Multiple sequence alignment - TraesCS2A01G129700

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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 TraesCS2A01G129700 chr2A 100.000 5204 0 0 1 5204 77536535 77541738 0.000000e+00 9611.0
1 TraesCS2A01G129700 chr2A 81.893 243 40 4 411 651 207761161 207761401 8.840000e-48 202.0
2 TraesCS2A01G129700 chr2A 80.702 228 28 12 407 620 534320032 534320257 4.170000e-36 163.0
3 TraesCS2A01G129700 chr2D 96.093 2457 70 14 2730 5175 76872999 76875440 0.000000e+00 3982.0
4 TraesCS2A01G129700 chr2D 96.180 1466 32 11 885 2340 76870802 76872253 0.000000e+00 2375.0
5 TraesCS2A01G129700 chr2D 87.566 378 39 3 1 371 76867980 76868356 1.040000e-116 431.0
6 TraesCS2A01G129700 chr2D 82.222 405 60 6 5 398 304267379 304267782 6.450000e-89 339.0
7 TraesCS2A01G129700 chr2D 90.367 218 8 2 2529 2733 76872667 76872884 1.850000e-69 274.0
8 TraesCS2A01G129700 chr2D 84.426 244 36 2 411 652 88404246 88404489 6.730000e-59 239.0
9 TraesCS2A01G129700 chr2D 78.902 346 48 15 421 748 195229487 195229825 1.470000e-50 211.0
10 TraesCS2A01G129700 chr2D 89.683 126 8 2 2409 2530 76872459 76872583 6.980000e-34 156.0
11 TraesCS2A01G129700 chr2D 77.686 121 25 2 683 802 377163874 377163755 7.230000e-09 73.1
12 TraesCS2A01G129700 chr2D 100.000 29 0 0 5147 5175 433310638 433310610 3.000000e-03 54.7
13 TraesCS2A01G129700 chr2B 94.817 2219 85 9 2730 4941 118631383 118633578 0.000000e+00 3434.0
14 TraesCS2A01G129700 chr2B 95.178 1887 51 14 874 2733 118629396 118631269 0.000000e+00 2944.0
15 TraesCS2A01G129700 chr2B 82.134 403 60 9 5 399 399839083 399839481 8.350000e-88 335.0
16 TraesCS2A01G129700 chr2B 82.086 374 52 5 407 778 118628753 118629113 6.550000e-79 305.0
17 TraesCS2A01G129700 chr6D 85.540 1065 150 4 3137 4200 468057336 468056275 0.000000e+00 1110.0
18 TraesCS2A01G129700 chr6D 85.302 1075 152 6 3137 4209 468168805 468167735 0.000000e+00 1105.0
19 TraesCS2A01G129700 chr6D 86.173 1027 135 4 3190 4212 468096638 468095615 0.000000e+00 1103.0
20 TraesCS2A01G129700 chr6D 85.311 1028 148 3 3192 4217 468147033 468146007 0.000000e+00 1059.0
21 TraesCS2A01G129700 chr6D 84.289 401 53 5 5 398 264689735 264690132 2.940000e-102 383.0
22 TraesCS2A01G129700 chr6D 84.328 402 51 7 6 398 422180449 422180051 2.940000e-102 383.0
23 TraesCS2A01G129700 chr6D 84.918 305 38 2 1782 2086 468059034 468058738 8.470000e-78 302.0
24 TraesCS2A01G129700 chr6D 73.664 767 149 31 1626 2379 468152487 468151761 1.120000e-61 248.0
25 TraesCS2A01G129700 chr6D 79.933 299 50 6 1034 1331 468171302 468171013 1.470000e-50 211.0
26 TraesCS2A01G129700 chr6D 83.582 201 33 0 1112 1312 468060691 468060491 6.880000e-44 189.0
27 TraesCS2A01G129700 chr6D 83.750 160 24 2 1124 1282 29769076 29769234 3.250000e-32 150.0
28 TraesCS2A01G129700 chr6D 75.309 324 68 11 1767 2085 1428984 1428668 1.510000e-30 145.0
29 TraesCS2A01G129700 chr6D 80.000 190 29 2 1112 1301 468153160 468152980 1.180000e-26 132.0
30 TraesCS2A01G129700 chr6D 79.355 155 22 7 2230 2382 34950638 34950492 3.320000e-17 100.0
31 TraesCS2A01G129700 chr6B 84.871 1084 159 5 3137 4217 714340767 714339686 0.000000e+00 1088.0
32 TraesCS2A01G129700 chr6B 73.575 772 150 35 1626 2386 714335942 714335214 4.020000e-61 246.0
33 TraesCS2A01G129700 chr6B 74.664 596 128 13 1505 2088 714409475 714408891 5.210000e-60 243.0
34 TraesCS2A01G129700 chr6B 86.667 195 21 3 4962 5151 239292938 239292744 1.470000e-50 211.0
35 TraesCS2A01G129700 chr6B 78.261 345 43 21 407 736 31017525 31017852 5.320000e-45 193.0
36 TraesCS2A01G129700 chr6B 84.737 190 29 0 1112 1301 714336624 714336435 1.910000e-44 191.0
37 TraesCS2A01G129700 chr6B 82.301 226 32 4 4939 5157 116579482 116579706 6.880000e-44 189.0
38 TraesCS2A01G129700 chr6B 80.543 221 34 6 4942 5157 116456819 116457035 1.500000e-35 161.0
39 TraesCS2A01G129700 chrUn 84.779 1084 155 8 3137 4217 346081754 346080678 0.000000e+00 1079.0
40 TraesCS2A01G129700 chrUn 85.423 1029 145 5 3192 4217 310899428 310900454 0.000000e+00 1064.0
41 TraesCS2A01G129700 chrUn 73.725 765 152 29 1626 2379 216381723 216382449 2.410000e-63 254.0
42 TraesCS2A01G129700 chrUn 74.664 596 128 13 1505 2088 211920601 211921185 5.210000e-60 243.0
43 TraesCS2A01G129700 chrUn 82.632 190 33 0 1112 1301 216381041 216381230 8.960000e-38 169.0
44 TraesCS2A01G129700 chrUn 75.563 311 67 7 1777 2082 51444015 51444321 1.510000e-30 145.0
45 TraesCS2A01G129700 chr1D 84.236 406 50 11 6 399 32758955 32759358 2.940000e-102 383.0
46 TraesCS2A01G129700 chr1D 89.091 110 11 1 694 802 400121725 400121616 9.090000e-28 135.0
47 TraesCS2A01G129700 chr1D 76.000 200 44 3 1887 2085 2461404 2461208 3.320000e-17 100.0
48 TraesCS2A01G129700 chr3A 83.586 396 58 2 6 395 201495737 201496131 1.060000e-96 364.0
49 TraesCS2A01G129700 chr3A 84.186 215 23 8 4941 5145 142557837 142557624 1.140000e-46 198.0
50 TraesCS2A01G129700 chr3A 78.431 204 35 3 4939 5134 679257903 679258105 1.970000e-24 124.0
51 TraesCS2A01G129700 chr3A 97.222 36 1 0 694 729 72476511 72476476 1.560000e-05 62.1
52 TraesCS2A01G129700 chr3B 83.375 403 51 11 5 399 642817688 642818082 4.950000e-95 359.0
53 TraesCS2A01G129700 chr4B 82.294 401 58 10 9 399 645310504 645310901 8.350000e-88 335.0
54 TraesCS2A01G129700 chr4B 83.796 216 26 4 4938 5145 113598324 113598110 4.110000e-46 196.0
55 TraesCS2A01G129700 chr4B 77.843 343 48 19 407 736 45786813 45787140 2.470000e-43 187.0
56 TraesCS2A01G129700 chr6A 78.995 438 67 14 412 843 597685519 597685101 5.130000e-70 276.0
57 TraesCS2A01G129700 chr6A 82.951 305 44 2 1782 2086 614164789 614164493 8.590000e-68 268.0
58 TraesCS2A01G129700 chr6A 83.249 197 30 2 4952 5145 599854053 599854249 1.490000e-40 178.0
59 TraesCS2A01G129700 chr6A 85.890 163 23 0 1112 1274 614165660 614165498 1.930000e-39 174.0
60 TraesCS2A01G129700 chr4A 79.947 374 59 11 411 781 576045770 576046130 1.440000e-65 261.0
61 TraesCS2A01G129700 chr4A 83.478 230 29 2 4931 5151 715069769 715069998 6.830000e-49 206.0
62 TraesCS2A01G129700 chr4A 84.127 189 26 3 4941 5126 632695403 632695590 4.140000e-41 180.0
63 TraesCS2A01G129700 chr7D 86.207 232 17 6 4941 5157 255788830 255788599 2.420000e-58 237.0
64 TraesCS2A01G129700 chr7D 77.541 423 71 19 407 821 83388812 83388406 3.130000e-57 233.0
65 TraesCS2A01G129700 chr7D 74.923 323 53 14 486 802 571187928 571188228 7.080000e-24 122.0
66 TraesCS2A01G129700 chr7D 84.545 110 16 1 694 802 203023368 203023259 1.980000e-19 108.0
67 TraesCS2A01G129700 chr5A 78.283 396 57 16 407 786 1902009 1901627 1.460000e-55 228.0
68 TraesCS2A01G129700 chr5A 83.028 218 27 4 4938 5145 120785170 120784953 6.880000e-44 189.0
69 TraesCS2A01G129700 chr5A 76.205 332 47 19 1769 2085 625738067 625737753 4.200000e-31 147.0
70 TraesCS2A01G129700 chr4D 79.224 361 48 18 407 748 69131875 69131523 5.240000e-55 226.0
71 TraesCS2A01G129700 chr4D 82.203 236 31 5 4932 5158 78843915 78844148 5.320000e-45 193.0
72 TraesCS2A01G129700 chr3D 84.444 225 24 4 4939 5153 152171983 152172206 1.470000e-50 211.0
73 TraesCS2A01G129700 chr3D 100.000 28 0 0 5148 5175 27833472 27833499 9.000000e-03 52.8
74 TraesCS2A01G129700 chr1A 75.926 378 55 28 423 781 529262516 529262876 1.500000e-35 161.0
75 TraesCS2A01G129700 chr7A 80.000 230 29 9 4939 5151 31864162 31863933 2.510000e-33 154.0
76 TraesCS2A01G129700 chr7A 76.025 317 56 12 494 803 241725900 241725597 4.200000e-31 147.0
77 TraesCS2A01G129700 chr7A 100.000 28 0 0 5148 5175 31422859 31422832 9.000000e-03 52.8
78 TraesCS2A01G129700 chr5B 77.244 312 39 19 1789 2085 633178623 633178329 2.510000e-33 154.0
79 TraesCS2A01G129700 chr5B 82.036 167 28 2 1124 1289 623167152 623167317 1.950000e-29 141.0
80 TraesCS2A01G129700 chr1B 81.208 149 26 2 2238 2385 22823894 22823747 9.150000e-23 119.0
81 TraesCS2A01G129700 chr7B 100.000 29 0 0 5147 5175 289596501 289596473 3.000000e-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 TraesCS2A01G129700 chr2A 77536535 77541738 5203 False 9611.000000 9611 100.000000 1 5204 1 chr2A.!!$F1 5203
1 TraesCS2A01G129700 chr2D 76867980 76875440 7460 False 1443.600000 3982 91.977800 1 5175 5 chr2D.!!$F4 5174
2 TraesCS2A01G129700 chr2B 118628753 118633578 4825 False 2227.666667 3434 90.693667 407 4941 3 chr2B.!!$F2 4534
3 TraesCS2A01G129700 chr6D 468095615 468096638 1023 True 1103.000000 1103 86.173000 3190 4212 1 chr6D.!!$R4 1022
4 TraesCS2A01G129700 chr6D 468146007 468147033 1026 True 1059.000000 1059 85.311000 3192 4217 1 chr6D.!!$R5 1025
5 TraesCS2A01G129700 chr6D 468167735 468171302 3567 True 658.000000 1105 82.617500 1034 4209 2 chr6D.!!$R8 3175
6 TraesCS2A01G129700 chr6D 468056275 468060691 4416 True 533.666667 1110 84.680000 1112 4200 3 chr6D.!!$R6 3088
7 TraesCS2A01G129700 chr6B 714335214 714340767 5553 True 508.333333 1088 81.061000 1112 4217 3 chr6B.!!$R3 3105
8 TraesCS2A01G129700 chr6B 714408891 714409475 584 True 243.000000 243 74.664000 1505 2088 1 chr6B.!!$R2 583
9 TraesCS2A01G129700 chrUn 346080678 346081754 1076 True 1079.000000 1079 84.779000 3137 4217 1 chrUn.!!$R1 1080
10 TraesCS2A01G129700 chrUn 310899428 310900454 1026 False 1064.000000 1064 85.423000 3192 4217 1 chrUn.!!$F3 1025
11 TraesCS2A01G129700 chrUn 211920601 211921185 584 False 243.000000 243 74.664000 1505 2088 1 chrUn.!!$F2 583
12 TraesCS2A01G129700 chrUn 216381041 216382449 1408 False 211.500000 254 78.178500 1112 2379 2 chrUn.!!$F4 1267
13 TraesCS2A01G129700 chr6A 614164493 614165660 1167 True 221.000000 268 84.420500 1112 2086 2 chr6A.!!$R2 974

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
883 3117 0.036765 TCCCCCGTGCATATATTCGC 60.037 55.000 0.00 0.0 0.0 4.70 F
1838 5115 0.108756 GACTGGTACCGCTTCTCCAC 60.109 60.000 7.57 0.0 0.0 4.02 F
1839 5116 1.153823 CTGGTACCGCTTCTCCACG 60.154 63.158 7.57 0.0 0.0 4.94 F
2354 5800 1.318576 GCACCGATAAATTCCCCCTG 58.681 55.000 0.00 0.0 0.0 4.45 F
2446 5899 1.657594 CTTAGCAGCACACATGTCTCG 59.342 52.381 0.00 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2240 5526 0.613260 TCCCATCACTCGAACAAGGG 59.387 55.000 0.0 0.0 36.15 3.95 R
3213 7503 3.795688 ATGCCACCTATTCCACCTATG 57.204 47.619 0.0 0.0 0.00 2.23 R
3798 8089 3.887716 GCCTTGATATGCCAAAGTCTGAT 59.112 43.478 0.0 0.0 0.00 2.90 R
4148 8439 3.206964 CGCTCTACTACCTCTGTCATCA 58.793 50.000 0.0 0.0 0.00 3.07 R
4295 8619 3.909732 TGGAACCAATGTGAAACCTTCT 58.090 40.909 0.0 0.0 34.36 2.85 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
44 45 9.630098 CCTCAAATCCATATTATTACATGCAAC 57.370 33.333 0.00 0.00 0.00 4.17
45 46 9.333497 CTCAAATCCATATTATTACATGCAACG 57.667 33.333 0.00 0.00 0.00 4.10
67 68 5.294552 ACGTAGCAATCTTAAAATGGAGCTC 59.705 40.000 4.71 4.71 32.70 4.09
78 79 1.068083 TGGAGCTCCATTCGATCGC 59.932 57.895 32.00 1.53 42.01 4.58
86 87 4.155733 ATTCGATCGCCGTGCCCA 62.156 61.111 11.09 0.00 39.75 5.36
88 89 4.889856 TCGATCGCCGTGCCCATG 62.890 66.667 11.09 0.00 39.75 3.66
90 91 3.272334 GATCGCCGTGCCCATGTC 61.272 66.667 0.00 0.00 0.00 3.06
97 98 3.192922 GTGCCCATGTCGTACGGC 61.193 66.667 14.12 14.12 41.99 5.68
122 124 2.520968 GCCCCCAGAGTGTTGGTT 59.479 61.111 0.00 0.00 36.45 3.67
129 131 0.307760 CAGAGTGTTGGTTCGGTTGC 59.692 55.000 0.00 0.00 0.00 4.17
130 132 0.180406 AGAGTGTTGGTTCGGTTGCT 59.820 50.000 0.00 0.00 0.00 3.91
147 149 4.021916 GTTGCTGGTAAGGTAGAGTAGGA 58.978 47.826 0.00 0.00 0.00 2.94
152 154 4.543689 TGGTAAGGTAGAGTAGGACATGG 58.456 47.826 0.00 0.00 0.00 3.66
169 171 2.126424 GGACACGAGCCGACTCAC 60.126 66.667 0.00 0.00 43.66 3.51
184 186 4.379243 CACGGGACTCAAGGCGCT 62.379 66.667 7.64 0.00 0.00 5.92
200 202 4.100084 CTGCCGTCTCCCATGCCA 62.100 66.667 0.00 0.00 0.00 4.92
211 213 3.389329 TCTCCCATGCCATACTCTTTCTC 59.611 47.826 0.00 0.00 0.00 2.87
217 219 1.536284 GCCATACTCTTTCTCGTCGGG 60.536 57.143 0.00 0.00 0.00 5.14
246 248 1.302431 CATTGGACGCTGGTGGACA 60.302 57.895 0.00 0.00 0.00 4.02
319 327 3.360340 GCACCAGGACTGCTGCAC 61.360 66.667 13.24 0.00 40.77 4.57
337 345 2.519622 CCATATGGGGCGCTGGAGA 61.520 63.158 14.52 0.00 0.00 3.71
355 363 0.108898 GAGTGTGACTCTGCATCGCT 60.109 55.000 0.00 0.00 41.88 4.93
359 367 1.153958 TGACTCTGCATCGCTGACG 60.154 57.895 0.00 0.00 42.01 4.35
465 714 4.554036 GTGGGATGAGCTCGGGGC 62.554 72.222 9.64 0.00 42.19 5.80
504 753 1.219124 GACTCAGATTCGCTGCCCA 59.781 57.895 0.00 0.00 44.52 5.36
555 806 3.338250 GCATGGGTGGTGGAGGGA 61.338 66.667 0.00 0.00 0.00 4.20
562 813 1.208165 GGTGGTGGAGGGAAGTGGAT 61.208 60.000 0.00 0.00 0.00 3.41
564 815 1.913419 GTGGTGGAGGGAAGTGGATTA 59.087 52.381 0.00 0.00 0.00 1.75
583 834 2.767644 AAAGTGGCTAGGGTTTGGTT 57.232 45.000 0.00 0.00 0.00 3.67
597 848 4.508128 GGTTCGGCGAGCGGATGA 62.508 66.667 17.37 0.00 0.00 2.92
598 849 2.508439 GTTCGGCGAGCGGATGAA 60.508 61.111 10.46 0.00 0.00 2.57
647 898 3.771160 GTGGGCTGGATCCGACGT 61.771 66.667 7.39 0.00 0.00 4.34
648 899 3.770040 TGGGCTGGATCCGACGTG 61.770 66.667 7.39 0.00 0.00 4.49
649 900 4.530857 GGGCTGGATCCGACGTGG 62.531 72.222 7.39 0.00 40.09 4.94
652 903 3.822192 CTGGATCCGACGTGGCGA 61.822 66.667 7.39 0.00 37.80 5.54
653 904 4.124351 TGGATCCGACGTGGCGAC 62.124 66.667 7.39 0.00 37.80 5.19
684 935 2.047061 GCCGGGATGCCTCCATATATA 58.953 52.381 10.44 0.00 44.08 0.86
685 936 2.639839 GCCGGGATGCCTCCATATATAT 59.360 50.000 10.44 0.00 44.08 0.86
686 937 3.838317 GCCGGGATGCCTCCATATATATA 59.162 47.826 10.44 0.00 44.08 0.86
687 938 4.322801 GCCGGGATGCCTCCATATATATAC 60.323 50.000 10.44 0.00 44.08 1.47
688 939 4.838423 CCGGGATGCCTCCATATATATACA 59.162 45.833 10.44 0.00 44.08 2.29
692 943 6.330250 GGGATGCCTCCATATATATACACCTT 59.670 42.308 10.44 0.00 44.08 3.50
749 1000 0.386352 GCGTTTAAGTCCCGTTTGCC 60.386 55.000 0.00 0.00 0.00 4.52
760 1011 2.357760 GTTTGCCACGCCCGTCTA 60.358 61.111 0.00 0.00 0.00 2.59
761 1012 1.962306 GTTTGCCACGCCCGTCTAA 60.962 57.895 0.00 0.00 0.00 2.10
762 1013 1.669760 TTTGCCACGCCCGTCTAAG 60.670 57.895 0.00 0.00 0.00 2.18
765 1016 2.967397 CCACGCCCGTCTAAGTCA 59.033 61.111 0.00 0.00 0.00 3.41
790 1041 1.153823 CGTGACCGGTCAGTGATCC 60.154 63.158 37.04 22.34 40.75 3.36
820 1071 3.555527 CCTGATGAGGCAGATTTGAGA 57.444 47.619 0.00 0.00 38.14 3.27
821 1072 3.204526 CCTGATGAGGCAGATTTGAGAC 58.795 50.000 0.00 0.00 38.14 3.36
822 1073 2.864946 CTGATGAGGCAGATTTGAGACG 59.135 50.000 0.00 0.00 38.14 4.18
824 1075 0.737367 TGAGGCAGATTTGAGACGCG 60.737 55.000 3.53 3.53 0.00 6.01
825 1076 0.737715 GAGGCAGATTTGAGACGCGT 60.738 55.000 13.85 13.85 0.00 6.01
868 3094 0.661020 CGTATGCACGGAATTTCCCC 59.339 55.000 9.87 0.00 44.59 4.81
883 3117 0.036765 TCCCCCGTGCATATATTCGC 60.037 55.000 0.00 0.00 0.00 4.70
931 3171 2.040178 CCGGAGCTTAATGACCTAGGT 58.960 52.381 16.26 16.26 0.00 3.08
937 3177 6.592870 GGAGCTTAATGACCTAGGTGTAATT 58.407 40.000 22.10 17.54 0.00 1.40
949 3189 2.493278 AGGTGTAATTTGCATGAGTGGC 59.507 45.455 0.00 0.00 0.00 5.01
1065 3306 3.166679 GCCGATAATCCTAGTCCTCCTT 58.833 50.000 0.00 0.00 0.00 3.36
1066 3307 3.056465 GCCGATAATCCTAGTCCTCCTTG 60.056 52.174 0.00 0.00 0.00 3.61
1067 3308 3.056465 CCGATAATCCTAGTCCTCCTTGC 60.056 52.174 0.00 0.00 0.00 4.01
1068 3309 3.574396 CGATAATCCTAGTCCTCCTTGCA 59.426 47.826 0.00 0.00 0.00 4.08
1069 3310 4.321601 CGATAATCCTAGTCCTCCTTGCAG 60.322 50.000 0.00 0.00 0.00 4.41
1070 3311 1.127343 ATCCTAGTCCTCCTTGCAGC 58.873 55.000 0.00 0.00 0.00 5.25
1071 3312 0.252239 TCCTAGTCCTCCTTGCAGCA 60.252 55.000 0.00 0.00 0.00 4.41
1091 3332 1.801332 CAGCAGCAGCATCAACTCC 59.199 57.895 3.17 0.00 45.49 3.85
1106 3347 4.168101 TCAACTCCCTTGATCTTACAGGT 58.832 43.478 0.00 0.00 33.65 4.00
1838 5115 0.108756 GACTGGTACCGCTTCTCCAC 60.109 60.000 7.57 0.00 0.00 4.02
1839 5116 1.153823 CTGGTACCGCTTCTCCACG 60.154 63.158 7.57 0.00 0.00 4.94
2240 5526 5.107065 CCGAAAACTGAATCCTGAGTTGTAC 60.107 44.000 0.00 0.00 32.66 2.90
2297 5583 2.216898 GAAGGCTATGACTGTCCATGC 58.783 52.381 5.17 6.42 0.00 4.06
2354 5800 1.318576 GCACCGATAAATTCCCCCTG 58.681 55.000 0.00 0.00 0.00 4.45
2385 5831 3.068873 GGTGATTGTGGGTAAGCACAAAA 59.931 43.478 0.00 0.00 45.90 2.44
2421 5870 7.634817 CACATTAATCGATTACAACCGTCTTTC 59.365 37.037 17.33 0.00 0.00 2.62
2434 5887 1.996191 CGTCTTTCTGTCCTTAGCAGC 59.004 52.381 0.00 0.00 34.21 5.25
2446 5899 1.657594 CTTAGCAGCACACATGTCTCG 59.342 52.381 0.00 0.00 0.00 4.04
2646 6197 4.248859 GCCTCTGCATCATTACGATACAT 58.751 43.478 0.00 0.00 37.47 2.29
2740 6778 5.184479 TGATTTCAAAGCCTCTTCCAAGATG 59.816 40.000 0.00 0.00 33.93 2.90
2742 6780 3.679389 TCAAAGCCTCTTCCAAGATGAC 58.321 45.455 0.00 0.00 33.93 3.06
2786 6826 6.224584 TGTGAAATGTAGTACGAACCAATCA 58.775 36.000 0.00 0.00 0.00 2.57
2796 6836 7.499321 AGTACGAACCAATCATTTGTAAACA 57.501 32.000 0.00 0.00 29.63 2.83
2844 6884 6.248433 ACACAGATGACCAACATAGGAAAAT 58.752 36.000 0.00 0.00 39.56 1.82
2847 6887 8.090214 CACAGATGACCAACATAGGAAAATTTT 58.910 33.333 2.28 2.28 39.56 1.82
2968 7008 6.349777 GGCTTCTACTCAGCTATCGACATATT 60.350 42.308 0.00 0.00 37.43 1.28
2969 7009 7.148222 GGCTTCTACTCAGCTATCGACATATTA 60.148 40.741 0.00 0.00 37.43 0.98
2970 7010 8.237949 GCTTCTACTCAGCTATCGACATATTAA 58.762 37.037 0.00 0.00 34.15 1.40
3213 7503 7.148507 TGTGAAATCATTTTGTTTTGTGTCCAC 60.149 33.333 0.00 0.00 0.00 4.02
3214 7504 6.875726 TGAAATCATTTTGTTTTGTGTCCACA 59.124 30.769 0.00 0.00 39.98 4.17
3231 7521 2.851195 CACATAGGTGGAATAGGTGGC 58.149 52.381 0.00 0.00 41.45 5.01
3498 7789 7.288852 AGTGGTACTATGCTAGAGAATGAACAT 59.711 37.037 0.00 0.00 0.00 2.71
3798 8089 3.787785 TGATAAGTTTGCGCCGAAGATA 58.212 40.909 4.18 0.00 0.00 1.98
4148 8439 4.708421 CCTTGATGTGGATCAAAGACCATT 59.292 41.667 0.00 0.00 45.89 3.16
4295 8619 5.499004 AAAGCATGTAAGGTAGGAACAGA 57.501 39.130 0.00 0.00 0.00 3.41
4690 11277 7.962934 TTTAATAAACGCATTTTCCATCTCG 57.037 32.000 0.00 0.00 0.00 4.04
4709 11296 0.173255 GGCATTGTGACATTTCCCCG 59.827 55.000 0.00 0.00 0.00 5.73
4961 11991 2.156098 GAGCATCTCTAGTAGACCCCG 58.844 57.143 0.00 0.00 36.93 5.73
4970 12000 6.845908 TCTCTAGTAGACCCCGTATAATGTT 58.154 40.000 0.00 0.00 0.00 2.71
4977 12007 1.223187 CCCGTATAATGTTGACCCGC 58.777 55.000 0.00 0.00 0.00 6.13
4997 12027 3.040099 GCAAAATGCGTTTACTGTTCGT 58.960 40.909 3.90 0.00 31.71 3.85
5007 12037 4.619760 CGTTTACTGTTCGTTGCAGATCTA 59.380 41.667 0.00 0.00 37.40 1.98
5025 12055 2.354510 TCTAATTTGCAGGGCGAATTCG 59.645 45.455 23.34 23.34 46.02 3.34
5181 12573 3.625745 GGACACATCCGTTCTTGGT 57.374 52.632 0.00 0.00 34.48 3.67
5183 12575 3.048337 GGACACATCCGTTCTTGGTAA 57.952 47.619 0.00 0.00 34.48 2.85
5184 12576 3.404899 GGACACATCCGTTCTTGGTAAA 58.595 45.455 0.00 0.00 34.48 2.01
5185 12577 3.187842 GGACACATCCGTTCTTGGTAAAC 59.812 47.826 0.00 0.00 34.48 2.01
5186 12578 2.803956 ACACATCCGTTCTTGGTAAACG 59.196 45.455 1.64 1.64 46.79 3.60
5188 12580 3.249080 CACATCCGTTCTTGGTAAACGTT 59.751 43.478 0.00 0.00 46.03 3.99
5189 12581 3.249080 ACATCCGTTCTTGGTAAACGTTG 59.751 43.478 0.00 7.16 46.03 4.10
5190 12582 1.598601 TCCGTTCTTGGTAAACGTTGC 59.401 47.619 0.00 0.00 46.03 4.17
5191 12583 1.331138 CCGTTCTTGGTAAACGTTGCA 59.669 47.619 0.00 0.00 46.03 4.08
5192 12584 2.031508 CCGTTCTTGGTAAACGTTGCAT 60.032 45.455 0.00 0.00 46.03 3.96
5193 12585 2.970609 CGTTCTTGGTAAACGTTGCATG 59.029 45.455 0.00 0.00 43.31 4.06
5195 12587 2.852449 TCTTGGTAAACGTTGCATGGA 58.148 42.857 0.00 0.00 0.00 3.41
5198 12590 4.098044 TCTTGGTAAACGTTGCATGGAAAA 59.902 37.500 0.00 0.00 0.00 2.29
5199 12591 3.707793 TGGTAAACGTTGCATGGAAAAC 58.292 40.909 0.00 0.00 0.00 2.43
5200 12592 3.130516 TGGTAAACGTTGCATGGAAAACA 59.869 39.130 0.00 0.00 0.00 2.83
5201 12593 4.113354 GGTAAACGTTGCATGGAAAACAA 58.887 39.130 0.00 0.00 0.00 2.83
5202 12594 4.567159 GGTAAACGTTGCATGGAAAACAAA 59.433 37.500 0.00 0.00 0.00 2.83
5203 12595 5.063564 GGTAAACGTTGCATGGAAAACAAAA 59.936 36.000 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.277538 GGAGCTCCATTTTAAGATTGCTACG 60.278 44.000 28.43 0.00 35.64 3.51
45 46 5.590259 TGGAGCTCCATTTTAAGATTGCTAC 59.410 40.000 32.00 0.00 42.01 3.58
67 68 3.640000 GGCACGGCGATCGAATGG 61.640 66.667 21.57 6.10 42.43 3.16
69 70 3.460672 ATGGGCACGGCGATCGAAT 62.461 57.895 21.57 0.00 42.43 3.34
78 79 2.883730 CGTACGACATGGGCACGG 60.884 66.667 10.44 0.00 0.00 4.94
86 87 4.508128 CAGCCGGCCGTACGACAT 62.508 66.667 26.15 0.00 35.47 3.06
105 106 1.603739 GAACCAACACTCTGGGGGC 60.604 63.158 0.00 0.00 41.16 5.80
113 115 1.101049 CCAGCAACCGAACCAACACT 61.101 55.000 0.00 0.00 0.00 3.55
122 124 1.822990 CTCTACCTTACCAGCAACCGA 59.177 52.381 0.00 0.00 0.00 4.69
129 131 4.585162 CCATGTCCTACTCTACCTTACCAG 59.415 50.000 0.00 0.00 0.00 4.00
130 132 4.543689 CCATGTCCTACTCTACCTTACCA 58.456 47.826 0.00 0.00 0.00 3.25
147 149 2.994995 TCGGCTCGTGTCCCATGT 60.995 61.111 0.00 0.00 0.00 3.21
152 154 2.126424 GTGAGTCGGCTCGTGTCC 60.126 66.667 13.21 0.00 44.48 4.02
162 164 1.213013 CCTTGAGTCCCGTGAGTCG 59.787 63.158 0.00 0.00 42.83 4.18
184 186 2.069430 TATGGCATGGGAGACGGCA 61.069 57.895 10.98 0.00 39.74 5.69
186 188 0.034059 GAGTATGGCATGGGAGACGG 59.966 60.000 10.98 0.00 0.00 4.79
198 200 1.067212 CCCCGACGAGAAAGAGTATGG 59.933 57.143 0.00 0.00 0.00 2.74
200 202 0.745468 GCCCCGACGAGAAAGAGTAT 59.255 55.000 0.00 0.00 0.00 2.12
217 219 2.036572 TCCAATGGGTTTCGGGCC 59.963 61.111 0.00 0.00 34.93 5.80
223 225 1.152830 ACCAGCGTCCAATGGGTTT 59.847 52.632 0.00 0.00 41.13 3.27
246 248 3.095332 ACGGATCCATCATCGATCTGAT 58.905 45.455 13.41 0.00 43.16 2.90
307 315 0.182061 CCATATGGTGCAGCAGTCCT 59.818 55.000 24.45 9.85 0.00 3.85
319 327 2.033141 CTCCAGCGCCCCATATGG 59.967 66.667 15.41 15.41 0.00 2.74
329 337 4.878774 GAGTCACACTCTCCAGCG 57.121 61.111 0.00 0.00 41.88 5.18
337 345 0.389556 CAGCGATGCAGAGTCACACT 60.390 55.000 0.00 0.00 0.00 3.55
341 349 1.153958 CGTCAGCGATGCAGAGTCA 60.154 57.895 0.00 0.00 41.33 3.41
447 696 4.227134 CCCCGAGCTCATCCCACG 62.227 72.222 15.40 0.00 0.00 4.94
465 714 3.760035 CACCTCCAGACCCGTCGG 61.760 72.222 3.60 3.60 34.09 4.79
504 753 3.771160 GGACGTCTCCGGCATGGT 61.771 66.667 16.46 0.00 46.78 3.55
555 806 3.591977 ACCCTAGCCACTTTAATCCACTT 59.408 43.478 0.00 0.00 0.00 3.16
562 813 3.887916 ACCAAACCCTAGCCACTTTAA 57.112 42.857 0.00 0.00 0.00 1.52
564 815 2.594131 GAACCAAACCCTAGCCACTTT 58.406 47.619 0.00 0.00 0.00 2.66
583 834 4.207281 CCTTCATCCGCTCGCCGA 62.207 66.667 0.00 0.00 40.02 5.54
597 848 3.072476 CCGACCCCACATATATTCACCTT 59.928 47.826 0.00 0.00 0.00 3.50
598 849 2.637872 CCGACCCCACATATATTCACCT 59.362 50.000 0.00 0.00 0.00 4.00
636 887 4.124351 GTCGCCACGTCGGATCCA 62.124 66.667 13.41 0.00 36.56 3.41
667 918 5.846714 AGGTGTATATATATGGAGGCATCCC 59.153 44.000 16.13 0.00 46.04 3.85
684 935 9.466497 CATATTCAGCCCAAATATAAGGTGTAT 57.534 33.333 0.00 0.00 30.13 2.29
685 936 8.664992 TCATATTCAGCCCAAATATAAGGTGTA 58.335 33.333 0.00 0.00 30.13 2.90
686 937 7.526041 TCATATTCAGCCCAAATATAAGGTGT 58.474 34.615 0.00 0.00 30.13 4.16
687 938 7.121759 CCTCATATTCAGCCCAAATATAAGGTG 59.878 40.741 5.09 0.00 32.84 4.00
688 939 7.177878 CCTCATATTCAGCCCAAATATAAGGT 58.822 38.462 5.09 0.00 32.84 3.50
692 943 6.484288 CACCCTCATATTCAGCCCAAATATA 58.516 40.000 0.00 0.00 30.13 0.86
729 980 0.308376 GCAAACGGGACTTAAACGCA 59.692 50.000 0.00 0.00 0.00 5.24
749 1000 1.504359 TTTTGACTTAGACGGGCGTG 58.496 50.000 0.00 0.00 0.00 5.34
756 1007 5.371629 CGGTCACGAAATTTTGACTTAGAC 58.628 41.667 18.06 13.24 44.60 2.59
760 1011 2.946990 ACCGGTCACGAAATTTTGACTT 59.053 40.909 18.06 5.30 44.60 3.01
761 1012 2.546789 GACCGGTCACGAAATTTTGACT 59.453 45.455 29.75 3.83 44.60 3.41
762 1013 2.288458 TGACCGGTCACGAAATTTTGAC 59.712 45.455 33.23 12.60 44.60 3.18
765 1016 2.289547 CACTGACCGGTCACGAAATTTT 59.710 45.455 33.23 9.50 44.60 1.82
802 1053 2.897436 CGTCTCAAATCTGCCTCATCA 58.103 47.619 0.00 0.00 0.00 3.07
809 1060 1.002366 ATCACGCGTCTCAAATCTGC 58.998 50.000 9.86 0.00 0.00 4.26
810 1061 2.413112 ACAATCACGCGTCTCAAATCTG 59.587 45.455 9.86 0.78 0.00 2.90
820 1071 1.560923 GAGCATCTACAATCACGCGT 58.439 50.000 5.58 5.58 0.00 6.01
865 3091 1.358725 CGCGAATATATGCACGGGGG 61.359 60.000 0.00 0.00 35.65 5.40
866 3092 0.389296 TCGCGAATATATGCACGGGG 60.389 55.000 6.20 1.47 38.74 5.73
867 3093 0.713883 GTCGCGAATATATGCACGGG 59.286 55.000 12.06 8.92 39.36 5.28
868 3094 0.362179 CGTCGCGAATATATGCACGG 59.638 55.000 12.06 0.00 34.41 4.94
870 3096 1.124297 CCACGTCGCGAATATATGCAC 59.876 52.381 12.06 0.00 0.00 4.57
871 3097 1.001158 TCCACGTCGCGAATATATGCA 60.001 47.619 12.06 0.00 0.00 3.96
872 3098 1.693467 TCCACGTCGCGAATATATGC 58.307 50.000 12.06 0.00 0.00 3.14
931 3171 5.192176 TCTATGCCACTCATGCAAATTACA 58.808 37.500 0.00 0.00 42.92 2.41
937 3177 1.211212 AGCTCTATGCCACTCATGCAA 59.789 47.619 0.00 0.00 42.92 4.08
1070 3311 1.154016 GTTGATGCTGCTGCTGCTG 60.154 57.895 27.67 16.73 40.48 4.41
1071 3312 1.303398 AGTTGATGCTGCTGCTGCT 60.303 52.632 27.67 15.76 40.48 4.24
1091 3332 2.421424 GCAGCAACCTGTAAGATCAAGG 59.579 50.000 0.00 0.00 41.26 3.61
2189 5475 2.095668 ACACTCGTCGATGTCTGAAGAC 60.096 50.000 4.21 3.41 44.97 3.01
2240 5526 0.613260 TCCCATCACTCGAACAAGGG 59.387 55.000 0.00 0.00 36.15 3.95
2297 5583 1.804151 TCGCCTTTCATTCCGAGTTTG 59.196 47.619 0.00 0.00 0.00 2.93
2354 5800 1.453155 CCACAATCACCTGTGCTACC 58.547 55.000 0.00 0.00 44.47 3.18
2385 5831 3.266636 TCGATTAATGTGGTGCGATGTT 58.733 40.909 0.00 0.00 0.00 2.71
2434 5887 3.706802 AGCTAGATCGAGACATGTGTG 57.293 47.619 1.15 0.00 0.00 3.82
2646 6197 5.569355 ACACCACATAAATCAAGATGGTCA 58.431 37.500 0.00 0.00 38.38 4.02
2776 6816 7.090173 AGGAATGTTTACAAATGATTGGTTCG 58.910 34.615 0.00 0.00 41.01 3.95
2844 6884 6.910191 TGGAGCATATGAATCCCTTAGAAAA 58.090 36.000 19.34 1.94 31.73 2.29
2847 6887 7.813087 TTATGGAGCATATGAATCCCTTAGA 57.187 36.000 19.34 6.08 31.73 2.10
2968 7008 6.366340 TGGTGTGAAGAACCACCTTTAATTA 58.634 36.000 9.93 0.00 42.82 1.40
2969 7009 5.205056 TGGTGTGAAGAACCACCTTTAATT 58.795 37.500 9.93 0.00 42.82 1.40
2970 7010 4.798882 TGGTGTGAAGAACCACCTTTAAT 58.201 39.130 9.93 0.00 42.82 1.40
2971 7011 4.237976 TGGTGTGAAGAACCACCTTTAA 57.762 40.909 9.93 0.00 42.82 1.52
3213 7503 3.795688 ATGCCACCTATTCCACCTATG 57.204 47.619 0.00 0.00 0.00 2.23
3214 7504 4.814224 AAATGCCACCTATTCCACCTAT 57.186 40.909 0.00 0.00 0.00 2.57
3231 7521 9.577110 AATGATATAGCCGCAATGATAAAAATG 57.423 29.630 0.00 0.00 0.00 2.32
3498 7789 5.586339 TGAATGATGACTTCGTTTGCAAAA 58.414 33.333 14.67 0.00 33.61 2.44
3798 8089 3.887716 GCCTTGATATGCCAAAGTCTGAT 59.112 43.478 0.00 0.00 0.00 2.90
4070 8361 8.100135 ACTATCAAGAATCTCCAAATCTCCTT 57.900 34.615 0.00 0.00 0.00 3.36
4148 8439 3.206964 CGCTCTACTACCTCTGTCATCA 58.793 50.000 0.00 0.00 0.00 3.07
4278 8602 5.342866 ACCTTCTCTGTTCCTACCTTACAT 58.657 41.667 0.00 0.00 0.00 2.29
4280 8604 5.741962 AACCTTCTCTGTTCCTACCTTAC 57.258 43.478 0.00 0.00 0.00 2.34
4295 8619 3.909732 TGGAACCAATGTGAAACCTTCT 58.090 40.909 0.00 0.00 34.36 2.85
4467 11052 4.994217 CGCCATTGTATGTGACCATATACA 59.006 41.667 13.28 13.28 41.52 2.29
4479 11064 9.729023 TTATTTATTGAACTTCGCCATTGTATG 57.271 29.630 0.00 0.00 0.00 2.39
4591 11176 8.956426 TGAAATGAAAAGGCTAGGTTAATACTG 58.044 33.333 0.00 0.00 0.00 2.74
4592 11177 9.528489 TTGAAATGAAAAGGCTAGGTTAATACT 57.472 29.630 0.00 0.00 0.00 2.12
4690 11277 0.173255 CGGGGAAATGTCACAATGCC 59.827 55.000 0.00 0.00 0.00 4.40
4709 11296 7.274447 TCCCAGCAATGGATAATCAAAAATTC 58.726 34.615 0.00 0.00 0.00 2.17
4871 11901 4.760530 TGAGATCTCGGATGGACAAAAT 57.239 40.909 17.76 0.00 0.00 1.82
4953 11983 3.642848 GGGTCAACATTATACGGGGTCTA 59.357 47.826 0.00 0.00 0.00 2.59
4961 11991 4.502645 GCATTTTGCGGGTCAACATTATAC 59.497 41.667 0.00 0.00 33.73 1.47
4977 12007 4.602957 GCAACGAACAGTAAACGCATTTTG 60.603 41.667 0.00 0.00 0.00 2.44
4991 12021 4.215185 TGCAAATTAGATCTGCAACGAACA 59.785 37.500 5.18 0.00 42.84 3.18
4994 12024 3.374988 CCTGCAAATTAGATCTGCAACGA 59.625 43.478 5.18 0.00 44.94 3.85
4995 12025 3.488047 CCCTGCAAATTAGATCTGCAACG 60.488 47.826 5.18 0.14 44.94 4.10
4997 12027 2.428171 GCCCTGCAAATTAGATCTGCAA 59.572 45.455 5.18 0.00 44.94 4.08
5007 12037 0.887933 ACGAATTCGCCCTGCAAATT 59.112 45.000 27.03 0.92 44.43 1.82
5025 12055 1.639298 GGGTCTGATCTGCAACGCAC 61.639 60.000 0.00 0.00 33.79 5.34
5175 12567 2.852449 TCCATGCAACGTTTACCAAGA 58.148 42.857 0.00 0.00 0.00 3.02
5176 12568 3.634568 TTCCATGCAACGTTTACCAAG 57.365 42.857 0.00 0.00 0.00 3.61
5177 12569 4.113354 GTTTTCCATGCAACGTTTACCAA 58.887 39.130 0.00 0.00 0.00 3.67
5178 12570 3.130516 TGTTTTCCATGCAACGTTTACCA 59.869 39.130 0.00 0.00 0.00 3.25
5179 12571 3.707793 TGTTTTCCATGCAACGTTTACC 58.292 40.909 0.00 0.00 0.00 2.85
5180 12572 5.704217 TTTGTTTTCCATGCAACGTTTAC 57.296 34.783 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.