Multiple sequence alignment - TraesCS5B01G047500

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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 TraesCS5B01G047500 chr5B 100.000 4403 0 0 1 4403 53537071 53541473 0.000000e+00 8131
1 TraesCS5B01G047500 chr5D 92.353 3557 222 22 886 4403 50644231 50647776 0.000000e+00 5016
2 TraesCS5B01G047500 chr5D 87.759 2941 314 31 886 3812 50574032 50576940 0.000000e+00 3395
3 TraesCS5B01G047500 chr5D 88.621 2118 207 19 1741 3836 42984172 42986277 0.000000e+00 2545
4 TraesCS5B01G047500 chr5D 86.237 1257 153 12 2194 3433 50927549 50926296 0.000000e+00 1345
5 TraesCS5B01G047500 chr5D 88.261 690 55 14 221 891 50643523 50644205 0.000000e+00 802
6 TraesCS5B01G047500 chr5D 86.074 596 67 14 886 1477 42983592 42984175 1.040000e-175 627
7 TraesCS5B01G047500 chr5D 90.278 144 14 0 1 144 50643380 50643523 5.810000e-44 189
8 TraesCS5B01G047500 chr5A 86.579 2675 316 34 886 3533 39927679 39930337 0.000000e+00 2911
9 TraesCS5B01G047500 chr5A 82.140 1383 208 22 2081 3434 40161043 40162415 0.000000e+00 1149
10 TraesCS5B01G047500 chr5A 82.399 642 92 17 1 625 39926296 39926933 1.390000e-149 540
11 TraesCS5B01G047500 chr7A 81.416 2190 345 44 1289 3434 6298726 6300897 0.000000e+00 1733
12 TraesCS5B01G047500 chr7A 83.210 1346 197 19 2087 3411 50235212 50233875 0.000000e+00 1206
13 TraesCS5B01G047500 chr4A 81.616 2067 322 35 1400 3428 737708690 737710736 0.000000e+00 1659


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 TraesCS5B01G047500 chr5B 53537071 53541473 4402 False 8131.000000 8131 100.000000 1 4403 1 chr5B.!!$F1 4402
1 TraesCS5B01G047500 chr5D 50574032 50576940 2908 False 3395.000000 3395 87.759000 886 3812 1 chr5D.!!$F1 2926
2 TraesCS5B01G047500 chr5D 50643380 50647776 4396 False 2002.333333 5016 90.297333 1 4403 3 chr5D.!!$F3 4402
3 TraesCS5B01G047500 chr5D 42983592 42986277 2685 False 1586.000000 2545 87.347500 886 3836 2 chr5D.!!$F2 2950
4 TraesCS5B01G047500 chr5D 50926296 50927549 1253 True 1345.000000 1345 86.237000 2194 3433 1 chr5D.!!$R1 1239
5 TraesCS5B01G047500 chr5A 39926296 39930337 4041 False 1725.500000 2911 84.489000 1 3533 2 chr5A.!!$F2 3532
6 TraesCS5B01G047500 chr5A 40161043 40162415 1372 False 1149.000000 1149 82.140000 2081 3434 1 chr5A.!!$F1 1353
7 TraesCS5B01G047500 chr7A 6298726 6300897 2171 False 1733.000000 1733 81.416000 1289 3434 1 chr7A.!!$F1 2145
8 TraesCS5B01G047500 chr7A 50233875 50235212 1337 True 1206.000000 1206 83.210000 2087 3411 1 chr7A.!!$R1 1324
9 TraesCS5B01G047500 chr4A 737708690 737710736 2046 False 1659.000000 1659 81.616000 1400 3428 1 chr4A.!!$F1 2028

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
311 317 0.109365 CGGCTCTCACTCACTGACAG 60.109 60.000 0.0 0.0 0.0 3.51 F
544 558 1.922447 TGTCAATAAGAGGTGGGGCAT 59.078 47.619 0.0 0.0 0.0 4.40 F
1926 2475 0.396435 TTCTCATGCGAACCACCTGT 59.604 50.000 0.0 0.0 0.0 4.00 F
2472 3043 2.189521 GGTGGAGGGCATGGTACG 59.810 66.667 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 2207 0.600557 AAATGGCGGCATTTCGTTCA 59.399 45.000 36.04 3.05 29.61 3.18 R
2149 2713 1.779157 CGTATGCGGTAACATGACTCG 59.221 52.381 0.00 0.00 0.00 4.18 R
2736 3308 1.192980 GCTTTGCCAATTTCTGTTGCG 59.807 47.619 0.00 0.00 0.00 4.85 R
4292 4917 2.041265 CCTAGGGGGTCCTGCTGT 59.959 66.667 0.00 0.00 44.61 4.40 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
106 108 3.054802 AGCCTCTCTCAATCCATCGTTTT 60.055 43.478 0.00 0.00 0.00 2.43
107 109 3.311048 GCCTCTCTCAATCCATCGTTTTC 59.689 47.826 0.00 0.00 0.00 2.29
109 111 4.937620 CCTCTCTCAATCCATCGTTTTCAA 59.062 41.667 0.00 0.00 0.00 2.69
123 125 2.178912 TTTCAACCGACTCCATGACC 57.821 50.000 0.00 0.00 0.00 4.02
146 148 5.068591 CCCAAAAGTTTACTTAGCACCAACT 59.931 40.000 0.00 0.00 34.61 3.16
157 159 1.615392 AGCACCAACTTTTGCCTCATC 59.385 47.619 0.00 0.00 39.75 2.92
158 160 1.337167 GCACCAACTTTTGCCTCATCC 60.337 52.381 0.00 0.00 32.21 3.51
165 167 5.248640 CAACTTTTGCCTCATCCTCTAAGA 58.751 41.667 0.00 0.00 0.00 2.10
192 194 9.382275 ACTAAATCAATTTTCAGTTTGCTTTGT 57.618 25.926 0.00 0.00 0.00 2.83
194 196 8.898983 AAATCAATTTTCAGTTTGCTTTGTTG 57.101 26.923 0.00 0.00 0.00 3.33
210 213 5.445407 GCTTTGTTGATGCTCGAATACGTTA 60.445 40.000 0.00 0.00 40.69 3.18
212 215 4.989044 TGTTGATGCTCGAATACGTTAGA 58.011 39.130 0.00 0.00 40.69 2.10
216 219 3.957671 TGCTCGAATACGTTAGATCGT 57.042 42.857 0.00 0.00 45.97 3.73
222 225 6.349973 TCGAATACGTTAGATCGTGTTAGT 57.650 37.500 0.00 0.00 42.96 2.24
226 229 8.616425 CGAATACGTTAGATCGTGTTAGTATTG 58.384 37.037 14.31 7.38 42.96 1.90
291 297 1.688197 CCCCATTGGATCAAAATCGGG 59.312 52.381 3.62 8.14 35.39 5.14
311 317 0.109365 CGGCTCTCACTCACTGACAG 60.109 60.000 0.00 0.00 0.00 3.51
355 362 8.393671 TCGCCCTAAGTTTTATAAGAAAAACA 57.606 30.769 13.02 0.00 46.88 2.83
409 419 3.070446 ACCGTGTGTTGGAATGAGAGTAA 59.930 43.478 0.00 0.00 0.00 2.24
462 473 4.156556 ACATGCCCATATTTATGTGATCGC 59.843 41.667 0.00 0.00 32.90 4.58
466 477 4.201685 GCCCATATTTATGTGATCGCGTAC 60.202 45.833 5.77 4.94 31.82 3.67
489 503 7.671495 ACCAGAATTTTATTTGGCAAACATC 57.329 32.000 16.00 7.46 33.98 3.06
494 508 9.995003 AGAATTTTATTTGGCAAACATCTGTTA 57.005 25.926 16.00 0.00 37.25 2.41
544 558 1.922447 TGTCAATAAGAGGTGGGGCAT 59.078 47.619 0.00 0.00 0.00 4.40
576 591 4.496539 GTTTTGACGGAAAACGACGAAAAT 59.503 37.500 0.00 0.00 46.53 1.82
577 592 5.676310 GTTTTGACGGAAAACGACGAAAATA 59.324 36.000 0.00 0.00 46.53 1.40
592 607 5.675538 ACGAAAATATCAGAGAAGGAAGGG 58.324 41.667 0.00 0.00 0.00 3.95
593 608 5.059833 CGAAAATATCAGAGAAGGAAGGGG 58.940 45.833 0.00 0.00 0.00 4.79
611 627 6.013379 GGAAGGGGAAAATCAAAAGAGGAAAT 60.013 38.462 0.00 0.00 0.00 2.17
616 632 6.070021 GGGAAAATCAAAAGAGGAAATGGGAT 60.070 38.462 0.00 0.00 0.00 3.85
635 651 4.337274 GGGATTTGGAAACATACGTAAGGG 59.663 45.833 0.00 0.00 42.32 3.95
652 668 5.278561 CGTAAGGGTAGATGAAGGATGAGTC 60.279 48.000 0.00 0.00 0.00 3.36
664 680 2.933573 GGATGAGTCCGAGAGAACCTA 58.066 52.381 0.00 0.00 34.13 3.08
666 682 3.254657 GGATGAGTCCGAGAGAACCTATG 59.745 52.174 0.00 0.00 34.13 2.23
676 1111 7.601508 GTCCGAGAGAACCTATGTCTTTTTAAA 59.398 37.037 0.00 0.00 30.41 1.52
728 1170 9.696917 CTTACTCCTGCAAGAAAAATTAAACAT 57.303 29.630 0.00 0.00 34.07 2.71
763 1205 3.558321 CGGATAGGTTGACAAGTTTCCCA 60.558 47.826 0.00 0.00 0.00 4.37
778 1220 2.806945 TCCCAAGGTGCTATTTGGAG 57.193 50.000 13.10 5.87 45.32 3.86
818 1271 5.762711 ACTTGCACACAGACACATACATTAA 59.237 36.000 0.00 0.00 0.00 1.40
857 1326 8.383619 GTGCATATACTAATAAATCTGCTTCGG 58.616 37.037 0.00 0.00 0.00 4.30
872 1344 2.103263 GCTTCGGGGAGTATGATGAAGT 59.897 50.000 0.00 0.00 36.19 3.01
907 1410 6.907212 CGACAAGCCAAAATATAGATTCACAC 59.093 38.462 0.00 0.00 0.00 3.82
919 1422 2.104111 AGATTCACACGGTCAACTTGGA 59.896 45.455 0.00 0.00 0.00 3.53
972 1475 3.003275 ACGAGTGTAAACAGCCACAATTG 59.997 43.478 3.24 3.24 31.90 2.32
1017 1520 3.696051 CCAACATGGTTGGATCTTTCGAT 59.304 43.478 20.66 0.00 42.06 3.59
1069 1572 2.103263 GCCACCCACAAAAATGGTTGTA 59.897 45.455 0.00 0.00 39.73 2.41
1073 1576 3.580895 ACCCACAAAAATGGTTGTATCCC 59.419 43.478 0.00 0.00 39.73 3.85
1116 1619 6.268566 GCACTATTGCTTCTTATTTTCCCTG 58.731 40.000 0.00 0.00 46.17 4.45
1196 1699 7.290110 ACTTCCTCCTTTTCCAAAATGTAAG 57.710 36.000 0.00 0.00 0.00 2.34
1279 1782 6.037172 GCCAACATCTTTAAGAGCGAATTAGA 59.963 38.462 0.03 0.00 0.00 2.10
1281 1784 8.066595 CCAACATCTTTAAGAGCGAATTAGATG 58.933 37.037 0.03 0.00 41.84 2.90
1321 1824 8.410030 TGAAATGTGTTGTCAAGATTTCTTTG 57.590 30.769 17.44 0.00 36.58 2.77
1421 1934 9.088987 ACACTAACATTTTGGAAATATTGAGGT 57.911 29.630 0.00 0.00 0.00 3.85
1434 1947 9.628500 GGAAATATTGAGGTAGTAGGTGAAAAT 57.372 33.333 0.00 0.00 0.00 1.82
1544 2063 7.269477 AGCTCATGAACCATAAAAATAGAGC 57.731 36.000 0.00 0.00 43.59 4.09
1605 2125 8.768019 CGATGCAGATACAATTCAGATTTCTTA 58.232 33.333 0.00 0.00 0.00 2.10
1687 2207 8.710749 ATCAGTTGCAACCCACAATTATATAT 57.289 30.769 25.62 0.00 0.00 0.86
1691 2211 8.413229 AGTTGCAACCCACAATTATATATGAAC 58.587 33.333 25.62 0.00 0.00 3.18
1693 2213 6.768381 TGCAACCCACAATTATATATGAACGA 59.232 34.615 0.00 0.00 0.00 3.85
1872 2421 7.923344 TCAAAATTTCGAAATAGAAGCCAACAA 59.077 29.630 22.99 0.00 0.00 2.83
1890 2439 4.134379 ACAATCTCTCTAGCCACACATG 57.866 45.455 0.00 0.00 0.00 3.21
1892 2441 1.560505 TCTCTCTAGCCACACATGCA 58.439 50.000 0.00 0.00 0.00 3.96
1926 2475 0.396435 TTCTCATGCGAACCACCTGT 59.604 50.000 0.00 0.00 0.00 4.00
1949 2509 5.010213 GTGATTTTGGTTAGTGGCTGGTTAA 59.990 40.000 0.00 0.00 0.00 2.01
1950 2510 5.777732 TGATTTTGGTTAGTGGCTGGTTAAT 59.222 36.000 0.00 0.00 0.00 1.40
2116 2680 5.770162 CCTTAACAAGACTTCAAACCCTGAT 59.230 40.000 0.00 0.00 32.78 2.90
2135 2699 6.183361 CCCTGATTCCAACCTCATATCTGTTA 60.183 42.308 0.00 0.00 0.00 2.41
2178 2742 4.935702 TGTTACCGCATACGCTAATTACT 58.064 39.130 0.00 0.00 38.22 2.24
2265 2834 8.523658 ACTATTCTAATTTTGTTTCTTGCCTCC 58.476 33.333 0.00 0.00 0.00 4.30
2329 2900 6.371809 AGTTGCGACAAAAGTTCTTCAATA 57.628 33.333 6.90 0.00 0.00 1.90
2472 3043 2.189521 GGTGGAGGGCATGGTACG 59.810 66.667 0.00 0.00 0.00 3.67
2661 3233 4.096984 CCCTTGTTGGCTTATGAGTTCATC 59.903 45.833 0.00 0.00 37.76 2.92
2709 3281 7.364522 TCTTCACAAGAAACCATTAAGATCG 57.635 36.000 0.00 0.00 33.83 3.69
2736 3308 4.932200 CCTTGGCGAGACATATTAAGGATC 59.068 45.833 2.43 0.00 36.23 3.36
2785 3357 2.262637 ACCTTCACTCGGGTATTTCCA 58.737 47.619 0.00 0.00 38.11 3.53
2816 3388 7.805542 CGTGATACACAGAGATATAAAGTCCAG 59.194 40.741 0.00 0.00 33.40 3.86
2964 3536 7.548075 CCTATGTACTTTTATTGTGGTCGTCTT 59.452 37.037 0.00 0.00 0.00 3.01
3069 3641 2.173669 CGGTGATGGGCTAGTTGCG 61.174 63.158 0.00 0.00 44.05 4.85
3078 3650 1.003851 GGCTAGTTGCGCGATTTGTA 58.996 50.000 12.10 0.00 44.05 2.41
3135 3707 5.602978 ACTAGATTCACGGGTAATTGAGGAT 59.397 40.000 0.00 0.00 0.00 3.24
3321 3910 4.038763 TCGACAATGAGGTATACATCACCC 59.961 45.833 21.50 10.31 39.61 4.61
3342 3937 4.202305 CCCATAAGGACAAGCTTAGAGGAG 60.202 50.000 0.00 0.00 38.24 3.69
3345 3940 3.176924 AGGACAAGCTTAGAGGAGACA 57.823 47.619 0.00 0.00 0.00 3.41
3397 3992 1.974957 TGTTGTCTGCAAGCTACCCTA 59.025 47.619 0.00 0.00 34.94 3.53
3402 3997 4.286707 TGTCTGCAAGCTACCCTAGATAA 58.713 43.478 0.00 0.00 0.00 1.75
3411 4006 7.815549 GCAAGCTACCCTAGATAATCTTACTTC 59.184 40.741 0.00 0.00 0.00 3.01
3414 4009 8.011290 AGCTACCCTAGATAATCTTACTTCCAA 58.989 37.037 0.00 0.00 0.00 3.53
3474 4069 3.243410 TGTGTTGTGTACGTTCGAACATC 59.757 43.478 26.71 16.05 0.00 3.06
3504 4099 6.901357 GTGCTTCAATTTGTTGTTGCTTTAAG 59.099 34.615 0.00 0.00 0.00 1.85
3583 4187 1.334869 GCTTCCTTCATAATGTGGGCG 59.665 52.381 0.00 0.00 0.00 6.13
3593 4197 2.852495 AATGTGGGCGCTCACCGTAG 62.852 60.000 36.01 0.00 39.71 3.51
3600 4204 0.169672 GCGCTCACCGTAGAGTACAA 59.830 55.000 0.00 0.00 39.71 2.41
3661 4265 7.864686 TCCATTGCTCACATAATAGAAATTCG 58.135 34.615 0.00 0.00 0.00 3.34
3818 4438 3.859745 ATCTGCGCGTACAACATATTG 57.140 42.857 8.43 0.00 41.98 1.90
3879 4499 4.276431 TCGCAACTTTTAAGGGACGATTTT 59.724 37.500 0.00 0.00 0.00 1.82
3915 4537 6.539173 TCTACCAGAGAGCTCTAGAAATAGG 58.461 44.000 18.25 12.69 37.98 2.57
4166 4791 7.927048 AGAATAGTTGTTGTTTTACAGTGACC 58.073 34.615 0.00 0.00 0.00 4.02
4179 4804 7.795482 TTTACAGTGACCGGATAAAATATGG 57.205 36.000 9.46 0.00 0.00 2.74
4186 4811 3.073946 ACCGGATAAAATATGGTGGGAGG 59.926 47.826 9.46 0.00 0.00 4.30
4278 4903 9.741647 TTTCACAATTTTAAATGGGCATTTTTC 57.258 25.926 0.00 0.00 40.99 2.29
4282 4907 7.012799 ACAATTTTAAATGGGCATTTTTCGTGT 59.987 29.630 0.00 0.00 40.99 4.49
4292 4917 5.463724 GGGCATTTTTCGTGTAAACAAATGA 59.536 36.000 10.16 0.00 31.27 2.57
4296 4921 6.561945 TTTTTCGTGTAAACAAATGACAGC 57.438 33.333 0.00 0.00 0.00 4.40
4297 4922 4.884458 TTCGTGTAAACAAATGACAGCA 57.116 36.364 0.00 0.00 0.00 4.41
4307 4932 0.253160 AATGACAGCAGGACCCCCTA 60.253 55.000 0.00 0.00 42.02 3.53
4329 4954 3.956199 AGGTATGCCCATGTGAAGAATTG 59.044 43.478 0.00 0.00 34.66 2.32
4377 5002 2.293677 TCTATTCGAAGGATCACTCGGC 59.706 50.000 13.73 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 4.040461 CCAGTTGAAGGGTGAGTCTAAAGA 59.960 45.833 0.00 0.00 0.00 2.52
40 42 4.040461 TCCAGTTGAAGGGTGAGTCTAAAG 59.960 45.833 0.00 0.00 0.00 1.85
106 108 0.834261 TGGGTCATGGAGTCGGTTGA 60.834 55.000 0.00 0.00 0.00 3.18
107 109 0.036164 TTGGGTCATGGAGTCGGTTG 59.964 55.000 0.00 0.00 0.00 3.77
109 111 0.768622 TTTTGGGTCATGGAGTCGGT 59.231 50.000 0.00 0.00 0.00 4.69
123 125 6.144078 AGTTGGTGCTAAGTAAACTTTTGG 57.856 37.500 0.00 0.00 37.40 3.28
146 148 5.505181 AGTTCTTAGAGGATGAGGCAAAA 57.495 39.130 0.00 0.00 0.00 2.44
178 180 4.362279 GAGCATCAACAAAGCAAACTGAA 58.638 39.130 0.00 0.00 33.17 3.02
180 182 2.722629 CGAGCATCAACAAAGCAAACTG 59.277 45.455 0.00 0.00 33.17 3.16
181 183 2.618241 TCGAGCATCAACAAAGCAAACT 59.382 40.909 0.00 0.00 33.17 2.66
182 184 2.998772 TCGAGCATCAACAAAGCAAAC 58.001 42.857 0.00 0.00 33.17 2.93
192 194 4.909880 CGATCTAACGTATTCGAGCATCAA 59.090 41.667 0.00 0.00 40.62 2.57
194 196 4.318593 CACGATCTAACGTATTCGAGCATC 59.681 45.833 13.84 0.00 44.76 3.91
210 213 5.934402 AAGGGTCAATACTAACACGATCT 57.066 39.130 0.00 0.00 0.00 2.75
254 260 9.332713 TCCAATGGGGAAAAGTAAAAATATTCT 57.667 29.630 0.00 0.00 44.80 2.40
277 283 2.118404 GCCGCCCGATTTTGATCCA 61.118 57.895 0.00 0.00 0.00 3.41
291 297 1.445238 GTCAGTGAGTGAGAGCCGC 60.445 63.158 0.00 0.00 35.13 6.53
311 317 3.860536 GCGAGTGAGAAGTTCTTATGTCC 59.139 47.826 6.88 0.00 0.00 4.02
387 397 1.416401 ACTCTCATTCCAACACACGGT 59.584 47.619 0.00 0.00 0.00 4.83
389 399 5.666969 TTTTACTCTCATTCCAACACACG 57.333 39.130 0.00 0.00 0.00 4.49
462 473 6.642950 TGTTTGCCAAATAAAATTCTGGTACG 59.357 34.615 0.00 0.00 0.00 3.67
466 477 7.388500 ACAGATGTTTGCCAAATAAAATTCTGG 59.612 33.333 15.26 0.00 35.20 3.86
544 558 2.045561 TCCGTCAAAACTGGCTCAAA 57.954 45.000 0.00 0.00 0.00 2.69
560 574 5.287752 TCTCTGATATTTTCGTCGTTTTCCG 59.712 40.000 0.00 0.00 38.13 4.30
567 582 5.460419 CCTTCCTTCTCTGATATTTTCGTCG 59.540 44.000 0.00 0.00 0.00 5.12
570 585 5.059833 CCCCTTCCTTCTCTGATATTTTCG 58.940 45.833 0.00 0.00 0.00 3.46
576 591 5.731187 TGATTTTCCCCTTCCTTCTCTGATA 59.269 40.000 0.00 0.00 0.00 2.15
577 592 4.541714 TGATTTTCCCCTTCCTTCTCTGAT 59.458 41.667 0.00 0.00 0.00 2.90
592 607 6.358974 TCCCATTTCCTCTTTTGATTTTCC 57.641 37.500 0.00 0.00 0.00 3.13
593 608 8.724229 CAAATCCCATTTCCTCTTTTGATTTTC 58.276 33.333 0.00 0.00 30.98 2.29
611 627 4.944930 CCTTACGTATGTTTCCAAATCCCA 59.055 41.667 0.00 0.00 0.00 4.37
616 632 6.357579 TCTACCCTTACGTATGTTTCCAAA 57.642 37.500 0.00 0.00 0.00 3.28
635 651 4.138290 TCTCGGACTCATCCTTCATCTAC 58.862 47.826 0.00 0.00 43.73 2.59
652 668 7.900782 TTTAAAAAGACATAGGTTCTCTCGG 57.099 36.000 0.00 0.00 0.00 4.63
728 1170 5.653330 TCAACCTATCCGTGTCTACAATACA 59.347 40.000 0.00 0.00 0.00 2.29
763 1205 4.411013 AGAAAAGCTCCAAATAGCACCTT 58.589 39.130 0.00 0.00 45.30 3.50
778 1220 9.405587 TGTGTGCAAGTTAAATATAAGAAAAGC 57.594 29.630 0.00 0.00 0.00 3.51
878 1350 4.839121 TCTATATTTTGGCTTGTCGTGGT 58.161 39.130 0.00 0.00 0.00 4.16
879 1351 6.038161 TGAATCTATATTTTGGCTTGTCGTGG 59.962 38.462 0.00 0.00 0.00 4.94
881 1353 6.597672 TGTGAATCTATATTTTGGCTTGTCGT 59.402 34.615 0.00 0.00 0.00 4.34
882 1354 6.907212 GTGTGAATCTATATTTTGGCTTGTCG 59.093 38.462 0.00 0.00 0.00 4.35
883 1355 6.907212 CGTGTGAATCTATATTTTGGCTTGTC 59.093 38.462 0.00 0.00 0.00 3.18
885 1357 6.183360 ACCGTGTGAATCTATATTTTGGCTTG 60.183 38.462 0.00 0.00 0.00 4.01
886 1358 5.885912 ACCGTGTGAATCTATATTTTGGCTT 59.114 36.000 0.00 0.00 0.00 4.35
888 1360 5.295787 TGACCGTGTGAATCTATATTTTGGC 59.704 40.000 0.00 0.00 0.00 4.52
889 1361 6.918892 TGACCGTGTGAATCTATATTTTGG 57.081 37.500 0.00 0.00 0.00 3.28
907 1410 4.438744 GGAAGCATTAATCCAAGTTGACCG 60.439 45.833 3.87 0.00 35.71 4.79
1017 1520 0.534877 ATCCTTGTGAGCACGTGCAA 60.535 50.000 39.21 25.59 45.16 4.08
1069 1572 1.913419 ACCTGTGTTTATGGACGGGAT 59.087 47.619 0.00 0.00 40.62 3.85
1073 1576 1.448985 CCCACCTGTGTTTATGGACG 58.551 55.000 0.00 0.00 33.80 4.79
1108 1611 3.541242 ACATGTTGATCCCAGGGAAAA 57.459 42.857 13.94 7.64 34.34 2.29
1254 1757 4.622701 ATTCGCTCTTAAAGATGTTGGC 57.377 40.909 0.00 0.00 0.00 4.52
1315 1818 6.707440 ACATATGTGACACCAAACAAAGAA 57.293 33.333 7.78 0.00 0.00 2.52
1321 1824 4.503741 AGCAACATATGTGACACCAAAC 57.496 40.909 9.63 0.00 0.00 2.93
1414 1927 9.838339 CAATAGATTTTCACCTACTACCTCAAT 57.162 33.333 0.00 0.00 0.00 2.57
1415 1928 8.822805 ACAATAGATTTTCACCTACTACCTCAA 58.177 33.333 0.00 0.00 0.00 3.02
1416 1929 8.375493 ACAATAGATTTTCACCTACTACCTCA 57.625 34.615 0.00 0.00 0.00 3.86
1421 1934 9.886132 GAAGGAACAATAGATTTTCACCTACTA 57.114 33.333 0.00 0.00 0.00 1.82
1461 1975 8.303876 GCATTTAAGACAACAAGAGGGATTTTA 58.696 33.333 0.00 0.00 0.00 1.52
1562 2082 8.432110 TCTGCATCGCATAACTAATTTTTAGA 57.568 30.769 1.47 0.00 38.13 2.10
1687 2207 0.600557 AAATGGCGGCATTTCGTTCA 59.399 45.000 36.04 3.05 29.61 3.18
1691 2211 4.466828 CTCTATAAAATGGCGGCATTTCG 58.533 43.478 39.44 28.54 34.06 3.46
1693 2213 4.469657 TCCTCTATAAAATGGCGGCATTT 58.530 39.130 36.04 36.04 36.44 2.32
1855 2403 5.814705 AGAGAGATTGTTGGCTTCTATTTCG 59.185 40.000 0.00 0.00 0.00 3.46
1872 2421 2.113807 TGCATGTGTGGCTAGAGAGAT 58.886 47.619 0.00 0.00 0.00 2.75
1890 2439 6.564873 GCATGAGAAAGGACGTAGATAATTGC 60.565 42.308 0.00 0.00 0.00 3.56
1892 2441 5.692204 CGCATGAGAAAGGACGTAGATAATT 59.308 40.000 0.00 0.00 0.00 1.40
1926 2475 3.237268 ACCAGCCACTAACCAAAATCA 57.763 42.857 0.00 0.00 0.00 2.57
1949 2509 9.131791 GTCAATATTTAACCCATGTAAGTCCAT 57.868 33.333 0.00 0.00 0.00 3.41
1950 2510 7.558444 GGTCAATATTTAACCCATGTAAGTCCA 59.442 37.037 5.72 0.00 0.00 4.02
1990 2550 6.365970 ACTATGTCTCAAATGAAGTGACCT 57.634 37.500 0.00 0.00 0.00 3.85
2116 2680 9.444600 GTTAAAGTAACAGATATGAGGTTGGAA 57.555 33.333 0.00 0.00 38.52 3.53
2149 2713 1.779157 CGTATGCGGTAACATGACTCG 59.221 52.381 0.00 0.00 0.00 4.18
2265 2834 6.798959 GCTTAAGCTTGCGGAATATTATCTTG 59.201 38.462 20.38 0.00 38.21 3.02
2275 2844 1.819928 TGATGCTTAAGCTTGCGGAA 58.180 45.000 26.90 6.44 42.66 4.30
2329 2900 4.437239 TGCAACAATTGTCCACGATTTTT 58.563 34.783 12.39 0.00 0.00 1.94
2516 3087 6.431234 ACTCTTGACCACAATATTTGACTTCC 59.569 38.462 0.00 0.00 35.37 3.46
2661 3233 3.931907 TCACATAGGGTTCCATTGGAG 57.068 47.619 5.36 0.00 31.21 3.86
2701 3273 3.887110 TCTCGCCAAGGTATCGATCTTAA 59.113 43.478 0.00 0.00 0.00 1.85
2709 3281 5.869888 CCTTAATATGTCTCGCCAAGGTATC 59.130 44.000 0.00 0.00 0.00 2.24
2736 3308 1.192980 GCTTTGCCAATTTCTGTTGCG 59.807 47.619 0.00 0.00 0.00 4.85
2785 3357 2.454336 TCTCTGTGTATCACGGGGAT 57.546 50.000 7.13 0.00 44.26 3.85
2816 3388 8.347771 TCAAAGCATCATCAAGAAGTATATTGC 58.652 33.333 0.00 0.00 0.00 3.56
3069 3641 4.625742 TCTGCAAGTAGTTCTACAAATCGC 59.374 41.667 11.73 7.21 33.76 4.58
3071 3643 6.651225 ACCTTCTGCAAGTAGTTCTACAAATC 59.349 38.462 11.73 0.58 33.76 2.17
3078 3650 6.431234 CCAATTTACCTTCTGCAAGTAGTTCT 59.569 38.462 0.00 0.00 33.76 3.01
3122 3694 3.244596 GCTACCTCCATCCTCAATTACCC 60.245 52.174 0.00 0.00 0.00 3.69
3135 3707 2.054799 ACTTCAACTTGGCTACCTCCA 58.945 47.619 0.00 0.00 0.00 3.86
3321 3910 5.127845 TGTCTCCTCTAAGCTTGTCCTTATG 59.872 44.000 9.86 0.00 0.00 1.90
3342 3937 7.761704 TCTTCTTGACTATATTGTCTGCTTGTC 59.238 37.037 16.53 0.00 37.79 3.18
3345 3940 8.535335 TCTTCTTCTTGACTATATTGTCTGCTT 58.465 33.333 16.53 0.00 37.79 3.91
3411 4006 6.748132 ACCAACTCTTTCACATGTAAATTGG 58.252 36.000 9.42 9.42 39.02 3.16
3414 4009 8.635765 ACATACCAACTCTTTCACATGTAAAT 57.364 30.769 0.00 0.00 0.00 1.40
3474 4069 3.178267 ACAACAAATTGAAGCACACACG 58.822 40.909 0.00 0.00 39.30 4.49
3583 4187 5.246145 AGTATTTGTACTCTACGGTGAGC 57.754 43.478 6.81 0.00 37.58 4.26
3600 4204 8.422577 ACCCAGCTTGAAGAAAAATAAGTATT 57.577 30.769 0.00 0.00 0.00 1.89
3723 4327 9.575783 TTTGAAATAGAAAATATTAACCGCACC 57.424 29.630 0.00 0.00 0.00 5.01
3781 4401 3.084039 CAGATTTGCAGGAAGTGGCTAA 58.916 45.455 0.00 0.00 0.00 3.09
3879 4499 4.878968 TCTCTGGTAGATATTGTCCACCA 58.121 43.478 1.18 1.18 44.83 4.17
4124 4749 9.299963 CAACTATTCTAGAGTCTTCTGTCATTG 57.700 37.037 0.00 0.00 34.79 2.82
4143 4768 6.238538 CCGGTCACTGTAAAACAACAACTATT 60.239 38.462 0.00 0.00 0.00 1.73
4159 4784 4.515191 CCACCATATTTTATCCGGTCACTG 59.485 45.833 0.00 0.00 0.00 3.66
4165 4790 3.073946 ACCTCCCACCATATTTTATCCGG 59.926 47.826 0.00 0.00 0.00 5.14
4166 4791 4.367039 ACCTCCCACCATATTTTATCCG 57.633 45.455 0.00 0.00 0.00 4.18
4206 4831 9.699410 ATTGAATGTTGAGATTTGACCCTAATA 57.301 29.630 0.00 0.00 0.00 0.98
4246 4871 9.784531 TGCCCATTTAAAATTGTGAAATAAAGA 57.215 25.926 0.00 0.00 0.00 2.52
4260 4885 8.336080 GTTTACACGAAAAATGCCCATTTAAAA 58.664 29.630 6.67 0.00 39.88 1.52
4278 4903 3.249799 TCCTGCTGTCATTTGTTTACACG 59.750 43.478 0.00 0.00 0.00 4.49
4282 4907 3.153919 GGGTCCTGCTGTCATTTGTTTA 58.846 45.455 0.00 0.00 0.00 2.01
4292 4917 2.041265 CCTAGGGGGTCCTGCTGT 59.959 66.667 0.00 0.00 44.61 4.40
4307 4932 3.956199 CAATTCTTCACATGGGCATACCT 59.044 43.478 0.00 0.00 41.11 3.08
4329 4954 3.382048 CCGTTAGGGTCTATTAGGCAC 57.618 52.381 0.00 0.00 0.00 5.01
4350 4975 6.203145 CGAGTGATCCTTCGAATAGACTTAGA 59.797 42.308 9.61 0.00 0.00 2.10
4353 4978 4.036971 CCGAGTGATCCTTCGAATAGACTT 59.963 45.833 15.17 0.00 0.00 3.01
4361 4986 2.771639 CCGCCGAGTGATCCTTCGA 61.772 63.158 15.17 0.00 0.00 3.71
4377 5002 3.605749 ATTATCGATGCCGGCCCCG 62.606 63.158 26.77 26.04 39.44 5.73


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

AutoCloner maintained by Alex Coulton.