Multiple sequence alignment - TraesCS3B01G035400

Loading Multiple Alignment...

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 TraesCS3B01G035400 chr3B 100.000 2458 0 0 1 2458 17317828 17320285 0.000000e+00 4540.0
1 TraesCS3B01G035400 chr3B 95.012 1624 58 5 750 2355 679712625 679711007 0.000000e+00 2529.0
2 TraesCS3B01G035400 chr3B 85.691 608 44 18 156 738 679713354 679712765 3.500000e-168 601.0
3 TraesCS3B01G035400 chr3B 96.078 102 4 0 2356 2457 679710770 679710669 1.510000e-37 167.0
4 TraesCS3B01G035400 chr3B 88.636 44 4 1 103 146 512418938 512418896 4.000000e-03 52.8
5 TraesCS3B01G035400 chr5A 90.953 2089 119 21 411 2457 65996129 65998189 0.000000e+00 2747.0
6 TraesCS3B01G035400 chr5A 93.273 1323 68 3 749 2050 427855212 427853890 0.000000e+00 1930.0
7 TraesCS3B01G035400 chr5A 94.484 562 30 1 1896 2457 66045698 66046258 0.000000e+00 865.0
8 TraesCS3B01G035400 chr5A 88.347 369 24 10 598 951 569170105 569169741 2.260000e-115 425.0
9 TraesCS3B01G035400 chr5A 87.433 374 34 4 2092 2452 139249236 139249609 3.780000e-113 418.0
10 TraesCS3B01G035400 chr4A 91.601 1905 102 18 603 2455 96105159 96107057 0.000000e+00 2579.0
11 TraesCS3B01G035400 chr4A 91.027 1772 107 22 507 2236 588546967 588548728 0.000000e+00 2344.0
12 TraesCS3B01G035400 chr4A 92.895 1323 72 5 748 2049 679660877 679659556 0.000000e+00 1903.0
13 TraesCS3B01G035400 chr4A 85.805 472 35 15 108 553 96104705 96105170 2.860000e-129 472.0
14 TraesCS3B01G035400 chr4A 86.014 429 30 14 108 510 588542240 588542664 1.350000e-117 433.0
15 TraesCS3B01G035400 chr4A 94.595 37 1 1 102 138 609550771 609550806 3.410000e-04 56.5
16 TraesCS3B01G035400 chrUn 91.050 1676 91 14 411 2049 19135000 19136653 0.000000e+00 2209.0
17 TraesCS3B01G035400 chr2D 91.007 1679 87 21 411 2049 142214674 142216328 0.000000e+00 2206.0
18 TraesCS3B01G035400 chr7D 90.882 1678 91 14 411 2049 292321263 292322917 0.000000e+00 2194.0
19 TraesCS3B01G035400 chr7D 87.368 1322 128 21 791 2085 69829416 69828107 0.000000e+00 1480.0
20 TraesCS3B01G035400 chr7D 82.979 141 19 4 469 605 69829640 69829501 3.320000e-24 122.0
21 TraesCS3B01G035400 chr7D 85.714 105 13 2 414 518 8995922 8995820 2.580000e-20 110.0
22 TraesCS3B01G035400 chr7D 97.143 35 1 0 105 139 28191693 28191727 2.640000e-05 60.2
23 TraesCS3B01G035400 chr1D 90.755 1655 93 12 414 2030 460576043 460574411 0.000000e+00 2154.0
24 TraesCS3B01G035400 chr1D 90.909 44 1 2 105 147 332679192 332679151 3.410000e-04 56.5
25 TraesCS3B01G035400 chr6A 92.587 1322 64 5 749 2049 517541439 517540131 0.000000e+00 1868.0
26 TraesCS3B01G035400 chr6A 80.289 1938 253 77 106 1968 464933300 464935183 0.000000e+00 1343.0
27 TraesCS3B01G035400 chr6A 87.003 377 35 5 2092 2455 464935182 464935557 1.760000e-111 412.0
28 TraesCS3B01G035400 chr6A 92.500 40 2 1 107 145 16366587 16366548 3.410000e-04 56.5
29 TraesCS3B01G035400 chr4D 90.352 1192 64 14 414 1563 215029922 215028740 0.000000e+00 1517.0
30 TraesCS3B01G035400 chr5B 83.412 1489 166 50 528 1968 593467915 593466460 0.000000e+00 1306.0
31 TraesCS3B01G035400 chr5B 83.210 1489 169 48 528 1968 593465036 593463581 0.000000e+00 1290.0
32 TraesCS3B01G035400 chr5B 88.715 319 34 2 2139 2455 593463527 593463209 2.960000e-104 388.0
33 TraesCS3B01G035400 chr5B 88.715 319 34 2 2139 2455 593466406 593466088 2.960000e-104 388.0
34 TraesCS3B01G035400 chr5B 100.000 32 0 0 107 138 271151272 271151241 2.640000e-05 60.2
35 TraesCS3B01G035400 chr7B 90.328 548 33 9 416 951 78142340 78141801 0.000000e+00 701.0
36 TraesCS3B01G035400 chr7B 88.969 553 41 11 411 951 85846515 85847059 0.000000e+00 665.0
37 TraesCS3B01G035400 chr6B 90.043 462 29 8 503 951 503880829 503881286 1.270000e-162 582.0
38 TraesCS3B01G035400 chr6B 88.410 371 25 8 598 953 159801191 159801558 4.860000e-117 431.0
39 TraesCS3B01G035400 chr6B 94.737 38 1 1 107 143 83932247 83932210 9.490000e-05 58.4
40 TraesCS3B01G035400 chr1B 93.609 266 17 0 2192 2457 28802961 28803226 4.930000e-107 398.0
41 TraesCS3B01G035400 chr4B 86.322 329 25 9 598 911 240151616 240151293 8.420000e-90 340.0
42 TraesCS3B01G035400 chr6D 92.857 112 5 1 1 112 338914821 338914929 2.530000e-35 159.0


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 TraesCS3B01G035400 chr3B 17317828 17320285 2457 False 4540.0 4540 100.000000 1 2458 1 chr3B.!!$F1 2457
1 TraesCS3B01G035400 chr3B 679710669 679713354 2685 True 1099.0 2529 92.260333 156 2457 3 chr3B.!!$R2 2301
2 TraesCS3B01G035400 chr5A 65996129 65998189 2060 False 2747.0 2747 90.953000 411 2457 1 chr5A.!!$F1 2046
3 TraesCS3B01G035400 chr5A 427853890 427855212 1322 True 1930.0 1930 93.273000 749 2050 1 chr5A.!!$R1 1301
4 TraesCS3B01G035400 chr5A 66045698 66046258 560 False 865.0 865 94.484000 1896 2457 1 chr5A.!!$F2 561
5 TraesCS3B01G035400 chr4A 588546967 588548728 1761 False 2344.0 2344 91.027000 507 2236 1 chr4A.!!$F2 1729
6 TraesCS3B01G035400 chr4A 679659556 679660877 1321 True 1903.0 1903 92.895000 748 2049 1 chr4A.!!$R1 1301
7 TraesCS3B01G035400 chr4A 96104705 96107057 2352 False 1525.5 2579 88.703000 108 2455 2 chr4A.!!$F4 2347
8 TraesCS3B01G035400 chrUn 19135000 19136653 1653 False 2209.0 2209 91.050000 411 2049 1 chrUn.!!$F1 1638
9 TraesCS3B01G035400 chr2D 142214674 142216328 1654 False 2206.0 2206 91.007000 411 2049 1 chr2D.!!$F1 1638
10 TraesCS3B01G035400 chr7D 292321263 292322917 1654 False 2194.0 2194 90.882000 411 2049 1 chr7D.!!$F2 1638
11 TraesCS3B01G035400 chr7D 69828107 69829640 1533 True 801.0 1480 85.173500 469 2085 2 chr7D.!!$R2 1616
12 TraesCS3B01G035400 chr1D 460574411 460576043 1632 True 2154.0 2154 90.755000 414 2030 1 chr1D.!!$R2 1616
13 TraesCS3B01G035400 chr6A 517540131 517541439 1308 True 1868.0 1868 92.587000 749 2049 1 chr6A.!!$R2 1300
14 TraesCS3B01G035400 chr6A 464933300 464935557 2257 False 877.5 1343 83.646000 106 2455 2 chr6A.!!$F1 2349
15 TraesCS3B01G035400 chr4D 215028740 215029922 1182 True 1517.0 1517 90.352000 414 1563 1 chr4D.!!$R1 1149
16 TraesCS3B01G035400 chr5B 593463209 593467915 4706 True 843.0 1306 86.013000 528 2455 4 chr5B.!!$R2 1927
17 TraesCS3B01G035400 chr7B 78141801 78142340 539 True 701.0 701 90.328000 416 951 1 chr7B.!!$R1 535
18 TraesCS3B01G035400 chr7B 85846515 85847059 544 False 665.0 665 88.969000 411 951 1 chr7B.!!$F1 540

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
39 40 0.107165 CGGGATTTGAAGGAGGGGTC 60.107 60.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1683 4868 1.435577 AGATTAAACGCGACACCCAC 58.564 50.0 15.93 0.0 0.0 4.61 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
22 23 2.591571 TCAGCATGAGAGATCAACGG 57.408 50.000 0.00 0.00 42.56 4.44
23 24 1.137675 TCAGCATGAGAGATCAACGGG 59.862 52.381 0.00 0.00 42.56 5.28
24 25 1.137675 CAGCATGAGAGATCAACGGGA 59.862 52.381 0.00 0.00 39.69 5.14
25 26 2.045524 AGCATGAGAGATCAACGGGAT 58.954 47.619 0.00 0.00 39.53 3.85
26 27 2.437281 AGCATGAGAGATCAACGGGATT 59.563 45.455 0.00 0.00 36.00 3.01
27 28 3.118112 AGCATGAGAGATCAACGGGATTT 60.118 43.478 0.00 0.00 36.00 2.17
28 29 3.003068 GCATGAGAGATCAACGGGATTTG 59.997 47.826 0.00 0.00 36.00 2.32
29 30 4.445453 CATGAGAGATCAACGGGATTTGA 58.555 43.478 0.00 0.00 39.79 2.69
30 31 4.551702 TGAGAGATCAACGGGATTTGAA 57.448 40.909 0.00 0.00 38.95 2.69
31 32 4.507710 TGAGAGATCAACGGGATTTGAAG 58.492 43.478 0.00 0.00 38.95 3.02
32 33 3.873952 GAGAGATCAACGGGATTTGAAGG 59.126 47.826 0.00 0.00 38.95 3.46
33 34 3.519510 AGAGATCAACGGGATTTGAAGGA 59.480 43.478 0.00 0.00 38.95 3.36
34 35 3.873952 GAGATCAACGGGATTTGAAGGAG 59.126 47.826 0.00 0.00 38.95 3.69
35 36 2.489938 TCAACGGGATTTGAAGGAGG 57.510 50.000 0.00 0.00 32.42 4.30
36 37 1.004277 TCAACGGGATTTGAAGGAGGG 59.996 52.381 0.00 0.00 32.42 4.30
37 38 0.331616 AACGGGATTTGAAGGAGGGG 59.668 55.000 0.00 0.00 0.00 4.79
38 39 0.845102 ACGGGATTTGAAGGAGGGGT 60.845 55.000 0.00 0.00 0.00 4.95
39 40 0.107165 CGGGATTTGAAGGAGGGGTC 60.107 60.000 0.00 0.00 0.00 4.46
40 41 0.107165 GGGATTTGAAGGAGGGGTCG 60.107 60.000 0.00 0.00 0.00 4.79
41 42 0.909623 GGATTTGAAGGAGGGGTCGA 59.090 55.000 0.00 0.00 0.00 4.20
42 43 1.490910 GGATTTGAAGGAGGGGTCGAT 59.509 52.381 0.00 0.00 0.00 3.59
43 44 2.092375 GGATTTGAAGGAGGGGTCGATT 60.092 50.000 0.00 0.00 0.00 3.34
44 45 3.621558 GATTTGAAGGAGGGGTCGATTT 58.378 45.455 0.00 0.00 0.00 2.17
45 46 3.518992 TTTGAAGGAGGGGTCGATTTT 57.481 42.857 0.00 0.00 0.00 1.82
46 47 4.644163 TTTGAAGGAGGGGTCGATTTTA 57.356 40.909 0.00 0.00 0.00 1.52
47 48 3.906720 TGAAGGAGGGGTCGATTTTAG 57.093 47.619 0.00 0.00 0.00 1.85
48 49 2.504175 TGAAGGAGGGGTCGATTTTAGG 59.496 50.000 0.00 0.00 0.00 2.69
49 50 0.837940 AGGAGGGGTCGATTTTAGGC 59.162 55.000 0.00 0.00 0.00 3.93
50 51 0.179026 GGAGGGGTCGATTTTAGGCC 60.179 60.000 0.00 0.00 0.00 5.19
55 56 2.640316 GGTCGATTTTAGGCCCAGAT 57.360 50.000 0.00 0.00 0.00 2.90
56 57 3.764237 GGTCGATTTTAGGCCCAGATA 57.236 47.619 0.00 0.00 0.00 1.98
57 58 4.081322 GGTCGATTTTAGGCCCAGATAA 57.919 45.455 0.00 0.00 0.00 1.75
58 59 4.652822 GGTCGATTTTAGGCCCAGATAAT 58.347 43.478 0.00 0.00 0.00 1.28
59 60 5.801380 GGTCGATTTTAGGCCCAGATAATA 58.199 41.667 0.00 0.00 0.00 0.98
60 61 5.642491 GGTCGATTTTAGGCCCAGATAATAC 59.358 44.000 0.00 0.00 0.00 1.89
61 62 5.642491 GTCGATTTTAGGCCCAGATAATACC 59.358 44.000 0.00 0.00 0.00 2.73
62 63 5.546499 TCGATTTTAGGCCCAGATAATACCT 59.454 40.000 0.00 0.00 34.42 3.08
63 64 6.043938 TCGATTTTAGGCCCAGATAATACCTT 59.956 38.462 0.00 0.00 31.79 3.50
64 65 6.715264 CGATTTTAGGCCCAGATAATACCTTT 59.285 38.462 0.00 0.00 31.79 3.11
65 66 7.094762 CGATTTTAGGCCCAGATAATACCTTTC 60.095 40.741 0.00 0.00 31.79 2.62
66 67 3.771577 AGGCCCAGATAATACCTTTCG 57.228 47.619 0.00 0.00 0.00 3.46
67 68 3.046374 AGGCCCAGATAATACCTTTCGT 58.954 45.455 0.00 0.00 0.00 3.85
68 69 3.139077 GGCCCAGATAATACCTTTCGTG 58.861 50.000 0.00 0.00 0.00 4.35
69 70 3.139077 GCCCAGATAATACCTTTCGTGG 58.861 50.000 0.00 0.00 0.00 4.94
70 71 3.181458 GCCCAGATAATACCTTTCGTGGA 60.181 47.826 0.00 0.00 0.00 4.02
71 72 4.505039 GCCCAGATAATACCTTTCGTGGAT 60.505 45.833 0.00 0.00 0.00 3.41
72 73 5.238583 CCCAGATAATACCTTTCGTGGATC 58.761 45.833 0.00 0.00 0.00 3.36
73 74 5.221641 CCCAGATAATACCTTTCGTGGATCA 60.222 44.000 0.00 0.00 0.00 2.92
74 75 6.288294 CCAGATAATACCTTTCGTGGATCAA 58.712 40.000 0.00 0.00 0.00 2.57
75 76 6.936900 CCAGATAATACCTTTCGTGGATCAAT 59.063 38.462 0.00 0.00 0.00 2.57
76 77 7.118390 CCAGATAATACCTTTCGTGGATCAATC 59.882 40.741 0.00 0.00 0.00 2.67
77 78 7.657354 CAGATAATACCTTTCGTGGATCAATCA 59.343 37.037 0.00 0.00 0.00 2.57
78 79 7.875041 AGATAATACCTTTCGTGGATCAATCAG 59.125 37.037 0.00 0.00 0.00 2.90
79 80 3.981071 ACCTTTCGTGGATCAATCAGA 57.019 42.857 0.00 0.00 0.00 3.27
80 81 3.866651 ACCTTTCGTGGATCAATCAGAG 58.133 45.455 0.00 0.00 0.00 3.35
81 82 3.201290 CCTTTCGTGGATCAATCAGAGG 58.799 50.000 0.00 0.00 0.00 3.69
82 83 3.118629 CCTTTCGTGGATCAATCAGAGGA 60.119 47.826 0.00 0.00 0.00 3.71
83 84 3.808466 TTCGTGGATCAATCAGAGGAG 57.192 47.619 0.00 0.00 0.00 3.69
84 85 3.018423 TCGTGGATCAATCAGAGGAGA 57.982 47.619 0.00 0.00 0.00 3.71
85 86 2.954989 TCGTGGATCAATCAGAGGAGAG 59.045 50.000 0.00 0.00 0.00 3.20
86 87 2.035704 CGTGGATCAATCAGAGGAGAGG 59.964 54.545 0.00 0.00 0.00 3.69
87 88 2.368221 GTGGATCAATCAGAGGAGAGGG 59.632 54.545 0.00 0.00 0.00 4.30
88 89 2.248423 TGGATCAATCAGAGGAGAGGGA 59.752 50.000 0.00 0.00 0.00 4.20
89 90 2.899256 GGATCAATCAGAGGAGAGGGAG 59.101 54.545 0.00 0.00 0.00 4.30
90 91 1.786937 TCAATCAGAGGAGAGGGAGC 58.213 55.000 0.00 0.00 0.00 4.70
91 92 1.290431 TCAATCAGAGGAGAGGGAGCT 59.710 52.381 0.00 0.00 0.00 4.09
92 93 1.413445 CAATCAGAGGAGAGGGAGCTG 59.587 57.143 0.00 0.00 0.00 4.24
93 94 0.636101 ATCAGAGGAGAGGGAGCTGT 59.364 55.000 0.00 0.00 0.00 4.40
94 95 0.411452 TCAGAGGAGAGGGAGCTGTT 59.589 55.000 0.00 0.00 0.00 3.16
95 96 1.203237 TCAGAGGAGAGGGAGCTGTTT 60.203 52.381 0.00 0.00 0.00 2.83
96 97 1.627834 CAGAGGAGAGGGAGCTGTTTT 59.372 52.381 0.00 0.00 0.00 2.43
97 98 2.039613 CAGAGGAGAGGGAGCTGTTTTT 59.960 50.000 0.00 0.00 0.00 1.94
98 99 2.039613 AGAGGAGAGGGAGCTGTTTTTG 59.960 50.000 0.00 0.00 0.00 2.44
99 100 0.884514 GGAGAGGGAGCTGTTTTTGC 59.115 55.000 0.00 0.00 0.00 3.68
100 101 1.546548 GGAGAGGGAGCTGTTTTTGCT 60.547 52.381 0.00 0.00 44.24 3.91
101 102 1.538950 GAGAGGGAGCTGTTTTTGCTG 59.461 52.381 0.00 0.00 41.30 4.41
102 103 1.133668 AGAGGGAGCTGTTTTTGCTGT 60.134 47.619 0.00 0.00 41.30 4.40
103 104 2.106511 AGAGGGAGCTGTTTTTGCTGTA 59.893 45.455 0.00 0.00 41.30 2.74
104 105 2.485814 GAGGGAGCTGTTTTTGCTGTAG 59.514 50.000 0.00 0.00 41.30 2.74
149 150 3.540617 ACGCACATATCTACAAATGGCA 58.459 40.909 0.00 0.00 0.00 4.92
153 154 4.682860 GCACATATCTACAAATGGCAATGC 59.317 41.667 0.00 0.00 0.00 3.56
168 169 2.814097 GCAATGCCGGTATGATAACCCT 60.814 50.000 5.55 0.00 36.03 4.34
187 188 2.232941 CCTAGAAGCGGTACCAGTTCAA 59.767 50.000 20.23 0.00 0.00 2.69
249 250 2.623416 CCCTGTGAGGTTTTCAACTTCC 59.377 50.000 0.00 0.00 37.61 3.46
257 258 4.710324 AGGTTTTCAACTTCCACGACATA 58.290 39.130 0.00 0.00 0.00 2.29
261 262 4.866508 TTCAACTTCCACGACATAGACT 57.133 40.909 0.00 0.00 0.00 3.24
290 292 5.460419 GTCGTGTTGGTTGCAATTATTGAAA 59.540 36.000 9.36 1.04 0.00 2.69
339 351 3.459969 ACCCTGGAAGAGTGTTCTTTTCT 59.540 43.478 0.00 0.00 43.63 2.52
364 376 3.688673 CAGTGATGGAAGAGAGGCTTTTC 59.311 47.826 0.00 0.00 36.83 2.29
372 385 3.661811 AAGAGAGGCTTTTCGACGGAGT 61.662 50.000 0.00 0.00 37.04 3.85
403 416 2.014128 ACCTAGTGTGTGTTTGTGTGC 58.986 47.619 0.00 0.00 0.00 4.57
404 417 2.013400 CCTAGTGTGTGTTTGTGTGCA 58.987 47.619 0.00 0.00 0.00 4.57
409 422 3.193267 AGTGTGTGTTTGTGTGCATTTCT 59.807 39.130 0.00 0.00 0.00 2.52
455 495 7.344441 GCTTTTGCTTCGTGTTTGAATTTATT 58.656 30.769 0.00 0.00 43.35 1.40
456 496 7.850492 GCTTTTGCTTCGTGTTTGAATTTATTT 59.150 29.630 0.00 0.00 43.35 1.40
1069 4225 0.818296 ACTTGCACGCCCTACTCTAG 59.182 55.000 0.00 0.00 0.00 2.43
1244 4408 4.385865 GGTAATCTCTCTCTCTGACCCTGA 60.386 50.000 0.00 0.00 0.00 3.86
1352 4518 9.774742 CTCTACATATTTTGTTCTGTTAAAGGC 57.225 33.333 0.00 0.00 39.87 4.35
1357 4523 9.271828 CATATTTTGTTCTGTTAAAGGCCTTTT 57.728 29.630 34.60 18.88 34.23 2.27
1451 4620 4.366586 AGAGTTCACATGATGCAGTATCG 58.633 43.478 0.00 0.00 38.71 2.92
1900 5113 3.179443 TGTTGCGGATCTTCTATGGAC 57.821 47.619 0.00 0.00 0.00 4.02
1936 5149 3.832527 ACCAAGCTTGCCTTCTCTTTAA 58.167 40.909 21.43 0.00 0.00 1.52
2121 5337 6.826231 TGAACTCTTTTGACACTTTGTGGATA 59.174 34.615 2.72 0.00 37.94 2.59
2236 5466 3.936372 AGCTTAGTTTGAGCGTGAGTA 57.064 42.857 0.00 0.00 44.71 2.59
2286 5516 7.163441 AGCATGCAAATTTTACTTGGAAGAAT 58.837 30.769 21.98 0.00 0.00 2.40
2311 5541 9.612066 ATTGTTGATGGTTGTTTCTATGTTTTT 57.388 25.926 0.00 0.00 0.00 1.94
2384 5851 1.546029 GGAGTTCCCAGCAATTGGTTC 59.454 52.381 7.57 1.76 46.25 3.62
2438 5905 5.705441 ACTGTGGTTATCCAACATGTTAGTG 59.295 40.000 11.53 0.00 46.15 2.74
2457 5924 8.720562 TGTTAGTGTGTTACATGATTCATTCTG 58.279 33.333 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.875727 CCGTTGATCTCTCATGCTGAAAT 59.124 43.478 0.00 0.00 0.00 2.17
1 2 3.264947 CCGTTGATCTCTCATGCTGAAA 58.735 45.455 0.00 0.00 0.00 2.69
2 3 2.419159 CCCGTTGATCTCTCATGCTGAA 60.419 50.000 0.00 0.00 0.00 3.02
3 4 1.137675 CCCGTTGATCTCTCATGCTGA 59.862 52.381 0.00 0.00 0.00 4.26
4 5 1.137675 TCCCGTTGATCTCTCATGCTG 59.862 52.381 0.00 0.00 0.00 4.41
5 6 1.489481 TCCCGTTGATCTCTCATGCT 58.511 50.000 0.00 0.00 0.00 3.79
6 7 2.540265 ATCCCGTTGATCTCTCATGC 57.460 50.000 0.00 0.00 0.00 4.06
7 8 4.445453 TCAAATCCCGTTGATCTCTCATG 58.555 43.478 0.00 0.00 32.56 3.07
8 9 4.760530 TCAAATCCCGTTGATCTCTCAT 57.239 40.909 0.00 0.00 32.56 2.90
9 10 4.507710 CTTCAAATCCCGTTGATCTCTCA 58.492 43.478 0.00 0.00 37.36 3.27
10 11 3.873952 CCTTCAAATCCCGTTGATCTCTC 59.126 47.826 0.00 0.00 37.36 3.20
11 12 3.519510 TCCTTCAAATCCCGTTGATCTCT 59.480 43.478 0.00 0.00 37.36 3.10
12 13 3.873910 TCCTTCAAATCCCGTTGATCTC 58.126 45.455 0.00 0.00 37.36 2.75
13 14 3.370953 CCTCCTTCAAATCCCGTTGATCT 60.371 47.826 0.00 0.00 37.36 2.75
14 15 2.945668 CCTCCTTCAAATCCCGTTGATC 59.054 50.000 0.00 0.00 37.36 2.92
15 16 2.357154 CCCTCCTTCAAATCCCGTTGAT 60.357 50.000 0.00 0.00 37.36 2.57
16 17 1.004277 CCCTCCTTCAAATCCCGTTGA 59.996 52.381 0.00 0.00 35.72 3.18
17 18 1.463674 CCCTCCTTCAAATCCCGTTG 58.536 55.000 0.00 0.00 0.00 4.10
18 19 0.331616 CCCCTCCTTCAAATCCCGTT 59.668 55.000 0.00 0.00 0.00 4.44
19 20 0.845102 ACCCCTCCTTCAAATCCCGT 60.845 55.000 0.00 0.00 0.00 5.28
20 21 0.107165 GACCCCTCCTTCAAATCCCG 60.107 60.000 0.00 0.00 0.00 5.14
21 22 0.107165 CGACCCCTCCTTCAAATCCC 60.107 60.000 0.00 0.00 0.00 3.85
22 23 0.909623 TCGACCCCTCCTTCAAATCC 59.090 55.000 0.00 0.00 0.00 3.01
23 24 3.283259 AATCGACCCCTCCTTCAAATC 57.717 47.619 0.00 0.00 0.00 2.17
24 25 3.739401 AAATCGACCCCTCCTTCAAAT 57.261 42.857 0.00 0.00 0.00 2.32
25 26 3.518992 AAAATCGACCCCTCCTTCAAA 57.481 42.857 0.00 0.00 0.00 2.69
26 27 3.054655 CCTAAAATCGACCCCTCCTTCAA 60.055 47.826 0.00 0.00 0.00 2.69
27 28 2.504175 CCTAAAATCGACCCCTCCTTCA 59.496 50.000 0.00 0.00 0.00 3.02
28 29 2.745482 GCCTAAAATCGACCCCTCCTTC 60.745 54.545 0.00 0.00 0.00 3.46
29 30 1.212195 GCCTAAAATCGACCCCTCCTT 59.788 52.381 0.00 0.00 0.00 3.36
30 31 0.837940 GCCTAAAATCGACCCCTCCT 59.162 55.000 0.00 0.00 0.00 3.69
31 32 0.179026 GGCCTAAAATCGACCCCTCC 60.179 60.000 0.00 0.00 0.00 4.30
32 33 0.179026 GGGCCTAAAATCGACCCCTC 60.179 60.000 0.84 0.00 34.23 4.30
33 34 0.917333 TGGGCCTAAAATCGACCCCT 60.917 55.000 4.53 0.00 40.04 4.79
34 35 0.465642 CTGGGCCTAAAATCGACCCC 60.466 60.000 4.53 0.00 40.04 4.95
35 36 0.544697 TCTGGGCCTAAAATCGACCC 59.455 55.000 4.53 0.00 41.24 4.46
36 37 2.640316 ATCTGGGCCTAAAATCGACC 57.360 50.000 4.53 0.00 0.00 4.79
37 38 5.642491 GGTATTATCTGGGCCTAAAATCGAC 59.358 44.000 4.53 0.00 0.00 4.20
38 39 5.546499 AGGTATTATCTGGGCCTAAAATCGA 59.454 40.000 4.53 0.00 0.00 3.59
39 40 5.805728 AGGTATTATCTGGGCCTAAAATCG 58.194 41.667 4.53 0.00 0.00 3.34
40 41 7.094762 CGAAAGGTATTATCTGGGCCTAAAATC 60.095 40.741 4.53 0.00 0.00 2.17
41 42 6.715264 CGAAAGGTATTATCTGGGCCTAAAAT 59.285 38.462 4.53 0.00 0.00 1.82
42 43 6.059484 CGAAAGGTATTATCTGGGCCTAAAA 58.941 40.000 4.53 0.00 0.00 1.52
43 44 5.131475 ACGAAAGGTATTATCTGGGCCTAAA 59.869 40.000 4.53 0.00 0.00 1.85
44 45 4.657039 ACGAAAGGTATTATCTGGGCCTAA 59.343 41.667 4.53 0.00 0.00 2.69
45 46 4.039973 CACGAAAGGTATTATCTGGGCCTA 59.960 45.833 4.53 0.00 0.00 3.93
46 47 3.046374 ACGAAAGGTATTATCTGGGCCT 58.954 45.455 4.53 0.00 0.00 5.19
47 48 3.139077 CACGAAAGGTATTATCTGGGCC 58.861 50.000 0.00 0.00 0.00 5.80
48 49 3.139077 CCACGAAAGGTATTATCTGGGC 58.861 50.000 0.00 0.00 0.00 5.36
49 50 4.682778 TCCACGAAAGGTATTATCTGGG 57.317 45.455 0.00 0.00 0.00 4.45
50 51 5.853936 TGATCCACGAAAGGTATTATCTGG 58.146 41.667 0.00 0.00 0.00 3.86
51 52 7.657354 TGATTGATCCACGAAAGGTATTATCTG 59.343 37.037 0.00 0.00 0.00 2.90
52 53 7.735917 TGATTGATCCACGAAAGGTATTATCT 58.264 34.615 0.00 0.00 0.00 1.98
53 54 7.872993 TCTGATTGATCCACGAAAGGTATTATC 59.127 37.037 0.00 0.00 0.00 1.75
54 55 7.735917 TCTGATTGATCCACGAAAGGTATTAT 58.264 34.615 0.00 0.00 0.00 1.28
55 56 7.119709 TCTGATTGATCCACGAAAGGTATTA 57.880 36.000 0.00 0.00 0.00 0.98
56 57 5.989477 TCTGATTGATCCACGAAAGGTATT 58.011 37.500 0.00 0.00 0.00 1.89
57 58 5.453903 CCTCTGATTGATCCACGAAAGGTAT 60.454 44.000 0.00 0.00 0.00 2.73
58 59 4.141937 CCTCTGATTGATCCACGAAAGGTA 60.142 45.833 0.00 0.00 0.00 3.08
59 60 3.369892 CCTCTGATTGATCCACGAAAGGT 60.370 47.826 0.00 0.00 0.00 3.50
60 61 3.118629 TCCTCTGATTGATCCACGAAAGG 60.119 47.826 0.00 0.00 0.00 3.11
61 62 4.118410 CTCCTCTGATTGATCCACGAAAG 58.882 47.826 0.00 0.00 0.00 2.62
62 63 3.769300 TCTCCTCTGATTGATCCACGAAA 59.231 43.478 0.00 0.00 0.00 3.46
63 64 3.365472 TCTCCTCTGATTGATCCACGAA 58.635 45.455 0.00 0.00 0.00 3.85
64 65 2.954989 CTCTCCTCTGATTGATCCACGA 59.045 50.000 0.00 0.00 0.00 4.35
65 66 2.035704 CCTCTCCTCTGATTGATCCACG 59.964 54.545 0.00 0.00 0.00 4.94
66 67 2.368221 CCCTCTCCTCTGATTGATCCAC 59.632 54.545 0.00 0.00 0.00 4.02
67 68 2.248423 TCCCTCTCCTCTGATTGATCCA 59.752 50.000 0.00 0.00 0.00 3.41
68 69 2.899256 CTCCCTCTCCTCTGATTGATCC 59.101 54.545 0.00 0.00 0.00 3.36
69 70 2.299867 GCTCCCTCTCCTCTGATTGATC 59.700 54.545 0.00 0.00 0.00 2.92
70 71 2.090606 AGCTCCCTCTCCTCTGATTGAT 60.091 50.000 0.00 0.00 0.00 2.57
71 72 1.290431 AGCTCCCTCTCCTCTGATTGA 59.710 52.381 0.00 0.00 0.00 2.57
72 73 1.413445 CAGCTCCCTCTCCTCTGATTG 59.587 57.143 0.00 0.00 0.00 2.67
73 74 1.008206 ACAGCTCCCTCTCCTCTGATT 59.992 52.381 0.00 0.00 0.00 2.57
74 75 0.636101 ACAGCTCCCTCTCCTCTGAT 59.364 55.000 0.00 0.00 0.00 2.90
75 76 0.411452 AACAGCTCCCTCTCCTCTGA 59.589 55.000 0.00 0.00 0.00 3.27
76 77 1.274712 AAACAGCTCCCTCTCCTCTG 58.725 55.000 0.00 0.00 0.00 3.35
77 78 2.037385 AAAACAGCTCCCTCTCCTCT 57.963 50.000 0.00 0.00 0.00 3.69
78 79 2.431454 CAAAAACAGCTCCCTCTCCTC 58.569 52.381 0.00 0.00 0.00 3.71
79 80 1.546548 GCAAAAACAGCTCCCTCTCCT 60.547 52.381 0.00 0.00 0.00 3.69
80 81 0.884514 GCAAAAACAGCTCCCTCTCC 59.115 55.000 0.00 0.00 0.00 3.71
81 82 1.538950 CAGCAAAAACAGCTCCCTCTC 59.461 52.381 0.00 0.00 41.14 3.20
82 83 1.133668 ACAGCAAAAACAGCTCCCTCT 60.134 47.619 0.00 0.00 41.14 3.69
83 84 1.322442 ACAGCAAAAACAGCTCCCTC 58.678 50.000 0.00 0.00 41.14 4.30
84 85 2.158608 ACTACAGCAAAAACAGCTCCCT 60.159 45.455 0.00 0.00 41.14 4.20
85 86 2.230660 ACTACAGCAAAAACAGCTCCC 58.769 47.619 0.00 0.00 41.14 4.30
86 87 3.990318 AACTACAGCAAAAACAGCTCC 57.010 42.857 0.00 0.00 41.14 4.70
87 88 5.674933 AGTAACTACAGCAAAAACAGCTC 57.325 39.130 0.00 0.00 41.14 4.09
88 89 6.289064 ACTAGTAACTACAGCAAAAACAGCT 58.711 36.000 0.00 0.00 44.62 4.24
89 90 6.541111 ACTAGTAACTACAGCAAAAACAGC 57.459 37.500 0.00 0.00 0.00 4.40
90 91 9.257651 ACTTACTAGTAACTACAGCAAAAACAG 57.742 33.333 11.38 0.00 31.21 3.16
91 92 9.037737 CACTTACTAGTAACTACAGCAAAAACA 57.962 33.333 11.38 0.00 31.96 2.83
92 93 9.038803 ACACTTACTAGTAACTACAGCAAAAAC 57.961 33.333 11.38 0.00 31.96 2.43
93 94 9.037737 CACACTTACTAGTAACTACAGCAAAAA 57.962 33.333 11.38 0.00 31.96 1.94
94 95 7.170320 GCACACTTACTAGTAACTACAGCAAAA 59.830 37.037 11.38 0.00 31.96 2.44
95 96 6.643770 GCACACTTACTAGTAACTACAGCAAA 59.356 38.462 11.38 0.00 31.96 3.68
96 97 6.154445 GCACACTTACTAGTAACTACAGCAA 58.846 40.000 11.38 0.00 31.96 3.91
97 98 5.242171 TGCACACTTACTAGTAACTACAGCA 59.758 40.000 11.38 13.91 31.96 4.41
98 99 5.572126 GTGCACACTTACTAGTAACTACAGC 59.428 44.000 13.17 11.82 31.96 4.40
99 100 5.793952 CGTGCACACTTACTAGTAACTACAG 59.206 44.000 18.64 4.25 31.96 2.74
100 101 5.239306 ACGTGCACACTTACTAGTAACTACA 59.761 40.000 18.64 3.64 31.96 2.74
101 102 5.566774 CACGTGCACACTTACTAGTAACTAC 59.433 44.000 18.64 4.31 31.96 2.73
102 103 5.692814 CACGTGCACACTTACTAGTAACTA 58.307 41.667 18.64 0.00 31.96 2.24
103 104 4.543692 CACGTGCACACTTACTAGTAACT 58.456 43.478 18.64 0.17 31.96 2.24
104 105 3.120782 GCACGTGCACACTTACTAGTAAC 59.879 47.826 34.52 2.55 41.59 2.50
149 150 4.164981 TCTAGGGTTATCATACCGGCATT 58.835 43.478 0.00 0.00 39.18 3.56
153 154 3.367087 CGCTTCTAGGGTTATCATACCGG 60.367 52.174 0.00 0.00 39.18 5.28
168 169 5.597806 CATATTGAACTGGTACCGCTTCTA 58.402 41.667 17.81 12.86 0.00 2.10
187 188 2.094675 GCTCCAACACACCTTGCATAT 58.905 47.619 0.00 0.00 0.00 1.78
257 258 2.396590 ACCAACACGACACAAAGTCT 57.603 45.000 0.00 0.00 45.32 3.24
261 262 0.881796 TGCAACCAACACGACACAAA 59.118 45.000 0.00 0.00 0.00 2.83
339 351 1.552337 GCCTCTCTTCCATCACTGTCA 59.448 52.381 0.00 0.00 0.00 3.58
364 376 3.450115 GGGGGACTCACTCCGTCG 61.450 72.222 0.00 0.00 40.82 5.12
372 385 0.192566 ACACTAGGTTGGGGGACTCA 59.807 55.000 0.00 0.00 0.00 3.41
428 468 3.065019 TCAAACACGAAGCAAAAGCTC 57.935 42.857 0.00 0.00 0.00 4.09
608 676 4.935205 CCGATTCACCTCACATTGTTCTAA 59.065 41.667 0.00 0.00 0.00 2.10
609 677 4.221924 TCCGATTCACCTCACATTGTTCTA 59.778 41.667 0.00 0.00 0.00 2.10
610 678 3.007940 TCCGATTCACCTCACATTGTTCT 59.992 43.478 0.00 0.00 0.00 3.01
636 704 6.927933 AAAATTGTCTTCTTTTTATCGGCG 57.072 33.333 0.00 0.00 0.00 6.46
1046 4202 2.925706 TAGGGCGTGCAAGTCCCA 60.926 61.111 25.31 10.68 42.52 4.37
1069 4225 1.821332 CGGATTGGAAGGAGCAGGC 60.821 63.158 0.00 0.00 0.00 4.85
1139 4295 1.689582 GGAGGATGGAGGAACCCGT 60.690 63.158 0.00 0.00 38.00 5.28
1244 4408 4.680537 ACGGGGAGGAGCAGACGT 62.681 66.667 0.00 0.00 0.00 4.34
1683 4868 1.435577 AGATTAAACGCGACACCCAC 58.564 50.000 15.93 0.00 0.00 4.61
1900 5113 3.815401 AGCTTGGTTACTAGCAACAACAG 59.185 43.478 8.10 1.87 45.99 3.16
2161 5390 5.634118 AGAATGAACATCCAGGTGAAAGAA 58.366 37.500 0.00 0.00 0.00 2.52
2220 5450 5.105877 ACTGCTATTACTCACGCTCAAACTA 60.106 40.000 0.00 0.00 0.00 2.24
2256 5486 6.364706 TCCAAGTAAAATTTGCATGCTAAACG 59.635 34.615 20.33 1.57 0.00 3.60
2311 5541 6.270927 TGGGGTGAACAAATTTGATTCCATTA 59.729 34.615 24.64 6.27 0.00 1.90
2322 5552 0.757188 TGCCGTGGGGTGAACAAATT 60.757 50.000 0.00 0.00 34.97 1.82
2327 5557 1.966451 CTTCTGCCGTGGGGTGAAC 60.966 63.158 0.00 0.00 34.97 3.18


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

AutoCloner maintained by Alex Coulton.