Multiple sequence alignment - TraesCS5A01G382600

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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 TraesCS5A01G382600 chr5A 100.000 4135 0 0 1 4135 580468427 580464293 0.000000e+00 7637.0
1 TraesCS5A01G382600 chr5A 88.085 235 22 4 2902 3131 580449644 580449877 1.460000e-69 274.0
2 TraesCS5A01G382600 chr5A 90.991 111 10 0 2474 2584 57376725 57376615 2.570000e-32 150.0
3 TraesCS5A01G382600 chr5A 97.727 44 1 0 2474 2517 575658477 575658520 4.430000e-10 76.8
4 TraesCS5A01G382600 chr5D 93.608 4083 149 57 1 4018 460397058 460393023 0.000000e+00 5991.0
5 TraesCS5A01G382600 chr5D 88.757 338 26 8 2832 3158 460225444 460225780 1.790000e-108 403.0
6 TraesCS5A01G382600 chr5D 95.798 119 5 0 4017 4135 460392861 460392743 4.220000e-45 193.0
7 TraesCS5A01G382600 chr5D 95.918 98 4 0 3915 4012 139441012 139440915 4.280000e-35 159.0
8 TraesCS5A01G382600 chr5D 90.351 114 11 0 2471 2584 66755390 66755503 2.570000e-32 150.0
9 TraesCS5A01G382600 chr5D 82.883 111 19 0 2474 2584 457777065 457777175 2.630000e-17 100.0
10 TraesCS5A01G382600 chr5B 94.182 2853 102 30 1307 4135 565931045 565928233 0.000000e+00 4290.0
11 TraesCS5A01G382600 chr5B 94.112 1087 24 17 252 1307 565932149 565931072 0.000000e+00 1616.0
12 TraesCS5A01G382600 chr5B 85.841 339 33 7 2824 3158 565897386 565897713 3.060000e-91 346.0
13 TraesCS5A01G382600 chr5B 90.800 250 20 3 1 248 565932635 565932387 8.570000e-87 331.0
14 TraesCS5A01G382600 chr5B 88.346 266 20 5 2902 3158 565880099 565880362 4.010000e-80 309.0
15 TraesCS5A01G382600 chr5B 93.694 111 7 0 3902 4012 166379073 166379183 2.560000e-37 167.0
16 TraesCS5A01G382600 chr5B 90.991 111 10 0 2474 2584 64266318 64266208 2.570000e-32 150.0
17 TraesCS5A01G382600 chr5B 82.883 111 19 0 2474 2584 559992112 559992222 2.630000e-17 100.0
18 TraesCS5A01G382600 chr7B 94.845 97 5 0 3915 4011 162120908 162120812 7.160000e-33 152.0
19 TraesCS5A01G382600 chr7B 92.381 105 7 1 3915 4018 632337871 632337767 9.260000e-32 148.0
20 TraesCS5A01G382600 chr3A 93.269 104 5 2 3910 4011 470095675 470095778 7.160000e-33 152.0
21 TraesCS5A01G382600 chr3A 96.429 56 2 0 2778 2833 147791563 147791618 4.400000e-15 93.5
22 TraesCS5A01G382600 chr4A 94.845 97 4 1 3915 4011 37060207 37060112 2.570000e-32 150.0
23 TraesCS5A01G382600 chr2B 93.204 103 6 1 3913 4015 480409375 480409476 2.570000e-32 150.0
24 TraesCS5A01G382600 chr3D 96.429 56 2 0 2778 2833 134083624 134083679 4.400000e-15 93.5
25 TraesCS5A01G382600 chr3B 96.429 56 2 0 2778 2833 190470961 190471016 4.400000e-15 93.5


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 TraesCS5A01G382600 chr5A 580464293 580468427 4134 True 7637 7637 100.000000 1 4135 1 chr5A.!!$R2 4134
1 TraesCS5A01G382600 chr5D 460392743 460397058 4315 True 3092 5991 94.703000 1 4135 2 chr5D.!!$R2 4134
2 TraesCS5A01G382600 chr5B 565928233 565932635 4402 True 2079 4290 93.031333 1 4135 3 chr5B.!!$R2 4134

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
683 930 0.253327 GGCTCCAACCTCCAAGTAGG 59.747 60.0 0.00 0.00 42.82 3.18 F
1865 2180 0.103208 CGGTACATGTCAGAGAGGGC 59.897 60.0 0.00 0.00 0.00 5.19 F
1927 2246 0.385390 CCACTGCAAAAAGGAAGCGT 59.615 50.0 0.00 0.00 0.00 5.07 F
2835 3171 0.249911 GACGTCCCATGGGAGTATGC 60.250 60.0 34.67 20.24 46.16 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 2637 0.390603 CCCTGGTCGACGCATAACAA 60.391 55.000 9.92 0.0 0.0 2.83 R
2722 3058 0.421495 TCTTCCCCTCATTCCCTGGA 59.579 55.000 0.00 0.0 0.0 3.86 R
2915 3251 0.512952 CAGCCGACGAAAGAAACTGG 59.487 55.000 0.00 0.0 0.0 4.00 R
3824 4162 1.067565 TGCCTCTGATCGTCTTCACAC 60.068 52.381 0.00 0.0 0.0 3.82 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
63 64 5.880054 TTACTTCTTGCCATCACTTTAGC 57.120 39.130 0.00 0.00 0.00 3.09
71 72 2.615912 GCCATCACTTTAGCATCACTCC 59.384 50.000 0.00 0.00 0.00 3.85
95 97 9.730705 TCCCATTGATGCTCTAGATAAATAAAG 57.269 33.333 0.00 0.00 0.00 1.85
169 176 6.053005 CCCGATTTTCATAAGCAGTACCTTA 58.947 40.000 0.00 0.00 0.00 2.69
231 238 8.622948 ACCTTAAGAAACCAAGTAAGAATCAG 57.377 34.615 3.36 0.00 0.00 2.90
256 421 4.668576 ATGTGATAACTGCAACAACTCG 57.331 40.909 0.00 0.00 0.00 4.18
382 625 3.003689 CCACAAAGAGCTAAACACTGTGG 59.996 47.826 13.09 12.65 44.46 4.17
564 811 2.027192 GCACTGGATCCAAGTTGGTAGA 60.027 50.000 21.35 2.82 39.03 2.59
574 821 1.349067 AGTTGGTAGACCTCCACACC 58.651 55.000 0.00 0.00 34.45 4.16
683 930 0.253327 GGCTCCAACCTCCAAGTAGG 59.747 60.000 0.00 0.00 42.82 3.18
780 1042 2.461695 TCACCACTTCATCTCTCCTCC 58.538 52.381 0.00 0.00 0.00 4.30
826 1088 2.283173 CCCCCACCCAGTTCTTGC 60.283 66.667 0.00 0.00 0.00 4.01
849 1111 1.272985 CCTCTCTCTCTTCCACCACCT 60.273 57.143 0.00 0.00 0.00 4.00
898 1160 4.142359 GCATACACGGAGAGAGAAAGAGAA 60.142 45.833 0.00 0.00 0.00 2.87
900 1162 2.230266 ACACGGAGAGAGAAAGAGAAGC 59.770 50.000 0.00 0.00 0.00 3.86
902 1164 1.821753 CGGAGAGAGAAAGAGAAGCCA 59.178 52.381 0.00 0.00 0.00 4.75
1149 1417 1.220206 CGGCATGCAGGAAGACTCT 59.780 57.895 21.36 0.00 0.00 3.24
1333 1638 9.827411 AATTTGATTTTTCTAGCTTCTACGAAC 57.173 29.630 0.00 0.00 0.00 3.95
1394 1699 6.919721 TGGTTGTTTAGCAAAAGATCCATAC 58.080 36.000 0.00 0.00 39.03 2.39
1442 1747 9.944376 ATATGTAGAGTTTGAACATGTGTAAGT 57.056 29.630 0.00 0.00 35.54 2.24
1444 1749 8.500753 TGTAGAGTTTGAACATGTGTAAGTTT 57.499 30.769 0.00 0.00 0.00 2.66
1445 1750 8.952278 TGTAGAGTTTGAACATGTGTAAGTTTT 58.048 29.630 0.00 0.00 0.00 2.43
1446 1751 9.434559 GTAGAGTTTGAACATGTGTAAGTTTTC 57.565 33.333 0.00 0.00 0.00 2.29
1448 1753 8.398665 AGAGTTTGAACATGTGTAAGTTTTCTC 58.601 33.333 0.00 0.00 0.00 2.87
1450 1755 9.391006 AGTTTGAACATGTGTAAGTTTTCTCTA 57.609 29.630 0.00 0.00 0.00 2.43
1451 1756 9.651718 GTTTGAACATGTGTAAGTTTTCTCTAG 57.348 33.333 0.00 0.00 0.00 2.43
1494 1799 8.221251 GGAACCTGATTAATTATCTCCTTTCCT 58.779 37.037 0.00 0.00 34.17 3.36
1495 1800 9.634021 GAACCTGATTAATTATCTCCTTTCCTT 57.366 33.333 0.00 0.00 34.17 3.36
1496 1801 9.634021 AACCTGATTAATTATCTCCTTTCCTTC 57.366 33.333 0.00 0.00 34.17 3.46
1531 1836 5.938125 TCTGGTTGTTTAGCTAAAGATCCAC 59.062 40.000 29.07 19.20 35.00 4.02
1534 1839 6.547880 TGGTTGTTTAGCTAAAGATCCACAAA 59.452 34.615 29.07 15.28 35.00 2.83
1582 1893 2.338015 CGAGCATGTGCAGGCCTTT 61.338 57.895 0.00 0.00 45.16 3.11
1592 1903 4.881920 TGTGCAGGCCTTTAATCTTTTTC 58.118 39.130 0.00 0.00 0.00 2.29
1596 1907 3.837731 CAGGCCTTTAATCTTTTTCCCCA 59.162 43.478 0.00 0.00 0.00 4.96
1639 1950 9.669353 TCGAGTTTGGATTCGTTATATACTTAC 57.331 33.333 0.00 0.00 36.51 2.34
1864 2179 0.747255 CCGGTACATGTCAGAGAGGG 59.253 60.000 0.00 0.00 0.00 4.30
1865 2180 0.103208 CGGTACATGTCAGAGAGGGC 59.897 60.000 0.00 0.00 0.00 5.19
1878 2193 4.015084 CAGAGAGGGCAAGAAAATGATGT 58.985 43.478 0.00 0.00 0.00 3.06
1895 2210 5.981088 TGATGTTGCATACACTTTCCATT 57.019 34.783 4.23 0.00 40.19 3.16
1926 2245 0.667993 TCCACTGCAAAAAGGAAGCG 59.332 50.000 0.00 0.00 0.00 4.68
1927 2246 0.385390 CCACTGCAAAAAGGAAGCGT 59.615 50.000 0.00 0.00 0.00 5.07
1928 2247 1.202405 CCACTGCAAAAAGGAAGCGTT 60.202 47.619 0.00 0.00 0.00 4.84
1929 2248 2.034053 CCACTGCAAAAAGGAAGCGTTA 59.966 45.455 0.00 0.00 0.00 3.18
1930 2249 3.305335 CCACTGCAAAAAGGAAGCGTTAT 60.305 43.478 0.00 0.00 0.00 1.89
1931 2250 4.298332 CACTGCAAAAAGGAAGCGTTATT 58.702 39.130 0.00 0.00 0.00 1.40
1932 2251 5.457140 CACTGCAAAAAGGAAGCGTTATTA 58.543 37.500 0.00 0.00 0.00 0.98
1933 2252 5.569059 CACTGCAAAAAGGAAGCGTTATTAG 59.431 40.000 0.00 0.00 0.00 1.73
1934 2253 4.481463 TGCAAAAAGGAAGCGTTATTAGC 58.519 39.130 0.00 0.00 0.00 3.09
1935 2254 4.022762 TGCAAAAAGGAAGCGTTATTAGCA 60.023 37.500 0.00 0.00 37.01 3.49
1944 2263 5.965918 GGAAGCGTTATTAGCAGTTTCATTC 59.034 40.000 0.00 0.00 37.01 2.67
1947 2266 5.294552 AGCGTTATTAGCAGTTTCATTCTCC 59.705 40.000 0.00 0.00 37.01 3.71
1950 2269 6.183360 CGTTATTAGCAGTTTCATTCTCCGTT 60.183 38.462 0.00 0.00 0.00 4.44
1951 2270 5.803020 ATTAGCAGTTTCATTCTCCGTTC 57.197 39.130 0.00 0.00 0.00 3.95
1954 2273 2.160417 GCAGTTTCATTCTCCGTTCTGG 59.840 50.000 0.00 0.00 40.09 3.86
1964 2284 2.144482 TCCGTTCTGGAAACGAAGAC 57.856 50.000 11.53 0.00 46.38 3.01
1972 2292 6.510478 CGTTCTGGAAACGAAGACATGTTTAA 60.510 38.462 0.00 0.00 45.64 1.52
2044 2367 1.269448 CATGTGGCGTTTGGCTAAAGT 59.731 47.619 0.00 0.00 42.94 2.66
2047 2370 0.671251 TGGCGTTTGGCTAAAGTTGG 59.329 50.000 0.00 0.00 42.94 3.77
2056 2379 1.067974 GGCTAAAGTTGGTGCCGTTTT 59.932 47.619 0.00 0.00 35.79 2.43
2057 2380 2.390938 GCTAAAGTTGGTGCCGTTTTC 58.609 47.619 0.00 0.00 0.00 2.29
2261 2588 6.884836 GGTTGGACTTGGAACTAGATTATGTT 59.115 38.462 0.00 0.00 0.00 2.71
2292 2619 8.200792 ACTGATTTGCAAGTGGTAAATGTAAAA 58.799 29.630 0.00 0.00 41.16 1.52
2310 2637 6.451393 TGTAAAATTTGTGGCTAATTTCGCT 58.549 32.000 0.00 0.00 34.91 4.93
2674 3007 0.824109 TTGCCTCGACTGGTATGGAG 59.176 55.000 0.00 0.00 0.00 3.86
2691 3024 4.222124 TGGAGGGAGCTTAGTTTGAATC 57.778 45.455 0.00 0.00 0.00 2.52
2695 3028 4.003648 AGGGAGCTTAGTTTGAATCAACG 58.996 43.478 0.00 0.00 0.00 4.10
2702 3035 2.571212 AGTTTGAATCAACGAGTGCCA 58.429 42.857 0.00 0.00 0.00 4.92
2710 3043 2.503331 TCAACGAGTGCCACAATCATT 58.497 42.857 0.00 0.00 0.00 2.57
2835 3171 0.249911 GACGTCCCATGGGAGTATGC 60.250 60.000 34.67 20.24 46.16 3.14
2940 3276 3.793797 TTCTTTCGTCGGCTGATGATA 57.206 42.857 18.10 12.43 39.80 2.15
3022 3358 0.321653 GCCATCGGTCTTGGTCAGTT 60.322 55.000 0.00 0.00 36.57 3.16
3031 3367 2.550180 GTCTTGGTCAGTTTCTTCAGCC 59.450 50.000 0.00 0.00 0.00 4.85
3044 3380 7.806960 CAGTTTCTTCAGCCAAAATTCTCTTAG 59.193 37.037 0.00 0.00 0.00 2.18
3045 3381 7.721399 AGTTTCTTCAGCCAAAATTCTCTTAGA 59.279 33.333 0.00 0.00 0.00 2.10
3136 3473 7.307455 GGACAAGTACAAGAACAAGAGCTAAAG 60.307 40.741 0.00 0.00 0.00 1.85
3168 3506 4.414337 AAGAGGAAGACTATGATGCCAC 57.586 45.455 0.00 0.00 0.00 5.01
3490 3828 6.381801 AGCACACTATTTTTGTAATCTGTGC 58.618 36.000 17.23 17.23 46.12 4.57
3504 3842 1.224069 CTGTGCGTGGTCAAGTGGAG 61.224 60.000 0.00 0.00 0.00 3.86
3512 3850 0.476771 GGTCAAGTGGAGGGGAACAA 59.523 55.000 0.00 0.00 0.00 2.83
3655 3993 2.436417 CCAGGGTTGTGGTGATAACAG 58.564 52.381 0.00 0.00 32.32 3.16
3824 4162 6.270815 CCTCAAAAGGAATATGCAGATGTTG 58.729 40.000 0.00 0.00 46.67 3.33
3883 4221 5.469373 TGCGTAATAGAAATGAACTGCTG 57.531 39.130 0.00 0.00 0.00 4.41
3896 4234 8.579850 AAATGAACTGCTGAAAGGATGTATTA 57.420 30.769 0.00 0.00 29.63 0.98
3897 4235 8.757982 AATGAACTGCTGAAAGGATGTATTAT 57.242 30.769 0.00 0.00 29.63 1.28
3898 4236 7.558161 TGAACTGCTGAAAGGATGTATTATG 57.442 36.000 0.00 0.00 29.63 1.90
3899 4237 6.038603 TGAACTGCTGAAAGGATGTATTATGC 59.961 38.462 0.00 0.00 29.63 3.14
3900 4238 4.512944 ACTGCTGAAAGGATGTATTATGCG 59.487 41.667 0.00 0.00 29.63 4.73
3901 4239 3.814842 TGCTGAAAGGATGTATTATGCGG 59.185 43.478 0.00 0.00 0.00 5.69
3953 4291 2.844122 AAGTGTCGCAGTTTTGAACC 57.156 45.000 0.00 0.00 0.00 3.62
3987 4325 5.479716 AACCTTAGTTCAAAACTGTGACG 57.520 39.130 2.65 0.00 42.84 4.35
4026 4527 6.439058 GGAGGGAGTAGCATCTAGACATTAAT 59.561 42.308 0.00 0.00 0.00 1.40
4124 4625 0.108472 CAGAGGCATCTCAACGCTCA 60.108 55.000 0.00 0.00 42.34 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 6.363357 GTGATGGCAAGAAGTAATTTTGTCAC 59.637 38.462 7.08 0.00 39.00 3.67
35 36 6.655078 AGTGATGGCAAGAAGTAATTTTGT 57.345 33.333 0.00 0.00 0.00 2.83
95 97 4.095610 GTTGTGTGCTTGAACTTGTGTAC 58.904 43.478 0.00 0.00 0.00 2.90
228 235 8.040727 AGTTGTTGCAGTTATCACATATACTGA 58.959 33.333 0.00 0.00 40.24 3.41
231 238 7.010183 ACGAGTTGTTGCAGTTATCACATATAC 59.990 37.037 0.00 0.00 0.00 1.47
306 549 8.654094 GGATTATTTTTGGATCCAGGATCAATT 58.346 33.333 27.79 13.80 40.50 2.32
314 557 9.264719 GCATTTAAGGATTATTTTTGGATCCAG 57.735 33.333 15.53 0.00 41.43 3.86
319 562 8.766476 TCCATGCATTTAAGGATTATTTTTGGA 58.234 29.630 0.00 0.00 0.00 3.53
343 586 4.216411 TGTGGCCTATGAGTTTTAGTCC 57.784 45.455 3.32 0.00 0.00 3.85
382 625 1.312815 GGTGTCCAGCTATCCATTGC 58.687 55.000 0.00 0.00 0.00 3.56
520 766 2.305928 TGAAATGTCAACAGGGTGGTG 58.694 47.619 0.00 0.00 36.12 4.17
521 767 2.746279 TGAAATGTCAACAGGGTGGT 57.254 45.000 0.00 0.00 0.00 4.16
522 768 3.129287 GCTATGAAATGTCAACAGGGTGG 59.871 47.826 0.00 0.00 37.30 4.61
564 811 1.119574 AGTTAGCACGGTGTGGAGGT 61.120 55.000 10.24 0.00 33.64 3.85
574 821 1.204062 CGTGTTGCCAGTTAGCACG 59.796 57.895 0.00 0.00 43.97 5.34
683 930 4.803088 CAGTTAGTTAGAGCATGAGTGAGC 59.197 45.833 0.00 0.00 0.00 4.26
780 1042 9.116067 CGTATATATAGAGGGAAGAGAAAGAGG 57.884 40.741 0.00 0.00 0.00 3.69
826 1088 2.495669 GTGGTGGAAGAGAGAGAGGAAG 59.504 54.545 0.00 0.00 0.00 3.46
849 1111 3.114606 TGGCTTGTGATTAGGAGATGGA 58.885 45.455 0.00 0.00 0.00 3.41
898 1160 0.107606 CAGCTGCTGATCTCTTGGCT 60.108 55.000 24.88 0.00 32.44 4.75
900 1162 2.395651 GCAGCTGCTGATCTCTTGG 58.604 57.895 32.30 3.57 38.21 3.61
1275 1544 7.463431 ACCAACAACCTACCATAATAAGTTGA 58.537 34.615 7.61 0.00 38.32 3.18
1276 1545 7.696992 ACCAACAACCTACCATAATAAGTTG 57.303 36.000 0.00 0.00 40.24 3.16
1329 1634 3.068307 AGGAGATAATCAGGTTCCGTTCG 59.932 47.826 0.00 0.00 33.16 3.95
1333 1638 4.101741 AGGAAAGGAGATAATCAGGTTCCG 59.898 45.833 0.00 0.00 38.09 4.30
1444 1749 9.981460 TCCATGCATAGAATCTATACTAGAGAA 57.019 33.333 0.00 0.00 38.38 2.87
1445 1750 9.981460 TTCCATGCATAGAATCTATACTAGAGA 57.019 33.333 3.23 0.00 38.38 3.10
1448 1753 8.976353 AGGTTCCATGCATAGAATCTATACTAG 58.024 37.037 17.64 0.00 31.66 2.57
1450 1755 7.455953 TCAGGTTCCATGCATAGAATCTATACT 59.544 37.037 18.50 5.25 31.66 2.12
1451 1756 7.615403 TCAGGTTCCATGCATAGAATCTATAC 58.385 38.462 18.50 2.53 31.66 1.47
1453 1758 6.692849 TCAGGTTCCATGCATAGAATCTAT 57.307 37.500 18.50 0.00 31.66 1.98
1494 1799 7.920682 GCTAAACAACCAGAATGAAAAGAAGAA 59.079 33.333 0.00 0.00 39.69 2.52
1495 1800 7.285401 AGCTAAACAACCAGAATGAAAAGAAGA 59.715 33.333 0.00 0.00 39.69 2.87
1496 1801 7.428826 AGCTAAACAACCAGAATGAAAAGAAG 58.571 34.615 0.00 0.00 39.69 2.85
1539 1850 8.172484 CGAGCTCTACATATGTCTAACTATGTC 58.828 40.741 12.68 0.00 38.94 3.06
1545 1856 5.049336 TGCTCGAGCTCTACATATGTCTAAC 60.049 44.000 35.27 3.12 42.66 2.34
1592 1903 7.985752 ACTCGAGAAAACTAGTTTATAATGGGG 59.014 37.037 21.68 10.80 31.63 4.96
1639 1950 7.009815 GCATGTCATGTTTTATTCAACATCCTG 59.990 37.037 14.26 0.00 44.08 3.86
1655 1966 1.268066 TGCCCATTTGCATGTCATGT 58.732 45.000 14.26 0.00 36.04 3.21
1864 2179 5.865552 AGTGTATGCAACATCATTTTCTTGC 59.134 36.000 0.00 0.00 41.10 4.01
1865 2180 7.878477 AAGTGTATGCAACATCATTTTCTTG 57.122 32.000 0.00 0.00 41.10 3.02
1919 2238 4.575885 TGAAACTGCTAATAACGCTTCCT 58.424 39.130 0.00 0.00 0.00 3.36
1921 2240 6.776094 AGAATGAAACTGCTAATAACGCTTC 58.224 36.000 0.00 0.00 0.00 3.86
1926 2245 6.663944 ACGGAGAATGAAACTGCTAATAAC 57.336 37.500 0.00 0.00 0.00 1.89
1927 2246 7.064609 CAGAACGGAGAATGAAACTGCTAATAA 59.935 37.037 0.00 0.00 0.00 1.40
1928 2247 6.535150 CAGAACGGAGAATGAAACTGCTAATA 59.465 38.462 0.00 0.00 0.00 0.98
1929 2248 5.352569 CAGAACGGAGAATGAAACTGCTAAT 59.647 40.000 0.00 0.00 0.00 1.73
1930 2249 4.690748 CAGAACGGAGAATGAAACTGCTAA 59.309 41.667 0.00 0.00 0.00 3.09
1931 2250 4.245660 CAGAACGGAGAATGAAACTGCTA 58.754 43.478 0.00 0.00 0.00 3.49
1932 2251 3.070018 CAGAACGGAGAATGAAACTGCT 58.930 45.455 0.00 0.00 0.00 4.24
1933 2252 2.160417 CCAGAACGGAGAATGAAACTGC 59.840 50.000 0.00 0.00 36.56 4.40
1934 2253 3.664107 TCCAGAACGGAGAATGAAACTG 58.336 45.455 0.00 0.00 39.64 3.16
1947 2266 2.800544 ACATGTCTTCGTTTCCAGAACG 59.199 45.455 5.04 5.04 44.29 3.95
1950 2269 6.934645 AGATTAAACATGTCTTCGTTTCCAGA 59.065 34.615 0.00 0.00 36.72 3.86
1951 2270 7.017645 CAGATTAAACATGTCTTCGTTTCCAG 58.982 38.462 0.00 0.00 36.72 3.86
1954 2273 8.922676 TCTACAGATTAAACATGTCTTCGTTTC 58.077 33.333 0.00 0.00 36.72 2.78
1972 2292 7.675195 AGCCTCAATCATCTATCTTCTACAGAT 59.325 37.037 0.00 0.00 45.08 2.90
1994 2317 2.488528 CCAGCATGATTATCCACAGCCT 60.489 50.000 0.00 0.00 39.69 4.58
2044 2367 4.082679 GGTGTATAATGAAAACGGCACCAA 60.083 41.667 0.00 0.00 43.13 3.67
2047 2370 4.688511 TGGTGTATAATGAAAACGGCAC 57.311 40.909 0.00 0.00 0.00 5.01
2085 2408 5.871834 TGTGGCAACTTTATGGTAGTAAGT 58.128 37.500 0.00 0.00 33.76 2.24
2192 2519 9.806203 CAAATAAGATTCTCCATTGCAATTGTA 57.194 29.630 9.83 0.00 0.00 2.41
2261 2588 3.472652 ACCACTTGCAAATCAGTTCGTA 58.527 40.909 0.00 0.00 0.00 3.43
2292 2619 4.519540 ACAAGCGAAATTAGCCACAAAT 57.480 36.364 0.00 0.00 34.64 2.32
2310 2637 0.390603 CCCTGGTCGACGCATAACAA 60.391 55.000 9.92 0.00 0.00 2.83
2394 2721 4.099419 GTCTCCTCCTCCTTCTTGATCTTC 59.901 50.000 0.00 0.00 0.00 2.87
2674 3007 4.000988 TCGTTGATTCAAACTAAGCTCCC 58.999 43.478 0.00 0.00 0.00 4.30
2691 3024 2.995466 AATGATTGTGGCACTCGTTG 57.005 45.000 19.83 0.00 0.00 4.10
2695 3028 8.986477 AAAAATAGTTAATGATTGTGGCACTC 57.014 30.769 19.83 9.57 0.00 3.51
2722 3058 0.421495 TCTTCCCCTCATTCCCTGGA 59.579 55.000 0.00 0.00 0.00 3.86
2835 3171 1.153549 GGGCGCAGGAGTGAAGTAG 60.154 63.158 10.83 0.00 0.00 2.57
2915 3251 0.512952 CAGCCGACGAAAGAAACTGG 59.487 55.000 0.00 0.00 0.00 4.00
2940 3276 4.159557 ACAAACATCCTGCAGGGTAATTT 58.840 39.130 32.23 24.06 36.25 1.82
3022 3358 8.463930 TTTCTAAGAGAATTTTGGCTGAAGAA 57.536 30.769 0.00 0.00 33.67 2.52
3136 3473 2.119495 TCTTCCTCTTACTGCCCCATC 58.881 52.381 0.00 0.00 0.00 3.51
3168 3506 2.030540 CACTGCAAGAACACCATCCTTG 60.031 50.000 0.00 0.00 40.00 3.61
3490 3828 1.764571 TTCCCCTCCACTTGACCACG 61.765 60.000 0.00 0.00 0.00 4.94
3504 3842 2.973082 GCACATGGCTTGTTCCCC 59.027 61.111 2.88 0.00 36.00 4.81
3655 3993 4.137543 AGCTTATGCAATGTACTTAGCCC 58.862 43.478 3.16 0.00 42.74 5.19
3767 4105 4.397420 ACAGCTGTGTGATTCCAATTGTA 58.603 39.130 20.97 0.00 34.75 2.41
3824 4162 1.067565 TGCCTCTGATCGTCTTCACAC 60.068 52.381 0.00 0.00 0.00 3.82
3883 4221 4.142600 GGCATCCGCATAATACATCCTTTC 60.143 45.833 0.00 0.00 41.24 2.62
3896 4234 5.186198 GGAGTATTTTATAGGCATCCGCAT 58.814 41.667 0.00 0.00 41.24 4.73
3897 4235 4.564821 GGGAGTATTTTATAGGCATCCGCA 60.565 45.833 0.00 0.00 41.24 5.69
3898 4236 3.939592 GGGAGTATTTTATAGGCATCCGC 59.060 47.826 0.00 0.00 37.44 5.54
3899 4237 5.420409 GAGGGAGTATTTTATAGGCATCCG 58.580 45.833 0.00 0.00 0.00 4.18
3900 4238 5.250774 TGGAGGGAGTATTTTATAGGCATCC 59.749 44.000 0.00 0.00 0.00 3.51
3901 4239 6.374417 TGGAGGGAGTATTTTATAGGCATC 57.626 41.667 0.00 0.00 0.00 3.91
3983 4321 3.194861 CTCCGATCCAAAATAAGCGTCA 58.805 45.455 0.00 0.00 0.00 4.35
3987 4325 3.142174 CTCCCTCCGATCCAAAATAAGC 58.858 50.000 0.00 0.00 0.00 3.09
4038 4539 2.082140 ATGCGGTAGGATAGTGACCA 57.918 50.000 0.00 0.00 32.39 4.02
4039 4540 3.573110 AGTTATGCGGTAGGATAGTGACC 59.427 47.826 0.00 0.00 32.26 4.02
4046 4547 6.646267 TCTTGTTTTAGTTATGCGGTAGGAT 58.354 36.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.