Multiple sequence alignment - TraesCS6A01G125300

Loading Multiple Alignment...

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 TraesCS6A01G125300 chr6A 100.000 5305 0 0 1 5305 98889120 98883816 0.000000e+00 9797.0
1 TraesCS6A01G125300 chr6A 86.306 4586 464 80 598 5138 99016589 99012123 0.000000e+00 4839.0
2 TraesCS6A01G125300 chr6A 83.414 4540 621 66 607 5106 98982766 98978319 0.000000e+00 4091.0
3 TraesCS6A01G125300 chr6A 81.104 3805 622 67 920 4675 98316058 98312302 0.000000e+00 2953.0
4 TraesCS6A01G125300 chr6A 82.245 3368 551 31 992 4340 98310005 98306666 0.000000e+00 2863.0
5 TraesCS6A01G125300 chr6A 79.216 2040 399 20 1018 3043 100368181 100366153 0.000000e+00 1395.0
6 TraesCS6A01G125300 chr6A 76.604 530 70 27 242 734 98917893 98917381 5.310000e-60 243.0
7 TraesCS6A01G125300 chr6A 83.019 159 21 6 4937 5091 98808926 98808770 7.160000e-29 139.0
8 TraesCS6A01G125300 chr6A 76.727 275 47 12 4777 5045 98312216 98311953 2.580000e-28 137.0
9 TraesCS6A01G125300 chr6A 96.226 53 2 0 212 264 98814391 98814339 2.630000e-13 87.9
10 TraesCS6A01G125300 chr6A 82.979 94 13 2 199 291 98257217 98257126 1.220000e-11 82.4
11 TraesCS6A01G125300 chr6D 90.934 4401 336 19 883 5256 82204115 82199751 0.000000e+00 5858.0
12 TraesCS6A01G125300 chr6D 87.108 3320 396 23 893 4197 82220616 82217314 0.000000e+00 3731.0
13 TraesCS6A01G125300 chr6D 82.463 3313 532 37 1071 4362 81773822 81770538 0.000000e+00 2854.0
14 TraesCS6A01G125300 chr6D 81.298 3545 597 45 920 4432 81926272 81922762 0.000000e+00 2813.0
15 TraesCS6A01G125300 chr6D 83.265 2444 380 25 590 3015 83108973 83106541 0.000000e+00 2220.0
16 TraesCS6A01G125300 chr6D 79.177 2430 391 56 635 3046 46901119 46903451 0.000000e+00 1578.0
17 TraesCS6A01G125300 chr6D 77.040 527 67 23 245 734 82210467 82209958 2.450000e-63 254.0
18 TraesCS6A01G125300 chr6D 74.922 642 89 44 4529 5135 82234111 82233507 1.490000e-55 228.0
19 TraesCS6A01G125300 chr6D 81.868 182 26 7 4935 5112 81916600 81916422 4.280000e-31 147.0
20 TraesCS6A01G125300 chr6D 85.106 94 11 2 199 291 81764754 81764663 5.660000e-15 93.5
21 TraesCS6A01G125300 chr6D 82.524 103 11 3 160 262 82970181 82970086 3.400000e-12 84.2
22 TraesCS6A01G125300 chr6B 90.638 3856 324 18 592 4436 157109801 157105972 0.000000e+00 5086.0
23 TraesCS6A01G125300 chr6B 80.855 3813 647 46 598 4382 157489694 157485937 0.000000e+00 2920.0
24 TraesCS6A01G125300 chr6B 81.752 3436 574 33 992 4392 156550978 156547561 0.000000e+00 2822.0
25 TraesCS6A01G125300 chr6B 81.534 3417 568 43 920 4307 156654927 156651545 0.000000e+00 2756.0
26 TraesCS6A01G125300 chr6B 92.029 690 35 8 1 678 157110483 157109802 0.000000e+00 952.0
27 TraesCS6A01G125300 chr6B 89.706 680 49 9 4477 5147 157104006 157103339 0.000000e+00 848.0
28 TraesCS6A01G125300 chr6B 82.901 848 110 19 837 1679 125052408 125051591 0.000000e+00 730.0
29 TraesCS6A01G125300 chr6B 77.551 637 100 25 4529 5138 157485187 157484567 1.410000e-90 344.0
30 TraesCS6A01G125300 chr6B 76.837 449 58 22 324 734 157131513 157131073 1.500000e-50 211.0
31 TraesCS6A01G125300 chr6B 93.407 91 6 0 5183 5273 157103342 157103252 9.270000e-28 135.0
32 TraesCS6A01G125300 chr6B 93.103 87 4 2 4935 5020 156650707 156650622 5.580000e-25 126.0
33 TraesCS6A01G125300 chr6B 79.861 144 28 1 379 521 157766549 157766406 2.610000e-18 104.0
34 TraesCS6A01G125300 chr6B 73.248 314 51 23 199 498 156534002 156533708 3.400000e-12 84.2
35 TraesCS6A01G125300 chr5B 84.034 119 16 3 128 244 20172831 20172948 1.560000e-20 111.0


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 TraesCS6A01G125300 chr6A 98883816 98889120 5304 True 9797.000000 9797 100.000000 1 5305 1 chr6A.!!$R4 5304
1 TraesCS6A01G125300 chr6A 99012123 99016589 4466 True 4839.000000 4839 86.306000 598 5138 1 chr6A.!!$R7 4540
2 TraesCS6A01G125300 chr6A 98978319 98982766 4447 True 4091.000000 4091 83.414000 607 5106 1 chr6A.!!$R6 4499
3 TraesCS6A01G125300 chr6A 98306666 98316058 9392 True 1984.333333 2953 80.025333 920 5045 3 chr6A.!!$R9 4125
4 TraesCS6A01G125300 chr6A 100366153 100368181 2028 True 1395.000000 1395 79.216000 1018 3043 1 chr6A.!!$R8 2025
5 TraesCS6A01G125300 chr6A 98917381 98917893 512 True 243.000000 243 76.604000 242 734 1 chr6A.!!$R5 492
6 TraesCS6A01G125300 chr6D 82199751 82204115 4364 True 5858.000000 5858 90.934000 883 5256 1 chr6D.!!$R5 4373
7 TraesCS6A01G125300 chr6D 82217314 82220616 3302 True 3731.000000 3731 87.108000 893 4197 1 chr6D.!!$R7 3304
8 TraesCS6A01G125300 chr6D 81770538 81773822 3284 True 2854.000000 2854 82.463000 1071 4362 1 chr6D.!!$R2 3291
9 TraesCS6A01G125300 chr6D 81922762 81926272 3510 True 2813.000000 2813 81.298000 920 4432 1 chr6D.!!$R4 3512
10 TraesCS6A01G125300 chr6D 83106541 83108973 2432 True 2220.000000 2220 83.265000 590 3015 1 chr6D.!!$R10 2425
11 TraesCS6A01G125300 chr6D 46901119 46903451 2332 False 1578.000000 1578 79.177000 635 3046 1 chr6D.!!$F1 2411
12 TraesCS6A01G125300 chr6D 82209958 82210467 509 True 254.000000 254 77.040000 245 734 1 chr6D.!!$R6 489
13 TraesCS6A01G125300 chr6D 82233507 82234111 604 True 228.000000 228 74.922000 4529 5135 1 chr6D.!!$R8 606
14 TraesCS6A01G125300 chr6B 156547561 156550978 3417 True 2822.000000 2822 81.752000 992 4392 1 chr6B.!!$R3 3400
15 TraesCS6A01G125300 chr6B 157103252 157110483 7231 True 1755.250000 5086 91.445000 1 5273 4 chr6B.!!$R7 5272
16 TraesCS6A01G125300 chr6B 157484567 157489694 5127 True 1632.000000 2920 79.203000 598 5138 2 chr6B.!!$R8 4540
17 TraesCS6A01G125300 chr6B 156650622 156654927 4305 True 1441.000000 2756 87.318500 920 5020 2 chr6B.!!$R6 4100
18 TraesCS6A01G125300 chr6B 125051591 125052408 817 True 730.000000 730 82.901000 837 1679 1 chr6B.!!$R1 842

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
425 438 0.250295 TCTTCTTGCCGTCCACTTGG 60.250 55.0 0.00 0.0 0.00 3.61 F
1264 1440 0.321034 TCACCTGCAGCACAGATGAC 60.321 55.0 8.66 0.0 41.40 3.06 F
2114 2295 0.512952 GTACAACAGCTTCAGTGGCG 59.487 55.0 0.00 0.0 34.52 5.69 F
3161 3342 0.531974 GTTGGCACGTCTCCTTGTCA 60.532 55.0 5.13 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 1930 0.170784 GAAGAGTTCGTCCGGGAGAC 59.829 60.000 0.00 0.0 42.54 3.36 R
3143 3324 0.531974 GTGACAAGGAGACGTGCCAA 60.532 55.000 0.00 0.0 44.26 4.52 R
3274 3458 2.165998 CTTTCTTCTCCCTTGCCTTGG 58.834 52.381 0.00 0.0 0.00 3.61 R
4310 10793 0.322975 ACCTGTTAGGCTCTGTGCAG 59.677 55.000 3.96 0.0 45.15 4.41 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
27 28 3.194062 CCGCAGAAAACAACACCAATTT 58.806 40.909 0.00 0.00 0.00 1.82
74 80 5.689383 ATGATTAATACATGGTGCGGTTC 57.311 39.130 0.00 0.00 0.00 3.62
155 167 2.740055 GTGCCAGAGCTCACACGG 60.740 66.667 17.77 11.52 40.80 4.94
166 178 0.966920 CTCACACGGTACCCAGTCTT 59.033 55.000 6.25 0.00 0.00 3.01
178 190 1.543429 CCCAGTCTTCTTTGAACCGCT 60.543 52.381 0.00 0.00 0.00 5.52
179 191 2.222027 CCAGTCTTCTTTGAACCGCTT 58.778 47.619 0.00 0.00 0.00 4.68
180 192 2.224314 CCAGTCTTCTTTGAACCGCTTC 59.776 50.000 0.00 0.00 0.00 3.86
181 193 2.224314 CAGTCTTCTTTGAACCGCTTCC 59.776 50.000 0.00 0.00 0.00 3.46
182 194 2.158813 AGTCTTCTTTGAACCGCTTCCA 60.159 45.455 0.00 0.00 0.00 3.53
183 195 2.616842 GTCTTCTTTGAACCGCTTCCAA 59.383 45.455 0.00 0.00 0.00 3.53
184 196 2.616842 TCTTCTTTGAACCGCTTCCAAC 59.383 45.455 0.00 0.00 0.00 3.77
197 209 4.222114 CGCTTCCAACTTCAGATGAAAAC 58.778 43.478 0.00 0.00 33.07 2.43
272 284 5.405269 GGAAAACAACAGCAAATGTATCCAC 59.595 40.000 11.97 0.00 43.00 4.02
275 287 4.088634 ACAACAGCAAATGTATCCACCAT 58.911 39.130 0.00 0.00 43.00 3.55
301 313 1.530441 GCTCGTACGCGTGATAACTGA 60.530 52.381 24.59 12.20 39.49 3.41
302 314 2.099621 CTCGTACGCGTGATAACTGAC 58.900 52.381 24.59 8.35 39.49 3.51
414 427 4.170292 ACATGATTGCACTTCTTCTTGC 57.830 40.909 0.00 0.00 39.33 4.01
416 429 1.536766 TGATTGCACTTCTTCTTGCCG 59.463 47.619 0.00 0.00 38.00 5.69
425 438 0.250295 TCTTCTTGCCGTCCACTTGG 60.250 55.000 0.00 0.00 0.00 3.61
469 486 0.659957 GCCGATGTTTGCTCTGGATC 59.340 55.000 0.00 0.00 0.00 3.36
522 539 0.886490 CCATCTGGCCGGCTGAATAC 60.886 60.000 28.56 9.02 0.00 1.89
580 600 3.457234 GCTTTTCCTGTTCACCAAAAGG 58.543 45.455 0.00 0.00 36.67 3.11
679 727 6.935771 AGGCATGCTGTAAAAATTCATCAAAA 59.064 30.769 18.92 0.00 0.00 2.44
680 728 7.444792 AGGCATGCTGTAAAAATTCATCAAAAA 59.555 29.630 18.92 0.00 0.00 1.94
745 881 4.460948 TGTACGGAAGAATGGGTAGTTC 57.539 45.455 0.00 0.00 0.00 3.01
750 886 3.933332 CGGAAGAATGGGTAGTTCACTTC 59.067 47.826 0.00 0.00 33.80 3.01
751 887 4.262617 GGAAGAATGGGTAGTTCACTTCC 58.737 47.826 0.00 0.00 42.77 3.46
783 919 3.192001 ACAGCATGCAACCAATAGTGAAG 59.808 43.478 21.98 0.00 42.53 3.02
792 928 5.565439 GCAACCAATAGTGAAGCACTGAAAT 60.565 40.000 10.15 0.00 45.01 2.17
817 956 2.101582 AGTATGAACTAGGAAGCTGCCG 59.898 50.000 4.63 0.00 32.84 5.69
818 957 0.462759 ATGAACTAGGAAGCTGCCGC 60.463 55.000 4.63 0.00 0.00 6.53
844 984 2.287608 GCTGGGAGCAGTTGTGTAAAAC 60.288 50.000 0.00 0.00 41.89 2.43
847 987 1.265905 GGAGCAGTTGTGTAAAACCCG 59.734 52.381 0.00 0.00 0.00 5.28
863 1003 2.952116 ACCCGATTTTCTTGACCCAAA 58.048 42.857 0.00 0.00 0.00 3.28
866 1006 4.021456 ACCCGATTTTCTTGACCCAAATTC 60.021 41.667 0.00 0.00 0.00 2.17
880 1020 4.261801 CCCAAATTCTTCGTGGTGACTAT 58.738 43.478 0.00 0.00 0.00 2.12
912 1073 2.229784 GACAGAACAAATGGGAGCAAGG 59.770 50.000 0.00 0.00 0.00 3.61
913 1074 1.067354 CAGAACAAATGGGAGCAAGGC 60.067 52.381 0.00 0.00 0.00 4.35
1006 1168 1.066143 CATAAGCTCAGGTTCCCGTGT 60.066 52.381 0.00 0.00 0.00 4.49
1024 1191 4.334481 CCGTGTTAGTTTCACCAGAAAACT 59.666 41.667 6.50 6.50 44.75 2.66
1037 1204 3.369147 CCAGAAAACTATGCAGACACTCG 59.631 47.826 0.00 0.00 0.00 4.18
1092 1265 0.631212 ATACCTTCCCTTGGCCTTGG 59.369 55.000 3.32 5.90 0.00 3.61
1203 1376 2.596851 AAGATGGTGGCCTCGCTGT 61.597 57.895 3.32 0.00 0.00 4.40
1211 1384 2.265739 GCCTCGCTGTGTCATGGA 59.734 61.111 0.00 0.00 0.00 3.41
1213 1386 0.745845 GCCTCGCTGTGTCATGGAAT 60.746 55.000 0.00 0.00 0.00 3.01
1264 1440 0.321034 TCACCTGCAGCACAGATGAC 60.321 55.000 8.66 0.00 41.40 3.06
1444 1620 4.273148 AGATGTCAGCTTTAACCGTCTT 57.727 40.909 0.00 0.00 0.00 3.01
1648 1829 3.915575 CCATCCTTGGCAGTGCTC 58.084 61.111 16.11 5.84 35.85 4.26
1838 2019 2.036346 GGAACACTTGAAGGCTTGCATT 59.964 45.455 3.46 0.00 0.00 3.56
1923 2104 4.006989 CCGGAGTCTATAGGTCATCTCAG 58.993 52.174 0.00 2.56 0.00 3.35
2039 2220 0.881118 GAGCAACAATTTCAGCGGGA 59.119 50.000 0.00 0.00 0.00 5.14
2069 2250 5.264395 CCAAGGTCAATTTCTCCAACCTAT 58.736 41.667 0.00 0.00 39.40 2.57
2084 2265 9.053472 TCTCCAACCTATCCAATCTAAAAACTA 57.947 33.333 0.00 0.00 0.00 2.24
2114 2295 0.512952 GTACAACAGCTTCAGTGGCG 59.487 55.000 0.00 0.00 34.52 5.69
2180 2361 3.994392 GCGTCTGTCTTCCAATAAGTTCA 59.006 43.478 0.00 0.00 0.00 3.18
2290 2471 6.989169 GTGCACTTCATATCCTTAAGAGATGT 59.011 38.462 10.32 1.05 43.42 3.06
2318 2499 2.483014 TACAACCCTGCTTATTGCGT 57.517 45.000 0.00 0.00 46.63 5.24
2450 2631 8.621532 ATGGATATCGAAGCTAGCAAATTTAA 57.378 30.769 18.83 0.00 0.00 1.52
2532 2713 3.356529 AAGCAACCTGTTCTATCTGGG 57.643 47.619 0.00 0.00 0.00 4.45
2631 2812 3.207452 CCCATTTAGACCCAAGGGC 57.793 57.895 4.70 0.00 39.32 5.19
2651 2832 4.402474 GGGCATTTGAGCTACCTGTTTATT 59.598 41.667 0.00 0.00 34.17 1.40
2729 2910 4.045636 AGCAACAACAAATTCACTGGTC 57.954 40.909 0.00 0.00 0.00 4.02
2774 2955 3.633361 AAAGCCCTCCTTTCACTCG 57.367 52.632 0.00 0.00 39.55 4.18
2785 2966 4.389374 TCCTTTCACTCGATTTCAGCTTT 58.611 39.130 0.00 0.00 0.00 3.51
2854 3035 2.548707 CCTGCAGCTGTTAGACTTGTCA 60.549 50.000 16.64 0.00 0.00 3.58
2878 3059 7.615365 TCAAGCAATAATCTAACAGGTGGAATT 59.385 33.333 0.00 0.00 0.00 2.17
3143 3324 5.473039 GAGGCATTGCTATTCTTTTGTTGT 58.527 37.500 8.82 0.00 0.00 3.32
3147 3328 5.615325 GCATTGCTATTCTTTTGTTGTTGGC 60.615 40.000 0.16 0.00 0.00 4.52
3148 3329 4.662468 TGCTATTCTTTTGTTGTTGGCA 57.338 36.364 0.00 0.00 0.00 4.92
3161 3342 0.531974 GTTGGCACGTCTCCTTGTCA 60.532 55.000 5.13 0.00 0.00 3.58
3180 3361 3.753797 GTCACAATCAGGAAGAAGGGTTC 59.246 47.826 0.00 0.00 0.00 3.62
3208 3392 5.354513 GGCAAAACATAGAAGGGAGAGTAAC 59.645 44.000 0.00 0.00 0.00 2.50
3259 3443 4.997395 TCCAGTTCAGAGCAAACATTAGTC 59.003 41.667 0.00 0.00 0.00 2.59
3274 3458 0.464036 TAGTCGTCATGTGGATGCCC 59.536 55.000 0.00 0.00 32.27 5.36
3894 4078 4.106197 GTTGCTACGTTGAGAGGTGATAG 58.894 47.826 0.00 0.00 0.00 2.08
4201 10364 5.841957 AATCAGCCAAGATACAATGAACC 57.158 39.130 0.00 0.00 0.00 3.62
4202 10365 4.299586 TCAGCCAAGATACAATGAACCA 57.700 40.909 0.00 0.00 0.00 3.67
4203 10366 4.009675 TCAGCCAAGATACAATGAACCAC 58.990 43.478 0.00 0.00 0.00 4.16
4204 10367 4.012374 CAGCCAAGATACAATGAACCACT 58.988 43.478 0.00 0.00 0.00 4.00
4205 10368 5.045942 TCAGCCAAGATACAATGAACCACTA 60.046 40.000 0.00 0.00 0.00 2.74
4206 10369 5.647658 CAGCCAAGATACAATGAACCACTAA 59.352 40.000 0.00 0.00 0.00 2.24
4207 10370 6.150976 CAGCCAAGATACAATGAACCACTAAA 59.849 38.462 0.00 0.00 0.00 1.85
4208 10371 6.151144 AGCCAAGATACAATGAACCACTAAAC 59.849 38.462 0.00 0.00 0.00 2.01
4226 10389 9.996554 CCACTAAACCACACATGATAGATAATA 57.003 33.333 0.00 0.00 0.00 0.98
4354 10837 4.392138 GCCATCTTGAGCTTTACGTACTTT 59.608 41.667 0.00 0.00 0.00 2.66
4592 12856 0.603975 AAGAACCGCAGAGTTGGAGC 60.604 55.000 0.00 0.00 0.00 4.70
4597 12861 1.294659 CCGCAGAGTTGGAGCTGAAC 61.295 60.000 0.00 0.00 34.06 3.18
4607 12871 2.972625 TGGAGCTGAACTACCGAATTG 58.027 47.619 0.00 0.00 0.00 2.32
4609 12873 1.666189 GAGCTGAACTACCGAATTGCC 59.334 52.381 0.00 0.00 0.00 4.52
4630 12895 3.568538 CAGCTACAGCAAATGTTTGGTC 58.431 45.455 7.17 0.00 46.06 4.02
4633 12898 0.031994 ACAGCAAATGTTTGGTCGGC 59.968 50.000 7.17 0.00 46.06 5.54
4702 12983 7.957484 CGACTACCATCTTTGAAATACAAACTG 59.043 37.037 0.00 0.00 42.57 3.16
4704 12985 9.349713 ACTACCATCTTTGAAATACAAACTGAA 57.650 29.630 0.00 0.00 42.57 3.02
4745 13048 1.338200 GCAGAACACGAGAGGAATGGT 60.338 52.381 0.00 0.00 0.00 3.55
4775 13108 2.613474 GCACCTACGTACCATGTCCAAA 60.613 50.000 0.00 0.00 0.00 3.28
4780 13113 5.183228 CCTACGTACCATGTCCAAAGATTT 58.817 41.667 0.00 0.00 0.00 2.17
4817 13153 1.078708 GGGCCTTGCAACGTAGCTA 60.079 57.895 0.84 0.00 34.99 3.32
4850 13208 2.879002 AGACACATACGCATCAGAGG 57.121 50.000 0.00 0.00 0.00 3.69
4868 13226 0.681243 GGACTTCCCAAGCATGGTCC 60.681 60.000 7.29 3.38 46.01 4.46
4889 13248 1.075896 GATCCCACCCGGACTCTCT 60.076 63.158 0.73 0.00 46.09 3.10
4897 13256 1.139095 CCGGACTCTCTACGGCAAC 59.861 63.158 0.00 0.00 41.23 4.17
4898 13257 1.139095 CGGACTCTCTACGGCAACC 59.861 63.158 0.00 0.00 0.00 3.77
4933 13299 1.594331 GCGGTCCAAGAAAAGACACT 58.406 50.000 0.00 0.00 34.58 3.55
5036 13402 2.874701 GGAGAAATAGATGCATGCGTGT 59.125 45.455 19.18 16.69 0.00 4.49
5144 13576 3.213402 GACTCGCCGGGAGAGAGG 61.213 72.222 30.79 9.19 46.23 3.69
5145 13577 3.700831 GACTCGCCGGGAGAGAGGA 62.701 68.421 30.79 2.03 46.23 3.71
5146 13578 2.904866 CTCGCCGGGAGAGAGGAG 60.905 72.222 21.64 2.11 46.23 3.69
5147 13579 3.707640 CTCGCCGGGAGAGAGGAGT 62.708 68.421 21.64 0.00 46.23 3.85
5148 13580 3.522731 CGCCGGGAGAGAGGAGTG 61.523 72.222 2.18 0.00 0.00 3.51
5149 13581 2.043852 GCCGGGAGAGAGGAGTGA 60.044 66.667 2.18 0.00 0.00 3.41
5150 13582 1.456705 GCCGGGAGAGAGGAGTGAT 60.457 63.158 2.18 0.00 0.00 3.06
5151 13583 1.743321 GCCGGGAGAGAGGAGTGATG 61.743 65.000 2.18 0.00 0.00 3.07
5152 13584 1.112315 CCGGGAGAGAGGAGTGATGG 61.112 65.000 0.00 0.00 0.00 3.51
5153 13585 1.112315 CGGGAGAGAGGAGTGATGGG 61.112 65.000 0.00 0.00 0.00 4.00
5154 13586 0.762461 GGGAGAGAGGAGTGATGGGG 60.762 65.000 0.00 0.00 0.00 4.96
5155 13587 0.263172 GGAGAGAGGAGTGATGGGGA 59.737 60.000 0.00 0.00 0.00 4.81
5156 13588 1.343478 GGAGAGAGGAGTGATGGGGAA 60.343 57.143 0.00 0.00 0.00 3.97
5157 13589 1.760029 GAGAGAGGAGTGATGGGGAAC 59.240 57.143 0.00 0.00 0.00 3.62
5158 13590 0.461961 GAGAGGAGTGATGGGGAACG 59.538 60.000 0.00 0.00 0.00 3.95
5159 13591 1.153349 GAGGAGTGATGGGGAACGC 60.153 63.158 0.00 0.00 43.69 4.84
5234 13666 0.809385 ACAGAGTAAGAGCGCGCTAA 59.191 50.000 36.69 20.10 0.00 3.09
5263 13695 2.598787 AATTCGGGTTCCTGCCGGA 61.599 57.895 5.05 0.00 37.60 5.14
5264 13696 2.536997 AATTCGGGTTCCTGCCGGAG 62.537 60.000 5.05 0.00 41.25 4.63
5273 13705 3.267974 CTGCCGGAGCTGGTTTTC 58.732 61.111 5.05 0.00 40.80 2.29
5274 13706 2.282180 TGCCGGAGCTGGTTTTCC 60.282 61.111 5.05 0.00 40.80 3.13
5275 13707 2.034221 GCCGGAGCTGGTTTTCCT 59.966 61.111 5.05 0.00 41.38 3.36
5276 13708 1.603739 GCCGGAGCTGGTTTTCCTT 60.604 57.895 5.05 0.00 41.38 3.36
5277 13709 1.179174 GCCGGAGCTGGTTTTCCTTT 61.179 55.000 5.05 0.00 41.38 3.11
5278 13710 0.881796 CCGGAGCTGGTTTTCCTTTC 59.118 55.000 0.00 0.00 41.38 2.62
5279 13711 1.545651 CCGGAGCTGGTTTTCCTTTCT 60.546 52.381 0.00 0.00 41.38 2.52
5280 13712 2.290071 CCGGAGCTGGTTTTCCTTTCTA 60.290 50.000 0.00 0.00 41.38 2.10
5281 13713 3.610911 CGGAGCTGGTTTTCCTTTCTAT 58.389 45.455 0.00 0.00 41.38 1.98
5282 13714 4.010349 CGGAGCTGGTTTTCCTTTCTATT 58.990 43.478 0.00 0.00 41.38 1.73
5283 13715 4.459337 CGGAGCTGGTTTTCCTTTCTATTT 59.541 41.667 0.00 0.00 41.38 1.40
5284 13716 5.048013 CGGAGCTGGTTTTCCTTTCTATTTT 60.048 40.000 0.00 0.00 41.38 1.82
5285 13717 6.516693 CGGAGCTGGTTTTCCTTTCTATTTTT 60.517 38.462 0.00 0.00 41.38 1.94
5286 13718 6.868864 GGAGCTGGTTTTCCTTTCTATTTTTC 59.131 38.462 0.00 0.00 41.38 2.29
5287 13719 6.447162 AGCTGGTTTTCCTTTCTATTTTTCG 58.553 36.000 0.00 0.00 41.38 3.46
5288 13720 6.040504 AGCTGGTTTTCCTTTCTATTTTTCGT 59.959 34.615 0.00 0.00 41.38 3.85
5289 13721 6.700081 GCTGGTTTTCCTTTCTATTTTTCGTT 59.300 34.615 0.00 0.00 41.38 3.85
5290 13722 7.223971 GCTGGTTTTCCTTTCTATTTTTCGTTT 59.776 33.333 0.00 0.00 41.38 3.60
5291 13723 9.093970 CTGGTTTTCCTTTCTATTTTTCGTTTT 57.906 29.630 0.00 0.00 41.38 2.43
5292 13724 9.438228 TGGTTTTCCTTTCTATTTTTCGTTTTT 57.562 25.926 0.00 0.00 41.38 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 53 6.978080 ACCGCACCATGTATTAATCATTTTTC 59.022 34.615 0.00 0.00 0.00 2.29
55 61 3.892284 TGGAACCGCACCATGTATTAAT 58.108 40.909 0.00 0.00 32.03 1.40
68 74 1.838568 GACGTGGTCTTTGGAACCGC 61.839 60.000 0.00 0.00 0.00 5.68
74 80 1.495584 CGTGTGGACGTGGTCTTTGG 61.496 60.000 0.00 0.00 40.91 3.28
155 167 3.064931 CGGTTCAAAGAAGACTGGGTAC 58.935 50.000 0.00 0.00 0.00 3.34
166 178 2.341846 AGTTGGAAGCGGTTCAAAGA 57.658 45.000 26.94 8.17 33.93 2.52
178 190 4.952957 TGTGGTTTTCATCTGAAGTTGGAA 59.047 37.500 0.00 0.00 35.21 3.53
179 191 4.531854 TGTGGTTTTCATCTGAAGTTGGA 58.468 39.130 0.00 0.00 35.21 3.53
180 192 4.339247 ACTGTGGTTTTCATCTGAAGTTGG 59.661 41.667 0.00 0.00 35.21 3.77
181 193 5.505173 ACTGTGGTTTTCATCTGAAGTTG 57.495 39.130 0.00 0.00 35.21 3.16
182 194 4.580580 GGACTGTGGTTTTCATCTGAAGTT 59.419 41.667 0.00 0.00 35.21 2.66
183 195 4.137543 GGACTGTGGTTTTCATCTGAAGT 58.862 43.478 0.00 0.00 35.21 3.01
184 196 4.136796 TGGACTGTGGTTTTCATCTGAAG 58.863 43.478 0.00 0.00 35.21 3.02
197 209 0.110295 TTGTGGACCATGGACTGTGG 59.890 55.000 21.47 0.00 42.55 4.17
211 223 3.128589 ACTGGCGCACTATTATTTTGTGG 59.871 43.478 10.83 0.00 32.85 4.17
212 224 4.097714 CACTGGCGCACTATTATTTTGTG 58.902 43.478 10.83 0.00 35.08 3.33
272 284 1.944676 GCGTACGAGCTTCGGATGG 60.945 63.158 21.65 1.60 45.59 3.51
275 287 3.425713 ACGCGTACGAGCTTCGGA 61.426 61.111 21.65 0.00 45.59 4.55
301 313 3.152341 CCTGAAGCATGAACTTCCTTGT 58.848 45.455 0.00 0.00 44.50 3.16
302 314 3.152341 ACCTGAAGCATGAACTTCCTTG 58.848 45.455 0.00 0.00 44.50 3.61
414 427 1.170290 GGACAAACCCAAGTGGACGG 61.170 60.000 0.00 0.00 37.39 4.79
416 429 1.029681 GTGGACAAACCCAAGTGGAC 58.970 55.000 0.00 0.00 38.06 4.02
425 438 2.948979 TCAATCAGTGTGTGGACAAACC 59.051 45.455 0.00 0.00 34.64 3.27
522 539 8.816640 AAAACAGTTGGTAAAGATATGCAAAG 57.183 30.769 0.00 0.00 0.00 2.77
555 575 0.310854 GGTGAACAGGAAAAGCCGTG 59.689 55.000 0.00 0.00 43.43 4.94
580 600 1.282157 ACCTCTACCCACATCCTTTGC 59.718 52.381 0.00 0.00 0.00 3.68
620 668 3.574396 CCCTGATATCGCTTCTCTTACCA 59.426 47.826 0.00 0.00 0.00 3.25
740 876 6.127423 GCTGTAATCTACTGGGAAGTGAACTA 60.127 42.308 0.00 0.00 0.00 2.24
745 881 4.471904 TGCTGTAATCTACTGGGAAGTG 57.528 45.455 0.00 0.00 0.00 3.16
750 886 3.198409 TGCATGCTGTAATCTACTGGG 57.802 47.619 20.33 0.00 0.00 4.45
751 887 3.313526 GGTTGCATGCTGTAATCTACTGG 59.686 47.826 20.33 0.00 0.00 4.00
792 928 5.011125 GGCAGCTTCCTAGTTCATACTGATA 59.989 44.000 0.00 0.00 35.78 2.15
799 935 0.462759 GCGGCAGCTTCCTAGTTCAT 60.463 55.000 0.00 0.00 41.01 2.57
818 957 4.335647 AACTGCTCCCAGCCCACG 62.336 66.667 0.00 0.00 43.02 4.94
829 969 2.335316 TCGGGTTTTACACAACTGCT 57.665 45.000 0.00 0.00 0.00 4.24
844 984 4.220602 AGAATTTGGGTCAAGAAAATCGGG 59.779 41.667 0.00 0.00 0.00 5.14
847 987 6.363357 CACGAAGAATTTGGGTCAAGAAAATC 59.637 38.462 0.00 0.00 32.29 2.17
863 1003 5.448768 CGTAGTCATAGTCACCACGAAGAAT 60.449 44.000 0.00 0.00 0.00 2.40
866 1006 3.373130 TCGTAGTCATAGTCACCACGAAG 59.627 47.826 0.00 0.00 34.38 3.79
880 1020 2.281539 TGTTCTGTCCCTCGTAGTCA 57.718 50.000 0.00 0.00 0.00 3.41
912 1073 0.251341 TGGGAAAGGAAGAAGCAGGC 60.251 55.000 0.00 0.00 0.00 4.85
913 1074 2.291153 TGATGGGAAAGGAAGAAGCAGG 60.291 50.000 0.00 0.00 0.00 4.85
923 1084 3.359033 TGAAAGAGCATGATGGGAAAGG 58.641 45.455 0.00 0.00 0.00 3.11
1006 1168 6.995686 TCTGCATAGTTTTCTGGTGAAACTAA 59.004 34.615 11.92 0.00 41.34 2.24
1024 1191 3.055458 TGGGAAAATCGAGTGTCTGCATA 60.055 43.478 2.64 0.00 0.00 3.14
1037 1204 5.048083 TGCTGTATGTCTTGTTGGGAAAATC 60.048 40.000 0.00 0.00 0.00 2.17
1092 1265 2.286872 AGCATATCAGCAGCACAAGAC 58.713 47.619 0.00 0.00 36.85 3.01
1203 1376 2.437651 TCCGAGCCATTATTCCATGACA 59.562 45.455 0.00 0.00 0.00 3.58
1211 1384 1.610522 GCAGCAATCCGAGCCATTATT 59.389 47.619 0.00 0.00 0.00 1.40
1213 1386 0.819259 GGCAGCAATCCGAGCCATTA 60.819 55.000 0.00 0.00 46.26 1.90
1264 1440 3.434641 CCAGCAAGACATCTGTAACAGTG 59.565 47.826 0.00 0.00 32.61 3.66
1444 1620 0.616964 ACTCATGCAGCTCTCCTCCA 60.617 55.000 0.00 0.00 0.00 3.86
1648 1829 3.745975 TGAATTGGTTGTAGCAGAGTTCG 59.254 43.478 0.00 0.00 0.00 3.95
1688 1869 1.741706 CATGGAGCAGCTACCAAGTTG 59.258 52.381 15.11 7.71 39.69 3.16
1749 1930 0.170784 GAAGAGTTCGTCCGGGAGAC 59.829 60.000 0.00 0.00 42.54 3.36
1838 2019 6.195600 ACCCAGATTACTGAGTTTACCAAA 57.804 37.500 0.00 0.00 46.03 3.28
1865 2046 6.298361 TGATGTTGTTCTCTCCAAGATCAAA 58.702 36.000 9.63 0.00 44.62 2.69
2039 2220 3.222603 AGAAATTGACCTTGGCGAGTTT 58.777 40.909 0.12 0.00 0.00 2.66
2084 2265 8.700051 ACTGAAGCTGTTGTACATAAGATCTAT 58.300 33.333 0.00 0.00 0.00 1.98
2114 2295 6.992063 TGAGTAGATGCTTTCTGGAATTTC 57.008 37.500 0.62 0.00 35.79 2.17
2180 2361 1.999648 TTTTCTGACAGCTGGCCATT 58.000 45.000 19.23 0.00 0.00 3.16
2212 2393 5.284582 AGTGATAGGAATGAGAGGGACTTT 58.715 41.667 0.00 0.00 41.55 2.66
2290 2471 7.308951 GCAATAAGCAGGGTTGTAAGTTTTCTA 60.309 37.037 0.00 0.00 44.79 2.10
2296 2477 2.747446 CGCAATAAGCAGGGTTGTAAGT 59.253 45.455 0.00 0.00 46.13 2.24
2302 2483 1.904287 TGAACGCAATAAGCAGGGTT 58.096 45.000 0.00 0.00 46.13 4.11
2318 2499 4.722526 TGATTTCTCCCCTGAAGTTGAA 57.277 40.909 0.00 0.00 0.00 2.69
2356 2537 8.822652 ACTGAAGATTTTCAAAACCATCAATC 57.177 30.769 0.00 0.00 42.48 2.67
2425 2606 8.621532 TTAAATTTGCTAGCTTCGATATCCAT 57.378 30.769 17.23 0.00 0.00 3.41
2532 2713 3.191162 TGTGAGGCTGTTGTTTGATATGC 59.809 43.478 0.00 0.00 0.00 3.14
2596 2777 5.441718 AATGGGCTTCACTCTTATCTGAA 57.558 39.130 0.00 0.00 0.00 3.02
2631 2812 8.225603 ACCATAATAAACAGGTAGCTCAAATG 57.774 34.615 0.00 0.00 31.32 2.32
2651 2832 4.897076 ACGGTATTGTAGTGATGGACCATA 59.103 41.667 7.05 0.00 0.00 2.74
2729 2910 1.212935 ACCAATCTCGAGGGGGATTTG 59.787 52.381 20.05 9.03 30.81 2.32
2774 2955 6.072112 TGTCAAGTGGTTAAAGCTGAAATC 57.928 37.500 0.00 0.00 0.00 2.17
2785 2966 4.394729 GGATTTGTCCTGTCAAGTGGTTA 58.605 43.478 0.00 0.00 0.00 2.85
2854 3035 7.068716 GGAATTCCACCTGTTAGATTATTGCTT 59.931 37.037 20.04 0.00 35.64 3.91
2878 3059 5.619132 TCAGTCTATTCAATGCATCTGGA 57.381 39.130 0.00 0.00 0.00 3.86
2883 3064 6.421485 AGGAAGTTCAGTCTATTCAATGCAT 58.579 36.000 5.01 0.00 0.00 3.96
3143 3324 0.531974 GTGACAAGGAGACGTGCCAA 60.532 55.000 0.00 0.00 44.26 4.52
3147 3328 2.733552 CTGATTGTGACAAGGAGACGTG 59.266 50.000 3.74 0.00 46.00 4.49
3148 3329 2.289072 CCTGATTGTGACAAGGAGACGT 60.289 50.000 3.74 0.00 0.00 4.34
3161 3342 5.339530 CCATAGAACCCTTCTTCCTGATTGT 60.340 44.000 0.00 0.00 41.14 2.71
3180 3361 5.684704 TCTCCCTTCTATGTTTTGCCATAG 58.315 41.667 0.00 0.00 43.69 2.23
3208 3392 4.472691 TGAAGTTGCTTCAACATCTTCG 57.527 40.909 8.89 0.00 45.84 3.79
3259 3443 2.271821 TGGGGCATCCACATGACG 59.728 61.111 0.00 0.00 39.27 4.35
3274 3458 2.165998 CTTTCTTCTCCCTTGCCTTGG 58.834 52.381 0.00 0.00 0.00 3.61
3894 4078 4.392138 GCATGACTACTCCAAAACTGTACC 59.608 45.833 0.00 0.00 0.00 3.34
4205 10368 9.353431 TGCAATATTATCTATCATGTGTGGTTT 57.647 29.630 0.00 0.00 0.00 3.27
4206 10369 8.922931 TGCAATATTATCTATCATGTGTGGTT 57.077 30.769 0.00 0.00 0.00 3.67
4207 10370 8.159447 ACTGCAATATTATCTATCATGTGTGGT 58.841 33.333 0.00 0.00 0.00 4.16
4208 10371 8.557592 ACTGCAATATTATCTATCATGTGTGG 57.442 34.615 0.00 0.00 0.00 4.17
4302 10677 2.983229 AGGCTCTGTGCAGAAATACAG 58.017 47.619 3.36 0.00 45.15 2.74
4310 10793 0.322975 ACCTGTTAGGCTCTGTGCAG 59.677 55.000 3.96 0.00 45.15 4.41
4358 10841 9.971922 GGAAGATGAATACCAAAATATTTCCTG 57.028 33.333 0.10 0.00 0.00 3.86
4399 10980 5.941788 ACAGAAACATCTAAAGGTCCTTGT 58.058 37.500 4.45 0.00 0.00 3.16
4580 12843 2.342179 GTAGTTCAGCTCCAACTCTGC 58.658 52.381 10.31 1.31 35.63 4.26
4592 12856 1.398390 GCTGGCAATTCGGTAGTTCAG 59.602 52.381 0.00 0.00 0.00 3.02
4597 12861 2.205074 CTGTAGCTGGCAATTCGGTAG 58.795 52.381 0.00 0.00 0.00 3.18
4607 12871 2.331194 CAAACATTTGCTGTAGCTGGC 58.669 47.619 5.38 0.00 42.66 4.85
4609 12873 3.568538 GACCAAACATTTGCTGTAGCTG 58.431 45.455 5.38 0.00 42.66 4.24
4633 12898 1.969923 TCCATTTGTTTGAGGCTTGGG 59.030 47.619 0.00 0.00 0.00 4.12
4640 12905 7.428020 TCAGTTTCTCATTCCATTTGTTTGAG 58.572 34.615 0.00 0.00 36.09 3.02
4702 12983 3.512680 AGTGACTGCGTGCTAAGTATTC 58.487 45.455 0.00 0.00 0.00 1.75
4704 12985 3.489398 GCTAGTGACTGCGTGCTAAGTAT 60.489 47.826 0.00 0.00 0.00 2.12
4705 12986 2.159421 GCTAGTGACTGCGTGCTAAGTA 60.159 50.000 0.00 0.00 0.00 2.24
4745 13048 2.426024 GGTACGTAGGTGCTTCTGATCA 59.574 50.000 0.00 0.00 0.00 2.92
4775 13108 2.092323 GTTTCTTGGCCGCCTAAATCT 58.908 47.619 11.61 0.00 0.00 2.40
4780 13113 1.302993 GTGGTTTCTTGGCCGCCTA 60.303 57.895 11.61 1.40 0.00 3.93
4832 13177 2.099921 AGTCCTCTGATGCGTATGTGTC 59.900 50.000 0.00 0.00 0.00 3.67
5144 13576 2.511600 CCGCGTTCCCCATCACTC 60.512 66.667 4.92 0.00 0.00 3.51
5145 13577 2.589157 TTCCGCGTTCCCCATCACT 61.589 57.895 4.92 0.00 0.00 3.41
5146 13578 2.046700 TTCCGCGTTCCCCATCAC 60.047 61.111 4.92 0.00 0.00 3.06
5147 13579 2.046700 GTTCCGCGTTCCCCATCA 60.047 61.111 4.92 0.00 0.00 3.07
5148 13580 2.822701 GGTTCCGCGTTCCCCATC 60.823 66.667 4.92 0.00 0.00 3.51
5149 13581 4.770874 CGGTTCCGCGTTCCCCAT 62.771 66.667 4.92 0.00 0.00 4.00
5159 13591 3.788766 CTGCTTTCCGCGGTTCCG 61.789 66.667 27.15 13.19 43.27 4.30
5160 13592 3.431725 CCTGCTTTCCGCGGTTCC 61.432 66.667 27.15 12.62 43.75 3.62
5161 13593 4.103103 GCCTGCTTTCCGCGGTTC 62.103 66.667 27.15 12.94 43.75 3.62
5162 13594 4.643387 AGCCTGCTTTCCGCGGTT 62.643 61.111 27.15 0.00 43.75 4.44
5165 13597 4.093952 CACAGCCTGCTTTCCGCG 62.094 66.667 0.00 0.00 43.27 6.46
5166 13598 3.741476 CCACAGCCTGCTTTCCGC 61.741 66.667 0.00 0.00 39.77 5.54
5167 13599 2.032528 TCCACAGCCTGCTTTCCG 59.967 61.111 0.00 0.00 0.00 4.30
5168 13600 2.338785 GCTCCACAGCCTGCTTTCC 61.339 63.158 0.00 0.00 40.14 3.13
5169 13601 2.684843 CGCTCCACAGCCTGCTTTC 61.685 63.158 0.00 0.00 43.56 2.62
5170 13602 2.670934 CGCTCCACAGCCTGCTTT 60.671 61.111 0.00 0.00 43.56 3.51
5234 13666 4.489771 CCGAATTGGGCCGGCTCT 62.490 66.667 29.93 7.19 39.22 4.09
5263 13695 6.040504 ACGAAAAATAGAAAGGAAAACCAGCT 59.959 34.615 0.00 0.00 0.00 4.24
5264 13696 6.213677 ACGAAAAATAGAAAGGAAAACCAGC 58.786 36.000 0.00 0.00 0.00 4.85
5266 13698 9.438228 AAAAACGAAAAATAGAAAGGAAAACCA 57.562 25.926 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.