Multiple sequence alignment - TraesCS4B01G377500

Loading Multiple Alignment...

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 TraesCS4B01G377500 chr4B 100.000 2954 0 0 1 2954 660338206 660335253 0.000000e+00 5456.0
1 TraesCS4B01G377500 chr4B 88.467 2870 211 53 6 2815 660357713 660360522 0.000000e+00 3356.0
2 TraesCS4B01G377500 chr4B 79.581 191 27 4 354 536 660289160 660288974 3.090000e-25 126.0
3 TraesCS4B01G377500 chr4B 100.000 39 0 0 2824 2862 590571842 590571804 4.080000e-09 73.1
4 TraesCS4B01G377500 chrUn 90.377 2785 203 24 43 2808 156680082 156682820 0.000000e+00 3598.0
5 TraesCS4B01G377500 chrUn 92.222 2160 153 8 656 2808 156734359 156736510 0.000000e+00 3044.0
6 TraesCS4B01G377500 chrUn 89.019 2468 200 36 383 2814 110266331 110263899 0.000000e+00 2990.0
7 TraesCS4B01G377500 chrUn 88.551 2463 193 37 383 2808 156615791 156618201 0.000000e+00 2904.0
8 TraesCS4B01G377500 chrUn 90.251 1795 129 17 853 2622 371511182 371509409 0.000000e+00 2303.0
9 TraesCS4B01G377500 chrUn 85.863 1054 86 29 383 1404 110203668 110202646 0.000000e+00 1062.0
10 TraesCS4B01G377500 chrUn 88.728 621 56 7 6 616 156733733 156734349 0.000000e+00 747.0
11 TraesCS4B01G377500 chrUn 98.947 95 1 0 2860 2954 458727105 458727199 1.410000e-38 171.0
12 TraesCS4B01G377500 chrUn 81.720 93 9 2 406 494 110237620 110237532 1.470000e-08 71.3
13 TraesCS4B01G377500 chr5A 90.640 2329 169 25 504 2814 699535937 699533640 0.000000e+00 3048.0
14 TraesCS4B01G377500 chr5A 87.642 2557 239 38 295 2808 699565617 699568139 0.000000e+00 2900.0
15 TraesCS4B01G377500 chr5A 87.564 2557 241 38 295 2808 700375713 700378235 0.000000e+00 2889.0
16 TraesCS4B01G377500 chr5A 87.524 2557 242 38 295 2808 699633214 699635736 0.000000e+00 2883.0
17 TraesCS4B01G377500 chr5A 87.446 2557 243 39 295 2808 699711859 699714380 0.000000e+00 2872.0
18 TraesCS4B01G377500 chr5A 94.166 1217 56 7 504 1710 699550892 699549681 0.000000e+00 1840.0
19 TraesCS4B01G377500 chr5A 94.166 1217 56 7 504 1710 699876203 699877414 0.000000e+00 1840.0
20 TraesCS4B01G377500 chr5A 82.026 306 37 12 149 449 699536244 699535952 8.180000e-61 244.0
21 TraesCS4B01G377500 chr5A 82.026 306 37 12 149 449 699551199 699550907 8.180000e-61 244.0
22 TraesCS4B01G377500 chr5A 82.026 306 37 12 149 449 699875896 699876188 8.180000e-61 244.0
23 TraesCS4B01G377500 chr5A 97.895 95 2 0 2860 2954 607203823 607203729 6.550000e-37 165.0
24 TraesCS4B01G377500 chr7D 98.947 95 1 0 2860 2954 231567650 231567556 1.410000e-38 171.0
25 TraesCS4B01G377500 chr7D 98.947 95 1 0 2860 2954 231617280 231617186 1.410000e-38 171.0
26 TraesCS4B01G377500 chr7D 97.436 39 1 0 2824 2862 307026899 307026937 1.900000e-07 67.6
27 TraesCS4B01G377500 chr6D 98.947 95 1 0 2860 2954 45515312 45515218 1.410000e-38 171.0
28 TraesCS4B01G377500 chr5D 98.947 95 1 0 2860 2954 483807327 483807233 1.410000e-38 171.0
29 TraesCS4B01G377500 chr5D 97.895 95 2 0 2860 2954 6184683 6184589 6.550000e-37 165.0
30 TraesCS4B01G377500 chr3D 98.947 95 1 0 2860 2954 598875061 598875155 1.410000e-38 171.0
31 TraesCS4B01G377500 chr1D 98.947 95 1 0 2860 2954 254402365 254402459 1.410000e-38 171.0
32 TraesCS4B01G377500 chr3A 95.745 47 1 1 2824 2869 108768018 108768064 1.140000e-09 75.0
33 TraesCS4B01G377500 chr5B 100.000 39 0 0 2824 2862 127801619 127801581 4.080000e-09 73.1
34 TraesCS4B01G377500 chr3B 100.000 39 0 0 2824 2862 201609236 201609198 4.080000e-09 73.1
35 TraesCS4B01G377500 chr2D 100.000 39 0 0 2824 2862 391007030 391006992 4.080000e-09 73.1
36 TraesCS4B01G377500 chr1B 100.000 39 0 0 2824 2862 638722916 638722878 4.080000e-09 73.1
37 TraesCS4B01G377500 chr1B 100.000 39 0 0 2824 2862 672549445 672549483 4.080000e-09 73.1
38 TraesCS4B01G377500 chr6B 100.000 38 0 0 2824 2861 320185033 320185070 1.470000e-08 71.3


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 TraesCS4B01G377500 chr4B 660335253 660338206 2953 True 5456.0 5456 100.000 1 2954 1 chr4B.!!$R3 2953
1 TraesCS4B01G377500 chr4B 660357713 660360522 2809 False 3356.0 3356 88.467 6 2815 1 chr4B.!!$F1 2809
2 TraesCS4B01G377500 chrUn 156680082 156682820 2738 False 3598.0 3598 90.377 43 2808 1 chrUn.!!$F2 2765
3 TraesCS4B01G377500 chrUn 110263899 110266331 2432 True 2990.0 2990 89.019 383 2814 1 chrUn.!!$R3 2431
4 TraesCS4B01G377500 chrUn 156615791 156618201 2410 False 2904.0 2904 88.551 383 2808 1 chrUn.!!$F1 2425
5 TraesCS4B01G377500 chrUn 371509409 371511182 1773 True 2303.0 2303 90.251 853 2622 1 chrUn.!!$R4 1769
6 TraesCS4B01G377500 chrUn 156733733 156736510 2777 False 1895.5 3044 90.475 6 2808 2 chrUn.!!$F4 2802
7 TraesCS4B01G377500 chrUn 110202646 110203668 1022 True 1062.0 1062 85.863 383 1404 1 chrUn.!!$R1 1021
8 TraesCS4B01G377500 chr5A 699565617 699568139 2522 False 2900.0 2900 87.642 295 2808 1 chr5A.!!$F1 2513
9 TraesCS4B01G377500 chr5A 700375713 700378235 2522 False 2889.0 2889 87.564 295 2808 1 chr5A.!!$F4 2513
10 TraesCS4B01G377500 chr5A 699633214 699635736 2522 False 2883.0 2883 87.524 295 2808 1 chr5A.!!$F2 2513
11 TraesCS4B01G377500 chr5A 699711859 699714380 2521 False 2872.0 2872 87.446 295 2808 1 chr5A.!!$F3 2513
12 TraesCS4B01G377500 chr5A 699533640 699536244 2604 True 1646.0 3048 86.333 149 2814 2 chr5A.!!$R2 2665
13 TraesCS4B01G377500 chr5A 699549681 699551199 1518 True 1042.0 1840 88.096 149 1710 2 chr5A.!!$R3 1561
14 TraesCS4B01G377500 chr5A 699875896 699877414 1518 False 1042.0 1840 88.096 149 1710 2 chr5A.!!$F5 1561

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
701 768 0.824182 ACGGGTGGCGAATTTTTCCA 60.824 50.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 2527 1.204941 AGTTAGCTTGCTAGTCGGTGG 59.795 52.381 0.0 0.0 0.0 4.61 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
126 128 5.681337 TTACTCTGCTGAGATGATACGAG 57.319 43.478 25.49 0.00 42.73 4.18
143 145 1.406898 CGAGATGTTCCTGCTCAGCTA 59.593 52.381 0.00 0.00 30.32 3.32
181 183 2.997986 CGTTTGGTTAGATAGGCACGTT 59.002 45.455 0.00 0.00 0.00 3.99
187 189 4.647853 TGGTTAGATAGGCACGTTCACTAT 59.352 41.667 3.76 3.76 0.00 2.12
194 196 1.126113 GGCACGTTCACTATTGTCGTG 59.874 52.381 19.64 19.64 45.38 4.35
361 383 7.786178 AGCTTGATTTTATGCGTTCTATACA 57.214 32.000 0.00 0.00 0.00 2.29
369 391 6.729391 TTATGCGTTCTATACAAACTTGCA 57.271 33.333 0.00 0.00 30.97 4.08
378 400 7.435068 TCTATACAAACTTGCAGAAAGAACC 57.565 36.000 0.00 0.00 39.38 3.62
382 404 1.594331 ACTTGCAGAAAGAACCGGAC 58.406 50.000 9.46 0.99 39.38 4.79
393 415 3.430042 AGAACCGGACTAGTAGTCACA 57.570 47.619 27.41 0.00 46.79 3.58
394 416 3.965694 AGAACCGGACTAGTAGTCACAT 58.034 45.455 27.41 13.08 46.79 3.21
449 477 4.106029 TCACGCATTAGTAGGTGACTTC 57.894 45.455 0.00 0.00 43.67 3.01
452 480 4.268644 CACGCATTAGTAGGTGACTTCATG 59.731 45.833 0.00 0.00 43.67 3.07
453 481 3.246226 CGCATTAGTAGGTGACTTCATGC 59.754 47.826 9.77 9.77 43.71 4.06
455 483 4.034510 GCATTAGTAGGTGACTTCATGCAC 59.965 45.833 12.98 0.00 45.09 4.57
494 522 5.030936 GCTAGAAAACGATTGATTGCCTTC 58.969 41.667 0.00 0.00 0.00 3.46
512 540 3.575687 CCTTCCATGACTTGGCTTTTCTT 59.424 43.478 2.42 0.00 46.01 2.52
575 605 8.754991 ACTATGACCTGGTATATGATAGTAGC 57.245 38.462 0.00 0.00 0.00 3.58
576 606 8.336987 ACTATGACCTGGTATATGATAGTAGCA 58.663 37.037 0.00 0.00 0.00 3.49
646 710 4.635765 TCATTTGTTTCTCTTGCCGGATAG 59.364 41.667 5.05 0.11 0.00 2.08
649 713 4.811969 TGTTTCTCTTGCCGGATAGTTA 57.188 40.909 5.05 0.00 0.00 2.24
690 757 2.335316 TAATAATGGTGACGGGTGGC 57.665 50.000 0.00 0.00 0.00 5.01
694 761 2.478335 AATGGTGACGGGTGGCGAAT 62.478 55.000 0.00 0.00 0.00 3.34
701 768 0.824182 ACGGGTGGCGAATTTTTCCA 60.824 50.000 0.00 0.00 0.00 3.53
706 773 2.036604 GGTGGCGAATTTTTCCAGGAAA 59.963 45.455 10.90 10.90 0.00 3.13
883 957 6.023357 TGCAAAATAGTTTAATCAGCAGCA 57.977 33.333 0.00 0.00 0.00 4.41
907 981 4.763793 AGAGACCATTTCAATCTGTTGGTG 59.236 41.667 0.00 0.00 40.67 4.17
936 1010 4.343526 CACCTGACTATGTCTATTGCTCCT 59.656 45.833 0.00 0.00 33.15 3.69
1006 1081 3.499048 CATGTTCAAAGCATCACTCAGC 58.501 45.455 0.00 0.00 0.00 4.26
1058 1133 6.969828 AAAGAAGAGCCAACGATACTAAAG 57.030 37.500 0.00 0.00 0.00 1.85
1181 1259 1.079197 TCGCCGACATGCATTCACT 60.079 52.632 0.00 0.00 0.00 3.41
1287 1398 7.323420 TCTGAGTTTACATGTTACATCTCCTG 58.677 38.462 2.30 2.83 0.00 3.86
1344 1456 2.981400 ACCCAATGAAAGTTAACGCG 57.019 45.000 3.53 3.53 0.00 6.01
1679 1791 1.895131 CCACTTCCAATTCAACCCCAG 59.105 52.381 0.00 0.00 0.00 4.45
1743 1855 0.846693 ACCCAGGGGCTATCACAATC 59.153 55.000 11.37 0.00 39.32 2.67
1884 1996 7.800380 CACAACTAAGTCAGACATTTGTTGATC 59.200 37.037 26.75 0.00 41.53 2.92
1943 2057 6.949352 TGAATTTCTCAAGCATCCTTATCC 57.051 37.500 0.00 0.00 0.00 2.59
1993 2107 2.771089 CTGTGTGTCTGTAAGCCATGT 58.229 47.619 0.00 0.00 0.00 3.21
2211 2328 8.251026 TCGGGAAATTCTACATATATAGTGCTG 58.749 37.037 0.00 0.00 0.00 4.41
2232 2349 2.420022 GGTGTGCAATACATGTGAGGTC 59.580 50.000 9.11 0.00 42.24 3.85
2250 2367 3.140895 AGGTCCTATAATGCCTGCCATTT 59.859 43.478 0.00 0.00 41.29 2.32
2287 2410 5.440207 GGGGTTCCCGGCTTTATATTATA 57.560 43.478 0.00 0.00 32.13 0.98
2323 2446 4.159693 TCACTGCATTACAACCGAGTAGAT 59.840 41.667 0.00 0.00 0.00 1.98
2482 2607 2.108075 ACATCCACCATGAACCAGAACA 59.892 45.455 0.00 0.00 36.21 3.18
2502 2627 2.564504 CAGAGAGGTGAGATGGACAACA 59.435 50.000 0.00 0.00 0.00 3.33
2614 2739 3.679389 GGAGCAAGATGAAAGGAGTCAA 58.321 45.455 0.00 0.00 0.00 3.18
2626 2751 1.760613 AGGAGTCAAAACACCGAGACA 59.239 47.619 0.00 0.00 40.72 3.41
2703 2832 1.279271 GACTGGGCAAGTGATGTACCT 59.721 52.381 0.00 0.00 40.07 3.08
2815 2945 3.965258 ATGCTCCGCCCACCAACA 61.965 61.111 0.00 0.00 0.00 3.33
2816 2946 4.947147 TGCTCCGCCCACCAACAC 62.947 66.667 0.00 0.00 0.00 3.32
2821 2951 4.690719 CGCCCACCAACACCGCTA 62.691 66.667 0.00 0.00 0.00 4.26
2822 2952 2.746277 GCCCACCAACACCGCTAG 60.746 66.667 0.00 0.00 0.00 3.42
2823 2953 2.046314 CCCACCAACACCGCTAGG 60.046 66.667 0.00 0.00 45.13 3.02
2824 2954 2.046314 CCACCAACACCGCTAGGG 60.046 66.667 0.00 0.00 43.47 3.53
2825 2955 2.746277 CACCAACACCGCTAGGGC 60.746 66.667 0.19 0.00 43.47 5.19
2826 2956 3.246112 ACCAACACCGCTAGGGCA 61.246 61.111 0.19 0.00 43.47 5.36
2827 2957 2.033448 CCAACACCGCTAGGGCAA 59.967 61.111 0.19 0.00 43.47 4.52
2828 2958 1.602323 CCAACACCGCTAGGGCAAA 60.602 57.895 0.19 0.00 43.47 3.68
2829 2959 1.579429 CAACACCGCTAGGGCAAAC 59.421 57.895 0.19 0.00 43.47 2.93
2830 2960 0.889186 CAACACCGCTAGGGCAAACT 60.889 55.000 0.19 0.00 43.47 2.66
2831 2961 0.688487 AACACCGCTAGGGCAAACTA 59.312 50.000 0.19 0.00 43.47 2.24
2832 2962 0.909623 ACACCGCTAGGGCAAACTAT 59.090 50.000 0.19 0.00 43.47 2.12
2833 2963 1.134491 ACACCGCTAGGGCAAACTATC 60.134 52.381 0.19 0.00 43.47 2.08
2834 2964 0.468648 ACCGCTAGGGCAAACTATCC 59.531 55.000 0.19 0.00 43.47 2.59
2835 2965 0.250338 CCGCTAGGGCAAACTATCCC 60.250 60.000 0.19 0.00 42.94 3.85
2836 2966 0.468226 CGCTAGGGCAAACTATCCCA 59.532 55.000 0.00 0.00 45.07 4.37
2837 2967 1.134220 CGCTAGGGCAAACTATCCCAA 60.134 52.381 0.00 0.00 45.07 4.12
2838 2968 2.682563 CGCTAGGGCAAACTATCCCAAA 60.683 50.000 0.00 0.00 45.07 3.28
2839 2969 3.361786 GCTAGGGCAAACTATCCCAAAA 58.638 45.455 0.00 0.00 45.07 2.44
2840 2970 3.767131 GCTAGGGCAAACTATCCCAAAAA 59.233 43.478 0.00 0.00 45.07 1.94
2861 2991 7.658525 AAAAAGGAATGGGCTTTTTCAAAAT 57.341 28.000 0.00 0.00 36.04 1.82
2862 2992 8.759481 AAAAAGGAATGGGCTTTTTCAAAATA 57.241 26.923 0.00 0.00 36.04 1.40
2863 2993 7.984422 AAAGGAATGGGCTTTTTCAAAATAG 57.016 32.000 0.00 0.00 0.00 1.73
2864 2994 6.933514 AGGAATGGGCTTTTTCAAAATAGA 57.066 33.333 0.00 0.00 0.00 1.98
2865 2995 6.939622 AGGAATGGGCTTTTTCAAAATAGAG 58.060 36.000 0.00 0.00 0.00 2.43
2866 2996 5.582269 GGAATGGGCTTTTTCAAAATAGAGC 59.418 40.000 0.00 0.00 0.00 4.09
2867 2997 4.173036 TGGGCTTTTTCAAAATAGAGCG 57.827 40.909 0.07 0.00 0.00 5.03
2868 2998 3.572255 TGGGCTTTTTCAAAATAGAGCGT 59.428 39.130 0.07 0.00 0.00 5.07
2869 2999 4.038642 TGGGCTTTTTCAAAATAGAGCGTT 59.961 37.500 0.07 0.00 0.00 4.84
2870 3000 5.241949 TGGGCTTTTTCAAAATAGAGCGTTA 59.758 36.000 0.07 0.00 0.00 3.18
2871 3001 6.153756 GGGCTTTTTCAAAATAGAGCGTTAA 58.846 36.000 0.07 0.00 0.00 2.01
2872 3002 6.811665 GGGCTTTTTCAAAATAGAGCGTTAAT 59.188 34.615 0.07 0.00 0.00 1.40
2873 3003 7.330946 GGGCTTTTTCAAAATAGAGCGTTAATT 59.669 33.333 0.07 0.00 0.00 1.40
2874 3004 8.373256 GGCTTTTTCAAAATAGAGCGTTAATTC 58.627 33.333 0.07 0.00 0.00 2.17
2875 3005 9.129209 GCTTTTTCAAAATAGAGCGTTAATTCT 57.871 29.630 0.00 0.00 0.00 2.40
2880 3010 9.607285 TTCAAAATAGAGCGTTAATTCTGAAAC 57.393 29.630 0.00 0.00 0.00 2.78
2881 3011 8.999431 TCAAAATAGAGCGTTAATTCTGAAACT 58.001 29.630 0.00 0.00 0.00 2.66
2882 3012 9.612620 CAAAATAGAGCGTTAATTCTGAAACTT 57.387 29.630 0.00 0.00 0.00 2.66
2884 3014 9.612620 AAATAGAGCGTTAATTCTGAAACTTTG 57.387 29.630 0.00 0.00 0.00 2.77
2885 3015 6.002062 AGAGCGTTAATTCTGAAACTTTGG 57.998 37.500 0.00 0.00 0.00 3.28
2886 3016 5.531287 AGAGCGTTAATTCTGAAACTTTGGT 59.469 36.000 0.00 0.00 0.00 3.67
2887 3017 6.708949 AGAGCGTTAATTCTGAAACTTTGGTA 59.291 34.615 0.00 0.00 0.00 3.25
2888 3018 7.390718 AGAGCGTTAATTCTGAAACTTTGGTAT 59.609 33.333 0.00 0.00 0.00 2.73
2889 3019 7.882179 AGCGTTAATTCTGAAACTTTGGTATT 58.118 30.769 0.00 0.00 0.00 1.89
2890 3020 8.357402 AGCGTTAATTCTGAAACTTTGGTATTT 58.643 29.630 0.00 0.00 0.00 1.40
2891 3021 8.635983 GCGTTAATTCTGAAACTTTGGTATTTC 58.364 33.333 0.00 0.00 35.73 2.17
2892 3022 9.893305 CGTTAATTCTGAAACTTTGGTATTTCT 57.107 29.630 0.00 0.00 36.09 2.52
2903 3033 8.642908 AACTTTGGTATTTCTTTTTCTTTCGG 57.357 30.769 0.00 0.00 0.00 4.30
2904 3034 8.002984 ACTTTGGTATTTCTTTTTCTTTCGGA 57.997 30.769 0.00 0.00 0.00 4.55
2905 3035 7.919091 ACTTTGGTATTTCTTTTTCTTTCGGAC 59.081 33.333 0.00 0.00 0.00 4.79
2906 3036 6.945938 TGGTATTTCTTTTTCTTTCGGACA 57.054 33.333 0.00 0.00 0.00 4.02
2907 3037 7.336161 TGGTATTTCTTTTTCTTTCGGACAA 57.664 32.000 0.00 0.00 0.00 3.18
2908 3038 7.773149 TGGTATTTCTTTTTCTTTCGGACAAA 58.227 30.769 0.00 0.00 0.00 2.83
2909 3039 8.251721 TGGTATTTCTTTTTCTTTCGGACAAAA 58.748 29.630 0.00 0.00 0.00 2.44
2910 3040 9.256477 GGTATTTCTTTTTCTTTCGGACAAAAT 57.744 29.630 0.00 0.00 0.00 1.82
2916 3046 9.471084 TCTTTTTCTTTCGGACAAAATAATTCC 57.529 29.630 0.00 0.00 0.00 3.01
2917 3047 8.596271 TTTTTCTTTCGGACAAAATAATTCCC 57.404 30.769 0.00 0.00 0.00 3.97
2918 3048 5.554822 TCTTTCGGACAAAATAATTCCCG 57.445 39.130 0.00 0.00 38.41 5.14
2919 3049 5.005094 TCTTTCGGACAAAATAATTCCCGT 58.995 37.500 0.00 0.00 38.25 5.28
2920 3050 6.171921 TCTTTCGGACAAAATAATTCCCGTA 58.828 36.000 0.00 0.00 38.25 4.02
2921 3051 6.314400 TCTTTCGGACAAAATAATTCCCGTAG 59.686 38.462 0.00 0.00 38.25 3.51
2922 3052 3.872771 TCGGACAAAATAATTCCCGTAGC 59.127 43.478 0.00 0.00 38.25 3.58
2923 3053 3.302870 CGGACAAAATAATTCCCGTAGCG 60.303 47.826 0.00 0.00 33.02 4.26
2924 3054 3.872771 GGACAAAATAATTCCCGTAGCGA 59.127 43.478 0.00 0.00 0.00 4.93
2925 3055 4.025145 GGACAAAATAATTCCCGTAGCGAG 60.025 45.833 0.00 0.00 0.00 5.03
2926 3056 4.761975 ACAAAATAATTCCCGTAGCGAGA 58.238 39.130 0.00 0.00 0.00 4.04
2927 3057 5.180271 ACAAAATAATTCCCGTAGCGAGAA 58.820 37.500 0.00 0.00 0.00 2.87
2928 3058 5.820947 ACAAAATAATTCCCGTAGCGAGAAT 59.179 36.000 0.00 0.00 0.00 2.40
2929 3059 5.924475 AAATAATTCCCGTAGCGAGAATG 57.076 39.130 0.00 0.00 30.80 2.67
2930 3060 2.240493 AATTCCCGTAGCGAGAATGG 57.760 50.000 0.00 0.00 30.80 3.16
2931 3061 0.393077 ATTCCCGTAGCGAGAATGGG 59.607 55.000 0.00 3.58 43.60 4.00
2932 3062 3.533720 CCCGTAGCGAGAATGGGA 58.466 61.111 3.86 0.00 44.84 4.37
2933 3063 0.469331 TCCCGTAGCGAGAATGGGAT 60.469 55.000 7.72 0.00 45.49 3.85
2934 3064 0.393077 CCCGTAGCGAGAATGGGATT 59.607 55.000 3.86 0.00 44.84 3.01
2935 3065 1.202651 CCCGTAGCGAGAATGGGATTT 60.203 52.381 3.86 0.00 44.84 2.17
2936 3066 2.135933 CCGTAGCGAGAATGGGATTTC 58.864 52.381 0.00 0.00 0.00 2.17
2937 3067 2.135933 CGTAGCGAGAATGGGATTTCC 58.864 52.381 0.00 0.00 0.00 3.13
2947 3077 1.732941 TGGGATTTCCACAACGATCG 58.267 50.000 14.88 14.88 41.46 3.69
2948 3078 0.377203 GGGATTTCCACAACGATCGC 59.623 55.000 16.60 0.00 37.91 4.58
2949 3079 1.083489 GGATTTCCACAACGATCGCA 58.917 50.000 16.60 0.00 35.64 5.10
2950 3080 1.466950 GGATTTCCACAACGATCGCAA 59.533 47.619 16.60 0.00 35.64 4.85
2951 3081 2.095466 GGATTTCCACAACGATCGCAAA 60.095 45.455 16.60 5.33 35.64 3.68
2952 3082 2.392933 TTTCCACAACGATCGCAAAC 57.607 45.000 16.60 0.00 0.00 2.93
2953 3083 0.589223 TTCCACAACGATCGCAAACC 59.411 50.000 16.60 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.483685 AGGCATTCAACACACTAGTAGAA 57.516 39.130 3.59 0.00 0.00 2.10
2 3 5.967088 ACTAGGCATTCAACACACTAGTAG 58.033 41.667 0.00 0.00 39.29 2.57
3 4 5.479027 TGACTAGGCATTCAACACACTAGTA 59.521 40.000 0.00 0.00 40.64 1.82
5 6 4.820897 TGACTAGGCATTCAACACACTAG 58.179 43.478 0.00 0.00 35.31 2.57
7 8 3.557898 CCTGACTAGGCATTCAACACACT 60.558 47.826 0.00 0.00 37.25 3.55
74 75 5.408356 TCCTCTTGCTACGAGTTTAATCAC 58.592 41.667 0.00 0.00 0.00 3.06
114 116 4.022416 AGCAGGAACATCTCGTATCATCTC 60.022 45.833 0.00 0.00 0.00 2.75
126 128 2.680312 TGTAGCTGAGCAGGAACATC 57.320 50.000 7.39 0.00 0.00 3.06
143 145 1.781786 ACGGAGAGCTATGACCATGT 58.218 50.000 0.00 0.00 0.00 3.21
181 183 3.585862 GAAGAAGCCACGACAATAGTGA 58.414 45.455 0.00 0.00 41.83 3.41
187 189 0.884704 GCAGGAAGAAGCCACGACAA 60.885 55.000 0.00 0.00 0.00 3.18
194 196 2.991250 TGAGTATTGCAGGAAGAAGCC 58.009 47.619 0.00 0.00 0.00 4.35
249 255 3.131396 GCCCCTGTTATCATCACGTTAG 58.869 50.000 0.00 0.00 0.00 2.34
251 257 1.559682 AGCCCCTGTTATCATCACGTT 59.440 47.619 0.00 0.00 0.00 3.99
333 352 8.986477 ATAGAACGCATAAAATCAAGCTTTTT 57.014 26.923 0.00 0.00 31.15 1.94
349 368 4.311606 TCTGCAAGTTTGTATAGAACGCA 58.688 39.130 0.00 0.00 33.76 5.24
352 374 7.803659 GGTTCTTTCTGCAAGTTTGTATAGAAC 59.196 37.037 15.74 15.74 36.32 3.01
361 383 2.357952 GTCCGGTTCTTTCTGCAAGTTT 59.642 45.455 0.00 0.00 33.66 2.66
369 391 4.458642 GTGACTACTAGTCCGGTTCTTTCT 59.541 45.833 12.79 0.00 44.44 2.52
378 400 8.325421 AGACATATAATGTGACTACTAGTCCG 57.675 38.462 12.79 0.00 44.44 4.79
393 415 9.277783 GGTGCATGACTTCTAAAGACATATAAT 57.722 33.333 0.00 0.00 40.90 1.28
394 416 7.715249 GGGTGCATGACTTCTAAAGACATATAA 59.285 37.037 0.00 0.00 40.90 0.98
449 477 3.520862 GGCCGACATGGGTGCATG 61.521 66.667 0.00 0.00 38.63 4.06
453 481 3.723235 CTCGAGGCCGACATGGGTG 62.723 68.421 3.91 0.00 40.30 4.61
455 483 4.899239 GCTCGAGGCCGACATGGG 62.899 72.222 15.58 0.00 40.30 4.00
456 484 2.413437 CTAGCTCGAGGCCGACATGG 62.413 65.000 15.58 0.00 43.05 3.66
512 540 6.318648 ACACAAAATCAGTCAAAGAGCAGTTA 59.681 34.615 0.00 0.00 0.00 2.24
574 604 5.255710 AGTATCCTGCGTATCTATCATGC 57.744 43.478 0.00 0.00 0.00 4.06
575 605 8.214721 TCTAAGTATCCTGCGTATCTATCATG 57.785 38.462 0.00 0.00 0.00 3.07
576 606 8.988546 ATCTAAGTATCCTGCGTATCTATCAT 57.011 34.615 0.00 0.00 0.00 2.45
690 757 4.402474 AGGGCTATTTCCTGGAAAAATTCG 59.598 41.667 24.44 12.38 35.11 3.34
701 768 0.259647 TGCATGCAGGGCTATTTCCT 59.740 50.000 18.46 0.00 34.39 3.36
706 773 1.037493 CACAATGCATGCAGGGCTAT 58.963 50.000 26.69 4.78 0.00 2.97
883 957 5.242393 CACCAACAGATTGAAATGGTCTCTT 59.758 40.000 0.00 0.00 42.30 2.85
960 1035 7.147637 TGCAGGGTGTGTATGTGTTTATATAGA 60.148 37.037 0.00 0.00 0.00 1.98
1006 1081 2.232452 TGTTCCTGTTTGTGTTTGTGGG 59.768 45.455 0.00 0.00 0.00 4.61
1058 1133 2.206576 AGAGGAGGTTGCCATTTGAC 57.793 50.000 0.00 0.00 0.00 3.18
1181 1259 4.130118 GACGAGAAACCGGATAGTACCTA 58.870 47.826 9.46 0.00 0.00 3.08
1344 1456 1.433534 CTGCCTTGAAGAAGTCGTCC 58.566 55.000 0.00 0.00 0.00 4.79
1743 1855 1.373246 CCCAAACACTGCATTGGCG 60.373 57.895 10.74 2.08 43.84 5.69
1884 1996 5.432157 GTTTATGCGATAATCTTCCGTGTG 58.568 41.667 0.00 0.00 0.00 3.82
2086 2200 6.894682 ACCCTGAATTTTTGTTTGTTATGGT 58.105 32.000 0.00 0.00 0.00 3.55
2211 2328 2.420022 GACCTCACATGTATTGCACACC 59.580 50.000 0.00 0.00 40.86 4.16
2232 2349 4.942761 AACAAATGGCAGGCATTATAGG 57.057 40.909 21.80 13.89 0.00 2.57
2250 2367 5.993748 GGAACCCCTTTTTCATCATAACA 57.006 39.130 0.00 0.00 0.00 2.41
2281 2402 9.348476 TGCAGTGATGGTTGCTTTATTATAATA 57.652 29.630 0.81 0.81 40.87 0.98
2282 2403 8.236585 TGCAGTGATGGTTGCTTTATTATAAT 57.763 30.769 2.97 2.97 40.87 1.28
2283 2404 7.637631 TGCAGTGATGGTTGCTTTATTATAA 57.362 32.000 0.00 0.00 40.87 0.98
2287 2410 5.410355 AATGCAGTGATGGTTGCTTTATT 57.590 34.783 0.00 0.00 40.87 1.40
2323 2446 3.058570 GTGATGGCGTGTGTTTGTATTGA 60.059 43.478 0.00 0.00 0.00 2.57
2403 2527 1.204941 AGTTAGCTTGCTAGTCGGTGG 59.795 52.381 0.00 0.00 0.00 4.61
2482 2607 2.894731 TGTTGTCCATCTCACCTCTCT 58.105 47.619 0.00 0.00 0.00 3.10
2502 2627 2.978156 TTTGGAGTCCTGGCTTCATT 57.022 45.000 11.33 0.00 0.00 2.57
2614 2739 4.159879 CCTATAGGTTCTGTCTCGGTGTTT 59.840 45.833 10.96 0.00 0.00 2.83
2626 2751 6.553857 ACATCGTATCCTTCCTATAGGTTCT 58.446 40.000 18.51 3.50 36.63 3.01
2703 2832 0.392706 ATGGAGTGTGTGAACGCTGA 59.607 50.000 0.00 0.00 0.00 4.26
2815 2945 0.468648 GGATAGTTTGCCCTAGCGGT 59.531 55.000 0.00 0.00 44.31 5.68
2816 2946 0.250338 GGGATAGTTTGCCCTAGCGG 60.250 60.000 0.00 0.00 44.31 5.52
2817 2947 0.468226 TGGGATAGTTTGCCCTAGCG 59.532 55.000 0.00 0.00 44.96 4.26
2818 2948 2.729028 TTGGGATAGTTTGCCCTAGC 57.271 50.000 0.00 0.00 44.96 3.42
2838 2968 8.217111 TCTATTTTGAAAAAGCCCATTCCTTTT 58.783 29.630 0.00 0.00 42.53 2.27
2839 2969 7.744733 TCTATTTTGAAAAAGCCCATTCCTTT 58.255 30.769 0.00 0.00 34.18 3.11
2840 2970 7.315066 TCTATTTTGAAAAAGCCCATTCCTT 57.685 32.000 0.00 0.00 0.00 3.36
2841 2971 6.575056 GCTCTATTTTGAAAAAGCCCATTCCT 60.575 38.462 0.00 0.00 0.00 3.36
2842 2972 5.582269 GCTCTATTTTGAAAAAGCCCATTCC 59.418 40.000 0.00 0.00 0.00 3.01
2843 2973 5.289434 CGCTCTATTTTGAAAAAGCCCATTC 59.711 40.000 7.11 0.00 0.00 2.67
2844 2974 5.170748 CGCTCTATTTTGAAAAAGCCCATT 58.829 37.500 7.11 0.00 0.00 3.16
2845 2975 4.220602 ACGCTCTATTTTGAAAAAGCCCAT 59.779 37.500 7.11 0.00 0.00 4.00
2846 2976 3.572255 ACGCTCTATTTTGAAAAAGCCCA 59.428 39.130 7.11 0.00 0.00 5.36
2847 2977 4.174411 ACGCTCTATTTTGAAAAAGCCC 57.826 40.909 7.11 0.00 0.00 5.19
2848 2978 7.812309 ATTAACGCTCTATTTTGAAAAAGCC 57.188 32.000 7.11 0.00 0.00 4.35
2849 2979 9.129209 AGAATTAACGCTCTATTTTGAAAAAGC 57.871 29.630 0.00 0.00 0.00 3.51
2854 2984 9.607285 GTTTCAGAATTAACGCTCTATTTTGAA 57.393 29.630 0.00 0.00 33.33 2.69
2855 2985 8.999431 AGTTTCAGAATTAACGCTCTATTTTGA 58.001 29.630 0.00 0.00 0.00 2.69
2856 2986 9.612620 AAGTTTCAGAATTAACGCTCTATTTTG 57.387 29.630 0.00 0.00 0.00 2.44
2858 2988 9.612620 CAAAGTTTCAGAATTAACGCTCTATTT 57.387 29.630 0.00 0.00 0.00 1.40
2859 2989 8.237267 CCAAAGTTTCAGAATTAACGCTCTATT 58.763 33.333 0.00 0.00 0.00 1.73
2860 2990 7.390718 ACCAAAGTTTCAGAATTAACGCTCTAT 59.609 33.333 0.00 0.00 0.00 1.98
2861 2991 6.708949 ACCAAAGTTTCAGAATTAACGCTCTA 59.291 34.615 0.00 0.00 0.00 2.43
2862 2992 5.531287 ACCAAAGTTTCAGAATTAACGCTCT 59.469 36.000 0.00 0.00 0.00 4.09
2863 2993 5.758924 ACCAAAGTTTCAGAATTAACGCTC 58.241 37.500 0.00 0.00 0.00 5.03
2864 2994 5.767816 ACCAAAGTTTCAGAATTAACGCT 57.232 34.783 0.00 0.00 0.00 5.07
2865 2995 8.515473 AAATACCAAAGTTTCAGAATTAACGC 57.485 30.769 0.00 0.00 0.00 4.84
2866 2996 9.893305 AGAAATACCAAAGTTTCAGAATTAACG 57.107 29.630 0.00 0.00 36.92 3.18
2877 3007 9.093970 CCGAAAGAAAAAGAAATACCAAAGTTT 57.906 29.630 0.00 0.00 0.00 2.66
2878 3008 8.471609 TCCGAAAGAAAAAGAAATACCAAAGTT 58.528 29.630 0.00 0.00 0.00 2.66
2879 3009 7.919091 GTCCGAAAGAAAAAGAAATACCAAAGT 59.081 33.333 0.00 0.00 0.00 2.66
2880 3010 7.918562 TGTCCGAAAGAAAAAGAAATACCAAAG 59.081 33.333 0.00 0.00 0.00 2.77
2881 3011 7.773149 TGTCCGAAAGAAAAAGAAATACCAAA 58.227 30.769 0.00 0.00 0.00 3.28
2882 3012 7.336161 TGTCCGAAAGAAAAAGAAATACCAA 57.664 32.000 0.00 0.00 0.00 3.67
2883 3013 6.945938 TGTCCGAAAGAAAAAGAAATACCA 57.054 33.333 0.00 0.00 0.00 3.25
2884 3014 8.637281 TTTTGTCCGAAAGAAAAAGAAATACC 57.363 30.769 0.00 0.00 33.14 2.73
2890 3020 9.471084 GGAATTATTTTGTCCGAAAGAAAAAGA 57.529 29.630 0.00 0.00 33.14 2.52
2891 3021 8.708742 GGGAATTATTTTGTCCGAAAGAAAAAG 58.291 33.333 0.00 0.00 33.14 2.27
2892 3022 7.382759 CGGGAATTATTTTGTCCGAAAGAAAAA 59.617 33.333 0.00 0.00 39.83 1.94
2893 3023 6.864165 CGGGAATTATTTTGTCCGAAAGAAAA 59.136 34.615 0.00 0.00 39.83 2.29
2894 3024 6.016108 ACGGGAATTATTTTGTCCGAAAGAAA 60.016 34.615 6.57 0.00 40.53 2.52
2895 3025 5.474189 ACGGGAATTATTTTGTCCGAAAGAA 59.526 36.000 6.57 0.00 40.53 2.52
2896 3026 5.005094 ACGGGAATTATTTTGTCCGAAAGA 58.995 37.500 6.57 0.00 40.53 2.52
2897 3027 5.305139 ACGGGAATTATTTTGTCCGAAAG 57.695 39.130 6.57 0.00 40.53 2.62
2898 3028 5.163733 GCTACGGGAATTATTTTGTCCGAAA 60.164 40.000 6.57 0.00 40.53 3.46
2899 3029 4.333372 GCTACGGGAATTATTTTGTCCGAA 59.667 41.667 6.57 0.00 40.53 4.30
2900 3030 3.872771 GCTACGGGAATTATTTTGTCCGA 59.127 43.478 6.57 0.00 40.53 4.55
2901 3031 3.302870 CGCTACGGGAATTATTTTGTCCG 60.303 47.826 0.00 0.00 42.69 4.79
2902 3032 3.872771 TCGCTACGGGAATTATTTTGTCC 59.127 43.478 0.00 0.00 0.00 4.02
2903 3033 4.807304 TCTCGCTACGGGAATTATTTTGTC 59.193 41.667 0.00 0.00 31.57 3.18
2904 3034 4.761975 TCTCGCTACGGGAATTATTTTGT 58.238 39.130 0.00 0.00 31.57 2.83
2905 3035 5.728351 TTCTCGCTACGGGAATTATTTTG 57.272 39.130 0.00 0.00 41.63 2.44
2914 3044 1.076559 TCCCATTCTCGCTACGGGA 60.077 57.895 0.00 0.00 43.77 5.14
2915 3045 0.393077 AATCCCATTCTCGCTACGGG 59.607 55.000 0.00 0.00 38.34 5.28
2916 3046 2.135933 GAAATCCCATTCTCGCTACGG 58.864 52.381 0.00 0.00 0.00 4.02
2917 3047 2.135933 GGAAATCCCATTCTCGCTACG 58.864 52.381 0.00 0.00 34.14 3.51
2918 3048 3.194005 TGGAAATCCCATTCTCGCTAC 57.806 47.619 0.00 0.00 40.82 3.58
2928 3058 1.732941 CGATCGTTGTGGAAATCCCA 58.267 50.000 7.03 0.00 44.25 4.37
2929 3059 0.377203 GCGATCGTTGTGGAAATCCC 59.623 55.000 17.81 0.00 34.29 3.85
2930 3060 1.083489 TGCGATCGTTGTGGAAATCC 58.917 50.000 17.81 0.00 0.00 3.01
2931 3061 2.892373 TTGCGATCGTTGTGGAAATC 57.108 45.000 17.81 0.00 0.00 2.17
2932 3062 2.351350 GGTTTGCGATCGTTGTGGAAAT 60.351 45.455 17.81 0.00 0.00 2.17
2933 3063 1.002251 GGTTTGCGATCGTTGTGGAAA 60.002 47.619 17.81 0.00 0.00 3.13
2934 3064 0.589223 GGTTTGCGATCGTTGTGGAA 59.411 50.000 17.81 0.37 0.00 3.53
2935 3065 2.240230 GGTTTGCGATCGTTGTGGA 58.760 52.632 17.81 0.00 0.00 4.02
2936 3066 4.838959 GGTTTGCGATCGTTGTGG 57.161 55.556 17.81 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.