Multiple sequence alignment - TraesCS1A01G427400

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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 TraesCS1A01G427400 chr1A 100.000 5177 0 0 1 5177 581833668 581828492 0.000000e+00 9561.0
1 TraesCS1A01G427400 chr1A 88.742 302 32 2 1299 1599 581851813 581851513 8.190000e-98 368.0
2 TraesCS1A01G427400 chr1A 87.402 127 13 3 509 635 581852279 581852156 5.400000e-30 143.0
3 TraesCS1A01G427400 chr1D 92.725 4742 188 68 509 5177 484419912 484415255 0.000000e+00 6700.0
4 TraesCS1A01G427400 chr1D 78.880 393 21 22 627 1005 484444312 484443968 5.250000e-50 209.0
5 TraesCS1A01G427400 chr1D 85.556 180 22 2 1 176 484445037 484444858 8.850000e-43 185.0
6 TraesCS1A01G427400 chr1D 87.805 82 9 1 26 106 484420444 484420363 1.530000e-15 95.3
7 TraesCS1A01G427400 chr1B 93.014 4137 171 50 955 5027 674671549 674667467 0.000000e+00 5930.0
8 TraesCS1A01G427400 chr1B 88.936 470 45 6 1 464 674672818 674672350 1.620000e-159 573.0
9 TraesCS1A01G427400 chr1B 82.781 302 20 10 509 789 674672168 674671878 1.860000e-59 241.0
10 TraesCS1A01G427400 chr1B 84.810 158 9 4 5035 5177 674667432 674667275 1.500000e-30 145.0
11 TraesCS1A01G427400 chr4B 85.882 510 39 23 4694 5177 544007423 544006921 3.580000e-141 512.0
12 TraesCS1A01G427400 chr5A 85.352 512 39 22 4694 5177 137852285 137852788 1.000000e-136 497.0
13 TraesCS1A01G427400 chr5B 87.215 438 36 18 4694 5118 70460759 70461189 1.010000e-131 481.0
14 TraesCS1A01G427400 chr3A 84.375 512 40 26 4694 5176 170520424 170519924 2.820000e-127 466.0
15 TraesCS1A01G427400 chr3A 80.538 632 88 25 1298 1904 413679079 413679700 2.200000e-123 453.0
16 TraesCS1A01G427400 chr4A 86.591 440 36 16 4694 5117 686721341 686721773 1.020000e-126 464.0
17 TraesCS1A01G427400 chr7B 86.836 433 33 17 4694 5110 671469856 671470280 3.650000e-126 462.0
18 TraesCS1A01G427400 chr7B 86.168 441 38 16 4694 5118 671511601 671512034 6.110000e-124 455.0
19 TraesCS1A01G427400 chr3D 80.507 631 90 23 1298 1904 316170638 316170017 2.200000e-123 453.0
20 TraesCS1A01G427400 chr3B 79.556 631 96 22 1298 1904 403905558 403906179 2.230000e-113 420.0


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 TraesCS1A01G427400 chr1A 581828492 581833668 5176 True 9561.00 9561 100.00000 1 5177 1 chr1A.!!$R1 5176
1 TraesCS1A01G427400 chr1A 581851513 581852279 766 True 255.50 368 88.07200 509 1599 2 chr1A.!!$R2 1090
2 TraesCS1A01G427400 chr1D 484415255 484420444 5189 True 3397.65 6700 90.26500 26 5177 2 chr1D.!!$R1 5151
3 TraesCS1A01G427400 chr1B 674667275 674672818 5543 True 1722.25 5930 87.38525 1 5177 4 chr1B.!!$R1 5176
4 TraesCS1A01G427400 chr4B 544006921 544007423 502 True 512.00 512 85.88200 4694 5177 1 chr4B.!!$R1 483
5 TraesCS1A01G427400 chr5A 137852285 137852788 503 False 497.00 497 85.35200 4694 5177 1 chr5A.!!$F1 483
6 TraesCS1A01G427400 chr3A 170519924 170520424 500 True 466.00 466 84.37500 4694 5176 1 chr3A.!!$R1 482
7 TraesCS1A01G427400 chr3A 413679079 413679700 621 False 453.00 453 80.53800 1298 1904 1 chr3A.!!$F1 606
8 TraesCS1A01G427400 chr3D 316170017 316170638 621 True 453.00 453 80.50700 1298 1904 1 chr3D.!!$R1 606
9 TraesCS1A01G427400 chr3B 403905558 403906179 621 False 420.00 420 79.55600 1298 1904 1 chr3B.!!$F1 606

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
751 948 0.498685 ACCCTCCTTCCTTCCTTCCT 59.501 55.000 0.0 0.0 0.00 3.36 F
911 1126 1.003003 GCTTGGACTTCTCTGGAGCTT 59.997 52.381 0.0 0.0 0.00 3.74 F
2162 2561 1.065273 GCATGCTGCGAAGAATGGG 59.935 57.895 13.7 0.0 31.71 4.00 F
3704 4124 1.131126 CAGTTACCCTCATGCTTTGCG 59.869 52.381 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2392 0.032952 CAAGCAACAGTGGCAAGCAT 59.967 50.000 1.78 0.00 0.00 3.79 R
2877 3285 0.409092 AATGCCATGTTGACCTGGGA 59.591 50.000 7.42 5.06 36.55 4.37 R
3872 4298 0.537371 AAGGGCACTCGGAACAAAGG 60.537 55.000 0.00 0.00 0.00 3.11 R
4530 4977 1.226603 CTCGTCTTTCTACGGGGCG 60.227 63.158 0.00 0.00 43.05 6.13 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
75 76 8.980610 CAATTTCAGATTGTGCAAATTAAGACA 58.019 29.630 0.00 0.00 30.85 3.41
76 77 9.545105 AATTTCAGATTGTGCAAATTAAGACAA 57.455 25.926 0.00 0.00 30.54 3.18
80 81 8.143193 TCAGATTGTGCAAATTAAGACAAACAT 58.857 29.630 0.00 0.00 32.34 2.71
88 89 8.845227 TGCAAATTAAGACAAACATTCTCACTA 58.155 29.630 0.00 0.00 0.00 2.74
109 110 7.557358 TCACTAGAATTGGATATGCACATGTTT 59.443 33.333 0.00 0.00 0.00 2.83
125 126 0.526739 GTTTGTTCACGGGGTTGTGC 60.527 55.000 0.00 0.00 39.73 4.57
127 128 0.965866 TTGTTCACGGGGTTGTGCAA 60.966 50.000 0.00 0.00 39.73 4.08
164 165 1.661341 AGCTTTGTCGATCATGAGGC 58.339 50.000 0.09 0.00 0.00 4.70
165 166 1.209019 AGCTTTGTCGATCATGAGGCT 59.791 47.619 0.09 0.00 0.00 4.58
179 180 2.211353 GAGGCTAGTAGCAAACCTCG 57.789 55.000 23.24 0.00 44.75 4.63
222 224 9.099454 CCAAAACAGAGGAATTATGAGTAGTAC 57.901 37.037 0.00 0.00 0.00 2.73
223 225 9.653287 CAAAACAGAGGAATTATGAGTAGTACA 57.347 33.333 2.52 0.00 0.00 2.90
278 295 7.419711 AGGAATTATCTTGTCTCGTTCCTAA 57.580 36.000 2.15 0.00 41.43 2.69
280 297 8.319146 AGGAATTATCTTGTCTCGTTCCTAAAA 58.681 33.333 2.15 0.00 41.43 1.52
281 298 8.943002 GGAATTATCTTGTCTCGTTCCTAAAAA 58.057 33.333 0.00 0.00 32.83 1.94
314 333 8.738645 ACTTTGAATGGATCTGTAGTTTATCC 57.261 34.615 0.00 0.00 39.76 2.59
315 334 7.495934 ACTTTGAATGGATCTGTAGTTTATCCG 59.504 37.037 0.00 0.00 41.81 4.18
368 391 5.991328 AATCGTGTATGCATTTCCTACAG 57.009 39.130 3.54 0.00 0.00 2.74
383 406 5.894298 TCCTACAGACCAAATGCATCTAT 57.106 39.130 0.00 0.00 0.00 1.98
386 409 6.014242 TCCTACAGACCAAATGCATCTATAGG 60.014 42.308 11.01 11.01 39.87 2.57
389 412 6.294473 ACAGACCAAATGCATCTATAGGAAG 58.706 40.000 0.00 0.00 0.00 3.46
395 418 7.836183 ACCAAATGCATCTATAGGAAGTTTTCT 59.164 33.333 0.00 0.00 0.00 2.52
440 468 5.890424 TTTCTATGAAAACCATCCGAACC 57.110 39.130 0.00 0.00 36.71 3.62
464 492 6.017770 CCGGATAAGGTTTAAATGACGCATTA 60.018 38.462 0.00 0.00 32.43 1.90
465 493 7.411274 CGGATAAGGTTTAAATGACGCATTAA 58.589 34.615 5.67 0.00 32.43 1.40
466 494 8.073768 CGGATAAGGTTTAAATGACGCATTAAT 58.926 33.333 5.67 0.00 32.43 1.40
477 505 8.856490 AAATGACGCATTAATAGAAAACCATC 57.144 30.769 5.67 0.00 32.43 3.51
478 506 6.371809 TGACGCATTAATAGAAAACCATCC 57.628 37.500 0.00 0.00 0.00 3.51
479 507 5.007234 TGACGCATTAATAGAAAACCATCCG 59.993 40.000 0.00 0.00 0.00 4.18
483 511 6.206498 GCATTAATAGAAAACCATCCGAACC 58.794 40.000 0.00 0.00 0.00 3.62
732 929 3.140073 ATTCAACGCCACCCACCCA 62.140 57.895 0.00 0.00 0.00 4.51
746 943 1.541620 ACCCACCCTCCTTCCTTCC 60.542 63.158 0.00 0.00 0.00 3.46
747 944 1.229984 CCCACCCTCCTTCCTTCCT 60.230 63.158 0.00 0.00 0.00 3.36
748 945 0.846870 CCCACCCTCCTTCCTTCCTT 60.847 60.000 0.00 0.00 0.00 3.36
749 946 0.621082 CCACCCTCCTTCCTTCCTTC 59.379 60.000 0.00 0.00 0.00 3.46
750 947 0.621082 CACCCTCCTTCCTTCCTTCC 59.379 60.000 0.00 0.00 0.00 3.46
751 948 0.498685 ACCCTCCTTCCTTCCTTCCT 59.501 55.000 0.00 0.00 0.00 3.36
752 949 1.132036 ACCCTCCTTCCTTCCTTCCTT 60.132 52.381 0.00 0.00 0.00 3.36
753 950 1.562008 CCCTCCTTCCTTCCTTCCTTC 59.438 57.143 0.00 0.00 0.00 3.46
754 951 2.556766 CCTCCTTCCTTCCTTCCTTCT 58.443 52.381 0.00 0.00 0.00 2.85
755 952 2.916269 CCTCCTTCCTTCCTTCCTTCTT 59.084 50.000 0.00 0.00 0.00 2.52
798 995 1.613630 TCCCAGCTCACTTCTCCCC 60.614 63.158 0.00 0.00 0.00 4.81
799 996 2.674220 CCCAGCTCACTTCTCCCCC 61.674 68.421 0.00 0.00 0.00 5.40
860 1057 2.124085 ATGACCCCTCCGACCCAA 59.876 61.111 0.00 0.00 0.00 4.12
911 1126 1.003003 GCTTGGACTTCTCTGGAGCTT 59.997 52.381 0.00 0.00 0.00 3.74
966 1326 2.570181 GCATGCCTGCTTGGTCAC 59.430 61.111 6.36 0.00 45.32 3.67
1200 1560 4.487412 GCTCTGTGCAATGCGGCC 62.487 66.667 0.00 0.00 42.31 6.13
1629 2015 1.330655 GCAGATCTTCGAGGTCCCCA 61.331 60.000 0.00 0.00 0.00 4.96
1668 2063 2.753029 GACAGCCTGCAGGAGGTT 59.247 61.111 37.21 16.45 44.97 3.50
1914 2309 3.382832 CGGTGAGACCCGCTCCTT 61.383 66.667 0.00 0.00 43.26 3.36
1915 2310 2.579738 GGTGAGACCCGCTCCTTC 59.420 66.667 0.00 0.00 43.26 3.46
1916 2311 2.579738 GTGAGACCCGCTCCTTCC 59.420 66.667 0.00 0.00 43.26 3.46
1917 2312 2.683933 TGAGACCCGCTCCTTCCC 60.684 66.667 0.00 0.00 43.26 3.97
1918 2313 2.364448 GAGACCCGCTCCTTCCCT 60.364 66.667 0.00 0.00 37.69 4.20
1919 2314 1.990614 GAGACCCGCTCCTTCCCTT 60.991 63.158 0.00 0.00 37.69 3.95
1920 2315 1.962321 GAGACCCGCTCCTTCCCTTC 61.962 65.000 0.00 0.00 37.69 3.46
1921 2316 1.990614 GACCCGCTCCTTCCCTTCT 60.991 63.158 0.00 0.00 0.00 2.85
1936 2331 2.354503 CCCTTCTCCATGCATATCTCCG 60.355 54.545 0.00 0.00 0.00 4.63
1945 2343 1.242076 GCATATCTCCGGCTGCATTT 58.758 50.000 0.50 0.00 34.77 2.32
2071 2469 2.872370 CAGCTGCTATTTTGCTTGTCC 58.128 47.619 0.00 0.00 34.51 4.02
2162 2561 1.065273 GCATGCTGCGAAGAATGGG 59.935 57.895 13.70 0.00 31.71 4.00
2190 2589 4.361451 AGATTGCATCATTTGTCGGTTC 57.639 40.909 0.00 0.00 0.00 3.62
2203 2602 6.627395 TTTGTCGGTTCATTGTAGTCAATT 57.373 33.333 0.00 0.00 41.66 2.32
2224 2623 7.812191 TCAATTAATGTGTTCTTAATGCGCTTT 59.188 29.630 9.73 11.90 31.03 3.51
2237 2644 3.317608 CGCTTTGCATCGCAGAATT 57.682 47.368 8.25 0.00 43.58 2.17
2321 2728 3.614159 ATTATCGTTTCGATCCGACGA 57.386 42.857 13.11 13.11 43.45 4.20
2397 2804 2.694628 GGCATTTCTGATGGCCACATTA 59.305 45.455 8.16 0.00 45.70 1.90
2479 2886 2.401699 CTGACCCTGCTGAGTGGCAA 62.402 60.000 0.00 0.00 41.94 4.52
2688 3096 2.413453 GGTCAGCGTCAGAATTCAGTTC 59.587 50.000 8.44 0.00 37.08 3.01
2698 3106 6.368791 CGTCAGAATTCAGTTCCTAACAATGA 59.631 38.462 8.44 0.00 37.56 2.57
2846 3254 1.702401 TCCACCAAACTGTCAGGCATA 59.298 47.619 4.53 0.00 0.00 3.14
2873 3281 7.255491 AGCTGATTCATATGTACATGTTGTG 57.745 36.000 18.81 11.32 0.00 3.33
2877 3285 7.998580 TGATTCATATGTACATGTTGTGCAAT 58.001 30.769 18.81 10.84 45.54 3.56
2914 3322 4.953579 GGCATTTGGGAGGTACAATTCTAA 59.046 41.667 0.00 0.00 0.00 2.10
2933 3341 3.478857 AAAACACACCGATGGACTACA 57.521 42.857 0.00 0.00 0.00 2.74
2943 3351 5.353956 CACCGATGGACTACAATCATTTTCA 59.646 40.000 0.00 0.00 0.00 2.69
3073 3481 5.957771 TCCTGAATAACATGAGGCTAGTT 57.042 39.130 0.00 0.00 0.00 2.24
3076 3484 3.871006 TGAATAACATGAGGCTAGTTGCG 59.129 43.478 0.00 0.00 44.05 4.85
3100 3508 1.342819 GCTCGAGCTCAGGGTAATGAT 59.657 52.381 29.88 0.00 38.21 2.45
3348 3765 4.202567 ACATAGGTTGACATGTTCCTGGTT 60.203 41.667 20.76 8.83 31.32 3.67
3349 3766 5.013704 ACATAGGTTGACATGTTCCTGGTTA 59.986 40.000 20.76 7.82 31.32 2.85
3350 3767 3.751518 AGGTTGACATGTTCCTGGTTAC 58.248 45.455 14.46 0.00 0.00 2.50
3351 3768 3.394606 AGGTTGACATGTTCCTGGTTACT 59.605 43.478 14.46 0.00 0.00 2.24
3352 3769 3.751698 GGTTGACATGTTCCTGGTTACTC 59.248 47.826 0.00 0.00 0.00 2.59
3353 3770 4.385825 GTTGACATGTTCCTGGTTACTCA 58.614 43.478 0.00 0.00 0.00 3.41
3376 3795 5.303078 CACCTAGTATGCTATTGACACCTCT 59.697 44.000 0.00 0.00 0.00 3.69
3391 3810 2.624838 CACCTCTCTGTTGGCATTGTTT 59.375 45.455 0.00 0.00 0.00 2.83
3469 3888 2.110213 GGTGACACGGAGGTTGCA 59.890 61.111 0.00 0.00 0.00 4.08
3673 4093 8.327941 TCATGTCCTTAATTATGCTAGATTGC 57.672 34.615 0.00 0.00 0.00 3.56
3674 4094 8.159447 TCATGTCCTTAATTATGCTAGATTGCT 58.841 33.333 0.00 0.00 0.00 3.91
3675 4095 9.440773 CATGTCCTTAATTATGCTAGATTGCTA 57.559 33.333 0.00 0.00 0.00 3.49
3676 4096 9.664332 ATGTCCTTAATTATGCTAGATTGCTAG 57.336 33.333 0.00 0.00 45.63 3.42
3704 4124 1.131126 CAGTTACCCTCATGCTTTGCG 59.869 52.381 0.00 0.00 0.00 4.85
3720 4140 2.309528 TGCGCCAGTTCTATACTTGG 57.690 50.000 4.18 0.00 33.85 3.61
3723 4143 3.267483 GCGCCAGTTCTATACTTGGAAA 58.733 45.455 0.00 0.00 33.85 3.13
3724 4144 3.063588 GCGCCAGTTCTATACTTGGAAAC 59.936 47.826 0.00 0.00 33.85 2.78
3765 4190 8.625786 TGCATATACTTATCTGTAGTCGGTTA 57.374 34.615 0.00 0.00 0.00 2.85
3766 4191 9.070179 TGCATATACTTATCTGTAGTCGGTTAA 57.930 33.333 0.00 0.00 0.00 2.01
3767 4192 9.557338 GCATATACTTATCTGTAGTCGGTTAAG 57.443 37.037 0.00 0.00 37.82 1.85
3774 4199 8.743085 TTATCTGTAGTCGGTTAAGTAGATGT 57.257 34.615 0.00 0.00 0.00 3.06
3785 4210 6.405953 CGGTTAAGTAGATGTCCTGACTGATT 60.406 42.308 0.00 0.00 0.00 2.57
3786 4211 7.331791 GGTTAAGTAGATGTCCTGACTGATTT 58.668 38.462 0.00 0.00 0.00 2.17
3937 4363 9.495572 AATAAACCTAACAACTCTCTTTCTCTG 57.504 33.333 0.00 0.00 0.00 3.35
3988 4424 5.598416 AAAAAGCTTCCAAGTTGCTAACT 57.402 34.783 0.00 0.00 45.46 2.24
4122 4558 1.487976 GTGAAGGAGATGATCTGCCCA 59.512 52.381 10.48 6.46 35.21 5.36
4185 4624 5.248248 TGTCTCCAATTCTTGAGGTCATACA 59.752 40.000 0.00 0.00 0.00 2.29
4310 4750 0.543277 CACCTCAGCAGCCTCCATTA 59.457 55.000 0.00 0.00 0.00 1.90
4371 4818 2.486191 CCATCATCCTGTTGCTAGTCCC 60.486 54.545 0.00 0.00 0.00 4.46
4445 4892 8.232412 TCATTTCCTACTATCACTAGTACCCAT 58.768 37.037 0.00 0.00 39.04 4.00
4453 4900 4.137116 TCACTAGTACCCATCATTGCAC 57.863 45.455 0.00 0.00 0.00 4.57
4505 4952 1.218585 CTGCTCTCTGCCACCTCAG 59.781 63.158 0.00 0.00 42.00 3.35
4506 4953 1.534959 TGCTCTCTGCCACCTCAGT 60.535 57.895 0.00 0.00 42.00 3.41
4507 4954 1.123861 TGCTCTCTGCCACCTCAGTT 61.124 55.000 0.00 0.00 42.00 3.16
4508 4955 0.390998 GCTCTCTGCCACCTCAGTTC 60.391 60.000 0.00 0.00 35.63 3.01
4509 4956 0.972134 CTCTCTGCCACCTCAGTTCA 59.028 55.000 0.00 0.00 35.63 3.18
4510 4957 1.554160 CTCTCTGCCACCTCAGTTCAT 59.446 52.381 0.00 0.00 35.63 2.57
4511 4958 1.552337 TCTCTGCCACCTCAGTTCATC 59.448 52.381 0.00 0.00 35.63 2.92
4512 4959 1.277273 CTCTGCCACCTCAGTTCATCA 59.723 52.381 0.00 0.00 35.63 3.07
4516 4963 2.306805 TGCCACCTCAGTTCATCATTCT 59.693 45.455 0.00 0.00 0.00 2.40
4528 4975 7.658982 TCAGTTCATCATTCTATACATTCTGCC 59.341 37.037 0.00 0.00 0.00 4.85
4530 4977 5.809001 TCATCATTCTATACATTCTGCCCC 58.191 41.667 0.00 0.00 0.00 5.80
4622 5085 5.454966 GAGGAGGAAGAGATAAGAAGAGGT 58.545 45.833 0.00 0.00 0.00 3.85
4629 5092 2.035321 GAGATAAGAAGAGGTCTGCCGG 59.965 54.545 0.00 0.00 40.50 6.13
4712 5175 2.194271 GTTATTCTGCGGAGGAACGAG 58.806 52.381 3.37 0.00 35.47 4.18
5089 5587 4.804108 CCATTTTCGCCAATGTTACAGAA 58.196 39.130 0.00 0.00 32.95 3.02
5127 5628 0.037697 ACTGCATTGCACATTGCTGG 60.038 50.000 20.82 14.54 45.31 4.85
5128 5629 1.358725 CTGCATTGCACATTGCTGGC 61.359 55.000 7.38 5.55 45.31 4.85
5129 5630 1.079405 GCATTGCACATTGCTGGCT 60.079 52.632 3.15 0.00 45.31 4.75
5130 5631 1.082117 GCATTGCACATTGCTGGCTC 61.082 55.000 3.15 0.00 45.31 4.70
5132 5633 0.530744 ATTGCACATTGCTGGCTCAG 59.469 50.000 0.00 0.00 45.31 3.35
5133 5634 0.537828 TTGCACATTGCTGGCTCAGA 60.538 50.000 6.40 0.00 45.31 3.27
5134 5635 0.958876 TGCACATTGCTGGCTCAGAG 60.959 55.000 6.40 0.00 45.31 3.35
5135 5636 0.675837 GCACATTGCTGGCTCAGAGA 60.676 55.000 0.00 0.00 40.96 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 6.888105 TGTGCATATCCAATTCTAGTGAGAA 58.112 36.000 0.00 0.00 45.75 2.87
88 89 6.534475 ACAAACATGTGCATATCCAATTCT 57.466 33.333 0.00 0.00 0.00 2.40
109 110 1.378646 TTGCACAACCCCGTGAACA 60.379 52.632 0.00 0.00 39.34 3.18
125 126 3.119849 GCTAGTTAGTGCCACATTGGTTG 60.120 47.826 0.00 0.00 40.46 3.77
127 128 2.305927 AGCTAGTTAGTGCCACATTGGT 59.694 45.455 0.00 0.00 40.46 3.67
164 165 6.128634 CCAAACTAAACGAGGTTTGCTACTAG 60.129 42.308 11.54 0.00 46.09 2.57
165 166 5.697633 CCAAACTAAACGAGGTTTGCTACTA 59.302 40.000 11.54 0.00 46.09 1.82
249 251 7.980099 GGAACGAGACAAGATAATTCCTAAGAA 59.020 37.037 0.00 0.00 36.15 2.52
253 255 8.529424 TTAGGAACGAGACAAGATAATTCCTA 57.471 34.615 5.87 5.87 42.03 2.94
302 321 9.329913 CATTTTCTTTGTTCGGATAAACTACAG 57.670 33.333 0.00 0.00 0.00 2.74
368 391 7.573968 AAACTTCCTATAGATGCATTTGGTC 57.426 36.000 0.00 0.00 0.00 4.02
383 406 6.200878 ACAAGGATTCCAGAAAACTTCCTA 57.799 37.500 5.29 0.00 33.33 2.94
386 409 7.043961 AGAAACAAGGATTCCAGAAAACTTC 57.956 36.000 5.29 0.00 0.00 3.01
389 412 7.886338 ACATAGAAACAAGGATTCCAGAAAAC 58.114 34.615 5.29 0.00 0.00 2.43
436 464 5.728621 GCGTCATTTAAACCTTATCCGGTTC 60.729 44.000 0.00 0.00 46.21 3.62
440 468 4.868450 TGCGTCATTTAAACCTTATCCG 57.132 40.909 0.00 0.00 0.00 4.18
478 506 9.002080 GTGTGTTTTTAAATATTATCCGGTTCG 57.998 33.333 0.00 0.00 0.00 3.95
653 849 9.160496 CTGAGCTGTAATTTCTATCTTTCTTGT 57.840 33.333 0.00 0.00 0.00 3.16
654 850 9.376075 TCTGAGCTGTAATTTCTATCTTTCTTG 57.624 33.333 0.00 0.00 0.00 3.02
732 929 0.498685 AGGAAGGAAGGAAGGAGGGT 59.501 55.000 0.00 0.00 0.00 4.34
735 932 3.843619 AGAAGAAGGAAGGAAGGAAGGAG 59.156 47.826 0.00 0.00 0.00 3.69
746 943 9.942850 AATAGAAGAAGAAGAAGAAGAAGGAAG 57.057 33.333 0.00 0.00 0.00 3.46
747 944 9.936759 GAATAGAAGAAGAAGAAGAAGAAGGAA 57.063 33.333 0.00 0.00 0.00 3.36
748 945 8.536175 GGAATAGAAGAAGAAGAAGAAGAAGGA 58.464 37.037 0.00 0.00 0.00 3.36
749 946 8.539544 AGGAATAGAAGAAGAAGAAGAAGAAGG 58.460 37.037 0.00 0.00 0.00 3.46
750 947 9.942850 AAGGAATAGAAGAAGAAGAAGAAGAAG 57.057 33.333 0.00 0.00 0.00 2.85
752 949 9.936759 GAAAGGAATAGAAGAAGAAGAAGAAGA 57.063 33.333 0.00 0.00 0.00 2.87
753 950 9.161629 GGAAAGGAATAGAAGAAGAAGAAGAAG 57.838 37.037 0.00 0.00 0.00 2.85
754 951 8.885346 AGGAAAGGAATAGAAGAAGAAGAAGAA 58.115 33.333 0.00 0.00 0.00 2.52
755 952 8.442660 AGGAAAGGAATAGAAGAAGAAGAAGA 57.557 34.615 0.00 0.00 0.00 2.87
844 1041 2.926242 GTTGGGTCGGAGGGGTCA 60.926 66.667 0.00 0.00 0.00 4.02
1914 2309 2.909006 GGAGATATGCATGGAGAAGGGA 59.091 50.000 10.16 0.00 0.00 4.20
1915 2310 2.354503 CGGAGATATGCATGGAGAAGGG 60.355 54.545 10.16 0.00 0.00 3.95
1916 2311 2.354503 CCGGAGATATGCATGGAGAAGG 60.355 54.545 10.16 2.56 0.00 3.46
1917 2312 2.934364 GCCGGAGATATGCATGGAGAAG 60.934 54.545 10.16 0.00 0.00 2.85
1918 2313 1.002430 GCCGGAGATATGCATGGAGAA 59.998 52.381 10.16 0.00 0.00 2.87
1919 2314 0.610174 GCCGGAGATATGCATGGAGA 59.390 55.000 10.16 0.00 0.00 3.71
1920 2315 0.612229 AGCCGGAGATATGCATGGAG 59.388 55.000 10.16 0.00 0.00 3.86
1921 2316 0.322648 CAGCCGGAGATATGCATGGA 59.677 55.000 10.16 0.00 0.00 3.41
1936 2331 0.101219 GGATCCAACGAAATGCAGCC 59.899 55.000 6.95 0.00 0.00 4.85
1945 2343 1.827394 GGATTCGGGGATCCAACGA 59.173 57.895 22.23 22.23 44.15 3.85
1994 2392 0.032952 CAAGCAACAGTGGCAAGCAT 59.967 50.000 1.78 0.00 0.00 3.79
2150 2549 3.750371 TCTTTCTTTCCCATTCTTCGCA 58.250 40.909 0.00 0.00 0.00 5.10
2162 2561 6.034256 CCGACAAATGATGCAATCTTTCTTTC 59.966 38.462 0.00 0.00 45.81 2.62
2203 2602 4.856487 GCAAAGCGCATTAAGAACACATTA 59.144 37.500 11.47 0.00 41.79 1.90
2224 2623 0.726827 GAACCGAATTCTGCGATGCA 59.273 50.000 3.52 0.00 36.92 3.96
2237 2644 2.270352 AAGCACTCCATTTGAACCGA 57.730 45.000 0.00 0.00 0.00 4.69
2300 2707 3.956233 TCGTCGGATCGAAACGATAATT 58.044 40.909 16.12 0.00 47.00 1.40
2301 2708 3.614159 TCGTCGGATCGAAACGATAAT 57.386 42.857 16.12 0.00 47.00 1.28
2321 2728 2.093869 ACATTGACACTACCGGCGTTAT 60.094 45.455 6.01 0.00 0.00 1.89
2332 2739 1.999735 CGATTACCGCACATTGACACT 59.000 47.619 0.00 0.00 0.00 3.55
2359 2766 3.557577 TGCCATTTCAGTCACAATTCG 57.442 42.857 0.00 0.00 0.00 3.34
2397 2804 1.780309 TCTCAACCATCCCAAACCTGT 59.220 47.619 0.00 0.00 0.00 4.00
2479 2886 3.416156 GCTCTCCACCTCATGAAGTTTT 58.584 45.455 0.00 0.00 0.00 2.43
2688 3096 5.982890 AGAAACATGGGTTCATTGTTAGG 57.017 39.130 12.37 0.00 35.82 2.69
2698 3106 3.434309 AGCTGCATAAGAAACATGGGTT 58.566 40.909 1.02 0.00 39.43 4.11
2846 3254 8.206867 ACAACATGTACATATGAATCAGCTACT 58.793 33.333 21.39 0.00 0.00 2.57
2873 3281 0.819582 CCATGTTGACCTGGGATTGC 59.180 55.000 0.00 0.00 0.00 3.56
2877 3285 0.409092 AATGCCATGTTGACCTGGGA 59.591 50.000 7.42 5.06 36.55 4.37
2914 3322 3.478857 TTGTAGTCCATCGGTGTGTTT 57.521 42.857 0.00 0.00 0.00 2.83
2933 3341 6.589907 GCTTGTACCGGAAAATGAAAATGATT 59.410 34.615 9.46 0.00 0.00 2.57
2943 3351 5.010617 ACTTTCAATGCTTGTACCGGAAAAT 59.989 36.000 9.46 0.00 0.00 1.82
3094 3502 4.274147 TGCCCGCCTTAAAAAGATCATTA 58.726 39.130 0.00 0.00 0.00 1.90
3100 3508 1.989706 ACTTGCCCGCCTTAAAAAGA 58.010 45.000 0.00 0.00 0.00 2.52
3348 3765 6.264744 GGTGTCAATAGCATACTAGGTGAGTA 59.735 42.308 0.00 0.00 44.87 2.59
3349 3766 5.069251 GGTGTCAATAGCATACTAGGTGAGT 59.931 44.000 0.00 0.00 42.69 3.41
3350 3767 5.303078 AGGTGTCAATAGCATACTAGGTGAG 59.697 44.000 0.00 0.00 30.78 3.51
3351 3768 5.208890 AGGTGTCAATAGCATACTAGGTGA 58.791 41.667 0.00 0.00 0.00 4.02
3352 3769 5.303078 AGAGGTGTCAATAGCATACTAGGTG 59.697 44.000 0.00 0.00 0.00 4.00
3353 3770 5.459505 AGAGGTGTCAATAGCATACTAGGT 58.540 41.667 0.00 0.00 0.00 3.08
3355 3772 6.264292 ACAGAGAGGTGTCAATAGCATACTAG 59.736 42.308 0.00 0.00 0.00 2.57
3365 3784 1.421268 TGCCAACAGAGAGGTGTCAAT 59.579 47.619 0.00 0.00 31.03 2.57
3376 3795 4.340666 TCAAGCTAAAACAATGCCAACAGA 59.659 37.500 0.00 0.00 0.00 3.41
3391 3810 1.202710 TCAACCCAACGCTCAAGCTAA 60.203 47.619 0.00 0.00 39.32 3.09
3408 3827 4.176271 CTCATAGTCTCGCACACAATCAA 58.824 43.478 0.00 0.00 0.00 2.57
3580 3999 1.291877 CGGGCGAATGTATAGCAGCC 61.292 60.000 0.00 0.00 43.47 4.85
3669 4089 6.958767 AGGGTAACTGAACAATACTAGCAAT 58.041 36.000 0.00 0.00 0.00 3.56
3670 4090 6.014070 TGAGGGTAACTGAACAATACTAGCAA 60.014 38.462 0.00 0.00 0.00 3.91
3671 4091 5.482526 TGAGGGTAACTGAACAATACTAGCA 59.517 40.000 0.00 0.00 0.00 3.49
3672 4092 5.974108 TGAGGGTAACTGAACAATACTAGC 58.026 41.667 0.00 0.00 0.00 3.42
3673 4093 6.480320 GCATGAGGGTAACTGAACAATACTAG 59.520 42.308 0.00 0.00 0.00 2.57
3674 4094 6.156256 AGCATGAGGGTAACTGAACAATACTA 59.844 38.462 0.00 0.00 0.00 1.82
3675 4095 5.045578 AGCATGAGGGTAACTGAACAATACT 60.046 40.000 0.00 0.00 0.00 2.12
3676 4096 5.186198 AGCATGAGGGTAACTGAACAATAC 58.814 41.667 0.00 0.00 0.00 1.89
3704 4124 7.769044 TGATAAGTTTCCAAGTATAGAACTGGC 59.231 37.037 0.00 0.00 38.88 4.85
3747 4168 8.838365 CATCTACTTAACCGACTACAGATAAGT 58.162 37.037 0.00 0.00 37.37 2.24
3758 4183 4.398673 AGTCAGGACATCTACTTAACCGAC 59.601 45.833 1.84 0.00 0.00 4.79
3765 4190 9.388506 CATTTAAATCAGTCAGGACATCTACTT 57.611 33.333 0.00 0.00 0.00 2.24
3766 4191 7.989741 CCATTTAAATCAGTCAGGACATCTACT 59.010 37.037 0.00 0.00 0.00 2.57
3767 4192 7.254932 GCCATTTAAATCAGTCAGGACATCTAC 60.255 40.741 0.00 0.00 0.00 2.59
3768 4193 6.767902 GCCATTTAAATCAGTCAGGACATCTA 59.232 38.462 0.00 0.00 0.00 1.98
3774 4199 4.922206 AGTGCCATTTAAATCAGTCAGGA 58.078 39.130 0.00 0.00 0.00 3.86
3785 4210 2.896685 CACCCCTGAAAGTGCCATTTAA 59.103 45.455 0.00 0.00 0.00 1.52
3786 4211 2.109128 TCACCCCTGAAAGTGCCATTTA 59.891 45.455 0.00 0.00 33.90 1.40
3872 4298 0.537371 AAGGGCACTCGGAACAAAGG 60.537 55.000 0.00 0.00 0.00 3.11
3947 4373 7.175641 AGCTTTTTACAGATTGCTACAGTTGAT 59.824 33.333 0.00 0.00 0.00 2.57
3948 4374 6.486657 AGCTTTTTACAGATTGCTACAGTTGA 59.513 34.615 0.00 0.00 0.00 3.18
3949 4375 6.672147 AGCTTTTTACAGATTGCTACAGTTG 58.328 36.000 0.00 0.00 0.00 3.16
3950 4376 6.884280 AGCTTTTTACAGATTGCTACAGTT 57.116 33.333 0.00 0.00 0.00 3.16
3951 4377 6.072452 GGAAGCTTTTTACAGATTGCTACAGT 60.072 38.462 0.00 0.00 28.67 3.55
3952 4378 6.072508 TGGAAGCTTTTTACAGATTGCTACAG 60.073 38.462 0.00 0.00 32.20 2.74
3953 4379 5.767665 TGGAAGCTTTTTACAGATTGCTACA 59.232 36.000 0.00 0.00 32.20 2.74
3954 4380 6.254281 TGGAAGCTTTTTACAGATTGCTAC 57.746 37.500 0.00 0.00 32.20 3.58
3955 4381 6.490040 ACTTGGAAGCTTTTTACAGATTGCTA 59.510 34.615 0.00 0.00 32.20 3.49
3956 4382 5.302823 ACTTGGAAGCTTTTTACAGATTGCT 59.697 36.000 0.00 0.00 32.20 3.91
3957 4383 5.532557 ACTTGGAAGCTTTTTACAGATTGC 58.467 37.500 0.00 0.00 31.64 3.56
3958 4384 6.074142 GCAACTTGGAAGCTTTTTACAGATTG 60.074 38.462 0.00 7.59 0.00 2.67
3959 4385 5.985530 GCAACTTGGAAGCTTTTTACAGATT 59.014 36.000 0.00 0.00 0.00 2.40
3961 4387 4.644685 AGCAACTTGGAAGCTTTTTACAGA 59.355 37.500 0.00 0.00 34.37 3.41
3962 4388 4.936891 AGCAACTTGGAAGCTTTTTACAG 58.063 39.130 0.00 0.00 34.37 2.74
3963 4389 6.096282 AGTTAGCAACTTGGAAGCTTTTTACA 59.904 34.615 0.00 0.00 39.04 2.41
3964 4390 6.417930 CAGTTAGCAACTTGGAAGCTTTTTAC 59.582 38.462 0.00 0.00 40.46 2.01
3965 4391 6.320164 TCAGTTAGCAACTTGGAAGCTTTTTA 59.680 34.615 0.00 0.00 40.46 1.52
3966 4392 5.127031 TCAGTTAGCAACTTGGAAGCTTTTT 59.873 36.000 0.00 0.00 40.46 1.94
3969 4395 3.820557 TCAGTTAGCAACTTGGAAGCTT 58.179 40.909 0.00 0.00 40.46 3.74
3971 4397 3.127721 GGATCAGTTAGCAACTTGGAAGC 59.872 47.826 0.00 0.00 40.46 3.86
4122 4558 5.406175 TGAATAGCGTAAAACGTGTAAGCTT 59.594 36.000 19.75 3.48 44.73 3.74
4185 4624 2.519302 GGTGCCACACTGCCACTT 60.519 61.111 0.00 0.00 34.40 3.16
4205 4644 4.890581 ACTCTATGCATCGAAGGACTAGTT 59.109 41.667 0.19 0.00 0.00 2.24
4371 4818 1.469940 CGAATGAAGGGTCAGGACTCG 60.470 57.143 0.00 0.00 37.14 4.18
4445 4892 1.246056 GCTCAAGGCTGGTGCAATGA 61.246 55.000 10.96 0.00 41.91 2.57
4453 4900 2.559668 TGAAAGAATTGCTCAAGGCTGG 59.440 45.455 0.00 0.00 42.39 4.85
4505 4952 6.150140 GGGGCAGAATGTATAGAATGATGAAC 59.850 42.308 0.00 0.00 39.31 3.18
4506 4953 6.240894 GGGGCAGAATGTATAGAATGATGAA 58.759 40.000 0.00 0.00 39.31 2.57
4507 4954 5.569428 CGGGGCAGAATGTATAGAATGATGA 60.569 44.000 0.00 0.00 39.31 2.92
4508 4955 4.633126 CGGGGCAGAATGTATAGAATGATG 59.367 45.833 0.00 0.00 39.31 3.07
4509 4956 4.836825 CGGGGCAGAATGTATAGAATGAT 58.163 43.478 0.00 0.00 39.31 2.45
4510 4957 3.557054 GCGGGGCAGAATGTATAGAATGA 60.557 47.826 0.00 0.00 39.31 2.57
4511 4958 2.744202 GCGGGGCAGAATGTATAGAATG 59.256 50.000 0.00 0.00 39.31 2.67
4512 4959 2.290323 GGCGGGGCAGAATGTATAGAAT 60.290 50.000 0.00 0.00 39.31 2.40
4516 4963 1.758592 GGGCGGGGCAGAATGTATA 59.241 57.895 0.00 0.00 39.31 1.47
4528 4975 2.186125 GTCTTTCTACGGGGCGGG 59.814 66.667 0.00 0.00 0.00 6.13
4530 4977 1.226603 CTCGTCTTTCTACGGGGCG 60.227 63.158 0.00 0.00 43.05 6.13
4629 5092 1.817941 TAATGAAGAAGCCGGCGCC 60.818 57.895 23.20 19.07 34.57 6.53
4712 5175 1.732683 CCAAAAATGGTGCGACCGC 60.733 57.895 7.53 7.53 42.58 5.68
4720 5183 2.926420 GCCCGACGCCAAAAATGGT 61.926 57.895 0.00 0.00 0.00 3.55
4954 5424 4.540824 GATTTGCAAGAACAGGAGACAAC 58.459 43.478 0.00 0.00 0.00 3.32
4963 5433 5.549742 AAAATGGAGGATTTGCAAGAACA 57.450 34.783 0.00 0.00 34.30 3.18
5089 5587 5.530915 TGCAGTTCAGTAAGTAGCAATTGTT 59.469 36.000 7.40 3.27 0.00 2.83
5142 5656 5.390040 CCGAACAATTGCGATACAACAGTTA 60.390 40.000 5.05 0.00 42.27 2.24
5149 5663 3.816091 CAAACCGAACAATTGCGATACA 58.184 40.909 5.05 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.