Multiple sequence alignment - TraesCS3D01G299300

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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 TraesCS3D01G299300 chr3D 100.000 3375 0 0 1 3375 414629618 414626244 0.000000e+00 6233.0
1 TraesCS3D01G299300 chr3B 94.743 2644 63 25 1 2616 540457168 540454573 0.000000e+00 4043.0
2 TraesCS3D01G299300 chr3B 93.396 636 39 3 2742 3375 540454560 540453926 0.000000e+00 939.0
3 TraesCS3D01G299300 chr3B 88.806 134 13 2 2626 2758 79116998 79117130 2.690000e-36 163.0
4 TraesCS3D01G299300 chr3A 94.737 2641 68 20 1 2595 535823537 535826152 0.000000e+00 4041.0
5 TraesCS3D01G299300 chr3A 90.926 540 40 7 2841 3375 535847133 535847668 0.000000e+00 717.0
6 TraesCS3D01G299300 chr1D 85.838 346 49 0 4 349 470081457 470081112 5.320000e-98 368.0
7 TraesCS3D01G299300 chr1D 76.821 151 27 7 1602 1745 155736961 155736812 1.000000e-10 78.7
8 TraesCS3D01G299300 chr2D 83.333 378 55 5 1 377 502574570 502574200 3.220000e-90 342.0
9 TraesCS3D01G299300 chr2D 90.400 125 11 1 2626 2750 420523723 420523846 2.690000e-36 163.0
10 TraesCS3D01G299300 chr2D 74.286 210 47 6 1908 2114 136832840 136833045 7.760000e-12 82.4
11 TraesCS3D01G299300 chr1A 82.732 388 57 7 4 385 563791754 563791371 1.500000e-88 337.0
12 TraesCS3D01G299300 chr1A 80.747 348 58 7 4 348 563770062 563769721 2.580000e-66 263.0
13 TraesCS3D01G299300 chr1A 77.844 167 29 6 1586 1745 185117755 185117920 2.770000e-16 97.1
14 TraesCS3D01G299300 chr2A 82.540 378 58 8 1 377 648027654 648027284 3.250000e-85 326.0
15 TraesCS3D01G299300 chr2A 75.132 189 40 6 1929 2114 164704305 164704121 7.760000e-12 82.4
16 TraesCS3D01G299300 chr2B 82.275 378 59 6 1 377 590228812 590228442 1.510000e-83 320.0
17 TraesCS3D01G299300 chr1B 83.478 345 54 2 4 348 652570322 652569981 5.430000e-83 318.0
18 TraesCS3D01G299300 chr1B 83.333 348 49 7 4 348 652468086 652467745 2.530000e-81 313.0
19 TraesCS3D01G299300 chr1B 81.600 375 63 4 1 369 652460125 652459751 4.230000e-79 305.0
20 TraesCS3D01G299300 chr1B 81.897 348 54 8 4 348 652519006 652518665 5.510000e-73 285.0
21 TraesCS3D01G299300 chr1B 78.710 155 24 7 1586 1733 236953778 236953930 9.970000e-16 95.3
22 TraesCS3D01G299300 chr6D 93.162 117 8 0 2626 2742 379516967 379516851 4.480000e-39 172.0
23 TraesCS3D01G299300 chr6A 93.043 115 7 1 2626 2740 22166224 22166337 2.080000e-37 167.0
24 TraesCS3D01G299300 chr6A 90.909 121 10 1 2626 2746 610391398 610391279 9.690000e-36 161.0
25 TraesCS3D01G299300 chr5D 90.984 122 11 0 2626 2747 478215940 478215819 7.490000e-37 165.0
26 TraesCS3D01G299300 chr6B 92.174 115 8 1 2626 2740 468305576 468305689 9.690000e-36 161.0
27 TraesCS3D01G299300 chr5B 90.833 120 11 0 2627 2746 219989670 219989551 9.690000e-36 161.0
28 TraesCS3D01G299300 chr4D 87.970 133 13 3 2626 2755 77835728 77835596 1.620000e-33 154.0


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 TraesCS3D01G299300 chr3D 414626244 414629618 3374 True 6233 6233 100.0000 1 3375 1 chr3D.!!$R1 3374
1 TraesCS3D01G299300 chr3B 540453926 540457168 3242 True 2491 4043 94.0695 1 3375 2 chr3B.!!$R1 3374
2 TraesCS3D01G299300 chr3A 535823537 535826152 2615 False 4041 4041 94.7370 1 2595 1 chr3A.!!$F1 2594
3 TraesCS3D01G299300 chr3A 535847133 535847668 535 False 717 717 90.9260 2841 3375 1 chr3A.!!$F2 534

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
472 478 0.108329 CACGGTTCCGCAGATAAGGT 60.108 55.0 11.32 0.0 0.0 3.5 F
907 946 0.324830 CCTCTCGTTCCTTCCTCCCT 60.325 60.0 0.00 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 1959 0.032678 CCTTCTCGCCGATGCATACT 59.967 55.0 0.0 0.0 37.32 2.12 R
2797 2859 0.632294 ACCTGGGAGGACCTAGAGTC 59.368 60.0 0.0 0.0 45.87 3.36 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
23 24 3.999297 GACGCGGGAGAGAGGAGGT 62.999 68.421 12.47 0.00 0.00 3.85
224 225 3.241530 TGCAGGCGGAGGAACTGT 61.242 61.111 0.00 0.00 41.55 3.55
461 467 4.322385 GTTGGCGTGCACGGTTCC 62.322 66.667 37.47 29.57 40.23 3.62
468 474 1.447140 GTGCACGGTTCCGCAGATA 60.447 57.895 11.32 0.00 39.20 1.98
469 475 1.017177 GTGCACGGTTCCGCAGATAA 61.017 55.000 11.32 0.00 39.20 1.75
472 478 0.108329 CACGGTTCCGCAGATAAGGT 60.108 55.000 11.32 0.00 0.00 3.50
541 547 1.333177 GCATACCGGATCTCAGAGGT 58.667 55.000 9.46 0.00 40.52 3.85
719 748 2.560861 CGGGCCGTGTGATGTTTG 59.439 61.111 19.97 0.00 0.00 2.93
907 946 0.324830 CCTCTCGTTCCTTCCTCCCT 60.325 60.000 0.00 0.00 0.00 4.20
908 947 1.562783 CTCTCGTTCCTTCCTCCCTT 58.437 55.000 0.00 0.00 0.00 3.95
909 948 1.478916 CTCTCGTTCCTTCCTCCCTTC 59.521 57.143 0.00 0.00 0.00 3.46
910 949 0.537653 CTCGTTCCTTCCTCCCTTCC 59.462 60.000 0.00 0.00 0.00 3.46
937 976 1.075600 CTCTCCCTCCCACTCTCCC 60.076 68.421 0.00 0.00 0.00 4.30
1021 1074 2.281484 GGAAGCTGTGCCCGAACA 60.281 61.111 0.00 0.00 0.00 3.18
1429 1485 4.961511 AAGCAAGCGTCGACGGCA 62.962 61.111 36.13 0.00 40.23 5.69
1781 1837 2.743838 CGCCCACGTATCCTACCAATTT 60.744 50.000 0.00 0.00 33.53 1.82
1782 1838 2.616842 GCCCACGTATCCTACCAATTTG 59.383 50.000 0.00 0.00 0.00 2.32
1783 1839 3.683281 GCCCACGTATCCTACCAATTTGA 60.683 47.826 0.00 0.00 0.00 2.69
1784 1840 3.875134 CCCACGTATCCTACCAATTTGAC 59.125 47.826 0.00 0.00 0.00 3.18
1785 1841 4.509616 CCACGTATCCTACCAATTTGACA 58.490 43.478 0.00 0.00 0.00 3.58
1786 1842 5.123227 CCACGTATCCTACCAATTTGACAT 58.877 41.667 0.00 0.00 0.00 3.06
1787 1843 5.007626 CCACGTATCCTACCAATTTGACATG 59.992 44.000 0.00 0.00 0.00 3.21
1788 1844 5.584649 CACGTATCCTACCAATTTGACATGT 59.415 40.000 0.00 0.00 0.00 3.21
1789 1845 6.759356 CACGTATCCTACCAATTTGACATGTA 59.241 38.462 0.00 0.00 0.00 2.29
1790 1846 6.759827 ACGTATCCTACCAATTTGACATGTAC 59.240 38.462 0.00 0.00 0.00 2.90
1791 1847 6.984474 CGTATCCTACCAATTTGACATGTACT 59.016 38.462 0.00 0.00 0.00 2.73
1870 1926 3.415087 GGCCTGCAGGGTCTGGAT 61.415 66.667 33.46 0.00 36.61 3.41
1903 1959 1.585006 GAACCTCTTCTCCGACGCA 59.415 57.895 0.00 0.00 0.00 5.24
2227 2283 1.064296 CGTCACGCTCTTCCGCTAT 59.936 57.895 0.00 0.00 0.00 2.97
2396 2452 1.257936 CGGACACCGCGAATAATCAAG 59.742 52.381 8.23 0.00 41.17 3.02
2397 2453 2.277084 GGACACCGCGAATAATCAAGT 58.723 47.619 8.23 0.00 0.00 3.16
2421 2477 2.268298 CTCGCGGTAGTGCTAATTTGT 58.732 47.619 6.13 0.00 0.00 2.83
2458 2519 5.366482 TCCAAGGACATCGAAATCCATTA 57.634 39.130 17.89 1.33 37.47 1.90
2459 2520 5.750524 TCCAAGGACATCGAAATCCATTAA 58.249 37.500 17.89 1.65 37.47 1.40
2460 2521 6.364701 TCCAAGGACATCGAAATCCATTAAT 58.635 36.000 17.89 0.00 37.47 1.40
2461 2522 6.833416 TCCAAGGACATCGAAATCCATTAATT 59.167 34.615 17.89 3.35 37.47 1.40
2595 2657 7.716998 TCTTATCTCTTCTATGGGAAAACATGC 59.283 37.037 0.00 0.00 33.07 4.06
2596 2658 5.178096 TCTCTTCTATGGGAAAACATGCA 57.822 39.130 0.00 0.00 33.07 3.96
2597 2659 5.759059 TCTCTTCTATGGGAAAACATGCAT 58.241 37.500 0.00 0.00 33.07 3.96
2598 2660 5.591472 TCTCTTCTATGGGAAAACATGCATG 59.409 40.000 25.09 25.09 33.07 4.06
2599 2661 5.263599 TCTTCTATGGGAAAACATGCATGT 58.736 37.500 26.61 26.61 44.20 3.21
2608 2670 5.039333 GGAAAACATGCATGTCTATGAAGC 58.961 41.667 31.45 14.65 40.80 3.86
2611 2673 3.211865 ACATGCATGTCTATGAAGCAGG 58.788 45.455 26.61 0.00 42.08 4.85
2616 2678 4.346127 TGCATGTCTATGAAGCAGGAGTAT 59.654 41.667 0.00 0.00 36.36 2.12
2618 2680 6.041979 TGCATGTCTATGAAGCAGGAGTATAA 59.958 38.462 0.00 0.00 36.36 0.98
2619 2681 6.589523 GCATGTCTATGAAGCAGGAGTATAAG 59.410 42.308 0.00 0.00 36.36 1.73
2620 2682 7.665690 CATGTCTATGAAGCAGGAGTATAAGT 58.334 38.462 0.00 0.00 36.36 2.24
2621 2683 7.278461 TGTCTATGAAGCAGGAGTATAAGTC 57.722 40.000 0.00 0.00 0.00 3.01
2623 2685 7.561722 TGTCTATGAAGCAGGAGTATAAGTCTT 59.438 37.037 0.00 0.00 0.00 3.01
2625 2687 8.417106 TCTATGAAGCAGGAGTATAAGTCTTTG 58.583 37.037 0.00 0.00 0.00 2.77
2626 2688 6.605471 TGAAGCAGGAGTATAAGTCTTTGA 57.395 37.500 0.00 0.00 0.00 2.69
2627 2689 6.398918 TGAAGCAGGAGTATAAGTCTTTGAC 58.601 40.000 0.00 0.00 0.00 3.18
2628 2690 5.346181 AGCAGGAGTATAAGTCTTTGACC 57.654 43.478 0.00 0.00 32.18 4.02
2629 2691 4.777896 AGCAGGAGTATAAGTCTTTGACCA 59.222 41.667 0.00 0.00 32.18 4.02
2630 2692 4.870991 GCAGGAGTATAAGTCTTTGACCAC 59.129 45.833 0.00 0.00 32.18 4.16
2631 2693 5.568825 GCAGGAGTATAAGTCTTTGACCACA 60.569 44.000 0.00 0.00 32.18 4.17
2632 2694 6.644347 CAGGAGTATAAGTCTTTGACCACAT 58.356 40.000 0.00 0.00 32.18 3.21
2633 2695 7.632898 GCAGGAGTATAAGTCTTTGACCACATA 60.633 40.741 0.00 0.00 32.18 2.29
2634 2696 7.707035 CAGGAGTATAAGTCTTTGACCACATAC 59.293 40.741 0.00 0.00 32.18 2.39
2635 2697 6.696148 GGAGTATAAGTCTTTGACCACATACG 59.304 42.308 0.00 0.00 31.88 3.06
2636 2698 6.570692 AGTATAAGTCTTTGACCACATACGG 58.429 40.000 0.00 0.00 31.88 4.02
2637 2699 5.670792 ATAAGTCTTTGACCACATACGGA 57.329 39.130 0.00 0.00 32.18 4.69
2638 2700 3.594603 AGTCTTTGACCACATACGGAG 57.405 47.619 0.00 0.00 32.18 4.63
2639 2701 2.000447 GTCTTTGACCACATACGGAGC 59.000 52.381 0.00 0.00 0.00 4.70
2640 2702 1.621317 TCTTTGACCACATACGGAGCA 59.379 47.619 0.00 0.00 0.00 4.26
2641 2703 2.037902 TCTTTGACCACATACGGAGCAA 59.962 45.455 0.00 0.00 0.00 3.91
2642 2704 2.552599 TTGACCACATACGGAGCAAA 57.447 45.000 0.00 0.00 0.00 3.68
2643 2705 2.552599 TGACCACATACGGAGCAAAA 57.447 45.000 0.00 0.00 0.00 2.44
2644 2706 3.066291 TGACCACATACGGAGCAAAAT 57.934 42.857 0.00 0.00 0.00 1.82
2645 2707 3.417101 TGACCACATACGGAGCAAAATT 58.583 40.909 0.00 0.00 0.00 1.82
2646 2708 4.580868 TGACCACATACGGAGCAAAATTA 58.419 39.130 0.00 0.00 0.00 1.40
2647 2709 4.634004 TGACCACATACGGAGCAAAATTAG 59.366 41.667 0.00 0.00 0.00 1.73
2648 2710 4.585879 ACCACATACGGAGCAAAATTAGT 58.414 39.130 0.00 0.00 0.00 2.24
2649 2711 5.736813 ACCACATACGGAGCAAAATTAGTA 58.263 37.500 0.00 0.00 0.00 1.82
2650 2712 6.174760 ACCACATACGGAGCAAAATTAGTAA 58.825 36.000 0.00 0.00 0.00 2.24
2651 2713 6.655848 ACCACATACGGAGCAAAATTAGTAAA 59.344 34.615 0.00 0.00 0.00 2.01
2652 2714 7.338449 ACCACATACGGAGCAAAATTAGTAAAT 59.662 33.333 0.00 0.00 0.00 1.40
2653 2715 7.855904 CCACATACGGAGCAAAATTAGTAAATC 59.144 37.037 0.00 0.00 0.00 2.17
2654 2716 8.612619 CACATACGGAGCAAAATTAGTAAATCT 58.387 33.333 0.00 0.00 0.00 2.40
2655 2717 9.826574 ACATACGGAGCAAAATTAGTAAATCTA 57.173 29.630 0.00 0.00 0.00 1.98
2657 2719 9.826574 ATACGGAGCAAAATTAGTAAATCTACA 57.173 29.630 0.00 0.00 0.00 2.74
2658 2720 7.971455 ACGGAGCAAAATTAGTAAATCTACAC 58.029 34.615 0.00 0.00 0.00 2.90
2659 2721 7.822822 ACGGAGCAAAATTAGTAAATCTACACT 59.177 33.333 0.00 0.00 0.00 3.55
2660 2722 8.328864 CGGAGCAAAATTAGTAAATCTACACTC 58.671 37.037 0.00 0.00 0.00 3.51
2661 2723 9.384764 GGAGCAAAATTAGTAAATCTACACTCT 57.615 33.333 0.00 0.00 0.00 3.24
2672 2734 9.726438 AGTAAATCTACACTCTAAAATGCAACT 57.274 29.630 0.00 0.00 0.00 3.16
2689 2751 9.494271 AAATGCAACTATATACATCTGTAGGTG 57.506 33.333 0.00 0.00 35.50 4.00
2690 2752 6.993079 TGCAACTATATACATCTGTAGGTGG 58.007 40.000 0.00 0.00 33.54 4.61
2691 2753 6.553476 TGCAACTATATACATCTGTAGGTGGT 59.447 38.462 0.00 0.00 33.54 4.16
2692 2754 7.091443 GCAACTATATACATCTGTAGGTGGTC 58.909 42.308 0.00 0.00 33.54 4.02
2693 2755 7.039644 GCAACTATATACATCTGTAGGTGGTCT 60.040 40.741 0.00 0.00 33.54 3.85
2694 2756 9.516546 CAACTATATACATCTGTAGGTGGTCTA 57.483 37.037 0.00 0.00 33.52 2.59
2699 2761 9.688091 ATATACATCTGTAGGTGGTCTATAGTG 57.312 37.037 0.00 0.00 38.08 2.74
2700 2762 6.014771 ACATCTGTAGGTGGTCTATAGTGA 57.985 41.667 0.00 0.00 38.08 3.41
2701 2763 6.432581 ACATCTGTAGGTGGTCTATAGTGAA 58.567 40.000 0.00 0.00 38.08 3.18
2702 2764 6.895756 ACATCTGTAGGTGGTCTATAGTGAAA 59.104 38.462 0.00 0.00 38.08 2.69
2703 2765 7.565398 ACATCTGTAGGTGGTCTATAGTGAAAT 59.435 37.037 0.00 0.00 38.08 2.17
2704 2766 7.584122 TCTGTAGGTGGTCTATAGTGAAATC 57.416 40.000 0.00 0.00 38.08 2.17
2705 2767 7.355101 TCTGTAGGTGGTCTATAGTGAAATCT 58.645 38.462 0.00 0.00 38.08 2.40
2706 2768 7.502895 TCTGTAGGTGGTCTATAGTGAAATCTC 59.497 40.741 0.00 0.00 38.08 2.75
2707 2769 7.355101 TGTAGGTGGTCTATAGTGAAATCTCT 58.645 38.462 0.00 0.00 0.00 3.10
2708 2770 8.500238 TGTAGGTGGTCTATAGTGAAATCTCTA 58.500 37.037 0.00 0.00 0.00 2.43
2709 2771 7.826918 AGGTGGTCTATAGTGAAATCTCTAC 57.173 40.000 0.00 0.00 0.00 2.59
2710 2772 7.355101 AGGTGGTCTATAGTGAAATCTCTACA 58.645 38.462 0.00 0.00 0.00 2.74
2711 2773 7.839705 AGGTGGTCTATAGTGAAATCTCTACAA 59.160 37.037 0.00 0.00 0.00 2.41
2712 2774 8.475639 GGTGGTCTATAGTGAAATCTCTACAAA 58.524 37.037 0.00 0.00 0.00 2.83
2713 2775 9.522804 GTGGTCTATAGTGAAATCTCTACAAAG 57.477 37.037 0.00 0.00 0.00 2.77
2714 2776 9.475620 TGGTCTATAGTGAAATCTCTACAAAGA 57.524 33.333 0.00 0.00 0.00 2.52
2715 2777 9.738832 GGTCTATAGTGAAATCTCTACAAAGAC 57.261 37.037 15.03 15.03 33.91 3.01
2735 2797 9.783256 CAAAGACTTATATTTAAAAACGGAGGG 57.217 33.333 0.00 0.00 0.00 4.30
2736 2798 9.743581 AAAGACTTATATTTAAAAACGGAGGGA 57.256 29.630 0.00 0.00 0.00 4.20
2737 2799 8.959705 AGACTTATATTTAAAAACGGAGGGAG 57.040 34.615 0.00 0.00 0.00 4.30
2797 2859 4.074970 ACTTGGAAATTGCTGTGGTAGAG 58.925 43.478 0.00 0.00 0.00 2.43
2865 2927 4.623167 CACTGAACGAGTACTTGAGGAATG 59.377 45.833 17.37 5.73 31.73 2.67
2888 2950 1.520494 TGAAGTCTACGCTGTCGACT 58.480 50.000 17.92 9.08 39.66 4.18
2894 2957 2.579241 CTACGCTGTCGACTCGGTGG 62.579 65.000 25.78 15.40 39.41 4.61
2959 3022 3.981071 TGGAAGAGATGGTTGTACCTG 57.019 47.619 0.00 0.00 39.58 4.00
2967 3030 3.846588 AGATGGTTGTACCTGAAGTGGAT 59.153 43.478 0.00 0.00 39.58 3.41
2978 3041 9.038072 TGTACCTGAAGTGGATAAGTAACATAA 57.962 33.333 0.00 0.00 0.00 1.90
2999 3062 3.804036 ACGTTTCAACTGAGGAACATGA 58.196 40.909 0.00 0.00 0.00 3.07
3023 3086 4.130118 ACACTGGATGAACTCTGTTTGAC 58.870 43.478 0.00 0.00 0.00 3.18
3043 3107 3.926616 ACCGGGCAATTCTAATCGATAG 58.073 45.455 6.32 0.00 0.00 2.08
3086 3150 9.914834 TTTTAGTAATGGTATATATGGCCCATC 57.085 33.333 0.00 0.00 36.69 3.51
3183 3247 4.035208 CCTTGTCACCAACTACAAACTGTC 59.965 45.833 0.00 0.00 35.32 3.51
3190 3254 4.161565 ACCAACTACAAACTGTCTGTCAGA 59.838 41.667 8.87 0.00 46.27 3.27
3203 3270 7.721402 ACTGTCTGTCAGATATGTTCTTATCC 58.279 38.462 5.68 0.00 46.27 2.59
3232 3299 5.254901 AGATTTCATCTTTTGCTGAGCTCT 58.745 37.500 16.19 0.00 35.76 4.09
3259 3326 8.725148 GTGAAGATGTTGTCTGACTAAATCAAT 58.275 33.333 19.74 11.01 36.69 2.57
3264 3331 9.979270 GATGTTGTCTGACTAAATCAATAACAG 57.021 33.333 14.83 0.00 36.69 3.16
3323 3390 2.029560 TGCTACAGTGTCAGAAGCAGAG 60.030 50.000 13.25 0.00 38.22 3.35
3368 3435 7.869429 GCTTGTCCATATAAAATCTCAAATGGG 59.131 37.037 0.00 0.00 35.61 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.553819 TCAGGCTACCTCCTCTCTCC 59.446 60.000 0.00 0.00 33.25 3.71
373 374 3.003897 CCTACTGAGTATTCTCGCAGGAC 59.996 52.174 7.51 0.00 43.09 3.85
444 450 4.322385 GGAACCGTGCACGCCAAC 62.322 66.667 33.17 21.29 38.18 3.77
472 478 1.760479 CGGTGGTGGACTGGTGGTAA 61.760 60.000 0.00 0.00 0.00 2.85
481 487 0.971386 TCTAAACTCCGGTGGTGGAC 59.029 55.000 8.63 0.00 33.48 4.02
541 547 0.839277 CCTATGACATCTGGTGCCCA 59.161 55.000 0.00 0.00 0.00 5.36
713 722 1.185315 CGGCCCATTTCTCCAAACAT 58.815 50.000 0.00 0.00 0.00 2.71
907 946 0.196118 AGGGAGAGAAACAGGGGGAA 59.804 55.000 0.00 0.00 0.00 3.97
908 947 0.252742 GAGGGAGAGAAACAGGGGGA 60.253 60.000 0.00 0.00 0.00 4.81
909 948 1.275421 GGAGGGAGAGAAACAGGGGG 61.275 65.000 0.00 0.00 0.00 5.40
910 949 1.275421 GGGAGGGAGAGAAACAGGGG 61.275 65.000 0.00 0.00 0.00 4.79
937 976 4.778415 CAGGACGCCCGACAGACG 62.778 72.222 0.00 0.00 42.18 4.18
1021 1074 2.181021 GGAGTCGTCGCGGTCATT 59.819 61.111 6.13 0.00 0.00 2.57
1143 1199 4.675029 CGGTCGAACGCCTGGGTT 62.675 66.667 11.19 0.00 0.00 4.11
1290 1346 1.475034 GCATGGCTTACGATGGAGGAA 60.475 52.381 0.00 0.00 0.00 3.36
1429 1485 6.201615 CGATGTACTGATGCATGATGTACTTT 59.798 38.462 22.66 15.34 35.76 2.66
1588 1644 3.889134 CTGCCAGAGCACGAAGCCA 62.889 63.158 0.00 0.00 46.52 4.75
1781 1837 6.095720 TGGAATACATCGTACAGTACATGTCA 59.904 38.462 21.97 15.21 42.70 3.58
1782 1838 6.417044 GTGGAATACATCGTACAGTACATGTC 59.583 42.308 21.97 13.68 42.70 3.06
1783 1839 6.270815 GTGGAATACATCGTACAGTACATGT 58.729 40.000 21.98 21.98 46.45 3.21
1784 1840 5.690409 GGTGGAATACATCGTACAGTACATG 59.310 44.000 11.37 14.11 0.00 3.21
1785 1841 5.361571 TGGTGGAATACATCGTACAGTACAT 59.638 40.000 11.37 1.34 30.79 2.29
1786 1842 4.705991 TGGTGGAATACATCGTACAGTACA 59.294 41.667 11.37 0.00 30.79 2.90
1787 1843 5.066893 TCTGGTGGAATACATCGTACAGTAC 59.933 44.000 0.00 0.00 30.79 2.73
1788 1844 5.195185 TCTGGTGGAATACATCGTACAGTA 58.805 41.667 0.00 0.00 30.79 2.74
1789 1845 4.021229 TCTGGTGGAATACATCGTACAGT 58.979 43.478 0.00 0.00 30.79 3.55
1790 1846 4.649088 TCTGGTGGAATACATCGTACAG 57.351 45.455 0.00 0.00 30.79 2.74
1791 1847 4.739436 GCATCTGGTGGAATACATCGTACA 60.739 45.833 0.00 0.00 30.79 2.90
1903 1959 0.032678 CCTTCTCGCCGATGCATACT 59.967 55.000 0.00 0.00 37.32 2.12
2396 2452 2.537792 TAGCACTACCGCGAGCACAC 62.538 60.000 8.23 0.00 36.85 3.82
2397 2453 1.868987 TTAGCACTACCGCGAGCACA 61.869 55.000 8.23 0.00 36.85 4.57
2421 2477 5.821470 TGTCCTTGGATTAACGTTGTTGTTA 59.179 36.000 11.99 0.00 33.32 2.41
2458 2519 7.554476 GTCTACAGAAAAGATTAGCCTGGAATT 59.446 37.037 0.00 0.00 0.00 2.17
2459 2520 7.051000 GTCTACAGAAAAGATTAGCCTGGAAT 58.949 38.462 0.00 0.00 0.00 3.01
2460 2521 6.407202 GTCTACAGAAAAGATTAGCCTGGAA 58.593 40.000 0.00 0.00 0.00 3.53
2461 2522 5.394224 CGTCTACAGAAAAGATTAGCCTGGA 60.394 44.000 0.00 0.00 0.00 3.86
2573 2635 5.759059 TGCATGTTTTCCCATAGAAGAGAT 58.241 37.500 0.00 0.00 35.40 2.75
2590 2652 3.118149 TCCTGCTTCATAGACATGCATGT 60.118 43.478 31.82 31.82 45.16 3.21
2595 2657 7.665690 ACTTATACTCCTGCTTCATAGACATG 58.334 38.462 0.00 0.00 0.00 3.21
2596 2658 7.728083 AGACTTATACTCCTGCTTCATAGACAT 59.272 37.037 0.00 0.00 0.00 3.06
2597 2659 7.063593 AGACTTATACTCCTGCTTCATAGACA 58.936 38.462 0.00 0.00 0.00 3.41
2598 2660 7.519032 AGACTTATACTCCTGCTTCATAGAC 57.481 40.000 0.00 0.00 0.00 2.59
2599 2661 8.417106 CAAAGACTTATACTCCTGCTTCATAGA 58.583 37.037 0.00 0.00 0.00 1.98
2608 2670 6.037786 TGTGGTCAAAGACTTATACTCCTG 57.962 41.667 0.00 0.00 32.47 3.86
2611 2673 6.696148 CCGTATGTGGTCAAAGACTTATACTC 59.304 42.308 0.00 0.00 32.47 2.59
2616 2678 4.619863 GCTCCGTATGTGGTCAAAGACTTA 60.620 45.833 0.00 0.00 32.47 2.24
2618 2680 2.353803 GCTCCGTATGTGGTCAAAGACT 60.354 50.000 0.00 0.00 32.47 3.24
2619 2681 2.000447 GCTCCGTATGTGGTCAAAGAC 59.000 52.381 0.00 0.00 0.00 3.01
2620 2682 1.621317 TGCTCCGTATGTGGTCAAAGA 59.379 47.619 0.00 0.00 0.00 2.52
2621 2683 2.093306 TGCTCCGTATGTGGTCAAAG 57.907 50.000 0.00 0.00 0.00 2.77
2623 2685 2.552599 TTTGCTCCGTATGTGGTCAA 57.447 45.000 0.00 0.00 0.00 3.18
2625 2687 4.634443 ACTAATTTTGCTCCGTATGTGGTC 59.366 41.667 0.00 0.00 0.00 4.02
2626 2688 4.585879 ACTAATTTTGCTCCGTATGTGGT 58.414 39.130 0.00 0.00 0.00 4.16
2627 2689 6.671614 TTACTAATTTTGCTCCGTATGTGG 57.328 37.500 0.00 0.00 0.00 4.17
2628 2690 8.612619 AGATTTACTAATTTTGCTCCGTATGTG 58.387 33.333 0.00 0.00 0.00 3.21
2629 2691 8.732746 AGATTTACTAATTTTGCTCCGTATGT 57.267 30.769 0.00 0.00 0.00 2.29
2631 2693 9.826574 TGTAGATTTACTAATTTTGCTCCGTAT 57.173 29.630 0.00 0.00 32.49 3.06
2632 2694 9.090692 GTGTAGATTTACTAATTTTGCTCCGTA 57.909 33.333 0.00 0.00 32.49 4.02
2633 2695 7.822822 AGTGTAGATTTACTAATTTTGCTCCGT 59.177 33.333 0.00 0.00 32.49 4.69
2634 2696 8.197988 AGTGTAGATTTACTAATTTTGCTCCG 57.802 34.615 0.00 0.00 32.49 4.63
2635 2697 9.384764 AGAGTGTAGATTTACTAATTTTGCTCC 57.615 33.333 0.00 0.00 32.49 4.70
2646 2708 9.726438 AGTTGCATTTTAGAGTGTAGATTTACT 57.274 29.630 0.00 0.00 0.00 2.24
2663 2725 9.494271 CACCTACAGATGTATATAGTTGCATTT 57.506 33.333 0.00 0.00 0.00 2.32
2664 2726 8.097038 CCACCTACAGATGTATATAGTTGCATT 58.903 37.037 0.00 0.00 0.00 3.56
2665 2727 7.235606 ACCACCTACAGATGTATATAGTTGCAT 59.764 37.037 0.00 0.00 0.00 3.96
2666 2728 6.553476 ACCACCTACAGATGTATATAGTTGCA 59.447 38.462 0.00 0.00 0.00 4.08
2667 2729 6.994221 ACCACCTACAGATGTATATAGTTGC 58.006 40.000 0.00 0.00 0.00 4.17
2668 2730 8.410673 AGACCACCTACAGATGTATATAGTTG 57.589 38.462 0.00 0.00 0.00 3.16
2673 2735 9.688091 CACTATAGACCACCTACAGATGTATAT 57.312 37.037 6.78 0.00 0.00 0.86
2674 2736 8.887393 TCACTATAGACCACCTACAGATGTATA 58.113 37.037 6.78 0.00 0.00 1.47
2675 2737 7.756614 TCACTATAGACCACCTACAGATGTAT 58.243 38.462 6.78 0.00 0.00 2.29
2676 2738 7.145474 TCACTATAGACCACCTACAGATGTA 57.855 40.000 6.78 0.00 0.00 2.29
2677 2739 6.014771 TCACTATAGACCACCTACAGATGT 57.985 41.667 6.78 0.00 0.00 3.06
2678 2740 6.961360 TTCACTATAGACCACCTACAGATG 57.039 41.667 6.78 0.00 0.00 2.90
2679 2741 8.007742 AGATTTCACTATAGACCACCTACAGAT 58.992 37.037 6.78 0.00 0.00 2.90
2680 2742 7.355101 AGATTTCACTATAGACCACCTACAGA 58.645 38.462 6.78 0.00 0.00 3.41
2681 2743 7.504238 AGAGATTTCACTATAGACCACCTACAG 59.496 40.741 6.78 0.00 0.00 2.74
2682 2744 7.355101 AGAGATTTCACTATAGACCACCTACA 58.645 38.462 6.78 0.00 0.00 2.74
2683 2745 7.826918 AGAGATTTCACTATAGACCACCTAC 57.173 40.000 6.78 0.00 0.00 3.18
2684 2746 8.500238 TGTAGAGATTTCACTATAGACCACCTA 58.500 37.037 6.78 0.00 0.00 3.08
2685 2747 7.355101 TGTAGAGATTTCACTATAGACCACCT 58.645 38.462 6.78 0.00 0.00 4.00
2686 2748 7.584122 TGTAGAGATTTCACTATAGACCACC 57.416 40.000 6.78 0.00 0.00 4.61
2687 2749 9.522804 CTTTGTAGAGATTTCACTATAGACCAC 57.477 37.037 6.78 0.00 0.00 4.16
2688 2750 9.475620 TCTTTGTAGAGATTTCACTATAGACCA 57.524 33.333 6.78 0.00 0.00 4.02
2689 2751 9.738832 GTCTTTGTAGAGATTTCACTATAGACC 57.261 37.037 6.78 0.00 29.69 3.85
2709 2771 9.783256 CCCTCCGTTTTTAAATATAAGTCTTTG 57.217 33.333 0.00 0.00 0.00 2.77
2710 2772 9.743581 TCCCTCCGTTTTTAAATATAAGTCTTT 57.256 29.630 0.00 0.00 0.00 2.52
2711 2773 9.392259 CTCCCTCCGTTTTTAAATATAAGTCTT 57.608 33.333 0.00 0.00 0.00 3.01
2712 2774 8.546322 ACTCCCTCCGTTTTTAAATATAAGTCT 58.454 33.333 0.00 0.00 0.00 3.24
2713 2775 8.728337 ACTCCCTCCGTTTTTAAATATAAGTC 57.272 34.615 0.00 0.00 0.00 3.01
2797 2859 0.632294 ACCTGGGAGGACCTAGAGTC 59.368 60.000 0.00 0.00 45.87 3.36
2865 2927 2.353889 TCGACAGCGTAGACTTCATACC 59.646 50.000 0.00 0.00 38.98 2.73
2959 3022 8.928733 TGAAACGTTATGTTACTTATCCACTTC 58.071 33.333 0.00 0.00 40.84 3.01
2967 3030 8.143193 TCCTCAGTTGAAACGTTATGTTACTTA 58.857 33.333 0.00 0.00 40.84 2.24
2978 3041 3.804036 TCATGTTCCTCAGTTGAAACGT 58.196 40.909 0.00 0.00 0.00 3.99
2999 3062 5.066505 GTCAAACAGAGTTCATCCAGTGTTT 59.933 40.000 0.00 0.00 38.35 2.83
3023 3086 3.262420 CCTATCGATTAGAATTGCCCGG 58.738 50.000 1.71 0.00 0.00 5.73
3086 3150 7.553881 AATCATAAATTGTCCTCCAAGTACG 57.446 36.000 0.00 0.00 36.25 3.67
3183 3247 5.777802 AGCGGATAAGAACATATCTGACAG 58.222 41.667 9.21 0.00 39.88 3.51
3190 3254 7.933577 TGAAATCTCAAGCGGATAAGAACATAT 59.066 33.333 0.00 0.00 0.00 1.78
3232 3299 7.216494 TGATTTAGTCAGACAACATCTTCACA 58.784 34.615 2.66 0.00 34.41 3.58
3323 3390 7.172361 GGACAAGCTCCAAGATACTTTGATATC 59.828 40.741 0.00 0.00 39.21 1.63


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

AutoCloner maintained by Alex Coulton.