Multiple sequence alignment - TraesCS3D01G499800

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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 TraesCS3D01G499800 chr3D 100.000 2464 0 0 1 2464 589433785 589431322 0.000000e+00 4551.0
1 TraesCS3D01G499800 chr3D 93.708 747 38 4 752 1496 589506226 589505487 0.000000e+00 1110.0
2 TraesCS3D01G499800 chr3D 91.766 753 42 6 752 1497 589426807 589426068 0.000000e+00 1029.0
3 TraesCS3D01G499800 chr3D 90.300 701 50 7 1763 2463 549376580 549377262 0.000000e+00 902.0
4 TraesCS3D01G499800 chr3D 91.896 654 37 6 811 1464 589493350 589492713 0.000000e+00 900.0
5 TraesCS3D01G499800 chr3D 86.198 768 70 17 753 1497 589418004 589417250 0.000000e+00 798.0
6 TraesCS3D01G499800 chr3D 85.428 748 83 15 991 1726 589572851 589572118 0.000000e+00 754.0
7 TraesCS3D01G499800 chr3D 87.736 212 21 4 752 963 589573117 589572911 2.450000e-60 243.0
8 TraesCS3D01G499800 chr3D 81.319 182 30 4 1280 1459 418705372 418705193 7.100000e-31 145.0
9 TraesCS3D01G499800 chr3D 90.698 43 1 2 1726 1765 83325992 83325950 1.000000e-03 54.7
10 TraesCS3D01G499800 chr6D 94.350 761 41 2 1 760 272855050 272854291 0.000000e+00 1166.0
11 TraesCS3D01G499800 chr6D 92.450 702 52 1 1762 2463 16177687 16178387 0.000000e+00 1002.0
12 TraesCS3D01G499800 chr6D 92.092 392 27 3 1 390 23829899 23830288 1.290000e-152 549.0
13 TraesCS3D01G499800 chr6D 93.333 45 0 3 1724 1765 454925447 454925403 2.050000e-06 63.9
14 TraesCS3D01G499800 chr4D 94.282 752 42 1 1 751 39595092 39595843 0.000000e+00 1149.0
15 TraesCS3D01G499800 chr3A 88.153 996 71 22 752 1726 719354305 719353336 0.000000e+00 1142.0
16 TraesCS3D01G499800 chr3A 87.310 725 59 17 799 1497 719337537 719336820 0.000000e+00 798.0
17 TraesCS3D01G499800 chr3A 84.898 735 75 22 780 1490 719361029 719360307 0.000000e+00 710.0
18 TraesCS3D01G499800 chr3A 80.488 246 35 9 1495 1728 719360273 719360029 2.520000e-40 176.0
19 TraesCS3D01G499800 chr3A 87.705 122 11 1 1547 1668 719346424 719346307 3.300000e-29 139.0
20 TraesCS3D01G499800 chr3B 86.314 1001 66 34 753 1709 787472320 787473293 0.000000e+00 1024.0
21 TraesCS3D01G499800 chr3B 83.874 1017 112 30 752 1730 787989985 787990987 0.000000e+00 922.0
22 TraesCS3D01G499800 chr3B 84.458 978 93 32 780 1731 788058784 788057840 0.000000e+00 909.0
23 TraesCS3D01G499800 chr3B 83.966 237 35 2 1502 1735 788067609 788067373 8.870000e-55 224.0
24 TraesCS3D01G499800 chr3B 83.544 237 36 2 1502 1735 788073031 788072795 4.130000e-53 219.0
25 TraesCS3D01G499800 chr2B 90.495 747 66 4 8 752 782453901 782454644 0.000000e+00 981.0
26 TraesCS3D01G499800 chr2B 93.750 48 3 0 1763 1810 733865915 733865962 3.400000e-09 73.1
27 TraesCS3D01G499800 chr5D 91.834 698 50 6 1766 2463 539037300 539036610 0.000000e+00 966.0
28 TraesCS3D01G499800 chr5D 85.510 628 57 15 1 627 3014727 3014133 2.080000e-175 625.0
29 TraesCS3D01G499800 chr5D 90.173 173 12 4 585 754 3014130 3013960 1.150000e-53 220.0
30 TraesCS3D01G499800 chr6B 91.348 705 55 5 1762 2463 27918234 27918935 0.000000e+00 959.0
31 TraesCS3D01G499800 chr6B 92.683 41 2 1 1726 1765 504071761 504071721 9.520000e-05 58.4
32 TraesCS3D01G499800 chr5A 91.298 701 61 0 1763 2463 73805185 73804485 0.000000e+00 957.0
33 TraesCS3D01G499800 chr5A 91.013 701 58 3 1762 2461 480477958 480478654 0.000000e+00 941.0
34 TraesCS3D01G499800 chr5A 90.523 707 62 3 1762 2463 685998462 685999168 0.000000e+00 929.0
35 TraesCS3D01G499800 chr5A 100.000 29 0 0 1724 1752 613577387 613577415 1.000000e-03 54.7
36 TraesCS3D01G499800 chr4A 91.155 701 57 3 1765 2463 727414150 727414847 0.000000e+00 946.0
37 TraesCS3D01G499800 chr4A 95.325 492 21 2 1 491 560752769 560752279 0.000000e+00 780.0
38 TraesCS3D01G499800 chr4A 89.328 253 21 3 505 751 560745728 560745476 1.840000e-81 313.0
39 TraesCS3D01G499800 chr1A 90.429 700 66 1 1765 2463 318552906 318552207 0.000000e+00 920.0
40 TraesCS3D01G499800 chr1A 100.000 29 0 0 1724 1752 471256795 471256767 1.000000e-03 54.7
41 TraesCS3D01G499800 chr1D 84.359 780 58 28 1 752 416541298 416542041 0.000000e+00 706.0
42 TraesCS3D01G499800 chr1D 95.238 42 2 0 1724 1765 427698939 427698980 1.580000e-07 67.6
43 TraesCS3D01G499800 chr1D 95.238 42 2 0 1724 1765 487265109 487265068 1.580000e-07 67.6
44 TraesCS3D01G499800 chr1B 91.463 492 36 2 266 751 301775868 301776359 0.000000e+00 671.0
45 TraesCS3D01G499800 chr1B 92.035 226 16 2 1 224 301775381 301775606 1.420000e-82 316.0
46 TraesCS3D01G499800 chr6A 90.191 367 28 6 396 754 577847623 577847257 2.870000e-129 472.0
47 TraesCS3D01G499800 chr6A 88.438 320 30 3 2 320 577847939 577847626 1.790000e-101 379.0
48 TraesCS3D01G499800 chr2D 93.333 150 10 0 601 750 631957137 631957286 3.190000e-54 222.0
49 TraesCS3D01G499800 chr7B 96.875 32 1 0 1724 1755 5178737 5178768 1.000000e-03 54.7


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 TraesCS3D01G499800 chr3D 589431322 589433785 2463 True 4551.0 4551 100.0000 1 2464 1 chr3D.!!$R5 2463
1 TraesCS3D01G499800 chr3D 589505487 589506226 739 True 1110.0 1110 93.7080 752 1496 1 chr3D.!!$R7 744
2 TraesCS3D01G499800 chr3D 589426068 589426807 739 True 1029.0 1029 91.7660 752 1497 1 chr3D.!!$R4 745
3 TraesCS3D01G499800 chr3D 549376580 549377262 682 False 902.0 902 90.3000 1763 2463 1 chr3D.!!$F1 700
4 TraesCS3D01G499800 chr3D 589492713 589493350 637 True 900.0 900 91.8960 811 1464 1 chr3D.!!$R6 653
5 TraesCS3D01G499800 chr3D 589417250 589418004 754 True 798.0 798 86.1980 753 1497 1 chr3D.!!$R3 744
6 TraesCS3D01G499800 chr3D 589572118 589573117 999 True 498.5 754 86.5820 752 1726 2 chr3D.!!$R8 974
7 TraesCS3D01G499800 chr6D 272854291 272855050 759 True 1166.0 1166 94.3500 1 760 1 chr6D.!!$R1 759
8 TraesCS3D01G499800 chr6D 16177687 16178387 700 False 1002.0 1002 92.4500 1762 2463 1 chr6D.!!$F1 701
9 TraesCS3D01G499800 chr4D 39595092 39595843 751 False 1149.0 1149 94.2820 1 751 1 chr4D.!!$F1 750
10 TraesCS3D01G499800 chr3A 719353336 719354305 969 True 1142.0 1142 88.1530 752 1726 1 chr3A.!!$R3 974
11 TraesCS3D01G499800 chr3A 719336820 719337537 717 True 798.0 798 87.3100 799 1497 1 chr3A.!!$R1 698
12 TraesCS3D01G499800 chr3A 719360029 719361029 1000 True 443.0 710 82.6930 780 1728 2 chr3A.!!$R4 948
13 TraesCS3D01G499800 chr3B 787472320 787473293 973 False 1024.0 1024 86.3140 753 1709 1 chr3B.!!$F1 956
14 TraesCS3D01G499800 chr3B 787989985 787990987 1002 False 922.0 922 83.8740 752 1730 1 chr3B.!!$F2 978
15 TraesCS3D01G499800 chr3B 788057840 788058784 944 True 909.0 909 84.4580 780 1731 1 chr3B.!!$R1 951
16 TraesCS3D01G499800 chr2B 782453901 782454644 743 False 981.0 981 90.4950 8 752 1 chr2B.!!$F2 744
17 TraesCS3D01G499800 chr5D 539036610 539037300 690 True 966.0 966 91.8340 1766 2463 1 chr5D.!!$R1 697
18 TraesCS3D01G499800 chr5D 3013960 3014727 767 True 422.5 625 87.8415 1 754 2 chr5D.!!$R2 753
19 TraesCS3D01G499800 chr6B 27918234 27918935 701 False 959.0 959 91.3480 1762 2463 1 chr6B.!!$F1 701
20 TraesCS3D01G499800 chr5A 73804485 73805185 700 True 957.0 957 91.2980 1763 2463 1 chr5A.!!$R1 700
21 TraesCS3D01G499800 chr5A 480477958 480478654 696 False 941.0 941 91.0130 1762 2461 1 chr5A.!!$F1 699
22 TraesCS3D01G499800 chr5A 685998462 685999168 706 False 929.0 929 90.5230 1762 2463 1 chr5A.!!$F3 701
23 TraesCS3D01G499800 chr4A 727414150 727414847 697 False 946.0 946 91.1550 1765 2463 1 chr4A.!!$F1 698
24 TraesCS3D01G499800 chr1A 318552207 318552906 699 True 920.0 920 90.4290 1765 2463 1 chr1A.!!$R1 698
25 TraesCS3D01G499800 chr1D 416541298 416542041 743 False 706.0 706 84.3590 1 752 1 chr1D.!!$F1 751
26 TraesCS3D01G499800 chr1B 301775381 301776359 978 False 493.5 671 91.7490 1 751 2 chr1B.!!$F1 750
27 TraesCS3D01G499800 chr6A 577847257 577847939 682 True 425.5 472 89.3145 2 754 2 chr6A.!!$R1 752

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
614 913 0.108019 AAAGGCGTTCGGGAGACTTT 59.892 50.0 0.0 0.99 39.59 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 2181 0.161446 GCGAAATTTTTGTGCGCCTG 59.839 50.0 4.18 0.0 41.65 4.85 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
363 594 3.295734 CCGACGAGAGGACGGTATA 57.704 57.895 0.00 0.00 45.14 1.47
389 622 3.917760 CTCCATCGCGTCTCCCCC 61.918 72.222 5.77 0.00 0.00 5.40
390 623 4.770362 TCCATCGCGTCTCCCCCA 62.770 66.667 5.77 0.00 0.00 4.96
457 690 1.079256 CCACCTCCACTCTCCTCCA 59.921 63.158 0.00 0.00 0.00 3.86
534 773 0.461339 GGTCGCTCGGGATTTTGCTA 60.461 55.000 0.00 0.00 0.00 3.49
546 785 4.523083 GGATTTTGCTATGTGGGAGTGTA 58.477 43.478 0.00 0.00 0.00 2.90
557 796 3.311028 TGTGGGAGTGTAGGGAATGGATA 60.311 47.826 0.00 0.00 0.00 2.59
614 913 0.108019 AAAGGCGTTCGGGAGACTTT 59.892 50.000 0.00 0.99 39.59 2.66
657 956 4.492160 GATGACGTGGCGAGCCGA 62.492 66.667 9.78 0.00 39.42 5.54
680 979 1.596954 GCGTCAAGATGTGTGCGTTTT 60.597 47.619 0.00 0.00 0.00 2.43
726 1025 1.126296 GGACGAGAAGCTAAAACGTGC 59.874 52.381 11.56 10.78 37.32 5.34
778 1077 1.296392 CCTGCCATCGTCCAACTCA 59.704 57.895 0.00 0.00 0.00 3.41
900 1205 3.414700 CACGCGCACCTCCAAGAC 61.415 66.667 5.73 0.00 0.00 3.01
946 1252 6.071320 TCTATAGCAAAGCACAGGATCTAGA 58.929 40.000 0.00 0.00 0.00 2.43
967 1281 1.228245 GCACAGGCAGGGTCAAGAA 60.228 57.895 0.00 0.00 40.72 2.52
968 1282 1.518903 GCACAGGCAGGGTCAAGAAC 61.519 60.000 0.00 0.00 40.72 3.01
969 1283 0.109342 CACAGGCAGGGTCAAGAACT 59.891 55.000 0.00 0.00 0.00 3.01
970 1284 0.398318 ACAGGCAGGGTCAAGAACTC 59.602 55.000 0.00 0.00 0.00 3.01
971 1285 0.397941 CAGGCAGGGTCAAGAACTCA 59.602 55.000 0.00 0.00 0.00 3.41
972 1286 1.140312 AGGCAGGGTCAAGAACTCAA 58.860 50.000 0.00 0.00 0.00 3.02
973 1287 1.072965 AGGCAGGGTCAAGAACTCAAG 59.927 52.381 0.00 0.00 0.00 3.02
974 1288 1.072331 GGCAGGGTCAAGAACTCAAGA 59.928 52.381 0.00 0.00 0.00 3.02
1209 1572 2.202676 GAGTTCCTCGAGCTGGCG 60.203 66.667 6.99 0.00 0.00 5.69
1210 1573 4.443266 AGTTCCTCGAGCTGGCGC 62.443 66.667 6.99 0.00 0.00 6.53
1319 1688 4.701437 ATGGAGGGGCAGGGGTGT 62.701 66.667 0.00 0.00 0.00 4.16
1468 1843 4.700268 AGATCATGATGAGCTAGCTACG 57.300 45.455 19.38 2.77 41.92 3.51
1485 1864 2.590092 GTAGCGCCTGGACCCAAT 59.410 61.111 2.29 0.00 0.00 3.16
1514 1930 1.459592 CCTTCGCTCGTTCGTTCATTT 59.540 47.619 0.00 0.00 0.00 2.32
1531 1947 9.650371 TCGTTCATTTATTCATTCATTCGATTC 57.350 29.630 0.00 0.00 0.00 2.52
1603 2034 9.479549 AATTGATCTATGTGAATACCTTTGGTT 57.520 29.630 0.00 0.00 37.09 3.67
1605 2036 8.877864 TGATCTATGTGAATACCTTTGGTTTT 57.122 30.769 0.00 0.00 37.09 2.43
1648 2085 4.657969 TGGAATTGGATTGTGGGTTTCTTT 59.342 37.500 0.00 0.00 0.00 2.52
1656 2093 6.014669 TGGATTGTGGGTTTCTTTAGGAATTG 60.015 38.462 0.00 0.00 33.53 2.32
1659 2096 4.522789 TGTGGGTTTCTTTAGGAATTGAGC 59.477 41.667 0.00 0.00 33.53 4.26
1674 2111 4.563140 ATTGAGCTGCCCAAAATGAATT 57.437 36.364 0.00 0.00 0.00 2.17
1711 2154 1.936547 GGATTGACTTGTCATCCTCGC 59.063 52.381 17.15 2.83 0.00 5.03
1713 2156 0.684535 TTGACTTGTCATCCTCGCCA 59.315 50.000 4.18 0.00 0.00 5.69
1716 2159 1.194781 ACTTGTCATCCTCGCCACCT 61.195 55.000 0.00 0.00 0.00 4.00
1718 2161 1.414181 CTTGTCATCCTCGCCACCTAT 59.586 52.381 0.00 0.00 0.00 2.57
1731 2174 2.373502 GCCACCTATCCCTTTAGAGCAT 59.626 50.000 0.00 0.00 0.00 3.79
1732 2175 3.558109 GCCACCTATCCCTTTAGAGCATC 60.558 52.174 0.00 0.00 0.00 3.91
1744 2187 1.427020 GAGCATCTTCAACAGGCGC 59.573 57.895 0.00 0.00 0.00 6.53
1745 2188 1.300971 GAGCATCTTCAACAGGCGCA 61.301 55.000 10.83 0.00 0.00 6.09
1746 2189 1.154150 GCATCTTCAACAGGCGCAC 60.154 57.895 10.83 0.00 0.00 5.34
1747 2190 1.855213 GCATCTTCAACAGGCGCACA 61.855 55.000 10.83 0.00 0.00 4.57
1748 2191 0.592637 CATCTTCAACAGGCGCACAA 59.407 50.000 10.83 0.00 0.00 3.33
1749 2192 1.001487 CATCTTCAACAGGCGCACAAA 60.001 47.619 10.83 0.00 0.00 2.83
1750 2193 1.098869 TCTTCAACAGGCGCACAAAA 58.901 45.000 10.83 0.00 0.00 2.44
1751 2194 1.474478 TCTTCAACAGGCGCACAAAAA 59.526 42.857 10.83 0.00 0.00 1.94
1752 2195 2.100584 TCTTCAACAGGCGCACAAAAAT 59.899 40.909 10.83 0.00 0.00 1.82
1753 2196 2.593346 TCAACAGGCGCACAAAAATT 57.407 40.000 10.83 0.00 0.00 1.82
1754 2197 2.898705 TCAACAGGCGCACAAAAATTT 58.101 38.095 10.83 0.00 0.00 1.82
1755 2198 2.863137 TCAACAGGCGCACAAAAATTTC 59.137 40.909 10.83 0.00 0.00 2.17
1756 2199 1.486439 ACAGGCGCACAAAAATTTCG 58.514 45.000 10.83 0.00 0.00 3.46
1757 2200 0.161446 CAGGCGCACAAAAATTTCGC 59.839 50.000 10.83 11.52 44.39 4.70
1759 2202 4.677432 CGCACAAAAATTTCGCGC 57.323 50.000 0.00 0.00 39.43 6.86
1760 2203 1.224816 CGCACAAAAATTTCGCGCG 60.225 52.632 26.76 26.76 39.43 6.86
1784 2227 1.002868 AGCATCTTCAACAGCCGCT 60.003 52.632 0.00 0.00 0.00 5.52
1828 2271 3.007940 TCAGAATACAACACTGGGTGAGG 59.992 47.826 4.62 0.00 36.96 3.86
2001 2451 6.028368 AGTACAAATGTGAGATAGTTCGTCG 58.972 40.000 0.00 0.00 0.00 5.12
2136 2590 0.684479 CTCGGTGATGTCCTCCTCCA 60.684 60.000 0.00 0.00 0.00 3.86
2202 2656 0.037790 GGACGATGCATCTCCTAGCC 60.038 60.000 25.69 14.98 0.00 3.93
2294 2749 4.465446 TCCCTCTCCGCCCTCCTG 62.465 72.222 0.00 0.00 0.00 3.86
2315 2770 0.319555 CGGCGAAGAACTGTTCCTCA 60.320 55.000 16.48 0.00 0.00 3.86
2378 2833 1.379977 TTCCTCGTCCATCTCGGCT 60.380 57.895 0.00 0.00 33.14 5.52
2379 2834 1.667154 TTCCTCGTCCATCTCGGCTG 61.667 60.000 0.00 0.00 33.14 4.85
2412 2867 3.382832 CCTGCCTCCGGTTCTCGT 61.383 66.667 0.00 0.00 37.11 4.18
2413 2868 2.125912 CTGCCTCCGGTTCTCGTG 60.126 66.667 0.00 0.00 37.11 4.35
2414 2869 2.599281 TGCCTCCGGTTCTCGTGA 60.599 61.111 0.00 0.00 37.11 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 112 1.490574 CCCCTCTCCAACTCTTCGAT 58.509 55.000 0.00 0.00 0.00 3.59
257 269 3.849951 CGCCACGCCCTCTATGGT 61.850 66.667 0.00 0.00 35.79 3.55
534 773 1.846439 CCATTCCCTACACTCCCACAT 59.154 52.381 0.00 0.00 0.00 3.21
546 785 3.718956 CTCCTTCACCTTATCCATTCCCT 59.281 47.826 0.00 0.00 0.00 4.20
557 796 1.417890 CCACACTGTCTCCTTCACCTT 59.582 52.381 0.00 0.00 0.00 3.50
651 950 0.869454 CATCTTGACGCTCTCGGCTC 60.869 60.000 0.00 0.00 45.91 4.70
657 956 1.010935 CGCACACATCTTGACGCTCT 61.011 55.000 0.00 0.00 0.00 4.09
680 979 1.752498 GTGCTCATTGCCATTGGATCA 59.248 47.619 6.95 0.00 42.00 2.92
726 1025 4.261031 GGAATCAATAAATCCCGAACGTGG 60.261 45.833 0.00 0.00 0.00 4.94
778 1077 0.388907 GTACGTACATGCCGTGTGGT 60.389 55.000 20.67 0.51 42.24 4.16
936 1242 2.093288 TGCCTGTGCTTTCTAGATCCTG 60.093 50.000 0.00 0.00 38.71 3.86
946 1252 0.825010 CTTGACCCTGCCTGTGCTTT 60.825 55.000 0.00 0.00 38.71 3.51
967 1281 7.255312 CGGATGCTTTAGTAGTAGATCTTGAGT 60.255 40.741 0.00 0.00 0.00 3.41
968 1282 7.081349 CGGATGCTTTAGTAGTAGATCTTGAG 58.919 42.308 0.00 0.00 0.00 3.02
969 1283 6.016192 CCGGATGCTTTAGTAGTAGATCTTGA 60.016 42.308 0.00 0.00 0.00 3.02
970 1284 6.153067 CCGGATGCTTTAGTAGTAGATCTTG 58.847 44.000 0.00 0.00 0.00 3.02
971 1285 5.279056 GCCGGATGCTTTAGTAGTAGATCTT 60.279 44.000 5.05 0.00 36.87 2.40
972 1286 4.218852 GCCGGATGCTTTAGTAGTAGATCT 59.781 45.833 5.05 0.00 36.87 2.75
973 1287 4.487019 GCCGGATGCTTTAGTAGTAGATC 58.513 47.826 5.05 0.00 36.87 2.75
974 1288 3.057456 CGCCGGATGCTTTAGTAGTAGAT 60.057 47.826 5.05 0.00 38.05 1.98
1032 1388 1.337260 CGGTCCAGTGACAAGAAGAGG 60.337 57.143 0.00 0.00 43.65 3.69
1341 1710 3.859414 GAGCCTGCCGAGCATCCT 61.859 66.667 0.00 0.00 38.13 3.24
1379 1748 4.166888 ATCATGGCGCGGCACTCT 62.167 61.111 38.63 20.36 0.00 3.24
1468 1843 1.523938 GATTGGGTCCAGGCGCTAC 60.524 63.158 7.64 0.38 0.00 3.58
1485 1864 4.023450 ACGAACGAGCGAAGGAATATATGA 60.023 41.667 8.50 0.00 34.83 2.15
1514 1930 8.210946 ACCTGGTAAGAATCGAATGAATGAATA 58.789 33.333 0.00 0.00 0.00 1.75
1531 1947 7.664758 ACAACTTTGTACTAGTACCTGGTAAG 58.335 38.462 26.41 21.21 40.16 2.34
1536 1952 7.088905 CCACTACAACTTTGTACTAGTACCTG 58.911 42.308 26.41 18.68 42.35 4.00
1537 1953 6.779539 ACCACTACAACTTTGTACTAGTACCT 59.220 38.462 26.41 7.09 42.35 3.08
1603 2034 1.999735 GAGCACGGACAATCGATCAAA 59.000 47.619 0.00 0.00 0.00 2.69
1605 2036 0.817654 AGAGCACGGACAATCGATCA 59.182 50.000 0.00 0.00 0.00 2.92
1648 2085 2.897271 TTTGGGCAGCTCAATTCCTA 57.103 45.000 9.01 0.00 0.00 2.94
1656 2093 6.799926 TTTTTAATTCATTTTGGGCAGCTC 57.200 33.333 0.00 0.00 0.00 4.09
1680 2117 4.990526 ACAAGTCAATCCCTTCACATTCT 58.009 39.130 0.00 0.00 0.00 2.40
1693 2136 1.278985 TGGCGAGGATGACAAGTCAAT 59.721 47.619 7.02 0.00 43.58 2.57
1711 2154 3.906846 AGATGCTCTAAAGGGATAGGTGG 59.093 47.826 0.00 0.00 0.00 4.61
1713 2156 5.219739 TGAAGATGCTCTAAAGGGATAGGT 58.780 41.667 0.00 0.00 0.00 3.08
1716 2159 6.408548 CCTGTTGAAGATGCTCTAAAGGGATA 60.409 42.308 0.00 0.00 0.00 2.59
1718 2161 4.323792 CCTGTTGAAGATGCTCTAAAGGGA 60.324 45.833 0.00 0.00 0.00 4.20
1731 2174 1.098869 TTTTGTGCGCCTGTTGAAGA 58.901 45.000 4.18 0.00 0.00 2.87
1732 2175 1.919918 TTTTTGTGCGCCTGTTGAAG 58.080 45.000 4.18 0.00 0.00 3.02
1733 2176 2.593346 ATTTTTGTGCGCCTGTTGAA 57.407 40.000 4.18 0.00 0.00 2.69
1734 2177 2.593346 AATTTTTGTGCGCCTGTTGA 57.407 40.000 4.18 0.00 0.00 3.18
1735 2178 2.347476 CGAAATTTTTGTGCGCCTGTTG 60.347 45.455 4.18 0.00 0.00 3.33
1736 2179 1.857837 CGAAATTTTTGTGCGCCTGTT 59.142 42.857 4.18 0.00 0.00 3.16
1737 2180 1.486439 CGAAATTTTTGTGCGCCTGT 58.514 45.000 4.18 0.00 0.00 4.00
1738 2181 0.161446 GCGAAATTTTTGTGCGCCTG 59.839 50.000 4.18 0.00 41.65 4.85
1739 2182 1.274798 CGCGAAATTTTTGTGCGCCT 61.275 50.000 4.18 0.00 44.31 5.52
1740 2183 1.127620 CGCGAAATTTTTGTGCGCC 59.872 52.632 4.18 0.00 44.31 6.53
1741 2184 4.677432 CGCGAAATTTTTGTGCGC 57.323 50.000 0.00 0.00 42.42 6.09
1743 2186 1.504854 GCGCGCGAAATTTTTGTGC 60.505 52.632 37.18 20.31 35.85 4.57
1744 2187 1.322865 TAGCGCGCGAAATTTTTGTG 58.677 45.000 37.18 0.00 0.00 3.33
1745 2188 1.976045 CTTAGCGCGCGAAATTTTTGT 59.024 42.857 37.18 7.74 0.00 2.83
1746 2189 2.238363 TCTTAGCGCGCGAAATTTTTG 58.762 42.857 37.18 14.16 0.00 2.44
1747 2190 2.505866 CTCTTAGCGCGCGAAATTTTT 58.494 42.857 37.18 9.28 0.00 1.94
1748 2191 1.790481 GCTCTTAGCGCGCGAAATTTT 60.790 47.619 37.18 10.06 0.00 1.82
1749 2192 0.247695 GCTCTTAGCGCGCGAAATTT 60.248 50.000 37.18 14.89 0.00 1.82
1750 2193 1.348594 GCTCTTAGCGCGCGAAATT 59.651 52.632 37.18 17.57 0.00 1.82
1751 2194 1.154205 ATGCTCTTAGCGCGCGAAAT 61.154 50.000 37.18 20.81 46.26 2.17
1752 2195 1.752501 GATGCTCTTAGCGCGCGAAA 61.753 55.000 37.18 24.71 46.26 3.46
1753 2196 2.202743 ATGCTCTTAGCGCGCGAA 60.203 55.556 37.18 26.01 46.26 4.70
1754 2197 2.613739 AAGATGCTCTTAGCGCGCGA 62.614 55.000 37.18 19.65 46.26 5.87
1755 2198 2.140034 GAAGATGCTCTTAGCGCGCG 62.140 60.000 28.44 28.44 46.26 6.86
1756 2199 1.148157 TGAAGATGCTCTTAGCGCGC 61.148 55.000 26.66 26.66 46.26 6.86
1757 2200 1.005557 GTTGAAGATGCTCTTAGCGCG 60.006 52.381 0.00 0.00 46.26 6.86
1758 2201 2.002586 TGTTGAAGATGCTCTTAGCGC 58.997 47.619 0.00 0.00 46.26 5.92
1759 2202 2.030213 GCTGTTGAAGATGCTCTTAGCG 59.970 50.000 0.00 0.00 46.26 4.26
1760 2203 2.354199 GGCTGTTGAAGATGCTCTTAGC 59.646 50.000 8.62 8.62 36.73 3.09
1802 2245 5.705441 TCACCCAGTGTTGTATTCTGATTTC 59.295 40.000 0.00 0.00 34.79 2.17
2136 2590 2.178521 CGCCTACGCTCAGACGTT 59.821 61.111 0.00 0.00 45.75 3.99
2202 2656 2.285602 CGGTCGCTAAATTCAACATCGG 60.286 50.000 0.00 0.00 0.00 4.18
2294 2749 0.319641 AGGAACAGTTCTTCGCCGAC 60.320 55.000 13.13 0.00 0.00 4.79
2315 2770 2.715749 TCCCGCAAGACATCATCAAT 57.284 45.000 0.00 0.00 43.02 2.57
2350 2805 1.153086 GACGAGGAAGCCATGGCAT 60.153 57.895 37.18 27.80 44.88 4.40
2351 2806 2.268920 GACGAGGAAGCCATGGCA 59.731 61.111 37.18 0.00 44.88 4.92


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

AutoCloner maintained by Alex Coulton.