Multiple sequence alignment - TraesCS6B01G390000

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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 TraesCS6B01G390000 chr6B 100.000 4889 0 0 1 4889 664476690 664481578 0.000000e+00 9029
1 TraesCS6B01G390000 chr6B 92.172 1533 83 14 617 2140 664525172 664523668 0.000000e+00 2132
2 TraesCS6B01G390000 chr6B 98.420 1076 15 2 3799 4873 540603265 540602191 0.000000e+00 1892
3 TraesCS6B01G390000 chr6B 80.656 2042 299 45 632 2634 3799634 3801618 0.000000e+00 1495
4 TraesCS6B01G390000 chr6B 80.065 1550 253 24 1107 2628 664506677 664505156 0.000000e+00 1099
5 TraesCS6B01G390000 chr6B 82.073 1177 140 42 2627 3793 664523239 664522124 0.000000e+00 939
6 TraesCS6B01G390000 chr6B 92.494 453 28 3 2177 2628 664523577 664523130 1.150000e-180 643
7 TraesCS6B01G390000 chr6B 89.571 163 17 0 453 615 151137077 151136915 1.780000e-49 207
8 TraesCS6B01G390000 chr6B 88.824 170 18 1 447 615 465147944 465148113 1.780000e-49 207
9 TraesCS6B01G390000 chr6B 99.115 113 1 0 2627 2739 664479205 664479317 2.310000e-48 204
10 TraesCS6B01G390000 chr6B 99.115 113 1 0 2516 2628 664479316 664479428 2.310000e-48 204
11 TraesCS6B01G390000 chr6B 97.727 88 2 0 980 1067 664507916 664508003 8.480000e-33 152
12 TraesCS6B01G390000 chr6B 94.667 75 4 0 1726 1800 664508049 664508123 3.090000e-22 117
13 TraesCS6B01G390000 chr6A 96.779 2639 71 4 1 2628 587889670 587892305 0.000000e+00 4390
14 TraesCS6B01G390000 chr6A 92.095 2024 117 13 617 2628 587972180 587970188 0.000000e+00 2811
15 TraesCS6B01G390000 chr6A 95.543 1077 41 4 3802 4873 407496323 407495249 0.000000e+00 1716
16 TraesCS6B01G390000 chr6A 81.457 1688 236 34 632 2294 775007 773372 0.000000e+00 1312
17 TraesCS6B01G390000 chr6A 93.503 785 41 4 3022 3801 587892546 587893325 0.000000e+00 1158
18 TraesCS6B01G390000 chr6A 81.129 1187 159 38 2627 3800 587970300 587969166 0.000000e+00 891
19 TraesCS6B01G390000 chr6A 97.458 354 9 0 2627 2980 587892193 587892546 5.410000e-169 604
20 TraesCS6B01G390000 chr6A 87.037 162 13 2 3641 3802 587889375 587889528 5.030000e-40 176
21 TraesCS6B01G390000 chr6D 96.742 2640 68 9 1 2628 439615435 439618068 0.000000e+00 4383
22 TraesCS6B01G390000 chr6D 93.435 2026 114 8 617 2628 439662513 439660493 0.000000e+00 2987
23 TraesCS6B01G390000 chr6D 96.967 1187 28 3 2627 3805 439617956 439619142 0.000000e+00 1986
24 TraesCS6B01G390000 chr6D 81.149 2037 278 47 632 2627 2133977 2135948 0.000000e+00 1537
25 TraesCS6B01G390000 chr6D 83.206 786 111 10 3022 3804 439660250 439659483 0.000000e+00 701
26 TraesCS6B01G390000 chr6D 78.637 763 106 26 1541 2294 4209039 4209753 2.070000e-123 453
27 TraesCS6B01G390000 chr6D 88.650 326 34 1 2629 2951 439660603 439660278 1.280000e-105 394
28 TraesCS6B01G390000 chr3A 98.599 1071 14 1 3804 4873 629042821 629041751 0.000000e+00 1893
29 TraesCS6B01G390000 chr4A 98.224 1070 18 1 3805 4873 609101819 609102888 0.000000e+00 1869
30 TraesCS6B01G390000 chr1A 97.292 1071 27 2 3804 4873 551522219 551523288 0.000000e+00 1816
31 TraesCS6B01G390000 chr3B 97.199 1071 29 1 3804 4873 373121598 373120528 0.000000e+00 1810
32 TraesCS6B01G390000 chr5A 96.179 1073 35 3 3805 4873 698340635 698339565 0.000000e+00 1749
33 TraesCS6B01G390000 chr7A 95.903 1074 36 4 3804 4873 18549427 18550496 0.000000e+00 1733
34 TraesCS6B01G390000 chr7A 88.623 167 18 1 453 618 16718366 16718200 8.300000e-48 202
35 TraesCS6B01G390000 chr7B 94.708 1077 48 5 3804 4873 629432878 629433952 0.000000e+00 1664
36 TraesCS6B01G390000 chr3D 91.975 162 13 0 453 614 409892008 409891847 1.370000e-55 228
37 TraesCS6B01G390000 chr7D 90.184 163 16 0 453 615 5492209 5492047 3.830000e-51 213
38 TraesCS6B01G390000 chr4B 88.068 176 20 1 441 615 9545111 9545286 1.780000e-49 207
39 TraesCS6B01G390000 chr1D 88.235 170 19 1 447 615 84712050 84712219 8.300000e-48 202


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 TraesCS6B01G390000 chr6B 664476690 664481578 4888 False 3145.666667 9029 99.410000 1 4889 3 chr6B.!!$F3 4888
1 TraesCS6B01G390000 chr6B 540602191 540603265 1074 True 1892.000000 1892 98.420000 3799 4873 1 chr6B.!!$R2 1074
2 TraesCS6B01G390000 chr6B 3799634 3801618 1984 False 1495.000000 1495 80.656000 632 2634 1 chr6B.!!$F1 2002
3 TraesCS6B01G390000 chr6B 664522124 664525172 3048 True 1238.000000 2132 88.913000 617 3793 3 chr6B.!!$R4 3176
4 TraesCS6B01G390000 chr6B 664505156 664506677 1521 True 1099.000000 1099 80.065000 1107 2628 1 chr6B.!!$R3 1521
5 TraesCS6B01G390000 chr6A 587969166 587972180 3014 True 1851.000000 2811 86.612000 617 3800 2 chr6A.!!$R3 3183
6 TraesCS6B01G390000 chr6A 407495249 407496323 1074 True 1716.000000 1716 95.543000 3802 4873 1 chr6A.!!$R2 1071
7 TraesCS6B01G390000 chr6A 587889375 587893325 3950 False 1582.000000 4390 93.694250 1 3802 4 chr6A.!!$F1 3801
8 TraesCS6B01G390000 chr6A 773372 775007 1635 True 1312.000000 1312 81.457000 632 2294 1 chr6A.!!$R1 1662
9 TraesCS6B01G390000 chr6D 439615435 439619142 3707 False 3184.500000 4383 96.854500 1 3805 2 chr6D.!!$F3 3804
10 TraesCS6B01G390000 chr6D 2133977 2135948 1971 False 1537.000000 1537 81.149000 632 2627 1 chr6D.!!$F1 1995
11 TraesCS6B01G390000 chr6D 439659483 439662513 3030 True 1360.666667 2987 88.430333 617 3804 3 chr6D.!!$R1 3187
12 TraesCS6B01G390000 chr6D 4209039 4209753 714 False 453.000000 453 78.637000 1541 2294 1 chr6D.!!$F2 753
13 TraesCS6B01G390000 chr3A 629041751 629042821 1070 True 1893.000000 1893 98.599000 3804 4873 1 chr3A.!!$R1 1069
14 TraesCS6B01G390000 chr4A 609101819 609102888 1069 False 1869.000000 1869 98.224000 3805 4873 1 chr4A.!!$F1 1068
15 TraesCS6B01G390000 chr1A 551522219 551523288 1069 False 1816.000000 1816 97.292000 3804 4873 1 chr1A.!!$F1 1069
16 TraesCS6B01G390000 chr3B 373120528 373121598 1070 True 1810.000000 1810 97.199000 3804 4873 1 chr3B.!!$R1 1069
17 TraesCS6B01G390000 chr5A 698339565 698340635 1070 True 1749.000000 1749 96.179000 3805 4873 1 chr5A.!!$R1 1068
18 TraesCS6B01G390000 chr7A 18549427 18550496 1069 False 1733.000000 1733 95.903000 3804 4873 1 chr7A.!!$F1 1069
19 TraesCS6B01G390000 chr7B 629432878 629433952 1074 False 1664.000000 1664 94.708000 3804 4873 1 chr7B.!!$F1 1069

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
126 424 0.107654 AGCGACTTGTCCTTATGCCC 60.108 55.000 0.00 0.00 0.00 5.36 F
262 560 1.378514 GGCCCTTCGCTTTGGATCA 60.379 57.895 0.00 0.00 37.74 2.92 F
1708 2062 0.620556 ATCGAGTGCCCAACAGGAAT 59.379 50.000 0.00 0.00 38.24 3.01 F
2608 3054 5.970317 TCATTCTTGACATTTGCAGATGT 57.030 34.783 21.79 21.79 42.68 3.06 F
2638 3084 0.035534 TCTTGCAGATTGGCGCCTTA 60.036 50.000 29.70 16.47 36.28 2.69 F
2639 3085 0.099436 CTTGCAGATTGGCGCCTTAC 59.901 55.000 29.70 17.75 36.28 2.34 F
2641 3087 0.394216 TGCAGATTGGCGCCTTACAT 60.394 50.000 29.70 14.21 36.28 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1267 1600 2.143008 GGTTTAAACCCGGTTGCTTG 57.857 50.000 24.50 0.0 43.43 4.01 R
2014 2373 2.698855 ATTGTGACCCTCGATGGAAG 57.301 50.000 14.21 0.0 38.35 3.46 R
2620 3066 0.099436 GTAAGGCGCCAATCTGCAAG 59.901 55.000 31.54 0.0 0.00 4.01 R
3638 4132 0.103208 GACTGATCGCTCGACCCAAT 59.897 55.000 0.00 0.0 0.00 3.16 R
3639 4133 1.511305 GACTGATCGCTCGACCCAA 59.489 57.895 0.00 0.0 0.00 4.12 R
3712 4206 1.748732 TGGAACCTGGTCCACCATAA 58.251 50.000 13.67 0.0 46.46 1.90 R
3906 4402 2.028112 CGGTCAAGAATGAGAGGTTCCA 60.028 50.000 0.00 0.0 35.88 3.53 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
37 333 8.437360 AGCGAGAATATGTAATGAAATCACAA 57.563 30.769 0.00 0.00 0.00 3.33
60 358 3.319972 TGAGCAAAACTACCGAGTACTGT 59.680 43.478 0.00 0.00 33.58 3.55
62 360 2.660236 GCAAAACTACCGAGTACTGTCG 59.340 50.000 0.00 0.00 39.77 4.35
126 424 0.107654 AGCGACTTGTCCTTATGCCC 60.108 55.000 0.00 0.00 0.00 5.36
146 444 1.762957 CTCCTATTCGCTCCCTTTGGA 59.237 52.381 0.00 0.00 38.75 3.53
169 467 7.604545 TGGATTCGACACTTTATTTATCACACA 59.395 33.333 0.00 0.00 0.00 3.72
262 560 1.378514 GGCCCTTCGCTTTGGATCA 60.379 57.895 0.00 0.00 37.74 2.92
386 684 5.418840 AGAAATTGTGAGGCCGTATTCAAAT 59.581 36.000 0.00 0.00 0.00 2.32
524 823 7.730084 ACTACAACATACAGATGCACATAGAT 58.270 34.615 0.00 0.00 36.43 1.98
526 825 7.953158 ACAACATACAGATGCACATAGATAC 57.047 36.000 0.00 0.00 36.43 2.24
615 914 6.901615 TTTATATTTGGGAACAGAGGGAGA 57.098 37.500 0.00 0.00 44.54 3.71
802 1105 9.683870 AATTAATGGCATATTTTCCAACACAAT 57.316 25.926 0.00 0.00 35.75 2.71
1267 1600 4.677378 GTCTATGACTGCATCGATGTGTAC 59.323 45.833 25.47 14.66 35.94 2.90
1418 1753 4.948341 TGCTTTAGTGTGTTCTACTCCA 57.052 40.909 0.00 0.00 0.00 3.86
1421 1756 6.999950 TGCTTTAGTGTGTTCTACTCCATTA 58.000 36.000 0.00 0.00 0.00 1.90
1647 2001 3.435026 CCCTGTTTGGATGGATACCGAAT 60.435 47.826 0.00 0.00 38.35 3.34
1708 2062 0.620556 ATCGAGTGCCCAACAGGAAT 59.379 50.000 0.00 0.00 38.24 3.01
1864 2218 7.843760 TGGGATGTTTTGATAGGGTTGATTATT 59.156 33.333 0.00 0.00 0.00 1.40
1877 2231 6.317893 AGGGTTGATTATTCCAATTGACGTAC 59.682 38.462 7.12 0.00 0.00 3.67
2014 2373 8.287503 GTCATATTTGGATGGTAACGGTTAATC 58.712 37.037 1.47 3.39 42.51 1.75
2138 2534 9.826574 TTGTACTCTACAACATTTGAGTAGTTT 57.173 29.630 0.00 6.01 43.23 2.66
2603 3049 8.959548 ACATAGTATTCATTCTTGACATTTGCA 58.040 29.630 0.00 0.00 0.00 4.08
2604 3050 9.447040 CATAGTATTCATTCTTGACATTTGCAG 57.553 33.333 0.00 0.00 0.00 4.41
2605 3051 7.692460 AGTATTCATTCTTGACATTTGCAGA 57.308 32.000 0.00 0.00 0.00 4.26
2606 3052 8.289939 AGTATTCATTCTTGACATTTGCAGAT 57.710 30.769 0.00 0.00 0.00 2.90
2607 3053 8.188799 AGTATTCATTCTTGACATTTGCAGATG 58.811 33.333 15.28 15.28 0.00 2.90
2608 3054 5.970317 TCATTCTTGACATTTGCAGATGT 57.030 34.783 21.79 21.79 42.68 3.06
2609 3055 6.335471 TCATTCTTGACATTTGCAGATGTT 57.665 33.333 22.41 7.98 40.21 2.71
2610 3056 7.451501 TCATTCTTGACATTTGCAGATGTTA 57.548 32.000 22.41 16.43 40.21 2.41
2611 3057 7.307694 TCATTCTTGACATTTGCAGATGTTAC 58.692 34.615 22.41 12.21 40.21 2.50
2612 3058 6.882610 TTCTTGACATTTGCAGATGTTACT 57.117 33.333 22.41 1.08 40.21 2.24
2613 3059 6.882610 TCTTGACATTTGCAGATGTTACTT 57.117 33.333 22.41 0.70 40.21 2.24
2614 3060 7.275888 TCTTGACATTTGCAGATGTTACTTT 57.724 32.000 22.41 0.00 40.21 2.66
2615 3061 7.715657 TCTTGACATTTGCAGATGTTACTTTT 58.284 30.769 22.41 0.00 40.21 2.27
2616 3062 8.845227 TCTTGACATTTGCAGATGTTACTTTTA 58.155 29.630 22.41 4.18 40.21 1.52
2617 3063 9.630098 CTTGACATTTGCAGATGTTACTTTTAT 57.370 29.630 22.41 0.00 40.21 1.40
2618 3064 9.979578 TTGACATTTGCAGATGTTACTTTTATT 57.020 25.926 22.41 0.00 40.21 1.40
2619 3065 9.979578 TGACATTTGCAGATGTTACTTTTATTT 57.020 25.926 22.41 0.00 40.21 1.40
2624 3070 8.519492 TTGCAGATGTTACTTTTATTTCTTGC 57.481 30.769 0.00 0.00 0.00 4.01
2625 3071 7.656412 TGCAGATGTTACTTTTATTTCTTGCA 58.344 30.769 0.00 0.00 0.00 4.08
2626 3072 7.809331 TGCAGATGTTACTTTTATTTCTTGCAG 59.191 33.333 0.00 0.00 0.00 4.41
2627 3073 8.023128 GCAGATGTTACTTTTATTTCTTGCAGA 58.977 33.333 0.00 0.00 0.00 4.26
2631 3077 9.643693 ATGTTACTTTTATTTCTTGCAGATTGG 57.356 29.630 0.00 0.00 0.00 3.16
2632 3078 7.598493 TGTTACTTTTATTTCTTGCAGATTGGC 59.402 33.333 0.00 0.00 0.00 4.52
2633 3079 5.163513 ACTTTTATTTCTTGCAGATTGGCG 58.836 37.500 0.00 0.00 36.28 5.69
2634 3080 2.849880 TATTTCTTGCAGATTGGCGC 57.150 45.000 0.00 0.00 36.28 6.53
2635 3081 0.174162 ATTTCTTGCAGATTGGCGCC 59.826 50.000 22.73 22.73 36.28 6.53
2636 3082 0.895100 TTTCTTGCAGATTGGCGCCT 60.895 50.000 29.70 8.29 36.28 5.52
2637 3083 0.895100 TTCTTGCAGATTGGCGCCTT 60.895 50.000 29.70 15.71 36.28 4.35
2638 3084 0.035534 TCTTGCAGATTGGCGCCTTA 60.036 50.000 29.70 16.47 36.28 2.69
2639 3085 0.099436 CTTGCAGATTGGCGCCTTAC 59.901 55.000 29.70 17.75 36.28 2.34
2640 3086 0.607762 TTGCAGATTGGCGCCTTACA 60.608 50.000 29.70 14.09 36.28 2.41
2641 3087 0.394216 TGCAGATTGGCGCCTTACAT 60.394 50.000 29.70 14.21 36.28 2.29
2642 3088 0.740737 GCAGATTGGCGCCTTACATT 59.259 50.000 29.70 2.90 0.00 2.71
2643 3089 1.134946 GCAGATTGGCGCCTTACATTT 59.865 47.619 29.70 6.84 0.00 2.32
2644 3090 2.417243 GCAGATTGGCGCCTTACATTTT 60.417 45.455 29.70 2.76 0.00 1.82
2645 3091 3.848726 CAGATTGGCGCCTTACATTTTT 58.151 40.909 29.70 0.00 0.00 1.94
2646 3092 3.859386 CAGATTGGCGCCTTACATTTTTC 59.141 43.478 29.70 8.81 0.00 2.29
2647 3093 3.509575 AGATTGGCGCCTTACATTTTTCA 59.490 39.130 29.70 0.00 0.00 2.69
2648 3094 3.951775 TTGGCGCCTTACATTTTTCAT 57.048 38.095 29.70 0.00 0.00 2.57
2649 3095 5.359576 AGATTGGCGCCTTACATTTTTCATA 59.640 36.000 29.70 0.00 0.00 2.15
2650 3096 5.392767 TTGGCGCCTTACATTTTTCATAA 57.607 34.783 29.70 4.82 0.00 1.90
2651 3097 4.739195 TGGCGCCTTACATTTTTCATAAC 58.261 39.130 29.70 0.00 0.00 1.89
2652 3098 4.218635 TGGCGCCTTACATTTTTCATAACA 59.781 37.500 29.70 0.00 0.00 2.41
2653 3099 5.105554 TGGCGCCTTACATTTTTCATAACAT 60.106 36.000 29.70 0.00 0.00 2.71
2654 3100 5.231991 GGCGCCTTACATTTTTCATAACATG 59.768 40.000 22.15 0.00 0.00 3.21
2655 3101 6.033341 GCGCCTTACATTTTTCATAACATGA 58.967 36.000 0.00 0.00 37.55 3.07
2656 3102 6.529829 GCGCCTTACATTTTTCATAACATGAA 59.470 34.615 0.00 0.00 46.77 2.57
2679 3125 9.552695 TGAATTAGATGTGATATCCTATCAGGT 57.447 33.333 14.92 2.37 36.53 4.00
2685 3131 9.781425 AGATGTGATATCCTATCAGGTTTATCT 57.219 33.333 14.92 0.00 36.53 1.98
2751 3197 3.318191 GCAGAGGGCAGGACTCAT 58.682 61.111 0.00 0.00 43.97 2.90
2792 3238 1.332375 GGGCGCGTGCTTCATTAAATA 59.668 47.619 21.89 0.00 42.25 1.40
2827 3276 3.202373 AGGTTAAAGGTAGCCAGGATTCC 59.798 47.826 0.00 0.00 33.11 3.01
3204 3693 6.867519 TCAAGAATACAACCATCCTCTGTA 57.132 37.500 0.00 0.00 0.00 2.74
3460 3954 6.701841 GGCTGTTCGAATTCATTAGATACAGA 59.298 38.462 18.18 0.00 35.42 3.41
3557 4051 3.614176 GCATTTTGCTTCGGAAGGATTTC 59.386 43.478 18.73 2.96 40.96 2.17
3638 4132 4.350816 CCCCAAATAGATACATGGTGGAGA 59.649 45.833 0.00 0.00 0.00 3.71
3639 4133 5.014544 CCCCAAATAGATACATGGTGGAGAT 59.985 44.000 0.00 0.00 0.00 2.75
3709 4203 4.137543 GCAAGGATTTCGGGATGACTATT 58.862 43.478 0.00 0.00 0.00 1.73
3712 4206 6.431234 GCAAGGATTTCGGGATGACTATTTAT 59.569 38.462 0.00 0.00 0.00 1.40
3737 4231 0.475632 TGGACCAGGTTCCATGAGGT 60.476 55.000 6.66 0.00 41.00 3.85
3897 4392 0.620556 ATCCAATGACGCACCTTCCT 59.379 50.000 0.00 0.00 0.00 3.36
3992 4489 2.595386 CGCCACTTCCATTAAAAGCAC 58.405 47.619 0.00 0.00 0.00 4.40
4159 4662 2.238144 CCACCTCCATCCATATGCTAGG 59.762 54.545 0.00 1.83 39.18 3.02
4873 5379 4.993905 AGGCGTTGGCTAACAAATTAATC 58.006 39.130 13.75 0.00 41.58 1.75
4874 5380 4.109766 GGCGTTGGCTAACAAATTAATCC 58.890 43.478 13.75 0.00 41.58 3.01
4875 5381 4.109766 GCGTTGGCTAACAAATTAATCCC 58.890 43.478 13.75 0.00 41.58 3.85
4876 5382 4.678622 CGTTGGCTAACAAATTAATCCCC 58.321 43.478 13.75 0.00 41.58 4.81
4877 5383 4.401202 CGTTGGCTAACAAATTAATCCCCT 59.599 41.667 13.75 0.00 41.58 4.79
4878 5384 5.449999 CGTTGGCTAACAAATTAATCCCCTC 60.450 44.000 13.75 0.00 41.58 4.30
4879 5385 4.542697 TGGCTAACAAATTAATCCCCTCC 58.457 43.478 0.00 0.00 0.00 4.30
4880 5386 3.895656 GGCTAACAAATTAATCCCCTCCC 59.104 47.826 0.00 0.00 0.00 4.30
4881 5387 3.568430 GCTAACAAATTAATCCCCTCCCG 59.432 47.826 0.00 0.00 0.00 5.14
4882 5388 2.067365 ACAAATTAATCCCCTCCCGC 57.933 50.000 0.00 0.00 0.00 6.13
4883 5389 1.569072 ACAAATTAATCCCCTCCCGCT 59.431 47.619 0.00 0.00 0.00 5.52
4884 5390 2.230660 CAAATTAATCCCCTCCCGCTC 58.769 52.381 0.00 0.00 0.00 5.03
4885 5391 1.821088 AATTAATCCCCTCCCGCTCT 58.179 50.000 0.00 0.00 0.00 4.09
4886 5392 1.353091 ATTAATCCCCTCCCGCTCTC 58.647 55.000 0.00 0.00 0.00 3.20
4887 5393 0.763223 TTAATCCCCTCCCGCTCTCC 60.763 60.000 0.00 0.00 0.00 3.71
4888 5394 2.996470 TAATCCCCTCCCGCTCTCCG 62.996 65.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 333 4.021368 ACAGTACTCGGTAGTTTTGCTCAT 60.021 41.667 0.00 0.00 37.15 2.90
89 387 2.353803 CGCTGCTTAGGTAGAACCAACT 60.354 50.000 0.00 0.00 41.95 3.16
126 424 1.762957 TCCAAAGGGAGCGAATAGGAG 59.237 52.381 0.00 0.00 38.64 3.69
262 560 2.528743 CGCGCGCTGGAGATCAATT 61.529 57.895 30.48 0.00 0.00 2.32
386 684 9.997482 GTTTTGTTAATTTGTCAGTAAGTGAGA 57.003 29.630 0.00 0.00 35.13 3.27
497 796 8.040727 TCTATGTGCATCTGTATGTTGTAGTTT 58.959 33.333 0.00 0.00 35.38 2.66
511 810 9.486497 CACTCTAAAATGTATCTATGTGCATCT 57.514 33.333 0.00 0.00 0.00 2.90
615 914 6.543430 TTATTGCCACCAAAAGATATGCTT 57.457 33.333 0.00 0.00 38.88 3.91
1267 1600 2.143008 GGTTTAAACCCGGTTGCTTG 57.857 50.000 24.50 0.00 43.43 4.01
1708 2062 5.449041 CCGTTACTACGCAGTATTGGAACTA 60.449 44.000 7.70 0.00 44.56 2.24
1738 2092 5.125257 TCAATATTGTGTGTTGCTATGGTGG 59.875 40.000 14.97 0.00 0.00 4.61
2014 2373 2.698855 ATTGTGACCCTCGATGGAAG 57.301 50.000 14.21 0.00 38.35 3.46
2138 2534 5.083122 TCTAAGGGCACAAAAATCATTCCA 58.917 37.500 0.00 0.00 0.00 3.53
2198 2622 7.475840 GGAATTCCTTCATGTACAGCTAAAAG 58.524 38.462 17.73 0.68 32.70 2.27
2205 2629 6.316140 TGAAATCGGAATTCCTTCATGTACAG 59.684 38.462 22.05 2.83 32.70 2.74
2277 2708 6.240549 TGCCAAAAACTAAGAATTTGGGAA 57.759 33.333 18.63 1.47 46.94 3.97
2321 2752 6.211384 ACATTTTGGGAAGGAAAGAGTAATGG 59.789 38.462 0.00 0.00 0.00 3.16
2458 2902 9.998106 AAGCTAAGAAGTTCTAAGTTATGTGAA 57.002 29.630 5.65 0.00 0.00 3.18
2620 3066 0.099436 GTAAGGCGCCAATCTGCAAG 59.901 55.000 31.54 0.00 0.00 4.01
2621 3067 0.607762 TGTAAGGCGCCAATCTGCAA 60.608 50.000 31.54 2.05 0.00 4.08
2622 3068 0.394216 ATGTAAGGCGCCAATCTGCA 60.394 50.000 31.54 19.03 0.00 4.41
2623 3069 0.740737 AATGTAAGGCGCCAATCTGC 59.259 50.000 31.54 13.76 0.00 4.26
2624 3070 3.508744 AAAATGTAAGGCGCCAATCTG 57.491 42.857 31.54 0.00 0.00 2.90
2625 3071 3.509575 TGAAAAATGTAAGGCGCCAATCT 59.490 39.130 31.54 12.51 0.00 2.40
2626 3072 3.843999 TGAAAAATGTAAGGCGCCAATC 58.156 40.909 31.54 17.94 0.00 2.67
2627 3073 3.951775 TGAAAAATGTAAGGCGCCAAT 57.048 38.095 31.54 19.88 0.00 3.16
2628 3074 3.951775 ATGAAAAATGTAAGGCGCCAA 57.048 38.095 31.54 14.16 0.00 4.52
2629 3075 4.218635 TGTTATGAAAAATGTAAGGCGCCA 59.781 37.500 31.54 8.23 0.00 5.69
2630 3076 4.739195 TGTTATGAAAAATGTAAGGCGCC 58.261 39.130 21.89 21.89 0.00 6.53
2631 3077 6.033341 TCATGTTATGAAAAATGTAAGGCGC 58.967 36.000 0.00 0.00 36.11 6.53
2653 3099 9.552695 ACCTGATAGGATATCACATCTAATTCA 57.447 33.333 4.83 0.00 37.67 2.57
2659 3105 9.781425 AGATAAACCTGATAGGATATCACATCT 57.219 33.333 18.42 0.00 38.72 2.90
2688 3134 8.959548 TGCAAATGTCAAGAATGAATACTATGT 58.040 29.630 0.00 0.00 37.30 2.29
2689 3135 9.447040 CTGCAAATGTCAAGAATGAATACTATG 57.553 33.333 0.00 0.00 37.30 2.23
2690 3136 9.399797 TCTGCAAATGTCAAGAATGAATACTAT 57.600 29.630 0.00 0.00 37.30 2.12
2691 3137 8.791327 TCTGCAAATGTCAAGAATGAATACTA 57.209 30.769 0.00 0.00 37.30 1.82
2692 3138 7.692460 TCTGCAAATGTCAAGAATGAATACT 57.308 32.000 0.00 0.00 37.30 2.12
2693 3139 7.972277 ACATCTGCAAATGTCAAGAATGAATAC 59.028 33.333 0.00 0.00 34.84 1.89
2694 3140 8.058667 ACATCTGCAAATGTCAAGAATGAATA 57.941 30.769 0.00 0.00 34.84 1.75
2695 3141 6.931838 ACATCTGCAAATGTCAAGAATGAAT 58.068 32.000 0.00 0.00 34.84 2.57
2696 3142 6.335471 ACATCTGCAAATGTCAAGAATGAA 57.665 33.333 0.00 0.00 34.84 2.57
2697 3143 5.970317 ACATCTGCAAATGTCAAGAATGA 57.030 34.783 0.00 0.00 34.84 2.57
2698 3144 7.310664 AGTAACATCTGCAAATGTCAAGAATG 58.689 34.615 6.03 0.00 38.92 2.67
2699 3145 7.458409 AGTAACATCTGCAAATGTCAAGAAT 57.542 32.000 6.03 0.00 38.92 2.40
2700 3146 6.882610 AGTAACATCTGCAAATGTCAAGAA 57.117 33.333 6.03 0.00 38.92 2.52
2701 3147 6.882610 AAGTAACATCTGCAAATGTCAAGA 57.117 33.333 6.03 0.00 38.92 3.02
2702 3148 7.935338 AAAAGTAACATCTGCAAATGTCAAG 57.065 32.000 6.03 0.00 38.92 3.02
2703 3149 9.979578 AATAAAAGTAACATCTGCAAATGTCAA 57.020 25.926 6.03 0.00 38.92 3.18
2704 3150 9.979578 AAATAAAAGTAACATCTGCAAATGTCA 57.020 25.926 6.03 0.00 38.92 3.58
2709 3155 8.977505 GCAAGAAATAAAAGTAACATCTGCAAA 58.022 29.630 0.00 0.00 0.00 3.68
2710 3156 8.140628 TGCAAGAAATAAAAGTAACATCTGCAA 58.859 29.630 0.00 0.00 0.00 4.08
2711 3157 7.656412 TGCAAGAAATAAAAGTAACATCTGCA 58.344 30.769 0.00 0.00 0.00 4.41
2712 3158 8.023128 TCTGCAAGAAATAAAAGTAACATCTGC 58.977 33.333 0.00 0.00 42.31 4.26
2751 3197 6.633811 CGCCCCATATAAATCACCCATGTATA 60.634 42.308 0.00 0.00 0.00 1.47
2827 3276 8.984891 TTTCAATACTTATCCAAATTGCACTG 57.015 30.769 0.00 0.00 30.99 3.66
3063 3552 6.793492 TCCAAGGTCAAAAACAAAAACAAG 57.207 33.333 0.00 0.00 0.00 3.16
3460 3954 1.288752 CCAAAACGCCAAATCGCCT 59.711 52.632 0.00 0.00 0.00 5.52
3511 4005 1.522580 GCCCATCTGCGGAGACTTC 60.523 63.158 9.49 0.00 0.00 3.01
3557 4051 3.722555 TCTTATGAACGCTGCTTTTCG 57.277 42.857 0.00 0.00 0.00 3.46
3638 4132 0.103208 GACTGATCGCTCGACCCAAT 59.897 55.000 0.00 0.00 0.00 3.16
3639 4133 1.511305 GACTGATCGCTCGACCCAA 59.489 57.895 0.00 0.00 0.00 4.12
3709 4203 3.853181 TGGAACCTGGTCCACCATAATAA 59.147 43.478 13.67 0.00 46.46 1.40
3712 4206 1.748732 TGGAACCTGGTCCACCATAA 58.251 50.000 13.67 0.00 46.46 1.90
3906 4402 2.028112 CGGTCAAGAATGAGAGGTTCCA 60.028 50.000 0.00 0.00 35.88 3.53
3992 4489 2.350804 CGAAGATGAGTTGGCTGTCATG 59.649 50.000 2.21 0.00 33.43 3.07
4119 4616 2.771943 TGGAGCTTATTGGTGACTAGGG 59.228 50.000 0.00 0.00 0.00 3.53
4159 4662 5.908341 AGAGAAGAACGACAATTATCCCTC 58.092 41.667 0.00 0.00 0.00 4.30
4385 4888 5.367945 TGGTGTTGGAGAAAGTAAGAGTT 57.632 39.130 0.00 0.00 0.00 3.01
4832 5338 8.350722 CAACGCCTACAGATAATTAGAAGTAGA 58.649 37.037 16.47 0.00 32.75 2.59


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

AutoCloner maintained by Alex Coulton.