Multiple sequence alignment - TraesCS5D01G202800

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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 TraesCS5D01G202800 chr5D 100.000 5302 0 0 1 5302 308216618 308221919 0.000000e+00 9792
1 TraesCS5D01G202800 chr5D 96.159 807 26 5 2489 3290 190800255 190801061 0.000000e+00 1314
2 TraesCS5D01G202800 chr5D 95.415 807 32 5 2489 3290 181872238 181873044 0.000000e+00 1280
3 TraesCS5D01G202800 chr5A 95.433 1861 47 17 3300 5141 389725275 389723434 0.000000e+00 2931
4 TraesCS5D01G202800 chr5A 89.892 1108 41 25 893 1974 389726845 389725783 0.000000e+00 1360
5 TraesCS5D01G202800 chr5A 89.978 908 60 14 1 894 389727975 389727085 0.000000e+00 1144
6 TraesCS5D01G202800 chr5A 81.346 520 22 23 2008 2470 389725786 389725285 2.350000e-93 353
7 TraesCS5D01G202800 chr5A 98.780 164 2 0 5139 5302 389723273 389723110 5.190000e-75 292
8 TraesCS5D01G202800 chr5B 94.792 1248 40 11 3355 4584 353015528 353016768 0.000000e+00 1921
9 TraesCS5D01G202800 chr5B 90.441 1224 44 17 767 1966 353013478 353014652 0.000000e+00 1544
10 TraesCS5D01G202800 chr5B 88.571 490 38 10 4618 5093 353016779 353017264 3.560000e-161 579
11 TraesCS5D01G202800 chr5B 90.426 282 12 8 50 329 353013168 353013436 1.820000e-94 357
12 TraesCS5D01G202800 chr5B 81.193 436 59 12 347 765 700136418 700136847 3.960000e-86 329
13 TraesCS5D01G202800 chr5B 83.871 279 18 13 2218 2470 353015050 353015327 1.910000e-59 241
14 TraesCS5D01G202800 chr5B 91.597 119 8 2 5185 5302 353017446 353017563 4.250000e-36 163
15 TraesCS5D01G202800 chr5B 93.878 49 3 0 2194 2242 353014998 353015046 2.050000e-09 75
16 TraesCS5D01G202800 chr7D 95.652 805 28 6 2489 3289 507097291 507096490 0.000000e+00 1286
17 TraesCS5D01G202800 chr7D 95.074 812 36 4 2489 3296 506706237 506707048 0.000000e+00 1275
18 TraesCS5D01G202800 chr7D 87.571 531 66 0 3554 4084 45106379 45105849 2.710000e-172 616
19 TraesCS5D01G202800 chr7D 83.101 503 72 6 3594 4084 45058169 45057668 3.770000e-121 446
20 TraesCS5D01G202800 chr7D 89.080 348 35 2 1400 1745 45107566 45107220 3.790000e-116 429
21 TraesCS5D01G202800 chr7D 82.524 412 66 2 3679 4084 45028168 45028579 1.820000e-94 357
22 TraesCS5D01G202800 chr7D 86.026 229 28 3 3858 4084 45222344 45222118 5.310000e-60 243
23 TraesCS5D01G202800 chr3D 95.533 806 30 6 2489 3290 246203479 246204282 0.000000e+00 1284
24 TraesCS5D01G202800 chr3D 76.327 245 50 8 3598 3838 359092954 359093194 2.000000e-24 124
25 TraesCS5D01G202800 chr1D 95.533 806 29 6 2489 3288 371718611 371717807 0.000000e+00 1282
26 TraesCS5D01G202800 chr1D 95.398 804 33 4 2489 3289 159426008 159425206 0.000000e+00 1277
27 TraesCS5D01G202800 chr1D 95.404 805 31 5 2489 3290 320042834 320042033 0.000000e+00 1277
28 TraesCS5D01G202800 chr1D 85.176 425 43 11 356 767 296736573 296736156 8.210000e-113 418
29 TraesCS5D01G202800 chr6D 95.415 807 30 7 2489 3291 366141643 366140840 0.000000e+00 1279
30 TraesCS5D01G202800 chr1B 85.047 428 49 10 346 767 556968492 556968074 6.350000e-114 422
31 TraesCS5D01G202800 chr7A 84.507 426 50 10 356 771 556101981 556101562 1.780000e-109 407
32 TraesCS5D01G202800 chr7A 84.511 368 46 8 409 771 556101324 556100963 2.350000e-93 353
33 TraesCS5D01G202800 chr7A 81.612 397 52 12 343 734 645061560 645061940 5.160000e-80 309
34 TraesCS5D01G202800 chr3A 85.025 394 45 9 1427 1808 8999397 8999006 6.440000e-104 388
35 TraesCS5D01G202800 chr3A 88.696 230 23 3 1155 1382 8999629 8999401 1.450000e-70 278
36 TraesCS5D01G202800 chr3A 75.820 244 53 6 3598 3838 478666305 478666545 9.330000e-23 119
37 TraesCS5D01G202800 chr2B 84.293 382 45 11 356 729 12602817 12603191 5.050000e-95 359
38 TraesCS5D01G202800 chr2B 80.315 381 58 14 357 733 751298530 751298163 6.770000e-69 272
39 TraesCS5D01G202800 chr4A 79.051 506 80 7 3579 4084 656772118 656771639 1.840000e-84 324
40 TraesCS5D01G202800 chrUn 78.854 506 81 7 3579 4084 245140201 245139722 8.570000e-83 318
41 TraesCS5D01G202800 chrUn 78.585 509 83 7 3576 4084 371970714 371971196 3.990000e-81 313


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 TraesCS5D01G202800 chr5D 308216618 308221919 5301 False 9792.000000 9792 100.000000 1 5302 1 chr5D.!!$F3 5301
1 TraesCS5D01G202800 chr5D 190800255 190801061 806 False 1314.000000 1314 96.159000 2489 3290 1 chr5D.!!$F2 801
2 TraesCS5D01G202800 chr5D 181872238 181873044 806 False 1280.000000 1280 95.415000 2489 3290 1 chr5D.!!$F1 801
3 TraesCS5D01G202800 chr5A 389723110 389727975 4865 True 1216.000000 2931 91.085800 1 5302 5 chr5A.!!$R1 5301
4 TraesCS5D01G202800 chr5B 353013168 353017563 4395 False 697.142857 1921 90.510857 50 5302 7 chr5B.!!$F2 5252
5 TraesCS5D01G202800 chr7D 507096490 507097291 801 True 1286.000000 1286 95.652000 2489 3289 1 chr7D.!!$R3 800
6 TraesCS5D01G202800 chr7D 506706237 506707048 811 False 1275.000000 1275 95.074000 2489 3296 1 chr7D.!!$F2 807
7 TraesCS5D01G202800 chr7D 45105849 45107566 1717 True 522.500000 616 88.325500 1400 4084 2 chr7D.!!$R4 2684
8 TraesCS5D01G202800 chr7D 45057668 45058169 501 True 446.000000 446 83.101000 3594 4084 1 chr7D.!!$R1 490
9 TraesCS5D01G202800 chr3D 246203479 246204282 803 False 1284.000000 1284 95.533000 2489 3290 1 chr3D.!!$F1 801
10 TraesCS5D01G202800 chr1D 371717807 371718611 804 True 1282.000000 1282 95.533000 2489 3288 1 chr1D.!!$R4 799
11 TraesCS5D01G202800 chr1D 159425206 159426008 802 True 1277.000000 1277 95.398000 2489 3289 1 chr1D.!!$R1 800
12 TraesCS5D01G202800 chr1D 320042033 320042834 801 True 1277.000000 1277 95.404000 2489 3290 1 chr1D.!!$R3 801
13 TraesCS5D01G202800 chr6D 366140840 366141643 803 True 1279.000000 1279 95.415000 2489 3291 1 chr6D.!!$R1 802
14 TraesCS5D01G202800 chr7A 556100963 556101981 1018 True 380.000000 407 84.509000 356 771 2 chr7A.!!$R1 415
15 TraesCS5D01G202800 chr3A 8999006 8999629 623 True 333.000000 388 86.860500 1155 1808 2 chr3A.!!$R1 653

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
975 1245 0.179045 GGCCTGTACATGCCTACCAG 60.179 60.000 28.83 0.75 44.46 4.00 F
1379 1649 0.398696 ACCGACCATGCACAACCTTA 59.601 50.000 0.00 0.00 0.00 2.69 F
1381 1651 0.447801 CGACCATGCACAACCTTAGC 59.552 55.000 0.00 0.00 0.00 3.09 F
1383 1653 1.200020 GACCATGCACAACCTTAGCAC 59.800 52.381 0.00 0.00 41.60 4.40 F
1384 1654 1.246649 CCATGCACAACCTTAGCACA 58.753 50.000 0.00 0.00 41.60 4.57 F
3381 4064 1.064803 CTCCTGCTGTCGCTAGTACTG 59.935 57.143 5.39 0.00 36.97 2.74 F
3383 4066 0.171231 CTGCTGTCGCTAGTACTGCA 59.829 55.000 21.61 21.61 45.71 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2336 0.236449 GCGAATCGACCACGGTTTTT 59.764 50.000 6.91 0.00 43.14 1.94 R
2278 2793 1.065102 CGCCAGCTTGAATTGAGGATG 59.935 52.381 0.00 0.00 0.00 3.51 R
2431 2978 1.474077 CTCCTTCAAATTCAAGGGGCG 59.526 52.381 13.68 3.05 40.93 6.13 R
3323 3987 1.478105 TCTGGTGGTGTGATCTCGATG 59.522 52.381 0.00 0.00 0.00 3.84 R
3383 4066 0.681564 AGCAGCCGTAGAGCAGTAGT 60.682 55.000 0.00 0.00 34.23 2.73 R
4247 4976 1.606350 CCTTGACGAACGACAGCGAC 61.606 60.000 0.14 0.00 41.64 5.19 R
4960 5695 1.758936 ATCAGATCGGTACCGTCACA 58.241 50.000 32.16 15.05 40.74 3.58 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
31 32 0.323633 CCCCCTTCATGCATGTGTGA 60.324 55.000 25.43 4.99 0.00 3.58
47 48 4.713553 TGTGTGAATGTTTTCCTCTGCTA 58.286 39.130 0.00 0.00 0.00 3.49
48 49 5.129634 TGTGTGAATGTTTTCCTCTGCTAA 58.870 37.500 0.00 0.00 0.00 3.09
85 96 7.716560 GCCATGCTAAAATCCCTAAAAATGAAT 59.283 33.333 0.00 0.00 0.00 2.57
115 126 3.315140 TCGTGTTGATGCCGGGGA 61.315 61.111 2.18 0.00 0.00 4.81
192 204 5.696724 AGACTTTGTCAATCTTAGAACGTGG 59.303 40.000 0.00 0.00 34.60 4.94
348 363 7.726033 AGCTTATTAGAGGGATACATTCGAT 57.274 36.000 0.00 0.00 39.74 3.59
351 366 9.303537 GCTTATTAGAGGGATACATTCGATAAC 57.696 37.037 0.00 0.00 39.74 1.89
354 369 4.404640 AGAGGGATACATTCGATAACGGA 58.595 43.478 0.00 0.00 38.19 4.69
366 381 4.258543 TCGATAACGGAATTTTGGAGCTT 58.741 39.130 0.00 0.00 40.21 3.74
512 533 9.770097 GAATGAAATACCTTGAGATGTGATCTA 57.230 33.333 0.00 0.00 40.38 1.98
572 593 8.986477 AATAGTATCAAATGTTGAAAAGCCAC 57.014 30.769 0.00 0.00 43.95 5.01
574 595 6.996509 AGTATCAAATGTTGAAAAGCCACAT 58.003 32.000 0.00 0.00 43.95 3.21
580 601 7.930325 TCAAATGTTGAAAAGCCACATATTTGA 59.070 29.630 0.00 0.00 37.46 2.69
612 634 8.354711 TGCACAACCCTTATTTCAACATATTA 57.645 30.769 0.00 0.00 0.00 0.98
618 640 7.340256 ACCCTTATTTCAACATATTACGTCCA 58.660 34.615 0.00 0.00 0.00 4.02
637 661 5.851177 CGTCCAGAAATTTTACACACATGTC 59.149 40.000 0.00 0.00 40.48 3.06
639 663 7.425606 GTCCAGAAATTTTACACACATGTCTT 58.574 34.615 0.00 0.00 40.48 3.01
642 666 8.542132 CCAGAAATTTTACACACATGTCTTTTG 58.458 33.333 0.00 0.00 40.48 2.44
644 668 9.651913 AGAAATTTTACACACATGTCTTTTGTT 57.348 25.926 0.00 0.00 40.48 2.83
650 674 6.942532 ACACACATGTCTTTTGTTATGTCT 57.057 33.333 0.00 0.00 31.55 3.41
651 675 9.549078 TTACACACATGTCTTTTGTTATGTCTA 57.451 29.630 0.00 0.00 40.48 2.59
652 676 8.621532 ACACACATGTCTTTTGTTATGTCTAT 57.378 30.769 0.00 0.00 31.55 1.98
661 685 8.108782 GTCTTTTGTTATGTCTATTACGTCTGC 58.891 37.037 0.00 0.00 0.00 4.26
664 688 9.589111 TTTTGTTATGTCTATTACGTCTGCATA 57.411 29.630 0.00 0.00 0.00 3.14
739 763 2.588464 TTCAAAAACCGGCCTCCATA 57.412 45.000 0.00 0.00 0.00 2.74
800 824 7.591426 TCTTGATTGTATCGACTTGATATGACG 59.409 37.037 0.00 0.00 41.49 4.35
860 884 1.244019 AAAGACAATCGTGGCCCTGC 61.244 55.000 0.00 0.00 30.22 4.85
861 885 3.499737 GACAATCGTGGCCCTGCG 61.500 66.667 0.00 2.14 0.00 5.18
894 918 2.225908 ACCCCCAGAAACCTCATACTCT 60.226 50.000 0.00 0.00 0.00 3.24
895 919 3.013648 ACCCCCAGAAACCTCATACTCTA 59.986 47.826 0.00 0.00 0.00 2.43
896 920 3.643792 CCCCCAGAAACCTCATACTCTAG 59.356 52.174 0.00 0.00 0.00 2.43
897 921 4.290942 CCCCAGAAACCTCATACTCTAGT 58.709 47.826 0.00 0.00 0.00 2.57
898 922 4.717280 CCCCAGAAACCTCATACTCTAGTT 59.283 45.833 0.00 0.00 0.00 2.24
899 923 5.897824 CCCCAGAAACCTCATACTCTAGTTA 59.102 44.000 0.00 0.00 0.00 2.24
900 924 6.183360 CCCCAGAAACCTCATACTCTAGTTAC 60.183 46.154 0.00 0.00 0.00 2.50
901 925 6.380274 CCCAGAAACCTCATACTCTAGTTACA 59.620 42.308 0.00 0.00 0.00 2.41
954 1224 4.401925 AGCTTCTCCATTATTACATGCCC 58.598 43.478 0.00 0.00 0.00 5.36
956 1226 4.217118 GCTTCTCCATTATTACATGCCCAG 59.783 45.833 0.00 0.00 0.00 4.45
957 1227 4.371624 TCTCCATTATTACATGCCCAGG 57.628 45.455 0.00 0.00 0.00 4.45
958 1228 2.821969 CTCCATTATTACATGCCCAGGC 59.178 50.000 0.38 0.38 42.35 4.85
959 1229 1.895131 CCATTATTACATGCCCAGGCC 59.105 52.381 6.14 0.00 41.09 5.19
960 1230 2.491455 CCATTATTACATGCCCAGGCCT 60.491 50.000 0.00 0.00 41.09 5.19
961 1231 2.363306 TTATTACATGCCCAGGCCTG 57.637 50.000 26.87 26.87 41.42 4.85
963 1233 1.221635 ATTACATGCCCAGGCCTGTA 58.778 50.000 30.63 19.15 45.46 2.74
964 1234 0.254747 TTACATGCCCAGGCCTGTAC 59.745 55.000 30.63 21.80 46.34 2.90
965 1235 0.912006 TACATGCCCAGGCCTGTACA 60.912 55.000 30.63 26.43 45.46 2.90
966 1236 1.228228 CATGCCCAGGCCTGTACAT 59.772 57.895 30.63 27.35 41.09 2.29
967 1237 1.105167 CATGCCCAGGCCTGTACATG 61.105 60.000 33.51 33.51 41.09 3.21
968 1238 2.830370 GCCCAGGCCTGTACATGC 60.830 66.667 30.63 19.72 34.56 4.06
973 1243 4.878878 GGCCTGTACATGCCTACC 57.121 61.111 28.83 7.91 44.46 3.18
974 1244 1.912220 GGCCTGTACATGCCTACCA 59.088 57.895 28.83 0.00 44.46 3.25
975 1245 0.179045 GGCCTGTACATGCCTACCAG 60.179 60.000 28.83 0.75 44.46 4.00
1091 1361 1.654954 CTCTGCCACCTTGCTCATGC 61.655 60.000 0.00 0.00 40.20 4.06
1379 1649 0.398696 ACCGACCATGCACAACCTTA 59.601 50.000 0.00 0.00 0.00 2.69
1381 1651 0.447801 CGACCATGCACAACCTTAGC 59.552 55.000 0.00 0.00 0.00 3.09
1382 1652 1.533625 GACCATGCACAACCTTAGCA 58.466 50.000 0.00 0.00 43.14 3.49
1383 1653 1.200020 GACCATGCACAACCTTAGCAC 59.800 52.381 0.00 0.00 41.60 4.40
1384 1654 1.246649 CCATGCACAACCTTAGCACA 58.753 50.000 0.00 0.00 41.60 4.57
1398 1668 2.319841 GCACAGCACAGCACGATCA 61.320 57.895 0.00 0.00 0.00 2.92
1427 1697 4.776647 AACGCGTACGGTACCGCC 62.777 66.667 33.62 22.55 46.83 6.13
1432 1702 2.107546 GTACGGTACCGCCATGGG 59.892 66.667 33.62 6.69 44.64 4.00
1434 1704 2.723237 TACGGTACCGCCATGGGTG 61.723 63.158 33.62 5.10 44.64 4.61
1680 1952 3.379445 GACCAGGAGACCGGCGAA 61.379 66.667 9.30 0.00 0.00 4.70
1752 2037 9.045223 CCGTACCAAAATTTATTACTACTACCC 57.955 37.037 0.00 0.00 0.00 3.69
1754 2039 9.904198 GTACCAAAATTTATTACTACTACCCCA 57.096 33.333 0.00 0.00 0.00 4.96
1756 2041 8.617491 ACCAAAATTTATTACTACTACCCCAGT 58.383 33.333 0.00 0.00 41.62 4.00
1798 2119 2.758979 ACCGGAGTTGATAGTACACTGG 59.241 50.000 9.46 0.00 38.24 4.00
1816 2137 3.005554 CTGGTGGTGATGAGTTCATGAC 58.994 50.000 0.00 1.16 39.30 3.06
1822 2143 4.074970 GGTGATGAGTTCATGACAACCTT 58.925 43.478 12.58 0.00 41.32 3.50
1824 2145 4.074259 TGATGAGTTCATGACAACCTTGG 58.926 43.478 0.00 0.00 36.57 3.61
1906 2229 3.375299 CAGCAGGTATACCTTGTTCTTGC 59.625 47.826 22.36 19.70 46.09 4.01
1966 2292 4.320421 GGACAACCGCGGTTTAAGTTTAAT 60.320 41.667 39.64 13.84 36.00 1.40
1967 2293 5.106752 GGACAACCGCGGTTTAAGTTTAATA 60.107 40.000 39.64 0.00 36.00 0.98
1969 2295 6.142139 ACAACCGCGGTTTAAGTTTAATAAC 58.858 36.000 39.64 0.00 36.00 1.89
1970 2296 6.017192 ACAACCGCGGTTTAAGTTTAATAACT 60.017 34.615 39.64 11.76 40.19 2.24
1971 2297 7.172361 ACAACCGCGGTTTAAGTTTAATAACTA 59.828 33.333 39.64 0.00 38.76 2.24
1972 2298 7.848223 ACCGCGGTTTAAGTTTAATAACTAT 57.152 32.000 28.70 0.00 43.74 2.12
1973 2299 8.940768 ACCGCGGTTTAAGTTTAATAACTATA 57.059 30.769 28.70 0.00 43.74 1.31
1974 2300 9.546428 ACCGCGGTTTAAGTTTAATAACTATAT 57.454 29.630 28.70 0.00 43.74 0.86
2066 2392 6.899393 TGATAAAGCTTGAAAACATCCAGT 57.101 33.333 0.00 0.00 0.00 4.00
2080 2406 6.560253 AACATCCAGTACTAGCAAAAGTTG 57.440 37.500 0.00 0.00 0.00 3.16
2175 2502 7.278203 TCTCTAACTCTCGACACATACTTAGTG 59.722 40.741 0.00 0.00 42.56 2.74
2186 2654 7.254658 CGACACATACTTAGTGAAGGTTTTTGT 60.255 37.037 0.00 0.00 40.16 2.83
2206 2694 4.467769 TGTCACTAGTATGTAGGTAGGCC 58.532 47.826 0.00 0.00 0.00 5.19
2277 2792 7.989741 CAGATATAGTGGGCATTAATTCCTAGG 59.010 40.741 0.82 0.82 0.00 3.02
2278 2793 3.229697 AGTGGGCATTAATTCCTAGGC 57.770 47.619 2.96 0.00 0.00 3.93
2283 2798 3.245407 GGGCATTAATTCCTAGGCATCCT 60.245 47.826 2.96 0.00 37.71 3.24
2371 2917 1.334059 CGCACGCACAACATTCTCTTT 60.334 47.619 0.00 0.00 0.00 2.52
2387 2933 5.490139 TCTCTTTGCAACACTTCTTGAAG 57.510 39.130 0.00 8.65 0.00 3.02
2405 2952 6.262273 TCTTGAAGGTGACAGGAAAAATACAC 59.738 38.462 0.00 0.00 0.00 2.90
2447 2994 1.270041 GCAACGCCCCTTGAATTTGAA 60.270 47.619 0.00 0.00 0.00 2.69
2464 3011 6.848562 ATTTGAAGGAGGTGATAGGGTTAT 57.151 37.500 0.00 0.00 0.00 1.89
2470 3017 8.217799 TGAAGGAGGTGATAGGGTTATTTAATG 58.782 37.037 0.00 0.00 0.00 1.90
2471 3018 7.091533 AGGAGGTGATAGGGTTATTTAATGG 57.908 40.000 0.00 0.00 0.00 3.16
2472 3019 6.045577 AGGAGGTGATAGGGTTATTTAATGGG 59.954 42.308 0.00 0.00 0.00 4.00
2474 3021 7.257419 GGAGGTGATAGGGTTATTTAATGGGAT 60.257 40.741 0.00 0.00 0.00 3.85
2475 3022 8.766492 AGGTGATAGGGTTATTTAATGGGATA 57.234 34.615 0.00 0.00 0.00 2.59
2476 3023 9.189750 AGGTGATAGGGTTATTTAATGGGATAA 57.810 33.333 0.00 0.00 0.00 1.75
2477 3024 9.990868 GGTGATAGGGTTATTTAATGGGATAAT 57.009 33.333 0.00 0.00 0.00 1.28
2556 3103 5.127682 CCTATTATGCTTTTGCCCTTTGACT 59.872 40.000 0.00 0.00 46.87 3.41
2724 3272 5.986135 CGAGTTTTAGCTCTTATGCTACCAT 59.014 40.000 0.00 0.00 44.15 3.55
2725 3273 6.480320 CGAGTTTTAGCTCTTATGCTACCATT 59.520 38.462 0.00 0.00 44.15 3.16
3035 3609 2.939103 GAGCTAAAACTCGGATGTGCAT 59.061 45.455 0.00 0.00 0.00 3.96
3089 3663 7.041721 TGACACTGACATATAGGTGATGTTTC 58.958 38.462 0.00 0.00 37.65 2.78
3091 3665 7.624549 ACACTGACATATAGGTGATGTTTCTT 58.375 34.615 0.00 0.00 37.65 2.52
3194 3858 4.218417 GTCAAAGGGCAAAAGCATAAGAGA 59.782 41.667 0.00 0.00 0.00 3.10
3229 3893 3.325425 TGGATAGAACCGGTGACTTTTGA 59.675 43.478 8.52 0.00 0.00 2.69
3239 3903 4.564821 CCGGTGACTTTTGAGAATTAGGGA 60.565 45.833 0.00 0.00 0.00 4.20
3291 3955 8.336987 AGGGGCATAAATCTAATTATCCCTTAC 58.663 37.037 0.00 0.00 36.76 2.34
3323 3987 2.609350 AGTACTCGTCAGTCTCGTCTC 58.391 52.381 0.00 0.00 33.62 3.36
3381 4064 1.064803 CTCCTGCTGTCGCTAGTACTG 59.935 57.143 5.39 0.00 36.97 2.74
3383 4066 0.171231 CTGCTGTCGCTAGTACTGCA 59.829 55.000 21.61 21.61 45.71 4.41
3524 4211 5.878332 TGAATTCACGTGCATTCATTACT 57.122 34.783 31.02 2.96 33.86 2.24
3545 4243 0.538977 AGTGGTGCATGCAGCTTCTT 60.539 50.000 40.09 24.31 45.94 2.52
3546 4244 0.316204 GTGGTGCATGCAGCTTCTTT 59.684 50.000 40.09 0.00 45.94 2.52
3736 4447 4.034258 GTCGTGGCCGAGACGTCA 62.034 66.667 19.50 0.00 45.26 4.35
4087 4811 1.769026 TCAAGCTCGCATCTCTACCT 58.231 50.000 0.00 0.00 0.00 3.08
4094 4818 1.069204 TCGCATCTCTACCTCAATGCC 59.931 52.381 0.00 0.00 41.08 4.40
4110 4834 2.125310 CCGTGGGTAAGCATCGCA 60.125 61.111 0.00 0.00 0.00 5.10
4111 4835 1.523711 CCGTGGGTAAGCATCGCAT 60.524 57.895 0.00 0.00 0.00 4.73
4170 4894 2.668457 GCTCCGTTCAACTCATGTAGTG 59.332 50.000 0.00 0.00 38.88 2.74
4247 4976 6.347240 GCCAGAAGCAATTACTAATCTGATCG 60.347 42.308 8.41 0.00 42.97 3.69
4355 5084 0.105778 CAAAATTTGGGGTGCACCGT 59.894 50.000 29.08 9.92 41.60 4.83
4475 5204 5.349824 CTTTTACTGCTCCAGTCAAAGTC 57.650 43.478 17.51 0.00 44.18 3.01
4760 5493 2.814336 AGCTCCGGTTTTGATCTGAAAC 59.186 45.455 0.00 13.52 36.51 2.78
4960 5695 4.408270 TCCAGAGCAGCTTGAATAGATTCT 59.592 41.667 0.00 0.00 37.67 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.022589 AGCAGAGGAAAACATTCACACATG 60.023 41.667 0.00 0.00 0.00 3.21
85 96 1.330213 CAACACGACACACTGCAATGA 59.670 47.619 0.26 0.00 0.00 2.57
115 126 3.118112 ACTCATTCTGAAATCCCAGCGAT 60.118 43.478 0.00 0.00 34.28 4.58
160 172 5.552870 AGATTGACAAAGTCTACACCAGT 57.447 39.130 0.00 0.00 33.15 4.00
161 173 7.378966 TCTAAGATTGACAAAGTCTACACCAG 58.621 38.462 0.00 0.00 33.15 4.00
192 204 6.403418 CGCTGTCTACTATAGCCCATAAGTAC 60.403 46.154 0.00 0.00 39.05 2.73
345 360 4.342772 CAAGCTCCAAAATTCCGTTATCG 58.657 43.478 0.00 0.00 0.00 2.92
348 363 2.230266 GCCAAGCTCCAAAATTCCGTTA 59.770 45.455 0.00 0.00 0.00 3.18
351 366 0.108662 GGCCAAGCTCCAAAATTCCG 60.109 55.000 0.00 0.00 0.00 4.30
354 369 1.269958 GGAGGCCAAGCTCCAAAATT 58.730 50.000 5.01 0.00 39.45 1.82
558 579 6.996509 AGTCAAATATGTGGCTTTTCAACAT 58.003 32.000 0.00 0.00 25.25 2.71
593 615 7.340256 TGGACGTAATATGTTGAAATAAGGGT 58.660 34.615 0.00 0.00 0.00 4.34
612 634 5.298276 ACATGTGTGTAAAATTTCTGGACGT 59.702 36.000 0.00 0.00 36.63 4.34
618 640 9.651913 AACAAAAGACATGTGTGTAAAATTTCT 57.348 25.926 1.15 0.00 39.09 2.52
623 645 9.509855 GACATAACAAAAGACATGTGTGTAAAA 57.490 29.630 1.15 0.00 39.09 1.52
637 661 7.959733 TGCAGACGTAATAGACATAACAAAAG 58.040 34.615 0.00 0.00 0.00 2.27
639 663 9.758651 ATATGCAGACGTAATAGACATAACAAA 57.241 29.630 0.00 0.00 0.00 2.83
645 669 9.325198 TGAAAAATATGCAGACGTAATAGACAT 57.675 29.630 0.00 0.00 0.00 3.06
646 670 8.710835 TGAAAAATATGCAGACGTAATAGACA 57.289 30.769 0.00 0.00 0.00 3.41
647 671 9.031360 TCTGAAAAATATGCAGACGTAATAGAC 57.969 33.333 0.00 0.00 34.02 2.59
648 672 9.594478 TTCTGAAAAATATGCAGACGTAATAGA 57.406 29.630 0.00 0.00 38.30 1.98
652 676 9.906660 AAAATTCTGAAAAATATGCAGACGTAA 57.093 25.926 0.00 0.00 38.30 3.18
714 738 3.527533 GAGGCCGGTTTTTGAAAGTTTT 58.472 40.909 1.90 0.00 0.00 2.43
717 741 1.037493 GGAGGCCGGTTTTTGAAAGT 58.963 50.000 1.90 0.00 0.00 2.66
718 742 1.036707 TGGAGGCCGGTTTTTGAAAG 58.963 50.000 1.90 0.00 0.00 2.62
739 763 1.298014 CTTTTGGAGCTCGGCCTCT 59.702 57.895 7.83 0.00 32.43 3.69
800 824 2.804527 GGGAGTTTTTACTGACCGACAC 59.195 50.000 0.00 0.00 0.00 3.67
841 865 1.244019 GCAGGGCCACGATTGTCTTT 61.244 55.000 6.18 0.00 0.00 2.52
860 884 3.681593 TCTGGGGGTAAGATTTTCAACG 58.318 45.455 0.00 0.00 0.00 4.10
861 885 5.279306 GGTTTCTGGGGGTAAGATTTTCAAC 60.279 44.000 0.00 0.00 0.00 3.18
894 918 2.360483 TCGGTCGTGGTTTGTGTAACTA 59.640 45.455 0.00 0.00 38.04 2.24
895 919 1.136695 TCGGTCGTGGTTTGTGTAACT 59.863 47.619 0.00 0.00 38.04 2.24
896 920 1.569708 TCGGTCGTGGTTTGTGTAAC 58.430 50.000 0.00 0.00 35.94 2.50
897 921 1.932511 GTTCGGTCGTGGTTTGTGTAA 59.067 47.619 0.00 0.00 0.00 2.41
898 922 1.134877 TGTTCGGTCGTGGTTTGTGTA 60.135 47.619 0.00 0.00 0.00 2.90
899 923 0.391395 TGTTCGGTCGTGGTTTGTGT 60.391 50.000 0.00 0.00 0.00 3.72
900 924 0.303493 CTGTTCGGTCGTGGTTTGTG 59.697 55.000 0.00 0.00 0.00 3.33
901 925 1.433837 GCTGTTCGGTCGTGGTTTGT 61.434 55.000 0.00 0.00 0.00 2.83
957 1227 0.830648 TCTGGTAGGCATGTACAGGC 59.169 55.000 23.73 23.73 37.39 4.85
958 1228 2.158900 CCTTCTGGTAGGCATGTACAGG 60.159 54.545 2.43 2.43 0.00 4.00
959 1229 3.185246 CCTTCTGGTAGGCATGTACAG 57.815 52.381 0.33 0.00 0.00 2.74
973 1243 3.588336 GCTTGCTCCAGCCTTCTG 58.412 61.111 0.00 0.00 41.18 3.02
1037 1307 3.467803 CCTCCTCCATGTCCGTTAATTC 58.532 50.000 0.00 0.00 0.00 2.17
1091 1361 1.341156 AATGCGAGGGAGAGGAAGGG 61.341 60.000 0.00 0.00 0.00 3.95
1379 1649 2.031516 GATCGTGCTGTGCTGTGCT 61.032 57.895 0.00 0.00 0.00 4.40
1381 1651 0.096454 CATGATCGTGCTGTGCTGTG 59.904 55.000 1.07 0.00 0.00 3.66
1382 1652 0.037046 TCATGATCGTGCTGTGCTGT 60.037 50.000 10.24 0.00 0.00 4.40
1383 1653 0.651031 CTCATGATCGTGCTGTGCTG 59.349 55.000 10.24 0.00 0.00 4.41
1384 1654 1.088340 GCTCATGATCGTGCTGTGCT 61.088 55.000 10.24 0.00 0.00 4.40
1398 1668 0.452987 TACGCGTTCGGTTAGCTCAT 59.547 50.000 20.78 0.00 40.69 2.90
1427 1697 3.258070 CTGCACACGCACACCCATG 62.258 63.158 0.00 0.00 45.36 3.66
1432 1702 4.000557 CGTCCTGCACACGCACAC 62.001 66.667 0.69 0.00 45.36 3.82
1680 1952 1.542030 CTGCTGTCCGTGAAGTAGACT 59.458 52.381 0.00 0.00 0.00 3.24
1752 2037 7.910162 GTCACATGCATGTTTTATTACTACTGG 59.090 37.037 29.48 12.94 39.39 4.00
1754 2039 7.201609 CGGTCACATGCATGTTTTATTACTACT 60.202 37.037 29.48 0.29 39.39 2.57
1755 2040 6.905076 CGGTCACATGCATGTTTTATTACTAC 59.095 38.462 29.48 14.59 39.39 2.73
1756 2041 6.037720 CCGGTCACATGCATGTTTTATTACTA 59.962 38.462 29.48 4.35 39.39 1.82
1769 2079 0.324614 ATCAACTCCGGTCACATGCA 59.675 50.000 0.00 0.00 0.00 3.96
1798 2119 3.189287 GGTTGTCATGAACTCATCACCAC 59.811 47.826 0.00 0.00 41.93 4.16
1811 2132 4.244862 GCAAATTACCCAAGGTTGTCATG 58.755 43.478 0.00 0.00 37.09 3.07
1816 2137 2.671596 CGTGCAAATTACCCAAGGTTG 58.328 47.619 0.00 0.00 37.09 3.77
1822 2143 1.832883 ATCAGCGTGCAAATTACCCA 58.167 45.000 0.00 0.00 0.00 4.51
1824 2145 2.440501 CGAATCAGCGTGCAAATTACC 58.559 47.619 0.00 0.00 0.00 2.85
1906 2229 0.583438 GAATCGTCCGTGCCATCATG 59.417 55.000 0.00 0.00 0.00 3.07
2000 2326 9.768662 AATCGACCACGGTTTTTATATATAGTT 57.231 29.630 0.00 0.00 40.03 2.24
2001 2327 9.415544 GAATCGACCACGGTTTTTATATATAGT 57.584 33.333 0.00 0.00 43.14 2.12
2002 2328 8.581263 CGAATCGACCACGGTTTTTATATATAG 58.419 37.037 0.00 0.00 43.14 1.31
2003 2329 7.062138 GCGAATCGACCACGGTTTTTATATATA 59.938 37.037 6.91 0.00 43.14 0.86
2004 2330 6.128742 GCGAATCGACCACGGTTTTTATATAT 60.129 38.462 6.91 0.00 43.14 0.86
2005 2331 5.175491 GCGAATCGACCACGGTTTTTATATA 59.825 40.000 6.91 0.00 43.14 0.86
2006 2332 4.025480 GCGAATCGACCACGGTTTTTATAT 60.025 41.667 6.91 0.00 43.14 0.86
2007 2333 3.306703 GCGAATCGACCACGGTTTTTATA 59.693 43.478 6.91 0.00 43.14 0.98
2008 2334 2.094734 GCGAATCGACCACGGTTTTTAT 59.905 45.455 6.91 0.00 43.14 1.40
2009 2335 1.460359 GCGAATCGACCACGGTTTTTA 59.540 47.619 6.91 0.00 43.14 1.52
2010 2336 0.236449 GCGAATCGACCACGGTTTTT 59.764 50.000 6.91 0.00 43.14 1.94
2058 2384 5.621193 ACAACTTTTGCTAGTACTGGATGT 58.379 37.500 10.90 0.45 0.00 3.06
2059 2385 6.560253 AACAACTTTTGCTAGTACTGGATG 57.440 37.500 10.90 0.00 0.00 3.51
2060 2386 6.367969 CGTAACAACTTTTGCTAGTACTGGAT 59.632 38.462 10.90 0.00 0.00 3.41
2062 2388 5.614013 GCGTAACAACTTTTGCTAGTACTGG 60.614 44.000 5.39 3.15 0.00 4.00
2064 2390 4.149396 CGCGTAACAACTTTTGCTAGTACT 59.851 41.667 0.00 0.00 0.00 2.73
2065 2391 4.380290 CGCGTAACAACTTTTGCTAGTAC 58.620 43.478 0.00 0.00 0.00 2.73
2066 2392 3.120923 GCGCGTAACAACTTTTGCTAGTA 60.121 43.478 8.43 0.00 0.00 1.82
2095 2421 0.384309 TGCTAATCCGGCAGAGTACG 59.616 55.000 0.00 0.00 34.56 3.67
2147 2473 5.736813 AGTATGTGTCGAGAGTTAGAGACT 58.263 41.667 0.00 0.00 42.70 3.24
2175 2502 7.876582 ACCTACATACTAGTGACAAAAACCTTC 59.123 37.037 5.39 0.00 0.00 3.46
2186 2654 4.726583 CTGGCCTACCTACATACTAGTGA 58.273 47.826 5.39 0.00 36.63 3.41
2277 2792 1.202382 GCCAGCTTGAATTGAGGATGC 60.202 52.381 0.00 0.00 0.00 3.91
2278 2793 1.065102 CGCCAGCTTGAATTGAGGATG 59.935 52.381 0.00 0.00 0.00 3.51
2283 2798 2.174334 GCTCGCCAGCTTGAATTGA 58.826 52.632 0.00 0.00 43.09 2.57
2341 2861 4.222847 TGCGTGCGGTGTGGTGTA 62.223 61.111 0.00 0.00 0.00 2.90
2371 2917 2.682856 GTCACCTTCAAGAAGTGTTGCA 59.317 45.455 8.83 0.00 36.72 4.08
2387 2933 8.050778 TGATAATGTGTATTTTTCCTGTCACC 57.949 34.615 0.00 0.00 0.00 4.02
2431 2978 1.474077 CTCCTTCAAATTCAAGGGGCG 59.526 52.381 13.68 3.05 40.93 6.13
2447 2994 6.045577 CCCATTAAATAACCCTATCACCTCCT 59.954 42.308 0.00 0.00 0.00 3.69
2475 3022 9.445973 TTTGGGAATTAGGGCATAAATCTAATT 57.554 29.630 6.90 5.62 42.73 1.40
2476 3023 9.445973 TTTTGGGAATTAGGGCATAAATCTAAT 57.554 29.630 6.90 0.00 35.83 1.73
2477 3024 8.846423 TTTTGGGAATTAGGGCATAAATCTAA 57.154 30.769 6.90 1.39 0.00 2.10
2478 3025 8.065007 ACTTTTGGGAATTAGGGCATAAATCTA 58.935 33.333 6.90 0.00 0.00 1.98
2479 3026 6.902974 ACTTTTGGGAATTAGGGCATAAATCT 59.097 34.615 6.90 0.00 0.00 2.40
2480 3027 7.124573 ACTTTTGGGAATTAGGGCATAAATC 57.875 36.000 0.00 0.00 0.00 2.17
2481 3028 6.671779 TGACTTTTGGGAATTAGGGCATAAAT 59.328 34.615 0.00 0.00 0.00 1.40
2482 3029 6.019748 TGACTTTTGGGAATTAGGGCATAAA 58.980 36.000 0.00 0.00 0.00 1.40
2484 3031 4.953579 GTGACTTTTGGGAATTAGGGCATA 59.046 41.667 0.00 0.00 0.00 3.14
2486 3033 3.161866 GTGACTTTTGGGAATTAGGGCA 58.838 45.455 0.00 0.00 0.00 5.36
2487 3034 3.193479 CAGTGACTTTTGGGAATTAGGGC 59.807 47.826 0.00 0.00 0.00 5.19
2556 3103 7.548427 TGAAATTTTCAAACTGATGCTCAAACA 59.452 29.630 9.36 0.00 36.59 2.83
2647 3195 8.454570 TGAATGCAAATGACACTGACATATAT 57.545 30.769 0.00 0.00 0.00 0.86
3091 3665 9.941325 ATGCAAATAAGATACCAAAATGTTCAA 57.059 25.926 0.00 0.00 0.00 2.69
3194 3858 4.762251 GGTTCTATCCAAGTCACTTTGCTT 59.238 41.667 0.00 0.00 0.00 3.91
3229 3893 9.413734 CCATTTCTCTGTTTTATCCCTAATTCT 57.586 33.333 0.00 0.00 0.00 2.40
3239 3903 7.595819 TTTGTGTCCCATTTCTCTGTTTTAT 57.404 32.000 0.00 0.00 0.00 1.40
3249 3913 2.430694 GCCCCTATTTGTGTCCCATTTC 59.569 50.000 0.00 0.00 0.00 2.17
3250 3914 2.225496 TGCCCCTATTTGTGTCCCATTT 60.225 45.455 0.00 0.00 0.00 2.32
3263 3927 8.659196 AGGGATAATTAGATTTATGCCCCTAT 57.341 34.615 10.09 0.00 45.97 2.57
3291 3955 7.545265 AGACTGACGAGTACTAGTACTGTTAAG 59.455 40.741 34.67 28.11 45.63 1.85
3296 3960 4.500117 CGAGACTGACGAGTACTAGTACTG 59.500 50.000 34.67 26.84 45.63 2.74
3298 3962 4.420168 ACGAGACTGACGAGTACTAGTAC 58.580 47.826 23.03 23.03 36.35 2.73
3323 3987 1.478105 TCTGGTGGTGTGATCTCGATG 59.522 52.381 0.00 0.00 0.00 3.84
3383 4066 0.681564 AGCAGCCGTAGAGCAGTAGT 60.682 55.000 0.00 0.00 34.23 2.73
3521 4208 1.278985 AGCTGCATGCACCACTTAGTA 59.721 47.619 18.46 0.00 45.94 1.82
3524 4211 1.167851 GAAGCTGCATGCACCACTTA 58.832 50.000 18.46 0.00 45.94 2.24
3546 4244 7.615365 AGGCACAACCATATGATTAGAGAAAAA 59.385 33.333 3.65 0.00 43.14 1.94
3617 4320 1.043673 GGGTCGTACCTCATCAGCCT 61.044 60.000 4.41 0.00 38.64 4.58
3913 4628 4.148825 ACCCTGACGGCGCTCATC 62.149 66.667 6.90 3.00 33.26 2.92
4087 4811 0.034574 ATGCTTACCCACGGCATTGA 60.035 50.000 0.00 0.00 43.02 2.57
4094 4818 1.643292 CATGCGATGCTTACCCACG 59.357 57.895 0.00 0.00 0.00 4.94
4110 4834 1.672363 ACGACATGAATTGCGATGCAT 59.328 42.857 0.00 0.00 38.76 3.96
4111 4835 1.062440 GACGACATGAATTGCGATGCA 59.938 47.619 0.00 0.00 36.47 3.96
4170 4894 0.389426 ACAGGACGCACGATTGTACC 60.389 55.000 0.00 0.00 0.00 3.34
4234 4963 3.059800 CGACAGCGACGATCAGATTAGTA 60.060 47.826 0.00 0.00 40.82 1.82
4247 4976 1.606350 CCTTGACGAACGACAGCGAC 61.606 60.000 0.14 0.00 41.64 5.19
4475 5204 3.653344 TGAGAAACCAGAATCACAGACG 58.347 45.455 0.00 0.00 0.00 4.18
4586 5316 8.623310 TCATTTAGTTTGTTTTTCGTTTCCTC 57.377 30.769 0.00 0.00 0.00 3.71
4760 5493 3.618594 CAGGTGACATCTCATTTGGTACG 59.381 47.826 0.00 0.00 0.00 3.67
4960 5695 1.758936 ATCAGATCGGTACCGTCACA 58.241 50.000 32.16 15.05 40.74 3.58
5212 6220 2.831685 TTTCAGGCGTGCTCTTCTAA 57.168 45.000 0.35 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.