Multiple sequence alignment - TraesCS2B01G305600

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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 TraesCS2B01G305600 chr2B 100.000 2886 0 0 1 2886 436017473 436014588 0.000000e+00 5330
1 TraesCS2B01G305600 chr2B 93.968 630 21 7 2270 2886 442462774 442463399 0.000000e+00 937
2 TraesCS2B01G305600 chr2D 95.946 1110 39 1 1090 2199 367224165 367223062 0.000000e+00 1796
3 TraesCS2B01G305600 chr2D 94.847 621 19 4 2279 2886 8653136 8652516 0.000000e+00 957
4 TraesCS2B01G305600 chr2D 88.268 358 26 11 661 1008 367224601 367224250 5.750000e-112 414
5 TraesCS2B01G305600 chr2D 97.619 84 2 0 1025 1108 367224260 367224177 8.330000e-31 145
6 TraesCS2B01G305600 chr2A 89.438 1316 63 16 1025 2279 497014667 497013367 0.000000e+00 1591
7 TraesCS2B01G305600 chr2A 88.989 663 59 6 1 650 497015724 497015063 0.000000e+00 808
8 TraesCS2B01G305600 chr2A 91.667 516 27 6 2268 2770 776273811 776273299 0.000000e+00 701
9 TraesCS2B01G305600 chr2A 88.736 364 20 5 660 1008 497015014 497014657 2.660000e-115 425
10 TraesCS2B01G305600 chr1D 95.315 619 14 6 2281 2886 23942834 23943450 0.000000e+00 968
11 TraesCS2B01G305600 chr4D 95.146 618 17 4 2282 2886 220179131 220179748 0.000000e+00 963
12 TraesCS2B01G305600 chr4D 94.507 619 19 6 2282 2886 201001998 201001381 0.000000e+00 941
13 TraesCS2B01G305600 chr5D 94.677 620 20 4 2280 2886 6688075 6687456 0.000000e+00 950
14 TraesCS2B01G305600 chr4A 94.728 607 28 3 2282 2886 653334334 653334938 0.000000e+00 941
15 TraesCS2B01G305600 chr6D 94.337 618 21 5 2282 2886 202940025 202939409 0.000000e+00 935
16 TraesCS2B01G305600 chr3D 93.781 611 32 5 2282 2886 539616058 539615448 0.000000e+00 913
17 TraesCS2B01G305600 chr3D 90.617 373 28 7 2280 2647 589844314 589844684 3.340000e-134 488
18 TraesCS2B01G305600 chr3A 90.523 612 50 5 2282 2886 403136438 403135828 0.000000e+00 802
19 TraesCS2B01G305600 chr3A 92.759 511 23 5 2273 2770 160291343 160290834 0.000000e+00 726
20 TraesCS2B01G305600 chr3A 92.085 518 27 5 2266 2770 181038650 181039166 0.000000e+00 717
21 TraesCS2B01G305600 chr7D 93.939 396 10 5 2282 2664 276091913 276091519 1.150000e-163 586


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 TraesCS2B01G305600 chr2B 436014588 436017473 2885 True 5330.000000 5330 100.000000 1 2886 1 chr2B.!!$R1 2885
1 TraesCS2B01G305600 chr2B 442462774 442463399 625 False 937.000000 937 93.968000 2270 2886 1 chr2B.!!$F1 616
2 TraesCS2B01G305600 chr2D 8652516 8653136 620 True 957.000000 957 94.847000 2279 2886 1 chr2D.!!$R1 607
3 TraesCS2B01G305600 chr2D 367223062 367224601 1539 True 785.000000 1796 93.944333 661 2199 3 chr2D.!!$R2 1538
4 TraesCS2B01G305600 chr2A 497013367 497015724 2357 True 941.333333 1591 89.054333 1 2279 3 chr2A.!!$R2 2278
5 TraesCS2B01G305600 chr2A 776273299 776273811 512 True 701.000000 701 91.667000 2268 2770 1 chr2A.!!$R1 502
6 TraesCS2B01G305600 chr1D 23942834 23943450 616 False 968.000000 968 95.315000 2281 2886 1 chr1D.!!$F1 605
7 TraesCS2B01G305600 chr4D 220179131 220179748 617 False 963.000000 963 95.146000 2282 2886 1 chr4D.!!$F1 604
8 TraesCS2B01G305600 chr4D 201001381 201001998 617 True 941.000000 941 94.507000 2282 2886 1 chr4D.!!$R1 604
9 TraesCS2B01G305600 chr5D 6687456 6688075 619 True 950.000000 950 94.677000 2280 2886 1 chr5D.!!$R1 606
10 TraesCS2B01G305600 chr4A 653334334 653334938 604 False 941.000000 941 94.728000 2282 2886 1 chr4A.!!$F1 604
11 TraesCS2B01G305600 chr6D 202939409 202940025 616 True 935.000000 935 94.337000 2282 2886 1 chr6D.!!$R1 604
12 TraesCS2B01G305600 chr3D 539615448 539616058 610 True 913.000000 913 93.781000 2282 2886 1 chr3D.!!$R1 604
13 TraesCS2B01G305600 chr3A 403135828 403136438 610 True 802.000000 802 90.523000 2282 2886 1 chr3A.!!$R2 604
14 TraesCS2B01G305600 chr3A 160290834 160291343 509 True 726.000000 726 92.759000 2273 2770 1 chr3A.!!$R1 497
15 TraesCS2B01G305600 chr3A 181038650 181039166 516 False 717.000000 717 92.085000 2266 2770 1 chr3A.!!$F1 504

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
955 1023 0.317603 GTGATCCGACACCCGATACG 60.318 60.0 0.0 0.0 41.76 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 2413 0.033601 ATCAATGGCCGCCTTAACCA 60.034 50.0 11.61 0.0 37.99 3.67 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
49 50 2.224744 TGCAACATGGACTGGTATGTGT 60.225 45.455 0.00 0.00 37.57 3.72
50 51 2.162208 GCAACATGGACTGGTATGTGTG 59.838 50.000 0.00 0.00 37.57 3.82
90 91 2.616960 TGTTCGAATTGTGGATCTCCG 58.383 47.619 0.00 0.00 39.43 4.63
91 92 1.327764 GTTCGAATTGTGGATCTCCGC 59.672 52.381 0.00 2.75 46.40 5.54
127 130 3.706140 CGCATGCCGGTACTTCTC 58.294 61.111 13.15 0.00 0.00 2.87
129 132 1.220749 GCATGCCGGTACTTCTCCA 59.779 57.895 6.36 0.00 0.00 3.86
132 135 1.264749 ATGCCGGTACTTCTCCAGCA 61.265 55.000 1.90 0.00 41.64 4.41
166 169 1.455773 ACATGGATCTCGAGCGGGA 60.456 57.895 7.81 0.00 0.00 5.14
219 222 1.087202 CCATTCCGGACGAAATGCGA 61.087 55.000 1.83 0.00 46.80 5.10
242 245 2.367512 GGGTGGCCCTCCTCATCT 60.368 66.667 12.79 0.00 41.34 2.90
261 264 0.385751 TACGAGCTCATGGTAGCAGC 59.614 55.000 15.40 2.40 45.30 5.25
262 265 1.593750 CGAGCTCATGGTAGCAGCC 60.594 63.158 15.40 0.00 45.30 4.85
263 266 1.524002 GAGCTCATGGTAGCAGCCA 59.476 57.895 9.40 1.69 45.30 4.75
272 275 2.682594 TGGTAGCAGCCATGACTAGAT 58.317 47.619 0.00 0.00 32.81 1.98
285 288 6.218746 CCATGACTAGATTCATCGATTCACA 58.781 40.000 0.00 0.00 33.74 3.58
289 292 7.664758 TGACTAGATTCATCGATTCACATGAT 58.335 34.615 0.00 0.00 0.00 2.45
293 296 5.404667 AGATTCATCGATTCACATGATGTCG 59.595 40.000 0.00 4.01 40.25 4.35
301 304 0.875908 CACATGATGTCGGTAGGCGG 60.876 60.000 0.00 0.00 0.00 6.13
310 313 1.520787 CGGTAGGCGGTGGTCAATC 60.521 63.158 0.00 0.00 0.00 2.67
319 322 1.334960 CGGTGGTCAATCAAAGTGTGC 60.335 52.381 0.00 0.00 0.00 4.57
320 323 1.680735 GGTGGTCAATCAAAGTGTGCA 59.319 47.619 0.00 0.00 0.00 4.57
321 324 2.287788 GGTGGTCAATCAAAGTGTGCAG 60.288 50.000 0.00 0.00 0.00 4.41
366 370 2.038837 CGACGGGGGAAAGGAAAGC 61.039 63.158 0.00 0.00 0.00 3.51
373 377 2.399356 GGAAAGGAAAGCGGCGGAG 61.399 63.158 9.78 0.00 0.00 4.63
410 414 4.379243 CGTGGAGGCAACCGAGCT 62.379 66.667 0.00 0.00 34.17 4.09
419 423 1.324005 GCAACCGAGCTAGGGAGAGT 61.324 60.000 17.90 0.00 35.02 3.24
434 438 1.002430 GAGAGTGACATCCAAGCCACA 59.998 52.381 0.00 0.00 32.35 4.17
435 439 1.421268 AGAGTGACATCCAAGCCACAA 59.579 47.619 0.00 0.00 32.35 3.33
439 443 0.890683 GACATCCAAGCCACAAAGGG 59.109 55.000 0.00 0.00 38.09 3.95
490 494 3.883997 TCAAATTTGAGGCGCAACC 57.116 47.368 16.91 0.00 35.91 3.77
496 500 1.013596 TTTGAGGCGCAACCGATATG 58.986 50.000 10.83 0.00 46.52 1.78
501 505 4.012895 CGCAACCGATATGCCGCC 62.013 66.667 2.23 0.00 40.72 6.13
508 512 0.868406 CCGATATGCCGCCTTCTTTC 59.132 55.000 0.00 0.00 0.00 2.62
567 572 2.355756 GCCGTGAACATGTCTATGCATT 59.644 45.455 3.54 0.00 37.85 3.56
568 573 3.546815 GCCGTGAACATGTCTATGCATTC 60.547 47.826 3.54 0.00 37.85 2.67
580 585 5.046304 TGTCTATGCATTCTAGGCCCTATTC 60.046 44.000 3.54 0.00 0.00 1.75
582 587 2.325484 TGCATTCTAGGCCCTATTCGA 58.675 47.619 0.00 0.00 0.00 3.71
586 591 3.814005 TTCTAGGCCCTATTCGACAAC 57.186 47.619 0.00 0.00 0.00 3.32
589 594 1.276622 AGGCCCTATTCGACAACACT 58.723 50.000 0.00 0.00 0.00 3.55
591 596 1.278238 GCCCTATTCGACAACACTCG 58.722 55.000 0.00 0.00 34.83 4.18
630 644 2.897350 GCGCCGGATTAGCAGCTT 60.897 61.111 5.05 0.00 0.00 3.74
643 657 7.418408 GGATTAGCAGCTTCCTAAATTACAAC 58.582 38.462 0.00 0.00 0.00 3.32
650 664 7.065803 GCAGCTTCCTAAATTACAACTACATGA 59.934 37.037 0.00 0.00 0.00 3.07
651 665 9.113838 CAGCTTCCTAAATTACAACTACATGAT 57.886 33.333 0.00 0.00 0.00 2.45
654 668 8.800370 TTCCTAAATTACAACTACATGATGCA 57.200 30.769 0.00 0.00 0.00 3.96
655 669 8.437360 TCCTAAATTACAACTACATGATGCAG 57.563 34.615 0.00 0.00 0.00 4.41
658 711 6.932356 AATTACAACTACATGATGCAGAGG 57.068 37.500 0.00 0.00 0.00 3.69
681 734 4.804665 GCTCTTAGTCCTACAAATTCGTCC 59.195 45.833 0.00 0.00 0.00 4.79
742 795 5.289675 CAGGAGCATAAACTCTTGTAAGACG 59.710 44.000 0.00 0.00 38.57 4.18
816 884 6.067263 GCATATAGGCCAACGTTGATTTTA 57.933 37.500 29.35 15.21 0.00 1.52
825 893 9.278978 AGGCCAACGTTGATTTTATTTATTTTT 57.721 25.926 29.35 0.00 0.00 1.94
907 975 2.353376 CGGCGGCGGCATTAAATG 60.353 61.111 32.59 11.08 42.47 2.32
923 991 8.223100 GGCATTAAATGTTCAACAGAATTTGTC 58.777 33.333 0.00 0.00 39.73 3.18
955 1023 0.317603 GTGATCCGACACCCGATACG 60.318 60.000 0.00 0.00 41.76 3.06
998 1066 3.365265 GCCGCACCAGGGTTTCAG 61.365 66.667 0.00 0.00 0.00 3.02
999 1067 2.429930 CCGCACCAGGGTTTCAGA 59.570 61.111 0.00 0.00 0.00 3.27
1000 1068 1.228124 CCGCACCAGGGTTTCAGAA 60.228 57.895 0.00 0.00 0.00 3.02
1001 1069 0.609131 CCGCACCAGGGTTTCAGAAT 60.609 55.000 0.00 0.00 0.00 2.40
1002 1070 0.523072 CGCACCAGGGTTTCAGAATG 59.477 55.000 0.00 0.00 37.54 2.67
1003 1071 0.890683 GCACCAGGGTTTCAGAATGG 59.109 55.000 0.00 0.00 36.16 3.16
1004 1072 0.890683 CACCAGGGTTTCAGAATGGC 59.109 55.000 0.98 0.00 36.16 4.40
1005 1073 0.482446 ACCAGGGTTTCAGAATGGCA 59.518 50.000 0.98 0.00 36.16 4.92
1006 1074 1.077663 ACCAGGGTTTCAGAATGGCAT 59.922 47.619 0.00 0.00 36.16 4.40
1007 1075 2.181975 CCAGGGTTTCAGAATGGCATT 58.818 47.619 13.54 13.54 36.16 3.56
1008 1076 2.568509 CCAGGGTTTCAGAATGGCATTT 59.431 45.455 14.93 1.72 36.16 2.32
1009 1077 3.008266 CCAGGGTTTCAGAATGGCATTTT 59.992 43.478 14.93 5.70 36.16 1.82
1010 1078 4.505390 CCAGGGTTTCAGAATGGCATTTTT 60.505 41.667 14.93 3.25 36.16 1.94
1075 1143 0.321564 TGATCTCGCCACCAAACCAG 60.322 55.000 0.00 0.00 0.00 4.00
1423 1521 2.119495 GCCAAGATTCAGAGGGTCCTA 58.881 52.381 0.00 0.00 0.00 2.94
1617 1715 3.319198 GGACGACCCTCCCAAGCA 61.319 66.667 0.00 0.00 0.00 3.91
1618 1716 2.266055 GACGACCCTCCCAAGCAG 59.734 66.667 0.00 0.00 0.00 4.24
1625 1723 0.679321 CCCTCCCAAGCAGAAGAAGC 60.679 60.000 0.00 0.00 0.00 3.86
1630 1728 1.538950 CCCAAGCAGAAGAAGCAAGAC 59.461 52.381 0.00 0.00 0.00 3.01
1895 2029 2.164827 TCCGTCATGTAACTGCGTGTAT 59.835 45.455 0.00 0.00 0.00 2.29
1905 2039 0.807667 CTGCGTGTATGTCCCTGCTC 60.808 60.000 0.00 0.00 0.00 4.26
1973 2107 9.132521 CCATGAGTGATTTGTTTGTAATTCTTC 57.867 33.333 0.00 0.00 0.00 2.87
2027 2161 6.801539 AATGCTTTCTGTCGAATAAGTGAA 57.198 33.333 0.00 0.00 0.00 3.18
2061 2195 6.705863 ATGTTGCTTAAGGAATCAGGAATC 57.294 37.500 12.87 0.00 0.00 2.52
2114 2248 9.899226 CTTGTTCAAAAATCCTTTACTCTTAGG 57.101 33.333 0.00 0.00 0.00 2.69
2133 2267 7.781056 TCTTAGGATTTGAAAATACAATGCCC 58.219 34.615 1.00 0.00 31.40 5.36
2209 2368 3.745546 CCAGGCCTGAATCTGGGA 58.254 61.111 34.91 0.00 44.99 4.37
2210 2369 1.530771 CCAGGCCTGAATCTGGGAG 59.469 63.158 34.91 10.00 44.99 4.30
2213 2372 0.030705 AGGCCTGAATCTGGGAGCTA 60.031 55.000 3.11 0.00 0.00 3.32
2229 2388 3.501445 GGAGCTATTGATCTTCATGGCAC 59.499 47.826 0.00 4.99 0.00 5.01
2247 2406 0.833287 ACTGATTCTGACATCCCCGG 59.167 55.000 0.00 0.00 0.00 5.73
2248 2407 0.833287 CTGATTCTGACATCCCCGGT 59.167 55.000 0.00 0.00 0.00 5.28
2249 2408 0.541392 TGATTCTGACATCCCCGGTG 59.459 55.000 0.00 0.00 0.00 4.94
2250 2409 0.179045 GATTCTGACATCCCCGGTGG 60.179 60.000 0.00 0.82 0.00 4.61
2316 2475 9.436957 AAATATGTTAACTAGTGACCTTCTGTG 57.563 33.333 7.22 0.00 0.00 3.66
2333 2493 3.259374 TCTGTGAGTGACCTGGAAGAATC 59.741 47.826 0.00 0.00 34.07 2.52
2426 2586 9.396022 ACTATAACGACCATTTTGATCAGAAAT 57.604 29.630 2.39 6.43 0.00 2.17
2465 2625 5.065218 ACACGAAATGGTCATAAAGCAGATC 59.935 40.000 0.00 0.00 39.11 2.75
2466 2626 4.576463 ACGAAATGGTCATAAAGCAGATCC 59.424 41.667 0.00 0.00 39.11 3.36
2582 2754 3.682436 GCCTATGTGTCATGTCCATGTGA 60.682 47.826 7.13 0.00 39.72 3.58
2821 2993 4.546829 TTTCTACGGTGCTTTCCTATGT 57.453 40.909 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.702048 AGGCGGCGTGTGGTATGT 61.702 61.111 9.37 0.00 0.00 2.29
34 35 1.210478 GCTCCACACATACCAGTCCAT 59.790 52.381 0.00 0.00 0.00 3.41
67 68 3.242870 GGAGATCCACAATTCGAACATGC 60.243 47.826 0.00 0.00 35.64 4.06
127 130 2.125229 AGTCATCGCTGCTGCTGG 60.125 61.111 14.03 3.10 36.97 4.85
129 132 1.153608 CTCAGTCATCGCTGCTGCT 60.154 57.895 14.03 0.00 36.49 4.24
132 135 0.822811 ATGTCTCAGTCATCGCTGCT 59.177 50.000 0.00 0.00 36.49 4.24
144 147 0.665298 CGCTCGAGATCCATGTCTCA 59.335 55.000 18.75 1.55 43.84 3.27
202 205 1.663695 ATTCGCATTTCGTCCGGAAT 58.336 45.000 5.23 0.00 39.67 3.01
242 245 0.385751 GCTGCTACCATGAGCTCGTA 59.614 55.000 8.44 3.97 43.27 3.43
261 264 6.218746 TGTGAATCGATGAATCTAGTCATGG 58.781 40.000 0.00 0.64 38.38 3.66
262 265 7.597743 TCATGTGAATCGATGAATCTAGTCATG 59.402 37.037 0.00 7.66 38.38 3.07
263 266 7.664758 TCATGTGAATCGATGAATCTAGTCAT 58.335 34.615 0.00 0.00 41.01 3.06
266 269 7.440198 ACATCATGTGAATCGATGAATCTAGT 58.560 34.615 0.00 0.00 39.09 2.57
272 275 3.803778 CCGACATCATGTGAATCGATGAA 59.196 43.478 16.81 0.00 39.09 2.57
285 288 1.441729 CACCGCCTACCGACATCAT 59.558 57.895 0.00 0.00 40.02 2.45
289 292 3.376078 GACCACCGCCTACCGACA 61.376 66.667 0.00 0.00 40.02 4.35
293 296 0.035820 TTGATTGACCACCGCCTACC 60.036 55.000 0.00 0.00 0.00 3.18
301 304 2.287788 CCTGCACACTTTGATTGACCAC 60.288 50.000 0.00 0.00 0.00 4.16
310 313 1.171308 CCATCCTCCTGCACACTTTG 58.829 55.000 0.00 0.00 0.00 2.77
351 355 2.750237 CCGCTTTCCTTTCCCCCG 60.750 66.667 0.00 0.00 0.00 5.73
366 370 1.966451 AACTTTCTTGCCTCCGCCG 60.966 57.895 0.00 0.00 0.00 6.46
381 385 3.832237 CTCCACGCAGGCACCAACT 62.832 63.158 0.00 0.00 37.29 3.16
403 407 0.394625 GTCACTCTCCCTAGCTCGGT 60.395 60.000 3.23 0.00 0.00 4.69
410 414 2.111384 GCTTGGATGTCACTCTCCCTA 58.889 52.381 0.00 0.00 0.00 3.53
419 423 1.619654 CCTTTGTGGCTTGGATGTCA 58.380 50.000 0.00 0.00 0.00 3.58
450 454 2.394563 GCCGAAGCCACTTCTCAGC 61.395 63.158 5.85 2.79 38.24 4.26
485 489 2.117941 GAAGGCGGCATATCGGTTGC 62.118 60.000 13.08 0.00 39.41 4.17
490 494 1.871080 AGAAAGAAGGCGGCATATCG 58.129 50.000 13.08 0.00 0.00 2.92
496 500 1.466558 CTTCTCAAGAAAGAAGGCGGC 59.533 52.381 0.00 0.00 45.61 6.53
508 512 9.921637 AACTCTCATCTAGTTTAACTTCTCAAG 57.078 33.333 1.94 0.00 33.39 3.02
524 529 5.363939 GCAACTATAGCCAAACTCTCATCT 58.636 41.667 0.00 0.00 0.00 2.90
542 547 2.831685 TAGACATGTTCACGGCAACT 57.168 45.000 0.00 0.00 0.00 3.16
549 554 5.049818 GCCTAGAATGCATAGACATGTTCAC 60.050 44.000 0.00 0.00 34.40 3.18
567 572 2.429610 GTGTTGTCGAATAGGGCCTAGA 59.570 50.000 19.74 8.15 0.00 2.43
568 573 2.431057 AGTGTTGTCGAATAGGGCCTAG 59.569 50.000 19.74 5.67 0.00 3.02
580 585 0.109689 GGAGGAGTCGAGTGTTGTCG 60.110 60.000 0.00 0.00 41.51 4.35
582 587 0.962489 CTGGAGGAGTCGAGTGTTGT 59.038 55.000 0.00 0.00 0.00 3.32
586 591 1.649390 CGTCCTGGAGGAGTCGAGTG 61.649 65.000 10.85 0.00 46.49 3.51
589 594 2.045242 CCGTCCTGGAGGAGTCGA 60.045 66.667 17.56 0.00 46.49 4.20
620 634 9.110502 GTAGTTGTAATTTAGGAAGCTGCTAAT 57.889 33.333 0.90 0.00 30.42 1.73
630 644 8.264347 TCTGCATCATGTAGTTGTAATTTAGGA 58.736 33.333 2.33 0.00 31.74 2.94
643 657 3.472283 AAGAGCCTCTGCATCATGTAG 57.528 47.619 0.00 0.00 41.13 2.74
650 664 2.173126 AGGACTAAGAGCCTCTGCAT 57.827 50.000 0.00 0.00 41.13 3.96
651 665 2.291605 TGTAGGACTAAGAGCCTCTGCA 60.292 50.000 0.00 0.00 41.13 4.41
654 668 5.163499 CGAATTTGTAGGACTAAGAGCCTCT 60.163 44.000 0.00 0.00 35.73 3.69
655 669 5.044558 CGAATTTGTAGGACTAAGAGCCTC 58.955 45.833 0.00 0.00 35.73 4.70
658 711 4.804665 GGACGAATTTGTAGGACTAAGAGC 59.195 45.833 0.00 0.00 0.00 4.09
681 734 2.838275 CCAACGACAATTGATGACACG 58.162 47.619 13.59 9.74 0.00 4.49
742 795 1.082117 CCGGTGTACTGGAATCGCAC 61.082 60.000 3.73 0.00 45.36 5.34
775 828 0.808755 GCCGAACCGAAATGGATGTT 59.191 50.000 0.00 0.00 42.00 2.71
907 975 4.668289 ACGGTTGACAAATTCTGTTGAAC 58.332 39.130 0.00 0.00 38.84 3.18
923 991 1.660607 CGGATCACATCTCAACGGTTG 59.339 52.381 14.62 14.62 0.00 3.77
959 1027 1.634702 GAATAGATGGCGAGCGATCC 58.365 55.000 14.84 0.00 32.63 3.36
960 1028 1.263776 CGAATAGATGGCGAGCGATC 58.736 55.000 11.33 11.33 0.00 3.69
1013 1081 8.458052 TCTTGAATGCTATTCTATTCGCAAAAA 58.542 29.630 9.34 0.00 36.36 1.94
1014 1082 7.910162 GTCTTGAATGCTATTCTATTCGCAAAA 59.090 33.333 9.34 0.00 36.36 2.44
1015 1083 7.409697 GTCTTGAATGCTATTCTATTCGCAAA 58.590 34.615 9.34 0.00 36.36 3.68
1016 1084 6.017934 GGTCTTGAATGCTATTCTATTCGCAA 60.018 38.462 9.34 0.00 36.36 4.85
1017 1085 5.466728 GGTCTTGAATGCTATTCTATTCGCA 59.533 40.000 9.34 0.00 36.36 5.10
1018 1086 5.388890 CGGTCTTGAATGCTATTCTATTCGC 60.389 44.000 9.34 0.00 36.36 4.70
1019 1087 5.920840 TCGGTCTTGAATGCTATTCTATTCG 59.079 40.000 9.34 7.54 36.36 3.34
1020 1088 7.064016 GGATCGGTCTTGAATGCTATTCTATTC 59.936 40.741 0.00 0.00 34.64 1.75
1021 1089 6.876257 GGATCGGTCTTGAATGCTATTCTATT 59.124 38.462 0.00 0.00 0.00 1.73
1022 1090 6.402222 GGATCGGTCTTGAATGCTATTCTAT 58.598 40.000 0.00 0.00 0.00 1.98
1023 1091 5.564848 CGGATCGGTCTTGAATGCTATTCTA 60.565 44.000 0.00 3.01 0.00 2.10
1029 1097 0.537188 ACGGATCGGTCTTGAATGCT 59.463 50.000 0.00 0.00 0.00 3.79
1075 1143 5.643379 TGTTTTCTCCTATGGTTTGCATC 57.357 39.130 0.00 0.00 0.00 3.91
1402 1500 0.462759 GGACCCTCTGAATCTTGGCG 60.463 60.000 0.00 0.00 0.00 5.69
1617 1715 2.611722 GGCTTCTCGTCTTGCTTCTTCT 60.612 50.000 0.00 0.00 0.00 2.85
1618 1716 1.729517 GGCTTCTCGTCTTGCTTCTTC 59.270 52.381 0.00 0.00 0.00 2.87
1625 1723 0.456995 GTCTCGGGCTTCTCGTCTTG 60.457 60.000 0.00 0.00 0.00 3.02
1630 1728 1.153745 CTTGGTCTCGGGCTTCTCG 60.154 63.158 0.00 0.00 0.00 4.04
1672 1770 3.199190 TACGGGTACGCGTACGGG 61.199 66.667 35.36 30.64 46.04 5.28
1874 2008 0.315886 ACACGCAGTTACATGACGGA 59.684 50.000 0.00 0.00 41.61 4.69
1895 2029 3.680786 CACCGTCGAGCAGGGACA 61.681 66.667 0.00 0.00 34.04 4.02
1973 2107 9.037737 TCGAAGACGTTTAAGGAAATATATTGG 57.962 33.333 0.00 0.00 40.69 3.16
2027 2161 8.951787 TTCCTTAAGCAACATATATACAACGT 57.048 30.769 0.00 0.00 0.00 3.99
2061 2195 2.191641 GCTCTAGGCTGCTTGGGG 59.808 66.667 0.00 0.00 38.06 4.96
2114 2248 7.671495 AAACAGGGCATTGTATTTTCAAATC 57.329 32.000 0.00 0.00 0.00 2.17
2208 2367 4.213694 CAGTGCCATGAAGATCAATAGCTC 59.786 45.833 0.00 0.00 0.00 4.09
2209 2368 4.135306 CAGTGCCATGAAGATCAATAGCT 58.865 43.478 0.00 0.00 0.00 3.32
2210 2369 4.132336 TCAGTGCCATGAAGATCAATAGC 58.868 43.478 0.00 0.00 0.00 2.97
2213 2372 5.299531 CAGAATCAGTGCCATGAAGATCAAT 59.700 40.000 0.00 0.00 31.76 2.57
2229 2388 0.833287 ACCGGGGATGTCAGAATCAG 59.167 55.000 6.32 0.00 0.00 2.90
2247 2406 1.376812 CCGCCTTAACCACCTCCAC 60.377 63.158 0.00 0.00 0.00 4.02
2248 2407 3.074281 CCGCCTTAACCACCTCCA 58.926 61.111 0.00 0.00 0.00 3.86
2249 2408 2.437895 GCCGCCTTAACCACCTCC 60.438 66.667 0.00 0.00 0.00 4.30
2250 2409 2.437895 GGCCGCCTTAACCACCTC 60.438 66.667 0.71 0.00 0.00 3.85
2254 2413 0.033601 ATCAATGGCCGCCTTAACCA 60.034 50.000 11.61 0.00 37.99 3.67
2298 2457 5.241064 GTCACTCACAGAAGGTCACTAGTTA 59.759 44.000 0.00 0.00 0.00 2.24
2316 2475 1.550976 ACCGATTCTTCCAGGTCACTC 59.449 52.381 0.00 0.00 29.76 3.51
2358 2518 6.048509 CCAAACAGCTTTTGACCAATTAGTT 58.951 36.000 17.53 0.00 0.00 2.24
2361 2521 4.202305 CCCCAAACAGCTTTTGACCAATTA 60.202 41.667 17.53 0.00 0.00 1.40
2465 2625 3.995199 TGATCAGCTAGAAATAAGGCGG 58.005 45.455 0.00 0.00 0.00 6.13
2466 2626 5.119898 GTCATGATCAGCTAGAAATAAGGCG 59.880 44.000 0.00 0.00 0.00 5.52
2582 2754 4.993028 TCACAACCTAGGGCAAAAACTAT 58.007 39.130 14.81 0.00 0.00 2.12
2657 2829 5.873179 TTTGACGAAGATATGACCCAAAC 57.127 39.130 0.00 0.00 0.00 2.93
2807 2979 5.163550 GGTTATTTGGACATAGGAAAGCACC 60.164 44.000 0.00 0.00 0.00 5.01
2821 2993 2.922955 TGGTGGAGGATGGTTATTTGGA 59.077 45.455 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.