Multiple sequence alignment - TraesCS3D01G508200

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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 TraesCS3D01G508200 chr3D 100.000 4987 0 0 1 4987 594493604 594498590 0.000000e+00 9210.0
1 TraesCS3D01G508200 chr3D 95.557 3106 86 19 1048 4137 594183631 594180562 0.000000e+00 4924.0
2 TraesCS3D01G508200 chr3D 92.945 1871 81 18 2291 4147 594363599 594365432 0.000000e+00 2676.0
3 TraesCS3D01G508200 chr3D 89.803 863 77 6 1048 1908 594362235 594363088 0.000000e+00 1096.0
4 TraesCS3D01G508200 chr3D 81.501 1346 195 34 2836 4164 594077812 594076504 0.000000e+00 1057.0
5 TraesCS3D01G508200 chr3D 86.397 544 71 3 12 554 594357567 594358108 4.300000e-165 592.0
6 TraesCS3D01G508200 chr3D 85.185 405 31 12 2068 2449 594079819 594079421 6.050000e-104 388.0
7 TraesCS3D01G508200 chr3D 84.938 405 30 14 2068 2449 594078971 594078575 1.010000e-101 381.0
8 TraesCS3D01G508200 chr3D 87.138 311 33 1 1923 2233 594363160 594363463 3.700000e-91 346.0
9 TraesCS3D01G508200 chr3D 95.425 153 7 0 1048 1200 594053635 594053483 1.390000e-60 244.0
10 TraesCS3D01G508200 chr3D 74.359 195 32 11 4248 4433 10709313 10709128 3.220000e-07 67.6
11 TraesCS3D01G508200 chr3B 93.503 3294 126 40 868 4147 797224774 797221555 0.000000e+00 4817.0
12 TraesCS3D01G508200 chr3B 91.873 2338 135 27 1923 4254 798107629 798109917 0.000000e+00 3214.0
13 TraesCS3D01G508200 chr3B 82.368 2297 301 55 1923 4164 798122890 798125137 0.000000e+00 1903.0
14 TraesCS3D01G508200 chr3B 94.644 1139 52 8 771 1908 798106428 798107558 0.000000e+00 1757.0
15 TraesCS3D01G508200 chr3B 81.313 1188 171 32 2991 4164 798093823 798094973 0.000000e+00 917.0
16 TraesCS3D01G508200 chr3B 85.362 649 72 5 1273 1899 797638549 797639196 0.000000e+00 651.0
17 TraesCS3D01G508200 chr3B 90.087 343 27 4 4521 4859 798110746 798111085 5.930000e-119 438.0
18 TraesCS3D01G508200 chr3B 83.742 326 47 4 733 1057 798121729 798122049 2.260000e-78 303.0
19 TraesCS3D01G508200 chr3B 80.168 358 56 13 690 1042 798090551 798090898 2.300000e-63 254.0
20 TraesCS3D01G508200 chr3B 93.478 138 9 0 4850 4987 798111264 798111401 6.540000e-49 206.0
21 TraesCS3D01G508200 chr3B 84.507 213 15 7 4240 4452 798110560 798110754 1.420000e-45 195.0
22 TraesCS3D01G508200 chr3B 96.471 85 3 0 1048 1132 797224645 797224561 1.870000e-29 141.0
23 TraesCS3D01G508200 chr3B 85.000 80 7 4 4208 4284 798109834 798109911 5.350000e-10 76.8
24 TraesCS3D01G508200 chr3B 100.000 28 0 0 4199 4226 798110580 798110607 9.000000e-03 52.8
25 TraesCS3D01G508200 chr3A 96.249 1706 43 12 2202 3900 725099851 725101542 0.000000e+00 2776.0
26 TraesCS3D01G508200 chr3A 96.784 1586 43 5 1048 2626 724947541 724949125 0.000000e+00 2639.0
27 TraesCS3D01G508200 chr3A 90.125 1438 62 19 1 1387 725097183 725098591 0.000000e+00 1796.0
28 TraesCS3D01G508200 chr3A 83.661 1677 225 33 2506 4164 725119760 725121405 0.000000e+00 1533.0
29 TraesCS3D01G508200 chr3A 92.075 1060 59 5 3929 4987 725102084 725103119 0.000000e+00 1469.0
30 TraesCS3D01G508200 chr3A 82.866 1570 217 34 2506 4053 725167876 725169415 0.000000e+00 1362.0
31 TraesCS3D01G508200 chr3A 90.843 688 58 2 4301 4987 725089495 725090178 0.000000e+00 917.0
32 TraesCS3D01G508200 chr3A 86.196 623 63 10 1048 1650 724797948 724797329 0.000000e+00 652.0
33 TraesCS3D01G508200 chr3A 84.663 652 77 10 1270 1899 724895217 724895867 3.280000e-176 628.0
34 TraesCS3D01G508200 chr3A 83.407 681 80 14 1270 1921 725167129 725167805 7.140000e-168 601.0
35 TraesCS3D01G508200 chr3A 83.763 659 77 9 1277 1908 725119028 725119683 9.240000e-167 597.0
36 TraesCS3D01G508200 chr3A 96.450 338 11 1 4201 4538 725149466 725149802 1.570000e-154 556.0
37 TraesCS3D01G508200 chr3A 87.955 440 53 0 1460 1899 725098817 725099256 2.060000e-143 520.0
38 TraesCS3D01G508200 chr3A 87.025 447 39 2 4541 4987 725153122 725153549 2.090000e-133 486.0
39 TraesCS3D01G508200 chr3A 83.114 533 61 15 1923 2454 725099344 725099848 4.550000e-125 459.0
40 TraesCS3D01G508200 chr3A 84.783 322 42 6 736 1057 725166692 725167006 2.900000e-82 316.0
41 TraesCS3D01G508200 chr3A 84.783 322 42 6 736 1057 725181722 725182036 2.900000e-82 316.0
42 TraesCS3D01G508200 chr3A 86.000 250 28 1 1984 2233 724949136 724949378 1.380000e-65 261.0
43 TraesCS3D01G508200 chr3A 90.761 184 10 7 4071 4248 725149367 725149549 6.450000e-59 239.0
44 TraesCS3D01G508200 chr3A 86.792 212 8 3 4095 4306 725088295 725088486 8.410000e-53 219.0
45 TraesCS3D01G508200 chr3A 97.849 93 1 1 623 715 724935095 724935186 5.170000e-35 159.0
46 TraesCS3D01G508200 chr3A 95.789 95 3 1 623 717 724939798 724939891 8.650000e-33 152.0
47 TraesCS3D01G508200 chr3A 95.789 95 3 1 623 717 724941073 724941166 8.650000e-33 152.0
48 TraesCS3D01G508200 chr3A 95.789 95 3 1 623 717 724943418 724943511 8.650000e-33 152.0
49 TraesCS3D01G508200 chr3A 95.789 95 3 1 623 717 724946908 724947001 8.650000e-33 152.0
50 TraesCS3D01G508200 chr3A 96.629 89 2 1 623 711 724936257 724936344 4.020000e-31 147.0
51 TraesCS3D01G508200 chr3A 94.737 95 4 1 623 717 724938645 724938738 4.020000e-31 147.0
52 TraesCS3D01G508200 chr3A 100.000 36 0 0 4208 4243 725088364 725088399 3.220000e-07 67.6
53 TraesCS3D01G508200 chr3A 86.567 67 2 4 4170 4229 725088405 725088471 3.220000e-07 67.6
54 TraesCS3D01G508200 chr3A 86.567 67 2 4 4170 4229 725102361 725102427 3.220000e-07 67.6
55 TraesCS3D01G508200 chr7A 81.906 2288 316 57 1923 4164 92363067 92360832 0.000000e+00 1842.0
56 TraesCS3D01G508200 chr7A 81.481 324 55 5 736 1057 92364250 92363930 1.380000e-65 261.0
57 TraesCS3D01G508200 chr7A 92.308 39 3 0 4244 4282 482569745 482569783 6.970000e-04 56.5
58 TraesCS3D01G508200 chrUn 82.866 1570 217 34 2506 4053 33329828 33331367 0.000000e+00 1362.0
59 TraesCS3D01G508200 chrUn 83.700 681 78 14 1270 1921 33329081 33329757 3.300000e-171 612.0
60 TraesCS3D01G508200 chrUn 84.783 322 42 6 736 1057 33328644 33328958 2.900000e-82 316.0
61 TraesCS3D01G508200 chrUn 95.789 95 3 1 623 717 341820333 341820426 8.650000e-33 152.0
62 TraesCS3D01G508200 chrUn 95.789 95 3 1 623 717 341821608 341821701 8.650000e-33 152.0
63 TraesCS3D01G508200 chr5D 90.845 142 11 2 22 162 486935175 486935035 6.590000e-44 189.0
64 TraesCS3D01G508200 chr7D 87.417 151 17 2 15 164 395926127 395925978 6.640000e-39 172.0
65 TraesCS3D01G508200 chr7D 100.000 30 0 0 4253 4282 534526108 534526137 6.970000e-04 56.5
66 TraesCS3D01G508200 chr2B 85.621 153 22 0 18 170 476417341 476417189 1.440000e-35 161.0
67 TraesCS3D01G508200 chr2B 84.906 159 22 2 15 172 377518348 377518505 5.170000e-35 159.0
68 TraesCS3D01G508200 chr4B 84.472 161 25 0 15 175 655783947 655783787 5.170000e-35 159.0
69 TraesCS3D01G508200 chr4B 94.915 59 3 0 4245 4303 450908181 450908239 5.320000e-15 93.5
70 TraesCS3D01G508200 chr5B 84.906 159 21 3 16 173 266346856 266346700 1.860000e-34 158.0
71 TraesCS3D01G508200 chr1A 83.636 165 24 3 9 172 298723946 298724108 8.650000e-33 152.0


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 TraesCS3D01G508200 chr3D 594493604 594498590 4986 False 9210.000000 9210 100.000000 1 4987 1 chr3D.!!$F2 4986
1 TraesCS3D01G508200 chr3D 594180562 594183631 3069 True 4924.000000 4924 95.557000 1048 4137 1 chr3D.!!$R3 3089
2 TraesCS3D01G508200 chr3D 594362235 594365432 3197 False 1372.666667 2676 89.962000 1048 4147 3 chr3D.!!$F3 3099
3 TraesCS3D01G508200 chr3D 594076504 594079819 3315 True 608.666667 1057 83.874667 2068 4164 3 chr3D.!!$R4 2096
4 TraesCS3D01G508200 chr3D 594357567 594358108 541 False 592.000000 592 86.397000 12 554 1 chr3D.!!$F1 542
5 TraesCS3D01G508200 chr3B 797221555 797224774 3219 True 2479.000000 4817 94.987000 868 4147 2 chr3B.!!$R1 3279
6 TraesCS3D01G508200 chr3B 798121729 798125137 3408 False 1103.000000 1903 83.055000 733 4164 2 chr3B.!!$F4 3431
7 TraesCS3D01G508200 chr3B 798106428 798111401 4973 False 848.514286 3214 91.369857 771 4987 7 chr3B.!!$F3 4216
8 TraesCS3D01G508200 chr3B 797638549 797639196 647 False 651.000000 651 85.362000 1273 1899 1 chr3B.!!$F1 626
9 TraesCS3D01G508200 chr3B 798090551 798094973 4422 False 585.500000 917 80.740500 690 4164 2 chr3B.!!$F2 3474
10 TraesCS3D01G508200 chr3A 725097183 725103119 5936 False 1181.266667 2776 89.347500 1 4987 6 chr3A.!!$F5 4986
11 TraesCS3D01G508200 chr3A 725119028 725121405 2377 False 1065.000000 1533 83.712000 1277 4164 2 chr3A.!!$F6 2887
12 TraesCS3D01G508200 chr3A 725166692 725169415 2723 False 759.666667 1362 83.685333 736 4053 3 chr3A.!!$F8 3317
13 TraesCS3D01G508200 chr3A 724797329 724797948 619 True 652.000000 652 86.196000 1048 1650 1 chr3A.!!$R1 602
14 TraesCS3D01G508200 chr3A 724895217 724895867 650 False 628.000000 628 84.663000 1270 1899 1 chr3A.!!$F1 629
15 TraesCS3D01G508200 chr3A 724935095 724949378 14283 False 440.111111 2639 95.017222 623 2626 9 chr3A.!!$F3 2003
16 TraesCS3D01G508200 chr3A 725149367 725153549 4182 False 427.000000 556 91.412000 4071 4987 3 chr3A.!!$F7 916
17 TraesCS3D01G508200 chr3A 725088295 725090178 1883 False 317.800000 917 91.050500 4095 4987 4 chr3A.!!$F4 892
18 TraesCS3D01G508200 chr7A 92360832 92364250 3418 True 1051.500000 1842 81.693500 736 4164 2 chr7A.!!$R1 3428
19 TraesCS3D01G508200 chrUn 33328644 33331367 2723 False 763.333333 1362 83.783000 736 4053 3 chrUn.!!$F1 3317

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
118 119 0.247460 CATGCCTGGTTCTCACGAGA 59.753 55.00 0.00 0.00 30.35 4.04 F
864 1034 0.665670 CGATCGAGATGCTTGGCGAT 60.666 55.00 10.26 0.00 45.07 4.58 F
1311 6463 0.757561 TGACACGGGAGGAACACAGA 60.758 55.00 0.00 0.00 0.00 3.41 F
1426 10103 1.028330 CCTGTGTGCCATGGTAGCTG 61.028 60.00 14.67 8.65 0.00 4.24 F
1435 10112 2.158842 GCCATGGTAGCTGATTCAGTCT 60.159 50.00 14.67 13.76 33.43 3.24 F
1748 14114 5.191727 TCATAACCATGGGTGTTCAGAAT 57.808 39.13 14.24 0.00 35.34 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 6463 1.009829 CAAGGCGCGCTTCTATCTTT 58.990 50.000 32.29 2.64 0.00 2.52 R
2289 15100 2.340210 TTTCAGCAGCCAGTGTTACA 57.660 45.000 0.00 0.00 0.00 2.41 R
3189 18299 1.913778 ATCACAAAGCATGTCAGCCA 58.086 45.000 0.00 0.00 41.46 4.75 R
3264 18374 4.003648 CGCCAGACTCATAAACTTCCTTT 58.996 43.478 0.00 0.00 0.00 3.11 R
3903 19025 5.740290 ACTGGGTTTCTTTTATCTCGAGA 57.260 39.130 19.19 19.19 0.00 4.04 R
4179 19818 6.279513 TGAACTTTGAACCAAGTTTGATGT 57.720 33.333 5.70 0.00 0.00 3.06 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
117 118 1.364626 GCATGCCTGGTTCTCACGAG 61.365 60.000 6.36 0.00 0.00 4.18
118 119 0.247460 CATGCCTGGTTCTCACGAGA 59.753 55.000 0.00 0.00 30.35 4.04
504 514 1.617018 CGCAGACCCATGGAGGAAGA 61.617 60.000 15.22 0.00 41.22 2.87
573 603 2.772077 TATGGGCGTTTGTGCTAGAA 57.228 45.000 0.00 0.00 34.52 2.10
577 607 1.539827 GGGCGTTTGTGCTAGAAATGT 59.460 47.619 0.00 0.00 34.52 2.71
580 610 4.320641 GGGCGTTTGTGCTAGAAATGTAAA 60.321 41.667 0.00 0.00 34.52 2.01
581 611 4.615541 GGCGTTTGTGCTAGAAATGTAAAC 59.384 41.667 0.00 0.00 34.52 2.01
584 615 6.032460 GCGTTTGTGCTAGAAATGTAAACATC 59.968 38.462 0.00 0.00 35.10 3.06
586 617 5.794687 TGTGCTAGAAATGTAAACATCCG 57.205 39.130 0.00 0.00 35.10 4.18
589 620 5.813672 GTGCTAGAAATGTAAACATCCGGTA 59.186 40.000 0.00 0.00 35.10 4.02
603 634 4.472108 ACATCCGGTATAGAAAACCCTTCA 59.528 41.667 0.00 0.00 33.10 3.02
606 637 5.433526 TCCGGTATAGAAAACCCTTCAATG 58.566 41.667 0.00 0.00 33.10 2.82
615 646 0.963962 ACCCTTCAATGTGCAGCAAG 59.036 50.000 0.00 0.00 0.00 4.01
617 648 1.342174 CCCTTCAATGTGCAGCAAGTT 59.658 47.619 0.00 0.00 0.00 2.66
618 649 2.224113 CCCTTCAATGTGCAGCAAGTTT 60.224 45.455 0.00 0.00 0.00 2.66
619 650 3.005684 CCCTTCAATGTGCAGCAAGTTTA 59.994 43.478 0.00 0.00 0.00 2.01
620 651 3.983344 CCTTCAATGTGCAGCAAGTTTAC 59.017 43.478 0.00 0.00 0.00 2.01
621 652 3.266541 TCAATGTGCAGCAAGTTTACG 57.733 42.857 0.00 0.00 0.00 3.18
858 1028 3.365465 CGTATCCTTCGATCGAGATGCTT 60.365 47.826 23.04 10.11 0.00 3.91
859 1029 2.498807 TCCTTCGATCGAGATGCTTG 57.501 50.000 18.54 3.46 0.00 4.01
860 1030 1.067669 TCCTTCGATCGAGATGCTTGG 59.932 52.381 18.54 12.15 0.00 3.61
864 1034 0.665670 CGATCGAGATGCTTGGCGAT 60.666 55.000 10.26 0.00 45.07 4.58
966 5943 0.920763 ACCTGCCCCCATCATCTTCA 60.921 55.000 0.00 0.00 0.00 3.02
1311 6463 0.757561 TGACACGGGAGGAACACAGA 60.758 55.000 0.00 0.00 0.00 3.41
1388 7723 1.854743 CTGTATCAATCAGTCACCGCG 59.145 52.381 0.00 0.00 0.00 6.46
1408 10085 5.195379 CGCGCATGTCTTAAAGTTTATACC 58.805 41.667 8.75 0.00 0.00 2.73
1425 10102 1.300963 CCTGTGTGCCATGGTAGCT 59.699 57.895 14.67 0.00 0.00 3.32
1426 10103 1.028330 CCTGTGTGCCATGGTAGCTG 61.028 60.000 14.67 8.65 0.00 4.24
1435 10112 2.158842 GCCATGGTAGCTGATTCAGTCT 60.159 50.000 14.67 13.76 33.43 3.24
1550 13901 5.817296 CCAGAAGAATACACCGATGATGAAA 59.183 40.000 0.00 0.00 0.00 2.69
1748 14114 5.191727 TCATAACCATGGGTGTTCAGAAT 57.808 39.130 14.24 0.00 35.34 2.40
2289 15100 5.552178 ACTTCTTACCTCTTTCATTTCGCT 58.448 37.500 0.00 0.00 0.00 4.93
2429 15265 7.780745 AGCAAGCTAGACTATACTAGAAGGAAA 59.219 37.037 0.00 0.00 41.42 3.13
3225 18335 7.908082 GCTTTGTGATTATGCGTGTTTCTTATA 59.092 33.333 0.00 0.00 0.00 0.98
3264 18374 5.538813 TCAGAGAACTTACAAAGAGGCTGTA 59.461 40.000 0.00 0.00 0.00 2.74
3705 18823 8.307483 TCTCGATGAATCCTCTATGATTTTACC 58.693 37.037 0.00 0.00 35.15 2.85
3909 19031 8.188799 TGTCAAAGTATAAGGTTACATCTCGAG 58.811 37.037 5.93 5.93 0.00 4.04
4176 19815 7.284074 TGAAAACAAGGGACTACATCAAACTA 58.716 34.615 0.00 0.00 38.49 2.24
4177 19816 7.227910 TGAAAACAAGGGACTACATCAAACTAC 59.772 37.037 0.00 0.00 38.49 2.73
4178 19817 6.435292 AACAAGGGACTACATCAAACTACT 57.565 37.500 0.00 0.00 38.49 2.57
4179 19818 7.549147 AACAAGGGACTACATCAAACTACTA 57.451 36.000 0.00 0.00 38.49 1.82
4180 19819 6.932947 ACAAGGGACTACATCAAACTACTAC 58.067 40.000 0.00 0.00 38.49 2.73
4181 19820 6.495872 ACAAGGGACTACATCAAACTACTACA 59.504 38.462 0.00 0.00 38.49 2.74
4182 19821 7.180408 ACAAGGGACTACATCAAACTACTACAT 59.820 37.037 0.00 0.00 38.49 2.29
4183 19822 7.349412 AGGGACTACATCAAACTACTACATC 57.651 40.000 0.00 0.00 36.02 3.06
4184 19823 6.895756 AGGGACTACATCAAACTACTACATCA 59.104 38.462 0.00 0.00 36.02 3.07
4185 19824 7.399191 AGGGACTACATCAAACTACTACATCAA 59.601 37.037 0.00 0.00 36.02 2.57
4186 19825 8.038944 GGGACTACATCAAACTACTACATCAAA 58.961 37.037 0.00 0.00 0.00 2.69
4187 19826 8.870879 GGACTACATCAAACTACTACATCAAAC 58.129 37.037 0.00 0.00 0.00 2.93
4188 19827 9.640963 GACTACATCAAACTACTACATCAAACT 57.359 33.333 0.00 0.00 0.00 2.66
4189 19828 9.998106 ACTACATCAAACTACTACATCAAACTT 57.002 29.630 0.00 0.00 0.00 2.66
4191 19830 8.099364 ACATCAAACTACTACATCAAACTTGG 57.901 34.615 0.00 0.00 0.00 3.61
4192 19831 7.719633 ACATCAAACTACTACATCAAACTTGGT 59.280 33.333 0.00 0.00 0.00 3.67
4193 19832 8.567948 CATCAAACTACTACATCAAACTTGGTT 58.432 33.333 0.00 0.00 0.00 3.67
4194 19833 8.149973 TCAAACTACTACATCAAACTTGGTTC 57.850 34.615 0.00 0.00 0.00 3.62
4195 19834 7.771361 TCAAACTACTACATCAAACTTGGTTCA 59.229 33.333 0.00 0.00 0.00 3.18
4196 19835 8.402472 CAAACTACTACATCAAACTTGGTTCAA 58.598 33.333 0.00 0.00 0.00 2.69
4197 19836 8.514330 AACTACTACATCAAACTTGGTTCAAA 57.486 30.769 0.00 0.00 0.00 2.69
4246 20555 6.849305 GGTTCAAACTACTACATCAAACGTTG 59.151 38.462 0.00 0.00 0.00 4.10
4275 20584 8.851145 TGCAAATTTGGTTCAAACTACTACATA 58.149 29.630 19.47 0.00 36.13 2.29
4405 21733 0.905357 CGTTCTCCAACCTCTCCCAT 59.095 55.000 0.00 0.00 0.00 4.00
4431 21759 3.350219 TTCTGTAAGCCCTCCAATCAC 57.650 47.619 0.00 0.00 0.00 3.06
4478 21806 2.025727 CTAACCCGCTCCGCTACG 59.974 66.667 0.00 0.00 0.00 3.51
4524 21852 0.257328 AGGAGAGCTCGATGTCCTCA 59.743 55.000 14.87 0.00 38.56 3.86
4554 25199 3.850273 CGTTCGCGTTCTTCTTGTATAGT 59.150 43.478 5.77 0.00 35.57 2.12
4557 25202 3.125829 TCGCGTTCTTCTTGTATAGTCGT 59.874 43.478 5.77 0.00 0.00 4.34
4722 25367 2.436109 GGGAAGTTGAGCCAGGCA 59.564 61.111 15.80 0.00 0.00 4.75
4767 25412 0.535553 TAATATTTCCCGTGCCGCCC 60.536 55.000 0.00 0.00 0.00 6.13
4820 25469 1.409427 GGCTCTTATGTGTAGCGGTCT 59.591 52.381 0.00 0.00 37.11 3.85
4878 25716 0.654683 GCTGAGGTATTTGCTCTGCG 59.345 55.000 0.00 0.00 33.72 5.18
4883 25721 3.202001 TATTTGCTCTGCGGCGGC 61.202 61.111 9.78 9.68 40.52 6.53
4945 25783 5.700832 GTGTTGATGTCATGTACTCCTTGAA 59.299 40.000 0.00 0.00 0.00 2.69
4971 25809 3.007074 TCTTACGGTGTAGGCATGAACAA 59.993 43.478 0.00 0.00 0.00 2.83
4976 25814 2.356135 GTGTAGGCATGAACAACCGAT 58.644 47.619 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.125673 CCTTGGTACACCTCGCGG 60.126 66.667 6.13 0.00 39.29 6.46
117 118 3.521560 TCGCTGGAGTACATTGATGTTC 58.478 45.455 1.46 0.00 41.97 3.18
118 119 3.610040 TCGCTGGAGTACATTGATGTT 57.390 42.857 1.46 0.00 41.97 2.71
374 376 4.944177 AGTAGGAAAGAGCCTAGTACCAA 58.056 43.478 0.00 0.00 41.34 3.67
573 603 7.283807 GGGTTTTCTATACCGGATGTTTACATT 59.716 37.037 9.46 0.00 35.08 2.71
577 607 6.564557 AGGGTTTTCTATACCGGATGTTTA 57.435 37.500 9.46 0.00 36.49 2.01
580 610 4.472108 TGAAGGGTTTTCTATACCGGATGT 59.528 41.667 9.46 0.00 36.49 3.06
581 611 5.031066 TGAAGGGTTTTCTATACCGGATG 57.969 43.478 9.46 0.00 36.49 3.51
584 615 5.065988 CACATTGAAGGGTTTTCTATACCGG 59.934 44.000 0.00 0.00 36.49 5.28
586 617 5.417580 TGCACATTGAAGGGTTTTCTATACC 59.582 40.000 0.00 0.00 34.82 2.73
589 620 4.082026 GCTGCACATTGAAGGGTTTTCTAT 60.082 41.667 0.00 0.00 0.00 1.98
603 634 1.336440 TGCGTAAACTTGCTGCACATT 59.664 42.857 0.00 0.13 0.00 2.71
606 637 0.307760 ACTGCGTAAACTTGCTGCAC 59.692 50.000 0.00 0.00 33.87 4.57
615 646 0.318360 GTTTGGGGCACTGCGTAAAC 60.318 55.000 9.29 9.29 0.00 2.01
617 648 0.752009 TTGTTTGGGGCACTGCGTAA 60.752 50.000 0.00 0.00 0.00 3.18
618 649 0.752009 TTTGTTTGGGGCACTGCGTA 60.752 50.000 0.00 0.00 0.00 4.42
619 650 2.055042 TTTGTTTGGGGCACTGCGT 61.055 52.632 0.00 0.00 0.00 5.24
620 651 1.591327 GTTTGTTTGGGGCACTGCG 60.591 57.895 0.00 0.00 0.00 5.18
621 652 0.107945 TTGTTTGTTTGGGGCACTGC 60.108 50.000 0.00 0.00 0.00 4.40
842 1012 0.857935 GCCAAGCATCTCGATCGAAG 59.142 55.000 19.92 13.02 0.00 3.79
860 1030 0.249911 AATCTGGACGGGCTTATCGC 60.250 55.000 0.00 0.00 38.13 4.58
864 1034 0.756903 GGCTAATCTGGACGGGCTTA 59.243 55.000 0.00 0.00 0.00 3.09
892 2277 2.292389 TGTTTGCCCCATCTCCATCATT 60.292 45.455 0.00 0.00 0.00 2.57
966 5943 1.377725 GGCAGTGGCAGTAGCATGT 60.378 57.895 12.58 0.00 44.61 3.21
1311 6463 1.009829 CAAGGCGCGCTTCTATCTTT 58.990 50.000 32.29 2.64 0.00 2.52
1388 7723 7.962918 CACACAGGTATAAACTTTAAGACATGC 59.037 37.037 0.00 0.00 0.00 4.06
1425 10102 6.072508 GCATAACAAACCAGAAGACTGAATCA 60.073 38.462 0.00 0.00 46.03 2.57
1426 10103 6.317857 GCATAACAAACCAGAAGACTGAATC 58.682 40.000 0.00 0.00 46.03 2.52
1435 10112 2.292016 CACCACGCATAACAAACCAGAA 59.708 45.455 0.00 0.00 0.00 3.02
1550 13901 6.091437 CCTCAAAGTACGACTCGTTAAGAAT 58.909 40.000 9.84 0.00 41.54 2.40
1707 14064 9.391006 GGTTATGATAACCAAACTAGTCAATCA 57.609 33.333 25.40 0.51 40.03 2.57
1748 14114 3.017442 TCACGGTGTGTTTTGAAATGGA 58.983 40.909 8.17 0.00 34.79 3.41
2274 15083 4.452455 AGTGTTACAGCGAAATGAAAGAGG 59.548 41.667 0.00 0.00 0.00 3.69
2289 15100 2.340210 TTTCAGCAGCCAGTGTTACA 57.660 45.000 0.00 0.00 0.00 2.41
3189 18299 1.913778 ATCACAAAGCATGTCAGCCA 58.086 45.000 0.00 0.00 41.46 4.75
3264 18374 4.003648 CGCCAGACTCATAAACTTCCTTT 58.996 43.478 0.00 0.00 0.00 3.11
3897 19019 7.548075 TGGGTTTCTTTTATCTCGAGATGTAAC 59.452 37.037 33.22 24.02 36.05 2.50
3900 19022 6.049955 TGGGTTTCTTTTATCTCGAGATGT 57.950 37.500 33.22 15.40 36.05 3.06
3901 19023 6.109359 ACTGGGTTTCTTTTATCTCGAGATG 58.891 40.000 33.22 18.95 36.05 2.90
3902 19024 6.301169 ACTGGGTTTCTTTTATCTCGAGAT 57.699 37.500 29.58 29.58 38.51 2.75
3903 19025 5.740290 ACTGGGTTTCTTTTATCTCGAGA 57.260 39.130 19.19 19.19 0.00 4.04
3906 19028 7.668525 AAGTTACTGGGTTTCTTTTATCTCG 57.331 36.000 0.00 0.00 0.00 4.04
4176 19815 7.122055 TGAACTTTGAACCAAGTTTGATGTAGT 59.878 33.333 5.70 0.00 0.00 2.73
4177 19816 7.479980 TGAACTTTGAACCAAGTTTGATGTAG 58.520 34.615 5.70 0.00 0.00 2.74
4178 19817 7.397892 TGAACTTTGAACCAAGTTTGATGTA 57.602 32.000 5.70 0.00 0.00 2.29
4179 19818 6.279513 TGAACTTTGAACCAAGTTTGATGT 57.720 33.333 5.70 0.00 0.00 3.06
4180 19819 7.331687 AGTTTGAACTTTGAACCAAGTTTGATG 59.668 33.333 5.70 0.00 35.21 3.07
4181 19820 7.386059 AGTTTGAACTTTGAACCAAGTTTGAT 58.614 30.769 5.70 0.00 35.21 2.57
4182 19821 6.754193 AGTTTGAACTTTGAACCAAGTTTGA 58.246 32.000 5.70 0.00 35.21 2.69
4183 19822 7.812669 AGTAGTTTGAACTTTGAACCAAGTTTG 59.187 33.333 1.20 0.00 40.37 2.93
4184 19823 7.892609 AGTAGTTTGAACTTTGAACCAAGTTT 58.107 30.769 1.20 0.00 40.37 2.66
4185 19824 7.462571 AGTAGTTTGAACTTTGAACCAAGTT 57.537 32.000 1.20 4.16 40.37 2.66
4186 19825 7.608761 TGTAGTAGTTTGAACTTTGAACCAAGT 59.391 33.333 1.20 0.00 40.37 3.16
4187 19826 7.981142 TGTAGTAGTTTGAACTTTGAACCAAG 58.019 34.615 1.20 0.00 40.37 3.61
4188 19827 7.925043 TGTAGTAGTTTGAACTTTGAACCAA 57.075 32.000 1.20 0.00 40.37 3.67
4189 19828 7.771361 TGATGTAGTAGTTTGAACTTTGAACCA 59.229 33.333 1.20 0.00 40.37 3.67
4190 19829 8.149973 TGATGTAGTAGTTTGAACTTTGAACC 57.850 34.615 1.20 0.00 40.37 3.62
4191 19830 9.997482 TTTGATGTAGTAGTTTGAACTTTGAAC 57.003 29.630 1.20 0.00 40.37 3.18
4192 19831 9.997482 GTTTGATGTAGTAGTTTGAACTTTGAA 57.003 29.630 1.20 0.00 40.37 2.69
4193 19832 9.391006 AGTTTGATGTAGTAGTTTGAACTTTGA 57.609 29.630 1.20 0.00 40.37 2.69
4196 19835 8.621286 CCAAGTTTGATGTAGTAGTTTGAACTT 58.379 33.333 1.20 0.00 40.37 2.66
4197 19836 7.773690 ACCAAGTTTGATGTAGTAGTTTGAACT 59.226 33.333 1.60 1.60 42.91 3.01
4246 20555 3.540617 AGTTTGAACCAAATTTGCACCC 58.459 40.909 12.92 2.47 35.74 4.61
4320 21644 6.295292 GCAATCTAGTCCAAATTTTGTTCCCT 60.295 38.462 8.26 1.61 0.00 4.20
4321 21645 5.869344 GCAATCTAGTCCAAATTTTGTTCCC 59.131 40.000 8.26 0.00 0.00 3.97
4322 21646 6.454795 TGCAATCTAGTCCAAATTTTGTTCC 58.545 36.000 8.26 0.00 0.00 3.62
4323 21647 9.076596 GTATGCAATCTAGTCCAAATTTTGTTC 57.923 33.333 8.26 1.48 0.00 3.18
4405 21733 2.119495 GGAGGGCTTACAGAATCAGGA 58.881 52.381 0.00 0.00 0.00 3.86
4431 21759 4.511246 ATGAGGGCCATGGCGGTG 62.511 66.667 29.90 0.00 43.06 4.94
4478 21806 1.751924 ACTCAGACTATGAAGGCGGTC 59.248 52.381 0.00 0.00 37.52 4.79
4554 25199 0.989602 TCCTGTACCCAGAGAGACGA 59.010 55.000 0.00 0.00 41.50 4.20
4557 25202 0.033011 GCCTCCTGTACCCAGAGAGA 60.033 60.000 5.68 0.00 41.50 3.10
4614 25259 2.025441 GCTCACGAGCGCCTCTAG 59.975 66.667 2.29 0.00 45.29 2.43
4722 25367 0.033796 CCTGCCTCCATGACACCAAT 60.034 55.000 0.00 0.00 0.00 3.16
4770 25415 1.067635 CGCATTTTTCCACCCTGAAGG 60.068 52.381 0.00 0.00 43.78 3.46
4773 25418 1.818060 CATCGCATTTTTCCACCCTGA 59.182 47.619 0.00 0.00 0.00 3.86
4775 25420 0.532115 GCATCGCATTTTTCCACCCT 59.468 50.000 0.00 0.00 0.00 4.34
4820 25469 2.678580 TGGGTCGCGGAGATCACA 60.679 61.111 6.13 0.00 0.00 3.58
4883 25721 2.432628 GACCTCTCACAACCGCCG 60.433 66.667 0.00 0.00 0.00 6.46
4945 25783 3.259876 TCATGCCTACACCGTAAGAACTT 59.740 43.478 0.00 0.00 43.02 2.66


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

AutoCloner maintained by Alex Coulton.