Multiple sequence alignment - TraesCS2D01G420200

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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 TraesCS2D01G420200 chr2D 100.000 3126 0 0 1 3126 534308456 534311581 0.000000e+00 5773.0
1 TraesCS2D01G420200 chr2D 78.195 532 112 3 1 532 324889816 324889289 1.390000e-88 337.0
2 TraesCS2D01G420200 chr2B 95.672 1756 47 14 645 2379 635022393 635024140 0.000000e+00 2795.0
3 TraesCS2D01G420200 chr2B 95.285 615 27 2 1 614 635021780 635022393 0.000000e+00 974.0
4 TraesCS2D01G420200 chr2B 91.016 512 28 7 2440 2940 635024155 635024659 0.000000e+00 675.0
5 TraesCS2D01G420200 chr2B 94.886 176 9 0 2949 3124 635024777 635024952 3.070000e-70 276.0
6 TraesCS2D01G420200 chr2B 73.443 546 132 13 3 542 379117449 379116911 3.180000e-45 193.0
7 TraesCS2D01G420200 chr6B 93.301 627 42 0 1 627 124473343 124472717 0.000000e+00 926.0
8 TraesCS2D01G420200 chr1A 81.922 614 106 4 1 611 50779376 50779987 5.980000e-142 514.0
9 TraesCS2D01G420200 chr3D 79.604 505 101 2 1 505 535911491 535911993 8.240000e-96 361.0
10 TraesCS2D01G420200 chr3D 77.401 177 29 8 2517 2691 507771054 507770887 9.230000e-16 95.3
11 TraesCS2D01G420200 chr6A 81.714 175 30 2 2 175 107835651 107835478 9.040000e-31 145.0
12 TraesCS2D01G420200 chr6A 80.420 143 24 4 2550 2690 538051458 538051318 4.260000e-19 106.0
13 TraesCS2D01G420200 chr7D 82.209 163 21 5 2543 2704 623793444 623793599 1.960000e-27 134.0
14 TraesCS2D01G420200 chr7D 89.394 66 6 1 2622 2687 87509784 87509848 7.190000e-12 82.4
15 TraesCS2D01G420200 chr5B 79.389 131 23 3 2 130 689583634 689583506 4.290000e-14 89.8
16 TraesCS2D01G420200 chr5B 95.122 41 1 1 2379 2419 134791650 134791689 2.600000e-06 63.9
17 TraesCS2D01G420200 chr3B 92.453 53 2 1 2377 2429 493117250 493117300 1.200000e-09 75.0
18 TraesCS2D01G420200 chr3B 100.000 28 0 0 2671 2698 434987342 434987369 6.000000e-03 52.8
19 TraesCS2D01G420200 chr4A 91.304 46 4 0 2379 2424 737843929 737843884 2.600000e-06 63.9
20 TraesCS2D01G420200 chr4A 91.304 46 4 0 2379 2424 738354670 738354715 2.600000e-06 63.9


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 TraesCS2D01G420200 chr2D 534308456 534311581 3125 False 5773 5773 100.00000 1 3126 1 chr2D.!!$F1 3125
1 TraesCS2D01G420200 chr2D 324889289 324889816 527 True 337 337 78.19500 1 532 1 chr2D.!!$R1 531
2 TraesCS2D01G420200 chr2B 635021780 635024952 3172 False 1180 2795 94.21475 1 3124 4 chr2B.!!$F1 3123
3 TraesCS2D01G420200 chr6B 124472717 124473343 626 True 926 926 93.30100 1 627 1 chr6B.!!$R1 626
4 TraesCS2D01G420200 chr1A 50779376 50779987 611 False 514 514 81.92200 1 611 1 chr1A.!!$F1 610
5 TraesCS2D01G420200 chr3D 535911491 535911993 502 False 361 361 79.60400 1 505 1 chr3D.!!$F1 504

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
67 68 0.323629 CGTCACCCCACCAGTATTGT 59.676 55.0 0.0 0.00 0.0 2.71 F
799 804 0.378257 GCTTGCACATACCGGTCATG 59.622 55.0 12.4 15.83 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 2066 0.250038 CGGGATCCGTTGAGCATCAT 60.250 55.0 5.45 0.00 41.53 2.45 R
2385 2410 0.172578 GATTGCTAACCGGGTTTGCC 59.827 55.0 32.90 19.72 41.88 4.52 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
18 19 3.861341 CACACATCTTCCACCGGAT 57.139 52.632 9.46 0.00 0.00 4.18
24 25 0.546598 ATCTTCCACCGGATGAACCC 59.453 55.000 9.46 0.00 38.93 4.11
67 68 0.323629 CGTCACCCCACCAGTATTGT 59.676 55.000 0.00 0.00 0.00 2.71
229 233 7.147949 CCACTGATTTTCTGAATAATTCTGGCT 60.148 37.037 0.00 0.00 0.00 4.75
380 384 2.435372 TGGGCTGAAAAAGACACTGT 57.565 45.000 0.00 0.00 34.40 3.55
407 411 2.056906 AACGCTCACTTTCTGCCCCT 62.057 55.000 0.00 0.00 0.00 4.79
524 528 1.739562 GTCACGGCAGGAGCTTCTG 60.740 63.158 18.48 18.48 41.70 3.02
551 555 3.323775 ACCCTTACTCCTTCCAAGTCAA 58.676 45.455 0.00 0.00 0.00 3.18
614 619 8.543862 TTCGGTTTAGAGAAGAAAAAGATACC 57.456 34.615 0.00 0.00 0.00 2.73
627 632 0.872449 AGATACCGGGATAGGGGGTT 59.128 55.000 6.32 0.00 35.28 4.11
628 633 2.084300 AGATACCGGGATAGGGGGTTA 58.916 52.381 6.32 0.00 35.28 2.85
629 634 2.455947 AGATACCGGGATAGGGGGTTAA 59.544 50.000 6.32 0.00 35.28 2.01
630 635 2.403899 TACCGGGATAGGGGGTTAAG 57.596 55.000 6.32 0.00 35.28 1.85
631 636 1.058428 ACCGGGATAGGGGGTTAAGC 61.058 60.000 6.32 0.00 35.02 3.09
632 637 1.057851 CCGGGATAGGGGGTTAAGCA 61.058 60.000 7.03 0.00 0.00 3.91
633 638 0.841289 CGGGATAGGGGGTTAAGCAA 59.159 55.000 7.03 0.00 0.00 3.91
634 639 1.202770 CGGGATAGGGGGTTAAGCAAG 60.203 57.143 7.03 0.00 0.00 4.01
635 640 1.478837 GGGATAGGGGGTTAAGCAAGC 60.479 57.143 7.03 0.00 0.00 4.01
636 641 1.495148 GGATAGGGGGTTAAGCAAGCT 59.505 52.381 7.03 0.00 32.59 3.74
637 642 2.709397 GGATAGGGGGTTAAGCAAGCTA 59.291 50.000 7.03 0.00 32.59 3.32
638 643 3.137728 GGATAGGGGGTTAAGCAAGCTAA 59.862 47.826 7.03 0.00 32.59 3.09
639 644 4.202577 GGATAGGGGGTTAAGCAAGCTAAT 60.203 45.833 7.03 0.00 32.59 1.73
640 645 3.757947 AGGGGGTTAAGCAAGCTAATT 57.242 42.857 7.03 0.00 32.59 1.40
641 646 4.873724 AGGGGGTTAAGCAAGCTAATTA 57.126 40.909 7.03 0.00 32.59 1.40
642 647 5.201363 AGGGGGTTAAGCAAGCTAATTAA 57.799 39.130 7.03 0.00 32.59 1.40
643 648 4.954202 AGGGGGTTAAGCAAGCTAATTAAC 59.046 41.667 15.11 15.11 38.23 2.01
646 651 4.348656 GGTTAAGCAAGCTAATTAACCGC 58.651 43.478 21.91 8.91 44.93 5.68
688 693 2.779506 AGGTGAATCAAACTCCGTTCC 58.220 47.619 0.00 0.00 0.00 3.62
694 699 4.642885 TGAATCAAACTCCGTTCCTTTTGT 59.357 37.500 0.00 0.00 32.02 2.83
741 746 2.104111 ACTTTGTGTGTTCCGATCTCCA 59.896 45.455 0.00 0.00 0.00 3.86
785 790 2.464157 AGTCAAGGACTACTGCTTGC 57.536 50.000 0.00 0.00 43.70 4.01
795 800 0.611200 TACTGCTTGCACATACCGGT 59.389 50.000 13.98 13.98 0.00 5.28
799 804 0.378257 GCTTGCACATACCGGTCATG 59.622 55.000 12.40 15.83 0.00 3.07
829 834 1.492319 TTTCGTGGAGAAACGCACGG 61.492 55.000 10.36 0.00 43.35 4.94
831 836 1.952133 CGTGGAGAAACGCACGGAA 60.952 57.895 0.00 0.00 38.50 4.30
870 880 2.557317 TGGTCCGAGAAAAGTGTGAAC 58.443 47.619 0.00 0.00 0.00 3.18
947 958 7.094463 GCAGTGCTATAAAAGGATATGAGCAAT 60.094 37.037 8.18 0.00 39.92 3.56
981 992 5.163622 CGCATCAATCACTCTTAACCCAAAT 60.164 40.000 0.00 0.00 0.00 2.32
985 996 3.695830 TCACTCTTAACCCAAATCGCT 57.304 42.857 0.00 0.00 0.00 4.93
1270 1281 2.802816 GCATCCCTTCACATCGTGTATC 59.197 50.000 0.00 0.00 34.79 2.24
1271 1282 3.741075 GCATCCCTTCACATCGTGTATCA 60.741 47.826 0.00 0.00 34.79 2.15
1272 1283 4.635223 CATCCCTTCACATCGTGTATCAT 58.365 43.478 0.00 0.00 34.79 2.45
1273 1284 4.753516 TCCCTTCACATCGTGTATCATT 57.246 40.909 0.00 0.00 34.79 2.57
1274 1285 4.693283 TCCCTTCACATCGTGTATCATTC 58.307 43.478 0.00 0.00 34.79 2.67
1294 1306 1.547372 CTTTTTGCAGTGGGATCAGGG 59.453 52.381 0.00 0.00 0.00 4.45
1336 1348 0.779997 AGGGTTCATCTTTGGTGGCT 59.220 50.000 0.00 0.00 0.00 4.75
1337 1349 1.992557 AGGGTTCATCTTTGGTGGCTA 59.007 47.619 0.00 0.00 0.00 3.93
1338 1350 2.092323 GGGTTCATCTTTGGTGGCTAC 58.908 52.381 0.00 0.00 0.00 3.58
1339 1351 2.290960 GGGTTCATCTTTGGTGGCTACT 60.291 50.000 0.00 0.00 0.00 2.57
1340 1352 2.749621 GGTTCATCTTTGGTGGCTACTG 59.250 50.000 0.00 0.00 0.00 2.74
1708 1720 2.507992 CAGTTCTGCGAGGAGGCG 60.508 66.667 0.00 0.00 35.06 5.52
1728 1740 1.228657 GGAGACAAGGAACCACACGC 61.229 60.000 0.00 0.00 0.00 5.34
1809 1821 3.788766 GCGCGCGGTCACTTCAAT 61.789 61.111 33.06 0.00 0.00 2.57
1826 1838 0.949105 AATCCTTCACGGACGCACAC 60.949 55.000 0.00 0.00 46.80 3.82
2030 2042 3.558931 CAGTATGCCACAAGGATACCA 57.441 47.619 1.33 0.00 36.89 3.25
2033 2045 0.921896 ATGCCACAAGGATACCAGCT 59.078 50.000 0.00 0.00 36.89 4.24
2047 2059 2.215191 CAGCTACTGGGATGAGGCA 58.785 57.895 0.00 0.00 0.00 4.75
2054 2066 2.481441 ACTGGGATGAGGCATACTTCA 58.519 47.619 0.00 0.00 0.00 3.02
2062 2074 3.736720 TGAGGCATACTTCATGATGCTC 58.263 45.455 16.39 12.54 46.27 4.26
2113 2125 0.033601 TCATGCCGGCCAATTACCTT 60.034 50.000 26.77 0.00 0.00 3.50
2133 2145 1.110442 CTGTGGCTCTAGGAGGTGAG 58.890 60.000 0.00 0.00 0.00 3.51
2298 2310 9.886132 AGATATATGTACCCCGAAAAATGATAC 57.114 33.333 0.00 0.00 0.00 2.24
2300 2312 4.205065 TGTACCCCGAAAAATGATACGT 57.795 40.909 0.00 0.00 0.00 3.57
2301 2313 5.336150 TGTACCCCGAAAAATGATACGTA 57.664 39.130 0.00 0.00 0.00 3.57
2302 2314 5.916318 TGTACCCCGAAAAATGATACGTAT 58.084 37.500 8.05 8.05 0.00 3.06
2303 2315 5.754406 TGTACCCCGAAAAATGATACGTATG 59.246 40.000 13.97 0.00 0.00 2.39
2305 2317 5.617252 ACCCCGAAAAATGATACGTATGAT 58.383 37.500 13.97 7.34 0.00 2.45
2306 2318 6.761312 ACCCCGAAAAATGATACGTATGATA 58.239 36.000 13.97 0.00 0.00 2.15
2309 2321 7.148639 CCCCGAAAAATGATACGTATGATACAG 60.149 40.741 13.97 1.53 0.00 2.74
2311 2323 9.140286 CCGAAAAATGATACGTATGATACAGAT 57.860 33.333 13.97 0.00 0.00 2.90
2342 2361 4.321745 GTGATGATGCGTGTCATGTTTTTC 59.678 41.667 9.00 0.00 38.88 2.29
2369 2394 1.078709 AGAAATGATGCGTGTCGGTG 58.921 50.000 0.00 0.00 0.00 4.94
2379 2404 1.125566 GCGTGTCGGTGCTAGTTTTAC 59.874 52.381 0.00 0.00 0.00 2.01
2384 2409 3.942351 GGTGCTAGTTTTACCGGGT 57.058 52.632 6.32 4.46 0.00 5.28
2385 2410 1.445871 GGTGCTAGTTTTACCGGGTG 58.554 55.000 10.66 0.00 0.00 4.61
2386 2411 1.445871 GTGCTAGTTTTACCGGGTGG 58.554 55.000 10.66 0.00 42.84 4.61
2387 2412 0.321830 TGCTAGTTTTACCGGGTGGC 60.322 55.000 10.66 0.00 39.70 5.01
2388 2413 0.321830 GCTAGTTTTACCGGGTGGCA 60.322 55.000 10.66 0.00 39.70 4.92
2390 2415 2.506444 CTAGTTTTACCGGGTGGCAAA 58.494 47.619 10.66 0.00 39.70 3.68
2391 2416 1.034356 AGTTTTACCGGGTGGCAAAC 58.966 50.000 10.66 15.01 40.02 2.93
2399 2424 3.676216 GGTGGCAAACCCGGTTAG 58.324 61.111 2.39 0.00 44.02 2.34
2400 2425 2.632544 GGTGGCAAACCCGGTTAGC 61.633 63.158 2.39 0.00 44.02 3.09
2401 2426 1.899534 GTGGCAAACCCGGTTAGCA 60.900 57.895 2.39 0.00 35.87 3.49
2402 2427 1.152735 TGGCAAACCCGGTTAGCAA 60.153 52.632 2.39 0.00 35.87 3.91
2403 2428 0.540830 TGGCAAACCCGGTTAGCAAT 60.541 50.000 2.39 0.00 35.87 3.56
2404 2429 0.172578 GGCAAACCCGGTTAGCAATC 59.827 55.000 2.39 0.00 0.00 2.67
2405 2430 1.173913 GCAAACCCGGTTAGCAATCT 58.826 50.000 2.39 0.00 0.00 2.40
2406 2431 1.132453 GCAAACCCGGTTAGCAATCTC 59.868 52.381 2.39 0.00 0.00 2.75
2407 2432 2.432444 CAAACCCGGTTAGCAATCTCA 58.568 47.619 2.39 0.00 0.00 3.27
2408 2433 2.817258 CAAACCCGGTTAGCAATCTCAA 59.183 45.455 2.39 0.00 0.00 3.02
2409 2434 2.871096 ACCCGGTTAGCAATCTCAAA 57.129 45.000 0.00 0.00 0.00 2.69
2410 2435 2.433436 ACCCGGTTAGCAATCTCAAAC 58.567 47.619 0.00 0.00 0.00 2.93
2411 2436 2.039879 ACCCGGTTAGCAATCTCAAACT 59.960 45.455 0.00 0.00 0.00 2.66
2412 2437 3.081804 CCCGGTTAGCAATCTCAAACTT 58.918 45.455 0.00 0.00 0.00 2.66
2413 2438 3.506067 CCCGGTTAGCAATCTCAAACTTT 59.494 43.478 0.00 0.00 0.00 2.66
2414 2439 4.475944 CCGGTTAGCAATCTCAAACTTTG 58.524 43.478 0.00 0.00 0.00 2.77
2415 2440 4.215399 CCGGTTAGCAATCTCAAACTTTGA 59.785 41.667 4.16 4.16 38.17 2.69
2416 2441 5.278266 CCGGTTAGCAATCTCAAACTTTGAA 60.278 40.000 5.72 0.00 39.58 2.69
2417 2442 6.381801 CGGTTAGCAATCTCAAACTTTGAAT 58.618 36.000 5.72 0.88 39.58 2.57
2418 2443 7.361713 CCGGTTAGCAATCTCAAACTTTGAATA 60.362 37.037 5.72 0.00 39.58 1.75
2419 2444 8.184192 CGGTTAGCAATCTCAAACTTTGAATAT 58.816 33.333 5.72 0.53 39.58 1.28
2420 2445 9.294030 GGTTAGCAATCTCAAACTTTGAATATG 57.706 33.333 5.72 5.90 39.58 1.78
2421 2446 8.801913 GTTAGCAATCTCAAACTTTGAATATGC 58.198 33.333 18.46 18.46 39.58 3.14
2422 2447 6.927416 AGCAATCTCAAACTTTGAATATGCA 58.073 32.000 23.42 0.00 39.58 3.96
2423 2448 7.380536 AGCAATCTCAAACTTTGAATATGCAA 58.619 30.769 23.42 0.00 39.58 4.08
2424 2449 7.874016 AGCAATCTCAAACTTTGAATATGCAAA 59.126 29.630 23.42 8.62 39.58 3.68
2425 2450 8.497554 GCAATCTCAAACTTTGAATATGCAAAA 58.502 29.630 19.91 0.00 39.58 2.44
2485 2510 0.322816 AGCCAGCACCGAAATCATGT 60.323 50.000 0.00 0.00 0.00 3.21
2503 2528 7.943079 ATCATGTCTGACAAACCAATCATAA 57.057 32.000 15.31 0.00 33.22 1.90
2509 2534 8.081633 TGTCTGACAAACCAATCATAACAAATC 58.918 33.333 8.27 0.00 0.00 2.17
2511 2536 8.637099 TCTGACAAACCAATCATAACAAATCAA 58.363 29.630 0.00 0.00 0.00 2.57
2514 2539 8.550710 ACAAACCAATCATAACAAATCAATGG 57.449 30.769 0.00 0.00 0.00 3.16
2541 2569 1.767759 ATTGCAGCTTACACCCCATC 58.232 50.000 0.00 0.00 0.00 3.51
2597 2632 7.939784 TGAGTTGGATGTATATAGATACGCT 57.060 36.000 3.21 0.00 40.87 5.07
2598 2633 8.349568 TGAGTTGGATGTATATAGATACGCTT 57.650 34.615 3.21 0.00 40.87 4.68
2599 2634 8.803235 TGAGTTGGATGTATATAGATACGCTTT 58.197 33.333 3.21 0.00 40.87 3.51
2600 2635 9.640963 GAGTTGGATGTATATAGATACGCTTTT 57.359 33.333 3.21 0.00 40.87 2.27
2627 2662 5.223382 TGTGTGTGTTTGTTCGTTCATTTT 58.777 33.333 0.00 0.00 0.00 1.82
2662 2697 9.403583 TGTAGTCCATATTAAAAGATCCAAACC 57.596 33.333 0.00 0.00 0.00 3.27
2724 2759 1.853963 TTAGAGCACCCCACTCTCTC 58.146 55.000 0.00 0.00 43.42 3.20
2735 2770 0.884514 CACTCTCTCGGCTGACTCAA 59.115 55.000 0.00 0.00 0.00 3.02
2742 2777 3.820467 CTCTCGGCTGACTCAATCTCTAT 59.180 47.826 0.00 0.00 0.00 1.98
2800 2835 0.455410 CTCACCTGAAGCCTCTCGAG 59.545 60.000 5.93 5.93 0.00 4.04
2837 2872 3.321682 GTCTCTCTCCATCTCAATCCCAG 59.678 52.174 0.00 0.00 0.00 4.45
2861 2896 3.199880 ACAGTGTTTCTCTCCCAACAG 57.800 47.619 0.00 0.00 33.55 3.16
2912 2947 0.684535 TCAACTCCAGAACGCCATGA 59.315 50.000 0.00 0.00 0.00 3.07
2914 2949 0.321653 AACTCCAGAACGCCATGACC 60.322 55.000 0.00 0.00 0.00 4.02
2940 2975 2.280660 CCGCCTGGCTGCTATCTG 60.281 66.667 17.92 0.00 0.00 2.90
2941 2976 2.503061 CGCCTGGCTGCTATCTGT 59.497 61.111 17.92 0.00 0.00 3.41
2942 2977 1.593750 CGCCTGGCTGCTATCTGTC 60.594 63.158 17.92 0.00 0.00 3.51
2943 2978 1.524002 GCCTGGCTGCTATCTGTCA 59.476 57.895 12.43 0.00 0.00 3.58
2944 2979 0.107508 GCCTGGCTGCTATCTGTCAA 60.108 55.000 12.43 0.00 0.00 3.18
2947 2982 2.277969 CTGGCTGCTATCTGTCAAGTG 58.722 52.381 0.00 0.00 0.00 3.16
2962 3107 1.111277 AAGTGGTTTCAGTTGGGTGC 58.889 50.000 0.00 0.00 35.39 5.01
2974 3119 1.250154 TTGGGTGCAGCAGTTATGGC 61.250 55.000 19.06 0.00 0.00 4.40
3003 3148 0.804989 CAACTTGATCCAACGGCTCC 59.195 55.000 0.00 0.00 0.00 4.70
3118 3263 1.026718 CCGGGTCAGGCTTGTCATTC 61.027 60.000 0.00 0.00 0.00 2.67
3124 3269 3.508840 GGCTTGTCATTCGGGCCG 61.509 66.667 22.51 22.51 33.30 6.13
3125 3270 3.508840 GCTTGTCATTCGGGCCGG 61.509 66.667 27.98 10.57 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.620556 AAGAGGATGCACGGGTTCAT 59.379 50.000 0.00 0.00 0.00 2.57
18 19 1.271856 TAAGAGGATGCACGGGTTCA 58.728 50.000 0.00 0.00 0.00 3.18
24 25 3.312828 GCTACTCATAAGAGGATGCACG 58.687 50.000 0.00 0.00 46.44 5.34
380 384 4.152402 GCAGAAAGTGAGCGTTGAGAAATA 59.848 41.667 0.00 0.00 0.00 1.40
407 411 7.678171 TGTCCTTGATATGTATTATCTGGCCTA 59.322 37.037 3.32 0.00 38.05 3.93
524 528 4.628963 TGGAAGGAGTAAGGGTTTGTAC 57.371 45.455 0.00 0.00 0.00 2.90
551 555 4.001652 CTGTCTCATGCTGAAACATCAGT 58.998 43.478 7.59 0.00 39.76 3.41
595 600 6.862469 TCCCGGTATCTTTTTCTTCTCTAA 57.138 37.500 0.00 0.00 0.00 2.10
596 601 7.232941 CCTATCCCGGTATCTTTTTCTTCTCTA 59.767 40.741 0.00 0.00 0.00 2.43
614 619 0.841289 TTGCTTAACCCCCTATCCCG 59.159 55.000 0.00 0.00 0.00 5.14
627 632 4.094294 CACAGCGGTTAATTAGCTTGCTTA 59.906 41.667 13.77 0.00 39.48 3.09
628 633 3.081804 ACAGCGGTTAATTAGCTTGCTT 58.918 40.909 13.77 6.49 39.48 3.91
629 634 2.420022 CACAGCGGTTAATTAGCTTGCT 59.580 45.455 11.65 11.65 39.48 3.91
630 635 2.161609 ACACAGCGGTTAATTAGCTTGC 59.838 45.455 0.00 8.33 39.48 4.01
631 636 4.419522 AACACAGCGGTTAATTAGCTTG 57.580 40.909 0.00 3.59 39.48 4.01
632 637 4.094442 GCTAACACAGCGGTTAATTAGCTT 59.906 41.667 20.61 0.00 41.37 3.74
633 638 3.621715 GCTAACACAGCGGTTAATTAGCT 59.378 43.478 20.61 0.00 41.37 3.32
634 639 3.936661 GCTAACACAGCGGTTAATTAGC 58.063 45.455 16.29 16.29 41.37 3.09
646 651 6.876257 ACCTTTTCTAGATGAAGCTAACACAG 59.124 38.462 9.71 0.00 35.89 3.66
769 774 1.882912 TGTGCAAGCAGTAGTCCTTG 58.117 50.000 0.00 0.00 40.97 3.61
773 778 1.927174 CGGTATGTGCAAGCAGTAGTC 59.073 52.381 0.00 0.00 0.00 2.59
827 832 2.096218 GCAAAGTCTGTGCTTAGTTCCG 60.096 50.000 7.83 0.00 39.00 4.30
829 834 4.470462 CATGCAAAGTCTGTGCTTAGTTC 58.530 43.478 16.07 0.00 42.69 3.01
831 836 2.816087 CCATGCAAAGTCTGTGCTTAGT 59.184 45.455 16.07 0.00 42.69 2.24
921 932 5.702670 TGCTCATATCCTTTTATAGCACTGC 59.297 40.000 0.00 0.00 33.84 4.40
981 992 3.192633 TCATACTGTACTGCTTTCAGCGA 59.807 43.478 0.00 0.00 46.26 4.93
985 996 4.776795 TCGTCATACTGTACTGCTTTCA 57.223 40.909 0.00 0.00 0.00 2.69
993 1004 2.980476 CCGCATGATCGTCATACTGTAC 59.020 50.000 0.00 0.00 34.28 2.90
995 1006 1.681264 TCCGCATGATCGTCATACTGT 59.319 47.619 0.00 0.00 34.28 3.55
996 1007 2.422276 TCCGCATGATCGTCATACTG 57.578 50.000 0.00 0.00 34.28 2.74
1270 1281 4.491676 CTGATCCCACTGCAAAAAGAATG 58.508 43.478 0.00 0.00 0.00 2.67
1271 1282 3.512724 CCTGATCCCACTGCAAAAAGAAT 59.487 43.478 0.00 0.00 0.00 2.40
1272 1283 2.892852 CCTGATCCCACTGCAAAAAGAA 59.107 45.455 0.00 0.00 0.00 2.52
1273 1284 2.517959 CCTGATCCCACTGCAAAAAGA 58.482 47.619 0.00 0.00 0.00 2.52
1274 1285 1.547372 CCCTGATCCCACTGCAAAAAG 59.453 52.381 0.00 0.00 0.00 2.27
1336 1348 7.997773 ATCCGCTTAGATATCAACTACAGTA 57.002 36.000 5.32 0.00 0.00 2.74
1337 1349 6.902771 ATCCGCTTAGATATCAACTACAGT 57.097 37.500 5.32 0.00 0.00 3.55
1338 1350 8.594881 AAAATCCGCTTAGATATCAACTACAG 57.405 34.615 5.32 0.00 0.00 2.74
1339 1351 8.958119 AAAAATCCGCTTAGATATCAACTACA 57.042 30.769 5.32 0.00 0.00 2.74
1340 1352 9.262358 AGAAAAATCCGCTTAGATATCAACTAC 57.738 33.333 5.32 0.00 0.00 2.73
1441 1453 4.838152 TGATGCTTCGGAGGCGGC 62.838 66.667 7.63 0.00 0.00 6.53
1651 1663 4.410743 GCTTGCTTGGAGCCGTGC 62.411 66.667 0.00 0.00 41.51 5.34
1708 1720 0.602905 CGTGTGGTTCCTTGTCTCCC 60.603 60.000 0.00 0.00 0.00 4.30
1765 1777 3.299977 GTCCCCAAAACGGTGGCC 61.300 66.667 0.00 0.00 37.34 5.36
1819 1831 4.619227 CGGAGGGGTTGTGTGCGT 62.619 66.667 0.00 0.00 0.00 5.24
1826 1838 2.125673 CACGTAGCGGAGGGGTTG 60.126 66.667 0.00 0.00 0.00 3.77
1954 1966 0.307760 CAACAAGTTGGACACGGAGC 59.692 55.000 7.96 0.00 36.95 4.70
2030 2042 1.974236 GTATGCCTCATCCCAGTAGCT 59.026 52.381 0.00 0.00 0.00 3.32
2033 2045 3.653164 TGAAGTATGCCTCATCCCAGTA 58.347 45.455 0.00 0.00 0.00 2.74
2054 2066 0.250038 CGGGATCCGTTGAGCATCAT 60.250 55.000 5.45 0.00 41.53 2.45
2113 2125 0.704664 TCACCTCCTAGAGCCACAGA 59.295 55.000 0.00 0.00 0.00 3.41
2133 2145 1.344942 CGTACTTGCTGCTCGTGTCC 61.345 60.000 0.00 0.00 0.00 4.02
2305 2317 9.520204 CACGCATCATCACAATATATATCTGTA 57.480 33.333 0.00 0.00 0.00 2.74
2306 2318 8.037166 ACACGCATCATCACAATATATATCTGT 58.963 33.333 0.00 0.96 0.00 3.41
2309 2321 8.411318 TGACACGCATCATCACAATATATATC 57.589 34.615 0.00 0.00 0.00 1.63
2311 2323 7.818930 ACATGACACGCATCATCACAATATATA 59.181 33.333 0.00 0.00 37.20 0.86
2348 2373 2.670905 CACCGACACGCATCATTTCTAA 59.329 45.455 0.00 0.00 0.00 2.10
2349 2374 2.267426 CACCGACACGCATCATTTCTA 58.733 47.619 0.00 0.00 0.00 2.10
2366 2391 1.445871 CACCCGGTAAAACTAGCACC 58.554 55.000 0.00 0.00 0.00 5.01
2369 2394 0.321830 TGCCACCCGGTAAAACTAGC 60.322 55.000 0.00 0.00 33.28 3.42
2382 2407 2.632544 GCTAACCGGGTTTGCCACC 61.633 63.158 28.49 7.77 46.46 4.61
2384 2409 0.540830 ATTGCTAACCGGGTTTGCCA 60.541 50.000 32.90 26.33 41.88 4.92
2385 2410 0.172578 GATTGCTAACCGGGTTTGCC 59.827 55.000 32.90 19.72 41.88 4.52
2386 2411 1.132453 GAGATTGCTAACCGGGTTTGC 59.868 52.381 30.80 30.80 42.61 3.68
2387 2412 2.432444 TGAGATTGCTAACCGGGTTTG 58.568 47.619 19.02 17.15 0.00 2.93
2388 2413 2.871096 TGAGATTGCTAACCGGGTTT 57.129 45.000 19.02 0.00 0.00 3.27
2390 2415 2.039879 AGTTTGAGATTGCTAACCGGGT 59.960 45.455 6.32 0.00 0.00 5.28
2391 2416 2.711542 AGTTTGAGATTGCTAACCGGG 58.288 47.619 6.32 0.00 0.00 5.73
2393 2418 5.356882 TCAAAGTTTGAGATTGCTAACCG 57.643 39.130 14.35 0.00 34.08 4.44
2394 2419 9.294030 CATATTCAAAGTTTGAGATTGCTAACC 57.706 33.333 17.36 0.00 41.38 2.85
2395 2420 8.801913 GCATATTCAAAGTTTGAGATTGCTAAC 58.198 33.333 25.64 9.59 41.38 2.34
2397 2422 8.054152 TGCATATTCAAAGTTTGAGATTGCTA 57.946 30.769 29.02 20.40 41.38 3.49
2398 2423 6.927416 TGCATATTCAAAGTTTGAGATTGCT 58.073 32.000 29.02 14.02 41.38 3.91
2399 2424 7.585286 TTGCATATTCAAAGTTTGAGATTGC 57.415 32.000 25.91 25.91 41.38 3.56
2438 2463 7.388437 CAAGGAATCTGATTTCATGGGAAAAA 58.612 34.615 11.14 0.00 45.52 1.94
2439 2464 6.574859 GCAAGGAATCTGATTTCATGGGAAAA 60.575 38.462 13.97 0.00 45.52 2.29
2440 2465 5.105228 GCAAGGAATCTGATTTCATGGGAAA 60.105 40.000 13.97 0.00 46.36 3.13
2441 2466 4.403432 GCAAGGAATCTGATTTCATGGGAA 59.597 41.667 13.97 0.00 0.00 3.97
2442 2467 3.956199 GCAAGGAATCTGATTTCATGGGA 59.044 43.478 13.97 0.00 0.00 4.37
2443 2468 3.958798 AGCAAGGAATCTGATTTCATGGG 59.041 43.478 13.97 1.66 0.00 4.00
2485 2510 8.175925 TGATTTGTTATGATTGGTTTGTCAGA 57.824 30.769 0.00 0.00 0.00 3.27
2511 2536 7.993183 GGGTGTAAGCTGCAATATATATACCAT 59.007 37.037 1.02 0.00 0.00 3.55
2514 2539 7.335627 TGGGGTGTAAGCTGCAATATATATAC 58.664 38.462 1.02 0.00 0.00 1.47
2531 2556 8.966155 TCTTATATATGTGAAGATGGGGTGTA 57.034 34.615 0.00 0.00 0.00 2.90
2532 2557 7.872061 TCTTATATATGTGAAGATGGGGTGT 57.128 36.000 0.00 0.00 0.00 4.16
2533 2558 8.728337 CATCTTATATATGTGAAGATGGGGTG 57.272 38.462 20.09 5.10 46.76 4.61
2572 2607 8.526667 AGCGTATCTATATACATCCAACTCAT 57.473 34.615 0.00 0.00 38.31 2.90
2600 2635 5.041287 TGAACGAACAAACACACACAAAAA 58.959 33.333 0.00 0.00 0.00 1.94
2605 2640 5.755330 AAAATGAACGAACAAACACACAC 57.245 34.783 0.00 0.00 0.00 3.82
2660 2695 5.278758 CCTCCGTTCACAAATGTAAAATGGT 60.279 40.000 14.13 0.00 33.85 3.55
2662 2697 5.048364 TCCCTCCGTTCACAAATGTAAAATG 60.048 40.000 0.00 0.00 0.00 2.32
2667 2702 2.635915 ACTCCCTCCGTTCACAAATGTA 59.364 45.455 0.00 0.00 0.00 2.29
2724 2759 3.998099 TGATAGAGATTGAGTCAGCCG 57.002 47.619 0.00 0.00 0.00 5.52
2772 2807 4.555689 AGGCTTCAGGTGAGAGATAGATT 58.444 43.478 0.00 0.00 0.00 2.40
2776 2811 3.561143 GAGAGGCTTCAGGTGAGAGATA 58.439 50.000 0.00 0.00 0.00 1.98
2777 2812 2.387757 GAGAGGCTTCAGGTGAGAGAT 58.612 52.381 0.00 0.00 0.00 2.75
2800 2835 2.183046 GACACCGAGAGCTCAGGC 59.817 66.667 23.14 9.20 39.06 4.85
2837 2872 3.194005 TGGGAGAGAAACACTGTTGAC 57.806 47.619 0.00 0.00 0.00 3.18
2861 2896 3.842925 TTGACGTGGGCAGGAAGGC 62.843 63.158 0.00 0.00 43.27 4.35
2937 2972 3.278574 CCAACTGAAACCACTTGACAGA 58.721 45.455 0.00 0.00 33.53 3.41
2938 2973 2.358898 CCCAACTGAAACCACTTGACAG 59.641 50.000 0.00 0.00 35.14 3.51
2939 2974 2.291282 ACCCAACTGAAACCACTTGACA 60.291 45.455 0.00 0.00 0.00 3.58
2940 2975 2.099098 CACCCAACTGAAACCACTTGAC 59.901 50.000 0.00 0.00 0.00 3.18
2941 2976 2.374184 CACCCAACTGAAACCACTTGA 58.626 47.619 0.00 0.00 0.00 3.02
2942 2977 1.202405 GCACCCAACTGAAACCACTTG 60.202 52.381 0.00 0.00 0.00 3.16
2943 2978 1.111277 GCACCCAACTGAAACCACTT 58.889 50.000 0.00 0.00 0.00 3.16
2944 2979 0.033601 TGCACCCAACTGAAACCACT 60.034 50.000 0.00 0.00 0.00 4.00
2947 2982 1.363807 GCTGCACCCAACTGAAACC 59.636 57.895 0.00 0.00 0.00 3.27
2962 3107 3.648339 ACTGTTTTGCCATAACTGCTG 57.352 42.857 5.14 0.00 0.00 4.41
2974 3119 5.229887 CGTTGGATCAAGTTGAACTGTTTTG 59.770 40.000 10.14 0.00 0.00 2.44
3003 3148 1.468914 TGTGAGAACGAGGAGTGATCG 59.531 52.381 0.00 0.00 45.54 3.69
3082 3227 2.517166 GCCTGGCCCGAGATTTCC 60.517 66.667 7.66 0.00 0.00 3.13
3106 3251 2.044946 GGCCCGAATGACAAGCCT 60.045 61.111 0.00 0.00 40.57 4.58


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

AutoCloner maintained by Alex Coulton.