Multiple sequence alignment - TraesCS3B01G519000

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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 TraesCS3B01G519000 chr3B 100.000 5939 0 0 1 5939 762025363 762031301 0.000000e+00 10968.0
1 TraesCS3B01G519000 chr3B 95.601 591 23 1 4 591 497423506 497422916 0.000000e+00 944.0
2 TraesCS3B01G519000 chr3B 87.937 315 37 1 4629 4943 762099953 762100266 2.610000e-98 370.0
3 TraesCS3B01G519000 chr3B 77.372 548 107 14 5328 5866 242754800 242754261 5.780000e-80 309.0
4 TraesCS3B01G519000 chr3D 91.718 5313 323 53 666 5904 571996039 571990770 0.000000e+00 7265.0
5 TraesCS3B01G519000 chr3D 81.606 386 49 12 4662 5045 573072880 573073245 3.480000e-77 300.0
6 TraesCS3B01G519000 chr3D 92.727 110 8 0 5151 5260 572960993 572961102 6.160000e-35 159.0
7 TraesCS3B01G519000 chr3A 93.174 4688 210 54 646 5266 707082148 707086792 0.000000e+00 6783.0
8 TraesCS3B01G519000 chr3A 82.389 653 94 12 5253 5899 707087840 707088477 3.130000e-152 549.0
9 TraesCS3B01G519000 chr3A 86.032 315 43 1 4629 4943 707093624 707093937 2.650000e-88 337.0
10 TraesCS3B01G519000 chrUn 95.638 596 22 2 1 593 52968483 52969077 0.000000e+00 953.0
11 TraesCS3B01G519000 chrUn 78.912 147 22 5 3754 3897 7465003 7464863 2.280000e-14 91.6
12 TraesCS3B01G519000 chr6B 95.302 596 21 2 1 593 126744700 126744109 0.000000e+00 939.0
13 TraesCS3B01G519000 chr4B 95.134 596 26 1 1 593 4602353 4602948 0.000000e+00 937.0
14 TraesCS3B01G519000 chr7B 94.799 596 28 1 1 593 678279501 678280096 0.000000e+00 926.0
15 TraesCS3B01G519000 chr6D 92.953 596 39 1 1 593 129739786 129740381 0.000000e+00 865.0
16 TraesCS3B01G519000 chr6D 78.224 597 114 15 5314 5904 264689675 264690261 9.400000e-98 368.0
17 TraesCS3B01G519000 chr5A 90.741 594 51 2 4 593 670544107 670544700 0.000000e+00 789.0
18 TraesCS3B01G519000 chr5A 78.328 586 114 11 5327 5904 403706524 403705944 3.380000e-97 366.0
19 TraesCS3B01G519000 chr7D 90.620 597 49 4 4 593 630259760 630259164 0.000000e+00 785.0
20 TraesCS3B01G519000 chr7D 78.311 521 98 13 5314 5828 74954530 74955041 7.420000e-84 322.0
21 TraesCS3B01G519000 chr1A 89.404 604 60 2 4 603 84625515 84624912 0.000000e+00 758.0
22 TraesCS3B01G519000 chr1A 79.791 574 107 7 5339 5904 107468654 107469226 5.540000e-110 409.0
23 TraesCS3B01G519000 chr1A 78.912 147 22 5 3751 3894 521258792 521258932 2.280000e-14 91.6
24 TraesCS3B01G519000 chr1B 80.070 572 98 15 5342 5904 161986952 161987516 1.540000e-110 411.0
25 TraesCS3B01G519000 chr1B 79.592 147 21 5 3751 3894 575711709 575711849 4.900000e-16 97.1
26 TraesCS3B01G519000 chr1D 79.613 569 101 14 5316 5877 607192 606632 1.550000e-105 394.0
27 TraesCS3B01G519000 chr1D 78.767 146 24 4 3751 3894 425674406 425674546 2.280000e-14 91.6
28 TraesCS3B01G519000 chr1D 78.082 146 25 4 3751 3894 425571257 425571397 1.060000e-12 86.1
29 TraesCS3B01G519000 chr1D 83.544 79 11 2 3820 3897 47988304 47988227 8.260000e-09 73.1
30 TraesCS3B01G519000 chr1D 84.000 75 12 0 3820 3894 460621151 460621225 8.260000e-09 73.1
31 TraesCS3B01G519000 chr4A 77.453 581 114 15 5316 5887 185993977 185993405 1.230000e-86 331.0


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 TraesCS3B01G519000 chr3B 762025363 762031301 5938 False 10968 10968 100.0000 1 5939 1 chr3B.!!$F1 5938
1 TraesCS3B01G519000 chr3B 497422916 497423506 590 True 944 944 95.6010 4 591 1 chr3B.!!$R2 587
2 TraesCS3B01G519000 chr3B 242754261 242754800 539 True 309 309 77.3720 5328 5866 1 chr3B.!!$R1 538
3 TraesCS3B01G519000 chr3D 571990770 571996039 5269 True 7265 7265 91.7180 666 5904 1 chr3D.!!$R1 5238
4 TraesCS3B01G519000 chr3A 707082148 707088477 6329 False 3666 6783 87.7815 646 5899 2 chr3A.!!$F2 5253
5 TraesCS3B01G519000 chrUn 52968483 52969077 594 False 953 953 95.6380 1 593 1 chrUn.!!$F1 592
6 TraesCS3B01G519000 chr6B 126744109 126744700 591 True 939 939 95.3020 1 593 1 chr6B.!!$R1 592
7 TraesCS3B01G519000 chr4B 4602353 4602948 595 False 937 937 95.1340 1 593 1 chr4B.!!$F1 592
8 TraesCS3B01G519000 chr7B 678279501 678280096 595 False 926 926 94.7990 1 593 1 chr7B.!!$F1 592
9 TraesCS3B01G519000 chr6D 129739786 129740381 595 False 865 865 92.9530 1 593 1 chr6D.!!$F1 592
10 TraesCS3B01G519000 chr6D 264689675 264690261 586 False 368 368 78.2240 5314 5904 1 chr6D.!!$F2 590
11 TraesCS3B01G519000 chr5A 670544107 670544700 593 False 789 789 90.7410 4 593 1 chr5A.!!$F1 589
12 TraesCS3B01G519000 chr5A 403705944 403706524 580 True 366 366 78.3280 5327 5904 1 chr5A.!!$R1 577
13 TraesCS3B01G519000 chr7D 630259164 630259760 596 True 785 785 90.6200 4 593 1 chr7D.!!$R1 589
14 TraesCS3B01G519000 chr7D 74954530 74955041 511 False 322 322 78.3110 5314 5828 1 chr7D.!!$F1 514
15 TraesCS3B01G519000 chr1A 84624912 84625515 603 True 758 758 89.4040 4 603 1 chr1A.!!$R1 599
16 TraesCS3B01G519000 chr1A 107468654 107469226 572 False 409 409 79.7910 5339 5904 1 chr1A.!!$F1 565
17 TraesCS3B01G519000 chr1B 161986952 161987516 564 False 411 411 80.0700 5342 5904 1 chr1B.!!$F1 562
18 TraesCS3B01G519000 chr1D 606632 607192 560 True 394 394 79.6130 5316 5877 1 chr1D.!!$R1 561
19 TraesCS3B01G519000 chr4A 185993405 185993977 572 True 331 331 77.4530 5316 5887 1 chr4A.!!$R1 571

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
161 162 0.835971 TGGTGCAGGAGGAGTTGCTA 60.836 55.0 0.00 0.00 40.87 3.49 F
1203 1233 0.865769 GCAACATTCAGGTTCGTCGT 59.134 50.0 0.00 0.00 0.00 4.34 F
1289 1320 0.030908 GATCTACTCCCCTCAACGCG 59.969 60.0 3.53 3.53 0.00 6.01 F
1308 1339 0.243907 GGATGCATGCATGATGGCTC 59.756 55.0 36.73 20.92 36.70 4.70 F
1558 1607 0.307760 AGGAAAAGCTTCGTGTTGCG 59.692 50.0 0.00 0.00 43.01 4.85 F
3707 3760 0.244994 TGCTCTGCTTCTCGGAAGAC 59.755 55.0 15.23 8.59 35.39 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1289 1320 0.243907 GAGCCATCATGCATGCATCC 59.756 55.000 30.07 15.22 33.90 3.51 R
2584 2633 1.375908 GAACCTCGCCATGAGCACA 60.376 57.895 0.00 0.00 43.82 4.57 R
3563 3612 4.899239 GAGGATGCCGCACTCCCG 62.899 72.222 14.59 0.00 31.49 5.14 R
3675 3724 2.492881 AGCAGAGCATCGAGGATATGAG 59.507 50.000 14.65 0.00 42.67 2.90 R
3709 3764 0.901827 AGTGTGTCACCATCGGCATA 59.098 50.000 0.00 0.00 34.49 3.14 R
5475 6629 0.178990 GGACCAACACTTTGAGGGCT 60.179 55.000 0.00 0.00 34.24 5.19 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
161 162 0.835971 TGGTGCAGGAGGAGTTGCTA 60.836 55.000 0.00 0.00 40.87 3.49
199 200 2.335712 GGGAGCTTGGAGCAAACCG 61.336 63.158 2.47 0.00 45.56 4.44
374 375 6.908825 TCTGTTGTGGCATCTTTATTTGTAC 58.091 36.000 0.00 0.00 0.00 2.90
403 405 3.691609 GTGAGCTAGCTGCCAACTTTATT 59.308 43.478 24.99 0.00 44.23 1.40
612 621 5.991328 AAAGGTATACATGACGCATCTTG 57.009 39.130 5.01 0.00 36.34 3.02
613 622 3.393800 AGGTATACATGACGCATCTTGC 58.606 45.455 5.01 0.00 40.69 4.01
627 636 5.379757 GCATCTTGCGGAAATTGTTATTG 57.620 39.130 0.00 0.00 31.71 1.90
628 637 5.101628 GCATCTTGCGGAAATTGTTATTGA 58.898 37.500 0.00 0.00 31.71 2.57
629 638 5.230726 GCATCTTGCGGAAATTGTTATTGAG 59.769 40.000 0.00 0.00 31.71 3.02
630 639 6.554419 CATCTTGCGGAAATTGTTATTGAGA 58.446 36.000 0.00 0.00 0.00 3.27
631 640 6.757897 TCTTGCGGAAATTGTTATTGAGAT 57.242 33.333 0.00 0.00 0.00 2.75
632 641 6.785191 TCTTGCGGAAATTGTTATTGAGATC 58.215 36.000 0.00 0.00 0.00 2.75
633 642 6.374053 TCTTGCGGAAATTGTTATTGAGATCA 59.626 34.615 0.00 0.00 0.00 2.92
634 643 6.507958 TGCGGAAATTGTTATTGAGATCAA 57.492 33.333 0.00 0.00 40.51 2.57
636 645 7.546358 TGCGGAAATTGTTATTGAGATCAATT 58.454 30.769 12.96 0.00 43.48 2.32
637 646 8.034215 TGCGGAAATTGTTATTGAGATCAATTT 58.966 29.630 12.96 12.38 46.22 1.82
638 647 8.872845 GCGGAAATTGTTATTGAGATCAATTTT 58.127 29.630 12.96 7.45 44.74 1.82
649 658 4.452114 TGAGATCAATTTTGAGGTCACACG 59.548 41.667 0.00 0.00 41.08 4.49
662 671 1.105167 TCACACGGACACTCGAACCT 61.105 55.000 0.00 0.00 0.00 3.50
664 673 1.201647 CACACGGACACTCGAACCTAT 59.798 52.381 0.00 0.00 0.00 2.57
665 674 1.891150 ACACGGACACTCGAACCTATT 59.109 47.619 0.00 0.00 0.00 1.73
670 679 4.643784 ACGGACACTCGAACCTATTATCTT 59.356 41.667 0.00 0.00 0.00 2.40
701 714 7.598759 TCTTAGAATTCTTAGGCTTACGGAT 57.401 36.000 18.73 0.00 0.00 4.18
704 717 4.654262 AGAATTCTTAGGCTTACGGATGGA 59.346 41.667 0.88 0.00 0.00 3.41
778 792 2.380064 TTCTGGCCCATTGAACAACT 57.620 45.000 0.00 0.00 0.00 3.16
852 866 3.849953 GCGATGTGAACCGCGTCC 61.850 66.667 4.92 0.00 42.02 4.79
895 916 4.993705 ACAGTGGAAATAGGACTCCAAA 57.006 40.909 0.00 0.00 43.32 3.28
905 926 2.257207 AGGACTCCAAATCTCCAACGA 58.743 47.619 0.00 0.00 0.00 3.85
912 933 3.260632 TCCAAATCTCCAACGATCAGACA 59.739 43.478 0.00 0.00 0.00 3.41
922 943 1.751924 ACGATCAGACACTTCCTAGGC 59.248 52.381 2.96 0.00 0.00 3.93
956 977 6.608002 GGATAGAGAAGAAGTGTAGGGAAAGA 59.392 42.308 0.00 0.00 0.00 2.52
993 1023 6.645827 AGAGTTGATCAATAGATTGCTCATCG 59.354 38.462 12.12 0.00 41.02 3.84
1041 1071 2.939103 GTCCATGGATTTCCTCAAGACG 59.061 50.000 19.62 0.00 36.82 4.18
1170 1200 2.586792 GACAAGCGATCCCAGGCT 59.413 61.111 0.00 0.00 42.33 4.58
1203 1233 0.865769 GCAACATTCAGGTTCGTCGT 59.134 50.000 0.00 0.00 0.00 4.34
1204 1234 1.136336 GCAACATTCAGGTTCGTCGTC 60.136 52.381 0.00 0.00 0.00 4.20
1205 1235 1.124297 CAACATTCAGGTTCGTCGTCG 59.876 52.381 0.00 0.00 38.55 5.12
1212 1242 0.879765 AGGTTCGTCGTCGATCTGTT 59.120 50.000 5.44 0.00 45.65 3.16
1224 1254 4.981054 CGTCGATCTGTTCATCTGATGATT 59.019 41.667 20.16 4.60 39.39 2.57
1226 1256 6.215121 GTCGATCTGTTCATCTGATGATTCT 58.785 40.000 20.16 5.08 39.39 2.40
1228 1258 5.342791 CGATCTGTTCATCTGATGATTCTCG 59.657 44.000 20.16 17.92 39.39 4.04
1266 1296 1.153025 TTCTCCGCCGAGCTAGCTA 60.153 57.895 19.38 0.00 35.94 3.32
1278 1308 4.153475 CCGAGCTAGCTAGTTGATCTACTC 59.847 50.000 19.38 14.66 0.00 2.59
1289 1320 0.030908 GATCTACTCCCCTCAACGCG 59.969 60.000 3.53 3.53 0.00 6.01
1301 1332 1.942223 CAACGCGGATGCATGCATG 60.942 57.895 36.73 23.74 42.97 4.06
1307 1338 1.524008 CGGATGCATGCATGATGGCT 61.524 55.000 36.73 13.12 36.70 4.75
1308 1339 0.243907 GGATGCATGCATGATGGCTC 59.756 55.000 36.73 20.92 36.70 4.70
1310 1341 0.536460 ATGCATGCATGATGGCTCGA 60.536 50.000 31.74 0.00 35.03 4.04
1339 1374 9.481340 TGATCTAGAAACTGATTAATCGGATTG 57.519 33.333 27.40 12.34 36.97 2.67
1394 1429 3.427638 CGACAGTTACGTGGATCACATCT 60.428 47.826 0.00 0.00 33.40 2.90
1409 1444 9.460019 TGGATCACATCTATCAACATGTTTTAA 57.540 29.630 8.77 0.00 30.48 1.52
1415 1450 7.962918 ACATCTATCAACATGTTTTAAAGCGAC 59.037 33.333 8.77 0.00 28.27 5.19
1429 1464 3.824414 AAGCGACCGAAATTTGTTAGG 57.176 42.857 0.00 0.00 0.00 2.69
1472 1511 7.363530 GGAGATTGACTGTATGTGTAACCTACA 60.364 40.741 0.00 0.00 43.98 2.74
1555 1604 4.003648 CTCCATAGGAAAAGCTTCGTGTT 58.996 43.478 0.00 0.00 32.14 3.32
1558 1607 0.307760 AGGAAAAGCTTCGTGTTGCG 59.692 50.000 0.00 0.00 43.01 4.85
1561 1610 0.592247 AAAAGCTTCGTGTTGCGCTG 60.592 50.000 9.73 0.00 41.07 5.18
1603 1652 4.260985 TGCAGTTCATCGATGGTATGTTT 58.739 39.130 24.61 2.14 0.00 2.83
1651 1700 9.533253 CCATAAACATCCCATTAGTTTGATTTC 57.467 33.333 0.00 0.00 36.29 2.17
1707 1756 1.375396 CGATGTTTCTCCGGTGCCA 60.375 57.895 0.00 0.00 0.00 4.92
1710 1759 3.723348 GTTTCTCCGGTGCCACGC 61.723 66.667 0.00 0.00 0.00 5.34
1949 1998 0.391263 CAACCACTACCCCGAGAAGC 60.391 60.000 0.00 0.00 0.00 3.86
1975 2024 1.641577 GCACGTTCTGGATGTACCTC 58.358 55.000 0.00 0.00 39.86 3.85
1984 2033 1.043673 GGATGTACCTCTGGGACGCT 61.044 60.000 0.00 0.00 36.25 5.07
2491 2540 3.071206 GAGACGCTGAGCCAGGGA 61.071 66.667 20.69 0.00 45.41 4.20
2518 2567 2.183046 GAGACGCCTCTGCAGGTC 59.817 66.667 15.13 13.03 42.74 3.85
2554 2603 1.233019 CCACCATCATCGGCAAGATC 58.767 55.000 0.00 0.00 37.52 2.75
2606 2655 1.817099 CTCATGGCGAGGTTCCTGC 60.817 63.158 0.00 0.79 38.18 4.85
2608 2657 1.377725 CATGGCGAGGTTCCTGCTT 60.378 57.895 0.00 0.00 0.00 3.91
3043 3092 3.423154 GGCAAGGACGGCAAGACG 61.423 66.667 0.00 0.00 40.31 4.18
3177 3226 0.530744 TCGGTGAAGAAGACGATGGG 59.469 55.000 0.00 0.00 0.00 4.00
3412 3461 4.736896 GGCGGCGAGAACGAGGTT 62.737 66.667 12.98 0.00 42.66 3.50
3433 3482 2.049802 AACGACGGGTACACGCTG 60.050 61.111 19.40 12.96 37.37 5.18
3583 3632 2.512515 GAGTGCGGCATCCTCACC 60.513 66.667 5.72 0.00 0.00 4.02
3675 3724 3.065371 CCAAAAATCCAGGCACGTATCTC 59.935 47.826 0.00 0.00 0.00 2.75
3676 3725 3.914426 AAAATCCAGGCACGTATCTCT 57.086 42.857 0.00 0.00 0.00 3.10
3677 3726 3.460857 AAATCCAGGCACGTATCTCTC 57.539 47.619 0.00 0.00 0.00 3.20
3686 3739 3.181505 GGCACGTATCTCTCATATCCTCG 60.182 52.174 0.00 0.00 0.00 4.63
3707 3760 0.244994 TGCTCTGCTTCTCGGAAGAC 59.755 55.000 15.23 8.59 35.39 3.01
3709 3764 1.067213 GCTCTGCTTCTCGGAAGACTT 60.067 52.381 15.23 0.00 35.39 3.01
3914 3969 2.954611 GCCGGAACAGAGGTTTGC 59.045 61.111 5.05 0.00 37.36 3.68
3916 3971 1.949257 CCGGAACAGAGGTTTGCAC 59.051 57.895 0.00 0.00 37.36 4.57
3927 3985 2.666862 TTTGCACCGTACTGCCCG 60.667 61.111 4.79 0.00 36.21 6.13
3941 3999 1.147153 GCCCGGCTATCTTCAGCTT 59.853 57.895 0.71 0.00 41.50 3.74
3942 4000 1.162800 GCCCGGCTATCTTCAGCTTG 61.163 60.000 0.71 0.00 41.50 4.01
3967 4026 2.315925 ATGGCATGAGGTTACACTCG 57.684 50.000 0.00 0.00 40.39 4.18
3981 4040 0.235665 CACTCGTTGCTTGCGATTGT 59.764 50.000 0.00 0.00 37.74 2.71
3987 4046 2.339400 CGTTGCTTGCGATTGTGAATTC 59.661 45.455 0.00 0.00 0.00 2.17
3997 4056 3.189080 CGATTGTGAATTCTCAGGTTGCA 59.811 43.478 9.91 0.00 30.14 4.08
4042 4101 0.031585 TGGACGACAACTTCTCCACG 59.968 55.000 0.00 0.00 30.73 4.94
4129 4188 4.922026 ACCGTCAACGTGGTGGCC 62.922 66.667 0.00 0.00 37.02 5.36
4150 4209 2.254459 CTCATGGTCAACTTCGTCTCG 58.746 52.381 0.00 0.00 0.00 4.04
4168 4227 1.899814 TCGGCATCTTTCACAGGTACT 59.100 47.619 0.00 0.00 43.88 2.73
4201 4260 6.547141 ACTGAAACTCCATTGATTCTTGACAA 59.453 34.615 0.00 0.00 0.00 3.18
4203 4262 7.954835 TGAAACTCCATTGATTCTTGACAAAT 58.045 30.769 0.00 0.00 0.00 2.32
4211 4270 7.123247 CCATTGATTCTTGACAAATAGGGTCTT 59.877 37.037 0.00 0.00 36.26 3.01
4213 4272 9.753674 ATTGATTCTTGACAAATAGGGTCTTTA 57.246 29.630 0.00 0.00 36.26 1.85
4236 4295 4.508662 CCATCTCCTGGTGTTCTCTTAAC 58.491 47.826 0.00 0.00 40.49 2.01
4241 4300 5.711036 TCTCCTGGTGTTCTCTTAACTAGAC 59.289 44.000 0.00 0.00 0.00 2.59
4245 4304 5.311265 TGGTGTTCTCTTAACTAGACTCGA 58.689 41.667 0.00 0.00 0.00 4.04
4411 4472 0.798776 GGCGACAACTTCATCACCAG 59.201 55.000 0.00 0.00 0.00 4.00
4581 4642 0.959553 ACCACACTCTCCTACACACG 59.040 55.000 0.00 0.00 0.00 4.49
4603 4678 8.450964 ACACGAGATCGAAATGAATTTGTATTT 58.549 29.630 9.58 0.00 43.02 1.40
4677 4752 4.753233 AGATGGAGAAGATCAACGTCTTG 58.247 43.478 0.00 0.00 38.51 3.02
4707 4782 1.078567 CAGCAGCTGGGTCTTCTCC 60.079 63.158 17.12 0.00 0.00 3.71
4945 5020 0.179215 GAGCGCCGTGTGATTTTGAG 60.179 55.000 2.29 0.00 0.00 3.02
4953 5028 4.290155 CCGTGTGATTTTGAGGACTTTTG 58.710 43.478 0.00 0.00 0.00 2.44
4957 5032 4.037923 TGTGATTTTGAGGACTTTTGGCTC 59.962 41.667 0.00 0.00 0.00 4.70
4993 5068 8.231007 TCTAGGAAGAGGAAGATATGTTGATCT 58.769 37.037 0.00 0.00 37.81 2.75
5022 5100 1.823828 GATCTTTGCATGCAGCTTCG 58.176 50.000 21.50 8.72 45.94 3.79
5312 6448 5.388654 AGTTGACAAATCCAACCTCTCAAT 58.611 37.500 0.00 0.00 43.50 2.57
5315 6451 3.347216 ACAAATCCAACCTCTCAATCGG 58.653 45.455 0.00 0.00 0.00 4.18
5317 6453 1.879575 ATCCAACCTCTCAATCGGGA 58.120 50.000 0.00 0.00 0.00 5.14
5318 6454 0.902531 TCCAACCTCTCAATCGGGAC 59.097 55.000 0.00 0.00 0.00 4.46
5363 6515 7.647715 CCGATCACGCCTTAAATAATTGATTTT 59.352 33.333 0.00 0.00 37.29 1.82
5409 6561 9.614792 AGAAACCTCAAATCCATACTATTACAC 57.385 33.333 0.00 0.00 0.00 2.90
5475 6629 2.285773 ATGTCCGACAGCTGGCTGA 61.286 57.895 26.42 14.76 46.30 4.26
5498 6653 2.654863 CCTCAAAGTGTTGGTCCAGTT 58.345 47.619 0.00 0.00 35.29 3.16
5506 6661 3.096633 TTGGTCCAGTTGCCGACGT 62.097 57.895 0.00 0.00 0.00 4.34
5561 6716 1.215647 GACTCGAGGCATCACCGTT 59.784 57.895 15.11 0.00 46.52 4.44
5620 6775 0.942962 GACGATACCGATGGACGTCT 59.057 55.000 16.46 0.00 46.00 4.18
5632 6787 2.297701 TGGACGTCTGATCGATGATGA 58.702 47.619 16.46 0.00 32.79 2.92
5820 6979 1.742831 GCCATGTTTGCATAGGACGAA 59.257 47.619 0.00 0.00 33.30 3.85
5878 7037 0.960364 GGATTGCGTGTCCACCACAT 60.960 55.000 0.00 0.00 44.78 3.21
5904 7063 0.172803 GACATTAGACGGACCGCACT 59.827 55.000 15.39 15.96 0.00 4.40
5905 7064 0.108804 ACATTAGACGGACCGCACTG 60.109 55.000 15.39 7.35 0.00 3.66
5906 7065 0.108804 CATTAGACGGACCGCACTGT 60.109 55.000 15.39 4.90 0.00 3.55
5907 7066 0.606604 ATTAGACGGACCGCACTGTT 59.393 50.000 15.39 3.43 0.00 3.16
5908 7067 0.319211 TTAGACGGACCGCACTGTTG 60.319 55.000 15.39 0.00 0.00 3.33
5909 7068 1.457823 TAGACGGACCGCACTGTTGT 61.458 55.000 15.39 0.00 0.00 3.32
5910 7069 2.587753 ACGGACCGCACTGTTGTG 60.588 61.111 15.39 0.00 46.37 3.33
5911 7070 2.279851 CGGACCGCACTGTTGTGA 60.280 61.111 0.00 0.00 46.55 3.58
5912 7071 1.885388 CGGACCGCACTGTTGTGAA 60.885 57.895 0.00 0.00 46.55 3.18
5913 7072 1.831389 CGGACCGCACTGTTGTGAAG 61.831 60.000 0.00 0.00 46.55 3.02
5914 7073 1.279840 GACCGCACTGTTGTGAAGC 59.720 57.895 0.00 0.00 46.55 3.86
5915 7074 2.249309 CCGCACTGTTGTGAAGCG 59.751 61.111 0.00 0.00 46.55 4.68
5916 7075 2.534019 CCGCACTGTTGTGAAGCGT 61.534 57.895 0.00 0.00 46.55 5.07
5917 7076 1.218875 CCGCACTGTTGTGAAGCGTA 61.219 55.000 0.00 0.00 46.55 4.42
5918 7077 0.161658 CGCACTGTTGTGAAGCGTAG 59.838 55.000 0.00 0.00 46.55 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
161 162 2.205074 CAGCAAACGAGTGTCAGAACT 58.795 47.619 0.00 0.00 0.00 3.01
199 200 1.072331 AGATCCGTAACCCCATGATGC 59.928 52.381 0.00 0.00 0.00 3.91
322 323 4.963318 ATTATGGCGAGATTTCCAGAGA 57.037 40.909 0.00 0.00 35.57 3.10
374 375 1.133790 GGCAGCTAGCTCACCAATTTG 59.866 52.381 22.95 9.00 44.79 2.32
593 602 3.795561 GCAAGATGCGTCATGTATACC 57.204 47.619 12.40 0.00 31.71 2.73
605 614 5.101628 TCAATAACAATTTCCGCAAGATGC 58.898 37.500 0.00 0.00 40.69 3.91
606 615 6.554419 TCTCAATAACAATTTCCGCAAGATG 58.446 36.000 0.00 0.00 43.02 2.90
607 616 6.757897 TCTCAATAACAATTTCCGCAAGAT 57.242 33.333 0.00 0.00 43.02 2.40
608 617 6.374053 TGATCTCAATAACAATTTCCGCAAGA 59.626 34.615 0.00 0.00 43.02 3.02
609 618 6.554419 TGATCTCAATAACAATTTCCGCAAG 58.446 36.000 0.00 0.00 0.00 4.01
610 619 6.507958 TGATCTCAATAACAATTTCCGCAA 57.492 33.333 0.00 0.00 0.00 4.85
611 620 6.507958 TTGATCTCAATAACAATTTCCGCA 57.492 33.333 0.00 0.00 0.00 5.69
612 621 7.992180 AATTGATCTCAATAACAATTTCCGC 57.008 32.000 5.88 0.00 45.06 5.54
619 628 9.076781 TGACCTCAAAATTGATCTCAATAACAA 57.923 29.630 5.88 0.00 45.06 2.83
620 629 8.514594 GTGACCTCAAAATTGATCTCAATAACA 58.485 33.333 5.88 0.00 45.06 2.41
621 630 8.514594 TGTGACCTCAAAATTGATCTCAATAAC 58.485 33.333 5.88 0.00 45.06 1.89
622 631 8.514594 GTGTGACCTCAAAATTGATCTCAATAA 58.485 33.333 5.88 0.00 45.06 1.40
623 632 7.148423 CGTGTGACCTCAAAATTGATCTCAATA 60.148 37.037 5.88 0.00 45.06 1.90
625 634 5.049474 CGTGTGACCTCAAAATTGATCTCAA 60.049 40.000 0.00 0.00 40.51 3.02
626 635 4.452114 CGTGTGACCTCAAAATTGATCTCA 59.548 41.667 0.00 0.00 36.46 3.27
627 636 4.142816 CCGTGTGACCTCAAAATTGATCTC 60.143 45.833 0.00 0.00 36.46 2.75
628 637 3.753272 CCGTGTGACCTCAAAATTGATCT 59.247 43.478 0.00 0.00 36.46 2.75
629 638 3.751175 TCCGTGTGACCTCAAAATTGATC 59.249 43.478 0.00 0.00 36.46 2.92
630 639 3.502211 GTCCGTGTGACCTCAAAATTGAT 59.498 43.478 0.00 0.00 38.09 2.57
631 640 2.875933 GTCCGTGTGACCTCAAAATTGA 59.124 45.455 0.00 0.00 38.09 2.57
632 641 2.616376 TGTCCGTGTGACCTCAAAATTG 59.384 45.455 0.00 0.00 43.78 2.32
633 642 2.616842 GTGTCCGTGTGACCTCAAAATT 59.383 45.455 0.00 0.00 43.78 1.82
634 643 2.158813 AGTGTCCGTGTGACCTCAAAAT 60.159 45.455 0.00 0.00 43.78 1.82
635 644 1.208535 AGTGTCCGTGTGACCTCAAAA 59.791 47.619 0.00 0.00 43.78 2.44
636 645 0.828022 AGTGTCCGTGTGACCTCAAA 59.172 50.000 0.00 0.00 43.78 2.69
637 646 0.387929 GAGTGTCCGTGTGACCTCAA 59.612 55.000 0.00 0.00 43.78 3.02
638 647 1.792118 CGAGTGTCCGTGTGACCTCA 61.792 60.000 0.00 0.00 43.78 3.86
639 648 1.081376 CGAGTGTCCGTGTGACCTC 60.081 63.158 0.00 0.00 43.78 3.85
640 649 1.105167 TTCGAGTGTCCGTGTGACCT 61.105 55.000 0.00 0.00 43.78 3.85
641 650 0.938168 GTTCGAGTGTCCGTGTGACC 60.938 60.000 0.00 0.00 43.78 4.02
642 651 0.938168 GGTTCGAGTGTCCGTGTGAC 60.938 60.000 0.00 0.00 44.72 3.67
643 652 1.105167 AGGTTCGAGTGTCCGTGTGA 61.105 55.000 0.00 0.00 0.00 3.58
644 653 0.594602 TAGGTTCGAGTGTCCGTGTG 59.405 55.000 0.00 0.00 0.00 3.82
649 658 6.145338 TGAAGATAATAGGTTCGAGTGTCC 57.855 41.667 0.00 0.00 0.00 4.02
682 691 4.957296 TCCATCCGTAAGCCTAAGAATTC 58.043 43.478 0.00 0.00 0.00 2.17
683 692 4.654262 TCTCCATCCGTAAGCCTAAGAATT 59.346 41.667 0.00 0.00 0.00 2.17
685 694 3.637229 CTCTCCATCCGTAAGCCTAAGAA 59.363 47.826 0.00 0.00 0.00 2.52
687 696 2.297597 CCTCTCCATCCGTAAGCCTAAG 59.702 54.545 0.00 0.00 0.00 2.18
701 714 2.501723 GAGTTGCTACATTCCCTCTCCA 59.498 50.000 0.13 0.00 0.00 3.86
704 717 4.917906 AAAGAGTTGCTACATTCCCTCT 57.082 40.909 0.13 0.00 0.00 3.69
852 866 2.093921 TGCTTTCATGCATCCCACAATG 60.094 45.455 0.00 0.00 38.12 2.82
895 916 3.118956 GGAAGTGTCTGATCGTTGGAGAT 60.119 47.826 0.00 0.00 0.00 2.75
905 926 2.763448 GACTGCCTAGGAAGTGTCTGAT 59.237 50.000 28.35 0.00 33.34 2.90
912 933 0.684805 CCCGAGACTGCCTAGGAAGT 60.685 60.000 23.58 23.58 39.73 3.01
922 943 3.216187 TCTTCTCTATCCCCGAGACTG 57.784 52.381 0.00 0.00 37.26 3.51
956 977 1.040646 TCAACTCTCTTGCAGTCCGT 58.959 50.000 0.00 0.00 0.00 4.69
1098 1128 4.273257 TTGACGAGCGTGCCGACA 62.273 61.111 0.00 6.73 0.00 4.35
1203 1233 6.402456 AGAATCATCAGATGAACAGATCGA 57.598 37.500 17.24 0.00 43.50 3.59
1204 1234 5.342791 CGAGAATCATCAGATGAACAGATCG 59.657 44.000 17.24 16.50 43.50 3.69
1205 1235 5.118971 GCGAGAATCATCAGATGAACAGATC 59.881 44.000 17.24 10.30 43.50 2.75
1212 1242 2.880890 TCGAGCGAGAATCATCAGATGA 59.119 45.455 15.69 15.69 44.55 2.92
1224 1254 3.280634 GGGCGAGATCGAGCGAGA 61.281 66.667 6.39 0.00 43.02 4.04
1266 1296 2.761208 CGTTGAGGGGAGTAGATCAACT 59.239 50.000 13.23 0.00 45.90 3.16
1289 1320 0.243907 GAGCCATCATGCATGCATCC 59.756 55.000 30.07 15.22 33.90 3.51
1301 1332 2.509569 TCTAGATCAGGTCGAGCCATC 58.490 52.381 11.73 12.94 40.61 3.51
1307 1338 7.640597 TTAATCAGTTTCTAGATCAGGTCGA 57.359 36.000 0.00 0.00 0.00 4.20
1308 1339 7.324856 CGATTAATCAGTTTCTAGATCAGGTCG 59.675 40.741 15.57 0.00 0.00 4.79
1310 1341 7.287927 TCCGATTAATCAGTTTCTAGATCAGGT 59.712 37.037 15.57 0.00 0.00 4.00
1363 1398 1.370900 GTAACTGTCGTCCACGCGT 60.371 57.895 5.58 5.58 39.60 6.01
1394 1429 5.408909 TCGGTCGCTTTAAAACATGTTGATA 59.591 36.000 12.82 6.07 0.00 2.15
1409 1444 2.486592 CCCTAACAAATTTCGGTCGCTT 59.513 45.455 0.00 0.00 0.00 4.68
1415 1450 3.023832 AGCCATCCCTAACAAATTTCGG 58.976 45.455 0.00 0.00 0.00 4.30
1429 1464 2.039480 TCTCCATCTATTGCAGCCATCC 59.961 50.000 0.00 0.00 0.00 3.51
1472 1511 7.827236 TGGTCAAGACGAATTTAATTCTACCAT 59.173 33.333 14.66 0.00 37.13 3.55
1555 1604 2.021584 CTTCTGCACGTACAGCGCA 61.022 57.895 11.47 4.06 46.11 6.09
1558 1607 2.391389 GGCCTTCTGCACGTACAGC 61.391 63.158 11.11 0.00 43.89 4.40
1561 1610 3.488090 GCGGCCTTCTGCACGTAC 61.488 66.667 0.00 0.00 43.99 3.67
1603 1652 1.965930 GTTGCCGGTGATGCAGACA 60.966 57.895 1.90 0.00 40.35 3.41
1651 1700 5.464722 CGATCAGAGGAACATATTTGGACAG 59.535 44.000 0.00 0.00 0.00 3.51
1663 1712 4.288670 TGTTACGATCGATCAGAGGAAC 57.711 45.455 24.34 19.62 0.00 3.62
1928 1977 1.196104 TTCTCGGGGTAGTGGTTGGG 61.196 60.000 0.00 0.00 0.00 4.12
1975 2024 2.759973 TCCTGGCTAGCGTCCCAG 60.760 66.667 9.00 10.02 46.49 4.45
1984 2033 2.675423 AGCGTCGTGTCCTGGCTA 60.675 61.111 0.00 0.00 31.03 3.93
2303 2352 2.858344 CGATGAACGAGTACCCATCAAC 59.142 50.000 0.00 0.00 45.77 3.18
2420 2469 2.710902 CCGTCACCAGCATCCTCGA 61.711 63.158 0.00 0.00 0.00 4.04
2443 2492 4.873129 CACTCCGTCCGCATCCCG 62.873 72.222 0.00 0.00 0.00 5.14
2518 2567 4.430423 GCGACGCCGTTGAGCTTG 62.430 66.667 9.14 0.00 38.24 4.01
2584 2633 1.375908 GAACCTCGCCATGAGCACA 60.376 57.895 0.00 0.00 43.82 4.57
3563 3612 4.899239 GAGGATGCCGCACTCCCG 62.899 72.222 14.59 0.00 31.49 5.14
3675 3724 2.492881 AGCAGAGCATCGAGGATATGAG 59.507 50.000 14.65 0.00 42.67 2.90
3676 3725 2.523245 AGCAGAGCATCGAGGATATGA 58.477 47.619 14.65 0.00 42.67 2.15
3677 3726 3.056678 AGAAGCAGAGCATCGAGGATATG 60.057 47.826 5.48 5.48 42.67 1.78
3686 3739 1.135915 TCTTCCGAGAAGCAGAGCATC 59.864 52.381 8.32 0.00 0.00 3.91
3707 3760 1.665679 GTGTGTCACCATCGGCATAAG 59.334 52.381 0.00 0.00 0.00 1.73
3709 3764 0.901827 AGTGTGTCACCATCGGCATA 59.098 50.000 0.00 0.00 34.49 3.14
3927 3985 2.998316 AGGACAAGCTGAAGATAGCC 57.002 50.000 0.00 0.00 44.76 3.93
3941 3999 3.521531 TGTAACCTCATGCCATAAGGACA 59.478 43.478 0.00 0.00 36.89 4.02
3942 4000 3.877508 GTGTAACCTCATGCCATAAGGAC 59.122 47.826 0.00 0.00 36.89 3.85
3967 4026 3.568538 AGAATTCACAATCGCAAGCAAC 58.431 40.909 8.44 0.00 37.18 4.17
3981 4040 3.822735 CTCCTTTGCAACCTGAGAATTCA 59.177 43.478 8.44 0.00 0.00 2.57
3987 4046 1.532868 CGTTCTCCTTTGCAACCTGAG 59.467 52.381 0.00 5.67 0.00 3.35
4042 4101 2.480073 CCATTTGGCCACGTTGATGATC 60.480 50.000 3.88 0.00 0.00 2.92
4066 4125 0.389296 TGTTGATGTACACGGAGCGG 60.389 55.000 0.00 0.00 0.00 5.52
4150 4209 1.740025 GCAGTACCTGTGAAAGATGCC 59.260 52.381 0.00 0.00 33.43 4.40
4168 4227 2.121291 TGGAGTTTCAGTTGTGTGCA 57.879 45.000 0.00 0.00 0.00 4.57
4169 4228 3.066621 TCAATGGAGTTTCAGTTGTGTGC 59.933 43.478 0.00 0.00 0.00 4.57
4170 4229 4.898829 TCAATGGAGTTTCAGTTGTGTG 57.101 40.909 0.00 0.00 0.00 3.82
4201 4260 4.660771 CCAGGAGATGGTAAAGACCCTATT 59.339 45.833 0.00 0.00 46.32 1.73
4203 4262 3.654273 CCAGGAGATGGTAAAGACCCTA 58.346 50.000 0.00 0.00 46.32 3.53
4257 4318 2.690778 GCGCGCTCCCTGAAACATT 61.691 57.895 26.67 0.00 0.00 2.71
4258 4319 3.127533 GCGCGCTCCCTGAAACAT 61.128 61.111 26.67 0.00 0.00 2.71
4411 4472 1.743772 CGATGTTCCTCCACATGACCC 60.744 57.143 0.00 0.00 37.52 4.46
4512 4573 4.292784 GGTGTTGAGCAGCTCTCC 57.707 61.111 23.15 15.24 41.18 3.71
4517 4578 0.601311 AGACGAAGGTGTTGAGCAGC 60.601 55.000 0.00 0.00 45.33 5.25
4617 4692 1.627864 TGAAGACCTGGATCGTCACA 58.372 50.000 0.00 0.45 33.00 3.58
4677 4752 2.821688 GCTGCTGAAGATGCCGCTC 61.822 63.158 0.00 0.00 37.60 5.03
4821 4896 3.432051 GATGACCAGGCCGACCGAG 62.432 68.421 0.00 0.00 42.76 4.63
4895 4970 3.165160 ATGGGCTGGTATCCGTCGC 62.165 63.158 0.00 0.00 0.00 5.19
4945 5020 3.885901 AGAGAAACAAGAGCCAAAAGTCC 59.114 43.478 0.00 0.00 0.00 3.85
4953 5028 4.464597 TCTTCCTAGAGAGAAACAAGAGCC 59.535 45.833 0.00 0.00 0.00 4.70
4989 5064 6.991485 TGCAAAGATCGTTTTCAAAAGATC 57.009 33.333 16.14 16.14 46.98 2.75
4993 5068 4.807834 TGCATGCAAAGATCGTTTTCAAAA 59.192 33.333 20.30 0.00 0.00 2.44
5022 5100 0.669625 GGCACGTCCTACACTGAACC 60.670 60.000 0.00 0.00 0.00 3.62
5268 5346 9.286170 TCAACTACGTCTATAGATGCTCTTATT 57.714 33.333 19.87 3.53 34.50 1.40
5287 6423 5.305585 TGAGAGGTTGGATTTGTCAACTAC 58.694 41.667 6.86 2.74 42.76 2.73
5288 6424 5.560722 TGAGAGGTTGGATTTGTCAACTA 57.439 39.130 6.86 0.00 42.76 2.24
5290 6426 5.617751 CGATTGAGAGGTTGGATTTGTCAAC 60.618 44.000 0.00 0.00 42.53 3.18
5302 6438 1.898154 CCGTCCCGATTGAGAGGTT 59.102 57.895 0.00 0.00 0.00 3.50
5317 6453 3.311110 ACTGTCCGTGGATGCCGT 61.311 61.111 0.00 0.00 0.00 5.68
5318 6454 2.815211 CACTGTCCGTGGATGCCG 60.815 66.667 0.00 0.00 40.02 5.69
5319 6455 1.741770 GTCACTGTCCGTGGATGCC 60.742 63.158 0.00 0.00 43.94 4.40
5321 6457 1.446099 CGGTCACTGTCCGTGGATG 60.446 63.158 6.56 0.00 43.94 3.51
5363 6515 7.983484 GGTTTCTAATTCGAGGTATCCAGTTAA 59.017 37.037 0.00 0.00 0.00 2.01
5453 6607 1.003355 CCAGCTGTCGGACATGGTT 60.003 57.895 18.48 2.42 0.00 3.67
5475 6629 0.178990 GGACCAACACTTTGAGGGCT 60.179 55.000 0.00 0.00 34.24 5.19
5483 6638 1.101049 CGGCAACTGGACCAACACTT 61.101 55.000 0.00 0.00 0.00 3.16
5498 6653 1.028330 CCTACTCTACCACGTCGGCA 61.028 60.000 0.00 0.00 39.03 5.69
5506 6661 0.639943 TCCCATGCCCTACTCTACCA 59.360 55.000 0.00 0.00 0.00 3.25
5528 6683 1.276421 CGAGTCCCATGAGTTGGTCTT 59.724 52.381 0.00 0.00 44.83 3.01
5529 6684 0.898320 CGAGTCCCATGAGTTGGTCT 59.102 55.000 0.00 0.00 44.83 3.85
5548 6703 0.394352 ATGGGAAACGGTGATGCCTC 60.394 55.000 6.35 0.00 34.25 4.70
5561 6716 1.213296 GGAAGAGTAGGGCATGGGAA 58.787 55.000 0.00 0.00 0.00 3.97
5598 6753 0.661552 CGTCCATCGGTATCGTCAGT 59.338 55.000 0.00 0.00 37.69 3.41
5620 6775 4.262335 CCAGGACAGATTCATCATCGATCA 60.262 45.833 0.00 0.00 36.93 2.92
5632 6787 0.915364 GGCTCCTTCCAGGACAGATT 59.085 55.000 0.00 0.00 40.06 2.40
5654 6809 1.736645 CACGTCGTGGTGGATGTCC 60.737 63.158 17.75 0.00 34.01 4.02
5727 6885 0.179145 CGGCGGTGAACGTAGAAGAT 60.179 55.000 0.00 0.00 46.52 2.40
5878 7037 3.677700 CGGTCCGTCTAATGTCCAAATGA 60.678 47.826 2.08 0.00 0.00 2.57
5904 7063 0.516877 GCATGCTACGCTTCACAACA 59.483 50.000 11.37 0.00 0.00 3.33
5905 7064 0.516877 TGCATGCTACGCTTCACAAC 59.483 50.000 20.33 0.00 0.00 3.32
5906 7065 1.233919 TTGCATGCTACGCTTCACAA 58.766 45.000 20.33 0.00 0.00 3.33
5907 7066 1.452110 ATTGCATGCTACGCTTCACA 58.548 45.000 20.33 0.00 0.00 3.58
5908 7067 2.549633 AATTGCATGCTACGCTTCAC 57.450 45.000 20.33 0.00 0.00 3.18
5909 7068 2.487372 TGAAATTGCATGCTACGCTTCA 59.513 40.909 20.33 16.79 0.00 3.02
5910 7069 3.135414 TGAAATTGCATGCTACGCTTC 57.865 42.857 20.33 14.61 0.00 3.86
5911 7070 3.574284 TTGAAATTGCATGCTACGCTT 57.426 38.095 20.33 5.98 0.00 4.68
5912 7071 3.574284 TTTGAAATTGCATGCTACGCT 57.426 38.095 20.33 0.00 0.00 5.07
5913 7072 4.644044 TTTTTGAAATTGCATGCTACGC 57.356 36.364 20.33 5.10 0.00 4.42


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

AutoCloner maintained by Alex Coulton.