Multiple sequence alignment - TraesCS1D01G223700

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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 TraesCS1D01G223700 chr1D 100.000 5233 0 0 1 5233 311679851 311685083 0.000000e+00 9664.0
1 TraesCS1D01G223700 chr1D 97.561 41 1 0 4630 4670 400168749 400168709 2.610000e-08 71.3
2 TraesCS1D01G223700 chr1B 93.049 2604 131 23 2072 4656 421418746 421421318 0.000000e+00 3760.0
3 TraesCS1D01G223700 chr1B 93.130 1412 69 5 610 2000 421417344 421418748 0.000000e+00 2045.0
4 TraesCS1D01G223700 chr1B 93.391 575 32 5 1 572 49637400 49636829 0.000000e+00 846.0
5 TraesCS1D01G223700 chr1B 94.203 552 30 2 4683 5233 421421386 421421936 0.000000e+00 841.0
6 TraesCS1D01G223700 chr1B 92.657 572 37 4 1 571 488413362 488412795 0.000000e+00 819.0
7 TraesCS1D01G223700 chr1B 90.368 353 27 5 4284 4633 421426247 421426595 1.720000e-124 457.0
8 TraesCS1D01G223700 chr1B 91.304 184 16 0 4779 4962 421498640 421498823 8.700000e-63 252.0
9 TraesCS1D01G223700 chr1B 90.217 184 18 0 4779 4962 421458485 421458668 1.880000e-59 241.0
10 TraesCS1D01G223700 chr1B 88.293 205 14 4 4787 4985 421426677 421426877 2.440000e-58 237.0
11 TraesCS1D01G223700 chr1B 94.203 69 4 0 4670 4738 421458414 421458482 7.170000e-19 106.0
12 TraesCS1D01G223700 chr1B 92.754 69 5 0 4670 4738 421498569 421498637 3.330000e-17 100.0
13 TraesCS1D01G223700 chr1B 100.000 31 0 0 4742 4772 421458506 421458536 2.040000e-04 58.4
14 TraesCS1D01G223700 chr1B 100.000 31 0 0 4742 4772 421498661 421498691 2.040000e-04 58.4
15 TraesCS1D01G223700 chr1A 92.776 2104 103 25 575 2647 391669627 391671712 0.000000e+00 2998.0
16 TraesCS1D01G223700 chr1A 92.254 2014 110 20 2626 4633 391672909 391674882 0.000000e+00 2813.0
17 TraesCS1D01G223700 chr1A 91.525 354 23 6 4284 4633 391679924 391680274 1.020000e-131 481.0
18 TraesCS1D01G223700 chr1A 91.525 354 23 6 4284 4633 391765027 391765377 1.020000e-131 481.0
19 TraesCS1D01G223700 chr1A 91.243 354 24 6 4284 4633 391795490 391795840 4.740000e-130 475.0
20 TraesCS1D01G223700 chr1A 87.436 390 45 3 4848 5233 391675161 391675550 3.720000e-121 446.0
21 TraesCS1D01G223700 chr1A 88.398 181 13 3 4670 4849 391674886 391675059 1.480000e-50 211.0
22 TraesCS1D01G223700 chr1A 95.652 69 3 0 4670 4738 391680278 391680346 1.540000e-20 111.0
23 TraesCS1D01G223700 chr1A 95.652 69 3 0 4670 4738 391765381 391765449 1.540000e-20 111.0
24 TraesCS1D01G223700 chr1A 94.203 69 4 0 4670 4738 391795844 391795912 7.170000e-19 106.0
25 TraesCS1D01G223700 chr1A 93.478 46 3 0 5188 5233 391682106 391682151 9.400000e-08 69.4
26 TraesCS1D01G223700 chr1A 93.478 46 3 0 5188 5233 391706393 391706438 9.400000e-08 69.4
27 TraesCS1D01G223700 chr1A 93.478 46 3 0 5188 5233 391767209 391767254 9.400000e-08 69.4
28 TraesCS1D01G223700 chr1A 93.478 46 3 0 5188 5233 391799408 391799453 9.400000e-08 69.4
29 TraesCS1D01G223700 chr1A 97.368 38 0 1 4735 4772 391704651 391704687 4.370000e-06 63.9
30 TraesCS1D01G223700 chr1A 100.000 31 0 0 4742 4772 391680370 391680400 2.040000e-04 58.4
31 TraesCS1D01G223700 chr1A 100.000 31 0 0 4742 4772 391765473 391765503 2.040000e-04 58.4
32 TraesCS1D01G223700 chr1A 100.000 31 0 0 4742 4772 391795936 391795966 2.040000e-04 58.4
33 TraesCS1D01G223700 chr4A 94.251 574 26 4 1 572 613573494 613572926 0.000000e+00 870.0
34 TraesCS1D01G223700 chr4A 93.333 45 3 0 4629 4673 656850236 656850192 3.380000e-07 67.6
35 TraesCS1D01G223700 chr5D 94.066 573 31 3 1 572 412269888 412270458 0.000000e+00 867.0
36 TraesCS1D01G223700 chr5B 93.380 574 33 4 1 572 14938359 14937789 0.000000e+00 845.0
37 TraesCS1D01G223700 chr4B 93.368 573 34 3 1 571 5775532 5774962 0.000000e+00 845.0
38 TraesCS1D01G223700 chr2A 93.031 574 36 3 1 572 441135925 441135354 0.000000e+00 835.0
39 TraesCS1D01G223700 chr7D 93.182 572 30 5 1 572 19569246 19568684 0.000000e+00 832.0
40 TraesCS1D01G223700 chr5A 92.696 575 37 4 1 572 569120362 569120934 0.000000e+00 824.0
41 TraesCS1D01G223700 chrUn 91.243 354 24 6 4284 4633 422087639 422087289 4.740000e-130 475.0
42 TraesCS1D01G223700 chrUn 96.000 50 2 0 4670 4719 422087285 422087236 1.210000e-11 82.4
43 TraesCS1D01G223700 chrUn 97.561 41 1 0 4631 4671 100784091 100784051 2.610000e-08 71.3
44 TraesCS1D01G223700 chrUn 95.238 42 2 0 4629 4670 41274934 41274975 3.380000e-07 67.6
45 TraesCS1D01G223700 chrUn 93.182 44 2 1 4735 4778 375644722 375644680 4.370000e-06 63.9
46 TraesCS1D01G223700 chr2D 94.545 55 3 0 1049 1103 480459831 480459777 9.340000e-13 86.1
47 TraesCS1D01G223700 chr2D 93.333 45 3 0 4629 4673 472025630 472025586 3.380000e-07 67.6
48 TraesCS1D01G223700 chr7A 100.000 40 0 0 4631 4670 584040667 584040706 2.020000e-09 75.0
49 TraesCS1D01G223700 chr3D 97.561 41 1 0 4630 4670 159576481 159576521 2.610000e-08 71.3
50 TraesCS1D01G223700 chr3A 97.561 41 1 0 4630 4670 595437438 595437478 2.610000e-08 71.3


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 TraesCS1D01G223700 chr1D 311679851 311685083 5232 False 9664.000000 9664 100.000000 1 5233 1 chr1D.!!$F1 5232
1 TraesCS1D01G223700 chr1B 421417344 421421936 4592 False 2215.333333 3760 93.460667 610 5233 3 chr1B.!!$F1 4623
2 TraesCS1D01G223700 chr1B 49636829 49637400 571 True 846.000000 846 93.391000 1 572 1 chr1B.!!$R1 571
3 TraesCS1D01G223700 chr1B 488412795 488413362 567 True 819.000000 819 92.657000 1 571 1 chr1B.!!$R2 570
4 TraesCS1D01G223700 chr1B 421426247 421426877 630 False 347.000000 457 89.330500 4284 4985 2 chr1B.!!$F2 701
5 TraesCS1D01G223700 chr1A 391669627 391675550 5923 False 1617.000000 2998 90.216000 575 5233 4 chr1A.!!$F1 4658
6 TraesCS1D01G223700 chr4A 613572926 613573494 568 True 870.000000 870 94.251000 1 572 1 chr4A.!!$R1 571
7 TraesCS1D01G223700 chr5D 412269888 412270458 570 False 867.000000 867 94.066000 1 572 1 chr5D.!!$F1 571
8 TraesCS1D01G223700 chr5B 14937789 14938359 570 True 845.000000 845 93.380000 1 572 1 chr5B.!!$R1 571
9 TraesCS1D01G223700 chr4B 5774962 5775532 570 True 845.000000 845 93.368000 1 571 1 chr4B.!!$R1 570
10 TraesCS1D01G223700 chr2A 441135354 441135925 571 True 835.000000 835 93.031000 1 572 1 chr2A.!!$R1 571
11 TraesCS1D01G223700 chr7D 19568684 19569246 562 True 832.000000 832 93.182000 1 572 1 chr7D.!!$R1 571
12 TraesCS1D01G223700 chr5A 569120362 569120934 572 False 824.000000 824 92.696000 1 572 1 chr5A.!!$F1 571

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
446 448 0.109919 TCGATCCGCCATTATCGACG 60.110 55.0 3.49 0.00 46.52 5.12 F
723 731 0.319405 CGTTACCAGAAAGACCCGGT 59.681 55.0 0.00 0.00 35.46 5.28 F
1091 1110 0.457337 GGCGACGACCTCAACGTAAT 60.457 55.0 0.00 0.00 43.97 1.89 F
2091 2126 0.391130 AATACACATGTCCGCAGCGT 60.391 50.0 15.05 0.00 0.00 5.07 F
3413 4685 0.851469 AGGCATGCCAGAATCATCCT 59.149 50.0 37.18 10.88 38.92 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1286 1305 0.534203 GGAATCCTATTTCCGCGGCA 60.534 55.000 23.51 6.92 36.12 5.69 R
2035 2070 2.228822 CACCAAAATAGCCTGACACACC 59.771 50.000 0.00 0.00 0.00 4.16 R
2807 4072 1.419762 TGTGTGGCCAGCTCTAAAAGA 59.580 47.619 5.11 0.00 0.00 2.52 R
3645 4921 1.414550 GATGGGGAGCCAGAGTAAGAC 59.585 57.143 0.00 0.00 0.00 3.01 R
4527 5809 0.040204 CTCCCCATTTCCTGCCTTGT 59.960 55.000 0.00 0.00 0.00 3.16 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
78 79 3.390521 AGGCCATCTTCGCGGTGA 61.391 61.111 6.13 5.21 0.00 4.02
335 336 1.469703 TCATCGTCGCGTTCCTTCTTA 59.530 47.619 5.77 0.00 0.00 2.10
336 337 2.095110 TCATCGTCGCGTTCCTTCTTAA 60.095 45.455 5.77 0.00 0.00 1.85
389 390 1.078143 GAGCTTGGTGGGCGATCTT 60.078 57.895 0.00 0.00 34.52 2.40
446 448 0.109919 TCGATCCGCCATTATCGACG 60.110 55.000 3.49 0.00 46.52 5.12
450 452 2.867287 TCCGCCATTATCGACGTTTA 57.133 45.000 0.00 0.00 0.00 2.01
527 531 4.212004 CCAGCACCTATCGTTGAATGTATG 59.788 45.833 0.00 0.00 0.00 2.39
547 551 3.784178 TGGGATGGTTGCTTTGGAATAA 58.216 40.909 0.00 0.00 0.00 1.40
597 601 1.541310 CGTGGTAGGTTGGAGCCTCA 61.541 60.000 0.00 0.00 39.94 3.86
723 731 0.319405 CGTTACCAGAAAGACCCGGT 59.681 55.000 0.00 0.00 35.46 5.28
977 996 4.870012 GGGTTCGGATTCGGGGCC 62.870 72.222 0.00 0.00 36.95 5.80
1011 1030 1.619669 GGGGGAGATGGACCAGGTT 60.620 63.158 0.00 0.00 0.00 3.50
1090 1109 1.081242 GGCGACGACCTCAACGTAA 60.081 57.895 0.00 0.00 43.97 3.18
1091 1110 0.457337 GGCGACGACCTCAACGTAAT 60.457 55.000 0.00 0.00 43.97 1.89
1113 1132 2.757099 CCAATCCCTGGCCTGCAC 60.757 66.667 3.32 0.00 38.76 4.57
1133 1152 2.028385 ACTGCGTTTACACTAGGAAGGG 60.028 50.000 0.00 0.00 0.00 3.95
1453 1473 4.579869 ACACGGAAAGATGTGATTTAGCT 58.420 39.130 0.00 0.00 39.38 3.32
1463 1483 6.240894 AGATGTGATTTAGCTTGAACCTTGA 58.759 36.000 0.00 0.00 0.00 3.02
1590 1614 7.337184 TGCGATTTAATGTTTCCAGTACCAATA 59.663 33.333 0.00 0.00 0.00 1.90
1613 1637 8.885693 ATATAGACAGGATAGTATGTGCAAGA 57.114 34.615 0.00 0.00 0.00 3.02
1614 1638 5.269505 AGACAGGATAGTATGTGCAAGAC 57.730 43.478 0.00 0.00 0.00 3.01
1641 1674 7.106439 TGAATGTCTCTCTCCACTTTATCTC 57.894 40.000 0.00 0.00 0.00 2.75
1856 1891 2.265367 TGTTTCCAGCTCATCCTACCA 58.735 47.619 0.00 0.00 0.00 3.25
1860 1895 0.755686 CCAGCTCATCCTACCAGGTC 59.244 60.000 0.00 0.00 36.53 3.85
1996 2031 9.778741 TTGGAATCTAAGCTAATGAATCGTTAT 57.221 29.630 0.00 0.00 0.00 1.89
2022 2057 5.895636 TGAGTTTATCTACCCGTACGAAA 57.104 39.130 18.76 4.30 0.00 3.46
2029 2064 2.166254 TCTACCCGTACGAAAATCACCC 59.834 50.000 18.76 0.00 0.00 4.61
2035 2070 2.671396 CGTACGAAAATCACCCCTGAAG 59.329 50.000 10.44 0.00 0.00 3.02
2057 2092 2.884639 GTGTGTCAGGCTATTTTGGTGT 59.115 45.455 0.00 0.00 0.00 4.16
2058 2093 2.884012 TGTGTCAGGCTATTTTGGTGTG 59.116 45.455 0.00 0.00 0.00 3.82
2063 2098 1.203050 AGGCTATTTTGGTGTGGTGCT 60.203 47.619 0.00 0.00 0.00 4.40
2091 2126 0.391130 AATACACATGTCCGCAGCGT 60.391 50.000 15.05 0.00 0.00 5.07
2267 2302 8.731275 TGATGATTTACGTTGTATTTCCAGAT 57.269 30.769 0.00 0.00 0.00 2.90
2283 2318 6.420913 TTCCAGATCCTGCTTATAGGTAAC 57.579 41.667 0.00 0.00 38.99 2.50
2301 2336 4.757149 GGTAACCCAAAGCTCTATATGCAG 59.243 45.833 0.00 0.00 0.00 4.41
2421 2457 9.277783 AGGTATGCAATGTCTATTCTGTATTTC 57.722 33.333 0.00 0.00 0.00 2.17
2440 2476 9.688091 TGTATTTCCTAATGGCAAACTATGTTA 57.312 29.630 0.00 0.00 0.00 2.41
2623 2668 8.558973 AGTATGGATAGAAAATAGCAATGCTC 57.441 34.615 12.53 0.00 40.44 4.26
2655 3920 9.892130 ACTTCATAACTAAATGGGACTTCTTAG 57.108 33.333 0.00 0.00 0.00 2.18
2690 3955 6.900189 TGTATGTGGTTGTGGTTTATTTACG 58.100 36.000 0.00 0.00 0.00 3.18
2714 3979 7.602644 ACGTTTCTGATATTTCTGAAAGCTGTA 59.397 33.333 15.17 0.00 45.05 2.74
2715 3980 7.900352 CGTTTCTGATATTTCTGAAAGCTGTAC 59.100 37.037 15.17 5.99 45.05 2.90
2717 3982 5.520288 TCTGATATTTCTGAAAGCTGTACGC 59.480 40.000 8.95 2.08 39.57 4.42
2821 4086 9.326413 TGTATATTTTAGTCTTTTAGAGCTGGC 57.674 33.333 0.00 0.00 0.00 4.85
2882 4147 4.321527 CCCATCTCTTTTTCCTCACAAAGC 60.322 45.833 0.00 0.00 31.15 3.51
3029 4298 7.264947 ACAGTTATTTTGACAAAACTTGGAGG 58.735 34.615 15.36 5.53 32.37 4.30
3055 4324 6.811665 GGCTAAAAGGACGCTTATTTTGAAAT 59.188 34.615 0.00 0.00 0.00 2.17
3056 4325 7.201435 GGCTAAAAGGACGCTTATTTTGAAATG 60.201 37.037 0.00 0.00 0.00 2.32
3084 4354 7.182930 AGGGAGTAAGAGAAAACCAAGACATAT 59.817 37.037 0.00 0.00 0.00 1.78
3128 4398 2.866156 CGTACCAGTTATGCACCATCTG 59.134 50.000 0.00 0.00 0.00 2.90
3138 4409 2.392662 TGCACCATCTGTTTTTGGGAA 58.607 42.857 0.00 0.00 37.32 3.97
3142 4413 4.821260 GCACCATCTGTTTTTGGGAAAAAT 59.179 37.500 0.00 0.00 41.85 1.82
3210 4481 4.448732 GCAGCATTTGTTAGTTTTTGGAGG 59.551 41.667 0.00 0.00 0.00 4.30
3226 4497 4.447138 TGGAGGTGTACAAGGTTTTGAT 57.553 40.909 0.00 0.00 37.73 2.57
3227 4498 4.798882 TGGAGGTGTACAAGGTTTTGATT 58.201 39.130 0.00 0.00 37.73 2.57
3318 4590 5.418840 CAGTTAATGCTGGTTCCCTTATGTT 59.581 40.000 0.00 0.00 33.11 2.71
3413 4685 0.851469 AGGCATGCCAGAATCATCCT 59.149 50.000 37.18 10.88 38.92 3.24
3414 4686 2.060275 AGGCATGCCAGAATCATCCTA 58.940 47.619 37.18 0.00 38.92 2.94
3415 4687 2.157738 GGCATGCCAGAATCATCCTAC 58.842 52.381 32.08 0.00 35.81 3.18
3418 4690 3.004106 GCATGCCAGAATCATCCTACAAC 59.996 47.826 6.36 0.00 0.00 3.32
3419 4691 4.458397 CATGCCAGAATCATCCTACAACT 58.542 43.478 0.00 0.00 0.00 3.16
3446 4720 4.102524 TGATGAGTTTATGCCCTTATCGGT 59.897 41.667 0.00 0.00 0.00 4.69
3452 4726 1.513858 ATGCCCTTATCGGTAACCCA 58.486 50.000 0.00 0.00 0.00 4.51
3453 4727 1.513858 TGCCCTTATCGGTAACCCAT 58.486 50.000 0.00 0.00 0.00 4.00
3549 4824 6.723298 AAATGACAGTTTTGGTAACCATGA 57.277 33.333 0.00 0.00 31.53 3.07
3550 4825 6.723298 AATGACAGTTTTGGTAACCATGAA 57.277 33.333 0.00 0.00 31.53 2.57
3551 4826 6.916360 ATGACAGTTTTGGTAACCATGAAT 57.084 33.333 0.00 0.00 31.53 2.57
3552 4827 6.723298 TGACAGTTTTGGTAACCATGAATT 57.277 33.333 0.00 0.00 31.53 2.17
3553 4828 7.825331 TGACAGTTTTGGTAACCATGAATTA 57.175 32.000 0.00 0.00 31.53 1.40
3604 4879 1.442526 GGTCCATCTGCATTGCGAGG 61.443 60.000 3.84 6.21 0.00 4.63
3633 4909 5.163509 CGTTCATGAGAGATTACCTTGAGGA 60.164 44.000 3.59 0.00 38.94 3.71
3635 4911 7.278875 GTTCATGAGAGATTACCTTGAGGATT 58.721 38.462 3.59 0.00 38.94 3.01
3639 4915 4.775236 AGAGATTACCTTGAGGATTGTGC 58.225 43.478 3.59 0.00 38.94 4.57
3667 4943 2.518407 TCTTACTCTGGCTCCCCATCTA 59.482 50.000 0.00 0.00 41.21 1.98
3672 4948 3.906846 ACTCTGGCTCCCCATCTATTTAG 59.093 47.826 0.00 0.00 41.21 1.85
3710 4988 4.881850 TGTTTTGTTCCTTTCTCTCTGTCC 59.118 41.667 0.00 0.00 0.00 4.02
3791 5070 5.612725 TGTTGAAAAGGCTGAAATTTCCT 57.387 34.783 15.48 3.43 33.23 3.36
3803 5082 7.121315 AGGCTGAAATTTCCTATGTTTACTGAC 59.879 37.037 15.48 0.00 0.00 3.51
3812 5091 7.979444 TCCTATGTTTACTGACCTTTTTCTG 57.021 36.000 0.00 0.00 0.00 3.02
3814 5093 6.206634 CCTATGTTTACTGACCTTTTTCTGCA 59.793 38.462 0.00 0.00 0.00 4.41
3819 5098 7.117092 TGTTTACTGACCTTTTTCTGCAAAAAC 59.883 33.333 6.37 0.00 36.70 2.43
4326 5605 2.635915 TCGGATCGGCCTATTAACCAAT 59.364 45.455 0.00 0.00 0.00 3.16
4334 5613 4.156922 CGGCCTATTAACCAATTGTGTTGA 59.843 41.667 17.44 12.20 0.00 3.18
4392 5672 2.798283 CAATCTGTGCTTGTTTTGCTGG 59.202 45.455 0.00 0.00 0.00 4.85
4416 5696 1.065126 CCTGATTCTTCCACCAGACCC 60.065 57.143 0.00 0.00 0.00 4.46
4463 5743 6.322491 GCCATGTTGTATCCAGTTTTTAGTC 58.678 40.000 0.00 0.00 0.00 2.59
4527 5809 2.655090 TCAAGTTTGGATGCAGGTGA 57.345 45.000 0.00 0.00 0.00 4.02
4531 5813 2.233271 AGTTTGGATGCAGGTGACAAG 58.767 47.619 0.00 0.00 0.00 3.16
4584 5867 5.353956 GGGTGTGATTTTTGCTTGTTTTCTT 59.646 36.000 0.00 0.00 0.00 2.52
4616 5899 0.108424 ATCGACCTCAAGCAGTGCTC 60.108 55.000 20.03 3.71 38.25 4.26
4636 5924 3.942748 CTCGTGCTTTAGTCTCTACTCCT 59.057 47.826 0.00 0.00 37.15 3.69
4644 5932 1.917568 AGTCTCTACTCCTTCCGTCCT 59.082 52.381 0.00 0.00 0.00 3.85
4658 5946 8.048534 TCCTTCCGTCCTATAATATAAGAACG 57.951 38.462 0.00 0.00 0.00 3.95
4659 5947 7.667219 TCCTTCCGTCCTATAATATAAGAACGT 59.333 37.037 0.00 0.00 0.00 3.99
4660 5948 8.302438 CCTTCCGTCCTATAATATAAGAACGTT 58.698 37.037 0.00 0.00 0.00 3.99
4677 6003 5.288472 AGAACGTTTTTGACACTTTGATTGC 59.712 36.000 0.46 0.00 0.00 3.56
4778 6115 7.602517 TTGTTAATTCAAAGTTGGTTGTTGG 57.397 32.000 0.00 0.00 0.00 3.77
4779 6116 6.702329 TGTTAATTCAAAGTTGGTTGTTGGT 58.298 32.000 0.00 0.00 0.00 3.67
4780 6117 6.814146 TGTTAATTCAAAGTTGGTTGTTGGTC 59.186 34.615 0.00 0.00 0.00 4.02
4781 6118 3.495670 TTCAAAGTTGGTTGTTGGTCG 57.504 42.857 0.00 0.00 0.00 4.79
4782 6119 2.438411 TCAAAGTTGGTTGTTGGTCGT 58.562 42.857 0.00 0.00 0.00 4.34
4783 6120 3.607741 TCAAAGTTGGTTGTTGGTCGTA 58.392 40.909 0.00 0.00 0.00 3.43
4887 6328 8.036575 ACAAACAAATGCATATTACAGCAGATT 58.963 29.630 0.00 0.00 44.94 2.40
4905 6346 6.072728 AGCAGATTATCAACGCAAAACACTAA 60.073 34.615 0.00 0.00 0.00 2.24
4918 6359 5.915196 GCAAAACACTAAGAACTGCCTAAAG 59.085 40.000 0.00 0.00 0.00 1.85
4921 6362 4.319177 ACACTAAGAACTGCCTAAAGCTG 58.681 43.478 0.00 0.00 44.23 4.24
5005 6453 9.622004 CATATTGGATATTTGCAAAGCTTAGAG 57.378 33.333 18.19 0.00 36.71 2.43
5030 6479 2.047274 CCCTCTCTTTTCGCCGCA 60.047 61.111 0.00 0.00 0.00 5.69
5044 6493 2.735772 CCGCATCCTGCTACCCACT 61.736 63.158 0.00 0.00 42.25 4.00
5060 6509 2.296471 CCCACTCATCACCTATACCGAC 59.704 54.545 0.00 0.00 0.00 4.79
5074 6523 2.543802 CCGACGCTAGATCGAGGCA 61.544 63.158 16.04 0.00 42.25 4.75
5075 6524 1.369448 CGACGCTAGATCGAGGCAC 60.369 63.158 10.44 0.00 42.25 5.01
5093 6545 1.153549 CCCGCTTCTCTTTCTCCCG 60.154 63.158 0.00 0.00 0.00 5.14
5101 6553 4.038642 GCTTCTCTTTCTCCCGAGTGATAT 59.961 45.833 0.00 0.00 0.00 1.63
5106 6558 4.956700 TCTTTCTCCCGAGTGATATGAACT 59.043 41.667 0.00 0.00 0.00 3.01
5138 6590 2.902484 CGAGCGCAAACAAACAAGATAC 59.098 45.455 11.47 0.00 0.00 2.24
5156 6608 5.094387 AGATACTCAAGAGAACAGGGGAAA 58.906 41.667 3.73 0.00 0.00 3.13
5190 6642 2.241176 TGGGTTTCAGATAGCCCGAATT 59.759 45.455 6.64 0.00 43.89 2.17
5198 6650 3.675225 CAGATAGCCCGAATTATGTCACG 59.325 47.826 0.00 0.00 0.00 4.35
5199 6651 2.519377 TAGCCCGAATTATGTCACGG 57.481 50.000 0.00 0.00 44.16 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 1.004560 CCACGCTGTCTCACCACAT 60.005 57.895 0.00 0.00 0.00 3.21
335 336 2.510613 CCGGTACCAATCAACACCTTT 58.489 47.619 13.54 0.00 0.00 3.11
336 337 1.884928 GCCGGTACCAATCAACACCTT 60.885 52.381 13.54 0.00 0.00 3.50
527 531 4.817318 TTTATTCCAAAGCAACCATCCC 57.183 40.909 0.00 0.00 0.00 3.85
552 556 2.661718 TGAAAAAGGTTTTCCCTCGCT 58.338 42.857 10.17 0.00 45.47 4.93
554 558 3.365969 CGGATGAAAAAGGTTTTCCCTCG 60.366 47.826 10.17 7.60 45.47 4.63
559 563 2.287970 ACGCCGGATGAAAAAGGTTTTC 60.288 45.455 5.05 6.53 0.00 2.29
563 567 1.241315 CCACGCCGGATGAAAAAGGT 61.241 55.000 5.05 0.00 36.56 3.50
572 576 2.582436 CAACCTACCACGCCGGAT 59.418 61.111 5.05 0.00 38.63 4.18
573 577 3.697747 CCAACCTACCACGCCGGA 61.698 66.667 5.05 0.00 38.63 5.14
597 601 2.163815 CGAAACTGACGTGGTATCCTCT 59.836 50.000 0.00 0.00 0.00 3.69
723 731 2.852075 GTGGGGGTGGTCTGTGGA 60.852 66.667 0.00 0.00 0.00 4.02
977 996 1.456705 CCCTCCTCTCCTCTTCCCG 60.457 68.421 0.00 0.00 0.00 5.14
1011 1030 0.768221 AGCTCCCCACCTTGTTCAGA 60.768 55.000 0.00 0.00 0.00 3.27
1113 1132 2.618053 CCCTTCCTAGTGTAAACGCAG 58.382 52.381 0.00 0.00 0.00 5.18
1151 1170 1.201825 CGATTTAGCGGCTAAGCGC 59.798 57.895 23.92 16.21 43.00 5.92
1155 1174 2.626266 TCATCCTCGATTTAGCGGCTAA 59.374 45.455 18.04 18.04 0.00 3.09
1286 1305 0.534203 GGAATCCTATTTCCGCGGCA 60.534 55.000 23.51 6.92 36.12 5.69
1312 1331 3.077359 CAGCTGAAAACCCTCGAAAGAT 58.923 45.455 8.42 0.00 40.84 2.40
1453 1473 0.555769 ACCCTGCCTTCAAGGTTCAA 59.444 50.000 5.03 0.00 33.28 2.69
1482 1505 2.088674 ATCGACTACCCATGCGAGGC 62.089 60.000 0.00 0.00 36.12 4.70
1590 1614 6.015010 GGTCTTGCACATACTATCCTGTCTAT 60.015 42.308 0.00 0.00 0.00 1.98
1613 1637 3.515562 AGTGGAGAGAGACATTCAAGGT 58.484 45.455 0.00 0.00 0.00 3.50
1614 1638 4.550076 AAGTGGAGAGAGACATTCAAGG 57.450 45.455 0.00 0.00 0.00 3.61
1641 1674 6.238759 GCTAAACATCTTTAGTATGGCCCAAG 60.239 42.308 0.00 0.00 40.73 3.61
1712 1745 6.332635 AGGAAACCATGGACATCCTTCATATA 59.667 38.462 21.47 0.00 37.20 0.86
1716 1751 2.649312 AGGAAACCATGGACATCCTTCA 59.351 45.455 21.47 0.00 37.20 3.02
1831 1866 5.529060 GGTAGGATGAGCTGGAAACAATAAG 59.471 44.000 0.00 0.00 42.06 1.73
1856 1891 5.001725 TCAGAATGTGAGGTTACCTGACCT 61.002 45.833 17.81 5.75 45.16 3.85
1860 1895 4.878397 GGAATCAGAATGTGAGGTTACCTG 59.122 45.833 9.39 0.00 39.07 4.00
1996 2031 7.566760 TCGTACGGGTAGATAAACTCATTTA 57.433 36.000 16.52 0.00 34.78 1.40
2009 2044 2.543641 GGGTGATTTTCGTACGGGTAG 58.456 52.381 16.52 0.00 0.00 3.18
2014 2049 2.373540 TCAGGGGTGATTTTCGTACG 57.626 50.000 9.53 9.53 0.00 3.67
2035 2070 2.228822 CACCAAAATAGCCTGACACACC 59.771 50.000 0.00 0.00 0.00 4.16
2057 2092 3.073209 TGTGTATTTGGTAGGAAGCACCA 59.927 43.478 2.96 0.00 44.35 4.17
2058 2093 3.681593 TGTGTATTTGGTAGGAAGCACC 58.318 45.455 0.00 0.00 39.35 5.01
2063 2098 4.509616 CGGACATGTGTATTTGGTAGGAA 58.490 43.478 1.15 0.00 0.00 3.36
2117 2152 4.872691 CCTAACAGCAGAACATAACAGAGG 59.127 45.833 0.00 0.00 0.00 3.69
2267 2302 4.384868 GCTTTGGGTTACCTATAAGCAGGA 60.385 45.833 21.28 0.00 41.60 3.86
2283 2318 4.454678 TGAACTGCATATAGAGCTTTGGG 58.545 43.478 0.00 0.00 0.00 4.12
2325 2361 5.178797 AGACCGACTGGATTCAAAATGTAG 58.821 41.667 0.00 0.00 39.21 2.74
2421 2457 7.744087 TGCTATAACATAGTTTGCCATTAGG 57.256 36.000 0.00 0.00 38.23 2.69
2623 2668 7.548075 AGTCCCATTTAGTTATGAAGTGTAACG 59.452 37.037 0.00 0.00 45.86 3.18
2655 3920 6.365789 CCACAACCACATACAAATCACAATTC 59.634 38.462 0.00 0.00 0.00 2.17
2690 3955 7.900352 CGTACAGCTTTCAGAAATATCAGAAAC 59.100 37.037 0.00 0.00 36.50 2.78
2714 3979 5.696724 GGTCATTGCTCAATATTACTAGCGT 59.303 40.000 10.38 2.32 37.80 5.07
2715 3980 5.696270 TGGTCATTGCTCAATATTACTAGCG 59.304 40.000 10.38 0.00 37.80 4.26
2800 4065 5.416013 GTGGCCAGCTCTAAAAGACTAAAAT 59.584 40.000 5.11 0.00 0.00 1.82
2805 4070 1.699634 TGTGGCCAGCTCTAAAAGACT 59.300 47.619 5.11 0.00 0.00 3.24
2806 4071 1.807142 GTGTGGCCAGCTCTAAAAGAC 59.193 52.381 5.11 0.00 0.00 3.01
2807 4072 1.419762 TGTGTGGCCAGCTCTAAAAGA 59.580 47.619 5.11 0.00 0.00 2.52
2808 4073 1.896220 TGTGTGGCCAGCTCTAAAAG 58.104 50.000 5.11 0.00 0.00 2.27
2821 4086 5.067153 TCACCAACACTCTAAATTTGTGTGG 59.933 40.000 12.09 15.30 43.11 4.17
2882 4147 5.416013 GTGGAGGAAAAGGAGAACTTAATGG 59.584 44.000 0.00 0.00 38.85 3.16
2938 4203 6.071984 TCCTACTTGCCCTTAAAAATGTCAA 58.928 36.000 0.00 0.00 0.00 3.18
3029 4298 4.157105 TCAAAATAAGCGTCCTTTTAGCCC 59.843 41.667 0.00 0.00 32.47 5.19
3055 4324 3.593942 TGGTTTTCTCTTACTCCCTCCA 58.406 45.455 0.00 0.00 0.00 3.86
3056 4325 4.286291 TCTTGGTTTTCTCTTACTCCCTCC 59.714 45.833 0.00 0.00 0.00 4.30
3108 4378 3.873910 ACAGATGGTGCATAACTGGTAC 58.126 45.455 13.20 0.00 33.57 3.34
3210 4481 7.927048 AGTTCACTAATCAAAACCTTGTACAC 58.073 34.615 0.00 0.00 33.94 2.90
3226 4497 3.805807 GCAAGGCACCACTAGTTCACTAA 60.806 47.826 0.00 0.00 0.00 2.24
3227 4498 2.289444 GCAAGGCACCACTAGTTCACTA 60.289 50.000 0.00 0.00 0.00 2.74
3273 4544 2.431057 GGGTACTAGGTCACAGGACATG 59.569 54.545 0.00 0.00 46.17 3.21
3284 4555 4.755266 CAGCATTAACTGGGTACTAGGT 57.245 45.455 0.00 0.00 43.06 3.08
3318 4590 8.925338 ACAATTAAACCCACACTTTTGGTTATA 58.075 29.630 0.00 0.00 41.40 0.98
3418 4690 4.686191 AGGGCATAAACTCATCAGAGAG 57.314 45.455 0.00 0.00 44.98 3.20
3419 4691 6.517362 CGATAAGGGCATAAACTCATCAGAGA 60.517 42.308 0.00 0.00 44.98 3.10
3482 4757 5.835280 ACCTGAAGGACTGAAATTGATGTTT 59.165 36.000 2.62 0.00 38.94 2.83
3497 4772 6.127647 GCAATCAAAATATGTCACCTGAAGGA 60.128 38.462 2.62 0.00 38.94 3.36
3498 4773 6.038356 GCAATCAAAATATGTCACCTGAAGG 58.962 40.000 0.00 0.00 42.17 3.46
3499 4774 6.860080 AGCAATCAAAATATGTCACCTGAAG 58.140 36.000 0.00 0.00 0.00 3.02
3500 4775 6.433716 TGAGCAATCAAAATATGTCACCTGAA 59.566 34.615 0.00 0.00 0.00 3.02
3501 4776 5.945191 TGAGCAATCAAAATATGTCACCTGA 59.055 36.000 0.00 0.00 0.00 3.86
3531 4806 8.245195 ACTTAATTCATGGTTACCAAAACTGT 57.755 30.769 8.63 0.00 36.95 3.55
3576 4851 5.380043 CAATGCAGATGGACCCTTAATAGT 58.620 41.667 0.00 0.00 0.00 2.12
3580 4855 2.378038 GCAATGCAGATGGACCCTTAA 58.622 47.619 0.00 0.00 0.00 1.85
3604 4879 3.804873 GGTAATCTCTCATGAACGCCTTC 59.195 47.826 0.00 0.00 0.00 3.46
3633 4909 4.511527 CAGAGTAAGACCATGAGCACAAT 58.488 43.478 0.00 0.00 0.00 2.71
3635 4911 2.234661 CCAGAGTAAGACCATGAGCACA 59.765 50.000 0.00 0.00 0.00 4.57
3639 4915 2.102252 GGAGCCAGAGTAAGACCATGAG 59.898 54.545 0.00 0.00 0.00 2.90
3645 4921 1.414550 GATGGGGAGCCAGAGTAAGAC 59.585 57.143 0.00 0.00 0.00 3.01
3791 5070 7.575414 TTGCAGAAAAAGGTCAGTAAACATA 57.425 32.000 0.00 0.00 0.00 2.29
3803 5082 5.575218 ACGTTAGTGTTTTTGCAGAAAAAGG 59.425 36.000 3.66 3.94 40.83 3.11
3814 5093 4.157105 AGGTCAGCAAACGTTAGTGTTTTT 59.843 37.500 0.00 0.00 39.94 1.94
3819 5098 2.476619 CTCAGGTCAGCAAACGTTAGTG 59.523 50.000 0.00 0.00 0.00 2.74
4326 5605 4.280677 GGATGGGAGTTTTCATCAACACAA 59.719 41.667 0.00 0.00 40.94 3.33
4334 5613 4.598036 AGTCATGGATGGGAGTTTTCAT 57.402 40.909 0.00 0.00 0.00 2.57
4392 5672 2.092753 TCTGGTGGAAGAATCAGGATGC 60.093 50.000 0.00 0.00 34.76 3.91
4416 5696 2.047560 GGTCCGGTCACCCTTTCG 60.048 66.667 0.00 0.00 0.00 3.46
4463 5743 6.094603 CACACCCAAAGATAGAGGAATTCAAG 59.905 42.308 7.93 0.00 0.00 3.02
4527 5809 0.040204 CTCCCCATTTCCTGCCTTGT 59.960 55.000 0.00 0.00 0.00 3.16
4531 5813 1.937191 TTTTCTCCCCATTTCCTGCC 58.063 50.000 0.00 0.00 0.00 4.85
4584 5867 3.074369 TCGATGAAGCCCTCCGCA 61.074 61.111 0.00 0.00 41.38 5.69
4616 5899 4.439016 GGAAGGAGTAGAGACTAAAGCACG 60.439 50.000 0.00 0.00 35.45 5.34
4656 5944 4.743493 AGCAATCAAAGTGTCAAAAACGT 58.257 34.783 0.00 0.00 0.00 3.99
4658 5946 7.862372 TCAGATAGCAATCAAAGTGTCAAAAAC 59.138 33.333 0.00 0.00 34.28 2.43
4659 5947 7.939782 TCAGATAGCAATCAAAGTGTCAAAAA 58.060 30.769 0.00 0.00 34.28 1.94
4660 5948 7.509141 TCAGATAGCAATCAAAGTGTCAAAA 57.491 32.000 0.00 0.00 34.28 2.44
4662 5950 7.391275 TCAATCAGATAGCAATCAAAGTGTCAA 59.609 33.333 0.00 0.00 34.28 3.18
4663 5951 6.880529 TCAATCAGATAGCAATCAAAGTGTCA 59.119 34.615 0.00 0.00 34.28 3.58
4664 5952 7.312657 TCAATCAGATAGCAATCAAAGTGTC 57.687 36.000 0.00 0.00 34.28 3.67
4665 5953 7.681304 GCATCAATCAGATAGCAATCAAAGTGT 60.681 37.037 0.00 0.00 34.43 3.55
4666 5954 6.637254 GCATCAATCAGATAGCAATCAAAGTG 59.363 38.462 0.00 0.00 34.43 3.16
4668 5956 6.971602 AGCATCAATCAGATAGCAATCAAAG 58.028 36.000 0.00 0.00 34.43 2.77
4673 5999 5.068591 TGCAAAGCATCAATCAGATAGCAAT 59.931 36.000 0.00 0.00 34.43 3.56
4677 6003 5.494632 TGTGCAAAGCATCAATCAGATAG 57.505 39.130 0.00 0.00 41.91 2.08
4773 6110 8.298140 CCCAAAATAAAATTACTACGACCAACA 58.702 33.333 0.00 0.00 0.00 3.33
4777 6114 5.967088 CGCCCAAAATAAAATTACTACGACC 59.033 40.000 0.00 0.00 0.00 4.79
4778 6115 5.967088 CCGCCCAAAATAAAATTACTACGAC 59.033 40.000 0.00 0.00 0.00 4.34
4779 6116 5.647225 ACCGCCCAAAATAAAATTACTACGA 59.353 36.000 0.00 0.00 0.00 3.43
4780 6117 5.882553 ACCGCCCAAAATAAAATTACTACG 58.117 37.500 0.00 0.00 0.00 3.51
4781 6118 8.212317 TCTACCGCCCAAAATAAAATTACTAC 57.788 34.615 0.00 0.00 0.00 2.73
4782 6119 8.842280 CATCTACCGCCCAAAATAAAATTACTA 58.158 33.333 0.00 0.00 0.00 1.82
4783 6120 7.558444 TCATCTACCGCCCAAAATAAAATTACT 59.442 33.333 0.00 0.00 0.00 2.24
4881 6322 4.475944 AGTGTTTTGCGTTGATAATCTGC 58.524 39.130 0.00 0.00 0.00 4.26
4887 6328 6.655062 CAGTTCTTAGTGTTTTGCGTTGATA 58.345 36.000 0.00 0.00 0.00 2.15
4905 6346 1.339535 GCTCCAGCTTTAGGCAGTTCT 60.340 52.381 0.00 0.00 44.79 3.01
4918 6359 1.174712 TCCTGTTTGCAAGCTCCAGC 61.175 55.000 14.67 0.00 42.49 4.85
4921 6362 2.888834 TTTTCCTGTTTGCAAGCTCC 57.111 45.000 14.67 0.00 0.00 4.70
5005 6453 1.814793 GAAAAGAGAGGGGAGTGTGC 58.185 55.000 0.00 0.00 0.00 4.57
5030 6479 1.765314 GTGATGAGTGGGTAGCAGGAT 59.235 52.381 0.00 0.00 0.00 3.24
5044 6493 1.977056 AGCGTCGGTATAGGTGATGA 58.023 50.000 0.00 0.00 0.00 2.92
5060 6509 2.336809 GGGTGCCTCGATCTAGCG 59.663 66.667 0.00 0.00 0.00 4.26
5074 6523 1.889530 CGGGAGAAAGAGAAGCGGGT 61.890 60.000 0.00 0.00 0.00 5.28
5075 6524 1.153549 CGGGAGAAAGAGAAGCGGG 60.154 63.158 0.00 0.00 0.00 6.13
5093 6545 6.636447 CGAGTTGATCTCAGTTCATATCACTC 59.364 42.308 5.65 5.65 42.88 3.51
5101 6553 2.414691 CGCTCGAGTTGATCTCAGTTCA 60.415 50.000 15.13 0.00 42.88 3.18
5106 6558 0.243636 TTGCGCTCGAGTTGATCTCA 59.756 50.000 15.13 0.00 42.88 3.27
5138 6590 3.071602 TCTGTTTCCCCTGTTCTCTTGAG 59.928 47.826 0.00 0.00 0.00 3.02
5156 6608 2.711009 TGAAACCCAATCACTCCTCTGT 59.289 45.455 0.00 0.00 0.00 3.41
5190 6642 6.330278 CAAGAGAACTTGTATCCGTGACATA 58.670 40.000 0.00 0.00 45.73 2.29


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

AutoCloner maintained by Alex Coulton.