Multiple sequence alignment - TraesCS5D01G512800

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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 TraesCS5D01G512800 chr5D 100.000 4577 0 0 1 4577 536882794 536878218 0.000000e+00 8453.0
1 TraesCS5D01G512800 chr4A 94.444 4050 178 11 542 4574 633067167 633071186 0.000000e+00 6189.0
2 TraesCS5D01G512800 chr4A 93.750 272 15 1 89 360 633066636 633066905 1.530000e-109 407.0
3 TraesCS5D01G512800 chr5B 91.906 3731 211 31 427 4098 677638560 677642258 0.000000e+00 5132.0
4 TraesCS5D01G512800 chr5B 89.320 309 16 6 4133 4425 677642264 677642571 5.590000e-99 372.0
5 TraesCS5D01G512800 chr5B 86.131 274 35 1 1 274 677649512 677649782 4.480000e-75 292.0
6 TraesCS5D01G512800 chr3D 76.143 503 100 12 1813 2296 601223234 601222733 3.540000e-61 246.0
7 TraesCS5D01G512800 chr3D 80.455 220 36 6 1046 1260 601223968 601223751 1.320000e-35 161.0
8 TraesCS5D01G512800 chr1D 73.577 738 156 21 1551 2258 433954664 433955392 3.540000e-61 246.0
9 TraesCS5D01G512800 chr1B 73.871 731 140 34 2435 3151 587524510 587525203 1.270000e-60 244.0
10 TraesCS5D01G512800 chrUn 77.869 122 23 4 1828 1947 2239334 2239215 6.350000e-09 73.1
11 TraesCS5D01G512800 chrUn 77.869 122 23 4 1828 1947 317660162 317660281 6.350000e-09 73.1
12 TraesCS5D01G512800 chrUn 77.869 122 23 4 1828 1947 318824144 318824025 6.350000e-09 73.1


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 TraesCS5D01G512800 chr5D 536878218 536882794 4576 True 8453.0 8453 100.000 1 4577 1 chr5D.!!$R1 4576
1 TraesCS5D01G512800 chr4A 633066636 633071186 4550 False 3298.0 6189 94.097 89 4574 2 chr4A.!!$F1 4485
2 TraesCS5D01G512800 chr5B 677638560 677642571 4011 False 2752.0 5132 90.613 427 4425 2 chr5B.!!$F2 3998
3 TraesCS5D01G512800 chr3D 601222733 601223968 1235 True 203.5 246 78.299 1046 2296 2 chr3D.!!$R1 1250
4 TraesCS5D01G512800 chr1D 433954664 433955392 728 False 246.0 246 73.577 1551 2258 1 chr1D.!!$F1 707
5 TraesCS5D01G512800 chr1B 587524510 587525203 693 False 244.0 244 73.871 2435 3151 1 chr1B.!!$F1 716

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
700 839 0.037790 ACGACCTCTTCAGCTTGCTC 60.038 55.0 0.0 0.00 0.00 4.26 F
1528 1735 0.249868 TGGCGAACTGTTCTGTCCAG 60.250 55.0 17.6 3.15 36.01 3.86 F
1531 1738 0.393077 CGAACTGTTCTGTCCAGGGT 59.607 55.0 17.6 0.00 34.16 4.34 F
1602 1818 0.397564 GGGTGGGTTGGTAGTTTCGA 59.602 55.0 0.0 0.00 0.00 3.71 F
1714 1936 0.603975 GTTCTGCTCCAGGGTGTGAC 60.604 60.0 0.0 0.00 31.51 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1959 1.382914 ATAGACCCCTTTGCCCAACT 58.617 50.000 0.0 0.0 0.00 3.16 R
2361 2601 3.630312 AGCTTCTTGTAGGTTTTCGCAAA 59.370 39.130 0.0 0.0 0.00 3.68 R
2616 2859 4.240096 GCAATCACCTTCATTGAACCTTG 58.760 43.478 0.0 0.0 33.69 3.61 R
3511 3768 5.050431 GCTGCAACGGAAACAATATTTTTGT 60.050 36.000 0.0 0.0 0.00 2.83 R
3615 3880 6.324770 GGGGAATCATCACATTGGTTTTCTAT 59.675 38.462 0.0 0.0 0.00 1.98 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
17 18 4.647825 TGTTTCCACACCGTGCTT 57.352 50.000 0.00 0.00 31.34 3.91
18 19 2.102554 TGTTTCCACACCGTGCTTG 58.897 52.632 0.00 0.00 31.34 4.01
19 20 0.393132 TGTTTCCACACCGTGCTTGA 60.393 50.000 0.00 0.00 31.34 3.02
20 21 0.951558 GTTTCCACACCGTGCTTGAT 59.048 50.000 0.00 0.00 31.34 2.57
21 22 0.950836 TTTCCACACCGTGCTTGATG 59.049 50.000 0.00 0.00 31.34 3.07
22 23 0.888736 TTCCACACCGTGCTTGATGG 60.889 55.000 0.00 0.00 36.68 3.51
23 24 1.302431 CCACACCGTGCTTGATGGA 60.302 57.895 0.00 0.00 34.36 3.41
24 25 1.300971 CCACACCGTGCTTGATGGAG 61.301 60.000 0.00 0.00 34.36 3.86
25 26 0.603707 CACACCGTGCTTGATGGAGT 60.604 55.000 0.00 0.00 35.06 3.85
26 27 0.320771 ACACCGTGCTTGATGGAGTC 60.321 55.000 0.00 0.00 28.97 3.36
27 28 1.079819 ACCGTGCTTGATGGAGTCG 60.080 57.895 0.00 0.00 34.36 4.18
28 29 2.456119 CCGTGCTTGATGGAGTCGC 61.456 63.158 0.00 0.00 31.27 5.19
29 30 2.456119 CGTGCTTGATGGAGTCGCC 61.456 63.158 0.00 0.00 37.10 5.54
37 38 2.749682 TGGAGTCGCCATGCACTT 59.250 55.556 0.00 0.00 43.33 3.16
38 39 1.672030 TGGAGTCGCCATGCACTTG 60.672 57.895 0.00 0.00 43.33 3.16
39 40 1.672356 GGAGTCGCCATGCACTTGT 60.672 57.895 0.00 0.00 36.34 3.16
40 41 1.237285 GGAGTCGCCATGCACTTGTT 61.237 55.000 0.00 0.00 36.34 2.83
41 42 0.110056 GAGTCGCCATGCACTTGTTG 60.110 55.000 0.00 0.00 0.00 3.33
42 43 0.819259 AGTCGCCATGCACTTGTTGT 60.819 50.000 0.00 0.00 0.00 3.32
43 44 0.385974 GTCGCCATGCACTTGTTGTC 60.386 55.000 0.00 0.00 0.00 3.18
44 45 0.534877 TCGCCATGCACTTGTTGTCT 60.535 50.000 0.00 0.00 0.00 3.41
45 46 1.155889 CGCCATGCACTTGTTGTCTA 58.844 50.000 0.00 0.00 0.00 2.59
46 47 1.739466 CGCCATGCACTTGTTGTCTAT 59.261 47.619 0.00 0.00 0.00 1.98
47 48 2.935849 CGCCATGCACTTGTTGTCTATA 59.064 45.455 0.00 0.00 0.00 1.31
48 49 3.001634 CGCCATGCACTTGTTGTCTATAG 59.998 47.826 0.00 0.00 0.00 1.31
49 50 3.242870 GCCATGCACTTGTTGTCTATAGC 60.243 47.826 0.00 0.00 0.00 2.97
50 51 3.940852 CCATGCACTTGTTGTCTATAGCA 59.059 43.478 0.00 0.00 35.03 3.49
51 52 4.201851 CCATGCACTTGTTGTCTATAGCAC 60.202 45.833 0.00 0.00 33.18 4.40
52 53 3.334691 TGCACTTGTTGTCTATAGCACC 58.665 45.455 0.00 0.00 0.00 5.01
53 54 3.007940 TGCACTTGTTGTCTATAGCACCT 59.992 43.478 0.00 0.00 0.00 4.00
54 55 4.221924 TGCACTTGTTGTCTATAGCACCTA 59.778 41.667 0.00 0.00 0.00 3.08
55 56 5.104941 TGCACTTGTTGTCTATAGCACCTAT 60.105 40.000 0.00 0.00 0.00 2.57
56 57 5.235186 GCACTTGTTGTCTATAGCACCTATG 59.765 44.000 0.00 0.00 0.00 2.23
71 72 5.021033 CACCTATGCTTCTCTGATTCTGT 57.979 43.478 0.00 0.00 0.00 3.41
72 73 4.809958 CACCTATGCTTCTCTGATTCTGTG 59.190 45.833 0.00 0.00 0.00 3.66
73 74 3.808726 CCTATGCTTCTCTGATTCTGTGC 59.191 47.826 0.00 0.00 0.00 4.57
74 75 2.845363 TGCTTCTCTGATTCTGTGCA 57.155 45.000 0.00 0.00 0.00 4.57
75 76 3.345508 TGCTTCTCTGATTCTGTGCAT 57.654 42.857 0.00 0.00 0.00 3.96
76 77 4.476628 TGCTTCTCTGATTCTGTGCATA 57.523 40.909 0.00 0.00 0.00 3.14
77 78 4.186926 TGCTTCTCTGATTCTGTGCATAC 58.813 43.478 0.00 0.00 0.00 2.39
78 79 3.559242 GCTTCTCTGATTCTGTGCATACC 59.441 47.826 0.00 0.00 0.00 2.73
79 80 3.443099 TCTCTGATTCTGTGCATACCG 57.557 47.619 0.00 0.00 0.00 4.02
80 81 1.863454 CTCTGATTCTGTGCATACCGC 59.137 52.381 0.00 0.00 42.89 5.68
105 106 1.464734 TAGTCGACAGGGAGAAGCTG 58.535 55.000 19.50 0.00 0.00 4.24
109 110 1.603236 CGACAGGGAGAAGCTGCTCT 61.603 60.000 21.44 4.41 35.26 4.09
187 188 2.591429 CTTGGTGGCACGCTGTCA 60.591 61.111 12.17 0.00 39.78 3.58
188 189 1.968017 CTTGGTGGCACGCTGTCAT 60.968 57.895 12.17 0.00 33.03 3.06
210 211 2.113860 TGAAACTAGTCCATGCTGCC 57.886 50.000 0.00 0.00 0.00 4.85
309 310 2.664851 CTCCGCGTGCCTTTGTCA 60.665 61.111 4.92 0.00 0.00 3.58
319 320 2.620112 CCTTTGTCACTGGGCTGCG 61.620 63.158 0.00 0.00 0.00 5.18
352 353 0.606401 GTAAGCTGCCTCTGTTGCCA 60.606 55.000 0.00 0.00 0.00 4.92
366 367 3.423154 GCCAGAGCAACCGTTCGG 61.423 66.667 9.81 9.81 39.53 4.30
367 368 2.342279 CCAGAGCAACCGTTCGGA 59.658 61.111 18.28 0.00 0.00 4.55
368 369 1.738099 CCAGAGCAACCGTTCGGAG 60.738 63.158 18.28 10.54 0.00 4.63
369 370 1.738099 CAGAGCAACCGTTCGGAGG 60.738 63.158 18.28 9.89 0.00 4.30
370 371 2.434359 GAGCAACCGTTCGGAGGG 60.434 66.667 18.28 0.00 36.86 4.30
371 372 4.699522 AGCAACCGTTCGGAGGGC 62.700 66.667 18.28 15.96 34.08 5.19
373 374 4.323477 CAACCGTTCGGAGGGCCA 62.323 66.667 18.28 0.00 34.08 5.36
374 375 4.324991 AACCGTTCGGAGGGCCAC 62.325 66.667 18.28 0.00 34.08 5.01
396 397 3.803082 CGGTCGCTGTTGGCCATG 61.803 66.667 6.09 0.65 37.74 3.66
397 398 2.359850 GGTCGCTGTTGGCCATGA 60.360 61.111 6.09 0.00 37.74 3.07
398 399 1.750399 GGTCGCTGTTGGCCATGAT 60.750 57.895 6.09 0.00 37.74 2.45
399 400 0.463654 GGTCGCTGTTGGCCATGATA 60.464 55.000 6.09 0.00 37.74 2.15
400 401 0.940126 GTCGCTGTTGGCCATGATAG 59.060 55.000 6.09 0.54 37.74 2.08
401 402 0.541392 TCGCTGTTGGCCATGATAGT 59.459 50.000 6.09 0.00 37.74 2.12
402 403 1.065491 TCGCTGTTGGCCATGATAGTT 60.065 47.619 6.09 0.00 37.74 2.24
424 425 0.249699 TGCAGTGATCCGTCGTTGTT 60.250 50.000 0.00 0.00 0.00 2.83
428 429 0.438830 GTGATCCGTCGTTGTTGAGC 59.561 55.000 0.00 0.00 0.00 4.26
435 436 2.222213 CCGTCGTTGTTGAGCACATTTA 59.778 45.455 0.00 0.00 34.43 1.40
443 444 6.075099 CGTTGTTGAGCACATTTATTTTCGTT 60.075 34.615 0.00 0.00 34.43 3.85
515 599 2.754664 AAAAGCAGAGCTGGACCGGG 62.755 60.000 6.32 0.00 39.62 5.73
530 619 2.548480 GACCGGGCAGCTATTGAATTAC 59.452 50.000 0.00 0.00 0.00 1.89
540 629 6.559886 GCAGCTATTGAATTACTAACGTCGAC 60.560 42.308 5.18 5.18 0.00 4.20
700 839 0.037790 ACGACCTCTTCAGCTTGCTC 60.038 55.000 0.00 0.00 0.00 4.26
775 917 1.341531 GCTGCGCTATTCCTCTCCTTA 59.658 52.381 9.73 0.00 0.00 2.69
789 931 4.707448 CCTCTCCTTACAGAAGTCTAAGCA 59.293 45.833 0.00 0.00 0.00 3.91
803 945 5.576128 AGTCTAAGCAGAACCTCTACTTCT 58.424 41.667 0.00 0.00 32.65 2.85
884 1026 6.928492 TCCATTTTCATTTTACCTTTCTGCAC 59.072 34.615 0.00 0.00 0.00 4.57
891 1033 2.596904 TACCTTTCTGCACGGATAGC 57.403 50.000 0.00 0.00 0.00 2.97
892 1034 0.460284 ACCTTTCTGCACGGATAGCG 60.460 55.000 0.00 0.00 33.85 4.26
991 1133 2.779430 TCCTTCATCCACCATATGCAGT 59.221 45.455 0.00 0.00 0.00 4.40
1008 1150 2.825387 TCGCCAGCCATGTCATGC 60.825 61.111 7.35 3.48 0.00 4.06
1016 1158 1.073444 AGCCATGTCATGCTGGGATAG 59.927 52.381 7.35 0.00 36.23 2.08
1018 1160 1.701292 CCATGTCATGCTGGGATAGGA 59.299 52.381 7.35 0.00 0.00 2.94
1031 1173 5.458215 GCTGGGATAGGATTTGGGATAAGTT 60.458 44.000 0.00 0.00 0.00 2.66
1069 1211 4.274459 GTGAGAAGCTTGTTGATGACAGTT 59.726 41.667 2.10 0.00 39.94 3.16
1092 1237 3.467776 GGCAGAAGTAGAGGCCAAG 57.532 57.895 5.01 0.00 45.70 3.61
1203 1348 1.606668 GGTTTCATTGACGACCTGCAA 59.393 47.619 9.95 0.00 0.00 4.08
1233 1378 9.643693 AATGATTTTTGGTGTCTTACATTCATC 57.356 29.630 0.00 0.00 0.00 2.92
1312 1467 9.965824 TTCTTAATTCCTGTTTCTGATTTGTTC 57.034 29.630 0.00 0.00 0.00 3.18
1321 1476 7.756722 CCTGTTTCTGATTTGTTCATGGTATTC 59.243 37.037 0.00 0.00 32.72 1.75
1325 1480 9.513906 TTTCTGATTTGTTCATGGTATTCTGTA 57.486 29.630 0.00 0.00 32.72 2.74
1464 1659 6.596888 GCTGAGCTATATTGGAGATGCATTTA 59.403 38.462 0.00 0.00 0.00 1.40
1467 1662 8.815912 TGAGCTATATTGGAGATGCATTTACTA 58.184 33.333 0.00 0.00 0.00 1.82
1483 1678 2.863401 ACTAGCATCGCGTATGTTGA 57.137 45.000 5.77 0.00 37.93 3.18
1486 1681 3.490896 ACTAGCATCGCGTATGTTGAATG 59.509 43.478 5.77 0.23 37.93 2.67
1491 1686 0.445829 CGCGTATGTTGAATGCACCA 59.554 50.000 0.00 0.00 0.00 4.17
1495 1690 3.365868 GCGTATGTTGAATGCACCAGAAA 60.366 43.478 0.00 0.00 0.00 2.52
1522 1729 3.674997 ACAACATATGGCGAACTGTTCT 58.325 40.909 17.60 2.46 29.74 3.01
1523 1730 3.436704 ACAACATATGGCGAACTGTTCTG 59.563 43.478 17.60 12.15 29.74 3.02
1524 1731 3.334583 ACATATGGCGAACTGTTCTGT 57.665 42.857 17.60 11.10 0.00 3.41
1525 1732 3.262420 ACATATGGCGAACTGTTCTGTC 58.738 45.455 17.60 12.91 0.00 3.51
1526 1733 2.380084 TATGGCGAACTGTTCTGTCC 57.620 50.000 17.60 15.01 0.00 4.02
1527 1734 0.396435 ATGGCGAACTGTTCTGTCCA 59.604 50.000 20.29 20.29 0.00 4.02
1528 1735 0.249868 TGGCGAACTGTTCTGTCCAG 60.250 55.000 17.60 3.15 36.01 3.86
1529 1736 0.951040 GGCGAACTGTTCTGTCCAGG 60.951 60.000 17.60 2.48 34.16 4.45
1531 1738 0.393077 CGAACTGTTCTGTCCAGGGT 59.607 55.000 17.60 0.00 34.16 4.34
1532 1739 1.202651 CGAACTGTTCTGTCCAGGGTT 60.203 52.381 17.60 0.00 34.16 4.11
1533 1740 2.495084 GAACTGTTCTGTCCAGGGTTC 58.505 52.381 13.13 0.00 34.16 3.62
1549 1756 2.633488 GGTTCATACTCTGGTCTTGGC 58.367 52.381 0.00 0.00 0.00 4.52
1556 1772 2.519013 ACTCTGGTCTTGGCCATTTTC 58.481 47.619 6.09 0.00 37.96 2.29
1602 1818 0.397564 GGGTGGGTTGGTAGTTTCGA 59.602 55.000 0.00 0.00 0.00 3.71
1605 1821 1.129917 TGGGTTGGTAGTTTCGACCA 58.870 50.000 0.00 0.00 45.38 4.02
1621 1837 2.267351 CCATGCTTTCGGTGTGGCA 61.267 57.895 0.00 0.00 39.06 4.92
1714 1936 0.603975 GTTCTGCTCCAGGGTGTGAC 60.604 60.000 0.00 0.00 31.51 3.67
1724 1946 2.026822 CCAGGGTGTGACTTTCTGCTAT 60.027 50.000 0.00 0.00 0.00 2.97
1728 1950 3.623510 GGGTGTGACTTTCTGCTATAAGC 59.376 47.826 0.00 0.00 42.82 3.09
1733 1955 5.814188 TGTGACTTTCTGCTATAAGCTCATG 59.186 40.000 0.03 0.00 42.97 3.07
1737 1959 8.424133 TGACTTTCTGCTATAAGCTCATGAATA 58.576 33.333 0.00 0.00 42.97 1.75
1773 1995 5.279056 GGGTCTATAGTGAATGCAGTAGTCC 60.279 48.000 0.00 0.00 33.64 3.85
1776 1998 2.370281 AGTGAATGCAGTAGTCCACG 57.630 50.000 0.00 0.00 0.00 4.94
1994 2219 1.707632 CAGCAGTGAAAGAGGTCGAG 58.292 55.000 0.00 0.00 0.00 4.04
2061 2301 6.922247 AGAAACATCTGATAATGTCTGCAG 57.078 37.500 7.63 7.63 38.92 4.41
2182 2422 0.734889 GCTCACGACATCCATTTGGG 59.265 55.000 0.00 0.00 35.41 4.12
2263 2503 5.013183 ACAGTATTCTCCAACCATATAGGGC 59.987 44.000 2.61 0.00 43.89 5.19
2273 2513 3.618126 ACCATATAGGGCAGACTGGCTG 61.618 54.545 26.27 16.61 43.20 4.85
2361 2601 1.898863 AGGGGACTATGATGTTGGCT 58.101 50.000 0.00 0.00 40.61 4.75
2690 2933 2.419673 CACCAAGCTGCGTGATGAAATA 59.580 45.455 17.13 0.00 31.36 1.40
2753 2996 5.578336 TCTCGAGTGTAAAGAATGCAATGAG 59.422 40.000 13.13 0.00 0.00 2.90
3044 3290 2.901839 ACAAATGGCAGCTGAAATCCTT 59.098 40.909 20.43 4.19 0.00 3.36
3051 3297 4.771577 TGGCAGCTGAAATCCTTGAAAATA 59.228 37.500 20.43 0.00 0.00 1.40
3511 3768 6.294508 GCTTTTAACTATTGCCTCCTGAAACA 60.295 38.462 0.00 0.00 0.00 2.83
3613 3878 1.146263 GGCTGATACCAGAACCCGG 59.854 63.158 0.00 0.00 43.02 5.73
3615 3880 1.904771 CTGATACCAGAACCCGGCA 59.095 57.895 0.00 0.00 43.02 5.69
3709 3974 1.059264 GTACAGCTCGTTTCGCATGTC 59.941 52.381 0.00 0.00 0.00 3.06
3715 3980 2.262211 CTCGTTTCGCATGTCATCTCA 58.738 47.619 0.00 0.00 0.00 3.27
3737 4002 1.074566 TGTGTCACAATATGGGGTGCA 59.925 47.619 2.31 0.00 35.04 4.57
4009 4275 5.643379 TTCTTGATGGCTACATGGTTTTC 57.357 39.130 0.00 0.00 37.47 2.29
4010 4276 4.661222 TCTTGATGGCTACATGGTTTTCA 58.339 39.130 0.00 0.00 37.47 2.69
4098 4364 2.512705 AGAGCTTTTCCAGAGCCAAAG 58.487 47.619 0.00 0.00 41.03 2.77
4099 4365 2.158549 AGAGCTTTTCCAGAGCCAAAGT 60.159 45.455 0.00 0.00 41.03 2.66
4142 4408 1.408969 GAAAGGGTGGTGGCAAAAGA 58.591 50.000 0.00 0.00 0.00 2.52
4147 4413 0.823356 GGTGGTGGCAAAAGAGCAGA 60.823 55.000 0.00 0.00 35.83 4.26
4151 4417 2.040278 TGGTGGCAAAAGAGCAGATACT 59.960 45.455 0.00 0.00 35.83 2.12
4155 4421 4.695455 GTGGCAAAAGAGCAGATACTTGTA 59.305 41.667 0.00 0.00 35.83 2.41
4283 4553 2.739784 CTAGGGATGGCCTGCTCG 59.260 66.667 3.32 0.00 0.00 5.03
4303 4573 5.410439 GCTCGTTACTTATGTTTCCCTTTCA 59.590 40.000 0.00 0.00 0.00 2.69
4372 4654 6.583427 AAGTGTTTCTTTTGGTTGTAAACGTC 59.417 34.615 0.00 0.00 39.69 4.34
4472 4754 4.390048 GGGAACCGTGCTTAAGCA 57.610 55.556 26.06 26.06 45.44 3.91
4518 4800 4.643463 CTCTGCGGAGGTTACTCTCTATA 58.357 47.826 15.27 0.00 43.46 1.31
4561 4843 2.438975 ACATGGTGCATCCCAGCG 60.439 61.111 2.18 0.00 44.80 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.393132 TCAAGCACGGTGTGGAAACA 60.393 50.000 10.24 0.00 33.64 2.83
1 2 0.951558 ATCAAGCACGGTGTGGAAAC 59.048 50.000 10.24 0.00 33.64 2.78
2 3 0.950836 CATCAAGCACGGTGTGGAAA 59.049 50.000 10.24 0.00 33.64 3.13
3 4 0.888736 CCATCAAGCACGGTGTGGAA 60.889 55.000 10.24 0.00 33.64 3.53
4 5 1.302431 CCATCAAGCACGGTGTGGA 60.302 57.895 10.24 5.58 33.64 4.02
5 6 1.300971 CTCCATCAAGCACGGTGTGG 61.301 60.000 10.24 9.02 33.64 4.17
6 7 0.603707 ACTCCATCAAGCACGGTGTG 60.604 55.000 10.24 1.07 36.51 3.82
7 8 0.320771 GACTCCATCAAGCACGGTGT 60.321 55.000 10.24 0.00 0.00 4.16
8 9 1.354337 CGACTCCATCAAGCACGGTG 61.354 60.000 3.15 3.15 0.00 4.94
9 10 1.079819 CGACTCCATCAAGCACGGT 60.080 57.895 0.00 0.00 0.00 4.83
10 11 2.456119 GCGACTCCATCAAGCACGG 61.456 63.158 0.00 0.00 0.00 4.94
11 12 2.456119 GGCGACTCCATCAAGCACG 61.456 63.158 0.00 0.00 34.01 5.34
12 13 1.375908 TGGCGACTCCATCAAGCAC 60.376 57.895 0.00 0.00 40.72 4.40
13 14 3.067985 TGGCGACTCCATCAAGCA 58.932 55.556 0.00 0.00 40.72 3.91
21 22 1.237285 AACAAGTGCATGGCGACTCC 61.237 55.000 0.00 0.00 0.00 3.85
22 23 0.110056 CAACAAGTGCATGGCGACTC 60.110 55.000 0.00 0.00 0.00 3.36
23 24 0.819259 ACAACAAGTGCATGGCGACT 60.819 50.000 0.00 0.00 0.00 4.18
24 25 0.385974 GACAACAAGTGCATGGCGAC 60.386 55.000 0.00 0.00 0.00 5.19
25 26 0.534877 AGACAACAAGTGCATGGCGA 60.535 50.000 0.00 0.00 0.00 5.54
26 27 1.155889 TAGACAACAAGTGCATGGCG 58.844 50.000 0.00 0.00 0.00 5.69
27 28 3.242870 GCTATAGACAACAAGTGCATGGC 60.243 47.826 3.21 0.00 0.00 4.40
28 29 3.940852 TGCTATAGACAACAAGTGCATGG 59.059 43.478 3.21 0.00 0.00 3.66
29 30 4.201851 GGTGCTATAGACAACAAGTGCATG 60.202 45.833 3.21 0.00 0.00 4.06
30 31 3.941483 GGTGCTATAGACAACAAGTGCAT 59.059 43.478 3.21 0.00 0.00 3.96
31 32 3.007940 AGGTGCTATAGACAACAAGTGCA 59.992 43.478 3.21 0.00 0.00 4.57
32 33 3.600388 AGGTGCTATAGACAACAAGTGC 58.400 45.455 3.21 0.00 0.00 4.40
33 34 6.834959 CATAGGTGCTATAGACAACAAGTG 57.165 41.667 3.21 1.60 0.00 3.16
49 50 4.809958 CACAGAATCAGAGAAGCATAGGTG 59.190 45.833 0.00 0.00 0.00 4.00
50 51 4.682859 GCACAGAATCAGAGAAGCATAGGT 60.683 45.833 0.00 0.00 0.00 3.08
51 52 3.808726 GCACAGAATCAGAGAAGCATAGG 59.191 47.826 0.00 0.00 0.00 2.57
52 53 4.439968 TGCACAGAATCAGAGAAGCATAG 58.560 43.478 0.00 0.00 0.00 2.23
53 54 4.476628 TGCACAGAATCAGAGAAGCATA 57.523 40.909 0.00 0.00 0.00 3.14
54 55 3.345508 TGCACAGAATCAGAGAAGCAT 57.654 42.857 0.00 0.00 0.00 3.79
55 56 2.845363 TGCACAGAATCAGAGAAGCA 57.155 45.000 0.00 0.00 0.00 3.91
56 57 3.559242 GGTATGCACAGAATCAGAGAAGC 59.441 47.826 0.00 0.00 0.00 3.86
57 58 3.801050 CGGTATGCACAGAATCAGAGAAG 59.199 47.826 0.00 0.00 0.00 2.85
58 59 3.785486 CGGTATGCACAGAATCAGAGAA 58.215 45.455 0.00 0.00 0.00 2.87
59 60 2.481969 GCGGTATGCACAGAATCAGAGA 60.482 50.000 0.00 0.00 45.45 3.10
60 61 1.863454 GCGGTATGCACAGAATCAGAG 59.137 52.381 0.00 0.00 45.45 3.35
61 62 1.939974 GCGGTATGCACAGAATCAGA 58.060 50.000 0.00 0.00 45.45 3.27
72 73 1.000607 TCGACTATCCTTGCGGTATGC 60.001 52.381 0.00 0.00 46.70 3.14
73 74 2.034179 TGTCGACTATCCTTGCGGTATG 59.966 50.000 17.92 0.00 0.00 2.39
74 75 2.293677 CTGTCGACTATCCTTGCGGTAT 59.706 50.000 17.92 0.00 0.00 2.73
75 76 1.674441 CTGTCGACTATCCTTGCGGTA 59.326 52.381 17.92 0.00 0.00 4.02
76 77 0.456221 CTGTCGACTATCCTTGCGGT 59.544 55.000 17.92 0.00 0.00 5.68
77 78 0.249073 CCTGTCGACTATCCTTGCGG 60.249 60.000 17.92 0.00 0.00 5.69
78 79 0.249073 CCCTGTCGACTATCCTTGCG 60.249 60.000 17.92 0.00 0.00 4.85
79 80 1.067821 CTCCCTGTCGACTATCCTTGC 59.932 57.143 17.92 0.00 0.00 4.01
80 81 2.656002 TCTCCCTGTCGACTATCCTTG 58.344 52.381 17.92 1.56 0.00 3.61
81 82 3.292460 CTTCTCCCTGTCGACTATCCTT 58.708 50.000 17.92 0.00 0.00 3.36
82 83 2.938838 CTTCTCCCTGTCGACTATCCT 58.061 52.381 17.92 0.00 0.00 3.24
83 84 1.338655 GCTTCTCCCTGTCGACTATCC 59.661 57.143 17.92 0.00 0.00 2.59
84 85 2.034053 CAGCTTCTCCCTGTCGACTATC 59.966 54.545 17.92 0.00 0.00 2.08
85 86 2.028130 CAGCTTCTCCCTGTCGACTAT 58.972 52.381 17.92 0.00 0.00 2.12
86 87 1.464734 CAGCTTCTCCCTGTCGACTA 58.535 55.000 17.92 2.26 0.00 2.59
87 88 1.882989 GCAGCTTCTCCCTGTCGACT 61.883 60.000 17.92 0.00 32.93 4.18
105 106 1.379642 CCTCCGGAATTGCCAAGAGC 61.380 60.000 5.23 0.00 44.14 4.09
109 110 0.331278 ATGTCCTCCGGAATTGCCAA 59.669 50.000 5.23 0.00 35.94 4.52
166 167 2.281070 AGCGTGCCACCAAGACAG 60.281 61.111 0.00 0.00 0.00 3.51
187 188 3.881688 GCAGCATGGACTAGTTTCATCAT 59.118 43.478 0.00 0.00 35.86 2.45
188 189 3.273434 GCAGCATGGACTAGTTTCATCA 58.727 45.455 0.00 0.00 35.86 3.07
210 211 4.463879 CAGGAGCCAGTGCCCGAG 62.464 72.222 0.00 0.00 38.69 4.63
304 305 3.555324 TCCGCAGCCCAGTGACAA 61.555 61.111 0.00 0.00 0.00 3.18
319 320 3.945304 CTTACGCCCGGTGTGGTCC 62.945 68.421 14.17 0.00 35.15 4.46
352 353 2.657237 CCTCCGAACGGTTGCTCT 59.343 61.111 12.93 0.00 36.47 4.09
379 380 3.803082 CATGGCCAACAGCGACCG 61.803 66.667 10.96 0.00 45.17 4.79
380 381 0.463654 TATCATGGCCAACAGCGACC 60.464 55.000 10.96 0.00 45.17 4.79
381 382 0.940126 CTATCATGGCCAACAGCGAC 59.060 55.000 10.96 0.00 45.17 5.19
382 383 0.541392 ACTATCATGGCCAACAGCGA 59.459 50.000 10.96 1.58 45.17 4.93
383 384 1.064505 CAACTATCATGGCCAACAGCG 59.935 52.381 10.96 0.65 45.17 5.18
384 385 2.368439 TCAACTATCATGGCCAACAGC 58.632 47.619 10.96 0.00 42.60 4.40
385 386 3.243301 GCATCAACTATCATGGCCAACAG 60.243 47.826 10.96 7.14 0.00 3.16
386 387 2.689471 GCATCAACTATCATGGCCAACA 59.311 45.455 10.96 0.00 0.00 3.33
387 388 2.689471 TGCATCAACTATCATGGCCAAC 59.311 45.455 10.96 0.00 0.00 3.77
388 389 2.953648 CTGCATCAACTATCATGGCCAA 59.046 45.455 10.96 0.00 0.00 4.52
389 390 2.092267 ACTGCATCAACTATCATGGCCA 60.092 45.455 8.56 8.56 0.00 5.36
390 391 2.292569 CACTGCATCAACTATCATGGCC 59.707 50.000 0.00 0.00 0.00 5.36
391 392 3.208594 TCACTGCATCAACTATCATGGC 58.791 45.455 0.00 0.00 0.00 4.40
392 393 4.454847 GGATCACTGCATCAACTATCATGG 59.545 45.833 0.00 0.00 0.00 3.66
393 394 4.151867 CGGATCACTGCATCAACTATCATG 59.848 45.833 0.00 0.00 0.00 3.07
394 395 4.202295 ACGGATCACTGCATCAACTATCAT 60.202 41.667 0.00 0.00 0.00 2.45
395 396 3.132824 ACGGATCACTGCATCAACTATCA 59.867 43.478 0.00 0.00 0.00 2.15
396 397 3.722147 ACGGATCACTGCATCAACTATC 58.278 45.455 0.00 0.00 0.00 2.08
397 398 3.722147 GACGGATCACTGCATCAACTAT 58.278 45.455 0.00 0.00 0.00 2.12
398 399 2.479560 CGACGGATCACTGCATCAACTA 60.480 50.000 0.00 0.00 0.00 2.24
399 400 1.737029 CGACGGATCACTGCATCAACT 60.737 52.381 0.00 0.00 0.00 3.16
400 401 0.647410 CGACGGATCACTGCATCAAC 59.353 55.000 0.00 0.00 0.00 3.18
401 402 0.246360 ACGACGGATCACTGCATCAA 59.754 50.000 0.00 0.00 0.00 2.57
402 403 0.246360 AACGACGGATCACTGCATCA 59.754 50.000 0.00 0.00 0.00 3.07
424 425 9.284594 GCTAATTAACGAAAATAAATGTGCTCA 57.715 29.630 0.00 0.00 0.00 4.26
435 436 5.960113 TGGCATGTGCTAATTAACGAAAAT 58.040 33.333 4.84 0.00 41.70 1.82
479 563 9.793252 CTCTGCTTTTAATAAATTAGCACATGT 57.207 29.630 7.75 0.00 0.00 3.21
483 567 7.433425 CCAGCTCTGCTTTTAATAAATTAGCAC 59.567 37.037 7.75 1.05 36.40 4.40
496 580 1.302832 CCGGTCCAGCTCTGCTTTT 60.303 57.895 0.00 0.00 36.40 2.27
498 582 3.710722 CCCGGTCCAGCTCTGCTT 61.711 66.667 0.00 0.00 36.40 3.91
515 599 5.457799 TCGACGTTAGTAATTCAATAGCTGC 59.542 40.000 0.00 0.00 0.00 5.25
520 604 8.746922 AAGTTGTCGACGTTAGTAATTCAATA 57.253 30.769 11.62 0.00 0.00 1.90
530 619 3.854286 AAGCAAAGTTGTCGACGTTAG 57.146 42.857 11.62 0.00 0.00 2.34
540 629 3.303791 GGACCGACAGTAAAGCAAAGTTG 60.304 47.826 0.00 0.00 0.00 3.16
775 917 4.156477 AGAGGTTCTGCTTAGACTTCTGT 58.844 43.478 0.00 0.00 0.00 3.41
789 931 5.272405 TCTTACCCAGAAGTAGAGGTTCT 57.728 43.478 0.00 0.00 34.45 3.01
827 969 2.827800 TGCTCCTGTGAACTCAAGAG 57.172 50.000 0.00 0.00 0.00 2.85
828 970 3.834813 AGTATGCTCCTGTGAACTCAAGA 59.165 43.478 0.00 0.00 0.00 3.02
884 1026 3.688136 CGTTCCACACGCTATCCG 58.312 61.111 0.00 0.00 43.37 4.18
904 1046 6.242396 AGATGATACTGTACTACCTAGCTGG 58.758 44.000 0.00 0.00 42.93 4.85
991 1133 2.825387 GCATGACATGGCTGGCGA 60.825 61.111 17.03 0.00 30.50 5.54
1008 1150 5.850046 ACTTATCCCAAATCCTATCCCAG 57.150 43.478 0.00 0.00 0.00 4.45
1016 1158 7.039714 ACTCTTCACAAAACTTATCCCAAATCC 60.040 37.037 0.00 0.00 0.00 3.01
1018 1160 7.505585 TGACTCTTCACAAAACTTATCCCAAAT 59.494 33.333 0.00 0.00 0.00 2.32
1069 1211 0.324943 GCCTCTACTTCTGCCCAACA 59.675 55.000 0.00 0.00 0.00 3.33
1092 1237 2.301346 CCCATGAACAGGGCATAACTC 58.699 52.381 0.00 0.00 39.96 3.01
1116 1261 0.321564 CTTTGACGGCCATGGACAGA 60.322 55.000 20.22 0.00 0.00 3.41
1203 1348 9.612066 AATGTAAGACACCAAAAATCATTGTTT 57.388 25.926 0.00 0.00 0.00 2.83
1306 1461 6.595326 CAGAGCTACAGAATACCATGAACAAA 59.405 38.462 0.00 0.00 0.00 2.83
1308 1463 5.187772 ACAGAGCTACAGAATACCATGAACA 59.812 40.000 0.00 0.00 0.00 3.18
1312 1467 8.668510 AAAATACAGAGCTACAGAATACCATG 57.331 34.615 0.00 0.00 0.00 3.66
1464 1659 2.863401 TCAACATACGCGATGCTAGT 57.137 45.000 15.93 0.00 39.39 2.57
1467 1662 1.003545 GCATTCAACATACGCGATGCT 60.004 47.619 15.93 0.36 39.39 3.79
1483 1678 1.202758 TGTCCGACTTTCTGGTGCATT 60.203 47.619 0.00 0.00 0.00 3.56
1486 1681 0.586802 GTTGTCCGACTTTCTGGTGC 59.413 55.000 0.00 0.00 0.00 5.01
1491 1686 3.270877 GCCATATGTTGTCCGACTTTCT 58.729 45.455 1.24 0.00 0.00 2.52
1495 1690 0.821517 TCGCCATATGTTGTCCGACT 59.178 50.000 1.24 0.00 0.00 4.18
1522 1729 2.187958 CCAGAGTATGAACCCTGGACA 58.812 52.381 0.07 0.00 46.84 4.02
1523 1730 2.168728 GACCAGAGTATGAACCCTGGAC 59.831 54.545 12.40 3.32 46.84 4.02
1524 1731 2.044492 AGACCAGAGTATGAACCCTGGA 59.956 50.000 12.40 0.00 46.84 3.86
1526 1733 3.369892 CCAAGACCAGAGTATGAACCCTG 60.370 52.174 0.00 0.00 0.00 4.45
1527 1734 2.840651 CCAAGACCAGAGTATGAACCCT 59.159 50.000 0.00 0.00 0.00 4.34
1528 1735 2.681097 GCCAAGACCAGAGTATGAACCC 60.681 54.545 0.00 0.00 0.00 4.11
1529 1736 2.633488 GCCAAGACCAGAGTATGAACC 58.367 52.381 0.00 0.00 0.00 3.62
1531 1738 2.265367 TGGCCAAGACCAGAGTATGAA 58.735 47.619 0.61 0.00 33.75 2.57
1532 1739 1.951209 TGGCCAAGACCAGAGTATGA 58.049 50.000 0.61 0.00 33.75 2.15
1533 1740 3.287867 AATGGCCAAGACCAGAGTATG 57.712 47.619 10.96 0.00 44.71 2.39
1549 1756 1.547372 CCAGAGGGCACAAGAAAATGG 59.453 52.381 0.00 0.00 0.00 3.16
1602 1818 2.268076 GCCACACCGAAAGCATGGT 61.268 57.895 0.00 0.00 39.66 3.55
1605 1821 4.421365 ATGCCACACCGAAAGCAT 57.579 50.000 0.00 0.00 41.01 3.79
1621 1837 7.228108 CAGCATGGTAATCTTGTTGTATCAGAT 59.772 37.037 0.00 0.00 30.74 2.90
1677 1899 5.335191 GCAGAACAAGGGAATACAAGACAAG 60.335 44.000 0.00 0.00 0.00 3.16
1714 1936 8.830201 ACTATTCATGAGCTTATAGCAGAAAG 57.170 34.615 10.71 0.00 45.56 2.62
1724 1946 4.502105 TGCCCAACTATTCATGAGCTTA 57.498 40.909 0.00 0.00 0.00 3.09
1728 1950 3.382546 CCCTTTGCCCAACTATTCATGAG 59.617 47.826 0.00 0.00 0.00 2.90
1733 1955 2.100197 GACCCCTTTGCCCAACTATTC 58.900 52.381 0.00 0.00 0.00 1.75
1737 1959 1.382914 ATAGACCCCTTTGCCCAACT 58.617 50.000 0.00 0.00 0.00 3.16
1773 1995 4.253685 TCCTTATCAAAGCCTCTTTCGTG 58.746 43.478 0.00 0.00 0.00 4.35
1776 1998 6.457528 CGACAATCCTTATCAAAGCCTCTTTC 60.458 42.308 0.00 0.00 0.00 2.62
1994 2219 2.836360 TGCGGATCGTCTACCCCC 60.836 66.667 0.00 0.00 0.00 5.40
2061 2301 2.096248 CTGGACTATATCGGGAGAGGC 58.904 57.143 0.00 0.00 45.48 4.70
2182 2422 6.960232 GTAGCCAATTGCCTTTGGATATTTCC 60.960 42.308 16.65 0.00 46.17 3.13
2273 2513 8.407457 TGAAATCTTGTTCATATGTCTCGTAC 57.593 34.615 1.90 0.00 32.56 3.67
2361 2601 3.630312 AGCTTCTTGTAGGTTTTCGCAAA 59.370 39.130 0.00 0.00 0.00 3.68
2616 2859 4.240096 GCAATCACCTTCATTGAACCTTG 58.760 43.478 0.00 0.00 33.69 3.61
2690 2933 6.066032 TGTGATCAATTCCATACTGCATGAT 58.934 36.000 0.00 0.00 36.69 2.45
2753 2996 5.919141 CCAAATAGCTATTTTCTGCAGCATC 59.081 40.000 25.71 0.00 37.78 3.91
2976 3222 9.814899 AATCAATCTAGTCAGACTGTGAATAAG 57.185 33.333 13.84 0.58 35.36 1.73
3455 3712 6.422100 CACACCATCTATGATAGTTTTCCGAG 59.578 42.308 0.00 0.00 0.00 4.63
3511 3768 5.050431 GCTGCAACGGAAACAATATTTTTGT 60.050 36.000 0.00 0.00 0.00 2.83
3613 3878 6.698766 GGAATCATCACATTGGTTTTCTATGC 59.301 38.462 0.00 0.00 0.00 3.14
3615 3880 6.324770 GGGGAATCATCACATTGGTTTTCTAT 59.675 38.462 0.00 0.00 0.00 1.98
3737 4002 5.627182 AGTCCTGATCTGCACTTATCAAT 57.373 39.130 0.00 0.00 31.97 2.57
3947 4213 1.002990 TGGACAGTGCAGCCATCAG 60.003 57.895 0.00 0.00 0.00 2.90
4009 4275 3.753797 GACTTCTAAAAGGCCTTGGTCTG 59.246 47.826 21.33 10.63 34.09 3.51
4010 4276 3.653352 AGACTTCTAAAAGGCCTTGGTCT 59.347 43.478 21.33 20.00 41.97 3.85
4098 4364 2.704572 ACCACTAGCTTGAAGCATGAC 58.295 47.619 20.45 0.00 45.56 3.06
4099 4365 3.515502 ACTACCACTAGCTTGAAGCATGA 59.484 43.478 20.45 3.12 45.56 3.07
4142 4408 6.234177 AGCTCTTTGTTTACAAGTATCTGCT 58.766 36.000 0.00 0.00 37.15 4.24
4147 4413 8.232913 TGGAAAAGCTCTTTGTTTACAAGTAT 57.767 30.769 0.00 0.00 37.15 2.12
4151 4417 5.163457 CCCTGGAAAAGCTCTTTGTTTACAA 60.163 40.000 0.00 0.00 32.36 2.41
4155 4421 2.103094 GCCCTGGAAAAGCTCTTTGTTT 59.897 45.455 0.00 0.00 32.36 2.83
4283 4553 7.981102 AGACTGAAAGGGAAACATAAGTAAC 57.019 36.000 0.00 0.00 39.30 2.50
4303 4573 5.816955 AGAAAAGAGCACTCCTTTAGACT 57.183 39.130 0.00 0.00 33.85 3.24
4372 4654 3.881089 ACTCTTTTACACAACCCGGAAAG 59.119 43.478 0.73 1.86 0.00 2.62
4468 4750 3.564352 CCCCCAATTAGTTTCTCCTGCTT 60.564 47.826 0.00 0.00 0.00 3.91
4470 4752 2.379005 CCCCCAATTAGTTTCTCCTGC 58.621 52.381 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.