Multiple sequence alignment - TraesCS2B01G174800

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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 TraesCS2B01G174800 chr2B 100.000 5239 0 0 1 5239 149846969 149841731 0.000000e+00 9675.0
1 TraesCS2B01G174800 chr2B 82.234 197 29 6 4811 5004 762363535 762363342 1.170000e-36 165.0
2 TraesCS2B01G174800 chr2B 100.000 54 0 0 4599 4652 149842317 149842264 3.340000e-17 100.0
3 TraesCS2B01G174800 chr2B 100.000 54 0 0 4653 4706 149842371 149842318 3.340000e-17 100.0
4 TraesCS2B01G174800 chr2D 93.288 4693 204 53 12 4624 98271285 98266624 0.000000e+00 6818.0
5 TraesCS2B01G174800 chr2D 86.222 225 18 4 4847 5070 98266471 98266259 1.130000e-56 231.0
6 TraesCS2B01G174800 chr2D 93.805 113 5 1 5065 5177 98266228 98266118 9.020000e-38 169.0
7 TraesCS2B01G174800 chr2D 90.909 77 6 1 2159 2235 47408235 47408310 9.280000e-18 102.0
8 TraesCS2B01G174800 chr2D 85.714 91 10 3 2148 2236 267707179 267707090 5.590000e-15 93.5
9 TraesCS2B01G174800 chr2D 84.000 100 9 6 583 675 69916528 69916627 7.230000e-14 89.8
10 TraesCS2B01G174800 chr2A 94.209 2435 110 19 2231 4652 96250423 96248007 0.000000e+00 3687.0
11 TraesCS2B01G174800 chr2A 95.299 1340 41 9 841 2159 96251770 96250432 0.000000e+00 2106.0
12 TraesCS2B01G174800 chr2A 83.632 446 33 17 4653 5070 96248062 96247629 2.960000e-102 383.0
13 TraesCS2B01G174800 chr2A 94.012 167 10 0 5073 5239 96247594 96247428 2.420000e-63 254.0
14 TraesCS2B01G174800 chr2A 84.242 165 15 8 4737 4892 6081428 6081266 3.270000e-32 150.0
15 TraesCS2B01G174800 chr2A 83.636 165 16 10 4737 4892 6185220 6185058 1.520000e-30 145.0
16 TraesCS2B01G174800 chr2A 83.030 165 17 10 4737 4892 6134173 6134011 7.070000e-29 139.0
17 TraesCS2B01G174800 chr2A 81.595 163 23 6 4737 4892 6277158 6276996 1.530000e-25 128.0
18 TraesCS2B01G174800 chr2A 100.000 35 0 0 4565 4599 4493696 4493730 1.220000e-06 65.8
19 TraesCS2B01G174800 chr2A 100.000 35 0 0 4565 4599 4552918 4552952 1.220000e-06 65.8
20 TraesCS2B01G174800 chr7B 89.130 230 18 4 2220 2442 326671138 326670909 4.000000e-71 279.0
21 TraesCS2B01G174800 chr7A 89.686 223 16 5 2220 2435 138739630 138739852 1.440000e-70 278.0
22 TraesCS2B01G174800 chr7A 87.952 166 13 4 1994 2159 138739386 138739544 6.930000e-44 189.0
23 TraesCS2B01G174800 chr7A 90.123 81 2 6 2154 2231 28447072 28447149 3.340000e-17 100.0
24 TraesCS2B01G174800 chr4D 91.192 193 17 0 2243 2435 503868560 503868368 4.020000e-66 263.0
25 TraesCS2B01G174800 chr4D 84.921 126 11 6 601 719 31802995 31803119 2.560000e-23 121.0
26 TraesCS2B01G174800 chr7D 90.674 193 18 0 2243 2435 424268173 424267981 1.870000e-64 257.0
27 TraesCS2B01G174800 chr7D 75.524 286 49 14 27 304 575004809 575005081 2.560000e-23 121.0
28 TraesCS2B01G174800 chr7D 95.652 69 3 0 2161 2229 46702731 46702663 1.540000e-20 111.0
29 TraesCS2B01G174800 chr7D 89.412 85 5 3 2146 2229 236822599 236822680 2.580000e-18 104.0
30 TraesCS2B01G174800 chr7D 90.000 80 5 3 2153 2231 252560704 252560781 3.340000e-17 100.0
31 TraesCS2B01G174800 chr7D 89.157 83 4 4 2158 2235 184573356 184573438 1.200000e-16 99.0
32 TraesCS2B01G174800 chr6D 78.345 411 63 13 330 722 248515710 248516112 5.240000e-60 243.0
33 TraesCS2B01G174800 chr6D 89.286 84 5 4 4572 4652 140156856 140156938 9.280000e-18 102.0
34 TraesCS2B01G174800 chr6B 76.832 423 71 17 335 740 349454289 349453877 4.110000e-51 213.0
35 TraesCS2B01G174800 chr6B 77.959 245 33 9 485 709 585816890 585817133 3.290000e-27 134.0
36 TraesCS2B01G174800 chrUn 82.099 162 23 5 4737 4892 348170463 348170624 3.290000e-27 134.0
37 TraesCS2B01G174800 chrUn 100.000 35 0 0 4565 4599 176201743 176201709 1.220000e-06 65.8
38 TraesCS2B01G174800 chr4A 77.966 236 32 16 4737 4958 626306502 626306731 4.260000e-26 130.0
39 TraesCS2B01G174800 chr1A 85.271 129 10 5 586 708 251347897 251347772 1.980000e-24 124.0
40 TraesCS2B01G174800 chr4B 86.842 114 8 3 586 693 652249211 652249099 2.560000e-23 121.0
41 TraesCS2B01G174800 chr3A 80.645 155 22 4 586 734 718561532 718561684 4.290000e-21 113.0
42 TraesCS2B01G174800 chr3A 86.364 66 4 3 4678 4739 713982724 713982660 3.390000e-07 67.6
43 TraesCS2B01G174800 chr3A 100.000 32 0 0 4568 4599 710835975 710836006 5.670000e-05 60.2
44 TraesCS2B01G174800 chr1D 92.105 76 4 2 2155 2229 464799720 464799794 7.180000e-19 106.0
45 TraesCS2B01G174800 chr3B 75.319 235 29 18 4678 4887 771767413 771767183 9.350000e-13 86.1
46 TraesCS2B01G174800 chr3B 100.000 32 0 0 4569 4600 704258325 704258294 5.670000e-05 60.2
47 TraesCS2B01G174800 chr3D 82.022 89 10 5 4568 4652 384530740 384530654 2.620000e-08 71.3
48 TraesCS2B01G174800 chr5B 97.059 34 1 0 4568 4601 608625489 608625522 2.040000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G174800 chr2B 149841731 149846969 5238 True 9675.0 9675 100.000 1 5239 1 chr2B.!!$R1 5238
1 TraesCS2B01G174800 chr2D 98266118 98271285 5167 True 2406.0 6818 91.105 12 5177 3 chr2D.!!$R2 5165
2 TraesCS2B01G174800 chr2A 96247428 96251770 4342 True 1607.5 3687 91.788 841 5239 4 chr2A.!!$R5 4398

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
478 507 1.000896 GCCAGTACCAAGCCACCAT 60.001 57.895 0.00 0.00 0.00 3.55 F
1342 1382 0.107456 CTCAGACTGTGGCTGGTTGT 59.893 55.000 1.59 0.00 34.20 3.32 F
2072 2125 1.003118 TGCAGGTACCAAAGTAGCCTG 59.997 52.381 15.94 0.81 46.12 4.85 F
2809 2878 0.389025 GCAAAACCAGAACCAGTGGG 59.611 55.000 15.21 0.00 39.65 4.61 F
3656 3726 1.205655 GAGGCAAAGCAAAATCCCCTC 59.794 52.381 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1416 1468 0.109342 ACTGCCTGTTGGAGTCCTTG 59.891 55.000 11.33 0.0 34.57 3.61 R
2714 2783 0.329596 AGGAACTGGAGGGATGTTGC 59.670 55.000 0.00 0.0 37.18 4.17 R
4012 4086 1.021202 TCGTGTGTTTTGGCTTCAGG 58.979 50.000 0.00 0.0 0.00 3.86 R
4140 4215 0.175302 AACACCACACAACCGACGTA 59.825 50.000 0.00 0.0 0.00 3.57 R
4572 4660 1.003233 GAGCTCGGCCTCCAAAAGT 60.003 57.895 0.00 0.0 0.00 2.66 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
51 53 2.054232 TTTTCACCCTAAACGTGCCA 57.946 45.000 0.00 0.00 0.00 4.92
55 57 1.228033 ACCCTAAACGTGCCACCAC 60.228 57.895 0.00 0.00 38.62 4.16
100 102 4.647615 CGCCTATCCCCGTCGCTG 62.648 72.222 0.00 0.00 0.00 5.18
135 137 1.203052 CCGCAAATTTGAGTCTGCCAT 59.797 47.619 22.31 0.00 0.00 4.40
142 144 2.887568 GAGTCTGCCATGCCGACG 60.888 66.667 5.23 0.00 45.07 5.12
144 146 2.434185 GTCTGCCATGCCGACGAA 60.434 61.111 0.00 0.00 33.66 3.85
214 217 2.758737 GTCCGTCCATCCCCGACT 60.759 66.667 0.00 0.00 0.00 4.18
230 243 4.778415 CTCTGTCGTGACCCCGCG 62.778 72.222 0.00 0.00 46.73 6.46
263 276 2.655364 CACCGCATCGCTACTCCG 60.655 66.667 0.00 0.00 0.00 4.63
288 301 1.067199 ACGTTGCGAATCGACCGTAC 61.067 55.000 6.91 8.07 0.00 3.67
294 307 2.156117 TGCGAATCGACCGTACTTTTTG 59.844 45.455 6.91 0.00 0.00 2.44
299 312 1.562575 CGACCGTACTTTTTGCCGCT 61.563 55.000 0.00 0.00 0.00 5.52
308 321 1.781025 TTTTTGCCGCTCCACTGACG 61.781 55.000 0.00 0.00 0.00 4.35
309 322 2.652382 TTTTGCCGCTCCACTGACGA 62.652 55.000 0.00 0.00 0.00 4.20
311 324 4.357947 GCCGCTCCACTGACGACA 62.358 66.667 0.00 0.00 0.00 4.35
320 333 1.736645 ACTGACGACATTTCCGCCG 60.737 57.895 0.00 0.00 0.00 6.46
357 385 4.275508 CCCAGCCACCACTGCACT 62.276 66.667 0.00 0.00 36.29 4.40
368 396 4.694233 CTGCACTGCCGCTCCACT 62.694 66.667 0.00 0.00 0.00 4.00
400 428 3.001838 CGAATCGATTGTATTTTCCGCCA 59.998 43.478 16.96 0.00 0.00 5.69
406 434 2.799126 TGTATTTTCCGCCACTCCAT 57.201 45.000 0.00 0.00 0.00 3.41
407 435 2.639065 TGTATTTTCCGCCACTCCATC 58.361 47.619 0.00 0.00 0.00 3.51
410 438 2.463589 TTTTCCGCCACTCCATCGCT 62.464 55.000 0.00 0.00 0.00 4.93
441 469 4.612412 TCCCCGCTGCGTTTTCGT 62.612 61.111 21.59 0.00 46.03 3.85
443 471 4.424430 CCCGCTGCGTTTTCGTCG 62.424 66.667 21.59 2.41 46.03 5.12
444 472 3.698463 CCGCTGCGTTTTCGTCGT 61.698 61.111 21.59 0.00 46.03 4.34
445 473 2.201885 CGCTGCGTTTTCGTCGTC 60.202 61.111 14.93 0.00 46.03 4.20
466 495 2.202878 GCCGCTCATTCGCCAGTA 60.203 61.111 0.00 0.00 0.00 2.74
477 506 2.434331 GCCAGTACCAAGCCACCA 59.566 61.111 0.00 0.00 0.00 4.17
478 507 1.000896 GCCAGTACCAAGCCACCAT 60.001 57.895 0.00 0.00 0.00 3.55
486 515 1.984026 CAAGCCACCATCCAACCCC 60.984 63.158 0.00 0.00 0.00 4.95
529 558 3.615709 AACTTTTGCCCCGCAGCC 61.616 61.111 0.00 0.00 40.61 4.85
549 578 2.579201 CACCCCGATTCGAGCACT 59.421 61.111 7.83 0.00 0.00 4.40
585 614 4.489771 CTCCGCCGCCCCAATTCT 62.490 66.667 0.00 0.00 0.00 2.40
586 615 3.995506 CTCCGCCGCCCCAATTCTT 62.996 63.158 0.00 0.00 0.00 2.52
587 616 2.124487 CCGCCGCCCCAATTCTTA 60.124 61.111 0.00 0.00 0.00 2.10
603 632 7.270047 CCAATTCTTACATCTCCATTTGCATT 58.730 34.615 0.00 0.00 0.00 3.56
636 665 5.762045 AGTTGCACTTTTACATCACACATC 58.238 37.500 0.00 0.00 0.00 3.06
641 670 6.025896 GCACTTTTACATCACACATCATCTG 58.974 40.000 0.00 0.00 0.00 2.90
647 676 4.005650 ACATCACACATCATCTGTTGGAC 58.994 43.478 0.00 0.00 35.29 4.02
659 688 3.214328 TCTGTTGGACTTGCCTCTTTTC 58.786 45.455 0.00 0.00 37.63 2.29
719 749 8.992073 ACTGTTTTAAATCTCCAAATTTGCATC 58.008 29.630 12.92 0.00 31.50 3.91
746 776 4.044065 TGTTGGACATGATTTTAGAGGGGT 59.956 41.667 0.00 0.00 0.00 4.95
747 777 4.235079 TGGACATGATTTTAGAGGGGTG 57.765 45.455 0.00 0.00 0.00 4.61
769 799 7.441836 GGTGAAATTTACCCAGTTTGATTTCT 58.558 34.615 0.00 0.00 35.57 2.52
779 809 4.942483 CCAGTTTGATTTCTGATGCTCTCT 59.058 41.667 0.00 0.00 34.02 3.10
780 810 5.064962 CCAGTTTGATTTCTGATGCTCTCTC 59.935 44.000 0.00 0.00 34.02 3.20
823 853 6.121590 TGAATTGCATACCACATATGTCACT 58.878 36.000 5.07 0.00 42.52 3.41
878 908 1.476833 GCACCTGAACTCCAACAAGGA 60.477 52.381 0.00 0.00 46.75 3.36
907 937 3.350219 TCTGCTTTTCTCCGCCTAATT 57.650 42.857 0.00 0.00 0.00 1.40
1242 1279 1.683385 AGGCTGCTGTTTCTTGAAACC 59.317 47.619 19.53 8.89 31.87 3.27
1331 1371 0.807667 GCATACCCGTGCTCAGACTG 60.808 60.000 0.00 0.00 41.82 3.51
1342 1382 0.107456 CTCAGACTGTGGCTGGTTGT 59.893 55.000 1.59 0.00 34.20 3.32
1389 1441 1.067916 GGTGGTTGTTTGCTGCAGG 59.932 57.895 17.12 0.00 0.00 4.85
1416 1468 4.637977 GGGTTCCAGAAGATTGACAAGATC 59.362 45.833 0.00 0.00 0.00 2.75
1463 1515 1.338579 GCTGGAAGAACTCACTGGGAG 60.339 57.143 5.13 5.13 43.44 4.30
1580 1632 4.213694 TGTGGCATGATGAAATTTTGCAAC 59.786 37.500 10.98 10.98 38.31 4.17
1757 1810 9.294030 CTAAATGACAAGAAGCAATTTATGGTC 57.706 33.333 0.00 0.00 39.29 4.02
1770 1823 3.512219 TTATGGTCCGTGGTTTCCTTT 57.488 42.857 0.00 0.00 0.00 3.11
1883 1936 5.878755 CCATGAGGAAGACGTGAGTACACT 61.879 50.000 0.00 0.00 41.07 3.55
2035 2088 4.162131 TCTTGGTGCTAATAGATGTGCTCA 59.838 41.667 0.00 0.00 0.00 4.26
2072 2125 1.003118 TGCAGGTACCAAAGTAGCCTG 59.997 52.381 15.94 0.81 46.12 4.85
2169 2222 9.557061 CAGGTAAAATTAAGTAATACTCCCTCC 57.443 37.037 0.00 0.00 0.00 4.30
2188 2241 4.466370 CCTCCGTCCCATAATATAAGAGCA 59.534 45.833 0.00 0.00 0.00 4.26
2189 2242 5.394663 CCTCCGTCCCATAATATAAGAGCAG 60.395 48.000 0.00 0.00 0.00 4.24
2206 2275 4.524714 AGAGCAGTTTTGACACTAGCTCTA 59.475 41.667 18.23 0.00 45.87 2.43
2220 2289 6.153000 ACACTAGCTCTAATATTATGGGACGG 59.847 42.308 0.00 0.00 0.00 4.79
2237 2306 3.813724 GGACGGAGGGAGTATAATTTTGC 59.186 47.826 0.00 0.00 0.00 3.68
2452 2521 6.426025 AGGTATTTTTACAGAAGTGTCGGAAC 59.574 38.462 0.00 0.00 38.19 3.62
2557 2626 5.594317 ACACAGCAAGTAAGTTTTCTGGAAT 59.406 36.000 0.00 0.00 0.00 3.01
2714 2783 2.554032 CACCTCTGTAAACCAAAGGCAG 59.446 50.000 0.00 0.00 0.00 4.85
2715 2784 1.541588 CCTCTGTAAACCAAAGGCAGC 59.458 52.381 0.00 0.00 0.00 5.25
2716 2785 2.229792 CTCTGTAAACCAAAGGCAGCA 58.770 47.619 0.00 0.00 0.00 4.41
2741 2810 5.131142 ACATCCCTCCAGTTCCTTTATACTG 59.869 44.000 0.00 0.00 41.08 2.74
2809 2878 0.389025 GCAAAACCAGAACCAGTGGG 59.611 55.000 15.21 0.00 39.65 4.61
2878 2947 7.093201 CCCAAGTAGGATGTGTAAACCTTACTA 60.093 40.741 0.00 0.00 41.22 1.82
2901 2970 8.311836 ACTAGGTTGAAGAATCTTGTTTATCGA 58.688 33.333 0.00 0.00 25.09 3.59
3260 3329 5.733226 TTGTTGTCAAGGTATGATATGCG 57.267 39.130 0.00 0.00 40.97 4.73
3472 3542 7.393234 TGGAGATAAAATGTCGGATGAAAAAGT 59.607 33.333 0.00 0.00 0.00 2.66
3594 3664 4.844655 AGTGGGGACAACTTAGTCAGTAAT 59.155 41.667 0.00 0.00 46.06 1.89
3627 3697 5.856156 ACATGACTTTGCATCAATTTTGGA 58.144 33.333 0.00 0.00 0.00 3.53
3656 3726 1.205655 GAGGCAAAGCAAAATCCCCTC 59.794 52.381 0.00 0.00 0.00 4.30
3743 3813 6.325993 TGGAGATAAAGAATCCCATGACAA 57.674 37.500 0.00 0.00 34.90 3.18
3871 3945 1.215382 CTCGCAGATCGTCAACCCA 59.785 57.895 0.00 0.00 39.67 4.51
3880 3954 4.454161 CAGATCGTCAACCCACATAACAAA 59.546 41.667 0.00 0.00 0.00 2.83
4012 4086 4.803426 CCGTGCAGGTCTCTCGCC 62.803 72.222 5.57 0.00 34.51 5.54
4091 4166 7.562454 TCCCCGTATGTAATTTTCTTTGATC 57.438 36.000 0.00 0.00 0.00 2.92
4106 4181 4.391830 TCTTTGATCGGTTCATTCTTTCCG 59.608 41.667 0.00 0.00 43.65 4.30
4140 4215 6.276832 TGTTAGCTTCGGATTGTTAGTAGT 57.723 37.500 0.00 0.00 0.00 2.73
4143 4218 4.918037 AGCTTCGGATTGTTAGTAGTACG 58.082 43.478 0.00 0.00 0.00 3.67
4219 4294 3.006967 GTGGTGACCAGTGAGAGTTATGT 59.993 47.826 3.58 0.00 32.34 2.29
4225 4300 7.268586 GTGACCAGTGAGAGTTATGTGATTAT 58.731 38.462 0.00 0.00 0.00 1.28
4375 4454 1.457346 CAGTTCTGGTGGCAAGATCC 58.543 55.000 0.00 0.00 0.00 3.36
4376 4455 1.004044 CAGTTCTGGTGGCAAGATCCT 59.996 52.381 0.00 0.00 0.00 3.24
4387 4466 5.047235 GGTGGCAAGATCCTACGAGTATAAT 60.047 44.000 0.00 0.00 0.00 1.28
4428 4507 0.951040 GGGATAAGCTGGCCGAATCG 60.951 60.000 0.00 0.00 0.00 3.34
4434 4513 2.892640 CTGGCCGAATCGAGGTGA 59.107 61.111 3.36 0.00 0.00 4.02
4447 4526 6.036083 CGAATCGAGGTGACAGATTTGTATTT 59.964 38.462 0.00 0.00 39.15 1.40
4449 4528 8.786826 AATCGAGGTGACAGATTTGTATTTAA 57.213 30.769 0.00 0.00 37.76 1.52
4450 4529 7.827819 TCGAGGTGACAGATTTGTATTTAAG 57.172 36.000 0.00 0.00 37.76 1.85
4451 4530 7.383687 TCGAGGTGACAGATTTGTATTTAAGT 58.616 34.615 0.00 0.00 37.76 2.24
4500 4588 5.222130 GGCCAGAATGAGGGGAATAATTCTA 60.222 44.000 0.00 0.00 39.69 2.10
4523 4611 1.072266 ACCTATTCAGCCACAACCCA 58.928 50.000 0.00 0.00 0.00 4.51
4535 4623 3.564225 GCCACAACCCAGCTGTTATATAC 59.436 47.826 13.81 0.00 0.00 1.47
4607 4695 1.453155 CTCCATGGAGGTCGGTTTTG 58.547 55.000 31.14 4.89 38.51 2.44
4610 4698 1.812571 CCATGGAGGTCGGTTTTGAAG 59.187 52.381 5.56 0.00 0.00 3.02
4613 4701 3.502123 TGGAGGTCGGTTTTGAAGAAT 57.498 42.857 0.00 0.00 0.00 2.40
4656 4746 8.716619 TCGTATTTTACATTTCAAAAAGTCGG 57.283 30.769 0.00 0.00 31.70 4.79
4657 4747 8.344098 TCGTATTTTACATTTCAAAAAGTCGGT 58.656 29.630 0.00 0.00 31.70 4.69
4658 4748 8.960075 CGTATTTTACATTTCAAAAAGTCGGTT 58.040 29.630 0.00 0.00 0.00 4.44
4661 4751 9.980780 ATTTTACATTTCAAAAAGTCGGTTTTG 57.019 25.926 11.36 11.36 45.71 2.44
4676 4766 9.810545 AAGTCGGTTTTGAAGAATTTAAATTCA 57.189 25.926 32.22 17.77 45.59 2.57
4677 4767 9.981114 AGTCGGTTTTGAAGAATTTAAATTCAT 57.019 25.926 32.22 25.01 45.59 2.57
4679 4769 9.973450 TCGGTTTTGAAGAATTTAAATTCATCA 57.027 25.926 30.69 30.69 45.72 3.07
4734 4824 5.822519 TGAAAGAACATACATACATGGAGGC 59.177 40.000 0.00 0.00 0.00 4.70
4747 4856 7.560991 ACATACATGGAGGCATAAATTTTCAGA 59.439 33.333 0.00 0.00 0.00 3.27
4756 4865 9.567848 GAGGCATAAATTTTCAGAACGAAATAA 57.432 29.630 0.00 0.00 43.12 1.40
4824 4937 4.463539 TGATTGTTCATCCCCAAAGTCATG 59.536 41.667 0.00 0.00 0.00 3.07
4901 5016 3.374988 CACGCATACACATCACATCCTTT 59.625 43.478 0.00 0.00 0.00 3.11
4995 5111 1.306141 TCCATGGAGGCCGAACTCT 60.306 57.895 11.44 0.00 37.63 3.24
4996 5112 1.153289 CCATGGAGGCCGAACTCTG 60.153 63.158 5.56 0.00 37.63 3.35
5005 5121 1.301401 CCGAACTCTGAAACGCCCA 60.301 57.895 0.00 0.00 0.00 5.36
5007 5123 1.156736 CGAACTCTGAAACGCCCAAT 58.843 50.000 0.00 0.00 0.00 3.16
5041 5159 3.753272 GTGTCTTAAGCAATCTCAAGCCA 59.247 43.478 0.00 0.00 0.00 4.75
5042 5160 3.753272 TGTCTTAAGCAATCTCAAGCCAC 59.247 43.478 0.00 0.00 0.00 5.01
5071 5225 3.262405 AGGTTTAACCCGAGCACTGATAA 59.738 43.478 10.93 0.00 39.75 1.75
5109 5263 1.664965 ACGCTTCGTCAGGTTCAGC 60.665 57.895 0.00 0.00 33.69 4.26
5229 5383 0.859232 CGACAGCGGCCATATTACAC 59.141 55.000 2.24 0.00 0.00 2.90
5231 5385 1.867233 GACAGCGGCCATATTACACAG 59.133 52.381 2.24 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.387445 TGAAAATCACCGGCGAGCG 61.387 57.895 9.30 0.00 0.00 5.03
165 167 0.318120 CGGCTTTCCAGGCACAAATT 59.682 50.000 0.00 0.00 46.30 1.82
190 193 4.530857 GATGGACGGACAGGCGGG 62.531 72.222 0.00 0.00 0.00 6.13
196 199 3.072468 GTCGGGGATGGACGGACA 61.072 66.667 0.00 0.00 37.88 4.02
200 203 2.005960 GACAGAGTCGGGGATGGACG 62.006 65.000 0.00 0.00 39.38 4.79
234 247 3.792736 GCGGTGGTGGCAGGGATA 61.793 66.667 0.00 0.00 0.00 2.59
272 285 2.068837 AAAGTACGGTCGATTCGCAA 57.931 45.000 10.34 0.00 0.00 4.85
288 301 0.040067 GTCAGTGGAGCGGCAAAAAG 60.040 55.000 1.45 0.00 0.00 2.27
294 307 3.649277 ATGTCGTCAGTGGAGCGGC 62.649 63.158 0.00 0.00 0.00 6.53
299 312 0.669318 GCGGAAATGTCGTCAGTGGA 60.669 55.000 0.00 0.00 0.00 4.02
308 321 3.861263 GGCGACGGCGGAAATGTC 61.861 66.667 15.06 0.00 41.24 3.06
352 380 4.687215 GAGTGGAGCGGCAGTGCA 62.687 66.667 18.61 0.00 37.31 4.57
385 413 3.080300 TGGAGTGGCGGAAAATACAAT 57.920 42.857 0.00 0.00 0.00 2.71
458 487 2.345991 GTGGCTTGGTACTGGCGA 59.654 61.111 0.00 0.00 0.00 5.54
461 490 0.394352 GGATGGTGGCTTGGTACTGG 60.394 60.000 0.00 0.00 0.00 4.00
464 493 1.173913 GTTGGATGGTGGCTTGGTAC 58.826 55.000 0.00 0.00 0.00 3.34
466 495 1.228862 GGTTGGATGGTGGCTTGGT 60.229 57.895 0.00 0.00 0.00 3.67
477 506 2.453497 TGGGTGTGGGGGTTGGAT 60.453 61.111 0.00 0.00 0.00 3.41
478 507 3.503839 GTGGGTGTGGGGGTTGGA 61.504 66.667 0.00 0.00 0.00 3.53
505 534 2.028925 GGGCAAAAGTTGTGCGGG 59.971 61.111 11.90 0.00 43.18 6.13
511 540 2.356194 GCTGCGGGGCAAAAGTTG 60.356 61.111 0.00 0.00 38.41 3.16
533 562 2.579201 CAGTGCTCGAATCGGGGT 59.421 61.111 4.15 0.00 0.00 4.95
586 615 9.234827 CCAATAGATAATGCAAATGGAGATGTA 57.765 33.333 0.00 0.00 0.00 2.29
587 616 7.946219 TCCAATAGATAATGCAAATGGAGATGT 59.054 33.333 0.00 0.00 32.29 3.06
636 665 2.486472 AGAGGCAAGTCCAACAGATG 57.514 50.000 0.00 0.00 37.29 2.90
641 670 5.531287 TCTTTAGAAAAGAGGCAAGTCCAAC 59.469 40.000 0.00 0.00 37.29 3.77
683 713 9.567776 TGGAGATTTAAAACAGTTACATCTTCA 57.432 29.630 0.00 0.95 29.08 3.02
702 732 7.767198 CCAACATAAGATGCAAATTTGGAGATT 59.233 33.333 19.47 16.27 30.13 2.40
719 749 7.013655 CCCCTCTAAAATCATGTCCAACATAAG 59.986 40.741 0.00 0.00 36.53 1.73
722 752 5.203528 CCCCTCTAAAATCATGTCCAACAT 58.796 41.667 0.00 0.00 39.91 2.71
746 776 8.243961 TCAGAAATCAAACTGGGTAAATTTCA 57.756 30.769 0.00 0.00 36.21 2.69
747 777 9.143631 CATCAGAAATCAAACTGGGTAAATTTC 57.856 33.333 0.00 0.00 34.75 2.17
761 791 7.110810 AGAAATGAGAGAGCATCAGAAATCAA 58.889 34.615 0.00 0.00 37.82 2.57
762 792 6.651086 AGAAATGAGAGAGCATCAGAAATCA 58.349 36.000 0.00 0.00 37.82 2.57
764 794 7.941431 AAAGAAATGAGAGAGCATCAGAAAT 57.059 32.000 0.00 0.00 37.82 2.17
769 799 5.563592 TCCAAAAGAAATGAGAGAGCATCA 58.436 37.500 0.00 0.00 37.82 3.07
780 810 9.815936 GCAATTCAAACTAATCCAAAAGAAATG 57.184 29.630 0.00 0.00 0.00 2.32
805 835 4.801147 CACAGTGACATATGTGGTATGC 57.199 45.455 14.43 0.00 43.30 3.14
828 858 5.003632 TGGTGACATGAGAGCATCTGGAG 62.004 52.174 0.00 0.00 40.91 3.86
878 908 4.142513 GCGGAGAAAAGCAGATGATTCTTT 60.143 41.667 0.00 0.00 32.54 2.52
993 1027 4.810184 GGCGAGGGGGAGGGGTTA 62.810 72.222 0.00 0.00 0.00 2.85
1146 1181 2.556459 CCTGGATCTCGCCGTCGAT 61.556 63.158 0.00 0.00 44.56 3.59
1242 1279 6.146673 ACGAACGAAATTGGTACTCCTAAAAG 59.853 38.462 0.14 0.00 34.23 2.27
1331 1371 1.826487 ACGGGAAACAACCAGCCAC 60.826 57.895 0.00 0.00 0.00 5.01
1342 1382 5.312895 TCAGAAATTCAGAATCACGGGAAA 58.687 37.500 0.00 0.00 0.00 3.13
1389 1441 4.335416 TGTCAATCTTCTGGAACCCATTC 58.665 43.478 0.00 0.00 30.82 2.67
1416 1468 0.109342 ACTGCCTGTTGGAGTCCTTG 59.891 55.000 11.33 0.00 34.57 3.61
1463 1515 1.817099 CGCTTGCACTCCCTCATCC 60.817 63.158 0.00 0.00 0.00 3.51
1580 1632 4.469945 TGGTACATTCTCCAGGTAAAGAGG 59.530 45.833 0.00 0.00 0.00 3.69
1757 1810 3.418047 ACAGGAATAAAGGAAACCACGG 58.582 45.455 0.00 0.00 0.00 4.94
1770 1823 6.061441 ACATGACACAACAAAGACAGGAATA 58.939 36.000 0.00 0.00 0.00 1.75
1960 2013 7.386299 GCAGTTTCAGGAGGTGTATATATGAAG 59.614 40.741 0.00 0.00 0.00 3.02
2035 2088 1.019278 GCAACACCATGACGACCGAT 61.019 55.000 0.00 0.00 0.00 4.18
2072 2125 6.258068 CGAATAGTTCAATCCTCTTGTTACCC 59.742 42.308 0.00 0.00 0.00 3.69
2162 2215 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2169 2222 7.441157 TCAAAACTGCTCTTATATTATGGGACG 59.559 37.037 0.00 0.00 0.00 4.79
2206 2275 3.870559 ACTCCCTCCGTCCCATAATATT 58.129 45.455 0.00 0.00 0.00 1.28
2260 2329 7.770897 AGGTACTTGGATGAGAATGTTAACATC 59.229 37.037 21.02 14.03 35.60 3.06
2444 2513 4.815308 TGTAAATTTCCTTTCGTTCCGACA 59.185 37.500 0.00 0.00 34.89 4.35
2714 2783 0.329596 AGGAACTGGAGGGATGTTGC 59.670 55.000 0.00 0.00 37.18 4.17
2715 2784 2.887151 AAGGAACTGGAGGGATGTTG 57.113 50.000 0.00 0.00 40.86 3.33
2716 2785 5.731678 AGTATAAAGGAACTGGAGGGATGTT 59.268 40.000 0.00 0.00 40.86 2.71
2741 2810 5.320549 TCGATACACCTTACAGTTCCTTC 57.679 43.478 0.00 0.00 0.00 3.46
2809 2878 6.679327 AAACAGTCTCCAGTTTAAACAGAC 57.321 37.500 21.25 21.25 36.28 3.51
2878 2947 8.043710 AGATCGATAAACAAGATTCTTCAACCT 58.956 33.333 0.00 0.00 0.00 3.50
2901 2970 8.691661 ACTTCAAACCACAACTTATAACAGAT 57.308 30.769 0.00 0.00 0.00 2.90
3260 3329 6.753107 ACCCAATACAAATACTAACACAGC 57.247 37.500 0.00 0.00 0.00 4.40
3344 3413 4.620982 ACTTGGCTTTTAGTTGAACATGC 58.379 39.130 0.00 0.00 0.00 4.06
3472 3542 4.402155 GTGCACAGAATTTCATTATCCCCA 59.598 41.667 13.17 0.00 0.00 4.96
3594 3664 5.826601 TGCAAAGTCATGTTGTTCTAACA 57.173 34.783 0.00 0.00 37.08 2.41
3605 3675 6.788684 TTCCAAAATTGATGCAAAGTCATG 57.211 33.333 0.00 0.00 0.00 3.07
3627 3697 6.430925 GGATTTTGCTTTGCCTCCTTTATTTT 59.569 34.615 0.00 0.00 0.00 1.82
3656 3726 7.393234 TCATTTTTATCTCCACCAAACTACCAG 59.607 37.037 0.00 0.00 0.00 4.00
3743 3813 2.609427 AGTATGCATGCGATGACACT 57.391 45.000 14.09 6.53 0.00 3.55
3805 3875 5.295787 TGCAAGTAGGAAAACAAGTGTGTAG 59.704 40.000 0.00 0.00 36.80 2.74
3871 3945 4.406456 TGTCTGGGATGCTTTTGTTATGT 58.594 39.130 0.00 0.00 0.00 2.29
3880 3954 1.528824 CGGGATGTCTGGGATGCTT 59.471 57.895 0.00 0.00 0.00 3.91
3916 3990 2.046892 CGGTTCTGCACAGGAGGG 60.047 66.667 0.00 0.00 0.00 4.30
4012 4086 1.021202 TCGTGTGTTTTGGCTTCAGG 58.979 50.000 0.00 0.00 0.00 3.86
4091 4166 2.518949 CAATGCGGAAAGAATGAACCG 58.481 47.619 0.00 0.00 46.74 4.44
4140 4215 0.175302 AACACCACACAACCGACGTA 59.825 50.000 0.00 0.00 0.00 3.57
4143 4218 3.761311 TTTAAACACCACACAACCGAC 57.239 42.857 0.00 0.00 0.00 4.79
4219 4294 7.225931 GGAAGGTATACGAGCAAACAATAATCA 59.774 37.037 0.00 0.00 0.00 2.57
4225 4300 4.546829 AGGAAGGTATACGAGCAAACAA 57.453 40.909 0.00 0.00 0.00 2.83
4387 4466 6.717540 TCCCCAATTTCTTCTTCGATTTACAA 59.282 34.615 0.00 0.00 0.00 2.41
4428 4507 9.654663 ACTACTTAAATACAAATCTGTCACCTC 57.345 33.333 0.00 0.00 36.96 3.85
4500 4588 3.136626 GGGTTGTGGCTGAATAGGTATCT 59.863 47.826 0.00 0.00 0.00 1.98
4523 4611 9.649167 AGTTAAAGTTGAACGTATATAACAGCT 57.351 29.630 0.00 0.00 31.85 4.24
4535 4623 9.931210 ACTTTCATCTTAAGTTAAAGTTGAACG 57.069 29.630 18.39 11.77 41.46 3.95
4572 4660 1.003233 GAGCTCGGCCTCCAAAAGT 60.003 57.895 0.00 0.00 0.00 2.66
4630 4720 9.337091 CCGACTTTTTGAAATGTAAAATACGAT 57.663 29.630 0.00 0.00 30.77 3.73
4631 4721 8.344098 ACCGACTTTTTGAAATGTAAAATACGA 58.656 29.630 0.00 0.00 30.77 3.43
4632 4722 8.496872 ACCGACTTTTTGAAATGTAAAATACG 57.503 30.769 0.00 0.00 0.00 3.06
4635 4725 9.980780 CAAAACCGACTTTTTGAAATGTAAAAT 57.019 25.926 9.85 0.00 45.54 1.82
4650 4740 9.810545 TGAATTTAAATTCTTCAAAACCGACTT 57.189 25.926 31.05 1.26 43.97 3.01
4651 4741 9.981114 ATGAATTTAAATTCTTCAAAACCGACT 57.019 25.926 31.05 0.84 43.97 4.18
4715 4805 7.744087 TTTATGCCTCCATGTATGTATGTTC 57.256 36.000 0.00 0.00 32.85 3.18
4724 4814 7.415095 CGTTCTGAAAATTTATGCCTCCATGTA 60.415 37.037 0.00 0.00 32.85 2.29
4726 4816 5.745294 CGTTCTGAAAATTTATGCCTCCATG 59.255 40.000 0.00 0.00 32.85 3.66
4729 4819 5.560966 TCGTTCTGAAAATTTATGCCTCC 57.439 39.130 0.00 0.00 0.00 4.30
4747 4856 6.894339 ACCCTCATTTCAACTTATTTCGTT 57.106 33.333 0.00 0.00 0.00 3.85
4756 4865 2.665165 TGCACAACCCTCATTTCAACT 58.335 42.857 0.00 0.00 0.00 3.16
4794 4906 2.101783 GGGATGAACAATCATGTGCCA 58.898 47.619 0.00 0.00 46.30 4.92
4882 4997 8.383318 AGTATAAAAGGATGTGATGTGTATGC 57.617 34.615 0.00 0.00 0.00 3.14
4991 5107 3.914426 ATAGATTGGGCGTTTCAGAGT 57.086 42.857 0.00 0.00 0.00 3.24
4995 5111 5.353394 AGAACTATAGATTGGGCGTTTCA 57.647 39.130 6.78 0.00 0.00 2.69
4996 5112 5.585047 ACAAGAACTATAGATTGGGCGTTTC 59.415 40.000 6.78 0.00 0.00 2.78
5005 5121 9.944376 TTGCTTAAGACACAAGAACTATAGATT 57.056 29.630 6.67 0.00 0.00 2.40
5007 5123 9.587772 GATTGCTTAAGACACAAGAACTATAGA 57.412 33.333 6.67 0.00 0.00 1.98
5041 5159 1.294459 GGGTTAAACCTCGCTCGGT 59.706 57.895 0.96 0.00 38.64 4.69
5042 5160 1.808390 CGGGTTAAACCTCGCTCGG 60.808 63.158 8.19 0.00 38.64 4.63
5071 5225 3.982058 CGTCGAGTTTCTTCAGTTAGCTT 59.018 43.478 0.00 0.00 0.00 3.74
5109 5263 1.093159 GGGAGCAAGCATGTCAGAAG 58.907 55.000 0.00 0.00 0.00 2.85
5186 5340 9.894783 TCGCTTGTAGAACTACTTGAATATATC 57.105 33.333 12.25 0.00 37.00 1.63
5198 5352 1.135489 CCGCTGTCGCTTGTAGAACTA 60.135 52.381 0.00 0.00 0.00 2.24
5202 5356 2.126071 GCCGCTGTCGCTTGTAGA 60.126 61.111 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.