Multiple sequence alignment - TraesCS5A01G083000

Loading Multiple Alignment...

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 TraesCS5A01G083000 chr5A 100.000 2252 0 0 1 2252 108743421 108745672 0.000000e+00 4159.0
1 TraesCS5A01G083000 chr5A 86.812 1471 148 26 8 1456 304711777 304713223 0.000000e+00 1600.0
2 TraesCS5A01G083000 chr5A 86.683 413 44 11 1841 2246 280528419 280528827 4.410000e-122 448.0
3 TraesCS5A01G083000 chr5A 86.232 414 46 11 1841 2247 280578392 280578801 2.660000e-119 438.0
4 TraesCS5A01G083000 chr5A 78.711 667 92 36 1617 2250 481595287 481595936 1.250000e-107 399.0
5 TraesCS5A01G083000 chr5A 80.261 537 76 20 1617 2135 481533920 481534444 5.870000e-101 377.0
6 TraesCS5A01G083000 chr4A 87.026 1742 167 42 7 1704 685919207 685920933 0.000000e+00 1910.0
7 TraesCS5A01G083000 chr4A 93.586 1185 76 0 520 1704 685935377 685936561 0.000000e+00 1768.0
8 TraesCS5A01G083000 chr4A 93.605 907 55 3 520 1423 490560337 490559431 0.000000e+00 1351.0
9 TraesCS5A01G083000 chr4A 93.134 568 38 1 1137 1704 685904061 685904627 0.000000e+00 832.0
10 TraesCS5A01G083000 chr4A 88.355 541 48 13 1 536 293466815 293466285 8.770000e-179 636.0
11 TraesCS5A01G083000 chr4A 82.148 689 93 20 1 671 395980665 395981341 4.200000e-157 564.0
12 TraesCS5A01G083000 chr4A 81.675 573 75 20 7 569 485810346 485810898 1.230000e-122 449.0
13 TraesCS5A01G083000 chr4A 82.801 407 48 13 1743 2135 54348076 54347678 5.950000e-91 344.0
14 TraesCS5A01G083000 chr4A 75.820 488 86 26 1786 2252 492775873 492776349 3.770000e-53 219.0
15 TraesCS5A01G083000 chr4A 91.781 73 6 0 1460 1532 386405395 386405467 3.960000e-18 102.0
16 TraesCS5A01G083000 chr4A 91.935 62 5 0 1460 1521 279765039 279764978 1.110000e-13 87.9
17 TraesCS5A01G083000 chr2A 87.192 1460 158 25 9 1446 275353623 275352171 0.000000e+00 1633.0
18 TraesCS5A01G083000 chr2A 85.714 1463 147 42 7 1422 661855892 661854445 0.000000e+00 1487.0
19 TraesCS5A01G083000 chr2A 90.724 539 38 8 1 536 416493027 416492498 0.000000e+00 708.0
20 TraesCS5A01G083000 chr2A 88.601 579 46 14 6 580 416500694 416500132 0.000000e+00 686.0
21 TraesCS5A01G083000 chr2A 87.824 386 36 10 1865 2247 427038894 427039271 2.050000e-120 442.0
22 TraesCS5A01G083000 chr2A 89.112 349 30 7 1905 2251 568381286 568380944 5.750000e-116 427.0
23 TraesCS5A01G083000 chr2A 87.123 365 38 8 1890 2252 454946941 454946584 2.690000e-109 405.0
24 TraesCS5A01G083000 chr2A 79.574 563 81 24 1696 2244 408094137 408094679 2.730000e-99 372.0
25 TraesCS5A01G083000 chr2A 97.248 109 3 0 1617 1725 387965161 387965053 3.820000e-43 185.0
26 TraesCS5A01G083000 chr2A 92.661 109 7 1 1617 1725 387957304 387957197 2.990000e-34 156.0
27 TraesCS5A01G083000 chr7A 94.365 834 47 0 520 1353 394888129 394887296 0.000000e+00 1280.0
28 TraesCS5A01G083000 chr7A 88.619 536 45 13 1 533 177670669 177671191 2.440000e-179 638.0
29 TraesCS5A01G083000 chr7A 94.458 415 18 4 1841 2252 341655608 341656020 3.160000e-178 634.0
30 TraesCS5A01G083000 chr7A 94.217 415 20 4 1841 2252 178460698 178461111 4.080000e-177 630.0
31 TraesCS5A01G083000 chr7A 87.873 536 47 14 5 536 549656145 549655624 4.110000e-172 614.0
32 TraesCS5A01G083000 chr7A 87.500 536 51 12 1 533 177662973 177663495 2.470000e-169 604.0
33 TraesCS5A01G083000 chr7A 81.261 571 77 21 7 567 156480857 156480307 3.430000e-118 435.0
34 TraesCS5A01G083000 chr7A 78.393 560 87 30 1696 2234 398674314 398673768 1.290000e-87 333.0
35 TraesCS5A01G083000 chr7A 79.006 543 70 35 1731 2250 301747139 301747660 4.640000e-87 331.0
36 TraesCS5A01G083000 chr7A 78.821 543 71 36 1731 2250 301668548 301669069 2.160000e-85 326.0
37 TraesCS5A01G083000 chr7A 77.583 571 84 30 1696 2247 315981559 315982104 2.810000e-79 305.0
38 TraesCS5A01G083000 chr7A 77.153 569 89 30 1696 2247 315998225 315998769 2.190000e-75 292.0
39 TraesCS5A01G083000 chr7A 91.558 154 12 1 1293 1446 391579998 391580150 6.300000e-51 211.0
40 TraesCS5A01G083000 chr7A 87.500 120 13 2 1428 1545 298161877 298161996 1.080000e-28 137.0
41 TraesCS5A01G083000 chr7A 94.118 51 1 2 1555 1604 590075926 590075975 2.400000e-10 76.8
42 TraesCS5A01G083000 chr1A 86.348 1194 111 34 200 1353 395584154 395585335 0.000000e+00 1254.0
43 TraesCS5A01G083000 chr1A 89.714 350 28 7 1905 2252 164739648 164739305 7.380000e-120 440.0
44 TraesCS5A01G083000 chr1A 85.545 422 47 14 1841 2252 387544489 387544906 1.600000e-116 429.0
45 TraesCS5A01G083000 chr6A 93.525 834 50 2 520 1353 395304816 395305645 0.000000e+00 1238.0
46 TraesCS5A01G083000 chr6A 84.444 675 82 18 9 671 378422865 378422202 0.000000e+00 643.0
47 TraesCS5A01G083000 chr6A 82.916 679 88 19 6 671 378455034 378454371 8.960000e-164 586.0
48 TraesCS5A01G083000 chr6A 82.007 578 76 18 1 569 107633429 107633987 1.220000e-127 466.0
49 TraesCS5A01G083000 chr6A 81.661 578 78 18 1 569 350624886 350625444 2.640000e-124 455.0
50 TraesCS5A01G083000 chr6A 81.282 577 78 21 1 568 350633002 350633557 7.380000e-120 440.0
51 TraesCS5A01G083000 chr6A 79.203 577 80 31 1696 2252 535656477 535655921 4.570000e-97 364.0
52 TraesCS5A01G083000 chr6A 82.469 405 53 12 1744 2135 539356473 539356872 2.770000e-89 339.0
53 TraesCS5A01G083000 chr3A 89.637 579 42 13 5 580 251705178 251704615 0.000000e+00 721.0
54 TraesCS5A01G083000 chr3A 88.390 534 52 6 5 536 251697546 251697021 3.160000e-178 634.0
55 TraesCS5A01G083000 chr3A 81.707 574 73 21 7 569 66669236 66668684 1.230000e-122 449.0
56 TraesCS5A01G083000 chr3A 77.746 346 44 23 1661 1996 141088610 141088288 4.940000e-42 182.0
57 TraesCS5A01G083000 chr6B 89.241 158 16 1 1290 1446 609239678 609239835 1.760000e-46 196.0


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 TraesCS5A01G083000 chr5A 108743421 108745672 2251 False 4159 4159 100.000 1 2252 1 chr5A.!!$F1 2251
1 TraesCS5A01G083000 chr5A 304711777 304713223 1446 False 1600 1600 86.812 8 1456 1 chr5A.!!$F4 1448
2 TraesCS5A01G083000 chr5A 481595287 481595936 649 False 399 399 78.711 1617 2250 1 chr5A.!!$F6 633
3 TraesCS5A01G083000 chr5A 481533920 481534444 524 False 377 377 80.261 1617 2135 1 chr5A.!!$F5 518
4 TraesCS5A01G083000 chr4A 685919207 685920933 1726 False 1910 1910 87.026 7 1704 1 chr4A.!!$F6 1697
5 TraesCS5A01G083000 chr4A 685935377 685936561 1184 False 1768 1768 93.586 520 1704 1 chr4A.!!$F7 1184
6 TraesCS5A01G083000 chr4A 490559431 490560337 906 True 1351 1351 93.605 520 1423 1 chr4A.!!$R4 903
7 TraesCS5A01G083000 chr4A 685904061 685904627 566 False 832 832 93.134 1137 1704 1 chr4A.!!$F5 567
8 TraesCS5A01G083000 chr4A 293466285 293466815 530 True 636 636 88.355 1 536 1 chr4A.!!$R3 535
9 TraesCS5A01G083000 chr4A 395980665 395981341 676 False 564 564 82.148 1 671 1 chr4A.!!$F2 670
10 TraesCS5A01G083000 chr4A 485810346 485810898 552 False 449 449 81.675 7 569 1 chr4A.!!$F3 562
11 TraesCS5A01G083000 chr2A 275352171 275353623 1452 True 1633 1633 87.192 9 1446 1 chr2A.!!$R1 1437
12 TraesCS5A01G083000 chr2A 661854445 661855892 1447 True 1487 1487 85.714 7 1422 1 chr2A.!!$R8 1415
13 TraesCS5A01G083000 chr2A 416492498 416493027 529 True 708 708 90.724 1 536 1 chr2A.!!$R4 535
14 TraesCS5A01G083000 chr2A 416500132 416500694 562 True 686 686 88.601 6 580 1 chr2A.!!$R5 574
15 TraesCS5A01G083000 chr2A 408094137 408094679 542 False 372 372 79.574 1696 2244 1 chr2A.!!$F1 548
16 TraesCS5A01G083000 chr7A 394887296 394888129 833 True 1280 1280 94.365 520 1353 1 chr7A.!!$R2 833
17 TraesCS5A01G083000 chr7A 177670669 177671191 522 False 638 638 88.619 1 533 1 chr7A.!!$F2 532
18 TraesCS5A01G083000 chr7A 549655624 549656145 521 True 614 614 87.873 5 536 1 chr7A.!!$R4 531
19 TraesCS5A01G083000 chr7A 177662973 177663495 522 False 604 604 87.500 1 533 1 chr7A.!!$F1 532
20 TraesCS5A01G083000 chr7A 156480307 156480857 550 True 435 435 81.261 7 567 1 chr7A.!!$R1 560
21 TraesCS5A01G083000 chr7A 398673768 398674314 546 True 333 333 78.393 1696 2234 1 chr7A.!!$R3 538
22 TraesCS5A01G083000 chr7A 301747139 301747660 521 False 331 331 79.006 1731 2250 1 chr7A.!!$F6 519
23 TraesCS5A01G083000 chr7A 301668548 301669069 521 False 326 326 78.821 1731 2250 1 chr7A.!!$F5 519
24 TraesCS5A01G083000 chr7A 315981559 315982104 545 False 305 305 77.583 1696 2247 1 chr7A.!!$F7 551
25 TraesCS5A01G083000 chr7A 315998225 315998769 544 False 292 292 77.153 1696 2247 1 chr7A.!!$F8 551
26 TraesCS5A01G083000 chr1A 395584154 395585335 1181 False 1254 1254 86.348 200 1353 1 chr1A.!!$F2 1153
27 TraesCS5A01G083000 chr6A 395304816 395305645 829 False 1238 1238 93.525 520 1353 1 chr6A.!!$F4 833
28 TraesCS5A01G083000 chr6A 378422202 378422865 663 True 643 643 84.444 9 671 1 chr6A.!!$R1 662
29 TraesCS5A01G083000 chr6A 378454371 378455034 663 True 586 586 82.916 6 671 1 chr6A.!!$R2 665
30 TraesCS5A01G083000 chr6A 107633429 107633987 558 False 466 466 82.007 1 569 1 chr6A.!!$F1 568
31 TraesCS5A01G083000 chr6A 350624886 350625444 558 False 455 455 81.661 1 569 1 chr6A.!!$F2 568
32 TraesCS5A01G083000 chr6A 350633002 350633557 555 False 440 440 81.282 1 568 1 chr6A.!!$F3 567
33 TraesCS5A01G083000 chr6A 535655921 535656477 556 True 364 364 79.203 1696 2252 1 chr6A.!!$R3 556
34 TraesCS5A01G083000 chr3A 251704615 251705178 563 True 721 721 89.637 5 580 1 chr3A.!!$R4 575
35 TraesCS5A01G083000 chr3A 251697021 251697546 525 True 634 634 88.390 5 536 1 chr3A.!!$R3 531
36 TraesCS5A01G083000 chr3A 66668684 66669236 552 True 449 449 81.707 7 569 1 chr3A.!!$R1 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
569 720 0.108992 GCGATGGTAGTGGTTCACGA 60.109 55.0 0.0 0.0 39.64 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1725 1878 0.824759 CCAGCTCTAACCCTAGCGTT 59.175 55.0 0.0 0.0 43.63 4.84 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
191 204 4.993584 AGATATGAGGCATTTGTCATCGTC 59.006 41.667 0.00 0.00 35.08 4.20
265 287 1.067776 CATATCGGTTCCGGTAGCTCC 60.068 57.143 11.37 1.56 0.00 4.70
502 575 5.275494 GTTCGAGTTCATAGAGGAAGTAGC 58.725 45.833 0.00 0.00 30.77 3.58
569 720 0.108992 GCGATGGTAGTGGTTCACGA 60.109 55.000 0.00 0.00 39.64 4.35
724 875 0.323633 TATGGTCCACCGGTCTTCGA 60.324 55.000 2.59 0.00 42.43 3.71
935 1086 5.183904 GGTTCTTGCAATGGTAGTGATTCTT 59.816 40.000 0.00 0.00 0.00 2.52
978 1130 2.289444 ACTTGACGGTTCCACATCGATT 60.289 45.455 0.00 0.00 0.00 3.34
1117 1269 1.667830 GTGCAGCTCTACACCGCAA 60.668 57.895 0.00 0.00 33.76 4.85
1129 1281 1.906574 ACACCGCAAAGGAGGAAGATA 59.093 47.619 0.00 0.00 45.00 1.98
1263 1415 1.126846 CGGTGCTGAACTTGACGAATC 59.873 52.381 0.00 0.00 0.00 2.52
1268 1420 2.872038 GCTGAACTTGACGAATCCTGGT 60.872 50.000 0.00 0.00 0.00 4.00
1375 1528 2.281414 TAGCAAGCACAGCCGCAA 60.281 55.556 0.00 0.00 31.16 4.85
1456 1609 3.005539 GAGGAGGAGCTGGTGGCA 61.006 66.667 0.00 0.00 44.79 4.92
1468 1621 1.002430 CTGGTGGCACTAGAAGAGCAA 59.998 52.381 24.94 0.00 33.31 3.91
1483 1636 3.024782 GCAACAGCAGAGCAGCTCG 62.025 63.158 16.99 12.59 44.54 5.03
1516 1669 2.892425 GCTCGCCGGAGTTGATGG 60.892 66.667 5.05 0.00 42.53 3.51
1591 1744 1.536073 CGTTGGAGGAGCTCAGGACA 61.536 60.000 17.19 5.80 31.08 4.02
1725 1878 1.152398 GTGGGGATCGGGCTAGGTA 60.152 63.158 0.00 0.00 0.00 3.08
1726 1879 0.761702 GTGGGGATCGGGCTAGGTAA 60.762 60.000 0.00 0.00 0.00 2.85
1777 1933 1.307084 GCCCAGTAGAGAAGGGGGT 60.307 63.158 0.00 0.00 43.04 4.95
1780 1936 1.657804 CCAGTAGAGAAGGGGGTTGT 58.342 55.000 0.00 0.00 0.00 3.32
1798 1954 2.692741 GCCTAGGCCTTGGGAGGT 60.693 66.667 30.95 0.00 45.44 3.85
1880 2071 5.105146 TGGCTGAACTCCTCTCTCTTATTTC 60.105 44.000 0.00 0.00 0.00 2.17
1881 2072 5.128663 GGCTGAACTCCTCTCTCTTATTTCT 59.871 44.000 0.00 0.00 0.00 2.52
1921 2122 9.741647 ATAACAAAGAAGAGAAGAAAAAGCAAG 57.258 29.630 0.00 0.00 0.00 4.01
1926 2127 4.445557 AGAGAAGAAAAAGCAAGGAGGT 57.554 40.909 0.00 0.00 0.00 3.85
1934 2135 2.604912 AAGCAAGGAGGTTTTAGGGG 57.395 50.000 0.00 0.00 33.25 4.79
1940 2141 4.336280 CAAGGAGGTTTTAGGGGAAGAAG 58.664 47.826 0.00 0.00 0.00 2.85
1950 2151 1.177401 GGGGAAGAAGTTGGACATGC 58.823 55.000 0.00 0.00 0.00 4.06
1979 2181 2.649531 TCCCGGACTCACAAAAATGT 57.350 45.000 0.73 0.00 0.00 2.71
2099 2302 3.891366 AGGAGTGTCCAAAAATGTTGAGG 59.109 43.478 0.00 0.00 39.61 3.86
2100 2303 3.636764 GGAGTGTCCAAAAATGTTGAGGT 59.363 43.478 0.00 0.00 36.28 3.85
2111 2314 5.428184 AAATGTTGAGGTTTTTGGTGGAA 57.572 34.783 0.00 0.00 0.00 3.53
2121 2324 1.975660 TTTGGTGGAACTCCGGAAAG 58.024 50.000 5.23 0.00 46.43 2.62
2137 2340 7.173390 ACTCCGGAAAGTGAAGAAAGAATTTAG 59.827 37.037 5.23 0.00 39.27 1.85
2154 2357 5.665916 ATTTAGGGCAAAGTTTGGAGATG 57.334 39.130 17.11 0.00 0.00 2.90
2156 2359 2.800250 AGGGCAAAGTTTGGAGATGAG 58.200 47.619 17.11 0.00 0.00 2.90
2162 2366 5.279657 GGCAAAGTTTGGAGATGAGGAATTT 60.280 40.000 17.11 0.00 0.00 1.82
2165 2369 7.309438 GCAAAGTTTGGAGATGAGGAATTTAGT 60.309 37.037 17.11 0.00 0.00 2.24
2174 2378 8.616942 GGAGATGAGGAATTTAGTAAGAAAAGC 58.383 37.037 0.00 0.00 0.00 3.51
2175 2379 9.167311 GAGATGAGGAATTTAGTAAGAAAAGCA 57.833 33.333 0.00 0.00 0.00 3.91
2176 2380 9.692325 AGATGAGGAATTTAGTAAGAAAAGCAT 57.308 29.630 0.00 0.00 0.00 3.79
2177 2381 9.727627 GATGAGGAATTTAGTAAGAAAAGCATG 57.272 33.333 0.00 0.00 0.00 4.06
2178 2382 8.055279 TGAGGAATTTAGTAAGAAAAGCATGG 57.945 34.615 0.00 0.00 0.00 3.66
2179 2383 7.888021 TGAGGAATTTAGTAAGAAAAGCATGGA 59.112 33.333 0.00 0.00 0.00 3.41
2180 2384 8.650143 AGGAATTTAGTAAGAAAAGCATGGAA 57.350 30.769 0.00 0.00 0.00 3.53
2181 2385 9.259832 AGGAATTTAGTAAGAAAAGCATGGAAT 57.740 29.630 0.00 0.00 0.00 3.01
2203 2412 4.727507 ATTTTGCAAGTGTGTTGTGGTA 57.272 36.364 0.00 0.00 0.00 3.25
2213 2422 5.901552 AGTGTGTTGTGGTAAATTCCAAAG 58.098 37.500 0.00 0.00 39.34 2.77
2214 2423 5.047188 GTGTGTTGTGGTAAATTCCAAAGG 58.953 41.667 0.00 0.00 39.34 3.11
2249 2460 6.848562 ATTATAGCCCCCTAATATTGGAGG 57.151 41.667 0.00 0.00 0.00 4.30
2250 2461 2.835696 AGCCCCCTAATATTGGAGGA 57.164 50.000 0.54 0.00 34.46 3.71
2251 2462 3.314059 AGCCCCCTAATATTGGAGGAT 57.686 47.619 0.54 0.00 34.46 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
265 287 2.009774 CTTTTGCACCGGTATCTCCAG 58.990 52.381 6.87 0.00 35.57 3.86
443 505 2.277084 CGCTTCAAAGGTATAACCGCT 58.723 47.619 0.00 0.00 44.90 5.52
569 720 3.192844 AGAACGTGAATGACTACCATCGT 59.807 43.478 0.00 0.00 35.58 3.73
906 1057 2.496899 ACCATTGCAAGAACCGAGAT 57.503 45.000 4.94 0.00 0.00 2.75
935 1086 7.912056 AGTACAACTACTCTACGTTGATACA 57.088 36.000 8.89 0.00 42.24 2.29
978 1130 2.408271 ACGATACGTGGACCTCTACA 57.592 50.000 0.00 0.00 39.18 2.74
1031 1183 3.309582 CCGATGGCACTAGGGTGT 58.690 61.111 0.00 0.00 44.65 4.16
1114 1266 2.625314 GCCCAATATCTTCCTCCTTTGC 59.375 50.000 0.00 0.00 0.00 3.68
1117 1269 3.723681 TCATGCCCAATATCTTCCTCCTT 59.276 43.478 0.00 0.00 0.00 3.36
1129 1281 2.124151 GGACGCCTCATGCCCAAT 60.124 61.111 0.00 0.00 36.24 3.16
1299 1451 2.609534 ATCAGCAAGCTGGCCTCCA 61.610 57.895 20.78 1.93 43.75 3.86
1358 1511 2.281414 TTGCGGCTGTGCTTGCTA 60.281 55.556 0.00 0.14 35.36 3.49
1375 1528 4.135153 CCGCTGCCTCGCTGTAGT 62.135 66.667 0.00 0.00 0.00 2.73
1434 1587 4.421554 CCAGCTCCTCCTCCCCCA 62.422 72.222 0.00 0.00 0.00 4.96
1456 1609 2.353605 GCTCTGCTGTTGCTCTTCTAGT 60.354 50.000 0.00 0.00 40.48 2.57
1591 1744 1.455959 CTCCTCGTTCCCGATCCCT 60.456 63.158 0.00 0.00 43.27 4.20
1725 1878 0.824759 CCAGCTCTAACCCTAGCGTT 59.175 55.000 0.00 0.00 43.63 4.84
1726 1879 1.043673 CCCAGCTCTAACCCTAGCGT 61.044 60.000 0.00 0.00 43.63 5.07
1777 1933 1.850289 TCCCAAGGCCTAGGCACAA 60.850 57.895 34.09 10.91 44.11 3.33
1780 1936 2.692368 CCTCCCAAGGCCTAGGCA 60.692 66.667 34.09 12.54 44.11 4.75
1798 1954 1.826921 CCTAAGGTCTAGCCGCCGA 60.827 63.158 0.00 0.00 43.70 5.54
1807 1963 2.509964 CCACCTAATTGGCCTAAGGTCT 59.490 50.000 7.52 0.00 40.39 3.85
1809 1965 1.569072 CCCACCTAATTGGCCTAAGGT 59.431 52.381 3.32 4.26 43.15 3.50
1862 2018 9.936759 CTGTTTTAGAAATAAGAGAGAGGAGTT 57.063 33.333 0.00 0.00 0.00 3.01
1899 2098 6.799512 TCCTTGCTTTTTCTTCTCTTCTTTG 58.200 36.000 0.00 0.00 0.00 2.77
1900 2099 6.040278 CCTCCTTGCTTTTTCTTCTCTTCTTT 59.960 38.462 0.00 0.00 0.00 2.52
1902 2101 5.069318 CCTCCTTGCTTTTTCTTCTCTTCT 58.931 41.667 0.00 0.00 0.00 2.85
1903 2102 4.824537 ACCTCCTTGCTTTTTCTTCTCTTC 59.175 41.667 0.00 0.00 0.00 2.87
1908 2107 6.216569 CCTAAAACCTCCTTGCTTTTTCTTC 58.783 40.000 0.00 0.00 0.00 2.87
1911 2111 4.262463 CCCCTAAAACCTCCTTGCTTTTTC 60.262 45.833 0.00 0.00 0.00 2.29
1918 2119 4.202577 ACTTCTTCCCCTAAAACCTCCTTG 60.203 45.833 0.00 0.00 0.00 3.61
1921 2122 4.079970 CAACTTCTTCCCCTAAAACCTCC 58.920 47.826 0.00 0.00 0.00 4.30
1926 2127 4.799715 TGTCCAACTTCTTCCCCTAAAA 57.200 40.909 0.00 0.00 0.00 1.52
1934 2135 1.808411 TCCGCATGTCCAACTTCTTC 58.192 50.000 0.00 0.00 0.00 2.87
1940 2141 4.359706 GGAAAATTATCCGCATGTCCAAC 58.640 43.478 0.00 0.00 0.00 3.77
1950 2151 2.870411 GTGAGTCCGGGAAAATTATCCG 59.130 50.000 0.00 6.96 40.62 4.18
1979 2181 6.627395 TTTTCTATTTTCTCGGAACAAGCA 57.373 33.333 0.00 0.00 0.00 3.91
2064 2266 1.271656 ACACTCCTAAAACCTCGTCCG 59.728 52.381 0.00 0.00 0.00 4.79
2099 2302 1.682740 TCCGGAGTTCCACCAAAAAC 58.317 50.000 0.00 0.00 35.14 2.43
2100 2303 2.438800 TTCCGGAGTTCCACCAAAAA 57.561 45.000 3.34 0.00 35.14 1.94
2111 2314 4.417426 TTCTTTCTTCACTTTCCGGAGT 57.583 40.909 3.34 0.00 0.00 3.85
2121 2324 6.749139 ACTTTGCCCTAAATTCTTTCTTCAC 58.251 36.000 0.00 0.00 0.00 3.18
2137 2340 1.821136 CCTCATCTCCAAACTTTGCCC 59.179 52.381 0.00 0.00 0.00 5.36
2154 2357 8.281212 TCCATGCTTTTCTTACTAAATTCCTC 57.719 34.615 0.00 0.00 0.00 3.71
2162 2366 9.801873 GCAAAATATTCCATGCTTTTCTTACTA 57.198 29.630 11.50 0.00 35.93 1.82
2165 2369 9.153721 CTTGCAAAATATTCCATGCTTTTCTTA 57.846 29.630 16.84 0.00 39.49 2.10
2174 2378 6.424509 ACAACACACTTGCAAAATATTCCATG 59.575 34.615 0.00 0.00 0.00 3.66
2175 2379 6.424509 CACAACACACTTGCAAAATATTCCAT 59.575 34.615 0.00 0.00 0.00 3.41
2176 2380 5.752472 CACAACACACTTGCAAAATATTCCA 59.248 36.000 0.00 0.00 0.00 3.53
2177 2381 5.177327 CCACAACACACTTGCAAAATATTCC 59.823 40.000 0.00 0.00 0.00 3.01
2178 2382 5.752955 ACCACAACACACTTGCAAAATATTC 59.247 36.000 0.00 0.00 0.00 1.75
2179 2383 5.669477 ACCACAACACACTTGCAAAATATT 58.331 33.333 0.00 0.00 0.00 1.28
2180 2384 5.275067 ACCACAACACACTTGCAAAATAT 57.725 34.783 0.00 0.00 0.00 1.28
2181 2385 4.727507 ACCACAACACACTTGCAAAATA 57.272 36.364 0.00 0.00 0.00 1.40
2213 2422 7.826747 AGGGGGCTATAATAAATATTCCATCC 58.173 38.462 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.