Multiple sequence alignment - TraesCS4A01G404100

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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 TraesCS4A01G404100 chr4A 100.000 2751 0 0 432 3182 677959092 677956342 0.000000e+00 5081.0
1 TraesCS4A01G404100 chr4A 90.745 1329 105 12 864 2186 677989004 677987688 0.000000e+00 1757.0
2 TraesCS4A01G404100 chr4A 90.143 1329 110 12 864 2182 677969653 677968336 0.000000e+00 1709.0
3 TraesCS4A01G404100 chr4A 100.000 113 0 0 1 113 677959523 677959411 3.220000e-50 209.0
4 TraesCS4A01G404100 chr4A 91.566 83 6 1 729 810 677989103 677989021 2.590000e-21 113.0
5 TraesCS4A01G404100 chr4A 91.549 71 3 3 2371 2439 331629607 331629538 9.400000e-16 95.3
6 TraesCS4A01G404100 chr4D 95.517 1740 53 13 618 2342 470122235 470120506 0.000000e+00 2758.0
7 TraesCS4A01G404100 chr4D 90.634 1324 108 8 864 2182 470138498 470137186 0.000000e+00 1744.0
8 TraesCS4A01G404100 chr4D 94.730 759 18 11 2438 3182 470120517 470119767 0.000000e+00 1160.0
9 TraesCS4A01G404100 chr4D 91.429 105 9 0 432 536 470122338 470122234 9.200000e-31 145.0
10 TraesCS4A01G404100 chr4D 92.941 85 6 0 28 112 470122701 470122617 1.200000e-24 124.0
11 TraesCS4A01G404100 chr4D 83.803 142 12 6 656 793 470130624 470130490 1.200000e-24 124.0
12 TraesCS4A01G404100 chr4D 90.411 73 5 1 2373 2443 4643586 4643514 9.400000e-16 95.3
13 TraesCS4A01G404100 chr4B 92.063 1726 91 24 640 2341 591909728 591908025 0.000000e+00 2386.0
14 TraesCS4A01G404100 chr4B 91.804 1513 85 18 757 2257 591539901 591538416 0.000000e+00 2071.0
15 TraesCS4A01G404100 chr4B 90.971 1329 102 10 864 2186 592079737 592078421 0.000000e+00 1773.0
16 TraesCS4A01G404100 chr4B 90.634 1324 99 12 867 2186 592188170 592186868 0.000000e+00 1735.0
17 TraesCS4A01G404100 chr4B 91.224 1242 97 5 943 2182 591955113 591953882 0.000000e+00 1679.0
18 TraesCS4A01G404100 chr4B 87.662 308 13 12 2893 3182 591907630 591907330 5.090000e-88 335.0
19 TraesCS4A01G404100 chr4B 89.062 192 18 2 2567 2756 591537954 591538144 5.310000e-58 235.0
20 TraesCS4A01G404100 chr4B 86.010 193 13 7 2996 3182 591537645 591537461 9.010000e-46 195.0
21 TraesCS4A01G404100 chr4B 94.017 117 7 0 2451 2567 591907673 591907789 9.070000e-41 178.0
22 TraesCS4A01G404100 chr4B 87.619 105 10 3 520 622 399783261 399783158 5.580000e-23 119.0
23 TraesCS4A01G404100 chr4B 87.629 97 5 1 2471 2567 591537821 591537910 4.340000e-19 106.0
24 TraesCS4A01G404100 chr4B 83.621 116 12 4 1 109 591911259 591911144 5.620000e-18 102.0
25 TraesCS4A01G404100 chr6D 93.023 86 6 0 534 619 427966112 427966197 3.330000e-25 126.0
26 TraesCS4A01G404100 chr3B 86.441 118 12 4 533 648 132527297 132527412 3.330000e-25 126.0
27 TraesCS4A01G404100 chrUn 89.796 98 9 1 525 622 135090811 135090715 1.200000e-24 124.0
28 TraesCS4A01G404100 chrUn 89.796 98 9 1 525 622 152687667 152687571 1.200000e-24 124.0
29 TraesCS4A01G404100 chr7B 92.045 88 7 0 535 622 611720339 611720252 1.200000e-24 124.0
30 TraesCS4A01G404100 chr7D 87.619 105 11 2 535 637 15083935 15083831 1.550000e-23 121.0
31 TraesCS4A01G404100 chr5D 90.323 93 8 1 528 620 504792925 504793016 1.550000e-23 121.0
32 TraesCS4A01G404100 chr5D 87.356 87 6 4 2352 2436 482340270 482340353 9.400000e-16 95.3
33 TraesCS4A01G404100 chr1B 89.362 94 10 0 535 628 396228200 396228107 5.580000e-23 119.0
34 TraesCS4A01G404100 chr5B 88.889 90 8 2 2350 2438 107390081 107390169 3.360000e-20 110.0
35 TraesCS4A01G404100 chr2D 88.372 86 8 2 2350 2434 579607246 579607162 5.620000e-18 102.0
36 TraesCS4A01G404100 chr2D 88.235 85 6 4 2352 2434 481697113 481697195 7.260000e-17 99.0
37 TraesCS4A01G404100 chr2D 87.692 65 6 2 2783 2847 37948843 37948781 1.220000e-09 75.0
38 TraesCS4A01G404100 chr2A 89.474 76 8 0 2368 2443 12299109 12299184 2.610000e-16 97.1
39 TraesCS4A01G404100 chr3D 88.608 79 4 4 2362 2438 597935113 597935038 1.220000e-14 91.6
40 TraesCS4A01G404100 chr3D 85.556 90 6 6 2355 2441 18699453 18699538 1.570000e-13 87.9


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 TraesCS4A01G404100 chr4A 677956342 677959523 3181 True 2645.00 5081 100.00000 1 3182 2 chr4A.!!$R3 3181
1 TraesCS4A01G404100 chr4A 677968336 677969653 1317 True 1709.00 1709 90.14300 864 2182 1 chr4A.!!$R2 1318
2 TraesCS4A01G404100 chr4A 677987688 677989103 1415 True 935.00 1757 91.15550 729 2186 2 chr4A.!!$R4 1457
3 TraesCS4A01G404100 chr4D 470137186 470138498 1312 True 1744.00 1744 90.63400 864 2182 1 chr4D.!!$R3 1318
4 TraesCS4A01G404100 chr4D 470119767 470122701 2934 True 1046.75 2758 93.65425 28 3182 4 chr4D.!!$R4 3154
5 TraesCS4A01G404100 chr4B 592078421 592079737 1316 True 1773.00 1773 90.97100 864 2186 1 chr4B.!!$R3 1322
6 TraesCS4A01G404100 chr4B 592186868 592188170 1302 True 1735.00 1735 90.63400 867 2186 1 chr4B.!!$R4 1319
7 TraesCS4A01G404100 chr4B 591953882 591955113 1231 True 1679.00 1679 91.22400 943 2182 1 chr4B.!!$R2 1239
8 TraesCS4A01G404100 chr4B 591537461 591539901 2440 True 1133.00 2071 88.90700 757 3182 2 chr4B.!!$R5 2425
9 TraesCS4A01G404100 chr4B 591907330 591911259 3929 True 941.00 2386 87.78200 1 3182 3 chr4B.!!$R6 3181

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
517 854 0.249489 ATAGCCTAACTCTTGCGCCG 60.249 55.0 4.18 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2359 3733 0.036164 AGGCAGCATACACGAAACCA 59.964 50.0 0.0 0.0 0.0 3.67 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
25 26 2.750637 GCCCTCGTCTCGGACTCA 60.751 66.667 3.15 0.00 0.00 3.41
32 33 1.154188 GTCTCGGACTCAGTCGTGC 60.154 63.158 0.00 0.00 32.65 5.34
50 58 2.445438 CCGCGTCGCCTTCTTCTTC 61.445 63.158 12.44 0.00 0.00 2.87
109 117 3.072944 GGACATGCTCCTTATCATCTGC 58.927 50.000 0.00 0.00 35.89 4.26
112 120 1.510492 TGCTCCTTATCATCTGCCCA 58.490 50.000 0.00 0.00 0.00 5.36
477 814 1.651240 CCTGGAAGCTTCATGCCACG 61.651 60.000 27.02 7.53 44.23 4.94
478 815 1.651240 CTGGAAGCTTCATGCCACGG 61.651 60.000 27.02 10.29 44.23 4.94
479 816 2.486966 GAAGCTTCATGCCACGGC 59.513 61.111 21.67 0.00 44.23 5.68
517 854 0.249489 ATAGCCTAACTCTTGCGCCG 60.249 55.000 4.18 0.00 0.00 6.46
523 860 1.517276 CTAACTCTTGCGCCGTTATCG 59.483 52.381 4.18 0.00 0.00 2.92
547 1705 3.118371 ACAAATGAATACTCCCTCCGTCC 60.118 47.826 0.00 0.00 0.00 4.79
548 1706 1.718280 ATGAATACTCCCTCCGTCCC 58.282 55.000 0.00 0.00 0.00 4.46
549 1707 0.337082 TGAATACTCCCTCCGTCCCA 59.663 55.000 0.00 0.00 0.00 4.37
550 1708 1.062428 TGAATACTCCCTCCGTCCCAT 60.062 52.381 0.00 0.00 0.00 4.00
551 1709 2.178325 TGAATACTCCCTCCGTCCCATA 59.822 50.000 0.00 0.00 0.00 2.74
552 1710 3.236896 GAATACTCCCTCCGTCCCATAA 58.763 50.000 0.00 0.00 0.00 1.90
553 1711 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
554 1712 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
555 1713 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
556 1714 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
557 1715 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
558 1716 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
559 1717 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
560 1718 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
562 1720 2.132762 CCGTCCCATAATGTAAGACGC 58.867 52.381 5.39 0.00 46.66 5.19
563 1721 2.223971 CCGTCCCATAATGTAAGACGCT 60.224 50.000 5.39 0.00 46.66 5.07
564 1722 3.454375 CGTCCCATAATGTAAGACGCTT 58.546 45.455 0.00 0.00 43.07 4.68
565 1723 3.869246 CGTCCCATAATGTAAGACGCTTT 59.131 43.478 0.00 0.00 43.07 3.51
566 1724 4.331717 CGTCCCATAATGTAAGACGCTTTT 59.668 41.667 0.00 0.00 43.07 2.27
567 1725 5.163794 CGTCCCATAATGTAAGACGCTTTTT 60.164 40.000 0.00 0.00 43.07 1.94
568 1726 6.027749 GTCCCATAATGTAAGACGCTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
569 1727 5.941058 TCCCATAATGTAAGACGCTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
570 1728 6.027749 CCCATAATGTAAGACGCTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
571 1729 6.348950 CCCATAATGTAAGACGCTTTTTGACA 60.349 38.462 0.00 0.00 0.00 3.58
572 1730 6.523201 CCATAATGTAAGACGCTTTTTGACAC 59.477 38.462 0.00 0.00 0.00 3.67
573 1731 5.751243 AATGTAAGACGCTTTTTGACACT 57.249 34.783 0.00 0.00 0.00 3.55
574 1732 6.854496 AATGTAAGACGCTTTTTGACACTA 57.146 33.333 0.00 0.00 0.00 2.74
575 1733 5.900339 TGTAAGACGCTTTTTGACACTAG 57.100 39.130 0.00 0.00 0.00 2.57
576 1734 5.353938 TGTAAGACGCTTTTTGACACTAGT 58.646 37.500 0.00 0.00 0.00 2.57
577 1735 6.506147 TGTAAGACGCTTTTTGACACTAGTA 58.494 36.000 0.00 0.00 0.00 1.82
610 1768 7.510549 AAAAATATCTGACATTATGGGACGG 57.489 36.000 0.00 0.00 0.00 4.79
612 1770 6.433847 AATATCTGACATTATGGGACGGAA 57.566 37.500 0.00 0.00 0.00 4.30
614 1772 2.158957 TCTGACATTATGGGACGGAAGC 60.159 50.000 0.00 0.00 0.00 3.86
682 1840 6.994221 AGTAGTACATACCACTGCCATTATC 58.006 40.000 2.52 0.00 34.67 1.75
717 1875 9.830975 TCCGAGACAAATATATCTTGAATTGAA 57.169 29.630 11.95 0.00 0.00 2.69
798 1957 4.349636 TCCTTCCTTTATGTTGACTGACCA 59.650 41.667 0.00 0.00 0.00 4.02
799 1958 5.014123 TCCTTCCTTTATGTTGACTGACCAT 59.986 40.000 0.00 0.00 0.00 3.55
816 1979 9.953697 GACTGACCATCTAACTAATTAGTGTAG 57.046 37.037 18.70 18.78 39.18 2.74
817 1980 9.476928 ACTGACCATCTAACTAATTAGTGTAGT 57.523 33.333 18.70 10.42 39.18 2.73
917 2094 2.286872 CACACAAGCTCATCCCATCTC 58.713 52.381 0.00 0.00 0.00 2.75
982 2168 4.941873 AGCCAAAGTAGCAATACAAGTACC 59.058 41.667 0.00 0.00 0.00 3.34
1320 2511 2.285743 GCCAACCTCCTCCTCCCT 60.286 66.667 0.00 0.00 0.00 4.20
1923 3114 1.512996 GCATCATGGGGCTCATCACG 61.513 60.000 0.00 0.00 32.92 4.35
1992 3183 1.550130 TTTCCCAGATCCTCGCCGTT 61.550 55.000 0.00 0.00 0.00 4.44
2182 3376 3.991725 GAGCTGGCTGCCCCTTGAG 62.992 68.421 17.53 7.44 44.23 3.02
2189 3383 1.601171 CTGCCCCTTGAGGACAGAG 59.399 63.158 12.17 0.00 39.83 3.35
2207 3401 3.624861 CAGAGAGACAAGTTTTGTGTGCT 59.375 43.478 0.00 0.00 45.52 4.40
2211 3405 5.914033 AGAGACAAGTTTTGTGTGCTACTA 58.086 37.500 0.00 0.00 45.52 1.82
2212 3406 5.986135 AGAGACAAGTTTTGTGTGCTACTAG 59.014 40.000 0.00 0.00 45.52 2.57
2213 3407 4.511826 AGACAAGTTTTGTGTGCTACTAGC 59.488 41.667 0.61 0.61 45.52 3.42
2214 3408 4.196193 ACAAGTTTTGTGTGCTACTAGCA 58.804 39.130 6.66 6.66 45.73 3.49
2290 3662 3.687212 TGCCTTTCATACATTGTGTACGG 59.313 43.478 0.00 0.00 35.42 4.02
2324 3698 9.461312 TCATTTTAGGTAGCACAGACAAATTAT 57.539 29.630 0.00 0.00 0.00 1.28
2325 3699 9.722056 CATTTTAGGTAGCACAGACAAATTATC 57.278 33.333 0.00 0.00 0.00 1.75
2328 3702 9.817809 TTTAGGTAGCACAGACAAATTATCTAG 57.182 33.333 0.00 0.00 0.00 2.43
2346 3720 9.765795 ATTATCTAGTACTATTCAGTTTGGTGC 57.234 33.333 2.33 0.00 36.14 5.01
2347 3721 6.852420 TCTAGTACTATTCAGTTTGGTGCT 57.148 37.500 2.33 0.00 36.14 4.40
2348 3722 6.864342 TCTAGTACTATTCAGTTTGGTGCTC 58.136 40.000 2.33 0.00 36.14 4.26
2349 3723 5.746990 AGTACTATTCAGTTTGGTGCTCT 57.253 39.130 0.00 0.00 36.14 4.09
2350 3724 5.482908 AGTACTATTCAGTTTGGTGCTCTG 58.517 41.667 0.00 0.00 36.14 3.35
2351 3725 4.357918 ACTATTCAGTTTGGTGCTCTGT 57.642 40.909 0.00 0.00 0.00 3.41
2352 3726 5.483685 ACTATTCAGTTTGGTGCTCTGTA 57.516 39.130 0.00 0.00 0.00 2.74
2353 3727 5.865085 ACTATTCAGTTTGGTGCTCTGTAA 58.135 37.500 0.00 0.00 0.00 2.41
2354 3728 5.934625 ACTATTCAGTTTGGTGCTCTGTAAG 59.065 40.000 0.00 0.00 0.00 2.34
2355 3729 4.415881 TTCAGTTTGGTGCTCTGTAAGA 57.584 40.909 0.00 0.00 43.69 2.10
2356 3730 3.728845 TCAGTTTGGTGCTCTGTAAGAC 58.271 45.455 0.00 0.00 38.67 3.01
2357 3731 3.388024 TCAGTTTGGTGCTCTGTAAGACT 59.612 43.478 0.00 0.00 38.67 3.24
2358 3732 4.130118 CAGTTTGGTGCTCTGTAAGACTT 58.870 43.478 0.00 0.00 38.67 3.01
2359 3733 4.576463 CAGTTTGGTGCTCTGTAAGACTTT 59.424 41.667 0.00 0.00 38.67 2.66
2360 3734 4.576463 AGTTTGGTGCTCTGTAAGACTTTG 59.424 41.667 0.00 0.00 38.67 2.77
2361 3735 3.126001 TGGTGCTCTGTAAGACTTTGG 57.874 47.619 0.00 0.00 38.67 3.28
2362 3736 2.438021 TGGTGCTCTGTAAGACTTTGGT 59.562 45.455 0.00 0.00 38.67 3.67
2363 3737 3.118038 TGGTGCTCTGTAAGACTTTGGTT 60.118 43.478 0.00 0.00 38.67 3.67
2364 3738 3.883489 GGTGCTCTGTAAGACTTTGGTTT 59.117 43.478 0.00 0.00 38.67 3.27
2365 3739 4.023963 GGTGCTCTGTAAGACTTTGGTTTC 60.024 45.833 0.00 0.00 38.67 2.78
2366 3740 3.807622 TGCTCTGTAAGACTTTGGTTTCG 59.192 43.478 0.00 0.00 38.67 3.46
2367 3741 3.808174 GCTCTGTAAGACTTTGGTTTCGT 59.192 43.478 0.00 0.00 38.67 3.85
2368 3742 4.318831 GCTCTGTAAGACTTTGGTTTCGTG 60.319 45.833 0.00 0.00 38.67 4.35
2369 3743 4.761975 TCTGTAAGACTTTGGTTTCGTGT 58.238 39.130 0.00 0.00 38.67 4.49
2370 3744 5.904941 TCTGTAAGACTTTGGTTTCGTGTA 58.095 37.500 0.00 0.00 38.67 2.90
2371 3745 6.518493 TCTGTAAGACTTTGGTTTCGTGTAT 58.482 36.000 0.00 0.00 38.67 2.29
2372 3746 6.422701 TCTGTAAGACTTTGGTTTCGTGTATG 59.577 38.462 0.00 0.00 38.67 2.39
2373 3747 4.483476 AAGACTTTGGTTTCGTGTATGC 57.517 40.909 0.00 0.00 0.00 3.14
2374 3748 3.740115 AGACTTTGGTTTCGTGTATGCT 58.260 40.909 0.00 0.00 0.00 3.79
2375 3749 3.498397 AGACTTTGGTTTCGTGTATGCTG 59.502 43.478 0.00 0.00 0.00 4.41
2376 3750 2.031157 ACTTTGGTTTCGTGTATGCTGC 60.031 45.455 0.00 0.00 0.00 5.25
2377 3751 0.878416 TTGGTTTCGTGTATGCTGCC 59.122 50.000 0.00 0.00 0.00 4.85
2378 3752 0.036164 TGGTTTCGTGTATGCTGCCT 59.964 50.000 0.00 0.00 0.00 4.75
2379 3753 0.447801 GGTTTCGTGTATGCTGCCTG 59.552 55.000 0.00 0.00 0.00 4.85
2380 3754 1.438651 GTTTCGTGTATGCTGCCTGA 58.561 50.000 0.00 0.00 0.00 3.86
2381 3755 2.009774 GTTTCGTGTATGCTGCCTGAT 58.990 47.619 0.00 0.00 0.00 2.90
2382 3756 1.655484 TTCGTGTATGCTGCCTGATG 58.345 50.000 0.00 0.00 0.00 3.07
2383 3757 0.536724 TCGTGTATGCTGCCTGATGT 59.463 50.000 0.00 0.00 0.00 3.06
2384 3758 0.654160 CGTGTATGCTGCCTGATGTG 59.346 55.000 0.00 0.00 0.00 3.21
2385 3759 1.019673 GTGTATGCTGCCTGATGTGG 58.980 55.000 0.00 0.00 0.00 4.17
2386 3760 0.107066 TGTATGCTGCCTGATGTGGG 60.107 55.000 0.00 0.00 0.00 4.61
2397 3771 5.535753 GCCTGATGTGGGCTTTATTAATT 57.464 39.130 0.00 0.00 45.57 1.40
2398 3772 5.917462 GCCTGATGTGGGCTTTATTAATTT 58.083 37.500 0.00 0.00 45.57 1.82
2399 3773 7.049799 GCCTGATGTGGGCTTTATTAATTTA 57.950 36.000 0.00 0.00 45.57 1.40
2400 3774 7.496747 GCCTGATGTGGGCTTTATTAATTTAA 58.503 34.615 0.00 0.00 45.57 1.52
2401 3775 7.984617 GCCTGATGTGGGCTTTATTAATTTAAA 59.015 33.333 0.00 0.00 45.57 1.52
2402 3776 9.533253 CCTGATGTGGGCTTTATTAATTTAAAG 57.467 33.333 6.41 6.41 40.56 1.85
2410 3784 6.727569 CTTTATTAATTTAAAGCCGGACGC 57.272 37.500 5.05 0.00 33.69 5.19
2426 3800 3.952811 GCTCTTGGCGTCTTCGTT 58.047 55.556 0.00 0.00 39.49 3.85
2427 3801 2.235546 GCTCTTGGCGTCTTCGTTT 58.764 52.632 0.00 0.00 39.49 3.60
2428 3802 0.586802 GCTCTTGGCGTCTTCGTTTT 59.413 50.000 0.00 0.00 39.49 2.43
2429 3803 1.796459 GCTCTTGGCGTCTTCGTTTTA 59.204 47.619 0.00 0.00 39.49 1.52
2430 3804 2.222445 GCTCTTGGCGTCTTCGTTTTAA 59.778 45.455 0.00 0.00 39.49 1.52
2431 3805 3.303526 GCTCTTGGCGTCTTCGTTTTAAA 60.304 43.478 0.00 0.00 39.49 1.52
2432 3806 4.787245 GCTCTTGGCGTCTTCGTTTTAAAA 60.787 41.667 0.00 0.00 39.49 1.52
2433 3807 5.232610 TCTTGGCGTCTTCGTTTTAAAAA 57.767 34.783 1.31 0.00 39.49 1.94
2434 3808 5.267776 TCTTGGCGTCTTCGTTTTAAAAAG 58.732 37.500 1.31 4.79 39.49 2.27
2435 3809 4.879104 TGGCGTCTTCGTTTTAAAAAGA 57.121 36.364 11.83 11.83 39.49 2.52
2436 3810 5.232610 TGGCGTCTTCGTTTTAAAAAGAA 57.767 34.783 22.39 22.39 39.49 2.52
2658 4032 3.902515 GCTGTTCAGAGAGACAGCA 57.097 52.632 20.00 0.00 44.08 4.41
2936 4434 3.828451 AGACAAACCCATTCCATCAACTG 59.172 43.478 0.00 0.00 0.00 3.16
3011 4518 7.217200 ACATATACCGACTTACAATGCTGAAT 58.783 34.615 0.00 0.00 0.00 2.57
3102 4618 6.238897 GGAATACAGACACAACAATTTGGTGA 60.239 38.462 20.90 0.00 37.20 4.02
3103 4619 4.370364 ACAGACACAACAATTTGGTGAC 57.630 40.909 20.90 10.05 37.20 3.67
3104 4620 3.761218 ACAGACACAACAATTTGGTGACA 59.239 39.130 20.90 0.00 37.20 3.58
3105 4621 4.402155 ACAGACACAACAATTTGGTGACAT 59.598 37.500 20.90 5.60 37.20 3.06
3106 4622 4.741185 CAGACACAACAATTTGGTGACATG 59.259 41.667 20.90 11.10 37.20 3.21
3108 4624 5.083533 ACACAACAATTTGGTGACATGTT 57.916 34.783 20.90 0.00 40.67 2.71
3127 4649 3.333680 TGTTAAGAGGGAATTTGGAGGCT 59.666 43.478 0.00 0.00 0.00 4.58
3143 4665 7.446106 TTGGAGGCTAGATATACCAGAAAAA 57.554 36.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.432628 AAGAAGAAGGCGACGCGG 60.433 61.111 14.61 0.00 0.00 6.46
62 70 4.108699 TCGTGATTGAATTGAATTGCCC 57.891 40.909 0.00 0.00 0.00 5.36
461 469 3.056313 GCCGTGGCATGAAGCTTCC 62.056 63.158 23.42 9.45 44.79 3.46
462 470 2.486966 GCCGTGGCATGAAGCTTC 59.513 61.111 19.89 19.89 44.79 3.86
477 814 2.457366 TTCTTGGAGAAGAAGACGCC 57.543 50.000 0.00 0.00 42.23 5.68
478 815 5.446607 GCTATTTTCTTGGAGAAGAAGACGC 60.447 44.000 0.00 0.00 46.53 5.19
479 816 5.064071 GGCTATTTTCTTGGAGAAGAAGACG 59.936 44.000 0.00 0.00 46.53 4.18
517 854 6.289064 AGGGAGTATTCATTTGTCCGATAAC 58.711 40.000 0.00 0.00 0.00 1.89
523 860 3.118371 ACGGAGGGAGTATTCATTTGTCC 60.118 47.826 0.00 0.00 0.00 4.02
547 1705 6.523201 GTGTCAAAAAGCGTCTTACATTATGG 59.477 38.462 0.00 0.00 0.00 2.74
548 1706 7.298122 AGTGTCAAAAAGCGTCTTACATTATG 58.702 34.615 0.00 0.00 0.00 1.90
549 1707 7.435068 AGTGTCAAAAAGCGTCTTACATTAT 57.565 32.000 0.00 0.00 0.00 1.28
550 1708 6.854496 AGTGTCAAAAAGCGTCTTACATTA 57.146 33.333 0.00 0.00 0.00 1.90
551 1709 5.751243 AGTGTCAAAAAGCGTCTTACATT 57.249 34.783 0.00 0.00 0.00 2.71
552 1710 5.989777 ACTAGTGTCAAAAAGCGTCTTACAT 59.010 36.000 0.00 0.00 0.00 2.29
553 1711 5.353938 ACTAGTGTCAAAAAGCGTCTTACA 58.646 37.500 0.00 0.00 0.00 2.41
554 1712 5.902051 ACTAGTGTCAAAAAGCGTCTTAC 57.098 39.130 0.00 0.00 0.00 2.34
555 1713 8.517878 ACTATACTAGTGTCAAAAAGCGTCTTA 58.482 33.333 5.39 0.00 37.69 2.10
556 1714 7.376615 ACTATACTAGTGTCAAAAAGCGTCTT 58.623 34.615 5.39 0.00 37.69 3.01
557 1715 6.921914 ACTATACTAGTGTCAAAAAGCGTCT 58.078 36.000 5.39 0.00 37.69 4.18
585 1743 7.444183 TCCGTCCCATAATGTCAGATATTTTTC 59.556 37.037 0.00 0.00 0.00 2.29
590 1748 5.569630 GCTTCCGTCCCATAATGTCAGATAT 60.570 44.000 0.00 0.00 0.00 1.63
592 1750 3.495100 GCTTCCGTCCCATAATGTCAGAT 60.495 47.826 0.00 0.00 0.00 2.90
596 1754 2.213499 CTGCTTCCGTCCCATAATGTC 58.787 52.381 0.00 0.00 0.00 3.06
598 1756 2.332063 ACTGCTTCCGTCCCATAATG 57.668 50.000 0.00 0.00 0.00 1.90
604 1762 3.602483 TGTTTAATACTGCTTCCGTCCC 58.398 45.455 0.00 0.00 0.00 4.46
610 1768 5.216566 TCGTGCATGTTTAATACTGCTTC 57.783 39.130 5.68 0.00 34.23 3.86
612 1770 5.621197 TTTCGTGCATGTTTAATACTGCT 57.379 34.783 5.68 0.00 34.23 4.24
839 2009 5.446473 GCAGGAAGATGTTAACAATGAGTCG 60.446 44.000 13.23 1.25 0.00 4.18
840 2010 5.645497 AGCAGGAAGATGTTAACAATGAGTC 59.355 40.000 13.23 5.20 0.00 3.36
917 2094 2.349886 GCTCCTGTTTGTTAGATGCTCG 59.650 50.000 0.00 0.00 0.00 5.03
982 2168 2.292016 CCATGACGTGTCCTAGCTAGAG 59.708 54.545 22.70 12.09 0.00 2.43
1944 3135 1.301244 GACGGCGATCATGATGCCT 60.301 57.895 29.91 22.21 46.67 4.75
1992 3183 3.119602 CGAACTTCTCGTGGAGGAACATA 60.120 47.826 0.00 0.00 42.89 2.29
2182 3376 4.034510 CACACAAAACTTGTCTCTCTGTCC 59.965 45.833 0.00 0.00 43.23 4.02
2189 3383 5.333416 GCTAGTAGCACACAAAACTTGTCTC 60.333 44.000 17.47 0.00 40.88 3.36
2207 3401 2.760650 AGCTACATGCACAGTGCTAGTA 59.239 45.455 25.83 23.29 45.31 1.82
2211 3405 1.552337 ACTAGCTACATGCACAGTGCT 59.448 47.619 25.83 9.01 45.31 4.40
2212 3406 1.662629 CACTAGCTACATGCACAGTGC 59.337 52.381 19.37 19.37 44.23 4.40
2214 3408 2.354103 CCACACTAGCTACATGCACAGT 60.354 50.000 0.00 0.00 45.94 3.55
2215 3409 2.274437 CCACACTAGCTACATGCACAG 58.726 52.381 0.00 0.00 45.94 3.66
2218 3412 0.904649 AGCCACACTAGCTACATGCA 59.095 50.000 0.00 0.00 45.94 3.96
2219 3413 1.134699 TCAGCCACACTAGCTACATGC 60.135 52.381 0.00 0.00 38.95 4.06
2220 3414 2.967599 TCAGCCACACTAGCTACATG 57.032 50.000 0.00 0.00 38.95 3.21
2221 3415 6.013379 AGTATATCAGCCACACTAGCTACAT 58.987 40.000 0.00 0.00 38.95 2.29
2222 3416 5.241728 CAGTATATCAGCCACACTAGCTACA 59.758 44.000 0.00 0.00 38.95 2.74
2223 3417 5.336055 CCAGTATATCAGCCACACTAGCTAC 60.336 48.000 0.00 0.00 38.95 3.58
2224 3418 4.767409 CCAGTATATCAGCCACACTAGCTA 59.233 45.833 0.00 0.00 38.95 3.32
2225 3419 3.576118 CCAGTATATCAGCCACACTAGCT 59.424 47.826 0.00 0.00 42.70 3.32
2226 3420 3.322254 ACCAGTATATCAGCCACACTAGC 59.678 47.826 0.00 0.00 0.00 3.42
2227 3421 4.342378 ACACCAGTATATCAGCCACACTAG 59.658 45.833 0.00 0.00 0.00 2.57
2264 3636 6.305399 CGTACACAATGTATGAAAGGCAAAAG 59.695 38.462 2.59 0.00 41.20 2.27
2290 3662 8.726988 TCTGTGCTACCTAAAATGAAACAATAC 58.273 33.333 0.00 0.00 0.00 1.89
2324 3698 6.663953 AGAGCACCAAACTGAATAGTACTAGA 59.336 38.462 8.85 0.00 35.69 2.43
2325 3699 6.754209 CAGAGCACCAAACTGAATAGTACTAG 59.246 42.308 8.85 0.00 35.69 2.57
2327 3701 5.012148 ACAGAGCACCAAACTGAATAGTACT 59.988 40.000 0.00 0.00 35.69 2.73
2328 3702 5.238583 ACAGAGCACCAAACTGAATAGTAC 58.761 41.667 0.00 0.00 35.69 2.73
2333 3707 4.757149 GTCTTACAGAGCACCAAACTGAAT 59.243 41.667 0.00 0.00 35.85 2.57
2334 3708 4.127171 GTCTTACAGAGCACCAAACTGAA 58.873 43.478 0.00 0.00 35.85 3.02
2335 3709 3.388024 AGTCTTACAGAGCACCAAACTGA 59.612 43.478 0.00 0.00 35.85 3.41
2336 3710 3.733337 AGTCTTACAGAGCACCAAACTG 58.267 45.455 0.00 0.00 37.62 3.16
2337 3711 4.423625 AAGTCTTACAGAGCACCAAACT 57.576 40.909 0.00 0.00 0.00 2.66
2338 3712 4.261197 CCAAAGTCTTACAGAGCACCAAAC 60.261 45.833 0.00 0.00 0.00 2.93
2339 3713 3.882888 CCAAAGTCTTACAGAGCACCAAA 59.117 43.478 0.00 0.00 0.00 3.28
2340 3714 3.118038 ACCAAAGTCTTACAGAGCACCAA 60.118 43.478 0.00 0.00 0.00 3.67
2341 3715 2.438021 ACCAAAGTCTTACAGAGCACCA 59.562 45.455 0.00 0.00 0.00 4.17
2342 3716 3.127425 ACCAAAGTCTTACAGAGCACC 57.873 47.619 0.00 0.00 0.00 5.01
2343 3717 4.318831 CGAAACCAAAGTCTTACAGAGCAC 60.319 45.833 0.00 0.00 0.00 4.40
2344 3718 3.807622 CGAAACCAAAGTCTTACAGAGCA 59.192 43.478 0.00 0.00 0.00 4.26
2345 3719 3.808174 ACGAAACCAAAGTCTTACAGAGC 59.192 43.478 0.00 0.00 0.00 4.09
2346 3720 4.809426 ACACGAAACCAAAGTCTTACAGAG 59.191 41.667 0.00 0.00 0.00 3.35
2347 3721 4.761975 ACACGAAACCAAAGTCTTACAGA 58.238 39.130 0.00 0.00 0.00 3.41
2348 3722 6.590357 CATACACGAAACCAAAGTCTTACAG 58.410 40.000 0.00 0.00 0.00 2.74
2349 3723 5.049954 GCATACACGAAACCAAAGTCTTACA 60.050 40.000 0.00 0.00 0.00 2.41
2350 3724 5.178809 AGCATACACGAAACCAAAGTCTTAC 59.821 40.000 0.00 0.00 0.00 2.34
2351 3725 5.178623 CAGCATACACGAAACCAAAGTCTTA 59.821 40.000 0.00 0.00 0.00 2.10
2352 3726 4.024048 CAGCATACACGAAACCAAAGTCTT 60.024 41.667 0.00 0.00 0.00 3.01
2353 3727 3.498397 CAGCATACACGAAACCAAAGTCT 59.502 43.478 0.00 0.00 0.00 3.24
2354 3728 3.810373 CAGCATACACGAAACCAAAGTC 58.190 45.455 0.00 0.00 0.00 3.01
2355 3729 2.031157 GCAGCATACACGAAACCAAAGT 60.031 45.455 0.00 0.00 0.00 2.66
2356 3730 2.584791 GCAGCATACACGAAACCAAAG 58.415 47.619 0.00 0.00 0.00 2.77
2357 3731 1.268352 GGCAGCATACACGAAACCAAA 59.732 47.619 0.00 0.00 0.00 3.28
2358 3732 0.878416 GGCAGCATACACGAAACCAA 59.122 50.000 0.00 0.00 0.00 3.67
2359 3733 0.036164 AGGCAGCATACACGAAACCA 59.964 50.000 0.00 0.00 0.00 3.67
2360 3734 0.447801 CAGGCAGCATACACGAAACC 59.552 55.000 0.00 0.00 0.00 3.27
2361 3735 1.438651 TCAGGCAGCATACACGAAAC 58.561 50.000 0.00 0.00 0.00 2.78
2362 3736 2.009051 CATCAGGCAGCATACACGAAA 58.991 47.619 0.00 0.00 0.00 3.46
2363 3737 1.066215 ACATCAGGCAGCATACACGAA 60.066 47.619 0.00 0.00 0.00 3.85
2364 3738 0.536724 ACATCAGGCAGCATACACGA 59.463 50.000 0.00 0.00 0.00 4.35
2365 3739 0.654160 CACATCAGGCAGCATACACG 59.346 55.000 0.00 0.00 0.00 4.49
2366 3740 1.019673 CCACATCAGGCAGCATACAC 58.980 55.000 0.00 0.00 0.00 2.90
2367 3741 0.107066 CCCACATCAGGCAGCATACA 60.107 55.000 0.00 0.00 0.00 2.29
2368 3742 2.711711 CCCACATCAGGCAGCATAC 58.288 57.895 0.00 0.00 0.00 2.39
2376 3750 9.533253 CTTTAAATTAATAAAGCCCACATCAGG 57.467 33.333 0.00 0.00 36.42 3.86
2387 3761 6.727569 GCGTCCGGCTTTAAATTAATAAAG 57.272 37.500 0.00 6.41 42.93 1.85
2409 3783 0.586802 AAAACGAAGACGCCAAGAGC 59.413 50.000 0.00 0.00 43.96 4.09
2410 3784 4.461992 TTTAAAACGAAGACGCCAAGAG 57.538 40.909 0.00 0.00 43.96 2.85
2411 3785 4.879104 TTTTAAAACGAAGACGCCAAGA 57.121 36.364 0.00 0.00 43.96 3.02
2412 3786 5.267776 TCTTTTTAAAACGAAGACGCCAAG 58.732 37.500 4.76 0.00 43.96 3.61
2413 3787 5.232610 TCTTTTTAAAACGAAGACGCCAA 57.767 34.783 4.76 0.00 43.96 4.52
2414 3788 4.879104 TCTTTTTAAAACGAAGACGCCA 57.121 36.364 4.76 0.00 43.96 5.69
2415 3789 5.740569 AGTTTCTTTTTAAAACGAAGACGCC 59.259 36.000 16.49 7.11 43.96 5.68
2416 3790 6.785633 AGTTTCTTTTTAAAACGAAGACGC 57.214 33.333 16.49 10.42 43.96 5.19
2658 4032 2.829741 GTGGAACTCTTCTGCTGACT 57.170 50.000 0.00 0.00 0.00 3.41
2704 4078 6.987403 TGCCCATGAGTACAGTACAATATA 57.013 37.500 13.37 0.00 0.00 0.86
2936 4434 8.978539 TCAGTTGTTGATAGATTAATGATACGC 58.021 33.333 0.00 0.00 0.00 4.42
3042 4557 4.082245 CCCGTGGCTATGAAAAACTGAATT 60.082 41.667 0.00 0.00 0.00 2.17
3102 4618 5.264395 CCTCCAAATTCCCTCTTAACATGT 58.736 41.667 0.00 0.00 0.00 3.21
3103 4619 4.098501 GCCTCCAAATTCCCTCTTAACATG 59.901 45.833 0.00 0.00 0.00 3.21
3104 4620 4.017130 AGCCTCCAAATTCCCTCTTAACAT 60.017 41.667 0.00 0.00 0.00 2.71
3105 4621 3.333680 AGCCTCCAAATTCCCTCTTAACA 59.666 43.478 0.00 0.00 0.00 2.41
3106 4622 3.969553 AGCCTCCAAATTCCCTCTTAAC 58.030 45.455 0.00 0.00 0.00 2.01
3108 4624 4.631234 TCTAGCCTCCAAATTCCCTCTTA 58.369 43.478 0.00 0.00 0.00 2.10
3144 4666 1.748493 TCTTCGCTGTTGGCTGTTTTT 59.252 42.857 0.00 0.00 39.13 1.94
3145 4667 1.388547 TCTTCGCTGTTGGCTGTTTT 58.611 45.000 0.00 0.00 39.13 2.43


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

AutoCloner maintained by Alex Coulton.