Multiple sequence alignment - TraesCS4B01G116700

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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 TraesCS4B01G116700 chr4B 100.000 2375 0 0 742 3116 134812818 134815192 0.000000e+00 4386.0
1 TraesCS4B01G116700 chr4B 100.000 480 0 0 1 480 134812077 134812556 0.000000e+00 887.0
2 TraesCS4B01G116700 chr4B 87.023 131 8 2 1367 1488 590429248 590429118 4.190000e-29 139.0
3 TraesCS4B01G116700 chr4D 92.649 1714 68 17 775 2463 95278304 95279984 0.000000e+00 2414.0
4 TraesCS4B01G116700 chr4D 91.875 480 16 7 1 480 95277809 95278265 0.000000e+00 649.0
5 TraesCS4B01G116700 chr4D 87.500 464 24 13 2686 3116 95280435 95280897 3.590000e-139 505.0
6 TraesCS4B01G116700 chr4D 86.555 119 16 0 2516 2634 95279998 95280116 7.010000e-27 132.0
7 TraesCS4B01G116700 chr4A 89.822 1906 100 28 784 2657 484732943 484731100 0.000000e+00 2359.0
8 TraesCS4B01G116700 chr4A 86.134 476 23 15 2683 3116 484731037 484730563 1.010000e-129 473.0
9 TraesCS4B01G116700 chr4A 85.512 283 24 10 1 271 484733380 484733103 2.370000e-71 279.0
10 TraesCS4B01G116700 chr4A 87.786 131 7 2 1367 1488 645308493 645308623 9.010000e-31 145.0
11 TraesCS4B01G116700 chr4A 93.478 92 5 1 371 461 484733077 484732986 5.420000e-28 135.0
12 TraesCS4B01G116700 chr2D 91.086 359 20 7 1249 1598 85755798 85756153 2.810000e-130 475.0
13 TraesCS4B01G116700 chr3B 100.000 70 0 0 2652 2721 417289465 417289534 2.520000e-26 130.0
14 TraesCS4B01G116700 chr3D 79.310 145 26 2 2520 2660 589430438 589430294 7.110000e-17 99.0
15 TraesCS4B01G116700 chr2B 95.745 47 2 0 1432 1478 22379432 22379386 3.330000e-10 76.8


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 TraesCS4B01G116700 chr4B 134812077 134815192 3115 False 2636.5 4386 100.00000 1 3116 2 chr4B.!!$F1 3115
1 TraesCS4B01G116700 chr4D 95277809 95280897 3088 False 925.0 2414 89.64475 1 3116 4 chr4D.!!$F1 3115
2 TraesCS4B01G116700 chr4A 484730563 484733380 2817 True 811.5 2359 88.73650 1 3116 4 chr4A.!!$R1 3115

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
420 458 0.890542 ATGCCATGTCACGCACACTT 60.891 50.0 0.0 0.0 38.04 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 2365 0.107214 GGCCATGCACTAACTAGGCA 60.107 55.0 0.0 0.0 43.72 4.75 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
106 107 2.161855 CTGGCTATTGTGCAAGGTGAA 58.838 47.619 0.00 0.00 30.62 3.18
130 131 2.761392 GCAATAACATGCATGCTCGA 57.239 45.000 26.53 9.58 45.70 4.04
131 132 3.069074 GCAATAACATGCATGCTCGAA 57.931 42.857 26.53 7.95 45.70 3.71
132 133 3.437428 GCAATAACATGCATGCTCGAAA 58.563 40.909 26.53 6.17 45.70 3.46
133 134 3.858812 GCAATAACATGCATGCTCGAAAA 59.141 39.130 26.53 0.00 45.70 2.29
134 135 4.326817 GCAATAACATGCATGCTCGAAAAA 59.673 37.500 26.53 0.00 45.70 1.94
258 288 4.001652 CACTGTACGAGTCTACTCCTCAA 58.998 47.826 4.58 0.00 39.79 3.02
285 315 6.042777 TCAACAAGATGGAAGCTAGTATTCG 58.957 40.000 0.00 0.00 0.00 3.34
309 339 3.723364 GATGTGCGTGCGTCATGCC 62.723 63.158 17.44 11.28 44.81 4.40
419 457 1.302752 ATGCCATGTCACGCACACT 60.303 52.632 0.00 0.00 38.04 3.55
420 458 0.890542 ATGCCATGTCACGCACACTT 60.891 50.000 0.00 0.00 38.04 3.16
430 469 1.803922 CGCACACTTGGCATGCATG 60.804 57.895 22.70 22.70 39.39 4.06
465 511 3.650070 TGAAACACACAAGCAAACACA 57.350 38.095 0.00 0.00 0.00 3.72
466 512 3.982475 TGAAACACACAAGCAAACACAA 58.018 36.364 0.00 0.00 0.00 3.33
467 513 3.738282 TGAAACACACAAGCAAACACAAC 59.262 39.130 0.00 0.00 0.00 3.32
763 809 2.280552 GCACTACAGGGTGGGTCGA 61.281 63.158 0.00 0.00 37.65 4.20
771 817 2.516930 GGTGGGTCGATGGCATGG 60.517 66.667 3.81 3.19 0.00 3.66
772 818 3.211963 GTGGGTCGATGGCATGGC 61.212 66.667 13.29 13.29 0.00 4.40
773 819 3.726144 TGGGTCGATGGCATGGCA 61.726 61.111 25.52 25.52 0.00 4.92
774 820 2.203394 GGGTCGATGGCATGGCAT 60.203 61.111 32.65 32.65 0.00 4.40
775 821 2.558286 GGGTCGATGGCATGGCATG 61.558 63.158 36.49 26.36 0.00 4.06
776 822 2.558286 GGTCGATGGCATGGCATGG 61.558 63.158 36.49 33.22 0.00 3.66
830 876 2.286359 GGTACACGGACAAACGGTTTTC 60.286 50.000 2.79 5.49 38.39 2.29
874 927 3.593442 ATCACAGCCTAGCTAGAGAGT 57.407 47.619 22.70 13.27 36.40 3.24
927 985 3.497405 GGAATGATGAGCAAGCTATCCCA 60.497 47.826 0.00 0.00 0.00 4.37
1075 1133 1.660607 CACACTCGCATAGTCGCATTT 59.339 47.619 0.00 0.00 35.76 2.32
1076 1134 1.660607 ACACTCGCATAGTCGCATTTG 59.339 47.619 0.00 0.00 35.76 2.32
1077 1135 0.652592 ACTCGCATAGTCGCATTTGC 59.347 50.000 0.00 0.00 30.33 3.68
1078 1136 0.652071 CTCGCATAGTCGCATTTGCA 59.348 50.000 3.13 0.00 42.21 4.08
1079 1137 0.373370 TCGCATAGTCGCATTTGCAC 59.627 50.000 3.13 0.82 42.21 4.57
1080 1138 0.096802 CGCATAGTCGCATTTGCACA 59.903 50.000 3.13 0.00 42.21 4.57
1081 1139 1.538276 GCATAGTCGCATTTGCACAC 58.462 50.000 3.13 0.00 42.21 3.82
1082 1140 1.135717 GCATAGTCGCATTTGCACACA 60.136 47.619 3.13 0.00 42.21 3.72
1083 1141 2.508867 CATAGTCGCATTTGCACACAC 58.491 47.619 3.13 0.00 42.21 3.82
1084 1142 0.871722 TAGTCGCATTTGCACACACC 59.128 50.000 3.13 0.00 42.21 4.16
1085 1143 1.100463 AGTCGCATTTGCACACACCA 61.100 50.000 3.13 0.00 42.21 4.17
1086 1144 0.934436 GTCGCATTTGCACACACCAC 60.934 55.000 3.13 0.00 42.21 4.16
1087 1145 1.661197 CGCATTTGCACACACCACC 60.661 57.895 3.13 0.00 42.21 4.61
1088 1146 1.661197 GCATTTGCACACACCACCG 60.661 57.895 0.00 0.00 41.59 4.94
1089 1147 1.732917 CATTTGCACACACCACCGT 59.267 52.632 0.00 0.00 0.00 4.83
1116 1174 3.036091 CAATCAATCCCATTCCCAGCTT 58.964 45.455 0.00 0.00 0.00 3.74
1123 1181 2.753043 ATTCCCAGCTTGCCTGCG 60.753 61.111 0.00 0.00 40.36 5.18
1172 1233 3.001406 ACCCCTCCAGCGTACACC 61.001 66.667 0.00 0.00 0.00 4.16
1224 1285 8.484575 TGAACTATATATCCTAGCTAGCGTACT 58.515 37.037 15.74 1.26 0.00 2.73
1393 1454 0.987294 CCTTCCTCAAGCCTTCCTCA 59.013 55.000 0.00 0.00 0.00 3.86
1403 1464 2.105466 CCTTCCTCAGCGAGCAAGC 61.105 63.158 0.00 0.00 26.94 4.01
1441 1511 2.683933 TCGTCCAGCCTCTTCCCC 60.684 66.667 0.00 0.00 0.00 4.81
1459 1529 4.361971 TCGTCCTCCTCCACCGCT 62.362 66.667 0.00 0.00 0.00 5.52
1528 1598 4.089239 TACCATGGCTTCGGCGCA 62.089 61.111 13.04 0.00 42.91 6.09
1582 1652 3.072468 TCCGCCAAGGAGGTACCG 61.072 66.667 6.18 0.00 45.98 4.02
1583 1653 4.157120 CCGCCAAGGAGGTACCGG 62.157 72.222 6.18 0.00 45.00 5.28
1584 1654 4.832608 CGCCAAGGAGGTACCGGC 62.833 72.222 15.67 15.67 44.74 6.13
1585 1655 3.400054 GCCAAGGAGGTACCGGCT 61.400 66.667 17.73 0.00 44.74 5.52
1586 1656 2.584608 CCAAGGAGGTACCGGCTG 59.415 66.667 6.18 2.92 44.74 4.85
1587 1657 2.291043 CCAAGGAGGTACCGGCTGT 61.291 63.158 6.18 0.00 44.74 4.40
1588 1658 1.079127 CAAGGAGGTACCGGCTGTG 60.079 63.158 6.18 0.00 44.74 3.66
1589 1659 1.229082 AAGGAGGTACCGGCTGTGA 60.229 57.895 6.18 0.00 44.74 3.58
1678 1760 2.086869 GAGAACAAAGCAGCTATGGCA 58.913 47.619 3.10 0.00 41.70 4.92
1686 1768 2.203126 AGCTATGGCAGAAGCGGC 60.203 61.111 16.23 1.36 43.63 6.53
1714 1796 3.702048 GACGTGGGGCTGGCAGTA 61.702 66.667 17.16 0.00 0.00 2.74
1780 1862 1.078143 GCAGATGGTGGTGGAGACC 60.078 63.158 0.00 0.00 43.48 3.85
1840 1922 2.659016 CTGCTCGCCCTCAACTCA 59.341 61.111 0.00 0.00 0.00 3.41
1943 2025 2.238144 TCGTACCACTACCAGCTCTAGT 59.762 50.000 0.00 0.00 0.00 2.57
1944 2026 2.613133 CGTACCACTACCAGCTCTAGTC 59.387 54.545 0.00 0.00 0.00 2.59
1945 2027 3.682155 CGTACCACTACCAGCTCTAGTCT 60.682 52.174 0.00 0.00 0.00 3.24
1946 2028 4.442612 CGTACCACTACCAGCTCTAGTCTA 60.443 50.000 0.00 0.00 0.00 2.59
1947 2029 4.799715 ACCACTACCAGCTCTAGTCTAT 57.200 45.455 0.00 0.00 0.00 1.98
1958 2044 4.761739 AGCTCTAGTCTATCTAGCAAGCAG 59.238 45.833 13.82 2.64 43.31 4.24
2254 2340 8.528917 TTAGTGCTTAAGTATATGTATTGCGG 57.471 34.615 4.02 0.00 0.00 5.69
2264 2350 3.637911 ATGTATTGCGGGGAGTTTGTA 57.362 42.857 0.00 0.00 0.00 2.41
2278 2364 3.728845 AGTTTGTACTAGTGTGTGCCTG 58.271 45.455 5.39 0.00 31.21 4.85
2279 2365 3.134081 AGTTTGTACTAGTGTGTGCCTGT 59.866 43.478 5.39 0.00 31.21 4.00
2280 2366 2.812358 TGTACTAGTGTGTGCCTGTG 57.188 50.000 5.39 0.00 0.00 3.66
2281 2367 1.270094 TGTACTAGTGTGTGCCTGTGC 60.270 52.381 5.39 0.00 38.26 4.57
2282 2368 0.320374 TACTAGTGTGTGCCTGTGCC 59.680 55.000 5.39 0.00 36.33 5.01
2283 2369 1.372683 CTAGTGTGTGCCTGTGCCT 59.627 57.895 0.00 0.00 36.33 4.75
2301 2387 2.565841 CCTAGTTAGTGCATGGCCTTC 58.434 52.381 3.32 0.00 0.00 3.46
2336 2422 4.331622 CATGCATGGACAGGTGCT 57.668 55.556 19.40 0.00 41.78 4.40
2341 2427 1.905894 TGCATGGACAGGTGCTACTAA 59.094 47.619 0.00 0.00 41.78 2.24
2343 2429 2.678336 GCATGGACAGGTGCTACTAAAC 59.322 50.000 0.00 0.00 38.30 2.01
2344 2430 3.270877 CATGGACAGGTGCTACTAAACC 58.729 50.000 0.00 0.00 36.66 3.27
2365 2451 5.262588 CCAATTGGTAGGGTTTGCTAATC 57.737 43.478 16.90 0.00 0.00 1.75
2374 2460 2.749621 GGGTTTGCTAATCACAGAGTGG 59.250 50.000 0.00 0.00 33.87 4.00
2383 2469 6.014070 TGCTAATCACAGAGTGGGTAACTAAA 60.014 38.462 0.00 0.00 40.07 1.85
2395 2481 7.762382 AGTGGGTAACTAAACTATGTACGTAC 58.238 38.462 18.90 18.90 37.36 3.67
2398 2484 6.905609 GGGTAACTAAACTATGTACGTACGTC 59.094 42.308 26.53 16.55 0.00 4.34
2404 2499 5.869753 AACTATGTACGTACGTCAAGTCT 57.130 39.130 26.53 9.94 0.00 3.24
2413 2508 2.708386 ACGTCAAGTCTGAGTGTAGC 57.292 50.000 0.00 0.00 30.14 3.58
2431 2526 8.263940 AGTGTAGCGTTTTGTGTTATATGAAT 57.736 30.769 0.00 0.00 0.00 2.57
2432 2527 8.726988 AGTGTAGCGTTTTGTGTTATATGAATT 58.273 29.630 0.00 0.00 0.00 2.17
2466 2561 4.960938 TGCTACTGAATGAGACTGTGTTT 58.039 39.130 0.00 0.00 0.00 2.83
2469 2564 6.423905 TGCTACTGAATGAGACTGTGTTTTAC 59.576 38.462 0.00 0.00 0.00 2.01
2470 2565 6.647067 GCTACTGAATGAGACTGTGTTTTACT 59.353 38.462 0.00 0.00 0.00 2.24
2471 2566 7.813148 GCTACTGAATGAGACTGTGTTTTACTA 59.187 37.037 0.00 0.00 0.00 1.82
2472 2567 9.347934 CTACTGAATGAGACTGTGTTTTACTAG 57.652 37.037 0.00 0.00 0.00 2.57
2473 2568 7.952671 ACTGAATGAGACTGTGTTTTACTAGA 58.047 34.615 0.00 0.00 0.00 2.43
2474 2569 8.589338 ACTGAATGAGACTGTGTTTTACTAGAT 58.411 33.333 0.00 0.00 0.00 1.98
2475 2570 9.429359 CTGAATGAGACTGTGTTTTACTAGATT 57.571 33.333 0.00 0.00 0.00 2.40
2476 2571 9.424319 TGAATGAGACTGTGTTTTACTAGATTC 57.576 33.333 0.00 0.00 0.00 2.52
2477 2572 9.424319 GAATGAGACTGTGTTTTACTAGATTCA 57.576 33.333 0.00 0.00 0.00 2.57
2478 2573 9.778741 AATGAGACTGTGTTTTACTAGATTCAA 57.221 29.630 0.00 0.00 0.00 2.69
2479 2574 8.818141 TGAGACTGTGTTTTACTAGATTCAAG 57.182 34.615 0.00 0.00 0.00 3.02
2480 2575 8.421784 TGAGACTGTGTTTTACTAGATTCAAGT 58.578 33.333 0.00 0.00 0.00 3.16
2481 2576 8.594881 AGACTGTGTTTTACTAGATTCAAGTG 57.405 34.615 0.00 0.00 0.00 3.16
2492 2587 7.527084 ACTAGATTCAAGTGAAAATAGCGAC 57.473 36.000 0.00 0.00 37.61 5.19
2493 2588 5.803020 AGATTCAAGTGAAAATAGCGACC 57.197 39.130 0.00 0.00 37.61 4.79
2494 2589 5.491982 AGATTCAAGTGAAAATAGCGACCT 58.508 37.500 0.00 0.00 37.61 3.85
2495 2590 5.352569 AGATTCAAGTGAAAATAGCGACCTG 59.647 40.000 0.00 0.00 37.61 4.00
2496 2591 2.742053 TCAAGTGAAAATAGCGACCTGC 59.258 45.455 0.00 0.00 46.98 4.85
2507 2602 0.784778 GCGACCTGCGATATGTAAGC 59.215 55.000 0.00 0.00 44.57 3.09
2508 2603 1.419374 CGACCTGCGATATGTAAGCC 58.581 55.000 0.00 0.00 44.57 4.35
2509 2604 1.419374 GACCTGCGATATGTAAGCCG 58.581 55.000 0.00 0.00 0.00 5.52
2510 2605 0.750850 ACCTGCGATATGTAAGCCGT 59.249 50.000 0.00 0.00 0.00 5.68
2511 2606 1.269621 ACCTGCGATATGTAAGCCGTC 60.270 52.381 0.00 0.00 0.00 4.79
2512 2607 1.000163 CCTGCGATATGTAAGCCGTCT 60.000 52.381 0.00 0.00 0.00 4.18
2513 2608 2.054363 CTGCGATATGTAAGCCGTCTG 58.946 52.381 0.00 0.00 0.00 3.51
2514 2609 1.679153 TGCGATATGTAAGCCGTCTGA 59.321 47.619 0.00 0.00 0.00 3.27
2517 2612 3.366476 GCGATATGTAAGCCGTCTGAGAT 60.366 47.826 0.00 0.00 0.00 2.75
2559 2654 9.832445 GTCAATTATCTGGACCATTAGACTAAA 57.168 33.333 0.00 0.00 0.00 1.85
2565 2660 7.451731 TCTGGACCATTAGACTAAAATCCAT 57.548 36.000 18.61 0.00 34.59 3.41
2570 2665 5.163195 ACCATTAGACTAAAATCCATCGCCT 60.163 40.000 0.00 0.00 0.00 5.52
2578 2673 4.456280 AAAATCCATCGCCTTCCTTTTC 57.544 40.909 0.00 0.00 0.00 2.29
2579 2674 2.058593 ATCCATCGCCTTCCTTTTCC 57.941 50.000 0.00 0.00 0.00 3.13
2583 2678 2.171003 CATCGCCTTCCTTTTCCCTTT 58.829 47.619 0.00 0.00 0.00 3.11
2585 2680 2.235891 TCGCCTTCCTTTTCCCTTTTC 58.764 47.619 0.00 0.00 0.00 2.29
2590 2685 2.579410 TCCTTTTCCCTTTTCCCTCG 57.421 50.000 0.00 0.00 0.00 4.63
2625 2720 3.052944 CCAACCATTCCTCCTCCCATAAA 60.053 47.826 0.00 0.00 0.00 1.40
2634 2729 4.130118 CCTCCTCCCATAAAATCGACTTG 58.870 47.826 0.00 0.00 0.00 3.16
2635 2730 3.541632 TCCTCCCATAAAATCGACTTGC 58.458 45.455 0.00 0.00 0.00 4.01
2636 2731 2.618709 CCTCCCATAAAATCGACTTGCC 59.381 50.000 0.00 0.00 0.00 4.52
2637 2732 3.545703 CTCCCATAAAATCGACTTGCCT 58.454 45.455 0.00 0.00 0.00 4.75
2643 3037 7.776030 TCCCATAAAATCGACTTGCCTAAATTA 59.224 33.333 0.00 0.00 0.00 1.40
2698 3130 5.945155 TGTGAAGAAATTAACATTACCGGC 58.055 37.500 0.00 0.00 0.00 6.13
2700 3132 4.399934 TGAAGAAATTAACATTACCGGCCC 59.600 41.667 0.00 0.00 0.00 5.80
2718 3150 2.697654 CCCTCTCTGAAACAGAAGCAG 58.302 52.381 0.00 0.00 40.18 4.24
2724 3156 2.551032 TCTGAAACAGAAGCAGTGCATG 59.449 45.455 19.20 14.96 37.57 4.06
2754 3187 7.926018 TCTTTTCAGGTTTTTCTGGCTTAATTC 59.074 33.333 0.00 0.00 35.58 2.17
2755 3188 5.722021 TCAGGTTTTTCTGGCTTAATTCC 57.278 39.130 0.00 0.00 35.58 3.01
2764 3198 6.569179 TTCTGGCTTAATTCCTTACACAAC 57.431 37.500 0.00 0.00 0.00 3.32
2765 3199 5.626142 TCTGGCTTAATTCCTTACACAACA 58.374 37.500 0.00 0.00 0.00 3.33
2766 3200 6.065374 TCTGGCTTAATTCCTTACACAACAA 58.935 36.000 0.00 0.00 0.00 2.83
2767 3201 6.547880 TCTGGCTTAATTCCTTACACAACAAA 59.452 34.615 0.00 0.00 0.00 2.83
2768 3202 7.068839 TCTGGCTTAATTCCTTACACAACAAAA 59.931 33.333 0.00 0.00 0.00 2.44
2770 3204 7.492994 TGGCTTAATTCCTTACACAACAAAAAC 59.507 33.333 0.00 0.00 0.00 2.43
2771 3205 7.492994 GGCTTAATTCCTTACACAACAAAAACA 59.507 33.333 0.00 0.00 0.00 2.83
2804 3257 2.484264 CCAAACTTGGTACTGTAGCAGC 59.516 50.000 17.89 0.00 43.43 5.25
2810 3263 1.201647 TGGTACTGTAGCAGCGAAGTC 59.798 52.381 15.14 0.00 34.37 3.01
2820 3276 1.849219 GCAGCGAAGTCGAAGTAGATG 59.151 52.381 4.59 0.00 43.02 2.90
2842 3298 3.895025 CAGGGTGCATCTGGAACG 58.105 61.111 10.94 0.00 0.00 3.95
2843 3299 2.045926 AGGGTGCATCTGGAACGC 60.046 61.111 0.00 0.00 0.00 4.84
2844 3300 2.359850 GGGTGCATCTGGAACGCA 60.360 61.111 0.00 0.00 0.00 5.24
2944 3417 0.399454 CCAGAGGCTCCCCATACATG 59.601 60.000 11.71 0.00 0.00 3.21
2965 3438 2.838736 CCTAGCTTTCTGTGTGTGTGT 58.161 47.619 0.00 0.00 0.00 3.72
3044 3521 1.637553 ACTGTTTGGGCTCTGATCCAT 59.362 47.619 0.00 0.00 32.48 3.41
3048 3525 0.624206 TTGGGCTCTGATCCATCCCA 60.624 55.000 7.72 7.72 44.64 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.280205 GCGGGGATCGAACATAAGAAATTATAT 59.720 37.037 0.00 0.00 42.43 0.86
12 13 4.753107 GCGGGGATCGAACATAAGAAATTA 59.247 41.667 0.00 0.00 42.43 1.40
131 132 7.599630 AATTTCGAGCATGCATGTTATTTTT 57.400 28.000 26.79 10.85 0.00 1.94
132 133 7.599630 AAATTTCGAGCATGCATGTTATTTT 57.400 28.000 26.79 14.42 0.00 1.82
133 134 7.599630 AAAATTTCGAGCATGCATGTTATTT 57.400 28.000 26.79 19.06 0.00 1.40
134 135 8.190122 TCTAAAATTTCGAGCATGCATGTTATT 58.810 29.630 26.79 14.64 0.00 1.40
135 136 7.706159 TCTAAAATTTCGAGCATGCATGTTAT 58.294 30.769 26.79 13.97 0.00 1.89
136 137 7.082700 TCTAAAATTTCGAGCATGCATGTTA 57.917 32.000 26.79 13.08 0.00 2.41
137 138 5.953183 TCTAAAATTTCGAGCATGCATGTT 58.047 33.333 26.79 22.13 0.00 2.71
138 139 5.565592 TCTAAAATTTCGAGCATGCATGT 57.434 34.783 26.79 14.24 0.00 3.21
139 140 6.874297 TTTCTAAAATTTCGAGCATGCATG 57.126 33.333 22.70 22.70 0.00 4.06
258 288 8.814038 AATACTAGCTTCCATCTTGTTGATTT 57.186 30.769 0.00 0.00 32.05 2.17
444 483 3.312828 TGTGTTTGCTTGTGTGTTTCAC 58.687 40.909 0.00 0.00 46.31 3.18
455 494 3.812053 TGTTTTTGCAGTTGTGTTTGCTT 59.188 34.783 0.00 0.00 40.87 3.91
741 787 1.613630 CCCACCCTGTAGTGCCTCT 60.614 63.158 0.00 0.00 36.38 3.69
742 788 1.900545 GACCCACCCTGTAGTGCCTC 61.901 65.000 0.00 0.00 36.38 4.70
743 789 1.918800 GACCCACCCTGTAGTGCCT 60.919 63.158 0.00 0.00 36.38 4.75
744 790 2.669240 GACCCACCCTGTAGTGCC 59.331 66.667 0.00 0.00 36.38 5.01
745 791 1.614241 ATCGACCCACCCTGTAGTGC 61.614 60.000 0.00 0.00 36.38 4.40
746 792 0.175760 CATCGACCCACCCTGTAGTG 59.824 60.000 0.00 0.00 37.51 2.74
747 793 0.976073 CCATCGACCCACCCTGTAGT 60.976 60.000 0.00 0.00 0.00 2.73
748 794 1.823295 CCATCGACCCACCCTGTAG 59.177 63.158 0.00 0.00 0.00 2.74
749 795 2.363975 GCCATCGACCCACCCTGTA 61.364 63.158 0.00 0.00 0.00 2.74
750 796 3.717294 GCCATCGACCCACCCTGT 61.717 66.667 0.00 0.00 0.00 4.00
753 799 2.516930 CATGCCATCGACCCACCC 60.517 66.667 0.00 0.00 0.00 4.61
763 809 3.147132 CATGCCATGCCATGCCAT 58.853 55.556 3.39 0.00 36.52 4.40
772 818 0.754217 AGGTTGCTAGGCATGCCATG 60.754 55.000 37.18 27.97 38.76 3.66
773 819 0.466922 GAGGTTGCTAGGCATGCCAT 60.467 55.000 37.18 23.86 38.76 4.40
774 820 1.077501 GAGGTTGCTAGGCATGCCA 60.078 57.895 37.18 21.91 38.76 4.92
775 821 0.394899 AAGAGGTTGCTAGGCATGCC 60.395 55.000 30.12 30.12 38.76 4.40
776 822 1.020437 GAAGAGGTTGCTAGGCATGC 58.980 55.000 9.90 9.90 38.76 4.06
777 823 1.293924 CGAAGAGGTTGCTAGGCATG 58.706 55.000 0.00 0.00 38.76 4.06
778 824 0.179000 CCGAAGAGGTTGCTAGGCAT 59.821 55.000 0.00 0.00 38.76 4.40
779 825 1.596934 CCGAAGAGGTTGCTAGGCA 59.403 57.895 0.00 0.00 36.47 4.75
780 826 1.815840 GCCGAAGAGGTTGCTAGGC 60.816 63.158 0.00 0.00 43.70 3.93
781 827 1.153349 GGCCGAAGAGGTTGCTAGG 60.153 63.158 0.00 0.00 43.70 3.02
782 828 0.179097 GAGGCCGAAGAGGTTGCTAG 60.179 60.000 0.00 0.00 43.70 3.42
852 905 4.285863 ACTCTCTAGCTAGGCTGTGATTT 58.714 43.478 20.58 0.75 40.10 2.17
853 906 3.909732 ACTCTCTAGCTAGGCTGTGATT 58.090 45.455 20.58 3.94 40.10 2.57
874 927 3.773418 TTTCCATTGACCTTGACCGTA 57.227 42.857 0.00 0.00 0.00 4.02
927 985 0.611896 GGTTTAGCTGGGCCATGTGT 60.612 55.000 6.72 0.00 0.00 3.72
1077 1135 3.935872 CGTGCACGGTGGTGTGTG 61.936 66.667 31.15 0.00 46.13 3.82
1082 1140 3.353836 GATTGCGTGCACGGTGGT 61.354 61.111 37.47 10.58 40.23 4.16
1083 1141 2.198906 ATTGATTGCGTGCACGGTGG 62.199 55.000 37.47 13.19 40.23 4.61
1084 1142 0.794229 GATTGATTGCGTGCACGGTG 60.794 55.000 37.47 13.57 40.23 4.94
1085 1143 1.501741 GATTGATTGCGTGCACGGT 59.498 52.632 37.47 5.74 40.23 4.83
1086 1144 1.226379 GGATTGATTGCGTGCACGG 60.226 57.895 37.47 20.93 40.23 4.94
1087 1145 1.226379 GGGATTGATTGCGTGCACG 60.226 57.895 34.01 34.01 43.27 5.34
1088 1146 0.457035 ATGGGATTGATTGCGTGCAC 59.543 50.000 6.82 6.82 0.00 4.57
1089 1147 1.134753 GAATGGGATTGATTGCGTGCA 59.865 47.619 0.00 0.00 0.00 4.57
1172 1233 4.554363 CTGCGAGGCTACGTCGGG 62.554 72.222 11.10 0.00 41.21 5.14
1441 1511 3.827898 GCGGTGGAGGAGGACGAG 61.828 72.222 0.00 0.00 0.00 4.18
1459 1529 0.895530 CGTAGCTGGTGGAGAAGGAA 59.104 55.000 0.00 0.00 0.00 3.36
1714 1796 0.677414 GGTCCGACGAGTCCTTCTCT 60.677 60.000 0.00 0.00 40.75 3.10
1796 1878 2.434884 CATGCTGCGGAGGTCGTT 60.435 61.111 5.93 0.00 41.72 3.85
1916 1998 0.452987 TGGTAGTGGTACGACGATGC 59.547 55.000 0.00 0.00 0.00 3.91
1965 2051 0.749818 CTCGAGACCTCAGCTGGCTA 60.750 60.000 15.13 0.00 0.00 3.93
2239 2325 5.163237 ACAAACTCCCCGCAATACATATACT 60.163 40.000 0.00 0.00 0.00 2.12
2240 2326 5.061179 ACAAACTCCCCGCAATACATATAC 58.939 41.667 0.00 0.00 0.00 1.47
2241 2327 5.298989 ACAAACTCCCCGCAATACATATA 57.701 39.130 0.00 0.00 0.00 0.86
2242 2328 4.164843 ACAAACTCCCCGCAATACATAT 57.835 40.909 0.00 0.00 0.00 1.78
2254 2340 3.064931 GCACACACTAGTACAAACTCCC 58.935 50.000 0.00 0.00 37.15 4.30
2264 2350 1.071471 GGCACAGGCACACACTAGT 59.929 57.895 0.00 0.00 43.71 2.57
2278 2364 1.017387 GCCATGCACTAACTAGGCAC 58.983 55.000 0.00 0.00 40.83 5.01
2279 2365 0.107214 GGCCATGCACTAACTAGGCA 60.107 55.000 0.00 0.00 43.72 4.75
2280 2366 0.181350 AGGCCATGCACTAACTAGGC 59.819 55.000 5.01 0.00 41.29 3.93
2281 2367 2.565841 GAAGGCCATGCACTAACTAGG 58.434 52.381 5.01 0.00 0.00 3.02
2282 2368 2.205074 CGAAGGCCATGCACTAACTAG 58.795 52.381 5.01 0.00 0.00 2.57
2283 2369 1.134521 CCGAAGGCCATGCACTAACTA 60.135 52.381 5.01 0.00 46.14 2.24
2301 2387 1.384525 TGGACCTTCACACAAAACCG 58.615 50.000 0.00 0.00 0.00 4.44
2343 2429 4.709397 TGATTAGCAAACCCTACCAATTGG 59.291 41.667 23.31 23.31 42.17 3.16
2344 2430 5.184864 TGTGATTAGCAAACCCTACCAATTG 59.815 40.000 0.00 0.00 0.00 2.32
2365 2451 6.698380 ACATAGTTTAGTTACCCACTCTGTG 58.302 40.000 0.00 0.00 36.88 3.66
2374 2460 7.461107 TGACGTACGTACATAGTTTAGTTACC 58.539 38.462 22.87 2.82 0.00 2.85
2383 2469 4.931601 TCAGACTTGACGTACGTACATAGT 59.068 41.667 22.87 19.94 0.00 2.12
2395 2481 1.069159 ACGCTACACTCAGACTTGACG 60.069 52.381 0.00 0.00 0.00 4.35
2398 2484 3.555956 ACAAAACGCTACACTCAGACTTG 59.444 43.478 0.00 0.00 0.00 3.16
2404 2499 6.869388 TCATATAACACAAAACGCTACACTCA 59.131 34.615 0.00 0.00 0.00 3.41
2413 2508 8.964420 ACAAGGAATTCATATAACACAAAACG 57.036 30.769 7.93 0.00 0.00 3.60
2431 2526 6.995686 TCATTCAGTAGCAAAGTTACAAGGAA 59.004 34.615 0.00 0.00 0.00 3.36
2432 2527 6.530120 TCATTCAGTAGCAAAGTTACAAGGA 58.470 36.000 0.00 0.00 0.00 3.36
2466 2561 9.084164 GTCGCTATTTTCACTTGAATCTAGTAA 57.916 33.333 0.00 0.00 33.54 2.24
2469 2564 6.758886 AGGTCGCTATTTTCACTTGAATCTAG 59.241 38.462 0.00 0.00 33.54 2.43
2470 2565 6.535150 CAGGTCGCTATTTTCACTTGAATCTA 59.465 38.462 0.00 0.00 33.54 1.98
2471 2566 5.352569 CAGGTCGCTATTTTCACTTGAATCT 59.647 40.000 0.00 0.00 33.54 2.40
2472 2567 5.563842 CAGGTCGCTATTTTCACTTGAATC 58.436 41.667 0.00 0.00 33.54 2.52
2473 2568 4.142600 GCAGGTCGCTATTTTCACTTGAAT 60.143 41.667 0.00 0.00 37.77 2.57
2474 2569 3.188460 GCAGGTCGCTATTTTCACTTGAA 59.812 43.478 0.00 0.00 37.77 2.69
2475 2570 2.742053 GCAGGTCGCTATTTTCACTTGA 59.258 45.455 0.00 0.00 37.77 3.02
2476 2571 2.474526 CGCAGGTCGCTATTTTCACTTG 60.475 50.000 0.00 0.00 39.08 3.16
2477 2572 1.732259 CGCAGGTCGCTATTTTCACTT 59.268 47.619 0.00 0.00 39.08 3.16
2478 2573 1.067142 TCGCAGGTCGCTATTTTCACT 60.067 47.619 0.00 0.00 39.08 3.41
2479 2574 1.355971 TCGCAGGTCGCTATTTTCAC 58.644 50.000 0.00 0.00 39.08 3.18
2480 2575 2.309528 ATCGCAGGTCGCTATTTTCA 57.690 45.000 0.00 0.00 39.08 2.69
2481 2576 3.741344 ACATATCGCAGGTCGCTATTTTC 59.259 43.478 0.00 0.00 39.08 2.29
2486 2581 2.351447 GCTTACATATCGCAGGTCGCTA 60.351 50.000 0.00 0.00 39.08 4.26
2488 2583 0.784778 GCTTACATATCGCAGGTCGC 59.215 55.000 0.00 0.00 38.27 5.19
2489 2584 1.419374 GGCTTACATATCGCAGGTCG 58.581 55.000 0.00 0.00 40.15 4.79
2490 2585 1.269621 ACGGCTTACATATCGCAGGTC 60.270 52.381 0.00 0.00 0.00 3.85
2492 2587 1.000163 AGACGGCTTACATATCGCAGG 60.000 52.381 0.00 0.00 0.00 4.85
2493 2588 2.054363 CAGACGGCTTACATATCGCAG 58.946 52.381 0.00 0.00 0.00 5.18
2494 2589 1.679153 TCAGACGGCTTACATATCGCA 59.321 47.619 0.00 0.00 0.00 5.10
2495 2590 2.031069 TCTCAGACGGCTTACATATCGC 60.031 50.000 0.00 0.00 0.00 4.58
2496 2591 3.898517 TCTCAGACGGCTTACATATCG 57.101 47.619 0.00 0.00 0.00 2.92
2540 2635 7.451731 TGGATTTTAGTCTAATGGTCCAGAT 57.548 36.000 13.21 0.00 31.39 2.90
2544 2639 5.179555 GCGATGGATTTTAGTCTAATGGTCC 59.820 44.000 9.74 9.74 0.00 4.46
2555 2650 5.450550 GGAAAAGGAAGGCGATGGATTTTAG 60.451 44.000 0.00 0.00 0.00 1.85
2559 2654 2.379005 GGAAAAGGAAGGCGATGGATT 58.621 47.619 0.00 0.00 0.00 3.01
2563 2658 1.839424 AAGGGAAAAGGAAGGCGATG 58.161 50.000 0.00 0.00 0.00 3.84
2565 2660 2.235891 GAAAAGGGAAAAGGAAGGCGA 58.764 47.619 0.00 0.00 0.00 5.54
2570 2665 2.444010 TCGAGGGAAAAGGGAAAAGGAA 59.556 45.455 0.00 0.00 0.00 3.36
2578 2673 1.003696 AGAAAGCTCGAGGGAAAAGGG 59.996 52.381 15.58 0.00 0.00 3.95
2579 2674 2.481289 AGAAAGCTCGAGGGAAAAGG 57.519 50.000 15.58 0.00 0.00 3.11
2583 2678 1.550976 GAGGAAGAAAGCTCGAGGGAA 59.449 52.381 15.58 0.00 0.00 3.97
2585 2680 0.176910 GGAGGAAGAAAGCTCGAGGG 59.823 60.000 15.58 0.00 0.00 4.30
2590 2685 2.568623 TGGTTGGAGGAAGAAAGCTC 57.431 50.000 0.00 0.00 0.00 4.09
2671 3065 9.716507 CCGGTAATGTTAATTTCTTCACAATAG 57.283 33.333 0.00 0.00 0.00 1.73
2672 3066 8.185505 GCCGGTAATGTTAATTTCTTCACAATA 58.814 33.333 1.90 0.00 0.00 1.90
2673 3067 7.033185 GCCGGTAATGTTAATTTCTTCACAAT 58.967 34.615 1.90 0.00 0.00 2.71
2674 3068 6.383415 GCCGGTAATGTTAATTTCTTCACAA 58.617 36.000 1.90 0.00 0.00 3.33
2676 3070 5.337554 GGCCGGTAATGTTAATTTCTTCAC 58.662 41.667 1.90 0.00 0.00 3.18
2678 3072 4.643334 AGGGCCGGTAATGTTAATTTCTTC 59.357 41.667 1.90 0.00 0.00 2.87
2681 3113 4.204799 AGAGGGCCGGTAATGTTAATTTC 58.795 43.478 1.90 0.00 0.00 2.17
2684 3116 3.046374 AGAGAGGGCCGGTAATGTTAAT 58.954 45.455 1.90 0.00 0.00 1.40
2693 3125 1.831652 CTGTTTCAGAGAGGGCCGGT 61.832 60.000 1.90 0.00 32.44 5.28
2698 3130 2.038295 ACTGCTTCTGTTTCAGAGAGGG 59.962 50.000 0.00 0.00 41.75 4.30
2700 3132 2.479656 GCACTGCTTCTGTTTCAGAGAG 59.520 50.000 0.00 3.19 41.75 3.20
2718 3150 4.510038 AACCTGAAAAGATCACATGCAC 57.490 40.909 0.00 0.00 33.47 4.57
2724 3156 4.984785 GCCAGAAAAACCTGAAAAGATCAC 59.015 41.667 0.00 0.00 36.29 3.06
2754 3187 3.453424 GGCCTGTTTTTGTTGTGTAAGG 58.547 45.455 0.00 0.00 0.00 2.69
2755 3188 3.118956 TGGGCCTGTTTTTGTTGTGTAAG 60.119 43.478 4.53 0.00 0.00 2.34
2764 3198 2.432510 TGGTAACTTGGGCCTGTTTTTG 59.567 45.455 17.63 0.00 37.61 2.44
2765 3199 2.753247 TGGTAACTTGGGCCTGTTTTT 58.247 42.857 17.63 2.12 37.61 1.94
2766 3200 2.463047 TGGTAACTTGGGCCTGTTTT 57.537 45.000 17.63 3.70 37.61 2.43
2767 3201 2.432874 GTTTGGTAACTTGGGCCTGTTT 59.567 45.455 17.63 5.30 37.61 2.83
2768 3202 2.036387 GTTTGGTAACTTGGGCCTGTT 58.964 47.619 16.87 16.87 37.61 3.16
2770 3204 1.995376 AGTTTGGTAACTTGGGCCTG 58.005 50.000 4.53 0.00 41.85 4.85
2799 3252 1.166129 TCTACTTCGACTTCGCTGCT 58.834 50.000 0.00 0.00 39.60 4.24
2804 3257 3.119955 TGGTGTCATCTACTTCGACTTCG 60.120 47.826 0.00 0.00 41.45 3.79
2810 3263 1.825474 ACCCTGGTGTCATCTACTTCG 59.175 52.381 0.00 0.00 0.00 3.79
2820 3276 1.377725 CCAGATGCACCCTGGTGTC 60.378 63.158 22.48 8.28 46.90 3.67
2844 3300 2.765969 CCAGATTGCACCCCTGGT 59.234 61.111 16.19 0.00 41.81 4.00
2845 3301 2.043652 CCCAGATTGCACCCCTGG 60.044 66.667 17.07 17.07 45.28 4.45
2848 3304 1.152881 CTAGCCCAGATTGCACCCC 60.153 63.158 0.00 0.00 0.00 4.95
2849 3305 0.475906 ATCTAGCCCAGATTGCACCC 59.524 55.000 0.00 0.00 41.49 4.61
2869 3342 0.181587 TTCCGTTTCCCAGCAACTCA 59.818 50.000 0.00 0.00 0.00 3.41
2944 3417 1.532868 CACACACACAGAAAGCTAGGC 59.467 52.381 0.00 0.00 0.00 3.93
3048 3525 2.227865 GGACACGCACCAACATAAATGT 59.772 45.455 0.00 0.00 44.20 2.71


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

AutoCloner maintained by Alex Coulton.