Multiple sequence alignment - TraesCS5D01G297600

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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 TraesCS5D01G297600 chr5D 100.000 3547 0 0 1 3547 394826238 394829784 0.000000e+00 6551.0
1 TraesCS5D01G297600 chr5B 92.015 2655 115 45 1 2619 474521145 474523738 0.000000e+00 3639.0
2 TraesCS5D01G297600 chr5B 87.104 473 9 12 3098 3547 474524291 474524734 4.120000e-134 488.0
3 TraesCS5D01G297600 chr5B 81.511 503 40 32 2608 3064 474523796 474524291 7.240000e-97 364.0
4 TraesCS5D01G297600 chr5A 87.670 2717 157 83 944 3547 496608404 496611055 0.000000e+00 2998.0
5 TraesCS5D01G297600 chr5A 85.427 995 50 47 2 961 496607446 496608380 0.000000e+00 946.0
6 TraesCS5D01G297600 chr2B 86.885 366 35 5 1586 1939 98404758 98404394 7.130000e-107 398.0
7 TraesCS5D01G297600 chr1B 96.250 80 3 0 1063 1142 552947874 552947953 7.990000e-27 132.0
8 TraesCS5D01G297600 chr4B 93.506 77 3 2 1068 1142 182233238 182233314 2.890000e-21 113.0
9 TraesCS5D01G297600 chr4A 97.959 49 1 0 1094 1142 95365266 95365218 6.310000e-13 86.1


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 TraesCS5D01G297600 chr5D 394826238 394829784 3546 False 6551 6551 100.000000 1 3547 1 chr5D.!!$F1 3546
1 TraesCS5D01G297600 chr5B 474521145 474524734 3589 False 1497 3639 86.876667 1 3547 3 chr5B.!!$F1 3546
2 TraesCS5D01G297600 chr5A 496607446 496611055 3609 False 1972 2998 86.548500 2 3547 2 chr5A.!!$F1 3545

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
656 694 0.032515 TACCCTGGCTAGCTGTGCTA 60.033 55.0 15.72 6.48 40.44 3.49 F
1269 1370 0.177836 GCTGCTTCTTCTCCTCCTCC 59.822 60.0 0.00 0.00 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2463 2597 0.035439 GGGGAGCAAAAGGTGATCGA 60.035 55.0 0.0 0.0 43.96 3.59 R
3058 3348 0.250513 AAATCTGCACCCGTCTCCTC 59.749 55.0 0.0 0.0 0.00 3.71 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
181 191 2.354422 ATCATCTGCTCGAGCGCG 60.354 61.111 30.75 23.70 45.83 6.86
208 226 2.229062 CAGCCAACAGTCTCTCTCGTTA 59.771 50.000 0.00 0.00 0.00 3.18
213 231 4.416620 CAACAGTCTCTCTCGTTACCATC 58.583 47.826 0.00 0.00 0.00 3.51
294 312 0.390078 CAGAGCAGAGCACAGTCCAG 60.390 60.000 0.00 0.00 0.00 3.86
295 313 1.741032 GAGCAGAGCACAGTCCAGC 60.741 63.158 0.00 0.00 0.00 4.85
296 314 2.031616 GCAGAGCACAGTCCAGCA 59.968 61.111 0.00 0.00 0.00 4.41
297 315 2.033755 GCAGAGCACAGTCCAGCAG 61.034 63.158 0.00 0.00 0.00 4.24
298 316 2.033755 CAGAGCACAGTCCAGCAGC 61.034 63.158 0.00 0.00 0.00 5.25
299 317 2.745492 GAGCACAGTCCAGCAGCC 60.745 66.667 0.00 0.00 0.00 4.85
300 318 4.694233 AGCACAGTCCAGCAGCCG 62.694 66.667 0.00 0.00 0.00 5.52
301 319 4.687215 GCACAGTCCAGCAGCCGA 62.687 66.667 0.00 0.00 0.00 5.54
492 525 1.524621 GACCGTGATGGCATCCTGG 60.525 63.158 25.17 25.17 43.94 4.45
493 526 2.257409 GACCGTGATGGCATCCTGGT 62.257 60.000 29.83 29.83 43.94 4.00
494 527 1.077501 CCGTGATGGCATCCTGGTT 60.078 57.895 23.92 0.00 0.00 3.67
495 528 0.180171 CCGTGATGGCATCCTGGTTA 59.820 55.000 23.92 1.77 0.00 2.85
496 529 1.299541 CGTGATGGCATCCTGGTTAC 58.700 55.000 23.92 13.22 0.00 2.50
651 689 0.749649 CACTCTACCCTGGCTAGCTG 59.250 60.000 15.72 7.95 0.00 4.24
655 693 1.306141 TACCCTGGCTAGCTGTGCT 60.306 57.895 15.72 0.00 43.41 4.40
656 694 0.032515 TACCCTGGCTAGCTGTGCTA 60.033 55.000 15.72 6.48 40.44 3.49
657 695 1.144936 CCCTGGCTAGCTGTGCTAC 59.855 63.158 15.72 0.00 40.44 3.58
658 696 1.227089 CCTGGCTAGCTGTGCTACG 60.227 63.158 15.72 0.00 40.44 3.51
659 697 1.513158 CTGGCTAGCTGTGCTACGT 59.487 57.895 15.72 0.00 40.44 3.57
727 765 1.534805 CGCAGACGCACAGATACAGAT 60.535 52.381 0.00 0.00 38.40 2.90
733 771 5.007724 CAGACGCACAGATACAGATGTAGTA 59.992 44.000 0.00 0.00 33.52 1.82
734 772 5.237561 AGACGCACAGATACAGATGTAGTAG 59.762 44.000 0.00 0.00 33.52 2.57
735 773 4.882427 ACGCACAGATACAGATGTAGTAGT 59.118 41.667 0.00 0.00 33.52 2.73
764 809 3.024547 GGCACAGACCACAGTATAGAGA 58.975 50.000 0.00 0.00 0.00 3.10
803 848 4.081406 TCTGTACCCTCGCTTAAACACTA 58.919 43.478 0.00 0.00 0.00 2.74
845 892 1.007721 CCCCTTCTCTCTTCTCCCTCA 59.992 57.143 0.00 0.00 0.00 3.86
883 930 1.866063 GCCACCACGATCGATCTCTTC 60.866 57.143 24.34 0.00 0.00 2.87
884 931 1.678627 CCACCACGATCGATCTCTTCT 59.321 52.381 24.34 0.00 0.00 2.85
887 934 2.359531 ACCACGATCGATCTCTTCTTCC 59.640 50.000 24.34 0.00 0.00 3.46
894 941 1.666700 CGATCTCTTCTTCCGTCTCGT 59.333 52.381 0.00 0.00 0.00 4.18
956 1051 0.927029 TCCGATGAAGGAGGAGGAGA 59.073 55.000 0.00 0.00 34.92 3.71
982 1077 2.168496 GGATAGATAGGTGGCTGCGTA 58.832 52.381 0.00 0.00 0.00 4.42
991 1086 1.149627 TGGCTGCGTAACAAAGGGT 59.850 52.632 0.00 0.00 0.00 4.34
999 1094 1.066716 CGTAACAAAGGGTCCGGATCA 60.067 52.381 18.43 0.00 0.00 2.92
1269 1370 0.177836 GCTGCTTCTTCTCCTCCTCC 59.822 60.000 0.00 0.00 0.00 4.30
1270 1371 1.864669 CTGCTTCTTCTCCTCCTCCT 58.135 55.000 0.00 0.00 0.00 3.69
1271 1372 1.756538 CTGCTTCTTCTCCTCCTCCTC 59.243 57.143 0.00 0.00 0.00 3.71
1316 1417 0.392863 TCGTTGATGATGCCAGTGGG 60.393 55.000 12.15 0.00 37.18 4.61
1319 1424 1.064758 GTTGATGATGCCAGTGGGGTA 60.065 52.381 12.15 0.00 39.65 3.69
1341 1446 3.119495 ACTCAAAACTCAACTGTGTTGGC 60.119 43.478 10.05 0.00 36.20 4.52
1386 1491 3.450115 CAGGACGAGACCGGGGTC 61.450 72.222 6.32 9.88 44.86 4.46
1517 1622 4.767255 CGCCGGCCTCAGCTTCTT 62.767 66.667 23.46 0.00 39.73 2.52
1619 1724 4.047125 CACCACGGCCCTCCCAAT 62.047 66.667 0.00 0.00 0.00 3.16
1622 1727 2.824041 CACGGCCCTCCCAATTCG 60.824 66.667 0.00 0.00 0.00 3.34
1659 1764 4.716784 TCTTGGTAGATCACAGCTAACCAT 59.283 41.667 0.00 0.00 0.00 3.55
1669 1774 1.004745 CAGCTAACCATTGGTCCCACT 59.995 52.381 9.22 1.95 33.12 4.00
1843 1951 1.892819 CGGGCTCTTCTTCCTCTGCA 61.893 60.000 0.00 0.00 0.00 4.41
2086 2200 2.001812 CCATGGTGACGAACAGAGAG 57.998 55.000 2.57 0.00 0.00 3.20
2230 2344 2.660064 GGTGATCCCCGTGTGCTCT 61.660 63.158 0.00 0.00 0.00 4.09
2277 2406 0.747255 AAGGATGACGATGACCGGAG 59.253 55.000 9.46 0.00 43.93 4.63
2320 2452 4.451150 TAGGCAAGGGCGCGTGAG 62.451 66.667 20.34 0.87 42.47 3.51
2364 2496 4.710423 TGAAGATGAAGAAGACGAGGAG 57.290 45.455 0.00 0.00 0.00 3.69
2403 2535 7.555914 TCAGTAGCTATATGATGAGATCAGTCC 59.444 40.741 0.00 0.00 43.53 3.85
2408 2540 3.742433 ATGATGAGATCAGTCCGGTTC 57.258 47.619 0.00 0.00 43.53 3.62
2418 2552 1.751924 CAGTCCGGTTCTAGAAGGGAG 59.248 57.143 20.38 10.03 0.00 4.30
2435 2569 2.412847 GGGAGTTTTGATCGCAAGTTCG 60.413 50.000 0.00 0.00 38.91 3.95
2436 2570 2.223377 GGAGTTTTGATCGCAAGTTCGT 59.777 45.455 0.00 0.00 38.91 3.85
2437 2571 3.303791 GGAGTTTTGATCGCAAGTTCGTT 60.304 43.478 0.00 0.00 38.91 3.85
2438 2572 3.873529 AGTTTTGATCGCAAGTTCGTTC 58.126 40.909 0.00 0.00 38.91 3.95
2449 2583 4.056050 GCAAGTTCGTTCCTCTGTCTAAA 58.944 43.478 0.00 0.00 0.00 1.85
2450 2584 4.691216 GCAAGTTCGTTCCTCTGTCTAAAT 59.309 41.667 0.00 0.00 0.00 1.40
2463 2597 8.375506 TCCTCTGTCTAAATTTGTGTAAGTGAT 58.624 33.333 0.00 0.00 0.00 3.06
2464 2598 8.660373 CCTCTGTCTAAATTTGTGTAAGTGATC 58.340 37.037 0.00 0.00 0.00 2.92
2465 2599 8.239681 TCTGTCTAAATTTGTGTAAGTGATCG 57.760 34.615 0.00 0.00 0.00 3.69
2466 2600 8.085909 TCTGTCTAAATTTGTGTAAGTGATCGA 58.914 33.333 0.00 0.00 0.00 3.59
2467 2601 8.771920 TGTCTAAATTTGTGTAAGTGATCGAT 57.228 30.769 0.00 0.00 0.00 3.59
2480 2619 2.632377 TGATCGATCACCTTTTGCTCC 58.368 47.619 23.99 0.00 0.00 4.70
2482 2621 0.035439 TCGATCACCTTTTGCTCCCC 60.035 55.000 0.00 0.00 0.00 4.81
2485 2624 0.332972 ATCACCTTTTGCTCCCCCTC 59.667 55.000 0.00 0.00 0.00 4.30
2486 2625 0.772124 TCACCTTTTGCTCCCCCTCT 60.772 55.000 0.00 0.00 0.00 3.69
2489 2628 0.254462 CCTTTTGCTCCCCCTCTCTC 59.746 60.000 0.00 0.00 0.00 3.20
2492 2631 0.618968 TTTGCTCCCCCTCTCTCTCC 60.619 60.000 0.00 0.00 0.00 3.71
2493 2632 2.520741 GCTCCCCCTCTCTCTCCG 60.521 72.222 0.00 0.00 0.00 4.63
2496 2635 1.701757 TCCCCCTCTCTCTCCGGAT 60.702 63.158 3.57 0.00 0.00 4.18
2497 2636 1.532794 CCCCCTCTCTCTCCGGATG 60.533 68.421 3.57 0.57 0.00 3.51
2498 2637 1.532794 CCCCTCTCTCTCCGGATGG 60.533 68.421 3.57 0.17 0.00 3.51
2499 2638 2.206536 CCCTCTCTCTCCGGATGGC 61.207 68.421 3.57 0.00 34.14 4.40
2500 2639 2.560119 CCTCTCTCTCCGGATGGCG 61.560 68.421 3.57 0.00 34.14 5.69
2501 2640 1.527148 CTCTCTCTCCGGATGGCGA 60.527 63.158 3.57 0.00 34.14 5.54
2502 2641 1.076995 TCTCTCTCCGGATGGCGAA 60.077 57.895 3.57 0.00 34.14 4.70
2503 2642 1.103987 TCTCTCTCCGGATGGCGAAG 61.104 60.000 3.57 0.00 34.14 3.79
2561 2705 7.340743 TGAATGAATATAGCTCTACTAGGGCTC 59.659 40.741 14.07 0.70 37.50 4.70
2599 2747 4.755411 TCGATCCTTCCTGTGTCAAATAC 58.245 43.478 0.00 0.00 0.00 1.89
2604 2752 5.091552 TCCTTCCTGTGTCAAATACCTAGT 58.908 41.667 0.00 0.00 0.00 2.57
2619 2839 7.881775 AATACCTAGTTCATCACCATTTTCC 57.118 36.000 0.00 0.00 0.00 3.13
2647 2867 1.589716 GCCTGCCTTCACATGTGTCC 61.590 60.000 24.63 12.07 0.00 4.02
2682 2914 1.134401 TGCTCGATCAGTCCATTTCCC 60.134 52.381 0.00 0.00 0.00 3.97
2684 2916 2.420687 GCTCGATCAGTCCATTTCCCTT 60.421 50.000 0.00 0.00 0.00 3.95
2686 2918 2.170607 TCGATCAGTCCATTTCCCTTCC 59.829 50.000 0.00 0.00 0.00 3.46
2693 2925 6.561294 TCAGTCCATTTCCCTTCCTTTTAAT 58.439 36.000 0.00 0.00 0.00 1.40
2694 2926 7.016296 TCAGTCCATTTCCCTTCCTTTTAATT 58.984 34.615 0.00 0.00 0.00 1.40
2706 2938 4.072131 TCCTTTTAATTGCGTCAGAAGCT 58.928 39.130 9.88 0.00 35.28 3.74
2717 2950 3.249080 GCGTCAGAAGCTAGTAGGAGTAG 59.751 52.174 0.37 0.00 0.00 2.57
2718 2951 3.810941 CGTCAGAAGCTAGTAGGAGTAGG 59.189 52.174 0.00 0.00 0.00 3.18
2720 2953 5.627135 GTCAGAAGCTAGTAGGAGTAGGAT 58.373 45.833 0.00 0.00 0.00 3.24
2721 2954 6.066032 GTCAGAAGCTAGTAGGAGTAGGATT 58.934 44.000 0.00 0.00 0.00 3.01
2729 2962 6.999871 GCTAGTAGGAGTAGGATTACTTGAGT 59.000 42.308 0.00 0.00 40.21 3.41
2740 2973 5.424895 AGGATTACTTGAGTGCTTCTGATCT 59.575 40.000 0.00 0.00 0.00 2.75
2761 2994 8.896744 TGATCTGATCTGATCAAAAATACAACC 58.103 33.333 31.60 10.89 46.60 3.77
2762 2995 8.812513 ATCTGATCTGATCAAAAATACAACCA 57.187 30.769 19.95 0.00 39.11 3.67
2765 2998 7.592938 TGATCTGATCAAAAATACAACCACAC 58.407 34.615 17.56 0.00 36.11 3.82
2766 2999 6.325919 TCTGATCAAAAATACAACCACACC 57.674 37.500 0.00 0.00 0.00 4.16
2767 3000 5.830457 TCTGATCAAAAATACAACCACACCA 59.170 36.000 0.00 0.00 0.00 4.17
2768 3001 6.493115 TCTGATCAAAAATACAACCACACCAT 59.507 34.615 0.00 0.00 0.00 3.55
2769 3002 7.015098 TCTGATCAAAAATACAACCACACCATT 59.985 33.333 0.00 0.00 0.00 3.16
2770 3003 6.927936 TGATCAAAAATACAACCACACCATTG 59.072 34.615 0.00 0.00 0.00 2.82
2772 3005 3.676291 AAATACAACCACACCATTGCC 57.324 42.857 0.00 0.00 0.00 4.52
2789 3054 4.540153 CATGGACCATGGACGGAC 57.460 61.111 24.65 0.00 38.11 4.79
2791 3056 2.731571 ATGGACCATGGACGGACGG 61.732 63.158 21.47 0.00 0.00 4.79
2792 3057 3.072468 GGACCATGGACGGACGGA 61.072 66.667 21.47 0.00 0.00 4.69
2793 3058 2.432300 GGACCATGGACGGACGGAT 61.432 63.158 21.47 0.00 0.00 4.18
2794 3059 1.227263 GACCATGGACGGACGGATG 60.227 63.158 21.47 0.00 0.00 3.51
2795 3060 2.588877 CCATGGACGGACGGATGC 60.589 66.667 5.56 0.00 0.00 3.91
2796 3061 2.501128 CATGGACGGACGGATGCT 59.499 61.111 0.00 0.00 0.00 3.79
2797 3062 1.884464 CATGGACGGACGGATGCTG 60.884 63.158 0.00 0.00 0.00 4.41
2798 3063 3.740128 ATGGACGGACGGATGCTGC 62.740 63.158 0.00 0.00 0.00 5.25
2804 3069 4.479993 GACGGATGCTGCCCTGCT 62.480 66.667 0.00 0.00 0.00 4.24
2805 3070 4.790962 ACGGATGCTGCCCTGCTG 62.791 66.667 0.00 0.00 0.00 4.41
2826 3091 1.003545 CCGCAGAGCATCAATTAACCG 60.004 52.381 0.00 0.00 37.82 4.44
2841 3106 4.781959 CCGGCCGTGCATTGCTTG 62.782 66.667 26.12 0.00 0.00 4.01
2847 3112 2.605030 GCCGTGCATTGCTTGATAAAA 58.395 42.857 10.49 0.00 0.00 1.52
2848 3113 2.992543 GCCGTGCATTGCTTGATAAAAA 59.007 40.909 10.49 0.00 0.00 1.94
2955 3233 2.775032 GAAAGCACCGGCCGTACTCA 62.775 60.000 26.12 0.00 42.56 3.41
2962 3240 1.585521 CGGCCGTACTCATCGACAC 60.586 63.158 19.50 0.00 0.00 3.67
2975 3253 1.112113 TCGACACCCTTATCAGGAGC 58.888 55.000 0.00 0.00 44.19 4.70
2977 3255 1.202463 CGACACCCTTATCAGGAGCTG 60.202 57.143 0.00 0.00 44.19 4.24
3064 3354 1.135094 GAGGCATTCATGGGAGGAGA 58.865 55.000 0.00 0.00 0.00 3.71
3070 3360 1.264749 TTCATGGGAGGAGACGGGTG 61.265 60.000 0.00 0.00 0.00 4.61
3072 3362 3.924013 ATGGGAGGAGACGGGTGCA 62.924 63.158 0.00 0.00 0.00 4.57
3073 3363 3.775654 GGGAGGAGACGGGTGCAG 61.776 72.222 0.00 0.00 0.00 4.41
3074 3364 2.680352 GGAGGAGACGGGTGCAGA 60.680 66.667 0.00 0.00 0.00 4.26
3075 3365 2.060980 GGAGGAGACGGGTGCAGAT 61.061 63.158 0.00 0.00 0.00 2.90
3076 3366 1.617947 GGAGGAGACGGGTGCAGATT 61.618 60.000 0.00 0.00 0.00 2.40
3077 3367 0.250513 GAGGAGACGGGTGCAGATTT 59.749 55.000 0.00 0.00 0.00 2.17
3078 3368 0.250513 AGGAGACGGGTGCAGATTTC 59.749 55.000 0.00 0.00 0.00 2.17
3079 3369 0.250513 GGAGACGGGTGCAGATTTCT 59.749 55.000 0.00 0.00 0.00 2.52
3080 3370 1.339151 GGAGACGGGTGCAGATTTCTT 60.339 52.381 0.00 0.00 0.00 2.52
3081 3371 2.003301 GAGACGGGTGCAGATTTCTTC 58.997 52.381 0.00 0.00 0.00 2.87
3082 3372 0.721718 GACGGGTGCAGATTTCTTCG 59.278 55.000 0.00 0.00 0.00 3.79
3083 3373 1.298859 ACGGGTGCAGATTTCTTCGC 61.299 55.000 0.00 0.00 0.00 4.70
3084 3374 1.298157 CGGGTGCAGATTTCTTCGCA 61.298 55.000 0.00 0.00 33.53 5.10
3086 3376 1.202222 GGGTGCAGATTTCTTCGCATG 60.202 52.381 0.00 0.00 36.66 4.06
3087 3377 1.542544 GTGCAGATTTCTTCGCATGC 58.457 50.000 7.91 7.91 36.66 4.06
3088 3378 1.135603 GTGCAGATTTCTTCGCATGCA 60.136 47.619 19.57 1.73 41.05 3.96
3089 3379 1.135603 TGCAGATTTCTTCGCATGCAC 60.136 47.619 19.57 0.00 38.64 4.57
3090 3380 1.135603 GCAGATTTCTTCGCATGCACA 60.136 47.619 19.57 0.00 33.92 4.57
3091 3381 2.669113 GCAGATTTCTTCGCATGCACAA 60.669 45.455 19.57 8.70 33.92 3.33
3092 3382 3.766151 CAGATTTCTTCGCATGCACAAT 58.234 40.909 19.57 7.45 0.00 2.71
3093 3383 3.546271 CAGATTTCTTCGCATGCACAATG 59.454 43.478 19.57 0.14 39.49 2.82
3094 3384 3.441222 AGATTTCTTCGCATGCACAATGA 59.559 39.130 19.57 3.00 38.72 2.57
3096 3386 1.812235 TCTTCGCATGCACAATGAGT 58.188 45.000 19.57 0.00 38.72 3.41
3166 3457 1.078759 CATGACGCCACGGAGAGAAC 61.079 60.000 0.00 0.00 0.00 3.01
3220 3522 1.228510 GGCCATGAAGGAAGAGGGG 59.771 63.158 0.00 0.00 41.22 4.79
3239 3541 1.647346 GCGACGAGAGAGAGAGAGAA 58.353 55.000 0.00 0.00 0.00 2.87
3240 3542 1.593006 GCGACGAGAGAGAGAGAGAAG 59.407 57.143 0.00 0.00 0.00 2.85
3241 3543 2.201732 CGACGAGAGAGAGAGAGAAGG 58.798 57.143 0.00 0.00 0.00 3.46
3242 3544 1.940613 GACGAGAGAGAGAGAGAAGGC 59.059 57.143 0.00 0.00 0.00 4.35
3248 3550 0.175531 GAGAGAGAGAAGGCTGTGGC 59.824 60.000 0.00 0.00 37.82 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 3.437049 AGCGGCTTTGTTAAGTTCATCTC 59.563 43.478 0.00 0.00 33.74 2.75
318 341 2.203126 CGGAGGCTTGGCTCCATC 60.203 66.667 32.64 14.03 39.62 3.51
607 645 3.474570 GGCGAGATGAGGCTGGGT 61.475 66.667 0.00 0.00 0.00 4.51
651 689 1.035932 TCCAGCTAGGGACGTAGCAC 61.036 60.000 21.58 0.00 46.81 4.40
659 697 2.759973 CGGCAGTCCAGCTAGGGA 60.760 66.667 0.00 0.00 38.24 4.20
727 765 5.821470 GTCTGTGCCTCTGTATACTACTACA 59.179 44.000 4.17 2.10 0.00 2.74
733 771 2.761208 GTGGTCTGTGCCTCTGTATACT 59.239 50.000 4.17 0.00 0.00 2.12
734 772 2.496070 TGTGGTCTGTGCCTCTGTATAC 59.504 50.000 0.00 0.00 0.00 1.47
735 773 2.760650 CTGTGGTCTGTGCCTCTGTATA 59.239 50.000 0.00 0.00 0.00 1.47
764 809 4.591321 ACAGACCTTCATCTCTCTCTCT 57.409 45.455 0.00 0.00 0.00 3.10
830 877 2.380249 TCTTGGTGAGGGAGAAGAGAGA 59.620 50.000 0.00 0.00 0.00 3.10
832 879 2.900546 GTTCTTGGTGAGGGAGAAGAGA 59.099 50.000 0.00 0.00 30.66 3.10
833 880 2.634940 TGTTCTTGGTGAGGGAGAAGAG 59.365 50.000 0.00 0.00 30.66 2.85
845 892 4.555709 TGCGGCGGTGTTCTTGGT 62.556 61.111 9.78 0.00 0.00 3.67
883 930 3.470567 GCGCACACGAGACGGAAG 61.471 66.667 0.30 0.00 43.93 3.46
884 931 3.973516 AGCGCACACGAGACGGAA 61.974 61.111 11.47 0.00 43.93 4.30
887 934 4.700365 TCCAGCGCACACGAGACG 62.700 66.667 11.47 0.00 43.93 4.18
928 978 1.572085 CCTTCATCGGATCATGGCGC 61.572 60.000 0.00 0.00 0.00 6.53
940 990 2.597455 CTCCTCTCCTCCTCCTTCATC 58.403 57.143 0.00 0.00 0.00 2.92
956 1051 1.079658 GCCACCTATCTATCCCCTCCT 59.920 57.143 0.00 0.00 0.00 3.69
982 1077 2.225017 ACATTGATCCGGACCCTTTGTT 60.225 45.455 6.12 0.00 0.00 2.83
991 1086 3.262151 TGGTTCTTGTACATTGATCCGGA 59.738 43.478 6.61 6.61 0.00 5.14
999 1094 2.816087 CTGCAGCTGGTTCTTGTACATT 59.184 45.455 17.12 0.00 0.00 2.71
1269 1370 2.277120 GCAAGCAAGCGCATCGAG 60.277 61.111 11.47 0.00 42.27 4.04
1270 1371 2.743538 AGCAAGCAAGCGCATCGA 60.744 55.556 11.47 0.00 42.27 3.59
1271 1372 2.277120 GAGCAAGCAAGCGCATCG 60.277 61.111 11.47 0.00 42.27 3.84
1316 1417 5.448632 CCAACACAGTTGAGTTTTGAGTACC 60.449 44.000 11.19 0.00 32.38 3.34
1319 1424 3.119495 GCCAACACAGTTGAGTTTTGAGT 60.119 43.478 11.19 0.00 32.38 3.41
1341 1446 0.884259 TGGCATCAACGACACACCAG 60.884 55.000 0.00 0.00 0.00 4.00
1386 1491 1.446907 CCTGCAGCAGGTTCTTGTAG 58.553 55.000 30.97 4.23 45.82 2.74
1439 1544 3.277211 GAGCGCACGGTGGTGTAGA 62.277 63.158 11.47 0.00 46.13 2.59
1527 1632 1.073722 CTGCTTCTTGGTCCTGGCA 59.926 57.895 0.00 0.00 0.00 4.92
1619 1724 0.828022 AGATCCGGTGGTATTGCGAA 59.172 50.000 0.00 0.00 0.00 4.70
1622 1727 1.308998 CCAAGATCCGGTGGTATTGC 58.691 55.000 0.00 0.00 0.00 3.56
1659 1764 1.150536 GCAGGAACAGTGGGACCAA 59.849 57.895 0.00 0.00 0.00 3.67
1669 1774 2.595463 GGCACTGCAGCAGGAACA 60.595 61.111 26.38 0.00 35.51 3.18
1820 1925 2.509561 GGAAGAAGAGCCCGCGAC 60.510 66.667 8.23 0.00 0.00 5.19
1825 1930 0.392327 GTGCAGAGGAAGAAGAGCCC 60.392 60.000 0.00 0.00 0.00 5.19
2296 2428 2.124529 GCCCTTGCCTAGTGCTCC 60.125 66.667 5.06 0.00 42.00 4.70
2364 2496 2.097791 AGCTACTGAACGTCGGAATCTC 59.902 50.000 0.00 0.00 0.00 2.75
2374 2506 7.756558 TGATCTCATCATATAGCTACTGAACG 58.243 38.462 10.88 6.72 33.59 3.95
2403 2535 4.267349 TCAAAACTCCCTTCTAGAACCG 57.733 45.455 0.00 0.00 0.00 4.44
2408 2540 3.861840 TGCGATCAAAACTCCCTTCTAG 58.138 45.455 0.00 0.00 0.00 2.43
2418 2552 2.971261 GGAACGAACTTGCGATCAAAAC 59.029 45.455 0.00 0.00 35.16 2.43
2435 2569 8.283291 CACTTACACAAATTTAGACAGAGGAAC 58.717 37.037 0.00 0.00 0.00 3.62
2436 2570 8.208224 TCACTTACACAAATTTAGACAGAGGAA 58.792 33.333 0.00 0.00 0.00 3.36
2437 2571 7.732025 TCACTTACACAAATTTAGACAGAGGA 58.268 34.615 0.00 0.00 0.00 3.71
2438 2572 7.962964 TCACTTACACAAATTTAGACAGAGG 57.037 36.000 0.00 0.00 0.00 3.69
2463 2597 0.035439 GGGGAGCAAAAGGTGATCGA 60.035 55.000 0.00 0.00 43.96 3.59
2464 2598 1.032114 GGGGGAGCAAAAGGTGATCG 61.032 60.000 0.00 0.00 43.96 3.69
2465 2599 0.332972 AGGGGGAGCAAAAGGTGATC 59.667 55.000 0.00 0.00 42.20 2.92
2466 2600 0.332972 GAGGGGGAGCAAAAGGTGAT 59.667 55.000 0.00 0.00 0.00 3.06
2467 2601 0.772124 AGAGGGGGAGCAAAAGGTGA 60.772 55.000 0.00 0.00 0.00 4.02
2474 2613 1.002274 GGAGAGAGAGGGGGAGCAA 59.998 63.158 0.00 0.00 0.00 3.91
2478 2617 1.701757 ATCCGGAGAGAGAGGGGGA 60.702 63.158 11.34 0.00 0.00 4.81
2480 2619 1.532794 CCATCCGGAGAGAGAGGGG 60.533 68.421 11.34 0.00 30.27 4.79
2482 2621 2.560119 CGCCATCCGGAGAGAGAGG 61.560 68.421 11.34 5.90 32.98 3.69
2485 2624 1.361993 CTTCGCCATCCGGAGAGAG 59.638 63.158 11.34 5.53 45.77 3.20
2486 2625 1.379977 ACTTCGCCATCCGGAGAGA 60.380 57.895 11.34 0.91 45.77 3.10
2499 2638 2.163010 TCTAAACCACCTAGCGACTTCG 59.837 50.000 0.00 0.00 43.27 3.79
2500 2639 3.863142 TCTAAACCACCTAGCGACTTC 57.137 47.619 0.00 0.00 0.00 3.01
2501 2640 3.118738 CCATCTAAACCACCTAGCGACTT 60.119 47.826 0.00 0.00 0.00 3.01
2502 2641 2.431057 CCATCTAAACCACCTAGCGACT 59.569 50.000 0.00 0.00 0.00 4.18
2503 2642 2.429610 TCCATCTAAACCACCTAGCGAC 59.570 50.000 0.00 0.00 0.00 5.19
2561 2705 3.583806 GATCGATCATGGCTTCTACTGG 58.416 50.000 20.52 0.00 0.00 4.00
2599 2747 5.126061 CCAAGGAAAATGGTGATGAACTAGG 59.874 44.000 0.00 0.00 33.08 3.02
2604 2752 3.509442 AGCCAAGGAAAATGGTGATGAA 58.491 40.909 0.00 0.00 40.23 2.57
2630 2850 1.162698 CAGGACACATGTGAAGGCAG 58.837 55.000 31.94 12.19 0.00 4.85
2632 2852 3.329300 ACAGGACACATGTGAAGGC 57.671 52.632 31.94 16.50 0.00 4.35
2647 2867 1.891060 GAGCAACGAACGAGCCACAG 61.891 60.000 0.14 0.00 0.00 3.66
2682 2914 4.853743 GCTTCTGACGCAATTAAAAGGAAG 59.146 41.667 0.77 0.00 0.00 3.46
2684 2916 4.072131 AGCTTCTGACGCAATTAAAAGGA 58.928 39.130 8.91 0.00 0.00 3.36
2686 2918 6.170675 ACTAGCTTCTGACGCAATTAAAAG 57.829 37.500 8.91 0.00 0.00 2.27
2693 2925 2.423892 CTCCTACTAGCTTCTGACGCAA 59.576 50.000 8.91 0.00 0.00 4.85
2694 2926 2.017782 CTCCTACTAGCTTCTGACGCA 58.982 52.381 8.91 0.00 0.00 5.24
2706 2938 6.771749 GCACTCAAGTAATCCTACTCCTACTA 59.228 42.308 0.00 0.00 37.39 1.82
2717 2950 5.523188 CAGATCAGAAGCACTCAAGTAATCC 59.477 44.000 0.00 0.00 0.00 3.01
2718 2951 6.336566 TCAGATCAGAAGCACTCAAGTAATC 58.663 40.000 0.00 0.00 0.00 1.75
2720 2953 5.728637 TCAGATCAGAAGCACTCAAGTAA 57.271 39.130 0.00 0.00 0.00 2.24
2721 2954 5.655974 AGATCAGATCAGAAGCACTCAAGTA 59.344 40.000 13.14 0.00 0.00 2.24
2740 2973 7.309133 GGTGTGGTTGTATTTTTGATCAGATCA 60.309 37.037 9.21 9.21 37.55 2.92
2750 2983 4.141620 TGGCAATGGTGTGGTTGTATTTTT 60.142 37.500 0.00 0.00 0.00 1.94
2755 2988 1.891811 CATGGCAATGGTGTGGTTGTA 59.108 47.619 0.00 0.00 0.00 2.41
2756 2989 0.680618 CATGGCAATGGTGTGGTTGT 59.319 50.000 0.00 0.00 0.00 3.32
2772 3005 1.521457 CGTCCGTCCATGGTCCATG 60.521 63.158 23.11 23.11 41.10 3.66
2803 3068 1.302366 TAATTGATGCTCTGCGGCAG 58.698 50.000 23.72 23.72 45.75 4.85
2804 3069 1.401552 GTTAATTGATGCTCTGCGGCA 59.598 47.619 1.29 1.29 46.63 5.69
2805 3070 1.268743 GGTTAATTGATGCTCTGCGGC 60.269 52.381 0.00 0.00 0.00 6.53
2806 3071 1.003545 CGGTTAATTGATGCTCTGCGG 60.004 52.381 0.00 0.00 0.00 5.69
2807 3072 1.003545 CCGGTTAATTGATGCTCTGCG 60.004 52.381 0.00 0.00 0.00 5.18
2812 3077 0.393808 ACGGCCGGTTAATTGATGCT 60.394 50.000 31.76 0.00 0.00 3.79
2826 3091 0.455410 TTATCAAGCAATGCACGGCC 59.545 50.000 8.35 0.00 0.00 6.13
2841 3106 7.114106 GCAGAGTCAAAGCAAAGAGTTTTTATC 59.886 37.037 0.00 0.00 0.00 1.75
2847 3112 3.549794 AGCAGAGTCAAAGCAAAGAGTT 58.450 40.909 0.00 0.00 0.00 3.01
2848 3113 3.137533 GAGCAGAGTCAAAGCAAAGAGT 58.862 45.455 0.00 0.00 0.00 3.24
2955 3233 1.689273 GCTCCTGATAAGGGTGTCGAT 59.311 52.381 0.00 0.00 0.00 3.59
2962 3240 4.766970 CGCAGCTCCTGATAAGGG 57.233 61.111 0.00 0.00 32.44 3.95
3058 3348 0.250513 AAATCTGCACCCGTCTCCTC 59.749 55.000 0.00 0.00 0.00 3.71
3064 3354 1.298859 GCGAAGAAATCTGCACCCGT 61.299 55.000 0.00 0.00 0.00 5.28
3070 3360 1.135603 TGTGCATGCGAAGAAATCTGC 60.136 47.619 14.09 0.00 0.00 4.26
3072 3362 3.441222 TCATTGTGCATGCGAAGAAATCT 59.559 39.130 14.09 0.00 32.13 2.40
3073 3363 3.761657 TCATTGTGCATGCGAAGAAATC 58.238 40.909 14.09 0.00 32.13 2.17
3074 3364 3.192001 ACTCATTGTGCATGCGAAGAAAT 59.808 39.130 14.09 5.35 32.13 2.17
3075 3365 2.553602 ACTCATTGTGCATGCGAAGAAA 59.446 40.909 14.09 3.07 32.13 2.52
3076 3366 2.095617 CACTCATTGTGCATGCGAAGAA 60.096 45.455 14.09 1.20 40.06 2.52
3077 3367 1.465777 CACTCATTGTGCATGCGAAGA 59.534 47.619 14.09 5.64 40.06 2.87
3078 3368 1.891178 CACTCATTGTGCATGCGAAG 58.109 50.000 14.09 6.26 40.06 3.79
3220 3522 1.593006 CTTCTCTCTCTCTCTCGTCGC 59.407 57.143 0.00 0.00 0.00 5.19
3239 3541 4.626081 GTGACCACGCCACAGCCT 62.626 66.667 0.00 0.00 34.81 4.58
3499 3833 4.032786 TCGATCAAATTCGACGTACGTAGA 59.967 41.667 24.53 24.53 42.81 2.59


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

AutoCloner maintained by Alex Coulton.