Multiple sequence alignment - TraesCS7D01G486800

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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 TraesCS7D01G486800 chr7D 100.000 3041 0 0 1 3041 596896632 596899672 0.000000e+00 5616
1 TraesCS7D01G486800 chr7D 90.979 1042 75 12 1470 2508 596946688 596947713 0.000000e+00 1386
2 TraesCS7D01G486800 chr7D 90.883 1042 76 12 1470 2508 596917269 596918294 0.000000e+00 1380
3 TraesCS7D01G486800 chr7D 90.787 1042 77 12 1470 2508 596929853 596930878 0.000000e+00 1375
4 TraesCS7D01G486800 chr7D 87.706 545 44 14 2507 3041 330089163 330089694 5.570000e-172 614
5 TraesCS7D01G486800 chr7D 84.153 366 48 5 2110 2473 597407482 597407839 2.240000e-91 346
6 TraesCS7D01G486800 chr7A 93.815 2506 128 16 1 2499 690053424 690055909 0.000000e+00 3744
7 TraesCS7D01G486800 chr7A 86.550 855 82 15 11 843 724999092 724998249 0.000000e+00 911
8 TraesCS7D01G486800 chr7A 85.965 855 87 13 11 843 160250650 160251493 0.000000e+00 883
9 TraesCS7D01G486800 chr7A 82.228 377 57 6 1781 2149 690106407 690106781 1.760000e-82 316
10 TraesCS7D01G486800 chr7B 93.072 2165 122 18 308 2469 675722607 675724746 0.000000e+00 3142
11 TraesCS7D01G486800 chr7B 87.150 607 47 7 1814 2403 675968744 675969336 0.000000e+00 660
12 TraesCS7D01G486800 chr7B 87.385 436 30 7 1814 2226 675750272 675750705 7.630000e-131 477
13 TraesCS7D01G486800 chr7B 88.095 210 23 2 40 247 675722383 675722592 6.510000e-62 248
14 TraesCS7D01G486800 chr7B 90.826 109 10 0 1786 1894 675840837 675840945 2.440000e-31 147
15 TraesCS7D01G486800 chrUn 90.883 1042 76 12 1470 2508 348606529 348607554 0.000000e+00 1380
16 TraesCS7D01G486800 chrUn 90.787 1042 77 12 1470 2508 373138745 373139770 0.000000e+00 1375
17 TraesCS7D01G486800 chrUn 90.000 350 30 3 2160 2508 320187656 320187311 5.980000e-122 448
18 TraesCS7D01G486800 chr1A 86.682 856 79 17 11 843 29463225 29462382 0.000000e+00 917
19 TraesCS7D01G486800 chr1A 86.449 856 81 15 11 843 166855187 166854344 0.000000e+00 905
20 TraesCS7D01G486800 chr1A 86.332 856 82 14 11 843 25115050 25115893 0.000000e+00 900
21 TraesCS7D01G486800 chr2A 86.565 856 78 16 11 843 198844977 198844136 0.000000e+00 909
22 TraesCS7D01G486800 chr2A 86.480 858 72 22 11 843 646009352 646010190 0.000000e+00 902
23 TraesCS7D01G486800 chr2A 84.162 543 62 18 2509 3041 256125886 256125358 3.500000e-139 505
24 TraesCS7D01G486800 chr3A 86.348 857 80 18 11 843 582009796 582008953 0.000000e+00 900
25 TraesCS7D01G486800 chr3A 89.776 313 23 4 531 843 622037075 622036772 2.840000e-105 392
26 TraesCS7D01G486800 chr3A 89.677 310 23 4 531 840 138897284 138897584 1.320000e-103 387
27 TraesCS7D01G486800 chr4A 85.897 858 83 20 11 843 241097172 241098016 0.000000e+00 880
28 TraesCS7D01G486800 chr4A 85.748 856 87 16 11 843 374399079 374398236 0.000000e+00 872
29 TraesCS7D01G486800 chr6A 85.915 710 70 12 11 697 92995480 92994778 0.000000e+00 730
30 TraesCS7D01G486800 chr6A 83.054 537 72 12 2507 3041 409087295 409087814 1.280000e-128 470
31 TraesCS7D01G486800 chr1D 90.993 544 33 11 2507 3041 41345790 41346326 0.000000e+00 719
32 TraesCS7D01G486800 chr1D 85.662 551 52 20 2505 3041 25574337 25573800 3.430000e-154 555
33 TraesCS7D01G486800 chr3B 90.164 549 36 10 2505 3041 797637474 797636932 0.000000e+00 699
34 TraesCS7D01G486800 chr3D 92.873 463 24 7 2505 2962 578435279 578435737 0.000000e+00 664
35 TraesCS7D01G486800 chr3D 86.162 542 58 15 2505 3041 3191475 3192004 1.220000e-158 569
36 TraesCS7D01G486800 chr1B 89.178 499 46 5 2548 3041 666271617 666271122 1.550000e-172 616
37 TraesCS7D01G486800 chr5A 89.457 313 24 4 531 843 269092618 269092315 1.320000e-103 387
38 TraesCS7D01G486800 chr5A 80.783 281 35 13 1 276 694384428 694384694 5.140000e-48 202


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 TraesCS7D01G486800 chr7D 596896632 596899672 3040 False 5616 5616 100.0000 1 3041 1 chr7D.!!$F2 3040
1 TraesCS7D01G486800 chr7D 596946688 596947713 1025 False 1386 1386 90.9790 1470 2508 1 chr7D.!!$F5 1038
2 TraesCS7D01G486800 chr7D 596917269 596918294 1025 False 1380 1380 90.8830 1470 2508 1 chr7D.!!$F3 1038
3 TraesCS7D01G486800 chr7D 596929853 596930878 1025 False 1375 1375 90.7870 1470 2508 1 chr7D.!!$F4 1038
4 TraesCS7D01G486800 chr7D 330089163 330089694 531 False 614 614 87.7060 2507 3041 1 chr7D.!!$F1 534
5 TraesCS7D01G486800 chr7A 690053424 690055909 2485 False 3744 3744 93.8150 1 2499 1 chr7A.!!$F2 2498
6 TraesCS7D01G486800 chr7A 724998249 724999092 843 True 911 911 86.5500 11 843 1 chr7A.!!$R1 832
7 TraesCS7D01G486800 chr7A 160250650 160251493 843 False 883 883 85.9650 11 843 1 chr7A.!!$F1 832
8 TraesCS7D01G486800 chr7B 675722383 675724746 2363 False 1695 3142 90.5835 40 2469 2 chr7B.!!$F4 2429
9 TraesCS7D01G486800 chr7B 675968744 675969336 592 False 660 660 87.1500 1814 2403 1 chr7B.!!$F3 589
10 TraesCS7D01G486800 chrUn 348606529 348607554 1025 False 1380 1380 90.8830 1470 2508 1 chrUn.!!$F1 1038
11 TraesCS7D01G486800 chrUn 373138745 373139770 1025 False 1375 1375 90.7870 1470 2508 1 chrUn.!!$F2 1038
12 TraesCS7D01G486800 chr1A 29462382 29463225 843 True 917 917 86.6820 11 843 1 chr1A.!!$R1 832
13 TraesCS7D01G486800 chr1A 166854344 166855187 843 True 905 905 86.4490 11 843 1 chr1A.!!$R2 832
14 TraesCS7D01G486800 chr1A 25115050 25115893 843 False 900 900 86.3320 11 843 1 chr1A.!!$F1 832
15 TraesCS7D01G486800 chr2A 198844136 198844977 841 True 909 909 86.5650 11 843 1 chr2A.!!$R1 832
16 TraesCS7D01G486800 chr2A 646009352 646010190 838 False 902 902 86.4800 11 843 1 chr2A.!!$F1 832
17 TraesCS7D01G486800 chr2A 256125358 256125886 528 True 505 505 84.1620 2509 3041 1 chr2A.!!$R2 532
18 TraesCS7D01G486800 chr3A 582008953 582009796 843 True 900 900 86.3480 11 843 1 chr3A.!!$R1 832
19 TraesCS7D01G486800 chr4A 241097172 241098016 844 False 880 880 85.8970 11 843 1 chr4A.!!$F1 832
20 TraesCS7D01G486800 chr4A 374398236 374399079 843 True 872 872 85.7480 11 843 1 chr4A.!!$R1 832
21 TraesCS7D01G486800 chr6A 92994778 92995480 702 True 730 730 85.9150 11 697 1 chr6A.!!$R1 686
22 TraesCS7D01G486800 chr6A 409087295 409087814 519 False 470 470 83.0540 2507 3041 1 chr6A.!!$F1 534
23 TraesCS7D01G486800 chr1D 41345790 41346326 536 False 719 719 90.9930 2507 3041 1 chr1D.!!$F1 534
24 TraesCS7D01G486800 chr1D 25573800 25574337 537 True 555 555 85.6620 2505 3041 1 chr1D.!!$R1 536
25 TraesCS7D01G486800 chr3B 797636932 797637474 542 True 699 699 90.1640 2505 3041 1 chr3B.!!$R1 536
26 TraesCS7D01G486800 chr3D 3191475 3192004 529 False 569 569 86.1620 2505 3041 1 chr3D.!!$F1 536

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
306 316 0.447801 GCAATAACGCCACTGACCTG 59.552 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2260 2317 0.693049 AGCAGGGAACAGGTAAGTGG 59.307 55.0 0.0 0.0 0.0 4.0 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
79 80 4.024048 ACTCGAAATTGTTGGTGCTAACAG 60.024 41.667 1.70 0.00 41.18 3.16
135 136 2.011947 TCTCCACACGGTCTATGTACG 58.988 52.381 0.00 0.00 0.00 3.67
221 222 3.254166 TCCTTGCTGCTTGAAGAATTGAC 59.746 43.478 0.00 0.00 0.00 3.18
259 264 1.302752 TGCAGATGCGTCAGCCTTT 60.303 52.632 19.31 0.00 45.83 3.11
291 301 3.880490 TGTTTCCACAGTTCTAACGCAAT 59.120 39.130 0.00 0.00 0.00 3.56
298 308 2.413796 CAGTTCTAACGCAATAACGCCA 59.586 45.455 0.00 0.00 36.19 5.69
306 316 0.447801 GCAATAACGCCACTGACCTG 59.552 55.000 0.00 0.00 0.00 4.00
316 326 2.749621 GCCACTGACCTGATAAACTTGG 59.250 50.000 0.00 0.00 0.00 3.61
368 385 3.667360 GCCAATGCTCCAGAAATTGTTT 58.333 40.909 0.00 0.00 30.84 2.83
517 542 5.159273 TGTAAGCCACACATGATTGAGTA 57.841 39.130 0.00 0.00 30.04 2.59
521 546 2.880890 GCCACACATGATTGAGTATCCC 59.119 50.000 0.00 0.00 31.87 3.85
522 547 3.434167 GCCACACATGATTGAGTATCCCT 60.434 47.826 0.00 0.00 31.87 4.20
523 548 4.132336 CCACACATGATTGAGTATCCCTG 58.868 47.826 0.00 0.00 31.87 4.45
526 551 4.471025 ACACATGATTGAGTATCCCTGTCA 59.529 41.667 0.00 0.00 30.16 3.58
527 552 5.131642 ACACATGATTGAGTATCCCTGTCAT 59.868 40.000 0.00 0.00 30.16 3.06
528 553 6.060136 CACATGATTGAGTATCCCTGTCATT 58.940 40.000 0.00 0.00 30.16 2.57
529 554 7.147497 ACACATGATTGAGTATCCCTGTCATTA 60.147 37.037 0.00 0.00 30.16 1.90
546 576 5.542635 TGTCATTACTGTCAAGGTTCCTAGT 59.457 40.000 0.00 0.00 0.00 2.57
603 633 6.748333 ACTGTTGATGATACTCCAAACATG 57.252 37.500 0.00 0.00 0.00 3.21
643 674 7.654022 TTAATTTTTCACAGTTCTCCCAGTT 57.346 32.000 0.00 0.00 0.00 3.16
644 675 8.754991 TTAATTTTTCACAGTTCTCCCAGTTA 57.245 30.769 0.00 0.00 0.00 2.24
645 676 7.654022 AATTTTTCACAGTTCTCCCAGTTAA 57.346 32.000 0.00 0.00 0.00 2.01
646 677 6.445357 TTTTTCACAGTTCTCCCAGTTAAC 57.555 37.500 0.00 0.00 0.00 2.01
647 678 5.367945 TTTCACAGTTCTCCCAGTTAACT 57.632 39.130 1.12 1.12 33.82 2.24
682 717 9.586435 AGCATTTTAAATTACTGCTTGATTACC 57.414 29.630 8.45 0.00 40.08 2.85
714 749 6.127814 GGGTAGCACCAGTAAACCTTATTTTC 60.128 42.308 7.49 0.00 41.02 2.29
755 790 5.078411 ACATCACCACAGCTCTACTTAAG 57.922 43.478 0.00 0.00 0.00 1.85
781 816 6.531594 TCTCATTGCCGAAATTATATCTAGCG 59.468 38.462 0.00 0.00 0.00 4.26
786 821 7.987268 TGCCGAAATTATATCTAGCGAATAG 57.013 36.000 0.00 0.00 0.00 1.73
787 822 7.768240 TGCCGAAATTATATCTAGCGAATAGA 58.232 34.615 0.89 0.89 44.65 1.98
916 951 5.026038 TCTAGACTCTACTGTGGACTAGC 57.974 47.826 11.55 0.00 0.00 3.42
921 956 2.948979 CTCTACTGTGGACTAGCTCTGG 59.051 54.545 0.00 0.00 0.00 3.86
946 981 4.935702 TGTTCTGTTCATTTTCTTGCAGG 58.064 39.130 0.00 0.00 0.00 4.85
1038 1073 3.801293 GCAACAATTCTTTGGCTCTTGCT 60.801 43.478 0.00 0.00 37.76 3.91
1060 1095 2.671070 CACGGCCAGGAATGGAGT 59.329 61.111 2.24 0.00 0.00 3.85
1551 1586 4.340617 TCCAAACACTTCCAGACAAGTTT 58.659 39.130 0.00 0.00 34.17 2.66
1579 1614 0.895559 TGCCGTGAGCTTCTCAGAGA 60.896 55.000 0.00 0.00 41.46 3.10
1617 1652 2.351276 GGTGGCCTGGACAACGAT 59.649 61.111 2.31 0.00 0.00 3.73
1713 1749 1.833630 CAGCTTAGTCCTGATGGGTCA 59.166 52.381 0.00 0.00 36.25 4.02
1725 1761 2.023015 TGATGGGTCATACCTCCTCACT 60.023 50.000 0.00 0.00 38.64 3.41
1806 1842 3.366374 GCAACATCAAGACCTTTACAGGC 60.366 47.826 0.00 0.00 45.56 4.85
1971 2022 0.669318 GTTCCGTCAATGAGACCGCA 60.669 55.000 0.00 0.00 44.66 5.69
2088 2139 7.950124 AGGAATTCCTGTAATATTTGGGTATGG 59.050 37.037 26.52 0.00 46.55 2.74
2091 2142 9.722317 AATTCCTGTAATATTTGGGTATGGAAA 57.278 29.630 0.00 0.00 34.23 3.13
2127 2178 0.317479 GGTACCGTGTTGCTCTGTCT 59.683 55.000 0.00 0.00 0.00 3.41
2128 2179 1.419374 GTACCGTGTTGCTCTGTCTG 58.581 55.000 0.00 0.00 0.00 3.51
2178 2229 6.690957 TCGAATTTTCAAACTGCTACTTGTTG 59.309 34.615 0.00 0.00 0.00 3.33
2192 2243 2.289257 ACTTGTTGAGTACCCTTACGGC 60.289 50.000 0.00 0.00 36.65 5.68
2193 2244 1.636148 TGTTGAGTACCCTTACGGCT 58.364 50.000 0.00 0.00 32.93 5.52
2194 2245 1.547372 TGTTGAGTACCCTTACGGCTC 59.453 52.381 0.00 0.00 32.93 4.70
2209 2266 3.275999 ACGGCTCTTGTTAAACTTGTGT 58.724 40.909 0.00 0.00 0.00 3.72
2241 2298 5.335661 GCCTTTTAATCACTAACTGGTGTGG 60.336 44.000 0.00 0.00 38.28 4.17
2250 2307 1.794714 AACTGGTGTGGTCTCTCTGT 58.205 50.000 0.00 0.00 0.00 3.41
2260 2317 4.220821 TGTGGTCTCTCTGTAAACCTGATC 59.779 45.833 0.00 0.00 32.82 2.92
2302 2359 6.453922 GCTGAATTACGTTGTCTAACTAGTGC 60.454 42.308 0.00 0.00 34.60 4.40
2317 2374 1.089920 AGTGCATCGAGTCAAATGCC 58.910 50.000 19.46 13.04 46.10 4.40
2334 2391 6.314400 TCAAATGCCGTTATAGTCTGTAAACC 59.686 38.462 0.00 0.00 0.00 3.27
2352 2409 9.503399 CTGTAAACCTACCTTTTTCTGTTAGAT 57.497 33.333 0.00 0.00 0.00 1.98
2484 2545 8.771920 TTTAGTCAATCGTAGATTGTCAACAT 57.228 30.769 18.59 4.50 45.12 2.71
2606 2668 2.347114 CGTGATGCCCCACAGTCA 59.653 61.111 6.42 0.00 36.89 3.41
2670 2734 3.046390 CGGCTCAAATTTAACGCAAACA 58.954 40.909 0.00 0.00 0.00 2.83
2674 2738 4.615121 GCTCAAATTTAACGCAAACATCGA 59.385 37.500 0.00 0.00 0.00 3.59
2749 2819 3.082579 GCTCCTCGCCGTCTCCATT 62.083 63.158 0.00 0.00 0.00 3.16
2760 2830 2.587194 CTCCATTGCCGCTCCTCG 60.587 66.667 0.00 0.00 38.08 4.63
2761 2831 3.376935 CTCCATTGCCGCTCCTCGT 62.377 63.158 0.00 0.00 36.19 4.18
2762 2832 2.892425 CCATTGCCGCTCCTCGTC 60.892 66.667 0.00 0.00 36.19 4.20
2861 2949 2.435693 GCCGTCCCTGCTGTATCCT 61.436 63.158 0.00 0.00 0.00 3.24
2870 2958 1.149401 GCTGTATCCTTCCCCTGGC 59.851 63.158 0.00 0.00 0.00 4.85
2873 2961 1.149401 GTATCCTTCCCCTGGCTGC 59.851 63.158 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 5.057819 TGTTAGCACCAACAATTTCGAGTA 58.942 37.500 0.00 0.00 35.53 2.59
79 80 6.129009 GCATCACAAAATCACACAAATCAGAC 60.129 38.462 0.00 0.00 0.00 3.51
135 136 9.780413 CAAAAGCATCTACCTTAGAAATTTCTC 57.220 33.333 23.70 6.09 38.50 2.87
202 203 4.652421 TTGTCAATTCTTCAAGCAGCAA 57.348 36.364 0.00 0.00 0.00 3.91
203 204 4.652421 TTTGTCAATTCTTCAAGCAGCA 57.348 36.364 0.00 0.00 0.00 4.41
213 214 5.656416 TGGAGTGTTCCTTTTTGTCAATTCT 59.344 36.000 0.00 0.00 44.36 2.40
221 222 3.799917 GCACCATGGAGTGTTCCTTTTTG 60.800 47.826 21.47 1.89 44.36 2.44
259 264 2.203084 TGGAAACAGAACCGCGCA 60.203 55.556 8.75 0.00 35.01 6.09
291 301 3.259876 AGTTTATCAGGTCAGTGGCGTTA 59.740 43.478 0.00 0.00 0.00 3.18
306 316 4.630069 AGTGTGTATGCGACCAAGTTTATC 59.370 41.667 0.00 0.00 0.00 1.75
316 326 1.135972 CAGCCAAAGTGTGTATGCGAC 60.136 52.381 0.00 0.00 0.00 5.19
368 385 3.506455 GGTTGTCAGCAGACTAGTAGTGA 59.494 47.826 7.76 0.00 45.20 3.41
517 542 3.846588 ACCTTGACAGTAATGACAGGGAT 59.153 43.478 25.21 10.60 35.19 3.85
521 546 4.899502 AGGAACCTTGACAGTAATGACAG 58.100 43.478 0.00 0.00 0.00 3.51
522 547 4.974645 AGGAACCTTGACAGTAATGACA 57.025 40.909 0.00 0.00 0.00 3.58
523 548 6.038997 ACTAGGAACCTTGACAGTAATGAC 57.961 41.667 9.04 0.00 0.00 3.06
526 551 6.681729 TGAACTAGGAACCTTGACAGTAAT 57.318 37.500 9.04 0.00 0.00 1.89
527 552 5.510861 GCTGAACTAGGAACCTTGACAGTAA 60.511 44.000 21.20 6.48 33.83 2.24
528 553 4.021368 GCTGAACTAGGAACCTTGACAGTA 60.021 45.833 21.20 2.42 33.83 2.74
529 554 3.244249 GCTGAACTAGGAACCTTGACAGT 60.244 47.826 21.20 10.19 33.83 3.55
546 576 2.203480 GCCACACAAGGGGCTGAA 60.203 61.111 0.59 0.00 46.74 3.02
590 620 5.877012 CAGTAGCAGAACATGTTTGGAGTAT 59.123 40.000 13.36 0.00 0.00 2.12
603 633 4.954092 AATTAAGCAGCAGTAGCAGAAC 57.046 40.909 0.00 0.00 45.49 3.01
682 717 3.958147 CTGGTGCTACCCAGTGCCG 62.958 68.421 8.86 0.00 45.81 5.69
714 749 6.706270 GTGATGTAACCCAGGTCAATATACAG 59.294 42.308 4.99 0.00 0.00 2.74
755 790 7.463383 CGCTAGATATAATTTCGGCAATGAGAC 60.463 40.741 0.00 0.00 0.00 3.36
786 821 8.979574 GCACAAGTAGTACCACAGATAATAATC 58.020 37.037 0.00 0.00 0.00 1.75
787 822 8.705594 AGCACAAGTAGTACCACAGATAATAAT 58.294 33.333 0.00 0.00 0.00 1.28
788 823 8.074613 AGCACAAGTAGTACCACAGATAATAA 57.925 34.615 0.00 0.00 0.00 1.40
789 824 7.655521 AGCACAAGTAGTACCACAGATAATA 57.344 36.000 0.00 0.00 0.00 0.98
790 825 6.546428 AGCACAAGTAGTACCACAGATAAT 57.454 37.500 0.00 0.00 0.00 1.28
791 826 5.995565 AGCACAAGTAGTACCACAGATAA 57.004 39.130 0.00 0.00 0.00 1.75
792 827 5.245301 ACAAGCACAAGTAGTACCACAGATA 59.755 40.000 0.00 0.00 0.00 1.98
916 951 5.762218 AGAAAATGAACAGAACAGACCAGAG 59.238 40.000 0.00 0.00 0.00 3.35
921 956 5.581605 TGCAAGAAAATGAACAGAACAGAC 58.418 37.500 0.00 0.00 0.00 3.51
946 981 9.294030 CCTGTCACAAAGAAAAATATAAGATGC 57.706 33.333 0.00 0.00 0.00 3.91
1060 1095 3.143515 TTGCTGCACGTTGCCCAA 61.144 55.556 0.00 7.82 44.23 4.12
1098 1133 2.088096 TTTCCCACCAGGCCCAAGA 61.088 57.895 0.00 0.00 34.51 3.02
1551 1586 1.186200 AGCTCACGGCAGTAATCTGA 58.814 50.000 0.00 0.00 43.76 3.27
1579 1614 4.074970 CCAGTGAAAACCTTATCTGCAGT 58.925 43.478 14.67 3.75 0.00 4.40
1617 1652 1.001974 CGAAGATCCCACCACTTGACA 59.998 52.381 0.00 0.00 0.00 3.58
1713 1749 3.259374 CCATCGCATTAGTGAGGAGGTAT 59.741 47.826 0.00 0.00 38.25 2.73
1725 1761 3.133691 GAGCTCATTGTCCATCGCATTA 58.866 45.455 9.40 0.00 0.00 1.90
1806 1842 3.817084 TCTTCTCAAAGTTGTGCTGATGG 59.183 43.478 0.00 0.00 33.95 3.51
1971 2022 2.757124 GGGCTCGGTGGGATGGAAT 61.757 63.158 0.00 0.00 0.00 3.01
2088 2139 2.224314 CCTGCGGTCTTCAGTTCTTTTC 59.776 50.000 0.00 0.00 0.00 2.29
2091 2142 0.759346 ACCTGCGGTCTTCAGTTCTT 59.241 50.000 0.00 0.00 0.00 2.52
2127 2178 3.129813 GCAATCCAGCATTCAATGTCTCA 59.870 43.478 0.00 0.00 0.00 3.27
2128 2179 3.380637 AGCAATCCAGCATTCAATGTCTC 59.619 43.478 0.00 0.00 36.85 3.36
2192 2243 7.134815 CAGAATGGACACAAGTTTAACAAGAG 58.865 38.462 0.00 0.00 0.00 2.85
2193 2244 6.459573 GCAGAATGGACACAAGTTTAACAAGA 60.460 38.462 0.00 0.00 35.86 3.02
2194 2245 5.687285 GCAGAATGGACACAAGTTTAACAAG 59.313 40.000 0.00 0.00 35.86 3.16
2209 2266 7.121168 CAGTTAGTGATTAAAAGGCAGAATGGA 59.879 37.037 0.00 0.00 35.86 3.41
2241 2298 4.464597 AGTGGATCAGGTTTACAGAGAGAC 59.535 45.833 0.00 0.00 0.00 3.36
2250 2307 5.280317 GGAACAGGTAAGTGGATCAGGTTTA 60.280 44.000 0.00 0.00 0.00 2.01
2260 2317 0.693049 AGCAGGGAACAGGTAAGTGG 59.307 55.000 0.00 0.00 0.00 4.00
2302 2359 4.745125 ACTATAACGGCATTTGACTCGATG 59.255 41.667 0.00 0.00 0.00 3.84
2317 2374 8.992835 AAAAGGTAGGTTTACAGACTATAACG 57.007 34.615 0.00 0.00 0.00 3.18
2334 2391 9.495572 AGAAACTCATCTAACAGAAAAAGGTAG 57.504 33.333 0.00 0.00 0.00 3.18
2390 2450 6.555315 AGGCAATCTTTTAGCTGAATTAACG 58.445 36.000 0.00 0.00 0.00 3.18
2396 2457 6.403866 TTTTGAGGCAATCTTTTAGCTGAA 57.596 33.333 0.00 0.00 0.00 3.02
2455 2516 9.653287 TTGACAATCTACGATTGACTAAAAGAT 57.347 29.630 19.96 0.00 33.51 2.40
2642 2706 3.121496 CGTTAAATTTGAGCCGTGTTTGC 60.121 43.478 0.00 0.00 0.00 3.68
2808 2882 1.491563 GCAACTACACGCGGTTCTG 59.508 57.895 12.47 1.02 0.00 3.02
2856 2944 2.078665 GGCAGCCAGGGGAAGGATA 61.079 63.158 6.55 0.00 0.00 2.59
2995 3084 1.437772 CTACCGCGACGAGATGGTCT 61.438 60.000 8.23 0.00 35.93 3.85


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

AutoCloner maintained by Alex Coulton.