Multiple sequence alignment - TraesCS3D01G418700

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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 TraesCS3D01G418700 chr3D 100.000 4484 0 0 1 4484 531353651 531358134 0.000000e+00 8281.0
1 TraesCS3D01G418700 chr3D 85.314 1498 137 42 3003 4484 531374205 531372775 0.000000e+00 1471.0
2 TraesCS3D01G418700 chr3D 84.793 1473 139 51 3037 4484 426408098 426409510 0.000000e+00 1400.0
3 TraesCS3D01G418700 chr3D 81.897 917 123 23 2110 2998 531375140 531374239 0.000000e+00 734.0
4 TraesCS3D01G418700 chr3D 82.444 581 66 16 1560 2115 531375446 531374877 4.060000e-130 475.0
5 TraesCS3D01G418700 chr3D 86.640 247 29 2 2755 2998 426407792 426408037 2.060000e-68 270.0
6 TraesCS3D01G418700 chr3D 86.283 226 30 1 1217 1441 531375829 531375604 1.250000e-60 244.0
7 TraesCS3D01G418700 chr3D 84.722 144 21 1 591 734 531376674 531376532 4.680000e-30 143.0
8 TraesCS3D01G418700 chr3D 84.397 141 9 4 974 1111 531376090 531375960 4.710000e-25 126.0
9 TraesCS3D01G418700 chr3D 91.549 71 5 1 1487 1557 400337743 400337674 3.690000e-16 97.1
10 TraesCS3D01G418700 chr3D 84.615 65 7 3 1486 1549 565181892 565181830 1.350000e-05 62.1
11 TraesCS3D01G418700 chr2D 97.308 2117 26 7 2376 4481 46685597 46687693 0.000000e+00 3565.0
12 TraesCS3D01G418700 chr2D 92.408 1462 77 17 1 1449 46683222 46684662 0.000000e+00 2054.0
13 TraesCS3D01G418700 chr2D 96.806 908 13 4 1447 2339 46684707 46685613 0.000000e+00 1502.0
14 TraesCS3D01G418700 chr2D 85.714 511 24 20 517 1003 13215780 13216265 1.120000e-135 494.0
15 TraesCS3D01G418700 chr2D 90.278 72 6 1 1486 1557 86087063 86086993 4.780000e-15 93.5
16 TraesCS3D01G418700 chr2D 91.176 68 3 1 1026 1093 13216261 13216325 6.180000e-14 89.8
17 TraesCS3D01G418700 chr3B 83.636 2090 229 48 2459 4484 702699507 702697467 0.000000e+00 1860.0
18 TraesCS3D01G418700 chr3B 86.409 1501 150 29 3004 4484 702848508 702847042 0.000000e+00 1592.0
19 TraesCS3D01G418700 chr3B 85.967 848 92 17 3651 4484 702830843 702830009 0.000000e+00 881.0
20 TraesCS3D01G418700 chr3B 85.450 756 84 12 2251 2998 702834520 702833783 0.000000e+00 763.0
21 TraesCS3D01G418700 chr3B 82.578 574 53 27 1562 2115 702849785 702849239 3.160000e-126 462.0
22 TraesCS3D01G418700 chr3B 82.847 548 60 13 883 1424 702701185 702700666 1.140000e-125 460.0
23 TraesCS3D01G418700 chr3B 85.330 409 47 5 2602 2998 702848951 702848544 1.160000e-110 411.0
24 TraesCS3D01G418700 chr3B 80.268 598 66 20 1560 2115 702700262 702699675 1.940000e-108 403.0
25 TraesCS3D01G418700 chr3B 86.010 386 35 6 3213 3595 702831215 702830846 3.250000e-106 396.0
26 TraesCS3D01G418700 chr3B 89.498 219 16 3 3003 3217 702833750 702833535 2.060000e-68 270.0
27 TraesCS3D01G418700 chr3B 93.220 177 12 0 1678 1854 702834824 702834648 1.240000e-65 261.0
28 TraesCS3D01G418700 chr3B 78.827 307 44 11 2110 2396 702699940 702699635 2.130000e-43 187.0
29 TraesCS3D01G418700 chr3B 79.012 243 28 9 899 1131 702836181 702835952 1.300000e-30 145.0
30 TraesCS3D01G418700 chr3A 87.941 1161 96 19 3003 4155 665985055 665983931 0.000000e+00 1328.0
31 TraesCS3D01G418700 chr3A 82.100 581 68 16 1560 2115 665986295 665985726 8.790000e-127 464.0
32 TraesCS3D01G418700 chr3A 87.580 314 23 9 4183 4484 665983933 665983624 2.570000e-92 350.0
33 TraesCS3D01G418700 chr3A 87.981 208 25 0 1217 1424 665986916 665986709 3.460000e-61 246.0
34 TraesCS3D01G418700 chr3A 83.902 205 29 3 591 794 665987926 665987725 4.580000e-45 193.0
35 TraesCS3D01G418700 chr4B 89.005 573 62 1 3637 4208 622125218 622124646 0.000000e+00 708.0
36 TraesCS3D01G418700 chr2A 91.463 82 6 1 1476 1557 86446965 86446885 1.320000e-20 111.0
37 TraesCS3D01G418700 chr2B 93.056 72 4 1 1486 1557 139078981 139078911 2.210000e-18 104.0
38 TraesCS3D01G418700 chr1D 82.474 97 11 6 1482 1577 233793788 233793697 3.720000e-11 80.5
39 TraesCS3D01G418700 chr6B 92.500 40 3 0 1470 1509 191534723 191534684 1.740000e-04 58.4
40 TraesCS3D01G418700 chr6A 92.500 40 3 0 1470 1509 127186205 127186166 1.740000e-04 58.4


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 TraesCS3D01G418700 chr3D 531353651 531358134 4483 False 8281.000000 8281 100.000000 1 4484 1 chr3D.!!$F1 4483
1 TraesCS3D01G418700 chr3D 426407792 426409510 1718 False 835.000000 1400 85.716500 2755 4484 2 chr3D.!!$F2 1729
2 TraesCS3D01G418700 chr3D 531372775 531376674 3899 True 532.166667 1471 84.176167 591 4484 6 chr3D.!!$R3 3893
3 TraesCS3D01G418700 chr2D 46683222 46687693 4471 False 2373.666667 3565 95.507333 1 4481 3 chr2D.!!$F2 4480
4 TraesCS3D01G418700 chr2D 13215780 13216325 545 False 291.900000 494 88.445000 517 1093 2 chr2D.!!$F1 576
5 TraesCS3D01G418700 chr3B 702847042 702849785 2743 True 821.666667 1592 84.772333 1562 4484 3 chr3B.!!$R3 2922
6 TraesCS3D01G418700 chr3B 702697467 702701185 3718 True 727.500000 1860 81.394500 883 4484 4 chr3B.!!$R1 3601
7 TraesCS3D01G418700 chr3B 702830009 702836181 6172 True 452.666667 881 86.526167 899 4484 6 chr3B.!!$R2 3585
8 TraesCS3D01G418700 chr3A 665983624 665987926 4302 True 516.200000 1328 85.900800 591 4484 5 chr3A.!!$R1 3893
9 TraesCS3D01G418700 chr4B 622124646 622125218 572 True 708.000000 708 89.005000 3637 4208 1 chr4B.!!$R1 571

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
149 150 0.041535 TCGCTCCAGGTTTAGGGGTA 59.958 55.000 0.00 0.0 0.00 3.69 F
1224 1936 0.462047 GTATACAAGCGCAGTGGCCT 60.462 55.000 11.47 0.0 36.38 5.19 F
2175 3524 1.002134 GCAAGCTGCAGTTCCCCTA 60.002 57.895 16.64 0.0 44.26 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 2078 0.176680 CTGGCGTTGTAGGAGCAGAT 59.823 55.000 0.0 0.0 0.00 2.90 R
2291 3640 0.317020 GGCGTGACTGAGCAACAAAC 60.317 55.000 0.0 0.0 34.54 2.93 R
3641 7494 3.153919 TGAAAGCGGCCTCTAAAATGTT 58.846 40.909 0.0 0.0 0.00 2.71 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
34 35 1.009829 GCCGATGCCAGTGTTTCTAG 58.990 55.000 0.00 0.00 0.00 2.43
47 48 7.094377 GCCAGTGTTTCTAGATGGTGATTTTTA 60.094 37.037 10.33 0.00 33.42 1.52
81 82 8.190326 TCCTACTTTTGTTCTGATGTAGAAGA 57.810 34.615 0.00 0.00 45.71 2.87
124 125 2.857186 TTCTGCTGTCATACAGGCAA 57.143 45.000 8.99 0.00 46.01 4.52
131 132 3.499918 GCTGTCATACAGGCAATACCATC 59.500 47.826 8.99 0.00 46.01 3.51
147 148 0.179045 CATCGCTCCAGGTTTAGGGG 60.179 60.000 0.00 0.00 0.00 4.79
148 149 0.620700 ATCGCTCCAGGTTTAGGGGT 60.621 55.000 0.00 0.00 0.00 4.95
149 150 0.041535 TCGCTCCAGGTTTAGGGGTA 59.958 55.000 0.00 0.00 0.00 3.69
150 151 0.464452 CGCTCCAGGTTTAGGGGTAG 59.536 60.000 0.00 0.00 0.00 3.18
151 152 1.875488 GCTCCAGGTTTAGGGGTAGA 58.125 55.000 0.00 0.00 0.00 2.59
152 153 2.193993 GCTCCAGGTTTAGGGGTAGAA 58.806 52.381 0.00 0.00 0.00 2.10
153 154 2.574824 GCTCCAGGTTTAGGGGTAGAAA 59.425 50.000 0.00 0.00 0.00 2.52
154 155 3.202373 GCTCCAGGTTTAGGGGTAGAAAT 59.798 47.826 0.00 0.00 0.00 2.17
302 308 3.814945 CCACTTTCTGACGATTCTTTGC 58.185 45.455 0.00 0.00 0.00 3.68
343 349 6.444633 TCAATCCCTCGTTTCGTAGATATTC 58.555 40.000 0.00 0.00 35.04 1.75
385 391 9.747898 CCCTCTGTAGACTAATATAAGATCAGT 57.252 37.037 0.00 0.00 0.00 3.41
428 434 4.511527 CTGACTTGTACCTGCTGATGATT 58.488 43.478 0.00 0.00 0.00 2.57
455 461 2.978156 ACTGGGCTTTCAGGAATCAA 57.022 45.000 7.06 0.00 38.98 2.57
529 535 4.259356 TGACATCTCTGCAATTTCAGGAG 58.741 43.478 5.23 2.48 34.91 3.69
641 647 4.408821 TGACATGCGCCTCACCCC 62.409 66.667 4.18 0.00 0.00 4.95
661 671 2.603473 AGCTACGGTGGGTCTGCA 60.603 61.111 0.00 0.00 32.68 4.41
740 759 2.280119 TGCTGGTCTGTGCGTCAC 60.280 61.111 3.44 3.44 34.56 3.67
781 806 3.646162 TGAGTTTCTTCTACTTCCAGCCA 59.354 43.478 0.00 0.00 0.00 4.75
782 807 4.287067 TGAGTTTCTTCTACTTCCAGCCAT 59.713 41.667 0.00 0.00 0.00 4.40
783 808 4.583871 AGTTTCTTCTACTTCCAGCCATG 58.416 43.478 0.00 0.00 0.00 3.66
784 809 4.042187 AGTTTCTTCTACTTCCAGCCATGT 59.958 41.667 0.00 0.00 0.00 3.21
785 810 3.616956 TCTTCTACTTCCAGCCATGTG 57.383 47.619 0.00 0.00 0.00 3.21
786 811 2.012673 CTTCTACTTCCAGCCATGTGC 58.987 52.381 0.00 0.00 41.71 4.57
813 949 4.481368 ACAGGCGTAATTATGTGGAGAA 57.519 40.909 6.55 0.00 0.00 2.87
972 1403 3.519107 TCACCATTAATCTCAGTCAGGCA 59.481 43.478 0.00 0.00 0.00 4.75
979 1410 0.894141 TCTCAGTCAGGCAAGAGAGC 59.106 55.000 0.00 0.00 32.57 4.09
980 1411 0.896923 CTCAGTCAGGCAAGAGAGCT 59.103 55.000 0.00 0.00 34.17 4.09
1064 1553 4.694233 CCTCGTGCTGGTGCTGCT 62.694 66.667 0.00 0.00 40.48 4.24
1065 1554 3.420606 CTCGTGCTGGTGCTGCTG 61.421 66.667 0.00 0.00 40.48 4.41
1152 1841 3.684788 ACACGCAGAGTATTTCATTCCAC 59.315 43.478 0.00 0.00 0.00 4.02
1185 1874 3.315470 CACCCTCGAATCGACTTCAGATA 59.685 47.826 0.00 0.00 33.10 1.98
1224 1936 0.462047 GTATACAAGCGCAGTGGCCT 60.462 55.000 11.47 0.00 36.38 5.19
1282 1994 3.649096 CACGGCGTGGAACATCAA 58.351 55.556 31.19 0.00 44.52 2.57
1334 2049 5.920840 CGACAACACCGACATAGATAATGAT 59.079 40.000 0.00 0.00 39.07 2.45
1362 2078 3.084536 TCAATCCTGCCATTAAGTGCA 57.915 42.857 2.17 2.17 35.86 4.57
1420 2136 3.052181 GGCTGTAAGTCGCTCCTTC 57.948 57.895 0.00 0.00 35.30 3.46
1437 2163 2.027561 CCTTCCGACACCAACTCCATTA 60.028 50.000 0.00 0.00 0.00 1.90
1445 2171 2.879103 CCAACTCCATTAGTGGGTGT 57.121 50.000 4.18 1.54 43.67 4.16
1453 2226 7.446106 ACTCCATTAGTGGGTGTATGATAAA 57.554 36.000 4.18 0.00 46.06 1.40
1455 2228 6.597562 TCCATTAGTGGGTGTATGATAAACC 58.402 40.000 3.04 3.04 46.06 3.27
1702 3028 6.552445 AGTTGCATGTTCTTATCCTAGTCT 57.448 37.500 0.00 0.00 0.00 3.24
2041 3389 8.744011 GTTAGAATAGTGCAAACAGAGTATACG 58.256 37.037 0.00 0.00 0.00 3.06
2175 3524 1.002134 GCAAGCTGCAGTTCCCCTA 60.002 57.895 16.64 0.00 44.26 3.53
2176 3525 1.028868 GCAAGCTGCAGTTCCCCTAG 61.029 60.000 16.64 0.00 44.26 3.02
2180 3529 1.834263 AGCTGCAGTTCCCCTAGTTAG 59.166 52.381 16.64 0.00 0.00 2.34
2218 3567 2.192443 CGGGCGAGAGAGGGACTA 59.808 66.667 0.00 0.00 41.55 2.59
2220 3569 2.188161 GGGCGAGAGAGGGACTACG 61.188 68.421 0.00 0.00 41.55 3.51
2335 3684 8.961294 CTCTTTCAGGAGATGTCATTTCTATT 57.039 34.615 3.57 0.00 35.52 1.73
2336 3685 8.728337 TCTTTCAGGAGATGTCATTTCTATTG 57.272 34.615 3.57 1.52 0.00 1.90
2337 3686 8.542926 TCTTTCAGGAGATGTCATTTCTATTGA 58.457 33.333 3.57 3.48 0.00 2.57
2338 3687 9.339850 CTTTCAGGAGATGTCATTTCTATTGAT 57.660 33.333 3.57 0.00 0.00 2.57
2339 3688 8.672823 TTCAGGAGATGTCATTTCTATTGATG 57.327 34.615 3.57 0.00 0.00 3.07
2340 3689 7.799081 TCAGGAGATGTCATTTCTATTGATGT 58.201 34.615 3.57 0.00 0.00 3.06
2341 3690 7.713942 TCAGGAGATGTCATTTCTATTGATGTG 59.286 37.037 3.57 0.00 0.00 3.21
2342 3691 6.485984 AGGAGATGTCATTTCTATTGATGTGC 59.514 38.462 3.57 0.00 0.00 4.57
2343 3692 6.485984 GGAGATGTCATTTCTATTGATGTGCT 59.514 38.462 3.57 0.00 0.00 4.40
2344 3693 7.013083 GGAGATGTCATTTCTATTGATGTGCTT 59.987 37.037 3.57 0.00 0.00 3.91
2345 3694 7.704271 AGATGTCATTTCTATTGATGTGCTTG 58.296 34.615 0.00 0.00 0.00 4.01
2346 3695 6.198650 TGTCATTTCTATTGATGTGCTTGG 57.801 37.500 0.00 0.00 0.00 3.61
2347 3696 5.711506 TGTCATTTCTATTGATGTGCTTGGT 59.288 36.000 0.00 0.00 0.00 3.67
2431 3780 8.329203 AGCTAGAAAAATGGAGTTTAACTCAG 57.671 34.615 24.09 11.85 46.79 3.35
2510 3931 6.720112 TGGTAGTGTTGTAGTTCTAGTTGT 57.280 37.500 0.00 0.00 0.00 3.32
2683 4146 4.696455 ACCAACATTTCTTGAAAAGCTGG 58.304 39.130 15.03 15.03 45.70 4.85
3302 7139 6.615726 AGCTACCATCTACCTTTTCCAATCTA 59.384 38.462 0.00 0.00 0.00 1.98
3303 7140 7.127339 AGCTACCATCTACCTTTTCCAATCTAA 59.873 37.037 0.00 0.00 0.00 2.10
3304 7141 7.773690 GCTACCATCTACCTTTTCCAATCTAAA 59.226 37.037 0.00 0.00 0.00 1.85
3305 7142 9.681062 CTACCATCTACCTTTTCCAATCTAAAA 57.319 33.333 0.00 0.00 0.00 1.52
3306 7143 8.950007 ACCATCTACCTTTTCCAATCTAAAAA 57.050 30.769 0.00 0.00 0.00 1.94
3426 7263 5.158141 TGTTCTTATCTATCCAGATGGGCT 58.842 41.667 0.00 0.00 41.75 5.19
3641 7494 3.125607 CGGCTGTCGGGCTGTATA 58.874 61.111 3.42 0.00 38.46 1.47
3653 7506 5.465724 GTCGGGCTGTATAACATTTTAGAGG 59.534 44.000 0.00 0.00 0.00 3.69
4055 7911 8.942033 GGGGTAATCCTAAACCTCTTTATTCTA 58.058 37.037 0.00 0.00 33.12 2.10
4283 8199 6.206829 GGGACTTGAGTTTTAACAGCATAACT 59.793 38.462 0.00 0.00 33.78 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.009829 CTAGAAACACTGGCATCGGC 58.990 55.000 0.00 0.00 40.13 5.54
17 18 2.868583 CCATCTAGAAACACTGGCATCG 59.131 50.000 0.00 0.00 0.00 3.84
19 20 3.264193 TCACCATCTAGAAACACTGGCAT 59.736 43.478 8.90 0.00 0.00 4.40
34 35 7.378181 AGGAAACACACATAAAAATCACCATC 58.622 34.615 0.00 0.00 0.00 3.51
47 48 6.601613 TCAGAACAAAAGTAGGAAACACACAT 59.398 34.615 0.00 0.00 0.00 3.21
124 125 2.368875 CCTAAACCTGGAGCGATGGTAT 59.631 50.000 0.00 0.00 33.17 2.73
131 132 0.464452 CTACCCCTAAACCTGGAGCG 59.536 60.000 0.00 0.00 0.00 5.03
181 182 0.179000 ACATTTAGCGGCTCCCTGAG 59.821 55.000 5.39 0.00 0.00 3.35
302 308 6.433404 AGGGATTGAATATGATGCTAAGCAAG 59.567 38.462 0.00 0.00 43.62 4.01
323 329 5.826737 AGAAGAATATCTACGAAACGAGGGA 59.173 40.000 0.00 0.00 0.00 4.20
325 331 7.916450 AGAAAGAAGAATATCTACGAAACGAGG 59.084 37.037 0.00 0.00 0.00 4.63
343 349 9.191479 TCTACAGAGGGAGTAATTAGAAAGAAG 57.809 37.037 0.00 0.00 0.00 2.85
428 434 0.110295 TGAAAGCCCAGTAGCTGCAA 59.890 50.000 4.12 0.00 44.11 4.08
455 461 0.815734 GCAATTGCAGAGATGCCACT 59.184 50.000 25.36 0.00 41.59 4.00
474 480 0.459237 CACCTTGACTCCTAGCGCAG 60.459 60.000 11.47 4.88 0.00 5.18
529 535 0.602638 TTGCACGGATGTCACCTGAC 60.603 55.000 0.00 0.00 44.97 3.51
542 548 3.837213 ACTGATTCCTGAAATTGCACG 57.163 42.857 0.00 0.00 0.00 5.34
701 715 3.136443 ACAAATCCAGTGAGAAGGTGTCA 59.864 43.478 0.00 0.00 0.00 3.58
740 759 7.621428 AACTCAGATAAAATCATCACACTGG 57.379 36.000 0.00 0.00 0.00 4.00
781 806 4.873746 ATTACGCCTGTATAGAGCACAT 57.126 40.909 0.00 0.00 0.00 3.21
782 807 4.665833 AATTACGCCTGTATAGAGCACA 57.334 40.909 0.00 0.00 0.00 4.57
783 808 6.089551 CACATAATTACGCCTGTATAGAGCAC 59.910 42.308 0.00 0.00 0.00 4.40
784 809 6.156519 CACATAATTACGCCTGTATAGAGCA 58.843 40.000 0.00 0.00 0.00 4.26
785 810 5.577164 CCACATAATTACGCCTGTATAGAGC 59.423 44.000 0.00 0.00 0.00 4.09
786 811 6.920817 TCCACATAATTACGCCTGTATAGAG 58.079 40.000 0.00 0.00 0.00 2.43
787 812 6.717997 TCTCCACATAATTACGCCTGTATAGA 59.282 38.462 0.00 0.00 0.00 1.98
788 813 6.920817 TCTCCACATAATTACGCCTGTATAG 58.079 40.000 0.00 0.00 0.00 1.31
789 814 6.904463 TCTCCACATAATTACGCCTGTATA 57.096 37.500 0.00 0.00 0.00 1.47
813 949 6.095432 TGGCACTTGCAGTTTTTGTATAAT 57.905 33.333 3.15 0.00 44.36 1.28
972 1403 4.908790 GCTTCGCTCAGCTCTCTT 57.091 55.556 0.00 0.00 36.79 2.85
979 1410 1.276415 GTGCTTCTAGCTTCGCTCAG 58.724 55.000 0.00 0.00 42.97 3.35
980 1411 0.456824 CGTGCTTCTAGCTTCGCTCA 60.457 55.000 0.00 0.00 42.97 4.26
996 1482 4.794439 TGCCGTCGCCTCATCGTG 62.794 66.667 0.00 0.00 0.00 4.35
1152 1841 3.955650 TTCGAGGGTGTTAAAGAGGAG 57.044 47.619 0.00 0.00 0.00 3.69
1334 2049 6.608405 ACTTAATGGCAGGATTGAATTCATGA 59.392 34.615 9.40 0.00 29.04 3.07
1349 2064 2.019249 GAGCAGATGCACTTAATGGCA 58.981 47.619 7.68 3.96 45.16 4.92
1362 2078 0.176680 CTGGCGTTGTAGGAGCAGAT 59.823 55.000 0.00 0.00 0.00 2.90
1420 2136 2.346803 CACTAATGGAGTTGGTGTCGG 58.653 52.381 0.00 0.00 42.45 4.79
1437 2163 4.713321 AGTACGGTTTATCATACACCCACT 59.287 41.667 0.00 0.00 0.00 4.00
1453 2226 9.820725 TGTACTAAATTGCATATTAAGTACGGT 57.179 29.630 15.88 0.00 34.22 4.83
1702 3028 5.815581 ACAGGGTAACATCTTGAAAGCATA 58.184 37.500 0.00 0.00 39.74 3.14
2041 3389 4.672409 ACTAAGCAACAAAGAAACTGTGC 58.328 39.130 0.00 0.00 0.00 4.57
2175 3524 2.154462 GGCATGCAACAGACACTAACT 58.846 47.619 21.36 0.00 0.00 2.24
2176 3525 1.879380 TGGCATGCAACAGACACTAAC 59.121 47.619 21.36 0.00 0.00 2.34
2180 3529 2.733227 GCTAATGGCATGCAACAGACAC 60.733 50.000 21.36 0.00 41.35 3.67
2218 3567 7.055378 ACAGATAGTCTATGAAAGTCTACCGT 58.945 38.462 0.00 0.00 30.15 4.83
2291 3640 0.317020 GGCGTGACTGAGCAACAAAC 60.317 55.000 0.00 0.00 34.54 2.93
2332 3681 6.446318 GTCTGAAAAACCAAGCACATCAATA 58.554 36.000 0.00 0.00 0.00 1.90
2333 3682 5.291971 GTCTGAAAAACCAAGCACATCAAT 58.708 37.500 0.00 0.00 0.00 2.57
2334 3683 4.681744 GTCTGAAAAACCAAGCACATCAA 58.318 39.130 0.00 0.00 0.00 2.57
2335 3684 3.243035 CGTCTGAAAAACCAAGCACATCA 60.243 43.478 0.00 0.00 0.00 3.07
2336 3685 3.243068 ACGTCTGAAAAACCAAGCACATC 60.243 43.478 0.00 0.00 0.00 3.06
2337 3686 2.687935 ACGTCTGAAAAACCAAGCACAT 59.312 40.909 0.00 0.00 0.00 3.21
2338 3687 2.088423 ACGTCTGAAAAACCAAGCACA 58.912 42.857 0.00 0.00 0.00 4.57
2339 3688 2.540973 GGACGTCTGAAAAACCAAGCAC 60.541 50.000 16.46 0.00 0.00 4.40
2340 3689 1.673920 GGACGTCTGAAAAACCAAGCA 59.326 47.619 16.46 0.00 0.00 3.91
2341 3690 1.947456 AGGACGTCTGAAAAACCAAGC 59.053 47.619 16.46 0.00 0.00 4.01
2342 3691 4.497507 GGAAAGGACGTCTGAAAAACCAAG 60.498 45.833 16.46 0.00 0.00 3.61
2343 3692 3.379057 GGAAAGGACGTCTGAAAAACCAA 59.621 43.478 16.46 0.00 0.00 3.67
2344 3693 2.946990 GGAAAGGACGTCTGAAAAACCA 59.053 45.455 16.46 0.00 0.00 3.67
2345 3694 3.211865 AGGAAAGGACGTCTGAAAAACC 58.788 45.455 16.46 9.92 0.00 3.27
2346 3695 4.895224 AAGGAAAGGACGTCTGAAAAAC 57.105 40.909 16.46 0.00 0.00 2.43
2347 3696 7.576861 AATAAAGGAAAGGACGTCTGAAAAA 57.423 32.000 16.46 0.00 0.00 1.94
2384 3733 8.553459 AGCTATTGGAAAAGTATATCGATTGG 57.447 34.615 1.71 0.00 0.00 3.16
2431 3780 1.562783 AGAAGTAGTGGGAGGCTGAC 58.437 55.000 0.00 0.00 0.00 3.51
2683 4146 4.748892 TCTTACAGATACTGCAACTGAGC 58.251 43.478 13.91 0.00 34.37 4.26
3245 7082 6.420913 AAACCACAGCTATCGATATACCTT 57.579 37.500 5.40 0.00 0.00 3.50
3310 7147 9.504708 CAGGATCATCAGCTTCTTAAGATTATT 57.495 33.333 5.89 0.00 0.00 1.40
3311 7148 8.658619 ACAGGATCATCAGCTTCTTAAGATTAT 58.341 33.333 5.89 0.00 0.00 1.28
3312 7149 7.930325 CACAGGATCATCAGCTTCTTAAGATTA 59.070 37.037 5.89 0.00 0.00 1.75
3313 7150 6.766944 CACAGGATCATCAGCTTCTTAAGATT 59.233 38.462 5.89 0.00 0.00 2.40
3314 7151 6.099413 TCACAGGATCATCAGCTTCTTAAGAT 59.901 38.462 5.89 0.00 0.00 2.40
3315 7152 5.423290 TCACAGGATCATCAGCTTCTTAAGA 59.577 40.000 0.00 0.00 0.00 2.10
3316 7153 5.668471 TCACAGGATCATCAGCTTCTTAAG 58.332 41.667 0.00 0.00 0.00 1.85
3317 7154 5.682234 TCACAGGATCATCAGCTTCTTAA 57.318 39.130 0.00 0.00 0.00 1.85
3641 7494 3.153919 TGAAAGCGGCCTCTAAAATGTT 58.846 40.909 0.00 0.00 0.00 2.71
3653 7506 5.646606 TCCTTTACAAATTATGAAAGCGGC 58.353 37.500 0.00 0.00 30.92 6.53
3806 7659 7.523052 GCACAACAGGTATCACCAATTCTAAAA 60.523 37.037 0.00 0.00 41.95 1.52
4055 7911 6.926630 AGTTTCTCAGAACTCTGTAGGAAT 57.073 37.500 6.61 0.00 44.12 3.01
4175 8056 3.396260 TTCCAAACAGTTCCTCGGTAG 57.604 47.619 0.00 0.00 0.00 3.18
4283 8199 1.063266 AGGGTTGGAGAAACTTTGCCA 60.063 47.619 0.00 0.00 38.92 4.92
4412 8332 6.238869 GGTTATTGCTCCCAAGAAATCTGATC 60.239 42.308 0.00 0.00 34.31 2.92


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

AutoCloner maintained by Alex Coulton.