Multiple sequence alignment - TraesCS5A01G113600

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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 TraesCS5A01G113600 chr5A 100.000 2428 0 0 1 2428 225611410 225613837 0 4484
1 TraesCS5A01G113600 chr6A 95.625 960 41 1 679 1638 613366160 613367118 0 1539
2 TraesCS5A01G113600 chr6A 92.508 961 64 4 683 1638 395871094 395870137 0 1369
3 TraesCS5A01G113600 chr6A 93.377 755 38 6 1 744 162276081 162275328 0 1107
4 TraesCS5A01G113600 chr6A 95.501 689 31 0 1 689 613365593 613366281 0 1101
5 TraesCS5A01G113600 chr6A 94.049 689 38 1 1 689 395871661 395870976 0 1042
6 TraesCS5A01G113600 chr7B 95.417 960 40 2 679 1638 228682868 228681913 0 1526
7 TraesCS5A01G113600 chr7B 93.168 966 55 9 679 1638 499717172 499716212 0 1408
8 TraesCS5A01G113600 chr6D 94.320 986 49 3 660 1638 15118878 15119863 0 1504
9 TraesCS5A01G113600 chr6D 92.135 801 46 15 1639 2427 263985474 263984679 0 1114
10 TraesCS5A01G113600 chr6D 91.960 796 56 6 1639 2428 125943300 125942507 0 1109
11 TraesCS5A01G113600 chr6D 93.352 722 35 6 1 715 15118308 15119023 0 1055
12 TraesCS5A01G113600 chr6B 93.444 961 58 2 683 1638 171789154 171788194 0 1421
13 TraesCS5A01G113600 chr6B 94.920 689 32 2 1 689 171789721 171789036 0 1075
14 TraesCS5A01G113600 chr2B 93.236 961 55 4 688 1638 77333473 77334433 0 1406
15 TraesCS5A01G113600 chr2B 94.118 697 28 6 1 687 77332900 77333593 0 1048
16 TraesCS5A01G113600 chr4D 94.086 930 43 4 716 1638 386931974 386932898 0 1402
17 TraesCS5A01G113600 chr4D 92.453 795 53 5 1639 2427 100848419 100847626 0 1129
18 TraesCS5A01G113600 chr4D 91.980 798 53 9 1638 2427 323419877 323419083 0 1109
19 TraesCS5A01G113600 chr4D 94.745 666 27 4 1 659 386931399 386932063 0 1029
20 TraesCS5A01G113600 chr1A 93.215 958 55 4 688 1638 565154697 565155651 0 1400
21 TraesCS5A01G113600 chr1A 93.660 694 32 6 1 687 565154123 565154811 0 1027
22 TraesCS5A01G113600 chr1D 92.803 792 50 7 1639 2426 108971796 108971008 0 1140
23 TraesCS5A01G113600 chr1D 91.970 797 52 8 1639 2427 467374529 467373737 0 1107
24 TraesCS5A01G113600 chr1D 92.092 784 60 2 1646 2427 225759162 225758379 0 1103
25 TraesCS5A01G113600 chr7D 92.250 800 47 12 1638 2427 324370882 324371676 0 1120
26 TraesCS5A01G113600 chr7D 91.960 796 53 8 1638 2427 353134058 353134848 0 1105
27 TraesCS5A01G113600 chr3D 93.377 755 40 6 1 747 61930649 61931401 0 1109


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 TraesCS5A01G113600 chr5A 225611410 225613837 2427 False 4484.0 4484 100.0000 1 2428 1 chr5A.!!$F1 2427
1 TraesCS5A01G113600 chr6A 613365593 613367118 1525 False 1320.0 1539 95.5630 1 1638 2 chr6A.!!$F1 1637
2 TraesCS5A01G113600 chr6A 395870137 395871661 1524 True 1205.5 1369 93.2785 1 1638 2 chr6A.!!$R2 1637
3 TraesCS5A01G113600 chr6A 162275328 162276081 753 True 1107.0 1107 93.3770 1 744 1 chr6A.!!$R1 743
4 TraesCS5A01G113600 chr7B 228681913 228682868 955 True 1526.0 1526 95.4170 679 1638 1 chr7B.!!$R1 959
5 TraesCS5A01G113600 chr7B 499716212 499717172 960 True 1408.0 1408 93.1680 679 1638 1 chr7B.!!$R2 959
6 TraesCS5A01G113600 chr6D 15118308 15119863 1555 False 1279.5 1504 93.8360 1 1638 2 chr6D.!!$F1 1637
7 TraesCS5A01G113600 chr6D 263984679 263985474 795 True 1114.0 1114 92.1350 1639 2427 1 chr6D.!!$R2 788
8 TraesCS5A01G113600 chr6D 125942507 125943300 793 True 1109.0 1109 91.9600 1639 2428 1 chr6D.!!$R1 789
9 TraesCS5A01G113600 chr6B 171788194 171789721 1527 True 1248.0 1421 94.1820 1 1638 2 chr6B.!!$R1 1637
10 TraesCS5A01G113600 chr2B 77332900 77334433 1533 False 1227.0 1406 93.6770 1 1638 2 chr2B.!!$F1 1637
11 TraesCS5A01G113600 chr4D 386931399 386932898 1499 False 1215.5 1402 94.4155 1 1638 2 chr4D.!!$F1 1637
12 TraesCS5A01G113600 chr4D 100847626 100848419 793 True 1129.0 1129 92.4530 1639 2427 1 chr4D.!!$R1 788
13 TraesCS5A01G113600 chr4D 323419083 323419877 794 True 1109.0 1109 91.9800 1638 2427 1 chr4D.!!$R2 789
14 TraesCS5A01G113600 chr1A 565154123 565155651 1528 False 1213.5 1400 93.4375 1 1638 2 chr1A.!!$F1 1637
15 TraesCS5A01G113600 chr1D 108971008 108971796 788 True 1140.0 1140 92.8030 1639 2426 1 chr1D.!!$R1 787
16 TraesCS5A01G113600 chr1D 467373737 467374529 792 True 1107.0 1107 91.9700 1639 2427 1 chr1D.!!$R3 788
17 TraesCS5A01G113600 chr1D 225758379 225759162 783 True 1103.0 1103 92.0920 1646 2427 1 chr1D.!!$R2 781
18 TraesCS5A01G113600 chr7D 324370882 324371676 794 False 1120.0 1120 92.2500 1638 2427 1 chr7D.!!$F1 789
19 TraesCS5A01G113600 chr7D 353134058 353134848 790 False 1105.0 1105 91.9600 1638 2427 1 chr7D.!!$F2 789
20 TraesCS5A01G113600 chr3D 61930649 61931401 752 False 1109.0 1109 93.3770 1 747 1 chr3D.!!$F1 746

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
616 649 0.247736 CTAGCTGCGGTGGTCTTCTT 59.752 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2257 0.988145 ATGATTTCCCCTCCGGCAGA 60.988 55.0 0.0 0.0 0.0 4.26 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
41 42 4.346418 TGGAGAAGGATTTCTAGCTCCATC 59.654 45.833 10.87 5.53 44.87 3.51
129 130 5.405571 AGAGTTATATAACTTGCGCCATTCG 59.594 40.000 25.25 0.00 45.84 3.34
160 161 4.873827 GGAATGTAGTGGAGCGAACATTTA 59.126 41.667 1.52 0.00 41.37 1.40
357 359 5.625197 GCACAAATTTGCAAGGGATAGACAT 60.625 40.000 18.12 0.00 42.49 3.06
508 510 7.253422 GCAACAACTAGCTGATGATATGTTTT 58.747 34.615 7.51 0.00 0.00 2.43
525 527 3.211045 GTTTTCTGAGTACCTTGTGGCA 58.789 45.455 0.00 0.00 36.63 4.92
574 576 6.096705 GGATGAGAGTATGATATGTAGCTGCT 59.903 42.308 7.57 7.57 0.00 4.24
576 578 5.184671 TGAGAGTATGATATGTAGCTGCTGG 59.815 44.000 13.43 0.00 0.00 4.85
592 594 0.961753 CTGGGGTGGTCTTCTTTTGC 59.038 55.000 0.00 0.00 0.00 3.68
613 646 2.266055 GCTAGCTGCGGTGGTCTT 59.734 61.111 7.70 0.00 0.00 3.01
614 647 1.811679 GCTAGCTGCGGTGGTCTTC 60.812 63.158 7.70 0.00 0.00 2.87
615 648 1.893786 CTAGCTGCGGTGGTCTTCT 59.106 57.895 0.00 0.00 0.00 2.85
616 649 0.247736 CTAGCTGCGGTGGTCTTCTT 59.752 55.000 0.00 0.00 0.00 2.52
617 650 0.685097 TAGCTGCGGTGGTCTTCTTT 59.315 50.000 0.00 0.00 0.00 2.52
618 651 0.886490 AGCTGCGGTGGTCTTCTTTG 60.886 55.000 0.00 0.00 0.00 2.77
619 652 1.856265 GCTGCGGTGGTCTTCTTTGG 61.856 60.000 0.00 0.00 0.00 3.28
620 653 0.535102 CTGCGGTGGTCTTCTTTGGT 60.535 55.000 0.00 0.00 0.00 3.67
621 654 0.759959 TGCGGTGGTCTTCTTTGGTA 59.240 50.000 0.00 0.00 0.00 3.25
622 655 1.349688 TGCGGTGGTCTTCTTTGGTAT 59.650 47.619 0.00 0.00 0.00 2.73
623 656 2.568062 TGCGGTGGTCTTCTTTGGTATA 59.432 45.455 0.00 0.00 0.00 1.47
624 657 3.195661 GCGGTGGTCTTCTTTGGTATAG 58.804 50.000 0.00 0.00 0.00 1.31
625 658 3.195661 CGGTGGTCTTCTTTGGTATAGC 58.804 50.000 0.00 0.00 0.00 2.97
626 659 3.118738 CGGTGGTCTTCTTTGGTATAGCT 60.119 47.826 3.20 0.00 0.00 3.32
627 660 4.098960 CGGTGGTCTTCTTTGGTATAGCTA 59.901 45.833 0.00 0.00 0.00 3.32
628 661 5.602628 GGTGGTCTTCTTTGGTATAGCTAG 58.397 45.833 0.00 1.38 0.00 3.42
629 662 5.051153 GTGGTCTTCTTTGGTATAGCTAGC 58.949 45.833 6.62 6.62 0.00 3.42
630 663 4.962995 TGGTCTTCTTTGGTATAGCTAGCT 59.037 41.667 23.12 23.12 0.00 3.32
702 771 1.602311 AGCTGCAGTGGTCTTCTTTG 58.398 50.000 16.64 0.00 0.00 2.77
703 772 0.595095 GCTGCAGTGGTCTTCTTTGG 59.405 55.000 16.64 0.00 0.00 3.28
704 773 1.815408 GCTGCAGTGGTCTTCTTTGGA 60.815 52.381 16.64 0.00 0.00 3.53
705 774 2.575532 CTGCAGTGGTCTTCTTTGGAA 58.424 47.619 5.25 0.00 0.00 3.53
706 775 3.152341 CTGCAGTGGTCTTCTTTGGAAT 58.848 45.455 5.25 0.00 0.00 3.01
707 776 4.326826 CTGCAGTGGTCTTCTTTGGAATA 58.673 43.478 5.25 0.00 0.00 1.75
708 777 4.326826 TGCAGTGGTCTTCTTTGGAATAG 58.673 43.478 0.00 0.00 0.00 1.73
709 778 3.127721 GCAGTGGTCTTCTTTGGAATAGC 59.872 47.826 0.00 0.00 0.00 2.97
710 779 4.583871 CAGTGGTCTTCTTTGGAATAGCT 58.416 43.478 0.00 0.00 30.68 3.32
711 780 5.734720 CAGTGGTCTTCTTTGGAATAGCTA 58.265 41.667 0.00 0.00 30.68 3.32
712 781 5.814705 CAGTGGTCTTCTTTGGAATAGCTAG 59.185 44.000 0.00 0.00 30.68 3.42
713 782 4.572795 GTGGTCTTCTTTGGAATAGCTAGC 59.427 45.833 6.62 6.62 30.68 3.42
714 783 4.471386 TGGTCTTCTTTGGAATAGCTAGCT 59.529 41.667 23.12 23.12 30.68 3.32
715 784 4.813697 GGTCTTCTTTGGAATAGCTAGCTG 59.186 45.833 27.68 7.80 0.00 4.24
716 785 4.272261 GTCTTCTTTGGAATAGCTAGCTGC 59.728 45.833 27.68 15.46 43.29 5.25
725 794 2.266055 GCTAGCTGCGGTGGTCTT 59.734 61.111 7.70 0.00 0.00 3.01
726 795 1.811679 GCTAGCTGCGGTGGTCTTC 60.812 63.158 7.70 0.00 0.00 2.87
727 796 1.893786 CTAGCTGCGGTGGTCTTCT 59.106 57.895 0.00 0.00 0.00 2.85
728 797 0.247736 CTAGCTGCGGTGGTCTTCTT 59.752 55.000 0.00 0.00 0.00 2.52
729 798 0.685097 TAGCTGCGGTGGTCTTCTTT 59.315 50.000 0.00 0.00 0.00 2.52
730 799 0.886490 AGCTGCGGTGGTCTTCTTTG 60.886 55.000 0.00 0.00 0.00 2.77
731 800 1.856265 GCTGCGGTGGTCTTCTTTGG 61.856 60.000 0.00 0.00 0.00 3.28
732 801 0.535102 CTGCGGTGGTCTTCTTTGGT 60.535 55.000 0.00 0.00 0.00 3.67
733 802 0.759959 TGCGGTGGTCTTCTTTGGTA 59.240 50.000 0.00 0.00 0.00 3.25
734 803 1.349688 TGCGGTGGTCTTCTTTGGTAT 59.650 47.619 0.00 0.00 0.00 2.73
735 804 2.568062 TGCGGTGGTCTTCTTTGGTATA 59.432 45.455 0.00 0.00 0.00 1.47
736 805 3.195661 GCGGTGGTCTTCTTTGGTATAG 58.804 50.000 0.00 0.00 0.00 1.31
737 806 3.195661 CGGTGGTCTTCTTTGGTATAGC 58.804 50.000 0.00 0.00 0.00 2.97
738 807 3.118738 CGGTGGTCTTCTTTGGTATAGCT 60.119 47.826 3.20 0.00 0.00 3.32
739 808 4.098960 CGGTGGTCTTCTTTGGTATAGCTA 59.901 45.833 0.00 0.00 0.00 3.32
740 809 5.602628 GGTGGTCTTCTTTGGTATAGCTAG 58.397 45.833 0.00 1.38 0.00 3.42
741 810 5.051153 GTGGTCTTCTTTGGTATAGCTAGC 58.949 45.833 6.62 6.62 0.00 3.42
742 811 4.962995 TGGTCTTCTTTGGTATAGCTAGCT 59.037 41.667 23.12 23.12 0.00 3.32
743 812 6.040616 GTGGTCTTCTTTGGTATAGCTAGCTA 59.959 42.308 26.09 26.09 0.00 3.32
744 813 6.782988 TGGTCTTCTTTGGTATAGCTAGCTAT 59.217 38.462 33.67 33.67 41.58 2.97
745 814 7.093992 GGTCTTCTTTGGTATAGCTAGCTATG 58.906 42.308 36.77 23.41 39.36 2.23
746 815 7.093992 GTCTTCTTTGGTATAGCTAGCTATGG 58.906 42.308 36.77 22.05 39.36 2.74
747 816 6.782988 TCTTCTTTGGTATAGCTAGCTATGGT 59.217 38.462 36.77 21.09 39.36 3.55
748 817 6.346477 TCTTTGGTATAGCTAGCTATGGTG 57.654 41.667 36.77 22.94 39.36 4.17
749 818 5.246203 TCTTTGGTATAGCTAGCTATGGTGG 59.754 44.000 36.77 23.64 39.36 4.61
750 819 4.127918 TGGTATAGCTAGCTATGGTGGT 57.872 45.455 36.77 19.80 39.36 4.16
751 820 4.087182 TGGTATAGCTAGCTATGGTGGTC 58.913 47.826 36.77 22.24 39.36 4.02
752 821 4.202684 TGGTATAGCTAGCTATGGTGGTCT 60.203 45.833 36.77 18.52 39.36 3.85
753 822 4.773149 GGTATAGCTAGCTATGGTGGTCTT 59.227 45.833 36.77 17.89 39.36 3.01
754 823 5.105675 GGTATAGCTAGCTATGGTGGTCTTC 60.106 48.000 36.77 18.87 39.36 2.87
755 824 3.039252 AGCTAGCTATGGTGGTCTTCT 57.961 47.619 17.69 0.00 0.00 2.85
756 825 3.379452 AGCTAGCTATGGTGGTCTTCTT 58.621 45.455 17.69 0.00 0.00 2.52
757 826 3.777522 AGCTAGCTATGGTGGTCTTCTTT 59.222 43.478 17.69 0.00 0.00 2.52
952 1085 1.122632 TCCTTGTAGAACCGTGGCCA 61.123 55.000 0.00 0.00 0.00 5.36
1020 1153 4.152647 AGATGGATGATGCATTGCTTGAT 58.847 39.130 10.49 3.05 0.00 2.57
1095 1228 0.734309 ATGTGTACACGCATGCCATG 59.266 50.000 20.61 13.46 44.53 3.66
1109 1242 1.355381 TGCCATGAGGAATGTGAAGGT 59.645 47.619 0.00 0.00 36.89 3.50
1132 1265 6.017605 GGTCAAGTGCAATAAGGATATCACAG 60.018 42.308 4.83 0.00 0.00 3.66
1195 1328 4.645136 ACTATGAGGTCGTTAGCAAGATCA 59.355 41.667 0.00 0.00 0.00 2.92
1359 1492 4.142881 GGCAGTAGCTTTACTAGTTTGTGC 60.143 45.833 0.00 1.15 41.70 4.57
1362 1495 6.293462 GCAGTAGCTTTACTAGTTTGTGCTTT 60.293 38.462 0.00 0.00 37.91 3.51
1627 1760 6.963796 ACTTAGTTGATGCTTTCAAGACAAG 58.036 36.000 3.33 8.69 44.89 3.16
1772 1905 1.426251 ATTGACCCAGTGCCCAGTGA 61.426 55.000 4.72 0.00 33.67 3.41
1779 1912 0.179048 CAGTGCCCAGTGACAGTTGA 60.179 55.000 0.00 0.00 33.67 3.18
1785 1918 3.146066 GCCCAGTGACAGTTGATGTTTA 58.854 45.455 0.00 0.00 44.17 2.01
1850 1984 3.680458 TCCAAACACCGCAAAACTTTTTC 59.320 39.130 0.00 0.00 0.00 2.29
2049 2185 2.524611 CCCTCGGGGTTAACCTAGG 58.475 63.158 23.69 23.61 40.20 3.02
2053 2189 2.181975 CTCGGGGTTAACCTAGGTCAA 58.818 52.381 23.69 3.42 40.03 3.18
2084 2226 1.153289 CGCAAGCCTCTGTAGCCAT 60.153 57.895 0.00 0.00 0.00 4.40
2104 2246 5.016173 CCATCAAAAACCAATCTAGACCCA 58.984 41.667 0.00 0.00 0.00 4.51
2110 2252 4.993705 AACCAATCTAGACCCAGTTTCA 57.006 40.909 0.00 0.00 0.00 2.69
2115 2257 2.609747 TCTAGACCCAGTTTCAGCACT 58.390 47.619 0.00 0.00 0.00 4.40
2162 2306 0.397941 GCCATCTTCATCATCCCGGA 59.602 55.000 0.73 0.00 0.00 5.14
2244 2390 8.305046 AGCTATGTGTTTAATCTCTCTCTCTT 57.695 34.615 0.00 0.00 0.00 2.85
2347 2499 9.730705 TCTATCTTGTGATGAATTGAGTTTTCT 57.269 29.630 0.00 0.00 34.32 2.52
2354 2506 8.853126 TGTGATGAATTGAGTTTTCTCTTTGAT 58.147 29.630 0.00 0.00 46.30 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.341531 GATGATACCGAGTGGACCTGG 59.658 57.143 0.00 0.00 39.21 4.45
87 88 2.154462 TCTTTAGCTGTTTGAGGCTGC 58.846 47.619 0.00 0.00 39.31 5.25
129 130 1.136305 TCCACTACATTCCTAGCACGC 59.864 52.381 0.00 0.00 0.00 5.34
190 192 3.702792 TGTCAAAGAAGGTTTGGGAACA 58.297 40.909 0.00 0.00 37.51 3.18
261 263 8.834465 GTTCATAGTAAGCAATTGTCATCTCAT 58.166 33.333 7.40 0.00 0.00 2.90
339 341 5.452255 ACATGATGTCTATCCCTTGCAAAT 58.548 37.500 0.00 0.00 32.09 2.32
357 359 7.204604 GCAATAACAAATCATCCATGACATGA 58.795 34.615 17.24 9.10 40.03 3.07
416 418 5.366460 AGTTGTCATCATCTGGATCATCAC 58.634 41.667 0.00 0.00 32.57 3.06
525 527 4.982241 TTCCATCTCTTGTTCTCCTTGT 57.018 40.909 0.00 0.00 0.00 3.16
574 576 0.260230 TGCAAAAGAAGACCACCCCA 59.740 50.000 0.00 0.00 0.00 4.96
576 578 2.164422 GCTATGCAAAAGAAGACCACCC 59.836 50.000 3.72 0.00 0.00 4.61
592 594 0.598680 GACCACCGCAGCTAGCTATG 60.599 60.000 18.86 12.58 42.61 2.23
606 639 5.051153 GCTAGCTATACCAAAGAAGACCAC 58.949 45.833 7.70 0.00 0.00 4.16
607 640 4.962995 AGCTAGCTATACCAAAGAAGACCA 59.037 41.667 17.69 0.00 0.00 4.02
608 641 5.293560 CAGCTAGCTATACCAAAGAAGACC 58.706 45.833 18.86 0.00 0.00 3.85
609 642 4.747605 GCAGCTAGCTATACCAAAGAAGAC 59.252 45.833 18.86 0.00 41.15 3.01
610 643 4.499865 CGCAGCTAGCTATACCAAAGAAGA 60.500 45.833 18.86 0.00 42.61 2.87
611 644 3.738282 CGCAGCTAGCTATACCAAAGAAG 59.262 47.826 18.86 1.09 42.61 2.85
612 645 3.492656 CCGCAGCTAGCTATACCAAAGAA 60.493 47.826 18.86 0.00 42.61 2.52
613 646 2.035961 CCGCAGCTAGCTATACCAAAGA 59.964 50.000 18.86 0.00 42.61 2.52
614 647 2.224066 ACCGCAGCTAGCTATACCAAAG 60.224 50.000 18.86 3.27 42.61 2.77
615 648 1.760613 ACCGCAGCTAGCTATACCAAA 59.239 47.619 18.86 0.00 42.61 3.28
616 649 1.068588 CACCGCAGCTAGCTATACCAA 59.931 52.381 18.86 0.00 42.61 3.67
617 650 0.673985 CACCGCAGCTAGCTATACCA 59.326 55.000 18.86 0.00 42.61 3.25
618 651 0.038159 CCACCGCAGCTAGCTATACC 60.038 60.000 18.86 5.40 42.61 2.73
619 652 0.674534 ACCACCGCAGCTAGCTATAC 59.325 55.000 18.86 9.19 42.61 1.47
620 653 0.959553 GACCACCGCAGCTAGCTATA 59.040 55.000 18.86 0.00 42.61 1.31
621 654 0.757188 AGACCACCGCAGCTAGCTAT 60.757 55.000 18.86 0.06 42.61 2.97
622 655 0.970937 AAGACCACCGCAGCTAGCTA 60.971 55.000 18.86 0.00 42.61 3.32
623 656 2.232298 GAAGACCACCGCAGCTAGCT 62.232 60.000 12.68 12.68 42.61 3.32
624 657 1.811679 GAAGACCACCGCAGCTAGC 60.812 63.158 6.62 6.62 40.87 3.42
625 658 0.247736 AAGAAGACCACCGCAGCTAG 59.752 55.000 0.00 0.00 0.00 3.42
626 659 0.685097 AAAGAAGACCACCGCAGCTA 59.315 50.000 0.00 0.00 0.00 3.32
627 660 0.179018 AAAAGAAGACCACCGCAGCT 60.179 50.000 0.00 0.00 0.00 4.24
628 661 0.040067 CAAAAGAAGACCACCGCAGC 60.040 55.000 0.00 0.00 0.00 5.25
629 662 1.308998 ACAAAAGAAGACCACCGCAG 58.691 50.000 0.00 0.00 0.00 5.18
630 663 2.623878 TACAAAAGAAGACCACCGCA 57.376 45.000 0.00 0.00 0.00 5.69
702 771 0.601311 CCACCGCAGCTAGCTATTCC 60.601 60.000 18.86 5.40 42.61 3.01
703 772 0.105039 ACCACCGCAGCTAGCTATTC 59.895 55.000 18.86 8.75 42.61 1.75
704 773 0.105039 GACCACCGCAGCTAGCTATT 59.895 55.000 18.86 0.00 42.61 1.73
705 774 0.757188 AGACCACCGCAGCTAGCTAT 60.757 55.000 18.86 0.06 42.61 2.97
706 775 0.970937 AAGACCACCGCAGCTAGCTA 60.971 55.000 18.86 0.00 42.61 3.32
707 776 2.232298 GAAGACCACCGCAGCTAGCT 62.232 60.000 12.68 12.68 42.61 3.32
708 777 1.811679 GAAGACCACCGCAGCTAGC 60.812 63.158 6.62 6.62 40.87 3.42
709 778 0.247736 AAGAAGACCACCGCAGCTAG 59.752 55.000 0.00 0.00 0.00 3.42
710 779 0.685097 AAAGAAGACCACCGCAGCTA 59.315 50.000 0.00 0.00 0.00 3.32
711 780 0.886490 CAAAGAAGACCACCGCAGCT 60.886 55.000 0.00 0.00 0.00 4.24
712 781 1.576421 CAAAGAAGACCACCGCAGC 59.424 57.895 0.00 0.00 0.00 5.25
713 782 0.535102 ACCAAAGAAGACCACCGCAG 60.535 55.000 0.00 0.00 0.00 5.18
714 783 0.759959 TACCAAAGAAGACCACCGCA 59.240 50.000 0.00 0.00 0.00 5.69
715 784 2.109425 ATACCAAAGAAGACCACCGC 57.891 50.000 0.00 0.00 0.00 5.68
716 785 3.118738 AGCTATACCAAAGAAGACCACCG 60.119 47.826 0.00 0.00 0.00 4.94
717 786 4.489306 AGCTATACCAAAGAAGACCACC 57.511 45.455 0.00 0.00 0.00 4.61
718 787 5.051153 GCTAGCTATACCAAAGAAGACCAC 58.949 45.833 7.70 0.00 0.00 4.16
719 788 4.962995 AGCTAGCTATACCAAAGAAGACCA 59.037 41.667 17.69 0.00 0.00 4.02
720 789 5.538849 AGCTAGCTATACCAAAGAAGACC 57.461 43.478 17.69 0.00 0.00 3.85
721 790 7.093992 CCATAGCTAGCTATACCAAAGAAGAC 58.906 42.308 31.75 0.00 37.16 3.01
722 791 6.782988 ACCATAGCTAGCTATACCAAAGAAGA 59.217 38.462 31.75 7.17 37.16 2.87
723 792 6.870965 CACCATAGCTAGCTATACCAAAGAAG 59.129 42.308 31.75 18.08 37.16 2.85
724 793 6.239600 CCACCATAGCTAGCTATACCAAAGAA 60.240 42.308 31.75 7.91 37.16 2.52
725 794 5.246203 CCACCATAGCTAGCTATACCAAAGA 59.754 44.000 31.75 8.66 37.16 2.52
726 795 5.012148 ACCACCATAGCTAGCTATACCAAAG 59.988 44.000 31.75 19.93 37.16 2.77
727 796 4.905456 ACCACCATAGCTAGCTATACCAAA 59.095 41.667 31.75 10.16 37.16 3.28
728 797 4.489737 ACCACCATAGCTAGCTATACCAA 58.510 43.478 31.75 10.91 37.16 3.67
729 798 4.087182 GACCACCATAGCTAGCTATACCA 58.913 47.826 31.75 11.66 37.16 3.25
730 799 4.345854 AGACCACCATAGCTAGCTATACC 58.654 47.826 31.75 18.15 37.16 2.73
731 800 5.712917 AGAAGACCACCATAGCTAGCTATAC 59.287 44.000 31.75 19.23 37.16 1.47
732 801 5.893500 AGAAGACCACCATAGCTAGCTATA 58.106 41.667 31.75 13.20 37.16 1.31
733 802 4.746466 AGAAGACCACCATAGCTAGCTAT 58.254 43.478 28.08 28.08 39.60 2.97
734 803 4.186077 AGAAGACCACCATAGCTAGCTA 57.814 45.455 26.09 26.09 0.00 3.32
735 804 3.039252 AGAAGACCACCATAGCTAGCT 57.961 47.619 23.12 23.12 0.00 3.32
736 805 3.828875 AAGAAGACCACCATAGCTAGC 57.171 47.619 6.62 6.62 0.00 3.42
737 806 5.491982 ACAAAAGAAGACCACCATAGCTAG 58.508 41.667 0.00 0.00 0.00 3.42
738 807 5.499004 ACAAAAGAAGACCACCATAGCTA 57.501 39.130 0.00 0.00 0.00 3.32
739 808 4.373156 ACAAAAGAAGACCACCATAGCT 57.627 40.909 0.00 0.00 0.00 3.32
740 809 6.017852 GCTATACAAAAGAAGACCACCATAGC 60.018 42.308 0.00 0.00 32.89 2.97
741 810 7.275920 AGCTATACAAAAGAAGACCACCATAG 58.724 38.462 0.00 0.00 0.00 2.23
742 811 7.195374 AGCTATACAAAAGAAGACCACCATA 57.805 36.000 0.00 0.00 0.00 2.74
743 812 6.067217 AGCTATACAAAAGAAGACCACCAT 57.933 37.500 0.00 0.00 0.00 3.55
744 813 5.499004 AGCTATACAAAAGAAGACCACCA 57.501 39.130 0.00 0.00 0.00 4.17
745 814 5.524281 GCTAGCTATACAAAAGAAGACCACC 59.476 44.000 7.70 0.00 0.00 4.61
746 815 6.256757 CAGCTAGCTATACAAAAGAAGACCAC 59.743 42.308 18.86 0.00 0.00 4.16
747 816 6.341316 CAGCTAGCTATACAAAAGAAGACCA 58.659 40.000 18.86 0.00 0.00 4.02
748 817 5.235401 GCAGCTAGCTATACAAAAGAAGACC 59.765 44.000 18.86 0.00 41.15 3.85
749 818 5.051374 CGCAGCTAGCTATACAAAAGAAGAC 60.051 44.000 18.86 0.00 42.61 3.01
750 819 5.043903 CGCAGCTAGCTATACAAAAGAAGA 58.956 41.667 18.86 0.00 42.61 2.87
751 820 4.210120 CCGCAGCTAGCTATACAAAAGAAG 59.790 45.833 18.86 1.09 42.61 2.85
752 821 4.119862 CCGCAGCTAGCTATACAAAAGAA 58.880 43.478 18.86 0.00 42.61 2.52
753 822 3.132289 ACCGCAGCTAGCTATACAAAAGA 59.868 43.478 18.86 0.00 42.61 2.52
754 823 3.246226 CACCGCAGCTAGCTATACAAAAG 59.754 47.826 18.86 3.27 42.61 2.27
755 824 3.194861 CACCGCAGCTAGCTATACAAAA 58.805 45.455 18.86 0.00 42.61 2.44
756 825 2.483013 CCACCGCAGCTAGCTATACAAA 60.483 50.000 18.86 0.00 42.61 2.83
757 826 1.068588 CCACCGCAGCTAGCTATACAA 59.931 52.381 18.86 0.00 42.61 2.41
946 1079 4.215613 CCTTGTAGTTACTTCTTTGGCCAC 59.784 45.833 3.88 0.00 0.00 5.01
952 1085 6.082707 TCCTCCTCCTTGTAGTTACTTCTTT 58.917 40.000 0.00 0.00 0.00 2.52
1020 1153 4.702831 TGTTGTGATGCTCAACTAAGACA 58.297 39.130 11.92 0.00 43.54 3.41
1095 1228 2.485814 GCACTTGACCTTCACATTCCTC 59.514 50.000 0.00 0.00 0.00 3.71
1109 1242 6.888105 TCTGTGATATCCTTATTGCACTTGA 58.112 36.000 0.00 0.00 0.00 3.02
1132 1265 7.067496 TCATCCTTCCACTTATGTTATCCTC 57.933 40.000 0.00 0.00 0.00 3.71
1195 1328 3.004734 CAGCCGAAACCACTTTGAGAAAT 59.995 43.478 0.00 0.00 0.00 2.17
1359 1492 3.383761 CCTTGTTAGCCTGCACAAAAAG 58.616 45.455 0.00 0.00 32.53 2.27
1362 1495 0.673437 GCCTTGTTAGCCTGCACAAA 59.327 50.000 0.00 0.00 32.53 2.83
1412 1545 9.650539 CATATGGACTCCTAGTTCTTGATTATG 57.349 37.037 0.00 0.00 0.00 1.90
1413 1546 9.386122 ACATATGGACTCCTAGTTCTTGATTAT 57.614 33.333 7.80 0.00 0.00 1.28
1426 1559 9.475620 TTGAATATACGATACATATGGACTCCT 57.524 33.333 7.80 0.00 0.00 3.69
1570 1703 8.733458 TCATATCTCCAAGCATGCAAATAATAC 58.267 33.333 21.98 0.00 0.00 1.89
1575 1708 5.831525 TCTTCATATCTCCAAGCATGCAAAT 59.168 36.000 21.98 2.20 0.00 2.32
1627 1760 3.817647 GGAGATGTATCAAATGGGCTCAC 59.182 47.826 0.00 0.00 0.00 3.51
1772 1905 8.491331 AAAAACAAGCAATAAACATCAACTGT 57.509 26.923 0.00 0.00 40.84 3.55
1805 1938 6.990349 GGACTCCGTTTGATATTGATTTCCTA 59.010 38.462 0.00 0.00 0.00 2.94
2049 2185 2.254350 GGCGGCGGAACTTTTGAC 59.746 61.111 9.78 0.00 0.00 3.18
2084 2226 5.319043 ACTGGGTCTAGATTGGTTTTTGA 57.681 39.130 0.00 0.00 0.00 2.69
2115 2257 0.988145 ATGATTTCCCCTCCGGCAGA 60.988 55.000 0.00 0.00 0.00 4.26
2137 2281 2.658285 GATGATGAAGATGGCCACCAA 58.342 47.619 8.16 0.00 36.95 3.67
2162 2306 1.351080 CCTCCTCATCATGGTGGCCT 61.351 60.000 6.03 0.00 32.43 5.19
2244 2390 3.726291 TCGTGACATCTCAAGAACACA 57.274 42.857 0.00 0.00 32.63 3.72


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

AutoCloner maintained by Alex Coulton.