Multiple sequence alignment - TraesCS2D01G189200

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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 TraesCS2D01G189200 chr2D 100.000 4471 0 0 1 4471 133034177 133038647 0.000000e+00 8257.0
1 TraesCS2D01G189200 chr2B 90.682 3606 199 56 1 3546 188713859 188717387 0.000000e+00 4671.0
2 TraesCS2D01G189200 chr2B 88.958 480 24 13 3970 4434 188717833 188718298 2.330000e-157 566.0
3 TraesCS2D01G189200 chr2B 91.707 205 15 1 3607 3809 188717382 188717586 2.630000e-72 283.0
4 TraesCS2D01G189200 chr2A 94.625 2456 93 20 1266 3692 140499751 140502196 0.000000e+00 3768.0
5 TraesCS2D01G189200 chr2A 90.602 2341 115 51 2 2275 139984136 139981834 0.000000e+00 3007.0
6 TraesCS2D01G189200 chr2A 95.134 1459 62 5 2268 3719 139981676 139980220 0.000000e+00 2292.0
7 TraesCS2D01G189200 chr2A 90.493 873 69 10 403 1267 140498724 140499590 0.000000e+00 1140.0
8 TraesCS2D01G189200 chr2A 88.688 442 28 12 4008 4434 140504053 140504487 1.840000e-143 520.0
9 TraesCS2D01G189200 chr2A 85.237 359 31 9 2 360 140497423 140497759 2.560000e-92 350.0
10 TraesCS2D01G189200 chr2A 84.573 363 19 9 1 360 140498384 140498712 4.310000e-85 326.0
11 TraesCS2D01G189200 chr2A 79.919 493 29 24 3973 4434 139979612 139979159 9.400000e-77 298.0
12 TraesCS2D01G189200 chr2A 95.161 62 1 1 3751 3810 140502197 140502258 3.680000e-16 97.1
13 TraesCS2D01G189200 chr2A 80.342 117 23 0 3855 3971 139980144 139980028 6.160000e-14 89.8
14 TraesCS2D01G189200 chr3B 81.757 148 24 3 2672 2817 512576507 512576653 2.180000e-23 121.0


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 TraesCS2D01G189200 chr2D 133034177 133038647 4470 False 8257.000000 8257 100.000000 1 4471 1 chr2D.!!$F1 4470
1 TraesCS2D01G189200 chr2B 188713859 188718298 4439 False 1840.000000 4671 90.449000 1 4434 3 chr2B.!!$F1 4433
2 TraesCS2D01G189200 chr2A 139979159 139984136 4977 True 1421.700000 3007 86.499250 2 4434 4 chr2A.!!$R1 4432
3 TraesCS2D01G189200 chr2A 140497423 140504487 7064 False 1033.516667 3768 89.796167 1 4434 6 chr2A.!!$F1 4433

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
668 1651 0.975040 TTTGCACCTGGTGGCAGTTT 60.975 50.0 27.02 0.00 41.68 2.66 F
1633 2840 0.615331 CAGCTTCTAGGGCCTGTCAA 59.385 55.0 18.53 4.85 0.00 3.18 F
2116 3323 0.665298 GCTTTAGCCAGCATACTGCC 59.335 55.0 0.00 0.00 43.02 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 3041 0.947244 CAAGGCCGTGAATATGCTCC 59.053 55.000 14.14 0.00 0.00 4.70 R
3425 4809 1.329906 GCACCATCTGAAGCTTCATCG 59.670 52.381 28.57 18.22 36.46 3.84 R
3859 6693 0.176680 CAGCCGTGCAAGTCTAGGAT 59.823 55.000 0.00 0.00 0.00 3.24 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 1043 1.000884 CTCCAAACGCGCCGTATTAA 58.999 50.000 5.73 0.00 39.99 1.40
215 1184 2.978824 GAAGCACCACGGCCTCTA 59.021 61.111 0.00 0.00 0.00 2.43
237 1206 2.820037 GCGTTGCCTAGCCACCTC 60.820 66.667 0.00 0.00 0.00 3.85
436 1418 1.003718 AACCGAGCAAGTAGGTGCC 60.004 57.895 0.00 0.00 46.14 5.01
507 1489 5.526846 CCTTCCTCTGTAAAATGAGATGCTC 59.473 44.000 0.00 0.00 32.44 4.26
642 1624 9.620259 TCCCTGTTTGCTTAAAATTAACAAATT 57.380 25.926 12.41 0.00 32.22 1.82
668 1651 0.975040 TTTGCACCTGGTGGCAGTTT 60.975 50.000 27.02 0.00 41.68 2.66
679 1662 1.933181 GTGGCAGTTTTTCAACTTGCC 59.067 47.619 15.76 15.76 46.67 4.52
680 1663 1.830477 TGGCAGTTTTTCAACTTGCCT 59.170 42.857 19.92 0.00 46.65 4.75
685 1668 4.679372 GCAGTTTTTCAACTTGCCTTGGTA 60.679 41.667 0.00 0.00 40.66 3.25
691 1674 3.686016 TCAACTTGCCTTGGTAGATTCC 58.314 45.455 0.00 0.00 0.00 3.01
692 1675 3.330701 TCAACTTGCCTTGGTAGATTCCT 59.669 43.478 0.00 0.00 0.00 3.36
693 1676 3.636153 ACTTGCCTTGGTAGATTCCTC 57.364 47.619 0.00 0.00 0.00 3.71
694 1677 2.093447 ACTTGCCTTGGTAGATTCCTCG 60.093 50.000 0.00 0.00 0.00 4.63
695 1678 1.568504 TGCCTTGGTAGATTCCTCGT 58.431 50.000 0.00 0.00 0.00 4.18
724 1707 7.041916 GCAACATTTTCCAATCTGACAAATGAA 60.042 33.333 9.34 0.00 37.95 2.57
869 1859 6.114187 TGGTCTTTATCGATTGCCAGATAT 57.886 37.500 1.71 0.00 0.00 1.63
879 1870 7.482654 TCGATTGCCAGATATTAGTTTTGAG 57.517 36.000 0.00 0.00 0.00 3.02
888 1879 8.616076 CCAGATATTAGTTTTGAGATGGTGTTC 58.384 37.037 0.00 0.00 0.00 3.18
921 1912 3.251016 TGTTCCCAATGGGTGATTCAA 57.749 42.857 19.28 0.39 44.74 2.69
964 1955 2.428544 TAACTTATGGCGCCCATGTT 57.571 45.000 26.77 24.81 44.84 2.71
999 1990 3.758755 TCTTATTCTGCAGATCGGCAT 57.241 42.857 20.95 10.19 43.97 4.40
1101 2092 4.118168 ACTGATGGTTTGAACATCCCTT 57.882 40.909 3.71 0.00 43.10 3.95
1111 2102 6.936335 GGTTTGAACATCCCTTTCATGATTTT 59.064 34.615 0.00 0.00 33.03 1.82
1112 2103 7.445096 GGTTTGAACATCCCTTTCATGATTTTT 59.555 33.333 0.00 0.00 33.03 1.94
1269 2423 5.708736 TGGTTCCTCTTTGGCTAATATCA 57.291 39.130 0.00 0.00 35.26 2.15
1317 2478 8.791327 TGATGTGTTAGAGATAAAATTGCTGA 57.209 30.769 0.00 0.00 0.00 4.26
1428 2600 6.528537 AAGCATTTCACATGGTAGCATAAA 57.471 33.333 7.18 5.50 0.00 1.40
1439 2611 8.971321 CACATGGTAGCATAAAGATAAAAATGC 58.029 33.333 7.18 0.00 43.97 3.56
1463 2644 7.487829 TGCACTTGAAACATTTTCAGAGTAAAC 59.512 33.333 12.20 8.42 0.00 2.01
1464 2645 7.487829 GCACTTGAAACATTTTCAGAGTAAACA 59.512 33.333 12.20 0.00 0.00 2.83
1465 2646 9.352784 CACTTGAAACATTTTCAGAGTAAACAA 57.647 29.630 12.20 0.00 0.00 2.83
1466 2647 9.921637 ACTTGAAACATTTTCAGAGTAAACAAA 57.078 25.926 11.47 0.00 0.00 2.83
1492 2674 2.556144 TGCATCACTTTGCTCTGTCT 57.444 45.000 0.00 0.00 43.18 3.41
1513 2695 6.374333 TGTCTTATCCCAAGTCAAATAGCAAC 59.626 38.462 0.00 0.00 0.00 4.17
1521 2703 5.164061 CCAAGTCAAATAGCAACGCAATTTC 60.164 40.000 0.00 0.00 0.00 2.17
1633 2840 0.615331 CAGCTTCTAGGGCCTGTCAA 59.385 55.000 18.53 4.85 0.00 3.18
1750 2957 5.105797 TGTCTGGCTATTGCAAACCTTATTG 60.106 40.000 1.71 0.00 41.91 1.90
1834 3041 2.299582 TGTTGAAGCAAACATCATGGGG 59.700 45.455 0.00 0.00 35.16 4.96
1861 3068 2.045561 TTCACGGCCTTGAACTGAAA 57.954 45.000 20.03 0.00 30.29 2.69
1911 3118 4.764172 AGAGTGAGAGTTATGGACAATGC 58.236 43.478 0.00 0.00 0.00 3.56
2008 3215 4.272261 GCAGCCTTACAAATAGAGAAGCTC 59.728 45.833 0.00 0.00 0.00 4.09
2083 3290 3.060602 GACTACGCTTGAGCAAAGACTT 58.939 45.455 3.65 0.00 42.21 3.01
2116 3323 0.665298 GCTTTAGCCAGCATACTGCC 59.335 55.000 0.00 0.00 43.02 4.85
2148 3355 5.983540 AGTTAGAATAGAGAAGCAACTGGG 58.016 41.667 0.00 0.00 0.00 4.45
2202 3409 6.183361 TGGAAGACTATTGATCATCTTGAGGG 60.183 42.308 12.83 0.00 31.58 4.30
2467 3839 6.529125 TCGAATACGTTCCATCTGTAGTTTTC 59.471 38.462 0.00 0.00 40.69 2.29
2530 3902 5.484173 TCGCTATGGAATTTAGTTGCTTG 57.516 39.130 0.00 0.00 0.00 4.01
2548 3920 2.940994 TGCACTGCTAGTTGGGTAAA 57.059 45.000 1.98 0.00 0.00 2.01
2585 3957 8.249638 TGTCTGTTTTGTTGATTCTGATTTCAA 58.750 29.630 0.87 0.87 0.00 2.69
2807 4179 4.364318 GCTGGAGGCTCAGGTAGA 57.636 61.111 17.69 0.00 38.06 2.59
2850 4229 4.219944 TCCTAACTGTAACTGCACCAGTAG 59.780 45.833 0.00 0.00 44.62 2.57
2877 4256 9.784531 AAATATAGTTGCACATATAGCTCAAGT 57.215 29.630 0.00 0.00 0.00 3.16
3224 4603 5.938125 AGTTGTTTCATGGTACTGATACACC 59.062 40.000 7.57 2.84 37.00 4.16
3391 4775 2.774439 AGCAACATTGACGAAACACC 57.226 45.000 0.00 0.00 0.00 4.16
3392 4776 2.020720 AGCAACATTGACGAAACACCA 58.979 42.857 0.00 0.00 0.00 4.17
3393 4777 2.116366 GCAACATTGACGAAACACCAC 58.884 47.619 0.00 0.00 0.00 4.16
3425 4809 0.315568 CGCTAGTAGAGTGGCATCCC 59.684 60.000 0.00 0.00 31.50 3.85
3447 4831 0.674581 TGAAGCTTCAGATGGTGCCG 60.675 55.000 25.16 0.00 32.50 5.69
3557 4941 5.800296 TGCATTTGTAACCTTAGTGAGCTA 58.200 37.500 0.00 0.00 0.00 3.32
3620 5005 4.549599 CAGCGCGAATGTAACTTGTAAAAG 59.450 41.667 12.10 0.00 0.00 2.27
3636 5021 8.818057 ACTTGTAAAAGCTTCATATGTATCGTC 58.182 33.333 0.00 0.00 0.00 4.20
3695 5080 6.618287 TGTATTAGCATACACAGATTTGCC 57.382 37.500 0.00 0.00 40.39 4.52
3730 5115 2.071778 AAGTGGCATGAGTTTGGTGT 57.928 45.000 0.00 0.00 0.00 4.16
3747 5132 3.574216 GTGTGTACACGTGGTTTGTAC 57.426 47.619 21.57 12.93 46.45 2.90
3759 5144 5.176223 ACGTGGTTTGTACGAGAGTTATTTG 59.824 40.000 4.43 0.00 46.40 2.32
3831 6665 5.046807 ACACGTAGCTTAGATGGTTAGGTTT 60.047 40.000 0.00 0.00 0.00 3.27
3835 6669 7.123247 ACGTAGCTTAGATGGTTAGGTTTCTTA 59.877 37.037 0.00 0.00 0.00 2.10
3876 6710 1.398390 CAAATCCTAGACTTGCACGGC 59.602 52.381 0.00 0.00 0.00 5.68
3892 6726 0.524816 CGGCTGCATGCACATTTCTC 60.525 55.000 18.46 0.51 45.15 2.87
3909 6746 7.009540 CACATTTCTCGAATTATTTTGGCCTTC 59.990 37.037 3.32 0.00 0.00 3.46
3915 6752 5.475220 TCGAATTATTTTGGCCTTCTCAACA 59.525 36.000 3.32 0.00 0.00 3.33
3944 6781 0.877071 GCTCATATGGGCATGAACGG 59.123 55.000 22.95 0.00 34.59 4.44
3960 6797 3.322541 TGAACGGTTTGTAGGAGTGATCA 59.677 43.478 0.00 0.00 0.00 2.92
3973 6810 4.588951 AGGAGTGATCATATAACGCAGGAA 59.411 41.667 0.00 0.00 0.00 3.36
3974 6811 4.926238 GGAGTGATCATATAACGCAGGAAG 59.074 45.833 0.00 0.00 0.00 3.46
3978 6815 6.258727 AGTGATCATATAACGCAGGAAGTTTG 59.741 38.462 0.00 0.00 33.42 2.93
3997 7302 4.935352 TTGCCTAAACTTGCAGTCATTT 57.065 36.364 0.00 0.00 38.95 2.32
3999 7304 4.144297 TGCCTAAACTTGCAGTCATTTCT 58.856 39.130 0.00 0.00 32.77 2.52
4001 7306 5.945784 TGCCTAAACTTGCAGTCATTTCTAT 59.054 36.000 0.00 0.00 32.77 1.98
4002 7307 7.109501 TGCCTAAACTTGCAGTCATTTCTATA 58.890 34.615 0.00 0.00 32.77 1.31
4003 7308 7.280876 TGCCTAAACTTGCAGTCATTTCTATAG 59.719 37.037 0.00 0.00 32.77 1.31
4004 7309 7.281100 GCCTAAACTTGCAGTCATTTCTATAGT 59.719 37.037 0.00 0.00 0.00 2.12
4037 7342 7.593825 ACAATTTAGCTTCAGTTATTCCACAC 58.406 34.615 0.00 0.00 0.00 3.82
4038 7343 7.230510 ACAATTTAGCTTCAGTTATTCCACACA 59.769 33.333 0.00 0.00 0.00 3.72
4039 7344 7.944729 ATTTAGCTTCAGTTATTCCACACAT 57.055 32.000 0.00 0.00 0.00 3.21
4075 7381 9.751542 ATTTAATCTCAGTTATTACAGGACGAG 57.248 33.333 0.00 0.00 0.00 4.18
4087 7393 3.366396 ACAGGACGAGGTCAAGTCATAT 58.634 45.455 0.00 0.00 39.01 1.78
4088 7394 3.131223 ACAGGACGAGGTCAAGTCATATG 59.869 47.826 0.00 0.00 39.01 1.78
4291 7641 1.762957 TCTCAGGTTCGATCCATTCCC 59.237 52.381 14.83 0.00 0.00 3.97
4305 7655 2.629639 CCATTCCCTCCTTCCACCTCTA 60.630 54.545 0.00 0.00 0.00 2.43
4325 7675 4.956700 TCTATCAACTCATCGGAACTCCTT 59.043 41.667 0.00 0.00 0.00 3.36
4346 7696 2.203126 CCCAGGATGCGGCTCTTC 60.203 66.667 0.00 0.00 31.97 2.87
4389 7739 1.004918 CGGTCTTCTTCCGGCAACT 60.005 57.895 0.00 0.00 43.68 3.16
4434 7784 2.345991 CCCGGTTTCTTCAGGCGA 59.654 61.111 0.00 0.00 0.00 5.54
4435 7785 2.033194 CCCGGTTTCTTCAGGCGAC 61.033 63.158 0.00 0.00 0.00 5.19
4436 7786 1.301401 CCGGTTTCTTCAGGCGACA 60.301 57.895 0.00 0.00 0.00 4.35
4437 7787 0.673644 CCGGTTTCTTCAGGCGACAT 60.674 55.000 0.00 0.00 0.00 3.06
4438 7788 0.443869 CGGTTTCTTCAGGCGACATG 59.556 55.000 0.00 0.00 0.00 3.21
4439 7789 0.804989 GGTTTCTTCAGGCGACATGG 59.195 55.000 0.00 0.00 0.00 3.66
4440 7790 0.804989 GTTTCTTCAGGCGACATGGG 59.195 55.000 0.00 0.00 0.00 4.00
4441 7791 0.690192 TTTCTTCAGGCGACATGGGA 59.310 50.000 0.00 0.00 0.00 4.37
4442 7792 0.911769 TTCTTCAGGCGACATGGGAT 59.088 50.000 0.00 0.00 0.00 3.85
4443 7793 0.465705 TCTTCAGGCGACATGGGATC 59.534 55.000 0.00 0.00 0.00 3.36
4444 7794 0.533755 CTTCAGGCGACATGGGATCC 60.534 60.000 1.92 1.92 0.00 3.36
4445 7795 0.982852 TTCAGGCGACATGGGATCCT 60.983 55.000 12.58 0.00 0.00 3.24
4446 7796 0.105709 TCAGGCGACATGGGATCCTA 60.106 55.000 12.58 5.82 0.00 2.94
4447 7797 0.319728 CAGGCGACATGGGATCCTAG 59.680 60.000 12.58 4.40 0.00 3.02
4448 7798 0.188587 AGGCGACATGGGATCCTAGA 59.811 55.000 12.58 0.00 0.00 2.43
4449 7799 0.318762 GGCGACATGGGATCCTAGAC 59.681 60.000 12.58 0.43 0.00 2.59
4450 7800 1.333177 GCGACATGGGATCCTAGACT 58.667 55.000 12.58 0.00 0.00 3.24
4451 7801 1.000283 GCGACATGGGATCCTAGACTG 60.000 57.143 12.58 3.51 0.00 3.51
4452 7802 2.311463 CGACATGGGATCCTAGACTGT 58.689 52.381 12.58 7.15 0.00 3.55
4453 7803 2.695666 CGACATGGGATCCTAGACTGTT 59.304 50.000 12.58 0.00 0.00 3.16
4454 7804 3.243569 CGACATGGGATCCTAGACTGTTC 60.244 52.174 12.58 1.58 0.00 3.18
4455 7805 3.964031 GACATGGGATCCTAGACTGTTCT 59.036 47.826 12.58 0.00 35.66 3.01
4456 7806 4.366267 ACATGGGATCCTAGACTGTTCTT 58.634 43.478 12.58 0.00 32.75 2.52
4457 7807 4.785376 ACATGGGATCCTAGACTGTTCTTT 59.215 41.667 12.58 0.00 32.75 2.52
4458 7808 5.251700 ACATGGGATCCTAGACTGTTCTTTT 59.748 40.000 12.58 0.00 32.75 2.27
4459 7809 5.843019 TGGGATCCTAGACTGTTCTTTTT 57.157 39.130 12.58 0.00 32.75 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 1043 0.834687 TCGGTTGTAAGAGCAGGGGT 60.835 55.000 0.00 0.00 0.00 4.95
174 1143 1.076777 GATGGGTGGATGTGGGGTG 60.077 63.158 0.00 0.00 0.00 4.61
175 1144 2.316586 GGATGGGTGGATGTGGGGT 61.317 63.158 0.00 0.00 0.00 4.95
178 1147 0.680921 GTGTGGATGGGTGGATGTGG 60.681 60.000 0.00 0.00 0.00 4.17
180 1149 1.198094 TCGTGTGGATGGGTGGATGT 61.198 55.000 0.00 0.00 0.00 3.06
228 1197 3.766691 GAACGGCGGAGGTGGCTA 61.767 66.667 13.24 0.00 0.00 3.93
301 1278 3.024547 TCCTCTAGACGAAATGGGTGAG 58.975 50.000 0.00 0.00 0.00 3.51
436 1418 7.219484 AGAAAGACATATCCCAAACTTGTTG 57.781 36.000 0.00 0.00 0.00 3.33
507 1489 1.003545 CGAGCGCAATGAACCCAATAG 60.004 52.381 11.47 0.00 0.00 1.73
642 1624 1.459158 ACCAGGTGCAAATTGGGCA 60.459 52.632 14.69 1.19 39.32 5.36
668 1651 4.522789 GGAATCTACCAAGGCAAGTTGAAA 59.477 41.667 7.16 0.00 0.00 2.69
679 1662 2.166459 TGCTCACGAGGAATCTACCAAG 59.834 50.000 0.00 0.00 0.00 3.61
680 1663 2.176045 TGCTCACGAGGAATCTACCAA 58.824 47.619 0.00 0.00 0.00 3.67
685 1668 3.340814 AATGTTGCTCACGAGGAATCT 57.659 42.857 4.23 0.00 40.79 2.40
691 1674 3.624326 TTGGAAAATGTTGCTCACGAG 57.376 42.857 0.00 0.00 0.00 4.18
692 1675 3.820467 AGATTGGAAAATGTTGCTCACGA 59.180 39.130 0.00 0.00 0.00 4.35
693 1676 3.916172 CAGATTGGAAAATGTTGCTCACG 59.084 43.478 0.00 0.00 0.00 4.35
694 1677 4.919754 GTCAGATTGGAAAATGTTGCTCAC 59.080 41.667 0.00 0.00 0.00 3.51
695 1678 4.583907 TGTCAGATTGGAAAATGTTGCTCA 59.416 37.500 0.00 0.00 0.00 4.26
809 1794 4.783764 ACCACTACAAATAAAAGCAGCC 57.216 40.909 0.00 0.00 0.00 4.85
855 1840 7.272244 TCTCAAAACTAATATCTGGCAATCGA 58.728 34.615 0.00 0.00 0.00 3.59
856 1841 7.482654 TCTCAAAACTAATATCTGGCAATCG 57.517 36.000 0.00 0.00 0.00 3.34
869 1859 8.999431 GTCATTAGAACACCATCTCAAAACTAA 58.001 33.333 0.00 0.00 0.00 2.24
879 1870 8.816640 AACAAATTTGTCATTAGAACACCATC 57.183 30.769 23.47 0.00 41.31 3.51
921 1912 5.329399 TCTAAAATGGCATGTTGTACCCTT 58.671 37.500 13.23 0.00 0.00 3.95
964 1955 6.534079 GCAGAATAAGAAAAGGCTAAGTACGA 59.466 38.462 0.00 0.00 0.00 3.43
999 1990 2.303022 GCCATTGGAGCTACTAGCCATA 59.697 50.000 6.95 0.00 43.77 2.74
1348 2520 9.454585 CATAATCATCATGCAAAATTACGACTT 57.545 29.630 0.00 0.00 0.00 3.01
1416 2588 8.917088 AGTGCATTTTTATCTTTATGCTACCAT 58.083 29.630 0.00 0.00 42.85 3.55
1439 2611 8.909708 TGTTTACTCTGAAAATGTTTCAAGTG 57.090 30.769 18.42 11.15 0.00 3.16
1492 2674 4.095782 GCGTTGCTATTTGACTTGGGATAA 59.904 41.667 0.00 0.00 0.00 1.75
1570 2777 9.691362 AATTTCTGCATTAACAAAACTACGAAT 57.309 25.926 0.00 0.00 0.00 3.34
1633 2840 4.922206 TCTCAATGTATTGCCTGTCCTTT 58.078 39.130 0.00 0.00 37.68 3.11
1750 2957 5.321983 CGATCAGCAAAGACTACATAAGC 57.678 43.478 0.00 0.00 0.00 3.09
1834 3041 0.947244 CAAGGCCGTGAATATGCTCC 59.053 55.000 14.14 0.00 0.00 4.70
1861 3068 7.993183 TCAGGAAATTTCTCAAGTTCAGTTAGT 59.007 33.333 17.42 0.00 38.49 2.24
1911 3118 2.100418 TGAGAATCAGACCGCATCAGAG 59.900 50.000 0.00 0.00 42.56 3.35
1961 3168 4.357918 TTTGCAGCTCCTCTTCTTTACT 57.642 40.909 0.00 0.00 0.00 2.24
2008 3215 3.479006 CATGTCCAAAGTTACGCTTTCG 58.521 45.455 0.00 0.00 44.95 3.46
2023 3230 5.063180 TCTCAATTTCACATTGCATGTCC 57.937 39.130 0.00 0.00 42.70 4.02
2026 3233 8.523523 TTAAACTCTCAATTTCACATTGCATG 57.476 30.769 0.00 0.00 0.00 4.06
2083 3290 3.441572 GGCTAAAGCTCTCAGCATCAAAA 59.558 43.478 14.05 0.00 45.56 2.44
2116 3323 7.968956 TGCTTCTCTATTCTAACTTTGTACTCG 59.031 37.037 0.00 0.00 0.00 4.18
2467 3839 7.548196 TGTTTCTGAACTTGTTTGGTAGTAG 57.452 36.000 0.00 0.00 36.70 2.57
2505 3877 6.787085 AGCAACTAAATTCCATAGCGATAC 57.213 37.500 0.00 0.00 0.00 2.24
2530 3902 3.756434 TGAATTTACCCAACTAGCAGTGC 59.244 43.478 7.13 7.13 0.00 4.40
2548 3920 6.547141 TCAACAAAACAGACAGATCCTTGAAT 59.453 34.615 0.00 0.00 0.00 2.57
2585 3957 6.008696 TCACCGGAAATGGGAAACTTATAT 57.991 37.500 9.46 0.00 0.00 0.86
2591 3963 2.194201 TCTCACCGGAAATGGGAAAC 57.806 50.000 9.46 0.00 0.00 2.78
2603 3975 3.997021 AGAGCAACACTTAAATCTCACCG 59.003 43.478 0.00 0.00 0.00 4.94
2830 4209 5.794726 TTCTACTGGTGCAGTTACAGTTA 57.205 39.130 15.58 5.47 42.59 2.24
3058 4437 1.376543 CTCATGCGATTCCTGCAGTT 58.623 50.000 13.81 0.00 46.98 3.16
3224 4603 4.329392 TCTACAATGGAGGCATATGCATG 58.671 43.478 28.07 17.36 44.36 4.06
3391 4775 2.501223 TAGCGCTTGGTTCTCCGGTG 62.501 60.000 18.68 0.00 36.30 4.94
3392 4776 2.227089 CTAGCGCTTGGTTCTCCGGT 62.227 60.000 18.68 0.00 36.30 5.28
3393 4777 1.519455 CTAGCGCTTGGTTCTCCGG 60.519 63.158 18.68 0.00 36.30 5.14
3425 4809 1.329906 GCACCATCTGAAGCTTCATCG 59.670 52.381 28.57 18.22 36.46 3.84
3447 4831 8.877779 CATCTAGCATCCTACATTATTTACTGC 58.122 37.037 0.00 0.00 0.00 4.40
3490 4874 7.645340 CACAAAGAATTATATACAGCAACTGCC 59.355 37.037 0.00 0.00 43.38 4.85
3620 5005 7.087007 TGAATCTGAGACGATACATATGAAGC 58.913 38.462 10.38 0.00 0.00 3.86
3629 5014 3.316588 TGAGGCTGAATCTGAGACGATAC 59.683 47.826 0.00 0.00 0.00 2.24
3636 5021 2.101249 GAGTCCTGAGGCTGAATCTGAG 59.899 54.545 0.00 0.00 0.00 3.35
3695 5080 5.771469 TGCCACTTACAACATTCTCATTTG 58.229 37.500 0.00 0.00 0.00 2.32
3747 5132 7.210174 TGATCCTATTGGACAAATAACTCTCG 58.790 38.462 0.00 0.00 46.51 4.04
3759 5144 7.939039 TGGAATATGTTTCTGATCCTATTGGAC 59.061 37.037 0.00 0.00 46.51 4.02
3831 6665 9.639563 TGAATGGGCTTATTTCAACATATAAGA 57.360 29.630 0.00 0.00 36.77 2.10
3835 6669 9.768662 GATTTGAATGGGCTTATTTCAACATAT 57.231 29.630 0.00 0.00 0.00 1.78
3859 6693 0.176680 CAGCCGTGCAAGTCTAGGAT 59.823 55.000 0.00 0.00 0.00 3.24
3876 6710 2.905959 TTCGAGAAATGTGCATGCAG 57.094 45.000 23.41 6.81 0.00 4.41
3885 6719 7.260603 AGAAGGCCAAAATAATTCGAGAAATG 58.739 34.615 5.01 0.00 0.00 2.32
3892 6726 5.708948 TGTTGAGAAGGCCAAAATAATTCG 58.291 37.500 5.01 0.00 0.00 3.34
3944 6781 6.700081 TGCGTTATATGATCACTCCTACAAAC 59.300 38.462 0.00 0.00 0.00 2.93
3960 6797 3.886123 AGGCAAACTTCCTGCGTTATAT 58.114 40.909 0.00 0.00 40.88 0.86
4056 7362 4.398358 TGACCTCGTCCTGTAATAACTGAG 59.602 45.833 0.00 0.00 0.00 3.35
4075 7381 2.945668 GTTCTGGCCATATGACTTGACC 59.054 50.000 5.51 0.00 0.00 4.02
4087 7393 2.359850 GGCGTCATGTTCTGGCCA 60.360 61.111 4.71 4.71 43.23 5.36
4088 7394 3.499737 CGGCGTCATGTTCTGGCC 61.500 66.667 0.00 0.00 40.36 5.36
4291 7641 4.026744 TGAGTTGATAGAGGTGGAAGGAG 58.973 47.826 0.00 0.00 0.00 3.69
4305 7655 3.429547 CGAAGGAGTTCCGATGAGTTGAT 60.430 47.826 0.00 0.00 42.08 2.57
4346 7696 1.477295 GAGGAACGAACTGAGGTAGGG 59.523 57.143 0.00 0.00 0.00 3.53
4406 7756 0.034476 GAAACCGGGGTCGAGAAACT 59.966 55.000 6.32 0.00 39.00 2.66
4434 7784 4.000928 AGAACAGTCTAGGATCCCATGT 57.999 45.455 8.55 3.62 29.93 3.21
4435 7785 5.365021 AAAGAACAGTCTAGGATCCCATG 57.635 43.478 8.55 2.95 32.16 3.66
4436 7786 6.394345 AAAAAGAACAGTCTAGGATCCCAT 57.606 37.500 8.55 0.00 32.16 4.00
4437 7787 5.843019 AAAAAGAACAGTCTAGGATCCCA 57.157 39.130 8.55 0.00 32.16 4.37


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

AutoCloner maintained by Alex Coulton.