Multiple sequence alignment - TraesCS4D01G224300

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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 TraesCS4D01G224300 chr4D 100.000 3432 0 0 1 3432 381101219 381097788 0.000000e+00 6338
1 TraesCS4D01G224300 chr4B 92.926 2290 74 33 479 2742 468456095 468453868 0.000000e+00 3251
2 TraesCS4D01G224300 chr4B 94.262 366 14 5 1 363 468456569 468456208 1.390000e-153 553
3 TraesCS4D01G224300 chr4A 94.571 1713 56 7 1135 2836 82404567 82406253 0.000000e+00 2614
4 TraesCS4D01G224300 chr4A 83.358 679 24 35 450 1087 82403921 82404551 2.330000e-151 545
5 TraesCS4D01G224300 chr4A 92.183 371 15 7 1 363 82403545 82403909 2.360000e-141 512
6 TraesCS4D01G224300 chr5D 94.301 579 24 1 2854 3432 431559411 431559980 0.000000e+00 878
7 TraesCS4D01G224300 chr5D 93.448 580 37 1 2854 3432 464612344 464611765 0.000000e+00 859
8 TraesCS4D01G224300 chr2D 92.123 584 41 1 2854 3432 127267993 127267410 0.000000e+00 819
9 TraesCS4D01G224300 chr2D 92.295 584 33 5 2852 3432 562893168 562893742 0.000000e+00 819
10 TraesCS4D01G224300 chr7D 94.227 537 25 5 2854 3385 75313916 75313381 0.000000e+00 815
11 TraesCS4D01G224300 chr6D 91.938 583 43 4 2851 3432 139290593 139291172 0.000000e+00 813
12 TraesCS4D01G224300 chr6D 92.110 583 32 5 2852 3432 321120731 321120161 0.000000e+00 809
13 TraesCS4D01G224300 chr6D 91.394 581 47 2 2852 3432 363868863 363868286 0.000000e+00 793
14 TraesCS4D01G224300 chr3A 90.816 588 47 3 2852 3432 649825271 649824684 0.000000e+00 780
15 TraesCS4D01G224300 chr2B 88.158 304 14 3 1335 1638 682132221 682132502 3.280000e-90 342
16 TraesCS4D01G224300 chr1D 96.571 175 6 0 1539 1713 8012973 8012799 1.200000e-74 291
17 TraesCS4D01G224300 chr1D 90.000 100 10 0 1335 1434 8013077 8012978 2.780000e-26 130
18 TraesCS4D01G224300 chr1B 95.000 180 8 1 1539 1717 658481279 658481100 7.250000e-72 281


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 TraesCS4D01G224300 chr4D 381097788 381101219 3431 True 6338.000000 6338 100.000000 1 3432 1 chr4D.!!$R1 3431
1 TraesCS4D01G224300 chr4B 468453868 468456569 2701 True 1902.000000 3251 93.594000 1 2742 2 chr4B.!!$R1 2741
2 TraesCS4D01G224300 chr4A 82403545 82406253 2708 False 1223.666667 2614 90.037333 1 2836 3 chr4A.!!$F1 2835
3 TraesCS4D01G224300 chr5D 431559411 431559980 569 False 878.000000 878 94.301000 2854 3432 1 chr5D.!!$F1 578
4 TraesCS4D01G224300 chr5D 464611765 464612344 579 True 859.000000 859 93.448000 2854 3432 1 chr5D.!!$R1 578
5 TraesCS4D01G224300 chr2D 127267410 127267993 583 True 819.000000 819 92.123000 2854 3432 1 chr2D.!!$R1 578
6 TraesCS4D01G224300 chr2D 562893168 562893742 574 False 819.000000 819 92.295000 2852 3432 1 chr2D.!!$F1 580
7 TraesCS4D01G224300 chr7D 75313381 75313916 535 True 815.000000 815 94.227000 2854 3385 1 chr7D.!!$R1 531
8 TraesCS4D01G224300 chr6D 139290593 139291172 579 False 813.000000 813 91.938000 2851 3432 1 chr6D.!!$F1 581
9 TraesCS4D01G224300 chr6D 321120161 321120731 570 True 809.000000 809 92.110000 2852 3432 1 chr6D.!!$R1 580
10 TraesCS4D01G224300 chr6D 363868286 363868863 577 True 793.000000 793 91.394000 2852 3432 1 chr6D.!!$R2 580
11 TraesCS4D01G224300 chr3A 649824684 649825271 587 True 780.000000 780 90.816000 2852 3432 1 chr3A.!!$R1 580


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
468 503 0.035725 TGAGGACGGACGAGCTAGAA 60.036 55.0 0.00 0.0 0.0 2.10 F
1069 1191 0.100861 CTCGCGTCCCTTCTACCTTC 59.899 60.0 5.77 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2389 2523 1.876714 CTTCACCGCATCCGTACCG 60.877 63.158 0.0 0.0 0.00 4.02 R
2823 2963 0.095762 CGGTAAAACGAACATCCGCC 59.904 55.000 0.0 0.0 35.47 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
124 125 5.624967 CGGAGCCTCGTAATATCTCTCTCTA 60.625 48.000 0.00 0.00 0.00 2.43
125 126 5.583457 GGAGCCTCGTAATATCTCTCTCTAC 59.417 48.000 0.00 0.00 0.00 2.59
126 127 6.368779 AGCCTCGTAATATCTCTCTCTACT 57.631 41.667 0.00 0.00 0.00 2.57
127 128 6.170506 AGCCTCGTAATATCTCTCTCTACTG 58.829 44.000 0.00 0.00 0.00 2.74
128 129 5.935789 GCCTCGTAATATCTCTCTCTACTGT 59.064 44.000 0.00 0.00 0.00 3.55
129 130 7.038870 AGCCTCGTAATATCTCTCTCTACTGTA 60.039 40.741 0.00 0.00 0.00 2.74
189 198 1.597027 CAGTTCCACACACGGGACC 60.597 63.158 0.00 0.00 33.18 4.46
218 227 1.746760 GCCACGATTCGCAATTCATC 58.253 50.000 5.86 0.00 0.00 2.92
345 356 2.930040 CGCTCCAAAACTCATGATACGT 59.070 45.455 0.00 0.00 0.00 3.57
346 357 4.109766 CGCTCCAAAACTCATGATACGTA 58.890 43.478 0.00 0.00 0.00 3.57
347 358 4.026804 CGCTCCAAAACTCATGATACGTAC 60.027 45.833 0.00 0.00 0.00 3.67
363 374 2.159531 ACGTACTACGAGTATTTGCGCA 60.160 45.455 15.49 5.66 46.05 6.09
364 375 2.847717 CGTACTACGAGTATTTGCGCAA 59.152 45.455 21.02 21.02 46.05 4.85
365 376 3.301379 CGTACTACGAGTATTTGCGCAAA 59.699 43.478 35.19 35.19 46.05 3.68
367 378 4.735662 ACTACGAGTATTTGCGCAAAAA 57.264 36.364 36.42 18.42 33.56 1.94
368 379 4.460505 ACTACGAGTATTTGCGCAAAAAC 58.539 39.130 36.42 24.50 33.56 2.43
372 398 3.728718 CGAGTATTTGCGCAAAAACACTT 59.271 39.130 36.42 22.31 33.56 3.16
380 406 4.286910 TGCGCAAAAACACTTGTATCTTC 58.713 39.130 8.16 0.00 0.00 2.87
385 411 6.513393 CGCAAAAACACTTGTATCTTCCTCTT 60.513 38.462 0.00 0.00 0.00 2.85
387 413 7.379797 GCAAAAACACTTGTATCTTCCTCTTTC 59.620 37.037 0.00 0.00 0.00 2.62
390 416 4.184629 CACTTGTATCTTCCTCTTTCCGG 58.815 47.826 0.00 0.00 0.00 5.14
396 422 2.885616 TCTTCCTCTTTCCGGTGTACT 58.114 47.619 0.00 0.00 0.00 2.73
400 426 2.821969 TCCTCTTTCCGGTGTACTGTAC 59.178 50.000 10.98 10.98 0.00 2.90
401 427 2.824341 CCTCTTTCCGGTGTACTGTACT 59.176 50.000 17.98 0.00 0.00 2.73
402 428 3.257624 CCTCTTTCCGGTGTACTGTACTT 59.742 47.826 17.98 0.00 0.00 2.24
404 430 5.376854 TCTTTCCGGTGTACTGTACTTAC 57.623 43.478 17.98 9.25 0.00 2.34
405 431 3.829886 TTCCGGTGTACTGTACTTACG 57.170 47.619 17.98 17.16 0.00 3.18
407 433 3.932822 TCCGGTGTACTGTACTTACGTA 58.067 45.455 17.98 0.00 0.00 3.57
408 434 4.320023 TCCGGTGTACTGTACTTACGTAA 58.680 43.478 17.98 7.94 0.00 3.18
411 437 5.106712 CCGGTGTACTGTACTTACGTAAGAA 60.107 44.000 35.60 21.08 43.62 2.52
412 438 6.370593 CGGTGTACTGTACTTACGTAAGAAA 58.629 40.000 35.60 22.21 43.62 2.52
414 440 7.149128 CGGTGTACTGTACTTACGTAAGAAAAC 60.149 40.741 35.60 27.66 43.62 2.43
415 441 7.862873 GGTGTACTGTACTTACGTAAGAAAACT 59.137 37.037 35.60 18.82 43.62 2.66
416 442 8.896826 GTGTACTGTACTTACGTAAGAAAACTC 58.103 37.037 35.60 20.61 43.62 3.01
417 443 8.840321 TGTACTGTACTTACGTAAGAAAACTCT 58.160 33.333 35.60 17.52 43.62 3.24
418 444 9.323963 GTACTGTACTTACGTAAGAAAACTCTC 57.676 37.037 35.60 17.61 43.62 3.20
419 445 7.366513 ACTGTACTTACGTAAGAAAACTCTCC 58.633 38.462 35.60 14.00 43.62 3.71
420 446 7.230309 ACTGTACTTACGTAAGAAAACTCTCCT 59.770 37.037 35.60 15.58 43.62 3.69
422 448 6.023357 ACTTACGTAAGAAAACTCTCCTCC 57.977 41.667 35.60 0.00 43.62 4.30
423 449 3.572604 ACGTAAGAAAACTCTCCTCCG 57.427 47.619 0.00 0.00 43.62 4.63
424 450 2.889678 ACGTAAGAAAACTCTCCTCCGT 59.110 45.455 0.00 0.00 43.62 4.69
426 452 4.202192 ACGTAAGAAAACTCTCCTCCGTTT 60.202 41.667 0.00 0.00 43.62 3.60
427 453 5.010012 ACGTAAGAAAACTCTCCTCCGTTTA 59.990 40.000 0.00 0.00 43.62 2.01
428 454 5.922544 CGTAAGAAAACTCTCCTCCGTTTAA 59.077 40.000 0.00 0.00 43.02 1.52
429 455 6.128982 CGTAAGAAAACTCTCCTCCGTTTAAC 60.129 42.308 0.00 0.00 43.02 2.01
430 456 4.639334 AGAAAACTCTCCTCCGTTTAACC 58.361 43.478 0.00 0.00 33.36 2.85
431 457 4.102054 AGAAAACTCTCCTCCGTTTAACCA 59.898 41.667 0.00 0.00 33.36 3.67
434 469 2.280628 CTCTCCTCCGTTTAACCATGC 58.719 52.381 0.00 0.00 0.00 4.06
468 503 0.035725 TGAGGACGGACGAGCTAGAA 60.036 55.000 0.00 0.00 0.00 2.10
558 603 4.888325 CCCAGGGAGCCGAGGGAT 62.888 72.222 0.00 0.00 43.32 3.85
567 612 2.765807 CCGAGGGATGGCTGGAGT 60.766 66.667 0.00 0.00 0.00 3.85
634 718 3.609703 TCGAGAGAGGGAGCAAGC 58.390 61.111 0.00 0.00 34.84 4.01
635 719 2.103934 CGAGAGAGGGAGCAAGCG 59.896 66.667 0.00 0.00 0.00 4.68
636 720 2.410687 CGAGAGAGGGAGCAAGCGA 61.411 63.158 0.00 0.00 0.00 4.93
637 721 1.437160 GAGAGAGGGAGCAAGCGAG 59.563 63.158 0.00 0.00 0.00 5.03
638 722 1.000270 AGAGAGGGAGCAAGCGAGA 60.000 57.895 0.00 0.00 0.00 4.04
709 793 1.453155 GAACTGACCGGCATTCATGT 58.547 50.000 0.00 0.00 0.00 3.21
741 840 3.085947 CCTGCCTGCCTGCCTCTA 61.086 66.667 0.00 0.00 0.00 2.43
742 841 2.505006 CTGCCTGCCTGCCTCTAG 59.495 66.667 0.00 0.00 0.00 2.43
743 842 3.085947 TGCCTGCCTGCCTCTAGG 61.086 66.667 0.00 0.00 40.95 3.02
753 852 3.230245 CCTCTAGGCTGAGCGGGG 61.230 72.222 0.00 0.00 33.02 5.73
754 853 3.922640 CTCTAGGCTGAGCGGGGC 61.923 72.222 0.00 0.00 0.00 5.80
913 1035 3.062639 GCAAAAGCCAGCCACCAT 58.937 55.556 0.00 0.00 0.00 3.55
914 1036 1.079612 GCAAAAGCCAGCCACCATC 60.080 57.895 0.00 0.00 0.00 3.51
915 1037 1.593265 CAAAAGCCAGCCACCATCC 59.407 57.895 0.00 0.00 0.00 3.51
916 1038 1.610379 AAAAGCCAGCCACCATCCC 60.610 57.895 0.00 0.00 0.00 3.85
917 1039 2.097978 AAAAGCCAGCCACCATCCCT 62.098 55.000 0.00 0.00 0.00 4.20
918 1040 2.793317 AAAGCCAGCCACCATCCCTG 62.793 60.000 0.00 0.00 0.00 4.45
960 1082 1.064240 AGTCCCAACCGAACAAAAGGT 60.064 47.619 0.00 0.00 43.68 3.50
961 1083 1.335810 GTCCCAACCGAACAAAAGGTC 59.664 52.381 0.00 0.00 40.37 3.85
962 1084 0.309612 CCCAACCGAACAAAAGGTCG 59.690 55.000 0.00 0.00 40.37 4.79
963 1085 1.018910 CCAACCGAACAAAAGGTCGT 58.981 50.000 2.10 0.00 40.37 4.34
970 1092 2.106418 GAACAAAAGGTCGTTCGTTGC 58.894 47.619 0.00 0.00 32.87 4.17
1069 1191 0.100861 CTCGCGTCCCTTCTACCTTC 59.899 60.000 5.77 0.00 0.00 3.46
1078 1200 5.270794 GTCCCTTCTACCTTCTTCTCCTTA 58.729 45.833 0.00 0.00 0.00 2.69
1110 1235 2.550180 GTCTCTGTTCTTTGAGTTGGGC 59.450 50.000 0.00 0.00 0.00 5.36
1474 1608 4.710167 TCCTCGCCGTCTCCGACA 62.710 66.667 0.00 0.00 35.63 4.35
1612 1746 2.125350 CTGAAGCAGTCCCTCGCC 60.125 66.667 0.00 0.00 0.00 5.54
2389 2523 2.738846 CTGTAGCGATATGAATGGTGGC 59.261 50.000 0.00 0.00 0.00 5.01
2425 2559 1.473258 AGAGCTGTCAGAGTAGCAGG 58.527 55.000 3.32 0.00 42.29 4.85
2513 2648 3.417101 TGTGTGAATATGGGGTGTCAAC 58.583 45.455 0.00 0.00 0.00 3.18
2540 2675 4.512944 GCTCTTGTGAGTCACATTTCTTCA 59.487 41.667 25.97 8.94 44.16 3.02
2593 2728 5.954296 AGTGAAGTGATCATCTTTGGTTG 57.046 39.130 0.00 0.00 40.97 3.77
2594 2729 4.763793 AGTGAAGTGATCATCTTTGGTTGG 59.236 41.667 0.00 0.00 40.97 3.77
2595 2730 4.520492 GTGAAGTGATCATCTTTGGTTGGT 59.480 41.667 0.00 0.00 40.97 3.67
2596 2731 5.705441 GTGAAGTGATCATCTTTGGTTGGTA 59.295 40.000 0.00 0.00 40.97 3.25
2743 2883 2.317040 GTCATCGGATCCTTGGAGGTA 58.683 52.381 10.75 0.00 36.53 3.08
2758 2898 2.369394 GAGGTAAGGCCAACTCCAATG 58.631 52.381 5.01 0.00 40.61 2.82
2783 2923 2.493713 ACGCATCGTCTGTTAGGATC 57.506 50.000 0.00 0.00 33.69 3.36
2784 2924 1.067212 ACGCATCGTCTGTTAGGATCC 59.933 52.381 2.48 2.48 33.69 3.36
2785 2925 1.772182 GCATCGTCTGTTAGGATCCG 58.228 55.000 5.98 0.00 30.25 4.18
2786 2926 1.772182 CATCGTCTGTTAGGATCCGC 58.228 55.000 5.98 1.45 30.25 5.54
2787 2927 0.311165 ATCGTCTGTTAGGATCCGCG 59.689 55.000 5.98 0.00 0.00 6.46
2788 2928 1.944676 CGTCTGTTAGGATCCGCGC 60.945 63.158 5.98 0.00 0.00 6.86
2789 2929 1.141019 GTCTGTTAGGATCCGCGCA 59.859 57.895 8.75 5.60 0.00 6.09
2790 2930 1.141019 TCTGTTAGGATCCGCGCAC 59.859 57.895 8.75 2.48 0.00 5.34
2791 2931 1.153647 CTGTTAGGATCCGCGCACA 60.154 57.895 8.75 7.10 0.00 4.57
2792 2932 1.148157 CTGTTAGGATCCGCGCACAG 61.148 60.000 8.75 16.41 0.00 3.66
2793 2933 1.141019 GTTAGGATCCGCGCACAGA 59.859 57.895 8.75 0.19 0.00 3.41
2794 2934 0.459585 GTTAGGATCCGCGCACAGAA 60.460 55.000 8.75 0.00 0.00 3.02
2795 2935 0.248012 TTAGGATCCGCGCACAGAAA 59.752 50.000 8.75 0.00 0.00 2.52
2796 2936 0.248012 TAGGATCCGCGCACAGAAAA 59.752 50.000 8.75 0.00 0.00 2.29
2797 2937 0.392998 AGGATCCGCGCACAGAAAAT 60.393 50.000 8.75 0.00 0.00 1.82
2798 2938 1.134521 AGGATCCGCGCACAGAAAATA 60.135 47.619 8.75 0.00 0.00 1.40
2799 2939 1.003866 GGATCCGCGCACAGAAAATAC 60.004 52.381 8.75 0.00 0.00 1.89
2800 2940 1.663643 GATCCGCGCACAGAAAATACA 59.336 47.619 8.75 0.00 0.00 2.29
2801 2941 0.793861 TCCGCGCACAGAAAATACAC 59.206 50.000 8.75 0.00 0.00 2.90
2802 2942 0.518355 CCGCGCACAGAAAATACACG 60.518 55.000 8.75 0.00 0.00 4.49
2803 2943 0.436913 CGCGCACAGAAAATACACGA 59.563 50.000 8.75 0.00 0.00 4.35
2804 2944 1.060553 CGCGCACAGAAAATACACGAT 59.939 47.619 8.75 0.00 0.00 3.73
2805 2945 2.694043 GCGCACAGAAAATACACGATC 58.306 47.619 0.30 0.00 0.00 3.69
2806 2946 2.536928 GCGCACAGAAAATACACGATCC 60.537 50.000 0.30 0.00 0.00 3.36
2807 2947 2.670905 CGCACAGAAAATACACGATCCA 59.329 45.455 0.00 0.00 0.00 3.41
2808 2948 3.483574 CGCACAGAAAATACACGATCCAC 60.484 47.826 0.00 0.00 0.00 4.02
2809 2949 3.181510 GCACAGAAAATACACGATCCACC 60.182 47.826 0.00 0.00 0.00 4.61
2810 2950 3.062099 CACAGAAAATACACGATCCACCG 59.938 47.826 0.00 0.00 0.00 4.94
2811 2951 3.259064 CAGAAAATACACGATCCACCGT 58.741 45.455 0.00 0.00 44.43 4.83
2812 2952 3.306166 CAGAAAATACACGATCCACCGTC 59.694 47.826 0.00 0.00 41.29 4.79
2813 2953 2.304751 AAATACACGATCCACCGTCC 57.695 50.000 0.00 0.00 41.29 4.79
2814 2954 1.187974 AATACACGATCCACCGTCCA 58.812 50.000 0.00 0.00 41.29 4.02
2815 2955 0.458669 ATACACGATCCACCGTCCAC 59.541 55.000 0.00 0.00 41.29 4.02
2816 2956 0.894642 TACACGATCCACCGTCCACA 60.895 55.000 0.00 0.00 41.29 4.17
2817 2957 1.736645 CACGATCCACCGTCCACAC 60.737 63.158 0.00 0.00 41.29 3.82
2818 2958 2.204461 ACGATCCACCGTCCACACA 61.204 57.895 0.00 0.00 38.56 3.72
2819 2959 1.005512 CGATCCACCGTCCACACAA 60.006 57.895 0.00 0.00 0.00 3.33
2820 2960 0.601576 CGATCCACCGTCCACACAAA 60.602 55.000 0.00 0.00 0.00 2.83
2821 2961 1.821216 GATCCACCGTCCACACAAAT 58.179 50.000 0.00 0.00 0.00 2.32
2822 2962 1.468520 GATCCACCGTCCACACAAATG 59.531 52.381 0.00 0.00 0.00 2.32
2823 2963 0.536233 TCCACCGTCCACACAAATGG 60.536 55.000 0.00 0.00 41.57 3.16
2824 2964 1.523154 CCACCGTCCACACAAATGGG 61.523 60.000 0.00 0.00 40.49 4.00
2825 2965 1.901464 ACCGTCCACACAAATGGGC 60.901 57.895 0.00 0.00 41.28 5.36
2827 2967 2.961768 GTCCACACAAATGGGCGG 59.038 61.111 0.00 0.00 40.49 6.13
2828 2968 1.602323 GTCCACACAAATGGGCGGA 60.602 57.895 0.00 0.00 40.49 5.54
2829 2969 0.965363 GTCCACACAAATGGGCGGAT 60.965 55.000 0.00 0.00 40.49 4.18
2830 2970 0.964860 TCCACACAAATGGGCGGATG 60.965 55.000 0.00 0.00 40.49 3.51
2831 2971 1.250154 CCACACAAATGGGCGGATGT 61.250 55.000 0.00 0.00 35.95 3.06
2832 2972 0.602562 CACACAAATGGGCGGATGTT 59.397 50.000 0.00 0.00 0.00 2.71
2833 2973 0.887933 ACACAAATGGGCGGATGTTC 59.112 50.000 0.00 0.00 0.00 3.18
2834 2974 0.179166 CACAAATGGGCGGATGTTCG 60.179 55.000 0.00 0.00 0.00 3.95
2835 2975 0.608035 ACAAATGGGCGGATGTTCGT 60.608 50.000 0.00 0.00 0.00 3.85
2836 2976 0.525761 CAAATGGGCGGATGTTCGTT 59.474 50.000 0.00 0.00 0.00 3.85
2837 2977 1.067915 CAAATGGGCGGATGTTCGTTT 60.068 47.619 0.00 0.00 0.00 3.60
2838 2978 1.253100 AATGGGCGGATGTTCGTTTT 58.747 45.000 0.00 0.00 0.00 2.43
2839 2979 2.116827 ATGGGCGGATGTTCGTTTTA 57.883 45.000 0.00 0.00 0.00 1.52
2840 2980 1.158434 TGGGCGGATGTTCGTTTTAC 58.842 50.000 0.00 0.00 0.00 2.01
2841 2981 0.448990 GGGCGGATGTTCGTTTTACC 59.551 55.000 0.00 0.00 0.00 2.85
2842 2982 0.095762 GGCGGATGTTCGTTTTACCG 59.904 55.000 0.00 0.00 42.63 4.02
2843 2983 1.070038 GCGGATGTTCGTTTTACCGA 58.930 50.000 0.00 0.00 42.40 4.69
2844 2984 1.460359 GCGGATGTTCGTTTTACCGAA 59.540 47.619 0.00 0.00 43.96 4.30
2860 3000 7.328493 GTTTTACCGAAAAATGCTTAGAGCAAT 59.672 33.333 6.72 0.00 41.21 3.56
2926 3066 2.978010 CGGACAAAAGTGGCGGCT 60.978 61.111 11.43 0.00 31.03 5.52
3009 3149 2.612471 CCAATTTTGAGCCGGATTTGCA 60.612 45.455 5.05 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 125 6.017523 CGAGTCTGATGACATACAGATACAGT 60.018 42.308 15.87 2.97 45.20 3.55
125 126 6.369799 CGAGTCTGATGACATACAGATACAG 58.630 44.000 15.87 6.37 45.20 2.74
126 127 5.239525 CCGAGTCTGATGACATACAGATACA 59.760 44.000 15.87 0.00 45.20 2.29
127 128 5.470437 TCCGAGTCTGATGACATACAGATAC 59.530 44.000 15.87 12.80 45.20 2.24
128 129 5.621193 TCCGAGTCTGATGACATACAGATA 58.379 41.667 15.87 0.00 45.20 1.98
129 130 4.464947 TCCGAGTCTGATGACATACAGAT 58.535 43.478 15.87 8.79 45.20 2.90
218 227 2.096406 CGCTTCAACATGCCGTCG 59.904 61.111 0.00 0.00 0.00 5.12
345 356 5.177142 TGTTTTTGCGCAAATACTCGTAGTA 59.823 36.000 37.90 23.47 34.68 1.82
346 357 4.024725 TGTTTTTGCGCAAATACTCGTAGT 60.025 37.500 37.90 0.00 34.68 2.73
347 358 4.317291 GTGTTTTTGCGCAAATACTCGTAG 59.683 41.667 37.90 0.00 34.68 3.51
363 374 7.255139 CGGAAAGAGGAAGATACAAGTGTTTTT 60.255 37.037 0.00 0.00 0.00 1.94
364 375 6.204882 CGGAAAGAGGAAGATACAAGTGTTTT 59.795 38.462 0.00 0.00 0.00 2.43
365 376 5.701290 CGGAAAGAGGAAGATACAAGTGTTT 59.299 40.000 0.00 0.00 0.00 2.83
367 378 4.322801 CCGGAAAGAGGAAGATACAAGTGT 60.323 45.833 0.00 0.00 0.00 3.55
368 379 4.184629 CCGGAAAGAGGAAGATACAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
372 398 3.170717 ACACCGGAAAGAGGAAGATACA 58.829 45.455 9.46 0.00 0.00 2.29
380 406 2.824341 AGTACAGTACACCGGAAAGAGG 59.176 50.000 9.46 0.00 0.00 3.69
385 411 3.829886 CGTAAGTACAGTACACCGGAA 57.170 47.619 9.46 0.00 0.00 4.30
400 426 5.094134 CGGAGGAGAGTTTTCTTACGTAAG 58.906 45.833 26.13 26.13 37.25 2.34
401 427 4.520492 ACGGAGGAGAGTTTTCTTACGTAA 59.480 41.667 7.94 7.94 32.53 3.18
402 428 4.074970 ACGGAGGAGAGTTTTCTTACGTA 58.925 43.478 0.00 0.00 32.53 3.57
404 430 3.572604 ACGGAGGAGAGTTTTCTTACG 57.427 47.619 0.00 0.00 32.53 3.18
405 431 6.146837 GGTTAAACGGAGGAGAGTTTTCTTAC 59.853 42.308 0.00 0.00 40.54 2.34
407 433 5.061853 GGTTAAACGGAGGAGAGTTTTCTT 58.938 41.667 0.00 0.00 40.54 2.52
408 434 4.102054 TGGTTAAACGGAGGAGAGTTTTCT 59.898 41.667 0.00 0.00 40.54 2.52
409 435 4.383173 TGGTTAAACGGAGGAGAGTTTTC 58.617 43.478 0.00 0.00 40.54 2.29
411 437 4.324267 CATGGTTAAACGGAGGAGAGTTT 58.676 43.478 0.00 0.00 42.43 2.66
412 438 3.868754 GCATGGTTAAACGGAGGAGAGTT 60.869 47.826 0.00 0.00 0.00 3.01
414 440 2.280628 GCATGGTTAAACGGAGGAGAG 58.719 52.381 0.00 0.00 0.00 3.20
415 441 1.065709 GGCATGGTTAAACGGAGGAGA 60.066 52.381 0.00 0.00 0.00 3.71
416 442 1.065418 AGGCATGGTTAAACGGAGGAG 60.065 52.381 0.00 0.00 0.00 3.69
417 443 0.988832 AGGCATGGTTAAACGGAGGA 59.011 50.000 0.00 0.00 0.00 3.71
418 444 1.094785 CAGGCATGGTTAAACGGAGG 58.905 55.000 0.00 0.00 0.00 4.30
419 445 1.821216 ACAGGCATGGTTAAACGGAG 58.179 50.000 2.31 0.00 0.00 4.63
420 446 1.883275 CAACAGGCATGGTTAAACGGA 59.117 47.619 2.31 0.00 0.00 4.69
422 448 2.346099 CCAACAGGCATGGTTAAACG 57.654 50.000 2.31 0.00 33.08 3.60
434 469 3.612247 CTCACCTCCGGCCAACAGG 62.612 68.421 2.24 6.83 0.00 4.00
499 534 1.797537 GTTTTGCGTCGCCATCTGC 60.798 57.895 15.88 0.00 0.00 4.26
558 603 2.230994 GATGAGACGCACTCCAGCCA 62.231 60.000 7.56 0.00 44.34 4.75
561 606 0.244721 TGTGATGAGACGCACTCCAG 59.755 55.000 7.56 0.00 44.34 3.86
565 610 2.224042 TGACTTTGTGATGAGACGCACT 60.224 45.455 0.00 0.00 36.05 4.40
566 611 2.096713 GTGACTTTGTGATGAGACGCAC 60.097 50.000 0.00 0.00 35.63 5.34
567 612 2.135139 GTGACTTTGTGATGAGACGCA 58.865 47.619 0.00 0.00 0.00 5.24
634 718 1.834822 GGACCATCTCCCCCTCTCG 60.835 68.421 0.00 0.00 31.83 4.04
635 719 0.762461 CTGGACCATCTCCCCCTCTC 60.762 65.000 0.00 0.00 38.49 3.20
636 720 1.231751 TCTGGACCATCTCCCCCTCT 61.232 60.000 0.00 0.00 38.49 3.69
637 721 1.051556 GTCTGGACCATCTCCCCCTC 61.052 65.000 0.00 0.00 38.49 4.30
638 722 1.003573 GTCTGGACCATCTCCCCCT 59.996 63.158 0.00 0.00 38.49 4.79
668 752 1.400500 GGTCGTTGGTGCGTTTAATGG 60.400 52.381 0.00 0.00 0.00 3.16
736 835 3.230245 CCCCGCTCAGCCTAGAGG 61.230 72.222 0.00 0.00 36.15 3.69
737 836 3.922640 GCCCCGCTCAGCCTAGAG 61.923 72.222 0.00 0.00 38.68 2.43
908 1030 2.590007 GCTAGCGCAGGGATGGTG 60.590 66.667 11.47 0.00 35.78 4.17
909 1031 4.227134 CGCTAGCGCAGGGATGGT 62.227 66.667 26.07 0.00 39.56 3.55
910 1032 4.227134 ACGCTAGCGCAGGGATGG 62.227 66.667 35.63 7.99 44.19 3.51
911 1033 2.659897 GACGCTAGCGCAGGGATG 60.660 66.667 35.63 8.77 44.19 3.51
912 1034 3.917760 GGACGCTAGCGCAGGGAT 61.918 66.667 35.63 16.46 44.19 3.85
919 1041 4.849329 GGTGGTCGGACGCTAGCG 62.849 72.222 34.27 34.27 46.03 4.26
939 1061 1.607148 CCTTTTGTTCGGTTGGGACTC 59.393 52.381 0.00 0.00 0.00 3.36
950 1072 2.106418 GCAACGAACGACCTTTTGTTC 58.894 47.619 0.14 0.00 41.28 3.18
960 1082 1.002576 TCTACGAACAGCAACGAACGA 60.003 47.619 0.14 0.00 0.00 3.85
961 1083 1.382419 CTCTACGAACAGCAACGAACG 59.618 52.381 0.00 0.00 0.00 3.95
962 1084 1.719780 CCTCTACGAACAGCAACGAAC 59.280 52.381 0.00 0.00 0.00 3.95
963 1085 1.336517 CCCTCTACGAACAGCAACGAA 60.337 52.381 0.00 0.00 0.00 3.85
970 1092 0.378962 CGAGCTCCCTCTACGAACAG 59.621 60.000 8.47 0.00 35.90 3.16
1069 1191 6.038825 AGAGACATACACATCGTAAGGAGAAG 59.961 42.308 0.00 0.00 32.59 2.85
1078 1200 5.392767 AAGAACAGAGACATACACATCGT 57.607 39.130 0.00 0.00 0.00 3.73
1122 1247 2.124903 CTCACAAGCAAGCAAAGCAAG 58.875 47.619 0.00 0.00 0.00 4.01
1471 1605 3.917760 CCCTCCGAGGCCGATGTC 61.918 72.222 9.17 0.00 38.22 3.06
2362 2496 5.098893 CCATTCATATCGCTACAGCTACTC 58.901 45.833 0.00 0.00 39.32 2.59
2363 2497 4.524714 ACCATTCATATCGCTACAGCTACT 59.475 41.667 0.00 0.00 39.32 2.57
2389 2523 1.876714 CTTCACCGCATCCGTACCG 60.877 63.158 0.00 0.00 0.00 4.02
2513 2648 0.315251 TGTGACTCACAAGAGCGGAG 59.685 55.000 9.54 0.00 46.09 4.63
2540 2675 1.662629 CGCAGAAATGCTGTTCGAGAT 59.337 47.619 0.00 0.00 46.62 2.75
2563 2698 2.677199 TGATCACTTCACTTCACGCTC 58.323 47.619 0.00 0.00 0.00 5.03
2593 2728 1.291877 CGGTGAAGTGTGCAGCTACC 61.292 60.000 0.00 0.00 0.00 3.18
2594 2729 0.600255 ACGGTGAAGTGTGCAGCTAC 60.600 55.000 0.00 0.00 0.00 3.58
2595 2730 0.319555 GACGGTGAAGTGTGCAGCTA 60.320 55.000 0.00 0.00 0.00 3.32
2596 2731 1.595382 GACGGTGAAGTGTGCAGCT 60.595 57.895 0.00 0.00 0.00 4.24
2743 2883 0.971386 CTTGCATTGGAGTTGGCCTT 59.029 50.000 3.32 0.00 0.00 4.35
2770 2910 1.944676 GCGCGGATCCTAACAGACG 60.945 63.158 8.83 3.38 0.00 4.18
2771 2911 1.141019 TGCGCGGATCCTAACAGAC 59.859 57.895 8.83 0.00 0.00 3.51
2772 2912 1.141019 GTGCGCGGATCCTAACAGA 59.859 57.895 8.83 0.00 0.00 3.41
2773 2913 1.148157 CTGTGCGCGGATCCTAACAG 61.148 60.000 8.83 13.21 0.00 3.16
2774 2914 1.153647 CTGTGCGCGGATCCTAACA 60.154 57.895 8.83 7.72 0.00 2.41
2775 2915 0.459585 TTCTGTGCGCGGATCCTAAC 60.460 55.000 10.13 3.26 0.00 2.34
2776 2916 0.248012 TTTCTGTGCGCGGATCCTAA 59.752 50.000 10.13 0.00 0.00 2.69
2777 2917 0.248012 TTTTCTGTGCGCGGATCCTA 59.752 50.000 10.13 0.00 0.00 2.94
2778 2918 0.392998 ATTTTCTGTGCGCGGATCCT 60.393 50.000 10.13 0.00 0.00 3.24
2779 2919 1.003866 GTATTTTCTGTGCGCGGATCC 60.004 52.381 10.13 0.00 0.00 3.36
2780 2920 1.663643 TGTATTTTCTGTGCGCGGATC 59.336 47.619 10.13 0.03 0.00 3.36
2781 2921 1.396996 GTGTATTTTCTGTGCGCGGAT 59.603 47.619 10.13 0.00 0.00 4.18
2782 2922 0.793861 GTGTATTTTCTGTGCGCGGA 59.206 50.000 8.83 4.21 0.00 5.54
2783 2923 0.518355 CGTGTATTTTCTGTGCGCGG 60.518 55.000 8.83 0.00 32.76 6.46
2784 2924 0.436913 TCGTGTATTTTCTGTGCGCG 59.563 50.000 0.00 0.00 36.70 6.86
2785 2925 2.536928 GGATCGTGTATTTTCTGTGCGC 60.537 50.000 0.00 0.00 0.00 6.09
2786 2926 2.670905 TGGATCGTGTATTTTCTGTGCG 59.329 45.455 0.00 0.00 0.00 5.34
2787 2927 3.181510 GGTGGATCGTGTATTTTCTGTGC 60.182 47.826 0.00 0.00 0.00 4.57
2788 2928 3.062099 CGGTGGATCGTGTATTTTCTGTG 59.938 47.826 0.00 0.00 0.00 3.66
2789 2929 3.259064 CGGTGGATCGTGTATTTTCTGT 58.741 45.455 0.00 0.00 0.00 3.41
2790 2930 3.259064 ACGGTGGATCGTGTATTTTCTG 58.741 45.455 0.00 0.00 42.21 3.02
2791 2931 3.518590 GACGGTGGATCGTGTATTTTCT 58.481 45.455 0.00 0.00 43.96 2.52
2792 2932 2.606272 GGACGGTGGATCGTGTATTTTC 59.394 50.000 0.00 0.00 43.96 2.29
2793 2933 2.027929 TGGACGGTGGATCGTGTATTTT 60.028 45.455 0.00 0.00 43.96 1.82
2794 2934 1.551430 TGGACGGTGGATCGTGTATTT 59.449 47.619 0.00 0.00 43.96 1.40
2795 2935 1.134907 GTGGACGGTGGATCGTGTATT 60.135 52.381 0.00 0.00 43.96 1.89
2796 2936 0.458669 GTGGACGGTGGATCGTGTAT 59.541 55.000 0.00 0.00 43.96 2.29
2797 2937 0.894642 TGTGGACGGTGGATCGTGTA 60.895 55.000 0.00 0.00 43.96 2.90
2798 2938 2.204461 TGTGGACGGTGGATCGTGT 61.204 57.895 0.00 0.00 43.96 4.49
2799 2939 1.736645 GTGTGGACGGTGGATCGTG 60.737 63.158 0.00 0.00 43.96 4.35
2800 2940 1.750341 TTGTGTGGACGGTGGATCGT 61.750 55.000 0.00 0.00 46.83 3.73
2801 2941 0.601576 TTTGTGTGGACGGTGGATCG 60.602 55.000 0.00 0.00 0.00 3.69
2802 2942 1.468520 CATTTGTGTGGACGGTGGATC 59.531 52.381 0.00 0.00 0.00 3.36
2803 2943 1.533625 CATTTGTGTGGACGGTGGAT 58.466 50.000 0.00 0.00 0.00 3.41
2804 2944 0.536233 CCATTTGTGTGGACGGTGGA 60.536 55.000 0.00 0.00 42.02 4.02
2805 2945 1.523154 CCCATTTGTGTGGACGGTGG 61.523 60.000 0.00 0.00 42.02 4.61
2806 2946 1.956043 CCCATTTGTGTGGACGGTG 59.044 57.895 0.00 0.00 42.02 4.94
2807 2947 1.901464 GCCCATTTGTGTGGACGGT 60.901 57.895 0.00 0.00 42.02 4.83
2808 2948 2.961768 GCCCATTTGTGTGGACGG 59.038 61.111 0.00 0.00 42.02 4.79
2809 2949 2.560861 CGCCCATTTGTGTGGACG 59.439 61.111 0.00 0.00 42.02 4.79
2810 2950 0.965363 ATCCGCCCATTTGTGTGGAC 60.965 55.000 0.00 0.00 43.46 4.02
2811 2951 0.964860 CATCCGCCCATTTGTGTGGA 60.965 55.000 0.00 0.00 44.66 4.02
2812 2952 1.250154 ACATCCGCCCATTTGTGTGG 61.250 55.000 0.00 0.00 39.05 4.17
2813 2953 0.602562 AACATCCGCCCATTTGTGTG 59.397 50.000 0.00 0.00 0.00 3.82
2814 2954 0.887933 GAACATCCGCCCATTTGTGT 59.112 50.000 0.00 0.00 0.00 3.72
2815 2955 0.179166 CGAACATCCGCCCATTTGTG 60.179 55.000 0.00 0.00 0.00 3.33
2816 2956 0.608035 ACGAACATCCGCCCATTTGT 60.608 50.000 0.00 0.00 0.00 2.83
2817 2957 0.525761 AACGAACATCCGCCCATTTG 59.474 50.000 0.00 0.00 0.00 2.32
2818 2958 1.253100 AAACGAACATCCGCCCATTT 58.747 45.000 0.00 0.00 0.00 2.32
2819 2959 1.253100 AAAACGAACATCCGCCCATT 58.747 45.000 0.00 0.00 0.00 3.16
2820 2960 1.741145 GTAAAACGAACATCCGCCCAT 59.259 47.619 0.00 0.00 0.00 4.00
2821 2961 1.158434 GTAAAACGAACATCCGCCCA 58.842 50.000 0.00 0.00 0.00 5.36
2822 2962 0.448990 GGTAAAACGAACATCCGCCC 59.551 55.000 0.00 0.00 0.00 6.13
2823 2963 0.095762 CGGTAAAACGAACATCCGCC 59.904 55.000 0.00 0.00 35.47 6.13
2824 2964 1.070038 TCGGTAAAACGAACATCCGC 58.930 50.000 0.00 0.00 40.34 5.54
2831 2971 8.250976 GCTCTAAGCATTTTTCGGTAAAACGAA 61.251 37.037 0.00 0.00 44.89 3.85
2832 2972 6.542574 TCTAAGCATTTTTCGGTAAAACGA 57.457 33.333 0.00 0.00 38.48 3.85
2833 2973 5.283012 GCTCTAAGCATTTTTCGGTAAAACG 59.717 40.000 0.00 0.00 41.89 3.60
2834 2974 6.612855 GCTCTAAGCATTTTTCGGTAAAAC 57.387 37.500 0.00 0.00 41.89 2.43
2846 2986 7.680587 CCGCATTGGAATTGCTCTAAGCATT 62.681 44.000 1.95 0.00 46.59 3.56
2847 2987 6.285829 CCGCATTGGAATTGCTCTAAGCAT 62.286 45.833 1.95 0.00 46.59 3.79
2848 2988 5.037457 CCGCATTGGAATTGCTCTAAGCA 62.037 47.826 0.00 0.00 45.97 3.91
2849 2989 2.542411 CCGCATTGGAATTGCTCTAAGC 60.542 50.000 0.00 0.00 42.00 3.09
2850 2990 2.542411 GCCGCATTGGAATTGCTCTAAG 60.542 50.000 0.00 0.00 42.00 2.18
2860 3000 3.636929 ATGGGTCGCCGCATTGGAA 62.637 57.895 0.00 0.00 41.05 3.53
2868 3008 3.192922 GGACGAAATGGGTCGCCG 61.193 66.667 0.00 0.00 45.00 6.46
2926 3066 4.912485 TTTGGGTCGGCGCGTTGA 62.912 61.111 8.43 2.59 0.00 3.18
2963 3103 2.587322 GAATGGGTCATCCGCGGACA 62.587 60.000 33.75 24.01 38.76 4.02
3037 3181 1.076923 GGGGAGAGGAGTAGACGCA 60.077 63.158 0.00 0.00 0.00 5.24
3041 3185 3.070987 GCCCGGGGAGAGGAGTAGA 62.071 68.421 25.28 0.00 0.00 2.59
3229 3389 3.042560 GCACGAGGCTTGCCTTTT 58.957 55.556 15.92 2.97 40.25 2.27



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

AutoCloner maintained by Alex Coulton.