Multiple sequence alignment - TraesCS5B01G058000

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 TraesCS5B01G058000 chr5B 100.000 2354 0 0 1 2354 63737297 63734944 0.000000e+00 4348.0
1 TraesCS5B01G058000 chr5B 92.308 637 49 0 1718 2354 72237796 72237160 0.000000e+00 905.0
2 TraesCS5B01G058000 chr7D 84.828 1661 216 23 82 1715 563518136 563516485 0.000000e+00 1639.0
3 TraesCS5B01G058000 chr7D 84.140 1652 209 32 102 1716 617593233 617594868 0.000000e+00 1550.0
4 TraesCS5B01G058000 chr1D 82.009 1623 248 29 132 1718 270035230 270036844 0.000000e+00 1339.0
5 TraesCS5B01G058000 chr1D 83.431 1364 216 10 1 1360 431769669 431771026 0.000000e+00 1258.0
6 TraesCS5B01G058000 chr1D 73.652 1298 308 28 26 1305 85203455 85204736 2.740000e-129 472.0
7 TraesCS5B01G058000 chr4B 78.916 1328 260 19 11 1327 546133475 546132157 0.000000e+00 883.0
8 TraesCS5B01G058000 chr4B 78.180 1297 267 12 12 1302 273234965 273233679 0.000000e+00 813.0
9 TraesCS5B01G058000 chr4B 78.731 268 53 4 1716 1981 637340357 637340622 2.400000e-40 176.0
10 TraesCS5B01G058000 chr1B 75.678 1328 283 34 26 1333 145446313 145445006 5.520000e-176 627.0
11 TraesCS5B01G058000 chr1B 78.723 329 53 15 1717 2039 604833546 604833863 1.100000e-48 204.0
12 TraesCS5B01G058000 chr1B 83.957 187 20 10 1544 1725 117270776 117270595 1.120000e-38 171.0
13 TraesCS5B01G058000 chr4A 74.505 1263 295 23 3 1250 319840148 319838898 7.450000e-145 523.0
14 TraesCS5B01G058000 chr4A 77.627 295 55 7 1747 2039 628702440 628702155 4.020000e-38 169.0
15 TraesCS5B01G058000 chr4A 96.154 78 3 0 2277 2354 586336876 586336953 6.830000e-26 128.0
16 TraesCS5B01G058000 chr4A 94.872 78 4 0 2277 2354 586333597 586333674 3.180000e-24 122.0
17 TraesCS5B01G058000 chr7A 73.988 1334 320 23 3 1321 641707743 641709064 1.250000e-142 516.0
18 TraesCS5B01G058000 chr7A 86.441 177 17 6 1544 1717 582110967 582110795 1.110000e-43 187.0
19 TraesCS5B01G058000 chr7A 96.154 78 3 0 2277 2354 20616789 20616866 6.830000e-26 128.0
20 TraesCS5B01G058000 chr7A 96.154 78 3 0 2277 2354 20620066 20620143 6.830000e-26 128.0
21 TraesCS5B01G058000 chr7B 80.308 325 62 2 1717 2039 682885161 682884837 6.500000e-61 244.0
22 TraesCS5B01G058000 chr7B 76.025 317 75 1 1717 2032 66186761 66187077 1.870000e-36 163.0
23 TraesCS5B01G058000 chr7B 82.716 162 27 1 1872 2032 14932347 14932186 2.440000e-30 143.0
24 TraesCS5B01G058000 chr6A 79.321 324 61 6 1718 2037 551645327 551645648 3.040000e-54 222.0
25 TraesCS5B01G058000 chr5A 77.204 329 60 13 1722 2044 550533331 550533650 6.690000e-41 178.0
26 TraesCS5B01G058000 chr3D 84.211 190 20 9 1534 1720 488575925 488575743 2.400000e-40 176.0
27 TraesCS5B01G058000 chr3D 83.598 189 21 8 1534 1717 397922118 397922301 4.020000e-38 169.0
28 TraesCS5B01G058000 chr2D 84.043 188 21 7 1534 1716 357862856 357862673 3.110000e-39 172.0
29 TraesCS5B01G058000 chr6B 82.653 196 26 6 1526 1716 545330464 545330272 1.450000e-37 167.0
30 TraesCS5B01G058000 chr5D 75.676 259 59 4 1768 2025 429978448 429978193 2.460000e-25 126.0
31 TraesCS5B01G058000 chr2B 89.189 74 7 1 1716 1789 799125689 799125761 8.960000e-15 91.6


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 TraesCS5B01G058000 chr5B 63734944 63737297 2353 True 4348 4348 100.000 1 2354 1 chr5B.!!$R1 2353
1 TraesCS5B01G058000 chr5B 72237160 72237796 636 True 905 905 92.308 1718 2354 1 chr5B.!!$R2 636
2 TraesCS5B01G058000 chr7D 563516485 563518136 1651 True 1639 1639 84.828 82 1715 1 chr7D.!!$R1 1633
3 TraesCS5B01G058000 chr7D 617593233 617594868 1635 False 1550 1550 84.140 102 1716 1 chr7D.!!$F1 1614
4 TraesCS5B01G058000 chr1D 270035230 270036844 1614 False 1339 1339 82.009 132 1718 1 chr1D.!!$F2 1586
5 TraesCS5B01G058000 chr1D 431769669 431771026 1357 False 1258 1258 83.431 1 1360 1 chr1D.!!$F3 1359
6 TraesCS5B01G058000 chr1D 85203455 85204736 1281 False 472 472 73.652 26 1305 1 chr1D.!!$F1 1279
7 TraesCS5B01G058000 chr4B 546132157 546133475 1318 True 883 883 78.916 11 1327 1 chr4B.!!$R2 1316
8 TraesCS5B01G058000 chr4B 273233679 273234965 1286 True 813 813 78.180 12 1302 1 chr4B.!!$R1 1290
9 TraesCS5B01G058000 chr1B 145445006 145446313 1307 True 627 627 75.678 26 1333 1 chr1B.!!$R2 1307
10 TraesCS5B01G058000 chr4A 319838898 319840148 1250 True 523 523 74.505 3 1250 1 chr4A.!!$R1 1247
11 TraesCS5B01G058000 chr7A 641707743 641709064 1321 False 516 516 73.988 3 1321 1 chr7A.!!$F1 1318

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
913 921 0.654683 GAGATGTCATGAACAGGCGC 59.345 55.0 0.0 0.0 42.37 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 1838 0.108186 TGGTGCACTTAGCCTCATCG 60.108 55.0 17.98 0.0 44.83 3.84 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
21 22 3.265791 CCTAGACTGCAATTCTGTGGAC 58.734 50.000 7.61 0.00 0.00 4.02
22 23 2.936919 AGACTGCAATTCTGTGGACA 57.063 45.000 0.00 0.00 0.00 4.02
46 47 1.332997 GATTCCTCAAATGCTGCGAGG 59.667 52.381 13.23 13.23 46.49 4.63
69 70 1.284491 TGGATTGGTAATGCAGCCTCA 59.716 47.619 0.00 0.00 34.08 3.86
109 110 4.356405 ACTCCTCAACACATCATTGACA 57.644 40.909 0.00 0.00 32.67 3.58
157 160 2.239150 GTTCCTTCTTCCTAAGGGGGTC 59.761 54.545 2.96 0.00 45.25 4.46
166 169 2.777692 TCCTAAGGGGGTCATTGCTAAG 59.222 50.000 0.00 0.00 35.33 2.18
243 247 4.597032 CTTGGTCAAGTGGGCCAA 57.403 55.556 8.40 2.90 39.66 4.52
251 255 2.365293 GTCAAGTGGGCCAAAATCTGTT 59.635 45.455 8.40 0.00 0.00 3.16
256 260 1.818060 TGGGCCAAAATCTGTTGATCG 59.182 47.619 2.13 0.00 31.51 3.69
448 452 3.075882 CCCCCATTTGGAAGGCTATCATA 59.924 47.826 0.00 0.00 37.39 2.15
463 467 8.230472 AGGCTATCATAAAGGTCAAAGATTTG 57.770 34.615 0.00 0.00 39.48 2.32
512 516 8.274322 TCATTAAATCTGGAAATCTTGCTAGGA 58.726 33.333 0.00 0.00 0.00 2.94
690 697 4.335416 CAATGGAGGGAAGTTCAAGCTAA 58.665 43.478 5.01 0.00 0.00 3.09
718 725 3.294214 GTCATGGCCTCTTTCCAATGAT 58.706 45.455 3.32 0.00 37.13 2.45
719 726 3.703052 GTCATGGCCTCTTTCCAATGATT 59.297 43.478 3.32 0.00 37.13 2.57
787 795 9.489084 CCACGAAATCAATCTAATGATTACCTA 57.511 33.333 3.21 0.00 46.57 3.08
913 921 0.654683 GAGATGTCATGAACAGGCGC 59.345 55.000 0.00 0.00 42.37 6.53
918 927 3.049674 CATGAACAGGCGCGGTGT 61.050 61.111 8.83 8.14 0.00 4.16
970 979 1.981256 AAGGGAAACATCGCAACACT 58.019 45.000 0.00 0.00 0.00 3.55
986 996 5.408604 CGCAACACTTATTCTTTACCTGTCT 59.591 40.000 0.00 0.00 0.00 3.41
1017 1030 1.072331 GTGATGTGGAGAACTGTGGGT 59.928 52.381 0.00 0.00 0.00 4.51
1049 1062 0.462789 ACGGACCGTTGCCCTAATAG 59.537 55.000 15.37 0.00 36.35 1.73
1051 1064 0.878961 GGACCGTTGCCCTAATAGCG 60.879 60.000 0.00 0.00 0.00 4.26
1114 1128 7.882755 TGATGGGGAGAGATTTTATACCTTTT 58.117 34.615 0.00 0.00 0.00 2.27
1128 1142 1.615392 ACCTTTTGCCTAGCTGCTTTG 59.385 47.619 7.79 0.00 0.00 2.77
1172 1187 4.636648 TCGCAACAAGAAAACCTTTGAGTA 59.363 37.500 0.00 0.00 31.42 2.59
1215 1230 5.859521 TTGATGTGGTTTATTTTGCATGC 57.140 34.783 11.82 11.82 0.00 4.06
1243 1258 2.860817 TACCTACTGGGCAGGTATGT 57.139 50.000 0.00 1.11 44.77 2.29
1283 1298 2.040012 AGGCAATGGAGCATGGATCTAG 59.960 50.000 0.00 0.00 35.83 2.43
1288 1303 2.263545 TGGAGCATGGATCTAGGATGG 58.736 52.381 0.00 0.00 0.00 3.51
1289 1304 1.065564 GGAGCATGGATCTAGGATGGC 60.066 57.143 0.00 0.00 0.00 4.40
1321 1336 2.805099 GCTTCGAACATGATGAGGATCC 59.195 50.000 2.48 2.48 0.00 3.36
1341 1356 1.443702 CGCGACGTCAAGTGATCCA 60.444 57.895 17.16 0.00 0.00 3.41
1347 1362 2.483877 GACGTCAAGTGATCCAATGCAA 59.516 45.455 11.55 0.00 0.00 4.08
1348 1363 2.485426 ACGTCAAGTGATCCAATGCAAG 59.515 45.455 0.00 0.00 0.00 4.01
1378 1400 3.521796 GCTTGCGGCTGGGGATTC 61.522 66.667 0.00 0.00 38.06 2.52
1379 1401 3.204827 CTTGCGGCTGGGGATTCG 61.205 66.667 0.00 0.00 0.00 3.34
1381 1403 2.947938 CTTGCGGCTGGGGATTCGAT 62.948 60.000 0.00 0.00 0.00 3.59
1384 1406 2.024918 CGGCTGGGGATTCGATTTG 58.975 57.895 0.00 0.00 0.00 2.32
1385 1407 1.447317 CGGCTGGGGATTCGATTTGG 61.447 60.000 0.00 0.00 0.00 3.28
1387 1409 1.025041 GCTGGGGATTCGATTTGGTC 58.975 55.000 0.00 0.00 0.00 4.02
1388 1410 1.681780 GCTGGGGATTCGATTTGGTCA 60.682 52.381 0.00 0.00 0.00 4.02
1390 1412 2.684881 CTGGGGATTCGATTTGGTCAAG 59.315 50.000 0.00 0.00 0.00 3.02
1391 1413 2.041081 TGGGGATTCGATTTGGTCAAGT 59.959 45.455 0.00 0.00 0.00 3.16
1392 1414 2.683362 GGGGATTCGATTTGGTCAAGTC 59.317 50.000 0.00 0.00 0.00 3.01
1394 1416 2.351726 GGATTCGATTTGGTCAAGTCGG 59.648 50.000 21.98 9.12 46.20 4.79
1395 1417 2.536761 TTCGATTTGGTCAAGTCGGT 57.463 45.000 21.98 0.00 46.20 4.69
1397 1419 2.139917 TCGATTTGGTCAAGTCGGTTG 58.860 47.619 21.98 2.09 46.20 3.77
1400 1422 3.242936 CGATTTGGTCAAGTCGGTTGTTT 60.243 43.478 17.07 0.00 43.71 2.83
1404 1426 2.169769 TGGTCAAGTCGGTTGTTTCTCT 59.830 45.455 0.00 0.00 37.43 3.10
1405 1427 2.544267 GGTCAAGTCGGTTGTTTCTCTG 59.456 50.000 0.00 0.00 37.43 3.35
1406 1428 2.032808 GTCAAGTCGGTTGTTTCTCTGC 60.033 50.000 0.00 0.00 37.43 4.26
1415 1459 3.249189 TTTCTCTGCGGGTGCCCT 61.249 61.111 5.64 0.00 41.78 5.19
1417 1461 2.351924 TTTCTCTGCGGGTGCCCTTT 62.352 55.000 5.64 0.00 41.78 3.11
1434 1478 0.106769 TTTGGCTGTTGCTGGTCTGA 60.107 50.000 0.00 0.00 39.59 3.27
1437 1481 1.339055 TGGCTGTTGCTGGTCTGATAC 60.339 52.381 0.00 0.00 39.59 2.24
1440 1484 2.813754 GCTGTTGCTGGTCTGATACAAA 59.186 45.455 0.00 0.00 36.03 2.83
1445 1489 7.144722 TGTTGCTGGTCTGATACAAATTTAG 57.855 36.000 0.00 0.00 0.00 1.85
1451 1495 6.177610 TGGTCTGATACAAATTTAGTGGGTC 58.822 40.000 0.00 0.00 0.00 4.46
1459 1503 3.806949 AATTTAGTGGGTCCTTGCTCA 57.193 42.857 0.00 0.00 0.00 4.26
1488 1532 2.686915 GCTTTTGATGCAGCCTATCTGT 59.313 45.455 0.00 0.00 44.66 3.41
1504 1548 3.788227 TCTGTTGAGGCTTGTAATGGT 57.212 42.857 0.00 0.00 0.00 3.55
1508 1552 1.544724 TGAGGCTTGTAATGGTTGGC 58.455 50.000 0.00 0.00 0.00 4.52
1517 1561 2.961741 TGTAATGGTTGGCTTGCTGAAA 59.038 40.909 0.00 0.00 0.00 2.69
1527 1571 3.640967 TGGCTTGCTGAAATGTTTAGGTT 59.359 39.130 0.00 0.00 0.00 3.50
1532 1576 7.145323 GCTTGCTGAAATGTTTAGGTTTCTTA 58.855 34.615 0.00 0.00 35.80 2.10
1605 1650 0.036306 GTGTCCATCGTGGGTTTCCT 59.964 55.000 4.52 0.00 38.32 3.36
1622 1667 3.678056 TCCTAGTGATGCGTTGAACTT 57.322 42.857 0.00 0.00 0.00 2.66
1628 1673 3.563808 AGTGATGCGTTGAACTTGCTTTA 59.436 39.130 0.00 0.00 0.00 1.85
1642 1687 5.314529 ACTTGCTTTACCCTTTCTAGGTTC 58.685 41.667 0.00 0.00 40.19 3.62
1649 1694 1.557188 CCCTTTCTAGGTTCCCTGGGA 60.557 57.143 12.53 12.53 40.19 4.37
1753 1802 1.296392 CAGCACCGACTGAATCCCA 59.704 57.895 0.00 0.00 40.25 4.37
1754 1803 1.021390 CAGCACCGACTGAATCCCAC 61.021 60.000 0.00 0.00 40.25 4.61
1760 1809 1.137086 CCGACTGAATCCCACGAGATT 59.863 52.381 0.00 0.00 39.19 2.40
1768 1817 1.064296 CCCACGAGATTCGACGGAG 59.936 63.158 5.38 3.86 43.74 4.63
1789 1838 2.166664 GACACACCTCTACACATCCTCC 59.833 54.545 0.00 0.00 0.00 4.30
1791 1840 1.005569 ACACCTCTACACATCCTCCGA 59.994 52.381 0.00 0.00 0.00 4.55
1810 1859 2.216898 GATGAGGCTAAGTGCACCATC 58.783 52.381 14.63 13.15 45.15 3.51
1811 1860 0.983467 TGAGGCTAAGTGCACCATCA 59.017 50.000 14.63 8.68 45.15 3.07
1826 1875 3.586174 CACCATCAGGACATGGATAGGAT 59.414 47.826 6.48 0.00 45.79 3.24
1857 1906 4.902448 ACCTTATTCCTACTGAGGGACATC 59.098 45.833 0.00 0.00 43.94 3.06
1862 1911 2.091830 TCCTACTGAGGGACATCGTCAT 60.092 50.000 0.00 0.00 43.94 3.06
1863 1912 2.294791 CCTACTGAGGGACATCGTCATC 59.705 54.545 0.00 0.00 39.23 2.92
1886 1935 1.152777 CACAGCCCCAACCAAGACA 60.153 57.895 0.00 0.00 0.00 3.41
1910 1959 6.539649 TTGAACCTAACAAAGATGAGAACG 57.460 37.500 0.00 0.00 0.00 3.95
1914 1963 5.607477 ACCTAACAAAGATGAGAACGTGAA 58.393 37.500 0.00 0.00 0.00 3.18
1951 2000 1.604378 CCAAGATCCTCCGCACCTT 59.396 57.895 0.00 0.00 0.00 3.50
1982 2031 3.944123 CCATCAATGGTGGGGCAG 58.056 61.111 4.21 0.00 43.05 4.85
1988 2037 1.076485 AATGGTGGGGCAGATCAGC 60.076 57.895 0.60 0.60 0.00 4.26
2099 2148 5.302568 TCATGGATGCATTCTTAATTCCCAC 59.697 40.000 6.53 0.00 0.00 4.61
2113 2162 2.225382 TCCCACGAGTACATGAAGGA 57.775 50.000 0.00 0.00 0.00 3.36
2197 2246 2.040544 CCCACGTTAAGGCAGCCAG 61.041 63.158 15.80 1.66 0.00 4.85
2224 2273 3.781605 GAGGCTAGCACATGGGCCC 62.782 68.421 18.42 17.59 45.07 5.80
2227 2276 3.797353 CTAGCACATGGGCCCGGT 61.797 66.667 18.42 15.81 0.00 5.28
2253 2302 9.085645 TCCGTTGAGAACCAGTTATATATGTAT 57.914 33.333 0.00 0.00 0.00 2.29
2276 2325 1.961435 GGGAAAGCAATGAGCCATCCA 60.961 52.381 9.88 0.00 45.57 3.41
2281 2330 1.521450 GCAATGAGCCATCCATCCGG 61.521 60.000 0.00 0.00 37.23 5.14
2297 2346 1.375396 CGGGCTTGGATCACGACAA 60.375 57.895 0.00 0.00 0.00 3.18
2312 2361 4.697756 CAACGGCGGCTTCCCTGA 62.698 66.667 13.24 0.00 0.00 3.86
2330 2379 1.982958 TGACACCCCCTACCTTTCTTC 59.017 52.381 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.016024 TGAGGAATCTTTTGTCCACAGAATTG 60.016 38.462 0.00 0.00 36.28 2.32
10 11 6.070656 TGAGGAATCTTTTGTCCACAGAATT 58.929 36.000 0.00 0.00 36.28 2.17
14 15 5.772825 TTTGAGGAATCTTTTGTCCACAG 57.227 39.130 0.00 0.00 36.14 3.66
21 22 3.611113 CGCAGCATTTGAGGAATCTTTTG 59.389 43.478 0.00 0.00 0.00 2.44
22 23 3.507233 TCGCAGCATTTGAGGAATCTTTT 59.493 39.130 0.00 0.00 0.00 2.27
46 47 1.202452 GGCTGCATTACCAATCCAAGC 60.202 52.381 0.50 0.00 0.00 4.01
88 89 4.356405 TGTCAATGATGTGTTGAGGAGT 57.644 40.909 0.00 0.00 36.35 3.85
185 188 1.401761 TGCTCTTGCCAGAAAAAGCA 58.598 45.000 0.00 0.00 38.71 3.91
243 247 6.294731 CCCTTTTTCCTTCGATCAACAGATTT 60.295 38.462 0.00 0.00 0.00 2.17
251 255 1.615919 GCCCCCTTTTTCCTTCGATCA 60.616 52.381 0.00 0.00 0.00 2.92
256 260 0.904865 CCAGGCCCCCTTTTTCCTTC 60.905 60.000 0.00 0.00 0.00 3.46
393 397 7.973048 AACCTGGTCTTAATAGATGTCACTA 57.027 36.000 0.00 0.00 31.86 2.74
448 452 7.264947 CAACAAGGTACAAATCTTTGACCTTT 58.735 34.615 22.75 16.40 45.49 3.11
463 467 4.820173 ACTACTTTTCTGCCAACAAGGTAC 59.180 41.667 0.00 0.00 40.61 3.34
597 601 3.534357 TCTCCCTAAATTTGGCCACAA 57.466 42.857 3.88 3.52 34.07 3.33
650 657 1.067295 TGCTCAAGGAGTGGTGGATT 58.933 50.000 0.00 0.00 31.39 3.01
690 697 1.142688 AAGAGGCCATGACCCCACTT 61.143 55.000 5.01 0.00 0.00 3.16
776 784 7.787424 AGCTAGGTTTCTCTCTAGGTAATCATT 59.213 37.037 0.00 0.00 40.97 2.57
787 795 2.183679 CACCCAGCTAGGTTTCTCTCT 58.816 52.381 0.00 0.00 38.39 3.10
970 979 8.372459 TCTAGCAACAAGACAGGTAAAGAATAA 58.628 33.333 0.00 0.00 0.00 1.40
986 996 3.578282 TCTCCACATCACTCTAGCAACAA 59.422 43.478 0.00 0.00 0.00 2.83
1070 1083 2.069273 CAGGAAGAAAGGTGTAGCACG 58.931 52.381 0.00 0.00 34.83 5.34
1114 1128 3.672293 GCACAAAGCAGCTAGGCA 58.328 55.556 0.00 0.00 44.79 4.75
1128 1142 0.463654 TATTCCACATCGCCCAGCAC 60.464 55.000 0.00 0.00 0.00 4.40
1215 1230 2.289819 TGCCCAGTAGGTAAGAAAACCG 60.290 50.000 0.00 0.00 44.77 4.44
1243 1258 1.417517 CTCCCGATCATCACCCATCAA 59.582 52.381 0.00 0.00 0.00 2.57
1283 1298 2.247437 GCGTTGATCCTCGCCATCC 61.247 63.158 17.00 0.00 45.54 3.51
1289 1304 0.640768 GTTCGAAGCGTTGATCCTCG 59.359 55.000 0.00 0.00 0.00 4.63
1330 1345 1.820519 GCCTTGCATTGGATCACTTGA 59.179 47.619 10.08 0.00 0.00 3.02
1341 1356 1.681327 CCCAGCTCAGCCTTGCATT 60.681 57.895 0.00 0.00 0.00 3.56
1362 1378 2.947938 ATCGAATCCCCAGCCGCAAG 62.948 60.000 0.00 0.00 0.00 4.01
1367 1384 0.395724 ACCAAATCGAATCCCCAGCC 60.396 55.000 0.00 0.00 0.00 4.85
1374 1396 3.000727 ACCGACTTGACCAAATCGAATC 58.999 45.455 14.05 0.00 36.70 2.52
1375 1397 3.053831 ACCGACTTGACCAAATCGAAT 57.946 42.857 14.05 0.86 36.70 3.34
1376 1398 2.536761 ACCGACTTGACCAAATCGAA 57.463 45.000 14.05 0.00 36.70 3.71
1378 1400 1.871039 ACAACCGACTTGACCAAATCG 59.129 47.619 6.62 6.62 33.59 3.34
1379 1401 3.982576 AACAACCGACTTGACCAAATC 57.017 42.857 0.35 0.00 33.59 2.17
1381 1403 3.349022 AGAAACAACCGACTTGACCAAA 58.651 40.909 0.35 0.00 33.59 3.28
1384 1406 2.544267 CAGAGAAACAACCGACTTGACC 59.456 50.000 0.35 0.00 33.59 4.02
1385 1407 2.032808 GCAGAGAAACAACCGACTTGAC 60.033 50.000 0.35 0.00 33.59 3.18
1387 1409 1.070577 CGCAGAGAAACAACCGACTTG 60.071 52.381 0.00 0.00 35.77 3.16
1388 1410 1.217882 CGCAGAGAAACAACCGACTT 58.782 50.000 0.00 0.00 0.00 3.01
1390 1412 1.566018 CCCGCAGAGAAACAACCGAC 61.566 60.000 0.00 0.00 0.00 4.79
1391 1413 1.301401 CCCGCAGAGAAACAACCGA 60.301 57.895 0.00 0.00 0.00 4.69
1392 1414 1.597027 ACCCGCAGAGAAACAACCG 60.597 57.895 0.00 0.00 0.00 4.44
1393 1415 1.949257 CACCCGCAGAGAAACAACC 59.051 57.895 0.00 0.00 0.00 3.77
1394 1416 1.282875 GCACCCGCAGAGAAACAAC 59.717 57.895 0.00 0.00 38.36 3.32
1395 1417 1.896660 GGCACCCGCAGAGAAACAA 60.897 57.895 0.00 0.00 41.24 2.83
1415 1459 0.106769 TCAGACCAGCAACAGCCAAA 60.107 50.000 0.00 0.00 0.00 3.28
1417 1461 0.983467 TATCAGACCAGCAACAGCCA 59.017 50.000 0.00 0.00 0.00 4.75
1426 1470 6.180472 ACCCACTAAATTTGTATCAGACCAG 58.820 40.000 0.00 0.00 0.00 4.00
1434 1478 5.580022 AGCAAGGACCCACTAAATTTGTAT 58.420 37.500 0.00 0.00 0.00 2.29
1437 1481 3.826157 TGAGCAAGGACCCACTAAATTTG 59.174 43.478 0.00 0.00 0.00 2.32
1440 1484 3.624777 CATGAGCAAGGACCCACTAAAT 58.375 45.455 0.00 0.00 0.00 1.40
1445 1489 3.595819 GCATGAGCAAGGACCCAC 58.404 61.111 0.00 0.00 41.58 4.61
1463 1507 1.848652 AGGCTGCATCAAAAGCTCAT 58.151 45.000 0.50 0.00 39.46 2.90
1488 1532 1.892474 GCCAACCATTACAAGCCTCAA 59.108 47.619 0.00 0.00 0.00 3.02
1504 1548 3.640967 ACCTAAACATTTCAGCAAGCCAA 59.359 39.130 0.00 0.00 0.00 4.52
1527 1571 7.822334 CCAGTGACACCATAACAACTATAAGAA 59.178 37.037 0.84 0.00 0.00 2.52
1532 1576 4.288626 ACCCAGTGACACCATAACAACTAT 59.711 41.667 0.84 0.00 0.00 2.12
1541 1585 1.039856 GCAAAACCCAGTGACACCAT 58.960 50.000 0.84 0.00 0.00 3.55
1605 1650 2.766313 AGCAAGTTCAACGCATCACTA 58.234 42.857 0.00 0.00 0.00 2.74
1622 1667 3.009805 GGGAACCTAGAAAGGGTAAAGCA 59.990 47.826 0.00 0.00 45.59 3.91
1642 1687 4.860022 ACAATCAGTTTTAGATCCCAGGG 58.140 43.478 0.00 0.00 0.00 4.45
1678 1727 5.451354 GGCATAACCCCTTTCCATTACTTA 58.549 41.667 0.00 0.00 0.00 2.24
1679 1728 4.286707 GGCATAACCCCTTTCCATTACTT 58.713 43.478 0.00 0.00 0.00 2.24
1729 1778 2.731691 TTCAGTCGGTGCTGGCCTTC 62.732 60.000 3.32 0.00 37.12 3.46
1733 1782 2.109126 GGATTCAGTCGGTGCTGGC 61.109 63.158 0.00 0.00 37.12 4.85
1737 1786 2.100631 CGTGGGATTCAGTCGGTGC 61.101 63.158 0.00 0.00 0.00 5.01
1753 1802 0.447011 GTGTCTCCGTCGAATCTCGT 59.553 55.000 0.00 0.00 41.35 4.18
1754 1803 0.446616 TGTGTCTCCGTCGAATCTCG 59.553 55.000 0.00 0.00 42.10 4.04
1760 1809 0.322648 TAGAGGTGTGTCTCCGTCGA 59.677 55.000 0.00 0.00 34.46 4.20
1768 1817 2.166664 GGAGGATGTGTAGAGGTGTGTC 59.833 54.545 0.00 0.00 0.00 3.67
1789 1838 0.108186 TGGTGCACTTAGCCTCATCG 60.108 55.000 17.98 0.00 44.83 3.84
1791 1840 1.561076 TGATGGTGCACTTAGCCTCAT 59.439 47.619 17.98 9.49 44.83 2.90
1802 1851 0.921166 ATCCATGTCCTGATGGTGCA 59.079 50.000 0.00 0.00 43.20 4.57
1810 1859 2.039480 CCCACATCCTATCCATGTCCTG 59.961 54.545 0.00 0.00 31.83 3.86
1811 1860 2.089982 TCCCACATCCTATCCATGTCCT 60.090 50.000 0.00 0.00 31.83 3.85
1826 1875 4.030913 CAGTAGGAATAAGGTCTCCCACA 58.969 47.826 0.00 0.00 31.50 4.17
1857 1906 1.517257 GGGCTGTGAGACGATGACG 60.517 63.158 0.00 0.00 45.75 4.35
1862 1911 2.741092 GTTGGGGCTGTGAGACGA 59.259 61.111 0.00 0.00 0.00 4.20
1863 1912 2.358737 GGTTGGGGCTGTGAGACG 60.359 66.667 0.00 0.00 0.00 4.18
1886 1935 6.710744 ACGTTCTCATCTTTGTTAGGTTCAAT 59.289 34.615 0.00 0.00 0.00 2.57
1972 2021 4.100084 CGCTGATCTGCCCCACCA 62.100 66.667 17.78 0.00 0.00 4.17
1995 2044 4.918201 CTTCCTCATCCCGCCGGC 62.918 72.222 19.07 19.07 0.00 6.13
2000 2049 1.490574 AAGTCTCCTTCCTCATCCCG 58.509 55.000 0.00 0.00 0.00 5.14
2005 2054 5.844516 TCCTTAAGAAAAGTCTCCTTCCTCA 59.155 40.000 3.36 0.00 30.70 3.86
2062 2111 9.664332 GAATGCATCCATGATTACTAGTAGAAT 57.336 33.333 3.59 0.00 0.00 2.40
2148 2197 0.676782 GTGGCAGTAATTGGGTCGCT 60.677 55.000 0.00 0.00 0.00 4.93
2202 2251 1.099879 CCCATGTGCTAGCCTCTTGC 61.100 60.000 13.29 0.00 41.71 4.01
2224 2273 0.249741 AACTGGTTCTCAACGGACCG 60.250 55.000 13.61 13.61 0.00 4.79
2225 2274 2.825861 TAACTGGTTCTCAACGGACC 57.174 50.000 0.00 0.00 0.00 4.46
2227 2276 7.356089 ACATATATAACTGGTTCTCAACGGA 57.644 36.000 0.00 0.00 0.00 4.69
2232 2281 9.488762 CCCCTATACATATATAACTGGTTCTCA 57.511 37.037 0.00 0.00 0.00 3.27
2253 2302 0.998928 TGGCTCATTGCTTTCCCCTA 59.001 50.000 0.00 0.00 42.39 3.53
2266 2315 3.877450 GCCCGGATGGATGGCTCA 61.877 66.667 0.73 0.00 42.01 4.26
2281 2330 1.635663 CCGTTGTCGTGATCCAAGCC 61.636 60.000 0.00 0.00 35.01 4.35
2312 2361 1.132168 AGGAAGAAAGGTAGGGGGTGT 60.132 52.381 0.00 0.00 0.00 4.16
2330 2379 0.341609 AGGAAGAGGGAGGAAGGAGG 59.658 60.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.