Multiple sequence alignment - TraesCS2B01G474600

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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 TraesCS2B01G474600 chr2B 100.000 3623 0 0 1 3623 671753689 671750067 0.000000e+00 6691
1 TraesCS2B01G474600 chr2B 91.387 1579 124 8 1009 2585 485444843 485443275 0.000000e+00 2152
2 TraesCS2B01G474600 chr2D 92.613 3100 149 28 596 3623 562168710 562165619 0.000000e+00 4383
3 TraesCS2B01G474600 chr2D 91.514 1579 125 8 1009 2585 411733652 411732081 0.000000e+00 2165
4 TraesCS2B01G474600 chr2D 86.201 587 60 12 4 573 562169349 562168767 1.850000e-172 616
5 TraesCS2B01G474600 chr2D 82.314 605 88 16 2851 3447 400302711 400302118 1.160000e-139 507
6 TraesCS2B01G474600 chr2D 86.667 210 27 1 3237 3445 126970583 126970792 7.820000e-57 231
7 TraesCS2B01G474600 chr2A 90.500 2421 149 33 352 2747 702853640 702851276 0.000000e+00 3121
8 TraesCS2B01G474600 chr6B 80.551 617 87 22 2846 3447 638502339 638502937 9.230000e-121 444
9 TraesCS2B01G474600 chr5B 79.248 612 86 22 2855 3447 570381132 570381721 4.390000e-104 388
10 TraesCS2B01G474600 chr5B 74.920 622 114 23 2845 3447 570381737 570381139 2.790000e-61 246
11 TraesCS2B01G474600 chr7D 80.810 469 68 20 2978 3437 4906106 4906561 7.450000e-92 348
12 TraesCS2B01G474600 chr7D 85.430 151 21 1 2852 3002 95570166 95570017 4.840000e-34 156
13 TraesCS2B01G474600 chr6A 78.454 608 69 27 2853 3447 611456666 611456108 1.250000e-89 340
14 TraesCS2B01G474600 chr5A 77.023 618 103 23 2852 3442 521018499 521019104 5.840000e-83 318
15 TraesCS2B01G474600 chr5A 76.271 413 94 3 1980 2388 540052857 540053269 2.190000e-52 217
16 TraesCS2B01G474600 chr7B 80.874 366 50 14 3094 3447 724932873 724932516 1.660000e-68 270
17 TraesCS2B01G474600 chr5D 89.071 183 18 2 3266 3447 389004049 389003868 3.640000e-55 226
18 TraesCS2B01G474600 chr5D 75.481 416 92 7 1980 2388 425839799 425840211 1.030000e-45 195
19 TraesCS2B01G474600 chr5D 86.525 141 19 0 3308 3448 455601587 455601447 4.840000e-34 156
20 TraesCS2B01G474600 chr7A 76.442 416 74 11 2841 3255 57896899 57897291 1.710000e-48 204
21 TraesCS2B01G474600 chr4B 87.919 149 18 0 2854 3002 650453310 650453458 3.720000e-40 176
22 TraesCS2B01G474600 chr4B 86.577 149 19 1 2854 3002 650440443 650440590 2.890000e-36 163
23 TraesCS2B01G474600 chr4A 84.066 182 27 2 2852 3033 63828730 63828551 1.340000e-39 174
24 TraesCS2B01G474600 chr4A 84.892 139 20 1 2864 3002 11192458 11192321 4.880000e-29 139


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 TraesCS2B01G474600 chr2B 671750067 671753689 3622 True 6691.0 6691 100.000 1 3623 1 chr2B.!!$R2 3622
1 TraesCS2B01G474600 chr2B 485443275 485444843 1568 True 2152.0 2152 91.387 1009 2585 1 chr2B.!!$R1 1576
2 TraesCS2B01G474600 chr2D 562165619 562169349 3730 True 2499.5 4383 89.407 4 3623 2 chr2D.!!$R3 3619
3 TraesCS2B01G474600 chr2D 411732081 411733652 1571 True 2165.0 2165 91.514 1009 2585 1 chr2D.!!$R2 1576
4 TraesCS2B01G474600 chr2D 400302118 400302711 593 True 507.0 507 82.314 2851 3447 1 chr2D.!!$R1 596
5 TraesCS2B01G474600 chr2A 702851276 702853640 2364 True 3121.0 3121 90.500 352 2747 1 chr2A.!!$R1 2395
6 TraesCS2B01G474600 chr6B 638502339 638502937 598 False 444.0 444 80.551 2846 3447 1 chr6B.!!$F1 601
7 TraesCS2B01G474600 chr5B 570381132 570381721 589 False 388.0 388 79.248 2855 3447 1 chr5B.!!$F1 592
8 TraesCS2B01G474600 chr5B 570381139 570381737 598 True 246.0 246 74.920 2845 3447 1 chr5B.!!$R1 602
9 TraesCS2B01G474600 chr6A 611456108 611456666 558 True 340.0 340 78.454 2853 3447 1 chr6A.!!$R1 594
10 TraesCS2B01G474600 chr5A 521018499 521019104 605 False 318.0 318 77.023 2852 3442 1 chr5A.!!$F1 590

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
277 290 0.033504 TCCAGTCCTCTGTTTGACGC 59.966 55.0 0.0 0.0 39.82 5.19 F
798 859 0.176910 CCAAGGCCCAACACGTTTTT 59.823 50.0 0.0 0.0 0.00 1.94 F
1472 1582 0.249741 GACTACGGCAACCACAGTGT 60.250 55.0 0.0 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1116 1220 0.403271 AGAGGCATGGAAGCACAGTT 59.597 50.0 0.0 0.0 35.83 3.16 R
2334 2444 0.881118 CAAGGTTGTTGCTGCCGTAT 59.119 50.0 0.0 0.0 0.00 3.06 R
3342 3562 0.392998 CCCCGATCAGTTTGGTCCAG 60.393 60.0 0.0 0.0 0.00 3.86 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
38 39 9.557061 AGTTAAGAAAAGTTCGTTTAATCTCCT 57.443 29.630 0.00 0.00 34.02 3.69
80 81 8.912988 TCAGAAATTTTACAATCCACTTGAACT 58.087 29.630 0.00 0.00 38.29 3.01
112 116 7.595819 AAATTCCCTACACATGAAAACTGAA 57.404 32.000 0.00 0.00 0.00 3.02
114 118 7.781324 ATTCCCTACACATGAAAACTGAAAT 57.219 32.000 0.00 0.00 0.00 2.17
120 124 5.291971 ACACATGAAAACTGAAATCAAGGC 58.708 37.500 0.00 0.00 0.00 4.35
133 137 3.951563 ATCAAGGCCCTTAACAGCATA 57.048 42.857 0.00 0.00 0.00 3.14
134 138 2.999331 TCAAGGCCCTTAACAGCATAC 58.001 47.619 0.00 0.00 0.00 2.39
139 143 3.521937 AGGCCCTTAACAGCATACTAACA 59.478 43.478 0.00 0.00 0.00 2.41
142 146 5.008712 GGCCCTTAACAGCATACTAACATTC 59.991 44.000 0.00 0.00 0.00 2.67
143 147 5.823045 GCCCTTAACAGCATACTAACATTCT 59.177 40.000 0.00 0.00 0.00 2.40
144 148 6.990349 GCCCTTAACAGCATACTAACATTCTA 59.010 38.462 0.00 0.00 0.00 2.10
145 149 7.497909 GCCCTTAACAGCATACTAACATTCTAA 59.502 37.037 0.00 0.00 0.00 2.10
192 205 7.802738 TGGTTCTTATTTGACTATGTTCGTTG 58.197 34.615 0.00 0.00 0.00 4.10
193 206 6.741358 GGTTCTTATTTGACTATGTTCGTTGC 59.259 38.462 0.00 0.00 0.00 4.17
196 209 6.533723 TCTTATTTGACTATGTTCGTTGCGAT 59.466 34.615 0.00 0.00 35.23 4.58
273 286 6.824305 ATATGTTTTCCAGTCCTCTGTTTG 57.176 37.500 0.00 0.00 39.82 2.93
274 287 4.229304 TGTTTTCCAGTCCTCTGTTTGA 57.771 40.909 0.00 0.00 39.82 2.69
275 288 3.945285 TGTTTTCCAGTCCTCTGTTTGAC 59.055 43.478 0.00 0.00 39.82 3.18
276 289 2.526304 TTCCAGTCCTCTGTTTGACG 57.474 50.000 0.00 0.00 39.82 4.35
277 290 0.033504 TCCAGTCCTCTGTTTGACGC 59.966 55.000 0.00 0.00 39.82 5.19
280 293 2.027625 GTCCTCTGTTTGACGCCCG 61.028 63.158 0.00 0.00 0.00 6.13
287 301 1.155424 TGTTTGACGCCCGTGTTCTC 61.155 55.000 0.00 0.00 0.00 2.87
291 305 0.604073 TGACGCCCGTGTTCTCAATA 59.396 50.000 0.00 0.00 0.00 1.90
301 315 4.259970 CCGTGTTCTCAATAGATTCTTGCG 60.260 45.833 0.00 0.00 0.00 4.85
317 331 4.060205 TCTTGCGTTTGTACCCTTCTTAC 58.940 43.478 0.00 0.00 0.00 2.34
331 345 4.838423 CCCTTCTTACCTTTTCCAAATGGT 59.162 41.667 12.76 12.76 45.23 3.55
339 353 4.218417 ACCTTTTCCAAATGGTCAGAATCG 59.782 41.667 4.20 0.00 41.09 3.34
361 375 2.226962 AGATGCCCAAAATGAGCTGT 57.773 45.000 0.00 0.00 0.00 4.40
381 395 3.605749 CTCCGGTTGACGCACCCAT 62.606 63.158 0.00 0.00 42.52 4.00
394 408 2.032550 CGCACCCATCATTCTTAGCAAG 59.967 50.000 0.00 0.00 0.00 4.01
401 415 6.097412 ACCCATCATTCTTAGCAAGGAATTTC 59.903 38.462 0.00 0.00 30.81 2.17
511 528 3.287222 CTTAGGAGCACTAGAGCAGAGT 58.713 50.000 14.80 0.00 36.85 3.24
512 529 1.762708 AGGAGCACTAGAGCAGAGTC 58.237 55.000 14.80 2.99 36.85 3.36
545 562 2.029244 CGACCATGATACAAGTGCGTTC 59.971 50.000 0.00 0.00 0.00 3.95
573 590 5.569413 CGCTGGAAATGACCTGTAAATAAC 58.431 41.667 0.00 0.00 0.00 1.89
575 592 6.555315 GCTGGAAATGACCTGTAAATAACTG 58.445 40.000 0.00 0.00 0.00 3.16
798 859 0.176910 CCAAGGCCCAACACGTTTTT 59.823 50.000 0.00 0.00 0.00 1.94
849 926 4.646492 AGGAAACAGAGCATTTTCAGTGTT 59.354 37.500 0.00 0.00 34.03 3.32
852 929 6.237915 GGAAACAGAGCATTTTCAGTGTTTTG 60.238 38.462 0.00 0.00 38.03 2.44
875 952 2.118683 CGCGGGTAAAAATGCATGATG 58.881 47.619 0.00 0.00 0.00 3.07
883 963 6.711645 GGGTAAAAATGCATGATGCCATTATT 59.288 34.615 15.70 4.92 44.23 1.40
904 984 3.052082 CCGTGTTCAGCAGGGCAG 61.052 66.667 0.00 0.00 44.82 4.85
916 996 1.115467 CAGGGCAGGTAGACACTAGG 58.885 60.000 0.00 0.00 0.00 3.02
978 1058 1.410850 ATATCGCCTCCCACCACCAG 61.411 60.000 0.00 0.00 0.00 4.00
987 1067 2.656646 CACCACCAGCACGCTCTA 59.343 61.111 0.00 0.00 0.00 2.43
1128 1232 1.883638 GCCAGATCAACTGTGCTTCCA 60.884 52.381 0.00 0.00 44.40 3.53
1194 1304 1.964373 CGGAAACAACCCCACCGAG 60.964 63.158 0.00 0.00 45.31 4.63
1275 1385 3.986006 GCGTGGGACGGTGACTCA 61.986 66.667 0.00 0.00 42.82 3.41
1301 1411 0.663568 AAGTTCTTGCCGTCGACGAG 60.664 55.000 37.65 26.32 43.02 4.18
1405 1515 1.006571 AGCCACACGTACACCTTCG 60.007 57.895 0.00 0.00 0.00 3.79
1406 1516 2.664436 GCCACACGTACACCTTCGC 61.664 63.158 0.00 0.00 0.00 4.70
1407 1517 2.369629 CCACACGTACACCTTCGCG 61.370 63.158 0.00 0.00 0.00 5.87
1408 1518 2.732094 ACACGTACACCTTCGCGC 60.732 61.111 0.00 0.00 0.00 6.86
1413 1523 3.057548 TACACCTTCGCGCTCCGA 61.058 61.111 5.56 0.00 45.77 4.55
1470 1580 1.006571 CGACTACGGCAACCACAGT 60.007 57.895 0.00 0.00 35.72 3.55
1472 1582 0.249741 GACTACGGCAACCACAGTGT 60.250 55.000 0.00 0.00 0.00 3.55
1480 1590 2.140792 AACCACAGTGTCTCCGGCT 61.141 57.895 0.00 0.00 0.00 5.52
2034 2144 2.642171 ACAACCTCACCTGGATCCTA 57.358 50.000 14.23 0.00 0.00 2.94
2334 2444 1.070758 GAGGTGTTCAAGCTCCAGACA 59.929 52.381 0.00 0.00 45.92 3.41
2352 2462 0.881118 CATACGGCAGCAACAACCTT 59.119 50.000 0.00 0.00 0.00 3.50
2524 2634 4.373116 GCAGGAAGGCCACGTCGA 62.373 66.667 5.01 0.00 36.29 4.20
2559 2669 3.055240 AGTCAGAAGCCATTCCTGAGAAG 60.055 47.826 0.00 0.00 35.94 2.85
2574 2687 1.000396 GAAGCAAGCCCATGGTCCT 60.000 57.895 11.73 3.48 0.00 3.85
2633 2746 2.949963 GCCAGACATAAATGGGCCTTCA 60.950 50.000 4.53 0.00 38.70 3.02
2669 2783 5.639506 CGAACAGACCATAGTGTGAGAAATT 59.360 40.000 0.00 0.00 39.62 1.82
2699 2813 3.750639 TTCTTTATTTAACCTGCGCGG 57.249 42.857 9.96 9.96 39.35 6.46
2729 2843 2.808543 GTTCGTGCATCTCAGAAAAGGT 59.191 45.455 0.00 0.00 0.00 3.50
2894 3033 6.806217 TCCCTCAAGTTCCCCAAAAATATAA 58.194 36.000 0.00 0.00 0.00 0.98
3222 3418 8.258007 TGTTATTTGACCACCAAAATTTACACA 58.742 29.630 0.00 0.00 46.64 3.72
3231 3427 5.689961 CACCAAAATTTACACACAACTAGCC 59.310 40.000 0.00 0.00 0.00 3.93
3232 3428 5.221362 ACCAAAATTTACACACAACTAGCCC 60.221 40.000 0.00 0.00 0.00 5.19
3342 3562 3.003275 TCAACGTGCTCAAAATCTGGTTC 59.997 43.478 0.00 0.00 0.00 3.62
3447 3669 4.041740 GAACTTGAGGGTCCAAAAACAC 57.958 45.455 0.00 0.00 0.00 3.32
3448 3670 2.021457 ACTTGAGGGTCCAAAAACACG 58.979 47.619 0.00 0.00 0.00 4.49
3449 3671 0.741915 TTGAGGGTCCAAAAACACGC 59.258 50.000 0.00 0.00 0.00 5.34
3450 3672 1.281656 GAGGGTCCAAAAACACGCG 59.718 57.895 3.53 3.53 0.00 6.01
3451 3673 2.354188 GGGTCCAAAAACACGCGC 60.354 61.111 5.73 0.00 0.00 6.86
3452 3674 2.724358 GGTCCAAAAACACGCGCG 60.724 61.111 30.96 30.96 0.00 6.86
3453 3675 3.383601 GTCCAAAAACACGCGCGC 61.384 61.111 32.58 23.91 0.00 6.86
3469 3696 4.409588 GCGCGCGTGTGTGTGTAG 62.410 66.667 32.35 0.00 38.36 2.74
3477 3704 2.135139 CGTGTGTGTGTAGTGCTCATT 58.865 47.619 0.00 0.00 0.00 2.57
3535 3774 0.808847 GCCGAACCGTGGAATCTACC 60.809 60.000 0.00 0.00 0.00 3.18
3544 3783 1.215423 GTGGAATCTACCAGGCCCATT 59.785 52.381 0.00 0.00 40.85 3.16
3546 3785 1.215423 GGAATCTACCAGGCCCATTGT 59.785 52.381 0.00 0.00 0.00 2.71
3576 3816 3.006940 TGTGCATTTGGTCGTCTATTCC 58.993 45.455 0.00 0.00 0.00 3.01
3596 3836 1.219522 ACACACTAAGCGCGGAACAC 61.220 55.000 8.83 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.652245 TCGTTGAAAAGGAGATTAAACGAAC 58.348 36.000 8.67 0.00 43.21 3.95
54 55 8.912988 AGTTCAAGTGGATTGTAAAATTTCTGA 58.087 29.630 0.00 0.00 40.05 3.27
83 84 9.981114 AGTTTTCATGTGTAGGGAATTTTAAAG 57.019 29.630 0.00 0.00 0.00 1.85
84 85 9.757227 CAGTTTTCATGTGTAGGGAATTTTAAA 57.243 29.630 0.00 0.00 0.00 1.52
87 88 7.595819 TCAGTTTTCATGTGTAGGGAATTTT 57.404 32.000 0.00 0.00 0.00 1.82
88 89 7.595819 TTCAGTTTTCATGTGTAGGGAATTT 57.404 32.000 0.00 0.00 0.00 1.82
89 90 7.595819 TTTCAGTTTTCATGTGTAGGGAATT 57.404 32.000 0.00 0.00 0.00 2.17
91 92 6.775142 TGATTTCAGTTTTCATGTGTAGGGAA 59.225 34.615 0.00 0.00 0.00 3.97
92 93 6.303054 TGATTTCAGTTTTCATGTGTAGGGA 58.697 36.000 0.00 0.00 0.00 4.20
112 116 2.603075 TGCTGTTAAGGGCCTTGATT 57.397 45.000 28.88 4.64 0.00 2.57
114 118 2.576191 AGTATGCTGTTAAGGGCCTTGA 59.424 45.455 28.88 18.57 0.00 3.02
120 124 8.958119 TTAGAATGTTAGTATGCTGTTAAGGG 57.042 34.615 0.00 0.00 0.00 3.95
147 151 9.596308 AGAACCAAACTGTATTAAAAGGGTAAT 57.404 29.630 0.00 0.00 0.00 1.89
148 152 8.999905 AGAACCAAACTGTATTAAAAGGGTAA 57.000 30.769 0.00 0.00 0.00 2.85
149 153 8.999905 AAGAACCAAACTGTATTAAAAGGGTA 57.000 30.769 0.00 0.00 0.00 3.69
150 154 7.907841 AAGAACCAAACTGTATTAAAAGGGT 57.092 32.000 0.00 0.00 0.00 4.34
165 178 8.385898 ACGAACATAGTCAAATAAGAACCAAA 57.614 30.769 0.00 0.00 0.00 3.28
211 224 4.335416 GGTCTTTTGATCACAGGGATTGA 58.665 43.478 0.00 0.00 36.00 2.57
213 226 3.075882 TGGGTCTTTTGATCACAGGGATT 59.924 43.478 0.00 0.00 36.00 3.01
273 286 1.135199 TCTATTGAGAACACGGGCGTC 60.135 52.381 0.00 0.00 0.00 5.19
274 287 0.892755 TCTATTGAGAACACGGGCGT 59.107 50.000 0.00 0.00 0.00 5.68
275 288 2.225068 ATCTATTGAGAACACGGGCG 57.775 50.000 0.00 0.00 34.61 6.13
276 289 3.798202 AGAATCTATTGAGAACACGGGC 58.202 45.455 0.00 0.00 34.61 6.13
277 290 4.034510 GCAAGAATCTATTGAGAACACGGG 59.965 45.833 0.00 0.00 34.61 5.28
280 293 5.786401 ACGCAAGAATCTATTGAGAACAC 57.214 39.130 0.00 0.00 43.62 3.32
287 301 5.354234 AGGGTACAAACGCAAGAATCTATTG 59.646 40.000 0.00 0.00 40.89 1.90
291 305 3.418684 AGGGTACAAACGCAAGAATCT 57.581 42.857 0.00 0.00 40.89 2.40
301 315 5.829391 TGGAAAAGGTAAGAAGGGTACAAAC 59.171 40.000 0.00 0.00 0.00 2.93
317 331 4.458989 TCGATTCTGACCATTTGGAAAAGG 59.541 41.667 3.01 0.00 38.94 3.11
331 345 3.348647 TTGGGCATCTTTCGATTCTGA 57.651 42.857 0.00 0.00 0.00 3.27
408 424 8.344831 CACTTAATTATCGCATCATCTTTTCCA 58.655 33.333 0.00 0.00 0.00 3.53
466 483 2.202570 GCGTACGATGCCACGTCT 60.203 61.111 21.65 0.00 45.32 4.18
511 528 4.415332 GGTCGCCGAGCTTGACGA 62.415 66.667 8.44 8.44 33.45 4.20
512 529 3.989698 ATGGTCGCCGAGCTTGACG 62.990 63.158 17.87 2.81 33.45 4.35
545 562 1.021390 AGGTCATTTCCAGCGCTTCG 61.021 55.000 7.50 0.00 0.00 3.79
573 590 4.828829 ACCTACAAGATTCGGTTAACCAG 58.171 43.478 24.14 16.15 35.14 4.00
575 592 7.854557 ATTTACCTACAAGATTCGGTTAACC 57.145 36.000 15.13 15.13 0.00 2.85
576 593 8.938906 TCAATTTACCTACAAGATTCGGTTAAC 58.061 33.333 0.00 0.00 0.00 2.01
577 594 8.938906 GTCAATTTACCTACAAGATTCGGTTAA 58.061 33.333 0.00 0.00 0.00 2.01
626 677 0.041312 CGACGAAAACAACAGCCAGG 60.041 55.000 0.00 0.00 0.00 4.45
787 848 3.467803 AGGAGAGGAGAAAAACGTGTTG 58.532 45.455 0.00 0.00 0.00 3.33
798 859 2.598467 GAGCGGGAGGAGAGGAGA 59.402 66.667 0.00 0.00 0.00 3.71
849 926 2.223735 TGCATTTTTACCCGCGAACAAA 60.224 40.909 8.23 0.69 0.00 2.83
852 929 1.917303 CATGCATTTTTACCCGCGAAC 59.083 47.619 8.23 0.00 0.00 3.95
875 952 3.486875 GCTGAACACGGTGTAATAATGGC 60.487 47.826 15.11 8.50 0.00 4.40
883 963 1.369692 CCCTGCTGAACACGGTGTA 59.630 57.895 15.11 0.00 0.00 2.90
904 984 2.101582 CTGTCCATGCCTAGTGTCTACC 59.898 54.545 0.00 0.00 0.00 3.18
916 996 3.076621 TGATTTCTGTCACTGTCCATGC 58.923 45.455 0.00 0.00 0.00 4.06
978 1058 2.815647 GGGCTGTGTAGAGCGTGC 60.816 66.667 0.00 0.00 40.13 5.34
987 1067 0.039472 TTGGCATGTATGGGCTGTGT 59.961 50.000 0.00 0.00 0.00 3.72
1115 1219 0.524862 GAGGCATGGAAGCACAGTTG 59.475 55.000 0.00 0.00 35.83 3.16
1116 1220 0.403271 AGAGGCATGGAAGCACAGTT 59.597 50.000 0.00 0.00 35.83 3.16
1275 1385 1.961277 CGGCAAGAACTTGGACGCT 60.961 57.895 14.95 0.00 40.74 5.07
1320 1430 1.067212 GATGGGTCTTGATACGACGCT 59.933 52.381 0.00 0.00 42.67 5.07
1466 1576 2.997897 GGGAGCCGGAGACACTGT 60.998 66.667 5.05 0.00 0.00 3.55
1470 1580 1.682684 GAAGAGGGAGCCGGAGACA 60.683 63.158 5.05 0.00 0.00 3.41
1472 1582 2.440430 CGAAGAGGGAGCCGGAGA 60.440 66.667 5.05 0.00 0.00 3.71
1480 1590 3.744719 CGTGACGCCGAAGAGGGA 61.745 66.667 0.00 0.00 41.48 4.20
1521 1631 1.006102 CTGGGACGCGTTGAAGTCT 60.006 57.895 15.53 0.00 37.52 3.24
1858 1968 1.145803 GCGCCGAATATGTAAGGGAC 58.854 55.000 0.00 0.00 0.00 4.46
2172 2282 1.229336 CCCTATCCCTCCGCTCCAT 60.229 63.158 0.00 0.00 0.00 3.41
2334 2444 0.881118 CAAGGTTGTTGCTGCCGTAT 59.119 50.000 0.00 0.00 0.00 3.06
2460 2570 3.499737 CAGCCGATCAACACCGCC 61.500 66.667 0.00 0.00 0.00 6.13
2524 2634 1.080501 CTGACTCGCACACGACCAT 60.081 57.895 0.00 0.00 45.12 3.55
2539 2649 2.355513 GCTTCTCAGGAATGGCTTCTGA 60.356 50.000 0.00 0.00 0.00 3.27
2559 2669 1.635817 TAGGAGGACCATGGGCTTGC 61.636 60.000 19.55 16.69 38.94 4.01
2574 2687 2.108250 AGAGCTTTTTGTTGGGCTAGGA 59.892 45.455 0.00 0.00 35.01 2.94
2610 2723 2.032981 GCCCATTTATGTCTGGCCG 58.967 57.895 0.00 0.00 36.07 6.13
2633 2746 4.761975 TGGTCTGTTCGTAACTTCTTTGT 58.238 39.130 0.00 0.00 0.00 2.83
2699 2813 5.348724 TCTGAGATGCACGAACTTTTGTATC 59.651 40.000 0.00 0.00 35.67 2.24
2729 2843 8.212317 AGCACGCATTATATATATGCAATGAA 57.788 30.769 17.12 0.61 41.05 2.57
2894 3033 1.518367 TGACCTTGAGGGACCAAGTT 58.482 50.000 1.54 0.00 41.34 2.66
3101 3290 4.141287 TCCTCGAATGTCAAAACACCATT 58.859 39.130 0.00 0.00 38.48 3.16
3232 3428 0.542702 ACAACCAAGATGCTTGGGGG 60.543 55.000 25.15 19.23 43.71 5.40
3342 3562 0.392998 CCCCGATCAGTTTGGTCCAG 60.393 60.000 0.00 0.00 0.00 3.86
3354 3574 2.762535 TCAAGTCTCAAACCCCGATC 57.237 50.000 0.00 0.00 0.00 3.69
3358 3578 2.505405 GTCCTTCAAGTCTCAAACCCC 58.495 52.381 0.00 0.00 0.00 4.95
3417 3639 3.329814 GGACCCTCAAGTTCCCTAAAAGA 59.670 47.826 0.00 0.00 0.00 2.52
3452 3674 4.409588 CTACACACACACGCGCGC 62.410 66.667 32.58 23.91 0.00 6.86
3453 3675 3.028019 ACTACACACACACGCGCG 61.028 61.111 30.96 30.96 0.00 6.86
3454 3676 2.544359 CACTACACACACACGCGC 59.456 61.111 5.73 0.00 0.00 6.86
3455 3677 1.876453 GAGCACTACACACACACGCG 61.876 60.000 3.53 3.53 0.00 6.01
3456 3678 0.874175 TGAGCACTACACACACACGC 60.874 55.000 0.00 0.00 0.00 5.34
3457 3679 1.783284 ATGAGCACTACACACACACG 58.217 50.000 0.00 0.00 0.00 4.49
3506 3745 0.596082 ACGGTTCGGCCAAATTTCTG 59.404 50.000 2.24 0.00 36.97 3.02
3544 3783 4.953010 ATGCACAGTGGGCGCACA 62.953 61.111 32.29 9.15 38.73 4.57
3546 3785 2.911509 AAATGCACAGTGGGCGCA 60.912 55.556 13.78 9.72 40.50 6.09
3576 3816 1.218875 TGTTCCGCGCTTAGTGTGTG 61.219 55.000 5.56 0.00 36.51 3.82
3596 3836 5.707298 AGCTATGGGAATGATTGATAAACCG 59.293 40.000 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.