Multiple sequence alignment - TraesCS4D01G296500

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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 TraesCS4D01G296500 chr4D 100.000 2273 0 0 1 2273 465909884 465907612 0.000000e+00 4198.0
1 TraesCS4D01G296500 chr4D 91.351 185 13 2 453 637 346470185 346470004 1.350000e-62 250.0
2 TraesCS4D01G296500 chr4B 91.895 765 35 13 631 1375 582957248 582956491 0.000000e+00 1044.0
3 TraesCS4D01G296500 chr4B 87.047 911 41 19 1385 2268 582921342 582920482 0.000000e+00 957.0
4 TraesCS4D01G296500 chr4B 89.552 469 31 4 2 453 582957699 582957232 1.510000e-161 579.0
5 TraesCS4D01G296500 chr4B 86.817 311 27 7 1587 1884 46197160 46197469 3.620000e-88 335.0
6 TraesCS4D01G296500 chr6D 87.540 313 26 8 1585 1886 2699216 2698906 1.290000e-92 350.0
7 TraesCS4D01G296500 chr6D 85.535 159 22 1 295 453 467161236 467161079 5.020000e-37 165.0
8 TraesCS4D01G296500 chr6D 81.875 160 19 9 231 383 417886371 417886527 2.370000e-25 126.0
9 TraesCS4D01G296500 chr5D 87.908 306 24 8 1584 1879 70388076 70387774 4.650000e-92 348.0
10 TraesCS4D01G296500 chr5D 93.714 175 11 0 460 634 386086898 386087072 1.730000e-66 263.0
11 TraesCS4D01G296500 chr4A 86.885 305 30 4 990 1287 641602477 641602778 1.300000e-87 333.0
12 TraesCS4D01G296500 chr4A 86.869 297 29 6 1001 1287 641610693 641610989 7.830000e-85 324.0
13 TraesCS4D01G296500 chr4A 82.574 373 29 17 961 1315 686385587 686385233 1.710000e-76 296.0
14 TraesCS4D01G296500 chr4A 83.502 297 20 11 1982 2267 4641133 4641411 1.350000e-62 250.0
15 TraesCS4D01G296500 chr4A 89.147 129 13 1 1414 1542 4638128 4638255 2.340000e-35 159.0
16 TraesCS4D01G296500 chr2D 84.076 314 34 8 1583 1884 599785829 599785520 2.860000e-74 289.0
17 TraesCS4D01G296500 chr2D 83.230 322 40 10 961 1276 582494889 582494576 1.330000e-72 283.0
18 TraesCS4D01G296500 chr2D 89.604 202 18 3 451 650 143253522 143253722 1.040000e-63 254.0
19 TraesCS4D01G296500 chr2D 89.947 189 17 2 453 641 563100892 563100706 2.260000e-60 243.0
20 TraesCS4D01G296500 chr2D 78.638 323 38 17 990 1288 488229209 488229524 3.860000e-43 185.0
21 TraesCS4D01G296500 chr3D 83.706 313 32 9 1585 1884 91382397 91382703 6.180000e-71 278.0
22 TraesCS4D01G296500 chr3D 90.761 184 15 2 447 630 506177319 506177138 6.270000e-61 244.0
23 TraesCS4D01G296500 chr3D 90.659 182 15 1 453 634 453280405 453280584 8.110000e-60 241.0
24 TraesCS4D01G296500 chr3D 76.987 239 19 13 231 452 559226237 559226456 1.110000e-18 104.0
25 TraesCS4D01G296500 chr5B 82.927 328 34 12 990 1305 441446349 441446032 2.220000e-70 276.0
26 TraesCS4D01G296500 chr2B 83.803 284 34 9 999 1276 701490936 701490659 2.240000e-65 259.0
27 TraesCS4D01G296500 chr2B 91.758 182 12 3 454 634 743582876 743583055 1.350000e-62 250.0
28 TraesCS4D01G296500 chr7B 83.162 291 38 6 1024 1308 630651794 630651509 2.900000e-64 255.0
29 TraesCS4D01G296500 chr1A 88.557 201 21 2 451 651 44475867 44476065 2.260000e-60 243.0
30 TraesCS4D01G296500 chr1A 88.889 198 20 2 446 643 578019678 578019483 2.260000e-60 243.0
31 TraesCS4D01G296500 chr1A 87.619 105 13 0 294 398 511634360 511634464 3.070000e-24 122.0
32 TraesCS4D01G296500 chr7A 83.396 265 38 3 1035 1293 662169731 662169467 8.110000e-60 241.0
33 TraesCS4D01G296500 chr7A 77.824 239 28 9 232 453 19165663 19165433 8.520000e-25 124.0
34 TraesCS4D01G296500 chr7A 77.406 239 26 15 231 453 709765816 709765590 1.430000e-22 117.0
35 TraesCS4D01G296500 chr6A 84.906 212 25 4 248 453 446783278 446783488 8.230000e-50 207.0
36 TraesCS4D01G296500 chr6A 100.000 28 0 0 426 453 604529848 604529875 4.000000e-03 52.8
37 TraesCS4D01G296500 chr5A 80.000 245 30 5 228 453 600947284 600947040 1.810000e-36 163.0
38 TraesCS4D01G296500 chr5A 95.918 49 2 0 1587 1635 342261211 342261163 1.870000e-11 80.5
39 TraesCS4D01G296500 chr1B 79.524 210 26 10 231 423 34992647 34992856 1.420000e-27 134.0
40 TraesCS4D01G296500 chr1B 95.588 68 3 0 231 298 34992308 34992375 2.390000e-20 110.0
41 TraesCS4D01G296500 chr1B 85.577 104 13 2 294 396 47204773 47204875 8.590000e-20 108.0
42 TraesCS4D01G296500 chrUn 79.781 183 20 8 231 396 94974848 94974666 1.430000e-22 117.0
43 TraesCS4D01G296500 chr7D 93.939 66 4 0 233 298 550475408 550475473 1.440000e-17 100.0


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 TraesCS4D01G296500 chr4D 465907612 465909884 2272 True 4198.0 4198 100.0000 1 2273 1 chr4D.!!$R2 2272
1 TraesCS4D01G296500 chr4B 582920482 582921342 860 True 957.0 957 87.0470 1385 2268 1 chr4B.!!$R1 883
2 TraesCS4D01G296500 chr4B 582956491 582957699 1208 True 811.5 1044 90.7235 2 1375 2 chr4B.!!$R2 1373
3 TraesCS4D01G296500 chr4A 4638128 4641411 3283 False 204.5 250 86.3245 1414 2267 2 chr4A.!!$F3 853

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
849 867 0.114364 GCTTTCTTTTCCCCTCCCCA 59.886 55.0 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1865 0.036952 CACCGATGCTCCAGTCTTGT 60.037 55.0 0.0 0.0 0.0 3.16 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
53 54 3.554692 CCATGGCGCTCGAACGTC 61.555 66.667 7.64 5.76 38.39 4.34
84 85 1.276421 CCTGGTCGTCAAGAAGATGGT 59.724 52.381 0.00 0.00 33.89 3.55
88 89 3.118775 TGGTCGTCAAGAAGATGGTATGG 60.119 47.826 0.00 0.00 33.89 2.74
132 133 6.512514 AGAGGAGAGATTTGGATATTGCTT 57.487 37.500 0.00 0.00 0.00 3.91
133 134 6.297582 AGAGGAGAGATTTGGATATTGCTTG 58.702 40.000 0.00 0.00 0.00 4.01
134 135 4.826183 AGGAGAGATTTGGATATTGCTTGC 59.174 41.667 0.00 0.00 0.00 4.01
135 136 4.826183 GGAGAGATTTGGATATTGCTTGCT 59.174 41.667 0.00 0.00 0.00 3.91
136 137 5.278364 GGAGAGATTTGGATATTGCTTGCTG 60.278 44.000 0.00 0.00 0.00 4.41
137 138 5.443283 AGAGATTTGGATATTGCTTGCTGA 58.557 37.500 0.00 0.00 0.00 4.26
138 139 5.298777 AGAGATTTGGATATTGCTTGCTGAC 59.701 40.000 0.00 0.00 0.00 3.51
139 140 3.763097 TTTGGATATTGCTTGCTGACG 57.237 42.857 0.00 0.00 0.00 4.35
140 141 2.689553 TGGATATTGCTTGCTGACGA 57.310 45.000 0.00 0.00 0.00 4.20
157 158 2.989840 GACGATGATGATGAACCGATCC 59.010 50.000 0.00 0.00 0.00 3.36
180 181 3.969899 TCAATCGTCAAGAGGATCGATG 58.030 45.455 0.54 2.19 42.67 3.84
185 186 0.670706 TCAAGAGGATCGATGGAGCG 59.329 55.000 0.54 0.00 42.67 5.03
205 206 2.029728 CGTGCGCTTATTTCTTGAGGAG 59.970 50.000 9.73 0.00 0.00 3.69
245 246 5.364778 AGCAGGGTGGTTAAAAATTTCAAC 58.635 37.500 6.95 6.95 0.00 3.18
287 288 7.579589 TTTGAAATTTCGCATATTTCAGTGG 57.420 32.000 13.34 0.00 46.66 4.00
298 299 2.668144 TTTCAGTGGGGTCCGAAATT 57.332 45.000 0.00 0.00 0.00 1.82
300 301 2.194201 TCAGTGGGGTCCGAAATTTC 57.806 50.000 8.20 8.20 0.00 2.17
322 340 3.491267 CGAGGCAGACTTAAATCGATTCC 59.509 47.826 11.83 5.64 32.13 3.01
453 471 6.737254 TTCAGTGAGGTCCGAAATTATTTC 57.263 37.500 7.56 7.56 36.32 2.17
454 472 5.800296 TCAGTGAGGTCCGAAATTATTTCA 58.200 37.500 16.57 0.00 39.63 2.69
455 473 5.874810 TCAGTGAGGTCCGAAATTATTTCAG 59.125 40.000 16.57 6.54 39.63 3.02
456 474 5.643777 CAGTGAGGTCCGAAATTATTTCAGT 59.356 40.000 16.57 0.00 39.63 3.41
457 475 6.149474 CAGTGAGGTCCGAAATTATTTCAGTT 59.851 38.462 16.57 0.00 39.63 3.16
458 476 6.715264 AGTGAGGTCCGAAATTATTTCAGTTT 59.285 34.615 16.57 0.00 39.63 2.66
459 477 6.801862 GTGAGGTCCGAAATTATTTCAGTTTG 59.198 38.462 16.57 1.42 39.63 2.93
460 478 6.488683 TGAGGTCCGAAATTATTTCAGTTTGT 59.511 34.615 16.57 0.00 39.63 2.83
461 479 6.909909 AGGTCCGAAATTATTTCAGTTTGTC 58.090 36.000 16.57 1.38 39.63 3.18
462 480 6.715264 AGGTCCGAAATTATTTCAGTTTGTCT 59.285 34.615 16.57 3.29 39.63 3.41
463 481 7.881232 AGGTCCGAAATTATTTCAGTTTGTCTA 59.119 33.333 16.57 0.00 39.63 2.59
464 482 8.508875 GGTCCGAAATTATTTCAGTTTGTCTAA 58.491 33.333 16.57 0.00 39.63 2.10
476 494 9.996554 TTTCAGTTTGTCTAATTCACATCTAGA 57.003 29.630 0.00 0.00 0.00 2.43
478 496 9.591792 TCAGTTTGTCTAATTCACATCTAGATG 57.408 33.333 27.63 27.63 44.15 2.90
508 526 8.561536 TTAAGGATATCACATCTAAACTCCCA 57.438 34.615 4.83 0.00 0.00 4.37
509 527 7.639062 AAGGATATCACATCTAAACTCCCAT 57.361 36.000 4.83 0.00 0.00 4.00
510 528 8.742125 AAGGATATCACATCTAAACTCCCATA 57.258 34.615 4.83 0.00 0.00 2.74
511 529 8.742125 AGGATATCACATCTAAACTCCCATAA 57.258 34.615 4.83 0.00 0.00 1.90
512 530 9.170890 AGGATATCACATCTAAACTCCCATAAA 57.829 33.333 4.83 0.00 0.00 1.40
513 531 9.965902 GGATATCACATCTAAACTCCCATAAAT 57.034 33.333 4.83 0.00 0.00 1.40
582 600 8.902540 AAAATAGATCACAAACAGAGTGTACA 57.097 30.769 0.00 0.00 38.16 2.90
583 601 9.507329 AAAATAGATCACAAACAGAGTGTACAT 57.493 29.630 0.00 0.00 38.16 2.29
584 602 8.709386 AATAGATCACAAACAGAGTGTACATC 57.291 34.615 0.00 0.00 38.16 3.06
585 603 6.101650 AGATCACAAACAGAGTGTACATCA 57.898 37.500 0.00 0.00 38.16 3.07
586 604 6.162079 AGATCACAAACAGAGTGTACATCAG 58.838 40.000 0.00 0.00 38.16 2.90
587 605 5.529581 TCACAAACAGAGTGTACATCAGA 57.470 39.130 0.00 0.00 38.16 3.27
588 606 6.101650 TCACAAACAGAGTGTACATCAGAT 57.898 37.500 0.00 0.00 38.16 2.90
589 607 6.524734 TCACAAACAGAGTGTACATCAGATT 58.475 36.000 0.00 0.00 38.16 2.40
590 608 7.666623 TCACAAACAGAGTGTACATCAGATTA 58.333 34.615 0.00 0.00 38.16 1.75
591 609 7.814587 TCACAAACAGAGTGTACATCAGATTAG 59.185 37.037 0.00 0.00 38.16 1.73
592 610 7.814587 CACAAACAGAGTGTACATCAGATTAGA 59.185 37.037 0.00 0.00 32.44 2.10
593 611 8.535335 ACAAACAGAGTGTACATCAGATTAGAT 58.465 33.333 0.00 0.00 0.00 1.98
636 654 8.052748 ACATCTATATGTGTCCTAGAGAGATCC 58.947 40.741 0.00 0.00 44.79 3.36
637 655 7.575499 TCTATATGTGTCCTAGAGAGATCCA 57.425 40.000 0.00 0.00 0.00 3.41
638 656 7.990055 TCTATATGTGTCCTAGAGAGATCCAA 58.010 38.462 0.00 0.00 0.00 3.53
639 657 8.448816 TCTATATGTGTCCTAGAGAGATCCAAA 58.551 37.037 0.00 0.00 0.00 3.28
640 658 9.253832 CTATATGTGTCCTAGAGAGATCCAAAT 57.746 37.037 0.00 0.00 0.00 2.32
641 659 6.821616 ATGTGTCCTAGAGAGATCCAAATT 57.178 37.500 0.00 0.00 0.00 1.82
642 660 7.921041 ATGTGTCCTAGAGAGATCCAAATTA 57.079 36.000 0.00 0.00 0.00 1.40
643 661 7.921041 TGTGTCCTAGAGAGATCCAAATTAT 57.079 36.000 0.00 0.00 0.00 1.28
644 662 8.324191 TGTGTCCTAGAGAGATCCAAATTATT 57.676 34.615 0.00 0.00 0.00 1.40
645 663 8.772250 TGTGTCCTAGAGAGATCCAAATTATTT 58.228 33.333 0.00 0.00 0.00 1.40
646 664 9.620259 GTGTCCTAGAGAGATCCAAATTATTTT 57.380 33.333 0.00 0.00 0.00 1.82
697 715 1.008995 CCGTTCCGTTTGCACTTGG 60.009 57.895 0.00 0.00 0.00 3.61
710 728 3.433343 TGCACTTGGGAAATCATCATGT 58.567 40.909 0.00 0.00 0.00 3.21
742 760 2.632987 AGTGGCCGTTAACTTGTCTT 57.367 45.000 3.71 0.00 0.00 3.01
750 768 6.369615 TGGCCGTTAACTTGTCTTCTTATTAC 59.630 38.462 3.71 0.00 0.00 1.89
754 772 9.367444 CCGTTAACTTGTCTTCTTATTACATCT 57.633 33.333 3.71 0.00 0.00 2.90
787 805 5.732331 ATCCAATCCAATCCAAGAAGGTA 57.268 39.130 0.00 0.00 39.02 3.08
819 837 4.794655 GCTCTCTTTCTCGTGTTCTGTTCT 60.795 45.833 0.00 0.00 0.00 3.01
830 848 4.788100 CGTGTTCTGTTCTGTTTCTGTTTG 59.212 41.667 0.00 0.00 0.00 2.93
849 867 0.114364 GCTTTCTTTTCCCCTCCCCA 59.886 55.000 0.00 0.00 0.00 4.96
862 880 3.372025 CCCCTCCCCAGCATATAATAAGC 60.372 52.174 0.00 0.00 0.00 3.09
882 909 4.699522 GCACGACCCCTGTCCACC 62.700 72.222 0.00 0.00 38.32 4.61
902 929 2.880719 AAAGCAACGCAACGCAAGCA 62.881 50.000 0.00 0.00 45.62 3.91
960 992 7.042321 CGTCTTCTCTTCTTCACGTAGATAGAT 60.042 40.741 0.00 0.00 0.00 1.98
988 1020 3.753797 AGTTTTCCATCTCGCTTTTCCTC 59.246 43.478 0.00 0.00 0.00 3.71
1013 1045 0.620556 GGCCTGATGGAGAACAAGGA 59.379 55.000 0.00 0.00 34.57 3.36
1239 1274 0.957888 GCTTCAAGCCTGACTCCACC 60.958 60.000 0.00 0.00 34.48 4.61
1245 1280 1.600916 GCCTGACTCCACCACCAAC 60.601 63.158 0.00 0.00 0.00 3.77
1285 1320 1.367782 CAGTAGATCGCCGTCGTCG 60.368 63.158 0.00 0.00 36.96 5.12
1294 1329 0.111354 CGCCGTCGTCGTCTAGATAC 60.111 60.000 0.00 0.00 35.01 2.24
1367 1410 2.101415 GGATCATGGGCCTTGTTTTAGC 59.899 50.000 17.94 2.80 0.00 3.09
1375 1418 0.603065 CCTTGTTTTAGCTGTGGGGC 59.397 55.000 0.00 0.00 0.00 5.80
1376 1419 0.603065 CTTGTTTTAGCTGTGGGGCC 59.397 55.000 0.00 0.00 0.00 5.80
1377 1420 0.187361 TTGTTTTAGCTGTGGGGCCT 59.813 50.000 0.84 0.00 0.00 5.19
1378 1421 1.068948 TGTTTTAGCTGTGGGGCCTA 58.931 50.000 0.84 0.00 0.00 3.93
1379 1422 1.638589 TGTTTTAGCTGTGGGGCCTAT 59.361 47.619 0.84 0.00 0.00 2.57
1380 1423 2.847449 TGTTTTAGCTGTGGGGCCTATA 59.153 45.455 0.84 0.00 0.00 1.31
1381 1424 3.461831 TGTTTTAGCTGTGGGGCCTATAT 59.538 43.478 0.84 0.00 0.00 0.86
1382 1425 4.079443 TGTTTTAGCTGTGGGGCCTATATT 60.079 41.667 0.84 0.00 0.00 1.28
1383 1426 5.132985 TGTTTTAGCTGTGGGGCCTATATTA 59.867 40.000 0.84 0.00 0.00 0.98
1521 1564 5.766174 TGTAGGACATGGTTTTGAAAGTACC 59.234 40.000 0.00 0.00 0.00 3.34
1532 1575 8.630917 TGGTTTTGAAAGTACCGATTTGATTTA 58.369 29.630 0.00 0.00 34.62 1.40
1534 1577 9.887406 GTTTTGAAAGTACCGATTTGATTTAGA 57.113 29.630 0.00 0.00 0.00 2.10
1538 1581 9.443323 TGAAAGTACCGATTTGATTTAGATTCA 57.557 29.630 0.00 0.00 0.00 2.57
1555 1666 6.540438 AGATTCATTACTAACGTTGGGAGA 57.460 37.500 16.48 0.00 0.00 3.71
1580 1691 1.925455 CTGGAAAGGAGGGGAGGCA 60.925 63.158 0.00 0.00 0.00 4.75
1600 1711 3.316308 GCAGGATAAGGCCTTGTACAATG 59.684 47.826 28.77 17.60 35.66 2.82
1622 1733 2.280628 GGACTGCTTATGTACAGGTGC 58.719 52.381 0.33 5.80 38.25 5.01
1679 1801 7.643569 AAAATTGATACATGTGCCTCATACA 57.356 32.000 9.11 0.00 34.67 2.29
1680 1802 6.872628 AATTGATACATGTGCCTCATACAG 57.127 37.500 9.11 0.00 34.67 2.74
1707 1832 5.685075 GCTTAGGCTGGATTAGTACATGTGT 60.685 44.000 9.11 0.00 35.22 3.72
1724 1849 6.415573 ACATGTGTTTAAGGAGAGGGAATAC 58.584 40.000 0.00 0.00 0.00 1.89
1726 1851 4.529377 TGTGTTTAAGGAGAGGGAATACGT 59.471 41.667 0.00 0.00 0.00 3.57
1727 1852 5.012354 TGTGTTTAAGGAGAGGGAATACGTT 59.988 40.000 0.00 0.00 0.00 3.99
1799 1924 0.320771 GCTTCCGTTGCCTCTCTGAA 60.321 55.000 0.00 0.00 0.00 3.02
1800 1925 1.719600 CTTCCGTTGCCTCTCTGAAG 58.280 55.000 0.00 0.00 0.00 3.02
1801 1926 0.320771 TTCCGTTGCCTCTCTGAAGC 60.321 55.000 0.00 0.00 0.00 3.86
1802 1927 1.004560 CCGTTGCCTCTCTGAAGCA 60.005 57.895 0.00 0.00 33.97 3.91
1803 1928 1.294659 CCGTTGCCTCTCTGAAGCAC 61.295 60.000 0.00 0.00 35.96 4.40
1804 1929 1.294659 CGTTGCCTCTCTGAAGCACC 61.295 60.000 0.00 0.00 35.96 5.01
1805 1930 0.036022 GTTGCCTCTCTGAAGCACCT 59.964 55.000 0.00 0.00 35.96 4.00
1806 1931 0.035881 TTGCCTCTCTGAAGCACCTG 59.964 55.000 0.00 0.00 35.96 4.00
1807 1932 1.078567 GCCTCTCTGAAGCACCTGG 60.079 63.158 0.00 0.00 0.00 4.45
1808 1933 1.835927 GCCTCTCTGAAGCACCTGGT 61.836 60.000 0.00 0.00 0.00 4.00
1809 1934 0.248843 CCTCTCTGAAGCACCTGGTC 59.751 60.000 0.00 0.00 0.00 4.02
1810 1935 0.972134 CTCTCTGAAGCACCTGGTCA 59.028 55.000 0.00 0.00 0.00 4.02
1811 1936 1.345741 CTCTCTGAAGCACCTGGTCAA 59.654 52.381 0.00 0.00 0.00 3.18
1812 1937 1.345741 TCTCTGAAGCACCTGGTCAAG 59.654 52.381 0.00 0.00 0.00 3.02
1813 1938 0.250467 TCTGAAGCACCTGGTCAAGC 60.250 55.000 0.00 0.00 0.00 4.01
1814 1939 0.535780 CTGAAGCACCTGGTCAAGCA 60.536 55.000 9.90 0.59 0.00 3.91
1815 1940 0.819259 TGAAGCACCTGGTCAAGCAC 60.819 55.000 9.90 4.70 0.00 4.40
1817 1942 2.983725 AAGCACCTGGTCAAGCACCC 62.984 60.000 9.90 0.00 46.18 4.61
1818 1943 2.515398 CACCTGGTCAAGCACCCA 59.485 61.111 0.00 0.00 46.18 4.51
1819 1944 1.898574 CACCTGGTCAAGCACCCAC 60.899 63.158 0.00 0.00 46.18 4.61
1820 1945 2.669569 CCTGGTCAAGCACCCACG 60.670 66.667 0.00 0.00 46.18 4.94
1821 1946 2.425592 CTGGTCAAGCACCCACGA 59.574 61.111 0.00 0.00 46.18 4.35
1822 1947 1.669115 CTGGTCAAGCACCCACGAG 60.669 63.158 0.00 0.00 46.18 4.18
1823 1948 3.050275 GGTCAAGCACCCACGAGC 61.050 66.667 0.00 0.00 39.69 5.03
1878 2004 1.089920 GAGGCACCTGCATTGTACAG 58.910 55.000 0.00 0.00 44.36 2.74
1900 2026 1.613520 GCCTAACCAACTCCCCTTGAC 60.614 57.143 0.00 0.00 0.00 3.18
1935 2062 6.978343 TTCAATAAACTTACCGACCTGATG 57.022 37.500 0.00 0.00 0.00 3.07
1997 4791 1.762957 GTACTATGGCCAGCTTGGAGA 59.237 52.381 13.05 0.00 40.96 3.71
2027 4821 2.487762 GGAGCGAACACATTGGAATTCA 59.512 45.455 7.93 0.00 0.00 2.57
2066 4860 0.036952 CAGAGGGCGTTCACTGTGAT 60.037 55.000 11.86 0.00 30.23 3.06
2068 4862 1.072331 AGAGGGCGTTCACTGTGATTT 59.928 47.619 11.86 0.00 0.00 2.17
2069 4863 1.464997 GAGGGCGTTCACTGTGATTTC 59.535 52.381 11.86 4.92 0.00 2.17
2070 4864 1.072331 AGGGCGTTCACTGTGATTTCT 59.928 47.619 11.86 3.05 0.00 2.52
2071 4865 2.301870 AGGGCGTTCACTGTGATTTCTA 59.698 45.455 11.86 0.00 0.00 2.10
2159 4962 7.686105 GATGTTAATCGTTTCACGTTTGTAG 57.314 36.000 3.44 0.00 43.14 2.74
2236 5041 3.491639 TGTGTCATAGTTTTCGAACACGG 59.508 43.478 8.70 3.65 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.376037 CTTCTTGACGACCAGGCCC 60.376 63.158 0.00 0.00 0.00 5.80
84 85 2.547855 CGCTCCATTGATCGGTTCCATA 60.548 50.000 0.00 0.00 0.00 2.74
88 89 1.202417 TCTCGCTCCATTGATCGGTTC 60.202 52.381 0.00 0.00 31.28 3.62
97 98 2.031120 CTCTCCTCTTCTCGCTCCATT 58.969 52.381 0.00 0.00 0.00 3.16
132 133 2.554142 GGTTCATCATCATCGTCAGCA 58.446 47.619 0.00 0.00 0.00 4.41
133 134 1.524355 CGGTTCATCATCATCGTCAGC 59.476 52.381 0.00 0.00 0.00 4.26
134 135 3.084070 TCGGTTCATCATCATCGTCAG 57.916 47.619 0.00 0.00 0.00 3.51
135 136 3.552890 GGATCGGTTCATCATCATCGTCA 60.553 47.826 0.00 0.00 0.00 4.35
136 137 2.989840 GGATCGGTTCATCATCATCGTC 59.010 50.000 0.00 0.00 0.00 4.20
137 138 2.365293 TGGATCGGTTCATCATCATCGT 59.635 45.455 0.00 0.00 0.00 3.73
138 139 3.030668 TGGATCGGTTCATCATCATCG 57.969 47.619 0.00 0.00 0.00 3.84
139 140 4.572909 TGATGGATCGGTTCATCATCATC 58.427 43.478 15.97 5.15 43.09 2.92
140 141 4.628963 TGATGGATCGGTTCATCATCAT 57.371 40.909 15.97 0.00 43.09 2.45
157 158 3.969899 TCGATCCTCTTGACGATTGATG 58.030 45.455 0.00 0.00 0.00 3.07
185 186 3.262420 TCTCCTCAAGAAATAAGCGCAC 58.738 45.455 11.47 0.00 0.00 5.34
264 265 6.098679 CCCACTGAAATATGCGAAATTTCAA 58.901 36.000 17.99 6.05 46.93 2.69
270 271 3.013921 GACCCCACTGAAATATGCGAAA 58.986 45.455 0.00 0.00 0.00 3.46
298 299 3.861276 TCGATTTAAGTCTGCCTCGAA 57.139 42.857 0.00 0.00 32.78 3.71
300 301 3.491267 GGAATCGATTTAAGTCTGCCTCG 59.509 47.826 12.81 0.00 0.00 4.63
423 441 1.860950 CGGACCTCACTGAAATATGCG 59.139 52.381 0.00 0.00 0.00 4.73
424 442 3.179443 TCGGACCTCACTGAAATATGC 57.821 47.619 0.00 0.00 0.00 3.14
482 500 8.998814 TGGGAGTTTAGATGTGATATCCTTAAA 58.001 33.333 0.00 0.00 0.00 1.52
483 501 8.561536 TGGGAGTTTAGATGTGATATCCTTAA 57.438 34.615 0.00 0.00 0.00 1.85
484 502 8.742125 ATGGGAGTTTAGATGTGATATCCTTA 57.258 34.615 0.00 0.00 0.00 2.69
485 503 7.639062 ATGGGAGTTTAGATGTGATATCCTT 57.361 36.000 0.00 0.00 0.00 3.36
486 504 8.742125 TTATGGGAGTTTAGATGTGATATCCT 57.258 34.615 0.00 0.00 0.00 3.24
487 505 9.965902 ATTTATGGGAGTTTAGATGTGATATCC 57.034 33.333 0.00 0.00 0.00 2.59
556 574 9.337396 TGTACACTCTGTTTGTGATCTATTTTT 57.663 29.630 0.00 0.00 38.65 1.94
557 575 8.902540 TGTACACTCTGTTTGTGATCTATTTT 57.097 30.769 0.00 0.00 38.65 1.82
558 576 9.155975 GATGTACACTCTGTTTGTGATCTATTT 57.844 33.333 0.00 0.00 38.65 1.40
559 577 8.314021 TGATGTACACTCTGTTTGTGATCTATT 58.686 33.333 0.00 0.00 38.65 1.73
560 578 7.840931 TGATGTACACTCTGTTTGTGATCTAT 58.159 34.615 0.00 0.00 38.65 1.98
561 579 7.176690 TCTGATGTACACTCTGTTTGTGATCTA 59.823 37.037 0.00 0.00 38.65 1.98
562 580 6.015095 TCTGATGTACACTCTGTTTGTGATCT 60.015 38.462 0.00 0.00 38.65 2.75
563 581 6.159293 TCTGATGTACACTCTGTTTGTGATC 58.841 40.000 0.00 0.00 38.65 2.92
564 582 6.101650 TCTGATGTACACTCTGTTTGTGAT 57.898 37.500 0.00 0.00 38.65 3.06
565 583 5.529581 TCTGATGTACACTCTGTTTGTGA 57.470 39.130 0.00 0.00 38.65 3.58
566 584 6.791887 AATCTGATGTACACTCTGTTTGTG 57.208 37.500 0.00 0.00 40.87 3.33
567 585 7.896811 TCTAATCTGATGTACACTCTGTTTGT 58.103 34.615 0.00 0.00 0.00 2.83
568 586 8.815189 CATCTAATCTGATGTACACTCTGTTTG 58.185 37.037 0.00 0.00 39.05 2.93
569 587 8.939201 CATCTAATCTGATGTACACTCTGTTT 57.061 34.615 0.00 5.90 39.05 2.83
611 629 8.052141 TGGATCTCTCTAGGACACATATAGATG 58.948 40.741 0.00 0.00 39.16 2.90
612 630 8.168905 TGGATCTCTCTAGGACACATATAGAT 57.831 38.462 0.00 0.00 0.00 1.98
613 631 7.575499 TGGATCTCTCTAGGACACATATAGA 57.425 40.000 0.00 0.00 0.00 1.98
614 632 8.642935 TTTGGATCTCTCTAGGACACATATAG 57.357 38.462 0.00 0.00 0.00 1.31
615 633 9.607333 AATTTGGATCTCTCTAGGACACATATA 57.393 33.333 0.00 0.00 0.00 0.86
616 634 8.503428 AATTTGGATCTCTCTAGGACACATAT 57.497 34.615 0.00 0.00 0.00 1.78
617 635 7.921041 AATTTGGATCTCTCTAGGACACATA 57.079 36.000 0.00 0.00 0.00 2.29
618 636 6.821616 AATTTGGATCTCTCTAGGACACAT 57.178 37.500 0.00 0.00 0.00 3.21
619 637 7.921041 ATAATTTGGATCTCTCTAGGACACA 57.079 36.000 0.00 0.00 0.00 3.72
620 638 9.620259 AAAATAATTTGGATCTCTCTAGGACAC 57.380 33.333 0.00 0.00 0.00 3.67
634 652 9.665719 GCTTCTTGGGAAATAAAATAATTTGGA 57.334 29.630 0.00 0.00 0.00 3.53
635 653 9.447157 TGCTTCTTGGGAAATAAAATAATTTGG 57.553 29.630 0.00 0.00 0.00 3.28
637 655 9.671279 CCTGCTTCTTGGGAAATAAAATAATTT 57.329 29.630 0.00 0.00 0.00 1.82
638 656 8.267183 CCCTGCTTCTTGGGAAATAAAATAATT 58.733 33.333 0.00 0.00 46.15 1.40
639 657 7.795047 CCCTGCTTCTTGGGAAATAAAATAAT 58.205 34.615 0.00 0.00 46.15 1.28
640 658 7.181569 CCCTGCTTCTTGGGAAATAAAATAA 57.818 36.000 0.00 0.00 46.15 1.40
641 659 6.790232 CCCTGCTTCTTGGGAAATAAAATA 57.210 37.500 0.00 0.00 46.15 1.40
642 660 5.682234 CCCTGCTTCTTGGGAAATAAAAT 57.318 39.130 0.00 0.00 46.15 1.82
653 671 2.183679 ACTCCTACTCCCTGCTTCTTG 58.816 52.381 0.00 0.00 0.00 3.02
697 715 4.035675 GGAGTTCGGAACATGATGATTTCC 59.964 45.833 21.86 12.64 36.24 3.13
710 728 1.005394 GCCACTTCGGAGTTCGGAA 60.005 57.895 4.38 2.73 39.77 4.30
787 805 0.680061 AGAAAGAGAGCGTCCCGTTT 59.320 50.000 0.00 0.00 0.00 3.60
819 837 5.175127 GGGAAAAGAAAGCAAACAGAAACA 58.825 37.500 0.00 0.00 0.00 2.83
830 848 0.114364 TGGGGAGGGGAAAAGAAAGC 59.886 55.000 0.00 0.00 0.00 3.51
849 867 3.997021 GTCGTGCCTGCTTATTATATGCT 59.003 43.478 10.67 0.00 0.00 3.79
862 880 4.394712 GGACAGGGGTCGTGCCTG 62.395 72.222 0.00 0.00 45.28 4.85
877 904 1.435515 GTTGCGTTGCTTTGGTGGA 59.564 52.632 0.00 0.00 0.00 4.02
882 909 1.554595 CTTGCGTTGCGTTGCTTTG 59.445 52.632 0.00 0.00 0.00 2.77
902 929 0.173255 GTGGTTGTGCTTGTGCTTGT 59.827 50.000 0.00 0.00 40.48 3.16
960 992 4.537135 AGCGAGATGGAAAACTTGTCTA 57.463 40.909 0.00 0.00 0.00 2.59
988 1020 1.626356 TTCTCCATCAGGCCCCGAAG 61.626 60.000 0.00 0.00 33.74 3.79
1064 1096 0.982673 CCTCTTAAAGCACGTCGACG 59.017 55.000 34.58 34.58 46.33 5.12
1313 1348 4.082125 AGTAGCAGCTAAAACAAGGCAAT 58.918 39.130 2.87 0.00 0.00 3.56
1314 1349 3.486383 AGTAGCAGCTAAAACAAGGCAA 58.514 40.909 2.87 0.00 0.00 4.52
1315 1350 3.140325 AGTAGCAGCTAAAACAAGGCA 57.860 42.857 2.87 0.00 0.00 4.75
1316 1351 4.505313 AAAGTAGCAGCTAAAACAAGGC 57.495 40.909 2.87 0.00 0.00 4.35
1317 1352 6.803154 ACTAAAGTAGCAGCTAAAACAAGG 57.197 37.500 2.87 0.00 0.00 3.61
1318 1353 9.760660 CATAACTAAAGTAGCAGCTAAAACAAG 57.239 33.333 2.87 1.47 0.00 3.16
1319 1354 9.496873 TCATAACTAAAGTAGCAGCTAAAACAA 57.503 29.630 2.87 0.00 0.00 2.83
1320 1355 9.151471 CTCATAACTAAAGTAGCAGCTAAAACA 57.849 33.333 2.87 0.00 0.00 2.83
1321 1356 8.604890 CCTCATAACTAAAGTAGCAGCTAAAAC 58.395 37.037 2.87 0.00 0.00 2.43
1322 1357 8.537016 TCCTCATAACTAAAGTAGCAGCTAAAA 58.463 33.333 2.87 0.00 0.00 1.52
1323 1358 8.074613 TCCTCATAACTAAAGTAGCAGCTAAA 57.925 34.615 2.87 0.00 0.00 1.85
1324 1359 7.655521 TCCTCATAACTAAAGTAGCAGCTAA 57.344 36.000 2.87 0.00 0.00 3.09
1325 1360 7.505923 TGATCCTCATAACTAAAGTAGCAGCTA 59.494 37.037 0.00 0.00 0.00 3.32
1326 1361 6.325028 TGATCCTCATAACTAAAGTAGCAGCT 59.675 38.462 0.00 0.00 0.00 4.24
1367 1410 7.989741 CAGATCTTATTAATATAGGCCCCACAG 59.010 40.741 0.00 0.00 0.00 3.66
1382 1425 9.784531 GATTTCACAAGGATCCAGATCTTATTA 57.215 33.333 15.82 0.00 37.92 0.98
1383 1426 7.723172 GGATTTCACAAGGATCCAGATCTTATT 59.277 37.037 15.82 0.00 39.30 1.40
1458 1501 2.159099 TGCCTTTACCTGCTCATACTCG 60.159 50.000 0.00 0.00 0.00 4.18
1532 1575 6.540438 TCTCCCAACGTTAGTAATGAATCT 57.460 37.500 9.13 0.00 0.00 2.40
1534 1577 7.989416 TTTTCTCCCAACGTTAGTAATGAAT 57.011 32.000 9.13 0.00 0.00 2.57
1580 1691 3.117512 CCCATTGTACAAGGCCTTATCCT 60.118 47.826 20.00 3.48 38.31 3.24
1600 1711 1.838077 ACCTGTACATAAGCAGTCCCC 59.162 52.381 0.00 0.00 0.00 4.81
1622 1733 4.391523 GCAAGCAAACTCTCTCTCCTTAAG 59.608 45.833 0.00 0.00 0.00 1.85
1658 1769 5.311265 CCTGTATGAGGCACATGTATCAAT 58.689 41.667 7.73 0.00 39.77 2.57
1659 1770 4.707105 CCTGTATGAGGCACATGTATCAA 58.293 43.478 7.73 0.00 39.77 2.57
1660 1771 4.341366 CCTGTATGAGGCACATGTATCA 57.659 45.455 7.73 3.94 39.77 2.15
1679 1801 2.482494 ACTAATCCAGCCTAAGCACCT 58.518 47.619 0.00 0.00 43.56 4.00
1680 1802 3.134081 TGTACTAATCCAGCCTAAGCACC 59.866 47.826 0.00 0.00 43.56 5.01
1740 1865 0.036952 CACCGATGCTCCAGTCTTGT 60.037 55.000 0.00 0.00 0.00 3.16
1741 1866 2.759783 CACCGATGCTCCAGTCTTG 58.240 57.895 0.00 0.00 0.00 3.02
1799 1924 2.113986 GGTGCTTGACCAGGTGCT 59.886 61.111 0.00 0.00 45.34 4.40
1806 1931 3.050275 GCTCGTGGGTGCTTGACC 61.050 66.667 0.00 0.00 45.28 4.02
1807 1932 1.444119 TTTGCTCGTGGGTGCTTGAC 61.444 55.000 0.00 0.00 33.89 3.18
1808 1933 0.749818 TTTTGCTCGTGGGTGCTTGA 60.750 50.000 0.00 0.00 33.89 3.02
1809 1934 0.102120 TTTTTGCTCGTGGGTGCTTG 59.898 50.000 0.00 0.00 33.89 4.01
1810 1935 2.499214 TTTTTGCTCGTGGGTGCTT 58.501 47.368 0.00 0.00 33.89 3.91
1811 1936 4.251246 TTTTTGCTCGTGGGTGCT 57.749 50.000 0.00 0.00 33.89 4.40
1843 1968 0.325933 CCTCCACAGGTGCATCAGAA 59.674 55.000 0.00 0.00 34.60 3.02
1844 1969 1.985614 CCTCCACAGGTGCATCAGA 59.014 57.895 0.00 0.00 34.60 3.27
1849 1975 4.269523 GGTGCCTCCACAGGTGCA 62.270 66.667 0.00 0.00 43.88 4.57
1878 2004 1.506907 AAGGGGAGTTGGTTAGGCCC 61.507 60.000 0.00 0.00 38.08 5.80
1935 2062 1.092921 TGGCCGCGACAATTACATCC 61.093 55.000 8.23 0.00 0.00 3.51
1964 2141 4.100189 GGCCATAGTACACTCAGAATGTCT 59.900 45.833 0.00 0.00 37.40 3.41
1980 2157 1.476471 CCTTCTCCAAGCTGGCCATAG 60.476 57.143 5.51 0.00 37.47 2.23
1997 4791 4.699522 GTTCGCTCCCGCACCCTT 62.700 66.667 0.00 0.00 35.30 3.95
2027 4821 0.469331 CAGCATTGGATCCCCTGCAT 60.469 55.000 27.88 15.60 34.82 3.96
2110 4913 6.019237 CGAGAAGTGATCACAATAACCATCAG 60.019 42.308 27.02 3.45 0.00 2.90
2188 4993 6.777256 CGTTTGCTTAAAATCGGTTAAAAACG 59.223 34.615 14.75 14.75 38.93 3.60


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

AutoCloner maintained by Alex Coulton.