Multiple sequence alignment - TraesCS4B01G180000

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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 TraesCS4B01G180000 chr4B 100.000 2573 0 0 1 2573 394385694 394383122 0.000000e+00 4752.0
1 TraesCS4B01G180000 chr4A 93.626 1616 63 11 876 2482 157561875 157563459 0.000000e+00 2377.0
2 TraesCS4B01G180000 chr4A 95.395 760 25 5 1 750 157560877 157561636 0.000000e+00 1201.0
3 TraesCS4B01G180000 chr4A 97.059 102 3 0 747 848 157561688 157561789 3.400000e-39 172.0
4 TraesCS4B01G180000 chr4A 92.308 39 2 1 2288 2326 690220614 690220577 1.000000e-03 54.7
5 TraesCS4B01G180000 chr4D 90.785 1617 79 17 903 2482 317198557 317196974 0.000000e+00 2097.0
6 TraesCS4B01G180000 chr4D 92.358 759 45 6 1 750 317199612 317198858 0.000000e+00 1068.0
7 TraesCS4B01G180000 chr4D 94.175 103 5 1 747 848 317198806 317198704 3.430000e-34 156.0
8 TraesCS4B01G180000 chr6B 84.048 746 98 15 892 1629 50396631 50397363 0.000000e+00 699.0
9 TraesCS4B01G180000 chr6D 84.423 719 99 10 915 1629 27521365 27520656 0.000000e+00 695.0
10 TraesCS4B01G180000 chr6A 84.254 724 102 8 910 1629 30466997 30467712 0.000000e+00 695.0
11 TraesCS4B01G180000 chrUn 84.043 94 15 0 2245 2338 235115315 235115222 9.800000e-15 91.6
12 TraesCS4B01G180000 chr3D 89.583 48 5 0 2279 2326 524715656 524715703 7.690000e-06 62.1
13 TraesCS4B01G180000 chr2D 100.000 28 0 0 2304 2331 351288369 351288342 5.000000e-03 52.8


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 TraesCS4B01G180000 chr4B 394383122 394385694 2572 True 4752 4752 100.000000 1 2573 1 chr4B.!!$R1 2572
1 TraesCS4B01G180000 chr4A 157560877 157563459 2582 False 1250 2377 95.360000 1 2482 3 chr4A.!!$F1 2481
2 TraesCS4B01G180000 chr4D 317196974 317199612 2638 True 1107 2097 92.439333 1 2482 3 chr4D.!!$R1 2481
3 TraesCS4B01G180000 chr6B 50396631 50397363 732 False 699 699 84.048000 892 1629 1 chr6B.!!$F1 737
4 TraesCS4B01G180000 chr6D 27520656 27521365 709 True 695 695 84.423000 915 1629 1 chr6D.!!$R1 714
5 TraesCS4B01G180000 chr6A 30466997 30467712 715 False 695 695 84.254000 910 1629 1 chr6A.!!$F1 719


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
843 915 0.034574 ATAATGCGTTGCCCTCCACA 60.035 50.0 0.08 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1885 2085 0.693049 CTACCAGAGCCACAAACCCT 59.307 55.0 0.0 0.0 0.0 4.34 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
173 180 4.148128 AGAGCTAACATGAACCATGGAG 57.852 45.455 21.47 3.29 45.16 3.86
225 232 1.898472 CTCGAGGGGATATCTGTGCAT 59.102 52.381 3.91 0.00 0.00 3.96
260 267 3.092301 AGTTTATGAAAAGGAGGGCAGC 58.908 45.455 0.00 0.00 0.00 5.25
324 337 2.554893 GCTGACCGGTCAAATTTAACCA 59.445 45.455 35.36 11.68 39.39 3.67
389 402 6.259829 GGCTAGCTTTTTAAGATGAGAAGAGG 59.740 42.308 15.72 0.00 0.00 3.69
393 406 8.105097 AGCTTTTTAAGATGAGAAGAGGAAAC 57.895 34.615 0.00 0.00 0.00 2.78
472 486 9.836864 TGGCTAATCAAGGTAATATATGCTATG 57.163 33.333 0.00 0.00 0.00 2.23
479 493 9.739276 TCAAGGTAATATATGCTATGGGAAAAG 57.261 33.333 0.00 0.00 0.00 2.27
505 522 9.696917 GGTCTCATTGAACAATAACAGAAAAAT 57.303 29.630 0.00 0.00 31.33 1.82
536 553 1.974957 TGAGGATCGTTTGAGTGGGAA 59.025 47.619 0.00 0.00 38.61 3.97
617 634 4.156373 TGATTCACATGTATGGTGCAAGTG 59.844 41.667 0.00 0.00 37.03 3.16
740 757 8.492673 AAAACAAGATCTTAGTTGATGCGATA 57.507 30.769 18.05 0.00 0.00 2.92
750 767 7.976175 TCTTAGTTGATGCGATACATGGATATC 59.024 37.037 0.00 0.00 39.84 1.63
751 768 6.041423 AGTTGATGCGATACATGGATATCA 57.959 37.500 4.83 0.00 39.84 2.15
752 769 5.871524 AGTTGATGCGATACATGGATATCAC 59.128 40.000 4.83 0.00 39.84 3.06
837 909 4.033932 GGAAAATTCAATAATGCGTTGCCC 59.966 41.667 0.08 0.00 0.00 5.36
843 915 0.034574 ATAATGCGTTGCCCTCCACA 60.035 50.000 0.08 0.00 0.00 4.17
844 916 0.250945 TAATGCGTTGCCCTCCACAA 60.251 50.000 0.08 0.00 0.00 3.33
845 917 0.899717 AATGCGTTGCCCTCCACAAT 60.900 50.000 0.00 0.00 0.00 2.71
846 918 1.315257 ATGCGTTGCCCTCCACAATC 61.315 55.000 0.00 0.00 0.00 2.67
847 919 2.700773 GCGTTGCCCTCCACAATCC 61.701 63.158 0.00 0.00 0.00 3.01
848 920 1.002134 CGTTGCCCTCCACAATCCT 60.002 57.895 0.00 0.00 0.00 3.24
849 921 1.308069 CGTTGCCCTCCACAATCCTG 61.308 60.000 0.00 0.00 0.00 3.86
850 922 1.304381 TTGCCCTCCACAATCCTGC 60.304 57.895 0.00 0.00 0.00 4.85
851 923 2.825836 GCCCTCCACAATCCTGCG 60.826 66.667 0.00 0.00 0.00 5.18
852 924 2.671070 CCCTCCACAATCCTGCGT 59.329 61.111 0.00 0.00 0.00 5.24
853 925 1.002134 CCCTCCACAATCCTGCGTT 60.002 57.895 0.00 0.00 0.00 4.84
854 926 1.308069 CCCTCCACAATCCTGCGTTG 61.308 60.000 0.00 0.00 0.00 4.10
867 939 3.039202 GCGTTGCCCTCCACAATCG 62.039 63.158 0.00 0.00 0.00 3.34
874 946 1.519455 CCTCCACAATCGAGACGGC 60.519 63.158 0.00 0.00 0.00 5.68
973 1158 2.978978 TGATCAACAAGAGGTGGAGGAA 59.021 45.455 0.00 0.00 31.44 3.36
1174 1361 1.384502 CATGGCCTAGACCCAGGGA 60.385 63.158 14.54 0.00 35.48 4.20
1184 1371 0.108019 GACCCAGGGAACTTCGTTGT 59.892 55.000 14.54 0.00 40.21 3.32
1296 1490 2.110627 GATGGGCAGAGCATCGCT 59.889 61.111 0.00 0.00 43.88 4.93
1312 1506 1.657751 CGCTCTGACATCGGACCTCA 61.658 60.000 0.00 0.00 0.00 3.86
1549 1743 3.009143 GGTCATGGAGGAAAGTTACACCT 59.991 47.826 0.00 0.00 36.68 4.00
1550 1744 4.506802 GGTCATGGAGGAAAGTTACACCTT 60.507 45.833 0.00 0.00 33.89 3.50
1622 1818 2.358267 CAGATCTGCATCCTGAAAAGGC 59.642 50.000 10.38 0.00 0.00 4.35
1651 1847 3.826157 TCTTGCTCGTTTGGGATTCATTT 59.174 39.130 0.00 0.00 0.00 2.32
1765 1961 9.667107 TTTTATACGAGGATTCTGAATTGAGTT 57.333 29.630 4.11 0.00 0.00 3.01
1783 1979 5.977635 TGAGTTCTCAGACAAGTTTCAGAA 58.022 37.500 0.00 0.00 0.00 3.02
1791 1987 6.611381 TCAGACAAGTTTCAGAAAAGTGTTG 58.389 36.000 12.03 9.33 28.67 3.33
1799 1995 6.868339 AGTTTCAGAAAAGTGTTGGTTTTCAG 59.132 34.615 10.12 3.48 43.48 3.02
1815 2011 4.875544 TTTCAGCACACAAGTACAAGTC 57.124 40.909 0.00 0.00 0.00 3.01
1816 2012 3.535280 TCAGCACACAAGTACAAGTCA 57.465 42.857 0.00 0.00 0.00 3.41
1817 2013 4.071961 TCAGCACACAAGTACAAGTCAT 57.928 40.909 0.00 0.00 0.00 3.06
1818 2014 4.450976 TCAGCACACAAGTACAAGTCATT 58.549 39.130 0.00 0.00 0.00 2.57
1819 2015 4.511454 TCAGCACACAAGTACAAGTCATTC 59.489 41.667 0.00 0.00 0.00 2.67
1820 2016 4.273235 CAGCACACAAGTACAAGTCATTCA 59.727 41.667 0.00 0.00 0.00 2.57
1821 2017 5.049198 CAGCACACAAGTACAAGTCATTCAT 60.049 40.000 0.00 0.00 0.00 2.57
1822 2018 5.049198 AGCACACAAGTACAAGTCATTCATG 60.049 40.000 0.00 0.00 0.00 3.07
1823 2019 5.049474 GCACACAAGTACAAGTCATTCATGA 60.049 40.000 0.00 0.00 0.00 3.07
1824 2020 6.348786 GCACACAAGTACAAGTCATTCATGAT 60.349 38.462 0.00 0.00 39.30 2.45
1825 2021 7.587629 CACACAAGTACAAGTCATTCATGATT 58.412 34.615 0.00 0.00 39.30 2.57
1826 2022 8.077991 CACACAAGTACAAGTCATTCATGATTT 58.922 33.333 0.00 0.00 39.30 2.17
1827 2023 9.283768 ACACAAGTACAAGTCATTCATGATTTA 57.716 29.630 0.00 0.00 39.30 1.40
1841 2037 5.003160 TCATGATTTATCAGGCCGTAATGG 58.997 41.667 0.00 0.00 40.64 3.16
1852 2048 5.354792 TCAGGCCGTAATGGTTTATTTACAC 59.645 40.000 0.00 0.00 41.21 2.90
1873 2073 1.598685 GGGTTCAGGTTTTCGCGGA 60.599 57.895 6.13 0.00 0.00 5.54
1885 2085 0.248012 TTCGCGGAGGTGATTTGCTA 59.752 50.000 6.13 0.00 31.66 3.49
1993 2193 3.572255 GGGATGCTTGGTTTTCAGTACAA 59.428 43.478 0.00 0.00 0.00 2.41
2124 2324 0.486879 TGGCTGGGGTTCAAGGATTT 59.513 50.000 0.00 0.00 0.00 2.17
2125 2325 1.713647 TGGCTGGGGTTCAAGGATTTA 59.286 47.619 0.00 0.00 0.00 1.40
2128 2328 4.017037 TGGCTGGGGTTCAAGGATTTATTA 60.017 41.667 0.00 0.00 0.00 0.98
2131 2335 6.239317 GGCTGGGGTTCAAGGATTTATTATTC 60.239 42.308 0.00 0.00 0.00 1.75
2250 2481 9.628500 GAAATACAAAATGTAGTAATCCCTCCT 57.372 33.333 0.00 0.00 36.14 3.69
2268 2499 6.781014 TCCCTCCTATTCATATTACTTGTCGT 59.219 38.462 0.00 0.00 0.00 4.34
2403 2634 8.295288 GCTAAGAATTGCATGCAGAAAGTATAT 58.705 33.333 21.50 5.92 0.00 0.86
2482 2713 2.737881 GGTAGTATGGGGCGGCACA 61.738 63.158 19.28 19.28 0.00 4.57
2483 2714 1.450211 GTAGTATGGGGCGGCACAT 59.550 57.895 30.64 30.64 0.00 3.21
2484 2715 0.682852 GTAGTATGGGGCGGCACATA 59.317 55.000 28.29 28.29 0.00 2.29
2485 2716 0.973632 TAGTATGGGGCGGCACATAG 59.026 55.000 31.93 0.00 30.80 2.23
2486 2717 1.054406 AGTATGGGGCGGCACATAGT 61.054 55.000 31.93 30.98 30.80 2.12
2487 2718 0.602905 GTATGGGGCGGCACATAGTC 60.603 60.000 31.93 18.66 30.80 2.59
2488 2719 1.051556 TATGGGGCGGCACATAGTCA 61.052 55.000 28.29 10.19 0.00 3.41
2489 2720 2.203070 GGGGCGGCACATAGTCAG 60.203 66.667 12.47 0.00 0.00 3.51
2490 2721 2.897350 GGGCGGCACATAGTCAGC 60.897 66.667 12.47 0.00 0.00 4.26
2491 2722 2.897350 GGCGGCACATAGTCAGCC 60.897 66.667 3.07 0.00 44.89 4.85
2492 2723 2.187946 GCGGCACATAGTCAGCCT 59.812 61.111 0.00 0.00 46.14 4.58
2493 2724 1.884926 GCGGCACATAGTCAGCCTC 60.885 63.158 0.00 0.00 46.14 4.70
2494 2725 1.819229 CGGCACATAGTCAGCCTCT 59.181 57.895 0.00 0.00 46.14 3.69
2495 2726 0.176680 CGGCACATAGTCAGCCTCTT 59.823 55.000 0.00 0.00 46.14 2.85
2496 2727 1.409064 CGGCACATAGTCAGCCTCTTA 59.591 52.381 0.00 0.00 46.14 2.10
2497 2728 2.544694 CGGCACATAGTCAGCCTCTTAG 60.545 54.545 0.00 0.00 46.14 2.18
2498 2729 2.478831 GCACATAGTCAGCCTCTTAGC 58.521 52.381 0.00 0.00 0.00 3.09
2499 2730 2.102252 GCACATAGTCAGCCTCTTAGCT 59.898 50.000 0.00 0.00 46.45 3.32
2500 2731 3.431486 GCACATAGTCAGCCTCTTAGCTT 60.431 47.826 0.00 0.00 42.61 3.74
2501 2732 4.202161 GCACATAGTCAGCCTCTTAGCTTA 60.202 45.833 0.00 0.00 42.61 3.09
2502 2733 5.682471 GCACATAGTCAGCCTCTTAGCTTAA 60.682 44.000 0.00 0.00 42.61 1.85
2503 2734 5.982516 CACATAGTCAGCCTCTTAGCTTAAG 59.017 44.000 0.00 0.00 42.61 1.85
2504 2735 5.894393 ACATAGTCAGCCTCTTAGCTTAAGA 59.106 40.000 6.67 0.00 42.61 2.10
2505 2736 6.553100 ACATAGTCAGCCTCTTAGCTTAAGAT 59.447 38.462 6.67 1.53 42.61 2.40
2506 2737 7.726291 ACATAGTCAGCCTCTTAGCTTAAGATA 59.274 37.037 6.67 0.26 42.61 1.98
2507 2738 8.580720 CATAGTCAGCCTCTTAGCTTAAGATAA 58.419 37.037 12.36 12.36 42.61 1.75
2508 2739 7.049799 AGTCAGCCTCTTAGCTTAAGATAAG 57.950 40.000 27.22 27.22 42.61 1.73
2509 2740 6.041523 AGTCAGCCTCTTAGCTTAAGATAAGG 59.958 42.308 30.39 21.76 42.61 2.69
2510 2741 5.305644 TCAGCCTCTTAGCTTAAGATAAGGG 59.694 44.000 30.39 28.58 42.47 3.95
2513 2744 4.900684 CTCTTAGCTTAAGATAAGGGGGC 58.099 47.826 30.39 5.22 43.32 5.80
2514 2745 4.303794 TCTTAGCTTAAGATAAGGGGGCA 58.696 43.478 30.39 14.96 42.47 5.36
2515 2746 4.102681 TCTTAGCTTAAGATAAGGGGGCAC 59.897 45.833 30.39 1.22 42.47 5.01
2516 2747 2.205342 AGCTTAAGATAAGGGGGCACA 58.795 47.619 6.67 0.00 0.00 4.57
2517 2748 2.580783 AGCTTAAGATAAGGGGGCACAA 59.419 45.455 6.67 0.00 0.00 3.33
2518 2749 3.205282 AGCTTAAGATAAGGGGGCACAAT 59.795 43.478 6.67 0.00 0.00 2.71
2519 2750 3.960755 GCTTAAGATAAGGGGGCACAATT 59.039 43.478 6.67 0.00 0.00 2.32
2520 2751 4.405680 GCTTAAGATAAGGGGGCACAATTT 59.594 41.667 6.67 0.00 0.00 1.82
2521 2752 5.104941 GCTTAAGATAAGGGGGCACAATTTT 60.105 40.000 6.67 0.00 0.00 1.82
2522 2753 6.576244 GCTTAAGATAAGGGGGCACAATTTTT 60.576 38.462 6.67 0.00 0.00 1.94
2552 2783 8.688747 ATCAAAGATATGATGACTTTTCCCTC 57.311 34.615 0.00 0.00 38.59 4.30
2553 2784 7.056635 TCAAAGATATGATGACTTTTCCCTCC 58.943 38.462 0.00 0.00 32.59 4.30
2554 2785 5.574970 AGATATGATGACTTTTCCCTCCC 57.425 43.478 0.00 0.00 0.00 4.30
2555 2786 4.352298 AGATATGATGACTTTTCCCTCCCC 59.648 45.833 0.00 0.00 0.00 4.81
2556 2787 2.059756 TGATGACTTTTCCCTCCCCT 57.940 50.000 0.00 0.00 0.00 4.79
2557 2788 1.916181 TGATGACTTTTCCCTCCCCTC 59.084 52.381 0.00 0.00 0.00 4.30
2558 2789 1.916181 GATGACTTTTCCCTCCCCTCA 59.084 52.381 0.00 0.00 0.00 3.86
2559 2790 1.827792 TGACTTTTCCCTCCCCTCAA 58.172 50.000 0.00 0.00 0.00 3.02
2560 2791 2.140224 TGACTTTTCCCTCCCCTCAAA 58.860 47.619 0.00 0.00 0.00 2.69
2561 2792 2.516277 TGACTTTTCCCTCCCCTCAAAA 59.484 45.455 0.00 0.00 0.00 2.44
2562 2793 3.052490 TGACTTTTCCCTCCCCTCAAAAA 60.052 43.478 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.228925 CGGTAACTACCTAGGAGCCTC 58.771 57.143 17.98 1.06 44.25 4.70
239 246 3.092301 GCTGCCCTCCTTTTCATAAACT 58.908 45.455 0.00 0.00 0.00 2.66
283 290 2.096496 GCTGGTCATGTACAGATTGCAC 59.904 50.000 18.93 0.00 36.86 4.57
324 337 0.032678 CGATATCCAGCGGCACTTCT 59.967 55.000 1.45 0.00 0.00 2.85
389 402 6.833342 AATGTGAAGCTTGTTTCATGTTTC 57.167 33.333 2.10 5.69 39.13 2.78
393 406 5.107607 GCTGAAATGTGAAGCTTGTTTCATG 60.108 40.000 18.39 14.95 39.13 3.07
471 485 4.177537 TGTTCAATGAGACCTTTTCCCA 57.822 40.909 0.00 0.00 0.00 4.37
472 486 5.728637 ATTGTTCAATGAGACCTTTTCCC 57.271 39.130 0.00 0.00 0.00 3.97
475 489 8.463930 TCTGTTATTGTTCAATGAGACCTTTT 57.536 30.769 8.11 0.00 0.00 2.27
479 493 9.696917 ATTTTTCTGTTATTGTTCAATGAGACC 57.303 29.630 8.11 0.00 0.00 3.85
505 522 5.762711 TCAAACGATCCTCATCTTCAAACAA 59.237 36.000 0.00 0.00 0.00 2.83
598 615 3.415457 TCACTTGCACCATACATGTGA 57.585 42.857 9.11 8.00 44.89 3.58
617 634 1.739562 CGTCTGGCAGGCAGAGTTC 60.740 63.158 26.45 14.14 0.00 3.01
740 757 3.473923 TGCATGTCGTGATATCCATGT 57.526 42.857 16.31 0.00 37.57 3.21
750 767 0.316442 GCGATGGATTGCATGTCGTG 60.316 55.000 0.00 0.00 37.15 4.35
751 768 0.462581 AGCGATGGATTGCATGTCGT 60.463 50.000 0.00 0.00 39.70 4.34
752 769 0.659427 AAGCGATGGATTGCATGTCG 59.341 50.000 0.00 0.00 39.70 4.35
837 909 1.503542 GCAACGCAGGATTGTGGAG 59.496 57.895 0.00 0.00 39.15 3.86
843 915 2.044946 GGAGGGCAACGCAGGATT 60.045 61.111 0.00 0.00 37.60 3.01
844 916 3.329889 TGGAGGGCAACGCAGGAT 61.330 61.111 0.00 0.00 37.60 3.24
845 917 4.329545 GTGGAGGGCAACGCAGGA 62.330 66.667 0.00 0.00 37.60 3.86
846 918 4.641645 TGTGGAGGGCAACGCAGG 62.642 66.667 0.00 0.00 37.60 4.85
847 919 1.926511 GATTGTGGAGGGCAACGCAG 61.927 60.000 0.00 0.00 37.60 5.18
848 920 1.971167 GATTGTGGAGGGCAACGCA 60.971 57.895 0.00 0.00 37.60 5.24
849 921 2.877691 GATTGTGGAGGGCAACGC 59.122 61.111 0.00 0.00 37.60 4.84
850 922 1.361668 CTCGATTGTGGAGGGCAACG 61.362 60.000 0.00 0.00 37.60 4.10
851 923 0.036388 TCTCGATTGTGGAGGGCAAC 60.036 55.000 0.00 0.00 32.34 4.17
852 924 0.036388 GTCTCGATTGTGGAGGGCAA 60.036 55.000 0.00 0.00 32.34 4.52
853 925 1.596934 GTCTCGATTGTGGAGGGCA 59.403 57.895 0.00 0.00 32.34 5.36
854 926 1.519455 CGTCTCGATTGTGGAGGGC 60.519 63.158 0.00 0.00 32.34 5.19
867 939 1.453155 AAATCACCATGTGCCGTCTC 58.547 50.000 0.00 0.00 32.98 3.36
965 1150 6.385649 TCTTGTATTTGTTGTTTCCTCCAC 57.614 37.500 0.00 0.00 0.00 4.02
1151 1338 0.548926 TGGGTCTAGGCCATGGTCAA 60.549 55.000 20.74 0.00 0.00 3.18
1152 1339 0.982852 CTGGGTCTAGGCCATGGTCA 60.983 60.000 20.74 3.57 0.00 4.02
1184 1371 5.050227 CGGTCGATTGTGTTTACCAAGTAAA 60.050 40.000 0.00 0.00 35.92 2.01
1296 1490 1.177401 CAGTGAGGTCCGATGTCAGA 58.823 55.000 0.00 0.00 0.00 3.27
1297 1491 0.459237 GCAGTGAGGTCCGATGTCAG 60.459 60.000 0.00 0.00 0.00 3.51
1549 1743 0.885150 TTTGCATACGGGCACGACAA 60.885 50.000 19.19 11.22 44.86 3.18
1550 1744 0.675208 ATTTGCATACGGGCACGACA 60.675 50.000 19.19 4.42 44.86 4.35
1622 1818 2.031682 CCCAAACGAGCAAGAAACAGAG 60.032 50.000 0.00 0.00 0.00 3.35
1651 1847 8.868522 ACAGAAATTCCAGATACATCTCAAAA 57.131 30.769 0.00 0.00 34.22 2.44
1727 1923 7.463961 TCCTCGTATAAAACTCTGAAGTCTT 57.536 36.000 0.00 0.00 33.48 3.01
1765 1961 6.173339 ACACTTTTCTGAAACTTGTCTGAGA 58.827 36.000 1.58 0.00 0.00 3.27
1783 1979 3.006323 TGTGTGCTGAAAACCAACACTTT 59.994 39.130 5.90 0.00 41.26 2.66
1791 1987 4.142469 ACTTGTACTTGTGTGCTGAAAACC 60.142 41.667 0.00 0.00 0.00 3.27
1799 1995 4.811555 TGAATGACTTGTACTTGTGTGC 57.188 40.909 0.00 0.00 0.00 4.57
1815 2011 6.558771 TTACGGCCTGATAAATCATGAATG 57.441 37.500 0.00 0.00 36.02 2.67
1816 2012 6.151648 CCATTACGGCCTGATAAATCATGAAT 59.848 38.462 0.00 0.00 36.02 2.57
1817 2013 5.473162 CCATTACGGCCTGATAAATCATGAA 59.527 40.000 0.00 0.00 36.02 2.57
1818 2014 5.003160 CCATTACGGCCTGATAAATCATGA 58.997 41.667 0.00 0.00 36.02 3.07
1819 2015 4.761739 ACCATTACGGCCTGATAAATCATG 59.238 41.667 0.00 0.00 39.03 3.07
1820 2016 4.985538 ACCATTACGGCCTGATAAATCAT 58.014 39.130 0.00 0.00 39.03 2.45
1821 2017 4.431416 ACCATTACGGCCTGATAAATCA 57.569 40.909 0.00 0.00 39.03 2.57
1822 2018 5.767816 AAACCATTACGGCCTGATAAATC 57.232 39.130 0.00 0.00 39.03 2.17
1823 2019 7.833285 AATAAACCATTACGGCCTGATAAAT 57.167 32.000 0.00 0.00 39.03 1.40
1824 2020 7.648039 AAATAAACCATTACGGCCTGATAAA 57.352 32.000 0.00 0.00 39.03 1.40
1825 2021 7.774157 TGTAAATAAACCATTACGGCCTGATAA 59.226 33.333 0.00 0.00 39.03 1.75
1826 2022 7.227116 GTGTAAATAAACCATTACGGCCTGATA 59.773 37.037 0.00 0.00 39.03 2.15
1827 2023 6.038936 GTGTAAATAAACCATTACGGCCTGAT 59.961 38.462 0.00 0.00 39.03 2.90
1828 2024 5.354792 GTGTAAATAAACCATTACGGCCTGA 59.645 40.000 0.00 0.00 39.03 3.86
1829 2025 5.124138 TGTGTAAATAAACCATTACGGCCTG 59.876 40.000 0.00 0.00 39.03 4.85
1830 2026 5.254901 TGTGTAAATAAACCATTACGGCCT 58.745 37.500 0.00 0.00 39.03 5.19
1841 2037 5.074804 ACCTGAACCCCTGTGTAAATAAAC 58.925 41.667 0.00 0.00 0.00 2.01
1852 2048 1.852067 CGCGAAAACCTGAACCCCTG 61.852 60.000 0.00 0.00 0.00 4.45
1873 2073 3.157087 CACAAACCCTAGCAAATCACCT 58.843 45.455 0.00 0.00 0.00 4.00
1885 2085 0.693049 CTACCAGAGCCACAAACCCT 59.307 55.000 0.00 0.00 0.00 4.34
1939 2139 7.165460 TCTTTGACGTCCAGATAATCTTACA 57.835 36.000 14.12 0.00 0.00 2.41
1993 2193 5.810074 CCAGAACGGAAAACAAGACAAAATT 59.190 36.000 0.00 0.00 36.56 1.82
2051 2251 7.228308 ACTTCTTTCTCAGATCCTTTTCTGTTG 59.772 37.037 1.76 0.00 43.02 3.33
2052 2252 7.286313 ACTTCTTTCTCAGATCCTTTTCTGTT 58.714 34.615 1.76 0.00 43.02 3.16
2053 2253 6.836242 ACTTCTTTCTCAGATCCTTTTCTGT 58.164 36.000 1.76 0.00 43.02 3.41
2054 2254 7.583230 CAACTTCTTTCTCAGATCCTTTTCTG 58.417 38.462 0.00 0.00 43.70 3.02
2055 2255 6.206438 GCAACTTCTTTCTCAGATCCTTTTCT 59.794 38.462 0.00 0.00 0.00 2.52
2056 2256 6.377780 GCAACTTCTTTCTCAGATCCTTTTC 58.622 40.000 0.00 0.00 0.00 2.29
2057 2257 5.242615 GGCAACTTCTTTCTCAGATCCTTTT 59.757 40.000 0.00 0.00 0.00 2.27
2058 2258 4.764308 GGCAACTTCTTTCTCAGATCCTTT 59.236 41.667 0.00 0.00 0.00 3.11
2059 2259 4.331108 GGCAACTTCTTTCTCAGATCCTT 58.669 43.478 0.00 0.00 0.00 3.36
2060 2260 3.949132 GGCAACTTCTTTCTCAGATCCT 58.051 45.455 0.00 0.00 0.00 3.24
2124 2324 6.838612 AGCCCCTTATGCAAACAAGAATAATA 59.161 34.615 0.00 0.00 0.00 0.98
2125 2325 5.662657 AGCCCCTTATGCAAACAAGAATAAT 59.337 36.000 0.00 0.00 0.00 1.28
2128 2328 3.444029 AGCCCCTTATGCAAACAAGAAT 58.556 40.909 0.00 0.00 0.00 2.40
2131 2335 2.427095 GGTAGCCCCTTATGCAAACAAG 59.573 50.000 0.00 0.00 0.00 3.16
2194 2425 3.726291 TTTGTTGGCCTCTGCTTAAAC 57.274 42.857 3.32 0.00 37.74 2.01
2203 2434 2.814336 CTCTACTGGTTTTGTTGGCCTC 59.186 50.000 3.32 0.00 0.00 4.70
2250 2481 9.602568 TTAAAGCCACGACAAGTAATATGAATA 57.397 29.630 0.00 0.00 0.00 1.75
2252 2483 7.908827 TTAAAGCCACGACAAGTAATATGAA 57.091 32.000 0.00 0.00 0.00 2.57
2268 2499 6.885952 TGTACTAAAGTTGCATTAAAGCCA 57.114 33.333 0.00 0.00 0.00 4.75
2403 2634 7.339721 CAGGAAGGACTCACTGTATTCTTAGTA 59.660 40.741 0.00 0.00 0.00 1.82
2416 2647 1.633774 TCTGGTCAGGAAGGACTCAC 58.366 55.000 0.00 0.00 37.91 3.51
2482 2713 8.713708 TTATCTTAAGCTAAGAGGCTGACTAT 57.286 34.615 0.00 0.00 46.90 2.12
2483 2714 7.231722 CCTTATCTTAAGCTAAGAGGCTGACTA 59.768 40.741 22.05 0.00 46.90 2.59
2484 2715 6.041523 CCTTATCTTAAGCTAAGAGGCTGACT 59.958 42.308 22.05 0.00 46.90 3.41
2485 2716 6.220201 CCTTATCTTAAGCTAAGAGGCTGAC 58.780 44.000 22.05 0.00 46.90 3.51
2486 2717 5.305644 CCCTTATCTTAAGCTAAGAGGCTGA 59.694 44.000 22.05 0.00 46.90 4.26
2487 2718 5.512232 CCCCTTATCTTAAGCTAAGAGGCTG 60.512 48.000 22.05 9.03 46.90 4.85
2488 2719 4.595350 CCCCTTATCTTAAGCTAAGAGGCT 59.405 45.833 22.05 0.00 46.90 4.58
2489 2720 4.263112 CCCCCTTATCTTAAGCTAAGAGGC 60.263 50.000 22.05 0.00 46.90 4.70
2490 2721 4.263112 GCCCCCTTATCTTAAGCTAAGAGG 60.263 50.000 22.05 18.97 46.90 3.69
2491 2722 4.348168 TGCCCCCTTATCTTAAGCTAAGAG 59.652 45.833 22.05 12.44 46.90 2.85
2493 2724 4.141482 TGTGCCCCCTTATCTTAAGCTAAG 60.141 45.833 16.01 16.01 37.13 2.18
2494 2725 3.783642 TGTGCCCCCTTATCTTAAGCTAA 59.216 43.478 0.00 0.00 0.00 3.09
2495 2726 3.389866 TGTGCCCCCTTATCTTAAGCTA 58.610 45.455 0.00 0.00 0.00 3.32
2496 2727 2.205342 TGTGCCCCCTTATCTTAAGCT 58.795 47.619 0.00 0.00 0.00 3.74
2497 2728 2.729028 TGTGCCCCCTTATCTTAAGC 57.271 50.000 0.00 0.00 0.00 3.09
2498 2729 6.544928 AAAATTGTGCCCCCTTATCTTAAG 57.455 37.500 0.00 0.00 0.00 1.85
2499 2730 6.943899 AAAAATTGTGCCCCCTTATCTTAA 57.056 33.333 0.00 0.00 0.00 1.85
2526 2757 9.784531 GAGGGAAAAGTCATCATATCTTTGATA 57.215 33.333 0.00 0.00 34.59 2.15
2527 2758 7.723172 GGAGGGAAAAGTCATCATATCTTTGAT 59.277 37.037 0.00 0.00 36.79 2.57
2528 2759 7.056635 GGAGGGAAAAGTCATCATATCTTTGA 58.943 38.462 0.00 0.00 32.74 2.69
2529 2760 6.264067 GGGAGGGAAAAGTCATCATATCTTTG 59.736 42.308 0.00 0.00 32.74 2.77
2530 2761 6.368805 GGGAGGGAAAAGTCATCATATCTTT 58.631 40.000 0.00 0.00 33.61 2.52
2531 2762 5.163045 GGGGAGGGAAAAGTCATCATATCTT 60.163 44.000 0.00 0.00 0.00 2.40
2532 2763 4.352298 GGGGAGGGAAAAGTCATCATATCT 59.648 45.833 0.00 0.00 0.00 1.98
2533 2764 4.352298 AGGGGAGGGAAAAGTCATCATATC 59.648 45.833 0.00 0.00 0.00 1.63
2534 2765 4.319515 AGGGGAGGGAAAAGTCATCATAT 58.680 43.478 0.00 0.00 0.00 1.78
2535 2766 3.716872 GAGGGGAGGGAAAAGTCATCATA 59.283 47.826 0.00 0.00 0.00 2.15
2536 2767 2.511637 GAGGGGAGGGAAAAGTCATCAT 59.488 50.000 0.00 0.00 0.00 2.45
2537 2768 1.916181 GAGGGGAGGGAAAAGTCATCA 59.084 52.381 0.00 0.00 0.00 3.07
2538 2769 1.916181 TGAGGGGAGGGAAAAGTCATC 59.084 52.381 0.00 0.00 0.00 2.92
2539 2770 2.059756 TGAGGGGAGGGAAAAGTCAT 57.940 50.000 0.00 0.00 0.00 3.06
2540 2771 1.827792 TTGAGGGGAGGGAAAAGTCA 58.172 50.000 0.00 0.00 0.00 3.41
2541 2772 2.971901 TTTGAGGGGAGGGAAAAGTC 57.028 50.000 0.00 0.00 0.00 3.01
2542 2773 3.699025 TTTTTGAGGGGAGGGAAAAGT 57.301 42.857 0.00 0.00 0.00 2.66



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

AutoCloner maintained by Alex Coulton.