Multiple sequence alignment - TraesCS1A01G338000

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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 TraesCS1A01G338000 chr1A 100.000 2587 0 0 1 2587 527756706 527759292 0.000000e+00 4778
1 TraesCS1A01G338000 chr1A 92.407 1778 102 14 1 1774 527785550 527787298 0.000000e+00 2505
2 TraesCS1A01G338000 chr1A 98.058 206 4 0 2382 2587 526888398 526888603 2.450000e-95 359
3 TraesCS1A01G338000 chr1A 97.596 208 3 1 2382 2587 86962240 86962447 3.170000e-94 355
4 TraesCS1A01G338000 chr1A 97.585 207 3 1 2382 2586 351136230 351136436 1.140000e-93 353
5 TraesCS1A01G338000 chr1D 92.121 1320 90 9 1 1316 430309799 430311108 0.000000e+00 1849
6 TraesCS1A01G338000 chr1D 90.883 351 26 1 1370 1720 430311108 430311452 1.400000e-127 466
7 TraesCS1A01G338000 chr1B 90.491 936 62 8 728 1661 581104352 581105262 0.000000e+00 1210
8 TraesCS1A01G338000 chr1B 87.580 628 69 7 1798 2418 175406044 175406669 0.000000e+00 719
9 TraesCS1A01G338000 chr3A 87.883 652 69 9 1798 2444 231746580 231745934 0.000000e+00 758
10 TraesCS1A01G338000 chr3A 98.058 206 4 0 2382 2587 34800927 34801132 2.450000e-95 359
11 TraesCS1A01G338000 chr5D 89.394 594 57 5 1804 2394 347261193 347261783 0.000000e+00 743
12 TraesCS1A01G338000 chr5D 89.744 585 53 5 1810 2390 193530079 193529498 0.000000e+00 741
13 TraesCS1A01G338000 chr7A 88.057 628 66 6 1807 2428 188751092 188751716 0.000000e+00 736
14 TraesCS1A01G338000 chr7A 87.923 621 65 7 1810 2428 281385669 281385057 0.000000e+00 723
15 TraesCS1A01G338000 chr3D 88.141 624 64 8 1804 2424 480927500 480928116 0.000000e+00 734
16 TraesCS1A01G338000 chr2B 89.438 587 55 5 1810 2392 58368300 58367717 0.000000e+00 734
17 TraesCS1A01G338000 chr6D 86.936 643 69 11 1810 2444 319407449 319406814 0.000000e+00 708
18 TraesCS1A01G338000 chr4A 81.139 790 118 25 1810 2587 469557191 469556421 2.850000e-169 604
19 TraesCS1A01G338000 chr4A 98.058 206 4 0 2382 2587 288788544 288788339 2.450000e-95 359
20 TraesCS1A01G338000 chr2A 98.058 206 4 0 2382 2587 176764362 176764157 2.450000e-95 359
21 TraesCS1A01G338000 chr2A 98.058 206 4 0 2382 2587 313284195 313284400 2.450000e-95 359
22 TraesCS1A01G338000 chr2A 98.058 206 4 0 2382 2587 668997239 668997444 2.450000e-95 359


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 TraesCS1A01G338000 chr1A 527756706 527759292 2586 False 4778.0 4778 100.000 1 2587 1 chr1A.!!$F4 2586
1 TraesCS1A01G338000 chr1A 527785550 527787298 1748 False 2505.0 2505 92.407 1 1774 1 chr1A.!!$F5 1773
2 TraesCS1A01G338000 chr1D 430309799 430311452 1653 False 1157.5 1849 91.502 1 1720 2 chr1D.!!$F1 1719
3 TraesCS1A01G338000 chr1B 581104352 581105262 910 False 1210.0 1210 90.491 728 1661 1 chr1B.!!$F2 933
4 TraesCS1A01G338000 chr1B 175406044 175406669 625 False 719.0 719 87.580 1798 2418 1 chr1B.!!$F1 620
5 TraesCS1A01G338000 chr3A 231745934 231746580 646 True 758.0 758 87.883 1798 2444 1 chr3A.!!$R1 646
6 TraesCS1A01G338000 chr5D 347261193 347261783 590 False 743.0 743 89.394 1804 2394 1 chr5D.!!$F1 590
7 TraesCS1A01G338000 chr5D 193529498 193530079 581 True 741.0 741 89.744 1810 2390 1 chr5D.!!$R1 580
8 TraesCS1A01G338000 chr7A 188751092 188751716 624 False 736.0 736 88.057 1807 2428 1 chr7A.!!$F1 621
9 TraesCS1A01G338000 chr7A 281385057 281385669 612 True 723.0 723 87.923 1810 2428 1 chr7A.!!$R1 618
10 TraesCS1A01G338000 chr3D 480927500 480928116 616 False 734.0 734 88.141 1804 2424 1 chr3D.!!$F1 620
11 TraesCS1A01G338000 chr2B 58367717 58368300 583 True 734.0 734 89.438 1810 2392 1 chr2B.!!$R1 582
12 TraesCS1A01G338000 chr6D 319406814 319407449 635 True 708.0 708 86.936 1810 2444 1 chr6D.!!$R1 634
13 TraesCS1A01G338000 chr4A 469556421 469557191 770 True 604.0 604 81.139 1810 2587 1 chr4A.!!$R2 777

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
176 177 0.458543 CTAGTTGCGACGCCAGACAT 60.459 55.0 18.69 6.39 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 1818 0.252197 GTGGCTCGGACCAACCTTAT 59.748 55.0 0.0 0.0 42.7 1.73 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
109 110 0.918983 CTACAATGGGAAGGGCAGGA 59.081 55.000 0.00 0.00 0.00 3.86
110 111 1.496429 CTACAATGGGAAGGGCAGGAT 59.504 52.381 0.00 0.00 0.00 3.24
144 145 1.806542 CCATGGAGAGAAACCAACACG 59.193 52.381 5.56 0.00 40.93 4.49
153 154 4.056050 GAGAAACCAACACGTGATACACT 58.944 43.478 25.01 11.74 31.34 3.55
168 169 1.909376 ACACTATGCTAGTTGCGACG 58.091 50.000 0.00 0.00 46.63 5.12
176 177 0.458543 CTAGTTGCGACGCCAGACAT 60.459 55.000 18.69 6.39 0.00 3.06
202 203 3.451141 TGGCCAACATTGAGAACAAAC 57.549 42.857 0.61 0.00 39.54 2.93
205 206 3.803778 GGCCAACATTGAGAACAAACTTG 59.196 43.478 0.00 0.00 39.54 3.16
223 224 4.220724 ACTTGTCCTCCACACTACACTAA 58.779 43.478 0.00 0.00 33.41 2.24
416 419 4.728772 ACTCAAGTTCCATCCAACATTCA 58.271 39.130 0.00 0.00 0.00 2.57
504 507 9.490379 GGTTCATTTAAGTATATGTCGGAGAAT 57.510 33.333 0.00 0.00 39.69 2.40
681 685 7.880160 TTGTTGGAGAAACTATAATGGATGG 57.120 36.000 0.00 0.00 39.70 3.51
702 706 6.173427 TGGGGTATATCTAACGGGTAAAAC 57.827 41.667 0.00 0.00 0.00 2.43
719 723 8.298140 CGGGTAAAACTGTAATTTGTAATTCCA 58.702 33.333 0.00 0.00 0.00 3.53
789 793 6.575649 GCACTGGTGGTTAGTCTAATTTAGGA 60.576 42.308 3.66 0.00 0.00 2.94
798 802 7.984050 GGTTAGTCTAATTTAGGAAGGTACCAC 59.016 40.741 15.94 7.63 0.00 4.16
1039 1045 7.447238 AGAATGAGAAACTAAATTGACCGGAAA 59.553 33.333 9.46 1.81 0.00 3.13
1044 1050 8.040716 AGAAACTAAATTGACCGGAAATACAG 57.959 34.615 9.46 10.45 0.00 2.74
1098 1106 1.135859 CATGGCGCTTCTCAAGAACAC 60.136 52.381 7.64 0.00 0.00 3.32
1121 1129 2.791868 GGGGTTTTGTGCTTGGCGT 61.792 57.895 0.00 0.00 0.00 5.68
1173 1181 1.598130 GTGATGCATCCTACGGGGC 60.598 63.158 23.67 0.00 34.39 5.80
1174 1182 2.357517 GATGCATCCTACGGGGCG 60.358 66.667 16.23 0.00 34.39 6.13
1176 1184 3.165160 ATGCATCCTACGGGGCGAC 62.165 63.158 0.00 0.00 34.39 5.19
1324 1334 1.549203 CTACAACTTTGGCCATGGCT 58.451 50.000 34.70 15.98 41.60 4.75
1363 1373 3.559171 GGTGTGCAGATGGAGAAGGTTTA 60.559 47.826 0.00 0.00 0.00 2.01
1402 1412 1.000396 GGACCAAGGCTGCAAGGAT 60.000 57.895 10.57 0.00 0.00 3.24
1405 1415 1.000521 CCAAGGCTGCAAGGATCCA 60.001 57.895 15.82 0.00 0.00 3.41
1429 1439 3.118261 TGAATGGAATCCCTAGTCAGTGC 60.118 47.826 0.00 0.00 0.00 4.40
1510 1520 1.805428 GAAAGCCCAACCGCATGTGT 61.805 55.000 5.38 0.00 0.00 3.72
1535 1545 4.291783 CTGCTATAAGTAGACACTTCCGC 58.708 47.826 0.00 0.00 44.04 5.54
1537 1547 2.205307 ATAAGTAGACACTTCCGCGC 57.795 50.000 0.00 0.00 44.04 6.86
1543 1553 0.949105 AGACACTTCCGCGCGAATTT 60.949 50.000 34.63 10.03 0.00 1.82
1561 1571 4.734398 ATTTGTGGAAGAGTGCAAAACA 57.266 36.364 0.00 0.00 34.99 2.83
1664 1674 2.735772 CCCGGGCAGTGCTACTCAT 61.736 63.158 16.11 0.00 0.00 2.90
1670 1680 3.545703 GGGCAGTGCTACTCATTACAAT 58.454 45.455 16.11 0.00 0.00 2.71
1687 1697 6.751514 TTACAATATTCAGCAATCAACGGT 57.248 33.333 0.00 0.00 0.00 4.83
1725 1735 3.629087 TCCCTACAACAGCTAGGAGTAC 58.371 50.000 0.72 0.00 33.65 2.73
1782 1792 9.845214 ACATAGGTAATAGGATTTCTGATACCT 57.155 33.333 12.61 12.61 43.99 3.08
1786 1796 9.670442 AGGTAATAGGATTTCTGATACCTACAA 57.330 33.333 8.18 0.00 41.98 2.41
1804 1814 8.687292 ACCTACAATATACTTGTAGTGATCGA 57.313 34.615 21.08 0.00 46.30 3.59
1805 1815 9.128404 ACCTACAATATACTTGTAGTGATCGAA 57.872 33.333 21.08 0.00 46.30 3.71
1851 1861 0.462937 TCCCACAATACCGCCGAATG 60.463 55.000 0.00 0.00 0.00 2.67
1971 1981 1.270252 CCACTGTTGGGAATTGTTGCC 60.270 52.381 0.00 0.00 39.57 4.52
1973 1983 2.890311 CACTGTTGGGAATTGTTGCCTA 59.110 45.455 1.98 0.00 42.41 3.93
2015 2031 5.434408 GCATAGGCAATGATCTATCCATGA 58.566 41.667 0.00 0.00 37.86 3.07
2030 2050 4.426736 TCCATGAAGATGCATAGCAAGA 57.573 40.909 0.00 0.00 43.62 3.02
2060 2081 4.592942 AGTGTGTCTACGTACCCTCATAA 58.407 43.478 0.00 0.00 0.00 1.90
2104 2125 1.829222 ACGGGGTTGATGTAGTCGAAT 59.171 47.619 0.00 0.00 0.00 3.34
2270 2291 4.849813 TGGTGATGATGAAGTGATCCTT 57.150 40.909 0.00 0.00 35.59 3.36
2274 2295 4.579340 GTGATGATGAAGTGATCCTTGCAT 59.421 41.667 1.70 5.40 32.03 3.96
2333 2355 1.637035 AGTAAATGGTAAAGGGGGCGT 59.363 47.619 0.00 0.00 0.00 5.68
2352 2374 2.574322 GTCGCACACAGCTAAACAATG 58.426 47.619 0.00 0.00 42.61 2.82
2355 2377 2.287547 CGCACACAGCTAAACAATGGTT 60.288 45.455 0.00 0.00 42.61 3.67
2370 2396 0.250124 TGGTTTCGTGTGTGCTAGGG 60.250 55.000 0.00 0.00 0.00 3.53
2372 2398 1.666553 TTTCGTGTGTGCTAGGGCG 60.667 57.895 0.00 0.00 42.25 6.13
2500 2533 3.073678 TGATCACAACATGAACTTCCCG 58.926 45.455 0.00 0.00 41.93 5.14
2501 2534 2.920724 TCACAACATGAACTTCCCGA 57.079 45.000 0.00 0.00 33.02 5.14
2502 2535 2.766313 TCACAACATGAACTTCCCGAG 58.234 47.619 0.00 0.00 33.02 4.63
2505 2538 4.062293 CACAACATGAACTTCCCGAGTAA 58.938 43.478 0.00 0.00 37.72 2.24
2506 2539 4.062991 ACAACATGAACTTCCCGAGTAAC 58.937 43.478 0.00 0.00 37.72 2.50
2507 2540 2.955614 ACATGAACTTCCCGAGTAACG 58.044 47.619 0.00 0.00 37.72 3.18
2508 2541 1.659098 CATGAACTTCCCGAGTAACGC 59.341 52.381 0.00 0.00 37.72 4.84
2509 2542 0.387622 TGAACTTCCCGAGTAACGCG 60.388 55.000 3.53 3.53 37.72 6.01
2510 2543 1.681025 GAACTTCCCGAGTAACGCGC 61.681 60.000 5.73 0.00 37.72 6.86
2511 2544 3.245315 CTTCCCGAGTAACGCGCG 61.245 66.667 30.96 30.96 41.07 6.86
2515 2550 3.530104 CCGAGTAACGCGCGTGAC 61.530 66.667 37.49 37.49 38.74 3.67
2526 2561 3.692406 GCGTGACCTTCCCCGAGT 61.692 66.667 0.00 0.00 0.00 4.18
2543 2578 4.380655 CCCGAGTACTAGGTTGAACTTCAG 60.381 50.000 19.33 0.00 0.00 3.02
2545 2580 4.082679 CGAGTACTAGGTTGAACTTCAGCT 60.083 45.833 0.00 2.90 0.00 4.24
2548 2583 7.299246 AGTACTAGGTTGAACTTCAGCTAAA 57.701 36.000 0.00 0.00 0.00 1.85
2550 2585 7.873505 AGTACTAGGTTGAACTTCAGCTAAAAG 59.126 37.037 0.00 6.50 0.00 2.27
2551 2586 5.998363 ACTAGGTTGAACTTCAGCTAAAAGG 59.002 40.000 11.53 0.00 0.00 3.11
2552 2587 4.793201 AGGTTGAACTTCAGCTAAAAGGT 58.207 39.130 11.53 5.76 0.00 3.50
2553 2588 4.580580 AGGTTGAACTTCAGCTAAAAGGTG 59.419 41.667 11.53 0.00 44.57 4.00
2554 2589 4.338400 GGTTGAACTTCAGCTAAAAGGTGT 59.662 41.667 11.53 0.00 43.70 4.16
2555 2590 5.505819 GGTTGAACTTCAGCTAAAAGGTGTC 60.506 44.000 11.53 7.10 43.70 3.67
2556 2591 4.134563 TGAACTTCAGCTAAAAGGTGTCC 58.865 43.478 11.53 0.00 43.70 4.02
2568 2603 0.542702 AGGTGTCCAAATGGGGCTTG 60.543 55.000 0.00 0.00 43.75 4.01
2584 2619 2.413837 GCTTGCGATATACCGTTGGAT 58.586 47.619 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.229304 TCCATCGGTTTGTGGATATTGT 57.771 40.909 0.00 0.00 39.51 2.71
109 110 3.721172 ATGGCTGGAGGGTCCCGAT 62.721 63.158 0.99 0.00 35.03 4.18
110 111 4.414956 ATGGCTGGAGGGTCCCGA 62.415 66.667 0.99 0.00 35.03 5.14
153 154 0.527600 CTGGCGTCGCAACTAGCATA 60.528 55.000 20.50 0.00 46.13 3.14
168 169 0.966875 TGGCCATTGACATGTCTGGC 60.967 55.000 34.84 34.84 45.12 4.85
202 203 4.810790 CTTAGTGTAGTGTGGAGGACAAG 58.189 47.826 0.00 0.00 35.91 3.16
205 206 2.826725 AGCTTAGTGTAGTGTGGAGGAC 59.173 50.000 0.00 0.00 0.00 3.85
470 473 3.629142 ACTTAAATGAACCTAGCGGCT 57.371 42.857 7.98 7.98 0.00 5.52
504 507 3.831323 TCATGGAGAAACTTTGCCTTCA 58.169 40.909 0.00 0.00 0.00 3.02
555 559 9.569122 AGTTGACTAGCTTTTGGTAATTTAAGA 57.431 29.630 0.00 0.00 31.45 2.10
565 569 8.134895 TCATTTGTTTAGTTGACTAGCTTTTGG 58.865 33.333 0.00 0.00 0.00 3.28
619 623 2.902705 AGAGCAACCGTGTTCAGTAA 57.097 45.000 0.00 0.00 37.44 2.24
681 685 6.820335 ACAGTTTTACCCGTTAGATATACCC 58.180 40.000 0.00 0.00 0.00 3.69
748 752 6.219473 CACCAGTGCCACATTTTAAATTACA 58.781 36.000 0.00 0.00 0.00 2.41
750 754 5.305644 ACCACCAGTGCCACATTTTAAATTA 59.694 36.000 0.00 0.00 0.00 1.40
762 766 2.018355 TAGACTAACCACCAGTGCCA 57.982 50.000 0.00 0.00 0.00 4.92
767 771 7.048512 CCTTCCTAAATTAGACTAACCACCAG 58.951 42.308 0.83 0.00 0.00 4.00
789 793 4.719773 TGGATAGCTTGTATGTGGTACCTT 59.280 41.667 14.36 0.50 32.03 3.50
959 964 8.446599 TTTAGGCTATTATCTTTGGCAGTAAC 57.553 34.615 0.00 0.00 0.00 2.50
963 968 8.000780 AGTTTTTAGGCTATTATCTTTGGCAG 57.999 34.615 0.00 0.00 0.00 4.85
971 976 8.343366 GCACAACCTAGTTTTTAGGCTATTATC 58.657 37.037 0.00 0.00 38.25 1.75
1030 1036 2.035449 CCTATCGCTGTATTTCCGGTCA 59.965 50.000 0.00 0.00 0.00 4.02
1039 1045 8.643324 ACTATTCTTTTTCTCCTATCGCTGTAT 58.357 33.333 0.00 0.00 0.00 2.29
1044 1050 7.169476 GGTACACTATTCTTTTTCTCCTATCGC 59.831 40.741 0.00 0.00 0.00 4.58
1121 1129 3.114606 TGGCAGATATCACAAGAAGGGA 58.885 45.455 5.32 0.00 0.00 4.20
1213 1223 0.464036 CCAGCCCGTTGTATAGAGCA 59.536 55.000 0.00 0.00 0.00 4.26
1228 1238 3.848272 TCATCGGAAAAATGTTCCAGC 57.152 42.857 2.74 0.00 38.49 4.85
1324 1334 7.941790 TCTGCACACCCAAGCATATATATTTAA 59.058 33.333 0.00 0.00 40.42 1.52
1363 1373 2.495669 CCAACCCACACAGAACTTGTTT 59.504 45.455 0.00 0.00 38.16 2.83
1405 1415 4.163078 CACTGACTAGGGATTCCATTCACT 59.837 45.833 4.80 0.00 32.94 3.41
1429 1439 4.747108 CCGTTATCTCTGCAGTAAATCTGG 59.253 45.833 14.67 6.24 43.78 3.86
1510 1520 5.661458 GGAAGTGTCTACTTATAGCAGCAA 58.339 41.667 0.00 0.00 46.79 3.91
1535 1545 1.725931 GCACTCTTCCACAAATTCGCG 60.726 52.381 0.00 0.00 0.00 5.87
1537 1547 3.624326 TTGCACTCTTCCACAAATTCG 57.376 42.857 0.00 0.00 0.00 3.34
1543 1553 4.734398 AAATGTTTTGCACTCTTCCACA 57.266 36.364 0.00 0.00 0.00 4.17
1596 1606 9.875675 GATAGACATAGATCAAACAATGCTTTC 57.124 33.333 0.00 0.00 0.00 2.62
1664 1674 6.456315 CGACCGTTGATTGCTGAATATTGTAA 60.456 38.462 0.00 0.00 0.00 2.41
1670 1680 2.670905 CACGACCGTTGATTGCTGAATA 59.329 45.455 0.00 0.00 0.00 1.75
1687 1697 0.454600 GGATCGCAACTACTCCACGA 59.545 55.000 0.00 0.00 37.15 4.35
1790 1800 9.314321 CAACCTTATATTTCGATCACTACAAGT 57.686 33.333 0.00 0.00 0.00 3.16
1791 1801 8.765219 CCAACCTTATATTTCGATCACTACAAG 58.235 37.037 0.00 0.00 0.00 3.16
1792 1802 8.262227 ACCAACCTTATATTTCGATCACTACAA 58.738 33.333 0.00 0.00 0.00 2.41
1793 1803 7.788026 ACCAACCTTATATTTCGATCACTACA 58.212 34.615 0.00 0.00 0.00 2.74
1794 1804 7.384387 GGACCAACCTTATATTTCGATCACTAC 59.616 40.741 0.00 0.00 35.41 2.73
1795 1805 7.439381 GGACCAACCTTATATTTCGATCACTA 58.561 38.462 0.00 0.00 35.41 2.74
1796 1806 6.289064 GGACCAACCTTATATTTCGATCACT 58.711 40.000 0.00 0.00 35.41 3.41
1797 1807 5.176958 CGGACCAACCTTATATTTCGATCAC 59.823 44.000 0.00 0.00 36.31 3.06
1798 1808 5.069383 TCGGACCAACCTTATATTTCGATCA 59.931 40.000 0.00 0.00 36.31 2.92
1799 1809 5.535333 TCGGACCAACCTTATATTTCGATC 58.465 41.667 0.00 0.00 36.31 3.69
1800 1810 5.539048 CTCGGACCAACCTTATATTTCGAT 58.461 41.667 0.00 0.00 36.31 3.59
1801 1811 4.738541 GCTCGGACCAACCTTATATTTCGA 60.739 45.833 0.00 0.00 36.31 3.71
1802 1812 3.493503 GCTCGGACCAACCTTATATTTCG 59.506 47.826 0.00 0.00 36.31 3.46
1803 1813 3.813724 GGCTCGGACCAACCTTATATTTC 59.186 47.826 0.00 0.00 36.31 2.17
1804 1814 3.201266 TGGCTCGGACCAACCTTATATTT 59.799 43.478 0.00 0.00 36.55 1.40
1805 1815 2.775384 TGGCTCGGACCAACCTTATATT 59.225 45.455 0.00 0.00 36.55 1.28
1808 1818 0.252197 GTGGCTCGGACCAACCTTAT 59.748 55.000 0.00 0.00 42.70 1.73
1851 1861 5.049267 TGCTTACCACCAACGTCTTATTTTC 60.049 40.000 0.00 0.00 0.00 2.29
1986 1996 4.185467 AGATCATTGCCTATGCGTAGAG 57.815 45.455 14.79 5.87 41.78 2.43
1995 2011 6.940430 TCTTCATGGATAGATCATTGCCTA 57.060 37.500 0.00 0.00 0.00 3.93
1997 2013 5.163642 GCATCTTCATGGATAGATCATTGCC 60.164 44.000 0.00 0.00 0.00 4.52
2015 2031 2.423947 CCCCCTTCTTGCTATGCATCTT 60.424 50.000 0.19 0.00 38.76 2.40
2082 2103 2.445427 TCGACTACATCAACCCCGTTA 58.555 47.619 0.00 0.00 0.00 3.18
2087 2108 5.220416 CGAAGAAATTCGACTACATCAACCC 60.220 44.000 4.44 0.00 46.52 4.11
2104 2125 1.018148 TTGGTTGAAGCGCGAAGAAA 58.982 45.000 12.10 0.00 0.00 2.52
2238 2259 0.540923 TCATCACCATCATCACGCCA 59.459 50.000 0.00 0.00 0.00 5.69
2245 2266 5.073280 AGGATCACTTCATCATCACCATCAT 59.927 40.000 0.00 0.00 0.00 2.45
2287 2308 5.121142 CCACGGTCATATTTTCGTAGTGTTT 59.879 40.000 0.00 0.00 34.31 2.83
2288 2309 4.628333 CCACGGTCATATTTTCGTAGTGTT 59.372 41.667 0.00 0.00 34.31 3.32
2289 2310 4.178540 CCACGGTCATATTTTCGTAGTGT 58.821 43.478 0.00 0.00 34.31 3.55
2333 2355 5.990399 AAACCATTGTTTAGCTGTGTGCGA 61.990 41.667 0.00 0.00 42.79 5.10
2352 2374 1.574702 GCCCTAGCACACACGAAACC 61.575 60.000 0.00 0.00 39.53 3.27
2355 2377 2.048597 CGCCCTAGCACACACGAA 60.049 61.111 0.00 0.00 39.83 3.85
2489 2522 2.005971 GCGTTACTCGGGAAGTTCAT 57.994 50.000 5.01 0.00 39.55 2.57
2500 2533 1.671880 GAAGGTCACGCGCGTTACTC 61.672 60.000 36.73 28.27 0.00 2.59
2501 2534 1.731969 GAAGGTCACGCGCGTTACT 60.732 57.895 36.73 28.93 0.00 2.24
2502 2535 2.723719 GGAAGGTCACGCGCGTTAC 61.724 63.158 35.90 34.17 0.00 2.50
2508 2541 4.796231 CTCGGGGAAGGTCACGCG 62.796 72.222 3.53 3.53 43.27 6.01
2509 2542 2.345760 TACTCGGGGAAGGTCACGC 61.346 63.158 0.00 0.00 0.00 5.34
2510 2543 0.964358 AGTACTCGGGGAAGGTCACG 60.964 60.000 0.00 0.00 0.00 4.35
2511 2544 2.022934 CTAGTACTCGGGGAAGGTCAC 58.977 57.143 0.00 0.00 0.00 3.67
2515 2550 1.755380 CAACCTAGTACTCGGGGAAGG 59.245 57.143 17.18 11.38 0.00 3.46
2522 2557 4.082679 AGCTGAAGTTCAACCTAGTACTCG 60.083 45.833 7.06 0.00 0.00 4.18
2524 2559 6.912951 TTAGCTGAAGTTCAACCTAGTACT 57.087 37.500 7.06 0.00 0.00 2.73
2526 2561 7.159372 CCTTTTAGCTGAAGTTCAACCTAGTA 58.841 38.462 7.06 1.42 0.00 1.82
2543 2578 2.233676 CCCCATTTGGACACCTTTTAGC 59.766 50.000 0.00 0.00 37.39 3.09
2545 2580 2.158234 AGCCCCATTTGGACACCTTTTA 60.158 45.455 0.00 0.00 37.39 1.52
2548 2583 0.190815 AAGCCCCATTTGGACACCTT 59.809 50.000 0.00 0.00 37.39 3.50
2550 2585 1.974543 CAAGCCCCATTTGGACACC 59.025 57.895 0.00 0.00 37.39 4.16
2551 2586 1.293179 GCAAGCCCCATTTGGACAC 59.707 57.895 0.00 0.00 37.39 3.67
2552 2587 2.274645 CGCAAGCCCCATTTGGACA 61.275 57.895 0.00 0.00 37.39 4.02
2553 2588 1.322538 ATCGCAAGCCCCATTTGGAC 61.323 55.000 0.00 0.00 35.07 4.02
2554 2589 0.257328 TATCGCAAGCCCCATTTGGA 59.743 50.000 0.00 0.00 35.07 3.53
2555 2590 1.331214 ATATCGCAAGCCCCATTTGG 58.669 50.000 0.00 0.00 37.18 3.28
2556 2591 2.228822 GGTATATCGCAAGCCCCATTTG 59.771 50.000 0.00 0.00 37.18 2.32


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

AutoCloner maintained by Alex Coulton.