Multiple sequence alignment - TraesCS1D01G171400

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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 TraesCS1D01G171400 chr1D 100.000 6488 0 0 1 6488 244757069 244750582 0.000000e+00 11982
1 TraesCS1D01G171400 chr1D 93.335 5101 275 32 1 5083 244189877 244184824 0.000000e+00 7476
2 TraesCS1D01G171400 chr1D 93.020 4914 248 35 1168 6062 244180621 244175784 0.000000e+00 7086
3 TraesCS1D01G171400 chr1D 87.955 2997 276 52 2124 5083 70841190 70844138 0.000000e+00 3456
4 TraesCS1D01G171400 chr1D 91.786 2167 159 16 2924 5083 80860164 80862318 0.000000e+00 2998
5 TraesCS1D01G171400 chr1D 91.624 2173 161 17 2917 5083 80851549 80853706 0.000000e+00 2985
6 TraesCS1D01G171400 chr1D 94.904 1413 63 6 5079 6487 180381447 180382854 0.000000e+00 2202
7 TraesCS1D01G171400 chr1D 96.572 1167 39 1 1 1167 254465348 254464183 0.000000e+00 1932
8 TraesCS1D01G171400 chr1D 85.745 463 53 11 1165 1621 73923465 73923920 1.640000e-130 477
9 TraesCS1D01G171400 chr1D 83.135 504 61 21 1168 1655 329372497 329372992 7.720000e-119 438
10 TraesCS1D01G171400 chr1D 79.233 626 91 29 1168 1776 432084982 432084379 3.640000e-107 399
11 TraesCS1D01G171400 chr1D 77.685 596 91 32 1200 1776 432092533 432091961 6.270000e-85 326
12 TraesCS1D01G171400 chr3D 90.420 3403 271 37 1168 4537 290773444 290776824 0.000000e+00 4427
13 TraesCS1D01G171400 chr3D 89.465 2430 224 28 2668 5083 361840327 361837916 0.000000e+00 3040
14 TraesCS1D01G171400 chr3D 90.943 2131 145 15 1847 3976 290753938 290756021 0.000000e+00 2822
15 TraesCS1D01G171400 chr3D 87.179 702 62 19 1168 1849 290745310 290746003 0.000000e+00 773
16 TraesCS1D01G171400 chr3D 77.986 586 96 31 1168 1738 241185651 241186218 2.900000e-88 337
17 TraesCS1D01G171400 chr3D 77.021 631 106 33 1168 1777 310611305 310611917 6.270000e-85 326
18 TraesCS1D01G171400 chr3D 79.310 174 18 15 1849 2009 82765577 82765409 8.900000e-19 106
19 TraesCS1D01G171400 chr2D 92.976 2164 135 16 2924 5083 373960711 373958561 0.000000e+00 3138
20 TraesCS1D01G171400 chr2D 83.958 480 61 15 1168 1640 449255678 449256148 4.620000e-121 446
21 TraesCS1D01G171400 chr2D 79.275 193 20 17 1831 2009 287359150 287359336 4.110000e-22 117
22 TraesCS1D01G171400 chr4D 92.212 2170 154 13 2924 5083 392434563 392436727 0.000000e+00 3057
23 TraesCS1D01G171400 chr4D 91.897 2172 157 16 2924 5083 392447249 392449413 0.000000e+00 3018
24 TraesCS1D01G171400 chr4D 96.218 1375 43 5 5079 6449 270704340 270702971 0.000000e+00 2242
25 TraesCS1D01G171400 chr5D 91.705 2170 156 19 2924 5083 518977574 518975419 0.000000e+00 2988
26 TraesCS1D01G171400 chr5D 95.782 1375 46 7 5079 6449 503318284 503316918 0.000000e+00 2207
27 TraesCS1D01G171400 chr5D 95.776 1373 48 6 5079 6446 6248490 6249857 0.000000e+00 2206
28 TraesCS1D01G171400 chr5D 96.401 1167 41 1 1 1167 503319440 503318275 0.000000e+00 1921
29 TraesCS1D01G171400 chr5D 96.315 1167 43 0 1 1167 6247333 6248499 0.000000e+00 1917
30 TraesCS1D01G171400 chr5D 83.992 481 59 16 1168 1640 215436932 215436462 4.620000e-121 446
31 TraesCS1D01G171400 chr5D 83.925 479 62 14 1168 1640 234917147 234917616 1.660000e-120 444
32 TraesCS1D01G171400 chr1A 96.374 1379 38 6 5079 6449 554486811 554485437 0.000000e+00 2259
33 TraesCS1D01G171400 chr1A 96.575 1168 39 1 1 1167 554487969 554486802 0.000000e+00 1934
34 TraesCS1D01G171400 chr1A 84.615 247 30 5 2414 2657 153376979 153376738 8.410000e-59 239
35 TraesCS1D01G171400 chr2B 96.369 1377 40 5 5079 6449 683732229 683730857 0.000000e+00 2257
36 TraesCS1D01G171400 chr2B 96.649 1164 39 0 1 1164 683734340 683733177 0.000000e+00 1934
37 TraesCS1D01G171400 chr7B 96.431 1373 40 6 5079 6446 662750283 662751651 0.000000e+00 2255
38 TraesCS1D01G171400 chr7B 96.478 1164 41 0 4 1167 662749129 662750292 0.000000e+00 1923
39 TraesCS1D01G171400 chr3A 96.361 1374 40 6 5079 6446 105552172 105553541 0.000000e+00 2252
40 TraesCS1D01G171400 chr3A 96.401 1167 42 0 1 1167 105551015 105552181 0.000000e+00 1923
41 TraesCS1D01G171400 chr3A 85.220 318 42 5 2753 3068 412598756 412599070 8.120000e-84 322
42 TraesCS1D01G171400 chr3A 92.157 153 11 1 2643 2794 281111805 281111653 1.420000e-51 215
43 TraesCS1D01G171400 chr3A 82.305 243 27 12 2419 2656 546932166 546931935 5.130000e-46 196
44 TraesCS1D01G171400 chr1B 95.930 1376 47 6 5079 6449 633752227 633750856 0.000000e+00 2222
45 TraesCS1D01G171400 chr1B 96.658 1167 39 0 1 1167 633722939 633721773 0.000000e+00 1940
46 TraesCS1D01G171400 chr6D 83.149 902 90 25 2643 3529 406143394 406144248 0.000000e+00 767
47 TraesCS1D01G171400 chr6D 89.444 540 52 5 2641 3176 406159931 406160469 0.000000e+00 676
48 TraesCS1D01G171400 chr5A 80.067 893 125 38 2643 3508 121483822 121482956 1.200000e-171 614
49 TraesCS1D01G171400 chr6A 87.018 493 60 4 2643 3133 387385014 387385504 2.640000e-153 553
50 TraesCS1D01G171400 chr7D 77.689 623 102 32 1168 1774 19646053 19646654 4.820000e-91 346
51 TraesCS1D01G171400 chr7D 78.534 191 19 19 1834 2009 247818776 247818593 8.900000e-19 106
52 TraesCS1D01G171400 chr7D 78.010 191 20 19 1834 2009 247810610 247810427 4.140000e-17 100
53 TraesCS1D01G171400 chr2A 84.858 317 42 4 2342 2657 227466742 227467053 1.360000e-81 315
54 TraesCS1D01G171400 chrUn 87.603 121 7 5 1851 1964 19515357 19515238 4.080000e-27 134


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 TraesCS1D01G171400 chr1D 244750582 244757069 6487 True 11982.0 11982 100.0000 1 6488 1 chr1D.!!$R3 6487
1 TraesCS1D01G171400 chr1D 244184824 244189877 5053 True 7476.0 7476 93.3350 1 5083 1 chr1D.!!$R2 5082
2 TraesCS1D01G171400 chr1D 244175784 244180621 4837 True 7086.0 7086 93.0200 1168 6062 1 chr1D.!!$R1 4894
3 TraesCS1D01G171400 chr1D 70841190 70844138 2948 False 3456.0 3456 87.9550 2124 5083 1 chr1D.!!$F1 2959
4 TraesCS1D01G171400 chr1D 80860164 80862318 2154 False 2998.0 2998 91.7860 2924 5083 1 chr1D.!!$F4 2159
5 TraesCS1D01G171400 chr1D 80851549 80853706 2157 False 2985.0 2985 91.6240 2917 5083 1 chr1D.!!$F3 2166
6 TraesCS1D01G171400 chr1D 180381447 180382854 1407 False 2202.0 2202 94.9040 5079 6487 1 chr1D.!!$F5 1408
7 TraesCS1D01G171400 chr1D 254464183 254465348 1165 True 1932.0 1932 96.5720 1 1167 1 chr1D.!!$R4 1166
8 TraesCS1D01G171400 chr1D 432084379 432084982 603 True 399.0 399 79.2330 1168 1776 1 chr1D.!!$R5 608
9 TraesCS1D01G171400 chr1D 432091961 432092533 572 True 326.0 326 77.6850 1200 1776 1 chr1D.!!$R6 576
10 TraesCS1D01G171400 chr3D 290773444 290776824 3380 False 4427.0 4427 90.4200 1168 4537 1 chr3D.!!$F4 3369
11 TraesCS1D01G171400 chr3D 361837916 361840327 2411 True 3040.0 3040 89.4650 2668 5083 1 chr3D.!!$R2 2415
12 TraesCS1D01G171400 chr3D 290753938 290756021 2083 False 2822.0 2822 90.9430 1847 3976 1 chr3D.!!$F3 2129
13 TraesCS1D01G171400 chr3D 290745310 290746003 693 False 773.0 773 87.1790 1168 1849 1 chr3D.!!$F2 681
14 TraesCS1D01G171400 chr3D 241185651 241186218 567 False 337.0 337 77.9860 1168 1738 1 chr3D.!!$F1 570
15 TraesCS1D01G171400 chr3D 310611305 310611917 612 False 326.0 326 77.0210 1168 1777 1 chr3D.!!$F5 609
16 TraesCS1D01G171400 chr2D 373958561 373960711 2150 True 3138.0 3138 92.9760 2924 5083 1 chr2D.!!$R1 2159
17 TraesCS1D01G171400 chr4D 392434563 392436727 2164 False 3057.0 3057 92.2120 2924 5083 1 chr4D.!!$F1 2159
18 TraesCS1D01G171400 chr4D 392447249 392449413 2164 False 3018.0 3018 91.8970 2924 5083 1 chr4D.!!$F2 2159
19 TraesCS1D01G171400 chr4D 270702971 270704340 1369 True 2242.0 2242 96.2180 5079 6449 1 chr4D.!!$R1 1370
20 TraesCS1D01G171400 chr5D 518975419 518977574 2155 True 2988.0 2988 91.7050 2924 5083 1 chr5D.!!$R2 2159
21 TraesCS1D01G171400 chr5D 503316918 503319440 2522 True 2064.0 2207 96.0915 1 6449 2 chr5D.!!$R3 6448
22 TraesCS1D01G171400 chr5D 6247333 6249857 2524 False 2061.5 2206 96.0455 1 6446 2 chr5D.!!$F2 6445
23 TraesCS1D01G171400 chr1A 554485437 554487969 2532 True 2096.5 2259 96.4745 1 6449 2 chr1A.!!$R2 6448
24 TraesCS1D01G171400 chr2B 683730857 683734340 3483 True 2095.5 2257 96.5090 1 6449 2 chr2B.!!$R1 6448
25 TraesCS1D01G171400 chr7B 662749129 662751651 2522 False 2089.0 2255 96.4545 4 6446 2 chr7B.!!$F1 6442
26 TraesCS1D01G171400 chr3A 105551015 105553541 2526 False 2087.5 2252 96.3810 1 6446 2 chr3A.!!$F2 6445
27 TraesCS1D01G171400 chr1B 633750856 633752227 1371 True 2222.0 2222 95.9300 5079 6449 1 chr1B.!!$R2 1370
28 TraesCS1D01G171400 chr1B 633721773 633722939 1166 True 1940.0 1940 96.6580 1 1167 1 chr1B.!!$R1 1166
29 TraesCS1D01G171400 chr6D 406143394 406144248 854 False 767.0 767 83.1490 2643 3529 1 chr6D.!!$F1 886
30 TraesCS1D01G171400 chr6D 406159931 406160469 538 False 676.0 676 89.4440 2641 3176 1 chr6D.!!$F2 535
31 TraesCS1D01G171400 chr5A 121482956 121483822 866 True 614.0 614 80.0670 2643 3508 1 chr5A.!!$R1 865
32 TraesCS1D01G171400 chr7D 19646053 19646654 601 False 346.0 346 77.6890 1168 1774 1 chr7D.!!$F1 606

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
183 185 0.107410 TGTGGTTGACCGATATGGCC 60.107 55.0 0.00 0.00 43.94 5.36 F
1715 2727 1.623542 GGTGCCGAACCCTATCCACT 61.624 60.0 0.00 0.00 44.02 4.00 F
3086 4164 0.771127 CACAACTTTCCCCCTCTGGA 59.229 55.0 0.00 0.00 35.39 3.86 F
3759 4867 0.872388 GACTGTTACTTTGTGGCGGG 59.128 55.0 0.00 0.00 0.00 6.13 F
4285 5399 0.609151 TGATCCGCGGTAAAAGGACA 59.391 50.0 27.15 11.44 36.81 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 2840 2.738213 GATGATGGCTCCGGGCGAAT 62.738 60.0 0.00 1.49 42.94 3.34 R
3553 4659 0.038526 GATCACGGCCCGGTAGTATG 60.039 60.0 8.57 0.00 0.00 2.39 R
4100 5213 0.036765 TCAGCACGCCGGTCTAAATT 60.037 50.0 1.90 0.00 0.00 1.82 R
4630 5748 0.105504 AAAGGGGGAGCAAAGCAACT 60.106 50.0 0.00 0.00 0.00 3.16 R
6165 7299 0.178958 AGGAGTATGGAGCCGGTAGG 60.179 60.0 1.90 0.00 41.62 3.18 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
139 140 2.685388 GCCATTCTAACTCTTCTTGGGC 59.315 50.000 0.00 0.00 0.00 5.36
183 185 0.107410 TGTGGTTGACCGATATGGCC 60.107 55.000 0.00 0.00 43.94 5.36
221 223 9.880157 AGCTATTGCATTTATTTTTCTCATTGT 57.120 25.926 1.12 0.00 42.74 2.71
292 294 5.086104 TCTTTTAGAAGCGCATACTCCTT 57.914 39.130 11.47 0.00 32.75 3.36
824 827 3.843422 TGAATGACCCCACTTTCAATGT 58.157 40.909 0.00 0.00 33.31 2.71
973 976 9.337396 CAACTACATTGATTTTAGTATAGGGCA 57.663 33.333 0.00 0.00 41.23 5.36
1003 1006 2.669950 GCACGCGGTTCCAAATTAATGT 60.670 45.455 12.47 0.00 0.00 2.71
1106 2063 7.095649 GGACACATTTTATTTGGCAGTTTTCTC 60.096 37.037 0.00 0.00 0.00 2.87
1232 2190 3.064207 TGCCACGTCACTTTGATTACTC 58.936 45.455 0.00 0.00 0.00 2.59
1253 2211 5.163683 ACTCTTGCTAATCTCGCGTTAGTTA 60.164 40.000 5.77 1.12 32.90 2.24
1259 2217 5.742926 GCTAATCTCGCGTTAGTTAGAAACT 59.257 40.000 19.40 0.00 45.40 2.66
1293 2264 5.634439 TCAAATCCGAAAATCATGCAAACAG 59.366 36.000 0.00 0.00 0.00 3.16
1299 2270 6.980978 TCCGAAAATCATGCAAACAGTAAAAA 59.019 30.769 0.00 0.00 0.00 1.94
1715 2727 1.623542 GGTGCCGAACCCTATCCACT 61.624 60.000 0.00 0.00 44.02 4.00
1739 2757 3.182263 CCCACAACCCCCACTCCA 61.182 66.667 0.00 0.00 0.00 3.86
1748 2771 2.997315 CCCACTCCACCTCGCTCA 60.997 66.667 0.00 0.00 0.00 4.26
1749 2772 2.575993 CCACTCCACCTCGCTCAG 59.424 66.667 0.00 0.00 0.00 3.35
1796 2821 3.632080 ATGACCCGACGCCAACCA 61.632 61.111 0.00 0.00 0.00 3.67
1816 2841 3.537874 GTCGCCGGAGCCACCTAT 61.538 66.667 5.05 0.00 36.31 2.57
1829 2854 3.546543 CCTATTCGCCCGGAGCCA 61.547 66.667 0.73 0.00 38.78 4.75
1976 3011 4.767255 GCGCCCACAGGACCTCAG 62.767 72.222 0.00 0.00 33.47 3.35
1978 3013 3.640407 GCCCACAGGACCTCAGCA 61.640 66.667 0.00 0.00 33.47 4.41
2043 3078 2.358615 CGCACAGCCTTGCCACTA 60.359 61.111 1.69 0.00 39.53 2.74
2056 3091 3.760035 CACTAGCCACCGGTCGCT 61.760 66.667 29.64 29.64 39.17 4.93
2084 3119 4.662961 CGTGACCTCCTGTGCGCA 62.663 66.667 5.66 5.66 0.00 6.09
2088 3123 3.315142 GACCTCCTGTGCGCATCCA 62.315 63.158 15.91 7.01 0.00 3.41
2352 3399 1.483004 TGTTGCCGCCTATTGCTACTA 59.517 47.619 0.00 0.00 38.05 1.82
2429 3480 2.414994 AGATGCTGCTATGCACTTGT 57.585 45.000 0.00 0.00 46.33 3.16
2482 3533 2.223829 ACCCATCGATTCTTCTACTGCG 60.224 50.000 0.00 0.00 0.00 5.18
2499 3553 3.955291 CGATAGCTGCTACTGCTGT 57.045 52.632 12.26 0.66 38.96 4.40
2500 3554 2.215907 CGATAGCTGCTACTGCTGTT 57.784 50.000 12.26 0.00 38.96 3.16
2836 3912 3.328382 TGGACTATTGACTTTGACCCG 57.672 47.619 0.00 0.00 0.00 5.28
3068 4145 4.395854 CACATCCTTAGCATAGCAAACACA 59.604 41.667 0.00 0.00 0.00 3.72
3086 4164 0.771127 CACAACTTTCCCCCTCTGGA 59.229 55.000 0.00 0.00 35.39 3.86
3164 4244 1.329256 CCGGTATCACCTCCTACTGG 58.671 60.000 0.00 0.00 37.88 4.00
3387 4491 5.563876 TCGCCTATTCCTTCTCTCTACTA 57.436 43.478 0.00 0.00 0.00 1.82
3445 4549 4.823442 TGGTTAATCCTATTCTGCTGCATG 59.177 41.667 1.31 0.00 37.07 4.06
3494 4600 4.229582 ACCCTTACCTGCAATCCTAAATGA 59.770 41.667 0.00 0.00 0.00 2.57
3553 4659 2.359850 TTGTCCGTCTGCCATGCC 60.360 61.111 0.00 0.00 0.00 4.40
3681 4789 1.065491 CAAGTGATTCCGATGTGGGGA 60.065 52.381 0.00 0.00 38.76 4.81
3704 4812 1.559682 GAAAGGACAGGTGGCTCCATA 59.440 52.381 8.51 0.00 39.02 2.74
3759 4867 0.872388 GACTGTTACTTTGTGGCGGG 59.128 55.000 0.00 0.00 0.00 6.13
3764 4872 2.472414 TTACTTTGTGGCGGGGCGAT 62.472 55.000 0.00 0.00 0.00 4.58
3837 4947 7.361894 GGTGTCCGCTGTTACTTTAAAATAAA 58.638 34.615 0.00 0.00 0.00 1.40
4045 5158 4.357947 GTCTGCTCACCGGTCGCA 62.358 66.667 22.64 22.64 0.00 5.10
4100 5213 1.685765 AGACCCCTGCACGCATAGA 60.686 57.895 0.00 0.00 0.00 1.98
4171 5284 1.218316 GTTGATCTTCCGAGGCCGT 59.782 57.895 0.00 0.00 0.00 5.68
4285 5399 0.609151 TGATCCGCGGTAAAAGGACA 59.391 50.000 27.15 11.44 36.81 4.02
4418 5533 1.186267 AGGATCGCCGGGTAGGATTC 61.186 60.000 2.18 0.00 45.00 2.52
4552 5670 0.836606 TTCTGCAGTTCAGTCCACCA 59.163 50.000 14.67 0.00 43.32 4.17
4571 5689 4.221703 CACCAATATTGCCCCTTTACACAA 59.778 41.667 10.11 0.00 0.00 3.33
4657 5776 1.000486 GCTCCCCCTTTTCCCCTTC 60.000 63.158 0.00 0.00 0.00 3.46
4739 5858 2.224719 ACAGTGACTCCTACTACACCGT 60.225 50.000 0.00 0.00 34.33 4.83
4755 5874 1.063417 ACCGTGGGTGCCTACTACTAT 60.063 52.381 3.33 0.00 32.98 2.12
4766 5885 2.695666 CCTACTACTATGTGCAGGCTGT 59.304 50.000 17.16 0.00 0.00 4.40
5089 6213 1.529796 GGGGGCGTCACATTATGGA 59.470 57.895 0.00 0.00 0.00 3.41
5322 6446 8.680903 CAGGAATTAATTGAGACTTTAGCATGT 58.319 33.333 5.17 0.00 0.00 3.21
5417 6541 3.242870 GCAAGATTGGTTGGATTAGCTCG 60.243 47.826 0.00 0.00 0.00 5.03
5673 6802 1.273606 CAGAGGGAGAAGAAGCGACAA 59.726 52.381 0.00 0.00 0.00 3.18
5864 6998 6.428771 AGACCTAGAGCTAACTATCGACATTC 59.571 42.308 0.00 0.00 0.00 2.67
5924 7058 4.343526 TGAATGTTTGTTACCAGGTGCAAT 59.656 37.500 0.76 0.00 0.00 3.56
5927 7061 5.854010 TGTTTGTTACCAGGTGCAATAAA 57.146 34.783 0.76 0.00 0.00 1.40
5933 7067 5.719085 TGTTACCAGGTGCAATAAAATCCAT 59.281 36.000 0.76 0.00 0.00 3.41
5958 7092 9.777008 ATTTGGTAAGGATAAAATACCCTTTCA 57.223 29.630 0.00 0.00 40.47 2.69
6136 7270 2.866762 GTTTGGTAGCTCATAAGGCTCG 59.133 50.000 0.00 0.00 40.74 5.03
6165 7299 0.963856 GGTTGTGGGTTCGATTCCCC 60.964 60.000 19.27 14.02 44.00 4.81
6204 7338 8.503458 ACTCCTTCTTTATGATATATGCATGC 57.497 34.615 11.82 11.82 0.00 4.06
6205 7339 7.555554 ACTCCTTCTTTATGATATATGCATGCC 59.444 37.037 16.68 0.00 0.00 4.40
6206 7340 7.636579 TCCTTCTTTATGATATATGCATGCCT 58.363 34.615 16.68 8.18 0.00 4.75
6207 7341 7.555195 TCCTTCTTTATGATATATGCATGCCTG 59.445 37.037 16.68 0.00 0.00 4.85
6240 7374 4.579454 ACATCATGCATTTGTATCTGGC 57.421 40.909 9.73 0.00 0.00 4.85
6297 7435 7.772166 ACAGTTTTTCTCGGAAGAAGAAAAAT 58.228 30.769 20.36 11.02 46.21 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 3.913548 TTGTGTTTGTGGATGGAATCG 57.086 42.857 0.00 0.00 46.86 3.34
183 185 5.717078 ATGCAATAGCTAAATGATGGTGG 57.283 39.130 12.65 0.00 42.74 4.61
221 223 4.397103 ACTTAGTTCGATACATGTGACCGA 59.603 41.667 9.11 11.39 0.00 4.69
562 565 7.560991 TGCCAATACATTATCCTCATTCTGTTT 59.439 33.333 0.00 0.00 0.00 2.83
803 806 3.573538 CACATTGAAAGTGGGGTCATTCA 59.426 43.478 0.00 0.00 33.43 2.57
824 827 0.251916 CAACCATAGGCTTCGACCCA 59.748 55.000 0.00 0.00 0.00 4.51
967 970 1.742411 GCGTGCATCTAAAGTGCCCTA 60.742 52.381 0.00 0.00 41.83 3.53
973 976 1.076332 GAACCGCGTGCATCTAAAGT 58.924 50.000 4.92 0.00 0.00 2.66
1057 1060 5.220662 CCCAAGCAGAAATATCACAAGTACG 60.221 44.000 0.00 0.00 0.00 3.67
1232 2190 5.271625 TCTAACTAACGCGAGATTAGCAAG 58.728 41.667 15.93 11.26 33.66 4.01
1253 2211 8.792830 TCGGATTTGAATTAGAATCAGTTTCT 57.207 30.769 12.66 0.00 46.53 2.52
1715 2727 3.503839 GGGGTTGTGGGGGTGTCA 61.504 66.667 0.00 0.00 0.00 3.58
1815 2840 2.738213 GATGATGGCTCCGGGCGAAT 62.738 60.000 0.00 1.49 42.94 3.34
1816 2841 3.460672 GATGATGGCTCCGGGCGAA 62.461 63.158 0.00 0.00 42.94 4.70
1849 2874 4.173701 GGGGAGGAGGACGGGGAT 62.174 72.222 0.00 0.00 0.00 3.85
2084 3119 4.760047 GTCGCGGCAGGTGTGGAT 62.760 66.667 5.47 0.00 0.00 3.41
2188 3224 3.565214 TGCGGTGGGAAGGAGCAA 61.565 61.111 0.00 0.00 34.66 3.91
2219 3255 3.552384 ACGAGGCCACGTTTGGGA 61.552 61.111 23.14 0.00 44.14 4.37
2323 3370 3.123620 GCGGCAACAGAGGAGCAG 61.124 66.667 0.00 0.00 0.00 4.24
2372 3419 4.555709 AGGCAACCGCGACAACCA 62.556 61.111 8.23 0.00 39.92 3.67
2375 3422 4.927782 AGCAGGCAACCGCGACAA 62.928 61.111 8.23 0.00 39.92 3.18
2429 3480 2.573869 GGTCAGCAGTAGCAGCGA 59.426 61.111 0.00 0.00 45.49 4.93
2482 3533 3.686726 ACAAAACAGCAGTAGCAGCTATC 59.313 43.478 5.14 0.00 45.49 2.08
2490 3544 4.498009 CCTCAACCAACAAAACAGCAGTAG 60.498 45.833 0.00 0.00 0.00 2.57
2492 3546 2.166254 CCTCAACCAACAAAACAGCAGT 59.834 45.455 0.00 0.00 0.00 4.40
2496 3550 1.535860 CGGCCTCAACCAACAAAACAG 60.536 52.381 0.00 0.00 0.00 3.16
2497 3551 0.457851 CGGCCTCAACCAACAAAACA 59.542 50.000 0.00 0.00 0.00 2.83
2498 3552 0.874175 GCGGCCTCAACCAACAAAAC 60.874 55.000 0.00 0.00 0.00 2.43
2499 3553 1.040339 AGCGGCCTCAACCAACAAAA 61.040 50.000 0.00 0.00 0.00 2.44
2500 3554 1.454847 AGCGGCCTCAACCAACAAA 60.455 52.632 0.00 0.00 0.00 2.83
2836 3912 0.252197 GTGTATGACAGGTGGGGTCC 59.748 60.000 0.00 0.00 34.36 4.46
2957 4034 9.482627 AAAGTATTCTCATCCGAGTTATGAATC 57.517 33.333 0.00 0.00 40.44 2.52
3068 4145 1.636003 GATCCAGAGGGGGAAAGTTGT 59.364 52.381 0.00 0.00 41.12 3.32
3164 4244 2.034812 CGGTGCTAGAGGTGACCTAATC 59.965 54.545 2.97 0.00 31.76 1.75
3387 4491 5.661056 TGCTACACTACTCTAATGCAAGT 57.339 39.130 0.00 0.00 0.00 3.16
3445 4549 1.470098 CTGTAGCAACAATGACAGGCC 59.530 52.381 0.00 0.00 36.48 5.19
3553 4659 0.038526 GATCACGGCCCGGTAGTATG 60.039 60.000 8.57 0.00 0.00 2.39
3636 4744 2.046023 TCTACGAGCCGACCCGAA 60.046 61.111 1.50 0.00 0.00 4.30
3681 4789 0.398318 GAGCCACCTGTCCTTTCAGT 59.602 55.000 0.00 0.00 34.02 3.41
3704 4812 4.007323 AGGCCCACCTCTACCGGT 62.007 66.667 13.98 13.98 46.34 5.28
3759 4867 1.227674 CTCAACCTGCCCTATCGCC 60.228 63.158 0.00 0.00 0.00 5.54
3764 4872 1.198759 GGTGGTCTCAACCTGCCCTA 61.199 60.000 0.00 0.00 46.60 3.53
3837 4947 7.876068 TCAAATACCAAGATCTCGTTAAGTGTT 59.124 33.333 0.00 0.00 0.00 3.32
4045 5158 2.006888 GCACACCTACATGTTGCGTAT 58.993 47.619 2.30 0.00 0.00 3.06
4100 5213 0.036765 TCAGCACGCCGGTCTAAATT 60.037 50.000 1.90 0.00 0.00 1.82
4171 5284 0.478072 ACACTTTCCTGGGTCATGCA 59.522 50.000 0.00 0.00 0.00 3.96
4285 5399 1.071228 GTCAAGGTACAACTCCGGGTT 59.929 52.381 0.00 1.37 38.93 4.11
4418 5533 5.219343 TCACCAAGTATCATCCATAGCAG 57.781 43.478 0.00 0.00 0.00 4.24
4552 5670 6.099125 GGGTATTTGTGTAAAGGGGCAATATT 59.901 38.462 0.00 0.00 0.00 1.28
4571 5689 7.553504 TCTACACTACATATGCATGGGTATT 57.446 36.000 10.16 3.23 36.39 1.89
4630 5748 0.105504 AAAGGGGGAGCAAAGCAACT 60.106 50.000 0.00 0.00 0.00 3.16
4657 5776 2.329379 CGACAACCGAGAAGAAAGGAG 58.671 52.381 0.00 0.00 41.76 3.69
4739 5858 1.760613 GCACATAGTAGTAGGCACCCA 59.239 52.381 0.00 0.00 0.00 4.51
4755 5874 1.713937 CGTTGTCAACAGCCTGCACA 61.714 55.000 15.79 0.00 0.00 4.57
4766 5885 4.395959 AACTACTCTTGGTCGTTGTCAA 57.604 40.909 0.00 0.00 33.47 3.18
5089 6213 1.408969 AATTGTGAAACGGTGCCCTT 58.591 45.000 0.00 0.00 42.39 3.95
5322 6446 0.534877 AAGGTGTGCGTTCATGAGCA 60.535 50.000 10.36 7.93 41.55 4.26
5417 6541 8.409358 AGTGAATATATAACCCATGGAAAAGC 57.591 34.615 15.22 0.00 0.00 3.51
5584 6710 9.535170 CCAAGTATAGGTTCTAATCCTAGATGA 57.465 37.037 0.00 0.00 40.32 2.92
5768 6902 4.620567 GCGGTAGGGATTGCAATTTTTCTT 60.621 41.667 14.33 3.54 0.00 2.52
5837 6971 6.120905 TGTCGATAGTTAGCTCTAGGTCTTT 58.879 40.000 0.00 0.00 37.40 2.52
5864 6998 1.105167 TACGTGTCCGGATAGCCCAG 61.105 60.000 7.81 0.00 38.78 4.45
5927 7061 9.154632 GGGTATTTTATCCTTACCAAATGGATT 57.845 33.333 6.42 0.00 40.62 3.01
5958 7092 9.872684 ATCACTTCCAGAAATCCATACAAATAT 57.127 29.630 0.00 0.00 0.00 1.28
6051 7185 3.007581 AGGGTTGGATACGCTCCTT 57.992 52.632 6.23 0.00 46.10 3.36
6110 7244 4.683400 GCCTTATGAGCTACCAAACTGCTA 60.683 45.833 0.00 0.00 37.16 3.49
6165 7299 0.178958 AGGAGTATGGAGCCGGTAGG 60.179 60.000 1.90 0.00 41.62 3.18
6316 7455 6.206634 AGACAATGGACGCTTTTCTTTCATAA 59.793 34.615 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.