Multiple sequence alignment - TraesCS1A01G209200

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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 TraesCS1A01G209200 chr1A 100.000 4421 0 0 1 4421 371315911 371320331 0.000000e+00 8165
1 TraesCS1A01G209200 chr1A 92.321 599 37 4 754 1350 562292723 562292132 0.000000e+00 843
2 TraesCS1A01G209200 chr5B 94.135 1381 72 6 1347 2721 472026411 472025034 0.000000e+00 2093
3 TraesCS1A01G209200 chr5B 94.649 598 31 1 754 1350 631209546 631210143 0.000000e+00 926
4 TraesCS1A01G209200 chr5B 85.714 595 56 6 1 570 472027206 472026616 6.330000e-168 601
5 TraesCS1A01G209200 chr5B 88.925 307 30 2 2266 2569 328278775 328278470 4.170000e-100 375
6 TraesCS1A01G209200 chr5B 88.710 186 19 1 572 755 472026579 472026394 4.450000e-55 226
7 TraesCS1A01G209200 chr2B 93.917 1381 75 6 1347 2721 222940147 222941524 0.000000e+00 2076
8 TraesCS1A01G209200 chr2B 92.453 636 37 5 3788 4421 707739610 707740236 0.000000e+00 898
9 TraesCS1A01G209200 chr2B 91.853 626 47 3 3007 3632 707737966 707738587 0.000000e+00 870
10 TraesCS1A01G209200 chr2B 91.536 638 41 8 3788 4421 407885658 407886286 0.000000e+00 867
11 TraesCS1A01G209200 chr2B 91.379 638 42 7 3788 4421 371367353 371366725 0.000000e+00 861
12 TraesCS1A01G209200 chr2B 85.428 549 53 9 47 570 222939397 222939943 3.010000e-151 545
13 TraesCS1A01G209200 chr2B 94.767 172 7 2 3632 3803 371367543 371367374 2.620000e-67 267
14 TraesCS1A01G209200 chr2B 93.820 178 9 2 3626 3803 407885462 407885637 2.620000e-67 267
15 TraesCS1A01G209200 chr2B 94.771 153 7 1 572 724 222939980 222940131 2.060000e-58 237
16 TraesCS1A01G209200 chr2B 82.486 177 21 6 1 175 376460744 376460576 3.560000e-31 147
17 TraesCS1A01G209200 chr7B 93.845 1381 79 4 1347 2721 478619336 478617956 0.000000e+00 2074
18 TraesCS1A01G209200 chr7B 85.333 600 79 8 754 1350 496648404 496648997 2.920000e-171 612
19 TraesCS1A01G209200 chr7B 87.292 480 60 1 92 570 478620021 478619542 8.360000e-152 547
20 TraesCS1A01G209200 chr7B 94.798 173 6 3 3632 3803 43124791 43124621 2.620000e-67 267
21 TraesCS1A01G209200 chr7B 88.770 187 18 2 572 755 478619505 478619319 4.450000e-55 226
22 TraesCS1A01G209200 chr4B 93.551 1380 81 6 1347 2719 115709337 115707959 0.000000e+00 2049
23 TraesCS1A01G209200 chr4B 87.772 597 63 4 754 1350 51452078 51452664 0.000000e+00 689
24 TraesCS1A01G209200 chr4B 83.878 490 55 11 105 570 115710031 115709542 3.140000e-121 446
25 TraesCS1A01G209200 chr4B 93.464 153 10 0 572 724 115709505 115709353 1.240000e-55 228
26 TraesCS1A01G209200 chr4B 83.750 160 17 5 20 177 434965326 434965478 4.610000e-30 143
27 TraesCS1A01G209200 chr4B 82.530 166 20 4 9 172 444498535 444498377 2.140000e-28 137
28 TraesCS1A01G209200 chr6B 93.560 1382 66 11 1347 2721 140954832 140956197 0.000000e+00 2037
29 TraesCS1A01G209200 chr6B 91.223 638 43 7 3788 4421 308976223 308976851 0.000000e+00 856
30 TraesCS1A01G209200 chr6B 90.909 638 45 7 3788 4421 570078675 570079303 0.000000e+00 845
31 TraesCS1A01G209200 chr6B 91.069 627 47 4 3007 3632 308974588 308975206 0.000000e+00 839
32 TraesCS1A01G209200 chr6B 95.930 172 5 2 3632 3803 361273066 361272897 1.210000e-70 278
33 TraesCS1A01G209200 chr6B 91.457 199 14 1 44 239 140947314 140947512 2.030000e-68 270
34 TraesCS1A01G209200 chr6B 93.820 178 8 3 3626 3803 570078480 570078654 9.430000e-67 265
35 TraesCS1A01G209200 chr6B 93.258 178 10 2 3626 3803 308976027 308976202 1.220000e-65 261
36 TraesCS1A01G209200 chr6B 92.258 155 12 0 570 724 140954662 140954816 2.070000e-53 220
37 TraesCS1A01G209200 chr6B 83.884 242 27 3 2683 2924 293587612 293587841 2.070000e-53 220
38 TraesCS1A01G209200 chrUn 93.761 1122 64 4 1605 2721 116803744 116802624 0.000000e+00 1679
39 TraesCS1A01G209200 chrUn 84.538 595 67 10 1 570 116804765 116804171 2.310000e-157 566
40 TraesCS1A01G209200 chr1B 94.303 983 50 4 1744 2721 278152290 278153271 0.000000e+00 1500
41 TraesCS1A01G209200 chr1B 93.049 633 35 3 3788 4420 519434570 519433947 0.000000e+00 917
42 TraesCS1A01G209200 chr3B 93.553 636 30 5 3788 4421 446527270 446527896 0.000000e+00 937
43 TraesCS1A01G209200 chr3B 93.322 584 39 0 3049 3632 522282125 522281542 0.000000e+00 863
44 TraesCS1A01G209200 chr3B 87.914 513 49 8 2266 2768 522246408 522245899 3.810000e-165 592
45 TraesCS1A01G209200 chr3B 85.321 327 47 1 1934 2259 434509613 434509939 1.970000e-88 337
46 TraesCS1A01G209200 chr3B 87.692 260 32 0 1991 2250 383355666 383355407 2.000000e-78 303
47 TraesCS1A01G209200 chr3B 94.253 174 8 2 3630 3803 446527078 446527249 9.430000e-67 265
48 TraesCS1A01G209200 chr3B 79.897 194 30 4 1 192 151832024 151831838 2.770000e-27 134
49 TraesCS1A01G209200 chr3A 92.982 627 41 3 3007 3632 87730092 87730716 0.000000e+00 911
50 TraesCS1A01G209200 chr3A 92.453 636 36 9 3788 4421 87731752 87732377 0.000000e+00 898
51 TraesCS1A01G209200 chr3A 92.453 636 35 8 3788 4421 476147871 476147247 0.000000e+00 896
52 TraesCS1A01G209200 chr3A 91.759 631 49 3 3004 3632 476157134 476156505 0.000000e+00 874
53 TraesCS1A01G209200 chr3A 91.547 627 49 3 3007 3632 679990336 679990959 0.000000e+00 861
54 TraesCS1A01G209200 chr3A 87.173 421 38 12 1355 1765 217011965 217012379 8.660000e-127 464
55 TraesCS1A01G209200 chr3A 86.682 428 39 15 1348 1765 216936493 216936912 4.030000e-125 459
56 TraesCS1A01G209200 chr3A 92.697 178 11 2 3626 3803 87731556 87731731 5.670000e-64 255
57 TraesCS1A01G209200 chr2A 93.802 597 36 1 754 1350 770167172 770166577 0.000000e+00 896
58 TraesCS1A01G209200 chr2A 91.820 599 43 2 753 1350 477613944 477613351 0.000000e+00 830
59 TraesCS1A01G209200 chr2A 80.928 194 27 6 1 192 488386288 488386103 1.280000e-30 145
60 TraesCS1A01G209200 chr6A 92.151 637 37 9 3788 4421 370481494 370482120 0.000000e+00 887
61 TraesCS1A01G209200 chr6A 91.707 627 47 5 3007 3632 29436178 29436800 0.000000e+00 865
62 TraesCS1A01G209200 chr6A 89.202 639 31 12 3788 4421 347378769 347378164 0.000000e+00 763
63 TraesCS1A01G209200 chr5A 91.879 628 47 4 3007 3632 564441686 564441061 0.000000e+00 874
64 TraesCS1A01G209200 chr5A 91.261 595 45 2 754 1348 408131773 408131186 0.000000e+00 804
65 TraesCS1A01G209200 chr7A 91.325 634 41 8 3788 4419 587285047 587284426 0.000000e+00 854
66 TraesCS1A01G209200 chr7A 91.200 625 51 4 3009 3632 587286694 587286073 0.000000e+00 846
67 TraesCS1A01G209200 chr2D 91.333 600 42 4 754 1350 303501395 303500803 0.000000e+00 811
68 TraesCS1A01G209200 chr2D 87.648 421 36 14 1355 1765 161651795 161651381 4.000000e-130 475
69 TraesCS1A01G209200 chr4D 90.297 639 24 14 3788 4421 255552770 255553375 0.000000e+00 802
70 TraesCS1A01G209200 chr4D 85.464 571 65 13 2443 3006 448360124 448359565 2.960000e-161 579
71 TraesCS1A01G209200 chr4D 93.258 178 10 2 3626 3803 255552574 255552749 1.220000e-65 261
72 TraesCS1A01G209200 chr3D 90.847 590 46 4 754 1342 227670788 227670206 0.000000e+00 784
73 TraesCS1A01G209200 chr3D 84.393 346 50 2 14 356 236112470 236112814 1.970000e-88 337
74 TraesCS1A01G209200 chr6D 89.671 639 28 12 3788 4421 225586819 225586214 0.000000e+00 780
75 TraesCS1A01G209200 chr6D 87.173 421 38 14 1355 1765 197263410 197263824 8.660000e-127 464
76 TraesCS1A01G209200 chr6D 86.041 437 46 13 1356 1782 338138541 338138110 5.210000e-124 455


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 TraesCS1A01G209200 chr1A 371315911 371320331 4420 False 8165.000000 8165 100.000000 1 4421 1 chr1A.!!$F1 4420
1 TraesCS1A01G209200 chr1A 562292132 562292723 591 True 843.000000 843 92.321000 754 1350 1 chr1A.!!$R1 596
2 TraesCS1A01G209200 chr5B 472025034 472027206 2172 True 973.333333 2093 89.519667 1 2721 3 chr5B.!!$R2 2720
3 TraesCS1A01G209200 chr5B 631209546 631210143 597 False 926.000000 926 94.649000 754 1350 1 chr5B.!!$F1 596
4 TraesCS1A01G209200 chr2B 222939397 222941524 2127 False 952.666667 2076 91.372000 47 2721 3 chr2B.!!$F1 2674
5 TraesCS1A01G209200 chr2B 707737966 707740236 2270 False 884.000000 898 92.153000 3007 4421 2 chr2B.!!$F3 1414
6 TraesCS1A01G209200 chr2B 407885462 407886286 824 False 567.000000 867 92.678000 3626 4421 2 chr2B.!!$F2 795
7 TraesCS1A01G209200 chr2B 371366725 371367543 818 True 564.000000 861 93.073000 3632 4421 2 chr2B.!!$R2 789
8 TraesCS1A01G209200 chr7B 478617956 478620021 2065 True 949.000000 2074 89.969000 92 2721 3 chr7B.!!$R2 2629
9 TraesCS1A01G209200 chr7B 496648404 496648997 593 False 612.000000 612 85.333000 754 1350 1 chr7B.!!$F1 596
10 TraesCS1A01G209200 chr4B 115707959 115710031 2072 True 907.666667 2049 90.297667 105 2719 3 chr4B.!!$R2 2614
11 TraesCS1A01G209200 chr4B 51452078 51452664 586 False 689.000000 689 87.772000 754 1350 1 chr4B.!!$F1 596
12 TraesCS1A01G209200 chr6B 140954662 140956197 1535 False 1128.500000 2037 92.909000 570 2721 2 chr6B.!!$F3 2151
13 TraesCS1A01G209200 chr6B 308974588 308976851 2263 False 652.000000 856 91.850000 3007 4421 3 chr6B.!!$F4 1414
14 TraesCS1A01G209200 chr6B 570078480 570079303 823 False 555.000000 845 92.364500 3626 4421 2 chr6B.!!$F5 795
15 TraesCS1A01G209200 chrUn 116802624 116804765 2141 True 1122.500000 1679 89.149500 1 2721 2 chrUn.!!$R1 2720
16 TraesCS1A01G209200 chr1B 278152290 278153271 981 False 1500.000000 1500 94.303000 1744 2721 1 chr1B.!!$F1 977
17 TraesCS1A01G209200 chr1B 519433947 519434570 623 True 917.000000 917 93.049000 3788 4420 1 chr1B.!!$R1 632
18 TraesCS1A01G209200 chr3B 522281542 522282125 583 True 863.000000 863 93.322000 3049 3632 1 chr3B.!!$R4 583
19 TraesCS1A01G209200 chr3B 446527078 446527896 818 False 601.000000 937 93.903000 3630 4421 2 chr3B.!!$F2 791
20 TraesCS1A01G209200 chr3B 522245899 522246408 509 True 592.000000 592 87.914000 2266 2768 1 chr3B.!!$R3 502
21 TraesCS1A01G209200 chr3A 476147247 476147871 624 True 896.000000 896 92.453000 3788 4421 1 chr3A.!!$R1 633
22 TraesCS1A01G209200 chr3A 476156505 476157134 629 True 874.000000 874 91.759000 3004 3632 1 chr3A.!!$R2 628
23 TraesCS1A01G209200 chr3A 679990336 679990959 623 False 861.000000 861 91.547000 3007 3632 1 chr3A.!!$F3 625
24 TraesCS1A01G209200 chr3A 87730092 87732377 2285 False 688.000000 911 92.710667 3007 4421 3 chr3A.!!$F4 1414
25 TraesCS1A01G209200 chr2A 770166577 770167172 595 True 896.000000 896 93.802000 754 1350 1 chr2A.!!$R3 596
26 TraesCS1A01G209200 chr2A 477613351 477613944 593 True 830.000000 830 91.820000 753 1350 1 chr2A.!!$R1 597
27 TraesCS1A01G209200 chr6A 370481494 370482120 626 False 887.000000 887 92.151000 3788 4421 1 chr6A.!!$F2 633
28 TraesCS1A01G209200 chr6A 29436178 29436800 622 False 865.000000 865 91.707000 3007 3632 1 chr6A.!!$F1 625
29 TraesCS1A01G209200 chr6A 347378164 347378769 605 True 763.000000 763 89.202000 3788 4421 1 chr6A.!!$R1 633
30 TraesCS1A01G209200 chr5A 564441061 564441686 625 True 874.000000 874 91.879000 3007 3632 1 chr5A.!!$R2 625
31 TraesCS1A01G209200 chr5A 408131186 408131773 587 True 804.000000 804 91.261000 754 1348 1 chr5A.!!$R1 594
32 TraesCS1A01G209200 chr7A 587284426 587286694 2268 True 850.000000 854 91.262500 3009 4419 2 chr7A.!!$R1 1410
33 TraesCS1A01G209200 chr2D 303500803 303501395 592 True 811.000000 811 91.333000 754 1350 1 chr2D.!!$R2 596
34 TraesCS1A01G209200 chr4D 448359565 448360124 559 True 579.000000 579 85.464000 2443 3006 1 chr4D.!!$R1 563
35 TraesCS1A01G209200 chr4D 255552574 255553375 801 False 531.500000 802 91.777500 3626 4421 2 chr4D.!!$F1 795
36 TraesCS1A01G209200 chr3D 227670206 227670788 582 True 784.000000 784 90.847000 754 1342 1 chr3D.!!$R1 588
37 TraesCS1A01G209200 chr6D 225586214 225586819 605 True 780.000000 780 89.671000 3788 4421 1 chr6D.!!$R1 633

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
704 767 0.103208 AGATAAGCTTGTCCGGCTCG 59.897 55.0 18.49 0.0 39.30 5.03 F
746 809 0.250295 CTTCCCGCAGTTCAAGGACA 60.250 55.0 0.00 0.0 0.00 4.02 F
747 810 0.250295 TTCCCGCAGTTCAAGGACAG 60.250 55.0 0.00 0.0 0.00 3.51 F
1724 1793 0.322456 GGGAGCCACTGTGCATTACA 60.322 55.0 1.29 0.0 37.78 2.41 F
2847 2928 0.110295 CATGTCCCAGTGTCCCACAA 59.890 55.0 0.00 0.0 36.74 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1768 0.543749 GCACAGTGGCTCCCTTATCT 59.456 55.0 1.84 0.0 0.00 1.98 R
1967 2038 0.999406 AGATGTTCGTCGCATTTCGG 59.001 50.0 0.00 0.0 39.05 4.30 R
2010 2081 2.094894 CGAATTCTCACTGTGTGGATGC 59.905 50.0 7.79 3.4 33.87 3.91 R
2974 3055 0.037139 TGTTCCATTCCCGTGTACCG 60.037 55.0 0.00 0.0 0.00 4.02 R
4375 5355 0.463620 GAGGAGCTTGTAGAGGCAGG 59.536 60.0 0.00 0.0 0.00 4.85 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
102 104 1.129058 CCTAAACCGCCTCCTACCAT 58.871 55.000 0.00 0.00 0.00 3.55
241 243 2.750350 CAACCCACTCCTCGCCTT 59.250 61.111 0.00 0.00 0.00 4.35
251 253 2.127869 CCTCGCCTTCATCCCTCGA 61.128 63.158 0.00 0.00 0.00 4.04
252 254 1.361993 CTCGCCTTCATCCCTCGAG 59.638 63.158 5.13 5.13 40.22 4.04
275 277 3.068691 CGCCGACTTCCTCCCTCA 61.069 66.667 0.00 0.00 0.00 3.86
298 300 3.319198 GCCGTCAACTCCCTCCCA 61.319 66.667 0.00 0.00 0.00 4.37
301 303 2.571216 CGTCAACTCCCTCCCACGT 61.571 63.158 0.00 0.00 0.00 4.49
303 305 1.458777 TCAACTCCCTCCCACGTGT 60.459 57.895 15.65 0.00 0.00 4.49
337 339 2.037527 ACCGGTCTCTGTCTCCCC 59.962 66.667 0.00 0.00 0.00 4.81
404 406 4.530857 CGCCGGTCATCACCTCCC 62.531 72.222 1.90 0.00 41.17 4.30
441 444 2.515523 CCTTCCTCCATGCGCCAG 60.516 66.667 4.18 0.00 0.00 4.85
488 514 0.106015 TCTCCCTCTGATGATGCCGA 60.106 55.000 0.00 0.00 0.00 5.54
495 521 2.321263 CTGATGATGCCGACCAGCCT 62.321 60.000 0.00 0.00 0.00 4.58
702 765 2.389715 AGTAGATAAGCTTGTCCGGCT 58.610 47.619 18.49 11.59 42.31 5.52
704 767 0.103208 AGATAAGCTTGTCCGGCTCG 59.897 55.000 18.49 0.00 39.30 5.03
705 768 1.491505 GATAAGCTTGTCCGGCTCGC 61.492 60.000 9.86 0.00 39.30 5.03
706 769 1.961180 ATAAGCTTGTCCGGCTCGCT 61.961 55.000 9.86 0.00 39.30 4.93
724 787 1.376543 CTCAGCCAGGTAAGCACATG 58.623 55.000 0.00 0.00 36.21 3.21
741 804 2.282180 GGGCTTCCCGCAGTTCAA 60.282 61.111 0.00 0.00 41.67 2.69
742 805 2.335712 GGGCTTCCCGCAGTTCAAG 61.336 63.158 0.00 0.00 41.67 3.02
743 806 2.335712 GGCTTCCCGCAGTTCAAGG 61.336 63.158 0.00 0.00 41.67 3.61
744 807 1.302511 GCTTCCCGCAGTTCAAGGA 60.303 57.895 0.00 0.00 38.92 3.36
745 808 1.578206 GCTTCCCGCAGTTCAAGGAC 61.578 60.000 0.00 0.00 38.92 3.85
746 809 0.250295 CTTCCCGCAGTTCAAGGACA 60.250 55.000 0.00 0.00 0.00 4.02
747 810 0.250295 TTCCCGCAGTTCAAGGACAG 60.250 55.000 0.00 0.00 0.00 3.51
748 811 2.328099 CCCGCAGTTCAAGGACAGC 61.328 63.158 0.00 0.00 0.00 4.40
749 812 1.597854 CCGCAGTTCAAGGACAGCA 60.598 57.895 0.00 0.00 32.26 4.41
750 813 1.165907 CCGCAGTTCAAGGACAGCAA 61.166 55.000 0.00 0.00 32.26 3.91
751 814 0.662619 CGCAGTTCAAGGACAGCAAA 59.337 50.000 0.00 0.00 32.26 3.68
893 959 7.654022 AAGGTACATCAAGGTGAAAGAAAAA 57.346 32.000 0.00 0.00 0.00 1.94
932 998 3.286329 AAGTTACCCAACGAACAAGGT 57.714 42.857 0.00 0.00 39.78 3.50
1010 1076 5.768980 AGTTCTCCTCCAATGATTGAAGA 57.231 39.130 6.76 1.62 0.00 2.87
1012 1078 6.120905 AGTTCTCCTCCAATGATTGAAGATG 58.879 40.000 6.76 0.00 0.00 2.90
1085 1151 0.546122 AGCAGTGAACACCACCTCAA 59.454 50.000 0.00 0.00 46.87 3.02
1182 1249 4.698201 TCTGAAGGTAATTCCACACACA 57.302 40.909 0.00 0.00 37.08 3.72
1243 1310 1.355381 TCCCTGACCTGCAAATGACAT 59.645 47.619 0.00 0.00 0.00 3.06
1247 1314 2.357009 CTGACCTGCAAATGACATAGCC 59.643 50.000 9.52 0.00 0.00 3.93
1308 1375 7.345653 TCTCTCAACCATGTCCTTAGTATTCAT 59.654 37.037 0.00 0.00 0.00 2.57
1344 1411 5.185635 TCATCATCCAGGCAAAAACCTTTAG 59.814 40.000 0.00 0.00 38.26 1.85
1520 1589 8.918961 AAAATCAGATCTAGTAGTTTGTCTCG 57.081 34.615 0.00 0.00 0.00 4.04
1525 1594 6.762187 CAGATCTAGTAGTTTGTCTCGGAGTA 59.238 42.308 4.69 0.00 0.00 2.59
1594 1663 5.456822 GCATGTTTAGATGAGATTTTTCCGC 59.543 40.000 0.00 0.00 0.00 5.54
1599 1668 2.487762 AGATGAGATTTTTCCGCGCAAA 59.512 40.909 8.75 0.00 0.00 3.68
1607 1676 1.584175 TTTCCGCGCAAACAGACTTA 58.416 45.000 8.75 0.00 0.00 2.24
1671 1740 0.379669 GGCATGCAACTCCTCGATTG 59.620 55.000 21.36 0.00 0.00 2.67
1689 1758 6.996106 TCGATTGTTAATTGCTAAACGGTAG 58.004 36.000 0.00 0.00 0.00 3.18
1699 1768 4.823157 TGCTAAACGGTAGCTGAACAATA 58.177 39.130 17.91 0.00 40.95 1.90
1712 1781 4.444876 GCTGAACAATAGATAAGGGAGCCA 60.445 45.833 0.00 0.00 0.00 4.75
1724 1793 0.322456 GGGAGCCACTGTGCATTACA 60.322 55.000 1.29 0.00 37.78 2.41
1754 1823 3.001168 CACAAGGTTTTTGCGTTTTCTCG 60.001 43.478 0.00 0.00 0.00 4.04
1756 1825 3.768468 AGGTTTTTGCGTTTTCTCGAA 57.232 38.095 0.00 0.00 0.00 3.71
1928 1998 4.053983 TCGATCAGCAGCATAAAGATCAC 58.946 43.478 0.00 0.00 35.91 3.06
1936 2006 3.059120 CAGCATAAAGATCACCATCAGCG 60.059 47.826 0.00 0.00 0.00 5.18
1967 2038 0.742635 GCTCTGGCTGTAGTCCAAGC 60.743 60.000 0.00 0.00 33.80 4.01
1979 2050 2.098298 CCAAGCCGAAATGCGACG 59.902 61.111 0.00 0.00 44.57 5.12
2010 2081 0.387622 CAAGCGTTGCACCCATTGAG 60.388 55.000 0.00 0.00 0.00 3.02
2028 2099 2.303890 TGAGCATCCACACAGTGAGAAT 59.696 45.455 7.81 0.00 35.23 2.40
2029 2100 3.244665 TGAGCATCCACACAGTGAGAATT 60.245 43.478 7.81 0.00 35.23 2.17
2031 2102 2.094894 GCATCCACACAGTGAGAATTCG 59.905 50.000 7.81 0.00 35.23 3.34
2156 2227 2.932614 CTCCACTTCACCAAAGCTATCG 59.067 50.000 0.00 0.00 38.67 2.92
2476 2550 9.071276 CCCAGCATGTATTTTATCATTAGTTCT 57.929 33.333 0.00 0.00 0.00 3.01
2598 2677 5.843019 TTCAGTTCATCTACTTCCCCTTT 57.157 39.130 0.00 0.00 0.00 3.11
2737 2818 7.429633 TCTCTGTTGTATAAGAAGCTAGATGC 58.570 38.462 0.00 0.00 43.29 3.91
2782 2863 7.338800 ACAACATTTTCAGTCATCTTGAGTT 57.661 32.000 0.00 0.00 0.00 3.01
2802 2883 6.371548 TGAGTTTGTTGCCTATATCACTTCAC 59.628 38.462 0.00 0.00 0.00 3.18
2806 2887 5.988287 TGTTGCCTATATCACTTCACATCA 58.012 37.500 0.00 0.00 0.00 3.07
2807 2888 6.594744 TGTTGCCTATATCACTTCACATCAT 58.405 36.000 0.00 0.00 0.00 2.45
2811 2892 8.158169 TGCCTATATCACTTCACATCATTTTC 57.842 34.615 0.00 0.00 0.00 2.29
2836 2917 1.714011 TTGGTCCAGTGCATGTCCCA 61.714 55.000 0.00 0.00 0.00 4.37
2837 2918 1.377725 GGTCCAGTGCATGTCCCAG 60.378 63.158 0.00 0.00 0.00 4.45
2838 2919 1.376466 GTCCAGTGCATGTCCCAGT 59.624 57.895 0.00 0.00 0.00 4.00
2839 2920 0.957395 GTCCAGTGCATGTCCCAGTG 60.957 60.000 0.00 0.00 34.25 3.66
2841 2922 0.957395 CCAGTGCATGTCCCAGTGTC 60.957 60.000 0.00 0.00 32.94 3.67
2842 2923 0.957395 CAGTGCATGTCCCAGTGTCC 60.957 60.000 0.00 0.00 0.00 4.02
2843 2924 1.675641 GTGCATGTCCCAGTGTCCC 60.676 63.158 0.00 0.00 0.00 4.46
2844 2925 2.152729 TGCATGTCCCAGTGTCCCA 61.153 57.895 0.00 0.00 0.00 4.37
2847 2928 0.110295 CATGTCCCAGTGTCCCACAA 59.890 55.000 0.00 0.00 36.74 3.33
2848 2929 1.075601 ATGTCCCAGTGTCCCACAAT 58.924 50.000 0.00 0.00 36.74 2.71
2849 2930 0.110295 TGTCCCAGTGTCCCACAATG 59.890 55.000 0.00 0.00 43.12 2.82
2850 2931 0.400213 GTCCCAGTGTCCCACAATGA 59.600 55.000 5.69 0.00 46.01 2.57
2851 2932 0.692476 TCCCAGTGTCCCACAATGAG 59.308 55.000 5.69 0.00 46.01 2.90
2852 2933 0.401738 CCCAGTGTCCCACAATGAGT 59.598 55.000 5.69 0.00 46.01 3.41
2861 2942 3.254629 CACAATGAGTGGACAGGGG 57.745 57.895 0.00 0.00 44.69 4.79
2871 2952 1.074951 GGACAGGGGAGTTGTTGGG 59.925 63.158 0.00 0.00 0.00 4.12
2873 2954 2.672996 CAGGGGAGTTGTTGGGCG 60.673 66.667 0.00 0.00 0.00 6.13
2876 2957 3.365265 GGGAGTTGTTGGGCGCTG 61.365 66.667 7.64 0.00 0.00 5.18
2888 2969 4.521075 GCGCTGCCATCTTCACTA 57.479 55.556 0.00 0.00 0.00 2.74
2892 2973 1.156645 GCTGCCATCTTCACTAGCCG 61.157 60.000 0.00 0.00 0.00 5.52
2894 2975 1.409064 CTGCCATCTTCACTAGCCGTA 59.591 52.381 0.00 0.00 0.00 4.02
2896 2977 2.434336 TGCCATCTTCACTAGCCGTAAT 59.566 45.455 0.00 0.00 0.00 1.89
2911 2992 3.318017 CCGTAATGCTATGAGTGGCTAC 58.682 50.000 0.00 0.00 32.28 3.58
2924 3005 4.559502 GCTACGGCCATTGGTCAT 57.440 55.556 8.26 0.00 0.00 3.06
2926 3007 0.463654 GCTACGGCCATTGGTCATCA 60.464 55.000 8.26 0.00 0.00 3.07
2929 3010 2.727123 ACGGCCATTGGTCATCATTA 57.273 45.000 8.26 0.00 0.00 1.90
2933 3014 3.554934 GGCCATTGGTCATCATTAGTCA 58.445 45.455 1.41 0.00 0.00 3.41
2935 3016 4.586001 GGCCATTGGTCATCATTAGTCATT 59.414 41.667 1.41 0.00 0.00 2.57
2937 3018 5.300034 GCCATTGGTCATCATTAGTCATTGA 59.700 40.000 4.26 0.00 0.00 2.57
2950 3031 4.336889 AGTCATTGACCGTTCTTCTTCA 57.663 40.909 13.14 0.00 32.18 3.02
2958 3039 1.608283 CCGTTCTTCTTCACCACCTCC 60.608 57.143 0.00 0.00 0.00 4.30
2974 3055 0.251634 CTCCCTGAAGGTCAGCTTCC 59.748 60.000 14.06 0.00 42.98 3.46
2995 3076 4.807105 CGGTACACGGGAATGGAACACA 62.807 54.545 0.00 0.00 39.76 3.72
3134 3215 1.264288 GTTGGACGGACTGCAAGAAAG 59.736 52.381 0.00 0.00 37.43 2.62
3165 3246 2.527123 TACAGACAACCCCCGCCA 60.527 61.111 0.00 0.00 0.00 5.69
3186 3267 1.546961 CCACACGGACTACTTCCTCT 58.453 55.000 0.00 0.00 43.25 3.69
3210 3291 3.861237 TCCTCATCCAGGTATGGGGCTA 61.861 54.545 11.31 0.00 45.76 3.93
3269 3351 1.409802 CCTCTTGCCATGCTCCTTCAT 60.410 52.381 0.00 0.00 0.00 2.57
3282 3364 5.573337 GCTCCTTCATGTATGAGCTTTTT 57.427 39.130 18.13 0.00 45.21 1.94
3410 3494 2.889512 TGAGAAGTCAAGGTGCCTAGA 58.110 47.619 0.00 0.00 0.00 2.43
3428 3512 5.188434 CCTAGAACCTGCTTGATGAAATGA 58.812 41.667 0.00 0.00 0.00 2.57
3432 3516 4.510038 ACCTGCTTGATGAAATGACAAC 57.490 40.909 0.00 0.00 0.00 3.32
3526 3611 4.395959 CCCCCAATCTGATGTGATTTTG 57.604 45.455 0.00 0.00 34.77 2.44
3539 3624 8.905660 TGATGTGATTTTGTTTGGATCAAATT 57.094 26.923 0.00 0.00 35.74 1.82
3567 3653 4.324402 CACAGAAAAGTTGCACACAAAGAC 59.676 41.667 0.00 0.00 37.58 3.01
3582 3668 6.583806 CACACAAAGACCATCTTCTAAAATGC 59.416 38.462 0.00 0.00 35.27 3.56
3666 4602 8.138074 TCAGATTATCGGAACAAGTTCTCATAG 58.862 37.037 12.22 1.26 39.45 2.23
3676 4612 5.790593 ACAAGTTCTCATAGACGCCTTTTA 58.209 37.500 0.00 0.00 0.00 1.52
3768 4704 4.752604 TGAATAAGAAGTGTGTAGCGCAAA 59.247 37.500 11.47 0.00 0.00 3.68
3802 4773 6.793492 AACTACTGCAAGAGTTCAAGAATC 57.207 37.500 7.01 0.00 37.43 2.52
3861 4832 1.014564 GTTCTGGGCAGTACAGACGC 61.015 60.000 0.00 0.00 44.07 5.19
4097 5071 9.791838 GCAACTTAGTTAAAACATGCATTTTAC 57.208 29.630 0.00 4.52 34.53 2.01
4237 5214 1.905354 GCTGCTTTTGGACTGCCCT 60.905 57.895 0.00 0.00 35.38 5.19
4265 5242 5.008019 AGCACGTCATTATAGATGGCAAAAG 59.992 40.000 0.00 0.00 0.00 2.27
4395 5375 1.484038 CTGCCTCTACAAGCTCCTCT 58.516 55.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 81 1.551883 GTAGGAGGCGGTTTAGGTTGA 59.448 52.381 0.00 0.00 0.00 3.18
102 104 3.190849 CGCGACGACTACCTCCGA 61.191 66.667 0.00 0.00 0.00 4.55
262 264 2.579738 GGCGTGAGGGAGGAAGTC 59.420 66.667 0.00 0.00 0.00 3.01
289 291 2.657237 GTGACACGTGGGAGGGAG 59.343 66.667 21.57 0.00 0.00 4.30
290 292 2.920912 GGTGACACGTGGGAGGGA 60.921 66.667 21.57 0.00 0.00 4.20
298 300 3.296709 GAGGATGGCGGTGACACGT 62.297 63.158 0.00 0.00 35.98 4.49
301 303 3.770040 CGGAGGATGGCGGTGACA 61.770 66.667 0.00 0.00 0.00 3.58
320 322 2.037527 GGGGAGACAGAGACCGGT 59.962 66.667 6.92 6.92 0.00 5.28
477 503 2.190313 GGCTGGTCGGCATCATCA 59.810 61.111 4.06 0.00 38.25 3.07
667 730 6.648725 GCTTATCTACTAGAAATGCAGGAAGG 59.351 42.308 0.00 0.00 0.00 3.46
702 765 2.282783 TGCTTACCTGGCTGAGCGA 61.283 57.895 0.00 0.00 37.94 4.93
704 767 0.393537 ATGTGCTTACCTGGCTGAGC 60.394 55.000 0.00 0.00 35.74 4.26
705 768 1.376543 CATGTGCTTACCTGGCTGAG 58.623 55.000 0.00 0.00 0.00 3.35
706 769 0.035152 CCATGTGCTTACCTGGCTGA 60.035 55.000 0.00 0.00 0.00 4.26
727 790 0.250295 TGTCCTTGAACTGCGGGAAG 60.250 55.000 0.00 0.00 0.00 3.46
729 792 1.371183 CTGTCCTTGAACTGCGGGA 59.629 57.895 0.00 0.00 0.00 5.14
730 793 2.328099 GCTGTCCTTGAACTGCGGG 61.328 63.158 0.00 0.00 34.97 6.13
732 795 0.662619 TTTGCTGTCCTTGAACTGCG 59.337 50.000 0.00 0.00 44.36 5.18
893 959 5.536497 ACTTTTCTTCCCCCTTGATGTAT 57.464 39.130 0.00 0.00 0.00 2.29
932 998 6.617371 AGGATTAAGCCTAGATTCAAGGAGAA 59.383 38.462 11.43 0.00 37.27 2.87
1010 1076 7.394144 AAGTCTTTAGGCATATTAGACCCAT 57.606 36.000 14.07 3.32 36.71 4.00
1012 1078 7.468768 GCAAAAGTCTTTAGGCATATTAGACCC 60.469 40.741 14.07 0.00 36.71 4.46
1085 1151 5.129320 AGGATTTCAACAAGCCTTTCTTTGT 59.871 36.000 0.00 0.00 31.27 2.83
1182 1249 6.959639 TTTTCAATTGTCTCTTTAGCCAGT 57.040 33.333 5.13 0.00 0.00 4.00
1243 1310 2.050144 GATGGGATCTCTTGTGGGCTA 58.950 52.381 0.00 0.00 0.00 3.93
1247 1314 3.920231 TGAAGATGGGATCTCTTGTGG 57.080 47.619 0.72 0.00 39.08 4.17
1308 1375 4.202430 CCTGGATGATGATCATGGACAAGA 60.202 45.833 14.30 0.00 37.20 3.02
1344 1411 3.859386 CACAACTTTGCTGTCCTTGAAAC 59.141 43.478 0.00 0.00 0.00 2.78
1520 1589 9.465985 GCAGTACTATACAGAAGAAATTACTCC 57.534 37.037 0.00 0.00 0.00 3.85
1525 1594 7.852263 AGGTGCAGTACTATACAGAAGAAATT 58.148 34.615 0.00 0.00 0.00 1.82
1594 1663 2.609459 CCATAGCCTAAGTCTGTTTGCG 59.391 50.000 0.00 0.00 0.00 4.85
1671 1740 5.789710 TCAGCTACCGTTTAGCAATTAAC 57.210 39.130 13.97 0.00 42.68 2.01
1689 1758 4.068599 GGCTCCCTTATCTATTGTTCAGC 58.931 47.826 0.00 0.00 0.00 4.26
1699 1768 0.543749 GCACAGTGGCTCCCTTATCT 59.456 55.000 1.84 0.00 0.00 1.98
1712 1781 5.900425 TGTGTTTCAATTGTAATGCACAGT 58.100 33.333 13.63 0.00 38.72 3.55
1724 1793 4.693095 ACGCAAAAACCTTGTGTTTCAATT 59.307 33.333 0.00 0.00 46.39 2.32
1928 1998 1.811266 CGACTTGGACCGCTGATGG 60.811 63.158 0.00 0.00 0.00 3.51
1936 2006 1.216710 CCAGAGCTCGACTTGGACC 59.783 63.158 13.22 0.00 31.75 4.46
1967 2038 0.999406 AGATGTTCGTCGCATTTCGG 59.001 50.000 0.00 0.00 39.05 4.30
1979 2050 2.918131 GCAACGCTTGGTGAAGATGTTC 60.918 50.000 0.00 0.00 30.92 3.18
2010 2081 2.094894 CGAATTCTCACTGTGTGGATGC 59.905 50.000 7.79 3.40 33.87 3.91
2028 2099 9.748708 AAATGTTCAAAGAAAAATGAGATCGAA 57.251 25.926 0.00 0.00 0.00 3.71
2029 2100 9.184062 CAAATGTTCAAAGAAAAATGAGATCGA 57.816 29.630 0.00 0.00 0.00 3.59
2031 2102 8.985805 AGCAAATGTTCAAAGAAAAATGAGATC 58.014 29.630 0.00 0.00 0.00 2.75
2156 2227 2.681097 GCTACACCTCCTCATTTGGACC 60.681 54.545 0.00 0.00 31.94 4.46
2220 2291 8.405531 TGACGAAGAATTGAACTGAAAAAGAAT 58.594 29.630 0.00 0.00 0.00 2.40
2476 2550 5.301551 TGCACTGATTCAGCTTTCCTTTTAA 59.698 36.000 13.64 0.00 34.37 1.52
2560 2639 6.003326 TGAACTGAAAGCCATGAACTATTGA 58.997 36.000 0.00 0.00 37.60 2.57
2570 2649 5.189180 GGAAGTAGATGAACTGAAAGCCAT 58.811 41.667 0.00 0.00 37.60 4.40
2573 2652 3.942115 GGGGAAGTAGATGAACTGAAAGC 59.058 47.826 0.00 0.00 37.60 3.51
2574 2653 5.428184 AGGGGAAGTAGATGAACTGAAAG 57.572 43.478 0.00 0.00 42.29 2.62
2747 2828 7.119699 TGACTGAAAATGTTGTTAGAGCATAGG 59.880 37.037 0.00 0.00 0.00 2.57
2755 2836 8.562892 ACTCAAGATGACTGAAAATGTTGTTAG 58.437 33.333 0.00 0.00 31.06 2.34
2757 2838 7.338800 ACTCAAGATGACTGAAAATGTTGTT 57.661 32.000 0.00 0.00 31.06 2.83
2782 2863 6.413892 TGATGTGAAGTGATATAGGCAACAA 58.586 36.000 0.00 0.00 41.41 2.83
2802 2883 5.242393 ACTGGACCAACAAGAGAAAATGATG 59.758 40.000 0.00 0.00 0.00 3.07
2806 2887 3.319122 GCACTGGACCAACAAGAGAAAAT 59.681 43.478 0.00 0.00 0.00 1.82
2807 2888 2.687935 GCACTGGACCAACAAGAGAAAA 59.312 45.455 0.00 0.00 0.00 2.29
2811 2892 1.538512 CATGCACTGGACCAACAAGAG 59.461 52.381 0.00 0.00 0.00 2.85
2843 2924 0.692476 TCCCCTGTCCACTCATTGTG 59.308 55.000 0.00 0.00 45.80 3.33
2844 2925 0.987294 CTCCCCTGTCCACTCATTGT 59.013 55.000 0.00 0.00 0.00 2.71
2847 2928 0.987294 CAACTCCCCTGTCCACTCAT 59.013 55.000 0.00 0.00 0.00 2.90
2848 2929 0.399949 ACAACTCCCCTGTCCACTCA 60.400 55.000 0.00 0.00 0.00 3.41
2849 2930 0.765510 AACAACTCCCCTGTCCACTC 59.234 55.000 0.00 0.00 0.00 3.51
2850 2931 0.474184 CAACAACTCCCCTGTCCACT 59.526 55.000 0.00 0.00 0.00 4.00
2851 2932 0.537371 CCAACAACTCCCCTGTCCAC 60.537 60.000 0.00 0.00 0.00 4.02
2852 2933 1.715019 CCCAACAACTCCCCTGTCCA 61.715 60.000 0.00 0.00 0.00 4.02
2861 2942 4.043200 GGCAGCGCCCAACAACTC 62.043 66.667 2.29 0.00 44.06 3.01
2871 2952 1.770085 GCTAGTGAAGATGGCAGCGC 61.770 60.000 0.00 0.00 0.00 5.92
2873 2954 1.156645 CGGCTAGTGAAGATGGCAGC 61.157 60.000 0.00 0.00 0.00 5.25
2876 2957 2.596904 TTACGGCTAGTGAAGATGGC 57.403 50.000 0.00 0.00 0.00 4.40
2887 2968 4.568236 AGCCACTCATAGCATTACGGCTA 61.568 47.826 0.00 0.00 46.47 3.93
2892 2973 3.318017 CCGTAGCCACTCATAGCATTAC 58.682 50.000 0.00 0.00 0.00 1.89
2894 2975 1.541233 GCCGTAGCCACTCATAGCATT 60.541 52.381 0.00 0.00 0.00 3.56
2896 2977 1.441729 GCCGTAGCCACTCATAGCA 59.558 57.895 0.00 0.00 0.00 3.49
2911 2992 2.549754 GACTAATGATGACCAATGGCCG 59.450 50.000 0.00 0.00 0.00 6.13
2924 3005 6.037786 AGAAGAACGGTCAATGACTAATGA 57.962 37.500 13.53 0.00 32.47 2.57
2926 3007 6.369065 GTGAAGAAGAACGGTCAATGACTAAT 59.631 38.462 13.53 0.00 32.47 1.73
2929 3010 4.058817 GTGAAGAAGAACGGTCAATGACT 58.941 43.478 13.53 0.00 32.47 3.41
2933 3014 3.139077 GTGGTGAAGAAGAACGGTCAAT 58.861 45.455 1.87 0.00 0.00 2.57
2935 3016 1.202604 GGTGGTGAAGAAGAACGGTCA 60.203 52.381 1.87 0.00 0.00 4.02
2937 3018 1.070289 GAGGTGGTGAAGAAGAACGGT 59.930 52.381 0.00 0.00 0.00 4.83
2974 3055 0.037139 TGTTCCATTCCCGTGTACCG 60.037 55.000 0.00 0.00 0.00 4.02
2989 3070 5.152097 CAACTGATGCTTCATCTTGTGTTC 58.848 41.667 2.33 0.00 41.06 3.18
3027 3108 5.757320 AGAGATGTATGTATTGCTGCTGTTC 59.243 40.000 0.00 0.00 0.00 3.18
3134 3215 5.050023 GGTTGTCTGTAGAACTGAGCTTTTC 60.050 44.000 0.00 0.00 0.00 2.29
3165 3246 2.359088 GGAAGTAGTCCGTGTGGGT 58.641 57.895 0.00 0.00 36.40 4.51
3186 3267 1.695664 CCCATACCTGGATGAGGACCA 60.696 57.143 0.00 0.00 46.33 4.02
3210 3291 4.080299 GGGAGGAATAGTTGGACTGATGTT 60.080 45.833 0.00 0.00 0.00 2.71
3269 3351 1.810151 GTGCCGGAAAAAGCTCATACA 59.190 47.619 5.05 0.00 0.00 2.29
3410 3494 4.262164 GGTTGTCATTTCATCAAGCAGGTT 60.262 41.667 0.00 0.00 38.75 3.50
3526 3611 6.317789 TCTGTGAGTCAATTTGATCCAAAC 57.682 37.500 1.78 0.00 36.13 2.93
3539 3624 3.126858 GTGTGCAACTTTTCTGTGAGTCA 59.873 43.478 0.00 0.00 38.04 3.41
3638 4574 7.158697 TGAGAACTTGTTCCGATAATCTGAAA 58.841 34.615 9.58 0.00 0.00 2.69
3647 4583 4.673441 CGTCTATGAGAACTTGTTCCGAT 58.327 43.478 9.58 5.32 0.00 4.18
3666 4602 3.323243 TGTAACAGAGCTAAAAGGCGTC 58.677 45.455 0.00 0.00 37.29 5.19
3676 4612 5.239525 CCTTTTAGCAAGTTGTAACAGAGCT 59.760 40.000 4.48 11.37 36.78 4.09
3768 4704 6.437793 ACTCTTGCAGTAGTTATACCTGAACT 59.562 38.462 0.00 0.00 40.27 3.01
3834 4805 4.720046 TGTACTGCCCAGAACAACAAATA 58.280 39.130 1.69 0.00 0.00 1.40
3861 4832 5.631096 CACACATGTACTACACAAGACTCTG 59.369 44.000 0.00 0.00 41.55 3.35
4017 4990 9.976511 ATTCAGAAATTGCACCAAATATATCAG 57.023 29.630 0.00 0.00 0.00 2.90
4161 5136 6.055588 CACCTACTCGATGGGAATTTACAAT 58.944 40.000 5.63 0.00 31.84 2.71
4162 5137 5.424757 CACCTACTCGATGGGAATTTACAA 58.575 41.667 5.63 0.00 31.84 2.41
4237 5214 4.631131 CCATCTATAATGACGTGCTTCCA 58.369 43.478 0.00 0.00 0.00 3.53
4335 5312 5.472137 GCCAGGTGTAAGTTTGAACTATCAA 59.528 40.000 0.00 0.00 43.70 2.57
4375 5355 0.463620 GAGGAGCTTGTAGAGGCAGG 59.536 60.000 0.00 0.00 0.00 4.85
4395 5375 3.197766 CCAGCTACTACCAAGTCATTCCA 59.802 47.826 0.00 0.00 37.15 3.53


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

AutoCloner maintained by Alex Coulton.