Multiple sequence alignment - TraesCS2D01G395900

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 TraesCS2D01G395900 chr2D 100.000 2891 0 0 1 2891 506943479 506940589 0.000000e+00 5339
1 TraesCS2D01G395900 chr2D 91.743 436 26 7 2464 2891 612936814 612937247 5.330000e-167 597
2 TraesCS2D01G395900 chr2D 86.667 120 16 0 3 122 602809007 602808888 1.810000e-27 134
3 TraesCS2D01G395900 chr2B 90.925 2226 83 40 121 2298 594984404 594982250 0.000000e+00 2881
4 TraesCS2D01G395900 chr2B 83.993 556 57 16 2347 2873 609150968 609151520 3.320000e-139 505
5 TraesCS2D01G395900 chr2A 91.636 1614 42 39 736 2298 651753757 651752186 0.000000e+00 2146
6 TraesCS2D01G395900 chr2A 93.312 613 16 3 130 726 651754672 651754069 0.000000e+00 881
7 TraesCS2D01G395900 chr4D 89.161 572 35 14 2347 2891 54128925 54129496 0.000000e+00 688
8 TraesCS2D01G395900 chr4D 88.596 570 33 12 2347 2891 132295112 132294550 0.000000e+00 664
9 TraesCS2D01G395900 chr4D 87.895 570 43 8 2347 2891 461277661 461278229 0.000000e+00 647
10 TraesCS2D01G395900 chr6A 89.720 535 48 6 2347 2876 126537052 126536520 0.000000e+00 676
11 TraesCS2D01G395900 chr6A 90.751 173 15 1 1567 1739 479834237 479834408 2.240000e-56 230
12 TraesCS2D01G395900 chr6A 90.683 161 15 0 1297 1457 479833997 479834157 6.270000e-52 215
13 TraesCS2D01G395900 chr6A 84.672 137 15 5 1605 1738 496016063 496015930 6.500000e-27 132
14 TraesCS2D01G395900 chr7D 88.462 572 35 16 2346 2891 572594978 572595544 0.000000e+00 662
15 TraesCS2D01G395900 chr7D 88.246 570 41 8 2347 2891 35188333 35188901 0.000000e+00 658
16 TraesCS2D01G395900 chr7D 87.324 568 40 12 2349 2891 147809531 147810091 3.160000e-174 621
17 TraesCS2D01G395900 chr7D 87.603 121 15 0 3 123 437411062 437411182 1.080000e-29 141
18 TraesCS2D01G395900 chr5A 87.500 576 38 7 2347 2891 644011682 644012254 4.060000e-178 634
19 TraesCS2D01G395900 chr5B 83.688 564 61 15 2341 2876 448445120 448445680 1.200000e-138 503
20 TraesCS2D01G395900 chr5B 82.874 508 63 13 2347 2834 446886308 446886811 4.420000e-118 435
21 TraesCS2D01G395900 chr5B 79.329 566 73 31 2347 2876 693157093 693157650 9.850000e-95 357
22 TraesCS2D01G395900 chr4B 81.786 571 61 23 2344 2878 524703177 524703740 3.420000e-119 438
23 TraesCS2D01G395900 chr4B 77.262 431 53 18 2344 2743 493048386 493048802 8.120000e-51 211
24 TraesCS2D01G395900 chr6B 78.995 557 78 26 2347 2876 490644366 490643822 7.670000e-91 344
25 TraesCS2D01G395900 chr6B 90.751 173 15 1 1567 1739 481089556 481089385 2.240000e-56 230
26 TraesCS2D01G395900 chr6B 81.338 284 44 7 1180 1457 481089915 481089635 3.750000e-54 222
27 TraesCS2D01G395900 chr6B 86.777 121 16 0 3 123 578296681 578296801 5.020000e-28 135
28 TraesCS2D01G395900 chr6B 86.777 121 16 0 3 123 626049206 626049326 5.020000e-28 135
29 TraesCS2D01G395900 chr6B 83.212 137 17 5 1605 1738 532902597 532902464 1.410000e-23 121
30 TraesCS2D01G395900 chr6D 78.053 565 100 18 1185 1739 339389596 339390146 4.620000e-88 335
31 TraesCS2D01G395900 chr6D 83.824 136 18 4 1605 1738 347434348 347434481 3.020000e-25 126
32 TraesCS2D01G395900 chr7A 87.603 121 15 0 3 123 326028366 326028246 1.080000e-29 141
33 TraesCS2D01G395900 chr5D 87.603 121 15 0 3 123 494788876 494788996 1.080000e-29 141
34 TraesCS2D01G395900 chr1D 86.777 121 16 0 3 123 205118608 205118728 5.020000e-28 135
35 TraesCS2D01G395900 chr1D 85.950 121 17 0 3 123 493219090 493218970 2.340000e-26 130
36 TraesCS2D01G395900 chr3B 85.950 121 17 0 3 123 305218517 305218637 2.340000e-26 130


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 TraesCS2D01G395900 chr2D 506940589 506943479 2890 True 5339.0 5339 100.0000 1 2891 1 chr2D.!!$R1 2890
1 TraesCS2D01G395900 chr2B 594982250 594984404 2154 True 2881.0 2881 90.9250 121 2298 1 chr2B.!!$R1 2177
2 TraesCS2D01G395900 chr2B 609150968 609151520 552 False 505.0 505 83.9930 2347 2873 1 chr2B.!!$F1 526
3 TraesCS2D01G395900 chr2A 651752186 651754672 2486 True 1513.5 2146 92.4740 130 2298 2 chr2A.!!$R1 2168
4 TraesCS2D01G395900 chr4D 54128925 54129496 571 False 688.0 688 89.1610 2347 2891 1 chr4D.!!$F1 544
5 TraesCS2D01G395900 chr4D 132294550 132295112 562 True 664.0 664 88.5960 2347 2891 1 chr4D.!!$R1 544
6 TraesCS2D01G395900 chr4D 461277661 461278229 568 False 647.0 647 87.8950 2347 2891 1 chr4D.!!$F2 544
7 TraesCS2D01G395900 chr6A 126536520 126537052 532 True 676.0 676 89.7200 2347 2876 1 chr6A.!!$R1 529
8 TraesCS2D01G395900 chr7D 572594978 572595544 566 False 662.0 662 88.4620 2346 2891 1 chr7D.!!$F4 545
9 TraesCS2D01G395900 chr7D 35188333 35188901 568 False 658.0 658 88.2460 2347 2891 1 chr7D.!!$F1 544
10 TraesCS2D01G395900 chr7D 147809531 147810091 560 False 621.0 621 87.3240 2349 2891 1 chr7D.!!$F2 542
11 TraesCS2D01G395900 chr5A 644011682 644012254 572 False 634.0 634 87.5000 2347 2891 1 chr5A.!!$F1 544
12 TraesCS2D01G395900 chr5B 448445120 448445680 560 False 503.0 503 83.6880 2341 2876 1 chr5B.!!$F2 535
13 TraesCS2D01G395900 chr5B 446886308 446886811 503 False 435.0 435 82.8740 2347 2834 1 chr5B.!!$F1 487
14 TraesCS2D01G395900 chr5B 693157093 693157650 557 False 357.0 357 79.3290 2347 2876 1 chr5B.!!$F3 529
15 TraesCS2D01G395900 chr4B 524703177 524703740 563 False 438.0 438 81.7860 2344 2878 1 chr4B.!!$F2 534
16 TraesCS2D01G395900 chr6B 490643822 490644366 544 True 344.0 344 78.9950 2347 2876 1 chr6B.!!$R1 529
17 TraesCS2D01G395900 chr6B 481089385 481089915 530 True 226.0 230 86.0445 1180 1739 2 chr6B.!!$R3 559
18 TraesCS2D01G395900 chr6D 339389596 339390146 550 False 335.0 335 78.0530 1185 1739 1 chr6D.!!$F1 554

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
899 1260 0.030369 CGAGCTCCATACGTACCACC 59.97 60.0 8.47 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2310 2753 1.035923 CGAAGGCTGAGGATGCTCTA 58.964 55.0 15.82 1.28 0.0 2.43 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
18 19 3.389741 CGCCATTGAACAGCTTGTC 57.610 52.632 0.00 0.00 0.00 3.18
19 20 0.453282 CGCCATTGAACAGCTTGTCG 60.453 55.000 0.00 0.00 0.00 4.35
20 21 0.874390 GCCATTGAACAGCTTGTCGA 59.126 50.000 0.00 0.00 0.00 4.20
21 22 1.266718 GCCATTGAACAGCTTGTCGAA 59.733 47.619 0.00 0.00 0.00 3.71
22 23 2.666619 GCCATTGAACAGCTTGTCGAAG 60.667 50.000 0.00 0.00 0.00 3.79
23 24 2.549754 CCATTGAACAGCTTGTCGAAGT 59.450 45.455 0.00 0.00 0.00 3.01
24 25 3.745975 CCATTGAACAGCTTGTCGAAGTA 59.254 43.478 0.00 0.00 0.00 2.24
25 26 4.377431 CCATTGAACAGCTTGTCGAAGTAC 60.377 45.833 0.00 0.00 0.00 2.73
26 27 3.728076 TGAACAGCTTGTCGAAGTACT 57.272 42.857 0.00 0.00 0.00 2.73
27 28 3.639538 TGAACAGCTTGTCGAAGTACTC 58.360 45.455 0.00 0.00 0.00 2.59
28 29 2.726832 ACAGCTTGTCGAAGTACTCC 57.273 50.000 0.00 0.00 0.00 3.85
29 30 2.240279 ACAGCTTGTCGAAGTACTCCT 58.760 47.619 0.00 0.00 0.00 3.69
30 31 2.029828 ACAGCTTGTCGAAGTACTCCTG 60.030 50.000 0.00 0.00 0.00 3.86
31 32 2.029828 CAGCTTGTCGAAGTACTCCTGT 60.030 50.000 0.00 0.00 0.00 4.00
32 33 2.229302 AGCTTGTCGAAGTACTCCTGTC 59.771 50.000 0.00 0.00 0.00 3.51
33 34 2.030185 GCTTGTCGAAGTACTCCTGTCA 60.030 50.000 0.00 0.00 0.00 3.58
34 35 3.367498 GCTTGTCGAAGTACTCCTGTCAT 60.367 47.826 0.00 0.00 0.00 3.06
35 36 4.416620 CTTGTCGAAGTACTCCTGTCATC 58.583 47.826 0.00 0.00 0.00 2.92
36 37 3.687125 TGTCGAAGTACTCCTGTCATCT 58.313 45.455 0.00 0.00 0.00 2.90
37 38 4.840271 TGTCGAAGTACTCCTGTCATCTA 58.160 43.478 0.00 0.00 0.00 1.98
38 39 5.437946 TGTCGAAGTACTCCTGTCATCTAT 58.562 41.667 0.00 0.00 0.00 1.98
39 40 6.589135 TGTCGAAGTACTCCTGTCATCTATA 58.411 40.000 0.00 0.00 0.00 1.31
40 41 6.482641 TGTCGAAGTACTCCTGTCATCTATAC 59.517 42.308 0.00 0.00 0.00 1.47
41 42 6.707161 GTCGAAGTACTCCTGTCATCTATACT 59.293 42.308 0.00 0.00 0.00 2.12
42 43 7.227116 GTCGAAGTACTCCTGTCATCTATACTT 59.773 40.741 0.00 0.00 34.85 2.24
43 44 8.427276 TCGAAGTACTCCTGTCATCTATACTTA 58.573 37.037 0.00 0.00 32.89 2.24
44 45 9.053840 CGAAGTACTCCTGTCATCTATACTTAA 57.946 37.037 0.00 0.00 32.89 1.85
50 51 9.875708 ACTCCTGTCATCTATACTTAATCTTCT 57.124 33.333 0.00 0.00 0.00 2.85
52 53 9.004717 TCCTGTCATCTATACTTAATCTTCTCG 57.995 37.037 0.00 0.00 0.00 4.04
53 54 8.788806 CCTGTCATCTATACTTAATCTTCTCGT 58.211 37.037 0.00 0.00 0.00 4.18
54 55 9.820229 CTGTCATCTATACTTAATCTTCTCGTC 57.180 37.037 0.00 0.00 0.00 4.20
55 56 8.496751 TGTCATCTATACTTAATCTTCTCGTCG 58.503 37.037 0.00 0.00 0.00 5.12
56 57 8.497554 GTCATCTATACTTAATCTTCTCGTCGT 58.502 37.037 0.00 0.00 0.00 4.34
57 58 9.053840 TCATCTATACTTAATCTTCTCGTCGTT 57.946 33.333 0.00 0.00 0.00 3.85
58 59 9.320406 CATCTATACTTAATCTTCTCGTCGTTC 57.680 37.037 0.00 0.00 0.00 3.95
59 60 8.659925 TCTATACTTAATCTTCTCGTCGTTCT 57.340 34.615 0.00 0.00 0.00 3.01
60 61 8.763356 TCTATACTTAATCTTCTCGTCGTTCTC 58.237 37.037 0.00 0.00 0.00 2.87
61 62 4.984205 ACTTAATCTTCTCGTCGTTCTCC 58.016 43.478 0.00 0.00 0.00 3.71
62 63 4.458295 ACTTAATCTTCTCGTCGTTCTCCA 59.542 41.667 0.00 0.00 0.00 3.86
63 64 3.495670 AATCTTCTCGTCGTTCTCCAG 57.504 47.619 0.00 0.00 0.00 3.86
64 65 2.180432 TCTTCTCGTCGTTCTCCAGA 57.820 50.000 0.00 0.00 0.00 3.86
65 66 2.501261 TCTTCTCGTCGTTCTCCAGAA 58.499 47.619 0.00 0.00 0.00 3.02
66 67 2.484651 TCTTCTCGTCGTTCTCCAGAAG 59.515 50.000 11.09 11.09 40.95 2.85
67 68 1.893544 TCTCGTCGTTCTCCAGAAGT 58.106 50.000 0.00 0.00 34.27 3.01
68 69 2.228059 TCTCGTCGTTCTCCAGAAGTT 58.772 47.619 0.00 0.00 34.27 2.66
69 70 2.031069 TCTCGTCGTTCTCCAGAAGTTG 60.031 50.000 0.00 0.00 34.27 3.16
79 80 1.151668 CCAGAAGTTGGTCTGCTTCG 58.848 55.000 0.00 0.00 43.18 3.79
80 81 1.541233 CCAGAAGTTGGTCTGCTTCGT 60.541 52.381 0.00 0.00 43.18 3.85
81 82 1.528586 CAGAAGTTGGTCTGCTTCGTG 59.471 52.381 0.00 0.00 44.07 4.35
82 83 0.235926 GAAGTTGGTCTGCTTCGTGC 59.764 55.000 0.00 0.00 43.25 5.34
83 84 0.179045 AAGTTGGTCTGCTTCGTGCT 60.179 50.000 5.00 0.00 43.37 4.40
84 85 0.179045 AGTTGGTCTGCTTCGTGCTT 60.179 50.000 5.00 0.00 43.37 3.91
85 86 1.070134 AGTTGGTCTGCTTCGTGCTTA 59.930 47.619 5.00 0.00 43.37 3.09
86 87 1.871039 GTTGGTCTGCTTCGTGCTTAA 59.129 47.619 5.00 0.00 43.37 1.85
87 88 2.472695 TGGTCTGCTTCGTGCTTAAT 57.527 45.000 5.00 0.00 43.37 1.40
88 89 2.076100 TGGTCTGCTTCGTGCTTAATG 58.924 47.619 5.00 0.00 43.37 1.90
89 90 1.202076 GGTCTGCTTCGTGCTTAATGC 60.202 52.381 5.00 0.00 43.37 3.56
103 104 4.808558 GCTTAATGCATTTGACTTGGTCA 58.191 39.130 18.75 0.00 40.22 4.02
104 105 5.229423 GCTTAATGCATTTGACTTGGTCAA 58.771 37.500 18.75 8.75 44.64 3.18
105 106 5.119125 GCTTAATGCATTTGACTTGGTCAAC 59.881 40.000 18.75 3.34 45.28 3.18
106 107 7.229673 GCTTAATGCATTTGACTTGGTCAACA 61.230 38.462 18.75 8.19 45.28 3.33
107 108 8.478844 GCTTAATGCATTTGACTTGGTCAACAT 61.479 37.037 18.75 9.82 45.28 2.71
117 118 8.463930 TTGACTTGGTCAACATCTCTAATTTT 57.536 30.769 8.75 0.00 45.88 1.82
118 119 8.099364 TGACTTGGTCAACATCTCTAATTTTC 57.901 34.615 0.00 0.00 39.78 2.29
119 120 7.174946 TGACTTGGTCAACATCTCTAATTTTCC 59.825 37.037 0.00 0.00 39.78 3.13
124 125 7.106239 GGTCAACATCTCTAATTTTCCTCTGA 58.894 38.462 0.00 0.00 0.00 3.27
731 1065 0.318445 CTTGCCAGCAGTTTGACAGC 60.318 55.000 0.00 0.00 0.00 4.40
895 1256 4.207203 CGCGAGCTCCATACGTAC 57.793 61.111 8.47 0.00 0.00 3.67
897 1258 1.731700 GCGAGCTCCATACGTACCA 59.268 57.895 8.47 0.00 0.00 3.25
898 1259 0.594284 GCGAGCTCCATACGTACCAC 60.594 60.000 8.47 0.00 0.00 4.16
899 1260 0.030369 CGAGCTCCATACGTACCACC 59.970 60.000 8.47 0.00 0.00 4.61
901 1262 0.032416 AGCTCCATACGTACCACCCT 60.032 55.000 0.00 0.00 0.00 4.34
902 1263 0.828677 GCTCCATACGTACCACCCTT 59.171 55.000 0.00 0.00 0.00 3.95
903 1264 1.472728 GCTCCATACGTACCACCCTTG 60.473 57.143 0.00 0.00 0.00 3.61
904 1265 0.538118 TCCATACGTACCACCCTTGC 59.462 55.000 0.00 0.00 0.00 4.01
905 1266 0.463116 CCATACGTACCACCCTTGCC 60.463 60.000 0.00 0.00 0.00 4.52
906 1267 0.539986 CATACGTACCACCCTTGCCT 59.460 55.000 0.00 0.00 0.00 4.75
995 1358 1.355066 GAGGAAGAAAGGCGCACTCG 61.355 60.000 10.83 0.00 39.07 4.18
1083 1446 1.872234 CGACGCCGACGACAATGAT 60.872 57.895 2.16 0.00 43.93 2.45
1100 1463 0.107165 GATGGTAGGGAAGGGTGTGC 60.107 60.000 0.00 0.00 0.00 4.57
1102 1465 2.267961 GTAGGGAAGGGTGTGCCG 59.732 66.667 0.00 0.00 33.40 5.69
1479 1869 0.027848 GCGCACTCTCCTCGTACTAC 59.972 60.000 0.30 0.00 0.00 2.73
1488 1888 3.931468 TCTCCTCGTACTACTTTCTCACG 59.069 47.826 0.00 0.00 0.00 4.35
1522 1939 4.213906 CCTGTTTGTTTTGGATTGATTGGC 59.786 41.667 0.00 0.00 0.00 4.52
1984 2402 5.398603 AATCTCCGAGGATTATGCTGTAG 57.601 43.478 0.00 0.00 34.59 2.74
1986 2404 4.981812 TCTCCGAGGATTATGCTGTAGTA 58.018 43.478 0.00 0.00 0.00 1.82
2275 2718 2.842462 TCCGTGGTGCAGACTGGT 60.842 61.111 4.26 0.00 0.00 4.00
2298 2741 4.116328 CGAAGACCAGCTCGCCGA 62.116 66.667 0.00 0.00 0.00 5.54
2299 2742 2.202676 GAAGACCAGCTCGCCGAG 60.203 66.667 10.36 10.36 0.00 4.63
2300 2743 2.676822 AAGACCAGCTCGCCGAGA 60.677 61.111 20.05 0.00 0.00 4.04
2301 2744 2.875684 GAAGACCAGCTCGCCGAGAC 62.876 65.000 20.05 9.37 0.00 3.36
2302 2745 4.500116 GACCAGCTCGCCGAGACC 62.500 72.222 20.05 0.19 0.00 3.85
2304 2747 3.842923 CCAGCTCGCCGAGACCAT 61.843 66.667 20.05 0.00 0.00 3.55
2305 2748 2.279120 CAGCTCGCCGAGACCATC 60.279 66.667 20.05 0.00 0.00 3.51
2306 2749 2.441164 AGCTCGCCGAGACCATCT 60.441 61.111 20.05 1.33 0.00 2.90
2307 2750 2.055042 AGCTCGCCGAGACCATCTT 61.055 57.895 20.05 0.00 0.00 2.40
2308 2751 1.590259 GCTCGCCGAGACCATCTTC 60.590 63.158 20.05 0.00 0.00 2.87
2309 2752 2.010582 GCTCGCCGAGACCATCTTCT 62.011 60.000 20.05 0.00 0.00 2.85
2310 2753 0.457851 CTCGCCGAGACCATCTTCTT 59.542 55.000 8.82 0.00 0.00 2.52
2311 2754 1.676529 CTCGCCGAGACCATCTTCTTA 59.323 52.381 8.82 0.00 0.00 2.10
2312 2755 1.676529 TCGCCGAGACCATCTTCTTAG 59.323 52.381 0.00 0.00 0.00 2.18
2313 2756 1.676529 CGCCGAGACCATCTTCTTAGA 59.323 52.381 0.00 0.00 34.21 2.10
2314 2757 2.287308 CGCCGAGACCATCTTCTTAGAG 60.287 54.545 0.00 0.00 32.92 2.43
2315 2758 2.544903 GCCGAGACCATCTTCTTAGAGC 60.545 54.545 0.00 0.00 32.92 4.09
2316 2759 2.690497 CCGAGACCATCTTCTTAGAGCA 59.310 50.000 0.00 0.00 32.92 4.26
2317 2760 3.320541 CCGAGACCATCTTCTTAGAGCAT 59.679 47.826 0.00 0.00 32.92 3.79
2318 2761 4.545610 CGAGACCATCTTCTTAGAGCATC 58.454 47.826 0.00 0.00 32.92 3.91
2319 2762 4.558496 CGAGACCATCTTCTTAGAGCATCC 60.558 50.000 0.00 0.00 33.66 3.51
2320 2763 4.555689 AGACCATCTTCTTAGAGCATCCT 58.444 43.478 0.00 0.00 33.66 3.24
2321 2764 4.588528 AGACCATCTTCTTAGAGCATCCTC 59.411 45.833 0.00 0.00 38.42 3.71
2322 2765 4.293494 ACCATCTTCTTAGAGCATCCTCA 58.707 43.478 0.00 0.00 40.68 3.86
2323 2766 4.344679 ACCATCTTCTTAGAGCATCCTCAG 59.655 45.833 0.00 0.00 40.68 3.35
2324 2767 4.309099 CATCTTCTTAGAGCATCCTCAGC 58.691 47.826 0.00 0.00 40.68 4.26
2325 2768 2.697751 TCTTCTTAGAGCATCCTCAGCC 59.302 50.000 0.00 0.00 40.68 4.85
2326 2769 2.468301 TCTTAGAGCATCCTCAGCCT 57.532 50.000 0.00 0.00 40.68 4.58
2327 2770 2.756907 TCTTAGAGCATCCTCAGCCTT 58.243 47.619 0.00 0.00 40.68 4.35
2328 2771 2.697751 TCTTAGAGCATCCTCAGCCTTC 59.302 50.000 0.00 0.00 40.68 3.46
2329 2772 1.035923 TAGAGCATCCTCAGCCTTCG 58.964 55.000 0.00 0.00 40.68 3.79
2330 2773 1.886777 GAGCATCCTCAGCCTTCGC 60.887 63.158 0.00 0.00 38.03 4.70
2331 2774 2.899339 GCATCCTCAGCCTTCGCC 60.899 66.667 0.00 0.00 34.57 5.54
2332 2775 2.203126 CATCCTCAGCCTTCGCCC 60.203 66.667 0.00 0.00 34.57 6.13
2333 2776 2.688666 ATCCTCAGCCTTCGCCCA 60.689 61.111 0.00 0.00 34.57 5.36
2334 2777 2.300967 ATCCTCAGCCTTCGCCCAA 61.301 57.895 0.00 0.00 34.57 4.12
2335 2778 2.262774 ATCCTCAGCCTTCGCCCAAG 62.263 60.000 0.00 0.00 34.57 3.61
2379 2822 1.357334 CCACCCCAAACAAACGTCG 59.643 57.895 0.00 0.00 0.00 5.12
2675 3188 3.630148 CATGCCCGTCGATGTCGC 61.630 66.667 3.52 5.49 39.60 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.453282 CGACAAGCTGTTCAATGGCG 60.453 55.000 0.00 0.00 38.04 5.69
1 2 0.874390 TCGACAAGCTGTTCAATGGC 59.126 50.000 0.00 0.00 0.00 4.40
2 3 2.549754 ACTTCGACAAGCTGTTCAATGG 59.450 45.455 0.00 0.00 32.09 3.16
3 4 3.885484 ACTTCGACAAGCTGTTCAATG 57.115 42.857 0.00 0.00 32.09 2.82
5 6 4.049186 GAGTACTTCGACAAGCTGTTCAA 58.951 43.478 0.00 0.00 32.09 2.69
6 7 3.552273 GGAGTACTTCGACAAGCTGTTCA 60.552 47.826 0.00 0.00 32.09 3.18
7 8 2.987821 GGAGTACTTCGACAAGCTGTTC 59.012 50.000 0.00 0.00 32.09 3.18
8 9 2.628657 AGGAGTACTTCGACAAGCTGTT 59.371 45.455 0.00 0.00 32.09 3.16
9 10 2.029828 CAGGAGTACTTCGACAAGCTGT 60.030 50.000 0.00 0.00 32.09 4.40
10 11 2.029828 ACAGGAGTACTTCGACAAGCTG 60.030 50.000 0.00 0.00 32.09 4.24
11 12 2.229302 GACAGGAGTACTTCGACAAGCT 59.771 50.000 0.00 0.00 32.09 3.74
12 13 2.030185 TGACAGGAGTACTTCGACAAGC 60.030 50.000 0.00 0.00 32.09 4.01
13 14 3.917329 TGACAGGAGTACTTCGACAAG 57.083 47.619 0.00 0.00 35.50 3.16
14 15 4.079970 AGATGACAGGAGTACTTCGACAA 58.920 43.478 0.00 0.00 0.00 3.18
15 16 3.687125 AGATGACAGGAGTACTTCGACA 58.313 45.455 0.00 0.00 0.00 4.35
16 17 6.707161 AGTATAGATGACAGGAGTACTTCGAC 59.293 42.308 0.00 0.00 0.00 4.20
17 18 6.828788 AGTATAGATGACAGGAGTACTTCGA 58.171 40.000 0.00 0.00 0.00 3.71
18 19 7.499321 AAGTATAGATGACAGGAGTACTTCG 57.501 40.000 0.00 0.00 0.00 3.79
24 25 9.875708 AGAAGATTAAGTATAGATGACAGGAGT 57.124 33.333 0.00 0.00 0.00 3.85
26 27 9.004717 CGAGAAGATTAAGTATAGATGACAGGA 57.995 37.037 0.00 0.00 0.00 3.86
27 28 8.788806 ACGAGAAGATTAAGTATAGATGACAGG 58.211 37.037 0.00 0.00 0.00 4.00
28 29 9.820229 GACGAGAAGATTAAGTATAGATGACAG 57.180 37.037 0.00 0.00 0.00 3.51
29 30 8.496751 CGACGAGAAGATTAAGTATAGATGACA 58.503 37.037 0.00 0.00 0.00 3.58
30 31 8.497554 ACGACGAGAAGATTAAGTATAGATGAC 58.502 37.037 0.00 0.00 0.00 3.06
31 32 8.604640 ACGACGAGAAGATTAAGTATAGATGA 57.395 34.615 0.00 0.00 0.00 2.92
32 33 9.320406 GAACGACGAGAAGATTAAGTATAGATG 57.680 37.037 0.00 0.00 0.00 2.90
33 34 9.275398 AGAACGACGAGAAGATTAAGTATAGAT 57.725 33.333 0.00 0.00 0.00 1.98
34 35 8.659925 AGAACGACGAGAAGATTAAGTATAGA 57.340 34.615 0.00 0.00 0.00 1.98
35 36 8.011106 GGAGAACGACGAGAAGATTAAGTATAG 58.989 40.741 0.00 0.00 0.00 1.31
36 37 7.496920 TGGAGAACGACGAGAAGATTAAGTATA 59.503 37.037 0.00 0.00 0.00 1.47
37 38 6.318144 TGGAGAACGACGAGAAGATTAAGTAT 59.682 38.462 0.00 0.00 0.00 2.12
38 39 5.645067 TGGAGAACGACGAGAAGATTAAGTA 59.355 40.000 0.00 0.00 0.00 2.24
39 40 4.458295 TGGAGAACGACGAGAAGATTAAGT 59.542 41.667 0.00 0.00 0.00 2.24
40 41 4.982999 TGGAGAACGACGAGAAGATTAAG 58.017 43.478 0.00 0.00 0.00 1.85
41 42 4.698780 TCTGGAGAACGACGAGAAGATTAA 59.301 41.667 0.00 0.00 0.00 1.40
42 43 4.259356 TCTGGAGAACGACGAGAAGATTA 58.741 43.478 0.00 0.00 0.00 1.75
43 44 3.082548 TCTGGAGAACGACGAGAAGATT 58.917 45.455 0.00 0.00 0.00 2.40
44 45 2.712709 TCTGGAGAACGACGAGAAGAT 58.287 47.619 0.00 0.00 0.00 2.40
45 46 2.180432 TCTGGAGAACGACGAGAAGA 57.820 50.000 0.00 0.00 0.00 2.87
46 47 2.857618 CTTCTGGAGAACGACGAGAAG 58.142 52.381 0.00 4.57 41.17 2.85
47 48 2.228059 ACTTCTGGAGAACGACGAGAA 58.772 47.619 0.00 0.00 32.86 2.87
48 49 1.893544 ACTTCTGGAGAACGACGAGA 58.106 50.000 0.00 0.00 0.00 4.04
49 50 2.320367 CAACTTCTGGAGAACGACGAG 58.680 52.381 0.00 0.00 0.00 4.18
50 51 2.417339 CAACTTCTGGAGAACGACGA 57.583 50.000 0.00 0.00 0.00 4.20
61 62 1.528586 CACGAAGCAGACCAACTTCTG 59.471 52.381 0.00 0.00 45.15 3.02
62 63 1.871080 CACGAAGCAGACCAACTTCT 58.129 50.000 0.00 0.00 40.12 2.85
63 64 0.235926 GCACGAAGCAGACCAACTTC 59.764 55.000 0.00 0.00 44.79 3.01
64 65 2.321213 GCACGAAGCAGACCAACTT 58.679 52.632 0.00 0.00 44.79 2.66
65 66 4.049393 GCACGAAGCAGACCAACT 57.951 55.556 0.00 0.00 44.79 3.16
77 78 8.697846 GACCAAGTCAAATGCATTAAGCACGA 62.698 42.308 13.39 0.28 43.76 4.35
78 79 6.623525 GACCAAGTCAAATGCATTAAGCACG 61.624 44.000 13.39 0.76 43.76 5.34
79 80 4.622740 GACCAAGTCAAATGCATTAAGCAC 59.377 41.667 13.39 7.07 43.76 4.40
80 81 4.808558 GACCAAGTCAAATGCATTAAGCA 58.191 39.130 13.39 0.00 44.50 3.91
81 82 4.808558 TGACCAAGTCAAATGCATTAAGC 58.191 39.130 13.39 5.69 39.78 3.09
93 94 7.174946 GGAAAATTAGAGATGTTGACCAAGTCA 59.825 37.037 0.00 0.00 41.09 3.41
94 95 7.391833 AGGAAAATTAGAGATGTTGACCAAGTC 59.608 37.037 0.00 0.00 0.00 3.01
95 96 7.234355 AGGAAAATTAGAGATGTTGACCAAGT 58.766 34.615 0.00 0.00 0.00 3.16
96 97 7.609532 AGAGGAAAATTAGAGATGTTGACCAAG 59.390 37.037 0.00 0.00 0.00 3.61
97 98 7.391554 CAGAGGAAAATTAGAGATGTTGACCAA 59.608 37.037 0.00 0.00 0.00 3.67
98 99 6.881065 CAGAGGAAAATTAGAGATGTTGACCA 59.119 38.462 0.00 0.00 0.00 4.02
99 100 7.106239 TCAGAGGAAAATTAGAGATGTTGACC 58.894 38.462 0.00 0.00 0.00 4.02
100 101 8.553459 TTCAGAGGAAAATTAGAGATGTTGAC 57.447 34.615 0.00 0.00 0.00 3.18
101 102 9.224267 CTTTCAGAGGAAAATTAGAGATGTTGA 57.776 33.333 0.00 0.00 42.18 3.18
102 103 9.224267 TCTTTCAGAGGAAAATTAGAGATGTTG 57.776 33.333 0.00 0.00 42.18 3.33
103 104 9.799106 TTCTTTCAGAGGAAAATTAGAGATGTT 57.201 29.630 0.00 0.00 42.18 2.71
104 105 9.799106 TTTCTTTCAGAGGAAAATTAGAGATGT 57.201 29.630 0.00 0.00 42.18 3.06
117 118 9.162764 CGGTATATTTTCTTTTCTTTCAGAGGA 57.837 33.333 0.00 0.00 0.00 3.71
118 119 7.910683 GCGGTATATTTTCTTTTCTTTCAGAGG 59.089 37.037 0.00 0.00 0.00 3.69
119 120 8.669243 AGCGGTATATTTTCTTTTCTTTCAGAG 58.331 33.333 0.00 0.00 0.00 3.35
124 125 8.106247 TGACAGCGGTATATTTTCTTTTCTTT 57.894 30.769 0.00 0.00 0.00 2.52
142 143 3.684305 TGACCATCTAAAACATGACAGCG 59.316 43.478 0.00 0.00 0.00 5.18
476 501 2.615262 CTTGGCTCGTCGGGCTCTAC 62.615 65.000 18.16 0.00 0.00 2.59
619 648 1.852157 TTCCCTGGACATGGCAGGT 60.852 57.895 3.63 3.63 34.42 4.00
731 1065 2.213499 GACGGGATGCAATTACTGGAG 58.787 52.381 0.00 0.00 0.00 3.86
772 1110 2.740055 CTCCACCGCTGACAGCAC 60.740 66.667 26.32 0.00 42.58 4.40
773 1111 3.233980 ACTCCACCGCTGACAGCA 61.234 61.111 26.32 6.25 42.58 4.41
892 1253 1.861982 TAGAGAGGCAAGGGTGGTAC 58.138 55.000 0.00 0.00 0.00 3.34
893 1254 2.679082 GATAGAGAGGCAAGGGTGGTA 58.321 52.381 0.00 0.00 0.00 3.25
894 1255 1.501582 GATAGAGAGGCAAGGGTGGT 58.498 55.000 0.00 0.00 0.00 4.16
895 1256 0.761802 GGATAGAGAGGCAAGGGTGG 59.238 60.000 0.00 0.00 0.00 4.61
897 1258 1.273838 TGTGGATAGAGAGGCAAGGGT 60.274 52.381 0.00 0.00 0.00 4.34
898 1259 1.415659 CTGTGGATAGAGAGGCAAGGG 59.584 57.143 0.00 0.00 0.00 3.95
899 1260 1.202627 GCTGTGGATAGAGAGGCAAGG 60.203 57.143 0.00 0.00 0.00 3.61
901 1262 0.461548 CGCTGTGGATAGAGAGGCAA 59.538 55.000 0.00 0.00 0.00 4.52
902 1263 0.684479 ACGCTGTGGATAGAGAGGCA 60.684 55.000 0.00 0.00 0.00 4.75
903 1264 0.249238 CACGCTGTGGATAGAGAGGC 60.249 60.000 1.40 0.00 0.00 4.70
904 1265 1.107114 ACACGCTGTGGATAGAGAGG 58.893 55.000 12.18 0.00 37.94 3.69
905 1266 2.164422 TGAACACGCTGTGGATAGAGAG 59.836 50.000 12.18 0.00 37.94 3.20
906 1267 2.167662 TGAACACGCTGTGGATAGAGA 58.832 47.619 12.18 0.00 37.94 3.10
974 1337 2.041115 GTGCGCCTTTCTTCCTCCC 61.041 63.158 4.18 0.00 0.00 4.30
995 1358 0.030101 CCTTCGCTCGGTCATCTCTC 59.970 60.000 0.00 0.00 0.00 3.20
1064 1427 3.541831 CATTGTCGTCGGCGTCGG 61.542 66.667 24.52 6.06 39.49 4.79
1065 1428 1.872234 ATCATTGTCGTCGGCGTCG 60.872 57.895 19.85 19.85 39.49 5.12
1066 1429 1.631072 CATCATTGTCGTCGGCGTC 59.369 57.895 10.18 3.95 39.49 5.19
1083 1446 2.228480 GGCACACCCTTCCCTACCA 61.228 63.158 0.00 0.00 0.00 3.25
1100 1463 1.017701 GCAGACGGGGAAAAGTACGG 61.018 60.000 0.00 0.00 0.00 4.02
1102 1465 0.323957 AGGCAGACGGGGAAAAGTAC 59.676 55.000 0.00 0.00 0.00 2.73
1464 1851 4.937015 GTGAGAAAGTAGTACGAGGAGAGT 59.063 45.833 0.00 0.00 0.00 3.24
1479 1869 1.004918 AGGAACGCCCGTGAGAAAG 60.005 57.895 0.00 0.00 40.87 2.62
1522 1939 1.934589 TCAACATCGGCGATAACCAG 58.065 50.000 23.53 12.29 0.00 4.00
1552 1969 4.182433 TCCCGCCACTGCACAACA 62.182 61.111 0.00 0.00 37.32 3.33
1553 1970 3.660111 GTCCCGCCACTGCACAAC 61.660 66.667 0.00 0.00 37.32 3.32
1984 2402 9.146984 GGTCAAGGCCAAAATAAAAATTACTAC 57.853 33.333 5.01 0.00 0.00 2.73
1986 2404 7.659799 GTGGTCAAGGCCAAAATAAAAATTACT 59.340 33.333 5.01 0.00 40.68 2.24
2298 2741 4.555689 AGGATGCTCTAAGAAGATGGTCT 58.444 43.478 0.00 0.00 0.00 3.85
2299 2742 4.343526 TGAGGATGCTCTAAGAAGATGGTC 59.656 45.833 15.82 0.00 0.00 4.02
2300 2743 4.293494 TGAGGATGCTCTAAGAAGATGGT 58.707 43.478 15.82 0.00 0.00 3.55
2301 2744 4.800249 GCTGAGGATGCTCTAAGAAGATGG 60.800 50.000 15.82 0.00 0.00 3.51
2302 2745 4.309099 GCTGAGGATGCTCTAAGAAGATG 58.691 47.826 15.82 0.00 0.00 2.90
2303 2746 3.324556 GGCTGAGGATGCTCTAAGAAGAT 59.675 47.826 15.82 0.00 0.00 2.40
2304 2747 2.697751 GGCTGAGGATGCTCTAAGAAGA 59.302 50.000 15.82 0.00 0.00 2.87
2305 2748 2.699846 AGGCTGAGGATGCTCTAAGAAG 59.300 50.000 15.82 5.04 0.00 2.85
2306 2749 2.756907 AGGCTGAGGATGCTCTAAGAA 58.243 47.619 15.82 0.00 0.00 2.52
2307 2750 2.468301 AGGCTGAGGATGCTCTAAGA 57.532 50.000 15.82 0.00 0.00 2.10
2308 2751 2.545532 CGAAGGCTGAGGATGCTCTAAG 60.546 54.545 15.82 6.50 0.00 2.18
2309 2752 1.410517 CGAAGGCTGAGGATGCTCTAA 59.589 52.381 15.82 0.00 0.00 2.10
2310 2753 1.035923 CGAAGGCTGAGGATGCTCTA 58.964 55.000 15.82 1.28 0.00 2.43
2311 2754 1.821936 CGAAGGCTGAGGATGCTCT 59.178 57.895 15.82 0.00 0.00 4.09
2312 2755 1.886777 GCGAAGGCTGAGGATGCTC 60.887 63.158 7.39 7.39 35.83 4.26
2313 2756 2.188994 GCGAAGGCTGAGGATGCT 59.811 61.111 0.00 0.00 35.83 3.79
2339 2782 3.423154 GTGGAGTTGGCTTCCGCG 61.423 66.667 0.00 0.00 36.88 6.46
2340 2783 3.056328 GGTGGAGTTGGCTTCCGC 61.056 66.667 7.87 7.87 0.00 5.54
2341 2784 2.742372 CGGTGGAGTTGGCTTCCG 60.742 66.667 0.00 0.00 0.00 4.30
2342 2785 3.056328 GCGGTGGAGTTGGCTTCC 61.056 66.667 0.00 0.00 0.00 3.46
2343 2786 3.423154 CGCGGTGGAGTTGGCTTC 61.423 66.667 0.00 0.00 0.00 3.86
2362 2805 1.357334 CCGACGTTTGTTTGGGGTG 59.643 57.895 0.00 0.00 0.00 4.61
2386 2829 2.630580 CCCCAAAGAAACAAAATCGGGA 59.369 45.455 0.00 0.00 34.10 5.14
2399 2842 4.794648 CCATCGGCGCCCCAAAGA 62.795 66.667 23.46 12.68 0.00 2.52
2649 3156 3.628646 GACGGGCATGGGCAGAAGT 62.629 63.158 0.00 0.00 43.71 3.01
2659 3166 4.891727 GGCGACATCGACGGGCAT 62.892 66.667 5.26 0.00 43.02 4.40


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

AutoCloner maintained by Alex Coulton.