Multiple sequence alignment - TraesCS2B01G311100

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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 TraesCS2B01G311100 chr2B 100.000 2453 0 0 1 2453 445171492 445173944 0.000000e+00 4530.0
1 TraesCS2B01G311100 chr2D 90.665 1789 89 33 640 2381 375026656 375028413 0.000000e+00 2307.0
2 TraesCS2B01G311100 chr2D 90.032 311 26 3 2 312 375026349 375026654 4.910000e-107 398.0
3 TraesCS2B01G311100 chr2D 95.385 65 3 0 2373 2437 375029511 375029575 1.200000e-18 104.0
4 TraesCS2B01G311100 chr2D 95.455 44 0 2 206 248 506776590 506776548 4.380000e-08 69.4
5 TraesCS2B01G311100 chr2A 91.206 1683 86 22 750 2386 507376110 507377776 0.000000e+00 2231.0
6 TraesCS2B01G311100 chr2A 88.158 304 30 3 16 314 507375259 507375561 8.340000e-95 357.0
7 TraesCS2B01G311100 chr2A 97.170 106 3 0 639 744 507375560 507375665 1.940000e-41 180.0
8 TraesCS2B01G311100 chr2A 95.000 60 3 0 2378 2437 507386177 507386236 7.220000e-16 95.3
9 TraesCS2B01G311100 chr2A 97.297 37 0 1 213 248 626591045 626591081 7.320000e-06 62.1
10 TraesCS2B01G311100 chr2A 89.130 46 4 1 210 254 670644363 670644318 3.410000e-04 56.5
11 TraesCS2B01G311100 chr5A 91.066 347 20 4 304 641 704042947 704043291 2.220000e-125 459.0
12 TraesCS2B01G311100 chr5A 91.066 347 20 4 304 641 704139539 704139883 2.220000e-125 459.0
13 TraesCS2B01G311100 chr5A 90.778 347 21 4 304 641 704111337 704111681 1.030000e-123 453.0
14 TraesCS2B01G311100 chr5A 90.778 347 21 4 304 641 704230191 704230535 1.030000e-123 453.0
15 TraesCS2B01G311100 chr5A 90.778 347 21 4 304 641 704269879 704270223 1.030000e-123 453.0
16 TraesCS2B01G311100 chr5A 82.544 338 43 10 313 640 643040267 643040598 1.440000e-72 283.0
17 TraesCS2B01G311100 chrUn 90.407 344 24 2 313 647 175794470 175794127 6.220000e-121 444.0
18 TraesCS2B01G311100 chrUn 90.407 344 24 2 313 647 378558788 378559131 6.220000e-121 444.0
19 TraesCS2B01G311100 chrUn 90.116 344 25 2 313 647 42736598 42736941 2.900000e-119 438.0
20 TraesCS2B01G311100 chrUn 90.116 344 25 2 313 647 42749482 42749825 2.900000e-119 438.0
21 TraesCS2B01G311100 chrUn 89.826 344 26 2 313 647 175777834 175777491 1.350000e-117 433.0
22 TraesCS2B01G311100 chrUn 89.826 344 26 2 313 647 461766949 461766606 1.350000e-117 433.0
23 TraesCS2B01G311100 chrUn 90.000 340 24 3 313 643 43139072 43139410 4.850000e-117 431.0
24 TraesCS2B01G311100 chrUn 89.535 344 27 2 313 647 315965672 315965329 6.270000e-116 427.0
25 TraesCS2B01G311100 chrUn 90.402 323 22 2 334 647 42751227 42751549 1.360000e-112 416.0
26 TraesCS2B01G311100 chr5D 88.255 298 24 4 371 659 270776888 270776593 1.810000e-91 346.0
27 TraesCS2B01G311100 chr3D 80.488 287 50 2 1154 1437 480850245 480850528 5.310000e-52 215.0
28 TraesCS2B01G311100 chr3B 81.022 274 46 2 1167 1437 641666763 641667033 1.910000e-51 213.0
29 TraesCS2B01G311100 chr3A 79.225 284 50 3 1154 1437 623616456 623616730 3.220000e-44 189.0
30 TraesCS2B01G311100 chr7B 97.436 39 0 1 210 247 218563132 218563094 5.660000e-07 65.8
31 TraesCS2B01G311100 chr7B 100.000 29 0 0 1865 1893 487798681 487798709 1.000000e-03 54.7
32 TraesCS2B01G311100 chr7D 97.368 38 0 1 211 247 242803668 242803705 2.040000e-06 63.9
33 TraesCS2B01G311100 chr1D 97.143 35 1 0 210 244 104571571 104571537 2.630000e-05 60.2
34 TraesCS2B01G311100 chr1B 97.143 35 1 0 210 244 161992244 161992278 2.630000e-05 60.2


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 TraesCS2B01G311100 chr2B 445171492 445173944 2452 False 4530.000000 4530 100.000000 1 2453 1 chr2B.!!$F1 2452
1 TraesCS2B01G311100 chr2D 375026349 375029575 3226 False 936.333333 2307 92.027333 2 2437 3 chr2D.!!$F1 2435
2 TraesCS2B01G311100 chr2A 507375259 507377776 2517 False 922.666667 2231 92.178000 16 2386 3 chr2A.!!$F3 2370
3 TraesCS2B01G311100 chrUn 42749482 42751549 2067 False 427.000000 438 90.259000 313 647 2 chrUn.!!$F4 334

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
443 2182 0.109781 CTTTTCCCCGATTGCGTGTG 60.11 55.0 0.0 0.0 35.23 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 4605 0.037734 TAGCTCAGACCCACGACTGA 59.962 55.0 0.0 0.0 40.22 3.41 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
37 38 8.420222 ACTCTAATGTCCATTGTCAGAGATTAG 58.580 37.037 18.45 9.90 42.99 1.73
38 39 7.212976 TCTAATGTCCATTGTCAGAGATTAGC 58.787 38.462 10.45 0.00 42.11 3.09
39 40 5.627182 ATGTCCATTGTCAGAGATTAGCT 57.373 39.130 0.00 0.00 0.00 3.32
40 41 5.426689 TGTCCATTGTCAGAGATTAGCTT 57.573 39.130 0.00 0.00 0.00 3.74
41 42 5.809001 TGTCCATTGTCAGAGATTAGCTTT 58.191 37.500 0.00 0.00 0.00 3.51
78 79 7.923344 GCTGATCAACTAGCTTCTAATGTCTAA 59.077 37.037 0.00 0.00 36.99 2.10
154 159 5.106555 CGTGTGGAAGAGTCATATTGCTTTT 60.107 40.000 0.00 0.00 0.00 2.27
189 194 2.290260 TGCCAAACTTCCGTGATCAGAT 60.290 45.455 0.00 0.00 0.00 2.90
200 205 3.366121 CCGTGATCAGATGATATCGTTGC 59.634 47.826 0.00 0.00 34.37 4.17
203 208 4.624882 GTGATCAGATGATATCGTTGCTCC 59.375 45.833 0.00 0.00 34.37 4.70
206 211 5.282055 TCAGATGATATCGTTGCTCCTTT 57.718 39.130 0.00 0.00 0.00 3.11
221 226 3.181480 GCTCCTTTGTAACTGCCAAAACA 60.181 43.478 0.00 0.00 31.86 2.83
300 306 7.798982 GTGACACTTTACTTCATTTTAGCACTC 59.201 37.037 0.00 0.00 0.00 3.51
321 327 1.483004 GCTTTCAGACCTACTCCCTCC 59.517 57.143 0.00 0.00 0.00 4.30
325 331 2.752030 TCAGACCTACTCCCTCCATTG 58.248 52.381 0.00 0.00 0.00 2.82
340 346 5.183904 CCCTCCATTGCTTTATATAAGGTGC 59.816 44.000 6.48 7.94 0.00 5.01
391 2121 5.774690 TGTAAGGTGCATTTCTTCCAATTCT 59.225 36.000 0.00 0.00 0.00 2.40
412 2142 6.399639 TCTTCAAAAATCCGTTTTTAGCCT 57.600 33.333 0.00 0.00 43.69 4.58
413 2143 6.443792 TCTTCAAAAATCCGTTTTTAGCCTC 58.556 36.000 0.00 0.00 43.69 4.70
414 2144 6.264518 TCTTCAAAAATCCGTTTTTAGCCTCT 59.735 34.615 0.00 0.00 43.69 3.69
415 2145 7.446013 TCTTCAAAAATCCGTTTTTAGCCTCTA 59.554 33.333 0.00 0.00 43.69 2.43
416 2146 7.141100 TCAAAAATCCGTTTTTAGCCTCTAG 57.859 36.000 0.00 0.00 43.69 2.43
417 2147 6.713450 TCAAAAATCCGTTTTTAGCCTCTAGT 59.287 34.615 0.00 0.00 43.69 2.57
439 2178 2.561569 AGTATCTTTTCCCCGATTGCG 58.438 47.619 0.00 0.00 37.24 4.85
443 2182 0.109781 CTTTTCCCCGATTGCGTGTG 60.110 55.000 0.00 0.00 35.23 3.82
453 2192 2.476619 CGATTGCGTGTGTCTCTTCTTT 59.523 45.455 0.00 0.00 0.00 2.52
567 2306 8.770010 TTTAGTCAAGGTTAATTTTCTCCCAA 57.230 30.769 0.00 0.00 0.00 4.12
568 2307 6.650427 AGTCAAGGTTAATTTTCTCCCAAC 57.350 37.500 0.00 0.00 0.00 3.77
586 2325 8.325787 TCTCCCAACTTGTGTATAATTATGTGT 58.674 33.333 8.28 0.00 0.00 3.72
595 2334 8.487313 TGTGTATAATTATGTGTCTTGGTCAC 57.513 34.615 8.28 0.00 36.48 3.67
596 2335 7.551262 TGTGTATAATTATGTGTCTTGGTCACC 59.449 37.037 8.28 0.00 35.25 4.02
599 2338 2.448926 TATGTGTCTTGGTCACCGTG 57.551 50.000 0.00 0.00 35.25 4.94
681 2420 3.940209 TTTGATTGCTTGGTCACATCC 57.060 42.857 0.00 0.00 0.00 3.51
744 2483 6.183360 GCTGCCGTATATAGTAGATAAGTGCT 60.183 42.308 10.21 0.00 0.00 4.40
760 2939 5.712152 AAGTGCTTCTTAAAATGGTCCTG 57.288 39.130 0.00 0.00 34.23 3.86
789 2968 5.652452 AGCATAATTTTGGGACAGGTCTAAC 59.348 40.000 0.00 0.00 42.39 2.34
802 2981 3.743396 CAGGTCTAACTGAAGTGTTGAGC 59.257 47.826 0.00 0.00 40.97 4.26
827 3006 8.539674 GCTTTGAAGTAGTGTAAAACCAATTTG 58.460 33.333 0.00 0.00 32.27 2.32
842 3023 5.288804 ACCAATTTGTTAAGCACACATGTC 58.711 37.500 0.00 0.00 33.98 3.06
851 3032 2.862541 AGCACACATGTCAAGCCTTAA 58.137 42.857 0.00 0.00 0.00 1.85
900 3081 6.183360 GGGCCAAATATTTCTGCTTGAATTTG 60.183 38.462 4.39 0.00 34.47 2.32
914 3095 5.600696 CTTGAATTTGGTGCCTGTAAACTT 58.399 37.500 0.00 0.00 0.00 2.66
915 3096 4.942852 TGAATTTGGTGCCTGTAAACTTG 58.057 39.130 0.00 0.00 0.00 3.16
957 3143 5.916661 TTATAGCGTCTCCTCTCTTGTTT 57.083 39.130 0.00 0.00 0.00 2.83
966 3152 4.524714 TCTCCTCTCTTGTTTCTGAACGAT 59.475 41.667 0.00 0.00 38.65 3.73
983 3179 7.498900 TCTGAACGATGATTACCATTTTAGCAT 59.501 33.333 0.00 0.00 35.17 3.79
1015 3212 1.860950 CCGAGATGGCAACTACATTCG 59.139 52.381 0.00 0.00 33.18 3.34
1347 3544 1.906824 GGACCAGTCGGACCAGTCA 60.907 63.158 22.25 0.00 45.54 3.41
1353 3550 1.134965 CAGTCGGACCAGTCATTCCTC 60.135 57.143 4.14 0.00 0.00 3.71
1488 3685 7.587629 CAGCACTAGTTTCATTCAATCTTTGA 58.412 34.615 0.00 0.00 38.04 2.69
1570 3775 1.788067 TTCTCACTTCGTCGCCGTCA 61.788 55.000 0.00 0.00 35.01 4.35
1595 3808 4.935352 TTAACCTGAGCAAGTGCATTTT 57.065 36.364 6.00 0.00 45.16 1.82
1627 3840 3.951663 TCTCTCTACGTTCTCATGTGGA 58.048 45.455 0.00 0.00 0.00 4.02
1631 3844 6.205658 TCTCTCTACGTTCTCATGTGGATATG 59.794 42.308 0.00 0.00 29.63 1.78
1647 3861 3.243873 GGATATGTGGAATCTGTCGAGCA 60.244 47.826 0.00 0.00 0.00 4.26
1729 3943 3.289062 TTCTCGCCACGTCCACGA 61.289 61.111 6.03 4.30 43.02 4.35
1757 3971 1.223763 GGGTGAATCTTCCCCGGAC 59.776 63.158 0.73 0.00 37.89 4.79
1758 3972 1.153429 GGTGAATCTTCCCCGGACG 60.153 63.158 0.73 0.00 0.00 4.79
1759 3973 1.610554 GGTGAATCTTCCCCGGACGA 61.611 60.000 0.73 0.00 0.00 4.20
1785 3999 3.904353 CCGCGCGCATTGCATTTG 61.904 61.111 32.61 11.04 46.97 2.32
1788 4002 1.225529 GCGCGCATTGCATTTGTTG 60.226 52.632 29.10 0.00 46.97 3.33
1789 4003 1.888958 GCGCGCATTGCATTTGTTGT 61.889 50.000 29.10 0.00 46.97 3.32
1790 4004 0.507785 CGCGCATTGCATTTGTTGTT 59.492 45.000 8.75 0.00 46.97 2.83
1791 4005 1.718178 CGCGCATTGCATTTGTTGTTA 59.282 42.857 8.75 0.00 46.97 2.41
1792 4006 2.345041 CGCGCATTGCATTTGTTGTTAT 59.655 40.909 8.75 0.00 46.97 1.89
1796 4015 3.367327 GCATTGCATTTGTTGTTATCGCA 59.633 39.130 3.15 0.00 0.00 5.10
2000 4231 9.670180 GGTGTATACGTACGTTTTTATAAACAC 57.330 33.333 27.92 23.88 43.05 3.32
2001 4232 9.379831 GTGTATACGTACGTTTTTATAAACACG 57.620 33.333 27.92 26.93 44.86 4.49
2081 4316 0.040425 GAAGCGTGCGTGTCCAAAAT 60.040 50.000 0.00 0.00 0.00 1.82
2283 4524 4.322349 CCGAATTAAAGGTGCCAAATGGAA 60.322 41.667 2.98 0.00 37.39 3.53
2344 4585 5.810587 AGCGTATCGAATTATTGTTGTCACT 59.189 36.000 0.00 0.00 0.00 3.41
2353 4595 7.009265 CGAATTATTGTTGTCACTACTCACGAT 59.991 37.037 0.00 0.00 0.00 3.73
2363 4605 6.321435 TGTCACTACTCACGATTCATAGGATT 59.679 38.462 0.00 0.00 0.00 3.01
2429 5777 1.735559 GCCTGGTCCGTCGTGTTAC 60.736 63.158 0.00 0.00 0.00 2.50
2433 5781 0.032403 TGGTCCGTCGTGTTACCAAG 59.968 55.000 0.00 0.00 39.02 3.61
2437 5785 3.367292 GGTCCGTCGTGTTACCAAGATTA 60.367 47.826 0.00 0.00 31.70 1.75
2438 5786 3.609807 GTCCGTCGTGTTACCAAGATTAC 59.390 47.826 0.00 0.00 31.70 1.89
2439 5787 3.507233 TCCGTCGTGTTACCAAGATTACT 59.493 43.478 0.00 0.00 31.70 2.24
2440 5788 3.611113 CCGTCGTGTTACCAAGATTACTG 59.389 47.826 0.00 0.00 31.70 2.74
2441 5789 4.232221 CGTCGTGTTACCAAGATTACTGT 58.768 43.478 0.00 0.00 31.70 3.55
2442 5790 5.393124 CGTCGTGTTACCAAGATTACTGTA 58.607 41.667 0.00 0.00 31.70 2.74
2443 5791 6.032094 CGTCGTGTTACCAAGATTACTGTAT 58.968 40.000 0.00 0.00 31.70 2.29
2444 5792 6.020916 CGTCGTGTTACCAAGATTACTGTATG 60.021 42.308 0.00 0.00 31.70 2.39
2445 5793 6.810182 GTCGTGTTACCAAGATTACTGTATGT 59.190 38.462 0.00 0.00 31.70 2.29
2446 5794 6.809689 TCGTGTTACCAAGATTACTGTATGTG 59.190 38.462 0.00 0.00 0.00 3.21
2447 5795 6.035650 CGTGTTACCAAGATTACTGTATGTGG 59.964 42.308 0.00 0.00 0.00 4.17
2448 5796 5.878116 TGTTACCAAGATTACTGTATGTGGC 59.122 40.000 6.53 0.00 0.00 5.01
2449 5797 4.568072 ACCAAGATTACTGTATGTGGCA 57.432 40.909 6.53 0.00 0.00 4.92
2450 5798 4.917385 ACCAAGATTACTGTATGTGGCAA 58.083 39.130 0.00 0.00 0.00 4.52
2451 5799 5.321102 ACCAAGATTACTGTATGTGGCAAA 58.679 37.500 0.00 0.00 0.00 3.68
2452 5800 5.951747 ACCAAGATTACTGTATGTGGCAAAT 59.048 36.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.804639 TGGACATTAGAGTACAAGCAATGT 58.195 37.500 12.23 12.23 46.36 2.71
55 56 9.810545 AACTTAGACATTAGAAGCTAGTTGATC 57.189 33.333 0.00 0.00 0.00 2.92
154 159 7.416213 CGGAAGTTTGGCATATCCATTTCTAAA 60.416 37.037 0.00 0.00 46.04 1.85
170 175 3.599343 TCATCTGATCACGGAAGTTTGG 58.401 45.455 0.00 0.00 46.40 3.28
179 184 4.233005 AGCAACGATATCATCTGATCACG 58.767 43.478 3.12 13.42 38.32 4.35
189 194 5.580691 CAGTTACAAAGGAGCAACGATATCA 59.419 40.000 3.12 0.00 0.00 2.15
200 205 4.647424 TGTTTTGGCAGTTACAAAGGAG 57.353 40.909 0.00 0.00 38.84 3.69
203 208 7.199766 TGTAAGATGTTTTGGCAGTTACAAAG 58.800 34.615 3.16 0.00 38.84 2.77
206 211 6.892658 ATGTAAGATGTTTTGGCAGTTACA 57.107 33.333 0.00 0.00 36.76 2.41
221 226 5.222130 ACCCCTCTGTTCACAAATGTAAGAT 60.222 40.000 0.00 0.00 0.00 2.40
250 256 2.206576 ACGTCCTACCCGTCTTTACT 57.793 50.000 0.00 0.00 31.97 2.24
251 257 3.010420 ACTACGTCCTACCCGTCTTTAC 58.990 50.000 0.00 0.00 39.60 2.01
253 259 2.206576 ACTACGTCCTACCCGTCTTT 57.793 50.000 0.00 0.00 39.60 2.52
300 306 1.135333 GAGGGAGTAGGTCTGAAAGCG 59.865 57.143 0.00 0.00 0.00 4.68
321 327 8.876275 ACAAATGCACCTTATATAAAGCAATG 57.124 30.769 16.21 17.74 35.45 2.82
361 2091 4.789012 AGAAATGCACCTTACATTGTGG 57.211 40.909 0.00 0.00 37.78 4.17
391 2121 6.399639 AGAGGCTAAAAACGGATTTTTGAA 57.600 33.333 8.57 0.00 45.53 2.69
412 2142 7.686127 GCAATCGGGGAAAAGATACTTACTAGA 60.686 40.741 0.00 0.00 0.00 2.43
413 2143 6.424207 GCAATCGGGGAAAAGATACTTACTAG 59.576 42.308 0.00 0.00 0.00 2.57
414 2144 6.285990 GCAATCGGGGAAAAGATACTTACTA 58.714 40.000 0.00 0.00 0.00 1.82
415 2145 5.123936 GCAATCGGGGAAAAGATACTTACT 58.876 41.667 0.00 0.00 0.00 2.24
416 2146 4.025145 CGCAATCGGGGAAAAGATACTTAC 60.025 45.833 0.00 0.00 0.00 2.34
417 2147 4.124238 CGCAATCGGGGAAAAGATACTTA 58.876 43.478 0.00 0.00 0.00 2.24
471 2210 2.497675 TGCACAATCAGGAGAGAGGTAC 59.502 50.000 0.00 0.00 0.00 3.34
474 2213 4.620589 ATATGCACAATCAGGAGAGAGG 57.379 45.455 0.00 0.00 0.00 3.69
540 2279 9.374711 TGGGAGAAAATTAACCTTGACTAAATT 57.625 29.630 0.00 0.00 0.00 1.82
547 2286 6.609616 ACAAGTTGGGAGAAAATTAACCTTGA 59.390 34.615 7.96 0.00 0.00 3.02
550 2289 5.897250 ACACAAGTTGGGAGAAAATTAACCT 59.103 36.000 13.26 0.00 0.00 3.50
561 2300 8.506168 ACACATAATTATACACAAGTTGGGAG 57.494 34.615 13.26 1.22 0.00 4.30
565 2304 9.773328 CCAAGACACATAATTATACACAAGTTG 57.227 33.333 0.00 0.00 0.00 3.16
567 2306 9.162764 GACCAAGACACATAATTATACACAAGT 57.837 33.333 0.00 0.00 0.00 3.16
568 2307 9.161629 TGACCAAGACACATAATTATACACAAG 57.838 33.333 0.00 0.00 0.00 3.16
578 2317 3.334691 CACGGTGACCAAGACACATAAT 58.665 45.455 0.74 0.00 39.65 1.28
586 2325 0.179234 TTTCAGCACGGTGACCAAGA 59.821 50.000 13.29 0.00 0.00 3.02
595 2334 5.560966 AAGGTGTATAATTTTCAGCACGG 57.439 39.130 0.00 0.00 32.91 4.94
596 2335 7.067532 TGTAAGGTGTATAATTTTCAGCACG 57.932 36.000 0.00 0.00 32.91 5.34
628 2367 3.454812 TGGCTAGAAAATACTCCCTCCAC 59.545 47.826 0.00 0.00 0.00 4.02
681 2420 8.668510 AAAGTATGGTGTTGATTGAGCTATAG 57.331 34.615 0.00 0.00 0.00 1.31
744 2483 6.071984 TGCTTTACCAGGACCATTTTAAGAA 58.928 36.000 0.00 0.00 0.00 2.52
760 2939 5.186992 ACCTGTCCCAAAATTATGCTTTACC 59.813 40.000 0.00 0.00 0.00 2.85
789 2968 4.889832 ACTTCAAAGCTCAACACTTCAG 57.110 40.909 0.00 0.00 0.00 3.02
802 2981 9.581099 ACAAATTGGTTTTACACTACTTCAAAG 57.419 29.630 0.00 0.00 0.00 2.77
827 3006 2.554032 AGGCTTGACATGTGTGCTTAAC 59.446 45.455 1.15 0.00 0.00 2.01
842 3023 3.399440 TTTTGGGTGCATTAAGGCTTG 57.601 42.857 13.92 0.00 34.04 4.01
900 3081 4.649088 AAAGAACAAGTTTACAGGCACC 57.351 40.909 0.00 0.00 0.00 5.01
928 3111 5.708230 AGAGAGGAGACGCTATAATAACAGG 59.292 44.000 0.00 0.00 42.18 4.00
942 3128 3.984633 CGTTCAGAAACAAGAGAGGAGAC 59.015 47.826 0.00 0.00 34.93 3.36
957 3143 6.821160 TGCTAAAATGGTAATCATCGTTCAGA 59.179 34.615 0.00 0.00 34.44 3.27
966 3152 6.019656 TGGGGTATGCTAAAATGGTAATCA 57.980 37.500 0.00 0.00 0.00 2.57
983 3179 1.306654 ATCTCGGGTGCTTGGGGTA 60.307 57.895 0.00 0.00 0.00 3.69
1015 3212 1.865788 TTGCAGAGAATTGGTGCCGC 61.866 55.000 0.00 0.00 36.31 6.53
1116 3313 0.320247 CTCTTGAGCCTGTCAGCGTT 60.320 55.000 0.00 0.00 36.21 4.84
1347 3544 4.111016 TGCGCGTCGTCGAGGAAT 62.111 61.111 18.54 0.00 39.71 3.01
1398 3595 1.305549 GAGGTCGGAGGTGGGGTAA 60.306 63.158 0.00 0.00 0.00 2.85
1464 3661 7.229306 TGTCAAAGATTGAATGAAACTAGTGCT 59.771 33.333 0.00 0.00 42.15 4.40
1488 3685 3.130869 GCAGATCAGATCAGACAGAGTGT 59.869 47.826 13.14 0.00 0.00 3.55
1508 3707 1.538849 CGACAGCTACATATGCAGGCA 60.539 52.381 1.58 0.00 0.00 4.75
1561 3766 1.193874 CAGGTTAAAGTTGACGGCGAC 59.806 52.381 16.62 8.59 0.00 5.19
1570 3775 3.287222 TGCACTTGCTCAGGTTAAAGTT 58.713 40.909 2.33 0.00 42.66 2.66
1595 3808 6.906659 AGAACGTAGAGAGAACGACAAAATA 58.093 36.000 2.27 0.00 42.90 1.40
1627 3840 3.132824 TGTGCTCGACAGATTCCACATAT 59.867 43.478 0.00 0.00 30.38 1.78
1631 3844 1.929836 GATGTGCTCGACAGATTCCAC 59.070 52.381 0.60 0.00 38.23 4.02
1647 3861 1.374252 GCCGTCCACGTCAAGATGT 60.374 57.895 0.00 0.00 37.74 3.06
1729 3943 3.568430 GGAAGATTCACCCGTTCTTGTTT 59.432 43.478 0.00 0.00 30.11 2.83
1788 4002 2.477863 GGGATGTTGTTGCTGCGATAAC 60.478 50.000 19.14 19.14 0.00 1.89
1789 4003 1.742831 GGGATGTTGTTGCTGCGATAA 59.257 47.619 0.00 0.00 0.00 1.75
1790 4004 1.339535 TGGGATGTTGTTGCTGCGATA 60.340 47.619 0.00 0.00 0.00 2.92
1791 4005 0.608856 TGGGATGTTGTTGCTGCGAT 60.609 50.000 0.00 0.00 0.00 4.58
1792 4006 0.608856 ATGGGATGTTGTTGCTGCGA 60.609 50.000 0.00 0.00 0.00 5.10
1796 4015 3.956199 CCAGATAATGGGATGTTGTTGCT 59.044 43.478 0.00 0.00 46.36 3.91
1828 4047 3.063997 GTCAAGTGACACACCTTTCTGTG 59.936 47.826 8.59 0.00 46.06 3.66
1829 4048 3.270877 GTCAAGTGACACACCTTTCTGT 58.729 45.455 8.59 0.00 44.18 3.41
1932 4154 3.438087 AGATCACAGCAATTTCGGAGTTG 59.562 43.478 0.00 0.00 0.00 3.16
1997 4228 3.705604 CAAAAGGTCTTTTCATGCGTGT 58.294 40.909 5.68 0.00 40.45 4.49
1998 4229 2.472488 GCAAAAGGTCTTTTCATGCGTG 59.528 45.455 0.00 0.00 40.45 5.34
2000 4231 1.715519 CGCAAAAGGTCTTTTCATGCG 59.284 47.619 19.47 19.47 44.85 4.73
2001 4232 2.061028 CCGCAAAAGGTCTTTTCATGC 58.939 47.619 5.79 7.02 40.45 4.06
2081 4316 1.135315 GTACAGGTACACGCGAATCCA 60.135 52.381 15.93 0.00 36.15 3.41
2196 4432 6.310467 GTCTTTTGTTTCCTCAACTTTTGTCC 59.690 38.462 0.00 0.00 36.21 4.02
2272 4513 2.969628 TCCCTTTTCTTCCATTTGGCA 58.030 42.857 0.00 0.00 34.44 4.92
2283 4524 3.166489 GTGATCGACGATCCCTTTTCT 57.834 47.619 29.72 0.00 38.20 2.52
2344 4585 6.293462 CGACTGAATCCTATGAATCGTGAGTA 60.293 42.308 0.00 0.00 0.00 2.59
2353 4595 3.104512 ACCCACGACTGAATCCTATGAA 58.895 45.455 0.00 0.00 0.00 2.57
2363 4605 0.037734 TAGCTCAGACCCACGACTGA 59.962 55.000 0.00 0.00 40.22 3.41
2429 5777 5.895636 TTTGCCACATACAGTAATCTTGG 57.104 39.130 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.