Multiple sequence alignment - TraesCS6A01G009800

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G009800 chr6A 100.000 2638 0 0 1 2638 4542940 4540303 0.000000e+00 4872.0
1 TraesCS6A01G009800 chr6A 100.000 29 0 0 541 569 4542618 4542590 1.000000e-03 54.7
2 TraesCS6A01G009800 chr6A 100.000 29 0 0 541 569 30737345 30737317 1.000000e-03 54.7
3 TraesCS6A01G009800 chr3A 95.802 1453 56 2 567 2019 713676175 713674728 0.000000e+00 2340.0
4 TraesCS6A01G009800 chr3A 96.488 541 19 0 1 541 740328986 740329526 0.000000e+00 894.0
5 TraesCS6A01G009800 chr7A 95.473 1458 65 1 567 2024 14787988 14789444 0.000000e+00 2326.0
6 TraesCS6A01G009800 chr7A 97.967 541 11 0 1 541 17674959 17674419 0.000000e+00 939.0
7 TraesCS6A01G009800 chr7A 96.488 541 19 0 1 541 268856377 268855837 0.000000e+00 894.0
8 TraesCS6A01G009800 chr6B 95.577 1447 58 3 567 2013 531710998 531712438 0.000000e+00 2313.0
9 TraesCS6A01G009800 chr6B 96.380 1188 38 2 567 1754 531698374 531699556 0.000000e+00 1951.0
10 TraesCS6A01G009800 chr6B 96.488 541 18 1 1 541 630855948 630856487 0.000000e+00 893.0
11 TraesCS6A01G009800 chr6B 90.625 352 31 2 1721 2072 345595557 345595906 1.430000e-127 466.0
12 TraesCS6A01G009800 chr6B 90.341 352 32 2 1721 2072 345583791 345584140 6.650000e-126 460.0
13 TraesCS6A01G009800 chr6B 89.577 355 33 3 1725 2079 7826197 7826547 5.180000e-122 448.0
14 TraesCS6A01G009800 chr5A 96.406 1280 41 2 567 1846 662379098 662377824 0.000000e+00 2104.0
15 TraesCS6A01G009800 chr5A 83.287 712 101 17 1375 2079 708621435 708620735 7.960000e-180 640.0
16 TraesCS6A01G009800 chr5A 89.616 443 39 3 2052 2488 536196290 536195849 8.250000e-155 556.0
17 TraesCS6A01G009800 chr5A 91.081 370 30 2 1730 2097 438247763 438247395 5.070000e-137 497.0
18 TraesCS6A01G009800 chr5A 85.231 325 32 10 2047 2359 662371934 662371614 1.180000e-83 320.0
19 TraesCS6A01G009800 chr5A 88.123 261 25 4 2043 2300 708620449 708620192 3.300000e-79 305.0
20 TraesCS6A01G009800 chr5A 84.161 322 39 7 2047 2359 438247230 438246912 4.270000e-78 302.0
21 TraesCS6A01G009800 chr3B 96.735 735 23 1 1020 1754 733559799 733559066 0.000000e+00 1223.0
22 TraesCS6A01G009800 chrUn 97.227 541 15 0 1 541 85056387 85056927 0.000000e+00 917.0
23 TraesCS6A01G009800 chrUn 77.436 390 71 14 1376 1763 218588105 218588479 1.590000e-52 217.0
24 TraesCS6A01G009800 chrUn 100.000 29 0 0 541 569 85056709 85056737 1.000000e-03 54.7
25 TraesCS6A01G009800 chrUn 100.000 29 0 0 541 569 184622783 184622755 1.000000e-03 54.7
26 TraesCS6A01G009800 chrUn 100.000 29 0 0 541 569 184637287 184637259 1.000000e-03 54.7
27 TraesCS6A01G009800 chr1B 97.227 541 15 0 1 541 49868020 49867480 0.000000e+00 917.0
28 TraesCS6A01G009800 chr1B 97.227 541 15 0 1 541 133448169 133448709 0.000000e+00 917.0
29 TraesCS6A01G009800 chr7B 96.488 541 19 0 1 541 44552085 44552625 0.000000e+00 894.0
30 TraesCS6A01G009800 chr5B 96.303 541 20 0 1 541 246145147 246145687 0.000000e+00 889.0
31 TraesCS6A01G009800 chr4B 88.413 630 71 2 716 1344 365181664 365182292 0.000000e+00 758.0
32 TraesCS6A01G009800 chr4B 87.727 440 42 7 2054 2489 439782426 439782857 1.090000e-138 503.0
33 TraesCS6A01G009800 chr4B 89.247 372 38 1 2121 2490 365183014 365183385 5.140000e-127 464.0
34 TraesCS6A01G009800 chr4B 85.886 333 32 8 2200 2532 439734930 439735247 9.040000e-90 340.0
35 TraesCS6A01G009800 chr4B 100.000 29 0 0 541 569 25807649 25807677 1.000000e-03 54.7
36 TraesCS6A01G009800 chr2D 87.475 503 52 8 2052 2549 35461277 35460781 1.060000e-158 569.0
37 TraesCS6A01G009800 chr5D 87.677 495 44 9 2053 2532 30649679 30649187 6.380000e-156 560.0
38 TraesCS6A01G009800 chr1A 91.395 337 27 2 1736 2072 583035192 583034858 6.650000e-126 460.0
39 TraesCS6A01G009800 chr1A 77.863 393 63 17 1376 1762 583035621 583035247 3.420000e-54 222.0
40 TraesCS6A01G009800 chr1A 100.000 29 0 0 541 569 10438876 10438848 1.000000e-03 54.7
41 TraesCS6A01G009800 chr1A 100.000 29 0 0 541 569 569397785 569397757 1.000000e-03 54.7
42 TraesCS6A01G009800 chr1D 83.333 450 42 8 2047 2490 8061480 8061058 4.120000e-103 385.0
43 TraesCS6A01G009800 chr2A 96.970 33 1 0 541 573 40058160 40058128 3.670000e-04 56.5


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 TraesCS6A01G009800 chr6A 4540303 4542940 2637 True 2463.35 4872 100.0000 1 2638 2 chr6A.!!$R2 2637
1 TraesCS6A01G009800 chr3A 713674728 713676175 1447 True 2340.00 2340 95.8020 567 2019 1 chr3A.!!$R1 1452
2 TraesCS6A01G009800 chr3A 740328986 740329526 540 False 894.00 894 96.4880 1 541 1 chr3A.!!$F1 540
3 TraesCS6A01G009800 chr7A 14787988 14789444 1456 False 2326.00 2326 95.4730 567 2024 1 chr7A.!!$F1 1457
4 TraesCS6A01G009800 chr7A 17674419 17674959 540 True 939.00 939 97.9670 1 541 1 chr7A.!!$R1 540
5 TraesCS6A01G009800 chr7A 268855837 268856377 540 True 894.00 894 96.4880 1 541 1 chr7A.!!$R2 540
6 TraesCS6A01G009800 chr6B 531710998 531712438 1440 False 2313.00 2313 95.5770 567 2013 1 chr6B.!!$F5 1446
7 TraesCS6A01G009800 chr6B 531698374 531699556 1182 False 1951.00 1951 96.3800 567 1754 1 chr6B.!!$F4 1187
8 TraesCS6A01G009800 chr6B 630855948 630856487 539 False 893.00 893 96.4880 1 541 1 chr6B.!!$F6 540
9 TraesCS6A01G009800 chr5A 662377824 662379098 1274 True 2104.00 2104 96.4060 567 1846 1 chr5A.!!$R3 1279
10 TraesCS6A01G009800 chr5A 708620192 708621435 1243 True 472.50 640 85.7050 1375 2300 2 chr5A.!!$R5 925
11 TraesCS6A01G009800 chr5A 438246912 438247763 851 True 399.50 497 87.6210 1730 2359 2 chr5A.!!$R4 629
12 TraesCS6A01G009800 chr3B 733559066 733559799 733 True 1223.00 1223 96.7350 1020 1754 1 chr3B.!!$R1 734
13 TraesCS6A01G009800 chrUn 85056387 85056927 540 False 485.85 917 98.6135 1 569 2 chrUn.!!$F2 568
14 TraesCS6A01G009800 chr1B 49867480 49868020 540 True 917.00 917 97.2270 1 541 1 chr1B.!!$R1 540
15 TraesCS6A01G009800 chr1B 133448169 133448709 540 False 917.00 917 97.2270 1 541 1 chr1B.!!$F1 540
16 TraesCS6A01G009800 chr7B 44552085 44552625 540 False 894.00 894 96.4880 1 541 1 chr7B.!!$F1 540
17 TraesCS6A01G009800 chr5B 246145147 246145687 540 False 889.00 889 96.3030 1 541 1 chr5B.!!$F1 540
18 TraesCS6A01G009800 chr4B 365181664 365183385 1721 False 611.00 758 88.8300 716 2490 2 chr4B.!!$F4 1774
19 TraesCS6A01G009800 chr1A 583034858 583035621 763 True 341.00 460 84.6290 1376 2072 2 chr1A.!!$R3 696

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
358 359 0.106369 ACCCGATGTCACCGATCCTA 60.106 55.0 0.0 0.0 0.0 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 2923 1.070289 GGACGTGAAACTCACCTTCCT 59.93 52.381 0.0 0.0 44.2 3.36 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
274 275 3.314080 TCTTTACGCAAAAAGGGAGTGTG 59.686 43.478 7.67 0.00 37.13 3.82
294 295 4.007659 GTGGGGATTAAAGTGAATGACGT 58.992 43.478 0.00 0.00 0.00 4.34
295 296 5.180271 GTGGGGATTAAAGTGAATGACGTA 58.820 41.667 0.00 0.00 0.00 3.57
307 308 6.793349 AGTGAATGACGTAATAGGTCACTAC 58.207 40.000 16.66 14.74 44.42 2.73
358 359 0.106369 ACCCGATGTCACCGATCCTA 60.106 55.000 0.00 0.00 0.00 2.94
541 542 6.630444 AGAAACATGAAGCTGCTATTATGG 57.370 37.500 18.57 5.46 0.00 2.74
542 543 5.533903 AGAAACATGAAGCTGCTATTATGGG 59.466 40.000 18.57 4.22 0.00 4.00
543 544 3.759581 ACATGAAGCTGCTATTATGGGG 58.240 45.455 18.57 2.97 0.00 4.96
544 545 2.276732 TGAAGCTGCTATTATGGGGC 57.723 50.000 0.90 0.00 0.00 5.80
545 546 1.776667 TGAAGCTGCTATTATGGGGCT 59.223 47.619 0.90 0.00 0.00 5.19
546 547 2.978978 TGAAGCTGCTATTATGGGGCTA 59.021 45.455 0.90 0.00 0.00 3.93
547 548 3.394274 TGAAGCTGCTATTATGGGGCTAA 59.606 43.478 0.90 0.00 0.00 3.09
548 549 3.710209 AGCTGCTATTATGGGGCTAAG 57.290 47.619 0.00 0.00 0.00 2.18
549 550 2.307098 AGCTGCTATTATGGGGCTAAGG 59.693 50.000 0.00 0.00 0.00 2.69
550 551 2.716217 CTGCTATTATGGGGCTAAGGC 58.284 52.381 0.00 0.00 37.82 4.35
551 552 2.040278 CTGCTATTATGGGGCTAAGGCA 59.960 50.000 0.00 0.00 40.87 4.75
552 553 2.445145 TGCTATTATGGGGCTAAGGCAA 59.555 45.455 0.00 0.00 40.87 4.52
553 554 3.084786 GCTATTATGGGGCTAAGGCAAG 58.915 50.000 0.00 0.00 40.87 4.01
554 555 2.683211 ATTATGGGGCTAAGGCAAGG 57.317 50.000 0.00 0.00 40.87 3.61
555 556 1.602440 TTATGGGGCTAAGGCAAGGA 58.398 50.000 0.00 0.00 40.87 3.36
556 557 1.140312 TATGGGGCTAAGGCAAGGAG 58.860 55.000 0.00 0.00 40.87 3.69
557 558 0.624500 ATGGGGCTAAGGCAAGGAGA 60.625 55.000 0.00 0.00 40.87 3.71
558 559 1.224870 GGGGCTAAGGCAAGGAGAC 59.775 63.158 0.00 0.00 40.87 3.36
559 560 1.224870 GGGCTAAGGCAAGGAGACC 59.775 63.158 0.00 0.00 40.87 3.85
560 561 1.224870 GGCTAAGGCAAGGAGACCC 59.775 63.158 0.00 0.00 40.87 4.46
561 562 1.153349 GCTAAGGCAAGGAGACCCG 60.153 63.158 0.00 0.00 38.54 5.28
562 563 1.614241 GCTAAGGCAAGGAGACCCGA 61.614 60.000 0.00 0.00 38.54 5.14
563 564 1.123928 CTAAGGCAAGGAGACCCGAT 58.876 55.000 0.00 0.00 37.58 4.18
564 565 0.830648 TAAGGCAAGGAGACCCGATG 59.169 55.000 0.00 0.00 37.58 3.84
565 566 1.201429 AAGGCAAGGAGACCCGATGT 61.201 55.000 0.00 0.00 37.58 3.06
583 584 1.464219 TGTCACGAATGTACGACGCTA 59.536 47.619 0.00 0.00 37.03 4.26
610 611 2.566724 AGCTCCACCTCTTCTTCTTGAG 59.433 50.000 0.00 0.00 0.00 3.02
643 644 2.049802 TGAAGCGAACGACGACCC 60.050 61.111 0.00 0.00 45.77 4.46
718 719 2.299582 TGCAAAGGCCACTTACGTAGTA 59.700 45.455 5.01 0.00 40.40 1.82
729 730 3.508793 ACTTACGTAGTACACTGCCACAT 59.491 43.478 0.38 0.00 45.76 3.21
736 737 4.142609 AGTACACTGCCACATATTCAGG 57.857 45.455 0.00 0.00 32.42 3.86
746 747 4.211374 GCCACATATTCAGGCGTACTTAAG 59.789 45.833 0.00 0.00 38.86 1.85
1056 1057 2.969950 TCTCGTTTCCCTTGAAGGAGAA 59.030 45.455 13.97 11.54 38.17 2.87
1560 1590 2.508439 GGCTCGGCGACATCGAAA 60.508 61.111 4.99 0.00 43.02 3.46
1580 1610 4.755507 TGGGCGGCATCATGGCAA 62.756 61.111 12.41 0.00 43.94 4.52
1604 1634 1.299620 CGTGTCGTTGTCCTTCCGT 60.300 57.895 0.00 0.00 0.00 4.69
1781 1891 0.686441 TTGACCTCCGGGACATCGAT 60.686 55.000 0.00 0.00 37.16 3.59
1840 1950 1.680522 ATGAGCTCCGGCGACTCATT 61.681 55.000 24.50 14.33 46.38 2.57
1854 1964 1.827344 ACTCATTGTCCTCATCGAGCA 59.173 47.619 0.00 0.00 0.00 4.26
1956 2066 1.299773 GAAGATGAGCTCCGGCGAG 60.300 63.158 9.30 5.11 44.37 5.03
1985 2458 0.382158 TCATCGAGCGGTGATGAGTC 59.618 55.000 19.06 0.00 45.37 3.36
1987 2460 1.095807 ATCGAGCGGTGATGAGTCGA 61.096 55.000 0.00 0.00 43.26 4.20
2157 2848 3.042560 GCTTTTGGCAACGCTCCT 58.957 55.556 0.00 0.00 41.35 3.69
2228 2923 8.754991 TTGTTAGATCAAAGTTTTACCCTTCA 57.245 30.769 0.00 0.00 0.00 3.02
2257 2952 3.942115 TGAGTTTCACGTCCATGTTGAAA 59.058 39.130 0.00 0.00 0.00 2.69
2268 2963 4.452455 GTCCATGTTGAAATTGTCGAGAGT 59.548 41.667 0.00 0.00 0.00 3.24
2291 2986 0.037605 CTGTACGCCGGTCTCCTTTT 60.038 55.000 1.90 0.00 0.00 2.27
2293 2988 0.794473 GTACGCCGGTCTCCTTTTTG 59.206 55.000 1.90 0.00 0.00 2.44
2363 3064 1.215117 GCTGCGTGAGAGAGAGCTT 59.785 57.895 0.00 0.00 0.00 3.74
2385 3086 0.464036 TGGTCTTTCTGTCTGCGTGT 59.536 50.000 0.00 0.00 0.00 4.49
2396 3097 3.268446 CTGCGTGTGTCGTCTTGCG 62.268 63.158 0.00 0.00 42.13 4.85
2424 3125 2.534298 CTGAGTCTTGTGCGTGGATAG 58.466 52.381 0.00 0.00 0.00 2.08
2425 3126 2.164422 CTGAGTCTTGTGCGTGGATAGA 59.836 50.000 0.00 0.00 0.00 1.98
2438 3139 4.240888 CGTGGATAGATGATGGATGTGAC 58.759 47.826 0.00 0.00 0.00 3.67
2469 3170 2.985847 GGGTGCTGGAGGTGTTGC 60.986 66.667 0.00 0.00 0.00 4.17
2471 3172 2.591715 GTGCTGGAGGTGTTGCGT 60.592 61.111 0.00 0.00 0.00 5.24
2490 3191 3.099619 GATGGATGTGTGCGTGCGG 62.100 63.158 0.00 0.00 0.00 5.69
2491 3192 3.899981 ATGGATGTGTGCGTGCGGT 62.900 57.895 0.00 0.00 0.00 5.68
2492 3193 4.088762 GGATGTGTGCGTGCGGTG 62.089 66.667 0.00 0.00 0.00 4.94
2493 3194 4.088762 GATGTGTGCGTGCGGTGG 62.089 66.667 0.00 0.00 0.00 4.61
2494 3195 4.617520 ATGTGTGCGTGCGGTGGA 62.618 61.111 0.00 0.00 0.00 4.02
2495 3196 3.899981 ATGTGTGCGTGCGGTGGAT 62.900 57.895 0.00 0.00 0.00 3.41
2496 3197 4.088762 GTGTGCGTGCGGTGGATG 62.089 66.667 0.00 0.00 0.00 3.51
2499 3200 4.094646 TGCGTGCGGTGGATGGAT 62.095 61.111 0.00 0.00 0.00 3.41
2500 3201 3.576356 GCGTGCGGTGGATGGATG 61.576 66.667 0.00 0.00 0.00 3.51
2501 3202 2.896854 CGTGCGGTGGATGGATGG 60.897 66.667 0.00 0.00 0.00 3.51
2502 3203 2.516930 GTGCGGTGGATGGATGGG 60.517 66.667 0.00 0.00 0.00 4.00
2503 3204 3.014538 TGCGGTGGATGGATGGGT 61.015 61.111 0.00 0.00 0.00 4.51
2504 3205 2.516930 GCGGTGGATGGATGGGTG 60.517 66.667 0.00 0.00 0.00 4.61
2505 3206 2.516930 CGGTGGATGGATGGGTGC 60.517 66.667 0.00 0.00 0.00 5.01
2506 3207 3.010144 GGTGGATGGATGGGTGCT 58.990 61.111 0.00 0.00 0.00 4.40
2507 3208 1.454479 GGTGGATGGATGGGTGCTG 60.454 63.158 0.00 0.00 0.00 4.41
2508 3209 1.454479 GTGGATGGATGGGTGCTGG 60.454 63.158 0.00 0.00 0.00 4.85
2509 3210 1.619057 TGGATGGATGGGTGCTGGA 60.619 57.895 0.00 0.00 0.00 3.86
2510 3211 1.150081 GGATGGATGGGTGCTGGAG 59.850 63.158 0.00 0.00 0.00 3.86
2511 3212 1.150081 GATGGATGGGTGCTGGAGG 59.850 63.158 0.00 0.00 0.00 4.30
2512 3213 1.620589 ATGGATGGGTGCTGGAGGT 60.621 57.895 0.00 0.00 0.00 3.85
2513 3214 1.929860 ATGGATGGGTGCTGGAGGTG 61.930 60.000 0.00 0.00 0.00 4.00
2514 3215 2.606587 GGATGGGTGCTGGAGGTGT 61.607 63.158 0.00 0.00 0.00 4.16
2515 3216 1.377725 GATGGGTGCTGGAGGTGTG 60.378 63.158 0.00 0.00 0.00 3.82
2516 3217 3.574074 ATGGGTGCTGGAGGTGTGC 62.574 63.158 0.00 0.00 0.00 4.57
2518 3219 4.626081 GGTGCTGGAGGTGTGCGT 62.626 66.667 0.00 0.00 0.00 5.24
2519 3220 3.349006 GTGCTGGAGGTGTGCGTG 61.349 66.667 0.00 0.00 0.00 5.34
2522 3223 4.969196 CTGGAGGTGTGCGTGCGT 62.969 66.667 0.00 0.00 0.00 5.24
2524 3225 4.961511 GGAGGTGTGCGTGCGTGA 62.962 66.667 0.00 0.00 0.00 4.35
2525 3226 3.406361 GAGGTGTGCGTGCGTGAG 61.406 66.667 0.00 0.00 0.00 3.51
2526 3227 4.221422 AGGTGTGCGTGCGTGAGT 62.221 61.111 0.00 0.00 0.00 3.41
2527 3228 3.269347 GGTGTGCGTGCGTGAGTT 61.269 61.111 0.00 0.00 0.00 3.01
2528 3229 2.053116 GTGTGCGTGCGTGAGTTG 60.053 61.111 0.00 0.00 0.00 3.16
2529 3230 3.935872 TGTGCGTGCGTGAGTTGC 61.936 61.111 0.00 0.00 0.00 4.17
2530 3231 4.666532 GTGCGTGCGTGAGTTGCC 62.667 66.667 0.00 0.00 0.00 4.52
2531 3232 4.908687 TGCGTGCGTGAGTTGCCT 62.909 61.111 0.00 0.00 0.00 4.75
2532 3233 3.649986 GCGTGCGTGAGTTGCCTT 61.650 61.111 0.00 0.00 0.00 4.35
2533 3234 2.249309 CGTGCGTGAGTTGCCTTG 59.751 61.111 0.00 0.00 0.00 3.61
2534 3235 2.243957 CGTGCGTGAGTTGCCTTGA 61.244 57.895 0.00 0.00 0.00 3.02
2535 3236 1.571460 GTGCGTGAGTTGCCTTGAG 59.429 57.895 0.00 0.00 0.00 3.02
2536 3237 0.880278 GTGCGTGAGTTGCCTTGAGA 60.880 55.000 0.00 0.00 0.00 3.27
2537 3238 0.179059 TGCGTGAGTTGCCTTGAGAA 60.179 50.000 0.00 0.00 0.00 2.87
2538 3239 1.160137 GCGTGAGTTGCCTTGAGAAT 58.840 50.000 0.00 0.00 0.00 2.40
2539 3240 1.135859 GCGTGAGTTGCCTTGAGAATG 60.136 52.381 0.00 0.00 0.00 2.67
2540 3241 1.466167 CGTGAGTTGCCTTGAGAATGG 59.534 52.381 0.00 0.00 0.00 3.16
2541 3242 1.815003 GTGAGTTGCCTTGAGAATGGG 59.185 52.381 0.00 0.00 0.00 4.00
2542 3243 1.425066 TGAGTTGCCTTGAGAATGGGT 59.575 47.619 0.00 0.00 0.00 4.51
2543 3244 2.087646 GAGTTGCCTTGAGAATGGGTC 58.912 52.381 0.00 0.00 0.00 4.46
2544 3245 1.707427 AGTTGCCTTGAGAATGGGTCT 59.293 47.619 0.00 0.00 40.25 3.85
2555 3256 3.044894 AGAATGGGTCTCTCCTTGATCC 58.955 50.000 0.00 0.00 35.36 3.36
2556 3257 1.813102 ATGGGTCTCTCCTTGATCCC 58.187 55.000 0.00 0.00 38.41 3.85
2557 3258 0.719015 TGGGTCTCTCCTTGATCCCT 59.281 55.000 0.00 0.00 38.59 4.20
2558 3259 1.343478 TGGGTCTCTCCTTGATCCCTC 60.343 57.143 0.00 0.00 38.59 4.30
2559 3260 1.062505 GGGTCTCTCCTTGATCCCTCT 60.063 57.143 0.00 0.00 36.48 3.69
2560 3261 2.038659 GGTCTCTCCTTGATCCCTCTG 58.961 57.143 0.00 0.00 0.00 3.35
2561 3262 1.412343 GTCTCTCCTTGATCCCTCTGC 59.588 57.143 0.00 0.00 0.00 4.26
2562 3263 0.388659 CTCTCCTTGATCCCTCTGCG 59.611 60.000 0.00 0.00 0.00 5.18
2563 3264 0.324738 TCTCCTTGATCCCTCTGCGT 60.325 55.000 0.00 0.00 0.00 5.24
2564 3265 0.179089 CTCCTTGATCCCTCTGCGTG 60.179 60.000 0.00 0.00 0.00 5.34
2565 3266 0.614697 TCCTTGATCCCTCTGCGTGA 60.615 55.000 0.00 0.00 0.00 4.35
2566 3267 0.250234 CCTTGATCCCTCTGCGTGAA 59.750 55.000 0.00 0.00 0.00 3.18
2567 3268 1.649664 CTTGATCCCTCTGCGTGAAG 58.350 55.000 0.00 0.00 0.00 3.02
2568 3269 0.250234 TTGATCCCTCTGCGTGAAGG 59.750 55.000 0.00 0.00 0.00 3.46
2569 3270 0.614697 TGATCCCTCTGCGTGAAGGA 60.615 55.000 0.25 0.25 39.43 3.36
2570 3271 0.755686 GATCCCTCTGCGTGAAGGAT 59.244 55.000 8.78 8.78 45.97 3.24
2571 3272 0.755686 ATCCCTCTGCGTGAAGGATC 59.244 55.000 4.41 0.00 40.99 3.36
2572 3273 0.324738 TCCCTCTGCGTGAAGGATCT 60.325 55.000 0.00 0.00 30.67 2.75
2573 3274 0.179089 CCCTCTGCGTGAAGGATCTG 60.179 60.000 0.00 0.00 0.00 2.90
2574 3275 0.534412 CCTCTGCGTGAAGGATCTGT 59.466 55.000 0.00 0.00 0.00 3.41
2575 3276 1.638133 CTCTGCGTGAAGGATCTGTG 58.362 55.000 0.00 0.00 0.00 3.66
2576 3277 0.390340 TCTGCGTGAAGGATCTGTGC 60.390 55.000 0.00 0.00 0.00 4.57
2577 3278 1.364626 CTGCGTGAAGGATCTGTGCC 61.365 60.000 0.00 0.00 0.00 5.01
2578 3279 1.078848 GCGTGAAGGATCTGTGCCT 60.079 57.895 0.00 0.00 37.35 4.75
2580 3281 1.813513 CGTGAAGGATCTGTGCCTTT 58.186 50.000 0.00 0.00 45.43 3.11
2581 3282 2.935238 GCGTGAAGGATCTGTGCCTTTA 60.935 50.000 0.00 0.00 45.43 1.85
2582 3283 3.535561 CGTGAAGGATCTGTGCCTTTAT 58.464 45.455 0.00 0.00 45.43 1.40
2583 3284 4.693283 CGTGAAGGATCTGTGCCTTTATA 58.307 43.478 0.00 0.00 45.43 0.98
2584 3285 5.300752 CGTGAAGGATCTGTGCCTTTATAT 58.699 41.667 0.00 0.00 45.43 0.86
2585 3286 6.455647 CGTGAAGGATCTGTGCCTTTATATA 58.544 40.000 0.00 0.00 45.43 0.86
2586 3287 6.587990 CGTGAAGGATCTGTGCCTTTATATAG 59.412 42.308 0.00 0.00 45.43 1.31
2587 3288 6.876257 GTGAAGGATCTGTGCCTTTATATAGG 59.124 42.308 4.93 4.93 45.43 2.57
2595 3296 1.739067 CCTTTATATAGGCAGGCGGC 58.261 55.000 0.00 0.00 43.74 6.53
2603 3304 3.476419 GGCAGGCGGCTAGGGTTA 61.476 66.667 12.74 0.00 44.01 2.85
2604 3305 2.203029 GCAGGCGGCTAGGGTTAC 60.203 66.667 12.74 0.00 40.25 2.50
2605 3306 2.504519 CAGGCGGCTAGGGTTACC 59.495 66.667 12.74 0.00 0.00 2.85
2617 3318 0.107165 GGGTTACCTGTGATCCCTGC 60.107 60.000 0.00 0.00 35.63 4.85
2618 3319 0.462047 GGTTACCTGTGATCCCTGCG 60.462 60.000 0.00 0.00 0.00 5.18
2619 3320 0.462047 GTTACCTGTGATCCCTGCGG 60.462 60.000 0.00 0.00 0.00 5.69
2620 3321 2.252072 TTACCTGTGATCCCTGCGGC 62.252 60.000 0.00 0.00 0.00 6.53
2621 3322 4.100084 CCTGTGATCCCTGCGGCA 62.100 66.667 1.29 1.29 0.00 5.69
2622 3323 2.046023 CTGTGATCCCTGCGGCAA 60.046 61.111 3.44 0.00 0.00 4.52
2623 3324 2.046023 TGTGATCCCTGCGGCAAG 60.046 61.111 3.44 0.00 0.00 4.01
2624 3325 2.825836 GTGATCCCTGCGGCAAGG 60.826 66.667 11.49 11.49 37.05 3.61
2625 3326 3.329889 TGATCCCTGCGGCAAGGT 61.330 61.111 16.80 5.11 35.34 3.50
2626 3327 1.992834 TGATCCCTGCGGCAAGGTA 60.993 57.895 16.80 5.06 35.34 3.08
2627 3328 1.227674 GATCCCTGCGGCAAGGTAG 60.228 63.158 16.80 0.00 35.34 3.18
2628 3329 3.406595 ATCCCTGCGGCAAGGTAGC 62.407 63.158 16.80 0.00 35.34 3.58
2629 3330 4.408821 CCCTGCGGCAAGGTAGCA 62.409 66.667 9.53 0.00 39.25 3.49
2630 3331 3.127533 CCTGCGGCAAGGTAGCAC 61.128 66.667 3.44 0.00 36.79 4.40
2631 3332 3.490759 CTGCGGCAAGGTAGCACG 61.491 66.667 3.44 0.00 36.79 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
252 253 3.314080 CACACTCCCTTTTTGCGTAAAGA 59.686 43.478 10.87 0.00 37.31 2.52
274 275 6.937436 ATTACGTCATTCACTTTAATCCCC 57.063 37.500 0.00 0.00 0.00 4.81
294 295 7.156673 GTGTGTTTGGAAGTAGTGACCTATTA 58.843 38.462 0.00 0.00 0.00 0.98
295 296 5.995897 GTGTGTTTGGAAGTAGTGACCTATT 59.004 40.000 0.00 0.00 0.00 1.73
307 308 0.389025 GCCCCTTGTGTGTTTGGAAG 59.611 55.000 0.00 0.00 0.00 3.46
358 359 9.388506 GTGAGCATATCAGCCACTATATTAAAT 57.611 33.333 0.00 0.00 39.07 1.40
440 441 2.907696 TGGAAATCCCTCCGTCAACTAA 59.092 45.455 0.00 0.00 38.44 2.24
541 542 1.224870 GGTCTCCTTGCCTTAGCCC 59.775 63.158 0.00 0.00 38.69 5.19
542 543 1.224870 GGGTCTCCTTGCCTTAGCC 59.775 63.158 0.00 0.00 38.69 3.93
543 544 1.153349 CGGGTCTCCTTGCCTTAGC 60.153 63.158 0.00 0.00 40.48 3.09
544 545 1.123928 ATCGGGTCTCCTTGCCTTAG 58.876 55.000 0.00 0.00 0.00 2.18
545 546 0.830648 CATCGGGTCTCCTTGCCTTA 59.169 55.000 0.00 0.00 0.00 2.69
546 547 1.201429 ACATCGGGTCTCCTTGCCTT 61.201 55.000 0.00 0.00 0.00 4.35
547 548 1.613630 ACATCGGGTCTCCTTGCCT 60.614 57.895 0.00 0.00 0.00 4.75
548 549 1.153349 GACATCGGGTCTCCTTGCC 60.153 63.158 1.55 0.00 43.46 4.52
549 550 4.522971 GACATCGGGTCTCCTTGC 57.477 61.111 1.55 0.00 43.46 4.01
557 558 1.468565 CGTACATTCGTGACATCGGGT 60.469 52.381 0.00 0.00 0.00 5.28
558 559 1.197055 CGTACATTCGTGACATCGGG 58.803 55.000 0.00 0.00 0.00 5.14
559 560 1.844357 GTCGTACATTCGTGACATCGG 59.156 52.381 0.00 0.00 0.00 4.18
560 561 1.507520 CGTCGTACATTCGTGACATCG 59.492 52.381 0.00 0.00 0.00 3.84
561 562 1.252015 GCGTCGTACATTCGTGACATC 59.748 52.381 0.00 0.00 0.00 3.06
562 563 1.135489 AGCGTCGTACATTCGTGACAT 60.135 47.619 0.00 0.00 0.00 3.06
563 564 0.239082 AGCGTCGTACATTCGTGACA 59.761 50.000 0.00 0.00 0.00 3.58
564 565 2.163826 TAGCGTCGTACATTCGTGAC 57.836 50.000 0.00 0.00 0.00 3.67
565 566 2.352342 TCATAGCGTCGTACATTCGTGA 59.648 45.455 0.00 0.00 0.00 4.35
583 584 0.820871 GAAGAGGTGGAGCTCGTCAT 59.179 55.000 7.83 0.21 0.00 3.06
610 611 1.321743 CTTCAGCGCGTCTTACATCAC 59.678 52.381 8.43 0.00 0.00 3.06
718 719 1.755179 GCCTGAATATGTGGCAGTGT 58.245 50.000 8.47 0.00 45.46 3.55
729 730 5.657474 CTGAACCTTAAGTACGCCTGAATA 58.343 41.667 0.97 0.00 0.00 1.75
736 737 3.323243 TGAAGCTGAACCTTAAGTACGC 58.677 45.455 0.97 0.00 0.00 4.42
746 747 6.051717 TGCTATAGAAGAATGAAGCTGAACC 58.948 40.000 3.21 0.00 0.00 3.62
792 793 3.140814 GCCGTCCATTTCCAGCCC 61.141 66.667 0.00 0.00 0.00 5.19
909 910 2.624838 ACACAAGAACAAGAAGGCATGG 59.375 45.455 0.00 0.00 0.00 3.66
1056 1057 4.074526 ATGACGGTGCTGCTCGCT 62.075 61.111 13.81 4.16 40.11 4.93
1143 1144 2.358737 GTCACACCCTTCGCCCAG 60.359 66.667 0.00 0.00 0.00 4.45
1213 1214 1.278985 TCACCTCCATTTCATCACGCT 59.721 47.619 0.00 0.00 0.00 5.07
1460 1489 2.474266 CCGCGGAACACAATGACG 59.526 61.111 24.07 0.00 0.00 4.35
1547 1577 2.452813 CCACCTTTCGATGTCGCCG 61.453 63.158 0.00 0.00 39.60 6.46
1560 1590 4.511246 CCATGATGCCGCCCACCT 62.511 66.667 0.00 0.00 0.00 4.00
1580 1610 1.374252 GGACAACGACACGGAGCAT 60.374 57.895 0.00 0.00 0.00 3.79
1714 1744 3.619054 GCTAGACGAAGATGCCGC 58.381 61.111 0.00 0.00 0.00 6.53
1781 1891 2.867333 GAACGCTGACGCCATCGAGA 62.867 60.000 1.07 0.00 45.53 4.04
1840 1950 1.135721 CATCACTGCTCGATGAGGACA 59.864 52.381 5.05 0.00 42.39 4.02
1854 1964 2.606587 GCCACCCCCACTCATCACT 61.607 63.158 0.00 0.00 0.00 3.41
1956 2066 2.024871 CTCGATGAGGACGACGCC 59.975 66.667 0.00 0.00 35.88 5.68
2157 2848 2.110835 ATGCACGCACACAGGTCA 59.889 55.556 0.00 0.00 0.00 4.02
2228 2923 1.070289 GGACGTGAAACTCACCTTCCT 59.930 52.381 0.00 0.00 44.20 3.36
2239 2934 5.255710 ACAATTTCAACATGGACGTGAAA 57.744 34.783 14.47 14.47 33.78 2.69
2257 2952 2.163815 CGTACAGGGAACTCTCGACAAT 59.836 50.000 0.00 0.00 40.21 2.71
2268 2963 2.283388 AGACCGGCGTACAGGGAA 60.283 61.111 6.01 0.00 0.00 3.97
2363 3064 1.412710 ACGCAGACAGAAAGACCAGAA 59.587 47.619 0.00 0.00 0.00 3.02
2377 3078 1.949133 GCAAGACGACACACGCAGA 60.949 57.895 0.00 0.00 46.94 4.26
2396 3097 3.128938 ACGCACAAGACTCAGGTATAGTC 59.871 47.826 0.00 0.00 43.06 2.59
2400 3101 1.066858 CCACGCACAAGACTCAGGTAT 60.067 52.381 0.00 0.00 0.00 2.73
2424 3125 0.530650 ACCGCGTCACATCCATCATC 60.531 55.000 4.92 0.00 0.00 2.92
2425 3126 0.811219 CACCGCGTCACATCCATCAT 60.811 55.000 4.92 0.00 0.00 2.45
2438 3139 4.175337 ACCCATCCATCCACCGCG 62.175 66.667 0.00 0.00 0.00 6.46
2469 3170 1.421093 CACGCACACATCCATCACG 59.579 57.895 0.00 0.00 0.00 4.35
2471 3172 2.389809 CGCACGCACACATCCATCA 61.390 57.895 0.00 0.00 0.00 3.07
2490 3191 1.454479 CCAGCACCCATCCATCCAC 60.454 63.158 0.00 0.00 0.00 4.02
2491 3192 1.619057 TCCAGCACCCATCCATCCA 60.619 57.895 0.00 0.00 0.00 3.41
2492 3193 1.150081 CTCCAGCACCCATCCATCC 59.850 63.158 0.00 0.00 0.00 3.51
2493 3194 1.150081 CCTCCAGCACCCATCCATC 59.850 63.158 0.00 0.00 0.00 3.51
2494 3195 1.620589 ACCTCCAGCACCCATCCAT 60.621 57.895 0.00 0.00 0.00 3.41
2495 3196 2.204136 ACCTCCAGCACCCATCCA 60.204 61.111 0.00 0.00 0.00 3.41
2496 3197 2.273449 CACCTCCAGCACCCATCC 59.727 66.667 0.00 0.00 0.00 3.51
2497 3198 1.377725 CACACCTCCAGCACCCATC 60.378 63.158 0.00 0.00 0.00 3.51
2498 3199 2.759114 CACACCTCCAGCACCCAT 59.241 61.111 0.00 0.00 0.00 4.00
2499 3200 4.269523 GCACACCTCCAGCACCCA 62.270 66.667 0.00 0.00 0.00 4.51
2501 3202 4.626081 ACGCACACCTCCAGCACC 62.626 66.667 0.00 0.00 0.00 5.01
2502 3203 3.349006 CACGCACACCTCCAGCAC 61.349 66.667 0.00 0.00 0.00 4.40
2505 3206 4.969196 ACGCACGCACACCTCCAG 62.969 66.667 0.00 0.00 0.00 3.86
2507 3208 4.961511 TCACGCACGCACACCTCC 62.962 66.667 0.00 0.00 0.00 4.30
2508 3209 3.406361 CTCACGCACGCACACCTC 61.406 66.667 0.00 0.00 0.00 3.85
2509 3210 3.733344 AACTCACGCACGCACACCT 62.733 57.895 0.00 0.00 0.00 4.00
2510 3211 3.269347 AACTCACGCACGCACACC 61.269 61.111 0.00 0.00 0.00 4.16
2511 3212 2.053116 CAACTCACGCACGCACAC 60.053 61.111 0.00 0.00 0.00 3.82
2512 3213 3.935872 GCAACTCACGCACGCACA 61.936 61.111 0.00 0.00 0.00 4.57
2513 3214 4.666532 GGCAACTCACGCACGCAC 62.667 66.667 0.00 0.00 0.00 5.34
2525 3226 2.206576 AGACCCATTCTCAAGGCAAC 57.793 50.000 0.00 0.00 0.00 4.17
2534 3235 3.044894 GGATCAAGGAGAGACCCATTCT 58.955 50.000 0.00 0.00 40.05 2.40
2535 3236 2.105649 GGGATCAAGGAGAGACCCATTC 59.894 54.545 0.00 0.00 42.65 2.67
2536 3237 2.131023 GGGATCAAGGAGAGACCCATT 58.869 52.381 0.00 0.00 42.65 3.16
2537 3238 1.296523 AGGGATCAAGGAGAGACCCAT 59.703 52.381 0.00 0.00 44.35 4.00
2538 3239 0.719015 AGGGATCAAGGAGAGACCCA 59.281 55.000 0.00 0.00 44.35 4.51
2539 3240 1.062505 AGAGGGATCAAGGAGAGACCC 60.063 57.143 0.00 0.00 43.11 4.46
2540 3241 2.038659 CAGAGGGATCAAGGAGAGACC 58.961 57.143 0.00 0.00 39.35 3.85
2541 3242 1.412343 GCAGAGGGATCAAGGAGAGAC 59.588 57.143 0.00 0.00 0.00 3.36
2542 3243 1.786937 GCAGAGGGATCAAGGAGAGA 58.213 55.000 0.00 0.00 0.00 3.10
2543 3244 0.388659 CGCAGAGGGATCAAGGAGAG 59.611 60.000 0.00 0.00 0.00 3.20
2544 3245 0.324738 ACGCAGAGGGATCAAGGAGA 60.325 55.000 0.00 0.00 0.00 3.71
2545 3246 0.179089 CACGCAGAGGGATCAAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
2546 3247 0.614697 TCACGCAGAGGGATCAAGGA 60.615 55.000 0.00 0.00 0.00 3.36
2547 3248 0.250234 TTCACGCAGAGGGATCAAGG 59.750 55.000 0.00 0.00 28.68 3.61
2548 3249 1.649664 CTTCACGCAGAGGGATCAAG 58.350 55.000 0.00 0.00 28.68 3.02
2549 3250 0.250234 CCTTCACGCAGAGGGATCAA 59.750 55.000 0.86 0.00 46.07 2.57
2550 3251 0.614697 TCCTTCACGCAGAGGGATCA 60.615 55.000 5.37 0.00 46.61 2.92
2551 3252 2.202866 TCCTTCACGCAGAGGGATC 58.797 57.895 5.37 0.00 46.61 3.36
2552 3253 4.461119 TCCTTCACGCAGAGGGAT 57.539 55.556 5.37 0.00 46.61 3.85
2554 3255 0.179089 CAGATCCTTCACGCAGAGGG 60.179 60.000 0.72 0.72 44.59 4.30
2555 3256 0.534412 ACAGATCCTTCACGCAGAGG 59.466 55.000 0.00 0.00 0.00 3.69
2556 3257 1.638133 CACAGATCCTTCACGCAGAG 58.362 55.000 0.00 0.00 0.00 3.35
2557 3258 0.390340 GCACAGATCCTTCACGCAGA 60.390 55.000 0.00 0.00 0.00 4.26
2558 3259 1.364626 GGCACAGATCCTTCACGCAG 61.365 60.000 0.00 0.00 0.00 5.18
2559 3260 1.375908 GGCACAGATCCTTCACGCA 60.376 57.895 0.00 0.00 0.00 5.24
2560 3261 0.674895 AAGGCACAGATCCTTCACGC 60.675 55.000 0.00 0.00 39.63 5.34
2561 3262 1.813513 AAAGGCACAGATCCTTCACG 58.186 50.000 0.00 0.00 42.75 4.35
2562 3263 6.876257 CCTATATAAAGGCACAGATCCTTCAC 59.124 42.308 0.00 0.00 42.75 3.18
2563 3264 7.009179 CCTATATAAAGGCACAGATCCTTCA 57.991 40.000 0.00 0.00 42.75 3.02
2576 3277 1.279271 AGCCGCCTGCCTATATAAAGG 59.721 52.381 0.00 2.66 42.71 3.11
2577 3278 2.770164 AGCCGCCTGCCTATATAAAG 57.230 50.000 0.00 0.00 42.71 1.85
2578 3279 2.500098 CCTAGCCGCCTGCCTATATAAA 59.500 50.000 0.00 0.00 42.71 1.40
2579 3280 2.108168 CCTAGCCGCCTGCCTATATAA 58.892 52.381 0.00 0.00 42.71 0.98
2580 3281 1.688311 CCCTAGCCGCCTGCCTATATA 60.688 57.143 0.00 0.00 42.71 0.86
2581 3282 0.978146 CCCTAGCCGCCTGCCTATAT 60.978 60.000 0.00 0.00 42.71 0.86
2582 3283 1.609501 CCCTAGCCGCCTGCCTATA 60.610 63.158 0.00 0.00 42.71 1.31
2583 3284 2.925170 CCCTAGCCGCCTGCCTAT 60.925 66.667 0.00 0.00 42.71 2.57
2584 3285 2.592778 TAACCCTAGCCGCCTGCCTA 62.593 60.000 0.00 0.00 42.71 3.93
2585 3286 3.995809 TAACCCTAGCCGCCTGCCT 62.996 63.158 0.00 0.00 42.71 4.75
2586 3287 3.476419 TAACCCTAGCCGCCTGCC 61.476 66.667 0.00 0.00 42.71 4.85
2587 3288 2.203029 GTAACCCTAGCCGCCTGC 60.203 66.667 0.00 0.00 41.71 4.85
2588 3289 2.064581 AGGTAACCCTAGCCGCCTG 61.065 63.158 0.00 0.00 40.19 4.85
2589 3290 2.064581 CAGGTAACCCTAGCCGCCT 61.065 63.158 0.00 0.00 39.89 5.52
2590 3291 2.364780 ACAGGTAACCCTAGCCGCC 61.365 63.158 0.00 0.00 39.89 6.13
2591 3292 1.153429 CACAGGTAACCCTAGCCGC 60.153 63.158 0.00 0.00 39.89 6.53
2592 3293 1.068741 GATCACAGGTAACCCTAGCCG 59.931 57.143 0.00 0.00 39.89 5.52
2593 3294 1.416772 GGATCACAGGTAACCCTAGCC 59.583 57.143 0.00 0.00 39.89 3.93
2594 3295 1.416772 GGGATCACAGGTAACCCTAGC 59.583 57.143 0.00 0.00 39.89 3.42
2598 3299 0.107165 GCAGGGATCACAGGTAACCC 60.107 60.000 0.00 0.00 40.71 4.11
2599 3300 0.462047 CGCAGGGATCACAGGTAACC 60.462 60.000 0.00 0.00 37.17 2.85
2600 3301 3.065575 CGCAGGGATCACAGGTAAC 57.934 57.895 0.00 0.00 0.00 2.50
2614 3315 3.490759 CGTGCTACCTTGCCGCAG 61.491 66.667 0.00 0.00 33.84 5.18


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

AutoCloner maintained by Alex Coulton.