Multiple sequence alignment - TraesCS2D01G073100

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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 TraesCS2D01G073100 chr2D 100.000 5513 0 0 1 5513 30654980 30660492 0.000000e+00 10181.0
1 TraesCS2D01G073100 chr2D 81.078 835 121 26 3215 4042 630088396 630089200 2.800000e-177 632.0
2 TraesCS2D01G073100 chr2D 86.949 544 63 6 3218 3757 630635299 630634760 6.110000e-169 604.0
3 TraesCS2D01G073100 chr2D 80.120 830 131 23 3218 4042 629728918 629728118 6.150000e-164 588.0
4 TraesCS2D01G073100 chr2D 100.000 83 0 0 906 988 30584287 30584369 2.660000e-33 154.0
5 TraesCS2D01G073100 chr2B 94.211 3403 130 20 2163 5513 43801488 43804875 0.000000e+00 5131.0
6 TraesCS2D01G073100 chr2B 93.987 2395 87 13 3156 5513 50486958 50484584 0.000000e+00 3572.0
7 TraesCS2D01G073100 chr2B 88.904 2208 167 35 1855 4042 50627142 50629291 0.000000e+00 2649.0
8 TraesCS2D01G073100 chr2B 90.523 2047 119 34 204 2226 50490083 50488088 0.000000e+00 2636.0
9 TraesCS2D01G073100 chr2B 92.148 1108 61 14 1937 3032 50488074 50486981 0.000000e+00 1541.0
10 TraesCS2D01G073100 chr2B 88.065 620 61 6 4040 4647 50629325 50629943 0.000000e+00 723.0
11 TraesCS2D01G073100 chr2B 86.329 651 56 16 1492 2137 43800873 43801495 0.000000e+00 678.0
12 TraesCS2D01G073100 chr2B 85.062 569 73 9 3218 3784 773734832 773734274 2.230000e-158 569.0
13 TraesCS2D01G073100 chr2B 83.960 505 46 11 4677 5159 50629937 50630428 8.420000e-123 451.0
14 TraesCS2D01G073100 chr2B 83.778 450 44 23 966 1402 43799926 43800359 3.090000e-107 399.0
15 TraesCS2D01G073100 chr2B 78.367 245 48 3 4418 4658 773734279 773734036 2.660000e-33 154.0
16 TraesCS2D01G073100 chr2B 92.857 98 7 0 891 988 50626089 50626186 5.760000e-30 143.0
17 TraesCS2D01G073100 chr2B 95.122 82 4 0 907 988 50345454 50345535 4.480000e-26 130.0
18 TraesCS2D01G073100 chr2A 93.657 3169 148 26 1937 5072 32917304 32920452 0.000000e+00 4689.0
19 TraesCS2D01G073100 chr2A 87.924 2211 174 49 1850 4042 33008140 33006005 0.000000e+00 2518.0
20 TraesCS2D01G073100 chr2A 91.426 1283 88 8 3249 4520 33023458 33022187 0.000000e+00 1740.0
21 TraesCS2D01G073100 chr2A 84.185 1214 66 33 909 2031 32915998 32917176 0.000000e+00 1062.0
22 TraesCS2D01G073100 chr2A 88.558 839 80 7 1 839 32929767 32930589 0.000000e+00 1003.0
23 TraesCS2D01G073100 chr2A 88.218 662 65 5 1 662 32888670 32889318 0.000000e+00 778.0
24 TraesCS2D01G073100 chr2A 88.069 637 53 11 4040 4656 33005971 33005338 0.000000e+00 734.0
25 TraesCS2D01G073100 chr2A 78.804 953 100 54 906 1822 33009136 33008250 1.040000e-151 547.0
26 TraesCS2D01G073100 chr2A 77.677 990 99 53 4566 5505 33022185 33021268 4.960000e-135 492.0
27 TraesCS2D01G073100 chr2A 83.632 391 42 8 4677 5046 33005353 33004964 1.140000e-91 348.0
28 TraesCS2D01G073100 chr2A 84.906 318 19 14 5197 5513 32920580 32920869 1.500000e-75 294.0
29 TraesCS2D01G073100 chr2A 80.237 253 42 6 4418 4665 760506920 760507169 3.390000e-42 183.0
30 TraesCS2D01G073100 chr2A 92.742 124 5 2 823 942 32912746 32912869 5.680000e-40 176.0
31 TraesCS2D01G073100 chr2A 80.315 254 23 12 1492 1721 108028481 108028231 3.420000e-37 167.0
32 TraesCS2D01G073100 chr2A 88.710 124 10 2 823 942 32930606 32930729 1.240000e-31 148.0
33 TraesCS2D01G073100 chr2A 98.765 81 1 0 908 988 32539968 32540048 1.600000e-30 145.0
34 TraesCS2D01G073100 chr2A 94.048 84 4 1 3129 3212 33023546 33023464 5.800000e-25 126.0
35 TraesCS2D01G073100 chr2A 88.636 88 6 2 2143 2226 32917203 32917290 2.720000e-18 104.0
36 TraesCS2D01G073100 chr2A 84.091 88 9 5 5074 5159 33004971 33004887 4.580000e-11 80.5
37 TraesCS2D01G073100 chr6D 83.392 572 55 17 1920 2478 447021218 447020674 1.380000e-135 494.0
38 TraesCS2D01G073100 chr3B 82.948 563 58 18 1929 2478 697171616 697171079 1.800000e-129 473.0
39 TraesCS2D01G073100 chr3B 87.037 108 7 5 1590 1693 697171758 697171654 1.250000e-21 115.0
40 TraesCS2D01G073100 chr7A 80.315 254 23 12 1492 1721 565752803 565752553 3.420000e-37 167.0
41 TraesCS2D01G073100 chr7A 100.000 28 0 0 1056 1083 125890395 125890368 1.000000e-02 52.8
42 TraesCS2D01G073100 chr4D 79.200 125 18 7 77 197 43139021 43138901 4.580000e-11 80.5
43 TraesCS2D01G073100 chr4A 96.774 31 1 0 1053 1083 565737490 565737520 1.000000e-02 52.8


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 TraesCS2D01G073100 chr2D 30654980 30660492 5512 False 10181.000000 10181 100.000000 1 5513 1 chr2D.!!$F2 5512
1 TraesCS2D01G073100 chr2D 630088396 630089200 804 False 632.000000 632 81.078000 3215 4042 1 chr2D.!!$F3 827
2 TraesCS2D01G073100 chr2D 630634760 630635299 539 True 604.000000 604 86.949000 3218 3757 1 chr2D.!!$R2 539
3 TraesCS2D01G073100 chr2D 629728118 629728918 800 True 588.000000 588 80.120000 3218 4042 1 chr2D.!!$R1 824
4 TraesCS2D01G073100 chr2B 50484584 50490083 5499 True 2583.000000 3572 92.219333 204 5513 3 chr2B.!!$R1 5309
5 TraesCS2D01G073100 chr2B 43799926 43804875 4949 False 2069.333333 5131 88.106000 966 5513 3 chr2B.!!$F2 4547
6 TraesCS2D01G073100 chr2B 50626089 50630428 4339 False 991.500000 2649 88.446500 891 5159 4 chr2B.!!$F3 4268
7 TraesCS2D01G073100 chr2B 773734036 773734832 796 True 361.500000 569 81.714500 3218 4658 2 chr2B.!!$R2 1440
8 TraesCS2D01G073100 chr2A 32912746 32920869 8123 False 1265.000000 4689 88.825200 823 5513 5 chr2A.!!$F4 4690
9 TraesCS2D01G073100 chr2A 33004887 33009136 4249 True 845.500000 2518 84.504000 906 5159 5 chr2A.!!$R2 4253
10 TraesCS2D01G073100 chr2A 33021268 33023546 2278 True 786.000000 1740 87.717000 3129 5505 3 chr2A.!!$R3 2376
11 TraesCS2D01G073100 chr2A 32888670 32889318 648 False 778.000000 778 88.218000 1 662 1 chr2A.!!$F2 661
12 TraesCS2D01G073100 chr2A 32929767 32930729 962 False 575.500000 1003 88.634000 1 942 2 chr2A.!!$F5 941
13 TraesCS2D01G073100 chr6D 447020674 447021218 544 True 494.000000 494 83.392000 1920 2478 1 chr6D.!!$R1 558
14 TraesCS2D01G073100 chr3B 697171079 697171758 679 True 294.000000 473 84.992500 1590 2478 2 chr3B.!!$R1 888

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 0.246635 AGTGATTCGTGAAGGACCCG 59.753 55.000 0.00 0.00 0.00 5.28 F
658 659 0.325272 AAAAGGAAGGCCTCTCCGTC 59.675 55.000 21.23 9.93 46.28 4.79 F
1420 5136 0.620556 GGGGATGAGTTCTTGGCTGA 59.379 55.000 0.00 0.00 0.00 4.26 F
1459 5175 1.025041 GGTTCCTCGAATGGATTGGC 58.975 55.000 0.00 0.00 35.83 4.52 F
1848 5723 1.123928 GGTCAGATGGGAGAACGGAT 58.876 55.000 0.00 0.00 0.00 4.18 F
3584 8021 1.480137 AGGAGCTCAATGAGGTTCTCG 59.520 52.381 16.93 0.00 41.58 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 5371 1.069022 CCAGCACAAATGGAGTGAACG 60.069 52.381 0.00 0.00 40.51 3.95 R
2226 6627 0.610174 TCTGCTGACATCAGGTCCAC 59.390 55.000 10.81 0.00 46.38 4.02 R
3215 7642 0.909623 GTGCCCTACCCATGTAGTGT 59.090 55.000 0.00 0.00 42.49 3.55 R
3584 8021 2.042686 TACCCTGCTGCAATGACATC 57.957 50.000 3.02 0.00 0.00 3.06 R
3919 8362 4.322198 CCACCTGGAGGACATTCAAATTTG 60.322 45.833 12.15 12.15 38.94 2.32 R
4678 9387 0.035458 ACAAGAGAACCAAGGAGCCG 59.965 55.000 0.00 0.00 0.00 5.52 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
25 26 3.130633 TGACAACTCCAACAGTGATTCG 58.869 45.455 0.00 0.00 34.56 3.34
36 37 0.246635 AGTGATTCGTGAAGGACCCG 59.753 55.000 0.00 0.00 0.00 5.28
50 51 4.141990 AGGACCCGGGATCATTTAGATA 57.858 45.455 32.02 0.00 37.00 1.98
107 108 4.694339 CCGATCCCCTAAAAGTCTACAAG 58.306 47.826 0.00 0.00 0.00 3.16
173 174 8.022550 GCCGAACTCCTAAAATCTATAGAGTAC 58.977 40.741 8.70 0.00 0.00 2.73
224 225 4.468510 CCCCCATGACGCCTAAATATACTA 59.531 45.833 0.00 0.00 0.00 1.82
227 228 5.187186 CCCATGACGCCTAAATATACTAGGT 59.813 44.000 10.90 0.00 38.59 3.08
375 376 1.239968 CCAAGAGCCTTCTGCCACAC 61.240 60.000 0.00 0.00 42.71 3.82
503 504 4.284550 GCACTGGCTCCAACCCCA 62.285 66.667 0.00 0.00 36.96 4.96
504 505 2.765969 CACTGGCTCCAACCCCAT 59.234 61.111 0.00 0.00 0.00 4.00
557 558 4.899239 GATGGTCGGCTGCCCTCG 62.899 72.222 14.12 1.26 0.00 4.63
571 572 4.680237 CTCGCACAACTCCCGGCA 62.680 66.667 0.00 0.00 0.00 5.69
587 588 1.066587 GCAACGGCGAGAGAGCTAT 59.933 57.895 16.62 0.00 37.29 2.97
625 626 3.691342 CGCGGTCACCAAGGAGGA 61.691 66.667 0.00 0.00 41.22 3.71
658 659 0.325272 AAAAGGAAGGCCTCTCCGTC 59.675 55.000 21.23 9.93 46.28 4.79
715 716 0.823356 GCCATCCATACGGCCATTGT 60.823 55.000 2.24 0.00 42.82 2.71
870 905 3.756933 ATGTTTCAGCCTGTTTGCAAT 57.243 38.095 0.00 0.00 0.00 3.56
917 960 5.820423 TGCATGATACGGGTATAAATATGCC 59.180 40.000 17.50 0.00 37.68 4.40
1312 4591 3.122323 TCCGGTCGGCGAAATTGC 61.122 61.111 12.92 0.00 34.68 3.56
1420 5136 0.620556 GGGGATGAGTTCTTGGCTGA 59.379 55.000 0.00 0.00 0.00 4.26
1427 5143 2.224597 TGAGTTCTTGGCTGAAGCATCA 60.225 45.455 4.43 0.00 44.36 3.07
1459 5175 1.025041 GGTTCCTCGAATGGATTGGC 58.975 55.000 0.00 0.00 35.83 4.52
1465 5193 2.358957 CTCGAATGGATTGGCTTGACA 58.641 47.619 0.00 0.00 0.00 3.58
1482 5210 3.609853 TGACACTTCTGCAAGTTCTTGT 58.390 40.909 13.04 0.00 41.24 3.16
1584 5371 3.459969 AGAAGGATGTTCTGGTATTCCCC 59.540 47.826 0.00 0.00 0.00 4.81
1681 5472 3.180507 GGGGAGCTAGGAGATGATGAAT 58.819 50.000 0.00 0.00 0.00 2.57
1695 5486 4.982241 TGATGAATATTCAGGGGAGGAC 57.018 45.455 21.97 7.63 41.08 3.85
1764 5555 5.252397 TCCTGGTAACTTCCTCTCTACACTA 59.748 44.000 0.00 0.00 37.61 2.74
1771 5562 6.723298 ACTTCCTCTCTACACTATTCATGG 57.277 41.667 0.00 0.00 0.00 3.66
1830 5621 7.044181 TCATTGTAACTTATTCTCTCTGCTGG 58.956 38.462 0.00 0.00 0.00 4.85
1848 5723 1.123928 GGTCAGATGGGAGAACGGAT 58.876 55.000 0.00 0.00 0.00 4.18
1875 5750 2.513895 ACTGGTGGTTTCCGGTGG 59.486 61.111 0.00 0.00 44.40 4.61
2048 6153 3.443052 TGACCTCCCAAACGTCCTATTA 58.557 45.455 0.00 0.00 0.00 0.98
2049 6154 3.449737 TGACCTCCCAAACGTCCTATTAG 59.550 47.826 0.00 0.00 0.00 1.73
2050 6155 3.447950 ACCTCCCAAACGTCCTATTAGT 58.552 45.455 0.00 0.00 0.00 2.24
2051 6156 3.450096 ACCTCCCAAACGTCCTATTAGTC 59.550 47.826 0.00 0.00 0.00 2.59
2152 6258 6.503524 TCAAACATTTCCTCAGTAAACTTGC 58.496 36.000 0.00 0.00 0.00 4.01
2226 6627 5.647589 AGATGTTGTATTGAGCAATTGCAG 58.352 37.500 30.89 0.00 45.16 4.41
2227 6628 4.852134 TGTTGTATTGAGCAATTGCAGT 57.148 36.364 30.89 12.70 45.16 4.40
2229 6630 3.853831 TGTATTGAGCAATTGCAGTGG 57.146 42.857 30.89 0.00 45.16 4.00
2253 6662 4.940046 ACCTGATGTCAGCAGATGTTAAAG 59.060 41.667 19.61 2.67 42.47 1.85
2254 6663 4.201891 CCTGATGTCAGCAGATGTTAAAGC 60.202 45.833 19.61 0.00 42.47 3.51
2277 6686 5.961843 GCAAGATCAGTGTGAAATGTAATCG 59.038 40.000 0.00 0.00 0.00 3.34
2341 6753 5.544176 AGTTCTCTTACCATGAAGTCCTCAA 59.456 40.000 0.00 0.00 37.67 3.02
2342 6755 5.667539 TCTCTTACCATGAAGTCCTCAAG 57.332 43.478 0.00 0.00 37.67 3.02
2407 6825 9.685276 TCATCAGTATTACTGTTCAAATCCATT 57.315 29.630 20.43 0.00 46.03 3.16
2414 6832 8.868522 ATTACTGTTCAAATCCATTCTCAAGA 57.131 30.769 0.00 0.00 0.00 3.02
2443 6861 6.919721 TGAATGTTGCATATCATCCATCATG 58.080 36.000 0.00 0.00 0.00 3.07
2625 7047 8.927721 TGTTGTGCATATCTGAAAATCATTTTG 58.072 29.630 0.00 0.00 31.94 2.44
2753 7175 9.112725 TCAGTTTACTTAATCATGATGATGGTG 57.887 33.333 9.46 4.71 37.15 4.17
2782 7204 7.201884 CCTTTCTTGATCTGCATGGAAATGTAT 60.202 37.037 0.00 0.00 32.35 2.29
2786 7208 7.774625 TCTTGATCTGCATGGAAATGTATTACA 59.225 33.333 0.00 0.00 0.00 2.41
2979 7403 9.557338 CTGTAAGTACTGTACTAGCTTACAAAG 57.443 37.037 19.97 10.31 45.76 2.77
3092 7518 6.545666 TCTCTTTTGTTGCCTGAATTGTTCTA 59.454 34.615 0.00 0.00 0.00 2.10
3245 7672 3.332485 TGGGTAGGGCACTAGAATGTTTT 59.668 43.478 0.00 0.00 0.00 2.43
3331 7759 6.675515 AGTTTCGATTTCAAATTTTCGCTC 57.324 33.333 5.34 0.29 0.00 5.03
3584 8021 1.480137 AGGAGCTCAATGAGGTTCTCG 59.520 52.381 16.93 0.00 41.58 4.04
3919 8362 7.056844 AGTTCTACAAGCAATCTATCCCTAC 57.943 40.000 0.00 0.00 0.00 3.18
3993 8445 9.780186 TCGGATATCATTCTCGATATACTACAT 57.220 33.333 4.83 0.00 38.44 2.29
4020 8472 5.298026 GGATTATCTTGCCCTCTTTGTCTTC 59.702 44.000 0.00 0.00 0.00 2.87
4021 8473 2.568623 TCTTGCCCTCTTTGTCTTCC 57.431 50.000 0.00 0.00 0.00 3.46
4254 8756 3.007635 GAGGGCTTTAACGTATGCACTT 58.992 45.455 2.83 0.00 39.49 3.16
4551 9216 1.194772 CTCGCTCGACAAAAACTTCCC 59.805 52.381 0.00 0.00 0.00 3.97
4644 9353 5.238650 CCCAAACAACCTGTAACTACTTCTG 59.761 44.000 0.00 0.00 0.00 3.02
4645 9354 5.277828 CCAAACAACCTGTAACTACTTCTGC 60.278 44.000 0.00 0.00 0.00 4.26
4646 9355 4.957684 ACAACCTGTAACTACTTCTGCT 57.042 40.909 0.00 0.00 0.00 4.24
4647 9356 6.415206 AACAACCTGTAACTACTTCTGCTA 57.585 37.500 0.00 0.00 0.00 3.49
4648 9357 5.780984 ACAACCTGTAACTACTTCTGCTAC 58.219 41.667 0.00 0.00 0.00 3.58
4649 9358 4.698583 ACCTGTAACTACTTCTGCTACG 57.301 45.455 0.00 0.00 0.00 3.51
4650 9359 4.330250 ACCTGTAACTACTTCTGCTACGA 58.670 43.478 0.00 0.00 0.00 3.43
4651 9360 4.395542 ACCTGTAACTACTTCTGCTACGAG 59.604 45.833 0.00 0.00 0.00 4.18
4652 9361 4.201930 CCTGTAACTACTTCTGCTACGAGG 60.202 50.000 0.00 0.00 0.00 4.63
4653 9362 4.330250 TGTAACTACTTCTGCTACGAGGT 58.670 43.478 0.00 0.00 0.00 3.85
4654 9363 4.763793 TGTAACTACTTCTGCTACGAGGTT 59.236 41.667 0.00 0.00 0.00 3.50
4655 9364 4.868314 AACTACTTCTGCTACGAGGTTT 57.132 40.909 0.00 0.00 0.00 3.27
4656 9365 5.972107 AACTACTTCTGCTACGAGGTTTA 57.028 39.130 0.00 0.00 0.00 2.01
4657 9366 5.307926 ACTACTTCTGCTACGAGGTTTAC 57.692 43.478 0.00 0.00 0.00 2.01
4658 9367 3.589495 ACTTCTGCTACGAGGTTTACC 57.411 47.619 0.00 0.00 0.00 2.85
4659 9368 2.233186 ACTTCTGCTACGAGGTTTACCC 59.767 50.000 0.00 0.00 36.42 3.69
4661 9370 1.822990 TCTGCTACGAGGTTTACCCTG 59.177 52.381 0.00 0.00 46.51 4.45
4662 9371 1.822990 CTGCTACGAGGTTTACCCTGA 59.177 52.381 0.00 0.00 46.51 3.86
4663 9372 2.232941 CTGCTACGAGGTTTACCCTGAA 59.767 50.000 0.00 0.00 46.51 3.02
4664 9373 2.835764 TGCTACGAGGTTTACCCTGAAT 59.164 45.455 0.00 0.00 46.51 2.57
4665 9374 3.195661 GCTACGAGGTTTACCCTGAATG 58.804 50.000 0.00 0.00 46.51 2.67
4666 9375 3.118884 GCTACGAGGTTTACCCTGAATGA 60.119 47.826 0.00 0.00 46.51 2.57
4667 9376 3.329929 ACGAGGTTTACCCTGAATGAC 57.670 47.619 0.00 0.00 46.51 3.06
4668 9377 2.635915 ACGAGGTTTACCCTGAATGACA 59.364 45.455 0.00 0.00 46.51 3.58
4669 9378 3.263425 ACGAGGTTTACCCTGAATGACAT 59.737 43.478 0.00 0.00 46.51 3.06
4670 9379 3.623060 CGAGGTTTACCCTGAATGACATG 59.377 47.826 0.00 0.00 46.51 3.21
4671 9380 3.356290 AGGTTTACCCTGAATGACATGC 58.644 45.455 0.00 0.00 44.08 4.06
4672 9381 2.427095 GGTTTACCCTGAATGACATGCC 59.573 50.000 0.00 0.00 0.00 4.40
4673 9382 3.088532 GTTTACCCTGAATGACATGCCA 58.911 45.455 0.00 0.00 0.00 4.92
4674 9383 3.668141 TTACCCTGAATGACATGCCAT 57.332 42.857 0.00 0.00 0.00 4.40
4675 9384 1.771565 ACCCTGAATGACATGCCATG 58.228 50.000 2.40 2.40 0.00 3.66
4676 9385 0.387929 CCCTGAATGACATGCCATGC 59.612 55.000 4.17 0.00 0.00 4.06
4677 9386 1.399714 CCTGAATGACATGCCATGCT 58.600 50.000 4.17 0.00 0.00 3.79
4678 9387 1.337071 CCTGAATGACATGCCATGCTC 59.663 52.381 4.17 2.69 0.00 4.26
4679 9388 1.002792 CTGAATGACATGCCATGCTCG 60.003 52.381 4.17 0.00 0.00 5.03
4712 9457 1.605710 TCTTGTTCTTGCTGAAGCTGC 59.394 47.619 3.61 0.00 42.66 5.25
4733 9478 7.278868 AGCTGCTGTTAGTTACTCATGTATTTC 59.721 37.037 0.00 0.00 0.00 2.17
4843 9629 6.098679 CCTGGCTTATATCAGATTCTTCGAG 58.901 44.000 0.00 0.00 33.11 4.04
4996 9790 3.450457 ACAGGCCTCTTATCTCTTCACAG 59.550 47.826 0.00 0.00 0.00 3.66
5131 9928 0.320247 ACTTGCACTTCTCCAGCGAG 60.320 55.000 0.00 0.00 43.74 5.03
5242 10087 6.115448 TCTTCTCAGTTTAGGCTTTTAGCT 57.885 37.500 0.00 0.00 41.99 3.32
5256 10101 2.561733 TTAGCTGATCGACGTCTTGG 57.438 50.000 14.70 0.00 0.00 3.61
5331 10177 0.034337 AAAAGCCATGCAAGTGCCAG 59.966 50.000 0.00 0.00 41.18 4.85
5341 10187 1.608801 GCAAGTGCCAGGAAAAATGGG 60.609 52.381 0.00 0.00 38.33 4.00
5347 10193 2.368221 TGCCAGGAAAAATGGGTTTCAG 59.632 45.455 0.00 0.00 38.93 3.02
5428 10293 6.294731 GCCTCCTGAAACAACAGATAATTTGT 60.295 38.462 0.00 0.00 39.94 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.546598 AATGATCCCGGGTCCTTCAC 59.453 55.000 22.86 5.91 0.00 3.18
36 37 8.072321 TCTGCTATGTCTATCTAAATGATCCC 57.928 38.462 0.00 0.00 36.65 3.85
68 69 5.337652 GGGATCGGCTAGAATTGCTATTAGT 60.338 44.000 0.00 0.00 0.00 2.24
239 240 2.733956 AGGCGGGCAAGATTTTAATCA 58.266 42.857 3.78 0.00 37.89 2.57
387 388 1.607467 GTGGGGACAAGCCAGCAAT 60.607 57.895 0.00 0.00 46.06 3.56
388 389 2.203480 GTGGGGACAAGCCAGCAA 60.203 61.111 0.00 0.00 46.06 3.91
458 459 4.368315 GACAGTGAACATTTTTCAACCCC 58.632 43.478 0.00 0.00 0.00 4.95
459 460 4.368315 GGACAGTGAACATTTTTCAACCC 58.632 43.478 0.00 0.00 0.00 4.11
460 461 4.041723 CGGACAGTGAACATTTTTCAACC 58.958 43.478 0.00 0.00 0.00 3.77
461 462 4.041723 CCGGACAGTGAACATTTTTCAAC 58.958 43.478 0.00 0.00 0.00 3.18
462 463 3.948473 TCCGGACAGTGAACATTTTTCAA 59.052 39.130 0.00 0.00 0.00 2.69
557 558 4.025401 CGTTGCCGGGAGTTGTGC 62.025 66.667 2.18 0.00 0.00 4.57
571 572 1.103803 TTCATAGCTCTCTCGCCGTT 58.896 50.000 0.00 0.00 0.00 4.44
577 578 2.541999 CCGTCGGTTTCATAGCTCTCTC 60.542 54.545 2.08 0.00 0.00 3.20
606 607 2.579201 CTCCTTGGTGACCGCGAT 59.421 61.111 8.23 0.00 0.00 4.58
611 612 2.047179 GCGTCCTCCTTGGTGACC 60.047 66.667 0.00 0.00 37.07 4.02
625 626 3.040147 TCCTTTTCTTCATCTTCGCGT 57.960 42.857 5.77 0.00 0.00 6.01
917 960 3.612247 CTCCAGGGACCCAACTGCG 62.612 68.421 14.60 0.00 33.43 5.18
1046 4287 3.764466 CGTCTCCGCTGCTTCCCT 61.764 66.667 0.00 0.00 0.00 4.20
1312 4591 1.308998 AGAAACAGGGCAAGAACACG 58.691 50.000 0.00 0.00 0.00 4.49
1427 5143 2.572284 GAACCTACGACCGCAGCT 59.428 61.111 0.00 0.00 0.00 4.24
1430 5146 2.693762 CGAGGAACCTACGACCGCA 61.694 63.158 0.00 0.00 0.00 5.69
1459 5175 4.095483 ACAAGAACTTGCAGAAGTGTCAAG 59.905 41.667 13.50 0.00 41.87 3.02
1465 5193 4.508124 CGAACTACAAGAACTTGCAGAAGT 59.492 41.667 18.05 11.86 44.79 3.01
1584 5371 1.069022 CCAGCACAAATGGAGTGAACG 60.069 52.381 0.00 0.00 40.51 3.95
1681 5472 2.667470 CTCTTCGTCCTCCCCTGAATA 58.333 52.381 0.00 0.00 0.00 1.75
1695 5486 3.573598 CGAATCCTGATCATCCTCTTCG 58.426 50.000 0.00 4.01 0.00 3.79
1764 5555 4.018141 TGTTTCCTCAGATCACCCATGAAT 60.018 41.667 0.00 0.00 38.69 2.57
1771 5562 4.162320 TCTGGTATGTTTCCTCAGATCACC 59.838 45.833 0.00 0.00 30.58 4.02
1830 5621 1.269309 CGATCCGTTCTCCCATCTGAC 60.269 57.143 0.00 0.00 0.00 3.51
1875 5750 3.188786 GTCGGACGAGCATGTGGC 61.189 66.667 0.00 0.00 45.30 5.01
2152 6258 1.374758 GAACGACTGGGGCACTGAG 60.375 63.158 0.00 0.00 0.00 3.35
2226 6627 0.610174 TCTGCTGACATCAGGTCCAC 59.390 55.000 10.81 0.00 46.38 4.02
2227 6628 1.208776 CATCTGCTGACATCAGGTCCA 59.791 52.381 10.81 0.02 46.38 4.02
2253 6662 5.961843 CGATTACATTTCACACTGATCTTGC 59.038 40.000 0.00 0.00 0.00 4.01
2254 6663 7.294676 TCGATTACATTTCACACTGATCTTG 57.705 36.000 0.00 0.00 0.00 3.02
2277 6686 8.139989 AGCAGAAATCATAAGGTGCAAAATATC 58.860 33.333 0.00 0.00 33.24 1.63
2395 6812 9.334947 TCATCTATCTTGAGAATGGATTTGAAC 57.665 33.333 0.00 0.00 0.00 3.18
2407 6825 9.433153 GATATGCAACATTCATCTATCTTGAGA 57.567 33.333 0.00 0.00 0.00 3.27
2443 6861 5.582689 ATCACAAAAGGTAGCATTAAGGC 57.417 39.130 3.37 3.37 0.00 4.35
2753 7175 4.012374 TCCATGCAGATCAAGAAAGGAAC 58.988 43.478 0.00 0.00 0.00 3.62
2782 7204 7.011499 TCCTGTAGACAAGCCTATTTTGTAA 57.989 36.000 0.00 0.00 38.78 2.41
2786 7208 6.408662 GGATCTCCTGTAGACAAGCCTATTTT 60.409 42.308 0.00 0.00 36.93 1.82
2979 7403 7.124573 AGATAAGGGGAAAAATGTTTATGCC 57.875 36.000 0.00 0.00 0.00 4.40
3215 7642 0.909623 GTGCCCTACCCATGTAGTGT 59.090 55.000 0.00 0.00 42.49 3.55
3584 8021 2.042686 TACCCTGCTGCAATGACATC 57.957 50.000 3.02 0.00 0.00 3.06
3708 8145 6.293955 GCCATTCAGAAGTACAGCTACAAAAA 60.294 38.462 0.00 0.00 0.00 1.94
3792 8230 8.567948 ACAAATAGACAAACAACACATCCTAAG 58.432 33.333 0.00 0.00 0.00 2.18
3836 8277 9.566432 CTAAGGAGAGATATAACTGGCAAAAAT 57.434 33.333 0.00 0.00 0.00 1.82
3919 8362 4.322198 CCACCTGGAGGACATTCAAATTTG 60.322 45.833 12.15 12.15 38.94 2.32
3993 8445 6.101734 AGACAAAGAGGGCAAGATAATCCATA 59.898 38.462 0.00 0.00 0.00 2.74
4021 8473 7.865706 AAGGTAATTAGTATGCCAAGTCTTG 57.134 36.000 5.53 5.53 0.00 3.02
4254 8756 2.030401 GACACGCAACGGTATGCCA 61.030 57.895 0.00 0.00 43.47 4.92
4551 9216 4.323562 GGTTTCCCTATAATCATCCCGGAG 60.324 50.000 0.73 0.00 0.00 4.63
4651 9360 2.427095 GGCATGTCATTCAGGGTAAACC 59.573 50.000 0.00 0.00 40.67 3.27
4652 9361 3.088532 TGGCATGTCATTCAGGGTAAAC 58.911 45.455 0.00 0.00 0.00 2.01
4653 9362 3.448093 TGGCATGTCATTCAGGGTAAA 57.552 42.857 0.00 0.00 0.00 2.01
4654 9363 3.289836 CATGGCATGTCATTCAGGGTAA 58.710 45.455 19.32 0.00 0.00 2.85
4655 9364 2.934887 CATGGCATGTCATTCAGGGTA 58.065 47.619 19.32 0.00 0.00 3.69
4656 9365 1.771565 CATGGCATGTCATTCAGGGT 58.228 50.000 19.32 0.00 0.00 4.34
4657 9366 0.387929 GCATGGCATGTCATTCAGGG 59.612 55.000 26.94 0.00 0.00 4.45
4658 9367 1.337071 GAGCATGGCATGTCATTCAGG 59.663 52.381 26.94 0.00 0.00 3.86
4659 9368 1.002792 CGAGCATGGCATGTCATTCAG 60.003 52.381 26.94 0.37 0.00 3.02
4660 9369 1.018910 CGAGCATGGCATGTCATTCA 58.981 50.000 26.94 0.00 0.00 2.57
4661 9370 0.309922 CCGAGCATGGCATGTCATTC 59.690 55.000 26.94 17.73 0.00 2.67
4662 9371 2.411535 CCGAGCATGGCATGTCATT 58.588 52.632 26.94 11.70 0.00 2.57
4663 9372 4.152644 CCGAGCATGGCATGTCAT 57.847 55.556 26.94 7.07 0.00 3.06
4671 9380 2.515523 CCAAGGAGCCGAGCATGG 60.516 66.667 0.00 0.00 0.00 3.66
4672 9381 1.372087 GAACCAAGGAGCCGAGCATG 61.372 60.000 0.00 0.00 0.00 4.06
4673 9382 1.078143 GAACCAAGGAGCCGAGCAT 60.078 57.895 0.00 0.00 0.00 3.79
4674 9383 2.172483 GAGAACCAAGGAGCCGAGCA 62.172 60.000 0.00 0.00 0.00 4.26
4675 9384 1.448717 GAGAACCAAGGAGCCGAGC 60.449 63.158 0.00 0.00 0.00 5.03
4676 9385 0.610687 AAGAGAACCAAGGAGCCGAG 59.389 55.000 0.00 0.00 0.00 4.63
4677 9386 0.321671 CAAGAGAACCAAGGAGCCGA 59.678 55.000 0.00 0.00 0.00 5.54
4678 9387 0.035458 ACAAGAGAACCAAGGAGCCG 59.965 55.000 0.00 0.00 0.00 5.52
4679 9388 2.155279 GAACAAGAGAACCAAGGAGCC 58.845 52.381 0.00 0.00 0.00 4.70
4712 9457 8.808529 CCTTCGAAATACATGAGTAACTAACAG 58.191 37.037 0.00 0.00 33.13 3.16
4733 9478 6.137794 TCTTCTATTCTGTAGCTTCCTTCG 57.862 41.667 0.00 0.00 0.00 3.79
4818 9563 4.629200 CGAAGAATCTGATATAAGCCAGGC 59.371 45.833 1.84 1.84 0.00 4.85
4843 9629 6.848296 GTCAAGCTCATATCGAAATTGCTTAC 59.152 38.462 12.99 9.55 37.20 2.34
4965 9759 5.495640 AGATAAGAGGCCTGTGAAGAAAAG 58.504 41.667 12.00 0.00 0.00 2.27
4996 9790 7.863375 AGTTATGTGTATTCACTCTCGCTTATC 59.137 37.037 4.01 0.00 44.14 1.75
5242 10087 2.959372 ACGCCAAGACGTCGATCA 59.041 55.556 10.46 0.00 44.43 2.92
5256 10101 2.411547 CGAAACTCATCTTGGACAACGC 60.412 50.000 0.00 0.00 0.00 4.84
5331 10177 6.358118 GTTTTGACTGAAACCCATTTTTCC 57.642 37.500 0.00 0.00 35.01 3.13
5341 10187 2.098443 TGGCTTCGGTTTTGACTGAAAC 59.902 45.455 2.82 0.00 38.49 2.78
5347 10193 4.394920 TCAATAGATGGCTTCGGTTTTGAC 59.605 41.667 0.00 0.00 0.00 3.18
5428 10293 2.608506 CGTGGTTGTGACCTACGATTGA 60.609 50.000 12.12 0.00 45.21 2.57


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

AutoCloner maintained by Alex Coulton.