Multiple sequence alignment - TraesCS1D01G089700

Loading Multiple Alignment...

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 TraesCS1D01G089700 chr1D 100.000 2459 0 0 753 3211 75842693 75845151 0.000000e+00 4542.0
1 TraesCS1D01G089700 chr1D 100.000 355 0 0 1 355 75841941 75842295 0.000000e+00 656.0
2 TraesCS1D01G089700 chr1D 93.950 281 16 1 76 355 346873399 346873119 1.060000e-114 424.0
3 TraesCS1D01G089700 chr1D 89.825 285 22 6 72 355 486378055 486377777 3.050000e-95 359.0
4 TraesCS1D01G089700 chr2B 96.765 1793 48 6 812 2595 82054211 82052420 0.000000e+00 2981.0
5 TraesCS1D01G089700 chr2B 96.621 1746 53 5 830 2572 333060285 333062027 0.000000e+00 2892.0
6 TraesCS1D01G089700 chr2B 93.189 1806 110 7 773 2575 229865569 229863774 0.000000e+00 2641.0
7 TraesCS1D01G089700 chr2B 90.909 44 3 1 2571 2613 678609197 678609154 1.240000e-04 58.4
8 TraesCS1D01G089700 chr5B 95.619 1826 72 3 755 2572 472274534 472276359 0.000000e+00 2922.0
9 TraesCS1D01G089700 chr7A 95.728 1826 54 8 771 2578 8546680 8548499 0.000000e+00 2918.0
10 TraesCS1D01G089700 chr4B 96.692 1723 45 4 860 2580 636701307 636703019 0.000000e+00 2856.0
11 TraesCS1D01G089700 chr3A 94.772 1798 85 8 754 2548 352716473 352718264 0.000000e+00 2791.0
12 TraesCS1D01G089700 chr3A 90.551 635 32 5 2598 3211 730984685 730984058 0.000000e+00 815.0
13 TraesCS1D01G089700 chr3A 90.190 632 31 7 2601 3211 644892854 644892233 0.000000e+00 795.0
14 TraesCS1D01G089700 chr3A 89.731 633 32 16 2601 3211 644896140 644895519 0.000000e+00 778.0
15 TraesCS1D01G089700 chr3A 89.748 634 26 10 2600 3211 644899173 644898557 0.000000e+00 774.0
16 TraesCS1D01G089700 chr3A 86.111 216 14 8 822 1024 577241722 577241510 5.390000e-53 219.0
17 TraesCS1D01G089700 chr3A 85.430 151 20 2 774 924 558213569 558213421 4.290000e-34 156.0
18 TraesCS1D01G089700 chr3A 95.062 81 3 1 2593 2673 534426364 534426443 3.360000e-25 126.0
19 TraesCS1D01G089700 chr3A 91.358 81 7 0 3095 3175 644898794 644898714 9.420000e-21 111.0
20 TraesCS1D01G089700 chr3A 90.123 81 8 0 3095 3175 644892471 644892391 4.380000e-19 106.0
21 TraesCS1D01G089700 chr3A 90.123 81 8 0 3095 3175 644895757 644895677 4.380000e-19 106.0
22 TraesCS1D01G089700 chr3D 94.969 1769 86 2 809 2574 170560795 170559027 0.000000e+00 2771.0
23 TraesCS1D01G089700 chr3D 88.456 641 38 14 2598 3211 110337950 110337319 0.000000e+00 741.0
24 TraesCS1D01G089700 chr3D 90.526 285 19 7 73 355 170561506 170561228 1.410000e-98 370.0
25 TraesCS1D01G089700 chr3D 97.297 37 1 0 2565 2601 298241066 298241102 2.670000e-06 63.9
26 TraesCS1D01G089700 chr3D 97.297 37 1 0 2565 2601 359726520 359726556 2.670000e-06 63.9
27 TraesCS1D01G089700 chr3D 89.796 49 3 2 2567 2614 348727129 348727082 9.620000e-06 62.1
28 TraesCS1D01G089700 chr2A 96.190 1680 61 2 896 2573 737335307 737336985 0.000000e+00 2745.0
29 TraesCS1D01G089700 chr2D 97.720 614 14 0 2598 3211 507440529 507441142 0.000000e+00 1057.0
30 TraesCS1D01G089700 chr2D 90.845 284 19 6 74 355 174334050 174333772 1.090000e-99 374.0
31 TraesCS1D01G089700 chr2D 90.813 283 18 7 74 355 592381026 592381301 3.910000e-99 372.0
32 TraesCS1D01G089700 chr2D 90.036 281 20 7 76 355 589196769 589196496 1.100000e-94 357.0
33 TraesCS1D01G089700 chr2D 88.000 50 3 3 2562 2610 525723774 525723821 4.470000e-04 56.5
34 TraesCS1D01G089700 chr6A 87.697 634 45 9 2600 3211 480043689 480044311 0.000000e+00 708.0
35 TraesCS1D01G089700 chr4D 92.803 264 16 3 68 330 245111678 245111417 2.340000e-101 379.0
36 TraesCS1D01G089700 chr6B 90.210 286 25 3 73 355 608336267 608336552 1.410000e-98 370.0
37 TraesCS1D01G089700 chr5A 90.175 285 20 6 72 355 69981430 69981707 6.550000e-97 364.0
38 TraesCS1D01G089700 chr7B 87.640 89 8 3 2600 2686 1744837 1744924 2.040000e-17 100.0
39 TraesCS1D01G089700 chr7B 90.909 44 3 1 2572 2615 136525244 136525202 1.240000e-04 58.4
40 TraesCS1D01G089700 chr1B 91.667 72 3 1 1 72 119250367 119250435 2.640000e-16 97.1
41 TraesCS1D01G089700 chr1A 90.769 65 5 1 1 65 76539868 76539931 5.710000e-13 86.1
42 TraesCS1D01G089700 chr5D 90.000 50 4 1 2565 2614 509219064 509219016 2.670000e-06 63.9
43 TraesCS1D01G089700 chr5D 88.679 53 2 4 2560 2610 276915688 276915738 9.620000e-06 62.1


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 TraesCS1D01G089700 chr1D 75841941 75845151 3210 False 2599.0 4542 100.000000 1 3211 2 chr1D.!!$F1 3210
1 TraesCS1D01G089700 chr2B 82052420 82054211 1791 True 2981.0 2981 96.765000 812 2595 1 chr2B.!!$R1 1783
2 TraesCS1D01G089700 chr2B 333060285 333062027 1742 False 2892.0 2892 96.621000 830 2572 1 chr2B.!!$F1 1742
3 TraesCS1D01G089700 chr2B 229863774 229865569 1795 True 2641.0 2641 93.189000 773 2575 1 chr2B.!!$R2 1802
4 TraesCS1D01G089700 chr5B 472274534 472276359 1825 False 2922.0 2922 95.619000 755 2572 1 chr5B.!!$F1 1817
5 TraesCS1D01G089700 chr7A 8546680 8548499 1819 False 2918.0 2918 95.728000 771 2578 1 chr7A.!!$F1 1807
6 TraesCS1D01G089700 chr4B 636701307 636703019 1712 False 2856.0 2856 96.692000 860 2580 1 chr4B.!!$F1 1720
7 TraesCS1D01G089700 chr3A 352716473 352718264 1791 False 2791.0 2791 94.772000 754 2548 1 chr3A.!!$F1 1794
8 TraesCS1D01G089700 chr3A 730984058 730984685 627 True 815.0 815 90.551000 2598 3211 1 chr3A.!!$R3 613
9 TraesCS1D01G089700 chr3A 644892233 644899173 6940 True 445.0 795 90.212167 2600 3211 6 chr3A.!!$R4 611
10 TraesCS1D01G089700 chr3D 170559027 170561506 2479 True 1570.5 2771 92.747500 73 2574 2 chr3D.!!$R3 2501
11 TraesCS1D01G089700 chr3D 110337319 110337950 631 True 741.0 741 88.456000 2598 3211 1 chr3D.!!$R1 613
12 TraesCS1D01G089700 chr2A 737335307 737336985 1678 False 2745.0 2745 96.190000 896 2573 1 chr2A.!!$F1 1677
13 TraesCS1D01G089700 chr2D 507440529 507441142 613 False 1057.0 1057 97.720000 2598 3211 1 chr2D.!!$F1 613
14 TraesCS1D01G089700 chr6A 480043689 480044311 622 False 708.0 708 87.697000 2600 3211 1 chr6A.!!$F1 611

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
27 28 0.032952 ACCTTGAAGTTGCGCGTAGA 59.967 50.0 8.43 0.00 0.0 2.59 F
316 319 0.183731 AATTTCATCCCCGGCTCCTC 59.816 55.0 0.00 0.00 0.0 3.71 F
916 931 0.670854 GAAGAAGCCGCGGAAGAAGT 60.671 55.0 33.48 8.57 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 1759 1.065410 TGCCCTTCTTGGTTCCCTCA 61.065 55.000 0.00 0.00 0.00 3.86 R
2188 2228 3.214123 CCACATGCGGGCTCCATG 61.214 66.667 12.03 12.03 44.28 3.66 R
2612 2652 1.894466 TCACGACGTTCAATCCCCTTA 59.106 47.619 0.00 0.00 0.00 2.69 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
21 22 1.795768 TGAGCTACCTTGAAGTTGCG 58.204 50.000 0.00 0.00 42.31 4.85
22 23 0.444260 GAGCTACCTTGAAGTTGCGC 59.556 55.000 0.00 0.00 42.31 6.09
23 24 1.132640 GCTACCTTGAAGTTGCGCG 59.867 57.895 0.00 0.00 0.00 6.86
24 25 1.566018 GCTACCTTGAAGTTGCGCGT 61.566 55.000 8.43 0.00 0.00 6.01
25 26 1.705256 CTACCTTGAAGTTGCGCGTA 58.295 50.000 8.43 0.00 0.00 4.42
26 27 1.654105 CTACCTTGAAGTTGCGCGTAG 59.346 52.381 8.43 0.63 0.00 3.51
27 28 0.032952 ACCTTGAAGTTGCGCGTAGA 59.967 50.000 8.43 0.00 0.00 2.59
28 29 1.337823 ACCTTGAAGTTGCGCGTAGAT 60.338 47.619 8.43 0.00 0.00 1.98
29 30 1.061131 CCTTGAAGTTGCGCGTAGATG 59.939 52.381 8.43 0.00 0.00 2.90
30 31 1.726791 CTTGAAGTTGCGCGTAGATGT 59.273 47.619 8.43 0.00 0.00 3.06
31 32 1.790755 TGAAGTTGCGCGTAGATGTT 58.209 45.000 8.43 0.00 0.00 2.71
32 33 1.724623 TGAAGTTGCGCGTAGATGTTC 59.275 47.619 8.43 5.54 0.00 3.18
33 34 1.724623 GAAGTTGCGCGTAGATGTTCA 59.275 47.619 8.43 0.00 0.00 3.18
34 35 1.350193 AGTTGCGCGTAGATGTTCAG 58.650 50.000 8.43 0.00 0.00 3.02
35 36 0.247301 GTTGCGCGTAGATGTTCAGC 60.247 55.000 8.43 0.00 0.00 4.26
36 37 1.358725 TTGCGCGTAGATGTTCAGCC 61.359 55.000 8.43 0.00 0.00 4.85
37 38 1.809619 GCGCGTAGATGTTCAGCCA 60.810 57.895 8.43 0.00 0.00 4.75
38 39 1.154205 GCGCGTAGATGTTCAGCCAT 61.154 55.000 8.43 0.00 0.00 4.40
39 40 1.868109 GCGCGTAGATGTTCAGCCATA 60.868 52.381 8.43 0.00 0.00 2.74
40 41 2.469826 CGCGTAGATGTTCAGCCATAA 58.530 47.619 0.00 0.00 0.00 1.90
41 42 2.218759 CGCGTAGATGTTCAGCCATAAC 59.781 50.000 0.00 0.00 0.00 1.89
42 43 2.544267 GCGTAGATGTTCAGCCATAACC 59.456 50.000 0.00 0.00 0.00 2.85
43 44 3.792401 CGTAGATGTTCAGCCATAACCA 58.208 45.455 0.00 0.00 0.00 3.67
44 45 3.555956 CGTAGATGTTCAGCCATAACCAC 59.444 47.826 0.00 0.00 0.00 4.16
45 46 4.680708 CGTAGATGTTCAGCCATAACCACT 60.681 45.833 0.00 0.00 0.00 4.00
46 47 5.451381 CGTAGATGTTCAGCCATAACCACTA 60.451 44.000 0.00 0.00 0.00 2.74
47 48 5.028549 AGATGTTCAGCCATAACCACTAG 57.971 43.478 0.00 0.00 0.00 2.57
48 49 4.716784 AGATGTTCAGCCATAACCACTAGA 59.283 41.667 0.00 0.00 0.00 2.43
49 50 4.202245 TGTTCAGCCATAACCACTAGAC 57.798 45.455 0.00 0.00 0.00 2.59
50 51 3.055385 TGTTCAGCCATAACCACTAGACC 60.055 47.826 0.00 0.00 0.00 3.85
51 52 2.116238 TCAGCCATAACCACTAGACCC 58.884 52.381 0.00 0.00 0.00 4.46
52 53 1.141053 CAGCCATAACCACTAGACCCC 59.859 57.143 0.00 0.00 0.00 4.95
53 54 1.209621 GCCATAACCACTAGACCCCA 58.790 55.000 0.00 0.00 0.00 4.96
54 55 1.134189 GCCATAACCACTAGACCCCAC 60.134 57.143 0.00 0.00 0.00 4.61
55 56 2.478292 CCATAACCACTAGACCCCACT 58.522 52.381 0.00 0.00 0.00 4.00
56 57 2.170607 CCATAACCACTAGACCCCACTG 59.829 54.545 0.00 0.00 0.00 3.66
57 58 3.104512 CATAACCACTAGACCCCACTGA 58.895 50.000 0.00 0.00 0.00 3.41
58 59 2.112279 AACCACTAGACCCCACTGAA 57.888 50.000 0.00 0.00 0.00 3.02
59 60 2.112279 ACCACTAGACCCCACTGAAA 57.888 50.000 0.00 0.00 0.00 2.69
60 61 1.978580 ACCACTAGACCCCACTGAAAG 59.021 52.381 0.00 0.00 42.29 2.62
61 62 2.257207 CCACTAGACCCCACTGAAAGA 58.743 52.381 0.00 0.00 37.43 2.52
62 63 2.028020 CCACTAGACCCCACTGAAAGAC 60.028 54.545 0.00 0.00 37.43 3.01
63 64 2.900546 CACTAGACCCCACTGAAAGACT 59.099 50.000 0.00 0.00 37.43 3.24
64 65 4.087182 CACTAGACCCCACTGAAAGACTA 58.913 47.826 0.00 0.00 37.43 2.59
65 66 4.158764 CACTAGACCCCACTGAAAGACTAG 59.841 50.000 0.00 0.00 37.43 2.57
66 67 3.261818 AGACCCCACTGAAAGACTAGT 57.738 47.619 0.00 0.00 37.43 2.57
67 68 4.399483 AGACCCCACTGAAAGACTAGTA 57.601 45.455 0.00 0.00 37.43 1.82
68 69 4.949121 AGACCCCACTGAAAGACTAGTAT 58.051 43.478 0.00 0.00 37.43 2.12
69 70 4.712337 AGACCCCACTGAAAGACTAGTATG 59.288 45.833 0.00 0.00 37.43 2.39
70 71 4.426704 ACCCCACTGAAAGACTAGTATGT 58.573 43.478 0.00 0.00 37.43 2.29
71 72 5.586877 ACCCCACTGAAAGACTAGTATGTA 58.413 41.667 0.00 0.00 37.43 2.29
81 82 9.239551 TGAAAGACTAGTATGTACTAAGAGCAA 57.760 33.333 0.00 0.00 38.24 3.91
85 86 8.269317 AGACTAGTATGTACTAAGAGCAAGTCT 58.731 37.037 11.15 11.15 37.41 3.24
105 106 2.046280 AGTAGAGCCCTCAAACCCTT 57.954 50.000 0.00 0.00 0.00 3.95
125 126 7.307550 ACCCTTAAACCCCTAAAAATAACTGT 58.692 34.615 0.00 0.00 0.00 3.55
173 175 5.321959 AGCCGTAGACTAAAACCTCTAAC 57.678 43.478 0.00 0.00 0.00 2.34
175 177 4.082026 GCCGTAGACTAAAACCTCTAACCA 60.082 45.833 0.00 0.00 0.00 3.67
176 178 5.394993 GCCGTAGACTAAAACCTCTAACCAT 60.395 44.000 0.00 0.00 0.00 3.55
177 179 6.271566 CCGTAGACTAAAACCTCTAACCATC 58.728 44.000 0.00 0.00 0.00 3.51
178 180 6.127535 CCGTAGACTAAAACCTCTAACCATCA 60.128 42.308 0.00 0.00 0.00 3.07
181 183 9.668497 GTAGACTAAAACCTCTAACCATCAAAT 57.332 33.333 0.00 0.00 0.00 2.32
214 217 5.801531 AAATAAAGGTCCAACCCTCAAAC 57.198 39.130 0.00 0.00 39.75 2.93
223 226 2.383855 CAACCCTCAAACTGTTTCCCA 58.616 47.619 2.13 0.00 0.00 4.37
244 247 1.978580 ACCTGTAGAAGTGAGGGTTGG 59.021 52.381 0.00 0.00 0.00 3.77
248 251 2.158219 TGTAGAAGTGAGGGTTGGGAGA 60.158 50.000 0.00 0.00 0.00 3.71
312 315 3.207452 GGAAATTTCATCCCCGGCT 57.793 52.632 19.49 0.00 0.00 5.52
315 318 0.631212 AAATTTCATCCCCGGCTCCT 59.369 50.000 0.00 0.00 0.00 3.69
316 319 0.183731 AATTTCATCCCCGGCTCCTC 59.816 55.000 0.00 0.00 0.00 3.71
317 320 1.709994 ATTTCATCCCCGGCTCCTCC 61.710 60.000 0.00 0.00 0.00 4.30
318 321 4.880426 TCATCCCCGGCTCCTCCC 62.880 72.222 0.00 0.00 0.00 4.30
831 846 3.717294 GCCCCCAAGAAGAGCCGA 61.717 66.667 0.00 0.00 0.00 5.54
916 931 0.670854 GAAGAAGCCGCGGAAGAAGT 60.671 55.000 33.48 8.57 0.00 3.01
1244 1271 1.451927 GGATGGATGCAAGCACCGA 60.452 57.895 0.00 0.00 0.00 4.69
1281 1308 4.883006 GGTAAACGGTATTGGCAAAGGATA 59.117 41.667 3.01 0.00 0.00 2.59
1729 1759 1.075659 GAGGAACTTGGGCAAGCCT 59.924 57.895 11.40 0.00 41.55 4.58
2103 2136 3.799755 GGATGTTCCGTGGTGCGC 61.800 66.667 0.00 0.00 39.71 6.09
2188 2228 0.952984 GGCGCCTATGGAGATGCTTC 60.953 60.000 22.15 0.00 0.00 3.86
2427 2467 1.231963 AGAACCCTCAAACCCAACCT 58.768 50.000 0.00 0.00 0.00 3.50
2436 2476 4.040339 CCTCAAACCCAACCTTTAAAGCAT 59.960 41.667 9.86 0.00 0.00 3.79
2455 2495 4.410555 AGCATTTTAAGGGTTGGGTTTGAA 59.589 37.500 0.00 0.00 0.00 2.69
2460 2500 2.561209 AGGGTTGGGTTTGAAGGTTT 57.439 45.000 0.00 0.00 0.00 3.27
2481 2521 6.407187 GGTTTTAGTCTTTGCCCCTGTTTTTA 60.407 38.462 0.00 0.00 0.00 1.52
2485 2525 4.714802 AGTCTTTGCCCCTGTTTTTAAACT 59.285 37.500 6.87 0.00 39.59 2.66
2529 2569 4.338400 GCACTTCTCAACCCTTAAAACTGT 59.662 41.667 0.00 0.00 0.00 3.55
2595 2635 2.330216 GCTGGTCATAGTGGGGAGTAT 58.670 52.381 0.00 0.00 0.00 2.12
2596 2636 2.300437 GCTGGTCATAGTGGGGAGTATC 59.700 54.545 0.00 0.00 0.00 2.24
2673 2714 2.537401 GTTCAACCTCCTTCGATACCG 58.463 52.381 0.00 0.00 37.07 4.02
2676 2717 2.012902 AACCTCCTTCGATACCGCCG 62.013 60.000 0.00 0.00 35.37 6.46
2707 2748 1.041447 CCCCACGTACGATCCCTTCT 61.041 60.000 24.41 0.00 0.00 2.85
2952 3001 4.036804 GCATTGTCGCGTGGCCAA 62.037 61.111 7.24 5.87 0.00 4.52
3098 3187 1.534175 CCGTCTCGGTCATGTAGCTTC 60.534 57.143 0.00 0.00 42.73 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.350522 CGCAACTTCAAGGTAGCTCAT 58.649 47.619 0.00 0.00 0.00 2.90
2 3 1.795768 CGCAACTTCAAGGTAGCTCA 58.204 50.000 0.00 0.00 0.00 4.26
3 4 0.444260 GCGCAACTTCAAGGTAGCTC 59.556 55.000 0.30 0.00 0.00 4.09
4 5 1.291877 CGCGCAACTTCAAGGTAGCT 61.292 55.000 8.75 0.00 0.00 3.32
7 8 1.270274 TCTACGCGCAACTTCAAGGTA 59.730 47.619 5.73 0.00 0.00 3.08
10 11 1.726791 ACATCTACGCGCAACTTCAAG 59.273 47.619 5.73 0.00 0.00 3.02
11 12 1.790755 ACATCTACGCGCAACTTCAA 58.209 45.000 5.73 0.00 0.00 2.69
12 13 1.724623 GAACATCTACGCGCAACTTCA 59.275 47.619 5.73 0.00 0.00 3.02
13 14 1.724623 TGAACATCTACGCGCAACTTC 59.275 47.619 5.73 0.17 0.00 3.01
14 15 1.726791 CTGAACATCTACGCGCAACTT 59.273 47.619 5.73 0.00 0.00 2.66
15 16 1.350193 CTGAACATCTACGCGCAACT 58.650 50.000 5.73 0.00 0.00 3.16
16 17 0.247301 GCTGAACATCTACGCGCAAC 60.247 55.000 5.73 0.00 0.00 4.17
17 18 1.358725 GGCTGAACATCTACGCGCAA 61.359 55.000 5.73 0.00 0.00 4.85
18 19 1.809619 GGCTGAACATCTACGCGCA 60.810 57.895 5.73 0.00 0.00 6.09
19 20 1.154205 ATGGCTGAACATCTACGCGC 61.154 55.000 5.73 0.00 0.00 6.86
20 21 2.134201 TATGGCTGAACATCTACGCG 57.866 50.000 3.53 3.53 32.39 6.01
21 22 2.544267 GGTTATGGCTGAACATCTACGC 59.456 50.000 4.82 0.00 32.39 4.42
22 23 3.555956 GTGGTTATGGCTGAACATCTACG 59.444 47.826 4.82 0.00 32.39 3.51
23 24 4.770795 AGTGGTTATGGCTGAACATCTAC 58.229 43.478 4.82 0.00 32.39 2.59
24 25 5.897250 TCTAGTGGTTATGGCTGAACATCTA 59.103 40.000 4.82 5.45 32.39 1.98
25 26 4.716784 TCTAGTGGTTATGGCTGAACATCT 59.283 41.667 4.82 4.76 32.39 2.90
26 27 4.811557 GTCTAGTGGTTATGGCTGAACATC 59.188 45.833 4.82 0.00 32.39 3.06
27 28 4.384208 GGTCTAGTGGTTATGGCTGAACAT 60.384 45.833 4.82 0.00 34.90 2.71
28 29 3.055385 GGTCTAGTGGTTATGGCTGAACA 60.055 47.826 4.82 0.00 0.00 3.18
29 30 3.532542 GGTCTAGTGGTTATGGCTGAAC 58.467 50.000 0.00 0.00 0.00 3.18
30 31 2.504175 GGGTCTAGTGGTTATGGCTGAA 59.496 50.000 0.00 0.00 0.00 3.02
31 32 2.116238 GGGTCTAGTGGTTATGGCTGA 58.884 52.381 0.00 0.00 0.00 4.26
32 33 1.141053 GGGGTCTAGTGGTTATGGCTG 59.859 57.143 0.00 0.00 0.00 4.85
33 34 1.274184 TGGGGTCTAGTGGTTATGGCT 60.274 52.381 0.00 0.00 0.00 4.75
34 35 1.134189 GTGGGGTCTAGTGGTTATGGC 60.134 57.143 0.00 0.00 0.00 4.40
35 36 2.170607 CAGTGGGGTCTAGTGGTTATGG 59.829 54.545 0.00 0.00 0.00 2.74
36 37 3.104512 TCAGTGGGGTCTAGTGGTTATG 58.895 50.000 0.00 0.00 0.00 1.90
37 38 3.484953 TCAGTGGGGTCTAGTGGTTAT 57.515 47.619 0.00 0.00 0.00 1.89
38 39 3.263369 TTCAGTGGGGTCTAGTGGTTA 57.737 47.619 0.00 0.00 0.00 2.85
39 40 2.112279 TTCAGTGGGGTCTAGTGGTT 57.888 50.000 0.00 0.00 0.00 3.67
40 41 1.978580 CTTTCAGTGGGGTCTAGTGGT 59.021 52.381 0.00 0.00 0.00 4.16
41 42 2.028020 GTCTTTCAGTGGGGTCTAGTGG 60.028 54.545 0.00 0.00 0.00 4.00
42 43 2.900546 AGTCTTTCAGTGGGGTCTAGTG 59.099 50.000 0.00 0.00 0.00 2.74
43 44 3.261818 AGTCTTTCAGTGGGGTCTAGT 57.738 47.619 0.00 0.00 0.00 2.57
44 45 4.345854 ACTAGTCTTTCAGTGGGGTCTAG 58.654 47.826 0.00 0.00 0.00 2.43
45 46 4.399483 ACTAGTCTTTCAGTGGGGTCTA 57.601 45.455 0.00 0.00 0.00 2.59
46 47 3.261818 ACTAGTCTTTCAGTGGGGTCT 57.738 47.619 0.00 0.00 0.00 3.85
47 48 4.466726 ACATACTAGTCTTTCAGTGGGGTC 59.533 45.833 0.00 0.00 0.00 4.46
48 49 4.426704 ACATACTAGTCTTTCAGTGGGGT 58.573 43.478 0.00 0.00 0.00 4.95
49 50 5.657302 AGTACATACTAGTCTTTCAGTGGGG 59.343 44.000 0.00 0.00 34.13 4.96
50 51 6.777213 AGTACATACTAGTCTTTCAGTGGG 57.223 41.667 0.00 0.00 34.13 4.61
51 52 9.175312 TCTTAGTACATACTAGTCTTTCAGTGG 57.825 37.037 0.00 0.00 39.69 4.00
53 54 8.895737 GCTCTTAGTACATACTAGTCTTTCAGT 58.104 37.037 0.00 0.00 39.69 3.41
54 55 8.894731 TGCTCTTAGTACATACTAGTCTTTCAG 58.105 37.037 0.00 0.00 39.69 3.02
55 56 8.803397 TGCTCTTAGTACATACTAGTCTTTCA 57.197 34.615 0.00 0.00 39.69 2.69
56 57 9.724839 CTTGCTCTTAGTACATACTAGTCTTTC 57.275 37.037 0.00 0.00 39.69 2.62
57 58 9.245481 ACTTGCTCTTAGTACATACTAGTCTTT 57.755 33.333 0.00 0.00 39.69 2.52
58 59 8.810990 ACTTGCTCTTAGTACATACTAGTCTT 57.189 34.615 0.00 0.00 39.69 3.01
59 60 8.269317 AGACTTGCTCTTAGTACATACTAGTCT 58.731 37.037 0.00 10.55 39.69 3.24
60 61 8.441312 AGACTTGCTCTTAGTACATACTAGTC 57.559 38.462 0.00 7.40 39.69 2.59
61 62 9.550406 CTAGACTTGCTCTTAGTACATACTAGT 57.450 37.037 0.00 0.00 39.69 2.57
62 63 9.550406 ACTAGACTTGCTCTTAGTACATACTAG 57.450 37.037 0.00 0.00 39.69 2.57
64 65 9.550406 CTACTAGACTTGCTCTTAGTACATACT 57.450 37.037 0.00 0.00 40.24 2.12
65 66 9.545105 TCTACTAGACTTGCTCTTAGTACATAC 57.455 37.037 0.00 0.00 0.00 2.39
66 67 9.767228 CTCTACTAGACTTGCTCTTAGTACATA 57.233 37.037 0.00 0.00 0.00 2.29
67 68 7.227910 GCTCTACTAGACTTGCTCTTAGTACAT 59.772 40.741 0.00 0.00 0.00 2.29
68 69 6.539464 GCTCTACTAGACTTGCTCTTAGTACA 59.461 42.308 0.00 0.00 0.00 2.90
69 70 6.017687 GGCTCTACTAGACTTGCTCTTAGTAC 60.018 46.154 0.00 0.00 0.00 2.73
70 71 6.056884 GGCTCTACTAGACTTGCTCTTAGTA 58.943 44.000 0.00 0.00 0.00 1.82
71 72 4.885325 GGCTCTACTAGACTTGCTCTTAGT 59.115 45.833 0.00 0.00 0.00 2.24
81 82 3.367321 GGTTTGAGGGCTCTACTAGACT 58.633 50.000 0.00 0.00 31.67 3.24
85 86 2.942604 AGGGTTTGAGGGCTCTACTA 57.057 50.000 0.00 0.00 0.00 1.82
163 165 4.918588 ACGGATTTGATGGTTAGAGGTTT 58.081 39.130 0.00 0.00 0.00 3.27
193 196 4.832823 CAGTTTGAGGGTTGGACCTTTATT 59.167 41.667 0.00 0.00 42.10 1.40
194 197 4.141018 ACAGTTTGAGGGTTGGACCTTTAT 60.141 41.667 0.00 0.00 42.10 1.40
197 200 1.569072 ACAGTTTGAGGGTTGGACCTT 59.431 47.619 0.00 0.00 42.10 3.50
214 217 3.815401 CACTTCTACAGGTTGGGAAACAG 59.185 47.826 0.00 0.00 0.00 3.16
223 226 2.372172 CCAACCCTCACTTCTACAGGTT 59.628 50.000 0.00 0.00 38.10 3.50
256 259 3.319198 GGAGTGCGAGTTGGGGGA 61.319 66.667 0.00 0.00 0.00 4.81
265 268 1.178276 GAGAGGAAAGAGGAGTGCGA 58.822 55.000 0.00 0.00 0.00 5.10
298 301 1.709994 GGAGGAGCCGGGGATGAAAT 61.710 60.000 2.18 0.00 0.00 2.17
322 325 4.847444 GAGGCGGCAGAAGGAGGC 62.847 72.222 13.08 0.00 0.00 4.70
323 326 4.521062 CGAGGCGGCAGAAGGAGG 62.521 72.222 13.08 0.00 0.00 4.30
1281 1308 6.407525 GCTTGATCCTACAATAGTTGTCCTCT 60.408 42.308 0.00 0.00 44.12 3.69
1729 1759 1.065410 TGCCCTTCTTGGTTCCCTCA 61.065 55.000 0.00 0.00 0.00 3.86
2188 2228 3.214123 CCACATGCGGGCTCCATG 61.214 66.667 12.03 12.03 44.28 3.66
2306 2346 7.860872 CCTCTAAACAAACTACCAAATGACAAC 59.139 37.037 0.00 0.00 0.00 3.32
2427 2467 6.502074 ACCCAACCCTTAAAATGCTTTAAA 57.498 33.333 0.00 0.00 36.73 1.52
2436 2476 4.363573 ACCTTCAAACCCAACCCTTAAAA 58.636 39.130 0.00 0.00 0.00 1.52
2455 2495 2.177016 ACAGGGGCAAAGACTAAAACCT 59.823 45.455 0.00 0.00 0.00 3.50
2460 2500 6.381707 AGTTTAAAAACAGGGGCAAAGACTAA 59.618 34.615 8.21 0.00 41.30 2.24
2481 2521 6.593770 CCAGTTTTTGGCACTTTTAAGAGTTT 59.406 34.615 0.00 0.00 40.87 2.66
2529 2569 5.520751 TCTCAAACCCTGAAACCCTTAAAA 58.479 37.500 0.00 0.00 32.17 1.52
2541 2581 6.522054 TGTCTAGTAAAACTCTCAAACCCTG 58.478 40.000 0.00 0.00 0.00 4.45
2612 2652 1.894466 TCACGACGTTCAATCCCCTTA 59.106 47.619 0.00 0.00 0.00 2.69
2676 2717 2.043953 GTGGGGATGAGGGTTGGC 60.044 66.667 0.00 0.00 0.00 4.52
2881 2930 3.315949 TGTGGGGTAGGTGGCGAC 61.316 66.667 0.00 0.00 0.00 5.19
2951 3000 1.302271 GGAGACGGGCGTTTTCCTT 60.302 57.895 0.00 0.00 32.77 3.36
2952 3001 2.346365 GGAGACGGGCGTTTTCCT 59.654 61.111 0.00 0.00 32.77 3.36


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

AutoCloner maintained by Alex Coulton.