Multiple sequence alignment - TraesCS4A01G040300

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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 TraesCS4A01G040300 chr4A 100.000 3156 0 0 1 3156 33647071 33643916 0 5829
1 TraesCS4A01G040300 chr4B 90.621 3220 126 75 1 3156 530208672 530205565 0 4111
2 TraesCS4A01G040300 chr4D 89.286 2268 101 60 947 3156 432428633 432426450 0 2712
3 TraesCS4A01G040300 chr4D 92.539 965 29 21 1 957 432429584 432428655 0 1343


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 TraesCS4A01G040300 chr4A 33643916 33647071 3155 True 5829.0 5829 100.0000 1 3156 1 chr4A.!!$R1 3155
1 TraesCS4A01G040300 chr4B 530205565 530208672 3107 True 4111.0 4111 90.6210 1 3156 1 chr4B.!!$R1 3155
2 TraesCS4A01G040300 chr4D 432426450 432429584 3134 True 2027.5 2712 90.9125 1 3156 2 chr4D.!!$R1 3155

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
528 530 0.321034 CCTCAGTTACAGCTGCTGCA 60.321 55.0 28.39 14.52 42.74 4.41 F
556 558 0.463474 GGCCTGAGCTAGCTTTGGAG 60.463 60.0 29.54 18.70 39.73 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1367 1446 0.034767 GTACCCCCTTGCTTGTACCC 60.035 60.0 0.0 0.0 0.00 3.69 R
2398 2540 0.242017 ACGGCACCTTCACGTAGTAC 59.758 55.0 0.0 0.0 41.61 2.73 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
81 82 7.501892 TGTGGCTGTATCTTTATTATGCATCAA 59.498 33.333 0.19 0.00 0.00 2.57
128 129 8.198109 TCTTCTTTATGAGAATTAGAGTTCGGG 58.802 37.037 0.00 0.00 43.23 5.14
129 130 6.817184 TCTTTATGAGAATTAGAGTTCGGGG 58.183 40.000 0.00 0.00 33.36 5.73
130 131 6.383147 TCTTTATGAGAATTAGAGTTCGGGGT 59.617 38.462 0.00 0.00 33.36 4.95
232 233 6.983906 ATGATATGATGGTCAGACAGTACA 57.016 37.500 2.17 0.00 0.00 2.90
233 234 6.790232 TGATATGATGGTCAGACAGTACAA 57.210 37.500 2.17 0.00 0.00 2.41
258 259 4.226168 AGAGGTTTTAAGACATGGGAGGAG 59.774 45.833 0.00 0.00 0.00 3.69
259 260 3.267031 AGGTTTTAAGACATGGGAGGAGG 59.733 47.826 0.00 0.00 0.00 4.30
300 301 0.550914 TGCCTTGTGGGTTTCACTCT 59.449 50.000 0.00 0.00 46.20 3.24
301 302 1.771854 TGCCTTGTGGGTTTCACTCTA 59.228 47.619 0.00 0.00 46.20 2.43
302 303 2.224523 TGCCTTGTGGGTTTCACTCTAG 60.225 50.000 0.00 0.00 46.20 2.43
303 304 2.427506 CCTTGTGGGTTTCACTCTAGC 58.572 52.381 0.00 0.00 46.20 3.42
437 438 1.341285 TGTTGCAGCAATAGATGGCCT 60.341 47.619 11.96 0.00 0.00 5.19
442 443 1.526917 GCAATAGATGGCCTGCCGT 60.527 57.895 3.32 1.68 39.42 5.68
461 463 0.938713 TTGTAGTTCCAACCAACGCG 59.061 50.000 3.53 3.53 0.00 6.01
481 483 1.165270 CACCGGTTTCTCCATTGGAC 58.835 55.000 2.97 0.00 35.57 4.02
482 484 0.768622 ACCGGTTTCTCCATTGGACA 59.231 50.000 0.00 0.00 35.57 4.02
528 530 0.321034 CCTCAGTTACAGCTGCTGCA 60.321 55.000 28.39 14.52 42.74 4.41
529 531 1.077123 CTCAGTTACAGCTGCTGCAG 58.923 55.000 28.39 24.80 42.74 4.41
552 554 2.124942 GCGGCCTGAGCTAGCTTT 60.125 61.111 20.42 0.00 38.78 3.51
553 555 2.467826 GCGGCCTGAGCTAGCTTTG 61.468 63.158 20.42 14.20 38.78 2.77
554 556 1.817099 CGGCCTGAGCTAGCTTTGG 60.817 63.158 20.42 22.82 39.73 3.28
555 557 1.604378 GGCCTGAGCTAGCTTTGGA 59.396 57.895 29.54 12.05 39.73 3.53
556 558 0.463474 GGCCTGAGCTAGCTTTGGAG 60.463 60.000 29.54 18.70 39.73 3.86
557 559 1.094650 GCCTGAGCTAGCTTTGGAGC 61.095 60.000 29.54 20.03 42.04 4.70
570 572 1.965414 TTGGAGCCCAGTGATCCTTA 58.035 50.000 9.51 0.00 33.81 2.69
588 590 5.790593 TCCTTACACTTACTAACAAGGCAG 58.209 41.667 0.00 0.00 33.96 4.85
626 628 1.384222 GGCCGGGCCTTGTAGATTTG 61.384 60.000 30.86 0.00 46.69 2.32
627 629 0.679960 GCCGGGCCTTGTAGATTTGT 60.680 55.000 8.12 0.00 0.00 2.83
628 630 1.094785 CCGGGCCTTGTAGATTTGTG 58.905 55.000 0.84 0.00 0.00 3.33
631 636 1.818674 GGGCCTTGTAGATTTGTGGTG 59.181 52.381 0.84 0.00 0.00 4.17
650 655 3.406200 CTCTCCTGGGCTGGGTGG 61.406 72.222 0.00 0.00 0.00 4.61
789 794 3.013932 CTGCCCTGCCCTCTCCTT 61.014 66.667 0.00 0.00 0.00 3.36
818 826 2.625617 GGGTTGGATGGAGGCCATTTAA 60.626 50.000 5.01 0.00 45.26 1.52
890 898 2.796304 CTGTAGAAGAGAAGCAGCTCG 58.204 52.381 0.00 0.00 39.87 5.03
891 899 1.135257 TGTAGAAGAGAAGCAGCTCGC 60.135 52.381 0.00 0.47 39.87 5.03
947 958 1.132643 GAGTACTCGAGTTCCGCACAT 59.867 52.381 25.44 0.79 38.37 3.21
972 1015 2.932184 TATAGGGAGTGGTGGTGTCA 57.068 50.000 0.00 0.00 0.00 3.58
973 1016 2.270434 ATAGGGAGTGGTGGTGTCAT 57.730 50.000 0.00 0.00 0.00 3.06
974 1017 1.568504 TAGGGAGTGGTGGTGTCATC 58.431 55.000 0.00 0.00 0.00 2.92
975 1018 0.473694 AGGGAGTGGTGGTGTCATCA 60.474 55.000 0.00 0.00 0.00 3.07
993 1037 1.829533 ACAACACCAGCCAAGCCAG 60.830 57.895 0.00 0.00 0.00 4.85
1022 1066 5.276773 CGATGAGCACTGAATTCTTTAGAGC 60.277 44.000 7.05 6.32 0.00 4.09
1137 1181 1.542547 GCCTCGGAGAAGAACACCAAA 60.543 52.381 6.58 0.00 34.09 3.28
1247 1291 0.464870 CACCTGGAGCTCCATCTCAG 59.535 60.000 35.11 22.33 46.46 3.35
1305 1349 0.545309 TCCAAGTGAGTCCCTCCCTG 60.545 60.000 0.00 0.00 0.00 4.45
1306 1350 0.838122 CCAAGTGAGTCCCTCCCTGT 60.838 60.000 0.00 0.00 0.00 4.00
1308 1352 0.489567 AAGTGAGTCCCTCCCTGTCT 59.510 55.000 0.00 0.00 0.00 3.41
1314 1358 1.132689 AGTCCCTCCCTGTCTGTCTTT 60.133 52.381 0.00 0.00 0.00 2.52
1319 1363 3.118592 CCCTCCCTGTCTGTCTTTATCAC 60.119 52.174 0.00 0.00 0.00 3.06
1320 1364 3.772025 CCTCCCTGTCTGTCTTTATCACT 59.228 47.826 0.00 0.00 0.00 3.41
1321 1365 4.956700 CCTCCCTGTCTGTCTTTATCACTA 59.043 45.833 0.00 0.00 0.00 2.74
1322 1366 5.068460 CCTCCCTGTCTGTCTTTATCACTAG 59.932 48.000 0.00 0.00 0.00 2.57
1323 1367 4.402793 TCCCTGTCTGTCTTTATCACTAGC 59.597 45.833 0.00 0.00 0.00 3.42
1342 1386 8.696374 TCACTAGCTAGCTAATTATTCTGTGTT 58.304 33.333 24.20 0.00 0.00 3.32
1343 1422 8.759641 CACTAGCTAGCTAATTATTCTGTGTTG 58.240 37.037 24.20 10.44 0.00 3.33
1369 1448 9.924650 GTATATACTTGTATGTTCTACCTTGGG 57.075 37.037 5.58 0.00 0.00 4.12
1370 1449 6.886178 ATACTTGTATGTTCTACCTTGGGT 57.114 37.500 0.00 0.00 40.16 4.51
1371 1450 7.983166 ATACTTGTATGTTCTACCTTGGGTA 57.017 36.000 0.00 0.00 37.09 3.69
1372 1451 6.046290 ACTTGTATGTTCTACCTTGGGTAC 57.954 41.667 0.00 0.00 37.09 3.34
1373 1452 5.544948 ACTTGTATGTTCTACCTTGGGTACA 59.455 40.000 0.00 0.00 37.09 2.90
1374 1453 6.043474 ACTTGTATGTTCTACCTTGGGTACAA 59.957 38.462 0.00 0.00 37.09 2.41
1389 1468 2.433436 GTACAAGCAAGGGGGTACAAG 58.567 52.381 0.00 0.00 36.87 3.16
1412 1491 6.609876 AGTCATTTCTCTCCATAGCTCTCTA 58.390 40.000 0.00 0.00 0.00 2.43
1459 1567 1.077645 GGCGCCGACACGTGTTAATA 61.078 55.000 24.26 0.00 34.88 0.98
1460 1568 0.925466 GCGCCGACACGTGTTAATAT 59.075 50.000 24.26 0.00 34.88 1.28
1461 1569 2.118683 GCGCCGACACGTGTTAATATA 58.881 47.619 24.26 0.00 34.88 0.86
1462 1570 2.152489 GCGCCGACACGTGTTAATATAG 59.848 50.000 24.26 11.62 34.88 1.31
1483 1591 4.648651 AGAGCCGGTAAAGTTAATTGTGT 58.351 39.130 1.90 0.00 0.00 3.72
1549 1657 0.391528 CTGTCGCACATGGACATGGA 60.392 55.000 15.94 2.05 42.97 3.41
1650 1758 0.391263 ACGCCCACGAGGAATCTTTC 60.391 55.000 0.00 0.00 43.93 2.62
1653 1761 2.799917 CGCCCACGAGGAATCTTTCTAG 60.800 54.545 0.00 0.00 43.93 2.43
1655 1763 3.383825 GCCCACGAGGAATCTTTCTAGTA 59.616 47.826 0.00 0.00 38.24 1.82
1656 1764 4.737055 GCCCACGAGGAATCTTTCTAGTAC 60.737 50.000 0.00 0.00 38.24 2.73
1657 1765 4.202131 CCCACGAGGAATCTTTCTAGTACC 60.202 50.000 0.00 0.00 38.24 3.34
1658 1766 4.401519 CCACGAGGAATCTTTCTAGTACCA 59.598 45.833 0.00 0.00 36.89 3.25
1659 1767 5.341617 CACGAGGAATCTTTCTAGTACCAC 58.658 45.833 0.00 0.00 0.00 4.16
1660 1768 4.096081 ACGAGGAATCTTTCTAGTACCACG 59.904 45.833 0.00 0.00 36.47 4.94
1661 1769 4.497674 CGAGGAATCTTTCTAGTACCACGG 60.498 50.000 0.00 0.00 0.00 4.94
1683 1805 4.274459 GGTTGCCTAGAAGATGCAAGTATG 59.726 45.833 3.90 0.00 44.84 2.39
1687 1813 5.163163 TGCCTAGAAGATGCAAGTATGGATT 60.163 40.000 0.00 0.00 37.78 3.01
1845 1972 2.435586 CAAGGAGCAGGGCGTGAG 60.436 66.667 12.03 0.00 0.00 3.51
1871 1998 0.385974 GCTCAACATGTCCACAACGC 60.386 55.000 0.00 0.00 0.00 4.84
1874 2001 1.227704 AACATGTCCACAACGCCGA 60.228 52.632 0.00 0.00 0.00 5.54
1893 2020 2.338984 GAGGCAGGTCGTCGTTGT 59.661 61.111 0.00 0.00 0.00 3.32
1955 2082 1.786582 GCAGCAGCGACAAAGAGAG 59.213 57.895 0.00 0.00 0.00 3.20
1956 2083 0.668706 GCAGCAGCGACAAAGAGAGA 60.669 55.000 0.00 0.00 0.00 3.10
1963 2090 1.009389 CGACAAAGAGAGACACCGCC 61.009 60.000 0.00 0.00 0.00 6.13
2169 2308 0.465705 CACTAGGCGGACATGATGGT 59.534 55.000 0.00 0.00 0.00 3.55
2194 2333 4.828072 AGAAAGGAAACCCTAGTAGCTG 57.172 45.455 0.00 0.00 32.65 4.24
2195 2334 4.168883 AGAAAGGAAACCCTAGTAGCTGT 58.831 43.478 0.00 0.00 32.65 4.40
2196 2335 5.339477 AGAAAGGAAACCCTAGTAGCTGTA 58.661 41.667 0.00 0.00 32.65 2.74
2197 2336 5.422650 AGAAAGGAAACCCTAGTAGCTGTAG 59.577 44.000 0.00 0.00 32.65 2.74
2198 2337 4.604784 AGGAAACCCTAGTAGCTGTAGA 57.395 45.455 0.00 0.00 30.72 2.59
2199 2338 4.279982 AGGAAACCCTAGTAGCTGTAGAC 58.720 47.826 0.00 0.00 30.72 2.59
2201 2340 3.752359 AACCCTAGTAGCTGTAGACCA 57.248 47.619 0.00 0.00 0.00 4.02
2203 2342 4.057063 ACCCTAGTAGCTGTAGACCAAA 57.943 45.455 0.00 0.00 0.00 3.28
2204 2343 3.768215 ACCCTAGTAGCTGTAGACCAAAC 59.232 47.826 0.00 0.00 0.00 2.93
2205 2344 3.132467 CCCTAGTAGCTGTAGACCAAACC 59.868 52.174 0.00 0.00 0.00 3.27
2206 2345 3.767673 CCTAGTAGCTGTAGACCAAACCA 59.232 47.826 0.00 0.00 0.00 3.67
2209 2348 5.043737 AGTAGCTGTAGACCAAACCAAAA 57.956 39.130 0.00 0.00 0.00 2.44
2210 2349 4.820173 AGTAGCTGTAGACCAAACCAAAAC 59.180 41.667 0.00 0.00 0.00 2.43
2211 2350 3.898482 AGCTGTAGACCAAACCAAAACT 58.102 40.909 0.00 0.00 0.00 2.66
2212 2351 5.043737 AGCTGTAGACCAAACCAAAACTA 57.956 39.130 0.00 0.00 0.00 2.24
2213 2352 5.063880 AGCTGTAGACCAAACCAAAACTAG 58.936 41.667 0.00 0.00 0.00 2.57
2214 2353 4.215613 GCTGTAGACCAAACCAAAACTAGG 59.784 45.833 0.00 0.00 0.00 3.02
2215 2354 4.721132 TGTAGACCAAACCAAAACTAGGG 58.279 43.478 0.00 0.00 0.00 3.53
2216 2355 3.965470 AGACCAAACCAAAACTAGGGT 57.035 42.857 0.00 0.00 39.65 4.34
2217 2356 3.562182 AGACCAAACCAAAACTAGGGTG 58.438 45.455 0.00 0.00 37.50 4.61
2218 2357 2.626266 GACCAAACCAAAACTAGGGTGG 59.374 50.000 6.98 6.98 39.83 4.61
2219 2358 2.245287 ACCAAACCAAAACTAGGGTGGA 59.755 45.455 13.75 0.00 38.27 4.02
2220 2359 3.301274 CCAAACCAAAACTAGGGTGGAA 58.699 45.455 13.75 0.00 37.53 3.53
2221 2360 3.901222 CCAAACCAAAACTAGGGTGGAAT 59.099 43.478 13.75 2.16 37.53 3.01
2222 2361 4.346709 CCAAACCAAAACTAGGGTGGAATT 59.653 41.667 13.75 6.95 37.53 2.17
2223 2362 5.510690 CCAAACCAAAACTAGGGTGGAATTC 60.511 44.000 13.75 0.00 37.53 2.17
2224 2363 3.774734 ACCAAAACTAGGGTGGAATTCC 58.225 45.455 18.17 18.17 35.67 3.01
2278 2420 5.239306 CGATGCATGTATGTTAATCAAGGGT 59.761 40.000 2.46 0.00 0.00 4.34
2294 2436 3.983044 AGGGTTGGAGCAAGTAAGTAG 57.017 47.619 0.00 0.00 0.00 2.57
2303 2445 7.101652 TGGAGCAAGTAAGTAGATCTTGTAG 57.898 40.000 0.00 0.00 40.14 2.74
2309 2451 9.934190 GCAAGTAAGTAGATCTTGTAGTAGTAC 57.066 37.037 0.00 0.37 40.14 2.73
2398 2540 3.558829 AGATTGATGCATGAACGCTGTAG 59.441 43.478 2.46 0.00 0.00 2.74
2402 2544 3.119137 TGATGCATGAACGCTGTAGTACT 60.119 43.478 2.46 0.00 0.00 2.73
2403 2545 4.097286 TGATGCATGAACGCTGTAGTACTA 59.903 41.667 2.46 0.00 0.00 1.82
2404 2546 3.766151 TGCATGAACGCTGTAGTACTAC 58.234 45.455 23.58 23.58 36.63 2.73
2405 2547 2.782192 GCATGAACGCTGTAGTACTACG 59.218 50.000 24.36 19.74 38.85 3.51
2406 2548 3.730061 GCATGAACGCTGTAGTACTACGT 60.730 47.826 24.36 17.33 38.85 3.57
2407 2549 3.460362 TGAACGCTGTAGTACTACGTG 57.540 47.619 24.36 24.22 38.85 4.49
2409 2551 3.498018 TGAACGCTGTAGTACTACGTGAA 59.502 43.478 28.63 14.54 38.85 3.18
2410 2552 3.736530 ACGCTGTAGTACTACGTGAAG 57.263 47.619 28.63 21.29 38.85 3.02
2411 2553 2.417933 ACGCTGTAGTACTACGTGAAGG 59.582 50.000 28.63 17.96 38.85 3.46
2412 2554 2.417933 CGCTGTAGTACTACGTGAAGGT 59.582 50.000 24.36 0.00 38.85 3.50
2413 2555 3.727079 CGCTGTAGTACTACGTGAAGGTG 60.727 52.174 24.36 13.70 38.85 4.00
2414 2556 3.756069 CTGTAGTACTACGTGAAGGTGC 58.244 50.000 24.36 1.38 38.85 5.01
2416 2558 0.524862 AGTACTACGTGAAGGTGCCG 59.475 55.000 0.00 0.00 0.00 5.69
2417 2559 0.242017 GTACTACGTGAAGGTGCCGT 59.758 55.000 0.00 0.00 38.53 5.68
2418 2560 0.523072 TACTACGTGAAGGTGCCGTC 59.477 55.000 0.00 0.00 36.12 4.79
2419 2561 1.445582 CTACGTGAAGGTGCCGTCC 60.446 63.158 0.00 0.00 36.12 4.79
2420 2562 1.874345 CTACGTGAAGGTGCCGTCCT 61.874 60.000 0.00 0.00 39.84 3.85
2470 2612 0.034089 GGCAATAGGGCAGTGAAGGT 60.034 55.000 0.00 0.00 42.77 3.50
2471 2613 1.098050 GCAATAGGGCAGTGAAGGTG 58.902 55.000 0.00 0.00 0.00 4.00
2609 2754 4.785453 GGGCCGAGGCAGTGAAGG 62.785 72.222 16.65 0.00 44.11 3.46
2682 2827 0.681243 GCACACTCCATTCCCTTCCC 60.681 60.000 0.00 0.00 0.00 3.97
2758 2903 6.260936 CAGAGTGAACAAACAATAACCTGAGT 59.739 38.462 0.00 0.00 0.00 3.41
2765 2910 7.668525 ACAAACAATAACCTGAGTTAGCTAC 57.331 36.000 0.00 0.00 41.66 3.58
2767 2912 7.387948 ACAAACAATAACCTGAGTTAGCTACAG 59.612 37.037 0.00 0.00 41.66 2.74
2771 2916 6.702716 ATAACCTGAGTTAGCTACAGAGAC 57.297 41.667 10.59 0.00 41.66 3.36
2772 2917 4.310022 ACCTGAGTTAGCTACAGAGACT 57.690 45.455 10.59 3.36 34.07 3.24
2774 2919 5.817784 ACCTGAGTTAGCTACAGAGACTTA 58.182 41.667 10.59 0.19 34.07 2.24
2776 2921 5.220970 CCTGAGTTAGCTACAGAGACTTAGC 60.221 48.000 10.59 0.00 40.98 3.09
2777 2922 5.254115 TGAGTTAGCTACAGAGACTTAGCA 58.746 41.667 7.27 0.00 42.78 3.49
2778 2923 5.124138 TGAGTTAGCTACAGAGACTTAGCAC 59.876 44.000 7.27 0.00 42.78 4.40
2779 2924 5.258051 AGTTAGCTACAGAGACTTAGCACT 58.742 41.667 7.27 1.18 42.78 4.40
2780 2925 5.355910 AGTTAGCTACAGAGACTTAGCACTC 59.644 44.000 7.27 0.00 42.78 3.51
2781 2926 3.963129 AGCTACAGAGACTTAGCACTCT 58.037 45.455 7.27 4.27 42.78 3.24
2782 2927 3.945285 AGCTACAGAGACTTAGCACTCTC 59.055 47.826 7.27 0.00 42.78 3.20
2783 2928 3.692101 GCTACAGAGACTTAGCACTCTCA 59.308 47.826 6.58 0.00 40.85 3.27
2784 2929 4.201910 GCTACAGAGACTTAGCACTCTCAG 60.202 50.000 6.58 8.00 40.85 3.35
2785 2930 2.491693 ACAGAGACTTAGCACTCTCAGC 59.508 50.000 6.58 0.00 40.85 4.26
2843 2992 2.322371 GCTGAGTGCAAAGCTACAAC 57.678 50.000 9.44 0.00 42.31 3.32
2844 2993 1.603802 GCTGAGTGCAAAGCTACAACA 59.396 47.619 9.44 0.00 42.31 3.33
2845 2994 2.603173 GCTGAGTGCAAAGCTACAACAC 60.603 50.000 9.44 0.00 42.31 3.32
2846 2995 2.613595 CTGAGTGCAAAGCTACAACACA 59.386 45.455 10.53 1.77 33.69 3.72
2847 2996 2.613595 TGAGTGCAAAGCTACAACACAG 59.386 45.455 10.53 0.00 33.69 3.66
2848 2997 1.334869 AGTGCAAAGCTACAACACAGC 59.665 47.619 10.53 0.00 39.41 4.40
2849 2998 1.065401 GTGCAAAGCTACAACACAGCA 59.935 47.619 0.00 0.00 41.66 4.41
2850 2999 1.955778 TGCAAAGCTACAACACAGCAT 59.044 42.857 0.00 0.00 41.66 3.79
2865 3014 4.042398 CACAGCATACGACACCTATACAC 58.958 47.826 0.00 0.00 0.00 2.90
2957 3119 2.809446 CAAGGCGTCGAATCTACATGA 58.191 47.619 0.00 0.00 0.00 3.07
2958 3120 2.493713 AGGCGTCGAATCTACATGAC 57.506 50.000 0.00 0.00 0.00 3.06
2959 3121 2.025155 AGGCGTCGAATCTACATGACT 58.975 47.619 0.00 0.00 0.00 3.41
2961 3123 3.003482 AGGCGTCGAATCTACATGACTAC 59.997 47.826 0.00 0.00 0.00 2.73
2962 3124 3.242969 GGCGTCGAATCTACATGACTACA 60.243 47.826 0.00 0.00 0.00 2.74
3040 3202 0.698818 ACTTGGCCCTAGGTTGGAAG 59.301 55.000 8.29 6.76 0.00 3.46
3041 3203 0.681243 CTTGGCCCTAGGTTGGAAGC 60.681 60.000 8.29 2.20 0.00 3.86
3042 3204 1.431195 TTGGCCCTAGGTTGGAAGCA 61.431 55.000 8.29 0.00 0.00 3.91
3043 3205 1.214305 TGGCCCTAGGTTGGAAGCAT 61.214 55.000 8.29 0.00 0.00 3.79
3044 3206 0.753111 GGCCCTAGGTTGGAAGCATG 60.753 60.000 8.29 0.00 0.00 4.06
3045 3207 1.387295 GCCCTAGGTTGGAAGCATGC 61.387 60.000 10.51 10.51 0.00 4.06
3046 3208 0.257039 CCCTAGGTTGGAAGCATGCT 59.743 55.000 16.30 16.30 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 5.455392 GCTGCGTTGATGCATAATAAAGAT 58.545 37.500 0.00 0.00 45.26 2.40
128 129 0.038166 TCATGGCTTTCTCCACCACC 59.962 55.000 0.00 0.00 39.25 4.61
129 130 1.909700 TTCATGGCTTTCTCCACCAC 58.090 50.000 0.00 0.00 39.25 4.16
130 131 2.449464 CATTCATGGCTTTCTCCACCA 58.551 47.619 0.00 0.00 39.25 4.17
232 233 5.280727 CCTCCCATGTCTTAAAACCTCTCTT 60.281 44.000 0.00 0.00 0.00 2.85
233 234 4.226168 CCTCCCATGTCTTAAAACCTCTCT 59.774 45.833 0.00 0.00 0.00 3.10
258 259 3.726144 AGCTTGCAGAGGCCTCCC 61.726 66.667 29.54 20.39 40.13 4.30
259 260 2.438075 CAGCTTGCAGAGGCCTCC 60.438 66.667 29.54 15.52 40.13 4.30
417 418 1.105457 GGCCATCTATTGCTGCAACA 58.895 50.000 18.51 4.93 0.00 3.33
418 419 1.066605 CAGGCCATCTATTGCTGCAAC 59.933 52.381 18.51 2.69 0.00 4.17
419 420 1.395635 CAGGCCATCTATTGCTGCAA 58.604 50.000 18.43 18.43 0.00 4.08
420 421 1.105167 GCAGGCCATCTATTGCTGCA 61.105 55.000 5.01 0.00 39.72 4.41
421 422 1.658673 GCAGGCCATCTATTGCTGC 59.341 57.895 5.01 0.00 35.31 5.25
422 423 1.512996 CGGCAGGCCATCTATTGCTG 61.513 60.000 5.01 6.12 36.79 4.41
442 443 0.938713 CGCGTTGGTTGGAACTACAA 59.061 50.000 0.00 0.00 0.00 2.41
461 463 0.608035 TCCAATGGAGAAACCGGTGC 60.608 55.000 8.52 3.13 42.61 5.01
530 532 4.152964 TAGCTCAGGCCGCAGCAG 62.153 66.667 25.58 8.13 42.56 4.24
531 533 4.152964 CTAGCTCAGGCCGCAGCA 62.153 66.667 25.58 13.60 42.56 4.41
533 535 2.866085 AAAGCTAGCTCAGGCCGCAG 62.866 60.000 19.65 0.00 39.73 5.18
552 554 1.204146 GTAAGGATCACTGGGCTCCA 58.796 55.000 2.20 0.00 0.00 3.86
553 555 1.134371 GTGTAAGGATCACTGGGCTCC 60.134 57.143 0.00 0.00 33.59 4.70
554 556 1.834263 AGTGTAAGGATCACTGGGCTC 59.166 52.381 0.00 0.00 43.32 4.70
555 557 1.958288 AGTGTAAGGATCACTGGGCT 58.042 50.000 0.00 0.00 43.32 5.19
556 558 2.789409 AAGTGTAAGGATCACTGGGC 57.211 50.000 0.00 0.00 44.03 5.36
557 559 6.070995 TGTTAGTAAGTGTAAGGATCACTGGG 60.071 42.308 0.00 0.00 44.03 4.45
570 572 2.105821 TGCCTGCCTTGTTAGTAAGTGT 59.894 45.455 0.00 0.00 0.00 3.55
608 610 0.679960 ACAAATCTACAAGGCCCGGC 60.680 55.000 0.00 0.00 0.00 6.13
609 611 1.094785 CACAAATCTACAAGGCCCGG 58.905 55.000 0.00 0.00 0.00 5.73
610 612 1.094785 CCACAAATCTACAAGGCCCG 58.905 55.000 0.00 0.00 0.00 6.13
626 628 4.416738 GCCCAGGAGAGCCACCAC 62.417 72.222 0.00 0.00 36.29 4.16
627 629 4.664267 AGCCCAGGAGAGCCACCA 62.664 66.667 0.00 0.00 36.29 4.17
628 630 4.106925 CAGCCCAGGAGAGCCACC 62.107 72.222 0.00 0.00 36.29 4.61
650 655 0.944386 CTGTACACGCCATAATGCCC 59.056 55.000 0.00 0.00 0.00 5.36
697 702 1.307866 TCCACCTCCTCCCCCATTC 60.308 63.158 0.00 0.00 0.00 2.67
775 780 1.584724 TTAAGAAGGAGAGGGCAGGG 58.415 55.000 0.00 0.00 0.00 4.45
781 786 3.372025 CCAACCCCATTAAGAAGGAGAGG 60.372 52.174 0.00 0.00 0.00 3.69
787 792 4.210331 CTCCATCCAACCCCATTAAGAAG 58.790 47.826 0.00 0.00 0.00 2.85
788 793 3.052944 CCTCCATCCAACCCCATTAAGAA 60.053 47.826 0.00 0.00 0.00 2.52
789 794 2.513738 CCTCCATCCAACCCCATTAAGA 59.486 50.000 0.00 0.00 0.00 2.10
818 826 3.195825 CGTGGACACTAAAGAAGGGATCT 59.804 47.826 0.56 0.00 41.32 2.75
890 898 2.235898 AGGTGAGGAGAATTGAGTGAGC 59.764 50.000 0.00 0.00 0.00 4.26
891 899 3.118811 GGAGGTGAGGAGAATTGAGTGAG 60.119 52.174 0.00 0.00 0.00 3.51
892 900 2.834549 GGAGGTGAGGAGAATTGAGTGA 59.165 50.000 0.00 0.00 0.00 3.41
893 901 2.836981 AGGAGGTGAGGAGAATTGAGTG 59.163 50.000 0.00 0.00 0.00 3.51
935 946 8.405418 TCCCTATATATATATGTGCGGAACTC 57.595 38.462 14.42 0.00 0.00 3.01
942 953 7.290248 ACCACCACTCCCTATATATATATGTGC 59.710 40.741 14.42 0.00 0.00 4.57
947 958 7.946381 TGACACCACCACTCCCTATATATATA 58.054 38.462 2.49 2.49 0.00 0.86
972 1015 1.181098 GGCTTGGCTGGTGTTGTGAT 61.181 55.000 0.00 0.00 0.00 3.06
973 1016 1.827789 GGCTTGGCTGGTGTTGTGA 60.828 57.895 0.00 0.00 0.00 3.58
974 1017 2.079020 CTGGCTTGGCTGGTGTTGTG 62.079 60.000 0.00 0.00 0.00 3.33
975 1018 1.829533 CTGGCTTGGCTGGTGTTGT 60.830 57.895 0.00 0.00 0.00 3.32
976 1019 1.521450 CTCTGGCTTGGCTGGTGTTG 61.521 60.000 1.75 0.00 0.00 3.33
977 1020 1.228367 CTCTGGCTTGGCTGGTGTT 60.228 57.895 1.75 0.00 0.00 3.32
993 1037 4.619973 AGAATTCAGTGCTCATCGATCTC 58.380 43.478 8.44 0.00 0.00 2.75
1022 1066 0.588252 CTCCTGGTGAAACTTGTGCG 59.412 55.000 0.00 0.00 36.74 5.34
1116 1160 1.446272 GGTGTTCTTCTCCGAGGCG 60.446 63.158 0.00 0.00 0.00 5.52
1137 1181 2.165437 GGAAGAAGACGAGCTGATCTGT 59.835 50.000 0.00 0.00 0.00 3.41
1305 1349 6.385649 AGCTAGCTAGTGATAAAGACAGAC 57.614 41.667 17.69 0.26 0.00 3.51
1306 1350 8.698973 ATTAGCTAGCTAGTGATAAAGACAGA 57.301 34.615 23.03 5.12 0.00 3.41
1319 1363 8.879342 ACAACACAGAATAATTAGCTAGCTAG 57.121 34.615 23.03 16.84 0.00 3.42
1343 1422 9.924650 CCCAAGGTAGAACATACAAGTATATAC 57.075 37.037 4.60 4.60 0.00 1.47
1367 1446 0.034767 GTACCCCCTTGCTTGTACCC 60.035 60.000 0.00 0.00 0.00 3.69
1368 1447 0.694196 TGTACCCCCTTGCTTGTACC 59.306 55.000 0.00 0.00 34.15 3.34
1369 1448 2.224695 ACTTGTACCCCCTTGCTTGTAC 60.225 50.000 0.00 0.00 35.32 2.90
1370 1449 2.039348 GACTTGTACCCCCTTGCTTGTA 59.961 50.000 0.00 0.00 0.00 2.41
1371 1450 0.850784 ACTTGTACCCCCTTGCTTGT 59.149 50.000 0.00 0.00 0.00 3.16
1372 1451 1.202879 TGACTTGTACCCCCTTGCTTG 60.203 52.381 0.00 0.00 0.00 4.01
1373 1452 1.145571 TGACTTGTACCCCCTTGCTT 58.854 50.000 0.00 0.00 0.00 3.91
1374 1453 1.372501 ATGACTTGTACCCCCTTGCT 58.627 50.000 0.00 0.00 0.00 3.91
1375 1454 2.215942 AATGACTTGTACCCCCTTGC 57.784 50.000 0.00 0.00 0.00 4.01
1376 1455 4.010349 GAGAAATGACTTGTACCCCCTTG 58.990 47.826 0.00 0.00 0.00 3.61
1377 1456 3.916989 AGAGAAATGACTTGTACCCCCTT 59.083 43.478 0.00 0.00 0.00 3.95
1378 1457 3.519913 GAGAGAAATGACTTGTACCCCCT 59.480 47.826 0.00 0.00 0.00 4.79
1379 1458 3.370633 GGAGAGAAATGACTTGTACCCCC 60.371 52.174 0.00 0.00 0.00 5.40
1380 1459 3.263425 TGGAGAGAAATGACTTGTACCCC 59.737 47.826 0.00 0.00 0.00 4.95
1389 1468 5.789643 AGAGAGCTATGGAGAGAAATGAC 57.210 43.478 0.00 0.00 0.00 3.06
1412 1491 7.425606 AGACATGCTCGATTTTGTTTTAGTTT 58.574 30.769 0.00 0.00 0.00 2.66
1459 1567 6.412214 ACACAATTAACTTTACCGGCTCTAT 58.588 36.000 0.00 0.00 0.00 1.98
1460 1568 5.797051 ACACAATTAACTTTACCGGCTCTA 58.203 37.500 0.00 0.00 0.00 2.43
1461 1569 4.648651 ACACAATTAACTTTACCGGCTCT 58.351 39.130 0.00 0.00 0.00 4.09
1462 1570 6.073112 TGTTACACAATTAACTTTACCGGCTC 60.073 38.462 0.00 0.00 33.73 4.70
1483 1591 4.496673 CCGCGCCATAAATAGCTTTTGTTA 60.497 41.667 0.00 0.00 0.00 2.41
1537 1645 3.836146 CCACCAATATCCATGTCCATGT 58.164 45.455 6.53 0.00 37.11 3.21
1643 1751 4.251268 GCAACCGTGGTACTAGAAAGATT 58.749 43.478 0.00 0.00 0.00 2.40
1650 1758 2.372264 TCTAGGCAACCGTGGTACTAG 58.628 52.381 14.40 14.40 32.91 2.57
1653 1761 1.547372 TCTTCTAGGCAACCGTGGTAC 59.453 52.381 0.00 0.00 37.17 3.34
1655 1763 1.066143 CATCTTCTAGGCAACCGTGGT 60.066 52.381 0.00 0.00 37.17 4.16
1656 1764 1.656652 CATCTTCTAGGCAACCGTGG 58.343 55.000 0.00 0.00 37.17 4.94
1657 1765 1.009829 GCATCTTCTAGGCAACCGTG 58.990 55.000 0.00 0.00 34.20 4.94
1658 1766 0.613260 TGCATCTTCTAGGCAACCGT 59.387 50.000 0.00 0.00 43.03 4.83
1659 1767 3.458872 TGCATCTTCTAGGCAACCG 57.541 52.632 0.00 0.00 43.03 4.44
1723 1849 6.097839 AGCACATTAAATCAAATGATGAGGCT 59.902 34.615 3.73 0.00 42.53 4.58
1845 1972 1.028868 GGACATGTTGAGCTCCAGGC 61.029 60.000 12.15 0.00 42.19 4.85
1893 2020 2.279851 CGGTGTTGCTGTCGTCCA 60.280 61.111 0.00 0.00 0.00 4.02
1963 2090 2.108514 AGCGATCATGTTGCCACCG 61.109 57.895 0.00 0.00 38.03 4.94
2054 2181 3.049674 CGGTGCCAACGACTGCAT 61.050 61.111 0.00 0.00 40.07 3.96
2084 2223 3.965539 GATGAGCTGCCGCCTGTGT 62.966 63.158 0.00 0.00 36.60 3.72
2133 2272 1.613630 TGGAGAAGGCTCAGGGTCC 60.614 63.158 0.00 0.00 43.14 4.46
2169 2308 5.783875 AGCTACTAGGGTTTCCTTTCTACAA 59.216 40.000 0.00 0.00 41.56 2.41
2194 2333 4.517832 CACCCTAGTTTTGGTTTGGTCTAC 59.482 45.833 0.00 0.00 30.70 2.59
2195 2334 4.446600 CCACCCTAGTTTTGGTTTGGTCTA 60.447 45.833 0.00 0.00 30.70 2.59
2196 2335 3.562182 CACCCTAGTTTTGGTTTGGTCT 58.438 45.455 0.00 0.00 30.70 3.85
2197 2336 2.626266 CCACCCTAGTTTTGGTTTGGTC 59.374 50.000 0.00 0.00 30.70 4.02
2198 2337 2.245287 TCCACCCTAGTTTTGGTTTGGT 59.755 45.455 2.39 0.00 30.70 3.67
2199 2338 2.952116 TCCACCCTAGTTTTGGTTTGG 58.048 47.619 2.39 0.00 30.70 3.28
2201 2340 4.591498 GGAATTCCACCCTAGTTTTGGTTT 59.409 41.667 20.04 0.00 35.64 3.27
2203 2342 3.141272 TGGAATTCCACCCTAGTTTTGGT 59.859 43.478 23.63 0.00 42.01 3.67
2204 2343 3.773560 TGGAATTCCACCCTAGTTTTGG 58.226 45.455 23.63 0.00 42.01 3.28
2223 2362 6.329197 TCCCTCCAAATACTAATCCTAGTTGG 59.671 42.308 0.00 0.00 39.23 3.77
2224 2363 7.374975 TCCCTCCAAATACTAATCCTAGTTG 57.625 40.000 0.00 0.00 39.23 3.16
2228 2367 5.138996 TCCCTCCCTCCAAATACTAATCCTA 59.861 44.000 0.00 0.00 0.00 2.94
2232 2371 3.981375 GGTCCCTCCCTCCAAATACTAAT 59.019 47.826 0.00 0.00 0.00 1.73
2238 2377 0.327576 ATCGGTCCCTCCCTCCAAAT 60.328 55.000 0.00 0.00 0.00 2.32
2244 2383 2.040464 ATGCATCGGTCCCTCCCT 60.040 61.111 0.00 0.00 0.00 4.20
2278 2420 6.360370 ACAAGATCTACTTACTTGCTCCAA 57.640 37.500 0.00 0.00 42.93 3.53
2398 2540 0.242017 ACGGCACCTTCACGTAGTAC 59.758 55.000 0.00 0.00 41.61 2.73
2402 2544 1.870055 GAGGACGGCACCTTCACGTA 61.870 60.000 0.00 0.00 41.40 3.57
2403 2545 3.222354 GAGGACGGCACCTTCACGT 62.222 63.158 0.00 0.00 44.35 4.49
2404 2546 2.432628 GAGGACGGCACCTTCACG 60.433 66.667 0.00 0.00 40.73 4.35
2405 2547 1.668151 GTGAGGACGGCACCTTCAC 60.668 63.158 0.00 2.69 40.73 3.18
2406 2548 1.837051 AGTGAGGACGGCACCTTCA 60.837 57.895 0.00 0.00 40.73 3.02
2407 2549 1.374758 CAGTGAGGACGGCACCTTC 60.375 63.158 0.00 0.30 40.73 3.46
2409 2551 2.140792 AACAGTGAGGACGGCACCT 61.141 57.895 0.00 0.00 43.64 4.00
2410 2552 1.961277 CAACAGTGAGGACGGCACC 60.961 63.158 0.00 0.00 36.95 5.01
2411 2553 2.607892 GCAACAGTGAGGACGGCAC 61.608 63.158 0.00 0.00 36.53 5.01
2412 2554 2.280797 GCAACAGTGAGGACGGCA 60.281 61.111 0.00 0.00 0.00 5.69
2413 2555 3.050275 GGCAACAGTGAGGACGGC 61.050 66.667 0.00 0.00 0.00 5.68
2414 2556 2.358737 GGGCAACAGTGAGGACGG 60.359 66.667 0.00 0.00 39.74 4.79
2416 2558 2.358737 CGGGGCAACAGTGAGGAC 60.359 66.667 0.00 0.00 39.74 3.85
2417 2559 3.636231 CCGGGGCAACAGTGAGGA 61.636 66.667 0.00 0.00 39.74 3.71
2523 2665 1.320344 TGGAGTACCTAGCAGCACCG 61.320 60.000 0.00 0.00 37.04 4.94
2571 2716 3.261897 CCAAATCCACTACTCCAGTCAGT 59.738 47.826 0.00 0.00 34.26 3.41
2572 2717 3.369892 CCCAAATCCACTACTCCAGTCAG 60.370 52.174 0.00 0.00 34.26 3.51
2573 2718 2.571653 CCCAAATCCACTACTCCAGTCA 59.428 50.000 0.00 0.00 34.26 3.41
2574 2719 2.681097 GCCCAAATCCACTACTCCAGTC 60.681 54.545 0.00 0.00 34.26 3.51
2682 2827 3.610911 GTGTTTTGGGGATAGGAGACAG 58.389 50.000 0.00 0.00 0.00 3.51
2712 2857 2.743928 GGGAGTCAGTGCGGCTTG 60.744 66.667 0.00 0.00 0.00 4.01
2758 2903 5.502079 AGAGTGCTAAGTCTCTGTAGCTAA 58.498 41.667 0.00 0.00 42.67 3.09
2779 2924 2.354401 CCTCGCCCTCTTGCTGAGA 61.354 63.158 8.51 0.26 45.39 3.27
2780 2925 2.186384 CCTCGCCCTCTTGCTGAG 59.814 66.667 1.17 1.17 42.30 3.35
2781 2926 3.393970 CCCTCGCCCTCTTGCTGA 61.394 66.667 0.00 0.00 0.00 4.26
2782 2927 4.479993 CCCCTCGCCCTCTTGCTG 62.480 72.222 0.00 0.00 0.00 4.41
2784 2929 4.475135 GACCCCTCGCCCTCTTGC 62.475 72.222 0.00 0.00 0.00 4.01
2785 2930 2.873557 TAGGACCCCTCGCCCTCTTG 62.874 65.000 0.00 0.00 34.61 3.02
2841 2990 3.887621 ATAGGTGTCGTATGCTGTGTT 57.112 42.857 0.00 0.00 0.00 3.32
2842 2991 3.697542 TGTATAGGTGTCGTATGCTGTGT 59.302 43.478 0.00 0.00 0.00 3.72
2843 2992 4.042398 GTGTATAGGTGTCGTATGCTGTG 58.958 47.826 0.00 0.00 0.00 3.66
2844 2993 3.242969 CGTGTATAGGTGTCGTATGCTGT 60.243 47.826 0.00 0.00 0.00 4.40
2845 2994 3.297472 CGTGTATAGGTGTCGTATGCTG 58.703 50.000 0.00 0.00 0.00 4.41
2846 2995 2.287427 GCGTGTATAGGTGTCGTATGCT 60.287 50.000 0.00 0.00 0.00 3.79
2847 2996 2.049228 GCGTGTATAGGTGTCGTATGC 58.951 52.381 0.00 0.00 0.00 3.14
2848 2997 3.343380 TGCGTGTATAGGTGTCGTATG 57.657 47.619 0.00 0.00 0.00 2.39
2849 2998 4.295870 CATTGCGTGTATAGGTGTCGTAT 58.704 43.478 0.00 0.00 0.00 3.06
2850 2999 3.697982 CATTGCGTGTATAGGTGTCGTA 58.302 45.455 0.00 0.00 0.00 3.43
2961 3123 1.087202 GCAATGGCCACATGCACATG 61.087 55.000 30.70 9.06 43.89 3.21
2962 3124 1.219664 GCAATGGCCACATGCACAT 59.780 52.632 30.70 2.93 43.89 3.21
3007 3169 2.282462 AAGTGCCTGCCGGAAAGG 60.282 61.111 17.23 17.23 44.97 3.11
3040 3202 1.093159 CCAAGGAACAGAGAGCATGC 58.907 55.000 10.51 10.51 0.00 4.06
3041 3203 2.289882 TGACCAAGGAACAGAGAGCATG 60.290 50.000 0.00 0.00 0.00 4.06
3042 3204 1.980765 TGACCAAGGAACAGAGAGCAT 59.019 47.619 0.00 0.00 0.00 3.79
3043 3205 1.070758 GTGACCAAGGAACAGAGAGCA 59.929 52.381 0.00 0.00 0.00 4.26
3044 3206 1.070758 TGTGACCAAGGAACAGAGAGC 59.929 52.381 0.00 0.00 0.00 4.09
3045 3207 2.869636 GCTGTGACCAAGGAACAGAGAG 60.870 54.545 22.13 8.16 43.22 3.20
3046 3208 1.070758 GCTGTGACCAAGGAACAGAGA 59.929 52.381 22.13 0.46 43.22 3.10
3127 3289 3.504134 GCACGAGCAATAGATCCTCTCTA 59.496 47.826 0.00 0.00 39.68 2.43


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

AutoCloner maintained by Alex Coulton.