Multiple sequence alignment - TraesCS2A01G254600

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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 TraesCS2A01G254600 chr2A 100.000 2954 0 0 1 2954 387774955 387777908 0.000000e+00 5456
1 TraesCS2A01G254600 chr2B 94.882 2247 82 15 1 2219 360483661 360481420 0.000000e+00 3482
2 TraesCS2A01G254600 chr2B 90.517 116 5 2 2839 2954 360481437 360481328 6.600000e-32 148
3 TraesCS2A01G254600 chr2D 96.561 1541 38 6 669 2200 307155283 307156817 0.000000e+00 2538
4 TraesCS2A01G254600 chr2D 86.620 284 25 5 180 460 307136955 307137228 4.780000e-78 302
5 TraesCS2A01G254600 chr2D 89.385 179 15 3 460 636 307146718 307146894 3.830000e-54 222
6 TraesCS2A01G254600 chr2D 95.652 115 5 0 2836 2950 307156804 307156918 5.030000e-43 185
7 TraesCS2A01G254600 chrUn 96.935 620 18 1 2221 2840 83929032 83928414 0.000000e+00 1038
8 TraesCS2A01G254600 chr6D 96.452 620 21 1 2221 2840 464465381 464465999 0.000000e+00 1022
9 TraesCS2A01G254600 chr6D 96.290 620 23 0 2221 2840 14615547 14616166 0.000000e+00 1018
10 TraesCS2A01G254600 chr5B 96.129 620 23 1 2221 2840 680927255 680927873 0.000000e+00 1011
11 TraesCS2A01G254600 chr5B 95.652 621 26 1 2221 2841 10581063 10581682 0.000000e+00 996
12 TraesCS2A01G254600 chr3B 95.813 621 24 2 2221 2840 2501182 2501801 0.000000e+00 1002
13 TraesCS2A01G254600 chr7B 95.307 618 29 0 2221 2838 138474858 138475475 0.000000e+00 981
14 TraesCS2A01G254600 chr5D 95.169 621 28 2 2221 2841 129238890 129239508 0.000000e+00 979
15 TraesCS2A01G254600 chr1D 95.169 621 29 1 2220 2840 472002086 472001467 0.000000e+00 979


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 TraesCS2A01G254600 chr2A 387774955 387777908 2953 False 5456.0 5456 100.0000 1 2954 1 chr2A.!!$F1 2953
1 TraesCS2A01G254600 chr2B 360481328 360483661 2333 True 1815.0 3482 92.6995 1 2954 2 chr2B.!!$R1 2953
2 TraesCS2A01G254600 chr2D 307155283 307156918 1635 False 1361.5 2538 96.1065 669 2950 2 chr2D.!!$F3 2281
3 TraesCS2A01G254600 chrUn 83928414 83929032 618 True 1038.0 1038 96.9350 2221 2840 1 chrUn.!!$R1 619
4 TraesCS2A01G254600 chr6D 464465381 464465999 618 False 1022.0 1022 96.4520 2221 2840 1 chr6D.!!$F2 619
5 TraesCS2A01G254600 chr6D 14615547 14616166 619 False 1018.0 1018 96.2900 2221 2840 1 chr6D.!!$F1 619
6 TraesCS2A01G254600 chr5B 680927255 680927873 618 False 1011.0 1011 96.1290 2221 2840 1 chr5B.!!$F2 619
7 TraesCS2A01G254600 chr5B 10581063 10581682 619 False 996.0 996 95.6520 2221 2841 1 chr5B.!!$F1 620
8 TraesCS2A01G254600 chr3B 2501182 2501801 619 False 1002.0 1002 95.8130 2221 2840 1 chr3B.!!$F1 619
9 TraesCS2A01G254600 chr7B 138474858 138475475 617 False 981.0 981 95.3070 2221 2838 1 chr7B.!!$F1 617
10 TraesCS2A01G254600 chr5D 129238890 129239508 618 False 979.0 979 95.1690 2221 2841 1 chr5D.!!$F1 620
11 TraesCS2A01G254600 chr1D 472001467 472002086 619 True 979.0 979 95.1690 2220 2840 1 chr1D.!!$R1 620

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
40 41 0.035820 GGGGCTTACACCGTGATTCA 60.036 55.0 5.28 0.0 0.0 2.57 F
259 261 0.320374 TGGAGAGTAGGCCAACAACG 59.680 55.0 5.01 0.0 0.0 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1268 1299 1.000060 CGAAACCGAACCCTACTGTCA 60.000 52.381 0.00 0.00 0.0 3.58 R
2157 2198 0.604578 AATTGAAGCGCTGCCAACAT 59.395 45.000 22.49 14.26 0.0 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
32 33 1.002502 GTCACTGGGGGCTTACACC 60.003 63.158 0.00 0.00 0.00 4.16
34 35 2.528378 ACTGGGGGCTTACACCGT 60.528 61.111 0.00 0.00 0.00 4.83
39 40 0.746923 GGGGGCTTACACCGTGATTC 60.747 60.000 5.28 0.00 0.00 2.52
40 41 0.035820 GGGGCTTACACCGTGATTCA 60.036 55.000 5.28 0.00 0.00 2.57
77 78 8.675705 TGAAGACTAATTTGTCATGTTTCTCA 57.324 30.769 19.82 8.92 39.27 3.27
78 79 8.777413 TGAAGACTAATTTGTCATGTTTCTCAG 58.223 33.333 19.82 0.00 39.27 3.35
105 107 5.462530 TGAGATGTAGAACTTCACCGAAA 57.537 39.130 0.00 0.00 0.00 3.46
106 108 5.849510 TGAGATGTAGAACTTCACCGAAAA 58.150 37.500 0.00 0.00 0.00 2.29
127 129 3.545703 ACTAGCAATCAGGGCATGTAAC 58.454 45.455 0.00 0.00 0.00 2.50
149 151 0.884704 GCCACATCACCACAACTCGT 60.885 55.000 0.00 0.00 0.00 4.18
164 166 3.733236 TCGTTCGCCGAGAATTGAT 57.267 47.368 0.00 0.00 41.60 2.57
166 168 1.135228 TCGTTCGCCGAGAATTGATCA 60.135 47.619 0.00 0.00 41.60 2.92
179 181 6.958193 CGAGAATTGATCAAACAAAGCTACTC 59.042 38.462 13.09 9.28 33.44 2.59
192 194 1.298413 CTACTCGACATGGCGACGG 60.298 63.158 22.34 14.61 36.17 4.79
259 261 0.320374 TGGAGAGTAGGCCAACAACG 59.680 55.000 5.01 0.00 0.00 4.10
265 267 1.029947 GTAGGCCAACAACGGATGGG 61.030 60.000 5.01 0.00 37.43 4.00
267 269 2.340328 GGCCAACAACGGATGGGAC 61.340 63.158 0.00 0.00 37.43 4.46
269 271 1.004320 CCAACAACGGATGGGACGA 60.004 57.895 0.00 0.00 33.54 4.20
272 274 0.395312 AACAACGGATGGGACGACTT 59.605 50.000 0.00 0.00 34.93 3.01
287 289 2.421073 ACGACTTATGTCATCGACGGAA 59.579 45.455 9.22 0.00 43.06 4.30
303 305 2.645797 ACGGAAAGTTAGGGATTTGGGA 59.354 45.455 0.00 0.00 0.00 4.37
309 311 2.102588 AGTTAGGGATTTGGGATCGTCG 59.897 50.000 0.00 0.00 0.00 5.12
329 334 2.504175 CGGAGAAGTTAGGGATTTGGGA 59.496 50.000 0.00 0.00 0.00 4.37
334 339 6.101296 GGAGAAGTTAGGGATTTGGGAGATAA 59.899 42.308 0.00 0.00 0.00 1.75
355 360 9.972106 AGATAAGAATTTTTGAAGAGAGGTGAT 57.028 29.630 0.00 0.00 0.00 3.06
357 362 6.734104 AGAATTTTTGAAGAGAGGTGATCG 57.266 37.500 0.00 0.00 0.00 3.69
368 373 2.026822 AGAGGTGATCGAGCCATTTTGT 60.027 45.455 0.00 0.00 0.00 2.83
369 374 2.086869 AGGTGATCGAGCCATTTTGTG 58.913 47.619 0.00 0.00 0.00 3.33
370 375 1.468054 GGTGATCGAGCCATTTTGTGC 60.468 52.381 0.00 0.00 0.00 4.57
371 376 1.199789 GTGATCGAGCCATTTTGTGCA 59.800 47.619 0.00 0.00 0.00 4.57
372 377 1.885233 TGATCGAGCCATTTTGTGCAA 59.115 42.857 0.00 0.00 0.00 4.08
373 378 2.295629 TGATCGAGCCATTTTGTGCAAA 59.704 40.909 0.00 0.00 0.00 3.68
374 379 2.879002 TCGAGCCATTTTGTGCAAAA 57.121 40.000 11.77 11.77 43.48 2.44
419 431 3.187842 GGGTCATTTCACTTAACACCGAC 59.812 47.826 0.00 0.00 0.00 4.79
423 435 2.867287 TTCACTTAACACCGACGTGA 57.133 45.000 0.00 0.00 43.14 4.35
460 472 2.964740 ACAGTGACTAGTACGAGCGTA 58.035 47.619 2.52 0.00 0.00 4.42
461 473 3.529533 ACAGTGACTAGTACGAGCGTAT 58.470 45.455 6.00 0.00 32.82 3.06
462 474 4.686972 ACAGTGACTAGTACGAGCGTATA 58.313 43.478 6.00 0.36 32.82 1.47
463 475 4.505922 ACAGTGACTAGTACGAGCGTATAC 59.494 45.833 6.00 0.00 32.82 1.47
464 476 3.733224 AGTGACTAGTACGAGCGTATACG 59.267 47.826 20.87 20.87 43.27 3.06
495 510 3.188460 ACCGTACATTCATGTCTTGTTGC 59.812 43.478 0.00 0.00 41.97 4.17
514 529 7.416154 TGTTGCATTTAGTAACTGTACTGAC 57.584 36.000 6.77 0.00 42.52 3.51
515 530 6.425721 TGTTGCATTTAGTAACTGTACTGACC 59.574 38.462 6.77 0.00 42.52 4.02
517 532 5.929992 TGCATTTAGTAACTGTACTGACCAC 59.070 40.000 6.77 1.64 40.89 4.16
521 536 8.999431 CATTTAGTAACTGTACTGACCACATTT 58.001 33.333 6.77 0.00 40.89 2.32
536 551 6.204688 TGACCACATTTTTGAGTACAGTGATC 59.795 38.462 0.00 0.00 0.00 2.92
539 554 7.068103 ACCACATTTTTGAGTACAGTGATCAAA 59.932 33.333 14.54 14.54 40.25 2.69
542 557 9.337396 ACATTTTTGAGTACAGTGATCAAAGTA 57.663 29.630 16.52 0.22 42.19 2.24
546 561 8.958119 TTTGAGTACAGTGATCAAAGTAAGTT 57.042 30.769 14.54 0.00 37.86 2.66
549 564 8.082852 TGAGTACAGTGATCAAAGTAAGTTCTC 58.917 37.037 0.00 7.01 0.00 2.87
550 565 7.085116 AGTACAGTGATCAAAGTAAGTTCTCG 58.915 38.462 0.00 0.00 0.00 4.04
557 573 3.807622 TCAAAGTAAGTTCTCGTGGCAAG 59.192 43.478 0.00 0.00 0.00 4.01
567 583 5.122396 AGTTCTCGTGGCAAGTTTAATGATC 59.878 40.000 0.00 0.00 0.00 2.92
570 586 4.832248 TCGTGGCAAGTTTAATGATCTCT 58.168 39.130 0.00 0.00 0.00 3.10
625 641 7.064866 TCTTTGATTTGATCTGCTGGGATTAT 58.935 34.615 0.00 0.00 0.00 1.28
687 713 7.439955 ACAAGAACACTGACATATTCGTACAAA 59.560 33.333 0.00 0.00 0.00 2.83
699 725 1.228033 GTACAAACACTGGGCCGGT 60.228 57.895 13.59 13.59 0.00 5.28
971 998 1.665916 CCACTCACGCACAGTCCTG 60.666 63.158 0.00 0.00 0.00 3.86
1246 1277 0.741915 AGAAGCAGGTACGAGCTAGC 59.258 55.000 6.62 6.62 43.11 3.42
1247 1278 0.741915 GAAGCAGGTACGAGCTAGCT 59.258 55.000 19.45 19.45 43.11 3.32
1254 1285 3.411418 TACGAGCTAGCTGCCGTGC 62.411 63.158 30.84 13.69 44.08 5.34
1268 1299 2.023771 CGTGCATGTGAGCGACAGT 61.024 57.895 0.00 0.00 38.23 3.55
1272 1303 0.945743 GCATGTGAGCGACAGTGACA 60.946 55.000 0.00 0.00 38.23 3.58
1322 1354 2.388121 GCGAATGAATATGTTGCAGCC 58.612 47.619 0.00 0.00 0.00 4.85
1502 1534 4.035112 TCTCCGTTATAATCAACCCCACT 58.965 43.478 0.00 0.00 0.00 4.00
1639 1678 6.764379 TCCTTCCTTTCTTCTTCTTCTTCTC 58.236 40.000 0.00 0.00 0.00 2.87
1667 1706 1.380785 ACCTGCATGCATTCCCCAG 60.381 57.895 22.97 7.39 0.00 4.45
2206 2247 8.975410 ATTGTGAAGAATGTGTTATCAATGTG 57.025 30.769 0.00 0.00 0.00 3.21
2207 2248 7.509141 TGTGAAGAATGTGTTATCAATGTGT 57.491 32.000 0.00 0.00 0.00 3.72
2208 2249 7.584108 TGTGAAGAATGTGTTATCAATGTGTC 58.416 34.615 0.00 0.00 0.00 3.67
2209 2250 7.445096 TGTGAAGAATGTGTTATCAATGTGTCT 59.555 33.333 0.00 0.00 0.00 3.41
2210 2251 8.935844 GTGAAGAATGTGTTATCAATGTGTCTA 58.064 33.333 0.00 0.00 0.00 2.59
2211 2252 9.671279 TGAAGAATGTGTTATCAATGTGTCTAT 57.329 29.630 0.00 0.00 0.00 1.98
2271 2312 2.404995 CGTAGGTCCGCCTCGTCTT 61.405 63.158 0.00 0.00 45.64 3.01
2505 2547 3.319405 TGTCTCCGGCAGATCTATCTTTC 59.681 47.826 0.00 0.00 34.22 2.62
2531 2573 1.089112 TTGCTCGGATCTCGTCGTTA 58.911 50.000 0.00 0.00 40.32 3.18
2589 2631 6.598064 CCTTCCAACCTACGTTATTCTTCATT 59.402 38.462 0.00 0.00 0.00 2.57
2642 2684 2.499685 GGGCCTTAGCACGACGAT 59.500 61.111 0.84 0.00 42.56 3.73
2680 2722 0.180406 AACAAGTTGTGCCCGACTCT 59.820 50.000 9.79 0.00 34.00 3.24
2815 2857 7.940688 TGTACTGCCATGATTGAAGATGAATAT 59.059 33.333 0.00 0.00 0.00 1.28
2895 2937 7.284034 CCTTAGCTGACTGGAATGTAAAATCAT 59.716 37.037 0.00 0.00 0.00 2.45
2909 2957 6.908825 TGTAAAATCATGTCAGTAACAAGGC 58.091 36.000 0.00 0.00 42.37 4.35
2910 2958 4.685169 AAATCATGTCAGTAACAAGGCG 57.315 40.909 0.00 0.00 42.37 5.52
2911 2959 1.438651 TCATGTCAGTAACAAGGCGC 58.561 50.000 0.00 0.00 42.37 6.53
2912 2960 1.155889 CATGTCAGTAACAAGGCGCA 58.844 50.000 10.83 0.00 42.37 6.09
2913 2961 1.129251 CATGTCAGTAACAAGGCGCAG 59.871 52.381 10.83 0.00 42.37 5.18
2914 2962 0.602638 TGTCAGTAACAAGGCGCAGG 60.603 55.000 10.83 0.00 34.03 4.85
2915 2963 0.320421 GTCAGTAACAAGGCGCAGGA 60.320 55.000 10.83 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.122632 TAAGCCCCCAGTGACGTTCA 61.123 55.000 0.00 0.00 0.00 3.18
14 15 1.002502 GGTGTAAGCCCCCAGTGAC 60.003 63.158 0.00 0.00 0.00 3.67
17 18 2.528378 ACGGTGTAAGCCCCCAGT 60.528 61.111 0.00 0.00 0.00 4.00
34 35 3.274095 TCAACAGGTGTGTGTGAATCA 57.726 42.857 0.00 0.00 36.84 2.57
39 40 2.632377 AGTCTTCAACAGGTGTGTGTG 58.368 47.619 0.00 0.00 36.84 3.82
40 41 4.481368 TTAGTCTTCAACAGGTGTGTGT 57.519 40.909 0.00 0.00 36.84 3.72
50 51 9.387123 GAGAAACATGACAAATTAGTCTTCAAC 57.613 33.333 0.00 0.00 39.27 3.18
77 78 5.233988 GTGAAGTTCTACATCTCAAGCACT 58.766 41.667 4.17 0.00 0.00 4.40
78 79 4.390297 GGTGAAGTTCTACATCTCAAGCAC 59.610 45.833 4.17 0.00 0.00 4.40
105 107 2.814805 ACATGCCCTGATTGCTAGTT 57.185 45.000 0.00 0.00 0.00 2.24
106 108 3.545703 GTTACATGCCCTGATTGCTAGT 58.454 45.455 0.00 0.00 0.00 2.57
127 129 0.603707 AGTTGTGGTGATGTGGCTCG 60.604 55.000 0.00 0.00 0.00 5.03
149 151 3.070748 TGTTTGATCAATTCTCGGCGAA 58.929 40.909 12.13 0.00 35.78 4.70
164 166 3.745975 CCATGTCGAGTAGCTTTGTTTGA 59.254 43.478 0.00 0.00 0.00 2.69
166 168 2.484264 GCCATGTCGAGTAGCTTTGTTT 59.516 45.455 0.00 0.00 0.00 2.83
269 271 4.451629 ACTTTCCGTCGATGACATAAGT 57.548 40.909 6.11 6.96 32.09 2.24
272 274 4.202080 CCCTAACTTTCCGTCGATGACATA 60.202 45.833 6.11 0.00 32.09 2.29
287 289 3.431766 CGACGATCCCAAATCCCTAACTT 60.432 47.826 0.00 0.00 0.00 2.66
303 305 2.431954 TCCCTAACTTCTCCGACGAT 57.568 50.000 0.00 0.00 0.00 3.73
309 311 3.780850 TCTCCCAAATCCCTAACTTCTCC 59.219 47.826 0.00 0.00 0.00 3.71
329 334 9.972106 ATCACCTCTCTTCAAAAATTCTTATCT 57.028 29.630 0.00 0.00 0.00 1.98
334 339 6.467677 TCGATCACCTCTCTTCAAAAATTCT 58.532 36.000 0.00 0.00 0.00 2.40
355 360 2.159184 TGTTTTGCACAAAATGGCTCGA 60.159 40.909 11.39 0.00 41.64 4.04
387 392 3.068590 AGTGAAATGACCCACTTTGCAAG 59.931 43.478 0.00 0.00 40.40 4.01
388 393 3.030291 AGTGAAATGACCCACTTTGCAA 58.970 40.909 0.00 0.00 40.40 4.08
389 394 2.665165 AGTGAAATGACCCACTTTGCA 58.335 42.857 0.00 0.00 40.40 4.08
419 431 0.663568 GACCAGTCCACGACTTCACG 60.664 60.000 0.00 0.00 41.37 4.35
423 435 0.828022 TGTTGACCAGTCCACGACTT 59.172 50.000 0.00 0.00 41.37 3.01
443 455 4.033711 CGTATACGCTCGTACTAGTCAC 57.966 50.000 13.08 0.00 33.01 3.67
463 475 1.014044 AATGTACGGTCACTGCAGCG 61.014 55.000 15.27 11.90 42.99 5.18
464 476 0.721718 GAATGTACGGTCACTGCAGC 59.278 55.000 15.27 0.00 0.00 5.25
466 478 2.289382 ACATGAATGTACGGTCACTGCA 60.289 45.455 0.00 0.00 39.68 4.41
467 479 2.346803 ACATGAATGTACGGTCACTGC 58.653 47.619 0.00 0.00 39.68 4.40
468 480 3.849911 AGACATGAATGTACGGTCACTG 58.150 45.455 0.00 4.32 41.95 3.66
469 481 4.245660 CAAGACATGAATGTACGGTCACT 58.754 43.478 0.00 0.00 41.95 3.41
495 510 8.547967 AATGTGGTCAGTACAGTTACTAAATG 57.452 34.615 0.00 0.00 36.31 2.32
514 529 6.558771 TGATCACTGTACTCAAAAATGTGG 57.441 37.500 0.00 0.00 0.00 4.17
515 530 8.131100 ACTTTGATCACTGTACTCAAAAATGTG 58.869 33.333 14.18 7.87 38.15 3.21
521 536 8.958119 AACTTACTTTGATCACTGTACTCAAA 57.042 30.769 13.18 13.18 36.74 2.69
536 551 3.560068 ACTTGCCACGAGAACTTACTTTG 59.440 43.478 0.00 0.00 0.00 2.77
539 554 3.470645 AACTTGCCACGAGAACTTACT 57.529 42.857 0.00 0.00 0.00 2.24
542 557 4.819630 TCATTAAACTTGCCACGAGAACTT 59.180 37.500 0.00 0.00 0.00 2.66
546 561 4.832248 AGATCATTAAACTTGCCACGAGA 58.168 39.130 0.00 0.00 0.00 4.04
549 564 4.631377 TCAGAGATCATTAAACTTGCCACG 59.369 41.667 0.00 0.00 0.00 4.94
550 565 6.493116 CATCAGAGATCATTAAACTTGCCAC 58.507 40.000 0.00 0.00 0.00 5.01
567 583 9.859427 TTTTGGATTAAGTAAAATGCATCAGAG 57.141 29.630 0.00 0.00 37.10 3.35
587 603 9.590451 GATCAAATCAAAGATTAGCATTTTGGA 57.410 29.630 0.00 0.00 33.70 3.53
625 641 1.378531 AGCACAAAAGAGTTGCGACA 58.621 45.000 6.90 0.00 0.00 4.35
699 725 4.557554 CCTGTCACACACTGGCAA 57.442 55.556 0.00 0.00 37.30 4.52
719 745 0.994995 GATCCGCATCGAATGATCCG 59.005 55.000 0.00 0.00 35.50 4.18
971 998 3.953874 GCTGTTTAGCTTAGCTTAGGC 57.046 47.619 13.44 6.80 46.57 3.93
1113 1144 1.216444 GTCAGATGCAGCCTCGTCA 59.784 57.895 0.00 0.00 0.00 4.35
1189 1220 2.893398 GGAGACCTTGACGGCGAT 59.107 61.111 16.62 0.00 35.61 4.58
1246 1277 4.156622 CGCTCACATGCACGGCAG 62.157 66.667 0.00 0.00 43.65 4.85
1247 1278 4.678499 TCGCTCACATGCACGGCA 62.678 61.111 0.00 1.01 44.86 5.69
1254 1285 1.066136 CTGTCACTGTCGCTCACATG 58.934 55.000 0.00 0.00 33.23 3.21
1268 1299 1.000060 CGAAACCGAACCCTACTGTCA 60.000 52.381 0.00 0.00 0.00 3.58
1272 1303 1.206371 CATCCGAAACCGAACCCTACT 59.794 52.381 0.00 0.00 0.00 2.57
1322 1354 2.051345 GCCTTGCCGAACACGTTG 60.051 61.111 0.00 0.00 0.00 4.10
1502 1534 2.232941 GTCGGTGATGGTCTTCTTGGTA 59.767 50.000 0.00 0.00 0.00 3.25
1639 1678 1.210931 CATGCAGGTGCGACAAAGG 59.789 57.895 0.00 0.00 45.83 3.11
1667 1706 2.034879 CCCACATCGTCAGCACACC 61.035 63.158 0.00 0.00 0.00 4.16
2157 2198 0.604578 AATTGAAGCGCTGCCAACAT 59.395 45.000 22.49 14.26 0.00 2.71
2210 2251 9.121658 GCAGAAACCCTAGCTTTTAACTTATAT 57.878 33.333 0.00 0.00 0.00 0.86
2211 2252 7.555195 GGCAGAAACCCTAGCTTTTAACTTATA 59.445 37.037 0.00 0.00 0.00 0.98
2212 2253 6.377429 GGCAGAAACCCTAGCTTTTAACTTAT 59.623 38.462 0.00 0.00 0.00 1.73
2213 2254 5.708697 GGCAGAAACCCTAGCTTTTAACTTA 59.291 40.000 0.00 0.00 0.00 2.24
2214 2255 4.523173 GGCAGAAACCCTAGCTTTTAACTT 59.477 41.667 0.00 0.00 0.00 2.66
2215 2256 4.079970 GGCAGAAACCCTAGCTTTTAACT 58.920 43.478 0.00 0.00 0.00 2.24
2216 2257 4.079970 AGGCAGAAACCCTAGCTTTTAAC 58.920 43.478 0.00 0.00 0.00 2.01
2217 2258 4.042934 AGAGGCAGAAACCCTAGCTTTTAA 59.957 41.667 0.00 0.00 31.41 1.52
2218 2259 3.587506 AGAGGCAGAAACCCTAGCTTTTA 59.412 43.478 0.00 0.00 31.41 1.52
2355 2397 1.880027 GCAGGACACAAACCCTAACAG 59.120 52.381 0.00 0.00 0.00 3.16
2443 2485 0.313987 CGATGCTAGATACACCGCCA 59.686 55.000 0.00 0.00 0.00 5.69
2451 2493 1.070134 GCCCACCAACGATGCTAGATA 59.930 52.381 0.00 0.00 0.00 1.98
2481 2523 0.955178 ATAGATCTGCCGGAGACACG 59.045 55.000 5.05 0.00 31.75 4.49
2493 2535 5.923204 AGCAAATCCACGAAAGATAGATCT 58.077 37.500 0.00 0.00 39.22 2.75
2505 2547 1.212616 GAGATCCGAGCAAATCCACG 58.787 55.000 0.00 0.00 0.00 4.94
2531 2573 3.973657 AGACACACAAACGTAGACGAAT 58.026 40.909 9.41 0.00 43.02 3.34
2642 2684 3.890756 TGTTGTAGTAGACAGTCGGGAAA 59.109 43.478 0.00 0.00 39.88 3.13
2680 2722 2.366837 ATCACCCCTCCATCGCCA 60.367 61.111 0.00 0.00 0.00 5.69
2895 2937 0.602638 CCTGCGCCTTGTTACTGACA 60.603 55.000 4.18 0.00 36.19 3.58
2909 2957 2.924185 CCTTGATGGCTATCCTGCG 58.076 57.895 7.68 0.00 32.09 5.18


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

AutoCloner maintained by Alex Coulton.