Multiple sequence alignment - TraesCS4D01G113000

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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 TraesCS4D01G113000 chr4D 100.000 4189 0 0 1 4189 93613863 93609675 0.000000e+00 7736.0
1 TraesCS4D01G113000 chr4D 79.986 1409 242 27 976 2368 93761531 93760147 0.000000e+00 1003.0
2 TraesCS4D01G113000 chr4D 79.787 658 102 20 1294 1943 97969992 97969358 2.300000e-122 449.0
3 TraesCS4D01G113000 chr4D 80.638 470 87 4 2777 3244 93760036 93759569 1.110000e-95 361.0
4 TraesCS4D01G113000 chr4B 95.334 1693 69 8 885 2572 132056852 132055165 0.000000e+00 2680.0
5 TraesCS4D01G113000 chr4B 92.131 1652 68 23 2558 4189 132055151 132053542 0.000000e+00 2274.0
6 TraesCS4D01G113000 chr4B 79.730 1406 247 26 975 2368 132295269 132293890 0.000000e+00 983.0
7 TraesCS4D01G113000 chr4B 79.444 647 108 14 1302 1943 139571945 139571319 6.430000e-118 435.0
8 TraesCS4D01G113000 chr4B 81.217 378 64 7 2860 3234 132293750 132293377 8.800000e-77 298.0
9 TraesCS4D01G113000 chr4A 93.225 1594 78 13 2035 3617 488249842 488251416 0.000000e+00 2318.0
10 TraesCS4D01G113000 chr4A 97.418 1123 28 1 885 2007 488248738 488249859 0.000000e+00 1912.0
11 TraesCS4D01G113000 chr4A 79.872 1411 240 33 975 2368 487916348 487917731 0.000000e+00 992.0
12 TraesCS4D01G113000 chr4A 96.757 555 15 3 3637 4189 488251486 488252039 0.000000e+00 922.0
13 TraesCS4D01G113000 chr4A 82.313 441 74 4 2767 3205 487917823 487918261 3.060000e-101 379.0
14 TraesCS4D01G113000 chr4A 89.796 98 6 2 3461 3558 487918432 487918525 5.690000e-24 122.0
15 TraesCS4D01G113000 chr1D 92.009 851 48 11 1 834 432384624 432383777 0.000000e+00 1177.0
16 TraesCS4D01G113000 chr1D 88.484 851 76 18 1 837 318720667 318721509 0.000000e+00 1009.0
17 TraesCS4D01G113000 chr1D 91.379 58 4 1 2529 2585 347784495 347784438 1.250000e-10 78.7
18 TraesCS4D01G113000 chr5A 92.723 797 50 6 1 791 531095822 531096616 0.000000e+00 1144.0
19 TraesCS4D01G113000 chr5A 91.092 797 60 10 2 791 567938425 567937633 0.000000e+00 1068.0
20 TraesCS4D01G113000 chr5A 85.636 550 40 17 320 843 501408927 501409463 3.680000e-150 542.0
21 TraesCS4D01G113000 chr5A 84.276 566 44 21 320 852 94099203 94099756 1.040000e-140 510.0
22 TraesCS4D01G113000 chr5A 87.282 401 30 15 452 843 71276690 71277078 4.970000e-119 438.0
23 TraesCS4D01G113000 chr5A 86.500 400 38 11 452 846 517622133 517621745 3.870000e-115 425.0
24 TraesCS4D01G113000 chr5A 85.995 407 36 11 447 843 709605388 709605783 2.330000e-112 416.0
25 TraesCS4D01G113000 chr5A 80.488 164 18 7 685 843 14026506 14026660 3.420000e-21 113.0
26 TraesCS4D01G113000 chr3A 91.801 805 47 10 3 791 716094087 716093286 0.000000e+00 1103.0
27 TraesCS4D01G113000 chr3A 80.269 223 35 9 2508 2725 55215366 55215584 4.330000e-35 159.0
28 TraesCS4D01G113000 chr2A 90.568 827 56 13 3 812 459912543 459913364 0.000000e+00 1075.0
29 TraesCS4D01G113000 chr2A 84.324 555 44 22 320 843 770627796 770628338 1.740000e-138 503.0
30 TraesCS4D01G113000 chr2A 78.947 589 95 20 1285 1863 32503543 32504112 1.420000e-99 374.0
31 TraesCS4D01G113000 chr6D 90.698 774 50 10 37 791 11412115 11411345 0.000000e+00 1011.0
32 TraesCS4D01G113000 chr6D 78.654 431 47 20 1295 1722 61003133 61003521 1.160000e-60 244.0
33 TraesCS4D01G113000 chr6D 72.790 577 127 27 1305 1863 101720843 101721407 7.200000e-38 169.0
34 TraesCS4D01G113000 chr6D 83.832 167 26 1 1284 1450 380576963 380576798 1.560000e-34 158.0
35 TraesCS4D01G113000 chr6D 77.083 144 28 3 2517 2656 98110949 98110807 1.250000e-10 78.7
36 TraesCS4D01G113000 chr7A 88.477 729 56 20 139 852 706347124 706347839 0.000000e+00 856.0
37 TraesCS4D01G113000 chr7A 92.178 473 29 5 323 789 688267838 688267368 0.000000e+00 662.0
38 TraesCS4D01G113000 chr7A 83.265 245 34 5 2489 2729 658932790 658932549 7.050000e-53 219.0
39 TraesCS4D01G113000 chr2D 92.557 524 19 8 1 506 540166337 540166858 0.000000e+00 734.0
40 TraesCS4D01G113000 chr2D 92.902 479 24 9 320 791 346165017 346164542 0.000000e+00 688.0
41 TraesCS4D01G113000 chr2D 80.710 451 67 13 1287 1730 21825404 21825841 2.410000e-87 333.0
42 TraesCS4D01G113000 chr2D 77.645 586 100 22 1285 1863 30479048 30479609 1.120000e-85 327.0
43 TraesCS4D01G113000 chr2D 75.152 656 138 15 1285 1932 8976731 8977369 6.850000e-73 285.0
44 TraesCS4D01G113000 chr2D 76.967 521 89 22 1357 1869 30462726 30462229 6.900000e-68 268.0
45 TraesCS4D01G113000 chr2B 78.947 589 95 20 1288 1869 49981364 49980798 1.420000e-99 374.0
46 TraesCS4D01G113000 chr5B 76.056 710 130 29 1229 1936 63844345 63845016 2.410000e-87 333.0
47 TraesCS4D01G113000 chr5B 75.387 711 145 21 1229 1936 63632022 63632705 2.430000e-82 316.0
48 TraesCS4D01G113000 chr5D 75.493 710 134 28 1229 1936 58677772 58678443 1.130000e-80 311.0
49 TraesCS4D01G113000 chr5D 75.070 714 142 26 1229 1936 58947044 58947727 2.450000e-77 300.0
50 TraesCS4D01G113000 chr5D 74.474 713 147 24 1229 1936 58659177 58659859 4.130000e-70 276.0
51 TraesCS4D01G113000 chr5D 84.058 69 8 3 2518 2584 497956684 497956617 3.500000e-06 63.9
52 TraesCS4D01G113000 chr3D 76.336 655 103 22 1294 1943 134964185 134963578 1.890000e-78 303.0
53 TraesCS4D01G113000 chr3D 85.253 217 30 1 2516 2730 374927413 374927629 5.450000e-54 222.0
54 TraesCS4D01G113000 chr3D 80.349 229 36 9 2508 2731 43244796 43245020 9.320000e-37 165.0
55 TraesCS4D01G113000 chr3B 84.337 249 30 7 2486 2731 766953135 766953377 7.000000e-58 235.0
56 TraesCS4D01G113000 chr3B 89.630 135 12 2 2516 2649 488531248 488531381 2.000000e-38 171.0
57 TraesCS4D01G113000 chr3B 77.953 254 47 7 2484 2731 67378364 67378614 2.610000e-32 150.0
58 TraesCS4D01G113000 chr6A 78.212 179 32 7 2475 2649 559849558 559849733 1.590000e-19 108.0
59 TraesCS4D01G113000 chr7D 87.368 95 9 3 2493 2584 279743812 279743718 5.730000e-19 106.0


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 TraesCS4D01G113000 chr4D 93609675 93613863 4188 True 7736.000000 7736 100.000000 1 4189 1 chr4D.!!$R1 4188
1 TraesCS4D01G113000 chr4D 93759569 93761531 1962 True 682.000000 1003 80.312000 976 3244 2 chr4D.!!$R3 2268
2 TraesCS4D01G113000 chr4D 97969358 97969992 634 True 449.000000 449 79.787000 1294 1943 1 chr4D.!!$R2 649
3 TraesCS4D01G113000 chr4B 132053542 132056852 3310 True 2477.000000 2680 93.732500 885 4189 2 chr4B.!!$R2 3304
4 TraesCS4D01G113000 chr4B 132293377 132295269 1892 True 640.500000 983 80.473500 975 3234 2 chr4B.!!$R3 2259
5 TraesCS4D01G113000 chr4B 139571319 139571945 626 True 435.000000 435 79.444000 1302 1943 1 chr4B.!!$R1 641
6 TraesCS4D01G113000 chr4A 488248738 488252039 3301 False 1717.333333 2318 95.800000 885 4189 3 chr4A.!!$F2 3304
7 TraesCS4D01G113000 chr4A 487916348 487918525 2177 False 497.666667 992 83.993667 975 3558 3 chr4A.!!$F1 2583
8 TraesCS4D01G113000 chr1D 432383777 432384624 847 True 1177.000000 1177 92.009000 1 834 1 chr1D.!!$R2 833
9 TraesCS4D01G113000 chr1D 318720667 318721509 842 False 1009.000000 1009 88.484000 1 837 1 chr1D.!!$F1 836
10 TraesCS4D01G113000 chr5A 531095822 531096616 794 False 1144.000000 1144 92.723000 1 791 1 chr5A.!!$F5 790
11 TraesCS4D01G113000 chr5A 567937633 567938425 792 True 1068.000000 1068 91.092000 2 791 1 chr5A.!!$R2 789
12 TraesCS4D01G113000 chr5A 501408927 501409463 536 False 542.000000 542 85.636000 320 843 1 chr5A.!!$F4 523
13 TraesCS4D01G113000 chr5A 94099203 94099756 553 False 510.000000 510 84.276000 320 852 1 chr5A.!!$F3 532
14 TraesCS4D01G113000 chr3A 716093286 716094087 801 True 1103.000000 1103 91.801000 3 791 1 chr3A.!!$R1 788
15 TraesCS4D01G113000 chr2A 459912543 459913364 821 False 1075.000000 1075 90.568000 3 812 1 chr2A.!!$F2 809
16 TraesCS4D01G113000 chr2A 770627796 770628338 542 False 503.000000 503 84.324000 320 843 1 chr2A.!!$F3 523
17 TraesCS4D01G113000 chr2A 32503543 32504112 569 False 374.000000 374 78.947000 1285 1863 1 chr2A.!!$F1 578
18 TraesCS4D01G113000 chr6D 11411345 11412115 770 True 1011.000000 1011 90.698000 37 791 1 chr6D.!!$R1 754
19 TraesCS4D01G113000 chr7A 706347124 706347839 715 False 856.000000 856 88.477000 139 852 1 chr7A.!!$F1 713
20 TraesCS4D01G113000 chr2D 540166337 540166858 521 False 734.000000 734 92.557000 1 506 1 chr2D.!!$F4 505
21 TraesCS4D01G113000 chr2D 30479048 30479609 561 False 327.000000 327 77.645000 1285 1863 1 chr2D.!!$F3 578
22 TraesCS4D01G113000 chr2D 8976731 8977369 638 False 285.000000 285 75.152000 1285 1932 1 chr2D.!!$F1 647
23 TraesCS4D01G113000 chr2B 49980798 49981364 566 True 374.000000 374 78.947000 1288 1869 1 chr2B.!!$R1 581
24 TraesCS4D01G113000 chr5B 63844345 63845016 671 False 333.000000 333 76.056000 1229 1936 1 chr5B.!!$F2 707
25 TraesCS4D01G113000 chr5B 63632022 63632705 683 False 316.000000 316 75.387000 1229 1936 1 chr5B.!!$F1 707
26 TraesCS4D01G113000 chr5D 58677772 58678443 671 False 311.000000 311 75.493000 1229 1936 1 chr5D.!!$F2 707
27 TraesCS4D01G113000 chr5D 58947044 58947727 683 False 300.000000 300 75.070000 1229 1936 1 chr5D.!!$F3 707
28 TraesCS4D01G113000 chr5D 58659177 58659859 682 False 276.000000 276 74.474000 1229 1936 1 chr5D.!!$F1 707
29 TraesCS4D01G113000 chr3D 134963578 134964185 607 True 303.000000 303 76.336000 1294 1943 1 chr3D.!!$R1 649

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
137 149 0.937304 ATCCGCATCCGATTTTGACG 59.063 50.0 0.00 0.0 36.29 4.35 F
870 923 1.382914 AACCAGGACTAATGGCCCTT 58.617 50.0 0.00 0.0 41.87 3.95 F
2368 2442 0.990374 AGAGGCTGCATCTTGAGGTT 59.010 50.0 11.54 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 2143 1.146263 CCGGGTCCAGATAGCCAAC 59.854 63.158 0.0 0.0 36.81 3.77 R
2611 2721 0.323725 AGCATGACAATTCCGCCCTT 60.324 50.000 0.0 0.0 0.00 3.95 R
3766 4047 0.178992 TGTTGGCTTGGTCCTTCAGG 60.179 55.000 0.0 0.0 0.00 3.86 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
137 149 0.937304 ATCCGCATCCGATTTTGACG 59.063 50.000 0.00 0.00 36.29 4.35
375 402 7.658575 TGGTCAAACTATGGTCAAACTACTTAC 59.341 37.037 0.00 0.00 0.00 2.34
476 520 6.708949 TGGTCAAATCTGGTCAAACTACTTAC 59.291 38.462 0.00 0.00 0.00 2.34
563 608 2.533266 AACGTGTGACTTCATGCTCT 57.467 45.000 0.00 0.00 0.00 4.09
575 620 5.105752 ACTTCATGCTCTAAGCTAAACTCG 58.894 41.667 0.11 0.00 42.97 4.18
623 668 9.179909 TCTTACTATTGTCAGGAAAACAACAAA 57.820 29.630 0.00 0.00 39.29 2.83
652 698 4.227527 ACTTGGAAACGAGGGGAATAGAAT 59.772 41.667 0.00 0.00 46.96 2.40
740 786 6.008331 TGATTTGGAATGATGAGGGATGATC 58.992 40.000 0.00 0.00 0.00 2.92
743 789 3.244805 TGGAATGATGAGGGATGATCAGC 60.245 47.826 1.26 1.26 32.20 4.26
772 818 9.671279 TTAGAGATTAAATTGAGCAGTGATGAA 57.329 29.630 0.00 0.00 0.00 2.57
774 820 8.045507 AGAGATTAAATTGAGCAGTGATGAAGA 58.954 33.333 0.00 0.00 0.00 2.87
775 821 8.571461 AGATTAAATTGAGCAGTGATGAAGAA 57.429 30.769 0.00 0.00 0.00 2.52
857 910 8.622948 ACTTCATAAAACTCTCTTTAACCAGG 57.377 34.615 0.00 0.00 0.00 4.45
858 911 8.437575 ACTTCATAAAACTCTCTTTAACCAGGA 58.562 33.333 0.00 0.00 0.00 3.86
859 912 8.617290 TTCATAAAACTCTCTTTAACCAGGAC 57.383 34.615 0.00 0.00 0.00 3.85
860 913 7.974504 TCATAAAACTCTCTTTAACCAGGACT 58.025 34.615 0.00 0.00 0.00 3.85
861 914 9.096823 TCATAAAACTCTCTTTAACCAGGACTA 57.903 33.333 0.00 0.00 0.00 2.59
862 915 9.720769 CATAAAACTCTCTTTAACCAGGACTAA 57.279 33.333 0.00 0.00 0.00 2.24
864 917 8.622948 AAAACTCTCTTTAACCAGGACTAATG 57.377 34.615 0.00 0.00 0.00 1.90
865 918 6.301169 ACTCTCTTTAACCAGGACTAATGG 57.699 41.667 0.00 0.00 43.87 3.16
866 919 5.099042 TCTCTTTAACCAGGACTAATGGC 57.901 43.478 0.00 0.00 41.87 4.40
867 920 4.080526 TCTCTTTAACCAGGACTAATGGCC 60.081 45.833 0.00 0.00 41.87 5.36
868 921 3.053917 TCTTTAACCAGGACTAATGGCCC 60.054 47.826 0.00 0.00 41.87 5.80
869 922 2.280308 TAACCAGGACTAATGGCCCT 57.720 50.000 0.00 0.00 41.87 5.19
870 923 1.382914 AACCAGGACTAATGGCCCTT 58.617 50.000 0.00 0.00 41.87 3.95
871 924 1.382914 ACCAGGACTAATGGCCCTTT 58.617 50.000 0.00 0.00 41.87 3.11
872 925 1.716503 ACCAGGACTAATGGCCCTTTT 59.283 47.619 0.00 0.00 41.87 2.27
873 926 2.111792 ACCAGGACTAATGGCCCTTTTT 59.888 45.455 0.00 0.00 41.87 1.94
1203 1257 1.606601 CACGGTGACCCTCCTCTCA 60.607 63.158 0.74 0.00 0.00 3.27
1451 1511 4.753662 CGACCTCCTCCCCGTCCA 62.754 72.222 0.00 0.00 0.00 4.02
1626 1692 3.382832 CTCCTCGCCGTCAAGGGT 61.383 66.667 0.00 0.00 41.48 4.34
2071 2143 2.048603 GCCCCTGCACTAAGCTTGG 61.049 63.158 9.86 9.13 45.94 3.61
2179 2252 6.424176 TTGTTCGATTCGCCAATGTAAATA 57.576 33.333 0.00 0.00 0.00 1.40
2276 2350 2.890847 AAGCGTCAAGATCCTCGGCG 62.891 60.000 0.00 0.00 0.00 6.46
2368 2442 0.990374 AGAGGCTGCATCTTGAGGTT 59.010 50.000 11.54 0.00 0.00 3.50
2370 2444 2.776536 AGAGGCTGCATCTTGAGGTTAT 59.223 45.455 11.54 0.00 0.00 1.89
2441 2515 7.592164 TGCAATCATCAATTTATATTGCTGACG 59.408 33.333 12.61 9.29 44.85 4.35
2461 2535 5.536538 TGACGATAATGCTTCCATCTAGAGT 59.463 40.000 0.00 0.00 0.00 3.24
2487 2566 5.429957 AGTTGTAGCTTTTCTTTGCAGAG 57.570 39.130 0.00 0.00 0.00 3.35
2505 2584 4.328440 GCAGAGATGATAAATCCCGAATCG 59.672 45.833 0.00 0.00 0.00 3.34
2597 2707 5.070770 TGACAAGCACAACAATTTTCTGT 57.929 34.783 0.00 0.00 0.00 3.41
2662 2772 1.956477 CTTGCCACCCCTTGCATATAC 59.044 52.381 0.00 0.00 37.33 1.47
2793 2903 4.755123 CCAATCTACAGTCCAACGAAACTT 59.245 41.667 0.00 0.00 0.00 2.66
2804 2914 3.074412 CAACGAAACTTATGAGCCCACT 58.926 45.455 0.00 0.00 0.00 4.00
2820 2977 0.031178 CACTGGCAAGCTCAACAACC 59.969 55.000 0.00 0.00 0.00 3.77
2837 2994 1.062488 ACCAGTTCTGGCAGGAGGTT 61.062 55.000 15.73 0.00 0.00 3.50
2949 3106 3.231889 CTGGAGAGCGCACTGGTGT 62.232 63.158 13.44 0.00 0.00 4.16
2954 3111 1.887242 GAGCGCACTGGTGTTGACA 60.887 57.895 11.47 0.00 0.00 3.58
3247 3409 5.365619 GTTTTGAGTTCTCTACCAGGTGAA 58.634 41.667 0.76 0.00 0.00 3.18
3273 3469 2.584835 TCCAGGGAAACAGATGGTTG 57.415 50.000 0.00 0.00 40.35 3.77
3312 3510 1.821936 TGCAAGGCACTGTTTTGGG 59.178 52.632 0.00 0.00 40.86 4.12
3327 3525 1.110442 TTGGGTCTTTGGCTTGTGTG 58.890 50.000 0.00 0.00 0.00 3.82
3370 3569 2.791347 TTATTTGCCTGGCGACCTTA 57.209 45.000 14.98 0.00 0.00 2.69
3405 3604 5.922544 GCATAAGACAAGTGTTGCTCAAATT 59.077 36.000 0.00 0.00 0.00 1.82
3415 3614 5.067674 AGTGTTGCTCAAATTGCAGTCTTTA 59.932 36.000 0.00 0.00 41.71 1.85
3494 3693 1.792993 GCTGATTGTGTCGCTGAATGC 60.793 52.381 0.00 0.00 38.57 3.56
3495 3694 1.736126 CTGATTGTGTCGCTGAATGCT 59.264 47.619 0.00 0.00 40.11 3.79
3496 3695 2.931969 CTGATTGTGTCGCTGAATGCTA 59.068 45.455 0.00 0.00 40.11 3.49
3537 3757 6.925610 ATTCGTGAGCTATTTCATGCTTTA 57.074 33.333 0.00 0.00 39.91 1.85
3538 3758 5.718649 TCGTGAGCTATTTCATGCTTTAC 57.281 39.130 0.00 0.00 39.91 2.01
3539 3759 5.419542 TCGTGAGCTATTTCATGCTTTACT 58.580 37.500 0.00 0.00 39.91 2.24
3540 3760 6.569780 TCGTGAGCTATTTCATGCTTTACTA 58.430 36.000 0.00 0.00 39.91 1.82
3541 3761 7.039270 TCGTGAGCTATTTCATGCTTTACTAA 58.961 34.615 0.00 0.00 39.91 2.24
3542 3762 7.710907 TCGTGAGCTATTTCATGCTTTACTAAT 59.289 33.333 0.00 0.00 39.91 1.73
3543 3763 8.338259 CGTGAGCTATTTCATGCTTTACTAATT 58.662 33.333 0.00 0.00 39.91 1.40
3546 3766 9.670719 GAGCTATTTCATGCTTTACTAATTTCC 57.329 33.333 0.00 0.00 39.91 3.13
3547 3767 9.413734 AGCTATTTCATGCTTTACTAATTTCCT 57.586 29.630 0.00 0.00 35.86 3.36
3552 3772 9.855021 TTTCATGCTTTACTAATTTCCTTTAGC 57.145 29.630 0.00 0.00 33.34 3.09
3553 3773 8.574251 TCATGCTTTACTAATTTCCTTTAGCA 57.426 30.769 0.00 0.00 40.00 3.49
3554 3774 8.458843 TCATGCTTTACTAATTTCCTTTAGCAC 58.541 33.333 0.00 0.00 38.72 4.40
3555 3775 7.753309 TGCTTTACTAATTTCCTTTAGCACA 57.247 32.000 0.00 0.00 33.34 4.57
3556 3776 8.348285 TGCTTTACTAATTTCCTTTAGCACAT 57.652 30.769 0.00 0.00 33.34 3.21
3557 3777 8.802267 TGCTTTACTAATTTCCTTTAGCACATT 58.198 29.630 0.00 0.00 33.34 2.71
3617 3837 2.290641 TGTGCCCGTCTGGAATGTTAAT 60.291 45.455 0.00 0.00 37.49 1.40
3642 3921 8.703604 TTGTAGTATTTGTCTCTGCTGTTATC 57.296 34.615 0.00 0.00 0.00 1.75
3643 3922 8.067751 TGTAGTATTTGTCTCTGCTGTTATCT 57.932 34.615 0.00 0.00 0.00 1.98
3644 3923 7.976175 TGTAGTATTTGTCTCTGCTGTTATCTG 59.024 37.037 0.00 0.00 0.00 2.90
3645 3924 6.940739 AGTATTTGTCTCTGCTGTTATCTGT 58.059 36.000 0.00 0.00 0.00 3.41
3646 3925 7.390027 AGTATTTGTCTCTGCTGTTATCTGTT 58.610 34.615 0.00 0.00 0.00 3.16
3647 3926 8.531982 AGTATTTGTCTCTGCTGTTATCTGTTA 58.468 33.333 0.00 0.00 0.00 2.41
3648 3927 9.319143 GTATTTGTCTCTGCTGTTATCTGTTAT 57.681 33.333 0.00 0.00 0.00 1.89
3714 3995 7.500992 TGTTCACATAACTAGGGATTCAGATC 58.499 38.462 0.00 0.00 0.00 2.75
3760 4041 9.494271 GAGTTGTATTAGAATTGCCATCTATGA 57.506 33.333 0.00 0.00 29.93 2.15
3883 4165 8.652810 TGAGTACTAGGTAACAAGTGAAAAAC 57.347 34.615 0.00 0.00 41.41 2.43
4094 4376 3.426859 CACTGAGACTACGAAACAGCAAG 59.573 47.826 0.00 0.00 32.67 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 122 1.444836 TCGGATGCGGATTTTCGTTT 58.555 45.000 6.82 0.00 0.00 3.60
111 123 1.663695 ATCGGATGCGGATTTTCGTT 58.336 45.000 6.82 0.00 0.00 3.85
563 608 5.726980 TTAACCCTCACGAGTTTAGCTTA 57.273 39.130 0.00 0.00 0.00 3.09
575 620 6.831976 AGATGTCAATCCTATTAACCCTCAC 58.168 40.000 0.00 0.00 32.77 3.51
623 668 1.611673 CCCTCGTTTCCAAGTCTGCAT 60.612 52.381 0.00 0.00 0.00 3.96
652 698 3.002791 CTGAGCATGCTTAACTTTCGGA 58.997 45.455 23.61 0.00 0.00 4.55
740 786 7.042187 ACTGCTCAATTTAATCTCTAATCGCTG 60.042 37.037 0.00 0.00 0.00 5.18
743 789 8.357796 TCACTGCTCAATTTAATCTCTAATCG 57.642 34.615 0.00 0.00 0.00 3.34
833 886 8.722394 GTCCTGGTTAAAGAGAGTTTTATGAAG 58.278 37.037 0.00 0.00 0.00 3.02
843 896 5.119694 GCCATTAGTCCTGGTTAAAGAGAG 58.880 45.833 0.00 0.00 36.10 3.20
845 898 4.200092 GGCCATTAGTCCTGGTTAAAGAG 58.800 47.826 0.00 0.00 36.10 2.85
852 905 1.382914 AAAGGGCCATTAGTCCTGGT 58.617 50.000 1.49 0.00 36.10 4.00
853 906 2.532250 AAAAGGGCCATTAGTCCTGG 57.468 50.000 1.49 0.00 36.81 4.45
872 925 6.347696 TCTAACGGTGAAACACTAGGAAAAA 58.652 36.000 0.00 0.00 39.98 1.94
873 926 5.916318 TCTAACGGTGAAACACTAGGAAAA 58.084 37.500 0.00 0.00 39.98 2.29
874 927 5.534207 TCTAACGGTGAAACACTAGGAAA 57.466 39.130 0.00 0.00 39.98 3.13
875 928 4.560108 GCTCTAACGGTGAAACACTAGGAA 60.560 45.833 0.00 0.00 39.98 3.36
876 929 3.057033 GCTCTAACGGTGAAACACTAGGA 60.057 47.826 0.00 0.00 39.98 2.94
877 930 3.251571 GCTCTAACGGTGAAACACTAGG 58.748 50.000 0.00 0.00 39.98 3.02
878 931 2.915463 CGCTCTAACGGTGAAACACTAG 59.085 50.000 0.00 0.00 39.98 2.57
879 932 2.937591 CGCTCTAACGGTGAAACACTA 58.062 47.619 0.00 0.00 39.98 2.74
880 933 1.779569 CGCTCTAACGGTGAAACACT 58.220 50.000 0.00 0.00 39.98 3.55
900 954 2.456443 GGGATGGGAGGAGGAAGCC 61.456 68.421 0.00 0.00 0.00 4.35
904 958 4.880426 GCGGGGATGGGAGGAGGA 62.880 72.222 0.00 0.00 0.00 3.71
2071 2143 1.146263 CCGGGTCCAGATAGCCAAC 59.854 63.158 0.00 0.00 36.81 3.77
2179 2252 6.547141 TCCATTTTTCAGAGACAACTTCACAT 59.453 34.615 0.00 0.00 0.00 3.21
2276 2350 3.067833 GGACTCCAAAGCACACTCTTAC 58.932 50.000 0.00 0.00 0.00 2.34
2368 2442 7.426606 TGCCAAAGTAAGTGATAGTGGTATA 57.573 36.000 0.00 0.00 0.00 1.47
2370 2444 5.748670 TGCCAAAGTAAGTGATAGTGGTA 57.251 39.130 0.00 0.00 0.00 3.25
2441 2515 7.930865 ACTTTGACTCTAGATGGAAGCATTATC 59.069 37.037 0.00 0.00 0.00 1.75
2461 2535 5.960113 TGCAAAGAAAAGCTACAACTTTGA 58.040 33.333 25.34 14.92 45.45 2.69
2611 2721 0.323725 AGCATGACAATTCCGCCCTT 60.324 50.000 0.00 0.00 0.00 3.95
2804 2914 0.395586 ACTGGTTGTTGAGCTTGCCA 60.396 50.000 0.00 0.00 0.00 4.92
2820 2977 0.607489 CCAACCTCCTGCCAGAACTG 60.607 60.000 0.00 0.00 0.00 3.16
2949 3106 1.872952 CACGATCACCAGCTTTGTCAA 59.127 47.619 0.00 0.00 0.00 3.18
2954 3111 1.873591 GTGAACACGATCACCAGCTTT 59.126 47.619 8.79 0.00 43.11 3.51
3247 3409 1.697432 TCTGTTTCCCTGGAATCACGT 59.303 47.619 5.73 0.00 33.79 4.49
3273 3469 1.927174 CGTAGACTGCAACATAGCACC 59.073 52.381 0.00 0.00 40.11 5.01
3337 3535 4.283467 AGGCAAATAAAAACCAGGAACTCC 59.717 41.667 0.00 0.00 34.60 3.85
3370 3569 6.432162 ACACTTGTCTTATGCATCAACATCTT 59.568 34.615 0.19 0.00 0.00 2.40
3415 3614 8.150296 GGCCAAAGCAAAATAAATAGACCATAT 58.850 33.333 0.00 0.00 42.56 1.78
3461 3660 4.940046 ACACAATCAGCAGAAATAGTGAGG 59.060 41.667 0.00 0.00 0.00 3.86
3494 3693 8.387354 CACGAATATATCTCTGTCTGCTAGTAG 58.613 40.741 0.63 0.63 0.00 2.57
3495 3694 8.095169 TCACGAATATATCTCTGTCTGCTAGTA 58.905 37.037 0.00 0.00 0.00 1.82
3496 3695 6.937465 TCACGAATATATCTCTGTCTGCTAGT 59.063 38.462 0.00 0.00 0.00 2.57
3537 3757 7.552687 TCGATGAATGTGCTAAAGGAAATTAGT 59.447 33.333 0.00 0.00 35.70 2.24
3538 3758 7.919690 TCGATGAATGTGCTAAAGGAAATTAG 58.080 34.615 0.00 0.00 36.24 1.73
3539 3759 7.857734 TCGATGAATGTGCTAAAGGAAATTA 57.142 32.000 0.00 0.00 0.00 1.40
3540 3760 6.757897 TCGATGAATGTGCTAAAGGAAATT 57.242 33.333 0.00 0.00 0.00 1.82
3541 3761 6.757897 TTCGATGAATGTGCTAAAGGAAAT 57.242 33.333 0.00 0.00 0.00 2.17
3542 3762 6.554419 CATTCGATGAATGTGCTAAAGGAAA 58.446 36.000 10.60 0.00 42.89 3.13
3543 3763 6.122850 CATTCGATGAATGTGCTAAAGGAA 57.877 37.500 10.60 0.00 42.89 3.36
3544 3764 5.739752 CATTCGATGAATGTGCTAAAGGA 57.260 39.130 10.60 0.00 42.89 3.36
3555 3775 3.334691 ACGGAACACACATTCGATGAAT 58.665 40.909 0.00 0.00 31.86 2.57
3556 3776 2.734606 GACGGAACACACATTCGATGAA 59.265 45.455 0.00 0.00 0.00 2.57
3557 3777 2.029380 AGACGGAACACACATTCGATGA 60.029 45.455 0.00 0.00 0.00 2.92
3617 3837 8.531982 AGATAACAGCAGAGACAAATACTACAA 58.468 33.333 0.00 0.00 0.00 2.41
3642 3921 9.929180 ATACCTAGTGCACATAACATATAACAG 57.071 33.333 21.04 0.00 0.00 3.16
3643 3922 9.923143 GATACCTAGTGCACATAACATATAACA 57.077 33.333 21.04 0.00 0.00 2.41
3644 3923 9.923143 TGATACCTAGTGCACATAACATATAAC 57.077 33.333 21.04 0.51 0.00 1.89
3648 3927 9.271828 CAAATGATACCTAGTGCACATAACATA 57.728 33.333 21.04 3.89 0.00 2.29
3649 3928 7.255242 GCAAATGATACCTAGTGCACATAACAT 60.255 37.037 21.04 12.30 32.29 2.71
3715 3996 1.132199 CGTTTCCGATCCACGACTCG 61.132 60.000 0.00 0.00 45.77 4.18
3760 4041 2.290960 GGCTTGGTCCTTCAGGTGTTAT 60.291 50.000 0.00 0.00 36.34 1.89
3766 4047 0.178992 TGTTGGCTTGGTCCTTCAGG 60.179 55.000 0.00 0.00 0.00 3.86
3883 4165 6.527023 CAGCAAGATTTGTTCTAATGAGCTTG 59.473 38.462 0.00 0.00 33.05 4.01
3972 4254 5.613329 TGTTGTTCTATCGTGTTAACCCTT 58.387 37.500 2.48 0.00 0.00 3.95
4094 4376 3.457234 CACCACAGAAAAGAAAAAGGGC 58.543 45.455 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.