Multiple sequence alignment - TraesCS1A01G144700

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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 TraesCS1A01G144700 chr1A 100.000 5155 0 0 1 5155 250549882 250555036 0.000000e+00 9520.0
1 TraesCS1A01G144700 chr1A 95.367 259 11 1 1 259 30569839 30569582 1.340000e-110 411.0
2 TraesCS1A01G144700 chr1A 96.970 66 2 0 3634 3699 250553451 250553516 1.520000e-20 111.0
3 TraesCS1A01G144700 chr1A 96.970 66 2 0 3570 3635 250553515 250553580 1.520000e-20 111.0
4 TraesCS1A01G144700 chr1B 94.556 3233 99 20 460 3635 279772969 279776181 0.000000e+00 4924.0
5 TraesCS1A01G144700 chr1B 99.154 591 5 0 3634 4224 279776116 279776706 0.000000e+00 1064.0
6 TraesCS1A01G144700 chr1B 93.448 580 25 9 4219 4793 279776762 279777333 0.000000e+00 848.0
7 TraesCS1A01G144700 chr1B 91.419 303 24 2 4799 5100 279777375 279777676 1.030000e-111 414.0
8 TraesCS1A01G144700 chr1D 96.281 1452 41 6 2085 3534 199363113 199364553 0.000000e+00 2370.0
9 TraesCS1A01G144700 chr1D 94.972 1233 29 9 281 1509 199360894 199362097 0.000000e+00 1903.0
10 TraesCS1A01G144700 chr1D 98.433 638 9 1 3538 4175 199364599 199365235 0.000000e+00 1122.0
11 TraesCS1A01G144700 chr1D 92.823 627 33 9 4171 4793 199365409 199366027 0.000000e+00 898.0
12 TraesCS1A01G144700 chr1D 91.317 357 27 2 4799 5155 199366069 199366421 7.760000e-133 484.0
13 TraesCS1A01G144700 chr1D 87.470 423 13 13 1510 1894 199362124 199362544 7.870000e-123 451.0
14 TraesCS1A01G144700 chr1D 91.071 168 4 3 1891 2049 199362595 199362760 3.130000e-52 217.0
15 TraesCS1A01G144700 chr1D 98.485 66 1 0 3634 3699 199364631 199364696 3.260000e-22 117.0
16 TraesCS1A01G144700 chr1D 95.455 66 3 0 3570 3635 199364695 199364760 7.060000e-19 106.0
17 TraesCS1A01G144700 chr3A 95.200 250 12 0 1 250 691401152 691400903 3.740000e-106 396.0
18 TraesCS1A01G144700 chr3A 94.400 250 14 0 1 250 637478399 637478648 8.100000e-103 385.0
19 TraesCS1A01G144700 chr3A 93.651 252 16 0 1 252 690219938 690219687 1.350000e-100 377.0
20 TraesCS1A01G144700 chr3A 93.701 254 13 3 1 252 726836952 726837204 1.350000e-100 377.0
21 TraesCS1A01G144700 chr3A 97.143 35 0 1 246 280 106621917 106621884 2.000000e-04 58.4
22 TraesCS1A01G144700 chr6A 94.400 250 14 0 1 250 588365416 588365665 8.100000e-103 385.0
23 TraesCS1A01G144700 chr6A 91.304 46 3 1 4478 4523 93932305 93932261 1.550000e-05 62.1
24 TraesCS1A01G144700 chr4A 94.422 251 12 1 1 251 556629182 556629430 8.100000e-103 385.0
25 TraesCS1A01G144700 chr4A 93.651 252 16 0 1 252 548568926 548568675 1.350000e-100 377.0
26 TraesCS1A01G144700 chr2D 93.651 252 16 0 1 252 343158292 343158041 1.350000e-100 377.0
27 TraesCS1A01G144700 chr5B 94.872 39 1 1 242 280 316157159 316157122 5.570000e-05 60.2
28 TraesCS1A01G144700 chr4B 91.111 45 3 1 243 287 122557425 122557468 5.570000e-05 60.2
29 TraesCS1A01G144700 chr2B 94.737 38 1 1 243 280 790587749 790587785 2.000000e-04 58.4


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 TraesCS1A01G144700 chr1A 250549882 250555036 5154 False 3247.333333 9520 97.980000 1 5155 3 chr1A.!!$F1 5154
1 TraesCS1A01G144700 chr1B 279772969 279777676 4707 False 1812.500000 4924 94.644250 460 5100 4 chr1B.!!$F1 4640
2 TraesCS1A01G144700 chr1D 199360894 199366421 5527 False 852.000000 2370 94.034111 281 5155 9 chr1D.!!$F1 4874


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
251 252 0.037590 TGCGGGGCATTGTCTAGTTT 59.962 50.000 0.0 0.0 31.71 2.66 F
252 253 0.451783 GCGGGGCATTGTCTAGTTTG 59.548 55.000 0.0 0.0 0.00 2.93 F
964 967 0.454452 TCGTTCATCGCTCACTCACG 60.454 55.000 0.0 0.0 39.67 4.35 F
1448 1459 0.380378 TGACAAACTTCTTGTGGCGC 59.620 50.000 0.0 0.0 31.96 6.53 F
1918 2077 2.698274 GTTTGGTTCCTTGTGGTGGAAT 59.302 45.455 0.0 0.0 44.27 3.01 F
2473 2959 1.611519 TTAACCGAGGCCCAACAAAG 58.388 50.000 0.0 0.0 0.00 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1296 1303 0.378257 ACGAATCACGCATGCCATTC 59.622 50.000 13.15 15.3 46.94 2.67 R
1309 1320 0.857311 CATCGCGCAAACCACGAATC 60.857 55.000 8.75 0.0 39.56 2.52 R
2359 2844 1.066143 ACCTAGCGTTGACCTGATTGG 60.066 52.381 0.00 0.0 42.93 3.16 R
2382 2867 1.442769 GTGACGTGAACATGAGGCAT 58.557 50.000 0.00 0.0 0.00 4.40 R
3466 3972 1.450531 GCAAATCCTCGGGCATCCAG 61.451 60.000 0.00 0.0 0.00 3.86 R
4417 5205 1.605710 GCATTGAGCTACCAATCGCAT 59.394 47.619 13.04 0.0 41.15 4.73 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 8.937634 ATGCATTAGAAAAGATCCATTTCAAC 57.062 30.769 18.57 7.72 38.86 3.18
26 27 7.894708 TGCATTAGAAAAGATCCATTTCAACA 58.105 30.769 18.57 9.45 38.86 3.33
27 28 8.533657 TGCATTAGAAAAGATCCATTTCAACAT 58.466 29.630 18.57 8.39 38.86 2.71
28 29 9.028185 GCATTAGAAAAGATCCATTTCAACATC 57.972 33.333 18.57 6.14 38.86 3.06
29 30 9.525409 CATTAGAAAAGATCCATTTCAACATCC 57.475 33.333 18.57 0.00 38.86 3.51
30 31 8.648698 TTAGAAAAGATCCATTTCAACATCCA 57.351 30.769 18.57 0.00 38.86 3.41
31 32 7.543359 AGAAAAGATCCATTTCAACATCCAA 57.457 32.000 18.57 0.00 38.86 3.53
32 33 8.142485 AGAAAAGATCCATTTCAACATCCAAT 57.858 30.769 18.57 0.00 38.86 3.16
33 34 8.038944 AGAAAAGATCCATTTCAACATCCAATG 58.961 33.333 18.57 0.00 38.86 2.82
34 35 7.484993 AAAGATCCATTTCAACATCCAATGA 57.515 32.000 0.00 0.00 30.66 2.57
35 36 6.710597 AGATCCATTTCAACATCCAATGAG 57.289 37.500 0.00 0.00 30.66 2.90
36 37 6.192773 AGATCCATTTCAACATCCAATGAGT 58.807 36.000 0.00 0.00 30.66 3.41
37 38 5.902613 TCCATTTCAACATCCAATGAGTC 57.097 39.130 0.00 0.00 30.66 3.36
38 39 5.323581 TCCATTTCAACATCCAATGAGTCA 58.676 37.500 0.00 0.00 30.66 3.41
39 40 5.953548 TCCATTTCAACATCCAATGAGTCAT 59.046 36.000 0.00 0.00 30.66 3.06
40 41 7.118060 TCCATTTCAACATCCAATGAGTCATA 58.882 34.615 5.94 0.00 30.66 2.15
41 42 7.614974 TCCATTTCAACATCCAATGAGTCATAA 59.385 33.333 5.94 0.00 30.66 1.90
42 43 7.919091 CCATTTCAACATCCAATGAGTCATAAG 59.081 37.037 5.94 2.30 30.66 1.73
43 44 8.680001 CATTTCAACATCCAATGAGTCATAAGA 58.320 33.333 5.94 6.76 30.66 2.10
44 45 8.634335 TTTCAACATCCAATGAGTCATAAGAA 57.366 30.769 5.94 0.23 0.00 2.52
45 46 8.634335 TTCAACATCCAATGAGTCATAAGAAA 57.366 30.769 5.94 0.00 0.00 2.52
46 47 8.634335 TCAACATCCAATGAGTCATAAGAAAA 57.366 30.769 5.94 0.00 0.00 2.29
47 48 8.733458 TCAACATCCAATGAGTCATAAGAAAAG 58.267 33.333 5.94 4.22 0.00 2.27
48 49 8.733458 CAACATCCAATGAGTCATAAGAAAAGA 58.267 33.333 5.94 0.00 0.00 2.52
49 50 9.471702 AACATCCAATGAGTCATAAGAAAAGAT 57.528 29.630 5.94 0.00 0.00 2.40
50 51 9.471702 ACATCCAATGAGTCATAAGAAAAGATT 57.528 29.630 5.94 0.00 0.00 2.40
51 52 9.947669 CATCCAATGAGTCATAAGAAAAGATTC 57.052 33.333 5.94 0.00 35.70 2.52
52 53 9.690913 ATCCAATGAGTCATAAGAAAAGATTCA 57.309 29.630 5.94 0.00 38.06 2.57
53 54 8.950210 TCCAATGAGTCATAAGAAAAGATTCAC 58.050 33.333 5.94 0.00 38.06 3.18
54 55 8.954350 CCAATGAGTCATAAGAAAAGATTCACT 58.046 33.333 5.94 0.00 38.06 3.41
57 58 9.730705 ATGAGTCATAAGAAAAGATTCACTTCA 57.269 29.630 3.05 0.00 37.93 3.02
58 59 9.559732 TGAGTCATAAGAAAAGATTCACTTCAA 57.440 29.630 0.00 0.00 37.93 2.69
59 60 9.818796 GAGTCATAAGAAAAGATTCACTTCAAC 57.181 33.333 0.00 0.00 37.93 3.18
60 61 9.342308 AGTCATAAGAAAAGATTCACTTCAACA 57.658 29.630 0.00 0.00 37.93 3.33
63 64 8.857216 CATAAGAAAAGATTCACTTCAACATGC 58.143 33.333 0.00 0.00 37.93 4.06
64 65 6.395426 AGAAAAGATTCACTTCAACATGCA 57.605 33.333 0.00 0.00 37.93 3.96
65 66 6.808829 AGAAAAGATTCACTTCAACATGCAA 58.191 32.000 0.00 0.00 37.93 4.08
66 67 7.267128 AGAAAAGATTCACTTCAACATGCAAA 58.733 30.769 0.00 0.00 37.93 3.68
67 68 6.833342 AAAGATTCACTTCAACATGCAAAC 57.167 33.333 0.00 0.00 37.93 2.93
68 69 5.518848 AGATTCACTTCAACATGCAAACA 57.481 34.783 0.00 0.00 0.00 2.83
69 70 6.092955 AGATTCACTTCAACATGCAAACAT 57.907 33.333 0.00 0.00 36.79 2.71
70 71 6.422701 AAGATTCACTTCAACATGCAAACATG 59.577 34.615 4.55 4.55 46.05 3.21
71 72 8.894473 AAGATTCACTTCAACATGCAAACATGC 61.894 37.037 5.97 0.00 45.24 4.06
225 226 8.908903 AGAAATGTATTACAAAATATTCCCGCA 58.091 29.630 0.00 0.00 30.42 5.69
226 227 9.522804 GAAATGTATTACAAAATATTCCCGCAA 57.477 29.630 0.00 0.00 30.42 4.85
227 228 8.865590 AATGTATTACAAAATATTCCCGCAAC 57.134 30.769 0.00 0.00 30.42 4.17
228 229 7.392494 TGTATTACAAAATATTCCCGCAACA 57.608 32.000 0.00 0.00 30.42 3.33
229 230 7.827701 TGTATTACAAAATATTCCCGCAACAA 58.172 30.769 0.00 0.00 30.42 2.83
230 231 7.755822 TGTATTACAAAATATTCCCGCAACAAC 59.244 33.333 0.00 0.00 30.42 3.32
231 232 3.570559 ACAAAATATTCCCGCAACAACG 58.429 40.909 0.00 0.00 0.00 4.10
232 233 3.004944 ACAAAATATTCCCGCAACAACGT 59.995 39.130 0.00 0.00 0.00 3.99
233 234 2.911819 AATATTCCCGCAACAACGTG 57.088 45.000 0.00 0.00 0.00 4.49
234 235 0.450184 ATATTCCCGCAACAACGTGC 59.550 50.000 0.00 0.00 41.32 5.34
241 242 3.669344 CAACAACGTGCGGGGCAT 61.669 61.111 0.00 0.00 41.91 4.40
242 243 2.909965 AACAACGTGCGGGGCATT 60.910 55.556 0.00 0.00 41.91 3.56
243 244 3.206211 AACAACGTGCGGGGCATTG 62.206 57.895 0.00 0.00 41.91 2.82
244 245 3.669344 CAACGTGCGGGGCATTGT 61.669 61.111 0.00 0.00 41.91 2.71
245 246 3.361977 AACGTGCGGGGCATTGTC 61.362 61.111 0.00 0.00 41.91 3.18
246 247 3.842925 AACGTGCGGGGCATTGTCT 62.843 57.895 0.00 0.00 41.91 3.41
247 248 2.125310 CGTGCGGGGCATTGTCTA 60.125 61.111 0.00 0.00 41.91 2.59
248 249 2.173669 CGTGCGGGGCATTGTCTAG 61.174 63.158 0.00 0.00 41.91 2.43
249 250 1.078426 GTGCGGGGCATTGTCTAGT 60.078 57.895 0.00 0.00 41.91 2.57
250 251 0.676782 GTGCGGGGCATTGTCTAGTT 60.677 55.000 0.00 0.00 41.91 2.24
251 252 0.037590 TGCGGGGCATTGTCTAGTTT 59.962 50.000 0.00 0.00 31.71 2.66
252 253 0.451783 GCGGGGCATTGTCTAGTTTG 59.548 55.000 0.00 0.00 0.00 2.93
253 254 1.094785 CGGGGCATTGTCTAGTTTGG 58.905 55.000 0.00 0.00 0.00 3.28
254 255 1.339631 CGGGGCATTGTCTAGTTTGGA 60.340 52.381 0.00 0.00 0.00 3.53
255 256 2.369394 GGGGCATTGTCTAGTTTGGAG 58.631 52.381 0.00 0.00 0.00 3.86
256 257 2.026262 GGGGCATTGTCTAGTTTGGAGA 60.026 50.000 0.00 0.00 0.00 3.71
257 258 3.561313 GGGGCATTGTCTAGTTTGGAGAA 60.561 47.826 0.00 0.00 0.00 2.87
258 259 3.691609 GGGCATTGTCTAGTTTGGAGAAG 59.308 47.826 0.00 0.00 0.00 2.85
259 260 4.327680 GGCATTGTCTAGTTTGGAGAAGT 58.672 43.478 0.00 0.00 0.00 3.01
260 261 4.762251 GGCATTGTCTAGTTTGGAGAAGTT 59.238 41.667 0.00 0.00 0.00 2.66
261 262 5.335191 GGCATTGTCTAGTTTGGAGAAGTTG 60.335 44.000 0.00 0.00 0.00 3.16
262 263 5.335191 GCATTGTCTAGTTTGGAGAAGTTGG 60.335 44.000 0.00 0.00 0.00 3.77
263 264 5.623956 TTGTCTAGTTTGGAGAAGTTGGA 57.376 39.130 0.00 0.00 0.00 3.53
264 265 4.957296 TGTCTAGTTTGGAGAAGTTGGAC 58.043 43.478 0.00 0.00 0.00 4.02
265 266 4.407621 TGTCTAGTTTGGAGAAGTTGGACA 59.592 41.667 0.00 0.00 0.00 4.02
266 267 5.104693 TGTCTAGTTTGGAGAAGTTGGACAA 60.105 40.000 0.00 0.00 0.00 3.18
267 268 5.236695 GTCTAGTTTGGAGAAGTTGGACAAC 59.763 44.000 7.08 7.08 41.45 3.32
268 269 3.963129 AGTTTGGAGAAGTTGGACAACA 58.037 40.909 16.58 0.00 43.47 3.33
269 270 4.536765 AGTTTGGAGAAGTTGGACAACAT 58.463 39.130 16.58 5.31 43.47 2.71
270 271 4.580580 AGTTTGGAGAAGTTGGACAACATC 59.419 41.667 16.58 13.85 43.47 3.06
278 279 3.884900 GGACAACATCCGAACGGG 58.115 61.111 13.29 0.91 37.88 5.28
279 280 1.743995 GGACAACATCCGAACGGGG 60.744 63.158 13.29 8.55 37.88 5.73
291 292 5.350504 TCCGAACGGGGTGTAAATATAAA 57.649 39.130 13.29 0.00 36.01 1.40
297 298 8.829612 CGAACGGGGTGTAAATATAAATAGTTT 58.170 33.333 0.00 0.00 0.00 2.66
446 447 3.383825 GGGGTACGATAAAAGAGCTCTGA 59.616 47.826 19.06 6.34 0.00 3.27
471 472 2.270986 GCCCGAATGGATCCATGGC 61.271 63.158 29.14 29.14 36.39 4.40
559 560 5.590530 TGCTCTAGAAGAATCTTGGAGTC 57.409 43.478 0.00 3.40 37.01 3.36
621 623 5.382618 AGTTAAGCTTTTGGCATGAAGAG 57.617 39.130 3.20 0.00 44.79 2.85
655 658 3.131709 ACAACCATCCTGACTTGTGAG 57.868 47.619 0.00 0.00 0.00 3.51
656 659 2.439507 ACAACCATCCTGACTTGTGAGT 59.560 45.455 0.00 0.00 39.32 3.41
657 660 3.117888 ACAACCATCCTGACTTGTGAGTT 60.118 43.478 0.00 0.00 35.88 3.01
658 661 3.131709 ACCATCCTGACTTGTGAGTTG 57.868 47.619 0.00 0.00 35.88 3.16
659 662 2.439507 ACCATCCTGACTTGTGAGTTGT 59.560 45.455 0.00 0.00 35.88 3.32
660 663 2.810274 CCATCCTGACTTGTGAGTTGTG 59.190 50.000 0.00 0.00 35.88 3.33
661 664 3.494924 CCATCCTGACTTGTGAGTTGTGA 60.495 47.826 0.00 0.00 35.88 3.58
774 777 2.666526 GCTAGCCGCCACATAGCC 60.667 66.667 2.29 0.00 36.70 3.93
964 967 0.454452 TCGTTCATCGCTCACTCACG 60.454 55.000 0.00 0.00 39.67 4.35
965 968 1.704582 GTTCATCGCTCACTCACGC 59.295 57.895 0.00 0.00 0.00 5.34
966 969 1.008875 GTTCATCGCTCACTCACGCA 61.009 55.000 0.00 0.00 0.00 5.24
967 970 1.008875 TTCATCGCTCACTCACGCAC 61.009 55.000 0.00 0.00 0.00 5.34
1296 1303 3.518998 GCCATCTGCTGCAGCCTG 61.519 66.667 34.64 26.38 41.18 4.85
1394 1405 5.180680 GGGTTTCAGACTTTGTGTGGTATAC 59.819 44.000 0.00 0.00 0.00 1.47
1440 1451 6.091437 GCGTAGTAGTATGTGACAAACTTCT 58.909 40.000 0.00 0.00 31.21 2.85
1447 1458 1.400142 TGTGACAAACTTCTTGTGGCG 59.600 47.619 0.00 0.00 31.96 5.69
1448 1459 0.380378 TGACAAACTTCTTGTGGCGC 59.620 50.000 0.00 0.00 31.96 6.53
1501 1512 4.615949 ACGTTCACATGCTGCAAAAATAA 58.384 34.783 6.36 0.00 0.00 1.40
1508 1545 8.909708 TCACATGCTGCAAAAATAAATAGTAC 57.090 30.769 6.36 0.00 0.00 2.73
1569 1609 6.998074 TCTCAGAAATAGTTGCTTGGAAGAAA 59.002 34.615 0.00 0.00 0.00 2.52
1570 1610 7.502226 TCTCAGAAATAGTTGCTTGGAAGAAAA 59.498 33.333 0.00 0.00 0.00 2.29
1658 1725 9.173939 GATTCTCAGTGTGATGTTTTAGTTTTG 57.826 33.333 0.00 0.00 0.00 2.44
1839 1941 4.770351 AACACAAAAGCATTGCGTTTAC 57.230 36.364 19.65 0.00 38.06 2.01
1843 1945 5.401079 ACACAAAAGCATTGCGTTTACATAC 59.599 36.000 19.65 0.00 38.06 2.39
1918 2077 2.698274 GTTTGGTTCCTTGTGGTGGAAT 59.302 45.455 0.00 0.00 44.27 3.01
2359 2844 3.211045 TGGCTACCGATGAAAATAAGGC 58.789 45.455 0.00 0.00 0.00 4.35
2382 2867 4.250464 CAATCAGGTCAACGCTAGGTAAA 58.750 43.478 0.00 0.00 0.00 2.01
2460 2945 7.065803 CCCTCCATTAGCATATGTAATTAACCG 59.934 40.741 4.29 0.00 0.00 4.44
2473 2959 1.611519 TTAACCGAGGCCCAACAAAG 58.388 50.000 0.00 0.00 0.00 2.77
2957 3444 4.085357 TCTTTTGCTCCATACAGTGTGT 57.915 40.909 5.88 0.00 0.00 3.72
3210 3700 7.495901 TCCTTTTGCATGTTTTGAAGTATGAA 58.504 30.769 0.00 0.00 0.00 2.57
3279 3785 4.201724 CCGCATAACTGACTTGCTAGTTTC 60.202 45.833 1.43 0.00 38.11 2.78
3466 3972 7.651704 GTGGCAAAAATATATCATGGTGGTAAC 59.348 37.037 0.00 0.00 0.00 2.50
3482 3988 1.141053 GTAACTGGATGCCCGAGGATT 59.859 52.381 0.00 0.00 34.29 3.01
3527 4033 8.691797 GCAGTTTAAAATCCATAATAACTCCCA 58.308 33.333 0.00 0.00 0.00 4.37
3670 4218 9.451206 AATGGGGGAAAGTCATGATATATTTTT 57.549 29.630 0.00 0.00 0.00 1.94
4039 4587 4.837896 TCACTTCTATGGTAGCAGATCG 57.162 45.455 0.00 0.00 0.00 3.69
4236 5022 5.872617 GTGTGTGAGCTAACATGTATGGTAA 59.127 40.000 7.31 0.00 31.49 2.85
4413 5201 8.713737 AATGCTATGTGTGCTATGATATACAG 57.286 34.615 0.00 0.00 0.00 2.74
4414 5202 7.232118 TGCTATGTGTGCTATGATATACAGT 57.768 36.000 0.00 0.00 0.00 3.55
4415 5203 8.348285 TGCTATGTGTGCTATGATATACAGTA 57.652 34.615 0.00 0.00 0.00 2.74
4416 5204 8.244113 TGCTATGTGTGCTATGATATACAGTAC 58.756 37.037 0.00 0.00 0.00 2.73
4417 5205 8.244113 GCTATGTGTGCTATGATATACAGTACA 58.756 37.037 0.00 0.00 0.00 2.90
4422 5210 6.072175 TGTGCTATGATATACAGTACATGCGA 60.072 38.462 0.00 0.00 0.00 5.10
4433 5221 2.430694 AGTACATGCGATTGGTAGCTCA 59.569 45.455 0.00 0.00 0.00 4.26
4434 5222 2.401583 ACATGCGATTGGTAGCTCAA 57.598 45.000 0.00 0.00 0.00 3.02
4461 5249 3.816580 GTCCGTCAAAGGGACTCTC 57.183 57.895 10.72 0.00 46.58 3.20
4604 5395 2.044946 GCGCTCCCCATCCTGTTT 60.045 61.111 0.00 0.00 0.00 2.83
4615 5406 0.478072 ATCCTGTTTGGTGGACAGCA 59.522 50.000 0.00 0.00 42.42 4.41
4865 5708 4.446413 GACGGATGGACGGCGGTT 62.446 66.667 13.24 0.00 38.39 4.44
4971 5814 2.484287 CTTCAATGCTGACCCGGGGT 62.484 60.000 27.92 21.21 39.44 4.95
5018 5861 3.790437 CTCTGCCTCCGGTGCCAT 61.790 66.667 14.59 0.00 0.00 4.40
5034 5877 1.750930 CATAGCCCTCATCACCGCT 59.249 57.895 0.00 0.00 35.34 5.52
5042 5885 0.599466 CTCATCACCGCTGCATCGAT 60.599 55.000 12.26 0.00 0.00 3.59
5044 5887 1.066136 CATCACCGCTGCATCGATAG 58.934 55.000 12.26 0.78 0.00 2.08
5055 5898 4.269183 CTGCATCGATAGTAGAGATCCCT 58.731 47.826 0.00 0.00 37.40 4.20
5115 5958 3.532155 GAGTGCGCCTCGATCCCT 61.532 66.667 4.18 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.533657 TGTTGAAATGGATCTTTTCTAATGCAT 58.466 29.630 17.00 0.00 35.72 3.96
1 2 7.894708 TGTTGAAATGGATCTTTTCTAATGCA 58.105 30.769 17.00 0.00 34.80 3.96
2 3 8.937634 ATGTTGAAATGGATCTTTTCTAATGC 57.062 30.769 17.00 5.16 34.80 3.56
3 4 9.525409 GGATGTTGAAATGGATCTTTTCTAATG 57.475 33.333 17.00 0.00 34.80 1.90
4 5 9.258629 TGGATGTTGAAATGGATCTTTTCTAAT 57.741 29.630 17.00 10.73 34.80 1.73
5 6 8.648698 TGGATGTTGAAATGGATCTTTTCTAA 57.351 30.769 17.00 10.28 34.80 2.10
6 7 8.648698 TTGGATGTTGAAATGGATCTTTTCTA 57.351 30.769 17.00 10.46 34.80 2.10
7 8 7.543359 TTGGATGTTGAAATGGATCTTTTCT 57.457 32.000 17.00 3.51 34.80 2.52
8 9 8.036575 TCATTGGATGTTGAAATGGATCTTTTC 58.963 33.333 12.12 12.12 33.14 2.29
9 10 7.909518 TCATTGGATGTTGAAATGGATCTTTT 58.090 30.769 0.00 0.00 33.14 2.27
10 11 7.179694 ACTCATTGGATGTTGAAATGGATCTTT 59.820 33.333 0.00 0.00 33.14 2.52
11 12 6.666546 ACTCATTGGATGTTGAAATGGATCTT 59.333 34.615 0.00 0.00 33.14 2.40
12 13 6.192773 ACTCATTGGATGTTGAAATGGATCT 58.807 36.000 0.00 0.00 33.14 2.75
13 14 6.095860 TGACTCATTGGATGTTGAAATGGATC 59.904 38.462 0.00 0.00 33.14 3.36
14 15 5.953548 TGACTCATTGGATGTTGAAATGGAT 59.046 36.000 0.00 0.00 33.14 3.41
15 16 5.323581 TGACTCATTGGATGTTGAAATGGA 58.676 37.500 0.00 0.00 33.14 3.41
16 17 5.648178 TGACTCATTGGATGTTGAAATGG 57.352 39.130 0.00 0.00 33.14 3.16
17 18 8.680001 TCTTATGACTCATTGGATGTTGAAATG 58.320 33.333 0.00 0.00 33.50 2.32
18 19 8.812513 TCTTATGACTCATTGGATGTTGAAAT 57.187 30.769 0.00 0.00 0.00 2.17
19 20 8.634335 TTCTTATGACTCATTGGATGTTGAAA 57.366 30.769 0.00 0.00 0.00 2.69
20 21 8.634335 TTTCTTATGACTCATTGGATGTTGAA 57.366 30.769 0.00 0.00 0.00 2.69
21 22 8.634335 TTTTCTTATGACTCATTGGATGTTGA 57.366 30.769 0.00 0.00 0.00 3.18
22 23 8.733458 TCTTTTCTTATGACTCATTGGATGTTG 58.267 33.333 0.00 0.00 0.00 3.33
23 24 8.868522 TCTTTTCTTATGACTCATTGGATGTT 57.131 30.769 0.00 0.00 0.00 2.71
24 25 9.471702 AATCTTTTCTTATGACTCATTGGATGT 57.528 29.630 0.00 0.00 0.00 3.06
25 26 9.947669 GAATCTTTTCTTATGACTCATTGGATG 57.052 33.333 0.00 0.00 0.00 3.51
26 27 9.690913 TGAATCTTTTCTTATGACTCATTGGAT 57.309 29.630 0.00 0.00 32.78 3.41
27 28 8.950210 GTGAATCTTTTCTTATGACTCATTGGA 58.050 33.333 0.00 0.00 32.78 3.53
28 29 8.954350 AGTGAATCTTTTCTTATGACTCATTGG 58.046 33.333 0.00 0.00 32.78 3.16
31 32 9.730705 TGAAGTGAATCTTTTCTTATGACTCAT 57.269 29.630 0.00 0.00 36.40 2.90
32 33 9.559732 TTGAAGTGAATCTTTTCTTATGACTCA 57.440 29.630 0.00 0.00 36.40 3.41
33 34 9.818796 GTTGAAGTGAATCTTTTCTTATGACTC 57.181 33.333 0.00 0.00 36.40 3.36
34 35 9.342308 TGTTGAAGTGAATCTTTTCTTATGACT 57.658 29.630 0.00 0.00 36.40 3.41
37 38 8.857216 GCATGTTGAAGTGAATCTTTTCTTATG 58.143 33.333 0.00 0.00 36.40 1.90
38 39 8.579006 TGCATGTTGAAGTGAATCTTTTCTTAT 58.421 29.630 0.00 0.00 36.40 1.73
39 40 7.939782 TGCATGTTGAAGTGAATCTTTTCTTA 58.060 30.769 0.00 0.00 36.40 2.10
40 41 6.808829 TGCATGTTGAAGTGAATCTTTTCTT 58.191 32.000 0.00 0.00 36.40 2.52
41 42 6.395426 TGCATGTTGAAGTGAATCTTTTCT 57.605 33.333 0.00 0.00 36.40 2.52
42 43 7.010367 TGTTTGCATGTTGAAGTGAATCTTTTC 59.990 33.333 0.00 0.00 36.40 2.29
43 44 6.817641 TGTTTGCATGTTGAAGTGAATCTTTT 59.182 30.769 0.00 0.00 36.40 2.27
44 45 6.339730 TGTTTGCATGTTGAAGTGAATCTTT 58.660 32.000 0.00 0.00 36.40 2.52
45 46 5.904941 TGTTTGCATGTTGAAGTGAATCTT 58.095 33.333 0.00 0.00 39.32 2.40
46 47 5.518848 TGTTTGCATGTTGAAGTGAATCT 57.481 34.783 0.00 0.00 0.00 2.40
47 48 6.148270 CATGTTTGCATGTTGAAGTGAATC 57.852 37.500 0.00 0.00 45.48 2.52
199 200 8.908903 TGCGGGAATATTTTGTAATACATTTCT 58.091 29.630 0.00 0.00 0.00 2.52
200 201 9.522804 TTGCGGGAATATTTTGTAATACATTTC 57.477 29.630 0.00 0.00 0.00 2.17
201 202 9.308318 GTTGCGGGAATATTTTGTAATACATTT 57.692 29.630 0.00 0.00 0.00 2.32
202 203 8.470805 TGTTGCGGGAATATTTTGTAATACATT 58.529 29.630 0.00 0.00 0.00 2.71
203 204 8.001881 TGTTGCGGGAATATTTTGTAATACAT 57.998 30.769 0.00 0.00 0.00 2.29
204 205 7.392494 TGTTGCGGGAATATTTTGTAATACA 57.608 32.000 0.00 0.00 0.00 2.29
205 206 7.044576 CGTTGTTGCGGGAATATTTTGTAATAC 60.045 37.037 0.00 0.00 0.00 1.89
206 207 6.967767 CGTTGTTGCGGGAATATTTTGTAATA 59.032 34.615 0.00 0.00 0.00 0.98
207 208 5.802956 CGTTGTTGCGGGAATATTTTGTAAT 59.197 36.000 0.00 0.00 0.00 1.89
208 209 5.154932 CGTTGTTGCGGGAATATTTTGTAA 58.845 37.500 0.00 0.00 0.00 2.41
209 210 4.215827 ACGTTGTTGCGGGAATATTTTGTA 59.784 37.500 0.00 0.00 35.98 2.41
210 211 3.004944 ACGTTGTTGCGGGAATATTTTGT 59.995 39.130 0.00 0.00 35.98 2.83
211 212 3.363426 CACGTTGTTGCGGGAATATTTTG 59.637 43.478 0.00 0.00 37.48 2.44
212 213 3.570559 CACGTTGTTGCGGGAATATTTT 58.429 40.909 0.00 0.00 37.48 1.82
213 214 2.669950 GCACGTTGTTGCGGGAATATTT 60.670 45.455 0.00 0.00 37.48 1.40
214 215 1.135517 GCACGTTGTTGCGGGAATATT 60.136 47.619 0.00 0.00 37.48 1.28
215 216 0.450184 GCACGTTGTTGCGGGAATAT 59.550 50.000 0.00 0.00 37.48 1.28
216 217 1.870383 GCACGTTGTTGCGGGAATA 59.130 52.632 0.00 0.00 37.48 1.75
217 218 2.642700 GCACGTTGTTGCGGGAAT 59.357 55.556 0.00 0.00 37.48 3.01
224 225 3.206211 AATGCCCCGCACGTTGTTG 62.206 57.895 0.00 0.00 43.04 3.33
225 226 2.909965 AATGCCCCGCACGTTGTT 60.910 55.556 0.00 0.00 43.04 2.83
226 227 3.669344 CAATGCCCCGCACGTTGT 61.669 61.111 0.00 0.00 43.04 3.32
227 228 3.609214 GACAATGCCCCGCACGTTG 62.609 63.158 0.00 0.00 43.04 4.10
228 229 2.457743 TAGACAATGCCCCGCACGTT 62.458 55.000 0.00 0.00 43.04 3.99
229 230 2.852495 CTAGACAATGCCCCGCACGT 62.852 60.000 0.00 0.00 43.04 4.49
230 231 2.125310 TAGACAATGCCCCGCACG 60.125 61.111 0.00 0.00 43.04 5.34
231 232 0.676782 AACTAGACAATGCCCCGCAC 60.677 55.000 0.00 0.00 43.04 5.34
232 233 0.037590 AAACTAGACAATGCCCCGCA 59.962 50.000 0.00 0.00 44.86 5.69
233 234 0.451783 CAAACTAGACAATGCCCCGC 59.548 55.000 0.00 0.00 0.00 6.13
234 235 1.094785 CCAAACTAGACAATGCCCCG 58.905 55.000 0.00 0.00 0.00 5.73
235 236 2.026262 TCTCCAAACTAGACAATGCCCC 60.026 50.000 0.00 0.00 0.00 5.80
236 237 3.350219 TCTCCAAACTAGACAATGCCC 57.650 47.619 0.00 0.00 0.00 5.36
237 238 4.327680 ACTTCTCCAAACTAGACAATGCC 58.672 43.478 0.00 0.00 0.00 4.40
238 239 5.335191 CCAACTTCTCCAAACTAGACAATGC 60.335 44.000 0.00 0.00 0.00 3.56
239 240 5.997746 TCCAACTTCTCCAAACTAGACAATG 59.002 40.000 0.00 0.00 0.00 2.82
240 241 5.998363 GTCCAACTTCTCCAAACTAGACAAT 59.002 40.000 0.00 0.00 0.00 2.71
241 242 5.104693 TGTCCAACTTCTCCAAACTAGACAA 60.105 40.000 0.00 0.00 0.00 3.18
242 243 4.407621 TGTCCAACTTCTCCAAACTAGACA 59.592 41.667 0.00 0.00 0.00 3.41
243 244 4.957296 TGTCCAACTTCTCCAAACTAGAC 58.043 43.478 0.00 0.00 0.00 2.59
244 245 5.104693 TGTTGTCCAACTTCTCCAAACTAGA 60.105 40.000 11.14 0.00 41.67 2.43
245 246 5.123227 TGTTGTCCAACTTCTCCAAACTAG 58.877 41.667 11.14 0.00 41.67 2.57
246 247 5.105567 TGTTGTCCAACTTCTCCAAACTA 57.894 39.130 11.14 0.00 41.67 2.24
247 248 3.963129 TGTTGTCCAACTTCTCCAAACT 58.037 40.909 11.14 0.00 41.67 2.66
248 249 4.261614 GGATGTTGTCCAACTTCTCCAAAC 60.262 45.833 19.32 4.83 46.96 2.93
249 250 3.888930 GGATGTTGTCCAACTTCTCCAAA 59.111 43.478 19.32 0.00 46.96 3.28
250 251 3.486383 GGATGTTGTCCAACTTCTCCAA 58.514 45.455 19.32 0.00 46.96 3.53
251 252 3.140325 GGATGTTGTCCAACTTCTCCA 57.860 47.619 19.32 0.00 46.96 3.86
261 262 1.743995 CCCCGTTCGGATGTTGTCC 60.744 63.158 13.08 0.00 44.10 4.02
262 263 1.004200 ACCCCGTTCGGATGTTGTC 60.004 57.895 13.08 0.00 0.00 3.18
263 264 1.302192 CACCCCGTTCGGATGTTGT 60.302 57.895 13.08 0.00 0.00 3.32
264 265 0.037139 TACACCCCGTTCGGATGTTG 60.037 55.000 19.95 11.06 0.00 3.33
265 266 0.686224 TTACACCCCGTTCGGATGTT 59.314 50.000 19.95 9.45 0.00 2.71
266 267 0.686224 TTTACACCCCGTTCGGATGT 59.314 50.000 19.15 19.15 0.00 3.06
267 268 2.032680 ATTTACACCCCGTTCGGATG 57.967 50.000 13.08 12.31 0.00 3.51
268 269 5.549742 TTATATTTACACCCCGTTCGGAT 57.450 39.130 13.08 0.00 0.00 4.18
269 270 5.350504 TTTATATTTACACCCCGTTCGGA 57.649 39.130 13.08 0.00 0.00 4.55
270 271 6.930722 ACTATTTATATTTACACCCCGTTCGG 59.069 38.462 4.08 4.08 0.00 4.30
271 272 7.951530 ACTATTTATATTTACACCCCGTTCG 57.048 36.000 0.00 0.00 0.00 3.95
446 447 0.109342 GATCCATTCGGGCTCCACAT 59.891 55.000 0.00 0.00 36.21 3.21
471 472 6.100004 TCTAGAAATGCTACCGAAACTTCTG 58.900 40.000 0.00 0.00 0.00 3.02
559 560 2.931320 GCTTAACTCGGAAGTCAGGGTG 60.931 54.545 0.00 0.00 33.48 4.61
621 623 1.073284 TGGTTGTTCTGAGGTAAGGGC 59.927 52.381 0.00 0.00 0.00 5.19
655 658 2.870411 ACCTTAACTCGCAAGTCACAAC 59.130 45.455 0.00 0.00 33.48 3.32
656 659 3.188159 ACCTTAACTCGCAAGTCACAA 57.812 42.857 0.00 0.00 33.48 3.33
657 660 2.902705 ACCTTAACTCGCAAGTCACA 57.097 45.000 0.00 0.00 33.48 3.58
658 661 3.059120 GGAAACCTTAACTCGCAAGTCAC 60.059 47.826 0.00 0.00 33.48 3.67
659 662 3.135994 GGAAACCTTAACTCGCAAGTCA 58.864 45.455 0.00 0.00 33.48 3.41
660 663 2.157085 CGGAAACCTTAACTCGCAAGTC 59.843 50.000 0.00 0.00 33.48 3.01
661 664 2.140717 CGGAAACCTTAACTCGCAAGT 58.859 47.619 0.00 0.00 37.32 3.16
1296 1303 0.378257 ACGAATCACGCATGCCATTC 59.622 50.000 13.15 15.30 46.94 2.67
1307 1318 1.792057 CGCGCAAACCACGAATCAC 60.792 57.895 8.75 0.00 0.00 3.06
1308 1319 1.295357 ATCGCGCAAACCACGAATCA 61.295 50.000 8.75 0.00 39.56 2.57
1309 1320 0.857311 CATCGCGCAAACCACGAATC 60.857 55.000 8.75 0.00 39.56 2.52
1424 1435 4.537015 GCCACAAGAAGTTTGTCACATAC 58.463 43.478 0.00 0.00 0.00 2.39
1425 1436 3.249799 CGCCACAAGAAGTTTGTCACATA 59.750 43.478 0.00 0.00 0.00 2.29
1426 1437 2.033299 CGCCACAAGAAGTTTGTCACAT 59.967 45.455 0.00 0.00 0.00 3.21
1440 1451 2.006888 GCTCAAACTATAGCGCCACAA 58.993 47.619 2.29 0.00 0.00 3.33
1528 1565 7.687941 TTTCTGAGATAAAGGGAACATGTTC 57.312 36.000 27.16 27.16 38.80 3.18
1658 1725 7.867909 CCAGAACTGAAAAATAGGGAGAAAAAC 59.132 37.037 3.19 0.00 0.00 2.43
2056 2224 2.539547 GCGTTCTATACTTGCGTCCGTA 60.540 50.000 0.00 0.00 0.00 4.02
2063 2231 3.781280 GCGTTCTTGCGTTCTATACTTGC 60.781 47.826 0.00 0.00 0.00 4.01
2342 2827 5.441500 TGATTGGCCTTATTTTCATCGGTA 58.558 37.500 3.32 0.00 0.00 4.02
2346 2831 5.360714 TGACCTGATTGGCCTTATTTTCATC 59.639 40.000 3.32 0.00 40.22 2.92
2359 2844 1.066143 ACCTAGCGTTGACCTGATTGG 60.066 52.381 0.00 0.00 42.93 3.16
2382 2867 1.442769 GTGACGTGAACATGAGGCAT 58.557 50.000 0.00 0.00 0.00 4.40
2460 2945 4.038642 TGTTTATCAACTTTGTTGGGCCTC 59.961 41.667 4.53 0.00 33.58 4.70
2728 3215 2.396590 TATTTCTGGAACTCACCCGC 57.603 50.000 0.00 0.00 0.00 6.13
2950 3437 8.848948 TGTTCAACATTAATTTACACACACTG 57.151 30.769 0.00 0.00 0.00 3.66
2957 3444 9.482627 GGTTCCAATGTTCAACATTAATTTACA 57.517 29.630 15.51 0.00 46.22 2.41
3279 3785 3.713288 TGACTACAACCAGTTGAACTCG 58.287 45.455 17.06 0.00 42.93 4.18
3466 3972 1.450531 GCAAATCCTCGGGCATCCAG 61.451 60.000 0.00 0.00 0.00 3.86
3527 4033 8.584157 TCATTTGAAAAGTGCACCTAATATGTT 58.416 29.630 14.63 0.00 33.04 2.71
3535 4041 9.590451 CATATATTTCATTTGAAAAGTGCACCT 57.410 29.630 14.63 0.00 45.81 4.00
3536 4042 8.819974 CCATATATTTCATTTGAAAAGTGCACC 58.180 33.333 14.63 0.00 45.81 5.01
3670 4218 4.253685 GTGCTGCCTGTGATAGTAAAAGA 58.746 43.478 0.00 0.00 0.00 2.52
4225 5011 7.307396 GCTGCAACTACTGTATTACCATACATG 60.307 40.741 0.00 0.00 43.60 3.21
4236 5022 3.034635 AGGCTAGCTGCAACTACTGTAT 58.965 45.455 15.72 0.00 45.15 2.29
4413 5201 2.821546 TGAGCTACCAATCGCATGTAC 58.178 47.619 0.00 0.00 0.00 2.90
4414 5202 3.535280 TTGAGCTACCAATCGCATGTA 57.465 42.857 0.00 0.00 0.00 2.29
4415 5203 2.401583 TTGAGCTACCAATCGCATGT 57.598 45.000 0.00 0.00 0.00 3.21
4416 5204 2.603892 GCATTGAGCTACCAATCGCATG 60.604 50.000 13.04 0.00 41.15 4.06
4417 5205 1.605710 GCATTGAGCTACCAATCGCAT 59.394 47.619 13.04 0.00 41.15 4.73
4433 5221 2.154462 CTTTGACGGACCTTCAGCATT 58.846 47.619 0.41 0.00 0.00 3.56
4434 5222 1.611673 CCTTTGACGGACCTTCAGCAT 60.612 52.381 0.41 0.00 0.00 3.79
4604 5395 3.484806 AACCCGTGCTGTCCACCA 61.485 61.111 0.00 0.00 41.53 4.17
4787 5579 1.959282 ACTAAGACGACCGTTGAACCT 59.041 47.619 0.00 0.00 0.00 3.50
4971 5814 0.608035 CGGTTTAAGAAGGCCCTGCA 60.608 55.000 0.00 0.00 0.00 4.41
5017 5860 1.750930 CAGCGGTGATGAGGGCTAT 59.249 57.895 9.50 0.00 33.72 2.97
5018 5861 3.094062 GCAGCGGTGATGAGGGCTA 62.094 63.158 20.69 0.00 33.72 3.93
5034 5877 4.308526 AGGGATCTCTACTATCGATGCA 57.691 45.455 8.54 0.00 0.00 3.96
5042 5885 2.695666 GCAGTGCAAGGGATCTCTACTA 59.304 50.000 11.09 0.00 0.00 1.82
5044 5887 1.208052 TGCAGTGCAAGGGATCTCTAC 59.792 52.381 17.26 0.00 34.76 2.59
5074 5917 2.635443 CGAAATGGCCCGGCAGTTT 61.635 57.895 12.58 11.13 0.00 2.66
5104 5947 2.586357 GTTGCGAGGGATCGAGGC 60.586 66.667 1.17 0.00 34.64 4.70
5106 5949 2.278857 CGGTTGCGAGGGATCGAG 60.279 66.667 1.17 0.00 34.64 4.04



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

AutoCloner maintained by Alex Coulton.