Multiple sequence alignment - TraesCS2D01G586300

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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 TraesCS2D01G586300 chr2D 100.000 2387 0 0 1 2387 644734568 644732182 0.000000e+00 4409.0
1 TraesCS2D01G586300 chr2D 81.481 783 126 9 771 1544 644981386 644980614 2.010000e-175 625.0
2 TraesCS2D01G586300 chr2D 100.000 29 0 0 91 119 25683187 25683159 1.000000e-03 54.7
3 TraesCS2D01G586300 chr2A 95.362 1574 55 6 716 2274 770023799 770022229 0.000000e+00 2486.0
4 TraesCS2D01G586300 chr2A 91.690 710 25 19 1 678 770024500 770023793 0.000000e+00 953.0
5 TraesCS2D01G586300 chr2A 81.202 782 129 7 773 1544 770291091 770290318 4.360000e-172 614.0
6 TraesCS2D01G586300 chr2A 82.857 245 35 6 204 443 655058225 655057983 1.860000e-51 213.0
7 TraesCS2D01G586300 chr3B 82.051 741 122 8 806 1544 48668647 48667916 2.610000e-174 621.0
8 TraesCS2D01G586300 chr3B 84.615 78 10 2 123 199 441469722 441469646 2.540000e-10 76.8
9 TraesCS2D01G586300 chr2B 81.330 782 128 9 773 1544 790623505 790624278 9.370000e-174 619.0
10 TraesCS2D01G586300 chr2B 87.127 536 32 16 1441 1945 790807298 790806769 7.400000e-160 573.0
11 TraesCS2D01G586300 chr2B 91.255 263 22 1 980 1241 790740475 790740737 8.110000e-95 357.0
12 TraesCS2D01G586300 chr2B 83.924 367 21 17 1800 2143 790740801 790741152 1.380000e-82 316.0
13 TraesCS2D01G586300 chr2B 76.610 295 63 5 995 1286 697228683 697228392 8.830000e-35 158.0
14 TraesCS2D01G586300 chr2B 78.603 229 45 3 1060 1286 697398636 697398410 5.320000e-32 148.0
15 TraesCS2D01G586300 chr2B 75.593 295 67 4 995 1286 697142484 697142192 8.900000e-30 141.0
16 TraesCS2D01G586300 chr2B 75.254 295 68 4 995 1286 697295149 697294857 4.140000e-28 135.0
17 TraesCS2D01G586300 chr4D 84.337 249 32 7 199 442 15456947 15456701 1.100000e-58 237.0
18 TraesCS2D01G586300 chr4D 81.452 248 36 9 200 442 355287149 355287391 6.730000e-46 195.0
19 TraesCS2D01G586300 chr4D 92.208 77 6 0 123 199 310362772 310362848 2.510000e-20 110.0
20 TraesCS2D01G586300 chr3D 84.739 249 25 11 200 442 424255295 424255054 1.100000e-58 237.0
21 TraesCS2D01G586300 chr3D 83.721 215 29 6 200 411 312905548 312905759 5.200000e-47 198.0
22 TraesCS2D01G586300 chr3A 83.468 248 31 9 200 442 564453089 564453331 3.090000e-54 222.0
23 TraesCS2D01G586300 chr3A 80.169 237 41 5 204 436 128271936 128271702 3.150000e-39 172.0
24 TraesCS2D01G586300 chr3A 97.297 37 1 0 1712 1748 746355832 746355796 1.980000e-06 63.9
25 TraesCS2D01G586300 chr5D 81.967 244 34 9 204 442 65946523 65946761 5.200000e-47 198.0
26 TraesCS2D01G586300 chr4A 87.640 89 9 2 3 90 696743376 696743463 4.200000e-18 102.0
27 TraesCS2D01G586300 chr7D 100.000 29 0 0 91 119 353408417 353408389 1.000000e-03 54.7
28 TraesCS2D01G586300 chr1B 100.000 29 0 0 91 119 435806279 435806307 1.000000e-03 54.7
29 TraesCS2D01G586300 chr5B 96.875 32 0 1 92 122 277602675 277602706 4.000000e-03 52.8


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 TraesCS2D01G586300 chr2D 644732182 644734568 2386 True 4409.0 4409 100.0000 1 2387 1 chr2D.!!$R2 2386
1 TraesCS2D01G586300 chr2D 644980614 644981386 772 True 625.0 625 81.4810 771 1544 1 chr2D.!!$R3 773
2 TraesCS2D01G586300 chr2A 770022229 770024500 2271 True 1719.5 2486 93.5260 1 2274 2 chr2A.!!$R3 2273
3 TraesCS2D01G586300 chr2A 770290318 770291091 773 True 614.0 614 81.2020 773 1544 1 chr2A.!!$R2 771
4 TraesCS2D01G586300 chr3B 48667916 48668647 731 True 621.0 621 82.0510 806 1544 1 chr3B.!!$R1 738
5 TraesCS2D01G586300 chr2B 790623505 790624278 773 False 619.0 619 81.3300 773 1544 1 chr2B.!!$F1 771
6 TraesCS2D01G586300 chr2B 790806769 790807298 529 True 573.0 573 87.1270 1441 1945 1 chr2B.!!$R5 504
7 TraesCS2D01G586300 chr2B 790740475 790741152 677 False 336.5 357 87.5895 980 2143 2 chr2B.!!$F2 1163

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
313 346 0.248458 AAAGCGTGCGAAAACACCTG 60.248 50.0 0.0 0.0 37.25 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2311 2410 0.031994 GCCTGGCACGACAAATTGTT 59.968 50.0 15.17 0.0 0.0 2.83 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
99 100 5.274881 TGTTTTCAAAACACATTGCACAC 57.725 34.783 11.83 0.00 0.00 3.82
116 117 3.747193 CACACGTGCATATGAGTTTTCC 58.253 45.455 17.22 0.00 0.00 3.13
118 119 3.188460 ACACGTGCATATGAGTTTTCCAC 59.812 43.478 17.22 2.20 0.00 4.02
119 120 2.415168 ACGTGCATATGAGTTTTCCACG 59.585 45.455 20.76 20.76 46.80 4.94
210 243 3.535280 TTTTCAACACCCAAAGCTTCC 57.465 42.857 0.00 0.00 0.00 3.46
303 336 1.255084 CTGAAAAACCAAAAGCGTGCG 59.745 47.619 0.00 0.00 0.00 5.34
313 346 0.248458 AAAGCGTGCGAAAACACCTG 60.248 50.000 0.00 0.00 37.25 4.00
545 578 8.486210 ACAATGCCTATCTACTTTATCTCAACA 58.514 33.333 0.00 0.00 0.00 3.33
619 652 5.573219 TGTTAGTGGGTGAGCTAGTTACTA 58.427 41.667 0.00 0.00 0.00 1.82
630 663 6.469595 GTGAGCTAGTTACTACATCTGTTTCG 59.530 42.308 0.00 0.00 0.00 3.46
697 730 7.039313 ACTTTAAGTAGGTCAAAGCTTTTGG 57.961 36.000 9.53 0.00 33.50 3.28
698 731 6.831868 ACTTTAAGTAGGTCAAAGCTTTTGGA 59.168 34.615 9.53 1.60 33.50 3.53
699 732 7.340999 ACTTTAAGTAGGTCAAAGCTTTTGGAA 59.659 33.333 9.53 0.00 33.50 3.53
700 733 7.648039 TTAAGTAGGTCAAAGCTTTTGGAAA 57.352 32.000 9.53 0.00 0.00 3.13
701 734 6.731292 AAGTAGGTCAAAGCTTTTGGAAAT 57.269 33.333 9.53 0.07 0.00 2.17
702 735 6.089249 AGTAGGTCAAAGCTTTTGGAAATG 57.911 37.500 9.53 0.00 0.00 2.32
703 736 3.732212 AGGTCAAAGCTTTTGGAAATGC 58.268 40.909 9.53 2.56 38.80 3.56
704 737 3.134442 AGGTCAAAGCTTTTGGAAATGCA 59.866 39.130 9.53 0.00 40.38 3.96
705 738 4.067192 GGTCAAAGCTTTTGGAAATGCAT 58.933 39.130 9.53 0.00 40.38 3.96
706 739 4.152938 GGTCAAAGCTTTTGGAAATGCATC 59.847 41.667 9.53 0.00 40.38 3.91
707 740 4.751098 GTCAAAGCTTTTGGAAATGCATCA 59.249 37.500 9.53 0.00 40.38 3.07
708 741 5.236911 GTCAAAGCTTTTGGAAATGCATCAA 59.763 36.000 9.53 0.00 40.38 2.57
709 742 5.821470 TCAAAGCTTTTGGAAATGCATCAAA 59.179 32.000 9.53 3.62 40.38 2.69
710 743 6.487331 TCAAAGCTTTTGGAAATGCATCAAAT 59.513 30.769 9.53 0.00 40.38 2.32
711 744 6.887626 AAGCTTTTGGAAATGCATCAAATT 57.112 29.167 11.52 0.00 40.38 1.82
712 745 6.249035 AGCTTTTGGAAATGCATCAAATTG 57.751 33.333 11.52 9.35 40.38 2.32
713 746 5.998981 AGCTTTTGGAAATGCATCAAATTGA 59.001 32.000 11.52 0.00 40.38 2.57
714 747 6.657541 AGCTTTTGGAAATGCATCAAATTGAT 59.342 30.769 11.52 2.07 40.38 2.57
855 898 9.167311 CACTTCTAAATGCTTAGTTGGATAAGT 57.833 33.333 0.00 0.00 36.63 2.24
883 926 8.402472 TCCAATTAATATTTGCCTCTTACAACG 58.598 33.333 0.00 0.00 0.00 4.10
942 989 2.301583 TCCACTCACATCACCGATTCAA 59.698 45.455 0.00 0.00 0.00 2.69
943 990 3.073678 CCACTCACATCACCGATTCAAA 58.926 45.455 0.00 0.00 0.00 2.69
1011 1058 3.047857 TCCAATAGCCATGAGGACATCA 58.952 45.455 0.00 0.00 43.70 3.07
1020 1067 2.775911 TGAGGACATCAAGCTTCCTG 57.224 50.000 8.67 5.98 40.02 3.86
1111 1159 4.794655 GCAACCAATTACGGAACACAACAT 60.795 41.667 0.00 0.00 0.00 2.71
1178 1226 2.676471 GGTGCTCGGCAATTGGGT 60.676 61.111 7.72 0.00 41.47 4.51
1388 1436 2.489073 CCTTTGCCAAGGTGAACTAGGT 60.489 50.000 8.44 0.00 44.46 3.08
1452 1503 8.776376 CAAATATGTTTGCTGGGTTTCTAATT 57.224 30.769 1.72 0.00 38.39 1.40
1624 1676 1.127766 GCGTGCGACAATGAACACATA 59.872 47.619 0.00 0.00 33.23 2.29
1716 1784 6.318144 AGCAATACCTGTGAAAGATGATCTTG 59.682 38.462 8.68 0.00 36.71 3.02
1749 1817 3.317430 CGGAGGGAGTATAACTTTAGCGT 59.683 47.826 0.00 0.00 0.00 5.07
1954 2039 0.041238 AGGAGATCACGTGGGGAGAA 59.959 55.000 17.00 0.00 0.00 2.87
2147 2246 4.568359 ACGACAGCATTGATTGTATCTGAC 59.432 41.667 0.00 0.00 0.00 3.51
2213 2312 4.092116 TGAGAAGGCTAGATCGATCTGA 57.908 45.455 33.22 18.00 37.76 3.27
2223 2322 6.975772 GGCTAGATCGATCTGATTATTACACC 59.024 42.308 33.22 16.43 37.47 4.16
2226 2325 7.767250 AGATCGATCTGATTATTACACCTGA 57.233 36.000 26.78 0.00 37.47 3.86
2274 2373 5.947228 TCAGTGAATCAAGTGGAATCAAC 57.053 39.130 0.00 0.00 37.19 3.18
2275 2374 5.624159 TCAGTGAATCAAGTGGAATCAACT 58.376 37.500 0.00 0.00 37.19 3.16
2276 2375 5.702670 TCAGTGAATCAAGTGGAATCAACTC 59.297 40.000 0.00 0.00 37.19 3.01
2277 2376 4.692625 AGTGAATCAAGTGGAATCAACTCG 59.307 41.667 0.00 0.00 37.19 4.18
2278 2377 4.002982 TGAATCAAGTGGAATCAACTCGG 58.997 43.478 0.00 0.00 32.53 4.63
2279 2378 1.808411 TCAAGTGGAATCAACTCGGC 58.192 50.000 0.00 0.00 0.00 5.54
2280 2379 0.804989 CAAGTGGAATCAACTCGGCC 59.195 55.000 0.00 0.00 0.00 6.13
2281 2380 0.400213 AAGTGGAATCAACTCGGCCA 59.600 50.000 2.24 0.00 0.00 5.36
2282 2381 2.171635 GTGGAATCAACTCGGCCAC 58.828 57.895 2.24 0.00 41.77 5.01
2283 2382 1.375396 TGGAATCAACTCGGCCACG 60.375 57.895 2.24 0.00 42.74 4.94
2300 2399 3.060866 GAGCCCACCACTCGAACT 58.939 61.111 0.00 0.00 0.00 3.01
2301 2400 1.374758 GAGCCCACCACTCGAACTG 60.375 63.158 0.00 0.00 0.00 3.16
2302 2401 2.100879 GAGCCCACCACTCGAACTGT 62.101 60.000 0.00 0.00 0.00 3.55
2303 2402 1.668151 GCCCACCACTCGAACTGTC 60.668 63.158 0.00 0.00 0.00 3.51
2304 2403 1.004918 CCCACCACTCGAACTGTCC 60.005 63.158 0.00 0.00 0.00 4.02
2305 2404 1.004918 CCACCACTCGAACTGTCCC 60.005 63.158 0.00 0.00 0.00 4.46
2306 2405 1.472662 CCACCACTCGAACTGTCCCT 61.473 60.000 0.00 0.00 0.00 4.20
2307 2406 0.319900 CACCACTCGAACTGTCCCTG 60.320 60.000 0.00 0.00 0.00 4.45
2308 2407 1.374758 CCACTCGAACTGTCCCTGC 60.375 63.158 0.00 0.00 0.00 4.85
2309 2408 1.734477 CACTCGAACTGTCCCTGCG 60.734 63.158 0.00 0.00 0.00 5.18
2310 2409 2.201022 ACTCGAACTGTCCCTGCGT 61.201 57.895 0.00 0.00 0.00 5.24
2311 2410 0.892358 ACTCGAACTGTCCCTGCGTA 60.892 55.000 0.00 0.00 0.00 4.42
2312 2411 0.242825 CTCGAACTGTCCCTGCGTAA 59.757 55.000 0.00 0.00 0.00 3.18
2313 2412 0.038892 TCGAACTGTCCCTGCGTAAC 60.039 55.000 0.00 0.00 0.00 2.50
2314 2413 0.319211 CGAACTGTCCCTGCGTAACA 60.319 55.000 0.00 0.00 0.00 2.41
2315 2414 1.870580 CGAACTGTCCCTGCGTAACAA 60.871 52.381 0.00 0.00 0.00 2.83
2316 2415 2.423577 GAACTGTCCCTGCGTAACAAT 58.576 47.619 0.00 0.00 0.00 2.71
2317 2416 2.561478 ACTGTCCCTGCGTAACAATT 57.439 45.000 0.00 0.00 0.00 2.32
2318 2417 2.858745 ACTGTCCCTGCGTAACAATTT 58.141 42.857 0.00 0.00 0.00 1.82
2319 2418 2.552315 ACTGTCCCTGCGTAACAATTTG 59.448 45.455 0.00 0.00 0.00 2.32
2320 2419 2.552315 CTGTCCCTGCGTAACAATTTGT 59.448 45.455 0.00 0.00 0.00 2.83
2321 2420 2.550606 TGTCCCTGCGTAACAATTTGTC 59.449 45.455 1.83 0.00 0.00 3.18
2322 2421 1.801771 TCCCTGCGTAACAATTTGTCG 59.198 47.619 1.83 4.49 0.00 4.35
2323 2422 1.533731 CCCTGCGTAACAATTTGTCGT 59.466 47.619 1.83 0.00 0.00 4.34
2324 2423 2.570169 CCTGCGTAACAATTTGTCGTG 58.430 47.619 1.83 1.78 0.00 4.35
2325 2424 1.969256 CTGCGTAACAATTTGTCGTGC 59.031 47.619 1.83 7.55 0.00 5.34
2326 2425 1.323791 GCGTAACAATTTGTCGTGCC 58.676 50.000 1.83 0.00 0.00 5.01
2327 2426 1.334239 GCGTAACAATTTGTCGTGCCA 60.334 47.619 1.83 0.00 0.00 4.92
2328 2427 2.570169 CGTAACAATTTGTCGTGCCAG 58.430 47.619 1.83 0.00 0.00 4.85
2329 2428 2.664424 CGTAACAATTTGTCGTGCCAGG 60.664 50.000 1.83 0.00 0.00 4.45
2330 2429 0.031994 AACAATTTGTCGTGCCAGGC 59.968 50.000 3.66 3.66 0.00 4.85
2331 2430 1.080569 CAATTTGTCGTGCCAGGCC 60.081 57.895 9.64 0.00 0.00 5.19
2332 2431 2.625823 AATTTGTCGTGCCAGGCCG 61.626 57.895 9.64 12.49 0.00 6.13
2346 2445 2.432972 GCCGGCTGCCAAAACATG 60.433 61.111 22.15 0.00 0.00 3.21
2347 2446 2.432972 CCGGCTGCCAAAACATGC 60.433 61.111 20.29 0.00 0.00 4.06
2348 2447 2.652530 CGGCTGCCAAAACATGCT 59.347 55.556 20.29 0.00 0.00 3.79
2349 2448 1.005867 CGGCTGCCAAAACATGCTT 60.006 52.632 20.29 0.00 0.00 3.91
2350 2449 0.600782 CGGCTGCCAAAACATGCTTT 60.601 50.000 20.29 0.00 0.00 3.51
2351 2450 1.596603 GGCTGCCAAAACATGCTTTT 58.403 45.000 15.17 0.00 0.00 2.27
2352 2451 1.948834 GGCTGCCAAAACATGCTTTTT 59.051 42.857 15.17 0.00 0.00 1.94
2378 2477 9.959749 TTTGGTCTGATTAAAATTTAGTCACAC 57.040 29.630 6.82 7.29 0.00 3.82
2379 2478 8.684386 TGGTCTGATTAAAATTTAGTCACACA 57.316 30.769 14.69 8.69 0.00 3.72
2380 2479 9.295825 TGGTCTGATTAAAATTTAGTCACACAT 57.704 29.630 14.69 0.00 0.00 3.21
2381 2480 9.774742 GGTCTGATTAAAATTTAGTCACACATC 57.225 33.333 14.69 3.03 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.886719 GTGAACTCTGTATTTCATTCATCATCA 58.113 33.333 0.00 0.00 34.34 3.07
106 107 4.471904 TCTATGCTCGTGGAAAACTCAT 57.528 40.909 0.00 0.00 0.00 2.90
164 196 9.964354 ATATGCACTAGAGGCAATGATATTTTA 57.036 29.630 15.65 3.81 45.60 1.52
210 243 5.920193 TTTCTGAATGATAAAAGGCCCTG 57.080 39.130 0.00 0.00 0.00 4.45
238 271 6.568869 TCCAAACACGATGAAACTTTTTGAT 58.431 32.000 0.00 0.00 0.00 2.57
272 305 8.282592 GCTTTTGGTTTTTCAGAAAATCCATAC 58.717 33.333 27.98 18.09 45.01 2.39
303 336 3.065371 CCAGTGTCAGTTCAGGTGTTTTC 59.935 47.826 0.00 0.00 0.00 2.29
313 346 2.543777 TTAGTGCCCAGTGTCAGTTC 57.456 50.000 0.00 0.00 0.00 3.01
427 460 7.679783 TCATGGAAATATGATACGTCTCCAAT 58.320 34.615 0.00 0.00 35.25 3.16
545 578 9.679661 AACTTGGTCAAAATTAAAAGGATTTGT 57.320 25.926 0.00 0.00 39.02 2.83
589 622 2.548480 GCTCACCCACTAACAAACTGTC 59.452 50.000 0.00 0.00 0.00 3.51
619 652 7.106239 AGATGGTTCTATTTCGAAACAGATGT 58.894 34.615 18.91 6.32 43.21 3.06
671 704 8.626526 CCAAAAGCTTTGACCTACTTAAAGTTA 58.373 33.333 13.54 0.00 34.69 2.24
672 705 7.340999 TCCAAAAGCTTTGACCTACTTAAAGTT 59.659 33.333 13.54 0.00 34.69 2.66
673 706 6.831868 TCCAAAAGCTTTGACCTACTTAAAGT 59.168 34.615 13.54 0.00 34.69 2.66
674 707 7.272037 TCCAAAAGCTTTGACCTACTTAAAG 57.728 36.000 13.54 0.00 35.18 1.85
675 708 7.648039 TTCCAAAAGCTTTGACCTACTTAAA 57.352 32.000 13.54 0.00 0.00 1.52
676 709 7.648039 TTTCCAAAAGCTTTGACCTACTTAA 57.352 32.000 13.54 0.00 0.00 1.85
677 710 7.657336 CATTTCCAAAAGCTTTGACCTACTTA 58.343 34.615 13.54 0.00 0.00 2.24
678 711 6.515832 CATTTCCAAAAGCTTTGACCTACTT 58.484 36.000 13.54 0.00 0.00 2.24
679 712 5.509670 GCATTTCCAAAAGCTTTGACCTACT 60.510 40.000 13.54 0.00 30.56 2.57
680 713 4.686091 GCATTTCCAAAAGCTTTGACCTAC 59.314 41.667 13.54 0.00 30.56 3.18
681 714 4.343526 TGCATTTCCAAAAGCTTTGACCTA 59.656 37.500 13.54 0.00 34.04 3.08
682 715 3.134442 TGCATTTCCAAAAGCTTTGACCT 59.866 39.130 13.54 0.00 34.04 3.85
683 716 3.465871 TGCATTTCCAAAAGCTTTGACC 58.534 40.909 13.54 0.00 34.04 4.02
684 717 4.751098 TGATGCATTTCCAAAAGCTTTGAC 59.249 37.500 13.54 0.00 34.04 3.18
685 718 4.958509 TGATGCATTTCCAAAAGCTTTGA 58.041 34.783 13.54 3.59 34.04 2.69
686 719 5.676532 TTGATGCATTTCCAAAAGCTTTG 57.323 34.783 13.54 7.04 34.04 2.77
687 720 6.887626 ATTTGATGCATTTCCAAAAGCTTT 57.112 29.167 13.97 5.69 34.04 3.51
688 721 6.487331 TCAATTTGATGCATTTCCAAAAGCTT 59.513 30.769 13.97 0.00 34.04 3.74
689 722 5.998981 TCAATTTGATGCATTTCCAAAAGCT 59.001 32.000 13.97 2.60 34.04 3.74
690 723 6.243811 TCAATTTGATGCATTTCCAAAAGC 57.756 33.333 13.97 0.00 34.08 3.51
693 726 9.504708 AGTTAATCAATTTGATGCATTTCCAAA 57.495 25.926 12.50 12.76 37.15 3.28
694 727 9.504708 AAGTTAATCAATTTGATGCATTTCCAA 57.495 25.926 12.50 0.00 37.15 3.53
695 728 9.504708 AAAGTTAATCAATTTGATGCATTTCCA 57.495 25.926 12.50 0.00 37.15 3.53
739 772 7.857885 GCATTTAGAAGCGCATTTATAAGAACT 59.142 33.333 11.47 0.00 0.00 3.01
745 778 6.934645 ACTAGGCATTTAGAAGCGCATTTATA 59.065 34.615 11.47 0.00 0.00 0.98
883 926 7.317722 AGATAGGGGTGGTTAAATAGACATC 57.682 40.000 0.00 0.00 0.00 3.06
942 989 7.016153 TGAGATAGTTATGTGGGACTTTGTT 57.984 36.000 0.00 0.00 0.00 2.83
943 990 6.620877 TGAGATAGTTATGTGGGACTTTGT 57.379 37.500 0.00 0.00 0.00 2.83
1111 1159 5.822519 CGATTGGTTCCAATCCATTCTCTAA 59.177 40.000 28.04 0.00 45.50 2.10
1178 1226 1.210967 ACTTTCCGAACTCCAACACCA 59.789 47.619 0.00 0.00 0.00 4.17
1216 1264 2.614057 CACTCACCACCTTGTTGAACTC 59.386 50.000 0.00 0.00 0.00 3.01
1388 1436 0.548989 ACTGTTGTTACTGCCACCCA 59.451 50.000 0.00 0.00 0.00 4.51
1432 1480 6.418057 TTCAATTAGAAACCCAGCAAACAT 57.582 33.333 0.00 0.00 32.05 2.71
1716 1784 0.464452 CTCCCTCCGTCCCACAATAC 59.536 60.000 0.00 0.00 0.00 1.89
1954 2039 2.930040 CGTCTGTTCATATTGGCGTTCT 59.070 45.455 0.00 0.00 0.00 3.01
1987 2072 0.384669 ACGACCTGCTAGATTACGGC 59.615 55.000 0.00 0.00 0.00 5.68
1993 2082 2.440253 AGACCTAGACGACCTGCTAGAT 59.560 50.000 0.00 0.00 36.97 1.98
2147 2246 7.651808 ACCCAGATCAATCTAAAATATTTGCG 58.348 34.615 0.39 0.00 34.85 4.85
2184 2283 6.586344 TCGATCTAGCCTTCTCAAAATCAAT 58.414 36.000 0.00 0.00 0.00 2.57
2213 2312 7.553044 GCAAGTTCCTTACTCAGGTGTAATAAT 59.447 37.037 0.00 0.00 44.37 1.28
2283 2382 1.374758 CAGTTCGAGTGGTGGGCTC 60.375 63.158 0.00 0.00 0.00 4.70
2284 2383 2.100879 GACAGTTCGAGTGGTGGGCT 62.101 60.000 2.32 0.00 0.00 5.19
2285 2384 1.668151 GACAGTTCGAGTGGTGGGC 60.668 63.158 2.32 0.00 0.00 5.36
2286 2385 1.004918 GGACAGTTCGAGTGGTGGG 60.005 63.158 2.32 0.00 0.00 4.61
2287 2386 1.004918 GGGACAGTTCGAGTGGTGG 60.005 63.158 2.32 0.00 0.00 4.61
2288 2387 0.319900 CAGGGACAGTTCGAGTGGTG 60.320 60.000 2.32 0.00 0.00 4.17
2289 2388 2.050269 CAGGGACAGTTCGAGTGGT 58.950 57.895 2.32 0.00 0.00 4.16
2290 2389 1.374758 GCAGGGACAGTTCGAGTGG 60.375 63.158 2.32 0.00 0.00 4.00
2291 2390 1.734477 CGCAGGGACAGTTCGAGTG 60.734 63.158 0.00 0.00 0.00 3.51
2292 2391 0.892358 TACGCAGGGACAGTTCGAGT 60.892 55.000 0.00 0.00 0.00 4.18
2293 2392 0.242825 TTACGCAGGGACAGTTCGAG 59.757 55.000 0.00 0.00 0.00 4.04
2294 2393 0.038892 GTTACGCAGGGACAGTTCGA 60.039 55.000 0.00 0.00 0.00 3.71
2295 2394 0.319211 TGTTACGCAGGGACAGTTCG 60.319 55.000 0.00 0.00 0.00 3.95
2296 2395 1.873698 TTGTTACGCAGGGACAGTTC 58.126 50.000 0.00 0.00 0.00 3.01
2297 2396 2.561478 ATTGTTACGCAGGGACAGTT 57.439 45.000 0.00 0.00 0.00 3.16
2298 2397 2.552315 CAAATTGTTACGCAGGGACAGT 59.448 45.455 0.00 0.00 0.00 3.55
2299 2398 2.552315 ACAAATTGTTACGCAGGGACAG 59.448 45.455 0.00 0.00 0.00 3.51
2300 2399 2.550606 GACAAATTGTTACGCAGGGACA 59.449 45.455 0.00 0.00 0.00 4.02
2301 2400 2.412325 CGACAAATTGTTACGCAGGGAC 60.412 50.000 0.00 0.00 0.00 4.46
2302 2401 1.801771 CGACAAATTGTTACGCAGGGA 59.198 47.619 0.00 0.00 0.00 4.20
2303 2402 1.533731 ACGACAAATTGTTACGCAGGG 59.466 47.619 0.00 0.00 0.00 4.45
2304 2403 2.570169 CACGACAAATTGTTACGCAGG 58.430 47.619 0.00 0.00 0.00 4.85
2305 2404 1.969256 GCACGACAAATTGTTACGCAG 59.031 47.619 0.00 0.00 0.00 5.18
2306 2405 1.334239 GGCACGACAAATTGTTACGCA 60.334 47.619 0.00 0.00 0.00 5.24
2307 2406 1.323791 GGCACGACAAATTGTTACGC 58.676 50.000 0.00 3.22 0.00 4.42
2308 2407 2.570169 CTGGCACGACAAATTGTTACG 58.430 47.619 0.00 2.75 0.00 3.18
2309 2408 2.920647 GCCTGGCACGACAAATTGTTAC 60.921 50.000 15.17 0.00 0.00 2.50
2310 2409 1.268352 GCCTGGCACGACAAATTGTTA 59.732 47.619 15.17 0.00 0.00 2.41
2311 2410 0.031994 GCCTGGCACGACAAATTGTT 59.968 50.000 15.17 0.00 0.00 2.83
2312 2411 1.659794 GCCTGGCACGACAAATTGT 59.340 52.632 15.17 0.00 0.00 2.71
2313 2412 1.080569 GGCCTGGCACGACAAATTG 60.081 57.895 22.05 0.00 0.00 2.32
2314 2413 2.625823 CGGCCTGGCACGACAAATT 61.626 57.895 22.05 0.00 0.00 1.82
2315 2414 3.055719 CGGCCTGGCACGACAAAT 61.056 61.111 22.05 0.00 0.00 2.32
2329 2428 2.432972 CATGTTTTGGCAGCCGGC 60.433 61.111 21.89 21.89 43.74 6.13
2330 2429 2.432972 GCATGTTTTGGCAGCCGG 60.433 61.111 7.03 0.00 0.00 6.13
2331 2430 0.600782 AAAGCATGTTTTGGCAGCCG 60.601 50.000 7.03 0.00 0.00 5.52
2332 2431 1.596603 AAAAGCATGTTTTGGCAGCC 58.403 45.000 8.40 3.66 0.00 4.85
2352 2451 9.959749 GTGTGACTAAATTTTAATCAGACCAAA 57.040 29.630 13.80 0.00 29.72 3.28
2353 2452 9.126151 TGTGTGACTAAATTTTAATCAGACCAA 57.874 29.630 19.07 5.20 33.79 3.67
2354 2453 8.684386 TGTGTGACTAAATTTTAATCAGACCA 57.316 30.769 19.07 9.25 33.79 4.02
2355 2454 9.774742 GATGTGTGACTAAATTTTAATCAGACC 57.225 33.333 19.07 6.82 33.79 3.85


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

AutoCloner maintained by Alex Coulton.