Multiple sequence alignment - TraesCS5D01G293600

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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 TraesCS5D01G293600 chr5D 100.000 3138 0 0 1 3138 390557313 390560450 0.000000e+00 5795.0
1 TraesCS5D01G293600 chr5D 90.779 1399 88 22 755 2138 390508427 390509799 0.000000e+00 1831.0
2 TraesCS5D01G293600 chr5D 96.194 762 28 1 1 762 308808060 308807300 0.000000e+00 1245.0
3 TraesCS5D01G293600 chr5D 95.932 762 30 1 1 762 30084403 30083643 0.000000e+00 1234.0
4 TraesCS5D01G293600 chr5D 81.310 733 72 17 2439 3136 510472255 510472957 4.610000e-148 534.0
5 TraesCS5D01G293600 chr5D 82.810 605 52 19 2573 3136 549798124 549798717 7.820000e-136 494.0
6 TraesCS5D01G293600 chr5D 82.178 606 62 19 2573 3136 116627271 116627872 2.190000e-131 479.0
7 TraesCS5D01G293600 chr5D 87.766 188 13 3 2573 2751 457555613 457555427 8.820000e-51 211.0
8 TraesCS5D01G293600 chr5A 92.051 1409 85 18 755 2147 493811710 493810313 0.000000e+00 1956.0
9 TraesCS5D01G293600 chr5A 80.662 755 83 26 2416 3136 670521740 670522465 7.710000e-146 527.0
10 TraesCS5D01G293600 chr5B 91.875 1403 89 13 755 2141 470624231 470625624 0.000000e+00 1936.0
11 TraesCS5D01G293600 chr5B 96.974 760 23 0 1380 2139 470661539 470662298 0.000000e+00 1277.0
12 TraesCS5D01G293600 chr5B 80.815 589 70 18 2573 3136 584254487 584255057 3.740000e-114 422.0
13 TraesCS5D01G293600 chr5B 92.748 262 16 2 1052 1312 470656150 470656409 2.950000e-100 375.0
14 TraesCS5D01G293600 chr5B 88.587 184 9 4 2165 2336 470625715 470625898 2.450000e-51 213.0
15 TraesCS5D01G293600 chr5B 93.243 74 5 0 2342 2415 470627303 470627376 3.310000e-20 110.0
16 TraesCS5D01G293600 chr4D 96.457 762 27 0 1 762 7235611 7236372 0.000000e+00 1258.0
17 TraesCS5D01G293600 chr4D 96.457 762 27 0 1 762 205285568 205286329 0.000000e+00 1258.0
18 TraesCS5D01G293600 chr4D 95.669 762 33 0 1 762 219711246 219712007 0.000000e+00 1225.0
19 TraesCS5D01G293600 chr4D 82.473 639 57 16 2425 3037 6430824 6430215 2.790000e-140 508.0
20 TraesCS5D01G293600 chr4D 85.230 501 48 10 2573 3048 387753022 387752523 2.810000e-135 492.0
21 TraesCS5D01G293600 chr4D 81.488 605 59 20 2565 3137 3583006 3583589 6.170000e-122 448.0
22 TraesCS5D01G293600 chr1D 96.194 762 29 0 1 762 275950902 275951663 0.000000e+00 1247.0
23 TraesCS5D01G293600 chr1D 83.505 194 22 5 2573 2757 484268344 484268536 4.160000e-39 172.0
24 TraesCS5D01G293600 chr1D 76.961 204 36 5 2215 2408 86512259 86512057 4.280000e-19 106.0
25 TraesCS5D01G293600 chr3D 96.189 761 29 0 1 761 349829918 349829158 0.000000e+00 1245.0
26 TraesCS5D01G293600 chr3D 87.371 483 46 13 2573 3046 61809090 61809566 9.900000e-150 540.0
27 TraesCS5D01G293600 chr3D 89.583 48 3 2 2416 2461 357643715 357643762 3.380000e-05 60.2
28 TraesCS5D01G293600 chr2D 95.817 765 32 0 1 765 160147414 160146650 0.000000e+00 1236.0
29 TraesCS5D01G293600 chr2D 81.250 192 19 5 2962 3136 35027953 35027762 4.220000e-29 139.0
30 TraesCS5D01G293600 chr7D 95.801 762 31 1 1 762 601047311 601046551 0.000000e+00 1229.0
31 TraesCS5D01G293600 chr7D 84.032 501 48 9 2578 3048 163390671 163390173 1.330000e-123 453.0
32 TraesCS5D01G293600 chr7D 79.344 305 56 4 1524 1823 58483253 58483555 1.140000e-49 207.0
33 TraesCS5D01G293600 chr7D 76.207 290 59 9 866 1152 156945396 156945114 9.070000e-31 145.0
34 TraesCS5D01G293600 chr6D 83.636 605 57 18 2573 3136 413266271 413266874 5.960000e-147 531.0
35 TraesCS5D01G293600 chr7B 83.306 605 59 15 2573 3136 336645057 336644454 1.290000e-143 520.0
36 TraesCS5D01G293600 chr7B 75.517 290 58 10 866 1152 6065302 6065023 2.540000e-26 130.0
37 TraesCS5D01G293600 chr4B 83.113 604 60 12 2573 3136 641804798 641804197 2.160000e-141 512.0
38 TraesCS5D01G293600 chr7A 85.800 500 45 11 2573 3048 144156439 144155942 1.000000e-139 507.0
39 TraesCS5D01G293600 chr7A 78.155 206 34 5 2215 2410 290620945 290620741 1.530000e-23 121.0
40 TraesCS5D01G293600 chr2B 85.800 500 46 5 2573 3048 77246997 77247495 1.000000e-139 507.0
41 TraesCS5D01G293600 chr2B 78.768 617 60 31 2448 3048 681716960 681716399 6.440000e-92 348.0
42 TraesCS5D01G293600 chr3B 82.064 591 60 14 2573 3131 190379394 190379970 2.200000e-126 462.0
43 TraesCS5D01G293600 chr6A 84.400 500 42 9 2573 3048 531420097 531420584 2.850000e-125 459.0
44 TraesCS5D01G293600 chr6B 81.457 604 65 17 2574 3136 710775701 710776298 4.770000e-123 451.0
45 TraesCS5D01G293600 chr6B 88.024 167 9 4 2578 2734 711429751 711429586 1.490000e-43 187.0
46 TraesCS5D01G293600 chr6B 94.845 97 4 1 2573 2669 635206799 635206894 1.950000e-32 150.0
47 TraesCS5D01G293600 chr6B 80.208 192 21 11 2962 3136 635266152 635266343 9.140000e-26 128.0
48 TraesCS5D01G293600 chr4A 80.361 499 64 8 2574 3048 601132787 601132299 6.440000e-92 348.0


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 TraesCS5D01G293600 chr5D 390557313 390560450 3137 False 5795 5795 100.000 1 3138 1 chr5D.!!$F3 3137
1 TraesCS5D01G293600 chr5D 390508427 390509799 1372 False 1831 1831 90.779 755 2138 1 chr5D.!!$F2 1383
2 TraesCS5D01G293600 chr5D 308807300 308808060 760 True 1245 1245 96.194 1 762 1 chr5D.!!$R2 761
3 TraesCS5D01G293600 chr5D 30083643 30084403 760 True 1234 1234 95.932 1 762 1 chr5D.!!$R1 761
4 TraesCS5D01G293600 chr5D 510472255 510472957 702 False 534 534 81.310 2439 3136 1 chr5D.!!$F4 697
5 TraesCS5D01G293600 chr5D 549798124 549798717 593 False 494 494 82.810 2573 3136 1 chr5D.!!$F5 563
6 TraesCS5D01G293600 chr5D 116627271 116627872 601 False 479 479 82.178 2573 3136 1 chr5D.!!$F1 563
7 TraesCS5D01G293600 chr5A 493810313 493811710 1397 True 1956 1956 92.051 755 2147 1 chr5A.!!$R1 1392
8 TraesCS5D01G293600 chr5A 670521740 670522465 725 False 527 527 80.662 2416 3136 1 chr5A.!!$F1 720
9 TraesCS5D01G293600 chr5B 470661539 470662298 759 False 1277 1277 96.974 1380 2139 1 chr5B.!!$F2 759
10 TraesCS5D01G293600 chr5B 470624231 470627376 3145 False 753 1936 91.235 755 2415 3 chr5B.!!$F4 1660
11 TraesCS5D01G293600 chr5B 584254487 584255057 570 False 422 422 80.815 2573 3136 1 chr5B.!!$F3 563
12 TraesCS5D01G293600 chr4D 7235611 7236372 761 False 1258 1258 96.457 1 762 1 chr4D.!!$F2 761
13 TraesCS5D01G293600 chr4D 205285568 205286329 761 False 1258 1258 96.457 1 762 1 chr4D.!!$F3 761
14 TraesCS5D01G293600 chr4D 219711246 219712007 761 False 1225 1225 95.669 1 762 1 chr4D.!!$F4 761
15 TraesCS5D01G293600 chr4D 6430215 6430824 609 True 508 508 82.473 2425 3037 1 chr4D.!!$R1 612
16 TraesCS5D01G293600 chr4D 3583006 3583589 583 False 448 448 81.488 2565 3137 1 chr4D.!!$F1 572
17 TraesCS5D01G293600 chr1D 275950902 275951663 761 False 1247 1247 96.194 1 762 1 chr1D.!!$F1 761
18 TraesCS5D01G293600 chr3D 349829158 349829918 760 True 1245 1245 96.189 1 761 1 chr3D.!!$R1 760
19 TraesCS5D01G293600 chr2D 160146650 160147414 764 True 1236 1236 95.817 1 765 1 chr2D.!!$R2 764
20 TraesCS5D01G293600 chr7D 601046551 601047311 760 True 1229 1229 95.801 1 762 1 chr7D.!!$R3 761
21 TraesCS5D01G293600 chr6D 413266271 413266874 603 False 531 531 83.636 2573 3136 1 chr6D.!!$F1 563
22 TraesCS5D01G293600 chr7B 336644454 336645057 603 True 520 520 83.306 2573 3136 1 chr7B.!!$R2 563
23 TraesCS5D01G293600 chr4B 641804197 641804798 601 True 512 512 83.113 2573 3136 1 chr4B.!!$R1 563
24 TraesCS5D01G293600 chr2B 681716399 681716960 561 True 348 348 78.768 2448 3048 1 chr2B.!!$R1 600
25 TraesCS5D01G293600 chr3B 190379394 190379970 576 False 462 462 82.064 2573 3131 1 chr3B.!!$F1 558
26 TraesCS5D01G293600 chr6B 710775701 710776298 597 False 451 451 81.457 2574 3136 1 chr6B.!!$F3 562

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
669 672 0.692476 CAGATGTGTGGGGGTCTTGA 59.308 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 2333 1.141665 GATTGGTTGGCGGCATTCC 59.858 57.895 14.32 18.68 0.0 3.01 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
86 87 5.896073 TCCTCTTCCTTCTCTGTTTTCTT 57.104 39.130 0.00 0.00 0.00 2.52
166 167 1.446272 GAAGGAGAAGACGGTGGCG 60.446 63.158 0.00 0.00 0.00 5.69
570 573 1.444250 GTTGTCGACCACACTGGGA 59.556 57.895 14.12 0.00 43.37 4.37
636 639 5.344743 AAAGCTAATCCGAGTGATGAGAA 57.655 39.130 0.00 0.00 34.15 2.87
669 672 0.692476 CAGATGTGTGGGGGTCTTGA 59.308 55.000 0.00 0.00 0.00 3.02
699 702 2.986728 TGAGGGGTAAAAGCTCTTTCCT 59.013 45.455 0.00 0.00 31.45 3.36
745 748 3.311110 GGGTGGCAGTCGACCTGA 61.311 66.667 13.01 0.00 44.49 3.86
792 795 6.708054 CCAAACAGAGAGTAAGAACATCAACT 59.292 38.462 0.00 0.00 0.00 3.16
839 842 3.476552 ACTTCGCTTCTGAAATCCAACA 58.523 40.909 0.00 0.00 0.00 3.33
846 860 3.469899 TCTGAAATCCAACATTTCGCG 57.530 42.857 0.00 0.00 40.02 5.87
853 867 2.560504 TCCAACATTTCGCGCTCATAT 58.439 42.857 5.56 0.00 0.00 1.78
972 986 3.332385 TACCCGGGCCAGGTTTCC 61.332 66.667 24.08 0.00 38.89 3.13
1021 1035 5.556915 ACATGGGACTCGTGAGAATTTTTA 58.443 37.500 0.27 0.00 41.32 1.52
1028 1042 7.237173 GGACTCGTGAGAATTTTTAATCACAG 58.763 38.462 3.44 4.31 41.67 3.66
1078 1098 2.149578 GGGCACTGATCATGCTATGTC 58.850 52.381 21.50 8.03 42.93 3.06
1082 1102 3.875727 GCACTGATCATGCTATGTCTTGT 59.124 43.478 17.57 0.00 40.08 3.16
1113 1133 2.032681 GCAAAGGACGGGAGCAGT 59.967 61.111 0.00 0.00 0.00 4.40
1162 1182 2.601067 TTACCACGGACCGGCTGA 60.601 61.111 20.00 0.00 0.00 4.26
1221 1241 2.017559 GCGACCTCTCCTACGCCAAT 62.018 60.000 0.00 0.00 44.27 3.16
1316 1340 4.754667 GTTCGTCCGCCCACCCTC 62.755 72.222 0.00 0.00 0.00 4.30
1330 1354 2.290514 CCACCCTCAGAATCTTGCTTGA 60.291 50.000 0.00 0.00 0.00 3.02
1333 1357 4.461781 CACCCTCAGAATCTTGCTTGATTT 59.538 41.667 6.29 0.00 36.86 2.17
1335 1359 4.142227 CCCTCAGAATCTTGCTTGATTTGG 60.142 45.833 6.29 6.78 36.86 3.28
1337 1361 5.649395 CCTCAGAATCTTGCTTGATTTGGTA 59.351 40.000 6.29 0.00 36.86 3.25
1338 1362 6.183360 CCTCAGAATCTTGCTTGATTTGGTAG 60.183 42.308 6.29 3.63 36.86 3.18
1342 1366 6.716628 AGAATCTTGCTTGATTTGGTAGTTCA 59.283 34.615 6.29 0.00 36.86 3.18
1366 1390 4.461081 AGGTGAACTAGACTCAGACATGTC 59.539 45.833 18.47 18.47 0.00 3.06
1803 1828 0.172803 GTCCACAACTACGAGCGGAT 59.827 55.000 0.00 0.00 0.00 4.18
1991 2016 0.797249 CTTCGGGTACGTCAAGCTCG 60.797 60.000 0.00 0.00 41.85 5.03
2219 2311 0.880278 CGATTGGATCGCCGTGGATT 60.880 55.000 0.00 0.00 46.55 3.01
2220 2312 1.604438 CGATTGGATCGCCGTGGATTA 60.604 52.381 0.00 0.00 46.55 1.75
2221 2313 2.069273 GATTGGATCGCCGTGGATTAG 58.931 52.381 0.00 0.00 36.79 1.73
2240 2333 3.611766 AGTTAAGGATTGGTGGAGTCG 57.388 47.619 0.00 0.00 0.00 4.18
2304 2406 6.485648 TCTTGTGATGATGCTTATCAATCTGG 59.514 38.462 0.00 0.00 36.41 3.86
2340 2444 7.971455 ACACTAGAGTATTTTTGAAATACGGC 58.029 34.615 14.44 11.75 37.98 5.68
2346 3849 2.993449 TTTTGAAATACGGCCGTTCC 57.007 45.000 38.94 22.07 0.00 3.62
2377 3880 2.990740 TGGTGGCCAAGGTTAAAGAT 57.009 45.000 7.24 0.00 0.00 2.40
2378 3881 2.524306 TGGTGGCCAAGGTTAAAGATG 58.476 47.619 7.24 0.00 0.00 2.90
2423 3926 2.427095 GGAGCAAAGCATTAAATCCGGT 59.573 45.455 0.00 0.00 0.00 5.28
2433 3936 3.791953 TTAAATCCGGTCCCTCAAACA 57.208 42.857 0.00 0.00 0.00 2.83
2467 3972 1.370064 GGGCACTGACCGTACACTT 59.630 57.895 0.00 0.00 0.00 3.16
2483 3988 3.748083 ACACTTCCTATATCCGCGTCTA 58.252 45.455 4.92 0.00 0.00 2.59
2513 4018 5.279960 CCATGTATCTCATATTTCGTCCCCA 60.280 44.000 0.00 0.00 34.67 4.96
2537 4042 7.818930 CCAATTTTCATACTAAACCATGCAACT 59.181 33.333 0.00 0.00 0.00 3.16
2538 4043 8.863049 CAATTTTCATACTAAACCATGCAACTC 58.137 33.333 0.00 0.00 0.00 3.01
2539 4044 6.509418 TTTCATACTAAACCATGCAACTCC 57.491 37.500 0.00 0.00 0.00 3.85
2543 4048 1.474077 CTAAACCATGCAACTCCCAGC 59.526 52.381 0.00 0.00 0.00 4.85
2544 4049 0.178953 AAACCATGCAACTCCCAGCT 60.179 50.000 0.00 0.00 0.00 4.24
2545 4050 0.610232 AACCATGCAACTCCCAGCTC 60.610 55.000 0.00 0.00 0.00 4.09
2548 4053 1.471119 CATGCAACTCCCAGCTCAAT 58.529 50.000 0.00 0.00 0.00 2.57
2550 4055 1.250328 TGCAACTCCCAGCTCAATTG 58.750 50.000 0.00 0.00 0.00 2.32
2551 4056 1.202915 TGCAACTCCCAGCTCAATTGA 60.203 47.619 8.12 8.12 0.00 2.57
2552 4057 2.097825 GCAACTCCCAGCTCAATTGAT 58.902 47.619 8.96 0.00 0.00 2.57
2553 4058 2.494870 GCAACTCCCAGCTCAATTGATT 59.505 45.455 8.96 0.00 0.00 2.57
2554 4059 3.428589 GCAACTCCCAGCTCAATTGATTC 60.429 47.826 8.96 4.23 0.00 2.52
2555 4060 3.726557 ACTCCCAGCTCAATTGATTCA 57.273 42.857 8.96 0.00 0.00 2.57
2556 4061 4.246712 ACTCCCAGCTCAATTGATTCAT 57.753 40.909 8.96 0.00 0.00 2.57
2557 4062 4.205587 ACTCCCAGCTCAATTGATTCATC 58.794 43.478 8.96 0.00 0.00 2.92
2558 4063 4.204799 CTCCCAGCTCAATTGATTCATCA 58.795 43.478 8.96 0.00 34.44 3.07
2601 4106 4.036380 ACGTAGATCATGAGCGAACATACA 59.964 41.667 16.30 0.00 0.00 2.29
2618 4123 5.537188 ACATACAAAATGCACAATCGGTTT 58.463 33.333 0.00 0.00 0.00 3.27
2672 4187 7.497595 AGATAGCCAAAGTTCACATAATACGA 58.502 34.615 0.00 0.00 0.00 3.43
2701 4216 9.615295 GACAAGTTCAAACTACAACTAAAAACA 57.385 29.630 0.00 0.00 38.57 2.83
2731 4256 1.993370 GACGAATCTTCACCACTTCCG 59.007 52.381 0.00 0.00 0.00 4.30
2786 4311 1.982938 GTAGGAGTCCACGGCAGGT 60.983 63.158 12.86 0.00 0.00 4.00
2864 4389 3.333898 GAAGCCTTGCAAGCGCCTC 62.334 63.158 26.37 21.78 37.32 4.70
2896 4421 2.203337 TTGGCGCTTGAGCTTGGT 60.203 55.556 7.64 0.00 39.32 3.67
2989 4547 4.065281 CCGTCGGGCCTTCGTCTT 62.065 66.667 2.34 0.00 0.00 3.01
3060 4635 3.842923 CGGGCGGACTCTGCAGAT 61.843 66.667 18.63 7.64 0.00 2.90
3091 4666 2.421739 CCGCCATCTCCCTAACCG 59.578 66.667 0.00 0.00 0.00 4.44
3103 4678 0.108138 CCTAACCGTCTGCCTCTTGG 60.108 60.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 3.354499 CTTCTTCGCGCGCTCCAAC 62.354 63.158 30.48 0.00 0.00 3.77
352 353 4.710167 TCAGTCTCGTCCGCCGGA 62.710 66.667 5.05 0.00 37.11 5.14
426 427 0.627986 AGGATGGGGAGGCAAAGAAG 59.372 55.000 0.00 0.00 0.00 2.85
570 573 3.003689 CGTGAAAATGTGCTTGAAGAGGT 59.996 43.478 0.00 0.00 0.00 3.85
636 639 4.758674 CACACATCTGGATCACTTTTGTCT 59.241 41.667 0.00 0.00 0.00 3.41
669 672 5.093677 AGCTTTTACCCCTCATTTGGATTT 58.906 37.500 0.00 0.00 0.00 2.17
699 702 4.562767 TGACTTGGGTAGGATTATGGCTA 58.437 43.478 0.00 0.00 0.00 3.93
745 748 3.157087 CCACAGGTCCTTGCAGTAAAAT 58.843 45.455 0.00 0.00 0.00 1.82
817 820 3.882888 TGTTGGATTTCAGAAGCGAAGTT 59.117 39.130 0.00 0.00 0.00 2.66
819 822 4.691860 ATGTTGGATTTCAGAAGCGAAG 57.308 40.909 0.00 0.00 0.00 3.79
823 826 3.609807 GCGAAATGTTGGATTTCAGAAGC 59.390 43.478 0.00 0.00 37.76 3.86
834 837 4.397382 CATATATGAGCGCGAAATGTTGG 58.603 43.478 12.10 0.00 0.00 3.77
839 842 2.698803 TGGCATATATGAGCGCGAAAT 58.301 42.857 17.10 1.41 0.00 2.17
877 891 1.331756 GTGCCCAATCTGATAAGCGTG 59.668 52.381 0.00 0.00 0.00 5.34
880 894 1.869767 CTCGTGCCCAATCTGATAAGC 59.130 52.381 0.00 0.00 0.00 3.09
882 896 1.486310 AGCTCGTGCCCAATCTGATAA 59.514 47.619 5.73 0.00 40.80 1.75
1021 1035 6.322201 ACACCTGAACATTTTCTTCTGTGATT 59.678 34.615 0.00 0.00 32.36 2.57
1072 1092 2.489329 CCTGCAACCCAACAAGACATAG 59.511 50.000 0.00 0.00 0.00 2.23
1078 1098 2.209315 CCCCCTGCAACCCAACAAG 61.209 63.158 0.00 0.00 0.00 3.16
1113 1133 1.920325 CTGGAACCCCTGGAGCTCA 60.920 63.158 17.19 0.61 0.00 4.26
1146 1166 2.363276 ATCAGCCGGTCCGTGGTA 60.363 61.111 11.06 0.00 0.00 3.25
1152 1172 1.153349 GTCCTTGATCAGCCGGTCC 60.153 63.158 1.90 0.00 0.00 4.46
1162 1182 1.282157 GTAGTTGGGCAGGTCCTTGAT 59.718 52.381 0.00 0.00 34.39 2.57
1245 1265 2.202610 TCGATCTGCGCGGTGAAG 60.203 61.111 17.37 0.00 40.61 3.02
1316 1340 6.506500 ACTACCAAATCAAGCAAGATTCTG 57.493 37.500 4.41 5.65 37.24 3.02
1342 1366 4.835615 ACATGTCTGAGTCTAGTTCACCTT 59.164 41.667 0.00 0.00 0.00 3.50
1803 1828 1.604308 TTCTCGTAGACGGGGCACA 60.604 57.895 1.44 0.00 40.92 4.57
2170 2209 4.283978 TGGACATCAATTTTGCCAATCACT 59.716 37.500 0.00 0.00 0.00 3.41
2171 2210 4.567971 TGGACATCAATTTTGCCAATCAC 58.432 39.130 0.00 0.00 0.00 3.06
2219 2311 3.449737 CCGACTCCACCAATCCTTAACTA 59.550 47.826 0.00 0.00 0.00 2.24
2220 2312 2.236395 CCGACTCCACCAATCCTTAACT 59.764 50.000 0.00 0.00 0.00 2.24
2221 2313 2.235402 TCCGACTCCACCAATCCTTAAC 59.765 50.000 0.00 0.00 0.00 2.01
2240 2333 1.141665 GATTGGTTGGCGGCATTCC 59.858 57.895 14.32 18.68 0.00 3.01
2273 2367 4.456280 AAGCATCATCACAAGACGAGTA 57.544 40.909 0.00 0.00 0.00 2.59
2283 2377 6.709397 TCTTCCAGATTGATAAGCATCATCAC 59.291 38.462 0.00 0.00 40.85 3.06
2304 2406 7.583860 AAATACTCTAGTGTTTCGCTTCTTC 57.416 36.000 2.25 0.00 34.93 2.87
2317 2419 6.257193 CGGCCGTATTTCAAAAATACTCTAGT 59.743 38.462 19.50 0.00 32.43 2.57
2346 3849 2.347490 CCACCAAGACTCCCACCG 59.653 66.667 0.00 0.00 0.00 4.94
2369 3872 4.398247 CAAAGCGAGCACTCATCTTTAAC 58.602 43.478 11.94 0.00 33.39 2.01
2371 3874 3.002791 CCAAAGCGAGCACTCATCTTTA 58.997 45.455 11.94 0.00 33.39 1.85
2377 3880 4.681421 CTCCAAAGCGAGCACTCA 57.319 55.556 0.00 0.00 0.00 3.41
2423 3926 2.267642 CCGCGGATGTTTGAGGGA 59.732 61.111 24.07 0.00 0.00 4.20
2461 3966 3.748083 AGACGCGGATATAGGAAGTGTA 58.252 45.455 12.47 0.00 0.00 2.90
2467 3972 2.810274 GTGTGTAGACGCGGATATAGGA 59.190 50.000 12.47 0.00 0.00 2.94
2483 3988 5.991606 CGAAATATGAGATACATGGGTGTGT 59.008 40.000 0.00 0.00 39.39 3.72
2513 4018 8.034804 GGAGTTGCATGGTTTAGTATGAAAATT 58.965 33.333 0.00 0.00 0.00 1.82
2537 4042 4.239428 TGATGAATCAATTGAGCTGGGA 57.761 40.909 14.54 0.00 33.08 4.37
2538 4043 4.994907 TTGATGAATCAATTGAGCTGGG 57.005 40.909 14.54 0.00 41.51 4.45
2539 4044 6.627243 TCTTTTGATGAATCAATTGAGCTGG 58.373 36.000 14.54 0.00 45.30 4.85
2554 4059 9.003112 CGTAGTTTTGCTATTGATCTTTTGATG 57.997 33.333 0.00 0.00 33.94 3.07
2555 4060 8.730680 ACGTAGTTTTGCTATTGATCTTTTGAT 58.269 29.630 0.00 0.00 37.78 2.57
2556 4061 8.094798 ACGTAGTTTTGCTATTGATCTTTTGA 57.905 30.769 0.00 0.00 37.78 2.69
2557 4062 9.478019 CTACGTAGTTTTGCTATTGATCTTTTG 57.522 33.333 14.66 0.00 37.78 2.44
2558 4063 9.431887 TCTACGTAGTTTTGCTATTGATCTTTT 57.568 29.630 21.53 0.00 37.78 2.27
2559 4064 8.997621 TCTACGTAGTTTTGCTATTGATCTTT 57.002 30.769 21.53 0.00 37.78 2.52
2560 4065 9.250624 GATCTACGTAGTTTTGCTATTGATCTT 57.749 33.333 21.53 0.00 37.78 2.40
2561 4066 8.414003 TGATCTACGTAGTTTTGCTATTGATCT 58.586 33.333 21.53 0.00 37.78 2.75
2562 4067 8.575565 TGATCTACGTAGTTTTGCTATTGATC 57.424 34.615 21.53 12.77 37.78 2.92
2563 4068 8.982685 CATGATCTACGTAGTTTTGCTATTGAT 58.017 33.333 21.53 4.04 37.78 2.57
2564 4069 8.194769 TCATGATCTACGTAGTTTTGCTATTGA 58.805 33.333 21.53 10.62 37.78 2.57
2565 4070 8.352752 TCATGATCTACGTAGTTTTGCTATTG 57.647 34.615 21.53 8.82 37.78 1.90
2566 4071 7.169982 GCTCATGATCTACGTAGTTTTGCTATT 59.830 37.037 21.53 0.00 37.78 1.73
2567 4072 6.642950 GCTCATGATCTACGTAGTTTTGCTAT 59.357 38.462 21.53 6.45 37.78 2.97
2568 4073 5.977725 GCTCATGATCTACGTAGTTTTGCTA 59.022 40.000 21.53 1.36 37.78 3.49
2569 4074 4.806247 GCTCATGATCTACGTAGTTTTGCT 59.194 41.667 21.53 2.02 37.78 3.91
2570 4075 4.317418 CGCTCATGATCTACGTAGTTTTGC 60.317 45.833 21.53 15.35 37.78 3.68
2571 4076 5.034797 TCGCTCATGATCTACGTAGTTTTG 58.965 41.667 21.53 14.41 37.78 2.44
2572 4077 5.244785 TCGCTCATGATCTACGTAGTTTT 57.755 39.130 21.53 8.59 37.78 2.43
2573 4078 4.895224 TCGCTCATGATCTACGTAGTTT 57.105 40.909 21.53 11.02 37.78 2.66
2574 4079 4.095932 TGTTCGCTCATGATCTACGTAGTT 59.904 41.667 21.53 14.00 37.78 2.24
2576 4081 4.210832 TGTTCGCTCATGATCTACGTAG 57.789 45.455 16.73 16.73 0.00 3.51
2577 4082 4.830826 ATGTTCGCTCATGATCTACGTA 57.169 40.909 0.00 0.00 0.00 3.57
2578 4083 3.717400 ATGTTCGCTCATGATCTACGT 57.283 42.857 0.00 0.00 0.00 3.57
2601 4106 7.655328 TCTTTTGATAAACCGATTGTGCATTTT 59.345 29.630 0.00 0.00 0.00 1.82
2618 4123 3.904800 TCCGGCTGTGATCTTTTGATA 57.095 42.857 0.00 0.00 39.67 2.15
2672 4187 4.510571 AGTTGTAGTTTGAACTTGTCCGT 58.489 39.130 1.20 0.00 40.37 4.69
2701 4216 7.607991 AGTGGTGAAGATTCGTCTTTATTTCAT 59.392 33.333 1.37 0.00 0.00 2.57
2715 4230 1.298859 GCGCGGAAGTGGTGAAGATT 61.299 55.000 8.83 0.00 43.14 2.40
2822 4347 1.268352 GTCATCTCCGATTCCTCCTCG 59.732 57.143 0.00 0.00 35.92 4.63
2864 4389 1.497278 CCAACAAGACCGCATCGTG 59.503 57.895 0.24 0.24 42.06 4.35
2989 4547 2.626780 CGGTCACTGACTGAGGCGA 61.627 63.158 12.11 0.00 41.05 5.54


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

AutoCloner maintained by Alex Coulton.