Multiple sequence alignment - TraesCS3D01G201700

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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 TraesCS3D01G201700 chr3D 100.000 2456 0 0 1 2456 241418403 241420858 0.000000e+00 4536
1 TraesCS3D01G201700 chr3B 93.460 1422 71 4 1 1415 338621632 338623038 0.000000e+00 2091
2 TraesCS3D01G201700 chr3B 91.379 580 48 2 1878 2456 338633429 338634007 0.000000e+00 793
3 TraesCS3D01G201700 chr3B 92.874 435 29 2 1449 1882 338623040 338623473 4.460000e-177 630


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 TraesCS3D01G201700 chr3D 241418403 241420858 2455 False 4536.0 4536 100.000 1 2456 1 chr3D.!!$F1 2455
1 TraesCS3D01G201700 chr3B 338621632 338623473 1841 False 1360.5 2091 93.167 1 1882 2 chr3B.!!$F2 1881
2 TraesCS3D01G201700 chr3B 338633429 338634007 578 False 793.0 793 91.379 1878 2456 1 chr3B.!!$F1 578

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
539 540 0.25361 ACCGCCGGGAACATTGAATA 59.746 50.0 8.57 0.0 36.97 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1747 1756 0.107643 GGCCTTGACTCCTCCTATGC 59.892 60.0 0.0 0.0 0.0 3.14 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
24 25 6.861065 TTATCTGTTGAAGACAAAGTGACC 57.139 37.500 0.00 0.00 37.88 4.02
62 63 5.567915 GCACTTTTATTAGTTTGCGGAAGAC 59.432 40.000 0.00 0.00 0.00 3.01
70 71 1.531578 GTTTGCGGAAGACTGTTCCTC 59.468 52.381 3.59 0.00 36.45 3.71
115 116 6.183360 GGCAGCTATGATTATAGGATGTACGA 60.183 42.308 6.64 0.00 37.37 3.43
126 127 2.108970 GGATGTACGAGAGGGGAGTTT 58.891 52.381 0.00 0.00 0.00 2.66
182 183 6.652053 TGATGTTCATGGACATTCATAGTGA 58.348 36.000 20.74 0.00 40.21 3.41
195 196 7.103641 ACATTCATAGTGAACGAAATGGTAGT 58.896 34.615 0.00 0.00 39.45 2.73
202 203 4.024387 GTGAACGAAATGGTAGTCAAGCAA 60.024 41.667 0.00 0.00 39.48 3.91
210 211 4.112634 TGGTAGTCAAGCAAGGGAATTT 57.887 40.909 0.00 0.00 31.13 1.82
211 212 3.826157 TGGTAGTCAAGCAAGGGAATTTG 59.174 43.478 0.00 0.00 31.13 2.32
215 216 3.766051 AGTCAAGCAAGGGAATTTGGATC 59.234 43.478 0.00 0.00 0.00 3.36
269 270 4.386867 TCGGTTCTGGTGAAGTGATATC 57.613 45.455 0.00 0.00 32.15 1.63
377 378 7.649533 TTATCATGTTCAAAGAGATGGCAAT 57.350 32.000 0.00 0.00 0.00 3.56
403 404 7.824289 TGTATGGGCTATTGATATTACTTCTGC 59.176 37.037 0.00 0.00 0.00 4.26
427 428 4.665009 TGGAAAGGAGGCATATGAAGGTAT 59.335 41.667 6.97 0.00 0.00 2.73
469 470 3.498774 ACAGAGGCACAAAGAAGATGT 57.501 42.857 0.00 0.00 0.00 3.06
472 473 3.817084 CAGAGGCACAAAGAAGATGTTGA 59.183 43.478 0.00 0.00 0.00 3.18
502 503 0.965866 TCAGCCAACTCGAGATCGGT 60.966 55.000 21.68 2.11 40.29 4.69
530 531 2.757099 GGAGAGTACCGCCGGGAA 60.757 66.667 8.57 0.00 36.97 3.97
533 534 1.673808 GAGAGTACCGCCGGGAACAT 61.674 60.000 8.57 0.00 36.97 2.71
539 540 0.253610 ACCGCCGGGAACATTGAATA 59.746 50.000 8.57 0.00 36.97 1.75
550 551 7.255590 CCGGGAACATTGAATATCTTTAGCATT 60.256 37.037 0.00 0.00 0.00 3.56
562 563 2.032680 TTAGCATTAACTGTCGGGGC 57.967 50.000 0.00 0.00 0.00 5.80
566 567 0.676466 CATTAACTGTCGGGGCTGCA 60.676 55.000 0.50 0.00 0.00 4.41
591 592 1.542547 GCCCGAGACAGTTCAGGAAAA 60.543 52.381 0.00 0.00 0.00 2.29
609 610 5.358160 AGGAAAATTGTAGCTTGATACAGCC 59.642 40.000 0.00 0.00 41.12 4.85
610 611 5.125417 GGAAAATTGTAGCTTGATACAGCCA 59.875 40.000 0.00 0.00 41.12 4.75
640 641 3.674528 TGCTTGGTCTTTCTCTCAGAG 57.325 47.619 0.00 0.00 0.00 3.35
680 681 5.609423 AGAGAGCACATGATATGAGGTTTC 58.391 41.667 0.00 0.00 34.41 2.78
705 706 5.543507 TTGGGTTTTAGACATGCATTTGT 57.456 34.783 0.00 0.00 0.00 2.83
716 717 6.544620 GACATGCATTTGTCGTTAAATCTG 57.455 37.500 4.76 0.00 36.93 2.90
740 741 0.324943 TCTTTGTGGAGGCCTAGTGC 59.675 55.000 4.42 0.00 40.16 4.40
790 791 7.766278 GTCAGCCTTAAATCTTTCAGTAGATCA 59.234 37.037 0.00 0.00 33.81 2.92
791 792 7.766278 TCAGCCTTAAATCTTTCAGTAGATCAC 59.234 37.037 0.00 0.00 33.81 3.06
804 805 7.095695 TCAGTAGATCACATATTGACGTTCA 57.904 36.000 0.00 0.00 36.92 3.18
855 856 7.928873 AGAGAATGGAGGTTTAGTGGATTTTA 58.071 34.615 0.00 0.00 0.00 1.52
910 911 2.023673 TGGGAGTTGTTGCAGTTTCTG 58.976 47.619 0.00 0.00 34.12 3.02
983 991 1.820519 TGGATGCAAATGAACTGGAGC 59.179 47.619 0.00 0.00 0.00 4.70
1015 1023 3.696548 GGAGTGGATGATGGAAGGTTTTC 59.303 47.826 0.00 0.00 0.00 2.29
1016 1024 4.335416 GAGTGGATGATGGAAGGTTTTCA 58.665 43.478 0.00 0.00 34.90 2.69
1037 1045 2.392662 TGAAATGGTGGACTTTTGCCA 58.607 42.857 0.00 0.00 35.28 4.92
1062 1070 4.666412 TTCAGATTTGGGGTATGTTGGA 57.334 40.909 0.00 0.00 0.00 3.53
1074 1082 4.263156 GGGTATGTTGGACTTCCTTACACA 60.263 45.833 6.10 0.98 35.33 3.72
1103 1111 3.624777 ACCATCAACAGGGCATTAGAAG 58.375 45.455 0.00 0.00 0.00 2.85
1112 1120 5.264395 ACAGGGCATTAGAAGCATAAAAGT 58.736 37.500 0.00 0.00 0.00 2.66
1194 1202 3.075148 TCGTCACCTTCAGACTACAGAG 58.925 50.000 0.00 0.00 33.89 3.35
1195 1203 2.814919 CGTCACCTTCAGACTACAGAGT 59.185 50.000 0.00 0.00 39.20 3.24
1205 1213 3.152261 GACTACAGAGTCGGACCATTG 57.848 52.381 4.14 3.75 42.73 2.82
1216 1224 1.464608 CGGACCATTGTGCACTACTTG 59.535 52.381 19.41 6.66 32.24 3.16
1253 1261 3.349927 CAAGTTGGCTCAATGATGGAGA 58.650 45.455 0.00 0.00 34.24 3.71
1336 1344 0.886490 CGAGAAAGCTTGGGTGCACT 60.886 55.000 17.98 0.00 34.99 4.40
1337 1345 1.608025 CGAGAAAGCTTGGGTGCACTA 60.608 52.381 17.98 3.30 34.99 2.74
1355 1363 0.620410 TACCATGGTGACCTGGGGAG 60.620 60.000 28.17 0.00 36.82 4.30
1384 1392 6.951971 AGTGAAGCTTTAGGTATTGTGAGAT 58.048 36.000 0.00 0.00 0.00 2.75
1394 1402 2.885135 ATTGTGAGATCCAGGTTGCA 57.115 45.000 0.00 0.00 0.00 4.08
1406 1414 1.827789 GGTTGCAGGTGTGGAGCAA 60.828 57.895 0.00 0.00 45.07 3.91
1415 1423 2.024414 GGTGTGGAGCAAAAGTGAGTT 58.976 47.619 0.00 0.00 0.00 3.01
1416 1424 2.427095 GGTGTGGAGCAAAAGTGAGTTT 59.573 45.455 0.00 0.00 0.00 2.66
1417 1425 3.438360 GTGTGGAGCAAAAGTGAGTTTG 58.562 45.455 0.00 0.00 40.72 2.93
1418 1426 2.426738 TGTGGAGCAAAAGTGAGTTTGG 59.573 45.455 0.34 0.00 38.64 3.28
1419 1427 1.408702 TGGAGCAAAAGTGAGTTTGGC 59.591 47.619 3.91 3.91 44.59 4.52
1423 1431 3.931285 GCAAAAGTGAGTTTGGCTTTG 57.069 42.857 4.88 0.00 41.40 2.77
1424 1432 3.261580 GCAAAAGTGAGTTTGGCTTTGT 58.738 40.909 4.88 0.00 41.40 2.83
1425 1433 3.306973 GCAAAAGTGAGTTTGGCTTTGTC 59.693 43.478 4.88 0.00 41.40 3.18
1426 1434 3.801114 AAAGTGAGTTTGGCTTTGTCC 57.199 42.857 0.00 0.00 32.03 4.02
1427 1435 1.308998 AGTGAGTTTGGCTTTGTCCG 58.691 50.000 0.00 0.00 0.00 4.79
1428 1436 1.021968 GTGAGTTTGGCTTTGTCCGT 58.978 50.000 0.00 0.00 0.00 4.69
1429 1437 2.158871 AGTGAGTTTGGCTTTGTCCGTA 60.159 45.455 0.00 0.00 0.00 4.02
1430 1438 2.614983 GTGAGTTTGGCTTTGTCCGTAA 59.385 45.455 0.00 0.00 0.00 3.18
1431 1439 3.065648 GTGAGTTTGGCTTTGTCCGTAAA 59.934 43.478 0.00 0.00 0.00 2.01
1432 1440 3.695060 TGAGTTTGGCTTTGTCCGTAAAA 59.305 39.130 0.00 0.00 0.00 1.52
1433 1441 4.158025 TGAGTTTGGCTTTGTCCGTAAAAA 59.842 37.500 0.00 0.00 0.00 1.94
1434 1442 4.678622 AGTTTGGCTTTGTCCGTAAAAAG 58.321 39.130 0.00 0.00 36.64 2.27
1435 1443 4.158949 AGTTTGGCTTTGTCCGTAAAAAGT 59.841 37.500 0.00 0.00 36.09 2.66
1436 1444 4.722361 TTGGCTTTGTCCGTAAAAAGTT 57.278 36.364 0.00 0.00 36.09 2.66
1437 1445 5.831702 TTGGCTTTGTCCGTAAAAAGTTA 57.168 34.783 0.00 0.00 36.09 2.24
1438 1446 5.831702 TGGCTTTGTCCGTAAAAAGTTAA 57.168 34.783 0.00 0.00 36.09 2.01
1439 1447 6.205101 TGGCTTTGTCCGTAAAAAGTTAAA 57.795 33.333 0.00 0.00 36.09 1.52
1440 1448 6.628185 TGGCTTTGTCCGTAAAAAGTTAAAA 58.372 32.000 0.00 0.00 36.09 1.52
1441 1449 7.095270 TGGCTTTGTCCGTAAAAAGTTAAAAA 58.905 30.769 0.00 0.00 36.09 1.94
1442 1450 7.063191 TGGCTTTGTCCGTAAAAAGTTAAAAAC 59.937 33.333 0.00 0.00 36.09 2.43
1443 1451 7.276218 GGCTTTGTCCGTAAAAAGTTAAAAACT 59.724 33.333 0.00 0.00 45.46 2.66
1444 1452 9.288124 GCTTTGTCCGTAAAAAGTTAAAAACTA 57.712 29.630 0.00 0.00 41.91 2.24
1447 1455 9.733219 TTGTCCGTAAAAAGTTAAAAACTATGG 57.267 29.630 0.00 0.00 41.91 2.74
1497 1505 2.064434 TGTTGTGCAAAGGACCATCA 57.936 45.000 0.00 0.00 0.00 3.07
1500 1508 0.178995 TGTGCAAAGGACCATCAGCA 60.179 50.000 0.00 0.00 0.00 4.41
1512 1520 4.704057 GGACCATCAGCAGAAGAGAAAAAT 59.296 41.667 0.00 0.00 0.00 1.82
1551 1559 2.566724 AGAACTTCTGGCAAGAGAGGAG 59.433 50.000 4.02 0.00 32.79 3.69
1598 1606 0.698238 CAATGGTTGACTGAGGGGGA 59.302 55.000 0.00 0.00 0.00 4.81
1609 1617 4.901849 TGACTGAGGGGGATAGAAATACAG 59.098 45.833 0.00 0.00 0.00 2.74
1611 1619 4.235372 CTGAGGGGGATAGAAATACAGGT 58.765 47.826 0.00 0.00 0.00 4.00
1637 1645 1.612726 CCAGACAAAGGCCAAGGAGAG 60.613 57.143 5.01 0.00 0.00 3.20
1685 1694 5.946972 CCCTTAAGACAGAGTCTAGTCAGAA 59.053 44.000 18.73 12.96 42.59 3.02
1692 1701 6.481976 AGACAGAGTCTAGTCAGAATATCACG 59.518 42.308 18.73 0.00 41.51 4.35
1693 1702 5.529430 ACAGAGTCTAGTCAGAATATCACGG 59.471 44.000 0.00 0.00 30.85 4.94
1694 1703 4.517453 AGAGTCTAGTCAGAATATCACGGC 59.483 45.833 0.00 0.00 30.85 5.68
1696 1705 4.517453 AGTCTAGTCAGAATATCACGGCTC 59.483 45.833 0.00 0.00 30.85 4.70
1742 1751 6.239036 GCCAAGGTCTTCTATCAAACTTTGTT 60.239 38.462 1.44 0.00 29.59 2.83
1747 1756 7.227512 AGGTCTTCTATCAAACTTTGTTCACAG 59.772 37.037 1.44 0.00 0.00 3.66
1750 1759 6.882610 TCTATCAAACTTTGTTCACAGCAT 57.117 33.333 1.44 0.00 0.00 3.79
1755 1764 5.239306 TCAAACTTTGTTCACAGCATAGGAG 59.761 40.000 1.44 0.00 0.00 3.69
1760 1769 2.497675 TGTTCACAGCATAGGAGGAGTC 59.502 50.000 0.00 0.00 0.00 3.36
1768 1777 0.760945 ATAGGAGGAGTCAAGGCCGG 60.761 60.000 0.00 0.00 0.00 6.13
1824 1833 7.763172 AGATAAACAGATGAATGAACGTCTC 57.237 36.000 0.00 0.00 34.42 3.36
1836 1845 0.318784 AACGTCTCTGTTCGCCAGTC 60.319 55.000 0.00 0.00 42.19 3.51
1838 1847 0.318699 CGTCTCTGTTCGCCAGTCAA 60.319 55.000 2.48 0.00 42.19 3.18
1887 1896 5.678132 TCATGATGCATCCTAACAAATCG 57.322 39.130 23.67 0.20 0.00 3.34
1931 1940 6.071560 ACACTCGGTTTCTACATCAGACATTA 60.072 38.462 0.00 0.00 31.12 1.90
1936 1945 6.292542 CGGTTTCTACATCAGACATTAGCATG 60.293 42.308 0.00 0.00 36.34 4.06
1958 1967 6.762702 TGTGATCAAACATGATGTATGCTT 57.237 33.333 0.00 0.00 40.59 3.91
1962 1971 3.110358 CAAACATGATGTATGCTTGGCG 58.890 45.455 0.00 0.00 38.57 5.69
1967 1976 0.304705 GATGTATGCTTGGCGGTTCG 59.695 55.000 0.00 0.00 0.00 3.95
2006 2015 1.678728 GGTCATGCCGGAGAATGTGAA 60.679 52.381 5.05 0.00 0.00 3.18
2010 2019 0.955428 TGCCGGAGAATGTGAACAGC 60.955 55.000 5.05 0.00 0.00 4.40
2030 2039 1.806542 CACTGTGTTGGTGCTCATACC 59.193 52.381 0.00 0.00 41.24 2.73
2062 2071 6.882768 AAGATCCCTAAGATTTGACTCAGT 57.117 37.500 0.00 0.00 34.42 3.41
2065 2074 5.578005 TCCCTAAGATTTGACTCAGTACG 57.422 43.478 0.00 0.00 0.00 3.67
2066 2075 4.401519 TCCCTAAGATTTGACTCAGTACGG 59.598 45.833 0.00 0.00 0.00 4.02
2125 2134 4.640771 TTGAAGGTGATTGCTCTTAGGT 57.359 40.909 0.00 0.00 0.00 3.08
2132 2141 3.935828 GTGATTGCTCTTAGGTTGAGACC 59.064 47.826 0.00 0.00 46.92 3.85
2190 2200 4.082733 GCTTTTGTTCCTCGAAGGCTTATT 60.083 41.667 0.00 0.00 38.82 1.40
2211 2221 5.778161 TTACAGACAATGTAATCACAGCG 57.222 39.130 0.00 0.00 46.96 5.18
2229 2239 3.999001 CAGCGTATGAGTGCATCCATTAT 59.001 43.478 8.72 0.00 35.94 1.28
2235 2245 7.412346 GCGTATGAGTGCATCCATTATCTAAAG 60.412 40.741 8.72 0.00 35.94 1.85
2247 2257 6.154363 TCCATTATCTAAAGCACAAAAAGGGG 59.846 38.462 0.00 0.00 0.00 4.79
2249 2259 7.310361 CCATTATCTAAAGCACAAAAAGGGGAA 60.310 37.037 0.00 0.00 0.00 3.97
2252 2262 3.819564 AAAGCACAAAAAGGGGAAGAC 57.180 42.857 0.00 0.00 0.00 3.01
2295 2305 2.961062 GGACATGGCAAAAGCCTATGAT 59.039 45.455 18.80 8.59 0.00 2.45
2297 2307 2.620115 ACATGGCAAAAGCCTATGATCG 59.380 45.455 18.80 0.00 0.00 3.69
2306 2316 0.039074 GCCTATGATCGGGTCGAGTG 60.039 60.000 0.00 0.00 39.91 3.51
2360 2370 3.304928 GGTTTTGCAGAGTTGTGGATCAG 60.305 47.826 0.00 0.00 0.00 2.90
2377 2387 4.342378 GGATCAGTAGAGTGATGGCTTGTA 59.658 45.833 4.56 0.00 37.29 2.41
2385 2395 5.128919 AGAGTGATGGCTTGTATTCAATCC 58.871 41.667 0.00 0.00 39.47 3.01
2404 2414 1.554392 CGCCTCATTCTCAGTTCGAG 58.446 55.000 0.00 0.00 43.80 4.04
2407 2417 3.427638 CGCCTCATTCTCAGTTCGAGTTA 60.428 47.826 0.00 0.00 42.88 2.24
2411 2421 5.521735 CCTCATTCTCAGTTCGAGTTAATGG 59.478 44.000 0.00 0.00 42.88 3.16
2425 2435 6.764085 TCGAGTTAATGGTGTTTTCTCTGAAA 59.236 34.615 0.00 0.00 0.00 2.69
2435 2445 7.815549 TGGTGTTTTCTCTGAAACTTTTAAACC 59.184 33.333 0.00 0.00 39.62 3.27
2436 2446 7.277098 GGTGTTTTCTCTGAAACTTTTAAACCC 59.723 37.037 0.00 0.00 39.62 4.11
2439 2449 6.613755 TTCTCTGAAACTTTTAAACCCTCG 57.386 37.500 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.118920 TCGGTCACTTTGTCTTCAACAGA 60.119 43.478 0.00 0.00 39.58 3.41
7 8 3.807622 TCATCGGTCACTTTGTCTTCAAC 59.192 43.478 0.00 0.00 32.93 3.18
14 15 4.202101 TGCAATTTTCATCGGTCACTTTGT 60.202 37.500 0.00 0.00 0.00 2.83
24 25 4.977741 AAAAGTGCTGCAATTTTCATCG 57.022 36.364 28.57 0.00 37.09 3.84
62 63 3.670625 TCCACCGTTAATTGAGGAACAG 58.329 45.455 3.21 0.00 0.00 3.16
70 71 4.638421 TGCCTTAGATTCCACCGTTAATTG 59.362 41.667 0.00 0.00 0.00 2.32
115 116 7.510675 TGTTAATATCTTGAAACTCCCCTCT 57.489 36.000 0.00 0.00 0.00 3.69
182 183 3.502211 CCTTGCTTGACTACCATTTCGTT 59.498 43.478 0.00 0.00 0.00 3.85
195 196 2.754552 CGATCCAAATTCCCTTGCTTGA 59.245 45.455 0.00 0.00 0.00 3.02
202 203 1.005924 ACCTTGCGATCCAAATTCCCT 59.994 47.619 0.00 0.00 31.94 4.20
210 211 1.134220 GGATACCAACCTTGCGATCCA 60.134 52.381 9.81 0.00 37.62 3.41
211 212 1.141053 AGGATACCAACCTTGCGATCC 59.859 52.381 7.76 7.76 37.80 3.36
215 216 8.561738 AATAAATATAGGATACCAACCTTGCG 57.438 34.615 0.00 0.00 38.76 4.85
249 250 3.118775 TGGATATCACTTCACCAGAACCG 60.119 47.826 4.83 0.00 0.00 4.44
251 252 7.445121 TGATATGGATATCACTTCACCAGAAC 58.555 38.462 4.83 0.00 42.96 3.01
253 254 7.616528 TTGATATGGATATCACTTCACCAGA 57.383 36.000 8.56 0.00 46.28 3.86
269 270 7.811236 GTGGCATAGATGAAAACATTGATATGG 59.189 37.037 0.00 0.00 36.01 2.74
337 338 6.182627 ACATGATAAACATTTCTCTCTGCCA 58.817 36.000 0.00 0.00 37.07 4.92
377 378 7.824289 GCAGAAGTAATATCAATAGCCCATACA 59.176 37.037 0.00 0.00 0.00 2.29
403 404 3.117738 ACCTTCATATGCCTCCTTTCCAG 60.118 47.826 0.00 0.00 0.00 3.86
427 428 8.700051 TCTGTACCATTTCTTTTGAATTTTCCA 58.300 29.630 0.00 0.00 38.37 3.53
464 465 5.703130 GGCTGAGTTTAAGTCTTCAACATCT 59.297 40.000 11.31 0.00 0.00 2.90
469 470 5.437060 AGTTGGCTGAGTTTAAGTCTTCAA 58.563 37.500 1.30 1.38 0.00 2.69
472 473 4.058817 CGAGTTGGCTGAGTTTAAGTCTT 58.941 43.478 1.30 0.00 0.00 3.01
524 525 5.530915 TGCTAAAGATATTCAATGTTCCCGG 59.469 40.000 0.00 0.00 0.00 5.73
533 534 8.826710 CCGACAGTTAATGCTAAAGATATTCAA 58.173 33.333 0.00 0.00 0.00 2.69
539 540 4.451900 CCCCGACAGTTAATGCTAAAGAT 58.548 43.478 0.00 0.00 0.00 2.40
550 551 2.662596 CTGCAGCCCCGACAGTTA 59.337 61.111 0.00 0.00 0.00 2.24
640 641 2.029290 TCTCTTAGCGGACAGTTTGGTC 60.029 50.000 0.00 0.00 37.06 4.02
680 681 3.634568 TGCATGTCTAAAACCCAAACG 57.365 42.857 0.00 0.00 0.00 3.60
705 706 5.468746 CCACAAAGACCTTCAGATTTAACGA 59.531 40.000 0.00 0.00 0.00 3.85
707 708 6.072452 CCTCCACAAAGACCTTCAGATTTAAC 60.072 42.308 0.00 0.00 0.00 2.01
716 717 0.402121 AGGCCTCCACAAAGACCTTC 59.598 55.000 0.00 0.00 0.00 3.46
754 755 1.592400 TAAGGCTGACCACGGAGTCG 61.592 60.000 0.00 0.00 41.61 4.18
760 761 3.751175 TGAAAGATTTAAGGCTGACCACG 59.249 43.478 0.00 0.00 39.06 4.94
790 791 7.615582 ATTTCTGACATGAACGTCAATATGT 57.384 32.000 0.00 6.63 44.97 2.29
866 867 7.255590 CCAACTATTCTTCCTTTTTGCTCTTGA 60.256 37.037 0.00 0.00 0.00 3.02
910 911 3.560068 ACGGATTATCAAATTGTCCTCGC 59.440 43.478 0.00 0.00 0.00 5.03
983 991 2.682594 TCATCCACTCCTCCCTGTATG 58.317 52.381 0.00 0.00 0.00 2.39
1015 1023 3.244146 TGGCAAAAGTCCACCATTTCATG 60.244 43.478 0.00 0.00 0.00 3.07
1016 1024 2.971330 TGGCAAAAGTCCACCATTTCAT 59.029 40.909 0.00 0.00 0.00 2.57
1037 1045 5.245977 CCAACATACCCCAAATCTGAAAACT 59.754 40.000 0.00 0.00 0.00 2.66
1062 1070 4.538490 TGGTTATCCCATGTGTAAGGAAGT 59.462 41.667 0.00 0.00 38.72 3.01
1103 1111 2.866762 CGGTCTAGCCTGACTTTTATGC 59.133 50.000 6.64 0.00 37.16 3.14
1112 1120 2.219449 TAGTGCCCGGTCTAGCCTGA 62.219 60.000 0.00 0.00 34.25 3.86
1187 1195 2.881074 CACAATGGTCCGACTCTGTAG 58.119 52.381 0.00 0.00 0.00 2.74
1194 1202 1.076332 GTAGTGCACAATGGTCCGAC 58.924 55.000 21.04 0.00 0.00 4.79
1195 1203 0.973632 AGTAGTGCACAATGGTCCGA 59.026 50.000 21.04 0.00 0.00 4.55
1196 1204 1.464608 CAAGTAGTGCACAATGGTCCG 59.535 52.381 21.04 0.00 0.00 4.79
1197 1205 2.226437 CACAAGTAGTGCACAATGGTCC 59.774 50.000 21.04 0.00 42.15 4.46
1198 1206 3.542712 CACAAGTAGTGCACAATGGTC 57.457 47.619 21.04 2.44 42.15 4.02
1216 1224 0.737219 CTTGGCTGCCTAATGCTCAC 59.263 55.000 21.03 0.00 42.00 3.51
1231 1239 2.426024 CTCCATCATTGAGCCAACTTGG 59.574 50.000 3.10 3.10 41.55 3.61
1242 1250 1.810755 CGATGCCCATCTCCATCATTG 59.189 52.381 6.69 0.00 38.14 2.82
1253 1261 4.806640 AAATGAAAAGTTCGATGCCCAT 57.193 36.364 0.00 0.00 0.00 4.00
1336 1344 0.620410 CTCCCCAGGTCACCATGGTA 60.620 60.000 19.28 3.34 34.58 3.25
1337 1345 1.925455 CTCCCCAGGTCACCATGGT 60.925 63.158 13.00 13.00 34.58 3.55
1345 1353 1.222936 CACTCATGCTCCCCAGGTC 59.777 63.158 0.00 0.00 0.00 3.85
1355 1363 5.355350 ACAATACCTAAAGCTTCACTCATGC 59.645 40.000 0.00 0.00 0.00 4.06
1384 1392 2.055689 CTCCACACCTGCAACCTGGA 62.056 60.000 0.00 0.00 34.43 3.86
1394 1402 1.212935 ACTCACTTTTGCTCCACACCT 59.787 47.619 0.00 0.00 0.00 4.00
1406 1414 2.099098 CGGACAAAGCCAAACTCACTTT 59.901 45.455 0.00 0.00 34.03 2.66
1415 1423 4.722361 AACTTTTTACGGACAAAGCCAA 57.278 36.364 6.18 0.00 33.92 4.52
1416 1424 5.831702 TTAACTTTTTACGGACAAAGCCA 57.168 34.783 6.18 0.00 33.92 4.75
1417 1425 7.276218 AGTTTTTAACTTTTTACGGACAAAGCC 59.724 33.333 6.18 0.00 39.04 4.35
1418 1426 8.176814 AGTTTTTAACTTTTTACGGACAAAGC 57.823 30.769 6.18 0.00 39.04 3.51
1421 1429 9.733219 CCATAGTTTTTAACTTTTTACGGACAA 57.267 29.630 0.00 0.00 42.81 3.18
1422 1430 8.351461 CCCATAGTTTTTAACTTTTTACGGACA 58.649 33.333 0.00 0.00 42.81 4.02
1423 1431 8.567104 TCCCATAGTTTTTAACTTTTTACGGAC 58.433 33.333 0.00 0.00 42.81 4.79
1424 1432 8.688747 TCCCATAGTTTTTAACTTTTTACGGA 57.311 30.769 0.00 0.00 42.81 4.69
1425 1433 8.785946 TCTCCCATAGTTTTTAACTTTTTACGG 58.214 33.333 0.00 0.00 42.81 4.02
1433 1441 8.971073 CCAATCAATCTCCCATAGTTTTTAACT 58.029 33.333 0.00 0.00 45.40 2.24
1434 1442 8.966868 TCCAATCAATCTCCCATAGTTTTTAAC 58.033 33.333 0.00 0.00 0.00 2.01
1435 1443 9.189156 CTCCAATCAATCTCCCATAGTTTTTAA 57.811 33.333 0.00 0.00 0.00 1.52
1436 1444 7.285401 GCTCCAATCAATCTCCCATAGTTTTTA 59.715 37.037 0.00 0.00 0.00 1.52
1437 1445 6.097412 GCTCCAATCAATCTCCCATAGTTTTT 59.903 38.462 0.00 0.00 0.00 1.94
1438 1446 5.595952 GCTCCAATCAATCTCCCATAGTTTT 59.404 40.000 0.00 0.00 0.00 2.43
1439 1447 5.136105 GCTCCAATCAATCTCCCATAGTTT 58.864 41.667 0.00 0.00 0.00 2.66
1440 1448 4.166725 TGCTCCAATCAATCTCCCATAGTT 59.833 41.667 0.00 0.00 0.00 2.24
1441 1449 3.718434 TGCTCCAATCAATCTCCCATAGT 59.282 43.478 0.00 0.00 0.00 2.12
1442 1450 4.070716 GTGCTCCAATCAATCTCCCATAG 58.929 47.826 0.00 0.00 0.00 2.23
1443 1451 3.181440 GGTGCTCCAATCAATCTCCCATA 60.181 47.826 0.00 0.00 0.00 2.74
1444 1452 2.423947 GGTGCTCCAATCAATCTCCCAT 60.424 50.000 0.00 0.00 0.00 4.00
1445 1453 1.064463 GGTGCTCCAATCAATCTCCCA 60.064 52.381 0.00 0.00 0.00 4.37
1446 1454 1.213926 AGGTGCTCCAATCAATCTCCC 59.786 52.381 7.70 0.00 35.89 4.30
1447 1455 2.295885 CAGGTGCTCCAATCAATCTCC 58.704 52.381 7.70 0.00 35.89 3.71
1453 1461 2.747460 GCGCAGGTGCTCCAATCA 60.747 61.111 0.30 0.00 39.32 2.57
1497 1505 7.230108 TCACTCATCAAATTTTTCTCTTCTGCT 59.770 33.333 0.00 0.00 0.00 4.24
1500 1508 8.915057 TCTCACTCATCAAATTTTTCTCTTCT 57.085 30.769 0.00 0.00 0.00 2.85
1567 1575 3.853330 CCATTGCACTCGCGACCG 61.853 66.667 3.71 0.00 42.97 4.79
1569 1577 1.154413 CAACCATTGCACTCGCGAC 60.154 57.895 3.71 0.00 42.97 5.19
1620 1628 0.322906 CCCTCTCCTTGGCCTTTGTC 60.323 60.000 3.32 0.00 0.00 3.18
1621 1629 1.770324 CCCTCTCCTTGGCCTTTGT 59.230 57.895 3.32 0.00 0.00 2.83
1637 1645 5.705609 TTTGATCTTGTTAACTCTTGCCC 57.294 39.130 7.22 0.00 0.00 5.36
1685 1694 4.375272 CAATTCTGACTGAGCCGTGATAT 58.625 43.478 0.00 0.00 0.00 1.63
1692 1701 2.160417 CGTTTCCAATTCTGACTGAGCC 59.840 50.000 0.00 0.00 0.00 4.70
1693 1702 3.067106 TCGTTTCCAATTCTGACTGAGC 58.933 45.455 0.00 0.00 0.00 4.26
1694 1703 4.310769 AGTCGTTTCCAATTCTGACTGAG 58.689 43.478 0.00 0.00 35.52 3.35
1696 1705 4.395581 CAGTCGTTTCCAATTCTGACTG 57.604 45.455 5.86 5.86 44.83 3.51
1742 1751 2.532250 TGACTCCTCCTATGCTGTGA 57.468 50.000 0.00 0.00 0.00 3.58
1747 1756 0.107643 GGCCTTGACTCCTCCTATGC 59.892 60.000 0.00 0.00 0.00 3.14
1750 1759 1.381327 CCGGCCTTGACTCCTCCTA 60.381 63.158 0.00 0.00 0.00 2.94
1755 1764 2.593956 AACCTCCGGCCTTGACTCC 61.594 63.158 0.00 0.00 0.00 3.85
1760 1769 1.966451 GTGACAACCTCCGGCCTTG 60.966 63.158 0.00 0.00 0.00 3.61
1804 1813 5.300752 ACAGAGACGTTCATTCATCTGTTT 58.699 37.500 0.01 0.00 43.52 2.83
1830 1839 3.209410 CACCTCCATATCTTTGACTGGC 58.791 50.000 0.00 0.00 0.00 4.85
1836 1845 4.712476 CCTTCTCCACCTCCATATCTTTG 58.288 47.826 0.00 0.00 0.00 2.77
1838 1847 2.708325 GCCTTCTCCACCTCCATATCTT 59.292 50.000 0.00 0.00 0.00 2.40
1876 1885 1.384222 GGCCCTGGCGATTTGTTAGG 61.384 60.000 1.37 0.00 43.06 2.69
1983 1992 3.106986 ATTCTCCGGCATGACCCCG 62.107 63.158 0.00 0.00 45.17 5.73
2010 2019 1.806542 GGTATGAGCACCAACACAGTG 59.193 52.381 0.00 0.00 38.55 3.66
2012 2021 2.183478 TGGTATGAGCACCAACACAG 57.817 50.000 0.00 0.00 45.65 3.66
2062 2071 6.096141 ACAATGCATAATGAAATTGGTCCGTA 59.904 34.615 0.00 0.00 36.99 4.02
2065 2074 5.754890 GGACAATGCATAATGAAATTGGTCC 59.245 40.000 0.00 0.00 36.99 4.46
2066 2075 6.576185 AGGACAATGCATAATGAAATTGGTC 58.424 36.000 0.00 0.00 36.99 4.02
2105 2114 4.041567 TCAACCTAAGAGCAATCACCTTCA 59.958 41.667 0.00 0.00 0.00 3.02
2109 2118 3.935828 GTCTCAACCTAAGAGCAATCACC 59.064 47.826 0.00 0.00 33.15 4.02
2125 2134 9.753674 AATTATTTCCTCAATAACAGGTCTCAA 57.246 29.630 0.00 0.00 39.66 3.02
2132 2141 9.512435 CTTCTGCAATTATTTCCTCAATAACAG 57.488 33.333 0.00 0.00 39.66 3.16
2137 2146 8.125978 TGTTCTTCTGCAATTATTTCCTCAAT 57.874 30.769 0.00 0.00 0.00 2.57
2143 2152 7.383300 AGCACTTTGTTCTTCTGCAATTATTTC 59.617 33.333 0.00 0.00 0.00 2.17
2178 2188 5.730550 ACATTGTCTGTAATAAGCCTTCGA 58.269 37.500 0.00 0.00 35.91 3.71
2179 2189 7.534085 TTACATTGTCTGTAATAAGCCTTCG 57.466 36.000 0.00 0.00 43.72 3.79
2190 2200 4.816392 ACGCTGTGATTACATTGTCTGTA 58.184 39.130 0.00 0.00 39.39 2.74
2209 2219 4.248859 AGATAATGGATGCACTCATACGC 58.751 43.478 4.32 0.00 36.28 4.42
2211 2221 7.388776 TGCTTTAGATAATGGATGCACTCATAC 59.611 37.037 4.32 1.27 34.01 2.39
2229 2239 4.583073 GTCTTCCCCTTTTTGTGCTTTAGA 59.417 41.667 0.00 0.00 0.00 2.10
2235 2245 0.313987 CCGTCTTCCCCTTTTTGTGC 59.686 55.000 0.00 0.00 0.00 4.57
2247 2257 2.174319 GGCGCATTCTCCCGTCTTC 61.174 63.158 10.83 0.00 0.00 2.87
2249 2259 2.650813 GATGGCGCATTCTCCCGTCT 62.651 60.000 10.83 0.00 33.00 4.18
2252 2262 1.375853 TTTGATGGCGCATTCTCCCG 61.376 55.000 10.83 0.00 0.00 5.14
2295 2305 1.784358 AATATTCCCACTCGACCCGA 58.216 50.000 0.00 0.00 0.00 5.14
2297 2307 3.134081 TCTCAAATATTCCCACTCGACCC 59.866 47.826 0.00 0.00 0.00 4.46
2306 2316 5.766670 TGCATCATCTGTCTCAAATATTCCC 59.233 40.000 0.00 0.00 0.00 3.97
2360 2370 7.183580 GATTGAATACAAGCCATCACTCTAC 57.816 40.000 0.00 0.00 39.46 2.59
2377 2387 3.118112 ACTGAGAATGAGGCGGATTGAAT 60.118 43.478 0.00 0.00 0.00 2.57
2385 2395 3.721625 TCGAACTGAGAATGAGGCG 57.278 52.632 0.00 0.00 0.00 5.52
2404 2414 8.926715 AAAGTTTCAGAGAAAACACCATTAAC 57.073 30.769 2.73 0.00 40.77 2.01
2407 2417 9.936759 TTTAAAAGTTTCAGAGAAAACACCATT 57.063 25.926 2.73 0.00 40.77 3.16
2411 2421 8.033038 AGGGTTTAAAAGTTTCAGAGAAAACAC 58.967 33.333 0.00 0.00 40.77 3.32


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

AutoCloner maintained by Alex Coulton.