Multiple sequence alignment - TraesCS2A01G212900

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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 TraesCS2A01G212900 chr2A 100.000 4124 0 0 1 4124 197567174 197563051 0.000000e+00 7616.0
1 TraesCS2A01G212900 chr2A 95.887 2407 95 3 1719 4124 197336140 197333737 0.000000e+00 3893.0
2 TraesCS2A01G212900 chr2A 91.169 2627 199 14 606 3218 166627709 166630316 0.000000e+00 3535.0
3 TraesCS2A01G212900 chr2A 90.552 1069 66 17 658 1720 197344858 197343819 0.000000e+00 1382.0
4 TraesCS2A01G212900 chr2A 88.173 761 65 10 3365 4124 166631166 166631902 0.000000e+00 883.0
5 TraesCS2A01G212900 chr2A 82.963 405 36 13 3722 4124 447944655 447944282 6.610000e-88 335.0
6 TraesCS2A01G212900 chr2A 84.397 282 31 10 595 868 166254198 166254474 8.790000e-67 265.0
7 TraesCS2A01G212900 chr2A 91.566 166 10 3 408 573 197345558 197345397 4.150000e-55 226.0
8 TraesCS2A01G212900 chr2A 91.228 114 9 1 204 317 197576000 197575888 1.990000e-33 154.0
9 TraesCS2A01G212900 chr2A 90.000 110 11 0 312 421 120719746 120719855 4.300000e-30 143.0
10 TraesCS2A01G212900 chr2A 93.750 80 5 0 2 81 197346819 197346740 2.010000e-23 121.0
11 TraesCS2A01G212900 chr2A 97.297 37 1 0 286 322 197346096 197346060 3.440000e-06 63.9
12 TraesCS2A01G212900 chr2D 96.340 3634 94 18 421 4052 182576461 182572865 0.000000e+00 5938.0
13 TraesCS2A01G212900 chr2D 91.336 2747 198 22 492 3218 156706962 156709688 0.000000e+00 3718.0
14 TraesCS2A01G212900 chr2D 87.648 761 60 11 3365 4124 156710547 156711274 0.000000e+00 854.0
15 TraesCS2A01G212900 chr2D 91.139 316 22 6 1 313 182576776 182576464 1.370000e-114 424.0
16 TraesCS2A01G212900 chr2D 82.562 281 33 12 599 868 156591781 156592056 2.480000e-57 233.0
17 TraesCS2A01G212900 chr2D 88.696 115 11 2 308 421 423290432 423290319 5.560000e-29 139.0
18 TraesCS2A01G212900 chr2B 91.111 2655 192 24 499 3145 214280671 214283289 0.000000e+00 3555.0
19 TraesCS2A01G212900 chr2B 90.923 2666 176 40 571 3218 214312540 214315157 0.000000e+00 3522.0
20 TraesCS2A01G212900 chr2B 87.664 762 61 10 3365 4124 214315993 214316723 0.000000e+00 856.0
21 TraesCS2A01G212900 chr2B 89.873 79 7 1 492 569 214312424 214312502 2.620000e-17 100.0
22 TraesCS2A01G212900 chr1B 90.143 2587 191 39 598 3169 148416653 148414116 0.000000e+00 3306.0
23 TraesCS2A01G212900 chr1D 89.712 2605 203 37 587 3169 93105558 93102997 0.000000e+00 3265.0
24 TraesCS2A01G212900 chr1D 90.000 110 11 0 315 424 458310934 458310825 4.300000e-30 143.0
25 TraesCS2A01G212900 chr1A 92.450 2212 156 5 962 3169 90163536 90161332 0.000000e+00 3149.0
26 TraesCS2A01G212900 chr5A 91.743 109 9 0 314 422 597799285 597799177 7.140000e-33 152.0
27 TraesCS2A01G212900 chr5A 89.655 116 11 1 308 422 448850240 448850355 3.320000e-31 147.0
28 TraesCS2A01G212900 chr5A 90.654 107 10 0 315 421 664849494 664849600 4.300000e-30 143.0
29 TraesCS2A01G212900 chr6A 90.741 108 10 0 314 421 100813399 100813506 1.190000e-30 145.0
30 TraesCS2A01G212900 chr6A 90.741 108 10 0 314 421 120966003 120965896 1.190000e-30 145.0
31 TraesCS2A01G212900 chr7A 90.654 107 10 0 315 421 646552518 646552624 4.300000e-30 143.0


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 TraesCS2A01G212900 chr2A 197563051 197567174 4123 True 7616.000000 7616 100.000000 1 4124 1 chr2A.!!$R2 4123
1 TraesCS2A01G212900 chr2A 197333737 197336140 2403 True 3893.000000 3893 95.887000 1719 4124 1 chr2A.!!$R1 2405
2 TraesCS2A01G212900 chr2A 166627709 166631902 4193 False 2209.000000 3535 89.671000 606 4124 2 chr2A.!!$F3 3518
3 TraesCS2A01G212900 chr2A 197343819 197346819 3000 True 448.225000 1382 93.291250 2 1720 4 chr2A.!!$R5 1718
4 TraesCS2A01G212900 chr2D 182572865 182576776 3911 True 3181.000000 5938 93.739500 1 4052 2 chr2D.!!$R2 4051
5 TraesCS2A01G212900 chr2D 156706962 156711274 4312 False 2286.000000 3718 89.492000 492 4124 2 chr2D.!!$F2 3632
6 TraesCS2A01G212900 chr2B 214280671 214283289 2618 False 3555.000000 3555 91.111000 499 3145 1 chr2B.!!$F1 2646
7 TraesCS2A01G212900 chr2B 214312424 214316723 4299 False 1492.666667 3522 89.486667 492 4124 3 chr2B.!!$F2 3632
8 TraesCS2A01G212900 chr1B 148414116 148416653 2537 True 3306.000000 3306 90.143000 598 3169 1 chr1B.!!$R1 2571
9 TraesCS2A01G212900 chr1D 93102997 93105558 2561 True 3265.000000 3265 89.712000 587 3169 1 chr1D.!!$R1 2582
10 TraesCS2A01G212900 chr1A 90161332 90163536 2204 True 3149.000000 3149 92.450000 962 3169 1 chr1A.!!$R1 2207

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
689 2054 0.325203 ACCCAACCTTTGTGCCAAGT 60.325 50.000 0.0 0.0 0.00 3.16 F
690 2055 0.389025 CCCAACCTTTGTGCCAAGTC 59.611 55.000 0.0 0.0 0.00 3.01 F
1011 2434 1.070445 CAAACCAATGGCCGCCAAA 59.930 52.632 18.0 0.0 36.95 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 3322 1.302832 GTCCAGGGTGGTGCTTCAG 60.303 63.158 0.00 0.0 39.03 3.02 R
2949 4377 1.740296 GCGCATGAACCGGTACAGT 60.740 57.895 8.00 0.0 0.00 3.55 R
3226 4731 1.939934 TGCATGGCGCTACAAGTATTC 59.060 47.619 7.64 0.0 43.06 1.75 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
81 83 6.015519 TGGTTATGCAAAGCTGAGTATTGTTT 60.016 34.615 0.00 0.00 0.00 2.83
84 86 4.609947 TGCAAAGCTGAGTATTGTTTGTG 58.390 39.130 0.00 0.00 31.96 3.33
89 121 7.612266 CAAAGCTGAGTATTGTTTGTGTTTTC 58.388 34.615 0.00 0.00 0.00 2.29
103 135 4.367450 TGTGTTTTCTGTTTTGGCTATGC 58.633 39.130 0.00 0.00 0.00 3.14
116 148 1.671556 GGCTATGCAAAACCCGTTTGG 60.672 52.381 0.00 0.00 45.79 3.28
132 164 6.505272 CCCGTTTGGTGTTTTATTTTGAGTA 58.495 36.000 0.00 0.00 0.00 2.59
178 212 1.259507 TCGAAAAAGCAAACTCGTCCG 59.740 47.619 0.00 0.00 33.15 4.79
182 216 4.376615 CGAAAAAGCAAACTCGTCCGAATA 60.377 41.667 0.00 0.00 0.00 1.75
198 232 3.259064 CGAATATCCCGTGTGAACTTGT 58.741 45.455 0.00 0.00 0.00 3.16
202 236 0.528901 TCCCGTGTGAACTTGTCGTG 60.529 55.000 0.00 0.00 0.00 4.35
226 260 3.703556 TCAAGTCATGGTCAAAAAGCCAA 59.296 39.130 0.00 0.00 38.38 4.52
255 289 1.095600 CAGAGCTCCGCTACAGTACA 58.904 55.000 10.93 0.00 39.88 2.90
319 762 4.453751 AGAATCAGACTAGGACGTACTCC 58.546 47.826 1.79 0.00 39.81 3.85
322 765 2.170187 TCAGACTAGGACGTACTCCCTC 59.830 54.545 1.79 0.00 40.53 4.30
323 766 1.490069 AGACTAGGACGTACTCCCTCC 59.510 57.143 1.79 0.00 40.53 4.30
327 770 0.679321 AGGACGTACTCCCTCCGTTC 60.679 60.000 0.00 0.00 40.53 3.95
329 772 0.962356 GACGTACTCCCTCCGTTCCA 60.962 60.000 0.00 0.00 34.51 3.53
330 773 0.540365 ACGTACTCCCTCCGTTCCAA 60.540 55.000 0.00 0.00 0.00 3.53
331 774 0.604578 CGTACTCCCTCCGTTCCAAA 59.395 55.000 0.00 0.00 0.00 3.28
335 778 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
338 781 4.533311 ACTCCCTCCGTTCCAAATTACTTA 59.467 41.667 0.00 0.00 0.00 2.24
339 782 5.191124 ACTCCCTCCGTTCCAAATTACTTAT 59.809 40.000 0.00 0.00 0.00 1.73
340 783 5.677567 TCCCTCCGTTCCAAATTACTTATC 58.322 41.667 0.00 0.00 0.00 1.75
342 785 5.296035 CCCTCCGTTCCAAATTACTTATCAC 59.704 44.000 0.00 0.00 0.00 3.06
343 786 5.006358 CCTCCGTTCCAAATTACTTATCACG 59.994 44.000 0.00 0.00 0.00 4.35
344 787 4.871557 TCCGTTCCAAATTACTTATCACGG 59.128 41.667 0.00 0.00 44.80 4.94
345 788 4.034742 CCGTTCCAAATTACTTATCACGGG 59.965 45.833 0.00 0.00 40.76 5.28
346 789 4.632688 CGTTCCAAATTACTTATCACGGGT 59.367 41.667 0.00 0.00 0.00 5.28
347 790 5.811613 CGTTCCAAATTACTTATCACGGGTA 59.188 40.000 0.00 0.00 0.00 3.69
348 791 6.480981 CGTTCCAAATTACTTATCACGGGTAT 59.519 38.462 0.00 0.00 0.00 2.73
349 792 7.517734 CGTTCCAAATTACTTATCACGGGTATG 60.518 40.741 0.00 0.00 0.00 2.39
350 793 7.127012 TCCAAATTACTTATCACGGGTATGA 57.873 36.000 0.00 0.00 0.00 2.15
351 794 7.566569 TCCAAATTACTTATCACGGGTATGAA 58.433 34.615 0.00 0.00 30.82 2.57
352 795 8.215050 TCCAAATTACTTATCACGGGTATGAAT 58.785 33.333 0.00 0.00 30.82 2.57
357 800 9.871238 ATTACTTATCACGGGTATGAATGTATC 57.129 33.333 0.00 0.00 30.82 2.24
358 801 7.540474 ACTTATCACGGGTATGAATGTATCT 57.460 36.000 0.00 0.00 30.82 1.98
359 802 8.645814 ACTTATCACGGGTATGAATGTATCTA 57.354 34.615 0.00 0.00 30.82 1.98
360 803 9.085645 ACTTATCACGGGTATGAATGTATCTAA 57.914 33.333 0.00 0.00 30.82 2.10
361 804 9.923143 CTTATCACGGGTATGAATGTATCTAAA 57.077 33.333 0.00 0.00 30.82 1.85
363 806 8.777865 ATCACGGGTATGAATGTATCTAAATG 57.222 34.615 0.00 0.00 30.82 2.32
364 807 7.732025 TCACGGGTATGAATGTATCTAAATGT 58.268 34.615 0.00 0.00 0.00 2.71
365 808 8.862085 TCACGGGTATGAATGTATCTAAATGTA 58.138 33.333 0.00 0.00 0.00 2.29
394 837 6.957150 AGTTCTAGATACGTCCATTTCTACG 58.043 40.000 0.00 0.00 44.47 3.51
396 839 6.536731 TCTAGATACGTCCATTTCTACGAC 57.463 41.667 0.00 0.00 41.55 4.34
399 842 5.579718 AGATACGTCCATTTCTACGACAAG 58.420 41.667 0.00 0.00 41.55 3.16
400 843 3.655276 ACGTCCATTTCTACGACAAGT 57.345 42.857 1.45 0.00 41.55 3.16
401 844 4.771590 ACGTCCATTTCTACGACAAGTA 57.228 40.909 1.45 0.00 41.55 2.24
403 846 5.717119 ACGTCCATTTCTACGACAAGTAAT 58.283 37.500 1.45 0.00 41.55 1.89
404 847 6.161381 ACGTCCATTTCTACGACAAGTAATT 58.839 36.000 1.45 0.00 41.55 1.40
405 848 6.647895 ACGTCCATTTCTACGACAAGTAATTT 59.352 34.615 1.45 0.00 41.55 1.82
406 849 6.953743 CGTCCATTTCTACGACAAGTAATTTG 59.046 38.462 0.00 0.00 41.55 2.32
412 1271 6.978343 TCTACGACAAGTAATTTGGAATGG 57.022 37.500 0.00 0.00 41.25 3.16
474 1333 4.689705 TGGAACAATAATGGGAGCTCATCC 60.690 45.833 17.19 9.15 41.74 3.51
486 1345 1.007721 AGCTCATCCCTGTACCAGACT 59.992 52.381 0.00 0.00 32.44 3.24
487 1346 1.834263 GCTCATCCCTGTACCAGACTT 59.166 52.381 0.00 0.00 32.44 3.01
488 1347 2.419297 GCTCATCCCTGTACCAGACTTG 60.419 54.545 0.00 0.00 32.44 3.16
489 1348 3.099905 CTCATCCCTGTACCAGACTTGA 58.900 50.000 0.00 0.00 32.44 3.02
495 1359 6.442541 TCCCTGTACCAGACTTGATAAAAA 57.557 37.500 0.00 0.00 32.44 1.94
622 1555 2.016704 GTATCCCATCGTCGCAGCG 61.017 63.158 9.06 9.06 0.00 5.18
685 2050 1.334384 ACCAACCCAACCTTTGTGCC 61.334 55.000 0.00 0.00 0.00 5.01
686 2051 1.333636 CCAACCCAACCTTTGTGCCA 61.334 55.000 0.00 0.00 0.00 4.92
687 2052 0.539051 CAACCCAACCTTTGTGCCAA 59.461 50.000 0.00 0.00 0.00 4.52
688 2053 0.829990 AACCCAACCTTTGTGCCAAG 59.170 50.000 0.00 0.00 0.00 3.61
689 2054 0.325203 ACCCAACCTTTGTGCCAAGT 60.325 50.000 0.00 0.00 0.00 3.16
690 2055 0.389025 CCCAACCTTTGTGCCAAGTC 59.611 55.000 0.00 0.00 0.00 3.01
772 2157 3.046087 CCTGCGTGCAGTCCACTG 61.046 66.667 19.58 2.06 46.40 3.66
922 2317 2.404215 CTGACACAGTAAAGACCACCG 58.596 52.381 0.00 0.00 0.00 4.94
944 2364 2.352342 GTCTGTACTCTGTACTCGAGCC 59.648 54.545 13.61 3.82 31.71 4.70
953 2373 1.282447 TGTACTCGAGCCCTTCTCTCT 59.718 52.381 13.61 0.00 39.70 3.10
954 2374 1.944709 GTACTCGAGCCCTTCTCTCTC 59.055 57.143 13.61 0.00 39.70 3.20
960 2380 1.188219 AGCCCTTCTCTCTCGCAACA 61.188 55.000 0.00 0.00 0.00 3.33
1011 2434 1.070445 CAAACCAATGGCCGCCAAA 59.930 52.632 18.00 0.00 36.95 3.28
1222 2649 2.431683 GTGCCAGGGTGAAGCTCA 59.568 61.111 0.00 0.00 0.00 4.26
1299 2726 1.153628 GAACGGCACCGACAGCTAT 60.154 57.895 17.40 0.00 42.83 2.97
1894 3322 1.802960 CTGACCATCTGACACACAAGC 59.197 52.381 0.00 0.00 0.00 4.01
2838 4266 2.687425 GTTTGCCAAGGTTGCCAAATTT 59.313 40.909 2.54 0.00 0.00 1.82
2949 4377 0.752658 CTGACTGCCGATCATACCCA 59.247 55.000 0.00 0.00 0.00 4.51
2962 4390 1.551430 CATACCCACTGTACCGGTTCA 59.449 52.381 15.04 14.25 30.62 3.18
3567 5745 8.306038 CAGAAACATTAATTGGGATGAACTGAA 58.694 33.333 0.00 0.00 0.00 3.02
3587 5766 6.214412 ACTGAAGGAAAGATAGGTTGATGACT 59.786 38.462 0.00 0.00 0.00 3.41
3588 5767 7.020827 TGAAGGAAAGATAGGTTGATGACTT 57.979 36.000 0.00 0.00 0.00 3.01
3766 5945 8.764287 CAGAAAACCAAACATATCAAAAACCTC 58.236 33.333 0.00 0.00 0.00 3.85
3792 5971 4.102524 AGTTAATACGGGGATCAATCTGCA 59.897 41.667 0.00 0.00 0.00 4.41
3859 6039 4.023536 GCCTGAAACAATCCGTGAGTTAAA 60.024 41.667 0.00 0.00 0.00 1.52
4087 6279 2.229675 TGGCTACATCATGAGAAGCG 57.770 50.000 16.21 0.61 0.00 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 44 5.911752 TGCATAACCAAAACACAAATCACT 58.088 33.333 0.00 0.00 0.00 3.41
46 48 5.821995 AGCTTTGCATAACCAAAACACAAAT 59.178 32.000 0.00 0.00 34.59 2.32
81 83 4.142071 TGCATAGCCAAAACAGAAAACACA 60.142 37.500 0.00 0.00 0.00 3.72
84 86 5.982465 TTTGCATAGCCAAAACAGAAAAC 57.018 34.783 0.00 0.00 32.20 2.43
153 187 6.084277 GGACGAGTTTGCTTTTTCGATAAAT 58.916 36.000 1.40 0.00 36.89 1.40
155 189 4.376615 CGGACGAGTTTGCTTTTTCGATAA 60.377 41.667 7.93 0.00 36.89 1.75
157 191 2.096417 CGGACGAGTTTGCTTTTTCGAT 60.096 45.455 7.93 0.00 36.89 3.59
158 192 1.259507 CGGACGAGTTTGCTTTTTCGA 59.740 47.619 7.93 0.00 36.89 3.71
159 193 1.259507 TCGGACGAGTTTGCTTTTTCG 59.740 47.619 0.00 0.00 38.88 3.46
160 194 3.328237 TTCGGACGAGTTTGCTTTTTC 57.672 42.857 0.00 0.00 0.00 2.29
166 200 1.865340 GGGATATTCGGACGAGTTTGC 59.135 52.381 0.00 0.00 0.00 3.68
178 212 3.306166 CGACAAGTTCACACGGGATATTC 59.694 47.826 0.00 0.00 0.00 1.75
182 216 0.391597 ACGACAAGTTCACACGGGAT 59.608 50.000 0.00 0.00 0.00 3.85
198 232 2.900716 TGACCATGACTTGAACACGA 57.099 45.000 0.00 0.00 0.00 4.35
202 236 4.051237 GGCTTTTTGACCATGACTTGAAC 58.949 43.478 0.00 0.00 0.00 3.18
226 260 0.814457 CGGAGCTCTGACTTACAGCT 59.186 55.000 18.26 0.00 45.38 4.24
255 289 2.358898 GTCCTTCGCAAATGCATGGTAT 59.641 45.455 0.00 0.00 42.21 2.73
319 762 5.006358 CGTGATAAGTAATTTGGAACGGAGG 59.994 44.000 0.00 0.00 0.00 4.30
322 765 4.034742 CCCGTGATAAGTAATTTGGAACGG 59.965 45.833 10.36 10.36 45.71 4.44
323 766 4.632688 ACCCGTGATAAGTAATTTGGAACG 59.367 41.667 0.00 0.00 0.00 3.95
327 770 7.795482 TTCATACCCGTGATAAGTAATTTGG 57.205 36.000 0.00 0.00 0.00 3.28
329 772 8.974060 ACATTCATACCCGTGATAAGTAATTT 57.026 30.769 0.00 0.00 0.00 1.82
331 774 9.871238 GATACATTCATACCCGTGATAAGTAAT 57.129 33.333 0.00 0.00 0.00 1.89
335 778 9.923143 TTTAGATACATTCATACCCGTGATAAG 57.077 33.333 0.00 0.00 0.00 1.73
338 781 8.375506 ACATTTAGATACATTCATACCCGTGAT 58.624 33.333 0.00 0.00 0.00 3.06
339 782 7.732025 ACATTTAGATACATTCATACCCGTGA 58.268 34.615 0.00 0.00 0.00 4.35
340 783 7.962964 ACATTTAGATACATTCATACCCGTG 57.037 36.000 0.00 0.00 0.00 4.94
369 812 7.928167 TCGTAGAAATGGACGTATCTAGAACTA 59.072 37.037 0.00 0.00 0.00 2.24
370 813 6.765036 TCGTAGAAATGGACGTATCTAGAACT 59.235 38.462 0.00 0.00 0.00 3.01
371 814 6.850317 GTCGTAGAAATGGACGTATCTAGAAC 59.150 42.308 0.00 0.00 39.69 3.01
372 815 6.539826 TGTCGTAGAAATGGACGTATCTAGAA 59.460 38.462 0.00 0.00 39.69 2.10
373 816 6.051074 TGTCGTAGAAATGGACGTATCTAGA 58.949 40.000 0.00 0.00 39.69 2.43
374 817 6.296365 TGTCGTAGAAATGGACGTATCTAG 57.704 41.667 0.00 0.00 39.69 2.43
376 819 5.125097 ACTTGTCGTAGAAATGGACGTATCT 59.875 40.000 0.00 0.00 39.69 1.98
377 820 5.338365 ACTTGTCGTAGAAATGGACGTATC 58.662 41.667 0.00 0.00 39.69 2.24
378 821 5.320549 ACTTGTCGTAGAAATGGACGTAT 57.679 39.130 0.00 0.00 39.69 3.06
379 822 4.771590 ACTTGTCGTAGAAATGGACGTA 57.228 40.909 0.00 0.00 39.69 3.57
380 823 3.655276 ACTTGTCGTAGAAATGGACGT 57.345 42.857 0.00 0.00 39.69 4.34
381 824 6.642683 AATTACTTGTCGTAGAAATGGACG 57.357 37.500 0.00 0.00 39.69 4.79
382 825 7.118680 TCCAAATTACTTGTCGTAGAAATGGAC 59.881 37.037 0.00 0.00 39.69 4.02
383 826 7.162761 TCCAAATTACTTGTCGTAGAAATGGA 58.837 34.615 0.00 0.00 39.69 3.41
384 827 7.372451 TCCAAATTACTTGTCGTAGAAATGG 57.628 36.000 0.00 0.00 39.69 3.16
385 828 9.277565 CATTCCAAATTACTTGTCGTAGAAATG 57.722 33.333 0.00 0.00 39.69 2.32
386 829 8.458843 CCATTCCAAATTACTTGTCGTAGAAAT 58.541 33.333 0.00 0.00 39.69 2.17
388 831 7.162761 TCCATTCCAAATTACTTGTCGTAGAA 58.837 34.615 0.00 0.00 39.69 2.10
390 833 6.037172 CCTCCATTCCAAATTACTTGTCGTAG 59.963 42.308 0.00 0.00 32.65 3.51
392 835 4.700213 CCTCCATTCCAAATTACTTGTCGT 59.300 41.667 0.00 0.00 32.65 4.34
393 836 4.941263 TCCTCCATTCCAAATTACTTGTCG 59.059 41.667 0.00 0.00 32.65 4.35
394 837 6.434340 ACTTCCTCCATTCCAAATTACTTGTC 59.566 38.462 0.00 0.00 32.65 3.18
396 839 6.840780 ACTTCCTCCATTCCAAATTACTTG 57.159 37.500 0.00 0.00 34.52 3.16
399 842 6.424032 AGGTACTTCCTCCATTCCAAATTAC 58.576 40.000 0.00 0.00 44.42 1.89
400 843 6.652205 AGGTACTTCCTCCATTCCAAATTA 57.348 37.500 0.00 0.00 44.42 1.40
401 844 5.536497 AGGTACTTCCTCCATTCCAAATT 57.464 39.130 0.00 0.00 44.42 1.82
403 846 6.652205 ATTAGGTACTTCCTCCATTCCAAA 57.348 37.500 0.00 0.00 44.42 3.28
404 847 7.404980 AGTTATTAGGTACTTCCTCCATTCCAA 59.595 37.037 0.00 0.00 44.42 3.53
405 848 6.906901 AGTTATTAGGTACTTCCTCCATTCCA 59.093 38.462 0.00 0.00 44.42 3.53
406 849 7.070821 TCAGTTATTAGGTACTTCCTCCATTCC 59.929 40.741 0.00 0.00 44.42 3.01
495 1359 0.681564 TTAACCATTCGGCGGCCATT 60.682 50.000 20.71 5.46 34.57 3.16
685 2050 3.934391 GACCGCCGGACTGGACTTG 62.934 68.421 11.71 0.00 42.00 3.16
686 2051 3.692406 GACCGCCGGACTGGACTT 61.692 66.667 11.71 0.00 42.00 3.01
687 2052 4.988716 TGACCGCCGGACTGGACT 62.989 66.667 11.71 0.00 42.00 3.85
688 2053 3.998672 TTGACCGCCGGACTGGAC 61.999 66.667 11.71 4.31 42.00 4.02
689 2054 3.998672 GTTGACCGCCGGACTGGA 61.999 66.667 11.71 0.00 42.00 3.86
772 2157 5.073827 AGGAGAGGGAAGGATTTAAATAGGC 59.926 44.000 0.00 0.00 0.00 3.93
922 2317 2.352342 GCTCGAGTACAGAGTACAGACC 59.648 54.545 15.13 0.00 37.99 3.85
927 2347 2.041251 AGGGCTCGAGTACAGAGTAC 57.959 55.000 15.13 11.19 37.99 2.73
929 2349 1.004979 AGAAGGGCTCGAGTACAGAGT 59.995 52.381 15.13 0.00 37.99 3.24
930 2350 1.673920 GAGAAGGGCTCGAGTACAGAG 59.326 57.143 15.13 12.37 38.68 3.35
931 2351 1.752683 GAGAAGGGCTCGAGTACAGA 58.247 55.000 15.13 0.00 33.17 3.41
944 2364 0.246086 AGCTGTTGCGAGAGAGAAGG 59.754 55.000 1.37 0.00 45.42 3.46
953 2373 1.153765 CTCGATGGAGCTGTTGCGA 60.154 57.895 0.00 0.00 45.42 5.10
954 2374 1.153765 TCTCGATGGAGCTGTTGCG 60.154 57.895 0.00 0.00 45.42 4.85
955 2375 0.108424 AGTCTCGATGGAGCTGTTGC 60.108 55.000 0.00 0.00 40.26 4.17
960 2380 2.451490 TCTTGAAGTCTCGATGGAGCT 58.549 47.619 0.00 0.00 40.26 4.09
1011 2434 1.439353 CGCAAATACCATCGCTGCCT 61.439 55.000 0.00 0.00 0.00 4.75
1077 2503 2.043450 CTCCCCGACAGCTCCTCT 60.043 66.667 0.00 0.00 0.00 3.69
1216 2643 2.048127 GGCGGACTCGTTGAGCTT 60.048 61.111 0.00 0.00 38.89 3.74
1240 2667 2.264166 GCTGCTCTCCTTGACGCT 59.736 61.111 0.00 0.00 0.00 5.07
1894 3322 1.302832 GTCCAGGGTGGTGCTTCAG 60.303 63.158 0.00 0.00 39.03 3.02
2949 4377 1.740296 GCGCATGAACCGGTACAGT 60.740 57.895 8.00 0.00 0.00 3.55
3226 4731 1.939934 TGCATGGCGCTACAAGTATTC 59.060 47.619 7.64 0.00 43.06 1.75
3567 5745 7.020827 TCAAAGTCATCAACCTATCTTTCCT 57.979 36.000 0.00 0.00 0.00 3.36
3587 5766 8.519799 AAACACTTCTCAACTTATCCTTCAAA 57.480 30.769 0.00 0.00 0.00 2.69
3588 5767 8.519799 AAAACACTTCTCAACTTATCCTTCAA 57.480 30.769 0.00 0.00 0.00 2.69
3766 5945 5.928839 CAGATTGATCCCCGTATTAACTGAG 59.071 44.000 0.00 0.00 0.00 3.35
3859 6039 5.596361 TGGAATGGTTACCAAATGCGATATT 59.404 36.000 8.63 0.00 36.95 1.28
3958 6150 8.173130 CGATTTGTTACCCTAGTTATGTTTGTC 58.827 37.037 0.00 0.00 0.00 3.18
4087 6279 1.538047 TGAAATGCTTCAGACCTGCC 58.462 50.000 0.00 0.00 36.62 4.85


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

AutoCloner maintained by Alex Coulton.