Multiple sequence alignment - TraesCS5A01G046500

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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 TraesCS5A01G046500 chr5A 100.000 2348 0 0 1 2348 41476200 41473853 0.000000e+00 4337.0
1 TraesCS5A01G046500 chr5A 90.698 43 4 0 1468 1510 41496845 41496803 9.060000e-05 58.4
2 TraesCS5A01G046500 chr5D 89.459 1404 91 17 464 1844 52394110 52392741 0.000000e+00 1720.0
3 TraesCS5A01G046500 chr5D 91.943 211 13 2 2135 2345 52375208 52375002 2.280000e-75 292.0
4 TraesCS5A01G046500 chr5D 79.365 441 71 11 4 427 90312119 90311682 2.280000e-75 292.0
5 TraesCS5A01G046500 chr5D 91.971 137 7 2 1967 2103 52375268 52375400 3.080000e-44 189.0
6 TraesCS5A01G046500 chr5D 90.698 43 4 0 1468 1510 52399400 52399358 9.060000e-05 58.4
7 TraesCS5A01G046500 chr5B 86.446 996 105 16 58 1052 55544627 55543661 0.000000e+00 1064.0
8 TraesCS5A01G046500 chr5B 88.707 549 38 5 1048 1573 55538449 55537902 0.000000e+00 649.0
9 TraesCS5A01G046500 chr5B 92.358 458 17 5 1893 2348 55534673 55534232 9.150000e-179 636.0
10 TraesCS5A01G046500 chr5B 100.000 48 0 0 1838 1885 55534709 55534662 3.210000e-14 89.8
11 TraesCS5A01G046500 chr5B 90.698 43 4 0 1468 1510 55549328 55549286 9.060000e-05 58.4
12 TraesCS5A01G046500 chr1D 80.471 425 72 7 58 474 79756903 79756482 4.870000e-82 315.0
13 TraesCS5A01G046500 chr1D 81.299 385 69 3 59 441 416091579 416091962 2.270000e-80 309.0
14 TraesCS5A01G046500 chr3A 80.769 390 70 5 59 443 528524184 528524573 1.360000e-77 300.0
15 TraesCS5A01G046500 chr3D 80.759 369 70 1 60 427 405814623 405814991 1.060000e-73 287.0
16 TraesCS5A01G046500 chr3D 80.270 370 70 3 55 423 19293400 19293767 2.300000e-70 276.0
17 TraesCS5A01G046500 chr4D 80.802 349 64 3 59 405 3331670 3331323 1.070000e-68 270.0
18 TraesCS5A01G046500 chr1B 77.632 456 82 9 4 443 130665605 130665154 2.310000e-65 259.0
19 TraesCS5A01G046500 chr7D 83.871 62 9 1 597 657 536458399 536458460 9.060000e-05 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G046500 chr5A 41473853 41476200 2347 True 4337.000000 4337 100.000000 1 2348 1 chr5A.!!$R1 2347
1 TraesCS5A01G046500 chr5D 52392741 52394110 1369 True 1720.000000 1720 89.459000 464 1844 1 chr5D.!!$R2 1380
2 TraesCS5A01G046500 chr5B 55543661 55544627 966 True 1064.000000 1064 86.446000 58 1052 1 chr5B.!!$R1 994
3 TraesCS5A01G046500 chr5B 55534232 55538449 4217 True 458.266667 649 93.688333 1048 2348 3 chr5B.!!$R3 1300

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
73 74 0.032515 TCATTCCGCTACCTCCAGGA 60.033 55.0 0.0 0.0 38.94 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 1941 1.282157 AGGGGGTGAAGTGCTAATCAC 59.718 52.381 7.52 7.52 45.98 3.06 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
32 33 2.737830 GCCCTAGGCGTCATCTCC 59.262 66.667 2.05 0.00 39.62 3.71
33 34 1.834822 GCCCTAGGCGTCATCTCCT 60.835 63.158 2.05 0.00 39.62 3.69
34 35 1.403687 GCCCTAGGCGTCATCTCCTT 61.404 60.000 2.05 0.00 39.62 3.36
35 36 0.390860 CCCTAGGCGTCATCTCCTTG 59.609 60.000 2.05 0.00 34.02 3.61
36 37 1.115467 CCTAGGCGTCATCTCCTTGT 58.885 55.000 0.00 0.00 34.02 3.16
37 38 1.482593 CCTAGGCGTCATCTCCTTGTT 59.517 52.381 0.00 0.00 34.02 2.83
38 39 2.544685 CTAGGCGTCATCTCCTTGTTG 58.455 52.381 0.00 0.00 34.02 3.33
39 40 0.976641 AGGCGTCATCTCCTTGTTGA 59.023 50.000 0.00 0.00 0.00 3.18
40 41 1.347707 AGGCGTCATCTCCTTGTTGAA 59.652 47.619 0.00 0.00 0.00 2.69
41 42 1.734465 GGCGTCATCTCCTTGTTGAAG 59.266 52.381 0.00 0.00 0.00 3.02
53 54 4.871993 CTTGTTGAAGGAATCATCGAGG 57.128 45.455 0.00 0.00 38.03 4.63
54 55 3.981071 TGTTGAAGGAATCATCGAGGT 57.019 42.857 0.00 0.00 38.03 3.85
55 56 3.861840 TGTTGAAGGAATCATCGAGGTC 58.138 45.455 0.00 0.00 38.03 3.85
56 57 3.260632 TGTTGAAGGAATCATCGAGGTCA 59.739 43.478 0.00 0.00 38.03 4.02
57 58 4.080919 TGTTGAAGGAATCATCGAGGTCAT 60.081 41.667 0.00 0.00 38.03 3.06
58 59 4.760530 TGAAGGAATCATCGAGGTCATT 57.239 40.909 0.00 0.00 31.50 2.57
59 60 4.697514 TGAAGGAATCATCGAGGTCATTC 58.302 43.478 7.78 7.78 31.50 2.67
60 61 3.760580 AGGAATCATCGAGGTCATTCC 57.239 47.619 18.03 18.03 43.26 3.01
61 62 2.036475 AGGAATCATCGAGGTCATTCCG 59.964 50.000 19.02 0.00 46.20 4.30
62 63 1.795286 GAATCATCGAGGTCATTCCGC 59.205 52.381 0.00 0.00 41.99 5.54
73 74 0.032515 TCATTCCGCTACCTCCAGGA 60.033 55.000 0.00 0.00 38.94 3.86
93 94 3.254892 GAGAAACCCTTGATCAGTCGAC 58.745 50.000 7.70 7.70 0.00 4.20
102 103 1.338020 TGATCAGTCGACCGGATGATG 59.662 52.381 21.07 8.44 32.68 3.07
103 104 1.609072 GATCAGTCGACCGGATGATGA 59.391 52.381 21.07 13.14 32.68 2.92
108 109 1.115326 TCGACCGGATGATGATGGCT 61.115 55.000 9.46 0.00 0.00 4.75
111 112 0.683973 ACCGGATGATGATGGCTCTC 59.316 55.000 9.46 0.00 0.00 3.20
116 117 3.056322 CGGATGATGATGGCTCTCATGTA 60.056 47.826 7.68 0.00 36.01 2.29
158 159 3.372206 GTCATTCTTGGAGGTGTTCATCG 59.628 47.826 0.00 0.00 0.00 3.84
162 163 0.036388 TTGGAGGTGTTCATCGGCTC 60.036 55.000 0.00 0.00 0.00 4.70
177 178 3.007973 GCTCGAGGGACCAGTGGAC 62.008 68.421 18.40 10.15 0.00 4.02
186 187 0.106149 GACCAGTGGACGGTTTCAGT 59.894 55.000 18.40 0.00 36.69 3.41
220 221 1.802300 GCATCTGACGCATCGACGAC 61.802 60.000 0.00 0.00 36.70 4.34
239 240 2.360726 TGGAGTCTCAGCGGCGTA 60.361 61.111 9.37 0.00 0.00 4.42
260 261 1.227853 ACAACAGGGTCTTGGCGAC 60.228 57.895 0.00 0.00 42.07 5.19
262 263 2.504274 AACAGGGTCTTGGCGACGA 61.504 57.895 0.00 0.00 43.79 4.20
266 267 2.750888 GGGTCTTGGCGACGAATGC 61.751 63.158 0.00 0.00 43.79 3.56
283 284 4.661649 CGAATGCGTGATAATAGACTTGCG 60.662 45.833 0.00 0.00 0.00 4.85
298 299 4.509737 GCGTAGGGAGGTGGCGTC 62.510 72.222 0.00 0.00 0.00 5.19
301 302 2.283388 TAGGGAGGTGGCGTCGTT 60.283 61.111 0.00 0.00 0.00 3.85
302 303 1.001020 TAGGGAGGTGGCGTCGTTA 60.001 57.895 0.00 0.00 0.00 3.18
304 305 2.508663 GGAGGTGGCGTCGTTAGC 60.509 66.667 0.00 0.00 0.00 3.09
375 377 1.111277 TTCTGAAGATGGATCGGCGA 58.889 50.000 13.87 13.87 0.00 5.54
386 388 0.462047 GATCGGCGAAAGATGGTGGT 60.462 55.000 15.93 0.00 0.00 4.16
406 408 4.079850 CAGCCTCTGGAGCGTGCT 62.080 66.667 0.00 0.00 34.64 4.40
407 409 3.317571 AGCCTCTGGAGCGTGCTT 61.318 61.111 0.00 0.00 34.64 3.91
419 421 2.749839 GTGCTTATGCGGTGCCCA 60.750 61.111 0.00 0.00 43.34 5.36
424 426 1.078497 TTATGCGGTGCCCACTGAG 60.078 57.895 11.25 0.00 40.06 3.35
433 435 2.667418 CCCACTGAGAGCCCACTG 59.333 66.667 0.00 0.00 0.00 3.66
437 439 1.157276 ACTGAGAGCCCACTGGACT 59.843 57.895 0.00 0.00 0.00 3.85
438 440 1.190833 ACTGAGAGCCCACTGGACTG 61.191 60.000 0.00 0.00 0.00 3.51
439 441 1.897225 CTGAGAGCCCACTGGACTGG 61.897 65.000 0.00 0.00 0.00 4.00
441 443 1.462238 AGAGCCCACTGGACTGGTT 60.462 57.895 0.00 0.00 0.00 3.67
442 444 1.062488 AGAGCCCACTGGACTGGTTT 61.062 55.000 0.00 0.00 0.00 3.27
445 447 1.282157 AGCCCACTGGACTGGTTTATC 59.718 52.381 0.00 0.00 0.00 1.75
447 449 2.711542 CCCACTGGACTGGTTTATCAC 58.288 52.381 0.00 0.00 0.00 3.06
449 451 2.618045 CCACTGGACTGGTTTATCACCC 60.618 54.545 0.00 0.00 46.68 4.61
451 453 0.035820 TGGACTGGTTTATCACCCGC 60.036 55.000 0.00 0.00 46.68 6.13
452 454 0.252197 GGACTGGTTTATCACCCGCT 59.748 55.000 0.00 0.00 46.68 5.52
453 455 1.369625 GACTGGTTTATCACCCGCTG 58.630 55.000 0.00 0.00 46.68 5.18
454 456 0.690762 ACTGGTTTATCACCCGCTGT 59.309 50.000 0.00 0.00 46.68 4.40
455 457 1.073284 ACTGGTTTATCACCCGCTGTT 59.927 47.619 0.00 0.00 46.68 3.16
456 458 1.468520 CTGGTTTATCACCCGCTGTTG 59.531 52.381 0.00 0.00 46.68 3.33
457 459 0.808755 GGTTTATCACCCGCTGTTGG 59.191 55.000 0.00 0.00 40.19 3.77
475 477 0.618458 GGGCAGATTGGTGTGAGGTA 59.382 55.000 0.00 0.00 0.00 3.08
477 479 2.292267 GGCAGATTGGTGTGAGGTATG 58.708 52.381 0.00 0.00 0.00 2.39
504 506 1.378911 GCCCTGATCATGTGCACCA 60.379 57.895 15.69 3.27 0.00 4.17
514 516 1.471287 CATGTGCACCACCTTCATCAG 59.529 52.381 15.69 0.00 32.73 2.90
533 535 0.100146 GGTTGGTAGGAGTAGCGACG 59.900 60.000 0.00 0.00 40.63 5.12
534 536 0.100146 GTTGGTAGGAGTAGCGACGG 59.900 60.000 0.00 0.00 32.60 4.79
546 548 2.741985 CGACGGATGTTGCCAGCA 60.742 61.111 0.00 0.00 0.00 4.41
547 549 2.743752 CGACGGATGTTGCCAGCAG 61.744 63.158 0.00 0.00 0.00 4.24
548 550 1.672356 GACGGATGTTGCCAGCAGT 60.672 57.895 0.00 0.00 38.11 4.40
549 551 1.915614 GACGGATGTTGCCAGCAGTG 61.916 60.000 0.00 0.00 35.53 3.66
550 552 1.968017 CGGATGTTGCCAGCAGTGT 60.968 57.895 0.00 0.00 0.00 3.55
551 553 1.518056 CGGATGTTGCCAGCAGTGTT 61.518 55.000 0.00 0.00 0.00 3.32
552 554 0.038892 GGATGTTGCCAGCAGTGTTG 60.039 55.000 0.00 0.00 0.00 3.33
553 555 0.670162 GATGTTGCCAGCAGTGTTGT 59.330 50.000 6.22 0.00 0.00 3.32
579 584 4.327680 GAAGGTGGCTTCAGACTAATTGT 58.672 43.478 0.00 0.00 33.80 2.71
605 610 7.653647 TGTATTACTTTGTAAGGCTTTGTTGG 58.346 34.615 4.45 0.00 0.00 3.77
638 645 0.241749 AATGGTTGTGTGCATCGCTG 59.758 50.000 0.00 0.00 0.00 5.18
653 660 4.790962 CTGCATGCAGAGGCCGGT 62.791 66.667 38.90 0.00 46.30 5.28
663 670 0.620700 AGAGGCCGGTGGTTATCCTT 60.621 55.000 1.90 0.00 34.23 3.36
669 676 2.823747 GCCGGTGGTTATCCTTCTTTTT 59.176 45.455 1.90 0.00 34.23 1.94
670 677 3.366985 GCCGGTGGTTATCCTTCTTTTTG 60.367 47.826 1.90 0.00 34.23 2.44
671 678 3.192633 CCGGTGGTTATCCTTCTTTTTGG 59.807 47.826 0.00 0.00 34.23 3.28
672 679 4.076394 CGGTGGTTATCCTTCTTTTTGGA 58.924 43.478 0.00 0.00 36.72 3.53
709 716 7.225734 GGTCAGCTCTATCTAGACCAAAAATTC 59.774 40.741 11.25 0.00 46.15 2.17
732 739 4.338964 CCAGCATCTGCCAATGTATACAAA 59.661 41.667 10.14 0.00 43.38 2.83
788 795 8.267183 TCATCCATAAAAGTCTCAAGATTGCTA 58.733 33.333 0.00 0.00 0.00 3.49
812 819 3.441496 ACTTTGAAGGTGCAACACATG 57.559 42.857 3.64 3.09 39.98 3.21
816 823 5.301551 ACTTTGAAGGTGCAACACATGATTA 59.698 36.000 3.64 0.00 39.98 1.75
828 835 7.338957 TGCAACACATGATTACATTATCCAGAA 59.661 33.333 0.00 0.00 34.15 3.02
945 952 6.067217 AGGCACTAACCTATTTGAATCTGT 57.933 37.500 0.00 0.00 38.67 3.41
960 967 0.255318 TCTGTACCGTCTCCTCTCCC 59.745 60.000 0.00 0.00 0.00 4.30
982 989 3.200825 CCTAGCTTCATTTCTCCCTTGGA 59.799 47.826 0.00 0.00 0.00 3.53
1089 1096 2.239654 TGGTGAGCCTTCCCTGAAATAG 59.760 50.000 0.00 0.00 35.27 1.73
1116 1123 7.932120 ATCTGAAGAATATAACGGTTTCTCG 57.068 36.000 0.00 0.00 0.00 4.04
1162 1169 3.005684 TGCTAAGCAAAATGGTGTCCTTG 59.994 43.478 0.00 0.00 34.76 3.61
1201 1208 1.755179 AGCAGGCGATTATTGCAAGT 58.245 45.000 4.94 0.00 40.22 3.16
1202 1209 1.402968 AGCAGGCGATTATTGCAAGTG 59.597 47.619 4.94 2.07 40.22 3.16
1206 1213 2.423538 AGGCGATTATTGCAAGTGGTTC 59.576 45.455 4.94 0.00 0.00 3.62
1233 1240 6.281405 CAAGACCTACACTACTTTTCACTGT 58.719 40.000 0.00 0.00 0.00 3.55
1242 1249 1.400494 ACTTTTCACTGTGCGGACAAC 59.600 47.619 11.97 0.00 0.00 3.32
1266 1273 4.395583 GCTGAGCACTGCCGCAAC 62.396 66.667 0.00 0.00 35.44 4.17
1368 1375 7.283807 TGCTGATGATGCTTGTGAAGTAATAAT 59.716 33.333 0.00 0.00 0.00 1.28
1396 1403 8.145316 TGTTGTGTGTTTATAAGGAAGTGTAC 57.855 34.615 0.00 0.00 0.00 2.90
1427 1435 4.112716 TCTATGTCGTATTTGCCGTGAA 57.887 40.909 0.00 0.00 0.00 3.18
1542 1571 4.383989 GGTCCTCTCTGCTGATGAAATCTT 60.384 45.833 0.00 0.00 45.81 2.40
1545 1574 6.820656 GTCCTCTCTGCTGATGAAATCTTTTA 59.179 38.462 0.00 0.00 45.81 1.52
1551 1580 7.541162 TCTGCTGATGAAATCTTTTATTGGTG 58.459 34.615 0.00 0.00 45.81 4.17
1584 1613 3.672808 AGACTGATGCCTTTGTCTCTTG 58.327 45.455 0.00 0.00 35.13 3.02
1586 1615 4.284490 AGACTGATGCCTTTGTCTCTTGTA 59.716 41.667 0.00 0.00 35.13 2.41
1598 1627 9.177608 CCTTTGTCTCTTGTATTATTGGAATCA 57.822 33.333 0.00 0.00 0.00 2.57
1729 1758 4.810191 AAGACCAATCTCCAGTAGACAC 57.190 45.455 0.00 0.00 36.93 3.67
1789 1913 8.371571 TCTATTATGCAGTGAGATCATACCAT 57.628 34.615 0.00 0.00 0.00 3.55
1791 1915 9.747293 CTATTATGCAGTGAGATCATACCATAG 57.253 37.037 0.00 0.00 0.00 2.23
1795 1919 5.221322 TGCAGTGAGATCATACCATAGTGTC 60.221 44.000 0.00 0.00 0.00 3.67
1806 1930 3.521727 ACCATAGTGTCTTCCTTCACCT 58.478 45.455 0.00 0.00 35.45 4.00
1809 1933 2.103153 AGTGTCTTCCTTCACCTGGA 57.897 50.000 0.00 0.00 35.45 3.86
1812 1936 2.104963 GTGTCTTCCTTCACCTGGAACT 59.895 50.000 0.00 0.00 38.53 3.01
1814 1938 2.104963 GTCTTCCTTCACCTGGAACTGT 59.895 50.000 0.00 0.00 38.53 3.55
1815 1939 2.777692 TCTTCCTTCACCTGGAACTGTT 59.222 45.455 0.00 0.00 38.53 3.16
1816 1940 2.638480 TCCTTCACCTGGAACTGTTG 57.362 50.000 0.00 0.00 0.00 3.33
1817 1941 1.142870 TCCTTCACCTGGAACTGTTGG 59.857 52.381 0.00 0.00 0.00 3.77
1818 1942 1.133792 CCTTCACCTGGAACTGTTGGT 60.134 52.381 0.00 0.00 0.00 3.67
1832 1956 3.815401 ACTGTTGGTGATTAGCACTTCAC 59.185 43.478 0.00 4.81 46.86 3.18
1879 4914 6.447084 AGGTGATTAAGAGGGACCATCTTAAA 59.553 38.462 33.42 21.36 46.69 1.52
1880 4915 7.129504 AGGTGATTAAGAGGGACCATCTTAAAT 59.870 37.037 33.42 24.38 46.69 1.40
1881 4916 7.780271 GGTGATTAAGAGGGACCATCTTAAATT 59.220 37.037 33.42 23.26 46.69 1.82
1882 4917 8.841300 GTGATTAAGAGGGACCATCTTAAATTC 58.159 37.037 33.42 27.98 46.69 2.17
1883 4918 8.781951 TGATTAAGAGGGACCATCTTAAATTCT 58.218 33.333 33.42 22.40 46.69 2.40
1884 4919 9.278978 GATTAAGAGGGACCATCTTAAATTCTC 57.721 37.037 33.42 25.11 46.69 2.87
1885 4920 5.283457 AGAGGGACCATCTTAAATTCTCG 57.717 43.478 1.91 0.00 0.00 4.04
1886 4921 3.809905 AGGGACCATCTTAAATTCTCGC 58.190 45.455 0.00 0.00 0.00 5.03
1887 4922 3.456277 AGGGACCATCTTAAATTCTCGCT 59.544 43.478 0.00 0.00 0.00 4.93
1888 4923 4.080299 AGGGACCATCTTAAATTCTCGCTT 60.080 41.667 0.00 0.00 0.00 4.68
1889 4924 5.130477 AGGGACCATCTTAAATTCTCGCTTA 59.870 40.000 0.00 0.00 0.00 3.09
1890 4925 5.998363 GGGACCATCTTAAATTCTCGCTTAT 59.002 40.000 0.00 0.00 0.00 1.73
1891 4926 6.486993 GGGACCATCTTAAATTCTCGCTTATT 59.513 38.462 0.00 0.00 0.00 1.40
1892 4927 7.013369 GGGACCATCTTAAATTCTCGCTTATTT 59.987 37.037 0.00 0.00 0.00 1.40
1893 4928 8.070769 GGACCATCTTAAATTCTCGCTTATTTC 58.929 37.037 0.00 0.00 0.00 2.17
1894 4929 8.738645 ACCATCTTAAATTCTCGCTTATTTCT 57.261 30.769 0.00 0.00 0.00 2.52
1895 4930 9.178758 ACCATCTTAAATTCTCGCTTATTTCTT 57.821 29.630 0.00 0.00 0.00 2.52
1965 5000 6.493189 AGGGACCATCTTAAAATCTCTCTC 57.507 41.667 0.00 0.00 0.00 3.20
2026 5063 1.906574 AGCTGTCCCCGTATCTTTTCA 59.093 47.619 0.00 0.00 0.00 2.69
2057 5094 8.428852 GTGGGCTTTAAATGGTCCATATATTTT 58.571 33.333 4.33 0.00 39.51 1.82
2058 5095 8.646900 TGGGCTTTAAATGGTCCATATATTTTC 58.353 33.333 4.33 0.00 31.74 2.29
2059 5096 8.646900 GGGCTTTAAATGGTCCATATATTTTCA 58.353 33.333 4.33 0.00 0.00 2.69
2060 5097 9.696917 GGCTTTAAATGGTCCATATATTTTCAG 57.303 33.333 4.33 0.00 0.00 3.02
2111 5148 4.150451 GCACAGCACAACATTTTGGATTAC 59.850 41.667 0.00 0.00 37.00 1.89
2112 5149 4.685628 CACAGCACAACATTTTGGATTACC 59.314 41.667 0.00 0.00 37.00 2.85
2113 5150 4.343526 ACAGCACAACATTTTGGATTACCA 59.656 37.500 0.00 0.00 45.34 3.25
2170 5207 3.326006 CCATGGCTGGCTATAAGAAGAGA 59.674 47.826 0.00 0.00 35.23 3.10
2173 5210 2.399448 GCTGGCTATAAGAAGAGACGC 58.601 52.381 0.00 0.00 0.00 5.19
2176 5213 2.764010 TGGCTATAAGAAGAGACGCCAA 59.236 45.455 0.00 0.00 42.48 4.52
2182 5219 0.976641 AGAAGAGACGCCAATCACCA 59.023 50.000 0.00 0.00 0.00 4.17
2227 5264 1.282653 CCCTTCCTTCCTTCCCTCCC 61.283 65.000 0.00 0.00 0.00 4.30
2247 5284 2.245806 CCCCCTTCATTCCTTCATTCCT 59.754 50.000 0.00 0.00 0.00 3.36
2265 5302 1.442526 CTTGGAGACATGGCGATGGC 61.443 60.000 13.62 10.35 42.32 4.40
2317 5354 1.093496 TGCTTCTGCTGATCATGCCG 61.093 55.000 12.62 7.98 40.48 5.69
2343 5380 0.038166 TTGCTCCCTGGTAAGCCTTG 59.962 55.000 13.78 0.00 37.73 3.61
2345 5382 1.077429 CTCCCTGGTAAGCCTTGCC 60.077 63.158 4.40 4.40 35.79 4.52
2346 5383 1.541368 TCCCTGGTAAGCCTTGCCT 60.541 57.895 12.97 0.00 36.27 4.75
2347 5384 1.379044 CCCTGGTAAGCCTTGCCTG 60.379 63.158 12.97 11.82 36.27 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.403687 AAGGAGATGACGCCTAGGGC 61.404 60.000 11.72 1.76 45.18 5.19
16 17 0.390860 CAAGGAGATGACGCCTAGGG 59.609 60.000 11.72 3.13 45.18 3.53
17 18 1.115467 ACAAGGAGATGACGCCTAGG 58.885 55.000 3.67 3.67 45.18 3.02
18 19 2.166459 TCAACAAGGAGATGACGCCTAG 59.834 50.000 0.00 0.00 45.18 3.02
19 20 2.176045 TCAACAAGGAGATGACGCCTA 58.824 47.619 0.00 0.00 45.18 3.93
21 22 1.734465 CTTCAACAAGGAGATGACGCC 59.266 52.381 0.00 0.00 36.22 5.68
32 33 4.256920 ACCTCGATGATTCCTTCAACAAG 58.743 43.478 0.00 0.00 38.03 3.16
33 34 4.253685 GACCTCGATGATTCCTTCAACAA 58.746 43.478 0.00 0.00 38.03 2.83
34 35 3.260632 TGACCTCGATGATTCCTTCAACA 59.739 43.478 0.00 0.00 38.03 3.33
35 36 3.861840 TGACCTCGATGATTCCTTCAAC 58.138 45.455 0.00 0.00 38.03 3.18
36 37 4.760530 ATGACCTCGATGATTCCTTCAA 57.239 40.909 0.00 0.00 38.03 2.69
37 38 4.443457 GGAATGACCTCGATGATTCCTTCA 60.443 45.833 9.28 0.00 40.46 3.02
38 39 4.061596 GGAATGACCTCGATGATTCCTTC 58.938 47.826 9.28 0.79 40.46 3.46
39 40 3.493350 CGGAATGACCTCGATGATTCCTT 60.493 47.826 13.23 0.00 41.16 3.36
40 41 2.036475 CGGAATGACCTCGATGATTCCT 59.964 50.000 13.23 0.00 41.16 3.36
41 42 2.408050 CGGAATGACCTCGATGATTCC 58.592 52.381 7.06 7.06 40.30 3.01
42 43 1.795286 GCGGAATGACCTCGATGATTC 59.205 52.381 0.00 0.00 36.31 2.52
43 44 1.414181 AGCGGAATGACCTCGATGATT 59.586 47.619 0.00 0.00 36.31 2.57
44 45 1.043816 AGCGGAATGACCTCGATGAT 58.956 50.000 0.00 0.00 36.31 2.45
45 46 1.337071 GTAGCGGAATGACCTCGATGA 59.663 52.381 0.00 0.00 36.31 2.92
46 47 1.603172 GGTAGCGGAATGACCTCGATG 60.603 57.143 0.00 0.00 36.31 3.84
47 48 0.674534 GGTAGCGGAATGACCTCGAT 59.325 55.000 0.00 0.00 36.31 3.59
48 49 0.395311 AGGTAGCGGAATGACCTCGA 60.395 55.000 0.00 0.00 39.46 4.04
49 50 2.116383 AGGTAGCGGAATGACCTCG 58.884 57.895 0.00 0.00 39.46 4.63
51 52 0.325296 TGGAGGTAGCGGAATGACCT 60.325 55.000 0.00 0.00 46.47 3.85
52 53 0.105039 CTGGAGGTAGCGGAATGACC 59.895 60.000 0.00 0.00 0.00 4.02
53 54 0.105039 CCTGGAGGTAGCGGAATGAC 59.895 60.000 0.00 0.00 0.00 3.06
54 55 0.032515 TCCTGGAGGTAGCGGAATGA 60.033 55.000 0.00 0.00 36.34 2.57
55 56 0.390860 CTCCTGGAGGTAGCGGAATG 59.609 60.000 16.19 0.00 36.34 2.67
56 57 0.261991 TCTCCTGGAGGTAGCGGAAT 59.738 55.000 23.00 0.00 36.34 3.01
57 58 0.040646 TTCTCCTGGAGGTAGCGGAA 59.959 55.000 23.00 6.06 36.34 4.30
58 59 0.040646 TTTCTCCTGGAGGTAGCGGA 59.959 55.000 23.00 0.00 36.34 5.54
59 60 0.175989 GTTTCTCCTGGAGGTAGCGG 59.824 60.000 23.00 0.00 36.34 5.52
60 61 0.175989 GGTTTCTCCTGGAGGTAGCG 59.824 60.000 23.00 0.00 36.34 4.26
61 62 0.542333 GGGTTTCTCCTGGAGGTAGC 59.458 60.000 23.00 18.51 36.34 3.58
62 63 2.237392 CAAGGGTTTCTCCTGGAGGTAG 59.763 54.545 23.00 0.00 37.20 3.18
68 69 2.307098 ACTGATCAAGGGTTTCTCCTGG 59.693 50.000 0.00 0.00 37.20 4.45
73 74 2.028020 GGTCGACTGATCAAGGGTTTCT 60.028 50.000 16.46 0.00 0.00 2.52
93 94 0.683412 TGAGAGCCATCATCATCCGG 59.317 55.000 0.00 0.00 0.00 5.14
102 103 3.321497 GGAACGATACATGAGAGCCATC 58.679 50.000 0.00 0.00 31.94 3.51
103 104 2.037772 GGGAACGATACATGAGAGCCAT 59.962 50.000 0.00 0.00 35.44 4.40
134 135 1.464997 GAACACCTCCAAGAATGACGC 59.535 52.381 0.00 0.00 0.00 5.19
135 136 2.766313 TGAACACCTCCAAGAATGACG 58.234 47.619 0.00 0.00 0.00 4.35
136 137 3.372206 CGATGAACACCTCCAAGAATGAC 59.628 47.826 0.00 0.00 0.00 3.06
158 159 3.775654 CCACTGGTCCCTCGAGCC 61.776 72.222 6.99 3.51 35.55 4.70
162 163 3.760035 CCGTCCACTGGTCCCTCG 61.760 72.222 0.00 0.00 0.00 4.63
177 178 1.227823 TGCTCCACCACTGAAACCG 60.228 57.895 0.00 0.00 0.00 4.44
205 206 2.202311 ACGTCGTCGATGCGTCAG 60.202 61.111 14.35 0.00 40.62 3.51
209 210 2.944557 CTCCACGTCGTCGATGCG 60.945 66.667 14.35 16.34 40.62 4.73
231 232 2.738521 CTGTTGTGCTACGCCGCT 60.739 61.111 0.00 0.00 0.00 5.52
233 234 3.118454 CCCTGTTGTGCTACGCCG 61.118 66.667 0.00 0.00 0.00 6.46
237 238 1.523758 CCAAGACCCTGTTGTGCTAC 58.476 55.000 0.00 0.00 0.00 3.58
239 240 1.529244 GCCAAGACCCTGTTGTGCT 60.529 57.895 0.00 0.00 0.00 4.40
242 243 1.227853 GTCGCCAAGACCCTGTTGT 60.228 57.895 0.00 0.00 43.95 3.32
244 245 2.030562 CGTCGCCAAGACCCTGTT 59.969 61.111 0.00 0.00 46.92 3.16
245 246 1.827399 ATTCGTCGCCAAGACCCTGT 61.827 55.000 0.00 0.00 46.92 4.00
260 261 4.661649 CGCAAGTCTATTATCACGCATTCG 60.662 45.833 0.00 0.00 42.43 3.34
262 263 4.715520 CGCAAGTCTATTATCACGCATT 57.284 40.909 0.00 0.00 0.00 3.56
279 280 4.077184 CGCCACCTCCCTACGCAA 62.077 66.667 0.00 0.00 0.00 4.85
283 284 1.315257 TAACGACGCCACCTCCCTAC 61.315 60.000 0.00 0.00 0.00 3.18
325 326 1.888018 CATTGACCTTGCCAGGCTG 59.112 57.895 14.15 7.75 45.56 4.85
358 360 1.863454 CTTTCGCCGATCCATCTTCAG 59.137 52.381 0.00 0.00 0.00 3.02
375 377 1.607467 GGCTGCCACCACCATCTTT 60.607 57.895 15.17 0.00 0.00 2.52
419 421 1.157276 AGTCCAGTGGGCTCTCAGT 59.843 57.895 11.55 0.00 0.00 3.41
424 426 0.690762 TAAACCAGTCCAGTGGGCTC 59.309 55.000 15.09 2.45 42.54 4.70
427 429 2.711542 GTGATAAACCAGTCCAGTGGG 58.288 52.381 9.92 0.00 42.54 4.61
439 441 0.808755 CCCAACAGCGGGTGATAAAC 59.191 55.000 14.98 0.00 41.83 2.01
449 451 1.973281 ACCAATCTGCCCAACAGCG 60.973 57.895 0.00 0.00 46.76 5.18
452 454 0.184692 TCACACCAATCTGCCCAACA 59.815 50.000 0.00 0.00 0.00 3.33
453 455 0.883833 CTCACACCAATCTGCCCAAC 59.116 55.000 0.00 0.00 0.00 3.77
454 456 0.251297 CCTCACACCAATCTGCCCAA 60.251 55.000 0.00 0.00 0.00 4.12
455 457 1.379916 CCTCACACCAATCTGCCCA 59.620 57.895 0.00 0.00 0.00 5.36
456 458 0.618458 TACCTCACACCAATCTGCCC 59.382 55.000 0.00 0.00 0.00 5.36
457 459 2.292267 CATACCTCACACCAATCTGCC 58.708 52.381 0.00 0.00 0.00 4.85
458 460 2.292267 CCATACCTCACACCAATCTGC 58.708 52.381 0.00 0.00 0.00 4.26
459 461 2.923121 CCCATACCTCACACCAATCTG 58.077 52.381 0.00 0.00 0.00 2.90
460 462 1.212935 GCCCATACCTCACACCAATCT 59.787 52.381 0.00 0.00 0.00 2.40
461 463 1.064758 TGCCCATACCTCACACCAATC 60.065 52.381 0.00 0.00 0.00 2.67
462 464 0.998928 TGCCCATACCTCACACCAAT 59.001 50.000 0.00 0.00 0.00 3.16
488 490 0.034767 AGGTGGTGCACATGATCAGG 60.035 55.000 20.43 5.68 35.86 3.86
490 492 1.073603 TGAAGGTGGTGCACATGATCA 59.926 47.619 20.43 12.68 35.86 2.92
514 516 0.100146 CGTCGCTACTCCTACCAACC 59.900 60.000 0.00 0.00 0.00 3.77
542 544 1.233019 CCTTCCTGACAACACTGCTG 58.767 55.000 0.00 0.00 0.00 4.41
543 545 0.839946 ACCTTCCTGACAACACTGCT 59.160 50.000 0.00 0.00 0.00 4.24
544 546 0.947244 CACCTTCCTGACAACACTGC 59.053 55.000 0.00 0.00 0.00 4.40
545 547 1.597742 CCACCTTCCTGACAACACTG 58.402 55.000 0.00 0.00 0.00 3.66
546 548 0.179018 GCCACCTTCCTGACAACACT 60.179 55.000 0.00 0.00 0.00 3.55
547 549 0.179018 AGCCACCTTCCTGACAACAC 60.179 55.000 0.00 0.00 0.00 3.32
548 550 0.550914 AAGCCACCTTCCTGACAACA 59.449 50.000 0.00 0.00 0.00 3.33
549 551 1.239347 GAAGCCACCTTCCTGACAAC 58.761 55.000 0.00 0.00 41.30 3.32
550 552 0.843309 TGAAGCCACCTTCCTGACAA 59.157 50.000 1.43 0.00 45.53 3.18
551 553 0.397941 CTGAAGCCACCTTCCTGACA 59.602 55.000 1.43 0.00 45.53 3.58
552 554 0.687354 TCTGAAGCCACCTTCCTGAC 59.313 55.000 1.43 0.00 45.53 3.51
553 555 0.687354 GTCTGAAGCCACCTTCCTGA 59.313 55.000 1.43 0.00 45.53 3.86
579 584 8.138712 CCAACAAAGCCTTACAAAGTAATACAA 58.861 33.333 0.00 0.00 0.00 2.41
639 646 2.535485 TAACCACCGGCCTCTGCATG 62.535 60.000 0.00 0.00 40.13 4.06
709 716 3.479489 TGTATACATTGGCAGATGCTGG 58.521 45.455 0.08 0.00 41.70 4.85
732 739 1.153086 GGGATGATGCAGCTCGGTT 60.153 57.895 2.53 0.00 0.00 4.44
788 795 3.446873 TGTGTTGCACCTTCAAAGTTCAT 59.553 39.130 0.00 0.00 32.73 2.57
816 823 7.893124 AGATGCATTTCTTTCTGGATAATGT 57.107 32.000 0.00 0.00 0.00 2.71
945 952 1.138568 CTAGGGGAGAGGAGACGGTA 58.861 60.000 0.00 0.00 0.00 4.02
960 967 3.200825 TCCAAGGGAGAAATGAAGCTAGG 59.799 47.826 0.00 0.00 0.00 3.02
982 989 7.177878 ACCTCCATGTCTTCAAGAATAAACAT 58.822 34.615 0.00 0.00 0.00 2.71
1116 1123 6.583806 CAGCATCAAACAAAGAATAGAACACC 59.416 38.462 0.00 0.00 0.00 4.16
1162 1169 3.365767 GCTTCAGATCCTGCAGTCAAAAC 60.366 47.826 13.81 0.00 28.06 2.43
1201 1208 2.047061 AGTGTAGGTCTTGCTGAACCA 58.953 47.619 5.06 0.00 31.28 3.67
1202 1209 2.841442 AGTGTAGGTCTTGCTGAACC 57.159 50.000 0.00 0.00 31.28 3.62
1206 1213 5.177696 GTGAAAAGTAGTGTAGGTCTTGCTG 59.822 44.000 0.00 0.00 0.00 4.41
1368 1375 7.988599 ACACTTCCTTATAAACACACAACAGTA 59.011 33.333 0.00 0.00 0.00 2.74
1396 1403 6.901887 GCAAATACGACATAGAAGTTCACATG 59.098 38.462 5.50 10.27 0.00 3.21
1427 1435 8.484214 TCACCTTTATTATACTGATCTGCTCT 57.516 34.615 0.00 0.00 0.00 4.09
1542 1571 9.653287 CAGTCTCTACTTATTCACACCAATAAA 57.347 33.333 0.00 0.00 31.97 1.40
1545 1574 7.482169 TCAGTCTCTACTTATTCACACCAAT 57.518 36.000 0.00 0.00 31.97 3.16
1551 1580 6.155475 AGGCATCAGTCTCTACTTATTCAC 57.845 41.667 0.00 0.00 31.97 3.18
1584 1613 9.241317 CATGCTCTGTTTTGATTCCAATAATAC 57.759 33.333 0.00 0.00 31.46 1.89
1586 1615 6.759827 GCATGCTCTGTTTTGATTCCAATAAT 59.240 34.615 11.37 0.00 31.46 1.28
1598 1627 4.240096 GCATTTGTAGCATGCTCTGTTTT 58.760 39.130 26.57 0.00 43.26 2.43
1599 1628 3.256383 TGCATTTGTAGCATGCTCTGTTT 59.744 39.130 26.57 4.93 46.22 2.83
1625 1654 3.389002 TGTCACAGCAGCTATGTCCATAT 59.611 43.478 0.00 0.00 0.00 1.78
1761 1790 9.964303 GGTATGATCTCACTGCATAATAGATAG 57.036 37.037 0.00 0.00 0.00 2.08
1772 1896 5.010516 AGACACTATGGTATGATCTCACTGC 59.989 44.000 0.00 0.00 0.00 4.40
1785 1909 3.261897 CAGGTGAAGGAAGACACTATGGT 59.738 47.826 0.00 0.00 37.22 3.55
1789 1913 3.254093 TCCAGGTGAAGGAAGACACTA 57.746 47.619 0.00 0.00 37.22 2.74
1791 1915 2.104963 AGTTCCAGGTGAAGGAAGACAC 59.895 50.000 0.00 0.00 45.27 3.67
1795 1919 2.880890 CAACAGTTCCAGGTGAAGGAAG 59.119 50.000 0.00 0.00 45.27 3.46
1806 1930 3.146066 GTGCTAATCACCAACAGTTCCA 58.854 45.455 0.00 0.00 39.79 3.53
1809 1933 4.275936 GTGAAGTGCTAATCACCAACAGTT 59.724 41.667 5.39 0.00 46.81 3.16
1817 1941 1.282157 AGGGGGTGAAGTGCTAATCAC 59.718 52.381 7.52 7.52 45.98 3.06
1818 1942 1.668826 AGGGGGTGAAGTGCTAATCA 58.331 50.000 0.00 0.00 0.00 2.57
1832 1956 7.020009 ACCTTCTAAGAGAGAATATTAGGGGG 58.980 42.308 0.00 0.00 43.39 5.40
1880 4915 9.877178 AGAGAGAATTTAAGAAATAAGCGAGAA 57.123 29.630 0.00 0.00 0.00 2.87
1881 4916 9.877178 AAGAGAGAATTTAAGAAATAAGCGAGA 57.123 29.630 0.00 0.00 0.00 4.04
1923 4958 8.671409 TGGTCCCTTTTAATTACCTTCTAAGAA 58.329 33.333 0.00 0.00 0.00 2.52
1938 4973 8.836735 AGAGAGATTTTAAGATGGTCCCTTTTA 58.163 33.333 0.00 0.00 0.00 1.52
1941 4976 6.445139 TGAGAGAGATTTTAAGATGGTCCCTT 59.555 38.462 0.00 0.00 0.00 3.95
1965 5000 4.008330 ACACTCCTCATTTGAGCAGAATG 58.992 43.478 5.53 0.63 40.75 2.67
2026 5063 2.497273 GACCATTTAAAGCCCACATGCT 59.503 45.455 0.00 0.00 45.43 3.79
2057 5094 3.696051 GCAATCTGCTGGGAATTTACTGA 59.304 43.478 0.00 0.00 40.96 3.41
2058 5095 4.037858 GCAATCTGCTGGGAATTTACTG 57.962 45.455 0.00 0.00 40.96 2.74
2111 5148 0.889994 TGCATTTACCTGCTGCTTGG 59.110 50.000 0.00 5.96 42.75 3.61
2112 5149 2.480759 GGATGCATTTACCTGCTGCTTG 60.481 50.000 0.00 0.00 42.75 4.01
2113 5150 1.753073 GGATGCATTTACCTGCTGCTT 59.247 47.619 0.00 0.00 42.75 3.91
2118 5155 3.555966 ACCTTAGGATGCATTTACCTGC 58.444 45.455 14.23 0.00 42.62 4.85
2119 5156 5.041191 AGACCTTAGGATGCATTTACCTG 57.959 43.478 14.23 2.33 35.52 4.00
2120 5157 4.721776 TGAGACCTTAGGATGCATTTACCT 59.278 41.667 4.77 10.10 37.76 3.08
2121 5158 5.036117 TGAGACCTTAGGATGCATTTACC 57.964 43.478 4.77 0.00 0.00 2.85
2133 5170 2.038295 GCCATGGAGGATGAGACCTTAG 59.962 54.545 18.40 0.00 40.73 2.18
2170 5207 0.179004 TCCAAACTGGTGATTGGCGT 60.179 50.000 0.00 0.00 43.29 5.68
2173 5210 2.165030 GCAGATCCAAACTGGTGATTGG 59.835 50.000 0.00 0.00 44.46 3.16
2176 5213 1.742761 CGCAGATCCAAACTGGTGAT 58.257 50.000 0.00 0.00 39.03 3.06
2182 5219 0.326264 AGAAGGCGCAGATCCAAACT 59.674 50.000 10.83 0.00 0.00 2.66
2227 5264 3.677156 AGGAATGAAGGAATGAAGGGG 57.323 47.619 0.00 0.00 0.00 4.79
2247 5284 1.451927 GCCATCGCCATGTCTCCAA 60.452 57.895 0.00 0.00 0.00 3.53
2268 5305 3.818787 GCACCATGAGCTTGGGCG 61.819 66.667 9.27 1.18 44.37 6.13
2302 5339 1.227468 GAGCGGCATGATCAGCAGA 60.227 57.895 16.85 0.00 31.75 4.26
2317 5354 0.978146 TACCAGGGAGCAAGAGGAGC 60.978 60.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.