Multiple sequence alignment - TraesCS4A01G277400

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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 TraesCS4A01G277400 chr4A 100.000 2282 0 0 1 2282 585394987 585397268 0.000000e+00 4215.0
1 TraesCS4A01G277400 chr4A 91.636 550 13 6 1 518 708549334 708549882 0.000000e+00 730.0
2 TraesCS4A01G277400 chr4D 85.547 941 63 30 920 1813 15373255 15372341 0.000000e+00 917.0
3 TraesCS4A01G277400 chr4D 90.892 527 28 10 1774 2280 15372338 15371812 0.000000e+00 689.0
4 TraesCS4A01G277400 chr4D 91.346 104 4 3 615 713 15373576 15373473 1.100000e-28 137.0
5 TraesCS4A01G277400 chr4D 89.000 100 5 3 516 615 15373719 15373626 3.980000e-23 119.0
6 TraesCS4A01G277400 chr1B 96.075 535 4 1 1 518 150532375 150532909 0.000000e+00 856.0
7 TraesCS4A01G277400 chr7A 94.173 532 14 1 1 515 652699762 652700293 0.000000e+00 795.0
8 TraesCS4A01G277400 chr2D 93.321 524 16 3 1 506 114544130 114543608 0.000000e+00 756.0
9 TraesCS4A01G277400 chr4B 83.969 655 45 25 1656 2280 25889673 25889049 7.070000e-160 573.0
10 TraesCS4A01G277400 chr4B 85.972 499 42 8 44 515 433092534 433092037 2.020000e-140 508.0
11 TraesCS4A01G277400 chr4B 80.210 763 62 29 892 1623 25890607 25889903 7.330000e-135 490.0
12 TraesCS4A01G277400 chr4B 94.915 59 3 0 752 810 25890807 25890749 2.410000e-15 93.5
13 TraesCS4A01G277400 chr3B 75.093 269 58 8 254 518 763733134 763732871 1.430000e-22 117.0
14 TraesCS4A01G277400 chr6B 75.097 257 54 10 268 520 37053422 37053172 6.660000e-21 111.0


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 TraesCS4A01G277400 chr4A 585394987 585397268 2281 False 4215.0 4215 100.000000 1 2282 1 chr4A.!!$F1 2281
1 TraesCS4A01G277400 chr4A 708549334 708549882 548 False 730.0 730 91.636000 1 518 1 chr4A.!!$F2 517
2 TraesCS4A01G277400 chr4D 15371812 15373719 1907 True 465.5 917 89.196250 516 2280 4 chr4D.!!$R1 1764
3 TraesCS4A01G277400 chr1B 150532375 150532909 534 False 856.0 856 96.075000 1 518 1 chr1B.!!$F1 517
4 TraesCS4A01G277400 chr7A 652699762 652700293 531 False 795.0 795 94.173000 1 515 1 chr7A.!!$F1 514
5 TraesCS4A01G277400 chr2D 114543608 114544130 522 True 756.0 756 93.321000 1 506 1 chr2D.!!$R1 505
6 TraesCS4A01G277400 chr4B 25889049 25890807 1758 True 385.5 573 86.364667 752 2280 3 chr4B.!!$R2 1528

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
738 825 0.027455 CGCACACTTTCAGAACGCAA 59.973 50.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 2292 0.036952 CTCGATGCTGGTTGTCTGGT 60.037 55.0 0.0 0.0 0.0 4.0 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
103 104 2.994186 TTCGTACCTCTTAATGGGCC 57.006 50.000 0.00 0.00 0.00 5.80
157 158 3.257561 CATCTTCTCGCACGCCGG 61.258 66.667 0.00 0.00 37.59 6.13
518 550 0.719465 CACAAACTCCGCGTCCATAC 59.281 55.000 4.92 0.00 0.00 2.39
519 551 0.319083 ACAAACTCCGCGTCCATACA 59.681 50.000 4.92 0.00 0.00 2.29
520 552 1.270412 ACAAACTCCGCGTCCATACAA 60.270 47.619 4.92 0.00 0.00 2.41
521 553 2.006888 CAAACTCCGCGTCCATACAAT 58.993 47.619 4.92 0.00 0.00 2.71
522 554 2.396590 AACTCCGCGTCCATACAATT 57.603 45.000 4.92 0.00 0.00 2.32
523 555 1.651987 ACTCCGCGTCCATACAATTG 58.348 50.000 4.92 3.24 0.00 2.32
526 558 1.083489 CCGCGTCCATACAATTGTGT 58.917 50.000 21.42 12.00 42.09 3.72
532 564 5.220586 CGCGTCCATACAATTGTGTATTTCT 60.221 40.000 21.42 0.00 46.74 2.52
533 565 6.551736 GCGTCCATACAATTGTGTATTTCTT 58.448 36.000 21.42 0.00 46.74 2.52
588 620 2.109799 CATAGAGCCAGCCCACCG 59.890 66.667 0.00 0.00 0.00 4.94
589 621 3.866582 ATAGAGCCAGCCCACCGC 61.867 66.667 0.00 0.00 37.98 5.68
727 814 4.017877 GAGCAAGCGCGCACACTT 62.018 61.111 35.10 16.37 45.49 3.16
728 815 3.527360 GAGCAAGCGCGCACACTTT 62.527 57.895 35.10 15.93 45.49 2.66
729 816 3.093449 GCAAGCGCGCACACTTTC 61.093 61.111 35.10 9.46 0.00 2.62
730 817 2.327592 CAAGCGCGCACACTTTCA 59.672 55.556 35.10 0.00 0.00 2.69
731 818 1.723542 CAAGCGCGCACACTTTCAG 60.724 57.895 35.10 7.55 0.00 3.02
732 819 1.887242 AAGCGCGCACACTTTCAGA 60.887 52.632 35.10 0.00 0.00 3.27
733 820 1.436195 AAGCGCGCACACTTTCAGAA 61.436 50.000 35.10 0.00 0.00 3.02
734 821 1.722507 GCGCGCACACTTTCAGAAC 60.723 57.895 29.10 0.00 0.00 3.01
735 822 1.437089 CGCGCACACTTTCAGAACG 60.437 57.895 8.75 0.00 0.00 3.95
736 823 1.722507 GCGCACACTTTCAGAACGC 60.723 57.895 0.30 0.00 37.93 4.84
737 824 1.641140 CGCACACTTTCAGAACGCA 59.359 52.632 0.00 0.00 0.00 5.24
738 825 0.027455 CGCACACTTTCAGAACGCAA 59.973 50.000 0.00 0.00 0.00 4.85
739 826 1.334059 CGCACACTTTCAGAACGCAAT 60.334 47.619 0.00 0.00 0.00 3.56
740 827 2.046313 GCACACTTTCAGAACGCAATG 58.954 47.619 0.00 0.00 0.00 2.82
741 828 2.046313 CACACTTTCAGAACGCAATGC 58.954 47.619 0.00 0.00 0.00 3.56
742 829 1.001378 ACACTTTCAGAACGCAATGCC 60.001 47.619 0.00 0.00 0.00 4.40
743 830 1.001487 CACTTTCAGAACGCAATGCCA 60.001 47.619 0.00 0.00 0.00 4.92
744 831 1.267806 ACTTTCAGAACGCAATGCCAG 59.732 47.619 0.00 0.00 0.00 4.85
745 832 0.597568 TTTCAGAACGCAATGCCAGG 59.402 50.000 0.00 0.00 0.00 4.45
746 833 1.865788 TTCAGAACGCAATGCCAGGC 61.866 55.000 3.66 3.66 0.00 4.85
779 866 1.976474 GGCAACATTTCCCAGGCGA 60.976 57.895 0.00 0.00 0.00 5.54
780 867 1.212751 GCAACATTTCCCAGGCGAC 59.787 57.895 0.00 0.00 0.00 5.19
810 899 2.203015 ACGCCACATGGTATCCGC 60.203 61.111 0.00 0.00 37.57 5.54
815 907 0.747644 CCACATGGTATCCGCAAGCA 60.748 55.000 0.00 0.00 0.00 3.91
816 908 1.093972 CACATGGTATCCGCAAGCAA 58.906 50.000 0.00 0.00 0.00 3.91
825 917 2.026014 CGCAAGCAAAGCAACGGT 59.974 55.556 0.00 0.00 0.00 4.83
826 918 2.295052 CGCAAGCAAAGCAACGGTG 61.295 57.895 0.00 0.00 0.00 4.94
827 919 1.950630 GCAAGCAAAGCAACGGTGG 60.951 57.895 0.90 0.00 0.00 4.61
829 921 3.150647 AAGCAAAGCAACGGTGGCC 62.151 57.895 0.90 0.00 0.00 5.36
830 922 3.605664 GCAAAGCAACGGTGGCCT 61.606 61.111 3.32 0.00 0.00 5.19
831 923 2.336088 CAAAGCAACGGTGGCCTG 59.664 61.111 3.32 0.00 0.00 4.85
832 924 2.912025 AAAGCAACGGTGGCCTGG 60.912 61.111 3.32 0.00 0.00 4.45
857 949 0.394762 ACGGTCGCCACCTGATACTA 60.395 55.000 0.00 0.00 41.17 1.82
858 950 0.030369 CGGTCGCCACCTGATACTAC 59.970 60.000 0.00 0.00 41.17 2.73
859 951 1.400737 GGTCGCCACCTGATACTACT 58.599 55.000 0.00 0.00 40.00 2.57
868 960 3.821600 CACCTGATACTACTGATAGGCGT 59.178 47.826 0.00 0.00 32.08 5.68
871 963 3.821600 CTGATACTACTGATAGGCGTGGT 59.178 47.826 0.00 0.00 32.08 4.16
888 1005 4.994471 TCACCACGCAGCAGCAGG 62.994 66.667 0.82 4.92 42.27 4.85
1255 1522 3.511595 CGCCGCCAGCAACATCAT 61.512 61.111 0.00 0.00 44.04 2.45
1272 1539 1.065199 TCATCATCCAAGGCCAGTGAC 60.065 52.381 5.01 0.00 0.00 3.67
1290 1557 3.746492 GTGACGCCAAATAGTTCTTCTGT 59.254 43.478 0.00 0.00 0.00 3.41
1293 1560 6.092259 GTGACGCCAAATAGTTCTTCTGTATT 59.908 38.462 0.00 0.00 0.00 1.89
1295 1562 6.407202 ACGCCAAATAGTTCTTCTGTATTCT 58.593 36.000 0.00 0.00 0.00 2.40
1296 1563 6.879458 ACGCCAAATAGTTCTTCTGTATTCTT 59.121 34.615 0.00 0.00 0.00 2.52
1297 1564 7.064728 ACGCCAAATAGTTCTTCTGTATTCTTC 59.935 37.037 0.00 0.00 0.00 2.87
1299 1566 7.201741 GCCAAATAGTTCTTCTGTATTCTTCCC 60.202 40.741 0.00 0.00 0.00 3.97
1300 1567 7.283354 CCAAATAGTTCTTCTGTATTCTTCCCC 59.717 40.741 0.00 0.00 0.00 4.81
1303 1570 4.852697 AGTTCTTCTGTATTCTTCCCCCTT 59.147 41.667 0.00 0.00 0.00 3.95
1304 1571 4.844349 TCTTCTGTATTCTTCCCCCTTG 57.156 45.455 0.00 0.00 0.00 3.61
1306 1573 5.347124 TCTTCTGTATTCTTCCCCCTTGTA 58.653 41.667 0.00 0.00 0.00 2.41
1307 1574 5.425539 TCTTCTGTATTCTTCCCCCTTGTAG 59.574 44.000 0.00 0.00 0.00 2.74
1308 1575 4.695606 TCTGTATTCTTCCCCCTTGTAGT 58.304 43.478 0.00 0.00 0.00 2.73
1310 1577 5.045869 TCTGTATTCTTCCCCCTTGTAGTTG 60.046 44.000 0.00 0.00 0.00 3.16
1311 1578 4.600111 TGTATTCTTCCCCCTTGTAGTTGT 59.400 41.667 0.00 0.00 0.00 3.32
1312 1579 3.502123 TTCTTCCCCCTTGTAGTTGTG 57.498 47.619 0.00 0.00 0.00 3.33
1313 1580 1.702957 TCTTCCCCCTTGTAGTTGTGG 59.297 52.381 0.00 0.00 0.00 4.17
1314 1581 0.774908 TTCCCCCTTGTAGTTGTGGG 59.225 55.000 0.00 0.00 39.37 4.61
1316 1583 1.767692 CCCCTTGTAGTTGTGGGCT 59.232 57.895 0.00 0.00 38.37 5.19
1317 1584 0.988832 CCCCTTGTAGTTGTGGGCTA 59.011 55.000 0.00 0.00 38.37 3.93
1318 1585 1.065418 CCCCTTGTAGTTGTGGGCTAG 60.065 57.143 0.00 0.00 38.37 3.42
1319 1586 1.679032 CCCTTGTAGTTGTGGGCTAGC 60.679 57.143 6.04 6.04 32.49 3.42
1320 1587 1.003118 CCTTGTAGTTGTGGGCTAGCA 59.997 52.381 18.24 0.00 0.00 3.49
1336 1603 4.294416 CTAGCAGTAGCAATGTACGAGT 57.706 45.455 0.00 0.00 45.49 4.18
1337 1604 5.419760 CTAGCAGTAGCAATGTACGAGTA 57.580 43.478 0.00 0.00 45.49 2.59
1338 1605 4.294416 AGCAGTAGCAATGTACGAGTAG 57.706 45.455 0.00 0.00 45.49 2.57
1339 1606 2.789893 GCAGTAGCAATGTACGAGTAGC 59.210 50.000 0.00 0.00 41.58 3.58
1340 1607 3.733988 GCAGTAGCAATGTACGAGTAGCA 60.734 47.826 0.00 0.00 41.58 3.49
1341 1608 4.611943 CAGTAGCAATGTACGAGTAGCAT 58.388 43.478 0.00 0.00 0.00 3.79
1342 1609 5.758924 CAGTAGCAATGTACGAGTAGCATA 58.241 41.667 0.00 0.00 0.00 3.14
1343 1610 6.206498 CAGTAGCAATGTACGAGTAGCATAA 58.794 40.000 0.00 0.00 0.00 1.90
1344 1611 6.863645 CAGTAGCAATGTACGAGTAGCATAAT 59.136 38.462 0.00 0.00 0.00 1.28
1345 1612 7.382488 CAGTAGCAATGTACGAGTAGCATAATT 59.618 37.037 0.00 0.00 0.00 1.40
1346 1613 7.926555 AGTAGCAATGTACGAGTAGCATAATTT 59.073 33.333 0.00 0.00 0.00 1.82
1347 1614 7.178712 AGCAATGTACGAGTAGCATAATTTC 57.821 36.000 0.00 0.00 0.00 2.17
1348 1615 6.202954 AGCAATGTACGAGTAGCATAATTTCC 59.797 38.462 0.00 0.00 0.00 3.13
1401 1702 3.692576 CACTAGTACTGCCGTCATGTAC 58.307 50.000 5.39 0.00 37.42 2.90
1404 1709 2.955614 AGTACTGCCGTCATGTACAAC 58.044 47.619 0.00 0.00 39.02 3.32
1426 1731 3.423539 AGAATGTAACCAAGCAGCTGA 57.576 42.857 20.43 0.00 0.00 4.26
1438 1743 2.264124 CAGCTGAATGCCAAGCTGT 58.736 52.632 8.42 0.00 46.67 4.40
1549 1854 6.622427 ATTTTAGCACTGGTAGTTACTCCT 57.378 37.500 0.00 0.00 0.00 3.69
1552 1857 3.240302 AGCACTGGTAGTTACTCCTTGT 58.760 45.455 0.00 0.00 0.00 3.16
1561 1866 6.104665 GGTAGTTACTCCTTGTGTTCCATAC 58.895 44.000 0.00 0.00 0.00 2.39
1565 1870 4.974645 ACTCCTTGTGTTCCATACTTGA 57.025 40.909 0.00 0.00 0.00 3.02
1582 1887 7.148239 CCATACTTGAAGTTCTATGTTTGACCC 60.148 40.741 1.97 0.00 0.00 4.46
1652 1957 5.651530 ACGATCCAGAGTGTAAACTGTATG 58.348 41.667 0.00 0.00 32.93 2.39
1685 2189 0.901580 AATGGCCAACAGGAAGCTGG 60.902 55.000 10.96 0.00 36.52 4.85
1772 2280 1.474478 AGCTATGGCCTATCGATGTCG 59.526 52.381 8.54 0.00 39.73 4.35
1780 2288 2.480416 GCCTATCGATGTCGGATGATCC 60.480 54.545 8.54 0.08 40.29 3.36
1801 2357 0.518636 CAACCAGACAACCAGCATCG 59.481 55.000 0.00 0.00 0.00 3.84
1852 2408 3.117794 CACTTGTCGTAACGGAACTGAA 58.882 45.455 0.00 0.00 0.00 3.02
1864 2437 7.384115 CGTAACGGAACTGAATGATATTACCAT 59.616 37.037 0.00 0.00 0.00 3.55
1889 2462 4.943142 TTTAAAGTACGGTATTTGGGCG 57.057 40.909 0.00 0.00 0.00 6.13
1932 2506 9.799223 AACACCCCATCTACCAGTATATATATT 57.201 33.333 0.00 0.00 0.00 1.28
1960 2542 4.758688 TGAGAAATATCACGTGCACATCT 58.241 39.130 18.64 10.26 0.00 2.90
1961 2543 4.567959 TGAGAAATATCACGTGCACATCTG 59.432 41.667 18.64 8.68 0.00 2.90
1977 2559 2.380084 TCTGTCACCACCGATTAAGC 57.620 50.000 0.00 0.00 0.00 3.09
2001 2583 0.033601 AACAACCACCAGCACTCCAA 60.034 50.000 0.00 0.00 0.00 3.53
2009 2591 1.302033 CAGCACTCCAAGCGAGGTT 60.302 57.895 0.00 0.00 43.57 3.50
2037 2619 4.268644 ACAATAGATTCACACGCGAAGATG 59.731 41.667 15.93 2.09 0.00 2.90
2041 2623 0.602638 TTCACACGCGAAGATGGCTT 60.603 50.000 15.93 0.00 36.96 4.35
2129 2711 4.272748 GCTTTGAGACGGTAAACTGAGTTT 59.727 41.667 15.57 15.57 39.24 2.66
2222 2804 1.354031 TGCTATTCTCCCCTGCAACAA 59.646 47.619 0.00 0.00 0.00 2.83
2271 2853 7.059202 ACCAAAAATTGAGAAGAGCAGAATT 57.941 32.000 0.00 0.00 0.00 2.17
2280 2862 7.426929 TGAGAAGAGCAGAATTAAAACACTC 57.573 36.000 0.00 0.00 0.00 3.51
2281 2863 7.220030 TGAGAAGAGCAGAATTAAAACACTCT 58.780 34.615 0.00 0.00 34.61 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 3.242220 CGAAGATGGAGTTCTTTGATGCG 60.242 47.826 0.00 0.00 38.79 4.73
157 158 2.586357 GGCAATCTCGGCGACCTC 60.586 66.667 4.99 0.00 0.00 3.85
532 564 6.228258 ACAGGAGCACGTTTCTTTATCTAAA 58.772 36.000 0.00 0.00 0.00 1.85
533 565 5.790593 ACAGGAGCACGTTTCTTTATCTAA 58.209 37.500 0.00 0.00 0.00 2.10
710 797 3.527360 AAAGTGTGCGCGCTTGCTC 62.527 57.895 33.29 20.87 43.87 4.26
713 800 1.723542 CTGAAAGTGTGCGCGCTTG 60.724 57.895 33.29 10.56 43.87 4.01
714 801 1.436195 TTCTGAAAGTGTGCGCGCTT 61.436 50.000 33.29 19.97 46.30 4.68
715 802 1.887242 TTCTGAAAGTGTGCGCGCT 60.887 52.632 33.29 10.95 36.97 5.92
716 803 1.722507 GTTCTGAAAGTGTGCGCGC 60.723 57.895 27.26 27.26 33.76 6.86
717 804 1.437089 CGTTCTGAAAGTGTGCGCG 60.437 57.895 0.00 0.00 33.76 6.86
718 805 1.722507 GCGTTCTGAAAGTGTGCGC 60.723 57.895 0.00 0.00 35.03 6.09
719 806 0.027455 TTGCGTTCTGAAAGTGTGCG 59.973 50.000 5.29 0.00 33.76 5.34
722 809 1.001378 GGCATTGCGTTCTGAAAGTGT 60.001 47.619 1.91 0.00 33.76 3.55
724 811 1.267806 CTGGCATTGCGTTCTGAAAGT 59.732 47.619 1.91 0.00 33.76 2.66
725 812 1.401931 CCTGGCATTGCGTTCTGAAAG 60.402 52.381 1.91 0.00 0.00 2.62
726 813 0.597568 CCTGGCATTGCGTTCTGAAA 59.402 50.000 1.91 0.00 0.00 2.69
727 814 1.865788 GCCTGGCATTGCGTTCTGAA 61.866 55.000 15.17 0.00 0.00 3.02
728 815 2.334946 GCCTGGCATTGCGTTCTGA 61.335 57.895 15.17 0.00 0.00 3.27
729 816 2.180017 GCCTGGCATTGCGTTCTG 59.820 61.111 15.17 0.00 0.00 3.02
730 817 3.434319 CGCCTGGCATTGCGTTCT 61.434 61.111 20.29 0.00 45.43 3.01
735 822 3.207669 CTCCTCGCCTGGCATTGC 61.208 66.667 20.29 0.00 0.00 3.56
736 823 3.207669 GCTCCTCGCCTGGCATTG 61.208 66.667 20.29 7.51 0.00 2.82
779 866 1.371558 GGCGTCCCTTTCTCTGTGT 59.628 57.895 0.00 0.00 0.00 3.72
780 867 0.951040 GTGGCGTCCCTTTCTCTGTG 60.951 60.000 0.00 0.00 0.00 3.66
810 899 1.950630 GCCACCGTTGCTTTGCTTG 60.951 57.895 0.00 0.00 0.00 4.01
815 907 2.912025 CCAGGCCACCGTTGCTTT 60.912 61.111 5.01 0.00 0.00 3.51
844 936 3.056465 GCCTATCAGTAGTATCAGGTGGC 60.056 52.174 0.00 0.00 0.00 5.01
849 941 3.821600 ACCACGCCTATCAGTAGTATCAG 59.178 47.826 0.00 0.00 0.00 2.90
857 949 0.902984 TGGTGACCACGCCTATCAGT 60.903 55.000 0.00 0.00 45.89 3.41
858 950 0.460284 GTGGTGACCACGCCTATCAG 60.460 60.000 20.19 0.00 44.95 2.90
859 951 1.594833 GTGGTGACCACGCCTATCA 59.405 57.895 20.19 0.00 44.95 2.15
871 963 4.994471 CCTGCTGCTGCGTGGTGA 62.994 66.667 11.21 0.00 43.34 4.02
888 1005 2.155279 GACAAAAGAGGGGTCAAGAGC 58.845 52.381 0.00 0.00 0.00 4.09
977 1178 4.093952 CTCAACCAGCCGCGCAAG 62.094 66.667 8.75 0.00 43.44 4.01
984 1185 2.437359 ATCAGCGCTCAACCAGCC 60.437 61.111 7.13 0.00 46.74 4.85
987 1188 1.078918 CTCCATCAGCGCTCAACCA 60.079 57.895 7.13 0.00 0.00 3.67
988 1189 0.179062 ATCTCCATCAGCGCTCAACC 60.179 55.000 7.13 0.00 0.00 3.77
990 1191 0.179065 CCATCTCCATCAGCGCTCAA 60.179 55.000 7.13 0.00 0.00 3.02
991 1192 1.044790 TCCATCTCCATCAGCGCTCA 61.045 55.000 7.13 0.00 0.00 4.26
1092 1356 2.516589 CGCCACGATCACCACGATG 61.517 63.158 0.00 0.00 33.17 3.84
1255 1522 1.296392 CGTCACTGGCCTTGGATGA 59.704 57.895 3.32 0.00 0.00 2.92
1272 1539 6.910536 AGAATACAGAAGAACTATTTGGCG 57.089 37.500 0.00 0.00 0.00 5.69
1290 1557 4.018779 CCACAACTACAAGGGGGAAGAATA 60.019 45.833 0.00 0.00 0.00 1.75
1293 1560 1.702957 CCACAACTACAAGGGGGAAGA 59.297 52.381 0.00 0.00 0.00 2.87
1295 1562 0.774908 CCCACAACTACAAGGGGGAA 59.225 55.000 0.00 0.00 37.80 3.97
1296 1563 1.785353 GCCCACAACTACAAGGGGGA 61.785 60.000 3.44 0.00 41.75 4.81
1297 1564 1.304134 GCCCACAACTACAAGGGGG 60.304 63.158 0.00 0.00 41.75 5.40
1299 1566 1.679032 GCTAGCCCACAACTACAAGGG 60.679 57.143 2.29 0.00 44.37 3.95
1300 1567 1.003118 TGCTAGCCCACAACTACAAGG 59.997 52.381 13.29 0.00 0.00 3.61
1303 1570 1.348064 ACTGCTAGCCCACAACTACA 58.652 50.000 13.29 0.00 0.00 2.74
1304 1571 2.738964 GCTACTGCTAGCCCACAACTAC 60.739 54.545 13.29 0.00 39.79 2.73
1306 1573 0.250513 GCTACTGCTAGCCCACAACT 59.749 55.000 13.29 0.00 39.79 3.16
1307 1574 0.036388 TGCTACTGCTAGCCCACAAC 60.036 55.000 13.29 0.00 44.45 3.32
1308 1575 0.690192 TTGCTACTGCTAGCCCACAA 59.310 50.000 13.29 6.94 44.45 3.33
1310 1577 1.303309 CATTGCTACTGCTAGCCCAC 58.697 55.000 13.29 0.00 44.45 4.61
1311 1578 0.911769 ACATTGCTACTGCTAGCCCA 59.088 50.000 13.29 0.00 44.45 5.36
1312 1579 2.484889 GTACATTGCTACTGCTAGCCC 58.515 52.381 13.29 0.00 44.45 5.19
1313 1580 2.128035 CGTACATTGCTACTGCTAGCC 58.872 52.381 13.29 0.00 44.45 3.93
1314 1581 3.046390 CTCGTACATTGCTACTGCTAGC 58.954 50.000 8.10 8.10 45.19 3.42
1316 1583 4.261072 GCTACTCGTACATTGCTACTGCTA 60.261 45.833 0.00 0.00 40.48 3.49
1317 1584 3.489398 GCTACTCGTACATTGCTACTGCT 60.489 47.826 0.00 0.00 40.48 4.24
1318 1585 2.789893 GCTACTCGTACATTGCTACTGC 59.210 50.000 0.00 0.00 40.20 4.40
1319 1586 4.028852 TGCTACTCGTACATTGCTACTG 57.971 45.455 0.00 0.00 0.00 2.74
1320 1587 4.920640 ATGCTACTCGTACATTGCTACT 57.079 40.909 0.00 0.00 0.00 2.57
1331 1598 4.137116 TGCTGGAAATTATGCTACTCGT 57.863 40.909 0.00 0.00 0.00 4.18
1332 1599 5.928839 ACTATGCTGGAAATTATGCTACTCG 59.071 40.000 0.00 0.00 0.00 4.18
1333 1600 6.931281 TGACTATGCTGGAAATTATGCTACTC 59.069 38.462 0.00 0.00 0.00 2.59
1334 1601 6.830912 TGACTATGCTGGAAATTATGCTACT 58.169 36.000 0.00 0.00 0.00 2.57
1335 1602 7.678947 ATGACTATGCTGGAAATTATGCTAC 57.321 36.000 0.00 0.00 0.00 3.58
1336 1603 7.824289 GGTATGACTATGCTGGAAATTATGCTA 59.176 37.037 0.00 0.00 0.00 3.49
1337 1604 6.656693 GGTATGACTATGCTGGAAATTATGCT 59.343 38.462 0.00 0.00 0.00 3.79
1338 1605 6.430925 TGGTATGACTATGCTGGAAATTATGC 59.569 38.462 0.00 0.00 0.00 3.14
1339 1606 7.445096 TGTGGTATGACTATGCTGGAAATTATG 59.555 37.037 0.00 0.00 0.00 1.90
1340 1607 7.517320 TGTGGTATGACTATGCTGGAAATTAT 58.483 34.615 0.00 0.00 0.00 1.28
1341 1608 6.894682 TGTGGTATGACTATGCTGGAAATTA 58.105 36.000 0.00 0.00 0.00 1.40
1342 1609 5.754782 TGTGGTATGACTATGCTGGAAATT 58.245 37.500 0.00 0.00 0.00 1.82
1343 1610 5.372343 TGTGGTATGACTATGCTGGAAAT 57.628 39.130 0.00 0.00 0.00 2.17
1344 1611 4.835284 TGTGGTATGACTATGCTGGAAA 57.165 40.909 0.00 0.00 0.00 3.13
1345 1612 5.372343 AATGTGGTATGACTATGCTGGAA 57.628 39.130 0.00 0.00 0.00 3.53
1346 1613 5.838521 TCTAATGTGGTATGACTATGCTGGA 59.161 40.000 0.00 0.00 0.00 3.86
1347 1614 6.101650 TCTAATGTGGTATGACTATGCTGG 57.898 41.667 0.00 0.00 0.00 4.85
1348 1615 7.874528 TCATTCTAATGTGGTATGACTATGCTG 59.125 37.037 2.80 0.00 37.65 4.41
1401 1702 4.697352 AGCTGCTTGGTTACATTCTAGTTG 59.303 41.667 0.00 0.00 0.00 3.16
1404 1709 4.507710 TCAGCTGCTTGGTTACATTCTAG 58.492 43.478 9.47 0.00 0.00 2.43
1426 1731 2.804212 GCAAAGAACACAGCTTGGCATT 60.804 45.455 0.00 0.00 41.05 3.56
1437 1742 1.338020 CCCTTGTGGAGCAAAGAACAC 59.662 52.381 0.00 0.00 36.53 3.32
1438 1743 1.064017 ACCCTTGTGGAGCAAAGAACA 60.064 47.619 0.00 0.00 36.53 3.18
1561 1866 6.263168 ACTTGGGTCAAACATAGAACTTCAAG 59.737 38.462 0.00 0.00 34.64 3.02
1582 1887 8.369218 AGCCAAATTTAAAGATGTTTGACTTG 57.631 30.769 11.73 0.00 34.38 3.16
1623 1928 8.308931 ACAGTTTACACTCTGGATCGTTTATAA 58.691 33.333 0.00 0.00 36.17 0.98
1624 1929 7.833786 ACAGTTTACACTCTGGATCGTTTATA 58.166 34.615 0.00 0.00 36.17 0.98
1625 1930 6.698380 ACAGTTTACACTCTGGATCGTTTAT 58.302 36.000 0.00 0.00 36.17 1.40
1659 2163 1.425066 TCCTGTTGGCCATTTCTCTGT 59.575 47.619 6.09 0.00 0.00 3.41
1664 2168 1.067354 CAGCTTCCTGTTGGCCATTTC 60.067 52.381 6.09 0.54 34.31 2.17
1672 2176 1.975407 CAGGGCCAGCTTCCTGTTG 60.975 63.158 6.18 4.20 44.03 3.33
1685 2189 2.035442 GTTTCAGGTCGAGCAGGGC 61.035 63.158 18.15 0.00 0.00 5.19
1732 2240 3.573598 CTCATCGGTATCAGATGTCAGC 58.426 50.000 8.99 0.00 44.20 4.26
1772 2280 0.107703 TGTCTGGTTGCGGATCATCC 60.108 55.000 0.00 0.00 35.54 3.51
1780 2288 1.518056 ATGCTGGTTGTCTGGTTGCG 61.518 55.000 0.00 0.00 0.00 4.85
1781 2289 0.242017 GATGCTGGTTGTCTGGTTGC 59.758 55.000 0.00 0.00 0.00 4.17
1782 2290 0.518636 CGATGCTGGTTGTCTGGTTG 59.481 55.000 0.00 0.00 0.00 3.77
1783 2291 0.396435 TCGATGCTGGTTGTCTGGTT 59.604 50.000 0.00 0.00 0.00 3.67
1784 2292 0.036952 CTCGATGCTGGTTGTCTGGT 60.037 55.000 0.00 0.00 0.00 4.00
1864 2437 5.357596 GCCCAAATACCGTACTTTAAATCCA 59.642 40.000 0.00 0.00 0.00 3.41
1874 2447 1.708193 GGCACGCCCAAATACCGTAC 61.708 60.000 0.00 0.00 33.39 3.67
1889 2462 4.509970 GGGTGTTTGTAAATTCTTTGGCAC 59.490 41.667 0.00 0.00 0.00 5.01
1932 2506 5.290885 GTGCACGTGATATTTCTCATGTACA 59.709 40.000 22.23 0.00 42.15 2.90
1960 2542 2.779755 ATGCTTAATCGGTGGTGACA 57.220 45.000 0.00 0.00 38.70 3.58
1961 2543 3.527533 TGTATGCTTAATCGGTGGTGAC 58.472 45.455 0.00 0.00 0.00 3.67
1977 2559 2.226437 GAGTGCTGGTGGTTGTTGTATG 59.774 50.000 0.00 0.00 0.00 2.39
2001 2583 5.705441 TGAATCTATTGTTTCAAACCTCGCT 59.295 36.000 0.00 0.00 31.32 4.93
2009 2591 4.449405 TCGCGTGTGAATCTATTGTTTCAA 59.551 37.500 5.77 0.00 34.76 2.69
2041 2623 2.137528 TGAGTTGGTGACGGCCTCA 61.138 57.895 0.00 0.26 0.00 3.86
2074 2656 5.825593 ACTTTCCAGAATCTGACCTGTTA 57.174 39.130 12.53 0.00 32.44 2.41
2129 2711 8.107095 ACTGCTATCCAAAGGTAATGAACTTTA 58.893 33.333 0.00 0.00 35.32 1.85
2222 2804 4.108570 TCATACTGAACCCCTTGTATGGT 58.891 43.478 10.70 0.00 41.24 3.55


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

AutoCloner maintained by Alex Coulton.