Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007470.1 Hibiscus syriacus cultivar Beakdansim tig00020517_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: 76694
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:13037 original size:55 final size:55
Alignment explanation
Indices: 12953--13227 Score: 401
Period size: 55 Copynumber: 5.0 Consensus size: 55
12943 ATTTCCAAAT
* * * *
12953 GGCACTATGCGTGCAAAACTAAGAAATTCATAATTAGTTTATGAATTTTTGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* *
13008 GGCACTTTGAGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTAT-GTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTT-TCGTATG
13063 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAAG-TTATTGAATTTTCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAAT-AAGTTTA-TGAATTTTCGTATG
** * *
13119 GGCACTTTGTGTGCAAAGTTAACAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
* *
13174 GGCACTTTGTGTGCAAAACTAAGAAATTCAAAATAAGTTTATGAATTTCCGTAT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
13228 TGTTAGTGGA
Statistics
Matches: 201, Mismatches: 14, Indels: 10
0.89 0.06 0.04
Matches are distributed among these distances:
55 151 0.75
56 50 0.25
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (55 bp):
GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATG
Found at i:13146 original size:111 final size:110
Alignment explanation
Indices: 12953--13227 Score: 408
Period size: 111 Copynumber: 2.5 Consensus size: 110
12943 ATTTCCAAAT
* * * *
12953 GGCACTATGCGTGCAAAACTAAGAAATTCATAATTAGTTTATGAATTTTTGTATGGGCACTTTGA
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGA
* * *
13018 GTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTATGTATG
66 GTGCAAAACTAACAAATTCATAATAAGTTTATGAATTTACGTATG
13063 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAAG-TTATTGAATTTTCGTATGGGCACTTT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAAT-AAGTTTA-TGAATTTTCGTATGGGCACTTT
* ** *
13127 GTGTGCAAAGTTAACAAATTCATAATAAGTTTATGAATTTCCGTATG
64 GAGTGCAAAACTAACAAATTCATAATAAGTTTATGAATTTACGTATG
* *
13174 GGCACTTTGTGTGCAAAACTAAGAAATTCAAAATAAGTTTATGAATTTCCGTAT
1 GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
13228 TGTTAGTGGA
Statistics
Matches: 149, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
110 50 0.34
111 99 0.66
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (110 bp):
GGCACTTTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGA
GTGCAAAACTAACAAATTCATAATAAGTTTATGAATTTACGTATG
Found at i:13296 original size:54 final size:53
Alignment explanation
Indices: 12963--13299 Score: 248
Period size: 55 Copynumber: 6.1 Consensus size: 53
12953 GGCACTATGC
* ** * ** *
12963 GTGCAAAACTAAGAAATTCATAATTAGTTTATGAATTTTTGTATGGGCACTTTGA
1 GTGCAAAAC-AAGAAATTCATAATAAGTTTATGAATTTCCGTATTGATAC-TTGT
* ** * **
13018 GTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTATGTATGGGCACTTTGT
1 GTGCAAAAC-AAGAAATTCATAATAAGTTTATGAATTTCCGTATTGATAC-TTGT
* * **
13073 GTGCAAAACTAAGAAATTCATAATAAAG-TTATTGAATTTTCGTATGGGCACTTTGT
1 GTGCAAAAC-AAGAAATTCATAAT-AAGTTTA-TGAATTTCCGTATTGATAC-TTGT
** * * **
13129 GTGCAAAGTTAACAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGT
1 GTGCAAA-ACAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGATAC-TTGT
* * * *
13184 GTGCAAAACTAAGAAATTCAAAATAAGTTTATGAATTTCCGTATTGTTAGTGGAT
1 GTGCAAAAC-AAGAAATTCATAATAAGTTTATGAATTTCCGTATTGATACTTG-T
* * *
13239 GTGCAACCAAC-ATAAATT-ATAATAAGTTTGTGAATTACCGTATTGATACTATGT
1 GTGCAA--AACAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGATACT-TGT
13293 GTGCAAA
1 GTGCAAA
13300 CTATAGACTT
Statistics
Matches: 246, Mismatches: 27, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
52 1 0.00
54 36 0.15
55 158 0.64
56 48 0.20
57 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (53 bp):
GTGCAAAACAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGATACTTGT
Found at i:13571 original size:46 final size:46
Alignment explanation
Indices: 13519--13606 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
13509 TTAGATGAAG
*
13519 AACAGTGCATAATTGGCAGGAAAGGATGCCATAAATGAAAATGTAT
1 AACAGTGCATAATTGGCAGGAAAGGATGCCACAAATGAAAATGTAT
13565 AACAGTGCATAATTGGCAGGAAAGGATGCCACAAATGAAAAT
1 AACAGTGCATAATTGGCAGGAAAGGATGCCACAAATGAAAAT
13607 ATGTAGAGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.19
Consensus pattern (46 bp):
AACAGTGCATAATTGGCAGGAAAGGATGCCACAAATGAAAATGTAT
Found at i:20508 original size:21 final size:20
Alignment explanation
Indices: 20484--20523 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20474 GAGAAATCAA
*
20484 GAAAAAGAAAGAATAAAATAG
1 GAAAAAG-AAGAAAAAAATAG
*
20505 GAAAATGAAGAAAAAAATA
1 GAAAAAGAAGAAAAAAATA
20524 AAAATGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.10
Consensus pattern (20 bp):
GAAAAAGAAGAAAAAAATAG
Found at i:21991 original size:59 final size:60
Alignment explanation
Indices: 21883--22027 Score: 238
Period size: 59 Copynumber: 2.4 Consensus size: 60
21873 TTTGTTGATC
21883 CTCAACTATTATAAAGGTTATAAAATGGTCCCTTTACTATATGACACTATTTTATTGAGTCT
1 CTCAACTATTA-AAA-GTTATAAAATGGTCCCTTTACTATATGACACTATTTTATTGAGTCT
* *
21945 CTCAACTATTAAAAGTTATAAAATGGTTCC-TTACTATATGATACTATTTTATTGAGTCT
1 CTCAACTATTAAAAGTTATAAAATGGTCCCTTTACTATATGACACTATTTTATTGAGTCT
*
22004 CCCAACTATTAAAAGTTATAAAAT
1 CTCAACTATTAAAAGTTATAAAAT
22028 TTTCACCTGA
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
59 51 0.64
60 15 0.19
61 3 0.04
62 11 0.14
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (60 bp):
CTCAACTATTAAAAGTTATAAAATGGTCCCTTTACTATATGACACTATTTTATTGAGTCT
Found at i:22770 original size:15 final size:15
Alignment explanation
Indices: 22750--22794 Score: 53
Period size: 13 Copynumber: 3.3 Consensus size: 15
22740 AAATATTTTA
22750 ATTTAAATAATATAT
1 ATTTAAATAATATAT
22765 ATTTAAA-AA-ATAT
1 ATTTAAATAATATAT
*
22778 ATTAAAAT-ATAT-T
1 ATTTAAATAATATAT
22791 ATTT
1 ATTT
22795 GTTTATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 15 0.58
14 4 0.15
15 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTAAATAATATAT
Found at i:23169 original size:41 final size:42
Alignment explanation
Indices: 23111--23209 Score: 166
Period size: 42 Copynumber: 2.4 Consensus size: 42
23101 AAATTATGGA
*
23111 TCGGGTCGGG-TCGGGCCGGA-TTTTTAAAGTTATGTTCATG
1 TCGGGTTGGGTTCGGGCCGGATTTTTTAAAGTTATGTTCATG
23151 TCGGGTTGGGTTCGGGCCGGATTTTTTAAAGTTATGTTCATG
1 TCGGGTTGGGTTCGGGCCGGATTTTTTAAAGTTATGTTCATG
*
23193 TCGGGTTGGGTTTGGGC
1 TCGGGTTGGGTTCGGGC
23210 TTAGGGTGAA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
40 9 0.16
41 10 0.18
42 36 0.65
ACGTcount: A:0.12, C:0.13, G:0.37, T:0.37
Consensus pattern (42 bp):
TCGGGTTGGGTTCGGGCCGGATTTTTTAAAGTTATGTTCATG
Found at i:23347 original size:18 final size:18
Alignment explanation
Indices: 23324--23358 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23314 AATTTTATTG
23324 AATAAAAATAATATTTTT
1 AATAAAAATAATATTTTT
* *
23342 AATAAATATATTATTTT
1 AATAAAAATAATATTTT
23359 AGATCAAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAAAAATAATATTTTT
Found at i:23717 original size:25 final size:25
Alignment explanation
Indices: 23688--23735 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
23678 GTTAAAATAA
*
23688 TCTACCCGGTATTAGGGTTCTCTTT
1 TCTACCCGATATTAGGGTTCTCTTT
*
23713 TCTACTCGATATTAGGGTTCTCT
1 TCTACCCGATATTAGGGTTCTCT
23736 ACCGCCTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (25 bp):
TCTACCCGATATTAGGGTTCTCTTT
Found at i:34478 original size:53 final size:52
Alignment explanation
Indices: 34420--34556 Score: 170
Period size: 51 Copynumber: 2.7 Consensus size: 52
34410 TATTTTACAT
*
34420 TAGTGTAAGTATGTGTTAAGTGTTGCACTTTTTTGTATTTAATTCACTTAAAC
1 TAGTGTAAGTATGTGTTAAGTGTTACACTTTTTT-TATTTAATTCACTTAAAC
* ** * * *
34473 TAGTGTAAGTATATGTTAAGTACTAAAC-TTTTTTATTTTATTCACTTACAC
1 TAGTGTAAGTATGTGTTAAGTGTTACACTTTTTTTATTTAATTCACTTAAAC
**
34524 CGGTGTAAGTATGTGTTAA-TGTTACACTTTTTT
1 TAGTGTAAGTATGTGTTAAGTGTTACACTTTTTT
34557 ATAGTACGAA
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
50 5 0.07
51 37 0.53
52 5 0.07
53 23 0.33
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.47
Consensus pattern (52 bp):
TAGTGTAAGTATGTGTTAAGTGTTACACTTTTTTTATTTAATTCACTTAAAC
Found at i:35328 original size:20 final size:20
Alignment explanation
Indices: 35277--35328 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
35267 GCATTTGATC
*
35277 CATCGATGCACAAGACCATG
1 CATCGATGCACTAGACCATG
35297 CATCGATGCACTAGACCATG
1 CATCGATGCACTAGACCATG
35317 CATCGATGCACT
1 CATCGATGCACT
35329 CAGGCTATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (20 bp):
CATCGATGCACTAGACCATG
Found at i:44060 original size:45 final size:46
Alignment explanation
Indices: 44011--44098 Score: 135
Period size: 45 Copynumber: 1.9 Consensus size: 46
44001 GAACATCGAA
* *
44011 TGCATTTTATGCATCGATGCAC-ATACCATG-ATTCGATGCACTTAG
1 TGCATTTAATGCATCGATGCACAAGACCATGCA-TCGATGCACTTAG
44056 TGCATTTAATGCATCGATGCACAAGACCATGCATCGATGCACT
1 TGCATTTAATGCATCGATGCACAAGACCATGCATCGATGCACT
44099 CAGGCTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
45 21 0.54
46 17 0.44
47 1 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (46 bp):
TGCATTTAATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
Found at i:46307 original size:60 final size:60
Alignment explanation
Indices: 46206--46322 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
46196 CATTTGACAT
* * * * * *
46206 GATGTCTTCAAGCTCCAAGGGGAAGCATTCAACTGCGAGCTTCTTCAACCTTAATGTCGA
1 GATGCCTTCAAGCTCCAAAGGGAAGCATGCAACTACCAGCTTCTTCAACCTAAATGTCGA
* * *
46266 GATGCCTTCAAG-TTCAAAGGGAATGCATGCAACTACCAGCTTGTTCGACCTAAATGT
1 GATGCCTTCAAGCTCCAAAGGGAA-GCATGCAACTACCAGCTTCTTCAACCTAAATGT
46323 AAACATCATG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 9 0.19
60 38 0.81
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (60 bp):
GATGCCTTCAAGCTCCAAAGGGAAGCATGCAACTACCAGCTTCTTCAACCTAAATGTCGA
Found at i:48844 original size:3 final size:3
Alignment explanation
Indices: 48827--48880 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
48817 TTGTTCTGAC
*
48827 TCA TCA CTC- TCA TCA TCA TCA TCA TTA TCA T-A TCCA TCA TCA TCA
1 TCA TCA -TCA TCA TCA TCA TCA TCA TCA TCA TCA T-CA TCA TCA TCA
*
48872 TCG TCA TCA
1 TCA TCA TCA
48881 GAAGAAGATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.09
3 35 0.81
4 4 0.09
ACGTcount: A:0.30, C:0.33, G:0.02, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:49808 original size:2 final size:2
Alignment explanation
Indices: 49801--49827 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49791 CATTGAAACA
49801 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
49828 ATTCTTAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50976 original size:15 final size:16
Alignment explanation
Indices: 50946--50981 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
50936 ATACAAAAAT
50946 TAATAAAATGTTAATA
1 TAATAAAATGTTAATA
50962 TAATAAAAT-TTAATA
1 TAATAAAATGTTAATA
*
50977 AAATA
1 TAATA
50982 TGAAAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TAATAAAATGTTAATA
Found at i:52413 original size:2 final size:2
Alignment explanation
Indices: 52406--52450 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
52396 TCGAATAACT
*
52406 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52448 TA T
1 TA T
52451 CACATCCCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53662 original size:17 final size:18
Alignment explanation
Indices: 53629--53665 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
53619 TAATAGTGAG
53629 TTATTATAAAATATATTT
1 TTATTATAAAATATATTT
*
53647 TTATTAT-AATTATATTT
1 TTATTATAAAATATATTT
53664 TT
1 TT
53666 GTTTGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTATAAAATATATTT
Found at i:53993 original size:26 final size:25
Alignment explanation
Indices: 53942--53996 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
53932 ACACTTTTAA
* * *
53942 AAAAATGTTGTAGAAATGAACTTTT
1 AAAAATGTTGTACAAAAGAACGTTT
*
53967 AAAAATGTTGTACAAAAGAGCAGTTT
1 AAAAATGTTGTACAAAAGAAC-GTTT
53993 AAAA
1 AAAA
53997 TTTAACTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.29
Consensus pattern (25 bp):
AAAAATGTTGTACAAAAGAACGTTT
Found at i:54158 original size:51 final size:51
Alignment explanation
Indices: 54097--54195 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
54087 ATATTTACAC
* * * *
54097 TTATATATGAATCATATTAGTTTAAACTATAATAAATTTTAAAAAATATTA
1 TTATATATGAATCATATCAATTTAAACTATAATAAAATATAAAAAATATTA
*
54148 TTATATATGAATTATATCAATTTAAACTATAATAAAATATAAAAAATA
1 TTATATATGAATCATATCAATTTAAACTATAATAAAATATAAAAAATA
54196 CAAATAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (51 bp):
TTATATATGAATCATATCAATTTAAACTATAATAAAATATAAAAAATATTA
Found at i:57039 original size:16 final size:16
Alignment explanation
Indices: 57018--57052 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
57008 AGCAATTTTG
57018 CCAAGATCTTTTCCCT
1 CCAAGATCTTTTCCCT
57034 CCAAGATCTTTTCCCT
1 CCAAGATCTTTTCCCT
57050 CCA
1 CCA
57053 TTTTTGTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.20, C:0.40, G:0.06, T:0.34
Consensus pattern (16 bp):
CCAAGATCTTTTCCCT
Found at i:58790 original size:49 final size:49
Alignment explanation
Indices: 58713--59055 Score: 488
Period size: 49 Copynumber: 7.0 Consensus size: 49
58703 AATACCATGG
** *
58713 GTGGCACCTTTTATGCCGAAATATACCGTTATGCATTTAACTTTCATTC
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
*
58762 GTGGCACCTTTTATGCCGAAATGCACCGTTATACATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* * *
58811 GTGGCACCTTTTATGCCTAAATGCACTGTTGTGCATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* * * *
58860 ATGGCACCTATTATGCCGAAATGCATCGTTATGCATTTAACTTTTATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* * * * *
58909 GTGGCACCTTTTATGCCAAAATGCACCGTCATGCTTTTAACTTTTATCA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* * * *
58958 GTGACACCTTTTATGCCGAAATACACCGATATGCATTTAACTTTTATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* *
59007 GTGTCACCTTTTATGCCGAAATGCACCATTATGCATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
59056 ATTCATTTTA
Statistics
Matches: 260, Mismatches: 34, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 260 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (49 bp):
GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
Found at i:65735 original size:49 final size:49
Alignment explanation
Indices: 65682--66024 Score: 479
Period size: 49 Copynumber: 7.0 Consensus size: 49
65672 AATACCATGG
65682 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* **
65731 GTGGCACCTTTTATGCCTAAATGCAATGTTATGCATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* *
65780 GTAGCACCTTTTATGCCTAAATGCACCGTTATGCATTTAACTTTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* * * * *
65829 ATGGCACCTTTTAAGCTGAAATGCACCATTATGCATTTAACTTTTATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* * * * *
65878 CTGGCACCTTTTATGTCGCAATGCACTGTTATGCATTTAACTTTTATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
* * ** *
65927 GTGGCACCTTTTAAGCCTAAATGCACCGTTATATATTTAACTTTTATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
** *
65976 GTGGCACCTTTTATGCCGAAATGCACTATTATGCATTTAACATTCATTA
1 GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
66025 ATTCATTTTA
Statistics
Matches: 258, Mismatches: 36, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 258 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (49 bp):
GTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTA
Found at i:69475 original size:18 final size:17
Alignment explanation
Indices: 69452--69490 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
69442 AGAGTGATCT
*
69452 AAAAAAGGATAAGACCTG
1 AAAAAA-GATAAAACCTG
*
69470 AAAAAAGTTAAAACCTG
1 AAAAAAGATAAAACCTG
69487 AAAA
1 AAAA
69491 GACTTGTGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (17 bp):
AAAAAAGATAAAACCTG
Found at i:71335 original size:32 final size:34
Alignment explanation
Indices: 71299--71368 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
71289 CCTTACAAAC
* *
71299 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACATT
*
71331 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACATT
71365 TCCC
1 TCCC
71369 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAGAACATT
Found at i:74706 original size:34 final size:33
Alignment explanation
Indices: 74653--74724 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
74643 CCTTACAAAC
*
74653 TCCCTAGTTTTTCCGGGCTAAACAAGAACC-TT
1 TCCCTAGTTTTACCGGGCTAAACAAGAACCTTT
* *
74685 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTTT
1 TCCCTAG-TTTTAC-CGGGCTAAACAAGAACCTTT
74720 TCCCT
1 TCCCT
74725 TTACAAAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 15 0.44
35 7 0.21
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (33 bp):
TCCCTAGTTTTACCGGGCTAAACAAGAACCTTT
Done.