Multiple sequence alignment - TraesCS3B01G228700

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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 TraesCS3B01G228700 chr3B 100.000 4370 0 0 1 4370 331556369 331552000 0.000000e+00 8070.0
1 TraesCS3B01G228700 chr3B 99.419 516 3 0 3855 4370 349956234 349956749 0.000000e+00 937.0
2 TraesCS3B01G228700 chr3D 91.391 2846 125 53 1 2815 246325546 246328302 0.000000e+00 3788.0
3 TraesCS3B01G228700 chr3D 93.889 1080 27 18 2802 3855 246328324 246329390 0.000000e+00 1592.0
4 TraesCS3B01G228700 chr3A 92.620 1084 41 20 2798 3853 337881072 337880000 0.000000e+00 1522.0
5 TraesCS3B01G228700 chr3A 93.271 862 32 8 1957 2816 337881926 337881089 0.000000e+00 1247.0
6 TraesCS3B01G228700 chr3A 93.760 625 24 10 1276 1898 337882561 337881950 0.000000e+00 924.0
7 TraesCS3B01G228700 chr3A 91.134 688 20 9 633 1291 337883255 337882580 0.000000e+00 894.0
8 TraesCS3B01G228700 chr3A 89.400 500 45 3 3855 4346 20561715 20562214 1.330000e-174 623.0
9 TraesCS3B01G228700 chr3A 89.897 485 41 3 3855 4331 20568100 20567616 6.210000e-173 617.0
10 TraesCS3B01G228700 chr3A 86.667 375 18 10 219 575 337884110 337883750 1.910000e-103 387.0
11 TraesCS3B01G228700 chr3A 91.031 223 17 2 1 221 337884445 337884224 9.190000e-77 298.0
12 TraesCS3B01G228700 chr3A 95.000 40 2 0 612 651 337883308 337883269 3.650000e-06 63.9
13 TraesCS3B01G228700 chr4B 98.069 518 7 1 3856 4370 88405647 88406164 0.000000e+00 898.0
14 TraesCS3B01G228700 chrUn 97.605 501 9 2 3855 4352 364763738 364764238 0.000000e+00 856.0
15 TraesCS3B01G228700 chrUn 97.634 465 7 2 3855 4316 283046319 283046782 0.000000e+00 795.0
16 TraesCS3B01G228700 chrUn 97.634 465 7 2 3855 4316 287221670 287222133 0.000000e+00 795.0
17 TraesCS3B01G228700 chr2A 91.734 496 33 4 3855 4346 698145023 698145514 0.000000e+00 682.0
18 TraesCS3B01G228700 chr5D 88.800 500 45 8 3855 4346 387823924 387823428 1.740000e-168 603.0
19 TraesCS3B01G228700 chr5D 96.774 31 1 0 1827 1857 38054217 38054247 8.000000e-03 52.8
20 TraesCS3B01G228700 chr7D 82.656 369 56 8 2993 3357 197150528 197150892 1.960000e-83 320.0
21 TraesCS3B01G228700 chr7D 96.875 32 1 0 1827 1858 614671426 614671457 2.000000e-03 54.7
22 TraesCS3B01G228700 chr7A 82.114 369 58 8 2993 3357 206582238 206582602 4.240000e-80 309.0
23 TraesCS3B01G228700 chr6D 100.000 32 0 0 1827 1858 393940485 393940454 4.720000e-05 60.2
24 TraesCS3B01G228700 chr2B 100.000 28 0 0 1800 1827 70878892 70878919 8.000000e-03 52.8
25 TraesCS3B01G228700 chr2B 96.774 31 1 0 1827 1857 624373441 624373471 8.000000e-03 52.8


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 TraesCS3B01G228700 chr3B 331552000 331556369 4369 True 8070.000000 8070 100.000000 1 4370 1 chr3B.!!$R1 4369
1 TraesCS3B01G228700 chr3B 349956234 349956749 515 False 937.000000 937 99.419000 3855 4370 1 chr3B.!!$F1 515
2 TraesCS3B01G228700 chr3D 246325546 246329390 3844 False 2690.000000 3788 92.640000 1 3855 2 chr3D.!!$F1 3854
3 TraesCS3B01G228700 chr3A 337880000 337884445 4445 True 762.271429 1522 91.926143 1 3853 7 chr3A.!!$R2 3852
4 TraesCS3B01G228700 chr4B 88405647 88406164 517 False 898.000000 898 98.069000 3856 4370 1 chr4B.!!$F1 514
5 TraesCS3B01G228700 chrUn 364763738 364764238 500 False 856.000000 856 97.605000 3855 4352 1 chrUn.!!$F3 497

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
339 462 0.447406 GCATACGTTGAGTGCATGCA 59.553 50.0 18.46 18.46 41.87 3.96 F
1235 1837 0.467384 ATTCAGGCATGTCTCCTCGG 59.533 55.0 0.00 0.00 0.00 4.63 F
1859 2512 0.527565 TCTTTACGGCGGGAGTACAC 59.472 55.0 13.24 0.00 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 2497 0.035534 TACAGTGTACTCCCGCCGTA 60.036 55.0 0.0 0.0 0.00 4.02 R
2639 3297 0.102300 GTTGTTGTTGTCCCTGCCAC 59.898 55.0 0.0 0.0 0.00 5.01 R
3674 4408 0.393077 ACCGTTTGGGAGAGACACAG 59.607 55.0 0.0 0.0 40.75 3.66 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
50 51 1.043816 ATGCCTACCAGATCACCTCG 58.956 55.000 0.00 0.00 0.00 4.63
60 61 1.207329 AGATCACCTCGCCTGGTTTAC 59.793 52.381 0.00 0.00 38.45 2.01
100 103 7.861872 TGGTTAGTTGGTAGTTTTAAATTTCGC 59.138 33.333 0.00 0.00 0.00 4.70
166 169 5.820423 TCCATTTTGGATGAATATCGTTCGT 59.180 36.000 0.00 0.00 42.67 3.85
206 209 0.903942 GAAATGGGCCAGGCATTTGA 59.096 50.000 19.38 0.00 0.00 2.69
215 218 2.363038 GCCAGGCATTTGATAATCTGCA 59.637 45.455 6.55 0.00 0.00 4.41
226 345 7.395190 TTTGATAATCTGCATTGTAGTTGCT 57.605 32.000 1.55 0.00 40.77 3.91
255 375 3.825014 AGCATACGTACTCATCCGGTATT 59.175 43.478 0.00 0.00 0.00 1.89
339 462 0.447406 GCATACGTTGAGTGCATGCA 59.553 50.000 18.46 18.46 41.87 3.96
372 495 5.163963 GCATTCCTTTCCTTGCAAATTTACG 60.164 40.000 0.00 0.00 35.22 3.18
447 586 2.048127 GCACGACACTCCAGTCCC 60.048 66.667 0.00 0.00 35.07 4.46
486 625 2.604139 CCCTTCCCTTTACCAAAAGCA 58.396 47.619 0.00 0.00 40.73 3.91
537 676 8.485392 AGTAAACTACAGTAGGAGTAGGAGTAG 58.515 40.741 12.42 0.00 42.47 2.57
538 677 5.892524 ACTACAGTAGGAGTAGGAGTAGG 57.107 47.826 12.42 0.00 42.47 3.18
539 678 5.536951 ACTACAGTAGGAGTAGGAGTAGGA 58.463 45.833 12.42 0.00 42.47 2.94
540 679 5.603813 ACTACAGTAGGAGTAGGAGTAGGAG 59.396 48.000 12.42 0.00 42.47 3.69
668 1244 8.794364 AGAATGATGATGGATATATAGCTCCA 57.206 34.615 7.40 7.40 45.27 3.86
734 1317 1.760480 GTGCTCCTCCTCCTCCTCC 60.760 68.421 0.00 0.00 0.00 4.30
736 1319 1.152546 GCTCCTCCTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
740 1323 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
741 1324 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
742 1325 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
879 1481 1.180029 GGCGAGTACTAGTCCCAACA 58.820 55.000 0.00 0.00 0.00 3.33
885 1487 3.320129 AGTACTAGTCCCAACACCCAAA 58.680 45.455 0.00 0.00 0.00 3.28
943 1545 1.217511 CTCGCACAGGAGCATCAGT 59.782 57.895 0.00 0.00 36.25 3.41
1024 1626 1.686052 CTGCACCCTACTCTCCATCTC 59.314 57.143 0.00 0.00 0.00 2.75
1025 1627 1.044611 GCACCCTACTCTCCATCTCC 58.955 60.000 0.00 0.00 0.00 3.71
1026 1628 1.689575 GCACCCTACTCTCCATCTCCA 60.690 57.143 0.00 0.00 0.00 3.86
1027 1629 2.969628 CACCCTACTCTCCATCTCCAT 58.030 52.381 0.00 0.00 0.00 3.41
1028 1630 2.896685 CACCCTACTCTCCATCTCCATC 59.103 54.545 0.00 0.00 0.00 3.51
1029 1631 2.794760 ACCCTACTCTCCATCTCCATCT 59.205 50.000 0.00 0.00 0.00 2.90
1030 1632 3.181423 ACCCTACTCTCCATCTCCATCTC 60.181 52.174 0.00 0.00 0.00 2.75
1031 1633 3.430453 CCTACTCTCCATCTCCATCTCC 58.570 54.545 0.00 0.00 0.00 3.71
1032 1634 3.181424 CCTACTCTCCATCTCCATCTCCA 60.181 52.174 0.00 0.00 0.00 3.86
1033 1635 3.634218 ACTCTCCATCTCCATCTCCAT 57.366 47.619 0.00 0.00 0.00 3.41
1034 1636 3.509442 ACTCTCCATCTCCATCTCCATC 58.491 50.000 0.00 0.00 0.00 3.51
1035 1637 3.142597 ACTCTCCATCTCCATCTCCATCT 59.857 47.826 0.00 0.00 0.00 2.90
1077 1679 3.060615 GCTGCCCTTGTCCTGCTG 61.061 66.667 0.00 0.00 0.00 4.41
1110 1712 2.127232 GTCGCGCTTCTTGGCAAC 60.127 61.111 5.56 0.00 0.00 4.17
1235 1837 0.467384 ATTCAGGCATGTCTCCTCGG 59.533 55.000 0.00 0.00 0.00 4.63
1434 2076 3.650070 TCCATCTCGTTAGCAGCTATG 57.350 47.619 2.02 0.00 0.00 2.23
1530 2172 1.202879 TGGGCTCTTGTTCGATTGGTT 60.203 47.619 0.00 0.00 0.00 3.67
1540 2182 2.519377 TCGATTGGTTGTCTTGTCGT 57.481 45.000 0.00 0.00 0.00 4.34
1635 2277 4.338539 GTGTCCGGCGTCTCGTGT 62.339 66.667 6.01 0.00 0.00 4.49
1784 2433 5.104610 AGGTCCGTAGTCTACTCTTGTCATA 60.105 44.000 8.37 0.00 0.00 2.15
1785 2434 5.236911 GGTCCGTAGTCTACTCTTGTCATAG 59.763 48.000 8.37 0.00 0.00 2.23
1791 2440 6.642707 AGTCTACTCTTGTCATAGCATACC 57.357 41.667 0.00 0.00 0.00 2.73
1793 2442 6.780031 AGTCTACTCTTGTCATAGCATACCAT 59.220 38.462 0.00 0.00 0.00 3.55
1803 2452 8.700439 TGTCATAGCATACCATTACAGTACTA 57.300 34.615 0.00 0.00 0.00 1.82
1804 2453 8.793592 TGTCATAGCATACCATTACAGTACTAG 58.206 37.037 0.00 0.00 0.00 2.57
1805 2454 8.794553 GTCATAGCATACCATTACAGTACTAGT 58.205 37.037 0.00 0.00 0.00 2.57
1809 2458 8.393671 AGCATACCATTACAGTACTAGTACTC 57.606 38.462 28.86 14.98 43.98 2.59
1810 2459 7.447853 AGCATACCATTACAGTACTAGTACTCC 59.552 40.741 28.86 6.73 43.98 3.85
1811 2460 7.309073 GCATACCATTACAGTACTAGTACTCCC 60.309 44.444 28.86 6.37 43.98 4.30
1812 2461 6.338591 ACCATTACAGTACTAGTACTCCCT 57.661 41.667 28.86 17.64 43.98 4.20
1813 2462 6.363882 ACCATTACAGTACTAGTACTCCCTC 58.636 44.000 28.86 5.29 43.98 4.30
1814 2463 6.160105 ACCATTACAGTACTAGTACTCCCTCT 59.840 42.308 28.86 12.61 43.98 3.69
1815 2464 6.487331 CCATTACAGTACTAGTACTCCCTCTG 59.513 46.154 28.86 20.36 43.98 3.35
1816 2465 6.633325 TTACAGTACTAGTACTCCCTCTGT 57.367 41.667 28.86 24.08 43.98 3.41
1817 2466 7.739995 TTACAGTACTAGTACTCCCTCTGTA 57.260 40.000 28.86 23.20 43.98 2.74
1818 2467 6.633325 ACAGTACTAGTACTCCCTCTGTAA 57.367 41.667 28.86 0.00 43.98 2.41
1819 2468 7.025520 ACAGTACTAGTACTCCCTCTGTAAA 57.974 40.000 28.86 0.00 43.98 2.01
1820 2469 7.111466 ACAGTACTAGTACTCCCTCTGTAAAG 58.889 42.308 28.86 16.79 43.98 1.85
1821 2470 7.037730 ACAGTACTAGTACTCCCTCTGTAAAGA 60.038 40.741 28.86 0.00 43.98 2.52
1822 2471 7.828223 CAGTACTAGTACTCCCTCTGTAAAGAA 59.172 40.741 28.86 0.00 43.98 2.52
1823 2472 8.389366 AGTACTAGTACTCCCTCTGTAAAGAAA 58.611 37.037 26.61 0.00 42.30 2.52
1824 2473 7.706100 ACTAGTACTCCCTCTGTAAAGAAAG 57.294 40.000 0.00 0.00 0.00 2.62
1825 2474 7.240167 ACTAGTACTCCCTCTGTAAAGAAAGT 58.760 38.462 0.00 0.00 0.00 2.66
1828 2477 8.667592 AGTACTCCCTCTGTAAAGAAAGTAAT 57.332 34.615 0.00 0.00 0.00 1.89
1849 2502 8.989980 AGTAATGCTCTTATATTTCTTTACGGC 58.010 33.333 0.00 0.00 0.00 5.68
1859 2512 0.527565 TCTTTACGGCGGGAGTACAC 59.472 55.000 13.24 0.00 0.00 2.90
1869 2522 1.271379 CGGGAGTACACTGTAAGCACA 59.729 52.381 0.00 0.00 37.60 4.57
1898 2551 7.097192 TGAATTCAAGTTACTGTAGCCTGTAG 58.903 38.462 5.45 0.00 0.00 2.74
1899 2552 6.607004 ATTCAAGTTACTGTAGCCTGTAGT 57.393 37.500 0.00 0.00 0.00 2.73
1900 2553 7.713734 ATTCAAGTTACTGTAGCCTGTAGTA 57.286 36.000 0.00 0.00 0.00 1.82
1901 2554 7.713734 TTCAAGTTACTGTAGCCTGTAGTAT 57.286 36.000 0.00 0.00 0.00 2.12
1902 2555 7.096884 TCAAGTTACTGTAGCCTGTAGTATG 57.903 40.000 0.00 0.00 0.00 2.39
1903 2556 6.662234 TCAAGTTACTGTAGCCTGTAGTATGT 59.338 38.462 0.00 0.00 0.00 2.29
1904 2557 7.830697 TCAAGTTACTGTAGCCTGTAGTATGTA 59.169 37.037 0.00 0.00 0.00 2.29
1905 2558 7.804843 AGTTACTGTAGCCTGTAGTATGTAG 57.195 40.000 0.00 0.00 0.00 2.74
1906 2559 6.771749 AGTTACTGTAGCCTGTAGTATGTAGG 59.228 42.308 0.00 0.00 34.67 3.18
1907 2560 5.384145 ACTGTAGCCTGTAGTATGTAGGA 57.616 43.478 0.00 0.00 33.33 2.94
1908 2561 5.954757 ACTGTAGCCTGTAGTATGTAGGAT 58.045 41.667 0.00 0.00 33.33 3.24
1909 2562 7.087895 ACTGTAGCCTGTAGTATGTAGGATA 57.912 40.000 0.00 0.00 33.33 2.59
1939 2592 6.339730 TGTCTTTGTTGCTGAATGAAATTGT 58.660 32.000 0.00 0.00 36.07 2.71
1940 2593 6.476380 TGTCTTTGTTGCTGAATGAAATTGTC 59.524 34.615 0.00 0.00 36.07 3.18
1941 2594 5.984926 TCTTTGTTGCTGAATGAAATTGTCC 59.015 36.000 0.00 0.00 36.07 4.02
1942 2595 3.899734 TGTTGCTGAATGAAATTGTCCG 58.100 40.909 0.00 0.00 36.07 4.79
1943 2596 3.317711 TGTTGCTGAATGAAATTGTCCGT 59.682 39.130 0.00 0.00 36.07 4.69
1944 2597 4.202101 TGTTGCTGAATGAAATTGTCCGTT 60.202 37.500 0.00 0.00 36.07 4.44
1945 2598 4.582701 TGCTGAATGAAATTGTCCGTTT 57.417 36.364 0.00 0.00 36.07 3.60
1946 2599 4.545610 TGCTGAATGAAATTGTCCGTTTC 58.454 39.130 0.00 0.00 36.07 2.78
1947 2600 4.037327 TGCTGAATGAAATTGTCCGTTTCA 59.963 37.500 4.06 4.06 46.16 2.69
1948 2601 4.981674 GCTGAATGAAATTGTCCGTTTCAA 59.018 37.500 5.52 0.00 45.50 2.69
1949 2602 5.461737 GCTGAATGAAATTGTCCGTTTCAAA 59.538 36.000 5.52 0.00 45.50 2.69
1950 2603 6.019156 GCTGAATGAAATTGTCCGTTTCAAAA 60.019 34.615 5.52 0.00 45.50 2.44
1951 2604 7.465245 GCTGAATGAAATTGTCCGTTTCAAAAA 60.465 33.333 5.52 0.00 45.50 1.94
2038 2691 0.593618 TGATATCGAGCAGAGCGGTC 59.406 55.000 6.48 6.48 38.84 4.79
2114 2767 7.364408 CCTCATGGATTTGACTGGATTTGATTT 60.364 37.037 0.00 0.00 34.57 2.17
2169 2822 1.219124 GCAGAGAGCATTGACCCGA 59.781 57.895 0.00 0.00 44.79 5.14
2211 2864 1.617018 TTGGCTCTCGCTAGGTGCAT 61.617 55.000 0.00 0.00 43.06 3.96
2299 2956 3.390639 TCCTAAGACGGAGGGAGTAGTAG 59.609 52.174 0.00 0.00 34.56 2.57
2324 2981 2.906458 CAGTAGAGCAGCAGGGGG 59.094 66.667 0.00 0.00 0.00 5.40
2387 3044 3.514706 TGGATGGATGGTTGTTGAAATGG 59.485 43.478 0.00 0.00 0.00 3.16
2388 3045 3.118665 GGATGGATGGTTGTTGAAATGGG 60.119 47.826 0.00 0.00 0.00 4.00
2389 3046 2.255406 TGGATGGTTGTTGAAATGGGG 58.745 47.619 0.00 0.00 0.00 4.96
2390 3047 2.256306 GGATGGTTGTTGAAATGGGGT 58.744 47.619 0.00 0.00 0.00 4.95
2391 3048 2.028203 GGATGGTTGTTGAAATGGGGTG 60.028 50.000 0.00 0.00 0.00 4.61
2392 3049 2.166907 TGGTTGTTGAAATGGGGTGT 57.833 45.000 0.00 0.00 0.00 4.16
2393 3050 1.759445 TGGTTGTTGAAATGGGGTGTG 59.241 47.619 0.00 0.00 0.00 3.82
2394 3051 1.760029 GGTTGTTGAAATGGGGTGTGT 59.240 47.619 0.00 0.00 0.00 3.72
2631 3289 1.064463 CCTCTCTGGTCTCTGCTCTCT 60.064 57.143 0.00 0.00 0.00 3.10
2639 3297 0.393673 TCTCTGCTCTCTGTCTCGGG 60.394 60.000 0.00 0.00 0.00 5.14
2794 3452 0.961753 TGGATGGATCGATCGTCTGG 59.038 55.000 18.81 0.00 0.00 3.86
2795 3453 0.962489 GGATGGATCGATCGTCTGGT 59.038 55.000 18.81 0.00 0.00 4.00
2796 3454 1.336332 GGATGGATCGATCGTCTGGTG 60.336 57.143 18.81 0.00 0.00 4.17
2797 3455 1.609072 GATGGATCGATCGTCTGGTGA 59.391 52.381 18.81 0.00 0.00 4.02
2798 3456 1.470051 TGGATCGATCGTCTGGTGAA 58.530 50.000 18.81 0.00 0.00 3.18
2799 3457 1.822371 TGGATCGATCGTCTGGTGAAA 59.178 47.619 18.81 0.00 0.00 2.69
2800 3458 2.430694 TGGATCGATCGTCTGGTGAAAT 59.569 45.455 18.81 0.00 0.00 2.17
2878 3570 2.151049 GACGACGGGGTGCTACAACT 62.151 60.000 0.00 0.00 0.00 3.16
2946 3638 3.508840 GCCATTTCGCCCACCTCG 61.509 66.667 0.00 0.00 0.00 4.63
3061 3753 1.205055 GGGTTACTGGCCTAGCTTCT 58.795 55.000 3.32 0.00 0.00 2.85
3475 4191 3.402628 TGTTCCACTAGTCTTTGCTCC 57.597 47.619 0.00 0.00 0.00 4.70
3526 4242 2.105993 GAGGGTGGGTTCACTACTTGTT 59.894 50.000 0.00 0.00 43.17 2.83
3527 4243 2.158667 AGGGTGGGTTCACTACTTGTTG 60.159 50.000 0.00 0.00 43.17 3.33
3528 4244 2.422377 GGGTGGGTTCACTACTTGTTGT 60.422 50.000 0.00 0.00 43.17 3.32
3582 4302 5.569413 AGTGTAGCTTCGTTTCAAAAACAG 58.431 37.500 0.00 0.00 0.00 3.16
3614 4348 0.244994 AACTCAGCACTACTCCAGCG 59.755 55.000 0.00 0.00 0.00 5.18
3626 4360 1.143305 CTCCAGCGCATACTACATGC 58.857 55.000 11.47 0.00 41.35 4.06
3627 4361 0.463620 TCCAGCGCATACTACATGCA 59.536 50.000 11.47 0.00 44.75 3.96
3628 4362 1.070601 TCCAGCGCATACTACATGCAT 59.929 47.619 11.47 0.00 44.75 3.96
3629 4363 1.196127 CCAGCGCATACTACATGCATG 59.804 52.381 25.09 25.09 44.75 4.06
3630 4364 0.870393 AGCGCATACTACATGCATGC 59.130 50.000 26.53 11.82 44.75 4.06
3631 4365 0.587768 GCGCATACTACATGCATGCA 59.412 50.000 26.53 25.04 43.74 3.96
3632 4366 1.198408 GCGCATACTACATGCATGCAT 59.802 47.619 27.46 27.46 43.74 3.96
3660 4394 4.260866 GCATGCATCAATTGTTTATTGCCC 60.261 41.667 14.21 0.00 42.79 5.36
3685 4419 1.999071 ATCGCTCGCTGTGTCTCTCC 61.999 60.000 0.00 0.00 0.00 3.71
3703 4437 2.290641 CTCCCAAACGGTTCTTCACTTG 59.709 50.000 0.00 0.00 0.00 3.16
3868 4604 8.872670 GAGTATTTCTCCGAGGTAATAGCACCT 61.873 44.444 0.00 0.00 43.04 4.00
3916 4652 5.013079 TGTGATGATCTAGTCCCAAACTTGT 59.987 40.000 0.00 0.00 39.55 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 0.036010 AAACCAGGCGAGGTGATCTG 60.036 55.000 5.43 0.00 42.25 2.90
42 43 1.276622 AGTAAACCAGGCGAGGTGAT 58.723 50.000 5.43 1.54 42.25 3.06
50 51 9.366216 CCAAATAAAATCTAAAGTAAACCAGGC 57.634 33.333 0.00 0.00 0.00 4.85
206 209 4.037208 GGCAGCAACTACAATGCAGATTAT 59.963 41.667 0.00 0.00 46.22 1.28
215 218 2.369394 GCTAAGGGCAGCAACTACAAT 58.631 47.619 0.00 0.00 41.40 2.71
255 375 2.160205 AGCAAGCACTACGTGTAGAGA 58.840 47.619 13.69 0.00 36.97 3.10
288 410 6.267817 AGAAACAACTCATGTCATGTGTTTG 58.732 36.000 25.79 21.80 42.37 2.93
424 547 2.029666 GGAGTGTCGTGCTGCTGT 59.970 61.111 0.00 0.00 0.00 4.40
509 648 8.169393 ACTCCTACTCCTACTGTAGTTTACTTT 58.831 37.037 13.42 0.00 36.56 2.66
734 1317 0.933700 AGAAGGAGGAGGAGGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
736 1319 1.290732 AGAAGAAGGAGGAGGAGGAGG 59.709 57.143 0.00 0.00 0.00 4.30
740 1323 4.352893 AGAAGAAGAAGAAGGAGGAGGAG 58.647 47.826 0.00 0.00 0.00 3.69
741 1324 4.412060 AGAAGAAGAAGAAGGAGGAGGA 57.588 45.455 0.00 0.00 0.00 3.71
742 1325 5.244755 CAAAGAAGAAGAAGAAGGAGGAGG 58.755 45.833 0.00 0.00 0.00 4.30
879 1481 2.015227 CTGCCGCTTGTTGTTTGGGT 62.015 55.000 0.00 0.00 0.00 4.51
885 1487 3.595758 GTGCCTGCCGCTTGTTGT 61.596 61.111 0.00 0.00 38.78 3.32
1024 1626 2.617658 TGGAGATGGAGATGGAGATGG 58.382 52.381 0.00 0.00 0.00 3.51
1025 1627 3.838903 TGATGGAGATGGAGATGGAGATG 59.161 47.826 0.00 0.00 0.00 2.90
1026 1628 3.839490 GTGATGGAGATGGAGATGGAGAT 59.161 47.826 0.00 0.00 0.00 2.75
1027 1629 3.237746 GTGATGGAGATGGAGATGGAGA 58.762 50.000 0.00 0.00 0.00 3.71
1028 1630 2.970640 TGTGATGGAGATGGAGATGGAG 59.029 50.000 0.00 0.00 0.00 3.86
1029 1631 3.050523 TGTGATGGAGATGGAGATGGA 57.949 47.619 0.00 0.00 0.00 3.41
1030 1632 3.307550 GGATGTGATGGAGATGGAGATGG 60.308 52.174 0.00 0.00 0.00 3.51
1031 1633 3.307550 GGGATGTGATGGAGATGGAGATG 60.308 52.174 0.00 0.00 0.00 2.90
1032 1634 2.911636 GGGATGTGATGGAGATGGAGAT 59.088 50.000 0.00 0.00 0.00 2.75
1033 1635 2.333069 GGGATGTGATGGAGATGGAGA 58.667 52.381 0.00 0.00 0.00 3.71
1034 1636 2.052468 TGGGATGTGATGGAGATGGAG 58.948 52.381 0.00 0.00 0.00 3.86
1035 1637 1.770658 GTGGGATGTGATGGAGATGGA 59.229 52.381 0.00 0.00 0.00 3.41
1077 1679 1.136984 GACATGAAGCAGCAGCAGC 59.863 57.895 3.17 0.46 45.49 5.25
1155 1757 1.988406 GACCCGCCTGTACCTCCTT 60.988 63.158 0.00 0.00 0.00 3.36
1156 1758 2.363925 GACCCGCCTGTACCTCCT 60.364 66.667 0.00 0.00 0.00 3.69
1530 2172 2.642254 CGGGCCCTACGACAAGACA 61.642 63.158 22.43 0.00 0.00 3.41
1628 2270 3.933048 GACCCCTCCGGACACGAGA 62.933 68.421 0.00 0.00 44.60 4.04
1629 2271 3.450115 GACCCCTCCGGACACGAG 61.450 72.222 0.00 0.00 44.60 4.18
1729 2371 2.050168 GACCGTGTCACGCCGTAA 60.050 61.111 20.01 0.00 40.91 3.18
1784 2433 7.447853 GGAGTACTAGTACTGTAATGGTATGCT 59.552 40.741 34.67 10.34 45.63 3.79
1785 2434 7.309073 GGGAGTACTAGTACTGTAATGGTATGC 60.309 44.444 34.67 17.67 45.63 3.14
1791 2440 7.055378 ACAGAGGGAGTACTAGTACTGTAATG 58.945 42.308 34.67 25.88 45.63 1.90
1793 2442 6.633325 ACAGAGGGAGTACTAGTACTGTAA 57.367 41.667 34.67 0.00 45.63 2.41
1803 2452 8.532819 CATTACTTTCTTTACAGAGGGAGTACT 58.467 37.037 0.00 0.00 0.00 2.73
1804 2453 7.278203 GCATTACTTTCTTTACAGAGGGAGTAC 59.722 40.741 0.00 0.00 0.00 2.73
1805 2454 7.180408 AGCATTACTTTCTTTACAGAGGGAGTA 59.820 37.037 0.00 0.00 0.00 2.59
1806 2455 6.013293 AGCATTACTTTCTTTACAGAGGGAGT 60.013 38.462 0.00 0.00 0.00 3.85
1807 2456 6.410540 AGCATTACTTTCTTTACAGAGGGAG 58.589 40.000 0.00 0.00 0.00 4.30
1808 2457 6.213600 AGAGCATTACTTTCTTTACAGAGGGA 59.786 38.462 0.00 0.00 0.00 4.20
1809 2458 6.410540 AGAGCATTACTTTCTTTACAGAGGG 58.589 40.000 0.00 0.00 0.00 4.30
1810 2459 7.913674 AAGAGCATTACTTTCTTTACAGAGG 57.086 36.000 0.00 0.00 0.00 3.69
1823 2472 8.989980 GCCGTAAAGAAATATAAGAGCATTACT 58.010 33.333 0.00 0.00 0.00 2.24
1824 2473 7.950496 CGCCGTAAAGAAATATAAGAGCATTAC 59.050 37.037 0.00 0.00 0.00 1.89
1825 2474 7.117236 CCGCCGTAAAGAAATATAAGAGCATTA 59.883 37.037 0.00 0.00 0.00 1.90
1828 2477 4.748102 CCGCCGTAAAGAAATATAAGAGCA 59.252 41.667 0.00 0.00 0.00 4.26
1844 2497 0.035534 TACAGTGTACTCCCGCCGTA 60.036 55.000 0.00 0.00 0.00 4.02
1849 2502 1.271379 TGTGCTTACAGTGTACTCCCG 59.729 52.381 1.43 0.00 0.00 5.14
1859 2512 5.009010 ACTTGAATTCAGGTTGTGCTTACAG 59.991 40.000 16.83 5.52 31.78 2.74
1869 2522 5.705905 GGCTACAGTAACTTGAATTCAGGTT 59.294 40.000 30.99 30.99 45.99 3.50
1900 2553 8.462016 GCAACAAAGACAAGATTTATCCTACAT 58.538 33.333 0.00 0.00 0.00 2.29
1901 2554 7.665559 AGCAACAAAGACAAGATTTATCCTACA 59.334 33.333 0.00 0.00 0.00 2.74
1902 2555 7.965107 CAGCAACAAAGACAAGATTTATCCTAC 59.035 37.037 0.00 0.00 0.00 3.18
1903 2556 7.882791 TCAGCAACAAAGACAAGATTTATCCTA 59.117 33.333 0.00 0.00 0.00 2.94
1904 2557 6.716628 TCAGCAACAAAGACAAGATTTATCCT 59.283 34.615 0.00 0.00 0.00 3.24
1905 2558 6.913170 TCAGCAACAAAGACAAGATTTATCC 58.087 36.000 0.00 0.00 0.00 2.59
1906 2559 8.857216 CATTCAGCAACAAAGACAAGATTTATC 58.143 33.333 0.00 0.00 0.00 1.75
1907 2560 8.579006 TCATTCAGCAACAAAGACAAGATTTAT 58.421 29.630 0.00 0.00 0.00 1.40
1908 2561 7.939782 TCATTCAGCAACAAAGACAAGATTTA 58.060 30.769 0.00 0.00 0.00 1.40
1909 2562 6.808829 TCATTCAGCAACAAAGACAAGATTT 58.191 32.000 0.00 0.00 0.00 2.17
1921 2574 3.317711 ACGGACAATTTCATTCAGCAACA 59.682 39.130 0.00 0.00 0.00 3.33
1954 2607 0.972883 TTAGCGCAGGGGCAATTTTT 59.027 45.000 11.47 0.00 41.24 1.94
1955 2608 0.972883 TTTAGCGCAGGGGCAATTTT 59.027 45.000 11.47 0.00 41.24 1.82
1956 2609 1.134729 CATTTAGCGCAGGGGCAATTT 60.135 47.619 11.47 0.00 41.24 1.82
1957 2610 0.461135 CATTTAGCGCAGGGGCAATT 59.539 50.000 11.47 0.00 41.24 2.32
1958 2611 0.395586 TCATTTAGCGCAGGGGCAAT 60.396 50.000 11.47 0.07 41.24 3.56
1959 2612 0.395586 ATCATTTAGCGCAGGGGCAA 60.396 50.000 11.47 0.00 41.24 4.52
1960 2613 1.102809 CATCATTTAGCGCAGGGGCA 61.103 55.000 11.47 0.00 41.24 5.36
1961 2614 1.656441 CATCATTTAGCGCAGGGGC 59.344 57.895 11.47 0.00 0.00 5.80
1994 2647 6.039159 ACGTTTTTACCCAACTTTTTCGGATA 59.961 34.615 0.00 0.00 0.00 2.59
2051 2704 2.131183 GAATCTATGTCCTCGCAGTGC 58.869 52.381 4.58 4.58 0.00 4.40
2114 2767 2.223618 GGAGTAAAAGCAACGGCAAACA 60.224 45.455 0.00 0.00 44.61 2.83
2169 2822 0.664767 GCAGACGAAGAAGCGACACT 60.665 55.000 0.00 0.00 34.83 3.55
2242 2899 8.647143 ACACCACATTAATGTCAAAAGAAAAG 57.353 30.769 18.25 3.49 39.39 2.27
2282 2939 4.227073 AGTTAACTACTACTCCCTCCGTCT 59.773 45.833 6.26 0.00 34.56 4.18
2324 2981 9.257651 ACTAGTGTTACTGTCTTGTTAATGTTC 57.742 33.333 0.00 0.00 0.00 3.18
2387 3044 0.958382 ACACACACACACACACACCC 60.958 55.000 0.00 0.00 0.00 4.61
2388 3045 0.167908 CACACACACACACACACACC 59.832 55.000 0.00 0.00 0.00 4.16
2389 3046 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2390 3047 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2391 3048 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2392 3049 2.457366 TACACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
2393 3050 2.538737 GCATACACACACACACACACAC 60.539 50.000 0.00 0.00 0.00 3.82
2394 3051 1.668237 GCATACACACACACACACACA 59.332 47.619 0.00 0.00 0.00 3.72
2457 3114 4.505217 CGTTGATGCTCGCACGCC 62.505 66.667 0.00 0.00 0.00 5.68
2586 3243 3.111098 GGATGATGCTCAAATCGCAAAC 58.889 45.455 0.00 0.00 41.26 2.93
2631 3289 4.631740 TCCCTGCCACCCGAGACA 62.632 66.667 0.00 0.00 0.00 3.41
2639 3297 0.102300 GTTGTTGTTGTCCCTGCCAC 59.898 55.000 0.00 0.00 0.00 5.01
2878 3570 1.597854 CGAACCCTGAGCACAGCAA 60.598 57.895 5.52 0.00 42.25 3.91
2946 3638 4.733542 TGGCCGCCTTTGTAGCCC 62.734 66.667 11.61 0.00 45.14 5.19
3105 3797 3.936203 GTGTCCACCACCTCGCCA 61.936 66.667 0.00 0.00 38.18 5.69
3423 4115 9.860898 CAGGAAGAAAGAAAGAAAGAAAGAAAA 57.139 29.630 0.00 0.00 0.00 2.29
3460 4152 4.799564 AGAAGAGGAGCAAAGACTAGTG 57.200 45.455 0.00 0.00 0.00 2.74
3461 4153 5.326069 TGTAGAAGAGGAGCAAAGACTAGT 58.674 41.667 0.00 0.00 0.00 2.57
3464 4156 4.156477 ACTGTAGAAGAGGAGCAAAGACT 58.844 43.478 0.00 0.00 0.00 3.24
3465 4157 4.529109 ACTGTAGAAGAGGAGCAAAGAC 57.471 45.455 0.00 0.00 0.00 3.01
3467 4159 7.913674 AATAAACTGTAGAAGAGGAGCAAAG 57.086 36.000 0.00 0.00 0.00 2.77
3468 4160 8.691661 AAAATAAACTGTAGAAGAGGAGCAAA 57.308 30.769 0.00 0.00 0.00 3.68
3475 4191 8.391075 TGGTTGGAAAATAAACTGTAGAAGAG 57.609 34.615 0.00 0.00 0.00 2.85
3526 4242 4.553330 GTCAGGAGACCCATCTTTTACA 57.447 45.455 0.00 0.00 38.89 2.41
3582 4302 2.288825 TGCTGAGTTGGCTACACTACAC 60.289 50.000 1.24 0.00 0.00 2.90
3674 4408 0.393077 ACCGTTTGGGAGAGACACAG 59.607 55.000 0.00 0.00 40.75 3.66
3685 4419 1.676006 AGCAAGTGAAGAACCGTTTGG 59.324 47.619 0.00 0.00 42.84 3.28
3703 4437 6.843069 GTACTACTAGTACTACTGTCCAGC 57.157 45.833 16.30 0.00 45.70 4.85
3806 4542 1.442526 GGATGGTCTGGCGCAATCAG 61.443 60.000 10.83 7.89 0.00 2.90
3843 4579 5.010820 GGTGCTATTACCTCGGAGAAATACT 59.989 44.000 6.58 0.00 37.74 2.12
3916 4652 5.786457 TGGGGTATGAGTTGGTCTAGTTTTA 59.214 40.000 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.