Multiple sequence alignment - TraesCS2D01G591000

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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 TraesCS2D01G591000 chr2D 100.000 3737 0 0 1 3737 646595771 646592035 0.000000e+00 6902
1 TraesCS2D01G591000 chr2D 91.166 815 63 5 2926 3734 647110100 647110911 0.000000e+00 1098
2 TraesCS2D01G591000 chr2A 95.275 3661 138 11 82 3734 773218023 773221656 0.000000e+00 5770
3 TraesCS2D01G591000 chr4A 77.143 875 192 6 2417 3286 18019130 18018259 5.570000e-138 501


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 TraesCS2D01G591000 chr2D 646592035 646595771 3736 True 6902 6902 100.000 1 3737 1 chr2D.!!$R1 3736
1 TraesCS2D01G591000 chr2D 647110100 647110911 811 False 1098 1098 91.166 2926 3734 1 chr2D.!!$F1 808
2 TraesCS2D01G591000 chr2A 773218023 773221656 3633 False 5770 5770 95.275 82 3734 1 chr2A.!!$F1 3652
3 TraesCS2D01G591000 chr4A 18018259 18019130 871 True 501 501 77.143 2417 3286 1 chr4A.!!$R1 869

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
633 634 0.038892 AAGCTTTTCCATGTGCAGCG 60.039 50.0 0.0 0.0 35.53 5.18 F
1305 1306 0.178068 CTAACCCTGGTGATCCCGTG 59.822 60.0 0.0 0.0 35.15 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 1858 1.078072 ACCGCATGCGAATGGGTAA 60.078 52.632 39.90 0.0 42.83 2.85 R
2923 2926 0.894184 GATATCCACGGGAGCCTCGA 60.894 60.000 1.29 0.0 34.05 4.04 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
28 29 7.118496 CCAGATCTGGTACTCTTAAACATCT 57.882 40.000 30.55 0.00 45.53 2.90
29 30 7.206687 CCAGATCTGGTACTCTTAAACATCTC 58.793 42.308 30.55 0.00 45.53 2.75
30 31 7.206687 CAGATCTGGTACTCTTAAACATCTCC 58.793 42.308 15.38 0.00 0.00 3.71
31 32 5.934402 TCTGGTACTCTTAAACATCTCCC 57.066 43.478 0.00 0.00 0.00 4.30
32 33 5.590818 TCTGGTACTCTTAAACATCTCCCT 58.409 41.667 0.00 0.00 0.00 4.20
33 34 5.657302 TCTGGTACTCTTAAACATCTCCCTC 59.343 44.000 0.00 0.00 0.00 4.30
34 35 5.338632 TGGTACTCTTAAACATCTCCCTCA 58.661 41.667 0.00 0.00 0.00 3.86
35 36 5.422331 TGGTACTCTTAAACATCTCCCTCAG 59.578 44.000 0.00 0.00 0.00 3.35
36 37 4.479786 ACTCTTAAACATCTCCCTCAGC 57.520 45.455 0.00 0.00 0.00 4.26
37 38 3.840666 ACTCTTAAACATCTCCCTCAGCA 59.159 43.478 0.00 0.00 0.00 4.41
38 39 4.187694 CTCTTAAACATCTCCCTCAGCAC 58.812 47.826 0.00 0.00 0.00 4.40
39 40 2.672961 TAAACATCTCCCTCAGCACG 57.327 50.000 0.00 0.00 0.00 5.34
40 41 0.687354 AAACATCTCCCTCAGCACGT 59.313 50.000 0.00 0.00 0.00 4.49
41 42 0.687354 AACATCTCCCTCAGCACGTT 59.313 50.000 0.00 0.00 0.00 3.99
42 43 0.687354 ACATCTCCCTCAGCACGTTT 59.313 50.000 0.00 0.00 0.00 3.60
43 44 1.338200 ACATCTCCCTCAGCACGTTTC 60.338 52.381 0.00 0.00 0.00 2.78
44 45 1.066573 CATCTCCCTCAGCACGTTTCT 60.067 52.381 0.00 0.00 0.00 2.52
45 46 1.919240 TCTCCCTCAGCACGTTTCTA 58.081 50.000 0.00 0.00 0.00 2.10
46 47 1.544691 TCTCCCTCAGCACGTTTCTAC 59.455 52.381 0.00 0.00 0.00 2.59
47 48 1.546476 CTCCCTCAGCACGTTTCTACT 59.454 52.381 0.00 0.00 0.00 2.57
48 49 1.544691 TCCCTCAGCACGTTTCTACTC 59.455 52.381 0.00 0.00 0.00 2.59
49 50 1.618861 CCTCAGCACGTTTCTACTCG 58.381 55.000 0.00 0.00 0.00 4.18
50 51 1.068472 CCTCAGCACGTTTCTACTCGT 60.068 52.381 0.00 0.00 40.99 4.18
51 52 2.243407 CTCAGCACGTTTCTACTCGTC 58.757 52.381 0.00 0.00 38.23 4.20
52 53 0.975544 CAGCACGTTTCTACTCGTCG 59.024 55.000 0.00 0.00 38.23 5.12
53 54 0.590195 AGCACGTTTCTACTCGTCGT 59.410 50.000 0.00 0.00 38.23 4.34
54 55 0.973423 GCACGTTTCTACTCGTCGTC 59.027 55.000 0.00 0.00 38.23 4.20
55 56 1.399471 GCACGTTTCTACTCGTCGTCT 60.399 52.381 0.00 0.00 38.23 4.18
56 57 2.913613 CACGTTTCTACTCGTCGTCTT 58.086 47.619 0.00 0.00 38.23 3.01
57 58 2.650765 CACGTTTCTACTCGTCGTCTTG 59.349 50.000 0.00 0.00 38.23 3.02
58 59 2.545526 ACGTTTCTACTCGTCGTCTTGA 59.454 45.455 0.00 0.00 35.30 3.02
59 60 3.002656 ACGTTTCTACTCGTCGTCTTGAA 59.997 43.478 0.00 0.00 35.30 2.69
60 61 3.357240 CGTTTCTACTCGTCGTCTTGAAC 59.643 47.826 0.00 0.00 0.00 3.18
61 62 4.535116 GTTTCTACTCGTCGTCTTGAACT 58.465 43.478 0.00 0.00 0.00 3.01
62 63 4.825546 TTCTACTCGTCGTCTTGAACTT 57.174 40.909 0.00 0.00 0.00 2.66
63 64 4.825546 TCTACTCGTCGTCTTGAACTTT 57.174 40.909 0.00 0.00 0.00 2.66
64 65 4.781071 TCTACTCGTCGTCTTGAACTTTC 58.219 43.478 0.00 0.00 0.00 2.62
65 66 3.712091 ACTCGTCGTCTTGAACTTTCT 57.288 42.857 0.00 0.00 0.00 2.52
66 67 4.043037 ACTCGTCGTCTTGAACTTTCTT 57.957 40.909 0.00 0.00 0.00 2.52
67 68 4.430908 ACTCGTCGTCTTGAACTTTCTTT 58.569 39.130 0.00 0.00 0.00 2.52
68 69 4.868734 ACTCGTCGTCTTGAACTTTCTTTT 59.131 37.500 0.00 0.00 0.00 2.27
69 70 5.350640 ACTCGTCGTCTTGAACTTTCTTTTT 59.649 36.000 0.00 0.00 0.00 1.94
120 121 6.837992 TGATTTTTAGTCGTAGCCATTCAAC 58.162 36.000 0.00 0.00 0.00 3.18
181 182 1.745232 TTCACGTTGGATATGTGGCC 58.255 50.000 0.00 0.00 42.83 5.36
183 184 0.393673 CACGTTGGATATGTGGCCCA 60.394 55.000 0.00 0.00 39.62 5.36
188 189 3.299503 GTTGGATATGTGGCCCAGAAAT 58.700 45.455 0.00 0.00 0.00 2.17
201 202 3.132824 GCCCAGAAATTATCCCCACAAAG 59.867 47.826 0.00 0.00 0.00 2.77
207 208 7.449247 CAGAAATTATCCCCACAAAGGAAAAA 58.551 34.615 0.00 0.00 41.22 1.94
237 238 3.414700 CCTCGCGCGCAGAAAGTT 61.415 61.111 32.61 0.00 0.00 2.66
238 239 2.551270 CTCGCGCGCAGAAAGTTT 59.449 55.556 32.61 0.00 0.00 2.66
239 240 1.507919 CTCGCGCGCAGAAAGTTTC 60.508 57.895 32.61 7.57 0.00 2.78
240 241 2.860659 CGCGCGCAGAAAGTTTCG 60.861 61.111 32.61 6.38 34.02 3.46
241 242 3.159460 GCGCGCAGAAAGTTTCGC 61.159 61.111 29.10 17.11 43.62 4.70
272 273 6.507771 CGCGATGTAAATATTTTTGCCAAAGG 60.508 38.462 0.00 0.00 0.00 3.11
282 283 3.552132 TTTGCCAAAGGAAAAAGACCC 57.448 42.857 0.00 0.00 25.14 4.46
287 288 2.231235 CCAAAGGAAAAAGACCCCATCG 59.769 50.000 0.00 0.00 0.00 3.84
289 290 0.404040 AGGAAAAAGACCCCATCGCA 59.596 50.000 0.00 0.00 0.00 5.10
290 291 0.811281 GGAAAAAGACCCCATCGCAG 59.189 55.000 0.00 0.00 0.00 5.18
291 292 0.811281 GAAAAAGACCCCATCGCAGG 59.189 55.000 0.00 0.00 0.00 4.85
292 293 0.404040 AAAAAGACCCCATCGCAGGA 59.596 50.000 0.00 0.00 0.00 3.86
293 294 0.322546 AAAAGACCCCATCGCAGGAC 60.323 55.000 0.00 0.00 0.00 3.85
294 295 1.488705 AAAGACCCCATCGCAGGACA 61.489 55.000 0.00 0.00 0.00 4.02
295 296 1.903877 AAGACCCCATCGCAGGACAG 61.904 60.000 0.00 0.00 0.00 3.51
300 301 1.145598 CCATCGCAGGACAGAGCAT 59.854 57.895 0.00 0.00 0.00 3.79
315 316 5.312895 ACAGAGCATATCTATCGTCTGAGT 58.687 41.667 4.24 0.00 36.10 3.41
319 320 6.149308 AGAGCATATCTATCGTCTGAGTTCAG 59.851 42.308 2.69 2.69 39.98 3.02
330 331 2.043664 TCTGAGTTCAGTCCCCATCTCT 59.956 50.000 8.85 0.00 44.12 3.10
334 335 1.617018 TTCAGTCCCCATCTCTGGCG 61.617 60.000 0.00 0.00 41.64 5.69
464 465 3.056465 CGAGAGGGATACATAAGGGAAGC 60.056 52.174 0.00 0.00 39.74 3.86
476 477 1.448717 GGGAAGCAGCCGACTCTTC 60.449 63.158 0.00 3.51 36.42 2.87
564 565 6.959639 TTTCTTCTTGCAAACACTAGGATT 57.040 33.333 0.00 0.00 0.00 3.01
632 633 3.302365 TTAAGCTTTTCCATGTGCAGC 57.698 42.857 3.20 0.00 0.00 5.25
633 634 0.038892 AAGCTTTTCCATGTGCAGCG 60.039 50.000 0.00 0.00 35.53 5.18
667 668 4.864334 GTCCATGGCCTCCCTGCG 62.864 72.222 6.96 0.00 0.00 5.18
724 725 7.109501 TGCATGCCTAACTTATCAAGAGTAAA 58.890 34.615 16.68 0.00 0.00 2.01
754 755 9.941664 CTTCTTCATAACATGGCAACTAAATAG 57.058 33.333 0.00 0.00 37.61 1.73
759 760 7.498900 TCATAACATGGCAACTAAATAGTGGAG 59.501 37.037 0.00 0.00 36.50 3.86
764 765 5.974108 TGGCAACTAAATAGTGGAGTACTC 58.026 41.667 14.87 14.87 38.05 2.59
771 772 8.743085 ACTAAATAGTGGAGTACTCGTATCAA 57.257 34.615 16.56 0.74 40.89 2.57
801 802 5.719173 ACAACTCTGCTATCTTCTCTTCAC 58.281 41.667 0.00 0.00 0.00 3.18
832 833 7.341256 TCTCAACGAGTATAAGTATCAACCCTT 59.659 37.037 0.00 0.00 0.00 3.95
895 896 4.900635 TTTTCTCTTTGTGCTTGGAGTC 57.099 40.909 0.00 0.00 0.00 3.36
963 964 5.373222 TGTTAATATATTTCTGGCAGCGGT 58.627 37.500 10.34 0.00 0.00 5.68
1036 1037 3.421919 TGAACATGCTGAGTTCCATCA 57.578 42.857 11.90 0.00 43.57 3.07
1048 1049 6.151817 GCTGAGTTCCATCATTTTCCTACTTT 59.848 38.462 0.00 0.00 0.00 2.66
1051 1052 7.094805 TGAGTTCCATCATTTTCCTACTTTTCG 60.095 37.037 0.00 0.00 0.00 3.46
1092 1093 4.162690 GCCTACCCCTCCACTGCG 62.163 72.222 0.00 0.00 0.00 5.18
1181 1182 3.341823 CCCTTGTCATTCTTGAGAGTGG 58.658 50.000 4.04 0.00 33.27 4.00
1305 1306 0.178068 CTAACCCTGGTGATCCCGTG 59.822 60.000 0.00 0.00 35.15 4.94
1400 1401 1.405105 GTCAACAGCCACAAAGAGCAA 59.595 47.619 0.00 0.00 0.00 3.91
1407 1408 1.265365 GCCACAAAGAGCAAGTCAGTC 59.735 52.381 0.00 0.00 0.00 3.51
1428 1429 1.144936 AGGCTTGCGGCTAGATGTC 59.855 57.895 15.54 1.79 45.31 3.06
1431 1432 0.878086 GCTTGCGGCTAGATGTCTCC 60.878 60.000 15.54 0.00 38.06 3.71
1483 1484 1.002468 CCTCTGTTTGGCAGTCGTTTG 60.002 52.381 0.00 0.00 45.23 2.93
1665 1666 1.783284 TCACTGAAGTTGCTAGCACG 58.217 50.000 19.17 5.27 0.00 5.34
1806 1807 0.684479 ACGAGATGCAGGGCTACTCA 60.684 55.000 0.00 0.00 33.84 3.41
1857 1858 4.713321 AGCCTAGCCATGAAATTTTGTGAT 59.287 37.500 0.00 0.00 0.00 3.06
2130 2131 1.527034 TGGATTGTGCTTGCAGAGTC 58.473 50.000 6.70 6.70 0.00 3.36
2131 2132 1.202794 TGGATTGTGCTTGCAGAGTCA 60.203 47.619 14.85 0.00 0.00 3.41
2152 2153 5.064325 GTCACCATTTTCCAGTATTACGGAC 59.936 44.000 6.83 0.00 0.00 4.79
2158 2159 4.741321 TTCCAGTATTACGGACCGAATT 57.259 40.909 23.38 6.67 0.00 2.17
2197 2198 4.756084 AACTGCTTGTTGTTATCAGAGC 57.244 40.909 0.00 0.00 37.52 4.09
2236 2237 1.137086 CAGAAGGTTCGTCCGATGGAT 59.863 52.381 0.00 0.00 41.99 3.41
2237 2238 1.137086 AGAAGGTTCGTCCGATGGATG 59.863 52.381 0.00 0.00 41.99 3.51
2305 2306 8.918202 AAGGATCACAACTATAGTTTGTTCAA 57.082 30.769 15.60 6.36 35.83 2.69
2347 2348 0.108138 AGGAATCTTGTTCTCCGCCG 60.108 55.000 0.00 0.00 34.22 6.46
2413 2414 0.616371 CATACCCGGGACACCAAAGA 59.384 55.000 32.02 0.08 36.13 2.52
2458 2459 3.055747 GGTAGCTACCAGCAACTTCTCTT 60.056 47.826 33.64 0.00 45.56 2.85
2478 2479 0.823356 TGAAGCTTGGAAGTGGTGGC 60.823 55.000 2.10 0.00 0.00 5.01
2486 2487 0.759060 GGAAGTGGTGGCTTTGGGTT 60.759 55.000 0.00 0.00 0.00 4.11
2556 2557 2.952310 GGAAAGTGTTCAGCAAGGAACT 59.048 45.455 14.36 0.00 45.74 3.01
2650 2651 1.005630 GCAGAGAAGTCGCACAGGT 60.006 57.895 0.00 0.00 0.00 4.00
2827 2830 2.890311 CCACTTGGACATAAAGCCACAA 59.110 45.455 0.00 0.00 37.39 3.33
2896 2899 6.303054 TGGACTGTCCAAAATGATAAACAGA 58.697 36.000 26.54 0.00 45.00 3.41
2923 2926 5.297776 CCAGAGCAAAATTATGACTCGGATT 59.702 40.000 0.00 0.00 32.39 3.01
3177 3180 1.208293 GGAGGAGGTCATGGAAGTGAC 59.792 57.143 0.00 0.00 46.04 3.67
3241 3244 1.006825 TCTTGATGTCAACGGTCGCG 61.007 55.000 0.00 0.00 0.00 5.87
3250 3253 1.522130 AACGGTCGCGAAGGTGTTT 60.522 52.632 12.06 0.00 0.00 2.83
3252 3255 2.241880 CGGTCGCGAAGGTGTTTGT 61.242 57.895 12.06 0.00 0.00 2.83
3281 3284 4.666253 GCTTGGAGGCTGCACCCA 62.666 66.667 8.71 4.98 40.58 4.51
3324 3327 5.973899 TTTGCATCAAATGGTGCTAGTAA 57.026 34.783 18.58 2.98 41.78 2.24
3420 3423 5.966742 TTCCATATCTGACTACGAGGATG 57.033 43.478 0.00 0.00 0.00 3.51
3454 3457 1.063492 TGCATCCTTCCATTCTGCCAT 60.063 47.619 0.00 0.00 31.89 4.40
3491 3494 5.713025 ACAATTTGGTGCATCACTATTCAC 58.287 37.500 0.00 0.00 34.40 3.18
3492 3495 5.243507 ACAATTTGGTGCATCACTATTCACA 59.756 36.000 0.00 0.00 31.64 3.58
3494 3497 5.375417 TTTGGTGCATCACTATTCACAAG 57.625 39.130 0.00 0.00 31.64 3.16
3550 3556 8.006298 TCTTGAGAAATTAAGGCAAAAGACAA 57.994 30.769 0.00 0.00 0.00 3.18
3562 3568 5.011943 AGGCAAAAGACAAATGGCAAGATAA 59.988 36.000 0.00 0.00 41.64 1.75
3584 3590 6.839124 AACCTATTCATTGCACATTCTCAA 57.161 33.333 0.00 0.00 0.00 3.02
3626 3634 4.250116 TCGTATTTGTGCCTTGCAAAAT 57.750 36.364 0.00 0.00 41.47 1.82
3675 3683 8.146479 TCATTTCTACTGCTATAATTGCACTG 57.854 34.615 0.00 0.00 36.37 3.66
3695 3703 3.049912 TGACTTTGACATCAACGAGACG 58.950 45.455 5.22 0.00 35.28 4.18
3734 3743 7.639378 AGGCCTTGTTTGGAACTAATTATCTA 58.361 34.615 0.00 0.00 0.00 1.98
3735 3744 8.113462 AGGCCTTGTTTGGAACTAATTATCTAA 58.887 33.333 0.00 0.00 0.00 2.10
3736 3745 8.188799 GGCCTTGTTTGGAACTAATTATCTAAC 58.811 37.037 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.206687 GGAGATGTTTAAGAGTACCAGATCTG 58.793 42.308 16.24 16.24 0.00 2.90
6 7 6.325286 GGGAGATGTTTAAGAGTACCAGATCT 59.675 42.308 0.00 0.00 0.00 2.75
7 8 6.325286 AGGGAGATGTTTAAGAGTACCAGATC 59.675 42.308 0.00 0.00 0.00 2.75
8 9 6.206042 AGGGAGATGTTTAAGAGTACCAGAT 58.794 40.000 0.00 0.00 0.00 2.90
9 10 5.590818 AGGGAGATGTTTAAGAGTACCAGA 58.409 41.667 0.00 0.00 0.00 3.86
10 11 5.422331 TGAGGGAGATGTTTAAGAGTACCAG 59.578 44.000 0.00 0.00 0.00 4.00
11 12 5.338632 TGAGGGAGATGTTTAAGAGTACCA 58.661 41.667 0.00 0.00 0.00 3.25
12 13 5.682730 GCTGAGGGAGATGTTTAAGAGTACC 60.683 48.000 0.00 0.00 0.00 3.34
13 14 5.105310 TGCTGAGGGAGATGTTTAAGAGTAC 60.105 44.000 0.00 0.00 0.00 2.73
14 15 5.023452 TGCTGAGGGAGATGTTTAAGAGTA 58.977 41.667 0.00 0.00 0.00 2.59
15 16 3.840666 TGCTGAGGGAGATGTTTAAGAGT 59.159 43.478 0.00 0.00 0.00 3.24
16 17 4.187694 GTGCTGAGGGAGATGTTTAAGAG 58.812 47.826 0.00 0.00 0.00 2.85
17 18 3.368427 CGTGCTGAGGGAGATGTTTAAGA 60.368 47.826 0.00 0.00 0.00 2.10
18 19 2.932614 CGTGCTGAGGGAGATGTTTAAG 59.067 50.000 0.00 0.00 0.00 1.85
19 20 2.301870 ACGTGCTGAGGGAGATGTTTAA 59.698 45.455 0.00 0.00 0.00 1.52
20 21 1.899814 ACGTGCTGAGGGAGATGTTTA 59.100 47.619 0.00 0.00 0.00 2.01
21 22 0.687354 ACGTGCTGAGGGAGATGTTT 59.313 50.000 0.00 0.00 0.00 2.83
22 23 0.687354 AACGTGCTGAGGGAGATGTT 59.313 50.000 0.00 0.00 0.00 2.71
23 24 0.687354 AAACGTGCTGAGGGAGATGT 59.313 50.000 0.00 0.00 0.00 3.06
24 25 1.066573 AGAAACGTGCTGAGGGAGATG 60.067 52.381 0.00 0.00 0.00 2.90
25 26 1.270907 AGAAACGTGCTGAGGGAGAT 58.729 50.000 0.00 0.00 0.00 2.75
26 27 1.544691 GTAGAAACGTGCTGAGGGAGA 59.455 52.381 0.00 0.00 0.00 3.71
27 28 1.546476 AGTAGAAACGTGCTGAGGGAG 59.454 52.381 0.00 0.00 0.00 4.30
28 29 1.544691 GAGTAGAAACGTGCTGAGGGA 59.455 52.381 0.00 0.00 0.00 4.20
29 30 1.732732 CGAGTAGAAACGTGCTGAGGG 60.733 57.143 0.00 0.00 0.00 4.30
30 31 1.068472 ACGAGTAGAAACGTGCTGAGG 60.068 52.381 0.00 0.00 41.17 3.86
31 32 2.243407 GACGAGTAGAAACGTGCTGAG 58.757 52.381 0.00 0.00 42.74 3.35
32 33 1.399343 CGACGAGTAGAAACGTGCTGA 60.399 52.381 0.00 0.00 42.74 4.26
33 34 0.975544 CGACGAGTAGAAACGTGCTG 59.024 55.000 0.00 0.00 42.74 4.41
34 35 0.590195 ACGACGAGTAGAAACGTGCT 59.410 50.000 0.00 0.00 42.74 4.40
35 36 0.973423 GACGACGAGTAGAAACGTGC 59.027 55.000 0.00 0.00 42.74 5.34
36 37 2.591066 AGACGACGAGTAGAAACGTG 57.409 50.000 0.00 0.00 42.74 4.49
37 38 2.545526 TCAAGACGACGAGTAGAAACGT 59.454 45.455 0.00 0.00 45.32 3.99
38 39 3.179010 TCAAGACGACGAGTAGAAACG 57.821 47.619 0.00 0.00 0.00 3.60
39 40 4.535116 AGTTCAAGACGACGAGTAGAAAC 58.465 43.478 0.00 0.00 0.00 2.78
40 41 4.825546 AGTTCAAGACGACGAGTAGAAA 57.174 40.909 0.00 0.00 0.00 2.52
41 42 4.825546 AAGTTCAAGACGACGAGTAGAA 57.174 40.909 0.00 0.00 0.00 2.10
42 43 4.514441 AGAAAGTTCAAGACGACGAGTAGA 59.486 41.667 0.00 0.00 0.00 2.59
43 44 4.785417 AGAAAGTTCAAGACGACGAGTAG 58.215 43.478 0.00 0.00 0.00 2.57
44 45 4.825546 AGAAAGTTCAAGACGACGAGTA 57.174 40.909 0.00 0.00 0.00 2.59
45 46 3.712091 AGAAAGTTCAAGACGACGAGT 57.288 42.857 0.00 0.00 0.00 4.18
46 47 5.391060 AAAAGAAAGTTCAAGACGACGAG 57.609 39.130 0.00 0.00 0.00 4.18
47 48 5.789710 AAAAAGAAAGTTCAAGACGACGA 57.210 34.783 0.00 0.00 0.00 4.20
66 67 9.950680 GTTAGTTCAAGATGACATTCTCAAAAA 57.049 29.630 0.00 0.00 30.60 1.94
67 68 8.282592 CGTTAGTTCAAGATGACATTCTCAAAA 58.717 33.333 0.00 0.00 30.60 2.44
68 69 7.441157 ACGTTAGTTCAAGATGACATTCTCAAA 59.559 33.333 0.00 0.00 30.60 2.69
69 70 6.929049 ACGTTAGTTCAAGATGACATTCTCAA 59.071 34.615 0.00 0.00 30.60 3.02
70 71 6.455647 ACGTTAGTTCAAGATGACATTCTCA 58.544 36.000 0.00 0.00 0.00 3.27
71 72 6.952935 ACGTTAGTTCAAGATGACATTCTC 57.047 37.500 0.00 0.00 0.00 2.87
72 73 7.441157 TCAAACGTTAGTTCAAGATGACATTCT 59.559 33.333 0.00 0.00 40.18 2.40
73 74 7.572759 TCAAACGTTAGTTCAAGATGACATTC 58.427 34.615 0.00 0.00 40.18 2.67
74 75 7.490962 TCAAACGTTAGTTCAAGATGACATT 57.509 32.000 0.00 0.00 40.18 2.71
75 76 7.672983 ATCAAACGTTAGTTCAAGATGACAT 57.327 32.000 0.00 0.00 40.18 3.06
76 77 7.490962 AATCAAACGTTAGTTCAAGATGACA 57.509 32.000 0.00 0.00 40.18 3.58
77 78 8.782533 AAAATCAAACGTTAGTTCAAGATGAC 57.217 30.769 0.00 0.00 40.18 3.06
81 82 9.925268 GACTAAAAATCAAACGTTAGTTCAAGA 57.075 29.630 0.00 0.00 40.18 3.02
82 83 8.879299 CGACTAAAAATCAAACGTTAGTTCAAG 58.121 33.333 0.00 0.00 40.18 3.02
83 84 8.389603 ACGACTAAAAATCAAACGTTAGTTCAA 58.610 29.630 0.00 0.00 40.18 2.69
120 121 4.234574 GGGCTGGAACTAAAAATCAAACG 58.765 43.478 0.00 0.00 0.00 3.60
181 182 4.609301 TCCTTTGTGGGGATAATTTCTGG 58.391 43.478 0.00 0.00 36.20 3.86
183 184 7.625498 TTTTTCCTTTGTGGGGATAATTTCT 57.375 32.000 0.00 0.00 36.20 2.52
221 222 1.507919 GAAACTTTCTGCGCGCGAG 60.508 57.895 37.18 26.30 0.00 5.03
223 224 2.860659 CGAAACTTTCTGCGCGCG 60.861 61.111 28.44 28.44 0.00 6.86
227 228 2.069277 GTGCGCGAAACTTTCTGCG 61.069 57.895 24.01 24.01 46.92 5.18
228 229 1.725973 GGTGCGCGAAACTTTCTGC 60.726 57.895 12.10 8.08 0.00 4.26
229 230 1.082104 GGGTGCGCGAAACTTTCTG 60.082 57.895 12.10 0.00 0.00 3.02
230 231 2.604174 CGGGTGCGCGAAACTTTCT 61.604 57.895 12.10 0.00 0.00 2.52
231 232 2.127383 CGGGTGCGCGAAACTTTC 60.127 61.111 12.10 0.00 0.00 2.62
232 233 4.322385 GCGGGTGCGCGAAACTTT 62.322 61.111 12.10 0.00 0.00 2.66
242 243 3.619233 AAATATTTACATCGCGGGTGC 57.381 42.857 6.13 0.00 37.91 5.01
272 273 0.811281 CCTGCGATGGGGTCTTTTTC 59.189 55.000 0.00 0.00 0.00 2.29
282 283 0.390492 TATGCTCTGTCCTGCGATGG 59.610 55.000 0.00 0.00 0.00 3.51
287 288 3.192422 ACGATAGATATGCTCTGTCCTGC 59.808 47.826 0.00 0.00 38.53 4.85
289 290 4.699735 CAGACGATAGATATGCTCTGTCCT 59.300 45.833 0.00 0.00 38.53 3.85
290 291 4.697828 TCAGACGATAGATATGCTCTGTCC 59.302 45.833 0.00 0.00 38.53 4.02
291 292 5.411361 ACTCAGACGATAGATATGCTCTGTC 59.589 44.000 0.00 0.00 38.42 3.51
292 293 5.312895 ACTCAGACGATAGATATGCTCTGT 58.687 41.667 0.00 0.00 41.38 3.41
293 294 5.878332 ACTCAGACGATAGATATGCTCTG 57.122 43.478 0.00 0.00 41.38 3.35
294 295 6.000840 TGAACTCAGACGATAGATATGCTCT 58.999 40.000 0.00 0.00 41.38 4.09
295 296 6.072728 ACTGAACTCAGACGATAGATATGCTC 60.073 42.308 13.61 0.00 46.59 4.26
300 301 5.064558 GGGACTGAACTCAGACGATAGATA 58.935 45.833 13.61 0.00 46.59 1.98
315 316 1.617018 CGCCAGAGATGGGGACTGAA 61.617 60.000 5.46 0.00 43.67 3.02
334 335 1.763545 GGTGATTCAGTAGGGGAGGTC 59.236 57.143 0.00 0.00 0.00 3.85
395 396 1.899437 AATCGACCACCGTGGATGCT 61.899 55.000 24.80 0.70 40.96 3.79
443 444 3.904339 TGCTTCCCTTATGTATCCCTCTC 59.096 47.826 0.00 0.00 0.00 3.20
476 477 3.156157 CTGCTTCCTCTTGGAGCAG 57.844 57.895 8.00 8.00 46.90 4.24
511 512 1.153939 CGAGGAGAGGAACTGTGCG 60.154 63.158 0.00 0.00 46.55 5.34
512 513 0.172352 CTCGAGGAGAGGAACTGTGC 59.828 60.000 3.91 0.00 41.55 4.57
539 540 6.377327 TCCTAGTGTTTGCAAGAAGAAAAG 57.623 37.500 0.00 0.00 0.00 2.27
619 620 1.266718 GAAGAACGCTGCACATGGAAA 59.733 47.619 0.00 0.00 0.00 3.13
626 627 2.199467 GACGACGAAGAACGCTGCAC 62.199 60.000 0.00 0.00 46.94 4.57
633 634 2.287427 TGGACTTGAGACGACGAAGAAC 60.287 50.000 0.00 0.00 0.00 3.01
667 668 3.214328 TCAGGTTCTTGGCTTCTTCAAC 58.786 45.455 0.00 0.00 0.00 3.18
724 725 4.226427 TGCCATGTTATGAAGAAGAGCT 57.774 40.909 0.00 0.00 0.00 4.09
732 733 7.831690 TCCACTATTTAGTTGCCATGTTATGAA 59.168 33.333 0.00 0.00 33.46 2.57
733 734 7.342581 TCCACTATTTAGTTGCCATGTTATGA 58.657 34.615 0.00 0.00 33.46 2.15
734 735 7.283127 ACTCCACTATTTAGTTGCCATGTTATG 59.717 37.037 0.00 0.00 33.46 1.90
738 739 5.179452 ACTCCACTATTTAGTTGCCATGT 57.821 39.130 0.00 0.00 33.46 3.21
754 755 3.734293 GCCTGTTGATACGAGTACTCCAC 60.734 52.174 17.23 6.78 0.00 4.02
759 760 3.581755 TGTTGCCTGTTGATACGAGTAC 58.418 45.455 0.00 0.00 0.00 2.73
764 765 3.067106 AGAGTTGTTGCCTGTTGATACG 58.933 45.455 0.00 0.00 0.00 3.06
771 772 2.304180 AGATAGCAGAGTTGTTGCCTGT 59.696 45.455 0.00 0.00 42.48 4.00
801 802 9.569167 TTGATACTTATACTCGTTGAGAACAAG 57.431 33.333 0.00 3.39 36.64 3.16
832 833 1.741706 GTCGGAGGACTTACGATGTGA 59.258 52.381 0.00 0.00 40.15 3.58
938 939 5.385617 CGCTGCCAGAAATATATTAACAGC 58.614 41.667 18.58 18.58 43.39 4.40
971 972 6.981722 TGTGCTTATATATGCTCGAAGAAGA 58.018 36.000 18.37 0.00 34.09 2.87
1036 1037 6.158169 AGGATAGGGACGAAAAGTAGGAAAAT 59.842 38.462 0.00 0.00 0.00 1.82
1048 1049 0.399949 ATGGGCAGGATAGGGACGAA 60.400 55.000 0.00 0.00 0.00 3.85
1051 1052 1.062488 ACCATGGGCAGGATAGGGAC 61.062 60.000 18.09 0.00 0.00 4.46
1092 1093 1.207791 TCCAGAGATTTGAGGGAGCC 58.792 55.000 0.00 0.00 0.00 4.70
1181 1182 0.108138 AAGTCGGTATGAGGTGCTGC 60.108 55.000 0.00 0.00 0.00 5.25
1305 1306 0.394762 TCAACATGGCATCCTGGCTC 60.395 55.000 0.00 0.00 44.10 4.70
1400 1401 2.358003 GCAAGCCTGCGACTGACT 60.358 61.111 0.00 0.00 39.20 3.41
1428 1429 1.675552 ACAACACAAGGTTTCCGGAG 58.324 50.000 3.34 0.00 37.72 4.63
1431 1432 3.495670 TCAAACAACACAAGGTTTCCG 57.504 42.857 0.00 0.00 37.72 4.30
1483 1484 3.016736 CCAATGTATCTGTTGGGTGGTC 58.983 50.000 0.00 0.00 40.90 4.02
1665 1666 7.307694 TGACAAATGCATAACAGTCTGATTTC 58.692 34.615 6.91 0.00 0.00 2.17
1857 1858 1.078072 ACCGCATGCGAATGGGTAA 60.078 52.632 39.90 0.00 42.83 2.85
2002 2003 2.612972 CGAGTGGTAGCAACTGATGGTT 60.613 50.000 0.00 0.00 40.93 3.67
2025 2026 6.812656 TGTTGTCACTGAAGTAAGAAACGTTA 59.187 34.615 0.00 0.00 0.00 3.18
2112 2113 1.198637 GTGACTCTGCAAGCACAATCC 59.801 52.381 0.00 0.00 34.28 3.01
2130 2131 4.334481 GGTCCGTAATACTGGAAAATGGTG 59.666 45.833 5.76 0.00 35.67 4.17
2131 2132 4.520179 GGTCCGTAATACTGGAAAATGGT 58.480 43.478 5.76 0.00 35.67 3.55
2152 2153 8.553696 GTTACCACCATTACTGTAATAATTCGG 58.446 37.037 12.39 11.37 0.00 4.30
2158 2159 7.190335 AGCAGTTACCACCATTACTGTAATA 57.810 36.000 12.39 0.00 40.02 0.98
2197 2198 4.545610 TCTGCCAGCGAAATTAGTTTTTG 58.454 39.130 0.00 0.00 0.00 2.44
2236 2237 6.539826 CCTTGTATCTTGATGTATGCTGAACA 59.460 38.462 0.00 0.00 0.00 3.18
2237 2238 6.512415 GCCTTGTATCTTGATGTATGCTGAAC 60.512 42.308 0.00 0.00 0.00 3.18
2290 2291 9.243105 ACCTGCAATTATTGAACAAACTATAGT 57.757 29.630 9.36 0.00 0.00 2.12
2347 2348 7.315142 TCTTTCTTGCACATTTTCCATATGAC 58.685 34.615 3.65 0.00 0.00 3.06
2458 2459 1.691196 CCACCACTTCCAAGCTTCAA 58.309 50.000 0.00 0.00 0.00 2.69
2478 2479 6.546034 TCTTTCCTTTGAAGACTAACCCAAAG 59.454 38.462 0.00 0.00 42.86 2.77
2486 2487 6.352222 CCTGCCTATCTTTCCTTTGAAGACTA 60.352 42.308 0.00 0.00 36.08 2.59
2556 2557 3.093057 GACCTCTGCTAAGAACTCCTCA 58.907 50.000 0.00 0.00 30.03 3.86
2650 2651 4.921515 GCACATGTACTCGTAGACAAGAAA 59.078 41.667 0.00 0.00 0.00 2.52
2725 2728 9.661563 ATTATGATGTTACGTCTAGTTTTCCAA 57.338 29.630 6.13 0.00 0.00 3.53
2754 2757 4.081087 GGTAAGACAAACCTCTGGCTATCA 60.081 45.833 0.00 0.00 31.62 2.15
2755 2758 4.162509 AGGTAAGACAAACCTCTGGCTATC 59.837 45.833 0.00 0.00 44.20 2.08
2827 2830 7.405292 TGAACCTATCATCAAGGAGAATGTTT 58.595 34.615 0.00 0.00 37.57 2.83
2896 2899 4.872691 CGAGTCATAATTTTGCTCTGGTCT 59.127 41.667 13.78 0.00 0.00 3.85
2923 2926 0.894184 GATATCCACGGGAGCCTCGA 60.894 60.000 1.29 0.00 34.05 4.04
2930 2933 1.711375 AGGAGCTAGATATCCACGGGA 59.289 52.381 10.60 0.00 38.12 5.14
3177 3180 1.210931 CACCACATTGCAAGCCTCG 59.789 57.895 4.94 0.00 0.00 4.63
3222 3225 1.006825 CGCGACCGTTGACATCAAGA 61.007 55.000 0.00 0.00 36.39 3.02
3241 3244 1.529865 GTCACGCCTACAAACACCTTC 59.470 52.381 0.00 0.00 0.00 3.46
3250 3253 1.080772 CAAGCTCGTCACGCCTACA 60.081 57.895 0.00 0.00 0.00 2.74
3252 3255 1.934220 CTCCAAGCTCGTCACGCCTA 61.934 60.000 0.00 0.00 0.00 3.93
3281 3284 4.976540 AACTAGGGACAAAGCTGTAGTT 57.023 40.909 0.00 0.00 35.30 2.24
3324 3327 0.613012 GGAAGAAGTTGGCCCTGCAT 60.613 55.000 0.00 0.00 0.00 3.96
3454 3457 9.383519 TGCACCAAATTGTTTACAAAAGATTTA 57.616 25.926 0.00 0.00 39.55 1.40
3550 3556 6.324512 TGCAATGAATAGGTTATCTTGCCATT 59.675 34.615 0.00 0.00 37.34 3.16
3562 3568 6.839124 TTTGAGAATGTGCAATGAATAGGT 57.161 33.333 0.00 0.00 0.00 3.08
3599 3605 4.273235 TGCAAGGCACAAATACGATATGAG 59.727 41.667 0.00 0.00 31.71 2.90
3613 3621 6.724694 TCATTATTCAATTTTGCAAGGCAC 57.275 33.333 0.00 0.00 38.71 5.01
3665 3673 6.437928 GTTGATGTCAAAGTCAGTGCAATTA 58.562 36.000 0.00 0.00 37.63 1.40
3675 3683 3.050619 ACGTCTCGTTGATGTCAAAGTC 58.949 45.455 8.20 0.00 40.66 3.01
3695 3703 7.065443 CCAAACAAGGCCTATAGTACACTAAAC 59.935 40.741 5.16 0.00 31.39 2.01
3697 3705 6.441284 TCCAAACAAGGCCTATAGTACACTAA 59.559 38.462 5.16 0.00 31.39 2.24
3700 3708 5.093849 TCCAAACAAGGCCTATAGTACAC 57.906 43.478 5.16 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.