Multiple sequence alignment - TraesCS5A01G319600

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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 TraesCS5A01G319600 chr5A 100.000 4470 0 0 1 4470 531465269 531469738 0.000000e+00 8255.0
1 TraesCS5A01G319600 chr5A 100.000 29 0 0 1742 1770 531466067 531466039 2.000000e-03 54.7
2 TraesCS5A01G319600 chr6D 94.712 1456 44 8 2123 3575 457140481 457139056 0.000000e+00 2231.0
3 TraesCS5A01G319600 chr6D 93.394 1105 41 8 666 1746 457142007 457140911 0.000000e+00 1607.0
4 TraesCS5A01G319600 chr6D 94.795 730 33 5 3744 4470 457138809 457138082 0.000000e+00 1133.0
5 TraesCS5A01G319600 chr6D 94.747 495 21 3 1 492 457143179 457142687 0.000000e+00 765.0
6 TraesCS5A01G319600 chr6D 89.071 366 18 11 1769 2124 457140860 457140507 6.870000e-118 435.0
7 TraesCS5A01G319600 chr6D 93.088 217 10 4 3575 3789 457129921 457129708 3.360000e-81 313.0
8 TraesCS5A01G319600 chr6D 94.828 174 8 1 3575 3748 457139095 457138923 2.050000e-68 270.0
9 TraesCS5A01G319600 chr6D 96.154 156 6 0 3420 3575 457130037 457129882 5.740000e-64 255.0
10 TraesCS5A01G319600 chr6D 95.935 123 5 0 537 659 457142550 457142428 2.730000e-47 200.0
11 TraesCS5A01G319600 chr6D 92.308 78 5 1 3346 3422 457133293 457133216 4.730000e-20 110.0
12 TraesCS5A01G319600 chr6D 100.000 29 0 0 1742 1770 457141874 457141902 2.000000e-03 54.7
13 TraesCS5A01G319600 chr6B 92.527 1472 57 19 2123 3574 695795898 695794460 0.000000e+00 2060.0
14 TraesCS5A01G319600 chr6B 93.037 675 32 9 1 667 695798819 695798152 0.000000e+00 972.0
15 TraesCS5A01G319600 chr6B 93.802 597 14 2 666 1239 695797795 695797199 0.000000e+00 876.0
16 TraesCS5A01G319600 chr6B 89.535 430 26 10 1319 1746 695796748 695796336 1.100000e-145 527.0
17 TraesCS5A01G319600 chr6B 92.603 365 16 4 1769 2124 695796286 695795924 8.570000e-142 514.0
18 TraesCS5A01G319600 chr6B 90.278 216 14 3 3575 3784 695794501 695794287 4.400000e-70 276.0
19 TraesCS5A01G319600 chr6B 100.000 29 0 0 1742 1770 695797662 695797690 2.000000e-03 54.7
20 TraesCS5A01G319600 chr6A 93.557 1071 45 5 2508 3575 604108542 604107493 0.000000e+00 1574.0
21 TraesCS5A01G319600 chr6A 91.701 976 35 6 672 1625 604115587 604114636 0.000000e+00 1312.0
22 TraesCS5A01G319600 chr6A 97.761 670 12 1 1 667 604116316 604115647 0.000000e+00 1151.0
23 TraesCS5A01G319600 chr6A 95.630 389 14 2 2123 2509 604109011 604108624 4.910000e-174 621.0
24 TraesCS5A01G319600 chr6A 89.503 362 23 7 1772 2124 604109392 604109037 1.140000e-120 444.0
25 TraesCS5A01G319600 chr6A 93.119 218 9 3 3575 3789 604107532 604107318 9.330000e-82 315.0
26 TraesCS5A01G319600 chr6A 91.045 134 5 2 1620 1746 604109577 604109444 1.650000e-39 174.0
27 TraesCS5A01G319600 chr6A 86.207 58 2 1 2020 2071 604109058 604109001 1.740000e-04 58.4
28 TraesCS5A01G319600 chr6A 100.000 29 0 0 1742 1770 604115460 604115488 2.000000e-03 54.7
29 TraesCS5A01G319600 chr2D 82.043 646 90 20 3834 4470 194646739 194646111 1.100000e-145 527.0
30 TraesCS5A01G319600 chr2D 81.090 587 84 22 3835 4412 410473043 410472475 1.140000e-120 444.0
31 TraesCS5A01G319600 chr2D 79.798 396 49 13 295 667 514999794 515000181 4.440000e-65 259.0
32 TraesCS5A01G319600 chr2D 79.545 396 50 13 295 667 515013141 515013528 2.060000e-63 254.0
33 TraesCS5A01G319600 chr3B 81.847 639 96 17 3835 4460 284015011 284014380 1.840000e-143 520.0
34 TraesCS5A01G319600 chr3B 80.745 644 97 21 3835 4470 132615365 132615989 1.120000e-130 477.0
35 TraesCS5A01G319600 chr1D 81.056 644 103 14 3835 4470 339563423 339564055 3.110000e-136 496.0
36 TraesCS5A01G319600 chr1D 80.691 637 104 15 3841 4470 475481614 475482238 1.120000e-130 477.0
37 TraesCS5A01G319600 chr3D 80.392 714 76 22 1 667 94651822 94651126 6.720000e-133 484.0
38 TraesCS5A01G319600 chr4A 80.878 638 98 22 3835 4462 16053425 16054048 8.700000e-132 481.0
39 TraesCS5A01G319600 chr7D 81.229 602 90 17 3835 4429 474362601 474363186 8.760000e-127 464.0
40 TraesCS5A01G319600 chr5D 84.855 449 45 13 223 667 337531864 337531435 8.880000e-117 431.0
41 TraesCS5A01G319600 chr5B 83.234 334 24 15 356 667 396326779 396326456 1.220000e-70 278.0
42 TraesCS5A01G319600 chrUn 79.798 396 49 13 295 667 269147941 269148328 4.440000e-65 259.0
43 TraesCS5A01G319600 chr2A 78.987 395 54 12 295 667 658994420 658994807 4.470000e-60 243.0
44 TraesCS5A01G319600 chr1B 91.045 134 12 0 534 667 4949342 4949475 9.880000e-42 182.0
45 TraesCS5A01G319600 chr2B 79.323 266 42 11 4205 4470 706419686 706419938 1.650000e-39 174.0
46 TraesCS5A01G319600 chr2B 91.139 79 4 3 4381 4457 686447064 686446987 2.200000e-18 104.0


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 TraesCS5A01G319600 chr5A 531465269 531469738 4469 False 8255.000000 8255 100.000000 1 4470 1 chr5A.!!$F1 4469
1 TraesCS5A01G319600 chr6D 457138082 457143179 5097 True 948.714286 2231 93.926000 1 4470 7 chr6D.!!$R2 4469
2 TraesCS5A01G319600 chr6D 457129708 457133293 3585 True 226.000000 313 93.850000 3346 3789 3 chr6D.!!$R1 443
3 TraesCS5A01G319600 chr6B 695794287 695798819 4532 True 870.833333 2060 91.963667 1 3784 6 chr6B.!!$R1 3783
4 TraesCS5A01G319600 chr6A 604114636 604116316 1680 True 1231.500000 1312 94.731000 1 1625 2 chr6A.!!$R2 1624
5 TraesCS5A01G319600 chr6A 604107318 604109577 2259 True 531.066667 1574 91.510167 1620 3789 6 chr6A.!!$R1 2169
6 TraesCS5A01G319600 chr2D 194646111 194646739 628 True 527.000000 527 82.043000 3834 4470 1 chr2D.!!$R1 636
7 TraesCS5A01G319600 chr2D 410472475 410473043 568 True 444.000000 444 81.090000 3835 4412 1 chr2D.!!$R2 577
8 TraesCS5A01G319600 chr3B 284014380 284015011 631 True 520.000000 520 81.847000 3835 4460 1 chr3B.!!$R1 625
9 TraesCS5A01G319600 chr3B 132615365 132615989 624 False 477.000000 477 80.745000 3835 4470 1 chr3B.!!$F1 635
10 TraesCS5A01G319600 chr1D 339563423 339564055 632 False 496.000000 496 81.056000 3835 4470 1 chr1D.!!$F1 635
11 TraesCS5A01G319600 chr1D 475481614 475482238 624 False 477.000000 477 80.691000 3841 4470 1 chr1D.!!$F2 629
12 TraesCS5A01G319600 chr3D 94651126 94651822 696 True 484.000000 484 80.392000 1 667 1 chr3D.!!$R1 666
13 TraesCS5A01G319600 chr4A 16053425 16054048 623 False 481.000000 481 80.878000 3835 4462 1 chr4A.!!$F1 627
14 TraesCS5A01G319600 chr7D 474362601 474363186 585 False 464.000000 464 81.229000 3835 4429 1 chr7D.!!$F1 594

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
306 339 6.511416 TGTATAAATATTGGCCAACATGTGC 58.489 36.00 23.27 9.06 0.00 4.57 F
369 402 8.919145 ACCTAAACAAAATGTCTCCAAAATGTA 58.081 29.63 0.00 0.00 0.00 2.29 F
1302 1894 0.036010 CCCTTGCGTCTGATTCTGGT 60.036 55.00 0.00 0.00 0.00 4.00 F
1766 2738 0.835941 GTGTGGCTCTGATCCTGGAT 59.164 55.00 9.42 9.42 0.00 3.41 F
2331 3379 1.315257 ATCACCCGCAATGTGAAGGC 61.315 55.00 0.00 0.00 45.15 4.35 F
3319 4455 0.809385 CAGGAGCATTCACTTGCCTG 59.191 55.00 0.00 0.00 43.83 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 1894 0.609151 TCACACGCCGATAAGGGAAA 59.391 50.000 0.0 0.0 41.48 3.13 R
1844 2846 0.678048 AAGTTCCCGCTCCAAGATGC 60.678 55.000 0.0 0.0 0.00 3.91 R
3098 4233 2.168936 TCCTTTTGATTCATGGGCATGC 59.831 45.455 9.9 9.9 38.65 4.06 R
3319 4455 1.429463 ATCGTCCAGTTTCGTCAAGC 58.571 50.000 0.0 0.0 0.00 4.01 R
3400 4536 1.684450 TCAAGCACCGACAGTACTTCA 59.316 47.619 0.0 0.0 28.97 3.02 R
4336 8789 0.107703 TTGCCTCACATGATCGGGAC 60.108 55.000 0.0 0.0 0.00 4.46 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
145 146 9.855021 GGCATCATACATTTTACAAGTAGTTTT 57.145 29.630 0.00 0.00 0.00 2.43
306 339 6.511416 TGTATAAATATTGGCCAACATGTGC 58.489 36.000 23.27 9.06 0.00 4.57
369 402 8.919145 ACCTAAACAAAATGTCTCCAAAATGTA 58.081 29.630 0.00 0.00 0.00 2.29
1301 1893 0.745845 CCCCTTGCGTCTGATTCTGG 60.746 60.000 0.00 0.00 0.00 3.86
1302 1894 0.036010 CCCTTGCGTCTGATTCTGGT 60.036 55.000 0.00 0.00 0.00 4.00
1331 2294 4.666532 GCGTGTGACGGTGCTTGC 62.667 66.667 0.00 0.00 42.82 4.01
1389 2352 2.914289 GAGGCAGATCAGGTGGGG 59.086 66.667 0.00 0.00 0.00 4.96
1390 2353 1.690633 GAGGCAGATCAGGTGGGGA 60.691 63.158 0.00 0.00 0.00 4.81
1391 2354 1.005289 AGGCAGATCAGGTGGGGAT 59.995 57.895 0.00 0.00 0.00 3.85
1415 2378 4.278170 TGTTTGTCCCAAAATGTAGCTCAG 59.722 41.667 0.00 0.00 0.00 3.35
1428 2391 1.168407 AGCTCAGTTTGCATGCGTGT 61.168 50.000 14.09 0.00 0.00 4.49
1436 2399 2.022346 GCATGCGTGTGATGCTCG 59.978 61.111 0.00 0.00 42.52 5.03
1460 2423 5.050295 GGTTCAGTTCAGTTAGTTGTACAGC 60.050 44.000 0.72 0.72 0.00 4.40
1479 2442 3.688185 CAGCTCACTATGTGCTCAATTGT 59.312 43.478 5.13 0.00 44.32 2.71
1504 2467 7.790823 ACTTTGTTTTCAGAATTGATTTGGG 57.209 32.000 0.00 0.00 32.27 4.12
1508 2471 4.970860 TTTCAGAATTGATTTGGGGCAA 57.029 36.364 0.00 0.00 32.27 4.52
1618 2581 7.153217 TGAATAGTGAACTGTCTGTCGATTA 57.847 36.000 0.00 0.00 0.00 1.75
1679 2644 2.950781 TCGGATGATAGGAAGAGTGCT 58.049 47.619 0.00 0.00 0.00 4.40
1699 2664 8.195165 AGTGCTTTGTAGGCTATATAGATTGA 57.805 34.615 14.16 0.00 0.00 2.57
1746 2718 3.907893 GCTATTGCAAATCCGCGC 58.092 55.556 1.71 0.00 39.41 6.86
1747 2719 2.005537 GCTATTGCAAATCCGCGCG 61.006 57.895 25.67 25.67 39.41 6.86
1749 2721 0.925267 CTATTGCAAATCCGCGCGTG 60.925 55.000 29.95 21.00 33.35 5.34
1750 2722 1.640210 TATTGCAAATCCGCGCGTGT 61.640 50.000 29.95 14.09 33.35 4.49
1751 2723 3.754041 TATTGCAAATCCGCGCGTGTG 62.754 52.381 29.95 17.58 33.35 3.82
1760 2732 3.558411 GCGCGTGTGGCTCTGATC 61.558 66.667 8.43 0.00 40.44 2.92
1761 2733 2.887568 CGCGTGTGGCTCTGATCC 60.888 66.667 0.00 0.00 40.44 3.36
1762 2734 2.581354 GCGTGTGGCTCTGATCCT 59.419 61.111 0.00 0.00 39.11 3.24
1763 2735 1.812922 GCGTGTGGCTCTGATCCTG 60.813 63.158 0.00 0.00 39.11 3.86
1764 2736 1.153489 CGTGTGGCTCTGATCCTGG 60.153 63.158 0.00 0.00 0.00 4.45
1765 2737 1.607801 CGTGTGGCTCTGATCCTGGA 61.608 60.000 0.00 0.00 0.00 3.86
1766 2738 0.835941 GTGTGGCTCTGATCCTGGAT 59.164 55.000 9.42 9.42 0.00 3.41
1798 2798 6.153000 ACTTCCTAATGATCAGTACGTCTTGT 59.847 38.462 0.09 0.00 0.00 3.16
1799 2799 6.132791 TCCTAATGATCAGTACGTCTTGTC 57.867 41.667 0.09 0.00 0.00 3.18
1800 2800 5.886474 TCCTAATGATCAGTACGTCTTGTCT 59.114 40.000 0.09 0.00 0.00 3.41
1801 2801 7.052248 TCCTAATGATCAGTACGTCTTGTCTA 58.948 38.462 0.09 0.00 0.00 2.59
1844 2846 5.450412 CGTGTTATTCCAAGGAATTCCCATG 60.450 44.000 21.22 18.88 41.55 3.66
1855 2857 1.700955 ATTCCCATGCATCTTGGAGC 58.299 50.000 6.39 0.00 36.26 4.70
1944 2947 7.905604 TTGGTTGTGAATTACTAGATCACTG 57.094 36.000 17.12 0.00 42.99 3.66
1964 2967 7.799081 TCACTGATTATGAATCTCCAACTGAT 58.201 34.615 1.24 0.00 38.72 2.90
2067 3070 7.859325 ATATATAACAGACACGGTTGCTTTT 57.141 32.000 0.00 0.00 0.00 2.27
2100 3119 2.665649 ACGCGTCAGATTTGGATGTA 57.334 45.000 5.58 0.00 0.00 2.29
2161 3207 3.012518 GCCATTGAGTTCATGTGTAGCT 58.987 45.455 0.00 0.00 0.00 3.32
2228 3275 9.533253 GAAATAACTGCAATTATTAGTGGCATT 57.467 29.630 13.11 0.00 34.37 3.56
2331 3379 1.315257 ATCACCCGCAATGTGAAGGC 61.315 55.000 0.00 0.00 45.15 4.35
2537 3670 5.235850 TGCACCTTTCTGAACATACCTTA 57.764 39.130 0.00 0.00 0.00 2.69
2598 3733 7.864307 GCTGAATGTTGATATAGCCAAATTC 57.136 36.000 0.00 0.00 0.00 2.17
2599 3734 6.865205 GCTGAATGTTGATATAGCCAAATTCC 59.135 38.462 3.28 0.00 0.00 3.01
2625 3760 7.464178 CGAGGTTATGTTGTAACTCTGCATAAC 60.464 40.741 13.94 13.94 45.13 1.89
2628 3763 7.910162 GGTTATGTTGTAACTCTGCATAACATG 59.090 37.037 20.16 0.00 46.45 3.21
2760 3895 8.727910 GCAATCATCTTCAATATGCTAATCTCA 58.272 33.333 0.00 0.00 0.00 3.27
2834 3969 1.662686 GCCCCTATAAGCCAGATCCT 58.337 55.000 0.00 0.00 0.00 3.24
2954 4089 6.115446 TCCCATTATGTAGCTTAGCATATGC 58.885 40.000 20.36 20.36 41.58 3.14
2974 4109 8.663025 CATATGCATGATTCCTATACAGTTCAC 58.337 37.037 10.16 0.00 33.67 3.18
2975 4110 6.239217 TGCATGATTCCTATACAGTTCACT 57.761 37.500 0.00 0.00 0.00 3.41
2976 4111 6.653020 TGCATGATTCCTATACAGTTCACTT 58.347 36.000 0.00 0.00 0.00 3.16
2977 4112 7.112122 TGCATGATTCCTATACAGTTCACTTT 58.888 34.615 0.00 0.00 0.00 2.66
2978 4113 7.066163 TGCATGATTCCTATACAGTTCACTTTG 59.934 37.037 0.00 0.00 0.00 2.77
3079 4214 7.900782 TTGAAAGCTCCACAGTAAGTTATAC 57.099 36.000 0.00 0.00 0.00 1.47
3080 4215 6.999950 TGAAAGCTCCACAGTAAGTTATACA 58.000 36.000 0.00 0.00 0.00 2.29
3081 4216 7.097192 TGAAAGCTCCACAGTAAGTTATACAG 58.903 38.462 0.00 0.00 0.00 2.74
3082 4217 6.607004 AAGCTCCACAGTAAGTTATACAGT 57.393 37.500 0.00 0.00 0.00 3.55
3083 4218 7.713734 AAGCTCCACAGTAAGTTATACAGTA 57.286 36.000 0.00 0.00 0.00 2.74
3102 4237 5.877012 ACAGTAGTTTCATACTTCCAGCATG 59.123 40.000 0.00 0.00 38.33 4.06
3162 4297 5.696724 TCGCTAAATGCTCCTTAATTCTAGC 59.303 40.000 0.00 0.00 40.11 3.42
3199 4335 4.201920 GGAGTTCAGGACAGTTTTTGTGAC 60.202 45.833 0.00 0.00 41.05 3.67
3200 4336 4.331968 AGTTCAGGACAGTTTTTGTGACA 58.668 39.130 0.00 0.00 41.05 3.58
3201 4337 4.396166 AGTTCAGGACAGTTTTTGTGACAG 59.604 41.667 0.00 0.00 41.05 3.51
3202 4338 3.950397 TCAGGACAGTTTTTGTGACAGT 58.050 40.909 0.00 0.00 41.05 3.55
3203 4339 4.331968 TCAGGACAGTTTTTGTGACAGTT 58.668 39.130 0.00 0.00 41.05 3.16
3204 4340 4.764823 TCAGGACAGTTTTTGTGACAGTTT 59.235 37.500 0.00 0.00 41.05 2.66
3205 4341 5.242838 TCAGGACAGTTTTTGTGACAGTTTT 59.757 36.000 0.00 0.00 41.05 2.43
3206 4342 5.345741 CAGGACAGTTTTTGTGACAGTTTTG 59.654 40.000 0.00 0.00 41.05 2.44
3207 4343 5.010617 AGGACAGTTTTTGTGACAGTTTTGT 59.989 36.000 0.00 0.00 41.05 2.83
3208 4344 5.118510 GGACAGTTTTTGTGACAGTTTTGTG 59.881 40.000 0.00 0.00 41.05 3.33
3209 4345 5.837437 ACAGTTTTTGTGACAGTTTTGTGA 58.163 33.333 0.00 0.00 38.99 3.58
3238 4374 2.484264 ACTTTTCCGATAGCTTGTGCAC 59.516 45.455 10.75 10.75 42.74 4.57
3319 4455 0.809385 CAGGAGCATTCACTTGCCTG 59.191 55.000 0.00 0.00 43.83 4.85
3334 4470 0.884704 GCCTGCTTGACGAAACTGGA 60.885 55.000 0.00 0.00 0.00 3.86
3352 4488 3.840594 CGATACGGCCCCCACGAA 61.841 66.667 0.00 0.00 34.93 3.85
3400 4536 2.030027 TCATGGTGTCTTCACTCCCT 57.970 50.000 0.00 0.00 43.41 4.20
3488 7806 0.032540 ACAGGAAACGTCGTACACCC 59.967 55.000 0.00 0.00 0.00 4.61
3535 7856 5.533482 AGCTGTATCGATCAGTTTATCCAC 58.467 41.667 19.33 4.34 35.60 4.02
3547 7868 4.218417 CAGTTTATCCACACCCTCCAAAAG 59.782 45.833 0.00 0.00 0.00 2.27
3548 7869 4.141018 AGTTTATCCACACCCTCCAAAAGT 60.141 41.667 0.00 0.00 0.00 2.66
3549 7870 5.073965 AGTTTATCCACACCCTCCAAAAGTA 59.926 40.000 0.00 0.00 0.00 2.24
3550 7871 5.789574 TTATCCACACCCTCCAAAAGTAT 57.210 39.130 0.00 0.00 0.00 2.12
3551 7872 3.433306 TCCACACCCTCCAAAAGTATG 57.567 47.619 0.00 0.00 0.00 2.39
3552 7873 2.983192 TCCACACCCTCCAAAAGTATGA 59.017 45.455 0.00 0.00 0.00 2.15
3553 7874 3.081804 CCACACCCTCCAAAAGTATGAC 58.918 50.000 0.00 0.00 0.00 3.06
3554 7875 3.244911 CCACACCCTCCAAAAGTATGACT 60.245 47.826 0.00 0.00 0.00 3.41
3555 7876 3.753272 CACACCCTCCAAAAGTATGACTG 59.247 47.826 0.00 0.00 0.00 3.51
3556 7877 2.749621 CACCCTCCAAAAGTATGACTGC 59.250 50.000 0.00 0.00 0.00 4.40
3557 7878 2.644798 ACCCTCCAAAAGTATGACTGCT 59.355 45.455 0.00 0.00 0.00 4.24
3558 7879 3.844211 ACCCTCCAAAAGTATGACTGCTA 59.156 43.478 0.00 0.00 0.00 3.49
3559 7880 4.080863 ACCCTCCAAAAGTATGACTGCTAG 60.081 45.833 0.00 0.00 0.00 3.42
3560 7881 4.162320 CCCTCCAAAAGTATGACTGCTAGA 59.838 45.833 0.00 0.00 0.00 2.43
3561 7882 5.338381 CCCTCCAAAAGTATGACTGCTAGAA 60.338 44.000 0.00 0.00 0.00 2.10
3562 7883 6.173339 CCTCCAAAAGTATGACTGCTAGAAA 58.827 40.000 0.00 0.00 0.00 2.52
3563 7884 6.314896 CCTCCAAAAGTATGACTGCTAGAAAG 59.685 42.308 0.00 0.00 0.00 2.62
3564 7885 7.004555 TCCAAAAGTATGACTGCTAGAAAGA 57.995 36.000 0.00 0.00 0.00 2.52
3565 7886 7.450074 TCCAAAAGTATGACTGCTAGAAAGAA 58.550 34.615 0.00 0.00 0.00 2.52
3566 7887 7.936847 TCCAAAAGTATGACTGCTAGAAAGAAA 59.063 33.333 0.00 0.00 0.00 2.52
3567 7888 8.734386 CCAAAAGTATGACTGCTAGAAAGAAAT 58.266 33.333 0.00 0.00 0.00 2.17
3571 7892 8.854614 AGTATGACTGCTAGAAAGAAATTTGT 57.145 30.769 0.00 0.00 0.00 2.83
3572 7893 9.289782 AGTATGACTGCTAGAAAGAAATTTGTT 57.710 29.630 0.00 0.00 0.00 2.83
3573 7894 9.899226 GTATGACTGCTAGAAAGAAATTTGTTT 57.101 29.630 12.70 12.70 0.00 2.83
3576 7897 9.730420 TGACTGCTAGAAAGAAATTTGTTTTAC 57.270 29.630 13.88 3.58 0.00 2.01
3577 7898 9.181805 GACTGCTAGAAAGAAATTTGTTTTACC 57.818 33.333 13.88 2.93 0.00 2.85
3578 7899 8.141909 ACTGCTAGAAAGAAATTTGTTTTACCC 58.858 33.333 13.88 2.61 0.00 3.69
3579 7900 8.245195 TGCTAGAAAGAAATTTGTTTTACCCT 57.755 30.769 13.88 9.17 0.00 4.34
3580 7901 8.357402 TGCTAGAAAGAAATTTGTTTTACCCTC 58.643 33.333 13.88 1.63 0.00 4.30
3581 7902 7.813148 GCTAGAAAGAAATTTGTTTTACCCTCC 59.187 37.037 13.88 1.02 0.00 4.30
3582 7903 7.669089 AGAAAGAAATTTGTTTTACCCTCCA 57.331 32.000 13.88 0.00 0.00 3.86
3583 7904 8.084985 AGAAAGAAATTTGTTTTACCCTCCAA 57.915 30.769 13.88 0.00 0.00 3.53
3584 7905 8.544622 AGAAAGAAATTTGTTTTACCCTCCAAA 58.455 29.630 13.88 0.00 0.00 3.28
3585 7906 9.168451 GAAAGAAATTTGTTTTACCCTCCAAAA 57.832 29.630 13.88 0.00 31.30 2.44
3672 7996 1.123077 TTACGGATGCATCAGGCTCT 58.877 50.000 27.07 11.46 45.15 4.09
3677 8001 0.469070 GATGCATCAGGCTCTGAGGT 59.531 55.000 21.92 0.88 44.08 3.85
3793 8236 7.667219 AGAAAACCATAGATGATGTTGTCACTT 59.333 33.333 0.00 0.00 40.28 3.16
3796 8239 4.260497 CCATAGATGATGTTGTCACTTGCG 60.260 45.833 0.00 0.00 40.28 4.85
3808 8251 3.000041 GTCACTTGCGTCATATTGGTGA 59.000 45.455 0.00 0.00 0.00 4.02
3814 8257 2.682352 TGCGTCATATTGGTGATGTTGG 59.318 45.455 0.00 0.00 37.43 3.77
3822 8265 1.378514 GGTGATGTTGGACGCCCAT 60.379 57.895 0.00 0.00 43.12 4.00
3825 8268 2.755469 ATGTTGGACGCCCATGCC 60.755 61.111 0.00 0.00 43.12 4.40
4039 8483 9.278978 TGTAGACAAGAAACATTAAGCAATACA 57.721 29.630 0.00 0.00 0.00 2.29
4154 8600 2.092103 AGAACCCACTACAAAGCACCAA 60.092 45.455 0.00 0.00 0.00 3.67
4155 8601 1.981256 ACCCACTACAAAGCACCAAG 58.019 50.000 0.00 0.00 0.00 3.61
4182 8631 4.204012 TGAAGAAAACCCATCGAACTTGT 58.796 39.130 0.00 0.00 0.00 3.16
4189 8639 4.568152 ACCCATCGAACTTGTCAAAAAG 57.432 40.909 0.00 0.00 0.00 2.27
4192 8642 5.126384 ACCCATCGAACTTGTCAAAAAGAAA 59.874 36.000 0.00 0.00 0.00 2.52
4336 8789 7.449395 ACACATCCACAAATTATATCAGATGGG 59.551 37.037 0.00 0.00 39.30 4.00
4463 8922 2.124570 ACATGGTCATGGAGGCGC 60.125 61.111 14.49 0.00 42.91 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 8.980143 TCATTATCGAGTTATTTCATGCGATA 57.020 30.769 0.00 0.00 39.02 2.92
306 339 5.657470 TCAATGAACAAACGAAGTCTGAG 57.343 39.130 0.00 0.00 45.00 3.35
369 402 1.034838 TTGAAAGCCGTTGCACCTGT 61.035 50.000 0.00 0.00 41.13 4.00
804 1351 2.113139 GTGTGGTGGGTGGGAGTG 59.887 66.667 0.00 0.00 0.00 3.51
1044 1598 1.958715 CATGTCGAACACCACGCCA 60.959 57.895 0.00 0.00 0.00 5.69
1301 1893 0.725117 CACACGCCGATAAGGGAAAC 59.275 55.000 0.00 0.00 41.48 2.78
1302 1894 0.609151 TCACACGCCGATAAGGGAAA 59.391 50.000 0.00 0.00 41.48 3.13
1415 2378 2.064387 GCATCACACGCATGCAAAC 58.936 52.632 19.57 0.00 45.19 2.93
1428 2391 1.344438 ACTGAACTGAACCGAGCATCA 59.656 47.619 0.00 0.00 33.17 3.07
1436 2399 5.050295 GCTGTACAACTAACTGAACTGAACC 60.050 44.000 0.00 0.00 0.00 3.62
1460 2423 6.974932 AAGTACAATTGAGCACATAGTGAG 57.025 37.500 13.59 0.00 35.23 3.51
1479 2442 7.930865 CCCCAAATCAATTCTGAAAACAAAGTA 59.069 33.333 0.00 0.00 34.49 2.24
1504 2467 4.173256 GTGCAAATGGTATTACACTTGCC 58.827 43.478 17.17 9.67 38.67 4.52
1508 2471 4.016444 CCAGGTGCAAATGGTATTACACT 58.984 43.478 9.79 0.00 29.27 3.55
1618 2581 6.045072 TCCTGAAATGTTAGTCCGTACATT 57.955 37.500 0.00 0.00 44.50 2.71
1679 2644 8.605947 AGCCATTCAATCTATATAGCCTACAAA 58.394 33.333 4.75 0.00 0.00 2.83
1699 2664 5.518848 TGCATATCAAATTTCGAGCCATT 57.481 34.783 0.00 0.00 0.00 3.16
1746 2718 1.153489 CCAGGATCAGAGCCACACG 60.153 63.158 7.64 0.00 0.00 4.49
1747 2719 0.835941 ATCCAGGATCAGAGCCACAC 59.164 55.000 7.64 0.00 0.00 3.82
1749 2721 2.224402 GGTAATCCAGGATCAGAGCCAC 60.224 54.545 7.64 0.00 0.00 5.01
1750 2722 2.050144 GGTAATCCAGGATCAGAGCCA 58.950 52.381 7.64 0.00 0.00 4.75
1751 2723 2.334023 AGGTAATCCAGGATCAGAGCC 58.666 52.381 1.11 0.00 35.89 4.70
1752 2724 4.591072 AGTAAGGTAATCCAGGATCAGAGC 59.409 45.833 1.11 1.36 35.89 4.09
1753 2725 6.239458 GGAAGTAAGGTAATCCAGGATCAGAG 60.239 46.154 1.11 0.00 35.89 3.35
1754 2726 5.602978 GGAAGTAAGGTAATCCAGGATCAGA 59.397 44.000 1.11 0.00 35.89 3.27
1755 2727 5.604650 AGGAAGTAAGGTAATCCAGGATCAG 59.395 44.000 1.11 0.00 34.30 2.90
1756 2728 5.538877 AGGAAGTAAGGTAATCCAGGATCA 58.461 41.667 1.11 0.00 34.30 2.92
1757 2729 7.613551 TTAGGAAGTAAGGTAATCCAGGATC 57.386 40.000 1.11 0.00 34.30 3.36
1759 2731 7.136885 TCATTAGGAAGTAAGGTAATCCAGGA 58.863 38.462 0.00 0.00 34.30 3.86
1760 2732 7.374975 TCATTAGGAAGTAAGGTAATCCAGG 57.625 40.000 0.00 0.00 34.30 4.45
1761 2733 8.651389 TGATCATTAGGAAGTAAGGTAATCCAG 58.349 37.037 0.00 0.00 34.30 3.86
1762 2734 8.561536 TGATCATTAGGAAGTAAGGTAATCCA 57.438 34.615 0.00 0.00 34.30 3.41
1763 2735 8.652290 ACTGATCATTAGGAAGTAAGGTAATCC 58.348 37.037 0.00 0.00 0.00 3.01
1766 2738 8.627403 CGTACTGATCATTAGGAAGTAAGGTAA 58.373 37.037 6.90 0.00 0.00 2.85
1844 2846 0.678048 AAGTTCCCGCTCCAAGATGC 60.678 55.000 0.00 0.00 0.00 3.91
1855 2857 3.822607 CAGAGAGTGGAAGTTCCCG 57.177 57.895 19.42 0.00 35.03 5.14
1921 2924 7.239763 TCAGTGATCTAGTAATTCACAACCA 57.760 36.000 15.17 0.00 41.71 3.67
1964 2967 4.191544 CGAGGACTGATGGCATTAAGAAA 58.808 43.478 15.57 0.00 0.00 2.52
2085 3104 7.493367 ACTAGTAAGCTACATCCAAATCTGAC 58.507 38.462 0.00 0.00 0.00 3.51
2100 3119 9.828039 AGTAAGTAAACAACAAACTAGTAAGCT 57.172 29.630 0.00 0.00 0.00 3.74
2161 3207 9.255304 GGCAGATTTTTACAATAACAAACAGAA 57.745 29.630 0.00 0.00 0.00 3.02
2331 3379 2.223688 TGGTGAAACAAATCAACTGCGG 60.224 45.455 0.00 0.00 39.98 5.69
2537 3670 4.284178 CAAGGATTGGGGAGATCAACATT 58.716 43.478 0.00 0.00 43.94 2.71
2598 3733 3.617263 GCAGAGTTACAACATAACCTCGG 59.383 47.826 0.00 0.00 0.00 4.63
2599 3734 4.242475 TGCAGAGTTACAACATAACCTCG 58.758 43.478 0.00 0.00 0.00 4.63
2760 3895 3.990092 TCTGCGTAAGTTTCAGATGTGT 58.010 40.909 0.00 0.00 41.68 3.72
2834 3969 3.702548 AGCAAATATGAAGCAATGGAGCA 59.297 39.130 0.00 0.00 36.85 4.26
2954 4089 7.281774 AGCAAAGTGAACTGTATAGGAATCATG 59.718 37.037 0.00 0.00 0.00 3.07
3098 4233 2.168936 TCCTTTTGATTCATGGGCATGC 59.831 45.455 9.90 9.90 38.65 4.06
3102 4237 4.632688 CACAATTCCTTTTGATTCATGGGC 59.367 41.667 0.00 0.00 0.00 5.36
3162 4297 3.857052 TGAACTCCGGCTTATGTAAGTG 58.143 45.455 0.00 0.00 35.75 3.16
3199 4335 8.531530 CGGAAAAGTTTAAGATTCACAAAACTG 58.468 33.333 10.10 0.00 40.35 3.16
3200 4336 8.463607 TCGGAAAAGTTTAAGATTCACAAAACT 58.536 29.630 0.00 5.65 42.40 2.66
3201 4337 8.623310 TCGGAAAAGTTTAAGATTCACAAAAC 57.377 30.769 0.00 0.00 33.11 2.43
3204 4340 8.234546 GCTATCGGAAAAGTTTAAGATTCACAA 58.765 33.333 5.94 0.00 0.00 3.33
3205 4341 7.606456 AGCTATCGGAAAAGTTTAAGATTCACA 59.394 33.333 0.00 0.00 0.00 3.58
3206 4342 7.975750 AGCTATCGGAAAAGTTTAAGATTCAC 58.024 34.615 0.00 0.00 0.00 3.18
3207 4343 8.450964 CAAGCTATCGGAAAAGTTTAAGATTCA 58.549 33.333 0.00 0.00 0.00 2.57
3208 4344 8.451748 ACAAGCTATCGGAAAAGTTTAAGATTC 58.548 33.333 0.00 0.00 0.00 2.52
3209 4345 8.237267 CACAAGCTATCGGAAAAGTTTAAGATT 58.763 33.333 0.00 0.00 0.00 2.40
3238 4374 4.406069 CAAGGCAAATGAATCAGTACACG 58.594 43.478 0.00 0.00 0.00 4.49
3319 4455 1.429463 ATCGTCCAGTTTCGTCAAGC 58.571 50.000 0.00 0.00 0.00 4.01
3352 4488 4.400567 GGCTTAACATCTTCAGGCAAAGAT 59.599 41.667 8.77 8.77 44.84 2.40
3400 4536 1.684450 TCAAGCACCGACAGTACTTCA 59.316 47.619 0.00 0.00 28.97 3.02
3488 7806 9.025020 GCTCGACATATACCATATTACATTCAG 57.975 37.037 0.00 0.00 0.00 3.02
3535 7856 2.749621 GCAGTCATACTTTTGGAGGGTG 59.250 50.000 0.00 0.00 0.00 4.61
3547 7868 9.899226 AAACAAATTTCTTTCTAGCAGTCATAC 57.101 29.630 0.00 0.00 0.00 2.39
3550 7871 9.730420 GTAAAACAAATTTCTTTCTAGCAGTCA 57.270 29.630 0.00 0.00 32.27 3.41
3551 7872 9.181805 GGTAAAACAAATTTCTTTCTAGCAGTC 57.818 33.333 0.00 0.00 32.27 3.51
3552 7873 8.141909 GGGTAAAACAAATTTCTTTCTAGCAGT 58.858 33.333 0.00 0.00 32.27 4.40
3553 7874 8.360390 AGGGTAAAACAAATTTCTTTCTAGCAG 58.640 33.333 0.00 0.00 32.27 4.24
3554 7875 8.245195 AGGGTAAAACAAATTTCTTTCTAGCA 57.755 30.769 0.00 0.00 32.27 3.49
3555 7876 7.813148 GGAGGGTAAAACAAATTTCTTTCTAGC 59.187 37.037 0.00 0.00 32.27 3.42
3556 7877 8.856103 TGGAGGGTAAAACAAATTTCTTTCTAG 58.144 33.333 0.00 0.00 32.27 2.43
3557 7878 8.770010 TGGAGGGTAAAACAAATTTCTTTCTA 57.230 30.769 0.00 0.00 32.27 2.10
3558 7879 7.669089 TGGAGGGTAAAACAAATTTCTTTCT 57.331 32.000 0.00 0.00 32.27 2.52
3559 7880 8.725405 TTTGGAGGGTAAAACAAATTTCTTTC 57.275 30.769 0.00 0.00 32.27 2.62
3560 7881 9.521841 TTTTTGGAGGGTAAAACAAATTTCTTT 57.478 25.926 0.00 0.00 33.40 2.52
3561 7882 9.693739 ATTTTTGGAGGGTAAAACAAATTTCTT 57.306 25.926 0.00 0.00 33.40 2.52
3566 7887 9.719355 GTCATATTTTTGGAGGGTAAAACAAAT 57.281 29.630 0.00 0.00 33.40 2.32
3567 7888 8.929487 AGTCATATTTTTGGAGGGTAAAACAAA 58.071 29.630 0.00 0.00 0.00 2.83
3568 7889 8.364142 CAGTCATATTTTTGGAGGGTAAAACAA 58.636 33.333 0.00 0.00 0.00 2.83
3569 7890 7.524698 GCAGTCATATTTTTGGAGGGTAAAACA 60.525 37.037 0.00 0.00 0.00 2.83
3570 7891 6.811665 GCAGTCATATTTTTGGAGGGTAAAAC 59.188 38.462 0.00 0.00 0.00 2.43
3571 7892 6.723977 AGCAGTCATATTTTTGGAGGGTAAAA 59.276 34.615 0.00 0.00 0.00 1.52
3572 7893 6.252995 AGCAGTCATATTTTTGGAGGGTAAA 58.747 36.000 0.00 0.00 0.00 2.01
3573 7894 5.826643 AGCAGTCATATTTTTGGAGGGTAA 58.173 37.500 0.00 0.00 0.00 2.85
3574 7895 5.450818 AGCAGTCATATTTTTGGAGGGTA 57.549 39.130 0.00 0.00 0.00 3.69
3575 7896 4.322057 AGCAGTCATATTTTTGGAGGGT 57.678 40.909 0.00 0.00 0.00 4.34
3576 7897 5.684704 TCTAGCAGTCATATTTTTGGAGGG 58.315 41.667 0.00 0.00 0.00 4.30
3577 7898 7.554118 TCTTTCTAGCAGTCATATTTTTGGAGG 59.446 37.037 0.00 0.00 0.00 4.30
3578 7899 8.498054 TCTTTCTAGCAGTCATATTTTTGGAG 57.502 34.615 0.00 0.00 0.00 3.86
3579 7900 8.862325 TTCTTTCTAGCAGTCATATTTTTGGA 57.138 30.769 0.00 0.00 0.00 3.53
3672 7996 3.916359 TTTCACGGCCATAATACCTCA 57.084 42.857 2.24 0.00 0.00 3.86
3677 8001 3.889196 GCGAATTTCACGGCCATAATA 57.111 42.857 2.24 0.00 0.00 0.98
3728 8053 6.875972 ACTCTACTAAATTCCAGTCACCAT 57.124 37.500 0.00 0.00 0.00 3.55
3793 8236 2.682352 CCAACATCACCAATATGACGCA 59.318 45.455 0.00 0.00 0.00 5.24
3796 8239 3.242739 GCGTCCAACATCACCAATATGAC 60.243 47.826 0.00 0.00 0.00 3.06
3825 8268 6.381481 TCATAGTCAAAAATAGCCATGCTG 57.619 37.500 0.00 0.00 40.10 4.41
3880 8323 8.471609 TGATTAACGGTCTACTTATCATGAACA 58.528 33.333 0.00 0.00 0.00 3.18
4154 8600 5.677319 TCGATGGGTTTTCTTCATAGACT 57.323 39.130 0.00 0.00 0.00 3.24
4155 8601 5.875359 AGTTCGATGGGTTTTCTTCATAGAC 59.125 40.000 0.00 0.00 0.00 2.59
4182 8631 8.734386 GCTCTCCAATCTATCTTTTCTTTTTGA 58.266 33.333 0.00 0.00 0.00 2.69
4189 8639 5.530171 TGCATGCTCTCCAATCTATCTTTTC 59.470 40.000 20.33 0.00 0.00 2.29
4192 8642 4.701651 TGCATGCTCTCCAATCTATCTT 57.298 40.909 20.33 0.00 0.00 2.40
4336 8789 0.107703 TTGCCTCACATGATCGGGAC 60.108 55.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.