Multiple sequence alignment - TraesCS2A01G179200

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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 TraesCS2A01G179200 chr2A 100.000 2783 0 0 1 2783 137950274 137953056 0.000000e+00 5140.0
1 TraesCS2A01G179200 chr2A 84.133 1147 124 31 720 1848 138084127 138085233 0.000000e+00 1057.0
2 TraesCS2A01G179200 chr2A 83.157 849 116 14 1010 1848 137936078 137936909 0.000000e+00 750.0
3 TraesCS2A01G179200 chr2A 80.556 1008 123 35 663 1656 137942043 137942991 0.000000e+00 708.0
4 TraesCS2A01G179200 chr2A 84.341 364 54 1 1238 1601 138084738 138085098 1.230000e-93 353.0
5 TraesCS2A01G179200 chr2A 81.149 435 68 10 1426 1848 137942800 137943232 1.230000e-88 337.0
6 TraesCS2A01G179200 chr2B 91.436 2055 141 14 1 2035 184908660 184910699 0.000000e+00 2787.0
7 TraesCS2A01G179200 chr2B 80.884 1245 159 46 781 2005 184876821 184878006 0.000000e+00 907.0
8 TraesCS2A01G179200 chr2B 88.616 571 63 2 999 1568 184899826 184900395 0.000000e+00 693.0
9 TraesCS2A01G179200 chr2B 88.307 573 59 6 2212 2783 184912067 184912632 0.000000e+00 680.0
10 TraesCS2A01G179200 chr2B 83.203 768 70 31 663 1426 184799935 184800647 0.000000e+00 649.0
11 TraesCS2A01G179200 chr2B 81.157 743 94 12 865 1599 184930515 184931219 3.130000e-154 555.0
12 TraesCS2A01G179200 chr2B 78.084 981 134 51 1348 2294 184800685 184801618 1.880000e-151 545.0
13 TraesCS2A01G179200 chr2B 78.367 735 127 24 1427 2142 184900170 184900891 5.470000e-122 448.0
14 TraesCS2A01G179200 chr2B 78.714 700 100 29 918 1599 184789291 184789959 3.310000e-114 422.0
15 TraesCS2A01G179200 chr2B 89.140 221 21 1 1631 1848 184789877 184790097 3.530000e-69 272.0
16 TraesCS2A01G179200 chr2B 92.391 184 13 1 2032 2214 184910855 184911038 7.650000e-66 261.0
17 TraesCS2A01G179200 chr2B 77.045 379 64 18 4 376 662343872 662344233 2.190000e-46 196.0
18 TraesCS2A01G179200 chr2B 86.782 174 13 1 664 837 184928205 184928368 4.730000e-43 185.0
19 TraesCS2A01G179200 chr2B 84.375 160 12 9 766 923 184899635 184899783 8.030000e-31 145.0
20 TraesCS2A01G179200 chr2B 75.152 165 41 0 280 444 77204618 77204454 8.260000e-11 78.7
21 TraesCS2A01G179200 chr2B 84.615 78 11 1 247 324 140529178 140529254 2.970000e-10 76.8
22 TraesCS2A01G179200 chr2B 92.857 42 2 1 2316 2357 772825389 772825349 2.990000e-05 60.2
23 TraesCS2A01G179200 chr2D 93.320 1512 80 11 890 2397 131316679 131318173 0.000000e+00 2213.0
24 TraesCS2A01G179200 chr2D 85.987 628 53 14 663 1288 131359905 131360499 8.400000e-180 640.0
25 TraesCS2A01G179200 chr2D 84.211 646 81 10 1216 1848 131360469 131361106 2.370000e-170 608.0
26 TraesCS2A01G179200 chr2D 87.500 472 53 6 1348 1818 131303396 131303862 8.770000e-150 540.0
27 TraesCS2A01G179200 chr2D 90.750 400 36 1 2385 2783 131318192 131318591 1.470000e-147 532.0
28 TraesCS2A01G179200 chr2D 77.306 965 144 40 1176 2108 131284477 131285398 1.490000e-137 499.0
29 TraesCS2A01G179200 chr2D 85.253 434 53 4 1 423 131314767 131315200 1.180000e-118 436.0
30 TraesCS2A01G179200 chr2D 97.838 185 4 0 654 838 131316485 131316669 1.240000e-83 320.0
31 TraesCS2A01G179200 chr2D 80.603 464 39 25 663 1120 131294986 131295404 7.480000e-81 311.0
32 TraesCS2A01G179200 chr2D 81.215 362 65 1 1238 1599 131360614 131360972 3.510000e-74 289.0
33 TraesCS2A01G179200 chr2D 89.954 219 9 7 455 670 131315201 131315409 1.270000e-68 270.0
34 TraesCS2A01G179200 chr2D 78.947 323 53 9 1 313 596568996 596568679 3.630000e-49 206.0
35 TraesCS2A01G179200 chr2D 82.160 213 27 8 897 1103 107845538 107845745 3.690000e-39 172.0
36 TraesCS2A01G179200 chr2D 80.233 86 15 2 2625 2709 86517677 86517593 2.310000e-06 63.9
37 TraesCS2A01G179200 chr2D 97.297 37 1 0 2316 2352 565117576 565117612 2.310000e-06 63.9
38 TraesCS2A01G179200 chr7B 76.606 654 98 26 913 1537 604334529 604335156 2.690000e-80 309.0
39 TraesCS2A01G179200 chr7B 84.848 66 10 0 2626 2691 623712370 623712435 1.790000e-07 67.6
40 TraesCS2A01G179200 chr1D 76.786 448 96 8 2 444 477426283 477426727 7.700000e-61 244.0
41 TraesCS2A01G179200 chr5B 73.394 436 106 10 2317 2748 631392917 631393346 1.330000e-33 154.0
42 TraesCS2A01G179200 chr3B 79.882 169 34 0 2404 2572 412055350 412055182 1.050000e-24 124.0
43 TraesCS2A01G179200 chr7D 82.143 140 23 2 2536 2674 452258705 452258567 4.870000e-23 119.0
44 TraesCS2A01G179200 chrUn 75.829 211 48 3 2547 2755 19062167 19061958 1.360000e-18 104.0
45 TraesCS2A01G179200 chr7A 84.158 101 13 1 732 829 642380503 642380603 8.210000e-16 95.3
46 TraesCS2A01G179200 chr5A 82.857 105 16 2 246 350 692056349 692056247 2.950000e-15 93.5
47 TraesCS2A01G179200 chr6B 89.091 55 4 1 2316 2370 224247655 224247603 1.790000e-07 67.6
48 TraesCS2A01G179200 chr3A 93.023 43 1 2 2314 2356 716799536 716799496 8.320000e-06 62.1
49 TraesCS2A01G179200 chr3A 94.595 37 2 0 2316 2352 713803560 713803524 1.080000e-04 58.4
50 TraesCS2A01G179200 chr4A 92.857 42 2 1 2316 2357 429713607 429713567 2.990000e-05 60.2
51 TraesCS2A01G179200 chr1A 92.500 40 1 2 2316 2354 298500891 298500853 3.870000e-04 56.5


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 TraesCS2A01G179200 chr2A 137950274 137953056 2782 False 5140.000000 5140 100.000000 1 2783 1 chr2A.!!$F2 2782
1 TraesCS2A01G179200 chr2A 137936078 137936909 831 False 750.000000 750 83.157000 1010 1848 1 chr2A.!!$F1 838
2 TraesCS2A01G179200 chr2A 138084127 138085233 1106 False 705.000000 1057 84.237000 720 1848 2 chr2A.!!$F4 1128
3 TraesCS2A01G179200 chr2A 137942043 137943232 1189 False 522.500000 708 80.852500 663 1848 2 chr2A.!!$F3 1185
4 TraesCS2A01G179200 chr2B 184908660 184912632 3972 False 1242.666667 2787 90.711333 1 2783 3 chr2B.!!$F7 2782
5 TraesCS2A01G179200 chr2B 184876821 184878006 1185 False 907.000000 907 80.884000 781 2005 1 chr2B.!!$F2 1224
6 TraesCS2A01G179200 chr2B 184799935 184801618 1683 False 597.000000 649 80.643500 663 2294 2 chr2B.!!$F5 1631
7 TraesCS2A01G179200 chr2B 184899635 184900891 1256 False 428.666667 693 83.786000 766 2142 3 chr2B.!!$F6 1376
8 TraesCS2A01G179200 chr2B 184928205 184931219 3014 False 370.000000 555 83.969500 664 1599 2 chr2B.!!$F8 935
9 TraesCS2A01G179200 chr2B 184789291 184790097 806 False 347.000000 422 83.927000 918 1848 2 chr2B.!!$F4 930
10 TraesCS2A01G179200 chr2D 131314767 131318591 3824 False 754.200000 2213 91.423000 1 2783 5 chr2D.!!$F6 2782
11 TraesCS2A01G179200 chr2D 131359905 131361106 1201 False 512.333333 640 83.804333 663 1848 3 chr2D.!!$F7 1185
12 TraesCS2A01G179200 chr2D 131284477 131285398 921 False 499.000000 499 77.306000 1176 2108 1 chr2D.!!$F2 932
13 TraesCS2A01G179200 chr7B 604334529 604335156 627 False 309.000000 309 76.606000 913 1537 1 chr7B.!!$F1 624

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
205 208 0.366871 CGATGGACGAAACGAGCTTG 59.633 55.0 0.0 0.0 45.77 4.01 F
413 426 0.892755 ACCGTCCGTCTGAGCATTTA 59.107 50.0 0.0 0.0 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1008 4286 1.147817 AGGGAGGCCATGTTGTTCTTT 59.852 47.619 5.01 0.0 0.0 2.52 R
2400 7515 0.317269 CTTGCTTGTGTTGTGGCTCG 60.317 55.000 0.00 0.0 0.0 5.03 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
66 67 2.430367 GGAGTGGAAAGTGGCGGT 59.570 61.111 0.00 0.00 0.00 5.68
70 71 4.196778 TGGAAAGTGGCGGTGGCA 62.197 61.111 0.00 0.00 42.47 4.92
99 101 1.354368 GAGGGGGAAAATGTGGACAGA 59.646 52.381 0.00 0.00 0.00 3.41
119 121 1.756408 TAGGGTTTTGGTGCCGACGA 61.756 55.000 0.00 0.00 0.00 4.20
205 208 0.366871 CGATGGACGAAACGAGCTTG 59.633 55.000 0.00 0.00 45.77 4.01
232 235 2.483889 GCCGGGTTTTGGATTGTTTTCA 60.484 45.455 2.18 0.00 0.00 2.69
238 241 5.047188 GGTTTTGGATTGTTTTCACGTGAT 58.953 37.500 20.80 2.29 0.00 3.06
242 245 4.647611 TGGATTGTTTTCACGTGATACCT 58.352 39.130 20.80 10.44 0.00 3.08
291 304 3.168528 AACGCCCCCATATCCGCT 61.169 61.111 0.00 0.00 0.00 5.52
311 324 5.163622 CCGCTTTATATTTGGGCTGGATATG 60.164 44.000 0.00 0.00 0.00 1.78
318 331 3.344535 TTGGGCTGGATATGAGAGGTA 57.655 47.619 0.00 0.00 0.00 3.08
324 337 3.231818 CTGGATATGAGAGGTACCGGTT 58.768 50.000 15.04 0.00 0.00 4.44
329 342 3.666345 ATGAGAGGTACCGGTTAGTCT 57.334 47.619 15.04 12.48 0.00 3.24
338 351 4.160252 GGTACCGGTTAGTCTGGACATTTA 59.840 45.833 15.04 0.00 45.09 1.40
343 356 4.623171 CGGTTAGTCTGGACATTTAAGGCT 60.623 45.833 3.51 0.00 0.00 4.58
361 374 3.411351 CGTTTGAGGCACCCGTCG 61.411 66.667 0.00 0.00 0.00 5.12
390 403 5.007039 CGAATTTTCATGATCGGTCAGTGAT 59.993 40.000 3.97 0.00 37.87 3.06
409 422 3.371063 GGACCGTCCGTCTGAGCA 61.371 66.667 0.65 0.00 41.64 4.26
413 426 0.892755 ACCGTCCGTCTGAGCATTTA 59.107 50.000 0.00 0.00 0.00 1.40
416 429 2.416836 CCGTCCGTCTGAGCATTTAAGA 60.417 50.000 0.00 0.00 0.00 2.10
425 438 4.215399 TCTGAGCATTTAAGACCGTTTTGG 59.785 41.667 0.00 0.00 46.41 3.28
426 439 3.254657 TGAGCATTTAAGACCGTTTTGGG 59.745 43.478 0.00 0.00 44.64 4.12
435 448 4.038080 CGTTTTGGGGTGCTCGGC 62.038 66.667 0.00 0.00 0.00 5.54
444 457 1.517832 GGTGCTCGGCTGTAGATGT 59.482 57.895 0.00 0.00 0.00 3.06
452 469 3.585862 TCGGCTGTAGATGTTCAGTTTC 58.414 45.455 0.00 0.00 34.57 2.78
550 575 6.371548 GTCTGATTTAGCAGTTCCATGTGTTA 59.628 38.462 0.00 0.00 37.20 2.41
551 576 7.066284 GTCTGATTTAGCAGTTCCATGTGTTAT 59.934 37.037 0.00 0.00 37.20 1.89
552 577 7.611467 TCTGATTTAGCAGTTCCATGTGTTATT 59.389 33.333 0.00 0.00 37.20 1.40
553 578 7.537715 TGATTTAGCAGTTCCATGTGTTATTG 58.462 34.615 0.00 0.00 0.00 1.90
554 579 6.892658 TTTAGCAGTTCCATGTGTTATTGT 57.107 33.333 0.00 0.00 0.00 2.71
555 580 6.892658 TTAGCAGTTCCATGTGTTATTGTT 57.107 33.333 0.00 0.00 0.00 2.83
641 666 3.316573 CTCCCTGCAGGTTCGGGTC 62.317 68.421 30.63 0.00 39.10 4.46
704 1828 3.230976 GTCCCCTCAACATTCCAAACTT 58.769 45.455 0.00 0.00 0.00 2.66
997 4275 2.322422 GCACACAGCATCGATCGC 59.678 61.111 11.09 10.63 44.79 4.58
1008 4286 2.946172 ATCGATCGCCCATGCTGCAA 62.946 55.000 11.09 0.00 34.43 4.08
1159 4448 2.597217 TGCCAAAGCCCCAACTCG 60.597 61.111 0.00 0.00 38.69 4.18
1278 4706 2.107041 CTGAAGTGCCACACCCCGTA 62.107 60.000 0.00 0.00 34.49 4.02
1509 5252 1.142870 CCAGAGGTGACAAAGGAACCA 59.857 52.381 0.00 0.00 36.37 3.67
1514 5257 2.430694 AGGTGACAAAGGAACCAAAAGC 59.569 45.455 0.00 0.00 36.37 3.51
1528 5271 2.902423 AAAAGCGCCACACCCTGTCA 62.902 55.000 2.29 0.00 0.00 3.58
1592 5401 1.302832 AAGAGTTGCCGAAGCCTGG 60.303 57.895 0.00 0.00 38.69 4.45
1764 5600 2.945890 GCCTGAATTCCACTTTCCGGAT 60.946 50.000 4.15 0.00 31.28 4.18
1826 5665 9.099454 GCATAGTGCCCATTATCTAAGTATTAC 57.901 37.037 0.00 0.00 37.42 1.89
1851 5698 7.027161 CACTATATACTATACATGTGTGCGCA 58.973 38.462 5.66 5.66 0.00 6.09
1898 5749 9.850628 GTGTGTGATTGTTAGAGTATGTAAGTA 57.149 33.333 0.00 0.00 0.00 2.24
1899 5750 9.850628 TGTGTGATTGTTAGAGTATGTAAGTAC 57.149 33.333 0.00 0.00 0.00 2.73
1933 5829 3.062774 TGTGTGTGTGTTGTACATGTTCG 59.937 43.478 2.30 0.00 42.24 3.95
1957 5860 0.750249 TTCAGTTCCTGACGACAGCA 59.250 50.000 9.50 0.00 40.46 4.41
2007 5910 1.662629 CTGCTCAATCTGTTGCCTACG 59.337 52.381 0.00 0.00 35.26 3.51
2050 6112 9.550406 TGCATGATGTATATGATATGTACATGG 57.450 33.333 18.81 6.60 44.31 3.66
2119 6194 5.156355 GTGTTTGGATTTGTGCATCACTAG 58.844 41.667 0.00 0.00 35.11 2.57
2136 6211 7.647715 GCATCACTAGAGAGAGTTCTTATGTTC 59.352 40.741 0.00 0.00 32.53 3.18
2151 6226 6.830912 TCTTATGTTCTGGCTACATTATGCT 58.169 36.000 5.95 0.00 37.42 3.79
2177 6254 4.389374 TGGACAAATTTCTTTCTCGAGCT 58.611 39.130 7.81 0.00 0.00 4.09
2178 6255 5.547465 TGGACAAATTTCTTTCTCGAGCTA 58.453 37.500 7.81 0.00 0.00 3.32
2226 7339 9.435570 AGTATTACTTAATAGAGAAGGCCTGAA 57.564 33.333 5.69 0.00 0.00 3.02
2270 7383 9.746711 CAGAAGCATAATAAGATATAACAACGC 57.253 33.333 0.00 0.00 0.00 4.84
2271 7384 9.712305 AGAAGCATAATAAGATATAACAACGCT 57.288 29.630 0.00 0.00 0.00 5.07
2272 7385 9.959775 GAAGCATAATAAGATATAACAACGCTC 57.040 33.333 0.00 0.00 0.00 5.03
2273 7386 9.712305 AAGCATAATAAGATATAACAACGCTCT 57.288 29.630 0.00 0.00 0.00 4.09
2283 7396 9.174166 AGATATAACAACGCTCTAACCAAAAAT 57.826 29.630 0.00 0.00 0.00 1.82
2298 7411 3.119779 CCAAAAATCTAGCGCCGGTTTAA 60.120 43.478 2.29 0.00 0.00 1.52
2333 7448 0.329931 TGAAATAGCCTTTCGCCCCA 59.670 50.000 5.25 0.00 38.78 4.96
2367 7482 2.565834 AGCAACCAACTAGTCCGTACAT 59.434 45.455 0.00 0.00 0.00 2.29
2368 7483 2.671396 GCAACCAACTAGTCCGTACATG 59.329 50.000 0.00 0.00 0.00 3.21
2400 7515 7.348201 CAACTCACTGACATAAAAGTCTGTTC 58.652 38.462 4.25 0.00 44.83 3.18
2402 7517 5.838529 TCACTGACATAAAAGTCTGTTCGA 58.161 37.500 4.25 0.00 44.83 3.71
2431 7577 4.126437 ACACAAGCAAGCCCAAATAAAAC 58.874 39.130 0.00 0.00 0.00 2.43
2480 7626 4.165950 ACCAAGTGGCCATAACATCATAGA 59.834 41.667 9.72 0.00 39.32 1.98
2487 7633 3.341823 CCATAACATCATAGAGCTGCCC 58.658 50.000 0.00 0.00 0.00 5.36
2488 7634 2.820059 TAACATCATAGAGCTGCCCG 57.180 50.000 0.00 0.00 0.00 6.13
2502 7648 2.203509 CCCGGGAGCCTAGACGAT 60.204 66.667 18.48 0.00 0.00 3.73
2503 7649 2.565645 CCCGGGAGCCTAGACGATG 61.566 68.421 18.48 0.00 0.00 3.84
2519 7665 1.202302 CGATGTGCCGAGTCATGTAGT 60.202 52.381 0.00 0.00 0.00 2.73
2525 7671 1.471501 GCCGAGTCATGTAGTGCATCA 60.472 52.381 0.00 0.00 35.19 3.07
2575 7722 3.074281 CCTAGCCAACGGGTCCAA 58.926 61.111 0.00 0.00 34.28 3.53
2578 7725 0.035439 CTAGCCAACGGGTCCAATGT 60.035 55.000 0.00 0.00 34.28 2.71
2589 7736 1.336755 GGTCCAATGTTGCAAGAACGT 59.663 47.619 0.00 0.00 0.00 3.99
2615 7762 8.744568 AAGAAAATTGAAGAAAGAGTCAGAGT 57.255 30.769 0.00 0.00 0.00 3.24
2621 7768 2.599677 AGAAAGAGTCAGAGTCCCGTT 58.400 47.619 1.19 0.00 0.00 4.44
2638 7785 0.884704 GTTGCAGAAAGACCCGCTCA 60.885 55.000 0.00 0.00 0.00 4.26
2663 7810 2.357009 ACCATCTTATTACGCGTCGTCT 59.643 45.455 18.63 0.87 41.54 4.18
2722 7869 1.214589 GCGTCGGTTCCTTCTAGCA 59.785 57.895 0.00 0.00 0.00 3.49
2726 7873 0.179111 TCGGTTCCTTCTAGCATGCG 60.179 55.000 13.01 0.00 0.00 4.73
2765 7912 2.245582 AGCTGGCAAGATTTGAAGCTT 58.754 42.857 0.00 0.00 44.63 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 3.864983 TTTCCCCCTCCTGTCCGCT 62.865 63.158 0.00 0.00 0.00 5.52
77 78 0.704664 GTCCACATTTTCCCCCTCCT 59.295 55.000 0.00 0.00 0.00 3.69
86 88 5.245977 CCAAAACCCTATCTGTCCACATTTT 59.754 40.000 0.00 0.00 0.00 1.82
99 101 0.675522 CGTCGGCACCAAAACCCTAT 60.676 55.000 0.00 0.00 0.00 2.57
193 196 2.730672 CGCTCCCAAGCTCGTTTCG 61.731 63.158 0.00 0.00 46.91 3.46
232 235 3.243434 GGATTGACGATGAGGTATCACGT 60.243 47.826 0.00 0.00 42.09 4.49
270 273 2.513259 GGATATGGGGGCGTTCGGA 61.513 63.158 0.00 0.00 0.00 4.55
274 277 2.279037 AAAGCGGATATGGGGGCGTT 62.279 55.000 0.00 0.00 0.00 4.84
275 278 1.412453 TAAAGCGGATATGGGGGCGT 61.412 55.000 0.00 0.00 0.00 5.68
291 304 7.018550 ACCTCTCATATCCAGCCCAAATATAAA 59.981 37.037 0.00 0.00 0.00 1.40
311 324 2.022934 CCAGACTAACCGGTACCTCTC 58.977 57.143 8.00 0.00 0.00 3.20
318 331 4.323257 CCTTAAATGTCCAGACTAACCGGT 60.323 45.833 0.00 0.00 0.00 5.28
324 337 3.767673 ACGAGCCTTAAATGTCCAGACTA 59.232 43.478 0.00 0.00 0.00 2.59
329 342 3.745799 TCAAACGAGCCTTAAATGTCCA 58.254 40.909 0.00 0.00 0.00 4.02
338 351 1.600916 GGTGCCTCAAACGAGCCTT 60.601 57.895 0.00 0.00 0.00 4.35
343 356 2.029964 GACGGGTGCCTCAAACGA 59.970 61.111 0.00 0.00 0.00 3.85
361 374 2.290641 CCGATCATGAAAATTCGACCCC 59.709 50.000 16.08 0.00 33.59 4.95
375 388 2.158900 GGTCCAATCACTGACCGATCAT 60.159 50.000 0.00 0.00 41.48 2.45
409 422 2.297880 GCACCCCAAAACGGTCTTAAAT 59.702 45.455 0.00 0.00 0.00 1.40
413 426 0.822121 GAGCACCCCAAAACGGTCTT 60.822 55.000 0.00 0.00 0.00 3.01
416 429 2.593436 CGAGCACCCCAAAACGGT 60.593 61.111 0.00 0.00 0.00 4.83
425 438 1.227380 CATCTACAGCCGAGCACCC 60.227 63.158 0.00 0.00 0.00 4.61
426 439 0.108138 AACATCTACAGCCGAGCACC 60.108 55.000 0.00 0.00 0.00 5.01
435 448 6.884280 AAAAGGGAAACTGAACATCTACAG 57.116 37.500 0.00 0.00 39.65 2.74
631 656 3.427573 CCCTAATTTTTGACCCGAACCT 58.572 45.455 0.00 0.00 0.00 3.50
636 661 3.881220 TCTAGCCCTAATTTTTGACCCG 58.119 45.455 0.00 0.00 0.00 5.28
673 1791 2.108075 TGTTGAGGGGACATGTGTGATT 59.892 45.455 1.15 0.00 0.00 2.57
704 1828 9.078990 CCATCTCTAGTTATGTGTGGTTAGATA 57.921 37.037 0.00 0.00 0.00 1.98
997 4275 2.137523 GTTGTTCTTTTGCAGCATGGG 58.862 47.619 0.00 0.00 35.86 4.00
1008 4286 1.147817 AGGGAGGCCATGTTGTTCTTT 59.852 47.619 5.01 0.00 0.00 2.52
1278 4706 3.850098 CTTTGGCACCTCCGGCACT 62.850 63.158 0.00 0.00 41.78 4.40
1336 4764 1.591863 GATGCGGTAGTTCGGGCTC 60.592 63.158 0.00 0.00 0.00 4.70
1509 5252 2.123897 ACAGGGTGTGGCGCTTTT 60.124 55.556 7.64 0.00 38.41 2.27
1514 5257 3.434319 GCATGACAGGGTGTGGCG 61.434 66.667 0.00 0.00 36.69 5.69
1528 5271 1.561542 CTCCTTTGGTACCTCTGGCAT 59.438 52.381 14.36 0.00 0.00 4.40
1574 5383 1.302832 CCAGGCTTCGGCAACTCTT 60.303 57.895 0.00 0.00 43.96 2.85
1826 5665 7.008357 GTGCGCACACATGTATAGTATATAGTG 59.992 40.741 34.52 13.57 46.61 2.74
1898 5749 6.340962 ACACACACACACATGTATAGTAGT 57.659 37.500 0.00 0.00 36.72 2.73
1899 5750 6.645003 ACAACACACACACACATGTATAGTAG 59.355 38.462 0.00 0.00 36.72 2.57
1957 5860 4.908601 TGGAACACCACTCAGACATAAT 57.091 40.909 0.00 0.00 0.00 1.28
2007 5910 2.690786 TGCATACACACGTAAAGGGAC 58.309 47.619 0.00 0.00 0.00 4.46
2050 6112 8.209917 ACTCCGAAGACCAAAACATATTTATC 57.790 34.615 0.00 0.00 0.00 1.75
2064 6129 7.041303 GGATCCAATATAAAAACTCCGAAGACC 60.041 40.741 6.95 0.00 0.00 3.85
2067 6132 9.726438 ATAGGATCCAATATAAAAACTCCGAAG 57.274 33.333 15.82 0.00 0.00 3.79
2119 6194 5.337578 AGCCAGAACATAAGAACTCTCTC 57.662 43.478 0.00 0.00 0.00 3.20
2136 6211 3.323115 TCCAGAGAGCATAATGTAGCCAG 59.677 47.826 0.00 0.00 0.00 4.85
2151 6226 5.853936 TCGAGAAAGAAATTTGTCCAGAGA 58.146 37.500 0.00 0.00 0.00 3.10
2226 7339 4.581309 TCTGATCAAATCTGGGCTTCTT 57.419 40.909 0.00 0.00 0.00 2.52
2227 7340 4.525024 CTTCTGATCAAATCTGGGCTTCT 58.475 43.478 0.00 0.00 0.00 2.85
2228 7341 3.066481 GCTTCTGATCAAATCTGGGCTTC 59.934 47.826 0.00 0.00 0.00 3.86
2270 7383 3.001330 CGGCGCTAGATTTTTGGTTAGAG 59.999 47.826 7.64 0.00 0.00 2.43
2271 7384 2.933906 CGGCGCTAGATTTTTGGTTAGA 59.066 45.455 7.64 0.00 0.00 2.10
2272 7385 2.031683 CCGGCGCTAGATTTTTGGTTAG 59.968 50.000 7.64 0.00 0.00 2.34
2273 7386 2.011222 CCGGCGCTAGATTTTTGGTTA 58.989 47.619 7.64 0.00 0.00 2.85
2274 7387 0.808755 CCGGCGCTAGATTTTTGGTT 59.191 50.000 7.64 0.00 0.00 3.67
2278 7391 4.004982 TCTTAAACCGGCGCTAGATTTTT 58.995 39.130 7.64 5.35 0.00 1.94
2283 7396 2.954318 ACTATCTTAAACCGGCGCTAGA 59.046 45.455 7.64 0.00 0.00 2.43
2400 7515 0.317269 CTTGCTTGTGTTGTGGCTCG 60.317 55.000 0.00 0.00 0.00 5.03
2402 7517 1.438814 GCTTGCTTGTGTTGTGGCT 59.561 52.632 0.00 0.00 0.00 4.75
2431 7577 6.205071 GTCTTTTTCCTGCTTTTCTCTTCTG 58.795 40.000 0.00 0.00 0.00 3.02
2487 7633 1.360551 CACATCGTCTAGGCTCCCG 59.639 63.158 0.00 0.00 0.00 5.14
2488 7634 1.068250 GCACATCGTCTAGGCTCCC 59.932 63.158 0.00 0.00 0.00 4.30
2502 7648 0.389817 GCACTACATGACTCGGCACA 60.390 55.000 0.00 0.00 0.00 4.57
2503 7649 0.389817 TGCACTACATGACTCGGCAC 60.390 55.000 0.00 0.00 0.00 5.01
2575 7722 7.199766 TCAATTTTCTTACGTTCTTGCAACAT 58.800 30.769 0.00 0.00 0.00 2.71
2578 7725 7.476667 TCTTCAATTTTCTTACGTTCTTGCAA 58.523 30.769 0.00 0.00 0.00 4.08
2589 7736 9.838339 ACTCTGACTCTTTCTTCAATTTTCTTA 57.162 29.630 0.00 0.00 0.00 2.10
2615 7762 1.072505 GGGTCTTTCTGCAACGGGA 59.927 57.895 0.00 0.00 0.00 5.14
2621 7768 0.036732 ATTGAGCGGGTCTTTCTGCA 59.963 50.000 8.82 0.00 41.26 4.41
2638 7785 3.734231 CGACGCGTAATAAGATGGTGATT 59.266 43.478 13.97 0.00 0.00 2.57
2684 7831 4.246458 CGCCTCTTCTAGCTAGTTTTTGT 58.754 43.478 20.10 0.00 0.00 2.83
2722 7869 4.827087 CAGGCCAGAGCGACGCAT 62.827 66.667 23.70 7.23 41.24 4.73
2726 7873 4.154347 CCTCCAGGCCAGAGCGAC 62.154 72.222 15.62 0.00 41.24 5.19
2765 7912 2.918248 CCCTCGGGCATGATTGGA 59.082 61.111 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.