Multiple sequence alignment - TraesCS1D01G298300

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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 TraesCS1D01G298300 chr1D 100.000 4685 0 0 1 4685 397066576 397071260 0.000000e+00 8652.0
1 TraesCS1D01G298300 chr1A 92.629 1940 101 13 2059 3972 494438788 494440711 0.000000e+00 2752.0
2 TraesCS1D01G298300 chr1A 85.675 1438 87 41 3 1410 494436481 494437829 0.000000e+00 1404.0
3 TraesCS1D01G298300 chr1A 88.795 589 58 6 1446 2030 494437823 494438407 0.000000e+00 715.0
4 TraesCS1D01G298300 chr1A 86.289 671 64 16 4020 4685 494440717 494441364 0.000000e+00 704.0
5 TraesCS1D01G298300 chr1B 92.321 1719 73 29 2058 3763 532162189 532163861 0.000000e+00 2388.0
6 TraesCS1D01G298300 chr1B 86.707 835 38 24 608 1410 532160451 532161244 0.000000e+00 859.0
7 TraesCS1D01G298300 chr1B 86.750 400 39 10 126 522 532159899 532160287 2.590000e-117 433.0
8 TraesCS1D01G298300 chr1B 89.037 301 19 8 1446 1736 532161238 532161534 1.240000e-95 361.0
9 TraesCS1D01G298300 chr1B 92.241 116 7 2 1 115 532154222 532154336 3.750000e-36 163.0
10 TraesCS1D01G298300 chr7D 85.095 738 94 14 3956 4685 553807079 553806350 0.000000e+00 739.0
11 TraesCS1D01G298300 chr7D 77.612 335 70 5 4352 4685 595500460 595500790 1.030000e-46 198.0
12 TraesCS1D01G298300 chr6B 77.001 787 129 29 3922 4685 638493305 638494062 2.030000e-108 403.0
13 TraesCS1D01G298300 chr6A 79.275 386 73 7 4304 4685 94265980 94265598 3.600000e-66 263.0
14 TraesCS1D01G298300 chr6A 76.298 443 90 11 4227 4661 550718962 550719397 6.100000e-54 222.0
15 TraesCS1D01G298300 chr4B 74.843 636 131 24 3924 4546 472141607 472140988 1.290000e-65 261.0
16 TraesCS1D01G298300 chr7A 77.926 376 78 5 4313 4685 438145694 438146067 3.650000e-56 230.0
17 TraesCS1D01G298300 chr7B 77.748 373 72 9 4319 4685 64899427 64899060 7.890000e-53 219.0
18 TraesCS1D01G298300 chr7B 72.150 614 133 19 4052 4659 104012440 104011859 8.120000e-33 152.0
19 TraesCS1D01G298300 chr3D 84.793 217 29 4 4298 4512 395814353 395814567 1.020000e-51 215.0
20 TraesCS1D01G298300 chr3A 75.515 388 85 5 4304 4685 56731549 56731166 1.040000e-41 182.0
21 TraesCS1D01G298300 chr2D 71.429 595 130 27 4108 4685 444538860 444539431 2.290000e-23 121.0
22 TraesCS1D01G298300 chr3B 72.836 335 71 18 3927 4249 58214999 58215325 3.860000e-16 97.1
23 TraesCS1D01G298300 chr5B 74.757 206 34 17 4049 4241 234890388 234890188 5.030000e-10 76.8


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 TraesCS1D01G298300 chr1D 397066576 397071260 4684 False 8652.00 8652 100.00000 1 4685 1 chr1D.!!$F1 4684
1 TraesCS1D01G298300 chr1A 494436481 494441364 4883 False 1393.75 2752 88.34700 3 4685 4 chr1A.!!$F1 4682
2 TraesCS1D01G298300 chr1B 532159899 532163861 3962 False 1010.25 2388 88.70375 126 3763 4 chr1B.!!$F2 3637
3 TraesCS1D01G298300 chr7D 553806350 553807079 729 True 739.00 739 85.09500 3956 4685 1 chr7D.!!$R1 729
4 TraesCS1D01G298300 chr6B 638493305 638494062 757 False 403.00 403 77.00100 3922 4685 1 chr6B.!!$F1 763
5 TraesCS1D01G298300 chr4B 472140988 472141607 619 True 261.00 261 74.84300 3924 4546 1 chr4B.!!$R1 622

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
115 119 0.098728 GCCACCGACATTGCATGTAC 59.901 55.0 0.00 0.00 45.03 2.90 F
1470 1634 0.109781 CGCAGCCGCAAAACATACTT 60.110 50.0 0.00 0.00 38.40 2.24 F
1615 1780 0.031857 TGCCCGACACTGCAAATTTG 59.968 50.0 14.03 14.03 33.87 2.32 F
2945 3671 0.103208 GACCCGGAGAGTGCTACATG 59.897 60.0 0.73 0.00 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1596 1761 0.031857 CAAATTTGCAGTGTCGGGCA 59.968 50.0 5.01 0.0 38.46 5.36 R
3437 4166 0.108138 CTTACCAGCAGTCTTCCCGG 60.108 60.0 0.00 0.0 0.00 5.73 R
3438 4167 0.895530 TCTTACCAGCAGTCTTCCCG 59.104 55.0 0.00 0.0 0.00 5.14 R
4413 5191 0.394488 TTTTTGGTGTGGGTCTCGCA 60.394 50.0 0.00 0.0 0.00 5.10 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
46 50 4.201950 GGTTAGCGCTCAAATCACATGATT 60.202 41.667 16.34 1.11 45.91 2.57
57 61 7.440198 TCAAATCACATGATTAACCTGCAAAA 58.560 30.769 7.52 0.00 43.41 2.44
59 63 4.793071 TCACATGATTAACCTGCAAAACG 58.207 39.130 0.00 0.00 0.00 3.60
109 113 4.120331 GCCTGCCACCGACATTGC 62.120 66.667 0.00 0.00 0.00 3.56
111 115 2.048023 CCTGCCACCGACATTGCAT 61.048 57.895 0.00 0.00 32.53 3.96
112 116 1.138036 CTGCCACCGACATTGCATG 59.862 57.895 0.00 0.00 32.53 4.06
114 118 0.322008 TGCCACCGACATTGCATGTA 60.322 50.000 0.00 0.00 45.03 2.29
115 119 0.098728 GCCACCGACATTGCATGTAC 59.901 55.000 0.00 0.00 45.03 2.90
116 120 1.737838 CCACCGACATTGCATGTACT 58.262 50.000 0.00 0.00 45.03 2.73
141 145 5.954296 AAACATATGCATGGCACTAGATC 57.046 39.130 10.16 0.00 43.04 2.75
260 265 2.914289 GGGCCTCATAGCAGCACT 59.086 61.111 0.84 0.00 0.00 4.40
269 274 1.585668 CATAGCAGCACTCGACTTTCG 59.414 52.381 0.00 0.00 42.10 3.46
430 435 6.653320 TGCACCTTTATATTATCACGGAATCC 59.347 38.462 0.00 0.00 0.00 3.01
493 508 2.348660 CATCGTTAACTGGCCCGTAAA 58.651 47.619 0.00 0.00 0.00 2.01
499 514 0.179051 AACTGGCCCGTAAAACGTCA 60.179 50.000 0.00 0.00 40.58 4.35
522 537 2.462456 TGACATCACAGGCAGAACTC 57.538 50.000 0.00 0.00 0.00 3.01
523 538 1.002430 TGACATCACAGGCAGAACTCC 59.998 52.381 0.00 0.00 0.00 3.85
524 539 0.326264 ACATCACAGGCAGAACTCCC 59.674 55.000 0.00 0.00 0.00 4.30
525 540 0.742281 CATCACAGGCAGAACTCCCG 60.742 60.000 0.00 0.00 0.00 5.14
526 541 2.527951 ATCACAGGCAGAACTCCCGC 62.528 60.000 0.00 0.00 0.00 6.13
527 542 4.379243 ACAGGCAGAACTCCCGCG 62.379 66.667 0.00 0.00 0.00 6.46
531 546 3.353836 GCAGAACTCCCGCGCAAA 61.354 61.111 8.75 0.00 0.00 3.68
532 547 2.903547 GCAGAACTCCCGCGCAAAA 61.904 57.895 8.75 0.00 0.00 2.44
533 548 1.652012 CAGAACTCCCGCGCAAAAA 59.348 52.632 8.75 0.00 0.00 1.94
735 882 1.312815 GATCTTTTCATCCCCGGCTG 58.687 55.000 0.00 0.00 0.00 4.85
782 929 1.224069 CCGGCATCTGCTAATCACGG 61.224 60.000 1.70 1.80 41.70 4.94
787 934 0.394565 ATCTGCTAATCACGGCTCCC 59.605 55.000 0.00 0.00 0.00 4.30
788 935 1.227674 CTGCTAATCACGGCTCCCC 60.228 63.158 0.00 0.00 0.00 4.81
817 964 2.734175 GCCGCGCTAAAAAGGCTTTATT 60.734 45.455 13.77 11.81 45.67 1.40
926 1085 1.133482 TCACTCAGTCCACACTCTCCA 60.133 52.381 0.00 0.00 0.00 3.86
960 1119 1.139947 GCTGAGCTACCGTCTCACC 59.860 63.158 0.00 0.00 35.81 4.02
989 1148 3.708544 CCGCCTACCCCGTGGAAA 61.709 66.667 0.00 0.00 32.29 3.13
990 1149 2.435410 CGCCTACCCCGTGGAAAC 60.435 66.667 0.00 0.00 34.81 2.78
991 1150 2.435410 GCCTACCCCGTGGAAACG 60.435 66.667 0.00 0.00 34.81 3.60
992 1151 2.946346 GCCTACCCCGTGGAAACGA 61.946 63.158 0.00 0.00 34.81 3.85
1210 1372 0.832135 GGAGGTCAGTCTCACCCACA 60.832 60.000 0.00 0.00 35.58 4.17
1211 1373 1.270907 GAGGTCAGTCTCACCCACAT 58.729 55.000 0.00 0.00 33.96 3.21
1212 1374 1.205893 GAGGTCAGTCTCACCCACATC 59.794 57.143 0.00 0.00 33.96 3.06
1242 1405 3.104512 CTCCCCACCCGCATCTATTATA 58.895 50.000 0.00 0.00 0.00 0.98
1244 1407 2.569853 CCCCACCCGCATCTATTATACA 59.430 50.000 0.00 0.00 0.00 2.29
1246 1409 3.369471 CCCACCCGCATCTATTATACAGG 60.369 52.174 0.00 0.00 0.00 4.00
1264 1427 1.131771 GGCTTTTTCTTTCACGCAGC 58.868 50.000 0.00 0.00 0.00 5.25
1337 1501 4.153117 TCTCAAAGCGCTTTCTCATTTCTC 59.847 41.667 31.63 0.00 0.00 2.87
1343 1507 3.124636 GCGCTTTCTCATTTCTCCGTTTA 59.875 43.478 0.00 0.00 0.00 2.01
1344 1508 4.378046 GCGCTTTCTCATTTCTCCGTTTAA 60.378 41.667 0.00 0.00 0.00 1.52
1352 1516 8.583810 TCTCATTTCTCCGTTTAATATAACCG 57.416 34.615 0.00 0.00 0.00 4.44
1353 1517 7.170320 TCTCATTTCTCCGTTTAATATAACCGC 59.830 37.037 0.00 0.00 0.00 5.68
1372 1536 2.778997 CGCTTTCCTCGCGTTCTCG 61.779 63.158 5.77 0.00 45.13 4.04
1399 1563 1.126846 CGTTTGCTTCGAAATCTCGCT 59.873 47.619 0.00 0.00 45.04 4.93
1415 1579 1.010350 GCTGCCGCGAATCAAGATG 60.010 57.895 8.23 0.00 0.00 2.90
1416 1580 1.010350 CTGCCGCGAATCAAGATGC 60.010 57.895 8.23 0.00 0.00 3.91
1423 1587 3.532892 GCGAATCAAGATGCGAATGAT 57.467 42.857 14.38 0.00 42.38 2.45
1424 1588 3.881795 GCGAATCAAGATGCGAATGATT 58.118 40.909 14.38 6.55 42.38 2.57
1437 1601 3.658757 GAATGATTCGAGGGAGGAGAG 57.341 52.381 0.00 0.00 0.00 3.20
1438 1602 3.226777 GAATGATTCGAGGGAGGAGAGA 58.773 50.000 0.00 0.00 0.00 3.10
1439 1603 2.060050 TGATTCGAGGGAGGAGAGAC 57.940 55.000 0.00 0.00 0.00 3.36
1440 1604 1.285078 TGATTCGAGGGAGGAGAGACA 59.715 52.381 0.00 0.00 0.00 3.41
1441 1605 1.679153 GATTCGAGGGAGGAGAGACAC 59.321 57.143 0.00 0.00 0.00 3.67
1442 1606 0.699399 TTCGAGGGAGGAGAGACACT 59.301 55.000 0.00 0.00 0.00 3.55
1443 1607 0.699399 TCGAGGGAGGAGAGACACTT 59.301 55.000 0.00 0.00 0.00 3.16
1444 1608 1.075698 TCGAGGGAGGAGAGACACTTT 59.924 52.381 0.00 0.00 0.00 2.66
1445 1609 1.203523 CGAGGGAGGAGAGACACTTTG 59.796 57.143 0.00 0.00 0.00 2.77
1446 1610 0.980423 AGGGAGGAGAGACACTTTGC 59.020 55.000 0.00 0.00 0.00 3.68
1447 1611 0.687354 GGGAGGAGAGACACTTTGCA 59.313 55.000 0.00 0.00 0.00 4.08
1448 1612 1.072331 GGGAGGAGAGACACTTTGCAA 59.928 52.381 0.00 0.00 0.00 4.08
1449 1613 2.487265 GGGAGGAGAGACACTTTGCAAA 60.487 50.000 12.14 12.14 0.00 3.68
1450 1614 3.416156 GGAGGAGAGACACTTTGCAAAT 58.584 45.455 13.23 0.00 0.00 2.32
1451 1615 3.438434 GGAGGAGAGACACTTTGCAAATC 59.562 47.826 13.23 7.75 0.00 2.17
1452 1616 3.070018 AGGAGAGACACTTTGCAAATCG 58.930 45.455 13.23 9.27 0.00 3.34
1453 1617 2.413371 GGAGAGACACTTTGCAAATCGC 60.413 50.000 13.23 9.46 42.89 4.58
1470 1634 0.109781 CGCAGCCGCAAAACATACTT 60.110 50.000 0.00 0.00 38.40 2.24
1473 1638 2.862140 GCAGCCGCAAAACATACTTGTT 60.862 45.455 0.00 0.00 42.32 2.83
1497 1662 2.623416 CCTTTTCAAGTGGAGTGGTTCC 59.377 50.000 0.00 0.00 46.98 3.62
1507 1672 2.031163 GTGGTTCCAGCGAGCAGT 59.969 61.111 0.00 0.00 0.00 4.40
1615 1780 0.031857 TGCCCGACACTGCAAATTTG 59.968 50.000 14.03 14.03 33.87 2.32
1631 1800 6.875926 CAAATTTGCAAGTAGTAATGCTCC 57.124 37.500 5.01 0.00 42.97 4.70
1635 1804 3.599343 TGCAAGTAGTAATGCTCCACTG 58.401 45.455 9.78 0.00 42.97 3.66
1697 1872 5.836024 ATAGGTTGTCACTTTCCCTGTTA 57.164 39.130 0.00 0.00 0.00 2.41
1708 1883 5.411669 CACTTTCCCTGTTAGCGAAGTAAAT 59.588 40.000 0.00 0.00 0.00 1.40
1740 2110 6.793518 ATCCTGGAAGAAATTCAGGGATAT 57.206 37.500 0.00 0.00 45.89 1.63
1749 2119 6.474630 AGAAATTCAGGGATATCTGAGCATC 58.525 40.000 2.05 0.25 43.64 3.91
1756 2126 4.013728 GGGATATCTGAGCATCGAGTAGT 58.986 47.826 2.05 0.00 38.61 2.73
1763 2133 4.097892 TCTGAGCATCGAGTAGTATTGCAA 59.902 41.667 0.00 0.00 38.61 4.08
1768 2138 4.025647 GCATCGAGTAGTATTGCAAGGTTC 60.026 45.833 4.94 0.00 33.58 3.62
1788 2158 0.108138 GTATGCTGCGGAGGAACTGT 60.108 55.000 0.46 0.00 41.55 3.55
1795 2165 1.336517 TGCGGAGGAACTGTAAGAACG 60.337 52.381 0.00 0.00 41.55 3.95
1803 2173 3.998341 GGAACTGTAAGAACGTGCCAATA 59.002 43.478 0.00 0.00 37.43 1.90
1815 2185 3.138304 CGTGCCAATAATGCTAGCCTAA 58.862 45.455 13.29 0.00 0.00 2.69
1829 2199 5.163248 TGCTAGCCTAATGGTGTAATTGCTA 60.163 40.000 13.29 0.00 35.27 3.49
1830 2200 5.179555 GCTAGCCTAATGGTGTAATTGCTAC 59.820 44.000 2.29 0.00 35.27 3.58
1912 2282 4.907809 ACTACAGTACTCTGCTAGTGTGA 58.092 43.478 0.00 0.00 44.77 3.58
1960 2330 1.019278 GTACGTGTGGGGCACTGATG 61.019 60.000 0.00 0.00 45.57 3.07
1967 2337 1.384191 GGGGCACTGATGTTTCCCT 59.616 57.895 0.00 0.00 36.90 4.20
1971 2341 3.161866 GGGCACTGATGTTTCCCTAAAA 58.838 45.455 0.00 0.00 35.01 1.52
1976 2346 6.330278 GCACTGATGTTTCCCTAAAAATACC 58.670 40.000 0.00 0.00 0.00 2.73
2028 2398 5.344743 TTTGGTGTGAAATTAAGGCAACA 57.655 34.783 0.00 0.00 41.41 3.33
2031 2401 4.586421 TGGTGTGAAATTAAGGCAACATGA 59.414 37.500 0.00 0.00 41.41 3.07
2035 2405 5.638657 TGTGAAATTAAGGCAACATGATTGC 59.361 36.000 18.79 18.79 44.22 3.56
2085 2806 9.055248 GTCATATTTTGTTGAAGATCTTGTTCG 57.945 33.333 14.00 0.00 0.00 3.95
2095 2816 5.694910 TGAAGATCTTGTTCGTGTTCCTTAC 59.305 40.000 14.00 0.00 0.00 2.34
2102 2823 4.312443 TGTTCGTGTTCCTTACTCCATTC 58.688 43.478 0.00 0.00 0.00 2.67
2104 2825 4.884668 TCGTGTTCCTTACTCCATTCTT 57.115 40.909 0.00 0.00 0.00 2.52
2112 2833 7.174946 TGTTCCTTACTCCATTCTTGATTTCAC 59.825 37.037 0.00 0.00 0.00 3.18
2138 2864 7.868415 CCTTAGTAAGTCATGTTCCTGCTATAC 59.132 40.741 9.05 0.00 0.00 1.47
2150 2876 9.632638 ATGTTCCTGCTATACATCTTTATTGTT 57.367 29.630 0.00 0.00 0.00 2.83
2190 2916 7.551974 TGATTTTGTTTCATGTGGTGTCATTTT 59.448 29.630 0.00 0.00 0.00 1.82
2369 3095 2.230508 CAGAGTGTGGAAATGCAGCAAT 59.769 45.455 0.00 0.00 0.00 3.56
2402 3128 4.909695 TGATACCATGAAGATCCATCCACT 59.090 41.667 0.00 0.00 0.00 4.00
2407 3133 4.349048 CCATGAAGATCCATCCACTTCCTA 59.651 45.833 0.00 0.00 39.14 2.94
2409 3135 6.359804 CATGAAGATCCATCCACTTCCTAAA 58.640 40.000 0.00 0.00 39.14 1.85
2519 3245 2.649331 CAGGCAAAAGCATTCCTGAG 57.351 50.000 3.90 0.00 46.80 3.35
2763 3489 1.759445 CACAGGAAGATGGTCGAGGAT 59.241 52.381 0.00 0.00 0.00 3.24
2841 3567 4.815269 CGAAGACTCTTCAGTTCAGGATT 58.185 43.478 17.23 0.00 30.63 3.01
2914 3640 1.693083 CGCGGAGATGGGAAAACGAC 61.693 60.000 0.00 0.00 0.00 4.34
2945 3671 0.103208 GACCCGGAGAGTGCTACATG 59.897 60.000 0.73 0.00 0.00 3.21
2946 3672 0.614979 ACCCGGAGAGTGCTACATGT 60.615 55.000 0.73 2.69 0.00 3.21
3071 3797 4.007644 GGCAAACCAGGGCAAGGC 62.008 66.667 0.00 0.00 35.26 4.35
3076 3802 0.829182 AAACCAGGGCAAGGCAGAAG 60.829 55.000 0.00 0.00 0.00 2.85
3196 3922 3.624300 CAGCCGAAGATGCGCTCG 61.624 66.667 9.73 9.63 0.00 5.03
3426 4155 0.952280 AGCTCGACTGTGAGTTCGAA 59.048 50.000 0.00 0.00 38.28 3.71
3435 4164 0.586802 GTGAGTTCGAAACTGCCACC 59.413 55.000 0.00 0.00 43.03 4.61
3436 4165 0.179234 TGAGTTCGAAACTGCCACCA 59.821 50.000 0.00 0.00 43.03 4.17
3437 4166 0.586802 GAGTTCGAAACTGCCACCAC 59.413 55.000 0.00 0.00 43.03 4.16
3438 4167 0.818040 AGTTCGAAACTGCCACCACC 60.818 55.000 0.00 0.00 41.01 4.61
3448 4177 2.347490 CCACCACCGGGAAGACTG 59.653 66.667 6.32 0.00 38.05 3.51
3489 4218 3.014604 ACGAAGAAGAAGAAGGTGTCG 57.985 47.619 0.00 0.00 0.00 4.35
3685 4414 0.670546 CTGCACCAAGGTCGTGTAGG 60.671 60.000 0.00 0.00 39.45 3.18
3696 4425 2.421424 GGTCGTGTAGGGTAGTGTAGTG 59.579 54.545 0.00 0.00 0.00 2.74
3697 4426 3.077359 GTCGTGTAGGGTAGTGTAGTGT 58.923 50.000 0.00 0.00 0.00 3.55
3698 4427 4.253685 GTCGTGTAGGGTAGTGTAGTGTA 58.746 47.826 0.00 0.00 0.00 2.90
3699 4428 4.331168 GTCGTGTAGGGTAGTGTAGTGTAG 59.669 50.000 0.00 0.00 0.00 2.74
3716 4445 6.793505 AGTGTAGTTAGTTATCTTCCCAGG 57.206 41.667 0.00 0.00 0.00 4.45
3774 4510 2.107950 TAAATGGTGCTCCTGGTTCG 57.892 50.000 6.34 0.00 34.23 3.95
3785 4521 1.595093 CCTGGTTCGGCCCACAATTC 61.595 60.000 0.00 0.00 36.04 2.17
3861 4608 1.630369 AGGTGGATGTTTAGCAGCTGA 59.370 47.619 20.43 0.00 33.29 4.26
3901 4648 9.705290 AATTTTGGTGTGATAACCTGTAAATTC 57.295 29.630 0.00 0.00 41.16 2.17
3907 4654 7.492994 GGTGTGATAACCTGTAAATTCTCTCTC 59.507 40.741 0.00 0.00 37.24 3.20
3925 4672 2.283966 CCGGGACTCACTGAGGGT 60.284 66.667 10.86 0.00 33.35 4.34
3949 4704 5.438698 TTTCTAACCGATCCCAATAACCA 57.561 39.130 0.00 0.00 0.00 3.67
3950 4705 5.640158 TTCTAACCGATCCCAATAACCAT 57.360 39.130 0.00 0.00 0.00 3.55
3983 4738 8.557592 AATAAAACCCGGTTTTACTTCTCTAG 57.442 34.615 29.56 0.00 46.20 2.43
3984 4739 3.606595 ACCCGGTTTTACTTCTCTAGC 57.393 47.619 0.00 0.00 0.00 3.42
3985 4740 3.171528 ACCCGGTTTTACTTCTCTAGCT 58.828 45.455 0.00 0.00 0.00 3.32
4014 4769 4.268687 GATCCCTAATCGGCGCTG 57.731 61.111 10.86 10.86 0.00 5.18
4028 4783 2.805295 CGGCGCTGGTGGAGAATAAATA 60.805 50.000 8.83 0.00 0.00 1.40
4029 4784 2.808543 GGCGCTGGTGGAGAATAAATAG 59.191 50.000 7.64 0.00 0.00 1.73
4122 4896 1.398692 CTCTTCCTCTTCTCCTCCCG 58.601 60.000 0.00 0.00 0.00 5.14
4158 4932 2.362632 CTCCCTCCGTCGTTCCCT 60.363 66.667 0.00 0.00 0.00 4.20
4160 4934 3.771160 CCCTCCGTCGTTCCCTGG 61.771 72.222 0.00 0.00 0.00 4.45
4175 4951 3.774599 CTGGCGCCCCTACATTCCC 62.775 68.421 26.77 0.00 0.00 3.97
4196 4974 4.335647 GCCGGATCCCATCGCCAT 62.336 66.667 5.05 0.00 0.00 4.40
4270 5048 4.980805 TTCAAGCGGCGCGTCCTT 62.981 61.111 27.59 12.65 0.00 3.36
4396 5174 3.959991 GAGCGTGAGGGACTTGGGC 62.960 68.421 0.00 0.00 41.55 5.36
4398 5176 2.656069 GCGTGAGGGACTTGGGCTA 61.656 63.158 0.00 0.00 41.55 3.93
4504 5285 1.675641 GCAAGTTCGGCTCCATGGT 60.676 57.895 12.58 0.00 0.00 3.55
4581 5362 4.265056 GCCGGGTGTGGTGACCTT 62.265 66.667 2.18 0.00 36.14 3.50
4619 5400 2.352032 CGGGAGGCGAGGAAGAACT 61.352 63.158 0.00 0.00 0.00 3.01
4660 5441 1.410882 GAGGAGTACATGGCAGACCTC 59.589 57.143 0.00 5.17 36.63 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.578021 TCTTCCTTTCTCCCATCCTTGG 59.422 50.000 0.00 0.00 43.23 3.61
9 10 2.418884 CGCTAACCTCTTCCTTTCTCCC 60.419 54.545 0.00 0.00 0.00 4.30
15 16 1.267121 TGAGCGCTAACCTCTTCCTT 58.733 50.000 11.50 0.00 0.00 3.36
46 50 4.274602 TCCACTATCGTTTTGCAGGTTA 57.725 40.909 0.00 0.00 0.00 2.85
57 61 0.322322 TTGGCGGTTTCCACTATCGT 59.678 50.000 0.00 0.00 35.50 3.73
59 63 2.357952 GGATTTGGCGGTTTCCACTATC 59.642 50.000 0.00 0.00 35.50 2.08
71 75 2.409870 GGGCTCTGTGGATTTGGCG 61.410 63.158 0.00 0.00 0.00 5.69
109 113 6.144854 GCCATGCATATGTTTACAGTACATG 58.855 40.000 0.00 5.98 36.89 3.21
111 115 5.065859 GTGCCATGCATATGTTTACAGTACA 59.934 40.000 0.00 0.00 41.91 2.90
112 116 5.296780 AGTGCCATGCATATGTTTACAGTAC 59.703 40.000 0.00 0.00 41.91 2.73
113 117 5.436175 AGTGCCATGCATATGTTTACAGTA 58.564 37.500 0.00 0.00 41.91 2.74
114 118 4.272489 AGTGCCATGCATATGTTTACAGT 58.728 39.130 0.00 0.00 41.91 3.55
115 119 4.906065 AGTGCCATGCATATGTTTACAG 57.094 40.909 0.00 0.00 41.91 2.74
116 120 5.679601 TCTAGTGCCATGCATATGTTTACA 58.320 37.500 0.00 0.00 41.91 2.41
141 145 3.330720 AGAGGCCGGGTTCTTGGG 61.331 66.667 2.18 0.00 0.00 4.12
242 247 2.590007 GTGCTGCTATGAGGCCCG 60.590 66.667 0.00 0.00 0.00 6.13
260 265 5.353938 CCCAACTTATAATCCGAAAGTCGA 58.646 41.667 0.00 0.00 43.74 4.20
269 274 4.024302 GTGCTTACGCCCAACTTATAATCC 60.024 45.833 0.00 0.00 34.43 3.01
299 304 2.659610 GCCGTTGCTCTCTCCTGT 59.340 61.111 0.00 0.00 33.53 4.00
404 409 6.854496 TTCCGTGATAATATAAAGGTGCAC 57.146 37.500 8.80 8.80 0.00 4.57
430 435 7.041167 TGCAGGTCGATGGATTATTTTTAGATG 60.041 37.037 0.00 0.00 0.00 2.90
468 483 1.060937 GCCAGTTAACGATGCGCAG 59.939 57.895 18.32 5.51 0.00 5.18
469 484 2.395360 GGCCAGTTAACGATGCGCA 61.395 57.895 14.96 14.96 0.00 6.09
470 485 2.403586 GGCCAGTTAACGATGCGC 59.596 61.111 0.00 0.00 0.00 6.09
471 486 2.808958 CGGGCCAGTTAACGATGCG 61.809 63.158 4.39 0.00 0.00 4.73
499 514 0.392706 TCTGCCTGTGATGTCAACGT 59.607 50.000 0.00 0.00 0.00 3.99
533 548 9.686683 AGTAGTTCTGCCTGTGATTATTATTTT 57.313 29.630 0.00 0.00 0.00 1.82
534 549 9.113838 CAGTAGTTCTGCCTGTGATTATTATTT 57.886 33.333 0.00 0.00 37.36 1.40
535 550 8.668510 CAGTAGTTCTGCCTGTGATTATTATT 57.331 34.615 0.00 0.00 37.36 1.40
550 565 7.009260 ACTGGCGTAGTAAAACAGTAGTTCTG 61.009 42.308 0.00 0.00 42.96 3.02
713 860 1.583054 CCGGGGATGAAAAGATCGTC 58.417 55.000 0.00 0.00 42.40 4.20
735 882 2.879462 CGAGTAACTGCGCCGGTC 60.879 66.667 4.18 0.00 0.00 4.79
745 892 1.074872 GGTGGTAGTGCGCGAGTAAC 61.075 60.000 12.10 5.89 0.00 2.50
817 964 0.466007 TGTGTCCGGTAGCGCCTATA 60.466 55.000 9.24 0.00 34.25 1.31
838 996 1.164041 AGTGTTTCCTTTGGGTCGCG 61.164 55.000 0.00 0.00 0.00 5.87
983 1142 3.912745 ATGGCCCCGTCGTTTCCAC 62.913 63.158 0.00 0.00 0.00 4.02
984 1143 3.642503 ATGGCCCCGTCGTTTCCA 61.643 61.111 0.00 0.00 0.00 3.53
985 1144 3.131478 CATGGCCCCGTCGTTTCC 61.131 66.667 0.00 0.00 0.00 3.13
986 1145 3.131478 CCATGGCCCCGTCGTTTC 61.131 66.667 0.00 0.00 0.00 2.78
1204 1366 4.779486 GGGGGAGGGGATGTGGGT 62.779 72.222 0.00 0.00 0.00 4.51
1242 1405 1.748493 TGCGTGAAAGAAAAAGCCTGT 59.252 42.857 0.00 0.00 0.00 4.00
1244 1407 1.269257 GCTGCGTGAAAGAAAAAGCCT 60.269 47.619 0.00 0.00 0.00 4.58
1246 1409 1.783140 CAGCTGCGTGAAAGAAAAAGC 59.217 47.619 0.00 0.00 0.00 3.51
1337 1501 2.137523 AGCGGCGGTTATATTAAACGG 58.862 47.619 5.44 0.00 33.99 4.44
1343 1507 2.490991 GAGGAAAGCGGCGGTTATATT 58.509 47.619 25.54 9.30 0.00 1.28
1344 1508 1.604693 CGAGGAAAGCGGCGGTTATAT 60.605 52.381 25.54 13.18 0.00 0.86
1399 1563 2.812122 CGCATCTTGATTCGCGGCA 61.812 57.895 6.13 0.00 43.84 5.69
1417 1581 3.005367 GTCTCTCCTCCCTCGAATCATTC 59.995 52.174 0.00 0.00 0.00 2.67
1418 1582 2.962421 GTCTCTCCTCCCTCGAATCATT 59.038 50.000 0.00 0.00 0.00 2.57
1419 1583 2.091610 TGTCTCTCCTCCCTCGAATCAT 60.092 50.000 0.00 0.00 0.00 2.45
1420 1584 1.285078 TGTCTCTCCTCCCTCGAATCA 59.715 52.381 0.00 0.00 0.00 2.57
1421 1585 1.679153 GTGTCTCTCCTCCCTCGAATC 59.321 57.143 0.00 0.00 0.00 2.52
1422 1586 1.286553 AGTGTCTCTCCTCCCTCGAAT 59.713 52.381 0.00 0.00 0.00 3.34
1423 1587 0.699399 AGTGTCTCTCCTCCCTCGAA 59.301 55.000 0.00 0.00 0.00 3.71
1424 1588 0.699399 AAGTGTCTCTCCTCCCTCGA 59.301 55.000 0.00 0.00 0.00 4.04
1425 1589 1.203523 CAAAGTGTCTCTCCTCCCTCG 59.796 57.143 0.00 0.00 0.00 4.63
1426 1590 1.066502 GCAAAGTGTCTCTCCTCCCTC 60.067 57.143 0.00 0.00 0.00 4.30
1427 1591 0.980423 GCAAAGTGTCTCTCCTCCCT 59.020 55.000 0.00 0.00 0.00 4.20
1428 1592 0.687354 TGCAAAGTGTCTCTCCTCCC 59.313 55.000 0.00 0.00 0.00 4.30
1429 1593 2.550830 TTGCAAAGTGTCTCTCCTCC 57.449 50.000 0.00 0.00 0.00 4.30
1430 1594 3.124297 CGATTTGCAAAGTGTCTCTCCTC 59.876 47.826 18.19 5.14 0.00 3.71
1431 1595 3.070018 CGATTTGCAAAGTGTCTCTCCT 58.930 45.455 18.19 0.00 0.00 3.69
1432 1596 2.413371 GCGATTTGCAAAGTGTCTCTCC 60.413 50.000 18.19 0.68 45.45 3.71
1433 1597 2.844281 GCGATTTGCAAAGTGTCTCTC 58.156 47.619 18.19 7.28 45.45 3.20
1434 1598 2.977405 GCGATTTGCAAAGTGTCTCT 57.023 45.000 18.19 0.00 45.45 3.10
1451 1615 4.817087 ACAAGTATGTTTTGCGGCTGCG 62.817 50.000 13.96 0.00 39.77 5.18
1452 1616 1.335872 ACAAGTATGTTTTGCGGCTGC 60.336 47.619 11.65 11.65 35.91 5.25
1453 1617 2.704725 ACAAGTATGTTTTGCGGCTG 57.295 45.000 0.00 0.00 35.91 4.85
1477 1642 3.990318 GGAACCACTCCACTTGAAAAG 57.010 47.619 0.00 0.00 44.67 2.27
1497 1662 1.280746 CAACAACCACTGCTCGCTG 59.719 57.895 0.00 0.00 0.00 5.18
1507 1672 2.112297 GGTCTCCCGCAACAACCA 59.888 61.111 0.00 0.00 0.00 3.67
1596 1761 0.031857 CAAATTTGCAGTGTCGGGCA 59.968 50.000 5.01 0.00 38.46 5.36
1615 1780 3.600388 ACAGTGGAGCATTACTACTTGC 58.400 45.455 0.00 0.00 39.17 4.01
1616 1781 5.536554 CAACAGTGGAGCATTACTACTTG 57.463 43.478 0.00 0.00 0.00 3.16
1631 1800 2.082231 CAGCCTCAAGATCCAACAGTG 58.918 52.381 0.00 0.00 0.00 3.66
1635 1804 2.686915 CCAATCAGCCTCAAGATCCAAC 59.313 50.000 0.00 0.00 0.00 3.77
1697 1872 8.621286 CCAGGATTAATGTAAATTTACTTCGCT 58.379 33.333 24.81 9.97 34.77 4.93
1732 2102 2.824936 ACTCGATGCTCAGATATCCCTG 59.175 50.000 0.00 0.00 35.55 4.45
1740 2110 3.632145 TGCAATACTACTCGATGCTCAGA 59.368 43.478 6.48 0.00 37.86 3.27
1749 2119 3.508762 ACGAACCTTGCAATACTACTCG 58.491 45.455 0.00 5.84 0.00 4.18
1756 2126 2.354510 GCAGCATACGAACCTTGCAATA 59.645 45.455 0.00 0.00 38.84 1.90
1763 2133 1.141881 CTCCGCAGCATACGAACCT 59.858 57.895 0.00 0.00 0.00 3.50
1768 2138 1.141881 AGTTCCTCCGCAGCATACG 59.858 57.895 0.00 0.00 0.00 3.06
1788 2158 4.272504 GCTAGCATTATTGGCACGTTCTTA 59.727 41.667 10.63 0.00 0.00 2.10
1795 2165 4.082571 CCATTAGGCTAGCATTATTGGCAC 60.083 45.833 18.24 0.00 0.00 5.01
1803 2173 5.010012 GCAATTACACCATTAGGCTAGCATT 59.990 40.000 18.24 6.63 39.06 3.56
1829 2199 2.725312 ATCCTGCTCGTGATGCCGT 61.725 57.895 0.00 0.00 0.00 5.68
1830 2200 2.107750 ATCCTGCTCGTGATGCCG 59.892 61.111 0.00 0.00 0.00 5.69
1871 2241 6.678878 TGTAGTACTTCACTTGCTCTGTTAG 58.321 40.000 0.00 0.00 38.80 2.34
1912 2282 4.421131 ACATAGAAGGACTGTCAAGGACT 58.579 43.478 10.38 4.22 33.15 3.85
1949 2319 0.623723 TAGGGAAACATCAGTGCCCC 59.376 55.000 0.00 0.00 41.67 5.80
1976 2346 3.248363 CACTACGCAATCCACCATACATG 59.752 47.826 0.00 0.00 0.00 3.21
1992 2362 2.259618 CACCAAATCGTCCTCACTACG 58.740 52.381 0.00 0.00 41.64 3.51
2035 2405 3.993081 CAGAACAGTGTTAGAGCCAGAAG 59.007 47.826 8.88 0.00 0.00 2.85
2085 2806 7.174946 TGAAATCAAGAATGGAGTAAGGAACAC 59.825 37.037 0.00 0.00 0.00 3.32
2095 2816 8.792830 TTACTAAGGTGAAATCAAGAATGGAG 57.207 34.615 0.00 0.00 0.00 3.86
2102 2823 8.553459 ACATGACTTACTAAGGTGAAATCAAG 57.447 34.615 0.00 0.00 0.00 3.02
2104 2825 7.606456 GGAACATGACTTACTAAGGTGAAATCA 59.394 37.037 0.00 0.00 0.00 2.57
2112 2833 5.091261 AGCAGGAACATGACTTACTAAGG 57.909 43.478 0.00 0.00 0.00 2.69
2158 2884 8.825745 ACACCACATGAAACAAAATCAATTTAC 58.174 29.630 0.00 0.00 0.00 2.01
2190 2916 4.425772 TCATGAGTTCTACCTCCTGGAAA 58.574 43.478 0.00 0.00 37.04 3.13
2394 3120 7.338710 TCTGTTCTATTTTAGGAAGTGGATGG 58.661 38.462 0.00 0.00 0.00 3.51
2407 3133 8.421249 TGGTCATCCATTTTCTGTTCTATTTT 57.579 30.769 0.00 0.00 39.03 1.82
2519 3245 2.430465 ACATCTTGACAGTGTCCATGC 58.570 47.619 20.43 0.00 0.00 4.06
2841 3567 1.974265 TCAACTTTTCGGCCATGACA 58.026 45.000 2.24 0.00 0.00 3.58
2945 3671 1.517276 CGACAGAAAGTGTGACGTCAC 59.483 52.381 36.01 36.01 46.59 3.67
2946 3672 1.402613 TCGACAGAAAGTGTGACGTCA 59.597 47.619 15.76 15.76 40.56 4.35
3071 3797 4.260784 CGTCCACTCTTTCCAAAACTTCTG 60.261 45.833 0.00 0.00 0.00 3.02
3076 3802 2.548480 CCTCGTCCACTCTTTCCAAAAC 59.452 50.000 0.00 0.00 0.00 2.43
3108 3834 1.536073 CCTTCCTGCTGGACTCGACA 61.536 60.000 12.53 0.00 43.06 4.35
3196 3922 4.459089 GTCAGACCGCAGCCTCCC 62.459 72.222 0.00 0.00 0.00 4.30
3210 3936 4.016444 GCCAGTTCAGGATTATTTGGTCA 58.984 43.478 0.00 0.00 0.00 4.02
3291 4020 4.717313 GCCTTCCGGGGTGTCACC 62.717 72.222 14.13 14.13 37.60 4.02
3310 4039 4.603946 GTAGATCCCCGTGCCCGC 62.604 72.222 0.00 0.00 0.00 6.13
3311 4040 4.280494 CGTAGATCCCCGTGCCCG 62.280 72.222 0.00 0.00 0.00 6.13
3426 4155 3.491598 CTTCCCGGTGGTGGCAGTT 62.492 63.158 0.00 0.00 0.00 3.16
3435 4164 1.541310 TACCAGCAGTCTTCCCGGTG 61.541 60.000 0.00 0.00 0.00 4.94
3436 4165 0.834687 TTACCAGCAGTCTTCCCGGT 60.835 55.000 0.00 0.00 0.00 5.28
3437 4166 0.108138 CTTACCAGCAGTCTTCCCGG 60.108 60.000 0.00 0.00 0.00 5.73
3438 4167 0.895530 TCTTACCAGCAGTCTTCCCG 59.104 55.000 0.00 0.00 0.00 5.14
3448 4177 2.886124 GCTCGCCGTCTTACCAGC 60.886 66.667 0.00 0.00 0.00 4.85
3489 4218 2.516460 CTCAGCATCTGCCCCAGC 60.516 66.667 0.00 0.00 43.38 4.85
3696 4425 4.501058 CGGCCTGGGAAGATAACTAACTAC 60.501 50.000 0.00 0.00 0.00 2.73
3697 4426 3.640029 CGGCCTGGGAAGATAACTAACTA 59.360 47.826 0.00 0.00 0.00 2.24
3698 4427 2.434702 CGGCCTGGGAAGATAACTAACT 59.565 50.000 0.00 0.00 0.00 2.24
3699 4428 2.169978 ACGGCCTGGGAAGATAACTAAC 59.830 50.000 0.00 0.00 0.00 2.34
3711 4440 3.832615 AATAAAGTACTACGGCCTGGG 57.167 47.619 0.00 0.00 0.00 4.45
3716 4445 5.809051 ACACAGCTTAATAAAGTACTACGGC 59.191 40.000 0.00 0.00 34.99 5.68
3774 4510 1.288752 CGGTTGTGAATTGTGGGCC 59.711 57.895 0.00 0.00 0.00 5.80
3785 4521 5.476752 GTACTACTAGTACTCCGGTTGTG 57.523 47.826 16.30 0.00 45.70 3.33
3901 4648 1.034838 CAGTGAGTCCCGGGAGAGAG 61.035 65.000 27.72 8.41 0.00 3.20
3907 4654 2.509931 TACCCTCAGTGAGTCCCGGG 62.510 65.000 16.85 16.85 37.70 5.73
3925 4672 7.139287 TGGTTATTGGGATCGGTTAGAAATA 57.861 36.000 0.00 0.00 0.00 1.40
3983 4738 2.737830 GATCGGCTAGGTCCCAGC 59.262 66.667 0.00 0.00 38.35 4.85
3984 4739 3.460995 GGATCGGCTAGGTCCCAG 58.539 66.667 1.26 0.00 44.58 4.45
4003 4758 1.609635 TTCTCCACCAGCGCCGATTA 61.610 55.000 2.29 0.00 0.00 1.75
4014 4769 5.301555 GCTGAGGACTATTTATTCTCCACC 58.698 45.833 0.00 0.00 0.00 4.61
4100 4874 2.292587 GGGAGGAGAAGAGGAAGAGGAA 60.293 54.545 0.00 0.00 0.00 3.36
4158 4932 3.804329 GGGAATGTAGGGGCGCCA 61.804 66.667 30.85 7.48 0.00 5.69
4160 4934 1.898574 CATGGGAATGTAGGGGCGC 60.899 63.158 0.00 0.00 0.00 6.53
4167 4943 0.400213 GATCCGGCCATGGGAATGTA 59.600 55.000 15.13 0.00 37.07 2.29
4170 4946 2.845345 GGGATCCGGCCATGGGAAT 61.845 63.158 15.13 0.00 37.07 3.01
4175 4951 2.359107 CGATGGGATCCGGCCATG 60.359 66.667 15.92 5.90 0.00 3.66
4309 5087 4.143333 CGGGGAAGTCGGCGATGT 62.143 66.667 14.79 3.43 0.00 3.06
4385 5163 1.686110 CTCCGTAGCCCAAGTCCCT 60.686 63.158 0.00 0.00 0.00 4.20
4413 5191 0.394488 TTTTTGGTGTGGGTCTCGCA 60.394 50.000 0.00 0.00 0.00 5.10
4474 5253 1.287041 GAACTTGCCACCGGTCGTAC 61.287 60.000 2.59 0.00 0.00 3.67
4504 5285 4.666397 TTTAGACACGCCGCCGCA 62.666 61.111 0.00 0.00 38.22 5.69


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

AutoCloner maintained by Alex Coulton.