Multiple sequence alignment - TraesCS1A01G102100

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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 TraesCS1A01G102100 chr1A 100.000 2283 0 0 393 2675 98024417 98022135 0.000000e+00 4217
1 TraesCS1A01G102100 chr1A 100.000 110 0 0 1 110 98024809 98024700 1.260000e-48 204
2 TraesCS1A01G102100 chr1D 90.926 2094 113 26 549 2606 79171838 79169786 0.000000e+00 2743
3 TraesCS1A01G102100 chr1D 96.296 81 2 1 1 80 79172333 79172253 6.010000e-27 132
4 TraesCS1A01G102100 chr1B 93.884 932 47 3 853 1774 130364353 130363422 0.000000e+00 1397
5 TraesCS1A01G102100 chr1B 90.194 826 46 16 1777 2577 130362574 130361759 0.000000e+00 1044
6 TraesCS1A01G102100 chr1B 90.024 421 25 4 402 813 130366320 130365908 1.820000e-146 529


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 TraesCS1A01G102100 chr1A 98022135 98024809 2674 True 2210.5 4217 100.000000 1 2675 2 chr1A.!!$R1 2674
1 TraesCS1A01G102100 chr1D 79169786 79172333 2547 True 1437.5 2743 93.611000 1 2606 2 chr1D.!!$R1 2605
2 TraesCS1A01G102100 chr1B 130361759 130366320 4561 True 990.0 1397 91.367333 402 2577 3 chr1B.!!$R1 2175

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
983 2546 0.32336 GCATTGCACCAAGTCCCCTA 60.323 55.0 3.15 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2636 5083 0.037326 TCCCAGTTAAGCAGCTGACG 60.037 55.0 20.43 3.29 35.12 4.35 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
57 58 8.870075 ACCTTTCTTTTTAGATGTCTAGCAAT 57.130 30.769 0.00 0.00 0.00 3.56
62 63 9.453572 TTCTTTTTAGATGTCTAGCAATCATGT 57.546 29.630 7.10 1.50 0.00 3.21
76 77 6.865411 AGCAATCATGTATGTATGTTGCAAA 58.135 32.000 0.00 0.00 41.75 3.68
77 78 6.976349 AGCAATCATGTATGTATGTTGCAAAG 59.024 34.615 0.00 0.00 41.75 2.77
79 80 7.482474 CAATCATGTATGTATGTTGCAAAGGA 58.518 34.615 0.00 0.00 0.00 3.36
82 83 5.895636 TGTATGTATGTTGCAAAGGAAGG 57.104 39.130 0.00 0.00 0.00 3.46
89 114 1.000938 GTTGCAAAGGAAGGAGCACAG 60.001 52.381 0.00 0.00 36.62 3.66
98 123 1.399791 GAAGGAGCACAGTAAGCATGC 59.600 52.381 10.51 10.51 39.74 4.06
105 130 2.478539 GCACAGTAAGCATGCCTAAAGC 60.479 50.000 15.66 6.73 44.14 3.51
106 131 2.098117 CACAGTAAGCATGCCTAAAGCC 59.902 50.000 15.66 0.00 42.71 4.35
107 132 1.678101 CAGTAAGCATGCCTAAAGCCC 59.322 52.381 15.66 0.00 42.71 5.19
108 133 1.284785 AGTAAGCATGCCTAAAGCCCA 59.715 47.619 15.66 0.00 42.71 5.36
109 134 1.405463 GTAAGCATGCCTAAAGCCCAC 59.595 52.381 15.66 0.00 42.71 4.61
414 439 2.540101 CACATCGGTTTCGCCTCTTATC 59.460 50.000 0.00 0.00 36.13 1.75
432 457 3.622514 CCCCCTCTCGTCCTCTTG 58.377 66.667 0.00 0.00 0.00 3.02
433 458 1.000486 CCCCCTCTCGTCCTCTTGA 60.000 63.158 0.00 0.00 0.00 3.02
434 459 0.614979 CCCCCTCTCGTCCTCTTGAA 60.615 60.000 0.00 0.00 0.00 2.69
435 460 0.820871 CCCCTCTCGTCCTCTTGAAG 59.179 60.000 0.00 0.00 0.00 3.02
436 461 1.551452 CCCTCTCGTCCTCTTGAAGT 58.449 55.000 0.00 0.00 0.00 3.01
437 462 1.474879 CCCTCTCGTCCTCTTGAAGTC 59.525 57.143 0.00 0.00 0.00 3.01
438 463 2.442413 CCTCTCGTCCTCTTGAAGTCT 58.558 52.381 0.00 0.00 0.00 3.24
458 483 0.914551 CGAATGACGATCGTGGTGTC 59.085 55.000 28.12 15.45 45.77 3.67
463 488 0.527817 GACGATCGTGGTGTCCATCC 60.528 60.000 28.12 2.67 35.28 3.51
465 490 1.813859 GATCGTGGTGTCCATCCGA 59.186 57.895 4.49 4.49 36.68 4.55
476 501 4.510340 GGTGTCCATCCGAACACAATATAC 59.490 45.833 7.80 0.00 45.99 1.47
479 504 5.599242 TGTCCATCCGAACACAATATACCTA 59.401 40.000 0.00 0.00 0.00 3.08
557 582 6.936968 AATAGTTAGCCTATAAGTGAGGGG 57.063 41.667 0.00 0.00 35.22 4.79
655 680 7.529158 TGACGACGACATGAATACTTACTTAA 58.471 34.615 0.00 0.00 0.00 1.85
695 720 8.867112 ATTTTAAGCTGCTCAATTATGATGTG 57.133 30.769 1.00 0.00 34.37 3.21
731 761 1.964373 GTGCAACAGTGGGGTACCG 60.964 63.158 5.65 0.00 45.61 4.02
754 784 4.956085 AGATTATTTAAAATTGCCCCGCC 58.044 39.130 0.00 0.00 0.00 6.13
797 835 7.706607 GGAAAATAGAAAATTCCAGTGGCATAC 59.293 37.037 3.51 0.00 41.80 2.39
802 840 5.954150 AGAAAATTCCAGTGGCATACAAGAT 59.046 36.000 3.51 0.00 0.00 2.40
983 2546 0.323360 GCATTGCACCAAGTCCCCTA 60.323 55.000 3.15 0.00 0.00 3.53
1011 2574 1.872234 CTACACGATGACCACCGCG 60.872 63.158 0.00 0.00 0.00 6.46
1587 3150 1.376553 GAGCTTCCCTGCAGTGTCC 60.377 63.158 13.81 0.00 34.99 4.02
1589 3152 2.743718 CTTCCCTGCAGTGTCCGT 59.256 61.111 13.81 0.00 0.00 4.69
1682 3245 2.947542 CGAGATCTAGACGCCGGG 59.052 66.667 2.18 0.00 0.00 5.73
1724 3289 1.543941 CTTGGCGAGCGATCGATGTC 61.544 60.000 29.29 12.76 34.64 3.06
1737 3302 1.796796 GATGTCGGCTTTGGCAGTC 59.203 57.895 0.00 0.00 40.87 3.51
1759 3324 1.003580 ACTTGTTCTCATGGCGATGGT 59.996 47.619 8.98 0.00 0.00 3.55
1763 3328 0.617935 TTCTCATGGCGATGGTGGAA 59.382 50.000 8.98 8.33 0.00 3.53
1823 4233 3.334691 CTCCTTCCTTGACGTGCATTAA 58.665 45.455 0.00 0.00 0.00 1.40
1873 4283 5.050227 CGTGGTATGTTCTTGTTCGGTTTTA 60.050 40.000 0.00 0.00 0.00 1.52
1986 4397 0.586802 GGCAAGCCGGTAATTCGATC 59.413 55.000 1.90 0.00 0.00 3.69
2014 4425 2.278142 ACGTTACGTATCGGCCGC 60.278 61.111 23.51 5.56 38.73 6.53
2035 4446 1.299850 CGCACGATCCTATTCCGCA 60.300 57.895 0.00 0.00 0.00 5.69
2113 4532 2.098298 CTGCACACGCCGCATTAC 59.902 61.111 0.00 0.00 39.02 1.89
2114 4533 2.666526 TGCACACGCCGCATTACA 60.667 55.556 0.00 0.00 37.32 2.41
2116 4535 1.081774 GCACACGCCGCATTACAAA 60.082 52.632 0.00 0.00 0.00 2.83
2117 4536 0.455972 GCACACGCCGCATTACAAAT 60.456 50.000 0.00 0.00 0.00 2.32
2154 4573 1.134068 GGTTAGCCCATTGACTCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
2165 4584 2.108566 CTCCTCCATCGCCTGCAG 59.891 66.667 6.78 6.78 0.00 4.41
2166 4585 4.166888 TCCTCCATCGCCTGCAGC 62.167 66.667 8.66 2.87 38.52 5.25
2180 4599 2.569657 CAGCCCTGCACGTACGTA 59.430 61.111 22.34 5.54 0.00 3.57
2181 4600 1.804326 CAGCCCTGCACGTACGTAC 60.804 63.158 22.34 16.78 0.00 3.67
2191 4629 2.656328 GTACGTACGATGGCGGCC 60.656 66.667 24.41 13.32 43.17 6.13
2424 4863 3.089874 CCTCATGAGCCGGGGGAA 61.090 66.667 17.76 0.00 0.00 3.97
2477 4921 3.771160 GTCCCATCGACCGCACCT 61.771 66.667 0.00 0.00 35.23 4.00
2487 4931 1.912371 GACCGCACCTTACTTGCAGC 61.912 60.000 0.00 0.00 40.20 5.25
2489 4933 2.176792 GCACCTTACTTGCAGCGC 59.823 61.111 0.00 0.00 39.93 5.92
2490 4934 2.328099 GCACCTTACTTGCAGCGCT 61.328 57.895 2.64 2.64 39.93 5.92
2491 4935 1.856265 GCACCTTACTTGCAGCGCTT 61.856 55.000 7.50 0.00 39.93 4.68
2539 4986 6.653526 TCTTGATTCTTTTCATGCCTTTGA 57.346 33.333 0.00 0.00 0.00 2.69
2549 4996 5.759506 TTCATGCCTTTGAAAGAAACGTA 57.240 34.783 6.49 0.00 32.82 3.57
2550 4997 5.957842 TCATGCCTTTGAAAGAAACGTAT 57.042 34.783 6.49 0.00 0.00 3.06
2551 4998 7.441890 TTCATGCCTTTGAAAGAAACGTATA 57.558 32.000 6.49 0.00 32.82 1.47
2555 5002 7.355332 TGCCTTTGAAAGAAACGTATAGTAC 57.645 36.000 6.49 0.00 0.00 2.73
2577 5024 1.690893 AGCATATGTGATGGCGTCTCT 59.309 47.619 8.40 0.00 0.00 3.10
2578 5025 2.103771 AGCATATGTGATGGCGTCTCTT 59.896 45.455 8.40 5.43 0.00 2.85
2580 5027 4.058124 GCATATGTGATGGCGTCTCTTAA 58.942 43.478 8.40 0.00 0.00 1.85
2581 5028 4.692625 GCATATGTGATGGCGTCTCTTAAT 59.307 41.667 8.40 0.00 0.00 1.40
2582 5029 5.180117 GCATATGTGATGGCGTCTCTTAATT 59.820 40.000 8.40 0.00 0.00 1.40
2583 5030 6.619446 GCATATGTGATGGCGTCTCTTAATTC 60.619 42.308 8.40 0.00 0.00 2.17
2586 5033 5.245531 TGTGATGGCGTCTCTTAATTCTTT 58.754 37.500 8.40 0.00 0.00 2.52
2587 5034 5.122239 TGTGATGGCGTCTCTTAATTCTTTG 59.878 40.000 8.40 0.00 0.00 2.77
2589 5036 5.937540 TGATGGCGTCTCTTAATTCTTTGAA 59.062 36.000 8.40 0.00 0.00 2.69
2590 5037 6.429692 TGATGGCGTCTCTTAATTCTTTGAAA 59.570 34.615 8.40 0.00 0.00 2.69
2591 5038 6.627395 TGGCGTCTCTTAATTCTTTGAAAA 57.373 33.333 0.00 0.00 0.00 2.29
2592 5039 6.668323 TGGCGTCTCTTAATTCTTTGAAAAG 58.332 36.000 0.00 0.00 37.36 2.27
2593 5040 6.485313 TGGCGTCTCTTAATTCTTTGAAAAGA 59.515 34.615 1.31 1.31 42.91 2.52
2596 5043 8.844690 GCGTCTCTTAATTCTTTGAAAAGATTG 58.155 33.333 6.33 0.00 43.92 2.67
2606 5053 9.985730 ATTCTTTGAAAAGATTGCATTTCACTA 57.014 25.926 11.72 4.29 43.20 2.74
2607 5054 8.801715 TCTTTGAAAAGATTGCATTTCACTAC 57.198 30.769 11.72 0.00 43.20 2.73
2608 5055 8.632679 TCTTTGAAAAGATTGCATTTCACTACT 58.367 29.630 11.72 0.00 43.20 2.57
2609 5056 9.897744 CTTTGAAAAGATTGCATTTCACTACTA 57.102 29.630 11.72 0.00 43.20 1.82
2610 5057 9.677567 TTTGAAAAGATTGCATTTCACTACTAC 57.322 29.630 11.72 0.00 43.20 2.73
2611 5058 8.621532 TGAAAAGATTGCATTTCACTACTACT 57.378 30.769 8.73 0.00 39.81 2.57
2612 5059 8.721478 TGAAAAGATTGCATTTCACTACTACTC 58.279 33.333 8.73 0.00 39.81 2.59
2613 5060 7.617041 AAAGATTGCATTTCACTACTACTCC 57.383 36.000 0.00 0.00 0.00 3.85
2614 5061 6.552445 AGATTGCATTTCACTACTACTCCT 57.448 37.500 0.00 0.00 0.00 3.69
2615 5062 7.661536 AGATTGCATTTCACTACTACTCCTA 57.338 36.000 0.00 0.00 0.00 2.94
2616 5063 7.493367 AGATTGCATTTCACTACTACTCCTAC 58.507 38.462 0.00 0.00 0.00 3.18
2617 5064 6.852420 TTGCATTTCACTACTACTCCTACT 57.148 37.500 0.00 0.00 0.00 2.57
2618 5065 6.852420 TGCATTTCACTACTACTCCTACTT 57.148 37.500 0.00 0.00 0.00 2.24
2619 5066 6.864342 TGCATTTCACTACTACTCCTACTTC 58.136 40.000 0.00 0.00 0.00 3.01
2620 5067 6.436218 TGCATTTCACTACTACTCCTACTTCA 59.564 38.462 0.00 0.00 0.00 3.02
2621 5068 7.124298 TGCATTTCACTACTACTCCTACTTCAT 59.876 37.037 0.00 0.00 0.00 2.57
2622 5069 7.982354 GCATTTCACTACTACTCCTACTTCATT 59.018 37.037 0.00 0.00 0.00 2.57
2623 5070 9.522804 CATTTCACTACTACTCCTACTTCATTC 57.477 37.037 0.00 0.00 0.00 2.67
2624 5071 8.645814 TTTCACTACTACTCCTACTTCATTCA 57.354 34.615 0.00 0.00 0.00 2.57
2625 5072 8.824756 TTCACTACTACTCCTACTTCATTCAT 57.175 34.615 0.00 0.00 0.00 2.57
2626 5073 8.226819 TCACTACTACTCCTACTTCATTCATG 57.773 38.462 0.00 0.00 0.00 3.07
2627 5074 7.834681 TCACTACTACTCCTACTTCATTCATGT 59.165 37.037 0.00 0.00 0.00 3.21
2628 5075 7.918033 CACTACTACTCCTACTTCATTCATGTG 59.082 40.741 0.00 0.00 0.00 3.21
2629 5076 6.859112 ACTACTCCTACTTCATTCATGTGT 57.141 37.500 0.00 0.00 0.00 3.72
2630 5077 7.246171 ACTACTCCTACTTCATTCATGTGTT 57.754 36.000 0.00 0.00 0.00 3.32
2631 5078 7.099764 ACTACTCCTACTTCATTCATGTGTTG 58.900 38.462 0.00 0.00 0.00 3.33
2632 5079 4.697352 ACTCCTACTTCATTCATGTGTTGC 59.303 41.667 0.00 0.00 0.00 4.17
2633 5080 4.650734 TCCTACTTCATTCATGTGTTGCA 58.349 39.130 0.00 0.00 0.00 4.08
2634 5081 5.255687 TCCTACTTCATTCATGTGTTGCAT 58.744 37.500 0.00 0.00 38.60 3.96
2635 5082 6.413892 TCCTACTTCATTCATGTGTTGCATA 58.586 36.000 0.00 0.00 35.74 3.14
2636 5083 6.316140 TCCTACTTCATTCATGTGTTGCATAC 59.684 38.462 0.00 0.00 35.74 2.39
2637 5084 4.973396 ACTTCATTCATGTGTTGCATACG 58.027 39.130 0.00 0.00 35.74 3.06
2638 5085 4.455533 ACTTCATTCATGTGTTGCATACGT 59.544 37.500 0.00 0.00 35.74 3.57
2639 5086 4.598406 TCATTCATGTGTTGCATACGTC 57.402 40.909 0.00 0.00 35.74 4.34
2640 5087 3.999663 TCATTCATGTGTTGCATACGTCA 59.000 39.130 0.00 0.00 35.74 4.35
2641 5088 4.093261 TCATTCATGTGTTGCATACGTCAG 59.907 41.667 0.00 0.00 35.74 3.51
2642 5089 1.731709 TCATGTGTTGCATACGTCAGC 59.268 47.619 0.00 0.00 35.74 4.26
2643 5090 1.733912 CATGTGTTGCATACGTCAGCT 59.266 47.619 12.54 0.00 35.74 4.24
2644 5091 1.147473 TGTGTTGCATACGTCAGCTG 58.853 50.000 7.63 7.63 0.00 4.24
2645 5092 0.179215 GTGTTGCATACGTCAGCTGC 60.179 55.000 9.47 3.23 36.45 5.25
2646 5093 0.320683 TGTTGCATACGTCAGCTGCT 60.321 50.000 9.47 0.00 36.84 4.24
2647 5094 0.798776 GTTGCATACGTCAGCTGCTT 59.201 50.000 9.47 0.40 36.84 3.91
2648 5095 1.999735 GTTGCATACGTCAGCTGCTTA 59.000 47.619 9.47 2.85 36.84 3.09
2649 5096 2.378445 TGCATACGTCAGCTGCTTAA 57.622 45.000 9.47 0.00 36.84 1.85
2650 5097 1.999735 TGCATACGTCAGCTGCTTAAC 59.000 47.619 9.47 0.32 36.84 2.01
2651 5098 2.271800 GCATACGTCAGCTGCTTAACT 58.728 47.619 9.47 0.00 33.15 2.24
2652 5099 2.029728 GCATACGTCAGCTGCTTAACTG 59.970 50.000 9.47 3.37 33.15 3.16
2653 5100 2.363788 TACGTCAGCTGCTTAACTGG 57.636 50.000 9.47 0.00 34.57 4.00
2654 5101 0.320771 ACGTCAGCTGCTTAACTGGG 60.321 55.000 9.47 0.00 34.57 4.45
2655 5102 0.037326 CGTCAGCTGCTTAACTGGGA 60.037 55.000 9.47 0.00 34.57 4.37
2656 5103 1.406069 CGTCAGCTGCTTAACTGGGAT 60.406 52.381 9.47 0.00 34.57 3.85
2657 5104 2.716217 GTCAGCTGCTTAACTGGGATT 58.284 47.619 9.47 0.00 34.57 3.01
2658 5105 2.421424 GTCAGCTGCTTAACTGGGATTG 59.579 50.000 9.47 0.00 34.57 2.67
2659 5106 1.747355 CAGCTGCTTAACTGGGATTGG 59.253 52.381 0.00 0.00 0.00 3.16
2660 5107 1.355720 AGCTGCTTAACTGGGATTGGT 59.644 47.619 0.00 0.00 0.00 3.67
2661 5108 2.576191 AGCTGCTTAACTGGGATTGGTA 59.424 45.455 0.00 0.00 0.00 3.25
2662 5109 2.683362 GCTGCTTAACTGGGATTGGTAC 59.317 50.000 0.00 0.00 0.00 3.34
2663 5110 3.279434 CTGCTTAACTGGGATTGGTACC 58.721 50.000 4.43 4.43 0.00 3.34
2664 5111 2.916934 TGCTTAACTGGGATTGGTACCT 59.083 45.455 14.36 0.00 0.00 3.08
2665 5112 3.332485 TGCTTAACTGGGATTGGTACCTT 59.668 43.478 14.36 0.00 0.00 3.50
2666 5113 4.202631 TGCTTAACTGGGATTGGTACCTTT 60.203 41.667 14.36 0.00 0.00 3.11
2667 5114 5.014333 TGCTTAACTGGGATTGGTACCTTTA 59.986 40.000 14.36 0.00 0.00 1.85
2668 5115 6.127101 GCTTAACTGGGATTGGTACCTTTAT 58.873 40.000 14.36 3.95 0.00 1.40
2669 5116 6.039382 GCTTAACTGGGATTGGTACCTTTATG 59.961 42.308 14.36 0.29 0.00 1.90
2670 5117 4.519906 ACTGGGATTGGTACCTTTATGG 57.480 45.455 14.36 0.94 42.93 2.74
2671 5118 3.204382 ACTGGGATTGGTACCTTTATGGG 59.796 47.826 14.36 1.72 41.11 4.00
2672 5119 2.516277 TGGGATTGGTACCTTTATGGGG 59.484 50.000 14.36 0.00 41.11 4.96
2673 5120 2.158370 GGGATTGGTACCTTTATGGGGG 60.158 54.545 14.36 0.00 41.11 5.40
2674 5121 2.594131 GATTGGTACCTTTATGGGGGC 58.406 52.381 14.36 0.00 41.11 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 6.095300 CCTTCCTTTGCAACATACATACATGA 59.905 38.462 0.00 0.00 0.00 3.07
62 63 4.640201 GCTCCTTCCTTTGCAACATACATA 59.360 41.667 0.00 0.00 0.00 2.29
76 77 1.352083 TGCTTACTGTGCTCCTTCCT 58.648 50.000 0.00 0.00 0.00 3.36
77 78 2.012673 CATGCTTACTGTGCTCCTTCC 58.987 52.381 0.00 0.00 0.00 3.46
79 80 1.457346 GCATGCTTACTGTGCTCCTT 58.543 50.000 11.37 0.00 36.02 3.36
82 83 2.315925 TAGGCATGCTTACTGTGCTC 57.684 50.000 18.92 0.00 38.83 4.26
89 114 1.405463 GTGGGCTTTAGGCATGCTTAC 59.595 52.381 18.92 2.41 44.01 2.34
392 417 0.034896 AAGAGGCGAAACCGATGTGT 59.965 50.000 0.00 0.00 46.52 3.72
393 418 2.004583 TAAGAGGCGAAACCGATGTG 57.995 50.000 0.00 0.00 46.52 3.21
394 419 2.483188 GGATAAGAGGCGAAACCGATGT 60.483 50.000 0.00 0.00 46.52 3.06
395 420 2.135933 GGATAAGAGGCGAAACCGATG 58.864 52.381 0.00 0.00 46.52 3.84
396 421 1.070289 GGGATAAGAGGCGAAACCGAT 59.930 52.381 0.00 0.00 46.52 4.18
397 422 0.462789 GGGATAAGAGGCGAAACCGA 59.537 55.000 0.00 0.00 46.52 4.69
398 423 0.532196 GGGGATAAGAGGCGAAACCG 60.532 60.000 0.00 0.00 46.52 4.44
399 424 0.179026 GGGGGATAAGAGGCGAAACC 60.179 60.000 0.00 0.00 39.61 3.27
400 425 3.398694 GGGGGATAAGAGGCGAAAC 57.601 57.895 0.00 0.00 0.00 2.78
448 473 0.108329 GTTCGGATGGACACCACGAT 60.108 55.000 0.00 0.00 35.80 3.73
458 483 6.990349 ACTTTAGGTATATTGTGTTCGGATGG 59.010 38.462 0.00 0.00 0.00 3.51
463 488 9.093970 TCAATGACTTTAGGTATATTGTGTTCG 57.906 33.333 0.00 0.00 35.69 3.95
476 501 8.571336 AGTTGTTTTGAGATCAATGACTTTAGG 58.429 33.333 0.00 0.00 35.55 2.69
523 548 5.857822 AGGCTAACTATTTTGTGAACGAC 57.142 39.130 0.00 0.00 0.00 4.34
557 582 7.121315 AGCCAGTTAGAAAACTCCACATAATTC 59.879 37.037 0.00 0.00 44.28 2.17
655 680 9.578439 GCAGCTTAAAATTTTCATAGAAGATGT 57.422 29.630 20.95 3.91 32.82 3.06
707 737 1.037030 CCCCACTGTTGCACTGTTGT 61.037 55.000 0.00 0.00 0.00 3.32
708 738 1.037030 ACCCCACTGTTGCACTGTTG 61.037 55.000 0.00 0.00 0.00 3.33
709 739 0.548989 TACCCCACTGTTGCACTGTT 59.451 50.000 0.00 0.00 0.00 3.16
710 740 0.179029 GTACCCCACTGTTGCACTGT 60.179 55.000 0.00 0.00 0.00 3.55
731 761 4.988540 GGCGGGGCAATTTTAAATAATCTC 59.011 41.667 0.00 0.00 0.00 2.75
754 784 4.359971 TTTCCAAATGATGCGATGACAG 57.640 40.909 0.00 0.00 0.00 3.51
802 840 8.977412 TGCATATATCTCGGGATAACTTTCATA 58.023 33.333 9.51 0.00 37.87 2.15
838 876 2.944349 CCACCATTGCAAAAGCAAAAGT 59.056 40.909 1.71 5.02 33.20 2.66
983 2546 0.738762 CATCGTGTAGTGCTGCAGCT 60.739 55.000 36.61 21.93 42.66 4.24
1011 2574 4.570874 GGCGGAATGGGAGGCTCC 62.571 72.222 25.80 25.80 35.23 4.70
1190 2753 2.897972 CGGAGGAAACGTAGGGGG 59.102 66.667 0.00 0.00 0.00 5.40
1724 3289 0.798776 CAAGTAGACTGCCAAAGCCG 59.201 55.000 0.00 0.00 38.69 5.52
1737 3302 2.868583 CCATCGCCATGAGAACAAGTAG 59.131 50.000 0.00 0.00 30.57 2.57
1804 4214 3.242413 CGATTAATGCACGTCAAGGAAGG 60.242 47.826 0.00 0.00 0.00 3.46
1805 4215 3.370978 ACGATTAATGCACGTCAAGGAAG 59.629 43.478 0.00 0.00 35.33 3.46
1806 4216 3.124466 CACGATTAATGCACGTCAAGGAA 59.876 43.478 0.00 0.00 38.18 3.36
1807 4217 2.670905 CACGATTAATGCACGTCAAGGA 59.329 45.455 0.00 0.00 38.18 3.36
1873 4283 1.275666 TCCAGGTCACGATGATGGTT 58.724 50.000 0.00 0.00 30.53 3.67
1906 4316 1.050204 AAGGTTGTACTGTACGGCCA 58.950 50.000 23.28 0.00 0.00 5.36
1981 4392 2.767445 CGTGCGTAGTGGGGATCGA 61.767 63.158 0.00 0.00 0.00 3.59
1986 4397 1.802715 CGTAACGTGCGTAGTGGGG 60.803 63.158 0.00 0.00 0.00 4.96
2014 4425 2.022129 GGAATAGGATCGTGCGCCG 61.022 63.158 4.18 8.64 38.13 6.46
2101 4520 1.592110 CGAGATTTGTAATGCGGCGTG 60.592 52.381 9.37 0.00 0.00 5.34
2165 4584 2.877582 CGTACGTACGTGCAGGGC 60.878 66.667 33.95 13.73 44.13 5.19
2174 4593 2.656328 GGCCGCCATCGTACGTAC 60.656 66.667 15.90 15.90 0.00 3.67
2175 4594 4.254672 CGGCCGCCATCGTACGTA 62.255 66.667 14.67 2.34 0.00 3.57
2215 4653 2.517166 GATGGCGCCTTCCCCTTC 60.517 66.667 29.70 9.03 0.00 3.46
2256 4695 0.528470 CCTCTTCCGCTTCTTCGTCT 59.472 55.000 0.00 0.00 0.00 4.18
2477 4921 3.371168 CAAAGAAAAGCGCTGCAAGTAA 58.629 40.909 12.58 0.00 35.30 2.24
2487 4931 2.916735 CTTGCAAGCAAAGAAAAGCG 57.083 45.000 14.65 0.00 35.33 4.68
2509 4953 8.103305 AGGCATGAAAAGAATCAAGAACTAGTA 58.897 33.333 0.00 0.00 32.06 1.82
2510 4954 6.944862 AGGCATGAAAAGAATCAAGAACTAGT 59.055 34.615 0.00 0.00 32.06 2.57
2511 4955 7.388460 AGGCATGAAAAGAATCAAGAACTAG 57.612 36.000 0.00 0.00 32.06 2.57
2512 4956 7.765695 AAGGCATGAAAAGAATCAAGAACTA 57.234 32.000 0.00 0.00 32.06 2.24
2549 4996 5.419155 ACGCCATCACATATGCTAGTACTAT 59.581 40.000 2.33 0.00 0.00 2.12
2550 4997 4.765339 ACGCCATCACATATGCTAGTACTA 59.235 41.667 1.58 1.89 0.00 1.82
2551 4998 3.574396 ACGCCATCACATATGCTAGTACT 59.426 43.478 1.58 0.00 0.00 2.73
2555 5002 3.056962 AGAGACGCCATCACATATGCTAG 60.057 47.826 1.58 0.00 0.00 3.42
2583 5030 8.807667 AGTAGTGAAATGCAATCTTTTCAAAG 57.192 30.769 13.33 0.00 43.44 2.77
2586 5033 8.621532 AGTAGTAGTGAAATGCAATCTTTTCA 57.378 30.769 8.73 8.73 41.27 2.69
2587 5034 8.178313 GGAGTAGTAGTGAAATGCAATCTTTTC 58.822 37.037 3.97 3.97 37.07 2.29
2589 5036 7.398024 AGGAGTAGTAGTGAAATGCAATCTTT 58.602 34.615 0.00 0.00 0.00 2.52
2590 5037 6.951971 AGGAGTAGTAGTGAAATGCAATCTT 58.048 36.000 0.00 0.00 0.00 2.40
2591 5038 6.552445 AGGAGTAGTAGTGAAATGCAATCT 57.448 37.500 0.00 0.00 0.00 2.40
2592 5039 7.493367 AGTAGGAGTAGTAGTGAAATGCAATC 58.507 38.462 0.00 0.00 0.00 2.67
2593 5040 7.425224 AGTAGGAGTAGTAGTGAAATGCAAT 57.575 36.000 0.00 0.00 0.00 3.56
2596 5043 6.864342 TGAAGTAGGAGTAGTAGTGAAATGC 58.136 40.000 0.00 0.00 0.00 3.56
2606 5053 6.859112 ACACATGAATGAAGTAGGAGTAGT 57.141 37.500 0.00 0.00 0.00 2.73
2607 5054 6.036517 GCAACACATGAATGAAGTAGGAGTAG 59.963 42.308 0.00 0.00 0.00 2.57
2608 5055 5.874810 GCAACACATGAATGAAGTAGGAGTA 59.125 40.000 0.00 0.00 0.00 2.59
2609 5056 4.697352 GCAACACATGAATGAAGTAGGAGT 59.303 41.667 0.00 0.00 0.00 3.85
2610 5057 4.696877 TGCAACACATGAATGAAGTAGGAG 59.303 41.667 0.00 0.00 0.00 3.69
2611 5058 4.650734 TGCAACACATGAATGAAGTAGGA 58.349 39.130 0.00 0.00 0.00 2.94
2612 5059 5.571784 ATGCAACACATGAATGAAGTAGG 57.428 39.130 0.00 0.00 37.70 3.18
2613 5060 6.183360 ACGTATGCAACACATGAATGAAGTAG 60.183 38.462 0.00 0.00 40.06 2.57
2614 5061 5.641636 ACGTATGCAACACATGAATGAAGTA 59.358 36.000 0.00 0.00 40.06 2.24
2615 5062 4.455533 ACGTATGCAACACATGAATGAAGT 59.544 37.500 0.00 0.00 40.06 3.01
2616 5063 4.973396 ACGTATGCAACACATGAATGAAG 58.027 39.130 0.00 0.00 40.06 3.02
2617 5064 4.453819 TGACGTATGCAACACATGAATGAA 59.546 37.500 0.00 0.00 40.06 2.57
2618 5065 3.999663 TGACGTATGCAACACATGAATGA 59.000 39.130 0.00 0.00 40.06 2.57
2619 5066 4.336932 CTGACGTATGCAACACATGAATG 58.663 43.478 0.00 0.00 40.06 2.67
2620 5067 3.181507 GCTGACGTATGCAACACATGAAT 60.182 43.478 0.00 0.00 40.06 2.57
2621 5068 2.159430 GCTGACGTATGCAACACATGAA 59.841 45.455 0.00 0.00 40.06 2.57
2622 5069 1.731709 GCTGACGTATGCAACACATGA 59.268 47.619 0.00 0.00 40.06 3.07
2623 5070 1.733912 AGCTGACGTATGCAACACATG 59.266 47.619 13.54 0.00 40.06 3.21
2624 5071 1.733912 CAGCTGACGTATGCAACACAT 59.266 47.619 8.42 0.00 43.18 3.21
2625 5072 1.147473 CAGCTGACGTATGCAACACA 58.853 50.000 8.42 0.00 0.00 3.72
2626 5073 0.179215 GCAGCTGACGTATGCAACAC 60.179 55.000 20.43 0.00 39.75 3.32
2627 5074 0.320683 AGCAGCTGACGTATGCAACA 60.321 50.000 20.43 0.00 42.45 3.33
2628 5075 0.798776 AAGCAGCTGACGTATGCAAC 59.201 50.000 20.43 0.00 42.45 4.17
2629 5076 2.378445 TAAGCAGCTGACGTATGCAA 57.622 45.000 20.43 0.00 42.45 4.08
2630 5077 1.999735 GTTAAGCAGCTGACGTATGCA 59.000 47.619 20.43 0.00 42.45 3.96
2631 5078 2.029728 CAGTTAAGCAGCTGACGTATGC 59.970 50.000 20.43 0.00 35.12 3.14
2632 5079 2.604914 CCAGTTAAGCAGCTGACGTATG 59.395 50.000 20.43 8.03 35.12 2.39
2633 5080 2.418746 CCCAGTTAAGCAGCTGACGTAT 60.419 50.000 20.43 0.00 35.12 3.06
2634 5081 1.067142 CCCAGTTAAGCAGCTGACGTA 60.067 52.381 20.43 8.73 35.12 3.57
2635 5082 0.320771 CCCAGTTAAGCAGCTGACGT 60.321 55.000 20.43 9.78 35.12 4.34
2636 5083 0.037326 TCCCAGTTAAGCAGCTGACG 60.037 55.000 20.43 3.29 35.12 4.35
2637 5084 2.409948 ATCCCAGTTAAGCAGCTGAC 57.590 50.000 20.43 9.11 35.12 3.51
2638 5085 2.618816 CCAATCCCAGTTAAGCAGCTGA 60.619 50.000 20.43 0.00 35.12 4.26
2639 5086 1.747355 CCAATCCCAGTTAAGCAGCTG 59.253 52.381 10.11 10.11 33.07 4.24
2640 5087 1.355720 ACCAATCCCAGTTAAGCAGCT 59.644 47.619 0.00 0.00 0.00 4.24
2641 5088 1.839424 ACCAATCCCAGTTAAGCAGC 58.161 50.000 0.00 0.00 0.00 5.25
2642 5089 3.054361 AGGTACCAATCCCAGTTAAGCAG 60.054 47.826 15.94 0.00 0.00 4.24
2643 5090 2.916934 AGGTACCAATCCCAGTTAAGCA 59.083 45.455 15.94 0.00 0.00 3.91
2644 5091 3.646736 AGGTACCAATCCCAGTTAAGC 57.353 47.619 15.94 0.00 0.00 3.09
2645 5092 6.546034 CCATAAAGGTACCAATCCCAGTTAAG 59.454 42.308 15.94 0.00 0.00 1.85
2646 5093 6.428295 CCATAAAGGTACCAATCCCAGTTAA 58.572 40.000 15.94 0.00 0.00 2.01
2647 5094 5.103855 CCCATAAAGGTACCAATCCCAGTTA 60.104 44.000 15.94 0.00 34.66 2.24
2648 5095 4.325816 CCCATAAAGGTACCAATCCCAGTT 60.326 45.833 15.94 0.00 34.66 3.16
2649 5096 3.204382 CCCATAAAGGTACCAATCCCAGT 59.796 47.826 15.94 0.00 34.66 4.00
2650 5097 3.436470 CCCCATAAAGGTACCAATCCCAG 60.436 52.174 15.94 0.00 34.66 4.45
2651 5098 2.516277 CCCCATAAAGGTACCAATCCCA 59.484 50.000 15.94 0.00 34.66 4.37
2652 5099 2.158370 CCCCCATAAAGGTACCAATCCC 60.158 54.545 15.94 0.00 34.66 3.85
2653 5100 2.755208 GCCCCCATAAAGGTACCAATCC 60.755 54.545 15.94 0.00 34.66 3.01
2654 5101 2.594131 GCCCCCATAAAGGTACCAATC 58.406 52.381 15.94 0.00 34.66 2.67
2655 5102 2.767644 GCCCCCATAAAGGTACCAAT 57.232 50.000 15.94 4.56 34.66 3.16


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

AutoCloner maintained by Alex Coulton.