Multiple sequence alignment - TraesCS2A01G311200

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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 TraesCS2A01G311200 chr2A 100.000 4527 0 0 1 4527 534635396 534630870 0.000000e+00 8360.0
1 TraesCS2A01G311200 chr2D 97.385 3059 76 2 1470 4527 396671769 396668714 0.000000e+00 5203.0
2 TraesCS2A01G311200 chr2D 92.152 446 19 5 1013 1451 396672267 396671831 2.310000e-172 616.0
3 TraesCS2A01G311200 chr2D 97.598 333 3 4 1 330 396712310 396711980 2.360000e-157 566.0
4 TraesCS2A01G311200 chr2D 95.238 231 7 2 375 605 396711112 396710886 3.330000e-96 363.0
5 TraesCS2A01G311200 chr2D 92.672 232 12 4 605 832 396672578 396672348 3.380000e-86 329.0
6 TraesCS2A01G311200 chr2B 93.206 2988 136 37 1514 4487 470067887 470064953 0.000000e+00 4331.0
7 TraesCS2A01G311200 chr2B 91.026 468 25 12 1 461 470070859 470070402 2.310000e-172 616.0
8 TraesCS2A01G311200 chr2B 84.890 589 37 24 741 1291 470068738 470068164 8.560000e-152 547.0
9 TraesCS2A01G311200 chr2B 96.104 77 3 0 529 605 470069445 470069369 4.750000e-25 126.0
10 TraesCS2A01G311200 chr2B 98.214 56 0 1 4472 4527 470064906 470064852 3.730000e-16 97.1
11 TraesCS2A01G311200 chr6D 86.189 782 97 8 2856 3628 411616115 411615336 0.000000e+00 835.0
12 TraesCS2A01G311200 chr6D 80.928 582 75 17 3959 4527 411615087 411614529 1.160000e-115 427.0
13 TraesCS2A01G311200 chr6D 81.269 331 57 5 2352 2680 411616862 411616535 3.470000e-66 263.0
14 TraesCS2A01G311200 chr6D 89.840 187 16 2 1791 1975 411617390 411617205 2.110000e-58 237.0
15 TraesCS2A01G311200 chr6D 90.683 161 15 0 2097 2257 411617207 411617047 9.860000e-52 215.0
16 TraesCS2A01G311200 chr6D 92.453 53 4 0 3697 3749 411615172 411615120 4.860000e-10 76.8
17 TraesCS2A01G311200 chr6A 84.248 838 115 9 2794 3615 556532211 556531375 0.000000e+00 800.0
18 TraesCS2A01G311200 chr6A 82.823 588 68 17 3956 4527 556531076 556530506 3.150000e-136 496.0
19 TraesCS2A01G311200 chr6A 79.648 398 68 10 2292 2680 556532942 556532549 1.600000e-69 274.0
20 TraesCS2A01G311200 chr6A 88.360 189 18 2 1791 1975 556533402 556533214 1.640000e-54 224.0
21 TraesCS2A01G311200 chr6A 87.730 163 18 1 2097 2259 556533216 556533056 5.980000e-44 189.0
22 TraesCS2A01G311200 chr6A 86.806 144 12 5 3697 3836 556531221 556531081 2.180000e-33 154.0
23 TraesCS2A01G311200 chr6B 86.047 731 97 4 2890 3615 618943154 618942424 0.000000e+00 780.0
24 TraesCS2A01G311200 chr6B 80.723 332 59 4 2352 2680 618943976 618943647 2.090000e-63 254.0
25 TraesCS2A01G311200 chr6B 91.111 180 13 2 1798 1975 618944472 618944294 1.630000e-59 241.0
26 TraesCS2A01G311200 chr6B 91.411 163 14 0 2097 2259 618944296 618944134 1.640000e-54 224.0
27 TraesCS2A01G311200 chr6B 85.315 143 17 3 3697 3836 618942133 618941992 1.310000e-30 145.0
28 TraesCS2A01G311200 chr7D 82.727 110 15 3 3832 3940 38097254 38097148 1.340000e-15 95.3


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 TraesCS2A01G311200 chr2A 534630870 534635396 4526 True 8360.000000 8360 100.000000 1 4527 1 chr2A.!!$R1 4526
1 TraesCS2A01G311200 chr2D 396668714 396672578 3864 True 2049.333333 5203 94.069667 605 4527 3 chr2D.!!$R1 3922
2 TraesCS2A01G311200 chr2D 396710886 396712310 1424 True 464.500000 566 96.418000 1 605 2 chr2D.!!$R2 604
3 TraesCS2A01G311200 chr2B 470064852 470070859 6007 True 1143.420000 4331 92.688000 1 4527 5 chr2B.!!$R1 4526
4 TraesCS2A01G311200 chr6D 411614529 411617390 2861 True 342.300000 835 86.893667 1791 4527 6 chr6D.!!$R1 2736
5 TraesCS2A01G311200 chr6A 556530506 556533402 2896 True 356.166667 800 84.935833 1791 4527 6 chr6A.!!$R1 2736
6 TraesCS2A01G311200 chr6B 618941992 618944472 2480 True 328.800000 780 86.921400 1798 3836 5 chr6B.!!$R1 2038

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
576 1487 0.038983 TTGCGCACGACAGCTTAGTA 60.039 50.000 11.12 0.0 0.00 1.82 F
1512 3078 0.246635 ACAAGGGAAGTGTCGATCCG 59.753 55.000 0.00 0.0 36.54 4.18 F
1782 3349 1.538512 CCAACACATTCTGCCACTCAG 59.461 52.381 0.00 0.0 44.21 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 3253 2.103263 ACTCCTTCCCATATTCGACAGC 59.897 50.000 0.0 0.0 0.0 4.40 R
3499 5495 0.391927 CGGACGGCAGAAATGGGTAA 60.392 55.000 0.0 0.0 0.0 2.85 R
3630 5953 4.693566 ACATATTTTATCCATACCGTGCCG 59.306 41.667 0.0 0.0 0.0 5.69 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
18 19 2.993130 GACGTTCTACACCGACGAC 58.007 57.895 0.00 0.00 39.85 4.34
81 82 1.045407 CCAAGGGGAATGGCATGATG 58.955 55.000 0.00 0.00 35.59 3.07
128 129 2.399856 GAACTGTGTTGCCGTTCCA 58.600 52.632 0.00 0.00 32.88 3.53
152 153 7.121168 CCATCAGTGTGGCTTCTTCTTTTATTA 59.879 37.037 0.00 0.00 31.43 0.98
153 154 8.680903 CATCAGTGTGGCTTCTTCTTTTATTAT 58.319 33.333 0.00 0.00 0.00 1.28
155 156 9.077885 TCAGTGTGGCTTCTTCTTTTATTATTT 57.922 29.630 0.00 0.00 0.00 1.40
247 250 5.291128 GGATGTTTTCGATGATTACACTCGT 59.709 40.000 0.00 0.00 32.92 4.18
273 276 1.301423 TACTGCCGTTGCGTCTTTTT 58.699 45.000 0.00 0.00 41.78 1.94
274 277 0.248458 ACTGCCGTTGCGTCTTTTTG 60.248 50.000 0.00 0.00 41.78 2.44
275 278 1.539776 CTGCCGTTGCGTCTTTTTGC 61.540 55.000 0.00 0.00 41.78 3.68
276 279 1.299089 GCCGTTGCGTCTTTTTGCT 60.299 52.632 0.00 0.00 0.00 3.91
278 281 1.598430 GCCGTTGCGTCTTTTTGCTTA 60.598 47.619 0.00 0.00 0.00 3.09
279 282 2.307049 CCGTTGCGTCTTTTTGCTTAG 58.693 47.619 0.00 0.00 0.00 2.18
280 283 1.708680 CGTTGCGTCTTTTTGCTTAGC 59.291 47.619 0.00 0.00 0.00 3.09
281 284 2.726633 GTTGCGTCTTTTTGCTTAGCA 58.273 42.857 1.39 1.39 36.47 3.49
311 317 5.630661 TGTAGACTGACTTCTCTGCTTAC 57.369 43.478 0.00 0.00 0.00 2.34
336 342 4.344679 TGATTTGCACAAGAGGGAAACATT 59.655 37.500 0.00 0.00 0.00 2.71
339 345 2.364970 TGCACAAGAGGGAAACATTTGG 59.635 45.455 0.00 0.00 0.00 3.28
344 350 1.077169 AGAGGGAAACATTTGGGGGAC 59.923 52.381 0.00 0.00 0.00 4.46
346 352 1.077169 AGGGAAACATTTGGGGGACTC 59.923 52.381 0.00 0.00 0.00 3.36
349 355 3.239449 GGAAACATTTGGGGGACTCTTT 58.761 45.455 0.00 0.00 0.00 2.52
364 370 6.127869 GGGGACTCTTTTAGCAGATTTTTCTC 60.128 42.308 0.00 0.00 0.00 2.87
365 371 6.431234 GGGACTCTTTTAGCAGATTTTTCTCA 59.569 38.462 0.00 0.00 0.00 3.27
366 372 7.040409 GGGACTCTTTTAGCAGATTTTTCTCAA 60.040 37.037 0.00 0.00 0.00 3.02
394 400 0.455972 GGCAGAAATTAAGCGCGCAA 60.456 50.000 35.10 20.69 0.00 4.85
395 401 1.335935 GCAGAAATTAAGCGCGCAAA 58.664 45.000 35.10 26.30 0.00 3.68
396 402 1.919918 GCAGAAATTAAGCGCGCAAAT 59.080 42.857 35.10 27.30 0.00 2.32
397 403 2.345341 GCAGAAATTAAGCGCGCAAATT 59.655 40.909 35.10 30.88 0.00 1.82
398 404 3.545873 GCAGAAATTAAGCGCGCAAATTA 59.454 39.130 31.47 21.41 0.00 1.40
403 409 8.479280 CAGAAATTAAGCGCGCAAATTAATATT 58.521 29.630 31.47 24.60 30.82 1.28
404 410 9.030301 AGAAATTAAGCGCGCAAATTAATATTT 57.970 25.926 31.47 23.63 34.29 1.40
491 1402 2.689646 AGAAGAGCCTGTCTTTTACGC 58.310 47.619 0.00 0.00 46.21 4.42
502 1413 6.153067 CCTGTCTTTTACGCCTATGAGATAG 58.847 44.000 0.00 0.00 0.00 2.08
503 1414 6.016192 CCTGTCTTTTACGCCTATGAGATAGA 60.016 42.308 0.00 0.00 34.77 1.98
504 1415 7.309499 CCTGTCTTTTACGCCTATGAGATAGAT 60.309 40.741 0.00 0.00 34.77 1.98
505 1416 8.631480 TGTCTTTTACGCCTATGAGATAGATA 57.369 34.615 0.00 0.00 34.77 1.98
516 1427 7.471260 GCCTATGAGATAGATAATCGAAGCCAT 60.471 40.741 0.00 0.00 39.79 4.40
517 1428 8.081633 CCTATGAGATAGATAATCGAAGCCATC 58.918 40.741 0.00 0.00 39.79 3.51
518 1429 7.658525 ATGAGATAGATAATCGAAGCCATCT 57.341 36.000 0.00 0.00 39.79 2.90
519 1430 6.861144 TGAGATAGATAATCGAAGCCATCTG 58.139 40.000 10.12 0.00 39.79 2.90
520 1431 6.127507 TGAGATAGATAATCGAAGCCATCTGG 60.128 42.308 10.12 0.00 39.79 3.86
521 1432 3.692257 AGATAATCGAAGCCATCTGGG 57.308 47.619 0.00 0.00 40.85 4.45
576 1487 0.038983 TTGCGCACGACAGCTTAGTA 60.039 50.000 11.12 0.00 0.00 1.82
610 1521 2.279650 GGGCCGTCGCGCTTATTA 60.280 61.111 5.56 0.00 44.27 0.98
613 1524 0.712222 GGCCGTCGCGCTTATTATAC 59.288 55.000 5.56 0.00 35.02 1.47
614 1525 1.668047 GGCCGTCGCGCTTATTATACT 60.668 52.381 5.56 0.00 35.02 2.12
615 1526 1.647702 GCCGTCGCGCTTATTATACTC 59.352 52.381 5.56 0.00 0.00 2.59
697 1994 1.357258 GGATGACTGCAGCAGTGACG 61.357 60.000 33.03 4.72 45.44 4.35
810 2218 0.951558 AACAATCGTGGCAGGTTCAC 59.048 50.000 7.12 0.00 0.00 3.18
846 2254 1.852067 AAAAGGACATGTCACCGCGC 61.852 55.000 26.47 8.67 0.00 6.86
856 2264 3.760035 CACCGCGCCCAGAGTAGT 61.760 66.667 0.00 0.00 0.00 2.73
858 2266 2.412112 CCGCGCCCAGAGTAGTAC 59.588 66.667 0.00 0.00 0.00 2.73
861 2269 0.307146 CGCGCCCAGAGTAGTACTAC 59.693 60.000 23.03 23.03 36.35 2.73
864 2272 2.807392 GCGCCCAGAGTAGTACTACTAG 59.193 54.545 30.80 24.91 45.63 2.57
867 2282 5.229423 CGCCCAGAGTAGTACTACTAGTAG 58.771 50.000 30.80 25.30 45.63 2.57
884 2299 7.006865 ACTAGTAGGAAAAGTCTTCTTTCCC 57.993 40.000 11.07 0.00 42.26 3.97
886 2301 7.954620 ACTAGTAGGAAAAGTCTTCTTTCCCTA 59.045 37.037 11.07 5.46 44.62 3.53
887 2302 7.247456 AGTAGGAAAAGTCTTCTTTCCCTAG 57.753 40.000 11.07 0.00 46.27 3.02
888 2303 6.788456 AGTAGGAAAAGTCTTCTTTCCCTAGT 59.212 38.462 11.07 6.71 46.27 2.57
910 2325 1.096416 ACAGTAGAGAGCAGTACGCC 58.904 55.000 6.15 0.00 44.04 5.68
911 2326 0.382515 CAGTAGAGAGCAGTACGCCC 59.617 60.000 6.15 0.00 44.04 6.13
912 2327 1.096386 AGTAGAGAGCAGTACGCCCG 61.096 60.000 6.15 0.00 44.04 6.13
913 2328 1.822613 TAGAGAGCAGTACGCCCGG 60.823 63.158 0.00 0.00 44.04 5.73
949 2381 0.975556 CAACATAAAGGCCCACCCCC 60.976 60.000 0.00 0.00 36.11 5.40
1008 2440 3.008330 CAGACCAAGGAAGATGAGCAAG 58.992 50.000 0.00 0.00 0.00 4.01
1087 2531 3.611766 TTTCTTCTTCCGATCCCACTC 57.388 47.619 0.00 0.00 0.00 3.51
1088 2532 1.103803 TCTTCTTCCGATCCCACTCG 58.896 55.000 0.00 0.00 38.37 4.18
1089 2533 1.103803 CTTCTTCCGATCCCACTCGA 58.896 55.000 0.00 0.00 41.12 4.04
1090 2534 1.683917 CTTCTTCCGATCCCACTCGAT 59.316 52.381 0.00 0.00 41.12 3.59
1099 2543 3.067461 CGATCCCACTCGATCTCTCTTTT 59.933 47.826 0.00 0.00 41.12 2.27
1222 2674 1.401905 CCAATTCGGGTGCTAAAGCTC 59.598 52.381 3.26 0.00 42.66 4.09
1281 2733 3.822192 CCCGGACATGACTCGCGA 61.822 66.667 9.26 9.26 0.00 5.87
1335 2787 3.876320 CTCCTGCTTTTTATCAGAGGCTC 59.124 47.826 6.34 6.34 32.26 4.70
1356 2808 3.834813 TCTTCTTGTCTGGATACTGCTGT 59.165 43.478 0.66 0.66 35.12 4.40
1378 2830 4.697352 GTCCTGCTGTTGTTCATATCTTGT 59.303 41.667 0.00 0.00 0.00 3.16
1379 2831 5.182001 GTCCTGCTGTTGTTCATATCTTGTT 59.818 40.000 0.00 0.00 0.00 2.83
1380 2832 5.769662 TCCTGCTGTTGTTCATATCTTGTTT 59.230 36.000 0.00 0.00 0.00 2.83
1381 2833 6.265196 TCCTGCTGTTGTTCATATCTTGTTTT 59.735 34.615 0.00 0.00 0.00 2.43
1382 2834 7.446931 TCCTGCTGTTGTTCATATCTTGTTTTA 59.553 33.333 0.00 0.00 0.00 1.52
1411 2863 3.426787 TCAAGAACCGAATTTAGCCCA 57.573 42.857 0.00 0.00 0.00 5.36
1498 2995 9.919348 GCATGCATTTTGTATTTATTTACAAGG 57.081 29.630 14.21 0.00 41.65 3.61
1512 3078 0.246635 ACAAGGGAAGTGTCGATCCG 59.753 55.000 0.00 0.00 36.54 4.18
1558 3124 6.704289 ACATGTGGGATGATATTTGTCAAG 57.296 37.500 0.00 0.00 0.00 3.02
1559 3125 6.189859 ACATGTGGGATGATATTTGTCAAGT 58.810 36.000 0.00 0.00 0.00 3.16
1573 3139 5.596268 TTGTCAAGTCAAATCATCTGTCG 57.404 39.130 0.00 0.00 0.00 4.35
1604 3170 7.147141 TGGACAATTATTCCATCAATAGACCCT 60.147 37.037 4.19 0.00 38.28 4.34
1645 3211 2.024176 ACCAATGAGTACGCACCATC 57.976 50.000 0.00 0.00 0.00 3.51
1649 3215 3.068165 CCAATGAGTACGCACCATCTAGA 59.932 47.826 0.00 0.00 0.00 2.43
1686 3253 8.456904 ACAATCAATTTTCGTCTGATGAATTG 57.543 30.769 12.73 14.15 38.28 2.32
1693 3260 2.094752 TCGTCTGATGAATTGCTGTCGA 60.095 45.455 0.00 0.00 0.00 4.20
1711 3278 3.104512 TCGAATATGGGAAGGAGTGTGT 58.895 45.455 0.00 0.00 0.00 3.72
1735 3302 3.250762 CCTGAAATTTCTTCGACTGTGCA 59.749 43.478 18.64 0.00 0.00 4.57
1782 3349 1.538512 CCAACACATTCTGCCACTCAG 59.461 52.381 0.00 0.00 44.21 3.35
2310 3972 7.326789 GCACAATTATGTCGCAAGCAATAATAT 59.673 33.333 0.00 0.00 37.82 1.28
2381 4048 9.825109 TCTGTACGATTATTCACCATTTTATGA 57.175 29.630 0.00 0.00 0.00 2.15
2393 4060 6.072008 TCACCATTTTATGACACCATGAGTTG 60.072 38.462 0.00 0.00 34.31 3.16
2904 4900 3.903714 TGACTGTTGAAGAAGAGGGATCA 59.096 43.478 0.00 0.00 0.00 2.92
3250 5246 3.808728 ACGGATGGTGAATATTGGTGAG 58.191 45.455 0.00 0.00 0.00 3.51
3360 5356 3.003275 GGAAATAAAGCAATCGCCGATGA 59.997 43.478 0.00 0.00 39.83 2.92
3852 6182 3.843027 TGGTTTTGGCATGTTCCCATTAT 59.157 39.130 0.00 0.00 31.26 1.28
3857 6187 5.606348 TTGGCATGTTCCCATTATAAACC 57.394 39.130 0.00 0.00 31.26 3.27
3881 6211 5.584649 CCGCCATCTCTTGTAAATACTTTGA 59.415 40.000 0.00 0.00 0.00 2.69
3911 6241 4.910195 TCTCTCTTAATGAAAAGGCAGCA 58.090 39.130 0.00 0.00 0.00 4.41
3929 6260 1.980772 ATCCTGCCAGTTGCTTGCC 60.981 57.895 0.00 0.00 42.00 4.52
3930 6261 2.718487 ATCCTGCCAGTTGCTTGCCA 62.718 55.000 0.00 0.00 42.00 4.92
3931 6262 2.500714 CCTGCCAGTTGCTTGCCAA 61.501 57.895 0.00 0.00 42.00 4.52
4205 6560 7.229707 GGATCTACTACACTCTCAAGCTTATCA 59.770 40.741 0.00 0.00 0.00 2.15
4214 6570 9.372369 ACACTCTCAAGCTTATCATAAAAGTAC 57.628 33.333 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 8.814038 ATAATAAAAGAAGAAGCCACACTGAT 57.186 30.769 0.00 0.00 0.00 2.90
152 153 7.497249 AGTTGATACGACGGTACTAGTAGAAAT 59.503 37.037 1.87 0.00 0.00 2.17
153 154 6.818644 AGTTGATACGACGGTACTAGTAGAAA 59.181 38.462 1.87 0.00 0.00 2.52
155 156 5.907207 AGTTGATACGACGGTACTAGTAGA 58.093 41.667 1.87 0.00 0.00 2.59
158 159 6.283694 TGATAGTTGATACGACGGTACTAGT 58.716 40.000 0.00 0.00 0.00 2.57
159 160 6.775939 TGATAGTTGATACGACGGTACTAG 57.224 41.667 0.00 0.00 0.00 2.57
223 224 5.291128 ACGAGTGTAATCATCGAAAACATCC 59.709 40.000 0.30 0.00 39.66 3.51
225 226 6.721571 AACGAGTGTAATCATCGAAAACAT 57.278 33.333 0.30 0.00 39.66 2.71
226 227 6.422701 AGAAACGAGTGTAATCATCGAAAACA 59.577 34.615 0.30 0.00 39.66 2.83
227 228 6.818416 AGAAACGAGTGTAATCATCGAAAAC 58.182 36.000 0.30 0.00 39.66 2.43
247 250 1.671845 ACGCAACGGCAGTAAAAGAAA 59.328 42.857 0.00 0.00 41.24 2.52
293 299 3.508012 TCAGGTAAGCAGAGAAGTCAGTC 59.492 47.826 0.00 0.00 0.00 3.51
311 317 2.205022 TCCCTCTTGTGCAAATCAGG 57.795 50.000 0.00 0.00 0.00 3.86
336 342 2.344592 TCTGCTAAAAGAGTCCCCCAA 58.655 47.619 0.00 0.00 0.00 4.12
339 345 5.712446 AGAAAAATCTGCTAAAAGAGTCCCC 59.288 40.000 0.00 0.00 0.00 4.81
374 380 1.586303 GCGCGCTTAATTTCTGCCC 60.586 57.895 26.67 0.00 0.00 5.36
377 383 5.678910 TTAATTTGCGCGCTTAATTTCTG 57.321 34.783 33.10 0.00 0.00 3.02
378 384 8.574196 AATATTAATTTGCGCGCTTAATTTCT 57.426 26.923 33.10 25.58 0.00 2.52
380 386 9.980780 AAAAATATTAATTTGCGCGCTTAATTT 57.019 22.222 33.10 24.78 35.46 1.82
425 431 2.227194 CGTAAAAGACAAGCACCCCTT 58.773 47.619 0.00 0.00 0.00 3.95
471 1382 2.613223 GGCGTAAAAGACAGGCTCTTCT 60.613 50.000 0.00 0.00 38.37 2.85
472 1383 1.732809 GGCGTAAAAGACAGGCTCTTC 59.267 52.381 0.00 0.00 38.37 2.87
479 1390 6.971602 TCTATCTCATAGGCGTAAAAGACAG 58.028 40.000 3.97 3.00 33.64 3.51
491 1402 7.340122 TGGCTTCGATTATCTATCTCATAGG 57.660 40.000 0.00 0.00 33.64 2.57
522 1433 2.825836 GCTCATCCGCCACCTTGG 60.826 66.667 0.00 0.00 41.55 3.61
576 1487 0.544697 CCCACGGGCTAGGTTATGTT 59.455 55.000 0.00 0.00 0.00 2.71
656 1953 1.987807 ATCCAGCGGAGGACCATTGG 61.988 60.000 0.00 0.00 41.30 3.16
657 1954 0.533755 GATCCAGCGGAGGACCATTG 60.534 60.000 0.00 0.00 41.30 2.82
697 1994 3.265070 ACGACTACACACTTCTTCGAC 57.735 47.619 0.00 0.00 0.00 4.20
725 2022 5.522460 CCACACACTTTTTCGAGTTAAGAGA 59.478 40.000 9.38 0.00 0.00 3.10
727 2024 4.034742 GCCACACACTTTTTCGAGTTAAGA 59.965 41.667 9.38 0.00 0.00 2.10
739 2036 0.106519 AAGAGCTGGCCACACACTTT 60.107 50.000 0.00 0.00 0.00 2.66
791 2199 0.951558 GTGAACCTGCCACGATTGTT 59.048 50.000 0.00 0.00 0.00 2.83
834 2242 4.758251 TCTGGGCGCGGTGACATG 62.758 66.667 8.83 0.00 0.00 3.21
840 2248 2.044650 TACTACTCTGGGCGCGGT 60.045 61.111 8.83 0.00 0.00 5.68
846 2254 6.992664 TCCTACTAGTAGTACTACTCTGGG 57.007 45.833 33.47 27.90 44.58 4.45
884 2299 3.616219 ACTGCTCTCTACTGTGGACTAG 58.384 50.000 0.00 0.00 0.00 2.57
885 2300 3.722908 ACTGCTCTCTACTGTGGACTA 57.277 47.619 0.00 0.00 0.00 2.59
886 2301 2.595750 ACTGCTCTCTACTGTGGACT 57.404 50.000 0.00 0.00 0.00 3.85
887 2302 2.096174 CGTACTGCTCTCTACTGTGGAC 59.904 54.545 0.00 0.00 0.00 4.02
888 2303 2.357075 CGTACTGCTCTCTACTGTGGA 58.643 52.381 0.00 0.00 0.00 4.02
912 2327 3.056313 GATGAAAGCTGTGGCGGCC 62.056 63.158 13.32 13.32 44.37 6.13
913 2328 1.865788 TTGATGAAAGCTGTGGCGGC 61.866 55.000 0.00 0.00 44.37 6.53
949 2381 4.367023 TTCCTCCGCCCGTTCGTG 62.367 66.667 0.00 0.00 0.00 4.35
1008 2440 3.403558 GGGGTGAGGAGGGCAGTC 61.404 72.222 0.00 0.00 0.00 3.51
1087 2531 4.106197 CCGTACCAAGAAAAGAGAGATCG 58.894 47.826 0.00 0.00 0.00 3.69
1088 2532 5.326200 TCCGTACCAAGAAAAGAGAGATC 57.674 43.478 0.00 0.00 0.00 2.75
1089 2533 5.740290 TTCCGTACCAAGAAAAGAGAGAT 57.260 39.130 0.00 0.00 0.00 2.75
1090 2534 5.540400 TTTCCGTACCAAGAAAAGAGAGA 57.460 39.130 0.00 0.00 0.00 3.10
1099 2543 1.138568 TGGGGTTTTCCGTACCAAGA 58.861 50.000 0.00 0.00 41.82 3.02
1122 2566 1.303091 ACTAACAAACATCGGCGGCC 61.303 55.000 9.54 9.54 0.00 6.13
1132 2576 5.616488 TTCTTGGGCGATTACTAACAAAC 57.384 39.130 0.00 0.00 0.00 2.93
1205 2657 3.478540 GGAGCTTTAGCACCCGAAT 57.521 52.632 6.92 0.00 44.49 3.34
1281 2733 7.121382 ACATCCACATGACAATAAAGATCCTT 58.879 34.615 0.00 0.00 33.72 3.36
1335 2787 4.180057 GACAGCAGTATCCAGACAAGAAG 58.820 47.826 0.00 0.00 0.00 2.85
1356 2808 4.910195 ACAAGATATGAACAACAGCAGGA 58.090 39.130 0.00 0.00 0.00 3.86
1382 2834 7.973944 GCTAAATTCGGTTCTTGATGGTAAAAT 59.026 33.333 0.00 0.00 0.00 1.82
1498 2995 4.153475 TCAAAATTTCGGATCGACACTTCC 59.847 41.667 0.00 0.00 34.89 3.46
1558 3124 5.062308 GTCCAGTAACGACAGATGATTTGAC 59.938 44.000 0.00 0.00 0.00 3.18
1559 3125 5.168569 GTCCAGTAACGACAGATGATTTGA 58.831 41.667 0.00 0.00 0.00 2.69
1645 3211 6.618287 TTGATTGTTGACCACACTTTCTAG 57.382 37.500 0.00 0.00 33.98 2.43
1649 3215 6.255453 CGAAAATTGATTGTTGACCACACTTT 59.745 34.615 0.00 0.00 33.98 2.66
1686 3253 2.103263 ACTCCTTCCCATATTCGACAGC 59.897 50.000 0.00 0.00 0.00 4.40
1693 3260 3.933861 GGACACACTCCTTCCCATATT 57.066 47.619 0.00 0.00 35.89 1.28
1711 3278 4.065088 CACAGTCGAAGAAATTTCAGGGA 58.935 43.478 19.99 10.32 39.69 4.20
1782 3349 3.065925 GCAAGTGGATCATCAGGTAAAGC 59.934 47.826 0.00 0.00 0.00 3.51
2169 3741 6.389906 ACAGAAAAATATTCCTCCTTTTGCG 58.610 36.000 0.00 0.00 0.00 4.85
2507 4176 2.764314 CGAAATTGGAGCCTGCCCG 61.764 63.158 0.00 0.00 0.00 6.13
2585 4254 0.822164 GTAGCCGCCTAGGAGTTGAA 59.178 55.000 14.75 0.00 45.00 2.69
2769 4442 8.912988 ACTAATTTGGTTGAATGAAAAGTCTGA 58.087 29.630 0.00 0.00 0.00 3.27
2777 4450 9.177608 CTCCTGATACTAATTTGGTTGAATGAA 57.822 33.333 0.00 0.00 0.00 2.57
2904 4900 4.018415 ACCATACAAGGCATTGAGGTTAGT 60.018 41.667 19.41 4.43 38.83 2.24
3250 5246 5.561679 AGACTATGGGGAGTTTCAAACTTC 58.438 41.667 3.76 1.32 43.03 3.01
3298 5294 4.536765 CCCCAGCTACAATAAATGTTCCT 58.463 43.478 0.00 0.00 43.63 3.36
3499 5495 0.391927 CGGACGGCAGAAATGGGTAA 60.392 55.000 0.00 0.00 0.00 2.85
3630 5953 4.693566 ACATATTTTATCCATACCGTGCCG 59.306 41.667 0.00 0.00 0.00 5.69
3686 6009 9.905171 AGAAATCAGACTTCTTAATTTGCTTTC 57.095 29.630 0.00 0.00 28.46 2.62
3781 6107 8.644374 TCACAAGGTAACCTAATAGCATTTTT 57.356 30.769 0.00 0.00 31.13 1.94
3852 6182 3.985019 TTACAAGAGATGGCGGGTTTA 57.015 42.857 0.00 0.00 0.00 2.01
3857 6187 5.584649 TCAAAGTATTTACAAGAGATGGCGG 59.415 40.000 0.00 0.00 35.03 6.13
3881 6211 8.955388 GCCTTTTCATTAAGAGAGAAGAGAAAT 58.045 33.333 10.68 0.00 0.00 2.17
3911 6241 2.718487 TGGCAAGCAACTGGCAGGAT 62.718 55.000 20.34 4.15 46.00 3.24
4214 6570 7.385752 AGTCATTCCAAAACATTATTGCACAAG 59.614 33.333 0.00 0.00 0.00 3.16
4224 6580 6.493166 TCAGGGATAGTCATTCCAAAACATT 58.507 36.000 0.00 0.00 31.11 2.71


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

AutoCloner maintained by Alex Coulton.