Multiple sequence alignment - TraesCS2B01G288200

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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 TraesCS2B01G288200 chr2B 100.000 2764 0 0 1 2764 397918804 397921567 0.000000e+00 5105
1 TraesCS2B01G288200 chr2A 92.501 2667 186 11 1 2658 435577362 435580023 0.000000e+00 3805
2 TraesCS2B01G288200 chr2D 93.308 2391 130 12 275 2658 329147849 329150216 0.000000e+00 3502
3 TraesCS2B01G288200 chr6B 85.799 338 40 6 187 519 656290751 656291085 4.380000e-93 351
4 TraesCS2B01G288200 chr7D 85.588 340 41 7 176 510 233875845 233876181 1.580000e-92 350
5 TraesCS2B01G288200 chr7D 86.164 318 35 8 181 492 512000102 512000416 4.410000e-88 335
6 TraesCS2B01G288200 chr7D 85.106 329 44 4 185 510 538241308 538241634 5.710000e-87 331
7 TraesCS2B01G288200 chr5D 84.071 339 46 6 176 510 355098219 355098553 1.240000e-83 320
8 TraesCS2B01G288200 chr7B 83.918 342 43 10 176 510 604800665 604800329 1.600000e-82 316
9 TraesCS2B01G288200 chr3B 83.333 348 50 7 176 518 458404149 458404493 5.750000e-82 315


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 TraesCS2B01G288200 chr2B 397918804 397921567 2763 False 5105 5105 100.000 1 2764 1 chr2B.!!$F1 2763
1 TraesCS2B01G288200 chr2A 435577362 435580023 2661 False 3805 3805 92.501 1 2658 1 chr2A.!!$F1 2657
2 TraesCS2B01G288200 chr2D 329147849 329150216 2367 False 3502 3502 93.308 275 2658 1 chr2D.!!$F1 2383

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
940 952 0.036294 GAGGGAAGGCAACGTTAGCT 60.036 55.0 17.89 0.0 46.39 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2724 2742 0.312416 CGATCCTAGTGGCCTCGAAG 59.688 60.0 3.32 3.69 39.17 3.79 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
31 32 7.477945 ACTTATAGTGCTATATGTGGGGTAC 57.522 40.000 13.52 0.00 36.01 3.34
65 66 6.721571 ACTATGCAGTTTGTGTACATGTAC 57.278 37.500 25.99 25.99 36.63 2.90
69 70 5.849510 TGCAGTTTGTGTACATGTACTAGT 58.150 37.500 30.69 16.22 37.00 2.57
73 74 3.394313 TGTGTACATGTACTAGTCGCG 57.606 47.619 30.69 0.00 37.00 5.87
90 91 2.872028 CGTTGAGCAAAGGTTGTGC 58.128 52.632 0.00 0.00 42.55 4.57
101 102 4.201950 GCAAAGGTTGTGCTATACATGGAG 60.202 45.833 0.00 0.00 39.48 3.86
103 104 4.142609 AGGTTGTGCTATACATGGAGTG 57.857 45.455 0.00 0.00 39.48 3.51
107 108 4.155063 TGTGCTATACATGGAGTGCAAT 57.845 40.909 8.92 0.00 33.42 3.56
113 114 6.772233 TGCTATACATGGAGTGCAATTTACAT 59.228 34.615 5.29 0.00 0.00 2.29
120 123 2.848302 GAGTGCAATTTACATCGCTTGC 59.152 45.455 0.00 0.00 43.25 4.01
123 126 1.578915 GCAATTTACATCGCTTGCACG 59.421 47.619 0.00 0.00 42.66 5.34
131 134 4.214383 CGCTTGCACGCTGATCCG 62.214 66.667 13.78 0.00 0.00 4.18
141 144 1.131883 ACGCTGATCCGTAGTGTGTAC 59.868 52.381 0.00 0.00 40.08 2.90
148 151 1.266718 TCCGTAGTGTGTACGTGGTTC 59.733 52.381 0.00 0.00 39.09 3.62
152 155 3.365666 CGTAGTGTGTACGTGGTTCTGAT 60.366 47.826 0.00 0.00 36.31 2.90
158 161 4.746115 TGTGTACGTGGTTCTGATGTTAAC 59.254 41.667 0.00 0.00 0.00 2.01
160 163 5.464389 GTGTACGTGGTTCTGATGTTAACTT 59.536 40.000 7.22 0.00 0.00 2.66
169 172 9.616156 TGGTTCTGATGTTAACTTACAACTTTA 57.384 29.630 7.22 0.00 0.00 1.85
185 190 4.207891 ACTTTATGGCTTGACTGTCGAT 57.792 40.909 2.98 0.00 0.00 3.59
187 192 2.602257 TATGGCTTGACTGTCGATGG 57.398 50.000 2.98 0.00 0.00 3.51
194 199 0.176449 TGACTGTCGATGGCAGATGG 59.824 55.000 5.28 0.00 37.40 3.51
201 206 0.395686 CGATGGCAGATGGGACTGAT 59.604 55.000 0.00 0.00 39.94 2.90
212 217 6.154192 GCAGATGGGACTGATAAGATCTATGA 59.846 42.308 0.00 0.00 39.94 2.15
229 234 8.423349 AGATCTATGAAGTGATTTCTCCTGAAG 58.577 37.037 0.00 0.00 36.71 3.02
231 236 8.316497 TCTATGAAGTGATTTCTCCTGAAGAT 57.684 34.615 0.00 0.00 36.71 2.40
239 244 4.494091 TTTCTCCTGAAGATGGGATGAC 57.506 45.455 0.00 0.00 32.82 3.06
249 254 1.417890 GATGGGATGACGGAAGATGGT 59.582 52.381 0.00 0.00 0.00 3.55
252 257 0.815615 GGATGACGGAAGATGGTGGC 60.816 60.000 0.00 0.00 0.00 5.01
253 258 0.107703 GATGACGGAAGATGGTGGCA 60.108 55.000 0.00 0.00 0.00 4.92
262 267 1.152881 GATGGTGGCAGTGGATCCC 60.153 63.158 9.90 0.11 0.00 3.85
268 273 4.899239 GCAGTGGATCCCGGAGCG 62.899 72.222 9.90 0.00 0.00 5.03
342 349 8.778358 GGTCATTGGATTAGATTGTCTGTTATC 58.222 37.037 0.00 0.00 0.00 1.75
367 374 5.451381 CGGACAAGGCACATCTGTATACTTA 60.451 44.000 4.17 0.00 0.00 2.24
388 395 8.095937 ACTTATAGGTGTAGCAACTTTGTTTC 57.904 34.615 0.00 0.00 31.86 2.78
418 425 2.556559 GGTGGCTTTGGGTTGATCCTTA 60.557 50.000 0.00 0.00 36.25 2.69
423 431 6.098266 GTGGCTTTGGGTTGATCCTTATATTT 59.902 38.462 0.00 0.00 36.25 1.40
492 500 4.424711 TGATGTGAAGGCCGGGGC 62.425 66.667 13.58 13.58 41.06 5.80
497 505 3.656280 TGAAGGCCGGGGCAATCA 61.656 61.111 23.67 21.69 44.11 2.57
511 519 2.030946 GGCAATCATCCTTCTCGAAACG 59.969 50.000 0.00 0.00 0.00 3.60
541 552 7.790782 ACCAATTTTTCTTACCCATACACAT 57.209 32.000 0.00 0.00 0.00 3.21
578 589 3.018423 AGGTTAGATTTCACCCATGCC 57.982 47.619 0.00 0.00 32.92 4.40
638 650 5.565509 TGGTCTATGCCAAATTTGTCTACA 58.434 37.500 16.73 9.58 35.25 2.74
639 651 5.647658 TGGTCTATGCCAAATTTGTCTACAG 59.352 40.000 16.73 7.39 35.25 2.74
719 731 4.159506 GGCATGGTTAGCATTTGGAGTTTA 59.840 41.667 0.00 0.00 0.00 2.01
733 745 5.552870 TGGAGTTTATAGAAGAGGCATCC 57.447 43.478 0.00 0.00 0.00 3.51
748 760 1.939934 GCATCCCGATCAATGAAACGA 59.060 47.619 12.93 0.00 0.00 3.85
841 853 2.257207 TCTCGTCTTCCCAACATTCCT 58.743 47.619 0.00 0.00 0.00 3.36
940 952 0.036294 GAGGGAAGGCAACGTTAGCT 60.036 55.000 17.89 0.00 46.39 3.32
943 955 1.234615 GGAAGGCAACGTTAGCTGCA 61.235 55.000 17.89 0.00 40.98 4.41
946 958 2.616330 GGCAACGTTAGCTGCAGCA 61.616 57.895 38.24 22.31 40.98 4.41
1029 1041 1.502163 GCTGCAGAGAACACAAGCGT 61.502 55.000 20.43 0.00 0.00 5.07
1065 1077 2.086869 CCACCATTGTCGCTCTTCATT 58.913 47.619 0.00 0.00 0.00 2.57
1067 1079 1.470098 ACCATTGTCGCTCTTCATTGC 59.530 47.619 0.00 0.00 0.00 3.56
1239 1251 1.146930 CAGCATGGGCCTGTACGAT 59.853 57.895 4.53 0.00 42.56 3.73
1265 1277 4.124910 CGTGGGATGCGCTAACAT 57.875 55.556 9.73 0.00 0.00 2.71
1290 1302 1.591594 CACTGCGAACGGTGTGACT 60.592 57.895 0.00 0.00 46.36 3.41
1311 1323 0.616111 ACGAGGACCTGGATGAGCTT 60.616 55.000 10.93 0.00 0.00 3.74
1368 1380 1.128188 AGAACGGAGGCCAGAACCTT 61.128 55.000 5.01 0.00 41.32 3.50
1371 1383 1.073199 CGGAGGCCAGAACCTTTGT 59.927 57.895 5.01 0.00 41.32 2.83
1413 1425 0.038435 TGTATTTCGCCGTCAACCGA 60.038 50.000 0.00 0.00 39.56 4.69
1419 1431 2.260434 GCCGTCAACCGACAGCTA 59.740 61.111 0.00 0.00 41.51 3.32
1422 1434 0.456221 CCGTCAACCGACAGCTATCT 59.544 55.000 0.00 0.00 42.74 1.98
1551 1563 1.613630 GCCCTCCCTCCTTGACTCA 60.614 63.158 0.00 0.00 0.00 3.41
1582 1594 1.270147 GCAGTCCAGGTCAGTAACGTT 60.270 52.381 5.88 5.88 0.00 3.99
1586 1598 3.830755 AGTCCAGGTCAGTAACGTTGTAT 59.169 43.478 11.99 0.00 0.00 2.29
1656 1669 4.755123 AGCTTATGTTATTATGTGGTCGGC 59.245 41.667 0.00 0.00 0.00 5.54
1658 1671 5.929992 GCTTATGTTATTATGTGGTCGGCTA 59.070 40.000 0.00 0.00 0.00 3.93
1668 1681 0.988832 TGGTCGGCTATTTGGTCCTT 59.011 50.000 0.00 0.00 0.00 3.36
1813 1826 1.070914 TGCAGAACCGTTGTACATCCA 59.929 47.619 0.00 0.00 0.00 3.41
1850 1863 0.396417 CGAGGGAGAGGACATGACCT 60.396 60.000 16.96 16.96 43.64 3.85
1992 2005 3.005684 GGACAACATTTGATGCAAGGACA 59.994 43.478 0.00 0.00 0.00 4.02
2052 2066 7.725251 ACTCTTGCTGAAACATTTCCATAAAA 58.275 30.769 2.00 0.00 36.36 1.52
2122 2136 4.370776 TCCAAGGAGACAAATATCCTCCA 58.629 43.478 9.92 0.00 46.34 3.86
2130 2144 6.381133 GGAGACAAATATCCTCCAAAAACCAT 59.619 38.462 0.00 0.00 44.42 3.55
2184 2198 6.530120 AGAAAAGTTGGGCCGATAAAATTTT 58.470 32.000 10.92 10.92 34.78 1.82
2258 2272 4.524714 TCTGAAATTAAATTGGGCGTTCCA 59.475 37.500 0.00 0.00 45.43 3.53
2294 2308 3.260740 CCTCTGACTGCTGAAGATGTTC 58.739 50.000 0.00 0.00 0.00 3.18
2309 2323 9.586150 CTGAAGATGTTCGTTAAATATGCATAC 57.414 33.333 8.99 0.00 35.17 2.39
2310 2324 8.272866 TGAAGATGTTCGTTAAATATGCATACG 58.727 33.333 8.99 10.62 35.17 3.06
2311 2325 6.590357 AGATGTTCGTTAAATATGCATACGC 58.410 36.000 8.99 0.00 39.24 4.42
2393 2407 5.465532 TGCATGCTTTTGATTGGACTTAA 57.534 34.783 20.33 0.00 0.00 1.85
2402 2416 4.695217 TGATTGGACTTAACGCAAATCC 57.305 40.909 0.00 0.00 0.00 3.01
2509 2526 7.152645 ACGTTAAACAGACACTCTCATATGTT 58.847 34.615 1.90 0.00 32.55 2.71
2563 2580 5.941948 ACACTATCCTTTGAACCTTTTCG 57.058 39.130 0.00 0.00 34.04 3.46
2591 2609 9.476761 GTTCAAACATTTCAAAGTCACAATTTC 57.523 29.630 0.00 0.00 0.00 2.17
2604 2622 8.574196 AAGTCACAATTTCGACAAAATTTAGG 57.426 30.769 6.74 0.00 43.51 2.69
2677 2695 8.931775 ACTCAAATAAAAATTATTTTCACCCGC 58.068 29.630 3.23 0.00 39.42 6.13
2678 2696 8.833231 TCAAATAAAAATTATTTTCACCCGCA 57.167 26.923 3.23 0.00 39.42 5.69
2679 2697 9.273016 TCAAATAAAAATTATTTTCACCCGCAA 57.727 25.926 3.23 0.00 39.42 4.85
2680 2698 9.884465 CAAATAAAAATTATTTTCACCCGCAAA 57.116 25.926 3.23 0.00 39.42 3.68
2725 2743 9.904198 AAATTAAAATAAACTAATGCATGGCCT 57.096 25.926 3.32 0.00 0.00 5.19
2726 2744 9.904198 AATTAAAATAAACTAATGCATGGCCTT 57.096 25.926 3.32 0.00 0.00 4.35
2727 2745 8.940768 TTAAAATAAACTAATGCATGGCCTTC 57.059 30.769 3.32 0.00 0.00 3.46
2728 2746 4.836125 ATAAACTAATGCATGGCCTTCG 57.164 40.909 3.32 0.00 0.00 3.79
2729 2747 2.418368 AACTAATGCATGGCCTTCGA 57.582 45.000 3.32 0.00 0.00 3.71
2730 2748 1.959042 ACTAATGCATGGCCTTCGAG 58.041 50.000 3.32 0.00 0.00 4.04
2731 2749 1.233019 CTAATGCATGGCCTTCGAGG 58.767 55.000 3.32 0.00 38.80 4.63
2740 2758 4.356979 CCTTCGAGGCCACTAGGA 57.643 61.111 5.01 0.00 36.89 2.94
2741 2759 2.827715 CCTTCGAGGCCACTAGGAT 58.172 57.895 5.01 0.00 36.89 3.24
2742 2760 0.676736 CCTTCGAGGCCACTAGGATC 59.323 60.000 5.01 0.00 36.89 3.36
2743 2761 0.312416 CTTCGAGGCCACTAGGATCG 59.688 60.000 5.01 3.26 43.19 3.69
2744 2762 1.735376 TTCGAGGCCACTAGGATCGC 61.735 60.000 5.01 0.00 42.21 4.58
2745 2763 2.490148 CGAGGCCACTAGGATCGCA 61.490 63.158 5.01 0.00 38.33 5.10
2746 2764 1.823295 GAGGCCACTAGGATCGCAA 59.177 57.895 5.01 0.00 36.89 4.85
2747 2765 0.394565 GAGGCCACTAGGATCGCAAT 59.605 55.000 5.01 0.00 36.89 3.56
2748 2766 0.394565 AGGCCACTAGGATCGCAATC 59.605 55.000 5.01 0.00 36.89 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.376299 TCGTACCCCACATATAGCACTATAAG 59.624 42.308 1.67 0.63 32.39 1.73
13 14 2.891580 CTCGTACCCCACATATAGCACT 59.108 50.000 0.00 0.00 0.00 4.40
43 44 6.968131 AGTACATGTACACAAACTGCATAG 57.032 37.500 32.02 0.00 38.48 2.23
45 46 6.464222 ACTAGTACATGTACACAAACTGCAT 58.536 36.000 32.02 13.80 38.48 3.96
65 66 0.716108 CCTTTGCTCAACGCGACTAG 59.284 55.000 15.93 7.60 43.27 2.57
69 70 1.092921 ACAACCTTTGCTCAACGCGA 61.093 50.000 15.93 0.00 43.27 5.87
89 90 6.618287 TGTAAATTGCACTCCATGTATAGC 57.382 37.500 0.00 0.00 0.00 2.97
90 91 7.513132 CGATGTAAATTGCACTCCATGTATAG 58.487 38.462 0.00 0.00 0.00 1.31
103 104 1.578915 CGTGCAAGCGATGTAAATTGC 59.421 47.619 0.00 0.00 46.36 3.56
107 108 0.165727 CAGCGTGCAAGCGATGTAAA 59.834 50.000 18.93 0.00 42.41 2.01
113 114 2.815211 GGATCAGCGTGCAAGCGA 60.815 61.111 18.93 18.12 43.00 4.93
120 123 0.109272 ACACACTACGGATCAGCGTG 60.109 55.000 12.18 12.18 0.00 5.34
123 126 1.131883 ACGTACACACTACGGATCAGC 59.868 52.381 5.02 0.00 44.38 4.26
131 134 3.631145 TCAGAACCACGTACACACTAC 57.369 47.619 0.00 0.00 0.00 2.73
141 144 6.202188 AGTTGTAAGTTAACATCAGAACCACG 59.798 38.462 8.61 0.00 0.00 4.94
148 151 8.730680 AGCCATAAAGTTGTAAGTTAACATCAG 58.269 33.333 8.61 0.00 0.00 2.90
152 155 8.347035 GTCAAGCCATAAAGTTGTAAGTTAACA 58.653 33.333 8.61 0.00 0.00 2.41
158 161 6.560253 ACAGTCAAGCCATAAAGTTGTAAG 57.440 37.500 0.00 0.00 0.00 2.34
160 163 4.688879 CGACAGTCAAGCCATAAAGTTGTA 59.311 41.667 0.41 0.00 0.00 2.41
169 172 0.745845 GCCATCGACAGTCAAGCCAT 60.746 55.000 0.41 0.00 0.00 4.40
185 190 2.763039 TCTTATCAGTCCCATCTGCCA 58.237 47.619 0.00 0.00 35.63 4.92
187 192 4.888326 AGATCTTATCAGTCCCATCTGC 57.112 45.455 0.00 0.00 35.63 4.26
194 199 9.995003 AAATCACTTCATAGATCTTATCAGTCC 57.005 33.333 0.00 0.00 0.00 3.85
201 206 9.426534 TCAGGAGAAATCACTTCATAGATCTTA 57.573 33.333 0.00 0.00 36.40 2.10
212 217 4.537688 TCCCATCTTCAGGAGAAATCACTT 59.462 41.667 0.00 0.00 38.06 3.16
221 226 1.069823 CCGTCATCCCATCTTCAGGAG 59.930 57.143 0.00 0.00 35.08 3.69
229 234 1.417890 ACCATCTTCCGTCATCCCATC 59.582 52.381 0.00 0.00 0.00 3.51
231 236 0.541392 CACCATCTTCCGTCATCCCA 59.459 55.000 0.00 0.00 0.00 4.37
239 244 1.746615 CCACTGCCACCATCTTCCG 60.747 63.158 0.00 0.00 0.00 4.30
249 254 3.083349 CTCCGGGATCCACTGCCA 61.083 66.667 15.23 0.00 34.29 4.92
252 257 3.461773 ACGCTCCGGGATCCACTG 61.462 66.667 15.23 2.24 0.00 3.66
253 258 3.461773 CACGCTCCGGGATCCACT 61.462 66.667 15.23 0.00 28.17 4.00
273 278 2.749865 CCATAACGTGCACCGCCTG 61.750 63.158 12.15 4.27 41.42 4.85
318 323 7.657354 CGGATAACAGACAATCTAATCCAATGA 59.343 37.037 11.57 0.00 32.94 2.57
321 326 6.099125 TCCGGATAACAGACAATCTAATCCAA 59.901 38.462 0.00 1.55 32.94 3.53
342 349 0.249120 TACAGATGTGCCTTGTCCGG 59.751 55.000 0.00 0.00 0.00 5.14
349 356 6.782988 ACACCTATAAGTATACAGATGTGCCT 59.217 38.462 5.50 0.00 0.00 4.75
367 374 4.083484 GCGAAACAAAGTTGCTACACCTAT 60.083 41.667 0.13 0.00 0.00 2.57
388 395 0.804989 CCAAAGCCACCTTCTAAGCG 59.195 55.000 0.00 0.00 0.00 4.68
418 425 8.877864 TTCACCAGAACCTGACAAATAAATAT 57.122 30.769 0.00 0.00 32.44 1.28
423 431 8.877864 AATTATTCACCAGAACCTGACAAATA 57.122 30.769 0.00 0.00 36.39 1.40
480 488 2.909457 GATGATTGCCCCGGCCTTCA 62.909 60.000 0.00 6.70 41.09 3.02
482 490 2.123726 GATGATTGCCCCGGCCTT 60.124 61.111 0.00 0.00 41.09 4.35
492 500 5.530519 TTTCGTTTCGAGAAGGATGATTG 57.469 39.130 0.00 0.00 37.14 2.67
518 526 8.966868 AGTATGTGTATGGGTAAGAAAAATTGG 58.033 33.333 0.00 0.00 0.00 3.16
558 569 2.582636 AGGCATGGGTGAAATCTAACCT 59.417 45.455 0.00 0.00 36.64 3.50
578 589 9.968870 AGCTATTTTAAGGTTTATCTCGAGTAG 57.031 33.333 13.13 2.67 0.00 2.57
638 650 1.204941 CGGCTTGACTACTTACAGGCT 59.795 52.381 0.00 0.00 38.74 4.58
639 651 1.203994 TCGGCTTGACTACTTACAGGC 59.796 52.381 0.00 0.00 38.16 4.85
719 731 2.894731 TGATCGGGATGCCTCTTCTAT 58.105 47.619 0.28 0.00 0.00 1.98
733 745 5.983720 AGTATAACCTCGTTTCATTGATCGG 59.016 40.000 10.35 0.00 0.00 4.18
748 760 7.705700 ACAACCCAAAAATAGGAGTATAACCT 58.294 34.615 5.30 5.30 41.05 3.50
841 853 1.992277 GGCAGGAGGAAGGAGAGCA 60.992 63.158 0.00 0.00 0.00 4.26
940 952 0.107752 TGGCTATCGAATGTGCTGCA 60.108 50.000 0.00 0.00 0.00 4.41
943 955 2.009774 GTGTTGGCTATCGAATGTGCT 58.990 47.619 0.00 0.00 0.00 4.40
946 958 3.052455 TGTGTGTTGGCTATCGAATGT 57.948 42.857 0.00 0.00 0.00 2.71
1067 1079 1.145819 GCTGGCTCTTGCTCCCTAG 59.854 63.158 0.00 0.00 39.59 3.02
1290 1302 1.323271 GCTCATCCAGGTCCTCGTCA 61.323 60.000 0.00 0.00 0.00 4.35
1311 1323 1.776667 CCAAGCTCCATGGATCCCTTA 59.223 52.381 16.63 0.00 40.56 2.69
1368 1380 2.280797 GCAGGGAGCGTGTCACAA 60.281 61.111 3.42 0.00 0.00 3.33
1392 1404 1.717194 GGTTGACGGCGAAATACAGA 58.283 50.000 16.62 0.00 0.00 3.41
1419 1431 0.465097 CCCGCATCTTTGGCTCAGAT 60.465 55.000 0.00 0.00 0.00 2.90
1422 1434 1.675310 CACCCGCATCTTTGGCTCA 60.675 57.895 0.00 0.00 0.00 4.26
1428 1440 2.629656 GCTGCACACCCGCATCTTT 61.630 57.895 0.00 0.00 42.06 2.52
1551 1563 5.324409 TGACCTGGACTGCTAATTTTCAAT 58.676 37.500 0.00 0.00 0.00 2.57
1582 1594 9.362151 AGGAAGAAATTAACAAGGAAACATACA 57.638 29.630 0.00 0.00 0.00 2.29
1586 1598 8.990163 ACTAGGAAGAAATTAACAAGGAAACA 57.010 30.769 0.00 0.00 0.00 2.83
1619 1632 8.823220 ATAACATAAGCTGGTGGTTCTTTTAT 57.177 30.769 0.00 0.00 35.36 1.40
1620 1633 8.644374 AATAACATAAGCTGGTGGTTCTTTTA 57.356 30.769 0.00 0.00 35.36 1.52
1621 1634 7.539034 AATAACATAAGCTGGTGGTTCTTTT 57.461 32.000 0.00 0.00 35.36 2.27
1631 1644 5.179368 CCGACCACATAATAACATAAGCTGG 59.821 44.000 0.00 0.00 0.00 4.85
1656 1669 4.701651 TGCATGAGTCAAAGGACCAAATAG 59.298 41.667 0.00 0.00 45.48 1.73
1658 1671 3.499338 TGCATGAGTCAAAGGACCAAAT 58.501 40.909 0.00 0.00 45.48 2.32
1668 1681 2.036571 CGCCTGCTGCATGAGTCAA 61.037 57.895 9.18 0.00 41.33 3.18
1694 1707 2.363683 AGCCTTGTCTTGATAAGCTGC 58.636 47.619 0.00 0.00 0.00 5.25
1773 1786 1.203162 AGGATGGGTGGTTCATTGCAA 60.203 47.619 0.00 0.00 0.00 4.08
1850 1863 2.423892 ACGTTGTGTTAATTGCACCACA 59.576 40.909 14.71 7.97 33.69 4.17
1992 2005 7.410120 AAAGAAGTTGGTGAACAAGAAGAAT 57.590 32.000 0.00 0.00 40.38 2.40
2052 2066 1.538047 CCAGTGTGCATGCCTAGTTT 58.462 50.000 16.68 0.00 0.00 2.66
2122 2136 8.524487 TGTACAAAACAGTTAGTGATGGTTTTT 58.476 29.630 0.00 0.00 39.02 1.94
2184 2198 8.742777 CCATCTAAAATCTCTGATTCAAAACCA 58.257 33.333 0.00 0.00 0.00 3.67
2258 2272 4.528596 AGTCAGAGGTGCAAGTACTGTATT 59.471 41.667 0.00 0.00 0.00 1.89
2259 2273 4.081972 CAGTCAGAGGTGCAAGTACTGTAT 60.082 45.833 0.00 0.00 0.00 2.29
2294 2308 4.897924 CACACAGCGTATGCATATTTAACG 59.102 41.667 10.16 11.98 46.23 3.18
2309 2323 2.805671 TGGACAAGTAATTCACACAGCG 59.194 45.455 0.00 0.00 0.00 5.18
2310 2324 3.363970 CGTGGACAAGTAATTCACACAGC 60.364 47.826 0.00 0.00 0.00 4.40
2311 2325 4.055360 TCGTGGACAAGTAATTCACACAG 58.945 43.478 0.00 0.00 0.00 3.66
2367 2381 4.693566 AGTCCAATCAAAAGCATGCATTTG 59.306 37.500 32.26 32.26 36.37 2.32
2393 2407 2.198827 TTCACATGAGGGATTTGCGT 57.801 45.000 0.00 0.00 0.00 5.24
2498 2513 6.600246 CAGATGTCCACAAACATATGAGAG 57.400 41.667 10.38 0.68 46.73 3.20
2509 2526 1.676968 CCCGGTCAGATGTCCACAA 59.323 57.895 0.00 0.00 0.00 3.33
2539 2556 6.204108 TCGAAAAGGTTCAAAGGATAGTGTTC 59.796 38.462 0.00 0.00 32.89 3.18
2563 2580 7.810766 TTGTGACTTTGAAATGTTTGAACTC 57.189 32.000 0.00 0.00 0.00 3.01
2591 2609 5.773239 TCGAACTAGCCTAAATTTTGTCG 57.227 39.130 0.00 0.00 0.00 4.35
2699 2717 9.904198 AGGCCATGCATTAGTTTATTTTAATTT 57.096 25.926 5.01 0.00 0.00 1.82
2700 2718 9.904198 AAGGCCATGCATTAGTTTATTTTAATT 57.096 25.926 5.01 0.00 28.34 1.40
2701 2719 9.546428 GAAGGCCATGCATTAGTTTATTTTAAT 57.454 29.630 5.01 0.00 31.02 1.40
2702 2720 7.704472 CGAAGGCCATGCATTAGTTTATTTTAA 59.296 33.333 5.01 0.00 31.02 1.52
2703 2721 7.067615 TCGAAGGCCATGCATTAGTTTATTTTA 59.932 33.333 5.01 0.00 31.02 1.52
2704 2722 6.042143 CGAAGGCCATGCATTAGTTTATTTT 58.958 36.000 5.01 0.00 31.02 1.82
2705 2723 5.359576 TCGAAGGCCATGCATTAGTTTATTT 59.640 36.000 5.01 0.00 31.02 1.40
2706 2724 4.887071 TCGAAGGCCATGCATTAGTTTATT 59.113 37.500 5.01 0.00 31.02 1.40
2707 2725 4.460263 TCGAAGGCCATGCATTAGTTTAT 58.540 39.130 5.01 0.00 31.02 1.40
2708 2726 3.876914 CTCGAAGGCCATGCATTAGTTTA 59.123 43.478 5.01 0.00 31.02 2.01
2709 2727 2.684881 CTCGAAGGCCATGCATTAGTTT 59.315 45.455 5.01 0.00 31.02 2.66
2710 2728 2.292267 CTCGAAGGCCATGCATTAGTT 58.708 47.619 5.01 0.00 31.02 2.24
2711 2729 1.475751 CCTCGAAGGCCATGCATTAGT 60.476 52.381 5.01 0.00 31.02 2.24
2712 2730 1.233019 CCTCGAAGGCCATGCATTAG 58.767 55.000 5.01 0.00 31.02 1.73
2713 2731 3.402186 CCTCGAAGGCCATGCATTA 57.598 52.632 5.01 0.00 31.02 1.90
2714 2732 4.247781 CCTCGAAGGCCATGCATT 57.752 55.556 5.01 0.00 34.48 3.56
2723 2741 0.676736 GATCCTAGTGGCCTCGAAGG 59.323 60.000 18.22 18.22 38.80 3.46
2724 2742 0.312416 CGATCCTAGTGGCCTCGAAG 59.688 60.000 3.32 3.69 39.17 3.79
2725 2743 1.735376 GCGATCCTAGTGGCCTCGAA 61.735 60.000 12.02 0.00 39.17 3.71
2726 2744 2.194212 GCGATCCTAGTGGCCTCGA 61.194 63.158 12.02 0.00 39.17 4.04
2727 2745 2.016393 TTGCGATCCTAGTGGCCTCG 62.016 60.000 3.32 3.78 39.54 4.63
2728 2746 0.394565 ATTGCGATCCTAGTGGCCTC 59.605 55.000 3.32 0.00 0.00 4.70
2729 2747 0.394565 GATTGCGATCCTAGTGGCCT 59.605 55.000 3.32 0.00 0.00 5.19
2730 2748 2.919971 GATTGCGATCCTAGTGGCC 58.080 57.895 2.08 0.00 0.00 5.36
2739 2757 2.938451 TGTCACAATGAGGATTGCGATC 59.062 45.455 5.25 5.25 42.54 3.69
2740 2758 2.679837 GTGTCACAATGAGGATTGCGAT 59.320 45.455 0.00 0.00 42.54 4.58
2741 2759 2.076100 GTGTCACAATGAGGATTGCGA 58.924 47.619 0.00 0.00 42.54 5.10
2742 2760 2.079158 AGTGTCACAATGAGGATTGCG 58.921 47.619 5.62 0.00 42.54 4.85


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

AutoCloner maintained by Alex Coulton.