Multiple sequence alignment - TraesCS2A01G478800

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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 TraesCS2A01G478800 chr2A 100.000 6597 0 0 1 6597 717214492 717207896 0.000000e+00 12183.0
1 TraesCS2A01G478800 chr2D 94.857 3850 137 29 2664 6490 579587033 579583222 0.000000e+00 5956.0
2 TraesCS2A01G478800 chr2D 93.412 1867 91 14 521 2378 579589167 579587324 0.000000e+00 2737.0
3 TraesCS2A01G478800 chr2D 92.363 419 21 4 1 412 579589609 579589195 2.650000e-163 586.0
4 TraesCS2A01G478800 chr2D 95.437 263 11 1 2418 2680 579587315 579587054 1.020000e-112 418.0
5 TraesCS2A01G478800 chr2D 85.034 147 21 1 3672 3818 590162797 590162942 1.480000e-31 148.0
6 TraesCS2A01G478800 chr2B 93.426 2160 119 11 13 2162 697588781 697586635 0.000000e+00 3181.0
7 TraesCS2A01G478800 chr2B 94.122 1361 52 10 4665 6016 697575941 697574600 0.000000e+00 2045.0
8 TraesCS2A01G478800 chr2B 91.311 1358 85 8 2664 3991 697578169 697576815 0.000000e+00 1823.0
9 TraesCS2A01G478800 chr2B 93.599 578 26 5 6025 6597 697572224 697571653 0.000000e+00 852.0
10 TraesCS2A01G478800 chr2B 92.806 556 26 3 3981 4535 697576788 697576246 0.000000e+00 793.0
11 TraesCS2A01G478800 chr2B 95.076 264 11 2 2418 2680 697578452 697578190 1.320000e-111 414.0
12 TraesCS2A01G478800 chr2B 91.880 234 16 3 2147 2378 697578693 697578461 2.290000e-84 324.0
13 TraesCS2A01G478800 chr2B 85.714 147 20 1 3672 3818 714792379 714792524 3.190000e-33 154.0
14 TraesCS2A01G478800 chr6B 82.812 1024 155 14 842 1858 458578247 458579256 0.000000e+00 896.0
15 TraesCS2A01G478800 chr6B 83.831 569 69 10 2823 3375 458580737 458581298 2.730000e-143 520.0
16 TraesCS2A01G478800 chr6B 84.958 359 49 4 4174 4531 458581855 458582209 6.290000e-95 359.0
17 TraesCS2A01G478800 chr6B 83.732 209 29 4 3428 3631 458581300 458581508 6.750000e-45 193.0
18 TraesCS2A01G478800 chr6B 77.130 223 44 6 3673 3891 468372146 468371927 8.980000e-24 122.0
19 TraesCS2A01G478800 chr6D 86.216 798 107 3 908 1703 294086773 294087569 0.000000e+00 861.0
20 TraesCS2A01G478800 chr6D 84.561 570 63 11 2823 3375 294089474 294090035 5.820000e-150 542.0
21 TraesCS2A01G478800 chr6D 84.469 367 52 4 4167 4532 294090587 294090949 2.260000e-94 357.0
22 TraesCS2A01G478800 chr6D 85.238 210 25 5 3428 3631 294090037 294090246 1.860000e-50 211.0
23 TraesCS2A01G478800 chr6D 80.989 263 24 8 440 702 294085712 294085948 1.130000e-42 185.0
24 TraesCS2A01G478800 chr6D 79.235 183 32 6 3698 3878 429211649 429211471 8.980000e-24 122.0
25 TraesCS2A01G478800 chr6A 84.091 572 66 11 2821 3375 426634482 426633919 4.530000e-146 529.0
26 TraesCS2A01G478800 chr6A 84.741 367 51 4 4167 4532 426633376 426633014 4.860000e-96 363.0
27 TraesCS2A01G478800 chr6A 82.524 206 22 6 3428 3631 426633917 426633724 1.140000e-37 169.0
28 TraesCS2A01G478800 chr5A 79.358 218 40 5 3634 3850 199229203 199228990 1.480000e-31 148.0
29 TraesCS2A01G478800 chr5D 78.713 202 39 4 3650 3850 187941996 187942194 1.490000e-26 132.0
30 TraesCS2A01G478800 chr5B 77.064 218 44 6 3634 3850 161065870 161066082 3.230000e-23 121.0
31 TraesCS2A01G478800 chr4D 73.810 252 51 12 3647 3891 468476306 468476063 1.180000e-12 86.1
32 TraesCS2A01G478800 chr4B 86.076 79 11 0 3813 3891 587011273 587011195 1.180000e-12 86.1


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 TraesCS2A01G478800 chr2A 717207896 717214492 6596 True 12183.000000 12183 100.000000 1 6597 1 chr2A.!!$R1 6596
1 TraesCS2A01G478800 chr2D 579583222 579589609 6387 True 2424.250000 5956 94.017250 1 6490 4 chr2D.!!$R1 6489
2 TraesCS2A01G478800 chr2B 697586635 697588781 2146 True 3181.000000 3181 93.426000 13 2162 1 chr2B.!!$R1 2149
3 TraesCS2A01G478800 chr2B 697571653 697578693 7040 True 1041.833333 2045 93.132333 2147 6597 6 chr2B.!!$R2 4450
4 TraesCS2A01G478800 chr6B 458578247 458582209 3962 False 492.000000 896 83.833250 842 4531 4 chr6B.!!$F1 3689
5 TraesCS2A01G478800 chr6D 294085712 294090949 5237 False 431.200000 861 84.294600 440 4532 5 chr6D.!!$F1 4092
6 TraesCS2A01G478800 chr6A 426633014 426634482 1468 True 353.666667 529 83.785333 2821 4532 3 chr6A.!!$R1 1711

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
267 268 0.671163 TGGTTATGTGGTTCGCCGTC 60.671 55.000 0.00 0.0 41.18 4.79 F
1200 1894 2.354704 CGAGCCAGATCCCAAAGTACAA 60.355 50.000 0.00 0.0 0.00 2.41 F
1509 2212 0.028770 TGCAGTTGTCTTTTTCGCGG 59.971 50.000 6.13 0.0 0.00 6.46 F
1510 2213 0.660300 GCAGTTGTCTTTTTCGCGGG 60.660 55.000 6.13 0.0 0.00 6.13 F
2946 4592 0.249489 CCTCGTGTATGCCACCTAGC 60.249 60.000 0.00 0.0 41.26 3.42 F
4040 5765 1.340405 ACCTTCCAGGCAAGCTGTATG 60.340 52.381 0.00 0.0 39.63 2.39 F
4708 6710 3.563508 TCTTTATTTGCGCATGTGTGTG 58.436 40.909 12.75 0.0 38.87 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 2144 0.106519 ACAGTTTGAGGGCACAGCTT 60.107 50.000 0.00 0.00 0.00 3.74 R
2916 4562 0.320374 TACACGAGGAACCAGCTTGG 59.680 55.000 0.00 1.16 45.02 3.61 R
2945 4591 2.230508 CCACCATGGATCATGCTATTGC 59.769 50.000 21.47 0.00 40.96 3.56 R
3279 4925 2.500098 TGTATAAGCAAAGTCGCCTCCT 59.500 45.455 0.00 0.00 0.00 3.69 R
4549 6327 0.466555 GGTGCTGTTGGTGGTGGTAA 60.467 55.000 0.00 0.00 0.00 2.85 R
4950 6957 1.565759 ACACCTGCACCATACCATGAT 59.434 47.619 0.00 0.00 0.00 2.45 R
6385 10778 1.196012 AGTTACACCAGGGCTCTAGC 58.804 55.000 0.00 0.00 41.14 3.42 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
124 125 3.083349 TGGCTGTCCAGATCCCCG 61.083 66.667 0.00 0.00 37.47 5.73
267 268 0.671163 TGGTTATGTGGTTCGCCGTC 60.671 55.000 0.00 0.00 41.18 4.79
294 295 5.864474 GTGGTGATGATAATACGACTGGATC 59.136 44.000 0.00 0.00 0.00 3.36
312 320 7.577303 ACTGGATCCTCTGCTTTTGATTATAA 58.423 34.615 14.23 0.00 0.00 0.98
313 321 8.223330 ACTGGATCCTCTGCTTTTGATTATAAT 58.777 33.333 14.23 0.00 0.00 1.28
337 345 3.947910 AATGTTGCAACTTCTGGATGG 57.052 42.857 28.61 0.00 0.00 3.51
342 350 4.218200 TGTTGCAACTTCTGGATGGTATTG 59.782 41.667 28.61 0.00 0.00 1.90
357 365 7.559533 TGGATGGTATTGTTAGTGCACAATTAT 59.440 33.333 21.04 8.04 43.54 1.28
358 366 8.413229 GGATGGTATTGTTAGTGCACAATTATT 58.587 33.333 21.04 0.00 43.54 1.40
364 372 8.980143 ATTGTTAGTGCACAATTATTAACACC 57.020 30.769 21.04 0.00 43.54 4.16
365 373 7.753309 TGTTAGTGCACAATTATTAACACCT 57.247 32.000 21.04 0.00 0.00 4.00
366 374 7.812648 TGTTAGTGCACAATTATTAACACCTC 58.187 34.615 21.04 0.00 0.00 3.85
367 375 7.663905 TGTTAGTGCACAATTATTAACACCTCT 59.336 33.333 21.04 0.00 0.00 3.69
368 376 9.158233 GTTAGTGCACAATTATTAACACCTCTA 57.842 33.333 21.04 0.00 0.00 2.43
369 377 9.727859 TTAGTGCACAATTATTAACACCTCTAA 57.272 29.630 21.04 0.00 0.00 2.10
370 378 8.807948 AGTGCACAATTATTAACACCTCTAAT 57.192 30.769 21.04 0.00 0.00 1.73
371 379 8.893727 AGTGCACAATTATTAACACCTCTAATC 58.106 33.333 21.04 0.00 0.00 1.75
405 413 8.064336 AGATTCAGTAAACGGATACACTAGTT 57.936 34.615 0.00 0.00 0.00 2.24
423 433 3.030291 AGTTCACACAAAATGCTCCCAA 58.970 40.909 0.00 0.00 0.00 4.12
467 477 2.981400 TAGCGCTAAAGGCACAAAAC 57.019 45.000 16.33 0.00 41.91 2.43
478 488 4.419522 AGGCACAAAACGTATGTTGATC 57.580 40.909 12.07 0.00 38.62 2.92
779 809 7.309177 TCTGAGAAGCAATATACTAATCTCGC 58.691 38.462 0.00 0.00 35.70 5.03
810 1498 4.153475 CCTTGCAGCCAAAATTTCATTCAG 59.847 41.667 0.00 0.00 0.00 3.02
812 1500 4.309099 TGCAGCCAAAATTTCATTCAGTC 58.691 39.130 0.00 0.00 0.00 3.51
882 1570 5.276868 GCATGGTATGTCTTCGTAATGTGTC 60.277 44.000 0.00 0.00 0.00 3.67
945 1636 9.691362 TTTATGCTTTTTATCAGTTGGTTCTTC 57.309 29.630 0.00 0.00 0.00 2.87
949 1640 6.293462 GCTTTTTATCAGTTGGTTCTTCGAGT 60.293 38.462 0.00 0.00 0.00 4.18
1110 1804 5.106237 ACCAGTGTTGACGAATCTACTAGAC 60.106 44.000 0.00 0.00 32.45 2.59
1131 1825 5.013079 AGACTTGTATGATCACAACTGGGAA 59.987 40.000 0.00 0.00 34.75 3.97
1147 1841 7.500559 ACAACTGGGAATTTATAGAAGCTGATC 59.499 37.037 0.00 0.00 0.00 2.92
1200 1894 2.354704 CGAGCCAGATCCCAAAGTACAA 60.355 50.000 0.00 0.00 0.00 2.41
1322 2016 3.728385 AAGGCAAGCTAACAAGAGGAT 57.272 42.857 0.00 0.00 0.00 3.24
1420 2114 5.292765 GTGTCAATGAGAAGACAGAGTTGA 58.707 41.667 0.00 0.00 44.62 3.18
1427 2121 4.038522 TGAGAAGACAGAGTTGACTGAAGG 59.961 45.833 0.00 0.00 40.63 3.46
1455 2149 1.080705 GCAAGAAGCAGGCAAGCTG 60.081 57.895 5.21 0.00 45.89 4.24
1456 2150 1.803366 GCAAGAAGCAGGCAAGCTGT 61.803 55.000 5.21 0.00 45.89 4.40
1457 2151 0.039437 CAAGAAGCAGGCAAGCTGTG 60.039 55.000 5.21 1.64 45.89 3.66
1502 2205 3.181476 GGGAACACATTGCAGTTGTCTTT 60.181 43.478 1.68 0.00 0.00 2.52
1509 2212 0.028770 TGCAGTTGTCTTTTTCGCGG 59.971 50.000 6.13 0.00 0.00 6.46
1510 2213 0.660300 GCAGTTGTCTTTTTCGCGGG 60.660 55.000 6.13 0.00 0.00 6.13
1515 2218 2.112297 TCTTTTTCGCGGGTGCCT 59.888 55.556 6.13 0.00 38.08 4.75
1526 2229 2.024414 GCGGGTGCCTATTGAAGAAAT 58.976 47.619 0.00 0.00 33.98 2.17
1538 2241 9.651913 GCCTATTGAAGAAATAAACATGGAAAA 57.348 29.630 0.00 0.00 30.24 2.29
1721 2425 9.844790 CTCACACTTTCTATTGATTTATTTGCA 57.155 29.630 0.00 0.00 0.00 4.08
2010 2733 3.069729 TGGCACTCTCTCTCATCATCATG 59.930 47.826 0.00 0.00 0.00 3.07
2032 2755 2.472029 TGTTGTGGGAAATTTGGTGGT 58.528 42.857 0.00 0.00 0.00 4.16
2036 2759 3.643237 TGTGGGAAATTTGGTGGTTACA 58.357 40.909 0.00 0.00 0.00 2.41
2086 2813 2.028020 GGTTCCAGGAGTCGATCAAGTT 60.028 50.000 0.00 0.00 0.00 2.66
2158 2887 3.909086 GACAGTGCACTCCAGGCCC 62.909 68.421 18.64 0.00 0.00 5.80
2211 2940 9.103861 CCTTGGTTTTATTGCTTTTTAGTTTGA 57.896 29.630 0.00 0.00 0.00 2.69
2260 2994 8.135529 GGGTTAGTTTCATAATAAACATCCTGC 58.864 37.037 0.00 0.00 40.97 4.85
2267 3001 8.815565 TTCATAATAAACATCCTGCTTTACCA 57.184 30.769 0.00 0.00 0.00 3.25
2274 3008 3.011708 ACATCCTGCTTTACCATTCCCTT 59.988 43.478 0.00 0.00 0.00 3.95
2307 3041 3.027412 TGGGCTCTGTTTTTACTTGCAA 58.973 40.909 0.00 0.00 0.00 4.08
2404 3714 8.328758 TCAGTTATGACTTCTTGGGAATACATT 58.671 33.333 0.00 0.00 32.54 2.71
2459 3782 9.677567 TTGTTAATTTCAGTGCTATTTTCTCAC 57.322 29.630 0.00 0.00 0.00 3.51
2739 4110 7.868415 CCTTGTTAACCTAGGATCTTAATCTCG 59.132 40.741 17.98 1.52 32.12 4.04
2815 4194 1.296056 ATACAAGGACGCGCACAACC 61.296 55.000 5.73 4.52 0.00 3.77
2916 4562 2.504367 TCTAAGCCTTCAGTGCCAAAC 58.496 47.619 0.00 0.00 0.00 2.93
2945 4591 1.399714 TCCTCGTGTATGCCACCTAG 58.600 55.000 0.00 0.00 41.26 3.02
2946 4592 0.249489 CCTCGTGTATGCCACCTAGC 60.249 60.000 0.00 0.00 41.26 3.42
3130 4776 1.753073 GTGGCAATGGGATTCTTCCTG 59.247 52.381 0.00 0.00 42.20 3.86
3171 4817 4.260907 CCACGCAATATCACATTCCAGAAG 60.261 45.833 0.00 0.00 0.00 2.85
3245 4891 4.530161 AGACTGCTTTGGAGATTGTCTAGT 59.470 41.667 0.00 0.00 31.42 2.57
3246 4892 4.573900 ACTGCTTTGGAGATTGTCTAGTG 58.426 43.478 0.00 0.00 0.00 2.74
3476 5122 8.434589 AGGAAATTTATCAAGGAATGTTGGAA 57.565 30.769 0.00 0.00 0.00 3.53
3998 5677 9.891828 TCTAATGCATATAATTAAAGCGGTTTG 57.108 29.630 22.16 5.00 0.00 2.93
4040 5765 1.340405 ACCTTCCAGGCAAGCTGTATG 60.340 52.381 0.00 0.00 39.63 2.39
4177 5955 7.486647 AGATTAATGTGGAAATGTTGAGCATC 58.513 34.615 0.00 0.00 36.67 3.91
4644 6646 3.954200 TGAATGGCTACATTTGAGCTGA 58.046 40.909 0.00 0.00 46.89 4.26
4708 6710 3.563508 TCTTTATTTGCGCATGTGTGTG 58.436 40.909 12.75 0.00 38.87 3.82
5303 7310 6.599638 GCCAAACTGTTTCTAATATCCTGACT 59.400 38.462 2.13 0.00 0.00 3.41
5312 7319 9.606631 GTTTCTAATATCCTGACTGAATTCTGT 57.393 33.333 16.88 16.88 0.00 3.41
5314 7321 9.823647 TTCTAATATCCTGACTGAATTCTGTTC 57.176 33.333 17.78 11.88 0.00 3.18
5315 7322 8.981659 TCTAATATCCTGACTGAATTCTGTTCA 58.018 33.333 17.78 14.99 0.00 3.18
5316 7323 9.605275 CTAATATCCTGACTGAATTCTGTTCAA 57.395 33.333 17.78 7.58 0.00 2.69
5318 7325 6.998968 ATCCTGACTGAATTCTGTTCAATC 57.001 37.500 17.78 6.76 0.00 2.67
5377 7384 3.213206 ACTGTGTCTCTGCAAATCCAA 57.787 42.857 0.00 0.00 0.00 3.53
5378 7385 3.759581 ACTGTGTCTCTGCAAATCCAAT 58.240 40.909 0.00 0.00 0.00 3.16
5441 7448 8.897752 GTGAAATCTTCTTGCCTAGATTATTGT 58.102 33.333 0.00 0.00 39.53 2.71
5469 7476 8.959734 ACTTTTAAGTTATACGTCAAAATGCC 57.040 30.769 0.00 0.00 35.21 4.40
5481 7488 6.612306 ACGTCAAAATGCCTAATCTTCTTTC 58.388 36.000 0.00 0.00 0.00 2.62
5608 7615 3.265791 GAACATCTGAAGTAGGTGCCTG 58.734 50.000 0.12 0.00 41.45 4.85
5701 7708 8.385898 TCCATTTTGTTATAACAGTCGTCTTT 57.614 30.769 17.36 0.00 40.50 2.52
5917 7934 5.733154 ACATGGGGGCTAATGATAGATATGT 59.267 40.000 0.00 0.00 0.00 2.29
5985 8005 2.030185 GCATATGCCCTCTGCTCATTTG 60.030 50.000 17.26 0.00 42.00 2.32
6000 8020 6.296026 TGCTCATTTGTATACCCCTCAATAC 58.704 40.000 0.00 0.00 0.00 1.89
6016 8036 4.951254 TCAATACAACGACAGTTCCTTGA 58.049 39.130 0.00 0.00 38.79 3.02
6023 8043 3.919216 ACGACAGTTCCTTGATCTTGAG 58.081 45.455 0.00 0.00 0.00 3.02
6079 10467 7.202038 GCCCATATGATGTCTCTATTATGGCTA 60.202 40.741 3.65 0.00 33.71 3.93
6081 10469 9.926158 CCATATGATGTCTCTATTATGGCTATC 57.074 37.037 3.65 0.00 0.00 2.08
6177 10568 8.271398 ACATATATATTATTTACCCTCCCCCG 57.729 38.462 0.00 0.00 0.00 5.73
6248 10640 6.418057 AAAATTCCATCTGGTAAAGCAACA 57.582 33.333 0.00 0.00 36.34 3.33
6253 10645 5.136828 TCCATCTGGTAAAGCAACAGAAAA 58.863 37.500 0.00 0.00 43.65 2.29
6297 10690 7.894376 ATTGAATGTTTCACCAAAATAGCTG 57.106 32.000 0.00 0.00 39.87 4.24
6323 10716 3.266510 TCTGATATTTCAAGTGGCGCT 57.733 42.857 7.64 0.00 0.00 5.92
6357 10750 3.668447 AGTTACATCAGCTGACCACAAG 58.332 45.455 20.97 7.51 0.00 3.16
6378 10771 5.878406 AGTGTTGATATTCTCCTACAGGG 57.122 43.478 0.00 0.00 35.41 4.45
6385 10778 7.841282 TGATATTCTCCTACAGGGTCTAAAG 57.159 40.000 0.00 0.00 36.25 1.85
6387 10780 3.759815 TCTCCTACAGGGTCTAAAGCT 57.240 47.619 0.00 0.00 36.25 3.74
6419 10812 5.184479 TGGTGTAACTATGAGTACTGGTCAC 59.816 44.000 0.00 0.15 36.74 3.67
6467 10860 6.312180 TCGAGATAACATATCATCTGCAATGC 59.688 38.462 0.00 0.00 31.63 3.56
6490 10883 4.910195 TGTCTTCATGCTTTGTCACCTAT 58.090 39.130 0.00 0.00 0.00 2.57
6505 10898 2.374504 CACCTATGGATCTGGATTGCCT 59.625 50.000 0.00 0.00 34.31 4.75
6556 10949 1.262151 CAAGCAGTGCATTTTGGTTGC 59.738 47.619 19.20 9.71 43.20 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 125 2.203029 GGGATTCGAAGCGGGGAC 60.203 66.667 7.41 0.00 0.00 4.46
267 268 5.463392 CCAGTCGTATTATCATCACCACAAG 59.537 44.000 0.00 0.00 0.00 3.16
294 295 9.390795 CATTTCGATTATAATCAAAAGCAGAGG 57.609 33.333 22.22 5.16 35.11 3.69
312 320 3.820467 TCCAGAAGTTGCAACATTTCGAT 59.180 39.130 30.11 9.44 0.00 3.59
313 321 3.210227 TCCAGAAGTTGCAACATTTCGA 58.790 40.909 30.11 16.60 0.00 3.71
327 335 5.065218 GTGCACTAACAATACCATCCAGAAG 59.935 44.000 10.32 0.00 0.00 2.85
342 350 8.040716 AGAGGTGTTAATAATTGTGCACTAAC 57.959 34.615 19.41 16.32 0.00 2.34
357 365 7.058525 TCTCCTATCACGATTAGAGGTGTTAA 58.941 38.462 0.00 0.00 35.67 2.01
358 366 6.598503 TCTCCTATCACGATTAGAGGTGTTA 58.401 40.000 0.00 0.00 35.67 2.41
360 368 5.050126 TCTCCTATCACGATTAGAGGTGT 57.950 43.478 0.00 0.00 35.67 4.16
362 370 6.307776 TGAATCTCCTATCACGATTAGAGGT 58.692 40.000 0.00 0.00 0.00 3.85
364 372 7.447374 ACTGAATCTCCTATCACGATTAGAG 57.553 40.000 0.00 0.00 0.00 2.43
365 373 8.919777 TTACTGAATCTCCTATCACGATTAGA 57.080 34.615 0.00 0.00 0.00 2.10
366 374 9.400638 GTTTACTGAATCTCCTATCACGATTAG 57.599 37.037 0.00 0.00 0.00 1.73
367 375 8.074370 CGTTTACTGAATCTCCTATCACGATTA 58.926 37.037 0.00 0.00 0.00 1.75
368 376 6.918569 CGTTTACTGAATCTCCTATCACGATT 59.081 38.462 0.00 0.00 0.00 3.34
369 377 6.439599 CGTTTACTGAATCTCCTATCACGAT 58.560 40.000 0.00 0.00 0.00 3.73
370 378 5.220989 CCGTTTACTGAATCTCCTATCACGA 60.221 44.000 0.00 0.00 0.00 4.35
371 379 4.976731 CCGTTTACTGAATCTCCTATCACG 59.023 45.833 0.00 0.00 0.00 4.35
378 386 5.903810 AGTGTATCCGTTTACTGAATCTCC 58.096 41.667 0.00 0.00 0.00 3.71
405 413 2.665165 ACTTGGGAGCATTTTGTGTGA 58.335 42.857 0.00 0.00 0.00 3.58
423 433 1.635817 ATGCGGTATGCCCCTGAACT 61.636 55.000 0.00 0.00 45.60 3.01
478 488 3.973135 GCAAAGCGAATAATCTGATGCAG 59.027 43.478 0.00 0.00 0.00 4.41
724 754 9.399403 GGATACTTTTCTCTGAAAATGTTGAAC 57.601 33.333 6.02 0.00 31.38 3.18
945 1636 5.635280 ACATCATACAGAAAGTGACAACTCG 59.365 40.000 0.00 0.00 34.77 4.18
949 1640 5.308014 AGCACATCATACAGAAAGTGACAA 58.692 37.500 0.00 0.00 38.10 3.18
1110 1804 6.764308 AATTCCCAGTTGTGATCATACAAG 57.236 37.500 0.00 0.00 40.89 3.16
1131 1825 6.708054 CCCGAAAGTGATCAGCTTCTATAAAT 59.292 38.462 12.58 0.00 0.00 1.40
1147 1841 2.443887 TCGGTTAGAACCCGAAAGTG 57.556 50.000 5.85 0.00 46.53 3.16
1200 1894 9.023962 TGGCTAAATGATCAAAACAAAGTAGAT 57.976 29.630 0.00 0.00 0.00 1.98
1244 1938 6.963322 AGGAGTTATAAGAGAAATGTTGCCT 58.037 36.000 0.00 0.00 0.00 4.75
1420 2114 1.072159 GCTGCAGTGGACCTTCAGT 59.928 57.895 16.64 0.00 36.86 3.41
1427 2121 1.168407 TGCTTCTTGCTGCAGTGGAC 61.168 55.000 16.64 0.00 43.37 4.02
1449 2143 0.313043 CAGTTTGAGGGCACAGCTTG 59.687 55.000 0.00 0.00 0.00 4.01
1450 2144 0.106519 ACAGTTTGAGGGCACAGCTT 60.107 50.000 0.00 0.00 0.00 3.74
1451 2145 0.106519 AACAGTTTGAGGGCACAGCT 60.107 50.000 0.00 0.00 0.00 4.24
1452 2146 0.746659 AAACAGTTTGAGGGCACAGC 59.253 50.000 0.00 0.00 0.00 4.40
1453 2147 1.750778 ACAAACAGTTTGAGGGCACAG 59.249 47.619 29.10 3.15 43.26 3.66
1454 2148 1.476085 CACAAACAGTTTGAGGGCACA 59.524 47.619 29.10 0.00 43.26 4.57
1455 2149 1.802508 GCACAAACAGTTTGAGGGCAC 60.803 52.381 29.10 7.81 43.26 5.01
1456 2150 0.459489 GCACAAACAGTTTGAGGGCA 59.541 50.000 29.10 0.00 43.26 5.36
1457 2151 0.249447 GGCACAAACAGTTTGAGGGC 60.249 55.000 29.10 25.44 43.26 5.19
1502 2205 0.321741 TTCAATAGGCACCCGCGAAA 60.322 50.000 8.23 0.00 39.92 3.46
1509 2212 6.980397 CCATGTTTATTTCTTCAATAGGCACC 59.020 38.462 0.00 0.00 0.00 5.01
1510 2213 7.771183 TCCATGTTTATTTCTTCAATAGGCAC 58.229 34.615 0.00 0.00 0.00 5.01
1526 2229 6.869315 TGAGAACATCGTTTTCCATGTTTA 57.131 33.333 0.18 0.00 42.15 2.01
1538 2241 5.812642 GTCAATGTATCCTTGAGAACATCGT 59.187 40.000 0.00 0.00 33.49 3.73
1540 2243 7.044181 TCTGTCAATGTATCCTTGAGAACATC 58.956 38.462 0.00 0.00 33.49 3.06
1694 2398 9.294030 GCAAATAAATCAATAGAAAGTGTGAGG 57.706 33.333 0.00 0.00 0.00 3.86
1736 2441 9.465985 TGCATATGTATAACAGAAATGCAAATG 57.534 29.630 17.78 0.00 43.39 2.32
1783 2506 4.287067 AGAAGACTATCAAACTCAGGGCAA 59.713 41.667 0.00 0.00 0.00 4.52
1977 2700 3.997681 GAGAGAGTGCCACTTTTAAGTCC 59.002 47.826 0.00 0.00 37.08 3.85
2010 2733 3.070878 ACCACCAAATTTCCCACAACATC 59.929 43.478 0.00 0.00 0.00 3.06
2032 2755 6.971756 CACAACATCAAACAGTCATTGTGTAA 59.028 34.615 6.13 0.00 40.74 2.41
2036 2759 5.833406 TCACAACATCAAACAGTCATTGT 57.167 34.783 0.00 0.00 43.45 2.71
2042 2765 5.240183 CCTCAGAATCACAACATCAAACAGT 59.760 40.000 0.00 0.00 0.00 3.55
2086 2813 2.039480 AGCTCTGCTTCATCAAAGGTGA 59.961 45.455 0.00 0.00 33.89 4.02
2158 2887 3.686016 TCTAAGCTAAAAACAGCCAGGG 58.314 45.455 0.00 0.00 42.84 4.45
2165 2894 6.071952 CCAAGGCAAGATCTAAGCTAAAAACA 60.072 38.462 16.77 0.00 0.00 2.83
2257 2991 5.728637 AAGAAAAGGGAATGGTAAAGCAG 57.271 39.130 0.00 0.00 0.00 4.24
2260 2994 8.731275 AAAACAAAGAAAAGGGAATGGTAAAG 57.269 30.769 0.00 0.00 0.00 1.85
2267 3001 4.887071 GCCCAAAAACAAAGAAAAGGGAAT 59.113 37.500 0.00 0.00 37.22 3.01
2274 3008 4.817318 ACAGAGCCCAAAAACAAAGAAA 57.183 36.364 0.00 0.00 0.00 2.52
2307 3041 3.874543 TGTTAACGAGTGCACTGAAATGT 59.125 39.130 27.27 11.52 0.00 2.71
2378 3113 7.252612 TGTATTCCCAAGAAGTCATAACTGA 57.747 36.000 0.00 0.00 35.36 3.41
2418 3728 9.965824 TGAAATTAACAAGAGTTTCTTCCATTC 57.034 29.630 0.00 0.00 39.15 2.67
2424 3734 8.000780 AGCACTGAAATTAACAAGAGTTTCTT 57.999 30.769 0.00 0.00 39.15 2.52
2459 3782 2.998670 CACACCAAGACTAGTGATGCAG 59.001 50.000 0.00 0.00 37.43 4.41
2499 3823 2.225727 GCACACAAGCCAAAGGTAGTAC 59.774 50.000 0.00 0.00 0.00 2.73
2775 4154 6.493115 TGTATGCTGGAGGATTTTGAAAGAAA 59.507 34.615 0.00 0.00 0.00 2.52
2777 4156 5.569355 TGTATGCTGGAGGATTTTGAAAGA 58.431 37.500 0.00 0.00 0.00 2.52
2815 4194 6.682423 TGTATAGTCCAATTCAATGCACTG 57.318 37.500 0.00 0.00 0.00 3.66
2916 4562 0.320374 TACACGAGGAACCAGCTTGG 59.680 55.000 0.00 1.16 45.02 3.61
2945 4591 2.230508 CCACCATGGATCATGCTATTGC 59.769 50.000 21.47 0.00 40.96 3.56
2946 4592 3.493334 ACCACCATGGATCATGCTATTG 58.507 45.455 21.47 1.25 40.96 1.90
3130 4776 3.532542 GTGGTATGTAGTGAAAGGGAGC 58.467 50.000 0.00 0.00 0.00 4.70
3171 4817 4.558538 AAGCGAAAGATTGACATATGCC 57.441 40.909 1.58 0.00 38.91 4.40
3279 4925 2.500098 TGTATAAGCAAAGTCGCCTCCT 59.500 45.455 0.00 0.00 0.00 3.69
3471 5117 4.092279 TGGCACATCCACATTTATTCCAA 58.908 39.130 0.00 0.00 40.72 3.53
3476 5122 6.070653 ACAATTTCTGGCACATCCACATTTAT 60.071 34.615 0.00 0.00 40.72 1.40
3998 5677 5.049818 GGTGCTGACTAATCATGCATACTTC 60.050 44.000 0.00 0.00 39.52 3.01
4040 5765 9.853177 TTAATCAAAGGAAAGATAGAAGGATCC 57.147 33.333 2.48 2.48 0.00 3.36
4121 5859 5.965033 ATTGGATCCTACATTCAGTCACT 57.035 39.130 14.23 0.00 0.00 3.41
4177 5955 5.302823 TGATGAGGACATGAGTATACACAGG 59.697 44.000 12.48 12.48 36.82 4.00
4229 6007 8.964150 CGACACACATTACGAATGAATATAAGA 58.036 33.333 12.53 0.00 41.46 2.10
4324 6102 7.040132 TCACCAACATACTCACAAATAAATGCA 60.040 33.333 0.00 0.00 0.00 3.96
4537 6315 6.086011 TGGTGGTGGTAATCATAAAGGAAT 57.914 37.500 0.00 0.00 0.00 3.01
4549 6327 0.466555 GGTGCTGTTGGTGGTGGTAA 60.467 55.000 0.00 0.00 0.00 2.85
4644 6646 7.287810 AGTACATAGAACCAAGGTTGAACTTT 58.712 34.615 9.61 0.00 38.60 2.66
4697 6699 4.625311 TCACTACTAAATCACACACATGCG 59.375 41.667 0.00 0.00 0.00 4.73
4816 6818 6.038271 ACCTCTGTGTTCAAATCTTGTGTTAC 59.962 38.462 0.00 0.00 0.00 2.50
4950 6957 1.565759 ACACCTGCACCATACCATGAT 59.434 47.619 0.00 0.00 0.00 2.45
5303 7310 8.625786 TGAGATTGAAGATTGAACAGAATTCA 57.374 30.769 8.44 0.00 0.00 2.57
5313 7320 9.730705 AGTCTAAAACATGAGATTGAAGATTGA 57.269 29.630 0.00 0.00 0.00 2.57
5316 7323 9.956640 AGAAGTCTAAAACATGAGATTGAAGAT 57.043 29.630 0.00 0.00 0.00 2.40
5377 7384 7.065443 GGAACGGTAGCTTGACAAAACTATTAT 59.935 37.037 0.00 0.00 0.00 1.28
5378 7385 6.369615 GGAACGGTAGCTTGACAAAACTATTA 59.630 38.462 0.00 0.00 0.00 0.98
5620 7627 9.325198 CATCTGTAACTATTAAGTGCACCATAA 57.675 33.333 14.63 13.81 35.62 1.90
5733 7740 5.818678 AACACTACACACTTGATTCCCTA 57.181 39.130 0.00 0.00 0.00 3.53
5952 7969 3.713764 AGGGCATATGCTACTTCTTCTGT 59.286 43.478 26.12 0.35 41.70 3.41
5958 7978 2.421619 GCAGAGGGCATATGCTACTTC 58.578 52.381 26.12 16.07 43.01 3.01
5959 7979 2.557920 GCAGAGGGCATATGCTACTT 57.442 50.000 26.12 7.94 43.01 2.24
5985 8005 5.163478 ACTGTCGTTGTATTGAGGGGTATAC 60.163 44.000 0.00 0.00 0.00 1.47
6000 8020 4.058124 TCAAGATCAAGGAACTGTCGTTG 58.942 43.478 0.00 3.38 46.41 4.10
6079 10467 9.333724 GATGATTTGATTGCTTTAAATTGGGAT 57.666 29.630 0.00 0.00 0.00 3.85
6081 10469 8.495361 TGATGATTTGATTGCTTTAAATTGGG 57.505 30.769 0.00 0.00 0.00 4.12
6161 10552 2.267160 TGTCGGGGGAGGGTAAATAA 57.733 50.000 0.00 0.00 0.00 1.40
6162 10553 2.500269 ATGTCGGGGGAGGGTAAATA 57.500 50.000 0.00 0.00 0.00 1.40
6297 10690 5.967674 CGCCACTTGAAATATCAGATGAAAC 59.032 40.000 0.00 0.00 36.78 2.78
6323 10716 8.892723 CAGCTGATGTAACTTCAATGGTAAATA 58.107 33.333 8.42 0.00 0.00 1.40
6357 10750 5.364157 AGACCCTGTAGGAGAATATCAACAC 59.636 44.000 0.00 0.00 39.89 3.32
6378 10771 2.112190 ACCAGGGCTCTAGCTTTAGAC 58.888 52.381 0.00 0.00 41.70 2.59
6385 10778 1.196012 AGTTACACCAGGGCTCTAGC 58.804 55.000 0.00 0.00 41.14 3.42
6387 10780 4.215908 CTCATAGTTACACCAGGGCTCTA 58.784 47.826 0.00 0.00 0.00 2.43
6419 10812 2.168521 TCTCCTTGGTGGCTTTATCTCG 59.831 50.000 0.00 0.00 35.26 4.04
6467 10860 3.144506 AGGTGACAAAGCATGAAGACAG 58.855 45.455 0.00 0.00 0.00 3.51
6490 10883 2.041485 TGAAACAGGCAATCCAGATCCA 59.959 45.455 0.00 0.00 33.74 3.41
6505 10898 4.183865 CTCTGTCTGACAACACTGAAACA 58.816 43.478 12.16 0.00 0.00 2.83
6556 10949 7.117667 CCAAATCAAAAGGAAATTAAGAACGGG 59.882 37.037 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.