Multiple sequence alignment - TraesCS2D01G352700

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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 TraesCS2D01G352700 chr2D 100.000 3222 0 0 1 3222 450997029 451000250 0.000000e+00 5951
1 TraesCS2D01G352700 chr2D 77.649 689 110 24 1 674 619434587 619435246 2.350000e-101 379
2 TraesCS2D01G352700 chr2B 92.818 2353 118 25 765 3099 531134947 531137266 0.000000e+00 3362
3 TraesCS2D01G352700 chr2B 97.183 71 1 1 3152 3222 531137266 531137335 5.650000e-23 119
4 TraesCS2D01G352700 chr2A 89.510 2326 166 33 377 2686 598617729 598615466 0.000000e+00 2872
5 TraesCS2D01G352700 chr2A 88.133 573 33 20 2684 3222 598615428 598614857 0.000000e+00 649
6 TraesCS2D01G352700 chr2A 78.300 447 72 12 230 674 750579587 750580010 6.850000e-67 265
7 TraesCS2D01G352700 chr2A 78.153 444 72 12 233 674 750615642 750616062 3.190000e-65 259
8 TraesCS2D01G352700 chr2A 77.852 447 74 12 230 674 750650263 750650686 1.480000e-63 254
9 TraesCS2D01G352700 chr7A 81.552 683 106 13 1 674 105491466 105490795 2.190000e-151 545
10 TraesCS2D01G352700 chr7A 75.134 374 71 14 1 361 285169746 285169382 4.300000e-34 156
11 TraesCS2D01G352700 chr7B 79.769 692 111 20 1 674 443848047 443847367 2.910000e-130 475
12 TraesCS2D01G352700 chr3B 86.957 414 37 10 1943 2344 680237234 680237642 1.760000e-122 449
13 TraesCS2D01G352700 chr3B 93.506 77 5 0 2488 2564 680245820 680245896 7.300000e-22 115
14 TraesCS2D01G352700 chr3D 81.522 552 66 19 77 625 571554678 571554160 3.840000e-114 422
15 TraesCS2D01G352700 chr3D 78.366 453 73 16 1 450 81054324 81053894 1.470000e-68 270
16 TraesCS2D01G352700 chr3D 90.055 181 12 2 2304 2479 517004308 517004129 2.500000e-56 230
17 TraesCS2D01G352700 chr3D 91.667 108 6 2 2460 2567 517004115 517004011 2.590000e-31 147
18 TraesCS2D01G352700 chr1B 80.777 489 81 10 154 635 106906439 106905957 1.410000e-98 370
19 TraesCS2D01G352700 chr1B 75.953 682 119 28 5 673 606584365 606585014 3.120000e-80 309
20 TraesCS2D01G352700 chr6B 85.714 259 32 5 370 625 27730818 27731074 5.300000e-68 268
21 TraesCS2D01G352700 chr6B 88.158 152 13 5 323 470 604114234 604114384 3.300000e-40 176
22 TraesCS2D01G352700 chr5B 77.193 285 45 14 368 637 145817212 145817491 7.200000e-32 148
23 TraesCS2D01G352700 chr6D 73.559 503 79 30 167 665 289517566 289517114 3.350000e-30 143
24 TraesCS2D01G352700 chr7D 74.230 357 67 15 16 359 368815671 368815327 3.370000e-25 126


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 TraesCS2D01G352700 chr2D 450997029 451000250 3221 False 5951.0 5951 100.0000 1 3222 1 chr2D.!!$F1 3221
1 TraesCS2D01G352700 chr2D 619434587 619435246 659 False 379.0 379 77.6490 1 674 1 chr2D.!!$F2 673
2 TraesCS2D01G352700 chr2B 531134947 531137335 2388 False 1740.5 3362 95.0005 765 3222 2 chr2B.!!$F1 2457
3 TraesCS2D01G352700 chr2A 598614857 598617729 2872 True 1760.5 2872 88.8215 377 3222 2 chr2A.!!$R1 2845
4 TraesCS2D01G352700 chr7A 105490795 105491466 671 True 545.0 545 81.5520 1 674 1 chr7A.!!$R1 673
5 TraesCS2D01G352700 chr7B 443847367 443848047 680 True 475.0 475 79.7690 1 674 1 chr7B.!!$R1 673
6 TraesCS2D01G352700 chr3D 571554160 571554678 518 True 422.0 422 81.5220 77 625 1 chr3D.!!$R2 548
7 TraesCS2D01G352700 chr1B 606584365 606585014 649 False 309.0 309 75.9530 5 673 1 chr1B.!!$F1 668

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
237 259 0.179040 ATCGTCCTCTCCGACTCCTC 60.179 60.0 0.00 0.0 37.12 3.71 F
926 970 0.321122 ACCAGAAGCAGCAGCAGTAC 60.321 55.0 3.17 0.0 45.49 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 1949 0.246635 CGTTGATCACCTTCTCCGGT 59.753 55.0 0.0 0.0 37.93 5.28 R
2414 2484 2.287009 GCCTGGAAGTTGTTATATGCGC 60.287 50.0 0.0 0.0 0.00 6.09 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
60 61 2.747855 GGGTCTACCGTCGGTCGT 60.748 66.667 22.74 0.00 37.09 4.34
143 144 0.460284 CCATTAAGCAGTCGGAGCGT 60.460 55.000 0.00 0.00 37.01 5.07
200 222 1.466024 GGTAGCAAGACAGAGTCGTCG 60.466 57.143 8.71 0.00 40.98 5.12
237 259 0.179040 ATCGTCCTCTCCGACTCCTC 60.179 60.000 0.00 0.00 37.12 3.71
238 260 1.820481 CGTCCTCTCCGACTCCTCC 60.820 68.421 0.00 0.00 0.00 4.30
241 263 1.152839 CCTCTCCGACTCCTCCTCC 60.153 68.421 0.00 0.00 0.00 4.30
244 272 1.149627 CTCCGACTCCTCCTCCGAT 59.850 63.158 0.00 0.00 0.00 4.18
249 277 0.748729 GACTCCTCCTCCGATGACGT 60.749 60.000 0.00 0.00 37.88 4.34
267 295 2.660552 CGACGACCACAACGCCTT 60.661 61.111 0.00 0.00 0.00 4.35
345 373 1.765727 GAAAGGGGAAAGGACCGGT 59.234 57.895 6.92 6.92 0.00 5.28
432 464 5.788055 TGTCGTCGTTTATGTGCATTATT 57.212 34.783 0.00 0.00 0.00 1.40
469 501 5.070001 TCTTTTGAAGATCCGTTGGTGATT 58.930 37.500 0.00 0.00 31.20 2.57
516 549 0.729116 TGTCCGATTCTACGTCCGTC 59.271 55.000 0.00 0.00 0.00 4.79
518 551 1.399791 GTCCGATTCTACGTCCGTCTT 59.600 52.381 0.00 0.00 0.00 3.01
559 593 9.634021 TTTATCCATGTTGCATGGTTTAGTATA 57.366 29.630 22.74 12.21 40.06 1.47
572 606 8.826765 CATGGTTTAGTATAGATGTAGGGGATT 58.173 37.037 0.00 0.00 0.00 3.01
674 710 1.248101 CGTTTGAGGGCCCGGATTTT 61.248 55.000 18.44 0.00 0.00 1.82
686 722 1.867233 CCGGATTTTCGGCTGTAGATG 59.133 52.381 0.00 0.00 43.71 2.90
731 767 1.331447 GCAAAGCCAAAGCCAAAAGTG 59.669 47.619 0.00 0.00 41.25 3.16
809 850 2.650322 TGTTTGGTCTCAACCCTCAAC 58.350 47.619 0.00 0.00 45.83 3.18
828 869 2.503061 CCTCCTGGCCACTCATCG 59.497 66.667 0.00 0.00 0.00 3.84
924 968 0.466922 AAACCAGAAGCAGCAGCAGT 60.467 50.000 3.17 0.00 45.49 4.40
926 970 0.321122 ACCAGAAGCAGCAGCAGTAC 60.321 55.000 3.17 0.00 45.49 2.73
927 971 1.023513 CCAGAAGCAGCAGCAGTACC 61.024 60.000 3.17 0.00 45.49 3.34
928 972 1.023513 CAGAAGCAGCAGCAGTACCC 61.024 60.000 3.17 0.00 45.49 3.69
929 973 1.003355 GAAGCAGCAGCAGTACCCA 60.003 57.895 3.17 0.00 45.49 4.51
931 975 0.607489 AAGCAGCAGCAGTACCCAAG 60.607 55.000 3.17 0.00 45.49 3.61
934 978 1.896220 CAGCAGCAGTACCCAAGAAA 58.104 50.000 0.00 0.00 0.00 2.52
935 979 1.537202 CAGCAGCAGTACCCAAGAAAC 59.463 52.381 0.00 0.00 0.00 2.78
960 1005 1.639298 GGCAGAGCCGAATCACACAC 61.639 60.000 0.00 0.00 39.62 3.82
962 1007 0.792640 CAGAGCCGAATCACACACAC 59.207 55.000 0.00 0.00 0.00 3.82
973 1018 1.766059 ACACACACCCTGCAGGAGA 60.766 57.895 34.91 0.00 39.89 3.71
974 1019 1.004080 CACACACCCTGCAGGAGAG 60.004 63.158 34.91 24.20 39.89 3.20
982 1027 3.072476 TGCAGGAGAGGCAGGAAC 58.928 61.111 0.00 0.00 36.11 3.62
1066 1111 0.823356 GTTCCTCACAAAGCAGGCCA 60.823 55.000 5.01 0.00 0.00 5.36
1108 1153 1.754380 TACGGTTGTGAGGTGCAGCT 61.754 55.000 20.31 20.31 0.00 4.24
1109 1154 1.005037 CGGTTGTGAGGTGCAGCTA 60.005 57.895 20.22 0.00 0.00 3.32
1140 1185 3.054875 CCCTGTCAGGATCACATGAAGAA 60.055 47.826 21.23 0.00 38.53 2.52
1145 1190 3.453717 TCAGGATCACATGAAGAAGAGGG 59.546 47.826 0.00 0.00 33.86 4.30
1230 1275 1.896660 TGGAGTTTCGGTGCTTGGC 60.897 57.895 0.00 0.00 0.00 4.52
1330 1379 1.363807 GGTTGGTTCTTGCTGCCAC 59.636 57.895 0.00 0.00 31.19 5.01
1406 1471 5.208463 AGTTCAGTTCAGAGGAAGTCTTC 57.792 43.478 3.80 3.80 34.43 2.87
1566 1631 1.066502 GCTGGGAAGAGGTGAGAACTC 60.067 57.143 0.00 0.00 35.20 3.01
1574 1639 1.402613 GAGGTGAGAACTCGAGCTACC 59.597 57.143 13.61 13.35 0.00 3.18
1586 1651 1.846782 CGAGCTACCGACAGAAATTCG 59.153 52.381 0.00 0.00 36.20 3.34
1600 1665 5.180117 ACAGAAATTCGGTCTTCAGAACATG 59.820 40.000 0.00 0.00 31.42 3.21
1601 1666 4.154918 AGAAATTCGGTCTTCAGAACATGC 59.845 41.667 0.00 0.00 31.42 4.06
1603 1668 2.839486 TCGGTCTTCAGAACATGCTT 57.161 45.000 0.00 0.00 0.00 3.91
1604 1669 2.416747 TCGGTCTTCAGAACATGCTTG 58.583 47.619 0.00 0.00 0.00 4.01
1613 1678 2.358582 CAGAACATGCTTGGTCACACAA 59.641 45.455 18.83 0.00 42.38 3.33
1615 1680 3.254166 AGAACATGCTTGGTCACACAATC 59.746 43.478 18.83 0.00 42.38 2.67
1628 1693 4.913924 GTCACACAATCTCTGATGCAAAAC 59.086 41.667 0.00 0.00 0.00 2.43
1629 1694 4.823442 TCACACAATCTCTGATGCAAAACT 59.177 37.500 0.00 0.00 0.00 2.66
1638 1703 4.627058 TCTGATGCAAAACTCGTGTTCTA 58.373 39.130 2.94 0.00 34.96 2.10
1641 1706 5.688823 TGATGCAAAACTCGTGTTCTAATG 58.311 37.500 2.94 2.88 34.96 1.90
1728 1793 2.039084 GGAGGGCCGATTATCTGTCATT 59.961 50.000 0.00 0.00 0.00 2.57
1770 1835 1.615384 GCAGGTGAGCCCTCAAGAAAT 60.615 52.381 0.00 0.00 43.86 2.17
1788 1853 6.272822 AGAAATTGTTCTTTCCTGGCATAC 57.727 37.500 0.00 0.00 41.55 2.39
1790 1855 5.904362 AATTGTTCTTTCCTGGCATACTC 57.096 39.130 0.00 0.00 0.00 2.59
1791 1856 4.365514 TTGTTCTTTCCTGGCATACTCA 57.634 40.909 0.00 0.00 0.00 3.41
1792 1857 4.574674 TGTTCTTTCCTGGCATACTCAT 57.425 40.909 0.00 0.00 0.00 2.90
1794 1859 5.324409 TGTTCTTTCCTGGCATACTCATTT 58.676 37.500 0.00 0.00 0.00 2.32
1795 1860 5.415701 TGTTCTTTCCTGGCATACTCATTTC 59.584 40.000 0.00 0.00 0.00 2.17
1796 1861 5.441718 TCTTTCCTGGCATACTCATTTCT 57.558 39.130 0.00 0.00 0.00 2.52
1797 1862 5.819991 TCTTTCCTGGCATACTCATTTCTT 58.180 37.500 0.00 0.00 0.00 2.52
1798 1863 6.957631 TCTTTCCTGGCATACTCATTTCTTA 58.042 36.000 0.00 0.00 0.00 2.10
1799 1864 7.050377 TCTTTCCTGGCATACTCATTTCTTAG 58.950 38.462 0.00 0.00 0.00 2.18
1800 1865 5.957771 TCCTGGCATACTCATTTCTTAGT 57.042 39.130 0.00 0.00 0.00 2.24
1828 1893 3.336468 ACTGTCTCACGGTACTGACTAG 58.664 50.000 9.17 2.72 35.60 2.57
2161 2230 5.754890 GGAATTATGTATTTTTGCAGGGCTG 59.245 40.000 0.00 0.00 0.00 4.85
2249 2318 1.542328 CCACTGGGTTCGTTCATCACA 60.542 52.381 0.00 0.00 0.00 3.58
2260 2329 6.961554 GGTTCGTTCATCACATAATCTGTTTC 59.038 38.462 0.00 0.00 35.29 2.78
2265 2334 9.425893 CGTTCATCACATAATCTGTTTCATTAC 57.574 33.333 0.00 0.00 35.29 1.89
2331 2400 8.946085 AGTACACATCATTTGTAACGATGATTT 58.054 29.630 5.67 0.00 40.14 2.17
2333 2402 8.451687 ACACATCATTTGTAACGATGATTTTG 57.548 30.769 5.67 4.69 40.14 2.44
2414 2484 0.034089 CCTAAAGGTGCCTTCAGGGG 60.034 60.000 11.59 5.11 37.72 4.79
2437 2507 3.287222 GCATATAACAACTTCCAGGCCA 58.713 45.455 5.01 0.00 0.00 5.36
2546 2616 7.600375 ACTGATACATGTAGAGTTGTTTCACTG 59.400 37.037 11.91 0.29 32.71 3.66
2564 2634 2.589540 CACTTGCCGGCCTCCATA 59.410 61.111 26.77 0.00 0.00 2.74
2565 2635 1.149174 CACTTGCCGGCCTCCATAT 59.851 57.895 26.77 0.00 0.00 1.78
2566 2636 0.396435 CACTTGCCGGCCTCCATATA 59.604 55.000 26.77 0.00 0.00 0.86
2567 2637 0.396811 ACTTGCCGGCCTCCATATAC 59.603 55.000 26.77 0.00 0.00 1.47
2568 2638 0.687354 CTTGCCGGCCTCCATATACT 59.313 55.000 26.77 0.00 0.00 2.12
2656 2726 6.273071 CGTCATGGAGTATGAGTGTGATTTA 58.727 40.000 0.00 0.00 46.09 1.40
2686 2756 2.091610 AGGCATCACTAGAGCTCCAGTA 60.092 50.000 14.70 4.48 0.00 2.74
2687 2757 2.896685 GGCATCACTAGAGCTCCAGTAT 59.103 50.000 14.70 6.49 0.00 2.12
2688 2758 4.082845 GGCATCACTAGAGCTCCAGTATA 58.917 47.826 14.70 6.73 0.00 1.47
2689 2759 4.709397 GGCATCACTAGAGCTCCAGTATAT 59.291 45.833 14.70 8.70 0.00 0.86
2691 2761 5.184864 GCATCACTAGAGCTCCAGTATATGT 59.815 44.000 24.49 7.84 0.00 2.29
2692 2762 6.619744 CATCACTAGAGCTCCAGTATATGTG 58.380 44.000 14.70 9.78 0.00 3.21
2693 2763 5.941788 TCACTAGAGCTCCAGTATATGTGA 58.058 41.667 14.70 11.67 0.00 3.58
2704 2817 7.363355 GCTCCAGTATATGTGATATGTAGCTGT 60.363 40.741 0.00 0.00 0.00 4.40
2742 2855 7.496529 TCAAAGTTCACTCAAATGGTTCTAG 57.503 36.000 0.00 0.00 0.00 2.43
2753 2874 8.494433 ACTCAAATGGTTCTAGGATATGCTAAA 58.506 33.333 5.40 1.07 0.00 1.85
2816 2962 5.356882 TGAGCAGCAACTACAACATAAAC 57.643 39.130 0.00 0.00 0.00 2.01
2960 3106 2.462456 TCACAGGCAAGCTAGAACAG 57.538 50.000 0.00 0.00 0.00 3.16
3039 3190 8.094798 TCTATGGTTAACTTTTGCTGTACTTG 57.905 34.615 5.42 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.443266 AAGTGAGGAGCCGCTCGC 62.443 66.667 14.21 9.30 37.98 5.03
60 61 2.222796 CGTCCGTATCTGTCGTCGTAAA 60.223 50.000 0.00 0.00 0.00 2.01
69 70 0.179171 CGTCAAGCGTCCGTATCTGT 60.179 55.000 0.00 0.00 35.54 3.41
74 75 1.499056 GAGTCGTCAAGCGTCCGTA 59.501 57.895 0.00 0.00 42.13 4.02
161 182 4.069232 CTGAGCTTCGCCACCCGA 62.069 66.667 0.00 0.00 45.77 5.14
165 186 3.642778 TACCGCTGAGCTTCGCCAC 62.643 63.158 1.78 0.00 0.00 5.01
244 272 1.298563 GTTGTGGTCGTCGACGTCA 60.299 57.895 34.40 28.65 40.80 4.35
249 277 3.141522 AAGGCGTTGTGGTCGTCGA 62.142 57.895 0.00 0.00 37.99 4.20
328 356 1.063654 TCACCGGTCCTTTCCCCTTT 61.064 55.000 2.59 0.00 0.00 3.11
340 368 1.052124 TTCACCACTTCCTCACCGGT 61.052 55.000 0.00 0.00 0.00 5.28
345 373 1.550524 CGGATCTTCACCACTTCCTCA 59.449 52.381 0.00 0.00 0.00 3.86
394 423 7.928908 ACGACGACAAAGTTTAAACTACATA 57.071 32.000 20.83 0.00 38.57 2.29
410 441 5.788055 AATAATGCACATAAACGACGACA 57.212 34.783 0.00 0.00 0.00 4.35
432 464 4.909696 TCAAAAGATCGCCAAAGTTCAA 57.090 36.364 0.00 0.00 0.00 2.69
469 501 5.776173 ATACACAATCCGTTCACCAAAAA 57.224 34.783 0.00 0.00 0.00 1.94
559 593 5.920347 TCTCATATCCAATCCCCTACATCT 58.080 41.667 0.00 0.00 0.00 2.90
572 606 5.076873 TCACATCCGTGTATCTCATATCCA 58.923 41.667 0.00 0.00 44.02 3.41
601 635 1.697432 ACCGGTCAGTCCTCAAATTGA 59.303 47.619 0.00 0.00 0.00 2.57
686 722 7.846592 GCACGTAAAATCTGAGTAAATAAGAGC 59.153 37.037 0.00 0.00 0.00 4.09
708 744 0.809241 TTTGGCTTTGGCTTTGCACG 60.809 50.000 0.00 0.00 38.73 5.34
737 773 4.380867 CGTGCCTAGCTCAATTGGATTTTT 60.381 41.667 5.42 0.00 0.00 1.94
741 777 1.475751 CCGTGCCTAGCTCAATTGGAT 60.476 52.381 5.42 0.00 0.00 3.41
746 787 1.153289 CTGCCGTGCCTAGCTCAAT 60.153 57.895 0.00 0.00 0.00 2.57
748 789 1.826340 TTTCTGCCGTGCCTAGCTCA 61.826 55.000 0.00 0.00 0.00 4.26
753 794 1.335496 GTTTGTTTTCTGCCGTGCCTA 59.665 47.619 0.00 0.00 0.00 3.93
809 850 2.693864 ATGAGTGGCCAGGAGGGG 60.694 66.667 5.11 0.00 37.04 4.79
899 943 1.247567 GCTGCTTCTGGTTTTGCCTA 58.752 50.000 0.00 0.00 38.35 3.93
924 968 1.213182 TGCCTGTGTGTTTCTTGGGTA 59.787 47.619 0.00 0.00 0.00 3.69
926 970 0.670162 CTGCCTGTGTGTTTCTTGGG 59.330 55.000 0.00 0.00 0.00 4.12
927 971 1.605710 CTCTGCCTGTGTGTTTCTTGG 59.394 52.381 0.00 0.00 0.00 3.61
928 972 1.002033 GCTCTGCCTGTGTGTTTCTTG 60.002 52.381 0.00 0.00 0.00 3.02
929 973 1.312815 GCTCTGCCTGTGTGTTTCTT 58.687 50.000 0.00 0.00 0.00 2.52
931 975 1.952263 GGCTCTGCCTGTGTGTTTC 59.048 57.895 0.73 0.00 46.69 2.78
960 1005 3.324930 TGCCTCTCCTGCAGGGTG 61.325 66.667 32.23 23.73 34.05 4.61
973 1018 1.650528 AGCTAGAAGTGTTCCTGCCT 58.349 50.000 0.00 0.00 0.00 4.75
974 1019 2.740256 GCTAGCTAGAAGTGTTCCTGCC 60.740 54.545 25.15 0.00 0.00 4.85
982 1027 4.557296 GCTCATCTCTGCTAGCTAGAAGTG 60.557 50.000 25.35 22.89 30.61 3.16
1090 1135 1.754380 TAGCTGCACCTCACAACCGT 61.754 55.000 1.02 0.00 0.00 4.83
1140 1185 2.204705 ACCCCCTCTCTCCCCTCT 60.205 66.667 0.00 0.00 0.00 3.69
1145 1190 1.003573 ACCATCACCCCCTCTCTCC 59.996 63.158 0.00 0.00 0.00 3.71
1356 1405 6.105397 AGAACAAAAACATCCTACGGAGTA 57.895 37.500 0.00 0.00 45.11 2.59
1358 1407 5.689819 CAAGAACAAAAACATCCTACGGAG 58.310 41.667 0.00 0.00 34.05 4.63
1359 1408 4.023536 GCAAGAACAAAAACATCCTACGGA 60.024 41.667 0.00 0.00 35.55 4.69
1360 1409 4.023193 AGCAAGAACAAAAACATCCTACGG 60.023 41.667 0.00 0.00 0.00 4.02
1361 1410 5.108385 AGCAAGAACAAAAACATCCTACG 57.892 39.130 0.00 0.00 0.00 3.51
1566 1631 1.846782 CGAATTTCTGTCGGTAGCTCG 59.153 52.381 0.00 0.00 34.85 5.03
1574 1639 3.575630 TCTGAAGACCGAATTTCTGTCG 58.424 45.455 13.22 2.58 36.03 4.35
1586 1651 2.485814 GACCAAGCATGTTCTGAAGACC 59.514 50.000 0.00 0.00 0.00 3.85
1588 1653 3.141398 GTGACCAAGCATGTTCTGAAGA 58.859 45.455 0.00 0.00 0.00 2.87
1589 1654 2.880268 TGTGACCAAGCATGTTCTGAAG 59.120 45.455 0.00 0.00 0.00 3.02
1600 1665 2.771089 TCAGAGATTGTGTGACCAAGC 58.229 47.619 0.00 0.00 0.00 4.01
1601 1666 3.126514 GCATCAGAGATTGTGTGACCAAG 59.873 47.826 0.00 0.00 29.56 3.61
1603 1668 2.038820 TGCATCAGAGATTGTGTGACCA 59.961 45.455 0.00 0.00 29.56 4.02
1604 1669 2.703416 TGCATCAGAGATTGTGTGACC 58.297 47.619 0.00 0.00 29.56 4.02
1613 1678 3.668447 ACACGAGTTTTGCATCAGAGAT 58.332 40.909 0.00 0.00 0.00 2.75
1615 1680 3.496130 AGAACACGAGTTTTGCATCAGAG 59.504 43.478 0.00 0.00 38.30 3.35
1628 1693 5.055642 TGGTGTCTACATTAGAACACGAG 57.944 43.478 0.00 0.00 37.53 4.18
1629 1694 4.521639 ACTGGTGTCTACATTAGAACACGA 59.478 41.667 0.00 0.00 37.53 4.35
1728 1793 2.412323 CCTACGAGTGGGCGCTACA 61.412 63.158 7.64 3.94 33.86 2.74
1770 1835 4.365514 TGAGTATGCCAGGAAAGAACAA 57.634 40.909 0.00 0.00 0.00 2.83
1788 1853 7.155328 AGACAGTTACCACACTAAGAAATGAG 58.845 38.462 0.00 0.00 0.00 2.90
1790 1855 6.929049 TGAGACAGTTACCACACTAAGAAATG 59.071 38.462 0.00 0.00 0.00 2.32
1791 1856 6.929606 GTGAGACAGTTACCACACTAAGAAAT 59.070 38.462 0.00 0.00 0.00 2.17
1792 1857 6.278363 GTGAGACAGTTACCACACTAAGAAA 58.722 40.000 0.00 0.00 0.00 2.52
1794 1859 4.023450 CGTGAGACAGTTACCACACTAAGA 60.023 45.833 0.00 0.00 0.00 2.10
1795 1860 4.227538 CGTGAGACAGTTACCACACTAAG 58.772 47.826 0.00 0.00 0.00 2.18
1796 1861 3.005050 CCGTGAGACAGTTACCACACTAA 59.995 47.826 0.00 0.00 0.00 2.24
1797 1862 2.555325 CCGTGAGACAGTTACCACACTA 59.445 50.000 0.00 0.00 0.00 2.74
1798 1863 1.340248 CCGTGAGACAGTTACCACACT 59.660 52.381 0.00 0.00 0.00 3.55
1799 1864 1.068127 ACCGTGAGACAGTTACCACAC 59.932 52.381 0.00 0.00 0.00 3.82
1800 1865 1.405872 ACCGTGAGACAGTTACCACA 58.594 50.000 0.00 0.00 0.00 4.17
1828 1893 0.599558 TCTTGGCAGTTTCAGCATGC 59.400 50.000 10.51 10.51 39.25 4.06
1884 1949 0.246635 CGTTGATCACCTTCTCCGGT 59.753 55.000 0.00 0.00 37.93 5.28
2102 2167 4.156455 AGTGACCACAGAAATCAACACT 57.844 40.909 2.78 0.00 33.47 3.55
2115 2180 5.299279 TCCTTTTGATGAGAAAAGTGACCAC 59.701 40.000 0.00 0.00 40.09 4.16
2161 2230 3.181483 CCTTGTAATGCCTCTTCCATTGC 60.181 47.826 0.00 0.00 36.32 3.56
2260 2329 6.429385 GGCATCCCTCATTTTCTCTAGTAATG 59.571 42.308 0.00 0.00 0.00 1.90
2265 2334 3.181461 ACGGCATCCCTCATTTTCTCTAG 60.181 47.826 0.00 0.00 0.00 2.43
2331 2400 7.715657 ACAATGTTCAATTTCTTCAGCTACAA 58.284 30.769 0.00 0.00 0.00 2.41
2333 2402 9.282247 CATACAATGTTCAATTTCTTCAGCTAC 57.718 33.333 0.00 0.00 0.00 3.58
2414 2484 2.287009 GCCTGGAAGTTGTTATATGCGC 60.287 50.000 0.00 0.00 0.00 6.09
2546 2616 2.965716 ATATGGAGGCCGGCAAGTGC 62.966 60.000 30.85 17.77 41.14 4.40
2656 2726 4.457257 GCTCTAGTGATGCCTTGAAAGTTT 59.543 41.667 0.00 0.00 0.00 2.66
2780 2902 5.541953 TGCTGCTCATATCATTCTGTAGT 57.458 39.130 0.00 0.00 0.00 2.73
2960 3106 6.127111 CCCTTCCTACCCTAGAGTTAACTTTC 60.127 46.154 10.02 0.00 0.00 2.62
3039 3190 8.519526 TGAAAAATATGTGTTGTATGAAGACCC 58.480 33.333 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.