Multiple sequence alignment - TraesCS3A01G130700

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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 TraesCS3A01G130700 chr3A 100.000 2864 0 0 1 2864 107567733 107564870 0.000000e+00 5289.0
1 TraesCS3A01G130700 chr3A 77.411 394 67 17 203 581 673208905 673209291 6.210000e-52 215.0
2 TraesCS3A01G130700 chr3A 84.177 158 25 0 1511 1668 63476469 63476312 1.370000e-33 154.0
3 TraesCS3A01G130700 chr3A 83.974 156 25 0 1511 1666 57148406 57148251 1.780000e-32 150.0
4 TraesCS3A01G130700 chr3A 77.632 228 38 7 1074 1288 107620494 107620267 3.000000e-25 126.0
5 TraesCS3A01G130700 chr3A 78.610 187 37 3 1046 1232 649567354 649567537 1.390000e-23 121.0
6 TraesCS3A01G130700 chr3A 96.923 65 2 0 2121 2185 40850580 40850644 3.020000e-20 110.0
7 TraesCS3A01G130700 chr3A 84.848 99 9 5 2126 2219 692361936 692361839 8.450000e-16 95.3
8 TraesCS3A01G130700 chr3D 90.981 1896 118 34 1 1879 91388135 91386276 0.000000e+00 2505.0
9 TraesCS3A01G130700 chr3D 76.480 642 119 21 1039 1667 45543222 45542600 1.280000e-83 320.0
10 TraesCS3A01G130700 chr3D 78.117 393 70 12 202 581 596968929 596968540 4.770000e-58 235.0
11 TraesCS3A01G130700 chr3D 87.791 172 18 3 1962 2131 91385037 91384867 6.260000e-47 198.0
12 TraesCS3A01G130700 chr3D 88.393 112 13 0 1048 1159 45428917 45428806 4.980000e-28 135.0
13 TraesCS3A01G130700 chr3D 89.796 98 10 0 1046 1143 514851489 514851586 3.000000e-25 126.0
14 TraesCS3A01G130700 chr3D 98.361 61 1 0 612 672 91387576 91387516 1.090000e-19 108.0
15 TraesCS3A01G130700 chr3B 93.728 1403 57 15 744 2130 141003743 141002356 0.000000e+00 2074.0
16 TraesCS3A01G130700 chr3B 76.825 630 119 21 1048 1665 71215806 71215192 2.130000e-86 329.0
17 TraesCS3A01G130700 chr3B 79.061 277 55 3 1039 1315 71297559 71297286 1.350000e-43 187.0
18 TraesCS3A01G130700 chr3B 87.261 157 20 0 1511 1667 71295545 71295389 2.270000e-41 180.0
19 TraesCS3A01G130700 chr3B 87.097 155 20 0 1511 1665 71173110 71172956 2.930000e-40 176.0
20 TraesCS3A01G130700 chr3B 97.368 38 0 1 576 613 85081010 85080974 2.380000e-06 63.9
21 TraesCS3A01G130700 chr4A 97.297 518 8 4 2351 2864 3997720 3997205 0.000000e+00 874.0
22 TraesCS3A01G130700 chr4A 90.688 247 16 7 2124 2363 3998637 3998391 3.560000e-84 322.0
23 TraesCS3A01G130700 chr4A 92.473 93 6 1 2123 2214 161260594 161260686 6.440000e-27 132.0
24 TraesCS3A01G130700 chr4A 91.398 93 7 1 2126 2217 12207132 12207040 3.000000e-25 126.0
25 TraesCS3A01G130700 chr4A 96.875 64 1 1 2125 2188 683639965 683639903 3.900000e-19 106.0
26 TraesCS3A01G130700 chr6B 78.919 370 56 17 204 556 422401670 422402034 6.170000e-57 231.0
27 TraesCS3A01G130700 chr6B 81.679 262 43 5 1039 1299 151682144 151681887 2.240000e-51 213.0
28 TraesCS3A01G130700 chr6B 87.952 83 9 1 1782 1864 151681547 151681466 2.350000e-16 97.1
29 TraesCS3A01G130700 chr6B 82.418 91 16 0 70 160 655852918 655852828 2.370000e-11 80.5
30 TraesCS3A01G130700 chr6B 95.000 40 1 1 577 616 692558762 692558724 8.570000e-06 62.1
31 TraesCS3A01G130700 chr2B 79.130 345 51 17 253 584 40458479 40458815 4.800000e-53 219.0
32 TraesCS3A01G130700 chr2B 95.000 40 1 1 577 616 790011115 790011077 8.570000e-06 62.1
33 TraesCS3A01G130700 chr5D 78.512 363 55 18 236 581 554159483 554159839 1.730000e-52 217.0
34 TraesCS3A01G130700 chr5D 100.000 29 0 0 2478 2506 552047002 552047030 1.000000e-03 54.7
35 TraesCS3A01G130700 chr6D 77.500 400 62 19 202 581 89812246 89811855 6.210000e-52 215.0
36 TraesCS3A01G130700 chr7D 80.000 285 54 2 1037 1321 549946231 549945950 1.040000e-49 207.0
37 TraesCS3A01G130700 chr7B 77.121 389 67 18 208 584 562822288 562822666 3.740000e-49 206.0
38 TraesCS3A01G130700 chr7B 76.168 428 75 21 172 584 712727326 712726911 1.740000e-47 200.0
39 TraesCS3A01G130700 chr7B 88.820 161 18 0 1507 1667 594179386 594179226 6.260000e-47 198.0
40 TraesCS3A01G130700 chr7B 83.673 98 10 5 2126 2219 516916550 516916455 1.410000e-13 87.9
41 TraesCS3A01G130700 chr7B 95.122 41 1 1 577 617 583169018 583169057 2.380000e-06 63.9
42 TraesCS3A01G130700 chr7B 100.000 29 0 0 2478 2506 562749841 562749813 1.000000e-03 54.7
43 TraesCS3A01G130700 chr7A 86.813 91 8 4 2126 2214 160423300 160423212 6.530000e-17 99.0
44 TraesCS3A01G130700 chr7A 84.783 92 10 4 2129 2218 16883160 16883071 3.930000e-14 89.8
45 TraesCS3A01G130700 chr5A 84.337 83 8 3 11 90 29766333 29766253 3.060000e-10 76.8
46 TraesCS3A01G130700 chr5A 96.774 31 1 0 2476 2506 702087301 702087331 5.000000e-03 52.8
47 TraesCS3A01G130700 chr5B 95.238 42 1 1 577 618 695754667 695754627 6.620000e-07 65.8
48 TraesCS3A01G130700 chr2A 97.436 39 0 1 577 615 675087556 675087519 6.620000e-07 65.8
49 TraesCS3A01G130700 chr1B 97.436 39 0 1 577 615 330837843 330837806 6.620000e-07 65.8
50 TraesCS3A01G130700 chr4B 93.182 44 1 2 577 620 592204276 592204235 2.380000e-06 63.9
51 TraesCS3A01G130700 chr4B 95.000 40 0 2 577 616 672944872 672944835 8.570000e-06 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 TraesCS3A01G130700 chr3A 107564870 107567733 2863 True 5289 5289 100.000000 1 2864 1 chr3A.!!$R3 2863
1 TraesCS3A01G130700 chr3D 91384867 91388135 3268 True 937 2505 92.377667 1 2131 3 chr3D.!!$R4 2130
2 TraesCS3A01G130700 chr3D 45542600 45543222 622 True 320 320 76.480000 1039 1667 1 chr3D.!!$R2 628
3 TraesCS3A01G130700 chr3B 141002356 141003743 1387 True 2074 2074 93.728000 744 2130 1 chr3B.!!$R4 1386
4 TraesCS3A01G130700 chr3B 71215192 71215806 614 True 329 329 76.825000 1048 1665 1 chr3B.!!$R2 617
5 TraesCS3A01G130700 chr4A 3997205 3998637 1432 True 598 874 93.992500 2124 2864 2 chr4A.!!$R3 740

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
160 161 0.617935 TCGATCAATGGAGGGTTGCA 59.382 50.0 0.0 0.0 0.00 4.08 F
287 288 0.900647 AGAAGAGTCCTGGTGGTCGG 60.901 60.0 0.0 0.0 34.23 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1255 1293 0.109342 CTGAGCAGGGTGTCCTTGTT 59.891 55.0 0.32 0.0 42.67 2.83 R
2054 3281 0.584876 CCACCTCCACGAAAACGTTC 59.415 55.0 0.00 0.0 0.00 3.95 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
75 76 3.188786 GACGTGGATCCGTGCAGC 61.189 66.667 7.39 0.00 41.98 5.25
127 128 1.071642 TCCGACCGGTCAATGCAAA 59.928 52.632 32.80 7.79 36.47 3.68
156 157 0.911769 TTGCTCGATCAATGGAGGGT 59.088 50.000 0.00 0.00 33.81 4.34
160 161 0.617935 TCGATCAATGGAGGGTTGCA 59.382 50.000 0.00 0.00 0.00 4.08
170 171 3.035363 TGGAGGGTTGCATTATACTCGA 58.965 45.455 0.00 0.00 0.00 4.04
202 203 1.795170 GACAGCCGGTGCACAACAAT 61.795 55.000 20.43 0.00 41.13 2.71
215 216 1.671054 AACAATGGACGGGCAGACG 60.671 57.895 0.00 0.00 40.31 4.18
216 217 3.499737 CAATGGACGGGCAGACGC 61.500 66.667 0.00 0.00 37.37 5.19
243 244 4.504596 GACCATGATGGGCCGCCA 62.505 66.667 17.04 0.00 40.64 5.69
287 288 0.900647 AGAAGAGTCCTGGTGGTCGG 60.901 60.000 0.00 0.00 34.23 4.79
310 311 1.605058 GGAGTTGGAGTAGAGGCGCA 61.605 60.000 10.83 0.00 0.00 6.09
355 356 5.903810 AGCTACGAAAACCGATCTTAGATT 58.096 37.500 0.00 0.00 41.76 2.40
357 358 7.486647 AGCTACGAAAACCGATCTTAGATTAA 58.513 34.615 0.00 0.00 41.76 1.40
358 359 7.977853 AGCTACGAAAACCGATCTTAGATTAAA 59.022 33.333 0.00 0.00 41.76 1.52
359 360 8.598075 GCTACGAAAACCGATCTTAGATTAAAA 58.402 33.333 0.00 0.00 41.76 1.52
390 391 4.516365 AGAAACACCGATTAAGACGACT 57.484 40.909 6.44 0.00 0.00 4.18
391 392 4.235360 AGAAACACCGATTAAGACGACTG 58.765 43.478 6.44 4.51 0.00 3.51
392 393 2.649331 ACACCGATTAAGACGACTGG 57.351 50.000 6.44 0.00 0.00 4.00
393 394 1.278238 CACCGATTAAGACGACTGGC 58.722 55.000 6.44 0.00 0.00 4.85
397 398 1.278238 GATTAAGACGACTGGCCACG 58.722 55.000 13.76 13.76 0.00 4.94
410 411 1.073125 TGGCCACGAGAGAAAAATCCA 59.927 47.619 0.00 0.00 0.00 3.41
423 424 7.983307 AGAGAAAAATCCAGATCAAAAGATCG 58.017 34.615 0.00 0.00 36.73 3.69
462 466 3.434258 CGATCAACATGACCGGTGA 57.566 52.632 14.63 2.52 27.45 4.02
523 527 1.966354 CATGGAGATCGATCACCCTGA 59.034 52.381 29.94 18.14 36.04 3.86
529 533 2.721971 ATCGATCACCCTGATGCGGC 62.722 60.000 0.00 0.00 37.20 6.53
569 573 2.103094 CGGCTAGGATTGTGGATCAAGA 59.897 50.000 0.00 0.00 39.55 3.02
570 574 3.471680 GGCTAGGATTGTGGATCAAGAC 58.528 50.000 0.00 0.00 39.55 3.01
571 575 3.135530 GGCTAGGATTGTGGATCAAGACT 59.864 47.826 0.00 0.00 39.55 3.24
572 576 4.345257 GGCTAGGATTGTGGATCAAGACTA 59.655 45.833 0.00 0.00 39.55 2.59
573 577 5.510520 GGCTAGGATTGTGGATCAAGACTAG 60.511 48.000 0.00 12.56 42.52 2.57
574 578 5.510520 GCTAGGATTGTGGATCAAGACTAGG 60.511 48.000 15.79 5.70 41.40 3.02
575 579 3.135530 AGGATTGTGGATCAAGACTAGGC 59.864 47.826 0.00 0.00 39.55 3.93
576 580 3.135530 GGATTGTGGATCAAGACTAGGCT 59.864 47.826 0.00 0.00 39.55 4.58
577 581 3.616956 TTGTGGATCAAGACTAGGCTG 57.383 47.619 0.00 0.00 0.00 4.85
578 582 2.820178 TGTGGATCAAGACTAGGCTGA 58.180 47.619 0.00 0.00 0.00 4.26
579 583 3.378512 TGTGGATCAAGACTAGGCTGAT 58.621 45.455 0.00 4.42 0.00 2.90
580 584 4.546674 TGTGGATCAAGACTAGGCTGATA 58.453 43.478 0.00 0.00 0.00 2.15
581 585 4.586421 TGTGGATCAAGACTAGGCTGATAG 59.414 45.833 0.00 0.00 0.00 2.08
582 586 4.830046 GTGGATCAAGACTAGGCTGATAGA 59.170 45.833 0.00 0.00 0.00 1.98
583 587 5.480073 GTGGATCAAGACTAGGCTGATAGAT 59.520 44.000 0.00 0.36 0.00 1.98
584 588 5.479724 TGGATCAAGACTAGGCTGATAGATG 59.520 44.000 0.00 0.00 0.00 2.90
585 589 5.714333 GGATCAAGACTAGGCTGATAGATGA 59.286 44.000 0.00 0.00 0.00 2.92
586 590 6.210385 GGATCAAGACTAGGCTGATAGATGAA 59.790 42.308 0.00 0.00 0.00 2.57
587 591 7.093377 GGATCAAGACTAGGCTGATAGATGAAT 60.093 40.741 0.00 0.00 0.00 2.57
588 592 8.891985 ATCAAGACTAGGCTGATAGATGAATA 57.108 34.615 0.00 0.00 0.00 1.75
589 593 8.347004 TCAAGACTAGGCTGATAGATGAATAG 57.653 38.462 0.00 0.00 0.00 1.73
590 594 8.166726 TCAAGACTAGGCTGATAGATGAATAGA 58.833 37.037 0.00 0.00 0.00 1.98
591 595 8.970020 CAAGACTAGGCTGATAGATGAATAGAT 58.030 37.037 0.00 0.00 0.00 1.98
592 596 8.752005 AGACTAGGCTGATAGATGAATAGATC 57.248 38.462 0.00 0.00 0.00 2.75
593 597 7.498900 AGACTAGGCTGATAGATGAATAGATCG 59.501 40.741 0.00 0.00 0.00 3.69
594 598 5.850557 AGGCTGATAGATGAATAGATCGG 57.149 43.478 0.00 0.00 0.00 4.18
595 599 5.514169 AGGCTGATAGATGAATAGATCGGA 58.486 41.667 0.00 0.00 0.00 4.55
596 600 5.954752 AGGCTGATAGATGAATAGATCGGAA 59.045 40.000 0.00 0.00 0.00 4.30
597 601 6.438741 AGGCTGATAGATGAATAGATCGGAAA 59.561 38.462 0.00 0.00 0.00 3.13
598 602 7.125507 AGGCTGATAGATGAATAGATCGGAAAT 59.874 37.037 0.00 0.00 0.00 2.17
599 603 7.768120 GGCTGATAGATGAATAGATCGGAAATT 59.232 37.037 0.00 0.00 0.00 1.82
600 604 9.160496 GCTGATAGATGAATAGATCGGAAATTT 57.840 33.333 0.00 0.00 0.00 1.82
605 609 8.304202 AGATGAATAGATCGGAAATTTTCTCG 57.696 34.615 8.93 10.38 0.00 4.04
606 610 6.287107 TGAATAGATCGGAAATTTTCTCGC 57.713 37.500 8.93 1.03 0.00 5.03
607 611 5.815222 TGAATAGATCGGAAATTTTCTCGCA 59.185 36.000 8.93 3.16 0.00 5.10
608 612 6.315144 TGAATAGATCGGAAATTTTCTCGCAA 59.685 34.615 8.93 0.00 0.00 4.85
609 613 6.677781 ATAGATCGGAAATTTTCTCGCAAA 57.322 33.333 8.93 0.00 0.00 3.68
610 614 5.371115 AGATCGGAAATTTTCTCGCAAAA 57.629 34.783 8.93 0.00 0.00 2.44
611 615 5.768317 AGATCGGAAATTTTCTCGCAAAAA 58.232 33.333 8.93 0.00 32.99 1.94
727 764 2.294233 TCAACAAATCTGAGCCAGCAAC 59.706 45.455 0.00 0.00 0.00 4.17
806 843 1.669604 TGTAACGCTCAACTTGCCAA 58.330 45.000 0.00 0.00 0.00 4.52
829 866 3.630769 TGTAATCTAGCTATATCCCGCGG 59.369 47.826 21.04 21.04 0.00 6.46
830 867 1.693627 ATCTAGCTATATCCCGCGGG 58.306 55.000 39.13 39.13 0.00 6.13
860 897 8.637986 TCAGGGATAACCATATTTATTTGTTGC 58.362 33.333 0.00 0.00 43.89 4.17
911 949 4.827692 TGTGTATCGTTGTAATCTTGGCT 58.172 39.130 0.00 0.00 0.00 4.75
1255 1293 0.735978 CTACATCTGCCGCGACAACA 60.736 55.000 8.23 0.00 0.00 3.33
1256 1294 0.319986 TACATCTGCCGCGACAACAA 60.320 50.000 8.23 0.00 0.00 2.83
1264 1302 1.433053 CCGCGACAACAACAAGGACA 61.433 55.000 8.23 0.00 0.00 4.02
1409 1453 0.682292 TACGTGACCATGGCAAGTGA 59.318 50.000 25.84 14.08 0.00 3.41
1428 1472 4.235762 ACGCCGTGTGGAAGCTGT 62.236 61.111 0.00 0.00 37.49 4.40
1670 1732 0.318784 GGCTACGCCGAGGTAATGAG 60.319 60.000 0.00 0.00 39.62 2.90
1673 1735 0.742505 TACGCCGAGGTAATGAGTGG 59.257 55.000 0.00 0.00 0.00 4.00
1706 1773 7.325821 GTGCAAATTGATCGTTCAGTTGATTTA 59.674 33.333 18.75 5.86 32.68 1.40
1750 1819 7.928307 TGCAAGTCTTAGCTCATTCTTTAAT 57.072 32.000 0.00 0.00 0.00 1.40
1753 1822 8.239998 GCAAGTCTTAGCTCATTCTTTAATTGT 58.760 33.333 0.00 0.00 0.00 2.71
1756 1825 9.507329 AGTCTTAGCTCATTCTTTAATTGTTGA 57.493 29.630 0.00 0.00 0.00 3.18
1895 1964 2.036475 AGTTGTCACTGCAGTCGAAGAT 59.964 45.455 18.64 0.00 40.67 2.40
1906 1984 3.686128 CAGTCGAAGATAGTTCTCACCG 58.314 50.000 0.00 0.00 40.67 4.94
1913 1991 3.698289 AGATAGTTCTCACCGACTTCCA 58.302 45.455 0.00 0.00 0.00 3.53
2035 3262 5.826208 TCCTCTTAGGAACAGGAAACAAAAC 59.174 40.000 0.00 0.00 42.51 2.43
2054 3281 4.488126 AACACATGAATCCTGTTGAACG 57.512 40.909 0.00 0.00 0.00 3.95
2111 3341 5.698741 TCTATGATGTGTTTGATCCCACT 57.301 39.130 8.25 0.00 32.76 4.00
2137 3367 7.048512 CCTAAATCTTAAAGGGTGTGTCTAGG 58.951 42.308 0.00 0.00 0.00 3.02
2190 3420 9.485206 TCACATCTAAGTATGACATCATCATTG 57.515 33.333 0.00 0.00 46.54 2.82
2196 3426 7.615582 AAGTATGACATCATCATTGTTCGTT 57.384 32.000 0.00 0.00 46.54 3.85
2220 3450 4.620567 GCCCTCTTGTTTGTTTGTTTGTCT 60.621 41.667 0.00 0.00 0.00 3.41
2225 3455 6.551736 TCTTGTTTGTTTGTTTGTCTCTAGC 58.448 36.000 0.00 0.00 0.00 3.42
2231 3461 5.676552 TGTTTGTTTGTCTCTAGCCTGTAA 58.323 37.500 0.00 0.00 0.00 2.41
2265 3495 0.387929 TAATTAGTCGCTCCAGCCCG 59.612 55.000 0.00 0.00 37.91 6.13
2266 3496 1.327690 AATTAGTCGCTCCAGCCCGA 61.328 55.000 0.00 0.00 37.91 5.14
2274 3504 3.672295 CTCCAGCCCGACAGGAAGC 62.672 68.421 0.00 0.00 41.02 3.86
2275 3505 3.710722 CCAGCCCGACAGGAAGCT 61.711 66.667 0.00 0.00 41.02 3.74
2289 3526 1.273606 GGAAGCTATCCTGCTATCGCA 59.726 52.381 7.46 0.00 45.56 5.10
2329 3566 1.491668 TAAGCATTCCGTGGCTCCTA 58.508 50.000 0.00 0.00 40.01 2.94
2451 4371 3.128764 GTGCCTTCCAATTAGCAGGTTAC 59.871 47.826 0.00 0.00 35.56 2.50
2466 4386 4.391358 CAGGTTACGATTAAACAACGCAG 58.609 43.478 0.00 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.189521 CCTTTCGGGCCATAGCGT 59.810 61.111 4.39 0.00 41.24 5.07
55 56 4.796231 GCACGGATCCACGTCGCT 62.796 66.667 13.41 0.00 46.75 4.93
75 76 4.796231 CCGTGGTTCTCCTCGCGG 62.796 72.222 6.13 0.00 45.64 6.46
77 78 4.452733 CCCCGTGGTTCTCCTCGC 62.453 72.222 3.66 0.00 45.64 5.03
79 80 1.911766 TCACCCCGTGGTTCTCCTC 60.912 63.158 0.00 0.00 44.75 3.71
80 81 2.203182 TCACCCCGTGGTTCTCCT 59.797 61.111 0.00 0.00 44.75 3.69
97 98 4.955774 GTCGGACCACAACGCCGT 62.956 66.667 0.00 0.00 45.02 5.68
103 104 1.760479 ATTGACCGGTCGGACCACAA 61.760 55.000 28.70 24.33 38.47 3.33
106 107 2.660206 CATTGACCGGTCGGACCA 59.340 61.111 28.70 9.61 38.47 4.02
107 108 2.818274 GCATTGACCGGTCGGACC 60.818 66.667 28.70 17.38 38.96 4.46
115 116 2.159707 CGAGTTACCTTTGCATTGACCG 60.160 50.000 0.00 0.00 0.00 4.79
139 140 1.303309 CAACCCTCCATTGATCGAGC 58.697 55.000 0.00 0.00 0.00 5.03
147 148 4.102524 TCGAGTATAATGCAACCCTCCATT 59.897 41.667 0.00 0.00 35.90 3.16
148 149 3.646162 TCGAGTATAATGCAACCCTCCAT 59.354 43.478 0.00 0.00 0.00 3.41
156 157 3.069586 CCCTGTCCTCGAGTATAATGCAA 59.930 47.826 12.31 0.00 0.00 4.08
160 161 2.958818 TGCCCTGTCCTCGAGTATAAT 58.041 47.619 12.31 0.00 0.00 1.28
170 171 2.743718 CTGTCGTTGCCCTGTCCT 59.256 61.111 0.00 0.00 0.00 3.85
191 192 1.285641 CCCGTCCATTGTTGTGCAC 59.714 57.895 10.75 10.75 0.00 4.57
192 193 2.560119 GCCCGTCCATTGTTGTGCA 61.560 57.895 0.00 0.00 0.00 4.57
216 217 3.751401 ATCATGGTCGTCGTCCGCG 62.751 63.158 0.00 0.00 39.92 6.46
227 228 4.820744 GTGGCGGCCCATCATGGT 62.821 66.667 17.97 0.00 44.51 3.55
230 231 4.856801 GACGTGGCGGCCCATCAT 62.857 66.667 17.97 0.00 44.51 2.45
260 261 0.677098 CAGGACTCTTCTCCGACCGA 60.677 60.000 0.00 0.00 35.20 4.69
287 288 1.677637 CCTCTACTCCAACTCCGGCC 61.678 65.000 0.00 0.00 0.00 6.13
332 333 4.978083 TCTAAGATCGGTTTTCGTAGCT 57.022 40.909 0.00 0.00 40.32 3.32
358 359 8.549338 TTAATCGGTGTTTCTTTTTGGTTTTT 57.451 26.923 0.00 0.00 0.00 1.94
359 360 8.035984 TCTTAATCGGTGTTTCTTTTTGGTTTT 58.964 29.630 0.00 0.00 0.00 2.43
360 361 7.490079 GTCTTAATCGGTGTTTCTTTTTGGTTT 59.510 33.333 0.00 0.00 0.00 3.27
361 362 6.976349 GTCTTAATCGGTGTTTCTTTTTGGTT 59.024 34.615 0.00 0.00 0.00 3.67
362 363 6.500910 GTCTTAATCGGTGTTTCTTTTTGGT 58.499 36.000 0.00 0.00 0.00 3.67
363 364 5.623673 CGTCTTAATCGGTGTTTCTTTTTGG 59.376 40.000 0.00 0.00 0.00 3.28
364 365 6.356190 GTCGTCTTAATCGGTGTTTCTTTTTG 59.644 38.462 1.49 0.00 0.00 2.44
369 370 4.235360 CAGTCGTCTTAATCGGTGTTTCT 58.765 43.478 1.49 0.00 0.00 2.52
370 371 3.367025 CCAGTCGTCTTAATCGGTGTTTC 59.633 47.826 1.49 0.00 0.00 2.78
374 375 1.278238 GCCAGTCGTCTTAATCGGTG 58.722 55.000 1.49 0.79 0.00 4.94
376 377 0.174845 TGGCCAGTCGTCTTAATCGG 59.825 55.000 0.00 0.00 0.00 4.18
377 378 1.278238 GTGGCCAGTCGTCTTAATCG 58.722 55.000 5.11 0.00 0.00 3.34
390 391 1.073125 TGGATTTTTCTCTCGTGGCCA 59.927 47.619 0.00 0.00 0.00 5.36
391 392 1.740025 CTGGATTTTTCTCTCGTGGCC 59.260 52.381 0.00 0.00 0.00 5.36
392 393 2.699954 TCTGGATTTTTCTCTCGTGGC 58.300 47.619 0.00 0.00 0.00 5.01
393 394 4.507710 TGATCTGGATTTTTCTCTCGTGG 58.492 43.478 0.00 0.00 0.00 4.94
439 443 1.723870 GGTCATGTTGATCGGCTGC 59.276 57.895 0.00 0.00 0.00 5.25
462 466 2.583472 CCCGTACCTAGGGTTCGTT 58.417 57.895 14.81 0.00 43.23 3.85
569 573 6.545666 CCGATCTATTCATCTATCAGCCTAGT 59.454 42.308 0.00 0.00 0.00 2.57
570 574 6.770303 TCCGATCTATTCATCTATCAGCCTAG 59.230 42.308 0.00 0.00 0.00 3.02
571 575 6.663734 TCCGATCTATTCATCTATCAGCCTA 58.336 40.000 0.00 0.00 0.00 3.93
572 576 5.514169 TCCGATCTATTCATCTATCAGCCT 58.486 41.667 0.00 0.00 0.00 4.58
573 577 5.843673 TCCGATCTATTCATCTATCAGCC 57.156 43.478 0.00 0.00 0.00 4.85
574 578 8.715191 AATTTCCGATCTATTCATCTATCAGC 57.285 34.615 0.00 0.00 0.00 4.26
579 583 9.411801 CGAGAAAATTTCCGATCTATTCATCTA 57.588 33.333 1.57 0.00 0.00 1.98
580 584 7.095439 GCGAGAAAATTTCCGATCTATTCATCT 60.095 37.037 16.61 0.00 0.00 2.90
581 585 7.012358 GCGAGAAAATTTCCGATCTATTCATC 58.988 38.462 16.61 0.00 0.00 2.92
582 586 6.483307 TGCGAGAAAATTTCCGATCTATTCAT 59.517 34.615 16.61 0.00 0.00 2.57
583 587 5.815222 TGCGAGAAAATTTCCGATCTATTCA 59.185 36.000 16.61 4.66 0.00 2.57
584 588 6.287107 TGCGAGAAAATTTCCGATCTATTC 57.713 37.500 16.61 0.58 0.00 1.75
585 589 6.677781 TTGCGAGAAAATTTCCGATCTATT 57.322 33.333 16.61 0.00 0.00 1.73
586 590 6.677781 TTTGCGAGAAAATTTCCGATCTAT 57.322 33.333 16.61 0.00 0.00 1.98
587 591 6.489127 TTTTGCGAGAAAATTTCCGATCTA 57.511 33.333 16.61 2.12 0.00 1.98
588 592 5.371115 TTTTGCGAGAAAATTTCCGATCT 57.629 34.783 16.61 1.56 0.00 2.75
608 612 5.882557 CACATGGTATCAGCCTAGTCTTTTT 59.117 40.000 0.00 0.00 0.00 1.94
609 613 5.189736 TCACATGGTATCAGCCTAGTCTTTT 59.810 40.000 0.00 0.00 0.00 2.27
610 614 4.716784 TCACATGGTATCAGCCTAGTCTTT 59.283 41.667 0.00 0.00 0.00 2.52
611 615 4.290093 TCACATGGTATCAGCCTAGTCTT 58.710 43.478 0.00 0.00 0.00 3.01
612 616 3.916035 TCACATGGTATCAGCCTAGTCT 58.084 45.455 0.00 0.00 0.00 3.24
613 617 4.672587 TTCACATGGTATCAGCCTAGTC 57.327 45.455 0.00 0.00 0.00 2.59
727 764 1.931841 CTCTGTTGAGATGTGCCGATG 59.068 52.381 0.00 0.00 42.73 3.84
806 843 4.278669 CCGCGGGATATAGCTAGATTACAT 59.721 45.833 20.10 0.00 0.00 2.29
1255 1293 0.109342 CTGAGCAGGGTGTCCTTGTT 59.891 55.000 0.32 0.00 42.67 2.83
1256 1294 1.757306 CTGAGCAGGGTGTCCTTGT 59.243 57.895 0.32 0.00 42.67 3.16
1301 1339 0.676151 CTCTGGAAGCTGGAGCAACC 60.676 60.000 0.65 4.50 45.16 3.77
1303 1341 1.681666 CCTCTGGAAGCTGGAGCAA 59.318 57.895 0.65 0.00 45.16 3.91
1409 1453 3.616721 AGCTTCCACACGGCGTCT 61.617 61.111 10.85 0.00 0.00 4.18
1428 1472 2.434185 GTCGTCATCCTTGCGCCA 60.434 61.111 4.18 0.00 0.00 5.69
1670 1732 3.641437 TCAATTTGCACAAGTAGCCAC 57.359 42.857 0.00 0.00 0.00 5.01
1673 1735 4.083581 ACGATCAATTTGCACAAGTAGC 57.916 40.909 0.00 0.00 0.00 3.58
1706 1773 5.332743 TGCAGTCCTAATGAAAGGGAAAAT 58.667 37.500 0.00 0.00 37.24 1.82
1750 1819 8.049721 ACCCTACCAAAAATGAAAAATCAACAA 58.950 29.630 0.00 0.00 0.00 2.83
1753 1822 8.897752 CAAACCCTACCAAAAATGAAAAATCAA 58.102 29.630 0.00 0.00 0.00 2.57
1754 1823 7.500559 CCAAACCCTACCAAAAATGAAAAATCA 59.499 33.333 0.00 0.00 0.00 2.57
1755 1824 7.717436 TCCAAACCCTACCAAAAATGAAAAATC 59.283 33.333 0.00 0.00 0.00 2.17
1756 1825 7.578203 TCCAAACCCTACCAAAAATGAAAAAT 58.422 30.769 0.00 0.00 0.00 1.82
1757 1826 6.958767 TCCAAACCCTACCAAAAATGAAAAA 58.041 32.000 0.00 0.00 0.00 1.94
1758 1827 6.384305 TCTCCAAACCCTACCAAAAATGAAAA 59.616 34.615 0.00 0.00 0.00 2.29
1759 1828 5.900123 TCTCCAAACCCTACCAAAAATGAAA 59.100 36.000 0.00 0.00 0.00 2.69
1762 1831 5.723295 CATCTCCAAACCCTACCAAAAATG 58.277 41.667 0.00 0.00 0.00 2.32
1865 1934 6.363626 CGACTGCAGTGACAACTATAATATCC 59.636 42.308 27.27 1.86 33.79 2.59
1895 1964 2.496070 CCATGGAAGTCGGTGAGAACTA 59.504 50.000 5.56 0.00 0.00 2.24
1906 1984 1.740025 CCGCTTCTTTCCATGGAAGTC 59.260 52.381 25.69 13.46 40.49 3.01
1913 1991 0.681243 GGCCTTCCGCTTCTTTCCAT 60.681 55.000 0.00 0.00 37.74 3.41
2012 3239 5.592688 TGTTTTGTTTCCTGTTCCTAAGAGG 59.407 40.000 0.00 0.00 43.06 3.69
2035 3262 4.466828 GTTCGTTCAACAGGATTCATGTG 58.533 43.478 4.51 0.27 34.76 3.21
2054 3281 0.584876 CCACCTCCACGAAAACGTTC 59.415 55.000 0.00 0.00 0.00 3.95
2069 3296 3.641436 AGAATGTTCCCTCAAAAACCACC 59.359 43.478 0.00 0.00 0.00 4.61
2070 3297 4.937201 AGAATGTTCCCTCAAAAACCAC 57.063 40.909 0.00 0.00 0.00 4.16
2111 3341 6.697641 AGACACACCCTTTAAGATTTAGGA 57.302 37.500 0.00 0.00 0.00 2.94
2137 3367 6.095432 AGTTATGTCACATCTAGATGAGGC 57.905 41.667 34.16 28.43 41.20 4.70
2186 3416 1.608590 ACAAGAGGGCAACGAACAATG 59.391 47.619 0.00 0.00 37.60 2.82
2190 3420 1.404035 ACAAACAAGAGGGCAACGAAC 59.596 47.619 0.00 0.00 37.60 3.95
2193 3423 2.192624 CAAACAAACAAGAGGGCAACG 58.807 47.619 0.00 0.00 37.60 4.10
2196 3426 3.007398 ACAAACAAACAAACAAGAGGGCA 59.993 39.130 0.00 0.00 0.00 5.36
2239 3469 4.153475 GCTGGAGCGACTAATTAACACAAA 59.847 41.667 0.00 0.00 0.00 2.83
2247 3477 1.144057 CGGGCTGGAGCGACTAATT 59.856 57.895 0.00 0.00 43.26 1.40
2289 3526 1.610522 AGTAGTTTGTACGCACGTCCT 59.389 47.619 0.00 0.00 0.00 3.85
2451 4371 3.806316 AGTTCCTGCGTTGTTTAATCG 57.194 42.857 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.