Multiple sequence alignment - TraesCS1D01G290400

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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 TraesCS1D01G290400 chr1D 100.000 2657 0 0 1 2657 388630778 388628122 0.000000e+00 4907.0
1 TraesCS1D01G290400 chr1D 97.849 837 14 2 1783 2619 388623435 388622603 0.000000e+00 1443.0
2 TraesCS1D01G290400 chr7D 92.978 826 53 5 1787 2611 116901224 116900403 0.000000e+00 1199.0
3 TraesCS1D01G290400 chr7D 87.995 833 96 4 1 831 249495002 249495832 0.000000e+00 981.0
4 TraesCS1D01G290400 chr7D 85.888 822 114 2 2 822 499836420 499837240 0.000000e+00 874.0
5 TraesCS1D01G290400 chr2D 92.668 832 45 9 1779 2608 575683268 575682451 0.000000e+00 1184.0
6 TraesCS1D01G290400 chr2D 92.476 824 56 2 1783 2605 610266426 610265608 0.000000e+00 1173.0
7 TraesCS1D01G290400 chr2D 92.354 824 57 2 1783 2605 610272015 610271197 0.000000e+00 1168.0
8 TraesCS1D01G290400 chr3A 92.597 824 60 1 1783 2605 294146260 294145437 0.000000e+00 1182.0
9 TraesCS1D01G290400 chr2B 92.579 822 60 1 2 822 693735517 693736338 0.000000e+00 1179.0
10 TraesCS1D01G290400 chr1B 90.247 933 47 19 863 1784 522007145 522006246 0.000000e+00 1179.0
11 TraesCS1D01G290400 chr5D 92.289 830 54 4 1778 2602 545133246 545132422 0.000000e+00 1170.0
12 TraesCS1D01G290400 chr5D 94.810 578 27 3 258 834 403623991 403623416 0.000000e+00 898.0
13 TraesCS1D01G290400 chr7A 91.696 843 64 2 1783 2619 699129258 699128416 0.000000e+00 1164.0
14 TraesCS1D01G290400 chr7A 89.538 822 86 0 1 822 711602658 711603479 0.000000e+00 1042.0
15 TraesCS1D01G290400 chr3D 91.647 838 67 3 1783 2619 17715624 17716459 0.000000e+00 1157.0
16 TraesCS1D01G290400 chr3D 81.697 825 140 10 3 821 561380584 561379765 0.000000e+00 676.0
17 TraesCS1D01G290400 chr3B 90.700 828 71 1 1 822 610180993 610180166 0.000000e+00 1098.0
18 TraesCS1D01G290400 chr3B 88.078 822 97 1 2 822 562915523 562914702 0.000000e+00 974.0
19 TraesCS1D01G290400 chr7B 90.743 821 58 1 1 821 732703368 732704170 0.000000e+00 1079.0
20 TraesCS1D01G290400 chr5B 87.728 823 99 2 2 822 560453126 560452304 0.000000e+00 959.0
21 TraesCS1D01G290400 chr5B 86.788 825 104 5 2 822 601388393 601387570 0.000000e+00 915.0
22 TraesCS1D01G290400 chr5B 81.643 828 141 9 3 825 704733390 704732569 0.000000e+00 676.0
23 TraesCS1D01G290400 chr1A 87.136 824 101 5 2 822 306671296 306670475 0.000000e+00 929.0
24 TraesCS1D01G290400 chr1A 86.804 826 67 28 861 1676 487695897 487695104 0.000000e+00 883.0
25 TraesCS1D01G290400 chr1A 80.387 826 125 25 3 822 540208873 540209667 6.330000e-166 593.0
26 TraesCS1D01G290400 chr1A 86.538 52 2 4 1684 1730 487695108 487695057 5.000000e-03 52.8
27 TraesCS1D01G290400 chr4B 86.634 823 101 3 2 822 596369188 596370003 0.000000e+00 902.0
28 TraesCS1D01G290400 chr4A 90.403 521 48 2 306 824 625881525 625882045 0.000000e+00 684.0
29 TraesCS1D01G290400 chr4A 81.588 831 140 10 3 825 610806122 610806947 0.000000e+00 675.0
30 TraesCS1D01G290400 chr6B 80.266 826 156 6 3 824 618145190 618144368 1.350000e-172 616.0
31 TraesCS1D01G290400 chrUn 80.828 725 105 22 1887 2592 386483299 386482590 3.010000e-149 538.0
32 TraesCS1D01G290400 chrUn 100.000 38 0 0 2620 2657 85481496 85481459 1.320000e-08 71.3
33 TraesCS1D01G290400 chr6D 100.000 38 0 0 2620 2657 28000181 28000218 1.320000e-08 71.3
34 TraesCS1D01G290400 chr6D 100.000 38 0 0 2620 2657 28004240 28004277 1.320000e-08 71.3
35 TraesCS1D01G290400 chr6D 100.000 38 0 0 2620 2657 75027074 75027037 1.320000e-08 71.3
36 TraesCS1D01G290400 chr6D 100.000 38 0 0 2620 2657 75163867 75163830 1.320000e-08 71.3
37 TraesCS1D01G290400 chr6D 100.000 38 0 0 2620 2657 99547281 99547244 1.320000e-08 71.3
38 TraesCS1D01G290400 chr6D 100.000 38 0 0 2620 2657 416664599 416664636 1.320000e-08 71.3
39 TraesCS1D01G290400 chr6D 100.000 38 0 0 2620 2657 416670194 416670231 1.320000e-08 71.3


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 TraesCS1D01G290400 chr1D 388628122 388630778 2656 True 4907.0 4907 100.000 1 2657 1 chr1D.!!$R2 2656
1 TraesCS1D01G290400 chr1D 388622603 388623435 832 True 1443.0 1443 97.849 1783 2619 1 chr1D.!!$R1 836
2 TraesCS1D01G290400 chr7D 116900403 116901224 821 True 1199.0 1199 92.978 1787 2611 1 chr7D.!!$R1 824
3 TraesCS1D01G290400 chr7D 249495002 249495832 830 False 981.0 981 87.995 1 831 1 chr7D.!!$F1 830
4 TraesCS1D01G290400 chr7D 499836420 499837240 820 False 874.0 874 85.888 2 822 1 chr7D.!!$F2 820
5 TraesCS1D01G290400 chr2D 575682451 575683268 817 True 1184.0 1184 92.668 1779 2608 1 chr2D.!!$R1 829
6 TraesCS1D01G290400 chr2D 610265608 610266426 818 True 1173.0 1173 92.476 1783 2605 1 chr2D.!!$R2 822
7 TraesCS1D01G290400 chr2D 610271197 610272015 818 True 1168.0 1168 92.354 1783 2605 1 chr2D.!!$R3 822
8 TraesCS1D01G290400 chr3A 294145437 294146260 823 True 1182.0 1182 92.597 1783 2605 1 chr3A.!!$R1 822
9 TraesCS1D01G290400 chr2B 693735517 693736338 821 False 1179.0 1179 92.579 2 822 1 chr2B.!!$F1 820
10 TraesCS1D01G290400 chr1B 522006246 522007145 899 True 1179.0 1179 90.247 863 1784 1 chr1B.!!$R1 921
11 TraesCS1D01G290400 chr5D 545132422 545133246 824 True 1170.0 1170 92.289 1778 2602 1 chr5D.!!$R2 824
12 TraesCS1D01G290400 chr5D 403623416 403623991 575 True 898.0 898 94.810 258 834 1 chr5D.!!$R1 576
13 TraesCS1D01G290400 chr7A 699128416 699129258 842 True 1164.0 1164 91.696 1783 2619 1 chr7A.!!$R1 836
14 TraesCS1D01G290400 chr7A 711602658 711603479 821 False 1042.0 1042 89.538 1 822 1 chr7A.!!$F1 821
15 TraesCS1D01G290400 chr3D 17715624 17716459 835 False 1157.0 1157 91.647 1783 2619 1 chr3D.!!$F1 836
16 TraesCS1D01G290400 chr3D 561379765 561380584 819 True 676.0 676 81.697 3 821 1 chr3D.!!$R1 818
17 TraesCS1D01G290400 chr3B 610180166 610180993 827 True 1098.0 1098 90.700 1 822 1 chr3B.!!$R2 821
18 TraesCS1D01G290400 chr3B 562914702 562915523 821 True 974.0 974 88.078 2 822 1 chr3B.!!$R1 820
19 TraesCS1D01G290400 chr7B 732703368 732704170 802 False 1079.0 1079 90.743 1 821 1 chr7B.!!$F1 820
20 TraesCS1D01G290400 chr5B 560452304 560453126 822 True 959.0 959 87.728 2 822 1 chr5B.!!$R1 820
21 TraesCS1D01G290400 chr5B 601387570 601388393 823 True 915.0 915 86.788 2 822 1 chr5B.!!$R2 820
22 TraesCS1D01G290400 chr5B 704732569 704733390 821 True 676.0 676 81.643 3 825 1 chr5B.!!$R3 822
23 TraesCS1D01G290400 chr1A 306670475 306671296 821 True 929.0 929 87.136 2 822 1 chr1A.!!$R1 820
24 TraesCS1D01G290400 chr1A 540208873 540209667 794 False 593.0 593 80.387 3 822 1 chr1A.!!$F1 819
25 TraesCS1D01G290400 chr1A 487695057 487695897 840 True 467.9 883 86.671 861 1730 2 chr1A.!!$R2 869
26 TraesCS1D01G290400 chr4B 596369188 596370003 815 False 902.0 902 86.634 2 822 1 chr4B.!!$F1 820
27 TraesCS1D01G290400 chr4A 625881525 625882045 520 False 684.0 684 90.403 306 824 1 chr4A.!!$F2 518
28 TraesCS1D01G290400 chr4A 610806122 610806947 825 False 675.0 675 81.588 3 825 1 chr4A.!!$F1 822
29 TraesCS1D01G290400 chr6B 618144368 618145190 822 True 616.0 616 80.266 3 824 1 chr6B.!!$R1 821
30 TraesCS1D01G290400 chrUn 386482590 386483299 709 True 538.0 538 80.828 1887 2592 1 chrUn.!!$R2 705

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
956 992 0.033601 TATCGCCTGCAAACCCCAAT 60.034 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2625 2707 2.105306 CCCCACATGTATGAGCATGAGA 59.895 50.0 12.27 0.0 46.65 3.27 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 0.106521 TGCTTGAGTGTACTGCTGCA 59.893 50.000 0.88 0.88 0.00 4.41
25 26 2.357517 AGTGTACTGCTGCACGGC 60.358 61.111 0.00 0.00 40.26 5.68
51 52 1.281867 TGGTCATTGGTGGATCAGGAC 59.718 52.381 0.00 0.00 0.00 3.85
395 397 1.526917 GTGGAGTTGGTGCAGCTGT 60.527 57.895 18.08 0.87 0.00 4.40
585 591 9.289782 GAGGTGGTGAAGCATATTAAAGATAAT 57.710 33.333 0.00 0.00 35.85 1.28
591 597 9.617975 GTGAAGCATATTAAAGATAATTCAGGC 57.382 33.333 0.00 0.00 33.75 4.85
610 616 1.943968 GCGGAAACTATGGTGCAGTCA 60.944 52.381 0.00 0.00 0.00 3.41
625 631 7.988737 TGGTGCAGTCATAAAAGAGATTATTG 58.011 34.615 0.00 0.00 0.00 1.90
743 775 0.314935 CATGGCCGCCATATTTGGTC 59.685 55.000 24.66 0.00 43.15 4.02
809 842 7.608761 ACCAACGATTGAATAAAGCCTAGTTTA 59.391 33.333 0.00 0.00 0.00 2.01
854 887 9.921637 AAAAACTTGTGTTCTAAAATTGTCTCA 57.078 25.926 0.00 0.00 34.96 3.27
855 888 9.921637 AAAACTTGTGTTCTAAAATTGTCTCAA 57.078 25.926 0.00 0.00 34.96 3.02
856 889 9.921637 AAACTTGTGTTCTAAAATTGTCTCAAA 57.078 25.926 0.00 0.00 34.96 2.69
857 890 9.921637 AACTTGTGTTCTAAAATTGTCTCAAAA 57.078 25.926 0.00 0.00 0.00 2.44
858 891 9.921637 ACTTGTGTTCTAAAATTGTCTCAAAAA 57.078 25.926 0.00 0.00 0.00 1.94
925 958 8.599792 GGGTTGGCCTGTCTATTATAAATAGTA 58.400 37.037 3.32 0.00 34.45 1.82
926 959 9.654663 GGTTGGCCTGTCTATTATAAATAGTAG 57.345 37.037 3.32 6.63 0.00 2.57
944 980 0.556747 AGTCTACCAGGGTATCGCCT 59.443 55.000 0.00 0.00 37.43 5.52
954 990 1.377987 GTATCGCCTGCAAACCCCA 60.378 57.895 0.00 0.00 0.00 4.96
956 992 0.033601 TATCGCCTGCAAACCCCAAT 60.034 50.000 0.00 0.00 0.00 3.16
961 997 0.835543 CCTGCAAACCCCAATCCCAA 60.836 55.000 0.00 0.00 0.00 4.12
962 998 1.278537 CTGCAAACCCCAATCCCAAT 58.721 50.000 0.00 0.00 0.00 3.16
974 1010 4.968080 CCCAATCCCAATCCCAATCTTAAA 59.032 41.667 0.00 0.00 0.00 1.52
984 1020 2.365582 CCAATCTTAAACCCACTCCCG 58.634 52.381 0.00 0.00 0.00 5.14
1019 1055 3.379445 GGCAGAGAACCGACCGGA 61.379 66.667 16.07 0.00 38.96 5.14
1063 1099 1.870055 GCGGTTCGTGGTCTCCTACA 61.870 60.000 0.00 0.00 0.00 2.74
1074 1110 2.992689 TCCTACAGCGCGAACCCA 60.993 61.111 12.10 0.00 0.00 4.51
1148 1184 2.995872 GCGAGACGGAGGAGCAGTT 61.996 63.158 0.00 0.00 0.00 3.16
1296 1335 4.379243 CGGTGCTTCGGCCTCACT 62.379 66.667 0.00 0.00 40.91 3.41
1318 1357 4.361971 AGACCCTCGTCGGCAGGA 62.362 66.667 7.03 0.00 44.28 3.86
1339 1378 2.596338 TGGAGCTCGACCACGTCA 60.596 61.111 7.83 0.00 40.69 4.35
1353 1392 4.065281 GTCAGCGGCACCTACGGT 62.065 66.667 1.45 0.00 43.47 4.83
1449 1488 1.363744 GGTTCATCAGCAACGAGGAG 58.636 55.000 0.00 0.00 0.00 3.69
1583 1622 5.030993 GAGGATCAGCGACGAAGAATTCAT 61.031 45.833 8.44 0.00 39.53 2.57
1617 1668 4.564782 TTTCATTGATGAGCTCCTGACT 57.435 40.909 12.15 0.00 38.19 3.41
1671 1722 3.873952 GCATTTAGAAGAGATCGGTGCTT 59.126 43.478 0.00 0.00 0.00 3.91
1672 1723 4.260538 GCATTTAGAAGAGATCGGTGCTTG 60.261 45.833 0.00 0.00 0.00 4.01
1673 1724 4.801330 TTTAGAAGAGATCGGTGCTTGA 57.199 40.909 0.00 0.00 0.00 3.02
1674 1725 4.801330 TTAGAAGAGATCGGTGCTTGAA 57.199 40.909 0.00 0.00 0.00 2.69
1675 1726 3.244033 AGAAGAGATCGGTGCTTGAAG 57.756 47.619 0.00 0.00 0.00 3.02
1676 1727 2.564947 AGAAGAGATCGGTGCTTGAAGT 59.435 45.455 0.00 0.00 0.00 3.01
1677 1728 2.376808 AGAGATCGGTGCTTGAAGTG 57.623 50.000 0.00 0.00 0.00 3.16
1678 1729 1.895798 AGAGATCGGTGCTTGAAGTGA 59.104 47.619 0.00 0.00 0.00 3.41
1679 1730 2.300152 AGAGATCGGTGCTTGAAGTGAA 59.700 45.455 0.00 0.00 0.00 3.18
1680 1731 2.670414 GAGATCGGTGCTTGAAGTGAAG 59.330 50.000 0.00 0.00 0.00 3.02
1681 1732 1.734465 GATCGGTGCTTGAAGTGAAGG 59.266 52.381 0.00 0.00 0.00 3.46
1682 1733 0.884704 TCGGTGCTTGAAGTGAAGGC 60.885 55.000 0.00 0.00 0.00 4.35
1711 1769 2.852449 TCTGGATGGTCCTTGGCTTAAT 59.148 45.455 0.00 0.00 37.46 1.40
1733 1796 1.970640 GTGCCCCCTTGAAACTTCAAT 59.029 47.619 5.38 0.00 45.26 2.57
1740 1803 5.047306 CCCCCTTGAAACTTCAATTTCCTAC 60.047 44.000 5.38 0.00 45.26 3.18
1753 1816 9.495572 CTTCAATTTCCTACTCTTTCTTGTACT 57.504 33.333 0.00 0.00 0.00 2.73
1755 1818 9.924650 TCAATTTCCTACTCTTTCTTGTACTAC 57.075 33.333 0.00 0.00 0.00 2.73
1756 1819 8.861101 CAATTTCCTACTCTTTCTTGTACTACG 58.139 37.037 0.00 0.00 0.00 3.51
1757 1820 7.516198 TTTCCTACTCTTTCTTGTACTACGT 57.484 36.000 0.00 0.00 0.00 3.57
1758 1821 8.621532 TTTCCTACTCTTTCTTGTACTACGTA 57.378 34.615 0.00 0.00 0.00 3.57
1759 1822 7.602517 TCCTACTCTTTCTTGTACTACGTAC 57.397 40.000 0.00 0.00 39.24 3.67
1762 1825 8.816144 CCTACTCTTTCTTGTACTACGTACTAG 58.184 40.741 8.61 8.61 40.99 2.57
1774 1837 6.111768 ACTACGTACTAGTATTTGTCACGG 57.888 41.667 14.57 3.02 33.53 4.94
1776 1839 4.974591 ACGTACTAGTATTTGTCACGGTC 58.025 43.478 14.57 0.00 32.52 4.79
2359 2438 1.611936 GGAAGGAGAAGTTCTGGTGCC 60.612 57.143 10.90 5.13 0.00 5.01
2547 2629 2.562298 TGTGACCTTTCGTATACCCGTT 59.438 45.455 0.00 0.00 0.00 4.44
2625 2707 3.564455 GTCGTGACGAGGTCTTGTT 57.436 52.632 8.41 0.00 36.23 2.83
2626 2708 1.406447 GTCGTGACGAGGTCTTGTTC 58.594 55.000 8.41 0.00 36.23 3.18
2627 2709 1.001597 GTCGTGACGAGGTCTTGTTCT 60.002 52.381 8.41 0.00 36.23 3.01
2628 2710 1.266175 TCGTGACGAGGTCTTGTTCTC 59.734 52.381 2.39 0.00 33.15 2.87
2629 2711 1.001706 CGTGACGAGGTCTTGTTCTCA 60.002 52.381 0.00 0.00 33.15 3.27
2630 2712 2.351835 CGTGACGAGGTCTTGTTCTCAT 60.352 50.000 0.00 0.00 33.15 2.90
2631 2713 2.989840 GTGACGAGGTCTTGTTCTCATG 59.010 50.000 0.00 0.00 33.15 3.07
2632 2714 1.996191 GACGAGGTCTTGTTCTCATGC 59.004 52.381 0.00 0.00 0.00 4.06
2633 2715 1.620819 ACGAGGTCTTGTTCTCATGCT 59.379 47.619 0.00 0.00 0.00 3.79
2634 2716 2.266554 CGAGGTCTTGTTCTCATGCTC 58.733 52.381 0.00 0.00 0.00 4.26
2635 2717 2.353109 CGAGGTCTTGTTCTCATGCTCA 60.353 50.000 0.00 0.00 0.00 4.26
2636 2718 3.678252 CGAGGTCTTGTTCTCATGCTCAT 60.678 47.826 0.00 0.00 0.00 2.90
2637 2719 4.440663 CGAGGTCTTGTTCTCATGCTCATA 60.441 45.833 0.00 0.00 0.00 2.15
2638 2720 4.764172 AGGTCTTGTTCTCATGCTCATAC 58.236 43.478 0.00 0.00 0.00 2.39
2639 2721 4.223700 AGGTCTTGTTCTCATGCTCATACA 59.776 41.667 0.00 0.00 0.00 2.29
2640 2722 5.104610 AGGTCTTGTTCTCATGCTCATACAT 60.105 40.000 0.00 0.00 0.00 2.29
2642 2724 5.583854 GTCTTGTTCTCATGCTCATACATGT 59.416 40.000 2.69 2.69 46.15 3.21
2643 2725 5.583457 TCTTGTTCTCATGCTCATACATGTG 59.417 40.000 9.11 2.84 46.15 3.21
2644 2726 4.193865 TGTTCTCATGCTCATACATGTGG 58.806 43.478 9.11 0.25 46.15 4.17
2645 2727 3.480505 TCTCATGCTCATACATGTGGG 57.519 47.619 9.11 0.00 46.15 4.61
2646 2728 2.105306 TCTCATGCTCATACATGTGGGG 59.895 50.000 9.11 1.30 46.15 4.96
2647 2729 2.105306 CTCATGCTCATACATGTGGGGA 59.895 50.000 9.11 2.18 46.15 4.81
2648 2730 2.509131 TCATGCTCATACATGTGGGGAA 59.491 45.455 9.11 0.00 46.15 3.97
2649 2731 3.053768 TCATGCTCATACATGTGGGGAAA 60.054 43.478 9.11 0.00 46.15 3.13
2650 2732 3.003394 TGCTCATACATGTGGGGAAAG 57.997 47.619 9.11 0.00 0.00 2.62
2651 2733 2.575735 TGCTCATACATGTGGGGAAAGA 59.424 45.455 9.11 0.00 0.00 2.52
2652 2734 3.010027 TGCTCATACATGTGGGGAAAGAA 59.990 43.478 9.11 0.00 0.00 2.52
2653 2735 3.378427 GCTCATACATGTGGGGAAAGAAC 59.622 47.826 9.11 0.00 0.00 3.01
2654 2736 3.947834 CTCATACATGTGGGGAAAGAACC 59.052 47.826 9.11 0.00 0.00 3.62
2655 2737 3.591527 TCATACATGTGGGGAAAGAACCT 59.408 43.478 9.11 0.00 0.00 3.50
2656 2738 2.586648 ACATGTGGGGAAAGAACCTC 57.413 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.652012 CAATGACCAAACACGCCGT 59.348 52.632 0.00 0.00 0.00 5.68
25 26 1.313772 TCCACCAATGACCAAACACG 58.686 50.000 0.00 0.00 0.00 4.49
51 52 4.000331 ACTCCGCAGATCATCAATTAGG 58.000 45.455 0.00 0.00 0.00 2.69
585 591 1.948611 GCACCATAGTTTCCGCCTGAA 60.949 52.381 0.00 0.00 0.00 3.02
591 597 2.093306 TGACTGCACCATAGTTTCCG 57.907 50.000 0.00 0.00 0.00 4.30
625 631 7.675637 GCAAGAATTAAAAGAAGATTGCCATGC 60.676 37.037 0.00 0.00 36.64 4.06
743 775 1.048601 AGTATCATGTGGTAGCCCCG 58.951 55.000 0.00 0.00 35.15 5.73
831 864 9.921637 TTTTGAGACAATTTTAGAACACAAGTT 57.078 25.926 0.00 0.00 41.64 2.66
832 865 9.921637 TTTTTGAGACAATTTTAGAACACAAGT 57.078 25.926 0.00 0.00 0.00 3.16
855 888 0.379316 GGCACGACCACGAAGTTTTT 59.621 50.000 0.00 0.00 41.61 1.94
856 889 2.019337 GGCACGACCACGAAGTTTT 58.981 52.632 0.00 0.00 41.61 2.43
857 890 3.727146 GGCACGACCACGAAGTTT 58.273 55.556 0.00 0.00 41.61 2.66
925 958 0.556747 AGGCGATACCCTGGTAGACT 59.443 55.000 2.05 0.00 40.58 3.24
926 959 0.674534 CAGGCGATACCCTGGTAGAC 59.325 60.000 2.05 0.00 46.93 2.59
927 960 3.127099 CAGGCGATACCCTGGTAGA 57.873 57.895 2.05 0.00 46.93 2.59
940 976 2.573340 GATTGGGGTTTGCAGGCG 59.427 61.111 0.00 0.00 0.00 5.52
944 980 1.274712 GATTGGGATTGGGGTTTGCA 58.725 50.000 0.00 0.00 0.00 4.08
954 990 4.968719 GGGTTTAAGATTGGGATTGGGATT 59.031 41.667 0.00 0.00 0.00 3.01
956 992 3.338214 TGGGTTTAAGATTGGGATTGGGA 59.662 43.478 0.00 0.00 0.00 4.37
961 997 3.052869 GGGAGTGGGTTTAAGATTGGGAT 60.053 47.826 0.00 0.00 0.00 3.85
962 998 2.310647 GGGAGTGGGTTTAAGATTGGGA 59.689 50.000 0.00 0.00 0.00 4.37
1000 1036 2.579201 CGGTCGGTTCTCTGCCAT 59.421 61.111 0.00 0.00 0.00 4.40
1001 1037 3.691342 CCGGTCGGTTCTCTGCCA 61.691 66.667 0.55 0.00 0.00 4.92
1003 1039 2.182030 CTCCGGTCGGTTCTCTGC 59.818 66.667 9.36 0.00 36.47 4.26
1019 1055 1.738099 GTGCTGTTCGCCATCGTCT 60.738 57.895 0.00 0.00 38.05 4.18
1058 1094 2.813908 GTGGGTTCGCGCTGTAGG 60.814 66.667 5.56 0.00 0.00 3.18
1083 1119 2.450502 AGCTTCACCACCAGGGGT 60.451 61.111 0.00 0.00 43.56 4.95
1318 1357 3.681835 GTGGTCGAGCTCCACGGT 61.682 66.667 16.64 0.00 44.34 4.83
1449 1488 0.458716 GAGCTCGAAGGTACCTGTGC 60.459 60.000 17.14 15.89 0.00 4.57
1583 1622 2.016318 CAATGAAATAGCCCGTGAGCA 58.984 47.619 0.00 0.00 34.23 4.26
1587 1626 3.304257 GCTCATCAATGAAATAGCCCGTG 60.304 47.826 4.20 0.00 36.18 4.94
1671 1722 2.105477 AGAAGCTTCAGCCTTCACTTCA 59.895 45.455 27.57 0.00 43.38 3.02
1672 1723 2.483491 CAGAAGCTTCAGCCTTCACTTC 59.517 50.000 27.57 0.00 43.38 3.01
1673 1724 2.502295 CAGAAGCTTCAGCCTTCACTT 58.498 47.619 27.57 0.28 43.38 3.16
1674 1725 1.271271 CCAGAAGCTTCAGCCTTCACT 60.271 52.381 27.57 1.05 43.38 3.41
1675 1726 1.163554 CCAGAAGCTTCAGCCTTCAC 58.836 55.000 27.57 0.00 43.38 3.18
1676 1727 1.059098 TCCAGAAGCTTCAGCCTTCA 58.941 50.000 27.57 2.04 43.38 3.02
1677 1728 2.015587 CATCCAGAAGCTTCAGCCTTC 58.984 52.381 27.57 0.00 43.38 3.46
1678 1729 1.340795 CCATCCAGAAGCTTCAGCCTT 60.341 52.381 27.57 4.18 43.38 4.35
1679 1730 0.255318 CCATCCAGAAGCTTCAGCCT 59.745 55.000 27.57 4.58 43.38 4.58
1680 1731 0.034670 ACCATCCAGAAGCTTCAGCC 60.035 55.000 27.57 1.65 43.38 4.85
1681 1732 1.377536 GACCATCCAGAAGCTTCAGC 58.622 55.000 27.57 2.05 42.49 4.26
1682 1733 1.558756 AGGACCATCCAGAAGCTTCAG 59.441 52.381 27.57 19.78 39.61 3.02
1711 1769 3.164080 TGAAGTTTCAAGGGGGCACCA 62.164 52.381 9.35 0.00 42.72 4.17
1733 1796 7.516198 ACGTAGTACAAGAAAGAGTAGGAAA 57.484 36.000 0.38 0.00 41.94 3.13
1753 1816 5.641636 TGACCGTGACAAATACTAGTACGTA 59.358 40.000 4.31 0.00 0.00 3.57
1755 1818 4.973396 TGACCGTGACAAATACTAGTACG 58.027 43.478 4.31 4.92 0.00 3.67
1756 1819 7.383300 AGTTTTGACCGTGACAAATACTAGTAC 59.617 37.037 4.31 0.00 37.15 2.73
1757 1820 7.383029 CAGTTTTGACCGTGACAAATACTAGTA 59.617 37.037 4.77 4.77 37.15 1.82
1758 1821 6.202188 CAGTTTTGACCGTGACAAATACTAGT 59.798 38.462 0.00 0.00 37.15 2.57
1759 1822 6.202188 ACAGTTTTGACCGTGACAAATACTAG 59.798 38.462 0.00 0.00 37.15 2.57
1762 1825 5.164606 ACAGTTTTGACCGTGACAAATAC 57.835 39.130 0.00 0.00 37.15 1.89
1774 1837 6.446318 TGCTCATATTTCCAACAGTTTTGAC 58.554 36.000 0.00 0.00 0.00 3.18
1776 1839 7.894376 ATTGCTCATATTTCCAACAGTTTTG 57.106 32.000 0.00 0.00 0.00 2.44
2547 2629 3.181486 TGTCTAAATTTTTGCCACGCACA 60.181 39.130 0.00 0.00 38.71 4.57
2619 2701 5.583457 CACATGTATGAGCATGAGAACAAGA 59.417 40.000 12.27 0.00 46.65 3.02
2620 2702 5.220796 CCACATGTATGAGCATGAGAACAAG 60.221 44.000 12.27 0.00 46.65 3.16
2621 2703 4.637091 CCACATGTATGAGCATGAGAACAA 59.363 41.667 12.27 0.00 46.65 2.83
2622 2704 4.193865 CCACATGTATGAGCATGAGAACA 58.806 43.478 12.27 0.00 46.65 3.18
2624 2706 3.434024 CCCCACATGTATGAGCATGAGAA 60.434 47.826 12.27 0.00 46.65 2.87
2625 2707 2.105306 CCCCACATGTATGAGCATGAGA 59.895 50.000 12.27 0.00 46.65 3.27
2626 2708 2.105306 TCCCCACATGTATGAGCATGAG 59.895 50.000 12.27 5.04 46.65 2.90
2627 2709 2.126057 TCCCCACATGTATGAGCATGA 58.874 47.619 12.27 0.00 46.65 3.07
2629 2711 3.202818 TCTTTCCCCACATGTATGAGCAT 59.797 43.478 0.00 0.00 0.00 3.79
2630 2712 2.575735 TCTTTCCCCACATGTATGAGCA 59.424 45.455 0.00 0.00 0.00 4.26
2631 2713 3.281727 TCTTTCCCCACATGTATGAGC 57.718 47.619 0.00 0.00 0.00 4.26
2632 2714 3.947834 GGTTCTTTCCCCACATGTATGAG 59.052 47.826 0.00 0.00 0.00 2.90
2633 2715 3.591527 AGGTTCTTTCCCCACATGTATGA 59.408 43.478 0.00 0.00 0.00 2.15
2634 2716 3.947834 GAGGTTCTTTCCCCACATGTATG 59.052 47.826 0.00 0.00 0.00 2.39
2635 2717 4.236527 GAGGTTCTTTCCCCACATGTAT 57.763 45.455 0.00 0.00 0.00 2.29
2636 2718 3.713826 GAGGTTCTTTCCCCACATGTA 57.286 47.619 0.00 0.00 0.00 2.29
2637 2719 2.586648 GAGGTTCTTTCCCCACATGT 57.413 50.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.