Multiple sequence alignment - TraesCS7B01G270100

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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 TraesCS7B01G270100 chr7B 100.000 1730 0 0 1 1730 495303204 495301475 0.000000e+00 3195.0
1 TraesCS7B01G270100 chr7B 87.872 874 73 13 107 969 389135545 389136396 0.000000e+00 996.0
2 TraesCS7B01G270100 chr7B 100.000 429 0 0 2007 2435 495301198 495300770 0.000000e+00 793.0
3 TraesCS7B01G270100 chr7B 88.399 431 28 5 2007 2435 108513697 108513287 1.300000e-137 499.0
4 TraesCS7B01G270100 chr7B 94.040 302 15 2 329 629 389137464 389137763 2.850000e-124 455.0
5 TraesCS7B01G270100 chr7B 90.265 226 21 1 107 332 389136970 389137194 6.580000e-76 294.0
6 TraesCS7B01G270100 chr7D 90.894 604 41 7 867 1460 581129352 581128753 0.000000e+00 798.0
7 TraesCS7B01G270100 chr7D 91.015 601 38 6 867 1456 124618043 124618638 0.000000e+00 797.0
8 TraesCS7B01G270100 chr7D 84.110 837 99 28 634 1459 408566139 408565326 0.000000e+00 778.0
9 TraesCS7B01G270100 chr7D 90.942 276 18 3 1455 1730 448440562 448440830 4.950000e-97 364.0
10 TraesCS7B01G270100 chr7D 89.892 277 26 2 1455 1730 307383322 307383047 2.980000e-94 355.0
11 TraesCS7B01G270100 chr7D 88.693 283 26 4 1449 1730 332474670 332474393 8.340000e-90 340.0
12 TraesCS7B01G270100 chr1D 90.986 588 38 2 869 1456 288836667 288837239 0.000000e+00 778.0
13 TraesCS7B01G270100 chr1D 88.835 412 30 7 587 987 32888630 32888224 2.180000e-135 492.0
14 TraesCS7B01G270100 chr1D 82.440 336 24 6 2102 2435 126626881 126626579 6.680000e-66 261.0
15 TraesCS7B01G270100 chr1D 85.903 227 22 8 107 328 488644885 488644664 1.460000e-57 233.0
16 TraesCS7B01G270100 chr1B 90.333 600 44 4 867 1456 29292360 29291765 0.000000e+00 774.0
17 TraesCS7B01G270100 chr1B 89.493 276 29 0 1455 1730 155669554 155669829 1.390000e-92 350.0
18 TraesCS7B01G270100 chr1B 85.714 224 22 8 107 327 616024963 616024747 6.770000e-56 228.0
19 TraesCS7B01G270100 chr1B 84.753 223 26 6 107 327 616026307 616026091 1.470000e-52 217.0
20 TraesCS7B01G270100 chr5A 89.850 601 52 6 867 1460 304461392 304461990 0.000000e+00 763.0
21 TraesCS7B01G270100 chr5A 88.136 590 61 6 874 1460 607480132 607479549 0.000000e+00 693.0
22 TraesCS7B01G270100 chr5D 90.169 590 51 7 868 1456 505017316 505016733 0.000000e+00 761.0
23 TraesCS7B01G270100 chr5D 87.306 386 31 11 587 961 41800899 41800521 2.240000e-115 425.0
24 TraesCS7B01G270100 chr5D 97.368 38 1 0 536 573 532833121 532833084 5.620000e-07 65.8
25 TraesCS7B01G270100 chr6B 91.423 548 45 2 867 1413 707811739 707812285 0.000000e+00 750.0
26 TraesCS7B01G270100 chr6B 88.631 431 27 5 2007 2435 432383146 432382736 2.790000e-139 505.0
27 TraesCS7B01G270100 chr6B 86.207 377 29 6 2062 2435 207220760 207221116 1.060000e-103 387.0
28 TraesCS7B01G270100 chr6B 85.953 299 22 4 2137 2435 217960856 217961134 3.930000e-78 302.0
29 TraesCS7B01G270100 chr6B 84.821 224 23 9 107 327 691455414 691455199 5.270000e-52 215.0
30 TraesCS7B01G270100 chr6B 84.375 224 25 8 107 327 691453488 691453272 6.820000e-51 211.0
31 TraesCS7B01G270100 chr6D 86.638 696 69 11 613 1288 225874248 225873557 0.000000e+00 749.0
32 TraesCS7B01G270100 chr6D 81.850 865 120 24 613 1460 225872938 225872094 0.000000e+00 693.0
33 TraesCS7B01G270100 chr6D 86.072 359 46 4 594 950 18304575 18304931 1.370000e-102 383.0
34 TraesCS7B01G270100 chr6D 89.855 276 28 0 1455 1730 159470288 159470563 2.980000e-94 355.0
35 TraesCS7B01G270100 chrUn 81.456 879 105 36 613 1460 321936311 321935460 0.000000e+00 667.0
36 TraesCS7B01G270100 chrUn 89.189 259 22 5 318 575 70553803 70553550 3.910000e-83 318.0
37 TraesCS7B01G270100 chrUn 84.167 120 15 4 370 485 395585261 395585142 1.980000e-21 113.0
38 TraesCS7B01G270100 chrUn 95.000 40 2 0 536 575 33065444 33065483 2.020000e-06 63.9
39 TraesCS7B01G270100 chr4B 88.631 431 27 7 2007 2435 82802476 82802066 2.790000e-139 505.0
40 TraesCS7B01G270100 chr4B 88.657 432 26 6 2007 2435 137247925 137248336 2.790000e-139 505.0
41 TraesCS7B01G270100 chr4B 88.426 432 27 7 2007 2435 361417162 361416751 1.300000e-137 499.0
42 TraesCS7B01G270100 chr4B 93.359 256 16 1 1455 1710 361417504 361417250 6.360000e-101 377.0
43 TraesCS7B01G270100 chr4B 87.415 294 17 4 2142 2435 506661528 506661255 1.090000e-83 320.0
44 TraesCS7B01G270100 chr2B 88.605 430 28 4 2007 2435 139039575 139039984 1.000000e-138 503.0
45 TraesCS7B01G270100 chr2B 93.275 342 22 1 2007 2347 440615735 440616076 1.000000e-138 503.0
46 TraesCS7B01G270100 chr2B 92.711 343 23 2 2007 2347 310122204 310122546 6.050000e-136 494.0
47 TraesCS7B01G270100 chr2B 89.394 396 21 4 2038 2432 23761394 23761769 1.690000e-131 479.0
48 TraesCS7B01G270100 chr2B 87.167 413 31 5 2025 2435 298508252 298507860 1.330000e-122 449.0
49 TraesCS7B01G270100 chr2B 89.781 274 21 3 1457 1730 415100370 415100636 6.450000e-91 344.0
50 TraesCS7B01G270100 chr3B 88.140 430 29 5 2008 2435 246353213 246352804 2.180000e-135 492.0
51 TraesCS7B01G270100 chr3B 92.920 339 22 2 2010 2346 369884647 369884309 2.180000e-135 492.0
52 TraesCS7B01G270100 chr3B 84.071 226 26 9 106 328 354976065 354975847 2.450000e-50 209.0
53 TraesCS7B01G270100 chr3D 86.458 384 43 1 611 985 499949307 499949690 1.740000e-111 412.0
54 TraesCS7B01G270100 chr3D 92.095 253 20 0 1458 1710 614866644 614866392 8.280000e-95 357.0
55 TraesCS7B01G270100 chr3D 92.308 91 5 2 2347 2435 150894230 150894140 7.070000e-26 128.0
56 TraesCS7B01G270100 chr2D 86.480 392 31 8 587 969 234771509 234771131 6.270000e-111 411.0
57 TraesCS7B01G270100 chr2D 86.630 359 44 4 594 950 573454969 573454613 6.310000e-106 394.0
58 TraesCS7B01G270100 chr2D 87.069 348 42 3 591 936 252170384 252170730 8.160000e-105 390.0
59 TraesCS7B01G270100 chr2D 89.781 274 28 0 1455 1728 76017807 76018080 3.850000e-93 351.0
60 TraesCS7B01G270100 chr2D 91.748 206 13 3 339 542 56886149 56885946 1.430000e-72 283.0
61 TraesCS7B01G270100 chr4D 86.630 359 44 4 594 950 452395225 452395581 6.310000e-106 394.0
62 TraesCS7B01G270100 chr7A 85.714 378 46 5 611 985 355196927 355196555 2.270000e-105 392.0
63 TraesCS7B01G270100 chr7A 89.961 259 23 2 318 575 528929348 528929604 5.020000e-87 331.0
64 TraesCS7B01G270100 chr4A 83.123 397 50 11 570 961 13583656 13584040 1.790000e-91 346.0
65 TraesCS7B01G270100 chr4A 84.375 224 29 6 107 327 607933543 607933763 5.270000e-52 215.0
66 TraesCS7B01G270100 chr3A 86.000 300 20 10 2137 2435 345788146 345787868 3.930000e-78 302.0
67 TraesCS7B01G270100 chr1A 84.167 120 15 4 370 485 584124038 584124157 1.980000e-21 113.0
68 TraesCS7B01G270100 chr1A 84.167 120 15 4 370 485 584159529 584159648 1.980000e-21 113.0
69 TraesCS7B01G270100 chr1A 84.167 120 15 4 370 485 584191594 584191713 1.980000e-21 113.0


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 TraesCS7B01G270100 chr7B 495300770 495303204 2434 True 1994.000000 3195 100.000000 1 2435 2 chr7B.!!$R2 2434
1 TraesCS7B01G270100 chr7B 389135545 389137763 2218 False 581.666667 996 90.725667 107 969 3 chr7B.!!$F1 862
2 TraesCS7B01G270100 chr7D 581128753 581129352 599 True 798.000000 798 90.894000 867 1460 1 chr7D.!!$R4 593
3 TraesCS7B01G270100 chr7D 124618043 124618638 595 False 797.000000 797 91.015000 867 1456 1 chr7D.!!$F1 589
4 TraesCS7B01G270100 chr7D 408565326 408566139 813 True 778.000000 778 84.110000 634 1459 1 chr7D.!!$R3 825
5 TraesCS7B01G270100 chr1D 288836667 288837239 572 False 778.000000 778 90.986000 869 1456 1 chr1D.!!$F1 587
6 TraesCS7B01G270100 chr1B 29291765 29292360 595 True 774.000000 774 90.333000 867 1456 1 chr1B.!!$R1 589
7 TraesCS7B01G270100 chr1B 616024747 616026307 1560 True 222.500000 228 85.233500 107 327 2 chr1B.!!$R2 220
8 TraesCS7B01G270100 chr5A 304461392 304461990 598 False 763.000000 763 89.850000 867 1460 1 chr5A.!!$F1 593
9 TraesCS7B01G270100 chr5A 607479549 607480132 583 True 693.000000 693 88.136000 874 1460 1 chr5A.!!$R1 586
10 TraesCS7B01G270100 chr5D 505016733 505017316 583 True 761.000000 761 90.169000 868 1456 1 chr5D.!!$R2 588
11 TraesCS7B01G270100 chr6B 707811739 707812285 546 False 750.000000 750 91.423000 867 1413 1 chr6B.!!$F3 546
12 TraesCS7B01G270100 chr6B 691453272 691455414 2142 True 213.000000 215 84.598000 107 327 2 chr6B.!!$R2 220
13 TraesCS7B01G270100 chr6D 225872094 225874248 2154 True 721.000000 749 84.244000 613 1460 2 chr6D.!!$R1 847
14 TraesCS7B01G270100 chrUn 321935460 321936311 851 True 667.000000 667 81.456000 613 1460 1 chrUn.!!$R2 847
15 TraesCS7B01G270100 chr4B 361416751 361417504 753 True 438.000000 499 90.892500 1455 2435 2 chr4B.!!$R3 980

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
101 102 0.298707 CTACATGCACGACGACATGC 59.701 55.0 25.01 15.84 46.08 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 3927 0.107312 CCATCCTCAACCTCTGCCTG 60.107 60.0 0.0 0.0 0.0 4.85 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
63 64 7.953158 ACCTCTTCATTTATGATATGTCACG 57.047 36.000 0.00 0.00 37.14 4.35
64 65 7.500992 ACCTCTTCATTTATGATATGTCACGT 58.499 34.615 0.00 0.00 37.14 4.49
65 66 7.439356 ACCTCTTCATTTATGATATGTCACGTG 59.561 37.037 9.94 9.94 37.14 4.49
66 67 7.095481 CCTCTTCATTTATGATATGTCACGTGG 60.095 40.741 17.00 0.00 37.14 4.94
67 68 5.922739 TCATTTATGATATGTCACGTGGC 57.077 39.130 14.58 14.58 37.14 5.01
68 69 5.363939 TCATTTATGATATGTCACGTGGCA 58.636 37.500 27.05 27.05 37.14 4.92
69 70 5.236263 TCATTTATGATATGTCACGTGGCAC 59.764 40.000 27.45 13.86 37.14 5.01
70 71 2.689553 ATGATATGTCACGTGGCACA 57.310 45.000 27.45 16.14 37.14 4.57
71 72 2.464157 TGATATGTCACGTGGCACAA 57.536 45.000 27.45 17.33 44.16 3.33
72 73 2.772287 TGATATGTCACGTGGCACAAA 58.228 42.857 27.45 14.55 44.16 2.83
73 74 3.142174 TGATATGTCACGTGGCACAAAA 58.858 40.909 27.45 11.83 44.16 2.44
74 75 3.188254 TGATATGTCACGTGGCACAAAAG 59.812 43.478 27.45 3.40 44.16 2.27
75 76 1.674359 ATGTCACGTGGCACAAAAGA 58.326 45.000 27.45 0.00 44.16 2.52
76 77 1.013596 TGTCACGTGGCACAAAAGAG 58.986 50.000 20.89 2.21 44.16 2.85
77 78 0.317020 GTCACGTGGCACAAAAGAGC 60.317 55.000 16.80 0.00 44.16 4.09
78 79 0.746204 TCACGTGGCACAAAAGAGCA 60.746 50.000 19.09 0.00 44.16 4.26
79 80 0.317269 CACGTGGCACAAAAGAGCAG 60.317 55.000 19.09 0.00 44.16 4.24
80 81 0.748005 ACGTGGCACAAAAGAGCAGT 60.748 50.000 19.09 0.55 44.16 4.40
81 82 0.317269 CGTGGCACAAAAGAGCAGTG 60.317 55.000 19.09 0.00 44.16 3.66
88 89 3.818387 CACAAAAGAGCAGTGCTACATG 58.182 45.455 19.77 16.49 39.88 3.21
89 90 2.227388 ACAAAAGAGCAGTGCTACATGC 59.773 45.455 19.77 4.98 39.88 4.06
98 99 4.162640 GCTACATGCACGACGACA 57.837 55.556 0.00 0.00 42.31 4.35
99 100 2.665777 GCTACATGCACGACGACAT 58.334 52.632 0.00 1.70 42.31 3.06
101 102 0.298707 CTACATGCACGACGACATGC 59.701 55.000 25.01 15.84 46.08 4.06
104 105 2.338257 TGCACGACGACATGCAGA 59.662 55.556 4.21 0.00 46.63 4.26
105 106 2.021584 TGCACGACGACATGCAGAC 61.022 57.895 4.21 0.00 46.63 3.51
154 155 0.323957 TCCTCTCACTCGAACGGAGA 59.676 55.000 9.25 9.25 46.23 3.71
157 158 2.010497 CTCTCACTCGAACGGAGATGA 58.990 52.381 9.85 0.00 46.23 2.92
166 167 4.878439 TCGAACGGAGATGAAAGAAGAAA 58.122 39.130 0.00 0.00 0.00 2.52
171 172 6.305693 ACGGAGATGAAAGAAGAAAAACAG 57.694 37.500 0.00 0.00 0.00 3.16
191 192 4.709397 ACAGTGGACACAAAAGATTTTCCA 59.291 37.500 5.14 0.00 0.00 3.53
192 193 5.186797 ACAGTGGACACAAAAGATTTTCCAA 59.813 36.000 5.14 0.00 0.00 3.53
196 197 4.202070 GGACACAAAAGATTTTCCAACCGA 60.202 41.667 0.00 0.00 0.00 4.69
268 269 1.135139 ACACTGGCTACATCGCTACAG 59.865 52.381 0.00 0.00 0.00 2.74
272 273 0.876342 GGCTACATCGCTACAGCACC 60.876 60.000 1.61 0.00 42.21 5.01
417 433 1.221414 CGCCATGAAGCTAGCTAACC 58.779 55.000 19.70 10.98 0.00 2.85
430 446 3.967332 AGCTAACCAACTAACCGCTTA 57.033 42.857 0.00 0.00 0.00 3.09
444 461 1.922545 CCGCTTAACCAAGTACTACGC 59.077 52.381 0.00 0.00 34.00 4.42
480 497 3.680786 CACGGCCGAGAGTCCACA 61.681 66.667 35.90 0.00 0.00 4.17
485 502 2.573869 CCGAGAGTCCACACGCAT 59.426 61.111 0.00 0.00 0.00 4.73
486 503 1.807226 CCGAGAGTCCACACGCATA 59.193 57.895 0.00 0.00 0.00 3.14
496 513 5.016831 AGTCCACACGCATATATCCATCTA 58.983 41.667 0.00 0.00 0.00 1.98
528 545 3.998672 TCCGCCGGTCTCCACAAC 61.999 66.667 1.63 0.00 0.00 3.32
529 546 4.003788 CCGCCGGTCTCCACAACT 62.004 66.667 1.90 0.00 0.00 3.16
530 547 2.642254 CCGCCGGTCTCCACAACTA 61.642 63.158 1.90 0.00 0.00 2.24
577 620 0.518195 CGCACATGCATGAACTGTCA 59.482 50.000 32.75 0.00 42.21 3.58
579 622 1.726892 GCACATGCATGAACTGTCACG 60.727 52.381 32.75 9.84 41.59 4.35
623 712 0.734889 GCACGAGCATGGCTTATTGT 59.265 50.000 0.00 0.00 39.88 2.71
631 720 3.828451 AGCATGGCTTATTGTCAACACTT 59.172 39.130 0.00 0.00 33.89 3.16
681 776 0.751643 AAGTTGTTGCAGCTCCCGTT 60.752 50.000 1.17 0.00 0.00 4.44
686 781 1.153066 TTGCAGCTCCCGTTGTTGA 60.153 52.632 0.00 0.00 0.00 3.18
1024 1393 2.972505 CCGCCAGTGACAAACGCT 60.973 61.111 0.00 0.00 40.24 5.07
1040 1409 1.889573 GCTGGAAGGATGTAGCCGC 60.890 63.158 0.00 0.00 0.00 6.53
1067 1436 2.254350 CGGACTCGAGCACAACGA 59.746 61.111 13.61 0.00 39.00 3.85
1198 1595 2.046285 GCTTATTGCCCTGCACCGT 61.046 57.895 0.00 0.00 38.71 4.83
1506 3760 0.178301 GATGGGGAAGTCCTCGAACC 59.822 60.000 0.00 0.00 40.19 3.62
1510 3764 1.154073 GGAAGTCCTCGAACCGACG 60.154 63.158 0.00 0.00 34.10 5.12
1541 3795 3.620785 GCTGGCGGATCGGAGGAT 61.621 66.667 4.16 0.00 34.96 3.24
1550 3804 1.587043 GATCGGAGGATCGGCGATGA 61.587 60.000 29.20 17.84 39.11 2.92
1552 3806 2.049985 GGAGGATCGGCGATGACG 60.050 66.667 29.20 0.00 38.26 4.35
1568 3822 2.307768 TGACGGATCGATAAAGAGCCT 58.692 47.619 0.00 0.00 44.03 4.58
1577 3831 1.346068 GATAAAGAGCCTGCGGAGGAT 59.654 52.381 29.09 23.05 42.28 3.24
1580 3834 1.965754 AAGAGCCTGCGGAGGATGAC 61.966 60.000 29.09 9.77 38.46 3.06
1591 3845 1.677637 GAGGATGACGGGGACACCTC 61.678 65.000 0.00 0.00 37.37 3.85
1643 3897 1.470979 GCCGCGATAAACCTCTCTTGA 60.471 52.381 8.23 0.00 0.00 3.02
1696 3950 0.179936 CAGAGGTTGAGGATGGAGGC 59.820 60.000 0.00 0.00 0.00 4.70
1700 3954 4.161295 TTGAGGATGGAGGCGGCG 62.161 66.667 0.51 0.51 0.00 6.46
2033 4287 1.208535 TGTTGGAGGAAATACCGCGAT 59.791 47.619 8.23 0.00 44.74 4.58
2036 4290 4.062991 GTTGGAGGAAATACCGCGATAAT 58.937 43.478 8.23 0.00 44.74 1.28
2068 4322 0.905809 TAGGCGGGAGTAACAAGGCA 60.906 55.000 0.00 0.00 0.00 4.75
2085 4575 6.755206 ACAAGGCAGGGTTACTAAAAATTTC 58.245 36.000 0.00 0.00 0.00 2.17
2100 4591 2.550830 ATTTCGATAAGGGCGAGCAT 57.449 45.000 0.00 0.00 39.14 3.79
2104 4595 3.777465 TCGATAAGGGCGAGCATATAC 57.223 47.619 0.00 0.00 33.33 1.47
2150 4642 0.249489 CGGAGTATTTGGGGAGCGAG 60.249 60.000 0.00 0.00 0.00 5.03
2178 4670 4.920112 TGACACGCCGGTTGTGGG 62.920 66.667 25.89 9.36 41.64 4.61
2186 4678 2.347490 CGGTTGTGGGCTGTAGCT 59.653 61.111 3.63 0.00 41.70 3.32
2190 4682 1.005037 TTGTGGGCTGTAGCTGACG 60.005 57.895 0.00 0.00 41.70 4.35
2206 4698 4.088421 CGCACCTTCTCGCGTAAT 57.912 55.556 5.77 0.00 46.23 1.89
2213 4705 3.004419 CACCTTCTCGCGTAATCCATAGA 59.996 47.826 5.77 0.00 0.00 1.98
2227 4719 6.492007 AATCCATAGACGTACTATACACCG 57.508 41.667 0.00 0.00 39.50 4.94
2334 4996 8.780616 TGATTTGAATTACATAATGGGGTCAT 57.219 30.769 0.00 0.00 34.56 3.06
2347 5009 0.250901 GGGTCATAGCGGCAATGGAT 60.251 55.000 1.45 0.00 0.00 3.41
2348 5010 0.877071 GGTCATAGCGGCAATGGATG 59.123 55.000 1.45 0.00 0.00 3.51
2350 5012 0.250858 TCATAGCGGCAATGGATGGG 60.251 55.000 1.45 0.00 0.00 4.00
2351 5013 0.538057 CATAGCGGCAATGGATGGGT 60.538 55.000 1.45 0.00 0.00 4.51
2352 5014 0.250901 ATAGCGGCAATGGATGGGTC 60.251 55.000 1.45 0.00 0.00 4.46
2353 5015 1.631071 TAGCGGCAATGGATGGGTCA 61.631 55.000 1.45 0.00 0.00 4.02
2354 5016 1.829533 GCGGCAATGGATGGGTCAT 60.830 57.895 0.00 0.00 0.00 3.06
2355 5017 0.537143 GCGGCAATGGATGGGTCATA 60.537 55.000 0.00 0.00 0.00 2.15
2356 5018 1.527034 CGGCAATGGATGGGTCATAG 58.473 55.000 0.00 0.00 0.00 2.23
2357 5019 1.251251 GGCAATGGATGGGTCATAGC 58.749 55.000 0.00 0.00 0.00 2.97
2358 5020 0.877071 GCAATGGATGGGTCATAGCG 59.123 55.000 0.00 0.00 0.00 4.26
2359 5021 1.527034 CAATGGATGGGTCATAGCGG 58.473 55.000 0.00 0.00 0.00 5.52
2360 5022 0.250901 AATGGATGGGTCATAGCGGC 60.251 55.000 0.00 0.00 0.00 6.53
2361 5023 1.418097 ATGGATGGGTCATAGCGGCA 61.418 55.000 1.45 0.00 0.00 5.69
2362 5024 1.148273 GGATGGGTCATAGCGGCAA 59.852 57.895 1.45 0.00 0.00 4.52
2363 5025 0.250901 GGATGGGTCATAGCGGCAAT 60.251 55.000 1.45 0.00 0.00 3.56
2364 5026 0.877071 GATGGGTCATAGCGGCAATG 59.123 55.000 1.45 0.00 0.00 2.82
2365 5027 0.473755 ATGGGTCATAGCGGCAATGA 59.526 50.000 1.45 0.00 0.00 2.57
2366 5028 0.254462 TGGGTCATAGCGGCAATGAA 59.746 50.000 1.45 0.00 35.23 2.57
2367 5029 1.133823 TGGGTCATAGCGGCAATGAAT 60.134 47.619 1.45 0.00 35.23 2.57
2368 5030 2.105649 TGGGTCATAGCGGCAATGAATA 59.894 45.455 1.45 0.00 35.23 1.75
2369 5031 3.146066 GGGTCATAGCGGCAATGAATAA 58.854 45.455 1.45 0.00 35.23 1.40
2384 5046 8.545420 GGCAATGAATAATGTTTGAATTGCTAG 58.455 33.333 14.81 0.00 44.78 3.42
2395 5057 7.826690 TGTTTGAATTGCTAGACCTTTTATCC 58.173 34.615 0.00 0.00 0.00 2.59
2397 5059 5.741011 TGAATTGCTAGACCTTTTATCCGT 58.259 37.500 0.00 0.00 0.00 4.69
2402 5064 4.098960 TGCTAGACCTTTTATCCGTAGTGG 59.901 45.833 0.00 0.00 40.09 4.00
2428 5090 6.592220 ACATGCAACTATATGTGTGTCGTAAA 59.408 34.615 0.00 0.00 36.26 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.556144 AAGGGAAAACCCGTAGTGAC 57.444 50.000 0.00 0.00 41.63 3.67
14 15 3.581265 AAAAGGGAAAACCCGTAGTGA 57.419 42.857 0.00 0.00 41.63 3.41
37 38 9.476202 CGTGACATATCATAAATGAAGAGGTTA 57.524 33.333 0.00 0.00 40.69 2.85
38 39 7.987458 ACGTGACATATCATAAATGAAGAGGTT 59.013 33.333 0.00 0.00 40.69 3.50
39 40 7.439356 CACGTGACATATCATAAATGAAGAGGT 59.561 37.037 10.90 0.00 40.69 3.85
40 41 7.095481 CCACGTGACATATCATAAATGAAGAGG 60.095 40.741 19.30 0.00 40.69 3.69
41 42 7.570140 GCCACGTGACATATCATAAATGAAGAG 60.570 40.741 19.30 0.00 40.69 2.85
42 43 6.202762 GCCACGTGACATATCATAAATGAAGA 59.797 38.462 19.30 0.00 40.69 2.87
43 44 6.018016 TGCCACGTGACATATCATAAATGAAG 60.018 38.462 19.30 0.00 40.69 3.02
44 45 5.819901 TGCCACGTGACATATCATAAATGAA 59.180 36.000 19.30 0.00 40.69 2.57
45 46 5.236263 GTGCCACGTGACATATCATAAATGA 59.764 40.000 19.30 0.00 41.70 2.57
46 47 5.007528 TGTGCCACGTGACATATCATAAATG 59.992 40.000 19.30 0.00 37.14 2.32
47 48 5.122519 TGTGCCACGTGACATATCATAAAT 58.877 37.500 19.30 0.00 37.14 1.40
48 49 4.508662 TGTGCCACGTGACATATCATAAA 58.491 39.130 19.30 0.00 37.14 1.40
49 50 4.130286 TGTGCCACGTGACATATCATAA 57.870 40.909 19.30 0.00 37.14 1.90
50 51 3.810310 TGTGCCACGTGACATATCATA 57.190 42.857 19.30 0.63 37.14 2.15
51 52 2.689553 TGTGCCACGTGACATATCAT 57.310 45.000 19.30 0.00 37.14 2.45
52 53 2.464157 TTGTGCCACGTGACATATCA 57.536 45.000 19.30 2.98 0.00 2.15
53 54 3.435327 TCTTTTGTGCCACGTGACATATC 59.565 43.478 19.30 0.00 0.00 1.63
54 55 3.407698 TCTTTTGTGCCACGTGACATAT 58.592 40.909 19.30 0.00 0.00 1.78
55 56 2.805671 CTCTTTTGTGCCACGTGACATA 59.194 45.455 19.30 7.28 0.00 2.29
56 57 1.603802 CTCTTTTGTGCCACGTGACAT 59.396 47.619 19.30 0.00 0.00 3.06
57 58 1.013596 CTCTTTTGTGCCACGTGACA 58.986 50.000 19.30 9.38 0.00 3.58
58 59 0.317020 GCTCTTTTGTGCCACGTGAC 60.317 55.000 19.30 5.85 33.24 3.67
59 60 0.746204 TGCTCTTTTGTGCCACGTGA 60.746 50.000 19.30 0.00 38.08 4.35
60 61 0.317269 CTGCTCTTTTGTGCCACGTG 60.317 55.000 9.08 9.08 38.08 4.49
61 62 0.748005 ACTGCTCTTTTGTGCCACGT 60.748 50.000 0.00 0.00 38.08 4.49
62 63 0.317269 CACTGCTCTTTTGTGCCACG 60.317 55.000 0.00 0.00 38.08 4.94
63 64 3.557207 CACTGCTCTTTTGTGCCAC 57.443 52.632 0.00 0.00 38.08 5.01
67 68 3.818387 CATGTAGCACTGCTCTTTTGTG 58.182 45.455 6.86 0.00 40.44 3.33
68 69 2.227388 GCATGTAGCACTGCTCTTTTGT 59.773 45.455 6.86 0.00 44.79 2.83
69 70 2.860062 GCATGTAGCACTGCTCTTTTG 58.140 47.619 6.86 3.11 44.79 2.44
81 82 0.298707 CATGTCGTCGTGCATGTAGC 59.701 55.000 17.79 0.00 45.96 3.58
89 90 0.664466 ACAGTCTGCATGTCGTCGTG 60.664 55.000 0.00 0.00 0.00 4.35
90 91 0.032130 AACAGTCTGCATGTCGTCGT 59.968 50.000 0.00 0.00 0.00 4.34
91 92 0.436150 CAACAGTCTGCATGTCGTCG 59.564 55.000 0.00 0.00 0.00 5.12
92 93 1.783284 TCAACAGTCTGCATGTCGTC 58.217 50.000 0.00 0.00 0.00 4.20
93 94 2.238942 TTCAACAGTCTGCATGTCGT 57.761 45.000 0.00 0.00 0.00 4.34
94 95 2.349817 GGTTTCAACAGTCTGCATGTCG 60.350 50.000 0.00 0.00 0.00 4.35
95 96 2.349817 CGGTTTCAACAGTCTGCATGTC 60.350 50.000 0.00 0.00 0.00 3.06
96 97 1.603802 CGGTTTCAACAGTCTGCATGT 59.396 47.619 0.00 0.00 0.00 3.21
97 98 1.664016 GCGGTTTCAACAGTCTGCATG 60.664 52.381 0.00 0.00 33.09 4.06
98 99 0.593128 GCGGTTTCAACAGTCTGCAT 59.407 50.000 0.00 0.00 33.09 3.96
99 100 0.746204 TGCGGTTTCAACAGTCTGCA 60.746 50.000 0.00 0.00 39.41 4.41
100 101 0.040958 CTGCGGTTTCAACAGTCTGC 60.041 55.000 0.00 0.00 0.00 4.26
101 102 0.040958 GCTGCGGTTTCAACAGTCTG 60.041 55.000 0.00 0.00 33.87 3.51
102 103 1.166531 GGCTGCGGTTTCAACAGTCT 61.167 55.000 0.00 0.00 33.27 3.24
103 104 1.282875 GGCTGCGGTTTCAACAGTC 59.717 57.895 0.00 0.00 33.87 3.51
104 105 2.193536 GGGCTGCGGTTTCAACAGT 61.194 57.895 0.00 0.00 33.87 3.55
105 106 1.856265 GAGGGCTGCGGTTTCAACAG 61.856 60.000 0.00 0.00 34.48 3.16
154 155 6.152661 TGTGTCCACTGTTTTTCTTCTTTCAT 59.847 34.615 0.00 0.00 0.00 2.57
157 158 5.975693 TGTGTCCACTGTTTTTCTTCTTT 57.024 34.783 0.00 0.00 0.00 2.52
166 167 6.106003 GGAAAATCTTTTGTGTCCACTGTTT 58.894 36.000 0.00 0.00 0.00 2.83
171 172 4.808895 GGTTGGAAAATCTTTTGTGTCCAC 59.191 41.667 0.00 0.00 0.00 4.02
225 226 2.876581 AGAGGAAAAAGATTTGGGCGT 58.123 42.857 0.00 0.00 0.00 5.68
268 269 2.738013 ACTCTTGTAAGTACCGGTGC 57.262 50.000 19.93 17.74 0.00 5.01
293 295 4.530553 TGAACTGTGTATAAAGCTCCCTCA 59.469 41.667 0.00 0.00 0.00 3.86
361 363 1.278985 CATGAGTTAGTGGGTGAGCCA 59.721 52.381 0.00 0.00 36.17 4.75
417 433 4.992951 AGTACTTGGTTAAGCGGTTAGTTG 59.007 41.667 7.20 1.25 37.43 3.16
430 446 1.340889 TCCAACGCGTAGTACTTGGTT 59.659 47.619 21.26 7.03 31.73 3.67
480 497 5.237996 GCATGCATTAGATGGATATATGCGT 59.762 40.000 14.21 0.00 39.45 5.24
485 502 5.882000 GTGGTGCATGCATTAGATGGATATA 59.118 40.000 25.64 0.00 39.45 0.86
486 503 4.703575 GTGGTGCATGCATTAGATGGATAT 59.296 41.667 25.64 0.00 39.45 1.63
496 513 2.689785 CGGACGTGGTGCATGCATT 61.690 57.895 25.64 6.04 0.00 3.56
528 545 0.250124 TGGCCAGGTCGTGTGTTTAG 60.250 55.000 0.00 0.00 0.00 1.85
529 546 0.250124 CTGGCCAGGTCGTGTGTTTA 60.250 55.000 26.14 0.00 0.00 2.01
530 547 1.525995 CTGGCCAGGTCGTGTGTTT 60.526 57.895 26.14 0.00 0.00 2.83
604 693 0.734889 ACAATAAGCCATGCTCGTGC 59.265 50.000 1.71 1.71 38.25 5.34
609 698 3.424703 AGTGTTGACAATAAGCCATGCT 58.575 40.909 0.00 0.00 42.56 3.79
623 712 2.712087 TGGCTTAAGGGGTAAGTGTTGA 59.288 45.455 4.29 0.00 41.28 3.18
631 720 2.124411 GAGGTCATGGCTTAAGGGGTA 58.876 52.381 4.29 0.00 0.00 3.69
681 776 1.656263 GCTCGTGACGACGTCAACA 60.656 57.895 30.68 18.92 44.49 3.33
714 815 2.224159 ATTGTGCCAGGTCGGGTCT 61.224 57.895 0.00 0.00 34.06 3.85
748 888 1.439228 CGGAGTCGTGATGGAGCAT 59.561 57.895 0.00 0.00 0.00 3.79
1024 1393 1.220749 GTGCGGCTACATCCTTCCA 59.779 57.895 0.00 0.00 0.00 3.53
1067 1436 2.125961 GGGAGGAGGCGTATGTCGT 61.126 63.158 0.00 0.00 42.13 4.34
1134 1530 2.760159 GCGTGTTATGGGTGCGCAT 61.760 57.895 15.91 0.00 46.23 4.73
1198 1595 2.594303 CTGCGGTTGAGGCCACAA 60.594 61.111 11.97 11.97 0.00 3.33
1479 3733 1.383248 ACTTCCCCATCCTCCCTCG 60.383 63.158 0.00 0.00 0.00 4.63
1480 3734 1.057275 GGACTTCCCCATCCTCCCTC 61.057 65.000 0.00 0.00 31.75 4.30
1537 3791 1.867919 GATCCGTCATCGCCGATCCT 61.868 60.000 0.00 0.00 32.61 3.24
1550 3804 1.269831 GCAGGCTCTTTATCGATCCGT 60.270 52.381 0.00 0.00 0.00 4.69
1552 3806 1.423395 CGCAGGCTCTTTATCGATCC 58.577 55.000 0.00 0.00 0.00 3.36
1568 3822 4.770362 TCCCCGTCATCCTCCGCA 62.770 66.667 0.00 0.00 0.00 5.69
1673 3927 0.107312 CCATCCTCAACCTCTGCCTG 60.107 60.000 0.00 0.00 0.00 4.85
2017 4271 4.312443 TCAATTATCGCGGTATTTCCTCC 58.688 43.478 6.13 0.00 0.00 4.30
2033 4287 7.612633 ACTCCCGCCTAGTAAAATTTTCAATTA 59.387 33.333 6.72 0.00 0.00 1.40
2036 4290 5.318630 ACTCCCGCCTAGTAAAATTTTCAA 58.681 37.500 6.72 0.00 0.00 2.69
2068 4322 7.067859 GCCCTTATCGAAATTTTTAGTAACCCT 59.932 37.037 0.00 0.00 0.00 4.34
2085 4575 3.784701 AGTATATGCTCGCCCTTATCG 57.215 47.619 0.00 0.00 0.00 2.92
2100 4591 5.607939 TCCCTCGCAATCTCAAAAGTATA 57.392 39.130 0.00 0.00 0.00 1.47
2104 4595 2.223433 GCATCCCTCGCAATCTCAAAAG 60.223 50.000 0.00 0.00 0.00 2.27
2168 4660 2.746277 GCTACAGCCCACAACCGG 60.746 66.667 0.00 0.00 34.31 5.28
2172 4664 1.005037 CGTCAGCTACAGCCCACAA 60.005 57.895 0.00 0.00 43.38 3.33
2178 4670 1.355066 GAAGGTGCGTCAGCTACAGC 61.355 60.000 11.04 0.00 41.59 4.40
2190 4682 0.459585 TGGATTACGCGAGAAGGTGC 60.460 55.000 15.93 0.00 0.00 5.01
2206 4698 4.991056 GTCGGTGTATAGTACGTCTATGGA 59.009 45.833 14.14 2.68 39.42 3.41
2213 4705 2.024176 ACCGTCGGTGTATAGTACGT 57.976 50.000 18.08 0.00 32.98 3.57
2227 4719 2.614057 CAAAATATCCTGGAGCACCGTC 59.386 50.000 1.52 0.00 39.42 4.79
2237 4729 6.539826 TGTGAGATGCAGTACAAAATATCCTG 59.460 38.462 0.00 0.00 0.00 3.86
2334 4996 1.148273 GACCCATCCATTGCCGCTA 59.852 57.895 0.00 0.00 0.00 4.26
2347 5009 0.254462 TTCATTGCCGCTATGACCCA 59.746 50.000 15.79 0.92 32.04 4.51
2348 5010 1.609208 ATTCATTGCCGCTATGACCC 58.391 50.000 15.79 0.00 32.04 4.46
2350 5012 5.362556 ACATTATTCATTGCCGCTATGAC 57.637 39.130 15.79 0.00 32.04 3.06
2351 5013 6.039159 TCAAACATTATTCATTGCCGCTATGA 59.961 34.615 12.69 12.69 0.00 2.15
2352 5014 6.207928 TCAAACATTATTCATTGCCGCTATG 58.792 36.000 8.34 8.34 0.00 2.23
2353 5015 6.389830 TCAAACATTATTCATTGCCGCTAT 57.610 33.333 0.00 0.00 0.00 2.97
2354 5016 5.826601 TCAAACATTATTCATTGCCGCTA 57.173 34.783 0.00 0.00 0.00 4.26
2355 5017 4.717233 TCAAACATTATTCATTGCCGCT 57.283 36.364 0.00 0.00 0.00 5.52
2356 5018 5.971895 ATTCAAACATTATTCATTGCCGC 57.028 34.783 0.00 0.00 0.00 6.53
2357 5019 6.036300 AGCAATTCAAACATTATTCATTGCCG 59.964 34.615 9.70 0.00 43.92 5.69
2358 5020 7.311364 AGCAATTCAAACATTATTCATTGCC 57.689 32.000 9.70 0.00 43.92 4.52
2359 5021 9.304731 TCTAGCAATTCAAACATTATTCATTGC 57.695 29.630 5.95 5.95 43.44 3.56
2361 5023 9.807649 GGTCTAGCAATTCAAACATTATTCATT 57.192 29.630 0.00 0.00 0.00 2.57
2362 5024 9.193806 AGGTCTAGCAATTCAAACATTATTCAT 57.806 29.630 0.00 0.00 0.00 2.57
2363 5025 8.579850 AGGTCTAGCAATTCAAACATTATTCA 57.420 30.769 0.00 0.00 0.00 2.57
2364 5026 9.860898 AAAGGTCTAGCAATTCAAACATTATTC 57.139 29.630 0.00 0.00 0.00 1.75
2368 5030 9.860898 GATAAAAGGTCTAGCAATTCAAACATT 57.139 29.630 0.00 0.00 0.00 2.71
2369 5031 8.470002 GGATAAAAGGTCTAGCAATTCAAACAT 58.530 33.333 0.00 0.00 0.00 2.71
2395 5057 5.175673 CACATATAGTTGCATGTCCACTACG 59.824 44.000 0.00 0.00 33.12 3.51
2397 5059 6.048509 CACACATATAGTTGCATGTCCACTA 58.951 40.000 0.00 0.00 33.12 2.74
2402 5064 4.566759 ACGACACACATATAGTTGCATGTC 59.433 41.667 0.00 0.00 33.12 3.06


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

AutoCloner maintained by Alex Coulton.