Multiple sequence alignment - TraesCS7D01G103100

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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 TraesCS7D01G103100 chr7D 100.000 4412 0 0 1 4412 62939310 62943721 0.000000e+00 8148.0
1 TraesCS7D01G103100 chr7D 96.263 1793 62 4 1 1792 62192936 62194724 0.000000e+00 2935.0
2 TraesCS7D01G103100 chr7D 95.997 1249 45 2 1792 3039 62194682 62195926 0.000000e+00 2025.0
3 TraesCS7D01G103100 chr7D 97.585 911 21 1 3502 4412 231374253 231375162 0.000000e+00 1559.0
4 TraesCS7D01G103100 chr7D 87.353 1107 127 8 1796 2898 62162474 62163571 0.000000e+00 1256.0
5 TraesCS7D01G103100 chr7D 85.539 733 95 9 1794 2522 62537466 62538191 0.000000e+00 756.0
6 TraesCS7D01G103100 chr7D 97.074 376 9 1 3117 3492 62196315 62196688 2.240000e-177 632.0
7 TraesCS7D01G103100 chr7D 88.816 304 28 3 2596 2898 62538182 62538480 6.970000e-98 368.0
8 TraesCS7D01G103100 chr7D 90.132 152 14 1 2748 2898 62465983 62466134 3.480000e-46 196.0
9 TraesCS7D01G103100 chr7D 80.247 243 24 9 3126 3364 62163808 62164030 1.270000e-35 161.0
10 TraesCS7D01G103100 chr7D 87.805 123 14 1 1670 1792 62162390 62162511 4.600000e-30 143.0
11 TraesCS7D01G103100 chr7D 96.078 51 2 0 3066 3116 62196222 62196272 2.830000e-12 84.2
12 TraesCS7D01G103100 chr7D 100.000 43 0 0 1750 1792 62941101 62941143 3.660000e-11 80.5
13 TraesCS7D01G103100 chr7A 95.749 1623 51 8 174 1792 65517389 65518997 0.000000e+00 2599.0
14 TraesCS7D01G103100 chr7A 94.541 806 24 1 2311 3116 65520904 65521689 0.000000e+00 1227.0
15 TraesCS7D01G103100 chr7A 85.841 1123 129 19 1794 2898 65494792 65495902 0.000000e+00 1166.0
16 TraesCS7D01G103100 chr7A 94.961 516 21 3 1792 2306 65518955 65519466 0.000000e+00 804.0
17 TraesCS7D01G103100 chr7A 96.825 378 7 4 3117 3492 65521732 65522106 1.040000e-175 627.0
18 TraesCS7D01G103100 chr7A 94.697 132 4 3 1 131 65517260 65517389 7.480000e-48 202.0
19 TraesCS7D01G103100 chr7A 82.018 228 17 5 3126 3349 65496140 65496347 5.870000e-39 172.0
20 TraesCS7D01G103100 chr2D 97.695 911 21 0 3502 4412 56733651 56732741 0.000000e+00 1567.0
21 TraesCS7D01G103100 chr2D 88.242 893 85 8 916 1792 485991494 485992382 0.000000e+00 1050.0
22 TraesCS7D01G103100 chr2D 80.576 834 132 22 922 1744 485985193 485986007 2.250000e-172 616.0
23 TraesCS7D01G103100 chr2D 78.130 631 108 22 2283 2898 485986229 485986844 1.500000e-99 374.0
24 TraesCS7D01G103100 chr2D 90.870 230 21 0 3126 3355 485993398 485993627 4.290000e-80 309.0
25 TraesCS7D01G103100 chr2D 87.330 221 27 1 3138 3358 485987093 485987312 7.330000e-63 252.0
26 TraesCS7D01G103100 chr2D 90.217 184 16 1 1795 1978 485992345 485992526 5.700000e-59 239.0
27 TraesCS7D01G103100 chr2D 89.831 59 3 3 335 392 473701184 473701128 6.120000e-09 73.1
28 TraesCS7D01G103100 chr2D 86.792 53 7 0 334 386 34682532 34682480 4.770000e-05 60.2
29 TraesCS7D01G103100 chr1D 97.590 913 20 2 3502 4412 409950521 409951433 0.000000e+00 1563.0
30 TraesCS7D01G103100 chr1D 97.368 912 23 1 3502 4412 256269251 256268340 0.000000e+00 1550.0
31 TraesCS7D01G103100 chr1D 82.609 115 19 1 1058 1171 203917228 203917114 2.810000e-17 100.0
32 TraesCS7D01G103100 chr3D 97.585 911 22 0 3502 4412 380944648 380945558 0.000000e+00 1561.0
33 TraesCS7D01G103100 chr3D 97.473 910 22 1 3502 4411 610150791 610149883 0.000000e+00 1552.0
34 TraesCS7D01G103100 chr5D 97.475 911 23 0 3502 4412 215869788 215870698 0.000000e+00 1555.0
35 TraesCS7D01G103100 chr6D 97.366 911 24 0 3502 4412 160410704 160411614 0.000000e+00 1550.0
36 TraesCS7D01G103100 chr4D 97.062 919 27 0 3494 4412 323958415 323959333 0.000000e+00 1548.0
37 TraesCS7D01G103100 chr4D 82.946 258 34 6 13 270 88146066 88146313 1.600000e-54 224.0
38 TraesCS7D01G103100 chr2B 87.298 1236 116 21 589 1792 570896183 570897409 0.000000e+00 1375.0
39 TraesCS7D01G103100 chr2B 88.793 232 24 1 3126 3355 570898349 570898580 2.600000e-72 283.0
40 TraesCS7D01G103100 chr2B 88.601 193 19 3 1795 1986 570897372 570897562 9.540000e-57 231.0
41 TraesCS7D01G103100 chr2B 89.655 58 4 2 335 392 554291555 554291500 6.120000e-09 73.1
42 TraesCS7D01G103100 chr2A 86.548 1182 120 17 645 1792 631538514 631539690 0.000000e+00 1266.0
43 TraesCS7D01G103100 chr2A 81.535 834 127 18 922 1743 631531349 631532167 0.000000e+00 662.0
44 TraesCS7D01G103100 chr2A 82.284 429 59 13 2479 2898 631532584 631533004 5.430000e-94 355.0
45 TraesCS7D01G103100 chr2A 92.478 226 17 0 3126 3351 631540618 631540843 1.530000e-84 324.0
46 TraesCS7D01G103100 chr2A 87.568 185 21 1 1795 1979 631539653 631539835 3.460000e-51 213.0
47 TraesCS7D01G103100 chrUn 85.402 733 96 9 1794 2522 367447018 367447743 0.000000e+00 750.0
48 TraesCS7D01G103100 chrUn 88.487 304 29 3 2596 2898 367447734 367448032 3.240000e-96 363.0
49 TraesCS7D01G103100 chr4B 81.181 271 33 11 1 271 124920050 124920302 7.480000e-48 202.0
50 TraesCS7D01G103100 chr5B 91.489 94 8 0 131 224 429072291 429072384 3.580000e-26 130.0
51 TraesCS7D01G103100 chr3A 75.556 270 51 10 1995 2251 20837788 20838055 7.750000e-23 119.0
52 TraesCS7D01G103100 chr1B 82.609 115 19 1 1058 1171 298163825 298163711 2.810000e-17 100.0


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 TraesCS7D01G103100 chr7D 62939310 62943721 4411 False 4114.250000 8148 100.000000 1 4412 2 chr7D.!!$F6 4411
1 TraesCS7D01G103100 chr7D 231374253 231375162 909 False 1559.000000 1559 97.585000 3502 4412 1 chr7D.!!$F2 910
2 TraesCS7D01G103100 chr7D 62192936 62196688 3752 False 1419.050000 2935 96.353000 1 3492 4 chr7D.!!$F4 3491
3 TraesCS7D01G103100 chr7D 62537466 62538480 1014 False 562.000000 756 87.177500 1794 2898 2 chr7D.!!$F5 1104
4 TraesCS7D01G103100 chr7D 62162390 62164030 1640 False 520.000000 1256 85.135000 1670 3364 3 chr7D.!!$F3 1694
5 TraesCS7D01G103100 chr7A 65517260 65522106 4846 False 1091.800000 2599 95.354600 1 3492 5 chr7A.!!$F2 3491
6 TraesCS7D01G103100 chr7A 65494792 65496347 1555 False 669.000000 1166 83.929500 1794 3349 2 chr7A.!!$F1 1555
7 TraesCS7D01G103100 chr2D 56732741 56733651 910 True 1567.000000 1567 97.695000 3502 4412 1 chr2D.!!$R2 910
8 TraesCS7D01G103100 chr2D 485991494 485993627 2133 False 532.666667 1050 89.776333 916 3355 3 chr2D.!!$F2 2439
9 TraesCS7D01G103100 chr2D 485985193 485987312 2119 False 414.000000 616 82.012000 922 3358 3 chr2D.!!$F1 2436
10 TraesCS7D01G103100 chr1D 409950521 409951433 912 False 1563.000000 1563 97.590000 3502 4412 1 chr1D.!!$F1 910
11 TraesCS7D01G103100 chr1D 256268340 256269251 911 True 1550.000000 1550 97.368000 3502 4412 1 chr1D.!!$R2 910
12 TraesCS7D01G103100 chr3D 380944648 380945558 910 False 1561.000000 1561 97.585000 3502 4412 1 chr3D.!!$F1 910
13 TraesCS7D01G103100 chr3D 610149883 610150791 908 True 1552.000000 1552 97.473000 3502 4411 1 chr3D.!!$R1 909
14 TraesCS7D01G103100 chr5D 215869788 215870698 910 False 1555.000000 1555 97.475000 3502 4412 1 chr5D.!!$F1 910
15 TraesCS7D01G103100 chr6D 160410704 160411614 910 False 1550.000000 1550 97.366000 3502 4412 1 chr6D.!!$F1 910
16 TraesCS7D01G103100 chr4D 323958415 323959333 918 False 1548.000000 1548 97.062000 3494 4412 1 chr4D.!!$F2 918
17 TraesCS7D01G103100 chr2B 570896183 570898580 2397 False 629.666667 1375 88.230667 589 3355 3 chr2B.!!$F1 2766
18 TraesCS7D01G103100 chr2A 631538514 631540843 2329 False 601.000000 1266 88.864667 645 3351 3 chr2A.!!$F2 2706
19 TraesCS7D01G103100 chr2A 631531349 631533004 1655 False 508.500000 662 81.909500 922 2898 2 chr2A.!!$F1 1976
20 TraesCS7D01G103100 chrUn 367447018 367448032 1014 False 556.500000 750 86.944500 1794 2898 2 chrUn.!!$F1 1104

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
510 516 0.109597 GAAATTGCCAGGCTCGTGTG 60.110 55.0 14.15 0.0 0.00 3.82 F
1554 1600 2.507407 TCTAAGGGTTGGGATTGCAC 57.493 50.0 0.00 0.0 0.00 4.57 F
1565 1611 0.253044 GGATTGCACCTGTAGCCTCA 59.747 55.0 0.00 0.0 0.00 3.86 F
2594 4095 0.843309 TTGTTCTCAAGAGCACCCCA 59.157 50.0 0.00 0.0 35.01 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 1611 0.469917 CATGGTTATCTGAGGGCCGT 59.530 55.000 0.0 0.0 0.00 5.68 R
3050 4583 0.537653 AAACAAAAACACGGGGGTGG 59.462 50.000 0.0 0.0 0.00 4.61 R
3052 4585 2.159268 CGTAAAACAAAAACACGGGGGT 60.159 45.455 0.0 0.0 0.00 4.95 R
3947 5835 0.169451 CGAAATACGCCAACCCAACC 59.831 55.000 0.0 0.0 34.51 3.77 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
78 79 1.202166 TGTCATGAATGAAATGCGGCG 60.202 47.619 0.51 0.51 38.75 6.46
120 122 2.549633 GCATGTTGCATGGTACAGAC 57.450 50.000 10.59 0.00 44.26 3.51
193 195 5.354792 CCAATGGCTAAAACAATTTGGATGG 59.645 40.000 0.78 0.00 32.36 3.51
195 197 3.326006 TGGCTAAAACAATTTGGATGGCA 59.674 39.130 0.78 0.00 0.00 4.92
248 250 7.326063 GCAATTAATGACTTGTAGTGTGGTTTC 59.674 37.037 0.00 0.00 0.00 2.78
322 324 2.218603 ACTGCCAAAAACCACTAGACG 58.781 47.619 0.00 0.00 0.00 4.18
370 372 6.682423 ATGATGTCAGATTTTTACGCATGA 57.318 33.333 0.00 0.00 0.00 3.07
377 379 7.023575 GTCAGATTTTTACGCATGAGAAATGT 58.976 34.615 2.50 0.00 0.00 2.71
443 449 2.095110 CCATTCAGCGAGCATGACAAAA 60.095 45.455 0.00 0.00 0.00 2.44
444 450 3.428452 CCATTCAGCGAGCATGACAAAAT 60.428 43.478 0.00 0.00 0.00 1.82
446 452 1.739466 TCAGCGAGCATGACAAAATCC 59.261 47.619 0.00 0.00 0.00 3.01
447 453 1.741706 CAGCGAGCATGACAAAATCCT 59.258 47.619 0.00 0.00 0.00 3.24
510 516 0.109597 GAAATTGCCAGGCTCGTGTG 60.110 55.000 14.15 0.00 0.00 3.82
529 535 5.058734 CGTGTGACGTAATTTGCCATAAAAC 59.941 40.000 0.00 0.00 36.74 2.43
655 661 6.045072 TCGTTGGTTGGAGTTACAATATCT 57.955 37.500 0.00 0.00 32.24 1.98
680 686 6.985653 TTCTGATCCCAGGAGTATAAGAAG 57.014 41.667 0.00 0.00 40.76 2.85
832 844 9.890629 TTCTCTACATGTTCTATTGCTTAACAT 57.109 29.630 2.30 0.00 42.91 2.71
838 850 8.982685 ACATGTTCTATTGCTTAACATATCTCG 58.017 33.333 0.00 0.00 40.83 4.04
1102 1129 2.665165 TGGGACACTGCAATTTTGAGT 58.335 42.857 0.00 0.00 0.00 3.41
1237 1278 9.099454 GACTTTAGGTCCATTATGTTCTTACTG 57.901 37.037 0.00 0.00 38.93 2.74
1363 1409 3.449018 CCCCATAGGTATCATTCTCTCCG 59.551 52.174 0.00 0.00 0.00 4.63
1554 1600 2.507407 TCTAAGGGTTGGGATTGCAC 57.493 50.000 0.00 0.00 0.00 4.57
1565 1611 0.253044 GGATTGCACCTGTAGCCTCA 59.747 55.000 0.00 0.00 0.00 3.86
1760 1806 5.124776 GGATTTTCCACGTTACATGAATCCA 59.875 40.000 0.00 0.00 40.45 3.41
1761 1807 6.349777 GGATTTTCCACGTTACATGAATCCAA 60.350 38.462 0.00 0.00 40.45 3.53
1762 1808 6.582677 TTTTCCACGTTACATGAATCCAAT 57.417 33.333 0.00 0.00 0.00 3.16
1763 1809 7.689446 TTTTCCACGTTACATGAATCCAATA 57.311 32.000 0.00 0.00 0.00 1.90
1764 1810 6.671614 TTCCACGTTACATGAATCCAATAC 57.328 37.500 0.00 0.00 0.00 1.89
1765 1811 5.120399 TCCACGTTACATGAATCCAATACC 58.880 41.667 0.00 0.00 0.00 2.73
1766 1812 5.104693 TCCACGTTACATGAATCCAATACCT 60.105 40.000 0.00 0.00 0.00 3.08
1767 1813 5.588648 CCACGTTACATGAATCCAATACCTT 59.411 40.000 0.00 0.00 0.00 3.50
1768 1814 6.238374 CCACGTTACATGAATCCAATACCTTC 60.238 42.308 0.00 0.00 0.00 3.46
1769 1815 6.315144 CACGTTACATGAATCCAATACCTTCA 59.685 38.462 0.00 0.00 33.75 3.02
1770 1816 7.012327 CACGTTACATGAATCCAATACCTTCAT 59.988 37.037 0.00 0.00 39.55 2.57
1771 1817 8.208224 ACGTTACATGAATCCAATACCTTCATA 58.792 33.333 0.00 0.00 37.48 2.15
1772 1818 8.712363 CGTTACATGAATCCAATACCTTCATAG 58.288 37.037 0.00 0.00 37.48 2.23
1773 1819 9.561069 GTTACATGAATCCAATACCTTCATAGT 57.439 33.333 0.00 0.00 37.48 2.12
1774 1820 9.559732 TTACATGAATCCAATACCTTCATAGTG 57.440 33.333 0.00 0.00 37.48 2.74
1775 1821 7.577303 ACATGAATCCAATACCTTCATAGTGT 58.423 34.615 0.00 0.00 37.48 3.55
1776 1822 8.055181 ACATGAATCCAATACCTTCATAGTGTT 58.945 33.333 0.00 0.00 37.48 3.32
1777 1823 7.864108 TGAATCCAATACCTTCATAGTGTTG 57.136 36.000 0.00 0.00 36.44 3.33
1778 1824 7.402054 TGAATCCAATACCTTCATAGTGTTGT 58.598 34.615 0.00 0.00 35.32 3.32
1779 1825 8.544622 TGAATCCAATACCTTCATAGTGTTGTA 58.455 33.333 0.00 0.00 35.32 2.41
1780 1826 9.391006 GAATCCAATACCTTCATAGTGTTGTAA 57.609 33.333 0.00 0.00 35.32 2.41
1781 1827 9.747898 AATCCAATACCTTCATAGTGTTGTAAA 57.252 29.630 0.00 0.00 35.32 2.01
1801 1847 9.778741 TTGTAAACTGATAGGATACATGAATCC 57.221 33.333 0.00 0.00 45.06 3.01
1802 1848 8.933653 TGTAAACTGATAGGATACATGAATCCA 58.066 33.333 0.00 0.00 46.81 3.41
2185 2244 2.167662 CCTTTGGCCGGAATACAAACT 58.832 47.619 5.05 0.00 31.51 2.66
2195 2254 6.653320 GGCCGGAATACAAACTGATATCATTA 59.347 38.462 5.05 0.00 0.00 1.90
2431 3931 6.942532 ACAAGAGTCAGATGCACTTTTTAA 57.057 33.333 0.00 0.00 0.00 1.52
2435 3935 7.516198 AGAGTCAGATGCACTTTTTAAACAT 57.484 32.000 0.00 0.00 0.00 2.71
2470 3971 9.200817 AGCACAAATATATTAACCCTCACATTT 57.799 29.630 0.00 0.00 0.00 2.32
2495 3996 2.879026 GTCCCAGGAAAGACAACTCAAC 59.121 50.000 0.00 0.00 33.08 3.18
2590 4091 4.372656 ACAGTAGTTGTTCTCAAGAGCAC 58.627 43.478 0.00 0.00 36.31 4.40
2594 4095 0.843309 TTGTTCTCAAGAGCACCCCA 59.157 50.000 0.00 0.00 35.01 4.96
3039 4572 8.739039 ACAGTGAATGCTTATAAAACATTGCTA 58.261 29.630 14.84 3.22 34.28 3.49
3040 4573 9.013490 CAGTGAATGCTTATAAAACATTGCTAC 57.987 33.333 14.84 11.52 34.28 3.58
3041 4574 8.190784 AGTGAATGCTTATAAAACATTGCTACC 58.809 33.333 14.84 4.74 34.28 3.18
3042 4575 7.435192 GTGAATGCTTATAAAACATTGCTACCC 59.565 37.037 14.84 4.23 34.28 3.69
3043 4576 5.845391 TGCTTATAAAACATTGCTACCCC 57.155 39.130 0.00 0.00 0.00 4.95
3044 4577 4.647399 TGCTTATAAAACATTGCTACCCCC 59.353 41.667 0.00 0.00 0.00 5.40
3148 5024 7.817418 AAAGAAACACTCTGGTAAGCAATAA 57.183 32.000 0.00 0.00 33.37 1.40
3249 5131 7.041780 CCAAGAGGATCAACATTTATTCCTACG 60.042 40.741 0.00 0.00 36.95 3.51
3403 5289 6.630443 CCTTTTTGCGAAAATAGATGATCTCG 59.370 38.462 12.26 0.00 34.45 4.04
3690 5578 8.306761 GTTGATCAAAGATGGTTATGTTTCCTT 58.693 33.333 10.35 0.00 28.23 3.36
3987 5875 4.709886 TCGAGATTAGGATTTGTCACTCCA 59.290 41.667 3.96 0.00 33.75 3.86
4170 6059 1.483415 TCTCGGGCAAGTAACATACCC 59.517 52.381 0.00 0.00 37.19 3.69
4246 6135 5.305902 TCGTAGAATATGTGGGAGCCAATAA 59.694 40.000 0.00 0.00 34.18 1.40
4320 6209 2.357009 TCTACATAGTTCTCGAACCCGC 59.643 50.000 6.20 0.00 42.06 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 6.072728 TGCATATATCGTGGATTTTTAGTGCC 60.073 38.462 0.00 0.00 0.00 5.01
120 122 4.032900 CCGTCCGATTTGAACATAAGAGTG 59.967 45.833 0.00 0.00 0.00 3.51
193 195 1.811965 TGTACATGTGTGCTTCCATGC 59.188 47.619 9.11 0.00 41.69 4.06
195 197 3.701205 TCTGTACATGTGTGCTTCCAT 57.299 42.857 9.11 0.00 0.00 3.41
387 389 6.902948 GCTTGCAATACGTTAATTCGACATAA 59.097 34.615 0.00 0.00 34.70 1.90
424 430 3.181493 GGATTTTGTCATGCTCGCTGAAT 60.181 43.478 0.00 0.00 0.00 2.57
470 476 1.814394 CTTCAGCAAGCATGGCAACTA 59.186 47.619 0.00 0.00 37.68 2.24
510 516 4.725359 ACGGTTTTATGGCAAATTACGTC 58.275 39.130 0.00 0.00 0.00 4.34
529 535 5.914085 TTTAAACATGCCAAATTGAACGG 57.086 34.783 0.00 0.00 0.00 4.44
594 600 5.814764 ACAGATGCTTTCAGATGTCATTC 57.185 39.130 0.00 0.00 0.00 2.67
655 661 8.235230 ACTTCTTATACTCCTGGGATCAGAATA 58.765 37.037 0.00 0.00 43.49 1.75
793 805 6.402222 ACATGTAGAGAAATCTGAACTGGAC 58.598 40.000 0.00 0.00 0.00 4.02
832 844 2.159240 ACGCAGCAATCACTTCGAGATA 60.159 45.455 0.00 0.00 30.59 1.98
838 850 3.536158 TGTTAACGCAGCAATCACTTC 57.464 42.857 0.26 0.00 0.00 3.01
935 962 3.881089 TGGATGAATGACAGCTGCTAATG 59.119 43.478 15.27 0.00 35.04 1.90
939 966 2.730934 ATGGATGAATGACAGCTGCT 57.269 45.000 15.27 0.00 35.04 4.24
1102 1129 2.555227 GGAAGATCCACTTTGGGAGCAA 60.555 50.000 0.00 0.00 45.76 3.91
1192 1220 7.621428 AAAGTCTCATCACTAACATGATTGG 57.379 36.000 0.00 0.00 37.20 3.16
1286 1328 4.634004 TGTGGTTTTATGAAGCTATGTCCG 59.366 41.667 0.00 0.00 0.00 4.79
1363 1409 8.758715 AGTAGTTTGTACGAAACTTTGTATGAC 58.241 33.333 20.78 14.07 40.58 3.06
1408 1454 6.597672 GTCCATGGTGTTGAATATGTAGTCAA 59.402 38.462 12.58 0.00 37.87 3.18
1565 1611 0.469917 CATGGTTATCTGAGGGCCGT 59.530 55.000 0.00 0.00 0.00 5.68
1619 1665 3.415212 CCATGCCAGTACCATTGATAGG 58.585 50.000 0.00 0.00 0.00 2.57
1760 1806 9.959721 ATCAGTTTACAACACTATGAAGGTATT 57.040 29.630 0.00 0.00 0.00 1.89
1763 1809 8.041323 CCTATCAGTTTACAACACTATGAAGGT 58.959 37.037 0.00 0.00 0.00 3.50
1764 1810 8.258007 TCCTATCAGTTTACAACACTATGAAGG 58.742 37.037 0.00 0.00 0.00 3.46
1765 1811 9.823647 ATCCTATCAGTTTACAACACTATGAAG 57.176 33.333 0.00 0.00 0.00 3.02
1771 1817 8.758829 TCATGTATCCTATCAGTTTACAACACT 58.241 33.333 0.00 0.00 0.00 3.55
1772 1818 8.942338 TCATGTATCCTATCAGTTTACAACAC 57.058 34.615 0.00 0.00 0.00 3.32
1775 1821 9.778741 GGATTCATGTATCCTATCAGTTTACAA 57.221 33.333 20.86 0.00 40.81 2.41
1776 1822 8.933653 TGGATTCATGTATCCTATCAGTTTACA 58.066 33.333 26.17 4.66 43.75 2.41
1777 1823 9.778741 TTGGATTCATGTATCCTATCAGTTTAC 57.221 33.333 26.17 2.45 43.75 2.01
1780 1826 9.950496 GTATTGGATTCATGTATCCTATCAGTT 57.050 33.333 26.17 10.62 43.75 3.16
1781 1827 8.543774 GGTATTGGATTCATGTATCCTATCAGT 58.456 37.037 26.17 10.92 43.75 3.41
1782 1828 8.766476 AGGTATTGGATTCATGTATCCTATCAG 58.234 37.037 26.17 0.00 43.75 2.90
1783 1829 8.685257 AGGTATTGGATTCATGTATCCTATCA 57.315 34.615 26.17 13.43 43.75 2.15
1784 1830 9.606631 GAAGGTATTGGATTCATGTATCCTATC 57.393 37.037 26.17 18.08 43.75 2.08
1785 1831 9.116080 TGAAGGTATTGGATTCATGTATCCTAT 57.884 33.333 26.17 25.05 43.75 2.57
1786 1832 8.504811 TGAAGGTATTGGATTCATGTATCCTA 57.495 34.615 26.17 21.07 43.75 2.94
1787 1833 7.392766 TGAAGGTATTGGATTCATGTATCCT 57.607 36.000 26.17 13.60 43.75 3.24
1788 1834 9.388506 CTATGAAGGTATTGGATTCATGTATCC 57.611 37.037 21.23 21.23 42.19 2.59
1790 1836 9.730705 CACTATGAAGGTATTGGATTCATGTAT 57.269 33.333 9.32 0.00 42.19 2.29
1792 1838 7.577303 ACACTATGAAGGTATTGGATTCATGT 58.423 34.615 9.32 4.08 42.19 3.21
1801 1847 9.214957 TCAGTTTACAACACTATGAAGGTATTG 57.785 33.333 0.00 0.00 0.00 1.90
1802 1848 9.959721 ATCAGTTTACAACACTATGAAGGTATT 57.040 29.630 0.00 0.00 0.00 1.89
2470 3971 2.243736 AGTTGTCTTTCCTGGGACCAAA 59.756 45.455 0.00 0.00 0.00 3.28
2495 3996 6.489127 TGTGTAAATAATTCACCACTTCCG 57.511 37.500 0.00 0.00 0.00 4.30
2590 4091 2.158667 ACCCGCTTTGTATCTAATGGGG 60.159 50.000 0.00 0.00 39.79 4.96
2594 4095 5.497474 AGAAACACCCGCTTTGTATCTAAT 58.503 37.500 0.00 0.00 0.00 1.73
2781 4288 9.521841 TGGTTCATGATTACCTACACAAAATTA 57.478 29.630 15.90 0.00 35.41 1.40
3047 4580 3.759910 AAAAACACGGGGGTGGGGG 62.760 63.158 0.00 0.00 0.00 5.40
3048 4581 2.123208 AAAAACACGGGGGTGGGG 60.123 61.111 0.00 0.00 0.00 4.96
3049 4582 1.331399 AACAAAAACACGGGGGTGGG 61.331 55.000 0.00 0.00 0.00 4.61
3050 4583 0.537653 AAACAAAAACACGGGGGTGG 59.462 50.000 0.00 0.00 0.00 4.61
3051 4584 2.388310 AAAACAAAAACACGGGGGTG 57.612 45.000 0.00 0.00 0.00 4.61
3052 4585 2.159268 CGTAAAACAAAAACACGGGGGT 60.159 45.455 0.00 0.00 0.00 4.95
3053 4586 2.461903 CGTAAAACAAAAACACGGGGG 58.538 47.619 0.00 0.00 0.00 5.40
3232 5114 6.460781 ACTGTGACGTAGGAATAAATGTTGA 58.539 36.000 0.00 0.00 0.00 3.18
3249 5131 7.148623 CGTATCTTCTTAAAGGGAAACTGTGAC 60.149 40.741 0.00 0.00 33.03 3.67
3403 5289 8.755696 TCACAAAATTTACATAATCAGGCAAC 57.244 30.769 0.00 0.00 0.00 4.17
3432 5318 8.100164 TCTGTGTATGTCAAATGTCCTATTTCA 58.900 33.333 0.00 0.00 0.00 2.69
3492 5378 6.474918 AGGGCATATTTCCTTGGATAAGAT 57.525 37.500 0.00 0.00 35.92 2.40
3499 5385 4.026356 CCTCTAGGGCATATTTCCTTGG 57.974 50.000 0.00 0.00 34.75 3.61
3866 5754 2.294074 GGTAGCACACAAAGTGTTCCA 58.706 47.619 0.00 0.00 45.08 3.53
3947 5835 0.169451 CGAAATACGCCAACCCAACC 59.831 55.000 0.00 0.00 34.51 3.77
4073 5962 9.516314 TCTTTACTCGTTCTGTAATACATCATG 57.484 33.333 0.00 0.00 31.13 3.07
4142 6031 2.787473 ACTTGCCCGAGATTCAATCA 57.213 45.000 0.00 0.00 0.00 2.57
4146 6035 3.627395 ATGTTACTTGCCCGAGATTCA 57.373 42.857 0.00 0.00 0.00 2.57
4170 6059 4.215399 ACATACGTTGTTCCCTTTGTCATG 59.785 41.667 0.00 0.00 33.74 3.07
4201 6090 4.202020 CGAAGATCTTTATCGGTCAGACCA 60.202 45.833 20.13 7.26 38.47 4.02
4246 6135 0.687757 TAGCGGAACCTGGATGCTCT 60.688 55.000 0.00 0.00 37.12 4.09
4320 6209 1.635663 CTTTAAGCGTGCGGACCCTG 61.636 60.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.