Multiple sequence alignment - TraesCS6A01G024500

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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 TraesCS6A01G024500 chr6A 100.000 2370 0 0 1 2370 12226441 12228810 0.000000e+00 4377.0
1 TraesCS6A01G024500 chr6A 85.714 196 24 2 1148 1343 12146483 12146674 1.110000e-48 204.0
2 TraesCS6A01G024500 chr5D 97.005 768 22 1 1604 2370 127236717 127237484 0.000000e+00 1290.0
3 TraesCS6A01G024500 chr5D 97.001 767 23 0 1604 2370 388201704 388200938 0.000000e+00 1290.0
4 TraesCS6A01G024500 chr5D 97.005 768 22 1 1604 2370 419871844 419871077 0.000000e+00 1290.0
5 TraesCS6A01G024500 chr3D 97.005 768 22 1 1604 2370 391678549 391677782 0.000000e+00 1290.0
6 TraesCS6A01G024500 chrUn 96.871 767 24 0 1604 2370 367230665 367231431 0.000000e+00 1284.0
7 TraesCS6A01G024500 chrUn 85.457 832 90 18 683 1497 385849814 385848997 0.000000e+00 837.0
8 TraesCS6A01G024500 chr6D 96.875 768 23 1 1604 2370 163344299 163343532 0.000000e+00 1284.0
9 TraesCS6A01G024500 chr6D 89.583 672 39 9 850 1495 10670850 10671516 0.000000e+00 824.0
10 TraesCS6A01G024500 chr6D 85.942 313 32 9 443 744 10670230 10670541 8.170000e-85 324.0
11 TraesCS6A01G024500 chr6D 78.788 396 54 23 972 1344 10666736 10667124 3.040000e-59 239.0
12 TraesCS6A01G024500 chr6D 94.643 56 3 0 3 58 302579997 302579942 1.170000e-13 87.9
13 TraesCS6A01G024500 chr4D 96.875 768 23 1 1604 2370 283384961 283385728 0.000000e+00 1284.0
14 TraesCS6A01G024500 chr4D 94.872 39 2 0 15 53 494097609 494097571 7.070000e-06 62.1
15 TraesCS6A01G024500 chr2D 96.875 768 23 1 1604 2370 153747956 153748723 0.000000e+00 1284.0
16 TraesCS6A01G024500 chr1D 96.875 768 23 1 1604 2370 294333191 294332424 0.000000e+00 1284.0
17 TraesCS6A01G024500 chr1D 95.238 42 2 0 17 58 398921764 398921723 1.520000e-07 67.6
18 TraesCS6A01G024500 chr1B 87.971 981 76 14 635 1592 589706990 589706029 0.000000e+00 1120.0
19 TraesCS6A01G024500 chr1B 87.362 633 65 9 4 635 589725963 589725345 0.000000e+00 712.0
20 TraesCS6A01G024500 chr1B 92.683 41 3 0 18 58 470871533 470871493 2.540000e-05 60.2
21 TraesCS6A01G024500 chr6B 85.815 853 71 18 683 1497 19450995 19450155 0.000000e+00 859.0
22 TraesCS6A01G024500 chr6B 87.879 627 60 11 528 1143 19983783 19984404 0.000000e+00 723.0
23 TraesCS6A01G024500 chr6B 86.096 374 34 10 1141 1497 19984431 19984803 1.030000e-103 387.0
24 TraesCS6A01G024500 chr7B 81.333 225 41 1 58 282 729063989 729064212 5.200000e-42 182.0
25 TraesCS6A01G024500 chr3B 92.857 56 4 0 3 58 487051372 487051317 5.430000e-12 82.4
26 TraesCS6A01G024500 chr7D 83.544 79 13 0 94 172 615769212 615769134 9.080000e-10 75.0
27 TraesCS6A01G024500 chr2B 95.349 43 2 0 15 57 611017560 611017602 4.230000e-08 69.4
28 TraesCS6A01G024500 chr5A 95.122 41 2 0 16 56 649405047 649405007 5.470000e-07 65.8


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 TraesCS6A01G024500 chr6A 12226441 12228810 2369 False 4377.000000 4377 100.0000 1 2370 1 chr6A.!!$F2 2369
1 TraesCS6A01G024500 chr5D 127236717 127237484 767 False 1290.000000 1290 97.0050 1604 2370 1 chr5D.!!$F1 766
2 TraesCS6A01G024500 chr5D 388200938 388201704 766 True 1290.000000 1290 97.0010 1604 2370 1 chr5D.!!$R1 766
3 TraesCS6A01G024500 chr5D 419871077 419871844 767 True 1290.000000 1290 97.0050 1604 2370 1 chr5D.!!$R2 766
4 TraesCS6A01G024500 chr3D 391677782 391678549 767 True 1290.000000 1290 97.0050 1604 2370 1 chr3D.!!$R1 766
5 TraesCS6A01G024500 chrUn 367230665 367231431 766 False 1284.000000 1284 96.8710 1604 2370 1 chrUn.!!$F1 766
6 TraesCS6A01G024500 chrUn 385848997 385849814 817 True 837.000000 837 85.4570 683 1497 1 chrUn.!!$R1 814
7 TraesCS6A01G024500 chr6D 163343532 163344299 767 True 1284.000000 1284 96.8750 1604 2370 1 chr6D.!!$R1 766
8 TraesCS6A01G024500 chr6D 10666736 10671516 4780 False 462.333333 824 84.7710 443 1495 3 chr6D.!!$F1 1052
9 TraesCS6A01G024500 chr4D 283384961 283385728 767 False 1284.000000 1284 96.8750 1604 2370 1 chr4D.!!$F1 766
10 TraesCS6A01G024500 chr2D 153747956 153748723 767 False 1284.000000 1284 96.8750 1604 2370 1 chr2D.!!$F1 766
11 TraesCS6A01G024500 chr1D 294332424 294333191 767 True 1284.000000 1284 96.8750 1604 2370 1 chr1D.!!$R1 766
12 TraesCS6A01G024500 chr1B 589706029 589706990 961 True 1120.000000 1120 87.9710 635 1592 1 chr1B.!!$R2 957
13 TraesCS6A01G024500 chr1B 589725345 589725963 618 True 712.000000 712 87.3620 4 635 1 chr1B.!!$R3 631
14 TraesCS6A01G024500 chr6B 19450155 19450995 840 True 859.000000 859 85.8150 683 1497 1 chr6B.!!$R1 814
15 TraesCS6A01G024500 chr6B 19983783 19984803 1020 False 555.000000 723 86.9875 528 1497 2 chr6B.!!$F1 969

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
352 354 0.107703 CGGCTAGCTTTGGATGACCA 60.108 55.0 15.72 0.0 45.34 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1511 4868 0.798776 CGGCAAAGCAGTAGGTTCTG 59.201 55.0 0.0 0.0 38.35 3.02 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
34 35 4.802039 CCATTCTTTGAAGCAATGGATTCG 59.198 41.667 19.32 0.00 42.27 3.34
49 50 3.454447 TGGATTCGGACATGGAGTACATT 59.546 43.478 0.00 0.00 37.84 2.71
53 54 4.036567 TCGGACATGGAGTACATTTACG 57.963 45.455 0.00 0.00 43.36 3.18
65 66 6.294564 GGAGTACATTTACGAGCATCCTATCA 60.295 42.308 0.00 0.00 32.93 2.15
74 75 3.744942 CGAGCATCCTATCAAACATCCAG 59.255 47.826 0.00 0.00 0.00 3.86
92 93 2.293677 CCAGATCAGAATTCAGCCATGC 59.706 50.000 8.44 0.00 0.00 4.06
108 109 3.495193 CCATGCTTGATGAGTTTGTTCG 58.505 45.455 0.22 0.00 33.31 3.95
109 110 3.495193 CATGCTTGATGAGTTTGTTCGG 58.505 45.455 0.00 0.00 33.31 4.30
132 133 1.847999 GCATCAACAAATTCGGCATCG 59.152 47.619 0.00 0.00 37.82 3.84
133 134 2.731968 GCATCAACAAATTCGGCATCGT 60.732 45.455 0.00 0.00 37.69 3.73
134 135 2.610219 TCAACAAATTCGGCATCGTG 57.390 45.000 0.00 0.00 37.69 4.35
135 136 0.984109 CAACAAATTCGGCATCGTGC 59.016 50.000 1.92 1.92 44.08 5.34
146 147 2.115348 GCATCGTGCAATTCATGAGG 57.885 50.000 0.00 7.14 43.39 3.86
174 175 3.359950 AGGAAGATTTGATTGAGCACCC 58.640 45.455 0.00 0.00 0.00 4.61
185 186 4.954970 AGCACCCGTGGGCAGTTG 62.955 66.667 4.41 0.00 39.32 3.16
189 190 2.672996 CCCGTGGGCAGTTGAAGG 60.673 66.667 0.00 0.00 0.00 3.46
217 218 6.072508 ACAACTGAAACATATGTGCTAGTTGG 60.073 38.462 33.87 25.06 44.71 3.77
218 219 5.560724 ACTGAAACATATGTGCTAGTTGGT 58.439 37.500 9.63 0.00 0.00 3.67
236 237 7.222000 AGTTGGTTTTCAAGTTTGAACTACA 57.778 32.000 6.79 4.11 45.99 2.74
298 299 8.902540 TTAGAACTATGATTTGATATGCGGTT 57.097 30.769 0.00 0.00 0.00 4.44
312 313 3.750639 TGCGGTTATTTTAAGCTTCCG 57.249 42.857 14.30 14.30 39.52 4.30
313 314 2.420722 TGCGGTTATTTTAAGCTTCCGG 59.579 45.455 18.63 0.00 37.44 5.14
314 315 2.679336 GCGGTTATTTTAAGCTTCCGGA 59.321 45.455 18.63 0.00 37.44 5.14
326 327 3.542648 AGCTTCCGGACTTAAAATAGGC 58.457 45.455 1.83 0.00 0.00 3.93
328 329 3.788937 CTTCCGGACTTAAAATAGGCGA 58.211 45.455 1.83 0.00 0.00 5.54
350 352 1.134670 AGTCGGCTAGCTTTGGATGAC 60.135 52.381 15.72 10.82 0.00 3.06
352 354 0.107703 CGGCTAGCTTTGGATGACCA 60.108 55.000 15.72 0.00 45.34 4.02
371 373 1.135575 CAGCTCCCGCATCAGTTTTTC 60.136 52.381 0.00 0.00 39.10 2.29
376 378 1.094785 CCGCATCAGTTTTTCCGGAT 58.905 50.000 4.15 0.00 38.04 4.18
381 383 3.673323 GCATCAGTTTTTCCGGATTGGTC 60.673 47.826 4.15 0.00 39.52 4.02
382 384 3.216187 TCAGTTTTTCCGGATTGGTCA 57.784 42.857 4.15 0.00 39.52 4.02
384 386 2.030274 CAGTTTTTCCGGATTGGTCACC 60.030 50.000 4.15 0.00 39.52 4.02
388 390 1.131303 TTCCGGATTGGTCACCACCT 61.131 55.000 4.15 0.00 44.17 4.00
410 412 3.555401 CGCGAACGGATATGGTGTA 57.445 52.632 0.00 0.00 34.97 2.90
411 413 1.126079 CGCGAACGGATATGGTGTAC 58.874 55.000 0.00 0.00 34.97 2.90
425 427 4.713824 TGGTGTACGATTTAGGAGTCAG 57.286 45.455 0.00 0.00 0.00 3.51
453 3506 2.222027 GATGCCCTAAATGTCCCTTCG 58.778 52.381 0.00 0.00 0.00 3.79
499 3552 0.682292 CCTCCCTCCGCTTTCTATCC 59.318 60.000 0.00 0.00 0.00 2.59
561 3624 2.330286 GGTTATTTTCAAAACCGCCCG 58.670 47.619 0.00 0.00 36.12 6.13
591 3654 0.387929 TCCTACCGAGCTTATTGGCG 59.612 55.000 0.00 0.00 35.56 5.69
704 3770 7.218773 CACGATTACTGCTGACAAAATATTTGG 59.781 37.037 0.39 0.55 0.00 3.28
707 3773 5.789643 ACTGCTGACAAAATATTTGGTGT 57.210 34.783 13.08 8.93 0.00 4.16
766 4035 2.357760 GGCCCTTACAACGCACGA 60.358 61.111 0.00 0.00 0.00 4.35
774 4043 1.222300 TACAACGCACGACAATTGCT 58.778 45.000 5.05 0.00 37.87 3.91
776 4045 0.771756 CAACGCACGACAATTGCTTG 59.228 50.000 5.05 3.89 37.87 4.01
834 4117 1.131928 ACCTAAGAACCGGGCCTTGT 61.132 55.000 17.52 7.71 0.00 3.16
931 4216 5.535783 CCATCTTGTATAAATGGACCATGCA 59.464 40.000 8.02 0.00 42.13 3.96
934 4219 4.518278 TGTATAAATGGACCATGCACCT 57.482 40.909 8.02 0.00 0.00 4.00
941 4227 2.669569 ACCATGCACCTGACGCAC 60.670 61.111 0.00 0.00 43.35 5.34
955 4241 1.812571 GACGCACCAAAACCATCTCAT 59.187 47.619 0.00 0.00 0.00 2.90
958 4244 3.270027 CGCACCAAAACCATCTCATAGA 58.730 45.455 0.00 0.00 0.00 1.98
1005 4298 3.751479 TCATTCATACCCACGATGGAG 57.249 47.619 5.71 0.00 40.96 3.86
1045 4344 4.803426 CGGTCACGCTGCTCCTCC 62.803 72.222 0.00 0.00 0.00 4.30
1054 4353 0.395686 GCTGCTCCTCCTCATATGCA 59.604 55.000 0.00 0.00 0.00 3.96
1079 4378 1.440060 CTACCCAGGCGCGATGTAA 59.560 57.895 12.10 0.00 0.00 2.41
1080 4379 0.033504 CTACCCAGGCGCGATGTAAT 59.966 55.000 12.10 0.00 0.00 1.89
1081 4380 0.466543 TACCCAGGCGCGATGTAATT 59.533 50.000 12.10 0.00 0.00 1.40
1082 4381 0.466543 ACCCAGGCGCGATGTAATTA 59.533 50.000 12.10 0.00 0.00 1.40
1097 4396 7.064728 GCGATGTAATTAATAATCCCTCCTGAC 59.935 40.741 0.00 0.00 0.00 3.51
1225 4553 1.734137 CTACGGGCTGTGCGTCTAT 59.266 57.895 9.79 0.00 0.00 1.98
1237 4565 3.951680 TGTGCGTCTATGATAAGAGGTCA 59.048 43.478 0.00 0.00 34.58 4.02
1376 4725 3.677190 TCTCCGATAGCTTAGCTACCTC 58.323 50.000 16.78 10.16 44.24 3.85
1384 4733 2.097791 AGCTTAGCTACCTCGTTCTTCG 59.902 50.000 4.30 0.00 36.99 3.79
1400 4750 6.811665 TCGTTCTTCGAGACAAATGTATGATT 59.188 34.615 0.00 0.00 44.01 2.57
1402 4752 7.009631 CGTTCTTCGAGACAAATGTATGATTCT 59.990 37.037 0.00 0.00 42.86 2.40
1405 4755 6.471233 TCGAGACAAATGTATGATTCTCCT 57.529 37.500 0.00 0.00 0.00 3.69
1407 4757 7.426410 TCGAGACAAATGTATGATTCTCCTAC 58.574 38.462 0.00 0.00 0.00 3.18
1472 4829 0.452184 CTACTTCTCTTGCGAGCGGA 59.548 55.000 0.00 0.00 37.19 5.54
1498 4855 3.655276 AAGCTTCTGCACAATCTTTGG 57.345 42.857 0.00 0.00 42.74 3.28
1501 4858 2.666619 GCTTCTGCACAATCTTTGGTCG 60.667 50.000 0.00 0.00 39.41 4.79
1502 4859 0.874390 TCTGCACAATCTTTGGTCGC 59.126 50.000 0.00 0.00 34.12 5.19
1503 4860 0.109597 CTGCACAATCTTTGGTCGCC 60.110 55.000 0.00 0.00 34.12 5.54
1504 4861 0.537143 TGCACAATCTTTGGTCGCCT 60.537 50.000 0.00 0.00 34.12 5.52
1505 4862 0.169009 GCACAATCTTTGGTCGCCTC 59.831 55.000 0.00 0.00 34.12 4.70
1506 4863 1.813513 CACAATCTTTGGTCGCCTCT 58.186 50.000 0.00 0.00 34.12 3.69
1507 4864 2.935238 GCACAATCTTTGGTCGCCTCTA 60.935 50.000 0.00 0.00 34.12 2.43
1508 4865 2.932614 CACAATCTTTGGTCGCCTCTAG 59.067 50.000 0.00 0.00 34.12 2.43
1509 4866 2.832129 ACAATCTTTGGTCGCCTCTAGA 59.168 45.455 0.00 0.00 34.12 2.43
1510 4867 3.452627 ACAATCTTTGGTCGCCTCTAGAT 59.547 43.478 0.00 0.00 34.12 1.98
1511 4868 4.054671 CAATCTTTGGTCGCCTCTAGATC 58.945 47.826 0.00 0.00 0.00 2.75
1512 4869 2.735151 TCTTTGGTCGCCTCTAGATCA 58.265 47.619 0.00 0.00 0.00 2.92
1513 4870 2.690497 TCTTTGGTCGCCTCTAGATCAG 59.310 50.000 0.00 0.00 29.61 2.90
1514 4871 2.437085 TTGGTCGCCTCTAGATCAGA 57.563 50.000 0.00 0.00 29.61 3.27
1526 4883 5.362430 CCTCTAGATCAGAACCTACTGCTTT 59.638 44.000 0.00 0.00 37.75 3.51
1556 4913 0.684535 TCCTCATGTTGCTCGGTCAA 59.315 50.000 0.00 0.00 0.00 3.18
1557 4914 0.798776 CCTCATGTTGCTCGGTCAAC 59.201 55.000 11.89 11.89 44.80 3.18
1570 4927 3.084039 TCGGTCAACAGACGTACCTTAT 58.916 45.455 1.72 0.00 33.01 1.73
1582 4939 9.139734 ACAGACGTACCTTATTATCAGGAAATA 57.860 33.333 0.00 0.00 35.14 1.40
1598 4955 8.660295 TCAGGAAATAGAACCAAACTACTAGA 57.340 34.615 0.00 0.00 0.00 2.43
1599 4956 9.268282 TCAGGAAATAGAACCAAACTACTAGAT 57.732 33.333 0.00 0.00 0.00 1.98
1600 4957 9.892130 CAGGAAATAGAACCAAACTACTAGATT 57.108 33.333 0.00 0.00 0.00 2.40
1795 5152 9.581289 TTGATCAAAGATGGTTAAGTTTCCTAA 57.419 29.630 5.45 0.00 0.00 2.69
1834 5191 5.123186 TGTCATTTGATTAACGGGATCACAC 59.877 40.000 0.00 0.00 33.51 3.82
1841 5198 5.129650 TGATTAACGGGATCACACCATTAGA 59.870 40.000 0.00 0.00 0.00 2.10
1854 5211 6.992063 ACACCATTAGAAGAATGATGTGAC 57.008 37.500 11.28 0.00 33.32 3.67
1884 5241 2.887152 CCCATTCCATTAGCTTAGCACC 59.113 50.000 7.07 0.00 0.00 5.01
1887 5244 0.468226 TCCATTAGCTTAGCACCCGG 59.532 55.000 7.07 0.00 0.00 5.73
2070 5427 1.982660 TGTTGGGTTGGCGTATTTCA 58.017 45.000 0.00 0.00 0.00 2.69
2099 5456 2.804697 TTTGTCACTCCGATTGTCGA 57.195 45.000 0.22 0.00 43.74 4.20
2118 5475 3.893324 GAGGTATCTCTGGGCCCC 58.107 66.667 22.27 0.22 37.07 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.923121 ACTCCATGTCCGAATCCATTG 58.077 47.619 0.00 0.00 0.00 2.82
34 35 3.802685 GCTCGTAAATGTACTCCATGTCC 59.197 47.826 0.00 0.00 32.82 4.02
49 50 5.163353 TGGATGTTTGATAGGATGCTCGTAA 60.163 40.000 0.00 0.00 0.00 3.18
53 54 4.965814 TCTGGATGTTTGATAGGATGCTC 58.034 43.478 0.00 0.00 0.00 4.26
65 66 4.643784 GGCTGAATTCTGATCTGGATGTTT 59.356 41.667 15.79 0.00 0.00 2.83
74 75 3.630769 TCAAGCATGGCTGAATTCTGATC 59.369 43.478 15.79 7.62 39.62 2.92
92 93 3.189080 TGCATCCGAACAAACTCATCAAG 59.811 43.478 0.00 0.00 0.00 3.02
108 109 2.195922 GCCGAATTTGTTGATGCATCC 58.804 47.619 23.67 9.97 0.00 3.51
109 110 2.878580 TGCCGAATTTGTTGATGCATC 58.121 42.857 20.14 20.14 0.00 3.91
132 133 4.380233 CCTTGAGTTCCTCATGAATTGCAC 60.380 45.833 0.00 0.00 40.39 4.57
133 134 3.760151 CCTTGAGTTCCTCATGAATTGCA 59.240 43.478 0.00 0.00 40.39 4.08
134 135 4.012374 TCCTTGAGTTCCTCATGAATTGC 58.988 43.478 0.00 0.00 40.39 3.56
135 136 5.942236 TCTTCCTTGAGTTCCTCATGAATTG 59.058 40.000 0.00 0.00 40.39 2.32
136 137 6.131972 TCTTCCTTGAGTTCCTCATGAATT 57.868 37.500 0.00 0.00 40.39 2.17
140 141 5.942236 TCAAATCTTCCTTGAGTTCCTCATG 59.058 40.000 0.00 0.00 40.39 3.07
141 142 6.131972 TCAAATCTTCCTTGAGTTCCTCAT 57.868 37.500 0.00 0.00 40.39 2.90
146 147 6.072286 TGCTCAATCAAATCTTCCTTGAGTTC 60.072 38.462 11.06 0.00 42.92 3.01
174 175 2.672996 CCCCTTCAACTGCCCACG 60.673 66.667 0.00 0.00 0.00 4.94
185 186 5.010282 ACATATGTTTCAGTTGTCCCCTTC 58.990 41.667 1.41 0.00 0.00 3.46
189 190 3.758554 AGCACATATGTTTCAGTTGTCCC 59.241 43.478 5.37 0.00 0.00 4.46
295 296 5.892160 AAGTCCGGAAGCTTAAAATAACC 57.108 39.130 5.23 0.00 0.00 2.85
312 313 4.033702 CCGACTTTCGCCTATTTTAAGTCC 59.966 45.833 0.00 0.00 40.83 3.85
313 314 4.493708 GCCGACTTTCGCCTATTTTAAGTC 60.494 45.833 0.00 0.00 40.62 3.01
314 315 3.373130 GCCGACTTTCGCCTATTTTAAGT 59.627 43.478 0.00 0.00 38.82 2.24
322 323 1.035932 AGCTAGCCGACTTTCGCCTA 61.036 55.000 12.13 0.00 38.82 3.93
324 325 1.019805 AAAGCTAGCCGACTTTCGCC 61.020 55.000 12.13 0.00 38.82 5.54
326 327 0.721718 CCAAAGCTAGCCGACTTTCG 59.278 55.000 12.13 0.00 40.07 3.46
328 329 2.027192 TCATCCAAAGCTAGCCGACTTT 60.027 45.455 12.13 2.13 36.56 2.66
371 373 0.837272 ATAGGTGGTGACCAATCCGG 59.163 55.000 5.57 0.00 45.98 5.14
376 378 1.600107 GCGGATAGGTGGTGACCAA 59.400 57.895 5.57 0.00 45.98 3.67
381 383 1.876714 CGTTCGCGGATAGGTGGTG 60.877 63.158 6.13 0.00 36.88 4.17
382 384 2.493030 CGTTCGCGGATAGGTGGT 59.507 61.111 6.13 0.00 36.88 4.16
410 412 3.306780 CCCAACACTGACTCCTAAATCGT 60.307 47.826 0.00 0.00 0.00 3.73
411 413 3.262420 CCCAACACTGACTCCTAAATCG 58.738 50.000 0.00 0.00 0.00 3.34
453 3506 2.439507 TGGAGACAATGCTCTTATCCCC 59.560 50.000 5.07 0.00 37.44 4.81
466 3519 1.717077 AGGGAGGAGTAGTGGAGACAA 59.283 52.381 0.00 0.00 46.06 3.18
561 3624 2.223618 GCTCGGTAGGAGAGACATGTTC 60.224 54.545 0.00 0.00 46.23 3.18
591 3654 6.806249 TGGCTTAACAATCGAAACATGATTTC 59.194 34.615 0.00 5.27 33.91 2.17
605 3668 8.259411 TGAATCAGCATTTATTGGCTTAACAAT 58.741 29.630 0.00 0.00 43.13 2.71
663 3729 4.921470 AATCGTGATTTACTTGTCGGTG 57.079 40.909 0.00 0.00 0.00 4.94
665 3731 5.500290 GCAGTAATCGTGATTTACTTGTCGG 60.500 44.000 0.00 0.00 32.50 4.79
704 3770 1.956477 AGGTGCCAACTGAATCAACAC 59.044 47.619 0.00 0.00 0.00 3.32
707 3773 6.418057 AATTTTAGGTGCCAACTGAATCAA 57.582 33.333 0.00 0.00 0.00 2.57
791 4067 8.557029 GGTATTAATTGCTTCGTTTGCTAGTAT 58.443 33.333 0.00 0.00 0.00 2.12
792 4068 7.767198 AGGTATTAATTGCTTCGTTTGCTAGTA 59.233 33.333 0.00 0.00 0.00 1.82
793 4069 6.598064 AGGTATTAATTGCTTCGTTTGCTAGT 59.402 34.615 0.00 0.00 0.00 2.57
801 4077 6.257193 CGGTTCTTAGGTATTAATTGCTTCGT 59.743 38.462 0.00 0.00 0.00 3.85
834 4117 6.647334 TGTGCTAAAGATTGTGGAAAATCA 57.353 33.333 0.27 0.00 38.74 2.57
852 4136 2.097825 GAGCATTGGGAAGATTGTGCT 58.902 47.619 0.00 0.00 44.75 4.40
919 4204 0.677731 CGTCAGGTGCATGGTCCATT 60.678 55.000 0.00 0.00 0.00 3.16
931 4216 0.467290 ATGGTTTTGGTGCGTCAGGT 60.467 50.000 0.00 0.00 0.00 4.00
934 4219 1.234821 GAGATGGTTTTGGTGCGTCA 58.765 50.000 0.00 0.00 0.00 4.35
941 4227 4.096984 GGCAGTTCTATGAGATGGTTTTGG 59.903 45.833 0.00 0.00 0.00 3.28
1045 4344 2.417924 GGGTAGCGAGGATGCATATGAG 60.418 54.545 6.97 0.00 37.31 2.90
1079 4378 3.587506 CGGGGTCAGGAGGGATTATTAAT 59.412 47.826 0.00 0.00 0.00 1.40
1080 4379 2.976882 CGGGGTCAGGAGGGATTATTAA 59.023 50.000 0.00 0.00 0.00 1.40
1081 4380 2.616524 CGGGGTCAGGAGGGATTATTA 58.383 52.381 0.00 0.00 0.00 0.98
1082 4381 1.435256 CGGGGTCAGGAGGGATTATT 58.565 55.000 0.00 0.00 0.00 1.40
1097 4396 1.889105 CATGATCAACGAGGCGGGG 60.889 63.158 0.00 0.00 0.00 5.73
1187 4515 1.677217 GGGCAAACTGATCTTCTCGCT 60.677 52.381 0.00 0.00 0.00 4.93
1225 4553 2.677836 GCACGCAAATGACCTCTTATCA 59.322 45.455 0.00 0.00 0.00 2.15
1237 4565 2.981560 CTCGCCCTTGCACGCAAAT 61.982 57.895 5.87 0.00 37.32 2.32
1376 4725 6.575083 ATCATACATTTGTCTCGAAGAACG 57.425 37.500 0.00 0.00 44.09 3.95
1400 4750 5.414789 TCAAAAACATCCATCGTAGGAGA 57.585 39.130 4.99 0.00 41.90 3.71
1402 4752 8.568676 TTATTTCAAAAACATCCATCGTAGGA 57.431 30.769 1.29 1.29 43.01 2.94
1407 4757 9.158364 CGTATCTTATTTCAAAAACATCCATCG 57.842 33.333 0.00 0.00 0.00 3.84
1472 4829 4.841422 AGATTGTGCAGAAGCTTATGACT 58.159 39.130 24.73 9.65 42.74 3.41
1498 4855 2.303175 AGGTTCTGATCTAGAGGCGAC 58.697 52.381 0.00 0.00 36.61 5.19
1501 4858 3.005367 GCAGTAGGTTCTGATCTAGAGGC 59.995 52.174 0.00 0.00 36.61 4.70
1502 4859 4.469657 AGCAGTAGGTTCTGATCTAGAGG 58.530 47.826 0.00 0.00 36.61 3.69
1503 4860 6.272318 CAAAGCAGTAGGTTCTGATCTAGAG 58.728 44.000 0.00 0.00 36.61 2.43
1504 4861 5.394663 GCAAAGCAGTAGGTTCTGATCTAGA 60.395 44.000 0.00 0.00 37.61 2.43
1505 4862 4.808364 GCAAAGCAGTAGGTTCTGATCTAG 59.192 45.833 0.00 0.00 37.61 2.43
1506 4863 4.383118 GGCAAAGCAGTAGGTTCTGATCTA 60.383 45.833 0.00 0.00 37.61 1.98
1507 4864 3.604582 GCAAAGCAGTAGGTTCTGATCT 58.395 45.455 0.00 0.00 37.61 2.75
1508 4865 2.680339 GGCAAAGCAGTAGGTTCTGATC 59.320 50.000 0.00 0.00 37.61 2.92
1509 4866 2.716217 GGCAAAGCAGTAGGTTCTGAT 58.284 47.619 0.00 0.00 37.61 2.90
1510 4867 1.608025 CGGCAAAGCAGTAGGTTCTGA 60.608 52.381 0.00 0.00 37.61 3.27
1511 4868 0.798776 CGGCAAAGCAGTAGGTTCTG 59.201 55.000 0.00 0.00 38.35 3.02
1512 4869 0.955919 GCGGCAAAGCAGTAGGTTCT 60.956 55.000 0.00 0.00 33.61 3.01
1513 4870 1.502190 GCGGCAAAGCAGTAGGTTC 59.498 57.895 0.00 0.00 33.61 3.62
1514 4871 1.971695 GGCGGCAAAGCAGTAGGTT 60.972 57.895 3.07 0.00 39.27 3.50
1556 4913 7.414222 TTTCCTGATAATAAGGTACGTCTGT 57.586 36.000 0.00 0.00 36.14 3.41
1557 4914 9.627395 CTATTTCCTGATAATAAGGTACGTCTG 57.373 37.037 0.00 0.00 36.14 3.51
1582 4939 9.892130 CCTTCATTAATCTAGTAGTTTGGTTCT 57.108 33.333 4.07 0.00 0.00 3.01
1592 4949 9.959721 GGGCATATTTCCTTCATTAATCTAGTA 57.040 33.333 0.00 0.00 0.00 1.82
1593 4950 8.673251 AGGGCATATTTCCTTCATTAATCTAGT 58.327 33.333 0.00 0.00 0.00 2.57
1596 4953 8.894592 TCTAGGGCATATTTCCTTCATTAATCT 58.105 33.333 0.00 0.00 34.75 2.40
1597 4954 9.171877 CTCTAGGGCATATTTCCTTCATTAATC 57.828 37.037 0.00 0.00 34.75 1.75
1598 4955 8.112183 CCTCTAGGGCATATTTCCTTCATTAAT 58.888 37.037 0.00 0.00 34.75 1.40
1599 4956 7.461749 CCTCTAGGGCATATTTCCTTCATTAA 58.538 38.462 0.00 0.00 34.75 1.40
1600 4957 7.020827 CCTCTAGGGCATATTTCCTTCATTA 57.979 40.000 0.00 0.00 34.75 1.90
1601 4958 5.885465 CCTCTAGGGCATATTTCCTTCATT 58.115 41.667 0.00 0.00 34.75 2.57
1602 4959 5.511386 CCTCTAGGGCATATTTCCTTCAT 57.489 43.478 0.00 0.00 34.75 2.57
1689 5046 8.402472 CACATGTGTTATGTTTCCGGTTAATAT 58.598 33.333 18.03 4.04 0.00 1.28
1708 5065 7.805700 TGTTTGTCTATGTATTCACACATGTG 58.194 34.615 24.25 24.25 46.91 3.21
1834 5191 7.046652 AGTCAGTCACATCATTCTTCTAATGG 58.953 38.462 0.00 0.00 0.00 3.16
1841 5198 4.999950 GGTCAAGTCAGTCACATCATTCTT 59.000 41.667 0.00 0.00 0.00 2.52
1854 5211 3.629398 GCTAATGGAATGGGTCAAGTCAG 59.371 47.826 0.00 0.00 0.00 3.51
1884 5241 2.613691 AGCAACATACTAAACGACCGG 58.386 47.619 0.00 0.00 0.00 5.28
1887 5244 6.345920 AGCAATAGCAACATACTAAACGAC 57.654 37.500 0.00 0.00 45.49 4.34
2070 5427 5.677319 TCGGAGTGACAAATCCTAATCTT 57.323 39.130 6.43 0.00 33.12 2.40
2118 5475 2.315925 AGTGATGTGCATTACCGAGG 57.684 50.000 0.00 0.00 0.00 4.63
2250 5608 3.627395 ATGTTACTTGCCCGAGATTCA 57.373 42.857 0.00 0.00 0.00 2.57
2343 5701 3.181440 GGAACCTGGATGCTCATATTGGA 60.181 47.826 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.