Multiple sequence alignment - TraesCS2B01G415400

Loading Multiple Alignment...

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 TraesCS2B01G415400 chr2B 100.000 4496 0 0 1 4496 593678064 593673569 0.000000e+00 8303
1 TraesCS2B01G415400 chr2B 84.389 442 58 8 2274 2709 601732129 601732565 1.500000e-114 424
2 TraesCS2B01G415400 chr2A 93.285 2338 60 24 1 2275 650658066 650655763 0.000000e+00 3358
3 TraesCS2B01G415400 chr2A 90.913 2234 104 34 2265 4442 650655063 650652873 0.000000e+00 2909
4 TraesCS2B01G415400 chr2A 85.294 170 20 4 2300 2466 80262282 80262449 2.150000e-38 171
5 TraesCS2B01G415400 chr2D 94.517 2061 77 17 710 2765 506166199 506164170 0.000000e+00 3147
6 TraesCS2B01G415400 chr2D 89.811 1747 87 25 2799 4496 506164173 506162469 0.000000e+00 2156
7 TraesCS2B01G415400 chr2D 86.115 749 48 22 4 703 506167056 506166315 0.000000e+00 756
8 TraesCS2B01G415400 chr7D 86.257 342 41 6 2369 2709 562395867 562395531 2.560000e-97 366


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 TraesCS2B01G415400 chr2B 593673569 593678064 4495 True 8303.000000 8303 100.000000 1 4496 1 chr2B.!!$R1 4495
1 TraesCS2B01G415400 chr2A 650652873 650658066 5193 True 3133.500000 3358 92.099000 1 4442 2 chr2A.!!$R1 4441
2 TraesCS2B01G415400 chr2D 506162469 506167056 4587 True 2019.666667 3147 90.147667 4 4496 3 chr2D.!!$R1 4492

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
283 322 1.055849 TGCCGTACTGCCATGGATAT 58.944 50.000 18.40 1.03 0.00 1.63 F
405 469 1.065199 TCTGCCCACTAATGCCAAGAG 60.065 52.381 0.00 0.00 0.00 2.85 F
1986 2171 1.005394 CTTAACCACGGGCGACAGT 60.005 57.895 0.00 0.00 40.29 3.55 F
3117 4026 1.059657 CATCAACGCGCCAGAAAACG 61.060 55.000 5.73 0.00 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1177 1359 3.160585 CCTTCCAGGTGTGGCTGA 58.839 61.111 0.00 0.00 44.60 4.26 R
2364 3259 1.348036 ACTTCCCTTGTTTCTCTCCCG 59.652 52.381 0.00 0.00 0.00 5.14 R
3403 4332 0.038166 CCTTTGGCAGGCTCCTGTTA 59.962 55.000 16.51 4.31 45.24 2.41 R
4356 5331 0.041238 AGGGAGTGGCTGTAGCTGTA 59.959 55.000 0.00 0.00 41.70 2.74 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
38 39 6.094464 AGGTTAGTGTTTCGCTGTAAAGTTTT 59.906 34.615 0.00 0.00 0.00 2.43
58 59 2.995283 TGAGCTTGTTGATGATCCTGG 58.005 47.619 0.00 0.00 0.00 4.45
119 122 7.259088 AGTGTTACTTTCCTTGTCATCCTAT 57.741 36.000 0.00 0.00 0.00 2.57
166 191 6.825721 AGCTCAAATAGTTTCCCTTCATACTG 59.174 38.462 0.00 0.00 0.00 2.74
178 203 5.885912 TCCCTTCATACTGGCTTATGTTTTC 59.114 40.000 6.59 0.00 32.17 2.29
183 208 7.843490 TCATACTGGCTTATGTTTTCTACAC 57.157 36.000 6.59 0.00 40.19 2.90
184 209 7.390823 TCATACTGGCTTATGTTTTCTACACA 58.609 34.615 6.59 0.00 40.19 3.72
224 249 4.348168 AGAGAAGTAGAAGCAAAGGTCCAA 59.652 41.667 0.00 0.00 0.00 3.53
247 272 7.365741 CAATCAAGATGGTATGCATTACTTCC 58.634 38.462 3.54 1.19 0.00 3.46
249 274 6.604171 TCAAGATGGTATGCATTACTTCCAT 58.396 36.000 3.54 11.49 38.21 3.41
283 322 1.055849 TGCCGTACTGCCATGGATAT 58.944 50.000 18.40 1.03 0.00 1.63
391 455 2.024306 GCCAAGTCCCTATTTCTGCCC 61.024 57.143 0.00 0.00 0.00 5.36
394 458 1.972588 AGTCCCTATTTCTGCCCACT 58.027 50.000 0.00 0.00 0.00 4.00
405 469 1.065199 TCTGCCCACTAATGCCAAGAG 60.065 52.381 0.00 0.00 0.00 2.85
415 479 3.463048 AATGCCAAGAGAGGGTTCAAT 57.537 42.857 0.00 0.00 0.00 2.57
496 560 9.176460 TGCATATCAGTTGATTTAAGTCATTGA 57.824 29.630 14.05 14.05 36.05 2.57
514 578 9.373450 AGTCATTGATAGTCTGACCATACTAAT 57.627 33.333 3.76 0.00 40.08 1.73
683 756 3.661648 GGAAGGGGAGCCTTGGCA 61.662 66.667 14.54 0.00 0.00 4.92
741 923 8.447200 TGGACTAATTAATCATTGGATCATCCA 58.553 33.333 0.66 0.66 46.61 3.41
775 957 8.786826 TGTACGATTGGTCTTTCTAATTGAAT 57.213 30.769 0.00 0.00 34.05 2.57
776 958 9.878667 TGTACGATTGGTCTTTCTAATTGAATA 57.121 29.630 0.00 0.00 34.05 1.75
778 960 8.786826 ACGATTGGTCTTTCTAATTGAATACA 57.213 30.769 0.00 0.00 34.05 2.29
779 961 8.883731 ACGATTGGTCTTTCTAATTGAATACAG 58.116 33.333 0.00 0.00 34.05 2.74
804 986 5.591099 AGTTTGCAAAATACTTCACACCTG 58.409 37.500 14.67 0.00 0.00 4.00
1615 1797 4.388469 GCTTTACTGCTCTCTTCAGTTGAG 59.612 45.833 0.77 2.10 41.61 3.02
1642 1824 7.481642 AGTATTCCGACTGAGTTGTTACATAG 58.518 38.462 0.00 0.00 0.00 2.23
1758 1940 1.598962 GAAGCTGCAGCCTCACACA 60.599 57.895 34.39 0.00 43.38 3.72
1828 2010 3.634910 ACGTTTGCACTAAAACCCATTCT 59.365 39.130 0.00 0.00 36.83 2.40
1986 2171 1.005394 CTTAACCACGGGCGACAGT 60.005 57.895 0.00 0.00 40.29 3.55
2291 3186 4.079787 TGCAGATCTATTTAGGCCCTGTTT 60.080 41.667 0.00 0.00 0.00 2.83
2305 3200 2.159393 CCCTGTTTGCAACGGATGTATG 60.159 50.000 0.00 0.00 40.26 2.39
2345 3240 8.802267 CAAAAACCTTTACAGGAATAGGATTGA 58.198 33.333 0.79 0.00 44.19 2.57
2364 3259 5.656213 TTGAGGTGCTAGTAGAAACCTAC 57.344 43.478 19.63 14.81 43.12 3.18
2398 3295 6.842676 ACAAGGGAAGTAGAAAATCAAGACT 58.157 36.000 0.00 0.00 0.00 3.24
2482 3382 1.228862 GACCCAAGCACCCCATGTT 60.229 57.895 0.00 0.00 0.00 2.71
2483 3383 1.533753 ACCCAAGCACCCCATGTTG 60.534 57.895 0.00 0.00 0.00 3.33
2484 3384 1.533753 CCCAAGCACCCCATGTTGT 60.534 57.895 0.00 0.00 0.00 3.32
2676 3585 9.341899 CTCTGTTTTATTTTCCTTTACATTCCG 57.658 33.333 0.00 0.00 0.00 4.30
2735 3644 4.039124 GTGTTGTCACCTGGAAATGGAAAT 59.961 41.667 0.00 0.00 38.51 2.17
2742 3651 9.265862 TGTCACCTGGAAATGGAAATAATATTT 57.734 29.630 0.00 0.00 0.00 1.40
2788 3697 6.093909 TCACTATGACCAACTCGACGTATTTA 59.906 38.462 0.00 0.00 0.00 1.40
2795 3704 7.041916 TGACCAACTCGACGTATTTAATGTTTT 60.042 33.333 0.00 0.00 0.00 2.43
2826 3735 5.769662 TGCTTCAAAGTATTGTTGGACATCT 59.230 36.000 0.00 0.00 37.79 2.90
2866 3775 3.944015 GGCTGCTGAAGATAGTTGTGATT 59.056 43.478 0.00 0.00 0.00 2.57
2892 3801 6.155475 TCCCCTTTTGAAACTATGTTGTTG 57.845 37.500 0.00 0.00 0.00 3.33
2893 3802 5.659079 TCCCCTTTTGAAACTATGTTGTTGT 59.341 36.000 0.00 0.00 0.00 3.32
2894 3803 6.155393 TCCCCTTTTGAAACTATGTTGTTGTT 59.845 34.615 0.00 0.00 0.00 2.83
2903 3812 6.601741 AACTATGTTGTTGTTTTGGCAATG 57.398 33.333 0.00 0.00 0.00 2.82
2922 3831 5.298777 GCAATGTTCAGATCAAGAGGCTATT 59.701 40.000 0.00 0.00 0.00 1.73
2934 3843 5.877012 TCAAGAGGCTATTGTTGAAGATGAC 59.123 40.000 20.24 0.00 0.00 3.06
3014 3923 3.336122 CAGCACCTGGAGCTTCTTT 57.664 52.632 16.28 0.00 41.14 2.52
3019 3928 2.042831 CCTGGAGCTTCTTTGGCCG 61.043 63.158 0.00 0.00 0.00 6.13
3023 3932 1.968540 GAGCTTCTTTGGCCGCTGT 60.969 57.895 5.21 0.00 31.96 4.40
3117 4026 1.059657 CATCAACGCGCCAGAAAACG 61.060 55.000 5.73 0.00 0.00 3.60
3166 4075 2.954318 AGCAGCAAGAAAGAAGCAGAAA 59.046 40.909 0.00 0.00 0.00 2.52
3209 4118 7.545265 TGCTATTTTTCAAACTGTTCATATGCC 59.455 33.333 0.00 0.00 0.00 4.40
3225 4134 6.957631 TCATATGCCCTTTTTCTCTACTGAA 58.042 36.000 0.00 0.00 0.00 3.02
3226 4135 7.577303 TCATATGCCCTTTTTCTCTACTGAAT 58.423 34.615 0.00 0.00 0.00 2.57
3282 4208 8.352942 AGTTAATTCCGGATGCTAAAATGATTC 58.647 33.333 4.15 0.00 0.00 2.52
3305 4231 9.675464 ATTCCAGAATCATTTATGTGCAAAAAT 57.325 25.926 0.00 0.00 0.00 1.82
3368 4297 5.872635 TGTAAGAAGACACGGTATCTAACG 58.127 41.667 0.00 0.00 0.00 3.18
3374 4303 6.541641 AGAAGACACGGTATCTAACGTAATCT 59.458 38.462 0.00 4.29 42.04 2.40
3387 4316 7.130917 TCTAACGTAATCTTAGTCGCTGATTC 58.869 38.462 0.00 0.00 33.24 2.52
3393 4322 7.595502 CGTAATCTTAGTCGCTGATTCCTATTT 59.404 37.037 0.00 0.00 33.24 1.40
3403 4332 5.278169 CGCTGATTCCTATTTAATTGCTGCT 60.278 40.000 0.00 0.00 0.00 4.24
3462 4391 0.531974 AAGAGCCGAAGTTCAACGCA 60.532 50.000 3.32 0.00 0.00 5.24
3483 4412 3.577649 TTCACAGGAAAGAGCTACTCG 57.422 47.619 0.00 0.00 35.36 4.18
3536 4465 1.001487 CAGCGACAACTTTGGCAATCA 60.001 47.619 0.00 0.00 35.35 2.57
3550 4479 3.119884 TGGCAATCAAACACGCTATCTTG 60.120 43.478 0.00 0.00 0.00 3.02
3582 4520 3.638160 TGTCTGGTTACCGTAGTGAACTT 59.362 43.478 0.00 0.00 0.00 2.66
3668 4607 2.754946 AAACGGTTTAGCTCGATGGA 57.245 45.000 3.90 0.00 0.00 3.41
3674 4613 3.246226 CGGTTTAGCTCGATGGAAATCTG 59.754 47.826 0.00 0.00 0.00 2.90
3760 4700 5.049167 CAGTCTAGTCTCATCAATTGCTCC 58.951 45.833 0.00 0.00 0.00 4.70
3829 4769 7.599998 CGATGATGATGTGACATAAACTATGGA 59.400 37.037 0.00 0.00 40.47 3.41
3861 4801 0.107017 GCAGGCAGGCCAGATTCTTA 60.107 55.000 13.63 0.00 38.92 2.10
3967 4909 3.475566 TTACTCAACAGAGTGCAGCTT 57.524 42.857 8.31 0.00 42.38 3.74
4006 4948 5.038683 CAGTATATGCATGTTGTTTGGCAG 58.961 41.667 10.16 0.00 39.95 4.85
4104 5051 5.028549 ACTATCTTTTGACCTGCGATGAT 57.971 39.130 0.00 0.00 0.00 2.45
4107 5054 3.186909 TCTTTTGACCTGCGATGATACG 58.813 45.455 0.00 0.00 0.00 3.06
4154 5101 5.473039 TCACTGACTGATTGTGACATGTAG 58.527 41.667 0.00 0.00 36.03 2.74
4155 5102 5.011023 TCACTGACTGATTGTGACATGTAGT 59.989 40.000 0.00 0.00 36.03 2.73
4156 5103 6.208599 TCACTGACTGATTGTGACATGTAGTA 59.791 38.462 0.00 0.00 36.03 1.82
4182 5130 6.817765 AAATTTTTCCTGCTCGTCTATCAA 57.182 33.333 0.00 0.00 0.00 2.57
4241 5197 3.393800 CCATATCTCCAACTACTTGGCG 58.606 50.000 0.00 0.00 46.15 5.69
4283 5249 3.822735 CCGGATGGCAAGTGAAATGATAT 59.177 43.478 0.00 0.00 0.00 1.63
4284 5250 5.003160 CCGGATGGCAAGTGAAATGATATA 58.997 41.667 0.00 0.00 0.00 0.86
4285 5251 5.106555 CCGGATGGCAAGTGAAATGATATAC 60.107 44.000 0.00 0.00 0.00 1.47
4314 5280 2.037136 CCAGGGTCTTTGCTCAGCG 61.037 63.158 0.00 0.00 0.00 5.18
4356 5331 2.969821 TGGTCCTGCCATTTTGTACT 57.030 45.000 0.00 0.00 43.61 2.73
4358 5333 3.681593 TGGTCCTGCCATTTTGTACTAC 58.318 45.455 0.00 0.00 43.61 2.73
4359 5334 3.073209 TGGTCCTGCCATTTTGTACTACA 59.927 43.478 0.00 0.00 43.61 2.74
4360 5335 3.689649 GGTCCTGCCATTTTGTACTACAG 59.310 47.826 0.00 0.00 37.17 2.74
4361 5336 3.127030 GTCCTGCCATTTTGTACTACAGC 59.873 47.826 0.00 0.00 0.00 4.40
4362 5337 3.009033 TCCTGCCATTTTGTACTACAGCT 59.991 43.478 0.00 0.00 0.00 4.24
4363 5338 4.224147 TCCTGCCATTTTGTACTACAGCTA 59.776 41.667 0.00 0.00 0.00 3.32
4364 5339 4.332819 CCTGCCATTTTGTACTACAGCTAC 59.667 45.833 0.00 0.00 0.00 3.58
4365 5340 4.900684 TGCCATTTTGTACTACAGCTACA 58.099 39.130 0.00 0.00 0.00 2.74
4366 5341 4.935205 TGCCATTTTGTACTACAGCTACAG 59.065 41.667 0.00 0.00 0.00 2.74
4367 5342 4.201822 GCCATTTTGTACTACAGCTACAGC 60.202 45.833 0.00 0.00 42.49 4.40
4453 5439 3.635373 GTCCATGGATCGAACCTGTACTA 59.365 47.826 19.62 0.00 0.00 1.82
4482 5471 1.093972 TTTGTGTAGCCGATGCATGG 58.906 50.000 2.46 1.62 41.13 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 2.573009 TCCAGGATCATCAACAAGCTCA 59.427 45.455 0.00 0.00 0.00 4.26
58 59 4.285775 TCCAAAGGATCCCAACCAAAATTC 59.714 41.667 8.55 0.00 0.00 2.17
178 203 7.782049 TCTTGGACCTGTTATTATCTGTGTAG 58.218 38.462 0.00 0.00 0.00 2.74
183 208 7.560368 ACTTCTCTTGGACCTGTTATTATCTG 58.440 38.462 0.00 0.00 0.00 2.90
184 209 7.741554 ACTTCTCTTGGACCTGTTATTATCT 57.258 36.000 0.00 0.00 0.00 1.98
224 249 6.604171 TGGAAGTAATGCATACCATCTTGAT 58.396 36.000 0.00 0.00 34.89 2.57
247 272 1.210931 CACCGAGTTGCAGGCAATG 59.789 57.895 10.21 0.16 38.28 2.82
249 274 3.286751 GCACCGAGTTGCAGGCAA 61.287 61.111 1.93 1.93 42.49 4.52
378 439 2.887152 GCATTAGTGGGCAGAAATAGGG 59.113 50.000 0.00 0.00 0.00 3.53
379 440 2.887152 GGCATTAGTGGGCAGAAATAGG 59.113 50.000 0.00 0.00 0.00 2.57
380 441 3.554934 TGGCATTAGTGGGCAGAAATAG 58.445 45.455 0.00 0.00 35.74 1.73
391 455 3.274288 GAACCCTCTCTTGGCATTAGTG 58.726 50.000 0.00 0.00 0.00 2.74
394 458 4.591321 ATTGAACCCTCTCTTGGCATTA 57.409 40.909 0.00 0.00 0.00 1.90
405 469 3.006752 TCAAATGCCACAATTGAACCCTC 59.993 43.478 13.59 0.00 31.45 4.30
415 479 6.040054 CCAGATTCATCTATCAAATGCCACAA 59.960 38.462 0.00 0.00 34.85 3.33
596 661 4.335594 AGGAACAACAAGAAAGTACTGTGC 59.664 41.667 0.00 0.00 0.00 4.57
657 730 1.779061 GCTCCCCTTCCCAGTTCACA 61.779 60.000 0.00 0.00 0.00 3.58
683 756 1.170290 GGCAACAGCTTTACCACCGT 61.170 55.000 0.00 0.00 0.00 4.83
741 923 9.832445 AGAAAGACCAATCGTACATACATTAAT 57.168 29.630 0.00 0.00 0.00 1.40
744 926 9.832445 ATTAGAAAGACCAATCGTACATACATT 57.168 29.630 0.00 0.00 0.00 2.71
775 957 8.339714 GTGTGAAGTATTTTGCAAACTACTGTA 58.660 33.333 31.16 23.03 35.42 2.74
776 958 7.193595 GTGTGAAGTATTTTGCAAACTACTGT 58.806 34.615 31.16 23.28 35.42 3.55
777 959 6.636850 GGTGTGAAGTATTTTGCAAACTACTG 59.363 38.462 31.16 0.00 35.42 2.74
778 960 6.546034 AGGTGTGAAGTATTTTGCAAACTACT 59.454 34.615 27.40 27.40 36.36 2.57
779 961 6.636850 CAGGTGTGAAGTATTTTGCAAACTAC 59.363 38.462 24.55 24.55 0.00 2.73
1168 1350 5.765510 TCCAGGTGTGGCTGAAAAATATAT 58.234 37.500 0.00 0.00 44.60 0.86
1177 1359 3.160585 CCTTCCAGGTGTGGCTGA 58.839 61.111 0.00 0.00 44.60 4.26
1615 1797 6.154445 TGTAACAACTCAGTCGGAATACTTC 58.846 40.000 0.00 0.00 0.00 3.01
1758 1940 3.515502 TCGAGATGTCCAGGAAATCAGTT 59.484 43.478 20.42 1.11 29.19 3.16
1986 2171 7.445707 TGTTTGTTGTTGTAAGCTACCATGATA 59.554 33.333 0.00 0.00 0.00 2.15
2291 3186 3.149981 TGTTTTCCATACATCCGTTGCA 58.850 40.909 0.00 0.00 0.00 4.08
2305 3200 6.811253 AAGGTTTTTGTTCCTTTGTTTTCC 57.189 33.333 0.00 0.00 40.64 3.13
2364 3259 1.348036 ACTTCCCTTGTTTCTCTCCCG 59.652 52.381 0.00 0.00 0.00 5.14
2398 3295 3.374042 TCCTTTCCTGTGAACCAAACA 57.626 42.857 0.00 0.00 0.00 2.83
2482 3382 1.569548 AGCTACTACTAGAGGCCCACA 59.430 52.381 0.00 0.00 0.00 4.17
2483 3383 2.368311 AGCTACTACTAGAGGCCCAC 57.632 55.000 0.00 0.00 0.00 4.61
2484 3384 3.399952 AAAGCTACTACTAGAGGCCCA 57.600 47.619 0.00 0.00 0.00 5.36
2595 3496 2.726832 ACGAACTGCTAGAACTCCAC 57.273 50.000 0.00 0.00 0.00 4.02
2596 3497 2.029290 GGAACGAACTGCTAGAACTCCA 60.029 50.000 0.00 0.00 0.00 3.86
2597 3498 2.231721 AGGAACGAACTGCTAGAACTCC 59.768 50.000 0.00 0.00 0.00 3.85
2598 3499 3.246619 CAGGAACGAACTGCTAGAACTC 58.753 50.000 0.00 0.00 0.00 3.01
2599 3500 3.305398 CAGGAACGAACTGCTAGAACT 57.695 47.619 0.00 0.00 0.00 3.01
2674 3583 1.539827 GTTTGAAGGGATTGTGGACGG 59.460 52.381 0.00 0.00 0.00 4.79
2676 3585 1.539827 CGGTTTGAAGGGATTGTGGAC 59.460 52.381 0.00 0.00 0.00 4.02
2795 3704 7.500892 TCCAACAATACTTTGAAGCAGACTAAA 59.499 33.333 0.00 0.00 36.64 1.85
2826 3735 4.821805 GCAGCCTATAGAAAAGTGGCATAA 59.178 41.667 0.00 0.00 45.42 1.90
2866 3775 7.189079 ACAACATAGTTTCAAAAGGGGAAAA 57.811 32.000 0.00 0.00 36.14 2.29
2892 3801 5.531634 TCTTGATCTGAACATTGCCAAAAC 58.468 37.500 0.00 0.00 0.00 2.43
2893 3802 5.279106 CCTCTTGATCTGAACATTGCCAAAA 60.279 40.000 0.00 0.00 0.00 2.44
2894 3803 4.219070 CCTCTTGATCTGAACATTGCCAAA 59.781 41.667 0.00 0.00 0.00 3.28
2903 3812 5.877012 TCAACAATAGCCTCTTGATCTGAAC 59.123 40.000 0.00 0.00 0.00 3.18
2922 3831 4.531854 TGAACTTTGGGTCATCTTCAACA 58.468 39.130 0.00 0.00 0.00 3.33
2934 3843 4.370917 CAGTGAATGGTTTGAACTTTGGG 58.629 43.478 0.00 0.00 0.00 4.12
3019 3928 2.974698 AGAACGTGCAGCCACAGC 60.975 61.111 0.00 0.00 42.17 4.40
3117 4026 2.167487 TGAACCAAACACAAGCTTTCCC 59.833 45.455 0.00 0.00 0.00 3.97
3238 4147 8.657074 AATTAACTTGAAAGGTTTAACTTGCC 57.343 30.769 0.00 0.00 0.00 4.52
3315 4241 8.877864 TGTCATACAGAATTGGAACCTTTAAT 57.122 30.769 0.00 0.00 0.00 1.40
3318 4244 7.781324 AATGTCATACAGAATTGGAACCTTT 57.219 32.000 0.00 0.00 0.00 3.11
3322 4248 7.820648 ACAGAAATGTCATACAGAATTGGAAC 58.179 34.615 0.00 0.00 0.00 3.62
3359 4288 7.571026 TCAGCGACTAAGATTACGTTAGATAC 58.429 38.462 0.00 0.00 32.67 2.24
3363 4292 6.360148 GGAATCAGCGACTAAGATTACGTTAG 59.640 42.308 0.00 0.00 32.51 2.34
3368 4297 8.819643 AAATAGGAATCAGCGACTAAGATTAC 57.180 34.615 0.00 0.00 33.69 1.89
3374 4303 7.715249 AGCAATTAAATAGGAATCAGCGACTAA 59.285 33.333 0.00 0.00 0.00 2.24
3387 4316 6.514048 GCTCCTGTTAGCAGCAATTAAATAGG 60.514 42.308 0.17 0.00 42.30 2.57
3393 4322 2.239654 AGGCTCCTGTTAGCAGCAATTA 59.760 45.455 0.17 0.00 44.64 1.40
3403 4332 0.038166 CCTTTGGCAGGCTCCTGTTA 59.962 55.000 16.51 4.31 45.24 2.41
3462 4391 3.511934 ACGAGTAGCTCTTTCCTGTGAAT 59.488 43.478 0.00 0.00 0.00 2.57
3529 4458 3.429085 CAAGATAGCGTGTTTGATTGCC 58.571 45.455 0.00 0.00 0.00 4.52
3536 4465 2.778299 TCCAAGCAAGATAGCGTGTTT 58.222 42.857 0.00 0.00 41.48 2.83
3550 4479 2.552743 GGTAACCAGACAACTTCCAAGC 59.447 50.000 0.00 0.00 0.00 4.01
3582 4520 3.186909 CGAATGCGAAGTGGAGATACAA 58.813 45.455 0.00 0.00 40.82 2.41
3760 4700 5.178996 CACAGTTCTGAATCAAAGAGTCTGG 59.821 44.000 6.83 0.00 34.60 3.86
3829 4769 3.644606 CCTGCCTGCCACTGAGGT 61.645 66.667 0.00 0.00 40.61 3.85
3861 4801 4.705507 ACATTGATTGCTCAAGCTCATCTT 59.294 37.500 3.32 0.00 44.32 2.40
3967 4909 8.433599 TGCATATACTGTTGGCCTACTTTAATA 58.566 33.333 18.31 10.66 0.00 0.98
4104 5051 3.342377 TTTGATGCCATGGACTTCGTA 57.658 42.857 18.40 4.63 0.00 3.43
4107 5054 4.724074 TCATTTTGATGCCATGGACTTC 57.276 40.909 18.40 14.38 0.00 3.01
4154 5101 9.865484 GATAGACGAGCAGGAAAAATTTATTAC 57.135 33.333 0.00 0.00 0.00 1.89
4155 5102 9.607988 TGATAGACGAGCAGGAAAAATTTATTA 57.392 29.630 0.00 0.00 0.00 0.98
4156 5103 8.506168 TGATAGACGAGCAGGAAAAATTTATT 57.494 30.769 0.00 0.00 0.00 1.40
4173 5121 4.041740 TCGGGAAGTTCATTGATAGACG 57.958 45.455 5.01 0.00 0.00 4.18
4178 5126 4.559862 AAGACTCGGGAAGTTCATTGAT 57.440 40.909 5.01 0.00 38.74 2.57
4182 5130 4.527038 TCAGTAAAGACTCGGGAAGTTCAT 59.473 41.667 5.01 0.00 38.74 2.57
4241 5197 3.206964 GGAGCTTTCAATACCCAGCTAC 58.793 50.000 0.00 0.00 42.80 3.58
4247 5213 2.222027 CATCCGGAGCTTTCAATACCC 58.778 52.381 11.34 0.00 0.00 3.69
4283 5249 2.520982 CCTGGATCTCGGCGGGTA 60.521 66.667 6.68 0.00 0.00 3.69
4314 5280 1.228063 AGCGTGATGATGGATGGGC 60.228 57.895 0.00 0.00 0.00 5.36
4356 5331 0.041238 AGGGAGTGGCTGTAGCTGTA 59.959 55.000 0.00 0.00 41.70 2.74
4357 5332 0.838122 AAGGGAGTGGCTGTAGCTGT 60.838 55.000 0.00 0.00 41.70 4.40
4358 5333 0.392193 CAAGGGAGTGGCTGTAGCTG 60.392 60.000 0.00 0.00 41.70 4.24
4359 5334 1.986413 CAAGGGAGTGGCTGTAGCT 59.014 57.895 3.63 0.00 41.70 3.32
4360 5335 1.746991 GCAAGGGAGTGGCTGTAGC 60.747 63.158 0.00 0.00 41.14 3.58
4361 5336 0.107945 GAGCAAGGGAGTGGCTGTAG 60.108 60.000 0.00 0.00 38.15 2.74
4362 5337 0.545309 AGAGCAAGGGAGTGGCTGTA 60.545 55.000 0.00 0.00 38.15 2.74
4363 5338 1.422161 AAGAGCAAGGGAGTGGCTGT 61.422 55.000 0.00 0.00 38.15 4.40
4364 5339 0.676151 GAAGAGCAAGGGAGTGGCTG 60.676 60.000 0.00 0.00 38.15 4.85
4365 5340 1.682257 GAAGAGCAAGGGAGTGGCT 59.318 57.895 0.00 0.00 41.35 4.75
4366 5341 1.377856 GGAAGAGCAAGGGAGTGGC 60.378 63.158 0.00 0.00 0.00 5.01
4367 5342 1.484240 CTAGGAAGAGCAAGGGAGTGG 59.516 57.143 0.00 0.00 0.00 4.00
4453 5439 0.386731 GCTACACAAATTTGCGCCGT 60.387 50.000 18.12 12.12 0.00 5.68


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

AutoCloner maintained by Alex Coulton.