Multiple sequence alignment - TraesCS5D01G224500

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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 TraesCS5D01G224500 chr5D 100.000 2663 0 0 1 2663 332430073 332427411 0.000000e+00 4918
1 TraesCS5D01G224500 chr5D 92.451 861 53 6 1 854 276712764 276713619 0.000000e+00 1219
2 TraesCS5D01G224500 chr5D 91.763 862 62 7 1 857 327217225 327216368 0.000000e+00 1190
3 TraesCS5D01G224500 chr5A 92.593 1485 68 22 853 2324 433234336 433232881 0.000000e+00 2095
4 TraesCS5D01G224500 chr5A 89.809 314 22 3 2350 2663 451267311 451267614 6.910000e-106 394
5 TraesCS5D01G224500 chr5B 92.081 1490 71 20 862 2323 388312473 388311003 0.000000e+00 2054
6 TraesCS5D01G224500 chr4D 93.481 859 50 3 1 854 16452116 16451259 0.000000e+00 1271
7 TraesCS5D01G224500 chr4D 92.899 859 49 9 1 852 212097797 212096944 0.000000e+00 1238
8 TraesCS5D01G224500 chr4D 92.218 861 61 4 1 857 37523296 37522438 0.000000e+00 1214
9 TraesCS5D01G224500 chr1D 92.700 863 57 5 1 859 23376144 23375284 0.000000e+00 1240
10 TraesCS5D01G224500 chr1D 90.159 315 19 4 2350 2663 322065093 322064790 1.490000e-107 399
11 TraesCS5D01G224500 chr1D 87.500 312 24 4 2350 2660 250150929 250151226 1.960000e-91 346
12 TraesCS5D01G224500 chr3D 92.111 862 58 7 1 856 176529895 176529038 0.000000e+00 1206
13 TraesCS5D01G224500 chr3D 91.628 860 63 7 1 854 362065867 362065011 0.000000e+00 1181
14 TraesCS5D01G224500 chr6D 92.047 855 63 2 4 854 392268855 392268002 0.000000e+00 1197
15 TraesCS5D01G224500 chr7D 92.675 314 23 0 2350 2663 603268785 603268472 1.120000e-123 453
16 TraesCS5D01G224500 chr7D 87.025 316 27 7 2350 2663 239661424 239661727 7.060000e-91 344
17 TraesCS5D01G224500 chr2D 91.720 314 23 2 2350 2663 40853567 40853877 1.460000e-117 433
18 TraesCS5D01G224500 chr2D 92.500 240 17 1 2423 2661 435265348 435265109 2.540000e-90 342
19 TraesCS5D01G224500 chr4A 88.217 314 29 4 2350 2663 677484185 677483880 4.190000e-98 368
20 TraesCS5D01G224500 chr7B 87.500 264 32 1 2350 2613 528015670 528015408 1.200000e-78 303


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 TraesCS5D01G224500 chr5D 332427411 332430073 2662 True 4918 4918 100.000 1 2663 1 chr5D.!!$R2 2662
1 TraesCS5D01G224500 chr5D 276712764 276713619 855 False 1219 1219 92.451 1 854 1 chr5D.!!$F1 853
2 TraesCS5D01G224500 chr5D 327216368 327217225 857 True 1190 1190 91.763 1 857 1 chr5D.!!$R1 856
3 TraesCS5D01G224500 chr5A 433232881 433234336 1455 True 2095 2095 92.593 853 2324 1 chr5A.!!$R1 1471
4 TraesCS5D01G224500 chr5B 388311003 388312473 1470 True 2054 2054 92.081 862 2323 1 chr5B.!!$R1 1461
5 TraesCS5D01G224500 chr4D 16451259 16452116 857 True 1271 1271 93.481 1 854 1 chr4D.!!$R1 853
6 TraesCS5D01G224500 chr4D 212096944 212097797 853 True 1238 1238 92.899 1 852 1 chr4D.!!$R3 851
7 TraesCS5D01G224500 chr4D 37522438 37523296 858 True 1214 1214 92.218 1 857 1 chr4D.!!$R2 856
8 TraesCS5D01G224500 chr1D 23375284 23376144 860 True 1240 1240 92.700 1 859 1 chr1D.!!$R1 858
9 TraesCS5D01G224500 chr3D 176529038 176529895 857 True 1206 1206 92.111 1 856 1 chr3D.!!$R1 855
10 TraesCS5D01G224500 chr3D 362065011 362065867 856 True 1181 1181 91.628 1 854 1 chr3D.!!$R2 853
11 TraesCS5D01G224500 chr6D 392268002 392268855 853 True 1197 1197 92.047 4 854 1 chr6D.!!$R1 850

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
601 605 0.54412 GAGGGTTTGGGGAAATGGCA 60.544 55.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2547 2597 0.1023 GTAAATGGCCACCGCAATCC 59.898 55.0 8.16 0.0 36.38 3.01 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
448 451 4.379243 CTCCTCCGGCGTGCACTT 62.379 66.667 16.19 0.00 0.00 3.16
601 605 0.544120 GAGGGTTTGGGGAAATGGCA 60.544 55.000 0.00 0.00 0.00 4.92
642 653 0.547075 TTGGTTTCTCCCACCGACAA 59.453 50.000 0.00 0.00 37.07 3.18
643 654 0.547075 TGGTTTCTCCCACCGACAAA 59.453 50.000 0.00 0.00 37.07 2.83
665 676 3.322466 CCAGGGGAGGACAAGCGT 61.322 66.667 0.00 0.00 0.00 5.07
704 715 1.168714 GTGCTGTCTGTTTCATCCCC 58.831 55.000 0.00 0.00 0.00 4.81
718 729 3.690280 CCCCAAACCGGCGCAAAT 61.690 61.111 10.83 0.00 0.00 2.32
878 894 3.323979 GGGGCGATCTTCCAATTCTACTA 59.676 47.826 0.00 0.00 0.00 1.82
948 964 0.784495 ACCCTCACCTCTCACCACTA 59.216 55.000 0.00 0.00 0.00 2.74
953 969 2.230025 CTCACCTCTCACCACTACACAG 59.770 54.545 0.00 0.00 0.00 3.66
967 985 1.051812 ACACAGGTCCTTGGACTGAG 58.948 55.000 17.99 14.21 36.17 3.35
993 1011 3.522731 CTCCTCCTCGGCTCCACG 61.523 72.222 0.00 0.00 0.00 4.94
994 1012 3.997400 CTCCTCCTCGGCTCCACGA 62.997 68.421 0.00 0.00 41.13 4.35
995 1013 3.827898 CCTCCTCGGCTCCACGAC 61.828 72.222 0.00 0.00 38.06 4.34
996 1014 3.827898 CTCCTCGGCTCCACGACC 61.828 72.222 0.00 0.00 38.06 4.79
997 1015 4.671590 TCCTCGGCTCCACGACCA 62.672 66.667 0.00 0.00 38.06 4.02
998 1016 4.436998 CCTCGGCTCCACGACCAC 62.437 72.222 0.00 0.00 38.06 4.16
1032 1050 3.379688 GGATCCAGAAAAGCATCTTCCAC 59.620 47.826 6.95 0.00 0.00 4.02
1077 1095 2.595878 CCGCAGCGCTGATGATCAG 61.596 63.158 40.21 17.83 46.90 2.90
1159 1177 3.217743 GGCGAGTAGGGGGAGACG 61.218 72.222 0.00 0.00 0.00 4.18
1341 1359 4.171005 CCGACAAAGACGTGTACATGTAT 58.829 43.478 20.49 15.07 0.00 2.29
1349 1367 6.615264 AGACGTGTACATGTATAGGTACTG 57.385 41.667 22.66 9.78 42.80 2.74
1382 1400 2.224079 GTGCAAAGCTCGTGATCTGAAA 59.776 45.455 1.62 0.00 0.00 2.69
1672 1690 2.028020 GCGGTAGCCTAGCCTGATTATT 60.028 50.000 0.00 0.00 37.42 1.40
1682 1700 7.890127 AGCCTAGCCTGATTATTGCATAATAAA 59.110 33.333 0.00 0.00 40.91 1.40
1772 1791 2.806945 AATCGAGGGGCAAATCAAGA 57.193 45.000 0.00 0.00 0.00 3.02
1844 1888 1.004440 AGAGACGTTGAAGCAGGGC 60.004 57.895 0.00 0.00 0.00 5.19
1946 1991 4.893424 AATATGTGCACATCCGGTTAAC 57.107 40.909 34.54 0.00 37.76 2.01
2002 2048 0.858583 GCACACGAAAATTTGGTGGC 59.141 50.000 21.48 17.59 42.74 5.01
2006 2052 2.363680 ACACGAAAATTTGGTGGCATGA 59.636 40.909 21.48 0.00 42.74 3.07
2126 2173 2.747799 GCCAAGAGGAAGCAAGGGATAG 60.748 54.545 0.00 0.00 36.89 2.08
2161 2211 1.583556 TCTAGCAGCTTGATGGGGAA 58.416 50.000 0.00 0.00 0.00 3.97
2175 2225 1.288752 GGGAACACAAATGGCACCG 59.711 57.895 0.00 0.00 0.00 4.94
2312 2362 0.251608 ATTTCTTTGGTGGGGGTCGG 60.252 55.000 0.00 0.00 0.00 4.79
2324 2374 1.270893 GGGGGTCGGCAGAGATTTATC 60.271 57.143 0.00 0.00 0.00 1.75
2325 2375 1.416401 GGGGTCGGCAGAGATTTATCA 59.584 52.381 0.00 0.00 0.00 2.15
2326 2376 2.484889 GGGTCGGCAGAGATTTATCAC 58.515 52.381 0.00 0.00 0.00 3.06
2327 2377 2.103263 GGGTCGGCAGAGATTTATCACT 59.897 50.000 0.00 0.00 0.00 3.41
2328 2378 3.432326 GGGTCGGCAGAGATTTATCACTT 60.432 47.826 0.00 0.00 0.00 3.16
2329 2379 3.804873 GGTCGGCAGAGATTTATCACTTC 59.195 47.826 0.00 0.00 0.00 3.01
2330 2380 4.442192 GGTCGGCAGAGATTTATCACTTCT 60.442 45.833 0.00 0.00 0.00 2.85
2331 2381 5.112686 GTCGGCAGAGATTTATCACTTCTT 58.887 41.667 0.00 0.00 0.00 2.52
2332 2382 5.233263 GTCGGCAGAGATTTATCACTTCTTC 59.767 44.000 0.00 0.00 0.00 2.87
2333 2383 4.208047 CGGCAGAGATTTATCACTTCTTCG 59.792 45.833 0.00 0.00 0.00 3.79
2334 2384 4.509600 GGCAGAGATTTATCACTTCTTCGG 59.490 45.833 0.00 0.00 0.00 4.30
2335 2385 5.112686 GCAGAGATTTATCACTTCTTCGGT 58.887 41.667 0.00 0.00 0.00 4.69
2336 2386 6.273825 GCAGAGATTTATCACTTCTTCGGTA 58.726 40.000 0.00 0.00 0.00 4.02
2337 2387 6.199342 GCAGAGATTTATCACTTCTTCGGTAC 59.801 42.308 0.00 0.00 0.00 3.34
2338 2388 7.258441 CAGAGATTTATCACTTCTTCGGTACA 58.742 38.462 0.00 0.00 0.00 2.90
2339 2389 7.759886 CAGAGATTTATCACTTCTTCGGTACAA 59.240 37.037 0.00 0.00 0.00 2.41
2340 2390 7.760340 AGAGATTTATCACTTCTTCGGTACAAC 59.240 37.037 0.00 0.00 0.00 3.32
2341 2391 6.817140 AGATTTATCACTTCTTCGGTACAACC 59.183 38.462 0.00 0.00 34.05 3.77
2342 2392 2.825861 TCACTTCTTCGGTACAACCC 57.174 50.000 0.00 0.00 33.75 4.11
2343 2393 1.345415 TCACTTCTTCGGTACAACCCC 59.655 52.381 0.00 0.00 33.75 4.95
2344 2394 1.346722 CACTTCTTCGGTACAACCCCT 59.653 52.381 0.00 0.00 33.75 4.79
2345 2395 1.346722 ACTTCTTCGGTACAACCCCTG 59.653 52.381 0.00 0.00 33.75 4.45
2346 2396 0.688487 TTCTTCGGTACAACCCCTGG 59.312 55.000 0.00 0.00 33.75 4.45
2347 2397 0.178926 TCTTCGGTACAACCCCTGGA 60.179 55.000 0.00 0.00 33.75 3.86
2348 2398 0.909623 CTTCGGTACAACCCCTGGAT 59.090 55.000 0.00 0.00 33.75 3.41
2349 2399 0.616371 TTCGGTACAACCCCTGGATG 59.384 55.000 0.00 0.00 33.75 3.51
2350 2400 0.252330 TCGGTACAACCCCTGGATGA 60.252 55.000 0.00 0.00 33.75 2.92
2351 2401 0.837272 CGGTACAACCCCTGGATGAT 59.163 55.000 0.00 0.00 33.75 2.45
2352 2402 1.211949 CGGTACAACCCCTGGATGATT 59.788 52.381 0.00 0.00 33.75 2.57
2353 2403 2.436542 CGGTACAACCCCTGGATGATTA 59.563 50.000 0.00 0.00 33.75 1.75
2354 2404 3.494398 CGGTACAACCCCTGGATGATTAG 60.494 52.174 0.00 0.00 33.75 1.73
2355 2405 3.714798 GGTACAACCCCTGGATGATTAGA 59.285 47.826 0.00 0.00 30.04 2.10
2356 2406 4.165372 GGTACAACCCCTGGATGATTAGAA 59.835 45.833 0.00 0.00 30.04 2.10
2357 2407 4.510167 ACAACCCCTGGATGATTAGAAG 57.490 45.455 0.00 0.00 0.00 2.85
2358 2408 4.111577 ACAACCCCTGGATGATTAGAAGA 58.888 43.478 0.00 0.00 0.00 2.87
2359 2409 4.728860 ACAACCCCTGGATGATTAGAAGAT 59.271 41.667 0.00 0.00 0.00 2.40
2360 2410 5.911178 ACAACCCCTGGATGATTAGAAGATA 59.089 40.000 0.00 0.00 0.00 1.98
2361 2411 6.183361 ACAACCCCTGGATGATTAGAAGATAC 60.183 42.308 0.00 0.00 0.00 2.24
2362 2412 4.846940 ACCCCTGGATGATTAGAAGATACC 59.153 45.833 0.00 0.00 0.00 2.73
2363 2413 5.097234 CCCCTGGATGATTAGAAGATACCT 58.903 45.833 0.00 0.00 0.00 3.08
2364 2414 5.188751 CCCCTGGATGATTAGAAGATACCTC 59.811 48.000 0.00 0.00 0.00 3.85
2365 2415 6.022315 CCCTGGATGATTAGAAGATACCTCT 58.978 44.000 0.00 0.00 0.00 3.69
2366 2416 6.500049 CCCTGGATGATTAGAAGATACCTCTT 59.500 42.308 0.00 0.00 44.53 2.85
2367 2417 7.017056 CCCTGGATGATTAGAAGATACCTCTTT 59.983 40.741 0.00 0.00 41.87 2.52
2368 2418 7.877097 CCTGGATGATTAGAAGATACCTCTTTG 59.123 40.741 0.00 0.00 41.87 2.77
2369 2419 7.739825 TGGATGATTAGAAGATACCTCTTTGG 58.260 38.462 0.00 0.00 41.87 3.28
2384 2434 6.485830 CCTCTTTGGTATGATAAGTGAGGA 57.514 41.667 0.00 0.00 40.49 3.71
2385 2435 6.520272 CCTCTTTGGTATGATAAGTGAGGAG 58.480 44.000 0.00 0.00 40.49 3.69
2386 2436 6.463614 CCTCTTTGGTATGATAAGTGAGGAGG 60.464 46.154 0.00 0.00 40.49 4.30
2387 2437 5.366768 TCTTTGGTATGATAAGTGAGGAGGG 59.633 44.000 0.00 0.00 0.00 4.30
2388 2438 3.587498 TGGTATGATAAGTGAGGAGGGG 58.413 50.000 0.00 0.00 0.00 4.79
2389 2439 3.051341 TGGTATGATAAGTGAGGAGGGGT 60.051 47.826 0.00 0.00 0.00 4.95
2390 2440 4.171243 TGGTATGATAAGTGAGGAGGGGTA 59.829 45.833 0.00 0.00 0.00 3.69
2391 2441 4.773149 GGTATGATAAGTGAGGAGGGGTAG 59.227 50.000 0.00 0.00 0.00 3.18
2392 2442 4.834406 ATGATAAGTGAGGAGGGGTAGA 57.166 45.455 0.00 0.00 0.00 2.59
2393 2443 4.620086 TGATAAGTGAGGAGGGGTAGAA 57.380 45.455 0.00 0.00 0.00 2.10
2394 2444 5.157770 TGATAAGTGAGGAGGGGTAGAAT 57.842 43.478 0.00 0.00 0.00 2.40
2395 2445 4.901849 TGATAAGTGAGGAGGGGTAGAATG 59.098 45.833 0.00 0.00 0.00 2.67
2396 2446 2.182516 AGTGAGGAGGGGTAGAATGG 57.817 55.000 0.00 0.00 0.00 3.16
2397 2447 1.651770 AGTGAGGAGGGGTAGAATGGA 59.348 52.381 0.00 0.00 0.00 3.41
2398 2448 2.045885 AGTGAGGAGGGGTAGAATGGAA 59.954 50.000 0.00 0.00 0.00 3.53
2399 2449 2.844348 GTGAGGAGGGGTAGAATGGAAA 59.156 50.000 0.00 0.00 0.00 3.13
2400 2450 3.459969 GTGAGGAGGGGTAGAATGGAAAT 59.540 47.826 0.00 0.00 0.00 2.17
2401 2451 4.079730 GTGAGGAGGGGTAGAATGGAAATT 60.080 45.833 0.00 0.00 0.00 1.82
2402 2452 4.544152 TGAGGAGGGGTAGAATGGAAATTT 59.456 41.667 0.00 0.00 0.00 1.82
2403 2453 5.130705 AGGAGGGGTAGAATGGAAATTTC 57.869 43.478 9.83 9.83 0.00 2.17
2404 2454 4.544152 AGGAGGGGTAGAATGGAAATTTCA 59.456 41.667 19.49 6.65 0.00 2.69
2405 2455 4.889995 GGAGGGGTAGAATGGAAATTTCAG 59.110 45.833 19.49 0.00 0.00 3.02
2406 2456 4.871822 AGGGGTAGAATGGAAATTTCAGG 58.128 43.478 19.49 0.00 0.00 3.86
2407 2457 3.960755 GGGGTAGAATGGAAATTTCAGGG 59.039 47.826 19.49 0.00 0.00 4.45
2408 2458 3.960755 GGGTAGAATGGAAATTTCAGGGG 59.039 47.826 19.49 0.00 0.00 4.79
2409 2459 3.960755 GGTAGAATGGAAATTTCAGGGGG 59.039 47.826 19.49 0.00 0.00 5.40
2453 2503 3.702555 GCGCGCGGATGTATGGTC 61.703 66.667 33.06 6.44 0.00 4.02
2454 2504 3.036084 CGCGCGGATGTATGGTCC 61.036 66.667 24.84 0.00 0.00 4.46
2462 2512 3.146618 GGATGTATGGTCCGCTATACG 57.853 52.381 0.00 0.00 40.56 3.06
2463 2513 2.527100 GATGTATGGTCCGCTATACGC 58.473 52.381 0.00 0.00 40.56 4.42
2464 2514 0.599558 TGTATGGTCCGCTATACGCC 59.400 55.000 0.00 0.00 40.56 5.68
2465 2515 0.599558 GTATGGTCCGCTATACGCCA 59.400 55.000 0.00 0.00 41.76 5.69
2466 2516 1.203994 GTATGGTCCGCTATACGCCAT 59.796 52.381 0.00 0.00 44.02 4.40
2467 2517 1.552578 ATGGTCCGCTATACGCCATA 58.447 50.000 0.00 0.00 41.21 2.74
2468 2518 0.599558 TGGTCCGCTATACGCCATAC 59.400 55.000 0.00 0.00 41.76 2.39
2480 2530 4.097828 CCATACGTGGCGGTGTAC 57.902 61.111 0.00 0.00 39.01 2.90
2510 2560 4.692475 GGCGGCCCACACGTACTT 62.692 66.667 8.12 0.00 0.00 2.24
2511 2561 2.262292 GCGGCCCACACGTACTTA 59.738 61.111 0.00 0.00 0.00 2.24
2512 2562 1.808390 GCGGCCCACACGTACTTAG 60.808 63.158 0.00 0.00 0.00 2.18
2513 2563 1.588082 CGGCCCACACGTACTTAGT 59.412 57.895 0.00 0.00 0.00 2.24
2514 2564 0.457337 CGGCCCACACGTACTTAGTC 60.457 60.000 0.00 0.00 0.00 2.59
2515 2565 0.108472 GGCCCACACGTACTTAGTCC 60.108 60.000 0.00 0.00 0.00 3.85
2516 2566 0.604578 GCCCACACGTACTTAGTCCA 59.395 55.000 0.00 0.00 0.00 4.02
2517 2567 1.670967 GCCCACACGTACTTAGTCCAC 60.671 57.143 0.00 0.00 0.00 4.02
2518 2568 1.067354 CCCACACGTACTTAGTCCACC 60.067 57.143 0.00 0.00 0.00 4.61
2519 2569 1.614903 CCACACGTACTTAGTCCACCA 59.385 52.381 0.00 0.00 0.00 4.17
2520 2570 2.608752 CCACACGTACTTAGTCCACCAC 60.609 54.545 0.00 0.00 0.00 4.16
2521 2571 1.615392 ACACGTACTTAGTCCACCACC 59.385 52.381 0.00 0.00 0.00 4.61
2522 2572 0.883833 ACGTACTTAGTCCACCACCG 59.116 55.000 0.00 0.00 0.00 4.94
2523 2573 0.457337 CGTACTTAGTCCACCACCGC 60.457 60.000 0.00 0.00 0.00 5.68
2524 2574 0.108472 GTACTTAGTCCACCACCGCC 60.108 60.000 0.00 0.00 0.00 6.13
2525 2575 1.597797 TACTTAGTCCACCACCGCCG 61.598 60.000 0.00 0.00 0.00 6.46
2526 2576 4.382320 TTAGTCCACCACCGCCGC 62.382 66.667 0.00 0.00 0.00 6.53
2544 2594 4.821935 CCCCCTCATTAATCCGGC 57.178 61.111 0.00 0.00 0.00 6.13
2545 2595 1.302511 CCCCCTCATTAATCCGGCG 60.303 63.158 0.00 0.00 0.00 6.46
2546 2596 1.966451 CCCCTCATTAATCCGGCGC 60.966 63.158 0.00 0.00 0.00 6.53
2547 2597 2.317609 CCCTCATTAATCCGGCGCG 61.318 63.158 0.00 0.00 0.00 6.86
2563 2613 3.140141 CGGATTGCGGTGGCCATT 61.140 61.111 9.72 0.00 38.85 3.16
2564 2614 2.709883 CGGATTGCGGTGGCCATTT 61.710 57.895 9.72 0.00 38.85 2.32
2565 2615 1.380403 CGGATTGCGGTGGCCATTTA 61.380 55.000 9.72 0.00 38.85 1.40
2566 2616 0.102300 GGATTGCGGTGGCCATTTAC 59.898 55.000 9.72 0.00 38.85 2.01
2567 2617 0.248458 GATTGCGGTGGCCATTTACG 60.248 55.000 9.72 13.21 38.85 3.18
2575 2625 4.886925 GCCATTTACGCCGCGCAG 62.887 66.667 13.88 0.00 0.00 5.18
2589 2639 3.621394 GCAGCGCCTCGTCGAATC 61.621 66.667 2.29 0.00 0.00 2.52
2590 2640 3.315521 CAGCGCCTCGTCGAATCG 61.316 66.667 2.29 10.35 0.00 3.34
2595 2645 4.847516 CCTCGTCGAATCGCCGCA 62.848 66.667 0.00 0.00 0.00 5.69
2596 2646 3.315521 CTCGTCGAATCGCCGCAG 61.316 66.667 0.00 0.00 0.00 5.18
2597 2647 4.111016 TCGTCGAATCGCCGCAGT 62.111 61.111 0.00 0.00 0.00 4.40
2598 2648 3.902063 CGTCGAATCGCCGCAGTG 61.902 66.667 0.00 0.00 0.00 3.66
2599 2649 2.809601 GTCGAATCGCCGCAGTGT 60.810 61.111 0.00 0.00 0.00 3.55
2600 2650 2.809174 TCGAATCGCCGCAGTGTG 60.809 61.111 0.00 0.00 0.00 3.82
2601 2651 3.853330 CGAATCGCCGCAGTGTGG 61.853 66.667 18.84 18.84 36.10 4.17
2602 2652 2.434185 GAATCGCCGCAGTGTGGA 60.434 61.111 27.04 6.75 34.74 4.02
2603 2653 2.434884 AATCGCCGCAGTGTGGAG 60.435 61.111 27.04 23.07 34.74 3.86
2604 2654 3.240134 AATCGCCGCAGTGTGGAGT 62.240 57.895 27.04 10.87 34.74 3.85
2605 2655 3.649277 ATCGCCGCAGTGTGGAGTC 62.649 63.158 27.04 7.81 34.74 3.36
2606 2656 4.363990 CGCCGCAGTGTGGAGTCT 62.364 66.667 27.04 0.00 34.74 3.24
2607 2657 2.970639 GCCGCAGTGTGGAGTCTA 59.029 61.111 27.04 0.00 34.74 2.59
2608 2658 1.292223 GCCGCAGTGTGGAGTCTAA 59.708 57.895 27.04 0.00 34.74 2.10
2609 2659 0.108138 GCCGCAGTGTGGAGTCTAAT 60.108 55.000 27.04 0.00 34.74 1.73
2610 2660 1.927895 CCGCAGTGTGGAGTCTAATC 58.072 55.000 18.34 0.00 34.74 1.75
2611 2661 1.550065 CGCAGTGTGGAGTCTAATCG 58.450 55.000 0.00 0.00 0.00 3.34
2612 2662 1.281899 GCAGTGTGGAGTCTAATCGC 58.718 55.000 0.00 0.00 0.00 4.58
2613 2663 1.134965 GCAGTGTGGAGTCTAATCGCT 60.135 52.381 0.00 0.00 0.00 4.93
2614 2664 2.534298 CAGTGTGGAGTCTAATCGCTG 58.466 52.381 0.00 0.00 0.00 5.18
2615 2665 1.478510 AGTGTGGAGTCTAATCGCTGG 59.521 52.381 0.00 0.00 0.00 4.85
2616 2666 0.175760 TGTGGAGTCTAATCGCTGGC 59.824 55.000 0.00 0.00 0.00 4.85
2617 2667 0.872021 GTGGAGTCTAATCGCTGGCG 60.872 60.000 8.80 8.80 41.35 5.69
2650 2700 2.180769 CGTCGATTCCCACGCTGA 59.819 61.111 0.00 0.00 0.00 4.26
2651 2701 2.158959 CGTCGATTCCCACGCTGAC 61.159 63.158 0.00 0.00 0.00 3.51
2653 2703 3.554692 CGATTCCCACGCTGACGC 61.555 66.667 0.00 0.00 45.53 5.19
2654 2704 2.125512 GATTCCCACGCTGACGCT 60.126 61.111 0.00 0.00 45.53 5.07
2655 2705 1.741770 GATTCCCACGCTGACGCTT 60.742 57.895 0.00 0.00 45.53 4.68
2656 2706 1.970917 GATTCCCACGCTGACGCTTG 61.971 60.000 0.00 0.00 45.53 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.280524 CCAAGGCACGACGGTCAA 60.281 61.111 9.10 0.00 0.00 3.18
257 259 4.221422 GCGCACGCCCTCCTCATA 62.221 66.667 0.30 0.00 34.56 2.15
448 451 4.735132 CAAGGAAGCCGCGGTCGA 62.735 66.667 28.70 0.00 38.10 4.20
578 581 1.101195 ATTTCCCCAAACCCTCCCAT 58.899 50.000 0.00 0.00 0.00 4.00
601 605 4.694987 CCCCACGCCCCATTTGGT 62.695 66.667 0.00 0.00 0.00 3.67
686 697 0.770499 TGGGGATGAAACAGACAGCA 59.230 50.000 0.00 0.00 0.00 4.41
704 715 1.564295 CCCAAATTTGCGCCGGTTTG 61.564 55.000 12.92 12.73 0.00 2.93
726 737 2.890474 CGCTTTCGACCCATCCCG 60.890 66.667 0.00 0.00 38.10 5.14
860 876 3.982058 GCCGTAGTAGAATTGGAAGATCG 59.018 47.826 0.00 0.00 0.00 3.69
948 964 1.051812 CTCAGTCCAAGGACCTGTGT 58.948 55.000 15.36 0.00 45.59 3.72
953 969 1.128188 ACCACCTCAGTCCAAGGACC 61.128 60.000 15.36 0.00 45.59 4.46
993 1011 1.379044 CCTGGGAAGCATGGTGGTC 60.379 63.158 0.00 0.00 0.00 4.02
994 1012 1.217057 ATCCTGGGAAGCATGGTGGT 61.217 55.000 0.00 0.00 0.00 4.16
995 1013 0.466922 GATCCTGGGAAGCATGGTGG 60.467 60.000 0.00 0.00 0.00 4.61
996 1014 0.466922 GGATCCTGGGAAGCATGGTG 60.467 60.000 3.84 0.00 0.00 4.17
997 1015 0.920763 TGGATCCTGGGAAGCATGGT 60.921 55.000 14.23 0.00 0.00 3.55
998 1016 0.178998 CTGGATCCTGGGAAGCATGG 60.179 60.000 14.23 0.00 0.00 3.66
1077 1095 2.281762 GTCAACGATGTTATCTCCACGC 59.718 50.000 0.00 0.00 0.00 5.34
1079 1097 4.508124 GGATGTCAACGATGTTATCTCCAC 59.492 45.833 0.00 0.00 0.00 4.02
1341 1359 1.112113 GTAGGCTGCAGCAGTACCTA 58.888 55.000 37.63 25.55 44.36 3.08
1349 1367 2.518836 CTTTGCACGTAGGCTGCAGC 62.519 60.000 30.88 30.88 45.21 5.25
1367 1385 5.582665 GGTTAAGAATTTCAGATCACGAGCT 59.417 40.000 0.00 0.00 0.00 4.09
1382 1400 1.555075 TCAGCCTCAGCGGTTAAGAAT 59.445 47.619 0.00 0.00 46.67 2.40
1570 1588 2.597805 ACGACGGTGAGCCAGAGT 60.598 61.111 0.00 0.00 34.09 3.24
1571 1589 2.179517 GACGACGGTGAGCCAGAG 59.820 66.667 0.00 0.00 34.09 3.35
1638 1656 1.413077 GCTACCGCCAGTAATCTCCTT 59.587 52.381 0.00 0.00 0.00 3.36
1682 1700 1.938577 GATCTCATGTTCGTGCATGCT 59.061 47.619 20.33 0.00 44.20 3.79
1699 1718 6.609237 TCTTGATCGATTTGTTCATGGATC 57.391 37.500 0.00 0.00 38.34 3.36
1772 1791 3.016736 CCTCACCTCGCATATTGGTTTT 58.983 45.455 0.00 0.00 30.72 2.43
1855 1899 3.646162 TCTGAACTAACCAGCCTGAAGAA 59.354 43.478 0.00 0.00 0.00 2.52
1974 2020 5.004345 CCAAATTTTCGTGTGCCGATTATTC 59.996 40.000 0.00 0.00 46.75 1.75
1981 2027 1.127701 CACCAAATTTTCGTGTGCCG 58.872 50.000 6.91 0.00 38.13 5.69
1984 2030 2.215907 TGCCACCAAATTTTCGTGTG 57.784 45.000 12.10 7.01 0.00 3.82
2002 2048 7.490079 ACAAATACAGTATTTTGCAGCATCATG 59.510 33.333 14.86 4.25 36.29 3.07
2006 2052 6.923012 TCACAAATACAGTATTTTGCAGCAT 58.077 32.000 14.86 0.00 36.29 3.79
2161 2211 0.602562 CATTCCGGTGCCATTTGTGT 59.397 50.000 0.00 0.00 0.00 3.72
2175 2225 3.136260 AGCTCCAGAGAAGATTCCATTCC 59.864 47.826 0.00 0.00 0.00 3.01
2298 2348 4.278513 CTGCCGACCCCCACCAAA 62.279 66.667 0.00 0.00 0.00 3.28
2302 2352 2.198304 AAATCTCTGCCGACCCCCAC 62.198 60.000 0.00 0.00 0.00 4.61
2303 2353 0.619255 TAAATCTCTGCCGACCCCCA 60.619 55.000 0.00 0.00 0.00 4.96
2312 2362 5.112686 ACCGAAGAAGTGATAAATCTCTGC 58.887 41.667 0.00 0.00 31.65 4.26
2324 2374 1.346722 AGGGGTTGTACCGAAGAAGTG 59.653 52.381 0.00 0.00 39.83 3.16
2325 2375 1.346722 CAGGGGTTGTACCGAAGAAGT 59.653 52.381 0.00 0.00 39.83 3.01
2326 2376 1.338769 CCAGGGGTTGTACCGAAGAAG 60.339 57.143 0.00 0.00 39.83 2.85
2327 2377 0.688487 CCAGGGGTTGTACCGAAGAA 59.312 55.000 0.00 0.00 39.83 2.52
2328 2378 0.178926 TCCAGGGGTTGTACCGAAGA 60.179 55.000 0.00 0.00 39.83 2.87
2329 2379 0.909623 ATCCAGGGGTTGTACCGAAG 59.090 55.000 0.00 0.00 39.83 3.79
2330 2380 0.616371 CATCCAGGGGTTGTACCGAA 59.384 55.000 0.00 0.00 39.83 4.30
2331 2381 0.252330 TCATCCAGGGGTTGTACCGA 60.252 55.000 0.00 0.00 39.83 4.69
2332 2382 0.837272 ATCATCCAGGGGTTGTACCG 59.163 55.000 0.00 0.00 39.83 4.02
2333 2383 3.714798 TCTAATCATCCAGGGGTTGTACC 59.285 47.826 0.00 0.00 37.60 3.34
2334 2384 5.130477 TCTTCTAATCATCCAGGGGTTGTAC 59.870 44.000 0.00 0.00 0.00 2.90
2335 2385 5.285401 TCTTCTAATCATCCAGGGGTTGTA 58.715 41.667 0.00 0.00 0.00 2.41
2336 2386 4.111577 TCTTCTAATCATCCAGGGGTTGT 58.888 43.478 0.00 0.00 0.00 3.32
2337 2387 4.778213 TCTTCTAATCATCCAGGGGTTG 57.222 45.455 0.00 0.00 0.00 3.77
2338 2388 5.310857 GGTATCTTCTAATCATCCAGGGGTT 59.689 44.000 0.00 0.00 0.00 4.11
2339 2389 4.846940 GGTATCTTCTAATCATCCAGGGGT 59.153 45.833 0.00 0.00 0.00 4.95
2340 2390 5.097234 AGGTATCTTCTAATCATCCAGGGG 58.903 45.833 0.00 0.00 0.00 4.79
2341 2391 6.022315 AGAGGTATCTTCTAATCATCCAGGG 58.978 44.000 0.00 0.00 28.57 4.45
2342 2392 7.552050 AAGAGGTATCTTCTAATCATCCAGG 57.448 40.000 0.00 0.00 42.25 4.45
2343 2393 7.877097 CCAAAGAGGTATCTTCTAATCATCCAG 59.123 40.741 0.00 0.00 45.25 3.86
2344 2394 7.739825 CCAAAGAGGTATCTTCTAATCATCCA 58.260 38.462 0.00 0.00 45.25 3.41
2361 2411 6.463614 CCTCCTCACTTATCATACCAAAGAGG 60.464 46.154 0.00 0.00 45.67 3.69
2362 2412 6.463614 CCCTCCTCACTTATCATACCAAAGAG 60.464 46.154 0.00 0.00 0.00 2.85
2363 2413 5.366768 CCCTCCTCACTTATCATACCAAAGA 59.633 44.000 0.00 0.00 0.00 2.52
2364 2414 5.455326 CCCCTCCTCACTTATCATACCAAAG 60.455 48.000 0.00 0.00 0.00 2.77
2365 2415 4.412199 CCCCTCCTCACTTATCATACCAAA 59.588 45.833 0.00 0.00 0.00 3.28
2366 2416 3.973973 CCCCTCCTCACTTATCATACCAA 59.026 47.826 0.00 0.00 0.00 3.67
2367 2417 3.051341 ACCCCTCCTCACTTATCATACCA 60.051 47.826 0.00 0.00 0.00 3.25
2368 2418 3.588569 ACCCCTCCTCACTTATCATACC 58.411 50.000 0.00 0.00 0.00 2.73
2369 2419 5.642165 TCTACCCCTCCTCACTTATCATAC 58.358 45.833 0.00 0.00 0.00 2.39
2370 2420 5.942977 TCTACCCCTCCTCACTTATCATA 57.057 43.478 0.00 0.00 0.00 2.15
2371 2421 4.834406 TCTACCCCTCCTCACTTATCAT 57.166 45.455 0.00 0.00 0.00 2.45
2372 2422 4.620086 TTCTACCCCTCCTCACTTATCA 57.380 45.455 0.00 0.00 0.00 2.15
2373 2423 4.284746 CCATTCTACCCCTCCTCACTTATC 59.715 50.000 0.00 0.00 0.00 1.75
2374 2424 4.077982 TCCATTCTACCCCTCCTCACTTAT 60.078 45.833 0.00 0.00 0.00 1.73
2375 2425 3.273886 TCCATTCTACCCCTCCTCACTTA 59.726 47.826 0.00 0.00 0.00 2.24
2376 2426 2.045885 TCCATTCTACCCCTCCTCACTT 59.954 50.000 0.00 0.00 0.00 3.16
2377 2427 1.651770 TCCATTCTACCCCTCCTCACT 59.348 52.381 0.00 0.00 0.00 3.41
2378 2428 2.176247 TCCATTCTACCCCTCCTCAC 57.824 55.000 0.00 0.00 0.00 3.51
2379 2429 2.961536 TTCCATTCTACCCCTCCTCA 57.038 50.000 0.00 0.00 0.00 3.86
2380 2430 4.797912 AATTTCCATTCTACCCCTCCTC 57.202 45.455 0.00 0.00 0.00 3.71
2381 2431 4.544152 TGAAATTTCCATTCTACCCCTCCT 59.456 41.667 15.48 0.00 0.00 3.69
2382 2432 4.867086 TGAAATTTCCATTCTACCCCTCC 58.133 43.478 15.48 0.00 0.00 4.30
2383 2433 4.889995 CCTGAAATTTCCATTCTACCCCTC 59.110 45.833 15.48 0.00 0.00 4.30
2384 2434 4.326132 CCCTGAAATTTCCATTCTACCCCT 60.326 45.833 15.48 0.00 0.00 4.79
2385 2435 3.960755 CCCTGAAATTTCCATTCTACCCC 59.039 47.826 15.48 0.00 0.00 4.95
2386 2436 3.960755 CCCCTGAAATTTCCATTCTACCC 59.039 47.826 15.48 0.00 0.00 3.69
2387 2437 3.960755 CCCCCTGAAATTTCCATTCTACC 59.039 47.826 15.48 0.00 0.00 3.18
2436 2486 3.702555 GACCATACATCCGCGCGC 61.703 66.667 27.36 23.91 0.00 6.86
2437 2487 3.036084 GGACCATACATCCGCGCG 61.036 66.667 25.67 25.67 0.00 6.86
2442 2492 2.734492 GCGTATAGCGGACCATACATCC 60.734 54.545 0.00 0.00 41.69 3.51
2443 2493 2.527100 GCGTATAGCGGACCATACATC 58.473 52.381 0.00 0.00 41.69 3.06
2444 2494 2.649331 GCGTATAGCGGACCATACAT 57.351 50.000 0.00 0.00 41.69 2.29
2464 2514 3.683055 CGTACACCGCCACGTATG 58.317 61.111 0.00 0.00 33.56 2.39
2493 2543 3.299524 TAAGTACGTGTGGGCCGCC 62.300 63.158 15.75 0.00 0.00 6.13
2494 2544 1.808390 CTAAGTACGTGTGGGCCGC 60.808 63.158 10.94 10.94 0.00 6.53
2495 2545 0.457337 GACTAAGTACGTGTGGGCCG 60.457 60.000 0.00 0.00 0.00 6.13
2496 2546 0.108472 GGACTAAGTACGTGTGGGCC 60.108 60.000 0.00 0.00 0.00 5.80
2497 2547 0.604578 TGGACTAAGTACGTGTGGGC 59.395 55.000 0.00 0.00 0.00 5.36
2498 2548 1.067354 GGTGGACTAAGTACGTGTGGG 60.067 57.143 0.00 0.00 0.00 4.61
2499 2549 1.614903 TGGTGGACTAAGTACGTGTGG 59.385 52.381 0.00 0.00 0.00 4.17
2500 2550 2.608752 GGTGGTGGACTAAGTACGTGTG 60.609 54.545 0.00 0.00 0.00 3.82
2501 2551 1.615392 GGTGGTGGACTAAGTACGTGT 59.385 52.381 0.00 0.00 0.00 4.49
2502 2552 1.401931 CGGTGGTGGACTAAGTACGTG 60.402 57.143 0.00 0.00 0.00 4.49
2503 2553 0.883833 CGGTGGTGGACTAAGTACGT 59.116 55.000 0.00 0.00 0.00 3.57
2504 2554 0.457337 GCGGTGGTGGACTAAGTACG 60.457 60.000 0.00 0.00 0.00 3.67
2505 2555 0.108472 GGCGGTGGTGGACTAAGTAC 60.108 60.000 0.00 0.00 0.00 2.73
2506 2556 1.597797 CGGCGGTGGTGGACTAAGTA 61.598 60.000 0.00 0.00 0.00 2.24
2507 2557 2.939261 CGGCGGTGGTGGACTAAGT 61.939 63.158 0.00 0.00 0.00 2.24
2508 2558 2.125673 CGGCGGTGGTGGACTAAG 60.126 66.667 0.00 0.00 0.00 2.18
2509 2559 4.382320 GCGGCGGTGGTGGACTAA 62.382 66.667 9.78 0.00 0.00 2.24
2527 2577 1.302511 CGCCGGATTAATGAGGGGG 60.303 63.158 5.05 6.76 33.69 5.40
2528 2578 1.966451 GCGCCGGATTAATGAGGGG 60.966 63.158 5.05 14.73 39.36 4.79
2529 2579 2.317609 CGCGCCGGATTAATGAGGG 61.318 63.158 5.05 0.00 0.00 4.30
2530 2580 3.244105 CGCGCCGGATTAATGAGG 58.756 61.111 5.05 0.00 0.00 3.86
2546 2596 1.380403 TAAATGGCCACCGCAATCCG 61.380 55.000 8.16 0.00 36.38 4.18
2547 2597 0.102300 GTAAATGGCCACCGCAATCC 59.898 55.000 8.16 0.00 36.38 3.01
2548 2598 0.248458 CGTAAATGGCCACCGCAATC 60.248 55.000 8.16 0.00 36.38 2.67
2549 2599 1.806568 CGTAAATGGCCACCGCAAT 59.193 52.632 8.16 0.00 36.38 3.56
2550 2600 2.983930 GCGTAAATGGCCACCGCAA 61.984 57.895 26.48 3.95 43.53 4.85
2551 2601 3.436055 GCGTAAATGGCCACCGCA 61.436 61.111 26.48 5.26 43.53 5.69
2558 2608 4.886925 CTGCGCGGCGTAAATGGC 62.887 66.667 24.46 5.50 0.00 4.40
2559 2609 4.886925 GCTGCGCGGCGTAAATGG 62.887 66.667 27.72 8.64 0.00 3.16
2572 2622 3.621394 GATTCGACGAGGCGCTGC 61.621 66.667 7.64 0.00 0.00 5.25
2573 2623 3.315521 CGATTCGACGAGGCGCTG 61.316 66.667 7.64 0.00 35.09 5.18
2582 2632 2.809601 ACACTGCGGCGATTCGAC 60.810 61.111 12.98 5.92 0.00 4.20
2583 2633 2.809174 CACACTGCGGCGATTCGA 60.809 61.111 12.98 0.00 0.00 3.71
2584 2634 3.853330 CCACACTGCGGCGATTCG 61.853 66.667 12.98 0.62 0.00 3.34
2585 2635 2.434185 TCCACACTGCGGCGATTC 60.434 61.111 12.98 0.00 0.00 2.52
2586 2636 2.434884 CTCCACACTGCGGCGATT 60.435 61.111 12.98 0.00 0.00 3.34
2587 2637 3.649277 GACTCCACACTGCGGCGAT 62.649 63.158 12.98 0.00 0.00 4.58
2588 2638 4.357947 GACTCCACACTGCGGCGA 62.358 66.667 12.98 0.00 0.00 5.54
2589 2639 2.486636 TTAGACTCCACACTGCGGCG 62.487 60.000 0.51 0.51 0.00 6.46
2590 2640 0.108138 ATTAGACTCCACACTGCGGC 60.108 55.000 0.00 0.00 0.00 6.53
2591 2641 1.799181 CGATTAGACTCCACACTGCGG 60.799 57.143 0.00 0.00 0.00 5.69
2592 2642 1.550065 CGATTAGACTCCACACTGCG 58.450 55.000 0.00 0.00 0.00 5.18
2593 2643 1.134965 AGCGATTAGACTCCACACTGC 60.135 52.381 0.00 0.00 0.00 4.40
2594 2644 2.534298 CAGCGATTAGACTCCACACTG 58.466 52.381 0.00 0.00 0.00 3.66
2595 2645 1.478510 CCAGCGATTAGACTCCACACT 59.521 52.381 0.00 0.00 0.00 3.55
2596 2646 1.927895 CCAGCGATTAGACTCCACAC 58.072 55.000 0.00 0.00 0.00 3.82
2597 2647 0.175760 GCCAGCGATTAGACTCCACA 59.824 55.000 0.00 0.00 0.00 4.17
2598 2648 0.872021 CGCCAGCGATTAGACTCCAC 60.872 60.000 6.06 0.00 42.83 4.02
2599 2649 1.035385 TCGCCAGCGATTAGACTCCA 61.035 55.000 11.27 0.00 44.01 3.86
2600 2650 1.734137 TCGCCAGCGATTAGACTCC 59.266 57.895 11.27 0.00 44.01 3.85
2633 2683 2.158959 GTCAGCGTGGGAATCGACG 61.159 63.158 0.00 0.00 45.70 5.12
2634 2684 2.158959 CGTCAGCGTGGGAATCGAC 61.159 63.158 0.00 0.00 0.00 4.20
2635 2685 2.180769 CGTCAGCGTGGGAATCGA 59.819 61.111 0.00 0.00 0.00 3.59
2636 2686 3.554692 GCGTCAGCGTGGGAATCG 61.555 66.667 0.00 0.00 40.81 3.34


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

AutoCloner maintained by Alex Coulton.