Multiple sequence alignment - TraesCS7D01G217500

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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 TraesCS7D01G217500 chr7D 100.000 3473 0 0 1 3473 178133447 178129975 0.000000e+00 6414.0
1 TraesCS7D01G217500 chr7D 82.232 439 38 20 2803 3230 178123276 178122867 3.320000e-90 342.0
2 TraesCS7D01G217500 chr7D 93.367 196 12 1 2306 2500 178125657 178125462 4.390000e-74 289.0
3 TraesCS7D01G217500 chr7D 89.333 75 8 0 2705 2779 178123350 178123276 1.030000e-15 95.3
4 TraesCS7D01G217500 chr7A 92.502 2574 90 45 673 3230 182124077 182121591 0.000000e+00 3589.0
5 TraesCS7D01G217500 chr7B 91.757 2584 105 47 664 3229 144112587 144110094 0.000000e+00 3493.0
6 TraesCS7D01G217500 chr7B 85.011 467 47 9 79 540 103621356 103621804 1.470000e-123 453.0
7 TraesCS7D01G217500 chr2D 99.539 651 3 0 1 651 602572555 602573205 0.000000e+00 1186.0
8 TraesCS7D01G217500 chr2D 98.677 529 7 0 1 529 321098102 321098630 0.000000e+00 939.0
9 TraesCS7D01G217500 chr2D 99.373 319 2 0 333 651 602573313 602573631 2.320000e-161 579.0
10 TraesCS7D01G217500 chr2D 90.863 197 16 1 3276 3472 105493232 105493426 2.660000e-66 263.0
11 TraesCS7D01G217500 chr2D 90.000 180 18 0 3294 3473 650889307 650889486 2.080000e-57 233.0
12 TraesCS7D01G217500 chr2D 98.529 68 1 0 561 628 602573249 602573316 1.690000e-23 121.0
13 TraesCS7D01G217500 chr2D 97.674 43 1 0 1 43 110874254 110874212 1.340000e-09 75.0
14 TraesCS7D01G217500 chr3D 99.078 651 6 0 1 651 343925620 343926270 0.000000e+00 1170.0
15 TraesCS7D01G217500 chr3D 98.300 647 5 1 3 649 380366349 380365709 0.000000e+00 1129.0
16 TraesCS7D01G217500 chr6D 98.476 656 9 1 1 655 69916134 69916789 0.000000e+00 1155.0
17 TraesCS7D01G217500 chr6D 99.333 300 2 0 1 300 297437653 297437952 8.480000e-151 544.0
18 TraesCS7D01G217500 chr6D 85.439 467 44 10 79 540 42450734 42451181 6.790000e-127 464.0
19 TraesCS7D01G217500 chr2B 93.934 544 29 1 1 540 596984200 596984743 0.000000e+00 819.0
20 TraesCS7D01G217500 chr2B 87.047 193 25 0 3281 3473 729496479 729496287 5.840000e-53 219.0
21 TraesCS7D01G217500 chr3B 91.919 198 15 1 3276 3473 717655164 717654968 3.410000e-70 276.0
22 TraesCS7D01G217500 chr1D 90.769 195 18 0 3279 3473 467366251 467366057 9.560000e-66 261.0
23 TraesCS7D01G217500 chr1D 90.769 195 18 0 3279 3473 467366782 467366588 9.560000e-66 261.0
24 TraesCS7D01G217500 chr1A 88.832 197 22 0 3277 3473 516451597 516451793 3.460000e-60 243.0
25 TraesCS7D01G217500 chr2A 87.500 200 21 3 3276 3472 645821509 645821707 9.700000e-56 228.0
26 TraesCS7D01G217500 chr1B 90.517 116 10 1 3280 3394 61315212 61315097 6.000000e-33 152.0


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 TraesCS7D01G217500 chr7D 178129975 178133447 3472 True 6414.000000 6414 100.000000 1 3473 1 chr7D.!!$R1 3472
1 TraesCS7D01G217500 chr7D 178122867 178125657 2790 True 242.100000 342 88.310667 2306 3230 3 chr7D.!!$R2 924
2 TraesCS7D01G217500 chr7A 182121591 182124077 2486 True 3589.000000 3589 92.502000 673 3230 1 chr7A.!!$R1 2557
3 TraesCS7D01G217500 chr7B 144110094 144112587 2493 True 3493.000000 3493 91.757000 664 3229 1 chr7B.!!$R1 2565
4 TraesCS7D01G217500 chr2D 321098102 321098630 528 False 939.000000 939 98.677000 1 529 1 chr2D.!!$F2 528
5 TraesCS7D01G217500 chr2D 602572555 602573631 1076 False 628.666667 1186 99.147000 1 651 3 chr2D.!!$F4 650
6 TraesCS7D01G217500 chr3D 343925620 343926270 650 False 1170.000000 1170 99.078000 1 651 1 chr3D.!!$F1 650
7 TraesCS7D01G217500 chr3D 380365709 380366349 640 True 1129.000000 1129 98.300000 3 649 1 chr3D.!!$R1 646
8 TraesCS7D01G217500 chr6D 69916134 69916789 655 False 1155.000000 1155 98.476000 1 655 1 chr6D.!!$F2 654
9 TraesCS7D01G217500 chr2B 596984200 596984743 543 False 819.000000 819 93.934000 1 540 1 chr2B.!!$F1 539
10 TraesCS7D01G217500 chr1D 467366057 467366782 725 True 261.000000 261 90.769000 3279 3473 2 chr1D.!!$R1 194

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
518 524 1.221414 GAGGTGTATGCTTCGATGCC 58.779 55.0 19.4 6.03 0.00 4.40 F
1368 1459 0.107848 GGATCATCGGGTTCGTGGTT 60.108 55.0 0.0 0.00 37.69 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2215 0.107214 CGATGTAACCCATGGTGCCT 60.107 55.0 11.73 0.0 35.34 4.75 R
2519 2658 0.095245 GACGACGACGACGACCAATA 59.905 55.0 25.15 0.0 42.66 1.90 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
518 524 1.221414 GAGGTGTATGCTTCGATGCC 58.779 55.000 19.40 6.03 0.00 4.40
651 657 1.369091 GCACGGGCAATGTCCTAGTG 61.369 60.000 3.77 4.88 40.72 2.74
657 746 2.565841 GGCAATGTCCTAGTGGATCAC 58.434 52.381 0.00 0.00 45.29 3.06
659 748 3.370953 GGCAATGTCCTAGTGGATCACTT 60.371 47.826 5.86 0.00 42.59 3.16
736 825 7.018550 AGGGGCATAATAGTCATTTCCATTCTA 59.981 37.037 0.00 0.00 0.00 2.10
805 896 2.825836 CGCCAATCAGACTGGGCC 60.826 66.667 13.63 0.00 43.50 5.80
809 900 1.622607 CCAATCAGACTGGGCCGGTA 61.623 60.000 20.19 2.83 0.00 4.02
878 969 1.515519 GCATCACAGCCGTGCATTG 60.516 57.895 0.00 0.00 43.28 2.82
935 1026 2.888447 GCTGTGCTCTCCACCCACT 61.888 63.158 0.00 0.00 44.01 4.00
971 1062 2.669240 GGAACCTTCCTCCCCACG 59.331 66.667 0.00 0.00 44.11 4.94
1020 1111 2.125832 GCGTTAGCGGCAGGTACA 60.126 61.111 1.45 0.00 38.78 2.90
1059 1150 0.250793 TCTTCCTCGTCTCTCTCGCT 59.749 55.000 0.00 0.00 0.00 4.93
1368 1459 0.107848 GGATCATCGGGTTCGTGGTT 60.108 55.000 0.00 0.00 37.69 3.67
1371 1462 1.004320 CATCGGGTTCGTGGTTGGA 60.004 57.895 0.00 0.00 37.69 3.53
1380 1471 2.124695 GTGGTTGGATCCCTCGCC 60.125 66.667 9.90 6.66 0.00 5.54
1661 1752 1.841302 ATCAAGAAGCAGGTGGGCGA 61.841 55.000 0.00 0.00 39.27 5.54
1662 1753 2.032681 AAGAAGCAGGTGGGCGAC 59.967 61.111 0.00 0.00 39.27 5.19
1663 1754 3.883744 AAGAAGCAGGTGGGCGACG 62.884 63.158 0.00 0.00 39.27 5.12
1870 1961 4.312231 TGCACAACGCGCTCAAGC 62.312 61.111 5.73 4.96 46.97 4.01
2518 2657 2.661594 GCCAAAGCTCCGTGTTTAAAG 58.338 47.619 0.00 0.00 35.50 1.85
2519 2658 2.034179 GCCAAAGCTCCGTGTTTAAAGT 59.966 45.455 0.00 0.00 35.50 2.66
2520 2659 3.251487 GCCAAAGCTCCGTGTTTAAAGTA 59.749 43.478 0.00 0.00 35.50 2.24
2521 2660 4.082949 GCCAAAGCTCCGTGTTTAAAGTAT 60.083 41.667 0.00 0.00 35.50 2.12
2522 2661 5.564063 GCCAAAGCTCCGTGTTTAAAGTATT 60.564 40.000 0.00 0.00 35.50 1.89
2523 2662 5.856455 CCAAAGCTCCGTGTTTAAAGTATTG 59.144 40.000 0.00 0.00 0.00 1.90
2524 2663 5.622770 AAGCTCCGTGTTTAAAGTATTGG 57.377 39.130 0.00 0.00 0.00 3.16
2547 2692 0.383491 TCGTCGTCGTCGTCTTCAAC 60.383 55.000 11.41 0.00 38.33 3.18
2614 3059 1.079336 GGGTCAGCGGGTCAAGTAC 60.079 63.158 0.00 0.00 0.00 2.73
2651 3096 1.952621 AAAGACCGGGAAGGAGATCA 58.047 50.000 6.32 0.00 45.00 2.92
2652 3097 1.952621 AAGACCGGGAAGGAGATCAA 58.047 50.000 6.32 0.00 45.00 2.57
2653 3098 2.182516 AGACCGGGAAGGAGATCAAT 57.817 50.000 6.32 0.00 45.00 2.57
2654 3099 2.482494 AGACCGGGAAGGAGATCAATT 58.518 47.619 6.32 0.00 45.00 2.32
2655 3100 3.654273 AGACCGGGAAGGAGATCAATTA 58.346 45.455 6.32 0.00 45.00 1.40
2656 3101 4.235372 AGACCGGGAAGGAGATCAATTAT 58.765 43.478 6.32 0.00 45.00 1.28
2657 3102 4.660771 AGACCGGGAAGGAGATCAATTATT 59.339 41.667 6.32 0.00 45.00 1.40
2658 3103 4.718961 ACCGGGAAGGAGATCAATTATTG 58.281 43.478 6.32 0.00 45.00 1.90
2659 3104 4.166144 ACCGGGAAGGAGATCAATTATTGT 59.834 41.667 6.32 0.00 45.00 2.71
2660 3105 5.368523 ACCGGGAAGGAGATCAATTATTGTA 59.631 40.000 6.32 0.00 45.00 2.41
2661 3106 5.701290 CCGGGAAGGAGATCAATTATTGTAC 59.299 44.000 4.77 1.21 45.00 2.90
2662 3107 6.288294 CGGGAAGGAGATCAATTATTGTACA 58.712 40.000 4.77 0.00 0.00 2.90
2663 3108 6.202954 CGGGAAGGAGATCAATTATTGTACAC 59.797 42.308 4.77 0.26 0.00 2.90
2664 3109 7.054124 GGGAAGGAGATCAATTATTGTACACA 58.946 38.462 4.77 0.00 0.00 3.72
2665 3110 7.556275 GGGAAGGAGATCAATTATTGTACACAA 59.444 37.037 4.77 0.00 40.51 3.33
2666 3111 8.956426 GGAAGGAGATCAATTATTGTACACAAA 58.044 33.333 4.77 0.00 39.55 2.83
2667 3112 9.994432 GAAGGAGATCAATTATTGTACACAAAG 57.006 33.333 4.77 0.00 39.55 2.77
2668 3113 9.520515 AAGGAGATCAATTATTGTACACAAAGT 57.479 29.630 4.77 0.00 39.55 2.66
2669 3114 9.520515 AGGAGATCAATTATTGTACACAAAGTT 57.479 29.630 4.77 0.00 39.55 2.66
2670 3115 9.774742 GGAGATCAATTATTGTACACAAAGTTC 57.225 33.333 4.77 0.00 39.55 3.01
2686 3131 9.950680 ACACAAAGTTCATCTACAAAACTATTG 57.049 29.630 0.00 0.00 33.08 1.90
2734 4777 5.818136 TTTCTTGACTTTGACTTGTCTGG 57.182 39.130 2.35 0.00 34.57 3.86
2746 4790 5.305585 TGACTTGTCTGGTTTGTAAGATCC 58.694 41.667 2.35 0.00 0.00 3.36
2752 4796 4.151867 GTCTGGTTTGTAAGATCCAACGAC 59.848 45.833 0.00 0.00 0.00 4.34
2765 4809 5.803967 AGATCCAACGACGTATCTAAACAAC 59.196 40.000 9.47 0.00 0.00 3.32
2766 4810 3.913763 TCCAACGACGTATCTAAACAACG 59.086 43.478 0.00 0.00 42.17 4.10
2768 4812 4.201428 CCAACGACGTATCTAAACAACGAC 60.201 45.833 0.00 0.00 39.80 4.34
2782 4826 9.016623 TCTAAACAACGACTATTAATCACATCG 57.983 33.333 0.00 0.36 35.74 3.84
2783 4827 5.637104 ACAACGACTATTAATCACATCGC 57.363 39.130 0.00 0.00 32.95 4.58
2784 4828 4.206404 ACAACGACTATTAATCACATCGCG 59.794 41.667 0.00 0.00 32.95 5.87
2785 4829 3.961182 ACGACTATTAATCACATCGCGT 58.039 40.909 5.77 0.00 32.95 6.01
2795 4839 3.274393 ACATCGCGTGATAAGAGCC 57.726 52.632 11.84 0.00 32.18 4.70
2796 4840 0.459899 ACATCGCGTGATAAGAGCCA 59.540 50.000 11.84 0.00 32.18 4.75
2797 4841 1.069204 ACATCGCGTGATAAGAGCCAT 59.931 47.619 11.84 0.00 32.18 4.40
2798 4842 1.458445 CATCGCGTGATAAGAGCCATG 59.542 52.381 11.84 0.00 32.18 3.66
2799 4843 0.249447 TCGCGTGATAAGAGCCATGG 60.249 55.000 7.63 7.63 0.00 3.66
2800 4844 1.224069 CGCGTGATAAGAGCCATGGG 61.224 60.000 15.13 0.00 0.00 4.00
2845 4889 1.901650 GCGTTACCTGCAGTGCACTC 61.902 60.000 18.64 12.59 33.79 3.51
2863 4907 4.499696 GCACTCATGTGGTAAGCACTTTTT 60.500 41.667 0.00 0.00 43.97 1.94
2886 4930 1.625315 AGCCAGTGCACTGATGTCTTA 59.375 47.619 41.50 0.00 46.59 2.10
2904 4948 0.108992 TAATTGGAACGAGTCGCGCT 60.109 50.000 13.59 0.89 46.04 5.92
2906 4950 2.486636 ATTGGAACGAGTCGCGCTCA 62.487 55.000 23.57 3.41 44.33 4.26
2907 4951 3.173240 GGAACGAGTCGCGCTCAC 61.173 66.667 23.57 15.86 44.33 3.51
2908 4952 3.173240 GAACGAGTCGCGCTCACC 61.173 66.667 23.57 12.07 44.33 4.02
2926 4970 1.762957 ACCTAGCTTCGTATGCATGGT 59.237 47.619 10.16 1.14 34.98 3.55
2927 4971 2.138320 CCTAGCTTCGTATGCATGGTG 58.862 52.381 10.16 0.00 0.00 4.17
2928 4972 2.483714 CCTAGCTTCGTATGCATGGTGT 60.484 50.000 10.16 0.00 0.00 4.16
2929 4973 1.656652 AGCTTCGTATGCATGGTGTC 58.343 50.000 10.16 0.00 0.00 3.67
2933 4977 2.871182 TCGTATGCATGGTGTCTCTC 57.129 50.000 10.16 0.00 0.00 3.20
2949 4996 0.323178 TCTCGTGGTAGTGGAGGACC 60.323 60.000 0.00 0.00 36.17 4.46
2950 4997 0.611062 CTCGTGGTAGTGGAGGACCA 60.611 60.000 0.00 0.00 43.55 4.02
2973 5023 4.469945 AGAGAAAATAGACCACCGGATCAA 59.530 41.667 9.46 0.00 0.00 2.57
2992 5042 7.330454 CGGATCAAGATCGATATGATGAAAGTT 59.670 37.037 23.59 5.88 37.47 2.66
2993 5043 9.645059 GGATCAAGATCGATATGATGAAAGTTA 57.355 33.333 23.59 0.01 37.47 2.24
3003 5056 8.076178 CGATATGATGAAAGTTAAATTGGGACC 58.924 37.037 0.00 0.00 0.00 4.46
3008 5061 3.653539 AAGTTAAATTGGGACCGCAAC 57.346 42.857 1.55 0.00 0.00 4.17
3024 5077 1.066918 AACGAAGACAAGTCGCCGT 59.933 52.632 13.93 13.93 42.27 5.68
3025 5078 0.529119 AACGAAGACAAGTCGCCGTT 60.529 50.000 20.88 20.88 42.59 4.44
3026 5079 0.529119 ACGAAGACAAGTCGCCGTTT 60.529 50.000 13.93 0.00 42.27 3.60
3027 5080 0.580104 CGAAGACAAGTCGCCGTTTT 59.420 50.000 8.39 0.00 34.09 2.43
3028 5081 1.396815 CGAAGACAAGTCGCCGTTTTC 60.397 52.381 8.39 0.00 34.09 2.29
3029 5082 0.942252 AAGACAAGTCGCCGTTTTCC 59.058 50.000 0.00 0.00 34.09 3.13
3030 5083 0.883370 AGACAAGTCGCCGTTTTCCC 60.883 55.000 0.00 0.00 34.09 3.97
3031 5084 1.848932 GACAAGTCGCCGTTTTCCCC 61.849 60.000 0.00 0.00 0.00 4.81
3032 5085 1.894756 CAAGTCGCCGTTTTCCCCA 60.895 57.895 0.00 0.00 0.00 4.96
3033 5086 1.895231 AAGTCGCCGTTTTCCCCAC 60.895 57.895 0.00 0.00 0.00 4.61
3034 5087 2.281276 GTCGCCGTTTTCCCCACT 60.281 61.111 0.00 0.00 0.00 4.00
3035 5088 2.281208 TCGCCGTTTTCCCCACTG 60.281 61.111 0.00 0.00 0.00 3.66
3036 5089 3.361977 CGCCGTTTTCCCCACTGG 61.362 66.667 0.00 0.00 0.00 4.00
3037 5090 2.203437 GCCGTTTTCCCCACTGGT 60.203 61.111 0.00 0.00 34.77 4.00
3038 5091 1.073548 GCCGTTTTCCCCACTGGTA 59.926 57.895 0.00 0.00 34.77 3.25
3039 5092 1.239296 GCCGTTTTCCCCACTGGTAC 61.239 60.000 0.00 0.00 34.77 3.34
3040 5093 0.607217 CCGTTTTCCCCACTGGTACC 60.607 60.000 4.43 4.43 34.77 3.34
3041 5094 0.952010 CGTTTTCCCCACTGGTACCG 60.952 60.000 7.57 4.79 34.77 4.02
3042 5095 1.073548 TTTTCCCCACTGGTACCGC 59.926 57.895 7.57 0.00 34.77 5.68
3043 5096 2.734948 TTTTCCCCACTGGTACCGCG 62.735 60.000 7.57 0.00 34.77 6.46
3090 5145 0.310543 TTGTTGTGTTCGCTGCATCC 59.689 50.000 0.00 0.00 0.00 3.51
3097 5152 1.005037 TTCGCTGCATCCGTTCACT 60.005 52.632 0.00 0.00 0.00 3.41
3108 5163 1.344438 TCCGTTCACTCTGTCATGCTT 59.656 47.619 0.00 0.00 0.00 3.91
3114 5169 1.197036 CACTCTGTCATGCTTGTGCTG 59.803 52.381 0.00 0.00 40.48 4.41
3133 5188 4.549516 GTCTACGTCGCGCCTCCC 62.550 72.222 0.00 0.00 0.00 4.30
3165 5220 7.765307 AACAGAGAAACTGGTGCAATTATATG 58.235 34.615 0.00 0.00 45.73 1.78
3173 5228 4.667262 TGGTGCAATTATATGTGCGAAAC 58.333 39.130 0.00 0.00 43.93 2.78
3188 5243 2.338500 CGAAACTCTACAGGTTCAGCC 58.662 52.381 0.00 0.00 45.62 4.85
3230 5291 0.379669 GCGACGGGAAGAATAGACGA 59.620 55.000 0.00 0.00 0.00 4.20
3231 5292 1.859197 GCGACGGGAAGAATAGACGAC 60.859 57.143 0.00 0.00 0.00 4.34
3232 5293 1.669779 CGACGGGAAGAATAGACGACT 59.330 52.381 0.00 0.00 0.00 4.18
3233 5294 2.097142 CGACGGGAAGAATAGACGACTT 59.903 50.000 0.00 0.00 0.00 3.01
3234 5295 3.693654 GACGGGAAGAATAGACGACTTC 58.306 50.000 0.00 0.00 39.16 3.01
3248 5309 2.537401 CGACTTCCGTTGGATAGAACC 58.463 52.381 0.00 0.00 0.00 3.62
3249 5310 2.094390 CGACTTCCGTTGGATAGAACCA 60.094 50.000 0.00 0.00 38.24 3.67
3250 5311 3.522553 GACTTCCGTTGGATAGAACCAG 58.477 50.000 0.00 0.00 41.19 4.00
3251 5312 2.280628 CTTCCGTTGGATAGAACCAGC 58.719 52.381 0.00 0.00 41.19 4.85
3252 5313 1.271856 TCCGTTGGATAGAACCAGCA 58.728 50.000 0.00 0.00 40.36 4.41
3253 5314 1.066430 TCCGTTGGATAGAACCAGCAC 60.066 52.381 0.00 0.00 40.36 4.40
3254 5315 1.369625 CGTTGGATAGAACCAGCACC 58.630 55.000 0.00 0.00 40.36 5.01
3255 5316 1.751437 GTTGGATAGAACCAGCACCC 58.249 55.000 0.00 0.00 41.19 4.61
3256 5317 1.004277 GTTGGATAGAACCAGCACCCA 59.996 52.381 0.00 0.00 41.19 4.51
3257 5318 0.911769 TGGATAGAACCAGCACCCAG 59.088 55.000 0.00 0.00 34.77 4.45
3258 5319 0.912486 GGATAGAACCAGCACCCAGT 59.088 55.000 0.00 0.00 0.00 4.00
3259 5320 1.407437 GGATAGAACCAGCACCCAGTG 60.407 57.143 0.00 0.00 36.51 3.66
3260 5321 0.620556 ATAGAACCAGCACCCAGTGG 59.379 55.000 0.63 0.63 39.98 4.00
3261 5322 2.124507 TAGAACCAGCACCCAGTGGC 62.125 60.000 2.61 0.00 37.34 5.01
3262 5323 4.954970 AACCAGCACCCAGTGGCG 62.955 66.667 2.61 0.00 37.34 5.69
3276 5337 4.785453 GGCGGAGACAAGCAGGGG 62.785 72.222 0.00 0.00 31.66 4.79
3277 5338 4.785453 GCGGAGACAAGCAGGGGG 62.785 72.222 0.00 0.00 0.00 5.40
3311 5372 1.339711 GCTAACTGCGGCAAAATGTG 58.660 50.000 3.44 0.00 0.00 3.21
3312 5373 1.981254 CTAACTGCGGCAAAATGTGG 58.019 50.000 3.44 0.00 0.00 4.17
3314 5375 0.314935 AACTGCGGCAAAATGTGGAG 59.685 50.000 3.44 0.00 0.00 3.86
3316 5377 0.109597 CTGCGGCAAAATGTGGAGAC 60.110 55.000 3.44 0.00 0.00 3.36
3384 5985 1.000145 GTTCCGGCTAGCGAAGAAAG 59.000 55.000 9.00 0.00 0.00 2.62
3411 6012 2.536728 CGCTCGCTCGCAAAAATGAATA 60.537 45.455 0.00 0.00 0.00 1.75
3420 6021 2.992543 GCAAAAATGAATACGCCAAGCA 59.007 40.909 0.00 0.00 0.00 3.91
3423 6024 2.418368 AATGAATACGCCAAGCAGGA 57.582 45.000 0.00 0.00 41.22 3.86
3425 6026 1.953559 TGAATACGCCAAGCAGGATC 58.046 50.000 0.00 0.00 41.22 3.36
3430 6031 2.464459 CGCCAAGCAGGATCCGAAC 61.464 63.158 5.98 0.00 41.22 3.95
3441 6042 1.334243 GGATCCGAACACTAGACCTCG 59.666 57.143 0.00 0.86 0.00 4.63
3446 6047 1.068472 CGAACACTAGACCTCGTGCTT 60.068 52.381 0.00 0.00 34.58 3.91
3448 6049 1.617322 ACACTAGACCTCGTGCTTCA 58.383 50.000 0.00 0.00 34.58 3.02
3460 6061 4.156664 TCGTGCTTCACAAGTACTACTC 57.843 45.455 0.00 0.00 41.29 2.59
3463 6064 4.155462 CGTGCTTCACAAGTACTACTCCTA 59.845 45.833 0.00 0.00 41.29 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
334 340 1.410083 GCATCACCAGGAGGGCAATTA 60.410 52.381 0.00 0.00 42.05 1.40
518 524 2.905959 TTTCTCATGCACATCAAGCG 57.094 45.000 0.00 0.00 33.85 4.68
627 633 2.903547 GACATTGCCCGTGCGTTGT 61.904 57.895 0.00 0.00 41.78 3.32
878 969 3.048337 TGAGGATTACCGTGTGGAAAC 57.952 47.619 0.00 0.00 41.83 2.78
935 1026 3.948719 GCGTGTGTGGGGGAGGAA 61.949 66.667 0.00 0.00 0.00 3.36
971 1062 1.280206 ACGTTTAGCTCGTTGGTCGC 61.280 55.000 0.00 0.00 38.38 5.19
1059 1150 1.153208 GACGAGGAGGAGGAGCGTA 60.153 63.158 0.00 0.00 35.09 4.42
2124 2215 0.107214 CGATGTAACCCATGGTGCCT 60.107 55.000 11.73 0.00 35.34 4.75
2513 2652 4.158384 GACGACGACGACCAATACTTTAA 58.842 43.478 15.32 0.00 42.66 1.52
2514 2653 3.724716 CGACGACGACGACCAATACTTTA 60.725 47.826 15.32 0.00 42.66 1.85
2515 2654 2.589014 GACGACGACGACCAATACTTT 58.411 47.619 15.32 0.00 42.66 2.66
2516 2655 1.464687 CGACGACGACGACCAATACTT 60.465 52.381 15.32 0.00 42.66 2.24
2518 2657 0.179215 ACGACGACGACGACCAATAC 60.179 55.000 25.15 0.00 42.66 1.89
2519 2658 0.095245 GACGACGACGACGACCAATA 59.905 55.000 25.15 0.00 42.66 1.90
2520 2659 1.154338 GACGACGACGACGACCAAT 60.154 57.895 25.15 3.08 42.66 3.16
2521 2660 2.249309 GACGACGACGACGACCAA 59.751 61.111 25.15 0.00 42.66 3.67
2547 2692 1.009078 CACGCATGACACATACCCAG 58.991 55.000 0.00 0.00 0.00 4.45
2655 3100 9.730420 GTTTTGTAGATGAACTTTGTGTACAAT 57.270 29.630 0.00 0.00 35.55 2.71
2656 3101 8.952278 AGTTTTGTAGATGAACTTTGTGTACAA 58.048 29.630 0.00 0.00 29.81 2.41
2657 3102 8.500753 AGTTTTGTAGATGAACTTTGTGTACA 57.499 30.769 0.00 0.00 29.81 2.90
2660 3105 9.950680 CAATAGTTTTGTAGATGAACTTTGTGT 57.049 29.630 0.00 0.00 35.43 3.72
2661 3106 9.950680 ACAATAGTTTTGTAGATGAACTTTGTG 57.049 29.630 0.00 0.00 35.66 3.33
2666 3111 9.772973 TGTGTACAATAGTTTTGTAGATGAACT 57.227 29.630 6.44 0.00 35.77 3.01
2677 3122 9.912634 CCAATCTCATTTGTGTACAATAGTTTT 57.087 29.630 0.00 0.00 35.55 2.43
2678 3123 8.522830 CCCAATCTCATTTGTGTACAATAGTTT 58.477 33.333 0.00 0.00 35.55 2.66
2734 4777 5.803967 AGATACGTCGTTGGATCTTACAAAC 59.196 40.000 1.78 0.00 0.00 2.93
2746 4790 4.614284 AGTCGTTGTTTAGATACGTCGTTG 59.386 41.667 1.78 0.00 36.70 4.10
2778 4822 1.458445 CATGGCTCTTATCACGCGATG 59.542 52.381 15.93 7.85 34.48 3.84
2779 4823 1.606480 CCATGGCTCTTATCACGCGAT 60.606 52.381 15.93 0.00 35.50 4.58
2780 4824 0.249447 CCATGGCTCTTATCACGCGA 60.249 55.000 15.93 0.00 0.00 5.87
2781 4825 1.224069 CCCATGGCTCTTATCACGCG 61.224 60.000 6.09 3.53 0.00 6.01
2782 4826 1.510480 GCCCATGGCTCTTATCACGC 61.510 60.000 6.09 0.00 46.69 5.34
2783 4827 2.621763 GCCCATGGCTCTTATCACG 58.378 57.895 6.09 0.00 46.69 4.35
2863 4907 0.109153 ACATCAGTGCACTGGCTCAA 59.891 50.000 39.04 24.26 43.91 3.02
2869 4913 4.696877 TCCAATTAAGACATCAGTGCACTG 59.303 41.667 36.07 36.07 45.08 3.66
2886 4930 1.352156 GAGCGCGACTCGTTCCAATT 61.352 55.000 12.10 0.00 41.68 2.32
2904 4948 2.224042 CCATGCATACGAAGCTAGGTGA 60.224 50.000 0.00 0.00 0.00 4.02
2906 4950 1.762957 ACCATGCATACGAAGCTAGGT 59.237 47.619 0.00 0.00 35.86 3.08
2907 4951 2.138320 CACCATGCATACGAAGCTAGG 58.862 52.381 0.00 0.00 34.37 3.02
2908 4952 2.797156 GACACCATGCATACGAAGCTAG 59.203 50.000 0.00 0.00 0.00 3.42
2926 4970 1.613520 CCTCCACTACCACGAGAGACA 60.614 57.143 0.00 0.00 0.00 3.41
2927 4971 1.096416 CCTCCACTACCACGAGAGAC 58.904 60.000 0.00 0.00 0.00 3.36
2928 4972 0.989602 TCCTCCACTACCACGAGAGA 59.010 55.000 0.00 0.00 0.00 3.10
2929 4973 1.096416 GTCCTCCACTACCACGAGAG 58.904 60.000 0.00 0.00 0.00 3.20
2933 4977 0.611062 TCTGGTCCTCCACTACCACG 60.611 60.000 0.00 0.00 40.84 4.94
2949 4996 3.887621 TCCGGTGGTCTATTTTCTCTG 57.112 47.619 0.00 0.00 0.00 3.35
2950 4997 4.030913 TGATCCGGTGGTCTATTTTCTCT 58.969 43.478 0.00 0.00 0.00 3.10
2992 5042 1.807742 CTTCGTTGCGGTCCCAATTTA 59.192 47.619 0.00 0.00 0.00 1.40
2993 5043 0.596082 CTTCGTTGCGGTCCCAATTT 59.404 50.000 0.00 0.00 0.00 1.82
2996 5049 1.595929 GTCTTCGTTGCGGTCCCAA 60.596 57.895 0.00 0.00 0.00 4.12
2998 5051 1.566018 CTTGTCTTCGTTGCGGTCCC 61.566 60.000 0.00 0.00 0.00 4.46
3003 5056 1.154836 GCGACTTGTCTTCGTTGCG 60.155 57.895 0.00 0.00 38.77 4.85
3008 5061 0.580104 AAAACGGCGACTTGTCTTCG 59.420 50.000 16.62 9.64 39.56 3.79
3024 5077 1.073548 GCGGTACCAGTGGGGAAAA 59.926 57.895 15.21 0.00 41.15 2.29
3025 5078 2.751688 GCGGTACCAGTGGGGAAA 59.248 61.111 15.21 0.00 41.15 3.13
3026 5079 3.697747 CGCGGTACCAGTGGGGAA 61.698 66.667 15.21 0.00 41.15 3.97
3059 5112 2.259204 CAACAATGCGCACCAGGG 59.741 61.111 14.90 2.76 0.00 4.45
3061 5114 0.248990 AACACAACAATGCGCACCAG 60.249 50.000 14.90 8.32 0.00 4.00
3062 5115 0.248825 GAACACAACAATGCGCACCA 60.249 50.000 14.90 0.00 0.00 4.17
3063 5116 1.268113 CGAACACAACAATGCGCACC 61.268 55.000 14.90 0.00 0.00 5.01
3065 5118 1.656875 GCGAACACAACAATGCGCA 60.657 52.632 14.96 14.96 43.45 6.09
3066 5119 1.370414 AGCGAACACAACAATGCGC 60.370 52.632 0.00 0.00 44.22 6.09
3067 5120 1.599422 GCAGCGAACACAACAATGCG 61.599 55.000 0.00 0.00 0.00 4.73
3068 5121 0.594540 TGCAGCGAACACAACAATGC 60.595 50.000 0.00 0.00 0.00 3.56
3069 5122 1.980844 GATGCAGCGAACACAACAATG 59.019 47.619 0.00 0.00 0.00 2.82
3070 5123 1.068333 GGATGCAGCGAACACAACAAT 60.068 47.619 0.00 0.00 0.00 2.71
3071 5124 0.310543 GGATGCAGCGAACACAACAA 59.689 50.000 0.00 0.00 0.00 2.83
3072 5125 1.840630 CGGATGCAGCGAACACAACA 61.841 55.000 0.00 0.00 0.00 3.33
3073 5126 1.154413 CGGATGCAGCGAACACAAC 60.154 57.895 0.00 0.00 0.00 3.32
3090 5145 2.096565 CACAAGCATGACAGAGTGAACG 60.097 50.000 0.00 0.00 0.00 3.95
3097 5152 0.607217 CCCAGCACAAGCATGACAGA 60.607 55.000 0.00 0.00 45.49 3.41
3108 5163 2.959372 CGACGTAGACCCAGCACA 59.041 61.111 0.00 0.00 0.00 4.57
3114 5169 4.549516 GAGGCGCGACGTAGACCC 62.550 72.222 12.10 0.00 0.00 4.46
3133 5188 4.177026 CACCAGTTTCTCTGTTCGATAGG 58.823 47.826 0.00 0.00 42.19 2.57
3165 5220 2.731976 CTGAACCTGTAGAGTTTCGCAC 59.268 50.000 0.00 0.00 0.00 5.34
3173 5228 1.134280 CCCATGGCTGAACCTGTAGAG 60.134 57.143 6.09 0.00 40.22 2.43
3188 5243 2.124736 AATGGACGTCGCCCCATG 60.125 61.111 17.25 0.00 41.98 3.66
3231 5292 2.280628 GCTGGTTCTATCCAACGGAAG 58.719 52.381 0.00 0.00 37.01 3.46
3232 5293 1.626321 TGCTGGTTCTATCCAACGGAA 59.374 47.619 0.00 0.00 37.01 4.30
3233 5294 1.066430 GTGCTGGTTCTATCCAACGGA 60.066 52.381 0.00 0.00 37.01 4.69
3234 5295 1.369625 GTGCTGGTTCTATCCAACGG 58.630 55.000 0.00 0.00 37.01 4.44
3235 5296 1.369625 GGTGCTGGTTCTATCCAACG 58.630 55.000 0.00 0.00 37.01 4.10
3236 5297 1.004277 TGGGTGCTGGTTCTATCCAAC 59.996 52.381 0.00 0.00 37.01 3.77
3237 5298 1.281867 CTGGGTGCTGGTTCTATCCAA 59.718 52.381 0.00 0.00 37.01 3.53
3238 5299 0.911769 CTGGGTGCTGGTTCTATCCA 59.088 55.000 0.00 0.00 36.00 3.41
3239 5300 0.912486 ACTGGGTGCTGGTTCTATCC 59.088 55.000 0.00 0.00 0.00 2.59
3240 5301 1.407437 CCACTGGGTGCTGGTTCTATC 60.407 57.143 0.00 0.00 31.34 2.08
3241 5302 0.620556 CCACTGGGTGCTGGTTCTAT 59.379 55.000 0.00 0.00 31.34 1.98
3242 5303 2.066340 CCACTGGGTGCTGGTTCTA 58.934 57.895 0.00 0.00 31.34 2.10
3243 5304 2.839098 CCACTGGGTGCTGGTTCT 59.161 61.111 0.00 0.00 31.34 3.01
3244 5305 2.985847 GCCACTGGGTGCTGGTTC 60.986 66.667 0.00 0.00 36.17 3.62
3245 5306 4.954970 CGCCACTGGGTGCTGGTT 62.955 66.667 0.00 0.00 37.98 3.67
3251 5312 3.177194 TTGTCTCCGCCACTGGGTG 62.177 63.158 0.00 0.00 44.61 4.61
3252 5313 2.847234 TTGTCTCCGCCACTGGGT 60.847 61.111 0.00 0.00 36.17 4.51
3253 5314 2.046892 CTTGTCTCCGCCACTGGG 60.047 66.667 0.00 0.00 37.18 4.45
3254 5315 2.743928 GCTTGTCTCCGCCACTGG 60.744 66.667 0.00 0.00 0.00 4.00
3255 5316 2.031012 TGCTTGTCTCCGCCACTG 59.969 61.111 0.00 0.00 0.00 3.66
3256 5317 2.345244 CTGCTTGTCTCCGCCACT 59.655 61.111 0.00 0.00 0.00 4.00
3257 5318 2.743928 CCTGCTTGTCTCCGCCAC 60.744 66.667 0.00 0.00 0.00 5.01
3258 5319 4.020617 CCCTGCTTGTCTCCGCCA 62.021 66.667 0.00 0.00 0.00 5.69
3259 5320 4.785453 CCCCTGCTTGTCTCCGCC 62.785 72.222 0.00 0.00 0.00 6.13
3260 5321 4.785453 CCCCCTGCTTGTCTCCGC 62.785 72.222 0.00 0.00 0.00 5.54
3261 5322 3.003173 TCCCCCTGCTTGTCTCCG 61.003 66.667 0.00 0.00 0.00 4.63
3262 5323 2.993853 CTCCCCCTGCTTGTCTCC 59.006 66.667 0.00 0.00 0.00 3.71
3263 5324 2.250741 GAGCTCCCCCTGCTTGTCTC 62.251 65.000 0.87 0.00 41.30 3.36
3264 5325 2.204059 AGCTCCCCCTGCTTGTCT 60.204 61.111 0.00 0.00 37.52 3.41
3265 5326 2.270527 GAGCTCCCCCTGCTTGTC 59.729 66.667 0.87 0.00 41.30 3.18
3266 5327 2.477190 TAGGAGCTCCCCCTGCTTGT 62.477 60.000 29.54 9.89 41.30 3.16
3267 5328 1.059006 ATAGGAGCTCCCCCTGCTTG 61.059 60.000 29.54 0.00 41.30 4.01
3268 5329 0.327964 AATAGGAGCTCCCCCTGCTT 60.328 55.000 29.54 11.45 41.30 3.91
3269 5330 0.327964 AAATAGGAGCTCCCCCTGCT 60.328 55.000 29.54 12.24 44.24 4.24
3270 5331 0.179006 CAAATAGGAGCTCCCCCTGC 60.179 60.000 29.54 2.90 35.30 4.85
3271 5332 0.179006 GCAAATAGGAGCTCCCCCTG 60.179 60.000 29.54 20.72 35.30 4.45
3272 5333 1.356494 GGCAAATAGGAGCTCCCCCT 61.356 60.000 29.54 13.83 37.80 4.79
3273 5334 1.151679 GGCAAATAGGAGCTCCCCC 59.848 63.158 29.54 15.43 36.42 5.40
3274 5335 1.227973 CGGCAAATAGGAGCTCCCC 60.228 63.158 29.54 19.98 36.42 4.81
3275 5336 1.894282 GCGGCAAATAGGAGCTCCC 60.894 63.158 29.54 12.48 36.42 4.30
3276 5337 0.393077 TAGCGGCAAATAGGAGCTCC 59.607 55.000 26.22 26.22 39.14 4.70
3277 5338 1.867865 GTTAGCGGCAAATAGGAGCTC 59.132 52.381 4.71 4.71 39.14 4.09
3411 6012 2.954684 TTCGGATCCTGCTTGGCGT 61.955 57.895 10.75 0.00 35.26 5.68
3420 6021 2.657143 GAGGTCTAGTGTTCGGATCCT 58.343 52.381 10.75 0.00 0.00 3.24
3423 6024 1.743958 CACGAGGTCTAGTGTTCGGAT 59.256 52.381 13.84 0.00 37.38 4.18
3425 6026 0.456312 GCACGAGGTCTAGTGTTCGG 60.456 60.000 11.66 6.89 38.27 4.30
3430 6031 1.269723 TGTGAAGCACGAGGTCTAGTG 59.730 52.381 6.83 6.83 37.14 2.74
3441 6042 4.522722 AGGAGTAGTACTTGTGAAGCAC 57.477 45.455 0.00 0.00 34.56 4.40
3446 6047 5.252586 AGTGGTAGGAGTAGTACTTGTGA 57.747 43.478 0.00 0.00 0.00 3.58
3448 6049 5.638133 TCAAGTGGTAGGAGTAGTACTTGT 58.362 41.667 0.00 0.00 43.17 3.16


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

AutoCloner maintained by Alex Coulton.