Multiple sequence alignment - TraesCS5B01G092100

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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 TraesCS5B01G092100 chr5B 100.000 5189 0 0 1 5189 120999918 121005106 0.000000e+00 9583.0
1 TraesCS5B01G092100 chr5D 92.324 3257 125 33 1970 5189 111952033 111955201 0.000000e+00 4514.0
2 TraesCS5B01G092100 chr5D 94.874 1307 28 11 697 1974 111950684 111951980 0.000000e+00 2006.0
3 TraesCS5B01G092100 chr5D 88.506 87 8 2 4900 4985 449052374 449052459 2.560000e-18 104.0
4 TraesCS5B01G092100 chr5D 87.209 86 9 2 4901 4985 370360156 370360240 4.280000e-16 97.1
5 TraesCS5B01G092100 chr5D 82.192 73 13 0 4817 4889 122624892 122624820 4.340000e-06 63.9
6 TraesCS5B01G092100 chr5A 94.380 2669 91 23 1970 4602 114704558 114707203 0.000000e+00 4043.0
7 TraesCS5B01G092100 chr5A 91.834 1298 46 28 697 1974 114703248 114704505 0.000000e+00 1755.0
8 TraesCS5B01G092100 chr5A 91.289 574 46 3 128 698 135137735 135138307 0.000000e+00 780.0
9 TraesCS5B01G092100 chr5A 87.413 429 13 14 4764 5189 114707285 114707675 6.130000e-124 455.0
10 TraesCS5B01G092100 chr5A 96.907 97 3 0 4654 4750 114707202 114707298 4.160000e-36 163.0
11 TraesCS5B01G092100 chr2A 95.157 413 20 0 286 698 90669310 90669722 0.000000e+00 652.0
12 TraesCS5B01G092100 chr2A 90.000 190 19 0 1 190 90669124 90669313 4.010000e-61 246.0
13 TraesCS5B01G092100 chr2A 93.478 46 3 0 4848 4893 12580234 12580279 9.320000e-08 69.4
14 TraesCS5B01G092100 chr7A 88.027 451 46 6 1971 2416 66457379 66457826 1.280000e-145 527.0
15 TraesCS5B01G092100 chr7A 95.652 46 2 0 1457 1502 250689012 250689057 2.000000e-09 75.0
16 TraesCS5B01G092100 chr6D 87.528 449 49 5 1970 2415 447742588 447743032 3.580000e-141 512.0
17 TraesCS5B01G092100 chr7D 87.907 430 43 4 1970 2398 63618850 63619271 1.000000e-136 497.0
18 TraesCS5B01G092100 chr7D 89.247 186 20 0 1970 2155 63635329 63635514 3.120000e-57 233.0
19 TraesCS5B01G092100 chr7D 97.826 46 1 0 1457 1502 532252976 532253021 4.310000e-11 80.5
20 TraesCS5B01G092100 chr7D 95.652 46 2 0 1457 1502 235576918 235576963 2.000000e-09 75.0
21 TraesCS5B01G092100 chr6B 84.749 459 48 9 1970 2415 676813397 676812948 1.720000e-119 440.0
22 TraesCS5B01G092100 chr6B 89.971 339 32 1 1975 2311 678218739 678219077 2.220000e-118 436.0
23 TraesCS5B01G092100 chr6B 91.026 78 7 0 1897 1974 678218613 678218690 7.110000e-19 106.0
24 TraesCS5B01G092100 chr6A 86.400 375 46 3 1970 2342 594341551 594341922 6.260000e-109 405.0
25 TraesCS5B01G092100 chr6A 97.872 47 1 0 1459 1505 255186874 255186920 1.200000e-11 82.4
26 TraesCS5B01G092100 chr7B 81.176 170 25 6 4817 4982 750596900 750597066 4.220000e-26 130.0
27 TraesCS5B01G092100 chr7B 85.714 63 6 2 4680 4742 672794510 672794451 4.340000e-06 63.9
28 TraesCS5B01G092100 chr4D 81.212 165 22 6 4817 4978 43624318 43624476 1.960000e-24 124.0
29 TraesCS5B01G092100 chr4D 82.558 86 13 2 4821 4905 313885567 313885483 2.000000e-09 75.0
30 TraesCS5B01G092100 chr3B 85.593 118 17 0 4819 4936 223938188 223938071 1.960000e-24 124.0
31 TraesCS5B01G092100 chr3B 97.143 35 1 0 4708 4742 697682403 697682369 5.610000e-05 60.2
32 TraesCS5B01G092100 chr4B 91.139 79 6 1 4901 4978 63120297 63120375 7.110000e-19 106.0
33 TraesCS5B01G092100 chr1D 89.412 85 7 2 4900 4983 65905163 65905080 7.110000e-19 106.0
34 TraesCS5B01G092100 chr1D 97.917 48 1 0 1460 1507 50709176 50709223 3.330000e-12 84.2
35 TraesCS5B01G092100 chr3A 87.356 87 9 2 4900 4985 515827534 515827449 1.190000e-16 99.0
36 TraesCS5B01G092100 chr3A 83.146 89 15 0 4821 4909 23322953 23322865 1.200000e-11 82.4
37 TraesCS5B01G092100 chr2D 85.714 91 11 2 4972 5061 27783639 27783728 1.540000e-15 95.3
38 TraesCS5B01G092100 chr2D 94.340 53 1 1 1457 1507 99733142 99733194 4.310000e-11 80.5
39 TraesCS5B01G092100 chr2D 100.000 30 0 0 4715 4744 641275732 641275703 7.260000e-04 56.5
40 TraesCS5B01G092100 chr3D 97.826 46 1 0 1459 1504 307935898 307935853 4.310000e-11 80.5
41 TraesCS5B01G092100 chr1B 88.060 67 2 4 4682 4744 368551684 368551748 2.000000e-09 75.0
42 TraesCS5B01G092100 chr1A 93.478 46 2 1 4706 4750 313743244 313743199 3.350000e-07 67.6


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 TraesCS5B01G092100 chr5B 120999918 121005106 5188 False 9583 9583 100.0000 1 5189 1 chr5B.!!$F1 5188
1 TraesCS5B01G092100 chr5D 111950684 111955201 4517 False 3260 4514 93.5990 697 5189 2 chr5D.!!$F3 4492
2 TraesCS5B01G092100 chr5A 114703248 114707675 4427 False 1604 4043 92.6335 697 5189 4 chr5A.!!$F2 4492
3 TraesCS5B01G092100 chr5A 135137735 135138307 572 False 780 780 91.2890 128 698 1 chr5A.!!$F1 570
4 TraesCS5B01G092100 chr2A 90669124 90669722 598 False 449 652 92.5785 1 698 2 chr2A.!!$F2 697

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
190 191 0.028902 GGCAAGAACGACAACACCAC 59.971 55.0 0.00 0.00 0.00 4.16 F
588 591 0.179015 TTAACCTCCTTGCACCGCAA 60.179 50.0 0.92 0.92 46.80 4.85 F
1984 2075 0.037447 AGGCCAGAGAAGTTTCCAGC 59.963 55.0 5.01 0.00 0.00 4.85 F
2438 2529 0.764890 TCTGGGTTGACAGTTCCTGG 59.235 55.0 0.00 0.00 39.48 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 1655 0.169672 CACATAAGCACAGCACCAGC 59.830 55.000 0.00 0.0 42.56 4.85 R
2087 2178 1.812235 GGCACATGACTCACACATGA 58.188 50.000 13.54 0.0 45.22 3.07 R
3166 3270 2.297880 TCGCCTGTAACAAGAACAGCTA 59.702 45.455 0.00 0.0 42.47 3.32 R
4289 4450 2.053865 CGGCCAAGGCACCATCAAT 61.054 57.895 13.87 0.0 44.11 2.57 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
22 23 4.467084 GTCCGCAATCCTGGCCGA 62.467 66.667 0.00 0.00 0.00 5.54
38 39 1.871408 GCCGACAGATGATACAGCCTG 60.871 57.143 0.00 0.00 0.00 4.85
52 53 1.006922 GCCTGTTGCAAGGACAAGC 60.007 57.895 8.71 1.72 40.02 4.01
58 59 1.702182 TTGCAAGGACAAGCAATCCA 58.298 45.000 0.00 0.00 44.98 3.41
73 74 3.181483 GCAATCCATCTCAAACATCACCC 60.181 47.826 0.00 0.00 0.00 4.61
84 85 3.020647 ATCACCCGCCCCATTCCA 61.021 61.111 0.00 0.00 0.00 3.53
92 93 1.613437 CCGCCCCATTCCATACAATTC 59.387 52.381 0.00 0.00 0.00 2.17
131 132 3.764434 TGTAGAAGAGCTTCAGATTCCGT 59.236 43.478 12.32 0.00 41.84 4.69
141 142 2.706890 TCAGATTCCGTTTGTAAGGCC 58.293 47.619 0.00 0.00 0.00 5.19
159 160 2.551504 GGCCGAACTTTGGTTAAGGAGA 60.552 50.000 0.00 0.00 38.23 3.71
166 167 5.333566 ACTTTGGTTAAGGAGATTCCCAA 57.666 39.130 0.00 0.00 37.19 4.12
190 191 0.028902 GGCAAGAACGACAACACCAC 59.971 55.000 0.00 0.00 0.00 4.16
192 193 0.661020 CAAGAACGACAACACCACCC 59.339 55.000 0.00 0.00 0.00 4.61
226 227 4.851252 CTCCCCAGCCTCCCCCAT 62.851 72.222 0.00 0.00 0.00 4.00
227 228 4.386100 TCCCCAGCCTCCCCCATT 62.386 66.667 0.00 0.00 0.00 3.16
228 229 3.825623 CCCCAGCCTCCCCCATTC 61.826 72.222 0.00 0.00 0.00 2.67
229 230 3.023116 CCCAGCCTCCCCCATTCA 61.023 66.667 0.00 0.00 0.00 2.57
231 232 2.276740 CAGCCTCCCCCATTCACC 59.723 66.667 0.00 0.00 0.00 4.02
232 233 2.204291 AGCCTCCCCCATTCACCA 60.204 61.111 0.00 0.00 0.00 4.17
233 234 1.623686 AGCCTCCCCCATTCACCAT 60.624 57.895 0.00 0.00 0.00 3.55
262 265 4.881920 AGGCTGCATCAACGTTTATTTTT 58.118 34.783 0.00 0.00 0.00 1.94
314 317 3.445805 GGGATTGGGCTTCGTTTGATTTA 59.554 43.478 0.00 0.00 0.00 1.40
358 361 1.068895 TGCCATTCAACAACTGCAAGG 59.931 47.619 0.00 0.00 39.30 3.61
386 389 1.576421 GCCTCGAAAGCAACACCTG 59.424 57.895 2.34 0.00 0.00 4.00
456 459 0.751277 CACAAGGTGCACAAGACCCA 60.751 55.000 20.43 0.00 33.51 4.51
468 471 3.947834 CACAAGACCCACAACTTCTTTCT 59.052 43.478 0.00 0.00 0.00 2.52
490 493 0.181350 CCGGGAGCTTAAAGATGGCT 59.819 55.000 0.00 0.00 39.16 4.75
588 591 0.179015 TTAACCTCCTTGCACCGCAA 60.179 50.000 0.92 0.92 46.80 4.85
702 705 6.501805 AGGGGATGACTATTATGTGCATTAGA 59.498 38.462 0.00 0.00 0.00 2.10
816 820 1.134098 CATGTCGTCCTAATTGGGCCT 60.134 52.381 4.53 0.00 37.05 5.19
864 868 3.828875 ACCCAAAATTTCTTTGCCGAA 57.171 38.095 0.00 0.00 0.00 4.30
1170 1184 2.235402 CCTCCAAGAAAGGTAACCGCTA 59.765 50.000 0.00 0.00 37.17 4.26
1343 1359 0.678048 GATGTGCCCTCCACCTGTTC 60.678 60.000 0.00 0.00 44.01 3.18
1438 1455 1.814248 GCGTTGTTTTGGAGGTCCTCT 60.814 52.381 18.58 0.00 36.82 3.69
1449 1466 1.751927 GGTCCTCTCGGCGTCCTTA 60.752 63.158 6.85 0.00 0.00 2.69
1450 1467 1.432657 GTCCTCTCGGCGTCCTTAC 59.567 63.158 6.85 0.00 0.00 2.34
1635 1655 0.879090 GTTGGAGTAGGGTTTTGCGG 59.121 55.000 0.00 0.00 0.00 5.69
1760 1790 4.759693 TGTTGAACTCCTAATTCATTGCGT 59.240 37.500 0.00 0.00 36.02 5.24
1941 1975 2.101582 CTCTGTTCCTCACCCTAATCCG 59.898 54.545 0.00 0.00 0.00 4.18
1942 1976 0.539986 TGTTCCTCACCCTAATCCGC 59.460 55.000 0.00 0.00 0.00 5.54
1984 2075 0.037447 AGGCCAGAGAAGTTTCCAGC 59.963 55.000 5.01 0.00 0.00 4.85
2032 2123 2.884012 CAGATTAGCACAACCAACCACA 59.116 45.455 0.00 0.00 0.00 4.17
2124 2215 4.041723 GTGCCGGATTTGAATAAATTCCG 58.958 43.478 5.05 12.24 41.42 4.30
2193 2284 5.041191 ACAACCTGGTCATTCCTATCATC 57.959 43.478 0.00 0.00 37.07 2.92
2264 2355 5.720202 CTGTACTTACAGCATGAAGTACCA 58.280 41.667 22.60 14.34 46.73 3.25
2269 2360 3.146104 ACAGCATGAAGTACCAGCTTT 57.854 42.857 0.00 0.00 39.69 3.51
2327 2418 5.633601 ACCGTACATGTATATGATGCTTTCG 59.366 40.000 9.18 3.20 37.73 3.46
2358 2449 7.989741 CACATCTACACTTTCCAGGAGATAAAT 59.010 37.037 0.00 0.00 0.00 1.40
2394 2485 1.740585 TGTTGTAAGCCACACACACAC 59.259 47.619 0.00 0.00 36.69 3.82
2395 2486 1.740585 GTTGTAAGCCACACACACACA 59.259 47.619 0.00 0.00 36.69 3.72
2396 2487 1.374560 TGTAAGCCACACACACACAC 58.625 50.000 0.00 0.00 30.04 3.82
2438 2529 0.764890 TCTGGGTTGACAGTTCCTGG 59.235 55.000 0.00 0.00 39.48 4.45
2441 2532 1.142870 TGGGTTGACAGTTCCTGGAAG 59.857 52.381 9.92 1.45 35.51 3.46
2644 2744 7.072030 GCATCACAGTTGATATTTATCCGAAC 58.928 38.462 0.00 0.00 40.79 3.95
2898 3001 5.182760 GGAGGCAAGCTAAGATCAAATATGG 59.817 44.000 0.00 0.00 0.00 2.74
3317 3423 5.649782 ACCTTTCTATTTCTGTGCATTGG 57.350 39.130 0.00 0.00 0.00 3.16
3664 3825 5.971763 TGTTTTGAAACTGTAACCATGCTT 58.028 33.333 7.97 0.00 39.59 3.91
3730 3891 7.974501 AGTAGTTAACTATCCGTGTCTTTCATG 59.025 37.037 18.03 0.00 36.36 3.07
3740 3901 8.731275 ATCCGTGTCTTTCATGTATTTAATGA 57.269 30.769 0.00 0.00 32.24 2.57
3909 4070 4.248058 TCCCGTCCTTCGATTTTTAGTTC 58.752 43.478 0.00 0.00 42.86 3.01
4081 4242 6.155910 AGTTTGACTACTCACCATCATCTCAT 59.844 38.462 0.00 0.00 0.00 2.90
4289 4450 2.620251 AGTGTGTGTGCTCTTTGCTA 57.380 45.000 0.00 0.00 43.37 3.49
4290 4451 3.131709 AGTGTGTGTGCTCTTTGCTAT 57.868 42.857 0.00 0.00 43.37 2.97
4534 4696 5.773176 TCCAGTGTCAGTTTACAGAGTATCA 59.227 40.000 0.00 0.00 37.82 2.15
4555 4717 5.288015 TCATGTTGCAATGTTTACCAGTTG 58.712 37.500 0.59 0.00 0.00 3.16
4579 4741 2.161855 CATTTCTGCAGGCTGGTTACA 58.838 47.619 17.64 4.44 0.00 2.41
4609 4771 5.533903 GTGTTAATCGATAGGGTCTCAGGTA 59.466 44.000 0.00 0.00 0.00 3.08
4613 4775 2.144730 CGATAGGGTCTCAGGTAGTCG 58.855 57.143 0.00 0.00 0.00 4.18
4745 4907 7.721286 AATTGAACGTTTTTATGGCAAATCA 57.279 28.000 0.46 0.00 0.00 2.57
4746 4908 7.721286 ATTGAACGTTTTTATGGCAAATCAA 57.279 28.000 0.46 0.00 0.00 2.57
4747 4909 6.761731 TGAACGTTTTTATGGCAAATCAAG 57.238 33.333 0.46 0.00 0.00 3.02
4748 4910 6.276847 TGAACGTTTTTATGGCAAATCAAGT 58.723 32.000 0.46 0.00 0.00 3.16
4749 4911 6.758886 TGAACGTTTTTATGGCAAATCAAGTT 59.241 30.769 0.46 0.00 0.00 2.66
4750 4912 7.278868 TGAACGTTTTTATGGCAAATCAAGTTT 59.721 29.630 0.46 0.00 0.00 2.66
4751 4913 7.546778 ACGTTTTTATGGCAAATCAAGTTTT 57.453 28.000 0.00 0.00 0.00 2.43
4752 4914 7.980062 ACGTTTTTATGGCAAATCAAGTTTTT 58.020 26.923 0.00 0.00 0.00 1.94
4771 4933 2.517650 TTTTTGCGGGGTGTCAAATC 57.482 45.000 0.00 0.00 32.92 2.17
4816 4978 6.442541 TTTTCTTGGACCCTGATAAGTGTA 57.557 37.500 0.00 0.00 0.00 2.90
4817 4979 5.416271 TTCTTGGACCCTGATAAGTGTAC 57.584 43.478 0.00 0.00 0.00 2.90
4818 4980 3.773119 TCTTGGACCCTGATAAGTGTACC 59.227 47.826 0.00 0.00 0.00 3.34
4819 4981 2.474112 TGGACCCTGATAAGTGTACCC 58.526 52.381 0.00 0.00 0.00 3.69
4820 4982 2.045326 TGGACCCTGATAAGTGTACCCT 59.955 50.000 0.00 0.00 0.00 4.34
4821 4983 2.434702 GGACCCTGATAAGTGTACCCTG 59.565 54.545 0.00 0.00 0.00 4.45
4822 4984 3.371965 GACCCTGATAAGTGTACCCTGA 58.628 50.000 0.00 0.00 0.00 3.86
4823 4985 3.967987 GACCCTGATAAGTGTACCCTGAT 59.032 47.826 0.00 0.00 0.00 2.90
4824 4986 5.145564 GACCCTGATAAGTGTACCCTGATA 58.854 45.833 0.00 0.00 0.00 2.15
4825 4987 5.535029 ACCCTGATAAGTGTACCCTGATAA 58.465 41.667 0.00 0.00 0.00 1.75
4837 4999 4.640771 ACCCTGATAAGTGTCACATGTT 57.359 40.909 5.62 0.00 0.00 2.71
4906 5079 3.585862 TGACACGAGGATAGCAACTTTC 58.414 45.455 0.00 0.00 0.00 2.62
4907 5080 2.599082 GACACGAGGATAGCAACTTTCG 59.401 50.000 0.00 0.00 0.00 3.46
4908 5081 2.029290 ACACGAGGATAGCAACTTTCGT 60.029 45.455 0.00 0.68 41.38 3.85
4909 5082 2.607187 ACGAGGATAGCAACTTTCGTG 58.393 47.619 5.07 0.00 39.49 4.35
4910 5083 1.324736 CGAGGATAGCAACTTTCGTGC 59.675 52.381 0.00 0.00 0.00 5.34
4911 5084 2.622436 GAGGATAGCAACTTTCGTGCT 58.378 47.619 4.14 4.14 42.12 4.40
4912 5085 3.003480 GAGGATAGCAACTTTCGTGCTT 58.997 45.455 3.99 0.00 39.79 3.91
4913 5086 3.412386 AGGATAGCAACTTTCGTGCTTT 58.588 40.909 3.99 0.00 39.79 3.51
4943 5116 2.605837 TGACAGAAACTTGCCGTGTA 57.394 45.000 0.00 0.00 0.00 2.90
4954 5127 2.102070 TGCCGTGTATCGTTGGAATT 57.898 45.000 0.00 0.00 37.94 2.17
4955 5128 2.428491 TGCCGTGTATCGTTGGAATTT 58.572 42.857 0.00 0.00 37.94 1.82
4956 5129 2.160615 TGCCGTGTATCGTTGGAATTTG 59.839 45.455 0.00 0.00 37.94 2.32
4957 5130 2.780993 CCGTGTATCGTTGGAATTTGC 58.219 47.619 0.00 0.00 37.94 3.68
4958 5131 2.477189 CCGTGTATCGTTGGAATTTGCC 60.477 50.000 0.00 0.00 37.94 4.52
4959 5132 2.160615 CGTGTATCGTTGGAATTTGCCA 59.839 45.455 0.00 0.00 35.78 4.92
4960 5133 3.181501 CGTGTATCGTTGGAATTTGCCAT 60.182 43.478 0.00 0.00 37.86 4.40
4961 5134 4.351192 GTGTATCGTTGGAATTTGCCATC 58.649 43.478 0.00 0.00 37.86 3.51
4962 5135 3.380004 TGTATCGTTGGAATTTGCCATCC 59.620 43.478 0.00 0.00 37.86 3.51
4963 5136 2.214376 TCGTTGGAATTTGCCATCCT 57.786 45.000 0.00 0.00 37.86 3.24
4964 5137 2.524306 TCGTTGGAATTTGCCATCCTT 58.476 42.857 0.00 0.00 37.86 3.36
4965 5138 2.230992 TCGTTGGAATTTGCCATCCTTG 59.769 45.455 0.00 0.00 37.86 3.61
4966 5139 2.674747 CGTTGGAATTTGCCATCCTTGG 60.675 50.000 0.00 0.00 46.66 3.61
4967 5140 2.302733 GTTGGAATTTGCCATCCTTGGT 59.697 45.455 0.00 0.00 45.57 3.67
4968 5141 1.901159 TGGAATTTGCCATCCTTGGTG 59.099 47.619 0.00 0.00 45.57 4.17
4969 5142 2.178580 GGAATTTGCCATCCTTGGTGA 58.821 47.619 0.00 0.00 45.57 4.02
4970 5143 2.094026 GGAATTTGCCATCCTTGGTGAC 60.094 50.000 0.00 0.00 45.57 3.67
4971 5144 2.610438 ATTTGCCATCCTTGGTGACT 57.390 45.000 0.00 0.00 45.57 3.41
4972 5145 1.619654 TTTGCCATCCTTGGTGACTG 58.380 50.000 0.00 0.00 45.57 3.51
4973 5146 0.251297 TTGCCATCCTTGGTGACTGG 60.251 55.000 0.00 0.00 45.57 4.00
4974 5147 1.133181 TGCCATCCTTGGTGACTGGA 61.133 55.000 0.00 0.00 45.57 3.86
4975 5148 0.038166 GCCATCCTTGGTGACTGGAA 59.962 55.000 0.00 0.00 45.57 3.53
4976 5149 1.341383 GCCATCCTTGGTGACTGGAAT 60.341 52.381 0.00 0.00 45.57 3.01
5060 5233 7.964559 CACCTGATGTGTGACACTTATTATTTG 59.035 37.037 17.47 1.47 40.26 2.32
5096 5269 9.679661 TTAGCAAACATATAAAATCCTGTCAGA 57.320 29.630 0.00 0.00 0.00 3.27
5125 5298 4.223255 TGAACATGGCATGGATTTGTCATT 59.777 37.500 29.49 12.50 39.85 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 0.178767 TCATCTGTCGGCCAGGATTG 59.821 55.000 2.24 0.00 41.83 2.67
11 12 1.135094 ATCATCTGTCGGCCAGGATT 58.865 50.000 2.24 0.00 41.83 3.01
21 22 2.611292 GCAACAGGCTGTATCATCTGTC 59.389 50.000 22.37 6.95 39.26 3.51
22 23 2.026915 TGCAACAGGCTGTATCATCTGT 60.027 45.455 22.37 0.00 45.15 3.41
52 53 3.065786 CGGGTGATGTTTGAGATGGATTG 59.934 47.826 0.00 0.00 0.00 2.67
58 59 0.394352 GGGCGGGTGATGTTTGAGAT 60.394 55.000 0.00 0.00 0.00 2.75
73 74 2.294233 CTGAATTGTATGGAATGGGGCG 59.706 50.000 0.00 0.00 0.00 6.13
84 85 6.043706 AGGCTATCAGGTTAGCTGAATTGTAT 59.956 38.462 18.17 3.34 43.37 2.29
92 93 3.891977 TCTACAGGCTATCAGGTTAGCTG 59.108 47.826 4.89 4.89 43.37 4.24
131 132 2.657143 ACCAAAGTTCGGCCTTACAAA 58.343 42.857 0.00 0.00 0.00 2.83
141 142 4.395231 GGGAATCTCCTTAACCAAAGTTCG 59.605 45.833 0.00 0.00 35.59 3.95
159 160 0.539438 TTCTTGCCGCTGTTGGGAAT 60.539 50.000 0.00 0.00 38.76 3.01
166 167 1.522806 TTGTCGTTCTTGCCGCTGT 60.523 52.632 0.00 0.00 0.00 4.40
190 191 0.954452 GCTATTGCAAGGGATTCGGG 59.046 55.000 4.94 0.00 39.41 5.14
192 193 1.876156 GGAGCTATTGCAAGGGATTCG 59.124 52.381 4.94 0.00 42.74 3.34
222 223 4.279169 CAGCCTACAATAATGGTGAATGGG 59.721 45.833 0.00 0.00 0.00 4.00
225 226 4.535781 TGCAGCCTACAATAATGGTGAAT 58.464 39.130 0.00 0.00 0.00 2.57
226 227 3.961849 TGCAGCCTACAATAATGGTGAA 58.038 40.909 0.00 0.00 0.00 3.18
227 228 3.643199 TGCAGCCTACAATAATGGTGA 57.357 42.857 0.00 0.00 0.00 4.02
228 229 3.884693 TGATGCAGCCTACAATAATGGTG 59.115 43.478 0.00 0.00 0.00 4.17
229 230 4.169059 TGATGCAGCCTACAATAATGGT 57.831 40.909 0.00 0.00 0.00 3.55
231 232 4.035558 ACGTTGATGCAGCCTACAATAATG 59.964 41.667 0.00 0.00 0.00 1.90
232 233 4.199310 ACGTTGATGCAGCCTACAATAAT 58.801 39.130 0.00 0.00 0.00 1.28
233 234 3.605634 ACGTTGATGCAGCCTACAATAA 58.394 40.909 0.00 0.00 0.00 1.40
358 361 2.855728 CTTTCGAGGCGCATGTTGGC 62.856 60.000 10.83 5.67 0.00 4.52
372 375 3.589988 AGACTATCAGGTGTTGCTTTCG 58.410 45.455 0.00 0.00 0.00 3.46
456 459 3.477530 CTCCCGGAAAGAAAGAAGTTGT 58.522 45.455 0.73 0.00 0.00 3.32
468 471 2.944094 GCCATCTTTAAGCTCCCGGAAA 60.944 50.000 0.73 0.00 0.00 3.13
490 493 5.337733 CCAATCTCCAATGGAAATGCTTCAA 60.338 40.000 2.61 0.00 39.12 2.69
541 544 1.064825 GGAGAGGTGGAGGTTTGGAA 58.935 55.000 0.00 0.00 0.00 3.53
588 591 5.510179 CCAGAAGATGGTGCTCATTTGTTTT 60.510 40.000 0.00 0.00 44.91 2.43
702 705 5.308825 AGAAATCTTCCGTTGTCAGAACAT 58.691 37.500 0.00 0.00 34.73 2.71
816 820 4.932105 GCCTGGTTGGTTGCCCCA 62.932 66.667 0.00 0.00 43.27 4.96
1291 1306 2.774234 CCAAAGGATCTAGCTTCCCTCA 59.226 50.000 0.00 0.00 33.45 3.86
1343 1359 2.202932 CAGCTCCCGAATCCACCG 60.203 66.667 0.00 0.00 0.00 4.94
1449 1466 1.601419 CGGATGGAGTACACGGTGGT 61.601 60.000 13.48 0.95 0.00 4.16
1450 1467 1.141019 CGGATGGAGTACACGGTGG 59.859 63.158 13.48 0.00 0.00 4.61
1586 1605 0.743688 ATCTGTGAGCTAGTCTGGCG 59.256 55.000 2.14 0.00 34.52 5.69
1635 1655 0.169672 CACATAAGCACAGCACCAGC 59.830 55.000 0.00 0.00 42.56 4.85
2087 2178 1.812235 GGCACATGACTCACACATGA 58.188 50.000 13.54 0.00 45.22 3.07
2103 2194 3.948473 TCGGAATTTATTCAAATCCGGCA 59.052 39.130 12.02 0.00 40.87 5.69
2124 2215 2.947448 AAAGCCTGCGGATTTGAATC 57.053 45.000 9.46 0.00 39.98 2.52
2134 2225 3.296322 TGGATTGTTTAAAAGCCTGCG 57.704 42.857 0.00 0.00 36.54 5.18
2249 2340 2.867109 AAGCTGGTACTTCATGCTGT 57.133 45.000 0.00 0.00 33.96 4.40
2327 2418 4.878397 CCTGGAAAGTGTAGATGTGGAATC 59.122 45.833 0.00 0.00 0.00 2.52
2358 2449 9.849166 GGCTTACAACATTTATTTTACTGCTAA 57.151 29.630 0.00 0.00 0.00 3.09
2394 2485 9.888878 GATGAATGTTGGAATATTCAGTATGTG 57.111 33.333 17.07 0.00 45.45 3.21
2395 2486 9.857656 AGATGAATGTTGGAATATTCAGTATGT 57.142 29.630 17.07 0.00 45.45 2.29
2438 2529 3.432592 GGAAGGAACAGCGACTTTACTTC 59.567 47.826 6.71 6.71 34.04 3.01
2441 2532 2.762745 TGGAAGGAACAGCGACTTTAC 58.237 47.619 0.00 0.00 0.00 2.01
2554 2653 6.127897 GCTGAAGGCAAGAACATACATACTTT 60.128 38.462 0.00 0.00 41.35 2.66
2555 2654 5.355350 GCTGAAGGCAAGAACATACATACTT 59.645 40.000 0.00 0.00 41.35 2.24
2556 2655 4.878397 GCTGAAGGCAAGAACATACATACT 59.122 41.667 0.00 0.00 41.35 2.12
2557 2656 4.260375 CGCTGAAGGCAAGAACATACATAC 60.260 45.833 0.00 0.00 41.91 2.39
2558 2657 3.871006 CGCTGAAGGCAAGAACATACATA 59.129 43.478 0.00 0.00 41.91 2.29
2559 2658 2.679837 CGCTGAAGGCAAGAACATACAT 59.320 45.455 0.00 0.00 41.91 2.29
2853 2956 7.918033 GCCTCCATAAATCTAAGAAGAAAAAGC 59.082 37.037 0.00 0.00 34.73 3.51
2898 3001 3.443099 AGCAAACTTCCACTCAAAAGC 57.557 42.857 0.00 0.00 0.00 3.51
3166 3270 2.297880 TCGCCTGTAACAAGAACAGCTA 59.702 45.455 0.00 0.00 42.47 3.32
3317 3423 2.354103 GGCTGAGCAAAAGGGGAAAATC 60.354 50.000 6.82 0.00 0.00 2.17
3359 3465 9.573133 GGTTCATGGTATTCAAAGTAAGAAATG 57.427 33.333 0.00 0.00 0.00 2.32
3644 3805 5.843673 TCAAGCATGGTTACAGTTTCAAA 57.156 34.783 10.31 0.00 0.00 2.69
3664 3825 9.129567 AATGATTCCATTCAGAACAAGCGTTCA 62.130 37.037 7.96 0.00 44.86 3.18
3718 3879 7.429340 GCCTTCATTAAATACATGAAAGACACG 59.571 37.037 0.00 0.00 39.59 4.49
3730 3891 7.442364 TCAGCTATGAGTGCCTTCATTAAATAC 59.558 37.037 5.50 0.00 38.65 1.89
3740 3901 4.592942 TCAAAATCAGCTATGAGTGCCTT 58.407 39.130 0.00 0.00 39.29 4.35
3890 4051 3.373130 GGGGAACTAAAAATCGAAGGACG 59.627 47.826 0.00 0.00 44.09 4.79
4081 4242 6.881065 AGAATTGAGTTTAGCAATACTGAGCA 59.119 34.615 0.00 0.00 35.06 4.26
4260 4421 4.157840 AGAGCACACACACTATGACGATAA 59.842 41.667 0.00 0.00 0.00 1.75
4289 4450 2.053865 CGGCCAAGGCACCATCAAT 61.054 57.895 13.87 0.00 44.11 2.57
4290 4451 2.676121 CGGCCAAGGCACCATCAA 60.676 61.111 13.87 0.00 44.11 2.57
4453 4615 6.945435 TGAACATGCCAGAAAAGAAGGTAATA 59.055 34.615 0.00 0.00 0.00 0.98
4534 4696 4.057432 GCAACTGGTAAACATTGCAACAT 58.943 39.130 0.00 0.00 40.33 2.71
4579 4741 4.481072 ACCCTATCGATTAACACCTAGCT 58.519 43.478 1.71 0.00 0.00 3.32
4609 4771 1.671979 TACTGCGTATAGGCACGACT 58.328 50.000 15.82 2.44 44.69 4.18
4613 4775 2.814280 ACCATACTGCGTATAGGCAC 57.186 50.000 15.82 0.00 38.17 5.01
4724 4886 6.276847 ACTTGATTTGCCATAAAAACGTTCA 58.723 32.000 0.00 0.00 0.00 3.18
4752 4914 1.757118 TGATTTGACACCCCGCAAAAA 59.243 42.857 0.00 0.00 37.52 1.94
4753 4915 1.403814 TGATTTGACACCCCGCAAAA 58.596 45.000 0.00 0.00 37.52 2.44
4754 4916 1.339610 CTTGATTTGACACCCCGCAAA 59.660 47.619 0.00 0.00 38.25 3.68
4755 4917 0.958091 CTTGATTTGACACCCCGCAA 59.042 50.000 0.00 0.00 0.00 4.85
4756 4918 0.179004 ACTTGATTTGACACCCCGCA 60.179 50.000 0.00 0.00 0.00 5.69
4757 4919 0.958822 AACTTGATTTGACACCCCGC 59.041 50.000 0.00 0.00 0.00 6.13
4758 4920 1.953686 ACAACTTGATTTGACACCCCG 59.046 47.619 0.00 0.00 0.00 5.73
4759 4921 3.716601 CAACAACTTGATTTGACACCCC 58.283 45.455 0.00 0.00 0.00 4.95
4760 4922 3.123050 GCAACAACTTGATTTGACACCC 58.877 45.455 0.00 0.00 0.00 4.61
4761 4923 2.788786 CGCAACAACTTGATTTGACACC 59.211 45.455 0.00 0.00 0.00 4.16
4762 4924 3.690422 TCGCAACAACTTGATTTGACAC 58.310 40.909 0.00 0.00 0.00 3.67
4763 4925 3.243035 CCTCGCAACAACTTGATTTGACA 60.243 43.478 0.00 0.00 0.00 3.58
4764 4926 3.003275 TCCTCGCAACAACTTGATTTGAC 59.997 43.478 0.00 0.00 0.00 3.18
4765 4927 3.210227 TCCTCGCAACAACTTGATTTGA 58.790 40.909 0.00 0.00 0.00 2.69
4766 4928 3.624326 TCCTCGCAACAACTTGATTTG 57.376 42.857 0.00 0.00 0.00 2.32
4767 4929 3.057315 CCATCCTCGCAACAACTTGATTT 60.057 43.478 0.00 0.00 0.00 2.17
4768 4930 2.489329 CCATCCTCGCAACAACTTGATT 59.511 45.455 0.00 0.00 0.00 2.57
4769 4931 2.086869 CCATCCTCGCAACAACTTGAT 58.913 47.619 0.00 0.00 0.00 2.57
4770 4932 1.522668 CCATCCTCGCAACAACTTGA 58.477 50.000 0.00 0.00 0.00 3.02
4771 4933 0.109597 GCCATCCTCGCAACAACTTG 60.110 55.000 0.00 0.00 0.00 3.16
4816 4978 4.640771 AACATGTGACACTTATCAGGGT 57.359 40.909 7.20 0.00 40.51 4.34
4817 4979 5.118990 CCTAACATGTGACACTTATCAGGG 58.881 45.833 7.20 0.00 0.00 4.45
4818 4980 5.734720 ACCTAACATGTGACACTTATCAGG 58.265 41.667 7.20 10.16 0.00 3.86
4819 4981 8.197439 TCATACCTAACATGTGACACTTATCAG 58.803 37.037 7.20 0.00 0.00 2.90
4820 4982 8.073467 TCATACCTAACATGTGACACTTATCA 57.927 34.615 7.20 0.00 0.00 2.15
4821 4983 7.169982 GCTCATACCTAACATGTGACACTTATC 59.830 40.741 7.20 0.00 0.00 1.75
4822 4984 6.986817 GCTCATACCTAACATGTGACACTTAT 59.013 38.462 7.20 0.00 0.00 1.73
4823 4985 6.071051 TGCTCATACCTAACATGTGACACTTA 60.071 38.462 7.20 0.00 0.00 2.24
4824 4986 5.178797 GCTCATACCTAACATGTGACACTT 58.821 41.667 7.20 0.00 0.00 3.16
4825 4987 4.222810 TGCTCATACCTAACATGTGACACT 59.777 41.667 7.20 0.00 0.00 3.55
4837 4999 3.862877 ATTGCCATGTGCTCATACCTA 57.137 42.857 0.04 0.00 42.00 3.08
4889 5051 2.607187 CACGAAAGTTGCTATCCTCGT 58.393 47.619 0.00 0.00 46.40 4.18
4906 5079 8.555166 TTCTGTCAAAAATAAACTAAAGCACG 57.445 30.769 0.00 0.00 0.00 5.34
4912 5085 9.308318 GGCAAGTTTCTGTCAAAAATAAACTAA 57.692 29.630 0.00 0.00 38.95 2.24
4913 5086 7.646130 CGGCAAGTTTCTGTCAAAAATAAACTA 59.354 33.333 0.00 0.00 38.95 2.24
4943 5116 2.738743 AGGATGGCAAATTCCAACGAT 58.261 42.857 8.26 0.00 39.96 3.73
4958 5131 3.367703 GCAAATTCCAGTCACCAAGGATG 60.368 47.826 0.00 0.00 0.00 3.51
4959 5132 2.827921 GCAAATTCCAGTCACCAAGGAT 59.172 45.455 0.00 0.00 0.00 3.24
4960 5133 2.238521 GCAAATTCCAGTCACCAAGGA 58.761 47.619 0.00 0.00 0.00 3.36
4961 5134 1.273327 GGCAAATTCCAGTCACCAAGG 59.727 52.381 0.00 0.00 0.00 3.61
4962 5135 1.962807 TGGCAAATTCCAGTCACCAAG 59.037 47.619 0.00 0.00 0.00 3.61
4963 5136 2.079170 TGGCAAATTCCAGTCACCAA 57.921 45.000 0.00 0.00 0.00 3.67
4964 5137 2.170166 GATGGCAAATTCCAGTCACCA 58.830 47.619 0.00 0.00 39.89 4.17
4965 5138 1.478105 GGATGGCAAATTCCAGTCACC 59.522 52.381 0.70 0.00 39.89 4.02
4966 5139 2.450476 AGGATGGCAAATTCCAGTCAC 58.550 47.619 8.26 0.00 39.89 3.67
4967 5140 2.827322 CAAGGATGGCAAATTCCAGTCA 59.173 45.455 8.26 0.00 39.89 3.41
4968 5141 2.167075 CCAAGGATGGCAAATTCCAGTC 59.833 50.000 8.26 0.00 40.58 3.51
4969 5142 2.181975 CCAAGGATGGCAAATTCCAGT 58.818 47.619 8.26 0.00 40.58 4.00
4970 5143 2.973694 CCAAGGATGGCAAATTCCAG 57.026 50.000 8.26 0.70 40.58 3.86
5096 5269 4.895668 ATCCATGCCATGTTCAGTTTTT 57.104 36.364 3.63 0.00 0.00 1.94
5125 5298 5.885912 GGATGGCAATTTTCTCTAGTAACCA 59.114 40.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.