
* * *
42289 TCTTTTACTCAATAGAGTTTAACTGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
* *
42318 TCTTTTACTCAACTGTATTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
*
42347 TCTTTTACTCAACAGTATTTAACCGTTCA
1 TCTTTTACTCAACAGTGTTTAACCGTTCA
42376 TCT
1 TCT
42379 AATTGGGATA
Statistics
Matches: 135, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 135 1.00
ACGTcount: A:0.25, C:0.22, G:0.09, T:0.44
Consensus pattern (29 bp):
TCTTTTACTCAACAGTGTTTAACCGTTCA
Found at i:42482 original size:81 final size:81
Alignment explanation
Indices: 42347--42501 Score: 206
Period size: 81 Copynumber: 1.9 Consensus size: 81
42337 TAACCGTTCA
* * * * *
42347 TCTTTTACTCAACAGTATTTAACCGTTCATCTAATTGGGATAATTGACACCTTTCTGT-CAAATA
1 TCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAATCGAAACCTTTCT-TCCAAATA
*
42411 CACAGTTAGGCCATTAT
65 CACAGCTAGGCCATTAT
* *
42428 TCTTTTACTCAACGGTATTTAACCATTCATCTAACTGGCATGAA-CGAAACCTTTCTTCCAAATG
1 TCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCAT-AATCGAAACCTTTCTTCCAAATA
42492 CACAGCTAGG
65 CACAGCTAGG
42502 ACTCAAAGGC
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 1 0.02
81 61 0.95
82 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (81 bp):
TCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAATCGAAACCTTTCTTCCAAATAC
ACAGCTAGGCCATTAT
Found at i:42558 original size:68 final size:68
Alignment explanation
Indices: 42453--43116 Score: 943
Period size: 68 Copynumber: 9.8 Consensus size: 68
42443 TATTTAACCA
* * * * * * *
42453 TTCATCTAACTGGCATGAACGAAACCTTTCT-TCCAAATGCACAGCTAGGACTCAAAGGCAGTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGT-CAAATACACAGTTAGGCCTCAAAGGCACTTA
42517 GCCT
65 GCCT
* * * * *
42521 TTCATCTAACTGGCATAAATGACATCTTCCTGTCAAATGCACAGCTAGACCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
42586 CCT
66 CCT
* * * *
42589 TTCATCTAACTGACATAAATGACACATTTATGTCAAATACACAGTTAGGCCTCAAAGGCACTTAA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
42654 CCT
66 CCT
* * * * *
42657 TTCATATAACTGGCATAAATGACACCTTTATTTCAAATCCACAGTTAGGCCTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
42722 CCT
66 CCT
*
42725 TTCATATAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
42790 CCT
66 CCT
* * *
42793 TTCATCTAACTAGCATAAATGACACCTTTCTGTCAAATCCACAGTAAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
42858 CCT
66 CCT
* * * * *
42861 TTCATCTAACTGGCATAAATGACACATTTCTATAAAATGCACAGTTAGGTCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
42926 CCT
66 CCT
* * *
42929 TTCATCTAACTGGCATAAATGACACTTTTATGTCAAATACACAGTTAGGCCTCAAAGGCACTTAA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
42994 CCT
66 CCT
* * * * *
42997 TTCATATAACTGGCATAAATGACACCTTTATTTCAAATCCACAGTTAGGCCTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
43062 CCT
66 CCT
* * *
43065 TTCATATAACTGGCATAAATGATACATTTCTGTCAAATACACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCT
43117 ATTAATCTTT
Statistics
Matches: 538, Mismatches: 57, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
68 537 1.00
69 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:43421 original size:55 final size:55
Alignment explanation
Indices: 43292--43443 Score: 170
Period size: 55 Copynumber: 2.8 Consensus size: 55
43282 ACATATATTT
*
43292 CCCATACGA-AAATTCATACACTTGGA-ATGAATTTCTTA-TTTCACACACATAGTG
1 CCCATAC-ATAAATTCATACACTT-AATATGAATTTCTTAGTTTCACACACATAGTG
* * *
43346 ACCAAACATAAATTTATACACTTAATATGAATTTCTTAGGTTTGCACACA-A-AGTG
1 CCCATACATAAATTCATACACTTAATATGAATTTCTTA-GTTT-CACACACATAGTG
* *
43401 CCCATACATAAATTCGTACACTTAATATTAATTTCTTAAGTTT
1 CCCATACATAAATTCATACACTTAATATGAATTTCTT-AGTTT
43444 TTGTACACTT
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
53 2 0.02
54 30 0.36
55 40 0.48
56 5 0.06
57 6 0.07
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (55 bp):
CCCATACATAAATTCATACACTTAATATGAATTTCTTAGTTTCACACACATAGTG
Found at i:48615 original size:2 final size:2
Alignment explanation
Indices: 48608--48653 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
48598 TACATTATCC
48608 AT AT AT AT AT 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 AT AT AT AT AT
48650 AT AT
1 AT AT
48654 CATCCCTTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48824 original size:29 final size:29
Alignment explanation
Indices: 48791--49025 Score: 371
Period size: 29 Copynumber: 8.1 Consensus size: 29
48781 AGTCCATTAT
* **
48791 TCTTTTACTCAACAGTGTTTAACTATTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
48820 TCTTTTACTCAACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
48849 TCTTTTACTCAACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
48878 TCTTTTACTCAACATTATTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
48907 TCTTTTACTCAACATTATTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
48936 TCTTTTACTCAACATTATTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
48965 TCTTTTACTCAACATTATTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
* *
48994 TCTTTTACTCAATAGTATTTAACAGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
49023 TCT
1 TCT
49026 AACTGGGATA
Statistics
Matches: 199, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 199 1.00
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.44
Consensus pattern (29 bp):
TCTTTTACTCAACAGTATTTAACCGTTCA
Found at i:49093 original size:81 final size:81
Alignment explanation
Indices: 48994--49148 Score: 195
Period size: 81 Copynumber: 1.9 Consensus size: 81
48984 TAACCGTTCA
* * * * * * ** *
48994 TCTTTTACTCAATAGTATTTAA-CAGTTCATCTAACTGGGATAATTGACACCTTTCTGTCAAATT
1 TCTTTTACTCAACAGTATTAAATC-GTTCATCTAACTGGCATAAATGAAACCTTTATACCAAATG
49058 CACAGTTAGGTCATTAT
65 CACAGTTAGGTCATTAT
* *
49075 TCTTTTACTCAACGGTATTAAATCGTTCATCTAACTGTCATAAATGAAACCTTTATACCAAATGC
1 TCTTTTACTCAACAGTATTAAATCGTTCATCTAACTGGCATAAATGAAACCTTTATACCAAATGC
49140 ACAGTTAGG
66 ACAGTTAGG
49149 CCTCAAAAGC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
81 61 0.98
82 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAACAGTATTAAATCGTTCATCTAACTGGCATAAATGAAACCTTTATACCAAATGC
ACAGTTAGGTCATTAT
Found at i:49191 original size:68 final size:68
Alignment explanation
Indices: 49100--49431 Score: 423
Period size: 68 Copynumber: 4.9 Consensus size: 68
49090 TATTAAATCG
* * ** * *
49100 TTCATCTAACTGTCATAAATGAAACCTTTATACCAAATGCACAGTTAGGCCTCAAAAGCATTTAG
1 TTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
49165 CCT
66 CCT
* * *
49168 TTCATCGAACTGGCATAAATGAAACCTTTATGTCAAATGCATAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
49233 CCT
66 CCT
* * * * * *
49236 TTCATCTAACTGGCATAAATGACACATTTCTATCAAATGCAAAGTTATGCCTCAAAGGCAATTAG
1 TTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
49301 CTT
66 CCT
* * * * * * *
49304 TTCATCTAACTGACATAAAT-AACACATTTCTGTCGAATCCATAGTTAGGCCTTAAAGGTACTTA
1 TTCATCTAACTGGCATAAATGAA-ACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
49368 GCCT
65 GCCT
* *
49372 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCA
1 TTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCA
49432 TGTCGCTACA
Statistics
Matches: 227, Mismatches: 35, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
67 1 0.00
68 225 0.99
69 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGAAACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:49347 original size:136 final size:136
Alignment explanation
Indices: 49100--49431 Score: 468
Period size: 136 Copynumber: 2.4 Consensus size: 136
49090 TATTAAATCG
* * * * * *
49100 TTCATCTAACTGTCATAAATGAAACCTTTATACCAAATGCACAGTTAGGCCTCAAAAGCATTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCAATTAG
* * *
49165 CCTTTCATCGAACTGGCATAAATGAAACCTTTATGTCAAATGCATAGTTAGGCCTCAAAGGCACT
66 CCTTTCATCGAACTGACATAAATGAAACATTTATGTCAAATCCATAGTTAGGCCTCAAAGGCACT
49230 TAGCCT
131 TAGCCT
* * *
49236 TTCATCTAACTGGCATAAATGACACATTTCTATCAAATGCAAAGTTATGCCTCAAAGGCAATTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCAATTAG
* * * * * *
49301 CTTTTCATCTAACTGACATAAAT-AACACATTTCTGTCGAATCCATAGTTAGGCCTTAAAGGTAC
66 CCTTTCATCGAACTGACATAAATGAA-ACATTTATGTCAAATCCATAGTTAGGCCTCAAAGGCAC
49365 TTAGCCT
130 TTAGCCT
* *
49372 TTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATACACAGTTAGGCCTCAAAGGCA
1 TTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCA
49432 TGTCGCTACA
Statistics
Matches: 172, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
135 2 0.01
136 170 0.99
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.30
Consensus pattern (136 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCAATTAG
CCTTTCATCGAACTGACATAAATGAAACATTTATGTCAAATCCATAGTTAGGCCTCAAAGGCACT
TAGCCT
Found at i:52413 original size:21 final size:21
Alignment explanation
Indices: 52389--52451 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
52379 TACCTGATTG
52389 ACTTCATAATTGTTAATCAAA
1 ACTTCATAATTGTTAATCAAA
* * * * *
52410 ACTTGA-ATTTTTTTATCATTA
1 ACTTCATAATTGTTAATCA-AA
*
52431 ACTTCATCATTGTTAATCAAA
1 ACTTCATAATTGTTAATCAAA
52452 GCCCAAACCA
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
20 9 0.31
21 12 0.41
22 8 0.28
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (21 bp):
ACTTCATAATTGTTAATCAAA
Found at i:53525 original size:30 final size:30
Alignment explanation
Indices: 53490--53580 Score: 173
Period size: 30 Copynumber: 3.0 Consensus size: 30
53480 TATTAGAGTG
53490 TGCCTAAAGACCAATCATATGATGATTGTA
1 TGCCTAAAGACCAATCATATGATGATTGTA
53520 TGCCTAAAGACCAATCATATGATGATTGTA
1 TGCCTAAAGACCAATCATATGATGATTGTA
*
53550 TGCCTAAAGATCAATCATATGATGATTGTA
1 TGCCTAAAGACCAATCATATGATGATTGTA
53580 T
1 T
53581 TGACATATTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (30 bp):
TGCCTAAAGACCAATCATATGATGATTGTA
Found at i:58887 original size:23 final size:23
Alignment explanation
Indices: 58848--58894 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
58838 GACGATCGGT
*
58848 TTTTTTACCGGATAAAAAACCGG
1 TTTTTTACCGGAAAAAAAACCGG
*
58871 TTTTTTATCC-GAAAAAAATCCGG
1 TTTTTTA-CCGGAAAAAAAACCGG
58894 T
1 T
58895 CCGGGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (23 bp):
TTTTTTACCGGAAAAAAAACCGG
Done.