Multiple sequence alignment - TraesCS6A01G190600

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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 TraesCS6A01G190600 chr6A 100.000 3516 0 0 1 3516 254935294 254938809 0.000000e+00 6493.0
1 TraesCS6A01G190600 chr6A 88.355 541 59 3 232 771 354885632 354885095 0.000000e+00 647.0
2 TraesCS6A01G190600 chr6A 86.975 238 21 3 3 231 354886240 354886004 3.480000e-65 259.0
3 TraesCS6A01G190600 chr6A 100.000 33 0 0 1134 1166 596750198 596750166 1.050000e-05 62.1
4 TraesCS6A01G190600 chr4A 95.442 2962 127 8 1 2958 651216685 651219642 0.000000e+00 4715.0
5 TraesCS6A01G190600 chr4A 88.778 704 69 6 74 771 731521169 731520470 0.000000e+00 854.0
6 TraesCS6A01G190600 chr4B 95.618 1666 72 1 1 1665 344470999 344472664 0.000000e+00 2671.0
7 TraesCS6A01G190600 chr4B 93.506 1001 63 2 111 1110 508212328 508211329 0.000000e+00 1487.0
8 TraesCS6A01G190600 chr4B 92.422 673 30 13 2288 2958 344472663 344473316 0.000000e+00 941.0
9 TraesCS6A01G190600 chr4B 91.250 400 28 4 1452 1850 228742526 228742919 3.990000e-149 538.0
10 TraesCS6A01G190600 chr4B 81.803 610 93 11 2310 2906 228743135 228743739 2.440000e-136 496.0
11 TraesCS6A01G190600 chr4B 94.783 115 6 0 1 115 508267415 508267301 2.790000e-41 180.0
12 TraesCS6A01G190600 chr4B 75.000 260 51 12 2704 2958 389782600 389782850 1.330000e-19 108.0
13 TraesCS6A01G190600 chr5B 86.931 1186 139 13 922 2104 167760644 167759472 0.000000e+00 1317.0
14 TraesCS6A01G190600 chr5B 89.661 619 55 7 2125 2739 496304631 496304018 0.000000e+00 780.0
15 TraesCS6A01G190600 chr5B 89.157 498 48 1 1353 1850 56020232 56020723 1.790000e-172 616.0
16 TraesCS6A01G190600 chr5B 84.000 325 26 11 141 461 167761561 167761259 4.440000e-74 289.0
17 TraesCS6A01G190600 chr5B 80.645 310 23 15 1 289 456978124 456978417 4.600000e-49 206.0
18 TraesCS6A01G190600 chr5B 100.000 37 0 0 1135 1171 558121423 558121387 6.300000e-08 69.4
19 TraesCS6A01G190600 chr3A 87.484 783 79 5 2 771 313183881 313183105 0.000000e+00 885.0
20 TraesCS6A01G190600 chr3A 88.746 702 71 4 74 770 709543242 709542544 0.000000e+00 852.0
21 TraesCS6A01G190600 chr3A 92.487 386 23 1 1452 1837 604999784 604999405 6.640000e-152 547.0
22 TraesCS6A01G190600 chr3A 86.353 447 49 8 2305 2740 523904425 523904870 8.830000e-131 477.0
23 TraesCS6A01G190600 chr3A 91.720 157 9 2 1216 1372 604999937 604999785 7.640000e-52 215.0
24 TraesCS6A01G190600 chr5D 89.331 703 67 4 74 771 30832116 30831417 0.000000e+00 876.0
25 TraesCS6A01G190600 chr5D 91.863 467 27 6 1 461 394746679 394746218 2.960000e-180 641.0
26 TraesCS6A01G190600 chr5D 92.537 402 29 1 2125 2525 559240054 559239653 3.040000e-160 575.0
27 TraesCS6A01G190600 chr5D 88.675 468 49 3 305 771 380294952 380294488 5.090000e-158 568.0
28 TraesCS6A01G190600 chr5D 84.314 561 78 8 2960 3514 217509826 217509270 1.110000e-149 540.0
29 TraesCS6A01G190600 chr5D 92.818 362 22 2 500 857 394746222 394745861 4.020000e-144 521.0
30 TraesCS6A01G190600 chr5D 86.585 246 31 2 2714 2958 393603634 393603390 1.610000e-68 270.0
31 TraesCS6A01G190600 chr5D 82.222 315 17 15 1 289 380840603 380840904 5.870000e-58 235.0
32 TraesCS6A01G190600 chr5D 89.474 114 8 1 136 245 380295063 380294950 1.320000e-29 141.0
33 TraesCS6A01G190600 chr5D 100.000 37 0 0 1135 1171 456342202 456342166 6.300000e-08 69.4
34 TraesCS6A01G190600 chr7A 89.189 703 68 4 74 771 617838699 617838000 0.000000e+00 870.0
35 TraesCS6A01G190600 chr7A 91.729 399 27 1 1452 1850 658724319 658724711 1.840000e-152 549.0
36 TraesCS6A01G190600 chr7A 90.864 405 24 3 1452 1850 728374749 728374352 6.680000e-147 531.0
37 TraesCS6A01G190600 chr7A 90.323 403 26 3 1448 1850 576381986 576381597 1.870000e-142 516.0
38 TraesCS6A01G190600 chr7A 78.136 869 94 49 1039 1848 81632670 81633501 6.870000e-127 464.0
39 TraesCS6A01G190600 chr7A 89.231 260 19 3 1118 1372 658724063 658724318 2.040000e-82 316.0
40 TraesCS6A01G190600 chr4D 89.047 703 69 4 74 771 444095331 444096030 0.000000e+00 865.0
41 TraesCS6A01G190600 chr4D 84.000 475 68 7 2959 3429 199829641 199830111 1.920000e-122 449.0
42 TraesCS6A01G190600 chr4D 91.364 220 17 1 1618 1837 444096254 444096471 2.050000e-77 300.0
43 TraesCS6A01G190600 chr1A 87.535 706 77 6 74 771 26056144 26055442 0.000000e+00 806.0
44 TraesCS6A01G190600 chr6D 91.434 572 41 4 2125 2692 49617992 49618559 0.000000e+00 778.0
45 TraesCS6A01G190600 chr6D 88.413 630 66 7 2116 2740 455720025 455719398 0.000000e+00 752.0
46 TraesCS6A01G190600 chr6D 100.000 33 0 0 1134 1166 451111125 451111093 1.050000e-05 62.1
47 TraesCS6A01G190600 chr2B 91.068 571 45 4 2125 2692 38902610 38902043 0.000000e+00 767.0
48 TraesCS6A01G190600 chr2B 94.783 115 6 0 1 115 253972040 253971926 2.790000e-41 180.0
49 TraesCS6A01G190600 chr7D 90.925 573 45 5 2125 2692 18030500 18031070 0.000000e+00 763.0
50 TraesCS6A01G190600 chr7D 80.231 865 85 50 1039 1848 78190180 78191013 3.940000e-159 571.0
51 TraesCS6A01G190600 chr7D 77.308 260 48 10 2704 2958 635928158 635927905 3.660000e-30 143.0
52 TraesCS6A01G190600 chr6B 88.455 615 63 4 162 771 545357172 545357783 0.000000e+00 736.0
53 TraesCS6A01G190600 chr6B 100.000 33 0 0 1134 1166 685201616 685201584 1.050000e-05 62.1
54 TraesCS6A01G190600 chr3B 86.305 701 65 13 74 769 190848963 190849637 0.000000e+00 734.0
55 TraesCS6A01G190600 chr3B 87.055 618 52 11 2125 2739 557795490 557796082 0.000000e+00 673.0
56 TraesCS6A01G190600 chr3B 83.242 549 84 7 2960 3503 341556124 341556669 6.780000e-137 497.0
57 TraesCS6A01G190600 chr7B 81.991 844 78 38 1039 1848 25587752 25588555 0.000000e+00 649.0
58 TraesCS6A01G190600 chr7B 86.851 289 34 1 2674 2958 25315774 25316062 1.570000e-83 320.0
59 TraesCS6A01G190600 chr7B 79.851 268 41 11 2700 2958 61013284 61013547 2.160000e-42 183.0
60 TraesCS6A01G190600 chr7B 78.070 228 39 10 2704 2927 634825347 634825567 2.200000e-27 134.0
61 TraesCS6A01G190600 chrUn 88.841 466 48 3 307 771 16405332 16404870 1.420000e-158 569.0
62 TraesCS6A01G190600 chrUn 88.841 466 48 3 307 771 203151818 203152280 1.420000e-158 569.0
63 TraesCS6A01G190600 chr1D 86.069 524 67 5 2996 3515 184490296 184489775 3.070000e-155 558.0
64 TraesCS6A01G190600 chr1D 82.938 422 64 6 3008 3423 168393901 168393482 1.190000e-99 374.0
65 TraesCS6A01G190600 chr1B 82.765 557 89 6 2961 3511 253769240 253768685 1.130000e-134 490.0
66 TraesCS6A01G190600 chr1B 78.469 209 36 9 2753 2958 86951729 86951931 1.020000e-25 128.0
67 TraesCS6A01G190600 chr2D 89.863 365 31 1 1290 1654 348066526 348066884 6.870000e-127 464.0
68 TraesCS6A01G190600 chr3D 83.524 437 63 8 2992 3423 583665477 583665909 1.970000e-107 399.0
69 TraesCS6A01G190600 chr3D 83.066 437 64 9 2992 3423 583710993 583711424 4.260000e-104 388.0
70 TraesCS6A01G190600 chr3D 82.273 440 70 7 2992 3427 583763134 583763569 1.190000e-99 374.0
71 TraesCS6A01G190600 chr3D 84.669 287 40 4 2674 2958 168364259 168364543 2.070000e-72 283.0
72 TraesCS6A01G190600 chr5A 100.000 37 0 0 1135 1171 574197825 574197789 6.300000e-08 69.4


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 TraesCS6A01G190600 chr6A 254935294 254938809 3515 False 6493.0 6493 100.0000 1 3516 1 chr6A.!!$F1 3515
1 TraesCS6A01G190600 chr6A 354885095 354886240 1145 True 453.0 647 87.6650 3 771 2 chr6A.!!$R2 768
2 TraesCS6A01G190600 chr4A 651216685 651219642 2957 False 4715.0 4715 95.4420 1 2958 1 chr4A.!!$F1 2957
3 TraesCS6A01G190600 chr4A 731520470 731521169 699 True 854.0 854 88.7780 74 771 1 chr4A.!!$R1 697
4 TraesCS6A01G190600 chr4B 344470999 344473316 2317 False 1806.0 2671 94.0200 1 2958 2 chr4B.!!$F3 2957
5 TraesCS6A01G190600 chr4B 508211329 508212328 999 True 1487.0 1487 93.5060 111 1110 1 chr4B.!!$R1 999
6 TraesCS6A01G190600 chr4B 228742526 228743739 1213 False 517.0 538 86.5265 1452 2906 2 chr4B.!!$F2 1454
7 TraesCS6A01G190600 chr5B 167759472 167761561 2089 True 803.0 1317 85.4655 141 2104 2 chr5B.!!$R3 1963
8 TraesCS6A01G190600 chr5B 496304018 496304631 613 True 780.0 780 89.6610 2125 2739 1 chr5B.!!$R1 614
9 TraesCS6A01G190600 chr3A 313183105 313183881 776 True 885.0 885 87.4840 2 771 1 chr3A.!!$R1 769
10 TraesCS6A01G190600 chr3A 709542544 709543242 698 True 852.0 852 88.7460 74 770 1 chr3A.!!$R2 696
11 TraesCS6A01G190600 chr3A 604999405 604999937 532 True 381.0 547 92.1035 1216 1837 2 chr3A.!!$R3 621
12 TraesCS6A01G190600 chr5D 30831417 30832116 699 True 876.0 876 89.3310 74 771 1 chr5D.!!$R1 697
13 TraesCS6A01G190600 chr5D 394745861 394746679 818 True 581.0 641 92.3405 1 857 2 chr5D.!!$R7 856
14 TraesCS6A01G190600 chr5D 217509270 217509826 556 True 540.0 540 84.3140 2960 3514 1 chr5D.!!$R2 554
15 TraesCS6A01G190600 chr5D 380294488 380295063 575 True 354.5 568 89.0745 136 771 2 chr5D.!!$R6 635
16 TraesCS6A01G190600 chr7A 617838000 617838699 699 True 870.0 870 89.1890 74 771 1 chr7A.!!$R2 697
17 TraesCS6A01G190600 chr7A 81632670 81633501 831 False 464.0 464 78.1360 1039 1848 1 chr7A.!!$F1 809
18 TraesCS6A01G190600 chr7A 658724063 658724711 648 False 432.5 549 90.4800 1118 1850 2 chr7A.!!$F2 732
19 TraesCS6A01G190600 chr4D 444095331 444096471 1140 False 582.5 865 90.2055 74 1837 2 chr4D.!!$F2 1763
20 TraesCS6A01G190600 chr1A 26055442 26056144 702 True 806.0 806 87.5350 74 771 1 chr1A.!!$R1 697
21 TraesCS6A01G190600 chr6D 49617992 49618559 567 False 778.0 778 91.4340 2125 2692 1 chr6D.!!$F1 567
22 TraesCS6A01G190600 chr6D 455719398 455720025 627 True 752.0 752 88.4130 2116 2740 1 chr6D.!!$R2 624
23 TraesCS6A01G190600 chr2B 38902043 38902610 567 True 767.0 767 91.0680 2125 2692 1 chr2B.!!$R1 567
24 TraesCS6A01G190600 chr7D 18030500 18031070 570 False 763.0 763 90.9250 2125 2692 1 chr7D.!!$F1 567
25 TraesCS6A01G190600 chr7D 78190180 78191013 833 False 571.0 571 80.2310 1039 1848 1 chr7D.!!$F2 809
26 TraesCS6A01G190600 chr6B 545357172 545357783 611 False 736.0 736 88.4550 162 771 1 chr6B.!!$F1 609
27 TraesCS6A01G190600 chr3B 190848963 190849637 674 False 734.0 734 86.3050 74 769 1 chr3B.!!$F1 695
28 TraesCS6A01G190600 chr3B 557795490 557796082 592 False 673.0 673 87.0550 2125 2739 1 chr3B.!!$F3 614
29 TraesCS6A01G190600 chr3B 341556124 341556669 545 False 497.0 497 83.2420 2960 3503 1 chr3B.!!$F2 543
30 TraesCS6A01G190600 chr7B 25587752 25588555 803 False 649.0 649 81.9910 1039 1848 1 chr7B.!!$F2 809
31 TraesCS6A01G190600 chr1D 184489775 184490296 521 True 558.0 558 86.0690 2996 3515 1 chr1D.!!$R2 519
32 TraesCS6A01G190600 chr1B 253768685 253769240 555 True 490.0 490 82.7650 2961 3511 1 chr1B.!!$R1 550

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
398 778 2.138656 CTGTCAGCAGCAAGGGCAAC 62.139 60.0 0.0 0.0 44.61 4.17 F
1285 1953 0.178967 TGCTTGCTTGATTGGGGTGA 60.179 50.0 0.0 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 2120 2.170607 AGTCTGTAACCACACAAGCACT 59.829 45.455 0.0 0.0 0.0 4.40 R
3076 3974 1.583054 GGACACGACTGTTCTTTGCT 58.417 50.000 0.0 0.0 0.0 3.91 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
59 60 4.529897 AGTATTCTGAATGATTGCTGGCA 58.470 39.130 13.01 0.00 0.00 4.92
134 143 4.562552 GCATGAGGGAGAGGTTCTTATAGC 60.563 50.000 0.00 0.00 0.00 2.97
168 177 2.238521 GGTCTTGACCTGCATTTTGGA 58.761 47.619 12.20 0.00 0.00 3.53
220 229 5.479716 AATTTTAGGTTATTCTCGGTGCG 57.520 39.130 0.00 0.00 0.00 5.34
398 778 2.138656 CTGTCAGCAGCAAGGGCAAC 62.139 60.000 0.00 0.00 44.61 4.17
413 793 2.925170 AACCTGCCCACGCTCTCT 60.925 61.111 0.00 0.00 35.36 3.10
582 1006 8.096414 CAGTGATGGTTAAGGGAAAAATCATTT 58.904 33.333 0.00 0.00 0.00 2.32
627 1051 5.805994 AGTACTTAGCGTGCATTTTCTACTC 59.194 40.000 0.00 0.00 0.00 2.59
636 1060 6.036083 GCGTGCATTTTCTACTCTGAGATTAA 59.964 38.462 12.44 0.00 0.00 1.40
653 1077 9.317936 CTGAGATTAATTACACAAGCTACATCA 57.682 33.333 0.00 0.00 0.00 3.07
783 1213 8.867112 CAAATAGCTGATTTGCAGTGATTAAT 57.133 30.769 12.57 0.00 45.97 1.40
816 1246 9.367444 CTTCAGAGTTAATTAGTGTTTCGGTAT 57.633 33.333 0.00 0.00 0.00 2.73
892 1543 3.452990 TGGATGGATGCTCGTAGGTTTTA 59.547 43.478 0.00 0.00 0.00 1.52
894 1545 4.879545 GGATGGATGCTCGTAGGTTTTAAA 59.120 41.667 0.00 0.00 0.00 1.52
992 1643 7.790782 TTTCTTCAGCTTTGGGGTATAATTT 57.209 32.000 0.00 0.00 0.00 1.82
1003 1654 7.487822 TTGGGGTATAATTTTTCTGCAATGA 57.512 32.000 0.00 0.00 0.00 2.57
1055 1706 2.428890 CTGGGTTCTACAAGAGCGAGAT 59.571 50.000 0.00 0.00 0.00 2.75
1062 1713 3.077556 AAGAGCGAGATGGGCGGT 61.078 61.111 0.00 0.00 42.69 5.68
1089 1740 3.770040 CCCGAGTCGCATGGGACA 61.770 66.667 35.60 6.38 46.41 4.02
1166 1820 0.389166 GTGCACAACCTCTCCGAGAG 60.389 60.000 17.34 17.34 41.96 3.20
1285 1953 0.178967 TGCTTGCTTGATTGGGGTGA 60.179 50.000 0.00 0.00 0.00 4.02
1305 1973 3.854669 CGGCGGAGGAGCAGGATT 61.855 66.667 0.00 0.00 39.27 3.01
1331 1999 3.884091 GAGAAGATGAAGGCATTGCAGAT 59.116 43.478 11.39 0.00 34.11 2.90
1402 2094 5.738619 ACCACTTTGTTTTTCTTTGTCCT 57.261 34.783 0.00 0.00 0.00 3.85
1417 2109 1.843851 TGTCCTTGAATTCGGGGCTAT 59.156 47.619 18.37 0.00 0.00 2.97
1428 2120 2.189676 TCGGGGCTATTGAGTTTGGTA 58.810 47.619 0.00 0.00 0.00 3.25
1505 2221 2.610433 TGAGTATCTGAAGCAACTGCG 58.390 47.619 0.00 0.00 40.80 5.18
1853 2618 2.441410 TGCAATTCGGCAAATCCACTA 58.559 42.857 0.00 0.00 41.65 2.74
1864 2629 4.941263 GGCAAATCCACTATAACTCACACA 59.059 41.667 0.00 0.00 34.01 3.72
1916 2762 4.629200 GTGGTTTTCACTGCAATTTGTCAA 59.371 37.500 0.00 0.00 42.86 3.18
1922 2768 4.738124 TCACTGCAATTTGTCAACGAAAA 58.262 34.783 0.00 0.00 0.00 2.29
2082 2928 4.628963 TTCCACTAGGTAAAGGGTGTTC 57.371 45.455 0.00 0.00 35.89 3.18
2099 2945 6.438425 AGGGTGTTCTTTATCATGCTTTTCAT 59.562 34.615 0.00 0.00 35.31 2.57
2597 3452 5.186797 AGTGAGAACAGGTAGAATGAGGAAG 59.813 44.000 0.00 0.00 0.00 3.46
2754 3647 3.322828 GCGTGGGGGTATTATAGAAGTGA 59.677 47.826 0.00 0.00 0.00 3.41
2784 3677 2.313317 TCCATTAGTAGTAGCGTGGGG 58.687 52.381 0.00 0.00 0.00 4.96
2801 3694 2.022820 TGGGGGTGGAATACTAGTAGCA 60.023 50.000 8.85 0.00 0.00 3.49
2802 3695 3.248888 GGGGGTGGAATACTAGTAGCAT 58.751 50.000 8.85 0.00 0.00 3.79
2824 3717 0.248949 GGCACTAGCGCTACTGGTAC 60.249 60.000 14.45 5.00 38.17 3.34
2864 3758 2.156917 GGGGTAAAACAAGCGCTACTT 58.843 47.619 12.05 1.11 40.05 2.24
2927 3821 4.499183 CTCCACTACTGCTAGTCCAAAAG 58.501 47.826 0.00 0.00 30.03 2.27
2948 3842 1.732259 CCAACGCTACTGCTAAGGTTG 59.268 52.381 0.00 0.00 36.92 3.77
2958 3852 6.900324 GCTACTGCTAAGGTTGTTCCTAGTAC 60.900 46.154 0.00 0.00 40.04 2.73
2975 3869 8.896722 TCCTAGTACCTTAAGAGAAAACTCAT 57.103 34.615 3.36 0.00 0.00 2.90
2984 3878 8.239998 CCTTAAGAGAAAACTCATGAAATGGAC 58.760 37.037 3.36 0.00 46.73 4.02
3017 3914 4.440839 AAAAATCTCATTCCCTTGCGAC 57.559 40.909 0.00 0.00 0.00 5.19
3037 3934 5.106908 GCGACTAAAGAAGCAAGAACTTCAT 60.107 40.000 7.01 0.00 46.97 2.57
3050 3947 8.587608 AGCAAGAACTTCATATTTCATTCCAAA 58.412 29.630 0.00 0.00 0.00 3.28
3071 3969 4.853924 AAAGTGGCAGATTGGTTACAAG 57.146 40.909 0.00 0.00 40.49 3.16
3075 3973 4.072131 GTGGCAGATTGGTTACAAGAGAA 58.928 43.478 0.00 0.00 40.49 2.87
3076 3974 4.518970 GTGGCAGATTGGTTACAAGAGAAA 59.481 41.667 0.00 0.00 40.49 2.52
3082 3981 6.860023 CAGATTGGTTACAAGAGAAAGCAAAG 59.140 38.462 4.10 0.00 43.76 2.77
3106 4005 1.904865 TCGTGTCCGGCACCTAAGT 60.905 57.895 19.09 0.00 44.97 2.24
3121 4020 4.041198 CACCTAAGTTAGTCTTCCCACCAA 59.959 45.833 9.05 0.00 37.56 3.67
3123 4022 4.041198 CCTAAGTTAGTCTTCCCACCAACA 59.959 45.833 9.05 0.00 37.56 3.33
3126 4025 1.416243 TAGTCTTCCCACCAACACGT 58.584 50.000 0.00 0.00 0.00 4.49
3322 4224 4.379243 CGGCGCACAGGGAGACTT 62.379 66.667 10.83 0.00 0.00 3.01
3391 4293 2.677875 CTTGAAGGGGTGCAGGGC 60.678 66.667 0.00 0.00 0.00 5.19
3392 4294 3.506743 TTGAAGGGGTGCAGGGCA 61.507 61.111 0.00 0.00 35.60 5.36
3409 4311 2.041265 ACTCCCTGCCTTCCGGAT 59.959 61.111 4.15 0.00 0.00 4.18
3506 4410 2.351276 GTGAGAACCCATGGGCGT 59.649 61.111 31.73 19.46 39.32 5.68
3511 4415 2.610859 AACCCATGGGCGTCCTCT 60.611 61.111 31.73 6.30 39.32 3.69
3515 4419 1.457643 CCATGGGCGTCCTCTCCTA 60.458 63.158 7.97 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 5.767665 TCCTACAAACAGTGCACACAATTAT 59.232 36.000 21.04 0.14 0.00 1.28
115 124 4.219919 ACAGCTATAAGAACCTCTCCCTC 58.780 47.826 0.00 0.00 0.00 4.30
168 177 0.856982 TTGGTCCAATTGGTCAGGGT 59.143 50.000 23.76 0.00 36.34 4.34
220 229 6.317391 AGCAACCTGATAGCAAATTCTTCTAC 59.683 38.462 0.00 0.00 0.00 2.59
398 778 4.154347 GGAGAGAGCGTGGGCAGG 62.154 72.222 0.00 0.00 43.41 4.85
413 793 4.934356 AGCAAGATTAAATTCCCAGTGGA 58.066 39.130 11.95 0.00 39.54 4.02
595 1019 3.056393 TGCACGCTAAGTACTTGTGGTAT 60.056 43.478 18.56 0.00 32.56 2.73
627 1051 9.317936 TGATGTAGCTTGTGTAATTAATCTCAG 57.682 33.333 0.00 0.00 0.00 3.35
861 1512 3.504906 CGAGCATCCATCCATAAAAGCAT 59.495 43.478 0.00 0.00 0.00 3.79
892 1543 6.966534 ACATTGACAGAATTTCAGTCCTTT 57.033 33.333 16.48 2.34 32.69 3.11
894 1545 7.770897 GGTATACATTGACAGAATTTCAGTCCT 59.229 37.037 16.48 4.51 32.69 3.85
1003 1654 2.770164 AAGTGCCGTCTAAATCTGCT 57.230 45.000 0.00 0.00 0.00 4.24
1062 1713 3.437795 GACTCGGGCTCGGACGAA 61.438 66.667 5.94 0.00 38.79 3.85
1305 1973 3.623060 GCAATGCCTTCATCTTCTCGTTA 59.377 43.478 0.00 0.00 31.27 3.18
1331 1999 4.569653 CCTTGTTGGAATTGGGTATCAGGA 60.570 45.833 0.00 0.00 38.35 3.86
1402 2094 3.644966 ACTCAATAGCCCCGAATTCAA 57.355 42.857 6.22 0.00 0.00 2.69
1417 2109 3.376859 CACACAAGCACTACCAAACTCAA 59.623 43.478 0.00 0.00 0.00 3.02
1428 2120 2.170607 AGTCTGTAACCACACAAGCACT 59.829 45.455 0.00 0.00 0.00 4.40
1505 2221 2.770164 ACTGACATGTACTTGGAGCC 57.230 50.000 12.86 1.11 0.00 4.70
1853 2618 7.480760 AAATAGGGCAATTTGTGTGAGTTAT 57.519 32.000 0.00 0.00 0.00 1.89
1864 2629 8.866093 ACAGTTACACTTAAAATAGGGCAATTT 58.134 29.630 0.00 0.00 0.00 1.82
1965 2811 9.944376 AGAAGCAGATTCACAGTAAATTAGTAA 57.056 29.630 0.31 0.00 40.67 2.24
1980 2826 8.097078 AGATACATTGCATTAGAAGCAGATTC 57.903 34.615 0.00 0.00 43.75 2.52
2069 2915 5.652452 AGCATGATAAAGAACACCCTTTACC 59.348 40.000 0.00 0.00 40.26 2.85
2099 2945 4.202514 TGGGTTGTTGGATGAACATAGACA 60.203 41.667 0.00 0.00 44.23 3.41
2299 3149 6.519679 TGAGAATATGCACTGAAATTTGCT 57.480 33.333 0.00 0.00 39.62 3.91
2597 3452 6.376978 AGTTGTCGTGTCTACTATTACACAC 58.623 40.000 6.43 0.00 44.98 3.82
2728 3614 3.434309 TCTATAATACCCCCACGCTACC 58.566 50.000 0.00 0.00 0.00 3.18
2784 3677 3.008049 CCCCATGCTACTAGTATTCCACC 59.992 52.174 2.33 0.00 0.00 4.61
2801 3694 1.762460 AGTAGCGCTAGTGCCCCAT 60.762 57.895 23.70 8.78 35.36 4.00
2802 3695 2.363795 AGTAGCGCTAGTGCCCCA 60.364 61.111 23.70 7.66 35.36 4.96
2824 3717 3.795101 CCCACGTTACTGCTAAATAGACG 59.205 47.826 0.00 0.00 35.39 4.18
2840 3733 1.788067 GCGCTTGTTTTACCCCACGT 61.788 55.000 0.00 0.00 0.00 4.49
2864 3758 3.554324 CGGCGCTACAGCTAATTTTTAGA 59.446 43.478 7.64 0.00 39.32 2.10
2907 3801 3.003480 GCTTTTGGACTAGCAGTAGTGG 58.997 50.000 0.00 0.00 39.78 4.00
2909 3803 2.637872 TGGCTTTTGGACTAGCAGTAGT 59.362 45.455 0.00 0.00 42.59 2.73
2948 3842 8.583296 TGAGTTTTCTCTTAAGGTACTAGGAAC 58.417 37.037 1.85 0.00 46.30 3.62
2958 3852 8.239998 GTCCATTTCATGAGTTTTCTCTTAAGG 58.760 37.037 1.85 0.00 46.30 2.69
2975 3869 2.516906 TCTGCAGCATTGTCCATTTCA 58.483 42.857 9.47 0.00 0.00 2.69
3003 3897 3.973206 TCTTTAGTCGCAAGGGAATGA 57.027 42.857 0.00 0.00 38.47 2.57
3050 3947 4.469657 TCTTGTAACCAATCTGCCACTTT 58.530 39.130 0.00 0.00 0.00 2.66
3059 3956 6.970484 TCTTTGCTTTCTCTTGTAACCAATC 58.030 36.000 0.00 0.00 0.00 2.67
3065 3963 6.238103 CGACTGTTCTTTGCTTTCTCTTGTAA 60.238 38.462 0.00 0.00 0.00 2.41
3071 3969 3.309954 ACACGACTGTTCTTTGCTTTCTC 59.690 43.478 0.00 0.00 0.00 2.87
3075 3973 1.940613 GGACACGACTGTTCTTTGCTT 59.059 47.619 0.00 0.00 0.00 3.91
3076 3974 1.583054 GGACACGACTGTTCTTTGCT 58.417 50.000 0.00 0.00 0.00 3.91
3082 3981 2.028484 TGCCGGACACGACTGTTC 59.972 61.111 5.05 0.00 44.60 3.18
3106 4005 1.764134 ACGTGTTGGTGGGAAGACTAA 59.236 47.619 0.00 0.00 0.00 2.24
3121 4020 3.009115 AGGCCCCATGCTACGTGT 61.009 61.111 0.00 0.00 40.92 4.49
3123 4022 3.480133 GGAGGCCCCATGCTACGT 61.480 66.667 0.00 0.00 40.92 3.57
3143 4042 2.513897 GACTATGCCCACGCCCAC 60.514 66.667 0.00 0.00 0.00 4.61
3263 4164 1.978617 CACCCATGCCCAAGTGGAC 60.979 63.158 0.00 0.00 37.72 4.02
3290 4191 3.083997 CCGCCCCTTAGCCTCACT 61.084 66.667 0.00 0.00 0.00 3.41
3322 4224 4.006357 GGGTTGTACACGCCCCGA 62.006 66.667 19.28 0.00 36.46 5.14
3368 4270 2.238521 CTGCACCCCTTCAAGCTTTAA 58.761 47.619 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.