Multiple sequence alignment - TraesCS3A01G447600

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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 TraesCS3A01G447600 chr3A 100.000 4724 0 0 1 4724 687591885 687596608 0.000000e+00 8724.0
1 TraesCS3A01G447600 chr3A 89.867 1204 86 10 2818 4012 687614129 687615305 0.000000e+00 1515.0
2 TraesCS3A01G447600 chr3A 88.854 314 22 4 4011 4313 687615391 687615702 1.610000e-99 374.0
3 TraesCS3A01G447600 chr3A 92.908 141 6 3 4499 4636 687616307 687616446 8.020000e-48 202.0
4 TraesCS3A01G447600 chr3A 88.679 53 6 0 4305 4357 456443358 456443306 1.100000e-06 65.8
5 TraesCS3A01G447600 chr3B 96.203 3266 94 5 773 4012 730283144 730286405 0.000000e+00 5317.0
6 TraesCS3A01G447600 chr3B 85.919 3004 382 27 774 3754 730309250 730312235 0.000000e+00 3166.0
7 TraesCS3A01G447600 chr3B 86.456 790 63 13 1 771 730282289 730283053 0.000000e+00 826.0
8 TraesCS3A01G447600 chr3B 89.931 288 19 3 4011 4298 730286491 730286768 3.470000e-96 363.0
9 TraesCS3A01G447600 chr3B 93.919 148 7 2 4551 4697 730288440 730288586 6.150000e-54 222.0
10 TraesCS3A01G447600 chr3B 93.814 97 6 0 3916 4012 730312331 730312427 3.810000e-31 147.0
11 TraesCS3A01G447600 chr3D 96.729 3118 87 3 906 4012 550660094 550663207 0.000000e+00 5179.0
12 TraesCS3A01G447600 chr3D 86.012 3024 382 25 774 3776 550668001 550671004 0.000000e+00 3203.0
13 TraesCS3A01G447600 chr3D 88.080 797 57 18 1 773 550659058 550659840 0.000000e+00 911.0
14 TraesCS3A01G447600 chr3D 88.791 339 28 3 4011 4349 550663292 550663620 1.580000e-109 407.0
15 TraesCS3A01G447600 chr3D 94.643 224 9 3 4499 4721 550663689 550663910 1.260000e-90 344.0
16 TraesCS3A01G447600 chr3D 93.478 138 5 2 773 906 550659929 550660066 8.020000e-48 202.0
17 TraesCS3A01G447600 chr4A 78.543 1785 329 37 2012 3778 532216194 532217942 0.000000e+00 1125.0
18 TraesCS3A01G447600 chr2A 79.147 1664 300 33 2123 3772 718119194 718120824 0.000000e+00 1107.0
19 TraesCS3A01G447600 chr2D 88.398 181 18 3 4535 4713 584841441 584841620 1.030000e-51 215.0
20 TraesCS3A01G447600 chr2B 86.559 186 17 7 4532 4713 705222662 705222843 1.040000e-46 198.0


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 TraesCS3A01G447600 chr3A 687591885 687596608 4723 False 8724.0 8724 100.00000 1 4724 1 chr3A.!!$F1 4723
1 TraesCS3A01G447600 chr3A 687614129 687616446 2317 False 697.0 1515 90.54300 2818 4636 3 chr3A.!!$F2 1818
2 TraesCS3A01G447600 chr3B 730282289 730288586 6297 False 1682.0 5317 91.62725 1 4697 4 chr3B.!!$F1 4696
3 TraesCS3A01G447600 chr3B 730309250 730312427 3177 False 1656.5 3166 89.86650 774 4012 2 chr3B.!!$F2 3238
4 TraesCS3A01G447600 chr3D 550668001 550671004 3003 False 3203.0 3203 86.01200 774 3776 1 chr3D.!!$F1 3002
5 TraesCS3A01G447600 chr3D 550659058 550663910 4852 False 1408.6 5179 92.34420 1 4721 5 chr3D.!!$F2 4720
6 TraesCS3A01G447600 chr4A 532216194 532217942 1748 False 1125.0 1125 78.54300 2012 3778 1 chr4A.!!$F1 1766
7 TraesCS3A01G447600 chr2A 718119194 718120824 1630 False 1107.0 1107 79.14700 2123 3772 1 chr2A.!!$F1 1649

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
47 48 0.322816 TCTTTGATGCTGCAGGACCC 60.323 55.000 17.12 9.15 0.00 4.46 F
388 393 0.323360 TCACATGTTGGCTTAGGGGC 60.323 55.000 0.00 0.00 41.27 5.80 F
585 604 1.084289 GTTCCATAGCGGACACAACC 58.916 55.000 0.00 0.00 46.36 3.77 F
2412 2575 1.002773 GTGGCCGAGGAAAACCTAAGA 59.997 52.381 0.00 0.00 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 2068 0.316442 GCGTTGTGATGATGATGCGG 60.316 55.000 0.00 0.0 0.00 5.69 R
2328 2491 0.397941 CAACCCAGAGCCTCACAAGA 59.602 55.000 0.00 0.0 0.00 3.02 R
2471 2634 1.275010 TGTCATGCATCGTACAGGTGT 59.725 47.619 0.00 0.0 32.28 4.16 R
4381 4671 0.100682 TCTACGCTTGCAGACGATCC 59.899 55.000 16.17 0.0 0.00 3.36 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
47 48 0.322816 TCTTTGATGCTGCAGGACCC 60.323 55.000 17.12 9.15 0.00 4.46
89 90 1.600957 GTGAATCATCGGCATGTGAGG 59.399 52.381 0.00 0.00 0.00 3.86
134 135 2.467838 GCCCGATTACTAGTTTCGTCC 58.532 52.381 20.06 10.88 0.00 4.79
138 139 4.142315 CCCGATTACTAGTTTCGTCCTCAA 60.142 45.833 20.06 0.45 0.00 3.02
146 147 6.861144 ACTAGTTTCGTCCTCAATTAGGTAC 58.139 40.000 0.00 0.00 46.62 3.34
161 162 8.726988 TCAATTAGGTACCGATTTTTCTCTTTG 58.273 33.333 6.18 0.00 0.00 2.77
163 164 8.857694 ATTAGGTACCGATTTTTCTCTTTGAA 57.142 30.769 6.18 0.00 0.00 2.69
164 165 8.680039 TTAGGTACCGATTTTTCTCTTTGAAA 57.320 30.769 6.18 0.00 42.33 2.69
254 259 3.009301 TGTCGGAAGAACGAGAAACTC 57.991 47.619 0.00 0.00 44.42 3.01
266 271 1.785430 GAGAAACTCCACGAACACGTC 59.215 52.381 0.00 0.00 38.21 4.34
295 300 4.094830 ACCAGGTTTAATCCTCGTGTTT 57.905 40.909 1.84 0.00 35.37 2.83
316 321 1.537202 GGCTGCAAAGTTAGACACCAG 59.463 52.381 0.50 0.00 0.00 4.00
327 332 4.602259 ACACCAGTGTCGCCGTGG 62.602 66.667 0.00 0.00 40.24 4.94
355 360 8.812513 ATATGACATATTGACATATGGGGTTG 57.187 34.615 7.80 0.00 44.79 3.77
359 364 1.458398 TTGACATATGGGGTTGCACG 58.542 50.000 7.80 0.00 0.00 5.34
388 393 0.323360 TCACATGTTGGCTTAGGGGC 60.323 55.000 0.00 0.00 41.27 5.80
397 402 3.228188 TGGCTTAGGGGCATATCAAAG 57.772 47.619 0.00 0.00 45.79 2.77
398 403 2.513738 TGGCTTAGGGGCATATCAAAGT 59.486 45.455 0.00 0.00 45.79 2.66
442 448 6.074088 GCATATGAGGTTCGACATCTTTGTAG 60.074 42.308 6.97 0.00 35.79 2.74
463 482 3.153919 GCATGTCCCTTTAAGGTGTTCA 58.846 45.455 10.40 4.07 31.93 3.18
464 483 3.572255 GCATGTCCCTTTAAGGTGTTCAA 59.428 43.478 10.40 0.00 31.93 2.69
467 486 6.389906 CATGTCCCTTTAAGGTGTTCAATTC 58.610 40.000 10.40 0.00 31.93 2.17
471 490 4.220602 CCCTTTAAGGTGTTCAATTCTGGG 59.779 45.833 10.40 0.00 31.93 4.45
485 504 7.460214 TCAATTCTGGGGGTGTATTTAGTAT 57.540 36.000 0.00 0.00 0.00 2.12
498 517 7.661847 GGTGTATTTAGTATTCCCTCCTTCATG 59.338 40.741 0.00 0.00 0.00 3.07
525 544 7.704789 AGAACATTTCAATTTTGCTGACTTC 57.295 32.000 0.00 0.00 0.00 3.01
585 604 1.084289 GTTCCATAGCGGACACAACC 58.916 55.000 0.00 0.00 46.36 3.77
685 710 6.371809 TCCTTCGTTCATAATGCCATTTAC 57.628 37.500 0.00 0.00 0.00 2.01
704 729 1.604308 CAGGCCCATGAGCACAACA 60.604 57.895 0.27 0.00 0.00 3.33
920 1073 9.119418 TCTCTCTGAACATATATATGAGCTAGC 57.881 37.037 26.05 6.62 37.15 3.42
933 1086 2.956333 TGAGCTAGCTTGCGACCTAATA 59.044 45.455 20.42 0.00 38.13 0.98
941 1094 4.947388 AGCTTGCGACCTAATATTTTTGGA 59.053 37.500 3.61 0.00 32.72 3.53
948 1101 7.757624 TGCGACCTAATATTTTTGGAATGAAAC 59.242 33.333 3.61 0.00 32.72 2.78
1126 1280 7.282675 ACCTGATTGATCTGAATGACAAGATTC 59.717 37.037 0.00 0.00 33.59 2.52
1140 1294 6.747125 TGACAAGATTCAGCAGATAGAGATC 58.253 40.000 0.00 0.00 0.00 2.75
1316 1470 4.580580 GGAAGAAGGTTTTCTGAAGAAGCA 59.419 41.667 13.11 0.00 42.80 3.91
1325 1479 5.954296 TTTCTGAAGAAGCATTTCCTCAG 57.046 39.130 7.63 7.63 46.40 3.35
1353 1507 4.943705 TCACATTATCTCCTGGTTTTCAGC 59.056 41.667 0.00 0.00 42.05 4.26
1362 1516 4.479158 TCCTGGTTTTCAGCCAAATTACT 58.521 39.130 0.00 0.00 42.05 2.24
1911 2068 3.124297 CACTCCAGAATTCTCGTGAAAGC 59.876 47.826 17.79 0.00 35.63 3.51
2069 2232 4.574013 CCAGCAGTGTCCTGATTATCTTTC 59.426 45.833 0.00 0.00 41.50 2.62
2256 2419 3.834489 AATCTGAGCTACCATGACCTG 57.166 47.619 0.00 0.00 0.00 4.00
2328 2491 1.048601 ACCCAATGTCACGTGAGACT 58.951 50.000 20.73 4.13 39.27 3.24
2412 2575 1.002773 GTGGCCGAGGAAAACCTAAGA 59.997 52.381 0.00 0.00 0.00 2.10
2471 2634 2.305927 GAGATGAACTGGGAAGGGTGAA 59.694 50.000 0.00 0.00 0.00 3.18
2490 2653 2.010145 ACACCTGTACGATGCATGAC 57.990 50.000 2.46 0.00 0.00 3.06
2907 3085 1.331214 AACTGCCAAGTGGGATTGTG 58.669 50.000 0.00 0.00 40.01 3.33
3115 3293 6.169094 AGAACTCTGTGGATTGACAACATAG 58.831 40.000 0.00 0.00 0.00 2.23
3783 3967 0.729116 GGTGCATCCACGTCATTCTG 59.271 55.000 0.00 0.00 43.00 3.02
3792 3976 6.460123 GCATCCACGTCATTCTGGATTTAATT 60.460 38.462 0.46 0.00 43.61 1.40
3848 4040 9.040939 CATTTTGTACTTCCATATCGTGATACA 57.959 33.333 0.00 0.00 0.00 2.29
4040 4319 0.318441 TGCTTGAGTTGAGAGTCCGG 59.682 55.000 0.00 0.00 0.00 5.14
4094 4380 6.033341 TGCAGTGTTTATTGTGTGAAGAAAC 58.967 36.000 0.00 0.00 0.00 2.78
4099 4385 8.303876 AGTGTTTATTGTGTGAAGAAACTGTTT 58.696 29.630 5.29 5.29 32.47 2.83
4131 4417 8.089115 AGTAACAGTAGTTTTGATTCTGCTTC 57.911 34.615 0.00 0.00 39.15 3.86
4157 4443 1.672737 GCTGCTGGGGTTTGTATTTGC 60.673 52.381 0.00 0.00 0.00 3.68
4165 4451 3.059166 GGGTTTGTATTTGCACAGCTTG 58.941 45.455 0.00 0.00 0.00 4.01
4231 4518 3.062466 GCTGGCTTTCCGTTCCCC 61.062 66.667 0.00 0.00 34.14 4.81
4232 4519 2.757077 CTGGCTTTCCGTTCCCCT 59.243 61.111 0.00 0.00 34.14 4.79
4235 4522 1.228459 GGCTTTCCGTTCCCCTTGT 60.228 57.895 0.00 0.00 0.00 3.16
4238 4525 1.435577 CTTTCCGTTCCCCTTGTACG 58.564 55.000 0.00 0.00 35.20 3.67
4244 4531 3.599285 TTCCCCTTGTACGGCTGCG 62.599 63.158 0.00 0.00 0.00 5.18
4299 4589 3.701040 ACCATGATGGGCATTTCAAGTAC 59.299 43.478 17.04 0.00 43.37 2.73
4304 4594 4.887071 TGATGGGCATTTCAAGTACCATAC 59.113 41.667 0.00 0.00 38.72 2.39
4333 4623 2.867156 AGGGTCCCCTTCTTCCGA 59.133 61.111 3.51 0.00 45.70 4.55
4371 4661 2.354539 CCTTGCCGCACCGTTTTG 60.355 61.111 0.00 0.00 0.00 2.44
4373 4663 1.370414 CTTGCCGCACCGTTTTGAG 60.370 57.895 0.00 0.00 0.00 3.02
4379 4669 4.174305 CACCGTTTTGAGGGGCTT 57.826 55.556 0.00 0.00 0.00 4.35
4380 4670 1.956802 CACCGTTTTGAGGGGCTTC 59.043 57.895 0.00 0.00 0.00 3.86
4381 4671 1.599797 ACCGTTTTGAGGGGCTTCG 60.600 57.895 0.00 0.00 0.00 3.79
4382 4672 2.332654 CCGTTTTGAGGGGCTTCGG 61.333 63.158 0.00 0.00 0.00 4.30
4383 4673 1.302192 CGTTTTGAGGGGCTTCGGA 60.302 57.895 0.00 0.00 0.00 4.55
4384 4674 0.676782 CGTTTTGAGGGGCTTCGGAT 60.677 55.000 0.00 0.00 0.00 4.18
4386 4676 0.392461 TTTTGAGGGGCTTCGGATCG 60.392 55.000 0.00 0.00 0.00 3.69
4387 4677 1.550130 TTTGAGGGGCTTCGGATCGT 61.550 55.000 0.00 0.00 0.00 3.73
4389 4679 2.042843 AGGGGCTTCGGATCGTCT 60.043 61.111 0.00 0.00 0.00 4.18
4390 4680 2.107141 GGGGCTTCGGATCGTCTG 59.893 66.667 0.00 0.00 0.00 3.51
4391 4681 2.586357 GGGCTTCGGATCGTCTGC 60.586 66.667 0.00 0.00 0.00 4.26
4392 4682 2.184322 GGCTTCGGATCGTCTGCA 59.816 61.111 0.00 0.00 0.00 4.41
4393 4683 1.447838 GGCTTCGGATCGTCTGCAA 60.448 57.895 0.00 0.00 0.00 4.08
4395 4685 2.002127 CTTCGGATCGTCTGCAAGC 58.998 57.895 0.00 0.00 0.00 4.01
4404 4991 0.448197 CGTCTGCAAGCGTAGAGAGA 59.552 55.000 1.89 0.00 34.21 3.10
4406 4993 0.453793 TCTGCAAGCGTAGAGAGAGC 59.546 55.000 0.00 0.00 29.60 4.09
4441 6234 2.037136 CGTTGGCTTGCAGGAGGAG 61.037 63.158 0.00 0.00 0.00 3.69
4457 6250 3.595173 GAGGAGGAAGAAAGAAGCAGAC 58.405 50.000 0.00 0.00 0.00 3.51
4459 6252 3.070748 GGAGGAAGAAAGAAGCAGACAC 58.929 50.000 0.00 0.00 0.00 3.67
4461 6254 1.195674 GGAAGAAAGAAGCAGACACGC 59.804 52.381 0.00 0.00 0.00 5.34
4478 6271 4.802424 CGAAGCGCAGATGAGAGT 57.198 55.556 11.47 0.00 0.00 3.24
4479 6272 3.041874 CGAAGCGCAGATGAGAGTT 57.958 52.632 11.47 0.00 0.00 3.01
4480 6273 1.354040 CGAAGCGCAGATGAGAGTTT 58.646 50.000 11.47 0.00 0.00 2.66
4481 6274 1.728971 CGAAGCGCAGATGAGAGTTTT 59.271 47.619 11.47 0.00 0.00 2.43
4482 6275 2.158449 CGAAGCGCAGATGAGAGTTTTT 59.842 45.455 11.47 0.00 0.00 1.94
4542 6337 0.752054 GCAGAGGAGGAGATCACCTG 59.248 60.000 17.19 3.78 40.73 4.00
4639 6496 1.269051 CGAGTGGGTTTGTTTTGCTCC 60.269 52.381 0.00 0.00 0.00 4.70
4640 6497 2.031870 GAGTGGGTTTGTTTTGCTCCT 58.968 47.619 0.00 0.00 0.00 3.69
4643 6500 2.093711 GTGGGTTTGTTTTGCTCCTTGT 60.094 45.455 0.00 0.00 0.00 3.16
4657 6514 5.278061 TGCTCCTTGTAGGGTTATCTTAGT 58.722 41.667 0.00 0.00 35.59 2.24
4699 6557 1.056660 GGAAAGAGTGTCAGGGGTGA 58.943 55.000 0.00 0.00 0.00 4.02
4717 6575 3.509184 GGTGACCGGGTATAAGATAGGAC 59.491 52.174 6.32 0.00 0.00 3.85
4718 6576 4.405548 GTGACCGGGTATAAGATAGGACT 58.594 47.826 6.32 0.00 0.00 3.85
4719 6577 5.515534 GGTGACCGGGTATAAGATAGGACTA 60.516 48.000 6.32 0.00 0.00 2.59
4720 6578 5.647225 GTGACCGGGTATAAGATAGGACTAG 59.353 48.000 6.32 0.00 0.00 2.57
4721 6579 5.549228 TGACCGGGTATAAGATAGGACTAGA 59.451 44.000 6.32 0.00 0.00 2.43
4722 6580 6.217074 TGACCGGGTATAAGATAGGACTAGAT 59.783 42.308 6.32 0.00 0.00 1.98
4723 6581 6.661777 ACCGGGTATAAGATAGGACTAGATC 58.338 44.000 6.32 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.098770 GCAGCATCAAAGAAGGGATGAC 59.901 50.000 5.86 0.00 42.73 3.06
134 135 8.494016 AAGAGAAAAATCGGTACCTAATTGAG 57.506 34.615 10.90 0.00 0.00 3.02
138 139 8.857694 TTCAAAGAGAAAAATCGGTACCTAAT 57.142 30.769 10.90 0.19 32.05 1.73
180 183 4.311606 TGCAAGCTGTGAACGAACTAATA 58.688 39.130 0.00 0.00 0.00 0.98
182 185 2.556257 TGCAAGCTGTGAACGAACTAA 58.444 42.857 0.00 0.00 0.00 2.24
186 189 1.675483 ACATTGCAAGCTGTGAACGAA 59.325 42.857 4.94 0.00 0.00 3.85
189 192 2.780065 TCACATTGCAAGCTGTGAAC 57.220 45.000 26.04 0.00 46.41 3.18
222 225 1.953686 CTTCCGACATGTGGTTTTGGT 59.046 47.619 1.15 0.00 0.00 3.67
295 300 1.133945 TGGTGTCTAACTTTGCAGCCA 60.134 47.619 0.00 0.00 0.00 4.75
316 321 2.203015 ATATGGCCACGGCGACAC 60.203 61.111 16.62 0.85 43.06 3.67
320 325 0.320334 TATGTCATATGGCCACGGCG 60.320 55.000 8.16 4.80 43.06 6.46
324 329 7.700505 CATATGTCAATATGTCATATGGCCAC 58.299 38.462 8.16 0.00 44.96 5.01
325 330 7.868906 CATATGTCAATATGTCATATGGCCA 57.131 36.000 8.56 8.56 44.96 5.36
329 334 8.680001 CAACCCCATATGTCAATATGTCATATG 58.320 37.037 20.74 20.74 46.54 1.78
330 335 7.340232 GCAACCCCATATGTCAATATGTCATAT 59.660 37.037 1.24 0.00 42.85 1.78
331 336 6.658816 GCAACCCCATATGTCAATATGTCATA 59.341 38.462 1.24 0.00 42.85 2.15
359 364 1.670674 CCAACATGTGACAGGCATTGC 60.671 52.381 0.00 0.00 0.00 3.56
368 373 1.463674 CCCCTAAGCCAACATGTGAC 58.536 55.000 0.00 0.00 0.00 3.67
370 375 0.611618 TGCCCCTAAGCCAACATGTG 60.612 55.000 0.00 0.00 0.00 3.21
391 396 9.471084 CCGGTACAGAAAAATTAAAACTTTGAT 57.529 29.630 0.00 0.00 0.00 2.57
392 397 7.435784 GCCGGTACAGAAAAATTAAAACTTTGA 59.564 33.333 1.90 0.00 0.00 2.69
393 398 7.222999 TGCCGGTACAGAAAAATTAAAACTTTG 59.777 33.333 1.90 0.00 0.00 2.77
397 402 8.803799 CATATGCCGGTACAGAAAAATTAAAAC 58.196 33.333 1.90 0.00 0.00 2.43
398 403 8.740906 TCATATGCCGGTACAGAAAAATTAAAA 58.259 29.630 1.90 0.00 0.00 1.52
442 448 3.153919 TGAACACCTTAAAGGGACATGC 58.846 45.455 0.00 0.00 40.58 4.06
463 482 7.295340 GGAATACTAAATACACCCCCAGAATT 58.705 38.462 0.00 0.00 0.00 2.17
464 483 6.183361 GGGAATACTAAATACACCCCCAGAAT 60.183 42.308 0.00 0.00 0.00 2.40
467 486 4.663592 AGGGAATACTAAATACACCCCCAG 59.336 45.833 0.00 0.00 33.97 4.45
471 490 6.100714 TGAAGGAGGGAATACTAAATACACCC 59.899 42.308 0.00 0.00 33.78 4.61
498 517 6.703165 AGTCAGCAAAATTGAAATGTTCTTCC 59.297 34.615 0.00 0.00 0.00 3.46
525 544 8.190122 TGGAATAAATAGCTGCAATTGTTACAG 58.810 33.333 7.40 7.21 34.48 2.74
585 604 9.779237 CGTGACTTACTTAATCGCTTAAATATG 57.221 33.333 0.00 0.00 0.00 1.78
653 678 8.592155 GGCATTATGAACGAAGGAAAATTTAAC 58.408 33.333 0.00 0.00 0.00 2.01
685 710 2.036098 TTGTGCTCATGGGCCTGG 59.964 61.111 16.70 0.00 0.00 4.45
913 1051 2.517650 ATTAGGTCGCAAGCTAGCTC 57.482 50.000 19.65 5.43 36.85 4.09
920 1073 7.479980 TCATTCCAAAAATATTAGGTCGCAAG 58.520 34.615 0.00 0.00 0.00 4.01
933 1086 6.096695 CGATAACCGGTTTCATTCCAAAAAT 58.903 36.000 27.64 7.91 33.91 1.82
941 1094 2.027007 TGGGACGATAACCGGTTTCATT 60.027 45.455 27.64 8.08 43.93 2.57
948 1101 3.310501 GTGTTAAATGGGACGATAACCGG 59.689 47.826 0.00 0.00 43.93 5.28
1039 1193 4.439289 GGCAACCTCATCAGCTAAAACATC 60.439 45.833 0.00 0.00 0.00 3.06
1083 1237 7.232534 TCAATCAGGTTACCAACTTTTGCTAAT 59.767 33.333 3.51 0.00 0.00 1.73
1126 1280 6.202570 GCTTTTAACTGGATCTCTATCTGCTG 59.797 42.308 0.00 0.00 32.29 4.41
1131 1285 7.220030 TCATGGCTTTTAACTGGATCTCTATC 58.780 38.462 0.00 0.00 0.00 2.08
1140 1294 3.980775 CGTTGTTCATGGCTTTTAACTGG 59.019 43.478 0.00 0.00 0.00 4.00
1325 1479 5.559148 AACCAGGAGATAATGTGATCCTC 57.441 43.478 0.00 0.00 40.23 3.71
1353 1507 7.331026 TCTTGACTACCTCATCAGTAATTTGG 58.669 38.462 0.00 0.00 0.00 3.28
1362 1516 6.775142 CCTTCTCTATCTTGACTACCTCATCA 59.225 42.308 0.00 0.00 0.00 3.07
1674 1831 1.134220 GTCTGAGACACAACCACCCAA 60.134 52.381 7.90 0.00 32.09 4.12
1911 2068 0.316442 GCGTTGTGATGATGATGCGG 60.316 55.000 0.00 0.00 0.00 5.69
2069 2232 8.594881 ATGAACTATAGATTTAGCAGTTTCCG 57.405 34.615 6.78 0.00 29.89 4.30
2256 2419 2.611722 GCAGTTTCTGAGGTCTCCAGAC 60.612 54.545 0.00 0.00 40.05 3.51
2328 2491 0.397941 CAACCCAGAGCCTCACAAGA 59.602 55.000 0.00 0.00 0.00 3.02
2412 2575 3.181487 GCATATTGCGGTGGATCAGTTTT 60.181 43.478 0.00 0.00 31.71 2.43
2471 2634 1.275010 TGTCATGCATCGTACAGGTGT 59.725 47.619 0.00 0.00 32.28 4.16
2490 2653 1.703438 GAGCCAGCTCTCGCACAATG 61.703 60.000 12.42 0.00 39.80 2.82
2907 3085 2.605366 GTGCCGTAGATTCTTGAGCTTC 59.395 50.000 0.00 0.00 0.00 3.86
3115 3293 1.727511 TTTGCACACTCAGCAGCACC 61.728 55.000 0.00 0.00 43.75 5.01
3848 4040 6.183360 ACACCGACATTTTCAGAACAGAAATT 60.183 34.615 0.00 0.00 37.35 1.82
3914 4106 7.935338 AGTTTTACAGCATGAAACTGAAATG 57.065 32.000 8.27 0.00 40.35 2.32
4040 4319 1.148498 CCTACCAAATCCCGCCTCC 59.852 63.158 0.00 0.00 0.00 4.30
4157 4443 4.082300 ACAGTAGAGATCAGTCAAGCTGTG 60.082 45.833 0.00 0.00 45.23 3.66
4353 4643 4.279043 AAAACGGTGCGGCAAGGC 62.279 61.111 3.23 0.00 0.00 4.35
4354 4644 2.354539 CAAAACGGTGCGGCAAGG 60.355 61.111 3.23 1.58 0.00 3.61
4355 4645 1.370414 CTCAAAACGGTGCGGCAAG 60.370 57.895 3.23 4.53 0.00 4.01
4358 4648 4.038080 CCCTCAAAACGGTGCGGC 62.038 66.667 0.00 0.00 0.00 6.53
4360 4650 4.038080 GCCCCTCAAAACGGTGCG 62.038 66.667 0.00 0.00 0.00 5.34
4361 4651 2.142357 GAAGCCCCTCAAAACGGTGC 62.142 60.000 0.00 0.00 0.00 5.01
4362 4652 1.852067 CGAAGCCCCTCAAAACGGTG 61.852 60.000 0.00 0.00 0.00 4.94
4363 4653 1.599797 CGAAGCCCCTCAAAACGGT 60.600 57.895 0.00 0.00 0.00 4.83
4365 4655 0.676782 ATCCGAAGCCCCTCAAAACG 60.677 55.000 0.00 0.00 0.00 3.60
4366 4656 1.095600 GATCCGAAGCCCCTCAAAAC 58.904 55.000 0.00 0.00 0.00 2.43
4367 4657 0.392461 CGATCCGAAGCCCCTCAAAA 60.392 55.000 0.00 0.00 0.00 2.44
4368 4658 1.220749 CGATCCGAAGCCCCTCAAA 59.779 57.895 0.00 0.00 0.00 2.69
4369 4659 1.956629 GACGATCCGAAGCCCCTCAA 61.957 60.000 0.00 0.00 0.00 3.02
4371 4661 2.128507 AGACGATCCGAAGCCCCTC 61.129 63.158 0.00 0.00 0.00 4.30
4373 4663 2.107141 CAGACGATCCGAAGCCCC 59.893 66.667 0.00 0.00 0.00 5.80
4378 4668 1.805539 CGCTTGCAGACGATCCGAA 60.806 57.895 4.58 0.00 0.00 4.30
4379 4669 1.650314 TACGCTTGCAGACGATCCGA 61.650 55.000 16.17 0.00 0.00 4.55
4380 4670 1.202973 CTACGCTTGCAGACGATCCG 61.203 60.000 16.17 2.06 0.00 4.18
4381 4671 0.100682 TCTACGCTTGCAGACGATCC 59.899 55.000 16.17 0.00 0.00 3.36
4382 4672 1.064208 TCTCTACGCTTGCAGACGATC 59.936 52.381 16.17 0.00 0.00 3.69
4383 4673 1.064803 CTCTCTACGCTTGCAGACGAT 59.935 52.381 16.17 4.61 0.00 3.73
4384 4674 0.448197 CTCTCTACGCTTGCAGACGA 59.552 55.000 16.17 1.14 0.00 4.20
4386 4676 1.797348 GCTCTCTCTACGCTTGCAGAC 60.797 57.143 0.00 0.00 0.00 3.51
4387 4677 0.453793 GCTCTCTCTACGCTTGCAGA 59.546 55.000 0.00 0.00 0.00 4.26
4389 4679 0.172127 CTGCTCTCTCTACGCTTGCA 59.828 55.000 0.00 0.00 0.00 4.08
4390 4680 1.145162 GCTGCTCTCTCTACGCTTGC 61.145 60.000 0.00 0.00 0.00 4.01
4391 4681 0.172127 TGCTGCTCTCTCTACGCTTG 59.828 55.000 0.00 0.00 0.00 4.01
4392 4682 0.455410 CTGCTGCTCTCTCTACGCTT 59.545 55.000 0.00 0.00 0.00 4.68
4393 4683 1.383456 CCTGCTGCTCTCTCTACGCT 61.383 60.000 0.00 0.00 0.00 5.07
4395 4685 0.662619 CTCCTGCTGCTCTCTCTACG 59.337 60.000 0.00 0.00 0.00 3.51
4406 4993 2.510238 GTACGCCTGCTCCTGCTG 60.510 66.667 0.00 0.00 40.48 4.41
4441 6234 1.195674 GCGTGTCTGCTTCTTTCTTCC 59.804 52.381 0.00 0.00 0.00 3.46
4461 6254 1.354040 AAACTCTCATCTGCGCTTCG 58.646 50.000 9.73 0.00 0.00 3.79
4485 6278 2.943036 AACTCTCGTGGCCCTAAAAA 57.057 45.000 0.00 0.00 0.00 1.94
4486 6279 4.563140 AATAACTCTCGTGGCCCTAAAA 57.437 40.909 0.00 0.00 0.00 1.52
4487 6280 4.563140 AAATAACTCTCGTGGCCCTAAA 57.437 40.909 0.00 0.00 0.00 1.85
4488 6281 4.563140 AAAATAACTCTCGTGGCCCTAA 57.437 40.909 0.00 0.00 0.00 2.69
4489 6282 4.563140 AAAAATAACTCTCGTGGCCCTA 57.437 40.909 0.00 0.00 0.00 3.53
4558 6414 2.419620 CACGGCCCACAAAAACCC 59.580 61.111 0.00 0.00 0.00 4.11
4639 6496 9.159364 GGTACAAAACTAAGATAACCCTACAAG 57.841 37.037 0.00 0.00 0.00 3.16
4640 6497 8.658619 TGGTACAAAACTAAGATAACCCTACAA 58.341 33.333 0.00 0.00 31.92 2.41
4643 6500 8.204903 TGTGGTACAAAACTAAGATAACCCTA 57.795 34.615 0.00 0.00 44.16 3.53
4657 6514 2.264005 ACAGCCGATGTGGTACAAAA 57.736 45.000 0.00 0.00 44.16 2.44
4699 6557 6.655376 ATCTAGTCCTATCTTATACCCGGT 57.345 41.667 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.