Multiple sequence alignment - TraesCS3A01G147600

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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 TraesCS3A01G147600 chr3A 100.000 3541 0 0 1 3541 130833725 130837265 0.000000e+00 6540.0
1 TraesCS3A01G147600 chr3A 88.029 685 46 24 1 673 493096542 493097202 0.000000e+00 778.0
2 TraesCS3A01G147600 chr3A 79.104 201 25 8 1 199 118452247 118452432 4.800000e-24 122.0
3 TraesCS3A01G147600 chr3B 93.049 2762 121 22 821 3541 175756113 175758844 0.000000e+00 3971.0
4 TraesCS3A01G147600 chr3B 93.478 46 3 0 783 828 771341747 771341702 6.340000e-08 69.4
5 TraesCS3A01G147600 chr3B 93.478 46 3 0 783 828 819036560 819036605 6.340000e-08 69.4
6 TraesCS3A01G147600 chr3D 93.594 1889 83 15 821 2696 123294748 123296611 0.000000e+00 2784.0
7 TraesCS3A01G147600 chr3D 90.394 864 40 17 2697 3541 123296660 123297499 0.000000e+00 1096.0
8 TraesCS3A01G147600 chr3D 89.333 675 45 18 1 666 603118574 603119230 0.000000e+00 822.0
9 TraesCS3A01G147600 chr3D 98.276 58 1 0 667 724 123294700 123294757 6.250000e-18 102.0
10 TraesCS3A01G147600 chr3D 94.000 50 3 0 743 792 588863474 588863425 3.790000e-10 76.8
11 TraesCS3A01G147600 chr6D 88.889 675 50 19 6 674 423361276 423361931 0.000000e+00 808.0
12 TraesCS3A01G147600 chr6D 88.053 678 56 16 7 674 22137589 22136927 0.000000e+00 780.0
13 TraesCS3A01G147600 chr6D 93.878 49 1 2 739 785 2528651 2528699 4.900000e-09 73.1
14 TraesCS3A01G147600 chr6D 85.965 57 5 3 772 828 97016245 97016298 1.370000e-04 58.4
15 TraesCS3A01G147600 chr2D 88.462 676 57 16 6 672 160320058 160320721 0.000000e+00 797.0
16 TraesCS3A01G147600 chr2D 97.059 34 1 0 745 778 14836445 14836412 1.370000e-04 58.4
17 TraesCS3A01G147600 chr7D 88.341 669 55 17 6 668 461778753 461778102 0.000000e+00 782.0
18 TraesCS3A01G147600 chr7D 87.722 676 56 15 6 672 134434011 134434668 0.000000e+00 763.0
19 TraesCS3A01G147600 chr1A 89.189 629 53 10 48 672 549883927 549883310 0.000000e+00 771.0
20 TraesCS3A01G147600 chr4A 86.812 690 66 15 1 676 89949971 89950649 0.000000e+00 747.0
21 TraesCS3A01G147600 chr4A 91.525 59 4 1 772 830 490530137 490530194 2.930000e-11 80.5
22 TraesCS3A01G147600 chr4A 93.478 46 3 0 783 828 179474259 179474304 6.340000e-08 69.4
23 TraesCS3A01G147600 chr4A 91.489 47 3 1 782 828 649878117 649878072 2.950000e-06 63.9
24 TraesCS3A01G147600 chr2A 83.858 254 28 10 1 253 678958239 678958480 2.750000e-56 230.0
25 TraesCS3A01G147600 chr2A 95.238 42 1 1 745 786 28674018 28674058 8.210000e-07 65.8
26 TraesCS3A01G147600 chr2B 93.617 47 3 0 783 829 697984241 697984287 1.760000e-08 71.3
27 TraesCS3A01G147600 chr6B 89.286 56 4 2 783 837 73901080 73901134 6.340000e-08 69.4
28 TraesCS3A01G147600 chr6B 91.837 49 4 0 782 830 192051573 192051621 6.340000e-08 69.4
29 TraesCS3A01G147600 chr4B 95.455 44 1 1 743 785 136524145 136524188 6.340000e-08 69.4
30 TraesCS3A01G147600 chr1B 91.837 49 2 2 740 786 668084845 668084893 2.280000e-07 67.6
31 TraesCS3A01G147600 chr1B 100.000 28 0 0 749 776 667325655 667325682 6.000000e-03 52.8
32 TraesCS3A01G147600 chr7B 92.857 42 3 0 749 790 507837196 507837155 1.060000e-05 62.1


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 TraesCS3A01G147600 chr3A 130833725 130837265 3540 False 6540.000000 6540 100.000 1 3541 1 chr3A.!!$F2 3540
1 TraesCS3A01G147600 chr3A 493096542 493097202 660 False 778.000000 778 88.029 1 673 1 chr3A.!!$F3 672
2 TraesCS3A01G147600 chr3B 175756113 175758844 2731 False 3971.000000 3971 93.049 821 3541 1 chr3B.!!$F1 2720
3 TraesCS3A01G147600 chr3D 123294700 123297499 2799 False 1327.333333 2784 94.088 667 3541 3 chr3D.!!$F2 2874
4 TraesCS3A01G147600 chr3D 603118574 603119230 656 False 822.000000 822 89.333 1 666 1 chr3D.!!$F1 665
5 TraesCS3A01G147600 chr6D 423361276 423361931 655 False 808.000000 808 88.889 6 674 1 chr6D.!!$F3 668
6 TraesCS3A01G147600 chr6D 22136927 22137589 662 True 780.000000 780 88.053 7 674 1 chr6D.!!$R1 667
7 TraesCS3A01G147600 chr2D 160320058 160320721 663 False 797.000000 797 88.462 6 672 1 chr2D.!!$F1 666
8 TraesCS3A01G147600 chr7D 461778102 461778753 651 True 782.000000 782 88.341 6 668 1 chr7D.!!$R1 662
9 TraesCS3A01G147600 chr7D 134434011 134434668 657 False 763.000000 763 87.722 6 672 1 chr7D.!!$F1 666
10 TraesCS3A01G147600 chr1A 549883310 549883927 617 True 771.000000 771 89.189 48 672 1 chr1A.!!$R1 624
11 TraesCS3A01G147600 chr4A 89949971 89950649 678 False 747.000000 747 86.812 1 676 1 chr4A.!!$F1 675

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
513 551 0.248539 CCAAAACGTCGCGGGAAAAA 60.249 50.000 6.13 0.0 0.00 1.94 F
515 554 0.248580 AAAACGTCGCGGGAAAAACC 60.249 50.000 6.13 0.0 38.08 3.27 F
882 931 1.135721 GCATGGCAGAAGGAAATCACC 59.864 52.381 0.00 0.0 0.00 4.02 F
2319 2385 0.107017 CCCGATCTTCATGGCAGGTT 60.107 55.000 0.00 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1531 1587 0.029567 CGAGCAAGGCGACTAGTAGG 59.970 60.0 5.08 0.0 42.68 3.18 R
1534 1590 0.109226 GAACGAGCAAGGCGACTAGT 60.109 55.0 0.00 0.0 42.68 2.57 R
2455 2521 0.579630 CGTCTCCTCGTCGAGATCAG 59.420 60.0 23.74 15.0 40.89 2.90 R
3316 3455 2.087501 TGGTACATAACAGGTGTGCG 57.912 50.0 0.00 0.0 33.68 5.34 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
18 21 3.876589 TTTCGAGAGGCACCACCGC 62.877 63.158 0.00 0.00 46.52 5.68
269 280 1.226547 CGCAAAAGCACAACCGTGT 60.227 52.632 0.00 0.00 45.50 4.49
376 393 2.993899 CTCTCGATAAAGCACAACCGTT 59.006 45.455 0.00 0.00 0.00 4.44
505 536 0.595567 GGGGAAAACCAAAACGTCGC 60.596 55.000 0.00 0.00 42.91 5.19
506 537 0.931202 GGGAAAACCAAAACGTCGCG 60.931 55.000 0.00 0.00 39.85 5.87
507 538 0.931202 GGAAAACCAAAACGTCGCGG 60.931 55.000 6.13 0.00 0.00 6.46
508 539 0.931202 GAAAACCAAAACGTCGCGGG 60.931 55.000 6.13 0.00 0.00 6.13
513 551 0.248539 CCAAAACGTCGCGGGAAAAA 60.249 50.000 6.13 0.00 0.00 1.94
515 554 0.248580 AAAACGTCGCGGGAAAAACC 60.249 50.000 6.13 0.00 38.08 3.27
721 770 4.033358 GCGCGAATATCCTGATATGAAAGG 59.967 45.833 12.10 0.00 34.45 3.11
722 771 5.171476 CGCGAATATCCTGATATGAAAGGT 58.829 41.667 0.00 0.00 34.45 3.50
723 772 6.330278 CGCGAATATCCTGATATGAAAGGTA 58.670 40.000 0.00 0.00 34.45 3.08
724 773 6.253727 CGCGAATATCCTGATATGAAAGGTAC 59.746 42.308 0.00 0.00 34.45 3.34
725 774 7.324178 GCGAATATCCTGATATGAAAGGTACT 58.676 38.462 0.57 0.00 35.29 2.73
726 775 7.819900 GCGAATATCCTGATATGAAAGGTACTT 59.180 37.037 0.57 0.00 41.48 2.24
727 776 9.712305 CGAATATCCTGATATGAAAGGTACTTT 57.288 33.333 0.57 0.00 46.15 2.66
744 793 8.442632 AGGTACTTTTTAGTACAAAGTTGACC 57.557 34.615 17.26 17.87 44.60 4.02
745 794 8.048514 AGGTACTTTTTAGTACAAAGTTGACCA 58.951 33.333 23.55 6.84 41.46 4.02
746 795 8.843262 GGTACTTTTTAGTACAAAGTTGACCAT 58.157 33.333 19.87 2.01 44.60 3.55
747 796 9.659830 GTACTTTTTAGTACAAAGTTGACCATG 57.340 33.333 17.26 0.00 40.83 3.66
748 797 8.288689 ACTTTTTAGTACAAAGTTGACCATGT 57.711 30.769 8.35 0.00 40.83 3.21
749 798 8.188139 ACTTTTTAGTACAAAGTTGACCATGTG 58.812 33.333 8.35 0.00 40.83 3.21
750 799 7.867305 TTTTAGTACAAAGTTGACCATGTGA 57.133 32.000 0.00 0.00 0.00 3.58
751 800 6.854496 TTAGTACAAAGTTGACCATGTGAC 57.146 37.500 0.00 0.00 0.00 3.67
752 801 4.776349 AGTACAAAGTTGACCATGTGACA 58.224 39.130 0.00 0.00 0.00 3.58
753 802 4.574828 AGTACAAAGTTGACCATGTGACAC 59.425 41.667 0.00 0.00 0.00 3.67
754 803 3.351740 ACAAAGTTGACCATGTGACACA 58.648 40.909 11.41 11.41 0.00 3.72
755 804 3.953612 ACAAAGTTGACCATGTGACACAT 59.046 39.130 15.48 15.48 39.91 3.21
768 817 5.963176 TGTGACACATGTGATAAGCAATT 57.037 34.783 31.94 6.16 0.00 2.32
769 818 5.941733 TGTGACACATGTGATAAGCAATTC 58.058 37.500 31.94 15.44 0.00 2.17
770 819 5.472820 TGTGACACATGTGATAAGCAATTCA 59.527 36.000 31.94 17.78 0.00 2.57
771 820 6.016443 TGTGACACATGTGATAAGCAATTCAA 60.016 34.615 31.94 9.59 0.00 2.69
772 821 6.862608 GTGACACATGTGATAAGCAATTCAAA 59.137 34.615 31.94 0.00 0.00 2.69
773 822 6.862608 TGACACATGTGATAAGCAATTCAAAC 59.137 34.615 31.94 1.41 0.00 2.93
774 823 6.985117 ACACATGTGATAAGCAATTCAAACT 58.015 32.000 31.94 0.06 0.00 2.66
775 824 8.109705 ACACATGTGATAAGCAATTCAAACTA 57.890 30.769 31.94 0.00 0.00 2.24
776 825 8.742777 ACACATGTGATAAGCAATTCAAACTAT 58.257 29.630 31.94 0.00 0.00 2.12
777 826 9.577110 CACATGTGATAAGCAATTCAAACTATT 57.423 29.630 21.64 0.00 0.00 1.73
819 868 9.893305 AAAGTTGAGTTATCTATTTTGAAACGG 57.107 29.630 0.00 0.00 0.00 4.44
820 869 8.842358 AGTTGAGTTATCTATTTTGAAACGGA 57.158 30.769 0.00 0.00 0.00 4.69
821 870 9.449719 AGTTGAGTTATCTATTTTGAAACGGAT 57.550 29.630 0.00 0.00 0.00 4.18
822 871 9.490663 GTTGAGTTATCTATTTTGAAACGGATG 57.509 33.333 0.00 0.00 0.00 3.51
823 872 9.443323 TTGAGTTATCTATTTTGAAACGGATGA 57.557 29.630 0.00 0.00 0.00 2.92
824 873 9.443323 TGAGTTATCTATTTTGAAACGGATGAA 57.557 29.630 0.00 0.00 0.00 2.57
832 881 7.624360 ATTTTGAAACGGATGAAGTATGCTA 57.376 32.000 0.00 0.00 0.00 3.49
833 882 7.624360 TTTTGAAACGGATGAAGTATGCTAT 57.376 32.000 0.00 0.00 0.00 2.97
835 884 8.902540 TTTGAAACGGATGAAGTATGCTATAT 57.097 30.769 0.00 0.00 0.00 0.86
853 902 6.327104 TGCTATATCTTGATGGGCCAAATTTT 59.673 34.615 11.89 0.00 0.00 1.82
882 931 1.135721 GCATGGCAGAAGGAAATCACC 59.864 52.381 0.00 0.00 0.00 4.02
903 952 3.334691 CCCACAGCGATTTGAGTTTCTA 58.665 45.455 0.00 0.00 0.00 2.10
1297 1349 8.940397 AAAATTCTCCTTCTCATTAACTTCCA 57.060 30.769 0.00 0.00 0.00 3.53
1298 1350 9.539194 AAAATTCTCCTTCTCATTAACTTCCAT 57.461 29.630 0.00 0.00 0.00 3.41
1323 1375 1.497278 CGTCTGCAACGTGGGATTG 59.503 57.895 11.62 0.00 46.42 2.67
1531 1587 1.512734 CGGCCACACGTACGTACTC 60.513 63.158 22.34 10.25 0.00 2.59
1532 1588 1.153958 GGCCACACGTACGTACTCC 60.154 63.158 22.34 15.34 0.00 3.85
1533 1589 1.589716 GGCCACACGTACGTACTCCT 61.590 60.000 22.34 3.10 0.00 3.69
1534 1590 1.086696 GCCACACGTACGTACTCCTA 58.913 55.000 22.34 0.00 0.00 2.94
1535 1591 1.202076 GCCACACGTACGTACTCCTAC 60.202 57.143 22.34 3.48 0.00 3.18
1536 1592 2.350522 CCACACGTACGTACTCCTACT 58.649 52.381 22.34 0.00 0.00 2.57
1537 1593 3.521560 CCACACGTACGTACTCCTACTA 58.478 50.000 22.34 0.00 0.00 1.82
1781 1847 1.007734 GCGACTGGACTGTCACGAA 60.008 57.895 10.38 0.00 36.82 3.85
1782 1848 1.276145 GCGACTGGACTGTCACGAAC 61.276 60.000 10.38 0.00 36.82 3.95
1783 1849 0.997226 CGACTGGACTGTCACGAACG 60.997 60.000 10.38 4.94 36.82 3.95
1784 1850 1.276145 GACTGGACTGTCACGAACGC 61.276 60.000 10.38 0.00 36.97 4.84
1785 1851 1.299850 CTGGACTGTCACGAACGCA 60.300 57.895 10.38 0.00 0.00 5.24
1786 1852 1.548973 CTGGACTGTCACGAACGCAC 61.549 60.000 10.38 0.00 0.00 5.34
1787 1853 2.645510 GGACTGTCACGAACGCACG 61.646 63.158 10.38 0.48 39.31 5.34
1788 1854 1.656263 GACTGTCACGAACGCACGA 60.656 57.895 2.24 0.00 37.03 4.35
1986 2052 1.909376 CTACAACCTGATGGACGTCG 58.091 55.000 9.92 0.00 37.04 5.12
2158 2224 2.425312 ACCTCAGTGAGCGATGAGTAAG 59.575 50.000 15.10 0.00 41.13 2.34
2165 2231 2.197577 GAGCGATGAGTAAGCTTCCAC 58.802 52.381 0.00 0.00 41.84 4.02
2259 2325 1.144936 GCGATGGACTCCAAGGAGG 59.855 63.158 19.62 2.65 45.88 4.30
2309 2375 2.790468 CGACGACAAGTACCCGATCTTC 60.790 54.545 0.00 0.00 0.00 2.87
2313 2379 3.458189 GACAAGTACCCGATCTTCATGG 58.542 50.000 0.00 0.00 0.00 3.66
2319 2385 0.107017 CCCGATCTTCATGGCAGGTT 60.107 55.000 0.00 0.00 0.00 3.50
2320 2386 1.683011 CCCGATCTTCATGGCAGGTTT 60.683 52.381 0.00 0.00 0.00 3.27
2325 2391 4.818546 CGATCTTCATGGCAGGTTTATCTT 59.181 41.667 0.00 0.00 0.00 2.40
2332 2398 2.222027 GGCAGGTTTATCTTAGCGCAT 58.778 47.619 11.47 0.00 0.00 4.73
2423 2489 1.270678 ACCGGTGACTACTTTTCAGGC 60.271 52.381 6.12 0.00 0.00 4.85
2455 2521 0.108138 ACTCTATGCACCGTCTTGGC 60.108 55.000 0.00 0.00 43.94 4.52
2488 2554 4.499865 CGAGGAGACGATGACCATTTACAT 60.500 45.833 0.00 0.00 35.09 2.29
2592 2658 0.169672 CGCTGAGAAATTGGCCAGTG 59.830 55.000 5.11 0.00 0.00 3.66
2607 2673 2.919228 CCAGTGTCCCTAATTGCTACC 58.081 52.381 0.00 0.00 0.00 3.18
2645 2711 9.696917 ATTGTAATTCAAAAGATTGGTTCAGAC 57.303 29.630 0.00 0.00 39.62 3.51
2665 2734 6.770303 TCAGACTTTTGGATGTTGTCACATAA 59.230 34.615 0.00 0.00 44.22 1.90
2765 2883 2.263077 CTGTATGACTCCTCGCAACAC 58.737 52.381 0.00 0.00 0.00 3.32
2766 2884 1.269166 GTATGACTCCTCGCAACACG 58.731 55.000 0.00 0.00 45.62 4.49
2767 2885 0.457853 TATGACTCCTCGCAACACGC 60.458 55.000 0.00 0.00 43.23 5.34
2768 2886 2.355837 GACTCCTCGCAACACGCA 60.356 61.111 0.00 0.00 42.60 5.24
2769 2887 1.954146 GACTCCTCGCAACACGCAA 60.954 57.895 0.00 0.00 42.60 4.85
2770 2888 2.159272 GACTCCTCGCAACACGCAAC 62.159 60.000 0.00 0.00 42.60 4.17
2771 2889 2.202946 TCCTCGCAACACGCAACA 60.203 55.556 0.00 0.00 42.60 3.33
2782 2900 4.545610 CAACACGCAACAATTATCACCTT 58.454 39.130 0.00 0.00 0.00 3.50
2783 2901 4.419522 ACACGCAACAATTATCACCTTC 57.580 40.909 0.00 0.00 0.00 3.46
2881 2999 3.257375 TCTGTAATGACTACACGGTGCTT 59.743 43.478 8.30 0.00 35.50 3.91
2987 3109 0.768221 AGCTCTTTGTCCCAGGTCCA 60.768 55.000 0.00 0.00 0.00 4.02
2990 3112 2.026262 GCTCTTTGTCCCAGGTCCAATA 60.026 50.000 0.00 0.00 0.00 1.90
3044 3168 3.053991 TCTTTGGACTTGAGGTTTCCACA 60.054 43.478 0.00 0.00 39.20 4.17
3140 3264 5.155278 ACAACAAATCATCCAATGCATGT 57.845 34.783 0.00 0.00 0.00 3.21
3143 3267 7.332557 ACAACAAATCATCCAATGCATGTTAT 58.667 30.769 0.00 0.00 32.67 1.89
3230 3354 8.635765 ACCACTGTTATTACACATGAGAAATT 57.364 30.769 0.00 0.00 0.00 1.82
3231 3355 9.077885 ACCACTGTTATTACACATGAGAAATTT 57.922 29.630 0.00 0.00 0.00 1.82
3243 3367 7.013655 ACACATGAGAAATTTCTAAACTGCTGT 59.986 33.333 20.51 11.13 37.73 4.40
3287 3426 6.692486 AGAGGATGGTATTTTATCTGTAGCG 58.308 40.000 0.00 0.00 0.00 4.26
3316 3455 9.793252 ATTTTGCAAGTAAATGATGTATCTGAC 57.207 29.630 0.00 0.00 0.00 3.51
3476 3615 6.206634 TGGAGACAGAATTGTTGGACATAAAC 59.793 38.462 0.00 0.00 37.76 2.01
3490 3629 6.554334 GGACATAAACTGTGCAAGAAGTTA 57.446 37.500 10.20 0.00 44.95 2.24
3491 3630 6.371389 GGACATAAACTGTGCAAGAAGTTAC 58.629 40.000 10.20 2.82 44.95 2.50
3497 3636 7.399245 AAACTGTGCAAGAAGTTACCTTAAA 57.601 32.000 10.20 0.00 35.60 1.52
3505 3644 8.567948 TGCAAGAAGTTACCTTAAATTTCTCAG 58.432 33.333 0.00 0.00 0.00 3.35
3526 3665 7.556275 TCTCAGGTTTTCTACAAATTTGACAGT 59.444 33.333 24.64 4.75 0.00 3.55
3535 3674 8.669946 TCTACAAATTTGACAGTTACACATGA 57.330 30.769 24.64 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 21 1.275471 TTGTGCTTTCGCGAGAGTCG 61.275 55.000 25.34 4.35 43.69 4.18
134 140 3.487536 CATGATTGTGCTTACGCGAAAA 58.512 40.909 15.93 5.71 39.65 2.29
269 280 1.792006 GGTTTTTCTTCCGCGAGAGA 58.208 50.000 8.23 7.58 0.00 3.10
376 393 1.607251 GGTTTTTCTTCCGCGAGAGGA 60.607 52.381 8.23 6.49 38.79 3.71
506 537 4.919206 TCGACTTTTAAACGGTTTTTCCC 58.081 39.130 11.87 0.00 0.00 3.97
507 538 6.867799 TTTCGACTTTTAAACGGTTTTTCC 57.132 33.333 11.87 0.00 0.00 3.13
508 539 6.883649 CGTTTTCGACTTTTAAACGGTTTTTC 59.116 34.615 19.31 1.08 46.06 2.29
721 770 9.659830 CATGGTCAACTTTGTACTAAAAAGTAC 57.340 33.333 9.49 8.43 44.93 2.73
722 771 9.398538 ACATGGTCAACTTTGTACTAAAAAGTA 57.601 29.630 9.49 0.00 44.93 2.24
724 773 8.402472 TCACATGGTCAACTTTGTACTAAAAAG 58.598 33.333 0.00 0.00 39.92 2.27
725 774 8.185505 GTCACATGGTCAACTTTGTACTAAAAA 58.814 33.333 0.00 0.00 0.00 1.94
726 775 7.337184 TGTCACATGGTCAACTTTGTACTAAAA 59.663 33.333 0.00 0.00 0.00 1.52
727 776 6.824196 TGTCACATGGTCAACTTTGTACTAAA 59.176 34.615 0.00 0.00 0.00 1.85
728 777 6.259167 GTGTCACATGGTCAACTTTGTACTAA 59.741 38.462 0.00 0.00 0.00 2.24
729 778 5.756347 GTGTCACATGGTCAACTTTGTACTA 59.244 40.000 0.00 0.00 0.00 1.82
730 779 4.574828 GTGTCACATGGTCAACTTTGTACT 59.425 41.667 0.00 0.00 0.00 2.73
731 780 4.334203 TGTGTCACATGGTCAACTTTGTAC 59.666 41.667 0.18 0.00 0.00 2.90
732 781 4.518249 TGTGTCACATGGTCAACTTTGTA 58.482 39.130 0.18 0.00 0.00 2.41
733 782 3.351740 TGTGTCACATGGTCAACTTTGT 58.648 40.909 0.18 0.00 0.00 2.83
734 783 4.572985 ATGTGTCACATGGTCAACTTTG 57.427 40.909 17.74 0.00 37.45 2.77
745 794 6.151480 TGAATTGCTTATCACATGTGTCACAT 59.849 34.615 24.63 12.87 39.91 3.21
746 795 5.472820 TGAATTGCTTATCACATGTGTCACA 59.527 36.000 24.63 8.40 0.00 3.58
747 796 5.941733 TGAATTGCTTATCACATGTGTCAC 58.058 37.500 24.63 11.82 0.00 3.67
748 797 6.572167 TTGAATTGCTTATCACATGTGTCA 57.428 33.333 24.63 14.58 0.00 3.58
749 798 7.086376 AGTTTGAATTGCTTATCACATGTGTC 58.914 34.615 24.63 12.23 0.00 3.67
750 799 6.985117 AGTTTGAATTGCTTATCACATGTGT 58.015 32.000 24.63 14.61 0.00 3.72
751 800 9.577110 AATAGTTTGAATTGCTTATCACATGTG 57.423 29.630 20.18 20.18 0.00 3.21
793 842 9.893305 CCGTTTCAAAATAGATAACTCAACTTT 57.107 29.630 0.00 0.00 0.00 2.66
794 843 9.280174 TCCGTTTCAAAATAGATAACTCAACTT 57.720 29.630 0.00 0.00 0.00 2.66
795 844 8.842358 TCCGTTTCAAAATAGATAACTCAACT 57.158 30.769 0.00 0.00 0.00 3.16
796 845 9.490663 CATCCGTTTCAAAATAGATAACTCAAC 57.509 33.333 0.00 0.00 0.00 3.18
797 846 9.443323 TCATCCGTTTCAAAATAGATAACTCAA 57.557 29.630 0.00 0.00 0.00 3.02
798 847 9.443323 TTCATCCGTTTCAAAATAGATAACTCA 57.557 29.630 0.00 0.00 0.00 3.41
799 848 9.922305 CTTCATCCGTTTCAAAATAGATAACTC 57.078 33.333 0.00 0.00 0.00 3.01
800 849 9.449719 ACTTCATCCGTTTCAAAATAGATAACT 57.550 29.630 0.00 0.00 0.00 2.24
804 853 8.345565 GCATACTTCATCCGTTTCAAAATAGAT 58.654 33.333 0.00 0.00 0.00 1.98
805 854 7.552687 AGCATACTTCATCCGTTTCAAAATAGA 59.447 33.333 0.00 0.00 0.00 1.98
806 855 7.697691 AGCATACTTCATCCGTTTCAAAATAG 58.302 34.615 0.00 0.00 0.00 1.73
807 856 7.624360 AGCATACTTCATCCGTTTCAAAATA 57.376 32.000 0.00 0.00 0.00 1.40
808 857 6.515272 AGCATACTTCATCCGTTTCAAAAT 57.485 33.333 0.00 0.00 0.00 1.82
809 858 5.957842 AGCATACTTCATCCGTTTCAAAA 57.042 34.783 0.00 0.00 0.00 2.44
810 859 8.902540 ATATAGCATACTTCATCCGTTTCAAA 57.097 30.769 0.00 0.00 0.00 2.69
811 860 8.367911 AGATATAGCATACTTCATCCGTTTCAA 58.632 33.333 0.00 0.00 0.00 2.69
812 861 7.896811 AGATATAGCATACTTCATCCGTTTCA 58.103 34.615 0.00 0.00 0.00 2.69
813 862 8.651588 CAAGATATAGCATACTTCATCCGTTTC 58.348 37.037 0.00 0.00 0.00 2.78
814 863 8.367911 TCAAGATATAGCATACTTCATCCGTTT 58.632 33.333 0.00 0.00 0.00 3.60
815 864 7.896811 TCAAGATATAGCATACTTCATCCGTT 58.103 34.615 0.00 0.00 0.00 4.44
816 865 7.468141 TCAAGATATAGCATACTTCATCCGT 57.532 36.000 0.00 0.00 0.00 4.69
817 866 7.437565 CCATCAAGATATAGCATACTTCATCCG 59.562 40.741 0.00 0.00 0.00 4.18
818 867 7.714377 CCCATCAAGATATAGCATACTTCATCC 59.286 40.741 0.00 0.00 0.00 3.51
819 868 7.226325 GCCCATCAAGATATAGCATACTTCATC 59.774 40.741 0.00 0.00 0.00 2.92
820 869 7.052873 GCCCATCAAGATATAGCATACTTCAT 58.947 38.462 0.00 0.00 0.00 2.57
821 870 6.409704 GCCCATCAAGATATAGCATACTTCA 58.590 40.000 0.00 0.00 0.00 3.02
822 871 5.819901 GGCCCATCAAGATATAGCATACTTC 59.180 44.000 0.00 0.00 0.00 3.01
823 872 5.251468 TGGCCCATCAAGATATAGCATACTT 59.749 40.000 0.00 0.00 0.00 2.24
824 873 4.784838 TGGCCCATCAAGATATAGCATACT 59.215 41.667 0.00 0.00 0.00 2.12
832 881 5.932455 CCAAAATTTGGCCCATCAAGATAT 58.068 37.500 12.23 0.00 45.17 1.63
833 882 5.356291 CCAAAATTTGGCCCATCAAGATA 57.644 39.130 12.23 0.00 45.17 1.98
835 884 3.699411 CCAAAATTTGGCCCATCAAGA 57.301 42.857 12.23 0.00 45.17 3.02
856 905 4.189188 CTTCTGCCATGCCTGCGC 62.189 66.667 0.00 0.00 0.00 6.09
864 913 1.342374 GGGGTGATTTCCTTCTGCCAT 60.342 52.381 0.00 0.00 0.00 4.40
882 931 2.154462 AGAAACTCAAATCGCTGTGGG 58.846 47.619 0.00 0.00 0.00 4.61
912 961 4.023365 GCTGCCTTATCTTCAAATAGCTGG 60.023 45.833 0.00 0.00 0.00 4.85
958 1009 1.516386 CGCGACAGAAGGTATGCGT 60.516 57.895 0.00 0.00 44.68 5.24
1080 1131 1.445410 CCTGATCGTGTCGCGGAAA 60.445 57.895 6.13 0.00 41.72 3.13
1084 1135 2.951745 GCTCCTGATCGTGTCGCG 60.952 66.667 0.00 0.00 43.01 5.87
1089 1140 0.879400 GCATCCTGCTCCTGATCGTG 60.879 60.000 0.00 0.00 40.96 4.35
1224 1275 4.746309 GCCATGCCCACCAGCTCA 62.746 66.667 0.00 0.00 0.00 4.26
1260 1311 2.096013 GGAGAATTTTACGTGCAGGAGC 59.904 50.000 14.38 0.00 42.57 4.70
1297 1349 4.778143 GTTGCAGACGGCCGGGAT 62.778 66.667 31.76 8.67 43.89 3.85
1369 1425 2.094182 CGGACGAATCTCCTTCCTCAAA 60.094 50.000 0.00 0.00 0.00 2.69
1531 1587 0.029567 CGAGCAAGGCGACTAGTAGG 59.970 60.000 5.08 0.00 42.68 3.18
1532 1588 0.733729 ACGAGCAAGGCGACTAGTAG 59.266 55.000 0.00 0.00 42.68 2.57
1533 1589 1.131883 GAACGAGCAAGGCGACTAGTA 59.868 52.381 0.00 0.00 42.68 1.82
1534 1590 0.109226 GAACGAGCAAGGCGACTAGT 60.109 55.000 0.00 0.00 42.68 2.57
1535 1591 0.171455 AGAACGAGCAAGGCGACTAG 59.829 55.000 0.00 0.00 42.68 2.57
1536 1592 0.170561 GAGAACGAGCAAGGCGACTA 59.829 55.000 0.00 0.00 42.68 2.59
1603 1663 2.115911 ACGTAGCTGAGGCGGAGAG 61.116 63.158 0.00 0.00 44.37 3.20
1783 1849 1.064654 GAAATTCAGCAGGGATCGTGC 59.935 52.381 10.04 10.04 44.27 5.34
1784 1850 1.328680 CGAAATTCAGCAGGGATCGTG 59.671 52.381 0.00 0.00 0.00 4.35
1785 1851 1.207089 TCGAAATTCAGCAGGGATCGT 59.793 47.619 0.00 0.00 0.00 3.73
1786 1852 1.594862 GTCGAAATTCAGCAGGGATCG 59.405 52.381 0.00 0.00 0.00 3.69
1787 1853 2.632377 TGTCGAAATTCAGCAGGGATC 58.368 47.619 0.00 0.00 0.00 3.36
1788 1854 2.787473 TGTCGAAATTCAGCAGGGAT 57.213 45.000 0.00 0.00 0.00 3.85
1952 2018 3.755628 TAGCAGTGCCCGACCGAC 61.756 66.667 12.58 0.00 0.00 4.79
2057 2123 2.602267 TTCGCGTGGAAGGAGGGA 60.602 61.111 5.77 0.00 0.00 4.20
2309 2375 2.031682 GCGCTAAGATAAACCTGCCATG 60.032 50.000 0.00 0.00 0.00 3.66
2313 2379 2.603173 GCATGCGCTAAGATAAACCTGC 60.603 50.000 9.73 0.00 34.30 4.85
2319 2385 4.916983 AAAATGGCATGCGCTAAGATAA 57.083 36.364 12.44 0.00 38.60 1.75
2320 2386 4.337836 TGAAAAATGGCATGCGCTAAGATA 59.662 37.500 12.44 0.00 38.60 1.98
2325 2391 2.166050 ACATGAAAAATGGCATGCGCTA 59.834 40.909 12.44 0.47 44.30 4.26
2332 2398 4.829968 CCCAACATACATGAAAAATGGCA 58.170 39.130 0.00 0.00 0.00 4.92
2366 2432 6.206634 TCATGTTTTTGTAGCAAACTCCCTAG 59.793 38.462 0.00 0.00 35.50 3.02
2423 2489 3.243737 TGCATAGAGTATACAGCGTTGGG 60.244 47.826 5.50 0.00 0.00 4.12
2455 2521 0.579630 CGTCTCCTCGTCGAGATCAG 59.420 60.000 23.74 15.00 40.89 2.90
2592 2658 5.718724 ATACTACGGTAGCAATTAGGGAC 57.281 43.478 14.91 0.00 0.00 4.46
2765 2883 2.159585 TGCGAAGGTGATAATTGTTGCG 60.160 45.455 0.00 0.00 0.00 4.85
2766 2884 3.119849 AGTGCGAAGGTGATAATTGTTGC 60.120 43.478 0.00 0.00 0.00 4.17
2767 2885 4.083324 ACAGTGCGAAGGTGATAATTGTTG 60.083 41.667 0.00 0.00 0.00 3.33
2768 2886 4.072131 ACAGTGCGAAGGTGATAATTGTT 58.928 39.130 0.00 0.00 0.00 2.83
2769 2887 3.674997 ACAGTGCGAAGGTGATAATTGT 58.325 40.909 0.00 0.00 0.00 2.71
2770 2888 4.271049 CCTACAGTGCGAAGGTGATAATTG 59.729 45.833 0.00 0.00 0.00 2.32
2771 2889 4.161565 TCCTACAGTGCGAAGGTGATAATT 59.838 41.667 6.65 0.00 0.00 1.40
2782 2900 1.476845 TTGGCCTTCCTACAGTGCGA 61.477 55.000 3.32 0.00 0.00 5.10
2783 2901 0.605319 TTTGGCCTTCCTACAGTGCG 60.605 55.000 3.32 0.00 0.00 5.34
2797 2915 3.129287 AGCATTGTACTACAGCATTTGGC 59.871 43.478 0.00 0.00 45.30 4.52
2841 2959 2.417933 CAGAAAGTCTATGGCACTGTGC 59.582 50.000 24.02 24.02 44.08 4.57
2881 2999 4.704540 ACCACTGATTTGTTCAACAGTCAA 59.295 37.500 8.51 0.00 40.84 3.18
2987 3109 9.747898 TTTTACCTGTAGATGTCATTTGGTATT 57.252 29.630 0.00 0.00 0.00 1.89
3018 3140 2.262423 ACCTCAAGTCCAAAGAGCAC 57.738 50.000 0.00 0.00 0.00 4.40
3230 3354 8.247562 ACATTGTTTTTGTACAGCAGTTTAGAA 58.752 29.630 0.00 0.00 0.00 2.10
3231 3355 7.767261 ACATTGTTTTTGTACAGCAGTTTAGA 58.233 30.769 0.00 0.00 0.00 2.10
3287 3426 7.707893 AGATACATCATTTACTTGCAAAATGCC 59.292 33.333 14.75 3.58 44.23 4.40
3316 3455 2.087501 TGGTACATAACAGGTGTGCG 57.912 50.000 0.00 0.00 33.68 5.34
3469 3608 6.313744 GGTAACTTCTTGCACAGTTTATGT 57.686 37.500 9.74 0.00 45.43 2.29
3490 3629 8.990163 TGTAGAAAACCTGAGAAATTTAAGGT 57.010 30.769 11.95 11.95 45.01 3.50
3497 3636 9.750125 GTCAAATTTGTAGAAAACCTGAGAAAT 57.250 29.630 17.47 0.00 0.00 2.17
3505 3644 9.016623 GTGTAACTGTCAAATTTGTAGAAAACC 57.983 33.333 22.78 8.31 0.00 3.27
3510 3649 8.669946 TCATGTGTAACTGTCAAATTTGTAGA 57.330 30.769 22.78 8.82 38.04 2.59


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

AutoCloner maintained by Alex Coulton.