Multiple sequence alignment - TraesCS3B01G416400

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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 TraesCS3B01G416400 chr3B 100.000 2511 0 0 416 2926 653151466 653153976 0.000000e+00 4638
1 TraesCS3B01G416400 chr3B 85.673 684 78 12 1641 2323 653617388 653618052 0.000000e+00 702
2 TraesCS3B01G416400 chr3B 92.814 334 22 2 2586 2918 637050709 637051041 1.580000e-132 483
3 TraesCS3B01G416400 chr3B 86.973 261 31 3 2315 2572 637049334 637049594 1.030000e-74 291
4 TraesCS3B01G416400 chr3B 100.000 94 0 0 1 94 653151051 653151144 1.080000e-39 174
5 TraesCS3B01G416400 chr3D 90.434 1683 62 38 527 2150 492130936 492132578 0.000000e+00 2124
6 TraesCS3B01G416400 chr3D 86.277 685 73 14 1641 2323 492612161 492612826 0.000000e+00 725
7 TraesCS3B01G416400 chr3D 86.127 519 50 13 1648 2163 492654706 492655205 9.230000e-150 540
8 TraesCS3B01G416400 chr3D 93.393 333 22 0 2586 2918 9198250 9198582 7.280000e-136 494
9 TraesCS3B01G416400 chr3D 93.393 333 22 0 2586 2918 341514138 341514470 7.280000e-136 494
10 TraesCS3B01G416400 chr3D 93.093 333 23 0 2586 2918 254088382 254088050 3.390000e-134 488
11 TraesCS3B01G416400 chr3D 85.401 274 35 5 2316 2586 148237937 148238208 2.220000e-71 279
12 TraesCS3B01G416400 chr3D 86.429 140 18 1 2185 2323 492655377 492655516 5.050000e-33 152
13 TraesCS3B01G416400 chr3A 87.941 1816 103 62 416 2150 633921468 633923248 0.000000e+00 2034
14 TraesCS3B01G416400 chr3A 85.602 889 95 22 1379 2262 634103251 634104111 0.000000e+00 902
15 TraesCS3B01G416400 chr3A 88.372 172 17 1 2152 2323 633923379 633923547 1.370000e-48 204
16 TraesCS3B01G416400 chr3A 87.097 93 11 1 1 93 633921095 633921186 1.430000e-18 104
17 TraesCS3B01G416400 chr4D 93.155 336 22 1 2583 2918 47979091 47979425 2.620000e-135 492
18 TraesCS3B01G416400 chr4D 87.805 123 15 0 1383 1505 68053667 68053789 8.450000e-31 145
19 TraesCS3B01G416400 chr7D 93.051 331 23 0 2588 2918 259284420 259284090 4.380000e-133 484
20 TraesCS3B01G416400 chr7D 92.793 333 24 0 2586 2918 365974304 365973972 1.580000e-132 483
21 TraesCS3B01G416400 chr7D 89.299 271 26 3 997 1265 262698961 262698692 1.300000e-88 337
22 TraesCS3B01G416400 chr7D 83.883 273 40 4 2317 2586 156097758 156098029 1.040000e-64 257
23 TraesCS3B01G416400 chr5A 92.793 333 24 0 2586 2918 448538583 448538915 1.580000e-132 483
24 TraesCS3B01G416400 chr5A 92.105 266 21 0 1001 1266 539093485 539093220 2.750000e-100 375
25 TraesCS3B01G416400 chr5A 88.722 266 28 2 2317 2581 448527115 448527379 1.010000e-84 324
26 TraesCS3B01G416400 chr5D 92.771 332 24 0 2587 2918 277132198 277131867 5.670000e-132 481
27 TraesCS3B01G416400 chr5D 92.857 266 19 0 1001 1266 425077485 425077220 1.270000e-103 387
28 TraesCS3B01G416400 chr5D 86.594 276 33 4 2313 2586 407925145 407925418 4.740000e-78 302
29 TraesCS3B01G416400 chr5D 83.150 273 38 8 2319 2586 424882808 424883077 2.910000e-60 243
30 TraesCS3B01G416400 chr1A 93.431 274 18 0 996 1269 463461702 463461429 9.760000e-110 407
31 TraesCS3B01G416400 chr1A 90.647 139 13 0 1378 1516 463461343 463461205 4.980000e-43 185
32 TraesCS3B01G416400 chr1D 92.647 272 20 0 997 1268 364625276 364625005 2.730000e-105 392
33 TraesCS3B01G416400 chr1D 88.235 136 15 1 1380 1515 364624923 364624789 8.390000e-36 161
34 TraesCS3B01G416400 chr5B 92.481 266 20 0 1001 1266 514279627 514279362 5.920000e-102 381
35 TraesCS3B01G416400 chr1B 91.241 274 24 0 995 1268 487951488 487951215 9.900000e-100 374
36 TraesCS3B01G416400 chr1B 81.884 276 45 5 2315 2586 101592156 101592430 8.160000e-56 228
37 TraesCS3B01G416400 chr1B 91.406 128 11 0 1378 1505 487951133 487951006 3.000000e-40 176
38 TraesCS3B01G416400 chr7A 83.594 256 39 3 2323 2575 482319861 482319606 1.360000e-58 237
39 TraesCS3B01G416400 chr4B 83.794 253 38 3 2336 2586 416644165 416644416 1.360000e-58 237
40 TraesCS3B01G416400 chr4B 88.618 123 14 0 1383 1505 100576909 100577031 1.820000e-32 150
41 TraesCS3B01G416400 chr4A 88.618 123 14 0 1383 1505 517884847 517884969 1.820000e-32 150


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 TraesCS3B01G416400 chr3B 653151051 653153976 2925 False 2406.000000 4638 100.000000 1 2926 2 chr3B.!!$F3 2925
1 TraesCS3B01G416400 chr3B 653617388 653618052 664 False 702.000000 702 85.673000 1641 2323 1 chr3B.!!$F1 682
2 TraesCS3B01G416400 chr3B 637049334 637051041 1707 False 387.000000 483 89.893500 2315 2918 2 chr3B.!!$F2 603
3 TraesCS3B01G416400 chr3D 492130936 492132578 1642 False 2124.000000 2124 90.434000 527 2150 1 chr3D.!!$F4 1623
4 TraesCS3B01G416400 chr3D 492612161 492612826 665 False 725.000000 725 86.277000 1641 2323 1 chr3D.!!$F5 682
5 TraesCS3B01G416400 chr3D 492654706 492655516 810 False 346.000000 540 86.278000 1648 2323 2 chr3D.!!$F6 675
6 TraesCS3B01G416400 chr3A 634103251 634104111 860 False 902.000000 902 85.602000 1379 2262 1 chr3A.!!$F1 883
7 TraesCS3B01G416400 chr3A 633921095 633923547 2452 False 780.666667 2034 87.803333 1 2323 3 chr3A.!!$F2 2322

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
76 77 0.320374 TTGTGTAAGGGACCTCTGCG 59.680 55.0 0.0 0.0 0.0 5.18 F
948 1026 0.482887 ACCTCCACCCCAAGAAAAGG 59.517 55.0 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1277 1367 0.027979 CCGATGCGCATTGAAATCGT 59.972 50.0 34.37 6.63 40.14 3.73 R
2793 4319 0.040958 CTGAAGCACACGGAAAGCAC 60.041 55.0 0.00 0.00 0.00 4.40 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
62 63 8.436046 ACAATCTTTTTGTGCAATATTTGTGT 57.564 26.923 0.00 0.00 0.00 3.72
72 73 4.947388 TGCAATATTTGTGTAAGGGACCTC 59.053 41.667 0.00 0.00 0.00 3.85
76 77 0.320374 TTGTGTAAGGGACCTCTGCG 59.680 55.000 0.00 0.00 0.00 5.18
77 78 1.448013 GTGTAAGGGACCTCTGCGC 60.448 63.158 0.00 0.00 0.00 6.09
78 79 1.609501 TGTAAGGGACCTCTGCGCT 60.610 57.895 9.73 0.00 0.00 5.92
79 80 1.142097 GTAAGGGACCTCTGCGCTC 59.858 63.158 9.73 0.00 0.00 5.03
82 83 2.125350 GGGACCTCTGCGCTCAAG 60.125 66.667 9.73 2.89 0.00 3.02
83 84 2.817396 GGACCTCTGCGCTCAAGC 60.817 66.667 9.73 0.00 37.78 4.01
450 451 4.320275 GCTGTACCAAAGCCAACTAAAGAC 60.320 45.833 0.00 0.00 34.45 3.01
452 453 3.306472 ACCAAAGCCAACTAAAGACCA 57.694 42.857 0.00 0.00 0.00 4.02
463 464 7.070696 AGCCAACTAAAGACCAAATTTAGGTTT 59.929 33.333 11.88 5.69 42.15 3.27
470 471 7.775053 AAGACCAAATTTAGGTTTAGATGCA 57.225 32.000 11.88 0.00 40.09 3.96
478 479 1.544691 AGGTTTAGATGCACGACGACT 59.455 47.619 0.00 0.00 0.00 4.18
522 541 7.380602 GTGTTCTTGATGAAAACAATTCTCTGG 59.619 37.037 0.00 0.00 41.42 3.86
531 553 7.610865 TGAAAACAATTCTCTGGAACAACTTT 58.389 30.769 0.00 0.00 38.70 2.66
538 560 3.454447 TCTCTGGAACAACTTTGTGGAGA 59.546 43.478 0.00 4.78 41.31 3.71
586 619 0.649993 CGTTTTGCAACCACCAAAGC 59.350 50.000 0.00 0.00 34.10 3.51
587 620 1.013596 GTTTTGCAACCACCAAAGCC 58.986 50.000 0.00 0.00 34.10 4.35
660 695 1.449601 CCGCGCCCACATCTTTACT 60.450 57.895 0.00 0.00 0.00 2.24
662 697 1.752501 CGCGCCCACATCTTTACTCG 61.753 60.000 0.00 0.00 0.00 4.18
666 701 1.560923 CCCACATCTTTACTCGCTCG 58.439 55.000 0.00 0.00 0.00 5.03
667 702 0.924090 CCACATCTTTACTCGCTCGC 59.076 55.000 0.00 0.00 0.00 5.03
668 703 0.924090 CACATCTTTACTCGCTCGCC 59.076 55.000 0.00 0.00 0.00 5.54
669 704 0.525668 ACATCTTTACTCGCTCGCCG 60.526 55.000 0.00 0.00 38.61 6.46
755 805 1.383799 CAGGCAGTCAAATCCCCCA 59.616 57.895 0.00 0.00 0.00 4.96
826 883 2.656947 ACCACCAAAAAGCTCTGCTA 57.343 45.000 0.00 0.00 38.25 3.49
859 916 1.141019 CCCATATATACGCGCGCCT 59.859 57.895 32.58 20.08 0.00 5.52
898 960 3.947041 ACCTCCACCTCCCCTGCT 61.947 66.667 0.00 0.00 0.00 4.24
919 993 1.279527 CGTACAACCGCGAGCTCAAA 61.280 55.000 15.40 0.00 0.00 2.69
946 1024 1.074889 GCTACCTCCACCCCAAGAAAA 59.925 52.381 0.00 0.00 0.00 2.29
948 1026 0.482887 ACCTCCACCCCAAGAAAAGG 59.517 55.000 0.00 0.00 0.00 3.11
949 1027 0.900182 CCTCCACCCCAAGAAAAGGC 60.900 60.000 0.00 0.00 0.00 4.35
951 1029 2.650778 CACCCCAAGAAAAGGCGC 59.349 61.111 0.00 0.00 0.00 6.53
952 1030 2.983592 ACCCCAAGAAAAGGCGCG 60.984 61.111 0.00 0.00 0.00 6.86
953 1031 4.419939 CCCCAAGAAAAGGCGCGC 62.420 66.667 25.94 25.94 0.00 6.86
954 1032 3.669344 CCCAAGAAAAGGCGCGCA 61.669 61.111 34.42 0.00 0.00 6.09
955 1033 2.126734 CCAAGAAAAGGCGCGCAG 60.127 61.111 34.42 10.87 0.00 5.18
956 1034 2.126734 CAAGAAAAGGCGCGCAGG 60.127 61.111 34.42 8.25 0.00 4.85
957 1035 3.365265 AAGAAAAGGCGCGCAGGG 61.365 61.111 34.42 0.00 46.11 4.45
1277 1367 2.422597 CAACAAGTAAGCACCCGATCA 58.577 47.619 0.00 0.00 0.00 2.92
1317 1407 1.904990 GCCTCCGCCTCTTCTTTCCT 61.905 60.000 0.00 0.00 0.00 3.36
1318 1408 0.176910 CCTCCGCCTCTTCTTTCCTC 59.823 60.000 0.00 0.00 0.00 3.71
1319 1409 1.190643 CTCCGCCTCTTCTTTCCTCT 58.809 55.000 0.00 0.00 0.00 3.69
1320 1410 0.898320 TCCGCCTCTTCTTTCCTCTG 59.102 55.000 0.00 0.00 0.00 3.35
1321 1411 0.742635 CCGCCTCTTCTTTCCTCTGC 60.743 60.000 0.00 0.00 0.00 4.26
1322 1412 1.080995 CGCCTCTTCTTTCCTCTGCG 61.081 60.000 0.00 0.00 34.52 5.18
1323 1413 0.036858 GCCTCTTCTTTCCTCTGCGT 60.037 55.000 0.00 0.00 0.00 5.24
1324 1414 2.003196 CCTCTTCTTTCCTCTGCGTC 57.997 55.000 0.00 0.00 0.00 5.19
1325 1415 1.404851 CCTCTTCTTTCCTCTGCGTCC 60.405 57.143 0.00 0.00 0.00 4.79
1326 1416 0.243907 TCTTCTTTCCTCTGCGTCCG 59.756 55.000 0.00 0.00 0.00 4.79
1327 1417 0.038159 CTTCTTTCCTCTGCGTCCGT 60.038 55.000 0.00 0.00 0.00 4.69
1328 1418 0.038526 TTCTTTCCTCTGCGTCCGTC 60.039 55.000 0.00 0.00 0.00 4.79
1329 1419 1.446272 CTTTCCTCTGCGTCCGTCC 60.446 63.158 0.00 0.00 0.00 4.79
1366 1459 3.352648 TGGGCAGTTATTGACTAAAGCC 58.647 45.455 0.00 0.00 39.95 4.35
1706 1811 3.612247 CTGCCCCGACCTGAACCTG 62.612 68.421 0.00 0.00 0.00 4.00
1712 1817 1.592223 CGACCTGAACCTGGACCTC 59.408 63.158 0.00 0.00 0.00 3.85
1937 2044 6.587990 GTCAATACATATAGCACACTAGGCAG 59.412 42.308 0.00 0.00 0.00 4.85
1942 2049 4.082523 GCACACTAGGCAGCCGGA 62.083 66.667 5.05 0.00 0.00 5.14
1967 2074 7.954788 AAAAACTCTGTACAAAGCACAAAAA 57.045 28.000 0.00 0.00 0.00 1.94
2017 2137 7.712639 GGTTTCTAATTGAGATAGCTGATGTGA 59.287 37.037 0.00 0.00 32.64 3.58
2018 2138 9.102757 GTTTCTAATTGAGATAGCTGATGTGAA 57.897 33.333 0.00 0.00 32.88 3.18
2019 2139 9.842775 TTTCTAATTGAGATAGCTGATGTGAAT 57.157 29.630 0.00 0.00 32.88 2.57
2020 2140 9.842775 TTCTAATTGAGATAGCTGATGTGAATT 57.157 29.630 0.00 0.43 31.17 2.17
2062 2185 4.452114 TCGCTTCATCCCAAATATGATTCG 59.548 41.667 0.00 0.00 33.52 3.34
2077 2201 4.322080 TGATTCGTTCTTCTCGCCATAT 57.678 40.909 0.00 0.00 0.00 1.78
2078 2202 4.693283 TGATTCGTTCTTCTCGCCATATT 58.307 39.130 0.00 0.00 0.00 1.28
2079 2203 4.745125 TGATTCGTTCTTCTCGCCATATTC 59.255 41.667 0.00 0.00 0.00 1.75
2208 2629 5.690464 AGTGAGAAAAGAGTGGCAGATAT 57.310 39.130 0.00 0.00 0.00 1.63
2227 2648 9.681692 GCAGATATAATTGTTTGATTGTGCATA 57.318 29.630 0.00 0.00 0.00 3.14
2240 2661 1.880796 TGCATACGATTCGGGCGTG 60.881 57.895 11.29 4.71 42.62 5.34
2301 2723 1.159285 GGCGTGTTTTGGGTAGGTAC 58.841 55.000 0.00 0.00 0.00 3.34
2302 2724 1.542987 GGCGTGTTTTGGGTAGGTACA 60.543 52.381 0.00 0.00 0.00 2.90
2308 2730 5.509501 CGTGTTTTGGGTAGGTACAGAACTA 60.510 44.000 0.00 0.00 34.09 2.24
2312 2734 6.691255 TTTGGGTAGGTACAGAACTAATGT 57.309 37.500 0.00 0.00 34.62 2.71
2338 2760 2.325082 GCCAACTCCAACGCACGAT 61.325 57.895 0.00 0.00 0.00 3.73
2345 2767 1.153369 CCAACGCACGATCCCATCT 60.153 57.895 0.00 0.00 0.00 2.90
2349 2771 0.460284 ACGCACGATCCCATCTTGTC 60.460 55.000 0.00 0.00 31.78 3.18
2352 2774 0.175760 CACGATCCCATCTTGTCCGT 59.824 55.000 0.00 0.00 0.00 4.69
2354 2776 0.249489 CGATCCCATCTTGTCCGTCC 60.249 60.000 0.00 0.00 0.00 4.79
2356 2778 0.976073 ATCCCATCTTGTCCGTCCGT 60.976 55.000 0.00 0.00 0.00 4.69
2361 2784 2.209064 ATCTTGTCCGTCCGTGTCCG 62.209 60.000 0.00 0.00 0.00 4.79
2364 2787 2.028043 GTCCGTCCGTGTCCGTTT 59.972 61.111 0.00 0.00 0.00 3.60
2366 2789 2.027897 CCGTCCGTGTCCGTTTGA 59.972 61.111 0.00 0.00 0.00 2.69
2369 2792 1.666872 GTCCGTGTCCGTTTGAGGG 60.667 63.158 0.00 0.00 0.00 4.30
2370 2793 2.135581 TCCGTGTCCGTTTGAGGGT 61.136 57.895 0.00 0.00 0.00 4.34
2384 2807 3.495434 TGAGGGTAACGGACAAAACAT 57.505 42.857 0.00 0.00 37.60 2.71
2393 2816 0.890683 GGACAAAACATGCCTCCCAG 59.109 55.000 0.00 0.00 0.00 4.45
2423 2847 1.072505 AAACAGGCCATCGTCCGTT 59.927 52.632 5.01 0.00 0.00 4.44
2426 2850 0.953960 ACAGGCCATCGTCCGTTTTC 60.954 55.000 5.01 0.00 0.00 2.29
2475 2899 2.548295 TTTGGGTCGAGTTTGCGGC 61.548 57.895 0.00 0.00 34.63 6.53
2481 2905 4.424430 CGAGTTTGCGGCCGAACG 62.424 66.667 33.48 15.45 39.79 3.95
2489 2913 4.953868 CGGCCGAACGGACACACA 62.954 66.667 24.07 0.00 45.70 3.72
2491 2915 2.586635 GCCGAACGGACACACACA 60.587 61.111 17.63 0.00 37.50 3.72
2495 2919 1.537289 CGAACGGACACACACAGACG 61.537 60.000 0.00 0.00 0.00 4.18
2496 2920 0.526954 GAACGGACACACACAGACGT 60.527 55.000 0.00 0.00 35.95 4.34
2525 2949 4.748144 GCCCTTGTCCTGCCCTGG 62.748 72.222 0.00 0.00 0.00 4.45
2526 2950 4.748144 CCCTTGTCCTGCCCTGGC 62.748 72.222 0.00 0.00 42.35 4.85
2545 2969 2.047274 CGCCCGTTGGTGAGACAT 60.047 61.111 0.00 0.00 45.51 3.06
2550 2975 0.107848 CCGTTGGTGAGACATACCCC 60.108 60.000 0.00 0.00 37.40 4.95
2572 2997 3.847184 CCTTTTTCTTCCTCTACCTCCCT 59.153 47.826 0.00 0.00 0.00 4.20
2575 3000 0.551879 TCTTCCTCTACCTCCCTCCG 59.448 60.000 0.00 0.00 0.00 4.63
2576 3001 1.076192 TTCCTCTACCTCCCTCCGC 60.076 63.158 0.00 0.00 0.00 5.54
2577 3002 2.905935 TTCCTCTACCTCCCTCCGCG 62.906 65.000 0.00 0.00 0.00 6.46
2656 4182 0.539438 TTGAGGTCAATGGCCACCAC 60.539 55.000 8.16 3.71 35.80 4.16
2662 4188 1.539827 GTCAATGGCCACCACTACAAC 59.460 52.381 8.16 0.00 35.80 3.32
2697 4223 1.549620 AGCTGATGGCATCTATCCTCG 59.450 52.381 26.49 8.61 44.79 4.63
2762 4288 4.476479 AGAAGAGATAGAGGTTTGCCCAAT 59.524 41.667 0.00 0.00 34.66 3.16
2765 4291 3.026694 AGATAGAGGTTTGCCCAATTGC 58.973 45.455 0.00 0.00 34.66 3.56
2785 4311 2.933056 GCAACAGAGTGCTAGGAAGGAC 60.933 54.545 0.00 0.00 43.97 3.85
2806 4332 2.551270 GAGCGTGCTTTCCGTGTG 59.449 61.111 0.00 0.00 0.00 3.82
2816 4342 1.795286 CTTTCCGTGTGCTTCAGTCTC 59.205 52.381 0.00 0.00 0.00 3.36
2818 4344 1.734477 CCGTGTGCTTCAGTCTCGG 60.734 63.158 0.00 0.00 33.32 4.63
2819 4345 2.375766 CGTGTGCTTCAGTCTCGGC 61.376 63.158 0.00 0.00 0.00 5.54
2820 4346 1.005630 GTGTGCTTCAGTCTCGGCT 60.006 57.895 0.00 0.00 0.00 5.52
2827 4353 1.067821 CTTCAGTCTCGGCTGGGTATC 59.932 57.143 0.00 0.00 37.12 2.24
2847 4373 1.127951 CGTTCGTAACCCTGCATTGAC 59.872 52.381 0.00 0.00 0.00 3.18
2860 4386 1.402968 GCATTGACATGGAGCACGAAT 59.597 47.619 0.00 0.00 0.00 3.34
2864 4390 2.279741 TGACATGGAGCACGAATAAGC 58.720 47.619 0.00 0.00 0.00 3.09
2868 4394 3.758554 ACATGGAGCACGAATAAGCTTTT 59.241 39.130 3.20 0.00 42.04 2.27
2869 4395 4.218417 ACATGGAGCACGAATAAGCTTTTT 59.782 37.500 3.20 2.19 42.04 1.94
2918 4444 3.273434 CACAACATGATCGTGGAGGATT 58.727 45.455 18.97 1.10 0.00 3.01
2919 4445 3.064408 CACAACATGATCGTGGAGGATTG 59.936 47.826 18.97 14.80 0.00 2.67
2920 4446 3.055167 ACAACATGATCGTGGAGGATTGA 60.055 43.478 18.97 0.00 0.00 2.57
2921 4447 3.912496 ACATGATCGTGGAGGATTGAA 57.088 42.857 18.97 0.00 0.00 2.69
2922 4448 4.220693 ACATGATCGTGGAGGATTGAAA 57.779 40.909 18.97 0.00 0.00 2.69
2923 4449 4.194640 ACATGATCGTGGAGGATTGAAAG 58.805 43.478 18.97 0.00 0.00 2.62
2924 4450 2.632377 TGATCGTGGAGGATTGAAAGC 58.368 47.619 0.00 0.00 0.00 3.51
2925 4451 2.027285 TGATCGTGGAGGATTGAAAGCA 60.027 45.455 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.710900 AAAGATTGTAAATCCATTTTCAAGGAC 57.289 29.630 9.19 4.99 39.33 3.85
62 63 0.902984 TTGAGCGCAGAGGTCCCTTA 60.903 55.000 11.47 0.00 46.24 2.69
437 438 6.075315 ACCTAAATTTGGTCTTTAGTTGGCT 58.925 36.000 0.00 0.00 35.39 4.75
445 446 8.088365 GTGCATCTAAACCTAAATTTGGTCTTT 58.912 33.333 11.23 6.33 36.69 2.52
447 448 6.128007 CGTGCATCTAAACCTAAATTTGGTCT 60.128 38.462 11.23 2.88 36.69 3.85
450 451 6.027749 GTCGTGCATCTAAACCTAAATTTGG 58.972 40.000 0.00 0.00 0.00 3.28
452 453 5.640357 TCGTCGTGCATCTAAACCTAAATTT 59.360 36.000 0.00 0.00 0.00 1.82
463 464 1.810755 ACTTGAGTCGTCGTGCATCTA 59.189 47.619 0.00 0.00 0.00 1.98
497 516 7.285172 TCCAGAGAATTGTTTTCATCAAGAACA 59.715 33.333 0.00 0.00 35.56 3.18
499 518 7.822161 TCCAGAGAATTGTTTTCATCAAGAA 57.178 32.000 0.00 0.00 0.00 2.52
502 521 7.345422 TGTTCCAGAGAATTGTTTTCATCAA 57.655 32.000 0.00 0.00 33.67 2.57
505 524 7.352079 AGTTGTTCCAGAGAATTGTTTTCAT 57.648 32.000 0.00 0.00 33.67 2.57
506 525 6.773976 AGTTGTTCCAGAGAATTGTTTTCA 57.226 33.333 0.00 0.00 33.67 2.69
515 534 4.080582 TCTCCACAAAGTTGTTCCAGAGAA 60.081 41.667 9.08 0.00 39.91 2.87
519 538 3.243201 GCTTCTCCACAAAGTTGTTCCAG 60.243 47.826 0.00 0.00 39.91 3.86
522 541 3.378427 AGTGCTTCTCCACAAAGTTGTTC 59.622 43.478 0.00 0.00 39.91 3.18
586 619 0.253327 GGAGTGGAGTAGCTTTGGGG 59.747 60.000 0.00 0.00 0.00 4.96
587 620 0.108138 CGGAGTGGAGTAGCTTTGGG 60.108 60.000 0.00 0.00 0.00 4.12
755 805 1.212935 CTCCATTGACCCGATCCCTTT 59.787 52.381 0.00 0.00 0.00 3.11
838 895 1.514087 CGCGCGTATATATGGGGGT 59.486 57.895 24.19 0.00 34.73 4.95
901 963 0.163146 GTTTGAGCTCGCGGTTGTAC 59.837 55.000 6.13 0.00 0.00 2.90
919 993 1.380112 GGTGGAGGTAGCTCGGAGT 60.380 63.158 15.43 0.00 0.00 3.85
949 1027 4.093952 CTGTTTCTGCCCTGCGCG 62.094 66.667 0.00 0.00 42.08 6.86
951 1029 2.684843 GCTCTGTTTCTGCCCTGCG 61.685 63.158 0.00 0.00 0.00 5.18
952 1030 2.684843 CGCTCTGTTTCTGCCCTGC 61.685 63.158 0.00 0.00 0.00 4.85
953 1031 2.037136 CCGCTCTGTTTCTGCCCTG 61.037 63.158 0.00 0.00 0.00 4.45
954 1032 2.348998 CCGCTCTGTTTCTGCCCT 59.651 61.111 0.00 0.00 0.00 5.19
955 1033 2.747855 CCCGCTCTGTTTCTGCCC 60.748 66.667 0.00 0.00 0.00 5.36
956 1034 1.301677 CTTCCCGCTCTGTTTCTGCC 61.302 60.000 0.00 0.00 0.00 4.85
957 1035 1.916697 GCTTCCCGCTCTGTTTCTGC 61.917 60.000 0.00 0.00 35.14 4.26
958 1036 0.603707 TGCTTCCCGCTCTGTTTCTG 60.604 55.000 0.00 0.00 40.11 3.02
965 1043 2.046507 CTGCTTGCTTCCCGCTCT 60.047 61.111 0.00 0.00 40.11 4.09
1044 1134 3.316573 CTCCTCCTTGGTCCACGCC 62.317 68.421 0.00 0.00 37.07 5.68
1277 1367 0.027979 CCGATGCGCATTGAAATCGT 59.972 50.000 34.37 6.63 40.14 3.73
1317 1407 4.988716 ACCAGGGACGGACGCAGA 62.989 66.667 0.00 0.00 0.00 4.26
1318 1408 3.530910 AAACCAGGGACGGACGCAG 62.531 63.158 0.00 0.00 0.00 5.18
1319 1409 3.524648 GAAACCAGGGACGGACGCA 62.525 63.158 0.00 0.00 0.00 5.24
1320 1410 2.726822 AAGAAACCAGGGACGGACGC 62.727 60.000 0.00 0.00 0.00 5.19
1321 1411 0.949105 CAAGAAACCAGGGACGGACG 60.949 60.000 0.00 0.00 0.00 4.79
1322 1412 0.605589 CCAAGAAACCAGGGACGGAC 60.606 60.000 0.00 0.00 0.00 4.79
1323 1413 0.765135 TCCAAGAAACCAGGGACGGA 60.765 55.000 0.00 0.00 0.00 4.69
1324 1414 0.321653 CTCCAAGAAACCAGGGACGG 60.322 60.000 0.00 0.00 0.00 4.79
1325 1415 0.685097 TCTCCAAGAAACCAGGGACG 59.315 55.000 0.00 0.00 0.00 4.79
1326 1416 2.619074 CCATCTCCAAGAAACCAGGGAC 60.619 54.545 0.00 0.00 0.00 4.46
1327 1417 1.635487 CCATCTCCAAGAAACCAGGGA 59.365 52.381 0.00 0.00 0.00 4.20
1328 1418 1.341383 CCCATCTCCAAGAAACCAGGG 60.341 57.143 0.00 0.00 0.00 4.45
1329 1419 1.957113 GCCCATCTCCAAGAAACCAGG 60.957 57.143 0.00 0.00 0.00 4.45
1427 1520 5.564848 CGTGTTCCAGTAGTTCTTGATCTCA 60.565 44.000 0.00 0.00 0.00 3.27
1547 1649 0.614979 CCGGAGAGGAAGGGAAGACA 60.615 60.000 0.00 0.00 45.00 3.41
1706 1811 2.037527 AGGTCCAGGTCGAGGTCC 59.962 66.667 0.00 0.00 34.97 4.46
1986 2093 8.103305 TCAGCTATCTCAATTAGAAACCTGTTT 58.897 33.333 0.00 0.00 37.89 2.83
1989 2109 7.714377 ACATCAGCTATCTCAATTAGAAACCTG 59.286 37.037 0.00 0.00 37.89 4.00
1990 2110 7.714377 CACATCAGCTATCTCAATTAGAAACCT 59.286 37.037 0.00 0.00 37.89 3.50
2062 2185 7.204496 TCTACTAGAATATGGCGAGAAGAAC 57.796 40.000 0.00 0.00 0.00 3.01
2079 2203 9.017669 GCTGCATGAAATTCAAAATTCTACTAG 57.982 33.333 0.00 0.00 0.00 2.57
2168 2438 0.947244 CTTGTGCCTCTGTGTGTTCC 59.053 55.000 0.00 0.00 0.00 3.62
2181 2602 2.287248 GCCACTCTTTTCTCACTTGTGC 60.287 50.000 0.00 0.00 0.00 4.57
2208 2629 7.427895 CGAATCGTATGCACAATCAAACAATTA 59.572 33.333 0.00 0.00 0.00 1.40
2227 2648 1.595929 AAACACACGCCCGAATCGT 60.596 52.632 0.82 0.00 41.28 3.73
2240 2661 5.880332 ACTATATCCCACATGACACAAACAC 59.120 40.000 0.00 0.00 0.00 3.32
2301 2723 8.281212 AGTTGGCCTAAATAACATTAGTTCTG 57.719 34.615 3.32 0.00 39.15 3.02
2302 2724 7.556635 GGAGTTGGCCTAAATAACATTAGTTCT 59.443 37.037 3.32 0.00 39.15 3.01
2308 2730 5.105917 CGTTGGAGTTGGCCTAAATAACATT 60.106 40.000 3.32 0.00 0.00 2.71
2312 2734 2.750712 GCGTTGGAGTTGGCCTAAATAA 59.249 45.455 3.32 0.00 0.00 1.40
2338 2760 1.608336 ACGGACGGACAAGATGGGA 60.608 57.895 0.00 0.00 0.00 4.37
2345 2767 2.295472 AAACGGACACGGACGGACAA 62.295 55.000 0.00 0.00 46.48 3.18
2349 2771 2.019951 CTCAAACGGACACGGACGG 61.020 63.158 0.00 0.00 46.48 4.79
2352 2774 0.827089 TACCCTCAAACGGACACGGA 60.827 55.000 0.00 0.00 46.48 4.69
2354 2776 2.516700 CGTTACCCTCAAACGGACACG 61.517 57.143 0.63 0.00 44.49 4.49
2356 2778 3.591979 CGTTACCCTCAAACGGACA 57.408 52.632 0.63 0.00 44.49 4.02
2361 2784 3.377798 TGTTTTGTCCGTTACCCTCAAAC 59.622 43.478 0.00 0.00 0.00 2.93
2364 2787 3.142951 CATGTTTTGTCCGTTACCCTCA 58.857 45.455 0.00 0.00 0.00 3.86
2366 2789 1.883926 GCATGTTTTGTCCGTTACCCT 59.116 47.619 0.00 0.00 0.00 4.34
2369 2792 2.095415 GGAGGCATGTTTTGTCCGTTAC 60.095 50.000 0.00 0.00 0.00 2.50
2370 2793 2.156098 GGAGGCATGTTTTGTCCGTTA 58.844 47.619 0.00 0.00 0.00 3.18
2402 2826 2.480555 GACGATGGCCTGTTTGCG 59.519 61.111 3.32 0.97 0.00 4.85
2409 2833 0.673644 CAGAAAACGGACGATGGCCT 60.674 55.000 3.32 0.00 0.00 5.19
2410 2834 0.953960 ACAGAAAACGGACGATGGCC 60.954 55.000 0.00 0.00 0.00 5.36
2411 2835 0.442699 GACAGAAAACGGACGATGGC 59.557 55.000 0.00 0.00 0.00 4.40
2416 2840 1.219522 AAGCGGACAGAAAACGGACG 61.220 55.000 0.00 0.00 0.00 4.79
2423 2847 0.601841 GGGTCGAAAGCGGACAGAAA 60.602 55.000 0.00 0.00 38.28 2.52
2426 2850 0.673644 AATGGGTCGAAAGCGGACAG 60.674 55.000 0.00 0.00 38.28 3.51
2463 2887 3.039588 GTTCGGCCGCAAACTCGA 61.040 61.111 23.51 0.00 0.00 4.04
2475 2899 1.066752 TCTGTGTGTGTCCGTTCGG 59.933 57.895 4.74 4.74 0.00 4.30
2481 2905 1.215655 GCTCACGTCTGTGTGTGTCC 61.216 60.000 0.00 0.00 46.49 4.02
2535 2959 2.053747 AAAGGGGGTATGTCTCACCA 57.946 50.000 0.00 0.00 37.84 4.17
2545 2969 3.848377 GGTAGAGGAAGAAAAAGGGGGTA 59.152 47.826 0.00 0.00 0.00 3.69
2550 2975 3.847184 AGGGAGGTAGAGGAAGAAAAAGG 59.153 47.826 0.00 0.00 0.00 3.11
2583 3008 0.531974 TGCAAACACCAGAGACCGTC 60.532 55.000 0.00 0.00 0.00 4.79
2584 3009 0.107410 TTGCAAACACCAGAGACCGT 60.107 50.000 0.00 0.00 0.00 4.83
2627 4153 3.891366 CCATTGACCTCAAAGTTCACCTT 59.109 43.478 0.00 0.00 39.55 3.50
2632 4158 2.029918 GTGGCCATTGACCTCAAAGTTC 60.030 50.000 9.72 0.00 39.55 3.01
2656 4182 7.015292 TCAGCTAGGTAATATCCCTTGTTGTAG 59.985 40.741 14.28 2.82 37.34 2.74
2662 4188 5.738909 CCATCAGCTAGGTAATATCCCTTG 58.261 45.833 0.00 0.03 33.35 3.61
2697 4223 1.416401 TCTTCACAAGAGTGGACCACC 59.584 52.381 21.32 12.48 45.91 4.61
2747 4273 2.300956 TGCAATTGGGCAAACCTCTA 57.699 45.000 7.72 0.00 41.65 2.43
2762 4288 2.550855 CCTTCCTAGCACTCTGTTGCAA 60.551 50.000 0.00 0.00 45.62 4.08
2765 4291 2.672478 CGTCCTTCCTAGCACTCTGTTG 60.672 54.545 0.00 0.00 0.00 3.33
2768 4294 1.135257 CACGTCCTTCCTAGCACTCTG 60.135 57.143 0.00 0.00 0.00 3.35
2793 4319 0.040958 CTGAAGCACACGGAAAGCAC 60.041 55.000 0.00 0.00 0.00 4.40
2801 4327 2.375766 GCCGAGACTGAAGCACACG 61.376 63.158 0.00 0.00 0.00 4.49
2806 4332 1.605058 TACCCAGCCGAGACTGAAGC 61.605 60.000 2.14 0.00 40.25 3.86
2816 4342 0.101040 TTACGAACGATACCCAGCCG 59.899 55.000 0.14 0.00 0.00 5.52
2818 4344 1.564207 GGTTACGAACGATACCCAGC 58.436 55.000 0.14 0.00 0.00 4.85
2827 4353 1.127951 GTCAATGCAGGGTTACGAACG 59.872 52.381 0.00 0.00 0.00 3.95
2847 4373 4.361451 AAAAGCTTATTCGTGCTCCATG 57.639 40.909 0.00 0.00 38.75 3.66
2860 4386 4.216257 GCAGTCATCACCTCAAAAAGCTTA 59.784 41.667 0.00 0.00 0.00 3.09
2864 4390 4.037208 ACAAGCAGTCATCACCTCAAAAAG 59.963 41.667 0.00 0.00 0.00 2.27
2868 4394 2.158769 ACACAAGCAGTCATCACCTCAA 60.159 45.455 0.00 0.00 0.00 3.02
2869 4395 1.417517 ACACAAGCAGTCATCACCTCA 59.582 47.619 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.