Multiple sequence alignment - TraesCS2A01G206200

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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 TraesCS2A01G206200 chr2A 100.000 2951 0 0 1 2951 185124860 185127810 0.000000e+00 5450.0
1 TraesCS2A01G206200 chr2A 88.761 436 31 4 2532 2950 30069450 30069016 4.360000e-143 518.0
2 TraesCS2A01G206200 chr2B 94.949 2277 75 23 47 2308 231971844 231974095 0.000000e+00 3531.0
3 TraesCS2A01G206200 chr2B 92.617 298 20 2 2571 2866 748193699 748193996 7.560000e-116 427.0
4 TraesCS2A01G206200 chr2D 97.257 1896 46 5 416 2308 165541746 165539854 0.000000e+00 3208.0
5 TraesCS2A01G206200 chr2D 88.372 430 27 10 2532 2946 590727133 590727554 2.040000e-136 496.0
6 TraesCS2A01G206200 chr2D 84.527 349 28 14 47 387 165542139 165541809 3.670000e-84 322.0
7 TraesCS2A01G206200 chr2D 90.625 224 18 2 2308 2531 54173157 54172937 8.000000e-76 294.0
8 TraesCS2A01G206200 chr2D 90.541 222 19 2 2310 2531 139519892 139520111 2.880000e-75 292.0
9 TraesCS2A01G206200 chr2D 90.141 213 17 3 2309 2521 639963036 639962828 1.040000e-69 274.0
10 TraesCS2A01G206200 chr2D 100.000 46 0 0 1 46 165542207 165542162 5.240000e-13 86.1
11 TraesCS2A01G206200 chr1B 90.802 424 34 3 2532 2950 109247875 109247452 1.990000e-156 562.0
12 TraesCS2A01G206200 chr4A 90.138 436 26 9 2532 2950 541171407 541170972 4.300000e-153 551.0
13 TraesCS2A01G206200 chr4A 92.308 325 23 2 2579 2901 711898505 711898829 7.450000e-126 460.0
14 TraesCS2A01G206200 chr1D 90.094 424 37 5 2532 2950 19480155 19480578 2.000000e-151 545.0
15 TraesCS2A01G206200 chr1D 89.952 418 30 6 2532 2944 19490541 19490951 2.010000e-146 529.0
16 TraesCS2A01G206200 chr1D 89.145 433 27 4 2532 2944 19480766 19481198 3.370000e-144 521.0
17 TraesCS2A01G206200 chr1D 87.500 440 35 4 2532 2951 19491145 19491584 9.500000e-135 490.0
18 TraesCS2A01G206200 chr3D 89.679 436 27 7 2532 2950 538576229 538575795 9.310000e-150 540.0
19 TraesCS2A01G206200 chr6B 88.050 318 23 1 2648 2950 168070987 168071304 2.160000e-96 363.0
20 TraesCS2A01G206200 chr3B 81.938 454 40 21 2532 2950 2393183 2392737 2.180000e-91 346.0
21 TraesCS2A01G206200 chrUn 91.111 225 19 1 2308 2531 88829830 88829606 1.330000e-78 303.0
22 TraesCS2A01G206200 chrUn 91.111 225 19 1 2308 2531 88849719 88849495 1.330000e-78 303.0
23 TraesCS2A01G206200 chr5D 90.667 225 15 5 2310 2531 311748323 311748102 8.000000e-76 294.0
24 TraesCS2A01G206200 chr4B 90.583 223 19 1 2309 2531 594148517 594148737 8.000000e-76 294.0
25 TraesCS2A01G206200 chr6A 88.559 236 23 4 2298 2531 326395568 326395801 1.730000e-72 283.0
26 TraesCS2A01G206200 chr7B 86.842 228 24 5 2306 2531 665382032 665381809 1.760000e-62 250.0


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 TraesCS2A01G206200 chr2A 185124860 185127810 2950 False 5450.000000 5450 100.0000 1 2951 1 chr2A.!!$F1 2950
1 TraesCS2A01G206200 chr2B 231971844 231974095 2251 False 3531.000000 3531 94.9490 47 2308 1 chr2B.!!$F1 2261
2 TraesCS2A01G206200 chr2D 165539854 165542207 2353 True 1205.366667 3208 93.9280 1 2308 3 chr2D.!!$R3 2307
3 TraesCS2A01G206200 chr1D 19480155 19481198 1043 False 533.000000 545 89.6195 2532 2950 2 chr1D.!!$F1 418
4 TraesCS2A01G206200 chr1D 19490541 19491584 1043 False 509.500000 529 88.7260 2532 2951 2 chr1D.!!$F2 419

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
310 342 1.067916 CAAGCCGCAGCCTGTTTTT 59.932 52.632 0.00 0.00 41.25 1.94 F
1534 1605 1.303309 GACCTCATGCATGTACAGGC 58.697 55.000 24.87 24.87 38.80 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1557 1628 0.456142 GTCGCACAGATCAGCACGTA 60.456 55.0 0.0 0.0 0.0 3.57 R
2335 2413 0.249073 CGTTCAGATGTAGAGGCCGG 60.249 60.0 0.0 0.0 0.0 6.13 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
97 120 8.519799 TTTGTAATTTCTCCTTCTCTGTGTTT 57.480 30.769 0.00 0.00 0.00 2.83
151 176 9.159254 ACAATATATGAAGAGGTATCTGGTGAA 57.841 33.333 0.00 0.00 35.37 3.18
154 179 5.965033 ATGAAGAGGTATCTGGTGAATGT 57.035 39.130 0.00 0.00 35.37 2.71
166 198 5.491070 TCTGGTGAATGTTACAAGATGAGG 58.509 41.667 0.00 0.00 0.00 3.86
171 203 7.286546 TGGTGAATGTTACAAGATGAGGAAAAA 59.713 33.333 0.00 0.00 0.00 1.94
205 237 8.010733 TGGTGAAAAAGAAATCATTCTGACTT 57.989 30.769 0.00 0.00 45.19 3.01
255 287 3.637998 AGCTGAATGAAGTTGCAAGTG 57.362 42.857 7.73 0.00 0.00 3.16
263 295 2.170397 TGAAGTTGCAAGTGTCTGAGGA 59.830 45.455 7.73 0.00 0.00 3.71
310 342 1.067916 CAAGCCGCAGCCTGTTTTT 59.932 52.632 0.00 0.00 41.25 1.94
340 372 9.000018 CGCAAAACTTATCAATTAGCTCTAAAC 58.000 33.333 0.00 0.00 0.00 2.01
357 389 6.072112 TCTAAACTTTGTTCATCACTTGCC 57.928 37.500 0.00 0.00 0.00 4.52
362 394 6.655078 ACTTTGTTCATCACTTGCCTAAAT 57.345 33.333 0.00 0.00 0.00 1.40
364 396 7.500141 ACTTTGTTCATCACTTGCCTAAATTT 58.500 30.769 0.00 0.00 0.00 1.82
365 397 7.986889 ACTTTGTTCATCACTTGCCTAAATTTT 59.013 29.630 0.00 0.00 0.00 1.82
440 506 7.823799 TCGCTAATAATAGATCATTTCATGCCA 59.176 33.333 0.00 0.00 0.00 4.92
452 518 5.889289 TCATTTCATGCCAGATCATCAGAAA 59.111 36.000 0.00 0.00 0.00 2.52
459 525 4.070716 GCCAGATCATCAGAAATACCCAG 58.929 47.826 0.00 0.00 0.00 4.45
528 595 5.295292 CAGGTAGATGTGTGAATGGCTTAAG 59.705 44.000 0.00 0.00 0.00 1.85
664 735 3.547054 TTTACGCCATATCTTTCCGGT 57.453 42.857 0.00 0.00 0.00 5.28
708 779 1.670406 CACAAGCGCTCTGAAGCCT 60.670 57.895 12.06 0.00 46.34 4.58
1356 1427 2.346365 GACGTCAAGTCCACCCCC 59.654 66.667 11.55 0.00 43.95 5.40
1512 1583 1.824272 GCAAGGTACGCAACGTCGTT 61.824 55.000 4.40 4.40 43.15 3.85
1530 1601 2.029244 CGTTTCGACCTCATGCATGTAC 59.971 50.000 25.43 13.90 0.00 2.90
1534 1605 1.303309 GACCTCATGCATGTACAGGC 58.697 55.000 24.87 24.87 38.80 4.85
1538 1609 1.417517 CTCATGCATGTACAGGCCCTA 59.582 52.381 27.91 11.61 37.30 3.53
1552 1623 6.054860 ACAGGCCCTAAATATATACTGCAG 57.945 41.667 13.48 13.48 0.00 4.41
1557 1628 4.081087 CCCTAAATATATACTGCAGGGCGT 60.081 45.833 19.93 0.00 35.18 5.68
1562 1633 0.382873 TATACTGCAGGGCGTACGTG 59.617 55.000 19.93 8.58 37.99 4.49
1574 1645 1.733416 CGTACGTGCTGATCTGTGCG 61.733 60.000 7.22 13.17 34.42 5.34
1983 2054 2.802556 GAGCAATTTCTGTCAGCTCG 57.197 50.000 0.00 0.00 41.75 5.03
2084 2155 4.691860 ATCGCAAAGATCCTTTGTTGAG 57.308 40.909 17.44 9.32 33.45 3.02
2188 2259 5.064452 CCACTTGTACATCAATCTTGAGCTC 59.936 44.000 6.82 6.82 41.08 4.09
2301 2379 1.425448 ACTGAGCTTGCTACCCCTTTT 59.575 47.619 0.00 0.00 0.00 2.27
2308 2386 4.228438 AGCTTGCTACCCCTTTTATCTCTT 59.772 41.667 0.00 0.00 0.00 2.85
2309 2387 4.950475 GCTTGCTACCCCTTTTATCTCTTT 59.050 41.667 0.00 0.00 0.00 2.52
2310 2388 5.419155 GCTTGCTACCCCTTTTATCTCTTTT 59.581 40.000 0.00 0.00 0.00 2.27
2311 2389 6.071334 GCTTGCTACCCCTTTTATCTCTTTTT 60.071 38.462 0.00 0.00 0.00 1.94
2333 2411 2.908688 TTTGAAAAAGGAGGCTTGCC 57.091 45.000 2.97 2.97 0.00 4.52
2334 2412 1.047801 TTGAAAAAGGAGGCTTGCCC 58.952 50.000 8.17 0.00 0.00 5.36
2335 2413 0.831711 TGAAAAAGGAGGCTTGCCCC 60.832 55.000 8.17 9.26 0.00 5.80
2336 2414 1.536418 AAAAAGGAGGCTTGCCCCC 60.536 57.895 8.17 6.00 0.00 5.40
2337 2415 3.886550 AAAAGGAGGCTTGCCCCCG 62.887 63.158 8.17 0.00 0.00 5.73
2348 2426 3.942439 GCCCCCGGCCTCTACATC 61.942 72.222 0.00 0.00 44.06 3.06
2349 2427 2.122813 CCCCCGGCCTCTACATCT 60.123 66.667 0.00 0.00 0.00 2.90
2350 2428 2.511452 CCCCCGGCCTCTACATCTG 61.511 68.421 0.00 0.00 0.00 2.90
2351 2429 1.457643 CCCCGGCCTCTACATCTGA 60.458 63.158 0.00 0.00 0.00 3.27
2352 2430 1.048724 CCCCGGCCTCTACATCTGAA 61.049 60.000 0.00 0.00 0.00 3.02
2353 2431 0.105039 CCCGGCCTCTACATCTGAAC 59.895 60.000 0.00 0.00 0.00 3.18
2354 2432 0.249073 CCGGCCTCTACATCTGAACG 60.249 60.000 0.00 0.00 0.00 3.95
2355 2433 0.738975 CGGCCTCTACATCTGAACGA 59.261 55.000 0.00 0.00 0.00 3.85
2356 2434 1.338337 CGGCCTCTACATCTGAACGAT 59.662 52.381 0.00 0.00 0.00 3.73
2364 2442 2.384899 CATCTGAACGATGCATGCAG 57.615 50.000 26.69 15.79 42.75 4.41
2365 2443 0.661552 ATCTGAACGATGCATGCAGC 59.338 50.000 25.69 25.69 45.96 5.25
2366 2444 1.063649 CTGAACGATGCATGCAGCC 59.936 57.895 28.76 19.54 44.83 4.85
2367 2445 1.650314 CTGAACGATGCATGCAGCCA 61.650 55.000 28.76 19.68 44.83 4.75
2368 2446 1.033202 TGAACGATGCATGCAGCCAT 61.033 50.000 28.76 18.23 44.83 4.40
2369 2447 0.946528 GAACGATGCATGCAGCCATA 59.053 50.000 28.76 2.58 44.83 2.74
2370 2448 1.538512 GAACGATGCATGCAGCCATAT 59.461 47.619 28.76 13.14 44.83 1.78
2371 2449 1.612676 ACGATGCATGCAGCCATATT 58.387 45.000 28.76 9.02 44.83 1.28
2372 2450 2.781923 ACGATGCATGCAGCCATATTA 58.218 42.857 28.76 0.09 44.83 0.98
2373 2451 3.349927 ACGATGCATGCAGCCATATTAT 58.650 40.909 28.76 7.39 44.83 1.28
2374 2452 3.760151 ACGATGCATGCAGCCATATTATT 59.240 39.130 28.76 6.59 44.83 1.40
2375 2453 4.943093 ACGATGCATGCAGCCATATTATTA 59.057 37.500 28.76 0.00 44.83 0.98
2376 2454 5.415389 ACGATGCATGCAGCCATATTATTAA 59.585 36.000 28.76 0.00 44.83 1.40
2377 2455 6.072008 ACGATGCATGCAGCCATATTATTAAA 60.072 34.615 28.76 0.00 44.83 1.52
2378 2456 6.807720 CGATGCATGCAGCCATATTATTAAAA 59.192 34.615 28.76 0.00 44.83 1.52
2379 2457 7.328982 CGATGCATGCAGCCATATTATTAAAAA 59.671 33.333 28.76 0.00 44.83 1.94
2405 2483 9.793259 AAATCTTAAAGTATCACAAGGTCTTCA 57.207 29.630 0.00 0.00 0.00 3.02
2406 2484 9.793259 AATCTTAAAGTATCACAAGGTCTTCAA 57.207 29.630 0.00 0.00 0.00 2.69
2407 2485 9.793259 ATCTTAAAGTATCACAAGGTCTTCAAA 57.207 29.630 0.00 0.00 0.00 2.69
2408 2486 9.273016 TCTTAAAGTATCACAAGGTCTTCAAAG 57.727 33.333 0.00 0.00 0.00 2.77
2409 2487 8.974060 TTAAAGTATCACAAGGTCTTCAAAGT 57.026 30.769 0.00 0.00 0.00 2.66
2412 2490 9.574516 AAAGTATCACAAGGTCTTCAAAGTATT 57.425 29.630 0.00 0.00 0.00 1.89
2414 2492 9.654663 AGTATCACAAGGTCTTCAAAGTATTAC 57.345 33.333 0.00 0.00 0.00 1.89
2415 2493 9.654663 GTATCACAAGGTCTTCAAAGTATTACT 57.345 33.333 0.00 0.00 0.00 2.24
2416 2494 7.962964 TCACAAGGTCTTCAAAGTATTACTG 57.037 36.000 0.00 0.00 0.00 2.74
2417 2495 6.426937 TCACAAGGTCTTCAAAGTATTACTGC 59.573 38.462 0.00 0.00 0.00 4.40
2418 2496 6.428159 CACAAGGTCTTCAAAGTATTACTGCT 59.572 38.462 0.00 0.00 0.00 4.24
2419 2497 6.651225 ACAAGGTCTTCAAAGTATTACTGCTC 59.349 38.462 0.00 0.00 0.00 4.26
2420 2498 5.411781 AGGTCTTCAAAGTATTACTGCTCG 58.588 41.667 0.00 0.00 0.00 5.03
2421 2499 4.033014 GGTCTTCAAAGTATTACTGCTCGC 59.967 45.833 0.00 0.00 0.00 5.03
2422 2500 4.625742 GTCTTCAAAGTATTACTGCTCGCA 59.374 41.667 0.00 0.00 0.00 5.10
2423 2501 5.120208 GTCTTCAAAGTATTACTGCTCGCAA 59.880 40.000 0.00 0.00 0.00 4.85
2424 2502 5.699001 TCTTCAAAGTATTACTGCTCGCAAA 59.301 36.000 0.00 0.00 0.00 3.68
2425 2503 5.933187 TCAAAGTATTACTGCTCGCAAAA 57.067 34.783 0.00 0.00 0.00 2.44
2426 2504 5.927030 TCAAAGTATTACTGCTCGCAAAAG 58.073 37.500 0.00 0.00 0.00 2.27
2427 2505 4.946784 AAGTATTACTGCTCGCAAAAGG 57.053 40.909 0.00 0.00 0.00 3.11
2428 2506 4.202245 AGTATTACTGCTCGCAAAAGGA 57.798 40.909 0.00 0.00 0.00 3.36
2429 2507 4.184629 AGTATTACTGCTCGCAAAAGGAG 58.815 43.478 0.00 0.00 40.29 3.69
2437 2515 3.354089 CTCGCAAAAGGAGCAAAGAAA 57.646 42.857 0.00 0.00 0.00 2.52
2438 2516 3.705604 CTCGCAAAAGGAGCAAAGAAAA 58.294 40.909 0.00 0.00 0.00 2.29
2439 2517 4.111916 CTCGCAAAAGGAGCAAAGAAAAA 58.888 39.130 0.00 0.00 0.00 1.94
2440 2518 4.692228 TCGCAAAAGGAGCAAAGAAAAAT 58.308 34.783 0.00 0.00 0.00 1.82
2441 2519 5.837437 TCGCAAAAGGAGCAAAGAAAAATA 58.163 33.333 0.00 0.00 0.00 1.40
2442 2520 6.276847 TCGCAAAAGGAGCAAAGAAAAATAA 58.723 32.000 0.00 0.00 0.00 1.40
2443 2521 6.758886 TCGCAAAAGGAGCAAAGAAAAATAAA 59.241 30.769 0.00 0.00 0.00 1.40
2444 2522 7.278868 TCGCAAAAGGAGCAAAGAAAAATAAAA 59.721 29.630 0.00 0.00 0.00 1.52
2445 2523 7.907563 CGCAAAAGGAGCAAAGAAAAATAAAAA 59.092 29.630 0.00 0.00 0.00 1.94
2459 2537 2.419198 AAAAACCGCAATGCCGCA 59.581 50.000 0.00 0.00 0.00 5.69
2460 2538 1.227380 AAAAACCGCAATGCCGCAA 60.227 47.368 0.00 0.00 0.00 4.85
2461 2539 1.494766 AAAAACCGCAATGCCGCAAC 61.495 50.000 0.00 0.00 0.00 4.17
2462 2540 3.857109 AAACCGCAATGCCGCAACC 62.857 57.895 0.00 0.00 0.00 3.77
2477 2555 3.947626 CGCAACCGGTATGAATTAAAGG 58.052 45.455 8.00 0.00 0.00 3.11
2478 2556 3.623960 CGCAACCGGTATGAATTAAAGGA 59.376 43.478 8.00 0.00 0.00 3.36
2479 2557 4.495184 CGCAACCGGTATGAATTAAAGGAC 60.495 45.833 8.00 0.00 0.00 3.85
2480 2558 4.638865 GCAACCGGTATGAATTAAAGGACT 59.361 41.667 8.00 0.00 0.00 3.85
2481 2559 5.818857 GCAACCGGTATGAATTAAAGGACTA 59.181 40.000 8.00 0.00 0.00 2.59
2482 2560 6.018180 GCAACCGGTATGAATTAAAGGACTAG 60.018 42.308 8.00 0.00 0.00 2.57
2483 2561 6.170846 ACCGGTATGAATTAAAGGACTAGG 57.829 41.667 4.49 0.00 0.00 3.02
2484 2562 5.071384 ACCGGTATGAATTAAAGGACTAGGG 59.929 44.000 4.49 0.00 0.00 3.53
2485 2563 4.995487 CGGTATGAATTAAAGGACTAGGGC 59.005 45.833 0.00 0.00 0.00 5.19
2486 2564 5.314529 GGTATGAATTAAAGGACTAGGGCC 58.685 45.833 0.00 0.00 0.00 5.80
2487 2565 3.945640 TGAATTAAAGGACTAGGGCCC 57.054 47.619 16.46 16.46 0.00 5.80
2488 2566 3.470868 TGAATTAAAGGACTAGGGCCCT 58.529 45.455 31.35 31.35 0.00 5.19
2489 2567 4.637600 TGAATTAAAGGACTAGGGCCCTA 58.362 43.478 30.08 30.08 31.36 3.53
2498 2576 2.390225 CTAGGGCCCTAGACTCATGT 57.610 55.000 44.67 15.42 46.56 3.21
2499 2577 2.243810 CTAGGGCCCTAGACTCATGTC 58.756 57.143 44.67 5.79 46.56 3.06
2500 2578 0.399233 AGGGCCCTAGACTCATGTCC 60.399 60.000 27.42 0.00 43.91 4.02
2501 2579 0.399233 GGGCCCTAGACTCATGTCCT 60.399 60.000 17.04 0.00 43.91 3.85
2502 2580 0.755686 GGCCCTAGACTCATGTCCTG 59.244 60.000 0.00 0.00 43.91 3.86
2503 2581 1.490574 GCCCTAGACTCATGTCCTGT 58.509 55.000 0.00 0.00 43.91 4.00
2504 2582 1.834263 GCCCTAGACTCATGTCCTGTT 59.166 52.381 0.00 0.00 43.91 3.16
2505 2583 3.031736 GCCCTAGACTCATGTCCTGTTA 58.968 50.000 0.00 0.00 43.91 2.41
2506 2584 3.643792 GCCCTAGACTCATGTCCTGTTAT 59.356 47.826 0.00 0.00 43.91 1.89
2507 2585 4.502259 GCCCTAGACTCATGTCCTGTTATG 60.502 50.000 0.00 0.00 43.91 1.90
2508 2586 4.502259 CCCTAGACTCATGTCCTGTTATGC 60.502 50.000 0.00 0.00 43.91 3.14
2509 2587 3.170791 AGACTCATGTCCTGTTATGCG 57.829 47.619 0.00 0.00 43.91 4.73
2510 2588 2.760650 AGACTCATGTCCTGTTATGCGA 59.239 45.455 0.00 0.00 43.91 5.10
2511 2589 2.860735 GACTCATGTCCTGTTATGCGAC 59.139 50.000 0.00 0.00 37.24 5.19
2512 2590 2.205074 CTCATGTCCTGTTATGCGACC 58.795 52.381 0.00 0.00 0.00 4.79
2513 2591 0.930310 CATGTCCTGTTATGCGACCG 59.070 55.000 0.00 0.00 0.00 4.79
2514 2592 0.810031 ATGTCCTGTTATGCGACCGC 60.810 55.000 7.53 7.53 42.35 5.68
2515 2593 2.171725 GTCCTGTTATGCGACCGCC 61.172 63.158 12.08 0.00 41.09 6.13
2516 2594 2.125310 CCTGTTATGCGACCGCCA 60.125 61.111 12.08 1.69 41.09 5.69
2517 2595 1.523711 CCTGTTATGCGACCGCCAT 60.524 57.895 12.08 8.00 41.09 4.40
2518 2596 1.498865 CCTGTTATGCGACCGCCATC 61.499 60.000 12.08 1.22 41.09 3.51
2519 2597 1.498865 CTGTTATGCGACCGCCATCC 61.499 60.000 12.08 0.00 41.09 3.51
2520 2598 1.522806 GTTATGCGACCGCCATCCA 60.523 57.895 12.08 0.00 41.09 3.41
2521 2599 1.092921 GTTATGCGACCGCCATCCAA 61.093 55.000 12.08 0.00 41.09 3.53
2522 2600 0.393132 TTATGCGACCGCCATCCAAA 60.393 50.000 12.08 0.00 41.09 3.28
2523 2601 1.092921 TATGCGACCGCCATCCAAAC 61.093 55.000 12.08 0.00 41.09 2.93
2524 2602 3.810896 GCGACCGCCATCCAAACC 61.811 66.667 2.55 0.00 34.56 3.27
2525 2603 3.496131 CGACCGCCATCCAAACCG 61.496 66.667 0.00 0.00 0.00 4.44
2526 2604 3.131478 GACCGCCATCCAAACCGG 61.131 66.667 0.00 0.00 45.80 5.28
2528 2606 2.675075 CCGCCATCCAAACCGGTT 60.675 61.111 15.86 15.86 36.18 4.44
2529 2607 2.566010 CGCCATCCAAACCGGTTG 59.434 61.111 23.08 14.70 36.94 3.77
2530 2608 1.969064 CGCCATCCAAACCGGTTGA 60.969 57.895 23.08 15.50 39.87 3.18
2690 3384 2.122144 CCCCCGGATCCATGGGTA 60.122 66.667 27.02 0.00 44.44 3.69
2873 3582 2.833582 GGCTCGTCCCGGATCTGA 60.834 66.667 0.73 0.00 0.00 3.27
2878 3587 0.106669 TCGTCCCGGATCTGATGACT 60.107 55.000 0.73 0.00 0.00 3.41
2931 3640 4.241555 GGCCGGCGATCTGGACAT 62.242 66.667 22.54 0.00 46.64 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 120 7.962964 AGAAGTGAAGAAAACGATACATTCA 57.037 32.000 0.00 0.00 0.00 2.57
205 237 6.542005 ACACACAGATTCAGATAAACAACACA 59.458 34.615 0.00 0.00 0.00 3.72
255 287 8.811017 TCTATTATGATGATTTCCTCCTCAGAC 58.189 37.037 0.00 0.00 32.86 3.51
263 295 8.776119 CCCCTGTATCTATTATGATGATTTCCT 58.224 37.037 0.00 0.00 0.00 3.36
310 342 5.417580 AGCTAATTGATAAGTTTTGCGGGAA 59.582 36.000 0.00 0.00 0.00 3.97
340 372 7.951530 AAATTTAGGCAAGTGATGAACAAAG 57.048 32.000 0.00 0.00 0.00 2.77
365 397 9.443323 ACAACAGCATAGTACAAATGTAATGTA 57.557 29.630 3.95 0.00 30.89 2.29
372 404 4.727734 GCGGACAACAGCATAGTACAAATG 60.728 45.833 0.00 0.00 37.19 2.32
387 419 0.532196 GGTATGGGCTAGCGGACAAC 60.532 60.000 9.00 3.11 0.00 3.32
452 518 9.914834 TTTAGTACTTGCATTTTATCTGGGTAT 57.085 29.630 0.00 0.00 0.00 2.73
483 549 5.242393 CCTGGCATCATGTAAAATTCCCTAG 59.758 44.000 0.00 0.00 0.00 3.02
487 554 5.827797 TCTACCTGGCATCATGTAAAATTCC 59.172 40.000 0.00 0.00 0.00 3.01
528 595 6.223351 AGCTTGAAATACTACTGGTAGGTC 57.777 41.667 11.73 4.99 37.49 3.85
639 710 5.212194 CGGAAAGATATGGCGTAAAAATGG 58.788 41.667 0.00 0.00 0.00 3.16
664 735 2.525629 TCTTCAGGGTGCGTGGGA 60.526 61.111 0.00 0.00 0.00 4.37
708 779 1.983119 GACCCCGGATTGGATGCTGA 61.983 60.000 0.73 0.00 42.00 4.26
1512 1583 2.418609 CCTGTACATGCATGAGGTCGAA 60.419 50.000 32.75 9.69 0.00 3.71
1530 1601 5.431765 CCTGCAGTATATATTTAGGGCCTG 58.568 45.833 18.53 0.00 0.00 4.85
1534 1605 4.081087 ACGCCCTGCAGTATATATTTAGGG 60.081 45.833 13.81 15.21 44.89 3.53
1538 1609 4.021719 ACGTACGCCCTGCAGTATATATTT 60.022 41.667 16.72 0.00 0.00 1.40
1552 1623 1.878522 CAGATCAGCACGTACGCCC 60.879 63.158 16.72 6.40 0.00 6.13
1557 1628 0.456142 GTCGCACAGATCAGCACGTA 60.456 55.000 0.00 0.00 0.00 3.57
1562 1633 1.922903 CATCGTCGCACAGATCAGC 59.077 57.895 0.00 0.00 0.00 4.26
1574 1645 2.821366 CCACCTGCCAGCATCGTC 60.821 66.667 0.00 0.00 0.00 4.20
1878 1949 2.564721 GGTGGCCCAGTTGTTGAGC 61.565 63.158 0.00 0.00 0.00 4.26
1983 2054 0.729140 CGTTCGTCCATTTTGCAGCC 60.729 55.000 0.00 0.00 0.00 4.85
2028 2099 5.746721 CCATCACTCGTCATATACAAAACGA 59.253 40.000 0.00 0.00 41.40 3.85
2029 2100 5.746721 TCCATCACTCGTCATATACAAAACG 59.253 40.000 0.00 0.00 36.50 3.60
2030 2101 7.438160 TCATCCATCACTCGTCATATACAAAAC 59.562 37.037 0.00 0.00 0.00 2.43
2034 2105 6.003950 TCTCATCCATCACTCGTCATATACA 58.996 40.000 0.00 0.00 0.00 2.29
2035 2106 6.404184 CCTCTCATCCATCACTCGTCATATAC 60.404 46.154 0.00 0.00 0.00 1.47
2036 2107 5.649831 CCTCTCATCCATCACTCGTCATATA 59.350 44.000 0.00 0.00 0.00 0.86
2037 2108 4.462132 CCTCTCATCCATCACTCGTCATAT 59.538 45.833 0.00 0.00 0.00 1.78
2084 2155 4.993584 CCTATGTGATCAGACCTGCATTAC 59.006 45.833 0.00 0.00 0.00 1.89
2207 2278 4.982295 CGTGGATGCTATCTTTGTAATCGA 59.018 41.667 0.00 0.00 0.00 3.59
2312 2390 3.540617 GGCAAGCCTCCTTTTTCAAAAA 58.459 40.909 3.29 0.00 0.00 1.94
2313 2391 2.158827 GGGCAAGCCTCCTTTTTCAAAA 60.159 45.455 11.40 0.00 36.10 2.44
2314 2392 1.416030 GGGCAAGCCTCCTTTTTCAAA 59.584 47.619 11.40 0.00 36.10 2.69
2315 2393 1.047801 GGGCAAGCCTCCTTTTTCAA 58.952 50.000 11.40 0.00 36.10 2.69
2316 2394 0.831711 GGGGCAAGCCTCCTTTTTCA 60.832 55.000 11.40 0.00 36.10 2.69
2317 2395 1.975327 GGGGCAAGCCTCCTTTTTC 59.025 57.895 11.40 0.00 36.10 2.29
2318 2396 4.215370 GGGGCAAGCCTCCTTTTT 57.785 55.556 11.40 0.00 36.10 1.94
2332 2410 2.122813 AGATGTAGAGGCCGGGGG 60.123 66.667 2.18 0.00 0.00 5.40
2333 2411 1.048724 TTCAGATGTAGAGGCCGGGG 61.049 60.000 2.18 0.00 0.00 5.73
2334 2412 0.105039 GTTCAGATGTAGAGGCCGGG 59.895 60.000 2.18 0.00 0.00 5.73
2335 2413 0.249073 CGTTCAGATGTAGAGGCCGG 60.249 60.000 0.00 0.00 0.00 6.13
2336 2414 0.738975 TCGTTCAGATGTAGAGGCCG 59.261 55.000 0.00 0.00 0.00 6.13
2346 2424 0.661552 GCTGCATGCATCGTTCAGAT 59.338 50.000 22.97 0.00 42.31 2.90
2347 2425 1.371337 GGCTGCATGCATCGTTCAGA 61.371 55.000 22.97 0.00 45.15 3.27
2348 2426 1.063649 GGCTGCATGCATCGTTCAG 59.936 57.895 22.97 8.76 45.15 3.02
2349 2427 1.033202 ATGGCTGCATGCATCGTTCA 61.033 50.000 22.97 14.74 45.15 3.18
2350 2428 0.946528 TATGGCTGCATGCATCGTTC 59.053 50.000 22.97 9.58 45.15 3.95
2351 2429 1.612676 ATATGGCTGCATGCATCGTT 58.387 45.000 22.97 10.26 45.15 3.85
2352 2430 1.612676 AATATGGCTGCATGCATCGT 58.387 45.000 22.97 19.00 45.15 3.73
2353 2431 4.365899 AATAATATGGCTGCATGCATCG 57.634 40.909 22.97 12.00 45.15 3.84
2354 2432 8.537049 TTTTTAATAATATGGCTGCATGCATC 57.463 30.769 22.97 17.75 45.15 3.91
2379 2457 9.793259 TGAAGACCTTGTGATACTTTAAGATTT 57.207 29.630 0.00 0.00 0.00 2.17
2380 2458 9.793259 TTGAAGACCTTGTGATACTTTAAGATT 57.207 29.630 0.00 0.00 0.00 2.40
2381 2459 9.793259 TTTGAAGACCTTGTGATACTTTAAGAT 57.207 29.630 0.00 0.00 0.00 2.40
2382 2460 9.273016 CTTTGAAGACCTTGTGATACTTTAAGA 57.727 33.333 0.00 0.00 0.00 2.10
2383 2461 9.057089 ACTTTGAAGACCTTGTGATACTTTAAG 57.943 33.333 0.00 0.00 0.00 1.85
2384 2462 8.974060 ACTTTGAAGACCTTGTGATACTTTAA 57.026 30.769 0.00 0.00 0.00 1.52
2386 2464 9.574516 AATACTTTGAAGACCTTGTGATACTTT 57.425 29.630 0.00 0.00 0.00 2.66
2388 2466 9.654663 GTAATACTTTGAAGACCTTGTGATACT 57.345 33.333 0.00 0.00 0.00 2.12
2389 2467 9.654663 AGTAATACTTTGAAGACCTTGTGATAC 57.345 33.333 0.00 0.00 0.00 2.24
2390 2468 9.653287 CAGTAATACTTTGAAGACCTTGTGATA 57.347 33.333 0.00 0.00 0.00 2.15
2391 2469 7.119846 GCAGTAATACTTTGAAGACCTTGTGAT 59.880 37.037 0.00 0.00 0.00 3.06
2392 2470 6.426937 GCAGTAATACTTTGAAGACCTTGTGA 59.573 38.462 0.00 0.00 0.00 3.58
2393 2471 6.428159 AGCAGTAATACTTTGAAGACCTTGTG 59.572 38.462 0.00 0.00 0.00 3.33
2394 2472 6.534634 AGCAGTAATACTTTGAAGACCTTGT 58.465 36.000 0.00 0.00 0.00 3.16
2395 2473 6.183360 CGAGCAGTAATACTTTGAAGACCTTG 60.183 42.308 0.00 0.00 0.00 3.61
2396 2474 5.869888 CGAGCAGTAATACTTTGAAGACCTT 59.130 40.000 0.00 0.00 0.00 3.50
2397 2475 5.411781 CGAGCAGTAATACTTTGAAGACCT 58.588 41.667 0.00 0.00 0.00 3.85
2398 2476 4.033014 GCGAGCAGTAATACTTTGAAGACC 59.967 45.833 0.00 0.00 0.00 3.85
2399 2477 4.625742 TGCGAGCAGTAATACTTTGAAGAC 59.374 41.667 0.00 0.00 0.00 3.01
2400 2478 4.816392 TGCGAGCAGTAATACTTTGAAGA 58.184 39.130 0.00 0.00 0.00 2.87
2401 2479 5.530519 TTGCGAGCAGTAATACTTTGAAG 57.469 39.130 0.00 0.00 0.00 3.02
2402 2480 5.933187 TTTGCGAGCAGTAATACTTTGAA 57.067 34.783 0.00 0.00 0.00 2.69
2403 2481 5.106712 CCTTTTGCGAGCAGTAATACTTTGA 60.107 40.000 0.00 0.00 0.00 2.69
2404 2482 5.088739 CCTTTTGCGAGCAGTAATACTTTG 58.911 41.667 0.00 0.00 0.00 2.77
2405 2483 5.001232 TCCTTTTGCGAGCAGTAATACTTT 58.999 37.500 0.00 0.00 0.00 2.66
2406 2484 4.575885 TCCTTTTGCGAGCAGTAATACTT 58.424 39.130 0.00 0.00 0.00 2.24
2407 2485 4.184629 CTCCTTTTGCGAGCAGTAATACT 58.815 43.478 0.00 0.00 0.00 2.12
2408 2486 4.522297 CTCCTTTTGCGAGCAGTAATAC 57.478 45.455 0.00 0.00 0.00 1.89
2417 2495 3.354089 TTTCTTTGCTCCTTTTGCGAG 57.646 42.857 0.00 0.00 0.00 5.03
2418 2496 3.791973 TTTTCTTTGCTCCTTTTGCGA 57.208 38.095 0.00 0.00 0.00 5.10
2419 2497 6.523676 TTATTTTTCTTTGCTCCTTTTGCG 57.476 33.333 0.00 0.00 0.00 4.85
2442 2520 1.227380 TTGCGGCATTGCGGTTTTT 60.227 47.368 16.35 0.00 37.81 1.94
2443 2521 1.953642 GTTGCGGCATTGCGGTTTT 60.954 52.632 16.35 0.00 37.81 2.43
2444 2522 2.355718 GTTGCGGCATTGCGGTTT 60.356 55.556 16.35 0.00 37.81 3.27
2445 2523 4.356442 GGTTGCGGCATTGCGGTT 62.356 61.111 16.35 0.00 37.81 4.44
2449 2527 2.770589 ATACCGGTTGCGGCATTGC 61.771 57.895 15.04 0.00 0.00 3.56
2450 2528 1.063972 CATACCGGTTGCGGCATTG 59.936 57.895 15.04 0.00 0.00 2.82
2451 2529 0.678366 TTCATACCGGTTGCGGCATT 60.678 50.000 15.04 0.00 0.00 3.56
2452 2530 0.465460 ATTCATACCGGTTGCGGCAT 60.465 50.000 15.04 0.00 0.00 4.40
2453 2531 0.678366 AATTCATACCGGTTGCGGCA 60.678 50.000 15.04 0.00 0.00 5.69
2454 2532 1.301423 TAATTCATACCGGTTGCGGC 58.699 50.000 15.04 0.00 0.00 6.53
2455 2533 3.242936 CCTTTAATTCATACCGGTTGCGG 60.243 47.826 15.04 0.00 0.00 5.69
2456 2534 3.623960 TCCTTTAATTCATACCGGTTGCG 59.376 43.478 15.04 0.97 0.00 4.85
2457 2535 4.638865 AGTCCTTTAATTCATACCGGTTGC 59.361 41.667 15.04 0.00 0.00 4.17
2458 2536 6.482308 CCTAGTCCTTTAATTCATACCGGTTG 59.518 42.308 15.04 11.55 0.00 3.77
2459 2537 6.408891 CCCTAGTCCTTTAATTCATACCGGTT 60.409 42.308 15.04 0.00 0.00 4.44
2460 2538 5.071384 CCCTAGTCCTTTAATTCATACCGGT 59.929 44.000 13.98 13.98 0.00 5.28
2461 2539 5.548406 CCCTAGTCCTTTAATTCATACCGG 58.452 45.833 0.00 0.00 0.00 5.28
2462 2540 4.995487 GCCCTAGTCCTTTAATTCATACCG 59.005 45.833 0.00 0.00 0.00 4.02
2463 2541 5.314529 GGCCCTAGTCCTTTAATTCATACC 58.685 45.833 0.00 0.00 0.00 2.73
2464 2542 5.314529 GGGCCCTAGTCCTTTAATTCATAC 58.685 45.833 17.04 0.00 33.65 2.39
2465 2543 5.578157 GGGCCCTAGTCCTTTAATTCATA 57.422 43.478 17.04 0.00 33.65 2.15
2466 2544 4.455070 GGGCCCTAGTCCTTTAATTCAT 57.545 45.455 17.04 0.00 33.65 2.57
2467 2545 3.945640 GGGCCCTAGTCCTTTAATTCA 57.054 47.619 17.04 0.00 33.65 2.57
2476 2554 0.556747 TGAGTCTAGGGCCCTAGTCC 59.443 60.000 44.13 36.10 44.59 3.85
2477 2555 2.243810 CATGAGTCTAGGGCCCTAGTC 58.756 57.143 44.13 39.91 44.59 2.59
2478 2556 1.576272 ACATGAGTCTAGGGCCCTAGT 59.424 52.381 44.13 32.88 44.59 2.57
2479 2557 2.243810 GACATGAGTCTAGGGCCCTAG 58.756 57.143 42.52 42.52 45.38 3.02
2480 2558 1.133136 GGACATGAGTCTAGGGCCCTA 60.133 57.143 30.08 30.08 44.36 3.53
2481 2559 0.399233 GGACATGAGTCTAGGGCCCT 60.399 60.000 31.35 31.35 44.36 5.19
2482 2560 0.399233 AGGACATGAGTCTAGGGCCC 60.399 60.000 16.46 16.46 44.36 5.80
2483 2561 0.755686 CAGGACATGAGTCTAGGGCC 59.244 60.000 0.00 0.00 44.36 5.80
2484 2562 1.490574 ACAGGACATGAGTCTAGGGC 58.509 55.000 0.00 0.00 44.36 5.19
2485 2563 4.502259 GCATAACAGGACATGAGTCTAGGG 60.502 50.000 0.00 0.00 44.36 3.53
2486 2564 4.626042 GCATAACAGGACATGAGTCTAGG 58.374 47.826 0.00 0.00 44.36 3.02
2487 2565 4.036852 TCGCATAACAGGACATGAGTCTAG 59.963 45.833 0.00 0.00 44.36 2.43
2488 2566 3.951680 TCGCATAACAGGACATGAGTCTA 59.048 43.478 0.00 0.00 44.36 2.59
2489 2567 2.760650 TCGCATAACAGGACATGAGTCT 59.239 45.455 0.00 0.00 44.36 3.24
2490 2568 2.860735 GTCGCATAACAGGACATGAGTC 59.139 50.000 0.00 0.00 44.21 3.36
2491 2569 2.418746 GGTCGCATAACAGGACATGAGT 60.419 50.000 0.00 0.00 32.39 3.41
2492 2570 2.205074 GGTCGCATAACAGGACATGAG 58.795 52.381 0.00 0.00 32.39 2.90
2493 2571 1.470805 CGGTCGCATAACAGGACATGA 60.471 52.381 0.00 0.00 32.39 3.07
2494 2572 0.930310 CGGTCGCATAACAGGACATG 59.070 55.000 0.00 0.00 32.39 3.21
2495 2573 0.810031 GCGGTCGCATAACAGGACAT 60.810 55.000 10.67 0.00 41.49 3.06
2496 2574 1.447140 GCGGTCGCATAACAGGACA 60.447 57.895 10.67 0.00 41.49 4.02
2497 2575 2.171725 GGCGGTCGCATAACAGGAC 61.172 63.158 17.21 0.00 44.11 3.85
2498 2576 1.966901 ATGGCGGTCGCATAACAGGA 61.967 55.000 17.21 0.00 44.11 3.86
2499 2577 1.498865 GATGGCGGTCGCATAACAGG 61.499 60.000 17.21 0.00 44.11 4.00
2500 2578 1.498865 GGATGGCGGTCGCATAACAG 61.499 60.000 17.21 0.00 44.11 3.16
2501 2579 1.522806 GGATGGCGGTCGCATAACA 60.523 57.895 17.21 6.12 44.11 2.41
2502 2580 1.092921 TTGGATGGCGGTCGCATAAC 61.093 55.000 17.21 5.24 44.11 1.89
2503 2581 0.393132 TTTGGATGGCGGTCGCATAA 60.393 50.000 17.21 2.61 44.11 1.90
2504 2582 1.092921 GTTTGGATGGCGGTCGCATA 61.093 55.000 17.21 5.89 44.11 3.14
2505 2583 2.045438 TTTGGATGGCGGTCGCAT 60.045 55.556 17.21 8.55 44.11 4.73
2506 2584 3.053291 GTTTGGATGGCGGTCGCA 61.053 61.111 17.21 4.04 44.11 5.10
2507 2585 3.810896 GGTTTGGATGGCGGTCGC 61.811 66.667 6.83 6.83 41.06 5.19
2508 2586 3.496131 CGGTTTGGATGGCGGTCG 61.496 66.667 0.00 0.00 0.00 4.79
2509 2587 3.131478 CCGGTTTGGATGGCGGTC 61.131 66.667 0.00 0.00 42.00 4.79
2510 2588 3.501040 AACCGGTTTGGATGGCGGT 62.501 57.895 15.86 0.00 42.00 5.68
2511 2589 2.675075 AACCGGTTTGGATGGCGG 60.675 61.111 15.86 0.00 42.00 6.13
2512 2590 1.969064 TCAACCGGTTTGGATGGCG 60.969 57.895 19.55 3.62 40.78 5.69
2513 2591 1.584495 GTCAACCGGTTTGGATGGC 59.416 57.895 19.55 4.19 40.78 4.40
2514 2592 1.873165 CGTCAACCGGTTTGGATGG 59.127 57.895 19.55 5.30 40.78 3.51
2515 2593 1.209127 GCGTCAACCGGTTTGGATG 59.791 57.895 19.55 18.70 41.73 3.51
2516 2594 1.969589 GGCGTCAACCGGTTTGGAT 60.970 57.895 19.55 0.00 42.00 3.41
2517 2595 2.592287 GGCGTCAACCGGTTTGGA 60.592 61.111 19.55 10.51 42.00 3.53
2518 2596 3.666253 GGGCGTCAACCGGTTTGG 61.666 66.667 19.55 7.84 46.41 3.28
2519 2597 3.666253 GGGGCGTCAACCGGTTTG 61.666 66.667 19.55 13.53 36.94 2.93
2520 2598 4.960866 GGGGGCGTCAACCGGTTT 62.961 66.667 19.55 0.00 36.94 3.27
2873 3582 4.203076 GCGCCGTCCGGTAGTCAT 62.203 66.667 7.66 0.00 37.65 3.06


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

AutoCloner maintained by Alex Coulton.