Multiple sequence alignment - TraesCS5D01G212000

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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 TraesCS5D01G212000 chr5D 100.000 7730 0 0 1 7730 320895065 320887336 0.000000e+00 14275.0
1 TraesCS5D01G212000 chr5D 89.928 278 27 1 6091 6367 320888895 320888618 2.650000e-94 357.0
2 TraesCS5D01G212000 chr5D 89.928 278 27 1 6171 6448 320888975 320888699 2.650000e-94 357.0
3 TraesCS5D01G212000 chr5D 86.647 337 22 13 1978 2298 320892662 320892333 1.230000e-92 351.0
4 TraesCS5D01G212000 chr5D 86.647 337 22 13 2404 2733 320893088 320892768 1.230000e-92 351.0
5 TraesCS5D01G212000 chr5D 84.211 304 32 9 1919 2214 320892378 320892083 1.640000e-71 281.0
6 TraesCS5D01G212000 chr5D 84.211 304 32 9 2688 2983 320893147 320892852 1.640000e-71 281.0
7 TraesCS5D01G212000 chr5D 86.364 242 22 2 2405 2646 320892313 320892083 3.580000e-63 254.0
8 TraesCS5D01G212000 chr5D 86.364 242 22 2 2753 2983 320892661 320892420 3.580000e-63 254.0
9 TraesCS5D01G212000 chr5D 98.113 53 1 0 2313 2365 320892719 320892667 8.260000e-15 93.5
10 TraesCS5D01G212000 chr5D 98.113 53 1 0 2347 2399 320892753 320892701 8.260000e-15 93.5
11 TraesCS5D01G212000 chr5A 95.598 2908 80 14 2404 5280 413410689 413413579 0.000000e+00 4617.0
12 TraesCS5D01G212000 chr5A 91.718 1449 85 18 6094 7522 413414432 413415865 0.000000e+00 1978.0
13 TraesCS5D01G212000 chr5A 96.886 1124 35 0 5324 6447 413413581 413414704 0.000000e+00 1882.0
14 TraesCS5D01G212000 chr5A 93.245 977 35 12 1364 2319 413410073 413411039 0.000000e+00 1410.0
15 TraesCS5D01G212000 chr5A 87.616 541 24 16 351 875 413408796 413409309 8.640000e-164 588.0
16 TraesCS5D01G212000 chr5A 91.457 398 17 2 928 1323 413409609 413409991 1.480000e-146 531.0
17 TraesCS5D01G212000 chr5A 89.925 268 27 0 6180 6447 413414356 413414623 5.740000e-91 346.0
18 TraesCS5D01G212000 chr5A 87.000 300 27 10 1919 2214 413410973 413411264 2.080000e-85 327.0
19 TraesCS5D01G212000 chr5A 87.726 277 34 0 6091 6367 413414510 413414786 2.690000e-84 324.0
20 TraesCS5D01G212000 chr5A 84.194 310 29 10 2688 2983 413410630 413410933 4.570000e-72 283.0
21 TraesCS5D01G212000 chr5A 88.017 242 18 2 2405 2646 413411034 413411264 7.640000e-70 276.0
22 TraesCS5D01G212000 chr5A 85.507 207 13 8 71 261 413407976 413408181 4.730000e-47 200.0
23 TraesCS5D01G212000 chr5A 85.792 183 6 2 7568 7730 413416332 413416514 7.970000e-40 176.0
24 TraesCS5D01G212000 chr5A 88.750 80 2 1 727 806 413410066 413409994 2.970000e-14 91.6
25 TraesCS5D01G212000 chr5A 84.722 72 2 5 7514 7576 413416226 413416297 6.480000e-06 63.9
26 TraesCS5D01G212000 chr5B 96.834 2464 57 5 2839 5281 372108848 372106385 0.000000e+00 4098.0
27 TraesCS5D01G212000 chr5B 92.462 2149 93 28 197 2314 372111647 372109537 0.000000e+00 3007.0
28 TraesCS5D01G212000 chr5B 93.638 1556 73 10 6094 7645 372105530 372103997 0.000000e+00 2302.0
29 TraesCS5D01G212000 chr5B 95.118 1147 42 7 5323 6465 372106385 372105249 0.000000e+00 1796.0
30 TraesCS5D01G212000 chr5B 95.444 439 10 4 2407 2845 372109460 372109032 0.000000e+00 691.0
31 TraesCS5D01G212000 chr5B 92.336 274 21 0 6094 6367 372105458 372105185 2.620000e-104 390.0
32 TraesCS5D01G212000 chr5B 86.842 342 20 11 2404 2733 372109881 372109553 7.380000e-95 359.0
33 TraesCS5D01G212000 chr5B 85.965 342 25 12 1981 2306 372109460 372109126 2.070000e-90 344.0
34 TraesCS5D01G212000 chr5B 85.473 296 31 4 6171 6465 372105614 372105330 1.630000e-76 298.0
35 TraesCS5D01G212000 chr5B 84.516 310 28 8 2688 2983 372109940 372109637 9.810000e-74 289.0
36 TraesCS5D01G212000 chr5B 93.258 89 6 0 2407 2495 372109122 372109034 1.750000e-26 132.0
37 TraesCS5D01G212000 chr5B 97.826 46 1 0 5277 5322 145944470 145944515 6.430000e-11 80.5
38 TraesCS5D01G212000 chr5B 97.826 46 1 0 5280 5325 455636110 455636065 6.430000e-11 80.5
39 TraesCS5D01G212000 chr6B 80.838 1623 194 65 2881 4411 615967736 615969333 0.000000e+00 1166.0
40 TraesCS5D01G212000 chr6B 78.492 358 47 14 6382 6715 615970690 615971041 2.830000e-49 207.0
41 TraesCS5D01G212000 chr6B 100.000 44 0 0 5279 5322 613158906 613158949 1.790000e-11 82.4
42 TraesCS5D01G212000 chr6D 80.069 1746 200 65 2779 4416 409753417 409755122 0.000000e+00 1160.0
43 TraesCS5D01G212000 chr6D 77.358 477 58 21 6382 6831 409756510 409756963 3.610000e-58 237.0
44 TraesCS5D01G212000 chr6D 80.255 314 44 10 1005 1305 409743418 409743726 3.630000e-53 220.0
45 TraesCS5D01G212000 chr6D 86.301 73 8 2 7150 7221 51198437 51198366 2.310000e-10 78.7
46 TraesCS5D01G212000 chr6D 91.111 45 3 1 7197 7241 94279332 94279375 8.380000e-05 60.2
47 TraesCS5D01G212000 chr6A 83.556 973 123 21 2880 3821 555220760 555221726 0.000000e+00 876.0
48 TraesCS5D01G212000 chr6A 80.806 521 63 17 3927 4411 555227278 555227797 2.630000e-99 374.0
49 TraesCS5D01G212000 chr2A 85.714 91 10 3 7151 7239 734597091 734597180 8.260000e-15 93.5
50 TraesCS5D01G212000 chr2A 86.047 86 10 2 7152 7236 501572193 501572109 2.970000e-14 91.6
51 TraesCS5D01G212000 chr3B 84.615 91 8 5 7153 7239 656601157 656601069 1.380000e-12 86.1
52 TraesCS5D01G212000 chr2B 84.706 85 12 1 7153 7236 56035881 56035797 4.970000e-12 84.2
53 TraesCS5D01G212000 chr7B 97.826 46 1 0 5280 5325 644471164 644471119 6.430000e-11 80.5
54 TraesCS5D01G212000 chr4D 97.826 46 1 0 5280 5325 123720225 123720180 6.430000e-11 80.5
55 TraesCS5D01G212000 chr4B 97.826 46 1 0 5277 5322 209073795 209073840 6.430000e-11 80.5
56 TraesCS5D01G212000 chr1D 97.826 46 1 0 5277 5322 141295905 141295950 6.430000e-11 80.5
57 TraesCS5D01G212000 chr1D 84.524 84 10 2 7153 7236 199841556 199841476 6.430000e-11 80.5
58 TraesCS5D01G212000 chr1D 97.826 46 1 0 5277 5322 298783186 298783231 6.430000e-11 80.5
59 TraesCS5D01G212000 chr1A 97.826 46 1 0 5280 5325 415668291 415668246 6.430000e-11 80.5
60 TraesCS5D01G212000 chrUn 95.122 41 1 1 7153 7192 24886462 24886422 6.480000e-06 63.9
61 TraesCS5D01G212000 chr1B 96.970 33 0 1 7209 7241 3881490 3881459 4.000000e-03 54.7


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 TraesCS5D01G212000 chr5D 320887336 320895065 7729 True 14275.000000 14275 100.000000 1 7730 1 chr5D.!!$R1 7729
1 TraesCS5D01G212000 chr5D 320888618 320893147 4529 True 267.300000 357 89.052600 1919 6448 10 chr5D.!!$R2 4529
2 TraesCS5D01G212000 chr5A 413407976 413416514 8538 False 928.707143 4617 89.243071 71 7730 14 chr5A.!!$F1 7659
3 TraesCS5D01G212000 chr5B 372103997 372111647 7650 True 1246.000000 4098 91.080545 197 7645 11 chr5B.!!$R2 7448
4 TraesCS5D01G212000 chr6B 615967736 615971041 3305 False 686.500000 1166 79.665000 2881 6715 2 chr6B.!!$F2 3834
5 TraesCS5D01G212000 chr6D 409753417 409756963 3546 False 698.500000 1160 78.713500 2779 6831 2 chr6D.!!$F3 4052
6 TraesCS5D01G212000 chr6A 555220760 555221726 966 False 876.000000 876 83.556000 2880 3821 1 chr6A.!!$F1 941
7 TraesCS5D01G212000 chr6A 555227278 555227797 519 False 374.000000 374 80.806000 3927 4411 1 chr6A.!!$F2 484

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
51 52 0.107945 GGCATCCCTCTGCGATATCC 60.108 60.0 0.00 0.0 43.23 2.59 F
117 118 0.304705 CGGGCGAATCTTCCGATTTG 59.695 55.0 5.45 0.0 45.96 2.32 F
1188 1992 0.324614 GATTTTTGGGGTTGGGGCAG 59.675 55.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1263 2067 1.068472 ACTGTCGTTGGAAGACGCTAG 60.068 52.381 0.0 0.0 42.50 3.42 R
1489 2336 1.235724 GAAGAACAACAACCCTCGGG 58.764 55.000 0.0 0.0 42.03 5.14 R
6754 8607 7.495934 GCAGTTTAATCCAGAATAAGCAGAGTA 59.504 37.037 0.0 0.0 0.00 2.59 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
31 32 4.093291 CCGAGGCAGCCAAGCTCT 62.093 66.667 15.80 0.00 36.40 4.09
32 33 2.818714 CGAGGCAGCCAAGCTCTG 60.819 66.667 15.80 0.00 36.40 3.35
40 41 3.004951 CCAAGCTCTGGCATCCCT 58.995 61.111 2.58 0.00 38.76 4.20
41 42 1.153005 CCAAGCTCTGGCATCCCTC 60.153 63.158 2.58 0.00 38.76 4.30
42 43 1.633915 CCAAGCTCTGGCATCCCTCT 61.634 60.000 2.58 0.00 38.76 3.69
43 44 0.464013 CAAGCTCTGGCATCCCTCTG 60.464 60.000 0.00 0.00 41.70 3.35
44 45 2.203181 GCTCTGGCATCCCTCTGC 60.203 66.667 0.00 0.00 41.53 4.26
45 46 2.108566 CTCTGGCATCCCTCTGCG 59.891 66.667 0.00 0.00 43.23 5.18
46 47 2.364186 TCTGGCATCCCTCTGCGA 60.364 61.111 0.00 0.00 43.23 5.10
47 48 1.756408 CTCTGGCATCCCTCTGCGAT 61.756 60.000 0.00 0.00 43.23 4.58
48 49 0.469892 TCTGGCATCCCTCTGCGATA 60.470 55.000 0.00 0.00 43.23 2.92
49 50 0.612229 CTGGCATCCCTCTGCGATAT 59.388 55.000 0.00 0.00 43.23 1.63
50 51 0.610174 TGGCATCCCTCTGCGATATC 59.390 55.000 0.00 0.00 43.23 1.63
51 52 0.107945 GGCATCCCTCTGCGATATCC 60.108 60.000 0.00 0.00 43.23 2.59
52 53 0.610174 GCATCCCTCTGCGATATCCA 59.390 55.000 0.00 0.00 31.49 3.41
53 54 1.405256 GCATCCCTCTGCGATATCCAG 60.405 57.143 12.51 12.51 31.49 3.86
54 55 2.174360 CATCCCTCTGCGATATCCAGA 58.826 52.381 17.63 17.63 37.71 3.86
57 58 3.398184 CTCTGCGATATCCAGAGCG 57.602 57.895 25.40 13.18 46.70 5.03
58 59 0.732196 CTCTGCGATATCCAGAGCGC 60.732 60.000 25.40 14.75 46.70 5.92
60 61 3.474034 GCGATATCCAGAGCGCGC 61.474 66.667 26.66 26.66 40.06 6.86
61 62 2.807045 CGATATCCAGAGCGCGCC 60.807 66.667 30.33 19.60 0.00 6.53
62 63 2.433318 GATATCCAGAGCGCGCCC 60.433 66.667 30.33 18.43 0.00 6.13
63 64 3.941657 GATATCCAGAGCGCGCCCC 62.942 68.421 30.33 20.47 0.00 5.80
117 118 0.304705 CGGGCGAATCTTCCGATTTG 59.695 55.000 5.45 0.00 45.96 2.32
118 119 1.379527 GGGCGAATCTTCCGATTTGT 58.620 50.000 0.00 0.00 41.28 2.83
125 126 1.872388 TCTTCCGATTTGTTGTGCGA 58.128 45.000 0.00 0.00 0.00 5.10
149 156 3.763897 GCAAATCATGGGGTAGAAACAGT 59.236 43.478 0.00 0.00 0.00 3.55
155 162 3.485463 TGGGGTAGAAACAGTGTTCAG 57.515 47.619 9.40 0.00 0.00 3.02
156 163 3.042682 TGGGGTAGAAACAGTGTTCAGA 58.957 45.455 9.40 0.00 0.00 3.27
157 164 3.456644 TGGGGTAGAAACAGTGTTCAGAA 59.543 43.478 9.40 0.00 0.00 3.02
159 166 4.695928 GGGGTAGAAACAGTGTTCAGAATC 59.304 45.833 9.40 2.66 0.00 2.52
160 167 5.305585 GGGTAGAAACAGTGTTCAGAATCA 58.694 41.667 9.40 0.00 0.00 2.57
161 168 5.179555 GGGTAGAAACAGTGTTCAGAATCAC 59.820 44.000 9.40 4.35 35.13 3.06
162 169 5.179555 GGTAGAAACAGTGTTCAGAATCACC 59.820 44.000 9.40 9.07 35.45 4.02
163 170 3.809832 AGAAACAGTGTTCAGAATCACCG 59.190 43.478 9.40 5.42 35.45 4.94
164 171 1.512926 ACAGTGTTCAGAATCACCGC 58.487 50.000 10.51 0.00 35.45 5.68
184 201 5.761234 ACCGCAATAAAACAGTGTTTAGAGA 59.239 36.000 21.14 8.11 0.00 3.10
185 202 6.261381 ACCGCAATAAAACAGTGTTTAGAGAA 59.739 34.615 21.14 6.00 0.00 2.87
191 208 9.952188 AATAAAACAGTGTTTAGAGAAAAGCTC 57.048 29.630 21.14 0.00 44.29 4.09
192 209 6.378710 AAACAGTGTTTAGAGAAAAGCTCC 57.621 37.500 19.59 0.00 45.10 4.70
194 211 5.437060 ACAGTGTTTAGAGAAAAGCTCCAA 58.563 37.500 0.00 0.00 45.10 3.53
356 897 3.679389 ACAAGATGGGCACAGTAAAGAG 58.321 45.455 0.00 0.00 0.00 2.85
387 928 2.200081 AGATGGTAGATGGGCACAGTT 58.800 47.619 0.00 0.00 0.00 3.16
388 929 2.578021 AGATGGTAGATGGGCACAGTTT 59.422 45.455 0.00 0.00 0.00 2.66
464 1011 1.266989 CTTTTCCCGGTCTTGTGAAGC 59.733 52.381 0.00 0.00 0.00 3.86
610 1157 4.408821 AAGCGCCGCAGAATCCCA 62.409 61.111 13.36 0.00 0.00 4.37
621 1168 3.699134 GAATCCCAGCCGTCCACCC 62.699 68.421 0.00 0.00 0.00 4.61
649 1196 1.004080 CACAGCACCTCACCTCCAG 60.004 63.158 0.00 0.00 0.00 3.86
652 1199 3.325753 GCACCTCACCTCCAGCCT 61.326 66.667 0.00 0.00 0.00 4.58
653 1200 2.985456 CACCTCACCTCCAGCCTC 59.015 66.667 0.00 0.00 0.00 4.70
654 1201 2.284995 ACCTCACCTCCAGCCTCC 60.285 66.667 0.00 0.00 0.00 4.30
655 1202 3.086600 CCTCACCTCCAGCCTCCC 61.087 72.222 0.00 0.00 0.00 4.30
656 1203 3.086600 CTCACCTCCAGCCTCCCC 61.087 72.222 0.00 0.00 0.00 4.81
657 1204 3.615811 TCACCTCCAGCCTCCCCT 61.616 66.667 0.00 0.00 0.00 4.79
658 1205 3.086600 CACCTCCAGCCTCCCCTC 61.087 72.222 0.00 0.00 0.00 4.30
659 1206 4.423209 ACCTCCAGCCTCCCCTCC 62.423 72.222 0.00 0.00 0.00 4.30
660 1207 4.101077 CCTCCAGCCTCCCCTCCT 62.101 72.222 0.00 0.00 0.00 3.69
661 1208 2.445654 CTCCAGCCTCCCCTCCTC 60.446 72.222 0.00 0.00 0.00 3.71
662 1209 4.465446 TCCAGCCTCCCCTCCTCG 62.465 72.222 0.00 0.00 0.00 4.63
689 1236 1.631071 CCTTCCCTGCCCTCTCCTTC 61.631 65.000 0.00 0.00 0.00 3.46
692 1239 3.474570 CCTGCCCTCTCCTTCCCG 61.475 72.222 0.00 0.00 0.00 5.14
772 1320 0.399376 TGACACACCCACTACCCACT 60.399 55.000 0.00 0.00 0.00 4.00
773 1321 1.133104 TGACACACCCACTACCCACTA 60.133 52.381 0.00 0.00 0.00 2.74
774 1322 1.274447 GACACACCCACTACCCACTAC 59.726 57.143 0.00 0.00 0.00 2.73
775 1323 0.611714 CACACCCACTACCCACTACC 59.388 60.000 0.00 0.00 0.00 3.18
776 1324 0.546027 ACACCCACTACCCACTACCC 60.546 60.000 0.00 0.00 0.00 3.69
777 1325 0.545787 CACCCACTACCCACTACCCA 60.546 60.000 0.00 0.00 0.00 4.51
778 1326 0.546027 ACCCACTACCCACTACCCAC 60.546 60.000 0.00 0.00 0.00 4.61
807 1355 2.122769 GGCCTCCCTAGACCCCTC 60.123 72.222 0.00 0.00 0.00 4.30
871 1429 2.041620 CTCCAGGATCAAGAACCCCAAA 59.958 50.000 0.00 0.00 0.00 3.28
942 1746 2.904131 CCGAGAAGAAGGGAGGGC 59.096 66.667 0.00 0.00 0.00 5.19
946 1750 1.578897 GAGAAGAAGGGAGGGCTCTT 58.421 55.000 0.00 0.00 37.60 2.85
1168 1972 0.875059 CTTGCACTCCCCGTTTCTTC 59.125 55.000 0.00 0.00 0.00 2.87
1187 1991 1.476007 CGATTTTTGGGGTTGGGGCA 61.476 55.000 0.00 0.00 0.00 5.36
1188 1992 0.324614 GATTTTTGGGGTTGGGGCAG 59.675 55.000 0.00 0.00 0.00 4.85
1189 1993 1.133181 ATTTTTGGGGTTGGGGCAGG 61.133 55.000 0.00 0.00 0.00 4.85
1190 1994 3.783239 TTTTGGGGTTGGGGCAGGG 62.783 63.158 0.00 0.00 0.00 4.45
1225 2029 1.202891 GGCAGGTAGGTTCTTGTTGGT 60.203 52.381 0.00 0.00 0.00 3.67
1254 2058 3.869272 GCGATGCCTTGCTCACCG 61.869 66.667 0.00 0.00 0.00 4.94
1263 2067 2.922335 GCCTTGCTCACCGAATTTGTTC 60.922 50.000 0.00 0.00 0.00 3.18
1266 2070 4.142816 CCTTGCTCACCGAATTTGTTCTAG 60.143 45.833 0.00 0.00 0.00 2.43
1277 2081 5.358298 AATTTGTTCTAGCGTCTTCCAAC 57.642 39.130 0.00 0.00 0.00 3.77
1278 2082 2.060326 TGTTCTAGCGTCTTCCAACG 57.940 50.000 0.00 0.00 45.31 4.10
1332 2138 4.833478 TCTTCCCAATCTCCTCAAAGAG 57.167 45.455 0.00 0.00 35.04 2.85
1336 2142 5.786121 TCCCAATCTCCTCAAAGAGAAAT 57.214 39.130 0.00 0.00 45.70 2.17
1383 2230 3.857052 TCGATTCACATAAAAGACGCCT 58.143 40.909 0.00 0.00 0.00 5.52
1433 2280 2.449137 ATCTTGCCTTCCATTCCCTG 57.551 50.000 0.00 0.00 0.00 4.45
1489 2336 6.967199 GGGAATCGTGTAAAATGTTCAGATTC 59.033 38.462 6.36 6.36 40.87 2.52
1513 2360 4.202111 CCGAGGGTTGTTGTTCTTCAAATT 60.202 41.667 0.00 0.00 37.81 1.82
1570 2428 1.899437 AACATCGATGGTGCCCGAGT 61.899 55.000 28.09 1.89 38.25 4.18
1694 2553 2.268298 AGGTTATTGCTTCGCTGTACG 58.732 47.619 0.00 0.00 45.62 3.67
1751 2610 8.537728 AAGGAAATGATTCATTGGCTATTACA 57.462 30.769 12.50 0.00 38.09 2.41
1779 2638 9.710979 CATTACGTCAAATCGGTGTATTTAAAT 57.289 29.630 5.89 5.89 34.94 1.40
1794 2653 9.579610 GTGTATTTAAATTTTTGCATGTGTGTC 57.420 29.630 5.91 0.00 0.00 3.67
1891 2750 4.333649 ACTTCAGATCTTGTTGTGTGTGTG 59.666 41.667 0.00 0.00 0.00 3.82
1893 2752 3.622612 TCAGATCTTGTTGTGTGTGTGTG 59.377 43.478 0.00 0.00 0.00 3.82
1895 2754 3.374988 AGATCTTGTTGTGTGTGTGTGTG 59.625 43.478 0.00 0.00 0.00 3.82
1896 2755 2.499197 TCTTGTTGTGTGTGTGTGTGT 58.501 42.857 0.00 0.00 0.00 3.72
1897 2756 2.225255 TCTTGTTGTGTGTGTGTGTGTG 59.775 45.455 0.00 0.00 0.00 3.82
6751 8604 5.713389 TGAACTCCTTTTCCGTCACTCTATA 59.287 40.000 0.00 0.00 0.00 1.31
6752 8605 6.380274 TGAACTCCTTTTCCGTCACTCTATAT 59.620 38.462 0.00 0.00 0.00 0.86
6753 8606 7.558807 TGAACTCCTTTTCCGTCACTCTATATA 59.441 37.037 0.00 0.00 0.00 0.86
6754 8607 8.480133 AACTCCTTTTCCGTCACTCTATATAT 57.520 34.615 0.00 0.00 0.00 0.86
6905 8759 9.083422 CATCCTCCTATAGATGTCTTTCTGTAA 57.917 37.037 0.00 0.00 36.06 2.41
7045 8905 2.763448 AGCATGGAGGTAGTTGAGACTC 59.237 50.000 0.00 0.00 37.33 3.36
7121 8983 8.282455 TCGAGAAAATCTCTGTCTAATACTGT 57.718 34.615 5.88 0.00 41.26 3.55
7122 8984 8.184848 TCGAGAAAATCTCTGTCTAATACTGTG 58.815 37.037 5.88 0.00 41.26 3.66
7189 9051 7.213252 TCGTAATATAAGAGCGTTTTGACAC 57.787 36.000 0.00 0.00 0.00 3.67
7194 9057 8.542497 AATATAAGAGCGTTTTGACACTACAA 57.458 30.769 0.00 0.00 0.00 2.41
7229 9094 9.877178 AAATTGCTCTTATATTATAGGACGGAG 57.123 33.333 0.00 0.00 0.00 4.63
7231 9096 6.728411 TGCTCTTATATTATAGGACGGAGGA 58.272 40.000 0.00 0.00 0.00 3.71
7289 9154 1.941999 GCTCCTTGCTTGCCATGGTC 61.942 60.000 14.67 6.41 39.25 4.02
7338 9208 9.981114 TCGTGAAACATATGTTCATATGACTAT 57.019 29.630 28.36 16.12 37.25 2.12
7340 9210 9.817365 GTGAAACATATGTTCATATGACTATGC 57.183 33.333 28.36 15.68 37.25 3.14
7341 9211 9.002600 TGAAACATATGTTCATATGACTATGCC 57.997 33.333 28.36 15.17 37.25 4.40
7342 9212 7.601073 AACATATGTTCATATGACTATGCCG 57.399 36.000 28.36 8.70 37.80 5.69
7408 9278 0.672401 GACGAGCATGGGAACGGAAA 60.672 55.000 0.00 0.00 0.00 3.13
7469 9340 6.218746 TCGCTGATATACGTACTTCTCAGTA 58.781 40.000 18.76 10.34 34.13 2.74
7495 9366 3.118112 ACCATGGTATGAAAGCTCTGGAG 60.118 47.826 18.10 0.00 34.85 3.86
7506 9377 3.185880 AGCTCTGGAGGTTACCTTACA 57.814 47.619 4.99 7.44 35.28 2.41
7508 9379 2.168728 GCTCTGGAGGTTACCTTACAGG 59.831 54.545 25.79 19.87 42.49 4.00
7650 9947 1.409241 GGATTTGAGCCAGAGCCATGA 60.409 52.381 0.00 0.00 41.25 3.07
7660 9957 2.124151 AGCCATGATTCCACCCGC 60.124 61.111 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.818714 CAGAGCTTGGCTGCCTCG 60.819 66.667 21.03 11.58 39.88 4.63
16 17 2.438075 CCAGAGCTTGGCTGCCTC 60.438 66.667 21.03 8.94 39.88 4.70
24 25 0.464013 CAGAGGGATGCCAGAGCTTG 60.464 60.000 5.86 0.00 40.80 4.01
25 26 1.913722 CAGAGGGATGCCAGAGCTT 59.086 57.895 5.86 0.00 40.80 3.74
26 27 2.744243 GCAGAGGGATGCCAGAGCT 61.744 63.158 5.86 0.00 40.43 4.09
27 28 2.203181 GCAGAGGGATGCCAGAGC 60.203 66.667 5.86 1.66 40.43 4.09
28 29 1.756408 ATCGCAGAGGGATGCCAGAG 61.756 60.000 5.86 0.00 43.63 3.35
29 30 0.469892 TATCGCAGAGGGATGCCAGA 60.470 55.000 5.86 0.00 43.63 3.86
30 31 0.612229 ATATCGCAGAGGGATGCCAG 59.388 55.000 5.86 0.00 43.63 4.85
31 32 0.610174 GATATCGCAGAGGGATGCCA 59.390 55.000 5.86 0.00 43.63 4.92
32 33 0.107945 GGATATCGCAGAGGGATGCC 60.108 60.000 0.00 0.00 43.63 4.40
33 34 0.610174 TGGATATCGCAGAGGGATGC 59.390 55.000 6.80 0.00 43.63 3.91
34 35 2.166050 CTCTGGATATCGCAGAGGGATG 59.834 54.545 27.24 13.57 43.63 3.51
35 36 2.455557 CTCTGGATATCGCAGAGGGAT 58.544 52.381 27.24 2.17 43.63 3.85
36 37 1.916506 CTCTGGATATCGCAGAGGGA 58.083 55.000 27.24 10.00 43.63 4.20
37 38 0.246086 GCTCTGGATATCGCAGAGGG 59.754 60.000 31.23 19.65 43.63 4.30
38 39 0.109365 CGCTCTGGATATCGCAGAGG 60.109 60.000 31.23 23.53 43.63 3.69
39 40 0.732196 GCGCTCTGGATATCGCAGAG 60.732 60.000 28.92 28.92 45.99 3.35
40 41 1.287191 GCGCTCTGGATATCGCAGA 59.713 57.895 17.63 17.63 45.99 4.26
41 42 2.085262 CGCGCTCTGGATATCGCAG 61.085 63.158 5.56 12.51 46.95 5.18
42 43 2.050077 CGCGCTCTGGATATCGCA 60.050 61.111 5.56 0.47 46.95 5.10
43 44 3.474034 GCGCGCTCTGGATATCGC 61.474 66.667 26.67 0.00 43.62 4.58
44 45 2.807045 GGCGCGCTCTGGATATCG 60.807 66.667 32.29 0.00 0.00 2.92
45 46 2.433318 GGGCGCGCTCTGGATATC 60.433 66.667 32.29 10.56 0.00 1.63
46 47 4.008933 GGGGCGCGCTCTGGATAT 62.009 66.667 32.56 0.00 0.00 1.63
57 58 4.803908 CTGGGAGAAAGGGGGCGC 62.804 72.222 0.00 0.00 0.00 6.53
58 59 4.803908 GCTGGGAGAAAGGGGGCG 62.804 72.222 0.00 0.00 0.00 6.13
59 60 2.001269 TAGCTGGGAGAAAGGGGGC 61.001 63.158 0.00 0.00 0.00 5.80
60 61 0.914417 TGTAGCTGGGAGAAAGGGGG 60.914 60.000 0.00 0.00 0.00 5.40
61 62 0.253327 GTGTAGCTGGGAGAAAGGGG 59.747 60.000 0.00 0.00 0.00 4.79
62 63 0.108138 CGTGTAGCTGGGAGAAAGGG 60.108 60.000 0.00 0.00 0.00 3.95
63 64 0.741221 GCGTGTAGCTGGGAGAAAGG 60.741 60.000 0.00 0.00 44.04 3.11
64 65 1.078759 CGCGTGTAGCTGGGAGAAAG 61.079 60.000 0.00 0.00 45.59 2.62
65 66 1.080093 CGCGTGTAGCTGGGAGAAA 60.080 57.895 0.00 0.00 45.59 2.52
66 67 2.571757 CGCGTGTAGCTGGGAGAA 59.428 61.111 0.00 0.00 45.59 2.87
67 68 3.449227 CCGCGTGTAGCTGGGAGA 61.449 66.667 4.92 0.00 45.59 3.71
117 118 1.921887 CCATGATTTGCATCGCACAAC 59.078 47.619 0.00 0.00 38.71 3.32
118 119 1.135053 CCCATGATTTGCATCGCACAA 60.135 47.619 0.00 0.00 38.71 3.33
125 126 4.352009 TGTTTCTACCCCATGATTTGCAT 58.648 39.130 0.00 0.00 37.85 3.96
149 156 5.009110 TGTTTTATTGCGGTGATTCTGAACA 59.991 36.000 0.00 0.00 0.00 3.18
155 162 4.794169 ACACTGTTTTATTGCGGTGATTC 58.206 39.130 10.04 0.00 42.77 2.52
156 163 4.846779 ACACTGTTTTATTGCGGTGATT 57.153 36.364 10.04 0.00 42.77 2.57
157 164 4.846779 AACACTGTTTTATTGCGGTGAT 57.153 36.364 10.04 0.00 42.77 3.06
159 166 5.753744 TCTAAACACTGTTTTATTGCGGTG 58.246 37.500 12.35 0.00 44.90 4.94
160 167 5.761234 TCTCTAAACACTGTTTTATTGCGGT 59.239 36.000 12.35 0.00 0.00 5.68
161 168 6.236017 TCTCTAAACACTGTTTTATTGCGG 57.764 37.500 12.35 0.00 0.00 5.69
162 169 8.555166 TTTTCTCTAAACACTGTTTTATTGCG 57.445 30.769 12.35 0.00 0.00 4.85
163 170 8.480066 GCTTTTCTCTAAACACTGTTTTATTGC 58.520 33.333 12.35 4.20 0.00 3.56
164 171 9.736023 AGCTTTTCTCTAAACACTGTTTTATTG 57.264 29.630 12.35 2.38 0.00 1.90
191 208 2.094854 GCAGAGAGGAAAGCATTGTTGG 60.095 50.000 0.00 0.00 0.00 3.77
192 209 2.818432 AGCAGAGAGGAAAGCATTGTTG 59.182 45.455 0.00 0.00 0.00 3.33
194 211 2.617532 GGAGCAGAGAGGAAAGCATTGT 60.618 50.000 0.00 0.00 0.00 2.71
248 265 0.973632 AAGGGAATTTGCGGGGTTTC 59.026 50.000 0.00 0.00 0.00 2.78
278 295 2.124507 TACCTGTGCTCACCCTTGGC 62.125 60.000 0.00 0.00 0.00 4.52
292 309 5.877012 TCTTATCTTTTGCTTCTGCTACCTG 59.123 40.000 0.00 0.00 40.48 4.00
331 348 5.472137 TCTTTACTGTGCCCATCTTGTTAAC 59.528 40.000 0.00 0.00 0.00 2.01
344 361 4.053295 TGTCGTTAACCTCTTTACTGTGC 58.947 43.478 0.00 0.00 0.00 4.57
356 897 4.809426 CCATCTACCATCTTGTCGTTAACC 59.191 45.833 0.00 0.00 0.00 2.85
464 1011 0.760945 CAGGGGCTACAGGAGTAGGG 60.761 65.000 4.97 0.00 46.30 3.53
604 1151 3.728373 GGGTGGACGGCTGGGATT 61.728 66.667 0.00 0.00 0.00 3.01
610 1157 3.476031 CTTGTGTGGGTGGACGGCT 62.476 63.158 0.00 0.00 0.00 5.52
621 1168 1.064621 GGTGCTGTGTGCTTGTGTG 59.935 57.895 0.00 0.00 43.37 3.82
642 1189 4.423209 GGAGGGGAGGCTGGAGGT 62.423 72.222 0.00 0.00 0.00 3.85
652 1199 3.752167 GAGGGACCGAGGAGGGGA 61.752 72.222 0.00 0.00 46.96 4.81
653 1200 4.862823 GGAGGGACCGAGGAGGGG 62.863 77.778 0.00 0.00 46.96 4.79
654 1201 4.862823 GGGAGGGACCGAGGAGGG 62.863 77.778 0.00 0.00 46.96 4.30
656 1203 1.758906 GAAGGGAGGGACCGAGGAG 60.759 68.421 0.00 0.00 40.11 3.69
657 1204 2.363361 GAAGGGAGGGACCGAGGA 59.637 66.667 0.00 0.00 40.11 3.71
658 1205 2.764547 GGAAGGGAGGGACCGAGG 60.765 72.222 0.00 0.00 40.11 4.63
659 1206 2.764547 GGGAAGGGAGGGACCGAG 60.765 72.222 0.00 0.00 40.11 4.63
660 1207 3.281787 AGGGAAGGGAGGGACCGA 61.282 66.667 0.00 0.00 40.11 4.69
661 1208 3.083997 CAGGGAAGGGAGGGACCG 61.084 72.222 0.00 0.00 40.11 4.79
662 1209 3.412408 GCAGGGAAGGGAGGGACC 61.412 72.222 0.00 0.00 38.08 4.46
663 1210 3.412408 GGCAGGGAAGGGAGGGAC 61.412 72.222 0.00 0.00 0.00 4.46
692 1239 2.668212 TGGGCGCTGTGTACTTGC 60.668 61.111 7.64 0.00 0.00 4.01
772 1320 3.215597 CTGTGCGACGGTGTGGGTA 62.216 63.158 0.00 0.00 0.00 3.69
773 1321 4.602259 CTGTGCGACGGTGTGGGT 62.602 66.667 0.00 0.00 0.00 4.51
807 1355 1.565305 CGAAATTGGCGAGAGAGAGG 58.435 55.000 0.00 0.00 0.00 3.69
878 1436 1.627297 CGGGGAGAAAAGAGGAGGGG 61.627 65.000 0.00 0.00 0.00 4.79
883 1441 2.125106 CGGCGGGGAGAAAAGAGG 60.125 66.667 0.00 0.00 0.00 3.69
892 1450 2.926242 AAGAAGAACCGGCGGGGA 60.926 61.111 31.78 0.00 39.97 4.81
923 1481 1.306226 CCCTCCCTTCTTCTCGGGT 60.306 63.158 0.00 0.00 41.40 5.28
926 1730 0.686112 AGAGCCCTCCCTTCTTCTCG 60.686 60.000 0.00 0.00 0.00 4.04
1168 1972 1.295101 GCCCCAACCCCAAAAATCG 59.705 57.895 0.00 0.00 0.00 3.34
1254 2058 5.383130 GTTGGAAGACGCTAGAACAAATTC 58.617 41.667 0.00 0.00 34.78 2.17
1263 2067 1.068472 ACTGTCGTTGGAAGACGCTAG 60.068 52.381 0.00 0.00 42.50 3.42
1266 2070 1.282930 GGACTGTCGTTGGAAGACGC 61.283 60.000 1.07 0.00 42.50 5.19
1277 2081 4.338815 TCCTAGGCAGGACTGTCG 57.661 61.111 2.96 0.00 46.58 4.35
1332 2138 9.584839 GTCAAATGCTAAACAATGAAACATTTC 57.415 29.630 0.00 0.00 34.88 2.17
1336 2142 5.174761 GCGTCAAATGCTAAACAATGAAACA 59.825 36.000 0.00 0.00 32.06 2.83
1489 2336 1.235724 GAAGAACAACAACCCTCGGG 58.764 55.000 0.00 0.00 42.03 5.14
1570 2428 4.499357 CGAACACCAACGGGGAAAATAAAA 60.499 41.667 2.06 0.00 41.15 1.52
1694 2553 6.473455 GGCATTTTTGCACTGTGAATAGATAC 59.527 38.462 12.86 0.00 36.33 2.24
1751 2610 2.695359 ACACCGATTTGACGTAATGCT 58.305 42.857 0.00 0.00 0.00 3.79
1779 2638 8.785329 TGTATCTATAGACACACATGCAAAAA 57.215 30.769 9.83 0.00 0.00 1.94
1891 2750 6.826893 ATATTTGAAAGCAAACACACACAC 57.173 33.333 0.00 0.00 45.94 3.82
1893 2752 7.326063 GGAGTATATTTGAAAGCAAACACACAC 59.674 37.037 0.00 0.00 45.94 3.82
1895 2754 6.806739 GGGAGTATATTTGAAAGCAAACACAC 59.193 38.462 0.00 0.00 45.94 3.82
1896 2755 6.491745 TGGGAGTATATTTGAAAGCAAACACA 59.508 34.615 0.00 0.00 45.94 3.72
1897 2756 6.919721 TGGGAGTATATTTGAAAGCAAACAC 58.080 36.000 0.00 0.00 45.94 3.32
6753 8606 9.553064 CAGTTTAATCCAGAATAAGCAGAGTAT 57.447 33.333 0.00 0.00 0.00 2.12
6754 8607 7.495934 GCAGTTTAATCCAGAATAAGCAGAGTA 59.504 37.037 0.00 0.00 0.00 2.59
6825 8679 4.324402 CCACAGCAGAATTTAATGAAACGC 59.676 41.667 0.00 0.00 0.00 4.84
6895 8749 6.035650 CCGTCTCGCAAAATATTACAGAAAGA 59.964 38.462 0.00 0.00 0.00 2.52
6905 8759 1.014352 GCCACCGTCTCGCAAAATAT 58.986 50.000 0.00 0.00 0.00 1.28
7045 8905 2.209838 ATGATCCAGCGAGTACAACG 57.790 50.000 7.86 7.86 0.00 4.10
7121 8983 6.412362 AGCAACAATAACCAATTTACCACA 57.588 33.333 0.00 0.00 0.00 4.17
7122 8984 5.867174 GGAGCAACAATAACCAATTTACCAC 59.133 40.000 0.00 0.00 0.00 4.16
7206 9069 7.179966 TCCTCCGTCCTATAATATAAGAGCAA 58.820 38.462 0.00 0.00 0.00 3.91
7207 9070 6.728411 TCCTCCGTCCTATAATATAAGAGCA 58.272 40.000 0.00 0.00 0.00 4.26
7229 9094 1.599542 GGCACGCAGAATGATACTTCC 59.400 52.381 0.00 0.00 39.69 3.46
7289 9154 4.529446 GCAAATGGCATGTTCACAAAAAG 58.471 39.130 0.00 0.00 43.97 2.27
7338 9208 2.159268 CATTTCAATGGTGCATACGGCA 60.159 45.455 0.00 0.00 44.83 5.69
7339 9209 2.462889 CATTTCAATGGTGCATACGGC 58.537 47.619 0.00 0.00 36.49 5.68
7340 9210 2.159268 TGCATTTCAATGGTGCATACGG 60.159 45.455 0.00 0.00 43.30 4.02
7341 9211 3.148026 TGCATTTCAATGGTGCATACG 57.852 42.857 0.00 0.00 43.30 3.06
7408 9278 2.011122 TCTCCCGTTTCTCTTCACCT 57.989 50.000 0.00 0.00 0.00 4.00
7469 9340 3.525199 AGAGCTTTCATACCATGGTTCCT 59.475 43.478 25.38 5.53 0.00 3.36
7506 9377 6.113411 CGTCTTCCAAAAATACAGTATCCCT 58.887 40.000 0.00 0.00 0.00 4.20
7508 9379 5.878669 ACCGTCTTCCAAAAATACAGTATCC 59.121 40.000 0.00 0.00 0.00 2.59
7650 9947 2.362375 ATTTGGCGCGGGTGGAAT 60.362 55.556 8.83 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.