Multiple sequence alignment - TraesCS1B01G345900

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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 TraesCS1B01G345900 chr1B 100.000 2387 0 0 1 2387 574269089 574266703 0 4409
1 TraesCS1B01G345900 chr1B 88.326 651 64 8 2 643 437539961 437539314 0 771
2 TraesCS1B01G345900 chr1A 88.500 1713 65 54 670 2355 520794140 520792533 0 1951
3 TraesCS1B01G345900 chr1D 87.674 1728 79 46 680 2364 424992577 424990941 0 1888
4 TraesCS1B01G345900 chr1D 87.771 646 70 6 1 640 493736644 493736002 0 747
5 TraesCS1B01G345900 chr3D 88.735 648 63 6 1 641 380180541 380179897 0 784
6 TraesCS1B01G345900 chr3D 88.099 647 68 5 1 641 414777713 414778356 0 760
7 TraesCS1B01G345900 chr2D 88.154 650 62 8 1 643 23303024 23303665 0 760
8 TraesCS1B01G345900 chr2D 87.865 651 68 8 1 643 27450574 27451221 0 754
9 TraesCS1B01G345900 chr6D 87.846 650 67 7 1 642 97128856 97129501 0 752
10 TraesCS1B01G345900 chr2B 87.692 650 68 8 1 642 100027635 100026990 0 747
11 TraesCS1B01G345900 chr5D 87.423 652 72 6 1 645 137227953 137228601 0 741


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 TraesCS1B01G345900 chr1B 574266703 574269089 2386 True 4409 4409 100.000 1 2387 1 chr1B.!!$R2 2386
1 TraesCS1B01G345900 chr1B 437539314 437539961 647 True 771 771 88.326 2 643 1 chr1B.!!$R1 641
2 TraesCS1B01G345900 chr1A 520792533 520794140 1607 True 1951 1951 88.500 670 2355 1 chr1A.!!$R1 1685
3 TraesCS1B01G345900 chr1D 424990941 424992577 1636 True 1888 1888 87.674 680 2364 1 chr1D.!!$R1 1684
4 TraesCS1B01G345900 chr1D 493736002 493736644 642 True 747 747 87.771 1 640 1 chr1D.!!$R2 639
5 TraesCS1B01G345900 chr3D 380179897 380180541 644 True 784 784 88.735 1 641 1 chr3D.!!$R1 640
6 TraesCS1B01G345900 chr3D 414777713 414778356 643 False 760 760 88.099 1 641 1 chr3D.!!$F1 640
7 TraesCS1B01G345900 chr2D 23303024 23303665 641 False 760 760 88.154 1 643 1 chr2D.!!$F1 642
8 TraesCS1B01G345900 chr2D 27450574 27451221 647 False 754 754 87.865 1 643 1 chr2D.!!$F2 642
9 TraesCS1B01G345900 chr6D 97128856 97129501 645 False 752 752 87.846 1 642 1 chr6D.!!$F1 641
10 TraesCS1B01G345900 chr2B 100026990 100027635 645 True 747 747 87.692 1 642 1 chr2B.!!$R1 641
11 TraesCS1B01G345900 chr5D 137227953 137228601 648 False 741 741 87.423 1 645 1 chr5D.!!$F1 644

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
503 506 0.107459 GGGGTGAAGAGGTGATCTGC 60.107 60.0 0.0 0.0 38.67 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2367 2440 0.315886 CACTACACGTGGGCACAGTA 59.684 55.0 21.57 0.0 40.02 2.74 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 1.137872 GTCTCGGAGTTGATGGCATCT 59.862 52.381 26.49 8.23 0.00 2.90
75 76 2.744202 GGCATCTTGTGTTTGTCGATCT 59.256 45.455 0.00 0.00 0.00 2.75
94 95 0.390078 TTTCAGATCGGCGGCGTTAA 60.390 50.000 31.06 12.96 0.00 2.01
156 157 2.311841 TCCATCAGGTGTGTCTCTCCTA 59.688 50.000 0.00 0.00 37.88 2.94
163 164 1.474879 GTGTGTCTCTCCTACTGCTCC 59.525 57.143 0.00 0.00 0.00 4.70
188 189 0.317770 CATTGTTGCGGCGTTGTCTT 60.318 50.000 9.37 0.00 0.00 3.01
264 266 2.224257 TGTGTATGCAAGTGACAGCTGA 60.224 45.455 23.35 0.00 0.00 4.26
294 296 3.548745 CATCTTGTGCTGGGTCTATGA 57.451 47.619 0.00 0.00 0.00 2.15
305 307 1.072965 GGGTCTATGATTGGAGGCTGG 59.927 57.143 0.00 0.00 0.00 4.85
313 315 3.719871 TGATTGGAGGCTGGTAGTTCTA 58.280 45.455 0.00 0.00 0.00 2.10
392 394 3.307906 CGGGGACACGTTCCTCCA 61.308 66.667 13.94 0.00 43.07 3.86
408 410 5.157940 TCCTCCAGTCTGATTCTTTCAAG 57.842 43.478 0.00 0.00 32.78 3.02
422 424 3.454082 TCTTTCAAGGGCAATGGTTTTGT 59.546 39.130 0.00 0.00 0.00 2.83
441 443 5.906113 TTGTTTCAGGCAAACTACTTTGA 57.094 34.783 2.66 0.00 44.35 2.69
476 479 0.320247 CTGATCAGTATGGAGCCGCC 60.320 60.000 14.95 0.00 36.16 6.13
503 506 0.107459 GGGGTGAAGAGGTGATCTGC 60.107 60.000 0.00 0.00 38.67 4.26
508 515 3.416156 GTGAAGAGGTGATCTGCCTTTT 58.584 45.455 10.08 10.44 38.67 2.27
509 516 3.823304 GTGAAGAGGTGATCTGCCTTTTT 59.177 43.478 10.08 8.36 38.67 1.94
533 542 1.294780 GGAGAGGGATATGCGCTGG 59.705 63.158 9.73 0.00 40.28 4.85
534 543 1.294780 GAGAGGGATATGCGCTGGG 59.705 63.158 9.73 0.00 40.28 4.45
539 548 1.111277 GGGATATGCGCTGGGTTTTT 58.889 50.000 9.73 0.00 0.00 1.94
656 665 1.948104 AAAAAGTTCGCCCCTTTTGC 58.052 45.000 7.11 0.00 40.32 3.68
657 666 0.827368 AAAAGTTCGCCCCTTTTGCA 59.173 45.000 5.95 0.00 39.86 4.08
658 667 1.047801 AAAGTTCGCCCCTTTTGCAT 58.952 45.000 0.00 0.00 0.00 3.96
659 668 1.917872 AAGTTCGCCCCTTTTGCATA 58.082 45.000 0.00 0.00 0.00 3.14
660 669 1.917872 AGTTCGCCCCTTTTGCATAA 58.082 45.000 0.00 0.00 0.00 1.90
661 670 1.544246 AGTTCGCCCCTTTTGCATAAC 59.456 47.619 0.00 0.00 0.00 1.89
662 671 1.544246 GTTCGCCCCTTTTGCATAACT 59.456 47.619 0.00 0.00 0.00 2.24
663 672 1.917872 TCGCCCCTTTTGCATAACTT 58.082 45.000 0.00 0.00 0.00 2.66
664 673 1.543802 TCGCCCCTTTTGCATAACTTG 59.456 47.619 0.00 0.00 0.00 3.16
678 687 1.466851 AACTTGCTCTTTGCCTGCCC 61.467 55.000 0.00 0.00 42.00 5.36
715 728 0.826256 TCGGGATCCCCAGATACGTG 60.826 60.000 25.73 7.70 45.83 4.49
717 730 1.407656 GGGATCCCCAGATACGTGCA 61.408 60.000 21.42 0.00 44.65 4.57
718 731 0.468226 GGATCCCCAGATACGTGCAA 59.532 55.000 0.00 0.00 30.90 4.08
719 732 1.072331 GGATCCCCAGATACGTGCAAT 59.928 52.381 0.00 0.00 30.90 3.56
720 733 2.301870 GGATCCCCAGATACGTGCAATA 59.698 50.000 0.00 0.00 30.90 1.90
721 734 3.589988 GATCCCCAGATACGTGCAATAG 58.410 50.000 0.00 0.00 30.90 1.73
722 735 1.070134 TCCCCAGATACGTGCAATAGC 59.930 52.381 0.00 0.00 42.57 2.97
723 736 1.070758 CCCCAGATACGTGCAATAGCT 59.929 52.381 0.00 0.00 42.74 3.32
725 738 2.545526 CCCAGATACGTGCAATAGCTTG 59.454 50.000 0.00 0.00 42.74 4.01
736 749 2.751806 GCAATAGCTTGGCTTGACTTCT 59.248 45.455 0.00 0.00 40.44 2.85
742 755 2.227626 GCTTGGCTTGACTTCTCCTTTC 59.772 50.000 0.00 0.00 0.00 2.62
781 795 3.190849 CTCATGCACCTCACGCCG 61.191 66.667 0.00 0.00 0.00 6.46
812 826 3.636231 CAACCGCACCCTCCCAGA 61.636 66.667 0.00 0.00 0.00 3.86
843 857 2.492090 CGTCCCTCTCGGCTCAAG 59.508 66.667 0.00 0.00 0.00 3.02
844 858 2.185608 GTCCCTCTCGGCTCAAGC 59.814 66.667 0.00 0.00 41.14 4.01
864 878 4.880537 CCCGCTCGCCACAGCTAG 62.881 72.222 0.00 0.00 37.25 3.42
865 879 4.880537 CCGCTCGCCACAGCTAGG 62.881 72.222 0.03 0.03 37.25 3.02
884 898 3.787001 CCCTTCCACCTCTCGCCC 61.787 72.222 0.00 0.00 0.00 6.13
885 899 4.148825 CCTTCCACCTCTCGCCCG 62.149 72.222 0.00 0.00 0.00 6.13
886 900 4.821589 CTTCCACCTCTCGCCCGC 62.822 72.222 0.00 0.00 0.00 6.13
945 959 2.536997 ATTCCGCCCTCCAAGAACCG 62.537 60.000 0.00 0.00 0.00 4.44
1338 1362 2.101575 GTCGACATGCGCTACGGA 59.898 61.111 11.55 0.00 40.61 4.69
1390 1414 4.081030 CGCTGCACAACTGAGGCG 62.081 66.667 0.00 0.00 35.01 5.52
1421 1449 2.359975 GGCGGGGTCAGTTCTTGG 60.360 66.667 0.00 0.00 0.00 3.61
1472 1500 0.321671 CTGGGTTCTTCAGCGAGGAA 59.678 55.000 0.00 0.37 0.00 3.36
1473 1501 0.762418 TGGGTTCTTCAGCGAGGAAA 59.238 50.000 5.07 0.00 29.87 3.13
1474 1502 1.270839 TGGGTTCTTCAGCGAGGAAAG 60.271 52.381 5.07 0.00 29.87 2.62
1577 1605 2.731348 GATCGATCGACGCCTGCC 60.731 66.667 22.06 0.21 42.26 4.85
1578 1606 3.200887 GATCGATCGACGCCTGCCT 62.201 63.158 22.06 0.76 42.26 4.75
1579 1607 3.490793 ATCGATCGACGCCTGCCTG 62.491 63.158 22.06 0.00 42.26 4.85
1581 1609 4.521062 GATCGACGCCTGCCTGCT 62.521 66.667 0.00 0.00 0.00 4.24
1582 1610 4.087892 ATCGACGCCTGCCTGCTT 62.088 61.111 0.00 0.00 0.00 3.91
1699 1734 5.297547 TCGTGTCATTTTTGCTCTAGTCTT 58.702 37.500 0.00 0.00 0.00 3.01
1813 1851 2.672874 CCGCTCGATTGTCAATTTCTCA 59.327 45.455 0.00 0.00 0.00 3.27
1881 1919 6.780706 TTTTCTTCTCTTTCACACGTATCC 57.219 37.500 0.00 0.00 0.00 2.59
1882 1920 4.092771 TCTTCTCTTTCACACGTATCCG 57.907 45.455 0.00 0.00 40.83 4.18
1895 1935 1.271876 GTATCCGTTCCGTTCCGTTC 58.728 55.000 0.00 0.00 0.00 3.95
1897 1937 0.319405 ATCCGTTCCGTTCCGTTCTT 59.681 50.000 0.00 0.00 0.00 2.52
1902 1942 2.539274 CGTTCCGTTCCGTTCTTAAACA 59.461 45.455 0.00 0.00 34.93 2.83
1903 1943 3.362304 CGTTCCGTTCCGTTCTTAAACAG 60.362 47.826 0.00 0.00 34.93 3.16
1904 1944 3.731652 TCCGTTCCGTTCTTAAACAGA 57.268 42.857 0.00 0.00 34.93 3.41
1905 1945 4.057406 TCCGTTCCGTTCTTAAACAGAA 57.943 40.909 0.00 0.00 39.39 3.02
1959 1999 0.469331 TGACCACCAGAAGACGAGGT 60.469 55.000 0.00 0.00 35.65 3.85
1963 2003 1.134965 CCACCAGAAGACGAGGTCATC 60.135 57.143 0.00 0.00 34.60 2.92
1968 2008 0.179134 GAAGACGAGGTCATCCGTGG 60.179 60.000 0.00 0.00 39.30 4.94
1975 2015 2.742372 GTCATCCGTGGCAGCGTT 60.742 61.111 8.28 0.00 0.00 4.84
1977 2017 1.599518 TCATCCGTGGCAGCGTTTT 60.600 52.632 8.28 0.00 0.00 2.43
1978 2018 1.442520 CATCCGTGGCAGCGTTTTG 60.443 57.895 8.28 1.06 0.00 2.44
1979 2019 3.267597 ATCCGTGGCAGCGTTTTGC 62.268 57.895 8.28 0.88 46.98 3.68
2153 2197 4.090057 GTCTCGGCCTTGCGTTGC 62.090 66.667 0.00 0.00 0.00 4.17
2162 2206 1.208870 CTTGCGTTGCGTGGCATTA 59.791 52.632 0.00 0.00 38.76 1.90
2247 2320 5.123502 ACTTGTGATGATGACTTCATTCTGC 59.876 40.000 5.39 0.00 45.29 4.26
2281 2354 5.871524 GTGGTAACTAACTTAACTACCTGGC 59.128 44.000 0.00 0.00 34.35 4.85
2287 2360 1.286248 CTTAACTACCTGGCCTGGGT 58.714 55.000 30.19 25.35 40.53 4.51
2343 2416 4.404394 TGACTTTGTGAGTAGGACAAGTCA 59.596 41.667 8.17 8.17 39.19 3.41
2364 2437 7.831753 AGTCACGAGTACTACTGTAACTACTA 58.168 38.462 0.00 0.00 0.00 1.82
2365 2438 8.307483 AGTCACGAGTACTACTGTAACTACTAA 58.693 37.037 0.00 0.00 0.00 2.24
2366 2439 8.376942 GTCACGAGTACTACTGTAACTACTAAC 58.623 40.741 0.00 1.16 0.00 2.34
2367 2440 8.307483 TCACGAGTACTACTGTAACTACTAACT 58.693 37.037 0.00 0.00 0.00 2.24
2368 2441 9.574458 CACGAGTACTACTGTAACTACTAACTA 57.426 37.037 0.00 0.00 0.00 2.24
2369 2442 9.575783 ACGAGTACTACTGTAACTACTAACTAC 57.424 37.037 0.00 0.00 0.00 2.73
2370 2443 9.796120 CGAGTACTACTGTAACTACTAACTACT 57.204 37.037 0.00 0.00 0.00 2.57
2374 2447 8.038492 ACTACTGTAACTACTAACTACTGTGC 57.962 38.462 0.00 0.00 32.24 4.57
2375 2448 6.264841 ACTGTAACTACTAACTACTGTGCC 57.735 41.667 0.00 0.00 0.00 5.01
2376 2449 5.184671 ACTGTAACTACTAACTACTGTGCCC 59.815 44.000 0.00 0.00 0.00 5.36
2377 2450 5.078949 TGTAACTACTAACTACTGTGCCCA 58.921 41.667 0.00 0.00 0.00 5.36
2378 2451 4.532314 AACTACTAACTACTGTGCCCAC 57.468 45.455 0.00 0.00 0.00 4.61
2379 2452 2.490903 ACTACTAACTACTGTGCCCACG 59.509 50.000 0.00 0.00 0.00 4.94
2380 2453 1.335145 ACTAACTACTGTGCCCACGT 58.665 50.000 0.00 0.00 0.00 4.49
2381 2454 1.000506 ACTAACTACTGTGCCCACGTG 59.999 52.381 9.08 9.08 0.00 4.49
2382 2455 1.000506 CTAACTACTGTGCCCACGTGT 59.999 52.381 15.65 0.00 0.00 4.49
2383 2456 1.042229 AACTACTGTGCCCACGTGTA 58.958 50.000 15.65 0.00 0.00 2.90
2384 2457 0.601558 ACTACTGTGCCCACGTGTAG 59.398 55.000 15.65 19.95 41.87 2.74
2385 2458 0.601558 CTACTGTGCCCACGTGTAGT 59.398 55.000 15.65 12.22 36.81 2.73
2386 2459 5.655195 AACTACTGTGCCCACGTGTAGTG 62.655 52.174 24.09 0.00 44.88 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 0.390078 TTAACGCCGCCGATCTGAAA 60.390 50.000 0.00 0.00 38.29 2.69
94 95 0.253044 CCGACACCATCCATGAACCT 59.747 55.000 0.00 0.00 0.00 3.50
129 130 1.448540 CACACCTGATGGAGTCGCC 60.449 63.158 0.00 0.00 34.94 5.54
156 157 1.779061 AACAATGGGGACGGAGCAGT 61.779 55.000 0.00 0.00 0.00 4.40
188 189 0.733150 CTGCTCCACTATGACGTCGA 59.267 55.000 11.62 0.00 0.00 4.20
198 199 0.111253 CAAAACCTCCCTGCTCCACT 59.889 55.000 0.00 0.00 0.00 4.00
246 248 3.748048 TCTTTCAGCTGTCACTTGCATAC 59.252 43.478 14.67 0.00 0.00 2.39
294 296 3.725634 ACTAGAACTACCAGCCTCCAAT 58.274 45.455 0.00 0.00 0.00 3.16
305 307 4.096231 GTCGGAGGAGGAAACTAGAACTAC 59.904 50.000 0.00 0.00 44.43 2.73
387 389 4.260170 CCTTGAAAGAATCAGACTGGAGG 58.740 47.826 1.81 0.00 39.77 4.30
392 394 3.795688 TGCCCTTGAAAGAATCAGACT 57.204 42.857 0.00 0.00 39.77 3.24
408 410 2.493035 CCTGAAACAAAACCATTGCCC 58.507 47.619 0.00 0.00 0.00 5.36
422 424 4.953579 ACCTTCAAAGTAGTTTGCCTGAAA 59.046 37.500 16.77 6.15 42.55 2.69
441 443 0.685097 TCAGCAGCTTTACGGACCTT 59.315 50.000 0.00 0.00 0.00 3.50
476 479 1.515020 CTCTTCACCCCAGCTCGAG 59.485 63.158 8.45 8.45 0.00 4.04
484 487 0.107459 GCAGATCACCTCTTCACCCC 60.107 60.000 0.00 0.00 29.16 4.95
508 515 3.494398 GCGCATATCCCTCTCCACTAAAA 60.494 47.826 0.30 0.00 0.00 1.52
509 516 2.037251 GCGCATATCCCTCTCCACTAAA 59.963 50.000 0.30 0.00 0.00 1.85
560 569 3.526931 ACATCGACATTACAGGACTGG 57.473 47.619 4.14 0.00 34.19 4.00
642 651 1.544246 AGTTATGCAAAAGGGGCGAAC 59.456 47.619 0.00 0.00 32.78 3.95
643 652 1.917872 AGTTATGCAAAAGGGGCGAA 58.082 45.000 0.00 0.00 0.00 4.70
645 654 1.994916 CAAGTTATGCAAAAGGGGCG 58.005 50.000 0.00 0.00 0.00 6.13
664 673 0.611896 TTTAGGGGCAGGCAAAGAGC 60.612 55.000 0.00 0.00 44.65 4.09
665 674 2.027385 GATTTAGGGGCAGGCAAAGAG 58.973 52.381 0.00 0.00 0.00 2.85
666 675 1.357420 TGATTTAGGGGCAGGCAAAGA 59.643 47.619 0.00 0.00 0.00 2.52
667 676 1.753073 CTGATTTAGGGGCAGGCAAAG 59.247 52.381 0.00 0.00 0.00 2.77
668 677 1.077005 ACTGATTTAGGGGCAGGCAAA 59.923 47.619 0.00 0.00 34.05 3.68
699 708 0.468226 TTGCACGTATCTGGGGATCC 59.532 55.000 1.92 1.92 33.71 3.36
700 709 2.550830 ATTGCACGTATCTGGGGATC 57.449 50.000 0.00 0.00 33.71 3.36
715 728 2.751806 AGAAGTCAAGCCAAGCTATTGC 59.248 45.455 0.00 0.00 38.25 3.56
717 730 3.265479 AGGAGAAGTCAAGCCAAGCTATT 59.735 43.478 0.00 0.00 38.25 1.73
718 731 2.843113 AGGAGAAGTCAAGCCAAGCTAT 59.157 45.455 0.00 0.00 38.25 2.97
719 732 2.260822 AGGAGAAGTCAAGCCAAGCTA 58.739 47.619 0.00 0.00 38.25 3.32
720 733 1.063183 AGGAGAAGTCAAGCCAAGCT 58.937 50.000 0.00 0.00 42.56 3.74
721 734 1.902938 AAGGAGAAGTCAAGCCAAGC 58.097 50.000 0.00 0.00 0.00 4.01
722 735 2.481952 CGAAAGGAGAAGTCAAGCCAAG 59.518 50.000 0.00 0.00 0.00 3.61
723 736 2.494059 CGAAAGGAGAAGTCAAGCCAA 58.506 47.619 0.00 0.00 0.00 4.52
725 738 0.799393 GCGAAAGGAGAAGTCAAGCC 59.201 55.000 0.00 0.00 0.00 4.35
736 749 0.391597 AAACAGAGACGGCGAAAGGA 59.608 50.000 16.62 0.00 0.00 3.36
742 755 4.354155 TGGAAAACAGAGACGGCG 57.646 55.556 4.80 4.80 0.00 6.46
812 826 1.969589 GGACGCGGTGGAAATTGGT 60.970 57.895 12.47 0.00 0.00 3.67
862 876 1.003051 GAGAGGTGGAAGGGGCCTA 59.997 63.158 0.84 0.00 31.89 3.93
863 877 2.285743 GAGAGGTGGAAGGGGCCT 60.286 66.667 0.84 0.00 34.93 5.19
864 878 3.787001 CGAGAGGTGGAAGGGGCC 61.787 72.222 0.00 0.00 0.00 5.80
865 879 4.475135 GCGAGAGGTGGAAGGGGC 62.475 72.222 0.00 0.00 0.00 5.80
1411 1439 3.202906 CGTCCAAGAAACCAAGAACTGA 58.797 45.455 0.00 0.00 0.00 3.41
1452 1480 0.832135 TCCTCGCTGAAGAACCCAGT 60.832 55.000 0.00 0.00 34.29 4.00
1474 1502 1.950909 ACAAGAGAGGACGATCGATCC 59.049 52.381 24.34 22.73 36.38 3.36
1530 1558 1.449070 GTAAGTCCTTTCCGGCCGG 60.449 63.158 39.13 39.13 0.00 6.13
1573 1601 1.602851 GATGTATGAGCAAGCAGGCAG 59.397 52.381 2.37 0.00 35.83 4.85
1574 1602 1.211212 AGATGTATGAGCAAGCAGGCA 59.789 47.619 2.37 0.00 35.83 4.75
1575 1603 1.872313 GAGATGTATGAGCAAGCAGGC 59.128 52.381 0.00 0.00 0.00 4.85
1576 1604 3.132160 CAGAGATGTATGAGCAAGCAGG 58.868 50.000 0.00 0.00 0.00 4.85
1577 1605 2.544686 GCAGAGATGTATGAGCAAGCAG 59.455 50.000 0.00 0.00 0.00 4.24
1578 1606 2.558378 GCAGAGATGTATGAGCAAGCA 58.442 47.619 0.00 0.00 0.00 3.91
1579 1607 1.526041 CGCAGAGATGTATGAGCAAGC 59.474 52.381 0.00 0.00 0.00 4.01
1580 1608 2.538861 CACGCAGAGATGTATGAGCAAG 59.461 50.000 0.00 0.00 0.00 4.01
1581 1609 2.543641 CACGCAGAGATGTATGAGCAA 58.456 47.619 0.00 0.00 0.00 3.91
1582 1610 1.803998 GCACGCAGAGATGTATGAGCA 60.804 52.381 0.00 0.00 0.00 4.26
1699 1734 3.556775 GGTAACGGCGAAATTATGCTACA 59.443 43.478 16.62 0.00 0.00 2.74
1813 1851 4.969196 CACGCCGTCAGCCACAGT 62.969 66.667 0.00 0.00 38.78 3.55
1849 1887 7.867403 GTGTGAAAGAGAAGAAAAATAATGGCA 59.133 33.333 0.00 0.00 0.00 4.92
1895 1935 8.078596 CCTGACCTCATTTTCTTTCTGTTTAAG 58.921 37.037 0.00 0.00 0.00 1.85
1897 1937 6.016276 GCCTGACCTCATTTTCTTTCTGTTTA 60.016 38.462 0.00 0.00 0.00 2.01
1902 1942 4.379302 AGCCTGACCTCATTTTCTTTCT 57.621 40.909 0.00 0.00 0.00 2.52
1903 1943 4.321527 CCAAGCCTGACCTCATTTTCTTTC 60.322 45.833 0.00 0.00 0.00 2.62
1904 1944 3.575687 CCAAGCCTGACCTCATTTTCTTT 59.424 43.478 0.00 0.00 0.00 2.52
1905 1945 3.160269 CCAAGCCTGACCTCATTTTCTT 58.840 45.455 0.00 0.00 0.00 2.52
1959 1999 1.599518 AAAACGCTGCCACGGATGA 60.600 52.632 0.00 0.00 37.37 2.92
1963 2003 4.263209 TGCAAAACGCTGCCACGG 62.263 61.111 0.00 0.00 41.90 4.94
1975 2015 0.886043 ATGAGAGCGCACAGTGCAAA 60.886 50.000 25.19 4.01 45.36 3.68
1977 2017 1.301953 AATGAGAGCGCACAGTGCA 60.302 52.632 25.19 4.84 45.36 4.57
1978 2018 1.134075 CAATGAGAGCGCACAGTGC 59.866 57.895 16.21 16.21 40.69 4.40
1979 2019 1.134075 GCAATGAGAGCGCACAGTG 59.866 57.895 11.47 16.74 34.54 3.66
1980 2020 2.037136 GGCAATGAGAGCGCACAGT 61.037 57.895 11.47 2.96 0.00 3.55
1981 2021 2.036571 TGGCAATGAGAGCGCACAG 61.037 57.895 11.47 0.00 0.00 3.66
1984 2024 3.120385 CGTGGCAATGAGAGCGCA 61.120 61.111 11.47 0.00 0.00 6.09
2153 2197 1.730176 CGAGCGAAATTAATGCCACG 58.270 50.000 0.00 0.00 0.00 4.94
2162 2206 0.949105 AACCACGAGCGAGCGAAATT 60.949 50.000 4.36 0.00 34.83 1.82
2247 2320 0.322322 TAGTTACCACGGCCACAAGG 59.678 55.000 2.24 0.10 38.23 3.61
2287 2360 1.471119 GTGTCCGTATCCCTGTCAGA 58.529 55.000 0.00 0.00 0.00 3.27
2343 2416 9.575783 GTAGTTAGTAGTTACAGTAGTACTCGT 57.424 37.037 0.00 5.37 36.12 4.18
2364 2437 1.000506 CTACACGTGGGCACAGTAGTT 59.999 52.381 21.57 0.00 36.07 2.24
2365 2438 0.601558 CTACACGTGGGCACAGTAGT 59.398 55.000 21.57 0.00 36.07 2.73
2366 2439 0.601558 ACTACACGTGGGCACAGTAG 59.398 55.000 21.57 12.50 41.43 2.57
2367 2440 0.315886 CACTACACGTGGGCACAGTA 59.684 55.000 21.57 0.00 40.02 2.74
2368 2441 1.069090 CACTACACGTGGGCACAGT 59.931 57.895 21.57 11.28 40.02 3.55
2369 2442 3.951332 CACTACACGTGGGCACAG 58.049 61.111 21.57 10.66 40.02 3.66


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

AutoCloner maintained by Alex Coulton.