Multiple sequence alignment - TraesCS7B01G195400

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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 TraesCS7B01G195400 chr7B 100.000 6190 0 0 1 6190 336255825 336262014 0.000000e+00 11431
1 TraesCS7B01G195400 chr7B 93.255 1527 64 14 4593 6104 345993255 345994757 0.000000e+00 2213
2 TraesCS7B01G195400 chr7B 92.868 1304 65 7 4593 5883 20342487 20341199 0.000000e+00 1868
3 TraesCS7B01G195400 chr7B 91.695 879 66 2 716 1587 345985530 345986408 0.000000e+00 1212
4 TraesCS7B01G195400 chr7B 92.838 740 46 2 850 1582 20347869 20347130 0.000000e+00 1066
5 TraesCS7B01G195400 chr7B 96.075 586 19 3 3158 3743 345988658 345989239 0.000000e+00 952
6 TraesCS7B01G195400 chr7B 88.734 719 78 3 1 717 137205059 137205776 0.000000e+00 876
7 TraesCS7B01G195400 chr7B 93.973 365 17 3 2798 3161 345987069 345987429 1.170000e-151 547
8 TraesCS7B01G195400 chr7B 94.955 337 14 1 2798 3134 20346463 20346130 5.500000e-145 525
9 TraesCS7B01G195400 chr7B 91.484 364 22 4 2798 3161 178422204 178422558 5.580000e-135 492
10 TraesCS7B01G195400 chr7B 85.281 231 16 4 1357 1587 178421352 178421564 8.080000e-54 222
11 TraesCS7B01G195400 chr7B 87.647 170 15 1 2908 3077 195422212 195422375 6.330000e-45 193
12 TraesCS7B01G195400 chr6B 96.409 5402 160 14 716 6102 587739355 587744737 0.000000e+00 8870
13 TraesCS7B01G195400 chr6B 92.354 1007 60 6 4593 5585 185006571 185007574 0.000000e+00 1417
14 TraesCS7B01G195400 chr6B 88.935 723 76 4 1 720 114446694 114445973 0.000000e+00 889
15 TraesCS7B01G195400 chr6B 88.260 724 81 4 1 720 134532241 134531518 0.000000e+00 863
16 TraesCS7B01G195400 chr6B 93.004 486 22 7 4111 4594 185001922 185002397 0.000000e+00 699
17 TraesCS7B01G195400 chr6B 81.924 603 95 12 734 1330 257980025 257979431 1.200000e-136 497
18 TraesCS7B01G195400 chr6B 92.045 88 7 0 6101 6188 613342471 613342558 2.340000e-24 124
19 TraesCS7B01G195400 chr3B 96.080 5408 149 20 716 6104 589662857 589657494 0.000000e+00 8754
20 TraesCS7B01G195400 chr3B 95.560 2455 96 7 716 3161 455487339 455489789 0.000000e+00 3917
21 TraesCS7B01G195400 chr3B 96.220 1561 52 5 3158 4713 455491299 455492857 0.000000e+00 2549
22 TraesCS7B01G195400 chr3B 95.461 1410 42 7 4709 6113 455493582 455494974 0.000000e+00 2230
23 TraesCS7B01G195400 chr3B 92.878 1011 54 6 4593 5585 648412372 648413382 0.000000e+00 1452
24 TraesCS7B01G195400 chr3B 90.416 1033 71 12 4792 5813 279515426 279514411 0.000000e+00 1334
25 TraesCS7B01G195400 chr3B 88.504 722 80 3 2 720 249613063 249612342 0.000000e+00 870
26 TraesCS7B01G195400 chr3B 88.308 727 73 11 1 717 162601486 162602210 0.000000e+00 861
27 TraesCS7B01G195400 chr3B 91.564 486 29 7 4111 4594 648407840 648408315 0.000000e+00 660
28 TraesCS7B01G195400 chr3B 88.433 268 28 3 2285 2550 763298803 763299069 2.780000e-83 320
29 TraesCS7B01G195400 chr3B 90.283 247 17 3 2563 2802 763302921 763303167 3.600000e-82 316
30 TraesCS7B01G195400 chr5B 96.586 4599 124 14 1518 6102 463405895 463401316 0.000000e+00 7592
31 TraesCS7B01G195400 chr5B 97.462 3349 60 8 1518 4841 22036233 22032885 0.000000e+00 5690
32 TraesCS7B01G195400 chr5B 95.360 1207 40 3 4894 6099 22032572 22031381 0.000000e+00 1905
33 TraesCS7B01G195400 chr5B 92.798 486 23 7 4111 4594 389236451 389236926 0.000000e+00 693
34 TraesCS7B01G195400 chr2B 93.433 1005 52 5 4593 5585 746309299 746308297 0.000000e+00 1478
35 TraesCS7B01G195400 chr2B 92.299 922 39 15 4593 5501 388574857 388573955 0.000000e+00 1280
36 TraesCS7B01G195400 chr2B 91.925 644 45 3 719 1355 685735021 685735664 0.000000e+00 894
37 TraesCS7B01G195400 chr2B 92.683 574 26 6 5529 6102 654442231 654441674 0.000000e+00 813
38 TraesCS7B01G195400 chr2B 91.152 486 31 7 4111 4594 746311632 746311157 0.000000e+00 649
39 TraesCS7B01G195400 chr2B 90.593 489 28 13 4111 4594 388577254 388576779 3.150000e-177 632
40 TraesCS7B01G195400 chr2B 85.792 366 43 4 2086 2451 184875722 184875366 4.530000e-101 379
41 TraesCS7B01G195400 chr2B 84.511 368 38 10 2434 2791 184875148 184874790 4.590000e-91 346
42 TraesCS7B01G195400 chr2B 83.188 345 55 3 1603 1945 184876077 184875734 4.660000e-81 313
43 TraesCS7B01G195400 chr2B 94.318 88 5 0 6101 6188 545065659 545065746 1.080000e-27 135
44 TraesCS7B01G195400 chr5A 92.324 938 66 4 3158 4092 337891739 337890805 0.000000e+00 1328
45 TraesCS7B01G195400 chr5A 93.605 516 26 4 5600 6114 216122016 216122525 0.000000e+00 763
46 TraesCS7B01G195400 chr2A 91.800 939 73 3 3158 4092 347861798 347862736 0.000000e+00 1304
47 TraesCS7B01G195400 chr7A 91.622 931 70 8 3158 4084 354945428 354946354 0.000000e+00 1280
48 TraesCS7B01G195400 chr3D 85.755 1053 108 16 1603 2628 596714479 596715516 0.000000e+00 1075
49 TraesCS7B01G195400 chr3D 94.444 90 5 0 6101 6190 160980467 160980378 8.370000e-29 139
50 TraesCS7B01G195400 chr3D 88.889 90 10 0 6101 6190 480002770 480002681 1.820000e-20 111
51 TraesCS7B01G195400 chr1B 89.088 724 72 6 1 720 290098927 290098207 0.000000e+00 893
52 TraesCS7B01G195400 chr1B 88.966 725 72 6 1 717 186052749 186053473 0.000000e+00 889
53 TraesCS7B01G195400 chr1B 88.935 723 77 3 1 720 568844255 568843533 0.000000e+00 889
54 TraesCS7B01G195400 chr1B 93.407 364 17 3 2798 3161 288550544 288550188 3.280000e-147 532
55 TraesCS7B01G195400 chr1B 86.752 234 17 3 1357 1590 288551393 288551174 1.330000e-61 248
56 TraesCS7B01G195400 chr1D 94.128 579 30 4 3518 4092 93821145 93821723 0.000000e+00 878
57 TraesCS7B01G195400 chr1D 86.930 329 34 3 716 1043 439885113 439885433 1.640000e-95 361
58 TraesCS7B01G195400 chr1D 92.222 90 7 0 6101 6190 342535978 342535889 1.810000e-25 128
59 TraesCS7B01G195400 chr5D 91.118 653 47 8 714 1361 249162378 249161732 0.000000e+00 874
60 TraesCS7B01G195400 chr5D 84.327 587 54 13 763 1338 98744715 98744156 1.960000e-149 540
61 TraesCS7B01G195400 chr5D 81.784 527 67 8 716 1240 175964687 175964188 1.240000e-111 414
62 TraesCS7B01G195400 chr5D 90.000 90 9 0 6101 6190 298618040 298618129 3.920000e-22 117
63 TraesCS7B01G195400 chr4B 88.504 722 75 7 2 717 350315552 350316271 0.000000e+00 867
64 TraesCS7B01G195400 chr4B 89.773 88 9 0 6101 6188 304486656 304486569 5.070000e-21 113
65 TraesCS7B01G195400 chr4D 93.846 520 25 7 5600 6116 460238992 460239507 0.000000e+00 776
66 TraesCS7B01G195400 chr4D 92.308 91 6 1 6101 6190 229155652 229155742 1.810000e-25 128
67 TraesCS7B01G195400 chr3A 89.195 435 32 5 716 1136 267366905 267366472 4.250000e-146 529
68 TraesCS7B01G195400 chr6A 93.333 90 6 0 6101 6190 512592527 512592616 3.890000e-27 134
69 TraesCS7B01G195400 chr7D 83.673 147 16 4 1832 1977 19154779 19154918 1.400000e-26 132


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 TraesCS7B01G195400 chr7B 336255825 336262014 6189 False 11431.000000 11431 100.000000 1 6190 1 chr7B.!!$F3 6189
1 TraesCS7B01G195400 chr7B 345993255 345994757 1502 False 2213.000000 2213 93.255000 4593 6104 1 chr7B.!!$F4 1511
2 TraesCS7B01G195400 chr7B 20341199 20347869 6670 True 1153.000000 1868 93.553667 850 5883 3 chr7B.!!$R1 5033
3 TraesCS7B01G195400 chr7B 345985530 345989239 3709 False 903.666667 1212 93.914333 716 3743 3 chr7B.!!$F6 3027
4 TraesCS7B01G195400 chr7B 137205059 137205776 717 False 876.000000 876 88.734000 1 717 1 chr7B.!!$F1 716
5 TraesCS7B01G195400 chr7B 178421352 178422558 1206 False 357.000000 492 88.382500 1357 3161 2 chr7B.!!$F5 1804
6 TraesCS7B01G195400 chr6B 587739355 587744737 5382 False 8870.000000 8870 96.409000 716 6102 1 chr6B.!!$F3 5386
7 TraesCS7B01G195400 chr6B 185006571 185007574 1003 False 1417.000000 1417 92.354000 4593 5585 1 chr6B.!!$F2 992
8 TraesCS7B01G195400 chr6B 114445973 114446694 721 True 889.000000 889 88.935000 1 720 1 chr6B.!!$R1 719
9 TraesCS7B01G195400 chr6B 134531518 134532241 723 True 863.000000 863 88.260000 1 720 1 chr6B.!!$R2 719
10 TraesCS7B01G195400 chr6B 257979431 257980025 594 True 497.000000 497 81.924000 734 1330 1 chr6B.!!$R3 596
11 TraesCS7B01G195400 chr3B 589657494 589662857 5363 True 8754.000000 8754 96.080000 716 6104 1 chr3B.!!$R3 5388
12 TraesCS7B01G195400 chr3B 455487339 455494974 7635 False 2898.666667 3917 95.747000 716 6113 3 chr3B.!!$F4 5397
13 TraesCS7B01G195400 chr3B 648412372 648413382 1010 False 1452.000000 1452 92.878000 4593 5585 1 chr3B.!!$F3 992
14 TraesCS7B01G195400 chr3B 279514411 279515426 1015 True 1334.000000 1334 90.416000 4792 5813 1 chr3B.!!$R2 1021
15 TraesCS7B01G195400 chr3B 249612342 249613063 721 True 870.000000 870 88.504000 2 720 1 chr3B.!!$R1 718
16 TraesCS7B01G195400 chr3B 162601486 162602210 724 False 861.000000 861 88.308000 1 717 1 chr3B.!!$F1 716
17 TraesCS7B01G195400 chr3B 763298803 763303167 4364 False 318.000000 320 89.358000 2285 2802 2 chr3B.!!$F5 517
18 TraesCS7B01G195400 chr5B 463401316 463405895 4579 True 7592.000000 7592 96.586000 1518 6102 1 chr5B.!!$R1 4584
19 TraesCS7B01G195400 chr5B 22031381 22036233 4852 True 3797.500000 5690 96.411000 1518 6099 2 chr5B.!!$R2 4581
20 TraesCS7B01G195400 chr2B 746308297 746311632 3335 True 1063.500000 1478 92.292500 4111 5585 2 chr2B.!!$R4 1474
21 TraesCS7B01G195400 chr2B 388573955 388577254 3299 True 956.000000 1280 91.446000 4111 5501 2 chr2B.!!$R3 1390
22 TraesCS7B01G195400 chr2B 685735021 685735664 643 False 894.000000 894 91.925000 719 1355 1 chr2B.!!$F2 636
23 TraesCS7B01G195400 chr2B 654441674 654442231 557 True 813.000000 813 92.683000 5529 6102 1 chr2B.!!$R1 573
24 TraesCS7B01G195400 chr2B 184874790 184876077 1287 True 346.000000 379 84.497000 1603 2791 3 chr2B.!!$R2 1188
25 TraesCS7B01G195400 chr5A 337890805 337891739 934 True 1328.000000 1328 92.324000 3158 4092 1 chr5A.!!$R1 934
26 TraesCS7B01G195400 chr5A 216122016 216122525 509 False 763.000000 763 93.605000 5600 6114 1 chr5A.!!$F1 514
27 TraesCS7B01G195400 chr2A 347861798 347862736 938 False 1304.000000 1304 91.800000 3158 4092 1 chr2A.!!$F1 934
28 TraesCS7B01G195400 chr7A 354945428 354946354 926 False 1280.000000 1280 91.622000 3158 4084 1 chr7A.!!$F1 926
29 TraesCS7B01G195400 chr3D 596714479 596715516 1037 False 1075.000000 1075 85.755000 1603 2628 1 chr3D.!!$F1 1025
30 TraesCS7B01G195400 chr1B 290098207 290098927 720 True 893.000000 893 89.088000 1 720 1 chr1B.!!$R1 719
31 TraesCS7B01G195400 chr1B 186052749 186053473 724 False 889.000000 889 88.966000 1 717 1 chr1B.!!$F1 716
32 TraesCS7B01G195400 chr1B 568843533 568844255 722 True 889.000000 889 88.935000 1 720 1 chr1B.!!$R2 719
33 TraesCS7B01G195400 chr1B 288550188 288551393 1205 True 390.000000 532 90.079500 1357 3161 2 chr1B.!!$R3 1804
34 TraesCS7B01G195400 chr1D 93821145 93821723 578 False 878.000000 878 94.128000 3518 4092 1 chr1D.!!$F1 574
35 TraesCS7B01G195400 chr5D 249161732 249162378 646 True 874.000000 874 91.118000 714 1361 1 chr5D.!!$R3 647
36 TraesCS7B01G195400 chr5D 98744156 98744715 559 True 540.000000 540 84.327000 763 1338 1 chr5D.!!$R1 575
37 TraesCS7B01G195400 chr4B 350315552 350316271 719 False 867.000000 867 88.504000 2 717 1 chr4B.!!$F1 715
38 TraesCS7B01G195400 chr4D 460238992 460239507 515 False 776.000000 776 93.846000 5600 6116 1 chr4D.!!$F2 516

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
93 94 0.325671 CCCCTCTGTTGCTCCCTAGA 60.326 60.000 0.00 0.00 0.00 2.43 F
882 897 1.181098 ACTGCCCAATGACAAGTGGC 61.181 55.000 5.73 5.73 40.34 5.01 F
1860 1895 0.468226 ACTCAACACAGGAAAGCCGA 59.532 50.000 0.00 0.00 39.96 5.54 F
2162 2222 0.826715 GATGTAGCTCACTGGCCAGA 59.173 55.000 39.19 17.43 0.00 3.86 F
2341 2407 1.502690 ACTGGTGACCCAAGTGTGTA 58.497 50.000 0.00 0.00 41.27 2.90 F
3404 11255 1.330213 TGCAACATTATGGACGATGCG 59.670 47.619 0.00 0.00 35.18 4.73 F
4342 12233 2.124151 GGTTGGCGGATGCTCCAT 60.124 61.111 0.00 0.00 42.25 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 1641 1.622607 CCAACCTGGATGCCGGAGTA 61.623 60.000 5.05 0.0 40.96 2.59 R
2162 2222 2.042831 GCTGGCATCGCAGGTTCTT 61.043 57.895 0.00 0.0 0.00 2.52 R
3099 7372 0.176680 GACATGGAGGAGCACGTCAT 59.823 55.000 6.20 0.0 33.25 3.06 R
3404 11255 6.476706 GCAATCCAAGCCAATATAAAAGACAC 59.523 38.462 0.00 0.0 0.00 3.67 R
4154 12037 7.777910 TCTTTCTCCCAACACAGATTAAAAAGA 59.222 33.333 0.00 0.0 0.00 2.52 R
4796 15421 0.667993 AGCAACAACCACGACAATGG 59.332 50.000 0.00 0.0 46.10 3.16 R
5593 16508 0.038310 CTTCCTTTCTTTCCCGGCCT 59.962 55.000 0.00 0.0 0.00 5.19 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
93 94 0.325671 CCCCTCTGTTGCTCCCTAGA 60.326 60.000 0.00 0.00 0.00 2.43
118 120 4.846137 CGTCGTCTTTATTTTTCCTGCTTG 59.154 41.667 0.00 0.00 0.00 4.01
157 160 5.896922 TGTTAAATTTGCACAATTCCACG 57.103 34.783 0.00 0.00 0.00 4.94
163 166 3.418913 CACAATTCCACGCGCGGA 61.419 61.111 35.22 20.06 0.00 5.54
267 271 2.872245 CCGAGTTCTGACTTTTCTTGCA 59.128 45.455 0.00 0.00 35.88 4.08
276 280 3.884693 TGACTTTTCTTGCATTCTGCTCA 59.115 39.130 0.34 0.00 45.31 4.26
303 311 2.765689 TTTCTTTTGCCTCCCTTCCA 57.234 45.000 0.00 0.00 0.00 3.53
312 320 1.216990 CCTCCCTTCCATTGCTACCT 58.783 55.000 0.00 0.00 0.00 3.08
339 347 2.979676 CCAAACAGCCGCTCTGCA 60.980 61.111 0.00 0.00 46.76 4.41
357 365 2.281484 GACTGCGGCTGGGTCAAA 60.281 61.111 11.64 0.00 0.00 2.69
386 395 3.624959 GCTACTTTTGGGAGGGCAAGTAT 60.625 47.826 0.00 0.00 32.59 2.12
409 418 1.434696 CCGATTGGAGCATTGGCAC 59.565 57.895 0.00 0.00 44.61 5.01
411 420 1.368345 CGATTGGAGCATTGGCACGA 61.368 55.000 0.00 0.00 44.61 4.35
458 469 4.070552 GCAGCCGGTCGAAGAGGT 62.071 66.667 1.90 0.00 36.95 3.85
485 496 1.742768 GGCCTAGACTATGTGCGCT 59.257 57.895 9.73 0.00 0.00 5.92
547 561 1.296392 CTTGCCCATCGGTCAGTCA 59.704 57.895 0.00 0.00 0.00 3.41
590 604 2.485814 GCAGGAGAAGTTTTAGGTGCTG 59.514 50.000 0.00 0.00 0.00 4.41
608 622 2.922758 GCTGACACACTACTTGTCCGAG 60.923 54.545 0.25 0.00 42.40 4.63
638 652 2.165845 GTGACACATAGTAGAAGGCGGT 59.834 50.000 0.00 0.00 0.00 5.68
882 897 1.181098 ACTGCCCAATGACAAGTGGC 61.181 55.000 5.73 5.73 40.34 5.01
906 921 1.374631 CTCACGCTTGCAGTGGCTA 60.375 57.895 13.98 0.00 41.91 3.93
1105 1132 3.464080 CTCTTCCTCCTCCCTACTCCTTA 59.536 52.174 0.00 0.00 0.00 2.69
1116 1143 3.306613 CCTACTCCTTAACGGATCCCTT 58.693 50.000 6.06 3.44 42.12 3.95
1257 1288 3.414136 TTGTGAAGCGGTGGTGCCT 62.414 57.895 0.00 0.00 34.65 4.75
1342 1374 1.941812 CGCCGACAGCTTCTTTGTT 59.058 52.632 0.00 0.00 40.39 2.83
1480 1512 1.318158 GGGGTTGCCAGAGAAGCATG 61.318 60.000 0.00 0.00 40.59 4.06
1609 1641 4.241076 ATCCGGCGATCCCCTCCT 62.241 66.667 9.30 0.00 0.00 3.69
1848 1883 5.480422 TCTTAGATCCAGCAGTAACTCAACA 59.520 40.000 0.00 0.00 0.00 3.33
1860 1895 0.468226 ACTCAACACAGGAAAGCCGA 59.532 50.000 0.00 0.00 39.96 5.54
2162 2222 0.826715 GATGTAGCTCACTGGCCAGA 59.173 55.000 39.19 17.43 0.00 3.86
2290 2356 5.069516 GGAATTTTCCATACATGCATGACCT 59.930 40.000 32.75 13.48 46.76 3.85
2341 2407 1.502690 ACTGGTGACCCAAGTGTGTA 58.497 50.000 0.00 0.00 41.27 2.90
2581 6818 5.069516 ACCCATCATCAGTTTTTGGCATATC 59.930 40.000 0.00 0.00 0.00 1.63
2983 7255 6.891624 TCAATTTGATCACTTTTGAGACTCG 58.108 36.000 0.00 0.00 34.35 4.18
2997 7269 7.406031 TTTGAGACTCGGTTAGAACAGATAT 57.594 36.000 0.00 0.00 32.84 1.63
3404 11255 1.330213 TGCAACATTATGGACGATGCG 59.670 47.619 0.00 0.00 35.18 4.73
4341 12232 4.424711 GGGTTGGCGGATGCTCCA 62.425 66.667 0.00 0.00 42.25 3.86
4342 12233 2.124151 GGTTGGCGGATGCTCCAT 60.124 61.111 0.00 0.00 42.25 3.41
4796 15421 3.492102 TCCTGTATATGCAAGAAGGGC 57.508 47.619 0.00 0.00 0.00 5.19
5302 16211 7.666623 CAAGTACATGGTTTTAAATGGGACTT 58.333 34.615 0.00 0.00 35.85 3.01
5548 16463 4.690719 AATTGCACCGGTCGGCGA 62.691 61.111 2.59 4.99 39.32 5.54
5574 16489 0.106918 AAACGCCTTTGTCACCCAGA 60.107 50.000 0.00 0.00 0.00 3.86
5581 16496 2.040278 CCTTTGTCACCCAGATGAGGAA 59.960 50.000 0.00 0.00 0.00 3.36
5582 16497 2.859165 TTGTCACCCAGATGAGGAAC 57.141 50.000 0.00 0.00 0.00 3.62
5583 16498 0.984230 TGTCACCCAGATGAGGAACC 59.016 55.000 0.00 0.00 0.00 3.62
5584 16499 0.108138 GTCACCCAGATGAGGAACCG 60.108 60.000 0.00 0.00 0.00 4.44
5585 16500 1.221840 CACCCAGATGAGGAACCGG 59.778 63.158 0.00 0.00 0.00 5.28
5586 16501 1.995626 ACCCAGATGAGGAACCGGG 60.996 63.158 6.32 0.00 39.72 5.73
5587 16502 1.689233 CCCAGATGAGGAACCGGGA 60.689 63.158 6.32 0.00 35.57 5.14
5588 16503 1.271840 CCCAGATGAGGAACCGGGAA 61.272 60.000 6.32 0.00 35.57 3.97
5589 16504 0.618458 CCAGATGAGGAACCGGGAAA 59.382 55.000 6.32 0.00 0.00 3.13
5590 16505 1.407437 CCAGATGAGGAACCGGGAAAG 60.407 57.143 6.32 0.00 0.00 2.62
5591 16506 1.555075 CAGATGAGGAACCGGGAAAGA 59.445 52.381 6.32 0.00 0.00 2.52
5592 16507 2.027192 CAGATGAGGAACCGGGAAAGAA 60.027 50.000 6.32 0.00 0.00 2.52
5593 16508 2.642807 AGATGAGGAACCGGGAAAGAAA 59.357 45.455 6.32 0.00 0.00 2.52
5594 16509 2.561478 TGAGGAACCGGGAAAGAAAG 57.439 50.000 6.32 0.00 0.00 2.62
5736 16651 6.811574 TGGGCTATCCTAATACCTCTTGATA 58.188 40.000 0.00 0.00 36.20 2.15
6042 16965 5.574443 GGTTCTTGCAGCATGAAACTATTTC 59.426 40.000 25.01 12.27 39.69 2.17
6064 16987 1.418373 TCGACAACATGTCTTCAGCG 58.582 50.000 0.00 0.00 44.85 5.18
6104 17027 3.369385 CGCAACGGGTCAACTAGTATAG 58.631 50.000 0.00 0.00 46.50 1.31
6105 17028 3.065786 CGCAACGGGTCAACTAGTATAGA 59.934 47.826 0.00 0.00 42.77 1.98
6112 17035 8.757982 ACGGGTCAACTAGTATAGATAAAAGA 57.242 34.615 0.00 0.00 42.77 2.52
6115 17038 8.586744 GGGTCAACTAGTATAGATAAAAGAGGG 58.413 40.741 0.00 0.00 42.77 4.30
6116 17039 9.145442 GGTCAACTAGTATAGATAAAAGAGGGT 57.855 37.037 0.00 0.00 42.77 4.34
6124 17047 7.884354 AGTATAGATAAAAGAGGGTAGTCTCCG 59.116 40.741 0.00 0.00 34.46 4.63
6125 17048 5.126699 AGATAAAAGAGGGTAGTCTCCGA 57.873 43.478 0.00 0.00 34.46 4.55
6126 17049 5.134661 AGATAAAAGAGGGTAGTCTCCGAG 58.865 45.833 0.00 0.00 34.46 4.63
6127 17050 1.476477 AAAGAGGGTAGTCTCCGAGC 58.524 55.000 0.00 0.00 34.46 5.03
6128 17051 0.626916 AAGAGGGTAGTCTCCGAGCT 59.373 55.000 0.00 0.00 34.46 4.09
6129 17052 0.181824 AGAGGGTAGTCTCCGAGCTC 59.818 60.000 2.73 2.73 34.46 4.09
6130 17053 0.181824 GAGGGTAGTCTCCGAGCTCT 59.818 60.000 12.85 0.00 0.00 4.09
6131 17054 0.626916 AGGGTAGTCTCCGAGCTCTT 59.373 55.000 12.85 0.00 0.00 2.85
6132 17055 1.026584 GGGTAGTCTCCGAGCTCTTC 58.973 60.000 12.85 0.00 0.00 2.87
6133 17056 1.409101 GGGTAGTCTCCGAGCTCTTCT 60.409 57.143 12.85 5.36 0.00 2.85
6134 17057 1.944709 GGTAGTCTCCGAGCTCTTCTC 59.055 57.143 12.85 0.00 38.47 2.87
6141 17064 3.212275 GAGCTCTTCTCGGGGGAC 58.788 66.667 6.43 0.00 31.20 4.46
6156 17079 2.545537 GGGACCCGGAATCTTCATAC 57.454 55.000 0.73 0.00 0.00 2.39
6157 17080 2.047830 GGGACCCGGAATCTTCATACT 58.952 52.381 0.73 0.00 0.00 2.12
6158 17081 2.438392 GGGACCCGGAATCTTCATACTT 59.562 50.000 0.73 0.00 0.00 2.24
6159 17082 3.644738 GGGACCCGGAATCTTCATACTTA 59.355 47.826 0.73 0.00 0.00 2.24
6160 17083 4.102054 GGGACCCGGAATCTTCATACTTAA 59.898 45.833 0.73 0.00 0.00 1.85
6161 17084 5.221864 GGGACCCGGAATCTTCATACTTAAT 60.222 44.000 0.73 0.00 0.00 1.40
6162 17085 6.013984 GGGACCCGGAATCTTCATACTTAATA 60.014 42.308 0.73 0.00 0.00 0.98
6163 17086 7.447594 GGACCCGGAATCTTCATACTTAATAA 58.552 38.462 0.73 0.00 0.00 1.40
6164 17087 7.935210 GGACCCGGAATCTTCATACTTAATAAA 59.065 37.037 0.73 0.00 0.00 1.40
6165 17088 9.333724 GACCCGGAATCTTCATACTTAATAAAA 57.666 33.333 0.73 0.00 0.00 1.52
6166 17089 9.689501 ACCCGGAATCTTCATACTTAATAAAAA 57.310 29.630 0.73 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.448582 TTGGTGGAGTGGACGGCTT 61.449 57.895 0.00 0.00 0.00 4.35
93 94 4.935808 AGCAGGAAAAATAAAGACGACGAT 59.064 37.500 0.00 0.00 0.00 3.73
157 160 1.463444 AGTTTGAAATACACTCCGCGC 59.537 47.619 0.00 0.00 0.00 6.86
163 166 7.013655 AGCATTCAACAGAGTTTGAAATACACT 59.986 33.333 2.61 0.00 46.06 3.55
288 295 0.975887 GCAATGGAAGGGAGGCAAAA 59.024 50.000 0.00 0.00 0.00 2.44
300 307 1.354031 TGGCAAGAAGGTAGCAATGGA 59.646 47.619 0.00 0.00 0.00 3.41
303 311 1.467920 GCTGGCAAGAAGGTAGCAAT 58.532 50.000 0.00 0.00 34.64 3.56
312 320 1.741525 GCTGTTTGGCTGGCAAGAA 59.258 52.632 16.39 8.36 0.00 2.52
339 347 2.129555 ATTTGACCCAGCCGCAGTCT 62.130 55.000 8.95 0.00 0.00 3.24
357 365 4.141459 GCCCTCCCAAAAGTAGCTAAGTAT 60.141 45.833 0.00 0.00 0.00 2.12
386 395 2.023673 CCAATGCTCCAATCGGCTAAA 58.976 47.619 0.00 0.00 0.00 1.85
409 418 0.663568 CGGCCGGCTTCTACTTATCG 60.664 60.000 28.56 13.40 0.00 2.92
411 420 1.746517 CCGGCCGGCTTCTACTTAT 59.253 57.895 34.96 0.00 0.00 1.73
458 469 0.775542 TAGTCTAGGCCGGCATCCTA 59.224 55.000 30.85 19.08 35.21 2.94
530 544 1.003839 GTGACTGACCGATGGGCAA 60.004 57.895 0.00 0.00 41.95 4.52
590 604 2.662700 CACTCGGACAAGTAGTGTGTC 58.337 52.381 0.00 0.00 41.96 3.67
608 622 6.754702 TCTACTATGTGTCACTTCCTACAC 57.245 41.667 4.27 0.00 44.97 2.90
611 625 5.360144 GCCTTCTACTATGTGTCACTTCCTA 59.640 44.000 4.27 0.00 0.00 2.94
882 897 2.049156 TGCAAGCGTGAGACGAGG 60.049 61.111 2.99 0.00 46.05 4.63
906 921 2.129555 AAATGACCCGCTGCTGACCT 62.130 55.000 0.00 0.00 0.00 3.85
958 973 4.641645 CAGGCAAGCCACGGGACA 62.642 66.667 14.40 0.00 38.92 4.02
1342 1374 4.823419 CACGGCCCCGCGTCATAA 62.823 66.667 4.92 0.00 44.19 1.90
1609 1641 1.622607 CCAACCTGGATGCCGGAGTA 61.623 60.000 5.05 0.00 40.96 2.59
1848 1883 2.690778 GCGCAATCGGCTTTCCTGT 61.691 57.895 0.30 0.00 41.67 4.00
1860 1895 4.024698 GAGCAGATCGAGCGCAAT 57.975 55.556 11.47 0.00 37.01 3.56
2162 2222 2.042831 GCTGGCATCGCAGGTTCTT 61.043 57.895 0.00 0.00 0.00 2.52
2290 2356 6.432783 ACAATGGAAATCACAAAACGGATCTA 59.567 34.615 0.00 0.00 0.00 1.98
2581 6818 6.403636 GGCATGGCGATATATAACTCAAAAGG 60.404 42.308 2.41 0.00 0.00 3.11
2892 7143 9.424319 ACATGTCCAAAAACTATATATAGCTCG 57.576 33.333 18.00 4.51 33.68 5.03
3099 7372 0.176680 GACATGGAGGAGCACGTCAT 59.823 55.000 6.20 0.00 33.25 3.06
3404 11255 6.476706 GCAATCCAAGCCAATATAAAAGACAC 59.523 38.462 0.00 0.00 0.00 3.67
4154 12037 7.777910 TCTTTCTCCCAACACAGATTAAAAAGA 59.222 33.333 0.00 0.00 0.00 2.52
4341 12232 4.969359 ACCACTAAGTAGGCTATTGGTCAT 59.031 41.667 0.00 0.00 30.02 3.06
4342 12233 4.359105 ACCACTAAGTAGGCTATTGGTCA 58.641 43.478 0.00 0.00 30.02 4.02
4569 12465 1.964608 CTCCTTGCTCCTGCGATCCA 61.965 60.000 0.00 0.00 43.34 3.41
4657 14539 5.395657 CCTGCTCATTAGTATGACAAGACCA 60.396 44.000 0.00 0.00 35.87 4.02
4796 15421 0.667993 AGCAACAACCACGACAATGG 59.332 50.000 0.00 0.00 46.10 3.16
4960 15847 6.641176 AACCATCAAAGAAACAAAACGTTC 57.359 33.333 0.00 0.00 36.59 3.95
5302 16211 1.969064 ATTGCGCTAAACGGCACCA 60.969 52.632 9.73 0.00 43.93 4.17
5430 16342 6.456501 ACTTCAATACTCGTTGTAGAAAGCT 58.543 36.000 1.21 0.00 34.24 3.74
5548 16463 1.134220 TGACAAAGGCGTTTCCTCAGT 60.134 47.619 0.42 0.00 46.94 3.41
5574 16489 2.290960 CCTTTCTTTCCCGGTTCCTCAT 60.291 50.000 0.00 0.00 0.00 2.90
5581 16496 2.033602 CGGCCTTTCTTTCCCGGT 59.966 61.111 0.00 0.00 37.21 5.28
5583 16498 2.750237 CCCGGCCTTTCTTTCCCG 60.750 66.667 0.00 0.00 40.39 5.14
5584 16499 0.541063 TTTCCCGGCCTTTCTTTCCC 60.541 55.000 0.00 0.00 0.00 3.97
5585 16500 0.888619 CTTTCCCGGCCTTTCTTTCC 59.111 55.000 0.00 0.00 0.00 3.13
5586 16501 1.905637 TCTTTCCCGGCCTTTCTTTC 58.094 50.000 0.00 0.00 0.00 2.62
5587 16502 2.375014 TTCTTTCCCGGCCTTTCTTT 57.625 45.000 0.00 0.00 0.00 2.52
5588 16503 2.239400 CTTTCTTTCCCGGCCTTTCTT 58.761 47.619 0.00 0.00 0.00 2.52
5589 16504 1.547901 CCTTTCTTTCCCGGCCTTTCT 60.548 52.381 0.00 0.00 0.00 2.52
5590 16505 0.888619 CCTTTCTTTCCCGGCCTTTC 59.111 55.000 0.00 0.00 0.00 2.62
5591 16506 0.481128 TCCTTTCTTTCCCGGCCTTT 59.519 50.000 0.00 0.00 0.00 3.11
5592 16507 0.481128 TTCCTTTCTTTCCCGGCCTT 59.519 50.000 0.00 0.00 0.00 4.35
5593 16508 0.038310 CTTCCTTTCTTTCCCGGCCT 59.962 55.000 0.00 0.00 0.00 5.19
5594 16509 0.965866 CCTTCCTTTCTTTCCCGGCC 60.966 60.000 0.00 0.00 0.00 6.13
5736 16651 8.379428 TGTTGTGCATATATGGAGATATAGGT 57.621 34.615 14.51 0.00 33.25 3.08
5748 16664 6.494893 AACGTGTCTTTGTTGTGCATATAT 57.505 33.333 0.00 0.00 0.00 0.86
6064 16987 2.409870 CCAAATGGCGCAGAGACCC 61.410 63.158 10.83 0.00 0.00 4.46
6104 17027 4.261698 GCTCGGAGACTACCCTCTTTTATC 60.262 50.000 9.69 0.00 33.79 1.75
6105 17028 3.637694 GCTCGGAGACTACCCTCTTTTAT 59.362 47.826 9.69 0.00 33.79 1.40
6112 17035 0.626916 AAGAGCTCGGAGACTACCCT 59.373 55.000 9.69 0.00 0.00 4.34
6124 17047 2.428085 GGTCCCCCGAGAAGAGCTC 61.428 68.421 5.27 5.27 40.38 4.09
6125 17048 2.364448 GGTCCCCCGAGAAGAGCT 60.364 66.667 0.00 0.00 0.00 4.09
6126 17049 3.471806 GGGTCCCCCGAGAAGAGC 61.472 72.222 0.00 0.00 32.13 4.09
6135 17058 1.353394 ATGAAGATTCCGGGTCCCCC 61.353 60.000 0.00 0.00 41.09 5.40
6136 17059 1.071857 GTATGAAGATTCCGGGTCCCC 59.928 57.143 0.00 0.00 0.00 4.81
6137 17060 2.047830 AGTATGAAGATTCCGGGTCCC 58.952 52.381 0.00 0.00 0.00 4.46
6138 17061 3.840124 AAGTATGAAGATTCCGGGTCC 57.160 47.619 0.00 0.00 0.00 4.46
6139 17062 8.897872 TTTATTAAGTATGAAGATTCCGGGTC 57.102 34.615 0.00 0.00 0.00 4.46
6140 17063 9.689501 TTTTTATTAAGTATGAAGATTCCGGGT 57.310 29.630 0.00 0.00 0.00 5.28
6163 17086 6.828273 TGCAGTATGTACCATGCTATCTTTTT 59.172 34.615 9.25 0.00 39.42 1.94
6164 17087 6.356556 TGCAGTATGTACCATGCTATCTTTT 58.643 36.000 9.25 0.00 39.42 2.27
6165 17088 5.928976 TGCAGTATGTACCATGCTATCTTT 58.071 37.500 9.25 0.00 39.42 2.52
6166 17089 5.551305 TGCAGTATGTACCATGCTATCTT 57.449 39.130 9.25 0.00 39.42 2.40
6167 17090 5.752036 ATGCAGTATGTACCATGCTATCT 57.248 39.130 0.00 0.00 39.42 1.98


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

AutoCloner maintained by Alex Coulton.