Multiple sequence alignment - TraesCS2B01G164900

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 TraesCS2B01G164900 chr2B 100.000 4418 0 0 1 4418 136949436 136953853 0.000000e+00 8159.0
1 TraesCS2B01G164900 chr2B 97.486 2347 30 8 1744 4085 137608256 137610578 0.000000e+00 3980.0
2 TraesCS2B01G164900 chr2B 98.438 2177 14 3 1744 3920 136806129 136808285 0.000000e+00 3814.0
3 TraesCS2B01G164900 chr2B 94.830 1702 87 1 1753 3454 137188537 137190237 0.000000e+00 2654.0
4 TraesCS2B01G164900 chr2B 86.475 1353 121 36 1 1316 136804466 136805793 0.000000e+00 1428.0
5 TraesCS2B01G164900 chr2B 86.897 725 75 11 1 714 137606761 137607476 0.000000e+00 795.0
6 TraesCS2B01G164900 chr2B 86.606 657 33 19 663 1309 137187596 137188207 0.000000e+00 675.0
7 TraesCS2B01G164900 chr2B 97.674 344 3 2 4079 4418 137610704 137611046 1.770000e-163 586.0
8 TraesCS2B01G164900 chr2B 96.497 314 10 1 1451 1763 136805794 136806107 6.550000e-143 518.0
9 TraesCS2B01G164900 chr2B 95.789 285 11 1 892 1176 137607566 137607849 4.030000e-125 459.0
10 TraesCS2B01G164900 chr2B 83.446 296 15 11 1451 1746 137188213 137188474 1.230000e-60 244.0
11 TraesCS2B01G164900 chr2B 87.442 215 10 1 1451 1665 137607954 137608151 9.560000e-57 231.0
12 TraesCS2B01G164900 chr2B 94.444 108 6 0 1209 1316 137607846 137607953 2.730000e-37 167.0
13 TraesCS2B01G164900 chr2B 92.941 85 6 0 752 836 137607469 137607553 1.670000e-24 124.0
14 TraesCS2B01G164900 chr2B 90.244 82 8 0 1665 1746 137608121 137608202 1.680000e-19 108.0
15 TraesCS2B01G164900 chr2D 96.413 2314 60 12 1744 4040 85389018 85391325 0.000000e+00 3792.0
16 TraesCS2B01G164900 chr2D 94.272 1711 97 1 1744 3454 85673435 85675144 0.000000e+00 2615.0
17 TraesCS2B01G164900 chr2D 92.999 1714 105 5 1744 3454 84916457 84918158 0.000000e+00 2486.0
18 TraesCS2B01G164900 chr2D 92.251 1226 75 8 1 1209 84914786 84916008 0.000000e+00 1720.0
19 TraesCS2B01G164900 chr2D 83.624 1374 116 44 1 1316 85671763 85673085 0.000000e+00 1190.0
20 TraesCS2B01G164900 chr2D 88.889 846 76 13 2 836 85387345 85388183 0.000000e+00 1026.0
21 TraesCS2B01G164900 chr2D 95.575 339 8 6 4082 4418 85391535 85391868 1.810000e-148 536.0
22 TraesCS2B01G164900 chr2D 96.296 297 10 1 1451 1746 85673086 85673382 1.850000e-133 486.0
23 TraesCS2B01G164900 chr2D 85.588 451 32 17 892 1316 85388196 85388639 4.060000e-120 442.0
24 TraesCS2B01G164900 chr2D 92.653 245 18 0 1451 1695 85388640 85388884 1.950000e-93 353.0
25 TraesCS2B01G164900 chr2D 91.892 185 15 0 1451 1635 84916145 84916329 4.380000e-65 259.0
26 TraesCS2B01G164900 chr2D 93.750 112 7 0 1205 1316 84916033 84916144 7.600000e-38 169.0
27 TraesCS2B01G164900 chr2D 93.519 108 7 0 1639 1746 85388858 85388965 1.270000e-35 161.0
28 TraesCS2B01G164900 chr2D 95.604 91 4 0 1655 1745 84916312 84916402 3.560000e-31 147.0
29 TraesCS2B01G164900 chr2D 82.812 128 20 2 1512 1638 499903448 499903322 3.610000e-21 113.0
30 TraesCS2B01G164900 chr2D 79.817 109 4 12 1541 1635 142675724 142675620 3.690000e-06 63.9
31 TraesCS2B01G164900 chr2A 90.157 1524 135 11 1939 3454 84154116 84152600 0.000000e+00 1969.0
32 TraesCS2B01G164900 chr2A 95.000 60 3 0 377 436 85801036 85801095 1.310000e-15 95.3
33 TraesCS2B01G164900 chr4B 96.870 639 16 3 3385 4021 446685640 446686276 0.000000e+00 1066.0
34 TraesCS2B01G164900 chr3B 95.775 639 21 5 3385 4021 124618410 124619044 0.000000e+00 1026.0
35 TraesCS2B01G164900 chr3B 76.382 1266 252 32 2178 3425 824391358 824392594 4.820000e-179 638.0
36 TraesCS2B01G164900 chrUn 76.531 1274 261 31 2178 3431 320961871 320963126 0.000000e+00 662.0
37 TraesCS2B01G164900 chrUn 93.651 63 4 0 377 439 177415099 177415037 1.310000e-15 95.3
38 TraesCS2B01G164900 chrUn 95.000 60 3 0 377 436 401398693 401398752 1.310000e-15 95.3
39 TraesCS2B01G164900 chr7A 75.524 1287 254 46 2179 3438 32413303 32414555 3.830000e-160 575.0
40 TraesCS2B01G164900 chr7A 97.626 337 5 2 4082 4418 571276508 571276841 3.830000e-160 575.0
41 TraesCS2B01G164900 chr7A 95.367 259 9 3 3787 4045 571276065 571276320 4.110000e-110 409.0
42 TraesCS2B01G164900 chr7A 82.105 190 25 7 1744 1927 522982772 522982958 2.130000e-33 154.0
43 TraesCS2B01G164900 chr4A 73.761 1231 260 45 2215 3418 717966792 717965598 4.080000e-115 425.0
44 TraesCS2B01G164900 chr4A 95.000 60 3 0 377 436 349795967 349796026 1.310000e-15 95.3
45 TraesCS2B01G164900 chr7D 74.393 1070 214 38 2215 3260 16708757 16709790 1.910000e-108 403.0
46 TraesCS2B01G164900 chr7D 82.143 112 10 5 1607 1718 633355352 633355453 2.190000e-13 87.9
47 TraesCS2B01G164900 chr7D 100.000 30 0 0 601 630 613966034 613966005 6.170000e-04 56.5
48 TraesCS2B01G164900 chr5D 76.316 266 26 14 1512 1751 234843008 234843262 1.680000e-19 108.0
49 TraesCS2B01G164900 chr5A 91.667 48 4 0 1523 1570 613462676 613462723 2.850000e-07 67.6
50 TraesCS2B01G164900 chr5A 76.812 138 19 9 1510 1635 309313457 309313593 1.030000e-06 65.8
51 TraesCS2B01G164900 chr4D 82.500 80 7 1 1610 1689 88516324 88516252 3.690000e-06 63.9
52 TraesCS2B01G164900 chr1D 97.297 37 1 0 3625 3661 38596749 38596713 3.690000e-06 63.9
53 TraesCS2B01G164900 chr1A 94.444 36 2 0 1676 1711 543652838 543652803 6.170000e-04 56.5


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 TraesCS2B01G164900 chr2B 136949436 136953853 4417 False 8159.000000 8159 100.000000 1 4418 1 chr2B.!!$F1 4417
1 TraesCS2B01G164900 chr2B 136804466 136808285 3819 False 1920.000000 3814 93.803333 1 3920 3 chr2B.!!$F2 3919
2 TraesCS2B01G164900 chr2B 137187596 137190237 2641 False 1191.000000 2654 88.294000 663 3454 3 chr2B.!!$F3 2791
3 TraesCS2B01G164900 chr2B 137606761 137611046 4285 False 806.250000 3980 92.864625 1 4418 8 chr2B.!!$F4 4417
4 TraesCS2B01G164900 chr2D 85671763 85675144 3381 False 1430.333333 2615 91.397333 1 3454 3 chr2D.!!$F3 3453
5 TraesCS2B01G164900 chr2D 85387345 85391868 4523 False 1051.666667 3792 92.106167 2 4418 6 chr2D.!!$F2 4416
6 TraesCS2B01G164900 chr2D 84914786 84918158 3372 False 956.200000 2486 93.299200 1 3454 5 chr2D.!!$F1 3453
7 TraesCS2B01G164900 chr2A 84152600 84154116 1516 True 1969.000000 1969 90.157000 1939 3454 1 chr2A.!!$R1 1515
8 TraesCS2B01G164900 chr4B 446685640 446686276 636 False 1066.000000 1066 96.870000 3385 4021 1 chr4B.!!$F1 636
9 TraesCS2B01G164900 chr3B 124618410 124619044 634 False 1026.000000 1026 95.775000 3385 4021 1 chr3B.!!$F1 636
10 TraesCS2B01G164900 chr3B 824391358 824392594 1236 False 638.000000 638 76.382000 2178 3425 1 chr3B.!!$F2 1247
11 TraesCS2B01G164900 chrUn 320961871 320963126 1255 False 662.000000 662 76.531000 2178 3431 1 chrUn.!!$F1 1253
12 TraesCS2B01G164900 chr7A 32413303 32414555 1252 False 575.000000 575 75.524000 2179 3438 1 chr7A.!!$F1 1259
13 TraesCS2B01G164900 chr7A 571276065 571276841 776 False 492.000000 575 96.496500 3787 4418 2 chr7A.!!$F3 631
14 TraesCS2B01G164900 chr4A 717965598 717966792 1194 True 425.000000 425 73.761000 2215 3418 1 chr4A.!!$R1 1203
15 TraesCS2B01G164900 chr7D 16708757 16709790 1033 False 403.000000 403 74.393000 2215 3260 1 chr7D.!!$F1 1045

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
253 260 0.333312 TGGGGTCAAAGTTGTGTGGT 59.667 50.000 0.00 0.00 0.0 4.16 F
317 325 1.002366 ATGATTCTTCGCAGCGTCAC 58.998 50.000 15.93 2.81 0.0 3.67 F
511 521 1.070134 TGATGATGCCGCTAAGGTACC 59.930 52.381 2.73 2.73 43.7 3.34 F
1445 1585 0.034896 AAGGTGAGCGTACTGGTTGG 59.965 55.000 0.00 0.00 0.0 3.77 F
1448 1588 0.604578 GTGAGCGTACTGGTTGGGTA 59.395 55.000 0.00 0.00 0.0 3.69 F
1449 1589 1.001181 GTGAGCGTACTGGTTGGGTAA 59.999 52.381 0.00 0.00 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1566 0.034896 CCAACCAGTACGCTCACCTT 59.965 55.0 0.0 0.0 0.00 3.50 R
1433 1573 0.322648 ACCTTACCCAACCAGTACGC 59.677 55.0 0.0 0.0 0.00 4.42 R
1558 1699 0.884704 GCTGTTCCTTCCTTCACGCA 60.885 55.0 0.0 0.0 0.00 5.24 R
2478 2749 2.530958 TAGCCCTACGCAAACCTGCC 62.531 60.0 0.0 0.0 46.56 4.85 R
3168 3469 5.279910 CCTCCTATCAAGGCTGATAAAGAGG 60.280 48.0 21.7 21.7 46.36 3.69 R
3758 4081 5.046878 TCTGACGGCCTTTATGAAGAACTTA 60.047 40.0 0.0 0.0 34.71 2.24 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
32 34 0.901114 TCCTTGGTCCGGACGATGAA 60.901 55.000 27.18 16.92 0.00 2.57
80 85 2.238521 GGCACCATCCTGAAGTTTGAA 58.761 47.619 0.00 0.00 0.00 2.69
121 126 2.234414 GTTGGCATGGTGGTCATTGATT 59.766 45.455 0.00 0.00 32.92 2.57
188 193 2.047061 TGAGACTGTGGTAGTTGGCTT 58.953 47.619 0.00 0.00 40.53 4.35
207 212 0.622136 TGGCTCTCTAGGTGTCCGTA 59.378 55.000 0.00 0.00 0.00 4.02
208 213 1.005097 TGGCTCTCTAGGTGTCCGTAA 59.995 52.381 0.00 0.00 0.00 3.18
216 221 1.557099 AGGTGTCCGTAAGCTCATCA 58.443 50.000 0.00 0.00 0.00 3.07
237 242 2.836262 TGGTACGTTTGTTGTAGTGGG 58.164 47.619 0.00 0.00 0.00 4.61
245 250 3.655615 TTGTTGTAGTGGGGTCAAAGT 57.344 42.857 0.00 0.00 0.00 2.66
249 256 2.925724 TGTAGTGGGGTCAAAGTTGTG 58.074 47.619 0.00 0.00 0.00 3.33
250 257 2.240160 TGTAGTGGGGTCAAAGTTGTGT 59.760 45.455 0.00 0.00 0.00 3.72
253 260 0.333312 TGGGGTCAAAGTTGTGTGGT 59.667 50.000 0.00 0.00 0.00 4.16
314 322 1.662629 CTTGATGATTCTTCGCAGCGT 59.337 47.619 15.93 0.00 0.00 5.07
317 325 1.002366 ATGATTCTTCGCAGCGTCAC 58.998 50.000 15.93 2.81 0.00 3.67
355 363 3.195661 GTCGCTCGTTTATTCCTGGATT 58.804 45.455 0.00 0.00 0.00 3.01
407 416 5.163322 TGTTGTTCATTTGGCTTGGATCTTT 60.163 36.000 0.00 0.00 0.00 2.52
415 424 2.025037 TGGCTTGGATCTTTATGTGGCT 60.025 45.455 0.00 0.00 0.00 4.75
470 480 6.478512 TGGTTGCTTCCTTTAAGTCAAAAT 57.521 33.333 0.00 0.00 37.53 1.82
511 521 1.070134 TGATGATGCCGCTAAGGTACC 59.930 52.381 2.73 2.73 43.70 3.34
541 551 3.182572 CGATATTTCCTTCGTAGCAGTGC 59.817 47.826 7.13 7.13 0.00 4.40
563 601 6.628856 GTGCGTGATTTATATTGTGTCATGTC 59.371 38.462 0.00 0.00 0.00 3.06
566 604 7.125755 CGTGATTTATATTGTGTCATGTCCAC 58.874 38.462 10.18 10.18 0.00 4.02
573 611 4.681074 TTGTGTCATGTCCACTGAGTTA 57.319 40.909 15.73 0.00 33.92 2.24
661 710 5.317733 TGAGTTTGCCCCGTTTATTTATG 57.682 39.130 0.00 0.00 0.00 1.90
794 864 2.226674 CTGACTAGCGAGGCGATTGATA 59.773 50.000 0.00 0.00 30.54 2.15
948 1019 2.024871 GCCGACGGATCTGACGAG 59.975 66.667 24.71 16.25 34.93 4.18
1117 1196 2.299582 TGCAGATTTGTTGGGTGGATTG 59.700 45.455 0.00 0.00 0.00 2.67
1316 1456 2.564947 AGGTGAGAGTCTTGCGAGATTT 59.435 45.455 7.00 0.00 33.70 2.17
1317 1457 3.764434 AGGTGAGAGTCTTGCGAGATTTA 59.236 43.478 7.00 0.00 33.70 1.40
1318 1458 4.404073 AGGTGAGAGTCTTGCGAGATTTAT 59.596 41.667 7.00 0.00 33.70 1.40
1319 1459 5.594725 AGGTGAGAGTCTTGCGAGATTTATA 59.405 40.000 7.00 0.00 33.70 0.98
1320 1460 6.096987 AGGTGAGAGTCTTGCGAGATTTATAA 59.903 38.462 7.00 0.00 33.70 0.98
1321 1461 6.926272 GGTGAGAGTCTTGCGAGATTTATAAT 59.074 38.462 7.00 0.00 33.70 1.28
1322 1462 7.439655 GGTGAGAGTCTTGCGAGATTTATAATT 59.560 37.037 7.00 0.00 33.70 1.40
1323 1463 8.821894 GTGAGAGTCTTGCGAGATTTATAATTT 58.178 33.333 7.00 0.00 33.70 1.82
1324 1464 8.820933 TGAGAGTCTTGCGAGATTTATAATTTG 58.179 33.333 7.00 0.00 33.70 2.32
1325 1465 8.723942 AGAGTCTTGCGAGATTTATAATTTGT 57.276 30.769 7.00 0.00 33.70 2.83
1326 1466 9.167311 AGAGTCTTGCGAGATTTATAATTTGTT 57.833 29.630 7.00 0.00 33.70 2.83
1418 1558 8.417884 AGATAAACTAGGTATTGAGAGTCTTGC 58.582 37.037 0.00 0.00 0.00 4.01
1419 1559 4.640789 ACTAGGTATTGAGAGTCTTGCG 57.359 45.455 0.00 0.00 0.00 4.85
1420 1560 4.270834 ACTAGGTATTGAGAGTCTTGCGA 58.729 43.478 0.00 0.00 0.00 5.10
1421 1561 3.791973 AGGTATTGAGAGTCTTGCGAG 57.208 47.619 0.00 0.00 0.00 5.03
1422 1562 3.357203 AGGTATTGAGAGTCTTGCGAGA 58.643 45.455 0.00 0.00 0.00 4.04
1423 1563 3.957497 AGGTATTGAGAGTCTTGCGAGAT 59.043 43.478 7.00 0.00 33.70 2.75
1424 1564 5.133941 AGGTATTGAGAGTCTTGCGAGATA 58.866 41.667 7.00 0.00 33.70 1.98
1425 1565 5.594725 AGGTATTGAGAGTCTTGCGAGATAA 59.405 40.000 7.00 0.00 33.70 1.75
1426 1566 6.096987 AGGTATTGAGAGTCTTGCGAGATAAA 59.903 38.462 7.00 0.00 33.70 1.40
1427 1567 6.757010 GGTATTGAGAGTCTTGCGAGATAAAA 59.243 38.462 7.00 0.00 33.70 1.52
1428 1568 6.900568 ATTGAGAGTCTTGCGAGATAAAAG 57.099 37.500 7.00 0.00 33.70 2.27
1429 1569 4.748892 TGAGAGTCTTGCGAGATAAAAGG 58.251 43.478 7.00 0.00 33.70 3.11
1430 1570 4.220821 TGAGAGTCTTGCGAGATAAAAGGT 59.779 41.667 7.00 0.00 33.70 3.50
1431 1571 4.499183 AGAGTCTTGCGAGATAAAAGGTG 58.501 43.478 7.00 0.00 33.70 4.00
1432 1572 4.220821 AGAGTCTTGCGAGATAAAAGGTGA 59.779 41.667 7.00 0.00 33.70 4.02
1433 1573 4.499183 AGTCTTGCGAGATAAAAGGTGAG 58.501 43.478 7.00 0.00 33.70 3.51
1434 1574 3.062774 GTCTTGCGAGATAAAAGGTGAGC 59.937 47.826 7.00 0.00 33.70 4.26
1435 1575 1.640428 TGCGAGATAAAAGGTGAGCG 58.360 50.000 0.00 0.00 0.00 5.03
1436 1576 1.067142 TGCGAGATAAAAGGTGAGCGT 60.067 47.619 0.00 0.00 0.00 5.07
1437 1577 2.164827 TGCGAGATAAAAGGTGAGCGTA 59.835 45.455 0.00 0.00 0.00 4.42
1438 1578 2.534757 GCGAGATAAAAGGTGAGCGTAC 59.465 50.000 0.00 0.00 0.00 3.67
1439 1579 3.734293 GCGAGATAAAAGGTGAGCGTACT 60.734 47.826 0.00 0.00 0.00 2.73
1440 1580 3.791887 CGAGATAAAAGGTGAGCGTACTG 59.208 47.826 0.00 0.00 0.00 2.74
1441 1581 4.113354 GAGATAAAAGGTGAGCGTACTGG 58.887 47.826 0.00 0.00 0.00 4.00
1442 1582 3.514309 AGATAAAAGGTGAGCGTACTGGT 59.486 43.478 0.00 0.00 0.00 4.00
1443 1583 2.632987 AAAAGGTGAGCGTACTGGTT 57.367 45.000 0.00 0.00 0.00 3.67
1444 1584 1.878953 AAAGGTGAGCGTACTGGTTG 58.121 50.000 0.00 0.00 0.00 3.77
1445 1585 0.034896 AAGGTGAGCGTACTGGTTGG 59.965 55.000 0.00 0.00 0.00 3.77
1446 1586 1.375523 GGTGAGCGTACTGGTTGGG 60.376 63.158 0.00 0.00 0.00 4.12
1447 1587 1.370064 GTGAGCGTACTGGTTGGGT 59.630 57.895 0.00 0.00 0.00 4.51
1448 1588 0.604578 GTGAGCGTACTGGTTGGGTA 59.395 55.000 0.00 0.00 0.00 3.69
1449 1589 1.001181 GTGAGCGTACTGGTTGGGTAA 59.999 52.381 0.00 0.00 0.00 2.85
1673 1861 2.478872 TCTATCTTAGGCTGGCAGGT 57.521 50.000 17.64 0.00 0.00 4.00
1720 1908 3.058160 GCATGGTGCAGGTTCGCT 61.058 61.111 0.00 0.00 44.26 4.93
1893 2139 2.270352 TTGGCTGACCGTTTTCAGAT 57.730 45.000 9.47 0.00 45.19 2.90
2171 2429 7.126726 AGCCTAAGTACTACCACATTTCCAATA 59.873 37.037 0.00 0.00 0.00 1.90
2478 2749 1.871418 TCCCACCTCTCCATCTCAAG 58.129 55.000 0.00 0.00 0.00 3.02
3168 3469 1.613925 GAGAAGTTGGAAAACTGGGCC 59.386 52.381 0.00 0.00 32.47 5.80
3758 4081 2.158475 TGTTGCAACCAGAGGAAGGAAT 60.158 45.455 26.14 0.00 0.00 3.01
4290 4799 2.629051 CAGCATGCATCTGAACTCTGA 58.371 47.619 21.98 0.00 33.54 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.003763 GTCCGGACCAAGGAGCCT 61.004 66.667 24.75 0.00 38.65 4.58
10 11 4.452733 CGTCCGGACCAAGGAGCC 62.453 72.222 28.52 0.46 38.65 4.70
32 34 6.214191 AGAGTGAACACGACATCATAGATT 57.786 37.500 0.00 0.00 36.20 2.40
183 188 0.545309 ACACCTAGAGAGCCAAGCCA 60.545 55.000 0.00 0.00 0.00 4.75
188 193 0.622136 TACGGACACCTAGAGAGCCA 59.378 55.000 0.00 0.00 0.00 4.75
207 212 3.674997 ACAAACGTACCATGATGAGCTT 58.325 40.909 0.00 0.00 0.00 3.74
208 213 3.334583 ACAAACGTACCATGATGAGCT 57.665 42.857 0.00 0.00 0.00 4.09
216 221 3.404899 CCCACTACAACAAACGTACCAT 58.595 45.455 0.00 0.00 0.00 3.55
237 242 0.744281 CCCACCACACAACTTTGACC 59.256 55.000 0.00 0.00 0.00 4.02
245 250 0.395036 CACAAGGACCCACCACACAA 60.395 55.000 0.00 0.00 42.04 3.33
249 256 2.597510 GCCACAAGGACCCACCAC 60.598 66.667 0.00 0.00 42.04 4.16
250 257 2.694920 TTGCCACAAGGACCCACCA 61.695 57.895 0.00 0.00 42.04 4.17
253 260 2.203280 CGTTGCCACAAGGACCCA 60.203 61.111 0.00 0.00 36.89 4.51
296 303 1.280982 GACGCTGCGAAGAATCATCA 58.719 50.000 30.47 0.00 0.00 3.07
355 363 2.569354 GCAACGGGGCCAACAATGA 61.569 57.895 4.39 0.00 0.00 2.57
377 385 2.495270 AGCCAAATGAACAACACACACA 59.505 40.909 0.00 0.00 0.00 3.72
415 424 0.035317 ACATCGAAGTGGCAGAAGCA 59.965 50.000 0.00 0.00 44.61 3.91
470 480 0.677731 CAATTCTCCCCGAGCAAGCA 60.678 55.000 0.00 0.00 0.00 3.91
511 521 4.103357 ACGAAGGAAATATCGACGAGTTG 58.897 43.478 3.01 0.00 41.43 3.16
541 551 7.011389 AGTGGACATGACACAATATAAATCACG 59.989 37.037 21.20 0.00 41.21 4.35
563 601 9.613957 CAGACGATAAACTATATAACTCAGTGG 57.386 37.037 0.00 0.00 0.00 4.00
794 864 1.002134 CAACCGATGGAAGCCACCT 60.002 57.895 0.00 0.00 35.80 4.00
961 1032 2.202892 GTGCCTACTGCTACCGGC 60.203 66.667 0.00 0.00 42.00 6.13
970 1041 2.973899 CCAGTCTGCGTGCCTACT 59.026 61.111 0.00 0.00 0.00 2.57
1117 1196 4.156455 TGGCTGATTCTAGTTTGGATCC 57.844 45.455 4.20 4.20 0.00 3.36
1392 1532 8.417884 GCAAGACTCTCAATACCTAGTTTATCT 58.582 37.037 0.00 0.00 0.00 1.98
1393 1533 7.380065 CGCAAGACTCTCAATACCTAGTTTATC 59.620 40.741 0.00 0.00 43.02 1.75
1394 1534 7.068348 TCGCAAGACTCTCAATACCTAGTTTAT 59.932 37.037 0.00 0.00 45.01 1.40
1395 1535 6.376299 TCGCAAGACTCTCAATACCTAGTTTA 59.624 38.462 0.00 0.00 45.01 2.01
1396 1536 5.185249 TCGCAAGACTCTCAATACCTAGTTT 59.815 40.000 0.00 0.00 45.01 2.66
1397 1537 4.705507 TCGCAAGACTCTCAATACCTAGTT 59.294 41.667 0.00 0.00 45.01 2.24
1398 1538 4.270834 TCGCAAGACTCTCAATACCTAGT 58.729 43.478 0.00 0.00 45.01 2.57
1399 1539 4.576873 TCTCGCAAGACTCTCAATACCTAG 59.423 45.833 0.00 0.00 45.01 3.02
1400 1540 4.524053 TCTCGCAAGACTCTCAATACCTA 58.476 43.478 0.00 0.00 45.01 3.08
1401 1541 3.357203 TCTCGCAAGACTCTCAATACCT 58.643 45.455 0.00 0.00 45.01 3.08
1402 1542 3.784701 TCTCGCAAGACTCTCAATACC 57.215 47.619 0.00 0.00 45.01 2.73
1403 1543 7.043059 CCTTTTATCTCGCAAGACTCTCAATAC 60.043 40.741 0.00 0.00 45.01 1.89
1404 1544 6.980978 CCTTTTATCTCGCAAGACTCTCAATA 59.019 38.462 0.00 0.00 45.01 1.90
1405 1545 5.814705 CCTTTTATCTCGCAAGACTCTCAAT 59.185 40.000 0.00 0.00 45.01 2.57
1406 1546 5.171476 CCTTTTATCTCGCAAGACTCTCAA 58.829 41.667 0.00 0.00 45.01 3.02
1407 1547 4.220821 ACCTTTTATCTCGCAAGACTCTCA 59.779 41.667 0.00 0.00 45.01 3.27
1408 1548 4.564769 CACCTTTTATCTCGCAAGACTCTC 59.435 45.833 0.00 0.00 45.01 3.20
1409 1549 4.220821 TCACCTTTTATCTCGCAAGACTCT 59.779 41.667 0.00 0.00 45.01 3.24
1410 1550 4.495422 TCACCTTTTATCTCGCAAGACTC 58.505 43.478 0.00 0.00 45.01 3.36
1411 1551 4.499183 CTCACCTTTTATCTCGCAAGACT 58.501 43.478 0.00 0.00 45.01 3.24
1412 1552 3.062774 GCTCACCTTTTATCTCGCAAGAC 59.937 47.826 0.00 0.00 45.01 3.01
1414 1554 2.029728 CGCTCACCTTTTATCTCGCAAG 59.970 50.000 0.00 0.00 0.00 4.01
1415 1555 1.999735 CGCTCACCTTTTATCTCGCAA 59.000 47.619 0.00 0.00 0.00 4.85
1416 1556 1.067142 ACGCTCACCTTTTATCTCGCA 60.067 47.619 0.00 0.00 0.00 5.10
1417 1557 1.641577 ACGCTCACCTTTTATCTCGC 58.358 50.000 0.00 0.00 0.00 5.03
1418 1558 3.791887 CAGTACGCTCACCTTTTATCTCG 59.208 47.826 0.00 0.00 0.00 4.04
1419 1559 4.113354 CCAGTACGCTCACCTTTTATCTC 58.887 47.826 0.00 0.00 0.00 2.75
1420 1560 3.514309 ACCAGTACGCTCACCTTTTATCT 59.486 43.478 0.00 0.00 0.00 1.98
1421 1561 3.858247 ACCAGTACGCTCACCTTTTATC 58.142 45.455 0.00 0.00 0.00 1.75
1422 1562 3.975168 ACCAGTACGCTCACCTTTTAT 57.025 42.857 0.00 0.00 0.00 1.40
1423 1563 3.395639 CAACCAGTACGCTCACCTTTTA 58.604 45.455 0.00 0.00 0.00 1.52
1424 1564 2.218603 CAACCAGTACGCTCACCTTTT 58.781 47.619 0.00 0.00 0.00 2.27
1425 1565 1.542547 CCAACCAGTACGCTCACCTTT 60.543 52.381 0.00 0.00 0.00 3.11
1426 1566 0.034896 CCAACCAGTACGCTCACCTT 59.965 55.000 0.00 0.00 0.00 3.50
1427 1567 1.671742 CCAACCAGTACGCTCACCT 59.328 57.895 0.00 0.00 0.00 4.00
1428 1568 1.375523 CCCAACCAGTACGCTCACC 60.376 63.158 0.00 0.00 0.00 4.02
1429 1569 0.604578 TACCCAACCAGTACGCTCAC 59.395 55.000 0.00 0.00 0.00 3.51
1430 1570 1.274167 CTTACCCAACCAGTACGCTCA 59.726 52.381 0.00 0.00 0.00 4.26
1431 1571 1.405121 CCTTACCCAACCAGTACGCTC 60.405 57.143 0.00 0.00 0.00 5.03
1432 1572 0.611714 CCTTACCCAACCAGTACGCT 59.388 55.000 0.00 0.00 0.00 5.07
1433 1573 0.322648 ACCTTACCCAACCAGTACGC 59.677 55.000 0.00 0.00 0.00 4.42
1434 1574 1.619827 TCACCTTACCCAACCAGTACG 59.380 52.381 0.00 0.00 0.00 3.67
1435 1575 2.369532 TGTCACCTTACCCAACCAGTAC 59.630 50.000 0.00 0.00 0.00 2.73
1436 1576 2.369532 GTGTCACCTTACCCAACCAGTA 59.630 50.000 0.00 0.00 0.00 2.74
1437 1577 1.142262 GTGTCACCTTACCCAACCAGT 59.858 52.381 0.00 0.00 0.00 4.00
1438 1578 1.420138 AGTGTCACCTTACCCAACCAG 59.580 52.381 0.00 0.00 0.00 4.00
1439 1579 1.513858 AGTGTCACCTTACCCAACCA 58.486 50.000 0.00 0.00 0.00 3.67
1440 1580 2.158726 TCAAGTGTCACCTTACCCAACC 60.159 50.000 0.00 0.00 0.00 3.77
1441 1581 3.202829 TCAAGTGTCACCTTACCCAAC 57.797 47.619 0.00 0.00 0.00 3.77
1442 1582 4.447138 AATCAAGTGTCACCTTACCCAA 57.553 40.909 0.00 0.00 0.00 4.12
1443 1583 4.141287 CAAATCAAGTGTCACCTTACCCA 58.859 43.478 0.00 0.00 0.00 4.51
1444 1584 4.142038 ACAAATCAAGTGTCACCTTACCC 58.858 43.478 0.00 0.00 0.00 3.69
1445 1585 5.767816 AACAAATCAAGTGTCACCTTACC 57.232 39.130 0.00 0.00 0.00 2.85
1446 1586 9.180678 CAAATAACAAATCAAGTGTCACCTTAC 57.819 33.333 0.00 0.00 0.00 2.34
1447 1587 7.865385 GCAAATAACAAATCAAGTGTCACCTTA 59.135 33.333 0.00 0.00 0.00 2.69
1448 1588 6.701400 GCAAATAACAAATCAAGTGTCACCTT 59.299 34.615 0.00 0.00 0.00 3.50
1449 1589 6.040842 AGCAAATAACAAATCAAGTGTCACCT 59.959 34.615 0.00 0.00 0.00 4.00
1558 1699 0.884704 GCTGTTCCTTCCTTCACGCA 60.885 55.000 0.00 0.00 0.00 5.24
1673 1861 6.726299 CACCCCTAAGATAGATAATGAGGTCA 59.274 42.308 0.00 0.00 0.00 4.02
1748 1950 0.908180 ACAAGCCTAACCGCCTACCT 60.908 55.000 0.00 0.00 0.00 3.08
1751 1953 1.078708 GCACAAGCCTAACCGCCTA 60.079 57.895 0.00 0.00 33.58 3.93
2478 2749 2.530958 TAGCCCTACGCAAACCTGCC 62.531 60.000 0.00 0.00 46.56 4.85
3168 3469 5.279910 CCTCCTATCAAGGCTGATAAAGAGG 60.280 48.000 21.70 21.70 46.36 3.69
3758 4081 5.046878 TCTGACGGCCTTTATGAAGAACTTA 60.047 40.000 0.00 0.00 34.71 2.24
4290 4799 2.962125 TGCGCTGATTGCATTGATTTT 58.038 38.095 9.73 0.00 43.06 1.82


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

AutoCloner maintained by Alex Coulton.