Multiple sequence alignment - TraesCS2A01G391700

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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 TraesCS2A01G391700 chr2A 100.000 5522 0 0 1 5522 641962485 641956964 0.000000e+00 10198
1 TraesCS2A01G391700 chr2D 94.612 5568 190 45 1 5522 497372300 497366797 0.000000e+00 8519
2 TraesCS2A01G391700 chr2D 76.141 482 95 16 3299 3774 637092092 637092559 9.250000e-58 235
3 TraesCS2A01G391700 chr2D 79.221 231 43 3 2273 2499 637091621 637091850 7.410000e-34 156
4 TraesCS2A01G391700 chr2B 95.969 3250 83 17 1878 5106 583681916 583678694 0.000000e+00 5232
5 TraesCS2A01G391700 chr2B 89.141 1851 111 40 1 1834 583683693 583681916 0.000000e+00 2222
6 TraesCS2A01G391700 chr2B 79.477 497 94 5 3076 3566 794502341 794501847 4.090000e-91 346
7 TraesCS2A01G391700 chr2B 85.903 227 16 6 5237 5458 583678532 583678317 1.550000e-55 228
8 TraesCS2A01G391700 chr2B 76.457 446 74 21 2051 2485 794502919 794502494 4.330000e-51 213
9 TraesCS2A01G391700 chr3D 80.169 237 26 12 5228 5450 460939668 460939897 2.060000e-34 158
10 TraesCS2A01G391700 chr3B 88.372 129 12 1 5322 5450 611179520 611179645 9.580000e-33 152
11 TraesCS2A01G391700 chr3A 79.237 236 27 12 5228 5448 603268174 603268402 1.600000e-30 145


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 TraesCS2A01G391700 chr2A 641956964 641962485 5521 True 10198.000000 10198 100.000000 1 5522 1 chr2A.!!$R1 5521
1 TraesCS2A01G391700 chr2D 497366797 497372300 5503 True 8519.000000 8519 94.612000 1 5522 1 chr2D.!!$R1 5521
2 TraesCS2A01G391700 chr2B 583678317 583683693 5376 True 2560.666667 5232 90.337667 1 5458 3 chr2B.!!$R1 5457
3 TraesCS2A01G391700 chr2B 794501847 794502919 1072 True 279.500000 346 77.967000 2051 3566 2 chr2B.!!$R2 1515

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
628 645 0.181350 CAATCCCTTTCCCCTCTCCG 59.819 60.0 0.00 0.0 0.00 4.63 F
1236 1268 0.317938 CTCCCGTTCCTAATCTCGCG 60.318 60.0 0.00 0.0 0.00 5.87 F
2711 2754 0.892755 ACCCTTGCACGAGTAATCGA 59.107 50.0 20.67 0.0 36.85 3.59 F
3530 3585 0.673437 CAAAGTGGTTTCCGGTGCAT 59.327 50.0 0.00 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2509 2552 1.538512 CCATGGCACTCAACAAGACTG 59.461 52.381 0.0 0.0 0.00 3.51 R
2996 3046 3.610040 AATTGAGCTGACGGTATCACA 57.390 42.857 0.0 0.0 32.37 3.58 R
4479 4536 1.672356 GCCATCAGCAACCACGTCT 60.672 57.895 0.0 0.0 42.97 4.18 R
4759 4816 1.318576 ACTTTCTCCAAAAGCCCACG 58.681 50.000 0.0 0.0 0.00 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
96 104 7.360861 GCTTTAACTTAAAAATGACCCATTGGC 60.361 37.037 0.00 0.00 34.04 4.52
97 105 4.551702 ACTTAAAAATGACCCATTGGCC 57.448 40.909 0.00 0.00 34.04 5.36
174 182 6.015772 TGTGTTATCTCTTAAAGGGGCAAAAC 60.016 38.462 0.00 0.00 0.00 2.43
186 194 0.601046 GGCAAAACTGCAAAGGAGCC 60.601 55.000 3.76 3.76 36.33 4.70
205 213 4.482990 AGCCAAGGAAAAGATTCTTCCAA 58.517 39.130 7.08 0.00 44.19 3.53
211 219 5.028131 AGGAAAAGATTCTTCCAATGGCAT 58.972 37.500 7.08 0.00 44.19 4.40
300 308 3.935203 CACTTAGTCCACACCACATGATC 59.065 47.826 0.00 0.00 0.00 2.92
304 312 4.412796 AGTCCACACCACATGATCATAG 57.587 45.455 8.15 5.79 0.00 2.23
391 403 6.958767 ACTATAAAAGAAGCTTTGGCCTCTA 58.041 36.000 3.32 0.00 38.19 2.43
396 408 3.115390 AGAAGCTTTGGCCTCTACCATA 58.885 45.455 3.32 0.00 37.47 2.74
467 479 1.662629 CTTGGCTGCGTCATTACTGAG 59.337 52.381 0.00 0.00 30.18 3.35
487 499 4.098807 TGAGAACCCACAGCTTTTTAAACC 59.901 41.667 0.00 0.00 0.00 3.27
548 560 2.749800 GCCTTTCACCCAAAGACTCACT 60.750 50.000 0.00 0.00 44.02 3.41
550 562 3.433598 CCTTTCACCCAAAGACTCACTCA 60.434 47.826 0.00 0.00 44.02 3.41
551 563 2.910688 TCACCCAAAGACTCACTCAC 57.089 50.000 0.00 0.00 0.00 3.51
554 566 0.320771 CCCAAAGACTCACTCACCCG 60.321 60.000 0.00 0.00 0.00 5.28
555 567 0.320771 CCAAAGACTCACTCACCCGG 60.321 60.000 0.00 0.00 0.00 5.73
556 568 0.951040 CAAAGACTCACTCACCCGGC 60.951 60.000 0.00 0.00 0.00 6.13
557 569 2.113243 AAAGACTCACTCACCCGGCC 62.113 60.000 0.00 0.00 0.00 6.13
558 570 2.997897 GACTCACTCACCCGGCCT 60.998 66.667 0.00 0.00 0.00 5.19
559 571 2.526873 ACTCACTCACCCGGCCTT 60.527 61.111 0.00 0.00 0.00 4.35
560 572 2.266055 CTCACTCACCCGGCCTTC 59.734 66.667 0.00 0.00 0.00 3.46
561 573 2.203788 TCACTCACCCGGCCTTCT 60.204 61.111 0.00 0.00 0.00 2.85
562 574 2.232298 CTCACTCACCCGGCCTTCTC 62.232 65.000 0.00 0.00 0.00 2.87
628 645 0.181350 CAATCCCTTTCCCCTCTCCG 59.819 60.000 0.00 0.00 0.00 4.63
828 856 3.941483 CTGAACAGATTCATACACCACCC 59.059 47.826 0.00 0.00 43.92 4.61
847 875 0.811281 CAAGAACCGCCCCTTGATTC 59.189 55.000 0.00 0.00 41.56 2.52
882 911 1.640428 TCTGCTCGCGAATTACTTGG 58.360 50.000 11.33 0.00 0.00 3.61
888 917 3.729716 GCTCGCGAATTACTTGGTAGTAG 59.270 47.826 11.33 0.00 38.09 2.57
891 920 6.624352 TCGCGAATTACTTGGTAGTAGTAT 57.376 37.500 6.20 0.00 38.09 2.12
892 921 7.031226 TCGCGAATTACTTGGTAGTAGTATT 57.969 36.000 6.20 0.00 38.09 1.89
893 922 7.483307 TCGCGAATTACTTGGTAGTAGTATTT 58.517 34.615 6.20 0.00 38.09 1.40
900 929 6.295719 ACTTGGTAGTAGTATTTCCACAGG 57.704 41.667 0.00 0.00 31.21 4.00
919 948 0.799393 GAGAACTGCTCCTTTTCCGC 59.201 55.000 0.00 0.00 37.69 5.54
920 949 0.398318 AGAACTGCTCCTTTTCCGCT 59.602 50.000 0.00 0.00 0.00 5.52
921 950 0.799393 GAACTGCTCCTTTTCCGCTC 59.201 55.000 0.00 0.00 0.00 5.03
922 951 0.398318 AACTGCTCCTTTTCCGCTCT 59.602 50.000 0.00 0.00 0.00 4.09
923 952 0.321122 ACTGCTCCTTTTCCGCTCTG 60.321 55.000 0.00 0.00 0.00 3.35
941 970 2.612212 TCTGTTTTCCGTGTTTCTCTGC 59.388 45.455 0.00 0.00 0.00 4.26
975 1004 1.191647 CGGTTCTTCCTCGTTTGTTCG 59.808 52.381 0.00 0.00 0.00 3.95
1236 1268 0.317938 CTCCCGTTCCTAATCTCGCG 60.318 60.000 0.00 0.00 0.00 5.87
1250 1282 1.591158 TCTCGCGTGTTCTTTGTTGAC 59.409 47.619 5.77 0.00 0.00 3.18
1291 1323 5.102953 TGGTAGATGTTAGCTGCAATCTT 57.897 39.130 1.02 0.00 0.00 2.40
1345 1378 1.593265 GCCTGCTTGGATTGGGTTG 59.407 57.895 0.49 0.00 38.35 3.77
1369 1402 3.204827 CGGAGGCCTTTGGATGCG 61.205 66.667 6.77 0.00 0.00 4.73
1679 1712 7.716998 AGATCAGTTCTCTCTTTTGCTTTAACA 59.283 33.333 0.00 0.00 0.00 2.41
1743 1776 2.146342 GCAAGCAGCTCAGTTTCACTA 58.854 47.619 0.00 0.00 41.15 2.74
1855 1888 3.125829 GCAGTTGACCATGTATGTGACTG 59.874 47.826 0.00 0.00 37.05 3.51
1857 1890 5.181009 CAGTTGACCATGTATGTGACTGAT 58.819 41.667 0.00 0.00 36.31 2.90
1931 1965 2.555757 GTTCTTCTGTGCTGCATTCCTT 59.444 45.455 5.27 0.00 0.00 3.36
2098 2135 2.352715 GGCAAATACTGAAACAGGCACC 60.353 50.000 0.00 0.00 35.51 5.01
2335 2372 5.359009 GGAGAATGGAGCATTTTCTGATCAA 59.641 40.000 0.00 0.00 42.21 2.57
2444 2484 4.476628 TCTGCTGATGCTAGTGAAATGA 57.523 40.909 0.00 0.00 40.48 2.57
2445 2485 4.186926 TCTGCTGATGCTAGTGAAATGAC 58.813 43.478 0.00 0.00 40.48 3.06
2446 2486 4.081254 TCTGCTGATGCTAGTGAAATGACT 60.081 41.667 0.00 0.00 40.48 3.41
2492 2535 8.243426 CCTAATGTGTTGCTGCTAAATAAGAAA 58.757 33.333 0.00 0.00 0.00 2.52
2706 2749 3.077484 AGTACTACCCTTGCACGAGTA 57.923 47.619 0.00 0.00 0.00 2.59
2707 2750 3.424703 AGTACTACCCTTGCACGAGTAA 58.575 45.455 0.00 0.00 0.00 2.24
2708 2751 4.021916 AGTACTACCCTTGCACGAGTAAT 58.978 43.478 0.00 0.00 0.00 1.89
2709 2752 3.521947 ACTACCCTTGCACGAGTAATC 57.478 47.619 0.00 0.00 0.00 1.75
2710 2753 2.159282 ACTACCCTTGCACGAGTAATCG 60.159 50.000 11.58 11.58 39.31 3.34
2711 2754 0.892755 ACCCTTGCACGAGTAATCGA 59.107 50.000 20.67 0.00 36.85 3.59
2712 2755 1.135083 ACCCTTGCACGAGTAATCGAG 60.135 52.381 20.67 12.90 36.85 4.04
2713 2756 1.135083 CCCTTGCACGAGTAATCGAGT 60.135 52.381 20.67 0.00 36.85 4.18
2714 2757 2.098607 CCCTTGCACGAGTAATCGAGTA 59.901 50.000 20.67 8.26 36.85 2.59
2850 2893 6.127703 CCTGCATCATCATTTCTCAAGAACTT 60.128 38.462 0.00 0.00 33.13 2.66
2851 2894 7.066645 CCTGCATCATCATTTCTCAAGAACTTA 59.933 37.037 0.00 0.00 33.13 2.24
2852 2895 8.515695 TGCATCATCATTTCTCAAGAACTTAT 57.484 30.769 0.00 0.00 33.13 1.73
2853 2896 9.617523 TGCATCATCATTTCTCAAGAACTTATA 57.382 29.630 0.00 0.00 33.13 0.98
3007 3057 8.813643 AAGCTATAATACTTTGTGATACCGTC 57.186 34.615 0.00 0.00 0.00 4.79
3028 3078 6.183360 CCGTCAGCTCAATTTACATTACCAAT 60.183 38.462 0.00 0.00 0.00 3.16
3500 3555 4.081476 GGGGCAAGTAATTCAAATGCTTCT 60.081 41.667 0.00 0.00 37.20 2.85
3530 3585 0.673437 CAAAGTGGTTTCCGGTGCAT 59.327 50.000 0.00 0.00 0.00 3.96
3751 3807 4.463050 ACCCTGGAAAATGTAGGTTCAA 57.537 40.909 0.00 0.00 0.00 2.69
3861 3918 2.575532 TGGTGCTTTTCTCTTCACTGG 58.424 47.619 0.00 0.00 0.00 4.00
3862 3919 1.882623 GGTGCTTTTCTCTTCACTGGG 59.117 52.381 0.00 0.00 0.00 4.45
4149 4206 7.372714 TCAATTCACACTTCATCATTTCCTTG 58.627 34.615 0.00 0.00 0.00 3.61
4411 4468 2.125147 TTCCTCTCAATGCGCGGG 60.125 61.111 8.83 0.00 0.00 6.13
4479 4536 4.383861 CGCAGCTCCACCTCAGCA 62.384 66.667 0.00 0.00 39.56 4.41
4524 4581 1.019805 GCCTCAAGCAACCGTAGACC 61.020 60.000 0.00 0.00 42.97 3.85
4759 4816 3.857010 GCTTGTGTTGGTTTCCATAGCAC 60.857 47.826 0.00 9.76 34.28 4.40
4910 4969 1.462283 CTTGAGCATGTTGGTGTCTCG 59.538 52.381 0.00 0.00 0.00 4.04
4922 4981 0.535335 GTGTCTCGATAACAGGCCCA 59.465 55.000 0.00 0.00 0.00 5.36
4984 5047 8.034804 CGGTATGTCTGAATGATTGATGGTATA 58.965 37.037 0.00 0.00 0.00 1.47
5069 5139 9.552695 TGATCTTTAGGTGACCTATGATATCAT 57.447 33.333 21.50 21.50 35.87 2.45
5096 5166 6.489700 TCTTCTTAAATCACAATGCTCCAACA 59.510 34.615 0.00 0.00 0.00 3.33
5103 5220 5.823209 TCACAATGCTCCAACATATTCTG 57.177 39.130 0.00 0.00 0.00 3.02
5106 5223 6.883756 TCACAATGCTCCAACATATTCTGTTA 59.116 34.615 0.00 0.00 46.43 2.41
5137 5254 8.429493 TGATCTAATATCTGTTTGTGCTTCTG 57.571 34.615 0.00 0.00 0.00 3.02
5168 5310 8.994429 AGTGAGAGTAGTAATTGAAGAATGTG 57.006 34.615 0.00 0.00 0.00 3.21
5214 5356 3.973206 CCCCCAAAAAGGAATTACACC 57.027 47.619 0.00 0.00 41.22 4.16
5231 5373 2.560542 ACACCTTGCAACAAAAGACACA 59.439 40.909 0.00 0.00 0.00 3.72
5234 5376 3.993736 ACCTTGCAACAAAAGACACAAAC 59.006 39.130 0.00 0.00 0.00 2.93
5263 5405 7.417612 ACTGGTCGAATGAATTATAAACATGC 58.582 34.615 8.56 6.60 0.00 4.06
5298 5441 5.757808 AGGAATTACATGTTGCAACAAAACC 59.242 36.000 34.06 26.06 43.03 3.27
5437 5584 7.880195 CCAAAGTGGAAGCTATAATACTAGCAT 59.120 37.037 5.94 0.00 42.44 3.79
5458 5605 3.591254 AAGCCACTCCTCGCGGAAC 62.591 63.158 6.13 0.00 39.29 3.62
5462 5609 4.698625 ACTCCTCGCGGAACCCCT 62.699 66.667 6.13 0.00 39.29 4.79
5478 5641 6.170506 GGAACCCCTGTTTTAAATTTCCATC 58.829 40.000 0.00 0.00 33.97 3.51
5485 5648 6.145371 CCTGTTTTAAATTTCCATCAACCACG 59.855 38.462 0.00 0.00 0.00 4.94
5487 5650 4.855715 TTAAATTTCCATCAACCACGCA 57.144 36.364 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 104 2.358582 TGAATATGCCATGAAAGCACGG 59.641 45.455 0.00 0.00 44.40 4.94
97 105 3.696281 TGAATATGCCATGAAAGCACG 57.304 42.857 0.00 0.00 44.40 5.34
111 119 4.948847 TGCACGTCTAGAGCAATGAATAT 58.051 39.130 2.84 0.00 43.26 1.28
174 182 1.331214 TTTCCTTGGCTCCTTTGCAG 58.669 50.000 0.00 0.00 34.04 4.41
186 194 5.173664 GCCATTGGAAGAATCTTTTCCTTG 58.826 41.667 6.95 0.00 43.63 3.61
205 213 1.756690 GCCCTCCATTTCTGATGCCAT 60.757 52.381 0.00 0.00 0.00 4.40
211 219 4.344104 CTTTAAAGGCCCTCCATTTCTGA 58.656 43.478 7.37 0.00 33.74 3.27
391 403 3.337301 GGAGGTAGGGGTAGAGATATGGT 59.663 52.174 0.00 0.00 0.00 3.55
396 408 2.990998 GAGAGGAGGTAGGGGTAGAGAT 59.009 54.545 0.00 0.00 0.00 2.75
467 479 4.394439 TGGTTTAAAAAGCTGTGGGTTC 57.606 40.909 6.24 0.00 37.31 3.62
548 560 1.120530 GATTAGAGAAGGCCGGGTGA 58.879 55.000 2.18 0.00 0.00 4.02
550 562 1.343075 TGAGATTAGAGAAGGCCGGGT 60.343 52.381 2.18 0.00 0.00 5.28
551 563 1.069358 GTGAGATTAGAGAAGGCCGGG 59.931 57.143 2.18 0.00 0.00 5.73
554 566 2.403561 AGGGTGAGATTAGAGAAGGCC 58.596 52.381 0.00 0.00 0.00 5.19
555 567 3.181459 GGAAGGGTGAGATTAGAGAAGGC 60.181 52.174 0.00 0.00 0.00 4.35
556 568 3.068873 CGGAAGGGTGAGATTAGAGAAGG 59.931 52.174 0.00 0.00 0.00 3.46
557 569 3.491792 GCGGAAGGGTGAGATTAGAGAAG 60.492 52.174 0.00 0.00 0.00 2.85
558 570 2.431057 GCGGAAGGGTGAGATTAGAGAA 59.569 50.000 0.00 0.00 0.00 2.87
559 571 2.032620 GCGGAAGGGTGAGATTAGAGA 58.967 52.381 0.00 0.00 0.00 3.10
560 572 2.035632 AGCGGAAGGGTGAGATTAGAG 58.964 52.381 0.00 0.00 0.00 2.43
561 573 2.160721 AGCGGAAGGGTGAGATTAGA 57.839 50.000 0.00 0.00 0.00 2.10
681 701 7.951591 TGTTCTTTATTTCCTTTTCCTTCTGG 58.048 34.615 0.00 0.00 0.00 3.86
828 856 0.811281 GAATCAAGGGGCGGTTCTTG 59.189 55.000 0.00 0.00 41.06 3.02
882 911 7.259161 CAGTTCTCCTGTGGAAATACTACTAC 58.741 42.308 0.00 0.00 36.37 2.73
888 917 3.935828 GAGCAGTTCTCCTGTGGAAATAC 59.064 47.826 0.00 0.00 43.55 1.89
891 920 2.550830 GAGCAGTTCTCCTGTGGAAA 57.449 50.000 0.00 0.00 43.55 3.13
900 929 0.799393 GCGGAAAAGGAGCAGTTCTC 59.201 55.000 0.00 0.00 41.15 2.87
913 942 0.941542 CACGGAAAACAGAGCGGAAA 59.058 50.000 0.00 0.00 0.00 3.13
915 944 0.179067 AACACGGAAAACAGAGCGGA 60.179 50.000 0.00 0.00 0.00 5.54
916 945 0.661020 AAACACGGAAAACAGAGCGG 59.339 50.000 0.00 0.00 0.00 5.52
917 946 1.597663 AGAAACACGGAAAACAGAGCG 59.402 47.619 0.00 0.00 0.00 5.03
918 947 2.872858 AGAGAAACACGGAAAACAGAGC 59.127 45.455 0.00 0.00 0.00 4.09
919 948 3.303395 GCAGAGAAACACGGAAAACAGAG 60.303 47.826 0.00 0.00 0.00 3.35
920 949 2.612212 GCAGAGAAACACGGAAAACAGA 59.388 45.455 0.00 0.00 0.00 3.41
921 950 2.614057 AGCAGAGAAACACGGAAAACAG 59.386 45.455 0.00 0.00 0.00 3.16
922 951 2.639065 AGCAGAGAAACACGGAAAACA 58.361 42.857 0.00 0.00 0.00 2.83
923 952 3.363178 CAAGCAGAGAAACACGGAAAAC 58.637 45.455 0.00 0.00 0.00 2.43
1108 1140 3.089284 GGAACAAGGGGATAACAACAGG 58.911 50.000 0.00 0.00 0.00 4.00
1221 1253 1.582502 GAACACGCGAGATTAGGAACG 59.417 52.381 15.93 0.00 0.00 3.95
1236 1268 3.764885 ACAGCAGTCAACAAAGAACAC 57.235 42.857 0.00 0.00 0.00 3.32
1250 1282 0.248458 AAACCGCAAACGAACAGCAG 60.248 50.000 0.00 0.00 43.93 4.24
1316 1348 1.306482 AAGCAGGCCCAGAGCTCTA 60.306 57.895 17.75 0.00 43.05 2.43
1345 1378 1.219393 CAAAGGCCTCCGAGACCTC 59.781 63.158 5.23 0.00 31.86 3.85
1369 1402 5.862924 TCGTTCCTCATGTTCAGAATTTC 57.137 39.130 0.00 0.00 0.00 2.17
1402 1435 8.991026 CAAACAAAATTCTGAATATCTGCCAAA 58.009 29.630 2.85 0.00 0.00 3.28
1465 1498 7.122353 GGTGTTCTAAGAAGTATCCTCTACACA 59.878 40.741 0.00 0.00 34.32 3.72
1472 1505 5.337652 GCACAGGTGTTCTAAGAAGTATCCT 60.338 44.000 0.91 0.00 0.00 3.24
1481 1514 3.111853 TGTCTGCACAGGTGTTCTAAG 57.888 47.619 0.91 0.00 0.00 2.18
1679 1712 3.453717 ACTGACTGTATGATGCCACAGAT 59.546 43.478 8.61 0.00 43.99 2.90
1743 1776 4.207165 AGGCATACCAAACGCAGATTATT 58.793 39.130 0.00 0.00 39.06 1.40
1931 1965 5.221521 GCTATCACAAGAGATGGTGGTATCA 60.222 44.000 0.00 0.00 35.74 2.15
2072 2106 6.039270 GTGCCTGTTTCAGTATTTGCCATATA 59.961 38.462 0.00 0.00 0.00 0.86
2098 2135 1.591183 CCCATTTCGCCAAAGTGGG 59.409 57.895 11.28 11.28 43.16 4.61
2335 2372 2.358258 TCCCCCATCTTCCAGAAGTTT 58.642 47.619 7.26 0.00 39.38 2.66
2386 2426 6.423302 CACAACTCTCTGAATATGATAGTGCC 59.577 42.308 0.00 0.00 0.00 5.01
2444 2484 7.741554 AGGAAATTAGAGATTACTGACCAGT 57.258 36.000 7.86 7.86 45.02 4.00
2509 2552 1.538512 CCATGGCACTCAACAAGACTG 59.461 52.381 0.00 0.00 0.00 3.51
2676 2719 4.020839 GCAAGGGTAGTACTACAAGAACCA 60.021 45.833 29.38 0.00 37.78 3.67
2677 2720 4.020839 TGCAAGGGTAGTACTACAAGAACC 60.021 45.833 29.38 21.45 37.78 3.62
2706 2749 6.127703 ACACAGTTACTAGCACATACTCGATT 60.128 38.462 0.00 0.00 0.00 3.34
2707 2750 5.357314 ACACAGTTACTAGCACATACTCGAT 59.643 40.000 0.00 0.00 0.00 3.59
2708 2751 4.698780 ACACAGTTACTAGCACATACTCGA 59.301 41.667 0.00 0.00 0.00 4.04
2709 2752 4.982999 ACACAGTTACTAGCACATACTCG 58.017 43.478 0.00 0.00 0.00 4.18
2711 2754 9.967346 CATTATACACAGTTACTAGCACATACT 57.033 33.333 0.00 0.00 0.00 2.12
2712 2755 8.700644 GCATTATACACAGTTACTAGCACATAC 58.299 37.037 0.00 0.00 0.00 2.39
2713 2756 8.417884 TGCATTATACACAGTTACTAGCACATA 58.582 33.333 0.00 0.00 0.00 2.29
2714 2757 7.272244 TGCATTATACACAGTTACTAGCACAT 58.728 34.615 0.00 0.00 0.00 3.21
2996 3046 3.610040 AATTGAGCTGACGGTATCACA 57.390 42.857 0.00 0.00 32.37 3.58
3313 3368 7.184862 ACTTCCATAACCAATCTCAAAGGAAT 58.815 34.615 0.00 0.00 32.75 3.01
3500 3555 1.140312 ACCACTTTGGCTTCTCAGGA 58.860 50.000 0.00 0.00 42.67 3.86
3530 3585 7.675962 ATACCTTTTAGCAATTTCGTGTGTA 57.324 32.000 0.00 0.00 0.00 2.90
3751 3807 7.964624 ACCTCTAAAGCTACTGAAACTAAAGT 58.035 34.615 0.00 0.00 0.00 2.66
3861 3918 5.180680 GGTTGGAAGTTCATAACAGTGTACC 59.819 44.000 18.27 0.00 0.00 3.34
3862 3919 5.995897 AGGTTGGAAGTTCATAACAGTGTAC 59.004 40.000 18.27 0.00 0.00 2.90
3922 3979 4.600111 TCCTTAGTGCCTTCTCCCTAAAAA 59.400 41.667 0.00 0.00 0.00 1.94
4114 4171 5.939883 TGAAGTGTGAATTGAATACAGAGGG 59.060 40.000 0.00 0.00 0.00 4.30
4149 4206 8.138074 GCTTCTCCTTGTTATTCCCAATAAATC 58.862 37.037 0.00 0.00 35.29 2.17
4167 4224 6.721704 AAAACAAATCAGAAAGCTTCTCCT 57.278 33.333 0.00 0.00 38.11 3.69
4411 4468 2.849294 AGAAGTTCTGCCTCTGGTTC 57.151 50.000 4.10 0.00 0.00 3.62
4479 4536 1.672356 GCCATCAGCAACCACGTCT 60.672 57.895 0.00 0.00 42.97 4.18
4524 4581 3.866449 GCCTGTTCCTAAGTTGGTCTCTG 60.866 52.174 0.00 0.00 0.00 3.35
4759 4816 1.318576 ACTTTCTCCAAAAGCCCACG 58.681 50.000 0.00 0.00 0.00 4.94
4910 4969 4.141251 TCCCTAAAAGATGGGCCTGTTATC 60.141 45.833 4.53 0.00 43.04 1.75
4922 4981 3.269381 TGACCTGCCATTCCCTAAAAGAT 59.731 43.478 0.00 0.00 0.00 2.40
5069 5139 6.003326 TGGAGCATTGTGATTTAAGAAGACA 58.997 36.000 0.00 0.00 0.00 3.41
5106 5223 8.834465 GCACAAACAGATATTAGATCAGAACAT 58.166 33.333 0.00 0.00 0.00 2.71
5124 5241 5.182487 TCACTAAGAACAGAAGCACAAACA 58.818 37.500 0.00 0.00 0.00 2.83
5198 5340 5.814705 TGTTGCAAGGTGTAATTCCTTTTTG 59.185 36.000 0.00 0.00 42.57 2.44
5212 5354 3.951775 TTGTGTCTTTTGTTGCAAGGT 57.048 38.095 0.00 0.00 0.00 3.50
5213 5355 3.060628 CGTTTGTGTCTTTTGTTGCAAGG 59.939 43.478 0.00 0.00 0.00 3.61
5214 5356 3.917380 TCGTTTGTGTCTTTTGTTGCAAG 59.083 39.130 0.00 0.00 0.00 4.01
5231 5373 3.380479 TTCATTCGACCAGTCTCGTTT 57.620 42.857 0.00 0.00 35.10 3.60
5234 5376 7.222031 TGTTTATAATTCATTCGACCAGTCTCG 59.778 37.037 0.00 0.00 34.83 4.04
5263 5405 7.547227 CAACATGTAATTCCTTTTTAGGGGAG 58.453 38.462 0.00 0.00 32.80 4.30
5458 5605 5.937540 GGTTGATGGAAATTTAAAACAGGGG 59.062 40.000 0.00 0.00 0.00 4.79
5462 5609 5.463724 GCGTGGTTGATGGAAATTTAAAACA 59.536 36.000 0.00 0.00 0.00 2.83
5478 5641 5.431420 TTGGCTATATAATTGCGTGGTTG 57.569 39.130 0.00 0.00 31.65 3.77


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

AutoCloner maintained by Alex Coulton.