Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005057.1 Hibiscus syriacus cultivar Beakdansim tig00011351_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: 64974
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:4806 original size:130 final size:130
Alignment explanation
Indices: 4573--4809 Score: 304
Period size: 130 Copynumber: 1.8 Consensus size: 130
4563 TAATTTTAAG
* *
4573 AGAGAAAATGATAATACCTAATGATTTCAGATCGAAAATAAATGACCTATCATGCTCTAAAGTAG
1 AGAGAAAATGATAATACCTAATGATTTCAGATCGAAAACAAATGACCTATCATGCTCTAAAGCAG
*
4638 TCATTTATTACTACAATCAAAATGAATAGATATTACTATTTTATCTTAAAATTCAATATTCATTA
66 TCAATTATTACTACAATCAAAATGAATAGATATTACTATTTTATCTTAAAATTCAATATTCATTA
* * * *
4703 AGAGAAAATGATAATATCC-AATTATTTCTA-ATCGAGAACAAATGATCTCTCATGC-CTTAAAG
1 AGAGAAAATGATAATA-CCTAATGATTTC-AGATCGAAAACAAATGACCTATCATGCTC-TAAAG
* * *
4765 CAGTCAATTATTATTCCAA-CTGAAATGGAA-AGATATTACTATTTT
63 CAGTCAATTATTACTACAATC-AAAAT-GAATAGATATTACTATTTT
4810 CAATGTTAAT
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
129 2 0.02
130 84 0.91
131 6 0.07
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.34
Consensus pattern (130 bp):
AGAGAAAATGATAATACCTAATGATTTCAGATCGAAAACAAATGACCTATCATGCTCTAAAGCAG
TCAATTATTACTACAATCAAAATGAATAGATATTACTATTTTATCTTAAAATTCAATATTCATTA
Found at i:7580 original size:42 final size:41
Alignment explanation
Indices: 7480--7586 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
7470 GCCCGAAGGT
* * * *
7480 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAATA
1 CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
* * *
7521 CTTATATATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGA
*
7563 CTTACT-GATGGCACGAAGGACTTA
1 CTTA-TAGATGGCCCGAAGGACTTA
7587 TTAAGTAAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 20 0.38
42 32 0.60
43 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:7728 original size:21 final size:21
Alignment explanation
Indices: 7704--7744 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
7694 TTTGTGAAAA
*
7704 CATCCTACCCGAAGGACTTAT
1 CATCCTACCCGAAAGACTTAT
* *
7725 CATCTTACTCGAAAGACTTA
1 CATCCTACCCGAAAGACTTA
7745 CAATGACCCG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (21 bp):
CATCCTACCCGAAAGACTTAT
Found at i:7785 original size:41 final size:40
Alignment explanation
Indices: 7710--7805 Score: 102
Period size: 41 Copynumber: 2.4 Consensus size: 40
7700 AAAACATCCT
* * *
7710 ACCCGAAGGACTTATCATCTTACTCGAAAGACTTACAATG
1 ACCCGAAGGACTTAGCATCATACTCGAAAAACTTACAATG
* * *
7750 ACCCGAAGGATTTAAGCATCATGCTCGAAAAACTTACTGATG
1 ACCCGAAGGACTT-AGCATCATACTCGAAAAACTTAC-AATG
* *
7792 GCCCGAATGACTTA
1 ACCCGAAGGACTTA
7806 CTAAGTAAGA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
40 12 0.27
41 20 0.44
42 13 0.29
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (40 bp):
ACCCGAAGGACTTAGCATCATACTCGAAAAACTTACAATG
Found at i:12193 original size:27 final size:28
Alignment explanation
Indices: 12149--12213 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 28
12139 ATTATAGAAT
12149 TACCTCTAAAGTGAAAAATGACC-AAAA
1 TACCTCTAAAGTGAAAAATGACCTAAAA
* * *
12176 TGCCTCTAAAGTGTAAAATGACCTAAAG
1 TACCTCTAAAGTGAAAAATGACCTAAAA
12204 TACCTCTAAA
1 TACCTCTAAA
12214 CCCTGGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (28 bp):
TACCTCTAAAGTGAAAAATGACCTAAAA
Found at i:22041 original size:3 final size:3
Alignment explanation
Indices: 22020--22056 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
22010 CTACACCAAT
* *
22020 TAA TAA AAA TAA CAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
22057 GTCGAAACGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:23274 original size:16 final size:16
Alignment explanation
Indices: 23253--23283 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23243 AGGGCTATAA
*
23253 CCATGCATGTCAAACC
1 CCATGCATATCAAACC
23269 CCATGCATATCAAAC
1 CCATGCATATCAAAC
23284 ATACGTCGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.10, T:0.19
Consensus pattern (16 bp):
CCATGCATATCAAACC
Found at i:27366 original size:23 final size:23
Alignment explanation
Indices: 27340--27385 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
27330 AACATCAATG
27340 ATTTTCGAAAAT-AATTTTTTTTT
1 ATTTT-GAAAATAAATTTTTTTTT
**
27363 ATTTTGAATTTAAATTTTTTTTT
1 ATTTTGAAAATAAATTTTTTTTT
27386 TGAAAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (23 bp):
ATTTTGAAAATAAATTTTTTTTT
Found at i:33396 original size:45 final size:46
Alignment explanation
Indices: 33311--33398 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
33301 AAATATCCTG
* *
33311 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
33357 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
33399 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 22 0.55
46 18 0.45
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:37481 original size:18 final size:17
Alignment explanation
Indices: 37450--37485 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
37440 ACTAAAATCA
37450 AATATTCATATAATAAT
1 AATATTCATATAATAAT
*
37467 AATATATCATGTAATAAT
1 AATAT-TCATATAATAAT
37485 A
1 A
37486 GGACTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (17 bp):
AATATTCATATAATAAT
Found at i:43140 original size:17 final size:19
Alignment explanation
Indices: 43095--43140 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
43085 ATATCACATG
*
43095 TATCCTAAAACCCGGTATA
1 TATCCCAAAACCCGGTATA
* *
43114 AATACCAAAACCC-G-ATA
1 TATCCCAAAACCCGGTATA
43131 TATCCCAAAA
1 TATCCCAAAA
43141 ACTCTCTCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
17 11 0.50
18 1 0.05
19 10 0.45
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.20
Consensus pattern (19 bp):
TATCCCAAAACCCGGTATA
Found at i:59170 original size:14 final size:15
Alignment explanation
Indices: 59149--59194 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
59139 GAAAAAAAGA
59149 AAAAAAATGAAAAAT
1 AAAAAAATGAAAAAT
*
59164 -GAAAAATG-AAAAT
1 AAAAAAATGAAAAAT
59177 AAAAAAATGAAAAA-
1 AAAAAAATGAAAAAT
59191 AAAA
1 AAAA
59195 CAAAACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 5 0.19
14 18 0.67
15 4 0.15
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (15 bp):
AAAAAAATGAAAAAT
Found at i:60857 original size:160 final size:159
Alignment explanation
Indices: 60540--61258 Score: 1081
Period size: 160 Copynumber: 4.5 Consensus size: 159
60530 GCAACAGAAG
* *
60540 ATTGTTCGAGTTCTACTCCCTGAAGAAAATAG-G-GCAGACCCGTAGGAAGATTATTTTTCGAGT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
* * * *
60603 TCTACTCTCTGAAGAAATAG-G-GTGGACCTGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTG
65 TCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTC-TACTCCCTG
60666 AAGAAATAGAGAGC-GAGCCCGTAGGAAGATT
129 AAGAAATAGAGAGCGGA-CCCGTAGGAAGATT
* *
60697 ATTGTTCGATTTCTACTTCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
*
60762 CTTACTCCCTGAAGAAAAAGAGAGTGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGA
66 C-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGA
* *
60827 AGAAATAGAGAGTGGACCCGGAGGAAGATT
130 AGAAATAGAGAGCGGACCCGTAGGAAGATT
*
60857 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
*
60922 CTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCTCTGA
66 C-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGA
60987 AGAAATAGAGAGCGGACCCGTAGGAAGATT
130 AGAAATAGAGAGCGGACCCGTAGGAAGATT
* *
61017 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCATAGGAAGATTATTGTTTGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
* * * *
61082 TCTACTCCCTGAAGAAATAGAGAGCGGACCCATAGGAAGATTATTATTCGAGTTCTACTCCTTGA
65 TCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGA
* * * *
61147 AGGAAGAGAGAGCAGACCCGTAGGAAGATA
130 AGAAATAGAGAGCGGACCCGTAGGAAGATT
** * *
61177 ATTGTTCGAGTTCTACTCCCTGAAGAAAAGAGAGAGC-GAGCCCGTAGGAAGAAGAATGTTTGAG
1 ATTGTTCGAGTTCTACTCCCTGAAGAAAA-AGAGAGCGGA-CCCGTAGGAAGATTATTGTTCGAG
61241 TTCTACTCCCTGAAGAAA
64 TTCTACTCCCTGAAGAAA
61259 GAGGAAGTGA
Statistics
Matches: 521, Mismatches: 32, Indels: 15
0.92 0.06 0.03
Matches are distributed among these distances:
156 2 0.00
157 28 0.05
158 30 0.06
159 34 0.07
160 344 0.66
161 83 0.16
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (159 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
CTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTACTCCCTGAA
GAAATAGAGAGCGGACCCGTAGGAAGATT
Found at i:61067 original size:267 final size:267
Alignment explanation
Indices: 60540--61258 Score: 1128
Period size: 267 Copynumber: 2.7 Consensus size: 267
60530 GCAACAGAAG
* *
60540 ATTGTTCGAGTTCTACTCCCTGAAGAAAATAG-G-GCAGACCCGTAGGAAGATTATTTTTCGAGT
1 ATTGTTCGAGTTCTACTCCCTGAAG-AAATAGAGAGCGGACCCGTAGGAAGATTATTATTCGAGT
* * *
60603 TCTACTCTCTGAAGAAATAG-G-GTGGACCTGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTG
65 TCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTG
* *
60666 AAGAAATAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGATTTCTACT-TCCTGAAGAAAAAGAG
130 AAGAAAAAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCT-CTGAAGAAAAAGAG
* *
60730 AGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGTGGACCCGT
194 AGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCAT
60795 AGGAAGATT
259 AGGAAGATT
* * *
60804 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGTGGACCCGGAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTATTCGAGTT
60869 CTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGA
66 CTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGA
*
60934 AGAAAAAGAGAGCG-GACCCGTAGGAAGATTATTGTTCGAGTTCTACTCTCTGAAGAAATAGAGA
131 AGAAAAAGAGAGCGAG-CCCGTAGGAAGATTATTGTTCGAGTTCTACTCTCTGAAGAAAAAGAGA
60998 GCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCATA
195 GCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCATA
61063 GGAAGATT
260 GGAAGATT
* *
61071 ATTGTTTGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCATAGGAAGATTATTATTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTATTCGAGTT
* * * * *
61136 CTACTCCTTGAAGGAAGAGAGAGCAGACCCGTAGGAAGATAATTGTTCGAGTTC-TACTCCCTGA
66 CTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGA
** * * *
61200 AGAAAAGAGAGAGCGAGCCCGTAGGAAGAAGAATGTTTGAGTTCTACTCCCTGAAGAAA
131 AGAAAA-AGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCTCTGAAGAAA
61259 GAGGAAGTGA
Statistics
Matches: 420, Mismatches: 27, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
263 6 0.01
264 26 0.06
265 45 0.11
266 18 0.04
267 323 0.77
268 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (267 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTATTCGAGTT
CTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGA
AGAAAAAGAGAGCGAGCCCGTAGGAAGATTATTGTTCGAGTTCTACTCTCTGAAGAAAAAGAGAG
CGGACCCGTAGGAAGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGCGGACCCATAG
GAAGATT
Found at i:61274 original size:107 final size:106
Alignment explanation
Indices: 60540--61258 Score: 1072
Period size: 107 Copynumber: 6.8 Consensus size: 106
60530 GCAACAGAAG
* *
60540 ATTGTTCGAGTTCTACTCCCTGAAGAAAATAG-G-GCAGACCCGTAGGAAGATTATTTTTCGAGT
1 ATTGTTCGAGTTCTACTCCCTGAAG-AAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
* * * *
60603 TCTACTCTCTGAAGAAATAG-G-GTGGACCTGTAGGAAGATT
65 TCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
*
60643 ATTGTTCGAGTTCTTACTCCCTGAAGAAATAGAGAGC-GAGCCCGTAGGAAGATTATTGTTCGAT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGA-CCCGTAGGAAGATTATTGTTCGAG
*
60707 TTCTACTTCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
64 TTCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
* *
60750 ATTGTTCGAGTTCTTACTCCCTGAAGAAAAAGAGAGTGGACCCGTAGGAAGATTATTGTTCGAGT
1 ATTGTTCGAGTTC-TACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGT
* * *
60815 TCTACTCCCTGAAGAAATAGAGAGTGGACCCGGAGGAAGATT
65 TCTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
60857 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
60922 CTTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
66 C-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
*
60964 ATTGTTCGAGTTCTACTCTCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
*
61029 CTTACTCCCTGAAGAAAAAGAGAGCGGACCCATAGGAAGATT
66 C-TACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
* * *
61071 ATTGTTTGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCATAGGAAGATTATTATTCGAGTT
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
* * * * *
61136 CTACTCCTTGAAGGAAGAGAGAGCAGACCCGTAGGAAGATA
66 CTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
* ** * *
61177 ATTGTTCGAGTTCTACTCCCTGAAGAAA-AGAGAGAGCGAGCCCGTAGGAAGAAGAATGTTTGAG
1 ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCG-GA-CCCGTAGGAAGATTATTGTTCGAG
61241 TTCTACTCCCTGAAGAAA
64 TTCTACTCCCTGAAGAAA
61259 GAGGAAGTGA
Statistics
Matches: 565, Mismatches: 41, Indels: 16
0.91 0.07 0.03
Matches are distributed among these distances:
103 19 0.03
104 15 0.03
105 49 0.09
106 115 0.20
107 365 0.65
108 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (106 bp):
ATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGCGGACCCGTAGGAAGATTATTGTTCGAGTT
CTACTCCCTGAAGAAAAAGAGAGCGGACCCGTAGGAAGATT
Found at i:61284 original size:53 final size:54
Alignment explanation
Indices: 60535--61274 Score: 633
Period size: 53 Copynumber: 13.9 Consensus size: 54
60525 GTGAAGCAAC
* *
60535 AGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAATAG-G-GC-AGACCCGTAGGA
1 AGAAGAATGTTCGAGTTCTACTCCCTGAAGAAAAGAGAGAGCGA-ACCCGTAGGA
** * * * * *
60587 AGATTATTTTTCGAGTTCTACTCTCTGAAGAAATAG-G-GTG-G-ACCTGTAGGA
1 AGAAGAATGTTCGAGTTCTACTCCCTGAAGAAA-AGAGAGAGCGAACCCGTAGGA
** * * *
60638 AGATTATTGTTCGAGTTCTTACTCCCTGAAG-AAATAGAGAGCGAGCCCGTAGGA
1 AGAAGAATGTTCGAGTTC-TACTCCCTGAAGAAAAGAGAGAGCGAACCCGTAGGA
** * * * *
60692 AGATTATTGTTCGATTTCTACTTCCTGAAGAAAA-AGAGAGCGGACCCGTAGGA
1 AGAAGAATGTTCGAGTTCTACTCCCTGAAGAAAAGAGAGAGCGAACCCGTAGGA
** * * *
60745 AGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAA-AGAGAGTGGACCCGTAGGA
1 AGAAGAATGTTCGAGTTC-TACTCCCTGAAGAAAAGAGAGAGCGAACCCGTAGGA
** * * *
60799 AGATTATTGTTCGAGTTCTACTCCCTGAAGAAATAGAGAGTG-G-ACCCGGAGGA
1 AGAAGAATGTTCGAGTTCTACTCCCTGAAGAAA-AGAGAGAGCGAACCCGTAGGA
** * * *
60852 AGATTATTGTTCGAGTTCTACTCCCTGAAG-AAATAGAGAGCGGACCCGTAGGA
1 AGAAGAATGTTCGAGTTCTACTCCCTGAAGAAAAGAGAGAGCGAACCCGTAGGA
** * *
60905 AGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAA-AGAGAGCGGACCCGTAGGA
1 AGAAGAATGTTCGAGTTC-TACTCCCTGAAGAAAAGAGAGAGCGAACCCGTAGGA
** * * * *
60959 AGATTATTGTTCGAGTTCTACTCTCTGAAG-AAATAGAGAGCGGACCCGTAGGA
1 AGAAGAATGTTCGAGTTCTACTCCCTGAAGAAAAGAGAGAGCGAACCCGTAGGA
** * * *
61012 AGATTATTGTTCGAGTTCTTACTCCCTGAAGAAAA-AGAGAGCGGACCCATAGGA
1 AGAAGAATGTTCGAGTTC-TACTCCCTGAAGAAAAGAGAGAGCGAACCCGTAGGA
** * * * * *
61066 AGATTATTGTTTGAGTTCTACTCCCTGAAG-AAATAGAGAGCGGACCCATAGGA
1 AGAAGAATGTTCGAGTTCTACTCCCTGAAGAAAAGAGAGAGCGAACCCGTAGGA
** * * * *
61119 AGATTATTATTCGAGTTCTACTCCTTGAAG-GAAGAGAGAGC-AGACCCGTAGGA
1 AGAAGAATGTTCGAGTTCTACTCCCTGAAGAAAAGAGAGAGCGA-ACCCGTAGGA
* *
61172 AGATA-ATTGTTCGAGTTCTACTCCCTGAAGAAAAGAGAGAGCGAGCCCGTAGGA
1 AGA-AGAATGTTCGAGTTCTACTCCCTGAAGAAAAGAGAGAGCGAACCCGTAGGA
* *
61226 AGAAGAATGTTTGAGTTCTACTCCCTGAAG-AAAGAG-GAAGTGAACCCGT
1 AGAAGAATGTTCGAGTTCTACTCCCTGAAGAAAAGAGAG-AGCGAACCCGT
61275 TGGCCGAAGA
Statistics
Matches: 618, Mismatches: 44, Indels: 51
0.87 0.06 0.07
Matches are distributed among these distances:
50 1 0.00
51 35 0.06
52 54 0.09
53 295 0.48
54 221 0.36
55 12 0.02
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (54 bp):
AGAAGAATGTTCGAGTTCTACTCCCTGAAGAAAAGAGAGAGCGAACCCGTAGGA
Done.