Multiple sequence alignment - TraesCS2A01G389500

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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 TraesCS2A01G389500 chr2A 100.000 4024 0 0 1 4024 638032822 638036845 0.000000e+00 7432.0
1 TraesCS2A01G389500 chr2D 94.911 3498 130 21 494 3969 492713125 492716596 0.000000e+00 5430.0
2 TraesCS2A01G389500 chr2D 85.654 237 22 6 1 237 492712749 492712973 5.200000e-59 239.0
3 TraesCS2A01G389500 chr2D 93.333 60 4 0 3965 4024 492716625 492716684 5.540000e-14 89.8
4 TraesCS2A01G389500 chr2B 93.636 1980 88 9 450 2417 579382229 579384182 0.000000e+00 2924.0
5 TraesCS2A01G389500 chr2B 96.966 758 20 3 2415 3171 579384410 579385165 0.000000e+00 1269.0
6 TraesCS2A01G389500 chr2B 89.655 464 26 12 3583 4024 579385795 579386258 4.510000e-159 571.0
7 TraesCS2A01G389500 chr2B 86.856 388 37 5 3210 3585 579385173 579385558 4.810000e-114 422.0
8 TraesCS2A01G389500 chr2B 92.893 197 13 1 48 244 579381855 579382050 6.580000e-73 285.0
9 TraesCS2A01G389500 chr2B 87.821 156 15 2 243 397 463024245 463024093 3.200000e-41 180.0
10 TraesCS2A01G389500 chr2B 87.742 155 14 3 243 395 458962289 458962440 4.130000e-40 176.0
11 TraesCS2A01G389500 chr2B 92.063 63 5 0 3385 3447 579385280 579385342 5.540000e-14 89.8
12 TraesCS2A01G389500 chr2B 97.500 40 1 0 413 452 579382087 579382126 7.220000e-08 69.4
13 TraesCS2A01G389500 chr2B 97.368 38 1 0 1 38 579381253 579381290 9.340000e-07 65.8
14 TraesCS2A01G389500 chr7A 90.132 152 11 2 247 397 498582735 498582883 1.140000e-45 195.0
15 TraesCS2A01G389500 chr3D 87.879 165 14 4 235 397 551595091 551594931 5.310000e-44 189.0
16 TraesCS2A01G389500 chr4B 87.821 156 15 2 243 397 111706932 111706780 3.200000e-41 180.0
17 TraesCS2A01G389500 chr4B 97.619 42 1 0 3165 3206 302866985 302867026 5.580000e-09 73.1
18 TraesCS2A01G389500 chr4B 93.617 47 3 0 3160 3206 660491587 660491541 2.010000e-08 71.3
19 TraesCS2A01G389500 chr7D 87.821 156 14 3 242 395 605142916 605142764 1.150000e-40 178.0
20 TraesCS2A01G389500 chr7D 87.662 154 14 3 244 395 34736214 34736064 1.490000e-39 174.0
21 TraesCS2A01G389500 chr5A 86.957 161 16 4 237 395 270828333 270828176 4.130000e-40 176.0
22 TraesCS2A01G389500 chr3B 87.742 155 13 4 244 395 786911618 786911769 4.130000e-40 176.0
23 TraesCS2A01G389500 chr1B 77.922 308 49 12 1733 2029 653733480 653733779 1.490000e-39 174.0
24 TraesCS2A01G389500 chr1B 77.597 308 50 12 1733 2029 653704614 653704913 6.920000e-38 169.0
25 TraesCS2A01G389500 chr1B 91.667 48 3 1 3171 3218 44932827 44932873 9.340000e-07 65.8
26 TraesCS2A01G389500 chr1D 95.556 45 2 0 3164 3208 474881320 474881276 5.580000e-09 73.1
27 TraesCS2A01G389500 chrUn 93.617 47 3 0 3160 3206 110464831 110464785 2.010000e-08 71.3
28 TraesCS2A01G389500 chr4D 100.000 38 0 0 3171 3208 79706059 79706022 2.010000e-08 71.3
29 TraesCS2A01G389500 chr4D 97.561 41 1 0 3168 3208 362116410 362116450 2.010000e-08 71.3
30 TraesCS2A01G389500 chr1A 93.333 45 3 0 3164 3208 570392125 570392081 2.600000e-07 67.6


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 TraesCS2A01G389500 chr2A 638032822 638036845 4023 False 7432.0 7432 100.000000 1 4024 1 chr2A.!!$F1 4023
1 TraesCS2A01G389500 chr2D 492712749 492716684 3935 False 1919.6 5430 91.299333 1 4024 3 chr2D.!!$F1 4023
2 TraesCS2A01G389500 chr2B 579381253 579386258 5005 False 712.0 2924 93.367125 1 4024 8 chr2B.!!$F2 4023

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
120 676 0.108472 CTCTTCTGTCGCCATCTGCA 60.108 55.0 0.0 0.0 41.33 4.41 F
697 1394 0.179100 CTACACCCTCCGCTGACATG 60.179 60.0 0.0 0.0 0.00 3.21 F
778 1475 0.248661 CCTGTCTCTGATGTACCGCG 60.249 60.0 0.0 0.0 0.00 6.46 F
959 1661 0.307760 GGAGCAAAACAGTGACCACG 59.692 55.0 0.0 0.0 36.20 4.94 F
1628 2340 0.392461 ACGTGTAGCCATTCCGCATT 60.392 50.0 0.0 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1460 2172 0.107410 AACGGAGCACTTGTTGGACA 60.107 50.000 0.00 0.0 0.00 4.02 R
1628 2340 1.068402 CATGAGTGCGATTGCCACAAA 60.068 47.619 1.50 0.0 41.78 2.83 R
1853 2575 2.616842 GACAAGCCGAGAAACCAAAAGA 59.383 45.455 0.00 0.0 0.00 2.52 R
2280 3002 2.686915 GGTGCGTAGACTAGCTTAAGGA 59.313 50.000 4.29 0.0 0.00 3.36 R
3265 4225 0.041576 GAACCACCGAAACAGCGAAC 60.042 55.000 0.00 0.0 0.00 3.95 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 4.625028 TCAGAGATTCAGAATATGCACCG 58.375 43.478 0.00 0.00 0.00 4.94
43 44 0.249447 TCAGAATATGCACCGGAGCG 60.249 55.000 19.24 2.89 37.31 5.03
120 676 0.108472 CTCTTCTGTCGCCATCTGCA 60.108 55.000 0.00 0.00 41.33 4.41
193 749 1.517242 CTGTGACTTCAAGAGCCCAC 58.483 55.000 0.00 0.00 34.62 4.61
203 759 4.593864 GAGCCCACCGATCGGAGC 62.594 72.222 39.55 33.14 38.96 4.70
213 769 1.067250 GATCGGAGCTGGACAGAGC 59.933 63.158 3.00 0.00 39.46 4.09
231 787 4.883585 CAGAGCTAAATAAATGAGCCCACA 59.116 41.667 0.00 0.00 36.87 4.17
244 800 3.068024 TGAGCCCACAAAAAGTTGCTTAG 59.932 43.478 0.00 0.00 38.39 2.18
246 802 3.319122 AGCCCACAAAAAGTTGCTTAGAG 59.681 43.478 0.00 0.00 38.39 2.43
248 804 3.005791 CCCACAAAAAGTTGCTTAGAGGG 59.994 47.826 0.00 0.00 38.39 4.30
250 806 4.499696 CCACAAAAAGTTGCTTAGAGGGTG 60.500 45.833 0.00 0.00 38.39 4.61
251 807 4.097892 CACAAAAAGTTGCTTAGAGGGTGT 59.902 41.667 0.00 0.00 38.39 4.16
252 808 4.709886 ACAAAAAGTTGCTTAGAGGGTGTT 59.290 37.500 0.00 0.00 38.39 3.32
253 809 5.186992 ACAAAAAGTTGCTTAGAGGGTGTTT 59.813 36.000 0.00 0.00 38.39 2.83
254 810 4.918810 AAAGTTGCTTAGAGGGTGTTTG 57.081 40.909 0.00 0.00 0.00 2.93
258 814 3.306472 TGCTTAGAGGGTGTTTGGTTT 57.694 42.857 0.00 0.00 0.00 3.27
260 816 3.219281 GCTTAGAGGGTGTTTGGTTTCA 58.781 45.455 0.00 0.00 0.00 2.69
261 817 3.253432 GCTTAGAGGGTGTTTGGTTTCAG 59.747 47.826 0.00 0.00 0.00 3.02
264 820 3.976015 AGAGGGTGTTTGGTTTCAGAAA 58.024 40.909 0.00 0.00 0.00 2.52
265 821 3.699538 AGAGGGTGTTTGGTTTCAGAAAC 59.300 43.478 16.63 16.63 40.65 2.78
266 822 3.699538 GAGGGTGTTTGGTTTCAGAAACT 59.300 43.478 22.60 2.60 41.14 2.66
269 825 5.012664 AGGGTGTTTGGTTTCAGAAACTTTT 59.987 36.000 22.60 0.31 41.14 2.27
291 847 6.844097 TTTTGTGTTGGGACTAGAAAAAGT 57.156 33.333 0.00 0.00 0.00 2.66
292 848 6.445357 TTTGTGTTGGGACTAGAAAAAGTC 57.555 37.500 0.00 0.00 44.31 3.01
302 858 6.483385 GACTAGAAAAAGTCCCTAGCAAAC 57.517 41.667 0.00 0.00 40.06 2.93
303 859 5.314529 ACTAGAAAAAGTCCCTAGCAAACC 58.685 41.667 0.00 0.00 34.70 3.27
304 860 4.178956 AGAAAAAGTCCCTAGCAAACCA 57.821 40.909 0.00 0.00 0.00 3.67
305 861 4.542697 AGAAAAAGTCCCTAGCAAACCAA 58.457 39.130 0.00 0.00 0.00 3.67
306 862 4.959839 AGAAAAAGTCCCTAGCAAACCAAA 59.040 37.500 0.00 0.00 0.00 3.28
307 863 4.665833 AAAAGTCCCTAGCAAACCAAAC 57.334 40.909 0.00 0.00 0.00 2.93
308 864 3.306472 AAGTCCCTAGCAAACCAAACA 57.694 42.857 0.00 0.00 0.00 2.83
309 865 2.583143 AGTCCCTAGCAAACCAAACAC 58.417 47.619 0.00 0.00 0.00 3.32
310 866 1.265905 GTCCCTAGCAAACCAAACACG 59.734 52.381 0.00 0.00 0.00 4.49
311 867 1.141254 TCCCTAGCAAACCAAACACGA 59.859 47.619 0.00 0.00 0.00 4.35
312 868 2.159382 CCCTAGCAAACCAAACACGAT 58.841 47.619 0.00 0.00 0.00 3.73
313 869 2.095263 CCCTAGCAAACCAAACACGATG 60.095 50.000 0.00 0.00 0.00 3.84
314 870 2.095263 CCTAGCAAACCAAACACGATGG 60.095 50.000 0.00 0.00 43.84 3.51
315 871 0.673437 AGCAAACCAAACACGATGGG 59.327 50.000 0.00 0.00 42.48 4.00
316 872 0.671251 GCAAACCAAACACGATGGGA 59.329 50.000 0.00 0.00 42.48 4.37
317 873 1.067821 GCAAACCAAACACGATGGGAA 59.932 47.619 0.00 0.00 42.48 3.97
318 874 2.288763 GCAAACCAAACACGATGGGAAT 60.289 45.455 0.00 0.00 42.48 3.01
319 875 3.801983 GCAAACCAAACACGATGGGAATT 60.802 43.478 0.00 0.00 42.48 2.17
320 876 4.376146 CAAACCAAACACGATGGGAATTT 58.624 39.130 0.00 0.00 42.48 1.82
321 877 4.681074 AACCAAACACGATGGGAATTTT 57.319 36.364 0.00 0.00 42.48 1.82
322 878 4.681074 ACCAAACACGATGGGAATTTTT 57.319 36.364 0.00 0.00 42.48 1.94
357 913 9.783256 TTGCTAAAAGTTCTTAGAAACACTTTC 57.217 29.630 9.95 1.57 38.28 2.62
538 1235 3.041508 TCAGAGAGCTGATATGCATGC 57.958 47.619 11.82 11.82 45.88 4.06
620 1317 1.374631 TGAGCACGCTCATGTGACC 60.375 57.895 17.54 0.00 46.80 4.02
687 1384 2.434359 GCACCGCACTACACCCTC 60.434 66.667 0.00 0.00 0.00 4.30
697 1394 0.179100 CTACACCCTCCGCTGACATG 60.179 60.000 0.00 0.00 0.00 3.21
735 1432 0.321653 GGCCCACACGTCATCTTCTT 60.322 55.000 0.00 0.00 0.00 2.52
749 1446 9.303116 ACGTCATCTTCTTAGTCCTATATCATT 57.697 33.333 0.00 0.00 0.00 2.57
753 1450 6.925211 TCTTCTTAGTCCTATATCATTGCCG 58.075 40.000 0.00 0.00 0.00 5.69
768 1465 2.513204 CCGCATGGCCTGTCTCTG 60.513 66.667 3.32 0.00 0.00 3.35
778 1475 0.248661 CCTGTCTCTGATGTACCGCG 60.249 60.000 0.00 0.00 0.00 6.46
918 1620 1.376037 CACCGGGGAAAGAGCAGAC 60.376 63.158 6.32 0.00 0.00 3.51
938 1640 1.605753 GACGGAAAGGTCAAAAGGCT 58.394 50.000 0.00 0.00 36.91 4.58
959 1661 0.307760 GGAGCAAAACAGTGACCACG 59.692 55.000 0.00 0.00 36.20 4.94
977 1679 1.437986 GGTAGGAGTACGCAGCCAG 59.562 63.158 0.00 0.00 0.00 4.85
1278 1990 2.126031 GTGTCCGCGTTCCTCCTC 60.126 66.667 4.92 0.00 0.00 3.71
1427 2139 6.588719 TGCTTATGCATTTTACCTGTTCTT 57.411 33.333 3.54 0.00 45.31 2.52
1431 2143 9.586435 GCTTATGCATTTTACCTGTTCTTAATT 57.414 29.630 3.54 0.00 39.41 1.40
1440 2152 4.236935 ACCTGTTCTTAATTGCAATTGCG 58.763 39.130 30.43 21.12 45.83 4.85
1442 2154 4.922692 CCTGTTCTTAATTGCAATTGCGAA 59.077 37.500 30.43 26.12 45.83 4.70
1443 2155 5.577945 CCTGTTCTTAATTGCAATTGCGAAT 59.422 36.000 30.43 18.13 45.83 3.34
1444 2156 6.392353 TGTTCTTAATTGCAATTGCGAATG 57.608 33.333 30.43 14.86 45.83 2.67
1445 2157 6.155136 TGTTCTTAATTGCAATTGCGAATGA 58.845 32.000 30.43 16.64 45.83 2.57
1458 2170 8.054236 GCAATTGCGAATGAAAATTGATCTAAG 58.946 33.333 15.87 0.00 41.64 2.18
1498 2210 1.181741 TCTGAAGTCTCGTGCCTGCT 61.182 55.000 0.00 0.00 0.00 4.24
1541 2253 6.120220 AGTGGGGCAGTAATAAATTCAGTAC 58.880 40.000 0.00 0.00 0.00 2.73
1554 2266 9.816354 AATAAATTCAGTACCATTTTGTATGGC 57.184 29.630 3.76 0.00 42.82 4.40
1559 2271 5.525745 TCAGTACCATTTTGTATGGCGTATG 59.474 40.000 3.76 0.00 42.82 2.39
1607 2319 5.724328 AGATATGTGGAGTATAATGCGTGG 58.276 41.667 0.00 0.00 0.00 4.94
1619 2331 4.367023 GCGTGGGACGTGTAGCCA 62.367 66.667 0.00 0.00 44.73 4.75
1628 2340 0.392461 ACGTGTAGCCATTCCGCATT 60.392 50.000 0.00 0.00 0.00 3.56
1640 2352 2.361797 CCGCATTTTGTGGCAATCG 58.638 52.632 0.00 0.00 41.59 3.34
1661 2373 2.259618 CACTCATGTGCCGTGTAGTAC 58.740 52.381 0.00 0.00 37.38 2.73
1670 2382 1.135527 GCCGTGTAGTACAGGTGCATA 59.864 52.381 21.37 0.00 33.53 3.14
1714 2426 4.436183 GCTCGTTGACCTTATCTTGAAAGC 60.436 45.833 0.00 0.00 0.00 3.51
1733 2445 7.767261 TGAAAGCTAGTTCTCTCAGATTAGAC 58.233 38.462 0.00 0.00 0.00 2.59
1768 2483 1.801178 GCTTCGCTGGCTGGATATTAC 59.199 52.381 0.00 0.00 0.00 1.89
1769 2484 2.548920 GCTTCGCTGGCTGGATATTACT 60.549 50.000 0.00 0.00 0.00 2.24
1770 2485 3.306088 GCTTCGCTGGCTGGATATTACTA 60.306 47.826 0.00 0.00 0.00 1.82
1814 2529 3.193479 GCTGCCTACTTTATTTGCCAAGT 59.807 43.478 0.00 0.00 37.08 3.16
1835 2550 9.774742 CCAAGTTTACAGAATTAACTTCTATGC 57.225 33.333 1.18 0.00 42.48 3.14
1853 2575 8.492673 TTCTATGCAAAGACTAATGATCGTTT 57.507 30.769 5.29 0.00 0.00 3.60
1873 2595 2.650322 TCTTTTGGTTTCTCGGCTTGT 58.350 42.857 0.00 0.00 0.00 3.16
1926 2648 8.303876 GTTTTCCTTGTGTATTTACCATGTGAT 58.696 33.333 0.00 0.00 0.00 3.06
1940 2662 4.685924 CCATGTGATTAGAATGGTTTGCC 58.314 43.478 0.00 0.00 36.82 4.52
2207 2929 6.553953 TCCTTGTATGTACCACACACATAT 57.446 37.500 0.00 0.00 35.23 1.78
2306 3028 1.825474 AGCTAGTCTACGCACCACAAT 59.175 47.619 0.00 0.00 0.00 2.71
2516 3469 6.547141 TCTCATTTGAACATTCTGTGGAGTTT 59.453 34.615 0.00 0.00 0.00 2.66
2697 3650 8.458573 TGTTGGCTACAAGAAAGAAATCTTTA 57.541 30.769 8.32 0.00 39.65 1.85
2889 3846 4.946157 TGAGCAAGAAGAATGGAGATTTCC 59.054 41.667 0.00 0.00 44.31 3.13
3139 4096 2.738213 CTTGAGGGCTCACACGGCTT 62.738 60.000 0.00 0.00 39.66 4.35
3277 4237 2.722629 TCTTACTTCGTTCGCTGTTTCG 59.277 45.455 0.00 0.00 0.00 3.46
3451 4419 7.220741 TGTAAAATTATTTGCAGTGTGCCTA 57.779 32.000 0.00 0.00 44.23 3.93
3461 4429 1.531149 CAGTGTGCCTAACAGAAACCG 59.469 52.381 0.00 0.00 40.26 4.44
3462 4430 1.414919 AGTGTGCCTAACAGAAACCGA 59.585 47.619 0.00 0.00 40.26 4.69
3478 4446 3.478857 ACCGACATAGTTTGGTTGTCA 57.521 42.857 0.00 0.00 39.75 3.58
3490 4458 0.759346 GGTTGTCAGACCACTGGAGT 59.241 55.000 0.71 0.00 43.60 3.85
3498 4466 3.773119 TCAGACCACTGGAGTAAATACCC 59.227 47.826 0.71 0.00 43.60 3.69
3560 4528 8.969260 TGAAGATGTGATGCTCTTTATAACAT 57.031 30.769 0.00 0.00 33.29 2.71
3561 4529 9.399797 TGAAGATGTGATGCTCTTTATAACATT 57.600 29.630 0.00 0.00 31.25 2.71
3562 4530 9.661187 GAAGATGTGATGCTCTTTATAACATTG 57.339 33.333 0.00 0.00 31.25 2.82
3653 4860 3.141398 TCAGAACCTGTGCAAAGATCAC 58.859 45.455 5.12 0.00 32.61 3.06
3773 4984 6.916360 TGATTAAATCTTCTTTTGCTGGGT 57.084 33.333 0.00 0.00 0.00 4.51
3776 4987 3.391506 AATCTTCTTTTGCTGGGTTGC 57.608 42.857 0.00 0.00 0.00 4.17
3839 5050 8.514330 TTAGTAAATCAACACAAGTCACCTTT 57.486 30.769 0.00 0.00 0.00 3.11
3841 5052 8.514330 AGTAAATCAACACAAGTCACCTTTAA 57.486 30.769 0.00 0.00 0.00 1.52
3851 5062 5.585047 ACAAGTCACCTTTAAGACACTTCAC 59.415 40.000 0.00 0.00 37.23 3.18
3852 5063 4.369182 AGTCACCTTTAAGACACTTCACG 58.631 43.478 0.00 0.00 37.23 4.35
3853 5064 3.493503 GTCACCTTTAAGACACTTCACGG 59.506 47.826 0.00 0.00 34.93 4.94
3854 5065 2.806244 CACCTTTAAGACACTTCACGGG 59.194 50.000 0.00 0.00 0.00 5.28
3902 5124 4.947388 TCAACCAGAACTTAAAAGCTGTGT 59.053 37.500 0.00 0.00 0.00 3.72
3967 5222 1.760192 AGGGCGGTACTGTACTGTAG 58.240 55.000 23.65 11.86 37.38 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 637 2.664185 AGACACACGCTGCAGCAG 60.664 61.111 36.03 28.81 42.21 4.24
90 646 2.412195 CGACAGAAGAGAGAGACACACG 60.412 54.545 0.00 0.00 0.00 4.49
120 676 6.947733 TGAATTGAATTCACACTTGTCCCTAT 59.052 34.615 16.04 0.00 43.84 2.57
193 749 2.069465 CTCTGTCCAGCTCCGATCGG 62.069 65.000 28.62 28.62 0.00 4.18
203 759 5.238214 GGCTCATTTATTTAGCTCTGTCCAG 59.762 44.000 0.00 0.00 36.48 3.86
213 769 8.711457 CAACTTTTTGTGGGCTCATTTATTTAG 58.289 33.333 0.00 0.00 0.00 1.85
221 777 2.041701 AGCAACTTTTTGTGGGCTCAT 58.958 42.857 0.00 0.00 35.95 2.90
231 787 5.395214 CCAAACACCCTCTAAGCAACTTTTT 60.395 40.000 0.00 0.00 0.00 1.94
244 800 3.699538 AGTTTCTGAAACCAAACACCCTC 59.300 43.478 25.22 1.05 42.34 4.30
246 802 4.465632 AAGTTTCTGAAACCAAACACCC 57.534 40.909 25.22 2.19 42.34 4.61
269 825 6.445357 GACTTTTTCTAGTCCCAACACAAA 57.555 37.500 0.00 0.00 38.88 2.83
279 835 5.411977 GGTTTGCTAGGGACTTTTTCTAGTC 59.588 44.000 0.00 0.00 43.05 2.59
280 836 5.163131 TGGTTTGCTAGGGACTTTTTCTAGT 60.163 40.000 0.00 0.00 41.75 2.57
281 837 5.313712 TGGTTTGCTAGGGACTTTTTCTAG 58.686 41.667 0.00 0.00 41.75 2.43
282 838 5.313280 TGGTTTGCTAGGGACTTTTTCTA 57.687 39.130 0.00 0.00 41.75 2.10
283 839 4.178956 TGGTTTGCTAGGGACTTTTTCT 57.821 40.909 0.00 0.00 41.75 2.52
284 840 4.929819 TTGGTTTGCTAGGGACTTTTTC 57.070 40.909 0.00 0.00 41.75 2.29
285 841 4.468153 TGTTTGGTTTGCTAGGGACTTTTT 59.532 37.500 0.00 0.00 41.75 1.94
286 842 4.027437 TGTTTGGTTTGCTAGGGACTTTT 58.973 39.130 0.00 0.00 41.75 2.27
287 843 3.383505 GTGTTTGGTTTGCTAGGGACTTT 59.616 43.478 0.00 0.00 41.75 2.66
288 844 2.956333 GTGTTTGGTTTGCTAGGGACTT 59.044 45.455 0.00 0.00 41.75 3.01
289 845 2.583143 GTGTTTGGTTTGCTAGGGACT 58.417 47.619 0.00 0.00 46.37 3.85
290 846 1.265905 CGTGTTTGGTTTGCTAGGGAC 59.734 52.381 0.00 0.00 0.00 4.46
291 847 1.141254 TCGTGTTTGGTTTGCTAGGGA 59.859 47.619 0.00 0.00 0.00 4.20
292 848 1.600023 TCGTGTTTGGTTTGCTAGGG 58.400 50.000 0.00 0.00 0.00 3.53
293 849 2.095263 CCATCGTGTTTGGTTTGCTAGG 60.095 50.000 0.00 0.00 0.00 3.02
294 850 2.095263 CCCATCGTGTTTGGTTTGCTAG 60.095 50.000 0.00 0.00 31.99 3.42
295 851 1.883275 CCCATCGTGTTTGGTTTGCTA 59.117 47.619 0.00 0.00 31.99 3.49
296 852 0.673437 CCCATCGTGTTTGGTTTGCT 59.327 50.000 0.00 0.00 31.99 3.91
297 853 0.671251 TCCCATCGTGTTTGGTTTGC 59.329 50.000 0.00 0.00 31.99 3.68
298 854 3.658757 ATTCCCATCGTGTTTGGTTTG 57.341 42.857 0.00 0.00 31.99 2.93
299 855 4.681074 AAATTCCCATCGTGTTTGGTTT 57.319 36.364 0.00 0.00 31.99 3.27
300 856 4.681074 AAAATTCCCATCGTGTTTGGTT 57.319 36.364 0.00 0.00 31.99 3.67
301 857 4.681074 AAAAATTCCCATCGTGTTTGGT 57.319 36.364 0.00 0.00 31.99 3.67
331 887 9.783256 GAAAGTGTTTCTAAGAACTTTTAGCAA 57.217 29.630 1.60 0.00 41.62 3.91
390 946 5.766174 GGGAACTGTCATACTAGGTCTCTAG 59.234 48.000 0.00 0.00 46.38 2.43
391 947 5.398809 GGGGAACTGTCATACTAGGTCTCTA 60.399 48.000 0.00 0.00 31.68 2.43
392 948 4.538738 GGGAACTGTCATACTAGGTCTCT 58.461 47.826 0.00 0.00 28.35 3.10
393 949 3.637694 GGGGAACTGTCATACTAGGTCTC 59.362 52.174 0.00 0.00 31.35 3.36
394 950 3.012502 TGGGGAACTGTCATACTAGGTCT 59.987 47.826 0.00 0.00 31.35 3.85
395 951 3.132467 GTGGGGAACTGTCATACTAGGTC 59.868 52.174 0.00 0.00 0.00 3.85
396 952 3.105283 GTGGGGAACTGTCATACTAGGT 58.895 50.000 0.00 0.00 0.00 3.08
397 953 2.100916 CGTGGGGAACTGTCATACTAGG 59.899 54.545 0.00 0.00 0.00 3.02
398 954 2.758979 ACGTGGGGAACTGTCATACTAG 59.241 50.000 0.00 0.00 0.00 2.57
399 955 2.756760 GACGTGGGGAACTGTCATACTA 59.243 50.000 0.00 0.00 34.50 1.82
400 956 1.549170 GACGTGGGGAACTGTCATACT 59.451 52.381 0.00 0.00 34.50 2.12
401 957 1.274167 TGACGTGGGGAACTGTCATAC 59.726 52.381 0.00 0.00 37.38 2.39
402 958 1.634960 TGACGTGGGGAACTGTCATA 58.365 50.000 0.00 0.00 37.38 2.15
403 959 0.984230 ATGACGTGGGGAACTGTCAT 59.016 50.000 0.00 1.12 42.69 3.06
404 960 0.320374 GATGACGTGGGGAACTGTCA 59.680 55.000 0.00 0.00 42.37 3.58
405 961 0.320374 TGATGACGTGGGGAACTGTC 59.680 55.000 0.00 0.00 34.76 3.51
406 962 0.762418 TTGATGACGTGGGGAACTGT 59.238 50.000 0.00 0.00 0.00 3.55
407 963 1.156736 GTTGATGACGTGGGGAACTG 58.843 55.000 0.00 0.00 0.00 3.16
408 964 0.036306 GGTTGATGACGTGGGGAACT 59.964 55.000 0.00 0.00 0.00 3.01
409 965 0.250553 TGGTTGATGACGTGGGGAAC 60.251 55.000 0.00 0.00 0.00 3.62
410 966 0.250553 GTGGTTGATGACGTGGGGAA 60.251 55.000 0.00 0.00 0.00 3.97
411 967 1.125093 AGTGGTTGATGACGTGGGGA 61.125 55.000 0.00 0.00 0.00 4.81
452 1009 8.262227 ACTCCTATCTCTATGTCTACTTATCCG 58.738 40.741 0.00 0.00 0.00 4.18
463 1125 7.603404 GTCACGTACATACTCCTATCTCTATGT 59.397 40.741 0.00 0.00 34.80 2.29
481 1144 0.317479 AGAAGCCTGTGGTCACGTAC 59.683 55.000 0.00 0.00 0.00 3.67
536 1233 1.941975 CACAATGCGATGATACAGGCA 59.058 47.619 0.00 0.00 40.06 4.75
537 1234 1.265095 CCACAATGCGATGATACAGGC 59.735 52.381 0.00 0.00 0.00 4.85
538 1235 1.265095 GCCACAATGCGATGATACAGG 59.735 52.381 0.00 0.00 0.00 4.00
620 1317 1.301244 AGACTTGGCGTGCTCACTG 60.301 57.895 0.00 0.00 0.00 3.66
697 1394 1.557443 CCGAATATTGCTCGACCGCC 61.557 60.000 0.00 0.00 38.61 6.13
735 1432 4.383010 CCATGCGGCAATGATATAGGACTA 60.383 45.833 6.82 0.00 0.00 2.59
753 1450 0.107312 ACATCAGAGACAGGCCATGC 60.107 55.000 5.01 0.00 0.00 4.06
778 1475 2.097825 ACCTACCAGTCATCGGTACAC 58.902 52.381 0.00 0.00 37.99 2.90
918 1620 0.237498 GCCTTTTGACCTTTCCGTCG 59.763 55.000 0.00 0.00 35.40 5.12
938 1640 0.257328 TGGTCACTGTTTTGCTCCCA 59.743 50.000 0.00 0.00 0.00 4.37
959 1661 1.437986 CTGGCTGCGTACTCCTACC 59.562 63.158 0.00 0.00 0.00 3.18
1427 2139 8.026341 TCAATTTTCATTCGCAATTGCAATTA 57.974 26.923 28.77 15.62 42.21 1.40
1431 2143 5.870433 AGATCAATTTTCATTCGCAATTGCA 59.130 32.000 28.77 12.04 42.21 4.08
1442 2154 9.246670 TGTTGGACATCTTAGATCAATTTTCAT 57.753 29.630 0.00 0.00 0.00 2.57
1443 2155 8.634335 TGTTGGACATCTTAGATCAATTTTCA 57.366 30.769 0.00 0.00 0.00 2.69
1444 2156 9.565213 CTTGTTGGACATCTTAGATCAATTTTC 57.435 33.333 0.00 0.00 0.00 2.29
1445 2157 9.082313 ACTTGTTGGACATCTTAGATCAATTTT 57.918 29.630 0.00 0.00 0.00 1.82
1458 2170 0.798776 CGGAGCACTTGTTGGACATC 59.201 55.000 0.00 0.00 0.00 3.06
1460 2172 0.107410 AACGGAGCACTTGTTGGACA 60.107 50.000 0.00 0.00 0.00 4.02
1498 2210 3.088532 ACTAAATGGCGGCTCAATTTCA 58.911 40.909 11.43 0.00 0.00 2.69
1528 2240 9.816354 GCCATACAAAATGGTACTGAATTTATT 57.184 29.630 5.94 0.00 41.17 1.40
1529 2241 8.134895 CGCCATACAAAATGGTACTGAATTTAT 58.865 33.333 5.94 0.00 41.17 1.40
1541 2253 3.988379 AGCATACGCCATACAAAATGG 57.012 42.857 0.00 0.00 41.99 3.16
1554 2266 8.723777 TTAGAAATCGATACACTTAGCATACG 57.276 34.615 0.00 0.00 0.00 3.06
1607 2319 2.171725 GCGGAATGGCTACACGTCC 61.172 63.158 0.00 0.00 33.00 4.79
1619 2331 2.620242 GATTGCCACAAAATGCGGAAT 58.380 42.857 0.00 0.00 0.00 3.01
1628 2340 1.068402 CATGAGTGCGATTGCCACAAA 60.068 47.619 1.50 0.00 41.78 2.83
1661 2373 5.353938 CCATCCAAAAGATTTATGCACCTG 58.646 41.667 0.00 0.00 30.59 4.00
1670 2382 5.025453 AGCATACACCCATCCAAAAGATTT 58.975 37.500 0.00 0.00 30.59 2.17
1714 2426 6.318648 ACAGCAGTCTAATCTGAGAGAACTAG 59.681 42.308 0.00 0.00 37.61 2.57
1733 2445 3.921969 CGAAGCTTCTATTCACAGCAG 57.078 47.619 23.50 0.24 35.88 4.24
1768 2483 6.238869 GCTCTTTTCCCCTTGCAAGATTATAG 60.239 42.308 28.05 15.86 0.00 1.31
1769 2484 5.594317 GCTCTTTTCCCCTTGCAAGATTATA 59.406 40.000 28.05 7.19 0.00 0.98
1770 2485 4.403752 GCTCTTTTCCCCTTGCAAGATTAT 59.596 41.667 28.05 0.00 0.00 1.28
1835 2550 8.076178 ACCAAAAGAAACGATCATTAGTCTTTG 58.924 33.333 2.83 0.06 35.92 2.77
1853 2575 2.616842 GACAAGCCGAGAAACCAAAAGA 59.383 45.455 0.00 0.00 0.00 2.52
1873 2595 4.083537 GCTTGTACCACAACAATGAATCGA 60.084 41.667 0.00 0.00 38.61 3.59
1936 2658 9.353431 ACATTACAACATATATGAGATTGGCAA 57.647 29.630 19.63 0.68 0.00 4.52
2207 2929 6.417258 TGAGATAGGTGCAAGATGAATGAAA 58.583 36.000 0.00 0.00 0.00 2.69
2280 3002 2.686915 GGTGCGTAGACTAGCTTAAGGA 59.313 50.000 4.29 0.00 0.00 3.36
2423 3375 3.128589 ACAATAACGGCAAAGCACTATGG 59.871 43.478 0.00 0.00 0.00 2.74
2424 3376 4.342772 GACAATAACGGCAAAGCACTATG 58.657 43.478 0.00 0.00 0.00 2.23
2697 3650 5.367302 GGATAAGCTGAGCTTCTTCAGAAT 58.633 41.667 24.63 9.59 46.77 2.40
2889 3846 3.467803 GTTCACGGGGAGGAAATATCAG 58.532 50.000 0.00 0.00 0.00 2.90
3208 4165 1.192312 CGTCACATTGTCACAACGAGG 59.808 52.381 0.00 0.00 32.17 4.63
3265 4225 0.041576 GAACCACCGAAACAGCGAAC 60.042 55.000 0.00 0.00 0.00 3.95
3451 4419 4.457466 ACCAAACTATGTCGGTTTCTGTT 58.543 39.130 0.00 0.00 35.09 3.16
3461 4429 4.385825 TGGTCTGACAACCAAACTATGTC 58.614 43.478 10.38 0.00 46.26 3.06
3462 4430 4.431416 TGGTCTGACAACCAAACTATGT 57.569 40.909 10.38 0.00 46.26 2.29
3478 4446 2.764572 CGGGTATTTACTCCAGTGGTCT 59.235 50.000 9.54 0.00 0.00 3.85
3490 4458 5.821995 GGTAAAATACAGGCACGGGTATTTA 59.178 40.000 9.41 0.00 45.50 1.40
3498 4466 1.662122 GACGGGTAAAATACAGGCACG 59.338 52.381 0.00 0.00 0.00 5.34
3653 4860 0.605589 GATCCTAGATGGGGACTGCG 59.394 60.000 0.00 0.00 35.51 5.18
3763 4970 1.412079 ATGACAGCAACCCAGCAAAA 58.588 45.000 0.00 0.00 36.85 2.44
3773 4984 2.995283 AGCTATGCAGAATGACAGCAA 58.005 42.857 0.00 0.00 43.66 3.91
3776 4987 5.556355 TTGAAAGCTATGCAGAATGACAG 57.444 39.130 0.00 0.00 39.69 3.51
3839 5050 0.971386 GGGTCCCGTGAAGTGTCTTA 59.029 55.000 0.00 0.00 0.00 2.10
3841 5052 2.214920 GGGGTCCCGTGAAGTGTCT 61.215 63.158 0.48 0.00 0.00 3.41
3851 5062 0.830023 AAATTGTGGTTGGGGTCCCG 60.830 55.000 0.48 0.00 39.42 5.14
3852 5063 2.300723 GTTAAATTGTGGTTGGGGTCCC 59.699 50.000 0.00 0.00 0.00 4.46
3853 5064 2.966516 TGTTAAATTGTGGTTGGGGTCC 59.033 45.455 0.00 0.00 0.00 4.46
3854 5065 4.627058 CTTGTTAAATTGTGGTTGGGGTC 58.373 43.478 0.00 0.00 0.00 4.46
3902 5124 5.417894 ACTGTAAACGTCCTCATCTGTGATA 59.582 40.000 0.00 0.00 32.98 2.15
3938 5160 2.098770 CAGTACCGCCCTTGTAGAGTAC 59.901 54.545 0.00 0.00 0.00 2.73
3940 5162 1.183549 CAGTACCGCCCTTGTAGAGT 58.816 55.000 0.00 0.00 0.00 3.24
3941 5163 1.183549 ACAGTACCGCCCTTGTAGAG 58.816 55.000 0.00 0.00 0.00 2.43
3942 5164 2.094675 GTACAGTACCGCCCTTGTAGA 58.905 52.381 0.00 0.00 0.00 2.59
3943 5165 2.097825 AGTACAGTACCGCCCTTGTAG 58.902 52.381 7.13 0.00 0.00 2.74
3946 5168 0.606604 ACAGTACAGTACCGCCCTTG 59.393 55.000 7.13 0.81 0.00 3.61
3951 5173 1.133790 CCCACTACAGTACAGTACCGC 59.866 57.143 7.13 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.