Multiple sequence alignment - TraesCS7B01G159500

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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 TraesCS7B01G159500 chr7B 100.000 5351 0 0 1 5351 216940221 216934871 0.000000e+00 9882.0
1 TraesCS7B01G159500 chr7B 94.606 241 3 1 1 231 662732654 662732414 1.100000e-96 364.0
2 TraesCS7B01G159500 chr7B 94.393 107 6 0 1888 1994 513654203 513654309 1.190000e-36 165.0
3 TraesCS7B01G159500 chr7B 80.000 200 35 5 2270 2467 534050314 534050118 5.590000e-30 143.0
4 TraesCS7B01G159500 chr7A 92.550 4859 246 36 235 5028 257124331 257129138 0.000000e+00 6861.0
5 TraesCS7B01G159500 chr7A 90.850 306 14 7 5034 5336 257129472 257129766 1.080000e-106 398.0
6 TraesCS7B01G159500 chr7A 94.393 107 6 0 1888 1994 554392261 554392367 1.190000e-36 165.0
7 TraesCS7B01G159500 chr7D 92.717 3762 161 40 1631 5336 241189662 241185958 0.000000e+00 5325.0
8 TraesCS7B01G159500 chr7D 94.950 1307 49 11 250 1553 241190972 241189680 0.000000e+00 2032.0
9 TraesCS7B01G159500 chr7D 96.679 271 9 0 250 520 241191364 241191094 8.170000e-123 451.0
10 TraesCS7B01G159500 chr7D 94.191 241 4 1 1 231 101578686 101578446 5.100000e-95 359.0
11 TraesCS7B01G159500 chr7D 91.342 231 19 1 1 231 16650879 16650650 1.120000e-81 315.0
12 TraesCS7B01G159500 chr7D 91.342 231 19 1 1 231 16652700 16652471 1.120000e-81 315.0
13 TraesCS7B01G159500 chr7D 90.476 231 21 1 1 231 16642020 16641791 2.420000e-78 303.0
14 TraesCS7B01G159500 chr1D 97.835 231 5 0 1 231 254531337 254531107 3.000000e-107 399.0
15 TraesCS7B01G159500 chr5D 94.191 241 4 1 1 231 503251520 503251280 5.100000e-95 359.0
16 TraesCS7B01G159500 chr5D 93.776 241 5 1 1 231 503251011 503250771 2.370000e-93 353.0
17 TraesCS7B01G159500 chr3A 93.361 241 6 1 1 231 672883289 672883529 1.100000e-91 348.0
18 TraesCS7B01G159500 chr3A 82.915 199 26 7 2273 2467 340284764 340284570 7.130000e-39 172.0
19 TraesCS7B01G159500 chr3A 92.523 107 8 0 1888 1994 261350994 261350888 2.580000e-33 154.0
20 TraesCS7B01G159500 chr3A 82.659 173 27 3 2275 2446 323258410 323258240 3.340000e-32 150.0
21 TraesCS7B01G159500 chr3A 83.654 104 12 5 1906 2006 557420814 557420915 5.710000e-15 93.5
22 TraesCS7B01G159500 chr3A 82.569 109 14 4 1903 2010 128524916 128524812 2.050000e-14 91.6
23 TraesCS7B01G159500 chr3A 84.524 84 13 0 2550 2633 616249595 616249678 3.430000e-12 84.2
24 TraesCS7B01G159500 chr3D 95.349 172 8 0 60 231 215290867 215291038 1.900000e-69 274.0
25 TraesCS7B01G159500 chr3D 94.059 101 6 0 1888 1988 190256484 190256584 2.580000e-33 154.0
26 TraesCS7B01G159500 chr3D 91.071 112 9 1 1887 1998 284818416 284818306 3.340000e-32 150.0
27 TraesCS7B01G159500 chr3D 91.525 59 3 2 1949 2006 570500023 570499966 4.440000e-11 80.5
28 TraesCS7B01G159500 chrUn 99.270 137 1 0 1 137 81096416 81096552 1.150000e-61 248.0
29 TraesCS7B01G159500 chrUn 93.443 122 4 3 112 231 447135314 447135195 1.530000e-40 178.0
30 TraesCS7B01G159500 chr2A 83.500 200 30 3 2269 2467 523864592 523864395 3.290000e-42 183.0
31 TraesCS7B01G159500 chr2A 85.714 84 11 1 2562 2645 423207541 423207459 2.650000e-13 87.9
32 TraesCS7B01G159500 chr2B 81.633 196 34 2 2273 2467 458243915 458243721 1.540000e-35 161.0
33 TraesCS7B01G159500 chr2B 94.118 51 1 2 2583 2633 423659844 423659892 5.750000e-10 76.8
34 TraesCS7B01G159500 chr2D 83.051 177 28 2 2269 2445 387187888 387187714 5.550000e-35 159.0
35 TraesCS7B01G159500 chr2D 91.525 59 3 2 1949 2006 532479099 532479156 4.440000e-11 80.5
36 TraesCS7B01G159500 chr2D 81.429 70 11 2 2551 2618 83101170 83101239 7.490000e-04 56.5
37 TraesCS7B01G159500 chr1B 93.396 106 7 0 1889 1994 301273502 301273397 2.000000e-34 158.0
38 TraesCS7B01G159500 chr1B 85.227 88 11 2 1920 2006 575712952 575712866 7.380000e-14 89.8
39 TraesCS7B01G159500 chr5B 94.118 102 4 2 1903 2003 501957046 501956946 2.580000e-33 154.0
40 TraesCS7B01G159500 chr5B 84.337 83 13 0 2558 2640 45388603 45388521 1.240000e-11 82.4
41 TraesCS7B01G159500 chr5A 91.818 110 8 1 1889 1998 559809527 559809635 9.280000e-33 152.0
42 TraesCS7B01G159500 chr4B 80.402 199 34 5 2271 2467 141486063 141485868 4.320000e-31 147.0
43 TraesCS7B01G159500 chr3B 91.304 69 6 0 2564 2632 829204560 829204628 1.590000e-15 95.3
44 TraesCS7B01G159500 chr3B 79.130 115 12 11 1906 2014 708518294 708518186 9.620000e-08 69.4
45 TraesCS7B01G159500 chr6B 81.905 105 13 6 1908 2008 585524753 585524855 3.430000e-12 84.2
46 TraesCS7B01G159500 chr4D 90.909 55 5 0 2582 2636 226631127 226631073 2.070000e-09 75.0


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 TraesCS7B01G159500 chr7B 216934871 216940221 5350 True 9882.000000 9882 100.0000 1 5351 1 chr7B.!!$R1 5350
1 TraesCS7B01G159500 chr7A 257124331 257129766 5435 False 3629.500000 6861 91.7000 235 5336 2 chr7A.!!$F2 5101
2 TraesCS7B01G159500 chr7D 241185958 241191364 5406 True 2602.666667 5325 94.7820 250 5336 3 chr7D.!!$R4 5086
3 TraesCS7B01G159500 chr7D 16650650 16652700 2050 True 315.000000 315 91.3420 1 231 2 chr7D.!!$R3 230
4 TraesCS7B01G159500 chr5D 503250771 503251520 749 True 356.000000 359 93.9835 1 231 2 chr5D.!!$R1 230

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
631 1009 1.203300 TCCAGAGGTCAGATCCAACCA 60.203 52.381 14.71 0.0 38.06 3.67 F
1656 2262 0.709467 CAATGAAAACATGCACGGCG 59.291 50.000 4.80 4.8 0.00 6.46 F
2355 2972 0.252197 ACCGGCTACCCATTCTCAAC 59.748 55.000 0.00 0.0 0.00 3.18 F
2373 2990 1.906990 ACTTGCTTCAAGCTGAGCAT 58.093 45.000 11.57 0.0 44.43 3.79 F
3877 4530 0.984230 TCCGTTGGAGAGGAGCATTT 59.016 50.000 0.00 0.0 31.95 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2337 2954 0.541863 AGTTGAGAATGGGTAGCCGG 59.458 55.0 6.45 0.0 0.00 6.13 R
2939 3585 2.283145 AAAGGAGTGATGCAGTTGCT 57.717 45.0 5.62 0.0 42.66 3.91 R
3672 4325 0.389391 CGAACGCAGGGGTGAGATAT 59.611 55.0 0.00 0.0 0.00 1.63 R
4004 4659 1.589716 GCAGACAGCCTTCCGCAAAT 61.590 55.0 0.00 0.0 41.38 2.32 R
4960 5663 0.971386 AATGCCCCTTTCTGCAACTG 59.029 50.0 0.00 0.0 41.50 3.16 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
138 139 5.017294 AGTGCTAGGAAGTGAAATAGAGC 57.983 43.478 0.00 0.00 0.00 4.09
141 152 4.410228 TGCTAGGAAGTGAAATAGAGCCAT 59.590 41.667 0.00 0.00 0.00 4.40
170 181 4.722220 CTTCCCTATGAAATGAGGCATGA 58.278 43.478 0.00 0.00 31.06 3.07
231 242 5.491982 AGAAGCTTCGGACTCATATTGTTT 58.508 37.500 20.43 0.00 0.00 2.83
233 244 6.758886 AGAAGCTTCGGACTCATATTGTTTAG 59.241 38.462 20.43 0.00 0.00 1.85
339 623 4.929707 CGCCCGGTCAATAGGCCC 62.930 72.222 0.00 0.00 44.13 5.80
570 948 2.096248 CTCCTCTTCACCTCTTACGCT 58.904 52.381 0.00 0.00 0.00 5.07
571 949 2.093106 TCCTCTTCACCTCTTACGCTC 58.907 52.381 0.00 0.00 0.00 5.03
574 952 3.056465 CCTCTTCACCTCTTACGCTCTTT 60.056 47.826 0.00 0.00 0.00 2.52
575 953 4.170256 CTCTTCACCTCTTACGCTCTTTC 58.830 47.826 0.00 0.00 0.00 2.62
631 1009 1.203300 TCCAGAGGTCAGATCCAACCA 60.203 52.381 14.71 0.00 38.06 3.67
641 1019 1.821753 AGATCCAACCAGACTCTCACG 59.178 52.381 0.00 0.00 0.00 4.35
755 1133 4.067192 AGTAATTTGTACGGTTCCACCAC 58.933 43.478 0.00 0.00 38.47 4.16
767 1145 4.410400 CACCACGCCCTCCCCTTC 62.410 72.222 0.00 0.00 0.00 3.46
881 1313 4.660168 ACATCACAGGATCTCAAAAGCTT 58.340 39.130 0.00 0.00 0.00 3.74
884 1316 4.579869 TCACAGGATCTCAAAAGCTTACC 58.420 43.478 0.00 0.00 0.00 2.85
887 1319 3.054065 CAGGATCTCAAAAGCTTACCCCT 60.054 47.826 0.00 0.00 0.00 4.79
921 1353 3.441572 GCATGCTTGTGTGGATACTCTTT 59.558 43.478 11.37 0.00 37.61 2.52
946 1378 8.634335 TGAGATCAATTGACACTTTGGAATTA 57.366 30.769 11.07 0.00 0.00 1.40
1065 1497 2.676471 ATGCCGTTCTTGCACCCC 60.676 61.111 0.00 0.00 42.38 4.95
1158 1590 5.385198 ACTGTTCATGTATCCTTTGTGGTT 58.615 37.500 0.00 0.00 37.07 3.67
1167 1599 3.517296 TCCTTTGTGGTTATCAAGGCA 57.483 42.857 0.00 0.00 37.07 4.75
1226 1658 1.987368 TGTGGTAAGGACTTAACCCCC 59.013 52.381 4.79 0.00 31.94 5.40
1352 1933 6.372659 AGAATGTTTGTTCTGCTGGTATAGTG 59.627 38.462 0.00 0.00 37.08 2.74
1367 1948 7.372451 TGGTATAGTGTCACAACTATTTTGC 57.628 36.000 5.62 0.00 39.80 3.68
1472 2055 7.604927 TGATGTGTTGGTATTTGAAGTACTACC 59.395 37.037 0.00 0.00 35.28 3.18
1587 2193 5.614324 TGCAGACTACTAACTATGGCAAT 57.386 39.130 0.00 0.00 0.00 3.56
1589 2195 5.128663 TGCAGACTACTAACTATGGCAATCA 59.871 40.000 0.00 0.00 0.00 2.57
1590 2196 6.183361 TGCAGACTACTAACTATGGCAATCAT 60.183 38.462 0.00 0.00 39.78 2.45
1591 2197 6.708054 GCAGACTACTAACTATGGCAATCATT 59.292 38.462 0.00 0.00 37.30 2.57
1656 2262 0.709467 CAATGAAAACATGCACGGCG 59.291 50.000 4.80 4.80 0.00 6.46
1710 2316 4.284178 AGGTGACTCTTAGGCGGTAATTA 58.716 43.478 0.00 0.00 32.90 1.40
1719 2325 1.154654 GCGGTAATTATGCTCGCGC 60.155 57.895 0.00 0.00 37.12 6.86
1777 2383 2.046314 TGCTCGCCTTAGGTTGCC 60.046 61.111 0.00 0.00 0.00 4.52
1782 2388 1.207329 CTCGCCTTAGGTTGCCTTACT 59.793 52.381 0.00 0.00 34.61 2.24
1785 2391 1.340114 GCCTTAGGTTGCCTTACTGCT 60.340 52.381 0.00 0.00 34.61 4.24
1897 2503 1.080498 TGGTTGGATGGTACTCCCTCT 59.920 52.381 0.00 0.00 34.12 3.69
1899 2505 1.134371 GTTGGATGGTACTCCCTCTGC 60.134 57.143 0.00 0.00 34.12 4.26
1918 2524 1.287425 CCCGGAATTACTTGTCGCTC 58.713 55.000 0.73 0.00 0.00 5.03
1946 2552 7.948357 ACGGATGTATCTAGCACTAAAATACA 58.052 34.615 11.81 11.81 37.26 2.29
1994 2600 3.373226 TTCCGGACGGAGGAAGTG 58.627 61.111 13.64 0.00 46.06 3.16
2027 2633 3.767131 TCACGATTGGTCTAGTGATTGGA 59.233 43.478 0.00 0.00 38.52 3.53
2091 2697 4.441079 GCCATGATCCTGTGGAATTTGAAG 60.441 45.833 11.77 0.00 37.72 3.02
2156 2773 5.222254 TGGACCAAGGGAGCTAATAGTTTTT 60.222 40.000 0.00 0.00 0.00 1.94
2213 2830 3.390521 CCCTGTGCTGGCTACCGA 61.391 66.667 0.00 0.00 0.00 4.69
2241 2858 1.734137 CGCTACGTCTGGCTACCAT 59.266 57.895 0.00 0.00 30.82 3.55
2255 2872 3.181474 GGCTACCATGTGAGAACTAGACC 60.181 52.174 0.00 0.00 0.00 3.85
2287 2904 4.260497 GGACGAACACCAACACTAGTTTTC 60.260 45.833 0.00 0.00 35.28 2.29
2342 2959 2.198304 GATCAACCTCCCAACCGGCT 62.198 60.000 0.00 0.00 0.00 5.52
2355 2972 0.252197 ACCGGCTACCCATTCTCAAC 59.748 55.000 0.00 0.00 0.00 3.18
2367 2984 3.255149 CCATTCTCAACTTGCTTCAAGCT 59.745 43.478 11.57 0.00 44.43 3.74
2373 2990 1.906990 ACTTGCTTCAAGCTGAGCAT 58.093 45.000 11.57 0.00 44.43 3.79
2425 3042 4.824537 GCTCCTGGAAAAAGAAGAGTTTCT 59.175 41.667 0.00 0.00 45.51 2.52
2451 3068 8.257602 TGTTGGTATGAGTAGCCTATTAATCA 57.742 34.615 0.00 0.00 32.89 2.57
2571 3204 9.707957 ATTGGTACTCTCTCCTATCCATATTAG 57.292 37.037 0.00 0.00 0.00 1.73
2580 3213 6.151312 TCTCCTATCCATATTAGTTGTCGCTC 59.849 42.308 0.00 0.00 0.00 5.03
2842 3488 2.298163 CTGCTTGGGATTGTTTTGCTCT 59.702 45.455 0.00 0.00 0.00 4.09
2843 3489 2.699846 TGCTTGGGATTGTTTTGCTCTT 59.300 40.909 0.00 0.00 0.00 2.85
2869 3515 5.367945 TTTGTGTACTCTTGGTCTTCCTT 57.632 39.130 0.00 0.00 34.23 3.36
2881 3527 4.693283 TGGTCTTCCTTTATATGAGTGCG 58.307 43.478 0.00 0.00 34.23 5.34
2932 3578 3.249080 ACGATATTTCCCCGTTATTTGCG 59.751 43.478 0.00 0.00 32.03 4.85
2939 3585 6.506500 TTTCCCCGTTATTTGCGTATTTAA 57.493 33.333 0.00 0.00 0.00 1.52
3265 3911 3.128589 ACGTGCATGTTGGACATTATTCC 59.871 43.478 5.51 0.00 38.73 3.01
3491 4144 5.059161 GCAAGCAATATGTGAGTATCCTCA 58.941 41.667 0.00 0.00 45.44 3.86
3625 4278 5.065218 CCAGCTTGTTCACTGGTAATGATAC 59.935 44.000 0.79 0.00 46.95 2.24
3877 4530 0.984230 TCCGTTGGAGAGGAGCATTT 59.016 50.000 0.00 0.00 31.95 2.32
4004 4659 4.222145 AGAACAAGTTAGGATTCGCCAGTA 59.778 41.667 0.00 0.00 40.02 2.74
4102 4757 4.436050 CCATGGTTTGTCGAGAAATCTTCG 60.436 45.833 17.99 7.34 34.02 3.79
4103 4758 3.724374 TGGTTTGTCGAGAAATCTTCGT 58.276 40.909 17.99 0.00 34.02 3.85
4104 4759 3.493129 TGGTTTGTCGAGAAATCTTCGTG 59.507 43.478 17.99 0.00 34.02 4.35
4105 4760 3.120649 GGTTTGTCGAGAAATCTTCGTGG 60.121 47.826 11.23 0.00 34.02 4.94
4106 4761 2.363788 TGTCGAGAAATCTTCGTGGG 57.636 50.000 0.00 0.00 34.02 4.61
4209 4878 4.025401 CCACGTGTTTCCCGCTGC 62.025 66.667 15.65 0.00 0.00 5.25
4354 5023 2.303311 GGGACATCTAGGGTCTAATGCC 59.697 54.545 13.00 4.53 35.61 4.40
4386 5055 3.506743 TGCCTTGTTGCCCCCTCA 61.507 61.111 0.00 0.00 0.00 3.86
4483 5179 8.138074 TGACTCCATATATGAGTTCTTCGAAAG 58.862 37.037 14.54 0.00 0.00 2.62
4550 5249 5.694006 CCATTTCGCCAACATTTTCTGTTTA 59.306 36.000 0.00 0.00 45.98 2.01
4584 5283 2.347490 GCCCTGACTGAGCCGAAA 59.653 61.111 0.00 0.00 0.00 3.46
4727 5426 0.734253 CTGAAGAACGAGTCGCAGGG 60.734 60.000 13.59 0.00 32.85 4.45
4811 5510 0.543174 AGACCTGTCTGTCACTCCCC 60.543 60.000 0.00 0.00 38.75 4.81
4863 5562 1.664016 CCACTTGCGTTCATGCACTTC 60.664 52.381 0.00 0.00 46.25 3.01
4960 5663 2.109181 GATCCCTACACGCCAGCC 59.891 66.667 0.00 0.00 0.00 4.85
4961 5664 2.687200 ATCCCTACACGCCAGCCA 60.687 61.111 0.00 0.00 0.00 4.75
4962 5665 2.650813 GATCCCTACACGCCAGCCAG 62.651 65.000 0.00 0.00 0.00 4.85
4963 5666 3.706373 CCCTACACGCCAGCCAGT 61.706 66.667 0.00 0.00 0.00 4.00
5151 6184 1.408405 CCTTGCCTGAGATGCAGTCAT 60.408 52.381 2.17 0.00 43.33 3.06
5152 6185 2.366533 CTTGCCTGAGATGCAGTCATT 58.633 47.619 2.17 0.00 43.33 2.57
5153 6186 2.034104 TGCCTGAGATGCAGTCATTC 57.966 50.000 2.17 0.00 43.33 2.67
5154 6187 1.279846 TGCCTGAGATGCAGTCATTCA 59.720 47.619 2.17 1.74 43.33 2.57
5158 6191 4.700700 CCTGAGATGCAGTCATTCATGTA 58.299 43.478 2.17 0.00 43.33 2.29
5235 6268 8.654230 TGGTTATCTGTAACTAGTACTCGTAG 57.346 38.462 0.00 0.00 40.06 3.51
5321 6356 2.287308 GCGTGTGAGCATCTAGTCTAGG 60.287 54.545 7.05 0.00 37.05 3.02
5337 6372 3.693411 GGGAAGATGCCCGCAAAA 58.307 55.556 0.00 0.00 38.58 2.44
5338 6373 1.971418 GGGAAGATGCCCGCAAAAA 59.029 52.632 0.00 0.00 38.58 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 181 3.695830 TTCTTCATAGTGGCTCCGTTT 57.304 42.857 0.00 0.00 0.00 3.60
231 242 2.290916 CGAGCCTCGCAACTCTAATCTA 59.709 50.000 0.00 0.00 31.14 1.98
233 244 1.482278 CGAGCCTCGCAACTCTAATC 58.518 55.000 0.00 0.00 31.14 1.75
283 567 1.899437 TTAACCTCGCTGAGCCAGGG 61.899 60.000 21.96 12.48 44.21 4.45
290 574 2.486548 GGCCCATTATTAACCTCGCTGA 60.487 50.000 0.00 0.00 0.00 4.26
319 603 4.929707 CCTATTGACCGGGCGGGC 62.930 72.222 11.50 2.29 45.60 6.13
339 623 0.245539 TACTTCACTTTCCGCCGAGG 59.754 55.000 0.00 0.00 42.97 4.63
570 948 4.018415 CAGTAGGAAGAATTGGGGGAAAGA 60.018 45.833 0.00 0.00 0.00 2.52
571 949 4.273318 CAGTAGGAAGAATTGGGGGAAAG 58.727 47.826 0.00 0.00 0.00 2.62
574 952 2.205342 CCAGTAGGAAGAATTGGGGGA 58.795 52.381 0.00 0.00 36.89 4.81
575 953 2.205342 TCCAGTAGGAAGAATTGGGGG 58.795 52.381 0.00 0.00 42.23 5.40
658 1036 3.871006 TCAATCGATCGATTTCCAACCAG 59.129 43.478 34.61 22.47 42.30 4.00
755 1133 2.421739 CATACGAAGGGGAGGGCG 59.578 66.667 0.00 0.00 0.00 6.13
767 1145 2.054687 TTATTCTACGGGCGCATACG 57.945 50.000 10.83 13.54 44.07 3.06
835 1267 3.252458 ACAGAACGCCAAAATTCTACCAC 59.748 43.478 0.00 0.00 33.35 4.16
838 1270 4.024387 TGTCACAGAACGCCAAAATTCTAC 60.024 41.667 0.00 0.00 33.35 2.59
881 1313 1.729276 CGTCGCGTTGATAGGGGTA 59.271 57.895 5.77 0.00 0.00 3.69
884 1316 1.591594 ATGCGTCGCGTTGATAGGG 60.592 57.895 13.38 0.00 0.00 3.53
887 1319 1.081556 AAGCATGCGTCGCGTTGATA 61.082 50.000 20.30 0.00 0.00 2.15
921 1353 7.528996 AATTCCAAAGTGTCAATTGATCTCA 57.471 32.000 12.12 2.04 0.00 3.27
946 1378 2.305343 ACAGAGCTTCCTGCAGAGAAAT 59.695 45.455 17.39 8.40 45.94 2.17
1158 1590 1.557099 ACGGAGTGTCTGCCTTGATA 58.443 50.000 0.00 0.00 42.51 2.15
1238 1670 8.153479 TGCTTATTCTTGCGTGATTTACATAT 57.847 30.769 0.00 0.00 0.00 1.78
1352 1933 9.810231 CAAAATAAATGGCAAAATAGTTGTGAC 57.190 29.630 0.00 0.00 0.00 3.67
1367 1948 6.819649 AGCATGGATTCACACAAAATAAATGG 59.180 34.615 0.00 0.00 0.00 3.16
1540 2123 7.510549 TCCTAATTCAAGAAGGTGTTCAAAG 57.489 36.000 0.00 0.00 34.82 2.77
1596 2202 6.711579 TCGCACGTTATTCCTTCATTATTTC 58.288 36.000 0.00 0.00 0.00 2.17
1614 2220 2.993899 ACAATTAGTTCTTCCTCGCACG 59.006 45.455 0.00 0.00 0.00 5.34
1734 2340 1.600107 CCCTAACACCTAAGGCGCA 59.400 57.895 10.83 0.00 0.00 6.09
1777 2383 9.013490 GTGCATCATTGTTTATAAAGCAGTAAG 57.987 33.333 0.00 0.00 0.00 2.34
1782 2388 6.188400 TCGTGCATCATTGTTTATAAAGCA 57.812 33.333 0.00 0.18 0.00 3.91
1897 2503 1.022451 GCGACAAGTAATTCCGGGCA 61.022 55.000 0.00 0.00 0.00 5.36
1899 2505 1.287425 GAGCGACAAGTAATTCCGGG 58.713 55.000 0.00 0.00 0.00 5.73
1918 2524 7.534085 TTTTAGTGCTAGATACATCCGTTTG 57.466 36.000 0.00 0.00 0.00 2.93
1946 2552 4.519350 TCGCTCAAACGGATGTATCTAGAT 59.481 41.667 10.73 10.73 0.00 1.98
1994 2600 9.477484 ACTAGACCAATCGTGATGTTAATAATC 57.523 33.333 0.00 0.00 0.00 1.75
2008 2614 4.060900 CCATCCAATCACTAGACCAATCG 58.939 47.826 0.00 0.00 0.00 3.34
2027 2633 8.792633 CCATACCACGATAATGTTAATTTCCAT 58.207 33.333 0.00 0.00 0.00 3.41
2091 2697 6.369065 GTGCACTATCAAGTATAATGTAGGGC 59.631 42.308 10.32 7.44 38.66 5.19
2164 2781 8.992073 GCAGAATGTTTGTTTGAGGAAAATAAT 58.008 29.630 0.00 0.00 39.31 1.28
2202 2819 2.347731 GCCTTATAATCGGTAGCCAGC 58.652 52.381 0.00 0.00 0.00 4.85
2213 2830 2.029290 CCAGACGTAGCGGCCTTATAAT 60.029 50.000 0.00 0.00 34.11 1.28
2241 2858 1.255667 GGGCCGGTCTAGTTCTCACA 61.256 60.000 5.77 0.00 0.00 3.58
2268 2885 5.007724 CAGGAGAAAACTAGTGTTGGTGTTC 59.992 44.000 2.08 0.00 36.39 3.18
2287 2904 1.294659 GAGGACAAAGTGCGCAGGAG 61.295 60.000 12.22 3.57 0.00 3.69
2337 2954 0.541863 AGTTGAGAATGGGTAGCCGG 59.458 55.000 6.45 0.00 0.00 6.13
2342 2959 4.365514 TGAAGCAAGTTGAGAATGGGTA 57.634 40.909 7.16 0.00 0.00 3.69
2355 2972 1.732732 GCATGCTCAGCTTGAAGCAAG 60.733 52.381 20.45 16.34 45.56 4.01
2367 2984 3.754965 ACCTCAAAGTTAAGCATGCTCA 58.245 40.909 22.93 2.34 0.00 4.26
2373 2990 3.317993 GCAAGGAACCTCAAAGTTAAGCA 59.682 43.478 0.00 0.00 0.00 3.91
2425 3042 8.710239 TGATTAATAGGCTACTCATACCAACAA 58.290 33.333 0.00 0.00 0.00 2.83
2451 3068 7.984475 TGTGCCTATAACATCCAGGTTAATAT 58.016 34.615 0.00 0.00 36.86 1.28
2536 3153 5.104735 AGGAGAGAGTACCAATTAAAGCCAG 60.105 44.000 0.00 0.00 0.00 4.85
2587 3220 7.192913 TGTTGCTGATTTAGTACAAAGTTGTG 58.807 34.615 6.94 0.00 42.31 3.33
2605 3238 7.080099 CCTCCGATTCATATTAATTGTTGCTG 58.920 38.462 0.00 0.00 0.00 4.41
2682 3318 3.423539 AAAGCTATGCTCCACTGTTCA 57.576 42.857 0.00 0.00 38.25 3.18
2751 3387 3.655276 AGCAAAAGGAAGCAATGACAG 57.345 42.857 0.00 0.00 0.00 3.51
2854 3500 7.560368 CACTCATATAAAGGAAGACCAAGAGT 58.440 38.462 0.00 0.00 38.94 3.24
2869 3515 4.818005 TCGTTCTAGGACGCACTCATATAA 59.182 41.667 19.16 0.00 42.50 0.98
2881 3527 9.916397 CAAATTGTATTGTATTCGTTCTAGGAC 57.084 33.333 0.00 0.00 0.00 3.85
2932 3578 5.355350 AGGAGTGATGCAGTTGCTTAAATAC 59.645 40.000 5.62 0.00 42.66 1.89
2939 3585 2.283145 AAAGGAGTGATGCAGTTGCT 57.717 45.000 5.62 0.00 42.66 3.91
3265 3911 3.763097 TTCGCATGCTGGTCAAAATAG 57.237 42.857 17.13 0.00 0.00 1.73
3672 4325 0.389391 CGAACGCAGGGGTGAGATAT 59.611 55.000 0.00 0.00 0.00 1.63
4004 4659 1.589716 GCAGACAGCCTTCCGCAAAT 61.590 55.000 0.00 0.00 41.38 2.32
4102 4757 2.370189 AGGCATAAGCTCATACTCCCAC 59.630 50.000 0.00 0.00 41.70 4.61
4103 4758 2.369860 CAGGCATAAGCTCATACTCCCA 59.630 50.000 0.00 0.00 41.70 4.37
4104 4759 2.873649 GCAGGCATAAGCTCATACTCCC 60.874 54.545 0.00 0.00 41.70 4.30
4105 4760 2.038295 AGCAGGCATAAGCTCATACTCC 59.962 50.000 0.00 0.00 41.70 3.85
4106 4761 3.065655 CAGCAGGCATAAGCTCATACTC 58.934 50.000 0.00 0.00 39.50 2.59
4209 4878 1.990799 TATTCTCGTTCACTGCACCG 58.009 50.000 0.00 0.00 0.00 4.94
4354 5023 3.793144 GCAGCGCTTTCTGACGGG 61.793 66.667 7.50 0.00 36.19 5.28
4386 5055 4.436852 CGCACAGTTCAGTGTTACAGTTTT 60.437 41.667 0.00 0.00 41.52 2.43
4483 5179 3.002656 CACATGGAACTGTCAAGTGTCAC 59.997 47.826 0.00 0.00 36.51 3.67
4509 5208 5.503031 CGAAATGGCGAATATGGATATCAGC 60.503 44.000 4.83 0.00 0.00 4.26
4550 5249 1.228154 GCGAAAAGTGGTCAGGGGT 60.228 57.895 0.00 0.00 0.00 4.95
4584 5283 4.025396 CGATGAAAATCAGCTATGCGAAGT 60.025 41.667 0.00 0.00 29.10 3.01
4727 5426 4.222847 GACGGCGAGACCCATCCC 62.223 72.222 16.62 0.00 33.26 3.85
4811 5510 6.704493 CCATCCATATTTTCATTCAAGGCAAG 59.296 38.462 0.00 0.00 0.00 4.01
4927 5626 5.461032 AGGGATCGATGAGTAACTGATTC 57.539 43.478 0.54 0.00 0.00 2.52
4960 5663 0.971386 AATGCCCCTTTCTGCAACTG 59.029 50.000 0.00 0.00 41.50 3.16
4961 5664 1.620323 GAAATGCCCCTTTCTGCAACT 59.380 47.619 0.00 0.00 41.50 3.16
4962 5665 1.620323 AGAAATGCCCCTTTCTGCAAC 59.380 47.619 5.51 0.00 42.43 4.17
4963 5666 1.895131 GAGAAATGCCCCTTTCTGCAA 59.105 47.619 9.86 0.00 43.69 4.08
5151 6184 2.763039 TGCATCCCTCTCCTACATGAA 58.237 47.619 0.00 0.00 0.00 2.57
5152 6185 2.477104 TGCATCCCTCTCCTACATGA 57.523 50.000 0.00 0.00 0.00 3.07
5153 6186 3.474600 CTTTGCATCCCTCTCCTACATG 58.525 50.000 0.00 0.00 0.00 3.21
5154 6187 2.441001 CCTTTGCATCCCTCTCCTACAT 59.559 50.000 0.00 0.00 0.00 2.29
5158 6191 1.211456 CTCCTTTGCATCCCTCTCCT 58.789 55.000 0.00 0.00 0.00 3.69
5231 6264 7.148950 GCTTTCATCCGAAATCACTATACTACG 60.149 40.741 0.00 0.00 40.32 3.51
5235 6268 6.844696 TGCTTTCATCCGAAATCACTATAC 57.155 37.500 0.00 0.00 40.32 1.47


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

AutoCloner maintained by Alex Coulton.