Multiple sequence alignment - TraesCS7D01G085000

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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 TraesCS7D01G085000 chr7D 100.000 3926 0 0 1 3926 52034239 52038164 0.000000e+00 7251.0
1 TraesCS7D01G085000 chr7D 86.058 1664 148 39 2 1623 52231842 52233463 0.000000e+00 1711.0
2 TraesCS7D01G085000 chr7D 93.280 1131 62 7 1670 2791 52267487 52268612 0.000000e+00 1655.0
3 TraesCS7D01G085000 chr7D 87.523 1090 105 16 545 1623 52292831 52293900 0.000000e+00 1230.0
4 TraesCS7D01G085000 chr7D 84.596 1201 101 35 2799 3926 52235846 52237035 0.000000e+00 1116.0
5 TraesCS7D01G085000 chr7D 90.147 680 29 5 715 1365 52266295 52266965 0.000000e+00 850.0
6 TraesCS7D01G085000 chr7D 85.238 840 94 20 796 1623 51954263 51953442 0.000000e+00 837.0
7 TraesCS7D01G085000 chr7D 92.167 383 17 3 3298 3668 52268618 52268999 2.690000e-146 529.0
8 TraesCS7D01G085000 chr7D 92.521 361 18 2 354 714 52260919 52261270 3.500000e-140 508.0
9 TraesCS7D01G085000 chr7D 84.047 514 49 11 2799 3308 52295218 52295702 7.680000e-127 464.0
10 TraesCS7D01G085000 chr7D 78.912 735 94 35 1829 2527 51953395 51952686 3.600000e-120 442.0
11 TraesCS7D01G085000 chr7D 83.871 496 45 18 2130 2597 52233850 52234338 1.290000e-119 440.0
12 TraesCS7D01G085000 chr7D 86.813 364 33 9 1 354 52259820 52260178 3.680000e-105 392.0
13 TraesCS7D01G085000 chr7D 81.200 500 42 25 2140 2597 52294609 52295098 4.830000e-94 355.0
14 TraesCS7D01G085000 chr7D 91.983 237 16 2 1829 2065 52293965 52294198 2.920000e-86 329.0
15 TraesCS7D01G085000 chr7D 82.838 303 40 10 2801 3095 51952493 51952195 1.080000e-65 261.0
16 TraesCS7D01G085000 chr7D 92.265 181 13 1 3747 3926 52270898 52271078 5.030000e-64 255.0
17 TraesCS7D01G085000 chr7D 83.696 184 26 4 1860 2041 596124225 596124406 1.880000e-38 171.0
18 TraesCS7D01G085000 chr7D 97.826 46 1 0 3711 3756 52268999 52269044 3.250000e-11 80.5
19 TraesCS7D01G085000 chr7D 97.500 40 0 1 2081 2119 611717981 611718020 2.530000e-07 67.6
20 TraesCS7D01G085000 chr4A 87.831 830 70 16 789 1598 666540633 666539815 0.000000e+00 944.0
21 TraesCS7D01G085000 chr4A 84.169 1017 115 24 628 1623 666811467 666812458 0.000000e+00 944.0
22 TraesCS7D01G085000 chr4A 87.168 865 63 15 1 840 666798456 666799297 0.000000e+00 939.0
23 TraesCS7D01G085000 chr4A 86.603 836 77 21 789 1594 666484794 666483964 0.000000e+00 891.0
24 TraesCS7D01G085000 chr4A 82.827 757 94 19 2800 3529 666813365 666814112 0.000000e+00 645.0
25 TraesCS7D01G085000 chr4A 89.336 497 53 0 1130 1626 666520108 666519612 3.330000e-175 625.0
26 TraesCS7D01G085000 chr4A 94.796 269 14 0 354 622 666922914 666923182 1.690000e-113 420.0
27 TraesCS7D01G085000 chr4A 92.096 291 22 1 1796 2085 666483889 666483599 3.650000e-110 409.0
28 TraesCS7D01G085000 chr4A 88.581 289 17 9 79 353 666921224 666921510 1.750000e-88 337.0
29 TraesCS7D01G085000 chr4A 86.395 294 33 5 1793 2085 666926353 666926640 8.190000e-82 315.0
30 TraesCS7D01G085000 chr4A 80.499 441 53 19 2130 2546 666539498 666539067 1.370000e-79 307.0
31 TraesCS7D01G085000 chr4A 86.245 269 23 9 2332 2597 666813002 666813259 2.990000e-71 279.0
32 TraesCS7D01G085000 chr4A 77.919 471 77 17 2137 2597 666926882 666927335 6.470000e-68 268.0
33 TraesCS7D01G085000 chr4A 87.069 232 22 6 3695 3926 666821406 666821629 5.030000e-64 255.0
34 TraesCS7D01G085000 chr4A 81.271 299 46 6 2804 3095 666538899 666538604 2.360000e-57 233.0
35 TraesCS7D01G085000 chr4A 83.471 242 25 7 542 776 666542622 666542389 1.110000e-50 211.0
36 TraesCS7D01G085000 chr4A 86.224 196 20 6 2404 2597 666483063 666482873 5.140000e-49 206.0
37 TraesCS7D01G085000 chr4A 84.404 218 17 5 2135 2335 666483595 666483378 8.600000e-47 198.0
38 TraesCS7D01G085000 chr4A 87.861 173 16 4 3532 3699 666814267 666814439 8.600000e-47 198.0
39 TraesCS7D01G085000 chr4A 81.526 249 25 13 9 242 13256241 13255999 6.700000e-43 185.0
40 TraesCS7D01G085000 chr4A 89.262 149 12 3 3672 3818 666929929 666930075 2.410000e-42 183.0
41 TraesCS7D01G085000 chr4A 88.333 120 14 0 1796 1915 666519557 666519438 1.140000e-30 145.0
42 TraesCS7D01G085000 chr7A 83.656 1034 109 34 628 1623 54773185 54772174 0.000000e+00 918.0
43 TraesCS7D01G085000 chr7A 88.060 804 53 24 851 1623 54758625 54757834 0.000000e+00 913.0
44 TraesCS7D01G085000 chr7A 79.310 725 89 28 1829 2525 54757787 54757096 5.980000e-123 451.0
45 TraesCS7D01G085000 chr7A 79.032 434 43 27 2130 2527 54771837 54771416 1.810000e-63 254.0
46 TraesCS7D01G085000 chr7A 81.469 286 43 6 2809 3084 54771195 54770910 3.950000e-55 226.0
47 TraesCS7D01G085000 chr5D 87.568 185 19 4 23 205 309687745 309687563 1.110000e-50 211.0
48 TraesCS7D01G085000 chr5D 100.000 33 0 0 2083 2115 191899029 191898997 1.180000e-05 62.1
49 TraesCS7D01G085000 chr5D 94.737 38 2 0 2077 2114 363323334 363323371 4.240000e-05 60.2
50 TraesCS7D01G085000 chr1D 86.885 183 18 5 2597 2775 443829378 443829558 2.390000e-47 200.0
51 TraesCS7D01G085000 chr1A 87.640 178 15 7 2597 2771 558098380 558098553 2.390000e-47 200.0
52 TraesCS7D01G085000 chr1A 86.957 184 15 7 2592 2771 504571165 504570987 8.600000e-47 198.0
53 TraesCS7D01G085000 chr1A 100.000 33 0 0 2083 2115 132133519 132133487 1.180000e-05 62.1
54 TraesCS7D01G085000 chr2D 84.286 210 25 7 11 215 49894570 49894776 8.600000e-47 198.0
55 TraesCS7D01G085000 chr4B 87.151 179 16 6 2598 2771 657626234 657626058 3.090000e-46 196.0
56 TraesCS7D01G085000 chr4B 83.105 219 31 6 1 215 132882241 132882025 1.110000e-45 195.0
57 TraesCS7D01G085000 chr4B 97.222 36 0 1 2081 2115 125833815 125833850 4.240000e-05 60.2
58 TraesCS7D01G085000 chr3D 82.427 239 28 10 1 230 84886196 84886429 3.090000e-46 196.0
59 TraesCS7D01G085000 chr3D 87.006 177 19 4 2597 2771 583468437 583468263 3.090000e-46 196.0
60 TraesCS7D01G085000 chr3B 87.500 176 15 6 2600 2771 676971337 676971165 3.090000e-46 196.0
61 TraesCS7D01G085000 chr6D 87.006 177 18 5 2598 2772 97032979 97033152 1.110000e-45 195.0
62 TraesCS7D01G085000 chr3A 87.006 177 18 5 2597 2771 180230955 180230782 1.110000e-45 195.0
63 TraesCS7D01G085000 chr3A 81.818 231 35 6 5 230 692722109 692722337 1.860000e-43 187.0
64 TraesCS7D01G085000 chr7B 90.526 95 9 0 2835 2929 674205343 674205249 4.120000e-25 126.0
65 TraesCS7D01G085000 chr5B 95.000 40 0 2 2076 2114 367794422 367794460 1.180000e-05 62.1
66 TraesCS7D01G085000 chr2A 95.000 40 0 2 2081 2118 733432209 733432248 1.180000e-05 62.1
67 TraesCS7D01G085000 chr6A 94.872 39 1 1 2081 2118 532658451 532658413 4.240000e-05 60.2


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 TraesCS7D01G085000 chr7D 52034239 52038164 3925 False 7251.000000 7251 100.000000 1 3926 1 chr7D.!!$F1 3925
1 TraesCS7D01G085000 chr7D 52231842 52237035 5193 False 1089.000000 1711 84.841667 2 3926 3 chr7D.!!$F4 3924
2 TraesCS7D01G085000 chr7D 52266295 52271078 4783 False 673.900000 1655 93.137000 715 3926 5 chr7D.!!$F6 3211
3 TraesCS7D01G085000 chr7D 52292831 52295702 2871 False 594.500000 1230 86.188250 545 3308 4 chr7D.!!$F7 2763
4 TraesCS7D01G085000 chr7D 51952195 51954263 2068 True 513.333333 837 82.329333 796 3095 3 chr7D.!!$R1 2299
5 TraesCS7D01G085000 chr7D 52259820 52261270 1450 False 450.000000 508 89.667000 1 714 2 chr7D.!!$F5 713
6 TraesCS7D01G085000 chr4A 666798456 666799297 841 False 939.000000 939 87.168000 1 840 1 chr4A.!!$F1 839
7 TraesCS7D01G085000 chr4A 666811467 666814439 2972 False 516.500000 944 85.275500 628 3699 4 chr4A.!!$F3 3071
8 TraesCS7D01G085000 chr4A 666482873 666484794 1921 True 426.000000 891 87.331750 789 2597 4 chr4A.!!$R2 1808
9 TraesCS7D01G085000 chr4A 666538604 666542622 4018 True 423.750000 944 83.268000 542 3095 4 chr4A.!!$R4 2553
10 TraesCS7D01G085000 chr4A 666519438 666520108 670 True 385.000000 625 88.834500 1130 1915 2 chr4A.!!$R3 785
11 TraesCS7D01G085000 chr4A 666921224 666930075 8851 False 304.600000 420 87.390600 79 3818 5 chr4A.!!$F4 3739
12 TraesCS7D01G085000 chr7A 54757096 54758625 1529 True 682.000000 913 83.685000 851 2525 2 chr7A.!!$R1 1674
13 TraesCS7D01G085000 chr7A 54770910 54773185 2275 True 466.000000 918 81.385667 628 3084 3 chr7A.!!$R2 2456

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
249 263 0.037303 ATGCCTCACTCACCAACCAG 59.963 55.0 0.0 0.0 0.0 4.00 F
680 2395 0.466555 AGAGCGAGCGTCCCTATCTT 60.467 55.0 0.0 0.0 0.0 2.40 F
2514 9629 0.456312 GGAGGCTGTTCACGACGTAG 60.456 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 5304 0.107897 TGTCGTATCTGCGGCCATTT 60.108 50.0 2.24 0.0 35.36 2.32 R
2636 9782 0.989805 CGCACACTAAAAACACGCCG 60.990 55.0 0.00 0.0 0.00 6.46 R
3892 16332 0.693049 ATCTGTCAGTCACCAACCCC 59.307 55.0 0.00 0.0 0.00 4.95 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
55 56 9.987726 ACATATGATACTATTCATCCTCTCAGA 57.012 33.333 10.38 0.00 37.51 3.27
249 263 0.037303 ATGCCTCACTCACCAACCAG 59.963 55.000 0.00 0.00 0.00 4.00
308 325 1.595993 GGCGACAGCTACAGTGGAGA 61.596 60.000 6.53 0.00 44.37 3.71
418 2113 1.274167 GGGGGATTTGAAACGTTTCCC 59.726 52.381 32.14 26.93 44.49 3.97
445 2140 1.908619 TGCCTGTGCTTCCAGAATCTA 59.091 47.619 0.94 0.00 38.71 1.98
528 2231 2.381589 TGTTACGCGATCGATGATGAC 58.618 47.619 21.57 9.31 39.41 3.06
577 2280 2.242926 TCCAATTTGGCAAATCGTCCA 58.757 42.857 24.51 6.02 37.47 4.02
606 2310 9.869844 CAGTTTTGTTTTGTTTACATTGAAACA 57.130 25.926 7.07 7.07 45.29 2.83
626 2335 0.676782 AAGGGAGAAAATGACCGGCG 60.677 55.000 0.00 0.00 0.00 6.46
652 2361 2.200092 GCTTCCCACCAAACCCCA 59.800 61.111 0.00 0.00 0.00 4.96
680 2395 0.466555 AGAGCGAGCGTCCCTATCTT 60.467 55.000 0.00 0.00 0.00 2.40
723 2438 3.960755 TCATACATGATCCCTTCTCGTGT 59.039 43.478 0.00 3.89 43.45 4.49
757 2481 1.418755 CGCCGGCGAAGTTTACTTC 59.581 57.895 44.86 11.68 46.63 3.01
769 2493 4.870221 AGTTTACTTCCGTTGTGTTGTC 57.130 40.909 0.00 0.00 0.00 3.18
806 4274 2.544359 CCGTCGCAAGTTGACACG 59.456 61.111 16.21 16.21 36.11 4.49
1302 4950 4.467084 ATCGTCAACCGCGGCCAT 62.467 61.111 28.58 9.34 36.19 4.40
1407 5304 2.584064 CCCACCGAGCACAGCATA 59.416 61.111 0.00 0.00 0.00 3.14
1434 5331 1.536922 CGCAGATACGACATGGAGCTT 60.537 52.381 0.00 0.00 34.06 3.74
1632 7617 1.027357 GGCAACATGGTATGCAGAGG 58.973 55.000 18.20 0.00 44.32 3.69
1645 7630 1.479323 TGCAGAGGACGGGTGTAATAC 59.521 52.381 0.00 0.00 0.00 1.89
1646 7631 1.755380 GCAGAGGACGGGTGTAATACT 59.245 52.381 0.00 0.00 0.00 2.12
1647 7632 2.167900 GCAGAGGACGGGTGTAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
1648 7633 3.382546 GCAGAGGACGGGTGTAATACTTA 59.617 47.826 0.00 0.00 0.00 2.24
1649 7634 4.142093 GCAGAGGACGGGTGTAATACTTAA 60.142 45.833 0.00 0.00 0.00 1.85
1650 7635 5.625197 GCAGAGGACGGGTGTAATACTTAAA 60.625 44.000 0.00 0.00 0.00 1.52
1651 7636 5.809051 CAGAGGACGGGTGTAATACTTAAAC 59.191 44.000 0.00 0.00 0.00 2.01
1652 7637 5.089970 AGGACGGGTGTAATACTTAAACC 57.910 43.478 0.00 0.00 41.91 3.27
1653 7638 4.779489 AGGACGGGTGTAATACTTAAACCT 59.221 41.667 6.28 0.00 42.23 3.50
1654 7639 5.249163 AGGACGGGTGTAATACTTAAACCTT 59.751 40.000 6.28 0.00 42.23 3.50
1655 7640 5.352293 GGACGGGTGTAATACTTAAACCTTG 59.648 44.000 6.28 3.09 42.23 3.61
1656 7641 5.868454 ACGGGTGTAATACTTAAACCTTGT 58.132 37.500 6.28 3.59 42.23 3.16
1657 7642 7.003402 ACGGGTGTAATACTTAAACCTTGTA 57.997 36.000 6.28 0.00 42.23 2.41
1658 7643 7.449247 ACGGGTGTAATACTTAAACCTTGTAA 58.551 34.615 6.28 0.00 42.23 2.41
1659 7644 7.603784 ACGGGTGTAATACTTAAACCTTGTAAG 59.396 37.037 6.28 0.00 42.23 2.34
1660 7645 7.603784 CGGGTGTAATACTTAAACCTTGTAAGT 59.396 37.037 6.28 2.70 42.23 2.24
1661 7646 9.942850 GGGTGTAATACTTAAACCTTGTAAGTA 57.057 33.333 6.28 6.53 44.22 2.24
1710 7695 6.848451 TGTAAGGAATAAAACGCTCCATTTC 58.152 36.000 0.00 0.00 0.00 2.17
1711 7696 4.616181 AGGAATAAAACGCTCCATTTCG 57.384 40.909 0.00 0.00 0.00 3.46
1712 7697 3.377172 AGGAATAAAACGCTCCATTTCGG 59.623 43.478 0.00 0.00 0.00 4.30
1783 7810 4.864916 AAGCTGCATGATACAACTAACG 57.135 40.909 1.02 0.00 0.00 3.18
1791 7818 5.615544 GCATGATACAACTAACGGCATCATC 60.616 44.000 0.00 0.00 32.29 2.92
1794 7821 5.293324 TGATACAACTAACGGCATCATCAAC 59.707 40.000 0.00 0.00 0.00 3.18
1843 7876 1.602311 CATGCATGGGGCTAACTCTC 58.398 55.000 19.40 0.00 45.15 3.20
2058 8179 3.625764 CCGTTTAATCCATTCACCGTCAT 59.374 43.478 0.00 0.00 0.00 3.06
2183 8955 4.025396 GCATTTCTAGACCATCACATGACG 60.025 45.833 0.00 0.00 0.00 4.35
2324 9127 6.580041 CGTCTTTCCTTCACTTTTGATTGATG 59.420 38.462 0.00 0.00 0.00 3.07
2349 9204 4.668576 ATTTAGATGTGTGCACAAGTCG 57.331 40.909 23.59 0.00 45.41 4.18
2396 9270 6.440010 TGGTTGGTGAATAATGATGGAATTGT 59.560 34.615 0.00 0.00 0.00 2.71
2514 9629 0.456312 GGAGGCTGTTCACGACGTAG 60.456 60.000 0.00 0.00 0.00 3.51
2600 9746 3.437049 GGTGCATTCAACTCTTGTCCTAC 59.563 47.826 0.00 0.00 0.00 3.18
2624 9770 5.928839 CGCATAGCTTTGGTCTTATATGACT 59.071 40.000 15.98 1.32 37.16 3.41
2636 9782 9.109393 TGGTCTTATATGACTTTGCTATTTGAC 57.891 33.333 15.98 0.00 37.16 3.18
2653 9799 1.328069 TGACGGCGTGTTTTTAGTGTG 59.672 47.619 21.19 0.00 0.00 3.82
2670 9816 1.011333 GTGCGTGTGTTAGTGTTGGT 58.989 50.000 0.00 0.00 0.00 3.67
2708 9854 3.699894 AGAGGCCAGGTGTGCTCG 61.700 66.667 5.01 0.00 0.00 5.03
2724 9870 6.092259 GGTGTGCTCGTTATGTTTCTATTCTT 59.908 38.462 0.00 0.00 0.00 2.52
2764 9910 6.183361 TGGCTCAAATAAAATCACCCTTTGTT 60.183 34.615 0.00 0.00 0.00 2.83
2775 9921 7.552458 AATCACCCTTTGTTGAAAAATTCAC 57.448 32.000 0.00 0.00 39.87 3.18
2776 9922 5.423886 TCACCCTTTGTTGAAAAATTCACC 58.576 37.500 0.00 0.00 39.87 4.02
2796 9942 2.810852 CCTCTTGTCCTTCAGCACTTTC 59.189 50.000 0.00 0.00 0.00 2.62
2853 11493 3.947612 ATGCAGGACATGGAGAAGAAT 57.052 42.857 0.00 0.00 37.70 2.40
2884 11524 1.277557 GTCAGGAGGTGAACAGCAGAT 59.722 52.381 6.76 0.00 36.74 2.90
2901 11541 4.020751 AGCAGATATATCAGCATGTTCCGT 60.021 41.667 26.23 5.82 41.18 4.69
2953 11597 7.349598 ACTAATGTTGATCCTCTGCCTAATTT 58.650 34.615 0.00 0.00 0.00 1.82
2955 11599 5.178096 TGTTGATCCTCTGCCTAATTTGA 57.822 39.130 0.00 0.00 0.00 2.69
3008 11653 7.846644 TGGTTATATGGTTTTTGTACGTAGG 57.153 36.000 0.00 0.00 0.00 3.18
3009 11654 7.393216 TGGTTATATGGTTTTTGTACGTAGGT 58.607 34.615 0.00 0.00 0.00 3.08
3010 11655 7.548780 TGGTTATATGGTTTTTGTACGTAGGTC 59.451 37.037 0.00 0.00 0.00 3.85
3024 11686 3.326880 ACGTAGGTCTTTCCATCCACTTT 59.673 43.478 0.00 0.00 39.02 2.66
3038 11700 5.771666 CCATCCACTTTGATGCCTTGTATAT 59.228 40.000 0.00 0.00 40.66 0.86
3045 11707 6.260050 ACTTTGATGCCTTGTATATGGTTACG 59.740 38.462 0.00 0.00 0.00 3.18
3096 11790 4.037089 TGTCCATGCATATCTTGATGTTGC 59.963 41.667 0.00 11.10 0.00 4.17
3145 11866 4.162698 ACATGATTATTGCCACTGCCATTT 59.837 37.500 0.00 0.00 36.33 2.32
3186 11908 5.041191 AGGCCTTGATTATGGTTGAGTAG 57.959 43.478 0.00 0.00 0.00 2.57
3187 11909 4.475016 AGGCCTTGATTATGGTTGAGTAGT 59.525 41.667 0.00 0.00 0.00 2.73
3188 11910 5.665812 AGGCCTTGATTATGGTTGAGTAGTA 59.334 40.000 0.00 0.00 0.00 1.82
3207 11931 5.099042 AGTACCTGCGAATGAAATAAGGT 57.901 39.130 0.00 0.00 40.95 3.50
3230 11954 4.883585 TCATCCATGGCTAATTCTTGTGTC 59.116 41.667 6.96 0.00 0.00 3.67
3288 12012 4.567959 CACTTTATGGCTAATTTTGGCAGC 59.432 41.667 12.11 1.79 43.06 5.25
3296 12020 2.985957 AATTTTGGCAGCACACAACT 57.014 40.000 0.00 0.00 0.00 3.16
3318 12042 6.127451 AACTTAGTGTTGTTTAGCTTTGGCTT 60.127 34.615 0.00 0.00 42.45 4.35
3472 12221 6.932356 TGAAGAATCATGCAAGGAATAGTC 57.068 37.500 0.00 0.00 0.00 2.59
3473 12222 5.525012 TGAAGAATCATGCAAGGAATAGTCG 59.475 40.000 0.00 0.00 0.00 4.18
3522 12271 2.096218 CCGTTGCTACAGCTCAAGAAAC 60.096 50.000 2.44 5.83 42.66 2.78
3612 12525 5.330233 TCAGGTACTCAAGTTGACTATGGA 58.670 41.667 0.08 0.00 34.60 3.41
3644 12563 2.313317 ACGGAGTACTCAACAGGTGAA 58.687 47.619 23.91 0.00 41.94 3.18
3718 14294 0.319083 CTTGTGTGCCATGTGCCATT 59.681 50.000 4.07 0.00 40.16 3.16
3778 16218 9.057089 AGTTCAATCTCGTAGAAAAGAAAACAT 57.943 29.630 0.00 0.00 34.09 2.71
3820 16260 4.261994 GCAATTACTGACTGCCCTTTTCAA 60.262 41.667 0.00 0.00 0.00 2.69
3892 16332 3.003480 GTCCAGAACTTTCTCATTCCGG 58.997 50.000 0.00 0.00 34.74 5.14
3903 16343 1.677633 CATTCCGGGGGTTGGTGAC 60.678 63.158 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
215 227 0.323725 GGCATTTTGGCTCTCCCTCA 60.324 55.000 0.00 0.00 40.14 3.86
249 263 4.038763 GGGTAAACTGGCTTTAATATGGCC 59.961 45.833 0.00 0.00 45.45 5.36
308 325 6.366061 GCTTTCATTTTCGGAGCAATTAGTTT 59.634 34.615 0.00 0.00 33.68 2.66
403 2098 5.277106 GCAAAATTCGGGAAACGTTTCAAAT 60.277 36.000 34.79 26.89 44.69 2.32
418 2113 1.000385 TGGAAGCACAGGCAAAATTCG 60.000 47.619 0.00 0.00 44.61 3.34
445 2140 8.415950 TTTTGTTCAGACCCATACATGTTAAT 57.584 30.769 2.30 0.00 0.00 1.40
528 2231 3.613494 TTGTTGGATCCATGCCATTTG 57.387 42.857 17.06 0.00 34.90 2.32
577 2280 9.442047 TTCAATGTAAACAAAACAAAACTGGAT 57.558 25.926 0.00 0.00 0.00 3.41
606 2310 1.545841 GCCGGTCATTTTCTCCCTTT 58.454 50.000 1.90 0.00 0.00 3.11
652 2361 1.527311 GACGCTCGCTCTCAAAAAGTT 59.473 47.619 0.00 0.00 0.00 2.66
723 2438 1.153784 GCGTCGTCCCATTCCGTTA 60.154 57.895 0.00 0.00 0.00 3.18
757 2481 1.275657 GACGCAGACAACACAACGG 59.724 57.895 0.00 0.00 0.00 4.44
769 2493 3.372954 GGCTTATACAGTACTGACGCAG 58.627 50.000 29.30 18.23 37.52 5.18
806 4274 3.321968 AGGTTGGAACATTTCAAGCCTTC 59.678 43.478 10.52 0.00 40.86 3.46
980 4511 2.520069 TGTTGTCTCTCTCCTGGTCTC 58.480 52.381 0.00 0.00 0.00 3.36
1035 4572 1.076632 GGCCGAGAAGAGGAGGAGA 60.077 63.158 0.00 0.00 0.00 3.71
1036 4573 1.076339 AGGCCGAGAAGAGGAGGAG 60.076 63.158 0.00 0.00 0.00 3.69
1037 4574 1.076632 GAGGCCGAGAAGAGGAGGA 60.077 63.158 0.00 0.00 0.00 3.71
1142 4790 3.189376 TTGATGTCGCCCCAGTGCA 62.189 57.895 0.00 0.00 0.00 4.57
1302 4950 3.588955 CTCGAACTTGACCATGATGTCA 58.411 45.455 0.00 0.00 43.26 3.58
1407 5304 0.107897 TGTCGTATCTGCGGCCATTT 60.108 50.000 2.24 0.00 35.36 2.32
1629 7614 5.111989 GGTTTAAGTATTACACCCGTCCTC 58.888 45.833 0.00 0.00 43.82 3.71
1666 7651 8.992073 CCTTACAAGGTTTAAGTATTACACGTT 58.008 33.333 0.00 0.00 39.16 3.99
1667 7652 8.367156 TCCTTACAAGGTTTAAGTATTACACGT 58.633 33.333 7.86 0.00 46.54 4.49
1668 7653 8.761575 TCCTTACAAGGTTTAAGTATTACACG 57.238 34.615 7.86 0.00 46.54 4.49
1676 7661 8.077991 GCGTTTTATTCCTTACAAGGTTTAAGT 58.922 33.333 7.86 0.00 46.54 2.24
1690 7675 3.377172 CCGAAATGGAGCGTTTTATTCCT 59.623 43.478 0.00 0.00 42.00 3.36
1692 7677 4.609691 TCCGAAATGGAGCGTTTTATTC 57.390 40.909 0.00 0.00 43.74 1.75
1730 7715 5.009210 TGCCGTTAATTAATGCATAAGTCCC 59.991 40.000 16.79 0.00 0.00 4.46
1783 7810 1.395635 TCATGCAGGTTGATGATGCC 58.604 50.000 0.00 0.00 39.22 4.40
1843 7876 1.059692 CAGCTGCGTTCGTACAAGATG 59.940 52.381 0.00 0.00 0.00 2.90
2183 8955 7.426169 CTTTTATTTGAAAGTTGCAAGTTGTGC 59.574 33.333 19.93 12.71 41.05 4.57
2219 8997 1.144913 TCCCTGCCAACTGCTAAGTTT 59.855 47.619 0.00 0.00 44.47 2.66
2324 9127 4.218417 ACTTGTGCACACATCTAAATTCCC 59.782 41.667 21.56 0.00 41.52 3.97
2349 9204 6.029607 CCATTCAATGCATGGCGTATAATAC 58.970 40.000 0.00 0.00 34.98 1.89
2514 9629 4.955811 ATGGGAGTGGAAAAAGAAAACC 57.044 40.909 0.00 0.00 0.00 3.27
2560 9704 6.605471 TGCACCAAGAGAATAGAAGACTTA 57.395 37.500 0.00 0.00 0.00 2.24
2576 9722 2.622942 GGACAAGAGTTGAATGCACCAA 59.377 45.455 0.00 0.00 0.00 3.67
2600 9746 5.928839 AGTCATATAAGACCAAAGCTATGCG 59.071 40.000 4.52 0.00 39.34 4.73
2624 9770 1.231221 ACACGCCGTCAAATAGCAAA 58.769 45.000 0.00 0.00 0.00 3.68
2636 9782 0.989805 CGCACACTAAAAACACGCCG 60.990 55.000 0.00 0.00 0.00 6.46
2653 9799 1.399089 ACAACCAACACTAACACACGC 59.601 47.619 0.00 0.00 0.00 5.34
2724 9870 4.603989 TGAGCCAAAATGAAGCATCAAA 57.396 36.364 0.00 0.00 39.49 2.69
2764 9910 5.890985 TGAAGGACAAGAGGTGAATTTTTCA 59.109 36.000 0.00 0.00 37.33 2.69
2775 9921 2.557920 AAGTGCTGAAGGACAAGAGG 57.442 50.000 4.72 0.00 38.96 3.69
2776 9922 2.810852 GGAAAGTGCTGAAGGACAAGAG 59.189 50.000 4.72 0.00 38.96 2.85
2819 11459 1.683011 CCTGCATGTAGGGTTGAAGGG 60.683 57.143 21.33 0.00 35.31 3.95
2884 11524 4.955811 AAGGACGGAACATGCTGATATA 57.044 40.909 0.00 0.00 0.00 0.86
2901 11541 6.475504 TCAATGTCTATTCTGCTCAAAAGGA 58.524 36.000 0.00 0.00 0.00 3.36
2932 11576 5.759059 TCAAATTAGGCAGAGGATCAACAT 58.241 37.500 0.00 0.00 37.82 2.71
2953 11597 5.726980 AAAAATAGCTGAAGCACCAATCA 57.273 34.783 4.90 0.00 45.16 2.57
2977 11621 9.777575 GTACAAAAACCATATAACCATGTACAC 57.222 33.333 0.00 0.00 39.98 2.90
2993 11638 4.815846 TGGAAAGACCTACGTACAAAAACC 59.184 41.667 0.00 0.00 39.86 3.27
2994 11639 5.989551 TGGAAAGACCTACGTACAAAAAC 57.010 39.130 0.00 0.00 39.86 2.43
3008 11653 3.119352 GGCATCAAAGTGGATGGAAAGAC 60.119 47.826 5.43 0.00 43.85 3.01
3009 11654 3.091545 GGCATCAAAGTGGATGGAAAGA 58.908 45.455 5.43 0.00 43.85 2.52
3010 11655 3.094572 AGGCATCAAAGTGGATGGAAAG 58.905 45.455 5.43 0.00 43.85 2.62
3024 11686 4.345547 TCCGTAACCATATACAAGGCATCA 59.654 41.667 0.00 0.00 0.00 3.07
3038 11700 6.313411 CGTGTTCCTTTATTATTCCGTAACCA 59.687 38.462 0.00 0.00 0.00 3.67
3045 11707 5.878669 ACTGGTCGTGTTCCTTTATTATTCC 59.121 40.000 0.00 0.00 0.00 3.01
3123 11817 4.330944 AATGGCAGTGGCAATAATCATG 57.669 40.909 24.45 0.00 42.43 3.07
3130 11824 3.008157 TCATTTCAAATGGCAGTGGCAAT 59.992 39.130 24.45 13.12 42.43 3.56
3160 11882 2.762327 CAACCATAATCAAGGCCTTGCT 59.238 45.455 36.24 26.95 40.24 3.91
3167 11889 6.986817 CAGGTACTACTCAACCATAATCAAGG 59.013 42.308 0.00 0.00 38.30 3.61
3168 11890 6.480320 GCAGGTACTACTCAACCATAATCAAG 59.520 42.308 0.00 0.00 38.30 3.02
3186 11908 4.873827 TGACCTTATTTCATTCGCAGGTAC 59.126 41.667 0.00 0.00 34.67 3.34
3187 11909 5.092554 TGACCTTATTTCATTCGCAGGTA 57.907 39.130 0.00 0.00 34.67 3.08
3188 11910 3.950397 TGACCTTATTTCATTCGCAGGT 58.050 40.909 0.00 0.00 37.35 4.00
3207 11931 4.858850 ACACAAGAATTAGCCATGGATGA 58.141 39.130 18.40 6.37 0.00 2.92
3230 11954 1.067974 TGGCTACGACGAATATGGGTG 59.932 52.381 0.00 0.00 0.00 4.61
3312 12036 1.946768 CGTTCTTTGGACTGAAGCCAA 59.053 47.619 0.00 0.00 43.31 4.52
3318 12042 4.142790 AGTCTAGACGTTCTTTGGACTGA 58.857 43.478 17.07 0.00 32.64 3.41
3356 12081 7.504403 ACAATCATGAGTATAAAGTGGGAGAG 58.496 38.462 0.09 0.00 0.00 3.20
3472 12221 1.068194 GGATAATCCTCTCAGGCGTCG 60.068 57.143 0.00 0.00 34.61 5.12
3473 12222 2.029470 CAGGATAATCCTCTCAGGCGTC 60.029 54.545 0.00 0.00 45.66 5.19
3510 12259 4.024893 TCAAACTTAGCGTTTCTTGAGCTG 60.025 41.667 0.00 0.00 43.75 4.24
3522 12271 8.394877 TCATGTTGGTAATATTCAAACTTAGCG 58.605 33.333 0.00 0.00 0.00 4.26
3718 14294 1.674359 ATTAATTCATGCCGGCGTCA 58.326 45.000 20.90 1.44 0.00 4.35
3804 16244 3.613432 GCTGATTTGAAAAGGGCAGTCAG 60.613 47.826 0.00 0.00 35.11 3.51
3808 16248 2.955614 CTGCTGATTTGAAAAGGGCAG 58.044 47.619 12.26 12.26 39.38 4.85
3835 16275 9.758651 GTCTAGTGTTCATTTAAAACCCAAAAT 57.241 29.630 0.00 0.00 0.00 1.82
3839 16279 7.883391 TTGTCTAGTGTTCATTTAAAACCCA 57.117 32.000 0.00 0.00 0.00 4.51
3869 16309 3.557054 CGGAATGAGAAAGTTCTGGACCA 60.557 47.826 0.00 0.00 37.73 4.02
3892 16332 0.693049 ATCTGTCAGTCACCAACCCC 59.307 55.000 0.00 0.00 0.00 4.95
3903 16343 2.746362 GGCAGGTCTTTCAATCTGTCAG 59.254 50.000 0.00 0.00 32.67 3.51


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

AutoCloner maintained by Alex Coulton.