Multiple sequence alignment - TraesCS2B01G211200

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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 TraesCS2B01G211200 chr2B 100.000 2934 0 0 1 2934 194955772 194952839 0.000000e+00 5419.0
1 TraesCS2B01G211200 chr2B 83.246 573 60 10 686 1252 195368636 195368094 7.300000e-136 494.0
2 TraesCS2B01G211200 chr2B 83.591 518 55 19 649 1157 194998189 194997693 2.660000e-125 459.0
3 TraesCS2B01G211200 chr2B 79.695 655 81 21 757 1399 195060045 195059431 2.700000e-115 425.0
4 TraesCS2B01G211200 chr2B 80.796 578 80 18 1511 2071 194997368 194996805 9.720000e-115 424.0
5 TraesCS2B01G211200 chr2B 76.602 671 93 46 1539 2173 195059435 195058793 7.900000e-81 311.0
6 TraesCS2B01G211200 chr2B 75.587 766 109 56 1539 2268 195167205 195166482 1.020000e-79 307.0
7 TraesCS2B01G211200 chr2B 85.171 263 29 7 1227 1488 194997696 194997443 8.070000e-66 261.0
8 TraesCS2B01G211200 chr2B 83.951 162 16 8 2548 2707 194996340 194996187 2.360000e-31 147.0
9 TraesCS2B01G211200 chr2B 84.354 147 20 1 1546 1692 222586510 222586367 1.100000e-29 141.0
10 TraesCS2B01G211200 chr2B 90.000 80 8 0 619 698 195369069 195368990 1.440000e-18 104.0
11 TraesCS2B01G211200 chr2D 89.386 1856 107 39 698 2505 136515733 136513920 0.000000e+00 2254.0
12 TraesCS2B01G211200 chr2D 80.030 1317 169 47 686 1945 136523592 136522313 0.000000e+00 889.0
13 TraesCS2B01G211200 chr2D 89.951 607 58 1 6 612 138689969 138690572 0.000000e+00 780.0
14 TraesCS2B01G211200 chr2D 85.752 751 65 24 634 1375 136634710 136633993 0.000000e+00 756.0
15 TraesCS2B01G211200 chr2D 83.005 659 77 17 750 1398 136526368 136525735 5.490000e-157 564.0
16 TraesCS2B01G211200 chr2D 81.435 641 66 29 759 1375 136613001 136612390 2.650000e-130 475.0
17 TraesCS2B01G211200 chr2D 82.137 571 60 13 685 1252 136651680 136651149 4.460000e-123 451.0
18 TraesCS2B01G211200 chr2D 78.117 754 108 38 1539 2268 136612184 136611464 2.700000e-115 425.0
19 TraesCS2B01G211200 chr2D 75.594 758 110 52 1539 2268 136607753 136607043 3.670000e-79 305.0
20 TraesCS2B01G211200 chr2D 83.436 163 16 7 2548 2707 136516046 136515892 1.100000e-29 141.0
21 TraesCS2B01G211200 chr2D 98.182 55 1 0 1321 1375 136607897 136607843 2.410000e-16 97.1
22 TraesCS2B01G211200 chr1B 89.170 1579 97 30 701 2231 512051622 512053174 0.000000e+00 1901.0
23 TraesCS2B01G211200 chr1B 87.960 598 68 2 12 609 431031759 431032352 0.000000e+00 702.0
24 TraesCS2B01G211200 chr1B 87.500 600 71 2 5 604 300959318 300958723 0.000000e+00 689.0
25 TraesCS2B01G211200 chr1B 91.494 435 26 4 2357 2786 512053244 512053672 3.260000e-164 588.0
26 TraesCS2B01G211200 chr2A 89.037 1578 100 29 701 2231 165104285 165105836 0.000000e+00 1888.0
27 TraesCS2B01G211200 chr2A 82.727 770 93 23 619 1375 164981130 164981872 0.000000e+00 649.0
28 TraesCS2B01G211200 chr2A 91.264 435 27 4 2357 2786 165105906 165106334 1.520000e-162 582.0
29 TraesCS2B01G211200 chr2A 78.902 929 115 47 1315 2215 165007071 165007946 3.300000e-154 555.0
30 TraesCS2B01G211200 chr2A 79.671 669 75 37 750 1398 164997651 164998278 2.700000e-115 425.0
31 TraesCS2B01G211200 chr2A 76.110 766 99 36 1345 2061 164876022 164876752 1.010000e-84 324.0
32 TraesCS2B01G211200 chr2A 82.301 226 19 9 697 914 164999177 164999389 3.010000e-40 176.0
33 TraesCS2B01G211200 chr2A 74.066 482 98 20 1546 2010 174787768 174787297 3.890000e-39 172.0
34 TraesCS2B01G211200 chr2A 95.556 90 1 1 2790 2876 165107150 165107239 1.100000e-29 141.0
35 TraesCS2B01G211200 chr2A 82.209 163 17 8 2548 2707 165008729 165008882 2.370000e-26 130.0
36 TraesCS2B01G211200 chr2A 88.043 92 7 1 616 703 164866812 164866903 4.000000e-19 106.0
37 TraesCS2B01G211200 chr2A 93.443 61 4 0 1315 1375 164878449 164878509 1.120000e-14 91.6
38 TraesCS2B01G211200 chr3B 89.256 605 64 1 5 609 708602406 708603009 0.000000e+00 756.0
39 TraesCS2B01G211200 chr3B 83.267 251 39 2 1511 1761 462061190 462060943 8.180000e-56 228.0
40 TraesCS2B01G211200 chr6D 90.070 574 50 4 5 576 396520130 396519562 0.000000e+00 737.0
41 TraesCS2B01G211200 chr4D 88.449 606 66 2 5 610 29640688 29640087 0.000000e+00 728.0
42 TraesCS2B01G211200 chr7A 87.685 609 69 4 4 612 198977466 198976864 0.000000e+00 704.0
43 TraesCS2B01G211200 chr7A 87.315 607 71 4 5 610 130498633 130499234 0.000000e+00 689.0
44 TraesCS2B01G211200 chr7D 87.500 608 70 3 5 612 168429304 168428703 0.000000e+00 697.0
45 TraesCS2B01G211200 chrUn 93.773 273 13 1 2357 2625 477031042 477030770 9.790000e-110 407.0


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 TraesCS2B01G211200 chr2B 194952839 194955772 2933 True 5419.000000 5419 100.000000 1 2934 1 chr2B.!!$R1 2933
1 TraesCS2B01G211200 chr2B 195058793 195060045 1252 True 368.000000 425 78.148500 757 2173 2 chr2B.!!$R5 1416
2 TraesCS2B01G211200 chr2B 194996187 194998189 2002 True 322.750000 459 83.377250 649 2707 4 chr2B.!!$R4 2058
3 TraesCS2B01G211200 chr2B 195166482 195167205 723 True 307.000000 307 75.587000 1539 2268 1 chr2B.!!$R2 729
4 TraesCS2B01G211200 chr2B 195368094 195369069 975 True 299.000000 494 86.623000 619 1252 2 chr2B.!!$R6 633
5 TraesCS2B01G211200 chr2D 136513920 136516046 2126 True 1197.500000 2254 86.411000 698 2707 2 chr2D.!!$R3 2009
6 TraesCS2B01G211200 chr2D 138689969 138690572 603 False 780.000000 780 89.951000 6 612 1 chr2D.!!$F1 606
7 TraesCS2B01G211200 chr2D 136633993 136634710 717 True 756.000000 756 85.752000 634 1375 1 chr2D.!!$R1 741
8 TraesCS2B01G211200 chr2D 136522313 136526368 4055 True 726.500000 889 81.517500 686 1945 2 chr2D.!!$R4 1259
9 TraesCS2B01G211200 chr2D 136651149 136651680 531 True 451.000000 451 82.137000 685 1252 1 chr2D.!!$R2 567
10 TraesCS2B01G211200 chr2D 136607043 136613001 5958 True 325.525000 475 83.332000 759 2268 4 chr2D.!!$R5 1509
11 TraesCS2B01G211200 chr1B 512051622 512053672 2050 False 1244.500000 1901 90.332000 701 2786 2 chr1B.!!$F2 2085
12 TraesCS2B01G211200 chr1B 431031759 431032352 593 False 702.000000 702 87.960000 12 609 1 chr1B.!!$F1 597
13 TraesCS2B01G211200 chr1B 300958723 300959318 595 True 689.000000 689 87.500000 5 604 1 chr1B.!!$R1 599
14 TraesCS2B01G211200 chr2A 165104285 165107239 2954 False 870.333333 1888 91.952333 701 2876 3 chr2A.!!$F6 2175
15 TraesCS2B01G211200 chr2A 164981130 164981872 742 False 649.000000 649 82.727000 619 1375 1 chr2A.!!$F2 756
16 TraesCS2B01G211200 chr2A 165007071 165008882 1811 False 342.500000 555 80.555500 1315 2707 2 chr2A.!!$F5 1392
17 TraesCS2B01G211200 chr2A 164997651 164999389 1738 False 300.500000 425 80.986000 697 1398 2 chr2A.!!$F4 701
18 TraesCS2B01G211200 chr2A 164876022 164878509 2487 False 207.800000 324 84.776500 1315 2061 2 chr2A.!!$F3 746
19 TraesCS2B01G211200 chr3B 708602406 708603009 603 False 756.000000 756 89.256000 5 609 1 chr3B.!!$F1 604
20 TraesCS2B01G211200 chr6D 396519562 396520130 568 True 737.000000 737 90.070000 5 576 1 chr6D.!!$R1 571
21 TraesCS2B01G211200 chr4D 29640087 29640688 601 True 728.000000 728 88.449000 5 610 1 chr4D.!!$R1 605
22 TraesCS2B01G211200 chr7A 198976864 198977466 602 True 704.000000 704 87.685000 4 612 1 chr7A.!!$R1 608
23 TraesCS2B01G211200 chr7A 130498633 130499234 601 False 689.000000 689 87.315000 5 610 1 chr7A.!!$F1 605
24 TraesCS2B01G211200 chr7D 168428703 168429304 601 True 697.000000 697 87.500000 5 612 1 chr7D.!!$R1 607

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
954 4225 0.037303 CATCCAGAGCCCGCCAATAT 59.963 55.0 0.0 0.0 0.0 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2626 14024 0.03563 AGATGCTCTGTCCCTGTTGC 60.036 55.0 0.0 0.0 0.0 4.17 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
110 111 1.070309 GGCGTACCTATCGTCGTAGTG 60.070 57.143 0.00 0.00 0.00 2.74
115 116 1.236628 CCTATCGTCGTAGTGGAGGG 58.763 60.000 0.00 0.00 0.00 4.30
236 239 0.256464 TTGTTGGGGAAGTGGACGTT 59.744 50.000 0.00 0.00 0.00 3.99
274 277 3.456431 CTCGTCTCCCAGTAGCGCG 62.456 68.421 0.00 0.00 0.00 6.86
345 348 4.506255 CCGATGGTGAAGGGGCCC 62.506 72.222 17.12 17.12 0.00 5.80
447 452 1.302993 GCGGTTGTGCTTCCCCTTA 60.303 57.895 0.00 0.00 0.00 2.69
515 521 0.838987 TTCGAGGCTAGGGTTTGGGT 60.839 55.000 0.00 0.00 0.00 4.51
530 536 2.940994 TGGGTCTGTCGGATTTTGAA 57.059 45.000 0.00 0.00 0.00 2.69
624 630 4.854924 TCGCCCCGTCCGATCGTA 62.855 66.667 15.09 0.00 0.00 3.43
625 631 4.619140 CGCCCCGTCCGATCGTAC 62.619 72.222 15.09 7.67 0.00 3.67
628 634 1.820906 CCCCGTCCGATCGTACTGA 60.821 63.158 15.09 0.54 0.00 3.41
655 662 4.664150 TTGGAAAAGCAAAACCAGGTAG 57.336 40.909 0.00 0.00 33.85 3.18
728 1104 3.057033 GTGGCAATTGAGCTCTGAAATGT 60.057 43.478 16.19 0.00 34.17 2.71
782 1159 2.290577 GCTCCCTCCAGACTGAAAATGT 60.291 50.000 3.32 0.00 0.00 2.71
799 1187 4.277009 TTGCCACCCGTCCATGCA 62.277 61.111 0.00 0.00 0.00 3.96
801 1189 2.191908 GCCACCCGTCCATGCATA 59.808 61.111 0.00 0.00 0.00 3.14
802 1190 1.228245 GCCACCCGTCCATGCATAT 60.228 57.895 0.00 0.00 0.00 1.78
803 1191 1.518056 GCCACCCGTCCATGCATATG 61.518 60.000 0.00 0.00 0.00 1.78
866 1262 1.133544 GTACCTCCTCCTCACCCGTAT 60.134 57.143 0.00 0.00 0.00 3.06
867 1263 0.397254 ACCTCCTCCTCACCCGTATG 60.397 60.000 0.00 0.00 0.00 2.39
868 1264 1.742768 CTCCTCCTCACCCGTATGC 59.257 63.158 0.00 0.00 0.00 3.14
869 1265 2.076622 CTCCTCCTCACCCGTATGCG 62.077 65.000 0.00 0.00 37.95 4.73
916 4187 1.067915 CCCACGGCAATTTCGTTTCAT 60.068 47.619 1.34 0.00 38.94 2.57
947 4218 1.372087 GCTGTTTCATCCAGAGCCCG 61.372 60.000 0.00 0.00 31.38 6.13
948 4219 1.372087 CTGTTTCATCCAGAGCCCGC 61.372 60.000 0.00 0.00 31.38 6.13
949 4220 2.115291 GTTTCATCCAGAGCCCGCC 61.115 63.158 0.00 0.00 0.00 6.13
950 4221 2.601702 TTTCATCCAGAGCCCGCCA 61.602 57.895 0.00 0.00 0.00 5.69
951 4222 2.135903 TTTCATCCAGAGCCCGCCAA 62.136 55.000 0.00 0.00 0.00 4.52
952 4223 1.925285 TTCATCCAGAGCCCGCCAAT 61.925 55.000 0.00 0.00 0.00 3.16
953 4224 1.053835 TCATCCAGAGCCCGCCAATA 61.054 55.000 0.00 0.00 0.00 1.90
954 4225 0.037303 CATCCAGAGCCCGCCAATAT 59.963 55.000 0.00 0.00 0.00 1.28
955 4226 0.326264 ATCCAGAGCCCGCCAATATC 59.674 55.000 0.00 0.00 0.00 1.63
956 4227 0.764369 TCCAGAGCCCGCCAATATCT 60.764 55.000 0.00 0.00 0.00 1.98
957 4228 0.321122 CCAGAGCCCGCCAATATCTC 60.321 60.000 0.00 0.00 0.00 2.75
963 4245 1.067060 GCCCGCCAATATCTCCAAAAC 59.933 52.381 0.00 0.00 0.00 2.43
965 4247 2.618709 CCCGCCAATATCTCCAAAACTC 59.381 50.000 0.00 0.00 0.00 3.01
1019 4303 3.825014 GAGATGGATGGTATGCTTGCATT 59.175 43.478 13.52 0.00 0.00 3.56
1037 4326 7.255520 GCTTGCATTTATGATCCATCTCTCTTT 60.256 37.037 0.00 0.00 0.00 2.52
1062 4355 6.515272 TTAATCATTCTTGGTTTCTCCTGC 57.485 37.500 0.00 0.00 37.07 4.85
1069 4362 0.324943 TGGTTTCTCCTGCTGGTAGC 59.675 55.000 9.73 4.67 42.82 3.58
1093 4398 3.935203 TGTTCTGCTTACTATTCTGCTGC 59.065 43.478 0.00 0.00 0.00 5.25
1099 4404 5.643664 TGCTTACTATTCTGCTGCAAATTG 58.356 37.500 3.02 9.84 0.00 2.32
1145 4450 5.972935 TGTTCTTCCTTGGTTTCTTTTTCC 58.027 37.500 0.00 0.00 0.00 3.13
1151 4456 1.694844 TGGTTTCTTTTTCCCCGTCC 58.305 50.000 0.00 0.00 0.00 4.79
1256 4564 2.936202 TCCATGGCAAAGGCTCTATTC 58.064 47.619 6.96 0.00 40.87 1.75
1290 4609 2.108344 TTTTTGTTCGGGTCTCGCGC 62.108 55.000 0.00 0.00 39.60 6.86
1308 4627 3.502237 CAGTTTTGCCTGCCATGTC 57.498 52.632 0.00 0.00 0.00 3.06
1309 4628 0.675083 CAGTTTTGCCTGCCATGTCA 59.325 50.000 0.00 0.00 0.00 3.58
1310 4629 0.675633 AGTTTTGCCTGCCATGTCAC 59.324 50.000 0.00 0.00 0.00 3.67
1311 4630 0.319813 GTTTTGCCTGCCATGTCACC 60.320 55.000 0.00 0.00 0.00 4.02
1312 4631 0.758310 TTTTGCCTGCCATGTCACCA 60.758 50.000 0.00 0.00 0.00 4.17
1313 4632 0.758310 TTTGCCTGCCATGTCACCAA 60.758 50.000 0.00 0.00 0.00 3.67
1317 4636 1.843368 CCTGCCATGTCACCAAGATT 58.157 50.000 0.00 0.00 0.00 2.40
1342 4661 2.877168 CTCTGCTATTTCCCTGTCATGC 59.123 50.000 0.00 0.00 0.00 4.06
1491 4820 0.030101 CGATCTCGAGTTCCTCTGCC 59.970 60.000 13.13 0.00 43.02 4.85
1492 4821 1.107114 GATCTCGAGTTCCTCTGCCA 58.893 55.000 13.13 0.00 0.00 4.92
1889 8101 2.948979 TCAAGTTTCGGCTTGATGTTGT 59.051 40.909 11.83 0.00 46.74 3.32
1890 8102 3.380004 TCAAGTTTCGGCTTGATGTTGTT 59.620 39.130 11.83 0.00 46.74 2.83
1997 8235 3.370840 TGGATCATTTTGGAGTCTGGG 57.629 47.619 0.00 0.00 0.00 4.45
2005 8243 3.474570 GGAGTCTGGGGATGCGCT 61.475 66.667 9.73 0.00 0.00 5.92
2021 8259 2.041244 GCGCTGTTTTGTTTAGTTCCG 58.959 47.619 0.00 0.00 0.00 4.30
2215 12981 4.343814 TGACTGTCTGTATGAACTTGGACA 59.656 41.667 9.51 0.00 33.19 4.02
2217 12983 4.345257 ACTGTCTGTATGAACTTGGACAGT 59.655 41.667 17.22 17.22 45.27 3.55
2269 13036 4.259356 GGTTGGAACCTAGTTATGTGACC 58.741 47.826 0.98 0.00 45.75 4.02
2283 13050 6.261381 AGTTATGTGACCGAGAGACTCTATTC 59.739 42.308 4.57 2.95 0.00 1.75
2306 13307 5.105351 TCCGTGAGCAGAATTTCTCATTCTA 60.105 40.000 0.00 0.00 40.89 2.10
2309 13310 6.700960 CGTGAGCAGAATTTCTCATTCTAGAT 59.299 38.462 0.00 0.00 40.89 1.98
2328 13333 2.519002 TGCGTTAGTAATTTGCAGCG 57.481 45.000 4.02 0.00 0.00 5.18
2335 13522 5.449304 GTTAGTAATTTGCAGCGAGTTGTT 58.551 37.500 0.54 0.00 0.00 2.83
2482 13819 3.160777 AGTCCGAACGACATGGTAATC 57.839 47.619 0.00 0.00 44.66 1.75
2507 13844 3.578688 CCTCCATAACAAAACTGCAAGC 58.421 45.455 0.00 0.00 37.60 4.01
2515 13852 3.374745 ACAAAACTGCAAGCAATTCGAG 58.625 40.909 0.00 0.00 37.60 4.04
2554 13942 0.690762 TTTGGAGGGAGGGAAACGAG 59.309 55.000 0.00 0.00 0.00 4.18
2618 14016 4.147449 CTGCGTCGATCCTGCCCA 62.147 66.667 0.00 0.00 0.00 5.36
2625 14023 3.415087 GATCCTGCCCACCTGCCT 61.415 66.667 0.00 0.00 0.00 4.75
2626 14024 3.711059 GATCCTGCCCACCTGCCTG 62.711 68.421 0.00 0.00 0.00 4.85
2742 14163 0.242017 GCAGCAGGACGAGCAAAAAT 59.758 50.000 0.00 0.00 0.00 1.82
2743 14164 1.336240 GCAGCAGGACGAGCAAAAATT 60.336 47.619 0.00 0.00 0.00 1.82
2748 14169 1.804748 AGGACGAGCAAAAATTCCGTC 59.195 47.619 0.00 0.00 45.98 4.79
2754 14175 3.667960 CGAGCAAAAATTCCGTCTCTTGG 60.668 47.826 0.00 0.00 0.00 3.61
2756 14177 2.296190 GCAAAAATTCCGTCTCTTGGGT 59.704 45.455 0.00 0.00 0.00 4.51
2757 14178 3.611766 GCAAAAATTCCGTCTCTTGGGTC 60.612 47.826 0.00 0.00 0.00 4.46
2786 14207 2.125912 CCTGGCCGAGACGAACAG 60.126 66.667 0.00 0.00 33.04 3.16
2866 15102 5.006386 TCTTTCTTGGAGATCTTTTGGCTC 58.994 41.667 0.00 0.00 0.00 4.70
2880 15116 3.389206 GCTCTAGCCTTTGCGTCG 58.611 61.111 0.00 0.00 44.33 5.12
2881 15117 1.153823 GCTCTAGCCTTTGCGTCGA 60.154 57.895 0.00 0.00 44.33 4.20
2882 15118 0.736325 GCTCTAGCCTTTGCGTCGAA 60.736 55.000 0.00 0.00 44.33 3.71
2883 15119 1.927895 CTCTAGCCTTTGCGTCGAAT 58.072 50.000 0.00 0.00 44.33 3.34
2884 15120 1.855360 CTCTAGCCTTTGCGTCGAATC 59.145 52.381 0.00 0.00 44.33 2.52
2885 15121 1.203758 TCTAGCCTTTGCGTCGAATCA 59.796 47.619 0.00 0.00 44.33 2.57
2886 15122 1.590238 CTAGCCTTTGCGTCGAATCAG 59.410 52.381 0.00 0.00 44.33 2.90
2887 15123 0.320771 AGCCTTTGCGTCGAATCAGT 60.321 50.000 0.00 0.00 44.33 3.41
2888 15124 0.179215 GCCTTTGCGTCGAATCAGTG 60.179 55.000 0.00 0.00 0.00 3.66
2889 15125 1.428448 CCTTTGCGTCGAATCAGTGA 58.572 50.000 0.00 0.00 0.00 3.41
2890 15126 1.126846 CCTTTGCGTCGAATCAGTGAC 59.873 52.381 0.00 0.00 0.00 3.67
2891 15127 1.792367 CTTTGCGTCGAATCAGTGACA 59.208 47.619 0.00 0.00 34.78 3.58
2892 15128 1.859383 TTGCGTCGAATCAGTGACAA 58.141 45.000 0.00 0.00 34.78 3.18
2893 15129 1.136690 TGCGTCGAATCAGTGACAAC 58.863 50.000 0.00 0.00 34.78 3.32
2894 15130 0.091344 GCGTCGAATCAGTGACAACG 59.909 55.000 0.00 4.58 34.78 4.10
2895 15131 1.405461 CGTCGAATCAGTGACAACGT 58.595 50.000 0.00 0.00 34.78 3.99
2896 15132 1.382419 CGTCGAATCAGTGACAACGTC 59.618 52.381 0.00 0.00 34.78 4.34
2897 15133 1.382419 GTCGAATCAGTGACAACGTCG 59.618 52.381 0.00 0.41 34.95 5.12
2898 15134 1.002142 TCGAATCAGTGACAACGTCGT 60.002 47.619 0.00 0.00 34.95 4.34
2899 15135 2.223845 TCGAATCAGTGACAACGTCGTA 59.776 45.455 0.00 0.00 34.95 3.43
2900 15136 3.120095 TCGAATCAGTGACAACGTCGTAT 60.120 43.478 0.00 0.00 34.95 3.06
2901 15137 4.093261 TCGAATCAGTGACAACGTCGTATA 59.907 41.667 0.00 0.00 34.95 1.47
2902 15138 4.968181 CGAATCAGTGACAACGTCGTATAT 59.032 41.667 0.00 0.00 34.95 0.86
2903 15139 5.108742 CGAATCAGTGACAACGTCGTATATG 60.109 44.000 0.00 0.00 34.95 1.78
2904 15140 4.950434 TCAGTGACAACGTCGTATATGA 57.050 40.909 0.00 0.00 34.95 2.15
2905 15141 5.494632 TCAGTGACAACGTCGTATATGAT 57.505 39.130 0.00 0.00 34.95 2.45
2906 15142 5.507974 TCAGTGACAACGTCGTATATGATC 58.492 41.667 0.00 0.00 34.95 2.92
2907 15143 5.296035 TCAGTGACAACGTCGTATATGATCT 59.704 40.000 0.00 0.00 34.95 2.75
2908 15144 5.971792 CAGTGACAACGTCGTATATGATCTT 59.028 40.000 0.00 0.00 34.95 2.40
2909 15145 5.971792 AGTGACAACGTCGTATATGATCTTG 59.028 40.000 0.00 5.65 34.95 3.02
2910 15146 4.738252 TGACAACGTCGTATATGATCTTGC 59.262 41.667 0.00 7.58 34.95 4.01
2911 15147 4.933330 ACAACGTCGTATATGATCTTGCT 58.067 39.130 0.00 1.94 0.00 3.91
2912 15148 4.976731 ACAACGTCGTATATGATCTTGCTC 59.023 41.667 0.00 0.00 0.00 4.26
2913 15149 5.215903 CAACGTCGTATATGATCTTGCTCT 58.784 41.667 0.00 0.00 0.00 4.09
2914 15150 4.788690 ACGTCGTATATGATCTTGCTCTG 58.211 43.478 0.00 0.00 0.00 3.35
2915 15151 3.605916 CGTCGTATATGATCTTGCTCTGC 59.394 47.826 0.00 0.00 0.00 4.26
2916 15152 4.550422 GTCGTATATGATCTTGCTCTGCA 58.450 43.478 0.00 0.00 36.47 4.41
2917 15153 5.167121 GTCGTATATGATCTTGCTCTGCAT 58.833 41.667 0.00 0.00 38.76 3.96
2918 15154 5.636965 GTCGTATATGATCTTGCTCTGCATT 59.363 40.000 0.00 0.00 38.76 3.56
2919 15155 6.146837 GTCGTATATGATCTTGCTCTGCATTT 59.853 38.462 0.00 0.00 38.76 2.32
2920 15156 6.707608 TCGTATATGATCTTGCTCTGCATTTT 59.292 34.615 0.00 0.00 38.76 1.82
2921 15157 6.795593 CGTATATGATCTTGCTCTGCATTTTG 59.204 38.462 0.00 0.00 38.76 2.44
2922 15158 3.226346 TGATCTTGCTCTGCATTTTGC 57.774 42.857 0.00 0.00 45.29 3.68
2923 15159 2.823747 TGATCTTGCTCTGCATTTTGCT 59.176 40.909 0.75 0.00 45.31 3.91
2924 15160 2.717580 TCTTGCTCTGCATTTTGCTG 57.282 45.000 0.75 0.60 45.31 4.41
2925 15161 1.068474 CTTGCTCTGCATTTTGCTGC 58.932 50.000 0.75 0.00 45.31 5.25
2926 15162 0.320073 TTGCTCTGCATTTTGCTGCC 60.320 50.000 0.00 0.00 45.31 4.85
2927 15163 1.290955 GCTCTGCATTTTGCTGCCA 59.709 52.632 0.00 0.00 45.31 4.92
2928 15164 0.320073 GCTCTGCATTTTGCTGCCAA 60.320 50.000 0.00 0.00 45.31 4.52
2929 15165 1.710013 CTCTGCATTTTGCTGCCAAG 58.290 50.000 0.00 0.00 45.31 3.61
2930 15166 1.271379 CTCTGCATTTTGCTGCCAAGA 59.729 47.619 0.00 0.00 45.31 3.02
2931 15167 1.897133 TCTGCATTTTGCTGCCAAGAT 59.103 42.857 0.00 0.00 45.31 2.40
2932 15168 2.300723 TCTGCATTTTGCTGCCAAGATT 59.699 40.909 0.00 0.00 45.31 2.40
2933 15169 3.071479 CTGCATTTTGCTGCCAAGATTT 58.929 40.909 0.00 0.00 45.31 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.201494 CTCCAGGACGAGCACGAT 58.799 61.111 11.40 0.00 42.66 3.73
115 116 3.839432 CCTCCTTCTCCCCGACGC 61.839 72.222 0.00 0.00 0.00 5.19
274 277 1.597742 ATCAACGCTGATGTATGCCC 58.402 50.000 0.00 0.00 40.94 5.36
322 325 1.632018 CCCTTCACCATCGGCCCTAA 61.632 60.000 0.00 0.00 0.00 2.69
447 452 1.593296 GGCTCTGGAACTACGACCGT 61.593 60.000 0.00 0.00 0.00 4.83
492 497 1.275291 CAAACCCTAGCCTCGAACTCA 59.725 52.381 0.00 0.00 0.00 3.41
515 521 2.615493 GGCCTCTTCAAAATCCGACAGA 60.615 50.000 0.00 0.00 0.00 3.41
547 553 2.646175 CGTCGTCCACACTCCCCAT 61.646 63.158 0.00 0.00 0.00 4.00
583 589 2.344025 GTCGCGGTCCTTCTTAAATGT 58.656 47.619 6.13 0.00 0.00 2.71
612 618 1.009900 GCTCAGTACGATCGGACGG 60.010 63.158 24.17 23.45 37.61 4.79
613 619 1.367782 CGCTCAGTACGATCGGACG 60.368 63.158 24.17 18.40 33.32 4.79
614 620 0.098376 AACGCTCAGTACGATCGGAC 59.902 55.000 23.21 23.21 37.57 4.79
615 621 0.806868 AAACGCTCAGTACGATCGGA 59.193 50.000 20.98 8.41 37.57 4.55
616 622 1.320555 CAAAACGCTCAGTACGATCGG 59.679 52.381 20.98 0.89 37.57 4.18
617 623 1.320555 CCAAAACGCTCAGTACGATCG 59.679 52.381 14.88 14.88 39.16 3.69
624 630 1.748493 TGCTTTTCCAAAACGCTCAGT 59.252 42.857 3.14 0.00 0.00 3.41
625 631 2.490328 TGCTTTTCCAAAACGCTCAG 57.510 45.000 3.14 0.00 0.00 3.35
655 662 7.298854 GGACAGTAAAATAGACTGCTTGTTTC 58.701 38.462 2.76 0.00 46.85 2.78
728 1104 5.299279 CAGCCTTTTCAGGTTTCAGTTTCTA 59.701 40.000 0.00 0.00 43.18 2.10
782 1159 2.203549 TATGCATGGACGGGTGGCAA 62.204 55.000 10.16 0.00 38.08 4.52
799 1187 3.744214 CGGTCAAGGTGGTACATGCATAT 60.744 47.826 0.00 0.00 44.52 1.78
801 1189 1.678728 CGGTCAAGGTGGTACATGCAT 60.679 52.381 0.00 0.00 44.52 3.96
802 1190 0.321210 CGGTCAAGGTGGTACATGCA 60.321 55.000 0.00 0.00 44.52 3.96
803 1191 0.036765 TCGGTCAAGGTGGTACATGC 60.037 55.000 0.00 0.00 44.52 4.06
867 1263 1.126846 CTACTTTATATGCAGCGCCGC 59.873 52.381 9.12 9.12 0.00 6.53
868 1264 1.726791 CCTACTTTATATGCAGCGCCG 59.273 52.381 2.29 0.00 0.00 6.46
869 1265 1.464997 GCCTACTTTATATGCAGCGCC 59.535 52.381 2.29 0.00 0.00 6.53
870 1266 1.126846 CGCCTACTTTATATGCAGCGC 59.873 52.381 0.00 0.00 35.58 5.92
947 4218 3.885901 GGAGGAGTTTTGGAGATATTGGC 59.114 47.826 0.00 0.00 0.00 4.52
948 4219 4.130118 CGGAGGAGTTTTGGAGATATTGG 58.870 47.826 0.00 0.00 0.00 3.16
949 4220 4.572389 CACGGAGGAGTTTTGGAGATATTG 59.428 45.833 0.00 0.00 0.00 1.90
950 4221 4.384208 CCACGGAGGAGTTTTGGAGATATT 60.384 45.833 0.00 0.00 41.22 1.28
951 4222 3.134804 CCACGGAGGAGTTTTGGAGATAT 59.865 47.826 0.00 0.00 41.22 1.63
952 4223 2.500098 CCACGGAGGAGTTTTGGAGATA 59.500 50.000 0.00 0.00 41.22 1.98
953 4224 1.279271 CCACGGAGGAGTTTTGGAGAT 59.721 52.381 0.00 0.00 41.22 2.75
954 4225 0.685097 CCACGGAGGAGTTTTGGAGA 59.315 55.000 0.00 0.00 41.22 3.71
955 4226 0.396811 ACCACGGAGGAGTTTTGGAG 59.603 55.000 2.94 0.00 41.22 3.86
956 4227 0.841289 AACCACGGAGGAGTTTTGGA 59.159 50.000 2.94 0.00 41.22 3.53
957 4228 2.423577 CTAACCACGGAGGAGTTTTGG 58.576 52.381 2.94 0.00 41.22 3.28
963 4245 1.272807 TTTCCCTAACCACGGAGGAG 58.727 55.000 2.94 0.00 41.22 3.69
965 4247 1.626825 TCTTTTCCCTAACCACGGAGG 59.373 52.381 0.00 0.00 45.67 4.30
1037 4326 8.055181 AGCAGGAGAAACCAAGAATGATTAATA 58.945 33.333 0.00 0.00 42.04 0.98
1062 4355 3.931578 AGTAAGCAGAACAAGCTACCAG 58.068 45.455 0.00 0.00 42.53 4.00
1069 4362 5.447010 GCAGCAGAATAGTAAGCAGAACAAG 60.447 44.000 0.00 0.00 0.00 3.16
1093 4398 4.201950 CCGGAGATCTTAAGCACCAATTTG 60.202 45.833 0.00 0.00 0.00 2.32
1099 4404 2.365617 TCATCCGGAGATCTTAAGCACC 59.634 50.000 11.34 0.00 0.00 5.01
1151 4456 0.318275 GATTGCTCTACGGCGAGGAG 60.318 60.000 16.62 20.17 32.82 3.69
1159 4464 5.613358 AAAGGAAACAAGATTGCTCTACG 57.387 39.130 0.00 0.00 29.97 3.51
1256 4564 0.756294 AAAAAGGCCAAGAAACCCCG 59.244 50.000 5.01 0.00 0.00 5.73
1290 4609 0.675083 TGACATGGCAGGCAAAACTG 59.325 50.000 0.00 0.00 41.41 3.16
1301 4620 2.028748 AGCAAAATCTTGGTGACATGGC 60.029 45.455 0.00 0.00 41.66 4.40
1302 4621 3.508793 AGAGCAAAATCTTGGTGACATGG 59.491 43.478 0.00 0.00 43.24 3.66
1303 4622 4.482386 CAGAGCAAAATCTTGGTGACATG 58.518 43.478 0.00 0.00 43.24 3.21
1304 4623 3.057033 GCAGAGCAAAATCTTGGTGACAT 60.057 43.478 0.00 0.00 43.24 3.06
1305 4624 2.294233 GCAGAGCAAAATCTTGGTGACA 59.706 45.455 0.00 0.00 43.24 3.58
1306 4625 2.555757 AGCAGAGCAAAATCTTGGTGAC 59.444 45.455 0.00 0.00 43.24 3.67
1307 4626 2.867624 AGCAGAGCAAAATCTTGGTGA 58.132 42.857 0.00 0.00 43.24 4.02
1308 4627 4.978083 ATAGCAGAGCAAAATCTTGGTG 57.022 40.909 0.00 0.00 43.24 4.17
1309 4628 5.105595 GGAAATAGCAGAGCAAAATCTTGGT 60.106 40.000 0.00 0.00 45.82 3.67
1310 4629 5.346522 GGAAATAGCAGAGCAAAATCTTGG 58.653 41.667 0.00 0.00 32.76 3.61
1311 4630 5.126707 AGGGAAATAGCAGAGCAAAATCTTG 59.873 40.000 0.00 0.00 35.49 3.02
1312 4631 5.126707 CAGGGAAATAGCAGAGCAAAATCTT 59.873 40.000 0.00 0.00 0.00 2.40
1313 4632 4.643784 CAGGGAAATAGCAGAGCAAAATCT 59.356 41.667 0.00 0.00 0.00 2.40
1317 4636 3.244875 TGACAGGGAAATAGCAGAGCAAA 60.245 43.478 0.00 0.00 0.00 3.68
1342 4661 7.600065 ACAAGAAGATGATCAAATCTTTGTGG 58.400 34.615 11.86 7.24 44.96 4.17
1451 4780 0.808125 TTATGAACATGCGTGTGGGC 59.192 50.000 13.39 6.12 38.92 5.36
1458 4787 3.914364 TCGAGATCGATTATGAACATGCG 59.086 43.478 0.00 0.00 44.22 4.73
1491 4820 1.437089 CGAACGCAAGAACACGCTG 60.437 57.895 0.00 0.00 43.62 5.18
1492 4821 2.928361 CGAACGCAAGAACACGCT 59.072 55.556 0.00 0.00 43.62 5.07
1640 7842 1.890510 GAACAAGGCGTGGAACCGT 60.891 57.895 5.22 0.00 0.00 4.83
1644 7852 1.153066 TGCAGAACAAGGCGTGGAA 60.153 52.632 5.22 0.00 0.00 3.53
1889 8101 1.353804 GGCACTGACGAAAACGCAA 59.646 52.632 0.00 0.00 0.00 4.85
1890 8102 1.815840 TGGCACTGACGAAAACGCA 60.816 52.632 0.00 0.00 0.00 5.24
1997 8235 3.282831 ACTAAACAAAACAGCGCATCC 57.717 42.857 11.47 0.00 0.00 3.51
2005 8243 4.034742 GCAGAGTCGGAACTAAACAAAACA 59.965 41.667 0.00 0.00 35.28 2.83
2021 8259 9.863845 AATTTCTAACTTAAGAGTAGCAGAGTC 57.136 33.333 10.09 0.00 34.21 3.36
2172 12886 1.471119 AAGCTGCTGCATGCTACAAT 58.529 45.000 20.33 5.76 43.37 2.71
2215 12981 7.814587 GGCTTCTGCTAAACAAATTCAAATACT 59.185 33.333 0.00 0.00 39.59 2.12
2217 12983 7.895759 AGGCTTCTGCTAAACAAATTCAAATA 58.104 30.769 0.00 0.00 39.59 1.40
2269 13036 2.032377 GCTCACGGAATAGAGTCTCTCG 60.032 54.545 5.39 6.39 35.36 4.04
2283 13050 3.937706 AGAATGAGAAATTCTGCTCACGG 59.062 43.478 0.00 0.00 43.26 4.94
2306 13307 3.242413 CGCTGCAAATTACTAACGCATCT 60.242 43.478 0.00 0.00 31.10 2.90
2309 13310 2.070028 TCGCTGCAAATTACTAACGCA 58.930 42.857 0.00 0.00 0.00 5.24
2328 13333 4.992381 AAGCGTAGTGATTGAACAACTC 57.008 40.909 0.00 0.00 0.00 3.01
2335 13522 4.319477 GCACAGAAAAAGCGTAGTGATTGA 60.319 41.667 0.00 0.00 0.00 2.57
2482 13819 2.094545 GCAGTTTTGTTATGGAGGCAGG 60.095 50.000 0.00 0.00 0.00 4.85
2507 13844 3.904136 ACCTTTCTTGCACTCGAATTG 57.096 42.857 0.00 0.00 0.00 2.32
2515 13852 1.234615 TGCGGCTACCTTTCTTGCAC 61.235 55.000 0.00 0.00 0.00 4.57
2554 13942 6.708054 TGATGAACTGTCTCCTTTTTCTCTTC 59.292 38.462 0.00 0.00 0.00 2.87
2625 14023 0.321919 GATGCTCTGTCCCTGTTGCA 60.322 55.000 0.00 0.00 34.88 4.08
2626 14024 0.035630 AGATGCTCTGTCCCTGTTGC 60.036 55.000 0.00 0.00 0.00 4.17
2627 14025 1.406614 GGAGATGCTCTGTCCCTGTTG 60.407 57.143 0.00 0.00 30.87 3.33
2628 14026 0.908198 GGAGATGCTCTGTCCCTGTT 59.092 55.000 0.00 0.00 30.87 3.16
2633 14031 0.179124 GTCGTGGAGATGCTCTGTCC 60.179 60.000 0.00 0.00 37.82 4.02
2715 14136 2.268920 GTCCTGCTGCCGAATCCA 59.731 61.111 0.00 0.00 0.00 3.41
2733 14154 3.366374 CCCAAGAGACGGAATTTTTGCTC 60.366 47.826 0.00 0.00 0.00 4.26
2742 14163 0.178944 TCCTGACCCAAGAGACGGAA 60.179 55.000 0.00 0.00 0.00 4.30
2743 14164 0.612174 CTCCTGACCCAAGAGACGGA 60.612 60.000 0.00 0.00 0.00 4.69
2748 14169 1.830477 CTTCTCCTCCTGACCCAAGAG 59.170 57.143 0.00 0.00 0.00 2.85
2754 14175 4.470764 AGGCTTCTCCTCCTGACC 57.529 61.111 0.00 0.00 43.20 4.02
2757 14178 2.588989 GCCAGGCTTCTCCTCCTG 59.411 66.667 3.29 1.47 45.52 3.86
2773 14194 0.179184 GAGACTCTGTTCGTCTCGGC 60.179 60.000 4.65 0.00 45.34 5.54
2774 14195 3.980136 GAGACTCTGTTCGTCTCGG 57.020 57.895 4.65 0.00 45.34 4.63
2786 14207 6.591313 AAGAAAGAAACAAAGACGAGACTC 57.409 37.500 0.00 0.00 0.00 3.36
2866 15102 1.590238 CTGATTCGACGCAAAGGCTAG 59.410 52.381 0.00 0.00 38.10 3.42
2876 15112 1.382419 GACGTTGTCACTGATTCGACG 59.618 52.381 7.55 7.55 42.43 5.12
2877 15113 1.382419 CGACGTTGTCACTGATTCGAC 59.618 52.381 0.00 0.00 32.09 4.20
2878 15114 1.002142 ACGACGTTGTCACTGATTCGA 60.002 47.619 1.48 0.00 32.09 3.71
2879 15115 1.405461 ACGACGTTGTCACTGATTCG 58.595 50.000 1.48 0.00 32.09 3.34
2880 15116 5.969435 TCATATACGACGTTGTCACTGATTC 59.031 40.000 12.83 0.00 32.09 2.52
2881 15117 5.886992 TCATATACGACGTTGTCACTGATT 58.113 37.500 12.83 0.00 32.09 2.57
2882 15118 5.494632 TCATATACGACGTTGTCACTGAT 57.505 39.130 12.83 2.39 32.09 2.90
2883 15119 4.950434 TCATATACGACGTTGTCACTGA 57.050 40.909 12.83 10.50 32.09 3.41
2884 15120 5.511571 AGATCATATACGACGTTGTCACTG 58.488 41.667 12.83 8.31 32.09 3.66
2885 15121 5.752892 AGATCATATACGACGTTGTCACT 57.247 39.130 12.83 1.25 32.09 3.41
2886 15122 5.331607 GCAAGATCATATACGACGTTGTCAC 60.332 44.000 12.83 0.00 32.09 3.67
2887 15123 4.738252 GCAAGATCATATACGACGTTGTCA 59.262 41.667 12.83 1.85 32.09 3.58
2888 15124 4.976731 AGCAAGATCATATACGACGTTGTC 59.023 41.667 12.83 0.00 0.00 3.18
2889 15125 4.933330 AGCAAGATCATATACGACGTTGT 58.067 39.130 14.07 14.07 0.00 3.32
2890 15126 5.116225 CAGAGCAAGATCATATACGACGTTG 59.884 44.000 5.50 0.00 0.00 4.10
2891 15127 5.215903 CAGAGCAAGATCATATACGACGTT 58.784 41.667 5.50 0.00 0.00 3.99
2892 15128 4.788690 CAGAGCAAGATCATATACGACGT 58.211 43.478 5.52 5.52 0.00 4.34
2893 15129 3.605916 GCAGAGCAAGATCATATACGACG 59.394 47.826 0.00 0.00 0.00 5.12
2894 15130 4.550422 TGCAGAGCAAGATCATATACGAC 58.450 43.478 0.00 0.00 34.76 4.34
2895 15131 4.853924 TGCAGAGCAAGATCATATACGA 57.146 40.909 0.00 0.00 34.76 3.43
2896 15132 6.477669 AAATGCAGAGCAAGATCATATACG 57.522 37.500 0.00 0.00 43.62 3.06
2897 15133 6.581542 GCAAAATGCAGAGCAAGATCATATAC 59.418 38.462 0.00 0.00 43.62 1.47
2898 15134 6.675026 GCAAAATGCAGAGCAAGATCATATA 58.325 36.000 0.00 0.00 43.62 0.86
2899 15135 5.529791 GCAAAATGCAGAGCAAGATCATAT 58.470 37.500 0.00 0.00 43.62 1.78
2900 15136 4.928601 GCAAAATGCAGAGCAAGATCATA 58.071 39.130 0.00 0.00 43.62 2.15
2901 15137 3.782046 GCAAAATGCAGAGCAAGATCAT 58.218 40.909 0.00 0.00 43.62 2.45
2902 15138 3.226346 GCAAAATGCAGAGCAAGATCA 57.774 42.857 0.00 0.00 43.62 2.92


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

AutoCloner maintained by Alex Coulton.