Multiple sequence alignment - TraesCS5D01G521700

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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 TraesCS5D01G521700 chr5D 100.000 3413 0 0 1 3413 542633311 542629899 0.000000e+00 6303.0
1 TraesCS5D01G521700 chr5D 81.951 1435 192 32 982 2396 540079264 540080651 0.000000e+00 1153.0
2 TraesCS5D01G521700 chr5D 85.590 229 28 5 2667 2891 382871972 382871745 5.690000e-58 235.0
3 TraesCS5D01G521700 chr5D 97.222 36 1 0 2439 2474 542630758 542630723 1.020000e-05 62.1
4 TraesCS5D01G521700 chr5D 97.222 36 1 0 2554 2589 542630873 542630838 1.020000e-05 62.1
5 TraesCS5D01G521700 chr4A 89.038 2764 228 49 11 2731 626384469 626387200 0.000000e+00 3356.0
6 TraesCS5D01G521700 chr4A 92.693 698 43 5 2721 3413 626387380 626388074 0.000000e+00 1000.0
7 TraesCS5D01G521700 chr4A 79.077 650 110 20 211 841 590429596 590428954 1.130000e-114 424.0
8 TraesCS5D01G521700 chr4A 97.297 37 1 0 2439 2475 626387030 626387066 2.840000e-06 63.9
9 TraesCS5D01G521700 chr5B 82.934 1418 178 28 996 2396 682398498 682399868 0.000000e+00 1219.0
10 TraesCS5D01G521700 chr5B 89.709 826 49 13 2613 3413 684372472 684371658 0.000000e+00 1022.0
11 TraesCS5D01G521700 chr5B 94.646 523 22 5 2085 2605 684373082 684372564 0.000000e+00 806.0
12 TraesCS5D01G521700 chr5B 79.199 649 109 20 211 841 505219319 505218679 8.750000e-116 427.0
13 TraesCS5D01G521700 chr5B 81.895 475 84 2 1913 2386 682369492 682369965 1.910000e-107 399.0
14 TraesCS5D01G521700 chr5B 97.222 36 1 0 2439 2474 684372614 684372579 1.020000e-05 62.1
15 TraesCS5D01G521700 chrUn 85.854 1124 138 9 1039 2159 323412892 323411787 0.000000e+00 1175.0
16 TraesCS5D01G521700 chrUn 86.885 549 57 6 1039 1587 354647469 354648002 4.870000e-168 601.0
17 TraesCS5D01G521700 chrUn 85.115 477 68 1 1686 2159 335761529 335762005 5.120000e-133 484.0
18 TraesCS5D01G521700 chrUn 86.885 244 31 1 2191 2434 323411793 323411551 4.340000e-69 272.0
19 TraesCS5D01G521700 chrUn 86.885 244 31 1 2191 2434 335761999 335762241 4.340000e-69 272.0
20 TraesCS5D01G521700 chrUn 81.900 221 31 7 2674 2891 268033790 268034004 9.730000e-41 178.0
21 TraesCS5D01G521700 chrUn 85.714 70 9 1 2822 2891 17300753 17300685 4.720000e-09 73.1
22 TraesCS5D01G521700 chr1B 85.765 1124 139 9 1039 2159 2559859 2558754 0.000000e+00 1170.0
23 TraesCS5D01G521700 chr1B 85.587 1124 141 9 1039 2159 2620602 2619497 0.000000e+00 1158.0
24 TraesCS5D01G521700 chr1B 81.522 1445 196 33 989 2392 603604413 603605827 0.000000e+00 1123.0
25 TraesCS5D01G521700 chr1B 86.885 244 31 1 2191 2434 2558760 2558518 4.340000e-69 272.0
26 TraesCS5D01G521700 chr2B 79.303 1435 237 38 983 2387 687634043 687635447 0.000000e+00 950.0
27 TraesCS5D01G521700 chr2B 84.746 236 32 4 2656 2888 636775360 636775594 2.050000e-57 233.0
28 TraesCS5D01G521700 chr2B 82.609 207 27 4 2694 2891 662897265 662897059 1.260000e-39 174.0
29 TraesCS5D01G521700 chr2D 79.091 1430 249 34 983 2387 572404229 572405633 0.000000e+00 939.0
30 TraesCS5D01G521700 chr2D 79.109 651 113 17 208 841 458731806 458731162 8.750000e-116 427.0
31 TraesCS5D01G521700 chr2A 79.013 1439 244 40 977 2386 711855862 711857271 0.000000e+00 931.0
32 TraesCS5D01G521700 chr2A 79.109 651 115 15 208 841 515503135 515503781 2.430000e-116 429.0
33 TraesCS5D01G521700 chr2A 73.046 1369 282 59 1060 2386 17118198 17119521 1.480000e-108 403.0
34 TraesCS5D01G521700 chr2A 72.614 1289 270 53 1121 2385 19471834 19473063 7.010000e-92 348.0
35 TraesCS5D01G521700 chr2A 72.016 997 214 52 1415 2386 15449650 15448694 5.690000e-58 235.0
36 TraesCS5D01G521700 chr1D 80.514 1011 146 32 1412 2386 476249194 476248199 0.000000e+00 728.0
37 TraesCS5D01G521700 chr1D 79.167 648 112 19 211 841 213374398 213373757 8.750000e-116 427.0
38 TraesCS5D01G521700 chr7A 80.000 650 107 16 211 841 634327936 634327291 3.100000e-125 459.0
39 TraesCS5D01G521700 chr3D 79.570 651 112 16 208 842 489527732 489528377 2.420000e-121 446.0
40 TraesCS5D01G521700 chr5A 79.109 651 111 20 208 842 390551292 390551933 3.150000e-115 425.0
41 TraesCS5D01G521700 chr3B 79.045 649 113 19 211 842 528711673 528711031 1.130000e-114 424.0
42 TraesCS5D01G521700 chr3B 84.848 231 29 5 2664 2891 493121881 493121654 9.530000e-56 228.0
43 TraesCS5D01G521700 chr6B 85.039 127 18 1 2762 2887 448666025 448665899 9.940000e-26 128.0


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 TraesCS5D01G521700 chr5D 542629899 542633311 3412 True 2142.400000 6303 98.148000 1 3413 3 chr5D.!!$R2 3412
1 TraesCS5D01G521700 chr5D 540079264 540080651 1387 False 1153.000000 1153 81.951000 982 2396 1 chr5D.!!$F1 1414
2 TraesCS5D01G521700 chr4A 626384469 626388074 3605 False 1473.300000 3356 93.009333 11 3413 3 chr4A.!!$F1 3402
3 TraesCS5D01G521700 chr4A 590428954 590429596 642 True 424.000000 424 79.077000 211 841 1 chr4A.!!$R1 630
4 TraesCS5D01G521700 chr5B 682398498 682399868 1370 False 1219.000000 1219 82.934000 996 2396 1 chr5B.!!$F2 1400
5 TraesCS5D01G521700 chr5B 684371658 684373082 1424 True 630.033333 1022 93.859000 2085 3413 3 chr5B.!!$R2 1328
6 TraesCS5D01G521700 chr5B 505218679 505219319 640 True 427.000000 427 79.199000 211 841 1 chr5B.!!$R1 630
7 TraesCS5D01G521700 chrUn 323411551 323412892 1341 True 723.500000 1175 86.369500 1039 2434 2 chrUn.!!$R2 1395
8 TraesCS5D01G521700 chrUn 354647469 354648002 533 False 601.000000 601 86.885000 1039 1587 1 chrUn.!!$F2 548
9 TraesCS5D01G521700 chrUn 335761529 335762241 712 False 378.000000 484 86.000000 1686 2434 2 chrUn.!!$F3 748
10 TraesCS5D01G521700 chr1B 2619497 2620602 1105 True 1158.000000 1158 85.587000 1039 2159 1 chr1B.!!$R1 1120
11 TraesCS5D01G521700 chr1B 603604413 603605827 1414 False 1123.000000 1123 81.522000 989 2392 1 chr1B.!!$F1 1403
12 TraesCS5D01G521700 chr1B 2558518 2559859 1341 True 721.000000 1170 86.325000 1039 2434 2 chr1B.!!$R2 1395
13 TraesCS5D01G521700 chr2B 687634043 687635447 1404 False 950.000000 950 79.303000 983 2387 1 chr2B.!!$F2 1404
14 TraesCS5D01G521700 chr2D 572404229 572405633 1404 False 939.000000 939 79.091000 983 2387 1 chr2D.!!$F1 1404
15 TraesCS5D01G521700 chr2D 458731162 458731806 644 True 427.000000 427 79.109000 208 841 1 chr2D.!!$R1 633
16 TraesCS5D01G521700 chr2A 711855862 711857271 1409 False 931.000000 931 79.013000 977 2386 1 chr2A.!!$F4 1409
17 TraesCS5D01G521700 chr2A 515503135 515503781 646 False 429.000000 429 79.109000 208 841 1 chr2A.!!$F3 633
18 TraesCS5D01G521700 chr2A 17118198 17119521 1323 False 403.000000 403 73.046000 1060 2386 1 chr2A.!!$F1 1326
19 TraesCS5D01G521700 chr2A 19471834 19473063 1229 False 348.000000 348 72.614000 1121 2385 1 chr2A.!!$F2 1264
20 TraesCS5D01G521700 chr2A 15448694 15449650 956 True 235.000000 235 72.016000 1415 2386 1 chr2A.!!$R1 971
21 TraesCS5D01G521700 chr1D 476248199 476249194 995 True 728.000000 728 80.514000 1412 2386 1 chr1D.!!$R2 974
22 TraesCS5D01G521700 chr1D 213373757 213374398 641 True 427.000000 427 79.167000 211 841 1 chr1D.!!$R1 630
23 TraesCS5D01G521700 chr7A 634327291 634327936 645 True 459.000000 459 80.000000 211 841 1 chr7A.!!$R1 630
24 TraesCS5D01G521700 chr3D 489527732 489528377 645 False 446.000000 446 79.570000 208 842 1 chr3D.!!$F1 634
25 TraesCS5D01G521700 chr5A 390551292 390551933 641 False 425.000000 425 79.109000 208 842 1 chr5A.!!$F1 634
26 TraesCS5D01G521700 chr3B 528711031 528711673 642 True 424.000000 424 79.045000 211 842 1 chr3B.!!$R2 631

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
402 420 0.178950 ATCTAGGAGGCTGCGGATCA 60.179 55.0 10.50 0.00 0.00 2.92 F
518 542 0.250124 TGCCTCCGTGTGATTCGTTT 60.250 50.0 0.00 0.00 0.00 3.60 F
595 625 0.798771 GATGAAGTCGCGTCGAGCTT 60.799 55.0 5.77 4.23 45.59 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 2043 0.240411 GTGTACGTCGTCTCCTGCTT 59.760 55.000 0.00 0.0 0.00 3.91 R
2376 2528 1.236616 TGGTTGCAGCCATGAACTCG 61.237 55.000 19.51 0.0 32.81 4.18 R
2449 2601 4.832248 TGGTCCTCACTGATAACAATCAC 58.168 43.478 0.00 0.0 0.00 3.06 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
35 36 1.357334 GCTCTCCTCCGTCGATGAC 59.643 63.158 6.11 0.00 0.00 3.06
40 41 0.835276 TCCTCCGTCGATGACCTCTA 59.165 55.000 6.11 0.00 0.00 2.43
41 42 1.211212 TCCTCCGTCGATGACCTCTAA 59.789 52.381 6.11 0.00 0.00 2.10
42 43 1.604755 CCTCCGTCGATGACCTCTAAG 59.395 57.143 6.11 0.00 0.00 2.18
44 45 2.286872 TCCGTCGATGACCTCTAAGTC 58.713 52.381 6.11 0.00 37.28 3.01
45 46 2.093075 TCCGTCGATGACCTCTAAGTCT 60.093 50.000 6.11 0.00 37.66 3.24
52 53 4.865776 GATGACCTCTAAGTCTTCGATGG 58.134 47.826 0.00 0.00 37.66 3.51
76 77 3.072468 GGGTCACCGGATCCGACA 61.072 66.667 35.42 15.31 42.83 4.35
78 79 2.642254 GGTCACCGGATCCGACACA 61.642 63.158 35.42 13.05 42.83 3.72
81 82 2.173669 CACCGGATCCGACACATGC 61.174 63.158 35.42 0.00 42.83 4.06
101 102 2.934553 GCGGATCGTTTTAGCTTTAGGT 59.065 45.455 0.00 0.00 0.00 3.08
102 103 3.373130 GCGGATCGTTTTAGCTTTAGGTT 59.627 43.478 0.00 0.00 0.00 3.50
103 104 4.142752 GCGGATCGTTTTAGCTTTAGGTTT 60.143 41.667 0.00 0.00 0.00 3.27
104 105 5.063817 GCGGATCGTTTTAGCTTTAGGTTTA 59.936 40.000 0.00 0.00 0.00 2.01
105 106 6.702897 CGGATCGTTTTAGCTTTAGGTTTAG 58.297 40.000 0.00 0.00 0.00 1.85
106 107 6.532657 CGGATCGTTTTAGCTTTAGGTTTAGA 59.467 38.462 0.00 0.00 0.00 2.10
126 127 3.010420 GACCCTAGCAGCTTAGGTTTTG 58.990 50.000 15.42 4.65 38.86 2.44
132 133 1.821666 GCAGCTTAGGTTTTGGGGTCA 60.822 52.381 0.00 0.00 0.00 4.02
134 135 2.755103 CAGCTTAGGTTTTGGGGTCATC 59.245 50.000 0.00 0.00 0.00 2.92
135 136 1.743394 GCTTAGGTTTTGGGGTCATCG 59.257 52.381 0.00 0.00 0.00 3.84
136 137 2.878526 GCTTAGGTTTTGGGGTCATCGT 60.879 50.000 0.00 0.00 0.00 3.73
137 138 2.483014 TAGGTTTTGGGGTCATCGTG 57.517 50.000 0.00 0.00 0.00 4.35
138 139 0.476771 AGGTTTTGGGGTCATCGTGT 59.523 50.000 0.00 0.00 0.00 4.49
139 140 1.133606 AGGTTTTGGGGTCATCGTGTT 60.134 47.619 0.00 0.00 0.00 3.32
140 141 1.000717 GGTTTTGGGGTCATCGTGTTG 60.001 52.381 0.00 0.00 0.00 3.33
144 158 1.303317 GGGGTCATCGTGTTGGCTT 60.303 57.895 0.00 0.00 0.00 4.35
145 159 0.893727 GGGGTCATCGTGTTGGCTTT 60.894 55.000 0.00 0.00 0.00 3.51
149 163 2.143122 GTCATCGTGTTGGCTTTGAGA 58.857 47.619 0.00 0.00 0.00 3.27
151 165 3.003275 GTCATCGTGTTGGCTTTGAGAAA 59.997 43.478 0.00 0.00 0.00 2.52
155 169 2.287009 CGTGTTGGCTTTGAGAAAGACC 60.287 50.000 0.00 2.04 46.27 3.85
185 199 4.227864 AGAAACTTAGGATCCTTGCCTG 57.772 45.455 22.03 8.43 36.96 4.85
187 201 4.289672 AGAAACTTAGGATCCTTGCCTGAA 59.710 41.667 22.03 5.86 36.96 3.02
190 204 3.846588 ACTTAGGATCCTTGCCTGAAGAA 59.153 43.478 22.03 3.46 36.96 2.52
192 206 1.064832 AGGATCCTTGCCTGAAGAAGC 60.065 52.381 9.02 0.00 33.59 3.86
198 212 1.808945 CTTGCCTGAAGAAGCGATTGT 59.191 47.619 0.00 0.00 32.82 2.71
200 214 1.806542 TGCCTGAAGAAGCGATTGTTC 59.193 47.619 15.60 15.60 0.00 3.18
209 223 6.876789 TGAAGAAGCGATTGTTCTTATGGTTA 59.123 34.615 21.68 0.00 42.95 2.85
221 235 7.418378 TGTTCTTATGGTTAGGGATGGATTTT 58.582 34.615 0.00 0.00 0.00 1.82
227 241 5.650283 TGGTTAGGGATGGATTTTGAAACT 58.350 37.500 0.00 0.00 0.00 2.66
238 252 7.496529 TGGATTTTGAAACTAGTCTGTTCAG 57.503 36.000 8.17 0.00 0.00 3.02
296 313 1.275291 GACTTGTGTCCTCCGAATCCA 59.725 52.381 0.00 0.00 37.24 3.41
304 321 1.416401 TCCTCCGAATCCATAGTTGCC 59.584 52.381 0.00 0.00 0.00 4.52
306 323 2.421388 CCTCCGAATCCATAGTTGCCAA 60.421 50.000 0.00 0.00 0.00 4.52
336 353 2.033755 CAGCACCTGCACAGAGCTC 61.034 63.158 5.27 5.27 45.94 4.09
392 410 1.875576 GCATCGGCAACATCTAGGAGG 60.876 57.143 0.00 0.00 40.72 4.30
393 411 0.394565 ATCGGCAACATCTAGGAGGC 59.605 55.000 0.00 0.00 0.00 4.70
402 420 0.178950 ATCTAGGAGGCTGCGGATCA 60.179 55.000 10.50 0.00 0.00 2.92
409 429 2.713770 GCTGCGGATCATGTGCTG 59.286 61.111 0.00 0.00 0.00 4.41
431 451 0.687920 TTCGTGGTTGGCAGGTATGA 59.312 50.000 0.00 0.00 0.00 2.15
446 466 5.629133 GCAGGTATGATTTACTCCTCCAACA 60.629 44.000 0.00 0.00 0.00 3.33
448 468 6.484643 CAGGTATGATTTACTCCTCCAACATG 59.515 42.308 0.00 0.00 0.00 3.21
454 474 7.103641 TGATTTACTCCTCCAACATGTTAGTC 58.896 38.462 11.53 0.00 0.00 2.59
455 475 6.428083 TTTACTCCTCCAACATGTTAGTCA 57.572 37.500 11.53 0.00 0.00 3.41
487 511 2.034685 TCAGATCTAAGTTCGATGGCGG 59.965 50.000 0.00 0.00 38.28 6.13
505 529 2.034221 GTCCAGGGTGTTGCCTCC 59.966 66.667 0.00 0.00 37.43 4.30
508 532 2.669569 CAGGGTGTTGCCTCCGTG 60.670 66.667 0.00 0.00 37.43 4.94
518 542 0.250124 TGCCTCCGTGTGATTCGTTT 60.250 50.000 0.00 0.00 0.00 3.60
534 558 1.731098 CGTTTAACGGCAATGGCTTCC 60.731 52.381 9.88 0.00 38.08 3.46
575 605 6.401047 TGAAGGTCCGTAAAGTATATCAGG 57.599 41.667 0.00 0.00 0.00 3.86
583 613 6.781014 TCCGTAAAGTATATCAGGGATGAAGT 59.219 38.462 0.00 0.00 0.00 3.01
595 625 0.798771 GATGAAGTCGCGTCGAGCTT 60.799 55.000 5.77 4.23 45.59 3.74
598 628 2.797866 GAAGTCGCGTCGAGCTTGGA 62.798 60.000 5.77 0.00 45.59 3.53
612 642 1.767681 GCTTGGATGAGGAGGTGATCT 59.232 52.381 0.00 0.00 0.00 2.75
616 646 4.475919 TGGATGAGGAGGTGATCTATCA 57.524 45.455 0.00 0.00 0.00 2.15
622 652 7.723172 GGATGAGGAGGTGATCTATCAATTTTT 59.277 37.037 0.00 0.00 38.75 1.94
649 679 2.410687 TGGTTGTTGTGGTGGTGCG 61.411 57.895 0.00 0.00 0.00 5.34
692 724 2.238395 GTCAAGCTCAGGGGATTCTTCT 59.762 50.000 0.00 0.00 0.00 2.85
699 731 2.573462 TCAGGGGATTCTTCTGTCTTGG 59.427 50.000 0.00 0.00 0.00 3.61
718 750 8.744652 TGTCTTGGTTGTAATTTTTCTTCTTGA 58.255 29.630 0.00 0.00 0.00 3.02
724 756 7.648112 GGTTGTAATTTTTCTTCTTGACTGGTC 59.352 37.037 0.00 0.00 0.00 4.02
763 795 7.920738 AGAATAGTGTTCTGTTGTCTTTTCAC 58.079 34.615 0.71 0.00 0.00 3.18
773 805 7.601856 TCTGTTGTCTTTTCACTTTTGTCATT 58.398 30.769 0.00 0.00 0.00 2.57
777 809 6.918626 TGTCTTTTCACTTTTGTCATTGTCA 58.081 32.000 0.00 0.00 0.00 3.58
780 812 7.542130 GTCTTTTCACTTTTGTCATTGTCAGTT 59.458 33.333 0.00 0.00 0.00 3.16
813 851 8.241367 TGACTTGCACACGATATACGATATAAT 58.759 33.333 0.00 0.00 45.77 1.28
819 857 9.452065 GCACACGATATACGATATAATTGAGAT 57.548 33.333 0.00 0.00 45.77 2.75
915 956 2.165030 GGAGCCATGCCATATGTAATGC 59.835 50.000 1.24 0.00 0.00 3.56
921 962 2.416747 TGCCATATGTAATGCGCTCTC 58.583 47.619 9.73 0.00 0.00 3.20
969 1010 1.203063 ACTACTGGTCTGCTCACTCCA 60.203 52.381 0.00 0.00 0.00 3.86
970 1011 1.203523 CTACTGGTCTGCTCACTCCAC 59.796 57.143 0.00 0.00 0.00 4.02
1030 1076 3.607987 GAATCGTGTCTCGGCGCG 61.608 66.667 0.00 0.00 42.91 6.86
1036 1082 3.672447 TGTCTCGGCGCGTGGTAA 61.672 61.111 8.43 0.00 0.00 2.85
1179 1242 1.566018 GAAAGGGGCTCAACGACGTG 61.566 60.000 0.00 0.00 0.00 4.49
1249 1315 2.797278 CCTTATGCCGGACGCCTCT 61.797 63.158 5.05 0.00 36.24 3.69
1399 1473 1.464734 GGACATCACCGACTCTCTCA 58.535 55.000 0.00 0.00 0.00 3.27
1434 1508 0.836400 TCTGGTCCTTCTTCCCGCTT 60.836 55.000 0.00 0.00 0.00 4.68
1687 1794 4.408821 GCTGCACCGTCCCCATCA 62.409 66.667 0.00 0.00 0.00 3.07
2028 2165 1.370064 GTCTACCGCCGGCCATATT 59.630 57.895 23.46 2.71 0.00 1.28
2030 2167 1.116536 TCTACCGCCGGCCATATTCA 61.117 55.000 23.46 0.00 0.00 2.57
2043 2183 2.489802 CCATATTCAGGAAAGGGGCCTC 60.490 54.545 0.84 0.00 32.12 4.70
2434 2586 7.337689 ACTGATTGTATCTCTTGCAGCAAAATA 59.662 33.333 9.65 5.04 0.00 1.40
2437 2589 9.525409 GATTGTATCTCTTGCAGCAAAATATTT 57.475 29.630 9.65 0.00 0.00 1.40
2449 2601 9.022915 TGCAGCAAAATATTTTATCATCTTTCG 57.977 29.630 12.98 0.00 0.00 3.46
2537 2691 3.692257 ATGGAGGTTCACTGAGTCTTG 57.308 47.619 0.00 0.00 0.00 3.02
2626 2864 2.486982 CCCTGAGTTGCTGATGTTTCTG 59.513 50.000 0.00 0.00 0.00 3.02
2687 2925 2.103537 AAACTGGACCCCGATAAACG 57.896 50.000 0.00 0.00 42.18 3.60
2713 2952 5.895636 ATGTTCGGATTTTAAGCATGTCA 57.104 34.783 0.00 0.00 0.00 3.58
2716 2955 3.680490 TCGGATTTTAAGCATGTCACCA 58.320 40.909 0.00 0.00 0.00 4.17
2717 2956 4.269183 TCGGATTTTAAGCATGTCACCAT 58.731 39.130 0.00 0.00 0.00 3.55
2793 3223 3.853355 AACATGGCAATTTTGTCCCAA 57.147 38.095 0.00 0.00 30.03 4.12
3145 3601 6.985117 ACCATTCAGCGCATATATGAAAAAT 58.015 32.000 17.10 5.42 36.59 1.82
3174 3630 9.788960 TCATCATCTATTAATAATCGTTCTCCG 57.211 33.333 0.00 0.00 38.13 4.63
3188 3644 8.571461 AATCGTTCTCCGTGTATTTACTATTC 57.429 34.615 0.00 0.00 37.94 1.75
3238 3694 5.600908 TTAGAAACTGTTTATCGTGTGCC 57.399 39.130 5.64 0.00 0.00 5.01
3276 3733 5.523438 TTTCTAAACGCTTCCATGGTTTT 57.477 34.783 12.58 7.34 35.64 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 0.835276 TAGAGGTCATCGACGGAGGA 59.165 55.000 0.00 0.00 32.65 3.71
26 27 3.942739 GAAGACTTAGAGGTCATCGACG 58.057 50.000 0.00 0.00 38.57 5.12
35 36 3.067461 CCTCACCATCGAAGACTTAGAGG 59.933 52.174 4.30 3.80 42.51 3.69
40 41 0.905357 CCCCTCACCATCGAAGACTT 59.095 55.000 0.00 0.00 42.51 3.01
41 42 0.978146 CCCCCTCACCATCGAAGACT 60.978 60.000 0.00 0.00 42.51 3.24
42 43 1.522569 CCCCCTCACCATCGAAGAC 59.477 63.158 0.00 0.00 42.51 3.01
63 64 2.173669 GCATGTGTCGGATCCGGTG 61.174 63.158 32.79 22.32 40.25 4.94
64 65 2.186903 GCATGTGTCGGATCCGGT 59.813 61.111 32.79 12.04 40.25 5.28
76 77 2.024176 AGCTAAAACGATCCGCATGT 57.976 45.000 0.00 0.00 0.00 3.21
78 79 3.560068 CCTAAAGCTAAAACGATCCGCAT 59.440 43.478 0.00 0.00 0.00 4.73
81 82 5.541098 AAACCTAAAGCTAAAACGATCCG 57.459 39.130 0.00 0.00 0.00 4.18
86 87 5.936372 AGGGTCTAAACCTAAAGCTAAAACG 59.064 40.000 0.00 0.00 45.66 3.60
101 102 3.721021 ACCTAAGCTGCTAGGGTCTAAA 58.279 45.455 21.28 0.00 42.57 1.85
102 103 3.399952 ACCTAAGCTGCTAGGGTCTAA 57.600 47.619 21.28 0.00 42.57 2.10
103 104 3.399952 AACCTAAGCTGCTAGGGTCTA 57.600 47.619 21.16 2.32 42.57 2.59
104 105 2.255770 AACCTAAGCTGCTAGGGTCT 57.744 50.000 21.16 12.05 42.57 3.85
105 106 3.010420 CAAAACCTAAGCTGCTAGGGTC 58.990 50.000 21.16 0.00 38.07 4.46
106 107 2.290960 CCAAAACCTAAGCTGCTAGGGT 60.291 50.000 21.28 19.38 40.99 4.34
112 113 0.888619 GACCCCAAAACCTAAGCTGC 59.111 55.000 0.00 0.00 0.00 5.25
113 114 2.286365 TGACCCCAAAACCTAAGCTG 57.714 50.000 0.00 0.00 0.00 4.24
126 127 0.893727 AAAGCCAACACGATGACCCC 60.894 55.000 0.00 0.00 0.00 4.95
132 133 3.251004 GTCTTTCTCAAAGCCAACACGAT 59.749 43.478 0.00 0.00 38.39 3.73
134 135 2.287009 GGTCTTTCTCAAAGCCAACACG 60.287 50.000 5.22 0.00 38.39 4.49
135 136 2.687935 TGGTCTTTCTCAAAGCCAACAC 59.312 45.455 8.71 0.00 39.79 3.32
136 137 3.011566 TGGTCTTTCTCAAAGCCAACA 57.988 42.857 8.71 0.00 39.79 3.33
137 138 3.569701 TCATGGTCTTTCTCAAAGCCAAC 59.430 43.478 12.90 0.00 43.11 3.77
138 139 3.831323 TCATGGTCTTTCTCAAAGCCAA 58.169 40.909 12.90 0.78 43.11 4.52
139 140 3.507162 TCATGGTCTTTCTCAAAGCCA 57.493 42.857 11.87 11.87 43.60 4.75
140 141 6.515272 TTATTCATGGTCTTTCTCAAAGCC 57.485 37.500 0.00 0.00 38.39 4.35
144 158 9.354673 AGTTTCTTTATTCATGGTCTTTCTCAA 57.645 29.630 0.00 0.00 0.00 3.02
145 159 8.924511 AGTTTCTTTATTCATGGTCTTTCTCA 57.075 30.769 0.00 0.00 0.00 3.27
149 163 9.807921 TCCTAAGTTTCTTTATTCATGGTCTTT 57.192 29.630 0.00 0.00 0.00 2.52
151 165 9.620259 GATCCTAAGTTTCTTTATTCATGGTCT 57.380 33.333 0.00 0.00 0.00 3.85
172 186 1.064832 GCTTCTTCAGGCAAGGATCCT 60.065 52.381 9.02 9.02 32.22 3.24
173 187 1.387539 GCTTCTTCAGGCAAGGATCC 58.612 55.000 2.48 2.48 32.22 3.36
181 195 2.079925 AGAACAATCGCTTCTTCAGGC 58.920 47.619 0.00 0.00 0.00 4.85
185 199 5.803020 ACCATAAGAACAATCGCTTCTTC 57.197 39.130 1.52 0.00 38.60 2.87
187 201 5.817816 CCTAACCATAAGAACAATCGCTTCT 59.182 40.000 0.00 0.00 0.00 2.85
190 204 4.163458 TCCCTAACCATAAGAACAATCGCT 59.837 41.667 0.00 0.00 0.00 4.93
192 206 5.470098 CCATCCCTAACCATAAGAACAATCG 59.530 44.000 0.00 0.00 0.00 3.34
198 212 7.647827 TCAAAATCCATCCCTAACCATAAGAA 58.352 34.615 0.00 0.00 0.00 2.52
200 214 7.896383 TTCAAAATCCATCCCTAACCATAAG 57.104 36.000 0.00 0.00 0.00 1.73
209 223 6.183347 CAGACTAGTTTCAAAATCCATCCCT 58.817 40.000 0.00 0.00 0.00 4.20
221 235 4.380531 CTTGCCTGAACAGACTAGTTTCA 58.619 43.478 7.96 7.96 0.00 2.69
227 241 2.237143 CCATCCTTGCCTGAACAGACTA 59.763 50.000 3.19 0.00 0.00 2.59
238 252 3.443045 CGCCACACCATCCTTGCC 61.443 66.667 0.00 0.00 0.00 4.52
263 280 4.074970 GACACAAGTCCACCATGAGAAAT 58.925 43.478 0.00 0.00 38.89 2.17
289 306 2.285220 CGTCTTGGCAACTATGGATTCG 59.715 50.000 0.00 0.00 37.61 3.34
291 308 3.350219 ACGTCTTGGCAACTATGGATT 57.650 42.857 0.00 0.00 37.61 3.01
296 313 2.484264 GAGCAAACGTCTTGGCAACTAT 59.516 45.455 0.00 0.00 37.61 2.12
325 342 1.304134 TACCTCCGAGCTCTGTGCA 60.304 57.895 12.85 0.00 45.94 4.57
328 345 0.394625 GGACTACCTCCGAGCTCTGT 60.395 60.000 12.85 6.25 0.00 3.41
330 347 0.106918 CTGGACTACCTCCGAGCTCT 60.107 60.000 12.85 0.00 43.03 4.09
336 353 2.482333 CGCTCCTGGACTACCTCCG 61.482 68.421 0.00 0.00 43.03 4.63
392 410 2.713770 CAGCACATGATCCGCAGC 59.286 61.111 0.00 0.00 0.00 5.25
393 411 2.184830 CCCAGCACATGATCCGCAG 61.185 63.158 0.00 0.00 0.00 5.18
402 420 1.150536 AACCACGAACCCAGCACAT 59.849 52.632 0.00 0.00 0.00 3.21
409 429 2.400269 TACCTGCCAACCACGAACCC 62.400 60.000 0.00 0.00 0.00 4.11
431 451 7.016153 TGACTAACATGTTGGAGGAGTAAAT 57.984 36.000 26.56 2.44 0.00 1.40
446 466 1.992557 ACACCCCCACATGACTAACAT 59.007 47.619 0.00 0.00 40.17 2.71
448 468 1.349688 TGACACCCCCACATGACTAAC 59.650 52.381 0.00 0.00 0.00 2.34
454 474 0.914644 AGATCTGACACCCCCACATG 59.085 55.000 0.00 0.00 0.00 3.21
455 475 2.568546 TAGATCTGACACCCCCACAT 57.431 50.000 5.18 0.00 0.00 3.21
487 511 2.034221 GAGGCAACACCCTGGACC 59.966 66.667 0.00 0.00 40.58 4.46
505 529 1.192757 TGCCGTTAAACGAATCACACG 59.807 47.619 0.00 0.00 46.05 4.49
508 532 3.168193 CCATTGCCGTTAAACGAATCAC 58.832 45.455 0.00 0.00 46.05 3.06
518 542 4.329831 GGGAAGCCATTGCCGTTA 57.670 55.556 0.00 0.00 37.15 3.18
554 581 5.461327 TCCCTGATATACTTTACGGACCTT 58.539 41.667 0.00 0.00 0.00 3.50
562 589 6.569801 CGCGACTTCATCCCTGATATACTTTA 60.570 42.308 0.00 0.00 0.00 1.85
575 605 2.224885 GCTCGACGCGACTTCATCC 61.225 63.158 15.93 0.00 0.00 3.51
583 613 2.202610 CATCCAAGCTCGACGCGA 60.203 61.111 15.93 2.20 45.59 5.87
595 625 4.475919 TGATAGATCACCTCCTCATCCA 57.524 45.455 0.00 0.00 0.00 3.41
622 652 2.900546 ACCACAACAACCACCAAAGAAA 59.099 40.909 0.00 0.00 0.00 2.52
639 669 3.036084 CGTGTCTCGCACCACCAC 61.036 66.667 0.00 0.00 44.97 4.16
667 699 0.616111 ATCCCCTGAGCTTGACGTCT 60.616 55.000 17.92 0.00 0.00 4.18
670 702 0.539051 AGAATCCCCTGAGCTTGACG 59.461 55.000 0.00 0.00 0.00 4.35
692 724 8.744652 TCAAGAAGAAAAATTACAACCAAGACA 58.255 29.630 0.00 0.00 0.00 3.41
699 731 8.406297 AGACCAGTCAAGAAGAAAAATTACAAC 58.594 33.333 0.00 0.00 0.00 3.32
741 773 7.865706 AAGTGAAAAGACAACAGAACACTAT 57.134 32.000 0.00 0.00 36.55 2.12
773 805 6.018262 GTGTGCAAGTCACTTATAAACTGACA 60.018 38.462 18.57 7.88 45.81 3.58
777 809 5.294356 TCGTGTGCAAGTCACTTATAAACT 58.706 37.500 4.63 0.00 45.81 2.66
780 812 7.377662 CGTATATCGTGTGCAAGTCACTTATAA 59.622 37.037 4.63 0.00 45.81 0.98
785 817 3.128068 TCGTATATCGTGTGCAAGTCACT 59.872 43.478 4.63 0.00 41.20 3.41
857 895 9.773328 CGGGTGCATATTGTAATTAATATCTTG 57.227 33.333 0.00 0.00 32.38 3.02
859 897 9.162764 GTCGGGTGCATATTGTAATTAATATCT 57.837 33.333 0.00 0.00 32.38 1.98
860 898 8.941977 TGTCGGGTGCATATTGTAATTAATATC 58.058 33.333 0.00 0.00 32.38 1.63
861 899 8.856153 TGTCGGGTGCATATTGTAATTAATAT 57.144 30.769 0.00 0.00 34.43 1.28
862 900 7.094975 GCTGTCGGGTGCATATTGTAATTAATA 60.095 37.037 0.00 0.00 0.00 0.98
863 901 6.293955 GCTGTCGGGTGCATATTGTAATTAAT 60.294 38.462 0.00 0.00 0.00 1.40
864 902 5.008217 GCTGTCGGGTGCATATTGTAATTAA 59.992 40.000 0.00 0.00 0.00 1.40
867 908 2.878406 GCTGTCGGGTGCATATTGTAAT 59.122 45.455 0.00 0.00 0.00 1.89
871 912 0.747644 TGGCTGTCGGGTGCATATTG 60.748 55.000 0.00 0.00 0.00 1.90
874 915 1.055849 ATATGGCTGTCGGGTGCATA 58.944 50.000 0.00 0.00 0.00 3.14
879 920 2.044806 GCTCCATATGGCTGTCGGGT 62.045 60.000 17.58 0.00 34.44 5.28
881 922 1.302033 GGCTCCATATGGCTGTCGG 60.302 63.158 17.58 4.01 34.44 4.79
921 962 1.346365 TAAGCTAAGTTGCGCAGACG 58.654 50.000 11.31 0.00 44.07 4.18
969 1010 1.903860 TCAGTTTACTATGCCACGGGT 59.096 47.619 0.00 0.00 0.00 5.28
970 1011 2.676342 GTTCAGTTTACTATGCCACGGG 59.324 50.000 0.00 0.00 0.00 5.28
1030 1076 1.073548 TTGGTTCCGGCCTTACCAC 59.926 57.895 17.14 0.28 41.42 4.16
1179 1242 0.889306 AAGCTAGACACTCCACGTCC 59.111 55.000 0.00 0.00 33.70 4.79
1287 1353 1.519719 GCTCTGGTTCTGAGGCGAT 59.480 57.895 0.00 0.00 31.52 4.58
1391 1465 1.384525 CCGAGGAACGATGAGAGAGT 58.615 55.000 0.00 0.00 45.77 3.24
1395 1469 1.320344 CCACCCGAGGAACGATGAGA 61.320 60.000 0.00 0.00 45.77 3.27
1399 1473 1.305046 AGACCACCCGAGGAACGAT 60.305 57.895 0.00 0.00 45.77 3.73
1909 2043 0.240411 GTGTACGTCGTCTCCTGCTT 59.760 55.000 0.00 0.00 0.00 3.91
2023 2160 2.811873 CGAGGCCCCTTTCCTGAATATG 60.812 54.545 0.00 0.00 33.24 1.78
2028 2165 2.840203 ATCCGAGGCCCCTTTCCTGA 62.840 60.000 0.00 0.00 33.24 3.86
2030 2167 2.042930 ATCCGAGGCCCCTTTCCT 59.957 61.111 0.00 0.00 36.46 3.36
2376 2528 1.236616 TGGTTGCAGCCATGAACTCG 61.237 55.000 19.51 0.00 32.81 4.18
2437 2589 9.599866 ACTGATAACAATCACGAAAGATGATAA 57.400 29.630 0.00 0.00 35.72 1.75
2449 2601 4.832248 TGGTCCTCACTGATAACAATCAC 58.168 43.478 0.00 0.00 0.00 3.06
2626 2864 1.757699 CTCTGGTACCTGGTAGGCTTC 59.242 57.143 17.82 0.00 39.63 3.86
2665 2903 4.002316 CGTTTATCGGGGTCCAGTTTTTA 58.998 43.478 0.00 0.00 35.71 1.52
2666 2904 2.815503 CGTTTATCGGGGTCCAGTTTTT 59.184 45.455 0.00 0.00 35.71 1.94
2667 2905 2.429478 CGTTTATCGGGGTCCAGTTTT 58.571 47.619 0.00 0.00 35.71 2.43
2668 2906 1.947212 GCGTTTATCGGGGTCCAGTTT 60.947 52.381 0.00 0.00 40.26 2.66
2671 2909 1.881252 CGCGTTTATCGGGGTCCAG 60.881 63.158 0.00 0.00 46.32 3.86
2733 3163 6.209192 TGCCATCTCATGTCAATTAAAGTTGT 59.791 34.615 0.00 0.00 0.00 3.32
2822 3253 0.753867 TAGTTGACGTGAGGTTGGCA 59.246 50.000 0.00 0.00 0.00 4.92
2854 3285 1.161843 CGTGGCTACCCGAACATTTT 58.838 50.000 0.00 0.00 0.00 1.82
2926 3357 5.300286 GCAAACATAGAGGTAGCAATGGAAT 59.700 40.000 0.00 0.00 0.00 3.01
2934 3365 5.639931 GCCTAATAGCAAACATAGAGGTAGC 59.360 44.000 0.00 0.00 0.00 3.58
3081 3515 7.749126 CGATGAACCTTTTTAAACTACATGACC 59.251 37.037 0.00 0.00 0.00 4.02
3112 3550 2.287547 TGCGCTGAATGGTTTCTCAAAC 60.288 45.455 9.73 0.00 40.65 2.93
3188 3644 6.866248 AGTAAATACACGGGAATTGCAAAAAG 59.134 34.615 1.71 0.00 0.00 2.27
3238 3694 9.356929 GCGTTTAGAAAAATGAAGAATTGTTTG 57.643 29.630 0.00 0.00 34.10 2.93
3366 3824 5.757886 TGTGAATCCACGAAGAACATTTTC 58.242 37.500 0.00 0.00 46.06 2.29


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

AutoCloner maintained by Alex Coulton.