Multiple sequence alignment - TraesCS7D01G127600

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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 TraesCS7D01G127600 chr7D 100.000 2540 0 0 1 2540 79963087 79965626 0.000000e+00 4691.0
1 TraesCS7D01G127600 chr7B 89.582 1891 84 51 4 1848 27066455 27068278 0.000000e+00 2296.0
2 TraesCS7D01G127600 chr7B 86.213 602 27 21 1963 2530 27068365 27068944 3.620000e-168 601.0
3 TraesCS7D01G127600 chr7B 97.619 42 1 0 2277 2318 27068631 27068672 3.510000e-09 73.1
4 TraesCS7D01G127600 chr7A 85.707 1840 88 65 786 2530 82942101 82943860 0.000000e+00 1779.0


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 TraesCS7D01G127600 chr7D 79963087 79965626 2539 False 4691.000000 4691 100.000 1 2540 1 chr7D.!!$F1 2539
1 TraesCS7D01G127600 chr7B 27066455 27068944 2489 False 990.033333 2296 91.138 4 2530 3 chr7B.!!$F1 2526
2 TraesCS7D01G127600 chr7A 82942101 82943860 1759 False 1779.000000 1779 85.707 786 2530 1 chr7A.!!$F1 1744

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
664 668 0.030773 TGTGTCTGTCGCTCACTCAC 59.969 55.0 0.0 0.0 33.82 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1705 0.039888 GCTCTGCTACCGCTAGCTAC 60.04 60.0 13.93 0.0 45.2 3.58 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
89 90 1.137282 GTTCACCTCTACTAGCTGCCC 59.863 57.143 0.00 0.00 0.00 5.36
90 91 0.397254 TCACCTCTACTAGCTGCCCC 60.397 60.000 0.00 0.00 0.00 5.80
97 98 1.207329 CTACTAGCTGCCCCGACTTTT 59.793 52.381 0.00 0.00 0.00 2.27
100 101 0.322187 TAGCTGCCCCGACTTTTTCC 60.322 55.000 0.00 0.00 0.00 3.13
102 103 2.281900 TGCCCCGACTTTTTCCCG 60.282 61.111 0.00 0.00 0.00 5.14
103 104 3.744719 GCCCCGACTTTTTCCCGC 61.745 66.667 0.00 0.00 0.00 6.13
104 105 2.033602 CCCCGACTTTTTCCCGCT 59.966 61.111 0.00 0.00 0.00 5.52
217 221 1.439679 GGGGATATTTGCGATCGACC 58.560 55.000 21.57 1.95 0.00 4.79
218 222 1.068474 GGGATATTTGCGATCGACCG 58.932 55.000 21.57 0.00 0.00 4.79
231 235 3.728474 GACCGATCGAGGCTCGTA 58.272 61.111 33.31 21.43 41.35 3.43
232 236 1.279238 GACCGATCGAGGCTCGTAC 59.721 63.158 33.31 25.45 41.35 3.67
233 237 1.434622 GACCGATCGAGGCTCGTACA 61.435 60.000 33.31 17.50 41.35 2.90
234 238 1.280142 CCGATCGAGGCTCGTACAG 59.720 63.158 33.31 22.30 41.35 2.74
235 239 1.437772 CCGATCGAGGCTCGTACAGT 61.438 60.000 33.31 16.81 41.35 3.55
236 240 1.215244 CGATCGAGGCTCGTACAGTA 58.785 55.000 33.31 15.99 41.35 2.74
269 273 2.499732 GCTTGTTAGCGTGCGTGC 60.500 61.111 0.00 0.00 37.71 5.34
293 297 1.064505 CATGATTTCGTGGAGCGCAAT 59.935 47.619 11.47 0.00 39.00 3.56
322 326 3.243877 CACCTTGTCAATTAGCTCGATCG 59.756 47.826 9.36 9.36 0.00 3.69
325 329 1.064952 TGTCAATTAGCTCGATCGCGA 59.935 47.619 13.09 13.09 45.71 5.87
335 339 2.504868 CTCGATCGCGATCAGAATCTC 58.495 52.381 39.26 18.93 46.80 2.75
389 393 3.428870 GTGACAGTTCGTACACATCCAAG 59.571 47.826 0.00 0.00 34.05 3.61
398 402 3.616317 CGTACACATCCAAGTCATCCACA 60.616 47.826 0.00 0.00 0.00 4.17
403 407 1.444933 TCCAAGTCATCCACACCCTT 58.555 50.000 0.00 0.00 0.00 3.95
418 422 0.329596 CCCTTTGGCCTCTGCTACTT 59.670 55.000 3.32 0.00 37.74 2.24
432 436 6.490381 CCTCTGCTACTTAAAATAAATCCCCC 59.510 42.308 0.00 0.00 0.00 5.40
447 451 0.689745 CCCCCGGATAAGTCACAGGA 60.690 60.000 0.73 0.00 0.00 3.86
454 458 2.287668 GGATAAGTCACAGGACCGATCG 60.288 54.545 8.51 8.51 45.48 3.69
466 470 1.292223 CCGATCGGACAACACACCT 59.708 57.895 30.62 0.00 37.50 4.00
474 478 1.488527 GACAACACACCTGACTCGAC 58.511 55.000 0.00 0.00 0.00 4.20
490 494 2.048503 ACCGAGTACCGCACAAGC 60.049 61.111 0.00 0.00 36.84 4.01
534 538 3.212685 GCCAATCCAAGAATCTCAGAGG 58.787 50.000 0.00 0.00 0.00 3.69
539 543 2.842496 TCCAAGAATCTCAGAGGTGCAT 59.158 45.455 0.00 0.00 0.00 3.96
540 544 2.943690 CCAAGAATCTCAGAGGTGCATG 59.056 50.000 0.00 0.00 0.00 4.06
541 545 2.943690 CAAGAATCTCAGAGGTGCATGG 59.056 50.000 0.00 0.00 0.00 3.66
542 546 1.134159 AGAATCTCAGAGGTGCATGGC 60.134 52.381 0.00 0.00 0.00 4.40
543 547 0.106819 AATCTCAGAGGTGCATGGCC 60.107 55.000 0.00 0.00 0.00 5.36
561 565 4.514577 AGCGCCGACCTCCAATCG 62.515 66.667 2.29 0.00 39.33 3.34
564 568 2.812499 GCCGACCTCCAATCGCTA 59.188 61.111 0.00 0.00 38.27 4.26
565 569 1.591863 GCCGACCTCCAATCGCTAC 60.592 63.158 0.00 0.00 38.27 3.58
566 570 2.017559 GCCGACCTCCAATCGCTACT 62.018 60.000 0.00 0.00 38.27 2.57
567 571 0.460311 CCGACCTCCAATCGCTACTT 59.540 55.000 0.00 0.00 38.27 2.24
568 572 1.134788 CCGACCTCCAATCGCTACTTT 60.135 52.381 0.00 0.00 38.27 2.66
569 573 2.618053 CGACCTCCAATCGCTACTTTT 58.382 47.619 0.00 0.00 31.96 2.27
570 574 3.000727 CGACCTCCAATCGCTACTTTTT 58.999 45.455 0.00 0.00 31.96 1.94
571 575 4.178540 CGACCTCCAATCGCTACTTTTTA 58.821 43.478 0.00 0.00 31.96 1.52
572 576 4.032558 CGACCTCCAATCGCTACTTTTTAC 59.967 45.833 0.00 0.00 31.96 2.01
573 577 3.930848 ACCTCCAATCGCTACTTTTTACG 59.069 43.478 0.00 0.00 0.00 3.18
574 578 3.308866 CCTCCAATCGCTACTTTTTACGG 59.691 47.826 0.00 0.00 0.00 4.02
575 579 4.178540 CTCCAATCGCTACTTTTTACGGA 58.821 43.478 0.00 0.00 0.00 4.69
576 580 4.178540 TCCAATCGCTACTTTTTACGGAG 58.821 43.478 0.00 0.00 0.00 4.63
577 581 3.242316 CCAATCGCTACTTTTTACGGAGC 60.242 47.826 0.00 0.00 0.00 4.70
578 582 2.728690 TCGCTACTTTTTACGGAGCA 57.271 45.000 0.00 0.00 32.55 4.26
579 583 2.331194 TCGCTACTTTTTACGGAGCAC 58.669 47.619 0.00 0.00 32.55 4.40
643 647 2.184167 ACCGGCGTCACACCAAAAG 61.184 57.895 6.01 0.00 0.00 2.27
645 649 2.542907 CGGCGTCACACCAAAAGCT 61.543 57.895 0.00 0.00 0.00 3.74
646 650 1.008538 GGCGTCACACCAAAAGCTG 60.009 57.895 0.00 0.00 0.00 4.24
647 651 1.724582 GGCGTCACACCAAAAGCTGT 61.725 55.000 0.00 0.00 0.00 4.40
657 661 0.940126 CAAAAGCTGTGTCTGTCGCT 59.060 50.000 0.00 0.00 0.00 4.93
658 662 1.070309 CAAAAGCTGTGTCTGTCGCTC 60.070 52.381 0.00 0.00 31.30 5.03
659 663 0.104855 AAAGCTGTGTCTGTCGCTCA 59.895 50.000 0.00 0.00 31.30 4.26
660 664 0.598680 AAGCTGTGTCTGTCGCTCAC 60.599 55.000 0.00 0.00 31.30 3.51
661 665 1.006805 GCTGTGTCTGTCGCTCACT 60.007 57.895 0.00 0.00 33.82 3.41
662 666 1.006314 GCTGTGTCTGTCGCTCACTC 61.006 60.000 0.00 0.00 33.82 3.51
663 667 0.312102 CTGTGTCTGTCGCTCACTCA 59.688 55.000 0.00 0.00 33.82 3.41
664 668 0.030773 TGTGTCTGTCGCTCACTCAC 59.969 55.000 0.00 0.00 33.82 3.51
665 669 0.999228 GTGTCTGTCGCTCACTCACG 60.999 60.000 0.00 0.00 0.00 4.35
686 692 1.080025 ACGCACCGGCTAGAAAGAC 60.080 57.895 0.00 0.00 38.10 3.01
687 693 1.080093 CGCACCGGCTAGAAAGACA 60.080 57.895 0.00 0.00 38.10 3.41
688 694 1.078759 CGCACCGGCTAGAAAGACAG 61.079 60.000 0.00 0.00 38.10 3.51
689 695 0.246635 GCACCGGCTAGAAAGACAGA 59.753 55.000 0.00 0.00 36.96 3.41
690 696 1.997669 CACCGGCTAGAAAGACAGAC 58.002 55.000 0.00 0.00 0.00 3.51
691 697 1.272490 CACCGGCTAGAAAGACAGACA 59.728 52.381 0.00 0.00 0.00 3.41
692 698 1.968493 ACCGGCTAGAAAGACAGACAA 59.032 47.619 0.00 0.00 0.00 3.18
693 699 2.028930 ACCGGCTAGAAAGACAGACAAG 60.029 50.000 0.00 0.00 0.00 3.16
694 700 2.231478 CCGGCTAGAAAGACAGACAAGA 59.769 50.000 0.00 0.00 0.00 3.02
708 714 1.064654 GACAAGAAATCCATCCAGCGC 59.935 52.381 0.00 0.00 0.00 5.92
735 741 4.722700 ATCACCGCACCACTGGCC 62.723 66.667 0.00 0.00 0.00 5.36
739 745 4.028490 CCGCACCACTGGCCCTAA 62.028 66.667 0.00 0.00 0.00 2.69
740 746 2.272146 CGCACCACTGGCCCTAAT 59.728 61.111 0.00 0.00 0.00 1.73
741 747 1.819632 CGCACCACTGGCCCTAATC 60.820 63.158 0.00 0.00 0.00 1.75
744 750 1.230149 ACCACTGGCCCTAATCCCA 60.230 57.895 0.00 0.00 0.00 4.37
749 755 1.133792 ACTGGCCCTAATCCCAAATCG 60.134 52.381 0.00 0.00 0.00 3.34
761 767 1.905843 CAAATCGCCCACCCACCAA 60.906 57.895 0.00 0.00 0.00 3.67
768 774 2.357034 CCACCCACCAACTCGACG 60.357 66.667 0.00 0.00 0.00 5.12
769 775 2.357034 CACCCACCAACTCGACGG 60.357 66.667 0.00 0.00 0.00 4.79
770 776 3.622826 ACCCACCAACTCGACGGG 61.623 66.667 0.00 0.00 43.02 5.28
772 778 4.308458 CCACCAACTCGACGGGCA 62.308 66.667 0.00 0.00 0.00 5.36
1328 1369 4.803426 CCAGCTCCTCGACGGCAC 62.803 72.222 0.00 0.00 0.00 5.01
1329 1370 3.753434 CAGCTCCTCGACGGCACT 61.753 66.667 0.00 0.00 0.00 4.40
1542 1595 1.203563 CGACGACGACGAGTGAACT 59.796 57.895 15.32 0.00 42.66 3.01
1559 1612 3.561120 CTGCTGTAAACCCCCGCCA 62.561 63.158 0.00 0.00 0.00 5.69
1573 1626 2.162681 CCCGCCAATTCTTCAGTTCTT 58.837 47.619 0.00 0.00 0.00 2.52
1578 1631 3.126000 GCCAATTCTTCAGTTCTTCTCCG 59.874 47.826 0.00 0.00 0.00 4.63
1579 1632 4.569943 CCAATTCTTCAGTTCTTCTCCGA 58.430 43.478 0.00 0.00 0.00 4.55
1581 1634 3.662247 TTCTTCAGTTCTTCTCCGACC 57.338 47.619 0.00 0.00 0.00 4.79
1586 1639 1.276421 CAGTTCTTCTCCGACCACCAT 59.724 52.381 0.00 0.00 0.00 3.55
1591 1647 0.834261 TTCTCCGACCACCATCACCA 60.834 55.000 0.00 0.00 0.00 4.17
1626 1682 8.068977 CCTAGTACTAGTGCGTCTTAATTAGTG 58.931 40.741 24.84 3.44 0.00 2.74
1732 1800 0.112995 AAGACATGGGGAAGCAAGCA 59.887 50.000 0.00 0.00 0.00 3.91
1739 1807 1.450531 GGGGAAGCAAGCATGGATCG 61.451 60.000 0.00 0.00 0.00 3.69
1744 1812 0.182061 AGCAAGCATGGATCGGACAT 59.818 50.000 0.00 0.00 0.00 3.06
1853 1925 1.767088 GGTTACTAAGTAGGGCCTGGG 59.233 57.143 18.53 3.95 0.00 4.45
1856 1928 0.640495 ACTAAGTAGGGCCTGGGCTA 59.360 55.000 18.53 7.68 41.60 3.93
1889 1961 0.321671 GCTTGGTGGCAGTAGACTCA 59.678 55.000 0.00 0.00 0.00 3.41
1893 1965 0.905337 GGTGGCAGTAGACTCAGGGT 60.905 60.000 0.00 0.00 0.00 4.34
1908 1980 2.588877 GGTGTGTGAGTGCGTGCT 60.589 61.111 0.00 0.00 0.00 4.40
1952 2036 3.110139 GTGCATGGCCATGTACCG 58.890 61.111 41.30 22.46 44.95 4.02
1996 2096 3.431922 TTGTAAAGAGAGATACCGGCG 57.568 47.619 0.00 0.00 0.00 6.46
2050 2155 1.466950 CGCACTCTCTCTTTCGTCTCT 59.533 52.381 0.00 0.00 0.00 3.10
2085 2191 0.106066 TTCCCACATCATCATGGCCC 60.106 55.000 0.00 0.00 34.37 5.80
2185 2298 3.373565 CCCACCCGCCTCAAAAGC 61.374 66.667 0.00 0.00 0.00 3.51
2188 2301 2.985847 ACCCGCCTCAAAAGCAGC 60.986 61.111 0.00 0.00 0.00 5.25
2189 2302 2.985282 CCCGCCTCAAAAGCAGCA 60.985 61.111 0.00 0.00 0.00 4.41
2404 2562 2.738135 CGTGTGTACGGCATATGATGA 58.262 47.619 6.97 0.00 46.23 2.92
2405 2563 3.317150 CGTGTGTACGGCATATGATGAT 58.683 45.455 6.97 0.00 46.23 2.45
2406 2564 3.121778 CGTGTGTACGGCATATGATGATG 59.878 47.826 6.97 0.00 46.23 3.07
2409 2567 2.637382 TGTACGGCATATGATGATGGGT 59.363 45.455 6.97 0.00 0.00 4.51
2421 2579 0.976641 TGATGGGTGTCAGTGGAGTC 59.023 55.000 0.00 0.00 0.00 3.36
2422 2580 1.270907 GATGGGTGTCAGTGGAGTCT 58.729 55.000 0.00 0.00 0.00 3.24
2423 2581 0.979665 ATGGGTGTCAGTGGAGTCTG 59.020 55.000 0.00 0.00 36.85 3.51
2424 2582 1.121407 TGGGTGTCAGTGGAGTCTGG 61.121 60.000 0.00 0.00 36.25 3.86
2425 2583 0.832135 GGGTGTCAGTGGAGTCTGGA 60.832 60.000 0.00 0.00 36.25 3.86
2426 2584 0.605589 GGTGTCAGTGGAGTCTGGAG 59.394 60.000 0.00 0.00 36.25 3.86
2427 2585 1.333177 GTGTCAGTGGAGTCTGGAGT 58.667 55.000 0.00 0.00 36.25 3.85
2428 2586 1.000283 GTGTCAGTGGAGTCTGGAGTG 60.000 57.143 0.00 0.00 36.25 3.51
2429 2587 0.605589 GTCAGTGGAGTCTGGAGTGG 59.394 60.000 0.00 0.00 36.25 4.00
2430 2588 0.482887 TCAGTGGAGTCTGGAGTGGA 59.517 55.000 0.00 0.00 36.25 4.02
2431 2589 0.605589 CAGTGGAGTCTGGAGTGGAC 59.394 60.000 0.00 0.00 0.00 4.02
2432 2590 0.543174 AGTGGAGTCTGGAGTGGACC 60.543 60.000 0.00 0.00 34.56 4.46
2433 2591 1.606601 TGGAGTCTGGAGTGGACCG 60.607 63.158 0.00 0.00 34.56 4.79
2434 2592 2.352032 GGAGTCTGGAGTGGACCGG 61.352 68.421 0.00 0.00 37.63 5.28
2435 2593 1.606889 GAGTCTGGAGTGGACCGGT 60.607 63.158 6.92 6.92 37.55 5.28
2469 2631 1.232621 ACGAGGTTTGGGTTTAGCGC 61.233 55.000 0.00 0.00 0.00 5.92
2530 2692 3.508402 TGCGTCTTATCGGGCTAATGATA 59.492 43.478 0.00 0.00 0.00 2.15
2531 2693 4.021807 TGCGTCTTATCGGGCTAATGATAA 60.022 41.667 0.00 0.00 36.10 1.75
2532 2694 5.109903 GCGTCTTATCGGGCTAATGATAAT 58.890 41.667 0.00 0.00 36.70 1.28
2533 2695 5.005779 GCGTCTTATCGGGCTAATGATAATG 59.994 44.000 0.00 0.00 36.70 1.90
2534 2696 6.330278 CGTCTTATCGGGCTAATGATAATGA 58.670 40.000 0.00 0.00 36.70 2.57
2535 2697 6.980978 CGTCTTATCGGGCTAATGATAATGAT 59.019 38.462 0.00 0.00 36.70 2.45
2536 2698 7.043125 CGTCTTATCGGGCTAATGATAATGATG 60.043 40.741 0.00 0.00 36.70 3.07
2537 2699 6.763135 TCTTATCGGGCTAATGATAATGATGC 59.237 38.462 0.00 0.00 36.70 3.91
2538 2700 3.261580 TCGGGCTAATGATAATGATGCG 58.738 45.455 0.00 0.00 0.00 4.73
2539 2701 2.223112 CGGGCTAATGATAATGATGCGC 60.223 50.000 0.00 0.00 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 1.226030 ACGAAGCGGGAAAAAGTCGG 61.226 55.000 0.00 0.00 32.96 4.79
90 91 0.584876 AACGAAGCGGGAAAAAGTCG 59.415 50.000 0.00 0.00 34.77 4.18
97 98 1.213537 CCGTCTAACGAAGCGGGAA 59.786 57.895 0.24 0.00 46.05 3.97
100 101 1.804326 CCACCGTCTAACGAAGCGG 60.804 63.158 16.75 16.75 46.05 5.52
102 103 1.012486 CCACCACCGTCTAACGAAGC 61.012 60.000 0.24 0.00 46.05 3.86
103 104 0.389426 CCCACCACCGTCTAACGAAG 60.389 60.000 0.24 0.00 46.05 3.79
104 105 1.667151 CCCACCACCGTCTAACGAA 59.333 57.895 0.24 0.00 46.05 3.85
199 203 1.068474 CGGTCGATCGCAAATATCCC 58.932 55.000 11.09 0.00 0.00 3.85
218 222 2.032722 CAGTACTGTACGAGCCTCGATC 60.033 54.545 22.80 13.07 43.74 3.69
269 273 0.247814 GCTCCACGAAATCATGCACG 60.248 55.000 0.00 0.00 0.00 5.34
293 297 4.020218 AGCTAATTGACAAGGTGTGAGCTA 60.020 41.667 0.00 0.00 36.04 3.32
300 304 3.243877 CGATCGAGCTAATTGACAAGGTG 59.756 47.826 10.26 0.00 0.00 4.00
322 326 0.228238 CGCAACGAGATTCTGATCGC 59.772 55.000 0.00 0.00 42.61 4.58
325 329 1.645034 CCACGCAACGAGATTCTGAT 58.355 50.000 0.00 0.00 0.00 2.90
358 362 1.335810 ACGAACTGTCACTGCGACTTA 59.664 47.619 0.00 0.00 45.60 2.24
389 393 1.250840 GGCCAAAGGGTGTGGATGAC 61.251 60.000 0.00 0.00 38.54 3.06
398 402 0.842467 AGTAGCAGAGGCCAAAGGGT 60.842 55.000 5.01 0.00 42.56 4.34
403 407 7.068226 GGATTTATTTTAAGTAGCAGAGGCCAA 59.932 37.037 5.01 0.00 42.56 4.52
418 422 6.999871 GTGACTTATCCGGGGGATTTATTTTA 59.000 38.462 0.00 0.00 39.79 1.52
432 436 1.100510 TCGGTCCTGTGACTTATCCG 58.899 55.000 0.00 0.00 41.47 4.18
447 451 1.005394 GGTGTGTTGTCCGATCGGT 60.005 57.895 32.15 0.00 36.47 4.69
454 458 0.387929 TCGAGTCAGGTGTGTTGTCC 59.612 55.000 0.00 0.00 0.00 4.02
474 478 2.094659 CAGCTTGTGCGGTACTCGG 61.095 63.158 0.00 0.00 45.42 4.63
490 494 2.609916 TCGTCTCGTCTTGAGCTATCAG 59.390 50.000 0.00 0.00 44.86 2.90
503 507 0.249120 TTGGATTGGCATCGTCTCGT 59.751 50.000 0.00 0.00 0.00 4.18
506 510 2.787473 TTCTTGGATTGGCATCGTCT 57.213 45.000 0.00 0.00 0.00 4.18
542 546 4.473520 ATTGGAGGTCGGCGCTGG 62.474 66.667 17.88 4.31 0.00 4.85
543 547 2.892425 GATTGGAGGTCGGCGCTG 60.892 66.667 10.86 10.86 0.00 5.18
558 562 2.928116 GTGCTCCGTAAAAAGTAGCGAT 59.072 45.455 0.00 0.00 35.95 4.58
561 565 3.064931 AGTGTGCTCCGTAAAAAGTAGC 58.935 45.455 0.00 0.00 0.00 3.58
562 566 4.151867 GGAAGTGTGCTCCGTAAAAAGTAG 59.848 45.833 0.00 0.00 0.00 2.57
564 568 2.876550 GGAAGTGTGCTCCGTAAAAAGT 59.123 45.455 0.00 0.00 0.00 2.66
565 569 2.096417 CGGAAGTGTGCTCCGTAAAAAG 60.096 50.000 3.30 0.00 41.62 2.27
566 570 1.868498 CGGAAGTGTGCTCCGTAAAAA 59.132 47.619 3.30 0.00 41.62 1.94
567 571 1.504359 CGGAAGTGTGCTCCGTAAAA 58.496 50.000 3.30 0.00 41.62 1.52
568 572 3.204505 CGGAAGTGTGCTCCGTAAA 57.795 52.632 3.30 0.00 41.62 2.01
569 573 4.979204 CGGAAGTGTGCTCCGTAA 57.021 55.556 3.30 0.00 41.62 3.18
643 647 1.006314 GAGTGAGCGACAGACACAGC 61.006 60.000 0.00 0.00 37.05 4.40
645 649 0.030773 GTGAGTGAGCGACAGACACA 59.969 55.000 0.00 0.00 36.51 3.72
646 650 0.999228 CGTGAGTGAGCGACAGACAC 60.999 60.000 0.00 0.00 34.72 3.67
647 651 1.164041 TCGTGAGTGAGCGACAGACA 61.164 55.000 0.00 0.00 31.76 3.41
657 661 2.027024 GGTGCGTGTCGTGAGTGA 59.973 61.111 0.00 0.00 0.00 3.41
658 662 3.394874 CGGTGCGTGTCGTGAGTG 61.395 66.667 0.00 0.00 0.00 3.51
659 663 4.640855 CCGGTGCGTGTCGTGAGT 62.641 66.667 0.00 0.00 0.00 3.41
662 666 4.710695 TAGCCGGTGCGTGTCGTG 62.711 66.667 1.90 0.00 44.33 4.35
663 667 4.415332 CTAGCCGGTGCGTGTCGT 62.415 66.667 1.90 0.00 44.33 4.34
664 668 3.620300 TTCTAGCCGGTGCGTGTCG 62.620 63.158 1.90 0.00 44.33 4.35
665 669 1.352156 CTTTCTAGCCGGTGCGTGTC 61.352 60.000 1.90 0.00 44.33 3.67
686 692 2.353889 CGCTGGATGGATTTCTTGTCTG 59.646 50.000 0.00 0.00 0.00 3.51
687 693 2.636830 CGCTGGATGGATTTCTTGTCT 58.363 47.619 0.00 0.00 0.00 3.41
688 694 1.064654 GCGCTGGATGGATTTCTTGTC 59.935 52.381 0.00 0.00 0.00 3.18
689 695 1.098050 GCGCTGGATGGATTTCTTGT 58.902 50.000 0.00 0.00 0.00 3.16
690 696 0.383231 GGCGCTGGATGGATTTCTTG 59.617 55.000 7.64 0.00 0.00 3.02
691 697 0.257039 AGGCGCTGGATGGATTTCTT 59.743 50.000 7.64 0.00 0.00 2.52
692 698 0.257039 AAGGCGCTGGATGGATTTCT 59.743 50.000 7.64 0.00 0.00 2.52
693 699 0.665298 GAAGGCGCTGGATGGATTTC 59.335 55.000 7.64 0.00 0.00 2.17
694 700 1.097547 CGAAGGCGCTGGATGGATTT 61.098 55.000 7.64 0.00 0.00 2.17
708 714 0.652592 GTGCGGTGATTCATCGAAGG 59.347 55.000 22.87 0.00 40.81 3.46
735 741 1.318576 GTGGGCGATTTGGGATTAGG 58.681 55.000 0.00 0.00 0.00 2.69
736 742 1.318576 GGTGGGCGATTTGGGATTAG 58.681 55.000 0.00 0.00 0.00 1.73
737 743 0.106419 GGGTGGGCGATTTGGGATTA 60.106 55.000 0.00 0.00 0.00 1.75
738 744 1.381191 GGGTGGGCGATTTGGGATT 60.381 57.895 0.00 0.00 0.00 3.01
739 745 2.278738 GGGTGGGCGATTTGGGAT 59.721 61.111 0.00 0.00 0.00 3.85
740 746 3.260888 TGGGTGGGCGATTTGGGA 61.261 61.111 0.00 0.00 0.00 4.37
741 747 3.068064 GTGGGTGGGCGATTTGGG 61.068 66.667 0.00 0.00 0.00 4.12
744 750 1.906333 GTTGGTGGGTGGGCGATTT 60.906 57.895 0.00 0.00 0.00 2.17
749 755 3.948719 TCGAGTTGGTGGGTGGGC 61.949 66.667 0.00 0.00 0.00 5.36
814 821 2.486951 TAGAGGCGATTAAGTGCGTC 57.513 50.000 13.53 13.53 44.11 5.19
1425 1469 4.935495 CCCATGCCGACCCCGATG 62.935 72.222 0.00 0.00 38.22 3.84
1480 1533 3.647771 GTCGGGGTTCTTGGCCCT 61.648 66.667 0.00 0.00 45.39 5.19
1542 1595 2.433646 ATTGGCGGGGGTTTACAGCA 62.434 55.000 0.00 0.00 0.00 4.41
1559 1612 4.040461 TGGTCGGAGAAGAACTGAAGAATT 59.960 41.667 0.00 0.00 39.69 2.17
1573 1626 1.229051 TGGTGATGGTGGTCGGAGA 60.229 57.895 0.00 0.00 0.00 3.71
1578 1631 0.981183 TGTAGGTGGTGATGGTGGTC 59.019 55.000 0.00 0.00 0.00 4.02
1579 1632 1.668826 ATGTAGGTGGTGATGGTGGT 58.331 50.000 0.00 0.00 0.00 4.16
1581 1634 2.771943 AGGTATGTAGGTGGTGATGGTG 59.228 50.000 0.00 0.00 0.00 4.17
1586 1639 5.722172 AGTACTAGGTATGTAGGTGGTGA 57.278 43.478 0.00 0.00 0.00 4.02
1591 1647 5.163258 ACGCACTAGTACTAGGTATGTAGGT 60.163 44.000 29.05 16.10 37.49 3.08
1646 1705 0.039888 GCTCTGCTACCGCTAGCTAC 60.040 60.000 13.93 0.00 45.20 3.58
1732 1800 0.548031 ACCTTGCATGTCCGATCCAT 59.452 50.000 0.00 0.00 0.00 3.41
1739 1807 0.889186 ACCGAACACCTTGCATGTCC 60.889 55.000 0.00 0.00 0.00 4.02
1744 1812 1.336440 CATTTCACCGAACACCTTGCA 59.664 47.619 0.00 0.00 0.00 4.08
1769 1837 1.299976 GTTTGGTCCCCGAGCTCAT 59.700 57.895 15.40 0.00 0.00 2.90
1770 1838 2.747686 GTTTGGTCCCCGAGCTCA 59.252 61.111 15.40 0.00 0.00 4.26
1781 1849 2.041891 TCCATTATTGGTCGGGTTTGGT 59.958 45.455 3.65 0.00 44.06 3.67
1784 1852 2.375146 GCTCCATTATTGGTCGGGTTT 58.625 47.619 3.65 0.00 44.06 3.27
1853 1925 2.727647 CTCGCCGTCGCTGATAGC 60.728 66.667 0.00 0.00 38.02 2.97
1856 1928 4.135153 AAGCTCGCCGTCGCTGAT 62.135 61.111 4.62 0.00 36.45 2.90
1877 1949 0.247736 CACACCCTGAGTCTACTGCC 59.752 60.000 0.00 0.00 0.00 4.85
1889 1961 2.108976 CACGCACTCACACACCCT 59.891 61.111 0.00 0.00 0.00 4.34
1893 1965 2.179547 CCAAGCACGCACTCACACA 61.180 57.895 0.00 0.00 0.00 3.72
1952 2036 6.095432 ACACTCTTATATCTGATGCAGGTC 57.905 41.667 0.00 0.00 31.51 3.85
1984 2081 1.274167 TGTTTGTTCGCCGGTATCTCT 59.726 47.619 1.90 0.00 0.00 3.10
1985 2082 1.717194 TGTTTGTTCGCCGGTATCTC 58.283 50.000 1.90 0.00 0.00 2.75
1996 2096 7.524294 TGATTCTTGAAGCTTTTGTTTGTTC 57.476 32.000 0.00 0.00 0.00 3.18
2050 2155 5.384336 TGTGGGAATCAAGATGAAGAAACA 58.616 37.500 0.00 0.00 0.00 2.83
2085 2191 0.731417 CTGCTGCTTTCCTGGAATCG 59.269 55.000 10.45 5.96 0.00 3.34
2314 2447 3.642503 CCCACCACCGGCTAACCA 61.643 66.667 0.00 0.00 34.57 3.67
2404 2562 0.979665 CAGACTCCACTGACACCCAT 59.020 55.000 0.00 0.00 39.94 4.00
2405 2563 1.121407 CCAGACTCCACTGACACCCA 61.121 60.000 0.00 0.00 39.94 4.51
2406 2564 0.832135 TCCAGACTCCACTGACACCC 60.832 60.000 0.00 0.00 39.94 4.61
2409 2567 1.332195 CACTCCAGACTCCACTGACA 58.668 55.000 0.00 0.00 39.94 3.58
2421 2579 2.923035 ACCACCGGTCCACTCCAG 60.923 66.667 2.59 0.00 0.00 3.86
2422 2580 3.238497 CACCACCGGTCCACTCCA 61.238 66.667 2.59 0.00 31.02 3.86
2423 2581 4.699522 GCACCACCGGTCCACTCC 62.700 72.222 2.59 0.00 31.02 3.85
2424 2582 2.227089 CTAGCACCACCGGTCCACTC 62.227 65.000 2.59 0.00 31.02 3.51
2425 2583 2.203728 TAGCACCACCGGTCCACT 60.204 61.111 2.59 2.18 31.02 4.00
2426 2584 2.264794 CTAGCACCACCGGTCCAC 59.735 66.667 2.59 0.00 31.02 4.02
2427 2585 3.000819 CCTAGCACCACCGGTCCA 61.001 66.667 2.59 0.00 31.02 4.02
2428 2586 3.001406 ACCTAGCACCACCGGTCC 61.001 66.667 2.59 0.00 31.02 4.46
2429 2587 2.264794 CACCTAGCACCACCGGTC 59.735 66.667 2.59 0.00 31.02 4.79
2430 2588 4.016706 GCACCTAGCACCACCGGT 62.017 66.667 0.00 0.00 44.79 5.28
2478 2640 2.994699 CCACGCACTAATCCCCCA 59.005 61.111 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.