Multiple sequence alignment - TraesCS4A01G488900

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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 TraesCS4A01G488900 chr4A 100.000 4711 0 0 1 4711 740176392 740181102 0.000000e+00 8700.0
1 TraesCS4A01G488900 chr4A 95.486 1174 50 1 2265 3438 739762064 739763234 0.000000e+00 1871.0
2 TraesCS4A01G488900 chr4A 95.936 1132 34 2 1098 2229 739760942 739762061 0.000000e+00 1825.0
3 TraesCS4A01G488900 chr4A 88.064 1131 130 3 2226 3355 650312967 650311841 0.000000e+00 1336.0
4 TraesCS4A01G488900 chr4A 93.133 830 24 17 263 1088 739759289 739760089 0.000000e+00 1186.0
5 TraesCS4A01G488900 chr4A 83.511 1031 130 19 1219 2217 650314289 650313267 0.000000e+00 926.0
6 TraesCS4A01G488900 chr4A 79.681 1127 205 13 2244 3363 716936582 716937691 0.000000e+00 791.0
7 TraesCS4A01G488900 chr4A 87.602 492 25 6 4255 4711 698935790 698936280 5.360000e-149 538.0
8 TraesCS4A01G488900 chr4A 97.701 174 4 0 1 174 739759059 739759232 2.760000e-77 300.0
9 TraesCS4A01G488900 chr4A 100.000 44 0 0 3448 3491 698935738 698935781 1.090000e-11 82.4
10 TraesCS4A01G488900 chr7A 87.951 1137 133 2 2226 3361 42454768 42453635 0.000000e+00 1338.0
11 TraesCS4A01G488900 chr7A 81.495 1124 191 11 2247 3363 16720130 16719017 0.000000e+00 907.0
12 TraesCS4A01G488900 chr7A 82.824 1048 134 26 1199 2217 42456098 42455068 0.000000e+00 896.0
13 TraesCS4A01G488900 chr7A 80.659 910 125 34 2366 3266 580655800 580654933 0.000000e+00 658.0
14 TraesCS4A01G488900 chr7D 87.588 1136 138 1 2226 3361 42801061 42799929 0.000000e+00 1314.0
15 TraesCS4A01G488900 chr7D 83.141 1038 135 21 1212 2217 42802390 42801361 0.000000e+00 911.0
16 TraesCS4A01G488900 chr7B 95.817 765 23 7 3495 4255 165607376 165606617 0.000000e+00 1227.0
17 TraesCS4A01G488900 chr7B 94.859 778 31 7 3495 4264 699249855 699249079 0.000000e+00 1206.0
18 TraesCS4A01G488900 chr7B 94.812 771 31 7 3492 4257 629026659 629027425 0.000000e+00 1194.0
19 TraesCS4A01G488900 chr7B 94.792 768 34 4 3492 4256 740016364 740017128 0.000000e+00 1192.0
20 TraesCS4A01G488900 chr7B 94.246 782 39 5 3492 4268 67874523 67875303 0.000000e+00 1190.0
21 TraesCS4A01G488900 chr7B 80.199 904 140 25 2366 3266 538206528 538205661 3.970000e-180 641.0
22 TraesCS4A01G488900 chr7B 91.258 469 29 6 4255 4711 467535589 467536057 3.090000e-176 628.0
23 TraesCS4A01G488900 chr7B 87.712 472 28 15 4255 4711 196386178 196385722 1.500000e-144 523.0
24 TraesCS4A01G488900 chr7B 86.965 491 28 18 4255 4709 604111663 604111173 1.940000e-143 520.0
25 TraesCS4A01G488900 chr7B 92.606 284 19 2 4255 4537 483221420 483221138 1.580000e-109 407.0
26 TraesCS4A01G488900 chr7B 79.839 124 17 7 719 837 62468077 62467957 3.020000e-12 84.2
27 TraesCS4A01G488900 chr7B 75.393 191 38 9 529 713 84637966 84637779 3.020000e-12 84.2
28 TraesCS4A01G488900 chr7B 78.226 124 21 6 719 837 701299933 701299811 1.820000e-09 75.0
29 TraesCS4A01G488900 chr3B 95.413 763 33 1 3495 4255 32986827 32986065 0.000000e+00 1214.0
30 TraesCS4A01G488900 chr3B 95.995 749 26 3 3505 4249 798202144 798202892 0.000000e+00 1214.0
31 TraesCS4A01G488900 chr3B 95.419 764 28 6 3495 4255 766595677 766594918 0.000000e+00 1210.0
32 TraesCS4A01G488900 chr3B 86.597 1052 124 14 2310 3354 70312235 70313276 0.000000e+00 1146.0
33 TraesCS4A01G488900 chr3B 91.064 470 18 8 4255 4711 365288767 365288309 8.660000e-172 614.0
34 TraesCS4A01G488900 chr6B 95.059 769 33 4 3492 4257 473644813 473645579 0.000000e+00 1205.0
35 TraesCS4A01G488900 chr6B 92.830 265 17 2 4448 4711 639535447 639535710 2.660000e-102 383.0
36 TraesCS4A01G488900 chr6B 97.872 47 1 0 3448 3494 506705560 506705514 1.090000e-11 82.4
37 TraesCS4A01G488900 chr6B 97.872 47 1 0 3448 3494 608109850 608109804 1.090000e-11 82.4
38 TraesCS4A01G488900 chr3A 84.396 878 96 16 2483 3354 56770483 56771325 0.000000e+00 824.0
39 TraesCS4A01G488900 chr3A 89.716 457 28 8 4255 4711 272766722 272767159 2.460000e-157 566.0
40 TraesCS4A01G488900 chr3A 86.538 208 28 0 2288 2495 56769756 56769963 3.670000e-56 230.0
41 TraesCS4A01G488900 chr5B 93.435 457 19 6 4255 4711 270326276 270325831 0.000000e+00 667.0
42 TraesCS4A01G488900 chr5B 92.235 425 32 1 4255 4678 23695512 23695936 6.750000e-168 601.0
43 TraesCS4A01G488900 chr5B 97.872 47 1 0 3448 3494 687987592 687987546 1.090000e-11 82.4
44 TraesCS4A01G488900 chr2B 90.175 458 32 3 4255 4711 395740199 395740644 6.790000e-163 584.0
45 TraesCS4A01G488900 chr2B 97.826 46 1 0 3446 3491 703576383 703576428 3.910000e-11 80.5
46 TraesCS4A01G488900 chr2B 92.593 54 4 0 3441 3494 796028740 796028687 1.410000e-10 78.7
47 TraesCS4A01G488900 chr4B 95.760 283 12 0 4255 4537 598264828 598265110 1.550000e-124 457.0
48 TraesCS4A01G488900 chr1B 92.409 303 16 6 4255 4551 61433362 61433061 4.360000e-115 425.0
49 TraesCS4A01G488900 chr1B 100.000 44 0 0 3448 3491 677532811 677532854 1.090000e-11 82.4
50 TraesCS4A01G488900 chr1B 97.826 46 1 0 3446 3491 374866146 374866191 3.910000e-11 80.5
51 TraesCS4A01G488900 chr1D 100.000 46 0 0 3446 3491 113862407 113862452 8.400000e-13 86.1
52 TraesCS4A01G488900 chr1D 81.395 86 9 6 639 720 471119835 471119917 3.940000e-06 63.9
53 TraesCS4A01G488900 chr6D 74.672 229 32 19 505 713 60551649 60551871 1.410000e-10 78.7
54 TraesCS4A01G488900 chr4D 82.895 76 8 5 651 723 49373679 49373606 3.940000e-06 63.9


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 TraesCS4A01G488900 chr4A 740176392 740181102 4710 False 8700.0 8700 100.0000 1 4711 1 chr4A.!!$F2 4710
1 TraesCS4A01G488900 chr4A 739759059 739763234 4175 False 1295.5 1871 95.5640 1 3438 4 chr4A.!!$F4 3437
2 TraesCS4A01G488900 chr4A 650311841 650314289 2448 True 1131.0 1336 85.7875 1219 3355 2 chr4A.!!$R1 2136
3 TraesCS4A01G488900 chr4A 716936582 716937691 1109 False 791.0 791 79.6810 2244 3363 1 chr4A.!!$F1 1119
4 TraesCS4A01G488900 chr4A 698935738 698936280 542 False 310.2 538 93.8010 3448 4711 2 chr4A.!!$F3 1263
5 TraesCS4A01G488900 chr7A 42453635 42456098 2463 True 1117.0 1338 85.3875 1199 3361 2 chr7A.!!$R3 2162
6 TraesCS4A01G488900 chr7A 16719017 16720130 1113 True 907.0 907 81.4950 2247 3363 1 chr7A.!!$R1 1116
7 TraesCS4A01G488900 chr7A 580654933 580655800 867 True 658.0 658 80.6590 2366 3266 1 chr7A.!!$R2 900
8 TraesCS4A01G488900 chr7D 42799929 42802390 2461 True 1112.5 1314 85.3645 1212 3361 2 chr7D.!!$R1 2149
9 TraesCS4A01G488900 chr7B 165606617 165607376 759 True 1227.0 1227 95.8170 3495 4255 1 chr7B.!!$R3 760
10 TraesCS4A01G488900 chr7B 699249079 699249855 776 True 1206.0 1206 94.8590 3495 4264 1 chr7B.!!$R8 769
11 TraesCS4A01G488900 chr7B 629026659 629027425 766 False 1194.0 1194 94.8120 3492 4257 1 chr7B.!!$F3 765
12 TraesCS4A01G488900 chr7B 740016364 740017128 764 False 1192.0 1192 94.7920 3492 4256 1 chr7B.!!$F4 764
13 TraesCS4A01G488900 chr7B 67874523 67875303 780 False 1190.0 1190 94.2460 3492 4268 1 chr7B.!!$F1 776
14 TraesCS4A01G488900 chr7B 538205661 538206528 867 True 641.0 641 80.1990 2366 3266 1 chr7B.!!$R6 900
15 TraesCS4A01G488900 chr3B 32986065 32986827 762 True 1214.0 1214 95.4130 3495 4255 1 chr3B.!!$R1 760
16 TraesCS4A01G488900 chr3B 798202144 798202892 748 False 1214.0 1214 95.9950 3505 4249 1 chr3B.!!$F2 744
17 TraesCS4A01G488900 chr3B 766594918 766595677 759 True 1210.0 1210 95.4190 3495 4255 1 chr3B.!!$R3 760
18 TraesCS4A01G488900 chr3B 70312235 70313276 1041 False 1146.0 1146 86.5970 2310 3354 1 chr3B.!!$F1 1044
19 TraesCS4A01G488900 chr6B 473644813 473645579 766 False 1205.0 1205 95.0590 3492 4257 1 chr6B.!!$F1 765
20 TraesCS4A01G488900 chr3A 56769756 56771325 1569 False 527.0 824 85.4670 2288 3354 2 chr3A.!!$F2 1066

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
36 37 0.671781 TGGCTGAGAGAAAGAAGCGC 60.672 55.0 0.00 0.00 36.50 5.92 F
1050 1072 0.243907 CCCGCCCACGACTATCATAG 59.756 60.0 0.00 0.00 43.93 2.23 F
1423 2294 0.661020 CGTGGTGTGGTTCCTGAAAC 59.339 55.0 0.00 0.00 37.12 2.78 F
2027 2922 0.607489 TCTAGATACGGTAGCGGGGC 60.607 60.0 19.72 6.86 0.00 5.80 F
3292 5040 0.540454 TCAGGCTCAGATTCAGGCAG 59.460 55.0 0.00 0.00 38.91 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 2200 0.034896 ATGTGGCGAGGACGAACTTT 59.965 50.0 0.00 0.0 42.66 2.66 R
1869 2752 0.107831 TGAGGAAACCCTGGTTGTCG 59.892 55.0 1.58 0.0 38.47 4.35 R
3156 4904 1.197430 CCCTCTGCTTGTCCTCCACT 61.197 60.0 0.00 0.0 0.00 4.00 R
3487 5238 0.629596 TAGGGGTGACGGATGAGACT 59.370 55.0 0.00 0.0 0.00 3.24 R
4598 6396 1.123928 CTTATCCTGAGCCGGACCTT 58.876 55.0 5.05 0.0 35.52 3.50 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
23 24 1.610673 GAGAGAGGTGGGTGGCTGA 60.611 63.158 0.00 0.00 0.00 4.26
29 30 0.768221 AGGTGGGTGGCTGAGAGAAA 60.768 55.000 0.00 0.00 0.00 2.52
36 37 0.671781 TGGCTGAGAGAAAGAAGCGC 60.672 55.000 0.00 0.00 36.50 5.92
185 203 2.672961 TCGCTGATGTGTCCCTTTAG 57.327 50.000 0.00 0.00 0.00 1.85
189 207 3.679917 CGCTGATGTGTCCCTTTAGTGAT 60.680 47.826 0.00 0.00 0.00 3.06
204 222 8.301002 CCCTTTAGTGATCTAGTAACATAGAGC 58.699 40.741 0.00 0.00 38.41 4.09
266 284 7.828508 TTTTAGAAAAGGGGGTTTACTTCTC 57.171 36.000 0.00 0.00 0.00 2.87
308 326 1.691196 TTTTGACTTGCCCCTGTCTG 58.309 50.000 0.00 0.00 34.57 3.51
314 332 1.207791 CTTGCCCCTGTCTGAGGTAT 58.792 55.000 0.00 0.00 40.87 2.73
348 366 3.285484 ACTGGGCTTGATGCTTCTTATG 58.715 45.455 0.88 0.00 42.39 1.90
349 367 3.054139 ACTGGGCTTGATGCTTCTTATGA 60.054 43.478 0.88 0.00 42.39 2.15
357 375 7.013655 GGCTTGATGCTTCTTATGAATTTCCTA 59.986 37.037 0.88 0.00 42.39 2.94
358 376 8.574737 GCTTGATGCTTCTTATGAATTTCCTAT 58.425 33.333 0.88 0.00 38.95 2.57
527 547 6.882768 TTTAATGGTAAATTGATGCCCCTT 57.117 33.333 0.00 0.00 0.00 3.95
533 553 6.142498 TGGTAAATTGATGCCCCTTATTCAT 58.858 36.000 0.00 0.00 0.00 2.57
534 554 6.267471 TGGTAAATTGATGCCCCTTATTCATC 59.733 38.462 0.00 0.00 37.65 2.92
536 556 2.566833 TGATGCCCCTTATTCATCCG 57.433 50.000 0.00 0.00 36.64 4.18
549 570 7.120726 CCCTTATTCATCCGTCTTACAAAACTT 59.879 37.037 0.00 0.00 0.00 2.66
552 573 5.223449 TCATCCGTCTTACAAAACTTCCT 57.777 39.130 0.00 0.00 0.00 3.36
816 838 5.235831 GGTTATCGGGTTTACAACTCATAGC 59.764 44.000 0.00 0.00 0.00 2.97
875 897 4.509230 GGATATATACATGCATGACGCTGG 59.491 45.833 32.75 4.95 43.06 4.85
897 919 3.052036 TCACGTTAGTGGCGACTAAAAC 58.948 45.455 21.07 12.62 44.54 2.43
914 936 6.270064 ACTAAAACAAAATTTGGGTCAGTCG 58.730 36.000 10.71 0.00 34.12 4.18
966 988 1.984066 ACTGGTAGCCGGTCTCTATC 58.016 55.000 1.90 0.00 39.13 2.08
973 995 3.074675 AGCCGGTCTCTATCGTCATAT 57.925 47.619 1.90 0.00 0.00 1.78
980 1002 3.092301 TCTCTATCGTCATATGGCCCTG 58.908 50.000 0.00 0.00 0.00 4.45
1011 1033 0.515127 CGCTGAACCGTTTATGCACA 59.485 50.000 0.00 0.00 0.00 4.57
1012 1034 1.130373 CGCTGAACCGTTTATGCACAT 59.870 47.619 0.00 0.00 0.00 3.21
1050 1072 0.243907 CCCGCCCACGACTATCATAG 59.756 60.000 0.00 0.00 43.93 2.23
1051 1073 0.243907 CCGCCCACGACTATCATAGG 59.756 60.000 0.00 0.00 43.93 2.57
1052 1074 1.244816 CGCCCACGACTATCATAGGA 58.755 55.000 0.00 0.00 43.93 2.94
1053 1075 1.819288 CGCCCACGACTATCATAGGAT 59.181 52.381 0.00 0.00 43.93 3.24
1088 1110 3.013219 TCGGCATGCAGCTTACAAATAA 58.987 40.909 21.36 0.00 44.79 1.40
1089 1111 3.631686 TCGGCATGCAGCTTACAAATAAT 59.368 39.130 21.36 0.00 44.79 1.28
1090 1112 3.732219 CGGCATGCAGCTTACAAATAATG 59.268 43.478 21.36 0.00 44.79 1.90
1091 1113 4.053295 GGCATGCAGCTTACAAATAATGG 58.947 43.478 21.36 0.00 44.79 3.16
1092 1114 3.492011 GCATGCAGCTTACAAATAATGGC 59.508 43.478 14.21 0.00 41.15 4.40
1093 1115 3.419264 TGCAGCTTACAAATAATGGCG 57.581 42.857 0.00 0.00 0.00 5.69
1094 1116 2.098934 TGCAGCTTACAAATAATGGCGG 59.901 45.455 0.00 0.00 0.00 6.13
1095 1117 2.731217 CAGCTTACAAATAATGGCGGC 58.269 47.619 0.00 0.00 0.00 6.53
1112 1977 1.006922 GCACTGCTTCCTTTGCACC 60.007 57.895 0.00 0.00 36.37 5.01
1159 2024 1.581447 CCCTGCTTTCGCTTTGGTC 59.419 57.895 0.00 0.00 36.97 4.02
1170 2035 1.078848 CTTTGGTCTCCTCCGCCTG 60.079 63.158 0.00 0.00 0.00 4.85
1335 2200 2.745100 CTCGACTCCGACCCGACA 60.745 66.667 0.00 0.00 40.30 4.35
1423 2294 0.661020 CGTGGTGTGGTTCCTGAAAC 59.339 55.000 0.00 0.00 37.12 2.78
1437 2308 0.762418 TGAAACAGACGACCATGGGT 59.238 50.000 18.09 4.80 39.44 4.51
1439 2310 2.028476 TGAAACAGACGACCATGGGTAG 60.028 50.000 18.09 9.24 35.25 3.18
1869 2752 1.828331 GCAACACGACCGTCACCTTC 61.828 60.000 0.00 0.00 0.00 3.46
2027 2922 0.607489 TCTAGATACGGTAGCGGGGC 60.607 60.000 19.72 6.86 0.00 5.80
2266 3452 1.100510 TCCCTACAAGATCGTCACCG 58.899 55.000 0.00 0.00 0.00 4.94
2496 4216 2.383170 GCATCTCATCGCGGTGAAA 58.617 52.632 24.22 11.52 0.00 2.69
2708 4428 4.320456 CCTGTGGAGCTGGCGTGT 62.320 66.667 0.00 0.00 0.00 4.49
3156 4904 2.911484 CGACCCGGACGTTGAGACA 61.911 63.158 0.73 0.00 0.00 3.41
3290 5038 2.220313 GAATCAGGCTCAGATTCAGGC 58.780 52.381 17.91 0.00 46.63 4.85
3291 5039 1.210538 ATCAGGCTCAGATTCAGGCA 58.789 50.000 0.00 0.00 38.91 4.75
3292 5040 0.540454 TCAGGCTCAGATTCAGGCAG 59.460 55.000 0.00 0.00 38.91 4.85
3369 5120 5.526479 GCTCAAGATTGAATGAGATGTGCTA 59.474 40.000 6.95 0.00 44.64 3.49
3372 5123 6.537660 TCAAGATTGAATGAGATGTGCTACAG 59.462 38.462 0.00 0.00 33.55 2.74
3426 5177 9.241317 CAGATTTATTGGTCTAAATGATGTTGC 57.759 33.333 0.00 0.00 32.74 4.17
3429 5180 8.755696 TTTATTGGTCTAAATGATGTTGCAAC 57.244 30.769 22.83 22.83 0.00 4.17
3433 5184 4.616802 GGTCTAAATGATGTTGCAACGTTG 59.383 41.667 24.49 23.90 0.00 4.10
3438 5189 4.621068 ATGATGTTGCAACGTTGGATAG 57.379 40.909 28.33 4.24 0.00 2.08
3439 5190 3.407698 TGATGTTGCAACGTTGGATAGT 58.592 40.909 28.33 14.53 0.00 2.12
3440 5191 3.818210 TGATGTTGCAACGTTGGATAGTT 59.182 39.130 28.33 11.82 0.00 2.24
3441 5192 4.998033 TGATGTTGCAACGTTGGATAGTTA 59.002 37.500 28.33 8.71 0.00 2.24
3442 5193 4.735662 TGTTGCAACGTTGGATAGTTAC 57.264 40.909 28.33 19.98 0.00 2.50
3443 5194 4.382291 TGTTGCAACGTTGGATAGTTACT 58.618 39.130 28.33 0.00 0.00 2.24
3444 5195 4.212425 TGTTGCAACGTTGGATAGTTACTG 59.788 41.667 28.33 0.49 0.00 2.74
3445 5196 4.260139 TGCAACGTTGGATAGTTACTGA 57.740 40.909 28.33 0.00 0.00 3.41
3446 5197 4.827692 TGCAACGTTGGATAGTTACTGAT 58.172 39.130 28.33 0.00 0.00 2.90
3556 5307 0.107508 ATCAACCCGCAGTCCATCTG 60.108 55.000 0.00 0.00 46.12 2.90
3563 5315 1.550065 CGCAGTCCATCTGTAAGTCG 58.450 55.000 0.00 0.00 45.23 4.18
3573 5325 4.478699 CATCTGTAAGTCGTAACGAACCA 58.521 43.478 0.00 0.00 37.72 3.67
3651 5404 7.201325 CGTCCATATTTAAGTCATACGAATCGG 60.201 40.741 7.80 0.00 0.00 4.18
3873 5629 6.103330 TGCAAACTTAATCTATAGTGCACGA 58.897 36.000 12.01 6.67 0.00 4.35
3917 5673 4.050553 CGGCGATCCAAATTGCAAATAAT 58.949 39.130 1.71 0.00 43.18 1.28
3918 5674 4.507388 CGGCGATCCAAATTGCAAATAATT 59.493 37.500 1.71 0.00 43.18 1.40
3919 5675 5.006552 CGGCGATCCAAATTGCAAATAATTT 59.993 36.000 1.71 0.00 43.18 1.82
4118 5880 1.732941 TTTCGTTGTGTGAGCAGTGT 58.267 45.000 0.00 0.00 0.00 3.55
4321 6084 2.806244 CGAGTCCCTACCTGTTTGTTTG 59.194 50.000 0.00 0.00 0.00 2.93
4324 6087 2.293399 GTCCCTACCTGTTTGTTTGCAG 59.707 50.000 0.00 0.00 0.00 4.41
4325 6088 2.173782 TCCCTACCTGTTTGTTTGCAGA 59.826 45.455 0.00 0.00 34.87 4.26
4374 6137 3.160748 GAGGCTCAGGAGAGGGCC 61.161 72.222 10.25 0.00 42.33 5.80
4413 6176 4.090057 GCTGCAACGAACCGAGGC 62.090 66.667 0.00 0.00 0.00 4.70
4429 6192 3.479269 GCAGAACGAACCGAGGCG 61.479 66.667 0.00 0.00 0.00 5.52
4619 6417 0.831307 GGTCCGGCTCAGGATAAGTT 59.169 55.000 0.00 0.00 43.04 2.66
4635 6433 3.653835 AAGTTCCAATAAGCTCCTCCC 57.346 47.619 0.00 0.00 0.00 4.30
4678 6476 5.010282 GTCCCAAATCACCACAATAAGTCT 58.990 41.667 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.615331 TCATGGGCGCTTCTTTCTCT 59.385 50.000 7.64 0.00 0.00 3.10
29 30 2.496942 CCAATTCATGGGCGCTTCT 58.503 52.632 7.64 0.00 46.27 2.85
60 61 7.158021 CCTGTACACTTGATTTCTTCTTCTCT 58.842 38.462 0.00 0.00 0.00 3.10
241 259 7.013559 CGAGAAGTAAACCCCCTTTTCTAAAAA 59.986 37.037 0.00 0.00 0.00 1.94
242 260 6.487668 CGAGAAGTAAACCCCCTTTTCTAAAA 59.512 38.462 0.00 0.00 0.00 1.52
243 261 5.999600 CGAGAAGTAAACCCCCTTTTCTAAA 59.000 40.000 0.00 0.00 0.00 1.85
244 262 5.072193 ACGAGAAGTAAACCCCCTTTTCTAA 59.928 40.000 0.00 0.00 0.00 2.10
245 263 4.594491 ACGAGAAGTAAACCCCCTTTTCTA 59.406 41.667 0.00 0.00 0.00 2.10
246 264 3.393609 ACGAGAAGTAAACCCCCTTTTCT 59.606 43.478 0.00 0.00 0.00 2.52
247 265 3.748083 ACGAGAAGTAAACCCCCTTTTC 58.252 45.455 0.00 0.00 0.00 2.29
248 266 3.393609 AGACGAGAAGTAAACCCCCTTTT 59.606 43.478 0.00 0.00 0.00 2.27
249 267 2.977580 AGACGAGAAGTAAACCCCCTTT 59.022 45.455 0.00 0.00 0.00 3.11
250 268 2.617658 AGACGAGAAGTAAACCCCCTT 58.382 47.619 0.00 0.00 0.00 3.95
251 269 2.322339 AGACGAGAAGTAAACCCCCT 57.678 50.000 0.00 0.00 0.00 4.79
252 270 3.413846 AAAGACGAGAAGTAAACCCCC 57.586 47.619 0.00 0.00 0.00 5.40
253 271 4.639334 AGAAAAGACGAGAAGTAAACCCC 58.361 43.478 0.00 0.00 0.00 4.95
254 272 5.405873 CAGAGAAAAGACGAGAAGTAAACCC 59.594 44.000 0.00 0.00 0.00 4.11
255 273 6.214399 TCAGAGAAAAGACGAGAAGTAAACC 58.786 40.000 0.00 0.00 0.00 3.27
256 274 7.140048 TCTCAGAGAAAAGACGAGAAGTAAAC 58.860 38.462 0.00 0.00 30.04 2.01
257 275 7.273320 TCTCAGAGAAAAGACGAGAAGTAAA 57.727 36.000 0.00 0.00 30.04 2.01
258 276 6.072397 CCTCTCAGAGAAAAGACGAGAAGTAA 60.072 42.308 2.09 0.00 32.61 2.24
259 277 5.413213 CCTCTCAGAGAAAAGACGAGAAGTA 59.587 44.000 2.09 0.00 32.61 2.24
260 278 4.217550 CCTCTCAGAGAAAAGACGAGAAGT 59.782 45.833 2.09 0.00 32.61 3.01
261 279 4.217550 ACCTCTCAGAGAAAAGACGAGAAG 59.782 45.833 2.09 0.00 32.61 2.85
262 280 4.022762 CACCTCTCAGAGAAAAGACGAGAA 60.023 45.833 2.09 0.00 32.61 2.87
263 281 3.504134 CACCTCTCAGAGAAAAGACGAGA 59.496 47.826 2.09 0.00 0.00 4.04
264 282 3.366883 CCACCTCTCAGAGAAAAGACGAG 60.367 52.174 2.09 0.00 0.00 4.18
265 283 2.558795 CCACCTCTCAGAGAAAAGACGA 59.441 50.000 2.09 0.00 0.00 4.20
266 284 2.558795 TCCACCTCTCAGAGAAAAGACG 59.441 50.000 2.09 0.00 0.00 4.18
308 326 5.163754 CCCAGTTGAAAAATCGACATACCTC 60.164 44.000 0.00 0.00 0.00 3.85
314 332 2.582052 AGCCCAGTTGAAAAATCGACA 58.418 42.857 0.00 0.00 0.00 4.35
370 388 9.927081 AAGAAGGGATAAATTAGTGTCATTGAT 57.073 29.630 0.00 0.00 0.00 2.57
411 429 7.553334 AGCATAATAGTGGAAGTTCTTTCGTA 58.447 34.615 2.25 0.00 36.62 3.43
501 521 7.871082 AGGGGCATCAATTTACCATTAAAATT 58.129 30.769 0.00 0.00 37.08 1.82
515 535 3.181429 ACGGATGAATAAGGGGCATCAAT 60.181 43.478 0.00 0.00 40.03 2.57
527 547 7.391620 AGGAAGTTTTGTAAGACGGATGAATA 58.608 34.615 0.00 0.00 0.00 1.75
533 553 6.126568 CAAAAGGAAGTTTTGTAAGACGGA 57.873 37.500 2.67 0.00 46.88 4.69
549 570 6.385649 AATAGTGAAAGTTTCGCAAAAGGA 57.614 33.333 26.46 8.54 42.49 3.36
611 632 8.359060 ACAAAATTTACACGTAATTTGCACAT 57.641 26.923 7.98 0.00 32.47 3.21
722 743 8.390143 AGTGTCCCCACAAATAATATATGCATA 58.610 33.333 9.27 9.27 44.39 3.14
723 744 7.240897 AGTGTCCCCACAAATAATATATGCAT 58.759 34.615 3.79 3.79 44.39 3.96
724 745 6.609876 AGTGTCCCCACAAATAATATATGCA 58.390 36.000 0.00 0.00 44.39 3.96
725 746 7.120726 GGTAGTGTCCCCACAAATAATATATGC 59.879 40.741 0.00 0.00 44.39 3.14
726 747 8.160765 TGGTAGTGTCCCCACAAATAATATATG 58.839 37.037 0.00 0.00 44.39 1.78
727 748 8.282801 TGGTAGTGTCCCCACAAATAATATAT 57.717 34.615 0.00 0.00 44.39 0.86
728 749 7.693533 TGGTAGTGTCCCCACAAATAATATA 57.306 36.000 0.00 0.00 44.39 0.86
729 750 6.584471 TGGTAGTGTCCCCACAAATAATAT 57.416 37.500 0.00 0.00 44.39 1.28
875 897 2.336554 TTAGTCGCCACTAACGTGAC 57.663 50.000 0.00 0.00 43.97 3.67
897 919 3.888934 CAGTCGACTGACCCAAATTTTG 58.111 45.455 36.73 8.90 46.74 2.44
914 936 7.813645 ACTAAAATACGAATTTTGGGTCAGTC 58.186 34.615 10.42 0.00 43.88 3.51
964 986 1.131638 ACACAGGGCCATATGACGAT 58.868 50.000 0.93 0.00 0.00 3.73
965 987 0.177836 CACACAGGGCCATATGACGA 59.822 55.000 0.93 0.00 0.00 4.20
966 988 1.439353 GCACACAGGGCCATATGACG 61.439 60.000 0.93 0.00 0.00 4.35
1011 1033 4.498009 CGGGAAAATTCTTATTCAGCGCAT 60.498 41.667 11.47 0.00 0.00 4.73
1012 1034 3.181501 CGGGAAAATTCTTATTCAGCGCA 60.182 43.478 11.47 0.00 0.00 6.09
1050 1072 2.242113 GAGCATGCATGGTCGATCC 58.758 57.895 35.33 18.62 44.12 3.36
1088 1110 3.574074 AAGGAAGCAGTGCCGCCAT 62.574 57.895 21.79 10.46 0.00 4.40
1089 1111 3.790416 AAAGGAAGCAGTGCCGCCA 62.790 57.895 21.79 0.00 0.00 5.69
1090 1112 2.985847 AAAGGAAGCAGTGCCGCC 60.986 61.111 12.58 13.63 0.00 6.13
1091 1113 2.256461 CAAAGGAAGCAGTGCCGC 59.744 61.111 12.58 3.63 0.00 6.53
1092 1114 2.256461 GCAAAGGAAGCAGTGCCG 59.744 61.111 12.58 0.00 0.00 5.69
1093 1115 1.006922 GTGCAAAGGAAGCAGTGCC 60.007 57.895 12.58 0.00 43.63 5.01
1094 1116 1.006922 GGTGCAAAGGAAGCAGTGC 60.007 57.895 7.13 7.13 43.63 4.40
1095 1117 0.746063 TTGGTGCAAAGGAAGCAGTG 59.254 50.000 0.00 0.00 43.63 3.66
1335 2200 0.034896 ATGTGGCGAGGACGAACTTT 59.965 50.000 0.00 0.00 42.66 2.66
1423 2294 1.226974 CGCTACCCATGGTCGTCTG 60.227 63.158 11.73 0.00 37.09 3.51
1578 2452 2.027625 GAGGAACTGGACGTTGCCG 61.028 63.158 0.00 0.00 44.16 5.69
1686 2569 1.075151 GGAGACGAGGAATCCCCCT 60.075 63.158 0.00 0.00 39.77 4.79
1717 2600 4.666253 TCCCGTCCCGAACTCCGT 62.666 66.667 0.00 0.00 36.31 4.69
1734 2617 3.537206 GACTGCCAGGCTGAACCGT 62.537 63.158 24.37 10.07 46.52 4.83
1869 2752 0.107831 TGAGGAAACCCTGGTTGTCG 59.892 55.000 1.58 0.00 38.47 4.35
1967 2862 1.517832 CCGTCAGTGTCCATCCTCC 59.482 63.158 0.00 0.00 0.00 4.30
2008 2903 0.607489 GCCCCGCTACCGTATCTAGA 60.607 60.000 0.00 0.00 0.00 2.43
2061 2956 2.031012 CTGTTGCAGCCTCCGTCA 59.969 61.111 0.00 0.00 0.00 4.35
2081 2976 1.738099 CCTTGCCTCGAGGACGTTG 60.738 63.158 35.69 17.64 37.20 4.10
2160 3055 1.749063 TCGATGTAGGTGTAGCCAGTG 59.251 52.381 0.00 0.00 40.61 3.66
2166 3061 0.928908 GCGCGTCGATGTAGGTGTAG 60.929 60.000 8.43 0.00 0.00 2.74
2266 3452 1.876156 CAGGAGACAGAACAGGCAAAC 59.124 52.381 0.00 0.00 0.00 2.93
2409 3598 1.260538 TGCCCAGCAGACTCTCGAAT 61.261 55.000 0.00 0.00 33.32 3.34
2472 3661 2.587194 GCGATGAGATGCGGCTGT 60.587 61.111 0.00 0.00 0.00 4.40
2496 4216 1.272490 TCGTTGGAGTCGATGAGCTTT 59.728 47.619 0.00 0.00 32.30 3.51
2693 4413 2.591429 CAACACGCCAGCTCCACA 60.591 61.111 0.00 0.00 0.00 4.17
2910 4630 2.027605 CACTCGGGCGCGATGTAT 59.972 61.111 26.78 9.74 0.00 2.29
3156 4904 1.197430 CCCTCTGCTTGTCCTCCACT 61.197 60.000 0.00 0.00 0.00 4.00
3206 4954 4.740822 GCGGGTTGGGCTCCATGT 62.741 66.667 0.00 0.00 31.53 3.21
3290 5038 2.262915 GACGGTCAGGGAGTGCTG 59.737 66.667 2.62 0.00 0.00 4.41
3291 5039 2.997897 GGACGGTCAGGGAGTGCT 60.998 66.667 10.76 0.00 0.00 4.40
3292 5040 4.436998 CGGACGGTCAGGGAGTGC 62.437 72.222 10.76 0.00 0.00 4.40
3369 5120 3.439857 TCAAAATAGCAAGGCCTCTGT 57.560 42.857 5.23 0.00 0.00 3.41
3372 5123 4.989279 TCAATCAAAATAGCAAGGCCTC 57.011 40.909 5.23 0.00 0.00 4.70
3411 5162 4.616802 CCAACGTTGCAACATCATTTAGAC 59.383 41.667 28.01 0.00 0.00 2.59
3425 5176 5.109903 AGATCAGTAACTATCCAACGTTGC 58.890 41.667 22.93 6.47 0.00 4.17
3426 5177 7.435488 CCTTAGATCAGTAACTATCCAACGTTG 59.565 40.741 21.47 21.47 0.00 4.10
3429 5180 5.921408 GCCTTAGATCAGTAACTATCCAACG 59.079 44.000 0.00 0.00 0.00 4.10
3433 5184 5.046950 CAGGGCCTTAGATCAGTAACTATCC 60.047 48.000 1.32 0.00 0.00 2.59
3438 5189 4.489306 AACAGGGCCTTAGATCAGTAAC 57.511 45.455 1.32 0.00 0.00 2.50
3439 5190 4.288626 ACAAACAGGGCCTTAGATCAGTAA 59.711 41.667 1.32 0.00 0.00 2.24
3440 5191 3.844211 ACAAACAGGGCCTTAGATCAGTA 59.156 43.478 1.32 0.00 0.00 2.74
3441 5192 2.644798 ACAAACAGGGCCTTAGATCAGT 59.355 45.455 1.32 0.00 0.00 3.41
3442 5193 3.356529 ACAAACAGGGCCTTAGATCAG 57.643 47.619 1.32 0.00 0.00 2.90
3443 5194 3.806949 AACAAACAGGGCCTTAGATCA 57.193 42.857 1.32 0.00 0.00 2.92
3444 5195 4.079253 TGAAACAAACAGGGCCTTAGATC 58.921 43.478 1.32 0.00 0.00 2.75
3445 5196 4.112634 TGAAACAAACAGGGCCTTAGAT 57.887 40.909 1.32 0.00 0.00 1.98
3446 5197 3.586470 TGAAACAAACAGGGCCTTAGA 57.414 42.857 1.32 0.00 0.00 2.10
3487 5238 0.629596 TAGGGGTGACGGATGAGACT 59.370 55.000 0.00 0.00 0.00 3.24
3488 5239 1.705873 ATAGGGGTGACGGATGAGAC 58.294 55.000 0.00 0.00 0.00 3.36
3489 5240 2.434336 CAAATAGGGGTGACGGATGAGA 59.566 50.000 0.00 0.00 0.00 3.27
3490 5241 2.838736 CAAATAGGGGTGACGGATGAG 58.161 52.381 0.00 0.00 0.00 2.90
3491 5242 1.134220 GCAAATAGGGGTGACGGATGA 60.134 52.381 0.00 0.00 0.00 2.92
3492 5243 1.308998 GCAAATAGGGGTGACGGATG 58.691 55.000 0.00 0.00 0.00 3.51
3493 5244 0.916086 TGCAAATAGGGGTGACGGAT 59.084 50.000 0.00 0.00 0.00 4.18
3585 5338 6.493458 TGAAATCTCAGGGGGTTTTCTAAAAG 59.507 38.462 0.00 0.00 0.00 2.27
3873 5629 1.069500 CGGTGCGAAAGAAAAACGGAT 60.069 47.619 0.00 0.00 0.00 4.18
3917 5673 7.432869 CCACTCAATCTGGTTTTAATGTGAAA 58.567 34.615 0.00 0.00 0.00 2.69
3918 5674 6.015519 CCCACTCAATCTGGTTTTAATGTGAA 60.016 38.462 0.00 0.00 0.00 3.18
3919 5675 5.476599 CCCACTCAATCTGGTTTTAATGTGA 59.523 40.000 0.00 0.00 0.00 3.58
4047 5805 3.023832 TCTCTCTCTCACACACACACAA 58.976 45.455 0.00 0.00 0.00 3.33
4118 5880 1.227321 GTGTTTCCGACGGTGGTCA 60.227 57.895 14.79 6.74 43.61 4.02
4321 6084 9.260190 GTGCAACATGGACTTATAAGTCTCTGC 62.260 44.444 33.70 30.20 45.44 4.26
4324 6087 5.294552 GGTGCAACATGGACTTATAAGTCTC 59.705 44.000 33.70 26.07 46.77 3.36
4325 6088 5.186198 GGTGCAACATGGACTTATAAGTCT 58.814 41.667 33.70 19.53 46.77 3.24
4374 6137 2.202932 CCTCCAATCGCCCGACAG 60.203 66.667 0.00 0.00 0.00 3.51
4404 6167 1.289800 GGTTCGTTCTGCCTCGGTTC 61.290 60.000 0.00 0.00 0.00 3.62
4413 6176 2.809601 CCGCCTCGGTTCGTTCTG 60.810 66.667 0.00 0.00 42.73 3.02
4541 6339 2.278857 CCTCTCGGTCCAATCGCG 60.279 66.667 0.00 0.00 0.00 5.87
4598 6396 1.123928 CTTATCCTGAGCCGGACCTT 58.876 55.000 5.05 0.00 35.52 3.50
4619 6417 2.023015 TCTCAGGGAGGAGCTTATTGGA 60.023 50.000 0.00 0.00 34.84 3.53
4635 6433 7.786030 TGGGACTTATCAAATAAGACTCTCAG 58.214 38.462 12.43 0.00 43.85 3.35


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

AutoCloner maintained by Alex Coulton.