Multiple sequence alignment - TraesCS4A01G210100

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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 TraesCS4A01G210100 chr4A 100.000 3028 0 0 1 3028 504174584 504171557 0.000000e+00 5592.0
1 TraesCS4A01G210100 chr4A 100.000 55 0 0 429 483 504174102 504174048 5.340000e-18 102.0
2 TraesCS4A01G210100 chr4A 100.000 55 0 0 483 537 504174156 504174102 5.340000e-18 102.0
3 TraesCS4A01G210100 chr4B 90.776 1160 45 22 1122 2267 128305147 128304036 0.000000e+00 1493.0
4 TraesCS4A01G210100 chr4B 90.881 636 39 11 491 1118 128305811 128305187 0.000000e+00 835.0
5 TraesCS4A01G210100 chr4B 87.679 349 18 12 1 341 128306388 128306057 1.700000e-102 383.0
6 TraesCS4A01G210100 chr4B 91.589 107 8 1 1413 1519 128304793 128304688 2.430000e-31 147.0
7 TraesCS4A01G210100 chr4B 95.745 47 1 1 437 483 128305811 128305766 1.160000e-09 75.0
8 TraesCS4A01G210100 chr4B 97.297 37 1 0 2216 2252 128267784 128267748 2.520000e-06 63.9
9 TraesCS4A01G210100 chr4D 93.340 961 48 4 1411 2357 92066929 92065971 0.000000e+00 1406.0
10 TraesCS4A01G210100 chr4D 92.656 640 36 6 483 1118 92067841 92067209 0.000000e+00 911.0
11 TraesCS4A01G210100 chr4D 88.657 432 29 6 62 483 92068206 92067785 2.690000e-140 508.0
12 TraesCS4A01G210100 chr4D 92.203 295 7 3 1122 1416 92067169 92066891 1.310000e-108 403.0
13 TraesCS4A01G210100 chr4D 83.571 140 12 6 1413 1544 92066830 92066694 1.470000e-23 121.0
14 TraesCS4A01G210100 chr5A 85.007 667 62 28 2371 3028 482427702 482428339 0.000000e+00 643.0
15 TraesCS4A01G210100 chr7D 81.575 635 79 27 2355 2979 94122423 94121817 9.760000e-135 490.0
16 TraesCS4A01G210100 chr3B 80.590 644 96 21 2371 3003 637099712 637099087 1.270000e-128 470.0
17 TraesCS4A01G210100 chr6D 80.460 609 79 28 2353 2947 46361330 46360748 2.160000e-116 429.0
18 TraesCS4A01G210100 chr5D 85.788 387 37 10 2357 2739 369069685 369070057 7.870000e-106 394.0
19 TraesCS4A01G210100 chr2A 78.211 693 78 37 2353 3023 756472251 756472892 2.850000e-100 375.0
20 TraesCS4A01G210100 chr2B 80.340 529 71 19 2367 2868 23060637 23060115 1.330000e-98 370.0
21 TraesCS4A01G210100 chr2D 79.081 631 61 32 2371 2997 271504722 271505285 4.770000e-98 368.0
22 TraesCS4A01G210100 chr2D 79.444 540 75 18 2352 2887 363320944 363320437 1.730000e-92 350.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G210100 chr4A 504171557 504174584 3027 True 1932.0 5592 100.0000 1 3028 3 chr4A.!!$R1 3027
1 TraesCS4A01G210100 chr4B 128304036 128306388 2352 True 586.6 1493 91.3340 1 2267 5 chr4B.!!$R2 2266
2 TraesCS4A01G210100 chr4D 92065971 92068206 2235 True 669.8 1406 90.0854 62 2357 5 chr4D.!!$R1 2295
3 TraesCS4A01G210100 chr5A 482427702 482428339 637 False 643.0 643 85.0070 2371 3028 1 chr5A.!!$F1 657
4 TraesCS4A01G210100 chr7D 94121817 94122423 606 True 490.0 490 81.5750 2355 2979 1 chr7D.!!$R1 624
5 TraesCS4A01G210100 chr3B 637099087 637099712 625 True 470.0 470 80.5900 2371 3003 1 chr3B.!!$R1 632
6 TraesCS4A01G210100 chr6D 46360748 46361330 582 True 429.0 429 80.4600 2353 2947 1 chr6D.!!$R1 594
7 TraesCS4A01G210100 chr2A 756472251 756472892 641 False 375.0 375 78.2110 2353 3023 1 chr2A.!!$F1 670
8 TraesCS4A01G210100 chr2B 23060115 23060637 522 True 370.0 370 80.3400 2367 2868 1 chr2B.!!$R1 501
9 TraesCS4A01G210100 chr2D 271504722 271505285 563 False 368.0 368 79.0810 2371 2997 1 chr2D.!!$F1 626
10 TraesCS4A01G210100 chr2D 363320437 363320944 507 True 350.0 350 79.4440 2352 2887 1 chr2D.!!$R1 535

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
46 47 0.312416 GAGAGCTGGTATGCGTCGAT 59.688 55.0 0.0 0.0 38.13 3.59 F
1490 1702 0.036388 ACGTCAAGTTCGGCATGGAT 60.036 50.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1855 0.250234 CGTGTCCATGTCCATGTCCT 59.750 55.0 6.53 0.0 37.11 3.85 R
2295 2570 0.531974 GGCGGATTTGATAGTGCGGA 60.532 55.0 0.00 0.0 0.00 5.54 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
38 39 4.364318 AGCACCGAGAGCTGGTAT 57.636 55.556 0.00 0.00 41.61 2.73
39 40 1.819229 AGCACCGAGAGCTGGTATG 59.181 57.895 0.00 0.00 41.61 2.39
40 41 1.884926 GCACCGAGAGCTGGTATGC 60.885 63.158 0.00 0.00 37.72 3.14
41 42 1.589993 CACCGAGAGCTGGTATGCG 60.590 63.158 0.00 0.00 37.72 4.73
42 43 2.052690 ACCGAGAGCTGGTATGCGT 61.053 57.895 0.00 0.00 38.15 5.24
43 44 1.299468 CCGAGAGCTGGTATGCGTC 60.299 63.158 0.00 0.00 38.13 5.19
44 45 1.655654 CGAGAGCTGGTATGCGTCG 60.656 63.158 0.00 0.00 37.71 5.12
45 46 1.728069 GAGAGCTGGTATGCGTCGA 59.272 57.895 0.00 0.00 38.13 4.20
46 47 0.312416 GAGAGCTGGTATGCGTCGAT 59.688 55.000 0.00 0.00 38.13 3.59
47 48 0.312416 AGAGCTGGTATGCGTCGATC 59.688 55.000 0.00 0.00 38.13 3.69
48 49 0.999228 GAGCTGGTATGCGTCGATCG 60.999 60.000 9.36 9.36 43.12 3.69
57 58 3.614659 CGTCGATCGCAGCAGCTG 61.615 66.667 18.93 18.93 39.10 4.24
81 82 0.376152 CAATCATGCGTGTCAGCCTC 59.624 55.000 5.68 0.00 36.02 4.70
244 253 2.072298 CCACGAAGAAGAAGGCAGAAG 58.928 52.381 0.00 0.00 0.00 2.85
245 254 2.072298 CACGAAGAAGAAGGCAGAAGG 58.928 52.381 0.00 0.00 0.00 3.46
246 255 1.082690 CGAAGAAGAAGGCAGAAGGC 58.917 55.000 0.00 0.00 43.74 4.35
296 305 1.148157 TGCTCTCTTCATTAGCGCGC 61.148 55.000 26.66 26.66 39.14 6.86
312 321 1.355971 GCGCGTCTTTTCCTACATGA 58.644 50.000 8.43 0.00 0.00 3.07
313 322 1.060698 GCGCGTCTTTTCCTACATGAC 59.939 52.381 8.43 0.00 0.00 3.06
315 324 1.659098 GCGTCTTTTCCTACATGACCG 59.341 52.381 0.00 0.00 0.00 4.79
350 359 1.070175 ACGCACGCAAACACTATCAAC 60.070 47.619 0.00 0.00 0.00 3.18
364 373 3.684788 ACTATCAACGTTCATCAACTGCC 59.315 43.478 0.00 0.00 0.00 4.85
367 376 2.226200 TCAACGTTCATCAACTGCCATG 59.774 45.455 0.00 0.00 0.00 3.66
377 386 3.765381 TCAACTGCCATGAAATCCTTGA 58.235 40.909 0.00 0.00 0.00 3.02
379 388 3.726557 ACTGCCATGAAATCCTTGAGA 57.273 42.857 0.00 0.00 0.00 3.27
390 399 5.885352 TGAAATCCTTGAGACTTGAAACACA 59.115 36.000 0.00 0.00 0.00 3.72
394 403 3.689161 CCTTGAGACTTGAAACACACACA 59.311 43.478 0.00 0.00 0.00 3.72
395 404 4.155826 CCTTGAGACTTGAAACACACACAA 59.844 41.667 0.00 0.00 0.00 3.33
396 405 5.335583 CCTTGAGACTTGAAACACACACAAA 60.336 40.000 0.00 0.00 0.00 2.83
398 407 4.517075 TGAGACTTGAAACACACACAAACA 59.483 37.500 0.00 0.00 0.00 2.83
400 409 4.277174 AGACTTGAAACACACACAAACACA 59.723 37.500 0.00 0.00 0.00 3.72
402 411 3.990318 TGAAACACACACAAACACACA 57.010 38.095 0.00 0.00 0.00 3.72
404 413 3.066760 TGAAACACACACAAACACACACA 59.933 39.130 0.00 0.00 0.00 3.72
406 415 1.950216 ACACACACAAACACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
408 417 1.950216 ACACACAAACACACACACACA 59.050 42.857 0.00 0.00 0.00 3.72
417 426 2.196749 CACACACACACACACTCTCTC 58.803 52.381 0.00 0.00 0.00 3.20
426 435 3.009723 CACACACTCTCTCTCTCTCTCC 58.990 54.545 0.00 0.00 0.00 3.71
439 598 2.632996 TCTCTCTCCCTCTCTCTCGATC 59.367 54.545 0.00 0.00 0.00 3.69
448 607 4.373527 CCTCTCTCTCGATCGAAACTCTA 58.626 47.826 19.92 2.67 0.00 2.43
449 608 4.994852 CCTCTCTCTCGATCGAAACTCTAT 59.005 45.833 19.92 0.00 0.00 1.98
450 609 5.468746 CCTCTCTCTCGATCGAAACTCTATT 59.531 44.000 19.92 0.00 0.00 1.73
451 610 6.017440 CCTCTCTCTCGATCGAAACTCTATTT 60.017 42.308 19.92 0.00 0.00 1.40
452 611 7.323049 TCTCTCTCGATCGAAACTCTATTTT 57.677 36.000 19.92 0.00 0.00 1.82
453 612 7.763356 TCTCTCTCGATCGAAACTCTATTTTT 58.237 34.615 19.92 0.00 0.00 1.94
473 632 5.407407 TTTTAACGAGGCAGAAGATCTCT 57.593 39.130 0.00 0.00 33.23 3.10
474 633 6.525578 TTTTAACGAGGCAGAAGATCTCTA 57.474 37.500 0.00 0.00 31.12 2.43
475 634 6.525578 TTTAACGAGGCAGAAGATCTCTAA 57.474 37.500 0.00 0.00 31.12 2.10
476 635 6.716934 TTAACGAGGCAGAAGATCTCTAAT 57.283 37.500 0.00 0.00 31.12 1.73
477 636 4.582701 ACGAGGCAGAAGATCTCTAATG 57.417 45.455 0.00 0.00 31.12 1.90
478 637 3.243704 ACGAGGCAGAAGATCTCTAATGC 60.244 47.826 0.00 4.33 37.04 3.56
479 638 3.005684 CGAGGCAGAAGATCTCTAATGCT 59.994 47.826 16.28 7.01 37.57 3.79
480 639 4.217334 CGAGGCAGAAGATCTCTAATGCTA 59.783 45.833 16.28 0.00 37.57 3.49
481 640 5.619757 CGAGGCAGAAGATCTCTAATGCTAG 60.620 48.000 16.28 0.00 37.57 3.42
482 641 5.147032 AGGCAGAAGATCTCTAATGCTAGT 58.853 41.667 16.28 4.59 37.57 2.57
483 642 5.243730 AGGCAGAAGATCTCTAATGCTAGTC 59.756 44.000 16.28 0.00 37.57 2.59
484 643 5.243730 GGCAGAAGATCTCTAATGCTAGTCT 59.756 44.000 16.28 2.02 37.57 3.24
485 644 6.381801 GCAGAAGATCTCTAATGCTAGTCTC 58.618 44.000 0.00 0.00 35.74 3.36
486 645 6.207417 GCAGAAGATCTCTAATGCTAGTCTCT 59.793 42.308 0.00 0.00 35.74 3.10
487 646 7.573843 GCAGAAGATCTCTAATGCTAGTCTCTC 60.574 44.444 0.00 0.00 35.74 3.20
488 647 7.663081 CAGAAGATCTCTAATGCTAGTCTCTCT 59.337 40.741 0.00 0.00 31.12 3.10
489 648 7.880195 AGAAGATCTCTAATGCTAGTCTCTCTC 59.120 40.741 0.00 0.00 30.22 3.20
490 649 6.166279 AGATCTCTAATGCTAGTCTCTCTCG 58.834 44.000 0.00 0.00 0.00 4.04
491 650 5.538849 TCTCTAATGCTAGTCTCTCTCGA 57.461 43.478 0.00 0.00 0.00 4.04
492 651 6.109156 TCTCTAATGCTAGTCTCTCTCGAT 57.891 41.667 0.00 0.00 0.00 3.59
493 652 6.163476 TCTCTAATGCTAGTCTCTCTCGATC 58.837 44.000 0.00 0.00 0.00 3.69
494 653 4.926832 TCTAATGCTAGTCTCTCTCGATCG 59.073 45.833 9.36 9.36 0.00 3.69
495 654 2.892784 TGCTAGTCTCTCTCGATCGA 57.107 50.000 18.32 18.32 0.00 3.59
496 655 3.180891 TGCTAGTCTCTCTCGATCGAA 57.819 47.619 19.92 9.28 0.00 3.71
497 656 3.532542 TGCTAGTCTCTCTCGATCGAAA 58.467 45.455 19.92 4.84 0.00 3.46
498 657 3.310227 TGCTAGTCTCTCTCGATCGAAAC 59.690 47.826 19.92 11.75 0.00 2.78
499 658 3.558418 GCTAGTCTCTCTCGATCGAAACT 59.442 47.826 19.92 17.47 0.00 2.66
500 659 4.318546 GCTAGTCTCTCTCGATCGAAACTC 60.319 50.000 19.92 7.75 0.00 3.01
501 660 3.869065 AGTCTCTCTCGATCGAAACTCT 58.131 45.455 19.92 9.79 0.00 3.24
502 661 5.013568 AGTCTCTCTCGATCGAAACTCTA 57.986 43.478 19.92 0.51 0.00 2.43
548 710 7.890515 TCTCTAATGCTAGTAGATCCATGTTG 58.109 38.462 0.00 0.00 0.00 3.33
684 846 4.723879 GCGATATGCTTTCCTCTTTCTC 57.276 45.455 0.00 0.00 41.73 2.87
685 847 4.376146 GCGATATGCTTTCCTCTTTCTCT 58.624 43.478 0.00 0.00 41.73 3.10
686 848 4.813697 GCGATATGCTTTCCTCTTTCTCTT 59.186 41.667 0.00 0.00 41.73 2.85
687 849 5.295540 GCGATATGCTTTCCTCTTTCTCTTT 59.704 40.000 0.00 0.00 41.73 2.52
717 879 7.713734 ATTGACTAACTACCTTGCTACTACA 57.286 36.000 0.00 0.00 0.00 2.74
790 952 7.950124 TCAATATTCCCAGGAAATTAGGATTCC 59.050 37.037 2.65 0.00 45.50 3.01
822 984 4.468765 TCCTCTGCTTCTCTCATGAAAG 57.531 45.455 0.00 0.00 0.00 2.62
842 1004 7.995289 TGAAAGAAAACTACTGCAAGATTCAA 58.005 30.769 9.64 0.00 37.43 2.69
865 1027 4.098914 TCAGGCCAAAGCTCTCTTAAAA 57.901 40.909 5.01 0.00 39.73 1.52
899 1064 9.358406 TCTGTCCTTTATGTCTATATAAACGGA 57.642 33.333 0.00 0.00 33.03 4.69
910 1080 9.407380 TGTCTATATAAACGGAACCAGTAAGTA 57.593 33.333 0.00 0.00 0.00 2.24
1003 1173 7.693951 CGCAAGATACTTTTTACTTTCAGATGG 59.306 37.037 0.00 0.00 43.02 3.51
1100 1270 2.127708 AGGTTAATTGCCCCGAGATCT 58.872 47.619 0.00 0.00 0.00 2.75
1118 1288 6.192234 AGATCTCAAATTGTGCATCAACTC 57.808 37.500 0.00 0.00 38.97 3.01
1119 1289 5.708697 AGATCTCAAATTGTGCATCAACTCA 59.291 36.000 0.00 0.00 38.97 3.41
1120 1290 5.112220 TCTCAAATTGTGCATCAACTCAC 57.888 39.130 0.00 0.00 38.97 3.51
1144 1350 5.604758 TCTTGATCCATGGACTAGACAAG 57.395 43.478 18.99 23.16 36.06 3.16
1145 1351 5.026121 TCTTGATCCATGGACTAGACAAGT 58.974 41.667 27.06 11.12 42.80 3.16
1146 1352 4.743057 TGATCCATGGACTAGACAAGTG 57.257 45.455 18.99 0.00 39.07 3.16
1147 1353 4.352893 TGATCCATGGACTAGACAAGTGA 58.647 43.478 18.99 0.00 39.07 3.41
1148 1354 4.160439 TGATCCATGGACTAGACAAGTGAC 59.840 45.833 18.99 0.00 39.07 3.67
1149 1355 3.506398 TCCATGGACTAGACAAGTGACA 58.494 45.455 11.44 0.00 39.07 3.58
1150 1356 3.901222 TCCATGGACTAGACAAGTGACAA 59.099 43.478 11.44 0.00 39.07 3.18
1232 1438 0.753262 AGAAGAGCAACACGGTGACT 59.247 50.000 16.29 8.86 0.00 3.41
1319 1525 4.164252 GACGTACAAGTCGCCAGG 57.836 61.111 0.00 0.00 0.00 4.45
1340 1546 0.698818 GGAACCAGATGAACCCCAGT 59.301 55.000 0.00 0.00 0.00 4.00
1444 1656 2.671619 GCCCCAAGCGCACAGTTA 60.672 61.111 11.47 0.00 0.00 2.24
1445 1657 2.978018 GCCCCAAGCGCACAGTTAC 61.978 63.158 11.47 0.00 0.00 2.50
1446 1658 2.677003 CCCCAAGCGCACAGTTACG 61.677 63.158 11.47 0.00 0.00 3.18
1447 1659 2.677003 CCCAAGCGCACAGTTACGG 61.677 63.158 11.47 0.00 0.00 4.02
1448 1660 2.173382 CAAGCGCACAGTTACGGC 59.827 61.111 11.47 0.00 0.00 5.68
1490 1702 0.036388 ACGTCAAGTTCGGCATGGAT 60.036 50.000 0.00 0.00 0.00 3.41
1637 1855 2.112297 GACCAAGGCCACGGACAA 59.888 61.111 16.90 0.00 0.00 3.18
1643 1861 1.779061 AAGGCCACGGACAAGGACAT 61.779 55.000 5.01 0.00 34.45 3.06
1661 1879 0.034186 ATGGACATGGACACGGCAAT 60.034 50.000 0.00 0.00 0.00 3.56
2017 2235 4.864334 GCCTAGCGCTGGGTGCAT 62.864 66.667 36.25 4.03 42.00 3.96
2042 2260 0.858583 TGTGATGAACTGAACACGCG 59.141 50.000 3.53 3.53 36.25 6.01
2074 2292 4.293415 CACATCAAAACCTTGCTCACTTC 58.707 43.478 0.00 0.00 32.14 3.01
2111 2337 1.003972 CACGTTGGTGTGTGTGATGTC 60.004 52.381 0.00 0.00 39.38 3.06
2171 2400 8.221965 TGTGTATACCACTACTCTGTAATCTG 57.778 38.462 0.00 0.00 44.81 2.90
2178 2453 5.533154 CCACTACTCTGTAATCTGTCCCTAG 59.467 48.000 0.00 0.00 0.00 3.02
2230 2505 7.387643 AGTCTGTAATCTTCCCTTAACTTGTC 58.612 38.462 0.00 0.00 0.00 3.18
2269 2544 9.851267 ATAATCCTAAATCTGTAATCTCCCTCT 57.149 33.333 0.00 0.00 0.00 3.69
2270 2545 6.985653 TCCTAAATCTGTAATCTCCCTCTG 57.014 41.667 0.00 0.00 0.00 3.35
2271 2546 6.683537 TCCTAAATCTGTAATCTCCCTCTGA 58.316 40.000 0.00 0.00 0.00 3.27
2272 2547 6.551601 TCCTAAATCTGTAATCTCCCTCTGAC 59.448 42.308 0.00 0.00 0.00 3.51
2273 2548 6.553100 CCTAAATCTGTAATCTCCCTCTGACT 59.447 42.308 0.00 0.00 0.00 3.41
2274 2549 6.882768 AAATCTGTAATCTCCCTCTGACTT 57.117 37.500 0.00 0.00 0.00 3.01
2275 2550 5.867903 ATCTGTAATCTCCCTCTGACTTG 57.132 43.478 0.00 0.00 0.00 3.16
2276 2551 4.678256 TCTGTAATCTCCCTCTGACTTGT 58.322 43.478 0.00 0.00 0.00 3.16
2277 2552 5.087323 TCTGTAATCTCCCTCTGACTTGTT 58.913 41.667 0.00 0.00 0.00 2.83
2278 2553 5.047021 TCTGTAATCTCCCTCTGACTTGTTG 60.047 44.000 0.00 0.00 0.00 3.33
2279 2554 4.593206 TGTAATCTCCCTCTGACTTGTTGT 59.407 41.667 0.00 0.00 0.00 3.32
2280 2555 5.778241 TGTAATCTCCCTCTGACTTGTTGTA 59.222 40.000 0.00 0.00 0.00 2.41
2281 2556 5.825593 AATCTCCCTCTGACTTGTTGTAA 57.174 39.130 0.00 0.00 0.00 2.41
2282 2557 4.602340 TCTCCCTCTGACTTGTTGTAAC 57.398 45.455 0.00 0.00 0.00 2.50
2283 2558 3.964688 TCTCCCTCTGACTTGTTGTAACA 59.035 43.478 0.00 0.00 37.08 2.41
2284 2559 4.593206 TCTCCCTCTGACTTGTTGTAACAT 59.407 41.667 0.00 0.00 38.95 2.71
2285 2560 4.894784 TCCCTCTGACTTGTTGTAACATC 58.105 43.478 0.00 0.00 38.95 3.06
2286 2561 4.003648 CCCTCTGACTTGTTGTAACATCC 58.996 47.826 0.00 0.00 38.95 3.51
2287 2562 4.263068 CCCTCTGACTTGTTGTAACATCCT 60.263 45.833 0.00 0.00 38.95 3.24
2288 2563 5.046591 CCCTCTGACTTGTTGTAACATCCTA 60.047 44.000 0.00 0.00 38.95 2.94
2289 2564 6.352222 CCCTCTGACTTGTTGTAACATCCTAT 60.352 42.308 0.00 0.00 38.95 2.57
2290 2565 7.147724 CCCTCTGACTTGTTGTAACATCCTATA 60.148 40.741 0.00 0.00 38.95 1.31
2291 2566 8.424918 CCTCTGACTTGTTGTAACATCCTATAT 58.575 37.037 0.00 0.00 38.95 0.86
2317 2592 1.172812 GCACTATCAAATCCGCCCCC 61.173 60.000 0.00 0.00 0.00 5.40
2318 2593 0.182537 CACTATCAAATCCGCCCCCA 59.817 55.000 0.00 0.00 0.00 4.96
2323 2598 4.726825 ACTATCAAATCCGCCCCCATATAT 59.273 41.667 0.00 0.00 0.00 0.86
2324 2599 3.364460 TCAAATCCGCCCCCATATATG 57.636 47.619 5.68 5.68 0.00 1.78
2327 2602 0.830648 ATCCGCCCCCATATATGTCG 59.169 55.000 11.73 8.85 0.00 4.35
2468 2743 6.148976 GCTATGCTCATCTGATGCATAAAAGA 59.851 38.462 17.92 3.78 45.28 2.52
2470 2745 6.954487 TGCTCATCTGATGCATAAAAGAAT 57.046 33.333 12.78 0.00 0.00 2.40
2500 2775 0.178998 GCTCATCTCATGCACCCCAT 60.179 55.000 0.00 0.00 33.39 4.00
2515 2791 1.922057 CCATACAGGGTGCATGGGA 59.078 57.895 0.00 0.00 37.58 4.37
2897 3373 9.813080 TTTTTGTTTACATTTTCAAAAAGGTCG 57.187 25.926 8.60 0.00 41.38 4.79
2918 3394 8.531146 AGGTCGGAATTTCAAATATGTTCAAAT 58.469 29.630 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 3.614659 CAGCTGCTGCGATCGACG 61.615 66.667 21.57 9.58 45.42 5.12
244 253 0.175989 CTCCGAGGTTAGGTTCTGCC 59.824 60.000 0.00 0.00 37.58 4.85
245 254 0.175989 CCTCCGAGGTTAGGTTCTGC 59.824 60.000 6.24 0.00 0.00 4.26
296 305 2.094390 TCCGGTCATGTAGGAAAAGACG 60.094 50.000 0.00 0.00 0.00 4.18
328 337 1.989864 TGATAGTGTTTGCGTGCGTAG 59.010 47.619 0.00 0.00 0.00 3.51
350 359 3.557577 TTTCATGGCAGTTGATGAACG 57.442 42.857 0.18 0.00 38.11 3.95
364 373 6.860023 GTGTTTCAAGTCTCAAGGATTTCATG 59.140 38.462 0.00 0.00 0.00 3.07
367 376 6.183360 TGTGTGTTTCAAGTCTCAAGGATTTC 60.183 38.462 0.00 0.00 0.00 2.17
377 386 4.277174 TGTGTTTGTGTGTGTTTCAAGTCT 59.723 37.500 0.00 0.00 0.00 3.24
379 388 4.202060 TGTGTGTTTGTGTGTGTTTCAAGT 60.202 37.500 0.00 0.00 0.00 3.16
390 399 1.950216 TGTGTGTGTGTGTGTTTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
394 403 2.742053 GAGAGTGTGTGTGTGTGTGTTT 59.258 45.455 0.00 0.00 0.00 2.83
395 404 2.028112 AGAGAGTGTGTGTGTGTGTGTT 60.028 45.455 0.00 0.00 0.00 3.32
396 405 1.550524 AGAGAGTGTGTGTGTGTGTGT 59.449 47.619 0.00 0.00 0.00 3.72
398 407 2.099921 GAGAGAGAGTGTGTGTGTGTGT 59.900 50.000 0.00 0.00 0.00 3.72
400 409 2.621055 GAGAGAGAGAGTGTGTGTGTGT 59.379 50.000 0.00 0.00 0.00 3.72
402 411 3.146066 GAGAGAGAGAGAGTGTGTGTGT 58.854 50.000 0.00 0.00 0.00 3.72
404 413 3.559171 GGAGAGAGAGAGAGAGTGTGTGT 60.559 52.174 0.00 0.00 0.00 3.72
406 415 2.026262 GGGAGAGAGAGAGAGAGTGTGT 60.026 54.545 0.00 0.00 0.00 3.72
408 417 2.505819 GAGGGAGAGAGAGAGAGAGTGT 59.494 54.545 0.00 0.00 0.00 3.55
417 426 2.039418 TCGAGAGAGAGGGAGAGAGAG 58.961 57.143 0.00 0.00 34.84 3.20
450 609 5.794894 AGAGATCTTCTGCCTCGTTAAAAA 58.205 37.500 0.00 0.00 33.93 1.94
451 610 5.407407 AGAGATCTTCTGCCTCGTTAAAA 57.593 39.130 0.00 0.00 33.93 1.52
452 611 6.525578 TTAGAGATCTTCTGCCTCGTTAAA 57.474 37.500 0.00 0.00 36.61 1.52
453 612 6.507900 CATTAGAGATCTTCTGCCTCGTTAA 58.492 40.000 0.00 0.00 36.61 2.01
454 613 5.508153 GCATTAGAGATCTTCTGCCTCGTTA 60.508 44.000 0.00 0.00 36.61 3.18
455 614 4.739137 GCATTAGAGATCTTCTGCCTCGTT 60.739 45.833 0.00 0.00 36.61 3.85
456 615 3.243704 GCATTAGAGATCTTCTGCCTCGT 60.244 47.826 0.00 0.00 36.61 4.18
457 616 3.005684 AGCATTAGAGATCTTCTGCCTCG 59.994 47.826 13.04 0.00 36.61 4.63
458 617 4.605640 AGCATTAGAGATCTTCTGCCTC 57.394 45.455 13.04 0.00 36.61 4.70
459 618 5.147032 ACTAGCATTAGAGATCTTCTGCCT 58.853 41.667 13.04 2.14 36.61 4.75
460 619 5.243730 AGACTAGCATTAGAGATCTTCTGCC 59.756 44.000 13.04 0.00 36.61 4.85
461 620 6.207417 AGAGACTAGCATTAGAGATCTTCTGC 59.793 42.308 0.00 4.26 36.61 4.26
462 621 7.663081 AGAGAGACTAGCATTAGAGATCTTCTG 59.337 40.741 0.00 0.00 36.61 3.02
463 622 7.749666 AGAGAGACTAGCATTAGAGATCTTCT 58.250 38.462 0.00 0.00 40.06 2.85
464 623 7.148573 CGAGAGAGACTAGCATTAGAGATCTTC 60.149 44.444 0.00 0.00 0.00 2.87
465 624 6.650807 CGAGAGAGACTAGCATTAGAGATCTT 59.349 42.308 0.00 0.00 0.00 2.40
466 625 6.014584 TCGAGAGAGACTAGCATTAGAGATCT 60.015 42.308 0.00 0.00 34.84 2.75
467 626 6.163476 TCGAGAGAGACTAGCATTAGAGATC 58.837 44.000 0.00 0.00 34.84 2.75
468 627 6.109156 TCGAGAGAGACTAGCATTAGAGAT 57.891 41.667 0.00 0.00 34.84 2.75
469 628 5.538849 TCGAGAGAGACTAGCATTAGAGA 57.461 43.478 0.00 0.00 34.84 3.10
548 710 7.276658 CACCAAAAGTACTGTACTGATCATCTC 59.723 40.741 20.34 0.00 39.39 2.75
717 879 4.338682 CCGGATCAACAACTACTAGCTACT 59.661 45.833 0.00 0.00 0.00 2.57
790 952 2.886862 AGCAGAGGATGAGTGAATCG 57.113 50.000 0.00 0.00 0.00 3.34
822 984 7.540055 CCTGAATTGAATCTTGCAGTAGTTTTC 59.460 37.037 0.00 0.00 0.00 2.29
842 1004 2.895242 AAGAGAGCTTTGGCCTGAAT 57.105 45.000 3.32 0.00 39.73 2.57
896 1061 5.981174 TCCCTAAAATACTTACTGGTTCCG 58.019 41.667 0.00 0.00 0.00 4.30
897 1062 7.832685 ACATTCCCTAAAATACTTACTGGTTCC 59.167 37.037 0.00 0.00 0.00 3.62
986 1156 5.356882 TGTCGCCATCTGAAAGTAAAAAG 57.643 39.130 0.00 0.00 33.76 2.27
1003 1173 2.470628 CGACTCTCATGATGATTGTCGC 59.529 50.000 25.32 6.87 41.28 5.19
1100 1270 5.300034 AGAAGTGAGTTGATGCACAATTTGA 59.700 36.000 2.79 0.00 40.76 2.69
1118 1288 5.105187 TGTCTAGTCCATGGATCAAGAAGTG 60.105 44.000 19.62 1.66 0.00 3.16
1119 1289 5.026121 TGTCTAGTCCATGGATCAAGAAGT 58.974 41.667 19.62 0.00 0.00 3.01
1120 1290 5.604758 TGTCTAGTCCATGGATCAAGAAG 57.395 43.478 19.62 9.31 0.00 2.85
1145 1351 7.095229 GCATACAGAAACATAAGTGAGTTGTCA 60.095 37.037 0.00 0.00 0.00 3.58
1146 1352 7.095229 TGCATACAGAAACATAAGTGAGTTGTC 60.095 37.037 0.00 0.00 0.00 3.18
1147 1353 6.710295 TGCATACAGAAACATAAGTGAGTTGT 59.290 34.615 0.00 0.00 0.00 3.32
1148 1354 7.132694 TGCATACAGAAACATAAGTGAGTTG 57.867 36.000 0.00 0.00 0.00 3.16
1149 1355 7.607607 TGATGCATACAGAAACATAAGTGAGTT 59.392 33.333 0.00 0.00 0.00 3.01
1150 1356 7.105588 TGATGCATACAGAAACATAAGTGAGT 58.894 34.615 0.00 0.00 0.00 3.41
1232 1438 2.599281 TCGAAGGAGCCGGACACA 60.599 61.111 5.05 0.00 0.00 3.72
1427 1639 2.671619 TAACTGTGCGCTTGGGGC 60.672 61.111 9.73 0.00 41.94 5.80
1428 1640 2.677003 CGTAACTGTGCGCTTGGGG 61.677 63.158 9.73 0.00 0.00 4.96
1429 1641 2.677003 CCGTAACTGTGCGCTTGGG 61.677 63.158 9.73 0.00 0.00 4.12
1430 1642 2.860293 CCGTAACTGTGCGCTTGG 59.140 61.111 9.73 0.20 0.00 3.61
1431 1643 2.173382 GCCGTAACTGTGCGCTTG 59.827 61.111 9.73 0.58 0.00 4.01
1432 1644 3.411351 CGCCGTAACTGTGCGCTT 61.411 61.111 9.73 0.00 41.95 4.68
1436 1648 3.308878 CTTGCCGCCGTAACTGTGC 62.309 63.158 0.00 0.00 0.00 4.57
1437 1649 2.860293 CTTGCCGCCGTAACTGTG 59.140 61.111 0.00 0.00 0.00 3.66
1438 1650 3.047877 GCTTGCCGCCGTAACTGT 61.048 61.111 0.00 0.00 0.00 3.55
1447 1659 4.760047 TCTTCTCCGGCTTGCCGC 62.760 66.667 26.48 0.00 38.13 6.53
1448 1660 2.815647 GTCTTCTCCGGCTTGCCG 60.816 66.667 25.17 25.17 0.00 5.69
1556 1774 0.532862 ACTGGACGTGCTTGGTCTTG 60.533 55.000 8.99 0.00 34.82 3.02
1613 1831 3.164977 TGGCCTTGGTCGTGGTGA 61.165 61.111 3.32 0.00 0.00 4.02
1637 1855 0.250234 CGTGTCCATGTCCATGTCCT 59.750 55.000 6.53 0.00 37.11 3.85
1643 1861 0.959867 CATTGCCGTGTCCATGTCCA 60.960 55.000 0.00 0.00 0.00 4.02
1673 1891 2.289882 GGTAGTTACCACCTTCGGCTTT 60.290 50.000 3.45 0.00 45.73 3.51
2017 2235 3.740832 GTGTTCAGTTCATCACATGACGA 59.259 43.478 0.00 0.00 39.39 4.20
2042 2260 2.456594 TTTTGATGTGCGCTCCGTGC 62.457 55.000 9.73 0.00 39.75 5.34
2111 2337 4.149617 CGTATCTACTCGCCTATCGTTTG 58.850 47.826 0.00 0.00 39.67 2.93
2206 2481 6.310711 CGACAAGTTAAGGGAAGATTACAGAC 59.689 42.308 0.00 0.00 0.00 3.51
2252 2527 5.723887 ACAAGTCAGAGGGAGATTACAGATT 59.276 40.000 0.00 0.00 0.00 2.40
2253 2528 5.276440 ACAAGTCAGAGGGAGATTACAGAT 58.724 41.667 0.00 0.00 0.00 2.90
2264 2539 4.003648 GGATGTTACAACAAGTCAGAGGG 58.996 47.826 0.00 0.00 43.03 4.30
2273 2548 8.995220 GCGGAATTATATAGGATGTTACAACAA 58.005 33.333 0.00 0.00 43.03 2.83
2274 2549 8.151596 TGCGGAATTATATAGGATGTTACAACA 58.848 33.333 0.00 0.00 44.06 3.33
2275 2550 8.440833 GTGCGGAATTATATAGGATGTTACAAC 58.559 37.037 0.00 0.00 0.00 3.32
2276 2551 8.372459 AGTGCGGAATTATATAGGATGTTACAA 58.628 33.333 0.00 0.00 0.00 2.41
2277 2552 7.903145 AGTGCGGAATTATATAGGATGTTACA 58.097 34.615 0.00 0.00 0.00 2.41
2280 2555 8.758829 TGATAGTGCGGAATTATATAGGATGTT 58.241 33.333 0.00 0.00 0.00 2.71
2281 2556 8.306313 TGATAGTGCGGAATTATATAGGATGT 57.694 34.615 0.00 0.00 0.00 3.06
2282 2557 9.599866 TTTGATAGTGCGGAATTATATAGGATG 57.400 33.333 0.00 0.00 0.00 3.51
2284 2559 9.817809 GATTTGATAGTGCGGAATTATATAGGA 57.182 33.333 0.00 0.00 0.00 2.94
2285 2560 9.046296 GGATTTGATAGTGCGGAATTATATAGG 57.954 37.037 0.00 0.00 0.00 2.57
2286 2561 8.755941 CGGATTTGATAGTGCGGAATTATATAG 58.244 37.037 0.00 0.00 0.00 1.31
2287 2562 7.223971 GCGGATTTGATAGTGCGGAATTATATA 59.776 37.037 0.00 0.00 0.00 0.86
2288 2563 6.037172 GCGGATTTGATAGTGCGGAATTATAT 59.963 38.462 0.00 0.00 0.00 0.86
2289 2564 5.350365 GCGGATTTGATAGTGCGGAATTATA 59.650 40.000 0.00 0.00 0.00 0.98
2290 2565 4.154195 GCGGATTTGATAGTGCGGAATTAT 59.846 41.667 0.00 0.00 0.00 1.28
2291 2566 3.496884 GCGGATTTGATAGTGCGGAATTA 59.503 43.478 0.00 0.00 0.00 1.40
2292 2567 2.290641 GCGGATTTGATAGTGCGGAATT 59.709 45.455 0.00 0.00 0.00 2.17
2293 2568 1.873591 GCGGATTTGATAGTGCGGAAT 59.126 47.619 0.00 0.00 0.00 3.01
2294 2569 1.295792 GCGGATTTGATAGTGCGGAA 58.704 50.000 0.00 0.00 0.00 4.30
2295 2570 0.531974 GGCGGATTTGATAGTGCGGA 60.532 55.000 0.00 0.00 0.00 5.54
2296 2571 1.507141 GGGCGGATTTGATAGTGCGG 61.507 60.000 0.00 0.00 0.00 5.69
2304 2579 2.647299 ACATATATGGGGGCGGATTTGA 59.353 45.455 16.96 0.00 0.00 2.69
2317 2592 2.254459 GCGAGTCTGCCGACATATATG 58.746 52.381 11.29 11.29 42.73 1.78
2318 2593 1.202582 GGCGAGTCTGCCGACATATAT 59.797 52.381 11.07 0.00 46.75 0.86
2338 2613 2.573609 CTTAAGGACTGCCCGGTCGG 62.574 65.000 0.00 1.86 40.87 4.79
2468 2743 3.201487 TGAGATGAGCATGGTTGAGGATT 59.799 43.478 0.00 0.00 0.00 3.01
2470 2745 2.190538 TGAGATGAGCATGGTTGAGGA 58.809 47.619 0.00 0.00 0.00 3.71
2500 2775 1.990424 CTGTCCCATGCACCCTGTA 59.010 57.895 0.00 0.00 0.00 2.74
2523 2799 2.524394 ACGAGTGTGAGGGCCAGT 60.524 61.111 6.18 0.00 0.00 4.00
2532 2808 1.006102 GTGGGTGAGGACGAGTGTG 60.006 63.158 0.00 0.00 0.00 3.82
2535 2811 0.697079 TCTAGTGGGTGAGGACGAGT 59.303 55.000 0.00 0.00 0.00 4.18
2761 3148 9.762933 TCTTTTGAAATTCCGATTTTTCTGAAT 57.237 25.926 0.00 0.00 35.65 2.57
2871 3347 9.813080 CGACCTTTTTGAAAATGTAAACAAAAA 57.187 25.926 0.00 0.00 44.29 1.94
2872 3348 8.443937 CCGACCTTTTTGAAAATGTAAACAAAA 58.556 29.630 0.00 0.00 39.38 2.44
2873 3349 7.817962 TCCGACCTTTTTGAAAATGTAAACAAA 59.182 29.630 0.00 0.00 28.93 2.83
2874 3350 7.321153 TCCGACCTTTTTGAAAATGTAAACAA 58.679 30.769 0.00 0.00 28.93 2.83
2875 3351 6.864342 TCCGACCTTTTTGAAAATGTAAACA 58.136 32.000 0.00 0.00 28.93 2.83
2881 3357 7.475771 TGAAATTCCGACCTTTTTGAAAATG 57.524 32.000 0.00 0.00 0.00 2.32
2893 3369 8.702163 ATTTGAACATATTTGAAATTCCGACC 57.298 30.769 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.