Multiple sequence alignment - TraesCS3D01G102800

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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 TraesCS3D01G102800 chr3D 100.000 2588 0 0 1 2588 55263083 55260496 0.000000e+00 4780.0
1 TraesCS3D01G102800 chr3D 93.068 678 43 4 1914 2588 47217015 47216339 0.000000e+00 989.0
2 TraesCS3D01G102800 chr3D 92.910 677 42 4 1914 2588 447796763 447796091 0.000000e+00 979.0
3 TraesCS3D01G102800 chr7B 91.507 1354 88 11 527 1868 656219918 656218580 0.000000e+00 1838.0
4 TraesCS3D01G102800 chr7B 91.857 1314 80 12 579 1885 655145665 655144372 0.000000e+00 1808.0
5 TraesCS3D01G102800 chr7B 88.213 263 26 1 3 260 656221307 656221045 2.500000e-80 309.0
6 TraesCS3D01G102800 chr7B 85.366 82 10 2 527 607 145727397 145727317 1.650000e-12 84.2
7 TraesCS3D01G102800 chr7D 83.291 1191 155 23 743 1910 585907214 585906045 0.000000e+00 1057.0
8 TraesCS3D01G102800 chr2D 93.639 676 41 2 1915 2588 439545937 439546612 0.000000e+00 1009.0
9 TraesCS3D01G102800 chr2D 92.342 679 44 6 1913 2588 352261956 352262629 0.000000e+00 959.0
10 TraesCS3D01G102800 chr2D 89.706 68 7 0 1803 1870 625455023 625454956 1.280000e-13 87.9
11 TraesCS3D01G102800 chr2D 97.778 45 1 0 1821 1865 423863881 423863837 7.680000e-11 78.7
12 TraesCS3D01G102800 chr7A 91.565 735 32 8 1186 1914 676302107 676301397 0.000000e+00 987.0
13 TraesCS3D01G102800 chr7A 83.836 928 116 18 993 1914 676425361 676424462 0.000000e+00 852.0
14 TraesCS3D01G102800 chr7A 92.405 158 7 2 922 1076 676302538 676302693 1.210000e-53 220.0
15 TraesCS3D01G102800 chr7A 88.406 69 8 0 1797 1865 112170043 112170111 1.650000e-12 84.2
16 TraesCS3D01G102800 chr7A 88.060 67 8 0 1797 1863 112123407 112123473 2.130000e-11 80.5
17 TraesCS3D01G102800 chr4D 92.920 678 46 2 1913 2588 414639975 414640652 0.000000e+00 985.0
18 TraesCS3D01G102800 chr5D 92.815 682 44 4 1912 2588 40181271 40180590 0.000000e+00 983.0
19 TraesCS3D01G102800 chr5D 92.773 678 43 6 1914 2588 302980826 302981500 0.000000e+00 976.0
20 TraesCS3D01G102800 chr5D 92.194 679 51 2 1912 2588 479443212 479442534 0.000000e+00 959.0
21 TraesCS3D01G102800 chr6D 92.330 678 46 6 1915 2588 237668757 237669432 0.000000e+00 959.0
22 TraesCS3D01G102800 chr1A 80.128 156 21 8 527 678 437164841 437164692 9.790000e-20 108.0
23 TraesCS3D01G102800 chr2A 85.000 100 11 4 533 629 515503018 515502920 5.890000e-17 99.0
24 TraesCS3D01G102800 chr2A 86.076 79 9 2 533 610 220359765 220359688 1.650000e-12 84.2
25 TraesCS3D01G102800 chr3B 79.675 123 17 5 538 657 383472714 383472831 5.940000e-12 82.4
26 TraesCS3D01G102800 chr6B 77.124 153 23 7 535 679 556795981 556796129 7.680000e-11 78.7
27 TraesCS3D01G102800 chr5B 84.810 79 11 1 533 610 568400608 568400530 7.680000e-11 78.7
28 TraesCS3D01G102800 chr4B 83.750 80 12 1 541 619 653119825 653119746 9.930000e-10 75.0
29 TraesCS3D01G102800 chr6A 100.000 28 0 0 415 442 1476851 1476878 5.000000e-03 52.8


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 TraesCS3D01G102800 chr3D 55260496 55263083 2587 True 4780.0 4780 100.000 1 2588 1 chr3D.!!$R2 2587
1 TraesCS3D01G102800 chr3D 47216339 47217015 676 True 989.0 989 93.068 1914 2588 1 chr3D.!!$R1 674
2 TraesCS3D01G102800 chr3D 447796091 447796763 672 True 979.0 979 92.910 1914 2588 1 chr3D.!!$R3 674
3 TraesCS3D01G102800 chr7B 655144372 655145665 1293 True 1808.0 1808 91.857 579 1885 1 chr7B.!!$R2 1306
4 TraesCS3D01G102800 chr7B 656218580 656221307 2727 True 1073.5 1838 89.860 3 1868 2 chr7B.!!$R3 1865
5 TraesCS3D01G102800 chr7D 585906045 585907214 1169 True 1057.0 1057 83.291 743 1910 1 chr7D.!!$R1 1167
6 TraesCS3D01G102800 chr2D 439545937 439546612 675 False 1009.0 1009 93.639 1915 2588 1 chr2D.!!$F2 673
7 TraesCS3D01G102800 chr2D 352261956 352262629 673 False 959.0 959 92.342 1913 2588 1 chr2D.!!$F1 675
8 TraesCS3D01G102800 chr7A 676301397 676302107 710 True 987.0 987 91.565 1186 1914 1 chr7A.!!$R1 728
9 TraesCS3D01G102800 chr7A 676424462 676425361 899 True 852.0 852 83.836 993 1914 1 chr7A.!!$R2 921
10 TraesCS3D01G102800 chr4D 414639975 414640652 677 False 985.0 985 92.920 1913 2588 1 chr4D.!!$F1 675
11 TraesCS3D01G102800 chr5D 40180590 40181271 681 True 983.0 983 92.815 1912 2588 1 chr5D.!!$R1 676
12 TraesCS3D01G102800 chr5D 302980826 302981500 674 False 976.0 976 92.773 1914 2588 1 chr5D.!!$F1 674
13 TraesCS3D01G102800 chr5D 479442534 479443212 678 True 959.0 959 92.194 1912 2588 1 chr5D.!!$R2 676
14 TraesCS3D01G102800 chr6D 237668757 237669432 675 False 959.0 959 92.330 1915 2588 1 chr6D.!!$F1 673

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
486 1319 0.10104 CGCATTTGTAGCATGGGTGG 59.899 55.0 0.0 0.0 31.55 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2232 3159 0.387929 TGGCGACCGGATATGAAGAC 59.612 55.0 9.46 0.0 0.0 3.01 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
46 47 1.501741 CGGGGCGTGATTTGTGAAG 59.498 57.895 0.00 0.00 0.00 3.02
52 53 2.095415 GGCGTGATTTGTGAAGTAACCC 60.095 50.000 0.00 0.00 0.00 4.11
72 78 4.424711 ACATGGGGCCGCGTCAAT 62.425 61.111 12.39 0.00 0.00 2.57
136 142 2.303022 ACCAGATATTATGGGGTCGCAG 59.697 50.000 11.44 0.00 42.48 5.18
152 158 2.739379 TCGCAGACGATAATTGCAACAA 59.261 40.909 0.00 0.00 45.12 2.83
155 161 5.064071 TCGCAGACGATAATTGCAACAATTA 59.936 36.000 13.47 13.47 45.12 1.40
156 162 5.909054 CGCAGACGATAATTGCAACAATTAT 59.091 36.000 20.09 20.09 43.93 1.28
158 164 7.746034 CGCAGACGATAATTGCAACAATTATAT 59.254 33.333 20.03 13.80 43.93 0.86
176 182 2.037620 ATGAGGAGCATGAGGGTCGC 62.038 60.000 0.00 0.00 45.03 5.19
210 216 5.925506 TGACCTAGATCAAACGATAACCA 57.074 39.130 0.00 0.00 0.00 3.67
214 220 4.738740 CCTAGATCAAACGATAACCACGTC 59.261 45.833 0.00 0.00 43.16 4.34
234 240 2.032377 TCGTTCGGATCTGTTGCAAAAC 60.032 45.455 0.00 0.00 0.00 2.43
237 243 1.266718 TCGGATCTGTTGCAAAACTGC 59.733 47.619 0.00 0.00 0.00 4.40
242 248 2.090760 TCTGTTGCAAAACTGCTGTGA 58.909 42.857 0.00 0.00 35.49 3.58
252 258 4.900635 AAACTGCTGTGATTCGAAAGTT 57.099 36.364 0.00 2.39 0.00 2.66
282 1109 7.778185 AGTCGATACATAAACCTATAAGGCT 57.222 36.000 0.00 0.00 39.63 4.58
283 1110 7.603651 AGTCGATACATAAACCTATAAGGCTG 58.396 38.462 0.00 0.00 39.63 4.85
332 1160 7.963532 AGACTTTTCTGATACCAACAACTCTA 58.036 34.615 0.00 0.00 0.00 2.43
344 1172 7.005709 ACCAACAACTCTATTAGTAAGCTGT 57.994 36.000 0.00 0.00 37.50 4.40
368 1196 8.855279 TGTAAGAAAACACAAAAATTCTCGTTG 58.145 29.630 0.00 0.00 31.20 4.10
370 1198 8.702163 AAGAAAACACAAAAATTCTCGTTGAT 57.298 26.923 0.00 0.00 31.20 2.57
371 1199 8.118893 AGAAAACACAAAAATTCTCGTTGATG 57.881 30.769 0.00 0.00 0.00 3.07
372 1200 7.759433 AGAAAACACAAAAATTCTCGTTGATGT 59.241 29.630 0.00 0.00 0.00 3.06
373 1201 7.826260 AAACACAAAAATTCTCGTTGATGTT 57.174 28.000 0.00 0.00 32.73 2.71
374 1202 7.449934 AACACAAAAATTCTCGTTGATGTTC 57.550 32.000 0.00 0.00 29.04 3.18
409 1242 4.740934 GCCGATCACTTACTTATTGCTCCT 60.741 45.833 0.00 0.00 0.00 3.69
410 1243 5.360591 CCGATCACTTACTTATTGCTCCTT 58.639 41.667 0.00 0.00 0.00 3.36
412 1245 6.316390 CCGATCACTTACTTATTGCTCCTTTT 59.684 38.462 0.00 0.00 0.00 2.27
417 1250 8.784043 TCACTTACTTATTGCTCCTTTTCTTTC 58.216 33.333 0.00 0.00 0.00 2.62
431 1264 5.739161 CCTTTTCTTTCATAATGTAGTGCGC 59.261 40.000 0.00 0.00 0.00 6.09
434 1267 7.546778 TTTCTTTCATAATGTAGTGCGCATA 57.453 32.000 15.91 0.00 0.00 3.14
442 1275 8.282592 TCATAATGTAGTGCGCATAGATTTTTC 58.717 33.333 15.91 0.00 0.00 2.29
447 1280 7.684670 TGTAGTGCGCATAGATTTTTCTTAAG 58.315 34.615 15.91 0.00 0.00 1.85
449 1282 6.776094 AGTGCGCATAGATTTTTCTTAAGAC 58.224 36.000 15.91 0.00 0.00 3.01
450 1283 5.965918 GTGCGCATAGATTTTTCTTAAGACC 59.034 40.000 15.91 0.00 0.00 3.85
470 1303 2.486203 CCAAACCTTAATGTAGTGCGCA 59.514 45.455 5.66 5.66 0.00 6.09
477 1310 5.064707 ACCTTAATGTAGTGCGCATTTGTAG 59.935 40.000 15.91 4.11 37.65 2.74
478 1311 3.405170 AATGTAGTGCGCATTTGTAGC 57.595 42.857 15.91 0.00 33.24 3.58
479 1312 1.802069 TGTAGTGCGCATTTGTAGCA 58.198 45.000 15.91 3.45 38.71 3.49
486 1319 0.101040 CGCATTTGTAGCATGGGTGG 59.899 55.000 0.00 0.00 31.55 4.61
488 1321 1.824230 GCATTTGTAGCATGGGTGGAA 59.176 47.619 0.00 0.00 0.00 3.53
511 1344 7.201839 GGAAAATAAATTATTCTACACCCGCCA 60.202 37.037 0.00 0.00 0.00 5.69
513 1346 3.637911 AATTATTCTACACCCGCCACA 57.362 42.857 0.00 0.00 0.00 4.17
519 1352 2.449031 CTACACCCGCCACAGAAGCA 62.449 60.000 0.00 0.00 0.00 3.91
522 1355 1.898574 ACCCGCCACAGAAGCAAAG 60.899 57.895 0.00 0.00 0.00 2.77
525 1358 1.205064 CGCCACAGAAGCAAAGACG 59.795 57.895 0.00 0.00 0.00 4.18
530 1396 2.614057 CCACAGAAGCAAAGACGAAACT 59.386 45.455 0.00 0.00 0.00 2.66
536 1402 4.389077 AGAAGCAAAGACGAAACTTATCCG 59.611 41.667 0.00 0.00 0.00 4.18
557 1424 2.750237 GCGTGGATCCAACACCCC 60.750 66.667 18.20 1.30 35.46 4.95
559 1426 2.602676 CGTGGATCCAACACCCCCT 61.603 63.158 18.20 0.00 35.46 4.79
563 1430 0.407918 GGATCCAACACCCCCTTCAA 59.592 55.000 6.95 0.00 0.00 2.69
568 1435 0.396417 CAACACCCCCTTCAACACCA 60.396 55.000 0.00 0.00 0.00 4.17
726 1606 6.282199 AGATTTACACACCACCTGTACTAG 57.718 41.667 0.00 0.00 0.00 2.57
833 1716 1.357137 TACTCCCCACTTGTCATGCA 58.643 50.000 0.00 0.00 0.00 3.96
839 1722 0.108992 CCACTTGTCATGCACATGCC 60.109 55.000 5.73 0.00 41.18 4.40
915 1799 6.536731 TGATGCATTAAAACGCAAACAATT 57.463 29.167 0.00 0.00 42.37 2.32
917 1801 7.727955 TGATGCATTAAAACGCAAACAATTAG 58.272 30.769 0.00 0.00 42.37 1.73
1344 2241 3.711059 GAGGGACGCCTACGAGGGA 62.711 68.421 0.00 0.00 43.93 4.20
1353 2250 1.051812 CCTACGAGGGATGCCTGAAT 58.948 55.000 12.02 0.00 0.00 2.57
1367 2264 1.134401 CCTGAATGACTATGCCACGGT 60.134 52.381 0.00 0.00 0.00 4.83
1460 2366 2.750350 CCGTGGGGTGAAGAGCTT 59.250 61.111 0.00 0.00 0.00 3.74
1461 2367 1.672356 CCGTGGGGTGAAGAGCTTG 60.672 63.158 0.00 0.00 0.00 4.01
1462 2368 1.672356 CGTGGGGTGAAGAGCTTGG 60.672 63.158 0.00 0.00 0.00 3.61
1463 2369 1.761174 GTGGGGTGAAGAGCTTGGA 59.239 57.895 0.00 0.00 0.00 3.53
1464 2370 0.322008 GTGGGGTGAAGAGCTTGGAG 60.322 60.000 0.00 0.00 0.00 3.86
1465 2371 0.473694 TGGGGTGAAGAGCTTGGAGA 60.474 55.000 0.00 0.00 0.00 3.71
1466 2372 0.251634 GGGGTGAAGAGCTTGGAGAG 59.748 60.000 0.00 0.00 0.00 3.20
1560 2466 9.297586 CGATACAAACTACTGCTAATTCACTTA 57.702 33.333 0.00 0.00 0.00 2.24
1659 2567 1.671901 AAATATGCGGGGTTTGGCCG 61.672 55.000 0.00 0.00 38.44 6.13
1687 2595 7.121759 ACCGTTACATAGCTAGTTTCTCAAGTA 59.878 37.037 0.00 0.00 0.00 2.24
1688 2596 7.431668 CCGTTACATAGCTAGTTTCTCAAGTAC 59.568 40.741 0.00 0.00 0.00 2.73
1689 2597 8.182881 CGTTACATAGCTAGTTTCTCAAGTACT 58.817 37.037 0.00 0.00 0.00 2.73
1751 2665 4.940046 AGAAGAGTAAACCGTCGAGTATCA 59.060 41.667 0.00 0.00 33.17 2.15
1907 2830 1.954146 GACGAGCAACAGTGGCGAA 60.954 57.895 0.00 0.00 36.08 4.70
1928 2851 2.169769 AGAGGACTGTCGGTGTCAAAAA 59.830 45.455 1.07 0.00 36.26 1.94
1929 2852 3.139077 GAGGACTGTCGGTGTCAAAAAT 58.861 45.455 1.07 0.00 36.26 1.82
1933 2857 1.002900 CTGTCGGTGTCAAAAATGCGT 60.003 47.619 0.00 0.00 0.00 5.24
1964 2888 2.280592 GGTCCCGAACTGTGCGTT 60.281 61.111 7.51 0.00 38.91 4.84
2133 3058 3.351794 AACCCTAAAAGTCTAGCCTGC 57.648 47.619 0.00 0.00 0.00 4.85
2177 3104 0.263765 ATGGACTAAGCCCTCCGGTA 59.736 55.000 0.00 0.00 0.00 4.02
2230 3157 5.272283 ACAAAGTCGGTTACAGAGAAAGA 57.728 39.130 0.00 0.00 0.00 2.52
2232 3159 5.753921 ACAAAGTCGGTTACAGAGAAAGAAG 59.246 40.000 0.00 0.00 0.00 2.85
2246 3173 5.659079 AGAGAAAGAAGTCTTCATATCCGGT 59.341 40.000 14.97 0.00 34.61 5.28
2282 3209 0.173708 CACGCTAAGGAGAGTCCCAC 59.826 60.000 1.17 0.00 37.19 4.61
2285 3212 0.617820 GCTAAGGAGAGTCCCACCCA 60.618 60.000 1.17 0.00 37.19 4.51
2335 3262 1.207089 CTTCACAGCCCATTAGTCCGA 59.793 52.381 0.00 0.00 0.00 4.55
2426 3353 2.223735 GCTTCAATGACGAGGTATCCGA 60.224 50.000 0.00 0.00 0.00 4.55
2461 3388 2.343387 GCATTGCAAGGCGGGTTT 59.657 55.556 21.32 0.00 0.00 3.27
2465 3392 1.047801 ATTGCAAGGCGGGTTTCTTT 58.952 45.000 4.94 0.00 0.00 2.52
2509 3436 1.563111 GAACTCAACGAACGTGTCCA 58.437 50.000 0.00 0.00 0.00 4.02
2521 3448 0.877071 CGTGTCCAGCTCTGCAAAAT 59.123 50.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.613482 GGTTTTAATTGTCCTAGTTAGAGCATC 58.387 37.037 0.00 0.00 0.00 3.91
4 5 6.592607 CGGTTTTAATTGTCCTAGTTAGAGCA 59.407 38.462 0.00 0.00 0.00 4.26
5 6 6.036844 CCGGTTTTAATTGTCCTAGTTAGAGC 59.963 42.308 0.00 0.00 0.00 4.09
12 13 2.686405 GCCCCGGTTTTAATTGTCCTAG 59.314 50.000 0.00 0.00 0.00 3.02
20 21 1.842052 AATCACGCCCCGGTTTTAAT 58.158 45.000 0.00 0.00 0.00 1.40
94 100 0.673644 AACTCCGCAAATCACTCCCG 60.674 55.000 0.00 0.00 0.00 5.14
97 103 1.464997 GGTCAACTCCGCAAATCACTC 59.535 52.381 0.00 0.00 0.00 3.51
136 142 9.546909 CCTCATATAATTGTTGCAATTATCGTC 57.453 33.333 22.56 0.00 35.26 4.20
139 145 9.565213 GCTCCTCATATAATTGTTGCAATTATC 57.435 33.333 22.56 8.93 35.26 1.75
143 149 6.964807 TGCTCCTCATATAATTGTTGCAAT 57.035 33.333 0.59 0.00 0.00 3.56
152 158 4.161189 CGACCCTCATGCTCCTCATATAAT 59.839 45.833 0.00 0.00 33.19 1.28
155 161 1.898472 CGACCCTCATGCTCCTCATAT 59.102 52.381 0.00 0.00 33.19 1.78
156 162 1.332195 CGACCCTCATGCTCCTCATA 58.668 55.000 0.00 0.00 33.19 2.15
158 164 2.725312 GCGACCCTCATGCTCCTCA 61.725 63.158 0.00 0.00 0.00 3.86
191 197 4.679662 ACGTGGTTATCGTTTGATCTAGG 58.320 43.478 0.00 0.00 38.38 3.02
194 200 3.176708 CGACGTGGTTATCGTTTGATCT 58.823 45.455 0.00 0.00 41.64 2.75
210 216 1.007336 GCAACAGATCCGAACGACGT 61.007 55.000 0.00 0.00 40.78 4.34
214 220 2.032030 AGTTTTGCAACAGATCCGAACG 60.032 45.455 0.00 0.00 35.05 3.95
234 240 6.414408 AATCTAACTTTCGAATCACAGCAG 57.586 37.500 0.00 0.00 0.00 4.24
237 243 7.696872 TCGACTAATCTAACTTTCGAATCACAG 59.303 37.037 0.00 0.00 32.86 3.66
306 1133 7.963532 AGAGTTGTTGGTATCAGAAAAGTCTA 58.036 34.615 3.97 0.00 30.85 2.59
315 1142 9.250624 GCTTACTAATAGAGTTGTTGGTATCAG 57.749 37.037 0.00 0.00 39.81 2.90
344 1172 9.796120 ATCAACGAGAATTTTTGTGTTTTCTTA 57.204 25.926 0.00 0.00 0.00 2.10
381 1214 5.050702 GCAATAAGTAAGTGATCGGCTTCTC 60.051 44.000 5.74 2.64 0.00 2.87
388 1221 6.910536 AAAGGAGCAATAAGTAAGTGATCG 57.089 37.500 0.00 0.00 0.00 3.69
409 1242 6.247727 TGCGCACTACATTATGAAAGAAAA 57.752 33.333 5.66 0.00 0.00 2.29
410 1243 5.871465 TGCGCACTACATTATGAAAGAAA 57.129 34.783 5.66 0.00 0.00 2.52
412 1245 6.512297 TCTATGCGCACTACATTATGAAAGA 58.488 36.000 14.90 0.00 0.00 2.52
417 1250 8.285394 AGAAAAATCTATGCGCACTACATTATG 58.715 33.333 14.90 0.00 0.00 1.90
442 1275 7.527457 GCACTACATTAAGGTTTGGTCTTAAG 58.473 38.462 0.00 0.00 39.24 1.85
447 1280 3.425758 GCGCACTACATTAAGGTTTGGTC 60.426 47.826 0.30 0.00 0.00 4.02
449 1282 2.486203 TGCGCACTACATTAAGGTTTGG 59.514 45.455 5.66 0.00 0.00 3.28
450 1283 3.822594 TGCGCACTACATTAAGGTTTG 57.177 42.857 5.66 0.00 0.00 2.93
461 1294 2.539547 CCATGCTACAAATGCGCACTAC 60.540 50.000 14.90 0.00 36.37 2.73
470 1303 6.865834 TTATTTTCCACCCATGCTACAAAT 57.134 33.333 0.00 0.00 0.00 2.32
477 1310 9.476202 GTAGAATAATTTATTTTCCACCCATGC 57.524 33.333 3.27 0.00 0.00 4.06
486 1319 7.646526 GTGGCGGGTGTAGAATAATTTATTTTC 59.353 37.037 3.27 0.00 0.00 2.29
488 1321 6.603997 TGTGGCGGGTGTAGAATAATTTATTT 59.396 34.615 3.27 0.00 0.00 1.40
511 1344 5.179555 GGATAAGTTTCGTCTTTGCTTCTGT 59.820 40.000 0.00 0.00 0.00 3.41
513 1346 4.389077 CGGATAAGTTTCGTCTTTGCTTCT 59.611 41.667 0.00 0.00 0.00 2.85
519 1352 2.410730 CGTGCGGATAAGTTTCGTCTTT 59.589 45.455 0.00 0.00 0.00 2.52
522 1355 0.024619 GCGTGCGGATAAGTTTCGTC 59.975 55.000 0.00 0.00 0.00 4.20
525 1358 0.247145 CACGCGTGCGGATAAGTTTC 60.247 55.000 28.16 0.00 44.69 2.78
530 1396 1.590525 GATCCACGCGTGCGGATAA 60.591 57.895 33.17 13.52 42.21 1.75
536 1402 3.047280 TGTTGGATCCACGCGTGC 61.047 61.111 33.17 19.74 0.00 5.34
550 1416 0.336737 TTGGTGTTGAAGGGGGTGTT 59.663 50.000 0.00 0.00 0.00 3.32
557 1424 1.806542 CTCGGTCATTGGTGTTGAAGG 59.193 52.381 0.00 0.00 0.00 3.46
559 1426 1.142060 ACCTCGGTCATTGGTGTTGAA 59.858 47.619 0.00 0.00 32.16 2.69
563 1430 1.292223 CGACCTCGGTCATTGGTGT 59.708 57.895 15.77 0.00 44.77 4.16
592 1459 3.597728 CCGTCCTCTAGCGGCTCC 61.598 72.222 5.39 0.00 41.53 4.70
600 1467 0.907486 TCCTTCGTCTCCGTCCTCTA 59.093 55.000 0.00 0.00 35.01 2.43
612 1479 0.471211 TCACCAGGGAGTTCCTTCGT 60.471 55.000 0.00 0.00 45.47 3.85
615 1482 1.481056 CCGTCACCAGGGAGTTCCTT 61.481 60.000 0.00 0.00 45.47 3.36
712 1592 6.656632 ATGATATGTCTAGTACAGGTGGTG 57.343 41.667 0.00 0.00 42.70 4.17
1248 2145 0.394216 CATCCAAGGATTCCACGGCA 60.394 55.000 5.29 0.00 31.62 5.69
1344 2241 2.579873 GTGGCATAGTCATTCAGGCAT 58.420 47.619 0.00 0.00 37.12 4.40
1353 2250 1.204704 CTTCTCACCGTGGCATAGTCA 59.795 52.381 0.00 0.00 0.00 3.41
1367 2264 0.391661 GCGGTTGATGGAGCTTCTCA 60.392 55.000 0.00 0.00 31.08 3.27
1460 2366 2.429767 CGGATCCAGCAGCTCTCCA 61.430 63.158 13.41 0.00 0.00 3.86
1461 2367 2.420890 CGGATCCAGCAGCTCTCC 59.579 66.667 13.41 0.00 0.00 3.71
1462 2368 2.420890 CCGGATCCAGCAGCTCTC 59.579 66.667 13.41 0.00 0.00 3.20
1463 2369 3.859414 GCCGGATCCAGCAGCTCT 61.859 66.667 15.38 0.00 0.00 4.09
1464 2370 3.859414 AGCCGGATCCAGCAGCTC 61.859 66.667 21.95 0.00 0.00 4.09
1465 2371 4.172512 CAGCCGGATCCAGCAGCT 62.173 66.667 21.95 15.12 0.00 4.24
1466 2372 3.472943 ATCAGCCGGATCCAGCAGC 62.473 63.158 21.95 13.11 0.00 5.25
1467 2373 1.597302 CATCAGCCGGATCCAGCAG 60.597 63.158 21.95 14.20 32.57 4.24
1468 2374 2.507452 CATCAGCCGGATCCAGCA 59.493 61.111 21.95 2.40 32.57 4.41
1560 2466 6.561519 ATGCCTAGTAGTTTACCATCAAGT 57.438 37.500 0.00 0.00 0.00 3.16
1659 2567 4.430908 AGAAACTAGCTATGTAACGGTGC 58.569 43.478 0.00 0.00 0.00 5.01
1687 2595 9.862371 CCGTTAAAGATGCTCTTATATCATAGT 57.138 33.333 0.00 0.00 35.27 2.12
1730 2641 5.125097 ACATGATACTCGACGGTTTACTCTT 59.875 40.000 0.00 0.00 0.00 2.85
1731 2642 4.639310 ACATGATACTCGACGGTTTACTCT 59.361 41.667 0.00 0.00 0.00 3.24
1732 2643 4.918037 ACATGATACTCGACGGTTTACTC 58.082 43.478 0.00 0.00 0.00 2.59
1751 2665 9.838339 CAAAGGAGAAAATATACACCTCTACAT 57.162 33.333 0.00 0.00 0.00 2.29
1900 2823 1.444553 CGACAGTCCTCTTCGCCAC 60.445 63.158 0.00 0.00 0.00 5.01
1907 2830 1.410004 TTTGACACCGACAGTCCTCT 58.590 50.000 0.00 0.00 35.15 3.69
1928 2851 0.898789 CCCCTACCCGAGATACGCAT 60.899 60.000 0.00 0.00 41.07 4.73
1929 2852 1.529948 CCCCTACCCGAGATACGCA 60.530 63.158 0.00 0.00 41.07 5.24
1933 2857 1.733387 GGGACCCCCTACCCGAGATA 61.733 65.000 0.00 0.00 41.34 1.98
1964 2888 5.568023 CGTCTCCTGTTACCATCAACCTTAA 60.568 44.000 0.00 0.00 0.00 1.85
2021 2945 7.015064 GGAAGTAGGGTATTACCTCCATAGAA 58.985 42.308 12.54 0.00 42.09 2.10
2133 3058 5.543405 AGGGAAGAGGAGAATCATAGTCATG 59.457 44.000 0.00 0.00 36.25 3.07
2177 3104 4.901785 ATCCCCTCCGGTGTCTATATAT 57.098 45.455 0.00 0.00 0.00 0.86
2198 3125 7.178274 TCTGTAACCGACTTTGTATAACCCTAA 59.822 37.037 0.00 0.00 0.00 2.69
2230 3157 1.068741 GGCGACCGGATATGAAGACTT 59.931 52.381 9.46 0.00 0.00 3.01
2232 3159 0.387929 TGGCGACCGGATATGAAGAC 59.612 55.000 9.46 0.00 0.00 3.01
2285 3212 1.828979 GAAGACTCTCTCCCGTGTCT 58.171 55.000 0.00 0.00 40.95 3.41
2335 3262 2.496942 CGGACTATGGTACGTGGGT 58.503 57.895 5.53 0.00 44.11 4.51
2426 3353 2.094659 CCGAAGACAATCTGCGCGT 61.095 57.895 8.43 0.00 44.09 6.01
2461 3388 6.591935 ACTGTGTTGGAGTATTCAGAAAAGA 58.408 36.000 0.00 0.00 0.00 2.52
2465 3392 5.808366 AGACTGTGTTGGAGTATTCAGAA 57.192 39.130 0.00 0.00 0.00 3.02
2509 3436 4.455877 GTGTGGTACTTATTTTGCAGAGCT 59.544 41.667 0.00 0.00 0.00 4.09
2521 3448 3.888323 TCTACGGTTGTGTGTGGTACTTA 59.112 43.478 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.