Multiple sequence alignment - TraesCS1B01G351300

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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 TraesCS1B01G351300 chr1B 100.000 8913 0 0 1 8913 581699396 581690484 0.000000e+00 16460.0
1 TraesCS1B01G351300 chr1B 86.111 576 70 7 787 1361 502631982 502631416 5.920000e-171 612.0
2 TraesCS1B01G351300 chr1B 85.659 258 31 2 5879 6136 581695572 581695321 5.310000e-67 267.0
3 TraesCS1B01G351300 chr1B 85.000 140 16 4 5005 5142 581692096 581691960 4.340000e-28 137.0
4 TraesCS1B01G351300 chr1B 85.000 140 16 4 7301 7437 581694392 581694255 4.340000e-28 137.0
5 TraesCS1B01G351300 chr1D 97.778 7247 128 18 1 7221 430573415 430566176 0.000000e+00 12460.0
6 TraesCS1B01G351300 chr1D 94.183 1719 76 11 7217 8913 430566149 430564433 0.000000e+00 2599.0
7 TraesCS1B01G351300 chr1D 85.788 774 94 13 787 1558 376058133 376057374 0.000000e+00 806.0
8 TraesCS1B01G351300 chr1D 83.784 777 110 13 786 1558 376066358 376065594 0.000000e+00 723.0
9 TraesCS1B01G351300 chr1D 85.659 258 31 2 5879 6136 430569589 430569338 5.310000e-67 267.0
10 TraesCS1B01G351300 chr1D 84.977 213 26 5 7301 7509 430568412 430568202 2.520000e-50 211.0
11 TraesCS1B01G351300 chr1D 72.471 603 102 43 4921 5482 430566153 430565574 1.560000e-27 135.0
12 TraesCS1B01G351300 chr1D 92.135 89 4 1 467 552 35756949 35756861 1.220000e-23 122.0
13 TraesCS1B01G351300 chr1D 76.562 256 38 15 5760 6010 430567779 430567541 4.370000e-23 121.0
14 TraesCS1B01G351300 chr1A 94.879 4804 147 19 2461 7221 528671408 528666661 0.000000e+00 7417.0
15 TraesCS1B01G351300 chr1A 93.858 1905 75 17 544 2436 528673284 528671410 0.000000e+00 2832.0
16 TraesCS1B01G351300 chr1A 92.807 1696 93 12 7230 8913 528666625 528664947 0.000000e+00 2429.0
17 TraesCS1B01G351300 chr1A 94.658 468 25 0 1 468 528673752 528673285 0.000000e+00 726.0
18 TraesCS1B01G351300 chr1A 86.609 575 69 6 787 1361 475305167 475304601 5.870000e-176 628.0
19 TraesCS1B01G351300 chr1A 86.695 233 28 1 5880 6112 528670045 528669816 1.150000e-63 255.0
20 TraesCS1B01G351300 chr1A 72.630 559 105 31 5005 5532 528666554 528666013 3.350000e-29 141.0
21 TraesCS1B01G351300 chr1A 88.000 75 6 2 6445 6518 350162571 350162499 1.590000e-12 86.1
22 TraesCS1B01G351300 chr3B 82.697 2358 317 52 2299 4618 679517 677213 0.000000e+00 2010.0
23 TraesCS1B01G351300 chr3B 86.356 1202 139 12 2872 4063 921195 922381 0.000000e+00 1288.0
24 TraesCS1B01G351300 chr3B 82.276 1072 132 28 637 1668 919041 920094 0.000000e+00 874.0
25 TraesCS1B01G351300 chr3B 87.097 744 89 5 2872 3613 904748 905486 0.000000e+00 835.0
26 TraesCS1B01G351300 chr3B 81.437 1072 146 25 2927 3986 529438 530468 0.000000e+00 828.0
27 TraesCS1B01G351300 chr3B 81.179 882 118 22 7080 7939 676467 675612 0.000000e+00 665.0
28 TraesCS1B01G351300 chr3B 81.779 697 79 25 4110 4794 906565 907225 2.830000e-149 540.0
29 TraesCS1B01G351300 chr3B 81.779 697 79 25 4110 4794 922380 923040 2.830000e-149 540.0
30 TraesCS1B01G351300 chr3B 76.336 917 125 45 7575 8441 571895 572769 3.000000e-109 407.0
31 TraesCS1B01G351300 chr3B 79.082 392 36 16 637 998 902857 903232 2.500000e-55 228.0
32 TraesCS1B01G351300 chr3B 82.158 241 36 4 7597 7832 907447 907685 5.460000e-47 200.0
33 TraesCS1B01G351300 chr3B 84.314 204 30 2 5874 6075 906321 906524 1.960000e-46 198.0
34 TraesCS1B01G351300 chr3B 84.314 204 30 2 5874 6075 922136 922339 1.960000e-46 198.0
35 TraesCS1B01G351300 chr3B 81.743 241 37 4 7597 7832 923262 923500 2.540000e-45 195.0
36 TraesCS1B01G351300 chr3B 84.530 181 26 2 6520 6699 544928724 544928545 2.560000e-40 178.0
37 TraesCS1B01G351300 chr3B 83.425 181 28 2 6520 6699 544836353 544836174 5.540000e-37 167.0
38 TraesCS1B01G351300 chr3B 84.416 154 22 2 6878 7030 676621 676469 5.570000e-32 150.0
39 TraesCS1B01G351300 chr3B 85.556 90 3 1 2792 2881 920967 921046 1.590000e-12 86.1
40 TraesCS1B01G351300 chr3A 85.859 1874 203 30 2164 4017 1209555 1211386 0.000000e+00 1936.0
41 TraesCS1B01G351300 chr3A 83.142 872 115 14 812 1668 1200567 1201421 0.000000e+00 767.0
42 TraesCS1B01G351300 chr3A 76.861 1236 185 55 7269 8442 1067668 1068864 9.900000e-169 604.0
43 TraesCS1B01G351300 chr3A 84.848 198 29 1 5874 6071 1211190 1211386 1.960000e-46 198.0
44 TraesCS1B01G351300 chrUn 86.060 1736 202 22 2497 4220 31955848 31954141 0.000000e+00 1829.0
45 TraesCS1B01G351300 chrUn 86.532 1136 127 12 2849 3983 31996338 31997448 0.000000e+00 1227.0
46 TraesCS1B01G351300 chrUn 86.356 1136 126 16 2849 3983 269076889 269075782 0.000000e+00 1212.0
47 TraesCS1B01G351300 chrUn 82.369 1072 131 28 637 1668 321410780 321409727 0.000000e+00 880.0
48 TraesCS1B01G351300 chrUn 84.337 498 48 17 7080 7569 31948514 31948039 2.270000e-125 460.0
49 TraesCS1B01G351300 chrUn 80.462 650 74 21 7266 7886 31870652 31871277 1.770000e-121 448.0
50 TraesCS1B01G351300 chrUn 80.101 397 69 3 6569 6963 31953284 31952896 4.070000e-73 287.0
51 TraesCS1B01G351300 chrUn 85.398 226 28 3 8251 8474 31997675 31997897 6.960000e-56 230.0
52 TraesCS1B01G351300 chrUn 85.398 226 28 3 8251 8474 269075555 269075333 6.960000e-56 230.0
53 TraesCS1B01G351300 chrUn 79.082 392 36 16 637 998 344639854 344639479 2.500000e-55 228.0
54 TraesCS1B01G351300 chrUn 79.082 392 36 16 637 998 344642278 344641903 2.500000e-55 228.0
55 TraesCS1B01G351300 chrUn 81.818 143 20 1 5709 5845 31997267 31997409 2.030000e-21 115.0
56 TraesCS1B01G351300 chrUn 82.143 140 19 1 5712 5845 269075960 269075821 2.030000e-21 115.0
57 TraesCS1B01G351300 chrUn 83.761 117 13 1 5709 5819 401019907 401020023 1.220000e-18 106.0
58 TraesCS1B01G351300 chrUn 85.556 90 3 1 2792 2881 321408854 321408775 1.590000e-12 86.1
59 TraesCS1B01G351300 chr3D 88.223 1401 144 13 2831 4220 3780198 3781588 0.000000e+00 1653.0
60 TraesCS1B01G351300 chr3D 77.561 1025 149 43 7266 8249 3856478 3855494 2.190000e-150 544.0
61 TraesCS1B01G351300 chr3D 82.780 482 62 11 4301 4777 3781586 3782051 2.320000e-110 411.0
62 TraesCS1B01G351300 chr3D 82.329 498 51 22 7080 7569 3782792 3783260 1.800000e-106 398.0
63 TraesCS1B01G351300 chr3D 81.687 486 65 12 7266 7732 3907985 3907505 5.050000e-102 383.0
64 TraesCS1B01G351300 chr3D 78.966 580 86 19 7388 7939 3902878 3902307 6.580000e-96 363.0
65 TraesCS1B01G351300 chr3D 79.668 482 67 14 7484 7939 3891481 3891005 1.440000e-82 318.0
66 TraesCS1B01G351300 chr3D 87.437 199 22 3 5874 6071 3781184 3781380 9.000000e-55 226.0
67 TraesCS1B01G351300 chr3D 81.955 266 34 9 6444 6699 171148373 171148112 7.010000e-51 213.0
68 TraesCS1B01G351300 chr3D 82.258 186 30 3 6520 6703 418561632 418561448 3.330000e-34 158.0
69 TraesCS1B01G351300 chr3D 88.333 120 14 0 7025 7144 3908225 3908106 2.590000e-30 145.0
70 TraesCS1B01G351300 chr3D 85.315 143 15 1 5709 5845 3781165 3781307 9.330000e-30 143.0
71 TraesCS1B01G351300 chr3D 88.172 93 5 5 7861 7951 3783247 3783335 1.220000e-18 106.0
72 TraesCS1B01G351300 chr2B 83.060 183 27 4 6519 6699 728387545 728387725 7.160000e-36 163.0
73 TraesCS1B01G351300 chr7D 82.258 186 30 3 6515 6699 449232611 449232794 3.330000e-34 158.0
74 TraesCS1B01G351300 chr7D 93.182 88 2 2 468 552 485090882 485090968 9.390000e-25 126.0
75 TraesCS1B01G351300 chr7D 88.158 76 6 2 6445 6519 72952271 72952344 4.430000e-13 87.9
76 TraesCS1B01G351300 chr7D 88.000 75 6 2 6445 6518 202244299 202244227 1.590000e-12 86.1
77 TraesCS1B01G351300 chr7D 87.179 78 7 2 6442 6518 436142518 436142593 1.590000e-12 86.1
78 TraesCS1B01G351300 chr7D 88.000 75 6 2 6445 6518 449593615 449593543 1.590000e-12 86.1
79 TraesCS1B01G351300 chr6D 82.514 183 28 4 6519 6699 337521323 337521143 3.330000e-34 158.0
80 TraesCS1B01G351300 chr6D 86.726 113 11 2 468 577 146072903 146072792 1.220000e-23 122.0
81 TraesCS1B01G351300 chr6D 88.000 75 5 2 6445 6519 125088537 125088467 1.590000e-12 86.1
82 TraesCS1B01G351300 chr6B 82.692 156 22 4 2623 2777 129851909 129851758 5.610000e-27 134.0
83 TraesCS1B01G351300 chr5D 92.391 92 2 2 462 548 373214568 373214659 9.390000e-25 126.0
84 TraesCS1B01G351300 chr5D 85.593 118 14 3 2667 2782 27977808 27977924 4.370000e-23 121.0
85 TraesCS1B01G351300 chr5D 91.209 91 4 2 468 554 240428122 240428032 4.370000e-23 121.0
86 TraesCS1B01G351300 chr4B 90.526 95 4 4 459 548 180553962 180553868 4.370000e-23 121.0
87 TraesCS1B01G351300 chr4B 85.586 111 15 1 2667 2776 575728241 575728131 2.030000e-21 115.0
88 TraesCS1B01G351300 chr4D 88.889 99 6 3 468 562 403409535 403409632 5.650000e-22 117.0
89 TraesCS1B01G351300 chr7B 88.776 98 5 4 456 549 517395776 517395871 2.030000e-21 115.0
90 TraesCS1B01G351300 chr2D 89.474 76 5 2 6445 6519 518263458 518263531 9.530000e-15 93.5


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 TraesCS1B01G351300 chr1B 581690484 581699396 8912 True 16460.000000 16460 100.000000 1 8913 1 chr1B.!!$R2 8912
1 TraesCS1B01G351300 chr1B 502631416 502631982 566 True 612.000000 612 86.111000 787 1361 1 chr1B.!!$R1 574
2 TraesCS1B01G351300 chr1D 430564433 430573415 8982 True 5064.666667 12460 88.144000 1 8913 3 chr1D.!!$R4 8912
3 TraesCS1B01G351300 chr1D 376057374 376058133 759 True 806.000000 806 85.788000 787 1558 1 chr1D.!!$R2 771
4 TraesCS1B01G351300 chr1D 376065594 376066358 764 True 723.000000 723 83.784000 786 1558 1 chr1D.!!$R3 772
5 TraesCS1B01G351300 chr1A 528664947 528673752 8805 True 2300.000000 7417 89.254500 1 8913 6 chr1A.!!$R3 8912
6 TraesCS1B01G351300 chr1A 475304601 475305167 566 True 628.000000 628 86.609000 787 1361 1 chr1A.!!$R2 574
7 TraesCS1B01G351300 chr3B 675612 679517 3905 True 941.666667 2010 82.764000 2299 7939 3 chr3B.!!$R3 5640
8 TraesCS1B01G351300 chr3B 529438 530468 1030 False 828.000000 828 81.437000 2927 3986 1 chr3B.!!$F1 1059
9 TraesCS1B01G351300 chr3B 919041 923500 4459 False 530.183333 1288 83.670667 637 7832 6 chr3B.!!$F4 7195
10 TraesCS1B01G351300 chr3B 571895 572769 874 False 407.000000 407 76.336000 7575 8441 1 chr3B.!!$F2 866
11 TraesCS1B01G351300 chr3B 902857 907685 4828 False 400.200000 835 82.886000 637 7832 5 chr3B.!!$F3 7195
12 TraesCS1B01G351300 chr3A 1209555 1211386 1831 False 1067.000000 1936 85.353500 2164 6071 2 chr3A.!!$F3 3907
13 TraesCS1B01G351300 chr3A 1200567 1201421 854 False 767.000000 767 83.142000 812 1668 1 chr3A.!!$F2 856
14 TraesCS1B01G351300 chr3A 1067668 1068864 1196 False 604.000000 604 76.861000 7269 8442 1 chr3A.!!$F1 1173
15 TraesCS1B01G351300 chrUn 31952896 31955848 2952 True 1058.000000 1829 83.080500 2497 6963 2 chrUn.!!$R2 4466
16 TraesCS1B01G351300 chrUn 31996338 31997897 1559 False 524.000000 1227 84.582667 2849 8474 3 chrUn.!!$F3 5625
17 TraesCS1B01G351300 chrUn 269075333 269076889 1556 True 519.000000 1212 84.632333 2849 8474 3 chrUn.!!$R3 5625
18 TraesCS1B01G351300 chrUn 321408775 321410780 2005 True 483.050000 880 83.962500 637 2881 2 chrUn.!!$R4 2244
19 TraesCS1B01G351300 chrUn 31870652 31871277 625 False 448.000000 448 80.462000 7266 7886 1 chrUn.!!$F1 620
20 TraesCS1B01G351300 chrUn 344639479 344642278 2799 True 228.000000 228 79.082000 637 998 2 chrUn.!!$R5 361
21 TraesCS1B01G351300 chr3D 3855494 3856478 984 True 544.000000 544 77.561000 7266 8249 1 chr3D.!!$R1 983
22 TraesCS1B01G351300 chr3D 3780198 3783335 3137 False 489.500000 1653 85.709333 2831 7951 6 chr3D.!!$F1 5120
23 TraesCS1B01G351300 chr3D 3902307 3902878 571 True 363.000000 363 78.966000 7388 7939 1 chr3D.!!$R3 551
24 TraesCS1B01G351300 chr3D 3907505 3908225 720 True 264.000000 383 85.010000 7025 7732 2 chr3D.!!$R6 707

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
236 237 0.316522 TCGCTCATGCTAGATCAGGC 59.683 55.000 0.00 0.0 36.97 4.85 F
1729 1945 1.094785 GTTATTGCGCCATCCACACT 58.905 50.000 4.18 0.0 0.00 3.55 F
1752 1968 1.137513 CCTCCTTCAACACGTCGTTC 58.862 55.000 0.00 0.0 34.86 3.95 F
3178 3644 4.388485 TCTGATGTTGTGCTGTGTTATGT 58.612 39.130 0.00 0.0 0.00 2.29 F
4268 5770 2.159028 GCCTTGCAAACACCTTTGGTAA 60.159 45.455 0.00 0.0 37.78 2.85 F
5077 6641 2.692557 TGCTGTTAAAGAAAGCTTGGCA 59.307 40.909 0.00 0.0 37.82 4.92 F
7037 8679 1.338020 GGCACACCTGAAAAGGACAAG 59.662 52.381 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 2035 0.251253 TGCATGCATGGTGTCCAGAA 60.251 50.000 27.34 0.00 36.75 3.02 R
3429 3897 1.062581 CATCCTTCCTCTCCCTCAGGA 60.063 57.143 0.00 0.00 41.08 3.86 R
4007 5450 9.274206 GAAACTTCATCCTTACTACAAGACTTT 57.726 33.333 0.00 0.00 0.00 2.66 R
4945 6509 3.029320 TGCAAATTGGCTAAGCTTGTG 57.971 42.857 9.86 2.92 34.04 3.33 R
5532 7133 4.100373 ACCTTCATCTTCAGGTTCTAGCT 58.900 43.478 0.00 0.00 40.85 3.32 R
7064 8706 1.812235 ATTCATTGCTCTGACGCACA 58.188 45.000 2.05 0.00 40.09 4.57 R
8128 10653 1.020861 TGCCATAGAAGTGCGCTGTG 61.021 55.000 9.73 0.00 0.00 3.66 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
104 105 1.623973 GCGCTGGTGTTCGGTAGTTC 61.624 60.000 0.00 0.00 0.00 3.01
121 122 0.834612 TTCTGGGTTTGAGTCGTGGT 59.165 50.000 0.00 0.00 0.00 4.16
177 178 1.358152 TGGATTGGTTCGGGAGTTCT 58.642 50.000 0.00 0.00 0.00 3.01
218 219 4.830600 TGGTTTCTAGGGTTTTGATGGTTC 59.169 41.667 0.00 0.00 0.00 3.62
236 237 0.316522 TCGCTCATGCTAGATCAGGC 59.683 55.000 0.00 0.00 36.97 4.85
311 313 2.983791 CTTGCCATTGCCCCCTTG 59.016 61.111 0.00 0.00 36.33 3.61
324 326 1.467432 CCCTTGGCCCTTGGGTAAA 59.533 57.895 14.63 1.79 36.32 2.01
327 329 1.256812 CTTGGCCCTTGGGTAAACAG 58.743 55.000 0.00 0.00 0.00 3.16
358 360 5.466728 TCGGCTGATTTCAACTATAGATTGC 59.533 40.000 6.78 0.00 0.00 3.56
367 369 6.391227 TCAACTATAGATTGCGTGAGATGA 57.609 37.500 6.78 0.00 0.00 2.92
645 649 5.294552 AGCAGTAGATCTGATTTTTAACGCC 59.705 40.000 5.18 0.00 46.27 5.68
1121 1311 1.279846 TCCTTTTCCGTACACATCCCC 59.720 52.381 0.00 0.00 0.00 4.81
1295 1485 3.675775 GCTGTGCAAACTCCAACAGAAAA 60.676 43.478 5.87 0.00 0.00 2.29
1577 1778 4.935352 TTCACCTTTGCATTTGTAGCTT 57.065 36.364 0.00 0.00 0.00 3.74
1729 1945 1.094785 GTTATTGCGCCATCCACACT 58.905 50.000 4.18 0.00 0.00 3.55
1744 1960 1.352622 ACACTGCCCCTCCTTCAACA 61.353 55.000 0.00 0.00 0.00 3.33
1752 1968 1.137513 CCTCCTTCAACACGTCGTTC 58.862 55.000 0.00 0.00 34.86 3.95
1801 2017 4.543590 TGCTTATTCTGGATAGCTAGCC 57.456 45.455 21.41 21.41 0.00 3.93
1819 2035 5.450965 GCTAGCCACAGCAAACAATTATGAT 60.451 40.000 2.29 0.00 43.56 2.45
2105 2348 9.740239 ATTTCATCTGCATATGTGTGAATTAAC 57.260 29.630 11.42 0.00 0.00 2.01
2246 2490 5.799827 TTGGGCATTAAGCTAAAACACTT 57.200 34.783 0.00 0.00 44.79 3.16
2412 2683 5.683681 TCATGTAGCTCTCCATTAATTGCA 58.316 37.500 0.00 0.00 0.00 4.08
3146 3607 5.807011 TCTTCTGATGATGTATGTCAACACG 59.193 40.000 0.00 0.00 31.94 4.49
3178 3644 4.388485 TCTGATGTTGTGCTGTGTTATGT 58.612 39.130 0.00 0.00 0.00 2.29
3429 3897 6.484288 TCATGTGATCATTCCCTTTGTAGTT 58.516 36.000 0.00 0.00 31.15 2.24
4007 5450 4.871933 TGAGTTCTGTGCTGAGATTACA 57.128 40.909 0.00 0.00 0.00 2.41
4268 5770 2.159028 GCCTTGCAAACACCTTTGGTAA 60.159 45.455 0.00 0.00 37.78 2.85
4348 5856 8.738645 ATAAATCCAATAGTTCCACTGAAGAC 57.261 34.615 0.00 0.00 0.00 3.01
4853 6417 4.496507 GCTGGCAGCAATAGTAAAGCTAAC 60.497 45.833 33.33 0.00 41.89 2.34
4990 6554 6.985188 TGCTATCCAAAGTTTGATGTAGTC 57.015 37.500 17.33 11.11 0.00 2.59
5077 6641 2.692557 TGCTGTTAAAGAAAGCTTGGCA 59.307 40.909 0.00 0.00 37.82 4.92
5100 6664 4.263905 ACAAGAATTAGGGCTGACATTCCA 60.264 41.667 0.00 0.00 0.00 3.53
5429 7030 5.601313 AGCTATACTAAAACCTCGGGATTGA 59.399 40.000 0.00 0.00 0.00 2.57
5532 7133 2.699321 CTGCAGAGGATCAGATTCTGGA 59.301 50.000 8.42 9.32 38.94 3.86
5676 7277 7.615039 ACTCTGAGGATGATGACTATGATTT 57.385 36.000 9.85 0.00 0.00 2.17
6366 7986 2.649190 TGTTTGCCTTGCTGTCAACTA 58.351 42.857 0.00 0.00 0.00 2.24
6926 8568 5.468746 TGTGTGTTTCACTAGCTTATGAACC 59.531 40.000 10.89 6.15 46.27 3.62
6928 8570 6.204882 GTGTGTTTCACTAGCTTATGAACCTT 59.795 38.462 10.89 0.00 43.13 3.50
6954 8596 6.888632 ACATATTTCCTCTTCATGCTGAAACT 59.111 34.615 0.00 0.00 35.73 2.66
7037 8679 1.338020 GGCACACCTGAAAAGGACAAG 59.662 52.381 0.00 0.00 0.00 3.16
7064 8706 5.921962 AAGAAAGTGAAGCAGGTTCTTTT 57.078 34.783 13.45 12.81 35.53 2.27
7233 8907 5.579511 CAGGTACTATGGTTTAACAGAACGG 59.420 44.000 0.00 0.00 36.02 4.44
7541 9412 6.595326 TCACATAAGAGTAGCATCCAACAAAG 59.405 38.462 0.00 0.00 0.00 2.77
7561 9433 0.593128 GCAGCACTCACGTGGAAAAT 59.407 50.000 17.00 0.00 41.51 1.82
7604 9488 5.747197 CCTAATGAATGCAAAAGTGATGCTC 59.253 40.000 0.00 0.00 44.14 4.26
7689 9573 0.539438 GACATTGGTGGTGGGCTGAA 60.539 55.000 0.00 0.00 0.00 3.02
7799 10067 4.287067 TGAAGAATACCTCCTCAAGCAGTT 59.713 41.667 0.00 0.00 0.00 3.16
7936 10373 6.268825 TGACGTTTCTAGCTAATGACTCTT 57.731 37.500 0.00 0.00 0.00 2.85
7937 10374 6.688578 TGACGTTTCTAGCTAATGACTCTTT 58.311 36.000 0.00 0.00 0.00 2.52
8029 10466 1.628340 CATGGTGGGTGTCTTACTCCA 59.372 52.381 1.07 0.00 33.60 3.86
8128 10653 3.423154 CTTGGAAGTGCCGTCGCC 61.423 66.667 0.00 0.00 40.66 5.54
8164 10689 2.373169 TGGCAGAGAATGGAAGACACTT 59.627 45.455 0.00 0.00 0.00 3.16
8173 10698 8.787852 AGAGAATGGAAGACACTTAACATTTTC 58.212 33.333 15.49 15.49 32.72 2.29
8182 10721 2.029380 ACTTAACATTTTCGCCTTGGGC 60.029 45.455 0.00 0.00 46.75 5.36
8260 10822 6.795098 TGTGTACATTGTTGATAAGTGACC 57.205 37.500 0.00 0.00 0.00 4.02
8334 10909 4.850680 TGGTACATGTTGTAATCTTCCCC 58.149 43.478 2.30 0.00 34.21 4.81
8340 10915 5.245977 ACATGTTGTAATCTTCCCCTTTTGG 59.754 40.000 0.00 0.00 39.97 3.28
8341 10916 4.810345 TGTTGTAATCTTCCCCTTTTGGT 58.190 39.130 0.00 0.00 38.10 3.67
8482 11061 2.285977 GGACGCCTTACCCAATACTTG 58.714 52.381 0.00 0.00 0.00 3.16
8507 11086 7.177744 TGCATGATATATGCCTGTTGAATCATT 59.822 33.333 9.15 0.00 43.94 2.57
8554 11133 7.604164 TCTTCTTCTTGTTGGTATTCTGATGAC 59.396 37.037 0.00 0.00 0.00 3.06
8572 11151 0.039326 ACTACAGTAGGACACCGCCT 59.961 55.000 12.42 0.00 42.15 5.52
8578 11157 2.756760 CAGTAGGACACCGCCTAGTTTA 59.243 50.000 0.00 0.00 41.23 2.01
8582 11161 4.089408 AGGACACCGCCTAGTTTAAAAA 57.911 40.909 0.00 0.00 36.22 1.94
8588 11167 4.621034 CACCGCCTAGTTTAAAAAGCATTG 59.379 41.667 0.00 0.00 0.00 2.82
8807 11388 3.426159 CCTTTCCGATTGTCCAATGTTCG 60.426 47.826 0.00 0.00 0.00 3.95
8834 11416 1.294857 GATGCTTTCTTCCTCTCGGC 58.705 55.000 0.00 0.00 0.00 5.54
8887 11469 1.668151 GTGAGTCCCGCTCCACAAC 60.668 63.158 0.00 0.00 43.48 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.633299 CGCGAAATCTAGCTTGAATGC 58.367 47.619 0.00 3.46 0.00 3.56
104 105 0.944386 CAACCACGACTCAAACCCAG 59.056 55.000 0.00 0.00 0.00 4.45
121 122 1.573829 GAATCACGAAGCCCGCACAA 61.574 55.000 0.00 0.00 43.32 3.33
177 178 0.323629 CACGCCCCCTCTTCTAAACA 59.676 55.000 0.00 0.00 0.00 2.83
236 237 0.387202 CAGATACAGAGCCCCGACTG 59.613 60.000 0.00 0.00 39.65 3.51
311 313 0.696501 TCTCTGTTTACCCAAGGGCC 59.303 55.000 4.70 0.00 39.32 5.80
324 326 3.244215 TGAAATCAGCCGAACTTCTCTGT 60.244 43.478 7.41 0.00 0.00 3.41
327 329 3.748568 AGTTGAAATCAGCCGAACTTCTC 59.251 43.478 0.00 0.00 0.00 2.87
358 360 2.681706 ACTTGAACAGCTCATCTCACG 58.318 47.619 0.00 0.00 32.78 4.35
367 369 2.546795 CCGTCTCAGAACTTGAACAGCT 60.547 50.000 0.00 0.00 34.81 4.24
645 649 3.331150 AGCACATTGTTGCAATGAATGG 58.669 40.909 25.84 19.08 45.62 3.16
1121 1311 1.541379 ATTTTTCCTTTCCCCCGACG 58.459 50.000 0.00 0.00 0.00 5.12
1295 1485 2.564721 GGTGGCTTCTTTGCGGCTT 61.565 57.895 0.00 0.00 0.00 4.35
1577 1778 8.171400 TGGAAGGGGTAATAACAAATGAAACTA 58.829 33.333 0.00 0.00 0.00 2.24
1729 1945 2.391724 GACGTGTTGAAGGAGGGGCA 62.392 60.000 0.00 0.00 0.00 5.36
1744 1960 1.019278 GCATGGATGTGGAACGACGT 61.019 55.000 0.00 0.00 42.39 4.34
1752 1968 1.065109 CATGCACGCATGGATGTGG 59.935 57.895 21.68 0.00 46.58 4.17
1801 2017 6.529125 GTCCAGAATCATAATTGTTTGCTGTG 59.471 38.462 0.00 0.00 0.00 3.66
1819 2035 0.251253 TGCATGCATGGTGTCCAGAA 60.251 50.000 27.34 0.00 36.75 3.02
2001 2217 2.503895 AAAGTGAATGCTCCCTCCAG 57.496 50.000 0.00 0.00 0.00 3.86
2143 2386 7.012044 GTGCCGGTTCAGAATTATTACACTAAT 59.988 37.037 1.90 0.00 0.00 1.73
2254 2499 7.946207 TGCACATTAAATAGGAAAGACAAACA 58.054 30.769 0.00 0.00 0.00 2.83
2412 2683 2.982488 AGGGACCAAAGAGACTCACATT 59.018 45.455 5.02 0.00 0.00 2.71
3146 3607 6.311200 ACAGCACAACATCAGAAAAGAAAAAC 59.689 34.615 0.00 0.00 0.00 2.43
3178 3644 8.538701 AGCATGGTCAATGATTAAAATGGTAAA 58.461 29.630 0.00 0.00 38.72 2.01
3194 3660 2.945440 GCAAGATGGGTAGCATGGTCAA 60.945 50.000 0.00 0.00 0.00 3.18
3429 3897 1.062581 CATCCTTCCTCTCCCTCAGGA 60.063 57.143 0.00 0.00 41.08 3.86
4007 5450 9.274206 GAAACTTCATCCTTACTACAAGACTTT 57.726 33.333 0.00 0.00 0.00 2.66
4580 6105 6.617879 GGTTCATAACCCAGTAAAACACATC 58.382 40.000 0.00 0.00 46.12 3.06
4831 6395 4.635765 TGTTAGCTTTACTATTGCTGCCAG 59.364 41.667 0.00 0.00 37.62 4.85
4832 6396 4.584874 TGTTAGCTTTACTATTGCTGCCA 58.415 39.130 0.00 0.00 37.62 4.92
4943 6507 5.121262 TGCAAATTGGCTAAGCTTGTGCT 62.121 43.478 20.37 4.19 42.60 4.40
4945 6509 3.029320 TGCAAATTGGCTAAGCTTGTG 57.971 42.857 9.86 2.92 34.04 3.33
4990 6554 3.914364 GCAAGAAAAATGAGGTGTAAGCG 59.086 43.478 0.00 0.00 40.95 4.68
5077 6641 4.263905 TGGAATGTCAGCCCTAATTCTTGT 60.264 41.667 0.00 0.00 31.20 3.16
5100 6664 5.147330 TGACAAAGACATACGAACCTGAT 57.853 39.130 0.00 0.00 0.00 2.90
5429 7030 4.327680 GACTCACTTTTTGGACAGCCTAT 58.672 43.478 0.00 0.00 34.31 2.57
5532 7133 4.100373 ACCTTCATCTTCAGGTTCTAGCT 58.900 43.478 0.00 0.00 40.85 3.32
5557 7158 5.006386 ACAAAATTCAGGTCATCAGAGTCC 58.994 41.667 0.00 0.00 0.00 3.85
5624 7225 6.125029 CAGAAGGTAATCCAAGGTCATCAAT 58.875 40.000 0.00 0.00 35.89 2.57
5676 7277 6.907741 TGCATCATTTCAATAACTTCGTCAA 58.092 32.000 0.00 0.00 0.00 3.18
6366 7986 7.979786 TCTGAATAAAGTAATCACTCTCCCT 57.020 36.000 0.00 0.00 32.29 4.20
6544 8169 5.482163 AGAGAAAGAGAGAAGGTGGAAAG 57.518 43.478 0.00 0.00 0.00 2.62
6954 8596 2.897271 TTCCCATAAGCCTGCTTTCA 57.103 45.000 10.01 0.00 37.47 2.69
7037 8679 2.959030 ACCTGCTTCACTTTCTTTTCCC 59.041 45.455 0.00 0.00 0.00 3.97
7064 8706 1.812235 ATTCATTGCTCTGACGCACA 58.188 45.000 2.05 0.00 40.09 4.57
7233 8907 6.412214 TCTTACTGGTTAAGCCTGTTTATCC 58.588 40.000 1.51 0.00 45.59 2.59
7477 9348 3.821033 ACCATTTCTCAACCTGTTAGCAC 59.179 43.478 0.00 0.00 0.00 4.40
7561 9433 3.387962 AGGATTCTCCTTGGTGCTATGA 58.612 45.455 0.00 0.00 46.91 2.15
7587 9471 4.859304 TTCAGAGCATCACTTTTGCATT 57.141 36.364 0.00 0.00 42.62 3.56
7604 9488 2.332104 CGATGGCGTATCCTCATTCAG 58.668 52.381 0.00 0.00 35.26 3.02
7689 9573 1.412079 TGGAGTGCTGGCATTTGTTT 58.588 45.000 0.00 0.00 0.00 2.83
7936 10373 1.452145 GGCCCGACTTGCAAGTTCAA 61.452 55.000 31.58 0.00 39.88 2.69
7937 10374 1.896660 GGCCCGACTTGCAAGTTCA 60.897 57.895 31.58 0.00 39.88 3.18
7968 10405 7.961827 CAGAGAAAGAATTAGTTGACTTGCATC 59.038 37.037 0.00 0.00 0.00 3.91
7969 10406 7.663081 TCAGAGAAAGAATTAGTTGACTTGCAT 59.337 33.333 0.00 0.00 0.00 3.96
8039 10478 3.119566 GGGAGTCCCATATATCGAACGAC 60.120 52.174 24.35 0.00 44.65 4.34
8041 10480 2.159421 CGGGAGTCCCATATATCGAACG 60.159 54.545 28.08 5.36 45.83 3.95
8128 10653 1.020861 TGCCATAGAAGTGCGCTGTG 61.021 55.000 9.73 0.00 0.00 3.66
8182 10721 4.553547 GCATAATTTAAGGAGACAGCAGCG 60.554 45.833 0.00 0.00 0.00 5.18
8260 10822 5.985530 TCATATGAACGATAAGCTGAACCTG 59.014 40.000 1.98 0.00 0.00 4.00
8290 10860 2.365617 ACGAGATCCACTGACACTGTTT 59.634 45.455 0.00 0.00 0.00 2.83
8334 10909 9.787532 CAGTACAACATATATTTCCACCAAAAG 57.212 33.333 0.00 0.00 0.00 2.27
8340 10915 8.181573 CACCAACAGTACAACATATATTTCCAC 58.818 37.037 0.00 0.00 0.00 4.02
8341 10916 8.103935 TCACCAACAGTACAACATATATTTCCA 58.896 33.333 0.00 0.00 0.00 3.53
8482 11061 6.505044 TGATTCAACAGGCATATATCATGC 57.495 37.500 0.55 0.55 43.85 4.06
8532 11111 7.819415 TGTAGTCATCAGAATACCAACAAGAAG 59.181 37.037 0.00 0.00 42.92 2.85
8546 11125 4.270834 GGTGTCCTACTGTAGTCATCAGA 58.729 47.826 13.42 0.27 36.81 3.27
8554 11133 1.948145 CTAGGCGGTGTCCTACTGTAG 59.052 57.143 7.87 7.87 37.99 2.74
8582 11161 9.768662 AAACTTTTGTAAGATCATTTCAATGCT 57.231 25.926 0.00 0.00 34.61 3.79
8611 11190 7.503492 CCCCCTTTTCCTTTATAAAATGGAA 57.497 36.000 12.61 12.61 43.53 3.53
8807 11388 2.003301 GGAAGAAAGCATCGTCACTCC 58.997 52.381 7.52 0.00 38.18 3.85
8834 11416 3.343941 TGACAAAAGGGGAATAGGTCG 57.656 47.619 0.00 0.00 0.00 4.79
8887 11469 2.484264 GGAATTCCGTGTCTTGTGAAGG 59.516 50.000 9.17 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.