Multiple sequence alignment - TraesCS6B01G089900

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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 TraesCS6B01G089900 chr6B 100.000 2507 0 0 1 2507 65159427 65156921 0.000000e+00 4630.0
1 TraesCS6B01G089900 chr6B 84.815 810 117 5 792 1598 53062065 53061259 0.000000e+00 809.0
2 TraesCS6B01G089900 chr6B 78.966 1122 208 19 809 1911 16255712 16256824 0.000000e+00 739.0
3 TraesCS6B01G089900 chr6B 85.969 449 47 8 2007 2440 53075052 53074605 1.360000e-127 466.0
4 TraesCS6B01G089900 chr6B 85.550 436 53 7 2006 2440 670600592 670600166 4.920000e-122 448.0
5 TraesCS6B01G089900 chr6B 80.396 454 49 11 2006 2440 15247915 15247483 2.420000e-80 309.0
6 TraesCS6B01G089900 chr6B 89.941 169 17 0 4 172 65174860 65174692 4.200000e-53 219.0
7 TraesCS6B01G089900 chr6B 88.202 178 21 0 1 178 16320844 16321021 1.950000e-51 213.0
8 TraesCS6B01G089900 chr6B 87.151 179 21 2 1 178 53076878 53076701 4.230000e-48 202.0
9 TraesCS6B01G089900 chr6B 86.111 180 25 0 1 180 15216598 15216419 7.080000e-46 195.0
10 TraesCS6B01G089900 chr6A 93.148 1328 64 10 1203 2505 35568297 35566972 0.000000e+00 1923.0
11 TraesCS6B01G089900 chr6A 84.783 782 115 3 792 1571 8994797 8994018 0.000000e+00 782.0
12 TraesCS6B01G089900 chr6A 79.474 989 186 14 869 1846 8623981 8622999 0.000000e+00 686.0
13 TraesCS6B01G089900 chr6A 78.693 1056 191 24 872 1911 30560042 30559005 0.000000e+00 673.0
14 TraesCS6B01G089900 chr6A 78.589 794 153 14 785 1571 9350655 9351438 2.220000e-140 508.0
15 TraesCS6B01G089900 chr6A 85.374 294 27 12 2161 2440 9366471 9366762 8.770000e-75 291.0
16 TraesCS6B01G089900 chr6A 90.116 172 17 0 1 172 35581332 35581161 9.020000e-55 224.0
17 TraesCS6B01G089900 chr5B 83.048 1109 171 11 812 1906 621235531 621234426 0.000000e+00 990.0
18 TraesCS6B01G089900 chr5D 82.262 1105 175 15 812 1900 499862136 499861037 0.000000e+00 935.0
19 TraesCS6B01G089900 chr5D 95.476 420 18 1 373 792 439495961 439496379 0.000000e+00 669.0
20 TraesCS6B01G089900 chr6D 82.597 747 120 7 792 1532 8968023 8968765 0.000000e+00 651.0
21 TraesCS6B01G089900 chr6D 79.574 940 167 15 872 1793 8578402 8577470 0.000000e+00 649.0
22 TraesCS6B01G089900 chr6D 83.559 444 53 8 2015 2440 34019275 34019716 5.020000e-107 398.0
23 TraesCS6B01G089900 chr2A 90.798 489 40 5 313 800 752919362 752918878 0.000000e+00 649.0
24 TraesCS6B01G089900 chr2A 90.368 353 30 4 319 670 752920479 752920130 6.320000e-126 460.0
25 TraesCS6B01G089900 chr2A 92.308 91 5 1 704 792 752920124 752920034 7.280000e-26 128.0
26 TraesCS6B01G089900 chr2B 79.189 937 174 13 873 1793 89495150 89496081 4.550000e-177 630.0
27 TraesCS6B01G089900 chr2B 78.298 940 188 13 869 1796 709487251 709486316 2.150000e-165 592.0
28 TraesCS6B01G089900 chr2B 80.914 744 138 4 792 1532 709425729 709424987 3.590000e-163 584.0
29 TraesCS6B01G089900 chr2B 86.517 178 24 0 1 178 89494890 89495067 1.970000e-46 196.0
30 TraesCS6B01G089900 chr2B 83.436 163 25 2 1750 1911 222791972 222791811 1.550000e-32 150.0
31 TraesCS6B01G089900 chr2B 82.209 163 27 2 1750 1911 710589240 710589079 3.360000e-29 139.0
32 TraesCS6B01G089900 chr4A 92.840 419 23 3 373 791 632021072 632021483 3.570000e-168 601.0
33 TraesCS6B01G089900 chr7A 79.755 736 137 11 794 1525 162578288 162579015 7.950000e-145 523.0
34 TraesCS6B01G089900 chr7A 89.103 156 10 3 229 377 13099399 13099244 1.180000e-43 187.0
35 TraesCS6B01G089900 chr7D 78.940 736 143 11 794 1525 161391094 161391821 8.060000e-135 490.0
36 TraesCS6B01G089900 chr7D 88.608 79 8 1 719 796 46847313 46847391 7.380000e-16 95.3
37 TraesCS6B01G089900 chr7D 96.875 32 1 0 515 546 11129108 11129077 1.000000e-03 54.7
38 TraesCS6B01G089900 chr7B 95.736 258 9 1 365 622 655809856 655810111 4.990000e-112 414.0
39 TraesCS6B01G089900 chr7B 96.104 77 3 0 720 796 655810096 655810172 2.620000e-25 126.0
40 TraesCS6B01G089900 chr7B 97.222 72 2 0 720 791 655810891 655810962 3.390000e-24 122.0
41 TraesCS6B01G089900 chr7B 98.462 65 1 0 558 622 655810842 655810906 5.670000e-22 115.0
42 TraesCS6B01G089900 chr5A 81.801 522 54 21 2006 2507 624201460 624200960 1.400000e-107 399.0
43 TraesCS6B01G089900 chr5A 89.286 196 16 4 229 421 496492738 496492931 8.960000e-60 241.0
44 TraesCS6B01G089900 chr4D 93.043 230 10 5 229 455 280789721 280789495 5.170000e-87 331.0
45 TraesCS6B01G089900 chr4D 91.667 228 11 6 229 455 280788526 280788306 2.420000e-80 309.0
46 TraesCS6B01G089900 chr1D 89.328 253 17 9 210 455 439141106 439141355 2.420000e-80 309.0
47 TraesCS6B01G089900 chr1D 87.156 218 13 13 231 443 35820496 35820289 1.500000e-57 233.0
48 TraesCS6B01G089900 chrUn 95.294 170 8 0 1 170 101057528 101057697 1.140000e-68 270.0
49 TraesCS6B01G089900 chr3B 93.413 167 9 2 229 394 761929246 761929411 1.930000e-61 246.0
50 TraesCS6B01G089900 chr3A 89.796 196 15 4 229 421 655085079 655084886 1.930000e-61 246.0
51 TraesCS6B01G089900 chr1B 89.560 182 19 0 1 182 630649809 630649990 5.390000e-57 231.0
52 TraesCS6B01G089900 chr3D 86.047 172 24 0 2 173 33330224 33330053 4.260000e-43 185.0
53 TraesCS6B01G089900 chr1A 96.429 112 4 0 498 609 586758311 586758200 4.260000e-43 185.0


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 TraesCS6B01G089900 chr6B 65156921 65159427 2506 True 4630.000000 4630 100.000 1 2507 1 chr6B.!!$R4 2506
1 TraesCS6B01G089900 chr6B 53061259 53062065 806 True 809.000000 809 84.815 792 1598 1 chr6B.!!$R3 806
2 TraesCS6B01G089900 chr6B 16255712 16256824 1112 False 739.000000 739 78.966 809 1911 1 chr6B.!!$F1 1102
3 TraesCS6B01G089900 chr6B 53074605 53076878 2273 True 334.000000 466 86.560 1 2440 2 chr6B.!!$R7 2439
4 TraesCS6B01G089900 chr6A 35566972 35568297 1325 True 1923.000000 1923 93.148 1203 2505 1 chr6A.!!$R4 1302
5 TraesCS6B01G089900 chr6A 8994018 8994797 779 True 782.000000 782 84.783 792 1571 1 chr6A.!!$R2 779
6 TraesCS6B01G089900 chr6A 8622999 8623981 982 True 686.000000 686 79.474 869 1846 1 chr6A.!!$R1 977
7 TraesCS6B01G089900 chr6A 30559005 30560042 1037 True 673.000000 673 78.693 872 1911 1 chr6A.!!$R3 1039
8 TraesCS6B01G089900 chr6A 9350655 9351438 783 False 508.000000 508 78.589 785 1571 1 chr6A.!!$F1 786
9 TraesCS6B01G089900 chr5B 621234426 621235531 1105 True 990.000000 990 83.048 812 1906 1 chr5B.!!$R1 1094
10 TraesCS6B01G089900 chr5D 499861037 499862136 1099 True 935.000000 935 82.262 812 1900 1 chr5D.!!$R1 1088
11 TraesCS6B01G089900 chr6D 8968023 8968765 742 False 651.000000 651 82.597 792 1532 1 chr6D.!!$F1 740
12 TraesCS6B01G089900 chr6D 8577470 8578402 932 True 649.000000 649 79.574 872 1793 1 chr6D.!!$R1 921
13 TraesCS6B01G089900 chr2A 752918878 752920479 1601 True 412.333333 649 91.158 313 800 3 chr2A.!!$R1 487
14 TraesCS6B01G089900 chr2B 709486316 709487251 935 True 592.000000 592 78.298 869 1796 1 chr2B.!!$R3 927
15 TraesCS6B01G089900 chr2B 709424987 709425729 742 True 584.000000 584 80.914 792 1532 1 chr2B.!!$R2 740
16 TraesCS6B01G089900 chr2B 89494890 89496081 1191 False 413.000000 630 82.853 1 1793 2 chr2B.!!$F1 1792
17 TraesCS6B01G089900 chr7A 162578288 162579015 727 False 523.000000 523 79.755 794 1525 1 chr7A.!!$F1 731
18 TraesCS6B01G089900 chr7D 161391094 161391821 727 False 490.000000 490 78.940 794 1525 1 chr7D.!!$F2 731
19 TraesCS6B01G089900 chr5A 624200960 624201460 500 True 399.000000 399 81.801 2006 2507 1 chr5A.!!$R1 501
20 TraesCS6B01G089900 chr4D 280788306 280789721 1415 True 320.000000 331 92.355 229 455 2 chr4D.!!$R1 226

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
900 1003 0.322546 GGGTGGTCAAGCCTAACCTG 60.323 60.0 1.26 0.0 43.63 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2485 4058 1.070758 ACTACAAGCACACACCAGAGG 59.929 52.381 0.0 0.0 0.0 3.69 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 0.759060 AGAAAACCCTGGCACCCAAC 60.759 55.000 0.00 0.00 30.80 3.77
110 111 2.119655 GCCTCGGACTCTCGCCTTA 61.120 63.158 0.00 0.00 0.00 2.69
114 115 1.002251 CTCGGACTCTCGCCTTATGAC 60.002 57.143 0.00 0.00 0.00 3.06
142 143 1.514443 CTCGTCTCGCTTTCCCGTC 60.514 63.158 0.00 0.00 0.00 4.79
151 152 1.673033 CGCTTTCCCGTCACAGATTCT 60.673 52.381 0.00 0.00 0.00 2.40
153 154 2.350522 CTTTCCCGTCACAGATTCTGG 58.649 52.381 17.66 7.14 35.51 3.86
173 174 0.749049 TGCAGATCCATCGTCTCCAG 59.251 55.000 0.00 0.00 0.00 3.86
178 179 2.037620 ATCCATCGTCTCCAGGCTGC 62.038 60.000 9.56 0.00 0.00 5.25
179 180 2.580815 CATCGTCTCCAGGCTGCA 59.419 61.111 9.56 0.00 0.00 4.41
180 181 1.812922 CATCGTCTCCAGGCTGCAC 60.813 63.158 9.56 4.21 0.00 4.57
181 182 1.986757 ATCGTCTCCAGGCTGCACT 60.987 57.895 9.56 0.00 0.00 4.40
182 183 2.236223 ATCGTCTCCAGGCTGCACTG 62.236 60.000 9.56 6.57 38.21 3.66
183 184 2.746359 GTCTCCAGGCTGCACTGT 59.254 61.111 9.56 0.00 36.75 3.55
184 185 1.072159 GTCTCCAGGCTGCACTGTT 59.928 57.895 9.56 0.00 36.75 3.16
185 186 1.071987 TCTCCAGGCTGCACTGTTG 59.928 57.895 9.56 0.00 36.75 3.33
186 187 1.970114 CTCCAGGCTGCACTGTTGG 60.970 63.158 9.56 8.16 36.75 3.77
187 188 3.677648 CCAGGCTGCACTGTTGGC 61.678 66.667 9.56 0.00 36.75 4.52
188 189 4.034258 CAGGCTGCACTGTTGGCG 62.034 66.667 0.00 0.00 33.81 5.69
216 217 4.683432 ACGCAGTGCCTCTTCTTC 57.317 55.556 10.11 0.00 42.51 2.87
217 218 2.053618 ACGCAGTGCCTCTTCTTCT 58.946 52.632 10.11 0.00 42.51 2.85
218 219 0.394565 ACGCAGTGCCTCTTCTTCTT 59.605 50.000 10.11 0.00 42.51 2.52
219 220 1.074752 CGCAGTGCCTCTTCTTCTTC 58.925 55.000 10.11 0.00 0.00 2.87
220 221 1.337635 CGCAGTGCCTCTTCTTCTTCT 60.338 52.381 10.11 0.00 0.00 2.85
221 222 2.094494 CGCAGTGCCTCTTCTTCTTCTA 60.094 50.000 10.11 0.00 0.00 2.10
222 223 3.258228 GCAGTGCCTCTTCTTCTTCTAC 58.742 50.000 2.85 0.00 0.00 2.59
223 224 3.855858 CAGTGCCTCTTCTTCTTCTACC 58.144 50.000 0.00 0.00 0.00 3.18
224 225 3.513515 CAGTGCCTCTTCTTCTTCTACCT 59.486 47.826 0.00 0.00 0.00 3.08
225 226 4.707448 CAGTGCCTCTTCTTCTTCTACCTA 59.293 45.833 0.00 0.00 0.00 3.08
226 227 5.362430 CAGTGCCTCTTCTTCTTCTACCTAT 59.638 44.000 0.00 0.00 0.00 2.57
227 228 5.362430 AGTGCCTCTTCTTCTTCTACCTATG 59.638 44.000 0.00 0.00 0.00 2.23
240 241 7.057894 TCTTCTACCTATGAACTCTCTCTTCC 58.942 42.308 0.00 0.00 0.00 3.46
241 242 6.584471 TCTACCTATGAACTCTCTCTTCCT 57.416 41.667 0.00 0.00 0.00 3.36
242 243 6.597562 TCTACCTATGAACTCTCTCTTCCTC 58.402 44.000 0.00 0.00 0.00 3.71
303 305 4.760204 CGGTGGGAAAAACTCATAAACTCT 59.240 41.667 0.00 0.00 0.00 3.24
357 362 1.087501 CTTTGCTTTCTACTCCCGGC 58.912 55.000 0.00 0.00 0.00 6.13
384 389 8.896320 AGACACACATACACTACATTGTTTTA 57.104 30.769 0.00 0.00 0.00 1.52
385 390 8.770828 AGACACACATACACTACATTGTTTTAC 58.229 33.333 0.00 0.00 0.00 2.01
394 399 1.133009 ACATTGTTTTACCCCAGCCCA 60.133 47.619 0.00 0.00 0.00 5.36
421 426 5.617751 CGGCCTCAAACTTTCTCATTAACTG 60.618 44.000 0.00 0.00 0.00 3.16
472 477 0.676151 GCTGACTTGCCAAGCTAGCT 60.676 55.000 12.68 12.68 37.62 3.32
473 478 1.085091 CTGACTTGCCAAGCTAGCTG 58.915 55.000 20.16 12.30 35.00 4.24
508 567 4.933400 CACACTAACCACTAACCCATGTAC 59.067 45.833 0.00 0.00 0.00 2.90
509 568 4.842380 ACACTAACCACTAACCCATGTACT 59.158 41.667 0.00 0.00 0.00 2.73
510 569 5.308759 ACACTAACCACTAACCCATGTACTT 59.691 40.000 0.00 0.00 0.00 2.24
511 570 6.497954 ACACTAACCACTAACCCATGTACTTA 59.502 38.462 0.00 0.00 0.00 2.24
512 571 6.815142 CACTAACCACTAACCCATGTACTTAC 59.185 42.308 0.00 0.00 0.00 2.34
513 572 4.460948 ACCACTAACCCATGTACTTACG 57.539 45.455 0.00 0.00 0.00 3.18
514 573 3.192466 CCACTAACCCATGTACTTACGC 58.808 50.000 0.00 0.00 0.00 4.42
515 574 3.368635 CCACTAACCCATGTACTTACGCA 60.369 47.826 0.00 0.00 0.00 5.24
516 575 3.615496 CACTAACCCATGTACTTACGCAC 59.385 47.826 0.00 0.00 0.00 5.34
517 576 3.512724 ACTAACCCATGTACTTACGCACT 59.487 43.478 0.00 0.00 0.00 4.40
518 577 4.706476 ACTAACCCATGTACTTACGCACTA 59.294 41.667 0.00 0.00 0.00 2.74
519 578 4.540359 AACCCATGTACTTACGCACTAA 57.460 40.909 0.00 0.00 0.00 2.24
520 579 3.853475 ACCCATGTACTTACGCACTAAC 58.147 45.455 0.00 0.00 0.00 2.34
521 580 3.512724 ACCCATGTACTTACGCACTAACT 59.487 43.478 0.00 0.00 0.00 2.24
522 581 4.020839 ACCCATGTACTTACGCACTAACTT 60.021 41.667 0.00 0.00 0.00 2.66
523 582 4.328983 CCCATGTACTTACGCACTAACTTG 59.671 45.833 0.00 0.00 0.00 3.16
524 583 4.328983 CCATGTACTTACGCACTAACTTGG 59.671 45.833 0.00 0.00 0.00 3.61
525 584 3.319755 TGTACTTACGCACTAACTTGGC 58.680 45.455 0.00 0.00 0.00 4.52
526 585 1.804601 ACTTACGCACTAACTTGGCC 58.195 50.000 0.00 0.00 0.00 5.36
527 586 0.719465 CTTACGCACTAACTTGGCCG 59.281 55.000 0.00 0.00 0.00 6.13
528 587 0.671163 TTACGCACTAACTTGGCCGG 60.671 55.000 0.00 0.00 0.00 6.13
529 588 3.799755 CGCACTAACTTGGCCGGC 61.800 66.667 21.18 21.18 0.00 6.13
530 589 2.671619 GCACTAACTTGGCCGGCA 60.672 61.111 30.85 12.04 0.00 5.69
531 590 2.978018 GCACTAACTTGGCCGGCAC 61.978 63.158 30.85 18.39 0.00 5.01
532 591 1.599518 CACTAACTTGGCCGGCACA 60.600 57.895 30.85 21.00 0.00 4.57
533 592 1.599797 ACTAACTTGGCCGGCACAC 60.600 57.895 30.85 12.03 0.00 3.82
534 593 1.302511 CTAACTTGGCCGGCACACT 60.303 57.895 30.85 10.70 0.00 3.55
535 594 1.298859 CTAACTTGGCCGGCACACTC 61.299 60.000 30.85 11.16 0.00 3.51
536 595 4.988598 ACTTGGCCGGCACACTCG 62.989 66.667 30.85 15.62 0.00 4.18
546 634 2.033194 GCACACTCGGCCACTAACC 61.033 63.158 2.24 0.00 0.00 2.85
576 664 1.077068 GATCCAAATGACCCGGCCA 60.077 57.895 2.24 0.00 0.00 5.36
577 665 0.682855 GATCCAAATGACCCGGCCAA 60.683 55.000 2.24 0.00 0.00 4.52
652 740 7.641249 ACTAACTAATCTGACCCACTACTAGT 58.359 38.462 0.00 0.00 0.00 2.57
682 770 8.631480 ATGCACACACATGATCTCATATTTAT 57.369 30.769 0.00 0.00 34.26 1.40
698 786 3.945981 TTTATGTGAGTACACTGCCGA 57.054 42.857 0.00 0.00 46.07 5.54
699 787 2.933495 TATGTGAGTACACTGCCGAC 57.067 50.000 0.00 0.00 46.07 4.79
700 788 0.966179 ATGTGAGTACACTGCCGACA 59.034 50.000 0.00 0.00 46.07 4.35
804 901 4.528596 AGTTCTGACATGCACTACTACCTT 59.471 41.667 0.00 0.00 0.00 3.50
805 902 5.715279 AGTTCTGACATGCACTACTACCTTA 59.285 40.000 0.00 0.00 0.00 2.69
840 937 3.998672 GACAACGTCCTCCGGGCA 61.999 66.667 0.00 0.00 42.24 5.36
867 970 2.429250 GAGGAGCTTCTACCTTCTCACC 59.571 54.545 0.00 0.00 35.44 4.02
894 997 2.936032 GAGGGGGTGGTCAAGCCT 60.936 66.667 0.00 0.00 46.42 4.58
898 1001 1.001269 GGGGTGGTCAAGCCTAACC 60.001 63.158 0.00 0.00 46.42 2.85
900 1003 0.322546 GGGTGGTCAAGCCTAACCTG 60.323 60.000 1.26 0.00 43.63 4.00
909 1012 1.078708 GCCTAACCTGGCGTTGCTA 60.079 57.895 0.00 0.00 43.74 3.49
1201 1307 0.959372 GACGAGGTCCAAGGAGTCGA 60.959 60.000 21.40 0.00 36.12 4.20
1329 1436 3.553105 CCCGGTATTACGCTGTAAAGTTC 59.447 47.826 0.00 0.00 0.00 3.01
1552 3023 6.826231 TGGTATGTTCATTATGTCATTCGGTT 59.174 34.615 9.65 0.00 0.00 4.44
1571 3042 1.442769 TGAGAAGAAAGCATCGCACC 58.557 50.000 0.00 0.00 0.00 5.01
1583 3054 2.621338 CATCGCACCACTATGACTTGT 58.379 47.619 0.00 0.00 0.00 3.16
1588 3059 3.003480 GCACCACTATGACTTGTCCTTC 58.997 50.000 0.00 0.00 0.00 3.46
1623 3111 5.937540 CACACATATTGGAACCAAGAGTGTA 59.062 40.000 25.49 11.38 41.98 2.90
1641 3130 2.625314 TGTAAGATCAGAGCATCCCTCG 59.375 50.000 0.00 0.00 45.54 4.63
1667 3157 5.122869 GTGCTTTGAAGTATGAATGAGCAGA 59.877 40.000 0.00 0.00 39.29 4.26
1715 3205 4.229876 GTTCTAAAATGGCTGTTGCAGTC 58.770 43.478 0.00 0.00 41.91 3.51
1739 3229 6.426025 TCTTGAATGCAATCCTCAATCTATCG 59.574 38.462 0.00 0.00 32.68 2.92
1817 3308 8.634335 ACTTTATTTTGGATGGAAATTTTGGG 57.366 30.769 0.00 0.00 0.00 4.12
1906 3397 3.822167 TGCTGAGAATGCAGTTTTGATCA 59.178 39.130 0.00 0.00 38.17 2.92
1939 3430 3.009033 AGCAGGCCATTGTTGACTAGTAA 59.991 43.478 5.01 0.00 0.00 2.24
1987 3481 5.012046 CCTTTTAGTTTTGGATGGCCTTCTT 59.988 40.000 17.48 0.00 34.31 2.52
1989 3483 2.962859 AGTTTTGGATGGCCTTCTTGT 58.037 42.857 17.48 0.00 34.31 3.16
2054 3586 7.322222 GCCTACTTGTATATCACTACGTAAACG 59.678 40.741 0.04 0.04 46.33 3.60
2127 3659 1.483827 TGCCATGGTGCTGAAAAACAA 59.516 42.857 14.67 0.00 0.00 2.83
2210 3743 9.612620 GCATTACCATGTTAATTTCTGCTATAC 57.387 33.333 0.00 0.00 32.28 1.47
2264 3802 5.061721 TCCATATAGATAGCGAGGGCATA 57.938 43.478 0.00 0.00 43.41 3.14
2378 3930 0.957395 CGGATGGGATGCCATGTAGC 60.957 60.000 25.10 8.83 0.00 3.58
2440 3992 1.607251 CCTCAGTGTACGAACCAACCC 60.607 57.143 0.00 0.00 0.00 4.11
2441 3993 1.343465 CTCAGTGTACGAACCAACCCT 59.657 52.381 0.00 0.00 0.00 4.34
2470 4043 2.158986 CCTGATGTGAGGCTGTAGAAGG 60.159 54.545 0.00 0.00 0.00 3.46
2476 4049 1.623811 TGAGGCTGTAGAAGGTGGAAC 59.376 52.381 0.00 0.00 0.00 3.62
2485 4058 5.305585 TGTAGAAGGTGGAACAAATGAGAC 58.694 41.667 0.00 0.00 44.16 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.473520 CAGCGGGTCCTTGGCGAT 62.474 66.667 0.00 0.00 0.00 4.58
99 100 1.269309 GCGATGTCATAAGGCGAGAGT 60.269 52.381 0.00 0.00 0.00 3.24
136 137 0.608130 CACCAGAATCTGTGACGGGA 59.392 55.000 9.63 0.00 0.00 5.14
142 143 2.286872 GGATCTGCACCAGAATCTGTG 58.713 52.381 9.63 8.66 44.04 3.66
151 152 0.461548 GAGACGATGGATCTGCACCA 59.538 55.000 0.00 0.00 41.83 4.17
153 154 0.461548 TGGAGACGATGGATCTGCAC 59.538 55.000 0.00 0.00 39.34 4.57
194 195 2.159819 GAAGAGGCACTGCGTGAGGA 62.160 60.000 11.94 0.00 41.55 3.71
195 196 1.739562 GAAGAGGCACTGCGTGAGG 60.740 63.158 11.94 0.00 41.55 3.86
196 197 0.320247 AAGAAGAGGCACTGCGTGAG 60.320 55.000 11.94 0.00 41.55 3.51
197 198 0.319900 GAAGAAGAGGCACTGCGTGA 60.320 55.000 11.94 0.00 41.55 4.35
198 199 0.320247 AGAAGAAGAGGCACTGCGTG 60.320 55.000 0.00 4.61 41.55 5.34
199 200 0.394565 AAGAAGAAGAGGCACTGCGT 59.605 50.000 0.00 0.00 41.55 5.24
200 201 1.074752 GAAGAAGAAGAGGCACTGCG 58.925 55.000 0.00 0.00 41.55 5.18
201 202 2.470983 AGAAGAAGAAGAGGCACTGC 57.529 50.000 0.00 0.00 41.55 4.40
202 203 3.513515 AGGTAGAAGAAGAAGAGGCACTG 59.486 47.826 0.00 0.00 41.55 3.66
204 205 5.361285 TCATAGGTAGAAGAAGAAGAGGCAC 59.639 44.000 0.00 0.00 0.00 5.01
205 206 5.519808 TCATAGGTAGAAGAAGAAGAGGCA 58.480 41.667 0.00 0.00 0.00 4.75
206 207 6.097696 AGTTCATAGGTAGAAGAAGAAGAGGC 59.902 42.308 0.00 0.00 0.00 4.70
207 208 7.559897 AGAGTTCATAGGTAGAAGAAGAAGAGG 59.440 40.741 0.00 0.00 0.00 3.69
208 209 8.519799 AGAGTTCATAGGTAGAAGAAGAAGAG 57.480 38.462 0.00 0.00 0.00 2.85
209 210 8.333235 AGAGAGTTCATAGGTAGAAGAAGAAGA 58.667 37.037 0.00 0.00 0.00 2.87
210 211 8.519799 AGAGAGTTCATAGGTAGAAGAAGAAG 57.480 38.462 0.00 0.00 0.00 2.85
211 212 8.333235 AGAGAGAGTTCATAGGTAGAAGAAGAA 58.667 37.037 0.00 0.00 0.00 2.52
212 213 7.867921 AGAGAGAGTTCATAGGTAGAAGAAGA 58.132 38.462 0.00 0.00 0.00 2.87
213 214 8.519799 AAGAGAGAGTTCATAGGTAGAAGAAG 57.480 38.462 0.00 0.00 0.00 2.85
214 215 7.558444 GGAAGAGAGAGTTCATAGGTAGAAGAA 59.442 40.741 0.00 0.00 0.00 2.52
215 216 7.057894 GGAAGAGAGAGTTCATAGGTAGAAGA 58.942 42.308 0.00 0.00 0.00 2.87
216 217 7.060421 AGGAAGAGAGAGTTCATAGGTAGAAG 58.940 42.308 0.00 0.00 0.00 2.85
217 218 6.975949 AGGAAGAGAGAGTTCATAGGTAGAA 58.024 40.000 0.00 0.00 0.00 2.10
218 219 6.388689 AGAGGAAGAGAGAGTTCATAGGTAGA 59.611 42.308 0.00 0.00 0.00 2.59
219 220 6.601332 AGAGGAAGAGAGAGTTCATAGGTAG 58.399 44.000 0.00 0.00 0.00 3.18
220 221 6.584471 AGAGGAAGAGAGAGTTCATAGGTA 57.416 41.667 0.00 0.00 0.00 3.08
221 222 5.466127 AGAGGAAGAGAGAGTTCATAGGT 57.534 43.478 0.00 0.00 0.00 3.08
222 223 5.656416 ACAAGAGGAAGAGAGAGTTCATAGG 59.344 44.000 0.00 0.00 0.00 2.57
223 224 6.773976 ACAAGAGGAAGAGAGAGTTCATAG 57.226 41.667 0.00 0.00 0.00 2.23
224 225 7.546250 AAACAAGAGGAAGAGAGAGTTCATA 57.454 36.000 0.00 0.00 0.00 2.15
225 226 6.432403 AAACAAGAGGAAGAGAGAGTTCAT 57.568 37.500 0.00 0.00 0.00 2.57
226 227 5.878406 AAACAAGAGGAAGAGAGAGTTCA 57.122 39.130 0.00 0.00 0.00 3.18
227 228 6.052360 ACAAAACAAGAGGAAGAGAGAGTTC 58.948 40.000 0.00 0.00 0.00 3.01
240 241 7.545362 TCTTGAGAGAAGAACAAAACAAGAG 57.455 36.000 0.00 0.00 37.92 2.85
241 242 7.921786 TTCTTGAGAGAAGAACAAAACAAGA 57.078 32.000 0.00 0.00 39.97 3.02
303 305 0.107897 GGTGAGGTGTGTGTGTGTGA 60.108 55.000 0.00 0.00 0.00 3.58
357 362 5.161358 ACAATGTAGTGTATGTGTGTCTCG 58.839 41.667 0.00 0.00 0.00 4.04
394 399 1.134220 TGAGAAAGTTTGAGGCCGTGT 60.134 47.619 0.00 0.00 0.00 4.49
421 426 7.759886 TCTCTTGTGTATATAAGTGTTGCACTC 59.240 37.037 2.04 0.00 44.62 3.51
508 567 0.719465 CGGCCAAGTTAGTGCGTAAG 59.281 55.000 2.24 0.00 43.44 2.34
509 568 0.671163 CCGGCCAAGTTAGTGCGTAA 60.671 55.000 2.24 0.00 0.00 3.18
510 569 1.079681 CCGGCCAAGTTAGTGCGTA 60.080 57.895 2.24 0.00 0.00 4.42
511 570 2.358247 CCGGCCAAGTTAGTGCGT 60.358 61.111 2.24 0.00 0.00 5.24
512 571 3.799755 GCCGGCCAAGTTAGTGCG 61.800 66.667 18.11 0.00 0.00 5.34
513 572 2.671619 TGCCGGCCAAGTTAGTGC 60.672 61.111 26.77 0.00 0.00 4.40
514 573 1.599518 TGTGCCGGCCAAGTTAGTG 60.600 57.895 26.77 0.00 0.00 2.74
515 574 1.599797 GTGTGCCGGCCAAGTTAGT 60.600 57.895 26.77 0.00 0.00 2.24
516 575 1.298859 GAGTGTGCCGGCCAAGTTAG 61.299 60.000 26.77 0.00 0.00 2.34
517 576 1.302192 GAGTGTGCCGGCCAAGTTA 60.302 57.895 26.77 0.00 0.00 2.24
518 577 2.594592 GAGTGTGCCGGCCAAGTT 60.595 61.111 26.77 10.36 0.00 2.66
519 578 4.988598 CGAGTGTGCCGGCCAAGT 62.989 66.667 26.77 15.23 0.00 3.16
528 587 2.033194 GGTTAGTGGCCGAGTGTGC 61.033 63.158 0.00 0.00 0.00 4.57
529 588 0.250124 TTGGTTAGTGGCCGAGTGTG 60.250 55.000 0.00 0.00 0.00 3.82
530 589 0.250166 GTTGGTTAGTGGCCGAGTGT 60.250 55.000 0.00 0.00 0.00 3.55
531 590 0.034896 AGTTGGTTAGTGGCCGAGTG 59.965 55.000 0.00 0.00 0.00 3.51
532 591 0.320697 GAGTTGGTTAGTGGCCGAGT 59.679 55.000 0.00 0.00 0.00 4.18
533 592 0.320374 TGAGTTGGTTAGTGGCCGAG 59.680 55.000 0.00 0.00 0.00 4.63
534 593 0.034337 GTGAGTTGGTTAGTGGCCGA 59.966 55.000 0.00 0.00 0.00 5.54
535 594 0.953960 GGTGAGTTGGTTAGTGGCCG 60.954 60.000 0.00 0.00 0.00 6.13
536 595 0.608308 GGGTGAGTTGGTTAGTGGCC 60.608 60.000 0.00 0.00 0.00 5.36
546 634 4.018490 TCATTTGGATCATGGGTGAGTTG 58.982 43.478 0.00 0.00 37.87 3.16
652 740 2.559231 AGATCATGTGTGTGCATGCAAA 59.441 40.909 24.58 15.92 44.20 3.68
676 764 5.105675 TGTCGGCAGTGTACTCACATAAATA 60.106 40.000 0.00 0.00 46.01 1.40
677 765 4.181578 GTCGGCAGTGTACTCACATAAAT 58.818 43.478 0.00 0.00 46.01 1.40
682 770 0.313987 CTGTCGGCAGTGTACTCACA 59.686 55.000 9.39 0.00 46.01 3.58
698 786 3.568853 GTCGTGTCCATATACTAGGCTGT 59.431 47.826 0.00 0.00 0.00 4.40
699 787 3.821600 AGTCGTGTCCATATACTAGGCTG 59.178 47.826 0.00 0.00 0.00 4.85
700 788 4.101645 AGTCGTGTCCATATACTAGGCT 57.898 45.455 0.00 0.00 0.00 4.58
701 789 4.758674 TGTAGTCGTGTCCATATACTAGGC 59.241 45.833 0.00 0.00 0.00 3.93
804 901 3.181422 TGTCAGAGGACCCAAAGAGAGTA 60.181 47.826 0.00 0.00 43.65 2.59
805 902 2.252714 GTCAGAGGACCCAAAGAGAGT 58.747 52.381 0.00 0.00 38.12 3.24
840 937 3.466395 AGGTAGAAGCTCCTCTTGAGT 57.534 47.619 0.00 0.00 43.48 3.41
867 970 2.055042 CACCCCCTCGAGGTCAGAG 61.055 68.421 29.25 13.79 34.56 3.35
894 997 4.582760 CGTAGCAACGCCAGGTTA 57.417 55.556 0.00 0.00 43.12 2.85
909 1012 3.141488 CCTAGCTCGCACTCCCGT 61.141 66.667 0.00 0.00 0.00 5.28
1201 1307 0.534412 AACTCAGAGCTACGCTGCAT 59.466 50.000 0.00 0.00 39.88 3.96
1329 1436 3.765511 TGAGCAATCCATTTTCCTTGAGG 59.234 43.478 0.00 0.00 0.00 3.86
1552 3023 1.270785 TGGTGCGATGCTTTCTTCTCA 60.271 47.619 0.00 0.00 0.00 3.27
1571 3042 4.808414 TGAGGAAGGACAAGTCATAGTG 57.192 45.455 2.29 0.00 0.00 2.74
1583 3054 5.698741 ATGTGTGTCAATATGAGGAAGGA 57.301 39.130 0.00 0.00 0.00 3.36
1588 3059 7.255242 GGTTCCAATATGTGTGTCAATATGAGG 60.255 40.741 0.00 0.00 0.00 3.86
1623 3111 1.962807 CTCGAGGGATGCTCTGATCTT 59.037 52.381 3.91 0.00 0.00 2.40
1641 3130 5.122869 TGCTCATTCATACTTCAAAGCACTC 59.877 40.000 0.00 0.00 33.88 3.51
1667 3157 8.671921 CATAAAGATACAGAGTGTGCAGAAATT 58.328 33.333 0.00 0.00 0.00 1.82
1715 3205 6.204301 ACGATAGATTGAGGATTGCATTCAAG 59.796 38.462 10.55 0.00 35.30 3.02
1739 3229 8.706035 CAAAATGAGAACATTCTTTCATGGAAC 58.294 33.333 0.00 0.00 44.67 3.62
1797 3288 5.259627 AGCCCAAAATTTCCATCCAAAAT 57.740 34.783 0.00 0.00 0.00 1.82
1798 3289 4.720775 AGCCCAAAATTTCCATCCAAAA 57.279 36.364 0.00 0.00 0.00 2.44
1843 3334 3.382546 CCAACTGACCATCAATGAATCCC 59.617 47.826 0.00 0.00 0.00 3.85
1849 3340 1.203052 GTGGCCAACTGACCATCAATG 59.797 52.381 7.24 0.00 38.46 2.82
1850 3341 1.203038 TGTGGCCAACTGACCATCAAT 60.203 47.619 7.24 0.00 38.46 2.57
1906 3397 5.264395 ACAATGGCCTGCTTAGAATAACTT 58.736 37.500 3.32 0.00 0.00 2.66
1987 3481 5.724854 ACTAGCCCCTAGAAAAGTATCAACA 59.275 40.000 6.29 0.00 37.49 3.33
1989 3483 5.962031 TGACTAGCCCCTAGAAAAGTATCAA 59.038 40.000 6.29 0.00 37.49 2.57
2054 3586 7.451566 ACAAATACCAGGGCATTAGAAATATCC 59.548 37.037 0.00 0.00 0.00 2.59
2127 3659 3.515104 CCCTTGTTGTATGAAATGCCCTT 59.485 43.478 0.00 0.00 0.00 3.95
2182 3715 4.739716 GCAGAAATTAACATGGTAATGCCG 59.260 41.667 16.65 7.30 41.21 5.69
2406 3958 7.553760 TCGTACACTGAGGTACATAGTAAATCA 59.446 37.037 10.40 0.00 42.95 2.57
2446 4019 3.173151 TCTACAGCCTCACATCAGGAAA 58.827 45.455 0.00 0.00 35.20 3.13
2470 4043 3.077359 CCAGAGGTCTCATTTGTTCCAC 58.923 50.000 0.55 0.00 0.00 4.02
2476 4049 2.810274 CACACACCAGAGGTCTCATTTG 59.190 50.000 0.55 0.00 31.02 2.32
2485 4058 1.070758 ACTACAAGCACACACCAGAGG 59.929 52.381 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.