Multiple sequence alignment - TraesCS4D01G337700

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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 TraesCS4D01G337700 chr4D 100.000 2570 0 0 1 2570 495128593 495131162 0.000000e+00 4747.0
1 TraesCS4D01G337700 chr4D 87.681 414 41 7 306 716 3100243 3099837 8.320000e-130 473.0
2 TraesCS4D01G337700 chr4D 87.681 414 41 7 306 716 3192771 3192365 8.320000e-130 473.0
3 TraesCS4D01G337700 chr4D 78.659 731 114 29 847 1571 495074300 495074994 5.040000e-122 448.0
4 TraesCS4D01G337700 chr4D 80.762 551 78 15 995 1540 495520366 495520893 3.080000e-109 405.0
5 TraesCS4D01G337700 chr4D 82.168 286 39 6 995 1268 495638638 495638923 4.280000e-58 235.0
6 TraesCS4D01G337700 chr4D 81.423 253 32 10 1000 1249 501675397 501675157 2.610000e-45 193.0
7 TraesCS4D01G337700 chr5A 93.099 1710 96 15 730 2434 674937104 674938796 0.000000e+00 2484.0
8 TraesCS4D01G337700 chr5A 79.862 581 79 17 995 1571 675319630 675319084 8.620000e-105 390.0
9 TraesCS4D01G337700 chr5A 80.479 543 73 21 1040 1571 674852048 674852568 4.010000e-103 385.0
10 TraesCS4D01G337700 chr5A 80.479 543 73 21 1040 1571 674893260 674893780 4.010000e-103 385.0
11 TraesCS4D01G337700 chr5A 83.212 274 37 9 398 666 657571014 657571283 2.550000e-60 243.0
12 TraesCS4D01G337700 chr5A 83.028 218 37 0 997 1214 675160712 675160495 5.610000e-47 198.0
13 TraesCS4D01G337700 chr4B 93.773 1654 61 14 730 2374 635029648 635031268 0.000000e+00 2446.0
14 TraesCS4D01G337700 chr4B 84.114 491 62 13 219 701 616989497 616989979 6.480000e-126 460.0
15 TraesCS4D01G337700 chr4B 81.125 551 65 23 1036 1571 635006275 635006801 3.080000e-109 405.0
16 TraesCS4D01G337700 chr4B 79.764 593 82 19 995 1571 635460564 635461134 1.850000e-106 396.0
17 TraesCS4D01G337700 chr4B 84.577 201 29 1 2368 2566 635042192 635042392 5.610000e-47 198.0
18 TraesCS4D01G337700 chr4B 90.141 142 12 2 1109 1249 645897540 645897400 1.570000e-42 183.0
19 TraesCS4D01G337700 chr5D 93.981 731 30 6 1 720 509441660 509440933 0.000000e+00 1094.0
20 TraesCS4D01G337700 chr5D 82.828 99 17 0 2471 2569 228786409 228786311 3.520000e-14 89.8
21 TraesCS4D01G337700 chr6D 93.810 727 33 4 1 716 116859009 116858284 0.000000e+00 1083.0
22 TraesCS4D01G337700 chr6D 93.239 710 36 4 17 715 79957605 79956897 0.000000e+00 1035.0
23 TraesCS4D01G337700 chr2B 92.160 727 45 5 1 716 733349881 733349156 0.000000e+00 1016.0
24 TraesCS4D01G337700 chr3A 91.071 728 51 6 1 716 724825308 724824583 0.000000e+00 972.0
25 TraesCS4D01G337700 chr3A 88.599 421 35 8 306 716 750721584 750722001 1.370000e-137 499.0
26 TraesCS4D01G337700 chr6B 90.922 727 54 7 1 716 135520143 135519418 0.000000e+00 966.0
27 TraesCS4D01G337700 chr6B 90.646 727 46 8 1 716 49731179 49731894 0.000000e+00 946.0
28 TraesCS4D01G337700 chr6B 89.674 736 60 11 1 723 581873769 581873037 0.000000e+00 924.0
29 TraesCS4D01G337700 chr3B 90.028 722 59 9 1 716 143071296 143072010 0.000000e+00 922.0
30 TraesCS4D01G337700 chr3B 88.480 408 43 4 306 712 572848781 572848377 8.260000e-135 490.0
31 TraesCS4D01G337700 chr3D 87.733 375 38 7 296 664 113028244 113027872 5.080000e-117 431.0
32 TraesCS4D01G337700 chr3D 82.222 90 14 2 2471 2559 43900057 43900145 2.740000e-10 76.8
33 TraesCS4D01G337700 chrUn 80.479 543 73 21 1040 1571 283623707 283624227 4.010000e-103 385.0
34 TraesCS4D01G337700 chrUn 78.641 103 18 4 1125 1225 475903255 475903155 5.940000e-07 65.8
35 TraesCS4D01G337700 chrUn 92.308 39 3 0 1183 1221 60909993 60910031 3.570000e-04 56.5
36 TraesCS4D01G337700 chrUn 90.476 42 4 0 1183 1224 171662323 171662282 3.570000e-04 56.5
37 TraesCS4D01G337700 chr1D 85.039 381 43 14 347 714 442672866 442673245 2.410000e-100 375.0
38 TraesCS4D01G337700 chr2A 90.164 61 5 1 657 716 712054085 712054145 7.620000e-11 78.7


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 TraesCS4D01G337700 chr4D 495128593 495131162 2569 False 4747 4747 100.000 1 2570 1 chr4D.!!$F2 2569
1 TraesCS4D01G337700 chr4D 495074300 495074994 694 False 448 448 78.659 847 1571 1 chr4D.!!$F1 724
2 TraesCS4D01G337700 chr4D 495520366 495520893 527 False 405 405 80.762 995 1540 1 chr4D.!!$F3 545
3 TraesCS4D01G337700 chr5A 674937104 674938796 1692 False 2484 2484 93.099 730 2434 1 chr5A.!!$F4 1704
4 TraesCS4D01G337700 chr5A 675319084 675319630 546 True 390 390 79.862 995 1571 1 chr5A.!!$R2 576
5 TraesCS4D01G337700 chr5A 674852048 674852568 520 False 385 385 80.479 1040 1571 1 chr5A.!!$F2 531
6 TraesCS4D01G337700 chr5A 674893260 674893780 520 False 385 385 80.479 1040 1571 1 chr5A.!!$F3 531
7 TraesCS4D01G337700 chr4B 635029648 635031268 1620 False 2446 2446 93.773 730 2374 1 chr4B.!!$F3 1644
8 TraesCS4D01G337700 chr4B 635006275 635006801 526 False 405 405 81.125 1036 1571 1 chr4B.!!$F2 535
9 TraesCS4D01G337700 chr4B 635460564 635461134 570 False 396 396 79.764 995 1571 1 chr4B.!!$F5 576
10 TraesCS4D01G337700 chr5D 509440933 509441660 727 True 1094 1094 93.981 1 720 1 chr5D.!!$R2 719
11 TraesCS4D01G337700 chr6D 116858284 116859009 725 True 1083 1083 93.810 1 716 1 chr6D.!!$R2 715
12 TraesCS4D01G337700 chr6D 79956897 79957605 708 True 1035 1035 93.239 17 715 1 chr6D.!!$R1 698
13 TraesCS4D01G337700 chr2B 733349156 733349881 725 True 1016 1016 92.160 1 716 1 chr2B.!!$R1 715
14 TraesCS4D01G337700 chr3A 724824583 724825308 725 True 972 972 91.071 1 716 1 chr3A.!!$R1 715
15 TraesCS4D01G337700 chr6B 135519418 135520143 725 True 966 966 90.922 1 716 1 chr6B.!!$R1 715
16 TraesCS4D01G337700 chr6B 49731179 49731894 715 False 946 946 90.646 1 716 1 chr6B.!!$F1 715
17 TraesCS4D01G337700 chr6B 581873037 581873769 732 True 924 924 89.674 1 723 1 chr6B.!!$R2 722
18 TraesCS4D01G337700 chr3B 143071296 143072010 714 False 922 922 90.028 1 716 1 chr3B.!!$F1 715
19 TraesCS4D01G337700 chrUn 283623707 283624227 520 False 385 385 80.479 1040 1571 1 chrUn.!!$F2 531

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
39 40 0.029989 GGTCCCCTCCTATCCACCTT 60.030 60.0 0.0 0.0 0.0 3.50 F
1268 1318 0.108615 CTCTGCGACCCCTACAACAG 60.109 60.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 1365 1.745141 GCTTGAATCGCAGGTCATCCT 60.745 52.381 0.0 0.0 46.37 3.24 R
2520 2601 0.108138 CCGACTTCCCTGTCCATGTC 60.108 60.000 0.0 0.0 33.70 3.06 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
39 40 0.029989 GGTCCCCTCCTATCCACCTT 60.030 60.000 0.00 0.00 0.00 3.50
229 230 4.373116 GTCGGCAGGTGGAGCGAA 62.373 66.667 0.00 0.00 0.00 4.70
266 267 0.179181 GACGACGACGAGTATTGGCA 60.179 55.000 15.32 0.00 42.66 4.92
287 288 1.645034 CATGGTGTAGCTGGTTCTCG 58.355 55.000 0.00 0.00 0.00 4.04
333 334 2.588989 GCAGGAGGAGGAAGCTGG 59.411 66.667 0.00 0.00 0.00 4.85
413 414 2.442272 CGAGGATGGACCGAGGGT 60.442 66.667 0.00 0.00 44.74 4.34
525 527 2.835764 ACACCCGGCTTTAGATGTTAGA 59.164 45.455 0.00 0.00 0.00 2.10
651 666 4.385825 TCACCTTGTATGGTCTTTGTGAC 58.614 43.478 0.00 0.00 44.63 3.67
707 723 0.620700 AGAAGCCGGGGTACATCCTT 60.621 55.000 2.18 0.00 36.25 3.36
839 855 8.728596 AAGCCATCTCATTATAAGGTAGTAGT 57.271 34.615 0.00 0.00 0.00 2.73
840 856 9.824216 AAGCCATCTCATTATAAGGTAGTAGTA 57.176 33.333 0.00 0.00 0.00 1.82
841 857 9.469097 AGCCATCTCATTATAAGGTAGTAGTAG 57.531 37.037 0.00 0.00 0.00 2.57
864 888 4.184629 GTCGAGTCCATAGCTTGTTTCAT 58.815 43.478 0.00 0.00 0.00 2.57
908 932 1.371595 GCCGCCGTTACCATTTCTAA 58.628 50.000 0.00 0.00 0.00 2.10
929 953 3.027412 ACTATCATCAGTTCTGTCGCCT 58.973 45.455 0.00 0.00 0.00 5.52
962 986 0.304705 GTGTTGTTGTGCTCCTGACG 59.695 55.000 0.00 0.00 0.00 4.35
1268 1318 0.108615 CTCTGCGACCCCTACAACAG 60.109 60.000 0.00 0.00 0.00 3.16
1285 1335 2.359850 GCAACGACAGCCCATCCA 60.360 61.111 0.00 0.00 0.00 3.41
1487 1549 4.003788 CCAGGACCCGTTCGCTGT 62.004 66.667 0.00 0.00 0.00 4.40
1585 1653 0.249953 CTAGCCAGGCTGCTCTCATG 60.250 60.000 25.59 0.14 41.68 3.07
1611 1679 4.797471 CGCAGGTGATTTCATTTTGAGAA 58.203 39.130 0.00 0.00 0.00 2.87
1651 1720 4.171663 TCGCACCGTAAGTTTGTGTATA 57.828 40.909 0.00 0.00 32.50 1.47
1770 1842 5.945784 TGCAGTGACCTAATTAAAGCAAGAT 59.054 36.000 0.00 0.00 0.00 2.40
1784 1856 4.104383 AGCAAGATTTGAGGAGTTTCCA 57.896 40.909 0.00 0.00 39.61 3.53
1820 1892 6.849085 AGATGCTGTATAGTAATCTGAGGG 57.151 41.667 6.18 0.00 32.04 4.30
1821 1893 6.556639 AGATGCTGTATAGTAATCTGAGGGA 58.443 40.000 6.18 0.00 32.04 4.20
1822 1894 6.663093 AGATGCTGTATAGTAATCTGAGGGAG 59.337 42.308 6.18 0.00 32.04 4.30
1823 1895 5.706447 TGCTGTATAGTAATCTGAGGGAGT 58.294 41.667 0.00 0.00 0.00 3.85
1842 1914 3.467803 AGTCCTCGGCTATTTTGTATGC 58.532 45.455 0.00 0.00 0.00 3.14
2021 2093 8.841300 TCTGTACTGTAATAAGCAGTAGATGAG 58.159 37.037 5.53 1.68 46.25 2.90
2061 2134 7.986889 GTCGTTTCCACCCCTACTAATTTTATA 59.013 37.037 0.00 0.00 0.00 0.98
2108 2182 3.013921 GTTAATGGAAATCAGCGGGTCA 58.986 45.455 0.00 0.00 0.00 4.02
2186 2260 3.096092 TGGACCAAACAAGCAAACTCTT 58.904 40.909 0.00 0.00 0.00 2.85
2268 2349 4.030452 GCGTGACAAGCTGGCCAC 62.030 66.667 0.00 0.00 0.00 5.01
2290 2371 4.095185 ACTCGTTCTCCGTATCTCTTTCTG 59.905 45.833 0.00 0.00 37.94 3.02
2313 2394 0.729116 CCATGTGATTCCACGAGTGC 59.271 55.000 0.00 0.00 46.06 4.40
2326 2407 3.425892 CCACGAGTGCACTACAGTAGTAC 60.426 52.174 21.73 8.43 35.60 2.73
2329 2410 4.869297 ACGAGTGCACTACAGTAGTACTAG 59.131 45.833 21.73 15.21 35.97 2.57
2330 2411 4.869297 CGAGTGCACTACAGTAGTACTAGT 59.131 45.833 21.73 3.18 37.23 2.57
2331 2412 6.038985 CGAGTGCACTACAGTAGTACTAGTA 58.961 44.000 21.73 0.00 37.23 1.82
2416 2497 2.089349 GCCGACGACAAGAGCACTC 61.089 63.158 0.00 0.00 0.00 3.51
2434 2515 2.279120 GATGCTCTCCCTGTCGCG 60.279 66.667 0.00 0.00 0.00 5.87
2435 2516 4.521062 ATGCTCTCCCTGTCGCGC 62.521 66.667 0.00 0.00 0.00 6.86
2437 2518 4.443266 GCTCTCCCTGTCGCGCTT 62.443 66.667 5.56 0.00 0.00 4.68
2438 2519 2.507992 CTCTCCCTGTCGCGCTTG 60.508 66.667 5.56 0.00 0.00 4.01
2439 2520 4.742201 TCTCCCTGTCGCGCTTGC 62.742 66.667 5.56 0.00 0.00 4.01
2444 2525 4.012895 CTGTCGCGCTTGCCGTTT 62.013 61.111 5.56 0.00 39.71 3.60
2445 2526 4.306471 TGTCGCGCTTGCCGTTTG 62.306 61.111 5.56 0.00 39.71 2.93
2446 2527 4.307908 GTCGCGCTTGCCGTTTGT 62.308 61.111 5.56 0.00 39.71 2.83
2447 2528 3.578272 TCGCGCTTGCCGTTTGTT 61.578 55.556 5.56 0.00 39.71 2.83
2448 2529 2.653766 CGCGCTTGCCGTTTGTTT 60.654 55.556 5.56 0.00 39.71 2.83
2449 2530 1.369448 CGCGCTTGCCGTTTGTTTA 60.369 52.632 5.56 0.00 39.71 2.01
2450 2531 0.930742 CGCGCTTGCCGTTTGTTTAA 60.931 50.000 5.56 0.00 39.71 1.52
2451 2532 1.201343 GCGCTTGCCGTTTGTTTAAA 58.799 45.000 0.00 0.00 39.71 1.52
2452 2533 1.790043 GCGCTTGCCGTTTGTTTAAAT 59.210 42.857 0.00 0.00 39.71 1.40
2453 2534 2.409624 GCGCTTGCCGTTTGTTTAAATG 60.410 45.455 0.00 0.00 39.71 2.32
2454 2535 3.046390 CGCTTGCCGTTTGTTTAAATGA 58.954 40.909 0.00 0.00 35.29 2.57
2455 2536 3.487574 CGCTTGCCGTTTGTTTAAATGAA 59.512 39.130 0.00 0.00 35.29 2.57
2456 2537 4.374906 CGCTTGCCGTTTGTTTAAATGAAG 60.375 41.667 0.00 0.00 35.29 3.02
2457 2538 4.506288 GCTTGCCGTTTGTTTAAATGAAGT 59.494 37.500 0.00 0.00 35.29 3.01
2458 2539 5.688176 GCTTGCCGTTTGTTTAAATGAAGTA 59.312 36.000 0.00 0.00 35.29 2.24
2459 2540 6.345487 GCTTGCCGTTTGTTTAAATGAAGTAC 60.345 38.462 0.00 0.00 35.29 2.73
2460 2541 6.380095 TGCCGTTTGTTTAAATGAAGTACT 57.620 33.333 0.00 0.00 35.29 2.73
2461 2542 7.493743 TGCCGTTTGTTTAAATGAAGTACTA 57.506 32.000 0.00 0.00 35.29 1.82
2462 2543 8.101654 TGCCGTTTGTTTAAATGAAGTACTAT 57.898 30.769 0.00 0.00 35.29 2.12
2463 2544 9.217278 TGCCGTTTGTTTAAATGAAGTACTATA 57.783 29.630 0.00 0.00 35.29 1.31
2464 2545 9.698617 GCCGTTTGTTTAAATGAAGTACTATAG 57.301 33.333 0.00 0.00 35.29 1.31
2465 2546 9.698617 CCGTTTGTTTAAATGAAGTACTATAGC 57.301 33.333 0.00 0.00 35.29 2.97
2478 2559 9.575868 TGAAGTACTATAGCTTATAGCAACTCT 57.424 33.333 0.00 0.00 45.56 3.24
2480 2561 9.575868 AAGTACTATAGCTTATAGCAACTCTCA 57.424 33.333 0.00 0.00 45.56 3.27
2481 2562 9.005777 AGTACTATAGCTTATAGCAACTCTCAC 57.994 37.037 0.00 0.00 45.56 3.51
2482 2563 6.904498 ACTATAGCTTATAGCAACTCTCACG 58.096 40.000 0.00 0.00 45.56 4.35
2483 2564 2.815478 AGCTTATAGCAACTCTCACGC 58.185 47.619 1.09 0.00 45.56 5.34
2484 2565 1.518929 GCTTATAGCAACTCTCACGCG 59.481 52.381 3.53 3.53 41.89 6.01
2485 2566 2.794981 GCTTATAGCAACTCTCACGCGA 60.795 50.000 15.93 0.00 41.89 5.87
2486 2567 2.470196 TATAGCAACTCTCACGCGAC 57.530 50.000 15.93 0.00 0.00 5.19
2487 2568 0.523546 ATAGCAACTCTCACGCGACG 60.524 55.000 15.93 2.89 0.00 5.12
2488 2569 1.571215 TAGCAACTCTCACGCGACGA 61.571 55.000 15.93 8.11 0.00 4.20
2489 2570 2.708059 GCAACTCTCACGCGACGAC 61.708 63.158 15.93 0.00 0.00 4.34
2490 2571 1.082038 CAACTCTCACGCGACGACT 60.082 57.895 15.93 0.00 0.00 4.18
2491 2572 1.060726 CAACTCTCACGCGACGACTC 61.061 60.000 15.93 0.00 0.00 3.36
2492 2573 1.504647 AACTCTCACGCGACGACTCA 61.505 55.000 15.93 0.00 0.00 3.41
2493 2574 1.299562 ACTCTCACGCGACGACTCAT 61.300 55.000 15.93 0.00 0.00 2.90
2494 2575 0.179187 CTCTCACGCGACGACTCATT 60.179 55.000 15.93 0.00 0.00 2.57
2495 2576 0.240145 TCTCACGCGACGACTCATTT 59.760 50.000 15.93 0.00 0.00 2.32
2496 2577 0.635731 CTCACGCGACGACTCATTTC 59.364 55.000 15.93 0.00 0.00 2.17
2497 2578 1.063412 TCACGCGACGACTCATTTCG 61.063 55.000 15.93 0.00 44.87 3.46
2503 2584 4.905085 CGACTCATTTCGTTCGCG 57.095 55.556 0.00 0.00 42.98 5.87
2504 2585 1.295220 CGACTCATTTCGTTCGCGC 60.295 57.895 0.00 0.00 41.05 6.86
2505 2586 1.295220 GACTCATTTCGTTCGCGCG 60.295 57.895 26.76 26.76 41.05 6.86
2506 2587 2.641663 CTCATTTCGTTCGCGCGC 60.642 61.111 27.95 23.91 41.05 6.86
2507 2588 4.477604 TCATTTCGTTCGCGCGCG 62.478 61.111 44.84 44.84 41.05 6.86
2508 2589 4.770102 CATTTCGTTCGCGCGCGT 62.770 61.111 46.54 27.68 41.05 6.01
2509 2590 4.479121 ATTTCGTTCGCGCGCGTC 62.479 61.111 46.54 36.80 41.05 5.19
2520 2601 4.676586 GCGCGTCCGTTTGGGTTG 62.677 66.667 8.43 0.00 37.00 3.77
2521 2602 2.968156 CGCGTCCGTTTGGGTTGA 60.968 61.111 0.00 0.00 37.00 3.18
2522 2603 2.635338 GCGTCCGTTTGGGTTGAC 59.365 61.111 0.00 0.00 37.00 3.18
2523 2604 2.181521 GCGTCCGTTTGGGTTGACA 61.182 57.895 0.00 0.00 37.00 3.58
2524 2605 1.512156 GCGTCCGTTTGGGTTGACAT 61.512 55.000 0.00 0.00 37.00 3.06
2525 2606 0.237235 CGTCCGTTTGGGTTGACATG 59.763 55.000 0.00 0.00 37.00 3.21
2526 2607 0.596082 GTCCGTTTGGGTTGACATGG 59.404 55.000 0.00 0.00 37.00 3.66
2527 2608 0.474614 TCCGTTTGGGTTGACATGGA 59.525 50.000 0.00 0.00 37.00 3.41
2528 2609 0.596082 CCGTTTGGGTTGACATGGAC 59.404 55.000 0.00 0.00 0.00 4.02
2529 2610 1.313772 CGTTTGGGTTGACATGGACA 58.686 50.000 0.00 0.00 0.00 4.02
2530 2611 1.266718 CGTTTGGGTTGACATGGACAG 59.733 52.381 0.00 0.00 0.00 3.51
2531 2612 1.613437 GTTTGGGTTGACATGGACAGG 59.387 52.381 0.00 0.00 0.00 4.00
2532 2613 0.112218 TTGGGTTGACATGGACAGGG 59.888 55.000 0.00 0.00 0.00 4.45
2533 2614 0.770166 TGGGTTGACATGGACAGGGA 60.770 55.000 0.00 0.00 0.00 4.20
2534 2615 0.404040 GGGTTGACATGGACAGGGAA 59.596 55.000 0.00 0.00 0.00 3.97
2535 2616 1.614317 GGGTTGACATGGACAGGGAAG 60.614 57.143 0.00 0.00 0.00 3.46
2536 2617 1.073923 GGTTGACATGGACAGGGAAGT 59.926 52.381 0.00 0.00 0.00 3.01
2537 2618 2.427506 GTTGACATGGACAGGGAAGTC 58.572 52.381 0.00 0.00 37.80 3.01
2538 2619 0.608130 TGACATGGACAGGGAAGTCG 59.392 55.000 0.00 0.00 39.42 4.18
2539 2620 0.108138 GACATGGACAGGGAAGTCGG 60.108 60.000 0.00 0.00 39.42 4.79
2540 2621 1.450312 CATGGACAGGGAAGTCGGC 60.450 63.158 0.00 0.00 39.42 5.54
2541 2622 2.670148 ATGGACAGGGAAGTCGGCC 61.670 63.158 0.00 0.00 39.42 6.13
2542 2623 3.003763 GGACAGGGAAGTCGGCCT 61.004 66.667 0.00 0.00 39.42 5.19
2543 2624 1.684734 GGACAGGGAAGTCGGCCTA 60.685 63.158 0.00 0.00 39.42 3.93
2544 2625 1.262640 GGACAGGGAAGTCGGCCTAA 61.263 60.000 0.00 0.00 39.42 2.69
2545 2626 0.108281 GACAGGGAAGTCGGCCTAAC 60.108 60.000 0.00 0.00 0.00 2.34
2546 2627 1.153628 CAGGGAAGTCGGCCTAACG 60.154 63.158 0.00 0.00 0.00 3.18
2547 2628 2.510918 GGGAAGTCGGCCTAACGC 60.511 66.667 0.00 0.00 0.00 4.84
2548 2629 2.884207 GGAAGTCGGCCTAACGCG 60.884 66.667 3.53 3.53 38.94 6.01
2549 2630 2.126189 GAAGTCGGCCTAACGCGT 60.126 61.111 5.58 5.58 38.94 6.01
2550 2631 2.126189 AAGTCGGCCTAACGCGTC 60.126 61.111 14.44 0.00 38.94 5.19
2551 2632 3.958822 AAGTCGGCCTAACGCGTCG 62.959 63.158 14.44 12.14 38.94 5.12
2552 2633 4.465512 GTCGGCCTAACGCGTCGA 62.466 66.667 14.44 14.70 38.94 4.20
2553 2634 3.511595 TCGGCCTAACGCGTCGAT 61.512 61.111 14.44 0.00 38.94 3.59
2554 2635 3.022914 CGGCCTAACGCGTCGATC 61.023 66.667 14.44 2.23 38.94 3.69
2555 2636 2.657620 GGCCTAACGCGTCGATCC 60.658 66.667 14.44 8.59 38.94 3.36
2556 2637 2.103538 GCCTAACGCGTCGATCCA 59.896 61.111 14.44 0.00 0.00 3.41
2557 2638 1.517694 GCCTAACGCGTCGATCCAA 60.518 57.895 14.44 0.00 0.00 3.53
2558 2639 1.079875 GCCTAACGCGTCGATCCAAA 61.080 55.000 14.44 0.00 0.00 3.28
2559 2640 0.643820 CCTAACGCGTCGATCCAAAC 59.356 55.000 14.44 0.00 0.00 2.93
2560 2641 1.342555 CTAACGCGTCGATCCAAACA 58.657 50.000 14.44 0.00 0.00 2.83
2561 2642 1.320555 CTAACGCGTCGATCCAAACAG 59.679 52.381 14.44 0.00 0.00 3.16
2562 2643 1.897398 AACGCGTCGATCCAAACAGC 61.897 55.000 14.44 0.00 0.00 4.40
2563 2644 2.785258 GCGTCGATCCAAACAGCC 59.215 61.111 0.00 0.00 0.00 4.85
2564 2645 3.081133 CGTCGATCCAAACAGCCG 58.919 61.111 0.00 0.00 0.00 5.52
2565 2646 2.785258 GTCGATCCAAACAGCCGC 59.215 61.111 0.00 0.00 0.00 6.53
2566 2647 2.813474 TCGATCCAAACAGCCGCG 60.813 61.111 0.00 0.00 0.00 6.46
2567 2648 4.520846 CGATCCAAACAGCCGCGC 62.521 66.667 0.00 0.00 0.00 6.86
2568 2649 4.520846 GATCCAAACAGCCGCGCG 62.521 66.667 25.67 25.67 0.00 6.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.307906 CGTCCGGGAGTGGGTCAA 61.308 66.667 0.00 0.00 0.00 3.18
228 229 0.179145 CGACGCGGTAGATCCAACTT 60.179 55.000 12.47 0.00 35.57 2.66
229 230 1.028330 TCGACGCGGTAGATCCAACT 61.028 55.000 12.47 0.00 35.57 3.16
266 267 0.987294 AGAACCAGCTACACCATGCT 59.013 50.000 0.00 0.00 40.54 3.79
281 282 0.982673 CACATCCGTCGTTCGAGAAC 59.017 55.000 5.93 5.93 42.86 3.01
287 288 0.242825 TCCAGACACATCCGTCGTTC 59.757 55.000 0.00 0.00 40.98 3.95
413 414 2.668632 GGCCGTCACCTCCATCAA 59.331 61.111 0.00 0.00 0.00 2.57
444 445 0.674895 GGCACACTCCCAGTAAGCAG 60.675 60.000 0.00 0.00 31.35 4.24
484 485 0.982852 CCCATCCAGCCACTACCTGA 60.983 60.000 0.00 0.00 32.03 3.86
525 527 1.967319 AACAGACATCGCACCAAAGT 58.033 45.000 0.00 0.00 0.00 2.66
612 623 4.392940 AGGTGATACATCAATAAGCCTGC 58.607 43.478 0.00 0.00 38.75 4.85
651 666 9.459640 GATGCATGCAGCCATATTATTAATTAG 57.540 33.333 25.21 0.00 44.83 1.73
725 741 8.773645 GCTGCCAACTAATTTCAACTAATTTTT 58.226 29.630 0.00 0.00 0.00 1.94
726 742 7.930865 TGCTGCCAACTAATTTCAACTAATTTT 59.069 29.630 0.00 0.00 0.00 1.82
727 743 7.441017 TGCTGCCAACTAATTTCAACTAATTT 58.559 30.769 0.00 0.00 0.00 1.82
728 744 6.991938 TGCTGCCAACTAATTTCAACTAATT 58.008 32.000 0.00 0.00 0.00 1.40
839 855 3.014304 ACAAGCTATGGACTCGACCTA 57.986 47.619 0.00 0.00 0.00 3.08
840 856 1.853963 ACAAGCTATGGACTCGACCT 58.146 50.000 0.00 0.00 0.00 3.85
841 857 2.674796 AACAAGCTATGGACTCGACC 57.325 50.000 0.00 0.00 0.00 4.79
908 932 3.027412 AGGCGACAGAACTGATGATAGT 58.973 45.455 8.87 0.00 0.00 2.12
929 953 6.514212 GCACAACAACACAACACAAGGATATA 60.514 38.462 0.00 0.00 0.00 0.86
1268 1318 2.359850 TGGATGGGCTGTCGTTGC 60.360 61.111 0.00 0.00 0.00 4.17
1315 1365 1.745141 GCTTGAATCGCAGGTCATCCT 60.745 52.381 0.00 0.00 46.37 3.24
1319 1369 3.874873 CGCTTGAATCGCAGGTCA 58.125 55.556 0.00 0.00 0.00 4.02
1543 1611 2.289532 GCAGCTCCAGGTCCAGAGT 61.290 63.158 9.90 0.00 32.47 3.24
1585 1653 2.352503 AATGAAATCACCTGCGCAAC 57.647 45.000 13.05 0.00 0.00 4.17
1611 1679 6.404734 GGTGCGATGATTGAGAAAAGGTATTT 60.405 38.462 0.00 0.00 0.00 1.40
1622 1690 2.540515 ACTTACGGTGCGATGATTGAG 58.459 47.619 0.00 0.00 0.00 3.02
1629 1698 1.873698 ACACAAACTTACGGTGCGAT 58.126 45.000 0.00 0.00 36.00 4.58
1651 1720 2.052690 CCCCACGAGGACACGATCT 61.053 63.158 0.00 0.00 38.24 2.75
1753 1823 7.890655 ACTCCTCAAATCTTGCTTTAATTAGGT 59.109 33.333 0.00 0.00 0.00 3.08
1784 1856 2.239150 ACAGCATCTTCAGCTTCCAGAT 59.761 45.455 0.00 0.00 41.14 2.90
1820 1892 3.495001 GCATACAAAATAGCCGAGGACTC 59.505 47.826 0.00 0.00 0.00 3.36
1821 1893 3.118408 TGCATACAAAATAGCCGAGGACT 60.118 43.478 0.00 0.00 0.00 3.85
1822 1894 3.202906 TGCATACAAAATAGCCGAGGAC 58.797 45.455 0.00 0.00 0.00 3.85
1823 1895 3.552132 TGCATACAAAATAGCCGAGGA 57.448 42.857 0.00 0.00 0.00 3.71
1842 1914 9.606631 AAGTCTTCCTTGAATTAACTAGCTATG 57.393 33.333 0.00 0.00 30.18 2.23
2021 2093 4.453136 TGGAAACGACCAATAAAGCAGTAC 59.547 41.667 0.00 0.00 36.96 2.73
2061 2134 4.365723 CGCCATAACCTAGTTCATTACGT 58.634 43.478 0.00 0.00 0.00 3.57
2108 2182 5.003804 CACTGGCAAAATTAGTAGTCCACT 58.996 41.667 0.00 0.00 41.62 4.00
2186 2260 3.895232 TTTGCCCAAACTAAGCAACAA 57.105 38.095 0.00 0.00 45.57 2.83
2290 2371 0.676466 TCGTGGAATCACATGGGTGC 60.676 55.000 0.00 0.00 44.87 5.01
2326 2407 5.893512 TTTGGCGCATATAAACGTACTAG 57.106 39.130 10.83 0.00 0.00 2.57
2329 2410 4.731480 CCTTTTTGGCGCATATAAACGTAC 59.269 41.667 10.83 0.00 0.00 3.67
2330 2411 4.911053 CCTTTTTGGCGCATATAAACGTA 58.089 39.130 10.83 0.00 0.00 3.57
2331 2412 3.765026 CCTTTTTGGCGCATATAAACGT 58.235 40.909 10.83 0.00 0.00 3.99
2377 2458 0.248661 CCGGCATCTGAGTCACTACG 60.249 60.000 0.00 0.00 0.00 3.51
2416 2497 2.279120 GCGACAGGGAGAGCATCG 60.279 66.667 0.00 0.00 42.67 3.84
2434 2515 4.506288 ACTTCATTTAAACAAACGGCAAGC 59.494 37.500 0.00 0.00 0.00 4.01
2435 2516 6.915843 AGTACTTCATTTAAACAAACGGCAAG 59.084 34.615 0.00 0.00 0.00 4.01
2436 2517 6.797454 AGTACTTCATTTAAACAAACGGCAA 58.203 32.000 0.00 0.00 0.00 4.52
2437 2518 6.380095 AGTACTTCATTTAAACAAACGGCA 57.620 33.333 0.00 0.00 0.00 5.69
2438 2519 9.698617 CTATAGTACTTCATTTAAACAAACGGC 57.301 33.333 0.00 0.00 0.00 5.68
2439 2520 9.698617 GCTATAGTACTTCATTTAAACAAACGG 57.301 33.333 0.00 0.00 0.00 4.44
2452 2533 9.575868 AGAGTTGCTATAAGCTATAGTACTTCA 57.424 33.333 0.00 0.00 42.97 3.02
2454 2535 9.575868 TGAGAGTTGCTATAAGCTATAGTACTT 57.424 33.333 0.00 0.00 42.97 2.24
2455 2536 9.005777 GTGAGAGTTGCTATAAGCTATAGTACT 57.994 37.037 0.00 0.00 42.97 2.73
2456 2537 7.958567 CGTGAGAGTTGCTATAAGCTATAGTAC 59.041 40.741 0.84 0.00 42.97 2.73
2457 2538 7.361031 GCGTGAGAGTTGCTATAAGCTATAGTA 60.361 40.741 0.84 0.00 42.97 1.82
2458 2539 6.568844 GCGTGAGAGTTGCTATAAGCTATAGT 60.569 42.308 0.84 0.00 42.97 2.12
2459 2540 5.797934 GCGTGAGAGTTGCTATAAGCTATAG 59.202 44.000 0.00 0.00 42.97 1.31
2460 2541 5.617087 CGCGTGAGAGTTGCTATAAGCTATA 60.617 44.000 0.00 0.00 42.97 1.31
2461 2542 4.551388 GCGTGAGAGTTGCTATAAGCTAT 58.449 43.478 0.03 0.00 42.97 2.97
2462 2543 3.548214 CGCGTGAGAGTTGCTATAAGCTA 60.548 47.826 0.00 0.00 42.97 3.32
2463 2544 2.796383 CGCGTGAGAGTTGCTATAAGCT 60.796 50.000 0.00 0.00 42.97 3.74
2464 2545 1.518929 CGCGTGAGAGTTGCTATAAGC 59.481 52.381 0.00 0.00 42.82 3.09
2465 2546 2.784380 GTCGCGTGAGAGTTGCTATAAG 59.216 50.000 5.77 0.00 0.00 1.73
2466 2547 2.790123 CGTCGCGTGAGAGTTGCTATAA 60.790 50.000 5.77 0.00 0.00 0.98
2467 2548 1.267882 CGTCGCGTGAGAGTTGCTATA 60.268 52.381 5.77 0.00 0.00 1.31
2468 2549 0.523546 CGTCGCGTGAGAGTTGCTAT 60.524 55.000 5.77 0.00 0.00 2.97
2469 2550 1.154282 CGTCGCGTGAGAGTTGCTA 60.154 57.895 5.77 0.00 0.00 3.49
2470 2551 2.429236 CGTCGCGTGAGAGTTGCT 60.429 61.111 5.77 0.00 0.00 3.91
2471 2552 2.428569 TCGTCGCGTGAGAGTTGC 60.429 61.111 5.77 0.00 0.00 4.17
2472 2553 1.060726 GAGTCGTCGCGTGAGAGTTG 61.061 60.000 5.77 0.00 0.00 3.16
2473 2554 1.207085 GAGTCGTCGCGTGAGAGTT 59.793 57.895 5.77 0.00 0.00 3.01
2474 2555 1.299562 ATGAGTCGTCGCGTGAGAGT 61.300 55.000 5.77 7.14 0.00 3.24
2475 2556 0.179187 AATGAGTCGTCGCGTGAGAG 60.179 55.000 5.77 0.00 0.00 3.20
2476 2557 0.240145 AAATGAGTCGTCGCGTGAGA 59.760 50.000 5.77 0.88 0.00 3.27
2477 2558 0.635731 GAAATGAGTCGTCGCGTGAG 59.364 55.000 5.77 0.00 0.00 3.51
2478 2559 1.063412 CGAAATGAGTCGTCGCGTGA 61.063 55.000 5.77 2.28 36.26 4.35
2479 2560 1.337150 CGAAATGAGTCGTCGCGTG 59.663 57.895 5.77 0.00 36.26 5.34
2480 2561 3.750162 CGAAATGAGTCGTCGCGT 58.250 55.556 5.77 0.00 36.26 6.01
2486 2567 1.295220 GCGCGAACGAAATGAGTCG 60.295 57.895 12.10 0.00 46.54 4.18
2487 2568 1.295220 CGCGCGAACGAAATGAGTC 60.295 57.895 28.94 0.00 43.93 3.36
2488 2569 2.769617 CGCGCGAACGAAATGAGT 59.230 55.556 28.94 0.00 43.93 3.41
2489 2570 2.641663 GCGCGCGAACGAAATGAG 60.642 61.111 37.18 0.00 43.93 2.90
2503 2584 4.676586 CAACCCAAACGGACGCGC 62.677 66.667 5.73 0.00 34.64 6.86
2504 2585 2.968156 TCAACCCAAACGGACGCG 60.968 61.111 3.53 3.53 34.64 6.01
2505 2586 1.512156 ATGTCAACCCAAACGGACGC 61.512 55.000 0.00 0.00 33.04 5.19
2506 2587 0.237235 CATGTCAACCCAAACGGACG 59.763 55.000 0.00 0.00 33.04 4.79
2507 2588 0.596082 CCATGTCAACCCAAACGGAC 59.404 55.000 0.00 0.00 34.64 4.79
2508 2589 0.474614 TCCATGTCAACCCAAACGGA 59.525 50.000 0.00 0.00 34.64 4.69
2509 2590 0.596082 GTCCATGTCAACCCAAACGG 59.404 55.000 0.00 0.00 37.81 4.44
2510 2591 1.266718 CTGTCCATGTCAACCCAAACG 59.733 52.381 0.00 0.00 0.00 3.60
2511 2592 1.613437 CCTGTCCATGTCAACCCAAAC 59.387 52.381 0.00 0.00 0.00 2.93
2512 2593 1.480312 CCCTGTCCATGTCAACCCAAA 60.480 52.381 0.00 0.00 0.00 3.28
2513 2594 0.112218 CCCTGTCCATGTCAACCCAA 59.888 55.000 0.00 0.00 0.00 4.12
2514 2595 0.770166 TCCCTGTCCATGTCAACCCA 60.770 55.000 0.00 0.00 0.00 4.51
2515 2596 0.404040 TTCCCTGTCCATGTCAACCC 59.596 55.000 0.00 0.00 0.00 4.11
2516 2597 1.073923 ACTTCCCTGTCCATGTCAACC 59.926 52.381 0.00 0.00 0.00 3.77
2517 2598 2.427506 GACTTCCCTGTCCATGTCAAC 58.572 52.381 0.00 0.00 0.00 3.18
2518 2599 1.001974 CGACTTCCCTGTCCATGTCAA 59.998 52.381 0.00 0.00 33.70 3.18
2519 2600 0.608130 CGACTTCCCTGTCCATGTCA 59.392 55.000 0.00 0.00 33.70 3.58
2520 2601 0.108138 CCGACTTCCCTGTCCATGTC 60.108 60.000 0.00 0.00 33.70 3.06
2521 2602 1.983224 CCGACTTCCCTGTCCATGT 59.017 57.895 0.00 0.00 33.70 3.21
2522 2603 1.450312 GCCGACTTCCCTGTCCATG 60.450 63.158 0.00 0.00 33.70 3.66
2523 2604 2.670148 GGCCGACTTCCCTGTCCAT 61.670 63.158 0.00 0.00 33.70 3.41
2524 2605 2.449967 TAGGCCGACTTCCCTGTCCA 62.450 60.000 0.00 0.00 33.70 4.02
2525 2606 1.262640 TTAGGCCGACTTCCCTGTCC 61.263 60.000 0.00 0.00 33.70 4.02
2526 2607 0.108281 GTTAGGCCGACTTCCCTGTC 60.108 60.000 0.00 0.00 32.65 3.51
2527 2608 1.885163 CGTTAGGCCGACTTCCCTGT 61.885 60.000 0.00 0.00 32.65 4.00
2528 2609 1.153628 CGTTAGGCCGACTTCCCTG 60.154 63.158 0.00 0.00 32.65 4.45
2529 2610 3.015312 GCGTTAGGCCGACTTCCCT 62.015 63.158 0.00 0.00 34.80 4.20
2530 2611 2.510918 GCGTTAGGCCGACTTCCC 60.511 66.667 0.00 0.00 34.80 3.97
2531 2612 2.884207 CGCGTTAGGCCGACTTCC 60.884 66.667 0.00 0.00 38.94 3.46
2532 2613 2.126189 ACGCGTTAGGCCGACTTC 60.126 61.111 5.58 0.00 38.94 3.01
2533 2614 2.126189 GACGCGTTAGGCCGACTT 60.126 61.111 15.53 0.00 38.94 3.01
2534 2615 4.471726 CGACGCGTTAGGCCGACT 62.472 66.667 15.53 0.00 38.94 4.18
2535 2616 3.746409 ATCGACGCGTTAGGCCGAC 62.746 63.158 20.04 1.25 37.97 4.79
2536 2617 3.459378 GATCGACGCGTTAGGCCGA 62.459 63.158 19.94 19.94 39.15 5.54
2537 2618 3.022914 GATCGACGCGTTAGGCCG 61.023 66.667 15.53 12.62 38.94 6.13
2538 2619 2.657620 GGATCGACGCGTTAGGCC 60.658 66.667 15.53 9.90 38.94 5.19
2539 2620 1.079875 TTTGGATCGACGCGTTAGGC 61.080 55.000 15.53 3.68 38.69 3.93
2540 2621 0.643820 GTTTGGATCGACGCGTTAGG 59.356 55.000 15.53 6.36 0.00 2.69
2541 2622 1.320555 CTGTTTGGATCGACGCGTTAG 59.679 52.381 15.53 11.61 0.00 2.34
2542 2623 1.342555 CTGTTTGGATCGACGCGTTA 58.657 50.000 15.53 5.25 0.00 3.18
2543 2624 1.897398 GCTGTTTGGATCGACGCGTT 61.897 55.000 15.53 0.00 0.00 4.84
2544 2625 2.380410 GCTGTTTGGATCGACGCGT 61.380 57.895 13.85 13.85 0.00 6.01
2545 2626 2.395690 GCTGTTTGGATCGACGCG 59.604 61.111 3.53 3.53 0.00 6.01
2546 2627 2.785258 GGCTGTTTGGATCGACGC 59.215 61.111 0.00 0.00 0.00 5.19
2547 2628 3.081133 CGGCTGTTTGGATCGACG 58.919 61.111 0.00 0.00 0.00 5.12
2548 2629 2.785258 GCGGCTGTTTGGATCGAC 59.215 61.111 0.00 0.00 0.00 4.20
2549 2630 2.813474 CGCGGCTGTTTGGATCGA 60.813 61.111 0.00 0.00 0.00 3.59
2550 2631 4.520846 GCGCGGCTGTTTGGATCG 62.521 66.667 8.83 0.00 0.00 3.69
2551 2632 4.520846 CGCGCGGCTGTTTGGATC 62.521 66.667 24.84 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.