Multiple sequence alignment - TraesCS7D01G067200

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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 TraesCS7D01G067200 chr7D 100.000 2527 0 0 1 2527 38173279 38170753 0.000000e+00 4667.0
1 TraesCS7D01G067200 chr7D 83.612 836 103 15 411 1220 153947451 153946624 0.000000e+00 754.0
2 TraesCS7D01G067200 chr7D 87.097 93 7 4 492 582 583094343 583094432 1.600000e-17 100.0
3 TraesCS7D01G067200 chr4A 85.061 1640 196 23 1 1610 642231838 642233458 0.000000e+00 1626.0
4 TraesCS7D01G067200 chr1B 82.452 1892 286 30 415 2276 523012707 523014582 0.000000e+00 1613.0
5 TraesCS7D01G067200 chr1B 82.095 1804 244 37 426 2193 471759157 471757397 0.000000e+00 1469.0
6 TraesCS7D01G067200 chr2A 85.804 1437 184 12 902 2332 516536966 516535544 0.000000e+00 1506.0
7 TraesCS7D01G067200 chr2A 85.235 149 18 4 2377 2522 254631199 254631052 1.570000e-32 150.0
8 TraesCS7D01G067200 chr1D 85.540 1390 188 12 902 2283 349780688 349779304 0.000000e+00 1441.0
9 TraesCS7D01G067200 chr4D 84.231 1522 189 25 734 2237 16237947 16239435 0.000000e+00 1434.0
10 TraesCS7D01G067200 chr4D 79.142 1889 330 50 492 2345 502108736 502106877 0.000000e+00 1247.0
11 TraesCS7D01G067200 chr4D 81.910 199 29 4 408 599 483037171 483037369 7.230000e-36 161.0
12 TraesCS7D01G067200 chr2D 85.350 1372 186 9 911 2273 573985454 573986819 0.000000e+00 1406.0
13 TraesCS7D01G067200 chr2D 80.579 587 81 18 401 964 5202241 5202817 3.010000e-114 422.0
14 TraesCS7D01G067200 chr2B 82.930 1611 225 40 950 2526 161990347 161991941 0.000000e+00 1406.0
15 TraesCS7D01G067200 chr2B 81.207 1591 266 28 810 2383 745673018 745674592 0.000000e+00 1251.0
16 TraesCS7D01G067200 chr2B 78.684 1398 226 52 428 1804 484611034 484612380 0.000000e+00 865.0
17 TraesCS7D01G067200 chr2B 85.263 95 13 1 492 586 534399009 534399102 2.070000e-16 97.1
18 TraesCS7D01G067200 chr5D 81.505 1595 260 28 813 2392 495795819 495794245 0.000000e+00 1279.0
19 TraesCS7D01G067200 chr5D 77.484 795 135 17 408 1173 450873119 450873898 1.070000e-118 436.0
20 TraesCS7D01G067200 chr5A 80.412 1552 268 27 813 2345 375291905 375290371 0.000000e+00 1149.0
21 TraesCS7D01G067200 chr7A 97.576 165 4 0 101 265 37694290 37694126 1.480000e-72 283.0
22 TraesCS7D01G067200 chr7B 75.668 374 64 18 415 773 494601950 494602311 7.230000e-36 161.0
23 TraesCS7D01G067200 chr5B 80.272 147 22 5 720 864 696452957 696453098 1.240000e-18 104.0


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 TraesCS7D01G067200 chr7D 38170753 38173279 2526 True 4667 4667 100.000 1 2527 1 chr7D.!!$R1 2526
1 TraesCS7D01G067200 chr7D 153946624 153947451 827 True 754 754 83.612 411 1220 1 chr7D.!!$R2 809
2 TraesCS7D01G067200 chr4A 642231838 642233458 1620 False 1626 1626 85.061 1 1610 1 chr4A.!!$F1 1609
3 TraesCS7D01G067200 chr1B 523012707 523014582 1875 False 1613 1613 82.452 415 2276 1 chr1B.!!$F1 1861
4 TraesCS7D01G067200 chr1B 471757397 471759157 1760 True 1469 1469 82.095 426 2193 1 chr1B.!!$R1 1767
5 TraesCS7D01G067200 chr2A 516535544 516536966 1422 True 1506 1506 85.804 902 2332 1 chr2A.!!$R2 1430
6 TraesCS7D01G067200 chr1D 349779304 349780688 1384 True 1441 1441 85.540 902 2283 1 chr1D.!!$R1 1381
7 TraesCS7D01G067200 chr4D 16237947 16239435 1488 False 1434 1434 84.231 734 2237 1 chr4D.!!$F1 1503
8 TraesCS7D01G067200 chr4D 502106877 502108736 1859 True 1247 1247 79.142 492 2345 1 chr4D.!!$R1 1853
9 TraesCS7D01G067200 chr2D 573985454 573986819 1365 False 1406 1406 85.350 911 2273 1 chr2D.!!$F2 1362
10 TraesCS7D01G067200 chr2D 5202241 5202817 576 False 422 422 80.579 401 964 1 chr2D.!!$F1 563
11 TraesCS7D01G067200 chr2B 161990347 161991941 1594 False 1406 1406 82.930 950 2526 1 chr2B.!!$F1 1576
12 TraesCS7D01G067200 chr2B 745673018 745674592 1574 False 1251 1251 81.207 810 2383 1 chr2B.!!$F4 1573
13 TraesCS7D01G067200 chr2B 484611034 484612380 1346 False 865 865 78.684 428 1804 1 chr2B.!!$F2 1376
14 TraesCS7D01G067200 chr5D 495794245 495795819 1574 True 1279 1279 81.505 813 2392 1 chr5D.!!$R1 1579
15 TraesCS7D01G067200 chr5D 450873119 450873898 779 False 436 436 77.484 408 1173 1 chr5D.!!$F1 765
16 TraesCS7D01G067200 chr5A 375290371 375291905 1534 True 1149 1149 80.412 813 2345 1 chr5A.!!$R1 1532

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
394 403 0.972883 TGTCATGTGTGTCCGGATGA 59.027 50.000 7.81 2.58 0.00 2.92 F
665 701 1.002544 GGGATAGCGCCAAATCTAGCT 59.997 52.381 2.29 0.00 43.07 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1319 0.180406 ACAAGGCTGACGAAAGGTGT 59.820 50.0 0.0 0.0 0.00 4.16 R
2392 2528 0.321564 CCGAATGAGTGGCAAGTCCA 60.322 55.0 0.0 0.0 44.18 4.02 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
63 64 2.334946 TTAGCTACACCGGTCGCGT 61.335 57.895 2.59 1.79 40.40 6.01
70 71 3.659092 ACCGGTCGCGTTCGTGTA 61.659 61.111 0.00 0.00 36.96 2.90
90 91 2.085320 ACGAGTAGCTCAGTGTAGGTG 58.915 52.381 0.00 0.00 0.00 4.00
108 109 3.030652 CGTGGCGGCAATATTCCC 58.969 61.111 15.50 0.00 0.00 3.97
126 127 1.645034 CCTGCTCAATGAGGTACACG 58.355 55.000 12.66 0.00 0.00 4.49
158 159 1.482182 AGGATCGTATTCTGCACAGCA 59.518 47.619 0.00 0.00 36.92 4.41
199 200 1.935933 ATGTACCTTGCCGAATCGAC 58.064 50.000 3.36 0.00 0.00 4.20
278 280 2.279517 GCCGAGCATCTACACCCG 60.280 66.667 0.00 0.00 0.00 5.28
286 288 1.075450 ATCTACACCCGGACCCTCC 60.075 63.158 0.73 0.00 0.00 4.30
314 320 1.024046 TCAATGAATGTGGGCGGACG 61.024 55.000 0.00 0.00 0.00 4.79
343 349 5.221742 GGTTATTGTCTGAATAGGAGAGGGG 60.222 48.000 0.00 0.00 0.00 4.79
344 350 2.478872 TGTCTGAATAGGAGAGGGGG 57.521 55.000 0.00 0.00 0.00 5.40
360 366 2.319025 GGGGGAAAAAGATGACCCAA 57.681 50.000 0.00 0.00 43.30 4.12
372 381 2.649531 TGACCCAACGAACCTTTCAT 57.350 45.000 0.00 0.00 0.00 2.57
376 385 4.048504 GACCCAACGAACCTTTCATTTTG 58.951 43.478 0.00 0.00 0.00 2.44
379 388 4.440802 CCCAACGAACCTTTCATTTTGTCA 60.441 41.667 0.00 0.00 0.00 3.58
383 392 5.280945 ACGAACCTTTCATTTTGTCATGTG 58.719 37.500 0.00 0.00 0.00 3.21
384 393 5.163561 ACGAACCTTTCATTTTGTCATGTGT 60.164 36.000 0.00 0.00 0.00 3.72
391 400 2.333688 TTTTGTCATGTGTGTCCGGA 57.666 45.000 0.00 0.00 0.00 5.14
394 403 0.972883 TGTCATGTGTGTCCGGATGA 59.027 50.000 7.81 2.58 0.00 2.92
406 415 3.905249 GGATGACCGCAAACCTCC 58.095 61.111 0.00 0.00 0.00 4.30
424 433 1.427368 TCCTAGGGCATGTTTGGTTGT 59.573 47.619 9.46 0.00 0.00 3.32
454 463 1.198094 TCCAATCAGGCCGAGTTGGA 61.198 55.000 25.37 25.37 45.68 3.53
484 493 2.418692 ACGTGTTTGATTGCATACGGA 58.581 42.857 0.00 0.00 33.43 4.69
494 504 2.281761 CATACGGATGGGCTGGCC 60.282 66.667 14.23 14.23 0.00 5.36
639 670 1.376683 CGGAAGATGGAAACCGGCA 60.377 57.895 0.00 0.00 41.41 5.69
665 701 1.002544 GGGATAGCGCCAAATCTAGCT 59.997 52.381 2.29 0.00 43.07 3.32
686 734 1.680989 ACCGCCCCATTTACTTGGC 60.681 57.895 0.00 0.00 40.54 4.52
730 783 4.406003 GGACTTCCTCTATTCTTAGCACCA 59.594 45.833 0.00 0.00 0.00 4.17
798 860 2.103143 CAGCACTCTCCGGTAGCG 59.897 66.667 7.49 7.49 0.00 4.26
845 907 3.141488 CCGTCTGGTCCTCCTCGG 61.141 72.222 0.00 0.00 37.08 4.63
903 976 4.552767 CGAATCCGATAAGCAACATGGAAC 60.553 45.833 0.00 0.00 38.22 3.62
904 977 6.926794 CGAATCCGATAAGCAACATGGAACA 61.927 44.000 0.00 0.00 40.33 3.18
935 1017 5.424252 CCCCTATGTTAGGTCAGTTGTTAGA 59.576 44.000 0.19 0.00 44.73 2.10
953 1035 1.972795 AGACCGTTAGGCAAGGTGTAA 59.027 47.619 0.00 0.00 42.76 2.41
1010 1096 2.829720 TGGACTAGGTTATGAACGCACT 59.170 45.455 0.00 0.00 0.00 4.40
1056 1150 4.436584 GCAACACTGATAGCTGTGATTCAC 60.437 45.833 22.62 9.93 44.06 3.18
1077 1171 1.752498 GCATGGCTCATGTTGATCCAA 59.248 47.619 14.21 0.00 44.68 3.53
1138 1234 7.581814 TCATTATGGTCCAATGTTAATCTGGA 58.418 34.615 0.00 0.34 36.89 3.86
1157 1253 1.342819 GAATCAGGAGGGGATGTCGAG 59.657 57.143 0.00 0.00 0.00 4.04
1195 1294 4.283467 ACAACTACAATGACACAGAGGCTA 59.717 41.667 0.00 0.00 0.00 3.93
1197 1296 5.269505 ACTACAATGACACAGAGGCTATC 57.730 43.478 0.00 0.00 0.00 2.08
1213 1312 3.255149 GGCTATCTGGATGCTTCAAATGG 59.745 47.826 1.64 0.00 0.00 3.16
1219 1319 5.078949 TCTGGATGCTTCAAATGGAAAGAA 58.921 37.500 1.64 0.00 34.44 2.52
1303 1404 2.037772 CCAGTGTGGAAGAGCAAGTAGT 59.962 50.000 0.00 0.00 40.96 2.73
1437 1538 1.412343 GGGAACTCAGAGGAGAGATGC 59.588 57.143 1.53 0.00 44.26 3.91
1481 1582 6.153000 GGACTCCTAACAAGATTCACACTAGA 59.847 42.308 0.00 0.00 0.00 2.43
1543 1646 7.118825 CAGTATGTAGTTCATGCCTTCATATGG 59.881 40.741 2.13 0.00 39.42 2.74
1563 1667 9.494271 CATATGGTTGTATTGTTCTGCTATAGT 57.506 33.333 0.84 0.00 0.00 2.12
1585 1689 6.179756 AGTCATAACACCATCTTGTAATGCA 58.820 36.000 0.00 0.00 0.00 3.96
1781 1887 5.816258 ACATGATGCTAACATTCTCAGTGAG 59.184 40.000 14.36 14.36 36.35 3.51
1806 1912 2.405559 TGAGTCATCCTGATGGCATCT 58.594 47.619 26.49 5.08 45.39 2.90
1830 1936 2.829023 TCCCCGATGGAAAGTTCTACT 58.171 47.619 0.00 0.00 41.40 2.57
1861 1967 1.281577 TGGCTATGCATGTTGTCCAGA 59.718 47.619 10.16 0.00 0.00 3.86
1873 1979 2.455674 TGTCCAGATGTTCTTCCACG 57.544 50.000 0.00 0.00 0.00 4.94
1879 1985 2.807967 CAGATGTTCTTCCACGCTTCAA 59.192 45.455 0.00 0.00 0.00 2.69
1882 1988 3.126001 TGTTCTTCCACGCTTCAAGAT 57.874 42.857 0.00 0.00 0.00 2.40
1936 2047 3.224269 GGACTATCCTAGGACTCCACAC 58.776 54.545 15.42 2.31 32.53 3.82
1957 2068 7.492669 CCACACGAACTATTTAATCTCAGACAT 59.507 37.037 0.00 0.00 0.00 3.06
1985 2096 4.698575 CCTTAGAGTTACCATTGAGAGGC 58.301 47.826 0.00 0.00 0.00 4.70
1998 2109 0.254178 GAGAGGCCATTTGGAGCTCA 59.746 55.000 17.19 0.00 37.39 4.26
2097 2208 8.117813 TGTCGCATTCTACATATAACTGGATA 57.882 34.615 0.00 0.00 0.00 2.59
2099 2210 9.025020 GTCGCATTCTACATATAACTGGATATG 57.975 37.037 9.16 9.16 42.93 1.78
2146 2257 1.821753 CTGAGGAGGAAGATGTGACGT 59.178 52.381 0.00 0.00 0.00 4.34
2151 2262 4.282496 AGGAGGAAGATGTGACGTCTAAT 58.718 43.478 17.92 10.11 0.00 1.73
2213 2327 2.222027 CGAAGCCTGGAGAACAAAAGT 58.778 47.619 0.00 0.00 0.00 2.66
2226 2340 5.892348 AGAACAAAAGTATGGAGTGGGAAT 58.108 37.500 0.00 0.00 0.00 3.01
2249 2363 3.589288 AGGGAATGTGGGATAATAGAGGC 59.411 47.826 0.00 0.00 0.00 4.70
2286 2421 6.122277 TGAAGAAGAAGAAGGAAAAGAGCAA 58.878 36.000 0.00 0.00 0.00 3.91
2287 2422 6.261826 TGAAGAAGAAGAAGGAAAAGAGCAAG 59.738 38.462 0.00 0.00 0.00 4.01
2290 2425 5.303259 AGAAGAAGGAAAAGAGCAAGAGT 57.697 39.130 0.00 0.00 0.00 3.24
2334 2470 3.837146 ACAGCAGATGAGGAGAAGAAGAA 59.163 43.478 0.00 0.00 0.00 2.52
2339 2475 5.105392 GCAGATGAGGAGAAGAAGAAGAAGA 60.105 44.000 0.00 0.00 0.00 2.87
2340 2476 6.567050 CAGATGAGGAGAAGAAGAAGAAGAG 58.433 44.000 0.00 0.00 0.00 2.85
2341 2477 5.658190 AGATGAGGAGAAGAAGAAGAAGAGG 59.342 44.000 0.00 0.00 0.00 3.69
2342 2478 5.004361 TGAGGAGAAGAAGAAGAAGAGGA 57.996 43.478 0.00 0.00 0.00 3.71
2343 2479 5.398236 TGAGGAGAAGAAGAAGAAGAGGAA 58.602 41.667 0.00 0.00 0.00 3.36
2344 2480 5.480073 TGAGGAGAAGAAGAAGAAGAGGAAG 59.520 44.000 0.00 0.00 0.00 3.46
2345 2481 4.222810 AGGAGAAGAAGAAGAAGAGGAAGC 59.777 45.833 0.00 0.00 0.00 3.86
2346 2482 4.503910 GAGAAGAAGAAGAAGAGGAAGCC 58.496 47.826 0.00 0.00 0.00 4.35
2347 2483 3.906846 AGAAGAAGAAGAAGAGGAAGCCA 59.093 43.478 0.00 0.00 0.00 4.75
2348 2484 4.349342 AGAAGAAGAAGAAGAGGAAGCCAA 59.651 41.667 0.00 0.00 0.00 4.52
2349 2485 4.713792 AGAAGAAGAAGAGGAAGCCAAA 57.286 40.909 0.00 0.00 0.00 3.28
2350 2486 4.650734 AGAAGAAGAAGAGGAAGCCAAAG 58.349 43.478 0.00 0.00 0.00 2.77
2351 2487 4.349342 AGAAGAAGAAGAGGAAGCCAAAGA 59.651 41.667 0.00 0.00 0.00 2.52
2352 2488 4.713792 AGAAGAAGAGGAAGCCAAAGAA 57.286 40.909 0.00 0.00 0.00 2.52
2353 2489 4.650734 AGAAGAAGAGGAAGCCAAAGAAG 58.349 43.478 0.00 0.00 0.00 2.85
2354 2490 4.349342 AGAAGAAGAGGAAGCCAAAGAAGA 59.651 41.667 0.00 0.00 0.00 2.87
2355 2491 4.713792 AGAAGAGGAAGCCAAAGAAGAA 57.286 40.909 0.00 0.00 0.00 2.52
2360 2496 4.824537 AGAGGAAGCCAAAGAAGAAAGAAC 59.175 41.667 0.00 0.00 0.00 3.01
2361 2497 3.891977 AGGAAGCCAAAGAAGAAAGAACC 59.108 43.478 0.00 0.00 0.00 3.62
2369 2505 5.163519 CCAAAGAAGAAAGAACCAGAAGCAA 60.164 40.000 0.00 0.00 0.00 3.91
2375 2511 5.136105 AGAAAGAACCAGAAGCAACAGAAT 58.864 37.500 0.00 0.00 0.00 2.40
2383 2519 5.936956 ACCAGAAGCAACAGAATAAGAAGAG 59.063 40.000 0.00 0.00 0.00 2.85
2386 2522 6.822676 CAGAAGCAACAGAATAAGAAGAGGAT 59.177 38.462 0.00 0.00 0.00 3.24
2389 2525 6.347696 AGCAACAGAATAAGAAGAGGATGAG 58.652 40.000 0.00 0.00 0.00 2.90
2392 2528 7.507829 CAACAGAATAAGAAGAGGATGAGGAT 58.492 38.462 0.00 0.00 0.00 3.24
2394 2530 6.043012 ACAGAATAAGAAGAGGATGAGGATGG 59.957 42.308 0.00 0.00 0.00 3.51
2396 2532 6.269769 AGAATAAGAAGAGGATGAGGATGGAC 59.730 42.308 0.00 0.00 0.00 4.02
2397 2533 3.704545 AGAAGAGGATGAGGATGGACT 57.295 47.619 0.00 0.00 0.00 3.85
2398 2534 4.006247 AGAAGAGGATGAGGATGGACTT 57.994 45.455 0.00 0.00 0.00 3.01
2399 2535 3.710677 AGAAGAGGATGAGGATGGACTTG 59.289 47.826 0.00 0.00 0.00 3.16
2401 2537 0.842635 AGGATGAGGATGGACTTGCC 59.157 55.000 0.00 0.00 37.10 4.52
2410 2546 3.231734 TGGACTTGCCACTCATTCG 57.768 52.632 0.00 0.00 43.33 3.34
2412 2548 0.321653 GGACTTGCCACTCATTCGGT 60.322 55.000 0.00 0.00 36.34 4.69
2414 2550 2.420129 GGACTTGCCACTCATTCGGTAT 60.420 50.000 0.00 0.00 36.34 2.73
2421 2670 4.067896 GCCACTCATTCGGTATCAATGAT 58.932 43.478 0.00 0.00 39.10 2.45
2426 2675 7.012704 CCACTCATTCGGTATCAATGATCTTTT 59.987 37.037 0.00 0.00 39.10 2.27
2434 2683 7.661437 TCGGTATCAATGATCTTTTCCCTATTG 59.339 37.037 0.00 0.00 0.00 1.90
2436 2685 9.354673 GGTATCAATGATCTTTTCCCTATTGAA 57.645 33.333 0.00 0.00 37.86 2.69
2441 2690 8.480501 CAATGATCTTTTCCCTATTGAACCATT 58.519 33.333 0.00 0.00 0.00 3.16
2444 2693 7.673504 TGATCTTTTCCCTATTGAACCATTTGA 59.326 33.333 0.00 0.00 0.00 2.69
2447 2696 6.588719 TTTCCCTATTGAACCATTTGACTG 57.411 37.500 0.00 0.00 0.00 3.51
2451 2700 7.410174 TCCCTATTGAACCATTTGACTGTTAT 58.590 34.615 0.00 0.00 0.00 1.89
2452 2701 8.553153 TCCCTATTGAACCATTTGACTGTTATA 58.447 33.333 0.00 0.00 0.00 0.98
2453 2702 9.354673 CCCTATTGAACCATTTGACTGTTATAT 57.645 33.333 0.00 0.00 0.00 0.86
2487 2738 6.622427 ATTTGTTAGTAGCTAGGGTGAACT 57.378 37.500 0.00 0.00 0.00 3.01
2489 2740 3.194968 TGTTAGTAGCTAGGGTGAACTGC 59.805 47.826 0.00 0.00 0.00 4.40
2490 2741 0.818296 AGTAGCTAGGGTGAACTGCG 59.182 55.000 0.00 0.00 0.00 5.18
2500 2751 2.607038 GGGTGAACTGCGATTTGTTTCC 60.607 50.000 0.00 0.00 0.00 3.13
2509 2760 2.288186 GCGATTTGTTTCCTAGCTAGGC 59.712 50.000 31.76 19.68 43.31 3.93
2510 2761 3.531538 CGATTTGTTTCCTAGCTAGGCA 58.468 45.455 31.76 21.24 43.31 4.75
2511 2762 3.309954 CGATTTGTTTCCTAGCTAGGCAC 59.690 47.826 31.76 27.81 43.31 5.01
2515 2766 2.269172 GTTTCCTAGCTAGGCACGAAC 58.731 52.381 31.76 25.51 43.31 3.95
2517 2768 2.723322 TCCTAGCTAGGCACGAACTA 57.277 50.000 31.76 11.84 43.31 2.24
2518 2769 3.225177 TCCTAGCTAGGCACGAACTAT 57.775 47.619 31.76 0.00 43.31 2.12
2519 2770 2.885266 TCCTAGCTAGGCACGAACTATG 59.115 50.000 31.76 6.88 43.31 2.23
2521 2772 3.068307 CCTAGCTAGGCACGAACTATGTT 59.932 47.826 26.62 0.00 36.53 2.71
2522 2773 2.893637 AGCTAGGCACGAACTATGTTG 58.106 47.619 0.00 0.00 0.00 3.33
2523 2774 2.496070 AGCTAGGCACGAACTATGTTGA 59.504 45.455 0.00 0.00 0.00 3.18
2524 2775 2.860735 GCTAGGCACGAACTATGTTGAG 59.139 50.000 0.00 0.00 0.00 3.02
2525 2776 3.428999 GCTAGGCACGAACTATGTTGAGA 60.429 47.826 0.00 0.00 0.00 3.27
2526 2777 2.960819 AGGCACGAACTATGTTGAGAC 58.039 47.619 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 3.167945 GTACACGAACGCGACCGG 61.168 66.667 15.93 0.00 41.64 5.28
69 70 3.268330 CACCTACACTGAGCTACTCGTA 58.732 50.000 0.00 0.00 32.35 3.43
70 71 2.085320 CACCTACACTGAGCTACTCGT 58.915 52.381 0.00 0.00 32.35 4.18
81 82 4.373116 CCGCCACGCACCTACACT 62.373 66.667 0.00 0.00 0.00 3.55
90 91 2.331451 GGAATATTGCCGCCACGC 59.669 61.111 0.00 0.00 0.00 5.34
99 100 4.467769 ACCTCATTGAGCAGGGAATATTG 58.532 43.478 8.23 0.00 33.57 1.90
108 109 1.645034 CCGTGTACCTCATTGAGCAG 58.355 55.000 8.23 0.00 0.00 4.24
126 127 2.528041 ACGATCCTCGCTTTATTCCC 57.472 50.000 0.00 0.00 45.12 3.97
158 159 2.346766 TACCCTTTCGATGCATGCAT 57.653 45.000 32.66 32.66 39.69 3.96
199 200 2.591429 TGGGCTGCTGTTGACGTG 60.591 61.111 0.00 0.00 0.00 4.49
237 238 3.514645 AGTGAGTTTGTGCTTTGCTTTG 58.485 40.909 0.00 0.00 0.00 2.77
278 280 1.492764 TGAAAGGATACGGAGGGTCC 58.507 55.000 0.00 0.00 46.39 4.46
286 288 4.498009 GCCCACATTCATTGAAAGGATACG 60.498 45.833 14.11 0.00 46.39 3.06
295 297 1.024046 CGTCCGCCCACATTCATTGA 61.024 55.000 0.00 0.00 0.00 2.57
314 320 4.137543 CCTATTCAGACAATAACCAGGCC 58.862 47.826 0.00 0.00 0.00 5.19
316 322 6.463614 CCTCTCCTATTCAGACAATAACCAGG 60.464 46.154 0.00 0.00 0.00 4.45
318 324 5.366768 CCCTCTCCTATTCAGACAATAACCA 59.633 44.000 0.00 0.00 0.00 3.67
324 330 2.764269 CCCCCTCTCCTATTCAGACAA 58.236 52.381 0.00 0.00 0.00 3.18
343 349 2.510613 TCGTTGGGTCATCTTTTTCCC 58.489 47.619 0.00 0.00 40.26 3.97
344 350 3.305131 GGTTCGTTGGGTCATCTTTTTCC 60.305 47.826 0.00 0.00 0.00 3.13
351 357 2.500229 TGAAAGGTTCGTTGGGTCATC 58.500 47.619 0.00 0.00 0.00 2.92
353 359 2.649531 ATGAAAGGTTCGTTGGGTCA 57.350 45.000 0.00 0.00 0.00 4.02
354 360 4.048504 CAAAATGAAAGGTTCGTTGGGTC 58.951 43.478 0.00 0.00 38.80 4.46
355 361 3.449377 ACAAAATGAAAGGTTCGTTGGGT 59.551 39.130 0.00 0.00 38.80 4.51
356 362 4.048504 GACAAAATGAAAGGTTCGTTGGG 58.951 43.478 0.00 0.00 38.80 4.12
357 363 4.677584 TGACAAAATGAAAGGTTCGTTGG 58.322 39.130 0.00 0.00 38.80 3.77
359 365 5.748152 CACATGACAAAATGAAAGGTTCGTT 59.252 36.000 0.00 0.00 40.47 3.85
360 366 5.163561 ACACATGACAAAATGAAAGGTTCGT 60.164 36.000 0.00 0.00 0.00 3.85
372 381 2.333688 TCCGGACACACATGACAAAA 57.666 45.000 0.00 0.00 0.00 2.44
376 385 1.359848 GTCATCCGGACACACATGAC 58.640 55.000 15.72 15.72 46.19 3.06
391 400 0.541863 CCTAGGAGGTTTGCGGTCAT 59.458 55.000 1.05 0.00 0.00 3.06
394 403 2.967946 GCCCTAGGAGGTTTGCGGT 61.968 63.158 11.48 0.00 31.93 5.68
400 409 1.005924 CCAAACATGCCCTAGGAGGTT 59.994 52.381 11.48 2.06 31.93 3.50
406 415 1.818674 GGACAACCAAACATGCCCTAG 59.181 52.381 0.00 0.00 35.97 3.02
424 433 1.140852 CCTGATTGGAGGTAATGCGGA 59.859 52.381 0.00 0.00 38.35 5.54
484 493 3.733507 CTGATGCAGGCCAGCCCAT 62.734 63.158 18.54 5.03 36.58 4.00
582 593 1.173043 CCTTGCATCCCTTTTGCGTA 58.827 50.000 0.00 0.00 43.10 4.42
583 594 1.966762 CCTTGCATCCCTTTTGCGT 59.033 52.632 0.00 0.00 43.10 5.24
665 701 1.540267 CAAGTAAATGGGGCGGTGAA 58.460 50.000 0.00 0.00 0.00 3.18
686 734 2.145397 TGTCCTAGAGCTAGTGGTGG 57.855 55.000 4.02 0.00 0.00 4.61
798 860 0.393673 GAAGGGAAGAAGCTGCTCCC 60.394 60.000 17.45 17.45 40.82 4.30
811 873 1.761174 GGTGCACAAGAGGAAGGGA 59.239 57.895 20.43 0.00 0.00 4.20
884 957 3.006940 GTGTTCCATGTTGCTTATCGGA 58.993 45.455 0.00 0.00 0.00 4.55
888 961 2.042979 AGGGGTGTTCCATGTTGCTTAT 59.957 45.455 0.00 0.00 37.22 1.73
903 976 1.435256 CTAACATAGGGGGAGGGGTG 58.565 60.000 0.00 0.00 0.00 4.61
904 977 0.271005 CCTAACATAGGGGGAGGGGT 59.729 60.000 0.00 0.00 42.42 4.95
935 1017 1.972795 TCTTACACCTTGCCTAACGGT 59.027 47.619 0.00 0.00 0.00 4.83
1010 1096 2.355108 GCCTGAACTACCAGCTTCATCA 60.355 50.000 0.00 0.00 32.97 3.07
1056 1150 3.839654 GATCAACATGAGCCATGCG 57.160 52.632 13.19 6.87 44.80 4.73
1077 1171 2.159142 ACCACGACGAACAACTCTCTTT 60.159 45.455 0.00 0.00 0.00 2.52
1138 1234 1.343478 ACTCGACATCCCCTCCTGATT 60.343 52.381 0.00 0.00 0.00 2.57
1195 1294 5.266788 TCTTTCCATTTGAAGCATCCAGAT 58.733 37.500 0.00 0.00 33.63 2.90
1197 1296 5.166398 GTTCTTTCCATTTGAAGCATCCAG 58.834 41.667 0.00 0.00 33.63 3.86
1219 1319 0.180406 ACAAGGCTGACGAAAGGTGT 59.820 50.000 0.00 0.00 0.00 4.16
1233 1333 0.397941 TCCTGAAGGTCTGCACAAGG 59.602 55.000 0.00 0.00 36.34 3.61
1407 1508 3.254166 CCTCTGAGTTCCCAAACAACATG 59.746 47.826 3.66 0.00 37.88 3.21
1416 1517 2.744760 CATCTCTCCTCTGAGTTCCCA 58.255 52.381 3.66 0.00 39.75 4.37
1437 1538 1.966451 GGCCGGTTGGTGACTTGAG 60.966 63.158 1.90 0.00 37.67 3.02
1465 1566 5.808366 TCTTGGTCTAGTGTGAATCTTGT 57.192 39.130 0.00 0.00 0.00 3.16
1537 1640 9.494271 ACTATAGCAGAACAATACAACCATATG 57.506 33.333 0.00 0.00 0.00 1.78
1563 1667 7.643569 ATTGCATTACAAGATGGTGTTATGA 57.356 32.000 8.13 0.00 42.87 2.15
1585 1689 9.617523 CTATTGCCCCAATGAAATCTTAAAATT 57.382 29.630 0.94 0.00 35.54 1.82
1597 1702 3.721575 AGTACCATCTATTGCCCCAATGA 59.278 43.478 0.94 0.00 35.54 2.57
1820 1926 5.627968 GCCAGCATCTCCTAAGTAGAACTTT 60.628 44.000 0.00 0.00 39.51 2.66
1830 1936 2.049372 TGCATAGCCAGCATCTCCTAA 58.951 47.619 0.00 0.00 37.02 2.69
1861 1967 3.126001 TCTTGAAGCGTGGAAGAACAT 57.874 42.857 0.00 0.00 0.00 2.71
1873 1979 6.529220 AGATGGTATCTGGTTATCTTGAAGC 58.471 40.000 0.00 0.00 38.44 3.86
1879 1985 5.833667 TCGTTGAGATGGTATCTGGTTATCT 59.166 40.000 0.00 0.00 40.38 1.98
1882 1988 4.954202 ACTCGTTGAGATGGTATCTGGTTA 59.046 41.667 0.00 0.00 40.38 2.85
1936 2047 8.648557 TGGAATGTCTGAGATTAAATAGTTCG 57.351 34.615 0.00 0.00 0.00 3.95
1957 2068 4.534500 TCAATGGTAACTCTAAGGCTGGAA 59.466 41.667 0.00 0.00 37.61 3.53
1985 2096 3.415212 TGTTCTTCTGAGCTCCAAATGG 58.585 45.455 12.15 0.00 0.00 3.16
2024 2135 4.403734 GGGAAAGTGTGGAATGGTTTCTA 58.596 43.478 0.00 0.00 32.16 2.10
2029 2140 0.856982 TGGGGAAAGTGTGGAATGGT 59.143 50.000 0.00 0.00 0.00 3.55
2075 2186 7.042456 GCCATATCCAGTTATATGTAGAATGCG 60.042 40.741 0.00 0.00 37.90 4.73
2086 2197 4.605813 ACCCCATTGCCATATCCAGTTATA 59.394 41.667 0.00 0.00 0.00 0.98
2087 2198 3.402366 ACCCCATTGCCATATCCAGTTAT 59.598 43.478 0.00 0.00 0.00 1.89
2097 2208 1.196911 CATCACAACCCCATTGCCAT 58.803 50.000 0.00 0.00 42.62 4.40
2099 2210 1.066929 GTTCATCACAACCCCATTGCC 60.067 52.381 0.00 0.00 42.62 4.52
2146 2257 5.452496 GGCTAGAGCTGACAACATCATTAGA 60.452 44.000 0.00 0.00 41.70 2.10
2151 2262 1.901833 TGGCTAGAGCTGACAACATCA 59.098 47.619 0.00 0.00 41.70 3.07
2213 2327 4.350816 CACATTCCCTATTCCCACTCCATA 59.649 45.833 0.00 0.00 0.00 2.74
2226 2340 4.783227 GCCTCTATTATCCCACATTCCCTA 59.217 45.833 0.00 0.00 0.00 3.53
2249 2363 4.815533 TCTTCTTCAGATCCTTGTCTGG 57.184 45.455 4.28 0.00 44.51 3.86
2286 2421 3.696045 TCTTCTCTTCTGCTGCTACTCT 58.304 45.455 0.00 0.00 0.00 3.24
2287 2422 4.423732 CTTCTTCTCTTCTGCTGCTACTC 58.576 47.826 0.00 0.00 0.00 2.59
2290 2425 2.564504 TGCTTCTTCTCTTCTGCTGCTA 59.435 45.455 0.00 0.00 0.00 3.49
2334 2470 4.713792 TTCTTCTTTGGCTTCCTCTTCT 57.286 40.909 0.00 0.00 0.00 2.85
2339 2475 3.891977 GGTTCTTTCTTCTTTGGCTTCCT 59.108 43.478 0.00 0.00 0.00 3.36
2340 2476 3.636764 TGGTTCTTTCTTCTTTGGCTTCC 59.363 43.478 0.00 0.00 0.00 3.46
2341 2477 4.580580 TCTGGTTCTTTCTTCTTTGGCTTC 59.419 41.667 0.00 0.00 0.00 3.86
2342 2478 4.536765 TCTGGTTCTTTCTTCTTTGGCTT 58.463 39.130 0.00 0.00 0.00 4.35
2343 2479 4.170468 TCTGGTTCTTTCTTCTTTGGCT 57.830 40.909 0.00 0.00 0.00 4.75
2344 2480 4.794329 GCTTCTGGTTCTTTCTTCTTTGGC 60.794 45.833 0.00 0.00 0.00 4.52
2345 2481 4.339247 TGCTTCTGGTTCTTTCTTCTTTGG 59.661 41.667 0.00 0.00 0.00 3.28
2346 2482 5.505173 TGCTTCTGGTTCTTTCTTCTTTG 57.495 39.130 0.00 0.00 0.00 2.77
2347 2483 5.418840 TGTTGCTTCTGGTTCTTTCTTCTTT 59.581 36.000 0.00 0.00 0.00 2.52
2348 2484 4.949856 TGTTGCTTCTGGTTCTTTCTTCTT 59.050 37.500 0.00 0.00 0.00 2.52
2349 2485 4.526970 TGTTGCTTCTGGTTCTTTCTTCT 58.473 39.130 0.00 0.00 0.00 2.85
2350 2486 4.576463 TCTGTTGCTTCTGGTTCTTTCTTC 59.424 41.667 0.00 0.00 0.00 2.87
2351 2487 4.526970 TCTGTTGCTTCTGGTTCTTTCTT 58.473 39.130 0.00 0.00 0.00 2.52
2352 2488 4.156455 TCTGTTGCTTCTGGTTCTTTCT 57.844 40.909 0.00 0.00 0.00 2.52
2353 2489 4.900635 TTCTGTTGCTTCTGGTTCTTTC 57.099 40.909 0.00 0.00 0.00 2.62
2354 2490 6.772716 TCTTATTCTGTTGCTTCTGGTTCTTT 59.227 34.615 0.00 0.00 0.00 2.52
2355 2491 6.299141 TCTTATTCTGTTGCTTCTGGTTCTT 58.701 36.000 0.00 0.00 0.00 2.52
2360 2496 5.353678 CCTCTTCTTATTCTGTTGCTTCTGG 59.646 44.000 0.00 0.00 0.00 3.86
2361 2497 6.169094 TCCTCTTCTTATTCTGTTGCTTCTG 58.831 40.000 0.00 0.00 0.00 3.02
2369 2505 6.043012 CCATCCTCATCCTCTTCTTATTCTGT 59.957 42.308 0.00 0.00 0.00 3.41
2375 2511 5.149584 AGTCCATCCTCATCCTCTTCTTA 57.850 43.478 0.00 0.00 0.00 2.10
2383 2519 0.548031 TGGCAAGTCCATCCTCATCC 59.452 55.000 0.00 0.00 40.72 3.51
2392 2528 0.321564 CCGAATGAGTGGCAAGTCCA 60.322 55.000 0.00 0.00 44.18 4.02
2394 2530 2.380084 TACCGAATGAGTGGCAAGTC 57.620 50.000 0.00 0.00 0.00 3.01
2396 2532 2.905075 TGATACCGAATGAGTGGCAAG 58.095 47.619 0.00 0.00 0.00 4.01
2397 2533 3.342377 TTGATACCGAATGAGTGGCAA 57.658 42.857 0.00 0.00 0.00 4.52
2398 2534 3.118445 TCATTGATACCGAATGAGTGGCA 60.118 43.478 0.00 0.00 35.38 4.92
2399 2535 3.466836 TCATTGATACCGAATGAGTGGC 58.533 45.455 0.00 0.00 35.38 5.01
2401 2537 7.488187 AAAGATCATTGATACCGAATGAGTG 57.512 36.000 0.00 0.00 41.83 3.51
2402 2538 7.227512 GGAAAAGATCATTGATACCGAATGAGT 59.772 37.037 0.00 0.00 41.83 3.41
2404 2540 6.486657 GGGAAAAGATCATTGATACCGAATGA 59.513 38.462 0.00 0.00 42.53 2.57
2405 2541 6.488006 AGGGAAAAGATCATTGATACCGAATG 59.512 38.462 0.00 0.00 32.91 2.67
2406 2542 6.605119 AGGGAAAAGATCATTGATACCGAAT 58.395 36.000 0.00 0.00 0.00 3.34
2407 2543 6.001449 AGGGAAAAGATCATTGATACCGAA 57.999 37.500 0.00 0.00 0.00 4.30
2408 2544 5.630415 AGGGAAAAGATCATTGATACCGA 57.370 39.130 0.00 0.00 0.00 4.69
2410 2546 8.924511 TCAATAGGGAAAAGATCATTGATACC 57.075 34.615 0.00 0.00 29.84 2.73
2412 2548 9.354673 GGTTCAATAGGGAAAAGATCATTGATA 57.645 33.333 0.00 0.00 33.70 2.15
2414 2550 7.181361 TGGTTCAATAGGGAAAAGATCATTGA 58.819 34.615 0.00 0.00 32.22 2.57
2421 2670 7.010160 AGTCAAATGGTTCAATAGGGAAAAGA 58.990 34.615 0.00 0.00 0.00 2.52
2426 2675 5.255397 ACAGTCAAATGGTTCAATAGGGA 57.745 39.130 0.00 0.00 0.00 4.20
2458 2707 9.430399 TCACCCTAGCTACTAACAAATATTAGT 57.570 33.333 3.84 3.84 45.33 2.24
2461 2710 8.769359 AGTTCACCCTAGCTACTAACAAATATT 58.231 33.333 0.00 0.00 0.00 1.28
2462 2711 8.204836 CAGTTCACCCTAGCTACTAACAAATAT 58.795 37.037 0.00 0.00 0.00 1.28
2463 2712 7.553334 CAGTTCACCCTAGCTACTAACAAATA 58.447 38.462 0.00 0.00 0.00 1.40
2464 2713 6.407202 CAGTTCACCCTAGCTACTAACAAAT 58.593 40.000 0.00 0.00 0.00 2.32
2465 2714 5.790593 CAGTTCACCCTAGCTACTAACAAA 58.209 41.667 0.00 0.00 0.00 2.83
2466 2715 4.322499 GCAGTTCACCCTAGCTACTAACAA 60.322 45.833 0.00 0.00 0.00 2.83
2468 2717 3.734293 CGCAGTTCACCCTAGCTACTAAC 60.734 52.174 0.00 0.00 0.00 2.34
2476 2727 2.699954 ACAAATCGCAGTTCACCCTAG 58.300 47.619 0.00 0.00 0.00 3.02
2481 2732 3.626028 AGGAAACAAATCGCAGTTCAC 57.374 42.857 0.00 0.00 0.00 3.18
2487 2738 3.531538 CCTAGCTAGGAAACAAATCGCA 58.468 45.455 32.79 0.00 46.63 5.10
2489 2740 3.309954 GTGCCTAGCTAGGAAACAAATCG 59.690 47.826 38.74 12.28 46.63 3.34
2490 2741 3.309954 CGTGCCTAGCTAGGAAACAAATC 59.690 47.826 38.74 20.59 46.63 2.17
2500 2751 3.992260 ACATAGTTCGTGCCTAGCTAG 57.008 47.619 14.20 14.20 0.00 3.42


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

AutoCloner maintained by Alex Coulton.