Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006620.1 Hibiscus syriacus cultivar Beakdansim tig00016260_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: 75314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:9613 original size:20 final size:20
Alignment explanation
Indices: 9590--9634 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
9580 AAAAGGTAGG
* *
9590 TATCGATACTCAAGGTTCAA
1 TATCAATACTCAAGGGTCAA
*
9610 TATCAATACTGAAGGGTCAA
1 TATCAATACTCAAGGGTCAA
9630 TATCA
1 TATCA
9635 GTACCATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (20 bp):
TATCAATACTCAAGGGTCAA
Found at i:12922 original size:20 final size:20
Alignment explanation
Indices: 12893--12930 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12883 TTTCAAAGGG
12893 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
12913 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
12931 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:13010 original size:65 final size:64
Alignment explanation
Indices: 12892--13036 Score: 159
Period size: 65 Copynumber: 2.2 Consensus size: 64
12882 TTTTCAAAGG
* * *
12892 GATGCACCGATGCACCAATCCATGCATCGATGCACCAATGAATAAATTGAACATCGAATGTAGTT
1 GATGCATCGATGCA-CAATCCATGCATCGATGCACCAATGAATAAATTGAACATCGAATGCA-CT
12957 T
64 T
* ** **
12958 GATGCATCGATGCACAATCCATGTATCGATGCACTC-A-GGCTATTTTGAAACATCGAATGCACT
1 GATGCATCGATGCACAATCCATGCATCGATGCAC-CAATGAATAAATTG-AACATCGAATGCACT
13021 T
64 T
*
13022 CATGCATCGATGCAC
1 GATGCATCGATGCAC
13037 TAAGGGCCCA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
64 22 0.32
65 32 0.47
66 14 0.21
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (64 bp):
GATGCATCGATGCACAATCCATGCATCGATGCACCAATGAATAAATTGAACATCGAATGCACTT
Found at i:18450 original size:23 final size:23
Alignment explanation
Indices: 18377--18453 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
18367 TAGCCAGTGA
*
18377 ATCGATGCATCCCTTTGAATGTGC
1 ATCGATGCATTCC-TTGAATGTGC
* * *
18401 ATCGATACA-T-CATGAA-GATAC
1 ATCGATGCATTCCTTGAATG-TGC
*
18422 ACCGATGCATTCCTTGAATGTGC
1 ATCGATGCATTCCTTGAATGTGC
18445 ATCGATGCA
1 ATCGATGCA
18454 CACTACCATG
Statistics
Matches: 40, Mismatches: 9, Indels: 9
0.69 0.16 0.16
Matches are distributed among these distances:
20 1 0.03
21 13 0.32
22 2 0.05
23 15 0.38
24 9 0.22
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (23 bp):
ATCGATGCATTCCTTGAATGTGC
Found at i:20251 original size:18 final size:18
Alignment explanation
Indices: 20218--20252 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20208 AGGGGGAGTA
*
20218 ATTTCAAACTTGATTTTG
1 ATTTCAAAATTGATTTTG
*
20236 ATTTCAAAATTTATTTT
1 ATTTCAAAATTGATTTT
20253 CAAAGAAAAT
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:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTTCAAAATTGATTTTG
Found at i:20583 original size:20 final size:20
Alignment explanation
Indices: 20554--20591 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20544 TTTCAAAGGG
20554 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
20574 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
20592 GAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:20690 original size:46 final size:44
Alignment explanation
Indices: 20637--20744 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 44
20627 ATTCACTCTC
* * *
20637 CATGCATCGATTCACTCAGG-TTTTAATGAAAACATCGAATGCATTT
1 CATGCATCGATGCACTCAGGCATTT--TG-AAACATCGAATGCACTT
*
20683 GATGCATCGATGCACTCAGGCCATTTTGAAACATCGAATGCACTT
1 CATGCATCGATGCACTCAGG-CATTTTGAAACATCGAATGCACTT
20728 CATGCATCGATGCACTC
1 CATGCATCGATGCACTC
20745 TTAGTACACC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
45 32 0.58
46 20 0.36
48 3 0.05
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (44 bp):
CATGCATCGATGCACTCAGGCATTTTGAAACATCGAATGCACTT
Found at i:29134 original size:11 final size:11
Alignment explanation
Indices: 29110--29146 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
29100 AAAATTTTAA
29110 ATTTAATATTTT
1 ATTTAAT-TTTT
29122 ATTTAATTTTT
1 ATTTAATTTTT
29133 ATTTAA-TTTT
1 ATTTAATTTTT
29143 ATTT
1 ATTT
29147 TGTAGATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 8 0.32
11 10 0.40
12 7 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTAATTTTT
Found at i:45211 original size:174 final size:173
Alignment explanation
Indices: 44908--45258 Score: 693
Period size: 174 Copynumber: 2.0 Consensus size: 173
44898 GTTCATATAG
44908 ATGCATTAGGAACTATAACTGCATTTGGTGGTTTGTATTTGTTCTGGCATATTTTGTAAATGGTG
1 ATGCATTAGGAACTATAACTGCATTTGGTGGTTTGTATTTGTTCTGGCATATTTTGTAAATGGTG
44973 CAATTTACGGGGAATGTTGTGTTTTGCTAATGATGTGCACGTTGAGGAAGCAAAGGGTGAGCGAA
66 CAATTTACGGGGAATGTTGTGTTTTGCTAATGATGTGCACGTTGAGGAAGCAAAGGGTGAGCGAA
45038 AGAGAATTGTCAAGGCAATTTGAGATGACTAAGCATGAGAAAA
131 AGAGAATTGTCAAGGCAATTTGAGATGACTAAGCATGAGAAAA
45081 ATGCATTAGGAACATATAACTGCATTTGGTGGTTTGTATTTGTTCTGGCATATTTTGTAAATGGT
1 ATGCATTAGGAAC-TATAACTGCATTTGGTGGTTTGTATTTGTTCTGGCATATTTTGTAAATGGT
45146 GCAATTTACGGGGAATGTTGTGTTTTGCTAATGATGTGCACGTTGAGGAAGCAAAGGGTGAGCGA
65 GCAATTTACGGGGAATGTTGTGTTTTGCTAATGATGTGCACGTTGAGGAAGCAAAGGGTGAGCGA
45211 AAGAGAATTGTCAAGGCAATTTGAGATGACTAAGCATGAGAAAA
130 AAGAGAATTGTCAAGGCAATTTGAGATGACTAAGCATGAGAAAA
45255 ATGC
1 ATGC
45259 CACGGAAGCT
Statistics
Matches: 177, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
173 13 0.07
174 164 0.93
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.32
Consensus pattern (173 bp):
ATGCATTAGGAACTATAACTGCATTTGGTGGTTTGTATTTGTTCTGGCATATTTTGTAAATGGTG
CAATTTACGGGGAATGTTGTGTTTTGCTAATGATGTGCACGTTGAGGAAGCAAAGGGTGAGCGAA
AGAGAATTGTCAAGGCAATTTGAGATGACTAAGCATGAGAAAA
Found at i:48619 original size:10 final size:10
Alignment explanation
Indices: 48604--48644 Score: 82
Period size: 10 Copynumber: 4.1 Consensus size: 10
48594 TTATCATCCT
48604 TCAAATTTTC
1 TCAAATTTTC
48614 TCAAATTTTC
1 TCAAATTTTC
48624 TCAAATTTTC
1 TCAAATTTTC
48634 TCAAATTTTC
1 TCAAATTTTC
48644 T
1 T
48645 ATTTGATCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (10 bp):
TCAAATTTTC
Found at i:50271 original size:38 final size:38
Alignment explanation
Indices: 50222--50330 Score: 209
Period size: 38 Copynumber: 2.9 Consensus size: 38
50212 AACTATACTC
50222 ACTCACTCTTTATTATTTGTGCGATTGTGTATAACGAT
1 ACTCACTCTTTATTATTTGTGCGATTGTGTATAACGAT
50260 ACTCACTCTTTATTATTTGTGCGATTGTGTATAACGAT
1 ACTCACTCTTTATTATTTGTGCGATTGTGTATAACGAT
*
50298 ACTCACTCTTTATTATTTGTGTGATTGTGTATA
1 ACTCACTCTTTATTATTTGTGCGATTGTGTATA
50331 CTTACACATA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 70 1.00
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.47
Consensus pattern (38 bp):
ACTCACTCTTTATTATTTGTGCGATTGTGTATAACGAT
Found at i:54050 original size:27 final size:27
Alignment explanation
Indices: 53980--54041 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
53970 GCCCTTAGAC
* *
53980 CCAAAATAACTAAAATAACCTCTAGCA
1 CCAAAATGACTAAAATAACCTCGAGCA
*
54007 CCAAAATGACTAAAATAACCTCGAGTA
1 CCAAAATGACTAAAATAACCTCGAGCA
*
54034 CTAAAATG
1 CCAAAATG
54042 GCCTAAATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.50, C:0.23, G:0.08, T:0.19
Consensus pattern (27 bp):
CCAAAATGACTAAAATAACCTCGAGCA
Found at i:54375 original size:21 final size:18
Alignment explanation
Indices: 54351--54391 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 18
54341 GTTTAGTTTG
54351 ATTTGACTATAAATCTTGAGA
1 ATTTGA-TATAAAT-TT-AGA
54372 ATTTGATATAAATTTAGA
1 ATTTGATATAAATTTAGA
54390 AT
1 AT
54392 ATTGCAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 2 0.10
20 7 0.35
21 6 0.30
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (18 bp):
ATTTGATATAAATTTAGA
Found at i:63387 original size:15 final size:15
Alignment explanation
Indices: 63369--63402 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
63359 GGTGTGATAC
*
63369 TTTCCTTTATTTGTT
1 TTTCCTTTATATGTT
63384 TTTCCTTTATATGTT
1 TTTCCTTTATATGTT
63399 TTTC
1 TTTC
63403 TTAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.15, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTCCTTTATATGTT
Found at i:65439 original size:41 final size:43
Alignment explanation
Indices: 65335--65456 Score: 133
Period size: 41 Copynumber: 2.9 Consensus size: 43
65325 AGTTAGCAGA
* * *
65335 GTTTTTGGAACAAATGTCGCAAAAGGTCGATATCTATAGCGAC
1 GTTTTTGGAACAAACGTCGCAAAAGGTAGATATATATAGCGAC
* * * *
65378 ATTTTTTGAA-TAACGTCGCAAAAGG-AGATATATATAGCGGC
1 GTTTTTGGAACAAACGTCGCAAAAGGTAGATATATATAGCGAC
* * *
65419 GTTTCTGGAACAAACG-CGCAAAAGGTTGATATCTATAG
1 GTTTTTGGAACAAACGTCGCAAAAGGTAGATATATATAG
65457 AGCAAAAGTC
Statistics
Matches: 64, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
41 29 0.45
42 27 0.42
43 8 0.12
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (43 bp):
GTTTTTGGAACAAACGTCGCAAAAGGTAGATATATATAGCGAC
Found at i:66538 original size:21 final size:21
Alignment explanation
Indices: 66512--66551 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
66502 AAAAATGTGT
66512 ATCGATGCACTACTACAGTGC
1 ATCGATGCACTACTACAGTGC
*
66533 ATCGATGCACTGCTACAGT
1 ATCGATGCACTACTACAGT
66552 AACTTCAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (21 bp):
ATCGATGCACTACTACAGTGC
Found at i:66891 original size:17 final size:18
Alignment explanation
Indices: 66862--66895 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
66852 TATTCTTATA
66862 TTTAATCTCCAATGAATC
1 TTTAATCTCCAATGAATC
66880 TTTAAT-TCCAATGAAT
1 TTTAATCTCCAATGAAT
66896 ATACTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (18 bp):
TTTAATCTCCAATGAATC
Found at i:67121 original size:59 final size:59
Alignment explanation
Indices: 67058--67169 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
67048 CTTACTCTTT
* *
67058 CATTTTAGCACACGAAGTACCCTAT-TCAAAAATCCATACCATTAGTATGATTTTGTTAC
1 CATTTTAGCACACAAAATACCCTATGT-AAAAATCCATACCATTAGTATGATTTTGTTAC
* * * *
67117 CATTTTAGCACATAAAATGCCCTATGTGAAAATCCATACCATTATTATGATTT
1 CATTTTAGCACACAAAATACCCTATGTAAAAATCCATACCATTAGTATGATTT
67170 CCTTATCCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.35
Consensus pattern (59 bp):
CATTTTAGCACACAAAATACCCTATGTAAAAATCCATACCATTAGTATGATTTTGTTAC
Found at i:67185 original size:59 final size:58
Alignment explanation
Indices: 67086--67363 Score: 190
Period size: 59 Copynumber: 4.7 Consensus size: 58
67076 ACCCTATTCA
** *
67086 AAAATCCATACCATTAGTATGATTTTGTTACCATTTTAGCACATAAAATGCCCTATGTG
1 AAAATCCATA-CATTAGTATGATTTCCTTACCATTTTAGCACATAAAATGCCCTATATG
* * * * * **
67145 AAAATCCATACCATTATTATGATTTCCTTATCC-TTATAGCACCCT-TAGTGCTTTATATG
1 AAAATCCATA-CATTAGTATGATTTCCTTA-CCATTTTAGCA-CATAAAATGCCCTATATG
* * * * *
67204 GAAATTCATACACTCAGTATGATTCCCTTACCATTTTAGCACATAAAATGCCCTATCTG
1 AAAATCCATACA-TTAGTATGATTTCCTTACCATTTTAGCACATAAAATGCCCTATATG
* ** * * * *
67263 GAAATCCATATTTTCAATATGATTTCCTTATCA-TTTAGCACACT-CAGTGCTCC-ATATGG
1 AAAATCCATACATT-AGTATGATTTCCTTACCATTTTAGCACA-TAAAATGC-CCTATAT-G
* * * *
67322 AAATATACACAC-TCAGTATGATTTCCTTATCATTTTAGCACA
1 AAA-ATCCATACATTAGTATGATTTCCTTACCATTTTAGCACA
67364 CAAAGTGACA
Statistics
Matches: 170, Mismatches: 38, Indels: 22
0.74 0.17 0.10
Matches are distributed among these distances:
58 40 0.24
59 121 0.71
60 9 0.05
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (58 bp):
AAAATCCATACATTAGTATGATTTCCTTACCATTTTAGCACATAAAATGCCCTATATG
Found at i:67241 original size:118 final size:117
Alignment explanation
Indices: 67113--67363 Score: 344
Period size: 117 Copynumber: 2.1 Consensus size: 117
67103 TATGATTTTG
* *
67113 TTACCATTTTAGCACATAAAATGCCCTATGTGAAAATCCATACCATT-ATTATGATTTCCTTATC
1 TTACCATTTTAGCACATAAAATGCCCTATCTGAAAATCCATA-CATTCAATATGATTTCCTTATC
* * * ** *
67177 CTTATAGCACCCTTAGTGCTTTATATGGAAAT-TCATACACTCAGTATGATTCCC
65 ATT-TAGCACACTCAGTGCTCCATATGGAAATAT-ACACACTCAGTATGATTCCC
* **
67231 TTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAAAATGCCCTATCTGAAAATCCATACATTCAATATGATTTCCTTATCA
*
67296 TTTAGCACACTCAGTGCTCCATATGGAAATATACACACTCAGTATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATATACACACTCAGTATGATTCCC
*
67348 TTATCATTTTAGCACA
1 TTACCATTTTAGCACA
67364 CAAAGTGACA
Statistics
Matches: 118, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
117 59 0.50
118 59 0.50
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (117 bp):
TTACCATTTTAGCACATAAAATGCCCTATCTGAAAATCCATACATTCAATATGATTTCCTTATCA
TTTAGCACACTCAGTGCTCCATATGGAAATATACACACTCAGTATGATTCCC
Found at i:67362 original size:117 final size:118
Alignment explanation
Indices: 67101--67363 Score: 352
Period size: 118 Copynumber: 2.2 Consensus size: 118
67091 CCATACCATT
** * *
67101 AGTATGATTTTGTTACCATTTTAGCACATAAAATGCCCTATGTGAAAATCCATACCATTATTATG
1 AGTATGATTTCCTTACCATTTTAGCACATAAAATGCCCTATCTGAAAATCCATACCATTAATATG
* * * ** *
67166 ATTTCCTTATCCTTATAGCACCCTTAGTGCTTTATATGGAAATTCATACACTC
66 ATTTCCTTATCATTATAGCACACTCAGTGCTCCATATGGAAATTCACACACTC
* * **
67219 AGTATGATTCCCTTACCATTTTAGCACATAAAATGCCCTATCTGGAAATCCATA-TTTTCAATAT
1 AGTATGATTTCCTTACCATTTTAGCACATAAAATGCCCTATCTGAAAATCCATACCATT-AATAT
67283 GATTTCCTTATCATT-TAGCACACTCAGTGCTCCATATGGAAATAT-ACACACTC
65 GATTTCCTTATCATTATAGCACACTCAGTGCTCCATATGGAAAT-TCACACACTC
*
67336 AGTATGATTTCCTTATCATTTTAGCACA
1 AGTATGATTTCCTTACCATTTTAGCACA
67364 CAAAGTGACA
Statistics
Matches: 127, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
117 59 0.46
118 68 0.54
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.37
Consensus pattern (118 bp):
AGTATGATTTCCTTACCATTTTAGCACATAAAATGCCCTATCTGAAAATCCATACCATTAATATG
ATTTCCTTATCATTATAGCACACTCAGTGCTCCATATGGAAATTCACACACTC
Found at i:74017 original size:17 final size:18
Alignment explanation
Indices: 73984--74017 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
73974 TATTCTGATA
73984 TTTAATCTCCAAGGAATC
1 TTTAATCTCCAAGGAATC
*
74002 TTTAAT-TCCAATGAAT
1 TTTAATCTCCAAGGAAT
74018 ATATTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (18 bp):
TTTAATCTCCAAGGAATC
Found at i:74110 original size:18 final size:19
Alignment explanation
Indices: 74074--74110 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
74064 TTTTGGAATC
74074 CATACATTCCATAGAAATT
1 CATACATTCCATAGAAATT
74093 CATACAATT-CAT-GAAATT
1 CATAC-ATTCCATAGAAATT
74111 TCCTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 8 0.47
20 3 0.18
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.32
Consensus pattern (19 bp):
CATACATTCCATAGAAATT
Found at i:74375 original size:57 final size:56
Alignment explanation
Indices: 74176--74384 Score: 151
Period size: 57 Copynumber: 3.7 Consensus size: 56
74166 TTCCCCTTTT
* * * * *
74176 CCATTTTAGCACACGAAGTGCCCTAT-TCAAAATCCATATCA-TAGTATGCTTCTGTTA
1 CCATTTTAGCACA-TAAATGCCCTATCT-GAAATCCATA-CACTAGTATGATTCTCTTA
* * *
74233 CCATTTTAGCACATGAAATGCCCTATGTGAAAATCCATACCATTAGTGTGATT-TCCTTA
1 CCATTTTAGCACAT-AAATGCCCTATCTG-AAATCCATA-CACTAGTATGATTCT-CTTA
* * * * * **
74292 TCC-TTGTAGTACCTTAGTGCTTTATCTAGAAA-CCATACACTCAGTATGATTCTCTTA
1 -CCATTTTAGCACATAAATGCCCTATCT-GAAATCCATACACT-AGTATGATTCTCTTA
74349 CCATTTTAGCACATAAATGCCCTATCTG-AATCCATA
1 CCATTTTAGCACATAAATGCCCTATCTGAAATCCATA
74385 TTTTTCAATA
Statistics
Matches: 117, Mismatches: 24, Indels: 23
0.71 0.15 0.14
Matches are distributed among these distances:
55 2 0.02
56 11 0.09
57 57 0.49
58 25 0.21
59 20 0.17
60 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (56 bp):
CCATTTTAGCACATAAATGCCCTATCTGAAATCCATACACTAGTATGATTCTCTTA
Found at i:74454 original size:114 final size:114
Alignment explanation
Indices: 74218--74484 Score: 265
Period size: 114 Copynumber: 2.3 Consensus size: 114
74208 TCCATATCAT
* * * * *
74218 AGTATGCTTCTGTTACCATTTTAGCACATGAAATGCCCTATGTGAAAATCCATACCATTAGTGTG
1 AGTATGATTCTCTTACCATTTTAGCACAT-AAATGCCCTATCTG-AAATCCATACCATTAATATG
* * ** *
74283 ATTTCCTTATCCTTGTAGTACCTTAGTGCTTTATCTAGAAACCATACACTC
64 ATTTCCTTATCATTGTAGTACCTCAGTGCTCCATATAGAAACCATACACTC
***
74334 AGTATGATTCTCTTACCATTTTAGCACATAAATGCCCTATCTG-AATCCATATTTTTCAATATGA
1 AGTATGATTCTCTTACCATTTTAGCACATAAATGCCCTATCTGAAATCCATACCATT-AATATGA
* *
74398 TTTCCTTATCATT-TAGCATA-CTCAGTGCTCCATATGGAAATCGATACACTC
65 TTTCCTTATCATTGTAG--TACCTCAGTGCTCCATATAGAAA-CCATACACTC
* * *
74449 A-TATGATT-TCCTAATCATTTTAGCACACAAAGTGCC
1 AGTATGATTCT-CTTACCATTTTAGCACATAAA-TGCC
74485 ATTCGGTAAT
Statistics
Matches: 127, Mismatches: 18, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
113 14 0.11
114 57 0.45
115 29 0.23
116 27 0.21
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (114 bp):
AGTATGATTCTCTTACCATTTTAGCACATAAATGCCCTATCTGAAATCCATACCATTAATATGAT
TTCCTTATCATTGTAGTACCTCAGTGCTCCATATAGAAACCATACACTC
Done.