Multiple sequence alignment - TraesCS2D01G018600

Loading Multiple Alignment...

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 TraesCS2D01G018600 chr2D 100.000 4100 0 0 1 4100 8715142 8719241 0.000000e+00 7572.0
1 TraesCS2D01G018600 chr2D 83.942 822 89 22 933 1720 8983197 8982385 0.000000e+00 747.0
2 TraesCS2D01G018600 chr2D 80.978 552 78 10 1973 2503 8928611 8929156 2.950000e-111 412.0
3 TraesCS2D01G018600 chr2D 76.009 917 140 44 856 1717 8888809 8889700 6.380000e-108 401.0
4 TraesCS2D01G018600 chr2D 84.559 408 54 7 1825 2226 8982352 8981948 2.970000e-106 396.0
5 TraesCS2D01G018600 chr2D 91.304 115 10 0 3835 3949 383561102 383561216 1.530000e-34 158.0
6 TraesCS2D01G018600 chr2D 93.939 66 4 0 1740 1805 8716824 8716889 2.610000e-17 100.0
7 TraesCS2D01G018600 chr2D 93.939 66 4 0 1683 1748 8716881 8716946 2.610000e-17 100.0
8 TraesCS2D01G018600 chr2B 97.513 2372 46 6 1740 4100 12026307 12023938 0.000000e+00 4041.0
9 TraesCS2D01G018600 chr2B 90.959 918 66 7 855 1755 12027152 12026235 0.000000e+00 1219.0
10 TraesCS2D01G018600 chr2B 93.548 744 33 7 4 737 12028647 12027909 0.000000e+00 1094.0
11 TraesCS2D01G018600 chr2B 84.091 836 93 22 919 1720 11984478 11985307 0.000000e+00 771.0
12 TraesCS2D01G018600 chr2B 79.871 929 123 34 839 1720 12077829 12076918 4.500000e-174 621.0
13 TraesCS2D01G018600 chr2B 80.343 875 111 32 1825 2652 11985340 11986200 1.260000e-169 606.0
14 TraesCS2D01G018600 chr2B 85.147 579 62 11 2872 3428 12075756 12075180 4.600000e-159 571.0
15 TraesCS2D01G018600 chr2B 87.226 501 44 11 2409 2898 12076250 12075759 1.670000e-153 553.0
16 TraesCS2D01G018600 chr2B 78.295 516 60 26 2314 2792 70880555 70880055 6.710000e-73 285.0
17 TraesCS2D01G018600 chr2B 89.600 125 10 3 3829 3951 545161638 545161515 5.490000e-34 156.0
18 TraesCS2D01G018600 chr2B 86.719 128 13 3 3831 3957 733875493 733875369 5.530000e-29 139.0
19 TraesCS2D01G018600 chr2B 93.443 61 1 2 737 794 12027317 12027257 2.030000e-13 87.9
20 TraesCS2D01G018600 chr2B 81.553 103 9 8 857 956 70882796 70882701 4.390000e-10 76.8
21 TraesCS2D01G018600 chr2A 96.965 1779 26 10 1740 3501 8370253 8368486 0.000000e+00 2961.0
22 TraesCS2D01G018600 chr2A 91.371 846 48 12 933 1754 8371026 8370182 0.000000e+00 1134.0
23 TraesCS2D01G018600 chr2A 97.892 427 8 1 3675 4100 8368485 8368059 0.000000e+00 737.0
24 TraesCS2D01G018600 chr2A 79.521 918 113 37 1825 2685 8046033 8046932 5.910000e-163 584.0
25 TraesCS2D01G018600 chr2A 81.622 555 75 10 1973 2506 8181678 8181130 6.290000e-118 435.0
26 TraesCS2D01G018600 chr2A 82.704 503 68 13 2409 2898 7921049 7921545 2.930000e-116 429.0
27 TraesCS2D01G018600 chr2A 78.537 615 102 19 1911 2507 7920178 7920780 1.080000e-100 377.0
28 TraesCS2D01G018600 chr2A 75.597 922 136 47 857 1717 7806656 7807549 1.390000e-99 374.0
29 TraesCS2D01G018600 chr2A 75.726 861 139 41 857 1675 8182748 8181916 6.470000e-98 368.0
30 TraesCS2D01G018600 chr2A 76.744 559 113 11 1895 2445 8314070 8313521 3.100000e-76 296.0
31 TraesCS2D01G018600 chr2A 80.398 352 51 13 1132 1474 7919447 7919789 6.800000e-63 252.0
32 TraesCS2D01G018600 chr2A 85.246 244 33 3 1067 1307 8045376 8045619 8.800000e-62 248.0
33 TraesCS2D01G018600 chr2A 79.205 327 40 14 1328 1626 8045610 8045936 6.950000e-48 202.0
34 TraesCS2D01G018600 chr2A 81.858 226 17 8 822 1038 7919125 7919335 7.050000e-38 169.0
35 TraesCS2D01G018600 chr2A 87.931 58 7 0 919 976 8045293 8045350 7.350000e-08 69.4
36 TraesCS2D01G018600 chr3D 85.997 757 82 14 988 1720 564006027 564005271 0.000000e+00 789.0
37 TraesCS2D01G018600 chr3D 86.700 406 49 4 1825 2226 564005238 564004834 2.910000e-121 446.0
38 TraesCS2D01G018600 chr3D 82.840 507 63 15 2409 2898 563861320 563861819 2.260000e-117 433.0
39 TraesCS2D01G018600 chr3D 79.248 612 103 12 1911 2507 563860449 563861051 4.930000e-109 405.0
40 TraesCS2D01G018600 chr3D 77.066 702 96 40 822 1474 563859375 563860060 1.090000e-90 344.0
41 TraesCS2D01G018600 chr7A 80.435 552 81 12 1973 2503 466508833 466509378 2.970000e-106 396.0
42 TraesCS2D01G018600 chr7A 79.221 462 74 18 2669 3125 466509838 466510282 6.660000e-78 302.0
43 TraesCS2D01G018600 chr7A 79.582 431 71 10 2020 2442 466492030 466492451 4.010000e-75 292.0
44 TraesCS2D01G018600 chr7A 77.326 516 78 26 2007 2497 466703178 466702677 6.760000e-68 268.0
45 TraesCS2D01G018600 chr7A 75.681 477 71 26 857 1312 466507641 466508093 3.230000e-46 196.0
46 TraesCS2D01G018600 chr5B 91.525 118 9 1 3835 3951 594753547 594753664 1.180000e-35 161.0
47 TraesCS2D01G018600 chr5B 84.259 108 12 5 434 539 59713730 59713834 2.610000e-17 100.0
48 TraesCS2D01G018600 chr6A 88.800 125 11 3 3835 3958 93890026 93889904 2.550000e-32 150.0
49 TraesCS2D01G018600 chr6A 81.308 107 13 7 485 589 616311 616412 3.400000e-11 80.5
50 TraesCS2D01G018600 chr6D 88.000 125 11 4 3835 3958 449507041 449506920 1.190000e-30 145.0
51 TraesCS2D01G018600 chr6D 79.167 120 16 7 474 589 2246038 2246152 1.580000e-09 75.0
52 TraesCS2D01G018600 chr3A 88.000 125 12 3 3833 3956 649707903 649707781 1.190000e-30 145.0
53 TraesCS2D01G018600 chr4B 83.898 118 17 2 1263 1379 515040648 515040532 1.200000e-20 111.0
54 TraesCS2D01G018600 chr7D 80.392 153 19 5 450 600 452161883 452162026 5.610000e-19 106.0
55 TraesCS2D01G018600 chrUn 72.141 341 86 5 1328 1662 11822681 11823018 1.210000e-15 95.3
56 TraesCS2D01G018600 chrUn 72.141 341 86 5 1328 1662 11858789 11859126 1.210000e-15 95.3
57 TraesCS2D01G018600 chrUn 74.375 160 38 2 1503 1662 400234488 400234332 9.510000e-07 65.8
58 TraesCS2D01G018600 chr5D 82.143 84 13 2 4016 4098 133538640 133538558 2.040000e-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 TraesCS2D01G018600 chr2D 8715142 8719241 4099 False 2590.666667 7572 95.959333 1 4100 3 chr2D.!!$F4 4099
1 TraesCS2D01G018600 chr2D 8981948 8983197 1249 True 571.500000 747 84.250500 933 2226 2 chr2D.!!$R1 1293
2 TraesCS2D01G018600 chr2D 8928611 8929156 545 False 412.000000 412 80.978000 1973 2503 1 chr2D.!!$F2 530
3 TraesCS2D01G018600 chr2D 8888809 8889700 891 False 401.000000 401 76.009000 856 1717 1 chr2D.!!$F1 861
4 TraesCS2D01G018600 chr2B 12023938 12028647 4709 True 1610.475000 4041 93.865750 4 4100 4 chr2B.!!$R3 4096
5 TraesCS2D01G018600 chr2B 11984478 11986200 1722 False 688.500000 771 82.217000 919 2652 2 chr2B.!!$F1 1733
6 TraesCS2D01G018600 chr2B 12075180 12077829 2649 True 581.666667 621 84.081333 839 3428 3 chr2B.!!$R4 2589
7 TraesCS2D01G018600 chr2A 8368059 8371026 2967 True 1610.666667 2961 95.409333 933 4100 3 chr2A.!!$R3 3167
8 TraesCS2D01G018600 chr2A 8181130 8182748 1618 True 401.500000 435 78.674000 857 2506 2 chr2A.!!$R2 1649
9 TraesCS2D01G018600 chr2A 7806656 7807549 893 False 374.000000 374 75.597000 857 1717 1 chr2A.!!$F1 860
10 TraesCS2D01G018600 chr2A 7919125 7921545 2420 False 306.750000 429 80.874250 822 2898 4 chr2A.!!$F2 2076
11 TraesCS2D01G018600 chr2A 8313521 8314070 549 True 296.000000 296 76.744000 1895 2445 1 chr2A.!!$R1 550
12 TraesCS2D01G018600 chr2A 8045293 8046932 1639 False 275.850000 584 82.975750 919 2685 4 chr2A.!!$F3 1766
13 TraesCS2D01G018600 chr3D 564004834 564006027 1193 True 617.500000 789 86.348500 988 2226 2 chr3D.!!$R1 1238
14 TraesCS2D01G018600 chr3D 563859375 563861819 2444 False 394.000000 433 79.718000 822 2898 3 chr3D.!!$F1 2076
15 TraesCS2D01G018600 chr7A 466507641 466510282 2641 False 298.000000 396 78.445667 857 3125 3 chr7A.!!$F2 2268
16 TraesCS2D01G018600 chr7A 466702677 466703178 501 True 268.000000 268 77.326000 2007 2497 1 chr7A.!!$R1 490

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
648 659 0.246910 TATTGTCGTTAGGTGCGCCA 59.753 50.0 20.59 1.18 37.19 5.69 F
1083 1828 0.253020 AGTTCCGGTGGGGGTTCTAT 60.253 55.0 0.00 0.00 36.01 1.98 F
1768 2740 0.181114 TGTCAAGCTGCCACAAGACT 59.819 50.0 0.00 0.00 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 2721 0.181114 AGTCTTGTGGCAGCTTGACA 59.819 50.000 10.83 0.0 29.15 3.58 R
1936 2947 3.490348 ACTTGGAGGTTTTGATCCAGTG 58.510 45.455 0.00 0.0 33.39 3.66 R
3587 5431 2.027100 CCTTCACTAGTCCAAAGGGTCC 60.027 54.545 15.83 0.0 35.63 4.46 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
22 23 2.362077 AGAAAAGGCTTGCACGACAATT 59.638 40.909 0.00 0.00 37.72 2.32
40 41 4.932799 ACAATTAGCGCATACAAGTACACA 59.067 37.500 11.47 0.00 0.00 3.72
49 50 6.522761 CGCATACAAGTACACACTAGAAAAC 58.477 40.000 0.00 0.00 33.48 2.43
63 64 8.674607 CACACTAGAAAACTAAAAAGGTTCACT 58.325 33.333 0.00 0.00 0.00 3.41
231 233 8.449397 CAAATTCAAAAGGTGTTCATGTTTTCA 58.551 29.630 0.00 0.00 0.00 2.69
314 317 7.841915 AAATTTGTCCGTGTTTTCAGAAAAT 57.158 28.000 11.54 0.00 32.22 1.82
393 396 1.259507 TCGCGTTTCCAAAACTTCTCG 59.740 47.619 5.77 0.00 0.00 4.04
471 474 8.492673 AACTTGAAGTTCCAAAAATTCTTTCC 57.507 30.769 4.45 0.00 39.57 3.13
476 479 8.251721 TGAAGTTCCAAAAATTCTTTCCGTTTA 58.748 29.630 0.00 0.00 39.57 2.01
555 558 2.991190 GGTTTCATGCAGCATTGAGTTG 59.009 45.455 4.69 0.00 0.00 3.16
579 582 8.375717 TGTTAAATATTCGCGTTGATCTTTTG 57.624 30.769 5.77 0.00 0.00 2.44
586 589 1.269517 GCGTTGATCTTTTGCCACCAA 60.270 47.619 0.00 0.00 0.00 3.67
633 644 5.645067 TGCAAGATGGTTGAGAGTTCTATTG 59.355 40.000 0.00 0.00 0.00 1.90
648 659 0.246910 TATTGTCGTTAGGTGCGCCA 59.753 50.000 20.59 1.18 37.19 5.69
650 661 0.604243 TTGTCGTTAGGTGCGCCAAT 60.604 50.000 20.59 0.20 37.19 3.16
757 1362 4.321527 GCTTTGCTAAAAGATGACAGGCTT 60.322 41.667 2.46 0.00 44.81 4.35
794 1399 4.083862 GGCCCTCCTCGTGTGTCC 62.084 72.222 0.00 0.00 0.00 4.02
795 1400 3.311110 GCCCTCCTCGTGTGTCCA 61.311 66.667 0.00 0.00 0.00 4.02
799 1404 2.520020 TCCTCGTGTGTCCACCGT 60.520 61.111 7.73 0.00 38.41 4.83
800 1405 2.049433 CCTCGTGTGTCCACCGTC 60.049 66.667 7.73 0.00 38.41 4.79
801 1406 2.561956 CCTCGTGTGTCCACCGTCT 61.562 63.158 7.73 0.00 38.41 4.18
802 1407 1.081376 CTCGTGTGTCCACCGTCTC 60.081 63.158 7.73 0.00 38.41 3.36
803 1408 2.428569 CGTGTGTCCACCGTCTCG 60.429 66.667 0.00 0.00 38.41 4.04
804 1409 2.733593 GTGTGTCCACCGTCTCGC 60.734 66.667 0.00 0.00 35.44 5.03
806 1411 4.736896 GTGTCCACCGTCTCGCCC 62.737 72.222 0.00 0.00 0.00 6.13
808 1413 4.736896 GTCCACCGTCTCGCCCAC 62.737 72.222 0.00 0.00 0.00 4.61
814 1419 3.382832 CGTCTCGCCCACCCTTCT 61.383 66.667 0.00 0.00 0.00 2.85
815 1420 2.943978 CGTCTCGCCCACCCTTCTT 61.944 63.158 0.00 0.00 0.00 2.52
816 1421 1.376037 GTCTCGCCCACCCTTCTTG 60.376 63.158 0.00 0.00 0.00 3.02
817 1422 1.535444 TCTCGCCCACCCTTCTTGA 60.535 57.895 0.00 0.00 0.00 3.02
820 1425 2.359975 GCCCACCCTTCTTGACGG 60.360 66.667 0.00 0.00 0.00 4.79
908 1583 2.438075 CTGCCTGCTGCTTCCTCC 60.438 66.667 0.00 0.00 42.00 4.30
913 1588 3.635268 CTGCTGCTTCCTCCACCCC 62.635 68.421 0.00 0.00 0.00 4.95
1025 1746 1.796796 GTTCCATGGTTCTGCTCGC 59.203 57.895 12.58 0.00 0.00 5.03
1082 1827 1.159184 AGTTCCGGTGGGGGTTCTA 59.841 57.895 0.00 0.00 36.01 2.10
1083 1828 0.253020 AGTTCCGGTGGGGGTTCTAT 60.253 55.000 0.00 0.00 36.01 1.98
1091 1843 2.514160 GGTGGGGGTTCTATGAAGGAAT 59.486 50.000 0.00 0.00 0.00 3.01
1489 2406 1.379642 GCTCATCAAGAAAGGCGGGG 61.380 60.000 0.00 0.00 0.00 5.73
1490 2407 0.749454 CTCATCAAGAAAGGCGGGGG 60.749 60.000 0.00 0.00 0.00 5.40
1491 2408 1.000896 CATCAAGAAAGGCGGGGGT 60.001 57.895 0.00 0.00 0.00 4.95
1493 2410 1.208165 ATCAAGAAAGGCGGGGGTCT 61.208 55.000 0.00 0.00 0.00 3.85
1733 2705 3.677963 CAGCCCTGGATTGGAACTT 57.322 52.632 0.00 0.00 0.00 2.66
1734 2706 2.806945 CAGCCCTGGATTGGAACTTA 57.193 50.000 0.00 0.00 0.00 2.24
1735 2707 3.085952 CAGCCCTGGATTGGAACTTAA 57.914 47.619 0.00 0.00 0.00 1.85
1736 2708 3.430453 CAGCCCTGGATTGGAACTTAAA 58.570 45.455 0.00 0.00 0.00 1.52
1737 2709 3.445096 CAGCCCTGGATTGGAACTTAAAG 59.555 47.826 0.00 0.00 0.00 1.85
1742 2714 5.325239 CCTGGATTGGAACTTAAAGGAGTT 58.675 41.667 0.00 0.00 42.31 3.01
1752 2724 6.378710 AACTTAAAGGAGTTCAGCTTTGTC 57.621 37.500 0.00 0.00 34.94 3.18
1753 2725 5.437060 ACTTAAAGGAGTTCAGCTTTGTCA 58.563 37.500 0.00 0.00 0.00 3.58
1754 2726 5.885912 ACTTAAAGGAGTTCAGCTTTGTCAA 59.114 36.000 0.00 0.00 0.00 3.18
1755 2727 4.907879 AAAGGAGTTCAGCTTTGTCAAG 57.092 40.909 0.00 0.00 0.00 3.02
1765 2737 2.129823 CTTTGTCAAGCTGCCACAAG 57.870 50.000 0.00 0.00 31.81 3.16
1766 2738 1.677576 CTTTGTCAAGCTGCCACAAGA 59.322 47.619 0.00 0.00 31.81 3.02
1767 2739 1.024271 TTGTCAAGCTGCCACAAGAC 58.976 50.000 0.00 0.00 0.00 3.01
1768 2740 0.181114 TGTCAAGCTGCCACAAGACT 59.819 50.000 0.00 0.00 0.00 3.24
1769 2741 0.590195 GTCAAGCTGCCACAAGACTG 59.410 55.000 0.00 0.00 0.00 3.51
1770 2742 0.181114 TCAAGCTGCCACAAGACTGT 59.819 50.000 0.00 0.00 35.63 3.55
1771 2743 0.590195 CAAGCTGCCACAAGACTGTC 59.410 55.000 0.00 0.00 31.64 3.51
1772 2744 0.536006 AAGCTGCCACAAGACTGTCC 60.536 55.000 3.76 0.00 31.64 4.02
1773 2745 1.227943 GCTGCCACAAGACTGTCCA 60.228 57.895 3.76 0.00 31.64 4.02
1774 2746 1.233285 GCTGCCACAAGACTGTCCAG 61.233 60.000 3.76 4.79 36.05 3.86
1775 2747 1.227943 TGCCACAAGACTGTCCAGC 60.228 57.895 3.76 1.53 31.64 4.85
1776 2748 1.968540 GCCACAAGACTGTCCAGCC 60.969 63.158 3.76 0.00 31.64 4.85
1777 2749 1.302832 CCACAAGACTGTCCAGCCC 60.303 63.158 3.76 0.00 31.64 5.19
1778 2750 1.757306 CACAAGACTGTCCAGCCCT 59.243 57.895 3.76 0.00 31.64 5.19
1779 2751 0.604780 CACAAGACTGTCCAGCCCTG 60.605 60.000 3.76 0.00 31.64 4.45
1805 2792 3.269906 AGGAACTTAGAGGAGTCCAGCTA 59.730 47.826 12.86 9.69 27.25 3.32
1811 2798 6.799827 ACTTAGAGGAGTCCAGCTATATCAT 58.200 40.000 12.86 0.00 0.00 2.45
1936 2947 4.233789 GACTCTGTTGACTGATCACTCAC 58.766 47.826 4.71 2.56 33.38 3.51
2464 3920 4.755266 TCAGGTTTAAGAGTAGATGCCC 57.245 45.455 0.00 0.00 0.00 5.36
3080 4912 0.889638 AGAGAGTTCGGTGCGAGTGA 60.890 55.000 0.00 0.00 37.14 3.41
3309 5148 2.031069 GCTGATTCTGGCTACATGCATG 60.031 50.000 25.09 25.09 45.15 4.06
3436 5280 3.164268 TGCTTGCCCATAATTTGACTGT 58.836 40.909 0.00 0.00 0.00 3.55
3442 5286 7.334171 GCTTGCCCATAATTTGACTGTTATTTT 59.666 33.333 0.00 0.00 0.00 1.82
3579 5423 1.108727 CCTTTTGTGGCAGGCTGTGA 61.109 55.000 17.16 0.00 0.00 3.58
3587 5431 0.524862 GGCAGGCTGTGAGTTTCATG 59.475 55.000 17.16 0.00 0.00 3.07
3672 5516 3.826729 AGTCTTGAAAAACTGGTATGGCC 59.173 43.478 0.00 0.00 37.90 5.36
3949 5793 9.818796 GTCTAAAAGAAACTAGCAAATCTTCAG 57.181 33.333 0.00 0.00 31.20 3.02
4092 5937 2.390225 AGATGGCGTTCTCTATCCCT 57.610 50.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.662619 TGTCGTGCAAGCCTTTTCTG 59.337 50.000 0.00 0.00 0.00 3.02
1 2 1.388547 TTGTCGTGCAAGCCTTTTCT 58.611 45.000 0.00 0.00 32.52 2.52
2 3 2.422276 ATTGTCGTGCAAGCCTTTTC 57.578 45.000 0.00 0.00 40.86 2.29
15 16 3.925688 ACTTGTATGCGCTAATTGTCG 57.074 42.857 9.73 0.00 0.00 4.35
22 23 3.861276 AGTGTGTACTTGTATGCGCTA 57.139 42.857 9.73 0.00 31.66 4.26
40 41 8.803397 ACAGTGAACCTTTTTAGTTTTCTAGT 57.197 30.769 0.00 0.00 33.61 2.57
333 336 9.921637 TCCTGAAAATACTTTTAAATGCGAATT 57.078 25.926 1.19 0.00 31.94 2.17
377 380 5.395642 TGAAACACGAGAAGTTTTGGAAAC 58.604 37.500 0.00 0.00 39.15 2.78
383 386 6.921307 ACACTTTTTGAAACACGAGAAGTTTT 59.079 30.769 0.00 0.00 39.15 2.43
446 449 7.277760 CGGAAAGAATTTTTGGAACTTCAAGTT 59.722 33.333 1.21 1.21 39.27 2.66
447 450 6.756542 CGGAAAGAATTTTTGGAACTTCAAGT 59.243 34.615 0.00 0.00 39.27 3.16
452 455 9.438228 TTTAAACGGAAAGAATTTTTGGAACTT 57.562 25.926 0.00 0.00 39.27 2.66
484 487 7.953158 TGTGAATAATTTTGAAAATGCCGAA 57.047 28.000 3.62 0.00 0.00 4.30
485 488 7.953158 TTGTGAATAATTTTGAAAATGCCGA 57.047 28.000 3.62 0.00 0.00 5.54
555 558 7.320077 GCAAAAGATCAACGCGAATATTTAAC 58.680 34.615 15.93 5.49 0.00 2.01
579 582 3.509575 TGGAACTAATGAATGTTGGTGGC 59.490 43.478 0.00 0.00 0.00 5.01
586 589 6.151144 GCACCTAAACTGGAACTAATGAATGT 59.849 38.462 0.00 0.00 0.00 2.71
633 644 0.519961 AAATTGGCGCACCTAACGAC 59.480 50.000 10.83 0.00 39.63 4.34
729 740 3.437049 GTCATCTTTTAGCAAAGCCTCGT 59.563 43.478 0.00 0.00 39.56 4.18
730 741 3.436704 TGTCATCTTTTAGCAAAGCCTCG 59.563 43.478 0.00 0.00 39.56 4.63
731 742 4.142513 CCTGTCATCTTTTAGCAAAGCCTC 60.143 45.833 0.00 0.00 39.56 4.70
732 743 3.760684 CCTGTCATCTTTTAGCAAAGCCT 59.239 43.478 0.00 0.00 39.56 4.58
734 745 3.192212 AGCCTGTCATCTTTTAGCAAAGC 59.808 43.478 0.00 0.00 39.56 3.51
735 746 5.382618 AAGCCTGTCATCTTTTAGCAAAG 57.617 39.130 0.00 0.00 40.91 2.77
745 1347 3.690460 CCCAAGTTTAAGCCTGTCATCT 58.310 45.455 0.00 0.00 0.00 2.90
757 1362 0.179015 TGCAGTTCGGCCCAAGTTTA 60.179 50.000 0.00 0.00 0.00 2.01
799 1404 1.535444 TCAAGAAGGGTGGGCGAGA 60.535 57.895 0.00 0.00 0.00 4.04
800 1405 1.376037 GTCAAGAAGGGTGGGCGAG 60.376 63.158 0.00 0.00 0.00 5.03
801 1406 2.747686 GTCAAGAAGGGTGGGCGA 59.252 61.111 0.00 0.00 0.00 5.54
802 1407 2.742372 CGTCAAGAAGGGTGGGCG 60.742 66.667 0.00 0.00 0.00 6.13
803 1408 2.359975 CCGTCAAGAAGGGTGGGC 60.360 66.667 0.00 0.00 0.00 5.36
804 1409 2.359975 GCCGTCAAGAAGGGTGGG 60.360 66.667 4.26 0.00 35.23 4.61
806 1411 2.317609 CGTGCCGTCAAGAAGGGTG 61.318 63.158 4.26 0.00 35.23 4.61
807 1412 2.030562 CGTGCCGTCAAGAAGGGT 59.969 61.111 4.26 0.00 35.23 4.34
808 1413 3.423154 GCGTGCCGTCAAGAAGGG 61.423 66.667 4.26 0.00 35.92 3.95
809 1414 3.423154 GGCGTGCCGTCAAGAAGG 61.423 66.667 0.00 0.00 0.00 3.46
906 1581 1.853565 GGGTTAGGGTTGGGGTGGA 60.854 63.158 0.00 0.00 0.00 4.02
908 1583 0.916809 CTAGGGTTAGGGTTGGGGTG 59.083 60.000 0.00 0.00 0.00 4.61
913 1588 1.153229 GCCGCTAGGGTTAGGGTTG 60.153 63.158 6.02 0.00 37.97 3.77
1025 1746 0.305922 GCTGAAATCAATCTCGCGGG 59.694 55.000 6.13 1.01 0.00 6.13
1082 1827 1.188863 GGTTGGCAGCATTCCTTCAT 58.811 50.000 3.14 0.00 0.00 2.57
1083 1828 0.899717 GGGTTGGCAGCATTCCTTCA 60.900 55.000 3.14 0.00 0.00 3.02
1091 1843 3.604667 CTTTGCGGGTTGGCAGCA 61.605 61.111 3.14 0.00 44.94 4.41
1489 2406 3.721706 CCAGACCCCAGCCAGACC 61.722 72.222 0.00 0.00 0.00 3.85
1490 2407 4.416738 GCCAGACCCCAGCCAGAC 62.417 72.222 0.00 0.00 0.00 3.51
1491 2408 4.664267 AGCCAGACCCCAGCCAGA 62.664 66.667 0.00 0.00 0.00 3.86
1732 2704 6.377327 CTTGACAAAGCTGAACTCCTTTAA 57.623 37.500 0.00 0.00 30.62 1.52
1734 2706 4.907879 CTTGACAAAGCTGAACTCCTTT 57.092 40.909 0.00 0.00 0.00 3.11
1746 2718 1.677576 TCTTGTGGCAGCTTGACAAAG 59.322 47.619 0.00 5.87 36.98 2.77
1747 2719 1.405105 GTCTTGTGGCAGCTTGACAAA 59.595 47.619 0.00 0.00 36.98 2.83
1748 2720 1.024271 GTCTTGTGGCAGCTTGACAA 58.976 50.000 0.00 0.00 36.98 3.18
1749 2721 0.181114 AGTCTTGTGGCAGCTTGACA 59.819 50.000 10.83 0.00 29.15 3.58
1751 2723 0.181114 ACAGTCTTGTGGCAGCTTGA 59.819 50.000 0.00 0.00 35.83 3.02
1752 2724 0.590195 GACAGTCTTGTGGCAGCTTG 59.410 55.000 0.00 0.00 37.76 4.01
1753 2725 0.536006 GGACAGTCTTGTGGCAGCTT 60.536 55.000 0.00 0.00 37.76 3.74
1754 2726 1.072159 GGACAGTCTTGTGGCAGCT 59.928 57.895 0.00 0.00 37.76 4.24
1755 2727 1.227943 TGGACAGTCTTGTGGCAGC 60.228 57.895 0.00 0.00 37.76 5.25
1756 2728 1.233285 GCTGGACAGTCTTGTGGCAG 61.233 60.000 0.00 0.00 37.76 4.85
1757 2729 1.227943 GCTGGACAGTCTTGTGGCA 60.228 57.895 0.00 0.00 37.76 4.92
1758 2730 1.968540 GGCTGGACAGTCTTGTGGC 60.969 63.158 0.00 0.00 37.76 5.01
1759 2731 1.302832 GGGCTGGACAGTCTTGTGG 60.303 63.158 3.73 0.00 37.76 4.17
1760 2732 0.604780 CAGGGCTGGACAGTCTTGTG 60.605 60.000 7.76 0.00 37.76 3.33
1761 2733 1.757306 CAGGGCTGGACAGTCTTGT 59.243 57.895 7.76 0.00 41.18 3.16
1762 2734 4.709840 CAGGGCTGGACAGTCTTG 57.290 61.111 3.73 2.65 33.88 3.02
1772 2744 3.309296 TCTAAGTTCCTATCCAGGGCTG 58.691 50.000 0.00 0.00 42.87 4.85
1773 2745 3.582164 CTCTAAGTTCCTATCCAGGGCT 58.418 50.000 0.00 0.00 42.87 5.19
1774 2746 2.635427 CCTCTAAGTTCCTATCCAGGGC 59.365 54.545 0.00 0.00 42.87 5.19
1775 2747 4.156477 CTCCTCTAAGTTCCTATCCAGGG 58.844 52.174 0.00 0.00 42.87 4.45
1776 2748 4.810345 ACTCCTCTAAGTTCCTATCCAGG 58.190 47.826 0.00 0.00 44.17 4.45
1777 2749 4.830600 GGACTCCTCTAAGTTCCTATCCAG 59.169 50.000 0.00 0.00 0.00 3.86
1778 2750 4.232122 TGGACTCCTCTAAGTTCCTATCCA 59.768 45.833 0.00 0.00 0.00 3.41
1779 2751 4.805744 TGGACTCCTCTAAGTTCCTATCC 58.194 47.826 0.00 0.00 0.00 2.59
1780 2752 4.279922 GCTGGACTCCTCTAAGTTCCTATC 59.720 50.000 0.00 0.00 0.00 2.08
1781 2753 4.078863 AGCTGGACTCCTCTAAGTTCCTAT 60.079 45.833 0.00 0.00 0.00 2.57
1782 2754 3.269906 AGCTGGACTCCTCTAAGTTCCTA 59.730 47.826 0.00 0.00 0.00 2.94
1783 2755 2.043801 AGCTGGACTCCTCTAAGTTCCT 59.956 50.000 0.00 0.00 0.00 3.36
1784 2756 2.462723 AGCTGGACTCCTCTAAGTTCC 58.537 52.381 0.00 0.00 0.00 3.62
1785 2757 6.717540 TGATATAGCTGGACTCCTCTAAGTTC 59.282 42.308 0.00 0.00 0.00 3.01
1786 2758 6.615617 TGATATAGCTGGACTCCTCTAAGTT 58.384 40.000 0.00 0.00 0.00 2.66
1787 2759 6.207509 TGATATAGCTGGACTCCTCTAAGT 57.792 41.667 0.00 0.00 0.00 2.24
1805 2792 3.470709 CGGGTGCAGAACTTGATGATAT 58.529 45.455 0.00 0.00 0.00 1.63
1811 2798 2.281484 GGCGGGTGCAGAACTTGA 60.281 61.111 0.00 0.00 45.35 3.02
1936 2947 3.490348 ACTTGGAGGTTTTGATCCAGTG 58.510 45.455 0.00 0.00 33.39 3.66
3080 4912 7.264373 ACATCTCAAATCTTCAACGTCTTTT 57.736 32.000 0.00 0.00 0.00 2.27
3222 5056 5.865085 ACAAGCCACTCAGTAGACATAAAA 58.135 37.500 0.00 0.00 0.00 1.52
3309 5148 5.751990 GGATTCATGCAGGAAAATCACAATC 59.248 40.000 18.75 8.11 31.25 2.67
3579 5423 2.447047 AGTCCAAAGGGTCCATGAAACT 59.553 45.455 0.00 0.00 34.93 2.66
3587 5431 2.027100 CCTTCACTAGTCCAAAGGGTCC 60.027 54.545 15.83 0.00 35.63 4.46
3631 5475 2.041081 ACTGCAATAGCCACTTACCCAA 59.959 45.455 0.00 0.00 41.13 4.12
3633 5477 2.092914 AGACTGCAATAGCCACTTACCC 60.093 50.000 0.00 0.00 41.13 3.69
3882 5726 5.594317 TGTAGTTAGCTCATGTATCTCTGCA 59.406 40.000 0.00 0.00 0.00 4.41
3949 5793 3.491267 CGGCCGTCTTCAGAGAAATATTC 59.509 47.826 19.50 0.00 32.66 1.75


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

AutoCloner maintained by Alex Coulton.