Multiple sequence alignment - TraesCS3A01G424800

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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 TraesCS3A01G424800 chr3A 100.000 3625 0 0 1 3625 667352188 667355812 0.000000e+00 6695.0
1 TraesCS3A01G424800 chr3A 84.901 755 76 19 44 771 577079414 577078671 0.000000e+00 728.0
2 TraesCS3A01G424800 chr3A 82.197 792 79 30 1540 2300 667345289 667346049 3.070000e-175 625.0
3 TraesCS3A01G424800 chr3A 77.819 541 100 15 887 1422 667314488 667315013 2.100000e-82 316.0
4 TraesCS3A01G424800 chr3A 83.871 248 38 2 1917 2163 667132901 667133147 6.050000e-58 235.0
5 TraesCS3A01G424800 chr3A 80.612 98 14 5 2784 2876 743533678 743533581 1.810000e-08 71.3
6 TraesCS3A01G424800 chr3B 90.314 2137 105 43 1540 3623 704324365 704326452 0.000000e+00 2706.0
7 TraesCS3A01G424800 chr3B 90.312 640 43 11 883 1512 704323633 704324263 0.000000e+00 821.0
8 TraesCS3A01G424800 chr3B 79.262 786 93 25 1544 2303 704311631 704312372 5.440000e-133 484.0
9 TraesCS3A01G424800 chr3B 77.840 537 96 15 892 1422 704309573 704310092 9.770000e-81 311.0
10 TraesCS3A01G424800 chr3B 83.534 249 37 4 1917 2163 704025611 704025857 2.820000e-56 230.0
11 TraesCS3A01G424800 chr3B 82.845 239 37 4 1917 2153 704109739 704109975 1.020000e-50 211.0
12 TraesCS3A01G424800 chr3D 88.961 1386 82 24 1710 3073 532170383 532171719 0.000000e+00 1646.0
13 TraesCS3A01G424800 chr3D 93.412 759 32 9 774 1516 532169253 532170009 0.000000e+00 1109.0
14 TraesCS3A01G424800 chr3D 87.891 768 47 16 44 771 304027020 304026259 0.000000e+00 861.0
15 TraesCS3A01G424800 chr3D 91.903 494 20 7 3137 3623 532172093 532172573 0.000000e+00 673.0
16 TraesCS3A01G424800 chr3D 79.494 790 90 26 1540 2303 532155760 532156503 2.510000e-136 496.0
17 TraesCS3A01G424800 chr3D 78.558 541 91 17 897 1430 532153632 532154154 2.090000e-87 333.0
18 TraesCS3A01G424800 chr3D 75.551 544 94 27 1917 2439 532105488 532106013 7.830000e-57 231.0
19 TraesCS3A01G424800 chr3D 82.639 144 22 3 384 526 596722764 596722623 1.370000e-24 124.0
20 TraesCS3A01G424800 chr7D 87.126 769 50 15 44 772 327396842 327397601 0.000000e+00 826.0
21 TraesCS3A01G424800 chr7D 89.706 68 5 1 3014 3079 461144020 461143953 6.450000e-13 86.1
22 TraesCS3A01G424800 chr7A 95.472 508 9 3 1 494 118160242 118160749 0.000000e+00 798.0
23 TraesCS3A01G424800 chr7A 97.419 310 8 0 463 772 118160750 118161059 2.480000e-146 529.0
24 TraesCS3A01G424800 chr5B 83.902 820 63 28 6 765 175230952 175230142 0.000000e+00 719.0
25 TraesCS3A01G424800 chr5B 93.333 45 3 0 728 772 612275646 612275602 2.340000e-07 67.6
26 TraesCS3A01G424800 chr2A 79.667 541 75 24 44 558 596411581 596412112 1.240000e-94 357.0
27 TraesCS3A01G424800 chr7B 87.342 79 6 2 3011 3085 350458220 350458298 1.790000e-13 87.9
28 TraesCS3A01G424800 chr7B 89.831 59 6 0 714 772 739079090 739079032 3.880000e-10 76.8
29 TraesCS3A01G424800 chr7B 91.111 45 4 0 728 772 451509014 451509058 1.090000e-05 62.1
30 TraesCS3A01G424800 chr5A 89.706 68 5 1 3013 3078 613545376 613545309 6.450000e-13 86.1
31 TraesCS3A01G424800 chr4A 82.000 100 13 5 2782 2876 612401294 612401393 3.000000e-11 80.5
32 TraesCS3A01G424800 chr4A 90.000 60 6 0 467 526 629945330 629945389 1.080000e-10 78.7
33 TraesCS3A01G424800 chr1B 85.714 70 10 0 702 771 669240812 669240743 1.400000e-09 75.0
34 TraesCS3A01G424800 chr1B 93.333 45 2 1 728 772 456189922 456189965 8.400000e-07 65.8
35 TraesCS3A01G424800 chr5D 90.741 54 3 2 3031 3082 491100931 491100878 1.810000e-08 71.3


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 TraesCS3A01G424800 chr3A 667352188 667355812 3624 False 6695.000000 6695 100.000000 1 3625 1 chr3A.!!$F4 3624
1 TraesCS3A01G424800 chr3A 577078671 577079414 743 True 728.000000 728 84.901000 44 771 1 chr3A.!!$R1 727
2 TraesCS3A01G424800 chr3A 667345289 667346049 760 False 625.000000 625 82.197000 1540 2300 1 chr3A.!!$F3 760
3 TraesCS3A01G424800 chr3A 667314488 667315013 525 False 316.000000 316 77.819000 887 1422 1 chr3A.!!$F2 535
4 TraesCS3A01G424800 chr3B 704323633 704326452 2819 False 1763.500000 2706 90.313000 883 3623 2 chr3B.!!$F4 2740
5 TraesCS3A01G424800 chr3B 704309573 704312372 2799 False 397.500000 484 78.551000 892 2303 2 chr3B.!!$F3 1411
6 TraesCS3A01G424800 chr3D 532169253 532172573 3320 False 1142.666667 1646 91.425333 774 3623 3 chr3D.!!$F3 2849
7 TraesCS3A01G424800 chr3D 304026259 304027020 761 True 861.000000 861 87.891000 44 771 1 chr3D.!!$R1 727
8 TraesCS3A01G424800 chr3D 532153632 532156503 2871 False 414.500000 496 79.026000 897 2303 2 chr3D.!!$F2 1406
9 TraesCS3A01G424800 chr3D 532105488 532106013 525 False 231.000000 231 75.551000 1917 2439 1 chr3D.!!$F1 522
10 TraesCS3A01G424800 chr7D 327396842 327397601 759 False 826.000000 826 87.126000 44 772 1 chr7D.!!$F1 728
11 TraesCS3A01G424800 chr7A 118160242 118161059 817 False 663.500000 798 96.445500 1 772 2 chr7A.!!$F1 771
12 TraesCS3A01G424800 chr5B 175230142 175230952 810 True 719.000000 719 83.902000 6 765 1 chr5B.!!$R1 759
13 TraesCS3A01G424800 chr2A 596411581 596412112 531 False 357.000000 357 79.667000 44 558 1 chr2A.!!$F1 514

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
39 40 2.063266 GTATCCAACGCTGTTCGAACA 58.937 47.619 28.07 28.07 41.67 3.18 F
1488 1774 0.618981 ACCCCGACTTCTTGATTCCC 59.381 55.000 0.00 0.00 0.00 3.97 F
1706 3423 0.101759 CATTCGAGCAAGGGCATTGG 59.898 55.000 14.30 0.00 44.61 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1687 3359 0.101759 CCAATGCCCTTGCTCGAATG 59.898 55.000 0.0 0.0 38.71 2.67 R
2350 4140 1.039068 CCATCTCCTCATCTCGTGCT 58.961 55.000 0.0 0.0 0.00 4.40 R
3506 5621 1.682854 TGCTTTTCTTGCCTCACTTGG 59.317 47.619 0.0 0.0 0.00 3.61 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
39 40 2.063266 GTATCCAACGCTGTTCGAACA 58.937 47.619 28.07 28.07 41.67 3.18
526 621 2.237393 TGTTTTTGCTTCCACCATGC 57.763 45.000 0.00 0.00 0.00 4.06
578 692 3.372554 GAGGGTGGCTACAGGCGAC 62.373 68.421 1.52 0.00 46.62 5.19
665 783 3.446310 TTTTGAAGGAAAAAGACGCCC 57.554 42.857 0.00 0.00 30.25 6.13
703 821 5.061853 AGAGAATCGTACGGCTATGAGTTA 58.938 41.667 16.52 0.00 42.67 2.24
779 908 3.197116 GCCTAGTAGTGGCCTGTTTAGAA 59.803 47.826 3.32 0.00 44.32 2.10
799 928 5.393962 AGAAAGCGTTCAAGTATTTGCATC 58.606 37.500 14.88 0.00 36.09 3.91
825 954 2.796557 TGTGTGATTTAAATGGGCCGA 58.203 42.857 5.17 0.00 0.00 5.54
869 998 2.159184 CGAGCCTGCTACAAGAAGATCA 60.159 50.000 0.00 0.00 0.00 2.92
876 1005 2.996621 GCTACAAGAAGATCACGCTGTT 59.003 45.455 0.00 0.00 0.00 3.16
1035 1178 0.830648 CGCCATTGTTCCTCTCCCTA 59.169 55.000 0.00 0.00 0.00 3.53
1036 1179 1.202580 CGCCATTGTTCCTCTCCCTAG 60.203 57.143 0.00 0.00 0.00 3.02
1037 1180 1.475930 GCCATTGTTCCTCTCCCTAGC 60.476 57.143 0.00 0.00 0.00 3.42
1423 1582 5.720041 AGGTGTGCCTCTCTTACAGTATAAA 59.280 40.000 0.00 0.00 42.67 1.40
1424 1583 5.811100 GGTGTGCCTCTCTTACAGTATAAAC 59.189 44.000 0.00 0.00 0.00 2.01
1425 1584 5.515626 GTGTGCCTCTCTTACAGTATAAACG 59.484 44.000 0.00 0.00 0.00 3.60
1426 1585 5.184479 TGTGCCTCTCTTACAGTATAAACGT 59.816 40.000 0.00 0.00 0.00 3.99
1427 1586 6.375174 TGTGCCTCTCTTACAGTATAAACGTA 59.625 38.462 0.00 0.00 0.00 3.57
1428 1587 6.690528 GTGCCTCTCTTACAGTATAAACGTAC 59.309 42.308 0.00 0.00 0.00 3.67
1429 1588 6.600822 TGCCTCTCTTACAGTATAAACGTACT 59.399 38.462 0.00 0.00 35.34 2.73
1430 1589 7.770433 TGCCTCTCTTACAGTATAAACGTACTA 59.230 37.037 0.00 0.00 33.29 1.82
1453 1708 2.010582 AAAAAGTTCTTGCGGCGCCA 62.011 50.000 30.82 18.70 0.00 5.69
1466 1723 1.081840 GCGCCAGTGTTCTTTGAGC 60.082 57.895 0.00 0.00 0.00 4.26
1487 1773 2.488153 CAAACCCCGACTTCTTGATTCC 59.512 50.000 0.00 0.00 0.00 3.01
1488 1774 0.618981 ACCCCGACTTCTTGATTCCC 59.381 55.000 0.00 0.00 0.00 3.97
1516 1802 5.475220 GCTACTGGAGATAGAGAGCAACATA 59.525 44.000 0.00 0.00 33.44 2.29
1518 1804 4.280677 ACTGGAGATAGAGAGCAACATAGC 59.719 45.833 0.00 0.00 0.00 2.97
1521 1807 4.280677 GGAGATAGAGAGCAACATAGCAGT 59.719 45.833 0.00 0.00 36.85 4.40
1522 1808 5.452078 AGATAGAGAGCAACATAGCAGTC 57.548 43.478 0.00 0.00 36.85 3.51
1523 1809 4.892345 AGATAGAGAGCAACATAGCAGTCA 59.108 41.667 0.00 0.00 36.85 3.41
1524 1810 3.969287 AGAGAGCAACATAGCAGTCAA 57.031 42.857 0.00 0.00 36.85 3.18
1526 1812 4.841422 AGAGAGCAACATAGCAGTCAAAT 58.159 39.130 0.00 0.00 36.85 2.32
1528 1814 4.330250 AGAGCAACATAGCAGTCAAATGT 58.670 39.130 0.00 0.00 35.40 2.71
1536 1822 3.996150 AGCAGTCAAATGTTGTTCAGG 57.004 42.857 0.00 0.00 0.00 3.86
1537 1823 2.035066 AGCAGTCAAATGTTGTTCAGGC 59.965 45.455 0.00 0.00 0.00 4.85
1538 1824 2.863704 GCAGTCAAATGTTGTTCAGGCC 60.864 50.000 0.00 0.00 0.00 5.19
1615 3286 6.605119 ACAGGATATTAAGGGTCCAAAGATG 58.395 40.000 6.40 0.00 34.42 2.90
1616 3287 5.474876 CAGGATATTAAGGGTCCAAAGATGC 59.525 44.000 6.40 0.00 34.42 3.91
1649 3321 3.306917 TTTGAGCAAGTTGGATGCATG 57.693 42.857 2.46 0.00 46.22 4.06
1675 3347 6.659824 TCAAATCAGGGGTATTAGAAACTCC 58.340 40.000 0.00 0.00 37.81 3.85
1687 3359 5.470047 TTAGAAACTCCACTCTTCCTGAC 57.530 43.478 0.00 0.00 0.00 3.51
1706 3423 0.101759 CATTCGAGCAAGGGCATTGG 59.898 55.000 14.30 0.00 44.61 3.16
1713 3435 2.560105 GAGCAAGGGCATTGGGATATTC 59.440 50.000 14.30 0.00 44.61 1.75
1720 3442 2.961062 GGCATTGGGATATTCAACTGCT 59.039 45.455 1.01 0.00 33.48 4.24
1759 3481 7.355778 GTCTGTTATTTTCCAACTCAACTCTG 58.644 38.462 0.00 0.00 0.00 3.35
1769 3491 1.622811 ACTCAACTCTGCTCTTCCTGG 59.377 52.381 0.00 0.00 0.00 4.45
1776 3498 0.321671 CTGCTCTTCCTGGTTTCGGA 59.678 55.000 0.00 0.00 0.00 4.55
1780 3502 2.417719 CTCTTCCTGGTTTCGGAACTG 58.582 52.381 6.53 0.00 35.70 3.16
1803 3537 6.054941 TGTTGGCATACACTATGTTCATAGG 58.945 40.000 19.63 12.76 38.43 2.57
1847 3593 5.168526 TGTTGCAAAGCTGTGTTACTTAG 57.831 39.130 5.61 0.00 0.00 2.18
1848 3594 4.638421 TGTTGCAAAGCTGTGTTACTTAGT 59.362 37.500 5.61 0.00 0.00 2.24
1849 3595 5.818336 TGTTGCAAAGCTGTGTTACTTAGTA 59.182 36.000 5.61 0.00 0.00 1.82
1850 3596 5.917541 TGCAAAGCTGTGTTACTTAGTAC 57.082 39.130 5.61 0.00 0.00 2.73
1851 3597 4.446385 TGCAAAGCTGTGTTACTTAGTACG 59.554 41.667 5.61 0.00 0.00 3.67
1852 3598 4.446719 GCAAAGCTGTGTTACTTAGTACGT 59.553 41.667 5.61 0.00 0.00 3.57
1853 3599 5.630680 GCAAAGCTGTGTTACTTAGTACGTA 59.369 40.000 5.61 0.00 0.00 3.57
1854 3600 6.183359 GCAAAGCTGTGTTACTTAGTACGTAG 60.183 42.308 5.61 0.00 0.00 3.51
1856 3602 7.672983 AAGCTGTGTTACTTAGTACGTAGTA 57.327 36.000 6.02 6.02 45.11 1.82
1873 3619 3.801114 AGTATGTGCATCGTGCTAGAA 57.199 42.857 10.54 0.00 45.31 2.10
1911 3658 6.494893 TGCACTCGATAAAAAGCTTAATGT 57.505 33.333 0.00 0.00 0.00 2.71
1915 3677 8.786028 GCACTCGATAAAAAGCTTAATGTAAAC 58.214 33.333 0.00 0.00 0.00 2.01
2033 3795 1.534595 GAAGAGCAAGCTCCAACACAG 59.465 52.381 17.81 0.00 43.70 3.66
2277 4067 5.798125 TTTGGTTGTTCTTGCATTGGATA 57.202 34.783 0.00 0.00 0.00 2.59
2350 4140 2.033448 AACGGGCATGGAAAGCGA 59.967 55.556 0.00 0.00 0.00 4.93
2398 4188 0.614697 TCCCATGCAAGAGAGTCCGA 60.615 55.000 0.00 0.00 0.00 4.55
2414 4204 4.321718 AGTCCGATGATATGCCAAATCTG 58.678 43.478 0.00 0.00 0.00 2.90
2529 4321 9.457110 CTTAAAGCTATGTGTAGATGTGTAGAG 57.543 37.037 0.00 0.00 0.00 2.43
2552 4344 2.501723 GGTCTGGAGCCATAGTTTCAGA 59.498 50.000 0.00 0.00 0.00 3.27
2565 4357 8.125448 GCCATAGTTTCAGATTTGTATCAAGTC 58.875 37.037 0.00 0.00 32.95 3.01
2685 4477 3.313803 TCGGCGCAAAATGCTAATATCAA 59.686 39.130 10.83 0.00 42.25 2.57
2688 4480 6.029607 CGGCGCAAAATGCTAATATCAATAT 58.970 36.000 10.83 0.00 42.25 1.28
2690 4487 7.696035 CGGCGCAAAATGCTAATATCAATATTA 59.304 33.333 10.83 3.19 42.25 0.98
3045 4849 7.731720 TCCGTAACATAATACAAGACGTTTTG 58.268 34.615 16.58 16.58 0.00 2.44
3101 4949 4.741321 TGTTACGGGGTATTTCACTAGG 57.259 45.455 0.00 0.00 0.00 3.02
3176 5285 3.961480 TGTGTACATGAGTGGGAGAAG 57.039 47.619 0.00 0.00 0.00 2.85
3401 5516 4.685924 CAAAAAGATTGCACAACTGAGGT 58.314 39.130 0.00 0.00 0.00 3.85
3445 5560 8.767436 AGGAGAAAGATTAGAAGAGCATAACTT 58.233 33.333 0.00 0.00 0.00 2.66
3480 5595 2.171448 AGTCAACTGGTCTGCACTCTTT 59.829 45.455 0.00 0.00 0.00 2.52
3492 5607 6.347725 GGTCTGCACTCTTTAACACTGTATTG 60.348 42.308 0.00 0.00 0.00 1.90
3583 5701 0.250124 CACAGGTGGCAGTTAACCGA 60.250 55.000 0.88 0.00 41.61 4.69
3623 5741 1.233019 CTGTGACCTTGCACCTTGAG 58.767 55.000 0.00 0.00 37.99 3.02
3624 5742 0.836606 TGTGACCTTGCACCTTGAGA 59.163 50.000 0.00 0.00 37.99 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.059352 GGATACAACACTCCTTGCTGT 57.941 47.619 0.00 0.00 38.17 4.40
30 31 0.389817 CAGCTCCCGATGTTCGAACA 60.390 55.000 31.41 31.41 43.74 3.18
39 40 4.473520 CCGGTTGCAGCTCCCGAT 62.474 66.667 20.76 0.00 44.41 4.18
656 774 0.179040 TTCTTTCACCGGGCGTCTTT 60.179 50.000 6.32 0.00 0.00 2.52
665 783 4.092091 CGATTCTCTCCTTTTCTTTCACCG 59.908 45.833 0.00 0.00 0.00 4.94
703 821 1.404391 ACTAGCAACGTCCGATCGAAT 59.596 47.619 18.66 0.00 34.70 3.34
772 901 6.635239 TGCAAATACTTGAACGCTTTCTAAAC 59.365 34.615 4.43 0.00 34.14 2.01
779 908 4.764679 TGATGCAAATACTTGAACGCTT 57.235 36.364 0.00 0.00 34.14 4.68
799 928 6.042143 GGCCCATTTAAATCACACATACTTG 58.958 40.000 0.00 0.00 0.00 3.16
857 986 3.244078 ACCAACAGCGTGATCTTCTTGTA 60.244 43.478 0.00 0.00 0.00 2.41
978 1115 1.814586 CTCTGCTGCTAGTGCTGGC 60.815 63.158 0.00 0.39 40.48 4.85
1035 1178 2.838225 CTGGTACGATCGGGGGCT 60.838 66.667 20.98 0.00 0.00 5.19
1036 1179 4.603946 GCTGGTACGATCGGGGGC 62.604 72.222 20.98 11.89 0.00 5.80
1037 1180 2.838225 AGCTGGTACGATCGGGGG 60.838 66.667 20.98 5.83 0.00 5.40
1404 1563 5.909621 ACGTTTATACTGTAAGAGAGGCA 57.090 39.130 0.00 0.00 37.43 4.75
1438 1693 4.626081 ACTGGCGCCGCAAGAACT 62.626 61.111 22.43 0.00 43.02 3.01
1453 1708 2.031870 GGGGTTTGCTCAAAGAACACT 58.968 47.619 0.00 0.00 0.00 3.55
1466 1723 2.488153 GGAATCAAGAAGTCGGGGTTTG 59.512 50.000 0.00 0.00 0.00 2.93
1487 1773 0.889638 TCTATCTCCAGTAGCGCCGG 60.890 60.000 2.29 0.00 0.00 6.13
1488 1774 0.519519 CTCTATCTCCAGTAGCGCCG 59.480 60.000 2.29 0.00 0.00 6.46
1516 1802 2.035066 GCCTGAACAACATTTGACTGCT 59.965 45.455 0.00 0.00 0.00 4.24
1518 1804 2.624838 AGGCCTGAACAACATTTGACTG 59.375 45.455 3.11 0.00 0.00 3.51
1521 1807 3.295093 TGAAGGCCTGAACAACATTTGA 58.705 40.909 5.69 0.00 0.00 2.69
1522 1808 3.553508 CCTGAAGGCCTGAACAACATTTG 60.554 47.826 5.69 0.00 0.00 2.32
1523 1809 2.629617 CCTGAAGGCCTGAACAACATTT 59.370 45.455 5.69 0.00 0.00 2.32
1524 1810 2.242043 CCTGAAGGCCTGAACAACATT 58.758 47.619 5.69 0.00 0.00 2.71
1526 1812 0.178992 CCCTGAAGGCCTGAACAACA 60.179 55.000 5.69 0.00 0.00 3.33
1528 1814 0.110486 GACCCTGAAGGCCTGAACAA 59.890 55.000 5.69 0.00 40.58 2.83
1530 1816 1.002011 GGACCCTGAAGGCCTGAAC 60.002 63.158 5.69 1.31 40.58 3.18
1532 1818 0.846427 ATTGGACCCTGAAGGCCTGA 60.846 55.000 5.69 0.00 40.58 3.86
1533 1819 0.682209 CATTGGACCCTGAAGGCCTG 60.682 60.000 5.69 0.00 40.58 4.85
1536 1822 0.613012 AAGCATTGGACCCTGAAGGC 60.613 55.000 0.00 0.00 40.58 4.35
1537 1823 1.180029 CAAGCATTGGACCCTGAAGG 58.820 55.000 0.00 0.00 43.94 3.46
1557 3222 4.712122 TGAAACTGACCCAAAACTCAAC 57.288 40.909 0.00 0.00 0.00 3.18
1594 3265 5.385198 TGCATCTTTGGACCCTTAATATCC 58.615 41.667 0.00 0.00 0.00 2.59
1615 3286 4.685169 TGCTCAAATAAGTTGCTACTGC 57.315 40.909 0.36 0.00 37.13 4.40
1616 3287 6.246420 ACTTGCTCAAATAAGTTGCTACTG 57.754 37.500 0.36 0.00 37.13 2.74
1644 3316 2.307496 ACCCCTGATTTGAACATGCA 57.693 45.000 0.00 0.00 0.00 3.96
1649 3321 7.067129 GGAGTTTCTAATACCCCTGATTTGAAC 59.933 40.741 0.00 0.00 30.99 3.18
1675 3347 2.266554 GCTCGAATGTCAGGAAGAGTG 58.733 52.381 0.00 0.00 0.00 3.51
1687 3359 0.101759 CCAATGCCCTTGCTCGAATG 59.898 55.000 0.00 0.00 38.71 2.67
1706 3423 2.213499 CACCGGAGCAGTTGAATATCC 58.787 52.381 9.46 0.00 0.00 2.59
1713 3435 0.729116 CATTAGCACCGGAGCAGTTG 59.271 55.000 26.04 14.84 36.85 3.16
1720 3442 1.153647 CAGACGCATTAGCACCGGA 60.154 57.895 9.46 0.00 42.27 5.14
1759 3481 3.625745 TTCCGAAACCAGGAAGAGC 57.374 52.632 0.00 0.00 42.33 4.09
1769 3491 2.550606 TGTATGCCAACAGTTCCGAAAC 59.449 45.455 0.00 0.00 35.50 2.78
1776 3498 5.312895 TGAACATAGTGTATGCCAACAGTT 58.687 37.500 1.64 0.00 39.79 3.16
1780 3502 5.049405 GCCTATGAACATAGTGTATGCCAAC 60.049 44.000 17.07 0.00 39.23 3.77
1803 3537 5.641209 ACAAGTAGATGAGAATGTTGTGAGC 59.359 40.000 0.00 0.00 0.00 4.26
1847 3593 2.466571 GCACGATGCACATACTACGTAC 59.533 50.000 0.00 0.00 44.26 3.67
1848 3594 2.723209 GCACGATGCACATACTACGTA 58.277 47.619 0.00 0.00 44.26 3.57
1849 3595 1.556564 GCACGATGCACATACTACGT 58.443 50.000 0.00 0.00 44.26 3.57
1864 3610 6.032775 CAGCATAACAACATTTTTCTAGCACG 59.967 38.462 0.00 0.00 0.00 5.34
1873 3619 4.023279 TCGAGTGCAGCATAACAACATTTT 60.023 37.500 0.00 0.00 0.00 1.82
1911 3658 7.884257 TGCACAGATTCAGATCAAAATGTTTA 58.116 30.769 0.00 0.00 34.60 2.01
1915 3677 6.560711 TCATGCACAGATTCAGATCAAAATG 58.439 36.000 0.00 0.00 34.60 2.32
2033 3795 3.190953 AGATTTTGAAAGAGCTGAGCTGC 59.809 43.478 13.71 3.47 39.88 5.25
2218 4008 8.552083 TCAGATTTCCGGATATGATGTATTTG 57.448 34.615 12.50 0.00 0.00 2.32
2277 4067 5.163426 TGTGTTTCTGCTCAATTGGTTGATT 60.163 36.000 5.42 0.00 43.08 2.57
2350 4140 1.039068 CCATCTCCTCATCTCGTGCT 58.961 55.000 0.00 0.00 0.00 4.40
2398 4188 3.825014 GCAGGACAGATTTGGCATATCAT 59.175 43.478 18.17 7.41 32.23 2.45
2414 4204 2.805099 CAAAAGTCTCAGTCTGCAGGAC 59.195 50.000 15.13 12.65 44.80 3.85
2475 4265 5.121811 AGCCATGTCAGTTCACATAATCTC 58.878 41.667 0.00 0.00 35.10 2.75
2529 4321 2.027192 TGAAACTATGGCTCCAGACCAC 60.027 50.000 0.00 0.00 40.82 4.16
2552 4344 4.406456 TGCAACTGGGACTTGATACAAAT 58.594 39.130 0.00 0.00 0.00 2.32
2565 4357 2.948979 TCTTACAACTGTTGCAACTGGG 59.051 45.455 31.76 25.93 32.82 4.45
2685 4477 8.978874 TGCACTGGTTACTGATTTGATAATAT 57.021 30.769 0.00 0.00 0.00 1.28
2688 4480 7.701539 AATGCACTGGTTACTGATTTGATAA 57.298 32.000 0.00 0.00 0.00 1.75
2690 4487 6.392354 CAAATGCACTGGTTACTGATTTGAT 58.608 36.000 0.00 0.00 33.22 2.57
2768 4565 8.046708 TGATTTGGTATTGTAGCTGTTGATAGT 58.953 33.333 0.00 0.00 0.00 2.12
3286 5398 4.764679 TTGTTTTAGCTGTATGCCTGTG 57.235 40.909 0.00 0.00 44.23 3.66
3401 5516 3.756434 CTCCTGGAATGGCGTTTTTCTTA 59.244 43.478 0.00 0.00 0.00 2.10
3445 5560 5.072600 ACCAGTTGACTACCACCTTTATTGA 59.927 40.000 0.00 0.00 0.00 2.57
3492 5607 5.354513 GCCTCACTTGGGTAAATTTAGAGAC 59.645 44.000 0.00 0.00 0.00 3.36
3503 5618 3.486383 CTTTTCTTGCCTCACTTGGGTA 58.514 45.455 0.00 0.00 0.00 3.69
3506 5621 1.682854 TGCTTTTCTTGCCTCACTTGG 59.317 47.619 0.00 0.00 0.00 3.61
3583 5701 7.122799 TCACAGTATAGTGTTAAGAGTGCAGAT 59.877 37.037 10.62 0.00 40.37 2.90


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

AutoCloner maintained by Alex Coulton.