Multiple sequence alignment - TraesCS4B01G306000

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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 TraesCS4B01G306000 chr4B 100.000 3624 0 0 1 3624 594867232 594870855 0.000000e+00 6693.0
1 TraesCS4B01G306000 chr7D 93.054 2030 99 18 1601 3624 78497910 78499903 0.000000e+00 2929.0
2 TraesCS4B01G306000 chr7D 92.102 747 29 12 738 1459 78497114 78497855 0.000000e+00 1026.0
3 TraesCS4B01G306000 chr7D 94.275 559 18 5 1 547 78496374 78496930 0.000000e+00 843.0
4 TraesCS4B01G306000 chr7D 94.643 112 5 1 573 684 78497015 78497125 4.810000e-39 172.0
5 TraesCS4B01G306000 chr4A 92.284 1970 120 22 1600 3560 679270504 679272450 0.000000e+00 2767.0
6 TraesCS4B01G306000 chr4A 92.910 818 39 8 738 1539 679269691 679270505 0.000000e+00 1171.0
7 TraesCS4B01G306000 chr4A 83.422 561 73 16 1 547 679268907 679269461 1.500000e-138 503.0
8 TraesCS4B01G306000 chr4D 93.556 1738 88 16 1496 3229 472511735 472513452 0.000000e+00 2567.0
9 TraesCS4B01G306000 chr4D 89.519 582 24 13 1 547 472501415 472501994 0.000000e+00 702.0
10 TraesCS4B01G306000 chr4D 94.985 339 14 3 933 1271 472511389 472511724 2.480000e-146 529.0
11 TraesCS4B01G306000 chr4D 82.196 337 40 14 3227 3560 472517365 472517684 4.610000e-69 272.0
12 TraesCS4B01G306000 chr2D 85.742 519 43 15 1048 1547 284553776 284553270 1.490000e-143 520.0
13 TraesCS4B01G306000 chr6D 84.557 395 31 14 1728 2105 467086400 467086019 7.390000e-97 364.0
14 TraesCS4B01G306000 chr6D 96.610 59 2 0 2484 2542 467085993 467085935 8.280000e-17 99.0
15 TraesCS4B01G306000 chr6D 84.536 97 7 4 2713 2801 467085944 467085848 4.980000e-14 89.8
16 TraesCS4B01G306000 chr6B 79.745 548 31 29 2382 2880 712263937 712263421 1.260000e-84 324.0


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 TraesCS4B01G306000 chr4B 594867232 594870855 3623 False 6693.000000 6693 100.000000 1 3624 1 chr4B.!!$F1 3623
1 TraesCS4B01G306000 chr7D 78496374 78499903 3529 False 1242.500000 2929 93.518500 1 3624 4 chr7D.!!$F1 3623
2 TraesCS4B01G306000 chr4A 679268907 679272450 3543 False 1480.333333 2767 89.538667 1 3560 3 chr4A.!!$F1 3559
3 TraesCS4B01G306000 chr4D 472511389 472517684 6295 False 1122.666667 2567 90.245667 933 3560 3 chr4D.!!$F2 2627
4 TraesCS4B01G306000 chr4D 472501415 472501994 579 False 702.000000 702 89.519000 1 547 1 chr4D.!!$F1 546
5 TraesCS4B01G306000 chr2D 284553270 284553776 506 True 520.000000 520 85.742000 1048 1547 1 chr2D.!!$R1 499
6 TraesCS4B01G306000 chr6B 712263421 712263937 516 True 324.000000 324 79.745000 2382 2880 1 chr6B.!!$R1 498

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
781 934 0.036388 TGGGCTAGAGAAAGCAACGG 60.036 55.0 0.0 0.0 44.64 4.44 F
1580 1792 0.179000 CCTGTGCCTCTATCCACACC 59.821 60.0 0.0 0.0 37.07 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1654 1866 0.548510 CTAGGGCTCAAAAGGGGGAG 59.451 60.000 0.00 0.00 0.00 4.30 R
3210 3484 1.004628 ACAACTGCATCTGGCCATGTA 59.995 47.619 5.51 0.32 43.89 2.29 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
27 28 6.491383 AGGTACAACCATAGTAACTCTCTCA 58.509 40.000 0.00 0.00 41.95 3.27
209 214 7.706179 TGCTCTATGTTTTCTTGTTTCCTTTTG 59.294 33.333 0.00 0.00 0.00 2.44
217 222 7.899178 TTTCTTGTTTCCTTTTGTTCCTTTC 57.101 32.000 0.00 0.00 0.00 2.62
320 367 7.456253 AGTTATCTTTTCACATGATTCGTTCG 58.544 34.615 0.00 0.00 0.00 3.95
563 642 4.130118 ACTGTCAATCTGGTCTTTGTGAC 58.870 43.478 0.00 0.00 44.63 3.67
622 775 8.596781 ATTACTCTACTTGTTCATCTGGTAGT 57.403 34.615 0.00 0.00 33.69 2.73
684 837 5.634118 TGACCATCCTGAAGTTTTCTGAAT 58.366 37.500 0.00 0.00 0.00 2.57
685 838 5.707298 TGACCATCCTGAAGTTTTCTGAATC 59.293 40.000 0.00 0.00 0.00 2.52
686 839 5.634118 ACCATCCTGAAGTTTTCTGAATCA 58.366 37.500 0.00 0.00 0.00 2.57
687 840 6.251471 ACCATCCTGAAGTTTTCTGAATCAT 58.749 36.000 0.00 0.00 0.00 2.45
688 841 6.376581 ACCATCCTGAAGTTTTCTGAATCATC 59.623 38.462 0.00 0.00 0.00 2.92
689 842 6.183360 CCATCCTGAAGTTTTCTGAATCATCC 60.183 42.308 0.00 0.00 0.00 3.51
690 843 5.256474 TCCTGAAGTTTTCTGAATCATCCC 58.744 41.667 0.00 0.00 0.00 3.85
691 844 4.400567 CCTGAAGTTTTCTGAATCATCCCC 59.599 45.833 0.00 0.00 0.00 4.81
692 845 4.009675 TGAAGTTTTCTGAATCATCCCCG 58.990 43.478 0.00 0.00 0.00 5.73
693 846 2.369394 AGTTTTCTGAATCATCCCCGC 58.631 47.619 0.00 0.00 0.00 6.13
694 847 2.091541 GTTTTCTGAATCATCCCCGCA 58.908 47.619 0.00 0.00 0.00 5.69
695 848 2.491693 GTTTTCTGAATCATCCCCGCAA 59.508 45.455 0.00 0.00 0.00 4.85
696 849 2.505650 TTCTGAATCATCCCCGCAAA 57.494 45.000 0.00 0.00 0.00 3.68
697 850 2.505650 TCTGAATCATCCCCGCAAAA 57.494 45.000 0.00 0.00 0.00 2.44
698 851 2.801483 TCTGAATCATCCCCGCAAAAA 58.199 42.857 0.00 0.00 0.00 1.94
757 910 0.661020 AGTTTTCTGAAACACGCGGG 59.339 50.000 6.92 6.92 46.01 6.13
781 934 0.036388 TGGGCTAGAGAAAGCAACGG 60.036 55.000 0.00 0.00 44.64 4.44
904 1057 3.621709 GCTCCTTAACCCTAAACCCTGAC 60.622 52.174 0.00 0.00 0.00 3.51
1284 1451 4.824166 CGCTTCCATGCTGTGCGC 62.824 66.667 0.00 0.00 40.15 6.09
1362 1537 2.040544 CGATGCCTCCTTGCGGTTT 61.041 57.895 0.00 0.00 0.00 3.27
1384 1559 4.269183 TGGTCAATTAACGAATGATGCCT 58.731 39.130 0.00 0.00 0.00 4.75
1459 1637 6.154203 AGCCCTCTTTTTCTTCTTTTTCTG 57.846 37.500 0.00 0.00 0.00 3.02
1460 1638 5.893824 AGCCCTCTTTTTCTTCTTTTTCTGA 59.106 36.000 0.00 0.00 0.00 3.27
1462 1640 6.644181 GCCCTCTTTTTCTTCTTTTTCTGATG 59.356 38.462 0.00 0.00 0.00 3.07
1487 1681 2.414994 ATGCACCAGAGGAGTCATTG 57.585 50.000 0.00 0.00 0.00 2.82
1489 1683 0.615331 GCACCAGAGGAGTCATTGGA 59.385 55.000 12.22 0.00 34.76 3.53
1516 1710 2.796383 GCGATGCAGTGTACCAGTAGAG 60.796 54.545 0.00 0.00 0.00 2.43
1547 1741 3.805807 GCGCTATAAATCAAGGTAGGGCA 60.806 47.826 0.00 0.00 46.27 5.36
1551 1745 2.808906 AAATCAAGGTAGGGCAGACC 57.191 50.000 0.00 0.00 40.67 3.85
1552 1746 0.541863 AATCAAGGTAGGGCAGACCG 59.458 55.000 1.80 0.00 46.96 4.79
1553 1747 0.325296 ATCAAGGTAGGGCAGACCGA 60.325 55.000 1.80 0.00 46.96 4.69
1554 1748 0.970937 TCAAGGTAGGGCAGACCGAG 60.971 60.000 1.80 0.00 46.96 4.63
1572 1784 2.759973 CCTCCGCCTGTGCCTCTA 60.760 66.667 0.00 0.00 0.00 2.43
1573 1785 2.136878 CCTCCGCCTGTGCCTCTAT 61.137 63.158 0.00 0.00 0.00 1.98
1574 1786 1.365633 CTCCGCCTGTGCCTCTATC 59.634 63.158 0.00 0.00 0.00 2.08
1575 1787 2.093537 CTCCGCCTGTGCCTCTATCC 62.094 65.000 0.00 0.00 0.00 2.59
1576 1788 2.434843 CCGCCTGTGCCTCTATCCA 61.435 63.158 0.00 0.00 0.00 3.41
1577 1789 1.227380 CGCCTGTGCCTCTATCCAC 60.227 63.158 0.00 0.00 0.00 4.02
1578 1790 1.907739 GCCTGTGCCTCTATCCACA 59.092 57.895 0.00 0.00 39.45 4.17
1579 1791 0.462759 GCCTGTGCCTCTATCCACAC 60.463 60.000 0.00 0.00 37.07 3.82
1580 1792 0.179000 CCTGTGCCTCTATCCACACC 59.821 60.000 0.00 0.00 37.07 4.16
1581 1793 0.904649 CTGTGCCTCTATCCACACCA 59.095 55.000 0.00 0.00 37.07 4.17
1582 1794 1.487976 CTGTGCCTCTATCCACACCAT 59.512 52.381 0.00 0.00 37.07 3.55
1583 1795 1.486310 TGTGCCTCTATCCACACCATC 59.514 52.381 0.00 0.00 37.07 3.51
1584 1796 1.765314 GTGCCTCTATCCACACCATCT 59.235 52.381 0.00 0.00 32.37 2.90
1585 1797 2.042464 TGCCTCTATCCACACCATCTC 58.958 52.381 0.00 0.00 0.00 2.75
1586 1798 1.346068 GCCTCTATCCACACCATCTCC 59.654 57.143 0.00 0.00 0.00 3.71
1587 1799 2.969628 CCTCTATCCACACCATCTCCT 58.030 52.381 0.00 0.00 0.00 3.69
1588 1800 3.312890 CCTCTATCCACACCATCTCCTT 58.687 50.000 0.00 0.00 0.00 3.36
1594 1806 2.040278 TCCACACCATCTCCTTTCTTGG 59.960 50.000 0.00 0.00 35.31 3.61
1604 1816 1.213430 TCCTTTCTTGGACCAAACCGT 59.787 47.619 8.59 0.00 0.00 4.83
1654 1866 3.426292 GCTAGGCCAAACTGAAATCGAAC 60.426 47.826 5.01 0.00 0.00 3.95
1655 1867 2.863809 AGGCCAAACTGAAATCGAACT 58.136 42.857 5.01 0.00 0.00 3.01
1667 1879 2.789409 ATCGAACTCCCCCTTTTGAG 57.211 50.000 0.00 0.00 34.73 3.02
1680 1892 0.109723 TTTTGAGCCCTAGGTTGCGT 59.890 50.000 8.29 0.00 0.00 5.24
1685 1897 2.202570 CCCTAGGTTGCGTCGTCG 60.203 66.667 8.29 0.00 40.37 5.12
1709 1921 5.239525 GCATCCGCTGGAATTTTCTTATACT 59.760 40.000 1.44 0.00 34.34 2.12
1717 1929 9.162764 GCTGGAATTTTCTTATACTGTTCTGTA 57.837 33.333 0.00 0.00 0.00 2.74
1948 2160 4.162690 ATCGCCTGGCCGGAGAAC 62.163 66.667 15.09 0.00 45.11 3.01
2023 2235 2.159156 TGTGAACGATGATCTTACCCGG 60.159 50.000 0.00 0.00 0.00 5.73
2029 2241 1.694696 GATGATCTTACCCGGGAGCTT 59.305 52.381 32.02 7.13 0.00 3.74
2224 2436 2.888051 GAGAGGAAGAAGGCGCGC 60.888 66.667 25.94 25.94 0.00 6.86
2230 2442 4.357947 AAGAAGGCGCGCGAGTCA 62.358 61.111 37.18 0.00 0.00 3.41
2236 2448 2.549282 GCGCGCGAGTCAAAGAAA 59.451 55.556 37.18 0.00 0.00 2.52
2296 2508 1.905894 GCCAAGGAGAAGAAGGAGAGT 59.094 52.381 0.00 0.00 0.00 3.24
2858 3121 1.606668 GGTCGTGGAATGCAGTTGAAA 59.393 47.619 0.00 0.00 0.00 2.69
2973 3243 6.311935 GGAGCGTTTTATTGTATCAGTGTGTA 59.688 38.462 0.00 0.00 0.00 2.90
2979 3250 9.893305 GTTTTATTGTATCAGTGTGTAAAGCTT 57.107 29.630 0.00 0.00 0.00 3.74
3016 3287 2.095768 CACTTGGTAATTGTGACTGCCG 60.096 50.000 0.00 0.00 33.95 5.69
3058 3331 9.334947 GGTTTCTTAAGTTATGTTCCCCTATAC 57.665 37.037 1.63 0.00 0.00 1.47
3072 3345 4.845796 TCCCCTATACATCTTGCATCATCA 59.154 41.667 0.00 0.00 0.00 3.07
3087 3361 2.229792 TCATCAACAAACCTCAGTGCC 58.770 47.619 0.00 0.00 0.00 5.01
3103 3377 1.738099 GCCTCACAATCAGCGTCGT 60.738 57.895 0.00 0.00 0.00 4.34
3192 3466 5.217978 ACAGATTTGGTTGTGATGCATTT 57.782 34.783 0.00 0.00 0.00 2.32
3210 3484 9.525409 GATGCATTTGTTCTTTCTTATTGCTAT 57.475 29.630 0.00 0.00 0.00 2.97
3228 3502 2.742428 ATACATGGCCAGATGCAGTT 57.258 45.000 13.05 0.00 43.89 3.16
3229 3503 1.753930 TACATGGCCAGATGCAGTTG 58.246 50.000 13.05 4.08 43.89 3.16
3289 7481 4.851558 GGAACAACTTTTGCATTAGCTACG 59.148 41.667 0.00 0.00 42.74 3.51
3378 7572 2.722094 CAGCTTGGTTGGTTATGCCTA 58.278 47.619 0.00 0.00 38.35 3.93
3438 7633 7.132863 GTGATGTTACACTTTCTCTGGAAAAC 58.867 38.462 0.00 0.00 40.41 2.43
3474 7669 6.909550 ACTTACAATGCCAGTATTTTCCAA 57.090 33.333 0.00 0.00 0.00 3.53
3476 7672 7.322664 ACTTACAATGCCAGTATTTTCCAATG 58.677 34.615 0.00 0.00 0.00 2.82
3500 7696 3.628008 TGTCTGTCTATATCGTGGTGGT 58.372 45.455 0.00 0.00 0.00 4.16
3607 7803 9.186837 TGTTGGTAAAATAACAAAAGGAGTGTA 57.813 29.630 0.00 0.00 37.08 2.90
3617 7813 5.941788 ACAAAAGGAGTGTAGAAAGATGGT 58.058 37.500 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.491383 TGAGAGAGTTACTATGGTTGTACCT 58.509 40.000 0.00 0.00 39.58 3.08
209 214 7.519809 GCAAGAGAAGAAGAAGAAGAAAGGAAC 60.520 40.741 0.00 0.00 0.00 3.62
217 222 8.562892 TGTAATTTGCAAGAGAAGAAGAAGAAG 58.437 33.333 0.00 0.00 0.00 2.85
250 293 8.670135 TGAATTCGAAAAGTAGTGAGACAAAAA 58.330 29.630 0.00 0.00 0.00 1.94
320 367 9.988350 ATCTGTGATGACGAATAAAAATGTAAC 57.012 29.630 0.00 0.00 0.00 2.50
464 511 5.212194 GTGTTCATGTTGAGCACGTAAAAT 58.788 37.500 8.40 0.00 45.80 1.82
563 642 7.974675 ACTAATCAAGTTCATATTTCGGTGTG 58.025 34.615 0.00 0.00 33.35 3.82
632 785 7.329962 TCGAAACGTTATTTTTGCTAGATGAGA 59.670 33.333 0.00 0.00 0.00 3.27
734 887 3.610677 CCGCGTGTTTCAGAAAACTTTTT 59.389 39.130 4.92 0.00 44.23 1.94
735 888 3.175929 CCGCGTGTTTCAGAAAACTTTT 58.824 40.909 4.92 0.00 44.23 2.27
736 889 2.478879 CCCGCGTGTTTCAGAAAACTTT 60.479 45.455 4.92 0.00 44.23 2.66
737 890 1.064952 CCCGCGTGTTTCAGAAAACTT 59.935 47.619 4.92 0.00 44.23 2.66
738 891 0.661020 CCCGCGTGTTTCAGAAAACT 59.339 50.000 4.92 0.00 44.23 2.66
739 892 0.317519 CCCCGCGTGTTTCAGAAAAC 60.318 55.000 4.92 0.00 44.18 2.43
740 893 1.448922 CCCCCGCGTGTTTCAGAAAA 61.449 55.000 4.92 0.00 0.00 2.29
741 894 1.894756 CCCCCGCGTGTTTCAGAAA 60.895 57.895 4.92 0.00 0.00 2.52
742 895 2.281208 CCCCCGCGTGTTTCAGAA 60.281 61.111 4.92 0.00 0.00 3.02
745 898 4.652131 ATGCCCCCGCGTGTTTCA 62.652 61.111 4.92 0.00 38.08 2.69
746 899 4.114997 CATGCCCCCGCGTGTTTC 62.115 66.667 4.92 0.00 45.38 2.78
757 910 0.821301 GCTTTCTCTAGCCCATGCCC 60.821 60.000 0.00 0.00 38.69 5.36
767 920 1.337447 CCCGTTCCGTTGCTTTCTCTA 60.337 52.381 0.00 0.00 0.00 2.43
781 934 2.853235 TTTCCCTTCTTCTCCCGTTC 57.147 50.000 0.00 0.00 0.00 3.95
820 973 0.528901 CGATAACGGCCCATCAACGA 60.529 55.000 0.00 0.00 35.72 3.85
1284 1451 0.533531 TAGAATGCAGCCAGCCATCG 60.534 55.000 0.00 0.00 44.83 3.84
1362 1537 4.096231 CAGGCATCATTCGTTAATTGACCA 59.904 41.667 0.00 0.00 0.00 4.02
1384 1559 2.300152 CTGAACCTGTCCTACTTGCTCA 59.700 50.000 0.00 0.00 0.00 4.26
1459 1637 6.153510 TGACTCCTCTGGTGCATATATACATC 59.846 42.308 0.00 0.00 0.00 3.06
1460 1638 6.019108 TGACTCCTCTGGTGCATATATACAT 58.981 40.000 0.00 0.00 0.00 2.29
1462 1640 5.984695 TGACTCCTCTGGTGCATATATAC 57.015 43.478 0.00 0.00 0.00 1.47
1466 1660 3.181447 CCAATGACTCCTCTGGTGCATAT 60.181 47.826 0.00 0.00 0.00 1.78
1474 1668 2.943690 CTGCATTCCAATGACTCCTCTG 59.056 50.000 3.35 0.00 38.70 3.35
1516 1710 5.227184 CCTTGATTTATAGCGCAAAACGTTC 59.773 40.000 11.47 2.93 46.11 3.95
1564 1776 1.765314 AGATGGTGTGGATAGAGGCAC 59.235 52.381 0.00 0.00 0.00 5.01
1565 1777 2.042464 GAGATGGTGTGGATAGAGGCA 58.958 52.381 0.00 0.00 0.00 4.75
1569 1781 4.624913 AGAAAGGAGATGGTGTGGATAGA 58.375 43.478 0.00 0.00 0.00 1.98
1570 1782 5.121811 CAAGAAAGGAGATGGTGTGGATAG 58.878 45.833 0.00 0.00 0.00 2.08
1571 1783 4.080356 CCAAGAAAGGAGATGGTGTGGATA 60.080 45.833 0.00 0.00 0.00 2.59
1572 1784 3.308688 CCAAGAAAGGAGATGGTGTGGAT 60.309 47.826 0.00 0.00 0.00 3.41
1573 1785 2.040278 CCAAGAAAGGAGATGGTGTGGA 59.960 50.000 0.00 0.00 0.00 4.02
1574 1786 2.040278 TCCAAGAAAGGAGATGGTGTGG 59.960 50.000 0.00 0.00 34.50 4.17
1575 1787 3.077359 GTCCAAGAAAGGAGATGGTGTG 58.923 50.000 0.00 0.00 38.64 3.82
1576 1788 2.040412 GGTCCAAGAAAGGAGATGGTGT 59.960 50.000 0.00 0.00 38.64 4.16
1577 1789 2.040278 TGGTCCAAGAAAGGAGATGGTG 59.960 50.000 0.00 0.00 38.64 4.17
1578 1790 2.348472 TGGTCCAAGAAAGGAGATGGT 58.652 47.619 0.00 0.00 38.64 3.55
1579 1791 3.439857 TTGGTCCAAGAAAGGAGATGG 57.560 47.619 0.00 0.00 38.64 3.51
1580 1792 3.507622 GGTTTGGTCCAAGAAAGGAGATG 59.492 47.826 4.09 0.00 38.64 2.90
1581 1793 3.767711 GGTTTGGTCCAAGAAAGGAGAT 58.232 45.455 4.09 0.00 38.64 2.75
1582 1794 2.486548 CGGTTTGGTCCAAGAAAGGAGA 60.487 50.000 4.09 0.00 38.64 3.71
1583 1795 1.880027 CGGTTTGGTCCAAGAAAGGAG 59.120 52.381 4.09 0.00 38.64 3.69
1584 1796 1.213430 ACGGTTTGGTCCAAGAAAGGA 59.787 47.619 4.09 0.00 34.64 3.36
1585 1797 1.607148 GACGGTTTGGTCCAAGAAAGG 59.393 52.381 4.09 0.00 0.00 3.11
1586 1798 1.263217 CGACGGTTTGGTCCAAGAAAG 59.737 52.381 4.09 1.15 33.30 2.62
1587 1799 1.301423 CGACGGTTTGGTCCAAGAAA 58.699 50.000 4.09 0.00 33.30 2.52
1588 1800 1.161563 GCGACGGTTTGGTCCAAGAA 61.162 55.000 4.09 0.00 33.30 2.52
1594 1806 1.445871 AATAAGGCGACGGTTTGGTC 58.554 50.000 0.00 0.00 0.00 4.02
1604 1816 2.179764 GGCTGCACAAATAAGGCGA 58.820 52.632 0.50 0.00 0.00 5.54
1654 1866 0.548510 CTAGGGCTCAAAAGGGGGAG 59.451 60.000 0.00 0.00 0.00 4.30
1655 1867 0.919289 CCTAGGGCTCAAAAGGGGGA 60.919 60.000 0.00 0.00 0.00 4.81
1667 1879 2.508663 GACGACGCAACCTAGGGC 60.509 66.667 14.81 6.85 0.00 5.19
1685 1897 2.947448 AAGAAAATTCCAGCGGATGC 57.053 45.000 0.00 0.00 43.24 3.91
1948 2160 1.959899 GCTTGTGCATCCAGTCGACG 61.960 60.000 10.46 5.16 39.41 5.12
1951 2163 0.671472 TGAGCTTGTGCATCCAGTCG 60.671 55.000 0.00 0.00 42.74 4.18
2023 2235 1.271379 TGGGTGTAGAAAGCAAGCTCC 60.271 52.381 0.00 0.00 0.00 4.70
2029 2241 0.771127 AAGCCTGGGTGTAGAAAGCA 59.229 50.000 0.00 0.00 0.00 3.91
2224 2436 3.059570 CCTTCGATCGTTTCTTTGACTCG 59.940 47.826 15.94 0.00 0.00 4.18
2230 2442 3.326747 CACCTCCTTCGATCGTTTCTTT 58.673 45.455 15.94 0.00 0.00 2.52
2236 2448 1.513158 CTGCACCTCCTTCGATCGT 59.487 57.895 15.94 0.00 0.00 3.73
2296 2508 2.422479 CCACTTCTTGACCGACTCGATA 59.578 50.000 0.00 0.00 0.00 2.92
2888 3156 9.755064 CAGCTGTAAACTGTAAATGTAATACAC 57.245 33.333 5.25 0.00 0.00 2.90
2889 3157 8.447833 GCAGCTGTAAACTGTAAATGTAATACA 58.552 33.333 16.64 0.00 37.47 2.29
2890 3158 8.665685 AGCAGCTGTAAACTGTAAATGTAATAC 58.334 33.333 16.64 0.00 37.47 1.89
2891 3159 8.664798 CAGCAGCTGTAAACTGTAAATGTAATA 58.335 33.333 16.64 0.00 37.47 0.98
2892 3160 7.174946 ACAGCAGCTGTAAACTGTAAATGTAAT 59.825 33.333 27.22 0.00 43.46 1.89
2893 3161 6.485313 ACAGCAGCTGTAAACTGTAAATGTAA 59.515 34.615 27.22 0.00 43.46 2.41
2894 3162 5.995282 ACAGCAGCTGTAAACTGTAAATGTA 59.005 36.000 27.22 0.00 43.46 2.29
2895 3163 4.821805 ACAGCAGCTGTAAACTGTAAATGT 59.178 37.500 27.22 0.00 43.46 2.71
2896 3164 5.149273 CACAGCAGCTGTAAACTGTAAATG 58.851 41.667 27.80 7.26 43.43 2.32
2897 3165 4.821805 ACACAGCAGCTGTAAACTGTAAAT 59.178 37.500 27.80 9.51 43.43 1.40
2898 3166 4.035091 CACACAGCAGCTGTAAACTGTAAA 59.965 41.667 27.80 0.00 43.43 2.01
2973 3243 7.054751 AGTGTTACTCCTTTCACTTAAGCTTT 58.945 34.615 3.20 0.00 37.81 3.51
2979 3250 6.243216 ACCAAGTGTTACTCCTTTCACTTA 57.757 37.500 8.67 0.00 45.36 2.24
3016 3287 8.667076 TTAAGAAACCAAAACTAGACTGTACC 57.333 34.615 0.00 0.00 0.00 3.34
3029 3300 7.070629 AGGGGAACATAACTTAAGAAACCAAA 58.929 34.615 10.09 0.00 0.00 3.28
3058 3331 5.068234 AGGTTTGTTGATGATGCAAGATG 57.932 39.130 0.00 0.00 0.00 2.90
3072 3345 1.064758 TGTGAGGCACTGAGGTTTGTT 60.065 47.619 0.00 0.00 41.55 2.83
3087 3361 3.179048 TGAATACGACGCTGATTGTGAG 58.821 45.455 0.00 0.00 0.00 3.51
3103 3377 5.441718 ACAGCAGAAAAGGAGGATGAATA 57.558 39.130 0.00 0.00 0.00 1.75
3192 3466 7.013274 GGCCATGTATAGCAATAAGAAAGAACA 59.987 37.037 0.00 0.00 0.00 3.18
3210 3484 1.004628 ACAACTGCATCTGGCCATGTA 59.995 47.619 5.51 0.32 43.89 2.29
3228 3502 5.305128 AGCAAGAAAAGAAAATGATCCCACA 59.695 36.000 0.00 0.00 0.00 4.17
3229 3503 5.636543 CAGCAAGAAAAGAAAATGATCCCAC 59.363 40.000 0.00 0.00 0.00 4.61
3263 7455 5.857268 AGCTAATGCAAAAGTTGTTCCAAT 58.143 33.333 0.00 0.00 42.74 3.16
3289 7481 3.623060 CCCATATAGCGCATATTGACACC 59.377 47.826 11.47 0.00 0.00 4.16
3366 7560 7.238486 ACAAAACATGAATAGGCATAACCAA 57.762 32.000 0.00 0.00 43.14 3.67
3378 7572 6.638873 TCGCATAAAAACGACAAAACATGAAT 59.361 30.769 0.00 0.00 32.45 2.57
3438 7633 5.278463 GGCATTGTAAGTTATAGTGCCCATG 60.278 44.000 26.16 8.13 43.60 3.66
3474 7669 6.042777 CACCACGATATAGACAGACAAACAT 58.957 40.000 0.00 0.00 0.00 2.71
3476 7672 4.804139 CCACCACGATATAGACAGACAAAC 59.196 45.833 0.00 0.00 0.00 2.93
3581 7777 8.068892 ACACTCCTTTTGTTATTTTACCAACA 57.931 30.769 0.00 0.00 32.98 3.33
3600 7796 4.455877 CCAACAACCATCTTTCTACACTCC 59.544 45.833 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.