Multiple sequence alignment - TraesCS7B01G086100

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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 TraesCS7B01G086100 chr7B 100.000 2672 0 0 1 2672 99132110 99129439 0.000000e+00 4935.0
1 TraesCS7B01G086100 chr7D 93.509 1895 82 23 764 2649 136253893 136252031 0.000000e+00 2780.0
2 TraesCS7B01G086100 chr7D 84.267 464 64 6 206 661 136254739 136254277 6.790000e-121 444.0
3 TraesCS7B01G086100 chr7D 96.602 206 6 1 1 206 136259744 136259540 9.160000e-90 340.0
4 TraesCS7B01G086100 chr7D 92.453 53 4 0 263 315 23581734 23581682 2.850000e-10 76.8
5 TraesCS7B01G086100 chr7D 89.796 49 5 0 261 309 555215173 555215125 2.220000e-06 63.9
6 TraesCS7B01G086100 chr7A 92.446 1165 44 11 764 1922 135902031 135900905 0.000000e+00 1624.0
7 TraesCS7B01G086100 chr7A 92.651 694 34 9 1914 2598 135900802 135900117 0.000000e+00 983.0
8 TraesCS7B01G086100 chr7A 87.130 676 67 11 1 660 135903090 135902419 0.000000e+00 749.0
9 TraesCS7B01G086100 chr7A 91.379 58 4 1 615 672 621317667 621317723 7.930000e-11 78.7
10 TraesCS7B01G086100 chr7A 91.071 56 5 0 261 316 664179514 664179569 2.850000e-10 76.8
11 TraesCS7B01G086100 chr5B 84.470 264 39 1 1295 1558 430680041 430679780 2.640000e-65 259.0
12 TraesCS7B01G086100 chr5B 85.340 191 24 4 364 552 354727703 354727891 7.550000e-46 195.0
13 TraesCS7B01G086100 chr5B 88.462 104 11 1 592 694 563677937 563677834 1.000000e-24 124.0
14 TraesCS7B01G086100 chr5D 84.959 246 37 0 1313 1558 364670752 364670507 1.590000e-62 250.0
15 TraesCS7B01G086100 chr5D 88.333 60 7 0 1343 1402 113391589 113391530 3.690000e-09 73.1
16 TraesCS7B01G086100 chr5A 83.396 265 42 1 1294 1558 465996839 465996577 7.390000e-61 244.0
17 TraesCS7B01G086100 chr5A 84.328 134 18 3 446 578 690555271 690555140 7.760000e-26 128.0
18 TraesCS7B01G086100 chr5A 85.938 64 9 0 253 316 485866043 485865980 4.770000e-08 69.4
19 TraesCS7B01G086100 chr6A 82.773 238 33 6 1315 1548 520869896 520870129 3.490000e-49 206.0
20 TraesCS7B01G086100 chr1B 81.148 244 40 5 351 590 646482065 646481824 9.760000e-45 191.0
21 TraesCS7B01G086100 chr1B 86.792 106 13 1 591 695 112617747 112617852 1.680000e-22 117.0
22 TraesCS7B01G086100 chr1B 95.652 46 2 0 261 306 344330475 344330520 1.030000e-09 75.0
23 TraesCS7B01G086100 chr4D 80.478 251 46 3 334 583 504565763 504565515 3.510000e-44 189.0
24 TraesCS7B01G086100 chr3B 82.569 218 33 5 368 582 662366016 662366231 1.260000e-43 187.0
25 TraesCS7B01G086100 chr3B 87.037 54 7 0 262 315 262089891 262089838 7.990000e-06 62.1
26 TraesCS7B01G086100 chr3B 88.462 52 3 3 349 399 642060467 642060516 2.870000e-05 60.2
27 TraesCS7B01G086100 chr6D 88.235 153 17 1 1315 1466 379724015 379723863 5.880000e-42 182.0
28 TraesCS7B01G086100 chr6D 94.737 38 2 0 257 294 395534266 395534303 2.870000e-05 60.2
29 TraesCS7B01G086100 chr6B 88.235 153 17 1 1315 1466 566535496 566535648 5.880000e-42 182.0
30 TraesCS7B01G086100 chr2A 79.184 245 43 7 350 590 104691378 104691138 2.130000e-36 163.0
31 TraesCS7B01G086100 chr1A 89.899 99 9 1 597 694 463458422 463458324 2.790000e-25 126.0
32 TraesCS7B01G086100 chr1A 81.250 112 18 3 592 701 12420149 12420259 1.320000e-13 87.9
33 TraesCS7B01G086100 chr2B 90.000 90 8 1 603 691 141739956 141739867 6.040000e-22 115.0
34 TraesCS7B01G086100 chr4B 77.885 208 27 5 385 590 67494771 67494581 7.820000e-21 111.0
35 TraesCS7B01G086100 chr1D 89.773 88 8 1 596 682 112916009 112915922 7.820000e-21 111.0
36 TraesCS7B01G086100 chr2D 86.275 102 8 5 592 691 589689904 589689807 3.640000e-19 106.0
37 TraesCS7B01G086100 chr2D 84.762 105 15 1 596 699 650689524 650689420 1.310000e-18 104.0


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 TraesCS7B01G086100 chr7B 99129439 99132110 2671 True 4935.000000 4935 100.000000 1 2672 1 chr7B.!!$R1 2671
1 TraesCS7B01G086100 chr7D 136252031 136254739 2708 True 1612.000000 2780 88.888000 206 2649 2 chr7D.!!$R4 2443
2 TraesCS7B01G086100 chr7A 135900117 135903090 2973 True 1118.666667 1624 90.742333 1 2598 3 chr7A.!!$R1 2597

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
310 318 0.178767 TCCTTCTGCATCCGTCCATG 59.821 55.0 0.00 0.0 0.0 3.66 F
311 319 0.178767 CCTTCTGCATCCGTCCATGA 59.821 55.0 0.00 0.0 0.0 3.07 F
682 698 0.242825 CCGTTTGAGGCGTCTGTCTA 59.757 55.0 8.06 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1200 1543 1.807573 GAGGTGAGCCGCTTCTTCG 60.808 63.158 0.00 0.00 40.50 3.79 R
1592 1938 2.279784 GATTGCTCGAGGCCGGAG 60.280 66.667 15.58 19.15 40.92 4.63 R
2548 3018 1.670967 GCTTGAAGGTTTCCATGCTGC 60.671 52.381 0.00 0.00 32.70 5.25 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
66 67 2.006805 TTGGCATGGACAAACATGGA 57.993 45.000 8.11 0.00 46.40 3.41
89 90 2.357952 GGATTAAATTCACCTGCCCGAC 59.642 50.000 0.00 0.00 0.00 4.79
244 252 7.872993 CACAAAGAACAATCTAGGAGAGTAACA 59.127 37.037 0.00 0.00 33.77 2.41
283 291 1.092348 GGCATCTTCAACGGTAACCC 58.908 55.000 0.00 0.00 0.00 4.11
297 305 2.823747 GGTAACCCGCAAATTTCCTTCT 59.176 45.455 0.00 0.00 0.00 2.85
304 312 2.533266 GCAAATTTCCTTCTGCATCCG 58.467 47.619 0.00 0.00 34.87 4.18
305 313 2.094545 GCAAATTTCCTTCTGCATCCGT 60.095 45.455 0.00 0.00 34.87 4.69
306 314 3.762779 CAAATTTCCTTCTGCATCCGTC 58.237 45.455 0.00 0.00 0.00 4.79
307 315 2.044123 ATTTCCTTCTGCATCCGTCC 57.956 50.000 0.00 0.00 0.00 4.79
308 316 0.690192 TTTCCTTCTGCATCCGTCCA 59.310 50.000 0.00 0.00 0.00 4.02
309 317 0.911769 TTCCTTCTGCATCCGTCCAT 59.088 50.000 0.00 0.00 0.00 3.41
310 318 0.178767 TCCTTCTGCATCCGTCCATG 59.821 55.000 0.00 0.00 0.00 3.66
311 319 0.178767 CCTTCTGCATCCGTCCATGA 59.821 55.000 0.00 0.00 0.00 3.07
312 320 1.407299 CCTTCTGCATCCGTCCATGAA 60.407 52.381 0.00 0.00 0.00 2.57
315 328 1.003003 TCTGCATCCGTCCATGAACAA 59.997 47.619 0.00 0.00 0.00 2.83
318 331 3.615155 TGCATCCGTCCATGAACAAATA 58.385 40.909 0.00 0.00 0.00 1.40
326 339 4.875536 CGTCCATGAACAAATAGATGTGGA 59.124 41.667 0.00 0.00 32.81 4.02
331 344 6.548622 CCATGAACAAATAGATGTGGAAGGAT 59.451 38.462 0.00 0.00 32.81 3.24
349 362 3.111853 GATACCATCCAATCGCAGTCA 57.888 47.619 0.00 0.00 0.00 3.41
371 384 4.495472 CACATACATTTCGAACCGCATTTC 59.505 41.667 0.00 0.00 0.00 2.17
379 392 3.132160 TCGAACCGCATTTCAACTAACA 58.868 40.909 0.00 0.00 0.00 2.41
382 395 4.464112 GAACCGCATTTCAACTAACAGAC 58.536 43.478 0.00 0.00 0.00 3.51
383 396 3.740115 ACCGCATTTCAACTAACAGACT 58.260 40.909 0.00 0.00 0.00 3.24
384 397 3.498397 ACCGCATTTCAACTAACAGACTG 59.502 43.478 0.00 0.00 0.00 3.51
401 414 1.944024 ACTGAAATTCACGCAAACCGA 59.056 42.857 0.00 0.00 41.02 4.69
402 415 2.552315 ACTGAAATTCACGCAAACCGAT 59.448 40.909 0.00 0.00 41.02 4.18
403 416 3.004315 ACTGAAATTCACGCAAACCGATT 59.996 39.130 0.00 0.00 41.02 3.34
417 430 6.198687 GCAAACCGATTGATATTCATCGAAA 58.801 36.000 15.53 0.00 41.85 3.46
425 438 9.616634 CGATTGATATTCATCGAAATTTGGATT 57.383 29.630 12.47 2.62 38.67 3.01
472 485 5.814314 GTAGCATGCGAATAAGTCTAGTG 57.186 43.478 13.01 0.00 0.00 2.74
473 486 3.126831 AGCATGCGAATAAGTCTAGTGC 58.873 45.455 13.01 0.00 0.00 4.40
510 523 9.559958 CAAATTTGACTACATTAACCAGATGTC 57.440 33.333 13.08 0.00 38.58 3.06
517 530 7.001674 ACTACATTAACCAGATGTCCAACAAA 58.998 34.615 0.00 0.00 38.58 2.83
524 537 5.288804 ACCAGATGTCCAACAAATTTTTCG 58.711 37.500 0.00 0.00 0.00 3.46
529 542 7.169645 CAGATGTCCAACAAATTTTTCGTCAAT 59.830 33.333 0.00 0.00 0.00 2.57
546 559 1.942657 CAATGGATCATGTCGTCCCAC 59.057 52.381 10.54 0.00 33.45 4.61
556 569 0.246635 GTCGTCCCACACATACTGCT 59.753 55.000 0.00 0.00 0.00 4.24
561 574 3.347216 GTCCCACACATACTGCTCATTT 58.653 45.455 0.00 0.00 0.00 2.32
583 598 7.667043 TTTAGCTTTATCCAACAGTGTGTAG 57.333 36.000 0.00 0.00 0.00 2.74
591 606 9.439500 TTTATCCAACAGTGTGTAGGTAAATAC 57.561 33.333 0.00 0.00 0.00 1.89
601 616 1.530283 GGTAAATACCCAGGCGCCT 59.470 57.895 27.08 27.08 40.53 5.52
637 653 7.458409 CCATATTTGGGTTTGATATGAGGAG 57.542 40.000 4.60 0.00 39.56 3.69
640 656 3.281727 TGGGTTTGATATGAGGAGTGC 57.718 47.619 0.00 0.00 0.00 4.40
642 658 2.213499 GGTTTGATATGAGGAGTGCCG 58.787 52.381 0.00 0.00 39.96 5.69
648 664 1.676678 TATGAGGAGTGCCGGTCAGC 61.677 60.000 1.90 0.00 39.96 4.26
660 676 3.423154 GTCAGCCCGGCGTTTGAG 61.423 66.667 6.01 0.00 0.00 3.02
661 677 3.621805 TCAGCCCGGCGTTTGAGA 61.622 61.111 6.01 0.00 0.00 3.27
662 678 3.423154 CAGCCCGGCGTTTGAGAC 61.423 66.667 6.01 0.00 0.00 3.36
663 679 4.699522 AGCCCGGCGTTTGAGACC 62.700 66.667 6.01 0.00 0.00 3.85
677 693 2.156051 GAGACCCGTTTGAGGCGTCT 62.156 60.000 8.06 0.00 41.34 4.18
681 697 1.006102 CCGTTTGAGGCGTCTGTCT 60.006 57.895 8.06 0.00 0.00 3.41
682 698 0.242825 CCGTTTGAGGCGTCTGTCTA 59.757 55.000 8.06 0.00 0.00 2.59
686 702 1.629043 TTGAGGCGTCTGTCTAGGTT 58.371 50.000 8.06 0.00 0.00 3.50
694 710 6.002082 AGGCGTCTGTCTAGGTTAAAATTTT 58.998 36.000 8.75 8.75 0.00 1.82
695 711 7.163441 AGGCGTCTGTCTAGGTTAAAATTTTA 58.837 34.615 6.54 6.54 0.00 1.52
709 725 9.726232 GGTTAAAATTTTATGATTAGGTCGTCC 57.274 33.333 11.33 0.00 0.00 4.79
710 726 9.429600 GTTAAAATTTTATGATTAGGTCGTCCG 57.570 33.333 11.33 0.00 39.05 4.79
711 727 5.668558 AATTTTATGATTAGGTCGTCCGC 57.331 39.130 0.00 0.00 39.05 5.54
712 728 4.395959 TTTTATGATTAGGTCGTCCGCT 57.604 40.909 0.00 0.00 39.05 5.52
715 731 0.745486 TGATTAGGTCGTCCGCTCGA 60.745 55.000 0.00 0.00 39.05 4.04
751 780 3.537874 GAGTGCCCGGCCGTAGAT 61.538 66.667 26.12 5.51 0.00 1.98
752 781 3.792053 GAGTGCCCGGCCGTAGATG 62.792 68.421 26.12 8.02 0.00 2.90
753 782 4.157120 GTGCCCGGCCGTAGATGT 62.157 66.667 26.12 0.00 0.00 3.06
754 783 3.395702 TGCCCGGCCGTAGATGTT 61.396 61.111 26.12 0.00 0.00 2.71
755 784 2.124860 GCCCGGCCGTAGATGTTT 60.125 61.111 26.12 0.00 0.00 2.83
756 785 1.144496 GCCCGGCCGTAGATGTTTA 59.856 57.895 26.12 0.00 0.00 2.01
757 786 0.462403 GCCCGGCCGTAGATGTTTAA 60.462 55.000 26.12 0.00 0.00 1.52
758 787 1.578583 CCCGGCCGTAGATGTTTAAG 58.421 55.000 26.12 3.25 0.00 1.85
759 788 0.935196 CCGGCCGTAGATGTTTAAGC 59.065 55.000 26.12 0.00 0.00 3.09
760 789 1.472728 CCGGCCGTAGATGTTTAAGCT 60.473 52.381 26.12 0.00 0.00 3.74
761 790 2.223876 CCGGCCGTAGATGTTTAAGCTA 60.224 50.000 26.12 0.00 0.00 3.32
762 791 2.793232 CGGCCGTAGATGTTTAAGCTAC 59.207 50.000 19.50 0.00 33.04 3.58
826 1169 5.841957 AAAAAGGATGACATGATACAGCC 57.158 39.130 14.76 14.76 42.05 4.85
827 1170 3.498774 AAGGATGACATGATACAGCCC 57.501 47.619 17.38 11.33 42.62 5.19
828 1171 2.411583 AGGATGACATGATACAGCCCA 58.588 47.619 17.38 0.00 42.62 5.36
829 1172 2.779430 AGGATGACATGATACAGCCCAA 59.221 45.455 17.38 0.00 42.62 4.12
830 1173 2.880890 GGATGACATGATACAGCCCAAC 59.119 50.000 0.00 0.00 36.70 3.77
831 1174 3.544684 GATGACATGATACAGCCCAACA 58.455 45.455 0.00 0.00 0.00 3.33
832 1175 3.650281 TGACATGATACAGCCCAACAT 57.350 42.857 0.00 0.00 0.00 2.71
847 1190 4.757594 CCCAACATGAGAGAGAAGAGAAG 58.242 47.826 0.00 0.00 0.00 2.85
848 1191 4.382901 CCCAACATGAGAGAGAAGAGAAGG 60.383 50.000 0.00 0.00 0.00 3.46
854 1197 3.837146 TGAGAGAGAAGAGAAGGCATTGT 59.163 43.478 0.00 0.00 0.00 2.71
875 1218 2.276732 TCTCTCTTGGGCAACAAAGG 57.723 50.000 0.00 0.00 38.91 3.11
1126 1469 2.609610 AAGCCTACTTCCCGCCCA 60.610 61.111 0.00 0.00 0.00 5.36
1149 1492 0.752009 TCGATCCTGCCGCTCTACTT 60.752 55.000 0.00 0.00 0.00 2.24
1200 1543 4.634184 TGAGTTTGACGCTATCCTACTC 57.366 45.455 0.00 0.00 37.31 2.59
1324 1670 3.535962 CCGCAGAGGAGGAGAGGC 61.536 72.222 0.00 0.00 45.00 4.70
1587 1933 3.393149 GAAGAAGGCCGCCTCCTCC 62.393 68.421 13.72 0.00 34.82 4.30
1588 1934 3.933542 AAGAAGGCCGCCTCCTCCT 62.934 63.158 13.72 5.12 34.82 3.69
1589 1935 3.855853 GAAGGCCGCCTCCTCCTC 61.856 72.222 13.72 1.86 34.82 3.71
1618 1964 1.364626 CTCGAGCAATCACAGTGGCC 61.365 60.000 0.00 0.00 0.00 5.36
1640 1986 1.523258 CCTCGGAGCCATGCAAGAG 60.523 63.158 0.00 0.00 0.00 2.85
1689 2035 9.912634 ATCGAATGAAATGTTGTTTTTACTCAT 57.087 25.926 0.00 0.00 0.00 2.90
1884 2231 5.411669 CAGGTTTTGGTACTTATCCTGTGTC 59.588 44.000 12.71 0.00 37.00 3.67
2064 2525 1.376812 GCGGGTGAACTACAAGGGG 60.377 63.158 0.00 0.00 0.00 4.79
2069 2530 3.774734 GGGTGAACTACAAGGGGAAAAT 58.225 45.455 0.00 0.00 0.00 1.82
2150 2611 4.831674 TCCACTTGATGATGTCATGAGT 57.168 40.909 0.00 2.12 36.54 3.41
2165 2626 7.889589 TGTCATGAGTTCAACTTGTATGTAG 57.110 36.000 0.00 0.00 0.00 2.74
2214 2675 1.320555 CTTCGTTGATGCCGACTTACG 59.679 52.381 0.00 0.00 42.18 3.18
2236 2697 2.508526 ACCTACCAGCTGCTTTTCTTG 58.491 47.619 8.66 0.00 0.00 3.02
2254 2715 2.190578 GGCAGCTAAGTCGCCCAT 59.809 61.111 0.47 0.00 40.07 4.00
2326 2788 8.462589 TGTATCTAGCAATTTTGGCATATGAA 57.537 30.769 6.97 0.00 0.00 2.57
2343 2810 7.201626 GGCATATGAATGTAGCATCAAGATCTC 60.202 40.741 6.97 0.00 35.38 2.75
2443 2911 3.189285 GCATGCCGCAAAACAAATCTAT 58.811 40.909 6.36 0.00 41.79 1.98
2497 2967 2.422303 GCCATGTGCATGCATAGGT 58.578 52.632 25.64 3.88 40.77 3.08
2548 3018 3.942829 TGAGCTTCAGGAGTTGGTATTG 58.057 45.455 0.00 0.00 0.00 1.90
2625 3095 6.712547 CCTAAAAACTAGGAGGAGGCATATTG 59.287 42.308 0.00 0.00 36.85 1.90
2626 3096 5.717119 AAAACTAGGAGGAGGCATATTGT 57.283 39.130 0.00 0.00 0.00 2.71
2649 3119 7.786030 TGTCTATTCAAATGGTTGTGGAAAAA 58.214 30.769 0.00 0.00 36.07 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.186942 TCCGCCTGTTGCTTTTACATATTA 58.813 37.500 0.00 0.00 38.05 0.98
42 43 2.438868 GTTTGTCCATGCCAAACTCC 57.561 50.000 22.17 5.99 45.13 3.85
66 67 2.686715 CGGGCAGGTGAATTTAATCCCT 60.687 50.000 0.00 0.00 0.00 4.20
179 180 3.797184 GCGAGGTTAGTGAGCATCTAAGG 60.797 52.174 0.00 0.00 34.92 2.69
221 229 7.235812 AGGTGTTACTCTCCTAGATTGTTCTTT 59.764 37.037 0.00 0.00 38.15 2.52
222 230 6.726764 AGGTGTTACTCTCCTAGATTGTTCTT 59.273 38.462 0.00 0.00 38.15 2.52
244 252 3.325135 GCCCTAAGTGCATCTACATAGGT 59.675 47.826 0.00 0.00 39.30 3.08
283 291 2.533266 GGATGCAGAAGGAAATTTGCG 58.467 47.619 3.87 0.00 39.34 4.85
292 300 0.178767 TCATGGACGGATGCAGAAGG 59.821 55.000 0.00 0.00 0.00 3.46
295 303 0.612744 TGTTCATGGACGGATGCAGA 59.387 50.000 0.00 0.00 0.00 4.26
297 305 1.902938 TTTGTTCATGGACGGATGCA 58.097 45.000 0.00 0.00 0.00 3.96
304 312 6.183360 CCTTCCACATCTATTTGTTCATGGAC 60.183 42.308 0.00 0.00 0.00 4.02
305 313 5.887598 CCTTCCACATCTATTTGTTCATGGA 59.112 40.000 0.00 0.00 0.00 3.41
306 314 5.887598 TCCTTCCACATCTATTTGTTCATGG 59.112 40.000 0.00 0.00 0.00 3.66
307 315 7.578310 ATCCTTCCACATCTATTTGTTCATG 57.422 36.000 0.00 0.00 0.00 3.07
308 316 7.721399 GGTATCCTTCCACATCTATTTGTTCAT 59.279 37.037 0.00 0.00 0.00 2.57
309 317 7.054124 GGTATCCTTCCACATCTATTTGTTCA 58.946 38.462 0.00 0.00 0.00 3.18
310 318 7.054124 TGGTATCCTTCCACATCTATTTGTTC 58.946 38.462 0.00 0.00 0.00 3.18
311 319 6.969043 TGGTATCCTTCCACATCTATTTGTT 58.031 36.000 0.00 0.00 0.00 2.83
312 320 6.575244 TGGTATCCTTCCACATCTATTTGT 57.425 37.500 0.00 0.00 0.00 2.83
315 328 6.380079 GGATGGTATCCTTCCACATCTATT 57.620 41.667 13.53 0.00 44.38 1.73
331 344 1.552792 TGTGACTGCGATTGGATGGTA 59.447 47.619 0.00 0.00 0.00 3.25
341 354 3.224884 TCGAAATGTATGTGACTGCGA 57.775 42.857 0.00 0.00 0.00 5.10
349 362 4.155099 TGAAATGCGGTTCGAAATGTATGT 59.845 37.500 0.00 0.00 0.00 2.29
371 384 5.140177 GCGTGAATTTCAGTCTGTTAGTTG 58.860 41.667 0.00 0.00 0.00 3.16
379 392 2.032030 CGGTTTGCGTGAATTTCAGTCT 60.032 45.455 0.00 0.00 0.00 3.24
382 395 2.679355 TCGGTTTGCGTGAATTTCAG 57.321 45.000 0.00 0.00 0.00 3.02
383 396 3.003793 TCAATCGGTTTGCGTGAATTTCA 59.996 39.130 0.00 0.00 35.16 2.69
384 397 3.560503 TCAATCGGTTTGCGTGAATTTC 58.439 40.909 0.00 0.00 35.16 2.17
425 438 9.719355 ACGTATGGATCATTTGTGCTATATTTA 57.281 29.630 0.00 0.00 0.00 1.40
430 443 5.639506 GCTACGTATGGATCATTTGTGCTAT 59.360 40.000 0.00 0.00 0.00 2.97
431 444 4.988540 GCTACGTATGGATCATTTGTGCTA 59.011 41.667 0.00 0.00 0.00 3.49
441 454 2.347697 TCGCATGCTACGTATGGATC 57.652 50.000 17.13 0.00 0.00 3.36
459 472 7.331934 TGAGACATTGTTGCACTAGACTTATTC 59.668 37.037 0.00 0.00 0.00 1.75
472 485 6.917477 TGTAGTCAAATTTGAGACATTGTTGC 59.083 34.615 21.05 5.66 37.98 4.17
473 486 9.467258 AATGTAGTCAAATTTGAGACATTGTTG 57.533 29.630 34.40 8.97 44.69 3.33
510 523 6.423302 TGATCCATTGACGAAAAATTTGTTGG 59.577 34.615 0.59 0.00 0.00 3.77
517 530 5.123820 ACGACATGATCCATTGACGAAAAAT 59.876 36.000 15.13 0.00 0.00 1.82
524 537 2.213499 GGGACGACATGATCCATTGAC 58.787 52.381 14.52 0.00 36.65 3.18
529 542 0.249120 GTGTGGGACGACATGATCCA 59.751 55.000 14.52 5.74 36.65 3.41
556 569 6.714810 ACACACTGTTGGATAAAGCTAAATGA 59.285 34.615 0.00 0.00 0.00 2.57
561 574 5.247564 ACCTACACACTGTTGGATAAAGCTA 59.752 40.000 9.46 0.00 44.30 3.32
564 577 7.972832 TTTACCTACACACTGTTGGATAAAG 57.027 36.000 9.46 0.00 44.30 1.85
567 580 7.364939 GGGTATTTACCTACACACTGTTGGATA 60.365 40.741 9.46 0.00 44.30 2.59
571 584 5.553123 TGGGTATTTACCTACACACTGTTG 58.447 41.667 6.71 0.00 45.72 3.33
583 598 0.534427 GAGGCGCCTGGGTATTTACC 60.534 60.000 38.41 11.75 45.71 2.85
591 606 2.348998 GATATGGAGGCGCCTGGG 59.651 66.667 38.41 0.00 37.63 4.45
594 609 4.008933 GCGGATATGGAGGCGCCT 62.009 66.667 33.48 33.48 37.63 5.52
601 616 2.025416 CCAAATATGGGGCGGATATGGA 60.025 50.000 0.00 0.00 43.51 3.41
624 639 1.837439 ACCGGCACTCCTCATATCAAA 59.163 47.619 0.00 0.00 0.00 2.69
626 642 1.040646 GACCGGCACTCCTCATATCA 58.959 55.000 0.00 0.00 0.00 2.15
652 668 0.234884 CTCAAACGGGTCTCAAACGC 59.765 55.000 0.00 0.00 37.46 4.84
653 669 0.865769 CCTCAAACGGGTCTCAAACG 59.134 55.000 0.00 0.00 0.00 3.60
654 670 0.591659 GCCTCAAACGGGTCTCAAAC 59.408 55.000 0.00 0.00 0.00 2.93
655 671 0.882927 CGCCTCAAACGGGTCTCAAA 60.883 55.000 0.00 0.00 0.00 2.69
656 672 1.301401 CGCCTCAAACGGGTCTCAA 60.301 57.895 0.00 0.00 0.00 3.02
657 673 2.342279 CGCCTCAAACGGGTCTCA 59.658 61.111 0.00 0.00 0.00 3.27
658 674 1.737008 GACGCCTCAAACGGGTCTC 60.737 63.158 0.00 0.00 39.41 3.36
659 675 2.207924 AGACGCCTCAAACGGGTCT 61.208 57.895 2.08 2.08 45.58 3.85
660 676 2.027625 CAGACGCCTCAAACGGGTC 61.028 63.158 0.00 0.00 41.98 4.46
661 677 2.030562 CAGACGCCTCAAACGGGT 59.969 61.111 0.00 0.00 34.00 5.28
662 678 2.027625 GACAGACGCCTCAAACGGG 61.028 63.158 0.00 0.00 34.00 5.28
663 679 0.242825 TAGACAGACGCCTCAAACGG 59.757 55.000 0.00 0.00 34.00 4.44
686 702 7.496591 AGCGGACGACCTAATCATAAAATTTTA 59.503 33.333 12.85 12.85 0.00 1.52
694 710 1.534163 CGAGCGGACGACCTAATCATA 59.466 52.381 1.72 0.00 35.09 2.15
695 711 0.311165 CGAGCGGACGACCTAATCAT 59.689 55.000 1.72 0.00 35.09 2.45
699 715 2.758089 GCTCGAGCGGACGACCTAA 61.758 63.158 23.61 0.00 37.37 2.69
700 716 3.200593 GCTCGAGCGGACGACCTA 61.201 66.667 23.61 0.00 37.37 3.08
710 726 2.695646 CGCCTTAAACGCTCGAGC 59.304 61.111 27.64 27.64 37.78 5.03
711 727 2.165301 CCCGCCTTAAACGCTCGAG 61.165 63.158 8.45 8.45 0.00 4.04
712 728 2.125832 CCCGCCTTAAACGCTCGA 60.126 61.111 0.00 0.00 0.00 4.04
715 731 1.520600 CCAAACCCGCCTTAAACGCT 61.521 55.000 0.00 0.00 0.00 5.07
722 751 2.597510 GCACTCCAAACCCGCCTT 60.598 61.111 0.00 0.00 0.00 4.35
744 773 5.527033 GGTAGGTAGCTTAAACATCTACGG 58.473 45.833 0.00 0.00 34.92 4.02
746 775 6.382869 TCGGTAGGTAGCTTAAACATCTAC 57.617 41.667 0.00 0.00 33.72 2.59
747 776 6.604795 AGTTCGGTAGGTAGCTTAAACATCTA 59.395 38.462 0.00 0.00 0.00 1.98
748 777 5.421374 AGTTCGGTAGGTAGCTTAAACATCT 59.579 40.000 0.00 0.00 0.00 2.90
749 778 5.658468 AGTTCGGTAGGTAGCTTAAACATC 58.342 41.667 0.00 0.00 0.00 3.06
751 780 4.768968 AGAGTTCGGTAGGTAGCTTAAACA 59.231 41.667 0.00 0.00 0.00 2.83
752 781 5.321959 AGAGTTCGGTAGGTAGCTTAAAC 57.678 43.478 0.00 0.41 0.00 2.01
753 782 5.067023 GCTAGAGTTCGGTAGGTAGCTTAAA 59.933 44.000 0.00 0.00 32.00 1.52
754 783 4.578105 GCTAGAGTTCGGTAGGTAGCTTAA 59.422 45.833 0.00 0.00 32.00 1.85
755 784 4.133078 GCTAGAGTTCGGTAGGTAGCTTA 58.867 47.826 0.00 0.00 32.00 3.09
756 785 2.950975 GCTAGAGTTCGGTAGGTAGCTT 59.049 50.000 0.00 0.00 32.00 3.74
757 786 2.173143 AGCTAGAGTTCGGTAGGTAGCT 59.827 50.000 0.00 0.00 38.68 3.32
758 787 2.549329 GAGCTAGAGTTCGGTAGGTAGC 59.451 54.545 0.00 0.00 34.38 3.58
759 788 3.140623 GGAGCTAGAGTTCGGTAGGTAG 58.859 54.545 0.00 0.00 0.00 3.18
760 789 2.507058 TGGAGCTAGAGTTCGGTAGGTA 59.493 50.000 0.00 0.00 0.00 3.08
761 790 1.284198 TGGAGCTAGAGTTCGGTAGGT 59.716 52.381 0.00 0.00 0.00 3.08
762 791 2.054232 TGGAGCTAGAGTTCGGTAGG 57.946 55.000 0.00 0.00 0.00 3.18
813 1151 3.544684 TCATGTTGGGCTGTATCATGTC 58.455 45.455 0.00 0.00 37.64 3.06
815 1153 3.812262 TCTCATGTTGGGCTGTATCATG 58.188 45.455 0.00 0.00 37.71 3.07
820 1163 2.820178 TCTCTCTCATGTTGGGCTGTA 58.180 47.619 0.00 0.00 0.00 2.74
821 1164 1.649321 TCTCTCTCATGTTGGGCTGT 58.351 50.000 0.00 0.00 0.00 4.40
822 1165 2.235650 TCTTCTCTCTCATGTTGGGCTG 59.764 50.000 0.00 0.00 0.00 4.85
823 1166 2.500910 CTCTTCTCTCTCATGTTGGGCT 59.499 50.000 0.00 0.00 0.00 5.19
824 1167 2.499289 TCTCTTCTCTCTCATGTTGGGC 59.501 50.000 0.00 0.00 0.00 5.36
825 1168 4.382901 CCTTCTCTTCTCTCTCATGTTGGG 60.383 50.000 0.00 0.00 0.00 4.12
826 1169 4.757594 CCTTCTCTTCTCTCTCATGTTGG 58.242 47.826 0.00 0.00 0.00 3.77
827 1170 4.183101 GCCTTCTCTTCTCTCTCATGTTG 58.817 47.826 0.00 0.00 0.00 3.33
828 1171 3.837146 TGCCTTCTCTTCTCTCTCATGTT 59.163 43.478 0.00 0.00 0.00 2.71
829 1172 3.439154 TGCCTTCTCTTCTCTCTCATGT 58.561 45.455 0.00 0.00 0.00 3.21
830 1173 4.675976 ATGCCTTCTCTTCTCTCTCATG 57.324 45.455 0.00 0.00 0.00 3.07
831 1174 4.470664 ACAATGCCTTCTCTTCTCTCTCAT 59.529 41.667 0.00 0.00 0.00 2.90
832 1175 3.837146 ACAATGCCTTCTCTTCTCTCTCA 59.163 43.478 0.00 0.00 0.00 3.27
847 1190 1.203287 GCCCAAGAGAGAAACAATGCC 59.797 52.381 0.00 0.00 0.00 4.40
848 1191 1.888512 TGCCCAAGAGAGAAACAATGC 59.111 47.619 0.00 0.00 0.00 3.56
854 1197 2.958355 CCTTTGTTGCCCAAGAGAGAAA 59.042 45.455 0.00 0.00 33.75 2.52
875 1218 3.119849 CCTTTTATAGTGTGGCACAGTGC 60.120 47.826 32.66 17.97 41.80 4.40
1104 1447 1.900545 GCGGGAAGTAGGCTTGAGGT 61.901 60.000 0.00 0.00 34.61 3.85
1126 1469 3.077556 AGCGGCAGGATCGAAGGT 61.078 61.111 1.45 0.00 0.00 3.50
1200 1543 1.807573 GAGGTGAGCCGCTTCTTCG 60.808 63.158 0.00 0.00 40.50 3.79
1288 1634 3.830192 GCCAAATCCAGCGCCAGG 61.830 66.667 2.29 7.04 0.00 4.45
1592 1938 2.279784 GATTGCTCGAGGCCGGAG 60.280 66.667 15.58 19.15 40.92 4.63
1779 2125 4.380867 CCCAGCCATCGCCATTAAATAATC 60.381 45.833 0.00 0.00 34.57 1.75
1824 2171 9.170890 ACATATTCCTGATAGGGAAACTGATTA 57.829 33.333 12.22 0.00 46.73 1.75
1863 2210 5.232463 TCGACACAGGATAAGTACCAAAAC 58.768 41.667 0.00 0.00 0.00 2.43
2112 2573 7.504403 TCAAGTGGAAGGCAAATTTCAAAATA 58.496 30.769 0.00 0.00 0.00 1.40
2121 2582 4.091549 ACATCATCAAGTGGAAGGCAAAT 58.908 39.130 0.00 0.00 0.00 2.32
2125 2586 2.715046 TGACATCATCAAGTGGAAGGC 58.285 47.619 0.00 0.00 33.02 4.35
2126 2587 4.520179 TCATGACATCATCAAGTGGAAGG 58.480 43.478 0.00 0.00 41.93 3.46
2128 2589 5.169992 ACTCATGACATCATCAAGTGGAA 57.830 39.130 0.00 0.00 41.93 3.53
2150 2611 6.540551 TCACAAAGCACTACATACAAGTTGAA 59.459 34.615 10.54 0.00 0.00 2.69
2165 2626 5.678483 CGATACATTAGCAATCACAAAGCAC 59.322 40.000 0.00 0.00 0.00 4.40
2214 2675 3.336138 AGAAAAGCAGCTGGTAGGTAC 57.664 47.619 20.51 9.29 0.00 3.34
2253 2714 7.281040 ACATTGCAAAACTATAGCATGCTAT 57.719 32.000 35.68 35.68 41.58 2.97
2254 2715 6.698008 ACATTGCAAAACTATAGCATGCTA 57.302 33.333 28.72 28.72 38.19 3.49
2326 2788 5.737860 TGTTGTGAGATCTTGATGCTACAT 58.262 37.500 0.00 0.00 0.00 2.29
2343 2810 7.095313 GCATCTCAGTGAATAGGATATGTTGTG 60.095 40.741 0.00 0.00 0.00 3.33
2490 2960 7.275560 GGATTAACAAAACATTCACACCTATGC 59.724 37.037 0.00 0.00 0.00 3.14
2491 2961 8.303156 TGGATTAACAAAACATTCACACCTATG 58.697 33.333 0.00 0.00 0.00 2.23
2493 2963 7.825331 TGGATTAACAAAACATTCACACCTA 57.175 32.000 0.00 0.00 0.00 3.08
2494 2964 6.723298 TGGATTAACAAAACATTCACACCT 57.277 33.333 0.00 0.00 0.00 4.00
2495 2965 7.778470 TTTGGATTAACAAAACATTCACACC 57.222 32.000 0.00 0.00 37.40 4.16
2496 2966 8.281893 CCATTTGGATTAACAAAACATTCACAC 58.718 33.333 0.00 0.00 42.91 3.82
2497 2967 8.206867 TCCATTTGGATTAACAAAACATTCACA 58.793 29.630 0.00 0.00 42.91 3.58
2524 2994 2.787994 ACCAACTCCTGAAGCTCATTG 58.212 47.619 0.00 0.00 0.00 2.82
2548 3018 1.670967 GCTTGAAGGTTTCCATGCTGC 60.671 52.381 0.00 0.00 32.70 5.25


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

AutoCloner maintained by Alex Coulton.