Multiple sequence alignment - TraesCS7D01G390700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G390700 chr7D 100.000 2372 0 0 1 2372 506094845 506097216 0.000000e+00 4381.0
1 TraesCS7D01G390700 chr7D 87.143 630 71 7 118 741 455356772 455357397 0.000000e+00 706.0
2 TraesCS7D01G390700 chr7D 83.439 628 90 10 122 741 364551636 364551015 2.640000e-159 571.0
3 TraesCS7D01G390700 chr7D 92.188 64 5 0 1052 1115 89279795 89279732 9.030000e-15 91.6
4 TraesCS7D01G390700 chr7A 93.864 1646 78 14 742 2372 573450297 573451934 0.000000e+00 2459.0
5 TraesCS7D01G390700 chr7B 95.667 854 32 3 744 1596 533845723 533846572 0.000000e+00 1367.0
6 TraesCS7D01G390700 chr7B 94.444 126 3 1 1583 1704 533846586 533846711 8.650000e-45 191.0
7 TraesCS7D01G390700 chr2B 88.504 635 55 10 122 745 45649526 45648899 0.000000e+00 752.0
8 TraesCS7D01G390700 chr3D 87.739 628 63 9 122 741 582157840 582158461 0.000000e+00 721.0
9 TraesCS7D01G390700 chr3D 87.500 624 66 10 125 741 608781649 608782267 0.000000e+00 710.0
10 TraesCS7D01G390700 chr3D 86.508 630 70 13 121 741 138061348 138060725 0.000000e+00 678.0
11 TraesCS7D01G390700 chr5D 88.072 612 63 7 125 731 238894725 238894119 0.000000e+00 717.0
12 TraesCS7D01G390700 chr4D 86.869 594 68 8 122 710 480038628 480038040 0.000000e+00 656.0
13 TraesCS7D01G390700 chr4D 83.133 83 13 1 2205 2286 499197869 499197787 9.090000e-10 75.0
14 TraesCS7D01G390700 chr1B 83.732 627 92 7 122 741 228244428 228243805 3.400000e-163 584.0
15 TraesCS7D01G390700 chr5A 87.179 78 8 2 2215 2290 679777064 679776987 1.170000e-13 87.9
16 TraesCS7D01G390700 chr1D 84.932 73 9 2 2214 2284 19902726 19902798 3.270000e-09 73.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G390700 chr7D 506094845 506097216 2371 False 4381 4381 100.0000 1 2372 1 chr7D.!!$F2 2371
1 TraesCS7D01G390700 chr7D 455356772 455357397 625 False 706 706 87.1430 118 741 1 chr7D.!!$F1 623
2 TraesCS7D01G390700 chr7D 364551015 364551636 621 True 571 571 83.4390 122 741 1 chr7D.!!$R2 619
3 TraesCS7D01G390700 chr7A 573450297 573451934 1637 False 2459 2459 93.8640 742 2372 1 chr7A.!!$F1 1630
4 TraesCS7D01G390700 chr7B 533845723 533846711 988 False 779 1367 95.0555 744 1704 2 chr7B.!!$F1 960
5 TraesCS7D01G390700 chr2B 45648899 45649526 627 True 752 752 88.5040 122 745 1 chr2B.!!$R1 623
6 TraesCS7D01G390700 chr3D 582157840 582158461 621 False 721 721 87.7390 122 741 1 chr3D.!!$F1 619
7 TraesCS7D01G390700 chr3D 608781649 608782267 618 False 710 710 87.5000 125 741 1 chr3D.!!$F2 616
8 TraesCS7D01G390700 chr3D 138060725 138061348 623 True 678 678 86.5080 121 741 1 chr3D.!!$R1 620
9 TraesCS7D01G390700 chr5D 238894119 238894725 606 True 717 717 88.0720 125 731 1 chr5D.!!$R1 606
10 TraesCS7D01G390700 chr4D 480038040 480038628 588 True 656 656 86.8690 122 710 1 chr4D.!!$R1 588
11 TraesCS7D01G390700 chr1B 228243805 228244428 623 True 584 584 83.7320 122 741 1 chr1B.!!$R1 619

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
74 75 0.109412 GCCAACAGCTTCTCATGTGC 60.109 55.0 0.0 0.0 38.99 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 1846 0.103937 ACATTTGTGTTTGCCCACGG 59.896 50.0 0.0 0.0 38.2 4.94 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.898171 ACAGGTAATGCTATCATATCCCAT 57.102 37.500 0.00 0.00 31.46 4.00
24 25 6.893583 ACAGGTAATGCTATCATATCCCATC 58.106 40.000 0.00 0.00 31.46 3.51
25 26 6.126652 ACAGGTAATGCTATCATATCCCATCC 60.127 42.308 0.00 0.00 31.46 3.51
26 27 6.100859 CAGGTAATGCTATCATATCCCATCCT 59.899 42.308 0.00 0.00 31.46 3.24
27 28 6.328672 AGGTAATGCTATCATATCCCATCCTC 59.671 42.308 0.00 0.00 31.46 3.71
28 29 4.952071 ATGCTATCATATCCCATCCTCG 57.048 45.455 0.00 0.00 0.00 4.63
29 30 3.713003 TGCTATCATATCCCATCCTCGT 58.287 45.455 0.00 0.00 0.00 4.18
30 31 3.701542 TGCTATCATATCCCATCCTCGTC 59.298 47.826 0.00 0.00 0.00 4.20
31 32 3.957497 GCTATCATATCCCATCCTCGTCT 59.043 47.826 0.00 0.00 0.00 4.18
32 33 4.404073 GCTATCATATCCCATCCTCGTCTT 59.596 45.833 0.00 0.00 0.00 3.01
33 34 5.594725 GCTATCATATCCCATCCTCGTCTTA 59.405 44.000 0.00 0.00 0.00 2.10
34 35 5.923733 ATCATATCCCATCCTCGTCTTAC 57.076 43.478 0.00 0.00 0.00 2.34
35 36 4.087182 TCATATCCCATCCTCGTCTTACC 58.913 47.826 0.00 0.00 0.00 2.85
36 37 2.777459 ATCCCATCCTCGTCTTACCT 57.223 50.000 0.00 0.00 0.00 3.08
37 38 1.776662 TCCCATCCTCGTCTTACCTG 58.223 55.000 0.00 0.00 0.00 4.00
38 39 1.006758 TCCCATCCTCGTCTTACCTGT 59.993 52.381 0.00 0.00 0.00 4.00
39 40 1.409427 CCCATCCTCGTCTTACCTGTC 59.591 57.143 0.00 0.00 0.00 3.51
40 41 1.065701 CCATCCTCGTCTTACCTGTCG 59.934 57.143 0.00 0.00 0.00 4.35
41 42 1.065701 CATCCTCGTCTTACCTGTCGG 59.934 57.143 0.00 0.00 0.00 4.79
42 43 0.679002 TCCTCGTCTTACCTGTCGGG 60.679 60.000 0.00 0.00 41.89 5.14
54 55 3.899052 CCTGTCGGGTAAGGTATTTGA 57.101 47.619 0.00 0.00 0.00 2.69
55 56 3.793559 CCTGTCGGGTAAGGTATTTGAG 58.206 50.000 0.00 0.00 0.00 3.02
56 57 3.195661 CTGTCGGGTAAGGTATTTGAGC 58.804 50.000 0.00 0.00 0.00 4.26
57 58 2.093341 TGTCGGGTAAGGTATTTGAGCC 60.093 50.000 0.00 0.00 0.00 4.70
58 59 2.093341 GTCGGGTAAGGTATTTGAGCCA 60.093 50.000 0.00 0.00 0.00 4.75
59 60 2.572556 TCGGGTAAGGTATTTGAGCCAA 59.427 45.455 0.00 0.00 0.00 4.52
60 61 2.681344 CGGGTAAGGTATTTGAGCCAAC 59.319 50.000 0.00 0.00 0.00 3.77
61 62 3.692690 GGGTAAGGTATTTGAGCCAACA 58.307 45.455 0.00 0.00 0.00 3.33
62 63 3.694566 GGGTAAGGTATTTGAGCCAACAG 59.305 47.826 0.00 0.00 0.00 3.16
63 64 3.128764 GGTAAGGTATTTGAGCCAACAGC 59.871 47.826 0.00 0.00 44.25 4.40
74 75 0.109412 GCCAACAGCTTCTCATGTGC 60.109 55.000 0.00 0.00 38.99 4.57
75 76 1.241165 CCAACAGCTTCTCATGTGCA 58.759 50.000 0.00 0.00 0.00 4.57
76 77 1.816835 CCAACAGCTTCTCATGTGCAT 59.183 47.619 0.00 0.00 0.00 3.96
77 78 2.230508 CCAACAGCTTCTCATGTGCATT 59.769 45.455 0.00 0.00 0.00 3.56
78 79 3.305813 CCAACAGCTTCTCATGTGCATTT 60.306 43.478 0.00 0.00 0.00 2.32
79 80 4.082625 CCAACAGCTTCTCATGTGCATTTA 60.083 41.667 0.00 0.00 0.00 1.40
80 81 5.463286 CAACAGCTTCTCATGTGCATTTAA 58.537 37.500 0.00 0.00 0.00 1.52
81 82 5.710513 ACAGCTTCTCATGTGCATTTAAA 57.289 34.783 0.00 0.00 0.00 1.52
82 83 5.464168 ACAGCTTCTCATGTGCATTTAAAC 58.536 37.500 0.00 0.00 0.00 2.01
83 84 5.242393 ACAGCTTCTCATGTGCATTTAAACT 59.758 36.000 0.00 0.00 0.00 2.66
84 85 6.430925 ACAGCTTCTCATGTGCATTTAAACTA 59.569 34.615 0.00 0.00 0.00 2.24
85 86 6.965500 CAGCTTCTCATGTGCATTTAAACTAG 59.035 38.462 0.00 0.00 0.00 2.57
86 87 6.656693 AGCTTCTCATGTGCATTTAAACTAGT 59.343 34.615 0.00 0.00 0.00 2.57
87 88 7.175641 AGCTTCTCATGTGCATTTAAACTAGTT 59.824 33.333 1.12 1.12 0.00 2.24
88 89 7.483059 GCTTCTCATGTGCATTTAAACTAGTTC 59.517 37.037 8.95 0.00 0.00 3.01
89 90 7.977789 TCTCATGTGCATTTAAACTAGTTCA 57.022 32.000 8.95 0.03 0.00 3.18
90 91 8.565896 TCTCATGTGCATTTAAACTAGTTCAT 57.434 30.769 8.95 2.58 0.00 2.57
91 92 9.013229 TCTCATGTGCATTTAAACTAGTTCATT 57.987 29.630 8.95 0.00 0.00 2.57
92 93 9.282247 CTCATGTGCATTTAAACTAGTTCATTC 57.718 33.333 8.95 0.00 0.00 2.67
93 94 8.791675 TCATGTGCATTTAAACTAGTTCATTCA 58.208 29.630 8.95 0.09 0.00 2.57
94 95 9.577110 CATGTGCATTTAAACTAGTTCATTCAT 57.423 29.630 8.95 3.98 0.00 2.57
95 96 8.969121 TGTGCATTTAAACTAGTTCATTCATG 57.031 30.769 8.95 8.36 0.00 3.07
96 97 8.575589 TGTGCATTTAAACTAGTTCATTCATGT 58.424 29.630 8.95 0.00 0.00 3.21
97 98 9.065871 GTGCATTTAAACTAGTTCATTCATGTC 57.934 33.333 8.95 5.16 0.00 3.06
98 99 9.013229 TGCATTTAAACTAGTTCATTCATGTCT 57.987 29.630 8.95 0.00 0.00 3.41
99 100 9.495754 GCATTTAAACTAGTTCATTCATGTCTC 57.504 33.333 8.95 0.00 0.00 3.36
100 101 9.994432 CATTTAAACTAGTTCATTCATGTCTCC 57.006 33.333 8.95 0.00 0.00 3.71
101 102 9.965902 ATTTAAACTAGTTCATTCATGTCTCCT 57.034 29.630 8.95 0.00 0.00 3.69
107 108 9.647918 ACTAGTTCATTCATGTCTCCTAATAGA 57.352 33.333 0.00 0.00 0.00 1.98
109 110 8.546083 AGTTCATTCATGTCTCCTAATAGAGT 57.454 34.615 0.00 0.00 35.28 3.24
110 111 9.647918 AGTTCATTCATGTCTCCTAATAGAGTA 57.352 33.333 0.00 0.00 35.28 2.59
117 118 9.310449 TCATGTCTCCTAATAGAGTAATTACCC 57.690 37.037 12.05 0.00 35.28 3.69
118 119 9.090103 CATGTCTCCTAATAGAGTAATTACCCA 57.910 37.037 12.05 0.00 35.28 4.51
119 120 9.845214 ATGTCTCCTAATAGAGTAATTACCCAT 57.155 33.333 12.05 1.45 35.28 4.00
155 156 2.110578 GGTACCCATTACCCACGTACT 58.889 52.381 0.00 0.00 44.41 2.73
156 157 2.159057 GGTACCCATTACCCACGTACTG 60.159 54.545 0.00 0.00 44.41 2.74
253 257 0.672342 CCATCGGGTAGAACGGGTAG 59.328 60.000 0.00 0.00 0.00 3.18
273 277 5.726793 GGTAGGGATATGGGATCACATAACT 59.273 44.000 21.23 19.50 36.94 2.24
360 366 5.712217 TTGTCGTGAGTTTGTCAACTTAG 57.288 39.130 0.00 0.00 43.79 2.18
368 374 9.878599 CGTGAGTTTGTCAACTTAGAATTTATT 57.121 29.630 0.00 0.00 43.79 1.40
416 422 3.626977 TGTTGATGTTTTGATGTGTCGC 58.373 40.909 0.00 0.00 0.00 5.19
477 484 5.406780 TGTTGTTTTGGATGTGTTGTTGTTC 59.593 36.000 0.00 0.00 0.00 3.18
480 487 6.169094 TGTTTTGGATGTGTTGTTGTTCATT 58.831 32.000 0.00 0.00 0.00 2.57
626 644 3.607163 GTCGGGTGACGGGTATGA 58.393 61.111 0.00 0.00 44.45 2.15
630 649 1.555992 TCGGGTGACGGGTATGAAAAT 59.444 47.619 0.00 0.00 44.45 1.82
640 659 7.281549 GTGACGGGTATGAAAATAATTGTACCT 59.718 37.037 0.00 0.00 33.72 3.08
642 661 9.498176 GACGGGTATGAAAATAATTGTACCTAT 57.502 33.333 0.00 0.00 33.72 2.57
679 698 2.092323 GGGTGATGGGTAAGCTCAAAC 58.908 52.381 0.00 0.00 0.00 2.93
687 706 1.336609 GGTAAGCTCAAACGAGACGGT 60.337 52.381 0.00 0.00 31.68 4.83
700 719 2.391678 GAGACGGTTAAGGGTATGGGA 58.608 52.381 0.00 0.00 0.00 4.37
710 729 1.352622 GGGTATGGGATGGCTCCACA 61.353 60.000 5.54 0.00 44.08 4.17
711 730 0.773644 GGTATGGGATGGCTCCACAT 59.226 55.000 5.54 3.14 44.08 3.21
712 731 1.985159 GGTATGGGATGGCTCCACATA 59.015 52.381 5.54 2.28 44.08 2.29
741 760 1.645710 CCTGCGGGTCTTATCCCTAT 58.354 55.000 2.29 0.00 44.95 2.57
745 764 0.613777 CGGGTCTTATCCCTATGCCC 59.386 60.000 0.25 0.00 44.95 5.36
746 765 1.742308 GGGTCTTATCCCTATGCCCA 58.258 55.000 0.00 0.00 43.85 5.36
747 766 2.279173 GGGTCTTATCCCTATGCCCAT 58.721 52.381 0.00 0.00 43.85 4.00
748 767 2.025887 GGGTCTTATCCCTATGCCCATG 60.026 54.545 0.00 0.00 43.85 3.66
749 768 2.025887 GGTCTTATCCCTATGCCCATGG 60.026 54.545 4.14 4.14 0.00 3.66
876 895 3.053544 TCCCACTCCTAAGTCTAGTCCAG 60.054 52.174 0.00 0.00 31.71 3.86
925 944 4.729595 TCGCTGTATATATAAGCACACCG 58.270 43.478 18.63 9.63 36.73 4.94
970 989 2.095768 CCATTTGTACACAGCTTCACGG 60.096 50.000 0.00 0.00 0.00 4.94
1032 1051 1.963338 GACGAACTGCAGCAAGCCT 60.963 57.895 15.27 0.00 44.83 4.58
1035 1054 1.963338 GAACTGCAGCAAGCCTCGT 60.963 57.895 15.27 0.00 44.83 4.18
1163 1182 1.969208 CATGGAGGAGCTCAGATGCTA 59.031 52.381 17.19 0.00 44.17 3.49
1167 1186 0.264359 AGGAGCTCAGATGCTACCCT 59.736 55.000 17.19 0.00 44.68 4.34
1169 1188 0.392336 GAGCTCAGATGCTACCCTGG 59.608 60.000 9.40 0.00 44.17 4.45
1333 1352 2.111384 TCAAGAGCAGATCCACCTACC 58.889 52.381 0.00 0.00 0.00 3.18
1435 1454 7.441017 TCCTGGAATTGGTTTTATCACTTTTG 58.559 34.615 0.00 0.00 0.00 2.44
1482 1502 9.964303 TTTCTTAGTGTTCTACGTATGTTTACA 57.036 29.630 0.00 0.00 0.00 2.41
1484 1504 9.563898 TCTTAGTGTTCTACGTATGTTTACATG 57.436 33.333 5.64 0.00 37.15 3.21
1710 1765 2.319841 GCGCTGCACTGACATCACA 61.320 57.895 0.00 0.00 0.00 3.58
1760 1815 8.556213 AAGATATTTGTAAGTTTCGGTGCTTA 57.444 30.769 0.00 0.00 0.00 3.09
2164 2224 9.184062 GCGAATGATTTTCTTATTGCATGAATA 57.816 29.630 0.00 0.00 0.00 1.75
2219 2279 3.377434 TTAAATGTCACGGCGATTTCG 57.623 42.857 16.62 0.00 43.27 3.46
2241 2302 2.294233 CGGCAATACTCATGATTTGGGG 59.706 50.000 0.00 0.00 0.00 4.96
2290 2351 4.960469 AGGATCTAGTTACGGGATTCACAA 59.040 41.667 0.00 0.00 0.00 3.33
2341 2402 5.472820 CCGTCTTAGAGGTAATACCCTACTG 59.527 48.000 5.71 4.07 39.75 2.74
2342 2403 5.048852 CGTCTTAGAGGTAATACCCTACTGC 60.049 48.000 5.71 0.65 39.75 4.40
2343 2404 5.243507 GTCTTAGAGGTAATACCCTACTGCC 59.756 48.000 5.71 0.00 39.75 4.85
2345 2406 2.176364 AGAGGTAATACCCTACTGCCGA 59.824 50.000 5.71 0.00 39.75 5.54
2346 2407 2.295629 GAGGTAATACCCTACTGCCGAC 59.704 54.545 5.71 0.00 39.75 4.79
2347 2408 1.342496 GGTAATACCCTACTGCCGACC 59.658 57.143 0.00 0.00 30.04 4.79
2353 2417 1.296056 CCCTACTGCCGACCGTTTTG 61.296 60.000 0.00 0.00 0.00 2.44
2364 2428 2.412089 CGACCGTTTTGATCAAGTCTCC 59.588 50.000 18.17 5.37 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.126652 GGATGGGATATGATAGCATTACCTGT 60.127 42.308 0.00 0.00 35.94 4.00
1 2 6.100859 AGGATGGGATATGATAGCATTACCTG 59.899 42.308 0.00 0.00 35.94 4.00
2 3 6.215786 AGGATGGGATATGATAGCATTACCT 58.784 40.000 0.00 0.00 35.94 3.08
3 4 6.506538 AGGATGGGATATGATAGCATTACC 57.493 41.667 0.00 3.21 35.94 2.85
4 5 6.183360 ACGAGGATGGGATATGATAGCATTAC 60.183 42.308 0.00 0.00 35.94 1.89
5 6 5.899547 ACGAGGATGGGATATGATAGCATTA 59.100 40.000 0.00 0.00 35.94 1.90
6 7 4.718774 ACGAGGATGGGATATGATAGCATT 59.281 41.667 0.00 0.00 35.94 3.56
8 9 3.701542 GACGAGGATGGGATATGATAGCA 59.298 47.826 0.00 0.00 0.00 3.49
10 11 6.039941 GGTAAGACGAGGATGGGATATGATAG 59.960 46.154 0.00 0.00 0.00 2.08
11 12 5.892119 GGTAAGACGAGGATGGGATATGATA 59.108 44.000 0.00 0.00 0.00 2.15
13 14 4.087182 GGTAAGACGAGGATGGGATATGA 58.913 47.826 0.00 0.00 0.00 2.15
14 15 4.081972 CAGGTAAGACGAGGATGGGATATG 60.082 50.000 0.00 0.00 0.00 1.78
15 16 4.090090 CAGGTAAGACGAGGATGGGATAT 58.910 47.826 0.00 0.00 0.00 1.63
16 17 3.117246 ACAGGTAAGACGAGGATGGGATA 60.117 47.826 0.00 0.00 0.00 2.59
17 18 2.320781 CAGGTAAGACGAGGATGGGAT 58.679 52.381 0.00 0.00 0.00 3.85
18 19 1.006758 ACAGGTAAGACGAGGATGGGA 59.993 52.381 0.00 0.00 0.00 4.37
19 20 1.409427 GACAGGTAAGACGAGGATGGG 59.591 57.143 0.00 0.00 0.00 4.00
20 21 1.065701 CGACAGGTAAGACGAGGATGG 59.934 57.143 0.00 0.00 0.00 3.51
21 22 1.065701 CCGACAGGTAAGACGAGGATG 59.934 57.143 0.00 0.00 0.00 3.51
22 23 1.390565 CCGACAGGTAAGACGAGGAT 58.609 55.000 0.00 0.00 0.00 3.24
23 24 0.679002 CCCGACAGGTAAGACGAGGA 60.679 60.000 0.00 0.00 35.12 3.71
24 25 1.807886 CCCGACAGGTAAGACGAGG 59.192 63.158 0.00 0.00 35.12 4.63
34 35 3.793559 CTCAAATACCTTACCCGACAGG 58.206 50.000 0.00 0.00 43.78 4.00
35 36 3.195661 GCTCAAATACCTTACCCGACAG 58.804 50.000 0.00 0.00 0.00 3.51
36 37 2.093341 GGCTCAAATACCTTACCCGACA 60.093 50.000 0.00 0.00 0.00 4.35
37 38 2.093341 TGGCTCAAATACCTTACCCGAC 60.093 50.000 0.00 0.00 0.00 4.79
38 39 2.189676 TGGCTCAAATACCTTACCCGA 58.810 47.619 0.00 0.00 0.00 5.14
39 40 2.681344 GTTGGCTCAAATACCTTACCCG 59.319 50.000 0.00 0.00 0.00 5.28
40 41 3.692690 TGTTGGCTCAAATACCTTACCC 58.307 45.455 0.00 0.00 0.00 3.69
41 42 3.128764 GCTGTTGGCTCAAATACCTTACC 59.871 47.826 0.00 0.00 38.06 2.85
42 43 4.357018 GCTGTTGGCTCAAATACCTTAC 57.643 45.455 0.00 0.00 38.06 2.34
55 56 0.109412 GCACATGAGAAGCTGTTGGC 60.109 55.000 0.00 0.00 42.19 4.52
56 57 1.241165 TGCACATGAGAAGCTGTTGG 58.759 50.000 0.00 0.00 0.00 3.77
57 58 3.570926 AATGCACATGAGAAGCTGTTG 57.429 42.857 0.00 0.00 0.00 3.33
58 59 5.710513 TTAAATGCACATGAGAAGCTGTT 57.289 34.783 0.00 0.03 0.00 3.16
59 60 5.242393 AGTTTAAATGCACATGAGAAGCTGT 59.758 36.000 0.00 0.00 0.00 4.40
60 61 5.706916 AGTTTAAATGCACATGAGAAGCTG 58.293 37.500 0.00 0.00 0.00 4.24
61 62 5.972107 AGTTTAAATGCACATGAGAAGCT 57.028 34.783 0.00 0.00 0.00 3.74
62 63 6.846350 ACTAGTTTAAATGCACATGAGAAGC 58.154 36.000 0.00 0.00 0.00 3.86
63 64 8.506437 TGAACTAGTTTAAATGCACATGAGAAG 58.494 33.333 10.02 0.00 0.00 2.85
64 65 8.389779 TGAACTAGTTTAAATGCACATGAGAA 57.610 30.769 10.02 0.00 0.00 2.87
65 66 7.977789 TGAACTAGTTTAAATGCACATGAGA 57.022 32.000 10.02 0.00 0.00 3.27
66 67 9.282247 GAATGAACTAGTTTAAATGCACATGAG 57.718 33.333 10.02 0.00 0.00 2.90
67 68 8.791675 TGAATGAACTAGTTTAAATGCACATGA 58.208 29.630 10.02 0.00 0.00 3.07
68 69 8.969121 TGAATGAACTAGTTTAAATGCACATG 57.031 30.769 10.02 0.00 0.00 3.21
69 70 9.577110 CATGAATGAACTAGTTTAAATGCACAT 57.423 29.630 10.02 3.10 0.00 3.21
70 71 8.575589 ACATGAATGAACTAGTTTAAATGCACA 58.424 29.630 10.02 0.61 0.00 4.57
71 72 8.970691 ACATGAATGAACTAGTTTAAATGCAC 57.029 30.769 10.02 0.00 0.00 4.57
72 73 9.013229 AGACATGAATGAACTAGTTTAAATGCA 57.987 29.630 10.02 9.38 0.00 3.96
73 74 9.495754 GAGACATGAATGAACTAGTTTAAATGC 57.504 33.333 10.02 4.02 0.00 3.56
74 75 9.994432 GGAGACATGAATGAACTAGTTTAAATG 57.006 33.333 10.02 12.88 0.00 2.32
75 76 9.965902 AGGAGACATGAATGAACTAGTTTAAAT 57.034 29.630 10.02 1.77 0.00 1.40
81 82 9.647918 TCTATTAGGAGACATGAATGAACTAGT 57.352 33.333 0.00 0.00 0.00 2.57
83 84 9.647918 ACTCTATTAGGAGACATGAATGAACTA 57.352 33.333 0.00 0.00 37.13 2.24
84 85 8.546083 ACTCTATTAGGAGACATGAATGAACT 57.454 34.615 0.00 0.00 37.13 3.01
91 92 9.310449 GGGTAATTACTCTATTAGGAGACATGA 57.690 37.037 15.05 0.00 37.13 3.07
92 93 9.090103 TGGGTAATTACTCTATTAGGAGACATG 57.910 37.037 16.35 0.00 37.13 3.21
93 94 9.845214 ATGGGTAATTACTCTATTAGGAGACAT 57.155 33.333 16.35 0.00 37.13 3.06
94 95 9.090103 CATGGGTAATTACTCTATTAGGAGACA 57.910 37.037 16.35 0.00 37.13 3.41
95 96 9.091220 ACATGGGTAATTACTCTATTAGGAGAC 57.909 37.037 16.35 0.00 37.13 3.36
98 99 9.543231 CCTACATGGGTAATTACTCTATTAGGA 57.457 37.037 21.07 2.59 0.00 2.94
116 117 1.624336 CCATTGCCATCCCTACATGG 58.376 55.000 0.00 0.00 45.70 3.66
117 118 1.133388 ACCCATTGCCATCCCTACATG 60.133 52.381 0.00 0.00 0.00 3.21
118 119 1.234806 ACCCATTGCCATCCCTACAT 58.765 50.000 0.00 0.00 0.00 2.29
119 120 1.493022 GTACCCATTGCCATCCCTACA 59.507 52.381 0.00 0.00 0.00 2.74
216 220 5.239525 CCGATGGGTTTGAGATTTTCCTATC 59.760 44.000 0.00 0.00 34.39 2.08
246 250 1.435563 TGATCCCATATCCCTACCCGT 59.564 52.381 0.00 0.00 0.00 5.28
253 257 5.762179 TGAGTTATGTGATCCCATATCCC 57.238 43.478 0.00 0.00 0.00 3.85
273 277 1.044231 ACATGGGTACGCGGGTATGA 61.044 55.000 15.92 3.37 0.00 2.15
337 343 5.870433 TCTAAGTTGACAAACTCACGACAAA 59.130 36.000 0.00 0.00 46.15 2.83
389 395 7.852454 CGACACATCAAAACATCAACATATAGG 59.148 37.037 0.00 0.00 0.00 2.57
606 623 1.000521 ATACCCGTCACCCGACAGA 60.001 57.895 0.00 0.00 42.74 3.41
640 659 5.601729 TCACCCGTACACATACCCATTAATA 59.398 40.000 0.00 0.00 0.00 0.98
642 661 3.773667 TCACCCGTACACATACCCATTAA 59.226 43.478 0.00 0.00 0.00 1.40
646 665 1.483004 CATCACCCGTACACATACCCA 59.517 52.381 0.00 0.00 0.00 4.51
654 673 0.538118 GCTTACCCATCACCCGTACA 59.462 55.000 0.00 0.00 0.00 2.90
679 698 1.068127 CCCATACCCTTAACCGTCTCG 59.932 57.143 0.00 0.00 0.00 4.04
687 706 2.062636 GGAGCCATCCCATACCCTTAA 58.937 52.381 0.00 0.00 40.03 1.85
700 719 3.436470 GGTTTGGGTATATGTGGAGCCAT 60.436 47.826 0.00 0.00 42.55 4.40
745 764 1.152984 TCCTTACCCGCATGCCATG 60.153 57.895 13.15 0.00 0.00 3.66
746 765 1.152963 GTCCTTACCCGCATGCCAT 60.153 57.895 13.15 0.00 0.00 4.40
747 766 0.978667 TAGTCCTTACCCGCATGCCA 60.979 55.000 13.15 0.00 0.00 4.92
748 767 0.179468 TTAGTCCTTACCCGCATGCC 59.821 55.000 13.15 0.00 0.00 4.40
749 768 2.143925 GATTAGTCCTTACCCGCATGC 58.856 52.381 7.91 7.91 0.00 4.06
750 769 3.469008 TGATTAGTCCTTACCCGCATG 57.531 47.619 0.00 0.00 0.00 4.06
751 770 4.389374 CAATGATTAGTCCTTACCCGCAT 58.611 43.478 0.00 0.00 0.00 4.73
752 771 3.804036 CAATGATTAGTCCTTACCCGCA 58.196 45.455 0.00 0.00 0.00 5.69
795 814 2.421073 TGTAGACCCATGTTCGTAGTCG 59.579 50.000 0.00 0.00 38.55 4.18
876 895 4.379499 GCCTTCACTGGTGTAAGTTATTGC 60.379 45.833 0.53 0.00 0.00 3.56
925 944 3.364366 GCATATGTTGAGCTAACCGCATC 60.364 47.826 4.29 0.00 42.61 3.91
940 959 3.953612 CTGTGTACAAATGGGGCATATGT 59.046 43.478 4.29 0.00 0.00 2.29
1060 1079 4.626081 GACACCACCACCGCTGCT 62.626 66.667 0.00 0.00 0.00 4.24
1119 1138 3.701604 GACGAGCAGGCCGACGATT 62.702 63.158 17.32 0.32 0.00 3.34
1144 1163 1.969923 GTAGCATCTGAGCTCCTCCAT 59.030 52.381 12.15 0.00 45.26 3.41
1167 1186 4.641645 CTGGTCTTGCCACGGCCA 62.642 66.667 2.24 0.00 43.61 5.36
1181 1200 4.103103 TCGACGTCGAGCAGCTGG 62.103 66.667 34.97 5.74 44.22 4.85
1333 1352 2.141517 CTTATCATCCTTCGCAGGCAG 58.858 52.381 0.00 0.00 40.58 4.85
1435 1454 8.824756 AGAAAAGACTAATTAAATTCTCCCCC 57.175 34.615 0.00 0.00 0.00 5.40
1784 1839 0.671251 TGTTTGCCCACGGTCATTTC 59.329 50.000 0.00 0.00 0.00 2.17
1791 1846 0.103937 ACATTTGTGTTTGCCCACGG 59.896 50.000 0.00 0.00 38.20 4.94
2136 2195 7.259882 TCATGCAATAAGAAAATCATTCGCTT 58.740 30.769 0.00 0.00 0.00 4.68
2199 2259 3.377434 CGAAATCGCCGTGACATTTAA 57.623 42.857 0.00 0.00 0.00 1.52
2212 2272 0.927537 TGAGTATTGCCGCGAAATCG 59.072 50.000 8.23 0.00 43.27 3.34
2219 2279 2.287788 CCCAAATCATGAGTATTGCCGC 60.288 50.000 0.09 0.00 0.00 6.53
2241 2302 1.063031 GCGCCTTGCTTCACAAAATC 58.937 50.000 0.00 0.00 41.73 2.17
2290 2351 3.705072 CCCGAACCTAGGTAAATCACTCT 59.295 47.826 16.67 0.00 0.00 3.24
2334 2395 1.004200 AAAACGGTCGGCAGTAGGG 60.004 57.895 0.00 0.00 0.00 3.53
2341 2402 0.872388 ACTTGATCAAAACGGTCGGC 59.128 50.000 9.88 0.00 0.00 5.54
2342 2403 2.412089 GAGACTTGATCAAAACGGTCGG 59.588 50.000 9.88 0.00 0.00 4.79
2343 2404 2.412089 GGAGACTTGATCAAAACGGTCG 59.588 50.000 9.88 0.00 0.00 4.79
2345 2406 3.771577 AGGAGACTTGATCAAAACGGT 57.228 42.857 9.88 3.61 37.44 4.83
2346 2407 5.419542 TCATAGGAGACTTGATCAAAACGG 58.580 41.667 9.88 0.06 43.67 4.44
2347 2408 6.941802 CATCATAGGAGACTTGATCAAAACG 58.058 40.000 9.88 0.44 43.67 3.60


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.