Multiple sequence alignment - TraesCS5A01G382200

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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 TraesCS5A01G382200 chr5A 100.000 2336 0 0 1 2336 580213291 580210956 0.000000e+00 4314.0
1 TraesCS5A01G382200 chr5A 83.844 947 138 9 541 1483 580200999 580200064 0.000000e+00 887.0
2 TraesCS5A01G382200 chr5A 85.146 855 117 5 540 1387 579326078 579326929 0.000000e+00 867.0
3 TraesCS5A01G382200 chr5A 93.023 172 11 1 351 521 579325804 579325975 1.390000e-62 250.0
4 TraesCS5A01G382200 chr5A 87.678 211 26 0 311 521 579399906 579400116 1.790000e-61 246.0
5 TraesCS5A01G382200 chr5A 90.476 42 4 0 1954 1995 579246306 579246347 3.240000e-04 56.5
6 TraesCS5A01G382200 chr5B 88.443 1419 128 13 548 1954 565512260 565510866 0.000000e+00 1679.0
7 TraesCS5A01G382200 chr5B 83.991 1268 174 19 540 1797 565686972 565685724 0.000000e+00 1190.0
8 TraesCS5A01G382200 chr5B 81.799 1434 225 27 540 1954 565546353 565544937 0.000000e+00 1170.0
9 TraesCS5A01G382200 chr5B 86.247 858 109 5 628 1483 565508763 565507913 0.000000e+00 922.0
10 TraesCS5A01G382200 chr5B 83.036 1008 153 13 540 1540 565502505 565501509 0.000000e+00 898.0
11 TraesCS5A01G382200 chr5B 85.238 840 111 8 588 1419 565492787 565491953 0.000000e+00 852.0
12 TraesCS5A01G382200 chr5B 85.062 482 36 13 94 542 565687532 565687054 2.120000e-125 459.0
13 TraesCS5A01G382200 chr5B 87.563 394 18 8 1950 2336 565510752 565510383 5.970000e-116 427.0
14 TraesCS5A01G382200 chr5B 88.655 238 26 1 302 538 565512591 565512354 2.940000e-74 289.0
15 TraesCS5A01G382200 chr5B 87.288 236 22 4 314 542 565493151 565492917 1.780000e-66 263.0
16 TraesCS5A01G382200 chr5B 91.192 193 17 0 345 537 565546632 565546440 1.780000e-66 263.0
17 TraesCS5A01G382200 chr5B 90.110 182 18 0 361 542 565426227 565426046 1.080000e-58 237.0
18 TraesCS5A01G382200 chr5B 86.538 208 28 0 314 521 565099546 565099339 1.810000e-56 230.0
19 TraesCS5A01G382200 chr5B 86.842 152 18 2 1658 1807 565491806 565491655 3.990000e-38 169.0
20 TraesCS5A01G382200 chr5D 90.360 861 80 2 548 1405 460072769 460071909 0.000000e+00 1127.0
21 TraesCS5A01G382200 chr5D 91.603 524 36 5 1437 1954 460071909 460071388 0.000000e+00 717.0
22 TraesCS5A01G382200 chr5D 91.139 395 18 3 1949 2336 460071244 460070860 9.570000e-144 520.0
23 TraesCS5A01G382200 chr5D 90.206 194 16 3 351 542 460061643 460061451 1.390000e-62 250.0
24 TraesCS5A01G382200 chr5D 79.012 405 52 15 1556 1952 460068058 460067679 1.790000e-61 246.0
25 TraesCS5A01G382200 chr4A 95.238 84 4 0 1 84 514347151 514347234 1.460000e-27 134.0


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 TraesCS5A01G382200 chr5A 580210956 580213291 2335 True 4314.00 4314 100.0000 1 2336 1 chr5A.!!$R2 2335
1 TraesCS5A01G382200 chr5A 580200064 580200999 935 True 887.00 887 83.8440 541 1483 1 chr5A.!!$R1 942
2 TraesCS5A01G382200 chr5A 579325804 579326929 1125 False 558.50 867 89.0845 351 1387 2 chr5A.!!$F3 1036
3 TraesCS5A01G382200 chr5B 565501509 565502505 996 True 898.00 898 83.0360 540 1540 1 chr5B.!!$R3 1000
4 TraesCS5A01G382200 chr5B 565507913 565512591 4678 True 829.25 1679 87.7270 302 2336 4 chr5B.!!$R5 2034
5 TraesCS5A01G382200 chr5B 565685724 565687532 1808 True 824.50 1190 84.5265 94 1797 2 chr5B.!!$R7 1703
6 TraesCS5A01G382200 chr5B 565544937 565546632 1695 True 716.50 1170 86.4955 345 1954 2 chr5B.!!$R6 1609
7 TraesCS5A01G382200 chr5B 565491655 565493151 1496 True 428.00 852 86.4560 314 1807 3 chr5B.!!$R4 1493
8 TraesCS5A01G382200 chr5D 460067679 460072769 5090 True 652.50 1127 88.0285 548 2336 4 chr5D.!!$R2 1788

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
155 156 0.032815 GAAGAGATAGGCCACGGAGC 59.967 60.0 5.01 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 6090 0.100682 TAGCTCTGACGCGTTCATCC 59.899 55.0 15.53 0.0 32.17 3.51 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
34 35 7.596749 AATGACCGTATTGACTAAGTTCTTG 57.403 36.000 0.00 0.00 0.00 3.02
35 36 6.335471 TGACCGTATTGACTAAGTTCTTGA 57.665 37.500 0.00 0.00 0.00 3.02
36 37 6.387465 TGACCGTATTGACTAAGTTCTTGAG 58.613 40.000 0.00 0.00 0.00 3.02
37 38 6.015688 TGACCGTATTGACTAAGTTCTTGAGT 60.016 38.462 0.00 0.00 0.00 3.41
38 39 7.175467 TGACCGTATTGACTAAGTTCTTGAGTA 59.825 37.037 0.00 0.00 0.00 2.59
39 40 8.064336 ACCGTATTGACTAAGTTCTTGAGTAT 57.936 34.615 0.00 0.00 0.00 2.12
40 41 9.182214 ACCGTATTGACTAAGTTCTTGAGTATA 57.818 33.333 0.00 0.00 0.00 1.47
41 42 9.666626 CCGTATTGACTAAGTTCTTGAGTATAG 57.333 37.037 0.00 0.00 0.00 1.31
42 43 9.666626 CGTATTGACTAAGTTCTTGAGTATAGG 57.333 37.037 0.00 0.00 0.00 2.57
47 48 9.702253 TGACTAAGTTCTTGAGTATAGGAATCT 57.298 33.333 0.00 0.00 0.00 2.40
53 54 9.702253 AGTTCTTGAGTATAGGAATCTAAGTGA 57.298 33.333 0.00 0.00 0.00 3.41
56 57 8.915036 TCTTGAGTATAGGAATCTAAGTGAACC 58.085 37.037 0.00 0.00 0.00 3.62
57 58 8.603898 TTGAGTATAGGAATCTAAGTGAACCA 57.396 34.615 0.00 0.00 0.00 3.67
58 59 8.239038 TGAGTATAGGAATCTAAGTGAACCAG 57.761 38.462 0.00 0.00 0.00 4.00
59 60 7.056844 AGTATAGGAATCTAAGTGAACCAGC 57.943 40.000 0.00 0.00 0.00 4.85
60 61 5.957771 ATAGGAATCTAAGTGAACCAGCA 57.042 39.130 0.00 0.00 0.00 4.41
61 62 4.640771 AGGAATCTAAGTGAACCAGCAA 57.359 40.909 0.00 0.00 0.00 3.91
62 63 4.583871 AGGAATCTAAGTGAACCAGCAAG 58.416 43.478 0.00 0.00 0.00 4.01
63 64 4.287067 AGGAATCTAAGTGAACCAGCAAGA 59.713 41.667 0.00 0.00 0.00 3.02
64 65 5.045286 AGGAATCTAAGTGAACCAGCAAGAT 60.045 40.000 0.00 0.00 0.00 2.40
65 66 6.156949 AGGAATCTAAGTGAACCAGCAAGATA 59.843 38.462 0.00 0.00 0.00 1.98
66 67 6.823689 GGAATCTAAGTGAACCAGCAAGATAA 59.176 38.462 0.00 0.00 0.00 1.75
67 68 7.011857 GGAATCTAAGTGAACCAGCAAGATAAG 59.988 40.741 0.00 0.00 0.00 1.73
68 69 6.360370 TCTAAGTGAACCAGCAAGATAAGT 57.640 37.500 0.00 0.00 0.00 2.24
69 70 7.476540 TCTAAGTGAACCAGCAAGATAAGTA 57.523 36.000 0.00 0.00 0.00 2.24
70 71 7.321153 TCTAAGTGAACCAGCAAGATAAGTAC 58.679 38.462 0.00 0.00 0.00 2.73
71 72 5.483685 AGTGAACCAGCAAGATAAGTACA 57.516 39.130 0.00 0.00 0.00 2.90
72 73 5.482908 AGTGAACCAGCAAGATAAGTACAG 58.517 41.667 0.00 0.00 0.00 2.74
73 74 5.012148 AGTGAACCAGCAAGATAAGTACAGT 59.988 40.000 0.00 0.00 0.00 3.55
74 75 5.120830 GTGAACCAGCAAGATAAGTACAGTG 59.879 44.000 0.00 0.00 0.00 3.66
75 76 5.011635 TGAACCAGCAAGATAAGTACAGTGA 59.988 40.000 0.00 0.00 0.00 3.41
76 77 4.822026 ACCAGCAAGATAAGTACAGTGAC 58.178 43.478 0.00 0.00 0.00 3.67
77 78 4.184629 CCAGCAAGATAAGTACAGTGACC 58.815 47.826 0.00 0.00 0.00 4.02
78 79 4.322725 CCAGCAAGATAAGTACAGTGACCA 60.323 45.833 0.00 0.00 0.00 4.02
79 80 5.423015 CAGCAAGATAAGTACAGTGACCAT 58.577 41.667 0.00 0.00 0.00 3.55
80 81 5.521735 CAGCAAGATAAGTACAGTGACCATC 59.478 44.000 0.00 0.00 0.00 3.51
81 82 5.187772 AGCAAGATAAGTACAGTGACCATCA 59.812 40.000 0.00 0.00 0.00 3.07
82 83 5.521735 GCAAGATAAGTACAGTGACCATCAG 59.478 44.000 0.00 0.00 0.00 2.90
83 84 6.634805 CAAGATAAGTACAGTGACCATCAGT 58.365 40.000 0.00 0.00 0.00 3.41
96 97 6.652481 AGTGACCATCAGTGAATTTTACTCAG 59.348 38.462 0.00 0.00 0.00 3.35
108 109 6.780031 TGAATTTTACTCAGGTGGAAATGGAA 59.220 34.615 0.00 0.00 0.00 3.53
114 115 5.336102 ACTCAGGTGGAAATGGAAATCAAT 58.664 37.500 0.00 0.00 0.00 2.57
122 123 6.697019 GTGGAAATGGAAATCAATGTATTCCG 59.303 38.462 12.50 0.00 44.48 4.30
124 125 6.697019 GGAAATGGAAATCAATGTATTCCGTG 59.303 38.462 12.64 0.00 44.48 4.94
125 126 7.403312 AAATGGAAATCAATGTATTCCGTGA 57.597 32.000 12.64 0.38 44.48 4.35
127 128 6.189677 TGGAAATCAATGTATTCCGTGAAC 57.810 37.500 12.50 0.00 44.48 3.18
148 149 0.386113 AGAACGCGAAGAGATAGGCC 59.614 55.000 15.93 0.00 0.00 5.19
149 150 0.102481 GAACGCGAAGAGATAGGCCA 59.898 55.000 15.93 0.00 0.00 5.36
150 151 0.179108 AACGCGAAGAGATAGGCCAC 60.179 55.000 15.93 0.00 0.00 5.01
152 153 1.300233 GCGAAGAGATAGGCCACGG 60.300 63.158 5.01 0.00 0.00 4.94
154 155 0.312416 CGAAGAGATAGGCCACGGAG 59.688 60.000 5.01 0.00 0.00 4.63
155 156 0.032815 GAAGAGATAGGCCACGGAGC 59.967 60.000 5.01 0.00 0.00 4.70
156 157 0.687757 AAGAGATAGGCCACGGAGCA 60.688 55.000 5.01 0.00 0.00 4.26
157 158 1.068250 GAGATAGGCCACGGAGCAC 59.932 63.158 5.01 0.00 0.00 4.40
233 240 2.031682 CGTTCAGTCTTTTCCTGGCTTG 60.032 50.000 0.00 0.00 0.00 4.01
259 266 2.754254 CCGCCCAAAACCCTAGCC 60.754 66.667 0.00 0.00 0.00 3.93
276 283 1.153628 CCGCCGTCCACTTTCCTAG 60.154 63.158 0.00 0.00 0.00 3.02
280 287 1.221021 CGTCCACTTTCCTAGCCCC 59.779 63.158 0.00 0.00 0.00 5.80
281 288 1.550130 CGTCCACTTTCCTAGCCCCA 61.550 60.000 0.00 0.00 0.00 4.96
282 289 0.035343 GTCCACTTTCCTAGCCCCAC 60.035 60.000 0.00 0.00 0.00 4.61
283 290 1.205460 TCCACTTTCCTAGCCCCACC 61.205 60.000 0.00 0.00 0.00 4.61
284 291 1.497309 CCACTTTCCTAGCCCCACCA 61.497 60.000 0.00 0.00 0.00 4.17
285 292 0.322546 CACTTTCCTAGCCCCACCAC 60.323 60.000 0.00 0.00 0.00 4.16
410 454 1.254975 TGAGCGGCTACCACTTGCTA 61.255 55.000 0.60 0.00 35.73 3.49
471 515 2.376808 CAAGTGGATCGACTCTTGCT 57.623 50.000 11.09 0.00 32.54 3.91
521 565 2.562298 TGTTCGTTACTATCCCAACGGT 59.438 45.455 6.97 0.00 45.70 4.83
543 671 1.293963 CGAGTCCGAGTACACCGACA 61.294 60.000 12.58 0.00 38.22 4.35
677 806 3.717400 GAGCATCTCCAGTACGATTCA 57.283 47.619 0.00 0.00 0.00 2.57
693 822 3.996363 CGATTCATTCACTGTCAAGGTCA 59.004 43.478 0.00 0.00 0.00 4.02
710 839 5.946942 AGGTCAATGTCACTATCATGAGT 57.053 39.130 0.09 0.00 0.00 3.41
753 884 2.927856 ATCCTGGTGCCACCGTCA 60.928 61.111 9.78 0.00 42.58 4.35
786 917 1.902508 CACTTAGGGCTTCTCCTGTCA 59.097 52.381 0.00 0.00 37.75 3.58
794 925 1.544314 GCTTCTCCTGTCAAGCAAGGT 60.544 52.381 0.00 0.00 43.87 3.50
903 1035 2.040813 AGAGCTCTTTGGGCTGATGAAA 59.959 45.455 11.45 0.00 40.40 2.69
946 1078 5.621422 CCATACGCATACATGACATTAAGC 58.379 41.667 0.00 0.00 0.00 3.09
1057 1195 3.174790 CTTGTTGCAGCAGACAAGC 57.825 52.632 24.79 5.38 44.14 4.01
1257 1395 4.514066 GGTTTCGAGCTTTTAACCAAGAGA 59.486 41.667 15.77 0.00 39.80 3.10
1361 1505 4.030216 TGAGGTTACAGTCCTGCATATCA 58.970 43.478 0.00 0.00 35.20 2.15
1378 1522 6.015010 TGCATATCATCATTTGCAATCATCCA 60.015 34.615 0.00 0.00 42.10 3.41
1416 1569 4.283363 AGACCCTGCATGCTATCTAATG 57.717 45.455 20.33 1.47 0.00 1.90
1464 1617 7.482169 TTCTGTATAGTCCTGTTCTCACAAT 57.518 36.000 0.00 0.00 30.36 2.71
1546 1705 5.492895 TGGTTTGACTATCTATGCGGAAAA 58.507 37.500 0.00 0.00 0.00 2.29
1547 1706 5.941058 TGGTTTGACTATCTATGCGGAAAAA 59.059 36.000 0.00 0.00 0.00 1.94
1610 1770 6.120220 ACTTGTAAGCCTTTCAACTAGTTGT 58.880 36.000 29.83 14.85 41.16 3.32
1713 5620 3.258372 CCCTTGTTCAGTACAGAGCACTA 59.742 47.826 4.29 0.00 38.19 2.74
1733 5640 6.313164 GCACTACTTATTTACCAGGTTCAGAC 59.687 42.308 0.00 0.00 0.00 3.51
1735 5642 8.041323 CACTACTTATTTACCAGGTTCAGACAT 58.959 37.037 0.00 0.00 0.00 3.06
1759 5669 3.581755 CATGTCTTGTTGAAATGCTGGG 58.418 45.455 0.00 0.00 34.02 4.45
1761 5671 3.030291 TGTCTTGTTGAAATGCTGGGTT 58.970 40.909 0.00 0.00 0.00 4.11
1827 5737 4.413495 TGCACGGCTACAAATTTTAGTC 57.587 40.909 0.00 0.00 0.00 2.59
1878 5794 7.439655 GCTAAGGTAGTGATCTTATGAAGGTTG 59.560 40.741 0.00 0.00 27.69 3.77
1879 5795 6.875972 AGGTAGTGATCTTATGAAGGTTGT 57.124 37.500 0.00 0.00 0.00 3.32
1931 5848 5.917087 ACAAGATTAGGATCCCATTTCCCTA 59.083 40.000 8.55 0.00 33.45 3.53
1977 6012 6.529125 CACTTGCGCAGAAATTCATTTTAGAT 59.471 34.615 11.31 0.00 0.00 1.98
1978 6013 7.062605 CACTTGCGCAGAAATTCATTTTAGATT 59.937 33.333 11.31 0.00 0.00 2.40
2021 6056 3.891366 ACATTCTTAATGGGTAGCCATGC 59.109 43.478 26.58 0.00 43.21 4.06
2028 6063 2.415983 TGGGTAGCCATGCCTAGTAT 57.584 50.000 10.27 0.00 0.00 2.12
2041 6076 6.998074 CCATGCCTAGTATAGAATTTCCACAA 59.002 38.462 0.00 0.00 42.77 3.33
2043 6078 7.195374 TGCCTAGTATAGAATTTCCACAAGT 57.805 36.000 0.00 0.00 42.77 3.16
2049 6084 8.918202 AGTATAGAATTTCCACAAGTTTGTCA 57.082 30.769 0.00 0.00 39.91 3.58
2055 6090 7.707893 AGAATTTCCACAAGTTTGTCAGATTTG 59.292 33.333 0.00 0.00 39.91 2.32
2062 6097 6.418819 CACAAGTTTGTCAGATTTGGATGAAC 59.581 38.462 4.05 0.00 39.91 3.18
2065 6100 1.731709 TGTCAGATTTGGATGAACGCG 59.268 47.619 3.53 3.53 0.00 6.01
2066 6101 1.732259 GTCAGATTTGGATGAACGCGT 59.268 47.619 5.58 5.58 0.00 6.01
2067 6102 1.999735 TCAGATTTGGATGAACGCGTC 59.000 47.619 14.44 7.01 0.00 5.19
2068 6103 1.731709 CAGATTTGGATGAACGCGTCA 59.268 47.619 14.44 13.24 41.67 4.35
2069 6104 2.002586 AGATTTGGATGAACGCGTCAG 58.997 47.619 14.44 0.00 40.43 3.51
2070 6105 1.999735 GATTTGGATGAACGCGTCAGA 59.000 47.619 14.44 0.53 40.43 3.27
2071 6106 1.428448 TTTGGATGAACGCGTCAGAG 58.572 50.000 14.44 0.00 40.43 3.35
2072 6107 1.014044 TTGGATGAACGCGTCAGAGC 61.014 55.000 14.44 1.40 40.43 4.09
2073 6108 1.153745 GGATGAACGCGTCAGAGCT 60.154 57.895 14.44 0.00 40.43 4.09
2074 6109 0.100682 GGATGAACGCGTCAGAGCTA 59.899 55.000 14.44 0.00 40.43 3.32
2075 6110 1.269309 GGATGAACGCGTCAGAGCTAT 60.269 52.381 14.44 0.00 40.43 2.97
2105 6140 8.851145 TGTTAGTTGGCTCATTACATTTAAACA 58.149 29.630 0.00 0.00 0.00 2.83
2142 6177 4.888326 ACTTTATTTCCCTTTGCATGCA 57.112 36.364 18.46 18.46 0.00 3.96
2145 6180 0.251073 ATTTCCCTTTGCATGCAGCC 59.749 50.000 21.50 0.00 44.83 4.85
2170 6208 5.834204 GGAGCTATTCTTAGTTCTGGGACTA 59.166 44.000 0.00 0.00 36.30 2.59
2192 6234 4.193826 TCTGCCTGTCACTTTACTCATC 57.806 45.455 0.00 0.00 0.00 2.92
2194 6236 2.560981 TGCCTGTCACTTTACTCATCGA 59.439 45.455 0.00 0.00 0.00 3.59
2206 6248 8.236586 CACTTTACTCATCGATGGAATTTTTGA 58.763 33.333 24.61 2.45 0.00 2.69
2219 6261 9.398170 GATGGAATTTTTGATATGAACATACCG 57.602 33.333 0.00 0.00 0.00 4.02
2262 6304 6.723298 TTTAAATGGGTGAATGACAACACT 57.277 33.333 13.23 0.50 38.06 3.55
2263 6305 6.723298 TTAAATGGGTGAATGACAACACTT 57.277 33.333 13.23 5.43 38.06 3.16
2264 6306 7.825331 TTAAATGGGTGAATGACAACACTTA 57.175 32.000 13.23 6.01 38.06 2.24
2265 6307 5.964958 AATGGGTGAATGACAACACTTAG 57.035 39.130 13.23 0.00 38.06 2.18
2266 6308 3.146066 TGGGTGAATGACAACACTTAGC 58.854 45.455 13.23 0.00 38.06 3.09
2267 6309 3.146066 GGGTGAATGACAACACTTAGCA 58.854 45.455 13.23 0.00 38.06 3.49
2268 6310 3.568007 GGGTGAATGACAACACTTAGCAA 59.432 43.478 13.23 0.00 38.06 3.91
2269 6311 4.218417 GGGTGAATGACAACACTTAGCAAT 59.782 41.667 13.23 0.00 38.06 3.56
2270 6312 5.156355 GGTGAATGACAACACTTAGCAATG 58.844 41.667 13.23 0.00 36.04 2.82
2271 6313 5.048782 GGTGAATGACAACACTTAGCAATGA 60.049 40.000 13.23 0.00 36.04 2.57
2272 6314 5.853282 GTGAATGACAACACTTAGCAATGAC 59.147 40.000 8.31 0.00 34.65 3.06
2273 6315 5.530543 TGAATGACAACACTTAGCAATGACA 59.469 36.000 0.00 0.00 0.00 3.58
2274 6316 6.207221 TGAATGACAACACTTAGCAATGACAT 59.793 34.615 0.00 0.00 0.00 3.06
2300 6342 5.993748 TTGTATACTATCGCCCATCATGA 57.006 39.130 0.00 0.00 0.00 3.07
2304 6346 6.661805 TGTATACTATCGCCCATCATGAACTA 59.338 38.462 0.00 0.00 0.00 2.24
2320 6362 6.672218 TCATGAACTAGAGGATTGGGTAAGAA 59.328 38.462 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.314321 CAAGAACTTAGTCAATACGGTCATTAT 57.686 33.333 0.00 0.00 0.00 1.28
9 10 8.525316 TCAAGAACTTAGTCAATACGGTCATTA 58.475 33.333 0.00 0.00 0.00 1.90
10 11 7.383687 TCAAGAACTTAGTCAATACGGTCATT 58.616 34.615 0.00 0.00 0.00 2.57
11 12 6.931838 TCAAGAACTTAGTCAATACGGTCAT 58.068 36.000 0.00 0.00 0.00 3.06
13 14 6.388278 ACTCAAGAACTTAGTCAATACGGTC 58.612 40.000 0.00 0.00 0.00 4.79
14 15 6.342338 ACTCAAGAACTTAGTCAATACGGT 57.658 37.500 0.00 0.00 0.00 4.83
15 16 9.666626 CTATACTCAAGAACTTAGTCAATACGG 57.333 37.037 0.00 0.00 0.00 4.02
16 17 9.666626 CCTATACTCAAGAACTTAGTCAATACG 57.333 37.037 0.00 0.00 0.00 3.06
21 22 9.702253 AGATTCCTATACTCAAGAACTTAGTCA 57.298 33.333 0.00 0.00 0.00 3.41
27 28 9.702253 TCACTTAGATTCCTATACTCAAGAACT 57.298 33.333 0.00 0.00 0.00 3.01
30 31 8.915036 GGTTCACTTAGATTCCTATACTCAAGA 58.085 37.037 0.00 0.00 0.00 3.02
31 32 8.696374 TGGTTCACTTAGATTCCTATACTCAAG 58.304 37.037 0.00 0.00 0.00 3.02
32 33 8.603898 TGGTTCACTTAGATTCCTATACTCAA 57.396 34.615 0.00 0.00 0.00 3.02
33 34 7.201920 GCTGGTTCACTTAGATTCCTATACTCA 60.202 40.741 0.00 0.00 0.00 3.41
34 35 7.149307 GCTGGTTCACTTAGATTCCTATACTC 58.851 42.308 0.00 0.00 0.00 2.59
35 36 6.611642 TGCTGGTTCACTTAGATTCCTATACT 59.388 38.462 0.00 0.00 0.00 2.12
36 37 6.817184 TGCTGGTTCACTTAGATTCCTATAC 58.183 40.000 0.00 0.00 0.00 1.47
37 38 7.344612 TCTTGCTGGTTCACTTAGATTCCTATA 59.655 37.037 0.00 0.00 0.00 1.31
38 39 5.957771 TGCTGGTTCACTTAGATTCCTAT 57.042 39.130 0.00 0.00 0.00 2.57
39 40 5.483937 TCTTGCTGGTTCACTTAGATTCCTA 59.516 40.000 0.00 0.00 0.00 2.94
40 41 4.287067 TCTTGCTGGTTCACTTAGATTCCT 59.713 41.667 0.00 0.00 0.00 3.36
41 42 4.579869 TCTTGCTGGTTCACTTAGATTCC 58.420 43.478 0.00 0.00 0.00 3.01
42 43 7.550906 ACTTATCTTGCTGGTTCACTTAGATTC 59.449 37.037 0.00 0.00 0.00 2.52
43 44 7.398024 ACTTATCTTGCTGGTTCACTTAGATT 58.602 34.615 0.00 0.00 0.00 2.40
44 45 6.951971 ACTTATCTTGCTGGTTCACTTAGAT 58.048 36.000 0.00 0.00 0.00 1.98
45 46 6.360370 ACTTATCTTGCTGGTTCACTTAGA 57.640 37.500 0.00 0.00 0.00 2.10
46 47 7.097192 TGTACTTATCTTGCTGGTTCACTTAG 58.903 38.462 0.00 0.00 0.00 2.18
47 48 6.999950 TGTACTTATCTTGCTGGTTCACTTA 58.000 36.000 0.00 0.00 0.00 2.24
48 49 5.865085 TGTACTTATCTTGCTGGTTCACTT 58.135 37.500 0.00 0.00 0.00 3.16
49 50 5.012148 ACTGTACTTATCTTGCTGGTTCACT 59.988 40.000 0.00 0.00 0.00 3.41
50 51 5.120830 CACTGTACTTATCTTGCTGGTTCAC 59.879 44.000 0.00 0.00 0.00 3.18
51 52 5.011635 TCACTGTACTTATCTTGCTGGTTCA 59.988 40.000 0.00 0.00 0.00 3.18
52 53 5.348997 GTCACTGTACTTATCTTGCTGGTTC 59.651 44.000 0.00 0.00 0.00 3.62
53 54 5.238583 GTCACTGTACTTATCTTGCTGGTT 58.761 41.667 0.00 0.00 0.00 3.67
54 55 4.322801 GGTCACTGTACTTATCTTGCTGGT 60.323 45.833 0.00 0.00 0.00 4.00
55 56 4.184629 GGTCACTGTACTTATCTTGCTGG 58.815 47.826 0.00 0.00 0.00 4.85
56 57 4.820897 TGGTCACTGTACTTATCTTGCTG 58.179 43.478 0.00 0.00 0.00 4.41
57 58 5.187772 TGATGGTCACTGTACTTATCTTGCT 59.812 40.000 0.00 0.00 0.00 3.91
58 59 5.419542 TGATGGTCACTGTACTTATCTTGC 58.580 41.667 0.00 0.00 0.00 4.01
59 60 6.533012 CACTGATGGTCACTGTACTTATCTTG 59.467 42.308 0.00 0.00 0.00 3.02
60 61 6.437477 TCACTGATGGTCACTGTACTTATCTT 59.563 38.462 0.00 0.00 0.00 2.40
61 62 5.952347 TCACTGATGGTCACTGTACTTATCT 59.048 40.000 0.00 0.00 0.00 1.98
62 63 6.208988 TCACTGATGGTCACTGTACTTATC 57.791 41.667 0.00 0.00 0.00 1.75
63 64 6.605471 TTCACTGATGGTCACTGTACTTAT 57.395 37.500 0.00 0.00 0.00 1.73
64 65 6.605471 ATTCACTGATGGTCACTGTACTTA 57.395 37.500 0.00 0.00 0.00 2.24
65 66 4.955811 TTCACTGATGGTCACTGTACTT 57.044 40.909 0.00 0.00 0.00 2.24
66 67 5.489792 AATTCACTGATGGTCACTGTACT 57.510 39.130 0.00 0.00 0.00 2.73
67 68 6.560253 AAAATTCACTGATGGTCACTGTAC 57.440 37.500 0.00 0.00 0.00 2.90
68 69 7.450074 AGTAAAATTCACTGATGGTCACTGTA 58.550 34.615 0.00 0.00 0.00 2.74
69 70 6.299141 AGTAAAATTCACTGATGGTCACTGT 58.701 36.000 0.00 0.00 0.00 3.55
70 71 6.427853 TGAGTAAAATTCACTGATGGTCACTG 59.572 38.462 0.00 0.00 0.00 3.66
71 72 6.533730 TGAGTAAAATTCACTGATGGTCACT 58.466 36.000 0.00 0.00 0.00 3.41
72 73 6.128172 CCTGAGTAAAATTCACTGATGGTCAC 60.128 42.308 0.00 0.00 0.00 3.67
73 74 5.939883 CCTGAGTAAAATTCACTGATGGTCA 59.060 40.000 0.00 0.00 0.00 4.02
74 75 5.940470 ACCTGAGTAAAATTCACTGATGGTC 59.060 40.000 0.00 0.00 0.00 4.02
75 76 5.707298 CACCTGAGTAAAATTCACTGATGGT 59.293 40.000 0.00 1.65 0.00 3.55
76 77 5.124457 CCACCTGAGTAAAATTCACTGATGG 59.876 44.000 0.00 1.15 0.00 3.51
77 78 5.939883 TCCACCTGAGTAAAATTCACTGATG 59.060 40.000 0.00 0.00 0.00 3.07
78 79 6.126863 TCCACCTGAGTAAAATTCACTGAT 57.873 37.500 0.00 0.00 0.00 2.90
79 80 5.560722 TCCACCTGAGTAAAATTCACTGA 57.439 39.130 0.00 0.00 0.00 3.41
80 81 6.633500 TTTCCACCTGAGTAAAATTCACTG 57.367 37.500 0.00 0.00 0.00 3.66
81 82 6.209391 CCATTTCCACCTGAGTAAAATTCACT 59.791 38.462 0.00 0.00 0.00 3.41
82 83 6.208599 TCCATTTCCACCTGAGTAAAATTCAC 59.791 38.462 0.00 0.00 0.00 3.18
83 84 6.310941 TCCATTTCCACCTGAGTAAAATTCA 58.689 36.000 0.00 0.00 0.00 2.57
84 85 6.834168 TCCATTTCCACCTGAGTAAAATTC 57.166 37.500 0.00 0.00 0.00 2.17
85 86 7.610580 TTTCCATTTCCACCTGAGTAAAATT 57.389 32.000 0.00 0.00 0.00 1.82
86 87 7.454380 TGATTTCCATTTCCACCTGAGTAAAAT 59.546 33.333 0.00 0.00 0.00 1.82
87 88 6.780031 TGATTTCCATTTCCACCTGAGTAAAA 59.220 34.615 0.00 0.00 0.00 1.52
88 89 6.310941 TGATTTCCATTTCCACCTGAGTAAA 58.689 36.000 0.00 0.00 0.00 2.01
89 90 5.886609 TGATTTCCATTTCCACCTGAGTAA 58.113 37.500 0.00 0.00 0.00 2.24
90 91 5.512942 TGATTTCCATTTCCACCTGAGTA 57.487 39.130 0.00 0.00 0.00 2.59
91 92 4.387026 TGATTTCCATTTCCACCTGAGT 57.613 40.909 0.00 0.00 0.00 3.41
92 93 5.186409 ACATTGATTTCCATTTCCACCTGAG 59.814 40.000 0.00 0.00 0.00 3.35
96 97 6.986231 GGAATACATTGATTTCCATTTCCACC 59.014 38.462 13.77 0.00 39.00 4.61
108 109 5.416083 TCTCGTTCACGGAATACATTGATT 58.584 37.500 0.00 0.00 40.29 2.57
114 115 2.587956 CGTTCTCGTTCACGGAATACA 58.412 47.619 0.00 0.00 40.29 2.29
122 123 0.703466 CTCTTCGCGTTCTCGTTCAC 59.297 55.000 5.77 0.00 39.49 3.18
124 125 1.897641 ATCTCTTCGCGTTCTCGTTC 58.102 50.000 5.77 0.00 39.49 3.95
125 126 2.223294 CCTATCTCTTCGCGTTCTCGTT 60.223 50.000 5.77 0.00 39.49 3.85
127 128 1.922444 GCCTATCTCTTCGCGTTCTCG 60.922 57.143 5.77 0.00 40.37 4.04
148 149 1.065928 GGTCTATCCGTGCTCCGTG 59.934 63.158 0.00 0.00 33.66 4.94
149 150 1.379443 TGGTCTATCCGTGCTCCGT 60.379 57.895 0.00 0.00 39.52 4.69
150 151 1.360551 CTGGTCTATCCGTGCTCCG 59.639 63.158 0.00 0.00 39.52 4.63
152 153 0.249238 CAGCTGGTCTATCCGTGCTC 60.249 60.000 5.57 0.00 43.15 4.26
154 155 0.175760 TTCAGCTGGTCTATCCGTGC 59.824 55.000 15.13 0.00 39.52 5.34
155 156 1.751351 TCTTCAGCTGGTCTATCCGTG 59.249 52.381 15.13 0.00 39.52 4.94
156 157 2.028130 CTCTTCAGCTGGTCTATCCGT 58.972 52.381 15.13 0.00 39.52 4.69
157 158 2.028130 ACTCTTCAGCTGGTCTATCCG 58.972 52.381 15.13 0.00 39.52 4.18
158 159 3.027412 TGACTCTTCAGCTGGTCTATCC 58.973 50.000 15.13 0.00 0.00 2.59
159 160 4.159506 ACTTGACTCTTCAGCTGGTCTATC 59.840 45.833 15.13 7.50 31.71 2.08
160 161 4.093011 ACTTGACTCTTCAGCTGGTCTAT 58.907 43.478 15.13 0.00 31.71 1.98
161 162 3.501349 ACTTGACTCTTCAGCTGGTCTA 58.499 45.455 15.13 9.09 31.71 2.59
162 163 2.324541 ACTTGACTCTTCAGCTGGTCT 58.675 47.619 15.13 0.00 31.71 3.85
163 164 2.805099 CAACTTGACTCTTCAGCTGGTC 59.195 50.000 15.13 13.48 31.71 4.02
207 214 2.872245 CAGGAAAAGACTGAACGCAGAA 59.128 45.455 0.00 0.00 45.17 3.02
211 218 0.238553 GCCAGGAAAAGACTGAACGC 59.761 55.000 0.00 0.00 38.20 4.84
233 240 1.605165 TTTTGGGCGGTGGATGGTC 60.605 57.895 0.00 0.00 0.00 4.02
259 266 1.810030 GCTAGGAAAGTGGACGGCG 60.810 63.158 4.80 4.80 0.00 6.46
300 307 4.059459 CGTGTGCGACTTGTCGGC 62.059 66.667 22.04 15.19 41.33 5.54
313 351 1.736586 GAGGAGATCGCCATCGTGT 59.263 57.895 18.44 0.00 36.96 4.49
410 454 0.248539 GCGAGTAGCCGACGATCTTT 60.249 55.000 0.00 0.00 40.81 2.52
471 515 3.319198 GCCTCCCACCTGGAACGA 61.319 66.667 0.00 0.00 44.57 3.85
521 565 1.293963 CGGTGTACTCGGACTCGTCA 61.294 60.000 0.00 0.00 37.69 4.35
543 671 1.678970 GCACCGGCTTCCCATCTTT 60.679 57.895 0.00 0.00 36.96 2.52
564 692 2.355756 TCGCGGTAGTCAAGGTATACAC 59.644 50.000 6.13 0.00 0.00 2.90
666 795 5.062683 CCTTGACAGTGAATGAATCGTACTG 59.937 44.000 0.00 4.34 43.20 2.74
669 798 5.147330 ACCTTGACAGTGAATGAATCGTA 57.853 39.130 0.00 0.00 0.00 3.43
677 806 4.516698 GTGACATTGACCTTGACAGTGAAT 59.483 41.667 0.00 0.00 0.00 2.57
710 839 0.894835 TGTCTCCTGCGCATAACTCA 59.105 50.000 12.24 5.55 0.00 3.41
775 906 2.149578 CACCTTGCTTGACAGGAGAAG 58.850 52.381 0.00 0.00 0.00 2.85
786 917 0.606401 CATCGACACCCACCTTGCTT 60.606 55.000 0.00 0.00 0.00 3.91
794 925 2.432444 GGAATTTGACATCGACACCCA 58.568 47.619 0.00 0.00 0.00 4.51
826 958 2.154462 CCGGTGAGCAGAAAATGTCTT 58.846 47.619 0.00 0.00 32.70 3.01
903 1035 0.252742 CCCCAGTAGTGGTTCCCTCT 60.253 60.000 15.60 0.00 43.23 3.69
946 1078 2.719798 CAAAGCGTTGAACACTTCTGG 58.280 47.619 6.52 0.00 36.83 3.86
964 1096 4.633175 TCCGTGTACATGAAAGTAAGCAA 58.367 39.130 16.87 0.00 0.00 3.91
1006 1138 2.622452 CCATGGCAGATTCCTCCTGTTT 60.622 50.000 0.00 0.00 34.29 2.83
1057 1195 2.358267 GCTTCAGCCTCTCCAAATCATG 59.642 50.000 0.00 0.00 34.31 3.07
1177 1315 1.901591 CTGAGGAACACCAAGCATGT 58.098 50.000 0.00 0.00 0.00 3.21
1257 1395 4.416848 AGATCCTTAATAACACCAGGGCAT 59.583 41.667 0.00 0.00 0.00 4.40
1361 1505 5.144832 TCTGGATGGATGATTGCAAATGAT 58.855 37.500 1.71 0.00 0.00 2.45
1378 1522 6.183347 CAGGGTCTTTATTCAGTTTCTGGAT 58.817 40.000 0.00 0.00 33.72 3.41
1446 1599 6.305272 ACATCATTGTGAGAACAGGACTAT 57.695 37.500 0.00 0.00 33.85 2.12
1464 1617 2.565391 AGGACCAACGTACATCACATCA 59.435 45.455 0.00 0.00 0.00 3.07
1549 1708 9.325198 CTGTTCACTAATTAGCACATATGGTTA 57.675 33.333 12.54 0.00 37.77 2.85
1583 1743 6.354130 ACTAGTTGAAAGGCTTACAAGTTCA 58.646 36.000 0.00 0.00 0.00 3.18
1610 1770 6.133356 ACAGAACTGGGTGAAATTTAAAGGA 58.867 36.000 6.76 0.00 34.19 3.36
1623 5529 1.701847 AGCAATCAGACAGAACTGGGT 59.298 47.619 6.76 0.00 38.31 4.51
1664 5571 1.166531 AACTCAGGAACCAGCGCAAC 61.167 55.000 11.47 0.00 0.00 4.17
1713 5620 7.037873 TGGTATGTCTGAACCTGGTAAATAAGT 60.038 37.037 0.00 0.00 36.67 2.24
1733 5640 5.803461 CAGCATTTCAACAAGACATGGTATG 59.197 40.000 0.00 0.00 41.73 2.39
1735 5642 4.218200 CCAGCATTTCAACAAGACATGGTA 59.782 41.667 0.00 0.00 41.73 3.25
1759 5669 5.870978 CCAATGATTTTTCACTGGATCCAAC 59.129 40.000 17.00 0.14 39.15 3.77
1761 5671 4.081531 GCCAATGATTTTTCACTGGATCCA 60.082 41.667 15.27 15.27 39.15 3.41
1808 5718 6.176975 TCATGACTAAAATTTGTAGCCGTG 57.823 37.500 0.00 1.43 0.00 4.94
1827 5737 7.307632 GCAGCCACTACTATGTTAGAAATCATG 60.308 40.741 0.00 0.00 0.00 3.07
1837 5747 3.775316 ACCTTAGCAGCCACTACTATGTT 59.225 43.478 0.00 0.00 0.00 2.71
1878 5794 0.954452 CTTGAGGCCAAACTCCACAC 59.046 55.000 5.01 0.00 36.66 3.82
1879 5795 0.550914 ACTTGAGGCCAAACTCCACA 59.449 50.000 5.01 0.00 36.66 4.17
1959 5994 9.860898 ACAAGGTAATCTAAAATGAATTTCTGC 57.139 29.630 0.00 0.00 32.27 4.26
2021 6056 9.449719 ACAAACTTGTGGAAATTCTATACTAGG 57.550 33.333 0.00 0.00 40.49 3.02
2028 6063 8.463930 AATCTGACAAACTTGTGGAAATTCTA 57.536 30.769 0.00 0.00 42.43 2.10
2041 6076 4.320494 GCGTTCATCCAAATCTGACAAACT 60.320 41.667 0.00 0.00 0.00 2.66
2043 6078 3.364864 CGCGTTCATCCAAATCTGACAAA 60.365 43.478 0.00 0.00 0.00 2.83
2049 6084 2.002586 CTGACGCGTTCATCCAAATCT 58.997 47.619 15.53 0.00 32.17 2.40
2055 6090 0.100682 TAGCTCTGACGCGTTCATCC 59.899 55.000 15.53 0.00 32.17 3.51
2062 6097 1.845266 ACATGAATAGCTCTGACGCG 58.155 50.000 3.53 3.53 34.40 6.01
2065 6100 5.007136 GCCAACTAACATGAATAGCTCTGAC 59.993 44.000 0.00 0.00 0.00 3.51
2066 6101 5.104776 AGCCAACTAACATGAATAGCTCTGA 60.105 40.000 0.00 0.00 0.00 3.27
2067 6102 5.121811 AGCCAACTAACATGAATAGCTCTG 58.878 41.667 0.00 1.15 0.00 3.35
2068 6103 5.104776 TGAGCCAACTAACATGAATAGCTCT 60.105 40.000 17.59 8.41 43.51 4.09
2069 6104 5.118990 TGAGCCAACTAACATGAATAGCTC 58.881 41.667 0.00 8.12 43.43 4.09
2070 6105 5.102953 TGAGCCAACTAACATGAATAGCT 57.897 39.130 0.00 0.00 0.00 3.32
2071 6106 6.382869 AATGAGCCAACTAACATGAATAGC 57.617 37.500 0.00 0.00 0.00 2.97
2072 6107 8.437360 TGTAATGAGCCAACTAACATGAATAG 57.563 34.615 0.00 4.21 0.00 1.73
2073 6108 8.978874 ATGTAATGAGCCAACTAACATGAATA 57.021 30.769 0.00 0.00 0.00 1.75
2074 6109 7.886629 ATGTAATGAGCCAACTAACATGAAT 57.113 32.000 0.00 0.00 0.00 2.57
2075 6110 7.701539 AATGTAATGAGCCAACTAACATGAA 57.298 32.000 0.00 0.00 0.00 2.57
2145 6180 3.637229 TCCCAGAACTAAGAATAGCTCCG 59.363 47.826 0.00 0.00 31.96 4.63
2170 6208 4.679106 CGATGAGTAAAGTGACAGGCAGAT 60.679 45.833 0.00 0.00 0.00 2.90
2192 6234 9.398170 GGTATGTTCATATCAAAAATTCCATCG 57.602 33.333 0.00 0.00 0.00 3.84
2194 6236 8.912988 ACGGTATGTTCATATCAAAAATTCCAT 58.087 29.630 4.34 0.00 0.00 3.41
2206 6248 8.635328 TCATTACAGTGTACGGTATGTTCATAT 58.365 33.333 1.43 0.00 30.12 1.78
2219 6261 9.654417 ATTTAAAAACGTGTCATTACAGTGTAC 57.346 29.630 1.43 0.00 35.91 2.90
2265 6307 7.011773 CGATAGTATACAAAGCATGTCATTGC 58.988 38.462 5.50 0.00 42.70 3.56
2266 6308 7.011773 GCGATAGTATACAAAGCATGTCATTG 58.988 38.462 5.50 0.21 40.39 2.82
2267 6309 6.147821 GGCGATAGTATACAAAGCATGTCATT 59.852 38.462 5.50 0.00 40.39 2.57
2268 6310 5.639506 GGCGATAGTATACAAAGCATGTCAT 59.360 40.000 5.50 0.00 40.39 3.06
2269 6311 4.988540 GGCGATAGTATACAAAGCATGTCA 59.011 41.667 5.50 0.00 40.39 3.58
2270 6312 4.389077 GGGCGATAGTATACAAAGCATGTC 59.611 45.833 5.50 0.00 40.39 3.06
2271 6313 4.202315 TGGGCGATAGTATACAAAGCATGT 60.202 41.667 5.50 0.67 42.11 3.21
2272 6314 4.314961 TGGGCGATAGTATACAAAGCATG 58.685 43.478 5.50 0.00 39.35 4.06
2273 6315 4.617253 TGGGCGATAGTATACAAAGCAT 57.383 40.909 5.50 0.00 39.35 3.79
2274 6316 4.039852 TGATGGGCGATAGTATACAAAGCA 59.960 41.667 5.50 0.00 39.35 3.91
2300 6342 6.239345 CGCTATTCTTACCCAATCCTCTAGTT 60.239 42.308 0.00 0.00 0.00 2.24
2304 6346 3.325135 CCGCTATTCTTACCCAATCCTCT 59.675 47.826 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.